Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012749.1 Corchorus capsularis cultivar CVL-1 contig12770, 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: 6585
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Found at i:330 original size:20 final size:18
Alignment explanation
Indices: 305--349 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
295 TCACCCAATT
305 TTTTTTTTAAAAAAAGTATA
1 TTTTTTTTAAAAAAA--ATA
**
325 TTTTTTTTTCAAAAAATA
1 TTTTTTTTAAAAAAAATA
343 TTTTTTT
1 TTTTTTT
350 AATCAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTTTTAAAAAAAATA
Found at i:357 original size:18 final size:18
Alignment explanation
Indices: 322--357 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
312 TAAAAAAAGT
*
322 ATATTTTTTTTTCAAAAA
1 ATATTTTTTTATCAAAAA
340 ATATTTTTTTAATCAAAA
1 ATATTTTTTT-ATCAAAA
358 TGTATGGCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTTTTTATCAAAAA
Found at i:789 original size:74 final size:74
Alignment explanation
Indices: 668--823 Score: 271
Period size: 74 Copynumber: 2.1 Consensus size: 74
658 CGGAGGTTTC
*
668 AATGAGTTTAGATAATAATAAATATTAGAAAGGCTTTGCTTCAATCTTTTTGGGGTTTGAAATTA
1 AATGAGTTTAGATAATAATAAATATTAGAAAGGCTTTACTTCAATCTTTTTGGGGTTTGAAATTA
733 AATGATAGT
66 AATGATAGT
*
742 AATGAGTTTAGATAATAATAAATATTTA-AATGGCTTTACTTCAATCTTTTTGGGGTTTGAAATT
1 AATGAGTTTAGATAATAATAAATA-TTAGAAAGGCTTTACTTCAATCTTTTTGGGGTTTGAAATT
806 AAATGATAGT
65 AAATGATAGT
816 AA-GAGTTT
1 AATGAGTTT
824 TGTTTTTTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
73 6 0.08
74 70 0.89
75 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (74 bp):
AATGAGTTTAGATAATAATAAATATTAGAAAGGCTTTACTTCAATCTTTTTGGGGTTTGAAATTA
AATGATAGT
Found at i:1369 original size:29 final size:29
Alignment explanation
Indices: 1335--1398 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 29
1325 ACTTTTGCTA
*
1335 CTTTTATCATTTTTACTCTTTTCTCACTCT
1 CTTTTAT-ATATTTACTCTTTTCTCACTCT
*
1365 -TTTTA-ATATTTACTCTTTTCTTACTCT
1 CTTTTATATATTTACTCTTTTCTCACTCT
1392 CTTTTAT
1 CTTTTAT
1399 TGATTACCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 20 0.67
28 5 0.17
29 5 0.17
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (29 bp):
CTTTTATATATTTACTCTTTTCTCACTCT
Found at i:1533 original size:35 final size:36
Alignment explanation
Indices: 1490--1561 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 36
1480 TTATCATCTT
1490 TACTGATTA-CTATTTTACTC-TTACTGATTACCTTC
1 TACTGATTATC-ATTTTACTCTTTACTGATTACCTTC
1525 TACTGATTATCATTTTACTCTTTACTGATTACCTTC
1 TACTGATTATCATTTTACTCTTTACTGATTACCTTC
1561 T
1 T
1562 TACTTTTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (36 bp):
TACTGATTATCATTTTACTCTTTACTGATTACCTTC
Found at i:1542 original size:22 final size:22
Alignment explanation
Indices: 1517--1682 Score: 119
Period size: 22 Copynumber: 8.0 Consensus size: 22
1507 CTCTTACTGA
1517 TTAC-CTTCTACTGATTATCATT
1 TTACTCTT-TACTGATTATCATT
*
1539 TTACTCTTTACTGATTA-CCTT
1 TTACTCTTTACTGATTATCATT
*
1560 CTTACTTTTTACTGATTAAT-ATT
1 -TTACTCTTTACTGATT-ATCATT
*
1583 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTATCATT
* *
1605 TTGCTC-TTACTGATTA-CCTT
1 TTACTCTTTACTGATTATCATT
1625 TTA--C--TA---ATTACT-ATT
1 TTACTCTTTACTGATTA-TCATT
*
1640 TTACTCTTTACTGATTA-CCTT
1 TTACTCTTTACTGATTATCATT
*
1661 CTTACT-TTTACTGATTACCATT
1 -TTACTCTTTACTGATTATCATT
1683 ACTTTTTACC
Statistics
Matches: 116, Mismatches: 11, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
14 4 0.03
15 5 0.04
17 3 0.03
18 1 0.01
19 2 0.02
20 5 0.04
21 27 0.23
22 63 0.54
23 6 0.05
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTCTTTACTGATTATCATT
Found at i:1612 original size:101 final size:100
Alignment explanation
Indices: 1486--1677 Score: 323
Period size: 101 Copynumber: 1.9 Consensus size: 100
1476 CTGATTATCA
* *
1486 TCTTTACTGATTACTATTTTACTCTTACTGATTACCTTCTACTGATTA-TCATTTTACTCTTTAC
1 TCTTTACTGATTACCATTTTACTCTTACTGATTACCTTCTACTAATTACT-ATTTTACTCTTTAC
1550 TGATTACCTTCTTACTTTTTACTGATTAATATTTTAC
65 TGATTACCTTCTTAC-TTTTACTGATTAATATTTTAC
* *
1587 TCTTTACTGATTACCATTTTGCTCTTACTGATTACCTTTTACTAATTACTATTTTACTCTTTACT
1 TCTTTACTGATTACCATTTTACTCTTACTGATTACCTTCTACTAATTACTATTTTACTCTTTACT
1652 GATTACCTTCTTACTTTTACTGATTA
66 GATTACCTTCTTACTTTTACTGATTA
1678 CCATTACTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
100 12 0.14
101 73 0.85
102 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.52
Consensus pattern (100 bp):
TCTTTACTGATTACCATTTTACTCTTACTGATTACCTTCTACTAATTACTATTTTACTCTTTACT
GATTACCTTCTTACTTTTACTGATTAATATTTTAC
Found at i:1654 original size:57 final size:57
Alignment explanation
Indices: 1561--1704 Score: 184
Period size: 57 Copynumber: 2.5 Consensus size: 57
1551 GATTACCTTC
* * * *
1561 TTACTTTTTACTGATTAATATTTTACTCTTTACTGATTACCATT-TTGCTCTTACTGA
1 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACC-TTCTTACTCTTACTGA
*
1618 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGA
1 TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTTCTTACTCTTACTGA
* ** *
1675 TTACC-ATTACTTTTTACCATTTTACTCTTT
1 TTACCTTTTACTAATTACTATTTTACTCTTT
1705 GAATTTAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
56 23 0.30
57 54 0.70
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (57 bp):
TTACCTTTTACTAATTACTATTTTACTCTTTACTGATTACCTTCTTACTCTTACTGA
Found at i:1672 original size:36 final size:35
Alignment explanation
Indices: 1589--1666 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
1579 TATTTTACTC
* * *
1589 TTTACTGATTACCATTTTGCTCTTACTGATTACCT
1 TTTACTAATTACTATTTTACTCTTACTGATTACCT
1624 TTTACTAATTACTATTTTACTCTTTACTGATTACCT
1 TTTACTAATTACTATTTTACTC-TTACTGATTACCT
1660 TCTTACT
1 T-TTACT
1667 TTTACTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 19 0.50
36 14 0.37
37 5 0.13
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (35 bp):
TTTACTAATTACTATTTTACTCTTACTGATTACCT
Found at i:1823 original size:26 final size:26
Alignment explanation
Indices: 1794--1847 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1784 CATTTTACTG
*
1794 ATTACTATTTT-ACTCTCTTGAATTTA
1 ATTACTATTTTCACTCT-TTGAACTTA
1820 ATTACTATTTTCACTCTTTGAACTTA
1 ATTACTATTTTCACTCTTTGAACTTA
1846 AT
1 AT
1848 CACCATTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTACTATTTTCACTCTTTGAACTTA
Found at i:1855 original size:26 final size:26
Alignment explanation
Indices: 1800--1855 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1790 ACTGATTACT
* * *
1800 ATTTTACTCTCTTGAATTTAATTACT
1 ATTTTACTCTCTTGAACTTAATCACC
1826 ATTTTCACTCT-TTGAACTTAATCACC
1 ATTTT-ACTCTCTTGAACTTAATCACC
1852 ATTT
1 ATTT
1856 GCCATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTTACTCTCTTGAACTTAATCACC
Found at i:1870 original size:32 final size:33
Alignment explanation
Indices: 1834--1897 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1824 CTATTTTCAC
*
1834 TCTTTGAACTTAATCACCA-TTTGCCATTTTAT
1 TCTTTGAACTTAATCACCATTTTACCATTTTAT
* *
1866 TCTTTGAATTTAATTACCATTTTACCATTTTA
1 TCTTTGAACTTAATCACCATTTTACCATTTTA
1898 CCCTTTACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50
Consensus pattern (33 bp):
TCTTTGAACTTAATCACCATTTTACCATTTTAT
Found at i:1983 original size:40 final size:41
Alignment explanation
Indices: 1939--2036 Score: 137
Period size: 40 Copynumber: 2.4 Consensus size: 41
1929 TTTTTATTCT
*
1939 TTACCGATTTACTGATCACTTCTTTTACTTTTACTC-TTAA
1 TTACCGATTTACTGATCACTTCTTTTACTTTGACTCTTTAA
*
1979 TTACC-ATTTTACTGATTACTTCTTTTACTTTGACTCTTTAA
1 TTACCGA-TTTACTGATCACTTCTTTTACTTTGACTCTTTAA
*
2020 TTACTGATTTCACTGAT
1 TTACCGATTT-ACTGAT
2037 AAATCTCTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
39 1 0.02
40 32 0.63
41 11 0.22
42 7 0.14
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.51
Consensus pattern (41 bp):
TTACCGATTTACTGATCACTTCTTTTACTTTGACTCTTTAA
Found at i:5751 original size:27 final size:27
Alignment explanation
Indices: 5709--5805 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
5699 AAGGTGAACT
*
5709 TAAAGAATGACTAAAATGCCCCC-GAGTG
1 TAAA-AATGACCAAAATGCCCCCGGA-TG
* *
5737 TAAAAATTACCAAAATGCCCCTGGATG
1 TAAAAATGACCAAAATGCCCCCGGATG
* * * **
5764 TTAAAATGACCAAAATACCCCTGGGCG
1 TAAAAATGACCAAAATGCCCCCGGATG
*
5791 CAAAAATGACCAAAA
1 TAAAAATGACCAAAA
5806 CACCCTTGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 52 0.90
28 6 0.10
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
TAAAAATGACCAAAATGCCCCCGGATG
Found at i:5810 original size:27 final size:27
Alignment explanation
Indices: 5766--5817 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5756 CCTGGATGTT
*
5766 AAAATGACCAAAATACCCCTGGGCGCA
1 AAAATGACCAAAACACCCCTGGGCGCA
*
5793 AAAATGACCAAAACACCCTTGGGCG
1 AAAATGACCAAAACACCCCTGGGCG
5818 ACCCTAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (27 bp):
AAAATGACCAAAACACCCCTGGGCGCA
Done.