Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004378.1 Hibiscus syriacus cultivar Beakdansim tig00009599_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: 60232
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5337 original size:31 final size:32
Alignment explanation
Indices: 5302--5362 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
5292 AGTTTAAATT
* * *
5302 TTTTAATTTAATTACT-TGACTTTCCAATTAC
1 TTTTAATTCAATCACTCTGACTTTCAAATTAC
5333 TTTTAATTCAATCACTCTGACTTTCAAATT
1 TTTTAATTCAATCACTCTGACTTTCAAATT
5363 TTTTTATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTTAATTCAATCACTCTGACTTTCAAATTAC
Found at i:5368 original size:31 final size:30
Alignment explanation
Indices: 5300--5374 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
5290 AAAGTTTAAA
* * *
5300 TTTTTTAATTTAATTACTTGACTTTCCAAT
1 TTTTTTAATTCAATCACTTGACTTTCAAAT
*
5330 TACTTTTAATTCAATCACTCTGACTTTCAAAT
1 T-TTTTTAATTCAATCACT-TGACTTTCAAAT
*
5362 TTTTTTATTTCAA
1 TTTTTTAATTCAA
5375 AATTATAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.03
31 24 0.65
32 12 0.32
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.53
Consensus pattern (30 bp):
TTTTTTAATTCAATCACTTGACTTTCAAAT
Found at i:15092 original size:2 final size:2
Alignment explanation
Indices: 15087--15124 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15077 AAAAATTACA
15087 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
15125 GTAAGATGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20280 original size:2 final size:2
Alignment explanation
Indices: 20273--20299 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20263 AAATTAAAAT
20273 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20300 TATTTATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30868 original size:24 final size:22
Alignment explanation
Indices: 30840--30892 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
30830 GTATTTAGTA
*
30840 TTTAAATTATTAA-TTTTAATTTAT
1 TTTAAATT-TAAACTTTT-ATTT-T
30864 TTTAATATTTAAACTTTTATTTT
1 TTTAA-ATTTAAACTTTTATTTT
30887 TTTAAA
1 TTTAAA
30893 ACAATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
23 6 0.23
24 12 0.46
25 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAAATTTAAACTTTTATTTT
Found at i:31065 original size:38 final size:37
Alignment explanation
Indices: 30992--31070 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
30982 AATTTAATGT
*
30992 TAAATTTTGAATGATAATACTAAAATGAAACAAAAAC
1 TAAATTTTGAATGATAATACTAAAATGAAAAAAAAAC
* *
31029 TAAAGTTTTTAATGATGGATACTAAAAT-AAAAAAAAAC
1 TAAA-TTTTGAATGAT-AATACTAAAATGAAAAAAAAAC
31067 TAAA
1 TAAA
31071 CTTTAGGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 4 0.11
38 23 0.62
39 10 0.27
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (37 bp):
TAAATTTTGAATGATAATACTAAAATGAAAAAAAAAC
Found at i:40759 original size:30 final size:30
Alignment explanation
Indices: 40720--40812 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
40710 AGTCACACAC
* *
40720 CGATAACTAATGTTATTGTTTGTTACAAAT
1 CGATTACTAACGTTATTGTTTGTTACAAAT
*
40750 CGATTACTAACGTTATTATTTGTTACAAAT
1 CGATTACTAACGTTATTGTTTGTTACAAAT
40780 CGATTACTAACGTTATTGTTTGTTACAAAT
1 CGATTACTAACGTTATTGTTTGTTACAAAT
40810 CGA
1 CGA
40813 CCAATCCACG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (30 bp):
CGATTACTAACGTTATTGTTTGTTACAAAT
Found at i:50309 original size:15 final size:16
Alignment explanation
Indices: 50272--50311 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
50262 TATAATTATC
*
50272 TATTAAATCTTTAAAA
1 TATTAAATTTTTAAAA
*
50288 TATTAAATTTTTATAA
1 TATTAAATTTTTAAAA
50304 -ATTAAATT
1 TATTAAATT
50312 AATAATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTAAATTTTTAAAA
Found at i:50887 original size:21 final size:21
Alignment explanation
Indices: 50863--50915 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
50853 ATTCTGACTA
*
50863 TCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
50884 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
50905 TCGCAATGCGA
1 TCGCATTGCGA
50916 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:50930 original size:20 final size:20
Alignment explanation
Indices: 50905--50998 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
50895 TTTTCCTAAT
50905 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
50925 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
50946 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
50966 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
50986 TCGCAACGCGAAT
1 TCGCAATGCGAAT
50999 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 48 0.75
21 16 0.25
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:51008 original size:20 final size:20
Alignment explanation
Indices: 50985--51031 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
50975 GAATACGTAA
*
50985 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
51005 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
51025 ATCGCAA
1 ATCGCAA
51032 TACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:52898 original size:20 final size:19
Alignment explanation
Indices: 52873--52961 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 19
52863 CAATGCGGAA
52873 ATCGCAACGTGAATATGACT
1 ATCGCAACG-GAATATGACT
52893 ATCGCAACACGGAA-ATGACT
1 ATCGC-A-ACGGAATATGACT
*
52913 ATCGCAACGCGGAAT-TAACT
1 ATCGCAA--CGGAATATGACT
*
52933 ATCGCAACGCGAAAATGACT
1 ATCGCAACG-GAATATGACT
52953 ATCGCAACG
1 ATCGCAACG
52962 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
18 3 0.05
19 4 0.07
20 45 0.76
21 4 0.07
22 3 0.05
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (19 bp):
ATCGCAACGGAATATGACT
Found at i:52934 original size:40 final size:40
Alignment explanation
Indices: 52873--52961 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
52863 CAATGCGGAA
* * *
52873 ATCGCAACGTGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGGGAATATAACTATCGCAACACGAAAATGACT
*
52913 ATCGCAACGCGGAAT-TAACTATCGCAACGCGAAAATGACT
1 ATCGCAACG-GGAATATAACTATCGCAACACGAAAATGACT
52953 ATCGCAACG
1 ATCGCAACG
52962 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
ATCGCAACGGGAATATAACTATCGCAACACGAAAATGACT
Found at i:52990 original size:33 final size:34
Alignment explanation
Indices: 52933--53031 Score: 155
Period size: 33 Copynumber: 2.9 Consensus size: 34
52923 GGAATTAACT
* **
52933 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
52967 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
53000 ATCGCAATGCGAAAATGAAAATCGCAACGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGA
53032 ATTTAGTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.51
34 29 0.49
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:53106 original size:33 final size:33
Alignment explanation
Indices: 53044--53138 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
53034 TTAGTTTCGT
**
53044 GTTGCGATTTTCATTTTCGCATTATGATTCTCTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCTCTC
53078 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* *
53111 GTTGCGATTGTCATTTCCGCGTTGCGAT
1 GTTGCGATTTTCATTT-CGCATTGCGAT
53139 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 33 0.59
34 23 0.41
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:54745 original size:42 final size:42
Alignment explanation
Indices: 54638--54745 Score: 96
Period size: 42 Copynumber: 2.6 Consensus size: 42
54628 TCTAGAATGT
* * * *
54638 TGGGAGG-GACCTCTTCAACGATGTTAGTGGCCTCTTGAAAGG
1 TGGGAGGTG-CCTCTTGAACGATGATAGGGGCCTCTTGAAAGA
* ** *
54680 TGGGAGGTGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGGTGCCTCTTGAACGATGATAGGGGCCTCTTGAAAGA
54722 TAGGG-GAG-GCCTCTTGAACGATGA
1 T-GGGAG-GTGCCTCTTGAACGATGA
54746 CAGGTGAGTC
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
42 47 0.90
43 5 0.10
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (42 bp):
TGGGAGGTGCCTCTTGAACGATGATAGGGGCCTCTTGAAAGA
Found at i:55252 original size:20 final size:20
Alignment explanation
Indices: 55229--55297 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
55219 GAAACTTAAA
**
55229 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
55249 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
**
55269 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAATTTGACT
55289 ATCGCAACG
1 ATCGCAACG
55298 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:55400 original size:21 final size:20
Alignment explanation
Indices: 55342--55409 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
55332 GATTCTTTCG
* **
55342 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
55362 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
55382 TTGCGATAGTCATTTTTCGCG
1 TTGCGATAGTCA-TTTTCGCA
55403 TTGCGAT
1 TTGCGAT
55410 TGTTGTTGCG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:57783 original size:22 final size:22
Alignment explanation
Indices: 57758--57833 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
57748 TGACCGTAAA
*
57758 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGCCGGAGATGGGGAC
* ***
57780 TGATATCGTTTGAGATGGGGAC
1 TGATTTCGCCGGAGATGGGGAC
**
57802 TGATTTCATCGGAGATGGGGAC
1 TGATTTCGCCGGAGATGGGGAC
* *
57824 GGATGTCGCC
1 TGATTTCGCC
57834 TTAGAGAGTG
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (22 bp):
TGATTTCGCCGGAGATGGGGAC
Found at i:58037 original size:20 final size:20
Alignment explanation
Indices: 58014--58125 Score: 181
Period size: 20 Copynumber: 5.7 Consensus size: 20
58004 CGATAGTCAG
58014 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
58034 ATTCGCATTACGATTTATGG
1 ATTCGCATTGCGATTTACGT
*
58054 ATTCGC-TTGCGATTTAAGT
1 ATTCGCATTGCGATTTACGT
58073 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
58093 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
58113 ATTCGCATTGCGA
1 ATTCGCATTGCGA
58126 ATTAGAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
19 16 0.19
20 68 0.81
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:58138 original size:20 final size:22
Alignment explanation
Indices: 58115--58167 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
58105 ATTTACGTAT
*
58115 TCGCATTGCGAA-TTAG-AAAA
1 TCGCAATGCGAATTTAGAAAAA
* *
58135 TCGCAACGCGAATTTGGAAAAA
1 TCGCAATGCGAATTTAGAAAAA
*
58157 TCGCAGTGCGA
1 TCGCAATGCGA
58168 TAGTCAGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.38
21 3 0.12
22 13 0.50
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCAATGCGAATTTAGAAAAA
Found at i:58626 original size:13 final size:13
Alignment explanation
Indices: 58608--58644 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
58598 TTAACAGCAC
58608 ATAAATCGTAATT
1 ATAAATCGTAATT
58621 ATAAATCGTAATT
1 ATAAATCGTAATT
58634 ATAAATCGTAA
1 ATAAATCGTAA
58645 AACAACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (13 bp):
ATAAATCGTAATT
Done.