Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012153.1 Corchorus capsularis cultivar CVL-1 contig12174, 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: 40725
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:8146 original size:49 final size:48
Alignment explanation
Indices: 8086--8361 Score: 365
Period size: 49 Copynumber: 5.6 Consensus size: 48
8076 AACATTAACA
* * * *
8086 CCTTCCATCCGGGAATGGCGTTTTTTGGAAAAAGAAGGTAAAAA-AGGTG
1 CCTTCCGTCCGGGAAGGGCG-TTTTGGGAAAAAGAA-GTAAAAATAAGTG
* *
8135 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAGGTAAAAATAAGTG
1 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAG-AAGTAAAAATAAGTG
* * *
8184 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCATGTAAAAAGAAGTG
1 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAG-AAGTAAAAATAAGTG
* * *
8233 ACTTCCGTCTGGGAAGGGCGTTTTGGGAAAAAGTAAGTAAAAATAAGCG
1 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAG-AAGTAAAAATAAGTG
8282 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGTG
1 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAG-AAGTAAAAATAAGTG
* *
8331 CCTTCCGTCAGGGAAGGGCATTTTGGGAAAA
1 CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA
8362 CGAGAACGAA
Statistics
Matches: 204, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
48 18 0.09
49 186 0.91
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (48 bp):
CCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGAAGTAAAAATAAGTG
Found at i:8294 original size:147 final size:147
Alignment explanation
Indices: 8087--8360 Score: 426
Period size: 147 Copynumber: 1.9 Consensus size: 147
8077 ACATTAACAC
* * * *
8087 CTTCCATCCGGGAATGGCGTTTTTTGGAAAAAGAAGGTAAAAAAGGTGCCTTCCGTCCGGGAAGG
1 CTTCCATCCGGGAAGGGCGTTTTTGGGAAAAAGAAGGTAAAAAAAGCGCCTTCCGTCCGGGAAGG
* * * *
8152 GCGTTTTGGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAG
66 GCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCAGGGAAGGGCATTTTGGGAAATAG
8217 CATGTAAAAAGAAGTGA
131 CATGTAAAAAGAAGTGA
* *
8234 CTTCCGTCTGGGAAGGGCG-TTTTGGGAAAAAGTAA-GTAAAAATAAGCGCCTTCCGTCCGGGAA
1 CTTCCATCCGGGAAGGGCGTTTTTGGGAAAAAG-AAGGTAAAAA-AAGCGCCTTCCGTCCGGGAA
8297 GGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCAGGGAAGGGCATTTTGGGAAA
64 GGGCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCAGGGAAGGGCATTTTGGGAAA
8361 ACGAGAACGA
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
146 19 0.17
147 96 0.83
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (147 bp):
CTTCCATCCGGGAAGGGCGTTTTTGGGAAAAAGAAGGTAAAAAAAGCGCCTTCCGTCCGGGAAGG
GCGTTTTGGGAAAAAGCAAGTAAAAATAAGTGCCTTCCGTCAGGGAAGGGCATTTTGGGAAATAG
CATGTAAAAAGAAGTGA
Found at i:8838 original size:19 final size:18
Alignment explanation
Indices: 8814--8849 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8804 TGAAGATTTC
8814 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
8833 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8850 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:14401 original size:28 final size:28
Alignment explanation
Indices: 14370--14423 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
14360 CCGACAAACA
14370 GTACGAACGCGCTGAAGAC-GTCAACACT
1 GTACGAACGCGCTGAAG-CTGTCAACACT
*
14398 GTACGGACGCGCTGAAGCTGTCAACA
1 GTACGAACGCGCTGAAGCTGTCAACA
14424 GCCTGGCGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (28 bp):
GTACGAACGCGCTGAAGCTGTCAACACT
Found at i:33850 original size:11 final size:11
Alignment explanation
Indices: 33834--33868 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
33824 TTGACAGCGC
33834 AACAAAAACAA
1 AACAAAAACAA
*
33845 AACAAAAACGA
1 AACAAAAACAA
33856 AACAAAAACAA
1 AACAAAAACAA
33867 AA
1 AA
33869 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:34215 original size:16 final size:17
Alignment explanation
Indices: 34189--34221 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
34179 AAAAACCTTT
34189 AAAGAAGAAAAAAAGAA
1 AAAGAAGAAAAAAAGAA
34206 AAAGAA-AAAAAAAGAA
1 AAAGAAGAAAAAAAGAA
34222 GATGAACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAAAAAGAA
Found at i:35150 original size:103 final size:103
Alignment explanation
Indices: 34988--35274 Score: 423
Period size: 103 Copynumber: 2.8 Consensus size: 103
34978 TTATAATATT
* * * **
34988 TTTTTATATAATTTGGGGCTACTAAACCTAAATGATTTAGGA-TTAGACTAAAATTCTAAAATTC
1 TTTTTATATAATTTGGGG---CTAAACCTAAGTGATTTGGGACTCA-ACTAAAATTCTAAAACCC
*
35052 TAGAAATAAATATTTTAAATTTAAGACATACCTTTAAAATAC
62 TAGAAATAAATATTTTAAATTCAAGACATACCTTTAAAATAC
*
35094 TTTTTATATAATTTGGGGCTAAACCTATGTGATTTGGGACTCAACTAAAATTCTAAAACCCTAGA
1 TTTTTATATAATTTGGGGCTAAACCTAAGTGATTTGGGACTCAACTAAAATTCTAAAACCCTAGA
**
35159 AATAAATATTTTAAATTCAAGACATACCTTTAAAATGT
66 AATAAATATTTTAAATTCAAGACATACCTTTAAAATAC
* * *
35197 TTTTTATATAATTTGGGGCTAAACCTAAGTGATTTGAGACTCAACTAAAATTTTAAAACCCTATA
1 TTTTTATATAATTTGGGGCTAAACCTAAGTGATTTGGGACTCAACTAAAATTCTAAAACCCTAGA
35262 AATAAATATTTTA
66 AATAAATATTTTA
35275 CCCTTAAAAT
Statistics
Matches: 167, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 147 0.88
104 2 0.01
106 18 0.11
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (103 bp):
TTTTTATATAATTTGGGGCTAAACCTAAGTGATTTGGGACTCAACTAAAATTCTAAAACCCTAGA
AATAAATATTTTAAATTCAAGACATACCTTTAAAATAC
Found at i:35546 original size:15 final size:15
Alignment explanation
Indices: 35526--35555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35516 TGATCATGTG
35526 AAAAAGAAAAAAAAT
1 AAAAAGAAAAAAAAT
*
35541 AAAAAGAAATAAAAT
1 AAAAAGAAAAAAAAT
35556 GGAAAAAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAAAGAAAAAAAAT
Found at i:37151 original size:55 final size:54
Alignment explanation
Indices: 37050--37163 Score: 174
Period size: 55 Copynumber: 2.1 Consensus size: 54
37040 AATTAAATCT
* * *
37050 TTTGATTCGATCTCTTGGAAAAGTCTCGAGGACTTGACAGCTTGATCTTGATGA
1 TTTGATTCGATCTCCTAGAAAAGTCTCGAGGACTTGACAGCTTGATCTAGATGA
* *
37104 TTTGATTCGATCTCCTAGAAAAGTTTTCGAGGACTTGATAGCTTGATCTAGATGA
1 TTTGATTCGATCTCCTAGAAAAG-TCTCGAGGACTTGACAGCTTGATCTAGATGA
37159 TTTGA
1 TTTGA
37164 AAGGAATGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 21 0.39
55 33 0.61
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (54 bp):
TTTGATTCGATCTCCTAGAAAAGTCTCGAGGACTTGACAGCTTGATCTAGATGA
Found at i:38285 original size:41 final size:41
Alignment explanation
Indices: 38234--38311 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
38224 CTTTATCAAA
**
38234 TAGGTGAATGAAGGTAACTGATTTTGATAATAGAGCAAATC
1 TAGGTGAATGAAGGTAACCAATTTTGATAATAGAGCAAATC
38275 TAGGTGAATGAAGGTAACCAATTTTGATAATAGAGCA
1 TAGGTGAATGAAGGTAACCAATTTTGATAATAGAGCA
38312 TATCAAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (41 bp):
TAGGTGAATGAAGGTAACCAATTTTGATAATAGAGCAAATC
Done.