Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004112.1 Hibiscus syriacus cultivar Beakdansim tig00008999_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: 77522
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:770 original size:23 final size:23
Alignment explanation
Indices: 727--770 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
717 CATTTTATAT
* *
727 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCAATCCTACGC
*
750 GGCACTTCGGTGCAATCCTAC
1 GGCACTACGGTGCAATCCTAC
771 TTGACAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATCCTACGC
Found at i:13753 original size:24 final size:23
Alignment explanation
Indices: 13716--13770 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
13706 AACAAGCTCG
*
13716 TTTATTAACATGTTTATCTACTAA
1 TTTA-TAACATGTTTATCTACCAA
*
13740 TTTATAACATTGTTTATCTACCCA
1 TTTATAACA-TGTTTATCTACCAA
13764 TTTATAA
1 TTTATAA
13771 GCTCGTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTATAACATGTTTATCTACCAA
Found at i:13778 original size:24 final size:24
Alignment explanation
Indices: 13716--13779 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
13706 AACAAGCTCG
*
13716 TTTATTAACAT-GTTTATCTACTAA
1 TTTA-TAACATCGTTTATCTACCAA
* *
13740 TTTATAACATTGTTTATCTACCCA
1 TTTATAACATCGTTTATCTACCAA
13764 TTTATAAGC-TCGTTTA
1 TTTATAA-CATCGTTTA
13780 CTCGATTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.17
24 28 0.80
25 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTATAACATCGTTTATCTACCAA
Found at i:15550 original size:2 final size:2
Alignment explanation
Indices: 15543--15568 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15533 AATAATCAAT
15543 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
15569 AACTAACCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17908 original size:31 final size:31
Alignment explanation
Indices: 17851--17910 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
17841 GTAATTCTTA
*
17851 TTTTTATCTTTTAGATTATTTCGTTTATTTT
1 TTTTTATCTTTTAGATAATTTCGTTTATTTT
* *
17882 TTTTTATCTTTT-TATAATTTATGTTTATT
1 TTTTTATCTTTTAGATAATTT-CGTTTATT
17911 CGTGTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (31 bp):
TTTTTATCTTTTAGATAATTTCGTTTATTTT
Found at i:19592 original size:24 final size:24
Alignment explanation
Indices: 19546--19594 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
19536 TTAAGACAAT
*
19546 AAAGACTAAGATCATAAAGATAAA
1 AAAGACTAAGATCATAAACATAAA
*
19570 AAAGACTAAGAAT-ATGAACATAAA
1 AAAGACTAAG-ATCATAAACATAAA
19594 A
1 A
19595 TAAAGAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.63, C:0.08, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAGACTAAGATCATAAACATAAA
Found at i:22692 original size:11 final size:12
Alignment explanation
Indices: 22672--22708 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
22662 TGAAAAGTGT
22672 AAAGTAAAAA-G
1 AAAGTAAAAATG
*
22683 AAAGTGAAAATG
1 AAAGTAAAAATG
22695 AAAG-AAAAATG
1 AAAGTAAAAATG
22706 AAA
1 AAA
22709 ACTTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (12 bp):
AAAGTAAAAATG
Found at i:26935 original size:44 final size:45
Alignment explanation
Indices: 26867--26996 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
26857 AAGAAGGTGG
* *
26867 ATCAAAATTTCG-TTCGATTGCATCACATATA-GAGTTGGATCAGC
1 ATCAACATTTCGCTTCGATTCCATCACATA-AGGAGTTGGATCAGC
* * * *
26911 ATCAATATTTTGC-TCGATTCCATCA-ATAAGGAGTTGGATTAAC
1 ATCAACATTTCGCTTCGATTCCATCACATAAGGAGTTGGATCAGC
* *
26954 ATCACCATTTCGCTTTG-TTCCATCACATAAGGAGTTGGATCAG
1 ATCAACATTTCGCTTCGATTCCATCACATAAGGAGTTGGATCAG
26997 TGTCAACTCG
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 32 0.45
44 38 0.54
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (45 bp):
ATCAACATTTCGCTTCGATTCCATCACATAAGGAGTTGGATCAGC
Found at i:27148 original size:39 final size:37
Alignment explanation
Indices: 27050--27161 Score: 127
Period size: 39 Copynumber: 3.0 Consensus size: 37
27040 TTCATTCAAG
* *
27050 ATTTTATCTCACTTGAGATTG-TTTTCCTTAAAACAA
1 ATTTTATCTTACTTGAGATTGTTTTTCCTCAAAACAA
* * *
27086 ATTTTGTCTTACTCGAGATTGTTTCTTCCTCAAAATTAA
1 ATTTTATCTTACTTGAGATTGTTT-TTCCTCAAAA-CAA
* * *
27125 TTTTTATCTTACTTGAGACTGTTTTTCTTCAAAACAA
1 ATTTTATCTTACTTGAGATTGTTTTTCCTCAAAACAA
27162 TTCTAGTTTC
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
36 18 0.29
37 4 0.06
38 18 0.29
39 22 0.35
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (37 bp):
ATTTTATCTTACTTGAGATTGTTTTTCCTCAAAACAA
Found at i:27304 original size:36 final size:36
Alignment explanation
Indices: 27242--27310 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
27232 TTATTGAGTT
* * * *
27242 TGTTTTTCTTAAGATATATTTTATCTCACTTGAGAC
1 TGTTTTTCTTAAAACAAATTTCATCTCACTTGAGAC
*
27278 TGTTTTTCTTAAAACAAATTTCATCTCTCTTGA
1 TGTTTTTCTTAAAACAAATTTCATCTCACTTGA
27311 AAGTGTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (36 bp):
TGTTTTTCTTAAAACAAATTTCATCTCACTTGAGAC
Found at i:27318 original size:36 final size:36
Alignment explanation
Indices: 27242--27323 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 36
27232 TTATTGAGTT
* * * * *
27242 TGTTTTTCTTAAGATATATTTTATCTCACTTGAGAC
1 TGTTTTTCTTAAAACAAATTTCATCTCACTTGAAAC
* *
27278 TGTTTTTCTTAAAACAAATTTCATCTCTCTTGAAAG
1 TGTTTTTCTTAAAACAAATTTCATCTCACTTGAAAC
*
27314 TGTTTCTCTT
1 TGTTTTTCTT
27324 GAAAGTGTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50
Consensus pattern (36 bp):
TGTTTTTCTTAAAACAAATTTCATCTCACTTGAAAC
Found at i:27323 original size:15 final size:15
Alignment explanation
Indices: 27303--27342 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
27293 AAATTTCATC
27303 TCTCTTGAAAGTGTT
1 TCTCTTGAAAGTGTT
27318 TCTCTTGAAAGTGTT
1 TCTCTTGAAAGTGTT
27333 TCTCTTGAAA
1 TCTCTTGAAA
27343 CAAATTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (15 bp):
TCTCTTGAAAGTGTT
Found at i:35402 original size:20 final size:20
Alignment explanation
Indices: 35355--35403 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
35345 ATTGAAGTGG
35355 CGAAG-AGAAGAAAAGTGAA
1 CGAAGAAGAAGAAAAGTGAA
*
35374 -GAGAAAAGAAGAAAAGTGAA
1 CGA-AGAAGAAGAAAAGTGAA
35394 CGAAGAAGAA
1 CGAAGAAGAA
35404 AAGAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 1 0.04
20 20 0.80
21 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.31, T:0.04
Consensus pattern (20 bp):
CGAAGAAGAAGAAAAGTGAA
Found at i:36065 original size:20 final size:20
Alignment explanation
Indices: 36039--36106 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
36029 TTAATATTAG
36039 GTCCTCTATTTTTAGGTTTA
1 GTCCTCTATTTTTAGGTTTA
*
36059 ATCCTCTATTTTTAGGTTTA
1 GTCCTCTATTTTTAGGTTTA
36079 GTCCTCTATTTTTAGGTTTA
1 GTCCTCTATTTTTAGGTTTA
36099 GTCCTCTA
1 GTCCTCTA
36107 GTTTCTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (20 bp):
GTCCTCTATTTTTAGGTTTA
Found at i:37395 original size:23 final size:23
Alignment explanation
Indices: 37361--37429 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
37351 CACCACAGCT
*
37361 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* * *
37384 CATAGAATTGCACCTAAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
*
37407 CGTAGAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
37430 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:39062 original size:21 final size:21
Alignment explanation
Indices: 39036--39090 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
39026 TTAAATTCTC
39036 ATGCATCGATGCATCCCCTTA
1 ATGCATCGATGCATCCCCTTA
* *
39057 ATGCATCGATACATCCCTTTA
1 ATGCATCGATGCATCCCCTTA
*
39078 ATGCATCAATGCA
1 ATGCATCGATGCA
39091 CCTTCAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCCCCTTA
Found at i:43288 original size:20 final size:20
Alignment explanation
Indices: 43265--43307 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
43255 AATCCACCAC
*
43265 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
43285 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
43305 ATG
1 ATG
43308 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:45922 original size:13 final size:13
Alignment explanation
Indices: 45906--45940 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
45896 AGGCAACTAG
45906 AAAGTGAAAGTAA
1 AAAGTGAAAGTAA
* *
45919 AAAGAGAAAGTGA
1 AAAGTGAAAGTAA
45932 AAAGTGAAA
1 AAAGTGAAA
45941 AATAAGTGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (13 bp):
AAAGTGAAAGTAA
Found at i:53657 original size:20 final size:20
Alignment explanation
Indices: 53634--53676 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53624 AATCCACCAC
*
53634 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
53654 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
53674 ATG
1 ATG
53677 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:55954 original size:21 final size:21
Alignment explanation
Indices: 55908--55954 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
55898 TTTTCTTCTT
* *
55908 ATTTTATTTATTTTATTTATC
1 ATTTTATTTATATTATTTACC
*
55929 TTTTTATTTACTATT-TTTACC
1 ATTTTATTTA-TATTATTTACC
55950 ATTTT
1 ATTTT
55955 TCATTTCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTATTTATATTATTTACC
Found at i:65042 original size:14 final size:14
Alignment explanation
Indices: 65023--65049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65013 ACATAAGGAC
65023 AGCTGGCACTGGAT
1 AGCTGGCACTGGAT
65037 AGCTGGCACTGGA
1 AGCTGGCACTGGA
65050 CAACTGTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.19
Consensus pattern (14 bp):
AGCTGGCACTGGAT
Found at i:66115 original size:17 final size:16
Alignment explanation
Indices: 66084--66117 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
66074 CACGTGAGGA
66084 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
66100 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
66117 T
1 T
66118 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:70225 original size:21 final size:21
Alignment explanation
Indices: 70201--70251 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
70191 AAACTAGAAT
70201 TATTGGTACACCAATATGGGG
1 TATTGGTACACCAATATGGGG
* *
70222 TATTGATACTCCAATATGGGG
1 TATTGGTACACCAATATGGGG
*
70243 TATCGGTAC
1 TATTGGTAC
70252 TACCTTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (21 bp):
TATTGGTACACCAATATGGGG
Found at i:70450 original size:64 final size:64
Alignment explanation
Indices: 70367--70498 Score: 237
Period size: 64 Copynumber: 2.1 Consensus size: 64
70357 ACTGTGCATA
* *
70367 GTATCGGTACCATTTCGTGGTTCTAGAATTTGAGCCTTTATGGTAGTATCGATACTACCTAGTG
1 GTATCGATACCATTTCGTGGTTCTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
*
70431 GTATCGATACCATTTCGTGGTTTTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
1 GTATCGATACCATTTCGTGGTTCTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
70495 GTAT
1 GTAT
70499 TGGTACTACT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (64 bp):
GTATCGATACCATTTCGTGGTTCTAGAATTTGAGCCTTCATGGTAGTATCGATACTACCTAGTG
Found at i:76180 original size:20 final size:20
Alignment explanation
Indices: 76136--76174 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
76126 AGAGAGAATA
*
76136 AAAGTTAAAATGAAAGAGAC
1 AAAGTTAAAATGAAAAAGAC
76156 AAAGTTAATAATGAAAAAG
1 AAAGTTAA-AATGAAAAAG
76175 GAAAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAGTTAAAATGAAAAAGAC
Done.