Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012977.1 Corchorus capsularis cultivar CVL-1 contig12998, 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: 26258
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:1530 original size:30 final size:31
Alignment explanation
Indices: 1489--1563 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
1479 CGGGTTGTGC
** *
1489 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
1519 CCGGTCATGTGCGA-TCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
1549 CCGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
1564 GGCATCCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.27
Consensus pattern (31 bp):
CCGGTCTTGTGCGATTCCCTCCATGCAATGG
Found at i:4430 original size:33 final size:33
Alignment explanation
Indices: 4388--4496 Score: 209
Period size: 33 Copynumber: 3.3 Consensus size: 33
4378 TTCTTTTCAC
4388 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
4421 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
4454 CTAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
4487 CCAAAACAGA
1 CCAAAACAGA
4497 TTTGTTTTCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:4526 original size:66 final size:66
Alignment explanation
Indices: 4388--4529 Score: 187
Period size: 66 Copynumber: 2.2 Consensus size: 66
4378 TTCTTTTCAC
* * *
4388 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
4453 A
66 A
* * * * *
4454 CTAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGC
*
4518 AT
65 AA
4520 CCAAAACAGA
1 CCAAAACAGA
4530 TTTAGTGTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 2 0.03
66 63 0.97
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.27
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
A
Found at i:4541 original size:33 final size:32
Alignment explanation
Indices: 4486--4573 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
4476 GCTATGATCA
* *
4486 ACCAAAACAGATTT-GTTTTCATCA-CAATTAGC
1 ACCAAAACAGATTTAG-TGTCATCACCAA-TAAC
4518 ATCCAAAACAGATTTAGTGTCATCACCAATAAC
1 A-CCAAAACAGATTTAGTGTCATCACCAATAAC
*
4551 ACTTAAAACAGATTTAGTGTCAT
1 AC-CAAAACAGATTTAGTGTCAT
4574 TGCAAACAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 2 0.04
33 43 0.88
34 4 0.08
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (32 bp):
ACCAAAACAGATTTAGTGTCATCACCAATAAC
Found at i:4585 original size:33 final size:33
Alignment explanation
Indices: 4522--4626 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
4512 ATTAGCATCC
* * *
4522 AAAACAGATTTAGTGTCATCACCAATAACACTT
1 AAAACAGATTTAGTGTCATCGCAAACAACACTT
* *
4555 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTGTCATCGCAAACAACACTT
** * *
4588 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTGTCATCGCAAACAACACT-T
4621 AAAACA
1 AAAACA
4627 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 1 0.02
33 57 0.98
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCGCAAACAACACTT
Found at i:7876 original size:21 final size:21
Alignment explanation
Indices: 7848--7900 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
7838 ACTAGCGTTG
*
7848 GGCG-CCCATGTGGTATGCTT
1 GGCGCCCCATGTGGTATGCCT
*
7868 GGCGCCCCATGTGGTTTGCCT
1 GGCGCCCCATGTGGTATGCCT
*
7889 CGCGCCCCATGT
1 GGCGCCCCATGT
7901 ACTCTAGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.08, C:0.34, G:0.32, T:0.26
Consensus pattern (21 bp):
GGCGCCCCATGTGGTATGCCT
Found at i:13820 original size:21 final size:21
Alignment explanation
Indices: 13787--13835 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
13777 AAGAATTGTA
**
13787 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
13807 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
13828 GCATTCCT
1 GC-TTCCT
13836 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:15162 original size:12 final size:12
Alignment explanation
Indices: 15120--15162 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
15110 GGCCATGATC
*
15120 GGCCAACGCATG
1 GGCCATCGCATG
* *
15132 GGGCATCGCACG
1 GGCCATCGCATG
*
15144 GGACATCGCATG
1 GGCCATCGCATG
15156 GGCCATC
1 GGCCATC
15163 CGGCCACAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.35, T:0.12
Consensus pattern (12 bp):
GGCCATCGCATG
Found at i:15187 original size:42 final size:42
Alignment explanation
Indices: 15135--15220 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
15125 ACGCATGGGG
* * *
15135 CATCGCACGGGACATCGCATGGGCCATCCGGCCACAACCGGC
1 CATCACACGGGACAACGCACGGGCCATCCGGCCACAACCGGC
* *
15177 CATCACACGGGCCAACGCACGGGCCATCCGGCCATAACCGGC
1 CATCACACGGGACAACGCACGGGCCATCCGGCCACAACCGGC
15219 CA
1 CA
15221 CTTGATCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08
Consensus pattern (42 bp):
CATCACACGGGACAACGCACGGGCCATCCGGCCACAACCGGC
Found at i:21735 original size:21 final size:21
Alignment explanation
Indices: 21711--21753 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
21701 CTTGCTCTTG
*
21711 TCAACGGACCCAAA-GGCATCT
1 TCAAAGGA-CCAAATGGCATCT
*
21732 TCAAAGGATCAAATGGCATCT
1 TCAAAGGACCAAATGGCATCT
21753 T
1 T
21754 AATGACATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
TCAAAGGACCAAATGGCATCT
Found at i:24773 original size:19 final size:18
Alignment explanation
Indices: 24740--24775 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24730 TTGAAATAAT
24740 TCTTCAATAATCTTCAAC
1 TCTTCAATAATCTTCAAC
*
24758 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
24776 ATAAGCCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAC
Done.