Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007042.1 Corchorus capsularis cultivar CVL-1 contig07063, 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: 48023
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:838 original size:2 final size:2
Alignment explanation
Indices: 831--865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
821 ATAGATCTAG
831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
866 GATCTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2011 original size:2 final size:2
Alignment explanation
Indices: 2004--2035 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1994 CAAAAAGAGG
2004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2036 TAATTGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2712 original size:40 final size:40
Alignment explanation
Indices: 2667--2744 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
2657 GAGCTAAGAG
2667 GGCAAAATGTTCAAAATTGAAATTCAAAAGACAAACGTTT
1 GGCAAAATGTTCAAAATTGAAATTCAAAAGACAAACGTTT
2707 GGCAAAATGTTCAAAATTGAAATTCAAAAGACAAACGT
1 GGCAAAATGTTCAAAATTGAAATTCAAAAGACAAACGT
2745 CCAGACGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (40 bp):
GGCAAAATGTTCAAAATTGAAATTCAAAAGACAAACGTTT
Found at i:3100 original size:74 final size:74
Alignment explanation
Indices: 3022--3178 Score: 233
Period size: 74 Copynumber: 2.1 Consensus size: 74
3012 TGGTCTTTTC
* * ** *
3022 ACACTTTTCGGGTGACTAAAAAGCCCCTTTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCAAATTCATTTTCCTTCTACCCTTT
3087 TTCGTAATT
66 TTCGTAATT
* * *
3096 ACACTTTTTGGATGACTAAAAAGTCTCTCTATGAGTTTCCCAAATTCATTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCAAATTCATTTTCCTTCTACCCTTT
3161 TTCGTAATT
66 TTCGTAATT
*
3170 ACACATTTC
1 ACACTTTTC
3179 CCTTACTTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCAAATTCATTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:7066 original size:2 final size:2
Alignment explanation
Indices: 7059--7088 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7049 GTTGGTATGC
7059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7089 CACACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8477 original size:2 final size:2
Alignment explanation
Indices: 8470--8501 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8460 ATTACTTTGA
8470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8502 TTAAAGGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15794 original size:24 final size:24
Alignment explanation
Indices: 15767--15814 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
15757 TCAAAATTCT
15767 CTCAAACCATTTCTAACTTTCTAA
1 CTCAAACCATTTCTAACTTTCTAA
*
15791 CTCAAATCATTTCTAACTTTCTAA
1 CTCAAACCATTTCTAACTTTCTAA
15815 ATTTTTAACT
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:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (24 bp):
CTCAAACCATTTCTAACTTTCTAA
Found at i:20632 original size:2 final size:2
Alignment explanation
Indices: 20619--20652 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20609 GTTATAAGTA
*
20619 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20653 TTCACCAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:47900 original size:18 final size:18
Alignment explanation
Indices: 47874--47911 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
47864 TCAACAAAAT
47874 AAGTAGAAAGATTGTGGG
1 AAGTAGAAAGATTGTGGG
*
47892 AAGTGGAAAGATTGTGGG
1 AAGTAGAAAGATTGTGGG
47910 AA
1 AA
47912 ACAAGAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (18 bp):
AAGTAGAAAGATTGTGGG
Done.