Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018584.1 Corchorus olitorius cultivar O-4 contig18617, 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: 26569
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1133 original size:24 final size:22
Alignment explanation
Indices: 1105--1152 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1095 CTAAAAACTC
*
1105 TATTTTTATTCATTATAACTATTT
1 TATTTTTA-CCATT-TAACTATTT
*
1129 TATTTTTACCATTTTACTATTT
1 TATTTTTACCATTTAACTATTT
1151 TA
1 TA
1153 ATTAAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 4 0.18
24 8 0.36
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTACCATTTAACTATTT
Found at i:3876 original size:58 final size:59
Alignment explanation
Indices: 3799--3972 Score: 287
Period size: 58 Copynumber: 3.0 Consensus size: 59
3789 GATACCATCT
3799 CGTATTGATTTTCAAAAGAAAGATTTAAGTGTGCAGATGATTTACATAGGCCTAACACC
1 CGTATTGATTTTCAAAAGAAAGATTTAAGTGTGCAGATGATTTACATAGGCCTAACACC
*
3858 CGTATTGA-TTTCAAAAGAAAGATTTAAGTGTGCAGATGATTTACATAGGTCTAACACC
1 CGTATTGATTTTCAAAAGAAAGATTTAAGTGTGCAGATGATTTACATAGGCCTAACACC
* * * * *
3916 CGTATTCATTTTCAAAAGGAAGATTTAAATGTGCGGATGATTTACTTAGGCCTAACA
1 CGTATTGATTTTCAAAAGAAAGATTTAAGTGTGCAGATGATTTACATAGGCCTAACA
3973 TATTTAAATT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
58 56 0.52
59 51 0.48
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (59 bp):
CGTATTGATTTTCAAAAGAAAGATTTAAGTGTGCAGATGATTTACATAGGCCTAACACC
Found at i:9804 original size:42 final size:44
Alignment explanation
Indices: 9753--9846 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 44
9743 AGTGCATTAT
* *
9753 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
* *
9794 CTGATATTCTACTCCTCCATCTGTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAA
9839 CTAATATT
1 CTAATATT
9847 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 3 0.07
42 8 0.18
43 2 0.05
45 31 0.70
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:12282 original size:19 final size:19
Alignment explanation
Indices: 12258--12294 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12248 GTACAGTACC
*
12258 TAATCTAATTTGTACAGTG
1 TAATCTAATATGTACAGTG
*
12277 TAATCTCATATGTACAGT
1 TAATCTAATATGTACAGT
12295 TGCTAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:17971 original size:35 final size:36
Alignment explanation
Indices: 17876--17972 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 36
17866 AGTAGTCCAC
*
17876 AAGT-AGCTTATTTCAGGGTAATTAAAG-AAACCAAT
1 AAGTAAGCTTAATTCAGGGTAATT-AAGTAAACCAAT
* *
17911 AAGTAAG-TTAATTCAGGGTAATTAAGTAAGCCATT
1 AAGTAAGCTTAATTCAGGGTAATTAAGTAAACCAAT
*
17946 AA-TCAGCTTAATTCAGGGTAATTAAGT
1 AAGTAAGCTTAATTCAGGGTAATTAAGT
17973 TGATTAAGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
34 6 0.11
35 47 0.85
36 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (36 bp):
AAGTAAGCTTAATTCAGGGTAATTAAGTAAACCAAT
Found at i:24821 original size:29 final size:30
Alignment explanation
Indices: 24761--24840 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
24751 GCTAAATACC
* * * *
24761 CAAAAAAATTCCTTATGTTTTGTTTTTGGGA
1 CAAAATAATCCCTTATG-TTTGATTTCGGGA
24792 CAAAATAATCCCTTATGTTT-ATTTCGGGA
1 CAAAATAATCCCTTATGTTTGATTTCGGGA
* *
24821 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
24841 CAAATATGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.58
30 3 0.07
31 15 0.35
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTGATTTCGGGA
Found at i:26089 original size:20 final size:20
Alignment explanation
Indices: 26064--26102 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
26054 CATATAAAAT
*
26064 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
26084 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
26103 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:26096 original size:27 final size:27
Alignment explanation
Indices: 26061--26113 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
26051 AATCATATAA
26061 AATAATAATAACTAA-TTTTTAAAAAT
1 AATAATAATAACTAATTTTTTAAAAAT
* *
26087 AATAACTAATTATTAATTTTTTAAAAA
1 AATAA-TAATAACTAATTTTTTAAAAA
26114 AAAGTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 8 0.35
28 10 0.43
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATAATAACTAATTTTTTAAAAAT
Found at i:26304 original size:17 final size:18
Alignment explanation
Indices: 26279--26325 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
26269 ATTGAGGTTT
*
26279 GAAAGTTTGAA-AATTGA
1 GAAATTTTGAAGAATTGA
26296 GAAATTTTGAGAGAATTGA
1 GAAATTTTGA-AGAATTGA
26315 -AAATTTTGAAG
1 GAAATTTTGAAG
26326 TTTGAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 10 0.37
19 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (18 bp):
GAAATTTTGAAGAATTGA
Done.