Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005452.1 Hibiscus syriacus cultivar Beakdansim tig00012491_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: 58300
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:6146 original size:138 final size:137
Alignment explanation
Indices: 5898--6346 Score: 769
Period size: 138 Copynumber: 3.3 Consensus size: 137
5888 TACTATTCAA
* * *
5898 GTGAAGGCGCGTTCTCGGGGGCGCGCTTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
5963 ATTATGTCACTCATGTCCCCCGAAAAACTATTCATGTCAGTACCTATTATTTATGAGGGGACTTG
66 ATTATGTCACTCATGTCCCCCG-AGAACTATTCATGTCAGTACCTATTATTTATGAGGGGACTTG
6028 GCAAAGTG
130 GCAAAGTG
*
6036 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCAT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
6101 ATTATGTCACTCATGTCCCCCAGAGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTG
66 ATTATGTCACTCATGTCCCCC-GAGAACTATTCATGTCAGTACCTATTATTTATGAGGGGACTTG
6166 GCAAAGTG
130 GCAAAGTG
* *
6174 GTGAAGGCGCGTTCCCGGGGGGGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
6239 ATTATGTCACTCATGTCCCCCGGAGAACTATTCATGTCAGTACCTATTATTTATGAGGGGATTTG
66 ATTATGTCACTCATGTCCCCC-GAGAACTATTCATGTCAGTACCTATTATTTATGAGGGGACTTG
6304 GCAAAGTG
130 GCAAAGTG
6312 GTGAAGGCGCGTTCCC-GGGG-GCGCCTTCC-TTATTT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT
6347 CATTTCCTAA
Statistics
Matches: 297, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
135 6 0.02
136 8 0.03
137 4 0.01
138 278 0.94
139 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (137 bp):
GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCCCGAGAACTATTCATGTCAGTACCTATTATTTATGAGGGGACTTGG
CAAAGTG
Found at i:10434 original size:21 final size:21
Alignment explanation
Indices: 10408--10465 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
10398 ATTTTTAATT
10408 AAATCTACTTAAAATCGACGA
1 AAATCTACTTAAAATCGACGA
* *
10429 ACATCTA-TCTAAAATCGATGA
1 AAATCTACT-TAAAATCGACGA
*
10450 AAATCTATCTAAAAAT
1 AAATCTA-CTTAAAAT
10466 TTAACTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 23 0.77
22 5 0.17
23 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATCTACTTAAAATCGACGA
Found at i:26869 original size:32 final size:31
Alignment explanation
Indices: 26833--26896 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
26823 GAGTGTAAAA
26833 TTAAATTATTAATAAAAA-T-ATAAATAAAATAT
1 TTAAATTA-TAA-AAAAATTAATAAA-AAAATAT
26865 TTAAATTATAAAAAAATTAATAAAAAAATAT
1 TTAAATTATAAAAAAATTAATAAAAAAATAT
26896 T
1 T
26897 GAAAATACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 5 0.17
31 12 0.40
32 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
TTAAATTATAAAAAAATTAATAAAAAAATAT
Found at i:27338 original size:36 final size:36
Alignment explanation
Indices: 27298--27442 Score: 200
Period size: 36 Copynumber: 4.0 Consensus size: 36
27288 TTAGGAATTG
*
27298 ATTAGTTGCTGAAGATAATGCTGGAATTTGAATTTT
1 ATTAGCTGCTGAAGATAATGCTGGAATTTGAATTTT
*
27334 ATTAGCTGCTGAAGATAATACTGGAATTTGAATTTT
1 ATTAGCTGCTGAAGATAATGCTGGAATTTGAATTTT
* * * *
27370 ATTAGTTGCTGAAGATAAGGTTGGAATTTGAAATTT
1 ATTAGCTGCTGAAGATAATGCTGGAATTTGAATTTT
** * *
27406 ATTAGCTGCTGAAGATAATTATAGAGTTTGAATTTT
1 ATTAGCTGCTGAAGATAATGCTGGAATTTGAATTTT
27442 A
1 A
27443 AATAAAATGA
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (36 bp):
ATTAGCTGCTGAAGATAATGCTGGAATTTGAATTTT
Found at i:27415 original size:72 final size:72
Alignment explanation
Indices: 27298--27442 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 72
27288 TTAGGAATTG
* * *
27298 ATTAGTTGCTGAAGATAATGCTGGAATTTGAATTTTATTAGCTGCTGAAGATAA-TACTGGAATT
1 ATTAGTTGCTGAAGATAAGGCTGGAATTTGAAATTTATTAGCTGCTGAAGATAATTA-TAGAATT
27362 TGAATTTT
65 TGAATTTT
* *
27370 ATTAGTTGCTGAAGATAAGGTTGGAATTTGAAATTTATTAGCTGCTGAAGATAATTATAGAGTTT
1 ATTAGTTGCTGAAGATAAGGCTGGAATTTGAAATTTATTAGCTGCTGAAGATAATTATAGAATTT
27435 GAATTTT
66 GAATTTT
27442 A
1 A
27443 AATAAAATGA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
72 65 0.97
73 2 0.03
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (72 bp):
ATTAGTTGCTGAAGATAAGGCTGGAATTTGAAATTTATTAGCTGCTGAAGATAATTATAGAATTT
GAATTTT
Found at i:43883 original size:23 final size:23
Alignment explanation
Indices: 43857--43901 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
43847 CACCACATCT
*
43857 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
43880 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
43902 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:45693 original size:64 final size:63
Alignment explanation
Indices: 45595--45755 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
45585 TAATGAAGGT
* * *
45595 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTTGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
45658 GG
62 GC
*
45660 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
45724 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
45756 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:47706 original size:24 final size:24
Alignment explanation
Indices: 47674--47727 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
47664 ACATTACTAT
47674 GATCCAAATATGCAACTATATCCA
1 GATCCAAATATGCAACTATATCCA
47698 GATCCAAATATGCAACTATATCCA
1 GATCCAAATATGCAACTATATCCA
47722 GATCCA
1 GATCCA
47728 TTGCAGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (24 bp):
GATCCAAATATGCAACTATATCCA
Found at i:49118 original size:23 final size:23
Alignment explanation
Indices: 49092--49136 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
49082 CACCACAGCT
*
49092 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
49115 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
49137 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:50927 original size:64 final size:63
Alignment explanation
Indices: 50829--50989 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
50819 TAATGAAGGT
* *
50829 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
50892 GG
62 GC
*
50894 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
50958 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
50990 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:53050 original size:5 final size:5
Alignment explanation
Indices: 53040--53073 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
53030 AGACTTAGAC
53040 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAA
1 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAA
53074 GCATGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (5 bp):
ACAAT
Done.