Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018421.1 Corchorus olitorius cultivar O-4 contig18454, 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: 53600
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:4406 original size:3 final size:3
Alignment explanation
Indices: 4398--4461 Score: 56
Period size: 3 Copynumber: 21.3 Consensus size: 3
4388 AAAGCACGTG
* * * * ** * *
4398 AGC AGC AGC AAC AAC AGC AGC AGC AGC AGC CGC AAC AGC CTC AAC ATC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
4446 AGC AGC AGC AGC AGC A
1 AGC AGC AGC AGC AGC A
4462 ACAACAACTG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.38, C:0.36, G:0.23, T:0.03
Consensus pattern (3 bp):
AGC
Found at i:4512 original size:3 final size:3
Alignment explanation
Indices: 4504--4584 Score: 54
Period size: 3 Copynumber: 27.0 Consensus size: 3
4494 AGAGGCATGC
* * * * * * * * *
4504 ACA ACA ACA GCA GCA GCA GCA ACA GCA ACA ACA GCA ACA GCA GCA GCA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
* * *
4552 GCA GCA ACA ACA ACA ACA ACA ACC ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
4585 GCCCCCACAG
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.52, C:0.35, G:0.14, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:4574 original size:9 final size:9
Alignment explanation
Indices: 4517--4572 Score: 67
Period size: 9 Copynumber: 6.2 Consensus size: 9
4507 ACAACAGCAG
*
4517 CAGCAGCAA
1 CAGCAACAA
4526 CAGCAACAA
1 CAGCAACAA
*
4535 CAGCAACAG
1 CAGCAACAA
* *
4544 CAGCAGCAG
1 CAGCAACAA
4553 CAGCAACAA
1 CAGCAACAA
*
4562 CAACAACAA
1 CAGCAACAA
4571 CA
1 CA
4573 ACCACAACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (9 bp):
CAGCAACAA
Found at i:4612 original size:18 final size:18
Alignment explanation
Indices: 4583--4631 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
4573 ACCACAACAA
* * *
4583 CAGCCCCCACAGTCTCAG
1 CAGCCCCAACAGCCGCAG
*
4601 CCGCCCCAACAGCCGCAG
1 CAGCCCCAACAGCCGCAG
*
4619 CAGCCCCAGCAGC
1 CAGCCCCAACAGC
4632 GAAGGGAGCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.53, G:0.20, T:0.04
Consensus pattern (18 bp):
CAGCCCCAACAGCCGCAG
Found at i:14989 original size:25 final size:24
Alignment explanation
Indices: 14960--15016 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
14950 ATGGATTGTA
* *
14960 AAATAGATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
14985 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
15009 AAA-AAATT
1 AAATAAATT
15017 CAAGGCTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:18067 original size:27 final size:27
Alignment explanation
Indices: 18037--18092 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
18027 TTTTCAATTT
*
18037 AATGACCCTTAAATGACCTAAATCGGA
1 AATGACCCTTAAATGACCTAAATCAGA
* *
18064 AATGACCTTTACATGACCTAAATCAGA
1 AATGACCCTTAAATGACCTAAATCAGA
18091 AA
1 AA
18093 GGTGTGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.23
Consensus pattern (27 bp):
AATGACCCTTAAATGACCTAAATCAGA
Found at i:31652 original size:22 final size:21
Alignment explanation
Indices: 31622--31671 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
31612 ATAGTTTAGA
*
31622 TTTAATTTATTCTGCTTTGT-TT
1 TTTAATTTAAT-TGCTTT-TCTT
*
31644 TTTAGTTTAATTGCTTTTCTT
1 TTTAATTTAATTGCTTTTCTT
31665 TTTAATT
1 TTTAATT
31672 GTTCTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 9 0.38
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (21 bp):
TTTAATTTAATTGCTTTTCTT
Found at i:35335 original size:10 final size:10
Alignment explanation
Indices: 35315--35349 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
35305 TGTTTTGAAA
35315 AAAACGAGAG
1 AAAACGAGAG
35325 AATAA-GAGAG
1 AA-AACGAGAG
35335 AAAACGAGAG
1 AAAACGAGAG
35345 AAAAC
1 AAAAC
35350 CAAGAACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 19 0.83
11 2 0.09
ACGTcount: A:0.63, C:0.09, G:0.26, T:0.03
Consensus pattern (10 bp):
AAAACGAGAG
Found at i:37956 original size:57 final size:57
Alignment explanation
Indices: 37816--38156 Score: 490
Period size: 57 Copynumber: 6.0 Consensus size: 57
37806 CAACAATACT
* * * * *
37816 TTTTGAAACAGAAACTCTCGACCAGAGACCTCGAACATGATTTTTAAACAAG-ACAAG-
1 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGA-TTTGAAA-AGGAACAAGA
* *** * *
37873 -CTTGAAGTGAAAACTCTCGAACAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
1 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
* *
37929 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACATGATTTTAAAAGGAACAAGA
1 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
* * *
37986 TTTTGAGACAAAAACCCTCTACCAGAGACCTCGAACAGGATTTGAAAAGAAACAAGA
1 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
*
38043 TATTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
1 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
38100 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
1 TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
38157 CATGATATTT
Statistics
Matches: 254, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
54 2 0.01
55 11 0.04
56 32 0.13
57 209 0.82
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (57 bp):
TTTTGAAACAAAAACTCTCTACCAGAGACCTCGAACAGGATTTGAAAAGGAACAAGA
Found at i:39171 original size:43 final size:41
Alignment explanation
Indices: 39061--39186 Score: 182
Period size: 43 Copynumber: 3.0 Consensus size: 41
39051 ATTTATTTCA
*
39061 CTTTTTCCGCCCTCTTTTTATTTTAGGCCAAGTTTTTTCTTT
1 CTTTTTCCGACCTCTTTTTATTTTAGGCCAAGTTTTTT-TTT
39103 -TTTTTCTCGACCTCTTTTTATTTTAGGCCAAGTATTTCTTTTT
1 CTTTTTC-CGACCTCTTTTTATTTTAGGCCAAGT-TTT-TTTTT
* *
39146 CTTTTTCCGACCTCTTTCTATTTTAGGCCGAGTTTTTTTTT
1 CTTTTTCCGACCTCTTTTTATTTTAGGCCAAGTTTTTTTTT
39187 AGCTTCCCCT
Statistics
Matches: 77, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
41 11 0.14
42 28 0.36
43 30 0.39
44 8 0.10
ACGTcount: A:0.11, C:0.21, G:0.10, T:0.57
Consensus pattern (41 bp):
CTTTTTCCGACCTCTTTTTATTTTAGGCCAAGTTTTTTTTT
Found at i:41682 original size:15 final size:16
Alignment explanation
Indices: 41649--41688 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
41639 TTACTTTGCT
41649 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
41665 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
41680 TTGCTTTCT
1 TTGTTTTCT
41689 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:53561 original size:2 final size:2
Alignment explanation
Indices: 53554--53593 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53544 GAATTAAGAT
53554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53594 ATACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.