Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006492.1 Hibiscus syriacus cultivar Beakdansim tig00015788_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: 75062
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:14868 original size:19 final size:19
Alignment explanation
Indices: 14844--14890 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
14834 ATCAAAATAA
14844 ATGAAAACTCTCTTTATAG
1 ATGAAAACTCTCTTTATAG
14863 ATGAAAACTCTCTTTATAG
1 ATGAAAACTCTCTTTATAG
14882 ATGAAAACT
1 ATGAAAACT
14891 ATTAGTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (19 bp):
ATGAAAACTCTCTTTATAG
Found at i:21000 original size:20 final size:21
Alignment explanation
Indices: 20967--21016 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
20957 ATTTTTGGCT
20967 CAAAGGATCGA-CCCTTAACA
1 CAAAGGATCGACCCCTTAACA
20987 CAAA-GATCGAACCCCTTAA-A
1 CAAAGGATCG-ACCCCTTAACA
21007 -AAAGGATCGA
1 CAAAGGATCGA
21017 TCATTTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 9 0.33
20 11 0.41
21 7 0.26
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (21 bp):
CAAAGGATCGACCCCTTAACA
Found at i:28788 original size:19 final size:20
Alignment explanation
Indices: 28742--28791 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
28732 ATTTTTTGCT
*
28742 CAAAAGATCG-ACCGCTTAA
1 CAAAAGATCGAACCACTTAA
28761 CACAAAGATCGAACCACTTAA
1 CA-AAAGATCGAACCACTTAA
28782 -AAAAGATCGA
1 CAAAAGATCGA
28792 TCCTTTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.39
20 9 0.32
21 8 0.29
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (20 bp):
CAAAAGATCGAACCACTTAA
Found at i:33987 original size:29 final size:29
Alignment explanation
Indices: 33945--34050 Score: 194
Period size: 29 Copynumber: 3.7 Consensus size: 29
33935 CTTCCCAACA
* *
33945 TAGGTCGCCATGCACTCCGGGTGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
33974 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
34003 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
34032 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
34051 CCTGCTCCTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.14, C:0.34, G:0.27, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:34157 original size:14 final size:14
Alignment explanation
Indices: 34110--34150 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
34100 GCTCGAATGG
34110 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
* *
34124 CATCGGGCGGATGC
1 CCTCGGTCGGATGC
34138 CCTCGGTCGGATG
1 CCTCGGTCGGATG
34151 GCTTCGGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.10, C:0.32, G:0.39, T:0.20
Consensus pattern (14 bp):
CCTCGGTCGGATGC
Found at i:42438 original size:3 final size:3
Alignment explanation
Indices: 42430--42518 Score: 96
Period size: 3 Copynumber: 29.0 Consensus size: 3
42420 TGACCTACAA
42430 AAT AAT AAT -AT AAT AA- AAT AAT AAAT AAAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT
42474 AGAT AAAT AAT AAT AAT AAT AAT -AT AAT AGAT AAAT AAT AAT AAT
1 A-AT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT
42519 TGTGTCTACA
Statistics
Matches: 77, Mismatches: 0, Indels: 18
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.10
3 52 0.68
4 15 0.19
5 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42467 original size:22 final size:22
Alignment explanation
Indices: 42439--42514 Score: 98
Period size: 22 Copynumber: 3.3 Consensus size: 22
42429 AAATAATAAT
42439 ATAATAAAATAATAAATAAATA
1 ATAATAAAATAATAAATAAATA
* *
42461 ATAATAATATAATAGATAAATA
1 ATAATAAAATAATAAATAAATA
*
42483 ATAATAATAATAATATAATAGATAA
1 ATAATAA-AATAATA-AATAAAT-A
42508 ATAATAA
1 ATAATAA
42515 TAATTGTGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 27 0.59
23 6 0.13
24 5 0.11
25 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
ATAATAAAATAATAAATAAATA
Found at i:42497 original size:28 final size:28
Alignment explanation
Indices: 42430--42518 Score: 141
Period size: 28 Copynumber: 3.3 Consensus size: 28
42420 TGACCTACAA
*
42430 AATAATAAT-ATAATAAAATA-ATAAAT
1 AATAATAATAATAATATAATAGATAAAT
42456 -A-AATAATAATAATATAATAGATAAAT
1 AATAATAATAATAATATAATAGATAAAT
42482 AATAATAATAATAATATAATAGATAAAT
1 AATAATAATAATAATATAATAGATAAAT
42510 AATAATAAT
1 AATAATAAT
42519 TGTGTCTACA
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
24 6 0.10
25 11 0.19
26 6 0.10
27 1 0.02
28 34 0.59
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
AATAATAATAATAATATAATAGATAAAT
Found at i:42515 original size:22 final size:20
Alignment explanation
Indices: 42430--42518 Score: 114
Period size: 19 Copynumber: 4.5 Consensus size: 20
42420 TGACCTACAA
42430 AATAATAATATAATAA-AAT
1 AATAATAATATAATAATAAT
42449 AATAAATAA-ATAATAATAAT
1 AAT-AATAATATAATAATAAT
42469 -ATAATAGATA-AATAATAAT
1 AATAATA-ATATAATAATAAT
42488 AATAATAATATAATAGATAAAT
1 AATAATAATATAATA-AT-AAT
42510 AATAATAAT
1 AATAATAAT
42519 TGTGTCTACA
Statistics
Matches: 62, Mismatches: 0, Indels: 13
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.06
19 25 0.40
20 19 0.31
21 2 0.03
22 12 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAATAATATAATAATAAT
Found at i:44371 original size:13 final size:13
Alignment explanation
Indices: 44353--44377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44343 GGAACGACCA
44353 TCGTACCCTCTAC
1 TCGTACCCTCTAC
44366 TCGTACCCTCTA
1 TCGTACCCTCTA
44378 ATCATCCCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.08, T:0.32
Consensus pattern (13 bp):
TCGTACCCTCTAC
Found at i:45035 original size:20 final size:20
Alignment explanation
Indices: 44999--45036 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44989 ATACTATTTC
**
44999 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
45019 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
45037 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:46252 original size:18 final size:17
Alignment explanation
Indices: 46198--46252 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
46188 TATTTTATTA
46198 ATTATATCTATTAGAATAT
1 ATTATAT-TATTA-AATAT
*
46217 TTTAT-TTATATAAA-AT
1 ATTATATTAT-TAAATAT
46233 ATTATATTATTAATATAT
1 ATTATATTATTAA-ATAT
46251 AT
1 AT
46253 CTCTACCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 7 0.23
19 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTATATTATTAAATAT
Found at i:46642 original size:2 final size:2
Alignment explanation
Indices: 46637--46682 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
46627 CAATATTTTA
46637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46679 AT AT
1 AT AT
46683 CAATTTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47342 original size:187 final size:188
Alignment explanation
Indices: 46987--47380 Score: 672
Period size: 187 Copynumber: 2.1 Consensus size: 188
46977 TTTTTTAATT
* * *
46987 TATATAAA-A-ATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATAT
1 TATATAAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATAT
*
47050 AATTATAAAATAAAAATTTTATATAAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
66 AATTATAAAATAAAAAATTTATATAAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
47115 TATTGGATCTTAAATTATTAATTGTGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
131 TATTGGATCTTAAATTATTAATTGTGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
* *
47173 TATATAAATATATTTAATATTTTTTAATTCAGAAAAACAATTTACAATTAATTTAAATAATATAT
1 TATATAAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATAT
*
47238 AATTATAAAATAAAAAATTTATATAAAA-TTTTTAATTAATTAATATTGATTTAGGTTTAAAAGT
66 AATTATAAAATAAAAAATTTATATAAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
*
47302 TATTGGATCTTAAATTATTAATT-TGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 TATTGGATCTTAAATTATTAATTGT-GTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
47360 TATAT-AATATATTTAATATTT
1 TATATAAATATATTTAATATTT
47381 AAAATTTTAT
Statistics
Matches: 197, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
186 25 0.13
187 96 0.49
188 76 0.39
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (188 bp):
TATATAAATATATTTAATATTTTATAATTCAAAAAAACAATTTACAATTAATTTAAATAATATAT
AATTATAAAATAAAAAATTTATATAAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
TATTGGATCTTAAATTATTAATTGTGTTTTAAATGGTTTGGGCTAAGCCCATATGTTA
Found at i:48355 original size:39 final size:39
Alignment explanation
Indices: 48291--48412 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 39
48281 GTTAAATATG
* * *
48291 AAGATTCCACGACTGTATGATGTCTTCAGACAAATGGAA
1 AAGACTCCACGACTATATGATGTCTTCAGACAAATGAAA
* *
48330 AAGACTCCACGACTATATGACGTCTTCAGTCAAATGAAA
1 AAGACTCCACGACTATATGATGTCTTCAGACAAATGAAA
* * * * *
48369 AAGACTTCACGATTATATGATGTTTTCAGGCAAATTAAA
1 AAGACTCCACGACTATATGATGTCTTCAGACAAATGAAA
48408 AAGAC
1 AAGAC
48413 CCTAAAAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (39 bp):
AAGACTCCACGACTATATGATGTCTTCAGACAAATGAAA
Found at i:48637 original size:2 final size:2
Alignment explanation
Indices: 48630--48662 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48620 CCCATTAATA
48630 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
48663 ACGCACACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:49070 original size:48 final size:48
Alignment explanation
Indices: 48999--49152 Score: 245
Period size: 48 Copynumber: 3.2 Consensus size: 48
48989 AATTCCTATC
* *
48999 TGTTTGGGTGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTAGGAAT
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
** *
49047 TGTTTGGATGATGCTTTGAATCTGGGAAAAAGTGAGCTTGCTGGGGAT
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
*
49095 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGCGAGCTTGCTGGGAAT
1 TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
*
49143 CGTTTGGATG
1 TGTTTGGATG
49153 GAATGAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 96 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.31
Consensus pattern (48 bp):
TGTTTGGATGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGAAT
Found at i:52083 original size:28 final size:28
Alignment explanation
Indices: 52043--52097 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
52033 CTCCGTTTAC
* * *
52043 ATTATATTGTCGAGTCAGTTCTTGAAAT
1 ATTATATTATCGAATCAGTGCTTGAAAT
*
52071 ATTATATTATCGAATTAGTGCTTGAAA
1 ATTATATTATCGAATCAGTGCTTGAAA
52098 ACGACGACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (28 bp):
ATTATATTATCGAATCAGTGCTTGAAAT
Found at i:57782 original size:21 final size:21
Alignment explanation
Indices: 57739--57788 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
57729 ATTTTGTGTA
* *
57739 TACAAAATTAGAAAGTTATAT
1 TACAAAATTAGAAAGTAAAAT
57760 TACAAAATTAGAAA-TAAAAAT
1 TACAAAATTAGAAAGT-AAAAT
*
57781 TATAAAAT
1 TACAAAAT
57789 ATTAGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (21 bp):
TACAAAATTAGAAAGTAAAAT
Found at i:61161 original size:60 final size:60
Alignment explanation
Indices: 61050--61162 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
61040 TATAGGGTAC
* * *
61050 TACTTTATTAAGTCCCTCAACTATTAAAAGTTACAAAATGATCCTCTGACTATAGAGTGT
1 TACTTTATTAAGTCCCTCAACTATTAAAAGTTAAAAAATGATCATCCGACTATAGAGTGT
* * * *
61110 TACTTTGTTGAGTCTCTCGACTATTAAAAGTTAAAAAATTG-TCATCCGACTAT
1 TACTTTATTAAGTCCCTCAACTATTAAAAGTTAAAAAA-TGATCATCCGACTAT
61163 TTATTATCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 43 0.96
61 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (60 bp):
TACTTTATTAAGTCCCTCAACTATTAAAAGTTAAAAAATGATCATCCGACTATAGAGTGT
Found at i:68919 original size:31 final size:30
Alignment explanation
Indices: 68866--68925 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
68856 GCTTTTGAAA
* **
68866 AAAATTGAAAGTTTAGGTACTAAAACGAATC
1 AAAACTGAAAGTTTAGACACTAAAA-GAATC
*
68897 AAAACTGATAGTTTAGACACTAAAAGAAT
1 AAAACTGAAAGTTTAGACACTAAAAGAAT
68926 AATTTACCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (30 bp):
AAAACTGAAAGTTTAGACACTAAAAGAATC
Found at i:71865 original size:2 final size:2
Alignment explanation
Indices: 71860--71889 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
71850 AACTAAATTA
71860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71890 GGATTGTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72257 original size:60 final size:59
Alignment explanation
Indices: 72176--72299 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 59
72166 GTAAAGTGCA
* *
72176 AAAATGGTCCCCAACTATAGGGT-ATTGCTTTGCGGATTCCCTTAATTATTAAAAGTTAC
1 AAAATGGTCCCCAACTATAGGGTGA-TGCTTTGCGGAGTCCCTTAACTATTAAAAGTTAC
* * ** *
72235 AAAATGGTGCCCCAGCTGTAGGGTGATGCTTTGTTGAGTCCCTTGACTATTAAAAGTTAC
1 AAAATGGT-CCCCAACTATAGGGTGATGCTTTGCGGAGTCCCTTAACTATTAAAAGTTAC
72295 AAAAT
1 AAAAT
72300 AATCACTCGA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
59 8 0.14
60 47 0.84
61 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAATGGTCCCCAACTATAGGGTGATGCTTTGCGGAGTCCCTTAACTATTAAAAGTTAC
Found at i:74198 original size:15 final size:14
Alignment explanation
Indices: 74175--74222 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
74165 AAAATGAAAG
74175 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
74189 TTAGGAGTAATCTGAAA
1 TTA-GAGTAAT-T-AAA
74206 GTTA-AGTAATTAAA
1 -TTAGAGTAATTAAA
74220 TTA
1 TTA
74223 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Done.