Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003958.1 Hibiscus syriacus cultivar Beakdansim tig00008558_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: 80102
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6047 original size:16 final size:16
Alignment explanation
Indices: 6017--6063 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6007 GAAACTGACT
*
6017 CAAATTTAACT-AAAC
1 CAAAATTAACTCAAAC
6032 CAAAATTAACTCAAA-
1 CAAAATTAACTCAAAC
*
6047 CATAAAGTAACTCAAAC
1 CA-AAATTAACTCAAAC
6064 ATAAAGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (16 bp):
CAAAATTAACTCAAAC
Found at i:6078 original size:15 final size:16
Alignment explanation
Indices: 6038--6078 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
6028 AAACCAAAAT
6038 TAACTCAAACATAAAG
1 TAACTCAAACATAAAG
6054 TAACTCAAACATAAAG
1 TAACTCAAACATAAAG
6070 TAA-TCAAAC
1 TAACTCAAAC
6079 TGAAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.20
Consensus pattern (16 bp):
TAACTCAAACATAAAG
Found at i:6106 original size:16 final size:15
Alignment explanation
Indices: 6081--6111 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
6071 AATCAAACTG
6081 AAAATAACCTGAATT
1 AAAATAACCTGAATT
6096 AAAATTAACCTGAATT
1 AAAA-TAACCTGAATT
6112 TAATTTGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAATAACCTGAATT
Found at i:11222 original size:16 final size:14
Alignment explanation
Indices: 11183--11224 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
11173 AAAAGAAAAG
11183 AATATGAAA-ATGA
1 AATATGAAATATGA
*
11196 AATATGGAATATGA
1 AATATGAAATATGA
11210 AAGTTATGAAATATG
1 AA--TATGAAATATG
11225 TTAGAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 6 0.25
16 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (14 bp):
AATATGAAATATGA
Found at i:11224 original size:7 final size:7
Alignment explanation
Indices: 11183--11224 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
11173 AAAAGAAAAG
11183 AATATGA
1 AATATGA
11190 AA-ATGA
1 AATATGA
*
11196 AATATGG
1 AATATGA
11203 AATATGA
1 AATATGA
11210 AAGTTATGA
1 AA--TATGA
11219 AATATG
1 AATATG
11225 TTAGAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
9 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (7 bp):
AATATGA
Found at i:16166 original size:15 final size:15
Alignment explanation
Indices: 16146--16175 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16136 TTGACTATGT
*
16146 GATATTTTAATGGAA
1 GATATTTCAATGGAA
16161 GATATTTCAATGGAA
1 GATATTTCAATGGAA
16176 AATGGTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (15 bp):
GATATTTCAATGGAA
Found at i:32710 original size:20 final size:21
Alignment explanation
Indices: 32663--32716 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
32653 AAAATGTCTC
32663 AGTATCGATACTGACCATCTG
1 AGTATCGATACTGACCATCTG
* *
32684 GGTATCGATATTGGACC-TC-G
1 AGTATCGATACT-GACCATCTG
32704 AGTATCGATACTG
1 AGTATCGATACTG
32717 TCTTTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 11 0.39
21 12 0.43
22 4 0.14
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (21 bp):
AGTATCGATACTGACCATCTG
Found at i:56086 original size:18 final size:18
Alignment explanation
Indices: 56063--56102 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
56053 TTTATGTACC
56063 ATGACAATTTGTAAATAG
1 ATGACAATTTGTAAATAG
*
56081 ATGACAATTTGTAAATAT
1 ATGACAATTTGTAAATAG
56099 ATGA
1 ATGA
56103 GAAAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (18 bp):
ATGACAATTTGTAAATAG
Found at i:65139 original size:26 final size:26
Alignment explanation
Indices: 65110--65163 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
65100 AAAAATGTTG
65110 TTTATCAATCGCACTCGAAGGTGCCA
1 TTTATCAATCGCACTCGAAGGTGCCA
* *
65136 TTTATCTATTGCACTCGAAGGTGCCA
1 TTTATCAATCGCACTCGAAGGTGCCA
65162 TT
1 TT
65164 ATACCAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (26 bp):
TTTATCAATCGCACTCGAAGGTGCCA
Found at i:66469 original size:20 final size:19
Alignment explanation
Indices: 66432--66476 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
66422 CCAAAATGGC
66432 CAATTTCACACACTAACAT
1 CAATTTCACACACTAACAT
66451 CAATTTCA-ACATTCTAACAT
1 CAATTTCACACA--CTAACAT
*
66471 TAATTT
1 CAATTT
66477 TCAGCATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 12 0.52
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACACACTAACAT
Found at i:73690 original size:80 final size:81
Alignment explanation
Indices: 73393--74042 Score: 817
Period size: 80 Copynumber: 8.1 Consensus size: 81
73383 TTTTAAAATG
* * ** *
73393 AAAGATTAAATCCCTAACTGTGCATTTGACAGAAATATGCCAATCATGCTAGTTAGATGAAAGAT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
* *
73458 TAAATGCCTTTGAATG
66 TAAATGCCTTTGAGTA
* * * * * *
73474 AAAGATTGAATACTTAACTGTGCATTT-GAAGGAAAGGTGTCAATCATGCTAGTTAGACGAAAGG
1 AAAGATTAAATGCCTAACTGTGCATTTGGCA-GAAAGGTGCCAATCATGCTAGTTAGATGAAAGG
73538 TTAAATGCCTTTGAGTA
65 TTAAATGCCTTTGAGTA
* * *
73555 AAAGTTTAAATGCCTAACTGTGCATTTGGCATAAAGGTGCCAATCATGCTAGTTAGATGAAATGT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
73620 TAAATGCCTTTGAGTA
66 TAAATGCCTTTGAGTA
* * *
73636 AAAGATT-AATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATTATGCTTGTTAGATG-AAGGT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
73699 TAAATGCCTTTGAGTA
66 TAAATGCCTTTGAGTA
* * * * *
73715 AAATA-TAAATACCTAATTGTGCATTTGG--TAAACGTGCCAATCATGCTAGTTAGATG-AAGGT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
73776 TAAATGCCTTTGAGT-
66 TAAATGCCTTTGAGTA
* *
73791 AAAGATTAAATGCCTAACTGTGCATTTGG-ATGAAAGGTACCAATCATGCTATTTAGATGAAAGG
1 AAAGATTAAATGCCTAACTGTGCATTTGGCA-GAAAGGTGCCAATCATGCTAGTTAGATGAAAGG
*
73855 TTAAAAGCC-TTGCAGTA
65 TTAAATGCCTTTG-AGTA
* * *
73872 AAA-ATTAAATGTCTAGCTGTGCATTTGGTAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
*
73936 TAAATGCCTTTGGGTA
66 TAAATGCCTTTGAGTA
* * * * *
73952 AAAGATTAAATGTCTAACTGTGCATTTGG-ATAAAGGTGCTAAT-AGTACAAGTTAGATGAAAGG
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCA-TGCTAGTTAGATGAAAGG
*
74015 TTAAATGCCTTTAGAG-G
65 TTAAATGCCTTT-GAGTA
74032 AAAGA-TAAATG
1 AAAGATTAAATG
74043 TTTAACAATG
Statistics
Matches: 499, Mismatches: 56, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
76 4 0.01
77 64 0.13
78 1 0.00
79 77 0.15
80 176 0.35
81 175 0.35
82 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (81 bp):
AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
TAAATGCCTTTGAGTA
Found at i:73839 original size:236 final size:239
Alignment explanation
Indices: 73393--74042 Score: 859
Period size: 236 Copynumber: 2.7 Consensus size: 239
73383 TTTTAAAATG
* * * *
73393 AAAGATTAAATCCCTAACTGTGCATTTGACAGAAATATGCCAATCATGCTAGTTAGATGAAAGAT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATCATGCTAGTTAGATGAAAGGT
* * * * *
73458 TAAATGCCTTTGAATGAAAGAT-TGAATACTTAACTGTGCATTTGAAGGAAAGGTGTCAATCATG
66 TAAATGCCTTTGAGT-AAA-ATATAAATACCTAACTGTGCATTTG--GTAAAGGTGCCAATCATG
* *
73522 CTAGTTAGACGAAAGGTTAAATGCCTTTGAGTAAAAGTTTAAATGCCTAACTGTGCATTTGGCAT
127 CTAGTTAGATGAAAGGTTAAATGCCTTTGAGT-AAAGATTAAATGCCTAACTGTGCATTTGGCAT
* * *
73587 AAAGGTGCCAATCATGCTAGTTAGATGAAATGTTAAATGCCTTTG-AGTA
191 AAAGGTACCAATCATGCTAGTTAGATGAAAGGTTAAAAGCC-TTGCAGTA
* *
73636 AAAGATT-AATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATTATGCTTGTTAGATG-AAGGT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATCATGCTAGTTAGATGAAAGGT
* *
73699 TAAATGCCTTTGAGTAAAATATAAATACCTAATTGTGCATTTGGTAAACGTGCCAATCATGCTAG
66 TAAATGCCTTTGAGTAAAATATAAATACCTAACTGTGCATTTGGTAAAGGTGCCAATCATGCTAG
73764 TTAGATG-AAGGTTAAATGCCTTTGAGTAAAGATTAAATGCCTAACTGTGCATTTGG-ATGAAAG
131 TTAGATGAAAGGTTAAATGCCTTTGAGTAAAGATTAAATGCCTAACTGTGCATTTGGCAT-AAAG
*
73827 GTACCAATCATGCTATTTAGATGAAAGGTTAAAAGCCTTGCAGTA
195 GTACCAATCATGCTAGTTAGATGAAAGGTTAAAAGCCTTGCAGTA
* * * *
73872 AAA-ATTAAATGTCTAGCTGTGCATTTGGTAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGT
1 AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATCATGCTAGTTAGATGAAAGGT
* * ** * *
73936 TAAATGCCTTTGGGTAAAAGATTAAATGTCTAACTGTGCATTTGGATAAAGGTGCTAAT-AGTAC
66 TAAATGCCTTTGAGTAAAATA-TAAATACCTAACTGTGCATTTGG-TAAAGGTGCCAATCA-TGC
* *
74000 AAGTTAGATGAAAGGTTAAATGCCTTTAGAGGAAAGA-TAAATG
128 TAGTTAGATGAAAGGTTAAATGCCTTT-GAGTAAAGATTAAATG
74043 TTTAACAATG
Statistics
Matches: 362, Mismatches: 35, Indels: 23
0.86 0.08 0.05
Matches are distributed among these distances:
235 8 0.02
236 117 0.32
237 44 0.12
238 46 0.13
239 24 0.07
240 44 0.12
241 26 0.07
242 46 0.13
243 7 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (239 bp):
AAAGATTAAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATCATGCTAGTTAGATGAAAGGT
TAAATGCCTTTGAGTAAAATATAAATACCTAACTGTGCATTTGGTAAAGGTGCCAATCATGCTAG
TTAGATGAAAGGTTAAATGCCTTTGAGTAAAGATTAAATGCCTAACTGTGCATTTGGCATAAAGG
TACCAATCATGCTAGTTAGATGAAAGGTTAAAAGCCTTGCAGTA
Found at i:74057 original size:317 final size:319
Alignment explanation
Indices: 73430--74057 Score: 856
Period size: 317 Copynumber: 2.0 Consensus size: 319
73420 GACAGAAATA
* *
73430 TGCCAATCATGCTAGTTAGATGAAAGATTAAATGCCTTTGAATGAAAGATTGAATACTTAACTGT
1 TGCCAATCATGCTAGTTAGATGAAAGATTAAATGCCTTTGAATGAAAGATTAAATACCTAACTGT
** * *
73495 GCATTTGAAGGAAAGGTGTCAATCATGCTAGTTAGACGAAAGGTTAAATGCCTTTGAGTAAAAGT
66 GCATTTGAAGGAAAGGTACCAATCATGCTAGTTAGACGAAAGGTTAAAAGCCTTTGAGTAAAAGA
* *
73560 TTAAATGCCTAACTGTGCATTTGGCATAAAGGTGCCAATCATGCTAGTTAGATGAAATGTTAAAT
131 TTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGTTAAAT
* **
73625 GCCTTTGAGTAAAAGATTAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATTATGCTTGTTA
196 GCCTTTGAGTAAAAGATTAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATTATACAAGTTA
* ***
73690 GATGAAGGTTAAATGCCTTTGAGTAAAATATAAATACCTAATTGTGCATTTGGTAAACG
261 GATGAAGGTTAAATGCCTTTGAGTAAAAGATAAATACCTAACAATGCATTTGGTAAACG
* * *
73749 TGCCAATCATGCTAGTTAGATG-AAGGTTAAATGCCTTTGAGT-AAAGATTAAATGCCTAACTGT
1 TGCCAATCATGCTAGTTAGATGAAAGATTAAATGCCTTTGAATGAAAGATTAAATACCTAACTGT
* * * *
73812 GCATTTGGATGAAAGGTACCAATCATGCTATTTAGATGAAAGGTTAAAAGCC-TTGCAGTAAAA-
66 GCATTTGAAGGAAAGGTACCAATCATGCTAGTTAGACGAAAGGTTAAAAGCCTTTG-AGTAAAAG
* * *
73875 ATTAAATGTCTAGCTGTGCATTTGGTAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGTTAAA
130 ATTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGTTAAA
* * * * *
73940 TGCCTTTGGGTAAAAGATTAAATGTCTAACTGTGCATTTGG-ATAAAGGTGCTAA-TAGTACAAG
195 TGCCTTTGAGTAAAAGATT-AATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATTA-TACAAG
* ***
74003 TTAGATGAAAGGTTAAATGCCTTTAGAG-GAAAGATAAATGTTTAACAATGCATTT
258 TTAGATG-AAGGTTAAATGCCTTT-GAGTAAAAGATAAATACCTAACAATGCATTT
74058 TGACATACAA
Statistics
Matches: 270, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
315 2 0.01
316 100 0.37
317 125 0.46
318 21 0.08
319 22 0.08
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (319 bp):
TGCCAATCATGCTAGTTAGATGAAAGATTAAATGCCTTTGAATGAAAGATTAAATACCTAACTGT
GCATTTGAAGGAAAGGTACCAATCATGCTAGTTAGACGAAAGGTTAAAAGCCTTTGAGTAAAAGA
TTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGAAAGGTTAAAT
GCCTTTGAGTAAAAGATTAATGCCTAACTGTGCATTTGGCAGAAAGATGCCAATTATACAAGTTA
GATGAAGGTTAAATGCCTTTGAGTAAAAGATAAATACCTAACAATGCATTTGGTAAACG
Found at i:74459 original size:26 final size:25
Alignment explanation
Indices: 74430--74481 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
74420 TCATTGTGTT
* *
74430 AAATAATTTGGTTTTAAAATTGAAAA
1 AAATAATGTGCTTTTAAAA-TGAAAA
* *
74456 AAATTATGTGCTTTTCAAATGAAAA
1 AAATAATGTGCTTTTAAAATGAAAA
74481 A
1 A
74482 TAAGGTCTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (25 bp):
AAATAATGTGCTTTTAAAATGAAAA
Found at i:75131 original size:24 final size:24
Alignment explanation
Indices: 75099--75147 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
75089 GAGAAGTTGC
*
75099 GTGGAGCTATATCGTTGTTAATGG
1 GTGGAGCTATATCGTTGCTAATGG
*
75123 GTGGAGCTATATTGTTGCTAATGG
1 GTGGAGCTATATCGTTGCTAATGG
75147 G
1 G
75148 ATCAGCTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.08, G:0.35, T:0.37
Consensus pattern (24 bp):
GTGGAGCTATATCGTTGCTAATGG
Done.