Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008579.1 Corchorus capsularis cultivar CVL-1 contig08600, 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: 7765
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Found at i:1884 original size:30 final size:30
Alignment explanation
Indices: 1824--1884 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1814 ACAAGTTGTG
* *
1824 CCATTTGATTCTGAAGGTTTGTGAGTTCTC
1 CCATTTGATTCTGAAGGCTTGTGAGCTCTC
* *
1854 CCATTTGATTCTTG-ATGCTTGTGTGCTCTC
1 CCATTTGATTC-TGAAGGCTTGTGAGCTCTC
1884 C
1 C
1885 ATCATATCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (30 bp):
CCATTTGATTCTGAAGGCTTGTGAGCTCTC
Found at i:5570 original size:45 final size:45
Alignment explanation
Indices: 5512--5597 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
5502 AAGATCTCAA
* * *
5512 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
5557 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
5598 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:5591 original size:22 final size:22
Alignment explanation
Indices: 5466--5940 Score: 151
Period size: 22 Copynumber: 21.7 Consensus size: 22
5456 TAAACTTTCT
* *
5466 TATGAAATTTTGTTAATCCTCCCT
1 TATGAAATTTTGATAA-CCT-CCA
* * * *
5490 TAAGGAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
5512 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
5535 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
5556 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
5579 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * *
5601 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
5623 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* * * * *
5644 CTTTAAAATTTTGATAATCACCC
1 -TATGAAATTTTGATAACCTCCA
* * **
5667 TATGAGATTGTGATAATATCGC-
1 TATGAAATTTTGATAACCTC-CA
* *
5689 TATGAAATTTTGATAAATCTTTC-
1 TATGAAATTTTGAT-AA-CCTCCA
* * *
5712 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * *
5735 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
*
5757 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * *
5774 TA-CAAATTTTGATAAGCTCCT
1 TATGAAATTTTGATAACCTCCA
**
5795 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* ** *
5816 TTATGAAATTTTGTTAATTTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
5839 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
5861 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
5883 TATGAAA-TTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* *
5903 CTATGAAAATTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
5926 TATGAAATTTTGATA
1 TATGAAATTTTGATA
5941 TTATCACTGA
Statistics
Matches: 330, Mismatches: 89, Indels: 66
0.68 0.18 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 6 0.02
21 26 0.08
22 201 0.61
23 70 0.21
24 13 0.04
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:5719 original size:23 final size:22
Alignment explanation
Indices: 5688--5772 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
5678 GATAATATCG
*
5688 CTATGAAATTTTGATAAATCTTT
1 CTATAAAATTTTGATAAA-CTTT
* **
5711 CTATAAAATTTTAATAAACCTCC
1 CTATAAAATTTTGATAAA-CTTT
5734 CTATAAAATTTTGAT-AACTTT
1 CTATAAAATTTTGATAAACTTT
* *
5755 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
5773 CTACAAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 3 0.06
22 14 0.28
23 33 0.66
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACTTT
Found at i:5981 original size:19 final size:19
Alignment explanation
Indices: 5931--5997 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
5921 CTTCATATGA
** *
5931 AATTTTGATATTATCACTG
1 AATTTTGATATCCTCCCTG
5950 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
* *
5969 AATTTTGGTATCCTCCCTAA
1 AATTTTGATATCCTCCCT-G
5989 AATTTTGAT
1 AATTTTGAT
5998 TACTCCATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 33 0.80
20 8 0.20
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:6129 original size:22 final size:22
Alignment explanation
Indices: 6103--6294 Score: 131
Period size: 22 Copynumber: 8.6 Consensus size: 22
6093 AATCGGATTT
*
6103 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
6125 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
6147 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
6169 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
6191 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
* ** **
6213 TGAAATTTTGATTACAACACTA
1 TGAAATTTTGATAACCTCTTTA
6235 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
*
6257 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-C--CTCTTTA
*
6281 TGAAATTTCGATAA
1 TGAAATTTTGATAA
6295 TCACTATATG
Statistics
Matches: 130, Mismatches: 30, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 13 0.10
22 96 0.74
23 2 0.02
24 3 0.02
25 11 0.08
26 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:6192 original size:66 final size:66
Alignment explanation
Indices: 6103--6288 Score: 191
Period size: 66 Copynumber: 2.8 Consensus size: 66
6093 AATCGGATTT
* * * * ** *
6103 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATCTTTATAAAATTTTG-TTGACCCCTC
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATGAAATTTTGATT-ACAACAC
6167 TA
65 TA
* * * *
6169 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATTACAACAC
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATC-TTTATGAAATTTTGATTACAACAC
6233 TA
65 TA
6235 TGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAATCATATCTTTATGAAATTT
1 TGAAATTTTGATAATC-TCATTATGAAATTTTGATAA-C--ATCTTTATGAAATTT
6289 CGATAATCAC
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
65 11 0.11
66 69 0.70
67 8 0.08
68 10 0.10
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (66 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATGAAATTTTGATTACAACACT
A
Found at i:6275 original size:18 final size:19
Alignment explanation
Indices: 6237--6275 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
6227 CAACACTATG
6237 AAATTTTGATAATCTTCATAT
1 AAATTTTGATAA--TTCATAT
6258 AAATTTTGATAA-TCATAT
1 AAATTTTGATAATTCATAT
6276 CTTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTTGATAATTCATAT
Found at i:6300 original size:66 final size:66
Alignment explanation
Indices: 6166--6330 Score: 146
Period size: 66 Copynumber: 2.5 Consensus size: 66
6156 GTTGACCCCT
* ** * * *
6166 CTATGAAATTTTGATAATC-ACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATTACAA
1 CTATGAAATTTTGATAATCTTCA-TATCAAATTTTGATAACATAGCTTTGAAATTTCGATTACAA
6230 CA
65 CA
*
6232 CTATGAAATTTTGATAATCTTCATAT-AAATTTTGATAATCATATCTTTATGAAATTTCGA-TA-
1 CTATGAAATTTTGATAATCTTCATATCAAATTTTGATAA-CATAGC-TT-TGAAATTTCGATTAC
*
6294 ATCA
63 AACA
* *
6298 CTAT-ATGA-TTTGATAATTTTC-TATCAAATTTTG
1 CTATGA-AATTTTGATAATCTTCATATCAAATTTTG
6331 GTACTCCTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
64 3 0.04
65 32 0.38
66 33 0.39
67 6 0.07
68 10 0.12
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (66 bp):
CTATGAAATTTTGATAATCTTCATATCAAATTTTGATAACATAGCTTTGAAATTTCGATTACAAC
A
Found at i:6382 original size:22 final size:22
Alignment explanation
Indices: 6353--6450 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
6343 AAATTGAGAC
6353 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTCATATGAAA
* *
6374 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTTCA-TATGAAA
** *
6396 TTTTGATAACCTTCCGATGAAG
1 TTTTGATAACCTTCATATGAAA
*
6418 TATT-AGTAACCTTC-TAATGAAA
1 TTTTGA-TAACCTTCAT-ATGAAA
*
6440 TTTTGTTAACC
1 TTTTGATAACC
6451 ACACTATAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
21 7 0.12
22 51 0.86
23 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCATATGAAA
Found at i:6645 original size:59 final size:59
Alignment explanation
Indices: 6550--6669 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
6540 AAATTTCAAT
* *
6550 AACCAACCTTAGAAATTTTAATAACTTGATCCTATGAAATTTTGGTAACCACTCTATGA
1 AACCAACCTTAGAAATTTTAATAACTTGATCATATGAAATTTTGGTAACCACACTATGA
6609 AACCAACCTTAGAAATTTTAATAACTTGATCATATGAAATTTTGGTAACCACACTATGA
1 AACCAACCTTAGAAATTTTAATAACTTGATCATATGAAATTTTGGTAACCACACTATGA
6668 AA
1 AA
6670 TTTTGATAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (59 bp):
AACCAACCTTAGAAATTTTAATAACTTGATCATATGAAATTTTGGTAACCACACTATGA
Done.