Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006475.1 Hibiscus syriacus cultivar Beakdansim tig00015693_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: 68198
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:11302 original size:16 final size:18
Alignment explanation
Indices: 11264--11304 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
11254 ATGCGAAAAT
*
11264 AATATATATATATATATAT
1 AATAT-TATATATATATAA
11283 AATATTATAT-TA-ATAA
1 AATATTATATATATATAA
11299 AATATT
1 AATATT
11305 TAATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 5 0.24
19 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTATATATATATAA
Found at i:12442 original size:2 final size:2
Alignment explanation
Indices: 12430--12476 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
12420 TATGAAAATG
12430 AT AT CAT 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
12473 AT AT
1 AT AT
12477 TAGTGTTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12899 original size:16 final size:15
Alignment explanation
Indices: 12877--12918 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
12867 GTTTTTCTTC
12877 TTTTTTATTATAATA
1 TTTTTTATTATAATA
*
12892 TATTTTTATTATAGTA
1 T-TTTTTATTATAATA
12908 TTTCTTTATTA
1 TTT-TTTATTA
12919 ATTTTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTTTATTATAATA
Found at i:13117 original size:23 final size:21
Alignment explanation
Indices: 13082--13147 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
13072 TTTTTAATAG
* *
13082 TTTTATCTTTATGACATGTCTTT
1 TTTTGTCTTTATGACACG--TTT
*
13105 TTTTGTCTCTATGACACGTTT
1 TTTTGTCTTTATGACACGTTT
*
13126 TTCTGTCTTTATGACACGTTT
1 TTTTGTCTTTATGACACGTTT
13147 T
1 T
13148 CGGTCTCTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 23 0.61
23 15 0.39
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTTGTCTTTATGACACGTTT
Found at i:13153 original size:20 final size:21
Alignment explanation
Indices: 13109--13155 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
13099 GTCTTTTTTT
*
13109 GTCTCTATGACACGTTTTTCT
1 GTCTCTATGACACGTTTTTCG
*
13130 GTCTTTATGACACG-TTTTCG
1 GTCTCTATGACACGTTTTTCG
13150 GTCTCT
1 GTCTCT
13156 TGCTCCTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
GTCTCTATGACACGTTTTTCG
Found at i:16940 original size:19 final size:20
Alignment explanation
Indices: 16912--16949 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
16902 AAAGTCTAAA
*
16912 AATTTATTAAAAATTAATAG
1 AATTTATTAAAAAATAATAG
16932 AATTT-TTAAAAAATAATA
1 AATTTATTAAAAAATAATA
16950 TTTGACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AATTTATTAAAAAATAATAG
Found at i:17549 original size:18 final size:18
Alignment explanation
Indices: 17526--17560 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17516 CGAAATATAT
* *
17526 TTGTTTATTTATTTATTA
1 TTGTTTAATAATTTATTA
17544 TTGTTTAATAATTTATT
1 TTGTTTAATAATTTATT
17561 TTTATTTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTGTTTAATAATTTATTA
Found at i:18601 original size:49 final size:49
Alignment explanation
Indices: 18544--18646 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
18534 ATCATTTATC
* *
18544 TAAATGAATATATTAATTAGAATATAATGATATATCAATATTTAGAATA
1 TAAATGAATATATTAATTAGAATATAATGATATATCAATAATTAAAATA
18593 TAAATGAATATATTAATTAGAATATAATGATATATCAATAATTAAAATA
1 TAAATGAATATATTAATTAGAATATAATGATATATCAATAATTAAAATA
18642 -AAATG
1 TAAATG
18647 TGTCGATTAC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
48 5 0.10
49 47 0.90
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (49 bp):
TAAATGAATATATTAATTAGAATATAATGATATATCAATAATTAAAATA
Found at i:18617 original size:24 final size:26
Alignment explanation
Indices: 18544--18646 Score: 121
Period size: 25 Copynumber: 4.2 Consensus size: 26
18534 ATCATTTATC
*
18544 TAAATGA-ATAT-ATTAATTAGAATA
1 TAAATGATATATCAATAATTAGAATA
*
18568 T-AATGATATATCAATATTTAGAATA
1 TAAATGATATATCAATAATTAGAATA
*
18593 TAAATGA-ATAT-ATTAATTAGAATA
1 TAAATGATATATCAATAATTAGAATA
*
18617 T-AATGATATATCAATAATTAAAATA
1 TAAATGATATATCAATAATTAGAATA
18642 -AAATG
1 TAAATG
18647 TGTCGATTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
23 10 0.15
24 21 0.31
25 31 0.46
26 5 0.07
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
TAAATGATATATCAATAATTAGAATA
Found at i:26329 original size:60 final size:60
Alignment explanation
Indices: 26263--26406 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 60
26253 TGGTCTTTAA
* * * *
26263 ACTTTTGAATATCCCAGTTTCATCCTTAAACTATGA-CTCCCATTCTAAATTAGGCCTTAC
1 ACTTTTGAAAATCACAATTTCATCCCTAAACTATGAGCT-CCATTCTAAATTAGGCCTTAC
* * * * * * *
26323 ACTTTTGAAAATTATAATTTCATCCCTAAACTATGAGCTTCTTTCTAAATTAGTCCATAA
1 ACTTTTGAAAATCACAATTTCATCCCTAAACTATGAGCTCCATTCTAAATTAGGCCTTAC
* *
26383 ACTTTT-TAAATC-CAATTTTATCCC
1 ACTTTTGAAAATCACAATTTCATCCC
26407 AAATTCATCC
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
58 10 0.15
59 4 0.06
60 52 0.76
61 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (60 bp):
ACTTTTGAAAATCACAATTTCATCCCTAAACTATGAGCTCCATTCTAAATTAGGCCTTAC
Found at i:27310 original size:2 final size:2
Alignment explanation
Indices: 27303--27329 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27293 AAAAACACTT
27303 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
27330 GATTGCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31228 original size:100 final size:100
Alignment explanation
Indices: 31066--31254 Score: 342
Period size: 100 Copynumber: 1.9 Consensus size: 100
31056 CTCAATATCC
*
31066 GTCATGTCGAACTATAAAATAATAAGTTCAATACTAGATGTGGAAGTGTATCTCACTCCATTGTT
1 GTCATGTCGAACTATAAAATAATAAGTTCAATACTAGATGCGGAAGTGTATCTCACTCCATTGTT
31131 AACTTATTTCTTGGAGATCACTACATATCTGTCAT
66 AACTTATTTCTTGGAGATCACTACATATCTGTCAT
* * *
31166 GTCATGTCGAACTATAAAATAATAAGTTCAGTGCTAGATGCGGTAGTGTATCTCACTCCATTGTT
1 GTCATGTCGAACTATAAAATAATAAGTTCAATACTAGATGCGGAAGTGTATCTCACTCCATTGTT
31231 AACTTATTTCTTGGAGATCACTAC
66 AACTTATTTCTTGGAGATCACTAC
31255 CTATTTGTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (100 bp):
GTCATGTCGAACTATAAAATAATAAGTTCAATACTAGATGCGGAAGTGTATCTCACTCCATTGTT
AACTTATTTCTTGGAGATCACTACATATCTGTCAT
Found at i:33430 original size:21 final size:23
Alignment explanation
Indices: 33406--33455 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
33396 TTAAATGATA
* *
33406 AAATTATTTAAAA-ATTTAAT-C
1 AAATAATTTAAAATAATTAATAC
33427 AAATAATTTAAAATAATTAATAC
1 AAATAATTTAAAATAATTAATAC
33450 AAATAA
1 AAATAA
33456 ATGTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 6 0.24
23 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATAATTTAAAATAATTAATAC
Found at i:39897 original size:17 final size:17
Alignment explanation
Indices: 39883--39920 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39873 AACTGACCTT
*
39883 TTGACTGACCTGACCCA
1 TTGAATGACCTGACCCA
*
39900 TTGAATGACCTGACCCG
1 TTGAATGACCTGACCCA
39917 TTGA
1 TTGA
39921 CCGTTGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (17 bp):
TTGAATGACCTGACCCA
Found at i:44723 original size:2 final size:2
Alignment explanation
Indices: 44716--44740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44706 GAATGGTCGG
44716 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44741 CTATTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45735 original size:85 final size:84
Alignment explanation
Indices: 45635--45798 Score: 224
Period size: 85 Copynumber: 1.9 Consensus size: 84
45625 ACAATCACGC
* *
45635 CACACGAATGTGTGTCATCTT-GTTTAATGACGTGTGCTTCAATGACACACAATGTA-AGTCATA
1 CACACGAATGTGTGTCATCTTCATTT-ATGACGTGGGCTTCAATGACACACAATG-AGA-TCATA
*
45698 CATGCGTGTCATAAATTTATGA
63 AATGCGTGTCATAAATTTATGA
* *
45720 CACACGAATGTGTGTCGTCTTCATTTATGACGTGGGCTTCAATGACACGCAATGAGCATCATAAA
1 CACACGAATGTGTGTCATCTTCATTTATGACGTGGGCTTCAATGACACACAATGAG-ATCATAAA
*
45785 TGTGTGTCATAAAT
65 TGCGTGTCATAAAT
45799 GCGTGTCATA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
84 1 0.01
85 65 0.93
86 4 0.06
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (84 bp):
CACACGAATGTGTGTCATCTTCATTTATGACGTGGGCTTCAATGACACACAATGAGATCATAAAT
GCGTGTCATAAATTTATGA
Found at i:45794 original size:13 final size:13
Alignment explanation
Indices: 45778--45811 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
45768 GCAATGAGCA
*
45778 TCATAAATGTGTG
1 TCATAAATGCGTG
45791 TCATAAATGCGTG
1 TCATAAATGCGTG
45804 TCATAAAT
1 TCATAAAT
45812 TTATGACGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:48160 original size:41 final size:41
Alignment explanation
Indices: 48106--48298 Score: 187
Period size: 41 Copynumber: 4.7 Consensus size: 41
48096 CTATAAATCA
* * * *
48106 AATCAAGTTGAATGATGAACTATTGTATGCTGCCATGATTG
1 AATCAAGTCGAATGATGAACTATTGCATGCTACCATGATCG
* *
48147 AATTGAA-TCGAATGATTAA-TCATTGCATGCTACCATGATCG
1 AA-TCAAGTCGAATGATGAACT-ATTGCATGCTACCATGATCG
* * * * *
48188 AATCAAGTTGGATGATGAACTATTGTATG-TCGCCATGATTG
1 AATCAAGTCGAATGATGAACTATTGCATGCT-ACCATGATCG
* * *
48229 AACTGAA-TCGAATGGTGAATTATTGCATGCTACCATGATCG
1 AA-TCAAGTCGAATGATGAACTATTGCATGCTACCATGATCG
*
48270 AATCAAGTTGAATGATGAACTATTGCATG
1 AATCAAGTCGAATGATGAACTATTGCATG
48299 TTAGAAAGAT
Statistics
Matches: 119, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
40 8 0.07
41 103 0.87
42 8 0.07
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (41 bp):
AATCAAGTCGAATGATGAACTATTGCATGCTACCATGATCG
Found at i:48207 original size:82 final size:82
Alignment explanation
Indices: 48106--48299 Score: 318
Period size: 82 Copynumber: 2.4 Consensus size: 82
48096 CTATAAATCA
* *
48106 AATCAAGTTGAATGATGAACTATTGTATG-CTGCCATGATTGAATTGAATCGAATGATTAATCAT
1 AATCAAGTTGAATGATGAACTATTGTATGTC-GCCATGATTGAACTGAATCGAATGATGAATCAT
48170 TGCATGCTACCATGATCG
65 TGCATGCTACCATGATCG
* * *
48188 AATCAAGTTGGATGATGAACTATTGTATGTCGCCATGATTGAACTGAATCGAATGGTGAATTATT
1 AATCAAGTTGAATGATGAACTATTGTATGTCGCCATGATTGAACTGAATCGAATGATGAATCATT
48253 GCATGCTACCATGATCG
66 GCATGCTACCATGATCG
*
48270 AATCAAGTTGAATGATGAACTATTGCATGT
1 AATCAAGTTGAATGATGAACTATTGTATGT
48300 TAGAAAGATC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 103 0.99
83 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (82 bp):
AATCAAGTTGAATGATGAACTATTGTATGTCGCCATGATTGAACTGAATCGAATGATGAATCATT
GCATGCTACCATGATCG
Found at i:63456 original size:41 final size:41
Alignment explanation
Indices: 63406--63604 Score: 194
Period size: 41 Copynumber: 4.9 Consensus size: 41
63396 ATAAACAACA
* *
63406 CCACAAAAGTATGAGTATATAGCGGCATTTGTATATAAACG
1 CCACAAAAGTATGAGTTTATAGCGGCGTTTGTATATAAACG
* * *
63447 CCACAAAAGTACGA--TTATACCGGCGTTTGTATAAAAACG
1 CCACAAAAGTATGAGTTTATAGCGGCGTTTGTATATAAACG
* *
63486 CCACTAAAA-TACT-AGTTTATAGCGGCGTTTATATAAAAACG
1 CCAC-AAAAGTA-TGAGTTTATAGCGGCGTTTGTATATAAACG
* * * *
63527 CCACTACAA-TACGATTTTTTAGCGGCGTTTGTATATAAACG
1 CCAC-AAAAGTATGAGTTTATAGCGGCGTTTGTATATAAACG
* * * *
63568 CCACGAAAGTATTAGTCTATAGC-GCGTTTATATATAA
1 CCACAAAAGTATGAGTTTATAGCGGCGTTTGTATATAA
63605 TTACCACTAA
Statistics
Matches: 130, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
39 28 0.22
40 19 0.15
41 83 0.64
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (41 bp):
CCACAAAAGTATGAGTTTATAGCGGCGTTTGTATATAAACG
Found at i:63589 original size:82 final size:80
Alignment explanation
Indices: 63396--63601 Score: 229
Period size: 80 Copynumber: 2.5 Consensus size: 80
63386 AGGGTAGAAC
* * * * *
63396 ATAAACAACACCACAAAAGTATGAGTATATAGCGGCATTTGTATATAAACGCCACAAAAGTACGA
1 ATAAA-AACGCCACAAAAGTATTAGTATATAGCGGCGTTTATATAAAAACGCCACAAAAGTACGA
63461 TTATACCGGCGTTTGT
65 TTATACCGGCGTTTGT
* * *
63477 ATAAAAACGCCACTAAAA-TACTAGTTTATAGCGGCGTTTATATAAAAACGCCACTACAA-TACG
1 ATAAAAACGCCAC-AAAAGTATTAGTATATAGCGGCGTTTATATAAAAACGCCAC-AAAAGTACG
* *
63540 ATTTTTTAGCGGCGTTTGT
64 A--TTATACCGGCGTTTGT
* * *
63559 ATATAAACGCCACGAAAGTATTAGTCTATAGC-GCGTTTATATA
1 ATAAAAACGCCACAAAAGTATTAGTATATAGCGGCGTTTATATA
63602 TAATTACCAC
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
80 42 0.40
81 26 0.25
82 38 0.36
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (80 bp):
ATAAAAACGCCACAAAAGTATTAGTATATAGCGGCGTTTATATAAAAACGCCACAAAAGTACGAT
TATACCGGCGTTTGT
Found at i:63648 original size:81 final size:82
Alignment explanation
Indices: 63467--63650 Score: 196
Period size: 82 Copynumber: 2.3 Consensus size: 82
63457 ACGATTATAC
* * * *
63467 CGGCGTTTGTATAAAAACGCCACTAAAATACTAGTTTATAGCGGCGTTTATATAAAAACGCCACT
1 CGGCGTTTATATAAAAACGCCACGAAAATACTAGTCTATAGCGGCGTTTATATAAAAACACCACT
* *
63532 ACAATACGATTTTTTAG
66 ACAATAAGATATTTTAG
* * * * * **
63549 CGGCGTTTGTATATAAACGCCACGAAAGTATTAGTCTATAGC-GCGTTTATATATAATTACCACT
1 CGGCGTTTATATAAAAACGCCACGAAAATACTAGTCTATAGCGGCGTTTATATAAAAACACCACT
63613 A-AAGTAAGAGTATTTT-G
66 ACAA-TAAGA-TATTTTAG
63630 CGGCGTTTAT-TCAAAAACGCC
1 CGGCGTTTATAT-AAAAACGCC
63651 GCTAAATGTA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
80 3 0.03
81 41 0.48
82 42 0.49
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (82 bp):
CGGCGTTTATATAAAAACGCCACGAAAATACTAGTCTATAGCGGCGTTTATATAAAAACACCACT
ACAATAAGATATTTTAG
Found at i:67782 original size:16 final size:17
Alignment explanation
Indices: 67743--67785 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
67733 ACTACTTGAA
67743 TAAATATTTAATAAATT
1 TAAATATTTAATAAATT
** *
67760 TTTATATTT-TTAAATT
1 TAAATATTTAATAAATT
67776 TAAATATTTA
1 TAAATATTTA
67786 TTTTTACATG
Statistics
Matches: 20, Mismatches: 5, Indels: 2
0.74 0.19 0.07
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATATTTAATAAATT
Done.