Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013457.1 Corchorus capsularis cultivar CVL-1 contig13478, 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: 17382
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Found at i:1159 original size:13 final size:13
Alignment explanation
Indices: 1141--1197 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1131 AATACCAAAT
1141 TACTAAATGAAAA
1 TACTAAATGAAAA
*
1154 TACTAATTGAAAA
1 TACTAAATGAAAA
* * *
1167 CACCATAATGCCAAA
1 TACTA-AATG-AAAA
1182 TCACTAAATGAAAA
1 T-ACTAAATGAAAA
1196 TA
1 TA
1198 TGCAAAAACT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 16 0.48
14 7 0.21
15 7 0.21
16 3 0.09
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (13 bp):
TACTAAATGAAAA
Found at i:1351 original size:27 final size:28
Alignment explanation
Indices: 1297--1366 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
1287 AGATGAACTT
* *
1297 AAAAATGACTAAAATGCCCCCGAGTGC-
1 AAAAATGACCAAAATGCCCCAGAGTGCA
1324 AAAAATGACCAAAATGCCCCTAGA-TGCA
1 AAAAATGACCAAAATGCCCC-AGAGTGCA
*
1352 AAAAATGATCAAAAT
1 AAAAATGACCAAAAT
1367 ACCCTTGGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCAGAGTGCA
Found at i:14035 original size:21 final size:21
Alignment explanation
Indices: 14011--14158 Score: 95
Period size: 22 Copynumber: 6.5 Consensus size: 21
14001 ATCATTATTT
14011 TACTGATTA-TTCTTTACTTTG
1 TACTGATTACTT-TTTACTTTG
14032 TACTGATTACTATTTTACTCTTG
1 TACTGATTACT-TTTTACT-TTG
*
14055 T--TGATTACCTTTTTACTTTT
1 TACTGATTA-CTTTTTACTTTG
* *
14075 TACTGATTACCATTTTACTATTT
1 TACTGATTA-CTTTTTACT-TTG
* *
14098 TACTGATTACTATTTTCTGCTCCTTTTT
1 TACTGATTAC---TTT-T--TAC-TTTG
*
14126 TACTGATTACTCTTTTACTTTT
1 TACTGATTACT-TTTTACTTTG
14148 TACTGATTACT
1 TACTGATTACT
14159 ATTTGACTCT
Statistics
Matches: 107, Mismatches: 5, Indels: 29
0.76 0.04 0.21
Matches are distributed among these distances:
20 3 0.03
21 22 0.21
22 40 0.37
23 19 0.18
25 4 0.04
26 3 0.03
28 15 0.14
29 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.56
Consensus pattern (21 bp):
TACTGATTACTTTTTACTTTG
Found at i:14107 original size:15 final size:15
Alignment explanation
Indices: 14089--14144 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
14079 GATTACCATT
14089 TTACTATTTTACTGA
1 TTACTATTTTACTGA
14104 TTACTATTTT-CTG-
1 TTACTATTTTACTGA
* * *
14117 CTCCTTTTTTACTGA
1 TTACTATTTTACTGA
*
14132 TTACTCTTTTACT
1 TTACTATTTTACT
14145 TTTTACTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 20 0.61
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTATTTTACTGA
Found at i:14241 original size:35 final size:35
Alignment explanation
Indices: 14202--14281 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
14192 CTGGTTACTG
14202 TTTTACTCTTAATGAG-TACCTTCTACTGATCACTA
1 TTTTACTCTTAATG-GCTACCTTCTACTGATCACTA
** * * *
14237 TTTTACTCTTAATGGCTGTCTTTTGCTGATTACTA
1 TTTTACTCTTAATGGCTACCTTCTACTGATCACTA
14272 TTTTACTCTT
1 TTTTACTCTT
14282 TACTGATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (35 bp):
TTTTACTCTTAATGGCTACCTTCTACTGATCACTA
Found at i:14318 original size:21 final size:22
Alignment explanation
Indices: 14272--14320 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
14262 CTGATTACTA
*
14272 TTTTACTCTTTACTGATTATTC
1 TTTTACTCTTTACTCATTATTC
*
14294 -TTTACTCTTTAC-CATTTTTC
1 TTTTACTCTTTACTCATTATTC
14314 TTTTACT
1 TTTTACT
14321 GATTACTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTACTCTTTACTCATTATTC
Found at i:14512 original size:71 final size:70
Alignment explanation
Indices: 14419--14574 Score: 183
Period size: 71 Copynumber: 2.2 Consensus size: 70
14409 GATCAATCCA
* * *
14419 TTGACTTTTAATTACTGATTTACTGATTAGTA-TTTTTACCTTGACT-CTTAATTACTGATTAAT
1 TTGACTTTTAATTACTAATTTACTGATTACTAGTTTTTA-CTTGACTACTGAATTACTGATT-A-
*
14482 CTCTTACC
63 CTATTACC
* *
14490 TTGACTTTTAATTA-TCAATTTACTGATTACTATGTTTTTACTTGATTACTGATTTACTGATTAC
1 TTGACTTTTAATTACT-AATTTACTGATTACTA-GTTTTTACTTGACTACTGAATTACTGATTAC
14554 TATTACC
64 TATTACC
*
14561 TTGACTTTTGATTA
1 TTGACTTTTAATTA
14575 ATCTCTTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
70 1 0.01
71 48 0.65
72 7 0.09
73 18 0.24
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (70 bp):
TTGACTTTTAATTACTAATTTACTGATTACTAGTTTTTACTTGACTACTGAATTACTGATTACTA
TTACC
Found at i:14636 original size:47 final size:47
Alignment explanation
Indices: 14535--14738 Score: 311
Period size: 47 Copynumber: 4.3 Consensus size: 47
14525 TTTTACTTGA
* * *
14535 TTACTGATTTACTGATTACTATTACCTTGACTTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGAC-TCTGATTAATCTCTTT
* *
14583 TTACTGATTTACTGATTACCATCACTTTGACTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTCTGATTAATCTCTTT
* *
14630 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTCTGATTAATCTCTTT
* *
14677 TTACTGATTTACTGATTACCATCACCTTGACTCTGTTTAAGCTCTTT
1 TTACTGATTTACTGATTACCATCACCTTGACTCTGATTAATCTCTTT
14724 TTACTGA-TTACTGAT
1 TTACTGATTTACTGAT
14739 CACCCCTTTT
Statistics
Matches: 147, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 8 0.05
47 111 0.76
48 28 0.19
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACCTTGACTCTGATTAATCTCTTT
Found at i:15128 original size:51 final size:50
Alignment explanation
Indices: 14957--15300 Score: 273
Period size: 51 Copynumber: 6.7 Consensus size: 50
14947 GAGAGTCATT
* * *
14957 TTAAAGATTCAATCTCTTTCATTCAAAGGTTAAAGT-TTTATTTACTAATCAC
1 TTAAAAATTCAATCT-TTT-ATTCAAAAGTTAAA-TCTTTATTTACCAATCAC
* ** * * * * * *
15009 TCTAAAGATTCAATCTTTTACCCGAACA-TGACATTTTTACTTACCAATTAC
1 T-TAAAAATTCAATCTTTTATTC-AAAAGTTAAATCTTTATTTACCAATCAC
*
15060 TTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTACTAATCAC
1 TTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTACCAATCAC
* * * * * * * *
15110 TCTAAAGATTCAATCTTTTACTC-AAAGATGACATTTTTGTTTACCCATTTAC
1 T-TAAAAATTCAATCTTTTATTCAAAAG-TTAAATCTTTATTTA-CCAATCAC
* *
15162 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATCAC
1 TTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTACCAATCAC
* * * * * * * *
15212 TCTAAACATTCAATCTTTTACTC-AAAGATGACATTTTTGTTTACCCATTTAC
1 T-TAAAAATTCAATCTTTTATTCAAAAG-TTAAATCTTTATTTA-CCAATCAC
*
15264 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
1 TTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTT
15301 TAGCAAAAGG
Statistics
Matches: 226, Mismatches: 54, Indels: 25
0.74 0.18 0.08
Matches are distributed among these distances:
49 3 0.01
50 50 0.22
51 135 0.60
52 24 0.11
53 14 0.06
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (50 bp):
TTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTACCAATCAC
Found at i:15211 original size:102 final size:102
Alignment explanation
Indices: 14957--15300 Score: 566
Period size: 102 Copynumber: 3.4 Consensus size: 102
14947 GAGAGTCATT
*
14957 TTAAAGATTCAATCTCTTTCATTCAAAGGTTAAAGT-TTTATTTACTAATCACTCTAAAGATTCA
1 TTAAAAATTCAATCT-TTT-ATTCAAAGGTTAAA-TCTTTATTTACTAATCACTCTAAAGATTCA
* * * ** *
15021 ATCTTTTACCCGAACATGACATTTTTACTTA-CCAATTAC
63 ATCTTTTACTCAAAGATGACATTTTTGTTTACCCATTTAC
*
15060 TTAAAAATTCAATCTTTTATTCAAAAGTTAAATCTTTATTTACTAATCACTCTAAAGATTCAATC
1 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATCACTCTAAAGATTCAATC
15125 TTTTACTCAAAGATGACATTTTTGTTTACCCATTTAC
66 TTTTACTCAAAGATGACATTTTTGTTTACCCATTTAC
*
15162 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATCACTCTAAACATTCAATC
1 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATCACTCTAAAGATTCAATC
15227 TTTTACTCAAAGATGACATTTTTGTTTACCCATTTAC
66 TTTTACTCAAAGATGACATTTTTGTTTACCCATTTAC
15264 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
1 TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTT
15301 TAGCAAAAGG
Statistics
Matches: 229, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
100 1 0.00
101 67 0.29
102 147 0.64
103 14 0.06
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (102 bp):
TTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATCACTCTAAAGATTCAATC
TTTTACTCAAAGATGACATTTTTGTTTACCCATTTAC
Found at i:15309 original size:20 final size:20
Alignment explanation
Indices: 15286--15324 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15276 TCTTTTATTC
*
15286 AAAGGTTAAATCTTTTAGCA
1 AAAGGTTAAACCTTTTAGCA
*
15306 AAAGGTTACACCTTTTAGC
1 AAAGGTTAAACCTTTTAGC
15325 CAAATATCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAGGTTAAACCTTTTAGCA
Done.