Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006451.1 Corchorus capsularis cultivar CVL-1 contig06472, 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: 25662
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1218 original size:6 final size:6
Alignment explanation
Indices: 1207--1263 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
1197 CTGCAAAATT
*
1207 AACAAA AAC--A AA-AAA AACAAA AACAAA AACAAA AACAAA ATAC-GA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA A-ACAAA
1252 AAC-AA AACAAA A
1 AACAAA AACAAA A
1264 CTAAAGGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 3 0.07
5 9 0.20
6 30 0.68
7 2 0.05
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.02
Consensus pattern (6 bp):
AACAAA
Found at i:5193 original size:108 final size:108
Alignment explanation
Indices: 5059--5279 Score: 397
Period size: 108 Copynumber: 2.0 Consensus size: 108
5049 TCTAACAAAG
5059 TAGTAAAAAACAAGGTTATAGTCTCAAGGAATTAATTTAAATACAAAACAAGACACCCAACAATA
1 TAGTAAAAAACAAGGTTATAGTCTCAAGGAATTAATTTAAATACAAAACAAGACACCCAACAATA
*
5124 TAAGCTAAAAGCAGGAGCTCAATTCATGTTTCATTATTTCTGC
66 TAAGCTAAAAGAAGGAGCTCAATTCATGTTTCATTATTTCTGC
* * * *
5167 TAGTCAAAAACAAGGTTATAGTCTCAAGGAATTAATTTAGATACAAAACAAGACACTCAGCAATA
1 TAGTAAAAAACAAGGTTATAGTCTCAAGGAATTAATTTAAATACAAAACAAGACACCCAACAATA
5232 TAAGCTAAAAGAAGGAGCTCAATTCATGTTTCATTATTTCTGC
66 TAAGCTAAAAGAAGGAGCTCAATTCATGTTTCATTATTTCTGC
5275 TAGTA
1 TAGTA
5280 TCCTCAATTC
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (108 bp):
TAGTAAAAAACAAGGTTATAGTCTCAAGGAATTAATTTAAATACAAAACAAGACACCCAACAATA
TAAGCTAAAAGAAGGAGCTCAATTCATGTTTCATTATTTCTGC
Found at i:16432 original size:79 final size:79
Alignment explanation
Indices: 16301--16455 Score: 265
Period size: 79 Copynumber: 2.0 Consensus size: 79
16291 CATTCTACCA
*
16301 ATATTACCCATTTTTCTCTCCCATTATTTATATGGTGAACTCTCTCCCATTATCACAGTATTATA
1 ATATTACCCATTTTTCTCTCCCATTATTTATATAGTGAACTCTCTCCCATTATCACAGTATTATA
16366 TGTACGAGAAACTC
66 TGTACGAGAAACTC
* * *
16380 ATATTACCCCTTTTTCTCTCCCATTATTTATATAGTGAACTCTCTCTCATTATTACAGTATTATA
1 ATATTACCCATTTTTCTCTCCCATTATTTATATAGTGAACTCTCTCCCATTATCACAGTATTATA
*
16445 TTTACGAGAAA
66 TGTACGAGAAA
16456 AATTAAATAG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (79 bp):
ATATTACCCATTTTTCTCTCCCATTATTTATATAGTGAACTCTCTCCCATTATCACAGTATTATA
TGTACGAGAAACTC
Found at i:22284 original size:36 final size:35
Alignment explanation
Indices: 22242--22360 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 35
22232 CTCTTTTTAG
* *
22242 ATTAAGTTGTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGAC-TCACTTAATTACCCTGA
22278 ATTAAGTTCTTTATT--CT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCACTTAATTACCCTGA
*
22310 ATTAAG-CCTTTTATTGACCTCACTTAATTACCCTGA
1 ATTAAGTTC-TTTATTGA-CTCACTTAATTACCCTGA
22346 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
22361 TTACTTAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
31 1 0.01
32 26 0.36
33 1 0.01
34 1 0.01
35 2 0.03
36 41 0.56
37 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (35 bp):
ATTAAGTTCTTTATTGACTCACTTAATTACCCTGA
Found at i:22304 original size:32 final size:32
Alignment explanation
Indices: 22263--22370 Score: 137
Period size: 32 Copynumber: 3.2 Consensus size: 32
22253 TATTGACTTC
*
22263 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTCT
*
22295 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACCT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT---CT
*
22330 CACTTAATTACCCTGAATTAAGTTCTTTATTTT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTCT
22363 ACTTAATT
1 ACTTAATT
22371 TCCTTTCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 34 0.52
33 1 0.02
35 2 0.03
36 27 0.41
37 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTCT
Found at i:22451 original size:36 final size:36
Alignment explanation
Indices: 22374--22675 Score: 364
Period size: 36 Copynumber: 8.5 Consensus size: 36
22364 CTTAATTTCC
* *
22374 TTTCC-TGAAATTAAGCCTGT-GTTT-TTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
*
22407 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTA-TCTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACT-TAA
* * *
22443 TTTCCTTGAAATTAAGCTAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
* *
22479 TTTCCTTGAGACTAAGCCAGTCTTTTCTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
* * *
22515 TTTCCTTGAAATTAAGTCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
*
22551 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
* * *
22587 TTTCCTTGAAATTAAGCAAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
* * * *
22623 TTTCCTTGAAATTCAGTC-TTC-TTTCTTTTACATAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTC-TTTACTTAA
*
22658 TTTTCTTGAAATTAAGCC
1 TTTCCTTGAAATTAAGCC
22676 CTTTGTCTGG
Statistics
Matches: 229, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
33 5 0.02
34 18 0.08
35 27 0.12
36 179 0.78
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (36 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACTTAA
Found at i:22728 original size:36 final size:36
Alignment explanation
Indices: 22706--22831 Score: 191
Period size: 36 Copynumber: 3.5 Consensus size: 36
22696 TCATCTGTGG
*
22706 ATTAAATCTTTGCTGACTTTACTTAATTCTTGTGAA
1 ATTAAATCTTTGCTAACTTTACTTAATTCTTGTGAA
* *
22742 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
1 ATTAAATCTTTGCTAACTTTACTTAATTCTTGTGAA
* *
22778 ATTAAGTCTTTGATAA-TTTACTTAATTCTTGTGAA
1 ATTAAATCTTTGCTAACTTTACTTAATTCTTGTGAA
*
22813 ATTAAGTCTTTGCTAACTT
1 ATTAAATCTTTGCTAACTT
22832 CTTTCAGTCT
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
35 34 0.40
36 50 0.60
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (36 bp):
ATTAAATCTTTGCTAACTTTACTTAATTCTTGTGAA
Found at i:22815 original size:20 final size:20
Alignment explanation
Indices: 22759--22815 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
22749 CTTTGCTAAT
22759 TTTACTTAATTCTTGTG-AA
1 TTTACTTAATTCTTGTGAAA
*
22778 ---A-TTAAGTCTT-TGATAA
1 TTTACTTAATTCTTGTGA-AA
22794 TTTACTTAATTCTTGTGAAA
1 TTTACTTAATTCTTGTGAAA
22814 TT
1 TT
22816 AAGTCTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 13
0.66 0.05 0.30
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 3 0.10
19 1 0.03
20 12 0.41
21 3 0.10
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTACTTAATTCTTGTGAAA
Found at i:22845 original size:11 final size:11
Alignment explanation
Indices: 22829--22975 Score: 177
Period size: 11 Copynumber: 13.0 Consensus size: 11
22819 TCTTTGCTAA
22829 CTTCTTTCAGT
1 CTTCTTTCAGT
22840 CTTCTTTCAGT
1 CTTCTTTCAGT
*
22851 CCTCTTTCAGT
1 CTTCTTTCAGT
*
22862 CTTGTTTTCAGT
1 CTT-CTTTCAGT
*
22874 CTTCTTTTCAAT
1 CTTC-TTTCAGT
*
22886 CTTCTTTCAAT
1 CTTCTTTCAGT
22897 CTTCTTTCAGT
1 CTTCTTTCAGT
*
22908 CTTCTTTTCAAT
1 CTTC-TTTCAGT
22920 CTTCTTTCAGT
1 CTTCTTTCAGT
*
22931 CTTGTTTCAGT
1 CTTCTTTCAGT
*
22942 CTTGTTTCAGT
1 CTTCTTTCAGT
*
22953 CTTGTTTTCAGT
1 CTT-CTTTCAGT
*
22965 CTTGTTTCAGT
1 CTTCTTTCAGT
22976 ATTTTTTTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
11 81 0.67
12 40 0.33
ACGTcount: A:0.11, C:0.24, G:0.10, T:0.55
Consensus pattern (11 bp):
CTTCTTTCAGT
Found at i:22871 original size:34 final size:34
Alignment explanation
Indices: 22867--22975 Score: 157
Period size: 34 Copynumber: 3.2 Consensus size: 34
22857 TCAGTCTTGT
* *
22867 TTTCAGTCTTCTTTTCAATCTTCTTTCAATCTTC
1 TTTCAGTCTTCTTTTCAATCTTCTTTCAGTCTTG
22901 TTTCAGTCTTCTTTTCAATCTTCTTTCAGTCTTG
1 TTTCAGTCTTCTTTTCAATCTTCTTTCAGTCTTG
* * *
22935 TTTCAGTCTT-GTTTCAGTCTTGTTTTCAGTCTTG
1 TTTCAGTCTTCTTTTCAATCTT-CTTTCAGTCTTG
22969 TTTCAGT
1 TTTCAGT
22976 ATTTTTTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
33 9 0.13
34 60 0.87
ACGTcount: A:0.12, C:0.22, G:0.10, T:0.56
Consensus pattern (34 bp):
TTTCAGTCTTCTTTTCAATCTTCTTTCAGTCTTG
Found at i:22874 original size:23 final size:23
Alignment explanation
Indices: 22829--22975 Score: 183
Period size: 23 Copynumber: 6.5 Consensus size: 23
22819 TCTTTGCTAA
*
22829 CTTCTTTCAGTCTT-CTTTCAGT
1 CTTCTTTCAGTCTTGTTTTCAGT
*
22851 CCTCTTTCAGTCTTGTTTTCAGT
1 CTTCTTTCAGTCTTGTTTTCAGT
* * *
22874 CTTCTTTTCAATCTT-CTTTCAAT
1 CTTC-TTTCAGTCTTGTTTTCAGT
* *
22897 CTTCTTTCAGTCTTCTTTTCAAT
1 CTTCTTTCAGTCTTGTTTTCAGT
22920 CTTCTTTCAGTCTTG-TTTCAGT
1 CTTCTTTCAGTCTTGTTTTCAGT
*
22942 CTTGTTTCAGTCTTGTTTTCAGT
1 CTTCTTTCAGTCTTGTTTTCAGT
*
22965 CTTGTTTCAGT
1 CTTCTTTCAGT
22976 ATTTTTTTTT
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
22 42 0.38
23 59 0.54
24 9 0.08
ACGTcount: A:0.11, C:0.24, G:0.10, T:0.55
Consensus pattern (23 bp):
CTTCTTTCAGTCTTGTTTTCAGT
Found at i:23150 original size:40 final size:40
Alignment explanation
Indices: 23058--23165 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
23048 TGTGCTCTGA
* **
23058 TGTTTTTACTTAATTACTATGAATTAAGTCTTTTAACTGT
1 TGTTTTTACTTAATTACTATGAATTAAGTCTCTTAACTAC
** * * *
23098 TGCTTCCT-CTTAATTTCTAGGAATTAAGTCTCTTGACTAC
1 TG-TTTTTACTTAATTACTATGAATTAAGTCTCTTAACTAC
*
23138 TGTTTTTACTTAATTCCTATGAATTAAG
1 TGTTTTTACTTAATTACTATGAATTAAG
23166 CCTTTGTGAT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.06
40 48 0.89
41 3 0.06
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (40 bp):
TGTTTTTACTTAATTACTATGAATTAAGTCTCTTAACTAC
Found at i:23206 original size:35 final size:34
Alignment explanation
Indices: 23141--23206 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
23131 TGACTACTGT
* * *
23141 TTTTACTTAATTCCTATGAATTAAGCCTTTGTGA
1 TTTTACCTAATTCCTACGAATTAAGACTTTGTGA
23175 TTTTACCTAATTTCCT-CGAATTAAGTACTTTG
1 TTTTACCTAA-TTCCTACGAATTAAG-ACTTTG
23207 ACTTCTCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 17 0.63
35 10 0.37
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (34 bp):
TTTTACCTAATTCCTACGAATTAAGACTTTGTGA
Done.