Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010328.1 Corchorus capsularis cultivar CVL-1 contig10349, 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: 94577
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:540 original size:16 final size:17
Alignment explanation
Indices: 509--543 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
499 GTTTGTTACT
*
509 TTTTATGAGCAAGAGTG
1 TTTTATAAGCAAGAGTG
526 TTTTATAAG-AAGAGTG
1 TTTTATAAGCAAGAGTG
542 TT
1 TT
544 CTTCATGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.40
Consensus pattern (17 bp):
TTTTATAAGCAAGAGTG
Found at i:7259 original size:2 final size:2
Alignment explanation
Indices: 7252--7280 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7242 ATTACCTCCA
7252 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7281 CAGTCATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10793 original size:12 final size:12
Alignment explanation
Indices: 10776--10817 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
10766 TTCCGGTGGA
* *
10776 GGTGATGTTGGT
1 GGTGATGGTGCT
10788 GGTGATGGTGCT
1 GGTGATGGTGCT
*
10800 GGTGCTGGTGCT
1 GGTGATGGTGCT
10812 GGTGAT
1 GGTGAT
10818 TGCTGGAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.07, G:0.50, T:0.36
Consensus pattern (12 bp):
GGTGATGGTGCT
Found at i:16795 original size:21 final size:21
Alignment explanation
Indices: 16769--16808 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16759 CAAAACCAAA
16769 GAGAAAATA-TAGTGATATAGT
1 GAGAAAATATTAGT-ATATAGT
*
16790 GAGAAATTATTAGTATATA
1 GAGAAAATATTAGTATATA
16809 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (21 bp):
GAGAAAATATTAGTATATAGT
Found at i:18895 original size:29 final size:28
Alignment explanation
Indices: 18828--18908 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
18818 GCTTAATACC
*
18828 CAAATTAGCCCCTTAACTATCTATTTTGGGA
1 CAAATTGGCCCCTTAACT-T-T-TTTTGGGA
* **
18859 TAAATTGGTTCCTTAACTTTTTTTGGGGA
1 CAAATTGGCCCCTTAACTTTTTTT-GGGA
18888 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAACTTTT
18909 AAAAACGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.10
29 23 0.55
30 1 0.02
31 14 0.33
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (28 bp):
CAAATTGGCCCCTTAACTTTTTTTGGGA
Found at i:19636 original size:29 final size:29
Alignment explanation
Indices: 19599--19656 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
19589 TCTTATTTTT
* * *
19599 AAAAGTTAAGGGGGCAATTTGTCCCAAAA
1 AAAAATTAAGGGGCCAAATTGTCCCAAAA
19628 AAAAATTAAGGGGCCAAATTGTCCCAAAA
1 AAAAATTAAGGGGCCAAATTGTCCCAAAA
19657 TGGATAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.19
Consensus pattern (29 bp):
AAAAATTAAGGGGCCAAATTGTCCCAAAA
Found at i:29018 original size:12 final size:12
Alignment explanation
Indices: 29001--29026 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28991 TTCATCACTG
29001 CAGAATCATGAA
1 CAGAATCATGAA
29013 CAGAATCATGAA
1 CAGAATCATGAA
29025 CA
1 CA
29027 ACATAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (12 bp):
CAGAATCATGAA
Found at i:31409 original size:6 final size:7
Alignment explanation
Indices: 31393--31417 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31383 TTGTCTTGGC
31393 AAAAAGA
1 AAAAAGA
31400 AAAAAGA
1 AAAAAGA
31407 AAAAAGA
1 AAAAAGA
31414 AAAA
1 AAAA
31418 TGGTCCTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:45252 original size:42 final size:45
Alignment explanation
Indices: 45197--45282 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 45
45187 TAAATTATAC
*
45197 TAATGGCTTAAAATGACGCTT-TTAGTGGGTTAA-TTA-TACTAA
1 TAATGGCTTAAAATGACACTTATTAGTGGGTTAAGTTATTACTAA
45239 TAATGG-TCTAAAATGACACTTATTAGTGGGTTAAGTTATTACTA
1 TAATGGCT-TAAAATGACACTTATTAGTGGGTTAAGTTATTACTA
45283 GTTACTCATG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 1 0.03
42 18 0.46
43 12 0.31
44 3 0.08
45 5 0.13
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (45 bp):
TAATGGCTTAAAATGACACTTATTAGTGGGTTAAGTTATTACTAA
Found at i:46289 original size:7 final size:7
Alignment explanation
Indices: 46265--46314 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
46255 ATTCATAAGC
46265 AAAGCC-
1 AAAGCCA
46271 AAAGCC-
1 AAAGCCA
46277 AAAGCCA
1 AAAGCCA
46284 AAAGCCA
1 AAAGCCA
46291 AAAGCCA
1 AAAGCCA
46298 AAAGCCA
1 AAAGCCA
46305 AAAGCCA
1 AAAGCCA
46312 AAA
1 AAA
46315 CCGTGTTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 12 0.28
7 31 0.72
ACGTcount: A:0.58, C:0.28, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGCCA
Found at i:49524 original size:19 final size:19
Alignment explanation
Indices: 49500--49536 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49490 ATACCATATG
* *
49500 ATAAATTTATTTTATAAAA
1 ATAAATTAATTATATAAAA
49519 ATAAATTAATTATATAAA
1 ATAAATTAATTATATAAA
49537 TTTATGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAATTAATTATATAAAA
Found at i:60342 original size:231 final size:231
Alignment explanation
Indices: 59939--60630 Score: 1384
Period size: 231 Copynumber: 3.0 Consensus size: 231
59929 GGATCACAAT
59939 ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
1 ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
60004 TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
66 TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
60069 TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
131 TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
60134 TACCCTTGCTCGTATCATATGGAAAGAAATATGAGG
196 TACCCTTGCTCGTATCATATGGAAAGAAATATGAGG
60170 ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
1 ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
60235 TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
66 TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
60300 TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
131 TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
60365 TACCCTTGCTCGTATCATATGGAAAGAAATATGAGG
196 TACCCTTGCTCGTATCATATGGAAAGAAATATGAGG
60401 ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
1 ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
60466 TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
66 TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
60531 TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
131 TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
60596 TACCCTTGCTCGTATCATATGGAAAGAAATATGAG
196 TACCCTTGCTCGTATCATATGGAAAGAAATATGAG
60631 CAGGACTACC
Statistics
Matches: 461, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 461 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (231 bp):
ATGGTAGGGGCTTTCAGATATAAATATCAGATTAAATTGCTTAGCCAAATCAATGAGTTAAAAAA
TTGAAGACTTTTGTTGAAATACAAACAAAGAAACTATTCCAACTATTTGGCTCTCAAGTACACTT
TGAAATTTGCAGCATCATACTAATTGCACAATTACAGGTGCATGCTTGAAGTTATCATGGGCAAA
TACCCTTGCTCGTATCATATGGAAAGAAATATGAGG
Found at i:71213 original size:7 final size:7
Alignment explanation
Indices: 71201--71226 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
71191 TTGTGATCCA
71201 TATGAGT
1 TATGAGT
71208 TATGAGT
1 TATGAGT
71215 TATGAGT
1 TATGAGT
71222 TATGA
1 TATGA
71227 CCCCAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
TATGAGT
Found at i:91950 original size:2 final size:2
Alignment explanation
Indices: 91945--91977 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
91935 TGTGTGTGTC
*
91945 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91978 GTATTAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94218 original size:2 final size:2
Alignment explanation
Indices: 94211--94237 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
94201 ACATACATAC
94211 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 A
94238 AAATGATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.