Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023924.1 Corchorus olitorius cultivar O-4 contig23957, 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: 22810
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1088 original size:21 final size:22
Alignment explanation
Indices: 1062--1104 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1052 TCTTTTTATA
1062 TTTA-TTTAAATTTCATTTTTT
1 TTTATTTTAAATTTCATTTTTT
* *
1083 TTTATTTTCATTTTCATTTTTT
1 TTTATTTTAAATTTCATTTTTT
1105 AATTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTAAATTTCATTTTTT
Found at i:3330 original size:17 final size:16
Alignment explanation
Indices: 3308--3364 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
3298 ACGTTCACCC
3308 CTTTTCTTTCTTTTTTT
1 CTTTTC-TTCTTTTTTT
3325 CTTTTCTTCTTTTTTTT
1 CTTTTCTTC-TTTTTTT
* * *
3342 CCTTTCTTCGTTTTCT
1 CTTTTCTTCTTTTTTT
3358 -TTTTCTT
1 CTTTTCTT
3365 TAATTTTGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 21 0.60
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (16 bp):
CTTTTCTTCTTTTTTT
Found at i:3332 original size:13 final size:13
Alignment explanation
Indices: 3309--3361 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
3299 CGTTCACCCC
3309 TTTTC-TTTCTTT
1 TTTTCTTTTCTTT
*
3321 TTTTCTTTTCTTC
1 TTTTCTTTTCTTT
*
3334 TTTT-TTTTCCTT
1 TTTTCTTTTCTTT
*
3346 TCTTCGTTTTCTTT
1 TTTTC-TTTTCTTT
3360 TT
1 TT
3362 CTTTAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 14 0.44
13 10 0.31
14 8 0.25
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:3423 original size:12 final size:11
Alignment explanation
Indices: 3406--3453 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
3396 AAGTCCCACC
3406 CCTTTTCTTTTT
1 CCTTTT-TTTTT
3418 CCTTTTTTTCTTT
1 CC-TTTTTT-TTT
*
3431 CTTTTTTCTTTT
1 CCTTTTT-TTTT
3443 CCTTTTTTTTT
1 CCTTTTTTTTT
3454 AACAACCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 4 0.13
12 18 0.58
13 9 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
CCTTTTTTTTT
Found at i:3529 original size:21 final size:21
Alignment explanation
Indices: 3485--3540 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3475 TTTTAATGAA
**
3485 TTGTTTTTTTATTTCTCTTTT
1 TTGTTTTTTTATTTCTCTGAT
* *
3506 TTGTTTTTTTCTTTTTCTGAT
1 TTGTTTTTTTATTTCTCTGAT
*
3527 TTGATTGTTTTATT
1 TTG-TTTTTTTATT
3541 ATTTCTTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (21 bp):
TTGTTTTTTTATTTCTCTGAT
Found at i:8332 original size:40 final size:40
Alignment explanation
Indices: 8272--8351 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
8262 AACTAATGAC
* * *
8272 TTTCTTTTCTTAACTTAACTTTCTTAAAAGCACTTATAAA
1 TTTCATTTCTTAACTGAACTTTCTTAAAAGAACTTATAAA
8312 TTTCATTTCTTAACTGAACTTTCTTAAAAGAACTTATAAA
1 TTTCATTTCTTAACTGAACTTTCTTAAAAGAACTTATAAA
8352 ATAAAACAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (40 bp):
TTTCATTTCTTAACTGAACTTTCTTAAAAGAACTTATAAA
Found at i:15173 original size:15 final size:15
Alignment explanation
Indices: 15137--15169 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
15127 AGGTTGACAG
15137 AAAACAATTAAACAT
1 AAAACAATTAAACAT
15152 AAAACAATTAAAC-T
1 AAAACAATTAAACAT
15166 AAAA
1 AAAA
15170 ACAAAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAACAATTAAACAT
Found at i:19686 original size:11 final size:11
Alignment explanation
Indices: 19670--19716 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
19660 CCTATGTGGC
19670 TTTTTTAAATA
1 TTTTTTAAATA
* *
19681 TTTTTTTATTA
1 TTTTTTAAATA
19692 TTTTTT-AA-A
1 TTTTTTAAATA
19701 TTTTTTAAATA
1 TTTTTTAAATA
19712 TTTTT
1 TTTTT
19717 ATTTTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 7 0.23
10 3 0.10
11 21 0.68
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:19715 original size:19 final size:20
Alignment explanation
Indices: 19693--19738 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
19683 TTTTTATTAT
19693 TTTTTAAATTT-TTTAAATA
1 TTTTTAAATTTCTTTAAATA
* *
19712 TTTTT-ATTTTCTTTTAATA
1 TTTTTAAATTTCTTTAAATA
19731 TTTTTAAA
1 TTTTTAAA
19739 CCGGCTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.18
19 17 0.77
20 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTAAATTTCTTTAAATA
Found at i:19738 original size:29 final size:30
Alignment explanation
Indices: 19670--19735 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
19660 CCTATGTGGC
19670 TTTTTTAAATATTTTTTTATTATTTTTTAAA
1 TTTTTTAAATA-TTTTTTATTATTTTTTAAA
19701 TTTTTTAAATA-TTTTTATT-TTCTTTTAATA
1 TTTTTTAAATATTTTTTATTATT-TTTTAA-A
19731 TTTTT
1 TTTTT
19736 AAACCGGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 2 0.06
29 14 0.42
30 6 0.18
31 11 0.33
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTTTAAATATTTTTTATTATTTTTTAAA
Found at i:20377 original size:72 final size:72
Alignment explanation
Indices: 20260--20403 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
20250 GAGTGTCCAC
20260 TGAACAAGCTGCAAAAGGAGGGGAAATAGGTTCAGAACAAGAAAAGGAGAGTTTTGAACATGCAA
1 TGAACAAGCTGCAAAAGGAGGGGAAATAGGTTCAGAACAAGAAAAGGAGAGTTTTGAACATGCAA
20325 GAAGTTT
66 GAAGTTT
20332 TGAACAAGCTGCAAAAGGAGGGGAAATAGGTTCAGAACAAGAAAAGGAGAGTTTTGAACATGCAA
1 TGAACAAGCTGCAAAAGGAGGGGAAATAGGTTCAGAACAAGAAAAGGAGAGTTTTGAACATGCAA
20397 GAAGTTT
66 GAAGTTT
20404 AAGAGAGTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.43, C:0.10, G:0.29, T:0.18
Consensus pattern (72 bp):
TGAACAAGCTGCAAAAGGAGGGGAAATAGGTTCAGAACAAGAAAAGGAGAGTTTTGAACATGCAA
GAAGTTT
Found at i:21709 original size:28 final size:28
Alignment explanation
Indices: 21669--21765 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
21659 ATTTACTGTT
*
21669 ATTTTGGTCATTTTGCATGGCCAGGGGC
1 ATTTTGGTCATTTTGCATGACCAGGGGC
21697 ATTTTGGTCATTTTGCATGACCAGGGGC
1 ATTTTGGTCATTTTGCATGACCAGGGGC
*
21725 ATTTTGGTCATTTTG--TGCACCCATGGGC
1 ATTTTGGTCATTTTGCATG-A-CCAGGGGC
21753 ATTTTGGTCATTT
1 ATTTTGGTCATTT
21766 CAAGAACCTT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 62 0.95
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.40
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATGACCAGGGGC
Found at i:22078 original size:85 final size:85
Alignment explanation
Indices: 21965--22136 Score: 344
Period size: 85 Copynumber: 2.0 Consensus size: 85
21955 ATTAGTAATA
21965 ATGGCCAATTGGTGAAAAAGAAAGGATAGAATGCTTATTGTTGGTTGCAAGTTTAGTAGTCCATT
1 ATGGCCAATTGGTGAAAAAGAAAGGATAGAATGCTTATTGTTGGTTGCAAGTTTAGTAGTCCATT
22030 TATTTTTTAAAAAGAAAGTC
66 TATTTTTTAAAAAGAAAGTC
22050 ATGGCCAATTGGTGAAAAAGAAAGGATAGAATGCTTATTGTTGGTTGCAAGTTTAGTAGTCCATT
1 ATGGCCAATTGGTGAAAAAGAAAGGATAGAATGCTTATTGTTGGTTGCAAGTTTAGTAGTCCATT
22115 TATTTTTTAAAAAGAAAGTC
66 TATTTTTTAAAAAGAAAGTC
22135 AT
1 AT
22137 ATTGTTACAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.34
Consensus pattern (85 bp):
ATGGCCAATTGGTGAAAAAGAAAGGATAGAATGCTTATTGTTGGTTGCAAGTTTAGTAGTCCATT
TATTTTTTAAAAAGAAAGTC
Done.