Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004726.1 Hibiscus syriacus cultivar Beakdansim tig00010657_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: 59134
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5286 original size:15 final size:16
Alignment explanation
Indices: 5259--5288 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5249 AAAACCCTGA
5259 CCCAAAGAATCAAAAT
1 CCCAAAGAATCAAAAT
5275 CCCAAA-AATCAAAA
1 CCCAAAGAATCAAAA
5289 GGGAATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.27, G:0.03, T:0.10
Consensus pattern (16 bp):
CCCAAAGAATCAAAAT
Found at i:7066 original size:20 final size:20
Alignment explanation
Indices: 7029--7067 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7019 TATAATTTTT
* * *
7029 AAAAATATTTTTATACTTTA
1 AAAAATAATTATAAACTTTA
7049 AAAAATAATTATAAACTTT
1 AAAAATAATTATAAACTTT
7068 TATATATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATAATTATAAACTTTA
Found at i:13198 original size:23 final size:23
Alignment explanation
Indices: 13172--13216 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
13162 CCTATCAAGG
13172 ACAACGATGAAGCCGTCAAAGCA
1 ACAACGATGAAGCCGTCAAAGCA
13195 ACAACGATGAAGCCGTCAAAGC
1 ACAACGATGAAGCCGTCAAAGC
13217 CTACGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.27, G:0.22, T:0.09
Consensus pattern (23 bp):
ACAACGATGAAGCCGTCAAAGCA
Found at i:14326 original size:31 final size:31
Alignment explanation
Indices: 14288--14363 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
14278 GTTTTCATCC
** * *
14288 AAATACCTAAAG-TATTTTTTTTTGTTAAAAT
1 AAATACCTAAAGTTA-TCATTTTGGTCAAAAT
*
14319 AAGTACCTAAAGTTATCATTTTGGTCAAAAT
1 AAATACCTAAAGTTATCATTTTGGTCAAAAT
14350 AAATACCTAAAGTT
1 AAATACCTAAAGTT
14364 TTCTTGCTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (31 bp):
AAATACCTAAAGTTATCATTTTGGTCAAAAT
Found at i:16091 original size:2 final size:2
Alignment explanation
Indices: 16084--16112 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16074 TTTGTTTCAA
16084 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 A
16113 GGTTCCGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18701 original size:31 final size:30
Alignment explanation
Indices: 18663--18722 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 30
18653 CAAAACGTCT
18663 AATTCTATGGCAAGATTTAGACTTGTTTCAC
1 AATTCTATGGCAAGATTTAGACTT-TTTCAC
18694 AATTCTATGGCAAGATTTAGACTTTTTCA
1 AATTCTATGGCAAGATTTAGACTTTTTCA
18723 ACATTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (30 bp):
AATTCTATGGCAAGATTTAGACTTTTTCAC
Found at i:26852 original size:10 final size:10
Alignment explanation
Indices: 26837--26861 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26827 ATAAATTACT
26837 AAAATCATTA
1 AAAATCATTA
26847 AAAATCATTA
1 AAAATCATTA
26857 AAAAT
1 AAAAT
26862 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATCATTA
Found at i:31452 original size:17 final size:17
Alignment explanation
Indices: 31424--31456 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31414 TATTAATATA
31424 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
31442 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
31457 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:32125 original size:130 final size:130
Alignment explanation
Indices: 31921--32168 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
31911 AATTTTCTTC
* *
31921 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* ** *
31986 CTTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
32051 TAATTAGGTGGTGACATGTGTCACCAATGACACATGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
32116 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
32169 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:32615 original size:35 final size:35
Alignment explanation
Indices: 32565--32640 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
32555 AATTGAATTT
* *
32565 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
32600 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
32635 AATTGA
1 AATTGA
32641 GGATTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:35720 original size:22 final size:22
Alignment explanation
Indices: 35692--35734 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35682 ATTTTTTTGG
35692 CGTCTTGCTTAGGATCTCCTGA
1 CGTCTTGCTTAGGATCTCCTGA
* *
35714 CGTCTTGTTTGGGATCTCCTG
1 CGTCTTGCTTAGGATCTCCTG
35735 GCGTTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (22 bp):
CGTCTTGCTTAGGATCTCCTGA
Found at i:35924 original size:22 final size:22
Alignment explanation
Indices: 35881--35926 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35871 CAGATCTAAC
*
35881 AAATTTTTAAATACTTTCTATA
1 AAATTTTTAAATACTTTATATA
*
35903 AAATTTTTATAA-ATTTTATATA
1 AAATTTTTA-AATACTTTATATA
35925 AA
1 AA
35927 TTTACTCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTTTAAATACTTTATATA
Found at i:36658 original size:21 final size:22
Alignment explanation
Indices: 36632--36680 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
36622 CCAGCACCCT
*
36632 CAAGACGTCGA-AAATCCCAAA
1 CAAGACGCCGAGAAATCCCAAA
*
36653 CAAGACGCCGAGAGATCCCAAA
1 CAAGACGCCGAGAAATCCCAAA
*
36675 TAAGAC
1 CAAGAC
36681 CCAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (22 bp):
CAAGACGCCGAGAAATCCCAAA
Found at i:43017 original size:34 final size:35
Alignment explanation
Indices: 42968--43039 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 35
42958 GGTAACTAAC
*
42968 AATTACTATCTATAAAAGAGCATTTTTGCCCTTAA
1 AATTACTATCCATAAAAGAGCATTTTTGCCCTTAA
43003 AATT-CTATCCATAAAAGAGCATTTTTGCCCTTAA
1 AATTACTATCCATAAAAGAGCATTTTTGCCCTTAA
43037 AAT
1 AAT
43040 AAAACGGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 32 0.89
35 4 0.11
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (35 bp):
AATTACTATCCATAAAAGAGCATTTTTGCCCTTAA
Found at i:46442 original size:24 final size:24
Alignment explanation
Indices: 46405--46450 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
46395 TACGACGTGC
* *
46405 CACGGAGAAGGAACTTGTCGTTGA
1 CACGGAAAACGAACTTGTCGTTGA
46429 CACGGAAAACGAACTTGTCGTT
1 CACGGAAAACGAACTTGTCGTT
46451 CCATGTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (24 bp):
CACGGAAAACGAACTTGTCGTTGA
Found at i:47787 original size:2 final size:2
Alignment explanation
Indices: 47782--47843 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
47772 TTTTATAAAC
* * *
47782 AT AT AT TT AT AT AT AT AT AT AT AT -T AC AT AT AT AT -T AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47822 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
47844 TATTTTCGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52206 original size:44 final size:43
Alignment explanation
Indices: 52154--52407 Score: 269
Period size: 43 Copynumber: 5.8 Consensus size: 43
52144 ATTAAAGACT
* * * *
52154 TCAATTATAAAAGTAAAAAGTGAGCTTGAAAAGAATTAGGGATC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGG-CC
*
52198 TCAATTATAAATGTAAAAAGTGAGATT-AAAAAAATTAGAGGCC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAG-GGCC
* * * * *
52241 TTAGTTATAAAGGTAGAAAGTAAGATTGAAAAAAA-TAGGGGC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGCC
*
52283 TCAATTATAAAGGTAAAAAGTGAGAATGAAAAAAAATTAGGGACC
1 TCAATTATAAAGGTAAAAAGTGAGATTG-AAAAAAATTAGGG-CC
* ** *
52328 TCAATTATAAATGTAAAAAGTGAGAATAAAAAAAAAATTATGGGAC
1 TCAATTATAAAGGTAAAAAGTGAG-AT-TGAAAAAAATTA-GGGCC
* *
52374 TCAATTATAAAGATAAAAAGCGAGATTAGAAAAA
1 TCAATTATAAAGGTAAAAAGTGAGATT-GAAAAA
52408 TTAAAGACTT
Statistics
Matches: 175, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
42 26 0.15
43 43 0.25
44 39 0.22
45 31 0.18
46 33 0.19
47 3 0.02
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (43 bp):
TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATTAGGGCC
Found at i:52249 original size:87 final size:84
Alignment explanation
Indices: 52154--52431 Score: 279
Period size: 87 Copynumber: 3.2 Consensus size: 84
52144 ATTAAAGACT
*
52154 TCAATTATAAAAGTAAAAAGTGAGCTTGAAAAGAATTAGGGATCTCAATTATAAATGTAAAAAGT
1 TCAATTATAAAAGTAAAAAGTGAGATTGAAAA-AATTAGGGA-CTCAATTATAAA-GTAAAAAGT
52219 GAGATTAAAAAAATTAGAGG-CC
63 GAGATTAAAAAAATTAG-GGACC
* * * * * * *
52241 TTAGTTATAAAGGTAGAAAGTAAGATTGAAAAAAATAGGGGCTCAATTATAAAGGTAAAAAGTGA
1 TCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACTCAATTATAAA-GTAAAAAGTGA
*
52306 GAATGAAAAAAAATTAGGGACC
65 G-AT-TAAAAAAATTAGGGACC
* **
52328 TCAATTATAAATGTAAAAAGTGAGAATAAAAAAAAAATTATGGGACTCAATTATAAAGATAAAAA
1 TCAATTATAAAAGTAAAAAGTGAG-AT--TGAAAAAATTA-GGGACTCAATTATAAAG-TAAAAA
* * ** *
52393 GCGAGATTAGAAAAATTAAAGACT
61 GTGAGATTAAAAAAATTAGGGACC
*
52417 TCAATAATAAAAGTA
1 TCAATTATAAAAGTA
52432 GATAATAGAA
Statistics
Matches: 156, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
85 24 0.15
86 11 0.07
87 58 0.37
88 2 0.01
89 25 0.16
90 11 0.07
91 25 0.16
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (84 bp):
TCAATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACTCAATTATAAAGTAAAAAGTGAG
ATTAAAAAAATTAGGGACC
Found at i:52421 original size:43 final size:42
Alignment explanation
Indices: 52150--52470 Score: 242
Period size: 43 Copynumber: 7.4 Consensus size: 42
52140 TTAAATTAAA
* *
52150 GACTTCAATTATAAAAGTAAAAAGTGAGCTTGAAAAGAATTAGG
1 GACTTCAATTAT-AAAGTAAAAAGTGAGATT-AAAAAAATTAGG
52194 GA-TCTCAATTATAAATGTAAAAAGTGAGATTAAAAAAATTAGAG
1 GACT-TCAATTATAAA-GTAAAAAGTGAGATTAAAAAAATTAG-G
* * * *
52238 GCCTT-AGTTATAAAGGTAGAAAGTAAGATTGAAAAAAA-TAGG
1 GACTTCAATTATAAA-GTAAAAAGTGAGATT-AAAAAAATTAGG
* *
52280 GGC-TCAATTATAAAGGTAAAAAGTGAGAATGAAAAAAAATTAGG
1 GACTTCAATTATAAA-GTAAAAAGTGAG-AT-TAAAAAAATTAGG
* *
52324 GACCTCAATTATAAATGTAAAAAGTGAGAATAAAAAAAAAATTATGG
1 GACTTCAATTATAAA-GTAAAAAGTGAG-AT--TAAAAAAATTA-GG
* * **
52371 GAC-TCAATTATAAAGATAAAAAGCGAGATTAGAAAAATTAAA
1 GACTTCAATTATAAAG-TAAAAAGTGAGATTAAAAAAATTAGG
* * * *
52413 GACTTCAATAATAAAAGTAGATAA-T-AGAATTTAAAAAATTAAG
1 GACTTCAATTAT-AAAGTA-AAAAGTGAG-ATTAAAAAAATTAGG
* *
52456 GATTTTAATTATAAA
1 GACTTCAATTATAAA
52471 AACAAAAACA
Statistics
Matches: 231, Mismatches: 29, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.00
42 30 0.13
43 86 0.37
44 47 0.20
45 30 0.13
46 32 0.14
47 5 0.02
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.25
Consensus pattern (42 bp):
GACTTCAATTATAAAGTAAAAAGTGAGATTAAAAAAATTAGG
Found at i:55969 original size:21 final size:21
Alignment explanation
Indices: 55945--56013 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
55935 TTAAGTATAT
55945 TAATTATTAAAAATTATAAAA
1 TAATTATTAAAAATTATAAAA
* * * *
55966 TAATCATTTAACATTA-AATATTT
1 TAATTATTAAAAATTATAA-A--A
*
55989 TAATTATTAAAAGTTATAAAA
1 TAATTATTAAAAATTATAAAA
56010 TAAT
1 TAAT
56014 CATTCGATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
20 2 0.06
21 18 0.51
23 13 0.37
24 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (21 bp):
TAATTATTAAAAATTATAAAA
Found at i:55992 original size:44 final size:44
Alignment explanation
Indices: 55934--56017 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
55924 ATGTTATTTT
*
55934 ATTAAGTATATTAATTATTAAAAATTATAAAATAATCATTTAAC
1 ATTAAATATATTAATTATTAAAAATTATAAAATAATCATTTAAC
* *
55978 ATTAAATATTTTAATTATTAAAAGTTATAAAATAATCATT
1 ATTAAATATATTAATTATTAAAAATTATAAAATAATCATT
56018 CGATTATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (44 bp):
ATTAAATATATTAATTATTAAAAATTATAAAATAATCATTTAAC
Found at i:56040 original size:44 final size:43
Alignment explanation
Indices: 55947--56042 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
55937 AAGTATATTA
* *
55947 ATTATTAAAAATTATAAAATAATCATTTAACATTAAATATTTT
1 ATTATTAAAAATTATAAAATAATCATTGAACATAAAATATTTT
* **
55990 AATTATTAAAAGTTATAAAATAATCATTCGATTATAAAATATTATT
1 -ATTATTAAAAATTATAAAATAATCATT-GAACATAAAATATT-TT
56036 -TTATTAA
1 ATTATTAA
56043 GTTCATTTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 33 0.73
45 10 0.22
46 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (43 bp):
ATTATTAAAAATTATAAAATAATCATTGAACATAAAATATTTT
Found at i:57826 original size:18 final size:18
Alignment explanation
Indices: 57800--57864 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
57790 AAATTACAAT
*
57800 AAGCTCAAGA-TTCGGTTC
1 AAGCCCAAGACTT-GGTTC
*
57818 AAGCCCAAGACTTTGTTC
1 AAGCCCAAGACTTGGTTC
57836 AAGCCCAAGACTTGGTTC
1 AAGCCCAAGACTTGGTTC
57854 AAGCCCAAGAC
1 AAGCCCAAGAC
57865 CCGGATTAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 41 0.95
19 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (18 bp):
AAGCCCAAGACTTGGTTC
Done.