Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008279.1 Hibiscus syriacus cultivar Beakdansim tig00110938_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: 62298
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:1798 original size:131 final size:129
Alignment explanation
Indices: 1551--1890 Score: 394
Period size: 131 Copynumber: 2.6 Consensus size: 129
1541 TAATTTTAAG
* * * *
1551 AGTGAAAACGATAATATCTAATTATTTTCAATCGAGAACAAATAACCTTTCGTGTATTAAAACAA
1 AGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAACCTTT-ATGCATTAAAACAA
* * * **
1616 TCATTTATTACTCCAATTGAAATAAAGAGATATGATTATTTCATATTAAAATTCAATATCGTTTC
65 TCATTTATTACTCCAATTGAAATAAAGAGATATGAATATTCCATA-TAAAAATCAATATCAATTC
1681 A
129 A
** * **
1682 AGTGAAAATAATAATATCTAATGATTTCCAATCGAGAATAAACGACCTTTAATGCATTAAAACAA
1 AGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAACCTTT-ATGCATTAAAACAA
* * * * *
1747 TCATTTATTA-TCCCAATTGAAATAAAGAGATATTAATATTCCGTCTAAAAATCGATATTAATTC
65 TCATTTATTACT-CCAATTGAAATAAAGAGATATGAATATTCCATATAAAAATCAATATCAATTC
*
1811 G
129 A
* * * * *
1812 AGAGAAAACGACAATATCCAATTATTTCCAATCGAAAATAAATAACCTCTTATGCCTTAAAACAA
1 AGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAACCT-TTATGCATTAAAACAA
*
1877 TCACTTATTACTCC
65 TCATTTATTACTCC
1891 GACGAAACGA
Statistics
Matches: 174, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
130 78 0.45
131 96 0.55
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (129 bp):
AGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAACCTTTATGCATTAAAACAAT
CATTTATTACTCCAATTGAAATAAAGAGATATGAATATTCCATATAAAAATCAATATCAATTCA
Found at i:1980 original size:17 final size:16
Alignment explanation
Indices: 1958--1991 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1948 AATCTATCGA
*
1958 AAAACACATACAAAAAC
1 AAAACAAATA-AAAAAC
1975 AAAACAAATAAAAAAC
1 AAAACAAATAAAAAAC
1991 A
1 A
1992 TACATCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAACAAATAAAAAAC
Found at i:4841 original size:23 final size:22
Alignment explanation
Indices: 4815--4892 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
4805 CACCACAGCT
4815 CATATAATTGCACCTAAGTGCCA
1 CATATAATTGCACCT-AGTGCCA
* * *
4838 CATATAATTGTACCGGAGTGCCG
1 CATATAATTGCACC-TAGTGCCA
* *
4861 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACC-TAGTGCCA
*
4884 TATAATAAT
1 CAT-ATAAT
4893 GTCCATAAGG
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
23 38 0.90
24 4 0.10
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (22 bp):
CATATAATTGCACCTAGTGCCA
Found at i:5070 original size:103 final size:103
Alignment explanation
Indices: 4891--5116 Score: 382
Period size: 103 Copynumber: 2.2 Consensus size: 103
4881 CCATATAATA
* * *
4891 ATGTCCAT-AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCC-TGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATAT
4955 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
4994 ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATATG
1 ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATG
*
5059 TCTCACCAGACTTCACACATGTTCTAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
5097 ATGTCCCGAAGGACCACATA
1 ATGTCCTGAAGGACCACATA
5117 GACCCTCGAC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 115 0.99
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:10266 original size:23 final size:23
Alignment explanation
Indices: 10240--10300 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
10230 CACCACAGCT
10240 CATATAATTGCACCGAAGTACCA
1 CATATAATTGCACCGAAGTACCA
* *
10263 CATATAATTGCACCGAAGTGCCG
1 CATATAATTGCACCGAAGTACCA
* *
10286 CGTAGAATTGCACCG
1 CATATAATTGCACCG
10301 TAGTGCCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTACCA
Found at i:10305 original size:23 final size:23
Alignment explanation
Indices: 10240--10308 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
10230 CACCACAGCT
* *
10240 CATATAATTGCACCGAAGTACCA
1 CATAGAATTGCACCGAAGTGCCA
* *
10263 CATATAATTGCACCGAAGTGCCG
1 CATAGAATTGCACCGAAGTGCCA
* *
10286 CGTAGAATTGCACCGTAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
10309 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:10495 original size:103 final size:103
Alignment explanation
Indices: 10324--10541 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
10314 TAATGTCCAT
* * * * *
10324 AAGGACCACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATTTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
10389 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
10427 AAGGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
10492 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
10530 AAGGACCACATA
1 AAGGACCACATA
10542 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:11519 original size:21 final size:21
Alignment explanation
Indices: 11493--11549 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
11483 TTTAACCTTG
* *
11493 ATGCATCGGTGCACTATGGAT
1 ATGCATCGATGCACTATGAAT
11514 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
11535 ATGCATCGATGCACT
1 ATGCATCGATGCACT
11550 CTACCCAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCACTATGAAT
Found at i:18880 original size:15 final size:15
Alignment explanation
Indices: 18860--18892 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18850 CGTAGGACCC
18860 CTACATCCCGAAAGA
1 CTACATCCCGAAAGA
*
18875 CTACATCCCGAAGGA
1 CTACATCCCGAAAGA
18890 CTA
1 CTA
18893 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAAGA
Found at i:19041 original size:23 final size:26
Alignment explanation
Indices: 19004--19072 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
18994 TTCTCTTGTG
19004 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
19028 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
19053 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
19073 AATATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:19054 original size:12 final size:12
Alignment explanation
Indices: 19037--19072 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
19027 TATCATGTTC
19037 TCATATCACATG
1 TCATATCACATG
*
19049 TCATATCACATA
1 TCATATCACATG
19061 TCATATCACATG
1 TCATATCACATG
19073 AATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:19488 original size:64 final size:63
Alignment explanation
Indices: 19380--19600 Score: 239
Period size: 64 Copynumber: 3.5 Consensus size: 63
19370 TAATGAAAGT
* * ** * **
19380 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* * **
19444 ATGTATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* **
19508 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTA--TTAATGGG
**
19571 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
19601 ACACCTTCAA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 127 0.95
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:20143 original size:3 final size:3
Alignment explanation
Indices: 20130--20159 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
20120 CACGCACAAG
20130 GAA GAAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GA
20160 GAACTCTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:44063 original size:30 final size:31
Alignment explanation
Indices: 43994--44067 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
43984 TTACGTCAAC
**
43994 GACCATATTATAAACAGACTAAATATTGAGG
1 GACCATATTGCAAACAGACTAAATATTGAGG
*
44025 GACCATATTGCAAACAGACTAAATGTT-AGG
1 GACCATATTGCAAACAGACTAAATATTGAGG
**
44055 GATTATATTGCAA
1 GACCATATTGCAA
44068 GTTTTAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 14 0.37
31 24 0.63
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATATTGAGG
Found at i:44326 original size:16 final size:17
Alignment explanation
Indices: 44298--44331 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44288 TTCTAAATTA
44298 TGATTTAAATTATAAAT
1 TGATTTAAATTATAAAT
*
44315 TGATTT-AATTATTAAT
1 TGATTTAAATTATAAAT
44331 T
1 T
44332 TTTATGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TGATTTAAATTATAAAT
Found at i:50844 original size:14 final size:14
Alignment explanation
Indices: 50827--50866 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
50817 GATTGGGTTA
*
50827 AACATAAATGAATG
1 AACATAAATGAAGG
50841 AACATAAATGAAGG
1 AACATAAATGAAGG
50855 AACATAAATGAA
1 AACATAAATGAA
50867 CATAACCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.17
Consensus pattern (14 bp):
AACATAAATGAAGG
Found at i:50869 original size:24 final size:24
Alignment explanation
Indices: 50837--50885 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
50827 AACATAAATG
* *
50837 AATGAACATAAATGAAGGAACATA
1 AATGAACATAAACGAACGAACATA
*
50861 AATGAACATAACCGAACGAACATA
1 AATGAACATAAACGAACGAACATA
50885 A
1 A
50886 CCGAACGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (24 bp):
AATGAACATAAACGAACGAACATA
Found at i:50881 original size:14 final size:14
Alignment explanation
Indices: 50864--50892 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
50854 GAACATAAAT
50864 GAACATAACCGAAC
1 GAACATAACCGAAC
50878 GAACATAACCGAAC
1 GAACATAACCGAAC
50892 G
1 G
50893 TTCACGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:50891 original size:24 final size:24
Alignment explanation
Indices: 50840--50891 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
50830 ATAAATGAAT
* * *
50840 GAACATAAATGAAGGAACATAAAT
1 GAACATAAACGAACGAACATAAAC
* *
50864 GAACATAACCGAACGAACATAACC
1 GAACATAAACGAACGAACATAAAC
50888 GAAC
1 GAAC
50892 GTTCACGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.19, G:0.15, T:0.12
Consensus pattern (24 bp):
GAACATAAACGAACGAACATAAAC
Done.