Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001804.1 Hibiscus syriacus cultivar Beakdansim tig00003647_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: 52796
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:6426 original size:21 final size:20
Alignment explanation
Indices: 6401--6473 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
6391 AAACCTTTGG
6401 TATGGATACCAGTTCATCCGA
1 TATGGATACCAGTT-ATCCGA
* *
6422 TATGGATACCAACTTACCCGA
1 TATGGATACC-AGTTATCCGA
*
6443 TATGGATACTAGTTTATCC-A
1 TATGGATACCAG-TTATCCGA
6463 GTATGGATACC
1 -TATGGATACC
6474 GACCCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.05
21 38 0.88
22 3 0.07
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (20 bp):
TATGGATACCAGTTATCCGA
Found at i:10282 original size:26 final size:26
Alignment explanation
Indices: 10245--10303 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
10235 CTACTCCATC
*
10245 GTTCAAACAACCCCTTAAGGTTTCAG
1 GTTCAAAAAACCCCTTAAGGTTTCAG
10271 GTTCAAAAAACCCCTTAAGGTTTCAG
1 GTTCAAAAAACCCCTTAAGGTTTCAG
10297 GTTCAAA
1 GTTCAAA
10304 TATTGTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (26 bp):
GTTCAAAAAACCCCTTAAGGTTTCAG
Found at i:12981 original size:44 final size:44
Alignment explanation
Indices: 12920--13192 Score: 316
Period size: 44 Copynumber: 6.2 Consensus size: 44
12910 TTTTGAAATT
*
12920 TAGCGGTGTTTTT-GGATACAAACGCCGCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* ** * *
12963 TAACAACATTTTTAGGATACAAACGCCGCTAAAGGTTTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * * * * *
13007 TAGAGGCGTTTTCAGTATATAAACACCGCTAAAGGTCTGGTTTA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
** * * *
13051 TAGCGGCGTTTTTATAATACAAATGCCACTAAAGATCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
** * *
13095 TAGCGGAATTTTTAGGATACAAACGACGCTAAAGGTCTGGTAGA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * *
13139 TAGCGGCGTTTTTAGAATACAAACGCTGCTAAAGGT-TGCTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
13182 TAGCGGCGTTT
1 TAGCGGCGTTT
13193 GTTAAAAAAA
Statistics
Matches: 186, Mismatches: 43, Indels: 2
0.81 0.19 0.01
Matches are distributed among these distances:
43 24 0.13
44 162 0.87
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (44 bp):
TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
Found at i:19160 original size:22 final size:22
Alignment explanation
Indices: 19133--19181 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
19123 CACGTTTTGA
19133 AAAGCTATTATTATCATATTCG
1 AAAGCTATTATTATCATATTCG
* **
19155 AAAGCTATTATTTTTGTATTCG
1 AAAGCTATTATTATCATATTCG
19177 AAAGC
1 AAAGC
19182 AAAAAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTATCATATTCG
Found at i:19805 original size:82 final size:81
Alignment explanation
Indices: 19701--19906 Score: 227
Period size: 82 Copynumber: 2.5 Consensus size: 81
19691 TTTGATAAAA
* * * * * *
19701 GCCGCTAAATTAATTCTCTATTGCGTCGTTTGTTGGACAAACGCCACTATAAGCAACCCTGTTGC
1 GCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGGA-AAACGCCACTATAAACAAACCTATT-C
*
19766 -GGCATTTTTA-TACAAAT
64 TGGCA-TTTTAGTACAAAC
* * * *
19783 GCCGCTAAATTACTACTCTATTGCGGCGTTTATTGAAAAAACGCCACTGTAAACAAATCTATTCT
1 GCCGCTAAATTACTACTCTATTGCGGCGTTTGTTG-GAAAACGCCACTATAAACAAACCTATTCT
*
19848 GGCATTTTAGTTATAAAC
65 GGCATTTTAG-TACAAAC
* *
19866 GCTGCTAAATTACCACTCTATTGCGGCGTTTGTTGGAAAAC
1 GCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGGAAAAC
19907 CACCGCTAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
81 6 0.06
82 60 0.58
83 38 0.37
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (81 bp):
GCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGGAAAACGCCACTATAAACAAACCTATTCTG
GCATTTTAGTACAAAC
Found at i:23062 original size:18 final size:17
Alignment explanation
Indices: 23034--23067 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
23024 CAGAATGGCA
23034 AAATGGTATCGATACCG
1 AAATGGTATCGATACCG
*
23051 AAATGTGTATCGGTACC
1 AAATG-GTATCGATACC
23068 ATAAAAGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (17 bp):
AAATGGTATCGATACCG
Found at i:26988 original size:23 final size:23
Alignment explanation
Indices: 26962--27054 Score: 77
Period size: 23 Copynumber: 4.1 Consensus size: 23
26952 GAGGGTTCTA
*
26962 TGGTCCTTCAGGA-AAAAGCTATT
1 TGGTCCTTCAGGACAAAA-CTATG
26985 TGGTCCTTCAGGACAAAACTATG
1 TGGTCCTTCAGGACAAAACTATG
* * * *
27008 TGGTCATTCGGGA-TAATCTTATG
1 TGGTCCTTCAGGACAAAAC-TATG
* *
27031 TGGTCCGTCGGGAC-AAA-TATG
1 TGGTCCTTCAGGACAAAACTATG
27052 TGG
1 TGG
27055 CACTTCGGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.12
22 3 0.05
23 45 0.76
24 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGTCCTTCAGGACAAAACTATG
Found at i:31211 original size:20 final size:21
Alignment explanation
Indices: 31186--31238 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31176 CCCTTCAAGG
31186 AGTATCAATACTC-G-GGGTCC
1 AGTATCAATACTCAGAGGG-CC
*
31206 AGTATCGATACTCAGAGGGCC
1 AGTATCAATACTCAGAGGGCC
*
31227 AGTATTAATACT
1 AGTATCAATACT
31239 GAGGTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 13 0.46
22 3 0.11
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
AGTATCAATACTCAGAGGGCC
Found at i:31925 original size:83 final size:82
Alignment explanation
Indices: 31838--32154 Score: 266
Period size: 83 Copynumber: 3.8 Consensus size: 82
31828 CAAACATCTT
* * * *
31838 AATAGAGTGGTAATTTAGCAGCGTTTATAGCTCAAACGTCAG-AATAGAGTTGTTTATAGTGGCG
1 AATAGAGTAGTAATTTAGCGGCGTTTATAGCACAAACATC-GTAATAG-GTTGTTTATAGTGGCG
* *
31902 TTTTTTCAATAAATGCCAC
64 TTTTTTCAAAAAATGACAC
* * * * * *
31921 AATAGAGTAGTAATGTAGCGGTGTTT-TTGTACAAACATCGTAATATGGTTATTTTATAGTGGCA
1 AATAGAGTAGTAATTTAGCGGCGTTTATAGCACAAACATCGTAATA-GGTT-GTTTATAGTGGCG
* * *
31985 TTTGTTCAACAAACGACAC
64 TTTTTTCAAAAAATGACAC
* * * *
32004 TATAGAGAAGTAATTTAGCGACGTTTATCA-AACAAACATCGTAATAGGGTTGTTTATAGTGGCG
1 AATAGAGTAGTAATTTAGCGGCGTTTAT-AGCACAAACATCGTAATA-GGTTGTTTATAGTGGCG
* * * *
32068 TTTATGCAAAAAATGTCAT
64 TTTTTTCAAAAAATGACAC
* * * * * *
32087 AATAGAGTAATATTTTAGTGGCGTTTGTAGCAC-AA-ATGCTGCAATATGTTGTTTATAGTGGCG
1 AATAGAGTAGTAATTTAGCGGCGTTTATAGCACAAACAT-C-GTAATAGGTTGTTTATAGTGGCG
32150 TTTTT
64 TTTTT
32155 ATAAAAATGT
Statistics
Matches: 185, Mismatches: 41, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
81 3 0.02
82 40 0.22
83 122 0.66
84 20 0.11
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (82 bp):
AATAGAGTAGTAATTTAGCGGCGTTTATAGCACAAACATCGTAATAGGTTGTTTATAGTGGCGTT
TTTTCAAAAAATGACAC
Found at i:33774 original size:82 final size:83
Alignment explanation
Indices: 33596--33799 Score: 243
Period size: 82 Copynumber: 2.5 Consensus size: 83
33586 TTTTCCTGCG
* * * * *
33596 TTTTTATACAAACATCGTAATAGGTGTAATCTATAGTGGCGTTTGAATAACAAACGCCGTAAAAT
1 TTTTTGTACAAACGTCGCAATAGGTGTAATCTATAGTGGCATTTGAATAACAAACACCGTAAAAT
** *
33661 ATTTATATTTTAGTGGCG
66 ATTTATACATTAGTGGCA
* * * ** *
33679 TTTTTGCACAAACGTCACAATAGGTCTAATCTATAGTGGCATTT-TTTCAACAAACACCG-CAAA
1 TTTTTGTACAAACGTCGCAATAGGTGTAATCTATAGTGGCATTTGAAT-AACAAACACCGTAAAA
33742 TATTTATACATTAGTGGCA
65 TATTTATACATTAGTGGCA
33761 TTTTTGTACAAACG-CTGCAATAGGTGTAATCTATAGTGG
1 TTTTTGTACAAACGTC-GCAATAGGTGTAATCTATAGTGG
33800 TGTTTGTTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
81 1 0.01
82 54 0.53
83 47 0.46
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (83 bp):
TTTTTGTACAAACGTCGCAATAGGTGTAATCTATAGTGGCATTTGAATAACAAACACCGTAAAAT
ATTTATACATTAGTGGCA
Found at i:33798 original size:41 final size:40
Alignment explanation
Indices: 33671--33799 Score: 97
Period size: 41 Copynumber: 3.1 Consensus size: 40
33661 ATTTATATTT
* * *
33671 TAGTGGCGTTTTTGCACAAACG-TCACAATAGGTCTAATCTA
1 TAGTGGCATTTTTGTACAAACGCT-GCAATAGGT-TAATCTA
* * *
33712 TAGTGGCATTTTT-TCAACAAACACCGCAAATA--TTTATAC-A
1 TAGTGGCATTTTTGT--ACAAACGCTGC-AATAGGTTAAT-CTA
33752 TTAGTGGCATTTTTGTACAAACGCTGCAATAGGTGTAATCTA
1 -TAGTGGCATTTTTGTACAAACGCTGCAATAGGT-TAATCTA
33794 TAGTGG
1 TAGTGG
33800 TGTTTGTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
39 4 0.06
40 13 0.19
41 35 0.51
42 12 0.18
43 4 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (40 bp):
TAGTGGCATTTTTGTACAAACGCTGCAATAGGTTAATCTA
Found at i:36396 original size:14 final size:15
Alignment explanation
Indices: 36367--36396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36357 GAAAGTGATT
36367 AGTTTTATACTATGC
1 AGTTTTATACTATGC
36382 AGTTTTATA-TATGC
1 AGTTTTATACTATGC
36396 A
1 A
36397 CCATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (15 bp):
AGTTTTATACTATGC
Found at i:41908 original size:21 final size:20
Alignment explanation
Indices: 41892--41982 Score: 69
Period size: 21 Copynumber: 4.3 Consensus size: 20
41882 AGGGAATCAA
41892 AGAGAGTAGCAGCGGAAGCAGCC
1 AGAGAG-AGCAGCGGAAGCA--C
* * *
41915 AGAG-CAGCAACGGAAGCAG
1 AGAGAGAGCAGCGGAAGCAC
41934 AGAGAGAAGCAGCGGTAA-CAC
1 AGAGAG-AGCAGCGG-AAGCAC
* *
41955 AGAGAGATGCAGCGGCATCAC
1 AGAGAGA-GCAGCGGAAGCAC
41976 AGAGAGA
1 AGAGAGA
41983 AGTAGCATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.07
20 2 0.04
21 44 0.79
22 2 0.04
23 4 0.07
ACGTcount: A:0.40, C:0.20, G:0.36, T:0.04
Consensus pattern (20 bp):
AGAGAGAGCAGCGGAAGCAC
Found at i:42418 original size:44 final size:43
Alignment explanation
Indices: 42306--42418 Score: 127
Period size: 44 Copynumber: 2.6 Consensus size: 43
42296 ATTTTGTGTT
* * *
42306 ATTTAGCGGTGTTTGTAACAAAAAATGCCGCAATATACCATAC
1 ATTTAGCGGCGTTTGTATCAAAAAATGCCGCAATATACCAGAC
* * **
42349 ATTTAGTGGCGTTTGTATCCTAAAAATGCCGTTATATACCAGAC
1 ATTTAGCGGCGTTTGTAT-CAAAAAATGCCGCAATATACCAGAC
* *
42393 CTTTAGCGACGTTTGTATCAGAAAAA
1 ATTTAGCGGCGTTTGTATCA-AAAAA
42419 CGTCGCGAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
43 16 0.28
44 41 0.72
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTATCAAAAAATGCCGCAATATACCAGAC
Found at i:42461 original size:43 final size:43
Alignment explanation
Indices: 42412--42496 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
42402 CGTTTGTATC
42412 AGAAAAACGTCGCGAAATCTCAACACTTATTGCGGCGTTTGTG
1 AGAAAAACGTCGCGAAATCTCAACACTTATTGCGGCGTTTGTG
* * *
42455 AGAAAAATGTCGCTAAATCTCAACGCTTATTGCGGCGTTTGT
1 AGAAAAACGTCGCGAAATCTCAACACTTATTGCGGCGTTTGT
42497 CGTTTGTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (43 bp):
AGAAAAACGTCGCGAAATCTCAACACTTATTGCGGCGTTTGTG
Found at i:42531 original size:18 final size:18
Alignment explanation
Indices: 42508--42545 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42498 GTTTGTGATA
42508 AAAACGCCGCTAAATCTC
1 AAAACGCCGCTAAATCTC
42526 AAAACGCCGCTAAATCTC
1 AAAACGCCGCTAAATCTC
42544 AA
1 AA
42546 CCCTTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAACGCCGCTAAATCTC
Found at i:42665 original size:43 final size:43
Alignment explanation
Indices: 42589--42671 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
42579 AAACATCTAA
* **
42589 ACCTATTACGGCGTTTGTCTTACAAACGTCACTAAATATCAAC
1 ACCTATTACGGCGTTTGTCTAACAAACACCACTAAATATCAAC
* *
42632 ACCTATTGCGGCGTTTGT-TGAACAAACACCACTATATATC
1 ACCTATTACGGCGTTTGTCT-AACAAACACCACTAAATATC
42672 GTTACCTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (43 bp):
ACCTATTACGGCGTTTGTCTAACAAACACCACTAAATATCAAC
Found at i:43911 original size:21 final size:21
Alignment explanation
Indices: 43887--43937 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
43877 AAGAAAGAAA
43887 AGAATGAAGAAAAGATGATGG
1 AGAATGAAGAAAAGATGATGG
43908 AGAATGAAGAAAAGATGATGG
1 AGAATGAAGAAAAGATGATGG
43929 AGAA-GAAGA
1 AGAATGAAGA
43938 CAAGGGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (21 bp):
AGAATGAAGAAAAGATGATGG
Found at i:52468 original size:15 final size:15
Alignment explanation
Indices: 52448--52477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52438 GATTAGTATC
52448 TTTCCTAAGTTAGAG
1 TTTCCTAAGTTAGAG
*
52463 TTTCCTAATTTAGAG
1 TTTCCTAAGTTAGAG
52478 ACATAATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (15 bp):
TTTCCTAAGTTAGAG
Done.