Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011479.1 Corchorus capsularis cultivar CVL-1 contig11500, 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: 19340
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:11936 original size:2 final size:2
Alignment explanation
Indices: 11931--11955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11921 AACGAATTGG
11931 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 A
11956 AAGCGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12568 original size:87 final size:87
Alignment explanation
Indices: 12464--12841 Score: 533
Period size: 87 Copynumber: 4.3 Consensus size: 87
12454 TGTATACACT
* * * *
12464 ATACATGATTTGGGGTTTGACCATTACAATTTG-GAATTTGATCTCATTACTAATAAGGTTTTGC
1 ATACATGATTTGGGGTTTGACCATTACAATTTGAG-GTTTGATCCCATTACTAGTAAGGGTTTGC
*
12528 CTAACCATGCTTTAAATTTCATC
65 CTAATCATGCTTTAAATTTCATC
** **
12551 ATACATGATTTGGGGTTTGACCATTATGATTTGAGGTTTGATCCCATTACTAGTAAGATTTTGCC
1 ATACATGATTTGGGGTTTGACCATTACAATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCC
12616 TAATCATGCTTTAAATTTCATC
66 TAATCATGCTTTAAATTTCATC
*
12638 ATACATGATTTGGGGTTTGACCATTACAATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGCC
1 ATACATGATTTGGGGTTTGACCATTACAATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCC
* * *
12703 TAATCATGCTTTATAGTTTAACC
66 TAATCATGCTTTA-AATTTCATC
* * * * *
12726 ATACATGATTTGGGGTTTGACCATTACACTTTGGGGTTTGATCCCATTACTACTAGGGGTTTGTC
1 ATACATGATTTGGGGTTTGACCATTACAATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCC
* *
12791 TTATCATGCTTTAAATTTCATT
66 TAATCATGCTTTAAATTTCATC
12813 ATACATGATTTGGGGTTTGATCTCATTAC
1 ATACATGATTTGGGGTTTGA-C-CATTAC
12842 TAGTAAGGGT
Statistics
Matches: 263, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
87 176 0.67
88 81 0.31
89 6 0.02
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (87 bp):
ATACATGATTTGGGGTTTGACCATTACAATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCC
TAATCATGCTTTAAATTTCATC
Found at i:12669 original size:21 final size:21
Alignment explanation
Indices: 12645--12775 Score: 61
Period size: 23 Copynumber: 6.0 Consensus size: 21
12635 ATCATACATG
12645 ATTTGGGGTTTGACCATTACA
1 ATTTGGGGTTTGACCATTACA
* *
12666 ATTTGAGGTTTGATCCCATTACT
1 ATTTGGGGTTTGA--CCATTACA
* * *
12689 AGTAGGGGTTTG-CC-TAATCA
1 ATTTGGGGTTTGACCATTA-CA
* *** *
12709 TGCTTTATAGTTTAACCA-TACA
1 --ATTTGGGGTTTGACCATTACA
12731 TGATTTGGGGTTTGACCATTACA
1 --ATTTGGGGTTTGACCATTACA
*
12754 CTTTGGGGTTTGATCCCATTAC
1 ATTTGGGGTTTGA--CCATTAC
12776 TACTAGGGGT
Statistics
Matches: 79, Mismatches: 21, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 24 0.30
22 20 0.25
23 30 0.38
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (21 bp):
ATTTGGGGTTTGACCATTACA
Found at i:12684 original size:23 final size:21
Alignment explanation
Indices: 12645--12687 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12635 ATCATACATG
*
12645 ATTTGGGGTTTGACCATTACA
1 ATTTGAGGTTTGACCATTACA
12666 ATTTGAGGTTTGATCCCATTAC
1 ATTTGAGGTTTGA--CCATTAC
12688 TAGTAGGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
ATTTGAGGTTTGACCATTACA
Found at i:12772 original size:23 final size:22
Alignment explanation
Indices: 12734--12788 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
12724 CCATACATGA
12734 TTTGGGGTTTGACCATTAC-AC
1 TTTGGGGTTTGACCATTACTAC
12755 TTTGGGGTTTGATCCCATTACTAC
1 TTTGGGGTTTGA--CCATTACTAC
*
12779 -TAGGGGTTTG
1 TTTGGGGTTTG
12789 TCTTATCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.40
23 16 0.53
24 2 0.07
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.40
Consensus pattern (22 bp):
TTTGGGGTTTGACCATTACTAC
Found at i:12811 original size:262 final size:265
Alignment explanation
Indices: 12326--12832 Score: 724
Period size: 262 Copynumber: 1.9 Consensus size: 265
12316 ATTATTTAGC
* * *
12326 CCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTACAATTTAATCATACATGATTTGGTGTTTG
1 CCCATTACTAGTAAGAGTTTGCCTAATCATGCTTTACAATTTAATCATACATGATTTGGGGTTTG
**
12391 ACCATTACGCTTTGGGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAAATTTCACTTG
66 ACCATTACAATTTGGGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTT-AA-TTCACTTG
*
12456 TATACACTATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCTCATTACTAATAAG
129 TATACACTATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCCCATTACTAATAAG
*
12521 GTTTTGCCTAACCATGCTTTAAATTTCATCATACATGATTTGGGGTTTGACCATTATGATTTGAG
194 GGTTTGCCTAACCATGCTTTAAATTTCATCATACATGATTTGGGGTTTGACCATTATGATTTGAG
12586 GTTTGAT
259 GTTTGAT
* *
12593 CCCATTACTAGTAAGATTTTGCCTAATCATGCTTTA-AATTTCATCATACATGATTTGGGGTTTG
1 CCCATTACTAGTAAGAGTTTGCCTAATCATGCTTTACAATTTAATCATACATGATTTGGGGTTTG
*
12657 ACCATTACAATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTT-A-T-AG
66 ACCATTACAATTT--GG---GATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAATTCAC
* ** *
12719 TT-TA-AC-C-ATACATGATTTGGGGTTTGACCATTACACTTTGGGGTTTGATCCCATTACTACT
126 TTGTATACACTATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCCCATTACTAAT
* * * * *
12780 AGGGGTTTGTCTTATCATGCTTTAAATTTCATTATACATGATTTGGGGTTTGA
191 AAGGGTTTGCCTAACCATGCTTTAAATTTCATCATACATGATTTGGGGTTTGA
12833 TCTCATTACT
Statistics
Matches: 216, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
262 96 0.44
263 1 0.00
264 2 0.01
265 2 0.01
266 40 0.19
267 34 0.16
268 2 0.01
269 1 0.00
271 38 0.18
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (265 bp):
CCCATTACTAGTAAGAGTTTGCCTAATCATGCTTTACAATTTAATCATACATGATTTGGGGTTTG
ACCATTACAATTTGGGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTAATTCACTTGTA
TACACTATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCCCATTACTAATAAGGG
TTTGCCTAACCATGCTTTAAATTTCATCATACATGATTTGGGGTTTGACCATTATGATTTGAGGT
TTGAT
Found at i:12819 original size:175 final size:174
Alignment explanation
Indices: 12463--12841 Score: 537
Period size: 175 Copynumber: 2.2 Consensus size: 174
12453 TTGTATACAC
* *
12463 TATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCTCATTACTAATAAGGTTTTGC
1 TATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCCCATTACTAATAAGGGTTTGC
* * *
12528 CTAACCATGCTTTAAATTTCATCATACATGATTTGGGGTTTGACCATTATGATTTGAGGTTTGAT
66 CTAACCATGCTTTAAATTTAACCATACATGATTTGGGGTTTGACCATTATCATTTGAGGTTTGAT
* *
12593 CCCATTACTAGTAAGATTTTGCCTAATCATGCTTTAAATTTCAT
131 CCCATTACTACTAAGAGTTTGCCTAATCATGCTTTAAATTTCAT
* * * *
12637 CATACATGATTTGGGGTTTGACCATTACAATTT-GAGGTTTGATCCCATTACTAGTAGGGGTTTG
1 TATACATGATTTGGGGTTTGACCATTACAATTTGGA-ATTTGATCCCATTACTAATAAGGGTTTG
* * *
12701 CCTAATCATGCTTTATAGTTTAACCATACATGATTTGGGGTTTGACCATTA-CACTTTGGGGTTT
65 CCTAACCATGCTTTA-AATTTAACCATACATGATTTGGGGTTTGACCATTATCA-TTTGAGGTTT
* * * *
12765 GATCCCATTACTACTAGGGGTTTGTCTTATCATGCTTTAAATTTCAT
128 GATCCCATTACTACTAAGAGTTTGCCTAATCATGCTTTAAATTTCAT
12812 TATACATGATTTGGGGTTTGATCTCATTAC
1 TATACATGATTTGGGGTTTGA-C-CATTAC
12842 TAGTAAGGGT
Statistics
Matches: 181, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
173 2 0.01
174 70 0.39
175 102 0.56
176 1 0.01
177 6 0.03
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (174 bp):
TATACATGATTTGGGGTTTGACCATTACAATTTGGAATTTGATCCCATTACTAATAAGGGTTTGC
CTAACCATGCTTTAAATTTAACCATACATGATTTGGGGTTTGACCATTATCATTTGAGGTTTGAT
CCCATTACTACTAAGAGTTTGCCTAATCATGCTTTAAATTTCAT
Found at i:12829 original size:66 final size:66
Alignment explanation
Indices: 12755--12905 Score: 234
Period size: 66 Copynumber: 2.3 Consensus size: 66
12745 ACCATTACAC
* * * *
12755 TTTGGGGTTTGATCCCATTACTACTAGGGGTTTGTCTTATCATGCTTTAAATTTCATTATACATG
1 TTTGGGGTTTGATCCCATTACTACTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATG
12820 A
66 A
* *
12821 TTTGGGGTTTGATCTCATTACTAGTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATG
1 TTTGGGGTTTGATCCCATTACTACTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATG
12886 A
66 A
12887 TTTGGGGTTTGA--CCATTAC
1 TTTGGGGTTTGATCCCATTAC
12906 GATTTGAGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
64 6 0.08
66 72 0.92
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (66 bp):
TTTGGGGTTTGATCCCATTACTACTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATG
A
Found at i:12976 original size:87 final size:87
Alignment explanation
Indices: 12819--12983 Score: 201
Period size: 87 Copynumber: 1.9 Consensus size: 87
12809 CATTATACAT
* * ** * *
12819 GATTTGGGGTTTGATCTCATTACTAGTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACA
1 GATTTGAGATTTGATCTCATTACTAGTAAGGGTTACCCTAATCATACTTTAAATTTCACCATACA
12884 TGATTTGGGGTTTGACCATTAC
66 TGATTTGGGGTTTGACCATTAC
* * *
12906 GATTTGAGATTTGATC-CAATTACTAGTAGGGGTTACCCTAATCATACTTTACAGTTTGACCATT
1 GATTTGAGATTTGATCTC-ATTACTAGTAAGGGTTACCCTAATCATACTTTA-AATTTCACCA-T
12970 A-A-GATTTGGGGTTT
63 ACATGATTTGGGGTTT
12984 CACAATGGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
86 1 0.02
87 55 0.83
88 8 0.12
89 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (87 bp):
GATTTGAGATTTGATCTCATTACTAGTAAGGGTTACCCTAATCATACTTTAAATTTCACCATACA
TGATTTGGGGTTTGACCATTAC
Found at i:12976 original size:153 final size:154
Alignment explanation
Indices: 12652--12983 Score: 431
Period size: 153 Copynumber: 2.2 Consensus size: 154
12642 ATGATTTGGG
* *
12652 GTTTGACCATTACA-ATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTA
1 GTTTGACCATTACAGATTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTA
* * * *
12716 TAGTTTAACCATACATGATTTGGGGTTTGACCATTACACTTTGGGGTTTGATCCCATTACTACTA
66 TAATTTAACCATACATGATTTGGGGTTTGACCATTACACTTTGAGATTTGATCCAATTACTACTA
*** * *
12781 GGGGTTTGTCTTATCATGCTTTAA
131 GGGGTTACCCTAATCATACTTTAA
* * ** *
12805 ATTTCATTA-TACATGATTTGGGGTTTGATCTCATTACTAGTAAGGGTTTGCCTAATCATGCTTT
1 GTTTGACCATTACA-GATTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTT
* * *
12869 A-AATTTCACTATACATGATTTGGGGTTTGACCATTACGA-TTTGAGATTTGATCCAATTACTAG
65 ATAATTTAACCATACATGATTTGGGGTTTGACCATTAC-ACTTTGAGATTTGATCCAATTACTAC
12932 TAGGGGTTACCCTAATCATACTTTACA
129 TAGGGGTTACCCTAATCATACTTTA-A
12959 GTTTGACCATTA-AGATTTGGGGTTT
1 GTTTGACCATTACAGATTTGGGGTTT
12984 CACAATGGAT
Statistics
Matches: 151, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
152 4 0.03
153 90 0.60
154 55 0.36
155 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.40
Consensus pattern (154 bp):
GTTTGACCATTACAGATTTGGGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTA
TAATTTAACCATACATGATTTGGGGTTTGACCATTACACTTTGAGATTTGATCCAATTACTACTA
GGGGTTACCCTAATCATACTTTAA
Found at i:14202 original size:19 final size:19
Alignment explanation
Indices: 14180--14216 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
14170 ACCCTCCCTC
14180 CCATTTTATTCCCTTTTAG
1 CCATTTTATTCCCTTTTAG
*
14199 CCATTTTATTCCTTTTTA
1 CCATTTTATTCCCTTTTA
14217 TCTTTTTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (19 bp):
CCATTTTATTCCCTTTTAG
Found at i:15409 original size:2 final size:2
Alignment explanation
Indices: 15402--15428 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15392 AATCTAAGGA
15402 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
15429 CACACATATT
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
Found at i:19307 original size:37 final size:37
Alignment explanation
Indices: 19212--19326 Score: 171
Period size: 36 Copynumber: 3.2 Consensus size: 37
19202 CTATTTTTAG
* * *
19212 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
*
19248 ATTAAGCC-TTTTATTGATGCTACTTAATTACCCTGA
1 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
*
19284 ATTAAGCCTTTTTATTGACGCTACTTAATTACCATGA
1 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
19321 ATTAAG
1 ATTAAG
19327 TCTCTAACTT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
36 38 0.54
37 33 0.46
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (37 bp):
ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
Done.