Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008682.1 Corchorus capsularis cultivar CVL-1 contig08703, 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: 54649
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:2180 original size:16 final size:16
Alignment explanation
Indices: 2159--2192 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2149 ACAATTCAGA
2159 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
2175 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
2191 AA
1 AA
2193 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:5178 original size:16 final size:16
Alignment explanation
Indices: 5157--5191 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5147 ACAATTCAGA
* *
5157 AAGCAGAAGAGCTCTG
1 AAGCAGAAAAACTCTG
5173 AAGCAGAAAAACTCTG
1 AAGCAGAAAAACTCTG
5189 AAG
1 AAG
5192 TATTTCAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAACTCTG
Found at i:6520 original size:18 final size:18
Alignment explanation
Indices: 6497--6562 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 18
6487 TATCATAGCA
6497 TAGCATAGCATTTGAATT
1 TAGCATAGCATTTGAATT
6515 TAGCATTAG-ATAGTTGAATGGT
1 TAGCA-TAGCAT--TTGAAT--T
*
6537 GGAAGCATAGCATTTGAATT
1 --TAGCATAGCATTTGAATT
6557 TAGCAT
1 TAGCAT
6563 CTTGGAGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 7 0.18
22 7 0.18
23 3 0.08
24 6 0.16
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (18 bp):
TAGCATAGCATTTGAATT
Found at i:6704 original size:21 final size:21
Alignment explanation
Indices: 6680--6885 Score: 231
Period size: 21 Copynumber: 9.9 Consensus size: 21
6670 CACAAAACTT
6680 TTGATGGTCAAACCCCAAATC
1 TTGATGGTCAAACCCCAAATC
6701 TTGATGGTCAAACCCCAAAGT-
1 TTGATGGTCAAACCCCAAA-TC
*
6722 TTGATTGTCAAA-CCCAATATC
1 TTGATGGTCAAACCCCAA-ATC
*** *
6743 AAAATGGTCACACCCCAAATC
1 TTGATGGTCAAACCCCAAATC
*
6764 TTGATAGTCAAACCCCAAAT-
1 TTGATGGTCAAACCCCAAATC
*
6784 TTGATGGTCAAATCCCAAATC
1 TTGATGGTCAAACCCCAAATC
* *
6805 TTGATAGTCTAACCCCAAAT-
1 TTGATGGTCAAACCCCAAATC
* *
6825 TTGATAGTCAAACCCTAAATC
1 TTGATGGTCAAACCCCAAATC
* *
6846 TTGATGGTCAAACCCTAAATA
1 TTGATGGTCAAACCCCAAATC
* *
6867 TTGATAGTCTAACCCCAAA
1 TTGATGGTCAAACCCCAAA
6886 GTTTCATATA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
20 42 0.27
21 108 0.69
22 6 0.04
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (21 bp):
TTGATGGTCAAACCCCAAATC
Found at i:6803 original size:41 final size:42
Alignment explanation
Indices: 6680--6885 Score: 231
Period size: 41 Copynumber: 5.0 Consensus size: 42
6670 CACAAAACTT
*
6680 TTGATGGTCAAACCCCAAATCTTGATGGTCAAACCCCAAAGT-
1 TTGATAGTCAAACCCCAAATCTTGATGGTCAAACCCCAAA-TC
* *** *
6722 TTGATTGTCAAA-CCCAATATCAAAATGGTCACACCCCAAATC
1 TTGATAGTCAAACCCCAA-ATCTTGATGGTCAAACCCCAAATC
*
6764 TTGATAGTCAAACCCCAAAT-TTGATGGTCAAATCCCAAATC
1 TTGATAGTCAAACCCCAAATCTTGATGGTCAAACCCCAAATC
* * *
6805 TTGATAGTCTAACCCCAAAT-TTGATAGTCAAACCCTAAATC
1 TTGATAGTCAAACCCCAAATCTTGATGGTCAAACCCCAAATC
* * * * *
6846 TTGATGGTCAAACCCTAAATATTGATAGTCTAACCCCAAA
1 TTGATAGTCAAACCCCAAATCTTGATGGTCAAACCCCAAA
6886 GTTTCATATA
Statistics
Matches: 140, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 76 0.54
42 59 0.42
43 5 0.04
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (42 bp):
TTGATAGTCAAACCCCAAATCTTGATGGTCAAACCCCAAATC
Found at i:6823 original size:62 final size:61
Alignment explanation
Indices: 6680--6885 Score: 254
Period size: 62 Copynumber: 3.3 Consensus size: 61
6670 CACAAAACTT
* * * *
6680 TTGATGGTCAAACCCCAAATCTTGATGGTCAAACCCCAAAGTTTGATTGTCAAACCCAATATC
1 TTGATAGTCTAACCCCAAATCTTGATAGTCAAACCCCAAA-TTTGATGGTCAAACCCAA-ATC
*** *
6743 AAAATGGTC-ACACCCCAAATCTTGATAGTCAAACCCCAAATTTGATGGTCAAATCCCAAATC
1 TTGATAGTCTA-ACCCCAAATCTTGATAGTCAAACCCCAAATTTGATGGTCAAA-CCCAAATC
* *
6805 TTGATAGTCTAACCCCAAAT-TTGATAGTCAAACCCTAAATCTTGATGGTCAAACCCTAAATA
1 TTGATAGTCTAACCCCAAATCTTGATAGTCAAACCCCAAAT-TTGATGGTCAAACCC-AAATC
6867 TTGATAGTCTAACCCCAAA
1 TTGATAGTCTAACCCCAAA
6886 GTTTCATATA
Statistics
Matches: 127, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
61 22 0.17
62 65 0.51
63 40 0.31
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (61 bp):
TTGATAGTCTAACCCCAAATCTTGATAGTCAAACCCCAAATTTGATGGTCAAACCCAAATC
Found at i:7608 original size:29 final size:29
Alignment explanation
Indices: 7562--7621 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
7552 CAATAAAAAC
* *
7562 TACCCATTTTAGATAAAAACTACCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
*
7591 TACCAATTTTAGAAAAAAACTACTCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
7620 TA
1 TA
7622 AGATAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (29 bp):
TACCAATTTTAGAAAAAAACTACCCATTA
Found at i:24479 original size:226 final size:226
Alignment explanation
Indices: 24074--24519 Score: 635
Period size: 226 Copynumber: 2.0 Consensus size: 226
24064 TTCGATTTAA
* *
24074 GGTCTAATCTTTCAACTTGGTGCATTGAATTAAGGTCTAACGTCAATTTTGATTCAAATAAGGGC
1 GGTCTAATCTTTCAACTCGGTGCATTGAATTAAGGTCTAACGCCAATTTTGATTCAAATAAGGGC
* * * * * *
24139 TCAGTGTGATTGTTAACCATTGAGAAATCGACATGTGACGCTACAAAATAGATTATGTATCTTAT
66 TCAGTGTGATTGTTAACCATTGAGAAATCGACACGTGACACTAAAAAATAGATCATATATCTCAT
* * * * * *
24204 TAGATCCTTATTTGAGTCAAAATTGAAATGTTAGATATGTTAGATCTTGATACGACCAAATT-AG
131 CAGACCCTTATTTAAGTCAAAATTGAAACGTTAGATATGTTAAATCTTGATACAACCAAATTGA-
24268 AAGGTTAAATCATAAAGCAAGCATTTCAATTT
195 AAGGTTAAATCATAAAGCAAGCATTTCAATTT
* *
24300 GGTCTAATCTTTCAACTCGGTGCGTTGAATTAAGGTCTAATC-CCAATTTTTATTCAAATAAGGG
1 GGTCTAATCTTTCAACTCGGTGCATTGAATTAAGGTCTAA-CGCCAATTTTGATTCAAATAAGGG
* * * * *
24364 CTTAGTGTGATTGTTAATCATTGAGAAATCGAGACGTGACACTAAAAAATGGATCCTATATCTCA
65 CTCAGTGTGATTGTTAACCATTGAGAAATCGACACGTGACACTAAAAAATAGATCATATATCTCA
*
24429 TCAGACCCTTATTTAAGTCAAAATTGAAACGTTAGATCTGTTAAATCTTGATACAACCAAATTGA
130 TCAGACCCTTATTTAAGTCAAAATTGAAACGTTAGATATGTTAAATCTTGATACAACCAAATTGA
* * *
24494 AAGGTTGAATCCTGAAGCAAGCATTT
195 AAGGTTAAATCATAAAGCAAGCATTT
24520 TCATAAGGTT
Statistics
Matches: 193, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
226 191 0.99
227 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (226 bp):
GGTCTAATCTTTCAACTCGGTGCATTGAATTAAGGTCTAACGCCAATTTTGATTCAAATAAGGGC
TCAGTGTGATTGTTAACCATTGAGAAATCGACACGTGACACTAAAAAATAGATCATATATCTCAT
CAGACCCTTATTTAAGTCAAAATTGAAACGTTAGATATGTTAAATCTTGATACAACCAAATTGAA
AGGTTAAATCATAAAGCAAGCATTTCAATTT
Found at i:33146 original size:9 final size:9
Alignment explanation
Indices: 33106--33146 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
33096 GGGTACATTT
33106 TTTTATATA
1 TTTTATATA
*
33115 TTATATATA
1 TTTTATATA
*
33124 TTATATATA
1 TTTTATATA
33133 TTTTTATATA
1 -TTTTATATA
33143 TTTT
1 TTTT
33147 TTGTATACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:34243 original size:11 final size:12
Alignment explanation
Indices: 34227--34259 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34217 TAACAAACCA
34227 TAAACGAAT-TT
1 TAAACGAATATT
*
34238 TAAACGAGTATT
1 TAAACGAATATT
34250 TAAACGAATA
1 TAAACGAATA
34260 ATAAACGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (12 bp):
TAAACGAATATT
Found at i:34276 original size:23 final size:23
Alignment explanation
Indices: 34226--34276 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
34216 TTAACAAACC
**
34226 ATAAACGAATTTTAAACGAGTAT
1 ATAAACGAATAATAAACGAGTAT
*
34249 TTAAACGAATAATAAACGAGCTA-
1 ATAAACGAATAATAAACGAG-TAT
34272 ATAAA
1 ATAAA
34277 TGAACATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (23 bp):
ATAAACGAATAATAAACGAGTAT
Found at i:35671 original size:19 final size:20
Alignment explanation
Indices: 35619--35676 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
35609 GCTGCTCTAA
35619 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTA-C
* *
35640 TAATCTAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAC
*
35659 TATTCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
35677 TGCTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:40339 original size:2 final size:2
Alignment explanation
Indices: 40332--40362 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40322 ATGTTAAAAT
40332 TA TA TA 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 TA TA TA T
40363 TCATTCACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41340 original size:22 final size:24
Alignment explanation
Indices: 41315--41374 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 24
41305 ATTTTTCTAT
* *
41315 TTTTTGTTTTTTTTAGATA-T-AA
1 TTTTTCTTTTTTTGAGATAGTGAA
**
41337 TTTTTCAATTTTTGAGATAGTGAA
1 TTTTTCTTTTTTTGAGATAGTGAA
41361 TTTTTCTTTTTTTG
1 TTTTTCTTTTTTTG
41375 GAGAAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 15 0.50
23 1 0.03
24 14 0.47
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (24 bp):
TTTTTCTTTTTTTGAGATAGTGAA
Found at i:46352 original size:66 final size:65
Alignment explanation
Indices: 46263--46431 Score: 223
Period size: 66 Copynumber: 2.6 Consensus size: 65
46253 TCAAAGTGTA
* *
46263 GTTATCAAAAATTCATAGGGAGGTTATCAAAATTTCAAGGTGTAGTTCTGAAATTTTGATAGGGA
1 GTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCAA-GTGTAGTTCTGAAATTTTGATAGGGA
46328 G
65 G
* * * * * *
46329 GTTAACAAAATTTCATAATGAGGTTATCGAAATTTCTTAGTGTAGTTTTTAAATTTTGATAGGGA
1 GTTATCAAAATTTCATAAGGAGGTTATCAAAATTTC-AAGTGTAGTTCTGAAATTTTGATAGGGA
46394 G
65 G
*
46395 GTTATCAAGATTTCAT-AGGAAGGTTATCAAAATTTCA
1 GTTATCAAAATTTCATAAGG-AGGTTATCAAAATTTCA
46432 TAGGGAAGTT
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.97
67 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (65 bp):
GTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCAAGTGTAGTTCTGAAATTTTGATAGGGAG
Found at i:46412 original size:22 final size:22
Alignment explanation
Indices: 46131--46450 Score: 186
Period size: 22 Copynumber: 14.6 Consensus size: 22
46121 GTCTATGTGT
* *
46131 GGTTATCACAATTTCATAGTG-
1 GGTTATCAAAATTTCATAGGGA
* * * *
46152 TGATATC-AAATTTCATTGAGA
1 GGTTATCAAAATTTCATAGGGA
* * * * *
46173 GGTAATCAGAATTGCATAGTGT
1 GGTTATCAAAATTTCATAGGGA
* * **
46195 TGTTATCAAAATTACAT-GACAA
1 GGTTATCAAAATTTCATAG-GGA
* * *
46217 TGTTATCAAAATTTCATTGGAAA
1 GGTTATCAAAATTTCATAGG-GA
* *
46240 GGTTATCAAAATTTCAAAGTGTA
1 GGTTATCAAAATTTCATAG-GGA
*
46263 -GTTATCAAAAATTCATAGGGA
1 GGTTATCAAAATTTCATAGGGA
46284 GGTTATCAAAATTTCA-AGGTGTA
1 GGTTATCAAAATTTCATAGG-G-A
* * * *
46307 -GTTCTGAAATTTTGATAGGGA
1 GGTTATCAAAATTTCATAGGGA
* **
46328 GGTTAACAAAATTTCATAATGA
1 GGTTATCAAAATTTCATAGGGA
* * *
46350 GGTTATCGAAATTTCTTAGTGTA
1 GGTTATCAAAATTTCATAG-GGA
* * * *
46373 -GTTTTTAAATTTTGATAGGGA
1 GGTTATCAAAATTTCATAGGGA
* *
46394 GGTTATCAAGATTTCATAGGAA
1 GGTTATCAAAATTTCATAGGGA
46416 GGTTATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGGGA
* *
46438 AGTTATCATAATT
1 GGTTATCAAAATT
46451 CAACAAGGTA
Statistics
Matches: 222, Mismatches: 64, Indels: 25
0.71 0.21 0.08
Matches are distributed among these distances:
20 10 0.05
21 18 0.08
22 168 0.76
23 25 0.11
24 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGGA
Found at i:48646 original size:2 final size:2
Alignment explanation
Indices: 48639--48667 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48629 AAGGAGTTTA
48639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48668 AAGTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51741 original size:25 final size:25
Alignment explanation
Indices: 51712--51783 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 25
51702 TTGGTTTGTG
*
51712 GAGACCGAGCGAGATTGCTCAAATA
1 GAGACCGAGCGAGAGTGCTCAAATA
*
51737 GAGACCGAGTGAGAGTGCTCAAATA
1 GAGACCGAGCGAGAGTGCTCAAATA
*
51762 GAGACTGAGCGAGAGTGCTCAA
1 GAGACCGAGCGAGAGTGCTCAA
51784 GATTGTTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (25 bp):
GAGACCGAGCGAGAGTGCTCAAATA
Found at i:51814 original size:19 final size:20
Alignment explanation
Indices: 51783--51820 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
51773 AGAGTGCTCA
*
51783 AGATTGTTTGGATTTGGTTT
1 AGATTGTTTGGATTGGGTTT
51803 AGATTG-TTGGATTGGGTT
1 AGATTGTTTGGATTGGGTT
51821 GAGAGATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (20 bp):
AGATTGTTTGGATTGGGTTT
Done.