Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005976.1 Hibiscus syriacus cultivar Beakdansim tig00014049_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: 53733
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:801 original size:13 final size:13
Alignment explanation
Indices: 783--810 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
773 TAACCAATGA
783 AAACATAGACAAT
1 AAACATAGACAAT
796 AAACATAGACAAT
1 AAACATAGACAAT
809 AA
1 AA
811 TCTCATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (13 bp):
AAACATAGACAAT
Found at i:2063 original size:19 final size:19
Alignment explanation
Indices: 2025--2070 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2015 TTGAACTACA
* *
2025 AAGTTCCTACCTTCATTTT
1 AAGTTCATACCTTCACTTT
*
2044 AAGTTCATACCTTCCCTTT
1 AAGTTCATACCTTCACTTT
*
2063 AAATTCAT
1 AAGTTCAT
2071 TGAGCAGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (19 bp):
AAGTTCATACCTTCACTTT
Found at i:5528 original size:31 final size:31
Alignment explanation
Indices: 5490--5614 Score: 223
Period size: 31 Copynumber: 4.0 Consensus size: 31
5480 TGACCTATGT
5490 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
5521 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
5552 AACTGTCCATATGTTCTGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
5583 AACTGTCCATATGTTTCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
5614 A
1 A
5615 CCCTCGACTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:6081 original size:19 final size:19
Alignment explanation
Indices: 6057--6104 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
6047 ACCTTAGCCT
6057 TGCTTTGATTCAATCCTAA
1 TGCTTTGATTCAATCCTAA
**
6076 TGCTTTGATTTGATCCTAA
1 TGCTTTGATTCAATCCTAA
*
6095 TTCTTTGATT
1 TGCTTTGATT
6105 GTTCCGGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (19 bp):
TGCTTTGATTCAATCCTAA
Found at i:7562 original size:20 final size:20
Alignment explanation
Indices: 7534--7587 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
7524 ATTTCTTCTT
7534 CTCTCTTTTCCTTTAAGAAC
1 CTCTCTTTTCCTTTAAGAAC
*
7554 CTTTCTTTTCCTTTAAGAAC
1 CTCTCTTTTCCTTTAAGAAC
7574 CTCTCTTTTCCTTT
1 CTCTCTTTTCCTTT
7588 CCTTTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.30, G:0.04, T:0.52
Consensus pattern (20 bp):
CTCTCTTTTCCTTTAAGAAC
Found at i:29144 original size:7 final size:7
Alignment explanation
Indices: 29132--29159 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29122 AAGGGGTCTG
29132 GGAATAT
1 GGAATAT
29139 GGAATAT
1 GGAATAT
29146 GGAATAT
1 GGAATAT
29153 GGAATAT
1 GGAATAT
29160 TTTAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
GGAATAT
Found at i:43095 original size:33 final size:32
Alignment explanation
Indices: 43049--43121 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
43039 TTTTTTATTT
* *
43049 ATTTTGTTTCTTAATGTTTTTATTTAATTATGG
1 ATTTT-TTTCTTAATGATTTCATTTAATTATGG
*
43082 ACTTTTTTTCTTAATGATTTCATTTAATTATGT
1 A-TTTTTTTCTTAATGATTTCATTTAATTATGG
43115 ATTTTTT
1 ATTTTTT
43122 ATTTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 6 0.17
33 26 0.72
34 4 0.11
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.64
Consensus pattern (32 bp):
ATTTTTTTCTTAATGATTTCATTTAATTATGG
Found at i:43139 original size:47 final size:44
Alignment explanation
Indices: 43084--43187 Score: 122
Period size: 47 Copynumber: 2.3 Consensus size: 44
43074 AATTATGGAC
* *
43084 TTTT-TTTCTTAATGATTT-CATTTAATTATGTATTTTTTATTTA
1 TTTTGTTTCTTAATG-TTTGCATTTAATTATGGACTTTTTATTTA
* *
43127 TTTATTTGTTTCTTGATGTTTGTATTTAATTATGGACTTTTTATTTA
1 --T-TTTGTTTCTTAATGTTTGCATTTAATTATGGACTTTTTATTTA
43174 TTTTGTTTCTTAAT
1 TTTTGTTTCTTAAT
43188 TTTTTATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 12 0.24
45 2 0.04
46 6 0.12
47 31 0.61
ACGTcount: A:0.20, C:0.05, G:0.09, T:0.66
Consensus pattern (44 bp):
TTTTGTTTCTTAATGTTTGCATTTAATTATGGACTTTTTATTTA
Found at i:43237 original size:13 final size:14
Alignment explanation
Indices: 43219--43253 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
43209 AATTGTAGCA
43219 TTTGTATTTAA-TG
1 TTTGTATTTAATTG
43232 TTTGTATTTAATTG
1 TTTGTATTTAATTG
*
43246 TTTTTATT
1 TTTGTATT
43254 ATTTAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (14 bp):
TTTGTATTTAATTG
Found at i:45405 original size:63 final size:63
Alignment explanation
Indices: 45330--45489 Score: 225
Period size: 63 Copynumber: 2.5 Consensus size: 63
45320 TCGAAATGGA
* * * * **
45330 GTGCATGGATGCACTGCATG-GTGCATCGATGCACTGCA-TGGTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGG--G
*
45393 GTGCATGAATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGGG
1 GTGCATGGATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGGG
45456 GTGCATGGATGCACTGCAGGAGTGCATGGATGCA
1 GTGCATGGATGCACTGCAGGAGTGCATGGATGCA
45490 ATTTGACACC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 52 0.60
64 17 0.20
65 18 0.21
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (63 bp):
GTGCATGGATGCACTGCAGGAGTGCATGGATGCACTGCAGGGGTGCATAGATGCACTACAGGG
Found at i:45419 original size:21 final size:21
Alignment explanation
Indices: 45327--45489 Score: 188
Period size: 21 Copynumber: 7.8 Consensus size: 21
45317 CATTCGAAAT
45327 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* *
45348 TG-GTGCATCGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* * *
45368 TG-GTGCATCGATGCACTAG-T
1 GGAGTGCATGGATGCACT-GCA
*
45388 GGCAGGTGCATGAATGCACTGCA
1 GG-A-GTGCATGGATGCACTGCA
45411 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* * *
45432 GGGGTGCATAGATGCACTACA
1 GGAGTGCATGGATGCACTGCA
*
45453 GGGGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
45474 GGAGTGCATGGATGCA
1 GGAGTGCATGGATGCA
45490 ATTTGACACC
Statistics
Matches: 123, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
20 35 0.28
21 71 0.58
22 2 0.02
23 15 0.12
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
GGAGTGCATGGATGCACTGCA
Found at i:46911 original size:19 final size:20
Alignment explanation
Indices: 46866--46913 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
46856 CTCTAAATCT
*
46866 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* * *
46886 CTCTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
46905 TTTTCAAAA
1 TTTTCAAAA
46914 GAAAATCATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:48083 original size:20 final size:22
Alignment explanation
Indices: 48058--48097 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
48048 TGTTGTATAT
48058 AGCCG-TTGGGGAT-ATTTTGA
1 AGCCGTTTGGGGATGATTTTGA
48078 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
48098 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGA
Found at i:48331 original size:21 final size:21
Alignment explanation
Indices: 48263--48447 Score: 198
Period size: 21 Copynumber: 8.7 Consensus size: 21
48253 TCGAAATGGA
*
48263 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * *
48283 GTGCATCGATACACTAG-TGGCAG
1 GTGCATGGATGCACT-GCAGG--G
48306 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
48327 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * *
48347 GTACATCGATGCACTAG-TGGCAG
1 GTGCATGGATGCACT-GCAGG--G
48370 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
48391 GTGCATGGATGCACTGCAAGG
1 GTGCATGGATGCACTGCAGGG
*
48412 GTGCATGGATGCACTGCAAGG
1 GTGCATGGATGCACTGCAGGG
48433 GTGCATGGATGCACT
1 GTGCATGGATGCACT
48448 TTTACACCCT
Statistics
Matches: 139, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
20 27 0.19
21 78 0.56
22 2 0.01
23 32 0.23
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:48340 original size:64 final size:64
Alignment explanation
Indices: 48263--48426 Score: 283
Period size: 64 Copynumber: 2.5 Consensus size: 64
48253 TCGAAATGGA
*
48263 GTGCATGGATGCACTGCATGGTGCATCGATACACTAGTGGCAGGTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
*
48327 GTGCATGGATGCACTGCATGGTACATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
* *
48391 GTGCATGGATGCACTGCAAGGGTGCATGGATGCACT
1 GTGCATGGATGCACTGC-ATGGTGCATCGATGCACT
48427 GCAAGGGTGC
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 79 0.84
65 15 0.16
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (64 bp):
GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGGCAGGTGCATGGATGCACTGCAGGG
Found at i:50474 original size:6 final size:6
Alignment explanation
Indices: 50449--50494 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
50439 AAGGGAGAGG
*
50449 GAAAGA GAAGAGA GGAAAGA GAAAGA GAAAGA GAAAGA GAGAGA GA
1 GAAAGA GAA-AGA -GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GA
50495 TTTAAATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 28 0.76
7 6 0.16
8 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:50490 original size:14 final size:13
Alignment explanation
Indices: 50425--50494 Score: 65
Period size: 12 Copynumber: 5.4 Consensus size: 13
50415 GAGAAGGCGG
50425 AGAGAAGAGGAGGAA
1 AGAGAAGA-GA-GAA
* *
50440 AG-GGAGAGGGAA
1 AGAGAAGAGAGAA
50452 AGAGAAGAGAGGAA
1 AGAGAAGAGA-GAA
50466 AGAGAA-AGAGAA
1 AGAGAAGAGAGAA
*
50478 AGAGAA-AGAGAG
1 AGAGAAGAGAGAA
50490 AGAGA
1 AGAGA
50495 TTTAAATGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
12 24 0.50
13 9 0.19
14 13 0.27
15 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (13 bp):
AGAGAAGAGAGAA
Done.