Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019082.1 Corchorus olitorius cultivar O-4 contig19115, 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: 21103
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:747 original size:42 final size:42
Alignment explanation
Indices: 694--778 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
684 ATGAAATGTA
*
694 CATATCTTTGTGTTGAATAAAGTTATCTCTGCAAAAATGCAG
1 CATATCCTTGTGTTGAATAAAGTTATCTCTGCAAAAATGCAG
736 CATATCCTTGTGTTGAATAAAGTTATCTCTGCAAAAATGCAG
1 CATATCCTTGTGTTGAATAAAGTTATCTCTGCAAAAATGCAG
778 C
1 C
779 CCAAATTGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (42 bp):
CATATCCTTGTGTTGAATAAAGTTATCTCTGCAAAAATGCAG
Found at i:5978 original size:54 final size:54
Alignment explanation
Indices: 5895--6000 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
5885 TACCAAATTT
*
5895 TGCAACTACATAGGCAACTTCTAATGGAGGACTCATTCAGATTAATCGAAACCC
1 TGCAACTACATAGGCAACTTCTAACGGAGGACTCATTCAGATTAATCGAAACCC
*
5949 TGCAACTACATAGGCAATTTCTAACGGAGGACTCATTCAGATTAATCGAAAC
1 TGCAACTACATAGGCAACTTCTAACGGAGGACTCATTCAGATTAATCGAAAC
6001 TCAATGTAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (54 bp):
TGCAACTACATAGGCAACTTCTAACGGAGGACTCATTCAGATTAATCGAAACCC
Found at i:6077 original size:66 final size:63
Alignment explanation
Indices: 5967--6095 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 63
5957 CATAGGCAAT
*
5967 TTCTAACGGAGGACTCATTCAGATTAATCGAAACTCAATGTAGCTAACC-GATTTTGCAACTAC
1 TTCTAACGGAGGACTCATTCAGATTAATCGAAACCCAATGTAGCT-ACCAGATTTTGCAACTAC
* *
6030 TTCTAACGGAGGACTCAATTTTCAGATTAATCGAAACCCAATTTAGCTACCATATTTTGCAACTA
1 TTCTAACGGAGGACTC-A--TTCAGATTAATCGAAACCCAATGTAGCTACCAGATTTTGCAACTA
6095 C
63 C
6096 ATAGGCAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
63 16 0.27
64 1 0.02
65 3 0.05
66 39 0.66
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (63 bp):
TTCTAACGGAGGACTCATTCAGATTAATCGAAACCCAATGTAGCTACCAGATTTTGCAACTAC
Found at i:7234 original size:31 final size:32
Alignment explanation
Indices: 7179--7238 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
7169 TCAACTTAAA
*
7179 GCTGAATTTATTTACTGAAAAAAACTTAAGCT
1 GCTGAACTTATTTACTGAAAAAAACTTAAGCT
7211 GCTGAACTTATTTACT-AAAAAAACTTAA
1 GCTGAACTTATTTACTGAAAAAAACTTAA
7239 ACTAGGCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (32 bp):
GCTGAACTTATTTACTGAAAAAAACTTAAGCT
Found at i:8069 original size:76 final size:76
Alignment explanation
Indices: 7938--8171 Score: 441
Period size: 76 Copynumber: 3.1 Consensus size: 76
7928 ATGCGAAAGC
*
7938 AAAAGACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTGGTT
1 AAAAAACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTGGTT
8003 AAAAAATAAAT
66 AAAAAATAAAT
8014 AAAAAACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTGGTT
1 AAAAAACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTGGTT
8079 AAAAAATAAAT
66 AAAAAATAAAT
* *
8090 AAATAACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTAGTT
1 AAAAAACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTGGTT
8155 AAAAAATAAAT
66 AAAAAATAAAT
8166 AAAAAA
1 AAAAAA
8172 TAAAATTAGT
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 154 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (76 bp):
AAAAAACCAACAATGTATTGATAAAAAGTGCTATCCAGATCCTCAAATGAAAAATAGAATTGGTT
AAAAAATAAAT
Found at i:9153 original size:16 final size:16
Alignment explanation
Indices: 9132--9189 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
9122 AGCGCAGCAA
9132 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
9148 AAACAAAAACAAAAAC-
1 AAAC-AAAACGAAAACG
*
9164 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
9179 ATACCAAACGA
1 AAACAAAACGA
9190 CCCCTGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 12 0.35
17 10 0.29
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:9155 original size:22 final size:25
Alignment explanation
Indices: 9129--9175 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
9119 GACAGCGCAG
9129 CAAAAAC-AAAAC-G-AAAACGAAA
1 CAAAAACAAAAACAGAAAAACGAAA
9151 CAAAAACAAAAACAGAAAAACGAAA
1 CAAAAACAAAAACAGAAAAACGAAA
9176 ACGATACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 1 0.05
25 9 0.41
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (25 bp):
CAAAAACAAAAACAGAAAAACGAAA
Found at i:10482 original size:16 final size:16
Alignment explanation
Indices: 10461--10493 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10451 AAGGAACTTG
10461 ATAATAT-ATAGTGTTT
1 ATAATATCATA-TGTTT
10477 ATAATATCATATGTTT
1 ATAATATCATATGTTT
10493 A
1 A
10494 CATTTTATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (16 bp):
ATAATATCATATGTTT
Found at i:11378 original size:13 final size:13
Alignment explanation
Indices: 11360--11384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11350 TCCCAAACTA
11360 TAATCTATCAAAT
1 TAATCTATCAAAT
11373 TAATCTATCAAA
1 TAATCTATCAAA
11385 AAAAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATCTATCAAAT
Found at i:11609 original size:25 final size:25
Alignment explanation
Indices: 11571--11619 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11561 CCAAACAATC
11571 TTGAACACTCTCGCTCGGTCTCTAT
1 TTGAACACTCTCGCTCGGTCTCTAT
* *
11596 TTGAGCACTTTCGCTCGGTCTCTA
1 TTGAACACTCTCGCTCGGTCTCTA
11620 CAAACCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.18, T:0.37
Consensus pattern (25 bp):
TTGAACACTCTCGCTCGGTCTCTAT
Done.