Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019729.1 Corchorus olitorius cultivar O-4 contig19762, 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: 20540
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3055 original size:21 final size:21
Alignment explanation
Indices: 3016--3064 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3006 TCAATGCTTT
**
3016 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
3038 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
3059 A-GAAGC
1 AGGAAGC
3065 TGCAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:7425 original size:201 final size:194
Alignment explanation
Indices: 7087--7481 Score: 711
Period size: 201 Copynumber: 2.0 Consensus size: 194
7077 ATCCTTAATT
7087 GTAATACCATTGATTTGATTAAAATAAAAAAATAATTACTAGTTCTTACAAATTTTGTGAATTGG
1 GTAATACCATTGATTTGATTAAAATAAAAAAATAATTACTAGTTCTTACAAATTTTGTGAATTGG
7152 GGATTGATGTGAATAAAAAGGACACTGTGGGGACCAAATTGAAGAGATTGCTAATGGTGGAGTAC
66 GGATTGATGTGAATAAAAAGGACACTGTGGGGACCAAATTGAAGAGATTGCTAATGGTGGAGTAC
7217 CAAGGGATAATTTGGACCAAGTC-TTTTTTTAATAAAAGCCCAAGTGCCCAACATCATCTTCCTC
131 CAAGGGATAATTTGG-CCAAGTCTTTTTTTTAATAAAAGCCCAAGTGCCCAACATCATCTTCCTC
7281 GTAATACCATTGATTTGATTAAAATAATAATAATAATAATAATTACTAGTTCTTACAAATTTTGT
1 GTAATACCATTGATTTGATT--AA-AAT-A-AA-AA-AATAATTACTAGTTCTTACAAATTTTGT
7346 GAATTGGGGATTGATGTGAATAAAAAGGACACTGTGGGGACCAAATTGAAGAGATTGCTAATGGT
59 GAATTGGGGATTGATGTGAATAAAAAGGACACTGTGGGGACCAAATTGAAGAGATTGCTAATGGT
7411 GGAGTACCAAGGGATAATTTGGCCAAGTCTTTTTTTTAATAAAAGCCCAAGTGCCCAACATCATC
124 GGAGTACCAAGGGATAATTTGGCCAAGTCTTTTTTTTAATAAAAGCCCAAGTGCCCAACATCATC
7476 TTCCTC
189 TTCCTC
7482 ATTATTTTTT
Statistics
Matches: 193, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
194 20 0.10
196 2 0.01
197 3 0.02
198 1 0.01
199 2 0.01
200 9 0.05
201 156 0.81
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (194 bp):
GTAATACCATTGATTTGATTAAAATAAAAAAATAATTACTAGTTCTTACAAATTTTGTGAATTGG
GGATTGATGTGAATAAAAAGGACACTGTGGGGACCAAATTGAAGAGATTGCTAATGGTGGAGTAC
CAAGGGATAATTTGGCCAAGTCTTTTTTTTAATAAAAGCCCAAGTGCCCAACATCATCTTCCTC
Found at i:8116 original size:16 final size:16
Alignment explanation
Indices: 8064--8122 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
8054 GGCGTGCGCA
8064 GGCCTGGTGCGCGCTG
1 GGCCTGGTGCGCGCTG
* * * *
8080 GACCAGCTGCGCGC-A
1 GGCCTGGTGCGCGCTG
8095 GGCCTGGTGCGCGCTG
1 GGCCTGGTGCGCGCTG
*
8111 GGCCTGGCGCGC
1 GGCCTGGTGCGC
8123 CTTGGTCCAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 11 0.33
16 22 0.67
ACGTcount: A:0.05, C:0.36, G:0.46, T:0.14
Consensus pattern (16 bp):
GGCCTGGTGCGCGCTG
Found at i:8267 original size:18 final size:17
Alignment explanation
Indices: 8219--8275 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
8209 CCCGTAAAAG
*
8219 GGAAA-AAAAAGACATAA
1 GGAAAGAAAAAGAGA-AA
8236 GGAAAGAAAAAGAGAAA
1 GGAAAGAAAAAGAGAAA
*
8253 GGAAGAGGAAAAGAGAAA
1 GGAA-AGAAAAAGAGAAA
*
8271 AGAAA
1 GGAAA
8276 AAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.34
18 23 0.66
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (17 bp):
GGAAAGAAAAAGAGAAA
Found at i:9115 original size:28 final size:28
Alignment explanation
Indices: 9048--9122 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
9038 TATGGGCATA
*
9048 AAATTACCA-TTTTACCCTAAGAATGAAT
1 AAATTA-CAGTTTTACCCTTAGAATGAAT
* **
9076 AAATTACCGTTTTACCCTTAGAA-GGTT
1 AAATTACAGTTTTACCCTTAGAATGAAT
*
9103 AAATTTACAGTTTTAACCTT
1 AAA-TTACAGTTTTACCCTT
9123 GTACTTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 6 0.15
28 33 0.85
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (28 bp):
AAATTACAGTTTTACCCTTAGAATGAAT
Found at i:9281 original size:28 final size:28
Alignment explanation
Indices: 9221--9273 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
9211 TATCATAAAA
* * *
9221 AAAATTATTGTTTTGCCCTTTGTTGAAT
1 AAAATTACTGTTTTGCCCTCTGTAGAAT
9249 AAAATTACTGTTTTGCCC-CTGTAGA
1 AAAATTACTGTTTTGCCCTCTGTAGA
9274 CTTAAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (28 bp):
AAAATTACTGTTTTGCCCTCTGTAGAAT
Found at i:9635 original size:13 final size:12
Alignment explanation
Indices: 9617--9661 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
9607 ATTTTATTAC
9617 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
9630 TGTTTTATAAAT
1 TGTTTTATAAAT
*
9642 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
9656 TGTTTT
1 TGTTTT
9662 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:11558 original size:4 final size:4
Alignment explanation
Indices: 11551--11581 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
11541 TTGAAAAAAA
11551 AATT AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AAT
11582 AATAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:16689 original size:19 final size:18
Alignment explanation
Indices: 16656--16691 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16646 TTGAGATAAT
16656 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
16674 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
16692 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:19312 original size:20 final size:20
Alignment explanation
Indices: 19287--19328 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19277 TAGTCAATAT
19287 AGAATTTTATCTAGATTAGA
1 AGAATTTTATCTAGATTAGA
19307 AGAATTTTATCTAGATTAGA
1 AGAATTTTATCTAGATTAGA
19327 AG
1 AG
19329 GTAACTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
AGAATTTTATCTAGATTAGA
Done.