Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007259.1 Hibiscus syriacus cultivar Beakdansim tig00019240_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: 60453
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:9300 original size:22 final size:23
Alignment explanation
Indices: 9258--9301 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9248 TTATGGTTTT
*
9258 TTTTATAATATCAATAGTTCTTA
1 TTTTATAATATCAAGAGTTCTTA
9281 TTTTATATATAT-AAGA-TTCTT
1 TTTTATA-ATATCAAGAGTTCTT
9302 CGTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTATAATATCAAGAGTTCTTA
Found at i:24956 original size:27 final size:24
Alignment explanation
Indices: 24915--24968 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
24905 ATGTTAAAGG
*
24915 TACTTGGATGGAAAATTATGAGAA
1 TACTTGGATGGAAAATTATGAAAA
24939 TACTCTGGTATGGTAAAATTATGAAAA
1 TACT-TGG-ATGG-AAAATTATGAAAA
24966 TAC
1 TAC
24969 CCTTATGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 3 0.12
26 4 0.15
27 15 0.58
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (24 bp):
TACTTGGATGGAAAATTATGAAAA
Found at i:24981 original size:27 final size:26
Alignment explanation
Indices: 24922--24975 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
24912 AGGTACTTGG
* *
24922 ATGG-AAAATTATGAGAATACTCTGGT
1 ATGGTAAAATTATGAAAATACCCT-GT
24948 ATGGTAAAATTATGAAAATACCCT-T
1 ATGGTAAAATTATGAAAATACCCTGT
24973 ATG
1 ATG
24976 TTGTAAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 4 0.16
27 17 0.68
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (26 bp):
ATGGTAAAATTATGAAAATACCCTGT
Found at i:32563 original size:12 final size:12
Alignment explanation
Indices: 32538--32607 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
32528 ACGAAGATAT
* *
32538 CAGAAATCAAAA
1 CAGAATTCAGAA
32550 CAGAATTCAGAA
1 CAGAATTCAGAA
32562 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
32574 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
32586 CAGAAATCAGAG
1 CAGAATTCAGAA
32598 CAGAATTCAG
1 CAGAATTCAG
32608 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:32607 original size:48 final size:47
Alignment explanation
Indices: 32536--32644 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
32526 AAACGAAGAT
*
32536 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
* ** ** *
32583 GATCAGAAATCAGAGCAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
32631 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
32645 TAAAATATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:32642 original size:24 final size:25
Alignment explanation
Indices: 32536--32644 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 25
32526 AAACGAAGAT
*
32536 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
32560 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
32584 ATCAGAAATCAGAGCAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
32608 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
32633 -TCGGAAATCAGA
1 ATCAGAAATCAGA
32645 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.03
24 61 0.91
25 4 0.06
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:33791 original size:18 final size:18
Alignment explanation
Indices: 33770--33805 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33760 CTTCCATCCG
*
33770 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
33788 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
33806 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:35133 original size:13 final size:13
Alignment explanation
Indices: 35115--35196 Score: 137
Period size: 13 Copynumber: 6.3 Consensus size: 13
35105 AACGGTCAAC
35115 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35128 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35141 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
35154 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
35167 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
35180 GGTAAACGGGTCG
1 GGTCAACGGGTCG
35193 GGTC
1 GGTC
35197 GGGTCGGGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 65 1.00
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:37304 original size:12 final size:12
Alignment explanation
Indices: 37279--37348 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
37269 ACGAAGATAT
* *
37279 CAGAAATCAAAA
1 CAGAATTCAGAA
37291 CAGAATTCAGAA
1 CAGAATTCAGAA
37303 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
37315 CAGAATCCAGAT
1 CAGAATTCAGAA
*
37327 CAGAAATCAGAA
1 CAGAATTCAGAA
37339 CAGAATTCAG
1 CAGAATTCAG
37349 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:37348 original size:48 final size:47
Alignment explanation
Indices: 37277--37385 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
37267 AAACGAAGAT
*
37277 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
37324 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
37372 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
37386 TAAATATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:37383 original size:24 final size:25
Alignment explanation
Indices: 37277--37385 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
37267 AAACGAAGAT
*
37277 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
37301 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
37325 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
37349 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
37374 -TCGGAAATCAGA
1 ATCAGAAATCAGA
37386 TAAATATTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:38531 original size:18 final size:18
Alignment explanation
Indices: 38510--38545 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38500 CTTCCATCCG
*
38510 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
38528 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
38546 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:39832 original size:10 final size:9
Alignment explanation
Indices: 39819--39873 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 9
39809 GTCAAAGTTT
39819 TGGTCAACAG
1 TGGTCAAC-G
39829 TGGTCAACG
1 TGGTCAACG
39838 TGGGTCAAC-
1 T-GGTCAACG
39847 -GGTCAACG
1 TGGTCAACG
39855 -GGTCAAC-
1 TGGTCAACG
39862 -GGTCAACG
1 TGGTCAACG
39870 -GGTC
1 TGGTC
39874 GGGTCAACGG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.33
8 11 0.26
9 2 0.05
10 15 0.36
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (9 bp):
TGGTCAACG
Found at i:39852 original size:7 final size:7
Alignment explanation
Indices: 39840--39870 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
39830 GGTCAACGTG
39840 GGTCAAC
1 GGTCAAC
39847 GGTCAAC
1 GGTCAAC
39854 GGGTCAAC
1 -GGTCAAC
39862 GGTCAAC
1 GGTCAAC
39869 GG
1 GG
39871 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:39860 original size:8 final size:8
Alignment explanation
Indices: 39820--39899 Score: 68
Period size: 8 Copynumber: 10.5 Consensus size: 8
39810 TCAAAGTTTT
39820 GGTCAACAG
1 GGTCAAC-G
39829 TGGTCAACGTG
1 -GGTCAAC--G
39840 GGTCAAC-
1 GGTCAACG
39847 GGTCAACG
1 GGTCAACG
39855 GGTCAAC-
1 GGTCAACG
39862 GGTCAACG
1 GGTCAACG
39870 GGT---CG
1 GGTCAACG
39875 GGTCAACG
1 GGTCAACG
39883 GGT---CG
1 GGTCAACG
39888 GGTCAACG
1 GGTCAACG
39896 GGTC
1 GGTC
39900 GGGTCAACTG
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
5 10 0.17
7 14 0.23
8 21 0.35
10 14 0.23
11 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.39, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:39880 original size:13 final size:13
Alignment explanation
Indices: 39847--39943 Score: 140
Period size: 13 Copynumber: 7.3 Consensus size: 13
39837 GTGGGTCAAC
*
39847 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
39862 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39875 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39888 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
39901 GGTCAACTGGTCG
1 GGTCAACGGGTCG
*
39914 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
39927 GGTAAACGGGTCG
1 GGTCAACGGGTCG
39940 GGTC
1 GGTC
39944 GGGTCGGGTT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
13 65 0.84
15 12 0.16
ACGTcount: A:0.19, C:0.22, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:43151 original size:27 final size:26
Alignment explanation
Indices: 43121--43171 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
43111 TTACTTTTAA
* * *
43121 AGTTTTCGATTTCGAGTCGAGCTCAGC
1 AGTTCTCGAGTTCGACTCG-GCTCAGC
43148 AGTTCTCGAGTTCGACTCGGCTCA
1 AGTTCTCGAGTTCGACTCGGCTCA
43172 TTTAACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (26 bp):
AGTTCTCGAGTTCGACTCGGCTCAGC
Found at i:50235 original size:11 final size:13
Alignment explanation
Indices: 50203--50232 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50193 TGGCCAAAGA
50203 TGAAAAGGTATGT
1 TGAAAAGGTATGT
50216 TGAAAAGGTATG-
1 TGAAAAGGTATGT
50228 TGAAA
1 TGAAA
50233 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:55069 original size:24 final size:24
Alignment explanation
Indices: 55034--55080 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
55024 ATACTAGAGG
*
55034 CAGGAGGCAGATCGGTCGGGCTCA
1 CAGGAGGAAGATCGGTCGGGCTCA
*
55058 CAGGAGGAAGATCTGTCGGGCTC
1 CAGGAGGAAGATCGGTCGGGCTC
55081 GTATGAGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.40, T:0.15
Consensus pattern (24 bp):
CAGGAGGAAGATCGGTCGGGCTCA
Done.