Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014492.1 Corchorus capsularis cultivar CVL-1 contig14513, 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: 27249
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1741 original size:12 final size:12
Alignment explanation
Indices: 1718--1752 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1708 TAATATGAAC
1718 ATGAAA-AAAAA
1 ATGAAACAAAAA
1729 ATGAAACAAAAA
1 ATGAAACAAAAA
*
1741 AAGAAACAAAAA
1 ATGAAACAAAAA
1753 TAAAAATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.80, C:0.06, G:0.09, T:0.06
Consensus pattern (12 bp):
ATGAAACAAAAA
Found at i:3670 original size:38 final size:38
Alignment explanation
Indices: 3619--3696 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
3609 TGATTCTCAG
**
3619 AAATATGAAAACAATATAGAATTTTCTCACATGAATTT
1 AAATATGAAAACAATATAGAATCCTCTCACATGAATTT
*
3657 AAATATGAAAACAATATAGAATCCTCTCATATGAATTT
1 AAATATGAAAACAATATAGAATCCTCTCACATGAATTT
3695 AA
1 AA
3697 TGGGTAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.32
Consensus pattern (38 bp):
AAATATGAAAACAATATAGAATCCTCTCACATGAATTT
Found at i:14545 original size:1 final size:1
Alignment explanation
Indices: 14539--14573 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
14529 CTCGTGTTGG
14539 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14574 GAGCAACTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15985 original size:2 final size:2
Alignment explanation
Indices: 15978--16005 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15968 TCGTATATCC
15978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16006 CTGTAGTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16065 original size:32 final size:32
Alignment explanation
Indices: 16019--16081 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
16009 TAGTTACATC
* *
16019 GAGTCCAGATTAATTCGGAGTTGAGTCGTGTT
1 GAGTCCAGATTAATTCGAAATTGAGTCGTGTT
*
16051 GAGTTCAGATTAATTCGAAATTGAGTCGTGT
1 GAGTCCAGATTAATTCGAAATTGAGTCGTGT
16082 CTTTCAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (32 bp):
GAGTCCAGATTAATTCGAAATTGAGTCGTGTT
Found at i:23787 original size:29 final size:30
Alignment explanation
Indices: 23745--23821 Score: 111
Period size: 33 Copynumber: 2.5 Consensus size: 30
23735 AAATGGTCAT
*
23745 CACATATTTGATTAT-AACAAAGGTGAGAA
1 CACAAATTTGATTATGAACAAAGGTGAGAA
23774 CACAAATTTGATTATCGGAAACAAAGGTGAGAA
1 CACAAATTTGATTAT--G-AACAAAGGTGAGAA
23807 CACAAATTTGATTAT
1 CACAAATTTGATTAT
23822 CGGAAACTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 14 0.33
33 29 0.67
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (30 bp):
CACAAATTTGATTATGAACAAAGGTGAGAA
Found at i:23802 original size:33 final size:33
Alignment explanation
Indices: 23760--23828 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
23750 ATTTGATTAT
23760 AACAAAGGTGAGAACACAAATTTGATTATCGGA
1 AACAAAGGTGAGAACACAAATTTGATTATCGGA
23793 AACAAAGGTGAGAACACAAATTTGATTATCGGA
1 AACAAAGGTGAGAACACAAATTTGATTATCGGA
23826 AAC
1 AAC
23829 TTGACTGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.20
Consensus pattern (33 bp):
AACAAAGGTGAGAACACAAATTTGATTATCGGA
Found at i:23965 original size:54 final size:55
Alignment explanation
Indices: 23880--23983 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 55
23870 CCCGTTCCTC
* *
23880 GGGAGGATTTTTTTTTTTTTAGTTTCTCATCCGGTATCCAGAGCTTTACTACGTT
1 GGGAGGATTTTCTTTTTTTTAGTTTCCCATCCGGTATCCAGAGCTTTACTACGTT
*
23935 GGGAGGA-TTTCTTTTTTTTGGTTTCCCATCCGGTATCCAGAGCTTTACT
1 GGGAGGATTTTCTTTTTTTTAGTTTCCCATCCGGTATCCAGAGCTTTACT
23984 CTGATTAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 39 0.85
55 7 0.15
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.45
Consensus pattern (55 bp):
GGGAGGATTTTCTTTTTTTTAGTTTCCCATCCGGTATCCAGAGCTTTACTACGTT
Done.