Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013020.1 Corchorus capsularis cultivar CVL-1 contig13041, 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: 8842
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:4304 original size:33 final size:32
Alignment explanation
Indices: 4207--4311 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
4197 TTGCAAAGAG
*
4207 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * *
4240 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
4273 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
4306 TGTTTT
1 TGTTTT
4312 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.05
33 52 0.87
34 5 0.08
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:4378 original size:33 final size:33
Alignment explanation
Indices: 4341--4445 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
4331 AACAAATCTA
4341 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
4374 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
* ** *
4407 TTTTGGTTGATTATAGCATTAAAAATAATTTTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
4440 TTTTGG
1 TTTTGG
4446 GTGAAAAGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (33 bp):
TTTTGGTTGATCATAGCATTGCAAATAATTCTG
Found at i:4824 original size:30 final size:30
Alignment explanation
Indices: 4788--4846 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4778 CAAGGGGGAG
4788 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
4818 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
4847 CTTAAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:6914 original size:6 final size:6
Alignment explanation
Indices: 6905--6931 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6895 AAAGCAAAGC
6905 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
6932 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:6943 original size:12 final size:13
Alignment explanation
Indices: 6928--6972 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
6918 AATCTAAATC
6928 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
6940 TAAAGCAAATTAA
1 TAAAGCAGATTAA
6953 TAAAGCAGATTAA
1 TAAAGCAGATTAA
6966 TAAAGCA
1 TAAAGCA
6973 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:6979 original size:25 final size:25
Alignment explanation
Indices: 6928--6980 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
6918 AATCTAAATC
*
6928 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
6953 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
6978 TAA
1 TAA
6981 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Done.