Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015634.1 Corchorus olitorius cultivar O-4 contig15667, 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: 37296
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1788 original size:15 final size:15
Alignment explanation
Indices: 1768--1809 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1758 ACAGAGATTG
1768 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
*
1783 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
*
1798 ACTAAAAAACAA
1 AC-AGAAAACAA
1810 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:8432 original size:22 final size:22
Alignment explanation
Indices: 8414--8460 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
8404 TAGATGGTCG
8414 GGCCCTAGCCGGGCAATGGCCA
1 GGCCCTAGCCGGGCAATGGCCA
8436 GGCCCTAGCCGGGCAATGGCC-
1 GGCCCTAGCCGGGCAATGGCCA
8457 GGCC
1 GGCC
8461 GAGCTAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.15, C:0.38, G:0.38, T:0.09
Consensus pattern (22 bp):
GGCCCTAGCCGGGCAATGGCCA
Found at i:9681 original size:13 final size:13
Alignment explanation
Indices: 9663--9709 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
9653 ATCAATCTTT
9663 CTTGCAACCTTAC
1 CTTGCAACCTTAC
9676 CTTGCAACCTTAC
1 CTTGCAACCTTAC
*
9689 CTT---ACCTTGC
1 CTTGCAACCTTAC
9699 CTTGCAACCTT
1 CTTGCAACCTT
9710 TCTTGTTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 9 0.30
13 21 0.70
ACGTcount: A:0.19, C:0.38, G:0.09, T:0.34
Consensus pattern (13 bp):
CTTGCAACCTTAC
Found at i:11411 original size:34 final size:34
Alignment explanation
Indices: 11373--11439 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
11363 CACATGGGTG
11373 CAATTCTCTATTTGAAACGTGAAGAGAAATATTA
1 CAATTCTCTATTTGAAACGTGAAGAGAAATATTA
11407 CAATTCTCTATTTGAAACGTGAAGAGAAATATT
1 CAATTCTCTATTTGAAACGTGAAGAGAAATATT
11440 TAATATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (34 bp):
CAATTCTCTATTTGAAACGTGAAGAGAAATATTA
Found at i:23865 original size:21 final size:21
Alignment explanation
Indices: 23841--23885 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23831 GGCGCCCACA
* *
23841 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGAACCCAAG
*
23862 TGGTTTGCTTGAGAACCCAAG
1 TGGTTTCCTTGAGAACCCAAG
23883 TGG
1 TGG
23886 GCAGTGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (21 bp):
TGGTTTCCTTGAGAACCCAAG
Found at i:25759 original size:41 final size:40
Alignment explanation
Indices: 25677--25757 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
25667 ATTCCTCTTA
*
25677 AATTTTATTTTGAAGACATTTAGAAATTTGATGAATTTTTT
1 AATTTTAATTTGAAGACATTTAGAAATTT-ATGAATTTTTT
*
25718 AATTTTAATTTGAAGACAATTTA-ATATTCT-TGAATTTTTT
1 AATTTTAATTTGAAGAC-ATTTAGAAATT-TATGAATTTTTT
25758 TAGTTCTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
40 10 0.28
41 20 0.56
42 6 0.17
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.52
Consensus pattern (40 bp):
AATTTTAATTTGAAGACATTTAGAAATTTATGAATTTTTT
Found at i:28348 original size:65 final size:65
Alignment explanation
Indices: 28242--28367 Score: 216
Period size: 65 Copynumber: 1.9 Consensus size: 65
28232 AGCTGGTCCT
* * *
28242 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCTTGGGCTAGTGCAGAAAGTTTGAATCATCCA
1 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTCGGCTAGTGCAGAAAGTTGGAATCATCCA
*
28307 ACCCATGCATGGGGTACTCTTGGCCTACCCACGCCTCGGCTAGTGCAGAAAGTTGGAATCA
1 ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTCGGCTAGTGCAGAAAGTTGGAATCA
28368 ATAGCAAGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.22
Consensus pattern (65 bp):
ACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTCGGCTAGTGCAGAAAGTTGGAATCATCCA
Found at i:28582 original size:21 final size:21
Alignment explanation
Indices: 28556--28597 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28546 GCATCTTAGG
*
28556 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
28577 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
28598 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:34505 original size:23 final size:22
Alignment explanation
Indices: 34458--34506 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
34448 TTATTTTTCG
*
34458 TTATTTTTTTTCTTGTTTTATTT
1 TTATTTTTTTTCTTG-TTTACTT
34481 TTATTTATTTTTCTTAG-TTACTT
1 TTATTT-TTTTTCTT-GTTTACTT
34504 TTA
1 TTA
34507 ATTGTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 14 0.61
24 8 0.35
25 1 0.04
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (22 bp):
TTATTTTTTTTCTTGTTTACTT
Found at i:35662 original size:21 final size:21
Alignment explanation
Indices: 35623--35671 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35613 TCAATGCTTT
**
35623 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
35645 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
35666 A-GAAGC
1 AGGAAGC
35672 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.