Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015656.1 Corchorus olitorius cultivar O-4 contig15689, 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: 64585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:20530 original size:13 final size:13
Alignment explanation
Indices: 20512--20538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20502 GATAAGTGTA
20512 AATATCTTGTGGT
1 AATATCTTGTGGT
20525 AATATCTTGTGGT
1 AATATCTTGTGGT
20538 A
1 A
20539 GCAAGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.44
Consensus pattern (13 bp):
AATATCTTGTGGT
Found at i:26323 original size:78 final size:78
Alignment explanation
Indices: 26194--26350 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
26184 GCCTTAAGTC
*
26194 ATTAGGATTTTAATATTTATGGTTTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGAATTA
1 ATTAGGATTCTAATATTTATGGTTTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGAATTA
26259 GGATTTTATGTTA
66 GGATTTTATGTTA
26272 ATTAGGATTCTAATATTTATGGTTTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGAATTA
1 ATTAGGATTCTAATATTTATGGTTTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGAATTA
26337 GGATTTTATGTTA
66 GGATTTTATGTTA
26350 A
1 A
26351 GTGTTTAGTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (78 bp):
ATTAGGATTCTAATATTTATGGTTTTTCCTAAAAGGATTAGGTTTTACTTTTCCTACCAGAATTA
GGATTTTATGTTA
Found at i:26785 original size:27 final size:27
Alignment explanation
Indices: 26723--26785 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
26713 CATATCACAA
*
26723 TGATGATGAGGACTCTGAGGACTATGC
1 TGATGATGGGGACTCTGAGGACTATGC
26750 TGATGATGGGGACTCTGAGGACTATGC
1 TGATGATGGGGACTCTGAGGACTATGC
26777 TGATGATGG
1 TGATGATGG
26786 TTCTGATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.27
Consensus pattern (27 bp):
TGATGATGGGGACTCTGAGGACTATGC
Found at i:30056 original size:56 final size:56
Alignment explanation
Indices: 29992--30106 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
29982 CCAATGAGCT
29992 TAATTTTCATTCTTATTTGAGGAAAAAAACCCATCATTCTAAATTAAGTTTAATCA
1 TAATTTTCATTCTTATTTGAGGAAAAAAACCCATCATTCTAAATTAAGTTTAATCA
30048 TAATTTTCATTCTTATTTGAGGAAAAAAACCCATCATTCTAAATTAAGTTTAATCA
1 TAATTTTCATTCTTATTTGAGGAAAAAAACCCATCATTCTAAATTAAGTTTAATCA
30104 TAA
1 TAA
30107 AGTGTAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (56 bp):
TAATTTTCATTCTTATTTGAGGAAAAAAACCCATCATTCTAAATTAAGTTTAATCA
Found at i:36511 original size:2 final size:2
Alignment explanation
Indices: 36504--36556 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
36494 TTCATAATCA
36504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- ACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
36544 AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT
36557 TATCTACCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37323 original size:27 final size:28
Alignment explanation
Indices: 37267--37324 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
37257 TCTGCCTCCT
37267 AAATTAGATGTTCTCTCTTATTGCCAAA
1 AAATTAGATGTTCTCTCTTATTGCCAAA
* *
37295 AAATTAGATGTTGTCTC-TATTGCTAAA
1 AAATTAGATGTTCTCTCTTATTGCCAAA
37322 AAA
1 AAA
37325 AAAAAAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (28 bp):
AAATTAGATGTTCTCTCTTATTGCCAAA
Found at i:37589 original size:20 final size:20
Alignment explanation
Indices: 37564--37647 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
37554 TAATTAAATT
37564 TTTATTTATAAATAAATACA
1 TTTATTTATAAATAAATACA
37584 TTTATTCTCATTAAA-AAA-A-A
1 TTTATT-T-A-TAAATAAATACA
* * * *
37604 TGT-TTTGT-AATAATTAAA
1 TTTATTTATAAATAAATACA
37622 TTTATTTATAAATAAATACA
1 TTTATTTATAAATAAATACA
37642 TTTATT
1 TTTATT
37648 CTCATTGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
15 2 0.04
16 3 0.06
17 1 0.02
18 4 0.08
19 6 0.12
20 23 0.47
21 2 0.04
22 4 0.08
23 4 0.08
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTATTTATAAATAAATACA
Found at i:37642 original size:58 final size:58
Alignment explanation
Indices: 37550--37666 Score: 200
Period size: 58 Copynumber: 2.0 Consensus size: 58
37540 ATTGGTATTG
37550 GTAATAATTAAATTTTTATTTATAAATAAATACATTTATTCTCATTAAAAAAAATGTTTT
1 GTAATAATTAAA-TTTTATTTATAAATAAATACATTTATTCTCATT-AAAAAAATGTTTT
*
37610 GTAATAATTAAA-TTTATTTATAAATAAATACATTTATTCTCATTGAAAAAATGTTTT
1 GTAATAATTAAATTTTATTTATAAATAAATACATTTATTCTCATTAAAAAAATGTTTT
37667 TATTTTTTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
57 12 0.21
58 32 0.57
60 12 0.21
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (58 bp):
GTAATAATTAAATTTTATTTATAAATAAATACATTTATTCTCATTAAAAAAATGTTTT
Found at i:52285 original size:25 final size:25
Alignment explanation
Indices: 52229--52290 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
52219 ACTTCATATG
* * *
52229 AATAAATTAATAATTATGTTATCTC
1 AATAAAATAATAATTATGTAATCAC
*
52254 AAAAAAATAATAATTATGTAAATCAC
1 AATAAAATAATAATTATGT-AATCAC
*
52280 -ATAAAAAAATA
1 AATAAAATAATA
52291 GAAGGCTTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (25 bp):
AATAAAATAATAATTATGTAATCAC
Found at i:60247 original size:27 final size:27
Alignment explanation
Indices: 60197--60249 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
60187 ACACGTAAAT
**
60197 AAAAATAATGAATTTCATCCCTAAAAA
1 AAAAATAATGAATTTCAAACCTAAAAA
*
60224 AAAAATAATGAATTTCAAATCTAAAA
1 AAAAATAATGAATTTCAAACCTAAAA
60250 TTACATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.58, C:0.11, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAAATAATGAATTTCAAACCTAAAAA
Found at i:61905 original size:15 final size:15
Alignment explanation
Indices: 61858--61908 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
61848 GATAAATTTT
61858 AATTATTAGGAAGGA
1 AATTATTAGGAAGGA
* ** *
61873 AATGATATAATAA-CA
1 AATTAT-TAGGAAGGA
61888 AATTATTAGGAAGGA
1 AATTATTAGGAAGGA
61903 AATTAT
1 AATTAT
61909 AATTACTATT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.51, C:0.02, G:0.18, T:0.29
Consensus pattern (15 bp):
AATTATTAGGAAGGA
Found at i:62443 original size:6 final size:6
Alignment explanation
Indices: 62434--62460 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
62424 AAATCTTATT
62434 GATATA GATATA GATATA GATATA GAT
1 GATATA GATATA GATATA GATATA GAT
62461 CGACACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (6 bp):
GATATA
Done.