Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001396.1 Hibiscus syriacus cultivar Beakdansim tig00002726_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: 227762
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:91087 original size:36 final size:36
Alignment explanation
Indices: 91019--91088 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
91009 AAAACAACAA
* *
91019 AATAGAATAAATAAAATAAAATAAAATTTAAAAAGT
1 AATAAAATAAATAAAATAAAATAAAATATAAAAAGT
* *
91055 AATAAAATAAATGAAAT-AAATATATATATAAAAA
1 AATAAAATAAATAAAATAAAATA-AAATATAAAAA
91089 CCATAATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (36 bp):
AATAAAATAAATAAAATAAAATAAAATATAAAAAGT
Found at i:93006 original size:106 final size:106
Alignment explanation
Indices: 92872--94239 Score: 2360
Period size: 106 Copynumber: 12.9 Consensus size: 106
92862 AGTCCAATAT
* * *
92872 CCTTCGTCGTGAAGTTGAAATTGTGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
92937 GGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
92978 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAATTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
93043 GGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
93084 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
93149 GGCTCCGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
93190 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
93255 GGCTCTGAAATTGAGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
93296 CCTTCGTCGTGAAATTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
93361 GGCTCTGAAATTGAGAAGTTAG-TTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTT-GTTTATTGACAACCAGCGGTC
* *
93402 CCTTCTTCGTGAAATTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
93467 GGCTCTGAATTTGAGAAGTTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
93508 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTTCAATATCCTTCATTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
93573 GGCTCTGAAATTGAGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
93614 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTAGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
93679 GGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
93720 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
93785 GGCTCTGAATTTGAGAAGTTGTTTATTGACAACTAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
93826 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
93891 GGCTCCGACATTGGGAAGTTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
93932 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAGTT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
93997 GGCTCTGAATTTGAGAAGTTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
* *
94038 CCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * *
94103 GGCTCTGAAATTGGGAAATTGTCTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
94144 CTTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * *
94209 GGCTCCGAAATTGGGAAATTGTTTGTTGACA
66 GGCTCTGAAATTGAGAAGTTGTTTATTGACA
94240 GACAACTTTT
Statistics
Matches: 1198, Mismatches: 62, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
105 1 0.00
106 1197 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
Found at i:96373 original size:26 final size:26
Alignment explanation
Indices: 96318--96375 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
96308 GAGACATGTG
*
96318 AATGCAATGAAAAAAAAAGGAATCAT
1 AATGCAATGAAAAAAAAAGGAATCAA
* * *
96344 AATGCGAATGTAAAGAAAAGTAA-CAA
1 AATGC-AATGAAAAAAAAAGGAATCAA
96370 AATGCA
1 AATGCA
96376 CAACATGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 12 0.44
27 14 0.52
ACGTcount: A:0.59, C:0.09, G:0.17, T:0.16
Consensus pattern (26 bp):
AATGCAATGAAAAAAAAAGGAATCAA
Found at i:98133 original size:9 final size:9
Alignment explanation
Indices: 98121--98179 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
98111 AAAAACAACA
*
98121 AAATAGAAT
1 AAATAAAAT
98130 AAATAAAAT
1 AAATAAAAT
98139 AAAATAAAATT
1 -AAATAAAA-T
* *
98150 TAA-AAAGT
1 AAATAAAAT
98158 -AATAAAAT
1 AAATAAAAT
*
98166 AAATGAAAT
1 AAATAAAAT
98175 AAATA
1 AAATA
98180 TATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 2 0.05
8 5 0.12
9 22 0.55
10 10 0.25
11 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:100397 original size:185 final size:185
Alignment explanation
Indices: 100076--100468 Score: 639
Period size: 185 Copynumber: 2.1 Consensus size: 185
100066 ATTAACTAAA
* * *
100076 ATAAAAT-TGTAAATATATTATATATAACATATGAGCTTAGCCCAAACTATTTAAAACTCAATTA
1 ATAAAATAT-TAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTA
100140 ATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAA
65 ATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAA
* *
100205 ATTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTCTGAATT
130 ATTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTT-TGAATT
*
100262 A-AAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAA
1 ATAAAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAA
* * *
100326 TAATTTAAGATCTAGTAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAA
66 TAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAA
*
100391 TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATT
131 TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATT
* *
100446 ATAAAATATTTAAT-TTTTATATA
1 ATAAAATATTAAATATATTATATA
100469 AATTAGAAAA
Statistics
Matches: 193, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
184 14 0.07
185 177 0.92
186 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (185 bp):
ATAAAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAA
TAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAA
TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATT
Found at i:102095 original size:21 final size:21
Alignment explanation
Indices: 102038--102100 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
102028 CATAAAACGA
*
102038 AAACTCTAAAATCACAAA-TTCT
1 AAACTC-AAAATCACAAACCT-T
*
102060 AAACTCAAAAACACAAACCTT
1 AAACTCAAAATCACAAACCTT
102081 AAATCTC-AAATCAC-AACCTT
1 AAA-CTCAAAATCACAAACCTT
102101 CATCGAGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.17
21 20 0.56
22 10 0.28
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACTCAAAATCACAAACCTT
Found at i:113045 original size:2 final size:2
Alignment explanation
Indices: 113032--113077 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
113022 TTTTAAGAAA
113032 AT AT AT -T A- AT AT AT -T A- 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 AT AT AT AT
113070 AT AT AT AT
1 AT AT AT AT
113078 TTAAATAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113442 original size:3 final size:3
Alignment explanation
Indices: 113434--113493 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
113424 TTATATGACT
*
113434 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT A-A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
113479 AT- ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA A
113494 ACATATAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:113474 original size:28 final size:28
Alignment explanation
Indices: 113434--113493 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
113424 TTATATGACT
*
113434 ATAATAATAATAAAT-AATAATAATAATA
1 ATAATAATAATAAATAAAT-ATAATAAAA
*
113462 ATAATAATAATAATTAAATATAATAAAA
1 ATAATAATAATAAATAAATATAATAAAA
113490 ATAA
1 ATAA
113494 ACATATAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATAATAATAAATAAATATAATAAAA
Found at i:115005 original size:13 final size:14
Alignment explanation
Indices: 114977--115008 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
114967 AATAGGCCTG
114977 TAATATTTATTTAA
1 TAATATTTATTTAA
114991 TAATATTTA-TTAA
1 TAATATTTATTTAA
115004 TAATA
1 TAATA
115009 ATAAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTATTTAA
Found at i:115007 original size:3 final size:3
Alignment explanation
Indices: 115001--115045 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
114991 TAATATTTAT
*
115001 TAA TAA TAA TAA AAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
115046 TACAAAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:115789 original size:45 final size:45
Alignment explanation
Indices: 115719--116155 Score: 662
Period size: 45 Copynumber: 9.7 Consensus size: 45
115709 AGGCTTTAAA
* * * *
115719 AAAACATTATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTCG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
115764 AAAACATTATGGACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
115809 AAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
115854 AAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
115899 AAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGATTTT-
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTG
* * *
115944 -AAACATCCTGTACTTAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
115988 AAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTG
* *
116034 AAAACATTATGCACTGAAGGGCTTACAGATTACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
116079 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTA
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTG
* * *
116125 AAAACATCCTGCACTGAAGGTCTTATAGATG
1 AAAACATCATGCACTGAAGGGCTTACAGATG
116156 TGGGAAATAG
Statistics
Matches: 363, Mismatches: 24, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
43 4 0.01
44 37 0.10
45 244 0.67
46 78 0.21
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
Found at i:116828 original size:22 final size:22
Alignment explanation
Indices: 116803--116879 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
116793 AATAAAGATT
*
116803 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
116825 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
* * *
116847 TCATCTTTGAAGAGTGTATCTA
1 TCATCTTTGAAAAGAGAATCTA
116869 TCATCTTTGAA
1 TCATCTTTGAA
116880 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:116880 original size:22 final size:22
Alignment explanation
Indices: 116820--116886 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
116810 TAAAAAGAGA
* * *
116820 ATCTATCATCTTTGAAAAGAGA
1 ATCTATCATCTTTGAAGAGTGT
*
116842 ATATATCATCTTTGAAGAGTGT
1 ATCTATCATCTTTGAAGAGTGT
*
116864 ATCTATCATCTTTGAAGAATGT
1 ATCTATCATCTTTGAAGAGTGT
116886 A
1 A
116887 GATGTAGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
ATCTATCATCTTTGAAGAGTGT
Found at i:125593 original size:18 final size:19
Alignment explanation
Indices: 125563--125599 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
125553 ATCATAAAAC
125563 TTTTTGTCCATTT-ATGAA
1 TTTTTGTCCATTTGATGAA
125581 TTTTT-TCCAATTTGATGAA
1 TTTTTGTCC-ATTTGATGAA
125600 CTGTCTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 9 0.53
19 5 0.29
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTTGTCCATTTGATGAA
Found at i:127118 original size:146 final size:148
Alignment explanation
Indices: 126911--127180 Score: 431
Period size: 146 Copynumber: 1.8 Consensus size: 148
126901 TAATTTTTAA
* * *
126911 AAAATATATTAATATATATATTTATCTAAATAAGATATTTATTTACTTAGAAATATCAGAAAATG
1 AAAATAAATTAATATATATATTTATCAAAATAAGATATTTATTTACTTAGAAATATCAGAAAAAG
*
126976 ACTTCTAGGTGCTTTAAGACAGCCTA-TTTCTTAATATTAAAAAATAAATAAATATTAATAAAAT
66 ACTTCTAGGTGCTTTAAGACAGCCCATTTTCTTAATATTAAAAAATAAATAAATATTAATAAAAT
127040 ATTTCTCTAAAAATAATT
131 ATTTCTCTAAAAATAATT
* * *
127058 AAAATAAATTAATGTATA-ATTTAT-AAAACTAGGATATTTATTTATTTA-AGAATATCAGAAAA
1 AAAATAAATTAATATATATATTTATCAAAA-TAAGATATTTATTTACTTAGA-AATATCAGAAAA
127120 AGACTTCTAGGTGCTTTAAGACAGCCCATTTTCTTAATATTAAAAAATAAATAAATATTAA
64 AGACTTCTAGGTGCTTTAAGACAGCCCATTTTCTTAATATTAAAAAATAAATAAATATTAA
127181 AATATTATTA
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
145 4 0.04
146 61 0.54
147 48 0.42
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (148 bp):
AAAATAAATTAATATATATATTTATCAAAATAAGATATTTATTTACTTAGAAATATCAGAAAAAG
ACTTCTAGGTGCTTTAAGACAGCCCATTTTCTTAATATTAAAAAATAAATAAATATTAATAAAAT
ATTTCTCTAAAAATAATT
Found at i:128771 original size:13 final size:14
Alignment explanation
Indices: 128743--128774 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
128733 AATAGGCATG
128743 TAATATTTATTTAA
1 TAATATTTATTTAA
128757 TAATATTTA-TTAA
1 TAATATTTATTTAA
128770 TAATA
1 TAATA
128775 ATAATAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTATTTAA
Found at i:128773 original size:3 final size:3
Alignment explanation
Indices: 128767--128812 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
128757 TAATATTTAT
128767 TAA TAA TAA TAA TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
128813 ACAAAATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:128779 original size:22 final size:22
Alignment explanation
Indices: 128767--128812 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
128757 TAATATTTAT
128767 TAATAATAATAATAATAGATAA
1 TAATAATAATAATAATAGATAA
128789 TAATAATAATAATAATA-ATAA
1 TAATAATAATAATAATAGATAA
128810 TAA
1 TAA
128813 ACAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAATAGATAA
Found at i:130104 original size:16 final size:17
Alignment explanation
Indices: 130065--130106 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
130055 ATGTATTTGG
*
130065 AATAAT-TTATAACATT
1 AATAATATTATAACATA
130081 AATAATATTATAA-ATA
1 AATAATATTATAACATA
*
130097 AATCATATTA
1 AATAATATTA
130107 AATTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATATTATAACATA
Found at i:132227 original size:21 final size:21
Alignment explanation
Indices: 132189--132228 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
132179 TGAATTTCAA
*
132189 AGTTCATATTTTATTCAATTT
1 AGTTCATATTTCATTCAATTT
132210 AGTTCATACTTTCA-TCAAT
1 AGTTCATA-TTTCATTCAAT
132229 ATTTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50
Consensus pattern (21 bp):
AGTTCATATTTCATTCAATTT
Found at i:132466 original size:3 final size:3
Alignment explanation
Indices: 132458--132502 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
132448 ACTGAATTTA
132458 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
132503 GTTATAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:133820 original size:20 final size:20
Alignment explanation
Indices: 133697--133868 Score: 102
Period size: 20 Copynumber: 8.6 Consensus size: 20
133687 AAATGACCAA
**
133697 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGATTTC
* **
133717 CAATTTCGCAAC-TTAGTTTC
1 CAAATTCGCAACGCGA-TTTC
* *
133737 CAAATTCGCAACGCGAATCTG
1 CAAATTCGCAACGCG-ATTTC
* ** *
133758 TAAA-TCGCAACGCGAACCTG
1 CAAATTCGCAACGCG-ATTTC
* *
133778 TAAA-TCGCAACAC-ATAATT-
1 CAAATTCGCAACGCGAT--TTC
133797 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACGCGATTTC
* *
133817 CAAATTCGCAACGTGATTTA
1 CAAATTCGCAACGCGATTTC
* *
133837 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACGCGATTTC
*
133857 CGAATTCGCAAC
1 CAAATTCGCAAC
133869 ACGAATTTTA
Statistics
Matches: 121, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
18 1 0.01
19 6 0.05
20 106 0.88
21 7 0.06
22 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:137184 original size:18 final size:18
Alignment explanation
Indices: 137161--137201 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
137151 AAGCAAAAGG
137161 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
137179 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
*
137197 CAATC
1 AAATC
137202 GGCTTCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:137322 original size:30 final size:30
Alignment explanation
Indices: 137286--137343 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
137276 GAATGCATAC
137286 ATTTTTAAATGCAAACGTTGTATTATGTGT
1 ATTTTTAAATGCAAACGTTGTATTATGTGT
137316 ATTTTTAAATGCAAACGTTGTATTATGT
1 ATTTTTAAATGCAAACGTTGTATTATGT
137344 TATCACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (30 bp):
ATTTTTAAATGCAAACGTTGTATTATGTGT
Found at i:137461 original size:29 final size:29
Alignment explanation
Indices: 137428--137485 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
137418 AAATTCGCAA
* **
137428 TGCAAAAATCGTAATGCGAATTTGACTTT
1 TGCAAAAATCGCAACACGAATTTGACTTT
*
137457 TGCAACAATCGCAACACGAATTTGACTTT
1 TGCAAAAATCGCAACACGAATTTGACTTT
137486 CGCGTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (29 bp):
TGCAAAAATCGCAACACGAATTTGACTTT
Found at i:137605 original size:25 final size:25
Alignment explanation
Indices: 137567--137616 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
137557 AAATCAATTA
* *
137567 AACATTGTTGTGGGTATATTATTTG
1 AACATTGTTATGGGTACATTATTTG
137592 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
137617 GAAATTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:139147 original size:29 final size:29
Alignment explanation
Indices: 139104--139161 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
139094 TCAGATTTTT
* *
139104 TGTTGTGATTGTTGCGAAAGTCAAATTCG
1 TGTTGCGATTATTGCGAAAGTCAAATTCG
139133 TGTTGCGATTATTGCGAAAGTCAAATTCG
1 TGTTGCGATTATTGCGAAAGTCAAATTCG
139162 AAACGCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (29 bp):
TGTTGCGATTATTGCGAAAGTCAAATTCG
Found at i:139169 original size:29 final size:29
Alignment explanation
Indices: 139110--139169 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
139100 TTTTTGTTGT
* ****
139110 GATTGTTGCGAAAGTCAAATTCGTGTTGC
1 GATTATTGCGAAAGTCAAATTCGAAACGC
139139 GATTATTGCGAAAGTCAAATTCGAAACGC
1 GATTATTGCGAAAGTCAAATTCGAAACGC
139168 GA
1 GA
139170 AATCGCAACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (29 bp):
GATTATTGCGAAAGTCAAATTCGAAACGC
Found at i:139179 original size:13 final size:13
Alignment explanation
Indices: 139163--139197 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
139153 TCAAATTCGA
139163 AACGCGAAATCGC
1 AACGCGAAATCGC
*
139176 AACGTGAAAATCGC
1 AACGCG-AAATCGC
139190 AACGCGAA
1 AACGCGAA
139198 TTTGACTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.43, C:0.26, G:0.23, T:0.09
Consensus pattern (13 bp):
AACGCGAAATCGC
Found at i:139210 original size:20 final size:20
Alignment explanation
Indices: 139185--139229 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
139175 CAACGTGAAA
*
139185 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAATTTGACT
139205 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAATTTGACT
*
139225 TTCGC
1 ATCGC
139230 GTTGCGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACACGAATTTGACT
Found at i:139344 original size:64 final size:64
Alignment explanation
Indices: 139276--139426 Score: 223
Period size: 64 Copynumber: 2.4 Consensus size: 64
139266 AATTTAAAAC
* * *
139276 AACAAATTAACTTTTACAAATCAATTAAACAAGTAAAAATTAAGAATTATTTACACATCAATTA
1 AACAAATTAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATGATTTACACATCAATTA
** * *
139340 AACAAATTAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTATGATTTCCTCATCAATTA
1 AACAAATTAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATGATTTACACATCAATTA
*
139404 AACAAATCAAC-TTTACAAATCAA
1 AACAAATTAACTTTTACAAATCAA
139427 CTTTTATAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 12 0.15
64 67 0.85
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (64 bp):
AACAAATTAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATGATTTACACATCAATTA
Found at i:139437 original size:14 final size:13
Alignment explanation
Indices: 139405--139430 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
139395 CATCAATTAA
139405 ACAAATCAACTTT
1 ACAAATCAACTTT
139418 ACAAATCAACTTT
1 ACAAATCAACTTT
139431 TATAAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
ACAAATCAACTTT
Found at i:140825 original size:21 final size:21
Alignment explanation
Indices: 140801--140880 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
140791 GGGAGGTACT
140801 TCTTGAACGATGACAGGGGCC
1 TCTTGAACGATGACAGGGGCC
* * *
140822 TCTTGAACGGTAAGAGGGGCC
1 TCTTGAACGATGACAGGGGCC
* *
140843 TCTTGAAGGATGATAGGGGCC
1 TCTTGAACGATGACAGGGGCC
140864 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
140881 TGCTTCGGGC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (21 bp):
TCTTGAACGATGACAGGGGCC
Found at i:141039 original size:12 final size:12
Alignment explanation
Indices: 141020--141061 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
141010 GAGCCTCTAA
*
141020 AAATAAATTAAT
1 AAATAAATCAAT
*
141032 ACATAAATCAAT
1 AAATAAATCAAT
141044 AAATAAA-CAAAT
1 AAATAAATC-AAT
141056 AAATAA
1 AAATAA
141062 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:141196 original size:21 final size:21
Alignment explanation
Indices: 141172--141230 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
141162 GTTGAGCGGC
*
141172 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
141193 TACCTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
141214 TACCTCACCACGTAAAG
1 TACCTCACCACGTAAAG
141231 CACCATTGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:141314 original size:21 final size:21
Alignment explanation
Indices: 141284--141330 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
141274 ACCATTGTCT
* * *
141284 TCACGTAAAGTACTTACCTCC
1 TCACGCAAAGCACTTACCTCA
*
141305 TCACGCAAAGCATTTACCTCA
1 TCACGCAAAGCACTTACCTCA
141326 TCACG
1 TCACG
141331 TAACTCCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.26
Consensus pattern (21 bp):
TCACGCAAAGCACTTACCTCA
Found at i:143069 original size:20 final size:20
Alignment explanation
Indices: 143028--143069 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
143018 GAAACTAAAA
* * *
143028 TCGTGTTGCGATTTTCATTT
1 TCGTGTTGCGAATTTAAGTT
143048 TCGTGTTGCGAATTTAAGTT
1 TCGTGTTGCGAATTTAAGTT
143068 TC
1 TC
143070 AAATAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (20 bp):
TCGTGTTGCGAATTTAAGTT
Found at i:143425 original size:22 final size:22
Alignment explanation
Indices: 143397--143476 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
143387 GATGGTGATA
143397 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
143419 GACGGATTTCGCCGGAGATGAG
1 GACGGATTTCGCCGGAGATGGG
*
143441 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
143463 GACGGATATCGCCG
1 GACGGATTTCGCCG
143477 TAGAGAATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.20, C:0.19, G:0.42, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:143666 original size:20 final size:20
Alignment explanation
Indices: 143643--143712 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
143633 TGACTTCTGT
143643 GTTGCGAATTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
*
143663 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
*
143683 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
143703 GTTGCGAATT
1 GTTGCGAATT
143713 TGTTGGTCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCGC
Found at i:143962 original size:20 final size:20
Alignment explanation
Indices: 143937--143975 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
143927 AATTTATAAA
143937 ATTTTTAA-AAATAAAAATAG
1 ATTTTTAATAAA-AAAAATAG
143957 ATTTTTAATAAAAAAAATA
1 ATTTTTAATAAAAAAAATA
143976 CATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTTTTAATAAAAAAAATAG
Found at i:145606 original size:16 final size:16
Alignment explanation
Indices: 145573--145641 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
145563 CATTTAATAA
*
145573 ATAAACGAACA--TAC
1 ATAAACGAACACGAAC
*
145587 ATAAACGACCACGAAC
1 ATAAACGAACACGAAC
145603 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
145619 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
145635 ATAAACG
1 ATAAACG
145642 TTGGAGACCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 10 0.21
16 38 0.79
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:146754 original size:14 final size:14
Alignment explanation
Indices: 146737--146789 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
146727 GAACATAAAT
146737 GAACATAACCGAAC
1 GAACATAACCGAAC
146751 GAACAT-A---AAC
1 GAACATAACCGAAC
146761 GAACATAACCGAAC
1 GAACATAACCGAAC
146775 GAACATAACCGAAC
1 GAACATAACCGAAC
146789 G
1 G
146790 TTCACGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.51, C:0.26, G:0.15, T:0.08
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:146799 original size:24 final size:24
Alignment explanation
Indices: 146727--146788 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
146717 ATAAATGAAT
*
146727 GAACATAAATGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
146751 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
146775 GAACATAACCGAAC
1 GAACATAAACGAAC
146789 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.24, G:0.13, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:147227 original size:29 final size:29
Alignment explanation
Indices: 147195--147258 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
147185 AAAAAATCAG
* *
147195 TTAATTCGGTTCTGTGAATAATTTTCAAA
1 TTAATTCAGTTCGGTGAATAATTTTCAAA
*
147224 TTAATTCAGTTCGGTTAATAATTTTCAAA
1 TTAATTCAGTTCGGTGAATAATTTTCAAA
*
147253 TAAATT
1 TTAATT
147259 TTGGTTCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
TTAATTCAGTTCGGTGAATAATTTTCAAA
Found at i:147350 original size:135 final size:135
Alignment explanation
Indices: 147185--147441 Score: 408
Period size: 135 Copynumber: 1.9 Consensus size: 135
147175 GGTTAAAGAA
* * * *
147185 AAAAAATCAGTTAATTCGGTTCTGTGAATAATTTTCAAATTAATTCAGTTCGGTTAATAATTTTC
1 AAAAAATCAGTCAATTCGGTGCGGTGAATAATGTTCAAATTAATTCAGTTCGGTTAATAATTTTC
* *
147250 AAATAAATTTTGGTTCGATTAA-CGAACAGAATTAACCGAATTTTTGCTTCGATTAATTCGATTA
66 AAATAAATTTTGGTTCGATTAACCGAAC-CAATTAACCGAAGTTTTGCTTCGATTAATTCGATTA
147314 ATAATT
130 ATAATT
* *
147320 AAAAAATCAGTCAATTCGGTGCGGTTAATAATGTTCAAATTAATTCTGTTCGGTTAATAATTTTC
1 AAAAAATCAGTCAATTCGGTGCGGTGAATAATGTTCAAATTAATTCAGTTCGGTTAATAATTTTC
* *
147385 AAATAAATTTTGGTTCGATTAACCGAGCCAATTAATCGAAGTTTTGCTTCGATTAAT
66 AAATAAATTTTGGTTCGATTAACCGAACCAATTAACCGAAGTTTTGCTTCGATTAAT
147442 AATTAAAAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 107 0.96
136 4 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (135 bp):
AAAAAATCAGTCAATTCGGTGCGGTGAATAATGTTCAAATTAATTCAGTTCGGTTAATAATTTTC
AAATAAATTTTGGTTCGATTAACCGAACCAATTAACCGAAGTTTTGCTTCGATTAATTCGATTAA
TAATT
Found at i:147365 original size:29 final size:29
Alignment explanation
Indices: 147332--147393 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
147322 AAAATCAGTC
*
147332 AATTCGGTGCGGTTAATAATGTTCAAATT
1 AATTCGGTGCGGTTAATAATGTTCAAATA
* * *
147361 AATTCTGTTCGGTTAATAATTTTCAAATA
1 AATTCGGTGCGGTTAATAATGTTCAAATA
147390 AATT
1 AATT
147394 TTGGTTCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (29 bp):
AATTCGGTGCGGTTAATAATGTTCAAATA
Found at i:147473 original size:28 final size:29
Alignment explanation
Indices: 147442--147498 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
147432 TTCGATTAAT
147442 AATTAA-AAAAATCGGTTAATAATTTTCA
1 AATTAATAAAAATCGGTTAATAATTTTCA
** **
147470 AATTAATTTAGTTCGGTTAATAATTTTCA
1 AATTAATAAAAATCGGTTAATAATTTTCA
147499 TACAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (29 bp):
AATTAATAAAAATCGGTTAATAATTTTCA
Found at i:147612 original size:29 final size:29
Alignment explanation
Indices: 147580--147643 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
147570 AAAAAATCAG
147580 TTAATTCGGTTCAGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
147609 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCGGTTCAGTTAATAATTTTCAAA
*
147638 TAAATT
1 TTAATT
147644 TTGGTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCAGTTAATAATTTTCAAA
Found at i:148125 original size:30 final size:30
Alignment explanation
Indices: 148091--148203 Score: 121
Period size: 30 Copynumber: 4.0 Consensus size: 30
148081 ATACTATGTA
*
148091 AATATTAAGAACCATATATAAAATTATGCC
1 AATATTAAGAACCAGATATAAAATTATGCC
*
148121 AATATTAAGGACCAGATATAAAATTATGCC
1 AATATTAAGAACCAGATATAAAATTATGCC
*
148151 -A-A-T---ACCCAGATATAAAATTATGCC
1 AATATTAAGAACCAGATATAAAATTATGCC
* * * *
148175 AATACTAAGGACCAAATATATAATTATGC
1 AATATTAAGAACCAGATATAAAATTATGC
148204 AAATTTATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
24 19 0.28
25 1 0.01
26 1 0.01
27 2 0.03
28 1 0.01
29 1 0.01
30 44 0.64
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (30 bp):
AATATTAAGAACCAGATATAAAATTATGCC
Found at i:148164 original size:24 final size:24
Alignment explanation
Indices: 148132--148179 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
148122 ATATTAAGGA
148132 CCAGATATAAAATTATGCCAATAC
1 CCAGATATAAAATTATGCCAATAC
148156 CCAGATATAAAATTATGCCAATAC
1 CCAGATATAAAATTATGCCAATAC
148180 TAAGGACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (24 bp):
CCAGATATAAAATTATGCCAATAC
Found at i:149090 original size:13 final size:14
Alignment explanation
Indices: 149074--149102 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
149064 CTTTTTTACA
149074 TTATTTTT-AAAAG
1 TTATTTTTCAAAAG
149087 TTATTTTTCAAAAG
1 TTATTTTTCAAAAG
149101 TT
1 TT
149103 GCGCCAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATTTTTCAAAAG
Found at i:152976 original size:10 final size:10
Alignment explanation
Indices: 152961--152990 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
152951 CGGAACAGTA
152961 ACCACGCGCC
1 ACCACGCGCC
152971 ACCACGCGCC
1 ACCACGCGCC
152981 ACCACTGCGC
1 ACCAC-GCGC
152991 GTGGGGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.20, C:0.57, G:0.20, T:0.03
Consensus pattern (10 bp):
ACCACGCGCC
Found at i:155585 original size:24 final size:24
Alignment explanation
Indices: 155558--155648 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
155548 TCAAATTTGA
*
155558 ATTCTGTTATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
155582 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
155605 ATTCTGATCTAATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
155629 ATTCCGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
155649 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:160232 original size:21 final size:22
Alignment explanation
Indices: 160206--160258 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
160196 GTTCCCTAAT
*
160206 TACATGA-ATATTCTGATATGA
1 TACATGACAGATTCTGATATGA
160227 TACATGACCTAGATTCTGATATGA
1 TACATGA-C-AGATTCTGATATGA
*
160251 TACTTGAC
1 TACATGAC
160259 TTGAATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
23 1 0.04
24 19 0.70
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TACATGACAGATTCTGATATGA
Found at i:166573 original size:17 final size:16
Alignment explanation
Indices: 166551--166598 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
166541 ATATTTTGTT
166551 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
*
166568 TTTAATTTTTTTAATA
1 TTTAATTTATTTAATA
* *
166584 TTTTATTTAATTAAT
1 TTTAATTTATTTAAT
166599 TTTTTTGCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:166576 original size:24 final size:23
Alignment explanation
Indices: 166527--166595 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
166517 TTAAGGTATA
**
166527 TTTTATTATATTTAATATTTTGT
1 TTTTATTATATTTAATATTTAAT
166550 TTTTAATT-TATTTAAGTATTTAAT
1 TTTT-ATTATATTTAA-TATTTAAT
166574 TTTT-TTAATATTT--TATTTAAT
1 TTTTATT-ATATTTAATATTTAAT
166595 T
1 T
166596 AATTTTTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 9 0.22
22 2 0.05
23 11 0.28
24 18 0.45
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (23 bp):
TTTTATTATATTTAATATTTAAT
Found at i:166588 original size:25 final size:26
Alignment explanation
Indices: 166549--166604 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
166539 TAATATTTTG
* *
166549 TTTTTAATTTATTTAAGTATTTAATT
1 TTTTTAATATATTTAAGTAATTAATT
**
166575 TTTTTAATAT-TTTATTTAATTAATT
1 TTTTTAATATATTTAAGTAATTAATT
166600 TTTTT
1 TTTTT
166605 GCAGATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTTAATATATTTAAGTAATTAATT
Found at i:166723 original size:19 final size:19
Alignment explanation
Indices: 166676--166723 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
166666 TGCTGATACG
* *
166676 ATAATATTTTAACGTTTTA
1 ATAATAATTTAAAGTTTTA
*
166695 AT-ATAATTTAAATTTTTA
1 ATAATAATTTAAAGTTTTA
166713 ATAATAATTTA
1 ATAATAATTTA
166724 TTTATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATAATAATTTAAAGTTTTA
Found at i:169823 original size:27 final size:27
Alignment explanation
Indices: 169793--169849 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
169783 AACAATCAAA
169793 GGGACCATCGCCATCCAAACATCTAAT
1 GGGACCATCGCCATCCAAACATCTAAT
*
169820 GGGACCATTGCCATCCAAACATCTAAT
1 GGGACCATCGCCATCCAAACATCTAAT
169847 GGG
1 GGG
169850 CCCCTCAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (27 bp):
GGGACCATCGCCATCCAAACATCTAAT
Found at i:171006 original size:17 final size:17
Alignment explanation
Indices: 170981--171022 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
170971 AATAATAATT
*
170981 AAATAAAATA-TTAAAA
1 AAATTAAATACTTAAAA
*
170997 AAATGTAAATACTTAAAT
1 AAAT-TAAATACTTAAAA
171015 AAATTAAA
1 AAATTAAA
171023 AATAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATTAAATACTTAAAA
Found at i:171030 original size:30 final size:30
Alignment explanation
Indices: 170974--171030 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
170964 GCAAAAAAAT
*
170974 AATAATTAAATAAAATATTAAAAAAATGTA
1 AATAATTAAATAAAATATAAAAAAAATGTA
* *
171004 AATACTTAAATAAATTA-AAAATAAAAT
1 AATAATTAAATAAAATATAAAA-AAAAT
171031 ATTAAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (30 bp):
AATAATTAAATAAAATATAAAAAAAATGTA
Found at i:171045 original size:23 final size:25
Alignment explanation
Indices: 170986--171045 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
170976 TAATTAAATA
*
170986 AAATATTAA-AAAAATGTAAATACTT
1 AAATA-TAATAAAAATGAAAATACTT
171011 AAATA-AATTAAAAAT-AAAATA-TT
1 AAATATAA-TAAAAATGAAAATACTT
171034 AAATATAATAAA
1 AAATATAATAAA
171046 TTATACCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 13 0.42
24 7 0.23
25 11 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
AAATATAATAAAAATGAAAATACTT
Found at i:172337 original size:9 final size:9
Alignment explanation
Indices: 172323--172368 Score: 67
Period size: 9 Copynumber: 5.0 Consensus size: 9
172313 TACATCAAAG
172323 AAAAAAAT-
1 AAAAAAATA
172331 AAAAAAATAA
1 AAAAAAAT-A
172341 AAAATAAATA
1 AAAA-AAATA
172351 AAAAAAATA
1 AAAAAAATA
172360 AAAAAAATA
1 AAAAAAATA
172369 GATAAATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.23
9 14 0.40
10 9 0.26
11 4 0.11
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Found at i:172374 original size:22 final size:20
Alignment explanation
Indices: 172323--172364 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
172313 TACATCAAAG
172323 AAAA-AAAT-AAAAAAATAA
1 AAAATAAATAAAAAAAATAA
172341 AAAATAAATAAAAAAAATAA
1 AAAATAAATAAAAAAAATAA
172361 AAAA
1 AAAA
172365 AATAGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAATAAATAAAAAAAATAA
Found at i:172387 original size:29 final size:28
Alignment explanation
Indices: 172295--172394 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 28
172285 AGAAAACATA
* * * *
172295 AAAAAATAATAATAATAATACATCAAAG
1 AAAAAATAAAAAAAATAATAAATCAATG
* * *
172323 AAAAAA-ATAAAAAAATAAAAAATAAATAA
1 AAAAAATA-AAAAAAATAATAAATCAAT-G
172352 AAAAAATAAAAAAAATAGATAAATCAATG
1 AAAAAATAAAAAAAATA-ATAAATCAATG
*
172381 AAAAAATGAAAAAA
1 AAAAAATAAAAAAA
172395 TGTTAAATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 19 0.33
29 28 0.49
30 9 0.16
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (28 bp):
AAAAAATAAAAAAAATAATAAATCAATG
Found at i:173671 original size:5 final size:5
Alignment explanation
Indices: 173663--173720 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
173653 CAAAAGAAGG
*
173663 AAATA AAAT- AAATA AAAT- AAAT- AAAT- AAATA ATAA-A TAAT- AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA A-AATA AAATA AAATA
173708 AAATA AAATA AAA
1 AAATA AAATA AAA
173721 AAACAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 21 0.46
5 23 0.50
6 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:173677 original size:4 final size:4
Alignment explanation
Indices: 173663--173729 Score: 66
Period size: 4 Copynumber: 16.2 Consensus size: 4
173653 CAAAAGAAGG
173663 AAAT AAAAT AAAT AAAAT AAAT AAAT AAAT -AAT AAAT -AAT AAAT AAAAT
1 AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT
* *
173712 AAAAT AAAA AAAC AAAT A
1 -AAAT AAAT AAAT AAAT A
173730 TATATTATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
3 6 0.11
4 32 0.58
5 17 0.31
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:173698 original size:7 final size:7
Alignment explanation
Indices: 173678--173708 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
173668 AAATAAATAA
173678 AATAAAT
1 AATAAAT
173685 AAATAAAT
1 -AATAAAT
173693 AATAAAT
1 AATAAAT
173700 AATAAAT
1 AATAAAT
173707 AA
1 AA
173709 AATAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAAAT
Found at i:173874 original size:40 final size:39
Alignment explanation
Indices: 173776--174110 Score: 291
Period size: 40 Copynumber: 8.9 Consensus size: 39
173766 TCAGAAAACA
* **
173776 TTTTCAAAACTATATAT-TATATATA---TTAAAAAATG
1 TTTTAAAAACTATATATATATATATATGTTTTCAAAATG
*
173811 TTTTCAAAAACTATATAATATATATATATATTTTTTCAAAATG
1 TTTT-AAAAAC--TAT-ATATATATATATATGTTTTCAAAATG
173854 TTTTAAAAACTATATAATATATATATATGTTTTCAAAATG
1 TTTTAAAAACTATAT-ATATATATATATGTTTTCAAAATG
*
173894 TTTTAAAAACTATATAT-TATATATATGTTTTCAAAATA
1 TTTTAAAAACTATATATATATATATATGTTTTCAAAATG
* *
173932 TTTTAAAAACTATATATATATATATA---TAT--ATAT-
1 TTTTAAAAACTATATATATATATATATGTTTTCAAAATG
* * * *
173965 ATATATATA-TATATATATATATATATGTTTTCAAAAAT-
1 TTTTAAAAACTATATATATATATATATGTTTTC-AAAATG
*
174003 TTTTAAAAAC----TATATA-ATATGTGTTTTCAAAATG
1 TTTTAAAAACTATATATATATATATATGTTTTCAAAATG
* * *
174037 TTTT-AAAA-T-TATATAT-TATTTATATATTCAAAATG
1 TTTTAAAAACTATATATATATATATATGTTTTCAAAATG
* *
174072 TTTTAAAAAGCTATATAATATATATATATATATTCAAAA
1 TTTTAAAAA-CTATAT-ATATATATATATGTTTTCAAAA
174111 ACCAATTTTT
Statistics
Matches: 249, Mismatches: 23, Indels: 50
0.77 0.07 0.16
Matches are distributed among these distances:
32 16 0.06
33 14 0.06
34 18 0.07
35 35 0.14
36 11 0.04
38 49 0.20
39 19 0.08
40 53 0.21
41 16 0.06
42 6 0.02
43 12 0.05
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (39 bp):
TTTTAAAAACTATATATATATATATATGTTTTCAAAATG
Found at i:173949 original size:2 final size:2
Alignment explanation
Indices: 173942--173990 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
173932 TTTTAAAAAC
173942 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
173984 TA TA TA T
1 TA TA TA T
173991 GTTTTCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:174087 original size:35 final size:34
Alignment explanation
Indices: 173870--174098 Score: 160
Period size: 35 Copynumber: 6.4 Consensus size: 34
173860 AAACTATATA
* *
173870 ATATATATATATGTTTTCAAAATGTTTTAAAAACT
1 ATATA-ATATATATATTCAAAATGTTTTAAAAACT
* *
173905 ATATATTATATATATGTTTTCAAAATATTTTAAAAACT
1 ATATA--ATATATA--TATTCAAAATGTTTTAAAAACT
* * * * *
173943 ATATATATATATATATAT-ATATATATATATATATA-T
1 ATATA-ATATATATAT-TCA-AAATGT-TTTAAAAACT
* *
173979 ATATATATATATGTTTTCAAAAAT-TTTTAAAAACT
1 ATATA-ATATATATATTC-AAAATGTTTTAAAAACT
* * *
174014 ATATAATATGTGTTTTCAAAATGTTTTAAAATTA-T
1 ATATAATATATATATTCAAAATGTTTTAAAA--ACT
* *
174049 ATATTATTTATATATTCAAAATGTTTTAAAAAGCT
1 ATATAATATATATATTCAAAATGTTTTAAAAA-CT
174084 ATATAATATATATAT
1 ATATAATATATATAT
174099 ATATATTCAA
Statistics
Matches: 159, Mismatches: 21, Indels: 28
0.76 0.10 0.13
Matches are distributed among these distances:
33 6 0.04
34 24 0.15
35 57 0.36
36 32 0.20
37 14 0.09
38 26 0.16
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATAATATATATATTCAAAATGTTTTAAAAACT
Found at i:175941 original size:2 final size:2
Alignment explanation
Indices: 175934--175959 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
175924 ATCCTAACTC
175934 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
175960 GTTCTGGATG
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:188972 original size:39 final size:40
Alignment explanation
Indices: 188899--189000 Score: 188
Period size: 39 Copynumber: 2.6 Consensus size: 40
188889 TCGTTTATTT
188899 ATTAAATGAACGAACATGAACAAGATTTTACGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGATTTTACGTTCGTTTA
188939 ATTAAATGAACGAACATG-ACAAGATTTTACGTTCGTTTA
1 ATTAAATGAACGAACATGAACAAGATTTTACGTTCGTTTA
*
188978 ATTAAATGAACGAACACGAACAA
1 ATTAAATGAACGAACATGAACAA
189001 AGGGCTCGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 38 0.63
40 22 0.37
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (40 bp):
ATTAAATGAACGAACATGAACAAGATTTTACGTTCGTTTA
Found at i:189011 original size:39 final size:39
Alignment explanation
Indices: 188899--189014 Score: 119
Period size: 39 Copynumber: 2.9 Consensus size: 39
188889 TCGTTTATTT
* ***
188899 ATTAAATGAACGAACATGAACAAGATTTTACGTTCGTTTA
1 ATTAAATGAACGAACACG-ACAAGAGGCTACGTTCGTTTA
* ***
188939 ATTAAATGAACGAACATGACAAGATTTTACGTTCGTTTA
1 ATTAAATGAACGAACACGACAAGAGGCTACGTTCGTTTA
188978 ATTAAATGAACGAACACGAACAA-AGGGCT-CGTTCGTT
1 ATTAAATGAACGAACACG-ACAAGA-GGCTACGTTCGTT
189015 CATTTACGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
39 47 0.67
40 23 0.33
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (39 bp):
ATTAAATGAACGAACACGACAAGAGGCTACGTTCGTTTA
Found at i:189352 original size:10 final size:10
Alignment explanation
Indices: 189337--189437 Score: 67
Period size: 10 Copynumber: 9.1 Consensus size: 10
189327 GTGTTTGTGT
189337 TGTTCGTTTA
1 TGTTCGTTTA
189347 TGTTCGTTTA
1 TGTTCGTTTA
*
189357 TTGTGTTCATTTA
1 ---TGTTCGTTTA
189370 TGTTCGTTTATTA
1 TGTTCG--T-TTA
*
189383 TGTTCTTTTA
1 TGTTCGTTTA
189393 TTTTCGTTCGTTTA
1 ---T-GTTCGTTTA
*
189407 CGTTCGTTTA
1 TGTTCGTTTA
*
189417 CGTTCGTTTA
1 TGTTCGTTTA
*
189427 TTTTCGTTTA
1 TGTTCGTTTA
189437 T
1 T
189438 CATTTAAATG
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
10 46 0.62
11 1 0.01
12 1 0.01
13 18 0.24
14 8 0.11
ACGTcount: A:0.11, C:0.12, G:0.16, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:189355 original size:23 final size:23
Alignment explanation
Indices: 189337--189428 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
189327 GTGTTTGTGT
*
189337 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTA
*
189360 TGTTCATTTATGTTCGTTTATTA
1 TGTTCGTTTATGTTCGTTTATTA
* *
189383 TGTTCTTTTATTTTCGTTCGT-TTA
1 TGTTCGTTTATGTTCGTT--TATTA
* *
189407 CGTTCGTTTACGTTCGTTTATT
1 TGTTCGTTTATGTTCGTTTATT
189429 TTCGTTTATC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.67
24 17 0.29
25 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.16, T:0.61
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTA
Found at i:195118 original size:36 final size:36
Alignment explanation
Indices: 195056--195273 Score: 236
Period size: 36 Copynumber: 6.2 Consensus size: 36
195046 AATTTACTCA
* *
195056 AAACAAAGTTTTGTATCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
195093 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
195129 AAACAAATTTTGTCTCTCTGGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
195165 AAACAAA------ATCT-TTGA-ATCTGTTTTCCTTA
1 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTG
* * **
195194 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
195230 GAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
195267 AAACAAA
1 AAACAAA
195274 ATCTTTGAAT
Statistics
Matches: 148, Mismatches: 23, Indels: 20
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.01
29 19 0.13
30 3 0.02
35 2 0.01
36 84 0.57
37 39 0.26
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:195268 original size:102 final size:102
Alignment explanation
Indices: 195084--195441 Score: 574
Period size: 102 Copynumber: 3.5 Consensus size: 102
195074 CTTGAGACAG
** * ** *
195084 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTTGTCTCTCT
1 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACAAAGTTTTGTCTCTCT
* *
195148 GGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
65 TGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTAT
*
195186 TTTCCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACAAAGTTTTGTCTCTCTT
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACAAAGTTTTGTCTCTCTT
195251 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTAT
66 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTAT
* *
195288 TTTCCTTGAAACAAATTTCGTCTCACTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACAAAGTTTTGTCTCTCTT
*
195353 GAGACAGTTTCCCTTGAAACAAAATCTTTGAAGCTAT
66 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTAT
*
195390 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTTCTTTTGGAACAAA
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA-GTTTCTTTTGGAACAAA
195442 AATCTTTGAA
Statistics
Matches: 238, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
101 40 0.17
102 183 0.77
103 15 0.06
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (102 bp):
TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACAAAGTTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTAT
Found at i:195545 original size:65 final size:65
Alignment explanation
Indices: 195344--195570 Score: 278
Period size: 65 Copynumber: 3.5 Consensus size: 65
195334 ACTAAGTTTT
* *
195344 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAGCTATTTTCCTTGAAACAAATTTC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTTTTTTCCTTGAAACAAATTTC
* * ** * *
195409 GTCTCCCTTGAGACATTTTTCTTTTGGAACAAAAATCTTTGAAT-TTATTTCCCTTGAAACAAAT
1 GTCTCTCTTGAGACA-GTTTCCCTTGAAAC-AAAATCTTTGAATCTT-TTTTCCTTGAAACAAAT
*
195473 TTT
63 TTC
* *
195476 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCATTGAATCTGTTTTTCATT-AAACAAATTT
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT-TTTTTCCTTGAAACAAATTT
195540 C
65 C
* * *
195541 GTCTCACTCGAGACAGTTTCTCTTGAAACA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACA
195571 CAAAAAAACT
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
65 63 0.46
66 28 0.21
67 45 0.33
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (65 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTTTTTTCCTTGAAACAAATTTC
Found at i:197546 original size:13 final size:13
Alignment explanation
Indices: 197528--197552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
197518 GTTCAAACTG
197528 AATTTTTAATTTA
1 AATTTTTAATTTA
197541 AATTTTTAATTT
1 AATTTTTAATTT
197553 TCGCATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTTTTAATTTA
Found at i:198032 original size:28 final size:29
Alignment explanation
Indices: 197992--198046 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
197982 ATATATAATA
*
197992 TTTAAAACATAAATTTAATATTTTTATAT
1 TTTAAAACATAAATTTAACATTTTTATAT
*
198021 TTTAAAA-TTAAATTTAACATTTTTAT
1 TTTAAAACATAAATTTAACATTTTTAT
198047 TTTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAAAACATAAATTTAACATTTTTATAT
Found at i:218325 original size:2 final size:2
Alignment explanation
Indices: 218312--218350 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
218302 ATTTCTAATA
* * *
218312 AT AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218351 AATTAACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:219874 original size:10 final size:11
Alignment explanation
Indices: 219859--219910 Score: 70
Period size: 11 Copynumber: 4.6 Consensus size: 11
219849 TAGGAAATAG
219859 AAATAATT-AA
1 AAATAATTAAA
219869 AAATAATTAAA
1 AAATAATTAAA
*
219880 AACATAAAATAAA
1 AA-AT-AATTAAA
219893 AAATAATTAAA
1 AAATAATTAAA
219904 AAATAAT
1 AAATAAT
219911 GAAGATTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 8 0.22
11 17 0.46
12 4 0.11
13 8 0.22
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAATTAAA
Found at i:220133 original size:12 final size:12
Alignment explanation
Indices: 220113--220171 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
220103 AATCACAAAC
220113 AACAATAAATAA
1 AACAATAAATAA
*
220125 AACAGTAAAT--
1 AACAATAAATAA
* *
220135 AACAA-ATAGAA
1 AACAATAAATAA
220146 AACAATAAATAA
1 AACAATAAATAA
220158 AACAGA-AAATAA
1 AACA-ATAAATAA
220170 AA
1 AA
220172 TATAACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
9 2 0.05
10 4 0.11
11 5 0.14
12 25 0.68
13 1 0.03
ACGTcount: A:0.73, C:0.08, G:0.05, T:0.14
Consensus pattern (12 bp):
AACAATAAATAA
Found at i:220255 original size:16 final size:16
Alignment explanation
Indices: 220244--220317 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 16
220234 ACAAAAAAAC
220244 AAAAACAAAAAAAATA
1 AAAAACAAAAAAAATA
* *
220260 AAAAACATAATAACATA
1 AAAAACA-AAAAAAATA
*
220277 AAACAATAAAAATAAATAA
1 AAA-AACAAAAA-AAAT-A
*
220296 AATAAATAAAATAAAATA
1 AA-AAACAAAA-AAAATA
220314 AAAA
1 AAAA
220318 CAGGAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.15
17 15 0.32
18 9 0.19
19 14 0.30
20 2 0.04
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAACAAAAAAAATA
Found at i:220269 original size:9 final size:8
Alignment explanation
Indices: 220236--220311 Score: 59
Period size: 9 Copynumber: 9.5 Consensus size: 8
220226 AAAGAATAAC
*
220236 AAAAAAAC
1 AAAAAAAT
*
220244 AAAAACA-
1 AAAAAAAT
220251 AAAAAAAT
1 AAAAAAAT
220259 AAAAAACAT
1 AAAAAA-AT
* *
220268 AATAACAT
1 AAAAAAAT
*
220276 AAAACAAT
1 AAAAAAAT
220284 --AAAAAT
1 AAAAAAAT
220290 AAATAAAAT
1 AAA-AAAAT
220299 AAATAAAAT
1 AAA-AAAAT
220308 AAAA
1 AAAA
220312 TAAAAACAGG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
6 5 0.09
7 6 0.11
8 21 0.38
9 23 0.42
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:220294 original size:35 final size:37
Alignment explanation
Indices: 220218--220306 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 37
220208 AATAACATAC
220218 AAATAAAAAAAGAATAACAAAAAAACAAAAACAAAAA
1 AAATAAAAAAAGAATAACAAAAAAACAAAAACAAAAA
* * * *
220255 AAATAAAAAACATAATAACATAAAACAATAAAAATAAATA
1 AAATAAAAAA-AGAATAACA-AAAA-AACAAAAACAAAAA
220295 AAATAAATAAAA
1 AAATAAA-AAAA
220307 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
37 10 0.23
38 8 0.18
39 4 0.09
40 19 0.43
41 3 0.07
ACGTcount: A:0.80, C:0.07, G:0.01, T:0.12
Consensus pattern (37 bp):
AAATAAAAAAAGAATAACAAAAAAACAAAAACAAAAA
Found at i:220300 original size:5 final size:5
Alignment explanation
Indices: 220207--220316 Score: 57
Period size: 5 Copynumber: 21.6 Consensus size: 5
220197 CAAAACATAT
* * * * *
220207 AAATA ACATA CAAATA AAAAA AGAATA ACAAAA AAACA AAA-A CAAAAA
1 AAATA AAATA -AAATA AAATA A-AATA A-AATA AAATA AAATA -AAATA
* * * *
220255 AAATA AAAAA CATAATA ACATA AAACA ATA-A AAAT- AAATA AAAT- AAATA
1 AAATA AAATA -A-AATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
220304 AAATA AAATA AAA
1 AAATA AAATA AAA
220317 ACAGGAAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
4 12 0.15
5 51 0.63
6 15 0.19
7 3 0.04
ACGTcount: A:0.78, C:0.07, G:0.01, T:0.14
Consensus pattern (5 bp):
AAATA
Found at i:220312 original size:23 final size:23
Alignment explanation
Indices: 220250--220315 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
220240 AAACAAAAAC
* *
220250 AAAAAAAATAAAA-AACAT-AAT
1 AAAATAAATAAAATAAAATAAAT
* *
220271 AACATAAA-ACAATAAAAATAAAT
1 AAAATAAATAAAAT-AAAATAAAT
220294 AAAATAAATAAAATAAAATAAA
1 AAAATAAATAAAATAAAATAAA
220316 AACAGGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 3 0.09
21 6 0.17
22 4 0.11
23 18 0.51
24 4 0.11
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAATAAATAAAATAAAATAAAT
Found at i:220564 original size:21 final size:21
Alignment explanation
Indices: 220538--220617 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
220528 AAAAAATGTA
*
220538 AGGAGTCAAGAATAGTAGATG
1 AGGAGTCAAGAACAGTAGATG
* * *
220559 AGGAGTTAAAAACAGTAGTTG
1 AGGAGTCAAGAACAGTAGATG
* * *
220580 AGGAGTCACGTACAATAGATG
1 AGGAGTCAAGAACAGTAGATG
* * *
220601 ATGAGTCACGAATAGTA
1 AGGAGTCAAGAACAGTA
220618 AATCGAGAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.21
Consensus pattern (21 bp):
AGGAGTCAAGAACAGTAGATG
Found at i:220782 original size:25 final size:26
Alignment explanation
Indices: 220748--220818 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
220738 GAAGGTTAGG
220748 GTTTGATTTGAAAAACAAAAC-AAAA
1 GTTTGATTTGAAAAACAAAACAAAAA
220773 GTTTGATTTGAAAAACAAAACAAAAA
1 GTTTGATTTGAAAAACAAAACAAAAA
*
220799 GTTTGTTTTGAAAAACAAAA
1 GTTTGATTTGAAAAACAAAA
220819 AGAACAAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 21 0.48
26 23 0.52
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.27
Consensus pattern (26 bp):
GTTTGATTTGAAAAACAAAACAAAAA
Found at i:220915 original size:93 final size:94
Alignment explanation
Indices: 220818--220987 Score: 222
Period size: 93 Copynumber: 1.8 Consensus size: 94
220808 GAAAAACAAA
* *
220818 AAGAACAAAGGAAGAACAATA-GATGAAAGTTTGGGTTTGAAC-CAAAAAA-AGAAGAAATTTTT
1 AAGAACAAAGGAAGAACAA-AGGATAAAAGTTAGGGTTTGAACTCAAAAAATA-AAG-AATTTTT
220880 ATGTTA-TTTGGATCTAGGAAAGAGATGTATG
63 ATGTTATTTTGGATCTAGGAAAGAGATGTATG
** * * *
220911 AAGAACAAATTAAGAATAAAGGATAAAAGTTAGGGTTTGATCTTAAAAAATAAAGAATTTTTATG
1 AAGAACAAAGGAAGAACAAAGGATAAAAGTTAGGGTTTGAACTCAAAAAATAAAGAATTTTTATG
220976 TTATTTTGGATC
66 TTATTTTGGATC
220988 GAAGAAATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
92 1 0.02
93 47 0.71
94 17 0.26
95 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (94 bp):
AAGAACAAAGGAAGAACAAAGGATAAAAGTTAGGGTTTGAACTCAAAAAATAAAGAATTTTTATG
TTATTTTGGATCTAGGAAAGAGATGTATG
Found at i:221566 original size:2 final size:2
Alignment explanation
Indices: 221559--222252 Score: 208
Period size: 2 Copynumber: 346.0 Consensus size: 2
221549 ATACATACTT
* * *
221559 TA TA TA TA TA GTT TA TA CTT TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
221603 TA TA TA GT- TCA TA T- TT TA CT- TA TA T- TA TA TA TA TA TA TA
1 TA TA TA -TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
221642 TA TA CTC TA TA CTT TA TA TA TA CTT TA TA GA TA TA AA CTA TA TG
1 TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * * * *
221686 TA TA T- TA TA TA TA AA TA TA AA CTA TA TA GTT TG TA CA AA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA
* * * * *
221730 TA TA -A TA GA TA TA GTA TA TG TA TG TA -A TT TCA TA TA CTT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA -TA TA
* *
221771 TA CTA TA TA TA TA TA TA TA TA GTC TA TA T- TA -A TA AA CT- TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * ** *
221811 CCA TA TC TA GC T- TT TA 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 TA TA TA TA TA TA TA TA
* * * * * *
221853 TA CA TA CA TA GTA TA CA TA -A T- TT TA TA TA T- TT TA TA TA AA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
221893 T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
221934 CA GTA TA TA AA CA -A TA TA GTT TA TA TA T- TG TA TA TGA -A TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA
* ** *
221974 TA GA CTA TA TA GC T- TA TA TA TA GT- TCA TA TA TA GTT TA -A CTA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA -TA TA TA -TA
* ** * * *
222016 TA TA GTT TA TA T- TA -A TA -A GC TA TA TA GTA TG TA TG TA TG TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
222057 TG TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA GTA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
*
222100 TA TA GTA TA TA CT- TA TA -A GTA TA -A TA TA TA TT TA TA T- TA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
222139 TA TA CT- TA TA -A GTA TA -A TG TA TA TT TA CA AA AA TA TA T- TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
222179 TA -A TG TA TA CT- TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222218 T- TA TA TA TA TA TA -A GTA TA TCA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA T-A TA TA
222253 CATTGTACTT
Statistics
Matches: 509, Mismatches: 101, Indels: 164
0.66 0.13 0.21
Matches are distributed among these distances:
1 40 0.08
2 419 0.82
3 50 0.10
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:221578 original size:31 final size:30
Alignment explanation
Indices: 221533--221598 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
221523 ATGTAATTTC
* *
221533 ATATATTTTTTACTTTATACATACTTTATAT
1 ATATAGTTTATACTTTATACATA-TTTATAT
*
221564 ATATAGTTTATACTTTATATATATTTATAT
1 ATATAGTTTATACTTTATACATATTTATAT
221594 ATATA
1 ATATA
221599 TATATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (30 bp):
ATATAGTTTATACTTTATACATATTTATAT
Found at i:221941 original size:35 final size:35
Alignment explanation
Indices: 221560--222246 Score: 202
Period size: 35 Copynumber: 19.4 Consensus size: 35
221550 TACATACTTT
* * *
221560 ATATATATAGTTTATACTT-TATA-TATATTTATAT
1 ATATATATA-TATATAGTTATATAGTATATATATAT
**
221594 ATATATATATATATAGTTCATATTTTACT-TATATTAT
1 ATATATATATATATAGTT-ATATAGTA-TATATA-TAT
* * *
221631 ATATATATATATATA-CTCTATACT-T-TATATAT
1 ATATATATATATATAGTTATATAGTATATATATAT
* * **
221663 ACTTTATAGATATA-AACTATAT-GTATATTATATAT
1 A-TATATATATATATAGTTATATAGTATA-TATATAT
* * * * *
221698 AAATATAAACTATATAGTT-TGTA-CAAATAGTATAT
1 ATATATATA-TATATAGTTATATAGTATATA-TATAT
* * * * *
221733 A-ATAGATATAGTATA-TGTATGTAATTTCATATACTTT
1 ATATATATATA-TATAGT-TATATAGTAT-ATATA-TAT
*
221770 ATACTATATATATATA--TATATAGTCTATAT-TA-
1 ATA-TATATATATATAGTTATATAGTATATATATAT
* * * *
221802 ATAAACTTACCATATCTAGCTTTTATA-TATATATATAT
1 ATATA--TA-TATATATAG-TTATATAGTATATATATAT
** * *
221840 ATATATATATATATACATACATAGTATACATA-ATT
1 ATATATATATATATAGTTATATAGTATATATATA-T
* * * *
221875 TTATATATTTTATATAAATTATATATATATATATATAT
1 ATATATA-TATATAT-AGTTATATA-GTATATATATAT
* * *
221913 ATATATATATATATAGTTATACAGTATATAAACA-
1 ATATATATATATATAGTTATATAGTATATATATAT
* * * *
221947 ATATAGTTTATATATTG-TATAT-GAATATAGACTAT
1 ATATA-TATATATATAGTTATATAGTATATATA-TAT
** *
221982 ATAGCT-TATATATAGTTCATATA-TAGTTTA-ACTAT
1 ATATATATATATATAGTT-ATATAGTA-TATATA-TAT
* * * *
222017 ATAGTTTATAT-TAATAAGCTATATAGTATGTATGTATGT
1 ATA-TATATATAT-AT-AGTTATATAGTA--TATATATAT
* *
222056 ATGTATATATATATAATATATATA-TATATATATAGT
1 ATATATATATATATAGT-TATATAGTATATATATA-T
*
222092 ATAAACTATATAGTATATACTTATA-AGTATA-ATATAT
1 AT--A-TATATA-TATATAGTTATATAGTATATATATAT
* * *
222129 ATTTATAT-TATATACTTATA-AGTATA-ATGTAT
1 ATATATATATATATAGTTATATAGTATATATATAT
* * * *
222161 ATTTACAAAAATATA-TTATA-ATGTATACT-TATATT
1 ATATATATATATATAGTTATATA-GTATA-TATATA-T
*
222196 ATATATATATATATA-TTATATATTATATATATAT
1 ATATATATATATATAGTTATATAGTATATATATAT
222230 AAGTATATCATATATAT
1 -A-TATAT-ATATATAT
222247 CATATACATT
Statistics
Matches: 491, Mismatches: 94, Indels: 133
0.68 0.13 0.19
Matches are distributed among these distances:
31 1 0.00
32 44 0.09
33 59 0.12
34 59 0.12
35 122 0.25
36 52 0.11
37 68 0.14
38 48 0.10
39 30 0.06
40 8 0.02
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
ATATATATATATATAGTTATATAGTATATATATAT
Found at i:221983 original size:79 final size:75
Alignment explanation
Indices: 221825--222009 Score: 191
Period size: 75 Copynumber: 2.4 Consensus size: 75
221815 ATCTAGCTTT
* * *
221825 TATATATATATATATATATATATATATA-TACATACATAGTATACATAATTTTATATATTTTATA
1 TATATATATATATATATATATATATATAGT-TATACATAGTATACATAAGTTTATATATTGTATA
*
221889 TAAATTATATA
65 TAAATTATAGA
221900 TATATATATATATATATATATATATATAGTTATACAGTA-TATAAACAATATAGTTTATATATTG
1 TATATATATATATATATATATATATATAGTTATACA-TAGTAT--AC-ATA-AGTTTATATATTG
*
221964 TATATGAA-TATAGA
61 TATATAAATTATAGA
**
221978 CTATATAGCT-TATATATAGT-TCATATATAGTT
1 -TATATATATATATATATA-TAT-ATATATAGTT
222010 TAACTATATA
Statistics
Matches: 94, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
75 36 0.38
76 3 0.03
77 2 0.02
78 17 0.18
79 36 0.38
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (75 bp):
TATATATATATATATATATATATATATAGTTATACATAGTATACATAAGTTTATATATTGTATAT
AAATTATAGA
Found at i:222017 original size:13 final size:12
Alignment explanation
Indices: 221979--222024 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
221969 GAATATAGAC
*
221979 TATATAGCTT-A
1 TATATAGTTTAA
*
221990 TATATAG-TTCA
1 TATATAGTTTAA
222001 TATATAGTTTAA
1 TATATAGTTTAA
222013 CTATATAGTTTA
1 -TATATAGTTTA
222025 TATTAATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 2 0.06
11 15 0.48
12 3 0.10
13 11 0.35
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (12 bp):
TATATAGTTTAA
Found at i:222083 original size:19 final size:19
Alignment explanation
Indices: 222059--222252 Score: 111
Period size: 21 Copynumber: 9.9 Consensus size: 19
222049 TGTATGTATG
222059 TATATATATATA-ATAT-A
1 TATATATATATATATATAA
222076 TATATATATATATAGTATAA
1 TATATATATATATA-TATAA
222096 -ACTATATAGTATATACTTATAA
1 TA-TATATA-TATATA--TATAA
* *
222118 GTATA-ATATATATTTATAT
1 -TATATATATATATATATAA
222137 TATATACT-TATA-AGTATAA
1 TATATA-TATATATA-TATAA
* * *
222156 TGTATAT-T-TACA-AAAA
1 TATATATATATATATATAA
* *
222172 TATAT-TATAATGTATACTTA
1 TATATATAT-ATATATA-TAA
*
222192 TATTATATATATATATATAT
1 TA-TATATATATATATATAA
222212 TATATATTATATATATATAA
1 TATATA-TATATATATATAA
222232 GTATATCATATATATCATATA
1 -TATAT-ATATATAT-ATATA
222253 CATTGTACTT
Statistics
Matches: 138, Mismatches: 16, Indels: 41
0.71 0.08 0.21
Matches are distributed among these distances:
15 1 0.01
16 8 0.06
17 14 0.10
18 10 0.07
19 27 0.20
20 26 0.19
21 32 0.23
22 17 0.12
23 2 0.01
24 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
TATATATATATATATATAA
Found at i:222316 original size:16 final size:13
Alignment explanation
Indices: 222171--222328 Score: 57
Period size: 13 Copynumber: 12.3 Consensus size: 13
222161 ATTTACAAAA
*
222171 ATATA-TTATAAT
1 ATATACTTATATT
*
222183 GTATACTTATATT
1 ATATACTTATATT
222196 ATATA--TATA-T
1 ATATACTTATATT
*
222206 ATATATTATATATT
1 ATATACT-TATATT
*
222220 ATATA--TATATA
1 ATATACTTATATT
*
222231 AGTATA-TCATA-T
1 A-TATACTTATATT
* *
222243 ATAT-CATATA-C
1 ATATACTTATATT
*
222254 ATTGTACTTATAGTAT
1 A-TATACTTATA-T-T
* * *
222270 AGATAATTATAAT
1 ATATACTTATATT
*
222283 GTATACTTATATT
1 ATATACTTATATT
222296 ATATACTTATATAGGT
1 ATATACTTATAT---T
*
222312 ATATACTTATAAT
1 ATATACTTATATT
222325 ATAT
1 ATAT
222329 GCATAAGTAT
Statistics
Matches: 108, Mismatches: 22, Indels: 31
0.67 0.14 0.19
Matches are distributed among these distances:
10 6 0.06
11 17 0.16
12 11 0.10
13 48 0.44
14 6 0.06
15 7 0.06
16 13 0.12
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (13 bp):
ATATACTTATATT
Found at i:222926 original size:16 final size:16
Alignment explanation
Indices: 222905--222945 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
222895 TTATGTGACC
222905 CGATCTGAACGAGATT
1 CGATCTGAACGAGATT
*
222921 CGATCTGAACGAGCTT
1 CGATCTGAACGAGATT
*
222937 CAATCTGAA
1 CGATCTGAA
222946 GTTCATCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (16 bp):
CGATCTGAACGAGATT
Done.