Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015196.1 Corchorus olitorius cultivar O-4 contig15229, 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: 10174
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:621 original size:57 final size:59
Alignment explanation
Indices: 551--667 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 59
541 GGGATTCGTG
551 CGGTAAAGAAATTAGA-ATTTGT-TAATATATATTTAATTTAATTGATAAATGAAATTA
1 CGGTAAAGAAATTAGAGATTTGTATAATATATATTTAATTTAATTGATAAATGAAATTA
* * *
608 CGGTAAAGAAATTAGAGTTTTTTAATAATATATATTTAATTTAATTGATAAATTAAATTA
1 CGGTAAAGAAATTAGAGATTTGT-ATAATATATATTTAATTTAATTGATAAATGAAATTA
668 TATATTAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 16 0.30
58 4 0.07
60 34 0.63
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (59 bp):
CGGTAAAGAAATTAGAGATTTGTATAATATATATTTAATTTAATTGATAAATGAAATTA
Found at i:690 original size:26 final size:25
Alignment explanation
Indices: 657--759 Score: 88
Period size: 26 Copynumber: 4.0 Consensus size: 25
647 TTTAATTGAT
657 AAATTAAATTATATATTAAACCTTAA
1 AAATTAAATTA-ATATTAAACCTTAA
* *
683 AAATTAAATCTAATATTTAA---GAA
1 AAATTAAAT-TAATATTAAACCTTAA
*
706 AAATGAAATTACATATTAAACCTTAA
1 AAATTAAATTA-ATATTAAACCTTAA
732 AAATGTCAAATCTAATATTTAAA-CTTAA
1 AAAT-T-AAAT-TAATA-TTAAACCTTAA
760 GAAAAAATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.03
23 17 0.27
26 22 0.35
27 2 0.03
28 12 0.19
29 7 0.11
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (25 bp):
AAATTAAATTAATATTAAACCTTAA
Found at i:722 original size:49 final size:51
Alignment explanation
Indices: 657--753 Score: 162
Period size: 49 Copynumber: 1.9 Consensus size: 51
647 TTTAATTGAT
* *
657 AAATTAAATTATATATTAAACCTTAAAAAT-T-AAATCTAATATTTAAGAA
1 AAATGAAATTACATATTAAACCTTAAAAATGTCAAATCTAATATTTAAGAA
706 AAATGAAATTACATATTAAACCTTAAAAATGTCAAATCTAATATTTAA
1 AAATGAAATTACATATTAAACCTTAAAAATGTCAAATCTAATATTTAA
754 ACTTAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 28 0.64
50 1 0.02
51 15 0.34
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (51 bp):
AAATGAAATTACATATTAAACCTTAAAAATGTCAAATCTAATATTTAAGAA
Found at i:790 original size:19 final size:20
Alignment explanation
Indices: 745--782 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
735 TGTCAAATCT
*
745 AATATTTAAACTTAAGAAAA
1 AATATTTAAAATTAAGAAAA
765 AATATTTAAAATTAAGAA
1 AATATTTAAAATTAAGAA
783 GGATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
AATATTTAAAATTAAGAAAA
Found at i:5173 original size:31 final size:32
Alignment explanation
Indices: 5119--5184 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
5109 GTTTTTTTTT
5119 ATCCTTTTGGCATTGGCCGTTTTTTTTATTTGG
1 ATCCTTTTGGCATTGG-CGTTTTTTTTATTTGG
*
5152 ATCCTTTTGGCATTGG-TTTTTTTTTATTTGG
1 ATCCTTTTGGCATTGGCGTTTTTTTTATTTGG
5183 AT
1 AT
5185 TGATAACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 16 0.50
33 16 0.50
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.58
Consensus pattern (32 bp):
ATCCTTTTGGCATTGGCGTTTTTTTTATTTGG
Found at i:5505 original size:14 final size:14
Alignment explanation
Indices: 5486--5515 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5476 TATCAACATT
*
5486 ACAAATTATTCTCC
1 ACAAATTACTCTCC
5500 ACAAATTACTCTCC
1 ACAAATTACTCTCC
5514 AC
1 AC
5516 CAGCAGTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATTACTCTCC
Found at i:9077 original size:27 final size:28
Alignment explanation
Indices: 9024--9079 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
9014 TCATGCACCC
* * *
9024 AAAATTATTTAATAAAATCATTTATAAA
1 AAAATAATTTAATAAAATCAGTAATAAA
9052 AAAATAATTTAATAAAA-CAGTAATAAA
1 AAAATAATTTAATAAAATCAGTAATAAA
9079 A
1 A
9080 TAGTTCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATAATTTAATAAAATCAGTAATAAA
Done.