Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003012.1 Hibiscus syriacus cultivar Beakdansim tig00006240_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: 58326
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:14428 original size:12 final size:12
Alignment explanation
Indices: 14411--14440 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
14401 GAGTATTGAT
14411 GATCAGTGGATC
1 GATCAGTGGATC
14423 GATCAGTGGATC
1 GATCAGTGGATC
14435 GATCAG
1 GATCAG
14441 AATACTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (12 bp):
GATCAGTGGATC
Found at i:18163 original size:39 final size:39
Alignment explanation
Indices: 18096--18184 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 39
18086 TTTAACTCTC
* * *
18096 CAACATGAGTGCCATTATTATTTAATTCACACGTGCCTT
1 CAACATGAGTGACATTATTACTTAATTCACACGCGCCTT
* * * **
18135 CAACATGAGTGACATTCTTCCTTGATTCACGTGCGCCTT
1 CAACATGAGTGACATTATTACTTAATTCACACGCGCCTT
*
18174 CAATATGAGTG
1 CAACATGAGTG
18185 GGATTTAACT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (39 bp):
CAACATGAGTGACATTATTACTTAATTCACACGCGCCTT
Found at i:18351 original size:105 final size:105
Alignment explanation
Indices: 18168--18381 Score: 338
Period size: 105 Copynumber: 2.0 Consensus size: 105
18158 GATTCACGTG
*
18168 CGCCTTCAATATGAGTGGGATTTAACTCATGTGTGCCCCCCAATTCATGTGCGCCATCATGATTT
1 CGCCTTCAATATGAATGGGATTTAACTCATGTGTGCCCCCCAATTCATGTGCGCCATCATGATTT
* * *
18233 CCATGTATACTTGTTGAATTGTCAAAACGGGTGGGCACCA
66 CCATGTACACTTGTTGAAGTATCAAAACGGGTGGGCACCA
* * * *
18273 CGCCTTCAATATGAATGGGATTTAACTCATGTGTGGCCCTCAATTCATGTGCGCTATCATGGTTT
1 CGCCTTCAATATGAATGGGATTTAACTCATGTGTGCCCCCCAATTCATGTGCGCCATCATGATTT
* *
18338 CCATGTGCGCTTGTTGAAGTATCAAAACGGGTGGGCACCA
66 CCATGTACACTTGTTGAAGTATCAAAACGGGTGGGCACCA
18378 CGCC
1 CGCC
18382 AGGAGGAGAT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 99 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (105 bp):
CGCCTTCAATATGAATGGGATTTAACTCATGTGTGCCCCCCAATTCATGTGCGCCATCATGATTT
CCATGTACACTTGTTGAAGTATCAAAACGGGTGGGCACCA
Found at i:24932 original size:19 final size:19
Alignment explanation
Indices: 24908--24944 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
24898 CTATAAGTAA
24908 AATCAAACTTCGAACGCCG
1 AATCAAACTTCGAACGCCG
24927 AATCAAACTTCGAACGCC
1 AATCAAACTTCGAACGCC
24945 CATTGTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (19 bp):
AATCAAACTTCGAACGCCG
Found at i:28806 original size:23 final size:23
Alignment explanation
Indices: 28780--28863 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
28770 CTCGTATAAA
28780 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
28803 TGCACAGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
28826 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
28849 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
28864 TATAATAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:29869 original size:21 final size:21
Alignment explanation
Indices: 29837--29879 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
29827 TGTTTGTTTA
29837 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
29858 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
29879 A
1 A
29880 CAACCCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:34068 original size:23 final size:23
Alignment explanation
Indices: 34042--34102 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
34032 CTCGTATAAA
*
34042 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
34065 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
34088 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
34103 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:38289 original size:2 final size:2
Alignment explanation
Indices: 38284--38315 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38274 ACACACACAC
38284 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
38316 GATGTCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42876 original size:2 final size:2
Alignment explanation
Indices: 42869--42902 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42859 GCTCCAATTC
42869 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
42903 CTTGTGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43212 original size:12 final size:12
Alignment explanation
Indices: 43197--43232 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
43187 GCTGGAGACA
43197 TGGGCACGACGC
1 TGGGCACGACGC
43209 TGGGCACGACGC
1 TGGGCACGACGC
43221 TGGGCACGACGC
1 TGGGCACGACGC
43233 GGTCTGACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.42, T:0.08
Consensus pattern (12 bp):
TGGGCACGACGC
Found at i:49838 original size:24 final size:23
Alignment explanation
Indices: 49811--49878 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
49801 AAGTTTTCTC
*
49811 TTTTCCTTTTCAAGTTCTTTTTAT
1 TTTTCCTTTTCAAGTT-TTATTAT
* *
49835 TTTTCTTTTTTATTA-TTTTATTAT
1 TTTTCCTTTTCA--AGTTTTATTAT
49859 TTTT-CTTTTCAAGTTTTATT
1 TTTTCCTTTTCAAGTTTTATT
49879 TTTATGCTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 1 0.03
22 7 0.19
23 5 0.14
24 20 0.56
25 2 0.06
26 1 0.03
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (23 bp):
TTTTCCTTTTCAAGTTTTATTAT
Found at i:51559 original size:13 final size:13
Alignment explanation
Indices: 51541--51567 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51531 AAGAAATTAT
51541 TTGAATTGTAAAA
1 TTGAATTGTAAAA
51554 TTGAATTGTAAAA
1 TTGAATTGTAAAA
51567 T
1 T
51568 AAATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGAATTGTAAAA
Found at i:52811 original size:42 final size:42
Alignment explanation
Indices: 52764--52845 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
52754 CAAAGATCAA
52764 ATTACATGGATATGAAACT-ACAAGTTAATGTCATTACATTAC
1 ATTACATGGATATGAAA-TAACAAGTTAATGTCATTACATTAC
*
52806 ATTACATGGATATGAAATAACAAGTTAATGTTATTACATT
1 ATTACATGGATATGAAATAACAAGTTAATGTCATTACATT
52846 TACGATGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (42 bp):
ATTACATGGATATGAAATAACAAGTTAATGTCATTACATTAC
Found at i:55450 original size:20 final size:22
Alignment explanation
Indices: 55416--55468 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
55406 CTGAAGAGAG
*
55416 GAAGAGAAAGA-GAAACAAGAA
1 GAAGAGAGAGAGGAAACAAGAA
*
55437 -AAGA-AGAGAGGAAAGAAGAA
1 GAAGAGAGAGAGGAAACAAGAA
55457 GAAGAGAGAGAG
1 GAAGAGAGAGAG
55469 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 4 0.15
22 6 0.22
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (22 bp):
GAAGAGAGAGAGGAAACAAGAA
Found at i:55464 original size:2 final size:2
Alignment explanation
Indices: 55459--55493 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55449 AAGAAGAAGA
55459 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55494 ACAACAGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.