Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007687.1 Hibiscus syriacus cultivar Beakdansim tig00109871_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: 56484
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2151 original size:21 final size:22
Alignment explanation
Indices: 2097--2151 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
2087 TGTGTAGAGT
* *
2097 TTTAGGATTT-AAGGTTTAGAG
1 TTTAGGATTTAAAGGTTGAGAA
*
2118 TTTAGGGTTTAAAGGTTGA-AA
1 TTTAGGATTTAAAGGTTGAGAA
2139 TTTAGGATTTAAA
1 TTTAGGATTTAAA
2152 TTATATGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (22 bp):
TTTAGGATTTAAAGGTTGAGAA
Found at i:2889 original size:48 final size:49
Alignment explanation
Indices: 2816--2916 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 49
2806 GAGCTCTATC
*
2816 ATGGGAAGATGAATGACGTGGGGAAGAAGAAA-GAAGAAGAGATTGATG
1 ATGGGAAGATGAATGACGTGCGGAAGAAGAAAGGAAGAAGAGATTGATG
* *
2864 ATGGGAAGATGGATGACGTGCGGAAGAAGAAAGCGGATGAAGAGATTGATG
1 ATGGGAAGATGAATGACGTGCGGAAGAAGAAA--GGAAGAAGAGATTGATG
2915 AT
1 AT
2917 AGGATATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
48 30 0.64
51 17 0.36
ACGTcount: A:0.41, C:0.04, G:0.40, T:0.16
Consensus pattern (49 bp):
ATGGGAAGATGAATGACGTGCGGAAGAAGAAAGGAAGAAGAGATTGATG
Found at i:21336 original size:27 final size:27
Alignment explanation
Indices: 21277--21330 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21267 TCGACCTGAT
21277 CAAGTTTTCAGGATACTCAATATTTAA
1 CAAGTTTTCAGGATACTCAATATTTAA
21304 CAAGTTTTCAGGATACTCAATATTTAA
1 CAAGTTTTCAGGATACTCAATATTTAA
21331 ACAGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (27 bp):
CAAGTTTTCAGGATACTCAATATTTAA
Found at i:25446 original size:18 final size:19
Alignment explanation
Indices: 25399--25455 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
25389 ATGTTTAATG
*
25399 AAAAAGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
25418 ACAAAAGGATACCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
*
25438 AAAAAGATACTAATTGTT
1 AAAAAGATACCAATTGTT
25456 GGAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:43513 original size:15 final size:15
Alignment explanation
Indices: 43493--43534 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
43483 CTTCATGGGG
*
43493 TAAGAAGACAACGTC
1 TAAGAAGAAAACGTC
43508 TAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
43523 AAAGAAGGAAAA
1 TAAGAA-GAAAA
43535 AGAAAGCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.57, C:0.12, G:0.21, T:0.10
Consensus pattern (15 bp):
TAAGAAGAAAACGTC
Found at i:47468 original size:51 final size:50
Alignment explanation
Indices: 47358--47468 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 50
47348 AACTTGTTGA
*
47358 AAAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGATGGAAAAAGAGAAAG
1 AAAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGAAGGAAAAAGAGAAAG
47408 AAAAGGAAGAGG-GTAAAGGAGAAGGGACACC-ACA-AAGGAAAAAG-GAAGAGG
1 AAAA-GAAGAGGAG-AAAGGAGAAGGGACACCGA-AGAAGGAAAAAGAGAA-A-G
47459 AGAAAGAAGA
1 A-AAAGAAGA
47469 AGGGACACCG
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
49 3 0.06
50 16 0.30
51 32 0.59
52 3 0.06
ACGTcount: A:0.56, C:0.06, G:0.36, T:0.02
Consensus pattern (50 bp):
AAAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGAAGGAAAAAGAGAAAG
Found at i:49437 original size:2 final size:2
Alignment explanation
Indices: 49430--49466 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49420 TCAATCTACA
49430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49467 ATTTTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49757 original size:28 final size:29
Alignment explanation
Indices: 49717--49774 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
49707 CAATGTAAAT
*
49717 CATACATGCGTGTCA-TAAATTTATGACG
1 CATAAATGCGTGTCACTAAATTTATGACG
* *
49745 CATAAATGTGTGTCATCTTAATTTATGACG
1 CATAAATGCGTGTCA-CTAAATTTATGACG
49775 GGGGCTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (29 bp):
CATAAATGCGTGTCACTAAATTTATGACG
Found at i:49816 original size:13 final size:13
Alignment explanation
Indices: 49798--49831 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
49788 CACTCAAAGA
*
49798 ACGTCATTAATGC
1 ACGTCATAAATGC
49811 ACGTCATAAATGC
1 ACGTCATAAATGC
*
49824 GCGTCATA
1 ACGTCATA
49832 GATTTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (13 bp):
ACGTCATAAATGC
Found at i:49821 original size:85 final size:85
Alignment explanation
Indices: 49526--49788 Score: 386
Period size: 85 Copynumber: 3.1 Consensus size: 85
49516 GACGTGTGCA
* * * * * * *
49526 TCAATAACACGCAATGTAAGTCATAAATGCGTGCCATAAATTTATGACACACAAATGTATATCAA
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTC-A
*
49591 GC--AGATTTATGACGGGGGCT
65 TCTTA-ATTTATGACGGGGGCT
*
49611 TTAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
*
49676 CTTAATTTATGACGGGAGCT
66 CTTAATTTATGACGGGGGCT
* *
49696 TCAATGACGCGCAATGTAAATCATACATGCGTGTCATAAATTTATGACGCATAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
49761 CTTAATTTATGACGGGGGCT
66 CTTAATTTATGACGGGGGCT
49781 TCAATGAC
1 TCAATGAC
49789 ACTCAAAGAA
Statistics
Matches: 162, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
84 2 0.01
85 159 0.98
86 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (85 bp):
TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
CTTAATTTATGACGGGGGCT
Found at i:50761 original size:30 final size:31
Alignment explanation
Indices: 50727--50787 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
50717 CAAATTAATT
*
50727 TATTTAATATTTTTATATTT-ATTTTAAAAA
1 TATTTAATATTTTTAAATTTAATTTTAAAAA
*
50757 TATTTTATATTTTTAAATTTACATTTTAAAA
1 TATTTAATATTTTTAAATTTA-ATTTTAAAA
50788 TAATTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 18 0.67
32 9 0.33
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTTAATATTTTTAAATTTAATTTTAAAAA
Found at i:51735 original size:27 final size:26
Alignment explanation
Indices: 51697--51756 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
51687 AAAAAAAACG
51697 ATTTTTT-CC-AAATCCGAT-TTCGGA
1 ATTTTTTGCCAAAATCCGATATTC-GA
51721 TATTTTTTGCACAAAATCCGATATTCGA
1 -ATTTTTTGC-CAAAATCCGATATTCGA
51749 ATTTTTTG
1 ATTTTTTG
51757 TGCACCTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 7 0.23
26 1 0.03
27 9 0.29
28 11 0.35
29 3 0.10
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.45
Consensus pattern (26 bp):
ATTTTTTGCCAAAATCCGATATTCGA
Found at i:51760 original size:29 final size:28
Alignment explanation
Indices: 51706--51761 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
51696 GATTTTTTCC
*
51706 AAATCCGATTTCGGATATTTTTTGCACA
1 AAATCCGATTTCGAATATTTTTTGCACA
51734 AAATCCGATATTCGAAT-TTTTTGTGCAC
1 AAATCCGAT-TTCGAATATTTTT-TGCAC
51762 CTCTGGGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (28 bp):
AAATCCGATTTCGAATATTTTTTGCACA
Found at i:55850 original size:5 final size:5
Alignment explanation
Indices: 55836--55881 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
55826 CCGCCGCCGC
* * *
55836 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGGCT CGGCT CGACT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
55882 GCACGGCACG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
4 4 0.10
5 35 0.90
ACGTcount: A:0.02, C:0.41, G:0.26, T:0.30
Consensus pattern (5 bp):
CGTCT
Found at i:55888 original size:5 final size:5
Alignment explanation
Indices: 55843--55926 Score: 96
Period size: 5 Copynumber: 16.8 Consensus size: 5
55833 CGCCGTCCGT
* * * * * * *
55843 CTCGT CTCGT CTCGT CTCGT CTCGG CTCGG CTCGA CTCGG CACGG CACGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
*
55893 CACGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
55927 TGGTCGTGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 74 1.00
ACGTcount: A:0.05, C:0.40, G:0.33, T:0.21
Consensus pattern (5 bp):
CTCGG
Done.