Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003712.1 Corchorus capsularis cultivar CVL-1 contig03720, 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: 5232
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:319 original size:101 final size:102
Alignment explanation
Indices: 168--418 Score: 316
Period size: 101 Copynumber: 2.5 Consensus size: 102
158 CTCCCGAGTA
* * * *
168 TTTTGGCTCTGTTTTTTGTTGATTTATTGAAGGCCACCAGCA-TCTATATGGAGTTGAAGACCAT
1 TTTTTGCTCCGTTTTTTGTTCATTTATTGAAGGCCACCAGCATTCTATATGGAGTTGAA-AAC-T
**
232 T-TGGAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT
64 TCTCCAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT
*
270 TTTTTGCTCCG-TTTTTGTTCATTTATTGAAGGCCACCAGCATTC-CTATGGAGTTGAAAACTTG
1 TTTTTGCTCCGTTTTTTGTTCATTTATTGAAGGCCACCAGCATTCTATATGGAGTTGAAAACTT-
* * *
333 CTCCAATGATGAATGAAGGTTTTGGGAGCTCCTGAAAT
65 CTCCAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT
* *
371 TTTTTGCTCTGTTTTTTGTTCCTTT-TGTGAAGGCCACCAGCATT-TATA
1 TTTTTGCTCCGTTTTTTGTTCATTTAT-TGAAGGCCACCAGCATTCTATA
419 GTTGTCTTTT
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
99 2 0.02
100 2 0.02
101 84 0.65
102 42 0.32
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (102 bp):
TTTTTGCTCCGTTTTTTGTTCATTTATTGAAGGCCACCAGCATTCTATATGGAGTTGAAAACTTC
TCCAATGATGAATGAAGATTTTGGAAGCTCCTAAAAT
Found at i:1780 original size:10 final size:10
Alignment explanation
Indices: 1749--1779 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1739 TGTAACATGG
1749 TTCTTTTTTT
1 TTCTTTTTTT
1759 TTCTTTTTTT
1 TTCTTTTTTT
1769 TT-TTTTTTT
1 TTCTTTTTTT
1778 TT
1 TT
1780 TGAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:2484 original size:16 final size:17
Alignment explanation
Indices: 2463--2495 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2453 GTACCCTTTG
2463 TATTTATATTT-TTAAT
1 TATTTATATTTATTAAT
*
2479 TATTTATTTTTATTAAT
1 TATTTATATTTATTAAT
2496 AAAAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATATTTATTAAT
Found at i:3184 original size:21 final size:21
Alignment explanation
Indices: 3144--3184 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3134 TTCTTGTTAT
*
3144 TAAGTTTAGCCCTAATTTAAC
1 TAAGTTTAGCCCTAAATTAAC
3165 TAAGTTTAG-CCTCAAATTAA
1 TAAGTTTAGCCCT-AAATTAA
3185 AATTTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAGTTTAGCCCTAAATTAAC
Found at i:4752 original size:11 final size:11
Alignment explanation
Indices: 4733--4775 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
4723 TATACTATAT
4733 CTAATTAATAG
1 CTAATTAATAG
* *
4744 CTAAGTAATAT
1 CTAATTAATAG
4755 CTAATTAATAG
1 CTAATTAATAG
*
4766 TTAATTAATA
1 CTAATTAATA
4776 ATGAATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:4757 original size:22 final size:22
Alignment explanation
Indices: 4729--4775 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4719 CCATTATACT
4729 ATATCTAATTAATAGCTAAGTA
1 ATATCTAATTAATAGCTAAGTA
* *
4751 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAAGTA
4773 ATA
1 ATA
4776 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAAGTA
Found at i:4970 original size:21 final size:21
Alignment explanation
Indices: 4944--4984 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4934 TGAGAGACTT
4944 CTTTCTTTTGTTTTCATTCAC
1 CTTTCTTTTGTTTTCATTCAC
4965 CTTTCTTTTGTTTTCATTCA
1 CTTTCTTTTGTTTTCATTCA
4985 TAAAGGCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.22, G:0.05, T:0.63
Consensus pattern (21 bp):
CTTTCTTTTGTTTTCATTCAC
Done.