Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001233.1 Hibiscus syriacus cultivar Beakdansim tig00002428_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: 33998
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2484 original size:64 final size:64
Alignment explanation
Indices: 2352--2493 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
2342 TGCACTAAGA
* *
2352 GTGCATCGATGCATGAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGTAT
** *
2416 GTGCATCGATGCATAAAATGCATTCG-TG-TTCAATTTAATCCATG-GTGCATCGATGCAT-GTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAAT-AGCC-TGAGTGCATCGATGCATGGTA
2477 TT
64 -T
*
2479 GGTGCATCGTTGCAT
1 -GTGCATCGATGCAT
2494 CACTTTGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
62 9 0.13
63 20 0.29
64 39 0.57
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGTAT
Found at i:8741 original size:29 final size:29
Alignment explanation
Indices: 8699--8754 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
8689 GACGTGTCAA
*
8699 AGGGTTACATTGATTTTTTATTAAGTTTT
1 AGGGTTAAATTGATTTTTTATTAAGTTTT
8728 AGGGTTAAATTGATTTTTTATTAAGTT
1 AGGGTTAAATTGATTTTTTATTAAGTT
8755 GCTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.54
Consensus pattern (29 bp):
AGGGTTAAATTGATTTTTTATTAAGTTTT
Found at i:10154 original size:42 final size:43
Alignment explanation
Indices: 10108--10257 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 43
10098 GTTTTTGTTA
*
10108 GTGTTGAT-ATTTAGCGGCATTTTCTCTA-AAACGCCGCAGTAG
1 GTGTTGATGTTTTAGCGGCATTTTCTC-ACAAACGCCGCAGTAG
* * *
10150 GTGTTGATGTTTTA-CGGCGTTTTCCCACAAACGCCGCAATAG
1 GTGTTGATGTTTTAGCGGCATTTTCTCACAAACGCCGCAGTAG
* * * *
10192 GTTTTGATGTTTTAACGTG-TTTTTCTCACAAACGCCACAGTAG
1 GTGTTGATGTTTTAGCG-GCATTTTCTCACAAACGCCGCAGTAG
* *
10235 GTATTGATGTTTT-GTGGCATTTT
1 GTGTTGATGTTTTAGCGGCATTTT
10258 TAGCAAAAAC
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 49 0.54
43 38 0.42
44 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (43 bp):
GTGTTGATGTTTTAGCGGCATTTTCTCACAAACGCCGCAGTAG
Found at i:10236 original size:43 final size:42
Alignment explanation
Indices: 10117--10247 Score: 149
Period size: 43 Copynumber: 3.1 Consensus size: 42
10107 AGTGTTGATA
* *
10117 TTTAGCGGCATTTTCTCTA-AAACGCCGCAGTAGGTGTTGATGT
1 TTTA-CGGCGTTTTCTC-ACAAACGCCGCAGTAGGTATTGATGT
* * *
10160 TTTACGGCGTTTTCCCACAAACGCCGCAATAGGTTTTGATGT
1 TTTACGGCGTTTTCTCACAAACGCCGCAGTAGGTATTGATGT
* *
10202 TTTAACGTG-TTTTTCTCACAAACGCCACAGTAGGTATTGATGT
1 TTT-ACG-GCGTTTTCTCACAAACGCCGCAGTAGGTATTGATGT
10245 TTT
1 TTT
10248 GTGGCATTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
41 1 0.01
42 35 0.46
43 39 0.51
44 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (42 bp):
TTTACGGCGTTTTCTCACAAACGCCGCAGTAGGTATTGATGT
Found at i:11596 original size:36 final size:35
Alignment explanation
Indices: 11547--11626 Score: 144
Period size: 36 Copynumber: 2.3 Consensus size: 35
11537 TGTTTGCAAC
11547 TTCTCTTAAGGATGAGATCATTCTTGAAGTATTTG
1 TTCTCTTAAGGATGAGATCATTCTTGAAGTATTTG
11582 TTCTCTTCAAGGATGAGATCATTCTTGAAGTATTTG
1 TTCTCTT-AAGGATGAGATCATTCTTGAAGTATTTG
11618 TTCT-TTAAG
1 TTCTCTTAAG
11627 AAGCTCTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 3 0.07
35 9 0.20
36 32 0.73
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (35 bp):
TTCTCTTAAGGATGAGATCATTCTTGAAGTATTTG
Found at i:19287 original size:42 final size:42
Alignment explanation
Indices: 19240--19355 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
19230 AAGGGACATA
* *
19240 CTATTGCGGCGTTTAT-TACAAAAAGGCCACTAAATTACAACT
1 CTATTGCGGCGTTTATGT-CAAAAACGCCACTAAAGTACAACT
19282 CTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACT
1 CTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACT
* *
19324 -TTTTAGCGGCGTTT-GGT-AACAAACGCCACTAA
1 CTATT-GCGGCGTTTATGTCAA-AAACGCCACTAA
19356 TTTAAGAGTA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
40 2 0.03
41 17 0.25
42 47 0.70
43 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
CTATTGCGGCGTTTATGTCAAAAACGCCACTAAAGTACAACT
Found at i:20741 original size:41 final size:41
Alignment explanation
Indices: 20705--20889 Score: 187
Period size: 41 Copynumber: 4.5 Consensus size: 41
20695 GACTATATAT
* *
20705 TTAACA-TTTTGCGGCGTTTATAAAAAAATGCCACTATTGA
1 TTAACACTATTGCGGCGTTTTTAAAAAAATGCCACTATTGA
*
20745 TT-ACACTATTGTGGCGTTTGTTAAAAAAATGCCACTATTGA
1 TTAACACTATTGCGGCGTTT-TTAAAAAAATGCCACTATTGA
* ** *
20786 TTGAA-ACTATTGCAGCGTTTTTCTAAAAACGCCACTATTGA
1 TT-AACACTATTGCGGCGTTTTTAAAAAAATGCCACTATTGA
* * ** * *
20827 TTAACATTATTGCGGCGTTTGTCTAAAAATGACACTATTTTA
1 TTAACACTATTGCGGCGTTTTTAAAAAAATGCCACTA-TTGA
* *
20869 TTATCACTATTGTGGCGTTTT
1 TTAACACTATTGCGGCGTTTT
20890 AGGAATAAAC
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.02
40 15 0.12
41 69 0.57
42 33 0.27
43 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (41 bp):
TTAACACTATTGCGGCGTTTTTAAAAAAATGCCACTATTGA
Found at i:20879 original size:83 final size:81
Alignment explanation
Indices: 20728--20907 Score: 193
Period size: 83 Copynumber: 2.2 Consensus size: 81
20718 GCGTTTATAA
* * *
20728 AAAAATGCCACTATTGATTACACTATTGTGGCGTTTGTTAAAAAAATGCCACTATTGATTGAAAC
1 AAAAACGCCACTATTGATTACACTATTGCGGCGTTTGTT-AAAAAATGACACTATTGATTGAAAC
* *
20793 TATTGCAGCGTTTTTCT
65 TATTGCAGCGTTTTACG
* *
20810 AAAAACGCCACTATTGATTAACATTATTGCGGCGTTTGTCT-AAAAATGACACTATTTTATT-AT
1 AAAAACGCCACTATTGATT-ACACTATTGCGGCGTTTGT-TAAAAAATGACACTA-TTGATTGA-
* ** *
20873 CACTATTGTGGCGTTTTAGG
62 AACTATTGCAGCGTTTTACG
20893 AATAAACGCCACTAT
1 AA-AAACGCCACTAT
20908 ATGTGTAATC
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
82 31 0.38
83 38 0.46
84 13 0.16
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTGCGGCGTTTGTTAAAAAATGACACTATTGATTGAAACT
ATTGCAGCGTTTTACG
Found at i:20962 original size:42 final size:38
Alignment explanation
Indices: 20913--21049 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 38
20903 ACTATATGTG
* *
20913 TAATCTATTACGGCATTTGTGGTAGAAACTCCGCTAATT
1 TAATCTATTGCGGCATTTGTGGTA-AAACGCCGCTAATT
* *
20952 TATCGATCTATTGCGGCGTTT-TGGCTAAAACGCCACTATATGT
1 TA---ATCTATTGCGGCATTTGTGG-TAAAACGCCGCTA-AT-T
**
20995 TAATCTATTGCAACATTTGTGGTATAAACGCCGCTAATT
1 TAATCTATTGCGGCATTTGTGGTA-AAACGCCGCTAATT
21034 TACCACTCTATTGCGG
1 TA--A-TCTATTGCGG
21050 TGTTTGTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
39 5 0.06
40 17 0.22
41 26 0.34
42 26 0.34
43 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (38 bp):
TAATCTATTGCGGCATTTGTGGTAAAACGCCGCTAATT
Found at i:21012 original size:82 final size:83
Alignment explanation
Indices: 20896--21054 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 83
20886 TTTTAGGAAT
** * *
20896 AAACGCCACTATATGTGTAATCTATTACGGCATTTGTGGTAGAAACTCCGCTAATTTATCGA-TC
1 AAACGCCACTATATGTGTAATCTATTACAACATTTGTGGTAGAAACGCCGCTAATTTA-CCACTC
20960 TATTGCGGCGTTTTGGCTA
65 TATTGCGGCGTTTTGGCTA
* *
20979 AAACGCCACTATATGT-TAATCTATTGCAACATTTGTGGTATAAACGCCGCTAATTTACCACTCT
1 AAACGCCACTATATGTGTAATCTATTACAACATTTGTGGTAGAAACGCCGCTAATTTACCACTCT
*
21043 ATTGCGGTGTTT
66 ATTGCGGCGTTT
21055 GTTAAAAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 2 0.03
82 50 0.74
83 16 0.24
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (83 bp):
AAACGCCACTATATGTGTAATCTATTACAACATTTGTGGTAGAAACGCCGCTAATTTACCACTCT
ATTGCGGCGTTTTGGCTA
Found at i:21056 original size:42 final size:39
Alignment explanation
Indices: 20915--21056 Score: 117
Period size: 42 Copynumber: 3.5 Consensus size: 39
20905 TATATGTGTA
* * *
20915 ATCTATTACGGCATTTGTGGTAGAAACTCCGCTAATTTATC
1 ATCTATTGCGGCGTTTGTGGTA-AAACGCCGCTAATTTA-C
*
20956 GATCTATTGCGGCGTTT-TGGCTAAAACGCCACTATATGTTA-
1 -ATCTATTGCGGCGTTTGTGG-TAAAACGCCGCTA-AT-TTAC
** *
20997 ATCTATTGCAACATTTGTGGTATAAACGCCGCTAATTTACC
1 ATCTATTGCGGCGTTTGTGGTA-AAACGCCGCTAATTTA-C
*
21038 ACTCTATTGCGGTGTTTGT
1 A-TCTATTGCGGCGTTTGT
21057 TAAAAAAACG
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
39 3 0.04
40 17 0.21
41 26 0.32
42 31 0.39
43 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (39 bp):
ATCTATTGCGGCGTTTGTGGTAAAACGCCGCTAATTTAC
Found at i:21096 original size:41 final size:42
Alignment explanation
Indices: 21020--21098 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
21010 TTTGTGGTAT
** *
21020 AAACGCCGCTAATTTACCACTCTATTGCGGTGTTTGTTAAAA
1 AAACGCCGCTAATAAACCACTCTATTGCGGCGTTTGTTAAAA
*
21062 AAACGCCGC-AATAAACCAC-CATATTGTGGCGTTTGTT
1 AAACGCCGCTAATAAACCACTC-TATTGCGGCGTTTGTT
21099 GTAAAAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.03
41 22 0.69
42 9 0.28
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (42 bp):
AAACGCCGCTAATAAACCACTCTATTGCGGCGTTTGTTAAAA
Found at i:21105 original size:41 final size:42
Alignment explanation
Indices: 21010--21110 Score: 98
Period size: 41 Copynumber: 2.4 Consensus size: 42
21000 TATTGCAACA
* * ** *
21010 TTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGCGGTG
1 TTTGTTGTAAAAACGCCGCTAATAAACCACTCTATTGCGGCG
** *
21052 TTTGTTAAAAAAACGCCGC-AATAAACCAC-CATATTGTGGCG
1 TTTGTTGTAAAAACGCCGCTAATAAACCACTC-TATTGCGGCG
*
21093 TTTGTTGTAAAAATGCCG
1 TTTGTTGTAAAAACGCCG
21111 TTATATGTCA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.02
41 31 0.66
42 15 0.32
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
TTTGTTGTAAAAACGCCGCTAATAAACCACTCTATTGCGGCG
Found at i:22582 original size:43 final size:43
Alignment explanation
Indices: 22497--22583 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
22487 ACATTGTTTA
* * **
22497 AAATTTTATTTTTTTACCGAAAATTTAATATCGGATGTTATTT
1 AAATATTATTTTTTTACCGAAAATTTAATATCAGATAATATTT
*
22540 AAATATTATTTTTTTACTGAAAATATTAATATCAG-TAATATTT
1 AAATATTATTTTTTTACCGAAAAT-TTAATATCAGATAATATTT
22583 A
1 A
22584 TTTTTAGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 29 0.76
44 9 0.24
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (43 bp):
AAATATTATTTTTTTACCGAAAATTTAATATCAGATAATATTT
Found at i:24217 original size:18 final size:18
Alignment explanation
Indices: 24178--24219 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
24168 GTAAGAAAAT
*
24178 ATTAAATTAATAAAAACG
1 ATTAAATTAATAAAAACA
*
24196 ATTAAA-TAAGTAAAAGCA
1 ATTAAATTAA-TAAAAACA
24214 ATTAAA
1 ATTAAA
24220 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (18 bp):
ATTAAATTAATAAAAACA
Done.