Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014904.1 Corchorus olitorius cultivar O-4 contig14937, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20660
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:855 original size:163 final size:162
Alignment explanation
Indices: 561--856 Score: 439
Period size: 163 Copynumber: 1.8 Consensus size: 162
551 TAGGTAATGG
* * * *
561 GAAAGTGTGGTAAATTAGATAGGAAAATAATTTTTCCATGTTTGGTTGGAGGATTCTAATTTTAG
1 GAAAGTGTGGTAAATTAGATAGGAAAATAACTTTCCCATGTTTGGTTGGAGGAATCTAATTTTAA
* * *
626 GTGGGAATGTCATTCCCATTACTTTACCACTCAAGTAGGAATGTGATAGAAATAACATTTCCATC
66 GTGGGAATGTCATTCCCATCACTTTACCACTCAAGTAGGAAAGTGATAGAAATAACATTCCCATC
691 TAAGGTTGCGTTTGGTTCGTGGAAAGTAGTGA
131 TAAGGTTGCGTTTGGTTCGTGGAAAGTAGTGA
* *
723 GAAAGTGTGGTAAGTTAGATAGGGAAAATAACTTTCCCATGTTTGGTTGGAGGAATCTAGTTTTA
1 GAAAGTGTGGTAAATTAGATA-GGAAAATAACTTTCCCATGTTTGGTTGGAGGAATCTAATTTTA
** * * * * *
788 AGTGGGAATGTCATTCCCATCACTTTACCACTTGAGTGGGAAAGTGGTGGGAATGACATTCCCAT
65 AGTGGGAATGTCATTCCCATCACTTTACCACTCAAGTAGGAAAGTGATAGAAATAACATTCCCAT
853 CTAA
130 CTAA
857 AAGGGTGGGA
Statistics
Matches: 117, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
162 20 0.17
163 97 0.83
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (162 bp):
GAAAGTGTGGTAAATTAGATAGGAAAATAACTTTCCCATGTTTGGTTGGAGGAATCTAATTTTAA
GTGGGAATGTCATTCCCATCACTTTACCACTCAAGTAGGAAAGTGATAGAAATAACATTCCCATC
TAAGGTTGCGTTTGGTTCGTGGAAAGTAGTGA
Found at i:1296 original size:231 final size:226
Alignment explanation
Indices: 853--1309 Score: 725
Period size: 231 Copynumber: 2.0 Consensus size: 226
843 ACATTCCCAT
* *
853 CTAAAAGGGTGGGAAAGTTCACTTTCCCAGGAAAGTGTTACTCTTTGTCCCTTGTCTTTCTCTTA
1 CTAAAAGGGTGGAAAAGTTAACTTTCCCAGGAAAGTGTTACTCTTTGTCCCTTGTCTTTCTCTTA
* ** *
918 TATTCTCAAAATTTATTAACTTTCCCATGTTAACCAAACATGGTAATCATATTCCCACAAAAATA
66 TATTCTCAAAATTTAATAACTTTCCCACATTAACCAAACATGGTAATCATATTCCCACAAAAAAA
*
983 AAAAAATTATACTTTCCCACTAAAATAACATTCCTAGGAAAGTAGTGTGAATGACATTCCCACGT
131 AAAAAATTATACTTTCCCACTAAAATAACATTCCTAGGAAAGTAGTGTGAATGACATTACCACGT
1048 GATACCTAAGATACCACGAACCAAACATAAC
196 GATACCTAAGATACCACGAACCAAACATAAC
* * * * *
1079 CTAAAAGGGTGGAAAAGTTAACTTTTCCATGAAAGTGTTACTCTTTTTCTCTTTGTCTTTCTTTT
1 CTAAAAGGGTGGAAAAGTTAACTTTCCCAGGAAAGTGTTACTCTTTGTC-CCTTGTCTTTCTCTT
*
1144 ATATTCTCAAAATTTAATAACTTTCCCACATTAACCAAACATGGTAATCTTATTCCCACACAAAT
65 ATATTCTCAAAATTTAATAACTTTCCCACATTAACCAAACATGGTAATCATATT-CC-CACAAA-
* *
1209 AAAAAATAAAATTATACTTTCCCACTAAAATAGCATTCCTAGGAAAGTAGTGTGAATGACATTAT
127 AAAAAA-AAAATTATACTTTCCCACTAAAATAACATTCCTAGGAAAGTAGTGTGAATGACATTAC
*
1274 CACGTGATACCTAAGATACCACGAACCAAACGTAAC
191 CACGTGATACCTAAGATACCACGAACCAAACATAAC
1310 GGATTTATAA
Statistics
Matches: 210, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
226 44 0.21
227 63 0.30
228 2 0.01
229 6 0.03
230 5 0.02
231 90 0.43
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (226 bp):
CTAAAAGGGTGGAAAAGTTAACTTTCCCAGGAAAGTGTTACTCTTTGTCCCTTGTCTTTCTCTTA
TATTCTCAAAATTTAATAACTTTCCCACATTAACCAAACATGGTAATCATATTCCCACAAAAAAA
AAAAAATTATACTTTCCCACTAAAATAACATTCCTAGGAAAGTAGTGTGAATGACATTACCACGT
GATACCTAAGATACCACGAACCAAACATAAC
Found at i:6211 original size:22 final size:25
Alignment explanation
Indices: 6185--6234 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
6175 TTAACAGCGC
6185 AACAAAAAC-AAAAC-G-AAAACGA
1 AACAAAAACAAAAACAGAAAAACGA
6207 AACAAAAACAGAAAACAGAAAAACGA
1 AACAAAAACA-AAAACAGAAAAACGA
6233 AA
1 AA
6235 ACGATGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
24 5 0.21
25 1 0.04
26 9 0.38
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (25 bp):
AACAAAAACAAAAACAGAAAAACGA
Found at i:6235 original size:6 final size:6
Alignment explanation
Indices: 6189--6238 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
6179 CAGCGCAACA
*
6189 AAAAC- AAAACG AAAACG -AAACA AAAACAG AAAACAG AAAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAAC-G AAAAC-G -AAAACG AAAACG
6238 A
1 A
6239 TGCCAAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 9 0.23
6 17 0.44
7 8 0.21
8 5 0.13
ACGTcount: A:0.72, C:0.16, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:9559 original size:25 final size:25
Alignment explanation
Indices: 9516--9563 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
9506 TAAACACTTA
*
9516 AAAACCTAATTCTGGTAGGAAAAGT
1 AAAACCTAATCCTGGTAGGAAAAGT
**
9541 AAAACCTAATCCTTTTAGGAAAA
1 AAAACCTAATCCTGGTAGGAAAA
9564 ATCCATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAACCTAATCCTGGTAGGAAAAGT
Found at i:10279 original size:17 final size:17
Alignment explanation
Indices: 10253--10303 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
10243 AGCATAACAA
10253 AAAC-AAAACGAAAACG
1 AAACAAAAACGAAAACG
*
10269 AAACAAAAACGAAAATG
1 AAACAAAAACGAAAACG
10286 AAACAAAAACGAAAACG
1 AAACAAAAACGAAAACG
10303 A
1 A
10304 TGCCAAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.71, C:0.16, G:0.12, T:0.02
Consensus pattern (17 bp):
AAACAAAAACGAAAACG
Found at i:10299 original size:11 final size:11
Alignment explanation
Indices: 10248--10282 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
10238 TTGAAAGCAT
*
10248 AACAAAAACAA
1 AACAAAAACGA
*
10259 AACGAAAACGA
1 AACAAAAACGA
10270 AACAAAAACGA
1 AACAAAAACGA
10281 AA
1 AA
10283 ATGAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (11 bp):
AACAAAAACGA
Found at i:10302 original size:6 final size:6
Alignment explanation
Indices: 10252--10303 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
10242 AAGCATAACA
* * *
10252 AAAAC- AAAACG AAAACG -AAACA AAAACG AAAATG -AAACA AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
10297 AAAACG A
1 AAAACG A
10304 TGCCAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
5 12 0.32
6 26 0.68
ACGTcount: A:0.71, C:0.15, G:0.12, T:0.02
Consensus pattern (6 bp):
AAAACG
Found at i:11007 original size:32 final size:32
Alignment explanation
Indices: 10966--11068 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
10956 TTGAGTCAGG
10966 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
* *
10998 TCGGGTTAAATTTGGATCAGGTTGATTTGAGT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
*
11030 TCGGGTTAAATTTGGATCAGGTTAATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
11062 TCGGGTT
1 TCGGGTT
11069 TGGGTTCGGG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (32 bp):
TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
Found at i:11020 original size:16 final size:16
Alignment explanation
Indices: 10969--11054 Score: 77
Period size: 16 Copynumber: 5.4 Consensus size: 16
10959 AGTCAGGTCG
10969 GGTTAAATTTGGATCA
1 GGTTAAATTTGGATCA
* * * *
10985 GGTT-GATTCGGGTTCG
1 GGTTAAATT-TGGATCA
11001 GGTTAAATTTGGATCA
1 GGTTAAATTTGGATCA
* * *
11017 GGTT-GATTTGAGTTCG
1 GGTTAAATTTG-GATCA
11033 GGTTAAATTTGGATCA
1 GGTTAAATTTGGATCA
11049 GGTTAA
1 GGTTAA
11055 TTCGGGTTCG
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
15 8 0.15
16 36 0.69
17 8 0.15
ACGTcount: A:0.23, C:0.07, G:0.31, T:0.38
Consensus pattern (16 bp):
GGTTAAATTTGGATCA
Found at i:11325 original size:16 final size:16
Alignment explanation
Indices: 11300--11351 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
11290 GAGTTTCAGA
11300 TTTTTT-GGGTTCTGG
1 TTTTTTCGGGTTCTGG
11315 TTTTTTCGGGTT-TGAG
1 TTTTTTCGGGTTCTG-G
*
11331 CTTTTTCGGGTTC-GG
1 TTTTTTCGGGTTCTGG
11346 TTTTTT
1 TTTTTT
11352 TGGTTTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.02, C:0.10, G:0.29, T:0.60
Consensus pattern (16 bp):
TTTTTTCGGGTTCTGG
Found at i:11352 original size:32 final size:31
Alignment explanation
Indices: 11276--11351 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
11266 TTCAGGTTCA
* *
11276 GTTCGGGTTTTATCGAGTTTCAGATTTTTTGG
1 GTTC-GGTTTTTTCGAGTTTCAGATTTTTCGG
* * *
11308 GTTCTGGTTTTTTCGGGTTTGAGCTTTTTCGG
1 GTTC-GGTTTTTTCGAGTTTCAGATTTTTCGG
11340 GTTCGGTTTTTT
1 GTTCGGTTTTTT
11352 TGGTTTGGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.07, C:0.11, G:0.29, T:0.54
Consensus pattern (31 bp):
GTTCGGTTTTTTCGAGTTTCAGATTTTTCGG
Found at i:11548 original size:33 final size:33
Alignment explanation
Indices: 11506--11609 Score: 120
Period size: 32 Copynumber: 3.1 Consensus size: 33
11496 GATTCGAACT
* *
11506 AAACTCTAAATTTGGCATTTTGGCAAAAAAAAA
1 AAACTCTAAACTTGGCATTTTGGCCAAAAAAAA
* *
11539 AAACTCTAAACTTGGCATTGT-GCCAAAAAGAA
1 AAACTCTAAACTTGGCATTTTGGCCAAAAAAAA
*
11571 AAAGTCTAAACTTGGCTACTTGTTGTGCCAAAAAAAA
1 AAACTCTAAACTTGGC-A-TT-TTG-GCCAAAAAAAA
11608 AA
1 AA
11610 CTTTGGCTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 24 0.41
33 20 0.34
34 2 0.03
35 1 0.02
37 12 0.20
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.25
Consensus pattern (33 bp):
AAACTCTAAACTTGGCATTTTGGCCAAAAAAAA
Found at i:12149 original size:21 final size:21
Alignment explanation
Indices: 12124--12167 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12114 AACTTATTTA
*
12124 AATTTTGATTTGCAAAGTTTG
1 AATTTTGATCTGCAAAGTTTG
*
12145 AATTTTGATCTGCAGAGTTTG
1 AATTTTGATCTGCAAAGTTTG
12166 AA
1 AA
12168 GGGAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (21 bp):
AATTTTGATCTGCAAAGTTTG
Found at i:12341 original size:8 final size:7
Alignment explanation
Indices: 12312--12341 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
12302 TTATAATTAA
12312 TTAAAAT
1 TTAAAAT
12319 TTAAAAT
1 TTAAAAT
12326 TTAAAAT
1 TTAAAAT
12333 TTCAAAAT
1 TT-AAAAT
12341 T
1 T
12342 CAAACATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.73
8 6 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (7 bp):
TTAAAAT
Found at i:15453 original size:2 final size:2
Alignment explanation
Indices: 15446--15470 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15436 TAGAAATGGT
15446 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15471 TTACAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.