Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014245.1 Corchorus capsularis cultivar CVL-1 contig14266, 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: 33282
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Found at i:3879 original size:75 final size:75
Alignment explanation
Indices: 3794--4028 Score: 359
Period size: 75 Copynumber: 3.1 Consensus size: 75
3784 CCTTCTGAGG
3794 GTTATACGGGGGCGCCAGTCTAGGCGCTC-GACCGTCTGCGGGTGGCGTTTGCTTGGACGCTCGA
1 GTTATACGGGGGCGCCAGTCTAGGCGCTCAG-CCGTCTGCGGGTGGCGTTTGCTTGGACGCTCGA
3858 CCTCGCTTAGA
65 CCTCGCTTAGA
3869 GTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTCTGCGGGTGGCGTTTGCTTGGACGCTCGAC
1 GTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTCTGCGGGTGGCGTTTGCTTGGACGCTCGAC
3934 CTCGCTTAGA
66 CTCGCTTAGA
* * * * **
3944 GTTATACGGGAGTGTCAGTCTAGGCGCTCAGTCGTCTGCGGGTGGCGCCTG-TTCAGG-CGCTCG
1 GTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTCTGCGGGTGGCGTTTGCTT--GGACGCTCG
*
4007 ACCTCGCTCAGA
64 ACCTCGCTTAGA
4019 GTTATACGGG
1 GTTATACGGG
4029 AGTTTGCACA
Statistics
Matches: 150, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
74 2 0.01
75 145 0.97
76 3 0.02
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (75 bp):
GTTATACGGGGGCGCCAGTCTAGGCGCTCAGCCGTCTGCGGGTGGCGTTTGCTTGGACGCTCGAC
CTCGCTTAGA
Found at i:11789 original size:42 final size:42
Alignment explanation
Indices: 11717--11797 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
11707 TTTTTTTTGA
*
11717 TATCTCATCCGGTATACAGAGATTTGCTCTAACTAATCTTGG
1 TATCACATCCGGTATACAGAGATTTGCTCTAACTAATCTTGG
* * * *
11759 TATCACATCTGGTATCCAGAGCTTTTCTCTAACTAATCT
1 TATCACATCCGGTATACAGAGATTTGCTCTAACTAATCT
11798 GGATCCGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (42 bp):
TATCACATCCGGTATACAGAGATTTGCTCTAACTAATCTTGG
Found at i:18749 original size:15 final size:16
Alignment explanation
Indices: 18722--18751 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18712 TGATCGTAAA
18722 CAAGTCTAGTGTTCAC
1 CAAGTCTAGTGTTCAC
18738 CAAGTC-AGTGTTCA
1 CAAGTCTAGTGTTCA
18752 TCTTGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (16 bp):
CAAGTCTAGTGTTCAC
Found at i:23913 original size:7 final size:7
Alignment explanation
Indices: 23901--23931 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
23891 TCAGTTATCC
23901 AAAAAAT
1 AAAAAAT
23908 AAAAAAT
1 AAAAAAT
23915 AAAAAAT
1 AAAAAAT
23922 AAAAAAT
1 AAAAAAT
23929 AAA
1 AAA
23932 TCTATGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:24153 original size:12 final size:12
Alignment explanation
Indices: 24136--24161 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24126 CCTAGAAGAA
24136 TTAGGTTTTACT
1 TTAGGTTTTACT
24148 TTAGGTTTTACT
1 TTAGGTTTTACT
24160 TT
1 TT
24162 TCCTATTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (12 bp):
TTAGGTTTTACT
Found at i:24897 original size:30 final size:30
Alignment explanation
Indices: 24858--24931 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
24848 GAGTATGACG
*
24858 AGGAGGAAGATTCTGATCTCTTTGTTTGTGT
1 AGGA-GAAGATTCTGATCTCTTTGTTTGTGA
24889 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
*
24919 AGGAGAAAATTCT
1 AGGAGAAGATTCT
24932 AATTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 37 0.90
31 4 0.10
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTGTTTGTGA
Found at i:27700 original size:12 final size:12
Alignment explanation
Indices: 27683--27708 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27673 CCTAGAAGAA
27683 TTAGGTTTTACT
1 TTAGGTTTTACT
27695 TTAGGTTTTACT
1 TTAGGTTTTACT
27707 TT
1 TT
27709 TCCTATTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (12 bp):
TTAGGTTTTACT
Done.