Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009851.1 Corchorus capsularis cultivar CVL-1 contig09872, 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: 40447
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:11684 original size:64 final size:63
Alignment explanation
Indices: 11578--11894 Score: 401
Period size: 64 Copynumber: 4.9 Consensus size: 63
11568 TAGTAATTAA
*
11578 TTGGCC-TTTT-GGATGTAAATAGAACTTCTCCCTTTGTGGGATACTGGAAAATGCCTTAGAT
1 TTGGCCTTTTTGGGATGTAAATAGAACTTCTCCCTTTGTGGGATACTGGAAAATGCCATAGAT
11639 TTGGCCTTTTTGGGATGTAAATAGAGAACTTCT-CCTTTGTGGGATACTACTGGGAAAATGCCAT
1 TTGGCCTTTTTGGGATGTAAAT--AGAACTTCTCCCTTTGTGGG--A-TACT-GGAAAATGCCAT
11703 AGAT
60 AGAT
* * *
11707 TTGGCCTTTTGGGGATGTAATTAGAACTTCTCCCTTTGTTGGGATACTGGAAAATGCCTTAGAT
1 TTGGCCTTTTTGGGATGTAAATAGAACTTCTCCCTTTG-TGGGATACTGGAAAATGCCATAGAT
11771 TTGGCCTTTTTGGGATGTAAATAGAACTTCT-CCTTTGTGGGATACTACTGGAAATTAAATGCCA
1 TTGGCCTTTTTGGGATGTAAATAGAACTTCTCCCTTTGTGGG--A-TACTGG--A--AAATGCCA
11835 TAGAT
59 TAGAT
* * *
11840 TTGGCCTTTTTGGGATGTAATTAGAACTTCTCCCTTTTTTGGGA-ATTGGAAAATG
1 TTGGCCTTTTTGGGATGTAAATAGAACTTCTCCC-TTTGTGGGATACTGGAAAATG
11895 GAAAATTGGG
Statistics
Matches: 227, Mismatches: 10, Indels: 36
0.83 0.04 0.13
Matches are distributed among these distances:
61 6 0.03
62 8 0.04
63 21 0.09
64 55 0.24
65 20 0.09
66 11 0.05
67 15 0.07
68 39 0.17
69 43 0.19
70 2 0.01
71 7 0.03
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (63 bp):
TTGGCCTTTTTGGGATGTAAATAGAACTTCTCCCTTTGTGGGATACTGGAAAATGCCATAGAT
Found at i:11779 original size:132 final size:131
Alignment explanation
Indices: 11578--11894 Score: 518
Period size: 132 Copynumber: 2.4 Consensus size: 131
11568 TAGTAATTAA
*
11578 TTGGCCTTTT-GGATGTAAATAGAACTTCTCCCTTTG-TGGGATACTGGAAAATGCCTTAGATTT
1 TTGGCCTTTTGGGATGTAATTAGAACTTCTCCCTTTGTTGGGATACTGGAAAATGCCTTAGATTT
*
11641 GGCCTTTTTGGGATGTAAATAGAGAACTTCTCCTTTGTGGGATACTACTGG-GA-AAATGCCATA
66 GGCCTTTTTGGGATGTAAAT--AGAACTTCTCCTTTGTGGGATACTACTGGAAATAAATGCCATA
11704 GAT
129 GAT
11707 TTGGCCTTTTGGGGATGTAATTAGAACTTCTCCCTTTGTTGGGATACTGGAAAATGCCTTAGATT
1 TTGGCCTTTT-GGGATGTAATTAGAACTTCTCCCTTTGTTGGGATACTGGAAAATGCCTTAGATT
11772 TGGCCTTTTTGGGATGTAAATAGAACTTCTCCTTTGTGGGATACTACTGGAAATTAAATGCCATA
65 TGGCCTTTTTGGGATGTAAATAGAACTTCTCCTTTGTGGGATACTACTGGAAA-TAAATGCCATA
11837 GAT
129 GAT
* *
11840 TTGGCCTTTTTGGGATGTAATTAGAACTTCTCCCTTTTTTGGGA-ATTGGAAAATG
1 TTGGCC-TTTTGGGATGTAATTAGAACTTCTCCCTTTGTTGGGATACTGGAAAATG
11895 GAAAATTGGG
Statistics
Matches: 177, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
129 10 0.06
130 29 0.16
131 26 0.15
132 57 0.32
133 51 0.29
134 4 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (131 bp):
TTGGCCTTTTGGGATGTAATTAGAACTTCTCCCTTTGTTGGGATACTGGAAAATGCCTTAGATTT
GGCCTTTTTGGGATGTAAATAGAACTTCTCCTTTGTGGGATACTACTGGAAATAAATGCCATAGA
T
Found at i:21125 original size:13 final size:14
Alignment explanation
Indices: 21107--21136 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21097 CGAACTGGGG
21107 AAAAAAAAGA-AAA
1 AAAAAAAAGAGAAA
21120 AAAAAAAAGAGAAA
1 AAAAAAAAGAGAAA
21134 AAA
1 AAA
21137 CTAAAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAGAAA
Found at i:21142 original size:15 final size:15
Alignment explanation
Indices: 21107--21136 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21097 CGAACTGGGG
21107 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
*
21122 AAAAAAGAGAAAAAA
1 AAAAAAAAGAAAAAA
21137 CTAAAACCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:29531 original size:14 final size:14
Alignment explanation
Indices: 29490--29524 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
29480 AAGTTAAACC
29490 AAGCAACAATATAG
1 AAGCAACAATATAG
*
29504 AAGGAACAATATAG
1 AAGCAACAATATAG
29518 AAGCAAC
1 AAGCAAC
29525 CACATAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.11
Consensus pattern (14 bp):
AAGCAACAATATAG
Found at i:33543 original size:5 final size:5
Alignment explanation
Indices: 33533--33559 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
33523 CTGAGAGAAA
33533 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
33560 GCAACTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Done.