Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012033.1 Corchorus olitorius cultivar O-4 contig12066, 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: 28043
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2127 original size:35 final size:32
Alignment explanation
Indices: 2037--2131 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 32
2027 TTAATTAAGG
2037 AATCCAAAAGGAGATTTTGGAAAATAAAAGGTA
1 AATCCAAAAGGAGATTTTGGAAAAT-AAAGGTA
* *
2070 ATTCCGAAAGGAGATTTTGGAAAATAAAGGTTAAA
1 AATCCAAAAGGAGATTTTGGAAAATAAAGG-T--A
* *
2105 AATCCAAAAGAAGATTATGGAAAATAA
1 AATCCAAAAGGAGATTTTGGAAAATAA
2132 TAAAATTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 5 0.09
33 24 0.45
35 24 0.45
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (32 bp):
AATCCAAAAGGAGATTTTGGAAAATAAAGGTA
Found at i:7128 original size:6 final size:7
Alignment explanation
Indices: 7111--7151 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
7101 TTTTTCCATT
7111 TTTTTCA
1 TTTTTCA
7118 TTTTTCA
1 TTTTTCA
*
7125 TTTTTCC
1 TTTTTCA
*
7132 TTTCTTCT
1 TTT-TTCA
7140 TTTTTCA
1 TTTTTCA
7147 TTTTT
1 TTTTT
7152 TCTTCAACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCA
Found at i:7146 original size:22 final size:23
Alignment explanation
Indices: 7100--7151 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
7090 AAATTTTATG
*
7100 ATTTTTCCATTTTTTTCATTTTTC
1 ATTTTTCCA-TTTCTTCATTTTTC
*
7124 ATTTTTCC-TTTCTTCTTTTTTC
1 ATTTTTCCATTTCTTCATTTTTC
7146 ATTTTT
1 ATTTTT
7152 TCTTCAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.69
24 8 0.31
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTTTCCATTTCTTCATTTTTC
Found at i:7152 original size:8 final size:8
Alignment explanation
Indices: 7100--7153 Score: 51
Period size: 7 Copynumber: 7.0 Consensus size: 8
7090 AAATTTTATG
*
7100 ATTTTTCC
1 ATTTTTTC
7108 ATTTTTTTC
1 A-TTTTTTC
7117 A-TTTTTC
1 ATTTTTTC
7124 A-TTTTTC
1 ATTTTTTC
* *
7131 CTTTCTTC
1 ATTTTTTC
7139 -TTTTTTC
1 ATTTTTTC
7146 ATTTTTTC
1 ATTTTTTC
7154 TTCAACTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
7 19 0.49
8 13 0.33
9 7 0.18
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTTC
Found at i:7154 original size:15 final size:15
Alignment explanation
Indices: 7110--7155 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
7100 ATTTTTCCAT
7110 TTTTTTCA-TTTTTC
1 TTTTTTCATTTTTTC
* * *
7124 ATTTTTCCTTTCTTC
1 TTTTTTCATTTTTTC
7139 TTTTTTCATTTTTTC
1 TTTTTTCATTTTTTC
7154 TT
1 TT
7156 CAACTTTGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTCATTTTTTC
Found at i:8240 original size:21 final size:22
Alignment explanation
Indices: 8210--8250 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
8200 GCATAATTTC
*
8210 TAAAATCAGGGGTCAAATTGAA
1 TAAAATCAGGGATCAAATTGAA
*
8232 TAAAA-CAGGGATTAAATTG
1 TAAAATCAGGGATCAAATTG
8251 CATTTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (22 bp):
TAAAATCAGGGATCAAATTGAA
Found at i:11189 original size:30 final size:30
Alignment explanation
Indices: 11153--11209 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
11143 AATGATCTTG
11153 TACTTCAAATCCTCTGGTGTAGGGAATGTT
1 TACTTCAAATCCTCTGGTGTAGGGAATGTT
11183 TACTTCAAATCCTCTGGTGTAGGGAAT
1 TACTTCAAATCCTCTGGTGTAGGGAAT
11210 TTTTTTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (30 bp):
TACTTCAAATCCTCTGGTGTAGGGAATGTT
Found at i:12859 original size:72 final size:72
Alignment explanation
Indices: 12742--12955 Score: 349
Period size: 72 Copynumber: 3.0 Consensus size: 72
12732 TGGGTGCCTC
* * *
12742 TGTTTGTTATTTGAGTTAATTTAAAGGTTGATTTGGTGATTGAGGCATGTAAATGTTCCAAATTT
1 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
* * *
12807 GGTTAAT
66 AGCTAAA
12814 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
1 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
12879 AGCTAAA
66 AGCTAAA
* *
12886 TGTTTGTTATTTGAGTT-AATTAAAAGTTGATTTGGTGATTTATGCATGTAAATGTTCTAAATTT
1 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
12950 AGCTAA
66 AGCTAA
12956 TTTATGAATA
Statistics
Matches: 134, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
71 51 0.38
72 83 0.62
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.45
Consensus pattern (72 bp):
TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
AGCTAAA
Found at i:16563 original size:21 final size:21
Alignment explanation
Indices: 16539--16630 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
16529 CTTAGGCAAT
*
16539 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
16560 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
16581 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
16602 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
16623 TCCAATGA
1 TCCAATGA
16631 TCTCCTAGCA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 3 0.04
21 66 0.96
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:20361 original size:25 final size:24
Alignment explanation
Indices: 20324--20370 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
20314 CTAGAAAATT
20324 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
20350 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
20371 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:21286 original size:21 final size:21
Alignment explanation
Indices: 21238--21287 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
21228 CTTAGGCAAT
*
21238 TCCAATAAGCTTGAAACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
21259 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGAAACCTT-C
21280 TCCAATGA
1 TCCAATGA
21288 TCTCCTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACCTTC
Found at i:25898 original size:21 final size:21
Alignment explanation
Indices: 25872--25912 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25862 TTGAAGCCCT
25872 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
25893 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
25913 GGGTTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:26511 original size:21 final size:21
Alignment explanation
Indices: 26472--26511 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26462 AGAAGATGCC
*
26472 GAAGATGCCATTTGATCCATT
1 GAAGATGCCATTAGATCCATT
*
26493 GAAGATGCCATTAGGTCCA
1 GAAGATGCCATTAGATCCA
26512 ATGACAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
GAAGATGCCATTAGATCCATT
Done.