Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001963.1 Hibiscus syriacus cultivar Beakdansim tig00003967_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: 56461
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:2245 original size:21 final size:21
Alignment explanation
Indices: 2219--2260 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2209 ACTGTGATTA
*
2219 CGGCCGTCACGGGTGCTATTG
1 CGGCCGTCACAGGTGCTATTG
*
2240 CGGCCGTCGCAGGTGCTATTG
1 CGGCCGTCACAGGTGCTATTG
2261 GACACTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.24
Consensus pattern (21 bp):
CGGCCGTCACAGGTGCTATTG
Found at i:2666 original size:14 final size:14
Alignment explanation
Indices: 2647--2677 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2637 TATATTTGTC
2647 CTAATTACTCTTAA
1 CTAATTACTCTTAA
2661 CTAATTACTCTTAA
1 CTAATTACTCTTAA
2675 CTA
1 CTA
2678 TTTTGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (14 bp):
CTAATTACTCTTAA
Found at i:7685 original size:21 final size:21
Alignment explanation
Indices: 7659--7706 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
7649 TAATTTTCAA
* *
7659 ACATTGTTGTATCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
7680 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
7701 ACATTG
1 ACATTG
7707 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:9273 original size:27 final size:27
Alignment explanation
Indices: 9222--9273 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
9212 CTCAAAACTC
** * *
9222 GGTCGGATGGAGGGTGTGTATTTTTCG
1 GGTCGGATGGAGAATGTATAATTTTCG
9249 GGTCGGATGGAGAATGTATAATTTT
1 GGTCGGATGGAGAATGTATAATTTT
9274 TGGATCGAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.38, T:0.37
Consensus pattern (27 bp):
GGTCGGATGGAGAATGTATAATTTTCG
Found at i:11593 original size:106 final size:105
Alignment explanation
Indices: 11409--11628 Score: 323
Period size: 106 Copynumber: 2.1 Consensus size: 105
11399 AGCAACGACA
* ** *
11409 ATACTAACAGACATTTTTAAAATATAATTTTATCATACTTTAATTAGTATATTAATGTCCAGCTC
1 ATACTAATAGACATCATTAAAATATAATTTTATCATACTTTAATTAATATATTAATGTCCAGCTC
* * *
11474 ATACGACCATTAATTTTTAACAAAAAAATGAGTTTAGAAC
66 AAACGACCATTAATTTTTAACAAAAAAACGAATTTAGAAC
* *
11514 ATACTAATAGACATCATTAAAATATGATTTTTATCATACTTTAATTAATATATTAGTGTCCAGCT
1 ATACTAATAGACATCATTAAAATAT-AATTTTATCATACTTTAATTAATATATTAATGTCCAGCT
* *
11579 CAAACGATCATTAATTTTTAATAAAAAAACGAATTTAGAAC
65 CAAACGACCATTAATTTTTAACAAAAAAACGAATTTAGAAC
11620 ATAACTAAT
1 AT-ACTAAT
11629 TAAATTATTT
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
105 22 0.22
106 74 0.73
107 6 0.06
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (105 bp):
ATACTAATAGACATCATTAAAATATAATTTTATCATACTTTAATTAATATATTAATGTCCAGCTC
AAACGACCATTAATTTTTAACAAAAAAACGAATTTAGAAC
Found at i:14228 original size:26 final size:26
Alignment explanation
Indices: 14189--14261 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 26
14179 CTCGAGTTTT
* * * *
14189 AAAATAACCAAAATACCCTTATA-CCT
1 AAAATGACTAAAATAACCTTA-ACCCC
* *
14215 AAAATGACTGAAATATCCTTAAGCCCC
1 AAAATGACTAAAATAACCTTAA-CCCC
14242 AAAATGACTAAAATAACCTT
1 AAAATGACTAAAATAACCTT
14262 GAGTACTGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 1 0.03
26 17 0.45
27 20 0.53
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAATGACTAAAATAACCTTAACCCC
Found at i:23908 original size:25 final size:26
Alignment explanation
Indices: 23852--23909 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
23842 GAACATTTTC
*
23852 AATAATAGATAGACTAAATTGATCCGTTT
1 AATAATAGATAGACTAAATTGA--C-TAT
*
23881 AATAATAGATAGGCTAAATTGA-TAT
1 AATAATAGATAGACTAAATTGACTAT
23906 AATA
1 AATA
23910 CTTATAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
29 21 0.78
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (26 bp):
AATAATAGATAGACTAAATTGACTAT
Found at i:30742 original size:6 final size:6
Alignment explanation
Indices: 30731--30755 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30721 GAAGACACGT
30731 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
30756 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:30761 original size:6 final size:6
Alignment explanation
Indices: 30752--30794 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
30742 CATTACCATT
30752 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
30795 GCCGTGCCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:36394 original size:22 final size:22
Alignment explanation
Indices: 36346--36399 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
36336 TTCAGCTGTT
* *
36346 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
36368 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
36390 ATAACTCCTG
1 ATAACTCCTG
36400 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:36685 original size:6 final size:6
Alignment explanation
Indices: 36674--36740 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
36664 GACACGTATT
* *
36674 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
36722 ACCACG ACCACG TCCACG A
1 ACCACG ACCACG ACCACG A
36741 GCCGAGCCGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:36748 original size:5 final size:5
Alignment explanation
Indices: 36738--36781 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
36728 ACCACGTCCA
* * *
36738 CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
36782 ACGGACGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.14, C:0.39, G:0.41, T:0.07
Consensus pattern (5 bp):
CGAGC
Found at i:42636 original size:6 final size:6
Alignment explanation
Indices: 42625--42649 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42615 GAAGACACGT
42625 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
42650 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:42655 original size:6 final size:6
Alignment explanation
Indices: 42646--42700 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
42636 CATTACCATT
42646 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
42694 ACCACG A
1 ACCACG A
42701 GCCGTGCCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:45151 original size:29 final size:29
Alignment explanation
Indices: 45109--45165 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
45099 AGTGTTGGTC
45109 GTAGATCGCCATGC-CTTCCGGGCGACCTT
1 GTAGATCGCCATGCAC-TCCGGGCGACCTT
* * *
45138 GTAGGTCGTCATGCACTCCGGGTGACCT
1 GTAGATCGCCATGCACTCCGGGCGACCT
45166 ACCCTTGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.25
Consensus pattern (29 bp):
GTAGATCGCCATGCACTCCGGGCGACCTT
Found at i:45252 original size:29 final size:29
Alignment explanation
Indices: 45219--45303 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
45209 TCCCAACACA
* *
45219 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGACATGCACTCCGGGCGACCTTG
* *
45248 TAGGTCGACATGCTCTCTGGGCGACCTTG
1 TAGGTCGACATGCACTCCGGGCGACCTTG
*
45277 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGACATGCACTCCGGGCGACCT
45304 ACCATTGCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.13, C:0.33, G:0.31, T:0.24
Consensus pattern (29 bp):
TAGGTCGACATGCACTCCGGGCGACCTTG
Found at i:45456 original size:29 final size:29
Alignment explanation
Indices: 45419--45505 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
45409 GCAATCTCTT
*
45419 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGGTCGCCGGGAAGACATGGCGACCTA
*
45448 GTAGGTCGCCGGGAAAACATGGCGACCTA
1 GTAGGTCGCCGGGAAGACATGGCGACCTA
* * *
45477 GTATGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCGGGAAGACATGGCGACCTA
45506 CGATGAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.24, C:0.26, G:0.34, T:0.15
Consensus pattern (29 bp):
GTAGGTCGCCGGGAAGACATGGCGACCTA
Found at i:50070 original size:20 final size:21
Alignment explanation
Indices: 50039--50078 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
50029 GATTAAGCTC
50039 TTTAACTTTGATAACCATTTT
1 TTTAACTTTGATAACCATTTT
*
50060 TTTAA-TTTGATAACTATTT
1 TTTAACTTTGATAACCATTT
50079 CTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAACTTTGATAACCATTTT
Found at i:53561 original size:21 final size:21
Alignment explanation
Indices: 53537--53597 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
53527 ATCTTTGAAA
53537 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
53558 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
53572 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
53593 AAATG
1 AAATG
53598 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:53643 original size:36 final size:36
Alignment explanation
Indices: 53501--53648 Score: 180
Period size: 35 Copynumber: 4.2 Consensus size: 36
53491 TGAAAGTATT
***
53501 AAAAATGGTTTTC-AAGTTTGGT-AA-CCATCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
53534 AAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 -AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
53571 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * * *
53606 AAAAATAGTTTTTTAAAGTTTGGTAGATGTTT-ATTG
1 AAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
53642 AAAAATG
1 AAAAATG
53649 ATAATGGGAT
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
34 13 0.13
35 45 0.44
36 16 0.16
37 28 0.27
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:53647 original size:72 final size:69
Alignment explanation
Indices: 53497--53648 Score: 175
Period size: 72 Copynumber: 2.2 Consensus size: 69
53487 TTGTTGAAAG
53497 TATT-AAAAATGGTTTTCAAGTTTGGTAACCATCTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
1 TATTGAAAAATGGTTTTCAAGTTTGGTAACCATCTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
53561 TGTT
66 TGTT
* *** * *
53565 TCTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-AAAAATAGTTTTTTAAAGTTTG
1 T-ATTGAAAAATGGTTTTC-AAGTTTGGT-AA-CCATCTTTGAAAAAAT-GGTTTTCAAAGTTTG
*
53628 GTAGATGTT
61 GTAAATGTT
53637 TATTGAAAAATG
1 TATTGAAAAATG
53649 ATAATGGGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
68 1 0.01
69 14 0.20
70 9 0.13
71 11 0.16
72 34 0.49
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (69 bp):
TATTGAAAAATGGTTTTCAAGTTTGGTAACCATCTTTGAAAAAATGGTTTTCAAAGTTTGGTAAA
TGTT
Done.