Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009659.1 Corchorus capsularis cultivar CVL-1 contig09680, 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: 19864
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Found at i:1050 original size:25 final size:27
Alignment explanation
Indices: 1003--1055 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
993 TAATATTCAA
1003 TTAAAACAAACTCTATGTAGCAAAAAAAC
1 TTAAAACAAACTC-ATG-AGCAAAAAAAC
1032 TTAAAACAAACTC-TG-GCAAAAAAA
1 TTAAAACAAACTCATGAGCAAAAAAA
1056 AAATTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.38
27 2 0.08
29 13 0.54
ACGTcount: A:0.57, C:0.17, G:0.08, T:0.19
Consensus pattern (27 bp):
TTAAAACAAACTCATGAGCAAAAAAAC
Found at i:1062 original size:27 final size:29
Alignment explanation
Indices: 1001--1067 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 29
991 TATAATATTC
* * *
1001 AATTAAAACAAACTCTATGTAGCAAAAAA
1 AATTAAAACAAACTCTAGGCAGAAAAAAA
*
1030 ACTTAAAACAAACTCT-GGCA-AAAAAAA
1 AATTAAAACAAACTCTAGGCAGAAAAAAA
1057 AATTAAAACAA
1 AATTAAAACAA
1068 CAATTGAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 16 0.48
28 2 0.06
29 15 0.45
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (29 bp):
AATTAAAACAAACTCTAGGCAGAAAAAAA
Found at i:10362 original size:17 final size:17
Alignment explanation
Indices: 10340--10387 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
10330 GGGGTGATCT
10340 TGATCTTAGATTACT-A
1 TGATCTTAGATTACTGA
*
10356 GTGATCTTAGATCACTGA
1 -TGATCTTAGATTACTGA
*
10374 TGATCTTTGATTAC
1 TGATCTTAGATTAC
10388 CTAGGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (17 bp):
TGATCTTAGATTACTGA
Found at i:12451 original size:12 final size:11
Alignment explanation
Indices: 12436--12473 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
12426 GTAATTAGAG
12436 ATATAATATAT
1 ATATAATATAT
12447 AATATAATATAT
1 -ATATAATATAT
12459 ATAATAATATA-
1 AT-ATAATATAT
12470 ATAT
1 ATAT
12474 GTACTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 4 0.16
12 19 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATAATATAT
Found at i:12465 original size:17 final size:17
Alignment explanation
Indices: 12436--12473 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
12426 GTAATTAGAG
12436 ATATAATATATAATATA
1 ATATAATATATAATATA
12453 ATAT-ATATAATAATATA
1 ATATAATAT-ATAATATA
12470 ATAT
1 ATAT
12474 GTACTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAATATATAATATA
Found at i:19235 original size:7 final size:7
Alignment explanation
Indices: 19211--19850 Score: 1114
Period size: 7 Copynumber: 93.3 Consensus size: 7
19201 TTTAGTGTCC
19211 TTTAGGG
1 TTTAGGG
19218 -TTATGGG
1 TTTA-GGG
*
19225 -TTAGTG
1 TTTAGGG
19231 TTTAGGG
1 TTTAGGG
*
19238 TTTAGAG
1 TTTAGGG
19245 TTTAGGG
1 TTTAGGG
*
19252 TATAGGG
1 TTTAGGG
19259 -TTAGGG
1 TTTAGGG
19265 TTTAGGG
1 TTTAGGG
19272 -TTAGGG
1 TTTAGGG
19278 -TTAGTCGG
1 TTTAG--GG
19286 -TTAGGG
1 TTTAGGG
19292 -TTAGGG
1 TTTAGGG
19298 TTTAGGG
1 TTTAGGG
19305 -TTAGGG
1 TTTAGGG
19311 TTTAGGG
1 TTTAGGG
19318 TTTAGGG
1 TTTAGGG
19325 TTTAGGG
1 TTTAGGG
19332 TTTAGGG
1 TTTAGGG
19339 TTTAGGG
1 TTTAGGG
19346 TTTAGGG
1 TTTAGGG
19353 TTTAGGG
1 TTTAGGG
19360 TTTAGGG
1 TTTAGGG
19367 TTTAGGG
1 TTTAGGG
19374 TTTAGGG
1 TTTAGGG
19381 TTTAGGG
1 TTTAGGG
19388 TTTAGGG
1 TTTAGGG
19395 TTTAGGG
1 TTTAGGG
19402 TTTAGGG
1 TTTAGGG
19409 TTTAGGG
1 TTTAGGG
19416 TTTAGGG
1 TTTAGGG
19423 TTTAGGG
1 TTTAGGG
19430 TTTAGGG
1 TTTAGGG
19437 TTTAGGG
1 TTTAGGG
19444 TTTAGGG
1 TTTAGGG
19451 TTTAGGG
1 TTTAGGG
19458 TTTAGGG
1 TTTAGGG
19465 TTTAGGG
1 TTTAGGG
19472 TTTAGGG
1 TTTAGGG
19479 TTTAGGG
1 TTTAGGG
19486 TTTAGGG
1 TTTAGGG
19493 TTTAGGG
1 TTTAGGG
19500 TTTAGGG
1 TTTAGGG
19507 TTTAGGG
1 TTTAGGG
19514 TTTAGGG
1 TTTAGGG
19521 TTTAGGG
1 TTTAGGG
19528 TTTAGGG
1 TTTAGGG
19535 TTTAGGG
1 TTTAGGG
19542 TTTAGGG
1 TTTAGGG
19549 TTTAGGG
1 TTTAGGG
19556 TTTAGGG
1 TTTAGGG
19563 TTTAGGG
1 TTTAGGG
19570 TTTAGGG
1 TTTAGGG
19577 TTTAGGG
1 TTTAGGG
19584 TTTAGGG
1 TTTAGGG
19591 TTTAGGG
1 TTTAGGG
19598 -TTAGGG
1 TTTAGGG
19604 TTTAGGG
1 TTTAGGG
19611 TTTAGGG
1 TTTAGGG
19618 TTTAGGG
1 TTTAGGG
19625 TTTAGGG
1 TTTAGGG
19632 TTTAGGG
1 TTTAGGG
19639 TTTAGGG
1 TTTAGGG
19646 TTTAGGG
1 TTTAGGG
19653 TTTAGGG
1 TTTAGGG
19660 -TTAGGG
1 TTTAGGG
19666 TTTAGGG
1 TTTAGGG
19673 TTTAGGG
1 TTTAGGG
19680 TTTAGGG
1 TTTAGGG
19687 TTTAGGG
1 TTTAGGG
19694 TTTAGGG
1 TTTAGGG
19701 TTTAGGG
1 TTTAGGG
19708 TTTAGGG
1 TTTAGGG
19715 TTTAGGG
1 TTTAGGG
19722 TTTAGGG
1 TTTAGGG
19729 TTTAGGG
1 TTTAGGG
19736 TTTAGGG
1 TTTAGGG
19743 -TTAGGG
1 TTTAGGG
19749 -TTAGGG
1 TTTAGGG
19755 TTTAGGG
1 TTTAGGG
19762 TTTAGGG
1 TTTAGGG
19769 TTTAGGG
1 TTTAGGG
19776 TTTAGGG
1 TTTAGGG
19783 TTTAGGG
1 TTTAGGG
19790 TTTAGGG
1 TTTAGGG
19797 TTTAGGG
1 TTTAGGG
19804 TTTAGGG
1 TTTAGGG
19811 -TTAGGG
1 TTTAGGG
19817 TTTAGGG
1 TTTAGGG
19824 TTTAGGG
1 TTTAGGG
19831 -TTAGGG
1 TTTAGGG
19837 -TTAGGG
1 TTTAGGG
19843 -TTAGGG
1 TTTAGGG
19849 TT
1 TT
19851 AGGTTAGGTT
Statistics
Matches: 615, Mismatches: 6, Indels: 24
0.95 0.01 0.04
Matches are distributed among these distances:
6 82 0.13
7 527 0.86
8 6 0.01
ACGTcount: A:0.15, C:0.00, G:0.43, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Done.