Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009546.1 Corchorus capsularis cultivar CVL-1 contig09567, 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: 20011
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:162 original size:32 final size:31
Alignment explanation
Indices: 104--164 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
94 TTAATTAAAA
104 TTTTTTTTACAATGTTTTCATAAAATATAAT
1 TTTTTTTTACAATGTTTTCATAAAATATAAT
*
135 TTTTTTTTGGCAATAGTTTTCAT-AAATATA
1 TTTTTTTT-ACAAT-GTTTTCATAAAATATA
165 CTATTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.30
32 11 0.41
33 8 0.30
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (31 bp):
TTTTTTTTACAATGTTTTCATAAAATATAAT
Found at i:276 original size:12 final size:12
Alignment explanation
Indices: 259--283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
249 AAATTATAGA
259 AAAGATGAATTC
1 AAAGATGAATTC
271 AAAGATGAATTC
1 AAAGATGAATTC
283 A
1 A
284 TCTAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
AAAGATGAATTC
Found at i:2805 original size:1 final size:1
Alignment explanation
Indices: 2799--2828 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2789 CTTTATATAT
2799 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2829 CCCAACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3605 original size:11 final size:11
Alignment explanation
Indices: 3589--3636 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3579 CAGCCCAACA
3589 AAAACAAAACG
1 AAAACAAAACG
*
3600 AAAACAAAACA
1 AAAACAAAACG
3611 AAAACAAAA--
1 AAAACAAAACG
*
3620 AACAAAAAAACG
1 AA-AACAAAACG
3632 AAAAC
1 AAAAC
3637 GATGTCAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 21 0.68
12 2 0.06
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAACAAAACG
Found at i:3635 original size:7 final size:6
Alignment explanation
Indices: 3585--3627 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
3575 TTGACAGCCC
*
3585 AACAAA AAC-AA AACGAA AAC-AA AACAAA AACAAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AAC-AAA AACAAA AA
3628 AACGAAAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.29
6 18 0.53
7 6 0.18
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:3635 original size:22 final size:21
Alignment explanation
Indices: 3585--3636 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3575 TTGACAGCCC
*
3585 AACAAAAACAAAACGAAAACAA
1 AACAAAAACAAAAC-AAAAAAA
3607 AACAAAAACAAAA-AACAAAAA
1 AACAAAAACAAAACAA-AAAAA
*
3628 AACGAAAAC
1 AACAAAAAC
3637 GATGTCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 12 0.44
22 13 0.48
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (21 bp):
AACAAAAACAAAACAAAAAAA
Found at i:8066 original size:17 final size:19
Alignment explanation
Indices: 8044--8081 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
8034 TATTATTTGC
8044 ATTTAT-GTTTGATTG-GT
1 ATTTATCGTTTGATTGAGT
*
8061 ATTTATCTTTTGATTGAGT
1 ATTTATCGTTTGATTGAGT
8080 AT
1 AT
8082 GGGCATGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (19 bp):
ATTTATCGTTTGATTGAGT
Found at i:9836 original size:2 final size:2
Alignment explanation
Indices: 9795--9823 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9785 TGTTTTTGTC
9795 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9824 GTTAAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11005 original size:2 final size:2
Alignment explanation
Indices: 10998--11024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10988 CTAAATTTAG
10998 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
11025 AGGCCCCATA
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:13281 original size:22 final size:22
Alignment explanation
Indices: 13239--13283 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13229 TATGTTACTC
*
13239 CAAGTATAGTATCCACCATTTT
1 CAAGTATAGTATCCACAATTTT
*
13261 CAAGTA-AGTACTCCATAATTTT
1 CAAGTATAGTA-TCCACAATTTT
13283 C
1 C
13284 TTCCAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (22 bp):
CAAGTATAGTATCCACAATTTT
Found at i:13635 original size:19 final size:19
Alignment explanation
Indices: 13613--13649 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
13603 ATTAAATTAC
13613 TTTCAATCAATACTAATTT
1 TTTCAATCAATACTAATTT
13632 TTTCAATCAATACTAATT
1 TTTCAATCAATACTAATT
13650 GTGCCCTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCAATACTAATTT
Found at i:15290 original size:8 final size:8
Alignment explanation
Indices: 15279--15307 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
15269 AGTTAAAATG
15279 GAAAAAAA
1 GAAAAAAA
15287 GAAAAAAA
1 GAAAAAAA
15295 G-AAAAAA
1 GAAAAAAA
15302 GAAAAA
1 GAAAAA
15308 GAAAAGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:15751 original size:53 final size:53
Alignment explanation
Indices: 15671--15781 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 53
15661 TTTAACTATG
15671 TGATATGTTAAACCGACTTAATTCGAATAAGATTAGTCATAAATCGTTAGGTT
1 TGATATGTTAAACCGACTTAATTCGAATAAGATTAGTCATAAATCGTTAGGTT
* * *
15724 TGATATGTTAAACCGATTTAATTCGAATAAGATTGGTTATAAATCGTTAGGTT
1 TGATATGTTAAACCGACTTAATTCGAATAAGATTAGTCATAAATCGTTAGGTT
15777 TGATA
1 TGATA
15782 ACGATACACG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (53 bp):
TGATATGTTAAACCGACTTAATTCGAATAAGATTAGTCATAAATCGTTAGGTT
Found at i:19241 original size:34 final size:34
Alignment explanation
Indices: 19198--19265 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
19188 ACTGAGAGCA
19198 TAACGGCTTGAGTTTTTACTACTCTCTCCGTTCC
1 TAACGGCTTGAGTTTTTACTACTCTCTCCGTTCC
19232 TAACGGCTTGAGTTTTTACTACTCTCTCCGTTCC
1 TAACGGCTTGAGTTTTTACTACTCTCTCCGTTCC
19266 AAATTATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (34 bp):
TAACGGCTTGAGTTTTTACTACTCTCTCCGTTCC
Done.