Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011763.1 Corchorus capsularis cultivar CVL-1 contig11784, 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: 62953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:232 original size:16 final size:18
Alignment explanation
Indices: 193--232 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
183 TTGGAACCAT
193 ATGACCCAAAACCGAAAA
1 ATGACCCAAAACCGAAAA
*
211 A-CACCC-AAACC-AAAA
1 ATGACCCAAAACCGAAAA
226 ATGACCC
1 ATGACCC
233 GACTTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 4 0.21
18 1 0.05
ACGTcount: A:0.53, C:0.35, G:0.07, T:0.05
Consensus pattern (18 bp):
ATGACCCAAAACCGAAAA
Found at i:739 original size:109 final size:109
Alignment explanation
Indices: 606--880 Score: 437
Period size: 109 Copynumber: 2.5 Consensus size: 109
596 AAAAAAATTA
606 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
* *
669 TAAAATTTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
714 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
779 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
823 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
881 CTATAATAGT
Statistics
Matches: 155, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
108 6 0.04
109 117 0.75
110 3 0.02
111 1 0.01
114 28 0.18
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:15912 original size:21 final size:20
Alignment explanation
Indices: 15886--15924 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
15876 TCTTCTTCTT
15886 TTTCTTCTCCTTTTCTCTTTC
1 TTTCTTCTCCTTTT-TCTTTC
*
15907 TTTCTTCTTCTTTTTCTT
1 TTTCTTCTCCTTTTTCTT
15925 CTATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCTTCTCCTTTTTCTTTC
Found at i:15932 original size:12 final size:11
Alignment explanation
Indices: 15872--15932 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 11
15862 CTCAAAGATG
15872 TTTTTCTTCTT
1 TTTTTCTTCTT
*
15883 CTTTTTCTTCTC
1 -TTTTTCTTCTT
*
15895 CTTTTC-TCTT
1 TTTTTCTTCTT
*
15905 TCTTTCTTCTT
1 TTTTTCTTCTT
*
15916 CTTTTTCTTCTA
1 -TTTTTCTTCTT
15928 TTTTT
1 TTTTT
15933 ACTATAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
10 7 0.17
11 14 0.35
12 19 0.47
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:31597 original size:92 final size:92
Alignment explanation
Indices: 31435--31613 Score: 342
Period size: 92 Copynumber: 1.9 Consensus size: 92
31425 ATTAATGCTG
31435 TTTTATAAAGACCACAAATGTGAACAATAGTGACAATAGCAAGCCAATAATTTAATAACCAACAG
1 TTTTATAAAGACCACAAATGTGAACAATAGTGACAATAGCAAGCCAATAATTTAATAACCAACAG
31500 AAAATGACCCTATTCCTATAACATAAA
66 AAAATGACCCTATTCCTATAACATAAA
31527 TTTTATAAAGACCACAAATGTGAACAATAGTGACAATAGCAAGCCAATAATTTAATAACCAACAT
1 TTTTATAAAGACCACAAATGTGAACAATAGTGACAATAGCAAGCCAATAATTTAATAACCAACA-
31592 G-AAATGACCCTATTCCTATAAC
65 GAAAATGACCCTATTCCTATAAC
31614 CATTTATGCT
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
92 85 0.99
93 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (92 bp):
TTTTATAAAGACCACAAATGTGAACAATAGTGACAATAGCAAGCCAATAATTTAATAACCAACAG
AAAATGACCCTATTCCTATAACATAAA
Found at i:49594 original size:2 final size:2
Alignment explanation
Indices: 49587--49619 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49577 CTGAATTACA
49587 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
49620 GTCAAAGAAG
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
Done.