Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015774.1 Corchorus capsularis cultivar CVL-1 contig15795, 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: 35302
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1263 original size:83 final size:80
Alignment explanation
Indices: 1159--1320 Score: 218
Period size: 83 Copynumber: 2.0 Consensus size: 80
1149 ACAGTTTCAT
* * * *
1159 TCTATGAATCCTATTTCAATCATTATGTTTGATTTTGTAACGTTA-TATAATAAATGTTTTTCAT
1 TCTATAAATCCTATTTAAATCATTATGTTTAATTTTGTAA---TAGAAT-ATAAATGTTTTTCAT
1223 TAAATGGAATTAATTTAGC
62 TAAATGGAATTAATTTAGC
* * *
1242 TCTATAAATTCTATTTAAATCATTATGTTTAATTTTTTAATAGAATATATATGTTTTTCATTAAA
1 TCTATAAATCCTATTTAAATCATTATGTTTAATTTTGTAATAGAATATAAATGTTTTTCATTAAA
1307 TGGAATTAATTTAG
66 TGGAATTAATTTAG
1321 GGTATTATCA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 34 0.48
81 2 0.03
83 35 0.49
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (80 bp):
TCTATAAATCCTATTTAAATCATTATGTTTAATTTTGTAATAGAATATAAATGTTTTTCATTAAA
TGGAATTAATTTAGC
Found at i:1730 original size:2 final size:2
Alignment explanation
Indices: 1723--1748 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1713 TTTTTGAATA
1723 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1749 CTTAAGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6992 original size:7 final size:7
Alignment explanation
Indices: 6982--7012 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6972 TTTTGTTTTG
6982 TTTTGTT
1 TTTTGTT
6989 TTTTGTT
1 TTTTGTT
6996 TTTTGTT
1 TTTTGTT
7003 TTTT-TT
1 TTTTGTT
7009 TTTT
1 TTTT
7013 CCTGTAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTGTT
Found at i:7001 original size:14 final size:13
Alignment explanation
Indices: 6972--7012 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 13
6962 TTTGCATCTT
6972 TTTTGTTTTGTTTTG
1 TTTT-TTTT-TTTTG
6987 TTTTTTGTTTTTTG
1 TTTTTT-TTTTTTG
7001 TTTTTTTTTTTT
1 TTTTTTTTTTTT
7013 CCTGTAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:7764 original size:29 final size:30
Alignment explanation
Indices: 7721--7782 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
7711 TCAACTGGTA
* *
7721 GGTGTATCGTGCCTGGGCCGTGAGGTCCTG
1 GGTGTATCCTGCCTGGACCGTGAGGTCCTG
7751 GGTGTA-CCTGCCTGGACCGTGAGGTCCTG
1 GGTGTATCCTGCCTGGACCGTGAGGTCCTG
7780 GGT
1 GGT
7783 TCAAGTCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.08, C:0.24, G:0.42, T:0.26
Consensus pattern (30 bp):
GGTGTATCCTGCCTGGACCGTGAGGTCCTG
Found at i:12936 original size:215 final size:215
Alignment explanation
Indices: 12565--13000 Score: 845
Period size: 215 Copynumber: 2.0 Consensus size: 215
12555 CATTTAGGAC
12565 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGACCCTTCATGTATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGACCCTTCATGTATATAAGGCAC
*
12630 CCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAGCC
66 CCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAACC
*
12695 CGGGACAACACCGAAATAGAACGGGCCTATACGTGGACACAACCGGGTCTGGGGCGCAACAGGAC
131 CGGGACAACACCGAAACAGAACGGGCCTATACGTGGACACAACCGGGTCTGGGGCGCAACAGGAC
12760 AGACCTGAGCTCTGATACCA
196 AGACCTGAGCTCTGATACCA
*
12780 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAGGCAC
1 TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGACCCTTCATGTATATAAGGCAC
12845 CCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAACC
66 CCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAACC
12910 CGGGACAACACCGAAACAGAACGGGCCTATACGTGGACACAACCGGGTCTGGGGCGCAACAGGAC
131 CGGGACAACACCGAAACAGAACGGGCCTATACGTGGACACAACCGGGTCTGGGGCGCAACAGGAC
12975 AGACCTGAGCTCTGATACCA
196 AGACCTGAGCTCTGATACCA
12995 TGTTAA
1 TGTTAA
13001 CTCATTAGAA
Statistics
Matches: 218, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
215 218 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (215 bp):
TGTTAAGCATCCAACCTAAAACCAATTGGCAATAGGTGGAGAGACCCTTCATGTATATAAGGCAC
CCAGTCATGTCAAACATAACCAATGTGGGATATTACCACTCTAACACGCCCCCTCACGTGTAACC
CGGGACAACACCGAAACAGAACGGGCCTATACGTGGACACAACCGGGTCTGGGGCGCAACAGGAC
AGACCTGAGCTCTGATACCA
Found at i:16723 original size:150 final size:150
Alignment explanation
Indices: 16541--16844 Score: 599
Period size: 150 Copynumber: 2.0 Consensus size: 150
16531 TGCTGGCGCT
16541 ACGGGCGTTTTTTTTTAGAATTATTATTTATCATCATGCATATATTAAAAGATTTTCGTCATAAA
1 ACGGGCGTTTTTTTTTAGAATTATTATTTATCATCATGCATATATTAAAAGATTTTCGTCATAAA
*
16606 TTTAAAATGGAGACAGTGCTTTGACGTGTTTATTAGGATTGTTCTATTTCCTTTTTTAAGGTACA
66 TTTAAAATGGAGACAGTGCTTTGACGTGTTTATTAGGATTGTTCTATTTCCTTTTTTAAGATACA
16671 GATTTTTCAAAAAATAATCG
131 GATTTTTCAAAAAATAATCG
16691 ACGGGCGTTTTTTTTTAGAATTATTATTTATCATCATGCATATATTAAAAGATTTTCGTCATAAA
1 ACGGGCGTTTTTTTTTAGAATTATTATTTATCATCATGCATATATTAAAAGATTTTCGTCATAAA
16756 TTTAAAATGGAGACAGTGCTTTGACGTGTTTATTAGGATTGTTCTATTTCCTTTTTTAAGATACA
66 TTTAAAATGGAGACAGTGCTTTGACGTGTTTATTAGGATTGTTCTATTTCCTTTTTTAAGATACA
16821 GATTTTTCAAAAAATAATCG
131 GATTTTTCAAAAAATAATCG
16841 ACGG
1 ACGG
16845 AAAAAAAAAC
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 153 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (150 bp):
ACGGGCGTTTTTTTTTAGAATTATTATTTATCATCATGCATATATTAAAAGATTTTCGTCATAAA
TTTAAAATGGAGACAGTGCTTTGACGTGTTTATTAGGATTGTTCTATTTCCTTTTTTAAGATACA
GATTTTTCAAAAAATAATCG
Found at i:17459 original size:45 final size:45
Alignment explanation
Indices: 17386--17475 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
17376 GATTACTTCT
* * * *
17386 CCAGCTCATCATTAATCCGGGGTTGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGAGATAGGGATCTTTTAATAATTCCAC
* *
17431 CCAGCTTATCATTAATTCGAGATAGGGATCTTTTAATAATTCCAC
1 CCAGCTCATCATTAATCCGAGATAGGGATCTTTTAATAATTCCAC
17476 TACTCTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGAGATAGGGATCTTTTAATAATTCCAC
Found at i:18894 original size:31 final size:28
Alignment explanation
Indices: 18823--18878 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
18813 TCTCATTTTT
*
18823 AAAACTTAA-GGGCCAATTTGTCCCAAA
1 AAAAATTAAGGGGCCAATTTGTCCCAAA
18850 AAAAATTAAGGGGCCAATTTGTCCCAAA
1 AAAAATTAAGGGGCCAATTTGTCCCAAA
18878 A
1 A
18879 TGGATAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (28 bp):
AAAAATTAAGGGGCCAATTTGTCCCAAA
Found at i:21531 original size:60 final size:59
Alignment explanation
Indices: 21392--21509 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 59
21382 TCCTTGAGCA
* * * *
21392 TATACATTAGGGCCCTATTTAACCAAATTAAAAGTATAAGCCCTAAATTGACCATTTTTG
1 TATACATTAAGGACCTATTTAACCAAATTAAAAGCATAAGCCCTAAATTGA-CATATTTG
* *
21452 TATACATTAAGGACATATTTAACCAAATT-AAAGCCATGAGCCCTAAATTGA-ATATTTG
1 TATACATTAAGGACCTATTTAACCAAATTAAAAG-CATAAGCCCTAAATTGACATATTTG
21510 CTCATATGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
58 6 0.12
59 4 0.08
60 41 0.80
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (59 bp):
TATACATTAAGGACCTATTTAACCAAATTAAAAGCATAAGCCCTAAATTGACATATTTG
Found at i:28388 original size:4 final size:4
Alignment explanation
Indices: 28381--28425 Score: 74
Period size: 4 Copynumber: 11.2 Consensus size: 4
28371 CTCGAGCAGC
28381 CTTT CTTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -TTT C
1 CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
28426 ATCTTCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.82
5 4 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:35279 original size:2 final size:2
Alignment explanation
Indices: 35272--35302 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35262 TAAATTAATT
35272 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
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
Done.