Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013421.1 Corchorus capsularis cultivar CVL-1 contig13442, 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: 29224
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4987 original size:2 final size:2
Alignment explanation
Indices: 4980--5004 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4970 AAATTTTATT
4980 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
5005 GTATGTATGT
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
Found at i:6164 original size:10 final size:11
Alignment explanation
Indices: 6148--6190 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
6138 AGAGAGAGAG
*
6148 AAAAAAAAAAC
1 AAAAACAAAAC
6159 AAAAA-AAAAC
1 AAAAACAAAAC
*
6169 AAAAACAAAAA
1 AAAAACAAAAC
6180 AAAAACAAAAC
1 AAAAACAAAAC
6191 CAGAACGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:6164 original size:11 final size:11
Alignment explanation
Indices: 6148--6190 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
6138 AGAGAGAGAG
6148 AAAAAAAAAAC
1 AAAAAAAAAAC
6159 -AAAAAAAAAC
1 AAAAAAAAAAC
6169 AAAAACAAAAA-
1 AAAAA-AAAAAC
*
6180 AAAAACAAAAC
1 AAAAAAAAAAC
6191 CAGAACGACG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 14 0.50
11 9 0.32
12 5 0.18
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:6172 original size:16 final size:17
Alignment explanation
Indices: 6148--6189 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
6138 AGAGAGAGAG
6148 AAAAA-AAAAAC-AAAA
1 AAAAACAAAAACAAAAA
6163 AAAAACAAAAACAAAAA
1 AAAAACAAAAACAAAAA
6180 AAAAACAAAA
1 AAAAACAAAA
6190 CCAGAACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.20
16 6 0.24
17 14 0.56
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAACAAAAA
Found at i:6190 original size:16 final size:15
Alignment explanation
Indices: 6148--6190 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
6138 AGAGAGAGAG
6148 AAAAAA-AAAACAAA
1 AAAAAACAAAACAAA
6162 AAAAAACAAAAACAAAA
1 AAAAAAC-AAAAC-AAA
6179 AAAAAACAAAAC
1 AAAAAACAAAAC
6191 CAGAACGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAACAAA
Found at i:11135 original size:46 final size:47
Alignment explanation
Indices: 11006--11156 Score: 205
Period size: 48 Copynumber: 3.2 Consensus size: 47
10996 ATACCTATTT
* *
11006 AGGAAGGCACGTGAGAGAATGAGTTGTATTGTGTAGAAGTTCCTAATA
1 AGGAAGGCAC-TGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
*
11054 AGGAAGGCACATGAGAGAACGAGTTGTATCGTGTAAAAGTTCCTAATA
1 AGGAAGGCAC-TGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
* * * *
11102 AGGAAGGCAC-GCGAGAATGAGTTGTATCATGTAAAACTTCCTAATG
1 AGGAAGGCACTGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
*
11148 AGGAGGGCA
1 AGGAAGGCA
11157 TGATTAGATA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
46 39 0.42
48 54 0.58
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (47 bp):
AGGAAGGCACTGAGAGAATGAGTTGTATCGTGTAAAAGTTCCTAATA
Found at i:13723 original size:15 final size:15
Alignment explanation
Indices: 13604--13723 Score: 170
Period size: 15 Copynumber: 8.0 Consensus size: 15
13594 GCCTTTGAAG
*
13604 AAGCAAG-GAGATGAG
1 AAGCAAGAG-GATGAC
*
13619 AAGCAAGAGGATGAG
1 AAGCAAGAGGATGAC
*
13634 AAGCAAGAGGATGCC
1 AAGCAAGAGGATGAC
*
13649 AAGCAAGAGGATGCC
1 AAGCAAGAGGATGAC
*
13664 AAGCAAAAGGATGAC
1 AAGCAAGAGGATGAC
*
13679 GAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
13694 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
13709 AAGCAAGAGGATGAC
1 AAGCAAGAGGATGAC
13724 CACCTTGCTG
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
15 96 0.99
16 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.35, T:0.07
Consensus pattern (15 bp):
AAGCAAGAGGATGAC
Found at i:14411 original size:117 final size:117
Alignment explanation
Indices: 14259--14625 Score: 716
Period size: 117 Copynumber: 3.1 Consensus size: 117
14249 GAAGGGACAC
14259 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
1 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
14324 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
66 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
14376 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
1 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
*
14441 GATAATGTGCCTGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
66 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
*
14493 GTGATTCAGAAGCAAAAACAAATAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
1 GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
14558 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
66 GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
14610 GTGATTCAGAAGCAAA
1 GTGATTCAGAAGCAAA
14626 GTCACTGAAG
Statistics
Matches: 247, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 247 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.22
Consensus pattern (117 bp):
GTGATTCAGAAGCAAAAACAAACAGACGTTCTGGAAAAAAGGTTGCTACTGTCGTTTCCAATGAA
GATAATGTGCCCGCTAATGTAGATGAAACTAAGAAAGAAAGTGGCACTGCGA
Found at i:18821 original size:57 final size:57
Alignment explanation
Indices: 18733--18905 Score: 220
Period size: 57 Copynumber: 3.0 Consensus size: 57
18723 CTCAGTATCC
18733 GGTAATCACATTAAGCTCCGACTAATCCGGAGTCGGGTTACATCGGACTATAAATGA
1 GGTAATCACATTAAGCTCCGACTAATCCGGAGTCGGGTTACATCGGACTATAAATGA
* * * *
18790 GGTAATCACATTAAACTCCGACTAATCCGGAGTCGGATTGCATCGGACCATAAATGA
1 GGTAATCACATTAAGCTCCGACTAATCCGGAGTCGGGTTACATCGGACTATAAATGA
* ** * * * * * * *
18847 GGTAACCACATTGGGCTCCAACTAATTCGGTGTCGGGTCACTTCAGACTCTAAATGA
1 GGTAATCACATTAAGCTCCGACTAATCCGGAGTCGGGTTACATCGGACTATAAATGA
18904 GG
1 GG
18906 GGAAAGCTCT
Statistics
Matches: 98, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 98 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (57 bp):
GGTAATCACATTAAGCTCCGACTAATCCGGAGTCGGGTTACATCGGACTATAAATGA
Found at i:25018 original size:6 final size:6
Alignment explanation
Indices: 25003--25036 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
24993 CCCAAAAAAC
25003 ACCC-A ACCCAA ACCCAA ACCCAA ACCCAA ACCCA
1 ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCA
25037 GTTTTGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCAA
Found at i:27413 original size:107 final size:104
Alignment explanation
Indices: 27302--27586 Score: 410
Period size: 107 Copynumber: 2.7 Consensus size: 104
27292 TTATCATATA
* * *
27302 GTTTTAGAAATAAGATATAAAACTAATTTCACTAAGTTTAGCCTCATATTAAAATTGTATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCC-CAAATTAAAATTATATTTTTA
*
27367 TTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGG
65 TTTTAAGGGTAAATTCCAAAATTAATAA--TATTGTTATAGG
* * *
27409 GTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAACCCCAAATTAAAATTTTATTTTTA
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTT-AGCCCAAATTAAAATTATATTTTTA
* *
27474 TTTTAAGGGTAACTTCCATAATTAATAATATTGTTATAGG
65 TTTTAAGGGTAAATTCCAAAATTAATAATATTGTTATAGG
* * * *
27514 GTTTTAGACATAAAATATATAACTAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTAT
1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTATATTTTTAT
27578 TTTAAGGGT
66 TTTAAGGGT
27587 TAGAAAAATA
Statistics
Matches: 162, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
103 31 0.19
104 12 0.07
105 35 0.22
107 81 0.50
108 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (104 bp):
GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTATATTTTTAT
TTTAAGGGTAAATTCCAAAATTAATAATATTGTTATAGG
Found at i:28055 original size:75 final size:74
Alignment explanation
Indices: 27967--28115 Score: 194
Period size: 75 Copynumber: 2.0 Consensus size: 74
27957 TCTGAATACC
* *
27967 CTCTGAAAATTACT-AAAGGCTCTCATCAACTTTTAACGTGGGAG-TGCCTTTTCGCCCCGTTTT
1 CTCTGAAAATTACTGAAA-GCCCCCATCAACTTTTAACGTGGGAGAT--CTTTTCGCCCCGTTTT
28030 GGTCTTTTCTCA
63 GGTCTTTTCTCA
* * * * *
28042 CTCTGAAATTTACTGATAGCCCCCATCAACTTTTAATGTTGGAGATCTTTTCGCTCCGTTTTGGT
1 CTCTGAAAATTACTGAAAGCCCCCATCAACTTTTAACGTGGGAGATCTTTTCGCCCCGTTTTGGT
28107 CTTTTCTCA
66 CTTTTCTCA
28116 ATTCATTAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
74 27 0.42
75 35 0.54
76 3 0.05
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (74 bp):
CTCTGAAAATTACTGAAAGCCCCCATCAACTTTTAACGTGGGAGATCTTTTCGCCCCGTTTTGGT
CTTTTCTCA
Found at i:28265 original size:14 final size:14
Alignment explanation
Indices: 28246--28276 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28236 AATTTTATAT
28246 TTTTTCCCTTTGCA
1 TTTTTCCCTTTGCA
*
28260 TTTTTCCCTTTGTA
1 TTTTTCCCTTTGCA
28274 TTT
1 TTT
28277 GGTAGGTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.23, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTTCCCTTTGCA
Done.