Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006369.1 Corchorus olitorius cultivar O-4 contig06394, 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, 991
Length: 1652
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Found at i:217 original size:31 final size:30
Alignment explanation
Indices: 179--260 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
169 AAGTGATAGC
179 TCAAAATTTTGTCATTTTGTACC-TTAAATTT
1 TCAAAATTTTGTCATTTTG--CCTTTAAATTT
*
210 TCAAAATTTTGCCATTTTGCCTTTTAAATTT
1 TCAAAATTTTGTCATTTTGCC-TTTAAATTT
*
241 TTAAAATTTTGTCATTTTGC
1 TCAAAATTTTGTCATTTTGC
261 TCCATACTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 2 0.04
31 44 0.96
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.52
Consensus pattern (30 bp):
TCAAAATTTTGTCATTTTGCCTTTAAATTT
Found at i:521 original size:2 final size:2
Alignment explanation
Indices: 514--543 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
504 ATTTTATTCC
514 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
544 GCATTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:743 original size:35 final size:37
Alignment explanation
Indices: 694--774 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 37
684 AAATATTCAC
* *
694 ATAT-AATAAAAAAAATTAGCATG-TGAAAATACAT-
1 ATATCAATAAAAAAAAATAGCATGTTAAAAATACATA
* *
728 ATATCAATAATAAAAAATAGTATGTTAAAAATACATAA
1 ATATCAATAAAAAAAAATAGCATGTTAAAAATACAT-A
766 ATATCAATA
1 ATATCAATA
775 TATTCAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.10
35 16 0.41
36 10 0.26
38 9 0.23
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (37 bp):
ATATCAATAAAAAAAAATAGCATGTTAAAAATACATA
Found at i:743 original size:36 final size:36
Alignment explanation
Indices: 694--774 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
684 AAATATTCAC
*
694 ATAT-AATAAAAAAAATTAGCATG-TGAAAATACAT-
1 ATATCAATAAAAAAAA-TAGCATGTTAAAAATACATA
*
728 ATATCAATAATAAAAAATAGTATGTTAAAAATACATAA
1 ATATCAATAA-AAAAAATAGCATGTTAAAAATACAT-A
766 ATATCAATA
1 ATATCAATA
775 TATTCAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 4 0.10
35 11 0.28
36 16 0.40
38 9 0.22
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (36 bp):
ATATCAATAAAAAAAATAGCATGTTAAAAATACATA
Found at i:856 original size:14 final size:14
Alignment explanation
Indices: 837--874 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
827 TATTTTTCCC
837 TCGTAAGATTTTAG
1 TCGTAAGATTTTAG
851 TCGTAAGATTTTAG
1 TCGTAAGATTTTAG
* *
865 GCATAAGATT
1 TCGTAAGATT
875 ATAAGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (14 bp):
TCGTAAGATTTTAG
Found at i:1017 original size:32 final size:32
Alignment explanation
Indices: 970--1030 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
960 TGTAAAACTT
*
970 TTGAATCGACTATTATATCCTTATTTTTCTAA
1 TTGAATCGACTATTATACCCTTATTTTTCTAA
1002 TTGAATCGA-TCATTATACCCTTATTTTTC
1 TTGAATCGACT-ATTATACCCTTATTTTTC
1031 AAATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (32 bp):
TTGAATCGACTATTATACCCTTATTTTTCTAA
Done.