Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003824.1 Hibiscus syriacus cultivar Beakdansim tig00008200_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: 54578
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:13500 original size:18 final size:18
Alignment explanation
Indices: 13477--13512 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13467 CATCATTCCC
13477 TGCTGCTGCAATTTCCAA
1 TGCTGCTGCAATTTCCAA
13495 TGCTGCTGCAATTTCCAA
1 TGCTGCTGCAATTTCCAA
13513 AACTGATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (18 bp):
TGCTGCTGCAATTTCCAA
Found at i:19557 original size:33 final size:33
Alignment explanation
Indices: 19512--19582 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
19502 TTATAGATGC
* *
19512 TTTGTTCATGAACATAAACGATCTGAATACACT
1 TTTGTTCATGAACATAAACGAACTGAACACACT
*
19545 TTTGTTCGTGAACATAAACGAACTGAACACACT
1 TTTGTTCATGAACATAAACGAACTGAACACACT
19578 TTTGT
1 TTTGT
19583 CATACTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
TTTGTTCATGAACATAAACGAACTGAACACACT
Found at i:25601 original size:17 final size:17
Alignment explanation
Indices: 25579--25616 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25569 AATTAAAAGT
25579 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
25596 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
25613 TAGT
1 TAGT
25617 AATGAACTAC
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:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:26424 original size:18 final size:19
Alignment explanation
Indices: 26389--26425 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
26379 CACGGAATGT
26389 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
26409 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
26426 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:28676 original size:14 final size:14
Alignment explanation
Indices: 28657--28770 Score: 77
Period size: 14 Copynumber: 8.8 Consensus size: 14
28647 TTGATTCTAA
28657 TTTTAATATTAATT
1 TTTTAATATTAATT
28671 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* * *
28681 ATTAAATAATAATT
1 TTTTAATATTAATT
*
28695 TTTTAATATT-ATA
1 TTTTAATATTAATT
*
28708 TTCTAGATATTAA--
1 TTTTA-ATATTAATT
28721 TTTTAATATTAATT
1 TTTTAATATTAATT
*
28735 TTTTAA-AATAA--
1 TTTTAATATTAATT
* *
28746 ATTAAATATTAATT
1 TTTTAATATTAATT
28760 TTTTAATATTA
1 TTTTAATATTA
28771 TATTATAGAT
Statistics
Matches: 75, Mismatches: 14, Indels: 22
0.68 0.13 0.20
Matches are distributed among these distances:
10 4 0.05
11 5 0.07
12 17 0.23
13 15 0.20
14 33 0.44
15 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:28727 original size:64 final size:64
Alignment explanation
Indices: 28634--28791 Score: 243
Period size: 65 Copynumber: 2.5 Consensus size: 64
28624 TTATATATAA
28634 TTTT-ATATTATATTT-GAT-TCTAATTTTAATATTAATTTTTT-AAATAAATTAAATAATAATT
1 TTTTAATATTATATTTAGATAT-TAATTTTAATATTAATTTTTTAAAATAAATTAAATAATAATT
*
28695 TTTTAATATTATATTCTAGATATTAATTTTAATATTAATTTTTTAAAATAAATTAAATATTAATT
1 TTTTAATATTATATT-TAGATATTAATTTTAATATTAATTTTTTAAAATAAATTAAATAATAATT
28760 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATT-TAGATA-TTAATTTTA
28792 TATCATATAA
Statistics
Matches: 89, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
61 4 0.04
62 10 0.11
63 1 0.01
64 24 0.27
65 41 0.46
66 9 0.10
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (64 bp):
TTTTAATATTATATTTAGATATTAATTTTAATATTAATTTTTTAAAATAAATTAAATAATAATT
Found at i:28846 original size:20 final size:19
Alignment explanation
Indices: 28786--28847 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
28776 TAGATATTTA
*
28786 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
28805 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
28823 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
28843 ATTTT
1 ATTTT
28848 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:29351 original size:31 final size:31
Alignment explanation
Indices: 29314--29373 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
29304 TAGTTGTATG
* * *
29314 AATTATTTAAATTTTAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
29345 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
29374 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:30078 original size:2 final size:2
Alignment explanation
Indices: 30073--30101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30063 AAATTAAAAT
30073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30102 TAAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31048 original size:55 final size:55
Alignment explanation
Indices: 30988--31103 Score: 180
Period size: 55 Copynumber: 2.1 Consensus size: 55
30978 CAAGGGTTTG
* *
30988 GGGTTTATTAGTGAACAAATTAGT-GGGAATTTCTTGAATTGAGAATTAGGCTTTT
1 GGGTTTATTAGTGAACAAATTA-TCAGGAATTTCTTGAATTGAGAATTAGGCTTTC
* *
31043 GGGTTTATTAGTGAAGAAATTATCAGGAATTTCTTGAATTGGGAATTAGGCTTTC
1 GGGTTTATTAGTGAACAAATTATCAGGAATTTCTTGAATTGAGAATTAGGCTTTC
31098 GGGTTT
1 GGGTTT
31104 TTGAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 1 0.02
55 55 0.98
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.40
Consensus pattern (55 bp):
GGGTTTATTAGTGAACAAATTATCAGGAATTTCTTGAATTGAGAATTAGGCTTTC
Found at i:36113 original size:22 final size:22
Alignment explanation
Indices: 36077--36119 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36067 TTTTCTCCTC
**
36077 AACAGTAAGTCTAAACTTATGG
1 AACAGTAAGGATAAACTTATGG
*
36099 AACAGTAAGGATAAAGTTATG
1 AACAGTAAGGATAAACTTATG
36120 TTCGACTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (22 bp):
AACAGTAAGGATAAACTTATGG
Found at i:41988 original size:19 final size:18
Alignment explanation
Indices: 41970--42027 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 18
41960 TAAATAATAT
41970 TAAATTATTCTAATTATA
1 TAAATTATTCTAATTATA
41988 T-AA-TATTCTAATTATA
1 TAAATTATTCTAATTATA
* *
42004 AAAATTCATTATAATTATA
1 TAAATT-ATTCTAATTATA
*
42023 AAAAT
1 TAAAT
42028 AATTATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 13 0.37
17 4 0.11
18 2 0.06
19 16 0.46
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTATTCTAATTATA
Found at i:42097 original size:30 final size:31
Alignment explanation
Indices: 42057--42118 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
42047 ATATAGTTGT
*
42057 ATATTCTTATTTAT-ATATA-TATATTATTAA
1 ATATTCTTATTTATAAAATAGTA-ATTATTAA
*
42087 ATATTTTTATTTATAAAATAGTAATTATTAA
1 ATATTCTTATTTATAAAATAGTAATTATTAA
42118 A
1 A
42119 GAAAGCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 13 0.46
31 13 0.46
32 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
ATATTCTTATTTATAAAATAGTAATTATTAA
Found at i:46762 original size:33 final size:33
Alignment explanation
Indices: 46725--46791 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
46715 GCTATATAAA
46725 ATTCCATGTCCAGAAGCACTTTTCAGATGATAC
1 ATTCCATGTCCAGAAGCACTTTTCAGATGATAC
*
46758 ATTCCATGTCCAGAAGCACTTTTTAGATGATAC
1 ATTCCATGTCCAGAAGCACTTTTCAGATGATAC
46791 A
1 A
46792 AAGTTAGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (33 bp):
ATTCCATGTCCAGAAGCACTTTTCAGATGATAC
Found at i:49023 original size:16 final size:16
Alignment explanation
Indices: 49000--49060 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
48990 TAATAAATGA
49000 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* **
49016 ATGAACATAAATAAAC
1 ACGAACATAAACGAAC
*
49032 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
49048 ACGAACATAAACG
1 ACGAACATAAACG
49061 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:49307 original size:12 final size:12
Alignment explanation
Indices: 49278--49369 Score: 95
Period size: 12 Copynumber: 7.9 Consensus size: 12
49268 CTCAAGACTC
49278 GAGCTCGA-T-T
1 GAGCTCGATTCT
49288 GAAGCTCGATTCT
1 G-AGCTCGATTCT
49301 GAGCTCGA-T-T
1 GAGCTCGATTCT
*
49311 GAAGCTTGATTCT
1 G-AGCTCGATTCT
49324 GAGCTCGATTCT
1 GAGCTCGATTCT
*
49336 GAGTTCGATTC-
1 GAGCTCGATTCT
*
49347 AAGCTCGATTCT
1 GAGCTCGATTCT
*
49359 GAGCTCTATTC
1 GAGCTCGATTC
49370 AAGCTTGACA
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
10 3 0.04
11 23 0.34
12 38 0.56
13 4 0.06
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.34
Consensus pattern (12 bp):
GAGCTCGATTCT
Found at i:49308 original size:23 final size:23
Alignment explanation
Indices: 49278--49333 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
49268 CTCAAGACTC
49278 GAGCTCGATTGAAGCTCGATTCT
1 GAGCTCGATTGAAGCTCGATTCT
*
49301 GAGCTCGATTGAAGCTTGATTCT
1 GAGCTCGATTGAAGCTCGATTCT
49324 GAGCTCGATT
1 GAGCTCGATT
49334 CTGAGTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTCT
Found at i:49329 original size:35 final size:35
Alignment explanation
Indices: 49290--49369 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
49280 GCTCGATTGA
* *
49290 AGCTCGATTCTGAGCTCGATTGAAGCTTGATTCTG
1 AGCTCGATTCTGAGCTCGATTCAAGCTCGATTCTG
*
49325 AGCTCGATTCTGAGTTCGATTCAAGCTCGATTCTG
1 AGCTCGATTCTGAGCTCGATTCAAGCTCGATTCTG
*
49360 AGCTCTATTC
1 AGCTCGATTC
49370 AAGCTTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (35 bp):
AGCTCGATTCTGAGCTCGATTCAAGCTCGATTCTG
Found at i:49351 original size:23 final size:23
Alignment explanation
Indices: 49290--49374 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
49280 GCTCGATTGA
*
49290 AGCTCGATTCTGAGCTCGA-T-TG
1 AGCTCGATTC-AAGCTCGATTCTG
* *
49312 AAGCTTGATTCTGAGCTCGATTCTG
1 -AGCTCGATTC-AAGCTCGATTCTG
*
49337 AGTTCGATTCAAGCTCGATTCTG
1 AGCTCGATTCAAGCTCGATTCTG
*
49360 AGCTCTATTCAAGCT
1 AGCTCGATTCAAGCT
49375 TGACATTTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
23 43 0.80
24 9 0.17
25 2 0.04
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTCTG
Found at i:50269 original size:24 final size:24
Alignment explanation
Indices: 50228--50325 Score: 128
Period size: 24 Copynumber: 4.1 Consensus size: 24
50218 GATTGGGTTA
*
50228 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
* *
50252 AACATAATCGAACAAACATAAACA
1 AACATAATCGAACGAACATAAACG
50276 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
50300 AACATAA-CTGAACGAACATAACCG
1 AACATAATC-GAACGAACATAAACG
50324 AA
1 AA
50326 TGTTCACGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
23 4 0.06
24 62 0.94
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:50271 original size:14 final size:14
Alignment explanation
Indices: 50252--50303 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
50242 AACATAAACG
50252 AACATAATCGAACA
1 AACATAATCGAACA
50266 AACAT-A---AACA
1 AACATAATCGAACA
*
50276 AACATAATCGAACG
1 AACATAATCGAACA
*
50290 AACATAAACGAACA
1 AACATAATCGAACA
50304 TAACTGAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.12
Consensus pattern (14 bp):
AACATAATCGAACA
Done.