Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015233.1 Corchorus capsularis cultivar CVL-1 contig15254, 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: 23593
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:376 original size:2 final size:2
Alignment explanation
Indices: 369--403 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
359 CGGGCCAATT
369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
404 TAAAGAGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:850 original size:75 final size:75
Alignment explanation
Indices: 732--877 Score: 229
Period size: 75 Copynumber: 1.9 Consensus size: 75
722 AAATCTGTAA
*
732 CTGCTCTCATAACCAGCTTTTTTAATTTGGTGATGAAAGTTTCTGTCAGAAGTTCCTCTATCAGA
1 CTGCTCTCATAACCAGCTTTTTTAATTTGGTGATGAAAATTTCTGTCAGAAGTTCCTCTATCAGA
797 TGCTCTGTTT
66 TGCTCTGTTT
* * * * * *
807 CTGCTCTTATGACCAGCTTTTTTCATTTGGTGATGAAAATTTCTGTCAGATGTTCCTCTGTTAGA
1 CTGCTCTCATAACCAGCTTTTTTAATTTGGTGATGAAAATTTCTGTCAGAAGTTCCTCTATCAGA
872 TGCTCT
66 TGCTCT
878 TCTGGTCTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (75 bp):
CTGCTCTCATAACCAGCTTTTTTAATTTGGTGATGAAAATTTCTGTCAGAAGTTCCTCTATCAGA
TGCTCTGTTT
Found at i:1438 original size:2 final size:2
Alignment explanation
Indices: 1431--1460 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1421 CCTTTCATCA
1431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1461 TATTTGGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2574 original size:2 final size:2
Alignment explanation
Indices: 2567--2596 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2557 ATAATTAAAG
2567 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
2597 ACAAAGTAGA
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:9941 original size:12 final size:12
Alignment explanation
Indices: 9924--9950 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9914 ATCTAAGGGC
9924 TGCATTGGGAGA
1 TGCATTGGGAGA
9936 TGCATTGGGAGA
1 TGCATTGGGAGA
9948 TGC
1 TGC
9951 GGCTTGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.41, T:0.26
Consensus pattern (12 bp):
TGCATTGGGAGA
Found at i:13338 original size:35 final size:35
Alignment explanation
Indices: 13297--13462 Score: 174
Period size: 35 Copynumber: 4.7 Consensus size: 35
13287 ATTTCATCAG
* *
13297 ATTCAGC-CATTGGGGGCTGCAGCAACCCCTTCATC
1 ATTCAGCAC-TTGGGGACTCCAGCAACCCCTTCATC
13332 ATTCAGCACTTGGGGACTCCAGCAACCCCTTCATC
1 ATTCAGCACTTGGGGACTCCAGCAACCCCTTCATC
* * * * *
13367 ATTCAACACTTGGGGACTCGAACAACCCCGTCCTC
1 ATTCAGCACTTGGGGACTCCAGCAACCCCTTCATC
* * * *
13402 ATTC-GACACTAGGGGACTCCAACAACCCATTTATC
1 ATTCAG-CACTTGGGGACTCCAGCAACCCCTTCATC
* * *
13437 ATTCAACAATTGGGTACTCCAGCAAC
1 ATTCAGCACTTGGGGACTCCAGCAAC
13463 TCATTCTTCT
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
35 108 0.99
36 1 0.01
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (35 bp):
ATTCAGCACTTGGGGACTCCAGCAACCCCTTCATC
Found at i:13957 original size:72 final size:71
Alignment explanation
Indices: 13877--14053 Score: 230
Period size: 72 Copynumber: 2.5 Consensus size: 71
13867 TAGCTGAGGT
* * *
13877 AGTTCCCACATTTGGCAGTCCTTCGCAAAATCCTTACATGACAATCTTCCATAATGCGGTTGTAG
1 AGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACACGACAATCTT-CACAATGCGGTTGTAG
*
13942 CCAAGTC
65 CCAAGAC
* * * ** *
13949 AGTTCCCACATTTGGTAGTCCTTCGCACAATTCTTATACGATTATCTTCACACTGCGGTTGTAGC
1 AGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACACGACAATCTTCACAATGCGGTTGTAGC
*
14014 CGAGAC
66 CAAGAC
*
14020 AGTTCCCACA-TTGGCAGTCTTTCGCACAATCCTT
1 AGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
14054 GCTACTACCT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
70 21 0.23
71 29 0.32
72 41 0.45
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (71 bp):
AGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACACGACAATCTTCACAATGCGGTTGTAGC
CAAGAC
Done.