Your Weeder Web Results

NEW: Starting a large job on file /tmp/motif_master/102_WEEDER/aiy_500.fa

Organism code: CE

Processing both strands

/ulhhmi/alok/local/programs/Weeder1.2/weederlauncher.out /tmp/motif_master/102_WEEDER/aiy_500.fa CE large S


Searching for motifs of length 6 with 1 mutations.....

(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/102_WEEDER/aiy_500.fa -R 50 -O CE -W 6 -e 1 -N -S -T 10 )
1) ATTTTT 1.60
2) ATGAGG 1.20
3) GGCTCA 1.19
4) TTGGCT 1.18
5) AGCCCA 1.14
6) CGACTA 1.13
7) TTGCAA 1.10
8) GCTCAA 1.08
9) GCATCG 1.08
10) CGTCAC 1.03

Elapsed time : 0 min. 0 sec.


Searching for motifs of length 8 with 2 mutations.....

(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/102_WEEDER/aiy_500.fa -R 50 -O CE -W 8 -e 2 -N -S -T 10 )
1) GGCTCAAT 2.19
2) ACGTCAGG 1.71
3) AATTGGCT 1.61
4) GCTTTAAC 1.58
5) GGCTTCGT 1.54
6) TGGCTCAA 1.53
7) TATTCATA 1.52
8) GCAACATG 1.51
9) CCAATATG 1.49
10) CGAAGTCA 1.48

Elapsed time : 0 min. 6 sec.


Searching for motifs of length 10 with 3 mutations.....

(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/102_WEEDER/aiy_500.fa -R 50 -O CE -W 10 -e 3 -N -S -T 10 )
1) GAAGGCATTG 2.33
2) TTGGCTTCGT 2.22
3) GCATTGAGCC 2.16
4) GTGAAGGCAT 2.06
5) ACACGTCACG 1.99
6) ATTGGCTTCG 1.97
7) GCCGTAGAAT 1.96
8) TGACTTCATC 1.94
9) TGAAGGCATT 1.91
10) TTGGCTCAAT 1.90

Elapsed time : 2 min. 25 sec.


Searching for motifs of length 12 with 4 mutations.....

(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/102_WEEDER/aiy_500.fa -R 50 -O CE -W 12 -e 4 -N -S -T 10 )
1) GTGAAGGCATTG 3.76
2) GAAGGCATTGAG 3.56
3) TAGATTAGACAA 3.49
4) ATTGGCTTCGTT 3.41
5) CCGATGTGAGAC 3.39
6) TGAAGGCATTGA 3.37
7) TAAATTAGCCAA 3.34
8) CGAAGTCAATTA 3.30
9) TATGAATAGGAG 3.28
10) GAGGAAGCCAAT 3.26

Elapsed time : 20 min. 34 sec.


Your sequences:

Sequence 1 : >III:5795689..5796188
Sequence 2 : >X:11767328..11767827
Sequence 3 : >III:7833475..7833974
Sequence 4 : >II:10912613..10913112
Sequence 5 : >I:14142002..14142501
Sequence 6 : >X:7118384..7118883
Sequence 7 : >IV:3625582..3626081
Sequence 8 : >X:15292788..15293287


**** MY ADVICE ****


*** Interesting motifs (highest-ranking) seem to be :


GGCTCAAT
ATTGAGCC

5 redundant motifs found:
TTGGCTCAAT - GCATTGAGCC - TGGCTCAA - GCTCAA - GGCTCA -

Best occurrences (match percentage):
Seq St oligo pos match
1 + [GTCTCATT] 37 (87.49)
1 + [TACTCAAT] 66 (88.69)
1 + .GGCTCAAT. 249 (100.00)
2 + [GATTCAAT] 44 (85.73)
2 + [GGTTAAAT] 365 (86.15)
2 + [TGCTCACT] 395 (86.94)
2 + .GGCTCAAT. 413 (100.00)
2 - [GACTCATT] 326 (87.49)
3 + [TGCTTAAT] 414 (85.35)
3 - [GGCTAATT] 224 (87.92)
3 - .GGCTCAGT. 65 (90.30)
4 + .TGCTCAAA. 116 (91.02)
4 - [GTCTCAAA] 286 (89.20)
5 + .TGCTCAAT. 34 (95.25)
5 + [AGCTCAAA] 374 (88.64)
5 - [GGCTCGTT] 246 (87.02)
5 - [GACTCGAT] 121 (86.40)
5 - .GGCTCAAT. 109 (100.00)
5 - [GGCTAATT] 52 (87.92)
5 - [GTCACAAT] 10 (85.91)
6 - [GTCACAAT] 471 (85.91)
6 - [TACTCAAT] 27 (88.69)
7 + [GGCACAAA] 98 (88.24)
7 + .TGCTCAAA. 118 (91.02)
7 + [AGCTCAAA] 126 (88.64)
7 + .GGCTCAAT. 249 (100.00)
7 - [GTCTCAAA] 435 (89.20)
7 - [GGCTCGAA] 256 (88.73)
8 + [TGCTAAAT] 134 (89.12)
8 + [GGCAAAAT] 249 (86.34)
8 + [GGTTAAAT] 454 (86.15)
8 - [GGTTCAAA] 393 (88.05)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 4 1 32 8| 0 0 5 3
2 5 1 34 5| 0 0 8 0
3 2 38 1 4| 0 8 0 0
4 4 3 2 36| 0 0 0 8
5 6 36 1 2| 0 8 0 0
6 39 1 5 0| 8 0 0 0
7 34 3 2 6| 7 0 1 0
8 9 3 2 31| 2 0 0 6






GAAGGCATTG
CAATGCCTTC

4 redundant motifs found:
TGAAGGCATTGA - GAAGGCATTGAG - GTGAAGGCATTG - TGAAGGCATT -

Best occurrences (match percentage):
Seq St oligo pos match
1 + [GAAGGCAGCA] 289 (86.52)
1 - .GAAGACACTG. 232 (93.79)
1 - .GAAGACGATG. 173 (90.20)
1 - .GGAGGCAATG. 53 (93.41)
2 + .GAAGACAATT. 75 (93.37)
2 + [AAAAACATTT] 190 (86.33)
2 + [GAAATAAGTG] 228 (85.94)
2 - .GAAGCCAATA. 245 (91.36)
2 - [GAAATCAGTG] 111 (89.67)
2 - [GAAAATATTA] 92 (86.42)
2 - .GAAGTTATTA. 12 (90.46)
3 + [GACGGCATCG] 3 (87.33)
3 + [AAAAACAATG] 43 (86.66)
3 + [GATGAAATTA] 75 (85.15)
3 + [GGTGACATTT] 246 (85.13)
3 - .CAACGCATTG. 48 (91.90)
4 + .GAAGGCTTTG. 280 (95.44)
4 + [AAACACATTG] 309 (87.98)
4 - .GGAGACATTT. 372 (90.67)
4 - [CAAAACATTT] 215 (87.85)
4 - [GATGAAATTT] 69 (86.04)
5 + .GAAGGCATTG. 103 (100.00)
5 - [GGAAAAATTG] 38 (85.58)
6 + .GAAGGAATTC. 6 (91.58)
6 + [CAACGAATTG] 51 (88.17)
6 + .GAAGCCAATT. 249 (92.25)
6 + [AAAAGCAATT] 262 (86.79)
6 + [AAAGCAATTT] 263 (85.11)
6 + .CAAATCATTG. 295 (90.53)
6 - [GAAACTATTT] 202 (86.19)
7 + .GAAGTCAATT. 217 (93.77)
7 + [GAATTCAATA] 341 (86.21)
7 + [GAAAGAAATA] 359 (87.52)
7 + .GAAGGAATTG. 381 (96.26)
7 - [GAAAGCTTTA] 487 (88.64)
8 + [CAAGCCGATG] 89 (85.25)
8 + .GATGGCAATT. 197 (90.24)
8 + [GAAGTCTCTG] 345 (89.64)
8 - .GAAGTCACTT. 11 (91.91)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 2 4 23 0| 0 2 15 0
2 25 0 3 1| 15 0 2 0
3 25 1 1 2| 16 0 0 1
4 4 3 21 1| 1 1 15 0
5 5 3 15 6| 4 2 7 4
6 4 22 0 3| 2 14 0 1
7 24 0 2 3| 15 0 1 1
8 7 3 2 17| 7 2 0 8
9 1 2 0 26| 0 0 0 17
10 4 2 17 6| 2 1 8 6






GTGAAGGCATTG
CAATGCCTTCAC

5 redundant motifs found:
TGAAGGCATTGA - GAAGGCATTGAG - TGAAGGCATT - GTGAAGGCAT - GAAGGCATTG -

Best occurrences (match percentage):
Seq St oligo pos match
1 - [GAGAAGACACTG] 232 (88.63)
1 - [GTCAAGACAGAG] 147 (85.19)
2 + [GTCAAATAATTT] 202 (85.49)
3 + [GTGACGGCATCG] 1 (85.94)
3 - [GGCAACGCATTG] 48 (87.88)
4 + .GAGAAGGCTTTG. 278 (91.19)
4 - [GTGATGAAATTT] 69 (86.04)
5 + .GTGAAGGCATTG. 101 (100.00)
6 + [CTGAAGGAATTC] 4 (89.14)
6 + [GGCAACGAATTG] 49 (85.11)
6 + [GACAAATCATTG] 293 (87.94)
6 - [GTGAAACTATTT] 202 (85.39)
7 + .GTGAAGGAATTG. 379 (97.22)
8 - [CTGAAGTCACTT] 11 (85.08)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 1 3 19 1| 0 0 3 0
2 4 2 2 16| 1 0 0 2
3 1 4 16 3| 0 0 3 0
4 22 0 1 1| 3 0 0 0
5 19 1 2 2| 3 0 0 0
6 4 3 15 2| 0 0 3 0
7 4 2 13 5| 0 0 3 0
8 5 16 0 3| 1 2 0 0
9 20 2 0 2| 2 0 0 1
10 1 2 3 18| 0 0 0 3
11 3 1 1 19| 0 0 0 3
12 3 3 14 4| 0 0 3 0





*** Interesting motifs (not highest-ranking) can also be :


TTGGCTTCGT
ACGAAGCCAA

4 redundant motifs found:
ATTGGCTTCGTT - TTGGCTCAAT - ATTGGCTTCG - GGCTTCGT -

Best occurrences (match percentage):
Seq St oligo pos match
1 + [TTGTCTCATT] 35 (86.93)
1 + [TTGTCTCTGT] 143 (87.60)
1 + .TTGACTTCAT. 154 (90.31)
1 + [TCGTCTTCTT] 175 (86.41)
1 + [TTGGCTCAAT] 247 (87.64)
1 - [TTGGCTGTGT] 279 (86.83)
2 + .TTGGCTTCGT. 247 (100.00)
2 - .TTGTCTTCGG. 73 (90.25)
3 + .TTGTCTTATT. 17 (91.11)
3 + [TTTGCTTTTT] 316 (87.06)
4 + [TTAGTTTAGT] 247 (85.08)
5 - [TTATCTTCTT] 289 (88.84)
5 - [TTAACTTCTT] 229 (86.63)
5 - [TGGGCTCCGT] 150 (88.48)
5 - [TTGGCTAATT] 52 (86.16)
6 + [TTTGTTTCTT] 61 (87.27)
6 - .TTGGCTTCCT. 247 (92.83)
6 - [TTGTGTTCTT] 120 (86.74)
7 + [TTGGCTCAAT] 247 (87.64)
7 - .TTGACTTCGT. 215 (94.57)
8 - [TTGTTTTTTT] 424 (85.25)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 2 2 2 31| 0 0 0 6
2 2 2 3 30| 0 0 0 6
3 4 1 28 4| 0 0 6 0
4 4 3 22 8| 2 0 2 2
5 2 27 2 6| 0 6 0 0
6 2 2 0 33| 0 0 0 6
7 2 7 2 26| 0 0 0 6
8 7 24 1 5| 1 5 0 0
9 5 2 19 11| 1 1 3 1
10 1 1 4 31| 0 0 1 5






GAAGGCATTGAG
CTCAATGCCTTC

3 redundant motifs found:
TGAAGGCATTGA - GTGAAGGCATTG - GAAGGCATTG -

Best occurrences (match percentage):
Seq St oligo pos match
1 - [GAAGACACTGCC] 230 (86.25)
1 - [GAAGACGATGAT] 171 (85.66)
1 - [GGAGGCAATGCG] 51 (89.81)
2 + [GAAGACAATTAT] 75 (89.52)
3 + [GGTGACATTTAG] 246 (86.39)
4 + .GAAGGCTTTGAG. 280 (95.43)
5 + .GAAGGCATTGAG. 103 (100.00)
5 - [GGAAAAATTGAG] 36 (88.51)
6 + [GAAGGAATTCAC] 6 (88.28)
6 + [CAAATCATTGCG] 295 (87.00)
7 + .GAAGTCAATTAG. 217 (92.42)
7 + [GAAGGAATTGGG] 381 (89.25)
7 - [GGAGATATGGAG] 172 (85.41)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 1 3 19 1| 0 0 3 0
2 17 2 4 1| 3 0 0 0
3 20 1 1 2| 3 0 0 0
4 4 3 16 1| 0 0 3 0
5 7 1 10 6| 0 0 2 1
6 4 17 0 3| 0 3 0 0
7 19 1 1 3| 2 0 0 1
8 5 2 1 16| 1 0 0 2
9 0 1 2 21| 0 0 0 3
10 1 3 16 4| 0 0 2 1
11 18 4 1 1| 3 0 0 0
12 2 3 15 4| 0 0 3 0






GGCTCA
TGAGCC

3 redundant motifs found:
TGGCTCAA - GGCTCAAT - GCTCAA -

Best occurrences (match percentage):
Seq St oligo pos match
1 + .GTCTCA. 37 (94.22)
1 + [TTCTCA] 239 (88.55)
1 + .GGCTCA. 249 (100.00)
1 + [TGATCA] 260 (87.70)
1 + .GGCGCA. 271 (91.96)
1 + .GGCTCT. 448 (90.10)
1 - [TGATCA] 260 (87.70)
2 + [GTCGCA] 58 (86.18)
2 + [TTCTCA] 216 (88.55)
2 + [TTCTCA] 303 (88.55)
2 + .TGCTCA. 395 (94.33)
2 + .GGCTCA. 413 (100.00)
2 - .GACTCA. 328 (90.10)
2 - [AGATCA] 155 (85.64)
3 + .GGATCA. 97 (93.37)
3 - .GGCTAA. 226 (91.96)
3 - .GGGTCA. 118 (90.10)
3 - [GTCTAA] 87 (86.18)
3 - .GGCTCA. 67 (100.00)
4 + .TGCTCA. 116 (94.33)
4 + .GGCGCA. 296 (91.96)
4 + [GGAGCA] 304 (85.33)
4 + [GGATAA] 423 (85.33)
4 + [TGCTAA] 457 (86.29)
4 - .GTCTCA. 288 (94.22)
4 - [TTCTCA] 277 (88.55)
4 - [GGCTGA] 98 (89.90)
5 + .TGCTCA. 34 (94.33)
5 + [AGCTCG] 135 (85.64)
5 + .GGCTCA. 145 (100.00)
5 + [GGAGCA] 169 (85.33)
5 + .AGCTCA. 374 (92.27)
5 - [TTCTCA] 387 (88.55)
5 - .GGCTCG. 248 (93.37)
5 - .GGCTCC. 152 (90.10)
5 - .GGCTCA. 111 (100.00)
5 - .GGATCA. 90 (93.37)
5 - .GGCTAA. 54 (91.96)
6 + .GGATCA. 450 (93.37)
6 - [GTCTAA] 290 (86.18)
6 - [TGCTCG] 276 (87.70)
7 + [GGCACA] 98 (89.90)
7 + [ATCTCA] 105 (86.49)
7 + .TGCTCA. 118 (94.33)
7 + .AGCTCA. 126 (92.27)
7 + .GGCTCA. 249 (100.00)
7 + [TTCTCA] 397 (88.55)
7 + .GGCTCG. 421 (93.37)
7 - .GTCTCA. 437 (94.22)
7 - [AGCTCG] 425 (85.64)
7 - [ATCTCA] 369 (86.49)
7 - .GGCTCG. 258 (93.37)
7 - [AGCTCG] 187 (85.64)
8 + [AGATCA] 85 (85.64)
8 + [TGCTAA] 134 (86.29)
8 - .GGTTCA. 395 (90.10)
8 - [ATCTCA] 289 (86.49)
8 - .GTCTCA. 99 (94.22)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 2 0 27 4| 2 0 25 4
2 1 0 28 4| 1 0 26 4
3 3 28 1 1| 3 26 1 1
4 1 0 2 30| 0 0 2 29
5 2 30 1 0| 2 29 0 0
6 28 1 3 1| 26 1 3 1






GCATTGAGCC
GGCTCAATGC

2 redundant motifs found:
TTGGCTCAAT - GGCTCAAT -

Best occurrences (match percentage):
Seq St oligo pos match
1 - [GTGTTGCGCC] 271 (87.58)
1 - .AAATTGAGCC. 249 (97.01)
1 - [AAATTGAGTA] 66 (86.79)
2 + [AAAATGAGTC] 324 (85.52)
2 - .AGATTGAGCC. 413 (91.25)
2 - [GTATTGAATC] 44 (87.60)
3 + .ACACTGAGCC. 63 (91.52)
3 + [ACAATGACCC] 114 (85.28)
4 + .GCTTTGAGAC. 284 (90.38)
5 + .GCATTGAGCC. 107 (100.00)
5 - [GTTTTGAGCT] 374 (86.28)
5 - .AAATTGAGCA. 34 (91.90)
7 + [GTTTTGAGAC] 433 (88.20)
7 - [GAATTGCGGC] 326 (86.65)
7 - .GAATTGAGCC. 249 (99.12)
7 - [AATTTGAGCT] 126 (85.47)
7 - [GATTTGTGCC] 98 (87.58)
8 + [ACTTTGAACC] 391 (89.39)
8 - [GAATTTAACC] 454 (87.37)
8 - [GAATTTAGCA] 134 (87.37)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 7 1 15 2| 4 0 3 0
2 8 11 1 5| 3 3 1 0
3 17 1 2 5| 6 0 0 1
4 2 2 1 20| 0 1 0 6
5 0 1 1 23| 0 0 0 7
6 1 0 22 2| 0 0 7 0
7 19 4 1 1| 7 0 0 0
8 3 2 19 1| 0 0 7 0
9 2 19 1 3| 1 6 0 0
10 3 19 2 1| 1 6 0 0






GTGAAGGCAT
ATGCCTTCAC

2 redundant motifs found:
GTGAAGGCATTG - TGAAGGCATT -

Best occurrences (match percentage):
Seq St oligo pos match
1 + [AAGAAGGCAG] 287 (86.50)
1 - [GTTAAAGCTT] 478 (86.07)
1 - [GAGAAGACAC] 234 (85.04)
1 - [ATGAAGTCAA] 154 (87.72)
1 - [GTCAAGACAG] 149 (86.44)
2 + [GTTAAAGCAG] 166 (86.48)
2 - [CTGATGGCTT] 35 (85.41)
3 + .GTGACGGCAT. 1 (91.47)
4 + .GAGAAGGCTT. 278 (90.45)
4 - [GTGATGAAAT] 71 (86.30)
5 + .GTGAAGGCAT. 101 (100.00)
6 + .CTGAAGGAAT. 4 (91.27)
6 + [ATGAGGTCAT] 181 (87.44)
6 - [GTCAAGATAT] 460 (86.44)
6 - [GTGAAACTAT] 204 (85.17)
7 + .GTGAAGGAAT. 379 (95.64)
7 - [CTGAAAGCTT] 489 (86.22)
8 - [ATGAGGGAAT] 216 (85.82)
8 - [GTGATGTCAG] 108 (87.44)
8 - [CTGAAGTCAC] 13 (86.58)

Frequency Matrix
All Occs Best Occs
ACGT ACGT
1 4 4 19 1| 0 1 4 0
2 4 1 1 22| 1 0 0 4
3 1 3 20 4| 0 0 5 0
4 26 0 1 1| 5 0 0 0
5 21 1 3 3| 4 1 0 0
6 4 1 21 2| 0 0 5 0
7 4 2 16 6| 0 0 5 0
8 4 19 1 4| 2 3 0 0
9 22 2 0 4| 4 0 0 1
10 3 2 4 19| 0 0 0 5