Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019913.1 Corchorus olitorius cultivar O-4 contig19946, 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: 21555
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Found at i:1200 original size:9 final size:9
Alignment explanation
Indices: 1186--1214 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1176 TTAAGGGACT
1186 AAATTGATG
1 AAATTGATG
1195 AAATTGATG
1 AAATTGATG
1204 AAATTGATG
1 AAATTGATG
1213 AA
1 AA
1215 TGAGAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (9 bp):
AAATTGATG
Found at i:6855 original size:31 final size:31
Alignment explanation
Indices: 6817--6879 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
6807 CTTATCTCGC
6817 AGTTGTATATTTATCACTTGTAATCATCTAT
1 AGTTGTATATTTATCACTTGTAATCATCTAT
6848 AGTTGTATATTTATCACTTGTAATCATCTAT
1 AGTTGTATATTTATCACTTGTAATCATCTAT
6879 A
1 A
6880 CTATAAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (31 bp):
AGTTGTATATTTATCACTTGTAATCATCTAT
Found at i:12817 original size:50 final size:50
Alignment explanation
Indices: 12740--12840 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
12730 TAATAGCCAT
* *
12740 CAAGCAGTCACTTTCAACAATGTAATCATTAAAGCCTTTGCTAAAAGCAA
1 CAAGCAGTCACTTTCAACAATGCAATCAGTAAAGCCTTTGCTAAAAGCAA
*
12790 CAAGCAGTCACTTTCAACAATGCAATCAGTAAAGCCTTTGTTAAAAGCAA
1 CAAGCAGTCACTTTCAACAATGCAATCAGTAAAGCCTTTGCTAAAAGCAA
12840 C
1 C
12841 TTGGAGACCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (50 bp):
CAAGCAGTCACTTTCAACAATGCAATCAGTAAAGCCTTTGCTAAAAGCAA
Found at i:16817 original size:370 final size:369
Alignment explanation
Indices: 16137--16877 Score: 1455
Period size: 370 Copynumber: 2.0 Consensus size: 369
16127 AGCTATACTG
16137 TAAGCAGGATCTTCATTCTCTAAACAGAATTCAGCCAGAGCACAGCCACTATAAAACCATCTTAA
1 TAAGCAGGATCTTCATTCTCTAAACAGAATTCAGCCAGAGCACAGCCACTATAAAACCATCTTAA
16202 ATTGCGAAAGGAGTGAGGTGCGTTAGATGAGGAAGAAGGCTAATAGCTGTAGTGGACAATTGCAA
66 ATTGCGAAAGGAGTGAGGTGCGTTAGATGAGGAAGAAGGCTAATAGCTGTAGTGGACAATTGCAA
16267 CTTAGATGAATCTAGGGCTTTGCTAATCAGATGGGGGAGAACCAAGATCAAGATGAAGAAAACAG
131 CTTAGATGAATCTAGGGCTTTGCTAATCAGATGGGGGAGAACCAAGATCAAGATGAAGAAAACAG
16332 AGTTTGACTATGGCTATACCAATTAGTATTGAATACAGAGAAGAAACATGAATAACAGAATCAGG
196 AGTTTGACTATGGCTATACCAATTAGTATTGAATACAGAGAAGAAACATGAATAACAGAATCAGG
*
16397 TAAGATTATGTGGTTCCCAGCTATAAGGCAAAAGCAGGGCTGCTTACAATGGATAAATGGATTGA
261 TAAGATTATGTGGTTCACAGCTATAAGGCAAAAGCAGGGCTGCTTACAATGGATAAATGGATTGA
16462 ATCTGCACATCCGCAGGGAACAACTTGCATTCCTCAGAGAAAAT
326 ATCTGCACATCCGCAGGGAACAACTTGCATTCCTCAGAGAAAAT
*
16506 TAAGCAGGATCTTCATTCTCTAAACAGAATTCAGCCAGAGCACGGCCACTATAAAACCATCTTAA
1 TAAGCAGGATCTTCATTCTCTAAACAGAATTCAGCCAGAGCACAGCCACTATAAAACCATCTTAA
16571 ATTGCGAAAGGAGTGAGGTGCGTTAGATGAGGAAGAAGGCTAATAGCTGTAGTGGACAATTGTCA
66 ATTGCGAAAGGAGTGAGGTGCGTTAGATGAGGAAGAAGGCTAATAGCTGTAGTGGACAATTG-CA
16636 ACTTAGATGAATCTAGGGCTTTGCTAATCAGATGGGGGAGAACCAAGATCAAGATGAAGAAAACA
130 ACTTAGATGAATCTAGGGCTTTGCTAATCAGATGGGGGAGAACCAAGATCAAGATGAAGAAAACA
16701 GAGTTTGACTATGGCTATACCAATTAGTATTGAATACAGAGAAGAAACATGAATAACAGAATCAG
195 GAGTTTGACTATGGCTATACCAATTAGTATTGAATACAGAGAAGAAACATGAATAACAGAATCAG
16766 GTAAGATTATGTGGTTCACAGCTATAAGGCAAAAGCAGGGCTGCTTACAATGGATAAATGGATTG
260 GTAAGATTATGTGGTTCACAGCTATAAGGCAAAAGCAGGGCTGCTTACAATGGATAAATGGATTG
16831 AATCTGCACATCCGCAGGGAACAACTTGCATTCCTCAGAGAAAAT
325 AATCTGCACATCCGCAGGGAACAACTTGCATTCCTCAGAGAAAAT
16876 TA
1 TA
16878 GAGCTTGTTT
Statistics
Matches: 369, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
369 126 0.34
370 243 0.66
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (369 bp):
TAAGCAGGATCTTCATTCTCTAAACAGAATTCAGCCAGAGCACAGCCACTATAAAACCATCTTAA
ATTGCGAAAGGAGTGAGGTGCGTTAGATGAGGAAGAAGGCTAATAGCTGTAGTGGACAATTGCAA
CTTAGATGAATCTAGGGCTTTGCTAATCAGATGGGGGAGAACCAAGATCAAGATGAAGAAAACAG
AGTTTGACTATGGCTATACCAATTAGTATTGAATACAGAGAAGAAACATGAATAACAGAATCAGG
TAAGATTATGTGGTTCACAGCTATAAGGCAAAAGCAGGGCTGCTTACAATGGATAAATGGATTGA
ATCTGCACATCCGCAGGGAACAACTTGCATTCCTCAGAGAAAAT
Done.