Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008739.1 Corchorus capsularis cultivar CVL-1 contig08760, 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: 45228
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:9495 original size:27 final size:29
Alignment explanation
Indices: 9465--9523 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
9455 AAATTGATCA
*
9465 AATCTGTATAAGAGAATAAATT-TAA-GT
1 AATCTGTATAAGAAAATAAATTATAATGT
9492 AATCTGTATAAGAAAATAAATTATAATGT
1 AATCTGTATAAGAAAATAAATTATAATGT
9521 AAT
1 AAT
9524 GTACCTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 21 0.72
28 3 0.10
29 5 0.17
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (29 bp):
AATCTGTATAAGAAAATAAATTATAATGT
Found at i:25760 original size:25 final size:26
Alignment explanation
Indices: 25727--25780 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
25717 CCCTTTTCAT
* *
25727 AAAATAGTTAGGAGTT-GGAACTTGG
1 AAAACAGTTACGAGTTGGGAACTTGG
25752 AAAACAGTTACGAGTTGGGGAACTTGG
1 AAAACAGTTACGAGTT-GGGAACTTGG
25779 AA
1 AA
25781 GATCAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.56
27 11 0.44
ACGTcount: A:0.37, C:0.07, G:0.31, T:0.24
Consensus pattern (26 bp):
AAAACAGTTACGAGTTGGGAACTTGG
Found at i:27859 original size:33 final size:33
Alignment explanation
Indices: 27822--27885 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
27812 GATGCCCCCT
*
27822 GGGA-CATCACCCCCTGTGGTGGGGCGCCCCATG
1 GGGACCATC-CCCCCCGTGGTGGGGCGCCCCATG
*
27855 GGGACGCCTCCCCCCCGTGGTGGGGCGCCCC
1 GGGAC-CATCCCCCCCGTGGTGGGGCGCCCC
27886 TTAGGGACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 4 0.15
34 20 0.74
35 3 0.11
ACGTcount: A:0.08, C:0.42, G:0.38, T:0.12
Consensus pattern (33 bp):
GGGACCATCCCCCCCGTGGTGGGGCGCCCCATG
Found at i:27875 original size:34 final size:34
Alignment explanation
Indices: 27831--27899 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
27821 TGGGACATCA
* *
27831 CCCCCTGTGGTGGGGCGCCCCATGGGGACGCCTC
1 CCCCCCGTGGTGGGGCGCCCCATAGGGACGCCTC
* *
27865 CCCCCCGTGGTGGGGCGCCCCTTAGGGACGTCTC
1 CCCCCCGTGGTGGGGCGCCCCATAGGGACGCCTC
27899 C
1 C
27900 GTGCTTGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.06, C:0.42, G:0.36, T:0.16
Consensus pattern (34 bp):
CCCCCCGTGGTGGGGCGCCCCATAGGGACGCCTC
Found at i:36807 original size:17 final size:17
Alignment explanation
Indices: 36785--36820 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
36775 AGATTATGGT
36785 GAATAGATTATTTTTTA
1 GAATAGATTATTTTTTA
36802 GAATAGATTATTTTTTA
1 GAATAGATTATTTTTTA
36819 GA
1 GA
36821 CATCGATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (17 bp):
GAATAGATTATTTTTTA
Found at i:44020 original size:27 final size:27
Alignment explanation
Indices: 43988--44041 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
43978 CAGTAAAATT
43988 CCATATCACTTCAAACTAGAATAATAC
1 CCATATCACTTCAAACTAGAATAATAC
*
44015 CCATATTACTTCAAACTAGAATAATAC
1 CCATATCACTTCAAACTAGAATAATAC
44042 TAAATGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (27 bp):
CCATATCACTTCAAACTAGAATAATAC
Done.