Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000982.1 Hibiscus syriacus cultivar Beakdansim tig00001965_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: 56396
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:241 original size:15 final size:15
Alignment explanation
Indices: 221--250 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
211 TACCTGCCTG
221 ATGGTATCAGTATCT
1 ATGGTATCAGTATCT
*
236 ATGGTATCGGTATCT
1 ATGGTATCAGTATCT
251 CCTTTAGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (15 bp):
ATGGTATCAGTATCT
Found at i:2899 original size:2 final size:2
Alignment explanation
Indices: 2892--2917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2882 CATGTTTTTA
2892 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
2918 TACATGTACC
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):
AT
Found at i:4145 original size:2 final size:2
Alignment explanation
Indices: 4138--4164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4128 TAATTATCAT
4138 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 T
4165 CCTTTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5598 original size:23 final size:24
Alignment explanation
Indices: 5555--5601 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
5545 TAAACAAAAT
*
5555 TTTATTAATCCGAAAATTCCTAAG
1 TTTATTAATCCGAAAAATCCTAAG
5579 TTTATTAATCC-AAAAATCCTAAG
1 TTTATTAATCCGAAAAATCCTAAG
5602 GAGAAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (24 bp):
TTTATTAATCCGAAAAATCCTAAG
Found at i:6390 original size:28 final size:28
Alignment explanation
Indices: 6336--6393 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
6326 CTTCAATTAT
*
6336 AATATTATGTCGTAGAGTCATTCTTTGA
1 AATATTATGTCGTAGAGTCAGTCTTTGA
* * *
6364 AATATTATGTCGTCGAGTTAGTGTTTGA
1 AATATTATGTCGTAGAGTCAGTCTTTGA
6392 AA
1 AA
6394 GCAACGATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (28 bp):
AATATTATGTCGTAGAGTCAGTCTTTGA
Found at i:7124 original size:78 final size:76
Alignment explanation
Indices: 7002--7232 Score: 385
Period size: 75 Copynumber: 3.0 Consensus size: 76
6992 AATTTTATCC
* * *
7002 TCAATTATTTAAATTTACTT-TTTTTTAGCACTTAAATGTATAATTATATTGTTTATTTTTTTAG
1 TCAATTATTTAAATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
*
7066 TTTATTAATTT
66 TTTATTAATGT
*
7077 TCAATTATTTAAATTTAATTAGTTTTTATAACACTAAAATGTATAATTATATTGTTTATTTTTTG
1 TCAATTATTTAAATTTAATTA-TTTTT-TAACACTTAAATGTATAATTATATTGTTTATTTTTTG
7142 AGTTTATTAATGT
64 AGTTTATTAATGT
7155 TCAATTATTT-AATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
1 TCAATTATTTAAATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
7219 TTTATTAATGT
66 TTTATTAATGT
7230 TCA
1 TCA
7233 TATTTATTAC
Statistics
Matches: 147, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
75 71 0.48
76 5 0.03
77 15 0.10
78 56 0.38
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (76 bp):
TCAATTATTTAAATTTAATTATTTTTTAACACTTAAATGTATAATTATATTGTTTATTTTTTGAG
TTTATTAATGT
Found at i:7229 original size:36 final size:36
Alignment explanation
Indices: 7114--7229 Score: 114
Period size: 36 Copynumber: 3.1 Consensus size: 36
7104 ATAACACTAA
7114 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
1 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
* **
7150 AATGT-TCAATTATTTAATT-TAATTATTTTTTAACACTTA--
1 AATGTAT-AATTA--T-ATTGT--TTATTTTTTGA-GTTTATT
7189 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
1 AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
7225 AATGT
1 AATGT
7230 TCATATTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
34 3 0.05
35 11 0.17
36 18 0.29
37 2 0.03
38 2 0.03
39 13 0.21
40 11 0.17
41 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.58
Consensus pattern (36 bp):
AATGTATAATTATATTGTTTATTTTTTGAGTTTATT
Found at i:21221 original size:19 final size:19
Alignment explanation
Indices: 21197--21235 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21187 AACTAGTACA
21197 TAGTGAAATAAACAATTCT
1 TAGTGAAATAAACAATTCT
*
21216 TAGTGAAATAAGCAATTCT
1 TAGTGAAATAAACAATTCT
21235 T
1 T
21236 CTCCTAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (19 bp):
TAGTGAAATAAACAATTCT
Found at i:33129 original size:25 final size:25
Alignment explanation
Indices: 33101--33160 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
33091 TCATAAACAA
33101 AATATGAGTTCATAATACATACCAT
1 AATATGAGTTCATAATACATACCAT
33126 AATATGAGTTCATAATACATACCAT
1 AATATGAGTTCATAATACATACCAT
33151 AATATGAGTT
1 AATATGAGTT
33161 AAAGTCCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (25 bp):
AATATGAGTTCATAATACATACCAT
Found at i:35758 original size:23 final size:23
Alignment explanation
Indices: 35727--35770 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35717 TACATTTATG
*
35727 GCACGTATGTGATATTGGTGCCT
1 GCACATATGTGATATTGGTGCCT
*
35750 GCACATATGTGATGTTGGTGC
1 GCACATATGTGATATTGGTGC
35771 GATGTATTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (23 bp):
GCACATATGTGATATTGGTGCCT
Found at i:43357 original size:18 final size:18
Alignment explanation
Indices: 43324--43374 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
43314 TTAATTAAAC
*
43324 ATACAT-ATAT-ATATAT
1 ATACATGATATAACATAT
*
43340 ATATAT-ATATAAACATAT
1 ATACATGATAT-AACATAT
43358 ATACATGATATAACATA
1 ATACATGATATAACATA
43375 ATAGTAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (18 bp):
ATACATGATATAACATAT
Found at i:45113 original size:3 final size:3
Alignment explanation
Indices: 45107--45145 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
45097 ATATTAGTAG
45107 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45146 CTTGGACGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47186 original size:81 final size:81
Alignment explanation
Indices: 47093--47982 Score: 1226
Period size: 81 Copynumber: 11.0 Consensus size: 81
47083 ATTGTTTTAA
* * *
47093 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTTAATCATGTCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
47158 AGGCTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
47174 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGAAAAAAAGGTGTAAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
47239 ATGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
47255 AGTAAAACATTAATTGTCTAGCTGTGCATTTGACAGAAATGTGTTAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
47320 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * * * * * *
47336 AGTAAAACATTAATTGCCTAGTTCTGCATTCGAAAGAAATGTATCAATAATG-CAGTAAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
47400 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * *
47416 AGTAAAAGATTCATTACCTAGCTGTGCATTTTACAAAAAGGTGTCAATCATGCTAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
* *
47481 AGGCTGAATACCTTTG
66 AGGTTAAATACCTTTG
* * ** * *
47497 AGTAAAAGATTCATTGCCTAGCTGTGCATTTGACATAAATATGTCAGTCATGCCAATTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
47562 AGGTTAAATACCTTTT
66 AGGTTAAATACCTTTG
* *
47578 AGTAAAAGATTAATTGCCTAGTTGTACATTTGACAGAAAGGTGTCGAA-CATGCCAGTTAGATGA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTC-AATCATGCCAGTTAGATGA
47642 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * *
47659 TGTAAAAGATTAATTACCTAGCTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
47724 AGGTTAAATATCTTTG
66 AGGTTAAATACCTTTG
* * * *
47740 AGTAAAAGATTAATTGCCTAGCTGTGCATTTAATATAAAGGTGTCAATCATGCCAATTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
* *
47805 ATGTTAAATACATTTG
66 AGGTTAAATACCTTTG
* * * *
47821 AGTAAAAGATTAATTGCCTAGTTTTTCATTTGACAGAAAGGTGTCAATCATACCAGTTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
47886 TGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
** * * * *
47902 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGGTAGAAAGGTGCCAATAATGCAAGGTAGATGAA
1 AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
*
47967 AGGTTAAATTCCTTTG
66 AGGTTAAATACCTTTG
47983 GCATGAAAAG
Statistics
Matches: 711, Mismatches: 95, Indels: 6
0.88 0.12 0.01
Matches are distributed among these distances:
80 69 0.10
81 641 0.90
82 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:48049 original size:46 final size:46
Alignment explanation
Indices: 47982--48244 Score: 341
Period size: 46 Copynumber: 5.7 Consensus size: 46
47972 AAATTCCTTT
*
47982 GGCATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
*
48028 GGCATGAAAGGATTG-CATAAATGAAAATGCATAACGGTACATTATA
1 GGCATGAAAGGA-TGCCATAAATGAAAATGCATAACGGTGCATTATA
* * *
48074 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGAATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * *
48120 GACATGAAAGGATGTCGTAAATGAAAATGCATAACGGTACATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * * *
48166 GGCATGAAA-GATGCAATAAATGAAAATGCTTAACGGTGAATAATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* ** *
48211 GGCATAAAAGGATGCCACCAATGAAAATACATAA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAA
48245 TGGTATATTA
Statistics
Matches: 186, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
45 38 0.20
46 146 0.78
47 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
Found at i:48237 original size:137 final size:138
Alignment explanation
Indices: 47984--48248 Score: 392
Period size: 137 Copynumber: 1.9 Consensus size: 138
47974 ATTCCTTTGG
*
47984 CATGAAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATAGGCATGAAAGGATTGCATAAA
1 CATGAAAAGATGCCATAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGATTGCATAAA
* * * *
48049 TGAAAATGCATAACGGTACATTATAGGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGA
66 TGAAAATGCATAACGGTACATAATAGGCATAAAAGGATGCCACAAATGAAAATACATAATGGTGA
48114 ATTATCGA
131 ATTATCGA
* * *
48122 CATGAAAGGATGTCGTAAATGAAAATGCATAACGGTACATTATAGGCATGAAA-GA-TGCAATAA
1 CATGAAAAGATGCCATAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGATTGC-ATAA
* * *
48185 ATGAAAATGCTTAACGGTGA-ATAATTGGCATAAAAGGATGCCACCAATGAAAATACATAATGGT
65 ATGAAAATGCATAACGGT-ACATAATAGGCATAAAAGGATGCCACAAATGAAAATACATAATGGT
48249 ATATTAACAA
Statistics
Matches: 114, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
136 3 0.03
137 61 0.54
138 50 0.44
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.23
Consensus pattern (138 bp):
CATGAAAAGATGCCATAAATGAAAATGCATAACGGTACATTATAGGCATGAAAGGATTGCATAAA
TGAAAATGCATAACGGTACATAATAGGCATAAAAGGATGCCACAAATGAAAATACATAATGGTGA
ATTATCGA
Done.