Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019367.1 Corchorus olitorius cultivar O-4 contig19400, 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: 20597
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:58 original size:23 final size:22
Alignment explanation
Indices: 5--197 Score: 156
Period size: 22 Copynumber: 8.6 Consensus size: 22
1 TGTA
* * **
5 GTTATCAAGATTTCATAATGAG
1 GTTATCAAAATTTTATAGGGAG
27 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTTATAGGGAG
*
49 GTTTATCAAAATTTTATAGGAAG
1 G-TTATCAAAATTTTATAGGGAG
*
72 GTATATCAAAATTTTCATAGCGAG
1 GT-TATCAAAATTTT-ATAGGGAG
* * * *
96 GTTATCACAATTTCATAGTGTG
1 GTTATCAAAATTTTATAGGGAG
* * *
118 GTTATCAATATATTATATGGAG
1 GTTATCAAAATTTTATAGGGAG
* * *
140 GTTATCAACATCTTATA-GTACTG
1 GTTATCAAAATTTTATAGGGA--G
* *
163 GTTATCAAAATTTAATTA-GGAA
1 GTTATCAAAATTTTA-TAGGGAG
185 GTTATCAAAATTT
1 GTTATCAAAATTT
198 GCTAGCTAGC
Statistics
Matches: 139, Mismatches: 26, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
21 2 0.01
22 69 0.50
23 56 0.40
24 12 0.09
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGGGAG
Found at i:300 original size:22 final size:22
Alignment explanation
Indices: 275--323 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
265 TTCCTTAGGG
* *
275 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
*
297 AGGTTAAAAAAATTTTATAAAA
1 AGGTTAAAAAAATTTCATAAAA
319 AGGTT
1 AGGTT
324 CTTGAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:3351 original size:22 final size:22
Alignment explanation
Indices: 3243--3441 Score: 117
Period size: 22 Copynumber: 9.1 Consensus size: 22
3233 TCAAAAACTT
* *
3243 ATAGGAAGATTAACAAAATCTTAC
1 ATAGGAAGGTTATCAAAAT-TT-C
*
3267 AT-GG-AGGTTATCAAAA-ATC
1 ATAGGAAGGTTATCAAAATTTC
* *
3286 ATATGAATGTTA-CAAAATTTC
1 ATAGGAAGGTTATCAAAATTTC
*
3307 ATAGGAAGGTTTATTAAAATTTC
1 ATAGGAAGG-TTATCAAAATTTC
** *
3330 ATAGTTAGGTTATCAAAGTTTC
1 ATAGGAAGGTTATCAAAATTTC
* * *
3352 ATATGG-AGTTTATCACAATTTT
1 ATA-GGAAGGTTATCAAAATTTC
*
3374 ATAGGTAA-ATTATCAAAATTTC
1 ATAGG-AAGGTTATCAAAATTTC
* * *
3396 ATAGCG-TGGTTGTCAAAATTTA
1 ATAG-GAAGGTTATCAAAATTTC
* * *
3418 ATAAGTA-GTTATCAAGATTTC
1 ATAGGAAGGTTATCAAAATTTC
3439 ATA
1 ATA
3442 AAAATATTCA
Statistics
Matches: 134, Mismatches: 30, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
19 3 0.02
20 7 0.05
21 31 0.23
22 71 0.53
23 20 0.15
24 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
ATAGGAAGGTTATCAAAATTTC
Found at i:11757 original size:15 final size:17
Alignment explanation
Indices: 11732--11763 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11722 CTCAAATCAG
11732 TCTTATTTCTC-TCCTC
1 TCTTATTTCTCTTCCTC
11748 TCTT-TTTCTCTTCCTC
1 TCTTATTTCTCTTCCTC
11764 CTACTGCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (17 bp):
TCTTATTTCTCTTCCTC
Found at i:16148 original size:20 final size:20
Alignment explanation
Indices: 16123--16162 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16113 AACATTCTAC
16123 CATCAGATCATATAACTATT
1 CATCAGATCATATAACTATT
16143 CATCAGATCATATAACTATT
1 CATCAGATCATATAACTATT
16163 GATGAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (20 bp):
CATCAGATCATATAACTATT
Found at i:20562 original size:2 final size:2
Alignment explanation
Indices: 20555--20594 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20545 ACACATATTT
20555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20595 CGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.