Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018592.1 Corchorus olitorius cultivar O-4 contig18625, 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: 24405
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Found at i:36 original size:21 final size:21
Alignment explanation
Indices: 10--51 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1 AAAATCAGA
10 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
31 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
52 GTCTGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19
Consensus pattern (21 bp):
ACAACTCCTGCCCAGGACTTG
Found at i:137 original size:72 final size:70
Alignment explanation
Indices: 1--134 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 70
* **
1 AAAATCAGAACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAAC
1 AAAATCAGAACAACTCCTGCCAAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGCGGAAAAAC
66 GGAAG
66 GGAAG
* * *
71 AAAATTCAGAACAAGTCTTGTCAAGGACTTCGACAACTCCTGCCCAGGACTT-GT-TGCGGAAAA
1 AAAA-TCAGAACAACTCCTGCCAAGGACTT-GACAACTCCTGCCCAGGACTTGGTCTGCGGAAAA
134 A
64 A
135 AACCTTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 12 0.21
71 23 0.41
72 21 0.38
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (70 bp):
AAAATCAGAACAACTCCTGCCAAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGCGGAAAAAC
GGAAG
Found at i:6547 original size:71 final size:71
Alignment explanation
Indices: 6417--6607 Score: 294
Period size: 71 Copynumber: 2.7 Consensus size: 71
6407 ATTAAAGCCT
* * * *
6417 AAAAA-CAGGACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAAGACCTGGTCTGTTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACATGGTCTGTTGAAAAA
6481 CGGAAG
66 CGGAAG
*
6487 AAAAATCAGAACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACATGGTCTGTTGAAAAA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACATGGTCTGTTGAAAAA
6552 CGGAAG
66 CGGAAG
* * *
6558 AAAATTCAGAACAAGTCCTGTCAAGGACTTGGACAACTCCTGCCCAGGAC
1 AAAAATCAGAACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGAC
6608 TTGTTGCGGA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
70 5 0.05
71 86 0.78
72 19 0.17
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (71 bp):
AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACATGGTCTGTTGAAAAA
CGGAAG
Found at i:6598 original size:22 final size:22
Alignment explanation
Indices: 6568--6610 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6558 AAAATTCAGA
* *
6568 ACAAGTCCTGTCAAGGACTTGG
1 ACAACTCCTGCCAAGGACTTGG
*
6590 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCAAGGACTTG
6611 TTGCGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCAAGGACTTGG
Found at i:19729 original size:15 final size:16
Alignment explanation
Indices: 19696--19735 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
19686 TTACTTTGTT
19696 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
19712 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
19727 TTGCTTTCT
1 TTGTTTTCT
19736 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:22952 original size:11 final size:11
Alignment explanation
Indices: 22936--22961 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22926 ATATAATTTC
22936 TTTTCTTCTAG
1 TTTTCTTCTAG
22947 TTTTCTTCTAG
1 TTTTCTTCTAG
22958 TTTT
1 TTTT
22962 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:23739 original size:15 final size:16
Alignment explanation
Indices: 23709--23749 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
23699 TTACTTTGCT
23709 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
23725 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
23740 TTGCTTTCTA
1 TTGTTTTCTA
23750 TCAATCTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.63
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:24141 original size:24 final size:25
Alignment explanation
Indices: 24101--24171 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
24091 GTTTGTTTTG
* *
24101 TGTTTTGCGTC-GAAAAATAAAATAC
1 TGTTTTGCGTCATAAAAAAAAAAT-C
*
24126 T-TTTTGCGTCATAAAAAAAAAATT
1 TGTTTTGCGTCATAAAAAAAAAATC
24150 TGTTTCTGCGTCATAAAAAAAA
1 TGTTT-TGCGTCATAAAAAAAA
24172 GAGTTTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 10 0.25
25 14 0.35
26 16 0.40
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (25 bp):
TGTTTTGCGTCATAAAAAAAAAATC
Found at i:24184 original size:25 final size:25
Alignment explanation
Indices: 24129--24185 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
24119 AAAATACTTT
*
24129 TTGCGTCATAAAAAAAAAATTTGTT
1 TTGCGTCATAAAAAAAAAATTTGTC
*
24154 TCTGCGTCATAAAAAAAAGAGTTT-TC
1 T-TGCGTCATAAAAAAAA-AATTTGTC
24180 TTGCGT
1 TTGCGT
24186 TTTTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.21
26 18 0.64
27 4 0.14
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (25 bp):
TTGCGTCATAAAAAAAAAATTTGTC
Done.