Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022233.1 Corchorus olitorius cultivar O-4 contig22266, 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: 33061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1535 original size:49 final size:48
Alignment explanation
Indices: 1461--1557 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 48
1451 AGGACTTGGG
* *
1461 CTGTTAGGAACGTAGAAATATAGGACAAGACCTGGGCAGGAGTTACCC
1 CTGTTAGGAACGCAGAAATACAGGACAAGACCTGGGCAGGAGTTACCC
*
1509 CTGTTGAGGAGCGCAGAAATACAGGACAAGACCTGGGCAGGAGTTACCC
1 CTGTT-AGGAACGCAGAAATACAGGACAAGACCTGGGCAGGAGTTACCC
1558 AAGTCCTGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 5 0.11
49 40 0.89
ACGTcount: A:0.32, C:0.21, G:0.31, T:0.16
Consensus pattern (48 bp):
CTGTTAGGAACGCAGAAATACAGGACAAGACCTGGGCAGGAGTTACCC
Found at i:5730 original size:15 final size:14
Alignment explanation
Indices: 5692--5755 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
5682 GATCATGTTC
5692 TTTTTTCTTTTTCA
1 TTTTTTCTTTTTCA
**
5706 TTTTCACTTTTTACA
1 TTTTTTCTTTTT-CA
* *
5721 TTTTTTCTTTCTCT
1 TTTTTTCTTTTTCA
*
5735 TTTTTTCTTTTCCA
1 TTTTTTCTTTTTCA
5749 TTTTTTC
1 TTTTTTC
5756 AGAGGGACAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 29 0.73
15 11 0.28
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTCTTTTTCA
Found at i:5738 original size:29 final size:28
Alignment explanation
Indices: 5692--5755 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
5682 GATCATGTTC
*
5692 TTTTTTCTTTTTCATTTTCACTTTTTACA
1 TTTTTTCTTTCTCATTTTCAC-TTTTACA
* ** *
5721 TTTTTTCTTTCTCTTTTTTTCTTTTCCA
1 TTTTTTCTTTCTCATTTTCACTTTTACA
5749 TTTTTTC
1 TTTTTTC
5756 AGAGGGACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTTTCTTTCTCATTTTCACTTTTACA
Found at i:14498 original size:19 final size:18
Alignment explanation
Indices: 14474--14509 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14464 TGAAGATTTA
14474 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
14493 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
14510 ATAATTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:15829 original size:22 final size:22
Alignment explanation
Indices: 15787--15829 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15777 TTTCTGATTA
**
15787 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
15809 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
15830 AATTATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:22429 original size:15 final size:15
Alignment explanation
Indices: 22390--22430 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
22380 CCCAATTTTT
22390 GATAAAATTTTTGAA
1 GATAAAATTTTTGAA
22405 -A-AAATGATTTTTGAA
1 GATAAA--ATTTTTGAA
22420 GATAAAATTTT
1 GATAAAATTTT
22431 GAATTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.14
14 1 0.05
15 14 0.64
16 1 0.05
17 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (15 bp):
GATAAAATTTTTGAA
Found at i:22733 original size:17 final size:18
Alignment explanation
Indices: 22711--22746 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22701 AATGGTAGTT
*
22711 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
22728 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
22746 T
1 T
22747 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:23612 original size:19 final size:18
Alignment explanation
Indices: 23588--23623 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23578 TGAAGATTCA
23588 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
23607 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
23624 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:23630 original size:30 final size:30
Alignment explanation
Indices: 23576--23635 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
23566 GAAGTTCGTG
* *
23576 TTTGAAGATTCATTGAAGACAATTTGAAGA
1 TTTGAAGATCCATTGAAGACAATTTCAAGA
*
23606 TTTGAAGA-CCATTGAAGAATAATTTCAAGA
1 TTTGAAGATCCATTGAAG-ACAATTTCAAGA
23636 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGATCCATTGAAGACAATTTCAAGA
Found at i:24946 original size:22 final size:22
Alignment explanation
Indices: 24904--24946 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24894 TTTCTGATTA
**
24904 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
24926 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
24947 AATTATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:30616 original size:34 final size:34
Alignment explanation
Indices: 30569--30639 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
30559 TGTTTCTTTC
* *
30569 TTTTACTTGTTTCAAAATTCCATATTAAGCATTA
1 TTTTACTTCTTTCAAAATTCCATATTAAGCACTA
* * *
30603 TTTTATTTCTTTCAAAATTTCGTATTAAGCACTA
1 TTTTACTTCTTTCAAAATTCCATATTAAGCACTA
30637 TTT
1 TTT
30640 AATAGTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.51
Consensus pattern (34 bp):
TTTTACTTCTTTCAAAATTCCATATTAAGCACTA
Found at i:32980 original size:34 final size:34
Alignment explanation
Indices: 32933--33003 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
32923 AGGTTCTTTC
*
32933 TTTTACCTTTTTCAAAATTCAATATTAAGCACTA
1 TTTTACCTTTTTCAAAATTCAATATTAAGAACTA
***
32967 TTTTA-CTTATTTCAAAATTTTGTATTAAGAACTA
1 TTTTACCTT-TTTCAAAATTCAATATTAAGAACTA
33001 TTT
1 TTT
33004 AATAGTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTTACCTTTTTCAAAATTCAATATTAAGAACTA
Done.