Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014063.1 Corchorus olitorius cultivar O-4 contig14096, 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: 45186
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:1223 original size:24 final size:24
Alignment explanation
Indices: 1191--1238 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1181 TTTGTCTTCC
1191 TACTTTTTTGCTTCAATTTAGTCA
1 TACTTTTTTGCTTCAATTTAGTCA
*
1215 TACTTTTTTGCTTCTATTTAGTCA
1 TACTTTTTTGCTTCAATTTAGTCA
1239 ATTAAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (24 bp):
TACTTTTTTGCTTCAATTTAGTCA
Found at i:5450 original size:16 final size:16
Alignment explanation
Indices: 5429--5460 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5419 CTAAGCTTAC
5429 AAAACTTATTAAGCAT
1 AAAACTTATTAAGCAT
5445 AAAACTTATTAAGCAT
1 AAAACTTATTAAGCAT
5461 GTAAGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAACTTATTAAGCAT
Found at i:11152 original size:11 final size:11
Alignment explanation
Indices: 11119--11164 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
11109 TCCATGTGCA
11119 CACGTGTCATC
1 CACGTGTCATC
*
11130 CAC--GTC-TA
1 CACGTGTCATC
*
11138 CACGTGTCTTC
1 CACGTGTCATC
11149 CACGTGTCATC
1 CACGTGTCATC
11160 CACGT
1 CACGT
11165 CAGCGCGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.14
9 3 0.10
10 3 0.10
11 19 0.66
ACGTcount: A:0.17, C:0.37, G:0.17, T:0.28
Consensus pattern (11 bp):
CACGTGTCATC
Found at i:11457 original size:43 final size:43
Alignment explanation
Indices: 11392--11479 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
11382 TCTGTTAGGG
* *
11392 CATAGTTTTGTGAAGTGGACTGTTAAATATTAGGATTAGAATT
1 CATAGTTTTGTGAAATGAACTGTTAAATATTAGGATTAGAATT
*
11435 CATAGTTTTGTGAAATGAACTGTTACATATTAGGATTAGAATT
1 CATAGTTTTGTGAAATGAACTGTTAAATATTAGGATTAGAATT
11478 CA
1 CA
11480 ATTCGTTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (43 bp):
CATAGTTTTGTGAAATGAACTGTTAAATATTAGGATTAGAATT
Found at i:36656 original size:20 final size:20
Alignment explanation
Indices: 36604--36658 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
36594 AATGTTAAGC
* * *
36604 TTTTCAATAACATTTTAAAT
1 TTTTTAATAACCTTATAAAT
* * *
36624 TTATTAGTCACCTTATAAAT
1 TTTTTAATAACCTTATAAAT
36644 TTTTTAATAACCTTA
1 TTTTTAATAACCTTA
36659 AAACCTTTTT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTTAATAACCTTATAAAT
Found at i:37315 original size:87 final size:88
Alignment explanation
Indices: 37212--37393 Score: 323
Period size: 88 Copynumber: 2.1 Consensus size: 88
37202 AAACCTTGTA
37212 AATTTCTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGC-TTTTTAAATAGTTTTCTTAA
1 AATTT-TTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTTAAATAGTTTTCTTAA
37276 ATTTATTCAATCACCTCATTTAAG
65 ATTTATTCAATCACCTCATTTAAG
*
37300 AATTTTTTGGTAAGCTTATAAATTTTTTATTAAACTTAAAAGCTTTTTTAAATAGTTTTCTTAAA
1 AATTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTTAAATAGTTTTCTTAAA
*
37365 TTTATTCAATCACCTCGTTTAAG
66 TTTATTCAATCACCTCATTTAAG
37388 -ATTTTT
1 AATTTTT
37394 GGTGATCTTA
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
87 43 0.47
88 48 0.53
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (88 bp):
AATTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTTAAATAGTTTTCTTAAA
TTTATTCAATCACCTCATTTAAG
Found at i:37416 original size:88 final size:87
Alignment explanation
Indices: 37212--37416 Score: 308
Period size: 88 Copynumber: 2.3 Consensus size: 87
37202 AAACCTTGTA
37212 AATTTCTTTGGTAAGCTTATAAAT-TTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAA
1 AATTT-TTTGGTAAGCTTATAAATGTTTT-ATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAA
37276 ATTTATTCAATCACCTCATTTAAG
64 ATTTATTCAATCACCTCATTTAAG
*
37300 AATTTTTTGGTAAGCTTATAAATTTTTTATTAAACTTAAAAGCTTTTTTAAATAGTTTTCTTAAA
1 AATTTTTTGGTAAGCTTATAAATGTTTTATTAAACTTAAAAGC-TTTTTAAATAGTTTTCTTAAA
*
37365 TTTATTCAATCACCTCGTTTAAG
65 TTTATTCAATCACCTCATTTAAG
* *
37388 -A-TTTTTGGTGATCTTATTAACATGTTTTA
1 AATTTTTTGGTAAGCTTA-TAA-ATGTTTTA
37417 GAGACCTTAC
Statistics
Matches: 109, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
86 13 0.12
87 37 0.34
88 59 0.54
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (87 bp):
AATTTTTTGGTAAGCTTATAAATGTTTTATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAAT
TTATTCAATCACCTCATTTAAG
Found at i:37524 original size:23 final size:23
Alignment explanation
Indices: 37481--37524 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
37471 TGAATTTTAG
*
37481 AGTAACCTTATGAAGTTTTTTTT
1 AGTAACCTTATGAAGTGTTTTTT
37504 AGTAACCTTATCG-AGTGTTTT
1 AGTAACCTTAT-GAAGTGTTTT
37525 AGAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (23 bp):
AGTAACCTTATGAAGTGTTTTTT
Found at i:37567 original size:80 final size:80
Alignment explanation
Indices: 37468--37639 Score: 326
Period size: 80 Copynumber: 2.1 Consensus size: 80
37458 TATAGTTAAC
37468 TTATGAATTTTAGAGTAACCTTATGAAGTTTTTTTTAGTAACCTTATCGAGTGTTTTAGAAATCT
1 TTATGAATTTTAGAGTAACCTTATGAAGTTTTTTTTAGTAACCTTATCGAGTGTTTTAGAAATCT
37533 TATAAAGTAACTTTA
66 TATAAAGTAACTTTA
*
37548 TTATGAATTTTATAGTAACCTTATGAAGTTTTTTTTAGTAACCTTATCGAGTGTTTTAGAAATCT
1 TTATGAATTTTAGAGTAACCTTATGAAGTTTTTTTTAGTAACCTTATCGAGTGTTTTAGAAATCT
37613 TATAAAGTAACTTTA
66 TATAAAGTAACTTTA
*
37628 TTAAGAATTTTA
1 TTATGAATTTTA
37640 CGCAACCTTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 90 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (80 bp):
TTATGAATTTTAGAGTAACCTTATGAAGTTTTTTTTAGTAACCTTATCGAGTGTTTTAGAAATCT
TATAAAGTAACTTTA
Found at i:37573 original size:20 final size:21
Alignment explanation
Indices: 37548--37594 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
37538 AGTAACTTTA
37548 TTATGAA-TTTTATAGTAACC
1 TTATGAATTTTTATAGTAACC
*
37568 TTATGAAGTTTTTTTTAGTAACC
1 TTATGAA--TTTTTATAGTAACC
37591 TTAT
1 TTAT
37595 CGAGTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
23 16 0.70
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (21 bp):
TTATGAATTTTTATAGTAACC
Found at i:37604 original size:23 final size:23
Alignment explanation
Indices: 37555--37605 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
37545 TTATTATGAA
*
37555 TTTTATAGTAACCTTATGAAGTT
1 TTTTATAGTAACCTTATGAAGTG
*
37578 TTTTTTAGTAACCTTATCG-AGTG
1 TTTTATAGTAACCTTAT-GAAGTG
37601 TTTTA
1 TTTTA
37606 GAAATCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (23 bp):
TTTTATAGTAACCTTATGAAGTG
Found at i:38027 original size:20 final size:20
Alignment explanation
Indices: 37990--38028 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37980 TATTATGCTT
* *
37990 TTTTAGTAACATTGTTAAGC
1 TTTTAATAACATTATTAAGC
*
38010 TTTTAATAACTTTATTAAG
1 TTTTAATAACATTATTAAG
38029 ACTGCTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTTAATAACATTATTAAGC
Found at i:38180 original size:20 final size:21
Alignment explanation
Indices: 38155--38195 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38145 TTTCCATATA
38155 TAAC-TTAGTAAGCATTTTAG
1 TAACTTTAGTAAGCATTTTAG
* *
38175 TAACTTTATTAAGCTTTTTAG
1 TAACTTTAGTAAGCATTTTAG
38196 AAAGCTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (21 bp):
TAACTTTAGTAAGCATTTTAG
Found at i:41302 original size:19 final size:19
Alignment explanation
Indices: 41278--41319 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
41268 AAACCAGAGT
41278 AAAACCAAGACAATAAATC
1 AAAACCAAGACAATAAATC
* *
41297 AAAACCAGGATAATAAATC
1 AAAACCAAGACAATAAATC
41316 AAAA
1 AAAA
41320 TGTCAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.64, C:0.17, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAACCAAGACAATAAATC
Found at i:43546 original size:2 final size:2
Alignment explanation
Indices: 43539--43574 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
43529 ACACCTAATT
*
43539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43575 CGGTATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:44328 original size:2 final size:2
Alignment explanation
Indices: 44321--44345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44311 ACCACTTATA
44321 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
44346 TTTTCTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.