Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008418.1 Corchorus capsularis cultivar CVL-1 contig08439, 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: 32423
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6217 original size:18 final size:18
Alignment explanation
Indices: 6194--6236 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6184 ATGTGATTTT
6194 ACAAAAAAAAAAAAACAA
1 ACAAAAAAAAAAAAACAA
* *
6212 ACAAAAAGAAAAAAAGAA
1 ACAAAAAAAAAAAAACAA
6230 A-AAAAAA
1 ACAAAAAA
6237 GGTTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (18 bp):
ACAAAAAAAAAAAAACAA
Found at i:7288 original size:7 final size:7
Alignment explanation
Indices: 7278--7305 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
7268 ATCAAAGACC
7278 AAAGAAA
1 AAAGAAA
7285 AAAGAAA
1 AAAGAAA
7292 AAAGAAA
1 AAAGAAA
7299 AAAGAAA
1 AAAGAAA
7306 TGAAGGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:13127 original size:136 final size:134
Alignment explanation
Indices: 12904--13158 Score: 352
Period size: 136 Copynumber: 1.9 Consensus size: 134
12894 TTATAACAAA
* * * * *
12904 ATGCCCCTACATAATGACGTTTCTAATAAATAAACGTCTCTAAACGGTTTATTTATTTTTTTTAT
1 ATGCCCCTAAATAATGACGTTTCTAATAAAAAAACGCCCCTAAACGGTTTATTTATTTTTTTAAT
* *
12969 CTTTCCTTGAATTATTTTGGGGGGGAATTTTTCCCACCCATATTTCTAATTTAGCGGCGTTTTTT
66 CTTTCCTTGAATTA-TTTGGGGGGAAAATTTTCCCA-CCATATTTCTAATTTAGCGGCGTTTTTT
13034 TCAGAC
129 TCAGAC
* *
13040 ATGCCCCTAAATAGTGGCGTTTCTAATAAAAAAACGCCCCTAAACGGTTTATTTA-TTTTTTAA-
1 ATGCCCCTAAATAATGACGTTTCTAATAAAAAAACGCCCCTAAACGGTTTATTTATTTTTTTAAT
* * *
13103 CTTTTCCTTGAATTATATTGGGGGGAAAATTTTCCCACCATTTTTTTTATTTAGCG
66 C-TTTCCTTGAATTAT-TTGGGGGGAAAATTTTCCCACCATATTTCTAATTTAGCG
13159 ACGATTCTCT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
134 18 0.17
135 38 0.36
136 49 0.47
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (134 bp):
ATGCCCCTAAATAATGACGTTTCTAATAAAAAAACGCCCCTAAACGGTTTATTTATTTTTTTAAT
CTTTCCTTGAATTATTTGGGGGGAAAATTTTCCCACCATATTTCTAATTTAGCGGCGTTTTTTTC
AGAC
Found at i:15823 original size:24 final size:25
Alignment explanation
Indices: 15778--15824 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
15768 TTGAAGTATA
**
15778 TATTTATCTTGTTGCTTAATTTTAT
1 TATTTATCTTGTTAATTAATTTTAT
*
15803 TATTT-TCTTGTTAATTTATTTT
1 TATTTATCTTGTTAATTAATTTT
15825 TATAGTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (25 bp):
TATTTATCTTGTTAATTAATTTTAT
Found at i:19437 original size:41 final size:40
Alignment explanation
Indices: 19386--19525 Score: 210
Period size: 41 Copynumber: 3.5 Consensus size: 40
19376 AAGCTGACGG
*
19386 CCCTAGATTGAAAACTTTGAAAATAACTTGATGGGATCTTT
1 CCCTAAATTGAAAACTTTGAAAA-AACTTGATGGGATCTTT
*
19427 CCCTAAATTGAAAACTTTGAAAAAAACTTGATGGAATCTTT
1 CCCTAAATTGAAAACTTTG-AAAAAACTTGATGGGATCTTT
* **
19468 CCCTAAATTGAAAACTTT-AAGAAACTTGATAAGATCTTT
1 CCCTAAATTGAAAACTTTGAAAAAACTTGATGGGATCTTT
19507 CCCTAAATTGAAAACTTTG
1 CCCTAAATTGAAAACTTTG
19526 GAAACTTCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
39 35 0.38
41 52 0.57
42 4 0.04
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (40 bp):
CCCTAAATTGAAAACTTTGAAAAAACTTGATGGGATCTTT
Found at i:22726 original size:19 final size:19
Alignment explanation
Indices: 22702--22741 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
22692 GGCAAGTAGG
22702 GGTCGAATCCCACAGAGAA
1 GGTCGAATCCCACAGAGAA
22721 GGTCGAATCCCACAGAGAA
1 GGTCGAATCCCACAGAGAA
22740 GG
1 GG
22742 GTAGTAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.30, T:0.10
Consensus pattern (19 bp):
GGTCGAATCCCACAGAGAA
Found at i:28940 original size:15 final size:15
Alignment explanation
Indices: 28922--28951 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28912 TTACTTTTGC
*
28922 TACTTTTATCATTTT
1 TACTTTTACCATTTT
28937 TACTTTTACCATTTT
1 TACTTTTACCATTTT
28952 CTTACTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:29104 original size:14 final size:14
Alignment explanation
Indices: 29085--29129 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
29075 ATTTTTTGAC
*
29085 CTTCTTACTCATTA
1 CTTCTTACTGATTA
29099 CTTCTTACTGATTA
1 CTTCTTACTGATTA
29113 CTT-TTACCTGATTA
1 CTTCTTA-CTGATTA
29127 CTT
1 CTT
29130 TTTTACTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 3 0.10
14 26 0.90
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.51
Consensus pattern (14 bp):
CTTCTTACTGATTA
Found at i:29172 original size:21 final size:22
Alignment explanation
Indices: 29148--29190 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
29138 CTCTTTGACA
*
29148 TTTTTA-CTCTTTACTGATTAC
1 TTTTTACCTCTTTACCGATTAC
*
29169 -TTTTACCTTTTTACCGATTAC
1 TTTTTACCTCTTTACCGATTAC
29190 T
1 T
29191 CTTAGCTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTTTACCTCTTTACCGATTAC
Found at i:29460 original size:33 final size:33
Alignment explanation
Indices: 29423--29718 Score: 266
Period size: 33 Copynumber: 9.3 Consensus size: 33
29413 CTAAACACTC
*
29423 CTTTTACTTTTACTCCATTTTTACTGATTACTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
* *
29456 CTTTTACTCTTTCTTCA-TTTTACTGATTACTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
* * * * *
29488 CTTCTACTGATTACTTCTC-TTGATTAC-CATT-TTT
1 CTTTTACT-CTTAC-TC-CATT-TTTACTGATTACTT
* *
29522 CTGATTACTTCTT-CTACA-TTTTACTGATTACTT
1 CT-TTTAC-TCTTACTCCATTTTTACTGATTACTT
*
29555 C---T--TC-TA---C--TTTTACTAATTACTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
*
29577 CGTTTACTCTTACTCCATTTTTACTGATTACTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
* * *
29610 CGTTTACTCTTGCTCCATTTTTACTGATTTCTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
*
29643 CTTTTACTCTTACTCCATTTTTACTGATTTCTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
*
29676 CTTTTACTCTTACTCCATTTTTACTGATTATTT
1 CTTTTACTCTTACTCCATTTTTACTGATTACTT
29709 CTTTTACTCT
1 CTTTTACTCT
29719 CTCCCTTAAG
Statistics
Matches: 216, Mismatches: 25, Indels: 44
0.76 0.09 0.15
Matches are distributed among these distances:
22 15 0.07
23 1 0.00
25 2 0.01
26 2 0.01
27 2 0.01
28 2 0.01
29 1 0.00
31 5 0.02
32 27 0.12
33 138 0.64
34 6 0.03
35 10 0.05
36 5 0.02
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.55
Consensus pattern (33 bp):
CTTTTACTCTTACTCCATTTTTACTGATTACTT
Found at i:29495 original size:16 final size:16
Alignment explanation
Indices: 29444--29538 Score: 78
Period size: 16 Copynumber: 6.2 Consensus size: 16
29434 ACTCCATTTT
*
29444 TACTGATTACTTCTTT
1 TACTGATTACTTCTTC
* * *
29460 TACT-CTTTCTTCATTT
1 TACTGATTACTTC-TTC
29476 TACTGATTACTTCTTC
1 TACTGATTACTTCTTC
29492 TACTGATTACTTC-TC
1 TACTGATTACTTCTTC
29507 T--TGATTACCATT-TT-
1 TACTGATTA-C-TTCTTC
29521 T-CTGATTACTTCTTC
1 TACTGATTACTTCTTC
29536 TAC
1 TAC
29539 ATTTTACTGA
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
13 8 0.12
14 5 0.08
15 19 0.29
16 27 0.42
17 6 0.09
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (16 bp):
TACTGATTACTTCTTC
Found at i:29511 original size:13 final size:15
Alignment explanation
Indices: 29479--29537 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
29469 TTCATTTTAC
29479 TGATTACTTCTTCTA
1 TGATTACTTCTTCTA
29494 CTGATTACTTC-TCT-
1 -TGATTACTTCTTCTA
*
29508 TGATTACCATT-TT-TC
1 TGATTA-C-TTCTTCTA
29523 TGATTACTTCTTCTA
1 TGATTACTTCTTCTA
29538 CATTTTACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
13 8 0.22
14 5 0.14
15 13 0.36
16 10 0.28
ACGTcount: A:0.19, C:0.22, G:0.07, T:0.53
Consensus pattern (15 bp):
TGATTACTTCTTCTA
Found at i:29541 original size:23 final size:23
Alignment explanation
Indices: 29515--29577 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
29505 TCTTGATTAC
*
29515 CATTTTTCTGATTACTTCTTCTA
1 CATTTTACTGATTACTTCTTCTA
29538 CATTTTACTGATTACTTCTTCTA
1 CATTTTACTGATTACTTCTTCTA
*
29561 C-TTTTACTAATTACTTC
1 CATTTTACTGATTACTTC
29578 GTTTACTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 15 0.39
23 23 0.61
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.54
Consensus pattern (23 bp):
CATTTTACTGATTACTTCTTCTA
Found at i:29568 original size:22 final size:22
Alignment explanation
Indices: 29517--29590 Score: 96
Period size: 22 Copynumber: 3.3 Consensus size: 22
29507 TTGATTACCA
*
29517 TTTTTCTGATTACTTCTTCTAC
1 TTTTACTGATTACTTCTTCTAC
29539 ATTTTACTGATTACTTCTTCTAC
1 -TTTTACTGATTACTTCTTCTAC
*
29562 TTTTACTAATTACTTCGTT-TAC
1 TTTTACTGATTACTTC-TTCTAC
*
29584 TCTTACT
1 TTTTACT
29591 CCATTTTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 24 0.51
23 23 0.49
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTTACTGATTACTTCTTCTAC
Found at i:29649 original size:16 final size:16
Alignment explanation
Indices: 29628--29683 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
29618 CTTGCTCCAT
29628 TTTTACTGATTTCTTC
1 TTTTACTGATTTCTTC
* * *
29644 TTTTACT-CTTACTCC
1 TTTTACTGATTTCTTC
29659 ATTTTTACTGATTTCTTC
1 --TTTTACTGATTTCTTC
29677 TTTTACT
1 TTTTACT
29684 CTTACTCCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 14 0.45
17 7 0.23
18 5 0.16
ACGTcount: A:0.14, C:0.21, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTTACTGATTTCTTC
Found at i:29849 original size:39 final size:38
Alignment explanation
Indices: 29723--29920 Score: 183
Period size: 38 Copynumber: 5.2 Consensus size: 38
29713 TACTCTCTCC
* * *
29723 CTTAAGTATCAA-TTTACTGATTAATC---CCTTGACT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
* * *
29757 CTTAATTA-CTGA-TTTACTGATTACTATTTTTACCTTGACT
1 CTTAATTATC-AATTTTACTGA-T--TATTCTTACTTTGACT
* *
29797 CTTGATTATCAATTTTACTGATTGTTCTTACTTTGACTT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGAC-T
* * *
29836 CTTAATTATCAATTTTTACTGATTACTATTAATTTGACT
1 CTTAATTATCAA-TTTTACTGATTATTCTTACTTTGACT
* *
29875 CTTAATTATCAATTTTACTGAATATCCTTACTTTGACT
1 CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
29913 CTTAATTA
1 CTTAATTA
29921 CTTAATTCAC
Statistics
Matches: 134, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
33 1 0.01
34 16 0.12
35 1 0.01
37 3 0.02
38 41 0.31
39 25 0.19
40 38 0.28
41 9 0.07
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (38 bp):
CTTAATTATCAATTTTACTGATTATTCTTACTTTGACT
Found at i:29883 original size:78 final size:76
Alignment explanation
Indices: 29751--29957 Score: 240
Period size: 78 Copynumber: 2.7 Consensus size: 76
29741 GATTAATCCC
* * * *
29751 TTGACTCTTAATTACT-GATTTACTGATTACTATTTTTACCTTGACTCTTGATTATCAATTTTAC
1 TTGACTCTTAATTACTCAATTCACTGATTACTA---TTATCTTGACTCTTAATTATCAATTTTAC
* * *
29815 TGATTGTTCTTACT
63 TGAATATCCTTACT
*
29829 TTGACTTCTTAATTA-TCAATTTTTACTGATTACTATTAAT-TTGACTCTTAATTATCAATTTTA
1 TTGAC-TCTTAATTACTCAA--TTCACTGATTACTATT-ATCTTGACTCTTAATTATCAATTTTA
29892 CTGAATATCCTTACT
62 CTGAATATCCTTACT
* *
29907 TTGACTCTTAATTACTTAATTCACTGGTTACTATTATCTTGACTCTTAATT
1 TTGACTCTTAATTACTCAATTCACTGATTACTATTATCTTGACTCTTAATT
29958 TATTGGGGTA
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
75 2 0.02
76 27 0.24
77 9 0.08
78 50 0.44
79 11 0.10
81 14 0.12
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.50
Consensus pattern (76 bp):
TTGACTCTTAATTACTCAATTCACTGATTACTATTATCTTGACTCTTAATTATCAATTTTACTGA
ATATCCTTACT
Found at i:31838 original size:1 final size:1
Alignment explanation
Indices: 31834--31871 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
31824 TTAGGCCCAG
31834 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31872 AGGCATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.