Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018374.1 Corchorus olitorius cultivar O-4 contig18407, 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: 32277
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:2634 original size:7 final size:7
Alignment explanation
Indices: 2622--2647 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2612 ATACTAATGT
2622 CTTGAAA
1 CTTGAAA
2629 CTTGAAA
1 CTTGAAA
2636 CTTGAAA
1 CTTGAAA
2643 CTTGA
1 CTTGA
2648 GAGGGAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (7 bp):
CTTGAAA
Found at i:3776 original size:19 final size:19
Alignment explanation
Indices: 3756--3792 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3746 AATTAATTAT
3756 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
3774 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
3793 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:15697 original size:6 final size:6
Alignment explanation
Indices: 15688--15712 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15678 TGTTTGATTA
15688 AGGCAC AGGCAC AGGCAC AGGCAC A
1 AGGCAC AGGCAC AGGCAC AGGCAC A
15713 TACGGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (6 bp):
AGGCAC
Found at i:24187 original size:33 final size:33
Alignment explanation
Indices: 24144--24244 Score: 175
Period size: 33 Copynumber: 3.1 Consensus size: 33
24134 AAAAAATCGG
*
24144 ACCACCATGGTCATGCCGCCCCAGGAGGGCGGC
1 ACCACTATGGTCATGCCGCCCCAGGAGGGCGGC
24177 ACCACTATGGTCATGCCGCCCCAGGAGGGCGGC
1 ACCACTATGGTCATGCCGCCCCAGGAGGGCGGC
* *
24210 ACCACTATGGTCATGTCGTCCCAGGAGGGCGGC
1 ACCACTATGGTCATGCCGCCCCAGGAGGGCGGC
24243 AC
1 AC
24245 TGGTTATTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.19, C:0.36, G:0.33, T:0.13
Consensus pattern (33 bp):
ACCACTATGGTCATGCCGCCCCAGGAGGGCGGC
Found at i:24363 original size:29 final size:28
Alignment explanation
Indices: 24324--24379 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
24314 GTTATTCCAC
*
24324 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
24353 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
24380 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:25557 original size:6 final size:6
Alignment explanation
Indices: 25540--25578 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
25530 AGGACCCCCA
* * *
25540 GGGTTT GTGTTT GGGTTT GGGTTT GAGTTT GAGTTT GGG
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGG
25579 AGGGATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.05, C:0.00, G:0.46, T:0.49
Consensus pattern (6 bp):
GGGTTT
Found at i:25563 original size:18 final size:18
Alignment explanation
Indices: 25540--25578 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25530 AGGACCCCCA
* *
25540 GGGTTTGTGTTTGGGTTT
1 GGGTTTGAGTTTGAGTTT
25558 GGGTTTGAGTTTGAGTTT
1 GGGTTTGAGTTTGAGTTT
25576 GGG
1 GGG
25579 AGGGATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.00, G:0.46, T:0.49
Consensus pattern (18 bp):
GGGTTTGAGTTTGAGTTT
Found at i:25951 original size:15 final size:15
Alignment explanation
Indices: 25931--25960 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25921 GAGTACTAGC
25931 TTTTATTGATGAAAT
1 TTTTATTGATGAAAT
25946 TTTTATTGATGAAAT
1 TTTTATTGATGAAAT
25961 CACATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTTATTGATGAAAT
Found at i:30594 original size:6 final size:6
Alignment explanation
Indices: 30585--30634 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
30575 CATCTACAGA
* * *
30585 AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG AGACGG AGACGG AGTCGG
1 AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG
30633 AG
1 AG
30635 AGAGCCTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.22, C:0.16, G:0.60, T:0.02
Consensus pattern (6 bp):
AGGCGG
Found at i:31175 original size:33 final size:35
Alignment explanation
Indices: 31132--31201 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 35
31122 GACTGATGAG
*
31132 ACACAAATTTAATTATAT-AAT-TATAATATATAC
1 ACACAAATTTAATTATATAAATATATAATACATAC
* *
31165 ACACACATTTATTTATATACAATATATAATACATAC
1 ACACAAATTTAATTATATA-AATATATAATACATAC
31201 A
1 A
31202 TAATAGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 16 0.52
35 3 0.10
36 12 0.39
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (35 bp):
ACACAAATTTAATTATATAAATATATAATACATAC
Done.