Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000173.1 Hibiscus syriacus cultivar Beakdansim tig00000304_pilon, 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: 46223
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5882 original size:12 final size:12
Alignment explanation
Indices: 5865--5899 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5855 ATATATGTTA
*
5865 ATGTGATATGAT
1 ATGTGATATGAC
5877 ATGTGATATGAC
1 ATGTGATATGAC
*
5889 CTGTGATATGA
1 ATGTGATATGA
5900 GAACATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (12 bp):
ATGTGATATGAC
Found at i:6083 original size:18 final size:15
Alignment explanation
Indices: 6044--6076 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6034 GAGGGTATAA
6044 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
6059 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
6074 TAG
1 TAG
6077 GAGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:18835 original size:12 final size:12
Alignment explanation
Indices: 18818--18842 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18808 ACAAAACACC
18818 ATTTGGTGCCTA
1 ATTTGGTGCCTA
18830 ATTTGGTGCCTA
1 ATTTGGTGCCTA
18842 A
1 A
18843 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:23440 original size:12 final size:12
Alignment explanation
Indices: 23423--23447 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23413 ACAAAGCACC
23423 ATTTGGTGCCTA
1 ATTTGGTGCCTA
23435 ATTTGGTGCCTA
1 ATTTGGTGCCTA
23447 A
1 A
23448 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:29799 original size:27 final size:28
Alignment explanation
Indices: 29751--29806 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
29741 CTAATTAATT
*
29751 TTATCATTAAATTTTTAAAATTAT-AAA
1 TTATCATTAAATTTATAAAATTATGAAA
* **
29778 TTATTATTAAATTTATCGAATTATGAAA
1 TTATCATTAAATTTATAAAATTATGAAA
29806 T
1 T
29807 AGTTACGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (28 bp):
TTATCATTAAATTTATAAAATTATGAAA
Found at i:29990 original size:23 final size:22
Alignment explanation
Indices: 29929--30010 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 22
29919 ATAAATTTAA
*
29929 TATTTTAAAAA-AAATATACATTT
1 TATTTTAAAAATATATATA-A-TT
*
29952 CTATTTTAGAAATATATATAATT
1 -TATTTTAAAAATATATATAATT
*
29975 TATTTTAAAAAT-TATAAAATT
1 TATTTTAAAAATATATATAATT
* *
29996 ATTTTTTTAAAATAT
1 -TATTTTAAAAATAT
30011 TTGACTCTCG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 8 0.16
22 21 0.43
23 3 0.06
24 11 0.22
25 6 0.12
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (22 bp):
TATTTTAAAAATATATATAATT
Found at i:31405 original size:13 final size:13
Alignment explanation
Indices: 31387--31415 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31377 GAACCGGTCC
31387 GACCCGACCCGTT
1 GACCCGACCCGTT
31400 GACCCGACCCGTT
1 GACCCGACCCGTT
31413 GAC
1 GAC
31416 TGTTGATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:33470 original size:21 final size:21
Alignment explanation
Indices: 33444--33491 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
33434 TGAGCAGAAG
33444 TTGAAGGGGGCCCTAACTATA
1 TTGAAGGGGGCCCTAACTATA
*
33465 TTGAAGGGGGCCCTAACTATG
1 TTGAAGGGGGCCCTAACTATA
33486 TTGAAG
1 TTGAAG
33492 AAATGGAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (21 bp):
TTGAAGGGGGCCCTAACTATA
Found at i:38565 original size:13 final size:13
Alignment explanation
Indices: 38542--38581 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
38532 CCGACCCGAG
38542 CCGACCCGTTGAC
1 CCGACCCGTTGAC
* *
38555 CTGACCTGTTGAC
1 CCGACCCGTTGAC
38568 CCGACCCGTTGAC
1 CCGACCCGTTGAC
38581 C
1 C
38582 ATTGACCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.15, C:0.42, G:0.23, T:0.20
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:41030 original size:3 final size:3
Alignment explanation
Indices: 41024--41068 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
41014 AATTATTATT
41024 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41069 ATGGGACAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:43418 original size:20 final size:20
Alignment explanation
Indices: 43384--43423 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43374 TAAAAAAATT
43384 AAAAGAGAAAAATTATGATTA
1 AAAAGAGAAAAATTAT-ATTA
*
43405 AAAAGAG-AATATTATATTA
1 AAAAGAGAAAAATTATATTA
43424 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (20 bp):
AAAAGAGAAAAATTATATTA
Done.