Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007228.1 Hibiscus syriacus cultivar Beakdansim tig00019131_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: 69386
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1809 original size:34 final size:35
Alignment explanation
Indices: 1765--1830 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
1755 GTGTATATAT
*
1765 ATTTACATTAAATATATGAATATTA-ATATATTTA
1 ATTTAAATTAAATATATGAATATTATATATATTTA
* *
1799 ATTTAAATTAAATTTATTAATATTATATATAT
1 ATTTAAATTAAATATATGAATATTATATATAT
1831 ATATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (35 bp):
ATTTAAATTAAATATATGAATATTATATATATTTA
Found at i:2460 original size:32 final size:32
Alignment explanation
Indices: 2423--2486 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2413 AAAAAATACC
2423 CCATTTCATGACCTACCAAACTATAAAAGAAG
1 CCATTTCATGACCTACCAAACTATAAAAGAAG
2455 CCATTTCATGACCTACCAAACTATAAAAGAAG
1 CCATTTCATGACCTACCAAACTATAAAAGAAG
2487 ATGAATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (32 bp):
CCATTTCATGACCTACCAAACTATAAAAGAAG
Found at i:3769 original size:5 final size:5
Alignment explanation
Indices: 3761--3786 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3751 TATATATTTT
3761 TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA T
3787 GTGAATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:11803 original size:31 final size:30
Alignment explanation
Indices: 11767--11825 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
11757 TTAAATTTTG
*
11767 AAAAAATTAAAAGTTTAGGTACTTAAACGGAT
1 AAAAAA-TAAAAGTTTAAGTAC-TAAACGGAT
* *
11799 AAAAAATGATAGTTTAAGTACTAAACG
1 AAAAAATAAAAGTTTAAGTACTAAACG
11826 TATTAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 12 0.50
32 6 0.25
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (30 bp):
AAAAAATAAAAGTTTAAGTACTAAACGGAT
Found at i:18755 original size:57 final size:57
Alignment explanation
Indices: 18664--18779 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
18654 ACCCATCGGC
* * *
18664 ATCAATAACGAATTATTTTGGCTACTTTGCACACCATGGGAAGCGACTTGCATATTT
1 ATCAATAACGAATTATTTTGGCTACTCTGAACACCATGGGAAGCAACTTGCATATTT
* *
18721 ATCAATGACGAGTTATTTTGGCTACTCTGAACACCATGGGAAGCAACTTGCATATTT
1 ATCAATAACGAATTATTTTGGCTACTCTGAACACCATGGGAAGCAACTTGCATATTT
18778 AT
1 AT
18780 GTTTCCTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (57 bp):
ATCAATAACGAATTATTTTGGCTACTCTGAACACCATGGGAAGCAACTTGCATATTT
Found at i:28102 original size:15 final size:15
Alignment explanation
Indices: 28082--28135 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
28072 CCGGATGTTA
28082 CGGGTACTCGGTAAT
1 CGGGTACTCGGTAAT
* **
28097 CGGGTACTCAGATTTT
1 CGGGTACTC-GGTAAT
28113 GCGGGTACTCGGTAAT
1 -CGGGTACTCGGTAAT
28129 CGGGTAC
1 CGGGTAC
28136 CCGATACCCG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 16 0.52
16 6 0.19
17 9 0.29
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (15 bp):
CGGGTACTCGGTAAT
Found at i:28169 original size:14 final size:14
Alignment explanation
Indices: 28147--28181 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28137 CGATACCCGG
* *
28147 TTTTTAATTTTTAA
1 TTTTAAATTATTAA
28161 TTTTAAATTATTAA
1 TTTTAAATTATTAA
28175 TTTTAAA
1 TTTTAAA
28182 AATATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTAAATTATTAA
Found at i:28989 original size:28 final size:28
Alignment explanation
Indices: 28912--28989 Score: 68
Period size: 32 Copynumber: 2.6 Consensus size: 28
28902 ATCCCTAGGC
* *
28912 TTAATAAATTTTTCTTTATTTATTTATTT
1 TTAA-AAATATTTATTTATTTATTTATTT
*
28941 TAAAAATTATCATTTTATTTATTTATTTATTT
1 TTAAAA--AT-A-TTTATTTATTTATTTATTT
28973 ATTAAAAATATTT-TTTA
1 -TTAAAAATATTTATTTA
28990 ATATAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
28 6 0.15
29 6 0.15
30 3 0.08
31 2 0.05
32 18 0.45
33 5 0.12
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (28 bp):
TTAAAAATATTTATTTATTTATTTATTT
Found at i:28989 original size:32 final size:32
Alignment explanation
Indices: 28920--28989 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
28910 GCTTAATAAA
*
28920 TTTTTCTTTATTTATTTATTTTAAAAATTATC
1 TTTTTATTTATTTATTTATTTTAAAAATTATC
*
28952 ATTTTATTTATTTATTTATTTATTAAAAA-TAT-
1 TTTTTATTTATTTATTTA-TT-TTAAAAATTATC
28984 TTTTTA
1 TTTTTA
28990 ATATAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 21 0.64
33 5 0.15
34 7 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTTTATTTATTTATTTATTTTAAAAATTATC
Found at i:29198 original size:20 final size:21
Alignment explanation
Indices: 29175--29218 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29165 CCAGAAATGT
*
29175 TAAAAAT-TTAATATTTTAGG
1 TAAAAATAATAATATTTTAGG
*
29195 TAAAAATAATAATGTTTTAGG
1 TAAAAATAATAATATTTTAGG
29216 TAA
1 TAA
29219 TTTTTTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGG
Found at i:30740 original size:16 final size:17
Alignment explanation
Indices: 30714--30747 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
30704 AAGAGAATTT
30714 TTTTATAAATATAATAA
1 TTTTATAAATATAATAA
30731 TTTT-TAAATATAATAA
1 TTTTATAAATATAATAA
30747 T
1 T
30748 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATAAATATAATAA
Found at i:30761 original size:16 final size:17
Alignment explanation
Indices: 30713--30762 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
30703 TAAGAGAATT
*
30713 TTTTTATAAATATAATAA
1 TTTTTA-AAAAATAATAA
30731 TTTTTAAATATAATAATAA
1 TTTTTAAA-A-AATAATAA
30750 -TTTTAAAAAATAA
1 TTTTTAAAAAATAA
30763 ATTTCAACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 5 0.17
17 3 0.10
18 14 0.48
19 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTTAAAAAATAATAA
Found at i:30762 original size:19 final size:19
Alignment explanation
Indices: 30720--30762 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
30710 ATTTTTTTAT
*
30720 AAAT-ATAATAATTTTTAA
1 AAATAATAATAATTTTAAA
*
30738 ATATAATAATAATTTTAAA
1 AAATAATAATAATTTTAAA
30757 AAATAA
1 AAATAA
30763 ATTTCAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATAATAATAATTTTAAA
Found at i:31622 original size:18 final size:18
Alignment explanation
Indices: 31601--31658 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
31591 GATAAATAAA
31601 TATTTTTTATTAAAATTT
1 TATTTTTTATTAAAATTT
***
31619 TATTTCCAATTATAAATTT
1 TATTTTTTATTA-AAATTT
* *
31638 AATACTTTTATTAAAATTT
1 TAT-TTTTTATTAAAATTT
31657 TA
1 TA
31659 AAAAATAATA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
18 9 0.31
19 15 0.52
20 5 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTTATTAAAATTT
Found at i:51124 original size:18 final size:18
Alignment explanation
Indices: 51075--51115 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
51065 ACGCATACCG
* *
51075 TAAAATTATTGTTTTAAT
1 TAAAATTAATATTTTAAT
51093 TAAAATTAATATTTT-AT
1 TAAAATTAATATTTTAAT
51110 TAAAAT
1 TAAAAT
51116 GATAAATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAAAATTAATATTTTAAT
Found at i:52190 original size:60 final size:60
Alignment explanation
Indices: 52114--52229 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
52104 GATTATAGGG
* *
52114 TGTTGCTTTATTAAGTCTCTCAACTATTAAAAGTTACAAAAT-AGTCATCCAACTATAAAA
1 TGTTACTTTATTAAGTCGCTCAACTATTAAAAGTTACAAAATGA-TCATCCAACTATAAAA
* * * *
52174 TGTTACTTTATTAAGTCGCTCTACTATTCAAAGTTATAAAATGATCATCTAACTAT
1 TGTTACTTTATTAAGTCGCTCAACTATTAAAAGTTACAAAATGATCATCCAACTAT
52230 TCATTATGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (60 bp):
TGTTACTTTATTAAGTCGCTCAACTATTAAAAGTTACAAAATGATCATCCAACTATAAAA
Found at i:53582 original size:31 final size:31
Alignment explanation
Indices: 53541--53621 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
53531 CGTTTAAAGT
53541 TGATAATTTAGGTACTAAAACGGATCAAAAC
1 TGATAATTTAGGTACTAAAACGGATCAAAAC
*
53572 TGATAGTTTAGGTACTAAAACGGATCAAAAC
1 TGATAATTTAGGTACTAAAACGGATCAAAAC
* **
53603 TAATAATTTATATACTAAA
1 TGATAATTTAGGTACTAAA
53622 CGCGTTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (31 bp):
TGATAATTTAGGTACTAAAACGGATCAAAAC
Found at i:53845 original size:30 final size:31
Alignment explanation
Indices: 53809--53868 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
53799 TCTTTGCTTT
* *
53809 TCCTTGTATTAT-AAGT-AATTATAGATTTAA
1 TCCTTGTAATATGAA-TAAATTATAAATTTAA
53839 TCCTTGTAATATGAATAAATTATAAATTTA
1 TCCTTGTAATATGAATAAATTATAAATTTA
53869 GTCTTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (31 bp):
TCCTTGTAATATGAATAAATTATAAATTTAA
Found at i:54298 original size:14 final size:14
Alignment explanation
Indices: 54260--54300 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
54250 ACCAACTCGT
*
54260 GGGATAACTCAGTA
1 GGGATAACTCGGTA
54274 GGGATAACTCGGTA
1 GGGATAACTCGGTA
54288 GGGATAACTCGGT
1 GGGATAACTCGGT
54301 TTGAGCTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (14 bp):
GGGATAACTCGGTA
Found at i:58220 original size:28 final size:29
Alignment explanation
Indices: 58180--58239 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
58170 TTACGGAATG
58180 AAACGTTAGACACCAAACT-AA-AATAAAA
1 AAACGTTAGACACCAAACTGAAGAA-AAAA
* *
58208 AAACGTTATACACTAAACTGAAGAAAAAA
1 AAACGTTAGACACCAAACTGAAGAAAAAA
58237 AAA
1 AAA
58240 GCATACATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.61
29 9 0.32
30 2 0.07
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (29 bp):
AAACGTTAGACACCAAACTGAAGAAAAAA
Found at i:58548 original size:46 final size:46
Alignment explanation
Indices: 58481--58581 Score: 184
Period size: 46 Copynumber: 2.2 Consensus size: 46
58471 ATCCTCTAAA
58481 TATAGGATGACATTTTATTAAGTCCATCGATTATTAAACATTTGAT
1 TATAGGATGACATTTTATTAAGTCCATCGATTATTAAACATTTGAT
**
58527 TATAGGATGATGTTTTATTAAGTCCATCGATTATTAAACATTTGAT
1 TATAGGATGACATTTTATTAAGTCCATCGATTATTAAACATTTGAT
58573 TATAGGATG
1 TATAGGATG
58582 TTACTTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (46 bp):
TATAGGATGACATTTTATTAAGTCCATCGATTATTAAACATTTGAT
Found at i:59637 original size:12 final size:12
Alignment explanation
Indices: 59620--59661 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
59610 TGACTTAACA
59620 TGTTTGACTGAC
1 TGTTTGACTGAC
59632 TGTTTG-CTGA-
1 TGTTTGACTGAC
*
59642 -GTTTGACCGAC
1 TGTTTGACTGAC
59653 TGTTTGACT
1 TGTTTGACT
59662 TCTTCTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 5 0.20
10 3 0.12
11 4 0.16
12 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (12 bp):
TGTTTGACTGAC
Done.