Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022260.1 Corchorus olitorius cultivar O-4 contig22293, 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: 60402
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:989 original size:33 final size:34
Alignment explanation
Indices: 890--1026 Score: 242
Period size: 33 Copynumber: 4.1 Consensus size: 34
880 ACAAATGAAA
*
890 TTGTTTTTATTAGTAAACCTCTTTTGTATACTCT
1 TTGTTTTTATTAGTAAACCTCTTTTGTAGACTCT
924 TTGTTTTTTATTAGTAAACCTCTTTTGTAGACTCT
1 TTG-TTTTTATTAGTAAACCTCTTTTGTAGACTCT
959 TTGTTTTTATTAGTAAACCTC-TTTGTAGACTCT
1 TTGTTTTTATTAGTAAACCTCTTTTGTAGACTCT
992 TTGTTTTTATTAGTAAACCTC-TTTGTAGACTCT
1 TTGTTTTTATTAGTAAACCTCTTTTGTAGACTCT
1025 TT
1 TT
1027 ATTTGTTTAG
Statistics
Matches: 101, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
33 47 0.47
34 21 0.21
35 33 0.33
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (34 bp):
TTGTTTTTATTAGTAAACCTCTTTTGTAGACTCT
Found at i:5671 original size:30 final size:31
Alignment explanation
Indices: 5635--5697 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5625 TTTGGATGAT
5635 TTCAAAAG-GAGATTTTGGAAAATAAAGAAA
1 TTCAAAAGAGAGATTTTGGAAAATAAAGAAA
* *
5665 TTCAAAAGAGAGATTTTGGAAATTAATGAAA
1 TTCAAAAGAGAGATTTTGGAAAATAAAGAAA
5696 TT
1 TT
5698 GGTAAGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (31 bp):
TTCAAAAGAGAGATTTTGGAAAATAAAGAAA
Found at i:13919 original size:22 final size:23
Alignment explanation
Indices: 13891--13933 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
13881 TAAAAGGAGT
13891 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
13913 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
13934 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:18969 original size:22 final size:23
Alignment explanation
Indices: 18941--18983 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
18931 TAGAAGGAGT
18941 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
18963 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
18984 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:22414 original size:32 final size:32
Alignment explanation
Indices: 22368--22452 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 32
22358 TTCGGGTATT
* * **
22368 TCGGATTCGGGTATTTTTGGGTTCGAGTTAAA
1 TCGGGTTCGGGTATTTTCGGACTCGAGTTAAA
* **
22400 TCGGGTTCGGGTATTTTCGGACTCGGGTTATG
1 TCGGGTTCGGGTATTTTCGGACTCGAGTTAAA
*
22432 TCGGGTTCGAGTATTTTCGGA
1 TCGGGTTCGGGTATTTTCGGA
22453 TTCGGTCTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.14, C:0.13, G:0.34, T:0.39
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGACTCGAGTTAAA
Found at i:22419 original size:16 final size:16
Alignment explanation
Indices: 22400--22457 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
22390 TCGAGTTAAA
*
22400 TCGGGTTCGGGTATTT
1 TCGGATTCGGGTATTT
* *
22416 TCGGACTCGGGT-TATG
1 TCGGATTCGGGTAT-TT
* *
22432 TCGGGTTCGAGTATTT
1 TCGGATTCGGGTATTT
22448 TCGGATTCGG
1 TCGGATTCGG
22458 TCTCAGGTAG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
15 1 0.03
16 29 0.94
17 1 0.03
ACGTcount: A:0.10, C:0.16, G:0.36, T:0.38
Consensus pattern (16 bp):
TCGGATTCGGGTATTT
Found at i:22476 original size:33 final size:32
Alignment explanation
Indices: 22402--22476 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
22392 GAGTTAAATC
* * *
22402 GGGTTCGGGTATTTTCGGACTCGGGTTATGTC
1 GGGTTCGAGTATTTTCGGACTCGGGTTAGGTA
*
22434 GGGTTCGAGTATTTTCGGATTC-GGTCTCAGGTA
1 GGGTTCGAGTATTTTCGGACTCGGGT-T-AGGTA
22467 GGGTTCGAGT
1 GGGTTCGAGT
22477 TTGGGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 21 0.57
33 13 0.35
ACGTcount: A:0.12, C:0.15, G:0.37, T:0.36
Consensus pattern (32 bp):
GGGTTCGAGTATTTTCGGACTCGGGTTAGGTA
Found at i:22965 original size:31 final size:31
Alignment explanation
Indices: 22930--23001 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
22920 TAAATTATTG
*
22930 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
22961 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
22992 CAAATTAAAA
1 CAAATTAAAA
23002 GTTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:31192 original size:20 final size:21
Alignment explanation
Indices: 31155--31198 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31145 AATAATAATT
* *
31155 AAAATCTAATTCATTTAAAAA
1 AAAAGCTAATCCATTTAAAAA
31176 AAAAGCTAATCCA-TTAAAAA
1 AAAAGCTAATCCATTTAAAAA
31196 AAA
1 AAA
31199 GTTGGTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAAGCTAATCCATTTAAAAA
Found at i:45145 original size:21 final size:21
Alignment explanation
Indices: 45107--45150 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
45097 GGAGTTGCCA
* *
45107 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTAGATCCAATG
*
45128 AAGATGCCATTAGGTCCAATG
1 AAGATGCCATTAGATCCAATG
45149 AA
1 AA
45151 AAGAGCAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGATGCCATTAGATCCAATG
Found at i:50942 original size:18 final size:19
Alignment explanation
Indices: 50909--50947 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
50899 AAATATCTCT
*
50909 AATTAGGTCTAATTGCACA
1 AATTAGATCTAATTGCACA
50928 AATTAGATC-AATTGCACA
1 AATTAGATCTAATTGCACA
50946 AA
1 AA
50948 AACAAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (19 bp):
AATTAGATCTAATTGCACA
Found at i:51841 original size:14 final size:15
Alignment explanation
Indices: 51822--51851 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51812 AACTAGGAAA
51822 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
51836 AATAAATAAACAAGG
1 AATAAATAAACAAGG
51851 A
1 A
51852 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Done.