Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011497.1 Corchorus capsularis cultivar CVL-1 contig11518, 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: 23479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1660 original size:45 final size:45
Alignment explanation
Indices: 1602--1687 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
1592 AAGACCTCAA
* * *
1602 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
1647 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
1688 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:1681 original size:22 final size:22
Alignment explanation
Indices: 1558--1718 Score: 110
Period size: 22 Copynumber: 7.3 Consensus size: 22
1548 TTAACTTTCT
* *
1558 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCA
* * *
1580 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
1602 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
1625 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
1646 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
1669 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * *
1691 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
1713 TATGAA
1 TATGAA
1719 TTGTTAGTAA
Statistics
Matches: 103, Mismatches: 31, Indels: 10
0.72 0.22 0.07
Matches are distributed among these distances:
21 3 0.03
22 80 0.78
23 20 0.19
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:1929 original size:22 final size:21
Alignment explanation
Indices: 1813--1958 Score: 84
Period size: 22 Copynumber: 6.8 Consensus size: 21
1803 GTAATCACAT
* * *
1813 TTTGAAAATTTGATAACCTCT
1 TTTGAAATTTTGATAACATCC
*
1834 TTATGAAATTTTGATAACATCT
1 TT-TGAAATTTTGATAACATCC
* * * *
1856 TTATAAAATTTTGTTGAC-CCTC
1 TT-TGAAATTTTGATAACATC-C
1878 TTTGAAA-TTTGA-AA-ATCAC
1 TTTGAAATTTTGATAACATC-C
* *
1897 ATTATGTAATTTTGATAACCTCGC
1 -TT-TGAAATTTTGATAACATC-C
*
1921 TTTGAAATTTTGATAACAACAC
1 TTTGAAATTTTGATAACATC-C
*
1943 TATGAAATTTTGATAA
1 TTTGAAATTTTGATAA
1959 TTTTCATATA
Statistics
Matches: 97, Mismatches: 20, Indels: 15
0.73 0.15 0.11
Matches are distributed among these distances:
19 3 0.03
20 6 0.06
21 11 0.11
22 70 0.72
23 4 0.04
24 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTGAAATTTTGATAACATCC
Found at i:2303 original size:24 final size:22
Alignment explanation
Indices: 2239--2348 Score: 80
Period size: 22 Copynumber: 4.9 Consensus size: 22
2229 TTGTGATAAT
* *
2239 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
2261 TAACCAACGTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
2283 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
2307 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
*
2329 TAACC-ACACTATGGAATTTT
1 TAACCAAC-CTATGAAATTTT
2349 GGTAACCTCC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.01
22 55 0.75
24 17 0.23
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:2321 original size:22 final size:22
Alignment explanation
Indices: 2293--2355 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
2283 TAACCTGATC
*
2293 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACA
2315 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
2337 CTATGGAATTTTGGTAACC
1 CTATGAAATTTTGGTAACC
2356 TCCCCATGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:2717 original size:30 final size:31
Alignment explanation
Indices: 2683--2747 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
2673 TGGCAATTTA
* * *
2683 GAAATATGTTTTTAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAAGGTACAATCG
2713 GAAATATGTTTTAAAAATAAAGGTACAATCG
1 GAAATATGTTTTAAAAATAAAGGTACAATCG
2744 GAAA
1 GAAA
2748 ACATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAAGGTACAATCG
Found at i:6640 original size:39 final size:39
Alignment explanation
Indices: 6556--6640 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
6546 TTTTAGGCGC
* * *
6556 TCTTGCACGTAGGTCGCACGATTATCGCACAATAGGCAT
1 TCTTGCACATAGGTCACACGATTATCGCACAATAGACAT
* *
6595 TCTTGCACATAGGTTACACGATTATCGCACAATAGACCT
1 TCTTGCACATAGGTCACACGATTATCGCACAATAGACAT
*
6634 TTTTGCA
1 TCTTGCA
6641 TTCTTTTCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (39 bp):
TCTTGCACATAGGTCACACGATTATCGCACAATAGACAT
Found at i:9746 original size:50 final size:50
Alignment explanation
Indices: 9671--9773 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
9661 GCTTTTATTC
9671 AGGATTGAGGTTTTCACCTTGGCTACTTGGCCTAATAGGGCTGAGTTAGG
1 AGGATTGAGGTTTTCACCTTGGCTACTTGGCCTAATAGGGCTGAGTTAGG
9721 AGGATTGAGGTTTTCACCTTGGCTACTTGGCCTAATAGGGCTGAGTTAGG
1 AGGATTGAGGTTTTCACCTTGGCTACTTGGCCTAATAGGGCTGAGTTAGG
9771 AGG
1 AGG
9774 TACTGTCCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (50 bp):
AGGATTGAGGTTTTCACCTTGGCTACTTGGCCTAATAGGGCTGAGTTAGG
Found at i:10320 original size:22 final size:23
Alignment explanation
Indices: 10277--10320 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
10267 CTTTGAAAAT
**
10277 ATTATTGAATTTATTTGGTTATC
1 ATTATTGAATTTATTTACTTATC
*
10300 ATTATTG-ATTTTTTTACTTAT
1 ATTATTGAATTTATTTACTTAT
10321 GTTTCAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (23 bp):
ATTATTGAATTTATTTACTTATC
Found at i:20358 original size:18 final size:20
Alignment explanation
Indices: 20335--20372 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
20325 AGCATTTAGG
20335 CTGTC-AATCCCT-CTAATT
1 CTGTCAAATCCCTACTAATT
20353 CTGTCAAATCCCTACTAATT
1 CTGTCAAATCCCTACTAATT
20373 AGTCTGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (20 bp):
CTGTCAAATCCCTACTAATT
Done.