Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006905.1 Corchorus capsularis cultivar CVL-1 contig06926, 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: 27944
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:1367 original size:18 final size:18
Alignment explanation
Indices: 1356--1408 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1346 ACACCCAATA
1356 GCCGCACCACACCAAGTG
1 GCCGCACCACACCAAGTG
*
1374 GTCGCACCACACCAAGTG
1 GCCGCACCACACCAAGTG
*
1392 GCCGCACCGCACCAAGT
1 GCCGCACCACACCAAGT
1409 TGCCACACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.26, C:0.43, G:0.23, T:0.08
Consensus pattern (18 bp):
GCCGCACCACACCAAGTG
Found at i:2289 original size:13 final size:13
Alignment explanation
Indices: 2271--2303 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2261 CTTGGAGAAG
2271 AAAAGAGCTTCGT
1 AAAAGAGCTTCGT
2284 AAAAGAGCTTCGT
1 AAAAGAGCTTCGT
2297 AAAAGAG
1 AAAAGAG
2304 TCAAGGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (13 bp):
AAAAGAGCTTCGT
Found at i:2759 original size:36 final size:36
Alignment explanation
Indices: 2693--2768 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
2683 CACCCAAGGT
* * *
2693 GATGGCACCGAAAGTGTTTACTACACTGAAAATGGC
1 GATGGCACCGAAACTGTTCACCACACTGAAAATGGC
* * * *
2729 GATGGCACCGAAACTGTTCACCGCAGTGAAAGTGGT
1 GATGGCACCGAAACTGTTCACCACACTGAAAATGGC
2765 GATG
1 GATG
2769 AAGTGATAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (36 bp):
GATGGCACCGAAACTGTTCACCACACTGAAAATGGC
Found at i:6385 original size:13 final size:13
Alignment explanation
Indices: 6367--6392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6357 AAGAAGATTT
6367 TTTTTTTTTTAAC
1 TTTTTTTTTTAAC
6380 TTTTTTTTTTAAC
1 TTTTTTTTTTAAC
6393 CTAGAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTAAC
Found at i:12573 original size:109 final size:109
Alignment explanation
Indices: 12420--12714 Score: 432
Period size: 109 Copynumber: 2.7 Consensus size: 109
12410 TAAATTAAAA
** *
12420 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATTGAAAATAGAGTTTTTAG
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATTGAAAATAGAGTTTTTAG
12484 TAGAATAAATTGTATAATAGAAAAAATTTTAATATATCCAAATTTTT
63 TAGAATAAATTGTATAATAGAAAAAATTTTAATATATCCAAATTTTT
*
12531 TTGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAA-TGAAAATAGAGTTTTTAGTAG
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATTGAAAATAGAGTTTTTAGTAG
* *
12595 AATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 AAT-AAATTGTATAATAGAAAAAATTTTAATATATCCAAATTTTT
* *
12640 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATTG----AAAATAGAGTTTTTA
12705 GTAGAATAAA
62 GTAGAATAAA
12715 ACTATAATAG
Statistics
Matches: 168, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
108 24 0.14
109 98 0.58
110 13 0.08
111 9 0.05
113 3 0.02
114 21 0.12
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATTGAAAATAGAGTTTTTAGTAG
AATAAATTGTATAATAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:18278 original size:34 final size:32
Alignment explanation
Indices: 18238--18303 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 32
18228 TTAATTGAAT
18238 ATAAATTGATATAGTTATAAATTGATATATATAC
1 ATAAATTGATATAGTTATAAA-T-ATATATATAC
18272 ATAAATTGATATAGTTATAAATATATATATAC
1 ATAAATTGATATAGTTATAAATATATATATAC
18304 CAAAATAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 10 0.31
33 1 0.03
34 21 0.66
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (32 bp):
ATAAATTGATATAGTTATAAATATATATATAC
Found at i:18300 original size:16 final size:16
Alignment explanation
Indices: 18237--18293 Score: 80
Period size: 16 Copynumber: 3.4 Consensus size: 16
18227 ATTAATTGAA
18237 TATAAATTGATATAGT
1 TATAAATTGATATAGT
18253 TATAAATTGATATA-T
1 TATAAATTGATATAGT
18268 ATACATAAATTGATATAGT
1 -T--ATAAATTGATATAGT
18287 TATAAAT
1 TATAAAT
18294 ATATATATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.03
16 21 0.57
18 14 0.38
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (16 bp):
TATAAATTGATATAGT
Found at i:18301 original size:18 final size:17
Alignment explanation
Indices: 18237--18302 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 17
18227 ATTAATTGAA
*
18237 TATAAATT-GATATAGT
1 TATAAATTATATATAGT
18253 TATAAATTGATATATA-T
1 TATAAATT-ATATATAGT
* *
18270 ACATAAATT-GATATAGT
1 -TATAAATTATATATAGT
18287 TATAAATATATATATA
1 TATAAAT-TATATATA
18303 CCAAAATAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 19 0.49
17 3 0.08
18 17 0.44
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (17 bp):
TATAAATTATATATAGT
Found at i:23541 original size:7 final size:7
Alignment explanation
Indices: 23529--23587 Score: 118
Period size: 7 Copynumber: 8.4 Consensus size: 7
23519 ATCATTCATT
23529 AATTGAA
1 AATTGAA
23536 AATTGAA
1 AATTGAA
23543 AATTGAA
1 AATTGAA
23550 AATTGAA
1 AATTGAA
23557 AATTGAA
1 AATTGAA
23564 AATTGAA
1 AATTGAA
23571 AATTGAA
1 AATTGAA
23578 AATTGAA
1 AATTGAA
23585 AAT
1 AAT
23588 GACAATTAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
AATTGAA
Found at i:24678 original size:2 final size:2
Alignment explanation
Indices: 24671--24699 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24661 GATTCAATAA
24671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24700 AGTATACTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25994 original size:31 final size:32
Alignment explanation
Indices: 25959--26046 Score: 106
Period size: 39 Copynumber: 2.6 Consensus size: 32
25949 TGTCTTACTT
25959 AAAAAAATACTTAAAACTTTTTTTA-AACATA
1 AAAAAAATACTTAAAACTTTTTTTATAACATA
25990 AAAAAAATACTTAAAACTGATTTTTTTTATTGCAACATA
1 AAAAAAATACTTAAAAC----TTTTTTTA-T--AACATA
26029 AAAAAAATACTTAAAACT
1 AAAAAAATACTTAAAACT
26047 GTTTAAGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
31 17 0.35
35 9 0.18
39 23 0.47
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.34
Consensus pattern (32 bp):
AAAAAAATACTTAAAACTTTTTTTATAACATA
Found at i:26768 original size:11 final size:11
Alignment explanation
Indices: 26752--26794 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
26742 TATAATATAT
26752 CTAATTAATAG
1 CTAATTAATAG
*
26763 CTAATTAATAT
1 CTAATTAATAG
26774 CTAATTAATAG
1 CTAATTAATAG
*
26785 TTAATTAATA
1 CTAATTAATA
26795 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:26775 original size:22 final size:22
Alignment explanation
Indices: 26748--26794 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
26738 CCATTATAAT
26748 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
26770 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
26792 ATA
1 ATA
26795 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Done.