Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004550.1 Hibiscus syriacus cultivar Beakdansim tig00010103_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: 58081
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1838 original size:2 final size:2
Alignment explanation
Indices: 1831--1859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1821 GCTTTTTCCG
1831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1860 TCGAAAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3307 original size:12 final size:13
Alignment explanation
Indices: 3270--3311 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3260 GAAAATTATT
*
3270 TAAATTATTAAAA
1 TAAATTAATAAAA
* *
3283 AAAATTAAAAAAA
1 TAAATTAATAAAA
3296 TAAA-TAATAAAA
1 TAAATTAATAAAA
3308 TAAA
1 TAAA
3312 AGAATAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATTAATAAAA
Found at i:7784 original size:21 final size:21
Alignment explanation
Indices: 7760--7812 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
7750 TAACAAAGGT
*
7760 AGTATCGATACTCTATTTAGG
1 AGTACCGATACTCTATTTAGG
7781 AGTACCGATACTCTATTTAGG
1 AGTACCGATACTCTATTTAGG
7802 AGTACCGATAC
1 AGTACCGATAC
7813 CCTCTATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (21 bp):
AGTACCGATACTCTATTTAGG
Found at i:17015 original size:3 final size:3
Alignment explanation
Indices: 17009--17055 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
16999 GATTCTCGTT
* *
17009 TTA TTA TTA TTA TTTA TTA TTA TTA TTA CTA TTAA TTA TTT TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
17056 CATATTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17026 original size:13 final size:13
Alignment explanation
Indices: 17008--17055 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
16998 GGATTCTCGT
17008 TTTATTATTATTA
1 TTTATTATTATTA
17021 TTTATTATTATTA
1 TTTATTATTATTA
*
17034 -TTACTATTAATTA
1 TTTATTATT-ATTA
17047 TTT-TTATTA
1 TTTATTATTA
17056 CATATTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 8 0.26
13 21 0.68
14 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:17033 original size:19 final size:19
Alignment explanation
Indices: 17009--17061 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
16999 GATTCTCGTT
* *
17009 TTATTATTATTATTTATTA
1 TTATTATTACTATTAATTA
17028 TTATTATTACTATTAATTA
1 TTATTATTACTATTAATTA
*
17047 TTTTTATTACATATT
1 TTATTATTAC-TATT
17062 TTTGCAGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTATTACTATTAATTA
Found at i:24344 original size:37 final size:37
Alignment explanation
Indices: 24301--24415 Score: 155
Period size: 36 Copynumber: 3.2 Consensus size: 37
24291 GTTGTCACTT
24301 TTGAGACAATTTCTTTTAAAAACAAATTTTGTCTCGC
1 TTGAGACAATTTCTTTTAAAAACAAATTTTGTCTCGC
* *
24338 TGGAGAC-A-GTCTTCTTAAAAACAAATTTTGTCTCGC
1 TTGAGACAATTTCTT-TTAAAAACAAATTTTGTCTCGC
* * *
24374 TTGAGACAATTT-ATCTCAAAACAAATTTTGTCTCGC
1 TTGAGACAATTTCTTTTAAAAACAAATTTTGTCTCGC
24410 TTGAGA
1 TTGAGA
24416 TATTTTTTTC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
35 4 0.06
36 55 0.81
37 8 0.12
38 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (37 bp):
TTGAGACAATTTCTTTTAAAAACAAATTTTGTCTCGC
Found at i:24679 original size:68 final size:65
Alignment explanation
Indices: 24570--24747 Score: 189
Period size: 68 Copynumber: 2.7 Consensus size: 65
24560 ATTGACAATC
* * * * *
24570 TTTGAGTCTTTTTCTCTTGAAATAAATTTTGTCACCCTTGAGACAGTTTCCCTTAAAACAAAATC
1 TTTGAGTCTGTTTCCCTTGAAACAAATTTT-TCTCTCTTGAGACAGTTTCCCTTAAAAC--AATC
24635 AGA
63 AGA
* * *
24638 TTTGAGTC-GTTTCCCTTGAAACAAATTTTTATCTCTCTTGAGAAAGTTTCTCTTGAAACAATCA
1 TTTGAGTCTGTTTCCCTTGAAACAAA-TTTT-TCTCTCTTGAGACAGTTTCCCTTAAAACAATCA
**
24702 TC
64 GA
* *
24704 TTTGAGTCTGTTTTCCTTGAAGCAAATTTTT-TCTCTTGAGACAG
1 TTTGAGTCTGTTTCCCTTGAAACAAATTTTTCTCTCTTGAGACAG
24748 CTTATATTGA
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
64 12 0.13
65 1 0.01
66 17 0.18
67 29 0.31
68 35 0.37
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (65 bp):
TTTGAGTCTGTTTCCCTTGAAACAAATTTTTCTCTCTTGAGACAGTTTCCCTTAAAACAATCAGA
Found at i:24786 original size:63 final size:66
Alignment explanation
Indices: 24638--24789 Score: 179
Period size: 63 Copynumber: 2.3 Consensus size: 66
24628 CAAAATCAGA
* * * *
24638 TTTGAGTCGTTTCCCTTGAAACAAATTTTTATCTCTCTTGAGAAAGTTTCTCTTGAAACAATCAT
1 TTTGAGTCGTTTCTCTTGAAACAAATTTTTATCTCTCTTGAGAAAGCTTATATTGAAACAATCAT
24703 C
66 C
* * *
24704 TTTGAGTCTGTTT-TCCTTGAAGCAAA-TTTT-T-TCTCTTGAGACAGCTTATATTGAAGC-ATC
1 TTTGAGTC-GTTTCT-CTTGAAACAAATTTTTATCTCTCTTGAGAAAGCTTATATTGAAACAATC
24764 ATC
64 ATC
24767 TTTGAGTCGGTTTCTCTTGAAAC
1 TTTGAGTC-GTTTCTCTTGAAAC
24790 CATTATCCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
63 25 0.34
64 22 0.30
65 1 0.01
66 12 0.16
67 14 0.19
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (66 bp):
TTTGAGTCGTTTCTCTTGAAACAAATTTTTATCTCTCTTGAGAAAGCTTATATTGAAACAATCAT
C
Found at i:25168 original size:134 final size:134
Alignment explanation
Indices: 24794--25235 Score: 493
Period size: 134 Copynumber: 3.3 Consensus size: 134
24784 TGAAACCATT
* * * * * * *
24794 ATCCCTAAAGATGGTCGACCGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTTCT
1 ATCCCTAAAGATAGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCT
* * * * * * *
24859 CATCACATAGGAGTCGTGTAAACCTTAGATAACCAGTCATCCTTATCACGTAGGAACCT-TG-T-
66 CATCACGTAGGAGTCGTGTCACCCCTAGATAACCAATCATCCTCATCACGTAAGAA-CTGTGTTA
24921 T-ATC
130 TCATC
* * *
24925 ATCCCTAAAGATTA-CCTGCCATCCTCATCACGTAGGAACTGTTTCATCCCTCCGACCAGACCTC
1 ATCCCTAAAGA-TAGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCCT-CGACCAGACCTC
* * * * *
24989 CTCATCATGTAGGAGCCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTATGAACTGTGTT
64 CTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAATCATCCTCATCACGTAAGAACTGTGTT
25054 ATCATC
129 ATCATC
* *
25060 ATCCCTAAAGATAGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCATCGACCAGATCTCCT
1 ATCCCTAAAGATAGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCT
* *
25125 CATCACGTAGAAGTCGTGTCACCCCTAGATAACCAACCATCCTCATCACGTAAGAA-TCGTGTTA
66 CATCACGTAGGAGTCGTGTCACCCCTAGATAACCAATCATCCTCATCACGTAAGAACT-GTGTTA
*
25189 TCACC
130 TCATC
* * * * * *
25194 CTCTCTAAAGAT-GACATGCCGTCCTCATCGCGTAGGAACCGT
1 ATCCCTAAAGATAG-CCTACCATCCTCATCACGTAGGAACCGT
25236 ATCAACCCCT
Statistics
Matches: 262, Mismatches: 40, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
131 42 0.16
132 61 0.23
133 3 0.01
134 109 0.42
135 47 0.18
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (134 bp):
ATCCCTAAAGATAGCCTACCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCT
CATCACGTAGGAGTCGTGTCACCCCTAGATAACCAATCATCCTCATCACGTAAGAACTGTGTTAT
CATC
Found at i:25174 original size:43 final size:42
Alignment explanation
Indices: 24979--25186 Score: 113
Period size: 43 Copynumber: 4.7 Consensus size: 42
24969 CATCCCTCCG
* * *
24979 ACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCCCTAGATA
1 ACCA-ACCTCCTCATCACGTAGAAGTCGTGTCACCCCTAGATA
* * *
25022 ACCAATCGTCCTCATCGCGTATGAACTGT-GTTATCATCATCCCTAAAGATA
1 ACCAA-CCTCCTCATCACGTA-GAA--GTCG-TGTCA-C--CCCT--AGATA
* * * * * *
25073 GCCTACCATCCTCATCACGTAGGAA-CCGTGTCATCCATCG---
1 ACCAACC-TCCTCATCACGTA-GAAGTCGTGTCACCCCTAGATA
*
25113 ACCAGATCTCCTCATCACGTAGAAGTCGTGTCACCCCTAGATA
1 ACCA-ACCTCCTCATCACGTAGAAGTCGTGTCACCCCTAGATA
25156 ACCAACCATCCTCATCACGTAAGAA-TCGTGT
1 ACCAACC-TCCTCATCACGT-AGAAGTCGTGT
25187 TATCACCCTC
Statistics
Matches: 122, Mismatches: 24, Indels: 38
0.66 0.13 0.21
Matches are distributed among these distances:
39 3 0.02
40 26 0.21
41 2 0.02
42 3 0.02
43 39 0.32
44 6 0.05
45 4 0.03
46 5 0.04
47 1 0.01
48 4 0.03
49 5 0.04
50 1 0.01
51 23 0.19
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (42 bp):
ACCAACCTCCTCATCACGTAGAAGTCGTGTCACCCCTAGATA
Found at i:25441 original size:3 final size:3
Alignment explanation
Indices: 25433--25481 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
25423 AGTTCTCGTT
* *
25433 TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA ATA TTAA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
25478 TTA T
1 TTA T
25482 AATTTTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28780 original size:29 final size:29
Alignment explanation
Indices: 28719--28795 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
28709 TATAGTTTCA
*
28719 ATTTTTCCTAATATTTATTATTATAGGATT
1 ATTTTT-CTAATATTTATTATTAGAGGATT
*
28749 ATTTTTCTAATATTTATTATTAG-GG-GT
1 ATTTTTCTAATATTTATTATTAGAGGATT
*
28776 ATATTTTATAATATTT-TTAT
1 AT-TTTTCTAATATTTATTAT
28796 AAGTGTCCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.16
28 14 0.33
29 16 0.37
30 6 0.14
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (29 bp):
ATTTTTCTAATATTTATTATTAGAGGATT
Found at i:35185 original size:16 final size:16
Alignment explanation
Indices: 35161--35194 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
35151 TATCACCGAC
*
35161 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
35177 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
35193 CG
1 CG
35195 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:38861 original size:17 final size:17
Alignment explanation
Indices: 38835--38867 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38825 TTTAGATTCA
38835 TTATTATAAATTAAATT
1 TTATTATAAATTAAATT
*
38852 TTATTTTAAATTAAAT
1 TTATTATAAATTAAAT
38868 CTAGCTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTATAAATTAAATT
Found at i:39452 original size:12 final size:12
Alignment explanation
Indices: 39437--39461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39427 CCACCGTCAC
39437 CCTCATTATCTT
1 CCTCATTATCTT
39449 CCTCATTATCTT
1 CCTCATTATCTT
39461 C
1 C
39462 TCTTAAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCATTATCTT
Found at i:41913 original size:9 final size:9
Alignment explanation
Indices: 41865--41920 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
41855 TATTTATTTA
*
41865 TTTTAAAAT
1 TTTTAATAT
41874 TTTTAAT-T
1 TTTTAATAT
*
41882 TAGTTAATAT
1 T-TTTAATAT
*
41892 TTATTATTAT
1 TT-TTAATAT
41902 TTTTAATAT
1 TTTTAATAT
41911 TTTTAATAT
1 TTTTAATAT
41920 T
1 T
41921 ATTATATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 2 0.05
9 27 0.69
10 10 0.26
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTAATAT
Found at i:41913 original size:37 final size:36
Alignment explanation
Indices: 41850--41934 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 36
41840 TTATTTTTAA
41850 ATTAATATTTA-T-TTATTTTAAAATTTTTAAT-TT
1 ATTAATATTTATTATTATTTTAAAATTTTTAATATT
*
41883 AGTTAATATTTATTATTATTTTTAATATTTTTAATATT
1 A-TTAATATTTATTATTA-TTTTAAAATTTTTAATATT
41921 ATT-ATATCTTATTA
1 ATTAATAT-TTATTA
41935 ATCTATATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
33 1 0.02
34 10 0.22
35 1 0.02
36 7 0.16
37 23 0.51
38 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (36 bp):
ATTAATATTTATTATTATTTTAAAATTTTTAATATT
Found at i:41916 original size:28 final size:27
Alignment explanation
Indices: 41872--41925 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
41862 TTATTTTAAA
41872 ATTTTTAATTTAGTTAATATTTATTATT
1 ATTTTTAATTTAGTTAATA-TTATTATT
*
41900 ATTTTTAATATT-TTTAATATTATTAT
1 ATTTTTAAT-TTAGTTAATATTATTAT
41926 ATCTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 15 0.62
29 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
ATTTTTAATTTAGTTAATATTATTATT
Done.