Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009149.1 Corchorus capsularis cultivar CVL-1 contig09170, 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: 10615
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Found at i:803 original size:132 final size:131
Alignment explanation
Indices: 553--804 Score: 407
Period size: 132 Copynumber: 1.9 Consensus size: 131
543 GAGAAGAATG
* *
553 TAGAAATTACCTGATGAAAATCTTGCAATGATGAATTTAACAATGCAAGAGTTAAATTGAGGGGA
1 TAGAAATGACCTAATGAAAATCTTGCAATGATGAATTTAACAATGCAAGAGTTAAATTGAGGGGA
* * *
618 AAAAACGCCATAAGATAAAAGGAAAACAAAAGCCCAAAATACGAAAACTCAAAGATACAGAGCAA
66 AAAAAC-CCATAACATAAAAGGAAAACAAAAGCCCAAAATACAAAAACACAAAGATACAGAGCAA
683 TT
130 TT
685 TAGAAATGACCTAATGAAAATCTTGCAATGATGAATTTAACAATGCAAGAGTTAAATTGAGGGGA
1 TAGAAATGACCTAATGAAAATCTTGCAATGATGAATTTAACAATGCAAGAGTTAAATTGAGGGGA
* *
750 AAATA-CCATAACATAAAAGTAAAACAAAAGCCCAAAATACAAAAACCCACAAAGA
66 AAAAACCCATAACATAAAAGGAAAACAAAAGCCCAAAATACAAAAA--CACAAAGA
805 GCAAAATACC
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
130 37 0.33
132 74 0.67
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (131 bp):
TAGAAATGACCTAATGAAAATCTTGCAATGATGAATTTAACAATGCAAGAGTTAAATTGAGGGGA
AAAAACCCATAACATAAAAGGAAAACAAAAGCCCAAAATACAAAAACACAAAGATACAGAGCAAT
T
Found at i:2020 original size:20 final size:20
Alignment explanation
Indices: 1995--2049 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1985 AAACTTTTTA
1995 TTTGCTACGTGTTGAATTGT
1 TTTGCTACGTGTTGAATTGT
*
2015 TTTGCTACGTGTTGGATTGT
1 TTTGCTACGTGTTGAATTGT
2035 TTTGCTACGTGTTGA
1 TTTGCTACGTGTTGA
2050 TTTGAAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (20 bp):
TTTGCTACGTGTTGAATTGT
Found at i:2563 original size:2 final size:2
Alignment explanation
Indices: 2519--2553 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2509 TATACTATGG
*
2519 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2554 GAGCATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3317 original size:23 final size:24
Alignment explanation
Indices: 3273--3326 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
3263 CTATATTATA
* * *
3273 ATAATTAATTTAGGATTTTAAAAAT
1 ATAATTAATTTA-GAATATAAAAAC
*
3298 ATAATTAATTTA-AATATAAATAC
1 ATAATTAATTTAGAATATAAAAAC
3321 ATAATT
1 ATAATT
3327 TACTCAACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 13 0.52
25 12 0.48
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
ATAATTAATTTAGAATATAAAAAC
Found at i:4203 original size:26 final size:26
Alignment explanation
Indices: 4151--4210 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
4141 TGATGGAATT
4151 AGGTTGAATTTTTTTGTTTGGTGAAA
1 AGGTTGAATTTTTTTGTTTGGTGAAA
*
4177 ATGTTGAA-TTTTTT-TTTGGTAGAAAA
1 AGGTTGAATTTTTTTGTTTGGT-G-AAA
4203 AGGTTGAA
1 AGGTTGAA
4211 AATTTAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.20
25 7 0.23
26 17 0.57
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (26 bp):
AGGTTGAATTTTTTTGTTTGGTGAAA
Found at i:5324 original size:29 final size:30
Alignment explanation
Indices: 5280--5348 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
5270 GCCCGGTATC
* *
5280 ATTTTTTTTTTCCAAAAAGCTTCATAAACA
1 ATTTTCTTTTTCCAAAAAGATTCATAAACA
* *
5310 ATTTTCTTTTT-CAAAGAGATTCATAAGCA
1 ATTTTCTTTTTCCAAAAAGATTCATAAACA
*
5339 AATTTCTTTT
1 ATTTTCTTTT
5349 GTTAGAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.46
Consensus pattern (30 bp):
ATTTTCTTTTTCCAAAAAGATTCATAAACA
Found at i:5569 original size:1 final size:1
Alignment explanation
Indices: 5563--5593 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
5553 GGCAAGCGAG
5563 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5594 GAACAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7749 original size:128 final size:128
Alignment explanation
Indices: 7556--7820 Score: 512
Period size: 128 Copynumber: 2.1 Consensus size: 128
7546 GTTTGTCATC
*
7556 TTAAAAGAATCAAAGTTGGTTTATAAGTATAAATGTTATATATGTGCATGTCAAAGACAGAATTG
1 TTAAATGAATCAAAGTTGGTTTATAAGTATAAATGTTATATATGTGCATGTCAAAGACAGAATTG
*
7621 CTAGGATTCATGAGGGTATTGCTTTTGTTATTTGGCTTATTTGTTAAATTGAACATATAATTG
66 CTAGGATTCATGAGGGTATTGCTTTTGTTATTTGGCTTATTTGGTAAATTGAACATATAATTG
7684 TTAAATGAATCAAAGTTGGTTTATAAGTATAAATGTTATATATGTGCATGTCAAAGACAGAATTG
1 TTAAATGAATCAAAGTTGGTTTATAAGTATAAATGTTATATATGTGCATGTCAAAGACAGAATTG
7749 CTAGGATTCATGAGGGTATTGCTTTTGTTATTTGGCTTATTTGGTAAATTGAACATATAATTG
66 CTAGGATTCATGAGGGTATTGCTTTTGTTATTTGGCTTATTTGGTAAATTGAACATATAATTG
7812 TTAAATGAA
1 TTAAATGAA
7821 GTAATGAAGT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 135 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.40
Consensus pattern (128 bp):
TTAAATGAATCAAAGTTGGTTTATAAGTATAAATGTTATATATGTGCATGTCAAAGACAGAATTG
CTAGGATTCATGAGGGTATTGCTTTTGTTATTTGGCTTATTTGGTAAATTGAACATATAATTG
Found at i:8789 original size:56 final size:56
Alignment explanation
Indices: 8729--8843 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
8719 TAGAAAATCA
8729 TTTGAAATACATCTAAATATAAATGGATCATGGTACAGTTTTGGGATAGAAAAATG
1 TTTGAAATACATCTAAATATAAATGGATCATGGTACAGTTTTGGGATAGAAAAATG
8785 TTTGAAATACATCTAAATATAAATGGATCATGGTACAGTTTTGGGATAGAAAAATG
1 TTTGAAATACATCTAAATATAAATGGATCATGGTACAGTTTTGGGATAGAAAAATG
8841 TTT
1 TTT
8844 AAAGTATTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (56 bp):
TTTGAAATACATCTAAATATAAATGGATCATGGTACAGTTTTGGGATAGAAAAATG
Found at i:9145 original size:16 final size:16
Alignment explanation
Indices: 9124--9160 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
9114 CGCATACACA
*
9124 TGTACCCAATTACTCG
1 TGTACCCAATTACTAG
9140 TGTACCCAATTACTAG
1 TGTACCCAATTACTAG
9156 TGTAC
1 TGTAC
9161 TTTGGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (16 bp):
TGTACCCAATTACTAG
Done.