Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016690.1 Corchorus olitorius cultivar O-4 contig16723, 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: 23927
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2650 original size:107 final size:107
Alignment explanation
Indices: 2459--2670 Score: 354
Period size: 107 Copynumber: 2.0 Consensus size: 107
2449 GTTTCAACCG
*
2459 CCAACTAGGGAAATAGGAACTAATTGTATAGTTGAATATGAATTAAACTTGTTGTGCATCATAAA
1 CCAACTAGGGAAATAGAAACTAATTGTATAGTTGAATATGAATTAAACTTGTTGTGCATCATAAA
*
2524 TTTACCATGTGTTTTAACTGGGTTTCAC-CGTTCCTATGCCCA
66 TTTACCATGTGTTTCAACTGGGTTTC-CTCGTTCCTATGCCCA
* *
2566 CCAACTAGGGAAATTGAAACTGATTGTATAGTTGAATATGAATTAAACTTGTTGTGCATCATAAA
1 CCAACTAGGGAAATAGAAACTAATTGTATAGTTGAATATGAATTAAACTTGTTGTGCATCATAAA
* *
2631 TTTCCCATTTGTTTCAACTGGGTTTCCTCGTTCCTATGCC
66 TTTACCATGTGTTTCAACTGGGTTTCCTCGTTCCTATGCC
2671 ATCACTTGTC
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 1 0.01
107 97 0.99
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (107 bp):
CCAACTAGGGAAATAGAAACTAATTGTATAGTTGAATATGAATTAAACTTGTTGTGCATCATAAA
TTTACCATGTGTTTCAACTGGGTTTCCTCGTTCCTATGCCCA
Found at i:6063 original size:24 final size:24
Alignment explanation
Indices: 6031--6078 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
6021 CCATGTCCCA
6031 GGTTCACTGAGAGAGGCAGGATAT
1 GGTTCACTGAGAGAGGCAGGATAT
6055 GGTTCACTGAGAGAGGCAGGATAT
1 GGTTCACTGAGAGAGGCAGGATAT
6079 ATTCAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.38, T:0.21
Consensus pattern (24 bp):
GGTTCACTGAGAGAGGCAGGATAT
Found at i:13981 original size:7 final size:7
Alignment explanation
Indices: 13962--14005 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
13952 TCAAGCACGA
13962 AATCAAT
1 AATCAAT
13969 -ATCAAT
1 AATCAAT
13975 AATCAAT
1 AATCAAT
13982 AATCAAT
1 AATCAAT
13989 AATCAAT
1 AATCAAT
13996 AATCAAT
1 AATCAAT
14003 AAT
1 AAT
14006 AAAAGTTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (7 bp):
AATCAAT
Found at i:18244 original size:24 final size:24
Alignment explanation
Indices: 18217--18269 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
18207 ACCTCCATCC
* *
18217 CTTCCACCACTCCATCCCCCACTT
1 CTTCCACCACTCCATCCACCACCT
*
18241 CTTCCACCACTCCTTCCACCACCT
1 CTTCCACCACTCCATCCACCACCT
18265 CTTCC
1 CTTCC
18270 GCTGCCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.15, C:0.58, G:0.00, T:0.26
Consensus pattern (24 bp):
CTTCCACCACTCCATCCACCACCT
Found at i:18269 original size:12 final size:12
Alignment explanation
Indices: 18216--18262 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
18206 CACCTCCATC
18216 CCTTCCACCACT
1 CCTTCCACCACT
* *
18228 CCATCCCCCACT
1 CCTTCCACCACT
*
18240 TCTTCCACCACT
1 CCTTCCACCACT
18252 CCTTCCACCAC
1 CCTTCCACCAC
18263 CTCTTCCGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.17, C:0.60, G:0.00, T:0.23
Consensus pattern (12 bp):
CCTTCCACCACT
Found at i:23738 original size:130 final size:131
Alignment explanation
Indices: 23486--23748 Score: 395
Period size: 130 Copynumber: 2.0 Consensus size: 131
23476 GCCATTAGAC
23486 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * *
23551 ATTAATTTTTACCATTTTACTATTTTAATTAAAAACTTATATATATTAGAAT-TTTTTAAATATA
66 ATTAATTTTTACCAATTTACTAATTTAATTAAAAACTTAGATATATTAGAATATTTTAAAATATA
23615 T
131 T
* * * * *
23616 TTTTATAGTTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * *
23681 TTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAA-ATTTTAAAATAT
66 ATTAATTTTTACCAATTTACTAATTTAATT-AAAAACTTAGATATATTAGAATATTTTAAAATAT
23745 AT
130 AT
23747 TT
1 TT
23749 CTTAAATGAC
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
130 85 0.71
131 34 0.29
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
ATTAATTTTTACCAATTTACTAATTTAATTAAAAACTTAGATATATTAGAATATTTTAAAATATA
T
Done.