Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold355
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: 530098
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 2 of 4
Found at i:119251 original size:23 final size:22
Alignment explanation
Indices: 119223--119275 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
119213 TTAAATTAAG
119223 AGATTTGGTGAGACAAATCTTCA
1 AGATTTGGTGAGAC-AATCTTCA
* * *
119246 ATATTTAGTTAGACAATCTTCA
1 AGATTTGGTGAGACAATCTTCA
119268 AGATTTGG
1 AGATTTGG
119276 GAATGAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (22 bp):
AGATTTGGTGAGACAATCTTCA
Found at i:121154 original size:29 final size:30
Alignment explanation
Indices: 121083--121154 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
121073 GCAAGCTCGT
121083 CAAAGCCCATATCATAATTTGAGCTTGCAG
1 CAAAGCCCATATCATAATTTGAGCTTGCAG
*
121113 TAAAGCCCATATCATAATTTGAGC-TGCAG
1 CAAAGCCCATATCATAATTTGAGCTTGCAG
*
121142 CAAAGCCCCTATC
1 CAAAGCCCATATC
121155 CACTTAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (30 bp):
CAAAGCCCATATCATAATTTGAGCTTGCAG
Found at i:125448 original size:20 final size:20
Alignment explanation
Indices: 125408--125467 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
125398 AATTTTTAAA
*
125408 AAATTAATATATAAAAATTT
1 AAATAAATATATAAAAATTT
* * *
125428 ATATAAATATATAATATTTT
1 AAATAAATATATAAAAATTT
*
125448 AAATAATAAAATATAAAAAT
1 AAAT-A-AATATATAAAAAT
125468 AAACAAACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 19 0.63
21 1 0.03
22 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAAATATATAAAAATTT
Found at i:125814 original size:8 final size:8
Alignment explanation
Indices: 125801--125876 Score: 61
Period size: 8 Copynumber: 9.6 Consensus size: 8
125791 CGAGATTTTA
125801 ATTTATAT
1 ATTTATAT
125809 ATTTATATT
1 ATTTATA-T
*
125818 ATATAATAT
1 AT-TTATAT
125827 AATTTATAT
1 -ATTTATAT
125836 ATTTATAT
1 ATTTATAT
125844 -TTTA-A-
1 ATTTATAT
*
125849 ATTTTTAT
1 ATTTATAT
* *
125857 AATTAAAT
1 ATTTATAT
125865 A-TTATAT
1 ATTTATAT
125872 ATTTA
1 ATTTA
125877 ATAAATTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
6 4 0.07
7 11 0.20
8 24 0.44
9 9 0.17
10 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATTTATAT
Found at i:125876 original size:21 final size:21
Alignment explanation
Indices: 125803--125876 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
125793 AGATTTTAAT
125803 TTATATATTTAT-ATTATATA
1 TTATATATTTATAATTATATA
* *
125823 ATATA-ATTTATATATTTATATT
1 TTATATATTTATA-A-TTATATA
* * *
125845 TTAAATTTTTATAATTAAATA
1 TTATATATTTATAATTATATA
125866 TTATATATTTA
1 TTATATATTTA
125877 ATAAATTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
19 6 0.15
20 4 0.10
21 15 0.37
22 10 0.24
23 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATATTTATAATTATATA
Found at i:125895 original size:17 final size:18
Alignment explanation
Indices: 125854--125897 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
125844 TTTAAATTTT
125854 TATAATTAAATATTATATA
1 TATAA-TAAATATTATATA
* *
125873 TTTAATAAATTTTA-ATA
1 TATAATAAATATTATATA
125890 TATAATAA
1 TATAATAA
125898 TTTATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATAATAAATATTATATA
Found at i:125951 original size:21 final size:21
Alignment explanation
Indices: 125918--125970 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
125908 AATTTTTTTG
* *
125918 ATATTTTTATAT-ATTTAAATT
1 ATATTTATATATAAATT-AATT
*
125939 ATATTTATGTATAAATTAATT
1 ATATTTATATATAAATTAATT
125960 ATATGTTATAT
1 ATAT-TTATAT
125971 TTTGATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATATTTATATATAAATTAATT
Found at i:125955 original size:17 final size:17
Alignment explanation
Indices: 125933--125965 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
125923 TTTATATATT
125933 TAAATTATATT-TATGTA
1 TAAATTA-ATTATATGTA
125950 TAAATTAATTATATGT
1 TAAATTAATTATATGT
125966 TATATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TAAATTAATTATATGTA
Found at i:126247 original size:11 final size:11
Alignment explanation
Indices: 126231--126294 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
126221 ATAATTTATA
126231 TATTTATATTT
1 TATTTATATTT
126242 TATTTATATATT
1 TATTTATAT-TT
* *
126254 GTA-TTATGTTA
1 -TATTTATATTT
*
126265 TAATTATATTT
1 TATTTATATTT
*
126276 TATATAT-TTT
1 TATTTATATTT
126286 ATATTTATA
1 -TATTTATA
126295 AATAAATTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
10 5 0.12
11 27 0.66
12 7 0.17
13 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
TATTTATATTT
Found at i:126274 original size:16 final size:16
Alignment explanation
Indices: 126224--126294 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
126214 AAATTTGATA
126224 ATTTATATATTTATATTTT
1 ATTTATATA-TTATA--TT
*
126243 ATTTATATATTGTATT
1 ATTTATATATTATATT
126259 ATGTTATA-ATTATA-T
1 AT-TTATATATTATATT
*
126274 -TTTATATATTTTA-T
1 ATTTATATATTATATT
126288 ATTTATA
1 ATTTATA
126295 AATAAATTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 5 0.11
14 7 0.15
15 7 0.15
16 9 0.20
17 5 0.11
18 4 0.09
19 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
ATTTATATATTATATT
Found at i:126280 original size:49 final size:49
Alignment explanation
Indices: 126225--126330 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
126215 AATTTGATAA
** *
126225 TTTATATA-TTTATATTTTATTTATATATTGT-ATTATGTTA-TAATTATAT
1 TTTATATATTTTATA-TTTATAAATAAATTGTGA-TATGTTAGTAATT-TAT
126274 TTTATATATTTTATATTTATAAATAAATTGTGATATGTTAGTAATTTAT
1 TTTATATATTTTATATTTATAAATAAATTGTGATATGTTAGTAATTTAT
*
126323 ATTATATA
1 TTTATATA
126331 GATTTTGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
49 38 0.76
50 12 0.24
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (49 bp):
TTTATATATTTTATATTTATAAATAAATTGTGATATGTTAGTAATTTAT
Found at i:126294 original size:13 final size:13
Alignment explanation
Indices: 126224--126294 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 13
126214 AAATTTGATA
126224 ATTTATATATTTAT
1 ATTTATAT-TTTAT
126238 ATTT-TATTTATAT
1 ATTTATATTT-TAT
*
126251 ATTGTATTATGTTAT
1 ATT-TA-TATTTTAT
*
126266 AATTATATTTTAT
1 ATTTATATTTTAT
*
126279 ATATTTTATATTTAT
1 AT-TTATAT-TTTAT
126294 A
1 A
126295 AATAAATTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.04
13 17 0.37
14 12 0.26
15 11 0.24
16 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (13 bp):
ATTTATATTTTAT
Found at i:126523 original size:55 final size:55
Alignment explanation
Indices: 126458--126615 Score: 181
Period size: 55 Copynumber: 2.9 Consensus size: 55
126448 AATCTGGTCT
* * * ***
126458 AACTTTTATTTTTTTACTGTTAGATATAGTAAGTGCGTGCATTTTAAGTTGGGGC
1 AACTTTTATTTCTTTACTGTTAGATATAGTAAATGCGTGCATTCTAAGTTAACGC
* * * *
126513 AACTTTTATTTCTTTAGTGTTTGATATAGTAAATACGTGCATTCTAGGTTAACGC
1 AACTTTTATTTCTTTACTGTTAGATATAGTAAATGCGTGCATTCTAAGTTAACGC
* * * * *
126568 GACTTCTATTTCTTTACTGTTAGAGATAATAAATGCGTGCACTCTAAG
1 AACTTTTATTTCTTTACTGTTAGATATAGTAAATGCGTGCATTCTAAG
126616 CTAATCTCGA
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 84 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (55 bp):
AACTTTTATTTCTTTACTGTTAGATATAGTAAATGCGTGCATTCTAAGTTAACGC
Found at i:128393 original size:18 final size:16
Alignment explanation
Indices: 128372--128421 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 16
128362 AAGAATATTG
128372 TGGTGGGTAAGGATAAAA
1 TGGTGGGTAAGGAT--AA
128390 TGGTGGGTAAGGATAA
1 TGGTGGGTAAGGATAA
*
128406 -GGTGGGTAAGGGTAA
1 TGGTGGGTAAGGATAA
128421 T
1 T
128422 ATGAAGGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 14 0.47
16 2 0.07
18 14 0.47
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (16 bp):
TGGTGGGTAAGGATAA
Found at i:128411 original size:15 final size:17
Alignment explanation
Indices: 128372--128416 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
128362 AAGAATATTG
128372 TGGTGGGTAAGGATAAAA
1 TGGTGGGTAAGGAT-AAA
128390 TGGTGGGTAAGGAT-AA
1 TGGTGGGTAAGGATAAA
128406 -GGTGGGTAAGG
1 TGGTGGGTAAGG
128417 GTAATATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.41
16 2 0.07
18 14 0.52
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (17 bp):
TGGTGGGTAAGGATAAA
Found at i:129454 original size:16 final size:16
Alignment explanation
Indices: 129433--129466 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
129423 AATTATGTAC
129433 AAGTAAAAAATATTTT
1 AAGTAAAAAATATTTT
129449 AAGTAAAAAATATTTT
1 AAGTAAAAAATATTTT
129465 AA
1 AA
129467 CTAGTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
AAGTAAAAAATATTTT
Found at i:130728 original size:18 final size:17
Alignment explanation
Indices: 130688--130730 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
130678 TTTGAAATCT
*
130688 TTATTTTCAACAAAAAG
1 TTATTTTCTACAAAAAG
130705 TT-TTTTCTACTAAAAAG
1 TTATTTTCTAC-AAAAAG
130722 TTATTTTCT
1 TTATTTTCT
130731 TTTCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 10 0.43
18 6 0.26
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (17 bp):
TTATTTTCTACAAAAAG
Found at i:131171 original size:36 final size:37
Alignment explanation
Indices: 131083--131228 Score: 118
Period size: 38 Copynumber: 3.9 Consensus size: 37
131073 ACCTAAGTAG
* * *
131083 CTTTTAAAGGT-TTTTTGTCATTTTAGGTCTAAAAGTA
1 CTTTTAAAGATATTTTGGTCATTTTAGGT-TAAAAATA
* *
131120 CTTTTTAGAGTTATTTTGGTCATTTTAGGTTAAAAAT-
1 C-TTTTAAAGATATTTTGGTCATTTTAGGTTAAAAATA
* * * *
131157 CTTTTAAAGATATTTTGGTCGTCTTAGGTTGAAGATA
1 CTTTTAAAGATATTTTGGTCATTTTAGGTTAAAAATA
* * * *
131194 CCTTTTATGAGA-ATTTTGTTCACTTTAGGTCAAAA
1 -CTTTTA-AAGATATTTTGGTCATTTTAGGTTAAAA
131229 GTACCATTAG
Statistics
Matches: 86, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
36 29 0.34
37 2 0.02
38 36 0.42
39 19 0.22
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (37 bp):
CTTTTAAAGATATTTTGGTCATTTTAGGTTAAAAATA
Found at i:136663 original size:14 final size:14
Alignment explanation
Indices: 136644--136671 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
136634 TCTCTAAAAG
136644 TAATAATAAAATAA
1 TAATAATAAAATAA
136658 TAATAATAAAATAA
1 TAATAATAAAATAA
136672 ATTAGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:138391 original size:16 final size:18
Alignment explanation
Indices: 138353--138391 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
138343 ATAATTAACT
*
138353 TTTCATGAAAATGAGTTA
1 TTTCATGAAAATGAGTAA
138371 TTTCATGAAAA-G-GTAA
1 TTTCATGAAAATGAGTAA
138387 TTTCA
1 TTTCA
138392 ATACCTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTCATGAAAATGAGTAA
Found at i:141179 original size:80 final size:79
Alignment explanation
Indices: 140909--141312 Score: 418
Period size: 80 Copynumber: 5.2 Consensus size: 79
140899 TCGAAATACA
140909 GGGTTGGAGTAT-CTCGAGATGAAAATTTTAATATTTTTG-AAATAAAAA-GGGGTTGGAGTATC
1 GGGTTGGAGTATCCTCGAGATGAAAA-TTTAATATTTTTGAAAATAAAAATGGGGTTGGAGTA-C
*
140971 CCC-TCAGAAATAATG
64 CCCTTCAAAAATAATG
* * *
140986 GGGTTGGAGTATCCTCGAGA--AAAATTTAATA-ATTTGAAAATAAAAACGGGGTT-GAGTA-TC
1 GGGTTGGAGTATCCTCGAGATGAAAATTTAATATTTTTGAAAATAAAAATGGGGTTGGAGTACCC
* * *
141046 CTCTCGAAATTGATG
66 CT-TCAAAAATAATG
* **
141061 GGGTTGGAGTATCC-AGAGATGAAAAATTTAGCATTTTTGAAAATAAAAATGGGGTTGGAGTACC
1 GGGTTGGAGTATCCTCGAGATG-AAAATTTAATATTTTTGAAAATAAAAATGGGGTTGGAGTACC
*
141125 CCTTCAAAAATAACG
65 CCTTCAAAAATAATG
* * * * *
141140 AGATTGGAGTATCCTCGAGATGTAAAATTTAATATTTTTGAAAATAAAAATGAGGTTAGAGTATC
1 GGGTTGGAGTATCCTCGAGATG-AAAATTTAATATTTTTGAAAATAAAAATGGGGTTGGAGTACC
* * * *
141205 CCTTTAGAATTGATG
65 CCTTCAAAAATAATG
* * * *
141220 GGGTTGGAGTATCCCCGAGATGAAAAATTTAATA-TTGTGGAAATAAAAATGGGGTTGAAGTATC
1 GGGTTGGAGTATCCTCGAGATG-AAAATTTAATATTTTTGAAAATAAAAATGGGGTTGGAGTA-C
* * *
141284 CTCTT-GAAAATAACG
64 CCCTTCAAAAATAATG
141299 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
141313 ACACGATGAA
Statistics
Matches: 268, Mismatches: 46, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
73 2 0.01
74 8 0.03
75 43 0.16
76 10 0.04
77 21 0.08
78 27 0.10
79 67 0.25
80 90 0.34
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (79 bp):
GGGTTGGAGTATCCTCGAGATGAAAATTTAATATTTTTGAAAATAAAAATGGGGTTGGAGTACCC
CTTCAAAAATAATG
Found at i:141264 original size:159 final size:154
Alignment explanation
Indices: 140909--141312 Score: 523
Period size: 159 Copynumber: 2.6 Consensus size: 154
140899 TCGAAATACA
* * *
140909 GGGTTGGAGTATCTCGAGATGAAAATTTTAATATTTTTGAAATAAAAA-GGGGTTGGAGTATCCC
1 GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
* * *
140973 C-TCAGAAATAATGGGGTTGGAGTATCCTCGAGAAAAATTTAATAATTTGAAAATAAAAACGGGG
66 CTTCAAAAATAACGGGGTTGGAGTATCCTCGAGAAAAATTTAATAATTTGAAAATAAAAACGAGG
*
141037 TTGAGTATCCTCTCGAAATTGATG
131 TTGAGTATCCTCTAGAAATTGATG
* *
141061 GGGTTGGAGTATCCAGAGATGAAAAATTTAGCAT-TTTTGAAAATAAAAATGGGGTTGGAGTA-C
1 GGGTTGGAGTATCCCGAGATGAAAAATTTA--ATATTTTGGAAATAAAAATGGGGTTGGAGTATC
* * *
141124 CCCTTCAAAAATAACGAGATTGGAGTATCCTCGAGATGTAAAATTTAATATTTTTGAAAATAAAA
64 CCCTTCAAAAATAACGGGGTTGGAGTATCCTCGAGA---AAAATTTAATA-ATTTGAAAATAAAA
* *
141189 ATGAGGTTAGAGTATCCCTTTAG-AATTGATG
125 ACGAGGTT-GAGTAT-CCTCTAGAAATTGATG
* *
141220 GGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTGTGGAAATAAAAATGGGGTTGAAGTATCC
1 GGGTTGGAGTAT-CCCGAGATGAAAAATTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCC
* *
141285 TCTT-GAAAATAACGGGGTTGGAGTATCC
65 CCTTCAAAAATAACGGGGTTGGAGTATCC
141313 ACACGATGAA
Statistics
Matches: 217, Mismatches: 22, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
152 27 0.12
153 17 0.08
154 42 0.19
157 11 0.05
158 21 0.10
159 72 0.33
160 27 0.12
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (154 bp):
GGGTTGGAGTATCCCGAGATGAAAAATTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCCC
CTTCAAAAATAACGGGGTTGGAGTATCCTCGAGAAAAATTTAATAATTTGAAAATAAAAACGAGG
TTGAGTATCCTCTAGAAATTGATG
Found at i:141310 original size:79 final size:78
Alignment explanation
Indices: 140909--141327 Score: 428
Period size: 79 Copynumber: 5.4 Consensus size: 78
140899 TCGAAATACA
* *
140909 GGGTTGGAGTAT-CTCGAGATGAAAATTTTAATATTTTTG-AAATAAAAA-GGGGTTGGAGTATC
1 GGGTTGGAGTATCCTCGAGATGAAAAATTTAATA-TTTTGAAAATAAAAATGGGGTTGAAGTATC
* *
140971 CCCTCAGAAATAATG
65 CCTTGA-AAATAATG
* *
140986 GGGTTGGAGTATCCTC--GA-GAAAAATTTAATAATTTGAAAATAAAAACGGGGTTG-AGTATCC
1 GGGTTGGAGTATCCTCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGAAGTATCC
* * *
141047 TCTCGAAATTGATG
66 -CTTGAAAATAATG
* * *
141061 GGGTTGGAGTATCC-AGAGATGAAAAATTTAGCAT-TTTTGAAAATAAAAATGGGGTTGGAGTAC
1 GGGTTGGAGTATCCTCGAGATGAAAAATTTA--ATATTTTGAAAATAAAAATGGGGTTGAAGTAT
* *
141124 CCCTTCAAAAATAACG
64 CCCTT-GAAAATAATG
* * * *
141140 AGATTGGAGTATCCTCGAGATGTAAAATTTAATATTTTTGAAAATAAAAATGAGGTT-AGAGTAT
1 GGGTTGGAGTATCCTCGAGATGAAAAATTTAATA-TTTTGAAAATAAAAATGGGGTTGA-AGTAT
* * *
141204 CCCTTTAGAATTGATG
64 CCCTTGA-AAATAATG
* * *
141220 GGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTGTGGAAATAAAAATGGGGTTGAAGTATCC
1 GGGTTGGAGTATCCTCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGAAGTATCC
*
141285 TCTTGAAAATAACG
66 -CTTGAAAATAATG
*
141299 GGGTTGGAGTATCCAC-ACGATGAAAAATT
1 GGGTTGGAGTATCCTCGA-GATGAAAAATT
141328 CGATGCTTTT
Statistics
Matches: 284, Mismatches: 39, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
74 4 0.01
75 48 0.17
76 13 0.05
77 22 0.08
78 29 0.10
79 84 0.30
80 84 0.30
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.30
Consensus pattern (78 bp):
GGGTTGGAGTATCCTCGAGATGAAAAATTTAATATTTTGAAAATAAAAATGGGGTTGAAGTATCC
CTTGAAAATAATG
Found at i:143772 original size:21 final size:21
Alignment explanation
Indices: 143725--143780 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
143715 ACAAAGTAGT
143725 TTTGTATCGATACATATTAGG
1 TTTGTATCGATACATATTAGG
** *
143746 CATGTATCGATACAT-TTACTG
1 TTTGTATCGATACATATTA-GG
143767 TTTGTATCGATACA
1 TTTGTATCGATACA
143781 AATTGTACAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (21 bp):
TTTGTATCGATACATATTAGG
Found at i:144712 original size:20 final size:20
Alignment explanation
Indices: 144673--144746 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
144663 TTCTACAATT
*
144673 TGTATCGATACAACAAGTTAA
1 TGTATCGATAC-ATAAGTTAA
144694 TGTATCGATACATAAGTTAA
1 TGTATCGATACATAAGTTAA
* *
144714 TGTATCGATATATAAGTGAA
1 TGTATCGATACATAAGTTAA
144734 TGTATCGATACAT
1 TGTATCGATACAT
144747 GCTTACAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 38 0.78
21 11 0.22
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATAAGTTAA
Found at i:148397 original size:290 final size:290
Alignment explanation
Indices: 147863--148423 Score: 917
Period size: 290 Copynumber: 1.9 Consensus size: 290
147853 TGGGCGTCAC
* * *
147863 AAAAAAGTTCATACCTCTTTGCACGTAACCAACTCCCGAACCTAATCAATGAATCTTCGAATCAC
1 AAAAAAGTTCATACCTCTTTGCACGTAACCAACCCCCGAACCCAATCAACGAATCTTCGAATCAC
* * * * *
147928 GTAGACTACGGGATTGATGTTTCGAGTTTCGTAACTCAAAATATAGGTTTCATTAGGCATCCGAT
66 GTAGACCACAGAATTGATGTTTCAAGTTTCGTAACTCAAAATATAGGTTTCAATAGGCATCCGAT
** *
147993 CATACCTAGCCTGAAATGATCGGTGGTGACTCCAAACCTTCGACCATCTTGTGGTGATCGTCAAG
131 CATACCTAGCCTGAAATGATCGGTGACGACTCCAAACCTTCGACCATCTTATGGTGATCGTCAAG
*
148058 GATCGATTAAATAGGCGATTCATCTACTGATCTTCCCCATTTTAATTAACGCATTTCTTATCATG
196 GATCGATTAAATAGGCGATTCATCTACTGATCTTCCCCATTTCAATTAACGCATTTCTTATCATG
148123 CCATAGAAATCTCCAATCCTGAGGGATATT
261 CCATAGAAATCTCCAATCCTGAGGGATATT
* * *
148153 AAAAATGTTCGTACCTCTTTGCGCGTAACCAACCCCCGAACCCAATCAACGAATCTTCGAATCAC
1 AAAAAAGTTCATACCTCTTTGCACGTAACCAACCCCCGAACCCAATCAACGAATCTTCGAATCAC
* *
148218 GTAGACCACAGAATTGATGTTTCAAGTTTTGTAACTCAAAATATAGGTTTCAATAGGCATCTGAT
66 GTAGACCACAGAATTGATGTTTCAAGTTTCGTAACTCAAAATATAGGTTTCAATAGGCATCCGAT
*
148283 CATGCCTAGCCTGAAATGATCGGTGACGACTCCAAACCTTCGACCATCTTATGGTGA-CTGTCAA
131 CATACCTAGCCTGAAATGATCGGTGACGACTCCAAACCTTCGACCATCTTATGGTGATC-GTCAA
* * *
148347 GGATCGATTAAATGGGCGATTCATCTGCTGATCTTCCCTATTTCAATTAACGCATTTCTTATCAT
195 GGATCGATTAAATAGGCGATTCATCTACTGATCTTCCCCATTTCAATTAACGCATTTCTTATCAT
148412 GCCATAGAAATC
260 GCCATAGAAATC
148424 CCTAATCGCG
Statistics
Matches: 249, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
289 1 0.00
290 248 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (290 bp):
AAAAAAGTTCATACCTCTTTGCACGTAACCAACCCCCGAACCCAATCAACGAATCTTCGAATCAC
GTAGACCACAGAATTGATGTTTCAAGTTTCGTAACTCAAAATATAGGTTTCAATAGGCATCCGAT
CATACCTAGCCTGAAATGATCGGTGACGACTCCAAACCTTCGACCATCTTATGGTGATCGTCAAG
GATCGATTAAATAGGCGATTCATCTACTGATCTTCCCCATTTCAATTAACGCATTTCTTATCATG
CCATAGAAATCTCCAATCCTGAGGGATATT
Found at i:155602 original size:52 final size:52
Alignment explanation
Indices: 155517--155641 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
155507 ATATGAAAAG
* *
155517 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
155569 TTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATTTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
155621 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
155642 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:155654 original size:52 final size:51
Alignment explanation
Indices: 155517--155661 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
155507 ATATGAAAAG
*
155517 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
155569 TTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATTTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
155621 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
155662 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:155668 original size:13 final size:13
Alignment explanation
Indices: 155650--155674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155640 CAAAGATCAG
155650 TGTATCGATACAA
1 TGTATCGATACAA
155663 TGTATCGATACA
1 TGTATCGATACA
155675 TTTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:155741 original size:19 final size:18
Alignment explanation
Indices: 155717--155814 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
155707 TAGCTTAAAT
155717 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
155736 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
155749 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
155768 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
155781 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
155801 TGTATCGATACAAA
1 TGTATCGATACAAA
155815 TTGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:155754 original size:13 final size:13
Alignment explanation
Indices: 155736--155792 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
155726 ACAAAACTTA
155736 TGTATCGATACAT
1 TGTATCGATACAT
155749 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
155767 ATGTATCGATACAT
1 -TGTATCGATACAT
155781 TGTATCGATACA
1 TGTATCGATACA
155793 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:155756 original size:32 final size:32
Alignment explanation
Indices: 155715--155812 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
155705 AGTAGCTTAA
*
155715 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
155747 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
155779 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
155812 A
1 A
155813 AATTGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:158070 original size:95 final size:94
Alignment explanation
Indices: 157960--158152 Score: 352
Period size: 95 Copynumber: 2.0 Consensus size: 94
157950 ATATGGAGTG
*
157960 TTTATACTCATTTAGTTCTTTCTCTTGAATCATATTCTAAAATATAGTATTTTAGTTGATTGATT
1 TTTAGACTCATTTAGTTCTTTCTCTTGAATCATATTCTAAAATATAGTATTTTAGTTGATTGATT
158025 C-AAGAGGACACTTGCCATTGTATTAGTCT
66 CGAA-AGGACACTTGCCATTGTATTAGTCT
158054 CTTTAGACTCATTTAGTTCTTTCTCTTGAATCATATTCTAAAATATAGTATTTTAGTTGATTGAT
1 -TTTAGACTCATTTAGTTCTTTCTCTTGAATCATATTCTAAAATATAGTATTTTAGTTGATTGAT
158119 TCGAAAGGACACTTGCCATTGTATTAGTCT
65 TCGAAAGGACACTTGCCATTGTATTAGTCT
158149 TTTA
1 TTTA
158153 ATCACTGGGA
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
94 4 0.04
95 90 0.94
96 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (94 bp):
TTTAGACTCATTTAGTTCTTTCTCTTGAATCATATTCTAAAATATAGTATTTTAGTTGATTGATT
CGAAAGGACACTTGCCATTGTATTAGTCT
Found at i:160162 original size:21 final size:23
Alignment explanation
Indices: 160138--160198 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
160128 TAAGGTTTTG
160138 TTTTATA-TATAA-AATTTATAT
1 TTTTATAGTATAATAATTTATAT
*
160159 TTTTATAGTATAATTATTTATA-
1 TTTTATAGTATAATAATTTATAT
*
160181 TTTTATAAGAATAATAAT
1 TTTTAT-AGTATAATAAT
160199 AATTTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.21
22 11 0.32
23 16 0.47
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (23 bp):
TTTTATAGTATAATAATTTATAT
Found at i:164503 original size:918 final size:920
Alignment explanation
Indices: 162318--165965 Score: 5220
Period size: 921 Copynumber: 4.0 Consensus size: 920
162308 AGTTTGATAC
* * * *
162318 TTCAACATGGCGTCAACGAATTTGACATCCTTTTTCTCAAAATTTTATTATGATTTAACAAAATA
1 TTCAACATGGCGTTAACGAATTGGACAT-CTTTTTCTCAAAATTTTATTATGATTTAAGAAAACA
* * *
162383 TGTTATCTAGTTTAAAATTTTCTTAATGATTCATATTATTGTAATAGGAGCCATAAGCCTATTTT
65 -CTTATCTAGTTTAAAATTTTCTT-ATGATTCATGTTATTGTAATAGGAGCCATAAGGCTATTTT
* * ** *
162448 TTCATTCGATATTGAAAAGCACCAGGCCTTTGGAATTATTATAATTAGCTCTG-GATCATTTTGC
128 TTCATTCTACATTGAAAAGCACCAGGCCTTTGGAATTATTATAATTATTTCTGTGATCATTTTAC
*
162512 TAAATACGTTTGGTC--------T--------TAT--T-TGTTCTCTATATTTTCAAACATTAAG
193 TAAATATGTTTGGTCTTATTTATTGAAAAAAATATAATGTGTTCTCTATATTTTCAAACATTAAG
* * * * *
162558 GTAGTTATTGAGAAATTTTTGATTTATCTATTGTTTTTATTTACAATGATTGCTAAGGAGTACAA
258 GCAATTATTGAGAAATTTTTGATTTACCTATTGTTTCTATTTACAATGATTGCTGAGGAGTACAA
*
162623 AAAAAATGGATCAATTTTTTGCCACACATGG-ATCGCTCATTTTCAAACTCTACCCTACACTTTT
323 AAAAAATGGATCAATTTTTTGCCACACATGGTATCGCTCATTTTCAAACTCTACCCTACACCTTT
* * *
162687 CAACATAATGGTTTTGACAAGCAATGGCACCCTATTATATCAAGTTTCACTTTTTACATTTTTTA
388 CAACATAATGGTTTTGACAAGCAATGGCACCCTATTACATCAAGTTTCACTTCTTACATCTTTTA
* *
162752 AGACCCATTATTTTCAAGCAACAACATATTTGAAAAATCAGATGCCTATTTTTTTACTTGATATG
453 AGACCCATTATTTTCAAGCAACAACATATTTGACAAATCAGATGCCTACTTTTTTACTTGATATG
* * *
162817 AAATTTTCATTTGAAACATTATTTAGTGAGAAATTGAATTACTTAAAACTCAAAGTATTTGGCAG
518 AAATTTTCATTTGAAACATTATTTAGAGAGAAATTGAATTACTTAAAACTCAAAGTATTTGGTAA
*
162882 GC-TTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCA-AGC
583 CCTTTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCATA-C
* *
162945 GCATGCCATGTATACTCTC-TTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAAT
647 ACATGTCATGTATACTCTCTTTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAAT
* * * * *
163009 TATTGTTTTAAGGCATGTTTGATTTATTGAATCTGATTTTTCATTTGCTATAAAGCTTAAGGCCA
712 TATTGTTTCAAGGCATGTTCGATTTATTGAATCTGATTTTCCATTTGCTGTAAAACTTAAGGCCA
*
163074 CATCCATCTTTCACTCCACTAGTAATGAAACTTCTATTGATTCTATCTCTTTAGGTACATTATTT
777 CATCCATCTTTCACTCCACTAGTAATGAAACTTCTATTGATTCTATCTCTTTAGGCACATTATTT
*
163139 TATACTATAACTTTGATGCATAACACCTCTATTACATGTCCTTAAACTATTCTTGAGTTGTAGGC
842 TATACTATAACTTTGATGCATAACACCTCTATTACATTTCCTTAAACTATTCTTGAGTTGTAGGC
163204 ATCATCCCCATAAT
907 ATCATCCCCATAAT
* *
163218 TTCAACATGGCGTTAACGAATTGTACATCATTTTCTCAAAATTTTATTATGATTTAAGAAAACAC
1 TTCAACATGGCGTTAACGAATTGGACATCTTTTTCTCAAAATTTTATTATGATTTAAGAAAACAC
* * *
163283 TTTATTTAGTTTAAAATTTTCTTATGATTCATGTTATTATAATAAGAGCCATAAGGCTATTTTTT
66 -TTATCTAGTTTAAAATTTTCTTATGATTCATGTTATTGTAATAGGAGCCATAAGGCTATTTTTT
* * * *
163348 CATTCTATATTGAAAAGCACCAAGCCTTTGGAATTATTATAATTATTTTTGCGATCATTTTACTA
130 CATTCTACATTGAAAAGCACCAGGCCTTTGGAATTATTATAATTATTTCTGTGATCATTTTACTA
* * *
163413 AATATATTTGGTCTTATTTAATGAAAAAAATATAATGTGTTCTTTATATTTTCAAACATTAAGGC
195 AATATGTTTGGTCTTATTTATTGAAAAAAATATAATGTGTTCTCTATATTTTCAAACATTAAGGC
* * *
163478 AATTATTGAGAAATTTTTTATTTACCTATTGTTTTTATTTACAATGATTGCTGAGG-G-GCATAA
260 AATTATTGAGAAATTTTTGATTTACCTATTGTTTCTATTTACAATGATTGCTGAGGAGTACA-AA
* * *
163541 AAAAATGGATCAATTTTTTGCCACGCATGGTATCGCTTATTTTCAAACTCTATCCTACACCTTTC
324 AAAAATGGATCAATTTTTTGCCACACATGGTATCGCTCATTTTCAAACTCTACCCTACACCTTTC
* * *
163606 AACATAATGGTTTTGATAAGCAATGGCACCCTATTACATTAAGTTTCACTTCTTAAATCTTTTAA
389 AACATAATGGTTTTGACAAGCAATGGCACCCTATTACATCAAGTTTCACTTCTTACATCTTTTAA
* * * *
163671 GACCTATTATTTTCAAGCAACAACATATTTGACAAACCAGATGCTTACTTTTTTACTTTATATGA
454 GACCCATTATTTTCAAGCAACAACATATTTGACAAATCAGATGCCTACTTTTTTACTTGATATGA
* * *
163736 AATTTTTATTTGAAACATTATTTAGAGAGAAATTGAATTA-TATAAAACTCAGAGTATATGGTAA
519 AATTTTCATTTGAAACATTATTTAGAGAGAAATTGAATTACT-TAAAACTCAAAGTATTTGGTAA
*
163800 CCTTTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCACACA
583 CCTTTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCATACA
163865 CATGTCATGTATACTCTCTTTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAATT
648 CATGTCATGTATACTCTCTTTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAATT
*
163930 ATTGTTTCAAGGCATGTTCGATTTATTGAATCTGATTTTTCATTTGCTGTAAAACTTAAGGCCAC
713 ATTGTTTCAAGGCATGTTCGATTTATTGAATCTGATTTTCCATTTGCTGTAAAACTTAAGGCCAC
*
163995 ATCCATCTTTCACTCCACTAGTAATGAAACTTTTATTGATTCTATCTCTTTAGGGCACATTATTT
778 ATCCATCTTTCACTCCACTAGTAATGAAACTTCTATTGATTCTATCTCTTTA-GGCACATTATTT
* *
164060 TATACTATAACTTTGATGCATAACACCTTTATTACATTTCCTTAAATTATTCTTGAGTTGTAGGC
842 TATACTATAACTTTGATGCATAACACCTCTATTACATTTCCTTAAACTATTCTTGAGTTGTAGGC
164125 ATCATCCCCATAAT
907 ATCATCCCCATAAT
* * *
164139 TTCAACATGGCTTTAACAAATTGGACATCTTTTTCTCAAAA-TTTATTATAATTTAAGAAAACAC
1 TTCAACATGGCGTTAACGAATTGGACATCTTTTTCTCAAAATTTTATTATGATTTAAGAAAACAC
* *
164203 -T-T-TAGTTTAAAATTTTCTTACGATTCATGTTATTGTAATAGGAGCCATGAGGCTATTTTTTC
66 TTATCTAGTTTAAAATTTTCTTATGATTCATGTTATTGTAATAGGAGCCATAAGGCTATTTTTTC
* * * *
164265 ATTCTACATTGAAAAGCACTAGGACTTTGGAATTATTATAATTATTTTTGTGATTATTTTACTAA
131 ATTCTACATTGAAAAGCACCAGGCCTTTGGAATTATTATAATTATTTCTGTGATCATTTTACTAA
* * * * *
164330 ATATGTTTGGTTTTATTTATTTAAAAAAATATAATTTGTTCTTTATATTTTCAAACATTAAGGGA
196 ATATGTTTGGTCTTATTTATTGAAAAAAATATAATGTGTTCTCTATATTTTCAAACATTAAGGCA
* *
164395 ATTATTGAGAAATTTTTGATTTACCTATTGTTTCTATTCACAATGATTGCTGATGAGTACAAAAA
261 ATTATTGAGAAATTTTTGATTTACCTATTGTTTCTATTTACAATGATTGCTGAGGAGTAC-AAAA
* * *
164460 AAAATGGATCAATTTTTTGCCACATATGGTATTGCTCATTTTCAAACTCTACCCTACACTTTTCA
325 AAAATGGATCAATTTTTTGCCACACATGGTATCGCTCATTTTCAAACTCTACCCTACACCTTTCA
*
164525 ACATAATGGTTTTGACAAGCAATGGCA-CCTATTACATCAAGTTTCACTTCTTACAGCTTTTAAG
390 ACATAATGGTTTTGACAAGCAATGGCACCCTATTACATCAAGTTTCACTTCTTACATCTTTTAAG
* * * *
164589 ACCCATTATTTTCAAGTAACAACATA-TT------T-AGATGCTTAATTTTTTACTTTATATGAA
455 ACCCATTATTTTCAAGCAACAACATATTTGACAAATCAGATGCCTACTTTTTTACTTGATATGAA
** *
164646 ATTTTCATTTGAAACATTATTCGGAGAGAAATTGAATTACTTAAAACTCAAAGTATTTGATAACC
520 ATTTTCATTTGAAACATTATTTAGAGAGAAATTGAATTACTTAAAACTCAAAGTATTTGGTAACC
* * * *
164711 TTTGTTGCCCTTAGTTAAGGCTATTCAATTCCAATAAACTACAACCTAAGAATAAACCATGCACA
585 TTTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCATACACA
* * * * * *
164776 TGTCATGTATACTTTCCTTTTCAAATTGCCTTTAGGTGTTATAATATTGTCATTGCTAAAATTAT
650 TGTCATGTATACTCTCTTTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAATTAT
* **
164841 TGTTTCAAGGCAGGTTCGATTTATTGAATCACATTTTCCATTTGCTGTAAAACTTAAGGCCACAT
715 TGTTTCAAGGCATGTTCGATTTATTGAATCTGATTTTCCATTTGCTGTAAAACTTAAGGCCACAT
* * * *
164906 CCATATTTCACTCCACTAGTAATGAAATTTCGATTGATTCTATCTCTTTAGGTACATTATTTTAT
780 CCATCTTTCACTCCACTAGTAATGAAACTTCTATTGATTCTATCTCTTTAGGCACATTATTTTAT
**
164971 ACTATAACTTTGATGCATAACACCTCTATTACATTTAATTAAACTATTCTTGAGTTGTAGGCATC
845 ACTATAACTTTGATGCATAACACCTCTATTACATTTCCTTAAACTATTCTTGAGTTGTAGGCATC
*
165036 TTCCCCATAAT
910 ATCCCCATAAT
* *
165047 TTCAACATCGCGTTAACGAATTGGACATCCTTTTCTCAAAATTTTATTATGATTTAAGAAAACAC
1 TTCAACATGGCGTTAACGAATTGGACATCTTTTTCTCAAAATTTTATTATGATTTAAGAAAACAC
*
165112 TTTATCTAGTTTAAAATTTTCTTATGATTCATGTTATTGTAATATGAGCCATAAGGCTATTTTTT
66 -TTATCTAGTTTAAAATTTTCTTATGATTCATGTTATTGTAATAGGAGCCATAAGGCTATTTTTT
* * * *
165177 CATTCTACATTGTAAAGCACCTGTCTTTTGGAATTATTATAATTATTTCTGTGATCATTTTACTA
130 CATTCTACATTGAAAAGCACCAGGCCTTTGGAATTATTATAATTATTTCTGTGATCATTTTACTA
** * * * *
165242 AATAACTTTAGTCTTATTTATTGAAAAAACTATAATGGGTTCTCTATATTTTCAAACATTGAGGC
195 AATATGTTTGGTCTTATTTATTGAAAAAAATATAATGTGTTCTCTATATTTTCAAACATTAAGGC
** * * * *
165307 AATTATTGA-ATTTTTTTTTATTTTCCTATTATTTCCATTTACAATGATTGCTGAGGAGTAC-AA
260 AATTATTGAGA-AATTTTTGATTTACCTATTGTTTCTATTTACAATGATTGCTGAGGAGTACAAA
** * *** * * *
165370 AAAGTTGGATCAATTTTTTGTCGTGCATGGTATCGTTCATTTTCAAACTCTTACCCTATATCTTT
324 AAAAATGGATCAATTTTTTGCCACACATGGTATCGCTCATTTTCAAACTC-TACCCTACACCTTT
* *
165435 CAACATAATGGTTTTGACAAGCTATGGCACCTTATTACATCAAGTTTCACTTCTTACATCTTTTA
388 CAACATAATGGTTTTGACAAGCAATGGCACCCTATTACATCAAGTTTCACTTCTTACATCTTTTA
* * * *
165500 AGACCTATTACTTTCAAGCAACAACATATTTGACATATCATATGCCTACTTTTTTACTTGATATG
453 AGACCCATTATTTTCAAGCAACAACATATTTGACAAATCAGATGCCTACTTTTTTACTTGATATG
* * * **
165565 AAATTTTCATTTGAAATATTATTTAGTGAGAAATTGGATTACTTAAAAC-CTGGAGTATTTGGTA
518 AAATTTTCATTTGAAACATTATTTAGAGAGAAATTGAATTACTTAAAACTC-AAAGTATTTGGTA
* * * * *
165629 GCCTTTGTTACCCTTAGTTAAGGCCATTTAATTCCAATAAACTACAACCTAAGAATATACCATGC
582 ACCTTTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCATAC
* * * * *
165694 ACATTTCATGTATACTTTCTTTTTCAAATTGTTTTTAGGTGTTATGATATTGTCGTTGGTAAAAT
647 ACATGTCATGTATACTCTCTTTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAAT
* * *
165759 TATTGTTTCAAAGCATGTTTGATTTATTGAATCTGATTTTCCATTTGCTGTAAAACTTATGGCCA
712 TATTGTTTCAAGGCATGTTCGATTTATTGAATCTGATTTTCCATTTGCTGTAAAACTTAAGGCCA
* *
165824 CATCCATCTTTCACTCCACTAGTCATGAAGCTTCTATTGATTCTATCTCTTTAGGTC-CATTA-T
777 CATCCATCTTTCACTCCACTAGTAATGAAACTTCTATTGATTCTATCTCTTTAGG-CACATTATT
* * * *
165887 TTATACTATGAC-TT--TG---AACACCTTTATTACATTTCCTTAAACTATTCTTGAGTTGCAAG
841 TTATACTATAACTTTGATGCATAACACCTCTATTACATTTCCTTAAACTATTCTTGAGTTGTAGG
**
165946 CATTTTCCCCATAAT
906 CATCATCCCCATAAT
165961 TTCAA
1 TTCAA
165966 TAAGTTTAAT
Statistics
Matches: 2470, Mismatches: 228, Indels: 86
0.89 0.08 0.03
Matches are distributed among these distances:
898 84 0.03
899 77 0.03
900 25 0.01
907 1 0.00
908 122 0.05
909 332 0.13
910 1 0.00
911 44 0.02
912 41 0.02
913 276 0.11
914 59 0.02
915 3 0.00
916 229 0.09
917 96 0.04
918 374 0.15
919 79 0.03
920 195 0.08
921 432 0.17
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (920 bp):
TTCAACATGGCGTTAACGAATTGGACATCTTTTTCTCAAAATTTTATTATGATTTAAGAAAACAC
TTATCTAGTTTAAAATTTTCTTATGATTCATGTTATTGTAATAGGAGCCATAAGGCTATTTTTTC
ATTCTACATTGAAAAGCACCAGGCCTTTGGAATTATTATAATTATTTCTGTGATCATTTTACTAA
ATATGTTTGGTCTTATTTATTGAAAAAAATATAATGTGTTCTCTATATTTTCAAACATTAAGGCA
ATTATTGAGAAATTTTTGATTTACCTATTGTTTCTATTTACAATGATTGCTGAGGAGTACAAAAA
AAATGGATCAATTTTTTGCCACACATGGTATCGCTCATTTTCAAACTCTACCCTACACCTTTCAA
CATAATGGTTTTGACAAGCAATGGCACCCTATTACATCAAGTTTCACTTCTTACATCTTTTAAGA
CCCATTATTTTCAAGCAACAACATATTTGACAAATCAGATGCCTACTTTTTTACTTGATATGAAA
TTTTCATTTGAAACATTATTTAGAGAGAAATTGAATTACTTAAAACTCAAAGTATTTGGTAACCT
TTGTTACCCTTAATTAAGGCCATTCAATTCCAATAAACTACAACCTAAGAATAAACCATACACAT
GTCATGTATACTCTCTTTTTCAAATTGCTTTTAGGTGTTATGATATGGTCATTGGTAAAATTATT
GTTTCAAGGCATGTTCGATTTATTGAATCTGATTTTCCATTTGCTGTAAAACTTAAGGCCACATC
CATCTTTCACTCCACTAGTAATGAAACTTCTATTGATTCTATCTCTTTAGGCACATTATTTTATA
CTATAACTTTGATGCATAACACCTCTATTACATTTCCTTAAACTATTCTTGAGTTGTAGGCATCA
TCCCCATAAT
Found at i:168184 original size:18 final size:18
Alignment explanation
Indices: 168157--168198 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
168147 ATAAAATATA
* *
168157 AATAACTAATTTTTAATT
1 AATAATTAATTATTAATT
168175 AATAATTAATTATTAATT
1 AATAATTAATTATTAATT
*
168193 ATTAAT
1 AATAAT
168199 AGAGTTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAATTAATTATTAATT
Found at i:172196 original size:88 final size:89
Alignment explanation
Indices: 172026--172231 Score: 288
Period size: 88 Copynumber: 2.3 Consensus size: 89
172016 AAAATCAATT
* * * * * *
172026 TAAAATTATCTAAGTAATCCCAAAGCCATTAGCTAAACATTCAAATTCAACCCTGATTTTTAATT
1 TAAAATGACCTAATTAATCCCAAAACCATTAGCTAAAAATTCAAATTCAACCCTAATTTTTAATT
*
172091 ACATATCACAAATAAAAATCAACC
66 ACATATCACAAATAAAAATAAACC
* * *
172115 TAAATTGACCTAATTAATCCCAAAACCATTTGTTAAAAATTCAAA-TCAACCCTAATTTTTAATT
1 TAAAATGACCTAATTAATCCCAAAACCATTAGCTAAAAATTCAAATTCAACCCTAATTTTTAATT
* * *
172179 ACATTTCACCATTAAAAATAAACC
66 ACATATCACAAATAAAAATAAACC
172203 TAAAATGACCTAATTAATCCCAAAACCAT
1 TAAAATGACCTAATTAATCCCAAAACCAT
172232 GAGGCAAAGT
Statistics
Matches: 103, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 66 0.64
89 37 0.36
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.30
Consensus pattern (89 bp):
TAAAATGACCTAATTAATCCCAAAACCATTAGCTAAAAATTCAAATTCAACCCTAATTTTTAATT
ACATATCACAAATAAAAATAAACC
Found at i:172249 original size:88 final size:89
Alignment explanation
Indices: 172026--172269 Score: 251
Period size: 88 Copynumber: 2.8 Consensus size: 89
172016 AAAATCAATT
* * * * * * * * *
172026 TAAAATTATCTAAGTAATCCCAAAGCCATTAGCT-AAACATTCAAATTCAACCCTGATTTTTAAT
1 TAAAATGACCTAATTAATCCCAAAACCATGAG-TGAAAAATCCAAAATCAACCCTAATTTTTAAT
*
172090 TACATATCACAAATAAAAATCAACC
65 TACATATCACAAATAAAAATAAACC
* ** * *
172115 TAAATTGACCTAATTAATCCCAAAACCATTTGTTAAAAATTC-AAATCAACCCTAATTTTTAATT
1 TAAAATGACCTAATTAATCCCAAAACCATGAGTGAAAAATCCAAAATCAACCCTAATTTTTAATT
* * *
172179 ACATTTCACCATTAAAAATAAACC
66 ACATATCACAAATAAAAATAAACC
* * * *
172203 TAAAATGACCTAATTAATCCCAAAACCATGAG-GCAAAGTCCAAAATCAATCCTAACGTTTTAAT
1 TAAAATGACCTAATTAATCCCAAAACCATGAGTGAAAAATCCAAAATCAACCCTAA-TTTTTAAT
172267 TAC
65 TAC
172270 GTACCATAAT
Statistics
Matches: 130, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
87 5 0.04
88 82 0.63
89 43 0.33
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (89 bp):
TAAAATGACCTAATTAATCCCAAAACCATGAGTGAAAAATCCAAAATCAACCCTAATTTTTAATT
ACATATCACAAATAAAAATAAACC
Found at i:173119 original size:7 final size:7
Alignment explanation
Indices: 173107--173135 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
173097 ATAAACTAAA
173107 CCTAATT
1 CCTAATT
173114 CCTAATT
1 CCTAATT
173121 CCTAATT
1 CCTAATT
173128 CCTAATT
1 CCTAATT
173135 C
1 C
173136 GAGATAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (7 bp):
CCTAATT
Found at i:173520 original size:23 final size:24
Alignment explanation
Indices: 173489--173539 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
173479 AAACTTGAAA
*
173489 TATATTAATATATT-AATA-ATTTT
1 TATAGTAATA-ATTAAATATATTTT
173512 TATAGTAATAATTAAATATATTTT
1 TATAGTAATAATTAAATATATTTT
173536 TATA
1 TATA
173540 ATTAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 3 0.12
23 13 0.52
24 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATAGTAATAATTAAATATATTTT
Found at i:173547 original size:23 final size:24
Alignment explanation
Indices: 173503--173554 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
173493 TTAATATATT
*
173503 AATAATTTTTATAGTAATAA-TTA
1 AATAATTTTTATAATAATAATTTA
*
173526 AATATATTTTTATAATTA-AATTTA
1 AATA-ATTTTTATAATAATAATTTA
173550 AATAA
1 AATAA
173555 AAAATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AATAATTTTTATAATAATAATTTA
Found at i:174329 original size:89 final size:90
Alignment explanation
Indices: 174174--174351 Score: 288
Period size: 89 Copynumber: 2.0 Consensus size: 90
174164 ATACAGTACG
* * *
174174 ACTTGAACATCAACATTTCAAGATCTCATCATTGAAATATTGAGAATTAAATGGTACTTTATTAA
1 ACTTGAACATAAACATTTCAAGATCTCATCATTGAAATATTGAGAATTAAATAGTACTTTAGTAA
174239 GTTATAAAATA-TAATATTTTCTAT
66 GTTATAAAATATTAATATTTTCTAT
* *
174263 ACTTGAACATAAACATTTCAAGATCTCATCATTGTAATATTGAGAATTAGATAGTA-TTCTAGTA
1 ACTTGAACATAAACATTTCAAGATCTCATCATTGAAATATTGAGAATTAAATAGTACTT-TAGTA
174327 AGTTATAAAATATTAATATTTTCTA
65 AGTTATAAAATATTAATATTTTCTA
174352 CAGGTTATAT
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
88 2 0.02
89 68 0.83
90 12 0.15
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (90 bp):
ACTTGAACATAAACATTTCAAGATCTCATCATTGAAATATTGAGAATTAAATAGTACTTTAGTAA
GTTATAAAATATTAATATTTTCTAT
Found at i:174835 original size:12 final size:12
Alignment explanation
Indices: 174819--174896 Score: 59
Period size: 12 Copynumber: 6.3 Consensus size: 12
174809 ATTTTAATTT
* *
174819 AATATAAAATAT
1 AATATAATATAA
174831 AATATAATATAA
1 AATATAATATAA
* * *
174843 AAAATAAAAAAA
1 AATATAATATAA
174855 TAATATAAATATATA
1 -AATAT-AATATA-A
* *
174870 AATATATTAAAA
1 AATATAATATAA
174882 AATAT-ATATAA
1 AATATAATATAA
174893 AATA
1 AATA
174897 AATTATAACA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
11 8 0.16
12 25 0.49
13 8 0.16
14 9 0.18
15 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATATAATATAA
Found at i:174838 original size:17 final size:17
Alignment explanation
Indices: 174813--174904 Score: 69
Period size: 19 Copynumber: 5.2 Consensus size: 17
174803 TATATGATTT
*
174813 TAATTTAATATAAAATA
1 TAATATAATATAAAATA
174830 TAATATAATATAAAAAATAA
1 TAATATAATAT--AAAAT-A
* *
174850 AAAAATAATATAAATATA
1 TAATATAATATAAA-ATA
* *
174868 TAAATATATTAAAAAATA
1 T-AATATAATATAAAATA
* *
174886 T-ATATAAAATAAATTA
1 TAATATAATATAAAATA
174902 TAA
1 TAA
174905 CAAATCAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
16 12 0.21
17 11 0.19
18 8 0.14
19 17 0.29
20 10 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATATAATATAAAATA
Found at i:174861 original size:30 final size:29
Alignment explanation
Indices: 174826--174893 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
174816 TTTAATATAA
174826 AATATAATATAATATAAAAAATAAAAAAAT
1 AATATAA-ATAATATAAAAAATAAAAAAAT
* *
174856 AATATAAAT-ATATAAATATATTAAAAAAT
1 AATATAAATAATATAAA-AAATAAAAAAAT
174885 ATATATAAA
1 A-ATATAAA
174894 ATAAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 7 0.21
29 13 0.38
30 14 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AATATAAATAATATAAAAAATAAAAAAAT
Found at i:175276 original size:21 final size:20
Alignment explanation
Indices: 175252--175289 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
175242 TTATATAAAT
175252 TTAATTATAAAATATAAAAAA
1 TTAA-TATAAAATATAAAAAA
175273 TTAATATAAAA-ATAAAA
1 TTAATATAAAATATAAAA
175290 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAATATAAAATATAAAAAA
Found at i:175442 original size:2 final size:2
Alignment explanation
Indices: 175435--175478 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
175425 TTTCATTCAC
175435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175476 TA T
1 TA T
175479 GGTCCTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175580 original size:23 final size:24
Alignment explanation
Indices: 175542--175588 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
175532 TAAATTTCTT
175542 ATTTAATAAATTA-TTTTTATTAA
1 ATTTAATAAATTATTTTTTATTAA
175565 ATTTAA-AAATTAATTTTTTATTAA
1 ATTTAATAAATT-ATTTTTTATTAA
175589 TATAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 7 0.32
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAATAAATTATTTTTTATTAA
Found at i:175759 original size:17 final size:18
Alignment explanation
Indices: 175737--175770 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
175727 CGTTTATTTT
*
175737 TAAATTAGTA-AAATTAA
1 TAAATTAATATAAATTAA
175754 TAAATTAATATAAATTA
1 TAAATTAATATAAATTA
175771 TTTCTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAATTAATATAAATTAA
Found at i:178310 original size:26 final size:25
Alignment explanation
Indices: 178271--178329 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
178261 AATTTTAGAT
*
178271 AAAAAATAAAAACATAATATAACATA
1 AAAAAATAAAAACATAACATAA-ATA
**
178297 AAAAAATACTAACATAACATAAATA
1 AAAAAATAAAAACATAACATAAATA
*
178322 AATAAATA
1 AAAAAATA
178330 TATTAATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.20
Consensus pattern (25 bp):
AAAAAATAAAAACATAACATAAATA
Found at i:178394 original size:20 final size:22
Alignment explanation
Indices: 178350--178394 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
178340 ACATATCAAA
* *
178350 AAATATATATATATAATATTTT
1 AAATATATATATATAATAATAT
178372 AAATATA-AT-TATAATAATAT
1 AAATATATATATATAATAATAT
178392 AAA
1 AAA
178395 ACATATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATATATATATAATAATAT
Found at i:181934 original size:3 final size:3
Alignment explanation
Indices: 181926--181967 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
181916 TGGAAAATTG
181926 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
181968 TATTCACACA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:184164 original size:13 final size:13
Alignment explanation
Indices: 184123--184171 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
184113 CTGTTACAAG
184123 CAATGTATCGATA
1 CAATGTATCGATA
184136 CAAT-T-TCG-T-
1 CAATGTATCGATA
184145 C-ATGTATCGATA
1 CAATGTATCGATA
184157 CAATGTATCGATA
1 CAATGTATCGATA
184170 CA
1 CA
184172 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:184187 original size:33 final size:34
Alignment explanation
Indices: 184123--184192 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
184113 CTGTTACAAG
*
184123 CAATGTATCGATACAATTTCGTCATGTATCGATA
1 CAATGTATCGATACAATTTCGCCATGTATCGATA
184157 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTATCGATACAATT-TCGCCATGTATCGATA
184190 CAA
1 CAA
184193 ATAGTGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCGCCATGTATCGATA
Found at i:184850 original size:20 final size:21
Alignment explanation
Indices: 184825--184875 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
184815 TTTCGTTTTA
184825 CTCCCCCTTAA-AAAAAAATT
1 CTCCCCCTTAATAAAAAAATT
* *
184845 CTCCCCCTTAATTAAAGAATTT
1 CTCCCCCTTAA-TAAAAAAATT
184867 CTCCCCCTT
1 CTCCCCCTT
184876 TGTCAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.31
Consensus pattern (21 bp):
CTCCCCCTTAATAAAAAAATT
Found at i:186728 original size:13 final size:13
Alignment explanation
Indices: 186710--186736 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
186700 AATAGTACCT
186710 AATGTATCGATAC
1 AATGTATCGATAC
186723 AATGTATCGATAC
1 AATGTATCGATAC
186736 A
1 A
186737 TTTTGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:186793 original size:24 final size:26
Alignment explanation
Indices: 186761--186812 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 26
186751 CAGAAAAGTG
186761 TAATTCAATCAT-AACA-AACAAACA
1 TAATTCAATCATAAACATAACAAACA
186785 TAATTCAATCATACAACATAACAAACA
1 TAATTCAATCATA-AACATAACAAACA
186812 T
1 T
186813 CAAAATTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.48
26 4 0.16
27 9 0.36
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (26 bp):
TAATTCAATCATAAACATAACAAACA
Found at i:196513 original size:20 final size:21
Alignment explanation
Indices: 196483--196541 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 21
196473 GCTACTACCA
*
196483 GTTTCATGTATTGATACAATT
1 GTTTCATGTATCGATACAATT
196504 GTTT-ATGTATCGATACAA-T
1 GTTTCATGTATCGATACAATT
**
196523 G-AGCATGTATCGATACAAT
1 GTTTCATGTATCGATACAAT
196542 GTATCGATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 16 0.48
20 13 0.39
21 4 0.12
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (21 bp):
GTTTCATGTATCGATACAATT
Found at i:196545 original size:13 final size:13
Alignment explanation
Indices: 196527--196553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
196517 TACAATGAGC
196527 ATGTATCGATACA
1 ATGTATCGATACA
196540 ATGTATCGATACA
1 ATGTATCGATACA
196553 A
1 A
196554 AGCAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:196569 original size:33 final size:32
Alignment explanation
Indices: 196508--196572 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
196498 ACAATTGTTT
*
196508 ATGTATCGATACAATGAGCATGTATCGATACA
1 ATGTATCGATACAAAGAGCATGTATCGATACA
*
196540 ATGTATCGATACAAAGCAGTATGTATCGATACA
1 ATGTATCGATACAAAG-AGCATGTATCGATACA
196573 TCTGGAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAGCATGTATCGATACA
Found at i:201533 original size:3 final size:3
Alignment explanation
Indices: 201525--201591 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
201515 ATAAAAATCT
201525 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
201573 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
201592 GCAATTGATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:205887 original size:13 final size:13
Alignment explanation
Indices: 205869--205897 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
205859 GTAAACCCAG
205869 AATGTATCGATAC
1 AATGTATCGATAC
205882 AATGTATCGATAC
1 AATGTATCGATAC
205895 AAT
1 AAT
205898 AAACAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:205895 original size:62 final size:63
Alignment explanation
Indices: 205820--205946 Score: 213
Period size: 62 Copynumber: 2.0 Consensus size: 63
205810 AAAATGCCTA
* *
205820 AATGTATCGATACATTGAAA-AATGTATCGATACATCTGGGT-AAACCCAGAATGTATCGATAC
1 AATGTATCGATACAAT-AAACAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
205882 AATGTATCGATACAATAAACAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
1 AATGTATCGATACAATAAACAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
205945 AA
1 AA
205947 ATTGTGAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 3 0.05
62 35 0.57
63 23 0.38
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (63 bp):
AATGTATCGATACAATAAACAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATAC
Found at i:206652 original size:61 final size:60
Alignment explanation
Indices: 206567--207159 Score: 621
Period size: 61 Copynumber: 9.8 Consensus size: 60
206557 AAATGGGTCT
* * * * ** *
206567 TGCTCCTTGGGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGCAAGGAGAAAGCATCC
1 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGCGTCC
* *
206628 TGCTCTTTGAGGATTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAGACGTCC
1 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-CGTCC
* *
206689 TGCTCTTTGAGGACTAGAAAAGTGCTACCAACTTGTGTGGGCTTCAAAAGGAAAAGACGTCC
1 TGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-CGTCC
* * * * *
206751 TGCTCTTTGAGGATTGGAAAGTGCCACCAACTTGTGTGGACTTTAAAAGGAAAGGCGTCT
1 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCC
* * * *
206811 TACTCTTTGAAGACT-GAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGACGTCC
1 TGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-CGTCC
* * * ** * * *
206872 TGCTCTTTGAGGACTAGAAAATACCACCAACTTATGCAGGCTTTAAAAAGAAAAGGTGTCT
1 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCGTCC
* *
206933 TGCTCCTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGCAAAAGGCGTCC
1 TGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCGTCC
*
206994 TGCTCTTTGAGGACT-GAACAGTGCCACCAACTTGTGTGGGTTTTTAAAA-GAAAAGGCGTCC
1 TGCTCTTTGAGGACTAGAA-AGTGCCACCAACTTGTGTGGG-CTTTAAAAGGAAAA-GCGTCC
* * * * * *
207055 TACTCCTTGAGGACT-GAAAAATGCCACCAACTTGTGTGTGCTTTAAAAGG--TA---TCA
1 TGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCC
* * * * *
207110 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTAGGCTTTGAAAGG
1 TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
207160 CGTCTTGCTC
Statistics
Matches: 456, Mismatches: 64, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
55 44 0.10
56 1 0.00
59 2 0.00
60 64 0.14
61 278 0.61
62 67 0.15
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (60 bp):
TGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCC
Found at i:207284 original size:55 final size:55
Alignment explanation
Indices: 207200--207332 Score: 194
Period size: 55 Copynumber: 2.4 Consensus size: 55
207190 GAAGAGAGCA
* ** *
207200 TCCTGCTCTTTAAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
*
207255 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
** *
207310 TCCTATTCTTTGAGAACTAAAAA
1 TCCTGCTCTTTGAGGACTAAAAA
207333 GGTGAAAGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
Found at i:207445 original size:61 final size:61
Alignment explanation
Indices: 207346--207462 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
207336 GAAAGAGAGA
** * *
207346 GCGTCCTGCTCTTTAAAGACTGGGAAGTGCCACAAACTTGTGTGGTCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTAAAGACTGAAAAATGCCACAAACTTGTGTGGGCTTTAAAAGGAGAAG
* * * * *
207407 GCGTCCTGCTCTTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
1 GCGTCCTGCTCTTTAAAGACTGAAAAATGCCACAAACTTGTGTGGGCTTTAAAAGG
207463 CGTCATGCTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (61 bp):
GCGTCCTGCTCTTTAAAGACTGAAAAATGCCACAAACTTGTGTGGGCTTTAAAAGGAGAAG
Found at i:207465 original size:155 final size:151
Alignment explanation
Indices: 207049--207576 Score: 623
Period size: 155 Copynumber: 3.5 Consensus size: 151
207039 AAAAGAAAAG
* * * ** * * ** *
207049 GCGTCCTACTCCTTGAGGACTGAAAAATGCCACCAACTTGTGTGTGCTTT--A--AAAGGTATCA
1 GCGTCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAGGCGTCC
* * * * *
207110 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTAGGCTTTGAAAGGCGT-CTTGCTCCTGA
66 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTTTCT-TTGA
*
207174 GGACTAAAAGGTCAAAGAAGAGA
130 GGACTAAAAGGTGAAAG-AGAGA
* *
207197 GCATCCTGCTCTTTAAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT--A--AAAGGCGTCC
1 GCGTCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAGGCGTCC
*
207258 TGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTATTCTTTGA
66 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCT-TTCTTTGA
*
207323 GAACTAAAAAGGTGAAAGAGAGA
130 GGACT-AAAAGGTGAAAGAGAGA
* * *
207346 GCGTCCTGCTCTTTAAAGACTGGGAAGTGCCACAAACTTGTGTGGTCTTTAAAAGGAGAAGGCGT
1 GCGTCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGA-AAGGCGT
* * *
207411 CCTGCTCTTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCATGCTCTTT
64 CCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCT-TTCTTT
*
207476 GAGGACTAAAGGGTGAAAGGAGAGA
128 GAGGACTAAAAGGTGAAA-GAGAGA
* * *
207501 GCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT----GAAAGGCGTCA
1 GCGTCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAGGCGTCC
207562 TGCTCTTTGAGGACT
66 TGCTCTTTGAGGACT
207577 AAAGGGTGAA
Statistics
Matches: 331, Mismatches: 39, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
148 98 0.30
149 81 0.24
150 16 0.05
152 1 0.00
154 11 0.03
155 124 0.37
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (151 bp):
GCGTCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAGGCGTCC
TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTTTCTTTGAG
GACTAAAAGGTGAAAGAGAGA
Found at i:207516 original size:94 final size:93
Alignment explanation
Indices: 207397--207650 Score: 377
Period size: 94 Copynumber: 2.7 Consensus size: 93
207387 GTGGTCTTTA
* * * *
207397 AAAGGAGAAGGCGTCCTGCTCTTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 AAAGGAGAA-GCGTCCTACTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
207462 GCGTCATGCTCTTTGAGGACTAAAGGGTG
65 GCGTCATGCTCTTTGAGGACTAAAGGGTG
*
207491 AAAGGAGAGAGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 AAAGGAGA-AGCGTCCTACTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
207556 GCGTCATGCTCTTTGAGGACTAAAGGGTG
65 GCGTCATGCTCTTTGAGGACTAAAGGGTG
* * *
207585 AAAGGAAAAAGCGTCCTATTCTTTGAGGACT-AGGAAGTGCCACCAACTTGCT-TGGGCTTTAAA
1 AAAGG-AGAAGCGTCCTACTCTTTGAGGACTGA-GAAGTGCCACCAACTTG-TGTGGGCTTTGAA
207648 AGG
63 AGG
207651 AAAAGGCGTC
Statistics
Matches: 147, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
94 143 0.97
95 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (93 bp):
AAAGGAGAAGCGTCCTACTCTTTGAGGACTGAGAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
CGTCATGCTCTTTGAGGACTAAAGGGTG
Found at i:211552 original size:28 final size:28
Alignment explanation
Indices: 211471--211552 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
211461 TTTTGGAGAT
*
211471 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
211499 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
211527 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
211553 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:211700 original size:51 final size:51
Alignment explanation
Indices: 211537--211705 Score: 185
Period size: 51 Copynumber: 3.3 Consensus size: 51
211527 AATAACGAGG
* * * *
211537 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAA
1 TTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGGGA
* * * * * *
211589 TTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGGGA
* * * *
211642 TTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGT
1 TTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGA
211693 TTGGAGTATCCCC
1 TTGGAGTATCCCC
211706 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 38 0.40
52 16 0.17
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGA
Found at i:214245 original size:13 final size:13
Alignment explanation
Indices: 214227--214252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
214217 ACAAAGATCC
214227 ATGTATCGATACA
1 ATGTATCGATACA
214240 ATGTATCGATACA
1 ATGTATCGATACA
214253 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:214248 original size:33 final size:33
Alignment explanation
Indices: 214206--214272 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
214196 AAAATTTCCA
***
214206 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
214239 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
214272 A
1 A
214273 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:214316 original size:19 final size:18
Alignment explanation
Indices: 214292--214359 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
214282 CAGTAGCTAA
214292 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
214311 TTATGTATCGGTAC--A-
1 TTATGTATCGATACAAAC
214326 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
214343 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
214360 TCGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:214336 original size:32 final size:32
Alignment explanation
Indices: 214295--214357 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
214285 TAGCTAATTA
* *
214295 TGTATCGATACAATACTTATGTATCGGTACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
214327 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
214358 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:225210 original size:78 final size:79
Alignment explanation
Indices: 225115--225487 Score: 361
Period size: 78 Copynumber: 4.7 Consensus size: 79
225105 AACGGGGCTG
** * * *
225115 GAGTATCCCCGATTATAGAAAATTG-TGTTCTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGG
1 GAGTATCCCCGATTATAGAAAATTGACATTTTGAAAATAAAACTGGGGTTGGAGTATCCCCTCGA
225179 AAATAACAGGGTTA
66 AAATAACAGGGTTA
*
225193 GAGTATCCCTGATTATAGAAAATTGACATTTTGAAAATAAAA-TCGGGG-TGGAGTATCCCCTCG
1 GAGTATCCCCGATTATAGAAAATTGACATTTTGAAAATAAAACT-GGGGTTGGAGTATCCCCTCG
225256 AAAATAACAGGGTTA
65 AAAATAACAGGGTTA
* * * *
225271 GAGTATCCCTGATTATAGAAAATCGACATTTTGAAAATAAAATTGGGGTTGGAGTATCCCCTCAA
1 GAGTATCCCCGATTATAGAAAATTGACATTTTGAAAATAAAACTGGGGTTGGAGTATCCCCTCGA
*
225336 AAATAAC-GGGATTG
66 AAATAACAGGG-TTA
* * * **
225350 GTGTATCCCCGACTGT-GAAAAATTGATGC-TTTT-AGAAATAAGGCTGGGGTTGGAGTAT-CCC
1 GAGTATCCCCGATTATAG-AAAATTGA--CATTTTGA-AAATAAAACTGGGGTTGGAGTATCCCC
* * *
225411 TGCCAAAATAACGGGGTTG
62 T-CGAAAATAACAGGGTTA
* * ** * * *
225430 GAGTATCCCCAATTGT-GAGAAATCAATATTTT-AGAAATAAAACCGGGGTTAGAGTATC
1 GAGTATCCCCGATTATAGA-AAATTGACATTTTGA-AAATAAAACTGGGGTTGGAGTATC
225488 TCCAAGATGA
Statistics
Matches: 253, Mismatches: 28, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
78 103 0.41
79 91 0.36
80 55 0.22
81 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
GAGTATCCCCGATTATAGAAAATTGACATTTTGAAAATAAAACTGGGGTTGGAGTATCCCCTCGA
AAATAACAGGGTTA
Found at i:225447 original size:80 final size:78
Alignment explanation
Indices: 225147--225487 Score: 230
Period size: 79 Copynumber: 4.3 Consensus size: 78
225137 TTGTGTTCTG
** * ** * *
225147 GAAATAAAACTGGGGTTGGAGTATCCCCTCGGAAATAACAGGG-TTAGAGTATCCCTGATTAT-A
1 GAAATAAAACTGGGGTTGGAGTAT-CCCTCAAAAATAAC-GGGATTGGAGTATCCCCAACTGTGA
** *
225210 GAAAATTGACATTTT-
64 -AAAATCAATATTTTA
* * ** * *
225225 GAAAATAAAA-TCGGGG-TGGAGTATCCCCTCGAAAATAACAGGG-TTAGAGTATCCCTGATTAT
1 G-AAATAAAACT-GGGGTTGGAGTAT-CCCTCAAAAATAAC-GGGATTGGAGTATCCCCAACTGT
* *
225287 -AGAAAATCGACATTTT-
62 GA-AAAATCAATATTTTA
* * *
225303 GAAAATAAAATTGGGGTTGGAGTATCCCCTCAAAAATAACGGGATTGGTGTATCCCCGACTGTGA
1 G-AAATAAAACTGGGGTTGGAGTAT-CCCTCAAAAATAACGGGATTGGAGTATCCCCAACTGTGA
** *
225368 AAAATTGATGCTTTTA
64 AAAATCAAT-ATTTTA
** * * * *
225384 GAAATAAGGCTGGGGTTGGAGTATCCCTGCCAAAATAACGGGGTTGGAGTATCCCCAATTGTGAG
1 GAAATAAAACTGGGGTTGGAGTATCCCT-CAAAAATAACGGGATTGGAGTATCCCCAACTGTGAA
225449 AAATCAATATTTTA
65 AAATCAATATTTTA
* *
225463 GAAATAAAACCGGGGTTAGAGTATC
1 GAAATAAAACTGGGGTTGGAGTATC
225488 TCCAAGATGA
Statistics
Matches: 227, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
78 79 0.35
79 86 0.38
80 61 0.27
81 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (78 bp):
GAAATAAAACTGGGGTTGGAGTATCCCTCAAAAATAACGGGATTGGAGTATCCCCAACTGTGAAA
AATCAATATTTTA
Found at i:227868 original size:69 final size:70
Alignment explanation
Indices: 227789--227942 Score: 224
Period size: 70 Copynumber: 2.2 Consensus size: 70
227779 AAAATGCCTG
**
227789 AATGTATCGATACTTTGAAA-AATGTAT-AGATACATCTGGGT-AAACCCAAAATGTAACGATAC
1 AATGTATCGATACAAT-AAACAATGTATCA-ATACATCTGGGTAAAACCCAAAATGTAACGATAC
227851 AATGAAC
64 AATGAAC
* * *
227858 AATGTATCGATACAATAAACAATGTATCAATACATCTGGGTAAAACCTAGAATGTATCGATACAA
1 AATGTATCGATACAATAAACAATGTATCAATACATCTGGGTAAAACCCAAAATGTAACGATACAA
227923 TGAAC
66 TGAAC
227928 AATGTATCGATACAA
1 AATGTATCGATACAA
227943 ATTGTGAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
68 3 0.04
69 33 0.43
70 41 0.53
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (70 bp):
AATGTATCGATACAATAAACAATGTATCAATACATCTGGGTAAAACCCAAAATGTAACGATACAA
TGAAC
Found at i:227884 original size:20 final size:20
Alignment explanation
Indices: 227838--227891 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
227828 GTAAACCCAA
* *
227838 AATGTAACGATACAATGAAC
1 AATGTATCGATACAATAAAC
227858 AATGTATCGATACAATAAAC
1 AATGTATCGATACAATAAAC
*
227878 AATGTATCAATACA
1 AATGTATCGATACA
227892 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAATAAAC
Found at i:228865 original size:93 final size:91
Alignment explanation
Indices: 228609--228858 Score: 279
Period size: 93 Copynumber: 2.7 Consensus size: 91
228599 ACAAGACCAA
* * * * *
228609 CCAATGAAGAATGTGGTTATTATGCTTATTAGCACATAAAAAAAGG-AAACCAAGATGCTTATCT
1 CCAATGAAGAATGTGATTGTAATGCTTATTAG-A-ATATAAAAAGGAAAACCATGATGCTTATCT
* *
228673 TTTAGATGTGCAAAATAAACCAACAATT
64 ATTAGATGTGCAAAATAAACCAACAAGT
* * * *
228701 CCAATGAAGAATGTGGTTGTAATGCTTATTAGCATATAAAAAGAGGAAAACCTTGATGCTTATGT
1 CCAATGAAGAATGTGATTGTAATGCTTATTAGAATAT-AAAA-AGGAAAACCATGATGCTTATCT
* * **
228766 ATTAGATGTGCAAAGTGAAGTAACAAGT
64 ATTAGATGTGCAAAATAAACCAACAAGT
*
228794 CTAATGGAA-AATGTGATTGTAATGCTTATTAGAATATAAAAAGGACAAAGCCATGATGCTTATC
1 CCAAT-GAAGAATGTGATTGTAATGCTTATTAGAATATAAAAAGGA-AAA-CCATGATGCTTATC
228858 T
63 T
228859 CCTAGATATG
Statistics
Matches: 134, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
90 3 0.02
91 8 0.06
92 40 0.30
93 80 0.60
94 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (91 bp):
CCAATGAAGAATGTGATTGTAATGCTTATTAGAATATAAAAAGGAAAACCATGATGCTTATCTAT
TAGATGTGCAAAATAAACCAACAAGT
Found at i:232242 original size:81 final size:81
Alignment explanation
Indices: 232149--232299 Score: 275
Period size: 81 Copynumber: 1.9 Consensus size: 81
232139 AAAAAGTAAG
* *
232149 TTGTGAGTAAAAAAATATATTACCATTTATGTTTATTACCAACATATTAAGAACTTAATGGGTTA
1 TTGTGAGTAAAAAAATATATTAACATTTATGTTTATTACCAACATATTAAGAACCTAATGGGTTA
232214 ACATAATAAAATGGAT
66 ACATAATAAAATGGAT
*
232230 TTGTGAGTAAAAAAATATATTAACGTTTATGTTTATTACCAACATATTAAGAACCTAATGGGTTA
1 TTGTGAGTAAAAAAATATATTAACATTTATGTTTATTACCAACATATTAAGAACCTAATGGGTTA
232295 ACATA
66 ACATA
232300 TTAAGTATGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (81 bp):
TTGTGAGTAAAAAAATATATTAACATTTATGTTTATTACCAACATATTAAGAACCTAATGGGTTA
ACATAATAAAATGGAT
Found at i:235632 original size:60 final size:58
Alignment explanation
Indices: 235539--235650 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 58
235529 ACCAAATTTC
* *
235539 CTTTAACTAGGATTCTCATATGTTACCAAAGGTTTTTTTTTCAGCCATTATAAATAAAAA
1 CTTTAACTAGGATTCTCATATGTGACCAAAGG-TTCTTTTTCAGCCA-TATAAATAAAAA
*
235599 CTTTAACTAGGATTCTTATACT-TGA-CATAAGGTTCTTTTTCAGCCATATAAA
1 CTTTAACTAGGATTCTCATA-TGTGACCA-AAGGTTCTTTTTCAGCCATATAAA
235651 GACTCATGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
58 6 0.13
59 15 0.32
60 25 0.53
61 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (58 bp):
CTTTAACTAGGATTCTCATATGTGACCAAAGGTTCTTTTTCAGCCATATAAATAAAAA
Found at i:237045 original size:21 final size:21
Alignment explanation
Indices: 237001--237057 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
236991 GGTAAGGAAA
*
237001 TGTATCGATACAT-TTTTCTG
1 TGTATCGATACATCTATTCTG
*
237021 TGTATCGATACATCTATTCTT
1 TGTATCGATACATCTATTCTG
237042 TGTATCGATACATCTA
1 TGTATCGATACATCTA
237058 GGAAGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATCTATTCTG
Found at i:239453 original size:52 final size:53
Alignment explanation
Indices: 239396--239517 Score: 158
Period size: 53 Copynumber: 2.3 Consensus size: 53
239386 ATTCTCCGTG
* * * * * *
239396 ATCGGGGATATTCCATCTCTGATTTTATTTTC-AAAAACACTAA-TTTTCTATA
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTC-ACA
*
239448 ATCGGGGATACCCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACA
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACA
239501 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
239518 CCCGTTAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
52 27 0.45
53 28 0.47
54 5 0.08
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (53 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACA
Found at i:239531 original size:27 final size:28
Alignment explanation
Indices: 239501--239575 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
239491 ATTTTTCACA
*
239501 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCATTATATC
*
239528 ATCGGGGATACTCCAACCCCATTATTTC
1 ATCGGGGATACTCCAACCCCATTATATC
*
239556 -TGAGGGGATACTCCAACCCC
1 AT-CGGGGATACTCCAACCCC
239576 TGCTTTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATATC
Found at i:239626 original size:51 final size:50
Alignment explanation
Indices: 239559--239778 Score: 227
Period size: 51 Copynumber: 4.4 Consensus size: 50
239549 TTATTTCTGA
* * * * *
239559 GGGGATACTCCAACCCCTGCTTTATTCTTAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTCTTAAAACACTAATTT-TCATAATC
239610 GGGGATACTCCAACCCCGGTTTTATTGC-TAAAACACTAATTTTTTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATT-CTTAAAACACTAA--TTTTCATAATC
239662 GGGGATACTCCAACCCCGGTTTTATT-TTCAAAACACTAATTTTCTATAATC
1 GGGGATACTCCAACCCCGGTTTTATTCTT-AAAACACTAATTTTC-ATAATC
** * * *
239713 GAAGATACTCCAACTCCGATTTTATT-TCTAAAACA-TCAATTTT--TCATC
1 GGGGATACTCCAACCCCGGTTTTATTCT-TAAAACACT-AATTTTCATAATC
*
239761 GGAGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
239779 TTAATCATCG
Statistics
Matches: 149, Mismatches: 12, Indels: 19
0.83 0.07 0.11
Matches are distributed among these distances:
48 20 0.13
50 6 0.04
51 74 0.50
52 46 0.31
53 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGGTTTTATTCTTAAAACACTAATTTTCATAATC
Found at i:239686 original size:103 final size:99
Alignment explanation
Indices: 239559--239778 Score: 257
Period size: 103 Copynumber: 2.2 Consensus size: 99
239549 TTATTTCTGA
* * * * **
239559 GGGGATACTCCAACCCCTGCTTTATTCTT-AAAATATTGA-TTTCTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGGCTTTATT-TTCAAAACACTAATTTTCT-ATAATCGAAGATACTCCA
*
239622 ACCCCGGTTTTATTGCTAAAACA-CTAATTTTTTCATAATC
64 ACCCCGATTTTATTGCTAAAACATC-AA-TTTTTC---ATC
*
239662 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCTATAATCGAAGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACTAATTTTCTATAATCGAAGATACTCCAAC
* *
239727 TCCGATTTTATTTCTAAAACATCAATTTTTCATC
66 CCCGATTTTATTGCTAAAACATCAATTTTTCATC
*
239761 GGAGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
239779 TTAATCATCG
Statistics
Matches: 103, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
99 20 0.19
102 8 0.08
103 69 0.67
104 6 0.06
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (99 bp):
GGGGATACTCCAACCCCGGCTTTATTTTCAAAACACTAATTTTCTATAATCGAAGATACTCCAAC
CCCGATTTTATTGCTAAAACATCAATTTTTCATC
Found at i:239795 original size:27 final size:27
Alignment explanation
Indices: 239756--239808 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
239746 CATCAATTTT
239756 TCATCGGAGATACTCCAACCCCGTTAA
1 TCATCGGAGATACTCCAACCCCGTTAA
239783 TCATCGG-GAATACTCCAACCCCGTTA
1 TCATCGGAG-ATACTCCAACCCCGTTA
239809 CCTCCGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (27 bp):
TCATCGGAGATACTCCAACCCCGTTAA
Found at i:239832 original size:28 final size:27
Alignment explanation
Indices: 239764--239833 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
239754 TTTCATCGGA
**
239764 GATACTCCAACCCCGTTAATCATCGGG
1 GATACTCCAACCCCGTTAATCAGAGGG
* * *
239791 AATACTCCAACCCCGTTACCTCCGAGGG
1 GATACTCCAACCCCGTTA-ATCAGAGGG
239819 GATACTCCAACCCCG
1 GATACTCCAACCCCG
239834 GCTTTATTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.26, C:0.39, G:0.17, T:0.19
Consensus pattern (27 bp):
GATACTCCAACCCCGTTAATCAGAGGG
Found at i:239936 original size:79 final size:79
Alignment explanation
Indices: 239787--239991 Score: 202
Period size: 79 Copynumber: 2.6 Consensus size: 79
239777 CGTTAATCAT
* ** *
239787 CGGGAATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
* * *
239852 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * ** *
239866 TGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGATG-TTT-TTTTC-TAAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCG--GCTTTATTCCCAAAAT
239928 CATCGATTTCTCACAAC
64 -ATCGATTTCTCACAAC
* * * *
239945 CGGGGATACTCCAGCCCCGTCATTT-TCAAGGGGACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCG
239992 TTATTATCTC
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
78 4 0.04
79 96 0.92
80 3 0.03
81 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:253504 original size:19 final size:19
Alignment explanation
Indices: 253447--253505 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
253437 TACAAGCCAA
* * *
253447 TGTATCAATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
253467 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
253487 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
253506 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.18
20 27 0.79
21 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:255610 original size:21 final size:20
Alignment explanation
Indices: 255581--255623 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
255571 GGCCAGTGTG
*
255581 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
255602 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
255622 GG
1 GG
255624 TGGTGATGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:256082 original size:13 final size:13
Alignment explanation
Indices: 256064--256102 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
256054 ATAATCCCCC
* *
256064 TGTATCGATATAG
1 TGTATCGATACAA
256077 TGTATCGATACAA
1 TGTATCGATACAA
256090 TGTATCGATACAA
1 TGTATCGATACAA
256103 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:262298 original size:13 final size:13
Alignment explanation
Indices: 262280--262304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
262270 CAATTTTTTG
262280 TGTATCGATACAT
1 TGTATCGATACAT
262293 TGTATCGATACA
1 TGTATCGATACA
262305 AGTTTGGCTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:263640 original size:23 final size:23
Alignment explanation
Indices: 263603--263650 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
263593 GCCCTAACCC
* * *
263603 AAAATATTGAGTTGATATTTTTG
1 AAAATATTGAATTGAAATTTATG
*
263626 AAAATATTTAATTGAAATTTATG
1 AAAATATTGAATTGAAATTTATG
263649 AA
1 AA
263651 TGCATTGTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAATATTGAATTGAAATTTATG
Found at i:269145 original size:14 final size:15
Alignment explanation
Indices: 269134--269226 Score: 55
Period size: 16 Copynumber: 5.9 Consensus size: 15
269124 ACAAATATGA
269134 TATAATAAATATAAT
1 TATAATAAATATAAT
* *
269149 TATAATACAATAAAAA
1 TATAATA-AATATAAT
*
269165 AATAATTAAAATATAAT
1 TATAA-T-AAATATAAT
* *
269182 ATAAAATAAAAAATAA-
1 -TATAAT-AAATATAAT
*
269198 TATGAATATAATATAAA
1 TAT-AATA-AATATAAT
269215 TAT-ATAAATATA
1 TATAATAAATATA
269227 TTAAAATCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.10
15 13 0.21
16 19 0.31
17 19 0.31
18 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (15 bp):
TATAATAAATATAAT
Found at i:269168 original size:28 final size:28
Alignment explanation
Indices: 269137--269210 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
269127 AATATGATAT
*
269137 AATAAATATAATTATAATACAATA-AAAA
1 AATAAATATAA-TATAATACAAAATAAAA
* * *
269165 AATAATTAAAATATAATATAAAATAAAA
1 AATAAATATAATATAATACAAAATAAAA
269193 AAT-AATATGAATATAATA
1 AATAAATAT-AATATAATA
269211 TAAATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (28 bp):
AATAAATATAATATAATACAAAATAAAA
Found at i:269191 original size:17 final size:17
Alignment explanation
Indices: 269171--269224 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
269161 AAAAAATAAT
269171 TAAAATATAATATAAAA
1 TAAAATATAATATAAAA
* *
269188 TAAAAAATAATAT-GAA
1 TAAAATATAATATAAAA
*
269204 TATAATATAAATATATAAA
1 TAAAATAT-AATATA-AAA
269223 TA
1 TA
269225 TATTAAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 8 0.28
17 17 0.59
19 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAATATAATATAAAA
Found at i:269205 original size:6 final size:5
Alignment explanation
Indices: 269127--269246 Score: 65
Period size: 5 Copynumber: 24.4 Consensus size: 5
269117 GATGTATACA
* * * * *
269127 AATAT GATAT AATA- AATAT AATTAT AATAC AATAAA AAAAT AATTAA
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AAT-AT AATAT AA-TAT
*
269174 AATAT AATAT AAAAT AA-A- AA-AT AATAT GAATAT AATAT AA-AT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT
* * *
269220 AAATAT ATTAA AATCT AA-AT AATAT AA
1 -AATAT AATAT AATAT AATAT AATAT AA
269247 ATTATGAACA
Statistics
Matches: 88, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
3 4 0.05
4 14 0.16
5 50 0.57
6 20 0.23
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:269210 original size:11 final size:11
Alignment explanation
Indices: 269138--269218 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
269128 ATATGATATA
269138 ATAAATATAAT
1 ATAAATATAAT
*
269149 -TATAATACAAT
1 ATA-AATATAAT
* *
269160 AAAAAAATAAT
1 ATAAATATAAT
269171 -TAAAATATAAT
1 AT-AAATATAAT
269182 ATAAA-AT-A-
1 ATAAATATAAT
269190 A-AAA-ATAAT
1 ATAAATATAAT
*
269199 ATGAATATAAT
1 ATAAATATAAT
269210 ATAAATATA
1 ATAAATATA
269219 TAAATATATT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 2 0.04
10 6 0.11
11 37 0.69
12 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:269211 original size:28 final size:28
Alignment explanation
Indices: 269161--269247 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
269151 TAATACAATA
269161 AAAAAATAATTAAAATATAATATAAAAT
1 AAAAAATAATTAAAATATAATATAAAAT
*
269189 AAAAAATAA-TATGAATATAATAT-AAAT
1 AAAAAATAATTA-AAATATAATATAAAAT
* * *
269216 ATATAAATATATTAAAATCTAA-ATAATAT
1 A-AAAAATA-ATTAAAATATAATATAAAAT
269245 AAA
1 AAA
269248 TTATGAACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
27 7 0.15
28 28 0.58
29 11 0.23
30 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAAAATAATTAAAATATAATATAAAAT
Found at i:269271 original size:32 final size:33
Alignment explanation
Indices: 269205--269273 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
269195 TAATATGAAT
* *
269205 ATAATATAAATATATAAATATATTAAAATCTAA
1 ATAATATAAATATATAAACATATCAAAATCTAA
* *
269238 ATAATATAAAT-TATGAACATATCAAAATTTAA
1 ATAATATAAATATATAAACATATCAAAATCTAA
269270 ATAA
1 ATAA
269274 AATATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 21 0.66
33 11 0.34
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (33 bp):
ATAATATAAATATATAAACATATCAAAATCTAA
Found at i:269318 original size:17 final size:18
Alignment explanation
Indices: 269298--269340 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
269288 TAAACATTAT
*
269298 TATATAACATA-TAAAAA
1 TATATAACATAGGAAAAA
*
269315 TATATAAACATAGGACAAA
1 TATAT-AACATAGGAAAAA
269334 TATATAA
1 TATATAA
269341 ATTATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 9 0.41
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (18 bp):
TATATAACATAGGAAAAA
Found at i:269864 original size:2 final size:2
Alignment explanation
Indices: 269859--269890 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
269849 TTTTTTTAGC
269859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
269891 TCTCTCAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272030 original size:17 final size:17
Alignment explanation
Indices: 272008--272040 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
271998 ATCCTAAAAA
272008 GAATTGCAAAAGCATGC
1 GAATTGCAAAAGCATGC
272025 GAATTGCAAAAGCATG
1 GAATTGCAAAAGCATG
272041 ACGATTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18
Consensus pattern (17 bp):
GAATTGCAAAAGCATGC
Found at i:273933 original size:20 final size:20
Alignment explanation
Indices: 273900--273952 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
273890 AAAGTTTTCG
* ** *
273900 AAAAAGATAAATAAATTTTT
1 AAAAATATAAATAAAAATTA
*
273920 AAAAATATATATAAAAATTA
1 AAAAATATAAATAAAAATTA
273940 AAAAATATAAATA
1 AAAAATATAAATA
273953 CTTTTATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATATAAATAAAAATTA
Found at i:276822 original size:30 final size:32
Alignment explanation
Indices: 276788--276857 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
276778 TCTATTTTTA
*
276788 TTTTATTGAAATTTGA-AATTAAATTTTGA-T
1 TTTTATTGAAATTTGATAATTAAATTTTCATT
* * *
276818 TTTTATTG-GATTTTATAATTCAATTTTCATT
1 TTTTATTGAAATTTGATAATTAAATTTTCATT
276849 TTTTATTGA
1 TTTTATTGA
276858 CTTTAGCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 5 0.15
30 19 0.58
31 9 0.27
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.59
Consensus pattern (32 bp):
TTTTATTGAAATTTGATAATTAAATTTTCATT
Found at i:277667 original size:25 final size:25
Alignment explanation
Indices: 277633--277685 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
277623 GGAAACGAGG
*
277633 AAAGAAGAAATGAA-AAAGAAAG-AA
1 AAAGAAGAAA-AAAGAAAGAAAGTAA
277657 AAAGAGAGAAAAAAGAAAGAAAGTAA
1 AAAGA-AGAAAAAAGAAAGAAAGTAA
277683 AAA
1 AAA
277686 ATAATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAGAAGAAAAAAGAAAGAAAGTAA
Found at i:277668 original size:9 final size:10
Alignment explanation
Indices: 277632--277678 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 10
277622 GGGAAACGAG
277632 GAAAGAAGAAA
1 GAAA-AAGAAA
277643 TGAAAAAGAAA
1 -GAAAAAGAAA
*
277654 GAAAAAGAGA
1 GAAAAAGAAA
277664 GAAAAAAGAAA
1 G-AAAAAGAAA
277675 GAAA
1 GAAA
277679 GTAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 13 0.41
11 15 0.47
12 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:280488 original size:2 final size:2
Alignment explanation
Indices: 280481--280519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
280471 TTTTAGGTTT
280481 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 T
280520 CTTATAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:280621 original size:19 final size:19
Alignment explanation
Indices: 280594--280632 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
280584 GGAATAAGTG
* *
280594 TGTAATTTTTTTATGATTA
1 TGTAATTTTATTATAATTA
*
280613 TGTATTTTTATTATAATTA
1 TGTAATTTTATTATAATTA
280632 T
1 T
280633 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (19 bp):
TGTAATTTTATTATAATTA
Found at i:280693 original size:27 final size:23
Alignment explanation
Indices: 280630--280701 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 23
280620 TTATTATAAT
280630 TATATTAAAAATATTATTTATATA
1 TATATT-AAAATATTATTTATATA
* *
280654 TATATTGACATATTATATATATATA
1 TATATTAAAATATTAT-T-TATATA
280679 TATATTTTAAAATATTTATTTAT
1 TATA--TTAAAATA-TTATTTAT
280702 TTTTTAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 8 0.21
24 7 0.18
25 10 0.26
26 3 0.08
27 7 0.18
28 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
TATATTAAAATATTATTTATATA
Found at i:280722 original size:20 final size:20
Alignment explanation
Indices: 280668--280726 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
280658 TTGACATATT
280668 ATATATATATATATATTTTAAA
1 ATAT-TATAT-TATATTTTAAA
**
280690 ATATT-TATT-TATTTTTTA
1 ATATTATATTATATTTTAAA
280708 ATATTATATTATATTTTAA
1 ATATTATATTATATTTTAA
280727 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 12 0.39
19 5 0.16
20 9 0.29
21 1 0.03
22 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTATATTATATTTTAAA
Found at i:281083 original size:22 final size:21
Alignment explanation
Indices: 281056--281118 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 21
281046 AATTTTCAAA
* *
281056 TTATATTATATTTTTGTTTTT
1 TTATATTATATTTATATTTTT
281077 TTAATATTAATATTTATATTTTT
1 TT-ATATT-ATATTTATATTTTT
281100 TTATATTATCA-TTATATTT
1 TTATATTAT-ATTTATATTT
281119 AAAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 12 0.32
22 11 0.30
23 14 0.38
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTATATTATATTTATATTTTT
Found at i:281547 original size:16 final size:15
Alignment explanation
Indices: 281511--281549 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
281501 ATTAAATTTA
281511 TTTTTTAATTTAAAT
1 TTTTTTAATTTAAAT
**
281526 AATTTTAGATTTAAAT
1 TTTTTTA-ATTTAAAT
281542 TTTTTTAA
1 TTTTTTAA
281550 GTTTGGATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTTTAATTTAAAT
Found at i:282808 original size:11 final size:11
Alignment explanation
Indices: 282792--282816 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
282782 AACATAAAAA
282792 ATAATATAAAT
1 ATAATATAAAT
282803 ATAATATAAAT
1 ATAATATAAAT
282814 ATA
1 ATA
282817 TAAACGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:283334 original size:23 final size:25
Alignment explanation
Indices: 283285--283339 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
283275 ATTGAAATAC
* *
283285 AATAT-AAGCACAATATAAGAAAAT
1 AATATAAAACACAACATAAGAAAAT
283309 AAT-TAAAACACAACATAA-AAAAT
1 AATATAAAACACAACATAAGAAAAT
283332 AATATAAA
1 AATATAAA
283340 TACTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (25 bp):
AATATAAAACACAACATAAGAAAAT
Found at i:286579 original size:23 final size:24
Alignment explanation
Indices: 286553--286603 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
286543 AATAACCCAT
*
286553 TATTAATATTTTTATTG-ATAATA
1 TATTAATAATTTTATTGCATAATA
*
286576 TATTATTAATTTTATTGCATAATA
1 TATTAATAATTTTATTGCATAATA
286600 -ATTA
1 TATTA
286604 GAAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
TATTAATAATTTTATTGCATAATA
Found at i:288371 original size:18 final size:18
Alignment explanation
Indices: 288348--288387 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
288338 GATTTCATTG
288348 GAAAAATACATGTTATAT
1 GAAAAATACATGTTATAT
288366 GAAAAATACATGTTATAT
1 GAAAAATACATGTTATAT
288384 GAAA
1 GAAA
288388 TAGTTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (18 bp):
GAAAAATACATGTTATAT
Found at i:288874 original size:17 final size:17
Alignment explanation
Indices: 288852--288894 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
288842 TATTATGTAC
288852 ATTCATGAAC-ATTGAAT
1 ATTCATGAACTA-TGAAT
288869 ATTCATGAACTATGAAT
1 ATTCATGAACTATGAAT
*
288886 ATACATGAA
1 ATTCATGAA
288895 TGATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
ATTCATGAACTATGAAT
Found at i:289589 original size:21 final size:21
Alignment explanation
Indices: 289550--289589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
289540 TACATGACCA
**
289550 AATGTATCGATACTTGTTAAG
1 AATGTATCGATACAGGTTAAG
289571 AATGTATCGATACAGGTTA
1 AATGTATCGATACAGGTTA
289590 TTGGCAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACAGGTTAAG
Done.