Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006803.1 Hibiscus syriacus cultivar Beakdansim tig00017267_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: 53275
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1908 original size:2 final size:2
Alignment explanation
Indices: 1887--1939 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
1877 ATTTTATAAC
1887 TA TA T- TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1926 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1940 ATAATTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8779 original size:28 final size:28
Alignment explanation
Indices: 8738--8812 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
8728 TCCCGAAGAC
*
8738 CTATGTCTCGAAGGACCACATATCACAT
1 CTATGTCCCGAAGGACCACATATCACAT
*
8766 CTATGTCCCAAAGGACCACATATCACAT
1 CTATGTCCCGAAGGACCACATATCACAT
8794 CTATGTCCCGAAGGACCAC
1 CTATGTCCCGAAGGACCAC
8813 TCCTTAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (28 bp):
CTATGTCCCGAAGGACCACATATCACAT
Found at i:8892 original size:21 final size:21
Alignment explanation
Indices: 8857--8915 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
8847 AATAGGTGTA
* * *
8857 CCAAAGTACCGCATATATGTT
1 CCAAAGGACCACATATATGTC
**
8878 CCAAAGGATTACATATATGTC
1 CCAAAGGACCACATATATGTC
*
8899 CCGAAGGACCACATATA
1 CCAAAGGACCACATATA
8916 AACTTCGACT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (21 bp):
CCAAAGGACCACATATATGTC
Found at i:17610 original size:14 final size:15
Alignment explanation
Indices: 17591--17632 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
17581 GCAAGCACTC
17591 AAAAGAAGAAAAGA-
1 AAAAGAAGAAAAGAG
17605 AAAAGAAGAAAA-AG
1 AAAAGAAGAAAAGAG
17619 AAAAGAAAGAAAAG
1 AAAAG-AAGAAAAG
17633 TTAAAGCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 17 0.68
15 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAGAG
Found at i:23410 original size:17 final size:16
Alignment explanation
Indices: 23388--23433 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 16
23378 TTGCTTTAGA
23388 AATTTAATTTTTTATAT
1 AATTTAATTTTTT-TAT
23405 AATTTAAATATTTTTTAT
1 AATTT-AAT-TTTTTTAT
23423 AATTTAATTTT
1 AATTTAATTTT
23434 GAATCTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.11
17 8 0.30
18 11 0.41
19 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTAATTTTTTTAT
Found at i:23797 original size:22 final size:22
Alignment explanation
Indices: 23765--23815 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
23755 GCGGACTGCT
*
23765 TGATTATTAGCTGTATCATATA
1 TGATTAATAGCTGTATCATATA
23787 TGATTAATAGCTGTATCATATA
1 TGATTAATAGCTGTATCATATA
23809 TGATTAA
1 TGATTAA
23816 GGACATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (22 bp):
TGATTAATAGCTGTATCATATA
Found at i:31051 original size:3 final size:3
Alignment explanation
Indices: 31043--31151 Score: 182
Period size: 3 Copynumber: 36.3 Consensus size: 3
31033 TACCCATATC
* *
31043 ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
31091 ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31139 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
31152 AATATATTAA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:31198 original size:22 final size:21
Alignment explanation
Indices: 31150--31195 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31140 TTATTATTAT
* *
31150 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
31171 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
31192 TAAA
1 TAAA
31196 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:31749 original size:15 final size:15
Alignment explanation
Indices: 31721--31762 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
31711 ACCACTCAGC
31721 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
*
31736 AAAGGAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
31751 GAAGAAAAGAAA
1 AAAGAAAAGAAA
31763 CTTACCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:32333 original size:30 final size:29
Alignment explanation
Indices: 32299--32357 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
32289 TAAAATAATA
32299 TATTTAGGATAAATAACAGATTTAATCCCT
1 TATTTAGGATAAATAACA-ATTTAATCCCT
** * *
32329 TATTTTTGATAAATAATATTTTAATCCCT
1 TATTTAGGATAAATAACAATTTAATCCCT
32358 AGTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (29 bp):
TATTTAGGATAAATAACAATTTAATCCCT
Found at i:33351 original size:18 final size:18
Alignment explanation
Indices: 33304--33351 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
33294 TTTCGAATTA
33304 TTTATTTTATTTATTATT
1 TTTATTTTATTTATTATT
***
33322 TTTATAAAATTTA-TATGT
1 TTTATTTTATTTATTAT-T
33340 TTTATTTTATTT
1 TTTATTTTATTT
33352 GCAAGTATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTATTTTATTTATTATT
Found at i:44410 original size:13 final size:13
Alignment explanation
Indices: 44392--44416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44382 TAAATTTTCA
44392 AAAAAAAAATTTT
1 AAAAAAAAATTTT
44405 AAAAAAAAATTT
1 AAAAAAAAATTT
44417 GTTTTTCAAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAAAAATTTT
Found at i:44410 original size:14 final size:15
Alignment explanation
Indices: 44383--44413 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
44373 CAAAAATTTT
44383 AAATTTTCAAAAAAA
1 AAATTTTCAAAAAAA
44398 AAATTTT-AAAAAAA
1 AAATTTTCAAAAAAA
44412 AA
1 AA
44414 TTTGTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTTTCAAAAAAA
Found at i:53052 original size:27 final size:26
Alignment explanation
Indices: 53004--53057 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
52994 CCGAATTCGG
*
53004 TGCCCCCTTAGCAGTCGTTTTTGACT
1 TGCCCCCTTAGCAGCCGTTTTTGACT
53030 TGCCCCCTTTTAGCAGCCG-TTTTGACT
1 TGCCCCC--TTAGCAGCCGTTTTTGACT
53057 T
1 T
53058 TACAATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 9 0.36
28 9 0.36
ACGTcount: A:0.11, C:0.31, G:0.19, T:0.39
Consensus pattern (26 bp):
TGCCCCCTTAGCAGCCGTTTTTGACT
Done.