Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006122.1 Hibiscus syriacus cultivar Beakdansim tig00014517_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: 72700
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:982 original size:24 final size:25
Alignment explanation
Indices: 934--989 Score: 105
Period size: 24 Copynumber: 2.3 Consensus size: 25
924 AAATGGTAGA
934 AGCATTATTAATTATAAATTCATCT
1 AGCATTATTAATTATAAATTCATCT
959 AGCATTATTAATTAT-AATTCATCT
1 AGCATTATTAATTATAAATTCATCT
983 AGCATTA
1 AGCATTA
990 ATATATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.43
Consensus pattern (25 bp):
AGCATTATTAATTATAAATTCATCT
Found at i:2241 original size:20 final size:18
Alignment explanation
Indices: 2197--2232 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2187 CAAGAAAAAA
2197 ATTAAAAATAAAAAATAT
1 ATTAAAAATAAAAAATAT
*
2215 ATTAAAAATATAAAATAT
1 ATTAAAAATAAAAAATAT
2233 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAAAAATAAAAAATAT
Found at i:4106 original size:20 final size:19
Alignment explanation
Indices: 4078--4145 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 19
4068 CCAAGCATAA
4078 CCGAACCGAGTTGATCTGAC
1 CCGAACCGAGTTGA-CTGAC
*
4098 CCAAACCGAGTTGACTCGAC
1 CCGAACCGAGTTGACT-GAC
4118 CCGAACCGAGTTGACCTGAC
1 CCGAACCGAGTTGA-CTGAC
4138 CCGAACCG
1 CCGAACCG
4146 CTGACCGCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.26, C:0.35, G:0.24, T:0.15
Consensus pattern (19 bp):
CCGAACCGAGTTGACTGAC
Found at i:4172 original size:22 final size:22
Alignment explanation
Indices: 4147--4194 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
4137 CCCGAACCGC
4147 TGACCGCTCTGACCATTGACTT
1 TGACCGCTCTGACCATTGACTT
*
4169 TGACCGGTCTGACCATTGACTT
1 TGACCGCTCTGACCATTGACTT
4191 TGAC
1 TGAC
4195 TTTGATAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (22 bp):
TGACCGCTCTGACCATTGACTT
Found at i:9446 original size:15 final size:16
Alignment explanation
Indices: 9421--9450 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9411 ATCCCAATTA
9421 TAGTATTAATAGATAT
1 TAGTATTAATAGATAT
9437 TAGT-TTAATAGATA
1 TAGTATTAATAGATA
9451 GAAATCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
TAGTATTAATAGATAT
Found at i:23671 original size:2 final size:2
Alignment explanation
Indices: 23664--23704 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
23654 AAGTCATCCT
23664 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
23705 TAAAATGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41832 original size:35 final size:35
Alignment explanation
Indices: 41781--41851 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
41771 CAGGACCTCC
*
41781 TCTGCCTCTGTGATCGATGGGATGCTGAATATAAG
1 TCTGACTCTGTGATCGATGGGATGCTGAATATAAG
* *
41816 TCTGACTCTGTGATCGATGGGATGTTGATTATAAG
1 TCTGACTCTGTGATCGATGGGATGCTGAATATAAG
41851 T
1 T
41852 TTTCTGATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (35 bp):
TCTGACTCTGTGATCGATGGGATGCTGAATATAAG
Found at i:41966 original size:30 final size:30
Alignment explanation
Indices: 41932--41997 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
41922 TCCTATAGCT
*
41932 ATTAAGATCATTAATGTATTTTCTTCAACC
1 ATTAAGATCATTAATGAATTTTCTTCAACC
*
41962 ATTAAGATCATTAATGAATTTTCTTTAACC
1 ATTAAGATCATTAATGAATTTTCTTCAACC
41992 ATTAAG
1 ATTAAG
41998 GTGCTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (30 bp):
ATTAAGATCATTAATGAATTTTCTTCAACC
Found at i:43196 original size:14 final size:14
Alignment explanation
Indices: 43177--43215 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
43167 TCTGTGTATA
43177 TTCGTTTATATCTG
1 TTCGTTTATATCTG
*
43191 TTCGTTTATGTCTG
1 TTCGTTTATATCTG
43205 TTCGTTTATAT
1 TTCGTTTATAT
43216 TTAGTCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (14 bp):
TTCGTTTATATCTG
Found at i:43295 original size:17 final size:18
Alignment explanation
Indices: 43255--43295 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
43245 AATAAGATCC
43255 AATC-ATTTTGAAACCCA
1 AATCAATTTTGAAACCCA
*
43272 AAT-AATTTT-AAACTCA
1 AATCAATTTTGAAACCCA
43288 AATCAATT
1 AATCAATT
43296 AAAGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.34
Consensus pattern (18 bp):
AATCAATTTTGAAACCCA
Found at i:43459 original size:10 final size:10
Alignment explanation
Indices: 43444--43507 Score: 74
Period size: 10 Copynumber: 6.1 Consensus size: 10
43434 ATTTTTGTGC
43444 ATGTTCGTTT
1 ATGTTCGTTT
*
43454 ATGTTCATTT
1 ATGTTCGTTT
*
43464 ATTGTGTTCGCTT
1 A---TGTTCGTTT
*
43477 ACGTTCGTTT
1 ATGTTCGTTT
43487 ATGTTCGTTT
1 ATGTTCGTTT
43497 ATGTTCGTTT
1 ATGTTCGTTT
43507 A
1 A
43508 CATCTGTTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
10 37 0.82
13 8 0.18
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:44744 original size:147 final size:147
Alignment explanation
Indices: 44471--44769 Score: 537
Period size: 147 Copynumber: 2.0 Consensus size: 147
44461 GAATTTATGA
44471 ATTCACCACCTTCAGGAGAAACGTTAGACCAGTTAACTCCATTCAAGAAAGCATTGAAGGATAAA
1 ATTCACCACCTTCAGGAGAAACGTTAGACCAGTTAACTCCATTCAAGAAAGCATTGAAGGATAAA
44536 GAAACAATGTCAGAAGATGCATTTCCTATGCCTCTCCATGTACCAGTCCCAATGGCTTATATTTC
66 GAAACAATGTCAGAAGATGCATTTCCTATGCCTCTCCATGTACCAGTCCCAATGGCTTATATTTC
44601 AGCCTTTTTATCAGTCG
131 AGCCTTTTTATCAGTCG
* *
44618 ATTCACCACCTTCAGTAGAAATGTTAGACCAGTTAACTCCATTCAAGAAAGCATTGAAGGATAAA
1 ATTCACCACCTTCAGGAGAAACGTTAGACCAGTTAACTCCATTCAAGAAAGCATTGAAGGATAAA
* * *
44683 GAAACAATGTCAGTAGATGCATTTCCTATGCTTCTCCATGTACCAGTCCTAATGG-TGTATATTT
66 GAAACAATGTCAGAAGATGCATTTCCTATGCCTCTCCATGTACCAGTCCCAATGGCT-TATATTT
44747 CAGCCTTTTTATCAGTCG
130 CAGCCTTTTTATCAGTCG
44765 ATTCA
1 ATTCA
44770 ACTGTCGGAG
Statistics
Matches: 146, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
146 1 0.01
147 145 0.99
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (147 bp):
ATTCACCACCTTCAGGAGAAACGTTAGACCAGTTAACTCCATTCAAGAAAGCATTGAAGGATAAA
GAAACAATGTCAGAAGATGCATTTCCTATGCCTCTCCATGTACCAGTCCCAATGGCTTATATTTC
AGCCTTTTTATCAGTCG
Found at i:46383 original size:12 final size:12
Alignment explanation
Indices: 46350--46382 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
46340 TCTCGTAATT
46350 GTGGTTAAAATC
1 GTGGTTAAAATC
*
46362 ATGGTTAAAATC
1 GTGGTTAAAATC
46374 GTGG-TAAAA
1 GTGGTTAAAA
46383 AAATGTGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.30
Consensus pattern (12 bp):
GTGGTTAAAATC
Found at i:47210 original size:17 final size:18
Alignment explanation
Indices: 47173--47213 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
47163 ATATTATGTA
*
47173 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
47191 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
47208 TTTACT
1 TTTACT
47214 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:50896 original size:24 final size:24
Alignment explanation
Indices: 50852--50898 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
50842 ATAAAGAACC
*
50852 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
50876 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
50899 CGACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:57050 original size:133 final size:134
Alignment explanation
Indices: 56535--57649 Score: 1045
Period size: 134 Copynumber: 8.2 Consensus size: 134
56525 GTGAATCAAA
* * ** * *
56535 CTCGATTCAATCTTCCCTGAAG-AATAGTGGAATGAATTAATGTCCCCAGATCTAATTTTCCCTC
1 CTCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTC
* * * * *
56599 AAGAAAAAGAGAAAAAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
65 AAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
***
56664 TCAAA
130 TCTGT
* * ** * *
56669 CTCGATTCAATCTTCCCTGAAG-AACAGTGGAATGAATTAACTTTTCTAAATCTGATTTTCCCTA
1 CTCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCT-
* * * * * * *
56733 AAACAAAAAAGCAGAACAGATCCCTTTCTTTCAAGATTTGATATTCACTGAGTAACTGTGGAACA
64 CAA-GAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
56798 AG--TGT
128 AGTCTGT
* * * ** *
56803 ACTTCCATTCAA-CATTCCCTGAGTAATAGTGGAATTAATCAACATATCCATATCTAATTTTCCC
1 -C-TCGATTCAATC-TTCCCTGAGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCC
* *
56867 TTAAGAAGTAA----AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGCAAC
63 TCAAGAAG-AAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAC
56928 AAGTCTGT
127 AAGTCTGT
* * *
56936 CTCGATTCAATCTTCCTTGAGTAACAATGGAATGAATCAACATCCCCATATCTGA-TTTCCCTTA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * *
57000 GGAAGAAGCGGAACAGATCCCTCCCTTTCAAGATTTGATAATCCCTGAGTAAAAGTGGAACAAGT
66 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
***
57065 CAAA
131 CTGT
* * * * * * *
57069 CTCGATTTAATCTTCCCTGAAG-AATAGTGGAATGAATCAACATCCACAGATTTGA-TTTACCTT
1 CTCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTC
* * * * ** *
57132 AAGGAGAAGAGGAACATATCCCTCTCTTTCAAGATTTGTTATTCTTTGAGTAATAGTGGAACAAG
65 AAGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
57197 TCTGT
130 TCTGT
* * ** *
57202 CTCAATTCAATCTTCCCTGATTTCCCTGAATAATAGTGGAATGAATCAATGTCCCAATATCTGAT
1 CTCGATTCAATCTTCCCTGA-------G--TAACAGTGGAATGAATCAACATCCCCATATCTGAT
* * *
57267 TTTCCCTCAAGAAGAAGTGAAACAAATCTCTCTCTCTCTTTCAA-ACTTTGATATTCCCTGAGTA
57 TTTCCCTCAAGAAGAAGCGGAACAGA--TC-C-CTCTCTTTCAAGA-TTTGATATTCCCTGAGTA
* * *
57331 ACAATGGAACAAGTTTGC
117 ACAGTGGAACAAGTCTGT
* * * *
57349 CTCAATTCAATCTTCCTTGAGTAACAGTGGAATGAATCAACATCCCCAGATTTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * * * *
57414 AGAATAAGCAGTACA-ATTTCCTCTCTTTCAAGATTTGATATTCCCTAAGTAGCAGTGGAACAAG
66 AGAAGAAGCGGAACAGA-TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
57478 TCTGC
130 TCTGT
* * * * * *
57483 CTCAATTCAATCTTCCCTGAGTAACAGTGGAATTAATCAACGTCCCTATGTCTGATTCTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * ** * *
57548 AAAAGAAGCAGAATTGATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGT
66 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
57613 CT-T
131 CTGT
* *
57616 CCTCGATTCAATCTTCCCTGAATAATAGTGGAAT
1 -CTCGATTCAATCTTCCCTGAGTAACAGTGGAAT
57650 TAGTAGACAT
Statistics
Matches: 812, Mismatches: 135, Indels: 68
0.80 0.13 0.07
Matches are distributed among these distances:
129 2 0.00
130 13 0.02
131 93 0.11
132 3 0.00
133 180 0.22
134 244 0.30
135 13 0.02
136 103 0.13
137 1 0.00
138 48 0.06
139 1 0.00
140 1 0.00
142 27 0.03
143 20 0.02
145 2 0.00
146 2 0.00
147 59 0.07
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTGT
Found at i:59214 original size:134 final size:134
Alignment explanation
Indices: 58879--59379 Score: 549
Period size: 134 Copynumber: 3.7 Consensus size: 134
58869 GAAGAGGAAC
* ** * *
58879 ATATCCCTCTCTTTCAAGATTTGTTATTCTTTGAGTAATAGTGGAACAAGTCTGTCTCAATTCAA
1 ATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCAATTCAA
** *
58944 TCTTCCCTGATTTCCCTGAGTACTAGTGAAATGAATCAACGTCCCAATATCTGATTTTCCCTCAA
66 ---T--C----TTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAATATCTGATTTTCCCTCAA
**
59009 GAAGAAGTGGAACA
122 GAAGAAGCAG-ACA
* * *
59023 A-ATCTCTCTCTCTTTTAAAATTTGATATTCCCTGAGTAACAGTGGAACAAGTTTGCCTCAATTC
1 ATATC-C-CTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCAATTC
* * * * * * *
59087 GATCTTCCTTGAGTAAAAGTGGAATGAATCAACATCCCCAGATTTGATTTTCCCTCAAGAATAAG
64 AATCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAATATCTGATTTTCCCTCAAGAAGAAG
59152 CAGTACA
129 CAG-ACA
* *
59159 AT-TCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAGCAGTGGAACAAGTCTGCCTCAATTCAA
1 ATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCAATTCAA
* * * * *
59223 TCTTCCCTGAGTAACAGTGGAATTAATCAACGTCCCTATATCTGATTCTCCCTCAAAAAGAAGCA
66 TCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAATATCTGATTTTCCCTCAAGAAGAAGCA
59288 GA-A
131 GACA
* * * * *
59291 TTGATCCCTCTCTTTCAAGATTTGATCTTCCTTGAGTAACAGTGGAACAAGTCTACCTCGATTCA
1 AT-ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCAATTCA
* *
59356 ATCTTCCCTGAATAATAGTGGAAT
65 ATCTTCCCTGAGTAAAAGTGGAAT
59380 CAGTAGACAT
Statistics
Matches: 306, Mismatches: 46, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
132 2 0.01
133 1 0.00
134 186 0.61
135 1 0.00
136 59 0.19
140 1 0.00
142 1 0.00
143 3 0.01
144 2 0.01
145 50 0.16
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (134 bp):
ATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCAATTCAA
TCTTCCCTGAGTAAAAGTGGAATGAATCAACGTCCCAATATCTGATTTTCCCTCAAGAAGAAGCA
GACA
Found at i:66410 original size:3 final size:3
Alignment explanation
Indices: 66402--66443 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
66392 AATATTTTAT
66402 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
66444 CATATACGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66652 original size:21 final size:21
Alignment explanation
Indices: 66614--66653 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
66604 TGGTTTATGT
* **
66614 AAAAATAAATATTTAAATTTA
1 AAAAATAAAAATAAAAATTTA
66635 AAAAATAAAAATAAAAATT
1 AAAAATAAAAATAAAAATT
66654 ATTAAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATAAAAATAAAAATTTA
Found at i:67057 original size:23 final size:23
Alignment explanation
Indices: 67003--67060 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
66993 ATAGTCTAAT
* *
67003 ATTATGGCCTCTATTAATATTTA
1 ATTATGGCTTCGATTAATATTTA
*
67026 ATTCTGGCTTCGATTAATATTTA
1 ATTATGGCTTCGATTAATATTTA
67049 ATTATGGCTTCG
1 ATTATGGCTTCG
67061 TCTCTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (23 bp):
ATTATGGCTTCGATTAATATTTA
Found at i:67071 original size:27 final size:26
Alignment explanation
Indices: 67011--67072 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 26
67001 ATATTATGGC
*
67011 CTCTATTAATATTTAATTCTGGCTTCG
1 CTCTA-TAATATTTAATTATGGCTTCG
*
67038 --AT-TAATATTTAATTATGGCTTCG
1 CTCTATAATATTTAATTATGGCTTCG
67061 TCTCTATAATAT
1 -CTCTATAATAT
67073 AATTGAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
23 20 0.71
25 1 0.04
26 1 0.04
27 6 0.21
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (26 bp):
CTCTATAATATTTAATTATGGCTTCG
Found at i:67142 original size:23 final size:23
Alignment explanation
Indices: 67098--67142 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
67088 TATTAAAAAG
*
67098 ACTAGAAATTAAATTATATATAA
1 ACTAGAAATTAAATAATATATAA
*
67121 ACTAG-AATTAAAATAATTTATA
1 ACTAGAAATT-AAATAATATATA
67143 TAAAGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (23 bp):
ACTAGAAATTAAATAATATATAA
Found at i:67226 original size:19 final size:19
Alignment explanation
Indices: 67179--67227 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
67169 AAATAAACTC
*
67179 TTCATCAAAAGTAAGTCTT
1 TTCATCAAATGTAAGTCTT
67198 TTCATCAAATGTAAGTCTT
1 TTCATCAAATGTAAGTCTT
67217 TTCATCAAATG
1 TTCATCAAATG
67228 GTCTTAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (19 bp):
TTCATCAAATGTAAGTCTT
Found at i:69865 original size:25 final size:25
Alignment explanation
Indices: 69837--69893 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
69827 AAATGGTAGA
69837 AGCATTATTAATTATAAATTCATCT
1 AGCATTATTAATTATAAATTCATCT
69862 AGCATTATTAATTATAAATTCATCT
1 AGCATTATTAATTATAAATTCATCT
69887 AGCATTA
1 AGCATTA
69894 ATTATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
AGCATTATTAATTATAAATTCATCT
Found at i:69896 original size:22 final size:23
Alignment explanation
Indices: 69842--69899 Score: 91
Period size: 25 Copynumber: 2.5 Consensus size: 23
69832 GTAGAAGCAT
69842 TATTAATTATAAATTCATCTAGC
1 TATTAATTATAAATTCATCTAGC
69865 ATTATTAATTATAAATTCATCTAGC
1 --TATTAATTATAAATTCATCTAGC
69890 -ATTAATTATA
1 TATTAATTATA
69900 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 10 0.30
25 23 0.70
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (23 bp):
TATTAATTATAAATTCATCTAGC
Found at i:71131 original size:14 final size:14
Alignment explanation
Indices: 71109--71143 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
71099 ATCCTCAAGA
71109 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
*
71123 AAAATATTAAAAAT
1 AAAAAATTAAAAAT
*
71137 ATAAAAT
1 AAAAAAT
71144 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Found at i:71142 original size:16 final size:15
Alignment explanation
Indices: 71117--71146 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
71107 GAAAAAAATT
71117 AAAAATAAAATATTA
1 AAAAATAAAATATTA
71132 AAAATATAAAATATT
1 AAAA-ATAAAATATT
71147 TTTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATAAAATATTA
Done.