Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008524.1 Corchorus capsularis cultivar CVL-1 contig08545, 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: 2414
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Found at i:848 original size:22 final size:22
Alignment explanation
Indices: 820--861 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
810 AAAAAAAAGG
820 AAAAATAATGGTCTGCAAAGAA
1 AAAAATAATGGTCTGCAAAGAA
842 AAAAATAATGGTCTGCAAAG
1 AAAAATAATGGTCTGCAAAG
862 TGCAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (22 bp):
AAAAATAATGGTCTGCAAAGAA
Found at i:1019 original size:92 final size:92
Alignment explanation
Indices: 862--1096 Score: 470
Period size: 92 Copynumber: 2.6 Consensus size: 92
852 GTCTGCAAAG
862 TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCATTGGA
1 TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCATTGGA
927 TGAAGAGAAAGCCAAATTATGAAGGTC
66 TGAAGAGAAAGCCAAATTATGAAGGTC
954 TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCATTGGA
1 TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCATTGGA
1019 TGAAGAGAAAGCCAAATTATGAAGGTC
66 TGAAGAGAAAGCCAAATTATGAAGGTC
1046 TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
1 TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
1097 TAGTACAAAG
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 143 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (92 bp):
TGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCATTGGA
TGAAGAGAAAGCCAAATTATGAAGGTC
Found at i:1391 original size:2 final size:2
Alignment explanation
Indices: 1384--1468 Score: 84
Period size: 2 Copynumber: 39.5 Consensus size: 2
1374 ATGTTCTCAA
1384 AT AT AT AT AT AT AT AT AT AT AT -T AT AT ACT GAT AT ACT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT A-T -AT AT
1427 AT AT -T AT AT ACT GAT AT ACT GAT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T -AT AT A-T -AT AT AT AT AT AT AT AT AT AT A
1469 ACAATGAATG
Statistics
Matches: 73, Mismatches: 0, Indels: 20
0.78 0.00 0.22
Matches are distributed among these distances:
1 2 0.03
2 59 0.81
3 8 0.11
4 4 0.05
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1426 original size:25 final size:25
Alignment explanation
Indices: 1398--1462 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
1388 ATATATATAT
1398 ATATATATTATATACTGATATACTG
1 ATATATATTATATACTGATATACTG
1423 ATATATATTATATACTGATATACTG
1 ATATATATTATATACTGATATACTG
1448 ATATATATATATATA
1 ATATATAT-TATATA
1463 TATATAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
25 33 0.85
26 6 0.15
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (25 bp):
ATATATATTATATACTGATATACTG
Found at i:1754 original size:16 final size:16
Alignment explanation
Indices: 1723--1809 Score: 88
Period size: 16 Copynumber: 5.5 Consensus size: 16
1713 GTTCGGGTAC
* *
1723 TTCGGGTTCGGATATT
1 TTCGGGTTTGGGTATT
*
1739 TTCGGATTTGGGTATT
1 TTCGGGTTTGGGTATT
*
1755 TTCGGGTTCGGGT-TCT
1 TTCGGGTTTGGGTAT-T
* *
1771 GTCGGGTTGGGGTA-T
1 TTCGGGTTTGGGTATT
*
1786 TACGGGTTTGGGTATT
1 TTCGGGTTTGGGTATT
1802 TTCGGGTT
1 TTCGGGTT
1810 CGGGCTCGAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
15 13 0.23
16 44 0.77
ACGTcount: A:0.08, C:0.10, G:0.38, T:0.44
Consensus pattern (16 bp):
TTCGGGTTTGGGTATT
Found at i:1796 original size:47 final size:47
Alignment explanation
Indices: 1712--1830 Score: 143
Period size: 47 Copynumber: 2.5 Consensus size: 47
1702 GGCGGGTTCA
*
1712 GGTTCGGGTACTTCGGGTTCGGATATTTTCGGATTTGGGTATTTTCG
1 GGTTCGGGTACTTCGGGTTCGGATATTTACGGATTTGGGTATTTTCG
* * * *
1759 GGTTCGGGTTCTGTCGGGTTGGGGTA-TTACGGGTTTGGGTATTTTCG
1 GGTTCGGGTACT-TCGGGTTCGGATATTTACGGATTTGGGTATTTTCG
*
1806 GGTTCGGGCT-CGATCGGGTTCGGAT
1 GGTTCGGG-TAC-TTCGGGTTCGGAT
1831 TCGGGCCCGG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
47 49 0.80
48 12 0.20
ACGTcount: A:0.08, C:0.13, G:0.39, T:0.39
Consensus pattern (47 bp):
GGTTCGGGTACTTCGGGTTCGGATATTTACGGATTTGGGTATTTTCG
Found at i:1827 original size:22 final size:23
Alignment explanation
Indices: 1802--1855 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1792 TTTGGGTATT
* *
1802 TTCGGGTTCGGGCTC-GATCGGG
1 TTCGGATTCGGGCCCGGATCGGG
*
1824 TTCGGATTCGGGCCCGGGTCGGG
1 TTCGGATTCGGGCCCGGATCGGG
1847 TTCGGATTC
1 TTCGGATTC
1856 ACTTTCGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.06, C:0.24, G:0.43, T:0.28
Consensus pattern (23 bp):
TTCGGATTCGGGCCCGGATCGGG
Done.