Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020564.1 Corchorus olitorius cultivar O-4 contig20597, 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: 7749
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:569 original size:32 final size:32
Alignment explanation
Indices: 528--588 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
518 TGTAAAACTT
*
528 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
*
560 TTGAATCGACCATTATACCTTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
589 AAACATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:6212 original size:30 final size:30
Alignment explanation
Indices: 6176--6589 Score: 515
Period size: 30 Copynumber: 13.7 Consensus size: 30
6166 ACTCTCTAAA
* *
6176 TGACACCAGAAGTTGTCATGGTCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
6206 TGACACCAGAAGTTGCCATGATCTTGTAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
6236 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
6266 TGACACCAGAAATTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
6296 TGACACCAAAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
6326 TGACACCATAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
6356 TGACACCAGAAATTGTTATGA-CTTTGCAAT
1 TGACACCAGAAGTTGTCATGATC-TTGCAAT
* *
6386 TGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
6416 TGACACCAGCAGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
6446 TGACACCAGAAGCTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
6476 TGACACCATAAGTTATCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
6506 TGACACCATAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
** * * * * *
6536 TGACACTTGAGGATGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
6568 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
6590 AATATTTCCA
Statistics
Matches: 334, Mismatches: 46, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
29 1 0.00
30 309 0.93
31 3 0.01
32 21 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:6571 original size:32 final size:32
Alignment explanation
Indices: 6532--6725 Score: 154
Period size: 32 Copynumber: 5.9 Consensus size: 32
6522 CATGATCTTG
*
6532 CAATTGACACTTGAGGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
** * * **
6564 CAATTGACACCAGAAGTTGTCATGATAATATTT
1 CAATTGACACTTGAAGATGTCATAATTTTA-TT
* * *
6597 CCAATAGAAACTTGAAAATGTCATAATTTTATT
1 -CAATTGACACTTGAAGATGTCATAATTTTATT
** * * **
6630 CAATTGACACCAGAAGTTGTCATGATAATATTT
1 CAATTGACACTTGAAGATGTCATAATTTTA-TT
* *
6663 CCAATAGACACTTGAAAATGTCATAATTTTATT
1 -CAATTGACACTTGAAGATGTCATAATTTTATT
** * *
6696 CAATTGACACCAGAAGTTGTCATGATTTTA
1 CAATTGACACTTGAAGATGTCATAATTTTA
6726 CCTTTCAATA
Statistics
Matches: 119, Mismatches: 39, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
32 68 0.57
33 8 0.07
34 43 0.36
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (32 bp):
CAATTGACACTTGAAGATGTCATAATTTTATT
Found at i:6619 original size:34 final size:34
Alignment explanation
Indices: 6581--6686 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 34
6571 CACCAGAAGT
*
6581 TGTCATGATAATATTTCCAATAGAAACTTGAAAA
1 TGTCATGATAATATTTCCAATAGACACTTGAAAA
* ** * ** **
6615 TGTCATAATTTTA-TT-CAATTGACACCAGAAGT
1 TGTCATGATAATATTTCCAATAGACACTTGAAAA
6647 TGTCATGATAATATTTCCAATAGACACTTGAAAA
1 TGTCATGATAATATTTCCAATAGACACTTGAAAA
6681 TGTCAT
1 TGTCAT
6687 AATTTTATTC
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
32 21 0.40
33 4 0.08
34 28 0.53
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (34 bp):
TGTCATGATAATATTTCCAATAGACACTTGAAAA
Found at i:6632 original size:66 final size:66
Alignment explanation
Indices: 6502--6721 Score: 349
Period size: 66 Copynumber: 3.4 Consensus size: 66
6492 CATGATTTTG
* * * * **
6502 CAATTGACACCATAAGTTGTCATG---AT-CTTGCAATTGACACTTGAGGATGTCATAATTTTAT
1 CAATTGACACCAGAAGTTGTCATGATAATATTTCCAATAGACACTTGAAAATGTCATAATTTTAT
6563 T
66 T
*
6564 CAATTGACACCAGAAGTTGTCATGATAATATTTCCAATAGAAACTTGAAAATGTCATAATTTTAT
1 CAATTGACACCAGAAGTTGTCATGATAATATTTCCAATAGACACTTGAAAATGTCATAATTTTAT
6629 T
66 T
6630 CAATTGACACCAGAAGTTGTCATGATAATATTTCCAATAGACACTTGAAAATGTCATAATTTTAT
1 CAATTGACACCAGAAGTTGTCATGATAATATTTCCAATAGACACTTGAAAATGTCATAATTTTAT
6695 T
66 T
6696 CAATTGACACCAGAAGTTGTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
6722 TTTACCTTTC
Statistics
Matches: 146, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
62 23 0.16
65 2 0.01
66 121 0.83
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (66 bp):
CAATTGACACCAGAAGTTGTCATGATAATATTTCCAATAGACACTTGAAAATGTCATAATTTTAT
T
Done.