Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005066.1 Hibiscus syriacus cultivar Beakdansim tig00011371_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: 87876
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:18444 original size:20 final size:21
Alignment explanation
Indices: 18419--18465 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18409 GTTTCCAATT
*
18419 TCGCAACT-CGAATCTGTAAA
1 TCGCAACTGCAAATCTGTAAA
*
18439 TCGCAA-TGCAAATTTGTAAA
1 TCGCAACTGCAAATCTGTAAA
18459 TCGCAAC
1 TCGCAAC
18466 ACATAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (21 bp):
TCGCAACTGCAAATCTGTAAA
Found at i:18494 original size:20 final size:20
Alignment explanation
Indices: 18459--18526 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
18449 AATTTGTAAA
* *
18459 TCGCAACACATAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
* * *
18479 TCACAACGCGATAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
*
18499 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
18519 TCGCAACG
1 TCGCAACG
18527 TGAATAGTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACGCAAAAGTCAAAT
Found at i:18503 original size:40 final size:41
Alignment explanation
Indices: 18456--18546 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 41
18446 GCAAATTTGT
* *
18456 AAATCGCAACACATAAGTCAAATTCACAACGCG-ATAGTCA
1 AAATCGCAACACAAAAGTCAAATTCACAACGCGAATAGTAA
* * *
18496 AATTCGCAACACAAAAGTCAAATTCGCAACGTGAATAGTAA
1 AAATCGCAACACAAAAGTCAAATTCACAACGCGAATAGTAA
18537 AAATCGCAAC
1 AAATCGCAAC
18547 GTGAATAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 29 0.66
41 15 0.34
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (41 bp):
AAATCGCAACACAAAAGTCAAATTCACAACGCGAATAGTAA
Found at i:18561 original size:20 final size:21
Alignment explanation
Indices: 18519--18567 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
18509 AAAGTCAAAT
18519 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGTAAAAA
18540 TCGCAACGTGAATAGT-AAAA
1 TCGCAACGTGAATAGTAAAAA
18560 TCGCAACG
1 TCGCAACG
18568 AATCTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
TCGCAACGTGAATAGTAAAAA
Found at i:18943 original size:21 final size:21
Alignment explanation
Indices: 18917--18968 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
18907 CAACGCGATT
18917 TTGCGA-TTTTCTAAATTCGCA
1 TTGCGATTTTTC-AAATTCGCA
*
18938 TTGCGATTTTTCAAATTCGCG
1 TTGCGATTTTTCAAATTCGCA
18959 TTGCGATTTT
1 TTGCGATTTT
18969 ACTATTCACG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.46
Consensus pattern (21 bp):
TTGCGATTTTTCAAATTCGCA
Found at i:18975 original size:20 final size:20
Alignment explanation
Indices: 18938--19050 Score: 118
Period size: 21 Copynumber: 5.5 Consensus size: 20
18928 TAAATTCGCA
* * *
18938 TTGCGATTTTTCAAATTCGCG
1 TTGCGATTTTAC-TATTCACG
18959 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
18979 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
* * *
18999 TTACGGTTTTTACTATTTACG
1 TTGC-GATTTTACTATTCACG
* *
19020 CTGCGATTTTTACTATTCACA
1 TTGCGA-TTTTACTATTCACG
*
19041 CTGCGATTTT
1 TTGCGATTTT
19051 GGATACTGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
20 34 0.43
21 45 0.57
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:18988 original size:41 final size:41
Alignment explanation
Indices: 18938--19039 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
18928 TAAATTCGCA
* *
18938 TTGCGATTTTTCAAATTCGCGTTGC-GATTTTACTATTCACG
1 TTGCGATTTTTC-AATTCACGTTACGGATTTTACTATTCACG
* * * *
18979 TTGCGATTTTACTATTCACGTTACGGTTTTTACTATTTACG
1 TTGCGATTTTTCAATTCACGTTACGGATTTTACTATTCACG
* *
19020 CTGCGATTTTTACTATTCAC
1 TTGCGATTTTT-CAATTCAC
19040 ACTGCGATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 9 0.18
41 34 0.67
42 8 0.16
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (41 bp):
TTGCGATTTTTCAATTCACGTTACGGATTTTACTATTCACG
Found at i:21502 original size:20 final size:21
Alignment explanation
Indices: 21479--21519 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21469 ATTAAATGAA
*
21479 ACTATTATT-GAGATTCGAAT
1 ACTAATATTCGAGATTCGAAT
*
21499 ACTAATATTCGATATTCGAAT
1 ACTAATATTCGAGATTCGAAT
21520 TGAAAGATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
ACTAATATTCGAGATTCGAAT
Found at i:23882 original size:2 final size:2
Alignment explanation
Indices: 23875--23910 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23865 TTCATTGGAC
*
23875 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23911 TCTTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29745 original size:20 final size:20
Alignment explanation
Indices: 29678--29753 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
29668 AACCCGACGG
* *
29678 ATGCATCGATGCATGGTCT-T
1 ATGCATCGATGCATTGT-TAA
*
29698 ATGCATCGATGCATAT-TCAA
1 ATGCATCGATGCAT-TGTTAA
29718 GGATGCATCGATGCATTGTTAA
1 --ATGCATCGATGCATTGTTAA
29740 ATGCATCGATGCAT
1 ATGCATCGATGCAT
29754 GAAGCACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
20 29 0.62
21 1 0.02
22 17 0.36
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (20 bp):
ATGCATCGATGCATTGTTAA
Found at i:33575 original size:22 final size:21
Alignment explanation
Indices: 33535--33574 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
33525 GAGTTTGTTT
33535 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
33556 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
33575 ATAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:40743 original size:16 final size:18
Alignment explanation
Indices: 40715--40752 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
40705 ATCGCTGACA
40715 AAATTTCACTATTCACG-
1 AAATTTCACTATTCACGT
40732 AAATTT-ACTATTCACGT
1 AAATTTCACTATTCACGT
40749 AAAT
1 AAAT
40753 AGTAATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTTCACTATTCACGT
Found at i:50012 original size:36 final size:36
Alignment explanation
Indices: 49963--50048 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
49953 AATTACATCC
* *
49963 ACTTTAGC-TTAGGTAAAAGCTTAAATGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
*
49998 ACTTTAACTTTAGGTAAAAGCTAAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
50034 ACTTTAGCTTTAGGT
1 ACTTTAGCTTTAGGT
50049 TAACTAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 7 0.15
36 39 0.85
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (36 bp):
ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
Found at i:51582 original size:15 final size:15
Alignment explanation
Indices: 51564--51592 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
51554 TTCATTTCAA
51564 AATTTTATAAAATAC
1 AATTTTATAAAATAC
51579 AATTTTATAAAATA
1 AATTTTATAAAATA
51593 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:53156 original size:36 final size:36
Alignment explanation
Indices: 53110--53361 Score: 364
Period size: 36 Copynumber: 7.0 Consensus size: 36
53100 AGTTTGCATT
* *
53110 GATTCAAGTCGAACGGAGGTAAGCATCGGCACTTCT
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
*
53146 GATTCAAGTCGAACGGAGGAAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* * *
53182 GATTCAAATCGAACGGAGGGAAGCATCGACTCTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* *
53218 GATTCAAGTCGAACGGAGGGAAGCATTGTCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
*
53254 GATTCAAATCGAACGGAGGGAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* * *
53290 GATTCAAATCGAACGAAAGGAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
*
53326 GATTCAAGT-GAACGG-GAGGAAGCATCGACACTTCC
1 GATTCAAGTCGAACGGAG-GGAAGCATCGGCACTTCC
53361 G
1 G
53362 GTTCTAGTGT
Statistics
Matches: 196, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
35 23 0.12
36 173 0.88
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (36 bp):
GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
Found at i:55180 original size:24 final size:24
Alignment explanation
Indices: 55152--55197 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
55142 GTTTGGAACA
*
55152 AAGCATTCAAAATTTGATCTTTCT
1 AAGCATTAAAAATTTGATCTTTCT
55176 AAGCATTAAAAATTTGATCTTT
1 AAGCATTAAAAATTTGATCTTT
55198 ACTACACGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (24 bp):
AAGCATTAAAAATTTGATCTTTCT
Found at i:57702 original size:15 final size:16
Alignment explanation
Indices: 57677--57711 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
57667 GCAGGCTATT
57677 CTGATTTTGCCTTAAG
1 CTGATTTTGCCTTAAG
57693 CTGA-TTTGCCTTAAG
1 CTGATTTTGCCTTAAG
57708 CTGA
1 CTGA
57712 CTGGCAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (16 bp):
CTGATTTTGCCTTAAG
Found at i:59101 original size:2 final size:2
Alignment explanation
Indices: 59094--59149 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
59084 ATGTGAAAGA
59094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59136 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
59150 TATGGTTAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61660 original size:22 final size:21
Alignment explanation
Indices: 61631--61672 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
61621 TGATCAAATG
61631 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
61652 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
61673 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:67401 original size:2 final size:2
Alignment explanation
Indices: 67394--67420 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67384 CACTTGCAAA
67394 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 A
67421 CTTGCCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75572 original size:33 final size:33
Alignment explanation
Indices: 75535--75600 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
75525 TCTATTGTAT
75535 TTGATAAGCTTAAATATACAAAAGGTGCCCAAC
1 TTGATAAGCTTAAATATACAAAAGGTGCCCAAC
*
75568 TTGATAAGCTTAAATATACAAAAGGTGTCCAAC
1 TTGATAAGCTTAAATATACAAAAGGTGCCCAAC
75601 GTATGCCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (33 bp):
TTGATAAGCTTAAATATACAAAAGGTGCCCAAC
Found at i:75783 original size:2 final size:2
Alignment explanation
Indices: 75778--75821 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
75768 AAAAATTAAA
75778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75820 AT
1 AT
75822 TCAAAAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77099 original size:79 final size:79
Alignment explanation
Indices: 76998--77153 Score: 260
Period size: 79 Copynumber: 2.0 Consensus size: 79
76988 TAAGCTGGAT
* *
76998 TAAACTTAACGTCGAGTTCGATGTAATACTCTTTCGATTTGAATATACAGAACCGAACAAAAACG
1 TAAACTTAACGTCGAGTCCGATGTAATACTCTTTCAATTTGAATATACAGAACCGAACAAAAACG
77063 ACAAAA-GAAAGGA
66 ACAAAAGGAAAGGA
* *
77076 TAAACTTAAACGTCGAGTCCGATGTGATACTCTTTCAATTTGAATATACAGATCCGAACAAAAAC
1 TAAACTT-AACGTCGAGTCCGATGTAATACTCTTTCAATTTGAATATACAGAACCGAACAAAAAC
77141 GACAAAAGGAAAG
65 GACAAAAGGAAAG
77154 AGCCACAGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 7 0.10
79 60 0.83
80 5 0.07
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (79 bp):
TAAACTTAACGTCGAGTCCGATGTAATACTCTTTCAATTTGAATATACAGAACCGAACAAAAACG
ACAAAAGGAAAGGA
Found at i:82155 original size:2 final size:2
Alignment explanation
Indices: 82150--82188 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
82140 ATTACCTTTA
82150 AT 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 AT A
82189 AATAATAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.