Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008870.1 Hibiscus syriacus cultivar Beakdansim tig00112105_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: 38476
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:186 original size:47 final size:47
Alignment explanation
Indices: 124--250 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 47
114 TCAACTTCTC
* **
124 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTTTA
1 AGAT-TGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
172 AGATTGATATTCCCTTC--AG-AAGCGGAACAAG--TCTCTTCTCCA
1 AGATTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
214 AGATTTGATATTCCCTTCAGAGTAAGT-GAACAAGTCT
1 AGA-TTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
251 GATTCAATGG
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
42 12 0.18
43 14 0.21
44 10 0.15
45 11 0.16
46 3 0.04
47 14 0.21
48 4 0.06
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (47 bp):
AGATTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:199 original size:108 final size:106
Alignment explanation
Indices: 15--209 Score: 286
Period size: 108 Copynumber: 1.8 Consensus size: 106
5 ATCACTCCCC
* * *
15 CAGATCTGATATTCCCTTTAGAGTAATTGGAACATGTCTCTCTCCAAGATTGATATTCCCTTCAG
1 CAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTCCAAGATTGATATTCCCTTCA-
*
80 AGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTTCT
65 AGTAAGCGGAACAAGTCT-CTTCGATTCAATGGATCAACTTCT
*
123 CAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTTTAAGATTGATATTCCCTT
1 CAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTC-TC--CAAGATTGATATTCCCTT
188 C-AG-AAGCGGAACAAGTCTCTTC
63 CAAGTAAGCGGAACAAGTCTCTTC
210 TCCAAGATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
107 4 0.05
108 53 0.67
109 4 0.05
111 18 0.23
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (106 bp):
CAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTCCAAGATTGATATTCCCTTCAA
GTAAGCGGAACAAGTCTCTTCGATTCAATGGATCAACTTCT
Found at i:310 original size:148 final size:152
Alignment explanation
Indices: 43--336 Score: 415
Period size: 149 Copynumber: 2.0 Consensus size: 152
33 TAGAGTAATT
*
43 GGAACATGTCTCTCTCCAAGATTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCGATTC
1 GGAACAAGTCTCTCTCCAAGATTGATATTCCCTTCAGAGTAAGTGGAACAAG-CTGCTTCGATTC
* * * ** *
108 AATGGATCAACTTCTCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTT-TA
65 AATGGATAAACTTCCCAGATCTGATATTCCCTTCAAAGTAAGCAGAACAGGTCTCTCTT-TTCCA
172 AGA-TTGATATTCCCTTCAGAAGC
129 AGATTTGATATTCCCTTCAGAAGC
195 GGAACAAGTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGT-GAACAAG-T-C-T-GATT
1 GGAACAAGTCTC-TCTCCAAGA-TTGATATTCCCTTCAGAGTAAGTGGAACAAGCTGCTTCGATT
*
255 CAATGGATAAACTTCCCCAGATCTGATATTCCCTTCAAAGTAA-CAGAACATGTCTCTCTTTTCC
64 CAATGGATAAACTT-CCCAGATCTGATATTCCCTTCAAAGTAAGCAGAACAGGTCTCTCTTTTCC
319 AAGATTTGATATTCCCTT
128 AAGATTTGATATTCCCTT
337 TAGAGAAAGT
Statistics
Matches: 129, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
147 2 0.02
148 35 0.27
149 40 0.31
150 1 0.01
151 1 0.01
152 11 0.09
153 16 0.12
154 23 0.18
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (152 bp):
GGAACAAGTCTCTCTCCAAGATTGATATTCCCTTCAGAGTAAGTGGAACAAGCTGCTTCGATTCA
ATGGATAAACTTCCCAGATCTGATATTCCCTTCAAAGTAAGCAGAACAGGTCTCTCTTTTCCAAG
ATTTGATATTCCCTTCAGAAGC
Found at i:459 original size:112 final size:112
Alignment explanation
Indices: 172--560 Score: 561
Period size: 113 Copynumber: 3.6 Consensus size: 112
162 CTCTTCTTTA
* *
172 AGAT-TGATATTCCCTTC--AG-AAGCGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
231 CAGAGTAAGT-GAACAAGTCT----GATTCAATGGATAAACTTCCCC
66 CAGAGTAAGTGGAACAAGTCTACCCGATTCAATGGATCAACTTCCCC
* * *
273 AGATCTGATATTCCCTTCAAAGTAA-CAGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * * *
337 TAGAGAAAGTGGAACAAGTCTACCCGATTCAATGGATCAGCTTTCCC
66 CAGAGTAAGTGGAACAAGTCTACCCGATTCAATGGATCAACTTCCCC
*
384 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTTTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
449 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAATGGATCAAC-TCCCTC
66 CAGAGTAAGTGGAACAAGTCTACCC-GATTCAATGGATCAACTTCCC-C
*
497 AGATCTGATATTCCCTTCAGATTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCT
561 GAGTGACAGT
Statistics
Matches: 256, Mismatches: 18, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
101 4 0.02
102 13 0.05
104 9 0.04
105 2 0.01
106 35 0.14
107 10 0.04
111 43 0.17
112 62 0.24
113 78 0.30
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (112 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTACCCGATTCAATGGATCAACTTCCCC
Found at i:1618 original size:13 final size:12
Alignment explanation
Indices: 1602--1644 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
1592 TAATAATGTT
1602 ATATATTACATAC
1 ATATATTA-ATAC
1615 ATATATTAATAC
1 ATATATTAATAC
*
1627 ATGATATATAATAA
1 AT-ATAT-TAATAC
1641 ATAT
1 ATAT
1645 TTTCTGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 6 0.22
13 14 0.52
14 7 0.26
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (12 bp):
ATATATTAATAC
Found at i:8825 original size:182 final size:184
Alignment explanation
Indices: 8451--8814 Score: 582
Period size: 182 Copynumber: 2.0 Consensus size: 184
8441 AAATTAAATG
*
8451 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
8516 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* *
8581 GAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTAATAT
131 GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
8635 TTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATAT-ATTATAAAATAAAAAATTT-
1 TTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTC
* * *
8697 ATAT-ATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
64 AGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
* *
8761 TTGGGTTTTAAATGGTTTGGGCTGAG-CCATATG-T-TATAT-ATATATTTAATAT
129 TTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
8813 TT
1 TT
8815 AAAATTTAAT
Statistics
Matches: 170, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
178 15 0.09
179 5 0.03
180 1 0.01
181 6 0.04
182 81 0.48
183 19 0.11
184 43 0.25
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (184 bp):
TTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTATATATAATATATTTAATAT
Found at i:22223 original size:87 final size:87
Alignment explanation
Indices: 22075--22249 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
22065 ACGCAAGTTT
*
22075 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGGATCCGGGG
1 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGCATCCGGGG
22140 GATGACTGATCGTAAACAACTC
66 GATGACTGATCGTAAACAACTC
*
22162 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGCATCCGTGG
1 CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGCATCCGGGG
*
22227 GATGACTGCTCGTAAACAACTC
66 GATGACTGATCGTAAACAACTC
22249 C
1 C
22250 GGTTCAAGAA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (87 bp):
CTTGCAAGGAAAGCATACAAGAATTTGTACCTCGCATCTGTTTCCATTCAAACAGGCATCCGGGG
GATGACTGATCGTAAACAACTC
Done.