Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023029.1 Corchorus olitorius cultivar O-4 contig23062, 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: 39596
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2552 original size:22 final size:23
Alignment explanation
Indices: 2522--2578 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2512 ATTGGGTCAG
*
2522 TCTTGAATTTTTAATGT-TTAAT
1 TCTTAAATTTTTAATGTCTTAAT
2544 TCTTAAATTTATTTAATGTCTTAAT
1 TCTTAAA-TT-TTTAATGTCTTAAT
* *
2569 TATTCAATTT
1 TCTTAAATTT
2579 ATTTTACAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 6 0.21
23 3 0.10
24 10 0.34
25 10 0.34
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (23 bp):
TCTTAAATTTTTAATGTCTTAAT
Found at i:2577 original size:25 final size:24
Alignment explanation
Indices: 2531--2582 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
2521 GTCTTGAATT
*
2531 TTTAATGTTTAATTCTTAAATTTA
1 TTTAATGTTTAATTATTAAATTTA
*
2555 TTTAATGTCTTAATTATTCAATTTA
1 TTTAATGT-TTAATTATTAAATTTA
2580 TTT
1 TTT
2583 TACAATCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTAATGTTTAATTATTAAATTTA
Found at i:10844 original size:22 final size:22
Alignment explanation
Indices: 10816--10858 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
10806 AAAATCAGGA
*
10816 CAAGTCCTGCCCAGTACTTGGC
1 CAAGTCCTGCCCAGGACTTGGC
10838 CAAGTCCTGCCCAGGACTTGG
1 CAAGTCCTGCCCAGGACTTGG
10859 TCTGCTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.21
Consensus pattern (22 bp):
CAAGTCCTGCCCAGGACTTGGC
Found at i:16224 original size:12 final size:12
Alignment explanation
Indices: 16207--16234 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16197 CCTTAATTCC
16207 TTTGATTGACTG
1 TTTGATTGACTG
16219 TTTGATTGACTG
1 TTTGATTGACTG
16231 TTTG
1 TTTG
16235 TTTCCCCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.25, T:0.54
Consensus pattern (12 bp):
TTTGATTGACTG
Found at i:16826 original size:25 final size:25
Alignment explanation
Indices: 16792--16841 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
16782 TCCTCCTGTT
16792 AATCCATGAGAACAAGGAACACAAG
1 AATCCATGAGAACAAGGAACACAAG
*
16817 AATCCGTGAGAACAAGGAACACAAG
1 AATCCATGAGAACAAGGAACACAAG
16842 CAGACGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.20, G:0.22, T:0.08
Consensus pattern (25 bp):
AATCCATGAGAACAAGGAACACAAG
Found at i:18184 original size:19 final size:19
Alignment explanation
Indices: 18164--18200 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18154 AATTAATTAT
18164 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
18182 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
18201 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:18211 original size:19 final size:19
Alignment explanation
Indices: 18170--18212 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
18160 TTATTTTAAT
* * * *
18170 ATTAAATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
18189 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
18208 ATTAT
1 ATTAT
18213 TCCTAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:19079 original size:6 final size:6
Alignment explanation
Indices: 19068--19093 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19058 AATATAATAA
19068 ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG AT
19094 TACAAGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:19493 original size:65 final size:65
Alignment explanation
Indices: 19413--19543 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
19403 TGAGAATTCA
19413 ACCCAAACTAGAAACTATCAACTACATACCTACCAAATAAACAAACAAATTACAAACAAACTCAC
1 ACCCAAACTAGAAACTATCAACTACATACCTACCAAATAAACAAACAAATTACAAACAAACTCAC
19478 ACCCAAACTAGAAACTATCAACTACATACCTACCAAATAAACAAACAAATTACAAACAAACTCAC
1 ACCCAAACTAGAAACTATCAACTACATACCTACCAAATAAACAAACAAATTACAAACAAACTCAC
19543 A
1 A
19544 TTCCGTGAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.54, C:0.29, G:0.02, T:0.15
Consensus pattern (65 bp):
ACCCAAACTAGAAACTATCAACTACATACCTACCAAATAAACAAACAAATTACAAACAAACTCAC
Found at i:22561 original size:21 final size:21
Alignment explanation
Indices: 22537--22584 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
22527 GTTCATGGGT
22537 CGGGCCGGACCGGGTTCGGGC
1 CGGGCCGGACCGGGTTCGGGC
22558 CGGGCCGGACCGGGTTCGGGC
1 CGGGCCGGACCGGGTTCGGGC
22579 CGGGCC
1 CGGGCC
22585 TAAGCTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.35, G:0.52, T:0.08
Consensus pattern (21 bp):
CGGGCCGGACCGGGTTCGGGC
Found at i:22796 original size:25 final size:26
Alignment explanation
Indices: 22751--22803 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
22741 TTTTGAACTC
*
22751 ATTATTTATTATTTAAAATATAT-TT
1 ATTATTTATTATATAAAATATATATT
*
22776 ATTATTTATT-TAATAATATATATATT
1 ATTATTTATTAT-ATAAAATATATATT
22802 AT
1 AT
22804 ATCTAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 19 0.79
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTATTTATTATATAAAATATATATT
Found at i:22801 original size:23 final size:22
Alignment explanation
Indices: 22721--22803 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
22711 TTTAGTAATT
*
22721 AAATATATATTATTTATTTATTTTG
1 AAATATATA-TA-TTATTTA-TTTA
*
22746 AACTCAT-TAT-TTA-TTATTTA
1 AAAT-ATATATATTATTTATTTA
*
22766 AAATATATTTATTATTTATTTA
1 AAATATATATATTATTTATTTA
22788 ATAATATATATATTAT
1 A-AATATATATATTAT
22804 ATCTAAGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.04
20 8 0.17
21 6 0.12
22 11 0.23
23 13 0.27
24 1 0.02
25 5 0.10
26 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (22 bp):
AAATATATATATTATTTATTTA
Found at i:23672 original size:22 final size:22
Alignment explanation
Indices: 23645--23690 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
23635 CTGCATTTTC
*
23645 TATTTGTTTTTTAGTCTTAGAA
1 TATTTGTTTTTTAATCTTAGAA
23667 TATTTGTTTTTTAATCTTAGAA
1 TATTTGTTTTTTAATCTTAGAA
23689 TA
1 TA
23691 GTATTCTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (22 bp):
TATTTGTTTTTTAATCTTAGAA
Found at i:35078 original size:18 final size:18
Alignment explanation
Indices: 35055--35090 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35045 CCAGAGTTCA
35055 CTGCATAAATAACAAATC
1 CTGCATAAATAACAAATC
35073 CTGCATAAATAACAAATC
1 CTGCATAAATAACAAATC
35091 TGTCTGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
CTGCATAAATAACAAATC
Found at i:38528 original size:21 final size:21
Alignment explanation
Indices: 38504--38543 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38494 TTTACACGCG
38504 CTCTGACATGCTGATGTGGCA
1 CTCTGACATGCTGATGTGGCA
*
38525 CTCTGACATGTTGATGTGG
1 CTCTGACATGCTGATGTGG
38544 ATGCCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (21 bp):
CTCTGACATGCTGATGTGGCA
Found at i:38713 original size:22 final size:22
Alignment explanation
Indices: 38685--38729 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38675 GTTACCCAAC
38685 ATTGGAATTGTGTTAAGAATGT
1 ATTGGAATTGTGTTAAGAATGT
38707 ATTGGAATTGTGTTAAGAATGT
1 ATTGGAATTGTGTTAAGAATGT
38729 A
1 A
38730 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (22 bp):
ATTGGAATTGTGTTAAGAATGT
Done.