MEME

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use MEME in your research, please cite the following paper:
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.

Discovered Motifs   |   Block diagrams of Motifs   |   Program information   |   Explanation

Discovered Motifs

Motif Overview

Motif 1
  • 2.6e-355
  • 38 sites
Motif 1 Logo
Motif 2
  • 6.1e-241
  • 25 sites
Motif 2 Logo
Motif 3
  • 6.9e-182
  • 37 sites
Motif 3 Logo
Motif 4
  • 1.7e-125
  • 18 sites
Motif 4 Logo
Motif 5
  • 7.8e-122
  • 27 sites
Motif 5 Logo
Motif 6
  • 1.2e-100
  • 13 sites
Motif 6 Logo
Motif 7
  • 2.1e-102
  • 40 sites
Motif 7 Logo
Motif 8
  • 2.4e-087
  • 8 sites
Motif 8 Logo
Motif 9
  • 1.2e-080
  • 12 sites
Motif 9 Logo
Motif 10
  • 9.6e-053
  • 10 sites
Motif 10 Logo
Motif 11
  • 8.6e-044
  • 10 sites
Motif 11 Logo
Motif 12
  • 3.0e-038
  • 33 sites
Motif 12 Logo
Motif 13
  • 2.4e-026
  • 14 sites
Motif 13 Logo
Motif 14
  • 6.6e-030
  • 23 sites
Motif 14 Logo
Motif 15
  • 3.2e-029
  • 10 sites
Motif 15 Logo
Motif 16
  • 1.5e-025
  • 9 sites
Motif 16 Logo
Motif 17
  • 5.6e-024
  • 4 sites
Motif 17 Logo
Motif 18
  • 3.0e-022
  • 9 sites
Motif 18 Logo
Motif 19
  • 1.1e-020
  • 7 sites
Motif 19 Logo
Motif 20
  • 6.4e-014
  • 4 sites
Motif 20 Logo

Further Analysis

Submit all motifs to  
      
      
 Mouse-over buttons for more information.

Motif 1

Next Top

Summary

Sequence Logo

E-value 2.6e-355
Width 15
Sites 38
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

QIKIWFQNRRMKWKK

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1514 1 5.93e-19 R QIKIWFQNRRMKWKK TYADFIASGR
1513 1 5.93e-19 R QIKIWFQNRRMKWKK DIMGEWGNEI
1512 1 5.93e-19 R QIKIWFQNRRMKWKK
1420 0 5.93e-19 QIKIWFQNRRMKWKK
1043 2 5.93e-19 CR QIKIWFQNRRMKWKK
1031 1 5.93e-19 A QIKIWFQNRRMKWKK
1020 9 5.93e-19 AHALCPPER QIKIWFQNRRMKWKK EN
1019 9 5.93e-19 AHALCLTER QIKIWFQNRRMKWKK EN
1494 1 3.76e-18 R QIKIWFPNRRMKWKK
1437 1 3.76e-18 R HIKIWFQNRRMKWKK
1042 2 3.76e-18 CR QIKIWFPNRRMKWKK C
1491 1 5.37e-18 R QIKIFFQNRRMKWKK
1501 1 5.81e-18 R QIKIWFQNRAMKWKK
1498 1 8.93e-18 R QIKIWFQNARMKWKK
1493 1 1.27e-17 R QIKIWFANRRMKWKK
1035 9 1.27e-17 AYALCLTER QIKIWFANRRMKWKK EN
1487 1 1.41e-17 R QIAIWFQNRRMKWKK
1511 1 1.65e-17 R QIKIWFQNRRMKWKA
1509 1 1.65e-17 R QIKIWFQNRRMKWAK
1488 1 1.65e-17 R QIKAWFQNRRMKWKK
1505 1 2.04e-17 R QIKIWFQNRRMAWKK
1483 1 2.04e-17 R QAKIWFQNRRMKWKK
1561 43 3.17e-17 IANALSLSER QIKIWFQNRRMKSKK DR
1431 1 3.74e-17 R AIKIWFQNRRMKWKK
1496 1 5.59e-17 R QIKIWFQARRMKWKK
1492 1 5.59e-17 R QIKIWAQNRRMKWKK
1507 1 7.19e-17 R QIKIWFQNRRMKAKK
1489 1 7.69e-17 R QIKIAFQNRRMKWKK
1503 1 1.01e-16 R QIKIWFQNRRAKWKK
1490 1 1.96e-16 R QIKIFFQNRRMKFKK
1499 1 2.66e-15 R QIKIWFQNMRRKWKK
1319 7 7.49e-14 LIRLWSH LIHIWFQNRRLKWKK K
1071 44 8.10e-14 LSSELGLNEA QIKIWFQNKRAKIKK ST
1515 1 1.02e-13 R QIRIWFQNRRMRWRR
1517 1 2.28e-12 R QPKIWFPNRRKPWKK
1543 1 9.98e-12 R VIRVWFQNKRCKDKK
1544 0 2.70e-10 RVIRWFQNKRCKDKK
1545 0 6.11e-10 RVIRWFQNKRSKDKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1019 5.93e-19
1020 5.93e-19
1031 5.93e-19
1035 1.27e-17
1042 3.76e-18
1043 5.93e-19
1071 8.10e-14
1319 7.49e-14
1420 5.93e-19
1431 3.74e-17
1437 3.76e-18
1483 2.04e-17
1487 1.41e-17
1488 1.65e-17
1489 7.69e-17
1490 1.96e-16
1491 5.37e-18
1492 5.59e-17
1493 1.27e-17
1494 3.76e-18
1496 5.59e-17
1498 8.93e-18
1499 2.66e-15
1501 5.81e-18
1503 1.01e-16
1505 2.04e-17
1507 7.19e-17
1509 1.65e-17
1511 1.65e-17
1512 5.93e-19
1513 5.93e-19
1514 5.93e-19
1515 1.02e-13
1517 2.28e-12
1543 9.98e-12
1544 2.70e-10
1545 6.11e-10
1561 3.17e-17
 
0
10
20
30
40
50
60

Time 7.3 secs.

Motif 2

Previous Next Top

Summary

Sequence Logo

E-value 6.1e-241
Width 15
Sites 25
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

RLWMRWYSPTTRRYG

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1477 0 1.48e-19 RLWMRWYSPTTRRYG
1479 0 2.91e-19 RLWMRWYSPWTRRYG
1262 0 4.06e-19 KLWMRWYSPTTRRYG
1433 0 8.49e-19 RAWMRWYSPTTRRYG
1028 0 8.49e-19 ALWMRWYSPTTRRYG
1474 0 1.26e-18 RLWMRWYSPTTRAYG
1473 0 1.26e-18 RLWMRWYSPTTARYG
1467 0 1.26e-18 RLWMAWYSPTTRRYG
1470 0 2.44e-18 RLWMRWYAPTTRRYG
1471 0 3.24e-18 RLWMRWYSPATRRYG
1472 0 3.85e-18 RLWMRWYSPTARRYG
1476 0 4.33e-18 RLWMRWYSPTTRRYA
1263 0 6.63e-18 KLWMRWYSPWTRRYG
1475 0 9.20e-18 RLWMRWYSPTTRRAG
1469 0 9.20e-18 RLWMRWASPTTRRYG
1468 0 1.39e-17 RLWMRAYSPTTRRYG
1459 0 1.39e-17 RLAMRWYSPTTRRYG
1478 0 1.99e-17 RLWMRWYSPWTRRWG
1261 0 2.49e-17 KLWMRWYSATTRRYG
1466 0 2.72e-17 RLWARWYSPTTRRYG
1481 0 3.63e-17 RLYMRYYSPTTRRYG
1460 0 4.80e-17 RLFMRFYSPTTRRYG
1465 0 1.92e-16 RLVMRVYSPTTRRYG
1462 0 5.87e-16 RLLMRLYSPTTRRYG
1461 0 9.13e-16 RLIMRIYSPTTRRYG

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1028 8.49e-19
1261 2.49e-17
1262 4.06e-19
1263 6.63e-18
1433 8.49e-19
1459 1.39e-17
1460 4.80e-17
1461 9.13e-16
1462 5.87e-16
1465 1.92e-16
1466 2.72e-17
1467 1.26e-18
1468 1.39e-17
1469 9.20e-18
1470 2.44e-18
1471 3.24e-18
1472 3.85e-18
1473 1.26e-18
1474 1.26e-18
1475 9.20e-18
1476 4.33e-18
1477 1.48e-19
1478 1.99e-17
1479 2.91e-19
1481 3.63e-17
 
0
2
4
6
8
10
12
14

Time 13.5 secs.

Motif 3

Previous Next Top

Summary

Sequence Logo

E-value 6.9e-182
Width 10
Sites 37
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[ML]IIFR[ID][LA][IA]SH

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1366 0 2.32e-14 MIIFRDLISH
1370 0 1.16e-13 MIIFRILISH KK
1367 0 4.74e-13 MIIFRIAASH KK
1384 0 4.90e-13 MIIYRDLISH
1386 0 1.38e-12 MIIYRIAASH KK
1365 0 1.38e-12 MIIFRALISH KK
1318 0 2.86e-12 LIIFRILISH RR
1317 0 2.86e-12 LIIFRILISH R
1316 0 2.86e-12 LIIFRILISH KK
1315 0 2.86e-12 LIIFRILISH K
1314 0 2.86e-12 LIIFRILISH HH
1313 0 2.86e-12 LIIFRILISH
1629 0 4.64e-12 WIIFRIAASH KK
1364 0 4.64e-12 MIIFRAAASH KK
1372 0 4.92e-12 MIISRDLISH
1368 0 4.92e-12 MIIFRIAATH KK
1377 0 7.04e-12 MIIYRALISH KK
1079 0 7.04e-12 FIIFRIAASH KK
1312 0 8.25e-12 LIIFRIAASH KK
1369 0 9.28e-12 MIIFRIAAYH KK
1362 0 1.02e-11 MIIFAIAASH KK
1628 0 1.42e-11 WIIFRALISH KK
1363 0 1.42e-11 MIIFKIAASH KK
1375 0 2.10e-11 MIIYRAEISH
1627 0 2.79e-11 WIIFRAAASH KK
1630 0 2.97e-11 WIIFRIAATH KK
1311 0 4.25e-11 LIIFAILISH KK
1631 0 5.06e-11 WIIFRIAAYH KK
1626 0 7.77e-11 WIIFKIAASH KK
1310 0 8.44e-11 LIIFAIAASH KK
1039 0 9.37e-11 CIISRDLISH
1419 0 1.49e-10 QIISRDLISH
1385 0 1.61e-10 MIIYRDLISK K
1379 0 7.29e-10 MIIYRDKKSH
1371 0 1.13e-09 MIIRRDLISE
1444 7 9.23e-09 RILQQLL FIHFRIGCRH SRI
1443 7 9.23e-09 RILQQLL FIHFRIGCRH

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1039 9.37e-11
1079 7.04e-12
1310 8.44e-11
1311 4.25e-11
1312 8.25e-12
1313 2.86e-12
1314 2.86e-12
1315 2.86e-12
1316 2.86e-12
1317 2.86e-12
1318 2.86e-12
1362 1.02e-11
1363 1.42e-11
1364 4.64e-12
1365 1.38e-12
1366 2.32e-14
1367 4.74e-13
1368 4.92e-12
1369 9.28e-12
1370 1.16e-13
1371 1.13e-09
1372 4.92e-12
1375 2.10e-11
1377 7.04e-12
1379 7.29e-10
1384 4.90e-13
1385 1.61e-10
1386 1.38e-12
1419 1.49e-10
1443 9.23e-09
1444 9.23e-09
1626 7.77e-11
1627 2.79e-11
1628 1.42e-11
1629 4.64e-12
1630 2.97e-11
1631 5.06e-11
 
0
5
10
15
20

Time 19.7 secs.

Motif 4

Previous Next Top

Summary

Sequence Logo

E-value 1.7e-125
Width 15
Sites 18
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

IILRRRIRKQAHAHS

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1339 2 1.27e-17 LL IILRRRIRKQAHAHS K
1338 2 1.27e-17 LL IILRRRIRKQAHAHS A
1304 2 1.27e-17 LA IILRRRIRKQAHAHS K
1025 2 1.27e-17 AL IILRRRIRKQAHAHS K
1327 2 3.34e-17 LL IIARRRIRKQAHAHS K
1331 2 9.08e-17 LL IILRRRARKQAHAHS K
1322 2 9.08e-17 LL AILRRRIRKQAHAHS K
1326 2 1.11e-16 LL IALRRRIRKQAHAHS K
1337 2 2.06e-16 LL IILRRRIRKQAHAHA K
1329 2 2.06e-16 LL IILRARIRKQAHAHS K
1328 2 2.06e-16 LL IILARRIRKQAHAHS K
1330 2 2.20e-16 LL IILRRAIRKQAHAHS K
1333 2 3.23e-16 LL IILRRRIRAQAHAHS K
1336 2 5.51e-16 LL IILRRRIRKQAHAAS K
1335 2 5.51e-16 LL IILRRRIRKQAAAHS K
1334 2 6.13e-16 LL IILRRRIRKAAHAHS K
1001 2 1.69e-14 AA AAARRRIRKQAHAHS K
1332 3 9.83e-13 LLI ILRRRIARKQAHAHS K

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1001 1.69e-14
1025 1.27e-17
1304 1.27e-17
1322 9.08e-17
1326 1.11e-16
1327 3.34e-17
1328 2.06e-16
1329 2.06e-16
1330 2.20e-16
1331 9.08e-17
1332 9.83e-13
1333 3.23e-16
1334 6.13e-16
1335 5.51e-16
1336 5.51e-16
1337 2.06e-16
1338 1.27e-17
1339 1.27e-17
 
0
2
4
6
8
10
12
14
16
18

Time 25.9 secs.

Motif 5

Previous Next Top

Summary

Sequence Logo

E-value 7.8e-122
Width 10
Sites 27
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[CS]RWRWK[CS][CS]KK

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1356 2 1.03e-12 MD CRWRWKCCKK
1267 3 1.03e-12 KMD CRWRWKCCKK
1215 2 1.03e-12 KD CRWRWKCCKK
1214 1 1.03e-12 K CRWRWKCCKK
1057 1 1.03e-12 D CRWRWKCCKK
1045 0 1.03e-12 CRWRWKCCKK
1269 3 3.45e-12 KMD CRWRWKCSKK
1048 0 3.45e-12 CRWRWKCSKK
1579 0 5.72e-12 SRWRWKCCKK
1274 3 5.72e-12 KMD SRWRWKCCKK
1271 3 7.99e-12 KMD CRWRWKSCKK
1580 0 1.71e-11 SRWRWKCSKK
1275 3 1.71e-11 KMD SRWRWKCSKK
1044 0 1.71e-11 CRWRFKCCKK
1041 0 1.78e-11 CRFRWKCCKK
1272 3 2.29e-11 KMD CRWRWKSSKK
1049 0 2.29e-11 CRWRWKSSKK
1581 0 2.79e-11 SRWRWKSCKK
1276 3 2.79e-11 KMD SRWRWKSCKK
1266 3 3.24e-11 KMD CRWRPKCCKK
1212 3 3.24e-11 KCG CRWRWKCGCK K
1047 0 3.24e-11 CRWRWKCGCK K
1297 0 6.74e-11 KRWRWKCCKK
1582 0 8.30e-11 SRWRWKSSKK
1277 3 8.30e-11 KMD SRWRWKSSKK
1040 0 2.76e-10 CRFRFKCCKK
1265 3 2.99e-09 KMD CRPRPKCCKK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1040 2.76e-10
1041 1.78e-11
1044 1.71e-11
1045 1.03e-12
1047 3.24e-11
1048 3.45e-12
1049 2.29e-11
1057 1.03e-12
1212 3.24e-11
1214 1.03e-12
1215 1.03e-12
1265 2.99e-09
1266 3.24e-11
1267 1.03e-12
1269 3.45e-12
1271 7.99e-12
1272 2.29e-11
1274 5.72e-12
1275 1.71e-11
1276 2.79e-11
1277 8.30e-11
1297 6.74e-11
1356 1.03e-12
1579 5.72e-12
1580 1.71e-11
1581 2.79e-11
1582 8.30e-11
 
0
2
4
6
8
10
12
14

Time 31.8 secs.

Motif 6

Previous Next Top

Summary

Sequence Logo

E-value 1.2e-100
Width 15
Sites 13
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

AAVALLPAVLLALLA

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1634 4 1.14e-17 WRFK AAVALLPAVLLALLA P
1455 13 1.14e-17 RRQRRRPPQC AAVALLPAVLLALLA P
1013 0 1.14e-17 AAVALLPAVLLALLA VTDQLGEDFF
1012 0 1.14e-17 AAVALLPAVLLALLA PVQRKRQKLM
1011 0 1.14e-17 AAVALLPAVLLALLA PSGASGLDKR
1010 0 1.14e-17 AAVALLPAVLLALLA PRRRRRR
1009 0 1.14e-17 AAVALLPAVLLALLA PRKKRRQRRR
1008 0 1.14e-17 AAVALLPAVLLALLA PRKKRRQRRR
1007 0 1.14e-17 AAVALLPAVLLALLA PEILLPNNYN
1006 0 1.14e-17 AAVALLPAVLLALLA P
1005 0 1.14e-17 AAVALLPAVLLALLA KKNNLKECGL
1004 0 1.14e-17 AAVALLPAVLLALLA KKNNLKDCGL
1003 0 1.14e-17 AAVALLPAVLLALLA K

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1003 1.14e-17
1004 1.14e-17
1005 1.14e-17
1006 1.14e-17
1007 1.14e-17
1008 1.14e-17
1009 1.14e-17
1010 1.14e-17
1011 1.14e-17
1012 1.14e-17
1013 1.14e-17
1455 1.14e-17
1634 1.14e-17
 
0
5
10
15
20
25
30
35
40

Time 37.7 secs.

Motif 7

Previous Next Top

Summary

Sequence Logo

E-value 2.1e-102
Width 15
Sites 40
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

L[LA][LG]K[LI][AN]LKAL[AK]A[LA][AL]K

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1344 6 9.77e-16 LNSAGY LLGKINLKALAALAK KIL
1325 0 9.77e-16 LLGKINLKALAALAK KIL
1175 9 9.77e-16 GWTLNSAGY LLGKINLKALAALAK KLL
1174 9 9.77e-16 GWTLNSAGY LLGKINLKALAALAK KIL
1172 9 9.77e-16 GWTLNPPGY LLGKINLKALAALAK KIL
1171 9 9.77e-16 GWTLNPAGY LLGKINLKALAALAK KIL
1017 3 9.77e-16 AGY LLGKINLKALAALAK KILTYADFIA
1016 3 9.77e-16 AGY LLGKINLKALAALAK KIL
1245 1 2.62e-13 K LALKLALKALKAALK LAGC
1244 1 2.62e-13 K LALKLALKALKAALK LA
1243 1 2.62e-13 K LALKLALKALKAALK
1246 1 4.58e-13 K LALKLALKALQAALQ LA
1176 9 1.28e-12 GWTLNSAGY LLGKINLKAPAALAK KIL
1179 3 1.87e-12 GWT LNSKINLKALAALAK KIL
1247 1 2.39e-12 K LALKLALKAWKAALK LA
1240 1 7.53e-12 K LALKAALKAWKAAAK LA
1421 1 1.17e-11 Q LALQLALQALQAALQ LA
1249 1 1.17e-11 K LALQLALQALQAALQ LA
1072 1 4.94e-11 E LALELALEALEAALE LA
1346 4 6.01e-11 LNSA GYLLGKLKALAALAK IL
1345 4 6.01e-11 LNSA GYLLGKLKALAALAK
1177 7 6.01e-11 GWTLNSA GYLLGKLKALAALAK KIL
1018 1 6.01e-11 A GYLLGKLKALAALAK KIL
1239 1 2.05e-10 K LALKAAAKAWKAAAK AA
1358 0 2.06e-09 MGLGLHLLVLAAALQ GAWSQPKKKR
1357 0 2.06e-09 MGLGLHLLVLAAALQ GAKKKRKV
1343 2 3.07e-09 LN SAGYLLGKALAALAK KIL
1248 1 1.39e-08 K LALKLALKWAKLALK AA
1250 1 2.00e-08 K LGLKLGLKGLKGGLK LG
1258 1 2.84e-08 K LLAKAALKWLLKALK AA
1029 1 2.84e-08 A LWMTLLKKVLKAAAK AALNAVLVGA
1224 1 7.40e-08 K ITLKLAIKAWKLALK AA
1389 10 8.45e-08 MVKSKIGSWI LVLFVAMWSDVGLCK KRPKP
1116 0 1.96e-07 GLFKALLKLLKSLWK LLLKA
1624 11 2.22e-07 EAKLAKALAK ALAKHLAKALAKALK ACEA
1354 8 2.22e-07 MANLGYWL LALFVTMWTDVGLCK KRPKP
1203 1 4.94e-07 K ALAKALAKLWKALAK AA
1341 0 2.47e-06 LLKTTALLKTTALLK TTA
1205 2 5.53e-06 KA LKLKLALALLAKLKL A
1082 0 1.95e-05 FLGKKFKKYFLQLLK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1016 9.77e-16
1017 9.77e-16
1018 6.01e-11
1029 2.84e-08
1072 4.94e-11
1082 1.95e-05
1116 1.96e-07
1171 9.77e-16
1172 9.77e-16
1174 9.77e-16
1175 9.77e-16
1176 1.28e-12
1177 6.01e-11
1179 1.87e-12
1203 4.94e-07
1205 5.53e-06
1224 7.40e-08
1239 2.05e-10
1240 7.53e-12
1243 2.62e-13
1244 2.62e-13
1245 2.62e-13
1246 4.58e-13
1247 2.39e-12
1248 1.39e-08
1249 1.17e-11
1250 2.00e-08
1258 2.84e-08
1325 9.77e-16
1341 2.47e-06
1343 3.07e-09
1344 9.77e-16
1345 6.01e-11
1346 6.01e-11
1354 2.22e-07
1357 2.06e-09
1358 2.06e-09
1389 8.45e-08
1421 1.17e-11
1624 2.22e-07
 
0
5
10
15
20
25
30
35

Time 44.1 secs.

Motif 8

Previous Next Top

Summary

Sequence Logo

E-value 2.4e-087
Width 15
Sites 8
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

KDVIDVRSVTTEINT

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1595 7 5.45e-22 TKRRITP KDVIDVRSVTTEINT
1591 8 5.45e-22 TKAARITP KDVIDVRSVTTEINT
1589 7 5.45e-22 TARRITP KDVIDVRSVTTEINT
1185 13 5.45e-22 HHHTKRRITP KDVIDVRSVTTEINT
1594 7 6.02e-22 TKRRITP KDVIDVESVTTEINT
1592 7 1.22e-21 TKRRITP DDVIDVRSVTTEINT
1596 7 9.92e-20 TKRRITP KDVIDVRSVTTKINT
1597 7 1.11e-19 TKRRITP KKVIDVRSVTTEINT

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1185 5.45e-22
1589 5.45e-22
1591 5.45e-22
1592 1.22e-21
1594 6.02e-22
1595 5.45e-22
1596 9.92e-20
1597 1.11e-19
 
0
5
10
15
20
25

Time 49.6 secs.

Motif 9

Previous Next Top

Summary

Sequence Logo

E-value 1.2e-080
Width 15
Sites 12
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

RRHHCRSKAKRSRHH

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1161 1 3.54e-18 G RRHHCRSKAKRSRHH
1576 1 2.52e-17 S RRHHCRSKAKRARHH
1572 1 2.52e-17 S RRHHCRAKAKRSRHH
1577 1 3.47e-17 S RRHHCRSKAKRSAHH
1575 1 3.47e-17 S RRHHCRSKAKASRHH
1566 1 3.47e-17 S RAHHCRSKAKRSRHH
1553 1 3.47e-17 S ARHHCRSKAKRSRHH
1574 1 7.75e-17 S RRHHCRSKAARSRHH
1573 1 7.75e-17 S RRHHCRSAAKRSRHH
1570 1 1.51e-16 S RRHACRSKAKRSRHH
1567 1 1.51e-16 S RRAHCRSKAKRSRHH
1571 1 5.18e-16 S RRHHARSKAKRSRHH

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1161 3.54e-18
1553 3.47e-17
1566 3.47e-17
1567 1.51e-16
1570 1.51e-16
1571 5.18e-16
1572 2.52e-17
1573 7.75e-17
1574 7.75e-17
1575 3.47e-17
1576 2.52e-17
1577 3.47e-17
 
0
2
4
6
8
10
12
14
16

Time 55 secs.

Motif 10

Previous Next Top

Summary

Sequence Logo

E-value 9.6e-053
Width 15
Sites 10
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[DE][STC][DC][CRV][PG][GP][AKT][CH][INS][CTQ][RNP]G[NCM]G[YCK]

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1101 13 5.10e-22 CPKILKKCRR DSDCPGACICRGNGY CGSGSD
1100 13 5.10e-22 CPKILKACRR DSDCPGACICRGNGY CGSGSD
1099 13 5.10e-22 CPKILAKCRR DSDCPGACICRGNGY CGSGSD
1098 13 5.10e-22 CPKILAACRR DSDCPGACICRGNGY CGSGSD
1097 13 5.10e-22 CPAILKKCRR DSDCPGACICRGNGY CGSGSD
1255 14 2.04e-13 GRTPIKFGKA DCDRPPKHSQNGMGK
1221 11 2.04e-13 GRTPIKFGKA DCDRPPKHSQNGMGK
1122 6 2.04e-13 GLPVCG ETCVGGTCNTPGCTC SWPKCTRN
1121 6 6.21e-13 GLPVCG ETCVGGTCNTPGCKC SWPVCTRN
1306 1 5.91e-11 L DTYSPELFCTIRNFY DADRPDRGAA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1097 5.10e-22
1098 5.10e-22
1099 5.10e-22
1100 5.10e-22
1101 5.10e-22
1121 6.21e-13
1122 2.04e-13
1221 2.04e-13
1255 2.04e-13
1306 5.91e-11
 
0
5
10
15
20
25
30

Time 60.7 secs.

Motif 11

Previous Next Top

Summary

Sequence Logo

E-value 8.6e-044
Width 15
Sites 10
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GRQLR[IR]AG[KR]RL[ER][GR]RS

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1550 6 1.68e-17 RVTSWL GRQLRIAGKRLEGRS K
1548 6 1.68e-17 RVRSWL GRQLRIAGKRLEGRS K
1538 7 1.68e-17 RRVTSWL GRQLRIAGKRLEGRS K
1486 11 1.68e-17 QGAARVTSWL GRQLRIAGKRLEGRS K
1154 0 1.68e-17 GRQLRIAGKRLEGRS K
1155 0 2.14e-16 GRQLRIAGKRLRGRS K
1156 0 5.64e-16 GRQLRIAGRRLRGRS R
1158 0 9.37e-15 GRQLRRAGRRLRGRS R
1157 0 2.36e-14 GRQLRIAGRRLRRRS R
1159 0 2.96e-13 GRQLRRAGRRLRRRS R

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1154 1.68e-17
1155 2.14e-16
1156 5.64e-16
1157 2.36e-14
1158 9.37e-15
1159 2.96e-13
1486 1.68e-17
1538 1.68e-17
1548 1.68e-17
1550 1.68e-17
 
0
5
10
15
20
25

Time 66.2 secs.

Motif 12

Previous Next Top

Summary

Sequence Logo

E-value 3.0e-038
Width 10
Sites 33
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GR[KR]KRRQRRR

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1647 1 9.76e-10 Y GRKKRRQRRR GCYGRKKRRQ
1646 1 9.76e-10 Y GRKKRRQRRR
1307 5 9.76e-10 LGISY GRKKRRQRRR PPQ
1217 15 9.76e-10 ETWWTEWSQP GRKKRRQRRR PPQ
1182 2 9.76e-10 GY GRKKRRQRRR G
1150 0 9.76e-10 GRKKRRQRRR PWQ
1149 0 9.76e-10 GRKKRRQRRR PPQTYADFIA
1148 0 9.76e-10 GRKKRRQRRR PPQGRKKRRQ
1147 0 9.76e-10 GRKKRRQRRR PPQC
1146 0 9.76e-10 GRKKRRQRRR PPQ
1145 0 9.76e-10 GRKKRRQRRR PP
1144 0 9.76e-10 GRKKRRQRRR C
1143 0 9.76e-10 GRKKRRQRRR
1081 10 9.76e-10 FITKALGISY GRKKRRQRRR PPQ
1142 0 6.68e-09 GRKKRRQRRP PQC
1140 0 1.71e-08 GRKKRRQRAR PPQC
1009 15 1.71e-08 LPAVLLALLA PRKKRRQRRR PPQC
1008 15 1.71e-08 LPAVLLALLA PRKKRRQRRR PPQ
1181 2 3.44e-08 GY GRKKRRGRRR THRLPRRRRR
1138 0 6.48e-08 GRKKRRQARA PPQC
1141 0 1.02e-07 GRKKRRQRPP QC
1650 1 3.13e-07 Y GRRARRRRRR
1651 1 5.42e-07 Y GRRRRRRRRR
1165 0 5.42e-07 GRRRRRRRRR PPQ
1139 0 5.70e-07 GRKKRRQPPQ C
1648 1 6.89e-07 Y GRRARRAARR
1649 1 8.36e-07 Y GRRARRRARR
1645 2 1.70e-06 YG RKKKRRQRRR
1644 1 2.05e-06 Y GRAARRAARR
1436 14 2.82e-06 RAVTRAQRRD GRRRRRSRRE SYSVYVYRVL
1642 1 5.38e-06 Y ARKARRAARR
1660 0 6.02e-06 YRRRRRRRRR R
1164 0 1.23e-05 GRRRRRERNK

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1008 1.71e-08
1009 1.71e-08
1081 9.76e-10
1138 6.48e-08
1139 5.70e-07
1140 1.71e-08
1141 1.02e-07
1142 6.68e-09
1143 9.76e-10
1144 9.76e-10
1145 9.76e-10
1146 9.76e-10
1147 9.76e-10
1148 9.76e-10
1149 9.76e-10
1150 9.76e-10
1164 1.23e-05
1165 5.42e-07
1181 3.44e-08
1182 9.76e-10
1217 9.76e-10
1307 9.76e-10
1436 2.82e-06
1642 5.38e-06
1644 2.05e-06
1645 1.70e-06
1646 9.76e-10
1647 9.76e-10
1648 6.89e-07
1649 8.36e-07
1650 3.13e-07
1651 5.42e-07
1660 6.02e-06
 
0
5
10
15
20
25
30
35

Time 71.7 secs.

Motif 13

Previous Next Top

Summary

Sequence Logo

E-value 2.4e-026
Width 10
Sites 14
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

GLWRALWR[AL]L

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1128 0 1.32e-11 GLWRALWRAL WRSLWKSKRK
1127 0 1.32e-11 GLWRALWRAL WRSLWKLKWK
1126 0 1.32e-11 GLWRALWRAL WRSLWKLKRK
1125 0 1.32e-11 GLWRALWRAL WRSLWKKKRK
1124 0 1.32e-11 GLWRALWRAL RSLWKLKRKV
1133 0 2.74e-11 GLWRALWRLL RSLWRLLWSQ
1132 0 2.74e-11 GLWRALWRLL RSLWRLLWRA
1131 0 2.74e-11 GLWRALWRLL RSLWRLLWKA
1130 0 3.85e-11 GLWRALWRGL RSLWKLKRKV
1129 0 3.85e-11 GLWRALWRGL RSLWKKKRKV
1117 0 1.08e-08 GLFRALLRLL RSLWRLLLRA
1480 0 7.96e-08 RLWRALPRVL RRLLRP
1115 0 2.16e-07 GLFEALLELL ESLWELLLEA
1134 0 2.71e-07 GLWWRLWWRL RSWFRLWFRA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1115 2.16e-07
1117 1.08e-08
1124 1.32e-11
1125 1.32e-11
1126 1.32e-11
1127 1.32e-11
1128 1.32e-11
1129 3.85e-11
1130 3.85e-11
1131 2.74e-11
1132 2.74e-11
1133 2.74e-11
1134 2.71e-07
1480 7.96e-08
 
0
5
10
15
20
25

Time 77.4 secs.

Motif 14

Previous Next Top

Summary

Sequence Logo

E-value 6.6e-030
Width 10
Sites 23
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[RW][SL][LQ][WP]K[KLY]K[RG]K[VF]

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1092 17 2.93e-11 LGAAGSTMGA WSQPKSKRKV
1358 17 6.53e-11 LVLAAALQGA WSQPKKKRKV
1218 11 6.53e-11 ETWWETWWTE WSQPKKKRKV
1216 11 6.53e-11 ETWFETWFTE WSQPKKKRKV
1133 17 6.53e-11 RLLRSLWRLL WSQPKKKRKV
1091 17 6.53e-11 LGAAGSTMGA WSQPKKKRKV
1128 11 3.15e-10 LWRALWRALW RSLWKSKRKV
1129 10 5.67e-10 GLWRALWRGL RSLWKKKRKV
1125 11 5.67e-10 LWRALWRALW RSLWKKKRKV
1130 10 7.09e-10 GLWRALWRGL RSLWKLKRKV
1126 11 7.09e-10 LWRALWRALW RSLWKLKRKV
1124 10 7.09e-10 GLWRALWRAL RSLWKLKRKV
1127 11 1.32e-09 LWRALWRALW RSLWKLKWKV
1090 17 5.40e-09 LAAALSLMGL WSQPKKKRRV
1192 9 9.14e-09 HYRIKPTFR RLKWKYKGKF A
1190 9 9.14e-09 HYRIKPTAR RLKWKYKGKF W
1183 9 9.14e-09 HARIKPTFR RLKWKYKGKF W
1036 9 9.14e-09 AYRIKPTFR RLKWKYKGKF W
1191 9 1.21e-08 HYRIKPTFR RLAWKYKGKF W
1119 12 2.27e-08 GSLLKKAGKK LKQPKSKRKV
1027 10 2.34e-07 ALWKTLLKKV LKAPKKKRKV
1635 0 5.15e-07 WRFKKSKRKV
1131 10 1.79e-05 GLWRALWRLL RSLWRLLWKA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1027 2.34e-07
1036 9.14e-09
1090 5.40e-09
1091 6.53e-11
1092 2.93e-11
1119 2.27e-08
1124 7.09e-10
1125 5.67e-10
1126 7.09e-10
1127 1.32e-09
1128 3.15e-10
1129 5.67e-10
1130 7.09e-10
1131 1.79e-05
1133 6.53e-11
1183 9.14e-09
1190 9.14e-09
1191 1.21e-08
1192 9.14e-09
1216 6.53e-11
1218 6.53e-11
1358 6.53e-11
1635 5.15e-07
 
0
5
10
15
20
25

Time 82.6 secs.

Motif 15

Previous Next Top

Summary

Sequence Logo

E-value 3.2e-029
Width 15
Sites 10
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

K[FP]GK[KA][TD][TC][TD][KR]P[TP]K[KH][PS][TGQ]

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1292 6 2.53e-16 KRIPNK KPGKKTTTKPTKKPT IKTTKKDLKP
1291 6 2.53e-16 KRIPNK KPGKKTTTKPTKKPT IKTTKKDLK
1290 6 2.53e-16 KRIPNK KPGKKTTTKPTKKPT IKTTKK
1289 6 2.53e-16 KRIPNK KPGKKTTTKPTKKPT IK
1233 1 2.53e-16 K KPGKKTTTKPTKKPT IKTTKK
1254 9 3.64e-16 KLIKGRTPI KFGKADCDRPPKHSQ NGM
1253 9 3.64e-16 KLIKGRTPI KFGKADCDRPPKHSQ NGK
1252 9 6.58e-16 KLIKGRTPI KFGKADCDRPPKHSG K
1256 9 1.64e-12 KLIKGRTPI KFGKARCRRPPKHSG K
1118 4 9.79e-10 GLGD KFGESIVNANTVLDD LNSRMPQSRH

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1118 9.79e-10
1233 2.53e-16
1252 6.58e-16
1253 3.64e-16
1254 3.64e-16
1256 1.64e-12
1289 2.53e-16
1290 2.53e-16
1291 2.53e-16
1292 2.53e-16
 
0
5
10
15
20
25
30
35

Time 88.2 secs.

Motif 16

Previous Next Top

Summary

Sequence Logo

E-value 1.5e-025
Width 14
Sites 9
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

[FY][AH][DT]F[IP][AQ][ST][AG][IR][TG][GV][GR][RA][NP]

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1663 7 1.53e-16 YTQDFNK FHTFPQTAIGVGAP
1309 10 1.53e-16 LGTYTQDFNK FHTFPQTAIGVGAP
1219 1 1.53e-16 K FHTFPQTAIGVGAP
1058 4 1.53e-16 DFNK FHTFPQTAIGVGAP
1536 12 1.38e-14 RRRRRRRRRT YADFIASGRTGRRN AI
1514 17 1.38e-14 QNRRMKWKKT YADFIASGRTGRRN AI
1149 14 1.38e-14 RRQRRRPPQT YADFIASGRTGRRN AI
1017 22 1.38e-14 LAALAKKILT YADFIASGRTGRRN AI
1094 10 4.56e-11 GDVYADAAPD LFDFLDSSVTTART INA

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1017 1.38e-14
1058 1.53e-16
1094 4.56e-11
1149 1.38e-14
1219 1.53e-16
1309 1.53e-16
1514 1.38e-14
1536 1.38e-14
1663 1.53e-16
 
0
5
10
15
20
25
30
35

Time 93.2 secs.

Motif 17

Previous Next Top

Summary

Sequence Logo

E-value 5.6e-024
Width 15
Sites 4
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

FQWQRNMRKVRGPPV

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1211 2 3.26e-20 KC FQWQRNMRKVRGPPV SSIKR
1210 2 3.26e-20 KC FQWQRNMRKVRGPPV SCIKR
1209 2 3.26e-20 KC FQWQRNMRKVRGPPV SC
1086 0 3.26e-20 FQWQRNMRKVRGPPV S

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1086 3.26e-20
1209 3.26e-20
1210 3.26e-20
1211 3.26e-20
 
0
5
10
15
20

Time 98.5 secs.

Motif 18

Previous Next Top

Summary

Sequence Logo

E-value 3.0e-022
Width 10
Sites 9
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

LPPPV[KHR]LPPP

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1609 2 1.01e-13 VH LPPPVHLPPP VHLPPP
1608 2 1.01e-13 VH LPPPVHLPPP
1607 2 1.82e-13 VE LPPPVELPPP VELPPP
1612 2 7.93e-13 VK LPPPVKLPPP VKLPPP
1611 2 7.93e-13 VK LPPPVKLPPP
1620 2 1.89e-12 VR LPPPVRLPPP VRLPPP
1619 2 1.89e-12 VR LPPPVRLPPP
1348 0 3.48e-09 LPHPVLHMGP LR
1050 2 4.95e-09 CS IPPEVKFNPF VYLI

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1050 4.95e-09
1348 3.48e-09
1607 1.82e-13
1608 1.01e-13
1609 1.01e-13
1611 7.93e-13
1612 7.93e-13
1619 1.89e-12
1620 1.89e-12
 
0
2
4
6
8
10
12
14
16
18

Time 103.9 secs.

Motif 19

Previous Next Top

Summary

Sequence Logo

E-value 1.1e-020
Width 10
Sites 7
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

PRPLPFPRPG

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1523 14 1.36e-12 PRPPRLPRPR PRPLPFPRPG
1463 6 1.36e-12 RLPRPR PRPLPFPRPG
1415 4 1.36e-12 PRPR PRPLPFPRPG
1414 2 1.36e-12 PR PRPLPFPRPG
1413 10 1.36e-12 PRPPRLPRPR PRPLPFPRPG
1412 0 1.36e-12 PRPLPFPRPG
1409 8 1.36e-12 PPRLPRPR PRPLPFPRPG

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1409 1.36e-12
1412 1.36e-12
1413 1.36e-12
1414 1.36e-12
1415 1.36e-12
1463 1.36e-12
1523 1.36e-12
 
0
5
10
15
20

Time 109.3 secs.

Motif 20

Previous Top

Summary

Sequence Logo

E-value 6.4e-014
Width 14
Sites 4
show more
PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Download LOGO
   Orientation:    SSC:    Format:    Width: cm    Height: cm   

Regular expression

AGLQ[FW]PVGRVHRLL

Further Analysis

Submit this motif to  
      
      
 Mouse-over buttons for more information.

Data Formats

View the motif in PSPM Format 
     PSSM Format 
     BLOCKS Format 
     FASTA Format 
     Raw Format 
     or Hide

Sites

Click on any row to highlight sequence in all motifs.

Name Start p-value Sites
1557 20 3.88e-18 RAKAKTRSSR AGLQFPVGRVHRLL RKGC
1556 20 3.88e-18 RAKAKTRSSR AGLQFPVGRVHRLL RKG
1430 1 3.88e-18 R AGLQFPVGRVHRLL RK
1604 5 4.13e-17 TRSSR AGLQWPVGRVHRLL RKGGC

Block Diagrams

The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. Mouse over the center of the motif blocks to see more information.

Name Lowest p-value Motif Location
1430 3.88e-18
1556 3.88e-18
1557 3.88e-18
1604 4.13e-17
 
0
5
10
15
20
25
30
35

Time 114.6 secs.

All Motifs

Top

Combined Block Diagrams

Non-overlapping sites with a p-value better than 0.0001.
The height of the motif "block" is proportional to -log(p-value), truncated at the height for a motif with a p-value of 1e-10.
Click on any row to highlight sequence in all motifs. The motif blocks have tool tips with more information.

Motif 1
Motif 2
Motif 3
Motif 4
Motif 5
Motif 6
Motif 7
Motif 8
Motif 9
Motif 10
Motif 11
Motif 12
Motif 13
Motif 14
Motif 15
Motif 16
Motif 17
Motif 18
Motif 19
Motif 20
Name Combined p-value Motif Location
1001 1.99e-05
1003 3.25e-14
1004 1.53e-10
1005 1.65e-10
1006 4.10e-14
1007 1.02e-12
1008 1.41e-15
1009 2.59e-15
1010 5.13e-12
1011 2.17e-10
1012 1.20e-11
1013 2.65e-10
1014 2.13e-05
1015 9.05e-05
1016 1.53e-08
1017 8.73e-16
1018 1.62e-04
1019 4.01e-06
1020 1.93e-06
1025 7.91e-08
1027 3.04e-04
1028 5.27e-10
1029 2.79e-07
1031 1.35e-06
1032 1.50e-02
1035 5.61e-06
1036 3.34e-02
1039 1.95e-06
1040 5.09e-06
1041 1.02e-06
1042 9.53e-06
1043 1.27e-06
1044 9.56e-07
1045 1.60e-07
1047 4.04e-06
1048 5.09e-07
1049 1.68e-06
1050 7.49e-03
1057 4.15e-07
1058 2.61e-10
1071 1.04e-05
1072 8.38e-08
1079 5.01e-07
1081 1.97e-03
1082 1.61e-01
1086 1.52e-10
1090 3.49e-06
1091 1.71e-06
1092 5.95e-07
1094 5.86e-07
1097 1.22e-10
1098 1.09e-11
1099 8.64e-11
1100 7.44e-11
1101 1.51e-10
1115 1.28e-05
1116 6.06e-04
1117 5.07e-03
1118 3.86e-10
1119 9.59e-05
1120 2.13e-03
1121 1.25e-06
1122 9.59e-07
1124 8.93e-08
1125 4.71e-07
1126 8.24e-07
1127 2.20e-06
1128 7.28e-08
1129 4.16e-07
1130 1.18e-06
1131 1.58e-04
1132 6.01e-04
1133 6.56e-07
1134 4.99e-01
1138 4.26e-03
1139 2.27e-03
1140 7.21e-03
1141 1.02e-03
1142 3.79e-04
1143 9.10e-06
1144 2.01e-05
1145 5.25e-05
1146 9.42e-05
1147 1.02e-03
1148 3.62e-01
1149 7.45e-10
1150 1.37e-04
1154 5.47e-09
1155 8.09e-08
1156 1.38e-07
1157 7.93e-06
1158 1.43e-07
1159 4.53e-06
1161 7.78e-08
1164 1.09e-03
1165 9.20e-03
1171 1.52e-08
1172 4.38e-08
1174 4.44e-09
1175 3.42e-09
1176 1.49e-07
1177 4.18e-04
1179 1.69e-05
1181 3.93e-01
1182 8.18e-05
1183 2.24e-02
1185 2.21e-12
1190 2.03e-02
1191 2.56e-02
1192 1.97e-02
1201 1.06e-02
1203 5.32e-03
1204 1.34e-01
1205 1.12e-01
1207 1.07e-01
1209 8.80e-10
1210 9.63e-10
1211 7.82e-10
1212 1.64e-04
1214 5.25e-07
1215 7.23e-07
1216 2.91e-03
1217 5.07e-03
1218 2.18e-02
1219 1.89e-09
1221 2.55e-15
1222 9.95e-02
1224 1.03e-02
1233 6.01e-06
1238 6.04e-02
1239 6.84e-05
1240 4.97e-05
1243 1.59e-07
1244 7.22e-06
1245 4.02e-06
1246 4.08e-06
1247 8.50e-05
1248 6.39e-03
1249 1.26e-06
1250 7.19e-03
1252 6.06e-07
1253 7.37e-08
1254 5.12e-08
1255 4.27e-15
1256 3.74e-05
1257 1.11e-01
1258 1.77e-02
1261 2.02e-10
1262 4.44e-10
1263 1.61e-07
1265 1.86e-04
1266 1.75e-05
1267 9.74e-07
1269 1.57e-06
1271 3.53e-06
1272 6.96e-06
1274 2.89e-06
1275 4.21e-06
1276 6.28e-06
1277 1.22e-05
1288 2.64e-01
1289 1.15e-05
1290 2.11e-05
1291 2.33e-05
1292 9.57e-05
1297 7.70e-06
1304 1.29e-07
1306 3.66e-05
1307 9.06e-03
1309 1.17e-08
1310 7.83e-06
1311 2.04e-06
1312 5.89e-07
1313 1.32e-07
1314 2.01e-07
1315 3.91e-08
1316 1.43e-07
1317 9.57e-08
1318 2.94e-07
1319 6.11e-04
1322 1.84e-06
1325 1.73e-07
1326 1.58e-06
1327 3.06e-07
1328 7.06e-08
1329 2.39e-07
1330 3.06e-09
1331 3.74e-08
1332 4.15e-05
1333 7.75e-07
1334 6.69e-07
1335 8.17e-07
1336 1.14e-06
1337 9.50e-07
1338 8.78e-08
1339 1.18e-07
1341 4.02e-02
1342 5.82e-02
1343 1.69e-04
1344 2.60e-08
1345 9.39e-05
1346 3.74e-04
1348 7.30e-06
1353 4.59e-03
1354 2.78e-02
1356 6.21e-07
1357 2.04e-07
1358 9.73e-11
1362 1.28e-06
1363 2.74e-06
1364 2.31e-07
1365 3.19e-08
1366 2.61e-09
1367 5.52e-08
1368 9.10e-07
1369 2.42e-06
1370 1.04e-08
1371 4.42e-06
1372 1.66e-07
1374 1.19e-02
1375 1.19e-06
1377 1.72e-07
1379 1.91e-05
1384 3.16e-08
1385 5.24e-07
1386 1.62e-07
1389 2.12e-03
1402 4.59e-02
1409 2.48e-03
1412 7.37e-08
1413 3.90e-03
1414 8.07e-09
1415 4.05e-07
1419 3.92e-06
1420 6.82e-07
1421 1.06e-06
1426 2.79e-03
1430 3.37e-10
1431 8.03e-06
1433 3.71e-10
1436 2.39e-02
1437 5.17e-06
1443 8.59e-04
1444 1.35e-03
1455 8.84e-11
1459 3.00e-09
1460 1.89e-10
1461 1.88e-09
1462 6.89e-09
1463 1.35e-03
1465 1.07e-11
1466 3.76e-08
1467 6.37e-10
1468 2.36e-09
1469 1.25e-09
1470 6.89e-09
1471 1.03e-08
1472 1.09e-08
1473 2.92e-10
1474 1.35e-09
1475 4.97e-09
1476 2.45e-09
1477 5.11e-10
1478 2.07e-06
1479 3.60e-08
1480 1.05e-02
1481 9.90e-10
1483 5.81e-06
1486 6.46e-07
1487 2.93e-06
1488 6.31e-06
1489 1.57e-05
1490 7.57e-06
1491 3.06e-06
1492 9.63e-06
1493 2.77e-06
1494 3.90e-06
1496 5.59e-06
1498 1.02e-06
1499 1.15e-04
1501 1.52e-06
1503 1.15e-05
1505 2.35e-06
1507 3.42e-06
1509 5.52e-06
1511 4.42e-06
1512 1.41e-06
1513 5.61e-08
1514 2.28e-16
1515 4.42e-04
1517 5.04e-03
1521 3.05e-01
1522 5.97e-01
1523 6.16e-03
1533 7.20e-02
1534 1.19e-01
1535 9.57e-01
1536 1.00e-06
1538 4.45e-07
1543 1.67e-03
1544 8.46e-03
1545 4.83e-03
1548 2.92e-06
1550 1.53e-06
1553 1.83e-07
1556 6.72e-09
1557 9.70e-09
1561 2.74e-07
1566 8.78e-08
1567 1.27e-06
1570 2.26e-06
1571 5.25e-06
1572 6.21e-07
1573 1.09e-06
1574 9.62e-07
1575 6.31e-08
1576 8.57e-07
1577 6.19e-07
1579 6.92e-07
1580 1.73e-06
1581 1.73e-06
1582 4.34e-06
1585 8.18e-03
1589 1.56e-13
1591 2.50e-13
1592 3.47e-14
1594 3.68e-14
1595 1.56e-13
1596 1.15e-11
1597 5.84e-11
1600 7.51e-01
1601 8.38e-01
1604 2.69e-07
1607 1.85e-06
1608 9.02e-09
1609 2.90e-06
1611 8.09e-08
1612 1.21e-04
1619 1.17e-07
1620 6.39e-05
1623 2.95e-04
1624 1.38e-02
1626 9.88e-06
1627 1.06e-06
1628 2.12e-07
1629 3.86e-07
1630 4.06e-06
1631 9.67e-06
1634 1.07e-11
1635 5.99e-04
1640 4.26e-02
1641 2.92e-02
1642 1.87e-02
1643 3.24e-02
1644 8.84e-03
1645 1.55e-02
1646 6.38e-05
1647 2.37e-01
1648 4.99e-03
1649 6.10e-03
1650 5.23e-03
1651 4.72e-03
1655 5.25e-02
1656 1.62e-02
1660 2.95e-02
1663 1.87e-08
 
0
10
20
30
40
50
60
Motif 1
Motif 2
Motif 3
Motif 4
Motif 5
Motif 6
Motif 7
Motif 8
Motif 9
Motif 10
Motif 11
Motif 12
Motif 13
Motif 14
Motif 15
Motif 16
Motif 17
Motif 18
Motif 19
Motif 20
Top
MEME version
4.7.0 (Release date: Wed Sep 28 17:30:10 EST 2011)
Reference
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
show training set...
Command line summary

Letter frequencies in dataset
A: 0.087   C: 0.020   D: 0.018   E: 0.019   F: 0.027   G: 0.047   H: 0.023   I: 0.054   K: 0.139   L: 0.094   M: 0.017   N: 0.024   P: 0.051   Q: 0.033   R: 0.179   S: 0.045   T: 0.039   V: 0.027   W: 0.037   Y: 0.020

Background letter frequencies (from dataset with add-one prior applied):
A: 0.087   C: 0.020   D: 0.018   E: 0.019   F: 0.027   G: 0.047   H: 0.023   I: 0.054   K: 0.139   L: 0.094   M: 0.017   N: 0.024   P: 0.051   Q: 0.033   R: 0.179   S: 0.045   T: 0.039   V: 0.027   W: 0.037   Y: 0.020

Stopping Reason
Stopped because nmotifs = 20 reached. Program ran on crdd.imtech.res.in.
show model parameters...

Explanation of MEME Results

Top

The MEME results consist of

  • The overview of all discovered motifs.
  • Information on each of the motifs MEME discovered, including:
    1. A summary table showing the width, number of contributing sites, log likelihood ratio, statistical significance, information content and relative entropy of the motif.
    2. A sequence LOGO.
    3. Downloadable LOGO files suitable for publication.
    4. A regular expression describing the motif.
    5. Some further analysis that can be performed on the motif.
    6. A list of data formats describing the motif.
    7. The contributing sites of the motif sorted by p-value and aligned with each other.
    8. The block diagrams of the contributing sites of the motif within each sequence in the training set.
  • A combined block diagram showing an optimized (non-overlapping) tiling of all of the motifs onto each of the sequences in the training set.
  • The version of MEME and the date it was released.
  • The reference to cite if you use MEME in your research.
  • A description of the sequences you submitted (the "training set") showing the name, "weight" and length of each sequence.
  • The command line summary detailing the parameters with which you ran MEME.
  • The reason why MEME stopped and the name of the CPU on which it ran.
  • This explanation of how to interpret MEME results.

Motifs

For each motif that it discovers in the training set, MEME prints the following information:

Summary Table

This summary table gives the main attributes of the motif.

E-value
The statistical significance of the motif. MEME usually finds the most statistically significant (low E-value) motifs first. The E-value of a motif is based on its log likelihood ratio, width, sites, the background letter frequencies (given in the command line summary), and the size of the training set. The E-value is an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and site count, that one would find in a similarly sized set of random sequences. (In random sequences each position is independent with letters chosen according to the background letter frequencies.)
Width
The width of the motif. Each motif describes a pattern of a fixed with as no gaps are allowed in MEME motifs.
Sites
The number of sites contributing to the construction of the motif.
Log Likelihood Ratio
The log likelihood ratio of the motif.The log likelihood ratio is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model (likelihood given the motif) versus their probability given the background model (likelihood given the null model). (Normally the background model is a 0-order Markov model using the background letter frequencies, but higher order Markov models may be specified via the -bfile option to MEME.)
Information Content
The information content of the motif in bits. It is equal to the sum of the uncorrected information content, R(), in the columns of the LOGO. This is equal relative entropy of the motif relative to a uniform background frequency model.
Relative Entropy
The relative entropy of the motif, computed in bits and relative to the background letter frequencies given in the command line summary. It is equal to the log-likelihood ratio (llr) divided by the number of contributing sites of the motif times 1/ln(2),

re = llr / (sites * ln(2)).
Sequence LOGO

MEME motifs are represented by position-specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif. These are displayed as "sequence LOGOS", containing stacks of letters at each position in the motif. The total height of the stack is the "information content" of that position in the motif in bits. The height of the individual letters in a stack is the probability of the letter at that position multiplied by the total information content of the stack.

Note: The MEME LOGO differs from those produced by the Weblogo program because a small-sample correction is NOT applied. However, MEME LOGOs in PNG and encapsulated postscript (EPS) formats with small-sample correction (SSC) are available by clicking on the download button with "SSC" set to "on" under Download LOGO. The MEME LOGOs without small sample correction are similarly available. Error bars are included in the LOGOs with small-sample correction.

Modern web browsers supporting the canvas element and it's text manipulation functions as described in the html 5 standard, can render the sequence LOGOs without needing the images. The browsers which work with this feature are:

  • Firefox 3.5 and above
  • Safari 4 and above
  • Google Chrome 4 and above

Unfortunately Internet Explorer 8 does not support any html 5 features.

The information content of each motif position is computed as described in the paper by Schneider and Stephens, "Sequence Logos: A New Way to Display Consensus Sequences" but the small-sample correction, e(n), is set to zero for the LOGO displayed in the MEME output. The corrected information content of position i is given by

            R(i) for amino acids   = log2(20) - (H(i) + e(n))   (1a) 
            R(i) for nucleic acids =    2    - (H(i) + e(n))    (1b)
          

where H(i) is the entropy of position i,

            H(l) = - (Sum f(a,i) * log2[ f(a,i) ]).             (2)
          

Here, f(a,i) is the frequency of base or amino acid a at position i, and e(n) is the small-sample correction for an alignment of n letters. The height of letter a in column i is given by

            height = f(a,i) * R(i)                              (3)
          

The approximation for the small-sample correction, e(n), is given by:

            e(n) = (s-1) / (2 * ln(2) * n),                     (4)
          

where s is 4 for nucleotides, 20 for amino acids, and n is the number of sequences in the alignment.

The letters in the logos are colored as follows.
For DNA sequences, the letter categories contain one letter each.

NUCLEIC ACIDS COLOR
A RED
C BLUE
G ORANGE
T GREEN

For proteins, the categories are based on the biochemical properties of the various amino acids.

AMINO ACIDS COLOR PROPERTIES
A, C, F, I, L, V, W and M BLUE Most hydrophobic[Kyte and Doolittle, 1982]
NQST GREEN Polar, non-charged, non-aliphatic residues
DE MAGENTA Acidic
KR RED Positively charged
H PINK  
G ORANGE  
P YELLOW  
Y TURQUOISE  

J. Kyte and R. Doolittle, 1982. "A Simple Method for Displaying the Hydropathic Character of a Protein", J. Mol Biol. 157, 105-132.

Note: the "text" output format of MEME preserves the historical MEME format where LOGOS are replaced by a simplified probability matrix, a relative entropy plot, and a multi-level consensus sequence.

Download LOGO

Logos can be generated on the fly by the meme webservice and you may specify a number of options to customize them to your needs. The options are:

Orientation
Only valid for nucleotide motifs. Generate the standard view or the reverse complemented view of the motif.
SSC
Use small sample correction and show errorbars on the image. Small sample correction is used by the Weblogo program.
Format
The format of the generated image. If the image is to be used on the web then png is recommend. If the image is to be published then eps is recommended.
Width
The width of the generated image in centimetres.
Height
The height of the generated image in centimetres.

Regular Expression

This is a regular expression (RE) describing the motif. In each column, all letters with observed frequencies greater than 0.2 are shown; less-frequent letters are not included in the RE. MEME regular expressions are interpreted as follows: single letters match that letter; groups of letters in square brackets match any of the letters in the group. Regular expressions can be used for searching for the motif in sequences (using, for example, PatMatch) but the search accuracy will usually be better with the PSSM (using, for example MAST.)

Further Analysis

Either as a group or individually the motifs have a number of options for further analysis.

MAST
Finds the best matching positions for a set of motifs in each sequence provided to it, ranked by the combined score of each sequence. For more information about MAST please read the introduction.
FIMO
Finds all matches for a motif. For more information about FIMO please read the introduction.
TOMTOM
Compares a single motif to a database of motifs. For more information about TOMTOM please read the introduction.
GOMO
Identifies possible roles of DNA binding motifs. For more information about GOMO please read the introduction.
BLOCKS
Submit to Blocks Multiple Alignment Processor where you can do several things like create phylogeny trees and search the blocks against a database of other blocks (protein only). For more information about BLOCKS Multiple Alignment Processor please visit the website.
Data Formats

The extracted data is avaliable in the following formats.

PSPM Format
The motif itself is a position-specific probability matrix giving, for each position in the pattern, the observed frequency ("probability") of each possible letter. The probability matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The motif is preceded by a line starting with "letter-probability matrix:" and containing the length of the alphabet, width of the motif, number of occurrences of the motif, and the E-value of the motif.
Note: Earlier versions of MEME gave the posterior probabilities--the probability after applying a prior on letter frequencies--rather than the observed frequencies. These versions of MEME also gave the number of possible positions for the motif rather than the actual number of occurrences. The output from these earlier versions of MEME can be distinguished by "n=" rather than "nsites=" in the line preceding the matrix.
PSSM Format
The position-specific scoring matrix corresponding to the motif is printed for use by database search programs such as MAST. This matrix is a log-odds matrix calculated by taking 100 times the log (base 2) of the ratio p/f at each position in the motif where p is the probability of a particular letter at that position in the motif, and f is the background frequency of the letter (given in the command line summary section.) This is the same matrix that is used above in computing the p-values of the occurrences of the motif in the Sites and Block Diagrams sections. The scoring matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The scoring matrix is preceded by a line starting with "log-odds matrix:" and containing the length of the alphabet, width of the motif, number of characters in the training set, the scoring threshold (obsolete) and the motif E-value.
Note: The probability p used to compute the PSSM is not exactly the same as the corresponding value in the Position Specific Probability Matrix (PSPM). The values of p used to compute the PSSM take into account the motif prior, whereas the values in the PSPM are just the observed frequencies of letters in the motif sites.
BLOCKS Format
For use with BLOCKS tools.
FASTA Format
The FASTA format as described here.
Raw Format
Just the sites of the sequences that contributed to the motif. One site per line.
Sites

MEME displays the occurrences (sites) of the motif in the training set. The sites are shown aligned with each other, and the ten sequence positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs, the strand (if both strands of DNA sequences are being used), and the position in the sequence where the site begins. When the DNA strand is specified, '+' means the sequence in the training set, and '-' means the reverse complement of the training set sequence. (For '-' strands, the 'start' position is actually the position on the positive strand where the site ends.) The sites are listed in order of increasing statistical significance (p-value). The p-value of a site is computed from the the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the position p-value by the MAST algorithm.)

Block Diagrams

The occurrences of the motif in the training set sequences are shown as coloured blocks on a line. One diagram is printed for each sequence showing all the sites contributating to that motif in that sequence. The sequences are listed in the same order as in the input to make it easier to compare multiple block diagrams. Additionally the best p-value for the sequence/motif combination is listed though this may not be in ascending order as with the sites. The p-value of an occurrence is the probability of a single random subsequence the length of the motif, generated according to the 0-order background model, having a score at least as high as the score of the occurrence. When the DNA strand is specified '+', it means the motif appears from left to right on the sequence, and '-' means the motif appears from right to left on the complementary strand. A sequence position scale is shown at the end of each table of block diagrams.

Combined Block Diagrams

The motif occurrences shown in the motif summary may not be exactly the same as those reported in each motif section because only motifs with a position p-value of 0.0001 that don't overlap other, more significant motif occurrences are shown.

See the documentation for MAST output for the definition of position and combined p-values.