Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006522.1 Corchorus olitorius cultivar O-4 contig06547, 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: 1668
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:75 original size:22 final size:22
Alignment explanation
Indices: 9--111 Score: 109
Period size: 22 Copynumber: 4.7 Consensus size: 22
1 AATGAAAA
* *
9 TATCAAAATTTCATAGAGGGGT
1 TATCAAAATTTCATAAAGAGGT
* * *
31 CAACAAAATTTTATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
53 TATCAAAATTTCATAAAGAGGT
1 TATCAAAATTTCATAAAGAGGT
* * *
75 TATCAAATTTTCA-AAATGTGAT
1 TATCAAAATTTCATAAA-GAGGT
*
97 TACCAAAATTTCATA
1 TATCAAAATTTCATA
112 GTCGTATTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
21 3 0.05
22 62 0.94
23 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
TATCAAAATTTCATAAAGAGGT
Found at i:240 original size:22 final size:22
Alignment explanation
Indices: 166--669 Score: 219
Period size: 22 Copynumber: 23.3 Consensus size: 22
156 CAAATTAGGA
* * *
166 AGGTTATTAAACTTTTACTATGG
1 AGGTTATCAAAATTTCA-TATGG
*
189 A-GTAATCAAAATTTC--ATGG
1 AGGTTATCAAAATTTCATATGG
* *
208 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGG
**
230 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATA-TGG
* *
253 A--TTTTCAAAATTTCATA-AG
1 AGGTTATCAAAATTTCATATGG
*
272 AGGGTTATCAAAATTTCATA-GT
1 A-GGTTATCAAAATTTCATATGG
* * *
294 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATATGG
* *
317 AGATTAACAAAATTTCATAAT-G
1 AGGTTATCAAAATTTCAT-ATGG
** **
339 AGGTTATCAAAAAATCATCGGG
1 AGGTTATCAAAATTTCATATGG
* *
361 AGGTTATCAGAA--T--T-TGT
1 AGGTTATCAAAATTTCATATGG
* * *
378 A-GTTATCAAGATTTCATAAGA
1 AGGTTATCAAAATTTCATATGG
* *
399 AGGTTAT-AAAATTTTATAAGG
1 AGGTTATCAAAATTTCATATGG
* *
420 AGGTTTATCAAAATTTTATA-GCA
1 AGG-TTATCAAAATTTCATATG-G
*
443 AGGTTATCACAATTTCATAGTGTG
1 AGGTTATCAAAATTTCATA-TG-G
*
467 A--TTATCAAAATTTCAGAGTGTG
1 AGGTTATCAAAATTTCATA-TG-G
*
489 A--TTA-CTAACAA-TTCAAATGG
1 AGGTTATC-AA-AATTTCATATGG
* * * **
509 AGGTTCTTAAATTTTCATAACG
1 AGGTTATCAAAATTTCATATGG
* * * *
531 TGGTTATCAATATATCATATGA
1 AGGTTATCAAAATTTCATATGG
* * *
553 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATA-TGG
* *
576 TGGTTATCAAAATTTCAT-TCAG
1 AGGTTATCAAAATTTCATAT-GG
*
598 AAGTTATCAAAATTTCATA-GTG
1 AGGTTATCAAAATTTCATATG-G
* * * * *
620 AGGTTTTTAAAATTCCTTAGGG
1 AGGTTATCAAAATTTCATATGG
*
642 AGGTTATCAAAATTTCATAAGG
1 AGGTTATCAAAATTTCATATGG
664 AGGTTA
1 AGGTTA
670 AAAAAAATTT
Statistics
Matches: 363, Mismatches: 85, Indels: 67
0.70 0.17 0.13
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
19 6 0.02
20 16 0.04
21 38 0.10
22 248 0.68
23 41 0.11
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGG
Found at i:585 original size:45 final size:44
Alignment explanation
Indices: 531--619 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 44
521 TTTCATAACG
* *
531 TGGTTATCAATATATCA-TATGAAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATTA-GAA-GTTATCAAAATCTCATAGTGT
* *
576 TGGTTATCAAAATTTCATTCAGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATT-AGAAGTTATCAAAATCTCATAGTG
620 AGGTTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 33 0.87
46 4 0.11
47 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (44 bp):
TGGTTATCAAAATATCATTAGAAGTTATCAAAATCTCATAGTGT
Found at i:1627 original size:2 final size:2
Alignment explanation
Indices: 1620--1667 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
1610 CTTTTATGTC
*
1620 AT AT AT AT AT AT AT AT A- AT -T AG ACT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
1660 AT AT AT AT
1 AT AT AT AT
1668 T
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Done.