Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003717.1 Hibiscus syriacus cultivar Beakdansim tig00007947_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: 56870
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:641 original size:16 final size:16
Alignment explanation
Indices: 622--690 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 16
612 AAAAAGTGTA
622 GAAAATTAAATTGTTG
1 GAAAATTAAATTGTTG
**
638 GAAAA-TAAATACTT-
1 GAAAATTAAATTGTTG
* * *
652 -AAATTTATA-TG-TA
1 GAAAATTAAATTGTTG
665 GAAAATTAAATTGTTG
1 GAAAATTAAATTGTTG
681 GAAAA-TAAAT
1 GAAAATTAAAT
691 ACTTAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 11
0.66 0.15 0.19
Matches are distributed among these distances:
12 1 0.03
13 3 0.08
14 10 0.26
15 14 0.36
16 11 0.28
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (16 bp):
GAAAATTAAATTGTTG
Found at i:666 original size:43 final size:43
Alignment explanation
Indices: 618--717 Score: 191
Period size: 43 Copynumber: 2.3 Consensus size: 43
608 AAAGAAAAAG
618 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
1 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
661 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
1 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
*
704 GGTAGAAAATTAAA
1 TGTAGAAAATTAAA
718 GATAAATTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (43 bp):
TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
Found at i:713 original size:23 final size:23
Alignment explanation
Indices: 644--713 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
634 GTTGGAAAAT
*
644 AAATACTTAAATTTATATGTAG-
1 AAATACTTAAATTTATAGGTAGA
* *
666 AAA-A-TTAAATTGT-T-GGAAAA
1 AAATACTTAAATT-TATAGGTAGA
686 TAAATACTTAAATTTATAGGTAGA
1 -AAATACTTAAATTTATAGGTAGA
710 AAAT
1 AAAT
714 TAAAGATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 5 0.14
22 5 0.14
23 12 0.33
24 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (23 bp):
AAATACTTAAATTTATAGGTAGA
Found at i:1929 original size:37 final size:38
Alignment explanation
Indices: 1867--1971 Score: 160
Period size: 37 Copynumber: 2.8 Consensus size: 38
1857 AAGCTGCAAC
* *
1867 TTTCAACAAGTTTCAC-TGCACATTTGGTGCACCACAA
1 TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
1904 TTTC-ACAATTTTCACTTGCATATTTGGTGCACCACAA
1 TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
* *
1941 TTTCAACAATTTCCACTTGCATATTCGGTGC
1 TTTCAACAATTTTCACTTGCATATTTGGTGC
1972 CTACCTTGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
36 10 0.16
37 28 0.45
38 24 0.39
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (38 bp):
TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
Found at i:13506 original size:56 final size:52
Alignment explanation
Indices: 13446--13556 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
13436 ACGGATTTAA
13446 ACTTTTAATATATTTT-CTTTAATTCTAAGGTTTTAATAAAGAATG-TTTTAATTTGG
1 ACTTTTAATATATTTTACTTT--TT-T-A-GTTTTAATAAAGAA-GATTTTAATTTGG
*
13502 ACTTTTAATATATTTTAAGTTTTTTAGTTTTAATAAAGAAGATTTTAATTTGG
1 ACTTTTAATATATTTT-ACTTTTTTAGTTTTAATAAAGAAGATTTTAATTTGG
13555 AC
1 AC
13557 ATTATATTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
52 1 0.02
53 27 0.53
54 1 0.02
55 1 0.02
56 18 0.35
58 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (52 bp):
ACTTTTAATATATTTTACTTTTTTAGTTTTAATAAAGAAGATTTTAATTTGG
Found at i:20262 original size:2 final size:2
Alignment explanation
Indices: 20255--20301 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
20245 ACTGGATTTA
20255 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
20297 AT AT A
1 AT AT A
20302 GGACTTTAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37230 original size:59 final size:59
Alignment explanation
Indices: 37148--37387 Score: 264
Period size: 59 Copynumber: 4.1 Consensus size: 59
37138 TATGCACCAA
* * * * *
37148 AGTGATAACCTGAATATGACACATAAGTTCGTTCCCACCATCTGCACTAGGTATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
* * *
37207 AGTGCTAACATGAATATGACACATAAGGTCGTGCCCACCATCTACACTAAATATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
* * * ** * * *
37266 AGTTCTAACATTAATATGACACAAAACATCGAACCCACCATTTGTACTAAGTATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
* * *** * * *
37325 TGTGCGAACCCAAATATAACACATAAGGTCATACCCACCATCTGCATTAAGTATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
37384 AGTG
1 AGTG
37388 TTGACCCGAA
Statistics
Matches: 147, Mismatches: 34, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 147 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (59 bp):
AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
Found at i:38049 original size:40 final size:40
Alignment explanation
Indices: 37989--38134 Score: 211
Period size: 40 Copynumber: 3.6 Consensus size: 40
37979 ATTATAGTTC
* *
37989 TACACATAAAGTCGTTCCCACCATATAAACCAAAGTGCAT
1 TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
* *
38029 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGCAT
1 TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
* *
38069 TACACATAAGGTCGTGCCCACCATATACACTAAAGTGCAT
1 TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
* * *
38109 TACACAAAAATTTGTGCCCACCATAT
1 TACACATAAAGTCGTGCCCACCATAT
38135 GCTCTTAGTG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 96 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (40 bp):
TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
Found at i:38489 original size:24 final size:24
Alignment explanation
Indices: 38456--38504 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
38446 AGTCTTCATG
*
38456 ATGATGTATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
38480 ATGATATATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
38504 A
1 A
38505 ATGTCATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (24 bp):
ATGATATATAAAACATCTATGTAC
Found at i:39095 original size:30 final size:31
Alignment explanation
Indices: 39037--39107 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
39027 ACAGCCATTT
* * * *
39037 ATAACTTTACCAAAATTATCAAATTGGTCCC
1 ATAACTTTTCAAAAATTATAAAAATGGTCCC
*
39068 TTAACTTTTCAAAAATTA-AAAAATGGTCCC
1 ATAACTTTTCAAAAATTATAAAAATGGTCCC
*
39098 AAAACTTTTC
1 ATAACTTTTC
39108 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (31 bp):
ATAACTTTTCAAAAATTATAAAAATGGTCCC
Found at i:43071 original size:20 final size:20
Alignment explanation
Indices: 43048--43086 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43038 TTATATGCTG
*
43048 GAAATT-AATGTTTGGATGTT
1 GAAATTGAA-GTTAGGATGTT
43068 GAAATTGAAGTTAGGATGT
1 GAAATTGAAGTTAGGATGT
43087 AAAATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
GAAATTGAAGTTAGGATGTT
Found at i:47145 original size:60 final size:59
Alignment explanation
Indices: 47003--47163 Score: 166
Period size: 59 Copynumber: 2.7 Consensus size: 59
46993 TGAAAAGTTA
* * * * * *
47003 TAAAAGTTTATAGACTAATTTATAATTATTGTCATAATTTGAGGATGAAAATGAAATAT
1 TAAAAGTTTAGAGACTAATTTAGAATGATAGTCATAATTTAAAGATGAAAATGAAATAT
* * *
47062 TCAAAGTTT-GAAGACTAATTTAGAATGATAGTCATAGTTTAAAGATGAAATTGGAACAT-T
1 TAAAAGTTTAG-AGACTAATTTAGAATGATAGTCATAATTTAAAGATGAAAAT-GAA-ATAT
* *
47122 TAAAAATTTAGAGACTAATTTAGAATGAGT-GACATAATTTAA
1 TAAAAGTTTAGAGACTAATTTAGAATGA-TAGTCATAATTTAA
47164 GGAAGTGTGT
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
59 42 0.50
60 38 0.45
61 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (59 bp):
TAAAAGTTTAGAGACTAATTTAGAATGATAGTCATAATTTAAAGATGAAAATGAAATAT
Found at i:49189 original size:39 final size:39
Alignment explanation
Indices: 49146--49293 Score: 156
Period size: 39 Copynumber: 3.8 Consensus size: 39
49136 GGCTCCTCGG
* * *
49146 CTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCTTATA
1 CTTTGTGCACATGGTAAGTCCTTACCACAGGCTCTTATA
** *
49185 CTTTGTGCACATGGTAAGTCCTTACTGCAGGCTCCTT-GA
1 CTTTGTGCACATGGTAAGTCCTTACCACAGGCT-CTTATA
* * * *
49224 CTTTGTGCTCAGGGTAAGTCCTTA-CAGCAGGCTCATATG
1 CTTTGTGCACATGGTAAGTCCTTACCA-CAGGCTCTTATA
* *
49263 CTTTGTTCACATGGTAAGTCCTTACCGCAGG
1 CTTTGTGCACATGGTAAGTCCTTACCACAGG
49294 TCCTTATGTT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.02
39 82 0.93
40 4 0.05
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (39 bp):
CTTTGTGCACATGGTAAGTCCTTACCACAGGCTCTTATA
Found at i:49267 original size:78 final size:78
Alignment explanation
Indices: 49129--49298 Score: 236
Period size: 78 Copynumber: 2.2 Consensus size: 78
49119 CTCGACTTTG
* * * *
49129 TACCGTAGGCTCCTCGGCTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCTTATACTTTGTGCA
1 TACCGCAGGCTCCTTGACTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCATATACTTTGTGCA
49194 CATGGTAAGTCCT
66 CATGGTAAGTCCT
* * * * *
49207 TACTGCAGGCTCCTTGACTTTGTGCTCAGGGTAAGTCCTTA-CAGCAGGCTCATATGCTTTGTTC
1 TACCGCAGGCTCCTTGACTTTGTGCTCAAGGTAAGTCCATACCA-CAGGCTCATATACTTTGTGC
49271 ACATGGTAAGTCCT
65 ACATGGTAAGTCCT
49285 TACCGCAGG-TCCTT
1 TACCGCAGGCTCCTT
49299 ATGTTGTGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
77 7 0.09
78 74 0.91
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.32
Consensus pattern (78 bp):
TACCGCAGGCTCCTTGACTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCATATACTTTGTGCA
CATGGTAAGTCCT
Found at i:49973 original size:27 final size:27
Alignment explanation
Indices: 49935--49989 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
49925 CCTTATAGAT
49935 TTATCCATTGAGTGCTATTAGAGGTCG
1 TTATCCATTGAGTGCTATTAGAGGTCG
49962 TTATCCATTGAGTGCTATTAGAGGTCG
1 TTATCCATTGAGTGCTATTAGAGGTCG
49989 T
1 T
49990 AGGCCAGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (27 bp):
TTATCCATTGAGTGCTATTAGAGGTCG
Found at i:51118 original size:16 final size:16
Alignment explanation
Indices: 51099--51180 Score: 58
Period size: 16 Copynumber: 5.1 Consensus size: 16
51089 GCATCCATGC
51099 ATGTATATATATATGT
1 ATGTATATATATATGT
* *
51115 ATGTGTGTATATATGT
1 ATGTATATATATATGT
* * * *
51131 ATGCATGTATGA-AAGC
1 ATGTATATAT-ATATGT
* * *
51147 ATGTATATATGTAAGC
1 ATGTATATATATATGT
*
51163 ATGTATATATGTATGT
1 ATGTATATATATATGT
51179 AT
1 AT
51181 AAAAATATAC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
16 52 0.98
17 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.43
Consensus pattern (16 bp):
ATGTATATATATATGT
Found at i:51125 original size:20 final size:20
Alignment explanation
Indices: 51100--51138 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
51090 CATCCATGCA
*
51100 TGTATATATATATGTATGTG
1 TGTATATATATATGCATGTG
*
51120 TGTATATATGTATGCATGT
1 TGTATATATATATGCATGT
51139 ATGAAAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (20 bp):
TGTATATATATATGCATGTG
Found at i:51141 original size:28 final size:28
Alignment explanation
Indices: 51110--51181 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
51100 TGTATATATA
* *
51110 TATGTATGTGTGTATATATGTATGCATG
1 TATGTATGTATGTATATATGTAAGCATG
* * *
51138 TATGAAAGCATGTATATATGTAAGCATG
1 TATGTATGTATGTATATATGTAAGCATG
*
51166 TATATATGTATGTATA
1 TATGTATGTATGTATA
51182 AAAATATACT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (28 bp):
TATGTATGTATGTATATATGTAAGCATG
Found at i:51259 original size:2 final size:2
Alignment explanation
Indices: 51252--51288 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51242 CATACCATAC
51252 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
51289 AAGTATGCAC
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:51411 original size:4 final size:4
Alignment explanation
Indices: 51402--51487 Score: 52
Period size: 4 Copynumber: 21.5 Consensus size: 4
51392 TCGAACAAAT
* * * *
51402 ATAC ATAC ATAC ATAAC ATAC ATAC AT-G ATAC ATGC ATTA- ATAA AT-T
1 ATAC ATAC ATAC AT-AC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC
** * *
51449 ATAC ATTT ATAC ATGC ATATC ATAC ATAC ATAG ATAC AT
1 ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATAC ATAC AT
51488 TATACATCAT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
3 6 0.10
4 47 0.76
5 9 0.15
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:51422 original size:13 final size:13
Alignment explanation
Indices: 51404--51428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51394 GAACAAATAT
51404 ACATACATACATA
1 ACATACATACATA
51417 ACATACATACAT
1 ACATACATACAT
51429 GATACATGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
ACATACATACATA
Found at i:55994 original size:20 final size:20
Alignment explanation
Indices: 55971--56020 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
55961 TTAGGAAAAT
55971 TTTCGAAACTCTCG-AGATAG
1 TTTCGAAACTCTCGTAGA-AG
*
55991 TTTCGAAACTCTTGTAGAAG
1 TTTCGAAACTCTCGTAGAAG
*
56011 TTTCAAAACT
1 TTTCGAAACT
56021 TCTGGTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TTTCGAAACTCTCGTAGAAG
Done.