Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005483.1 Corchorus capsularis cultivar CVL-1 contig05501, 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: 12815
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:1459 original size:198 final size:197
Alignment explanation
Indices: 1030--1689 Score: 844
Period size: 198 Copynumber: 3.3 Consensus size: 197
1020 GGCACAAAAC
* *
1030 CTTCTTAACCCGCTTATGGAGTCCAAATTTTACACTGACATTGTATTGTATAATAATCCTATAA-
1 CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAG
* * * *
1094 AAAAATTTATACAATATACCGTCAGTGGAGTTTAGCAAACTGCAAGTGCAGGGTTTAACTTTAAG
66 AAAAA-TTATACAATA-CCCGTTAGTGGAGTTTAGCAGACTGCACGTGCA-GG----A-TTTAAG
*
1159 GGTTGACATGTGTGCGCTTAGGGAATATGTATTAATATTAAATA--T-A-TAATTATGAAATGAG
123 GGTTGACATGTGT-CCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAG
1220 GTATGTGTCAA
187 GTATGTGTCAA
* * *
1231 CTTCTTAACCCGTTTATAGAGTCCAAAATTTACACTGAGAGTGTATTGTATAATAATCCTATAAG
1 CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAG
* * *
1296 AAAAATTATACAATACCCGTTACTGGACTATAGCAGACTGCACGTGCAGGATTTAAGGGTTGACA
66 AAAAATTATACAATACCCGTTAGTGGAGTTTAGCAGACTGCACGTGCAGGATTTAAGGGTTGACA
* *
1361 TGTGTCCCCTTAGGGAATATATATTAATATTAAATATTTAATTAATTATGAAATGTGGTATGTGT
131 TGTGT-CCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATGTGT
1426 CAA
195 CAA
* * *
1429 CTTCTTAACTCGCTTATGGAGTCCAAAATTTATATTGACAGTGTATTGTATAATAATCCTATAAG
1 CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAG
* * ** * *
1494 AAAAATTATGCAATACACAGTTAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTCAGGGTTGAC
66 AAAAATTATACAATAC-CCGTTAGTGGAGTTTAGCAGACTGCACGTGCAGGATTTAAGGGTTGAC
* * *
1559 ATGTATCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATTAAATGGGGTATGTGT
130 ATGTGTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATGTGT
*
1624 TAA
195 CAA
** ** * * *
1627 CTTCTTAATTCATTTATGGACGTCAAAAAATTTACATTGACAGTGTTTTTGTATAATAATCCT
1 CTTCTTAACCCGCTTATGGA-GTC-CAAAATTTACACTGACAGTG-TATTGTATAATAATCCT
1690 TTATTTAAAC
Statistics
Matches: 408, Mismatches: 42, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
194 47 0.12
195 1 0.00
196 1 0.00
197 1 0.00
198 174 0.43
199 50 0.12
200 44 0.11
201 85 0.21
202 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (197 bp):
CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAG
AAAAATTATACAATACCCGTTAGTGGAGTTTAGCAGACTGCACGTGCAGGATTTAAGGGTTGACA
TGTGTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATGTGTC
AA
Found at i:2622 original size:6 final size:6
Alignment explanation
Indices: 2613--2659 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
2603 ATTTTTCTGT
* *
2613 TTTTTG TTTTTG -TTTTG TTTTTG -TTTTG CTTTT- ATTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
2658 TT
1 TT
2660 ACGCTGTCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 14 0.39
6 22 0.61
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:2630 original size:11 final size:11
Alignment explanation
Indices: 2614--2659 Score: 74
Period size: 11 Copynumber: 4.2 Consensus size: 11
2604 TTTTTCTGTT
2614 TTTTGTTTTTG
1 TTTTGTTTTTG
2625 TTTTGTTTTTG
1 TTTTGTTTTTG
* *
2636 TTTTGCTTTTA
1 TTTTGTTTTTG
2647 TTTTGTTTTTG
1 TTTTGTTTTTG
2658 TT
1 TT
2660 ACGCTGTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:4881 original size:18 final size:18
Alignment explanation
Indices: 4842--4883 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4832 AGATGTGTTG
*
4842 AAGAAATCTGAGAGATGG
1 AAGAAATCTGAGAGATGA
* *
4860 AAGAGATCTGAGATATGA
1 AAGAAATCTGAGAGATGA
4878 AAGAAA
1 AAGAAA
4884 ATCCCTATGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.29, T:0.17
Consensus pattern (18 bp):
AAGAAATCTGAGAGATGA
Found at i:5728 original size:24 final size:25
Alignment explanation
Indices: 5682--5733 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
5672 TATCTAAGCA
*
5682 AAATTATATATATTATTTTTATT-T
1 AAATTATATATATTATTTATATTAT
5706 AAATTATATATA-TATTATATATTAT
1 AAATTATATATATTATT-TATATTAT
5731 AAA
1 AAA
5734 GTAAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 17 0.68
25 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTATATATATTATTTATATTAT
Found at i:5767 original size:64 final size:66
Alignment explanation
Indices: 5630--5800 Score: 251
Period size: 64 Copynumber: 2.6 Consensus size: 66
5620 TTTGATTTTG
* *
5630 ATTTTTATTTGAA-T-TATATATATTATATATTATATAAAGTAATATCTAAGCAAAATTATATAT
1 ATTTTTATTTAAATTATATATATATTATATA-T-TATAAAGTAAAATCTAAGCAAAATTATATAT
5693 ATT
64 ATT
* *
5696 ATTTTTATTTAAATTATATATATATTATATATTATAAAGTAAAATTTGAGCAAAATT-T-TATAT
1 ATTTTTATTTAAATTATATATATATTATATATTATAAAGTAAAATCTAAGCAAAATTATATATAT
5759 T
66 T
*
5760 ATTTTTATTTAAATTATATATATATTATATATTCTAAAGTA
1 ATTTTTATTTAAATTATATATATATTATATATTATAAAGTA
5801 TTATAAATTA
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
64 46 0.47
65 1 0.01
66 34 0.35
67 2 0.02
68 15 0.15
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (66 bp):
ATTTTTATTTAAATTATATATATATTATATATTATAAAGTAAAATCTAAGCAAAATTATATATAT
T
Done.