Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011671.1 Corchorus capsularis cultivar CVL-1 contig11692, 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: 39598
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:815 original size:32 final size:33
Alignment explanation
Indices: 734--819 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
724 GAGCCGCCCA
*
734 AGCCATGGGTAAGGCCGCCCAAGCTGGGCGGCT
1 AGCCATGGGCAAGGCCGCCCAAGCTGGGCGGCT
*
767 AGCCATGGGCAAGGCCGCCCACGCTGGGCGGCT
1 AGCCATGGGCAAGGCCGCCCAAGCTGGGCGGCT
800 AGCCAT-GGCAAGGCCGCCCA
1 AGCCATGGGCAAGGCCGCCCA
820 GTTTGGGCGG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 14 0.27
33 37 0.73
ACGTcount: A:0.19, C:0.35, G:0.37, T:0.09
Consensus pattern (33 bp):
AGCCATGGGCAAGGCCGCCCAAGCTGGGCGGCT
Found at i:827 original size:32 final size:32
Alignment explanation
Indices: 734--831 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 32
724 GAGCCGCCCA
*
734 AGCCATGGGTAAGGCCGCCCAAGCTGGGCGGCT
1 AGCCATGGGCAAGGCCGCCC-AGCTGGGCGGCT
767 AGCCATGGGCAAGGCCGCCCACGCTGGGCGGCT
1 AGCCATGGGCAAGGCCGCCCA-GCTGGGCGGCT
*
800 AGCCAT-GGCAAGGCCGCCCAGTTTGGGCGGCT
1 AGCCATGGGCAAGGCCGCCCAG-CTGGGCGGCT
832 CGGCTATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.02
32 24 0.39
33 36 0.59
ACGTcount: A:0.16, C:0.33, G:0.39, T:0.12
Consensus pattern (32 bp):
AGCCATGGGCAAGGCCGCCCAGCTGGGCGGCT
Found at i:938 original size:15 final size:14
Alignment explanation
Indices: 903--979 Score: 58
Period size: 11 Copynumber: 5.6 Consensus size: 14
893 TTAAAATTAC
*
903 TTAGTTTATTAGTTTA
1 TTAGTTTATT--TTAA
919 TTAGTTTATGTTTAA
1 TTAGTTTAT-TTTAA
*
934 TTAG--TA-TCTAA
1 TTAGTTTATTTTAA
945 TTAGTTTATTATTAA
1 TTAGTTTATT-TTAA
960 TTAG--TA-TTTAA
1 TTAGTTTATTTTAA
971 TTAGTTTAT
1 TTAGTTTAT
980 GATTAAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
11 16 0.32
12 1 0.02
13 8 0.16
14 1 0.02
15 14 0.28
16 9 0.18
17 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.10, T:0.58
Consensus pattern (14 bp):
TTAGTTTATTTTAA
Found at i:949 original size:26 final size:26
Alignment explanation
Indices: 918--985 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
908 TTATTAGTTT
918 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
944 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
970 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
986 AATGAAGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:985 original size:15 final size:14
Alignment explanation
Indices: 898--985 Score: 53
Period size: 15 Copynumber: 6.4 Consensus size: 14
888 GTTAATTAAA
*
898 ATTACTTAGTTTATT
1 ATTAATTAGTTTA-T
*
913 AGTTTATTAGTTTAT
1 A-TTAATTAGTTTAT
*
928 GTTTAATTAG--TAT
1 -ATTAATTAGTTTAT
*
941 -CTAATTAGTTTATT
1 ATTAATTAGTTTA-T
955 ATTAATTAG--TAT
1 ATTAATTAGTTTAT
967 -TTAATTAGTTTAT
1 ATTAATTAGTTTAT
980 GATTAA
1 -ATTAA
986 AATGAAGCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
11 15 0.26
12 1 0.02
13 10 0.18
14 1 0.02
15 20 0.35
16 10 0.18
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTAATTAGTTTAT
Found at i:1037 original size:10 final size:10
Alignment explanation
Indices: 1022--1047 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1012 TGTTAGAAAT
1022 GAAGTTTGAA
1 GAAGTTTGAA
1032 GAAGTTTGAA
1 GAAGTTTGAA
1042 GAAGTT
1 GAAGTT
1048 GTTAGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
GAAGTTTGAA
Found at i:1160 original size:21 final size:21
Alignment explanation
Indices: 1134--1177 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1124 CAAAAATGTA
*
1134 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGACGGTATTTAGC
*
1155 AAAAGGGGGACGGTGTTTAGC
1 AAAAGGGGGACGGTATTTAGC
1176 AA
1 AA
1178 TCCAGTTAAA
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:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGACGGTATTTAGC
Found at i:1586 original size:37 final size:37
Alignment explanation
Indices: 1543--1637 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
1533 AATTTTGTTT
1543 TTTGTTTCCAACGTCCTATTTAATTTTGAC-TTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTG-CTTTTTGTC
* *
1580 TTTGTTTCCAACGTTGC-ACTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAACG-TCCTATTTAATTTTGCTTTTTGTC
* *
1617 TTTGTCTCCAGCGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
1638 GGATTTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 3 0.06
37 44 0.90
38 2 0.04
ACGTcount: A:0.14, C:0.21, G:0.13, T:0.53
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTTTGTC
Found at i:2859 original size:13 final size:14
Alignment explanation
Indices: 2836--2864 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2826 AAGAAAGAAG
2836 TTTGTTTTTTGTTT
1 TTTGTTTTTTGTTT
2850 TTTG-TTTTTGTTT
1 TTTGTTTTTTGTTT
2863 TT
1 TT
2865 GGACAGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTGTTTTTTGTTT
Found at i:2865 original size:6 final size:7
Alignment explanation
Indices: 2836--2864 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2826 AAGAAAGAAG
2836 TTTGTTT
1 TTTGTTT
2843 TTTGTTT
1 TTTGTTT
2850 TTTG-TT
1 TTTGTTT
2856 TTTGTTT
1 TTTGTTT
2863 TT
1 TT
2865 GGACAGACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTGTTT
Found at i:3881 original size:21 final size:21
Alignment explanation
Indices: 3856--3903 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3846 CTAAGGGAAG
3856 TTTTTATAAAAAAAATTGAAT
1 TTTTTATAAAAAAAATTGAAT
3877 TTTTTATAAAAAAAATTGAAT
1 TTTTTATAAAAAAAATTGAAT
3898 TTTTTA
1 TTTTTA
3904 AAATCTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
TTTTTATAAAAAAAATTGAAT
Found at i:4718 original size:24 final size:24
Alignment explanation
Indices: 4685--4733 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
4675 TGGTTGTTGT
*
4685 TGTTCTACTATAAACCCAGAAAGG
1 TGTTCCACTATAAACCCAGAAAGG
*
4709 TGTTCCACTATAGACCCAGAAAGG
1 TGTTCCACTATAAACCCAGAAAGG
4733 T
1 T
4734 TATTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (24 bp):
TGTTCCACTATAAACCCAGAAAGG
Found at i:7581 original size:21 final size:21
Alignment explanation
Indices: 7556--7599 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
7546 AACTTATTTA
*
7556 AATTTTGATTTGCAAAGTTTG
1 AATTTTGATCTGCAAAGTTTG
*
7577 AATTTTGATCTGCAGAGTTTG
1 AATTTTGATCTGCAAAGTTTG
7598 AA
1 AA
7600 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:12631 original size:12 final size:12
Alignment explanation
Indices: 12578--12637 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
12568 CAATCGAGAA
12578 AATTAAAGAAAAC
1 AATT-AAGAAAAC
*
12591 AATTAATAAAA-
1 AATTAAGAAAAC
** *
12602 AAGCAGAGAATA-
1 AATTA-AGAAAAC
12614 AATTAAGAAAAC
1 AATTAAGAAAAC
12626 AATTAAGAAAAC
1 AATTAAGAAAAC
12638 CCTCCAACAT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
11 8 0.22
12 25 0.68
13 4 0.11
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (12 bp):
AATTAAGAAAAC
Found at i:13885 original size:318 final size:318
Alignment explanation
Indices: 13301--13942 Score: 1097
Period size: 318 Copynumber: 2.0 Consensus size: 318
13291 ATATTTTATG
*
13301 AGAAAAAAATACATAAAAACCTAGACCTAAGGAGGCTATTTATAGTGGAAAAATAACCTAAAGAC
1 AGAAAAGAATACATAAAAACCTAGACCTAAGGAGGCTATTTATAGTGGAAAAATAACCTAAAGAC
* *
13366 TCGAACTACACTTAGGATAGGACTCTAGGTCGTTTTCAACCTCTAACTTGGTCTCCAAGTTCGAT
66 TCCAACTACACTTAGGATAGGACTCTAGGTCGGTTTCAACCTCTAACTTGGTCTCCAAGTTCGAT
* * *
13431 TAAGAGTCTTCCCAACCGAAATTAGGGGTTAAAATCGGATCCTGGAATTTTCTGGAATCGCACAG
131 TAAAAGTCTTCCCAACCGAAATTAGGGGTTAAAATCGGAGCCTAGAATTTTCTGGAATCGCACAG
* * *
13496 CAACTTCGACAGCAATTTCGAGCTTGAAAACAGCATAACTGGCTTTGGACTTCAAAGGAAAATTG
196 CAACTTCGACAACAATTCCGAGCTTGAAAACAGCAGAACTGGCTTTGGACTTCAAAGGAAAATTG
* *
13561 TAGATCTCGGAGTTAGCTTTCCAACGCCTACTCACGGGCCTAAAACGGATATCTGAAC
261 TAGATCTCGGAGTTAACTTTCCAACACCTACTCACGGGCCTAAAACGGATATCTGAAC
13619 AGAAAAGAATACATAAAAACCTAGACCTAAGGAGGCTATTTATAGTGGAAAAATAACCTAAAGAC
1 AGAAAAGAATACATAAAAACCTAGACCTAAGGAGGCTATTTATAGTGGAAAAATAACCTAAAGAC
* *
13684 TCCAATTACACTTAGGATAGGACTCTAGGTCGGTTTCAACCTCTAACTTGGTCTCCAAGTTGGAT
66 TCCAACTACACTTAGGATAGGACTCTAGGTCGGTTTCAACCTCTAACTTGGTCTCCAAGTTCGAT
13749 TAAAAGTCTTCCCAACCGAAATTAGGGGTTAAAATCGGAGCCTAGAATTTTCTGGAATCGCACAG
131 TAAAAGTCTTCCCAACCGAAATTAGGGGTTAAAATCGGAGCCTAGAATTTTCTGGAATCGCACAG
* * * *
13814 CAACTTCGACAACAATTCCGTGCTTGAAAACGGCAGAACTGGCTTTGGACTTCAGAGGAAAGTTG
196 CAACTTCGACAACAATTCCGAGCTTGAAAACAGCAGAACTGGCTTTGGACTTCAAAGGAAAATTG
* * *
13879 TAGATCTTGGAGTTAACTTTCCAACACCTACTCACGGGCCTAAAATGGATATCTGAGC
261 TAGATCTCGGAGTTAACTTTCCAACACCTACTCACGGGCCTAAAACGGATATCTGAAC
13937 A-AAAAG
1 AGAAAAG
13943 TTATGGCCTT
Statistics
Matches: 304, Mismatches: 20, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
317 5 0.02
318 299 0.98
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (318 bp):
AGAAAAGAATACATAAAAACCTAGACCTAAGGAGGCTATTTATAGTGGAAAAATAACCTAAAGAC
TCCAACTACACTTAGGATAGGACTCTAGGTCGGTTTCAACCTCTAACTTGGTCTCCAAGTTCGAT
TAAAAGTCTTCCCAACCGAAATTAGGGGTTAAAATCGGAGCCTAGAATTTTCTGGAATCGCACAG
CAACTTCGACAACAATTCCGAGCTTGAAAACAGCAGAACTGGCTTTGGACTTCAAAGGAAAATTG
TAGATCTCGGAGTTAACTTTCCAACACCTACTCACGGGCCTAAAACGGATATCTGAAC
Found at i:17632 original size:10 final size:10
Alignment explanation
Indices: 17617--17644 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
17607 GGACTAGTAT
17617 GCGGGAATAA
1 GCGGGAATAA
17627 GCGGGAATAA
1 GCGGGAATAA
17637 GCGGGAAT
1 GCGGGAAT
17645 TGGATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.36, C:0.11, G:0.43, T:0.11
Consensus pattern (10 bp):
GCGGGAATAA
Found at i:25281 original size:17 final size:16
Alignment explanation
Indices: 25256--25298 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
25246 TTTTCTTCAG
25256 AAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAACA
*
25272 AAAAACAAAACAAAACA
1 AAAAA-AAAAAAAAACA
*
25289 AAAGAAAAAA
1 AAAAAAAAAA
25299 GGGGACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAACA
Found at i:30645 original size:10 final size:10
Alignment explanation
Indices: 30630--30657 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
30620 AGATGAGGAC
30630 TCTGGAATTT
1 TCTGGAATTT
30640 TCTGGAATTT
1 TCTGGAATTT
30650 TCTGGAAT
1 TCTGGAAT
30658 CTGGCAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.46
Consensus pattern (10 bp):
TCTGGAATTT
Done.