Your Weeder Web Results

NEW: Starting a large job on file /tmp/motif_master/12048_WEEDER/mec3_top20_u2t_3_19.fa

Organism code: CE

Processing both strands

/ulhhmi/alok/local/programs/Weeder1.2/weederlauncher.out /tmp/motif_master/12048_WEEDER/mec3_top20_u2t_3_19.fa CE large S


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

(Actual commandline is :
./weederTFBS.out -f /tmp/motif_master/12048_WEEDER/mec3_top20_u2t_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/12048_WEEDER/mec3_top20_u2t_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/12048_WEEDER/mec3_top20_u2t_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/12048_WEEDER/mec3_top20_u2t_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. 55 sec.


Your sequences:

Sequence 1 : >ID1926163_Y48G8AL.8a_u2k_truncated
Sequence 2 : >ID1931660_C06A8.3_u2k_truncated
Sequence 3 : >ID1939832_Y45F10D.12_u2k_truncated
Sequence 4 : >ID1948027_C03A3.3_u2k_truncated


**** 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
ACGT ACGT
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
ACGT ACGT
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
ACGT ACGT
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
ACGT ACGT
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
ACGT ACGT
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
ACGT ACGT
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
ACGT ACGT
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
ACGT ACGT
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