Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007059.1 Corchorus capsularis cultivar CVL-1 contig07080, 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: 19985
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:7917 original size:30 final size:30
Alignment explanation
Indices: 7877--7935 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
7867 TGTCTTCAAG
7877 TCCATAATAAGTCCTT-GGCCCATCATTCCT
1 TCCATAATAAG-CCTTCGGCCCATCATTCCT
* *
7907 TCCATGATAAGCCTTCGGCGCATCATTCC
1 TCCATAATAAGCCTTCGGCCCATCATTCC
7936 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTCGGCCCATCATTCCT
Found at i:9051 original size:30 final size:30
Alignment explanation
Indices: 9015--9073 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9005 TGTCTTCAAG
*
9015 TCCATGATAAGTCCTT-GGCGTATCATTCCT
1 TCCATGATAAG-CCTTGGGCGCATCATTCCT
9045 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATGATAAGCCTTGGGCGCATCATTCC
9074 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCT
Found at i:11214 original size:33 final size:33
Alignment explanation
Indices: 11172--11280 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
11162 TTCTTTTCAC
** *
11172 CCAAAACAGAATTATTTTTAATGCTATAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
11205 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
11238 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
11271 CCAAAACAGA
1 CCAAAACAGA
11281 TTTGCTTTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:11343 original size:33 final size:33
Alignment explanation
Indices: 11305--11401 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
11295 AATTAGCATC
* *
11305 CAAAACATATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * * *
11338 TAAAACAGACTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
**
11371 CAAATTAGATTTAGTATCATCGCAAACAACA
1 CAAAACAGATTTAGTATCATCGCAAACAACA
11402 TCTAAAATAC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:17728 original size:33 final size:32
Alignment explanation
Indices: 17686--17810 Score: 117
Period size: 33 Copynumber: 3.8 Consensus size: 32
17676 AGCTAAAGGA
*
17686 TCATATGGCCGGTTGTGGCCGGGCATGGCCGA-G
1 TCATGTGGCCGG-TGTGGCCGGGCATGGCC-ATG
17719 TCATGTGGCCGGGTGTGGCCGGGCATGGCCATG
1 TCATGTGGCC-GGTGTGGCCGGGCATGGCCATG
** **
17752 TCGCGTGGCCGGTGATGGCCGGGCATCTCCATG
1 TCATGTGGCCGGTG-TGGCCGGGCATGGCCATG
*** *
17785 TCGCATGGCCGGTGTTGCGCGGGCAT
1 TCATGTGGCCGGTGTGGC-CGGGCAT
17811 CTCCAAGTCG
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
32 8 0.10
33 71 0.88
34 2 0.02
ACGTcount: A:0.10, C:0.26, G:0.42, T:0.22
Consensus pattern (32 bp):
TCATGTGGCCGGTGTGGCCGGGCATGGCCATG
Found at i:17811 original size:33 final size:33
Alignment explanation
Indices: 17723--17830 Score: 130
Period size: 33 Copynumber: 3.3 Consensus size: 33
17713 GCCGAGTCAT
* **
17723 GTGGCCGGGTGTGGC-CGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTTGCGCGGGCATCTCCATGTCGC
*
17756 GTGGCCGGTGATG-GCCGGGCATCTCCATGTCGC
1 GTGGCCGGTGTTGCG-CGGGCATCTCCATGTCGC
* *
17789 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTTGCGCGGGCATCTCCATGTCGC
17822 GTGGCCGGT
1 GTGGCCGGT
17831 CACTTATGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 5 0.08
33 58 0.91
34 1 0.02
ACGTcount: A:0.08, C:0.29, G:0.43, T:0.20
Consensus pattern (33 bp):
GTGGCCGGTGTTGCGCGGGCATCTCCATGTCGC
Found at i:19653 original size:33 final size:33
Alignment explanation
Indices: 19576--19691 Score: 139
Period size: 33 Copynumber: 3.6 Consensus size: 33
19566 TTTTCGTCAC
* *
19576 CCAAAACAGATTTATTTTCAATG-T-T-ATCTA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
19606 CCAAAACAGGATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* * *
19639 CCAAAACAAAATTATTTTTAATGCTATGTTCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
19672 CCAAAACAGAATTGTTTTCA
1 CCAAAACAGAATTATTTTCA
19692 TCACAATTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.28
31 1 0.01
32 1 0.01
33 49 0.69
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:19744 original size:33 final size:33
Alignment explanation
Indices: 19707--19811 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 33
19697 ATTAGCATCC
*
19707 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* *
19740 AAAACAGATTTAGTGTCATTGCAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
19773 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
19806 AAAACA
1 AAAACA
19812 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Done.