Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010567.1 Corchorus capsularis cultivar CVL-1 contig10588, 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: 95673
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:586 original size:7 final size:7
Alignment explanation
Indices: 574--618 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
564 GCCCAATGAT
574 ACAAAAA
1 ACAAAAA
581 ACAAAACA
1 ACAAAA-A
589 A-ACAAAA
1 ACA-AAAA
596 A-AAAAA
1 ACAAAAA
602 ACAAAAA
1 ACAAAAA
609 ACAAAAA
1 ACAAAAA
616 ACA
1 ACA
619 TCATCAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.14
7 25 0.71
8 5 0.14
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:600 original size:19 final size:19
Alignment explanation
Indices: 576--616 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
566 CCAATGATAC
576 AAAAAACAAAACAAACAAAAA
1 AAAAAAC-AAA-AAACAAAAA
597 AAAAAACAAAAAACAAAAA
1 AAAAAACAAAAAACAAAAA
616 A
1 A
617 CATCATCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 3 0.15
21 7 0.35
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAACAAAAA
Found at i:3555 original size:27 final size:27
Alignment explanation
Indices: 3516--3579 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
3506 AAAATAATAC
*
3516 TCCCTCTGTTCCTTTTTAATTGTCCCTT
1 TCCCT-TGTTCCTTTTTAATTGTCACTT
3544 TCCCTTGTTCCTTTTTAATTGTCACTT
1 TCCCTTGTTCCTTTTTAATTGTCACTT
3571 TCCCTTGTT
1 TCCCTTGTT
3580 TTCCAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.08, C:0.30, G:0.08, T:0.55
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCACTT
Found at i:5952 original size:60 final size:60
Alignment explanation
Indices: 5859--6158 Score: 510
Period size: 60 Copynumber: 5.0 Consensus size: 60
5849 CCTTTGGCAG
* * * *
5859 TTCAACAGTCAAGTCAATAATGTACTTTGCAGACCCTGCCCAATCAGTTGGTACGTTTCC
1 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
5919 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
1 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
* * *
5979 TTCAACAGTCAAGTCAATGATGTTCTTTGCAGACCCTGCCCTCTCAGTCAGTACATTTCC
1 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
* *
6039 TTCAACAGTCAAGTCGATAATGTTCTTTGCAGACCCTGCCCTATCAGTCAGTACATTTCC
1 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
*
6099 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTTGGTACATTTCC
1 TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
6159 GTCCAATTTA
Statistics
Matches: 227, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 227 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (60 bp):
TTCAACAGTCAAGTCAATAATGTTCTTTGCAGACCCTGCCCTATCAGTCGGTACATTTCC
Found at i:38583 original size:1 final size:1
Alignment explanation
Indices: 38577--38619 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
38567 TTGGTTTGGG
38577 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38620 AATATTAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38745 original size:28 final size:28
Alignment explanation
Indices: 38705--38759 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
38695 TGTTCTTTGC
38705 AGCTTGAACTATAAAAGTTAACAAATGT
1 AGCTTGAACTATAAAAGTTAACAAATGT
38733 AGCTTGAACTATAAAAGTTAACAAATG
1 AGCTTGAACTATAAAAGTTAACAAATG
38760 AACGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (28 bp):
AGCTTGAACTATAAAAGTTAACAAATGT
Found at i:66396 original size:20 final size:20
Alignment explanation
Indices: 66373--66412 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
66363 GTTTTTCATC
66373 TATGATTTAAAGAACAAATT
1 TATGATTTAAAGAACAAATT
66393 TATGATTTAAAGAACAAATT
1 TATGATTTAAAGAACAAATT
66413 CACATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
TATGATTTAAAGAACAAATT
Found at i:87834 original size:1 final size:1
Alignment explanation
Indices: 87828--87856 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
87818 ATTGAAGCTG
87828 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
87857 CCCCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:88664 original size:1 final size:1
Alignment explanation
Indices: 88658--88689 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
88648 AGATTGGTGG
88658 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
88690 GAGAATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:89604 original size:38 final size:38
Alignment explanation
Indices: 89558--89637 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
89548 TGTTTCTGAA
*
89558 TTTT-TATTCTTTCTCCTCTGAAAAATTTGATTCCAGG
1 TTTTGTATTCTTTCTCCTCTGAAAAATTTGATCCCAGG
*
89595 TTTTGTATTCTTTCTCCTCTGAAAATTTTGATCCCAGG
1 TTTTGTATTCTTTCTCCTCTGAAAAATTTGATCCCAGG
89633 TTTTG
1 TTTTG
89638 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (38 bp):
TTTTGTATTCTTTCTCCTCTGAAAAATTTGATCCCAGG
Done.