Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006506.1 Corchorus capsularis cultivar CVL-1 contig06527, 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: 15543
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1323 original size:17 final size:17
Alignment explanation
Indices: 1297--1333 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1287 AAAAAAATAT
*
1297 CATAACATACAGTCTTC
1 CATAAAATACAGTCTTC
1314 CATAAAATACAGTCTTC
1 CATAAAATACAGTCTTC
1331 CAT
1 CAT
1334 TAGTAGTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (17 bp):
CATAAAATACAGTCTTC
Found at i:5977 original size:31 final size:28
Alignment explanation
Indices: 5907--5991 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 28
5897 GTTAAGAAAT
*
5907 TGAAAGGTTTAGGACCAAATTGAGCGGG
1 TGAAAGGTTTAGGACCAAATCGAGCGGG
* *
5935 TCAGAAGGTTTATGACCAAATCGAGCGGACCG
1 TGA-AAGGTTTAGGACCAAATCGAGCGG---G
5967 TGAAAGGTTTAGGACCAAATCGAGC
1 TGAAAGGTTTAGGACCAAATCGAGC
5992 ATTTAGCCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.04
29 22 0.46
31 21 0.44
32 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (28 bp):
TGAAAGGTTTAGGACCAAATCGAGCGGG
Found at i:7299 original size:35 final size:35
Alignment explanation
Indices: 7260--7327 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
7250 ATCTCTAGGT
7260 TTCTTAGCTCTTCATTTTTACAACAACACAGAAGG
1 TTCTTAGCTCTTCATTTTTACAACAACACAGAAGG
*
7295 TTCTTAGCTCTTCATTTTTACAGCAACACAGAA
1 TTCTTAGCTCTTCATTTTTACAACAACACAGAA
7328 AATACAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (35 bp):
TTCTTAGCTCTTCATTTTTACAACAACACAGAAGG
Found at i:9246 original size:65 final size:67
Alignment explanation
Indices: 9013--9315 Score: 321
Period size: 65 Copynumber: 4.5 Consensus size: 67
9003 TTTTATTTTC
* * *
9013 TCTTTCCAAAAATACCCTTCCAGTCGAAGGGTCAGTTTCATCAGATTGTTGCATTTAAGTCTAGT
1 TCTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTCATC--ATTGTTGCATTTAAGTCTAGT
9078 ATTT
64 ATTT
* * * * *
9082 TCATTT-C-AAAATACCCTTTCGGTCAAAGGGTCAATTTCGTCCTT-TTACATTTAAGTTTAGTA
1 TC-TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTCATCATTGTTGCATTTAAGTCTAGTA
9144 TTTT
65 -TTT
* ** * * * *
9148 TGTTTCCAGGAATACCCTTTCGGTCGAAGGGTCAATTTCGTC-TTTTTGCATTTAGGTTTAGT-T
1 TCTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTCATCATTGTTGCATTTAAGTCTAGTAT
9211 TT
66 TT
* * *
9213 ACTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAGT
1 TCTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTCATCA--TTGTTGCATTTAAGTCTAGT
*
9278 -CTT
64 ATTT
*
9281 TCTTTCCAAAGAATACCCTTTCGGTCAAAGGGTCA
1 TCTTTCCAAA-AATACCCTTTCGGTCGAAGGGTCA
9316 GTGCTGTCAT
Statistics
Matches: 197, Mismatches: 28, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
65 57 0.29
66 9 0.05
67 46 0.23
68 57 0.29
69 25 0.13
70 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (67 bp):
TCTTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTCATCATTGTTGCATTTAAGTCTAGTAT
TT
Found at i:9877 original size:3 final size:3
Alignment explanation
Indices: 9869--9901 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9859 TCATTTCCCC
*
9869 CAT CAT CAT CAT CAT CAT CAA CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
9902 TTCCGTGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (3 bp):
CAT
Found at i:10456 original size:10 final size:10
Alignment explanation
Indices: 10441--10476 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
10431 AATTTAATAT
10441 GGATATTTAC
1 GGATATTTAC
*
10451 GGATATTTAT
1 GGATATTTAC
*
10461 AGATATTTAC
1 GGATATTTAC
10471 GGATAT
1 GGATAT
10477 ATCGAGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:10484 original size:20 final size:20
Alignment explanation
Indices: 10442--10484 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
10432 ATTTAATATG
* *
10442 GATATTTACGGATATTTATA
1 GATATTTACGGATATATAGA
*
10462 GATATTTACGGATATATCGA
1 GATATTTACGGATATATAGA
10482 GAT
1 GAT
10485 TTATCGAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (20 bp):
GATATTTACGGATATATAGA
Found at i:13632 original size:30 final size:32
Alignment explanation
Indices: 13572--13650 Score: 117
Period size: 30 Copynumber: 2.5 Consensus size: 32
13562 AATCATATTC
13572 AACATTGTGAAAGCTTACTGATTAAAAAAAAA
1 AACATTGTGAAAGCTTACTGATTAAAAAAAAA
*
13604 AACATTGCGAAAGCTTACTGA-T-AAAAAAAA
1 AACATTGTGAAAGCTTACTGATTAAAAAAAAA
* *
13634 ATCATTATGAAAGCTTA
1 AACATTGTGAAAGCTTA
13651 GGGTGCCCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 22 0.51
31 1 0.02
32 20 0.47
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (32 bp):
AACATTGTGAAAGCTTACTGATTAAAAAAAAA
Found at i:13632 original size:31 final size:32
Alignment explanation
Indices: 13572--13634 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
13562 AATCATATTC
*
13572 AACATTGTGAAAGCTTACTGATTAAAAAAAAA
1 AACATTGCGAAAGCTTACTGATTAAAAAAAAA
13604 AACATTGCGAAAGCTTACTGA-TAAAAAAAAA
1 AACATTGCGAAAGCTTACTGATTAAAAAAAAA
13635 TCATTATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (32 bp):
AACATTGCGAAAGCTTACTGATTAAAAAAAAA
Found at i:15423 original size:169 final size:168
Alignment explanation
Indices: 15077--15524 Score: 618
Period size: 169 Copynumber: 2.7 Consensus size: 168
15067 TGAGTCATTT
* ** *
15077 GTCAATTGAGAAATGACCAAGAATTTTAGTTATTTAATTCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAAATTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** *
15142 TTAAGTAATCTAT-CAAGTAGGAAAAGACGAAAAAGAATTAGTTCTCTAGCTCATCATCAATCCT
66 TTAAATAATCTGTCCAAGTAGGAAAAGACGAAAAAGAATTAGTTCTCTAACTCAAAAGCAATCCT
** *
15206 TGATGGGGATCTTTTAGTAATTCCACTACTATATTCAA
131 TGATAAGGATCTTTTAGTAATTCCACTACTATATTAAA
* *
15244 GTCCATTGAGAAATGACCAAAAAAATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGAACA
1 GTCAATTGAGAAATGACCAAAAAAATTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGG-ACA
* *
15309 TTTAAATAATATGTCCAAGTAGGAAAAGACGAAAAAG-ATTGGTTCTCTAACTCCAAAAGCAAGT
65 TTTAAATAATCTGTCCAAGTAGGAAAAGACGAAAAAGAATTAGTTCTCTAACT-CAAAAGCAA-T
* *
15373 -CTTGGTAAGGATCTTTTAGTAATTCCACTACTCTATTAAA
128 CCTTGATAAGGATCTTTTAGTAATTCCACTACTATATTAAA
* *
15413 GTCAATTGAGAAATGACC-AAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGATA
1 GTCAATTGAGAAATGACCAAAAAAAT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA
* *
15477 TTTAAATAATCTG-CCAAGTGGGAAAAGACGAAAAAAAATTAGTTCTCT
65 TTTAAATAATCTGTCCAAGTAGGAAAAGACGAAAAAGAATTAGTTCTCT
15525 CGTTCCTCAT
Statistics
Matches: 248, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
167 76 0.31
168 57 0.23
169 114 0.46
170 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (168 bp):
GTCAATTGAGAAATGACCAAAAAAATTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
TTAAATAATCTGTCCAAGTAGGAAAAGACGAAAAAGAATTAGTTCTCTAACTCAAAAGCAATCCT
TGATAAGGATCTTTTAGTAATTCCACTACTATATTAAA
Done.