Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007670.1 Corchorus capsularis cultivar CVL-1 contig07691, 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: 10070
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Found at i:5244 original size:22 final size:22
Alignment explanation
Indices: 5219--5494 Score: 172
Period size: 22 Copynumber: 12.5 Consensus size: 22
5209 GCTCTTTAAG
*
5219 ATTTTGATAACCTCCTTGTGAA
1 ATTTTGATAACCTCCTTATGAA
***
5241 ATTTTGATAACCAGATTAT-AA
1 ATTTTGATAACCTCCTTATGAA
* * *
5262 AATTTGATAACCTTCATATGAA
1 ATTTTGATAACCTCCTTATGAA
* * *
5284 ATTTTCATAATCTGATCC-TATAAA
1 ATTTTGATAA-C--CTCCTTATGAA
* *
5308 ATTTTGATAA-CTACTCTATAAA
1 ATTTTGATAACCTCCT-TATGAA
* *
5330 ATTTTGATAATCTTCC-TATCAA
1 ATTTTGATAA-CCTCCTTATGAA
*
5352 ATTTTGGTAACCATCC-TATGAA
1 ATTTTGATAACC-TCCTTATGAA
* **
5374 A-TTTCAGTAACCTCAC-CGTGAA
1 ATTTTGA-TAACCTC-CTTATGAA
* *
5396 ATTTTGATAACCTCATTGTGAA
1 ATTTTGATAACCTCCTTATGAA
* *
5418 ATTTTGATAACCTTCTTATAAA
1 ATTTTGATAACCTCCTTATGAA
* *
5440 ATTAT-AGTAACCTCCTTGTGAA
1 ATTTTGA-TAACCTCCTTATGAA
* * *
5462 ATTTTGATAATCTCGTTACGAA
1 ATTTTGATAACCTCCTTATGAA
5484 ATTTTGATAAC
1 ATTTTGATAAC
5495 TACATAGAGA
Statistics
Matches: 195, Mismatches: 44, Indels: 30
0.72 0.16 0.11
Matches are distributed among these distances:
20 2 0.01
21 23 0.12
22 146 0.75
23 6 0.03
24 16 0.08
25 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
ATTTTGATAACCTCCTTATGAA
Found at i:5376 original size:44 final size:43
Alignment explanation
Indices: 5190--5474 Score: 177
Period size: 44 Copynumber: 6.5 Consensus size: 43
5180 CATTAGATCT
* * * *
5190 CTATGGAATTTTGATAATC-GCTCTTTAAGATTTTGATAACCTC
1 CTATGAAATTTTGATAATCTTC-CTATAAAATTTTGATAACCTC
* * ****
5233 CTTGTGAAATTTTGATAACCAGATTATAAAA-TTTGATAACCTTC
1 C-TATGAAATTTTGATAATCTTCCTATAAAATTTTGATAACC-TC
* *
5277 ATATGAAATTTTCATAATCTGATCCTATAAAATTTTGATAA-CTAC
1 CTATGAAATTTTGATAATCT--TCCTATAAAATTTTGATAACCT-C
* * *
5322 TCTATAAAATTTTGATAATCTTCCTATCAAATTTTGGTAACCATC
1 -CTATGAAATTTTGATAATCTTCCTATAAAATTTTGATAACC-TC
* * ** *
5367 CTATGAAA-TTTCAGTAA-CCTCACCGTGAAATTTTGATAACCTC
1 CTATGAAATTTTGA-TAATCTTC-CTATAAAATTTTGATAACCTC
* * * * *
5410 ATTGTGAAATTTTGATAACCTTCTTATAAAATTAT-AGTAACCTC
1 -CTATGAAATTTTGATAATCTTCCTATAAAATTTTGA-TAACCTC
*
5454 CTTGTGAAATTTTGATAATCT
1 C-TATGAAATTTTGATAATCT
5475 CGTTACGAAA
Statistics
Matches: 187, Mismatches: 38, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
43 36 0.19
44 106 0.57
45 19 0.10
46 26 0.14
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCTTCCTATAAAATTTTGATAACCTC
Found at i:6934 original size:117 final size:121
Alignment explanation
Indices: 6712--6977 Score: 362
Period size: 120 Copynumber: 2.2 Consensus size: 121
6702 ATTATTATAA
* *
6712 TTTTATTCTACTAAAAACTTTATTTTTATTTAATTAAATATAATATCTTTATAATTACTTTATTT
1 TTTTATTCTAATAAAAACTTTATTTTCATTTAATTAAATATAATATCTTTATAATTAC-TTATTT
** *
6777 TTACCATTTTACTATTTTTCATTAAAAACTAGGATATATT-ATTTTTTAATATACAG
65 TTACCATTTTACTATTTTTCATTAAAAACTAGGATATATTAAAATTTTAACATACAG
* * *
6833 TTTTATTCTAGTAAAAACTTTATTTTCATTTAATTAAAT-TCAATAT-TTTTTTATTA-TTA-TT
1 TTTTATTCTAATAAAAACTTTATTTTCATTTAATTAAATAT-AATATCTTTATAATTACTTATTT
* *
6894 TTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAAAATTTTAACATATAG
65 TTACCATTTTACTATTTTTCATTAAAAACTAGGATATATT--AAAATTTTAACATACAG
*
6953 TTTTATTCTAATAAAAACTCTATTT
1 TTTTATTCTAATAAAAACTTTATTT
6978 ATTGTGATTG
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
117 41 0.32
118 3 0.02
120 44 0.34
121 42 0.32
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (121 bp):
TTTTATTCTAATAAAAACTTTATTTTCATTTAATTAAATATAATATCTTTATAATTACTTATTTT
TACCATTTTACTATTTTTCATTAAAAACTAGGATATATTAAAATTTTAACATACAG
Found at i:8172 original size:16 final size:16
Alignment explanation
Indices: 8120--8190 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
8110 TAGGAAATTT
* *
8120 TCTCGAGTCATTCGGG
1 TCTCGGGTCATGCGGG
* * **
8136 TTTCGGCTCATATGGG
1 TCTCGGGTCATGCGGG
8152 T-TCGGGTCATGCGGG
1 TCTCGGGTCATGCGGG
8167 TCTCGGGTC-TGCTGGG
1 TCTCGGGTCATGC-GGG
8183 TCTCGGGT
1 TCTCGGGT
8191 TAGACGGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 15 0.33
16 30 0.67
ACGTcount: A:0.07, C:0.23, G:0.38, T:0.32
Consensus pattern (16 bp):
TCTCGGGTCATGCGGG
Found at i:9524 original size:17 final size:17
Alignment explanation
Indices: 9502--9534 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9492 TTATTACATC
9502 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
9519 AATTAATAATATAAAT
1 AATTAATAATATAAAT
9535 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Done.