Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012605.1 Corchorus capsularis cultivar CVL-1 contig12626, 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: 27031
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:6017 original size:108 final size:112
Alignment explanation
Indices: 5818--6033 Score: 271
Period size: 108 Copynumber: 1.9 Consensus size: 112
5808 AGAATCTTAG
* * *
5818 AAATTTTAAAGGAAGAACGAACAGAATATCGAAATTCAGAACCCTAGCATTTTACCCATTTCCAT
1 AAATTTTAAAAGAAGAACGAACAGAATATCGAAA-TCA-AACCCTAGAATTTTACCCATTTCAAT
* * *
5883 TTTAAACATGCTAATGTTGCAATTAAACACAAAA-CCCAACAACCGTAT
64 TTCAAACAAGCAAATGTTGCAATTAAACACAAAACCCCAACAACCGTAT
* * * *
5931 AAATTTTAAAAGAAGAATGAACAGAATATCG-AA-C-TACCCTAGAATTTTACCTATTTTAATTT
1 AAATTTTAAAAGAAGAACGAACAGAATATCGAAATCAAACCCTAGAATTTTACCCATTTCAATTT
*
5993 CAAACAAAG-AAATGTTGCATTTAAACACAAAACCCCAACAA
66 CAAAC-AAGCAAATGTTGCAATTAAACACAAAACCCCAACAA
6034 ATAACTAAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
108 48 0.53
109 10 0.11
110 1 0.01
112 2 0.02
113 29 0.32
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (112 bp):
AAATTTTAAAAGAAGAACGAACAGAATATCGAAATCAAACCCTAGAATTTTACCCATTTCAATTT
CAAACAAGCAAATGTTGCAATTAAACACAAAACCCCAACAACCGTAT
Found at i:6381 original size:24 final size:23
Alignment explanation
Indices: 6354--6402 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
6344 GAAATTTCCG
6354 TTTGCTAATTTTTTAA-AATTATAA
1 TTTGC-AATTTTTTAATAATT-TAA
*
6378 TTTGCGATTTTTTAATAATTTAA
1 TTTGCAATTTTTTAATAATTTAA
6401 TT
1 TT
6403 GCCACGTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTGCAATTTTTTAATAATTTAA
Found at i:10349 original size:21 final size:20
Alignment explanation
Indices: 10307--10348 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
10297 AATAAGGGGG
* *
10307 TTGCTAATACCGCCCTAGTT
1 TTGCTAATACCACCCCAGTT
10327 TTGCTAAATACCACCCCA-TT
1 TTGCT-AATACCACCCCAGTT
10347 TT
1 TT
10349 TTACACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.36
Consensus pattern (20 bp):
TTGCTAATACCACCCCAGTT
Found at i:10481 original size:32 final size:32
Alignment explanation
Indices: 10440--10575 Score: 213
Period size: 32 Copynumber: 4.3 Consensus size: 32
10430 CCCTCCCCAC
* *
10440 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
1 TGGGGCGGCTTTGCCACCGCAGGCCGCCCTCA
10472 TGGGGCGGCTTTGCCACCGCAGGCCGCCCT-A
1 TGGGGCGGCTTTGCCACCGCAGGCCGCCCTCA
*
10503 TGGCGCGGC-TTGCCACCGCAGGCCGCCCTCA
1 TGGGGCGGCTTTGCCACCGCAGGCCGCCCTCA
* *
10534 TGGGGCGGGTTTGCCACGGCAGGCCGCCCTCA
1 TGGGGCGGCTTTGCCACCGCAGGCCGCCCTCA
10566 TGGGGCGGCT
1 TGGGGCGGCT
10576 AGACCAAAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
30 20 0.21
31 17 0.18
32 58 0.61
ACGTcount: A:0.09, C:0.38, G:0.38, T:0.15
Consensus pattern (32 bp):
TGGGGCGGCTTTGCCACCGCAGGCCGCCCTCA
Found at i:10524 original size:62 final size:64
Alignment explanation
Indices: 10444--10575 Score: 214
Period size: 62 Copynumber: 2.1 Consensus size: 64
10434 CCCCACTGGG
*
10444 GCGGCTTCGCCACGGCAGGCCGCCCTCATGGGGCGGCTTTGCCACCGCAGGCCGCCCT-ATGGC
1 GCGGCTTCGCCACCGCAGGCCGCCCTCATGGGGCGGCTTTGCCACCGCAGGCCGCCCTCATGGC
* * *
10507 GCGGCTT-GCCACCGCAGGCCGCCCTCATGGGGCGGGTTTGCCACGGCAGGCCGCCCTCATGGG
1 GCGGCTTCGCCACCGCAGGCCGCCCTCATGGGGCGGCTTTGCCACCGCAGGCCGCCCTCATGGC
10570 GCGGCT
1 GCGGCT
10576 AGACCAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 47 0.73
63 17 0.27
ACGTcount: A:0.09, C:0.39, G:0.37, T:0.14
Consensus pattern (64 bp):
GCGGCTTCGCCACCGCAGGCCGCCCTCATGGGGCGGCTTTGCCACCGCAGGCCGCCCTCATGGC
Found at i:11315 original size:60 final size:60
Alignment explanation
Indices: 11221--11338 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
11211 ATTTATAGTC
*
11221 ATTTTGGTGCTTGTATTTTTCTTTAAATCTAATAGTTCATTGCACTTTATATTGTTTGGT
1 ATTTTGGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTATATTGTTTGGT
*
11281 ATTTTGGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTG
1 ATTTTGGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTATATTGTTTG
11339 CTATGTGTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.54
Consensus pattern (60 bp):
ATTTTGGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTATATTGTTTGGT
Found at i:11474 original size:107 final size:109
Alignment explanation
Indices: 11286--11501 Score: 391
Period size: 107 Copynumber: 2.0 Consensus size: 109
11276 TTGGTATTTT
11286 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGTGTGCTT
11351 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
* *
11395 GGTGCTTGTA-TTTTCTTT-AATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGTGTGCTT
*
11458 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
11502 ATAATAATAA
Statistics
Matches: 104, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
107 86 0.83
108 8 0.08
109 10 0.10
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGCTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:11499 original size:3 final size:3
Alignment explanation
Indices: 11491--11584 Score: 147
Period size: 3 Copynumber: 32.0 Consensus size: 3
11481 ACCACACAAT
* *
11491 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTA T-T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
11537 TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11585 AACTCACTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 3 0.04
3 82 0.96
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:11753 original size:11 final size:11
Alignment explanation
Indices: 11714--11747 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
11704 ATAGTAGGTA
11714 TAATTATCAAA-
1 TAATTAT-AAAT
11725 TAATTATAAAT
1 TAATTATAAAT
11736 TAATTATAAAT
1 TAATTATAAAT
11747 T
1 T
11748 TGTTATGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:12520 original size:187 final size:186
Alignment explanation
Indices: 12201--12731 Score: 731
Period size: 187 Copynumber: 2.8 Consensus size: 186
12191 GGTTCCTCAT
* * * * * *
12201 CATTTAAATTTAAAATGATTTGATTTATGAATATTCAGTTGTATAGTTGATAACATCATGTATGG
1 CATTCAAATTTAAAATGATTTGATTTATGAATATTCGGTTGTATAGTTGATAGCATCCTATATAG
* * * *
12266 TTTATACTTCCATTATCCTACTTCTATCAAAACAATGTTGCATATATTATATCAAATACAACAGA
66 TTTAAACTTCCATTATCCTACTTCTATCAAAACACTGTTGTATATATTATACCAAATACAACAGA
* * * * *
12331 AGTAAATTACCTTTCCCAAACAATTCTTCTGATAAATGATCTTTATTTACCCATAG
131 AGTAAATTATCTTTCCTAATCAATTCTTCTGATAAATGATCTTCATTTACCCACAG
* *
12387 CATTCAAATTTAATATGATTTGATTTAAGAATATTCGGTTGTATAGTTGATAGCATCCTATATAG
1 CATTCAAATTTAAAATGATTTGATTTATGAATATTCGGTTGTATAGTTGATAGCATCCTATATAG
*
12452 TTTAAACTTTCATGTATCCTACTTCTATCAAAACACTGTTGTATATATTATACCAAATACAACAG
66 TTTAAACTTCCAT-TATCCTACTTCTATCAAAACACTGTTGTATATATTATACCAAATACAACAG
** * * * *
12517 AAGTAAACCATCTTTCCTAATCAATTCTTCTGATTAATGATCTTCGTTTATCTACAG
130 AAGTAAATTATCTTTCCTAATCAATTCTTCTGATAAATGATCTTCATTTACCCACAG
* * ** *
12574 CAATCAAATTTAAAATGATTTGATTTATTAGGATTCGGTTGTATAATTGATAGCATCCTATATAG
1 CATTCAAATTTAAAATGATTTGATTTATGAATATTCGGTTGTATAGTTGATAGCATCCTATATAG
* ** * *
12639 TTTAAACTTCCATATATCTTACTTCTATCAAAACACTACTATTTATATTATACC-AATACAACAG
66 TTTAAACTTCCAT-TATCCTACTTCTATCAAAACACTGTTGTATATATTATACCAAATACAACAG
12703 AAGTAAATTATCTTTCCTAATCAATTCTT
130 AAGTAAATTATCTTTCCTAATCAATTCTT
12732 ATATAAGGTA
Statistics
Matches: 304, Mismatches: 40, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
186 105 0.35
187 199 0.65
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (186 bp):
CATTCAAATTTAAAATGATTTGATTTATGAATATTCGGTTGTATAGTTGATAGCATCCTATATAG
TTTAAACTTCCATTATCCTACTTCTATCAAAACACTGTTGTATATATTATACCAAATACAACAGA
AGTAAATTATCTTTCCTAATCAATTCTTCTGATAAATGATCTTCATTTACCCACAG
Found at i:15579 original size:15 final size:16
Alignment explanation
Indices: 15559--15592 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
15549 TTTTAGCGGC
15559 AAAAGAAAAAAAAG-A
1 AAAAGAAAAAAAAGTA
*
15574 AAAAGAAAATAAAGTA
1 AAAAGAAAAAAAAGTA
15590 AAA
1 AAA
15593 CCCCATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAAAAGTA
Found at i:16371 original size:24 final size:24
Alignment explanation
Indices: 16344--16417 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
16334 ATACATTTAA
16344 CAGAAACAGAGCATGCCTAAAACT
1 CAGAAACAGAGCATGCCTAAAACT
*
16368 CAGAAACATAGCATGCCTAAAACT
1 CAGAAACAGAGCATGCCTAAAACT
* * *
16392 CAGAAATAGAGCAAGCTTAAAA-T
1 CAGAAACAGAGCATGCCTAAAACT
16415 CAG
1 CAG
16418 GGCAATGCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (24 bp):
CAGAAACAGAGCATGCCTAAAACT
Found at i:21499 original size:17 final size:17
Alignment explanation
Indices: 21477--21511 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21467 TGCCCACCCC
21477 TAGTGCGGAAGACAATT
1 TAGTGCGGAAGACAATT
21494 TAGTGCGGAAGACAATT
1 TAGTGCGGAAGACAATT
21511 T
1 T
21512 CCGCCATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (17 bp):
TAGTGCGGAAGACAATT
Found at i:23606 original size:20 final size:20
Alignment explanation
Indices: 23553--23613 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
23543 ATTCAAGGCG
23553 ATCAAAAAATTAATATTAAC
1 ATCAAAAAATTAATATTAAC
* * *
23573 AT-ACACATTTAATATTAAC
1 ATCAAAAAATTAATATTAAC
23592 ATCAAAAAATTAATATTAAC
1 ATCAAAAAATTAATATTAAC
23612 AT
1 AT
23614 ACTATTAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCAAAAAATTAATATTAAC
Found at i:26147 original size:47 final size:47
Alignment explanation
Indices: 26078--26178 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 47
26068 ATCAACAATA
*
26078 TTTATTACTTGGTTTAATGAAGTTAAAGAGTTATTATTTGGTAAATC
1 TTTATTACTTGGTCTAATGAAGTTAAAGAGTTATTATTTGGTAAATC
26125 TTTATTACTTGGTCTAATGAAGTTAAAGAGTTATTATTTGGTAAATC
1 TTTATTACTTGGTCTAATGAAGTTAAAGAGTTATTATTTGGTAAATC
*
26172 TTAATTA
1 TTTATTA
26179 ATATATACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (47 bp):
TTTATTACTTGGTCTAATGAAGTTAAAGAGTTATTATTTGGTAAATC
Done.