Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009988.1 Corchorus capsularis cultivar CVL-1 contig10009, 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: 21643
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:6369 original size:19 final size:18
Alignment explanation
Indices: 6345--6381 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6335 TTGAAGATTT
6345 CTTGAAGACAATTTGAAGA
1 CTTGAAGACAA-TTGAAGA
*
6364 CTTGAAGACCATTGAAGA
1 CTTGAAGACAATTGAAGA
6382 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (18 bp):
CTTGAAGACAATTGAAGA
Found at i:9982 original size:18 final size:16
Alignment explanation
Indices: 9956--10005 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
9946 AAAAAAGGAG
*
9956 AAAAGTCAAATCAGAAAA
1 AAAAATCAAAT-A-AAAA
9974 AAAAATCAAAT-AAAA
1 AAAAATCAAATAAAAA
*
9989 AAAAA-GAAATAAAAA
1 AAAAATCAAATAAAAA
10004 AA
1 AA
10006 GTGATGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 4 0.14
15 15 0.52
18 10 0.34
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAATCAAATAAAAA
Found at i:9988 original size:15 final size:14
Alignment explanation
Indices: 9970--10005 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
9960 GTCAAATCAG
9970 AAAAAAAAATCAAAT
1 AAAAAAAAA-CAAAT
*
9985 AAAAAAAAAGAAAT
1 AAAAAAAAACAAAT
9999 AAAAAAA
1 AAAAAAA
10006 GTGATGGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (14 bp):
AAAAAAAAACAAAT
Found at i:14470 original size:17 final size:17
Alignment explanation
Indices: 14448--14481 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14438 GTTTGGTTGA
*
14448 AGGGGTTGCAAGGGGTG
1 AGGGGTAGCAAGGGGTG
*
14465 AGGGGTAGGAAGGGGTG
1 AGGGGTAGCAAGGGGTG
14482 GTCATCACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.62, T:0.15
Consensus pattern (17 bp):
AGGGGTAGCAAGGGGTG
Found at i:15108 original size:15 final size:15
Alignment explanation
Indices: 15090--15131 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
15080 CCAACTCCTC
*
15090 CCCCTCCCTACCCCA
1 CCCCTCCCCACCCCA
15105 CCCCTCCCCACCCCA
1 CCCCTCCCCACCCCA
15120 CCCCTCCTCCAC
1 CCCCTCC-CCAC
15132 TTGAACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.12, C:0.76, G:0.00, T:0.12
Consensus pattern (15 bp):
CCCCTCCCCACCCCA
Found at i:20073 original size:22 final size:22
Alignment explanation
Indices: 20032--20430 Score: 170
Period size: 22 Copynumber: 18.5 Consensus size: 22
20022 AGCATCACTA
20032 TTTTACTGTATTA-T-TCTTTACT
1 TTTTACTG-ATTACTAT-TTTACT
*
20054 TTGTACTGATTACTATTTTACT
1 TTTTACTGATTACTATTTTACT
*
20076 CTTGTTA---ATTACCT-TCTTACT
1 -TT-TTACTGATTA-CTATTTTACT
*
20097 TTTTACTGATTACCATTTTACT
1 TTTTACTGATTACTATTTTACT
*
20119 CTTTTACTGATTACTATTTTCTGCTCCTT
1 -TTTTACTGATTACTA--TT-T--TAC-T
*
20148 TTTTACTGATTACTCTTTTACT
1 TTTTACTGATTACTATTTTACT
* * *
20170 TTTTACTGATTGC-CTTTTGCT
1 TTTTACTGATTACTATTTTACT
20191 TTTTACTGATTACCT-TTTTACT
1 TTTTACTGATTA-CTATTTTACT
* *
20213 TCTTGCTGATTAGCT-TTTTACT
1 TTTTACTGATTA-CTATTTTACT
* *
20235 CTTTACTGATCACCT-TTTTAC-
1 TTTTACTGATTA-CTATTTTACT
* * *
20256 TCTTACCGA-T-CTCCTTTTACT
1 TTTTACTGATTACT-ATTTTACT
* *
20277 TCTTACTTATTAC-----T--T
1 TTTTACTGATTACTATTTTACT
*
20292 TTTTACTGATTACTATTTACA-T
1 TTTTACTGATTACTATTT-TACT
*
20314 TTT-ACTGACTACTATTTTACT
1 TTTTACTGATTACTATTTTACT
* * *
20335 CTTGT--TGATTACCT-TCTTAAT
1 -TTTTACTGATTA-CTATTTTACT
20356 TTTTACTGATTACTATTTTACT
1 TTTTACTGATTACTATTTTACT
* * * *
20378 CTTTACTAATTACCATTTTACC
1 TTTTACTGATTACTATTTTACT
* *
20400 CTTT-CAGA-TACCT-TTTTACT
1 TTTTACTGATTA-CTATTTTACT
20420 TTTTACTGATT
1 TTTTACTGATT
20431 GCATGCTATT
Statistics
Matches: 288, Mismatches: 49, Indels: 80
0.69 0.12 0.19
Matches are distributed among these distances:
15 12 0.04
17 1 0.00
18 2 0.01
19 3 0.01
20 23 0.08
21 78 0.27
22 124 0.43
23 20 0.07
24 2 0.01
25 3 0.01
26 3 0.01
28 16 0.06
29 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTACTGATTACTATTTTACT
Found at i:20132 original size:15 final size:15
Alignment explanation
Indices: 20114--20169 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
20104 GATTACCATT
20114 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
20129 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
20142 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
20157 TTACTCTTTTACT
1 TTACTCTTTTACT
20170 TTTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:20153 original size:116 final size:113
Alignment explanation
Indices: 20032--20244 Score: 259
Period size: 116 Copynumber: 1.8 Consensus size: 113
20022 AGCATCACTA
*
20032 TTTTACTGTATTATTC-TTTACTTTGTACTGATTACTATTTTACTCTTGTTA-ATTACCTTCTTA
1 TTTTACTG-ATTACTCTTTTACTTTGTACTGATTAC-ATTTTACT-TT-TTACATTACCTTCTTA
*
20095 CTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTTTCTGCTCCTT
62 CTTCTTACTGATTACCATTTTACTC-TTTACTGATTACTATTTTCTGCTCCTT
* * * * *
20148 TTTTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTGCTTTTTACTGATTACCTTTTTACT
1 TTTTACTGATTACTCTTTTACTTTGTACTGATTACATTTTACTTTTTAC--ATTACCTTCTTACT
* * *
20213 TCTTGCTGATTAGCTTTTTACTCTTTACTGAT
64 TCTTACTGATTACCATTTTACTCTTTACTGAT
20245 CACCTTTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
113 3 0.04
114 2 0.02
115 21 0.25
116 57 0.69
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (113 bp):
TTTTACTGATTACTCTTTTACTTTGTACTGATTACATTTTACTTTTTACATTACCTTCTTACTTC
TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTCTGCTCCTT
Found at i:20194 original size:43 final size:43
Alignment explanation
Indices: 20147--20432 Score: 174
Period size: 43 Copynumber: 6.8 Consensus size: 43
20137 TTCTGCTCCT
* *
20147 TTTTTACTGATTA-CTCTTTTACTTTTTACTGATTGCCTTTTGC
1 TTTTTACTGATTACCT-TTTTACTTCTTACTGATTGCCTTTTAC
* *
20190 TTTTTACTGATTACCTTTTTACTTCTTGCTGATTAGCTTTTTAC
1 TTTTTACTGATTACCTTTTTACTTCTTACTGATT-GCCTTTTAC
* * *
20234 TCTTTACTGATCACCTTTTTAC-TCTTACCGATCT-CCTTTTAC
1 TTTTTACTGATTACCTTTTTACTTCTTACTGAT-TGCCTTTTAC
* * *
20276 TTCTTACTTATTA-C---TT--TT-TTACTGATT-ACTATTTAC
1 TTTTTACTGATTACCTTTTTACTTCTTACTGATTGCCT-TTTAC
* * ** * *
20312 ATTTTACTGACTA-CTATTTTAC-TCTTGTTGATTACCTTCTTAA
1 TTTTTACTGATTACCT-TTTTACTTCTTACTGATTGCCTT-TTAC
* *
20355 TTTTTACTGATTA-CTATTTTAC-TCTTTACTAATTACCATTTTAC
1 TTTTTACTGATTACCT-TTTTACTTC-TTACTGATTGCC-TTTTAC
** * *
20399 CCTTT-CAGA-TACCTTTTTACTTTTTACTGATTGC
1 TTTTTACTGATTACCTTTTTACTTCTTACTGATTGC
20433 ATGCTATTCT
Statistics
Matches: 190, Mismatches: 35, Indels: 37
0.73 0.13 0.14
Matches are distributed among these distances:
35 3 0.02
36 22 0.12
37 1 0.01
38 2 0.01
40 2 0.01
41 2 0.01
42 41 0.22
43 70 0.37
44 45 0.24
45 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (43 bp):
TTTTTACTGATTACCTTTTTACTTCTTACTGATTGCCTTTTAC
Found at i:20359 original size:64 final size:64
Alignment explanation
Indices: 20291--20430 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 64
20281 ACTTATTACT
* * * *
20291 TTTTTACTGATTACTA-TTTACAT-TTTACTGACTACTATTTTACTCTTGT-TGATTACCTTCTT
1 TTTTTACTGATTACTATTTTAC-TCTTTACTAACTACCATTTTACCCTT-TCAGA-TACCTTCTT
20353 AA
63 AA
* * *
20355 TTTTTACTGATTACTATTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATACCTTTTTAC
1 TTTTTACTGATTACTATTTTACTCTTTACTAACTACCATTTTACCCTTTCAGATACCTTCTTAA
20419 TTTTTACTGATT
1 TTTTTACTGATT
20431 GCATGCTATT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
64 39 0.59
65 27 0.41
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.54
Consensus pattern (64 bp):
TTTTTACTGATTACTATTTTACTCTTTACTAACTACCATTTTACCCTTTCAGATACCTTCTTAA
Found at i:20417 original size:143 final size:143
Alignment explanation
Indices: 20145--20426 Score: 320
Period size: 143 Copynumber: 2.0 Consensus size: 143
20135 TTTTCTGCTC
* * * * * * * *
20145 CTTTTTTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTGCTTTTTACTGATTACCTTTTT
1 CTTTTTTACTGATTACTCATTTACATTTTACTGACTACATTTTACTTTGTA-TGATTACCTTCTT
* * * * * *
20210 ACTTCTTGCTGATTAGCTTTTTACTCTTTACTGATCACCTTTTTACTCTTACCGATCTCCTTTTA
65 AATTCTTACTGATTAGCTTTTTACTCTTTACTAATCACCATTTTACCCTTACAGATCTCCTTTTA
20275 CTTCTTACTTATTA
130 CTTCTTACTTATTA
20289 CTTTTTTACTGATTACT-ATTTACATTTTACTGACTACTATTTTACTCTTGT-TGATTACCTTCT
1 CTTTTTTACTGATTACTCATTTACATTTTACTGACTAC-ATTTTACT-TTGTATGATTACCTTCT
* * * *
20352 TAATTTTTACTGATTA-CTATTTTACTCTTTACTAATTACCATTTTACCCTTTCAGATAC-CTTT
64 TAATTCTTACTGATTAGCT-TTTTACTCTTTACTAATCACCATTTTACCCTTACAGAT-CTCCTT
*
20415 TTACTTTTTACT
127 TTACTTCTTACT
20427 GATTGCATGC
Statistics
Matches: 115, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
142 2 0.02
143 86 0.75
144 24 0.21
145 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (143 bp):
CTTTTTTACTGATTACTCATTTACATTTTACTGACTACATTTTACTTTGTATGATTACCTTCTTA
ATTCTTACTGATTAGCTTTTTACTCTTTACTAATCACCATTTTACCCTTACAGATCTCCTTTTAC
TTCTTACTTATTA
Found at i:20682 original size:63 final size:62
Alignment explanation
Indices: 20615--20734 Score: 190
Period size: 63 Copynumber: 1.9 Consensus size: 62
20605 CATTTTAACT
20615 CTTAATTA-TCGATTTACTGATTACTATTACT-TTGACTCTGATTAATCTCTTTTTACTTAATTA
1 CTTAATTACT-GATTTACTGATTACTATTACTCTTGA--CTGATTAATCTCTTTTTACTTAATTA
*
20678 CTTAATTACTGATTTACTGATTACTATTACTCTTTACTGATTAATCTCTTTTTACTT
1 CTTAATTACTGATTTACTGATTACTATTACTCTTGACTGATTAATCTCTTTTTACTT
20735 TTTAGATTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
62 21 0.39
63 29 0.54
64 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (62 bp):
CTTAATTACTGATTTACTGATTACTATTACTCTTGACTGATTAATCTCTTTTTACTTAATTA
Found at i:21489 original size:101 final size:102
Alignment explanation
Indices: 21379--21643 Score: 293
Period size: 102 Copynumber: 2.6 Consensus size: 102
21369 AACTAATCAA
* ** *** *
21379 TTTATTTACTAATGA-TCTAAAAAGTTTAAACTTCTAATTCAAAGGTGACA-TTTTACTTACTAA
1 TTTATTTACTAATGACTCTAAAAA-TTCAAACTT-TAACCCAAAGACAACACTTTTACTTACCAA
* *
21442 TTACTTAAAAATTC-AATCTTTTATTCAAATGTTAAAGC
64 TTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAAGC
* * * *
21480 TTTATTTACTAATGACTCTAAAGATTCAATCTTTTACCCAAAGACAACACTTTTATTTACCAATT
1 TTTATTTACTAATGACTCTAAAAATTCAAACTTTAACCCAAAGACAACACTTTTACTTACCAATT
*
21545 ACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATC
66 ACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAAGC
* * * * ** * *
21582 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCA
1 TTTATTTACTAATGACTCTAAAAATTCAAACTTTAACCCAAAGACAACACTTTTACTTACCA
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
100 10 0.07
101 46 0.32
102 87 0.61
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (102 bp):
TTTATTTACTAATGACTCTAAAAATTCAAACTTTAACCCAAAGACAACACTTTTACTTACCAATT
ACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAAGC
Found at i:21510 original size:51 final size:48
Alignment explanation
Indices: 21430--21617 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 48
21420 AAGGTGACAT
*
21430 TTTACTTACTAATTACTTAAAAATTCAATCTTTTATTCAAATGTTAAAGC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAA-GTTAAA-C
* * ** **
21480 TTTATTTACTAATGACTCTAAAGATTCAATCTTTTACCCAAAGACAACAC
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGTTAA-AC
* *
21530 TTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATC
1 -TTTATTTACTAATTACTTAAAAATTC-AATCTTTTATTCAAA-GTTAAA-C
*
21582 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTA
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTA
21618 CCCAAAGATG
Statistics
Matches: 113, Mismatches: 18, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
50 26 0.23
51 76 0.67
52 11 0.10
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.42
Consensus pattern (48 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGTTAAAC
Found at i:21587 original size:102 final size:101
Alignment explanation
Indices: 21429--21643 Score: 340
Period size: 102 Copynumber: 2.1 Consensus size: 101
21419 AAAGGTGACA
* * * *
21429 TTTTACTTACTAATTACTTAAAAATTCAATCTTTTATTCAAATGTTAAAGCTTTATTTACTAATG
1 TTTTATTTACCAATTACTTAAAAATCCAATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATG
21494 ACTCTAAAGATTCAATCTTTTACCCAAAGACAACAC
66 ACTCTAAAGATTCAATCTTTTACCCAAAGACAACAC
*
21530 TTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAAT
1 TTTTATTTACCAATTACTTAAAAATCC-AATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAAT
* ** *
21595 TACTCTAAAGATTCAATCTTTTACCCAAAGATGACAT
65 GACTCTAAAGATTCAATCTTTTACCCAAAGACAACAC
21632 TTTTATTTACCA
1 TTTTATTTACCA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 24 0.23
102 80 0.77
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (101 bp):
TTTTATTTACCAATTACTTAAAAATCCAATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATG
ACTCTAAAGATTCAATCTTTTACCCAAAGACAACAC
Found at i:21637 original size:51 final size:50
Alignment explanation
Indices: 21418--21641 Score: 200
Period size: 51 Copynumber: 4.4 Consensus size: 50
21408 ACTTCTAATT
* * **
21418 CAAAGGTGACA-TTTTACTTACTAATTACTTAAAAATTCAATCTTTTATT
1 CAAAGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTACC
* * ** * *
21467 CAAATG-TTAAAGCTTTATTTACTAATGACTCTAAAGATTCAATCTTTTACC
1 CAAA-GATGACATTTTTATTTACTAATTACT-TAAAAATTCAATCTTTTACC
** * * * **
21518 CAAAGACAACACTTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATT
1 CAAAGATGACATTTTTATTTACTAATTACTTAAAAATTC-AATCTTTTACC
* * * * *
21569 CAAAGGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAATCTTTTACC
1 CAAAGATGACATTTTTATTTACTAATTACT-TAAAAATTCAATCTTTTACC
21620 CAAAGATGACATTTTTATTTAC
1 CAAAGATGACATTTTTATTTAC
21642 CA
Statistics
Matches: 135, Mismatches: 34, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
49 7 0.05
50 24 0.18
51 97 0.72
52 7 0.05
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (50 bp):
CAAAGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTACC
Done.