Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015130.1 Corchorus capsularis cultivar CVL-1 contig15151, 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: 55436
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:373 original size:11 final size:11
Alignment explanation
Indices: 353--383 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
343 AAGATATCAA
353 CTGAAGATTAT
1 CTGAAGATTAT
*
364 CTGGAGATTAT
1 CTGAAGATTAT
375 CTGAAGATT
1 CTGAAGATT
384 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:4898 original size:15 final size:15
Alignment explanation
Indices: 4880--4913 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4870 TCATCATCAC
*
4880 TCTCCTTATCCAATT
1 TCTCCTTATCCAAAT
*
4895 TCTCCTTTTCCAAAT
1 TCTCCTTATCCAAAT
4910 TCTC
1 TCTC
4914 TTTCAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCCTTATCCAAAT
Found at i:10265 original size:14 final size:13
Alignment explanation
Indices: 10246--10276 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
10236 TCCATAGTCC
10246 ATATTACTCCATAT
1 ATATTACTCCAT-T
10260 ATATTACTCCATT
1 ATATTACTCCATT
10273 ATAT
1 ATAT
10277 GAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTACTCCATT
Found at i:10429 original size:12 final size:11
Alignment explanation
Indices: 10412--10446 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
10402 AACGAATTAT
*
10412 AAAAAACAGAGA
1 AAAAAACA-AAA
10424 AAAAAACAAAA
1 AAAAAACAAAA
10435 AAAAAACAAAA
1 AAAAAACAAAA
10446 A
1 A
10447 CTCTATTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.86, C:0.09, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:16119 original size:6 final size:6
Alignment explanation
Indices: 16110--16134 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16100 ATATAAAAAC
16110 AGAACA AGAACA AGAACA AGAACA A
1 AGAACA AGAACA AGAACA AGAACA A
16135 AAATCTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAACA
Found at i:19916 original size:22 final size:21
Alignment explanation
Indices: 19885--19928 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
19875 TATAGTATGT
19885 GAAAAGAAAAAAAAATGAAAA
1 GAAAAGAAAAAAAAATGAAAA
*
19906 GAAAAGAAAAATAAAATGCAAA
1 GAAAAGAAAAA-AAAATGAAAA
19928 G
1 G
19929 GAACTTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (21 bp):
GAAAAGAAAAAAAAATGAAAA
Found at i:19928 original size:17 final size:17
Alignment explanation
Indices: 19884--19921 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
19874 TTATAGTATG
19884 TGAAAAGAAAA-AAAAA
1 TGAAAAGAAAAGAAAAA
19900 TGAAAAGAAAAGAAAAA
1 TGAAAAGAAAAGAAAAA
19917 T-AAAA
1 TGAAAA
19922 TGCAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (17 bp):
TGAAAAGAAAAGAAAAA
Found at i:27565 original size:79 final size:77
Alignment explanation
Indices: 27453--27718 Score: 303
Period size: 79 Copynumber: 3.5 Consensus size: 77
27443 TACATATCTC
** *
27453 CTTTTGTCATCACATATATCATTTATTCATTAATTTTGAGGTAAAATTCATAATTATGTT-GATT
1 CTTTTGTCGCCACACATATCATTT-TTCATTAATTTTGAGGTAAAATTCAT--TT-TGTTCGATT
27517 TCATAAGTGTATCTAT
62 TCATAAGTGTATCTAT
*
27533 CTTTTGTCGCCACACATATCATTTTTCATTAATTTTGAGAGGTAAAATTCATTTTTTTCGATTTC
1 CTTTTGTCGCCACACATATCATTTTTCATTAATTTT--GAGGTAAAATTCATTTTGTTCGATTTC
*
27598 ATAAGTGTATCTTT
64 ATAAGTGTATCTAT
* *
27612 CTTTTGTCGCCACACATATCATTTTTCATTAATTCTAAGGTAAAATTCATTTT-TT-G---TCAT
1 CTTTTGTCGCCACACATATCATTTTTCATTAATTTTGAGGTAAAATTCATTTTGTTCGATTTCAT
* ** *
27672 ATGAATATCTTT
66 AAGTGTATCTAT
* * *
27684 CTTTTGTCGTCACACGTATCA-TTATCATTAATTTT
1 CTTTTGTCGCCACACATATCATTTTTCATTAATTTT
27719 CTTGTCGATT
Statistics
Matches: 169, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
71 12 0.07
72 32 0.19
75 1 0.01
76 2 0.01
77 16 0.09
78 3 0.02
79 68 0.40
80 21 0.12
81 14 0.08
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (77 bp):
CTTTTGTCGCCACACATATCATTTTTCATTAATTTTGAGGTAAAATTCATTTTGTTCGATTTCAT
AAGTGTATCTAT
Found at i:38426 original size:33 final size:34
Alignment explanation
Indices: 38359--38442 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 34
38349 ACTCTGTTCT
38359 AAACAGAAGCAAACAATTGATGTAAAAAAAAAAAA
1 AAACAGAAGCAAACAATTGATGT-AAAAAAAAAAA
*
38394 AAACAGAAGCAAACAATTGTTGT-AAAAAAAAAA
1 AAACAGAAGCAAACAATTGATGTAAAAAAAAAAA
38427 AAACAGAAGCAAACAA
1 AAACAGAAGCAAACAA
38443 AGAAATAGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 26 0.54
35 22 0.46
ACGTcount: A:0.67, C:0.11, G:0.12, T:0.11
Consensus pattern (34 bp):
AAACAGAAGCAAACAATTGATGTAAAAAAAAAAA
Found at i:41729 original size:1 final size:1
Alignment explanation
Indices: 41686--41711 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
41676 GACTTTGTTG
41686 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
41712 CACTAGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42566 original size:20 final size:20
Alignment explanation
Indices: 42541--42581 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
42531 TAAACAATGA
42541 TGTAAGTTCTT-GGGAAGGAG
1 TGTAAGTTCTTAGGG-AGGAG
42561 TGTAAGTTCTTAGGGAGGAG
1 TGTAAGTTCTTAGGGAGGAG
42581 T
1 T
42582 ATCATGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.24, C:0.05, G:0.39, T:0.32
Consensus pattern (20 bp):
TGTAAGTTCTTAGGGAGGAG
Found at i:52124 original size:16 final size:15
Alignment explanation
Indices: 52102--52138 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
52092 CACCCAATTT
52102 TTTTTTTTAAAAATA
1 TTTTTTTTAAAAATA
52117 TATTTTTTTAAAAATA
1 T-TTTTTTTAAAAATA
52133 TTTTTT
1 TTTTTT
52139 AATCAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTTTTAAAAATA
Done.