Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000845.1 Hibiscus syriacus cultivar Beakdansim tig00001629_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: 84562
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:14539 original size:21 final size:21
Alignment explanation
Indices: 14497--14540 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
14487 TTAAAATTAT
* *
14497 TATATATTTTTTAATTTTTTA
1 TATATATTTTTTAATATGTTA
14518 TATATATTTTTTGAA-ATGTTA
1 TATATATTTTTT-AATATGTTA
14539 TA
1 TA
14541 AATTCGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TATATATTTTTTAATATGTTA
Found at i:26972 original size:2 final size:2
Alignment explanation
Indices: 26965--26995 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26955 TTATCAAAAT
26965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26996 TTAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30700 original size:3 final size:3
Alignment explanation
Indices: 30692--30732 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
30682 TAAAATTATT
30692 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
30733 CGGGACGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:31137 original size:136 final size:137
Alignment explanation
Indices: 30892--31286 Score: 521
Period size: 136 Copynumber: 2.9 Consensus size: 137
30882 CAACTGGTGT
*
30892 ATGACATTGTTCCTTTGTGATGAGGACGA-CTGGCCATCTTTGAAGATATTTGAGATAACATGGT
1 ATGACATTGTTCCTTTGTGATGAGGAC-ATCTGGCCATCTTTAAAGATATTTGAGATAACATGGT
* * * * *
30956 TCCTTCGTGATGAGGACGTATGGTTATCTGAGGATGACTCGGCTCC-TACGTGATGAGGAGTTTT
65 TCATTCGTGATGAGGACATCTGGTTATCTAAGGATGACTCGGCTCCTTA-GTGATGAGGAGTTCT
*
31020 GGTCAGTGG
129 GATCAGTGG
* * *
31029 ATGACATTGTTCCTTCGTGATGAGGACATCTAGCCATCTTT-AAGATATTTGAGATGACATGGTT
1 ATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATGGTT
* * *
31093 CATTCGTGATGAGGTCATCTGGCTATCTAAAGATGA-T-GATGCTCCTTAGTGATGAGGAGTTCT
66 CATTCGTGATGAGGACATCTGGTTATCTAAGGATGACTCG--GCTCCTTAGTGATGAGGAGTTCT
31156 GATCAGTGG
129 GATCAGTGG
* * * **
31165 ATGGCATTGTTCCTTTGTGATGAGGACATCTGGTCATCTTTAAAAATATTTGAGATAACACAGTT
1 ATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATGGTT
* * * *
31230 CTTTCGTGATGAGGACATCTGGTTATCTAAGGATGACGCGACTCCTTCGTGATGAGG
66 CATTCGTGATGAGGACATCTGGTTATCTAAGGATGACTCGGCTCCTTAGTGATGAGG
31287 TTGAGCTTTG
Statistics
Matches: 224, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
134 1 0.00
135 1 0.00
136 116 0.52
137 105 0.47
139 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (137 bp):
ATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATGGTT
CATTCGTGATGAGGACATCTGGTTATCTAAGGATGACTCGGCTCCTTAGTGATGAGGAGTTCTGA
TCAGTGG
Found at i:34853 original size:23 final size:22
Alignment explanation
Indices: 34827--34890 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
34817 CAGCTCATAT
34827 AATTGCACCTAAGTGCCACGTAA
1 AATTGCACCT-AGTGCCACGTAA
* * *
34850 AATTACA-CTGGAGTGCCGCGTAG
1 AATTGCACCT--AGTGCCACGTAA
34873 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
34891 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
22 2 0.06
23 28 0.88
24 1 0.03
25 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAA
Found at i:35037 original size:103 final size:103
Alignment explanation
Indices: 34909--35226 Score: 591
Period size: 103 Copynumber: 3.1 Consensus size: 103
34899 TGTCCATAAA
34909 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
34974 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
* * *
35012 GACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTATCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
35077 CTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
35115 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTAACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
35180 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
35218 GACCACATA
1 GACCACATA
35227 GACCCTCTAC
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:40438 original size:17 final size:17
Alignment explanation
Indices: 40418--40456 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
40408 CCTACACCAT
40418 CATGATATCTACCCAAA
1 CATGATATCTACCCAAA
*
40435 CATGCTATCTACCCAAA
1 CATGATATCTACCCAAA
40452 -ATGAT
1 CATGAT
40457 TTTCCAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (17 bp):
CATGATATCTACCCAAA
Found at i:41065 original size:12 final size:12
Alignment explanation
Indices: 41048--41072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41038 ATATAAGGAT
41048 ATAAAAAATAAA
1 ATAAAAAATAAA
41060 ATAAAAAATAAA
1 ATAAAAAATAAA
41072 A
1 A
41073 AAATGAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:42345 original size:6 final size:6
Alignment explanation
Indices: 42321--42373 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
42311 AAAACATAAC
* *
42321 AAAA-T AAAATCT AAAATT CAAATT CAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAAT-T AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
42369 AAAAT
1 AAAAT
42374 GCGAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 4 0.09
6 34 0.77
7 6 0.14
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:50433 original size:30 final size:32
Alignment explanation
Indices: 50350--50434 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 32
50340 TATCTATTAC
**
50350 TAAATATGTTTATGTTCCGTTATTTTACATTTT
1 TAAATATGTTTATGTTCATTTATTTTA-ATTTT
* *
50383 TAATATCATATTTGTGTTCATTTA-TTT-ATTTT
1 TAA-AT-ATGTTTATGTTCATTTATTTTAATTTT
*
50415 TGAATATGTTTATGTTCATT
1 TAAATATGTTTATGTTCATT
50435 CGTTTAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
30 13 0.30
31 2 0.05
32 7 0.16
33 3 0.07
34 5 0.12
35 13 0.30
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (32 bp):
TAAATATGTTTATGTTCATTTATTTTAATTTT
Found at i:50487 original size:24 final size:24
Alignment explanation
Indices: 50448--50510 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
50438 TTAGTATTCA
* *
50448 CGAACATATTCATTTATATGTTAG
1 CGAACATGTTCGTTTATATGTTAG
* * *
50472 TGAACTTGTTCGTTTATATGTTCG
1 CGAACATGTTCGTTTATATGTTAG
50496 CGAACATGTTCGTTT
1 CGAACATGTTCGTTT
50511 GTAAGCTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.44
Consensus pattern (24 bp):
CGAACATGTTCGTTTATATGTTAG
Found at i:51153 original size:21 final size:22
Alignment explanation
Indices: 51127--51176 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
51117 GACTTAAATA
*
51127 TAAGGGGGGCGAACTAAAATT-
1 TAAGGGGGACGAACTAAAATTC
* *
51148 TCA-GGGTACGAACTAAAATTC
1 TAAGGGGGACGAACTAAAATTC
51169 TAAGGGGG
1 TAAGGGGG
51177 TGACTGCCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 15 0.68
21 4 0.18
22 3 0.14
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (22 bp):
TAAGGGGGACGAACTAAAATTC
Found at i:61540 original size:27 final size:24
Alignment explanation
Indices: 61509--61583 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 24
61499 GAAAATAAAA
61509 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATTTTT-AA-TAAGTTAAT
* *
61535 CGTAAAATATATTTAATAAGTTAAT
1 -ATAAAATATTTTTAATAAGTTAAT
*
61560 ATAAAA-ATATTT--TAAGTTAAT
1 ATAAAATATTTTTAATAAGTTAAT
61581 ATA
1 ATA
61584 TATATATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.27
23 6 0.13
24 5 0.11
25 9 0.20
26 2 0.04
27 11 0.24
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (24 bp):
ATAAAATATTTTTAATAAGTTAAT
Found at i:61566 original size:25 final size:25
Alignment explanation
Indices: 61509--61579 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 25
61499 GAAAATAAAA
61509 ATAAAATATTTTTAAATTAAGTTAATC
1 ATAAAATA-TTTT-AATTAAGTTAATC
*
61536 GTAAAATATATTTAA-TAAGTTAAT-
1 ATAAAATAT-TTTAATTAAGTTAATC
61560 ATAAAAATATTTTAAGTTAA
1 AT-AAAATATTTTAA-TTAA
61580 TATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 6 0.16
25 16 0.42
26 6 0.16
27 10 0.26
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (25 bp):
ATAAAATATTTTAATTAAGTTAATC
Found at i:61584 original size:23 final size:23
Alignment explanation
Indices: 61526--61596 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 23
61516 ATTTTTAAAT
*
61526 TAAGTTAATCGTAAAATATATTTAA
1 TAAGTTAAT-ATAAAATATATTT-A
61551 TAAGTTAATATAAAA-ATATTT-
1 TAAGTTAATATAAAATATATTTA
* *
61572 TAAGTTAATAT-ATATATATATA
1 TAAGTTAATATAAAATATATTTA
61594 TAA
1 TAA
61597 TTATATTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.05
21 16 0.39
22 3 0.07
23 6 0.15
24 5 0.12
25 9 0.22
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (23 bp):
TAAGTTAATATAAAATATATTTA
Found at i:61897 original size:39 final size:39
Alignment explanation
Indices: 61853--61958 Score: 96
Period size: 39 Copynumber: 2.7 Consensus size: 39
61843 TTTTAAAAAT
61853 AATTTAGAAAGTTAATGTGAAATAATTTAAGAAATT-GTG
1 AATTTAGAAAGTTAATGTGAAATAATTTAAGAAATTAG-G
* *
61892 AATTTA-AAACATT-ATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAAA-GTTAAT-GTG-AAATAATTTAAGAAATTAGG
* *
61931 ATTTTAGAATGTTAGA-GTGAAATAATTT
1 AATTTAGAAAGTTA-ATGTGAAATAATTT
61959 GAGGATTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
38 7 0.13
39 40 0.75
40 5 0.09
41 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (39 bp):
AATTTAGAAAGTTAATGTGAAATAATTTAAGAAATTAGG
Found at i:62371 original size:30 final size:31
Alignment explanation
Indices: 62335--62409 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
62325 TTAACTTCGG
* *
62335 GTGACCACATCTTAATTAAAT-AAAATGAAA
1 GTGACCATATCTTAATTAAATAAAAATAAAA
62365 GTGACCATATCTTAATTAAATAAAAATAAAA
1 GTGACCATATCTTAATTAAATAAAAATAAAA
*
62396 GTGATCATATCTTA
1 GTGACCATATCTTA
62410 TGTTTTTCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
GTGACCATATCTTAATTAAATAAAAATAAAA
Found at i:74929 original size:16 final size:17
Alignment explanation
Indices: 74908--74941 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
74898 CATTTTTATT
*
74908 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
74924 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
74941 A
1 A
74942 AAATAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:78423 original size:46 final size:45
Alignment explanation
Indices: 78353--78529 Score: 203
Period size: 46 Copynumber: 3.9 Consensus size: 45
78343 AACTGAATCT
*
78353 ATAACTAAAATGCATGAAAA-GATGCATTAAGGCATGAAAGCATTTC
1 ATAACTAAAATGCAT-AAAAGGATGCATTAAGGCATGAAAG-ATGTC
78399 ATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAAAGATGTC
1 ATAACTAAAATGCATAAAAGGATGCATTAAGGCATG-AAAGATGTC
* * *
78445 ATAACTAAAATGCATGAAAGGATGCGTTAGGGCATGAAAGGATGTC
1 ATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAA-GATGTC
* * * * * ** *
78491 ATGATTAAAATGTATGAACGGATATATTAATGCATGAAA
1 ATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAA
78530 AAAAGACCAT
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
45 7 0.06
46 104 0.90
47 4 0.03
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (45 bp):
ATAACTAAAATGCATAAAAGGATGCATTAAGGCATGAAAGATGTC
Found at i:78468 original size:26 final size:25
Alignment explanation
Indices: 78353--78469 Score: 83
Period size: 26 Copynumber: 5.0 Consensus size: 25
78343 AACTGAATCT
*
78353 ATAACTAAAATGCATGAAAAGATGC
1 ATAACTAAAATGCATGAAAGGATGC
* * *
78378 AT---T--AAGGCATGAAAGCATTTC
1 ATAACTAAAATGCATGAAAGGA-TGC
*
78399 ATAACTAAAATGCATAAAAGGATGC
1 ATAACTAAAATGCATGAAAGGATGC
* *
78424 AT---T--AAGGCATGAAAAGATGTC
1 ATAACTAAAATGCATGAAAGGATG-C
78445 ATAACTAAAATGCATGAAAGGATGC
1 ATAACTAAAATGCATGAAAGGATGC
78470 GTTAGGGCAT
Statistics
Matches: 67, Mismatches: 13, Indels: 24
0.64 0.12 0.23
Matches are distributed among these distances:
20 24 0.36
21 7 0.10
22 2 0.03
24 2 0.03
25 7 0.10
26 25 0.37
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (25 bp):
ATAACTAAAATGCATGAAAGGATGC
Found at i:78520 original size:92 final size:92
Alignment explanation
Indices: 78353--78530 Score: 239
Period size: 92 Copynumber: 1.9 Consensus size: 92
78343 AACTGAATCT
*
78353 ATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGCATTTCATAACTAAAATGCATAAAA
1 ATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGCATGTCATAACTAAAATGCATAAAA
*
78418 GGATGCATTAAGGCATGAAAAGATGTC
66 GGATACATTAAGGCATGAAAAGATGTC
* * * * * * * * *
78445 ATAACTAAAATGCATGAAAGGATGCGTTAGGGCATGAAAGGATGTCATGATTAAAATGTATGAAC
1 ATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGCATGTCATAACTAAAATGCATAAAA
* *
78510 GGATATATTAATGCATGAAAA
66 GGATACATTAAGGCATGAAAA
78531 AAAGACCATA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (92 bp):
ATAACTAAAATGCATGAAAAGATGCATTAAGGCATGAAAGCATGTCATAACTAAAATGCATAAAA
GGATACATTAAGGCATGAAAAGATGTC
Done.