Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022387.1 Corchorus olitorius cultivar O-4 contig22420, 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: 13743
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Found at i:1024 original size:27 final size:27
Alignment explanation
Indices: 977--1029 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
967 AAATTAACAA
977 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACA-AAAGATAAATCT
*
1005 GAAATCATAAAATAC-CAAGATAAAT
1 GAAATCATAAAA-ACAAAAGATAAAT
1030 AATCAGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 12 0.52
29 2 0.09
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCATAAAAACAAAAGATAAATCT
Found at i:3602 original size:50 final size:48
Alignment explanation
Indices: 3536--3629 Score: 143
Period size: 50 Copynumber: 1.9 Consensus size: 48
3526 AAAAAATTTA
* *
3536 TTATAAATTTTCAATTTTGACCGAATTATGATACCTAAAAGAACTAAGAT
1 TTATAAAATTTAAATTTTGACCGAATTA--ATACCTAAAAGAACTAAGAT
*
3586 TTATAAAATTTAAATTTTGACTGAATTAATACCTAAAAGAACTA
1 TTATAAAATTTAAATTTTGACCGAATTAATACCTAAAAGAACTA
3630 GAATTAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 16 0.39
50 25 0.61
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (48 bp):
TTATAAAATTTAAATTTTGACCGAATTAATACCTAAAAGAACTAAGAT
Found at i:6586 original size:15 final size:16
Alignment explanation
Indices: 6560--6589 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6550 AAAATAATAT
6560 TATAATATATTTTTAG
1 TATAATATATTTTTAG
6576 TATAA-ATATTTTTA
1 TATAATATATTTTTA
6590 ATGATAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TATAATATATTTTTAG
Found at i:6596 original size:16 final size:16
Alignment explanation
Indices: 6560--6597 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6550 AAAATAATAT
*
6560 TATAATATATTTTTAG
1 TATAATATATTTTTAA
6576 TATAA-ATATTTTTAA
1 TATAATATATTTTTAA
6591 TGATAAT
1 T-ATAAT
6598 GAAAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TATAATATATTTTTAA
Found at i:8385 original size:25 final size:24
Alignment explanation
Indices: 8330--8386 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
8320 GTCAGCCTTG
* *
8330 AATTT-TTTAATGTTTCATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
8353 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
8378 AATTTATTT
1 AATTTATTT
8387 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:9190 original size:78 final size:80
Alignment explanation
Indices: 9070--9230 Score: 263
Period size: 78 Copynumber: 2.0 Consensus size: 80
9060 CTTTTATAGC
* * *
9070 TTTACTCAATTAAAAACTCTATATTTATTTAATTAAATCT-A-ATATCTTTATACCTATTTTATT
1 TTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATATCTTTATAACTATTTTAGT
9133 TTACCATTTTACTAT
66 TTACCATTTTACTAT
* *
9148 TTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATATCTTTATAACTGTTTTAGT
1 TTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATATCTTTATAACTATTTTAGT
9213 TTACCATTTTACTAT
66 TTACCATTTTACTAT
9228 TTT
1 TTT
9231 GATTAAAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 38 0.50
79 1 0.01
80 37 0.49
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.52
Consensus pattern (80 bp):
TTTACTCAACTAAAAACTCTATATTTATTTAATTAAATCTAATATATCTTTATAACTATTTTAGT
TTACCATTTTACTAT
Found at i:11130 original size:17 final size:17
Alignment explanation
Indices: 11108--11140 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11098 TACATCAATT
11108 TCAATTTGAATGAAATA
1 TCAATTTGAATGAAATA
11125 TCAATTTGAATGAAAT
1 TCAATTTGAATGAAAT
11141 TTACTGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
TCAATTTGAATGAAATA
Found at i:13503 original size:42 final size:44
Alignment explanation
Indices: 13452--13545 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
13442 CGTCCATTAC
*
13452 CTAA-ATTCTACTCCTT-C-TC-TAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTTCCATCTTAGATAATTCATCAAAATAAAG
*
13493 CTAATATTCTACTCTTCCATCTTTAGATAATTTATCAAAATAAAG
1 CTAATATTCTACTCTTCCATC-TTAGATAATTCATCAAAATAAAG
*
13538 TTAATATT
1 CTAATATT
13546 AATTGTTACT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 7 0.16
42 9 0.20
43 2 0.04
45 27 0.60
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (44 bp):
CTAATATTCTACTCTTCCATCTTAGATAATTCATCAAAATAAAG
Done.