Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010295.1 Corchorus capsularis cultivar CVL-1 contig10316, 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: 8492
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Found at i:89 original size:27 final size:27
Alignment explanation
Indices: 47--100 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
37 TCCGCCGTTT
47 CTCCACCTTCTACCCTTCGACGAGAGG
1 CTCCACCTTCTACCCTTCGACGAGAGG
* *
74 CTCCACCTTTTCCCCTTCGACGAGAGG
1 CTCCACCTTCTACCCTTCGACGAGAGG
101 GGTTGGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.41, G:0.19, T:0.24
Consensus pattern (27 bp):
CTCCACCTTCTACCCTTCGACGAGAGG
Found at i:621 original size:28 final size:28
Alignment explanation
Indices: 590--727 Score: 89
Period size: 28 Copynumber: 5.1 Consensus size: 28
580 ATTTGCTTCG
590 ATTTTAACTTACATTTACTTTAAATTAC
1 ATTTTAACTTACATTTACTTTAAATTAC
* * **
618 A-TTTACATTTGCATTTACATTT-GCTT-C
1 ATTTTA-ACTTACATTTAC-TTTAAATTAC
*
645 GTTTTTAACTTACATTTACTTTAAATTAC
1 -ATTTTAACTTACATTTACTTTAAATTAC
* * **
674 A-TTTACATTTACATTTGC-TT--CGT--
1 ATTTTA-ACTTACATTTACTTTAAATTAC
697 -TTTTAACTTACATTTACTTTAAATTAC
1 ATTTTAACTTACATTTACTTTAAATTAC
724 ATTT
1 ATTT
728 ACATTTGCTT
Statistics
Matches: 78, Mismatches: 18, Indels: 28
0.63 0.15 0.23
Matches are distributed among these distances:
22 10 0.13
23 6 0.08
25 2 0.03
27 14 0.18
28 38 0.49
29 8 0.10
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (28 bp):
ATTTTAACTTACATTTACTTTAAATTAC
Found at i:623 original size:6 final size:6
Alignment explanation
Indices: 598--689 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
588 CGATTTTAAC
* * *
598 TTACAT TTAC-T TTA-AA TTACAT TTACAT TTGCAT TTACAT TTGC-T
1 TTACAT TTACAT TTACAT TTACAT TTACAT TTACAT TTACAT TTACAT
**** * *
643 TCGTTT TTA-AC TTACAT TTAC-T TTA-AA TTACAT TTACAT TTACAT
1 TTACAT TTACAT TTACAT TTACAT TTACAT TTACAT TTACAT TTACAT
688 TT
1 TT
690 GCTTCGTTTT
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
5 20 0.30
6 46 0.70
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.52
Consensus pattern (6 bp):
TTACAT
Found at i:623 original size:22 final size:22
Alignment explanation
Indices: 562--627 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
552 GTCAGTGAAA
*
562 ACTTTAAATTACATGTACATTT
1 ACTTTAAATTACATTTACATTT
* * ** *
584 GCTTCGATTTTA-ACTTACATTT
1 ACTT-TAAATTACATTTACATTT
606 ACTTTAAATTACATTTACATTT
1 ACTTTAAATTACATTTACATTT
628 GCATTTACAT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
21 4 0.13
22 23 0.74
23 4 0.13
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (22 bp):
ACTTTAAATTACATTTACATTT
Found at i:660 original size:22 final size:23
Alignment explanation
Indices: 632--745 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 23
622 ACATTTGCAT
632 TTACATTTGCTTCGTTTTTA-AC
1 TTACATTTGCTTCGTTTTTACAC
* ** *
654 TTACATTTACTTTAAATTACATTTACAT
1 TTACATTTGC-TT-CGTT---TTTACAC
682 TTACATTTGCTTCGTTTTTA-AC
1 TTACATTTGCTTCGTTTTTACAC
* ** *
704 TTACATTTACTT--TAAATTACAT
1 TTACATTTGCTTCGT-TTTTACAC
726 TTACATTTGCTTCGTTTTTA
1 TTACATTTGCTTCGTTTTTA
746 GGAGGGTTTA
Statistics
Matches: 67, Mismatches: 15, Indels: 19
0.66 0.15 0.19
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 33 0.49
23 9 0.13
24 3 0.04
26 2 0.03
27 6 0.09
28 10 0.15
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (23 bp):
TTACATTTGCTTCGTTTTTACAC
Found at i:663 original size:56 final size:56
Alignment explanation
Indices: 577--735 Score: 267
Period size: 50 Copynumber: 2.9 Consensus size: 56
567 AAATTACATG
*
577 TACATTTGCTTCGATTTTAACTTACATTTACTTTAAATTACATTTACATTTGCATT
1 TACATTTGCTTCGTTTTTAACTTACATTTACTTTAAATTACATTTACATTTGCATT
633 TACATTTGCTTCGTTTTTAACTTACATTTACTTTAAATTACATTT--A----CATT
1 TACATTTGCTTCGTTTTTAACTTACATTTACTTTAAATTACATTTACATTTGCATT
683 TACATTTGCTTCGTTTTTAACTTACATTTACTTTAAATTACATTTACATTTGC
1 TACATTTGCTTCGTTTTTAACTTACATTTACTTTAAATTACATTTACATTTGC
736 TTCGTTTTTA
Statistics
Matches: 96, Mismatches: 1, Indels: 12
0.88 0.01 0.11
Matches are distributed among these distances:
50 49 0.51
52 1 0.01
54 1 0.01
56 45 0.47
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (56 bp):
TACATTTGCTTCGTTTTTAACTTACATTTACTTTAAATTACATTTACATTTGCATT
Found at i:859 original size:42 final size:42
Alignment explanation
Indices: 812--898 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
802 CGGGCTTTTG
812 CTGGATCGGAAACTCGGAAACTCTGCCCATGGGTCGGAAAAC
1 CTGGATCGGAAACTCGGAAACTCTGCCCATGGGTCGGAAAAC
*
854 CTGGATCGGAAACTTGGAAACTCTGCCCATGGGTCGGAAAAC
1 CTGGATCGGAAACTCGGAAACTCTGCCCATGGGTCGGAAAAC
896 CTG
1 CTG
899 AGCATTCGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.29, T:0.18
Consensus pattern (42 bp):
CTGGATCGGAAACTCGGAAACTCTGCCCATGGGTCGGAAAAC
Done.