Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001112.1 Hibiscus syriacus cultivar Beakdansim tig00002194_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: 68921
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5742 original size:14 final size:15
Alignment explanation
Indices: 5723--5764 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
5713 TCATGTACCG
*
5723 AGAAAAATAAATGA-
1 AGAAAAATAAAGGAC
*
5737 AGAAAAATTAAGGAC
1 AGAAAAATAAAGGAC
5752 AGTAAAAATAAAG
1 AG-AAAAATAAAG
5765 CTAACTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 2 0.09
16 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.14
Consensus pattern (15 bp):
AGAAAAATAAAGGAC
Found at i:8404 original size:13 final size:13
Alignment explanation
Indices: 8386--8413 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8376 CATGCACTCC
8386 CAACAACTATCTT
1 CAACAACTATCTT
8399 CAACAACTATCTT
1 CAACAACTATCTT
8412 CA
1 CA
8414 CACTAAGTCA
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:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (13 bp):
CAACAACTATCTT
Found at i:9364 original size:31 final size:31
Alignment explanation
Indices: 9324--9383 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
9314 AGTTACGTCG
* *
9324 GGGATCATATTACAAACTGACTAAATGTTAA
1 GGGACCATATTACAAACAGACTAAATGTTAA
*
9355 GGGACCATATTGCAAACAGACTAAATGTT
1 GGGACCATATTACAAACAGACTAAATGTT
9384 GGGGGATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (31 bp):
GGGACCATATTACAAACAGACTAAATGTTAA
Found at i:19861 original size:11 final size:12
Alignment explanation
Indices: 19845--19903 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
19835 TTAAAAACTA
19845 AAAAATAAA-AT
1 AAAAATAAAGAT
19856 AAAAATAAAGAT
1 AAAAATAAAGAT
*
19868 AAATATAATATAATAT
1 -AA-A-AATA-AAGAT
*
19884 AAAAATAAA-AC
1 AAAAATAAAGAT
19895 AAAAATAAA
1 AAAAATAAA
19904 TAATATTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 19 0.46
12 4 0.10
13 6 0.15
14 2 0.05
15 6 0.15
16 4 0.10
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (12 bp):
AAAAATAAAGAT
Found at i:19905 original size:28 final size:28
Alignment explanation
Indices: 19849--19905 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
19839 AAACTAAAAA
* *
19849 ATAAAATAAAAATAAAGATAAATATAAT
1 ATAAAATAAAAATAAACAAAAATATAAT
*
19877 ATAATATAAAAATAAAACAAAAATA-AAT
1 ATAAAATAAAAAT-AAACAAAAATATAAT
19905 A
1 A
19906 ATATTTACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (28 bp):
ATAAAATAAAAATAAACAAAAATATAAT
Found at i:24001 original size:43 final size:42
Alignment explanation
Indices: 23925--24148 Score: 279
Period size: 43 Copynumber: 5.2 Consensus size: 42
23915 TTAATTACCG
* *
23925 TTACAGTTCCCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGT-CCTTTGTTGTGTGCAAGGGTAAGCC
* * *
23968 TTACAGTTCCTCCAAGACCATTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCC-TTTGTTGTGTGCAAGGGTAAGCC
* * *
24011 TTACAGTTCCCCCGGGTCCCTTTGTTGTGTACAAGGGTAAACC
1 TTACAGTTCCCCCAGGT-CCTTTGTTGTGTGCAAGGGTAAGCC
*
24054 TTACAGTTTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAG--TTCCCCCAGG-TCCTTTGTTGTGTGCAAGGGTAAGCC
*
24099 TTACAGTT-TCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGG-TCCTTTGTTGTGTGCAAGGGTAAGCC
*
24141 ATACAGTT
1 TTACAGTT
24149 TTCCCAGGCT
Statistics
Matches: 158, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
42 41 0.26
43 77 0.49
44 2 0.01
45 37 0.23
46 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (42 bp):
TTACAGTTCCCCCAGGTCCTTTGTTGTGTGCAAGGGTAAGCC
Found at i:24172 original size:43 final size:43
Alignment explanation
Indices: 23925--24187 Score: 262
Period size: 43 Copynumber: 6.1 Consensus size: 43
23915 TTAATTACCG
** * *
23925 TTACAGTTCCCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCC
1 TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
23968 TTACAG-TTCCTCCAAG-ACCATTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTTC-CCAGGTTCC-TTTGCTGTGTGCAAGGGTAAGCC
** * * * * *
24011 TTACAGTTCCCCCGGGTCCCTTTGTTGTGTACAAGGGTAAACC
1 TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
24054 TTACAGTTTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTT--CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
24099 TTACAG-TTTCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * * *
24141 ATACAGTTTTCCCAGGCTCTTTTACTATGTGCAAGGATAAGACC
1 TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CC
24185 TTA
1 TTA
24188 TCGTTTTTGC
Statistics
Matches: 185, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
42 42 0.23
43 97 0.52
44 12 0.06
45 34 0.18
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (43 bp):
TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:24194 original size:131 final size:131
Alignment explanation
Indices: 23931--24187 Score: 333
Period size: 131 Copynumber: 2.0 Consensus size: 131
23921 ACCGTTACAG
23931 TTCCCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTTCCTCCAAGACCATTTGTTGT
1 TTCCCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTTCCTCCAAGACCATTTGTTGT
* * * *
23996 GTGCAAGGGTAAGCCTTACAGTTCCCCCGGGTCCCTTTGTTGTGTACAAGGGTAAACCTTACAGT
66 GTGCAAGGGTAAGCCATACAGTTCCCCCAGGTCCCTTTGTTATGTACAAGGATAAACCTTACAGT
24061 T
131 T
* * * * *
24062 TTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTC-CCAGGTTCC-TTTGTTG
1 TTCCCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTTCCTCCAAG-ACCATTTGTTG
** * *
24125 TGTGCAAGGGTAAGCCATACAGTTTTCCCAGG-CTCTTT-TACTATGTGCAAGGATAAGACCTTA
65 TGTGCAAGGGTAAGCCATACAGTTCCCCCAGGTCCCTTTGT--TATGTACAAGGATAA-ACCTTA
24188 TCGTTTTTGC
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
128 1 0.01
129 5 0.05
130 51 0.47
131 52 0.48
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (131 bp):
TTCCCCCAGGTCCCTTTGCTGTATGCAAGGGTAAGCCTTACAGTTCCTCCAAGACCATTTGTTGT
GTGCAAGGGTAAGCCATACAGTTCCCCCAGGTCCCTTTGTTATGTACAAGGATAAACCTTACAGT
T
Found at i:27134 original size:24 final size:24
Alignment explanation
Indices: 27102--27147 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
27092 ATAAGAAATG
27102 TTAGTTTTACTTGGAAATTATGAA
1 TTAGTTTTACTTGGAAATTATGAA
27126 TTAGTTTTACTTGGAAATTATG
1 TTAGTTTTACTTGGAAATTATG
27148 GATAATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.48
Consensus pattern (24 bp):
TTAGTTTTACTTGGAAATTATGAA
Found at i:29127 original size:43 final size:43
Alignment explanation
Indices: 29065--29294 Score: 300
Period size: 43 Copynumber: 5.3 Consensus size: 43
29055 TTAATTACCG
* * *
29065 TTACAGTTCCCTCAAGTCCCTTTGTTGTGTGCAAGTGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
*
29108 TTACAGTTCCCCTAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* *
29151 TTAAAGTTCCCCCAGGTCCCTTTGTTGTGTACAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* * * **
29194 TTATAGTTTTCCCCCAGATTCCTTTGTTGTGTTAAAGGGTAAGCC
1 TTACAG--TTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* *
29239 TTACAGTT-TCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* *
29281 ATACAGTTTCCCCA
1 TTACAGTTCCCCCA
29295 TGCTCTTTTG
Statistics
Matches: 165, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 37 0.22
43 90 0.55
45 38 0.23
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
Found at i:29327 original size:131 final size:131
Alignment explanation
Indices: 29083--29334 Score: 328
Period size: 130 Copynumber: 1.9 Consensus size: 131
29073 CCCTCAAGTC
* *
29083 CCTTTGTTGTGTGCAAGTGTAAGCCTTACAGTTCCCCTAGGTCCCTTTGTTGTGTGCAAGGGTAA
1 CCTTTGTTGTGTGAAAGGGTAAGCCTTACAGTTCCCCTAGGTCCCTTTGTTGTGTGCAAGGGTAA
* * * * * *
29148 GCCTTAAAGTTCCCCCAGGTCCCTTTGTTGTGTACAAGGGTAAGCCTTATAGTTTTCCCCCAGAT
66 GCCATAAAGTTCCCCCAGCTCCCTTTGCTATGTACAAGGATAAACCTTATAGTTTTCCCCCAGAT
29213 T
131 T
* * *
29214 CCTTTGTTGTGTTAAAGGGTAAGCCTTACAGTTTCCC-AGGTTCCTTTGTTGTGTGCAAGGGTAA
1 CCTTTGTTGTGTGAAAGGGTAAGCCTTACAGTTCCCCTAGGTCCCTTTGTTGTGTGCAAGGGTAA
* * * * *
29278 GCCATACAGTTTCCCCATGCT-CTTTTGCTATGTGCAAGGATAATACCTTATCGTTTT
66 GCCATAAAGTTCCCCCA-GCTCCCTTTGCTATGTACAAGGATAA-ACCTTATAGTTTT
29335 TGCATGCTCC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 57 0.55
131 46 0.45
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (131 bp):
CCTTTGTTGTGTGAAAGGGTAAGCCTTACAGTTCCCCTAGGTCCCTTTGTTGTGTGCAAGGGTAA
GCCATAAAGTTCCCCCAGCTCCCTTTGCTATGTACAAGGATAAACCTTATAGTTTTCCCCCAGAT
T
Found at i:31445 original size:169 final size:169
Alignment explanation
Indices: 31112--31445 Score: 463
Period size: 169 Copynumber: 2.0 Consensus size: 169
31102 TATATTTATT
*
31112 TATTTATGTAAATCCAAATCTCTAAGTCAAGGGGTCAAGCATATCTATTGCAACAATTGCCCTCT
1 TATTTATGTAAATCCAAATCCCTAAGTCAAGGGGTCAAGCATATCTATTGCAACAATTGCCCTCT
*
31177 CCAAACTATTTGGCTTTGGATGGAGGGTCCTTAAGAGTATGAAAACTATGGTTTTTCGATATAGA
66 CCAAACTATTTGGCTTTGAATGGAGGGTCCTTAAGAGTATGAAAACTATGGTTTTTCGATATAGA
* **
31242 TAGATCAGTATGCATGCATGTATGTATAATGTATGTATA
131 TAGATCAGTATGCATACATGTATACATAATGTATGTATA
* * * * * * *
31281 TATTTATGTAAATTCAAGTCCCTATGTCAAGTGGTCAAGCATCTCTATTGCAATAATTGTCCTCT
1 TATTTATGTAAATCCAAATCCCTAAGTCAAGGGGTCAAGCATATCTATTGCAACAATTGCCCTCT
* * * ** *
31346 TCGAACTATTTGGCTTTGAATGGAGGGTTCTTAA-AGTATGAAAACTATGGTTTTTTTATGTAGA
66 CCAAACTATTTGGCTTTGAATGGAGGGTCCTTAAGAGTATGAAAACTATGGTTTTTCGATATAGA
* * *
31410 TAGATCAGTATGTATATATGTATACATGCATGTATG
131 TAGATCAGTATGCATACATGTATACAT-AATGTATG
31446 AATGTCTATA
Statistics
Matches: 143, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
168 49 0.34
169 94 0.66
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (169 bp):
TATTTATGTAAATCCAAATCCCTAAGTCAAGGGGTCAAGCATATCTATTGCAACAATTGCCCTCT
CCAAACTATTTGGCTTTGAATGGAGGGTCCTTAAGAGTATGAAAACTATGGTTTTTCGATATAGA
TAGATCAGTATGCATACATGTATACATAATGTATGTATA
Found at i:33760 original size:16 final size:16
Alignment explanation
Indices: 33730--33760 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33720 TAATATTGAA
*
33730 GCTTGAACTCGAAAAG
1 GCTTGAACTCAAAAAG
33746 GCTTGAACTCAAAAA
1 GCTTGAACTCAAAAA
33761 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
GCTTGAACTCAAAAAG
Found at i:36328 original size:22 final size:23
Alignment explanation
Indices: 36285--36329 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
36275 CCTAAAAGTT
*
36285 ATTAAAAATAAATTTAATACTAA
1 ATTAAAAATAAATTTAACACTAA
36308 ATTAAAAA-AATATTT-ACACTAA
1 ATTAAAAATAA-ATTTAACACTAA
36330 TTCTCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTAAAAATAAATTTAACACTAA
Found at i:49192 original size:31 final size:31
Alignment explanation
Indices: 49157--49216 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
49147 AATAGATACT
*
49157 AACATTTTCTAAGAGAATGCAATGAAGCTTG
1 AACATTTTCTAAGAAAATGCAATGAAGCTTG
49188 AACATTTTCTAAGAAAATGCAATGAAGCT
1 AACATTTTCTAAGAAAATGCAATGAAGCT
49217 GAAAAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (31 bp):
AACATTTTCTAAGAAAATGCAATGAAGCTTG
Found at i:52732 original size:2 final size:2
Alignment explanation
Indices: 52687--52717 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
52677 CATGTACTTA
*
52687 AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
52718 TATATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54472 original size:21 final size:20
Alignment explanation
Indices: 54447--54489 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
54437 TCATAAATAT
54447 AAACAT-GCAATCTATGAATTC
1 AAACATAGCAAT-TATG-ATTC
*
54468 AAACATAGCACTTATGATTC
1 AAACATAGCAATTATGATTC
54488 AA
1 AA
54490 TATACATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (20 bp):
AAACATAGCAATTATGATTC
Found at i:54804 original size:31 final size:31
Alignment explanation
Indices: 54768--54847 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
54758 CCATAGATTT
* *
54768 CAAAGAACCTAGGTAATCAGTCCATATGTCC
1 CAAAGAACATAGGTAAACAGTCCATATGTCC
* *
54799 TAAAGAACATAGATAAACAGTCCATATGTCC
1 CAAAGAACATAGGTAAACAGTCCATATGTCC
*
54830 CGAAGAACATAGGTAAAC
1 CAAAGAACATAGGTAAAC
54848 CCTCGACCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (31 bp):
CAAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:65203 original size:21 final size:20
Alignment explanation
Indices: 65177--65235 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 20
65167 ATTATCCAAT
65177 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
65198 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
*
65219 CAACTTGAACTCCATAA
1 AAACTTGAA-TCCATAA
65236 TAATAAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.05, T:0.20
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Done.