Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014367.1 Corchorus capsularis cultivar CVL-1 contig14388, 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: 74907
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:15862 original size:31 final size:31
Alignment explanation
Indices: 15803--15862 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
15793 TTAATTTGTT
* *
15803 AAAATAGACACAGATACATGGATGTCAAAAC
1 AAAAAAGACACAGATACATGAATGTCAAAAC
15834 AAAAAAGACACAGATACATGTAAT-TCAAA
1 AAAAAAGACACAGATACATG-AATGTCAAA
15863 TGAATTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (31 bp):
AAAAAAGACACAGATACATGAATGTCAAAAC
Found at i:22052 original size:79 final size:79
Alignment explanation
Indices: 21916--22098 Score: 357
Period size: 79 Copynumber: 2.3 Consensus size: 79
21906 ATTGAAGGGC
*
21916 CACCTAAAGAAGTTGGGGTGATGGCTTTTGGGCAAACTCTACAACGTCACAACCTCATGGAAGAT
1 CACCCAAAGAAGTTGGGGTGATGGCTTTTGGGCAAACTCTACAACGTCACAACCTCATGGAAGAT
21981 TTTTGGACACCCAA
66 TTTTGGACACCCAA
21995 CACCCAAAGAAGTTGGGGTGATGGCTTTTGGGCAAACTCTACAACGTCACAACCTCATGGAAGAT
1 CACCCAAAGAAGTTGGGGTGATGGCTTTTGGGCAAACTCTACAACGTCACAACCTCATGGAAGAT
22060 TTTTGGACACCCAA
66 TTTTGGACACCCAA
22074 CACCCAAAGAAGTTGGGGTGATGGC
1 CACCCAAAGAAGTTGGGGTGATGGC
22099 GCCATGAGAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 103 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (79 bp):
CACCCAAAGAAGTTGGGGTGATGGCTTTTGGGCAAACTCTACAACGTCACAACCTCATGGAAGAT
TTTTGGACACCCAA
Found at i:23085 original size:19 final size:18
Alignment explanation
Indices: 23057--23098 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
23047 AATTAATTGT
23057 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
23075 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
23094 CTTAA
1 TTTAA
23099 AAACTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:29277 original size:14 final size:14
Alignment explanation
Indices: 29258--29286 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29248 GATTGATTAC
29258 TACAAATACAATAA
1 TACAAATACAATAA
29272 TACAAATACAATAA
1 TACAAATACAATAA
29286 T
1 T
29287 CTAACCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (14 bp):
TACAAATACAATAA
Found at i:35009 original size:17 final size:17
Alignment explanation
Indices: 34987--35022 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34977 GGAGGTATCA
34987 TTATAAATAATAGTTTT
1 TTATAAATAATAGTTTT
35004 TTATAAATAATAGTTTT
1 TTATAAATAATAGTTTT
35021 TT
1 TT
35023 GTTTTGATCT
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:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATAAATAATAGTTTT
Found at i:53136 original size:3 final size:3
Alignment explanation
Indices: 53118--53160 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
53108 GTTTTCAAAT
*
53118 ATA A-A ATA ACA ATA ATA ATA ATA ATA ATA ATGA CATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A -ATA ATA ATA
53161 CTCAAATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.83
4 2 0.06
5 2 0.06
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:62791 original size:29 final size:30
Alignment explanation
Indices: 62736--62819 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 30
62726 CGGAGCCGTT
* *
62736 AAGTTGAGGGGGTAAAATGTTCCAAAATTG
1 AAGTTTAGGGGGCAAAATGTTCCAAAATTG
*
62766 ATGTTTAGGGGGCAAAATGTT-CAAAATTG
1 AAGTTTAGGGGGCAAAATGTTCCAAAATTG
*
62795 AAGTTTAGGGGGCAAAACG-TCCAAA
1 AAGTTTAGGGGGCAAAATGTTCCAAA
62820 CGCTACAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 1 0.02
29 29 0.60
30 18 0.38
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.25
Consensus pattern (30 bp):
AAGTTTAGGGGGCAAAATGTTCCAAAATTG
Found at i:70330 original size:24 final size:25
Alignment explanation
Indices: 70303--70356 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
70293 GTACTCTTTA
*
70303 TTTTCACGAATTT-G-AACTGGGTAT
1 TTTTCA-GAATTTCGAAACTGGGTAC
* *
70327 TTTTGAGAATTTCGAAATTGGGTAC
1 TTTTCAGAATTTCGAAACTGGGTAC
70352 TTTTC
1 TTTTC
70357 TTGTTTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 6 0.25
24 6 0.25
25 12 0.50
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (25 bp):
TTTTCAGAATTTCGAAACTGGGTAC
Done.