Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015579.1 Corchorus capsularis cultivar CVL-1 contig15600, 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: 1767
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Found at i:440 original size:20 final size:22
Alignment explanation
Indices: 401--440 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
391 ATGAAATGTC
*
401 CTATATATATGTAATGCAAGAA
1 CTATAGATATGTAATGCAAGAA
423 CTATAGATATG-AAT-CAAG
1 CTATAGATATGTAATGCAAG
441 TTGATACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (22 bp):
CTATAGATATGTAATGCAAGAA
Found at i:676 original size:15 final size:15
Alignment explanation
Indices: 644--677 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
634 GGGCGGGTTC
**
644 GGGTTCGGGTCATCT
1 GGGTTCGGGTCAAAT
659 GGGTTCGGGTCAAAT
1 GGGTTCGGGTCAAAT
674 GGGT
1 GGGT
678 CAGACAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.15, G:0.44, T:0.29
Consensus pattern (15 bp):
GGGTTCGGGTCAAAT
Found at i:720 original size:16 final size:16
Alignment explanation
Indices: 688--760 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
678 CAGACAGTTT
* *
688 TCTCGGGCCATACGGG
1 TCTCGGGTCATTCGGG
* *
704 TTTCGGGTCATTTGGG
1 TCTCGGGTCATTCGGG
720 TCTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
*
736 T-TCCAGGTCATTCGGG
1 TCT-CGGGTCATTCGGG
752 TCTCGGGTC
1 TCTCGGGTC
761 TACCGGTTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 45 0.96
17 1 0.02
ACGTcount: A:0.08, C:0.25, G:0.36, T:0.32
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:725 original size:32 final size:32
Alignment explanation
Indices: 688--775 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
678 CAGACAGTTT
* *
688 TCTCGGGCCATACGGGTTTCGGGTCATTTGGG
1 TCTCGGGTCATACGGGTTTCGGGTCATTCGGG
* * *
720 TCTCGGGTCATTCGGGTTCCAGGTCATTCGGG
1 TCTCGGGTCATACGGGTTTCGGGTCATTCGGG
*
752 TCTCGGGTC-TACCGGTTCTCGGGT
1 TCTCGGGTCATACGGGTT-TCGGGT
776 TTTGGCATCG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 6 0.13
32 40 0.87
ACGTcount: A:0.08, C:0.25, G:0.35, T:0.32
Consensus pattern (32 bp):
TCTCGGGTCATACGGGTTTCGGGTCATTCGGG
Found at i:1597 original size:16 final size:16
Alignment explanation
Indices: 1574--1710 Score: 154
Period size: 16 Copynumber: 8.6 Consensus size: 16
1564 AGGGTTAACT
*
1574 TCTCGGGTTATTCGGG
1 TCTCGGGTCATTCGGG
* *
1590 TTTCGGGTCATACGGG
1 TCTCGGGTCATTCGGG
*
1606 TCTCGGGTCACTCGGG
1 TCTCGGGTCATTCGGG
1622 T-TACGGGTCATTCGGG
1 TCT-CGGGTCATTCGGG
* **
1638 TTTCGGGTCATTTAGG
1 TCTCGGGTCATTCGGG
1654 TCTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
1670 TCTCGGGTCA-TCTGGG
1 TCTCGGGTCATTC-GGG
*
1686 T-TGCGGGTCACTCGGG
1 TCT-CGGGTCATTCGGG
1702 TCTCGGGTC
1 TCTCGGGTC
1711 GGGCGGGTTC
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
15 4 0.04
16 95 0.92
17 4 0.04
ACGTcount: A:0.08, C:0.23, G:0.37, T:0.32
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:1605 original size:9 final size:8
Alignment explanation
Indices: 1592--1710 Score: 74
Period size: 7 Copynumber: 14.9 Consensus size: 8
1582 TATTCGGGTT
1592 TCGGGTCA
1 TCGGGTCA
1600 TACGGGTC-
1 T-CGGGTCA
1608 TCGGGTCA
1 TCGGGTCA
*
1616 CTCGGGTTA
1 -TCGGGTCA
1625 -CGGGTCA
1 TCGGGTCA
*
1632 TTCGGGT-T
1 -TCGGGTCA
1640 TCGGGTCA
1 TCGGGTCA
**
1648 TTTAGGTC-
1 -TCGGGTCA
1656 TCGGGTCA
1 TCGGGTCA
1664 TTCGGGTC-
1 -TCGGGTCA
1672 TCGGGTCA
1 TCGGGTCA
1680 TCTGGGT--
1 TC-GGGTCA
1687 TGCGGGTCA
1 T-CGGGTCA
1696 CTCGGGTC-
1 -TCGGGTCA
1704 TCGGGTC
1 TCGGGTC
1711 GGGCGGGTTC
Statistics
Matches: 88, Mismatches: 8, Indels: 31
0.69 0.06 0.24
Matches are distributed among these distances:
7 42 0.48
8 5 0.06
9 40 0.45
10 1 0.01
ACGTcount: A:0.08, C:0.24, G:0.38, T:0.30
Consensus pattern (8 bp):
TCGGGTCA
Found at i:1635 original size:48 final size:47
Alignment explanation
Indices: 1574--1710 Score: 170
Period size: 48 Copynumber: 2.9 Consensus size: 47
1564 AGGGTTAACT
*
1574 TCTCGGGTTATTCGGGTTTCGGGTCATACGGGTCTCGGGTCACTCGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCAT-CGGGTCTCGGGTCACTCGGG
** *
1622 T-TACGGGTCATTCGGGTTTCGGGTCATTTAGGTCTCGGGTCATTCGGG
1 TCT-CGGGTCATTCGGGTTTCGGGTCA-TCGGGTCTCGGGTCACTCGGG
*
1670 TCTCGGGTCA-TCTGGGTTGCGGGTCACTCGGGTCTCGGGTC
1 TCTCGGGTCATTC-GGGTTTCGGGTCA-TCGGGTCTCGGGTC
1711 GGGCGGGTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
47 3 0.04
48 72 0.94
49 2 0.03
ACGTcount: A:0.08, C:0.23, G:0.37, T:0.32
Consensus pattern (47 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATCGGGTCTCGGGTCACTCGGG
Done.