Your Weeder Web Results
NEW: Starting a large job on file /tmp/motif_master/12050_WEEDER/mec3_top20_u2_3_19.fa
Organism code: CE
Processing both strands
/ulhhmi/alok/local/programs/Weeder1.2/weederlauncher.out /tmp/motif_master/12050_WEEDER/mec3_top20_u2_3_19.fa CE large S
Searching for motifs of length 6 with 1 mutations.....
(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/12050_WEEDER/mec3_top20_u2_3_19.fa -R 50 -O CE -W 6 -e 1 -N -S -T 10 )
1) CGCTGC 2.22
2) GCGAGA 2.19
3) CCATCG 2.18
4) AGGGCG 1.96
5) GCGTCG 1.96
6) TCGCTG 1.90
7) TACGGT 1.88
8) CGCCGT 1.82
9) GGAGCG 1.81
10) TGAGCG 1.79
Elapsed time : 0 min. 0 sec.
Searching for motifs of length 8 with 2 mutations.....
(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/12050_WEEDER/mec3_top20_u2_3_19.fa -R 50 -O CE -W 8 -e 2 -N -S -T 10 )
1) CGCCGTTT 3.07
2) GCGCCGTT 2.75
3) GAGCGTCG 2.72
4) CATCGCTG 2.70
5) AAAGGGCG 2.70
6) TGCGATGG 2.66
7) AACGGCGG 2.65
8) GCGTAACC 2.61
9) GCCCCGTG 2.58
10) TCGCTGCG 2.55
Elapsed time : 0 min. 1 sec.
Searching for motifs of length 10 with 3 mutations.....
(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/12050_WEEDER/mec3_top20_u2_3_19.fa -R 50 -O CE -W 10 -e 3 -N -S -T 10 )
1) GCGTAACCGT 4.01
2) ATGAGCGTCG 3.77
3) CGTAACCGTA 3.74
4) TGAGGCAGTA 3.65
5) CCTCCCGCAC 3.40
6) CGCGTAACCG 3.39
7) CGACGCACAT 3.38
8) GCCTAAAATG 3.37
9) AAACGGCGGC 3.30
10) CGGCACAGAG 3.28
Elapsed time : 0 min. 36 sec.
Searching for motifs of length 12 with 4 mutations.....
(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/12050_WEEDER/mec3_top20_u2_3_19.fa -R 50 -O CE -W 12 -e 4 -N -S -T 10 )
1) GATGAGGCAGTA 5.40
2) GCGGCACAGAGA 5.25
3) CGCGTAACCGTA 5.17
4) GAGCGAAAGGGC 5.07
5) TAGAAAACGGCG 5.02
6) AGATGAGGCAGT 4.94
7) GCGCCTTTGAAT 4.83
8) AGCGAAAGGGCG 4.82
9) ACGCGTAACCGT 4.75
10) AAACGGCGGCCC 4.66
Elapsed time : 4 min. 54 sec.
Your sequences:
Sequence 1 : >ID1043663_Y48G8AL.8a_upstream_2kb
Sequence 2 : >ID1049160_C06A8.3_upstream_2kb
Sequence 3 : >ID1057333_Y45F10D.12_upstream_2kb
Sequence 4 : >ID1065528_C03A3.3_upstream_2kb
**** MY ADVICE ****
*** Interesting motifs (highest-ranking) seem to be :
CGCTGC
GCAGCG
2 redundant motifs found:
TCGCTGCG - TCGCTG -
Best occurrences (match percentage):
Seq St oligo pos match
1 + .CGCGGC. 72 (93.38)
1 + .CGCTGC. 87 (100.00)
1 - .CGCAGC. 88 (93.38)
1 - .CGCCGC. 73 (93.38)
2 - .CGCTCA. 176 (90.35)
2 - .CGCTCC. 117 (95.29)
2 - .CGCTGA. 54 (95.05)
2 - .CGCTGA. 22 (95.05)
3 + [CGCAAC] 14 (86.76)
3 + [CACTCC] 22 (88.43)
3 + .CGCTCC. 27 (95.29)
3 + [CGCAAC] 45 (86.76)
3 - .CCCTGC. 204 (93.14)
3 - .CGCTAC. 129 (93.38)
3 - .CGTTGC. 46 (95.05)
3 - .CGTTGC. 15 (95.05)
3 - [CGCGCC] 10 (88.67)
4 + [CGTGGC] 60 (88.43)
4 + .CACTGC. 146 (93.14)
4 - .CGCTCA. 117 (90.35)
4 - .CGCTGC. 10 (100.00)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 0 | 14 | 0 | 0 | | | | 0 | 16 | 0 | 0 |
2 | | 1 | 1 | 12 | 0 | | | | 1 | 1 | 14 | 0 |
3 | | 0 | 12 | 0 | 2 | | | | 0 | 14 | 0 | 2 |
4 | | 1 | 1 | 1 | 11 | | | | 1 | 1 | 1 | 13 |
5 | | 1 | 2 | 11 | 0 | | | | 1 | 4 | 11 | 0 |
6 | | 2 | 12 | 0 | 0 | | | | 4 | 12 | 0 | 0 |
CGCCGTTT
AAACGGCG
4 redundant motifs found:
AAACGGCGGC - AACGGCGG - GCGCCGTT - CGCCGT -
Best occurrences (match percentage):
Seq St oligo pos match
1 + .CGCCTTTA. 111 (94.30)
1 + [CGATTATT] 130 (88.17)
1 + .GGCCTTTT. 142 (94.30)
1 + .CGCCGTTT. 181 (100.00)
1 + .CGTTTTTT. 184 (94.38)
1 + [TGTTTTTT] 194 (89.00)
1 - .CGCATTTT. 175 (96.21)
1 - [CGAAATGT] 122 (85.10)
1 - [CGATCTTG] 66 (85.93)
1 - [TGTCGATT] 58 (86.58)
1 - [TGATTTTT] 28 (88.17)
1 - .CGTTGTTT. 9 (94.70)
2 + .CGTCGATT. 180 (91.96)
2 - .CGCCCTTT. 123 (97.44)
3 + .CGCCTTTG. 62 (94.30)
3 + .CGTTTTTT. 113 (94.38)
3 + [TGCCGGTT] 141 (89.23)
3 + .CGTTGTTT. 153 (94.70)
3 + [TGATTTTT] 184 (88.17)
3 + .CGTTATTT. 194 (90.73)
3 - [TGTCGTTG] 16 (86.58)
3 - .CGCCCTGT. 6 (93.47)
4 + [CGATGGTT] 151 (88.48)
4 + [CGCACATT] 177 (88.58)
4 + .CGACATTT. 259 (92.55)
4 + [CGTATTTG] 369 (88.17)
4 - .CGCTTTTT. 335 (97.03)
4 - [CGTATTGT] 327 (89.58)
4 - .CGACTTTT. 168 (96.21)
4 - .CGCAGTGT. 145 (92.55)
4 - [CGCTCATT] 115 (89.41)
4 - [TGAAGTTT] 71 (87.66)
4 - .CGCCGTTT. 48 (100.00)
4 - [TGCATTTG] 36 (85.43)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 0 | 14 | 1 | 1 | | | | 0 | 17 | 1 | 0 |
2 | | 0 | 0 | 16 | 0 | | | | 0 | 0 | 18 | 0 |
3 | | 2 | 11 | 0 | 3 | | | | 2 | 10 | 0 | 6 |
4 | | 2 | 11 | 0 | 3 | | | | 2 | 10 | 0 | 6 |
5 | | 1 | 2 | 7 | 6 | | | | 2 | 2 | 6 | 8 |
6 | | 1 | 0 | 1 | 14 | | | | 1 | 0 | 0 | 17 |
7 | | 0 | 0 | 2 | 14 | | | | 0 | 0 | 2 | 16 |
8 | | 1 | 0 | 1 | 14 | | | | 1 | 0 | 1 | 16 |
GCGTAACCGT
ACGGTTACGC
5 redundant motifs found:
ACGCGTAACCGT - CGCGTAACCGTA - CGCGTAACCG - CGTAACCGTA - GCGTAACC -
Best occurrences (match percentage):
Seq St oligo pos match
1 - .GCGCAAGCGA. 104 (96.41)
1 - .GCGAAACCGT. 98 (98.87)
4 + .GCGGCCCCGT. 53 (94.33)
4 + .GCGTAACCGT. 362 (100.00)
4 - .GCGTAATTGA. 354 (95.27)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 0 | 0 | 5 | 0 | | | | 0 | 0 | 5 | 0 |
2 | | 0 | 5 | 0 | 0 | | | | 0 | 5 | 0 | 0 |
3 | | 0 | 0 | 5 | 0 | | | | 0 | 0 | 5 | 0 |
4 | | 1 | 1 | 1 | 2 | | | | 1 | 1 | 1 | 2 |
5 | | 4 | 1 | 0 | 0 | | | | 4 | 1 | 0 | 0 |
6 | | 4 | 1 | 0 | 0 | | | | 4 | 1 | 0 | 0 |
7 | | 0 | 3 | 1 | 1 | | | | 0 | 3 | 1 | 1 |
8 | | 0 | 4 | 0 | 1 | | | | 0 | 4 | 0 | 1 |
9 | | 0 | 0 | 5 | 0 | | | | 0 | 0 | 5 | 0 |
10 | | 2 | 0 | 0 | 3 | | | | 2 | 0 | 0 | 3 |
GATGAGGCAGTA
TACTGCCTCATC
2 redundant motifs found:
AGATGAGGCAGT - TGAGGCAGTA -
Best occurrences (match percentage):
Seq St oligo pos match
1 - .GGAGAGGCAACA. 41 (93.97)
2 - .GATGAGGGATGT. 213 (93.97)
2 - .GATCATAGATGA. 94 (91.08)
2 - .GATGAGACAGTA. 87 (99.13)
3 + .ATTGAGGGAATA. 75 (96.00)
4 + .GATGAGGCAGTA. 23 (100.00)
4 - .AATCATACAGTA. 284 (94.20)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 2 | 0 | 4 | 0 | | | | 2 | 0 | 5 | 0 |
2 | | 4 | 0 | 1 | 1 | | | | 5 | 0 | 1 | 1 |
3 | | 1 | 0 | 0 | 5 | | | | 1 | 0 | 0 | 6 |
4 | | 0 | 1 | 5 | 0 | | | | 0 | 2 | 5 | 0 |
5 | | 6 | 0 | 0 | 0 | | | | 7 | 0 | 0 | 0 |
6 | | 0 | 0 | 5 | 1 | | | | 0 | 0 | 5 | 2 |
7 | | 2 | 0 | 4 | 0 | | | | 3 | 0 | 4 | 0 |
8 | | 0 | 4 | 2 | 0 | | | | 0 | 4 | 3 | 0 |
9 | | 6 | 0 | 0 | 0 | | | | 7 | 0 | 0 | 0 |
10 | | 2 | 0 | 3 | 1 | | | | 2 | 0 | 3 | 2 |
11 | | 0 | 1 | 1 | 4 | | | | 0 | 1 | 2 | 4 |
12 | | 5 | 0 | 0 | 1 | | | | 6 | 0 | 0 | 1 |
*** Interesting motifs (not highest-ranking) can also be :
GCGCCGTT
AACGGCGC
3 redundant motifs found:
GCCCCGTG - CGCCGTTT - CGCCGT -
Best occurrences (match percentage):
Seq St oligo pos match
1 + .GCGCCTTT. 110 (99.24)
1 + .GGGCCTTT. 141 (94.93)
1 + [GGCCTTTT] 142 (86.12)
1 + [GCCTTTTT] 143 (88.38)
1 + .GCGCCGTT. 180 (100.00)
1 + [CCGTTTTT] 183 (89.85)
1 + [CTGTTTTT] 193 (85.54)
1 - .GCGCATTT. 176 (94.93)
1 - [GTGTCGAT] 59 (89.14)
1 - .GCGTTGTT. 10 (93.63)
2 + .GCGTCGAT. 179 (93.45)
2 - .CCGCCCTT. 124 (94.93)
2 - [CGCCCTTT] 123 (87.42)
3 + .GCGCCTTT. 61 (99.24)
3 + [GTGTTTTT] 134 (88.55)
3 + [CGGTTTTT] 144 (85.54)
3 + .CCGTTGTT. 152 (90.61)
3 - .GTGTCGTT. 17 (93.63)
3 - .GCGCCCTG. 7 (94.93)
4 + .GCCCCGTG. 56 (92.49)
4 + [CCGTATTT] 368 (89.85)
4 - .CCGCCGTT. 49 (96.98)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 0 | 2 | 10 | 0 | | | | 0 | 3 | 10 | 0 |
2 | | 0 | 10 | 1 | 1 | | | | 0 | 11 | 1 | 1 |
3 | | 0 | 1 | 11 | 0 | | | | 0 | 1 | 12 | 0 |
4 | | 0 | 9 | 0 | 3 | | | | 0 | 9 | 0 | 4 |
5 | | 1 | 10 | 0 | 1 | | | | 1 | 10 | 0 | 2 |
6 | | 0 | 2 | 6 | 4 | | | | 0 | 2 | 7 | 4 |
7 | | 1 | 0 | 0 | 11 | | | | 1 | 0 | 0 | 12 |
8 | | 0 | 0 | 2 | 10 | | | | 0 | 0 | 2 | 11 |
CGTAACCGTA
TACGGTTACG
2 redundant motifs found:
CGCGTAACCGTA - GCGTAACCGT -
Best occurrences (match percentage):
Seq St oligo pos match
1 - .CGCAAGCGAA. 103 (94.79)
1 - .CGAAACCGTA. 97 (97.91)
3 + .TTTTACCGTA. 117 (95.49)
3 - .CTTTACGGTA. 120 (95.83)
4 + .CGTAACCGTA. 363 (100.00)
4 - .CGTAATTGAA. 353 (94.79)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 0 | 5 | 0 | 1 | | | | 0 | 5 | 0 | 1 |
2 | | 0 | 0 | 4 | 2 | | | | 0 | 0 | 4 | 2 |
3 | | 1 | 1 | 0 | 4 | | | | 1 | 1 | 0 | 4 |
4 | | 4 | 0 | 0 | 2 | | | | 4 | 0 | 0 | 2 |
5 | | 6 | 0 | 0 | 0 | | | | 6 | 0 | 0 | 0 |
6 | | 0 | 4 | 1 | 1 | | | | 0 | 4 | 1 | 1 |
7 | | 0 | 4 | 1 | 1 | | | | 0 | 4 | 1 | 1 |
8 | | 0 | 0 | 6 | 0 | | | | 0 | 0 | 6 | 0 |
9 | | 2 | 0 | 0 | 4 | | | | 2 | 0 | 0 | 4 |
10 | | 6 | 0 | 0 | 0 | | | | 6 | 0 | 0 | 0 |
CGCGTAACCGTA
TACGGTTACGCG
4 redundant motifs found:
ACGCGTAACCGT - CGCGTAACCG - CGTAACCGTA - GCGTAACCGT -
Best occurrences (match percentage):
Seq St oligo pos match
1 + .CGCGAAAAATTA. 15 (92.56)
1 - .GGCGCAAGCGAA. 103 (93.29)
1 - .AGCGAAACCGTA. 97 (95.88)
2 + [AGGGAGAGAGAA] 157 (87.36)
2 - [CGCTCATAGTCA] 170 (85.17)
3 + .CGCGCAACGACA. 12 (90.97)
4 + .CGCGTAACCGTA. 361 (100.00)
4 - .CGGTTACGCGTA. 359 (93.39)
4 - .CGCGTAATTGAA. 353 (95.10)
4 - .CGCTTTTTCGTA. 331 (92.39)
4 - .CGGTTGACAGTA. 97 (93.07)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 1 | 7 | 1 | 0 | | | | 1 | 7 | 1 | 0 |
2 | | 0 | 0 | 9 | 0 | | | | 0 | 0 | 9 | 0 |
3 | | 0 | 7 | 2 | 0 | | | | 0 | 7 | 2 | 0 |
4 | | 0 | 0 | 6 | 3 | | | | 0 | 0 | 6 | 3 |
5 | | 2 | 2 | 0 | 5 | | | | 2 | 2 | 0 | 5 |
6 | | 7 | 0 | 1 | 1 | | | | 7 | 0 | 1 | 1 |
7 | | 7 | 1 | 0 | 1 | | | | 7 | 1 | 0 | 1 |
8 | | 1 | 4 | 2 | 2 | | | | 1 | 4 | 2 | 2 |
9 | | 2 | 5 | 1 | 1 | | | | 2 | 5 | 1 | 1 |
10 | | 1 | 0 | 7 | 1 | | | | 1 | 0 | 7 | 1 |
11 | | 2 | 1 | 0 | 6 | | | | 2 | 1 | 0 | 6 |
12 | | 9 | 0 | 0 | 0 | | | | 9 | 0 | 0 | 0 |
CATCGCTG
CAGCGATG
2 redundant motifs found:
TCGCTGCG - TCGCTG -
Best occurrences (match percentage):
Seq St oligo pos match
1 + .GATCGCGG. 69 (93.76)
1 + .CATCGCTG. 84 (100.00)
1 - .CAGCGATG. 84 (94.30)
2 + .CAGCGATT. 23 (90.41)
2 + [CAGCGAAC] 55 (86.52)
2 + .CATCTATG. 95 (96.07)
2 + .CATCCCTC. 214 (92.47)
2 - .CATAGATG. 95 (94.30)
2 - .GTTCGCTG. 55 (93.54)
2 - .AATCGCTG. 23 (96.36)
4 + [AAGAGATG] 19 (86.55)
4 + .CTGCGATG. 148 (90.19)
4 + [GATCTATT] 267 (89.83)
4 - [AATAGATC] 267 (86.77)
4 - .CATCGCAG. 148 (96.11)
4 - .GATCTCTC. 122 (91.42)
4 - .CATCTCTT. 19 (93.76)
Frequency Matrix | All Occs | | | Best Occs |
---|
| | A | C | G | T | | | A | C | G | T |
---|
1 | | 1 | 7 | 2 | 0 | | | | 1 | 9 | 3 | 0 |
2 | | 9 | 0 | 0 | 1 | | | | 11 | 0 | 0 | 2 |
3 | | 0 | 0 | 1 | 9 | | | | 0 | 0 | 3 | 10 |
4 | | 1 | 9 | 0 | 0 | | | | 1 | 12 | 0 | 0 |
5 | | 0 | 1 | 7 | 2 | | | | 0 | 1 | 9 | 3 |
6 | | 3 | 7 | 0 | 0 | | | | 5 | 8 | 0 | 0 |
7 | | 1 | 0 | 1 | 8 | | | | 1 | 0 | 1 | 11 |
8 | | 0 | 1 | 8 | 1 | | | | 0 | 2 | 9 | 2 |