Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014696.1 Corchorus olitorius cultivar O-4 contig14729, 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: 32622
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:12661 original size:2 final size:2
Alignment explanation
Indices: 12654--12685 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12644 CTATTACTAG
12654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12686 ATAATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13600 original size:62 final size:62
Alignment explanation
Indices: 13523--13658 Score: 206
Period size: 62 Copynumber: 2.2 Consensus size: 62
13513 AATGTTTGTC
* *
13523 AAAATACTC-AA-ATAAGGGTCTGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATC-
1 AAAATACTCAAATATAAGGGTCTGATCTTTTAATTTGACCAAATAAGGACCTAACGTTATCG
* *
13582 AAGAATGCTCAAATATAAGGGTCTGATCTTTTAATTTGACTAAATAAGGACCTAACGTTATCG
1 AA-AATACTCAAATATAAGGGTCTGATCTTTTAATTTGACCAAATAAGGACCTAACGTTATCG
13645 AAAATACTCAAATA
1 AAAATACTCAAATA
13659 AGGGACTGGC
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
59 2 0.03
60 6 0.09
61 2 0.03
62 56 0.82
63 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (62 bp):
AAAATACTCAAATATAAGGGTCTGATCTTTTAATTTGACCAAATAAGGACCTAACGTTATCG
Found at i:13784 original size:60 final size:60
Alignment explanation
Indices: 13729--13866 Score: 206
Period size: 60 Copynumber: 2.3 Consensus size: 60
13719 CATTTTTGAT
* *
13729 AATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGCCCTTATTTGAGTATTTTGACA
1 AATGTTAAGCCCTTATTTGGCCAAATTAAAAAATCAGGCCCTTATTTGAGTATTTTGACA
* * * **
13789 AAAGTTATGCCCTTATTTGGCCAAATTAAAAAATCATGCTTTTATTTGAGTATTTTGACA
1 AATGTTAAGCCCTTATTTGGCCAAATTAAAAAATCAGGCCCTTATTTGAGTATTTTGACA
13849 AATG-TAAGCCCTTATTTG
1 AATGTTAAGCCCTTATTTG
13867 AGGACGAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 13 0.19
60 57 0.81
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (60 bp):
AATGTTAAGCCCTTATTTGGCCAAATTAAAAAATCAGGCCCTTATTTGAGTATTTTGACA
Found at i:21854 original size:14 final size:14
Alignment explanation
Indices: 21835--21865 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21825 ACTTTAATTA
21835 ATAGTAGTATATAT
1 ATAGTAGTATATAT
*
21849 ATAGTATTATATAT
1 ATAGTAGTATATAT
21863 ATA
1 ATA
21866 TATATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (14 bp):
ATAGTAGTATATAT
Found at i:23080 original size:23 final size:22
Alignment explanation
Indices: 23045--23087 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
23035 ATATTGAATA
*
23045 TTTTAAATAAATAAATATATTT
1 TTTTAAAAAAATAAATATATTT
23067 TTTTGAAAAAAATAAATATAT
1 TTTT-AAAAAAATAAATATAT
23088 ATTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTTAAAAAAATAAATATATTT
Found at i:31231 original size:45 final size:45
Alignment explanation
Indices: 31162--31250 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
31152 AAACCATTCC
* *
31162 ATGCAAATGATACATCCAAGTATCAACCAGCCCTTATACATCTAA
1 ATGCAAATGATACATCCAAATATCAACCAGCCCTTACACATCTAA
31207 ATGCAAATGATACATCCAAATATCAACCAGCCCTTACACATCTA
1 ATGCAAATGATACATCCAAATATCAACCAGCCCTTACACATCTA
31251 TCGAACACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (45 bp):
ATGCAAATGATACATCCAAATATCAACCAGCCCTTACACATCTAA
Found at i:32002 original size:36 final size:36
Alignment explanation
Indices: 31961--32031 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
31951 CTCCAAACCT
*
31961 TCACCTCTGTCACTAATCCACCATTTCTTCCTCCAG
1 TCACCTCTATCACTAATCCACCATTTCTTCCTCCAG
31997 TCACCTCTATCACTAATCCACCATTTCTTCCTCCA
1 TCACCTCTATCACTAATCCACCATTTCTTCCTCCA
32032 AAAATTCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.42, G:0.03, T:0.34
Consensus pattern (36 bp):
TCACCTCTATCACTAATCCACCATTTCTTCCTCCAG
Done.