Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007525.1 Corchorus capsularis cultivar CVL-1 contig07546, 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: 28438
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8367 original size:182 final size:182
Alignment explanation
Indices: 8060--8424 Score: 649
Period size: 182 Copynumber: 2.0 Consensus size: 182
8050 GCTCCATAAA
8060 CAAATACTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTCTTATTCTTTATGCTATTTA
1 CAAATACTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTCTTATTCTTTATGCTATTTA
* *
8125 ATCCTTTACAATAATGGGTTGAACGATTTAACCCTTCGGATTTTATATTTGTATTTTTTTTGTTC
66 ATCCTTTACAATAATGGGTTGAACGATTTAACCCTTCGGATTTTATATTTGAATTTTTTTTGTCC
*
8190 TCTTTGTCAGATTAAGCTGATTCAAGTGCCTATTAAAATGTGATTTCATGAT
131 TATTTGTCAGATTAAGCTGATTCAAGTGCCTATTAAAATGTGATTTCATGAT
*
8242 CAAATACTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTTTTATTCTTTATGCTATTTA
1 CAAATACTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTCTTATTCTTTATGCTATTTA
* * *
8307 ATCCTTTACAATTATGGGTTGGACGATTTAACCCTTCGGATTTTATTTTTGAATTTTTTTTGTCC
66 ATCCTTTACAATAATGGGTTGAACGATTTAACCCTTCGGATTTTATATTTGAATTTTTTTTGTCC
* *
8372 TATTTGTCTGATTAAGGTGATTCAAGTGCCTATTAAAATGTGATTTCATGAT
131 TATTTGTCAGATTAAGCTGATTCAAGTGCCTATTAAAATGTGATTTCATGAT
8424 C
1 C
8425 TACAACTTTC
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 174 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (182 bp):
CAAATACTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTCTTATTCTTTATGCTATTTA
ATCCTTTACAATAATGGGTTGAACGATTTAACCCTTCGGATTTTATATTTGAATTTTTTTTGTCC
TATTTGTCAGATTAAGCTGATTCAAGTGCCTATTAAAATGTGATTTCATGAT
Found at i:22586 original size:43 final size:43
Alignment explanation
Indices: 22529--22610 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
22519 AACCACACTG
* * *
22529 TGAAAATTTGATAACCTCATTATGAAATTTCAATAACCTCCTA
1 TGAAAATTTCATAACCACACTATGAAATTTCAATAACCTCCTA
22572 TGAAAATTTCATAACCACACTATGAAATTTCAATAACCT
1 TGAAAATTTCATAACCACACTATGAAATTTCAATAACCT
22611 TAGCGTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (43 bp):
TGAAAATTTCATAACCACACTATGAAATTTCAATAACCTCCTA
Found at i:22607 original size:22 final size:23
Alignment explanation
Indices: 22517--22609 Score: 106
Period size: 22 Copynumber: 4.3 Consensus size: 23
22507 AGAAATATTG
* *
22517 ATAACCACACTGTGAAAATTT-G
1 ATAACCACACTATGAAAATTTCA
* *
22539 ATAACCTCATTATG-AAATTTCA
1 ATAACCACACTATGAAAATTTCA
*
22561 ATAACCTC-CTATGAAAATTTC-
1 ATAACCACACTATGAAAATTTCA
22582 ATAACCACACTATG-AAATTTCA
1 ATAACCACACTATGAAAATTTCA
22604 ATAACC
1 ATAACC
22610 TTAGCGTGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
21 24 0.39
22 37 0.61
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (23 bp):
ATAACCACACTATGAAAATTTCA
Found at i:22629 original size:22 final size:22
Alignment explanation
Indices: 22529--22651 Score: 74
Period size: 22 Copynumber: 5.6 Consensus size: 22
22519 AACCACACTG
* *
22529 TGAAAATTTGATAACCTCA-TTA
1 TGAAATTTTGATAACCT-AGCTA
** *
22551 TGAAATTTCAATAACCT-CCTA
1 TGAAATTTTGATAACCTAGCTA
* * *
22572 TGAAAATTTCATAACC-ACACTA
1 TGAAATTTTGATAACCTA-GCTA
** *
22594 TGAAATTTCAATAACCTTAGC-G
1 TGAAATTTTGATAACC-TAGCTA
*
22616 TGAAATTTTGATAATCTAGCTA
1 TGAAATTTTGATAACCTAGCTA
*
22638 TAAAATTTTGATAA
1 TGAAATTTTGATAA
22652 TAGCACTATA
Statistics
Matches: 77, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
21 19 0.25
22 56 0.73
23 1 0.01
24 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (22 bp):
TGAAATTTTGATAACCTAGCTA
Found at i:22991 original size:22 final size:22
Alignment explanation
Indices: 22956--23004 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
22946 GCAAATTTTA
* *
22956 ATAATCTTTTTATGAAAATTTG
1 ATAACCTTTGTATGAAAATTTG
* *
22978 GTAACCTTTGTATGAAATTTTG
1 ATAACCTTTGTATGAAAATTTG
23000 ATAAC
1 ATAAC
23005 TACACTATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (22 bp):
ATAACCTTTGTATGAAAATTTG
Found at i:23013 original size:22 final size:23
Alignment explanation
Indices: 22988--23089 Score: 104
Period size: 22 Copynumber: 4.6 Consensus size: 23
22978 GTAACCTTTG
22988 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCTACAC
* ** *
23010 TATGAAGTTTTGATAATTTTCA-
1 TATGAAATTTTGATAACCTACAC
* *
23032 TATGAAATTTTGGTAACC-AAAC
1 TATGAAATTTTGATAACCTACAC
*
23054 TATGAAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACCTACAC
*
23076 TATGTAATTTTGAT
1 TATGAAATTTTGAT
23090 TTGATTGTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 1 0.02
22 60 0.94
23 3 0.05
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (23 bp):
TATGAAATTTTGATAACCTACAC
Found at i:23014 original size:44 final size:44
Alignment explanation
Indices: 22966--23089 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
22956 ATAATCTTTT
* * * * *
22966 TATGAAAATTTGGTAACCTTTGTATGAAATTTTGATAACTACAC
1 TATGAAATTTTGATAACCTTTATATGAAATTTTGATAACCAAAC
* * *
23010 TATGAAGTTTTGATAA-TTTTCATATGAAATTTTGGTAACCAAAC
1 TATGAAATTTTGATAACCTTT-ATATGAAATTTTGATAACCAAAC
** *
23054 TATGAAATTTTGATAACCTTCCTATGTAATTTTGAT
1 TATGAAATTTTGATAACCTTTATATGAAATTTTGAT
23090 TTGATTGTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
43 3 0.05
44 59 0.92
45 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTTATATGAAATTTTGATAACCAAAC
Done.