Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009202.1 Corchorus capsularis cultivar CVL-1 contig09223, 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: 62532
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4601 original size:69 final size:69
Alignment explanation
Indices: 4473--4601 Score: 204
Period size: 69 Copynumber: 1.9 Consensus size: 69
4463 ATTGAGGTGC
* ** **
4473 GATTTCATCAAAATCAATCCCAATGTGACTACCAGATACCGGAGGGTTTGTACTGAAAGAGAAGA
1 GATTTCATCAAAATCAACCCCAATGTGACTACCAGATACCAAAGGGTTTGTACCAAAAGAGAAGA
4538 CTCA
66 CTCA
*
4542 GATTTCATCAAAATCAGCCCCAATGTGACTACCAGATACCAAAGGGTTTGTACCAAAAGA
1 GATTTCATCAAAATCAACCCCAATGTGACTACCAGATACCAAAGGGTTTGTACCAAAAGA
4602 TAGGGCTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (69 bp):
GATTTCATCAAAATCAACCCCAATGTGACTACCAGATACCAAAGGGTTTGTACCAAAAGAGAAGA
CTCA
Found at i:17381 original size:1 final size:1
Alignment explanation
Indices: 17375--17401 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
17365 ACAATCTGGG
17375 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
17402 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:17878 original size:18 final size:18
Alignment explanation
Indices: 17855--17904 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
17845 GGCCACAACT
*
17855 TGATCAGTAG-AGCCACCC
1 TGATCAGCAGCAG-CACCC
17873 TGATCAGCAGCAGCACCC
1 TGATCAGCAGCAGCACCC
* *
17891 TGCTCAGCTGCAGC
1 TGATCAGCAGCAGC
17905 CTCCTGCCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (18 bp):
TGATCAGCAGCAGCACCC
Found at i:17910 original size:18 final size:18
Alignment explanation
Indices: 17868--17923 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
17858 TCAGTAGAGC
*
17868 CACCCTGATCAGCAGCAG
1 CACCCTGCTCAGCAGCAG
*
17886 CACCCTGCTCAGCTGCAG
1 CACCCTGCTCAGCAGCAG
* *
17904 C-CTCCTGCCCTGCAGCAG
1 CAC-CCTGCTCAGCAGCAG
17922 CA
1 CA
17924 TCAGGTTCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.20, C:0.45, G:0.21, T:0.14
Consensus pattern (18 bp):
CACCCTGCTCAGCAGCAG
Found at i:27035 original size:24 final size:24
Alignment explanation
Indices: 26987--27036 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
26977 GAGCAATACG
* * **
26987 TGAAGCTCGTGAAAGGGCTTTTGC
1 TGAAGCCCGCGAAAGGGCTGCTGC
27011 TGAAGCCCGCGAAAGGGCTGCTGC
1 TGAAGCCCGCGAAAGGGCTGCTGC
27035 TG
1 TG
27037 GAAGAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (24 bp):
TGAAGCCCGCGAAAGGGCTGCTGC
Found at i:34669 original size:32 final size:33
Alignment explanation
Indices: 34612--34673 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
34602 ATTGAACCCT
*
34612 TACCAAACAACAAAGTATTAGTACCATCTTTTG
1 TACCAAACAACAAAGTATTAATACCATCTTTTG
34645 TACCAAACAGA-AAA-TATTAATACCATCTT
1 TACCAAACA-ACAAAGTATTAATACCATCTT
34674 ACATATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (33 bp):
TACCAAACAACAAAGTATTAATACCATCTTTTG
Found at i:35620 original size:2 final size:2
Alignment explanation
Indices: 35613--35645 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35603 GTAGAAGCGA
35613 AT AT 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 AT AT A
35646 GTGTAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37129 original size:162 final size:162
Alignment explanation
Indices: 36862--37186 Score: 596
Period size: 162 Copynumber: 2.0 Consensus size: 162
36852 TAAGTTGTAT
* *
36862 TTGGGATACAACTAAGCCGCTTAAGAACATCCAAGGAAGAAGTTGAAGAATTGATTGTTTCAGGG
1 TTGGGATACAACTAAGCCGCTTAAGAACATCCAAGGAAGAAGTAGAAGAATTGATTGGTTCAGGG
*
36927 GAAAAACACGTTCCTATTTATAAAAAGTGAAAGAACATAACCTCTGGAAATTGTCTCCTCATTAA
66 GAAAAACACGTTCCTATTTATAAAAAGTGAAAGAACATAACCTCTGGAAACTGTCTCCTCATTAA
*
36992 AAGGTATCTATCAGATAAAAGACAGTTTTTGG
131 AAAGTATCTATCAGATAAAAGACAGTTTTTGG
*
37024 TTGGGATACAACTAAGCCGCTTAAGAACATCCAAGGAAGAAGTAGAATAATTGATTGGTTCAGGG
1 TTGGGATACAACTAAGCCGCTTAAGAACATCCAAGGAAGAAGTAGAAGAATTGATTGGTTCAGGG
*
37089 GAAAAACACGTTCCTATTTATAAAAAGTGAAAGAACATAACCTCTGGAAACTGTTTCCTCATTAA
66 GAAAAACACGTTCCTATTTATAAAAAGTGAAAGAACATAACCTCTGGAAACTGTCTCCTCATTAA
37154 AAAGTATCTATCAGATAAAAGACAGTTTTTGG
131 AAAGTATCTATCAGATAAAAGACAGTTTTTGG
37186 T
1 T
37187 AGTTTATACC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 157 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (162 bp):
TTGGGATACAACTAAGCCGCTTAAGAACATCCAAGGAAGAAGTAGAAGAATTGATTGGTTCAGGG
GAAAAACACGTTCCTATTTATAAAAAGTGAAAGAACATAACCTCTGGAAACTGTCTCCTCATTAA
AAAGTATCTATCAGATAAAAGACAGTTTTTGG
Found at i:37483 original size:16 final size:16
Alignment explanation
Indices: 37462--37493 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37452 ATCTACTAGC
37462 CCACATGTTATCCAAA
1 CCACATGTTATCCAAA
37478 CCACATGTTATCCAAA
1 CCACATGTTATCCAAA
37494 GACAACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (16 bp):
CCACATGTTATCCAAA
Found at i:40627 original size:70 final size:71
Alignment explanation
Indices: 40544--40776 Score: 310
Period size: 70 Copynumber: 3.2 Consensus size: 71
40534 TAACTAAAAT
* *
40544 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
40608 TAGTTG
66 TAGTTG
*
40614 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
40679 GAGTTTTTAGTTG
59 GAGTTTTTAGTTG
* * * * *
40692 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
40756 TAGTTG
66 TAGTTG
40762 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
40777 ACCTAAACAA
Statistics
Matches: 147, Mismatches: 7, Indels: 18
0.85 0.04 0.10
Matches are distributed among these distances:
70 71 0.48
71 5 0.03
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 63 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:40627 original size:78 final size:77
Alignment explanation
Indices: 40538--40776 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
40528 GCTTTTTAAC
*
40538 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
40603 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
40616 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
40681 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
40694 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
40752 TTTTTAGTTGAG
66 TTTTTAGTTGAG
40764 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
40777 ACCTAAACAA
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:51694 original size:2 final size:2
Alignment explanation
Indices: 51687--51722 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
51677 AAGAAAATAG
51687 AT AT AT AT AT 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 AT AT AT AT AT
51723 GAAGACATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59088 original size:221 final size:215
Alignment explanation
Indices: 58703--59138 Score: 701
Period size: 221 Copynumber: 2.0 Consensus size: 215
58693 TACTAATATA
* * *
58703 TACTAAGCCTTATTTGAGATACCCAATGAAATTACTAAAGGCTCCAAACCAGAATAATGAGAGTC
1 TACTAAACCTTATTTGAGATACCCAATGAAATTACTAAAGACTCCAAACCAGAATAATGAGAGCC
* *
58768 AATATTTTGGCTTTTTTTTTCTTTTTTGATTTGCCAGATTACTGAGAAGCCCTCAATCAGTTTCT
66 AATATTTTAGCTTTTTTTTTCTTTTCTGATTTGCCAGATTACTGAGAAGCCCTCAATCAGTTTCT
** *
58833 TACACTTTCTTTCCCCTGTCCTATTTTGGTAATTGATTATTTTGGTAATAAATACTTAAATAGTG
131 TACACTTTCTTTCCCCTACCCTATTTTGGTAATTGACTATTTTGGTAATAAATACTTAAATAGTG
58898 TCATTAATATGTAATTTTAT
196 TCATTAATATGTAATTTTAT
* *
58918 TACTAAACCTTATTTGAGATACCCAATGAAATTACTAAAGACTCCAAAGCAGGATTAATGAGGAG
1 TACTAAACCTTATTTGAGATACCCAATGAAATTACTAAAGACTCCAAACCA-GAATAATGA-GAG
* * *
58983 CCAGTATTTTATCTTCTTTTTTTGTCTTTTCTGATTTGCCAGATTACTGAGAAGCCACTCAATTA
64 CCAATATTTTAGC-T-TTTTTTT-TCTTTTCTGATTTGCCAGATTACTGAGAAGCC-CTCAATCA
59048 GTTTCTTACACTTTCTTTCCCCTACCCTATTTTGGTAATTGACTATTTTGGTAATAAATACTTAA
125 GTTTCTTACACTTTCTTTCCCCTACCCTATTTTGGTAATTGACTATTTTGGTAATAAATACTTAA
59113 ATAGTGTCATTAATATGTAATTTTAT
190 ATAGTGTCATTAATATGTAATTTTAT
59139 CAACTATTCT
Statistics
Matches: 202, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
215 48 0.24
216 8 0.04
217 12 0.06
218 1 0.00
219 7 0.03
220 31 0.15
221 95 0.47
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (215 bp):
TACTAAACCTTATTTGAGATACCCAATGAAATTACTAAAGACTCCAAACCAGAATAATGAGAGCC
AATATTTTAGCTTTTTTTTTCTTTTCTGATTTGCCAGATTACTGAGAAGCCCTCAATCAGTTTCT
TACACTTTCTTTCCCCTACCCTATTTTGGTAATTGACTATTTTGGTAATAAATACTTAAATAGTG
TCATTAATATGTAATTTTAT
Found at i:59630 original size:345 final size:345
Alignment explanation
Indices: 58999--59632 Score: 1029
Period size: 345 Copynumber: 1.8 Consensus size: 345
58989 TTTTATCTTC
* * *
58999 TTTTTTTGTCTTTTCTGATTTGCCAGATTACTGAGAAGCCACTCAATTAGTTTCTTACACTTTCT
1 TTTTTTTGTCTTTTATGACTTGCCAGATTACTGAAAAGCCACTCAATTAGTTTCTTACACTTTCT
* *
59064 TTCCCCTACCCTATTTTGGTAATTGACTATTTTGGTAATAAATACTTAAATAGTGTCATTAATAT
66 TTCCCCTACCCTATTTTGGGAATTGACTATTTTGGTAATAAATACTTAAATAGTATCATTAATAT
* * *
59129 GTAATTTTATCAACTATTCTTACGGACAATTTCTTGGCTCTCTGTTTATCAAACTGACTTCACTA
131 GTAATTTAATCAACTATTCTCACGAACAATTTCTTGGCTCTCTGTTTATCAAACTGACTTCACTA
* * ** *
59194 TCAAATGATTGAATAAGCCTAGCAACAACTTTGTTTGACACTGATTCGCAAGGCTGATTTTTCCA
196 TCAAATGATTGAATAAGCCTAACAACAACTTTGCTTGACACTGATTCGCAAAACTGATGTTTCCA
* * *
59259 GGGTGATGTTTCTGAGGGTCACAATGAAAATGTCTCCCAATGAAATTACTAAAGGCTCCAAACCA
261 AGGTGATGTTTATGAGGGTAACAATGAAAATGTCTCCCAATGAAATTACTAAAGGCTCCAAACCA
59324 GAATTGATGAGGAGCTTTTT
326 GAATTGATGAGGAGCTTTTT
* * *
59344 TTTTTTTGTCTTTTATGACTTGCCGGATTACTGAAAAGCC-CCCTAATTAGTTTCTTACATTTTC
1 TTTTTTTGTCTTTTATGACTTGCCAGATTACTGAAAAGCCACTC-AATTAGTTTCTTACACTTTC
59408 TTTCCCCTACCCTATTTTGGGAATTGACTATTTTGGTAATAAATACTTAAATAGTATCATTAATA
65 TTTCCCCTACCCTATTTTGGGAATTGACTATTTTGGTAATAAATACTTAAATAGTATCATTAATA
*
59473 TTTAATTTAATCAACTATTCTCACGAACAAGTTT-TTGGCTCTCTGTTTATCAAACTGACTTCAC
130 TGTAATTTAATCAACTATTCTCACGAACAA-TTTCTTGGCTCTCTGTTTATCAAACTGACTTCAC
* * *
59537 TATCCAATGATTGAATAAGCCTAACAACAACTTTGCTTGACACTGATTGGCAAAATTGATGTTTC
194 TATCAAATGATTGAATAAGCCTAACAACAACTTTGCTTGACACTGATTCGCAAAACTGATGTTTC
59602 CAAGGTGATGTTTATGAGGGTAACAATGAAA
259 CAAGGTGATGTTTATGAGGGTAACAATGAAA
59633 TTTTCTCTAA
Statistics
Matches: 264, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
344 2 0.01
345 259 0.98
346 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (345 bp):
TTTTTTTGTCTTTTATGACTTGCCAGATTACTGAAAAGCCACTCAATTAGTTTCTTACACTTTCT
TTCCCCTACCCTATTTTGGGAATTGACTATTTTGGTAATAAATACTTAAATAGTATCATTAATAT
GTAATTTAATCAACTATTCTCACGAACAATTTCTTGGCTCTCTGTTTATCAAACTGACTTCACTA
TCAAATGATTGAATAAGCCTAACAACAACTTTGCTTGACACTGATTCGCAAAACTGATGTTTCCA
AGGTGATGTTTATGAGGGTAACAATGAAAATGTCTCCCAATGAAATTACTAAAGGCTCCAAACCA
GAATTGATGAGGAGCTTTTT
Done.