Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015979.1 Corchorus olitorius cultivar O-4 contig16012, 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: 45292
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:7809 original size:99 final size:99
Alignment explanation
Indices: 7638--7838 Score: 366
Period size: 99 Copynumber: 2.0 Consensus size: 99
7628 AGTAAAGGAT
*
7638 AAAGATTGCAAAACAATAACGAATATGCTCGAAGAATCATGAGAAGAGCAGATACAAAAAAGGAG
1 AAAGACTGCAAAACAATAACGAATATGCTCGAAGAATCATGAGAAGAGCAGATACAAAAAAGGAG
*
7703 GGCCAGAATGAAATCAACATCTCTTTACAAACAG
66 GGCCAGAATGAAATCAACATCTCTTTAAAAACAG
*
7737 AAAGACTGCAAAACAATAACGAATATGCTCGAAGAATCATGAGAAGAGCAGATACAAAAAAGGGG
1 AAAGACTGCAAAACAATAACGAATATGCTCGAAGAATCATGAGAAGAGCAGATACAAAAAAGGAG
*
7802 GGCCAGAATGGAATCAACATCTCTTTAAAAACAG
66 GGCCAGAATGAAATCAACATCTCTTTAAAAACAG
7836 AAA
1 AAA
7839 TACTACAATC
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.15
Consensus pattern (99 bp):
AAAGACTGCAAAACAATAACGAATATGCTCGAAGAATCATGAGAAGAGCAGATACAAAAAAGGAG
GGCCAGAATGAAATCAACATCTCTTTAAAAACAG
Found at i:38918 original size:53 final size:53
Alignment explanation
Indices: 38838--38943 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
38828 GTTTCGGCTT
38838 CGGCTTCGGGGCACACAAGGAAATTGTACAAAAGTATTGGCAAAATATTCATA
1 CGGCTTCGGGGCACACAAGGAAATTGTACAAAAGTATTGGCAAAATATTCATA
38891 CGGCTTCGGGGCACACAAGGAAATTGTACAAAAGTATTGGCAAAATATTCATA
1 CGGCTTCGGGGCACACAAGGAAATTGTACAAAAGTATTGGCAAAATATTCATA
38944 TATAGAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (53 bp):
CGGCTTCGGGGCACACAAGGAAATTGTACAAAAGTATTGGCAAAATATTCATA
Found at i:40112 original size:146 final size:146
Alignment explanation
Indices: 39848--40138 Score: 573
Period size: 146 Copynumber: 2.0 Consensus size: 146
39838 ATCCCCAAAA
*
39848 CCAAGCCTCCCATGTTCCCCTCTTCCCCAACCATACACCTAAGATGAAAGATACAAGCAAAGATA
1 CCAAGCCTCCCATGTTCCCCTCTTCCCCAACCATACACCTAAGATGAAAGATACAAGCAAAAATA
39913 TTAGGTTTCACAGAAACAGAATATTATAGGCGCTGCAAAGCTGGGAGGTACACAAGAAACCAGCA
66 TTAGGTTTCACAGAAACAGAATATTATAGGCGCTGCAAAGCTGGGAGGTACACAAGAAACCAGCA
39978 AAAGCATACACATAAC
131 AAAGCATACACATAAC
39994 CCAAGCCTCCCATGTTCCCCTCTTCCCCAACCATACACCTAAGATGAAAGATACAAGCAAAAATA
1 CCAAGCCTCCCATGTTCCCCTCTTCCCCAACCATACACCTAAGATGAAAGATACAAGCAAAAATA
40059 TTAGGTTTCACAGAAACAGAATATTATAGGCGCTGCAAAGCTGGGAGGTACACAAGAAACCAGCA
66 TTAGGTTTCACAGAAACAGAATATTATAGGCGCTGCAAAGCTGGGAGGTACACAAGAAACCAGCA
40124 AAAGCATACACATAA
131 AAAGCATACACATAA
40139 ATAAAGCAAC
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 144 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (146 bp):
CCAAGCCTCCCATGTTCCCCTCTTCCCCAACCATACACCTAAGATGAAAGATACAAGCAAAAATA
TTAGGTTTCACAGAAACAGAATATTATAGGCGCTGCAAAGCTGGGAGGTACACAAGAAACCAGCA
AAAGCATACACATAAC
Done.