Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001304.1 Hibiscus syriacus cultivar Beakdansim tig00002544_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: 57034
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3397 original size:17 final size:16
Alignment explanation
Indices: 3352--3399 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
3342 TCTTTGATAA
*
3352 CATTTCTATCCATTT-
1 CATTTCTTTCCATTTC
*
3367 AATTTCTTTCCATTTC
1 CATTTCTTTCCATTTC
*
3383 CATTTCCTTTTCATTTC
1 CATTT-CTTTCCATTTC
3400 TTAATTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 13 0.48
16 4 0.15
17 10 0.37
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (16 bp):
CATTTCTTTCCATTTC
Found at i:5328 original size:17 final size:16
Alignment explanation
Indices: 5283--5330 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
5273 TCTTTGATAA
*
5283 CATTTCTATCCATTT-
1 CATTTCTTTCCATTTC
*
5298 AATTTCTTTCCATTTC
1 CATTTCTTTCCATTTC
*
5314 CATTTCCTTTTCATTTC
1 CATTT-CTTTCCATTTC
5331 TTAATTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 13 0.48
16 4 0.15
17 10 0.37
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (16 bp):
CATTTCTTTCCATTTC
Found at i:7260 original size:17 final size:16
Alignment explanation
Indices: 7215--7262 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
7205 TCTTTGATAA
*
7215 CATTTCTATCCATTT-
1 CATTTCTTTCCATTTC
*
7230 AATTTCTTTCCATTTC
1 CATTTCTTTCCATTTC
*
7246 CATTTCCTTTTCATTTC
1 CATTT-CTTTCCATTTC
7263 TTAATTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 13 0.48
16 4 0.15
17 10 0.37
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (16 bp):
CATTTCTTTCCATTTC
Found at i:18186 original size:19 final size:20
Alignment explanation
Indices: 18162--18212 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
18152 CGTCCAAGAG
*
18162 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
18181 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
18201 CATGTATTTTCA
1 CATGTATTTTCA
18213 AAGGGATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:33986 original size:10 final size:10
Alignment explanation
Indices: 33971--33996 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
33961 TAAGGTATTT
33971 AGCTCATAAC
1 AGCTCATAAC
33981 AGCTCATAAC
1 AGCTCATAAC
33991 AGCTCA
1 AGCTCA
33997 ATATCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (10 bp):
AGCTCATAAC
Found at i:35324 original size:4 final size:5
Alignment explanation
Indices: 35293--35329 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
35283 TCCGGCACTC
35293 AAAAG AAAAAG AAAAG AAAAG AAAAG -AAAG AAAAG AA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
35330 GTTGAAGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35324 original size:9 final size:9
Alignment explanation
Indices: 35300--35329 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
35290 CTCAAAAGAA
35300 AAAGAAAAG
1 AAAGAAAAG
35309 AAAAGAAAAG
1 -AAAGAAAAG
35319 AAAGAAAAG
1 AAAGAAAAG
35328 AA
1 AA
35330 GTTGAAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:42776 original size:79 final size:79
Alignment explanation
Indices: 42663--42815 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 79
42653 TCTTATTTTT
* *
42663 TGATGTAAGGTACTCTTACCTTATAGATTGATTGTGAATCTAGGAAGGAAGCAAAATAACATGCA
1 TGATGTAAGGAACTCTTACCTTATAGATTGATTGTGAATCTAGGAAGGAAGCAAAACAACATGCA
*
42728 TCAGTGAATGGCTC
66 TAAGTGAATGGCTC
* * * ** * *
42742 TGATGTAAGGAACT-TGTACCTTGTCGATTGATTGTGGATCTATTAAGGAAGTAAAACAACCTGC
1 TGATGTAAGGAACTCT-TACCTTATAGATTGATTGTGAATCTAGGAAGGAAGCAAAACAACATGC
42806 ATAAGTGAAT
65 ATAAGTGAAT
42816 AGCTTAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 1 0.02
79 62 0.98
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (79 bp):
TGATGTAAGGAACTCTTACCTTATAGATTGATTGTGAATCTAGGAAGGAAGCAAAACAACATGCA
TAAGTGAATGGCTC
Found at i:54194 original size:21 final size:21
Alignment explanation
Indices: 54168--54216 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
54158 CCAGCTGAGT
54168 TGAGCTTTCCTTAGTGTTCCA
1 TGAGCTTTCCTTAGTGTTCCA
*
54189 TGAGCTTTCCTTAGTGTTTCA
1 TGAGCTTTCCTTAGTGTTCCA
54210 TGAGCTT
1 TGAGCTT
54217 CCATGTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (21 bp):
TGAGCTTTCCTTAGTGTTCCA
Found at i:56550 original size:24 final size:26
Alignment explanation
Indices: 56523--56576 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
56513 CTTTCTTTTA
*
56523 TTTTCTT-TTTTTTGAGTGCTTC-AT
1 TTTTCTTCTTTTTGGAGTGCTTCAAT
56547 TTTTCTTCTTTTTGGAGTGCTTCAAT
1 TTTTCTTCTTTTTGGAGTGCTTCAAT
56573 TTTT
1 TTTT
56577 TTGCTGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 14 0.52
26 6 0.22
ACGTcount: A:0.09, C:0.13, G:0.13, T:0.65
Consensus pattern (26 bp):
TTTTCTTCTTTTTGGAGTGCTTCAAT
Done.