Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 137 of 141
Found at i:41155973 original size:157 final size:157
Alignment explanation
Indices: 41155805--41156134 Score: 606
Period size: 157 Copynumber: 2.1 Consensus size: 157
41155795 TATGTACAAG
41155805 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
1 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
* *
41155870 TTACATAATACATAACTTATATGTAAACATACATAATACATAACTTATAAATTTTTTTTATATAA
66 TTACATAATACATAACTTACATGTAAACATACATAATACATAACTTATAAAATTTTTTTATATAA
*
41155935 ACTTACATAATACATTACTTACATATT
131 ACTTACATAACACATTACTTACATATT
41155962 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
1 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
* *
41156027 TTACATAATACATAACTTACATGTTAACTTACATAATACATAACTTATAAAATTTTTTTATATAA
66 TTACATAATACATAACTTACATGTAAACATACATAATACATAACTTATAAAATTTTTTTATATAA
41156092 ACTTACATAACACATTACTTACATATT
131 ACTTACATAACACATTACTTACATATT
*
41156119 AACTTACATAAGTTAT
1 AACTTACATAACTTAT
41156135 CTACAAGCTT
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 167 1.00
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.39
Consensus pattern (157 bp):
AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
TTACATAATACATAACTTACATGTAAACATACATAATACATAACTTATAAAATTTTTTTATATAA
ACTTACATAACACATTACTTACATATT
Found at i:41156045 original size:16 final size:16
Alignment explanation
Indices: 41156024--41156073 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
41156014 CTTATATGTA
41156024 AACTTACATAATACAT
1 AACTTACATAATACAT
*
41156040 AACTTACAT-GT---T
1 AACTTACATAATACAT
41156052 AACTTACATAATACAT
1 AACTTACATAATACAT
41156068 AACTTA
1 AACTTA
41156074 TAAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:41156189 original size:157 final size:157
Alignment explanation
Indices: 41155805--41156197 Score: 564
Period size: 157 Copynumber: 2.5 Consensus size: 157
41155795 TATGTACAAG
* * *
41155805 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
1 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAAAAC
* *
41155870 TTACATAATACATAACTTATATGTAAACATACATAATACATAACTTATAAATTTTTTTTATATAA
66 TTACATAATACATAACTTACATGTAAACATACATAATACATAACTTATAAAATTTTTTTATATAA
*
41155935 ACTTACATAATACATTACTTACATATT
131 ACTTACATAACACATTACTTACATATT
* * *
41155962 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTAAAC
1 AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAAAAC
* *
41156027 TTACATAATACATAACTTACATGTTAACTTACATAATACATAACTTATAAAATTTTTTTATATAA
66 TTACATAATACATAACTTACATGTAAACATACATAATACATAACTTATAAAATTTTTTTATATAA
41156092 ACTTACATAACACATTACTTACATATT
131 ACTTACATAACACATTACTTACATATT
* * *
41156119 AACTTACATAAGTTATCTACA-AGCTTATATATAAACTTGCATAACT-T-ACGT-AA-TAACAT-
1 AACTTACATAACTTAT-TA-ATA--TT-TATATAAACTTACATAACTATCACATAAACTAACATG
41156178 AACAACTTACATAATACATA
61 AA-AACTTACATAATACATA
41156198 GCATACGTAA
Statistics
Matches: 219, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
156 1 0.00
157 188 0.86
158 5 0.02
159 4 0.02
160 3 0.01
161 18 0.08
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (157 bp):
AACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAAAAC
TTACATAATACATAACTTACATGTAAACATACATAATACATAACTTATAAAATTTTTTTATATAA
ACTTACATAACACATTACTTACATATT
Found at i:41156209 original size:25 final size:25
Alignment explanation
Indices: 41156181--41156440 Score: 112
Period size: 25 Copynumber: 10.1 Consensus size: 25
41156171 ATAACATAAC
*
41156181 AACTTACATAA-TACATAGCATACGT
1 AACTTACATAACTACATA-CATACAT
*
41156206 AACTTACATAACTTACATA-ATACAA
1 AACTTACATAAC-TACATACATACAT
* *
41156231 AACTTCCATAACTTACATAACCTACAT
1 AACTTACATAAC-TACAT-ACATACAT
* *
41156258 AACCTACATAA-TACATTTAACTTACAT
1 AACTTACATAACTACA--T-ACATACAT
41156285 AACTTACATAACTTACATA-ATACATAAT
1 AACTTACATAAC-TACATACATAC---AT
*
41156313 AACTTAC--AACTTAAATAACATACAT
1 AACTTACATAAC-TACAT-ACATACAT
* ** *
41156338 TACTTTGATAACTTACATAACTTACAT
1 AACTTACATAAC-TACAT-ACATACAT
* * *
41156365 AA--TACACAACTTACATAGCTTACTT
1 AACTTACATAAC-TACATA-CATACAT
*
41156390 AAC--ACATAACT-TATACACGTACAT
1 AACTTACATAACTACATACA--TACAT
*
41156414 AACTTACATAACTTACTTA-ATACAT
1 AACTTACATAAC-TACATACATACAT
41156439 AA
1 AA
41156441 ATATATATCA
Statistics
Matches: 185, Mismatches: 27, Indels: 46
0.72 0.10 0.18
Matches are distributed among these distances:
22 1 0.01
23 3 0.02
24 9 0.05
25 77 0.42
26 17 0.09
27 59 0.32
28 15 0.08
29 4 0.02
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTACATACATACAT
Found at i:41156217 original size:9 final size:9
Alignment explanation
Indices: 41156181--41156429 Score: 195
Period size: 9 Copynumber: 28.8 Consensus size: 9
41156171 ATAACATAAC
41156181 AACTTACAT
1 AACTTACAT
41156190 AA--TACAT
1 AACTTACAT
* * *
41156197 AGCATACGT
1 AACTTACAT
41156206 AACTTACAT
1 AACTTACAT
41156215 AACTTACAT
1 AACTTACAT
*
41156224 AA--TACAA
1 AACTTACAT
*
41156231 AACTTCCAT
1 AACTTACAT
41156240 AACTTACAT
1 AACTTACAT
*
41156249 AACCTACAT
1 AACTTACAT
*
41156258 AACCTACAT
1 AACTTACAT
41156267 AA--TACATTT
1 AACTTACA--T
41156276 AACTTACAT
1 AACTTACAT
41156285 AACTTACAT
1 AACTTACAT
41156294 AACTTACAT
1 AACTTACAT
*
41156303 AATACATA-AT
1 -A-ACTTACAT
41156313 AACTTAC--
1 AACTTACAT
*
41156320 AACTTAAAT
1 AACTTACAT
*
41156329 AACATACAT
1 AACTTACAT
* **
41156338 TACTTTGAT
1 AACTTACAT
41156347 AACTTACAT
1 AACTTACAT
41156356 AACTTACAT
1 AACTTACAT
*
41156365 AA--TACAC
1 AACTTACAT
41156372 AACTTACAT
1 AACTTACAT
* *
41156381 AGCTTACTT
1 AACTTACAT
41156390 AAC--ACAT
1 AACTTACAT
41156397 AACTT--AT
1 AACTTACAT
*
41156404 ACACGTACAT
1 A-ACTTACAT
41156414 AACTTACAT
1 AACTTACAT
41156423 AACTTAC
1 AACTTAC
41156430 TTAATACATA
Statistics
Matches: 190, Mismatches: 30, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
7 37 0.19
8 7 0.04
9 132 0.69
10 6 0.03
11 8 0.04
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:41156235 original size:70 final size:68
Alignment explanation
Indices: 41156161--41156437 Score: 173
Period size: 71 Copynumber: 4.0 Consensus size: 68
41156151 AAACTTGCAT
*
41156161 AACTTACGTAA-TAACATAACAACTTACATAA-TACATAGCATAC-GTAACTTACATAACTTACA
1 AACTTACATAACTAACATAAC--C-TACATAACTACATA--ATACAGTAACTTACATAACTTACA
41156223 TAATACAA
61 TAATACAA
* * *
41156231 AACTTCCATAACTTACATAACCTACATAACCTACATAATACATTTAACTTACATAACTTACATAA
1 AACTTACATAACTAACATAACCTACATAA-CTACATAATACA-GTAACTTACATAACTTACATAA
*
41156296 CTTACAT
64 --TACAA
* * * *
41156303 AA--TACATAA-TAACTTACAACTTAAATAACATACAT--TACTTTGATAACTTACATAACTTAC
1 AACTTACATAACTAAC--ATAACCTACATAAC-TACATAATAC--AG-TAACTTACATAACTTAC
*
41156363 ATAATACAC
60 ATAATACAA
* * * * *
41156372 AACTTACATAGCTTACTTAA-C-ACATAACT-TATACACGTACA-TAACTTACATAACTTACTTA
1 AACTTACATAACTAACATAACCTACATAACTACATA-A--TACAGTAACTTACATAACTTACATA
41156433 ATACA
63 ATACA
41156438 TAAATATATA
Statistics
Matches: 164, Mismatches: 22, Indels: 45
0.71 0.10 0.19
Matches are distributed among these distances:
66 2 0.01
67 25 0.15
68 17 0.10
69 13 0.08
70 45 0.27
71 53 0.32
72 9 0.05
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (68 bp):
AACTTACATAACTAACATAACCTACATAACTACATAATACAGTAACTTACATAACTTACATAATA
CAA
Found at i:41156241 original size:79 final size:77
Alignment explanation
Indices: 41156151--41156308 Score: 203
Period size: 79 Copynumber: 2.0 Consensus size: 77
41156141 GCTTATATAT
* * * *
41156151 AAACTTGCATAACTTACGTAA-TAACATAACAACTTACATAATACA-TAGCATACGTAACTTACA
1 AAACTTCCATAACTTACATAACT-ACATAAC--C-TACATAATACATTAACATACATAACTTACA
41156214 TAACTTACATAATACA
62 TAACTTACATAATACA
*
41156230 AAACTTCCATAACTTACATAACCTACATAACCTACATAATACATTTAACTTACATAACTTACATA
1 AAACTTCCATAACTTACATAA-CTACATAACCTACATAATACA-TTAACATACATAACTTACATA
41156295 ACTTACATAATACA
64 ACTTACATAATACA
41156309 TAATAACTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
77 11 0.16
78 1 0.01
79 50 0.71
80 7 0.10
81 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (77 bp):
AAACTTCCATAACTTACATAACTACATAACCTACATAATACATTAACATACATAACTTACATAAC
TTACATAATACA
Found at i:41162416 original size:43 final size:41
Alignment explanation
Indices: 41162363--41162635 Score: 237
Period size: 43 Copynumber: 6.4 Consensus size: 41
41162353 AATCTCAAAA
*
41162363 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACAT-TTCT
1 TTAGCGGCGTTTTTT-T-AAAGCGCCGCTAAAGAACATGTTCT
* * * * *
41162405 TTCCGCGGCGTTTGTGATGAAAGCGCCACTAAAGAACATGATCT
1 TT-AGCGGCGTTT-T-TTTAAAGCGCCGCTAAAGAACATGTTCT
* *
41162449 ATAGCGGCCTTTTTTTACCAAGCGCCGCTAAAGAACAT-TATCT
1 TTAGCGGCGTTTTTTTA--AAGCGCCGCTAAAGAACATGT-TCT
* *
41162492 TTAGCGGCGTCTTTATTTTAAGCGCCGCTAAAGAAAATGTTCT
1 TTAGCGGCGT-TTT-TTTAAAGCGCCGCTAAAGAACATGTTCT
* * * *
41162535 TTAGCGGCGTTTTTTGTTAAGTGCCACTAAAGAACATGATCT
1 TTAGCGGCGTTTTTT-TAAAGCGCCGCTAAAGAACATGTTCT
** *
41162577 TTAGCGGCGTTTTTTTTTTAAA-TACCGCTAAAGAACATGATCT
1 TTAGCGGCG---TTTTTTTAAAGCGCCGCTAAAGAACATGTTCT
*
41162620 TTAGCGGCATTTTTTT
1 TTAGCGGCGTTTTTTT
41162636 CTGTAAACGC
Statistics
Matches: 192, Mismatches: 25, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
40 7 0.04
41 4 0.02
42 37 0.19
43 122 0.64
44 12 0.06
45 10 0.05
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTTAAAGCGCCGCTAAAGAACATGTTCT
Found at i:41162582 original size:128 final size:129
Alignment explanation
Indices: 41162382--41162627 Score: 327
Period size: 128 Copynumber: 1.9 Consensus size: 129
41162372 TTTTTTATAA
* *
41162382 AAGCGCCGCTAAAGAACATTTCTTTCCGCGGCGTTTGTGATGAAAGCGCCACTAAAGAACATGAT
1 AAGCGCCGCTAAAGAAAATTTCTTTCAGCGGCGTTTGTGATGAAAGCGCCACTAAAGAACATGAT
* * *
41162447 CTATAGCGGCCTTTTTTTACCAAGCGCCGCTAAAGAACATTATCTTTAGCGGCGTCTTTATTTT
66 CTATAGCGGCCTTTTTTTACCAAACACCGCTAAAGAACATGATCTTTAGCGGCGTCTTTATTTT
* * *
41162511 AAGCGCCGCTAAAGAAAATGTTCTTT-AGCGGCGTTT-T-TTGTTAAGTGCCACTAAAGAACATG
1 AAGCGCCGCTAAAGAAAAT-TTCTTTCAGCGGCGTTTGTGATG-AAAGCGCCACTAAAGAACATG
* * *** *
41162573 ATCTTTAGCGGCGTTTTTTTTTTAAATACCGCTAAAGAACATGATCTTTAGCGGC
64 ATCTATAGCGGCCTTTTTTTACCAAACACCGCTAAAGAACATGATCTTTAGCGGC
41162628 ATTTTTTTCT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
127 2 0.02
128 66 0.65
129 27 0.27
130 6 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (129 bp):
AAGCGCCGCTAAAGAAAATTTCTTTCAGCGGCGTTTGTGATGAAAGCGCCACTAAAGAACATGAT
CTATAGCGGCCTTTTTTTACCAAACACCGCTAAAGAACATGATCTTTAGCGGCGTCTTTATTTT
Found at i:41162596 original size:85 final size:85
Alignment explanation
Indices: 41162425--41162635 Score: 262
Period size: 85 Copynumber: 2.5 Consensus size: 85
41162415 TTTGTGATGA
* * * * *
41162425 AAGCGCCACTAAAGAACATGATCTATAGCGGCCTTTTTTTACCAAGCGCCGCTAAAGAACATTAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTA-CAAGCGCCACTAAAGAACATGAT
41162490 CTTTAGCGGCGTCTTTATTTT
65 CTTTAGCGGCGTCTTTATTTT
* * * * *
41162511 AAGCGCCGCTAAAGAAAATGTTCTTTAGCGGCGTTTTTTGT-TAAGTGCCACTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTT-TACAAGCGCCACTAAAGAACATGAT
* *
41162575 CTTTAGCGGCGTTTTTTTTTT
65 CTTTAGCGGCGTCTTTATTTT
***
41162596 AAATACCGCTAAAGAACATGATCTTTAGCGGCATTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTT
41162636 CTGTAAACGC
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
84 1 0.01
85 71 0.66
86 34 0.32
87 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTACAAGCGCCACTAAAGAACATGATC
TTTAGCGGCGTCTTTATTTT
Found at i:41166754 original size:21 final size:21
Alignment explanation
Indices: 41166728--41166768 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41166718 AGACGAGCAA
* *
41166728 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
41166749 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
41166769 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:41168707 original size:16 final size:16
Alignment explanation
Indices: 41168674--41168707 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41168664 GGAGATTGTT
* *
41168674 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
41168690 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
41168706 AA
1 AA
41168708 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:41169621 original size:20 final size:20
Alignment explanation
Indices: 41169585--41169628 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41169575 TTTTGAGAAA
*
41169585 TATTTTTACTGAGTTTAAAC
1 TATTTTTAATGAGTTTAAAC
*
41169605 TATTTTTAATGTA-TTTAAAG
1 TATTTTTAATG-AGTTTAAAC
41169625 TATT
1 TATT
41169629 ATAAATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (20 bp):
TATTTTTAATGAGTTTAAAC
Found at i:41169803 original size:13 final size:13
Alignment explanation
Indices: 41169785--41169814 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41169775 TGTTTTATTT
41169785 AAAATATTAAATA
1 AAAATATTAAATA
41169798 AAAATATTAAATA
1 AAAATATTAAATA
41169811 AAAA
1 AAAA
41169815 AAAGCCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATATTAAATA
Found at i:41172748 original size:54 final size:54
Alignment explanation
Indices: 41172712--41172872 Score: 232
Period size: 54 Copynumber: 3.0 Consensus size: 54
41172702 CAATGTATTA
41172712 TTCATTTCCCCATATGATGTCATAGCAAACGGCTAGGCCTTACACTATATGGTC
1 TTCATTTCCCCATATGATGTCATAGCAAACGGCTAGGCCTTACACTATATGGTC
* * * *
41172766 TTCATTTCCCCATATGATGCCATAACAAACGACTAGGGCTTACACTATATGGTC
1 TTCATTTCCCCATATGATGTCATAGCAAACGGCTAGGCCTTACACTATATGGTC
* * * * * *
41172820 TTTATTTCCCAATATAAAGTCATTGCAAATGGCTAGGCCTTACACTATATGGT
1 TTCATTTCCCCATATGATGTCATAGCAAACGGCTAGGCCTTACACTATATGGT
41172873 ATTCGCTTAC
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (54 bp):
TTCATTTCCCCATATGATGTCATAGCAAACGGCTAGGCCTTACACTATATGGTC
Found at i:41180851 original size:40 final size:40
Alignment explanation
Indices: 41180792--41180904 Score: 181
Period size: 40 Copynumber: 2.8 Consensus size: 40
41180782 GAACATTGGA
* *
41180792 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGTTAAGACCCGAAGGCAATTATGCGAGTTC
*
41180832 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTC
1 ATATATCCGGGTTAAGACCCGAAGGCAATTATGCGAGTTC
* *
41180872 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGTTAAGACCCGAAGGCAATTATG
41180905 TTTGCGGCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGTTAAGACCCGAAGGCAATTATGCGAGTTC
Found at i:41189552 original size:40 final size:40
Alignment explanation
Indices: 41189493--41189645 Score: 234
Period size: 40 Copynumber: 3.8 Consensus size: 40
41189483 GAACATTGGA
* *
41189493 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
41189533 ACATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
41189573 ATATATCCGGGCTAAGACCCGAATGCAATTATGCGAGTTC
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
41189613 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
41189646 TTTGCGGCTG
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:41198111 original size:40 final size:40
Alignment explanation
Indices: 41198061--41198428 Score: 664
Period size: 40 Copynumber: 9.2 Consensus size: 40
41198051 TGAGCATTGG
41198061 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
41198101 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
41198141 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
41198181 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
41198221 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
41198261 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
* *
41198301 GAAGGCAATTATGCGAGTTAATATGTCCGGGCTATGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
* *
41198341 GAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
* * * *
41198381 GAAGGCAATTATGCAAGTTGATATGTCCGGGTTAAGACCC
1 GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
41198421 GAAGGCAA
1 GAAGGCAA
41198429 ATGTGTTTGC
Statistics
Matches: 318, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 318 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
GAAGGCAATTATGCGAGTTAATATATCCGGGCTAAGACCC
Found at i:41202048 original size:28 final size:28
Alignment explanation
Indices: 41202008--41202063 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
41201998 ACCCAAACGA
41202008 AGCACAATCGCTTTCATGTGCTCTTTCC
1 AGCACAATCGCTTTCATGTGCTCTTTCC
*
41202036 AGCACAATCGCTTTCATGTGTTCTTTCC
1 AGCACAATCGCTTTCATGTGCTCTTTCC
41202064 CTTCTCTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (28 bp):
AGCACAATCGCTTTCATGTGCTCTTTCC
Found at i:41213491 original size:37 final size:37
Alignment explanation
Indices: 41213449--41213532 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
41213439 GTGAAACATG
*
41213449 GCCATGGAAAATGGTGGGATATATTGCCAACAGAAAT
1 GCCATGGAAAATGGTGGGATATATTCCCAACAGAAAT
*
41213486 GCCATGGTAAATGGTGGGATATATTCCCAACAGAAAT
1 GCCATGGAAAATGGTGGGATATATTCCCAACAGAAAT
41213523 GCCATGGAAA
1 GCCATGGAAA
41213533 TTCCAGGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.21
Consensus pattern (37 bp):
GCCATGGAAAATGGTGGGATATATTCCCAACAGAAAT
Found at i:41222802 original size:66 final size:66
Alignment explanation
Indices: 41222696--41222828 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
41222686 AAACATGTAG
41222696 GTTTTGGACTTGTCAAGAAGCCATGGTGTCAGTTTGGGACCACCACATCACCCATCGAACTTTTA
1 GTTTTGGACTTGTCAAGAAGCCATGGTGTCAGTTTGGGACCACCACATCACCCATCGAACTTTTA
41222761 A
66 A
** *
41222762 GTTTTGGACTTGTTGAGAAGCCATGGTGTCAGTTTGGGACCATCACATCACCCATCGAACTTTTA
1 GTTTTGGACTTGTCAAGAAGCCATGGTGTCAGTTTGGGACCACCACATCACCCATCGAACTTTTA
41222827 A
66 A
41222828 G
1 G
41222829 GTTGTATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (66 bp):
GTTTTGGACTTGTCAAGAAGCCATGGTGTCAGTTTGGGACCACCACATCACCCATCGAACTTTTA
A
Found at i:41225758 original size:17 final size:17
Alignment explanation
Indices: 41225738--41225786 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
41225728 AGAAAACAAA
41225738 AAATTTTAATATTATAT
1 AAATTTTAATATTATAT
** *
41225755 AAATAATAAAATTATAT
1 AAATTTTAATATTATAT
41225772 AAATAATTTAATATT
1 AAAT--TTTAATATT
41225787 TGTGAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 18 0.75
19 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTTAATATTATAT
Found at i:41233703 original size:160 final size:155
Alignment explanation
Indices: 41233440--41233901 Score: 594
Period size: 160 Copynumber: 3.0 Consensus size: 155
41233430 ATCTTAAGAA
* *
41233440 AAAGTTTAGATTTTTAAATATAAAAATATATTTTTTAGTCATTTTAAAGGAATGTTTAAATTTTT
1 AAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGGAAAGTTTAAATTTTT
** *
41233505 AAAACAAAAATTTGATTTTTGTTTTCAACTATTTCGAAATAAAATTTTTGATCTTTAAGAAAAGT
66 AAAACAAAGTTTTGATTTTTGTTTTCAACTATTTCGAAATAAAA-TTTTAATCTTTAAGAAAAGT
*
41233570 AGTGATTTTTTAAAAGAAAAAAATTAGAG
130 AGTAATTTTTTAAAAGAAAAAAA--A-AG
* * *
41233599 AAAGTTTATATTTTTAAAAATAAAAATATATTATTTTAGTCATTTCAAAGGAAAGTTAAAATTTT
1 AAAGTTTAGATTTTTAAAAATAAAAATATATT-TTTTAGTCATTTTAAAGGAAAGTTTAAATTTT
* * * * *
41233664 TGAAACAAAGTTTTGATTTTTGTTTTCAACTATTTCGAAATAATAACTTTCATCTTTAATAAAAA
65 TAAAACAAAGTTTTGATTTTTGTTTTCAACTATTTCGAAATAA-AATTTTAATCTTTAAGAAAAG
*
41233729 TAGCAATTTTTTAAAAG-AAAAAAAAG
129 TAGTAATTTTTTAAAAGAAAAAAAAAG
* * * *
41233755 AAA-TTTAGATTTTTAAAAATAAAAATTTGTTTTTTAATTCATTTTAAAGAAAAAGTTTAAATTT
1 AAAGTTTAGATTTTTAAAAATAAAAATATATTTTTT-AGTCATTTTAAAG-GAAAGTTTAAATTT
* * *
41233819 TTAAAACAAAGTTTTGA--TCT-TTTTCAACTATTTCGAAAT-AAGTTTTAATTTTTAAGAAAAG
64 TTAAAACAAAGTTTTGATTTTTGTTTTCAACTATTTCGAAATAAAATTTTAATCTTTAAGAAAAG
*
41233880 TAGTAATTTTTTTTAAAGAAAA
129 TAGTAA-TTTTTTAAAAGAAAA
41233902 CTTTGATTTT
Statistics
Matches: 266, Mismatches: 31, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
151 20 0.08
152 11 0.04
153 22 0.08
154 6 0.02
155 36 0.14
156 33 0.12
157 1 0.00
159 36 0.14
160 99 0.37
161 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (155 bp):
AAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGGAAAGTTTAAATTTTT
AAAACAAAGTTTTGATTTTTGTTTTCAACTATTTCGAAATAAAATTTTAATCTTTAAGAAAAGTA
GTAATTTTTTAAAAGAAAAAAAAAG
Found at i:41233788 original size:21 final size:23
Alignment explanation
Indices: 41233746--41233791 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
41233736 TTTTTAAAAG
41233746 AAAAAAAAGAAATTTAGATTTTT
1 AAAAAAAAGAAATTTAGATTTTT
* *
41233769 AAAAATAA-AAATTT-GTTTTTT
1 AAAAAAAAGAAATTTAGATTTTT
41233790 AA
1 AA
41233792 TTCATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
AAAAAAAAGAAATTTAGATTTTT
Found at i:41244200 original size:36 final size:35
Alignment explanation
Indices: 41244104--41244211 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 35
41244094 TGTTAATATT
* * *
41244104 TTTTTTATTCTGATTCGCAAGTTAAGCATGCTATT-
1 TTTTTGATTCTGATT-GCATGTTAAGCATGCCATTA
* * * *
41244139 CTTTTGATTTTGACTTACATATTAAGCATGCCATTA
1 TTTTTGATTCTGA-TTGCATGTTAAGCATGCCATTA
41244175 TTTTTGATTCTGATTGGCATGTTAAGCATGCCATTA
1 TTTTTGATTCTGATT-GCATGTTAAGCATGCCATTA
41244211 T
1 T
41244212 GTTAAACTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
35 27 0.46
36 32 0.54
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (35 bp):
TTTTTGATTCTGATTGCATGTTAAGCATGCCATTA
Found at i:41244955 original size:20 final size:20
Alignment explanation
Indices: 41244911--41244958 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
41244901 GTGGACTTTA
*
41244911 ATTTTGGACTTTGGTTTTGG
1 ATTTGGGACTTTGGTTTTGG
*
41244931 TTTTGGGACTTTGGATTTT-G
1 ATTTGGGACTTTGG-TTTTGG
41244951 ATTTGGGA
1 ATTTGGGA
41244959 ATTATTCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.12, C:0.04, G:0.31, T:0.52
Consensus pattern (20 bp):
ATTTGGGACTTTGGTTTTGG
Found at i:41256810 original size:17 final size:18
Alignment explanation
Indices: 41256778--41256812 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41256768 TATTATTCCT
41256778 AGGAAACAAAAAAGAAAA
1 AGGAAACAAAAAAGAAAA
*
41256796 AGGAAA-AAAAGAGAAAA
1 AGGAAACAAAAAAGAAAA
41256813 CTTACAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AGGAAACAAAAAAGAAAA
Found at i:41258112 original size:51 final size:51
Alignment explanation
Indices: 41257987--41258165 Score: 168
Period size: 51 Copynumber: 3.5 Consensus size: 51
41257977 GATGGTCAGG
* * * * * *
41257987 TGTGTGGTACTATGTGCAGGCTACTACGTGTTCCAGAAT-G-AA-GGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGTAATGATCACA
* *
41258036 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGT-TTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGTAAT-GATCACA
* * * * * * *
41258087 TGTGTAGTACTATGTGCAGACTACTACGTGTATCGGATGGTAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGTAATGATCACA
*
41258138 TGTGTAGTACTATGTGTAGGCTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTATG
41258166 TGAATCGAAC
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.04
49 31 0.30
51 69 0.66
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGTAATGATCACA
Found at i:41258230 original size:45 final size:45
Alignment explanation
Indices: 41258174--41258260 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
41258164 TGTGAATCGA
* * * *
41258174 ACATTATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGGGCTGAATCCACCGG
41258219 ACATCATTGATTAATAAGGTGGTTGCTATGGGCTGAATCCAC
1 ACATCATTGATTAATAAGGTGGTTGCTATGGGCTGAATCCAC
41258261 TGAGTATCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGGGCTGAATCCACCGG
Found at i:41260813 original size:15 final size:16
Alignment explanation
Indices: 41260783--41260822 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
41260773 ATCGAAACTT
41260783 TTAAAAATACAAAAAA
1 TTAAAAATACAAAAAA
* *
41260799 TTAAACATAAAAAAAA
1 TTAAAAATACAAAAAA
*
41260815 TTAGAAAT
1 TTAAAAAT
41260823 TGACTTAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (16 bp):
TTAAAAATACAAAAAA
Found at i:41261195 original size:23 final size:24
Alignment explanation
Indices: 41261160--41261238 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
41261150 TACTCTCTCC
*
41261160 TAGGG-TTATGGTTTTAAATATTTT
1 TAGGGTTTAGGGTTTT-AATATTTT
* *
41261184 TA-GGTTTAGGTTTTTAATATTCT
1 TAGGGTTTAGGGTTTTAATATTTT
41261207 TAGGGTTTAGGGTTTTAATATTTT
1 TAGGGTTTAGGGTTTTAATATTTT
*
41261231 TATGGTTT
1 TAGGGTTT
41261239 TTTGGCTTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.23
24 36 0.77
ACGTcount: A:0.22, C:0.01, G:0.22, T:0.56
Consensus pattern (24 bp):
TAGGGTTTAGGGTTTTAATATTTT
Found at i:41263828 original size:36 final size:36
Alignment explanation
Indices: 41263788--41263867 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
41263778 GATGCGACCG
*
41263788 AGGAAGAAAATCCTAATGAGCAAGAAGATGCAGTCA
1 AGGAAGAAAATCCTAATAAGCAAGAAGATGCAGTCA
** * *
41263824 AGGAAGATGATCCTAATAAGCAAGAAGATGCGGTCG
1 AGGAAGAAAATCCTAATAAGCAAGAAGATGCAGTCA
41263860 AGGAAGAA
1 AGGAAGAA
41263868 GATGCAAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.12, G:0.29, T:0.14
Consensus pattern (36 bp):
AGGAAGAAAATCCTAATAAGCAAGAAGATGCAGTCA
Found at i:41263830 original size:18 final size:18
Alignment explanation
Indices: 41263809--41263873 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
41263799 CCTAATGAGC
41263809 AAGAAGATGCAGTCAAGG
1 AAGAAGATGCAGTCAAGG
* * * *
41263827 AAGATGATCCTAAT-AAGC
1 AAGAAGATGC-AGTCAAGG
* *
41263845 AAGAAGATGCGGTCGAGG
1 AAGAAGATGCAGTCAAGG
41263863 AAGAAGATGCA
1 AAGAAGATGCA
41263874 AGTGAGGAAC
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
17 1 0.03
18 31 0.91
19 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.31, T:0.14
Consensus pattern (18 bp):
AAGAAGATGCAGTCAAGG
Found at i:41263880 original size:18 final size:18
Alignment explanation
Indices: 41263770--41263882 Score: 54
Period size: 18 Copynumber: 6.3 Consensus size: 18
41263760 GGTGCAGATT
* **
41263770 AGGAAGAAGATGCGACCG
1 AGGAAGAAGATGCAAGTG
* *
41263788 AGGAAGAAAATCCTAA-TG
1 AGGAAGAAGATGC-AAGTG
* *
41263806 AGCAAGAAGATGC-AGTCA
1 AGGAAGAAGATGCAAGT-G
* * *
41263824 AGGAAGATGATCCTAA-TA
1 AGGAAGAAGATGC-AAGTG
* *
41263842 AGCAAGAAGATGC-GGTCG
1 AGGAAGAAGATGCAAGT-G
41263860 AGGAAGAAGATGCAAGTG
1 AGGAAGAAGATGCAAGTG
41263878 AGGAA
1 AGGAA
41263883 CAAGGAACAG
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
16 1 0.01
17 2 0.03
18 61 0.88
19 4 0.06
20 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.32, T:0.12
Consensus pattern (18 bp):
AGGAAGAAGATGCAAGTG
Found at i:41265656 original size:51 final size:50
Alignment explanation
Indices: 41265549--41265704 Score: 240
Period size: 51 Copynumber: 3.1 Consensus size: 50
41265539 GATCACTCAT
* * *
41265549 CACTTGTCCCTAATCAGATAAGTGTAGCTAAGTTACCACTTATCACTTGC
1 CACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGC
41265599 CACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGC
1 CACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGC
* * *
41265650 CACTTGTCACTGATCAGAAAAGTGTAGCTGAAGCTACTACTTATCACTTGT
1 CACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGC
41265701 CACT
1 CACT
41265705 GATCAGAAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 27 0.28
51 71 0.72
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (50 bp):
CACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGC
Found at i:41271432 original size:18 final size:18
Alignment explanation
Indices: 41271406--41271440 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41271396 ACGATGTGCC
*
41271406 AAACTATTTTCATGCTTG
1 AAACCATTTTCATGCTTG
*
41271424 AAACCATTTTGATGCTT
1 AAACCATTTTCATGCTT
41271441 CTTGTTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AAACCATTTTCATGCTTG
Found at i:41281575 original size:15 final size:15
Alignment explanation
Indices: 41281555--41281604 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
41281545 GGAGATAAAA
41281555 AAAAAAGCATCCTAT
1 AAAAAAGCATCCTAT
** *
41281570 AAAAAA-CATTTTAA
1 AAAAAAGCATCCTAT
41281584 AAAAAAGCATCCTAT
1 AAAAAAGCATCCTAT
41281599 AAAAAA
1 AAAAAA
41281605 CATTTTCAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.62, C:0.14, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAAAAGCATCCTAT
Found at i:41281594 original size:29 final size:29
Alignment explanation
Indices: 41281553--41281610 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41281543 TTGGAGATAA
41281553 AAAAAAAAGCATCCTATAAAAAACATTTT
1 AAAAAAAAGCATCCTATAAAAAACATTTT
41281582 AAAAAAAAGCATCCTATAAAAAACATTTT
1 AAAAAAAAGCATCCTATAAAAAACATTTT
41281611 CAATCACGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (29 bp):
AAAAAAAAGCATCCTATAAAAAACATTTT
Found at i:41281824 original size:72 final size:72
Alignment explanation
Indices: 41281743--41281891 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
41281733 ATTTTAAGTT
*
41281743 TTTTTAATTAATATTTTTGGTATATTAGCTATTTTAGTTAGATAGTTAGCTATCTGTGATTTCAT
1 TTTTTAATTAATATTTTTGGTATATTAGCTATTTTAGTTAGATAGTTAGATATCTGTGATTTCAT
41281808 CTTTGAG
66 CTTTGAG
41281815 TTTTTAATTAATATTTTTGGTATATTAGCTATTTTAGTTAGATAGTTAGATATCTGTGATTTCAT
1 TTTTTAATTAATATTTTTGGTATATTAGCTATTTTAGTTAGATAGTTAGATATCTGTGATTTCAT
41281880 CTTTGAG
66 CTTTGAG
41281887 TTTTT
1 TTTTT
41281892 TATTTCATGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (72 bp):
TTTTTAATTAATATTTTTGGTATATTAGCTATTTTAGTTAGATAGTTAGATATCTGTGATTTCAT
CTTTGAG
Found at i:41285023 original size:22 final size:22
Alignment explanation
Indices: 41284996--41285065 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
41284986 AAATGTCTAA
41284996 GACCCTAGTTGAAAGATATTAT
1 GACCCTAGTTGAAAGATATTAT
* ** *
41285018 GGCCCTAACCTGAAA-ATATGTAA
1 GACCCT-AGTTGAAAGATAT-TAT
*
41285041 GACCATAGTTGAAAGATATTAT
1 GACCCTAGTTGAAAGATATTAT
41285063 GAC
1 GAC
41285066 ATTAAATTCA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (22 bp):
GACCCTAGTTGAAAGATATTAT
Found at i:41296502 original size:24 final size:24
Alignment explanation
Indices: 41296451--41296510 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
41296441 AGAATTGGTG
* * **
41296451 GCTTCATCCACAACCTATATGATG
1 GCTTCGTCCACAACCTACATGACA
*
41296475 GCTTCGTCCACAACCTACATGGCA
1 GCTTCGTCCACAACCTACATGACA
*
41296499 GCTT-GTCTACAA
1 GCTTCGTCCACAA
41296511 ATATTGGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (24 bp):
GCTTCGTCCACAACCTACATGACA
Found at i:41296900 original size:17 final size:17
Alignment explanation
Indices: 41296878--41296910 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41296868 TAGAATTGGG
41296878 TTGAGAATATT-ATTTAA
1 TTGAGAA-ATTAATTTAA
41296895 TTGAGAAATTAATTTA
1 TTGAGAAATTAATTTA
41296911 TATAAATTAA
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:0.12, T:0.45
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:41297914 original size:50 final size:50
Alignment explanation
Indices: 41297730--41297921 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
41297720 GGGAATGAGA
* *
41297730 TCCCATATAAGACCATGTCTGGGACA-GGCATTGGCATCTTTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAGG
* * * *
41297785 TCCCATGTAAGATCATGTCTGGGACATAGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
** * **
41297835 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
* * *
41297885 TCCCATGTAAGACCATATCTGGAATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41297922 GTACAGGAAA
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 80 0.70
51 2 0.02
55 25 0.22
56 8 0.07
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGG
Found at i:41305490 original size:50 final size:50
Alignment explanation
Indices: 41305387--41305629 Score: 231
Period size: 50 Copynumber: 4.8 Consensus size: 50
41305377 AGGGAATGAG
*
41305387 ATCCCATGTAAGACTATGTCTGGGACATGGCATTGGCATCTTTGAGATTATGAGAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAGAC
* * *
41305443 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATGAGAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAC
* * * *
41305493 GTCCC-TCGTAAGACCATGTCTAGGACATGGCATGGGCACTGATATGAGA-
1 ATCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAC
* * * * * * * * *
41305542 ACTCTCATGTAAGACCATATCTCGGATATGGAATTGGCAGT-ACAGGAAAC
1 A-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAC
*
41305592 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41305630 TGTTAAATTC
Statistics
Matches: 156, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
49 37 0.24
50 78 0.50
51 1 0.01
53 3 0.02
55 1 0.01
56 36 0.23
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (50 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAC
Found at i:41307939 original size:18 final size:18
Alignment explanation
Indices: 41307916--41307953 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41307906 TACAAAAGAT
41307916 ATAATAGAGAAATGTGAA
1 ATAATAGAGAAATGTGAA
41307934 ATAATAGAGAAATGTGAA
1 ATAATAGAGAAATGTGAA
41307952 AT
1 AT
41307954 TAAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATAATAGAGAAATGTGAA
Found at i:41310408 original size:20 final size:20
Alignment explanation
Indices: 41310366--41310404 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41310356 ATAAACATTA
*
41310366 AATTAATTTAATATTGAGAT
1 AATTAATTTAATATTGAAAT
*
41310386 AATTATTTTAATATT-AAAT
1 AATTAATTTAATATTGAAAT
41310405 TAATAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTAATTTAATATTGAAAT
Found at i:41310446 original size:37 final size:36
Alignment explanation
Indices: 41310399--41310468 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
41310389 TATTTTAATA
*
41310399 TTAAATTAATA-AAATACTATTAAGATAAGTATTAAAT
1 TTAAATTAATATAAA-ACTATTAAAATAA-TATTAAAT
* *
41310436 TTAATTTAATATTAAACTATTAAAATAATATTA
1 TTAAATTAATATAAAACTATTAAAATAATATTA
41310469 TTTTTAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 22 0.76
38 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAAATTAATATAAAACTATTAAAATAATATTAAAT
Found at i:41317238 original size:48 final size:48
Alignment explanation
Indices: 41317134--41317279 Score: 132
Period size: 48 Copynumber: 3.0 Consensus size: 48
41317124 GCGTATCGAT
* * * *
41317134 AATCTGTTATGACACGAGGGTGGCACGGACTGTGTGCAGGCCACCAAT
1 AATCTGTTAAGACACAAGGGTGGCACGGACTATGTGCAGGCCACCAAG
* **
41317182 AA-CTTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCACCGGG
1 AATC-TGTTAAGACACAAGGGTGGCACGGACTATGTGCAGGCCACCAAG
** * * ** * * *
41317230 AATCTGTTATTACACAAAGGTGGTACAAACTGTGTGTAGGCCACCGAG
1 AATCTGTTAAGACACAAGGGTGGCACGGACTATGTGCAGGCCACCAAG
41317278 AA
1 AA
41317280 ATCTATTTTT
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
47 1 0.01
48 77 0.97
49 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (48 bp):
AATCTGTTAAGACACAAGGGTGGCACGGACTATGTGCAGGCCACCAAG
Found at i:41322969 original size:37 final size:37
Alignment explanation
Indices: 41322912--41323017 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
41322902 TATGATCACT
*
41322912 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
41322947 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
*
41322984 TATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
41323018 GAAGCTATCA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 54 0.84
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:41323059 original size:52 final size:52
Alignment explanation
Indices: 41322980--41323196 Score: 293
Period size: 52 Copynumber: 4.2 Consensus size: 52
41322970 TAAGTGTAGC
* *
41322980 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
41323033 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
41323085 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * ** *
41323131 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
41323183 CACTTTGTCACTTG
1 CACTTT-TCACTTG
41323197 ATCAGAAGTA
Statistics
Matches: 145, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.30
49 1 0.01
52 86 0.59
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:41323102 original size:46 final size:46
Alignment explanation
Indices: 41323030--41323202 Score: 231
Period size: 46 Copynumber: 3.7 Consensus size: 46
41323020 AGCTATCACT
*
41323030 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
41323075 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
41323121 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
41323173 TACCACTTATCACTTTGTCACTTGATCAGA
1 TATCACTTATCACTTTGTCACTTGATCAGA
41323203 AGTACTCAAA
Statistics
Matches: 113, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
45 12 0.11
46 59 0.52
48 1 0.01
50 1 0.01
52 40 0.35
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (46 bp):
TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:41323146 original size:98 final size:98
Alignment explanation
Indices: 41322979--41323202 Score: 394
Period size: 98 Copynumber: 2.3 Consensus size: 98
41322969 ATAAGTGTAG
* *
41322979 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
*
41323044 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
* *
41323077 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
*
41323142 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
41323175 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
41323203 AGTACTCAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 119 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
Found at i:41327661 original size:48 final size:48
Alignment explanation
Indices: 41327590--41327794 Score: 241
Period size: 48 Copynumber: 4.2 Consensus size: 48
41327580 CTATGCTTAT
*
41327590 CGATAATCTGTTATGACACAAGGGTGGCACAGACTGTGTGCAGGCCAC
1 CGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
* *
41327638 CGATATTCTGTTGTGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
1 CGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
* * * * * *
41327686 CAATAA-CTTGTTAAGATACAAGGGTGACACGGACTATGTGCAGGTCAC
1 CGATAATC-TGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
* * * * * *
41327734 CGAGAATCTGTTATTACACAAAGGTGGTACGAACTGTGTGTAGGCCAC
1 CGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
*
41327782 CGAGAAATCTGTT
1 CGA-TAATCTGTT
41327795 TTTATTCCGA
Statistics
Matches: 130, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.01
48 120 0.92
49 9 0.07
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
CGATAATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCAC
Found at i:41333044 original size:111 final size:111
Alignment explanation
Indices: 41332845--41333074 Score: 370
Period size: 111 Copynumber: 2.1 Consensus size: 111
41332835 CTTCTTTTCC
* *
41332845 TAAACATACAGAACTCAGACTAATAACTTTGGACAGACAATCATTATTCACACACACATACACTG
1 TAAAGATACAGAACTCAGACTAATAACTTTGGACAAACAATCATTATTCACACACACATACACTG
*
41332910 ATCATTATTTAAAGAGTAAGAATACTTACCTTATAATATTATAAAG
66 ATCATCATTTAAAGAGTAAGAATACTTACCTTATAATATTATAAAG
* * * *
41332956 TAAAGATACATAACTCAGACTAATAACTTTGGATAAACAATCATTATTCACACATAGATACACTG
1 TAAAGATACAGAACTCAGACTAATAACTTTGGACAAACAATCATTATTCACACACACATACACTG
* *
41333021 ATCATCCTTTAAAGAGTAAGAATACTTACCTTCTAATATTATAAAG
66 ATCATCATTTAAAGAGTAAGAATACTTACCTTATAATATTATAAAG
*
41333067 TGAAGATA
1 TAAAGATA
41333075 ATCACAACAC
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (111 bp):
TAAAGATACAGAACTCAGACTAATAACTTTGGACAAACAATCATTATTCACACACACATACACTG
ATCATCATTTAAAGAGTAAGAATACTTACCTTATAATATTATAAAG
Found at i:41339372 original size:54 final size:54
Alignment explanation
Indices: 41339304--41339413 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
41339294 AATAATGAAA
*
41339304 TCAGCAGGACAAATAAATTTATCGAATCTTACCAAAACATCCTCGATCTTTCCT
1 TCAGCAGGAAAAATAAATTTATCGAATCTTACCAAAACATCCTCGATCTTTCCT
* *
41339358 TCAGCAGGAAAAATAAATTTATTGACTCTTACCAAAACATCCTCGATCTTTCCT
1 TCAGCAGGAAAAATAAATTTATCGAATCTTACCAAAACATCCTCGATCTTTCCT
41339412 TC
1 TC
41339414 GGGATATGCT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (54 bp):
TCAGCAGGAAAAATAAATTTATCGAATCTTACCAAAACATCCTCGATCTTTCCT
Found at i:41344017 original size:46 final size:46
Alignment explanation
Indices: 41343950--41344038 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
41343940 AAGGAGCATC
41343950 ACCTTTACTGCACTGCAACAGTCGCTCCCCTCCTAAGAGTCCTTTA
1 ACCTTTACTGCACTGCAACAGTCGCTCCCCTCCTAAGAGTCCTTTA
41343996 ACCTTTACTGCACTGCAACAGTCGCTCCCCTCCTAAGAGTCCT
1 ACCTTTACTGCACTGCAACAGTCGCTCCCCTCCTAAGAGTCCT
41344039 GTTGCATCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.38, G:0.13, T:0.27
Consensus pattern (46 bp):
ACCTTTACTGCACTGCAACAGTCGCTCCCCTCCTAAGAGTCCTTTA
Found at i:41346301 original size:32 final size:32
Alignment explanation
Indices: 41346265--41346345 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
41346255 AGTGTACATG
41346265 AATTAAATGGAAGTTTCTAGTGATATGATTTC
1 AATTAAATGGAAGTTTCTAGTGATATGATTTC
*
41346297 AATTAAATGGAAGTTTCTAGTGATATGATTTG
1 AATTAAATGGAAGTTTCTAGTGATATGATTTC
*
41346329 AATTAAATGGAAATTTC
1 AATTAAATGGAAGTTTC
41346346 ATATTTATGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (32 bp):
AATTAAATGGAAGTTTCTAGTGATATGATTTC
Found at i:41349668 original size:41 final size:39
Alignment explanation
Indices: 41349605--41350046 Score: 335
Period size: 41 Copynumber: 10.6 Consensus size: 39
41349595 CTTTGAATGT
* * *
41349605 AAGGGGTTGCTAAGTGCAGATTCCCAGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAT--AA
* * *
41349646 AAGGGGTTGCTATGTGCGGATTCCCCGTATCATTGAGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGA-TAA
* * *
41349686 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGGTTGGGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATT-GAT--AA
* *
41349730 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGA-TAA
* * * *
41349770 AAGGTGGTCGCTAAGTGCTGATTTCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGA-TTCCCCGTATCATTGA---TAA
* * *
41349814 AAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGA-TAA
* * * *
41349854 AAGGTGGTCGCTAAGTGCTGATTTCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGA-TTCCCCGTATCATTGA---TAA
* * *
41349898 AAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGA-TAA
* * * *
41349938 AAGGTGGTCGCTAAGTGCTGATTTCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGA-TTCCCCGTATCATTGA---TAA
* * *
41349982 AAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGA-TAA
*
41350022 AAGGTGGTTGCTAAGTGCTAATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
41350047 ACCAGGATCC
Statistics
Matches: 315, Mismatches: 66, Indels: 40
0.75 0.16 0.10
Matches are distributed among these distances:
40 21 0.07
41 111 0.35
42 105 0.33
43 62 0.20
44 16 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (39 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATAA
Found at i:41349752 original size:84 final size:84
Alignment explanation
Indices: 41349645--41350058 Score: 711
Period size: 84 Copynumber: 4.9 Consensus size: 84
41349635 CATTGATCAA
* * * * *
41349645 AAAGGGGTTGCTATGTGCGGATTCCCCGTATCATTGAGTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
* *
41349710 CACCGTATCCTTGGTTGGG
66 CACCGTATCCTTGATTGTG
*
41349729 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
1 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
41349794 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
41349813 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
1 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
41349878 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
41349897 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
1 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
41349962 CACCGTATCCTTGATTGTG
66 CACCGTATCCTTGATTGTG
* * *
41349981 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTAATTC
1 AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
*
41350046 CACCAGGATCCTT
66 CACC-GTATCCTT
41350059 TGAACATGAG
Statistics
Matches: 318, Mismatches: 11, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
84 311 0.98
85 7 0.02
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (84 bp):
AAAGAGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTCGCTAAGTGCTGATTT
CACCGTATCCTTGATTGTG
Found at i:41351311 original size:96 final size:96
Alignment explanation
Indices: 41351147--41351335 Score: 360
Period size: 96 Copynumber: 2.0 Consensus size: 96
41351137 ATGTTGAACT
41351147 CGACCATACTTATAATACTTACGCTATATGTTTATTTGGCTAACATGTGTAGTGTACACGCTTAA
1 CGACCATACTTATAATACTTACGCTATATGTTTATTTGGCTAACATGTGTAGTGTACACGCTTAA
*
41351212 GCTTTGGCCAAGTGGTGGCTGAATTATGTCA
66 GCTTTGGCCAAGTGGTAGCTGAATTATGTCA
41351243 CGACCATACTTATAATACTTACGCTATATGTTTATTTGGCTAACATGTGTAGTGTACACGCTTAA
1 CGACCATACTTATAATACTTACGCTATATGTTTATTTGGCTAACATGTGTAGTGTACACGCTTAA
*
41351308 GCTTTGGCCAAGTGGTAGTTGAATTATG
66 GCTTTGGCCAAGTGGTAGCTGAATTATG
41351336 CCAGGTTAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (96 bp):
CGACCATACTTATAATACTTACGCTATATGTTTATTTGGCTAACATGTGTAGTGTACACGCTTAA
GCTTTGGCCAAGTGGTAGCTGAATTATGTCA
Found at i:41370067 original size:46 final size:48
Alignment explanation
Indices: 41370000--41370093 Score: 156
Period size: 46 Copynumber: 2.0 Consensus size: 48
41369990 TGAGGAAATT
41370000 CTGTTGAATCCTTTATCATTGCAAGTTA-GC-AACTTAGGTGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTAACTTAGGTGTTTTTA
* *
41370046 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGTGTTTTTA
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTAACTTAGGTGTTTTTA
41370094 AGCAAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 27 0.61
47 2 0.05
48 15 0.34
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCTAACTTAGGTGTTTTTA
Found at i:41375210 original size:48 final size:48
Alignment explanation
Indices: 41375135--41375229 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
41375125 TGAGAGAATT
41375135 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCATTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCATTTTTG
* **
41375183 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCATTTTT
41375230 AAGCAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCAACTTAGGCATTTTTG
Found at i:41392955 original size:85 final size:85
Alignment explanation
Indices: 41392812--41393153 Score: 675
Period size: 85 Copynumber: 4.0 Consensus size: 85
41392802 AAATTCTGTC
*
41392812 AAAACCCTTTTCACCTTCAATTTCTTCATATTGATTTACCTCAAATACTTTAATTTTGCTATTTG
1 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
41392877 AATCAATTTCATATTAATAG
66 AATCAATTTCATATTAATAG
41392897 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
1 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
41392962 AATCAATTTCATATTAATAG
66 AATCAATTTCATATTAATAG
41392982 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
1 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
41393047 AATCAATTTCATATTAATAG
66 AATCAATTTCATATTAATAG
41393067 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
1 AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
41393132 AATCAATTTCATATTAATAG
66 AATCAATTTCATATTAATAG
41393152 AA
1 AA
41393154 GGGCAAATGG
Statistics
Matches: 256, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 256 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (85 bp):
AAAACCCTTTTCACCTTCAATTTCTTCATATTGGTTTACCTCAAATACTTTAATTTTGCTATTTG
AATCAATTTCATATTAATAG
Found at i:41394516 original size:27 final size:27
Alignment explanation
Indices: 41394485--41394662 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41394475 TAAATTGTAC
41394485 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41394512 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41394538 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41394566 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41394594 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41394621 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41394648 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41394663 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41394599 original size:82 final size:81
Alignment explanation
Indices: 41394486--41394641 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41394476 AAATTGTACA
* *
41394486 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41394550 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41394567 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41394632 TGCGAGTTGA
65 TGCGAATTGA
41394642 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41394653 original size:82 final size:81
Alignment explanation
Indices: 41394482--41394662 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41394472 GATTAAATTG
* *
41394482 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41394547 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41394563 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41394627 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41394645 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41394663 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41402579 original size:27 final size:27
Alignment explanation
Indices: 41402548--41402725 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41402538 TAAATTGTAC
41402548 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41402575 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41402601 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41402629 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41402657 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41402684 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41402711 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41402726 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41402662 original size:82 final size:81
Alignment explanation
Indices: 41402549--41402704 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41402539 AAATTGTACA
* *
41402549 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41402613 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41402630 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41402695 TGCGAGTTGA
65 TGCGAATTGA
41402705 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41402716 original size:82 final size:81
Alignment explanation
Indices: 41402545--41402725 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41402535 GATTAAATTG
* *
41402545 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41402610 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41402626 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41402690 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41402708 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41402726 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41424231 original size:12 final size:13
Alignment explanation
Indices: 41424214--41424243 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
41424204 CTCACACATG
41424214 AATAAATAAA-GC
1 AATAAATAAATGC
41424226 AATAAATAAATGC
1 AATAAATAAATGC
41424239 AATAA
1 AATAA
41424244 TTATATCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:41434108 original size:14 final size:14
Alignment explanation
Indices: 41434089--41434142 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
41434079 ACTTTCGTCA
*
41434089 TTCTTTTTTTCTTT
1 TTCTTTTTCTCTTT
* *
41434103 TTCTTTTCACTCCTT
1 TTCTTTT-TCTCTTT
*
41434118 TTGTTTTTCTCTTT
1 TTCTTTTTCTCTTT
41434132 TTCTTTTTCTC
1 TTCTTTTTCTC
41434143 GCTTAATGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:41447697 original size:33 final size:34
Alignment explanation
Indices: 41447631--41447712 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
41447621 TCCTGCCCCA
* *
41447631 CATGCAATTCAATCAAAGACATTTCAAACAATTC
1 CATGCAATTCAATCAAAGACATTTAAAAAAATTC
* *
41447665 CATGCAATTCAGTCAAA-TCATTTAAAAAAATTC
1 CATGCAATTCAATCAAAGACATTTAAAAAAATTC
*
41447698 CACGCAATTCAATCA
1 CATGCAATTCAATCA
41447713 GAATTATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 26 0.62
34 16 0.38
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (34 bp):
CATGCAATTCAATCAAAGACATTTAAAAAAATTC
Found at i:41455244 original size:13 final size:13
Alignment explanation
Indices: 41455211--41455249 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
41455201 ACATACATAT
*
41455211 AATTTAATTAAAC
1 AATTTAATTACAC
* *
41455224 CATATAATTACAC
1 AATTTAATTACAC
41455237 AATTTAATTACAC
1 AATTTAATTACAC
41455250 GAACTTACCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTTAATTACAC
Found at i:41458315 original size:39 final size:39
Alignment explanation
Indices: 41458242--41458342 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 39
41458232 TAACACTCCA
* * * *
41458242 CGTTGTGGCTAAGCCACTGTATATTACAGTCAAGCTGAAT
1 CGTTGTGGTTAAGCCACTGAATACTACAGACAAGCT-AAT
* *
41458282 -GTTGTGGTTAAGCCACTGAATACTGCAGACAAGCTACT
1 CGTTGTGGTTAAGCCACTGAATACTACAGACAAGCTAAT
* * *
41458320 CGTTGTGGTAAAACCATTGAATA
1 CGTTGTGGTTAAGCCACTGAATA
41458343 ACGTTGTGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 2 0.04
39 49 0.96
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (39 bp):
CGTTGTGGTTAAGCCACTGAATACTACAGACAAGCTAAT
Found at i:41458381 original size:63 final size:62
Alignment explanation
Indices: 41458282--41458485 Score: 196
Period size: 63 Copynumber: 3.2 Consensus size: 62
41458272 CAAGCTGAAT
** * * *
41458282 GTTGTGGTTAAGCCACTGAATA-CTGCAGACAAGCTACTCGTTGTGGTAAAACCATTGAATAAC
1 GTTGTGGCCAAGCCACTCAATATC-GCAAACAAGCTAC-CGTTGTGGTCAAACCATTGAATAAC
* * * * *
41458345 GTTGTGGCCAAGCCACTCAATATCGCATACAAGCTACACATTGTGGTCAAGCCACTGAATAAT
1 GTTGTGGCCAAGCCACTCAATATCGCAAACAAGCTAC-CGTTGTGGTCAAACCATTGAATAAC
* * * * * *
41458408 GTTGTGACCAAGCCATTCAATATTGTAAACAAGCTACAGACTGTGGTCAAACCACTT-AATAAC
1 GTTGTGGCCAAGCCACTCAATATCGCAAACAAGCTACCG-TTGTGGTCAAACCA-TTGAATAAC
*
41458471 ATTGTGGCCAAGCCA
1 GTTGTGGCCAAGCCA
41458486 TATAGTATTG
Statistics
Matches: 115, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
63 113 0.98
64 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (62 bp):
GTTGTGGCCAAGCCACTCAATATCGCAAACAAGCTACCGTTGTGGTCAAACCATTGAATAAC
Found at i:41458486 original size:63 final size:63
Alignment explanation
Indices: 41458323--41458486 Score: 204
Period size: 63 Copynumber: 2.6 Consensus size: 63
41458313 AGCTACTCGT
* * * *
41458323 TGTGGTAAAACCA-TTGAATAACGTTGTGGCCAAGCCACTCAATATCGCATACAAGCTACACAT
1 TGTGGTCAAACCACTT-AATAACGTTGTGGCCAAGCCATTCAATATCGCAAACAAGCTACACAC
* * * * * * *
41458386 TGTGGTCAAGCCACTGAATAATGTTGTGACCAAGCCATTCAATATTGTAAACAAGCTACAGAC
1 TGTGGTCAAACCACTTAATAACGTTGTGGCCAAGCCATTCAATATCGCAAACAAGCTACACAC
*
41458449 TGTGGTCAAACCACTTAATAACATTGTGGCCAAGCCAT
1 TGTGGTCAAACCACTTAATAACGTTGTGGCCAAGCCAT
41458487 ATAGTATTGC
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
63 83 0.99
64 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (63 bp):
TGTGGTCAAACCACTTAATAACGTTGTGGCCAAGCCATTCAATATCGCAAACAAGCTACACAC
Found at i:41469142 original size:20 final size:21
Alignment explanation
Indices: 41469117--41469163 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
41469107 TTTAGATTAT
41469117 AATAAAAT-AATAA-TAAATGA
1 AATAAAATGAA-AATTAAATGA
41469137 AAT-AAATGAAAATTAAATGA
1 AATAAAATGAAAATTAAATGA
*
41469157 AAGAAAA
1 AATAAAA
41469164 ACAAGAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 6 0.26
20 14 0.61
21 3 0.13
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (21 bp):
AATAAAATGAAAATTAAATGA
Found at i:41469763 original size:24 final size:24
Alignment explanation
Indices: 41469736--41469782 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
41469726 AAATAAAGTG
* *
41469736 TAAACCCTAAAAGAAAAGAAAAAC
1 TAAAACCTAAAACAAAAGAAAAAC
* *
41469760 TAAAATCTAAAACTAAAGAAAAA
1 TAAAACCTAAAACAAAAGAAAAA
41469783 ATTATACAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.13, G:0.06, T:0.13
Consensus pattern (24 bp):
TAAAACCTAAAACAAAAGAAAAAC
Found at i:41486757 original size:40 final size:40
Alignment explanation
Indices: 41486665--41486805 Score: 132
Period size: 40 Copynumber: 3.5 Consensus size: 40
41486655 ATGCTGTCCG
* * * *
41486665 GGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCA
*
41486703 GGACTAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-AATCCG
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATAA-CCA
*
41486744 GGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCA
1 GGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCA
*
41486784 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
41486806 AACGAGGAGC
Statistics
Matches: 85, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
38 2 0.02
39 16 0.19
40 55 0.65
41 11 0.13
42 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCA
Found at i:41491978 original size:36 final size:36
Alignment explanation
Indices: 41491931--41492003 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
41491921 TCAGAGCTAC
41491931 GGTTTAGTCGATTCTAGGACTACCGTAATGCGTTGG
1 GGTTTAGTCGATTCTAGGACTACCGTAATGCGTTGG
41491967 GGTTTAGTCGATTCTAGGACTACCGTAATGCGTTGG
1 GGTTTAGTCGATTCTAGGACTACCGTAATGCGTTGG
41492003 G
1 G
41492004 TCTAGCTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.33
Consensus pattern (36 bp):
GGTTTAGTCGATTCTAGGACTACCGTAATGCGTTGG
Found at i:41498433 original size:39 final size:40
Alignment explanation
Indices: 41498338--41498560 Score: 273
Period size: 39 Copynumber: 5.7 Consensus size: 40
41498328 TTGAATGATG
*
41498338 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
41498376 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
41498417 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
41498456 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
41498495 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
41498534 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41498561 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
39 93 0.56
40 61 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41498524 original size:79 final size:81
Alignment explanation
Indices: 41498338--41498560 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
41498328 TTGAATGATG
* * *
41498338 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
41498399 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
41498417 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
41498479 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
41498495 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
41498559 TG
66 TG
41498561 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:41498582 original size:79 final size:79
Alignment explanation
Indices: 41498338--41498593 Score: 224
Period size: 79 Copynumber: 3.3 Consensus size: 79
41498328 TTGAATGATG
* * * *
41498338 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
41498399 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
41498417 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
41498481 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
41498495 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
41498559 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
41498575 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41498594 TACGTGATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.29
79 70 0.46
80 36 0.24
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:41501325 original size:51 final size:51
Alignment explanation
Indices: 41501267--41501442 Score: 209
Period size: 51 Copynumber: 3.5 Consensus size: 51
41501257 CTGGTTCGCA
*
41501267 TAGTAGCCTGCACATAGTACTACACATGTGACCGTTACTATTC-GATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCG-TACTATTCTGGTACACG
* * * * * *
41501318 TAGTAGCCTGCACATAGTACAACACACGTGATCGAAGCTA-TCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCGTA-CTATTCTGGTACACG
* *
41501369 TAGTAGCCTGC-CATAGTACTACACATGCGACCAT-C-ATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCGTACTATTCTGGTACACG
*
41501417 TAGTAGCCTGCACACAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
41501443 ATTGACCATC
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.01
48 21 0.20
49 13 0.12
50 20 0.19
51 50 0.48
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCGTACTATTCTGGTACACG
Found at i:41501436 original size:99 final size:102
Alignment explanation
Indices: 41501257--41501442 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 102
41501247 ATTAATGATA
* * *
41501257 CTGGTTCGCATAGTAGCCTGCACATAGTACTACACATGTGACCGTTACTATTCGATACACGTAGT
1 CTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCGATACTATTCGATACACGTAGT
*
41501322 AGCCTGCACATAGTACAACACACGTGATCGAAGCTAT
66 AGCCTGCACACAGTACAACACACGTGATCGAAGCTAT
*
41501359 CTGGTACGCATAGTAGCCTGC-CATAGTACTACACATGCGACC-AT-C-ATTCTGGTACACGTAG
1 CTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCGATACTATTC-GATACACGTAG
*
41501420 TAGCCTGCACACAGTACTACACA
65 TAGCCTGCACACAGTACAACACA
41501443 ATTGACCATC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
98 4 0.05
99 32 0.42
100 1 0.01
101 20 0.26
102 20 0.26
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (102 bp):
CTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCGATACTATTCGATACACGTAGT
AGCCTGCACACAGTACAACACACGTGATCGAAGCTAT
Found at i:41507094 original size:147 final size:147
Alignment explanation
Indices: 41506827--41507120 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
41506817 GGCTCGATTT
41506827 AATTCAACACATACGTATCATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTAC
1 AATTCAACACATACGTATCATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTAC
41506892 AGCAAGCTCATTCGTTACCAATTCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAA
66 AGCAAGCTCATTCGTTACCAATTCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAA
41506957 TTGCCTTCGGGACATAG
131 TTGCCTTCGGGACATAG
41506974 AATTCAACACATACGTATCATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTAC
1 AATTCAACACATACGTATCATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTAC
41507039 AGCAAGCTCATTCGTTACCAATTCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAA
66 AGCAAGCTCATTCGTTACCAATTCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAA
41507104 TTGCCTTCGGGACATAG
131 TTGCCTTCGGGACATAG
41507121 CACGGATTTA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (147 bp):
AATTCAACACATACGTATCATATCCCCATATTGGGATGTTTTTCGAGTATTCGCTGGAATTTTAC
AGCAAGCTCATTCGTTACCAATTCACGTACCTTCGGGATTTAACCGGATATAGCTCCTCGTTCAA
TTGCCTTCGGGACATAG
Found at i:41507149 original size:40 final size:40
Alignment explanation
Indices: 41507105--41507193 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
41507095 CTCGTTCAAT
* *
41507105 TGCCTTCGGGACATAGCACGGATTTAACAACTCGCACGAA
1 TGCCTTCGGGACATAACACGGATTTAACAACTCGCACAAA
* * ** *
41507145 TGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAA
1 TGCCTTCGGGACATAACACGGATTTAACAACTCGCACAAA
*
41507185 GGCCTTCGG
1 TGCCTTCGG
41507194 ATCTTAATCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACATAACACGGATTTAACAACTCGCACAAA
Found at i:41507246 original size:40 final size:40
Alignment explanation
Indices: 41507146--41507246 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
41507136 TCGCACGAAT
* *
41507146 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGATATAGTATCTAGCACAAAG
* *
41507186 GCCTTC-GGATCTTAATCCGGATATATTCA-CTTAGCACAAA-
1 GCCTTCGGGA-CTTAACCCGGATATAGT-ATC-TAGCACAAAG
*
41507226 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
41507247 CAGCATTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
39 3 0.06
40 36 0.71
41 12 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGATATAGTATCTAGCACAAAG
Found at i:41510598 original size:51 final size:51
Alignment explanation
Indices: 41510540--41510730 Score: 255
Period size: 51 Copynumber: 3.8 Consensus size: 51
41510530 CCGGCTCACA
* *
41510540 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACGCG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACGCG
* *
41510591 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACGCG
* * * *
41510642 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACGCG
41510692 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
41510731 TTCACTTTCA
Statistics
Matches: 122, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
49 4 0.03
50 42 0.34
51 73 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACGCG
Found at i:41510719 original size:101 final size:102
Alignment explanation
Indices: 41510538--41510722 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
41510528 AACCGGCTCA
* *
41510538 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACGCGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
41510603 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* *
41510640 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
41510703 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
41510723 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 39 0.50
102 35 0.45
103 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:41510746 original size:101 final size:102
Alignment explanation
Indices: 41510530--41510722 Score: 291
Period size: 102 Copynumber: 1.9 Consensus size: 102
41510520 ATTAATGAAA
* * *
41510530 CCGGCTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACGCGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
*
41510595 AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
* * * *
41510632 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAG
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAG
41510695 TAGCCTGCACATAGTACTACACACGTGA
65 TAGCCTGCACATAGTACTACACACGTGA
41510723 CCATCACTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 39 0.47
102 40 0.48
103 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
AGCCTGCACATAGTACTACACACGTGATCCAAGCTAT
Found at i:41513429 original size:12 final size:12
Alignment explanation
Indices: 41513414--41513464 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
41513404 ATTAGTTTAA
*
41513414 TATTTTAATTAT
1 TATTTTCATTAT
*
41513426 TATTATCATTAT
1 TATTTTCATTAT
* * *
41513438 TATTTTTACTAC
1 TATTTTCATTAT
41513450 TATTTTCATTAT
1 TATTTTCATTAT
41513462 TAT
1 TAT
41513465 CAATATTTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTTCATTAT
Found at i:41513441 original size:24 final size:24
Alignment explanation
Indices: 41513414--41513464 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
41513404 ATTAGTTTAA
* *
41513414 TATTTTAATTATTATTATCATTAT
1 TATTTTAACTACTATTATCATTAT
* *
41513438 TATTTTTACTACTATTTTCATTAT
1 TATTTTAACTACTATTATCATTAT
41513462 TAT
1 TAT
41513465 CAATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTAACTACTATTATCATTAT
Found at i:41513484 original size:33 final size:32
Alignment explanation
Indices: 41513423--41513494 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
41513413 ATATTTTAAT
* * *
41513423 TATTATTATCATTATTATTTTTACTACTATTT
1 TATTATTATCAATATTATTTCTACTACTATTA
*
41513455 TCATTATTATCAATATT-TTTACTATTACTATTA
1 T-ATTATTATCAATATTATTT-CTACTACTATTA
41513488 TATTATT
1 TATTATT
41513495 CGTTTGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 10 0.29
33 24 0.71
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTATTATCAATATTATTTCTACTACTATTA
Found at i:41522470 original size:28 final size:27
Alignment explanation
Indices: 41522398--41522486 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 27
41522388 CTATTCAGTG
* *
41522398 ACAGTACAGTGAGGGCCTTAGCCCAAT
1 ACAGTACAGTGTGGGCCTTAGCCTAAT
* * * * *
41522425 TCAATAGCAATGTCGGCCCTAGCCTAAT
1 ACAGTA-CAGTGTGGGCCTTAGCCTAAT
41522453 ACAGTATCAGTGTGGGCCTTAG-CTCAAT
1 ACAGTA-CAGTGTGGGCCTTAGCCT-AAT
41522481 ACAGTA
1 ACAGTA
41522487 ACATTATAGT
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
27 6 0.13
28 41 0.87
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (27 bp):
ACAGTACAGTGTGGGCCTTAGCCTAAT
Found at i:41522886 original size:27 final size:27
Alignment explanation
Indices: 41522856--41522920 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
41522846 AGGGATATAA
41522856 CAGTCATTTTACCCTAT-AGAGGTATTT
1 CAGTCATTTTACCCTATGAG-GGTATTT
*
41522883 CAGTTATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
*
41522910 CGGTCATTTTA
1 CAGTCATTTTA
41522921 GTATAAATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGAGGGTATTT
Found at i:41534366 original size:56 final size:50
Alignment explanation
Indices: 41534275--41534454 Score: 155
Period size: 50 Copynumber: 3.5 Consensus size: 50
41534265 GGGAATGAGA
* **
41534275 TCCCATGTAAGACCATGTCTGGGGCATGAAATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGAAATTGGC---ACCGA-G--ATGAGAGG
**
41534331 TCCCATGTAAGACCATGTCTGGGACAT-AGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGA-AATTGGCACCGAGATGAGAGG
* * ** * * * **
41534381 TCCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACTGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGAAATTGGCACCGAGATGAGAGG
*
41534431 TCCCATGTAAGACCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
41534455 AATGGCATTG
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
50 69 0.66
52 1 0.01
53 3 0.03
55 1 0.01
56 31 0.30
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGAAATTGGCACCGAGATGAGAGG
Found at i:41534460 original size:50 final size:50
Alignment explanation
Indices: 41534322--41534467 Score: 193
Period size: 50 Copynumber: 2.9 Consensus size: 50
41534312 TTATTGAGGT
* *
41534322 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * * * *
41534372 GATGAGAGGTCCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACTGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * *
41534422 TATGAGAACTCCCATGTAAGACCATATCTGGGAAATGGCATTGGCA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41534468 GTACAAAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:41534741 original size:20 final size:20
Alignment explanation
Indices: 41534716--41534753 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41534706 ATGAGTTATT
41534716 CAAGTAAGCA-AGTAAGTATA
1 CAAGTAAG-AGAGTAAGTATA
41534736 CAAGTAAGAGAGTAAGTA
1 CAAGTAAGAGAGTAAGTA
41534754 AAGAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (20 bp):
CAAGTAAGAGAGTAAGTATA
Found at i:41539429 original size:24 final size:24
Alignment explanation
Indices: 41539380--41539429 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
41539370 TTTTCGAATT
* * *
41539380 TCCTTGATTTTCTCCCCAATCTCC
1 TCCTTGATTTGCTCCCAAAACTCC
41539404 TCCTTGATTTGCTCCACAAAAC-CC
1 TCCTTGATTTGCTCC-CAAAACTCC
41539428 TC
1 TC
41539430 TAAGACCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.18, C:0.40, G:0.06, T:0.36
Consensus pattern (24 bp):
TCCTTGATTTGCTCCCAAAACTCC
Found at i:41558692 original size:48 final size:48
Alignment explanation
Indices: 41558621--41558713 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
41558611 CTGATTTTAG
* *
41558621 GGAAAGGTTCTTGCATTTCTGGATTTGATGAGTTTTTATTGGACAAAT
1 GGAAAGATTCTTGCATTTCTGGATTCGATGAGTTTTTATTGGACAAAT
*
41558669 GGAAAGATTCTTGCATTTTTGGATTCGATGAGTTTTTATTGGACA
1 GGAAAGATTCTTGCATTTCTGGATTCGATGAGTTTTTATTGGACA
41558714 GATTGCACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.42
Consensus pattern (48 bp):
GGAAAGATTCTTGCATTTCTGGATTCGATGAGTTTTTATTGGACAAAT
Found at i:41562143 original size:103 final size:104
Alignment explanation
Indices: 41562025--41562230 Score: 369
Period size: 103 Copynumber: 2.0 Consensus size: 104
41562015 TAAGTAATAA
*
41562025 AGACATTACAAACTAGCAAATCCATAAGGAAATAAACCTTTTTAATATGGCTATTATAATCATCT
1 AGACATTACAAACTAGCAAATCCATAAGGAAATAAACCATTTTAATATGGCTATTATAATCATCT
41562090 TCAATAAGACAAAGTACGATCTTCAAAACA-TTATCTAG
66 TCAATAAGACAAAGTACGATCTTCAAAACATTTATCTAG
*
41562128 AGACATTACAAACTAGCAAATCCATAAGGAAATAAACCATTTTAATATGGCTATTATAATCATTT
1 AGACATTACAAACTAGCAAATCCATAAGGAAATAAACCATTTTAATATGGCTATTATAATCATCT
**
41562193 TCAATTCGACAAAGTACGATCTTCAAAACATTTATCTA
66 TCAATAAGACAAAGTACGATCTTCAAAACATTTATCTA
41562231 ATCTATACAT
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 91 0.93
104 7 0.07
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (104 bp):
AGACATTACAAACTAGCAAATCCATAAGGAAATAAACCATTTTAATATGGCTATTATAATCATCT
TCAATAAGACAAAGTACGATCTTCAAAACATTTATCTAG
Found at i:41562745 original size:260 final size:260
Alignment explanation
Indices: 41562284--41562788 Score: 938
Period size: 260 Copynumber: 1.9 Consensus size: 260
41562274 AGATAATAGA
41562284 TAGGGTGATGAACTTGCTGACAATCCCCGAGCTTGAAGCTTGATCTTTAAGTCTATAAAATAGAA
1 TAGGGTGATGAACTTGCTGACAATCCCCGAGCTTGAAGCTTGATCTTTAAGTCTATAAAATAGAA
* *
41562349 AAACATAAGTAAACAAAGTAAGTTTTTATAGCTTAGTAAGTCTATAGCATAACAACAAATATATT
66 AAACATAAGTAAACAAAGTAAGCTTTTATAACTTAGTAAGTCTATAGCATAACAACAAATATATT
41562414 TATAAAAATTATAAATTTTCCTGGTACACTTAATGAATTCTCAAATACTGTATATATATTAACAA
131 TATAAAAATTATAAATTTTCCTGGTACACTTAATGAATTCTCAAATACTGTATATATATTAACAA
* *
41562479 ATACTTATAGATAAATGTATACATACTTACCAACAATTAAAACCGAGTATATATACACTTTAATG
196 ATACTTATAGATAAATGCATACATAATTACCAACAATTAAAACCGAGTATATATACACTTTAATG
*
41562544 TAGGGTGATGAACTTGCTGACAATCCCCGAGCTTGAAGGTTGATCTTTAAGTCTATAAAATAGAA
1 TAGGGTGATGAACTTGCTGACAATCCCCGAGCTTGAAGCTTGATCTTTAAGTCTATAAAATAGAA
41562609 AAACATAAGTAAACAAAGTAAGCTTTTATAACTTAGTAAGTCTATAGCATAACAACAAATATATT
66 AAACATAAGTAAACAAAGTAAGCTTTTATAACTTAGTAAGTCTATAGCATAACAACAAATATATT
* *
41562674 TATAAAAATTATAAATTTTCCTGGTACACTTAATGAATTCTCAAATATTGTATATATATTAACTA
131 TATAAAAATTATAAATTTTCCTGGTACACTTAATGAATTCTCAAATACTGTATATATATTAACAA
*
41562739 ATACTTATAGATAAATGCATACATAATTATCAACAATTAAAACCGAGTAT
196 ATACTTATAGATAAATGCATACATAATTACCAACAATTAAAACCGAGTAT
41562789 TAACATAAAT
Statistics
Matches: 237, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
260 237 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (260 bp):
TAGGGTGATGAACTTGCTGACAATCCCCGAGCTTGAAGCTTGATCTTTAAGTCTATAAAATAGAA
AAACATAAGTAAACAAAGTAAGCTTTTATAACTTAGTAAGTCTATAGCATAACAACAAATATATT
TATAAAAATTATAAATTTTCCTGGTACACTTAATGAATTCTCAAATACTGTATATATATTAACAA
ATACTTATAGATAAATGCATACATAATTACCAACAATTAAAACCGAGTATATATACACTTTAATG
Found at i:41563193 original size:181 final size:181
Alignment explanation
Indices: 41563003--41563363 Score: 659
Period size: 181 Copynumber: 2.0 Consensus size: 181
41562993 TTATCATGTG
*
41563003 CATATAATTGATCATACACATATATACCAATCACATTTAATATTCATTTGTATATATATATATAC
1 CATATAATTGATCATACACATATATACCAATCACATTTAATATTCATTTGTATATATATATACAC
41563068 ATATATATACTCATTATGAATTTATACCTGAATACATAGCTAATACATACATTCGAATATATATA
66 ATATATATACTCATTATGAATTTATACCTGAATACATAGCTAATACATACATTCGAATATATATA
* *
41563133 CATATTCTTCATATACATATAAATGAGTACATTTATATATATCTCAAATGC
131 CATATTCTTAATATACATATAAATAAGTACATTTATATATATCTCAAATGC
* * *
41563184 CATATAATTGATCATACACATATATACCAATCACATTTTATATTCGTTTGTATATATATATACAT
1 CATATAATTGATCATACACATATATACCAATCACATTTAATATTCATTTGTATATATATATACAC
*
41563249 ATATATATACTCATTATGAATTTATACCTGAATACATAGCTAATACATGCATTCGAATATATATA
66 ATATATATACTCATTATGAATTTATACCTGAATACATAGCTAATACATACATTCGAATATATATA
41563314 CATATTCTTAATATACATATAAATAAGTACATTTATATATATCTCAAATG
131 CATATTCTTAATATACATATAAATAAGTACATTTATATATATCTCAAATG
41563364 TATACAAAAA
Statistics
Matches: 173, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 173 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (181 bp):
CATATAATTGATCATACACATATATACCAATCACATTTAATATTCATTTGTATATATATATACAC
ATATATATACTCATTATGAATTTATACCTGAATACATAGCTAATACATACATTCGAATATATATA
CATATTCTTAATATACATATAAATAAGTACATTTATATATATCTCAAATGC
Found at i:41563575 original size:161 final size:159
Alignment explanation
Indices: 41563393--41563711 Score: 548
Period size: 161 Copynumber: 2.0 Consensus size: 159
41563383 AACACATAGG
*
41563393 CTCAATATATATATTTAACAACCGCATATCACCATATGCATTTATAAATGCAACAATCGCATATA
1 CTCAATATATATATTTAACAACCGCATATCACCATATGCATTTATAAATGCAACAATCACATATA
* *
41563458 CCTAATATACATATGCCTTTCTTAATTGTATATACCGAATGCATACAATTATGTTTAACCAATGC
66 CCTAATATACATATGCCTTTATTAATTGTATATACCAAATGCATACAATTATGTTTAACCAATGC
*
41563523 AAAAAAAAAACCTGAATGTAGGTGTATACTC
131 --AAAAAAAACCTGAATGTAGGCGTATACTC
* *
41563554 CTCAATATATATATTTAACAACCGCATATCACCATATGGATTTATAAATTCAACAATCACATATA
1 CTCAATATATATATTTAACAACCGCATATCACCATATGCATTTATAAATGCAACAATCACATATA
* *
41563619 CCTAATGTACATATGCCTTTATTAATTGTATATACCAAATGCATACAATTATTTTTAACCAATGC
66 CCTAATATACATATGCCTTTATTAATTGTATATACCAAATGCATACAATTATGTTTAACCAATGC
41563684 AAAAAAAACCTGAATGTAGGCGTATACT
131 AAAAAAAACCTGAATGTAGGCGTATACT
41563712 TACCAAACAT
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
159 27 0.18
161 123 0.82
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (159 bp):
CTCAATATATATATTTAACAACCGCATATCACCATATGCATTTATAAATGCAACAATCACATATA
CCTAATATACATATGCCTTTATTAATTGTATATACCAAATGCATACAATTATGTTTAACCAATGC
AAAAAAAACCTGAATGTAGGCGTATACTC
Found at i:41563930 original size:97 final size:97
Alignment explanation
Indices: 41563764--41563956 Score: 359
Period size: 97 Copynumber: 2.0 Consensus size: 97
41563754 CATCGATTTC
*
41563764 ATATAATCAAAATCATAGATATATCAATTGCATATTCCCATATAATTTAAACATATTCACCGGCA
1 ATATAATCAAAATCATAGATATATCAATTGCATATTCCCATATAATTTAAACAGATTCACCGGCA
*
41563829 CTTAGCCTGCTAGGTTTTAAAACCTGATTCGA
66 CTTAGCCTGCTAGGTTTTAAAACCTAATTCGA
*
41563861 ATATAATCAAAATCATAGATATATCAATTGCATATTCCTATATAATTTAAACAGATTCACCGGCA
1 ATATAATCAAAATCATAGATATATCAATTGCATATTCCCATATAATTTAAACAGATTCACCGGCA
41563926 CTTAGCCTGCTAGGTTTTAAAACCTAATTCG
66 CTTAGCCTGCTAGGTTTTAAAACCTAATTCG
41563957 GTACACCGGC
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 93 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (97 bp):
ATATAATCAAAATCATAGATATATCAATTGCATATTCCCATATAATTTAAACAGATTCACCGGCA
CTTAGCCTGCTAGGTTTTAAAACCTAATTCGA
Found at i:41566704 original size:212 final size:212
Alignment explanation
Indices: 41566337--41566759 Score: 742
Period size: 212 Copynumber: 2.0 Consensus size: 212
41566327 TCAAGCATTC
*
41566337 ATCAATGGTAAAACTCAAAATCACTATCAAATTCTAAATTAAAACATGGGCTAAATAATACACGA
1 ATCAATGGTAAAACTCAAAATCACTATCAAATTCTAAAATAAAACATGGGCTAAATAATACACGA
*
41566402 AACAATGATCACAAAAACATAAAAATCATAAAAAAATCGAGACCAAAATATACCTCAATTAAACC
66 AACAAAGATCACAAAAACATAAAAATCATAAAAAAATCGAGACCAAAATATACCTCAATTAAACC
* *
41566467 AAGCAATTGCTGAAACCCTAAAGGCCATAGTTGAGTTCTTCTTAGCTTATTTTC-AGCTTTGGAG
131 AAGCAATTGCGGAAACCCTAAAGGCCATAGTTGAGTTCTTCTTAGCTTAGTTTCGA-CTTTGGAG
41566531 AAGATGAATGACACAAAA
195 AAGATGAATGACACAAAA
41566549 ATCAATGGTAAAACTCAAAATCACTATCAAATTCTAAAAATAAAACATGGGCTAAATAATACACG
1 ATCAATGGTAAAACTCAAAATCACTATCAAATTCT-AAAATAAAACATGGGCTAAATAATACACG
* * *
41566614 AAACAAAGATCACAAAAACATAAAAATCAT-CAAAAATCGGGACCAAAATATACCTCAATTAAGC
65 AAACAAAGATCACAAAAACATAAAAATCATAAAAAAATCGAGACCAAAATATACCTCAATTAAAC
*
41566678 CAAGGAATTGCGGAAACCCTAAAGGCCATAGTTGAGTTCTTCTTAGCTTAGTTTCGACTTTGGAG
130 CAAGCAATTGCGGAAACCCTAAAGGCCATAGTTGAGTTCTTCTTAGCTTAGTTTCGACTTTGGAG
41566743 AAGATGAATGACACAAA
195 AAGATGAATGACACAAA
41566760 TTTTAACTTT
Statistics
Matches: 201, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
212 143 0.71
213 58 0.29
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (212 bp):
ATCAATGGTAAAACTCAAAATCACTATCAAATTCTAAAATAAAACATGGGCTAAATAATACACGA
AACAAAGATCACAAAAACATAAAAATCATAAAAAAATCGAGACCAAAATATACCTCAATTAAACC
AAGCAATTGCGGAAACCCTAAAGGCCATAGTTGAGTTCTTCTTAGCTTAGTTTCGACTTTGGAGA
AGATGAATGACACAAAA
Found at i:41567029 original size:13 final size:13
Alignment explanation
Indices: 41567011--41567035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41567001 TCAAACTATC
41567011 AAATTTTCACACG
1 AAATTTTCACACG
41567024 AAATTTTCACAC
1 AAATTTTCACAC
41567036 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:41568356 original size:13 final size:13
Alignment explanation
Indices: 41568338--41568363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41568328 TCAAACTATC
41568338 AAATTTTCACACA
1 AAATTTTCACACA
41568351 AAATTTTCACACA
1 AAATTTTCACACA
41568364 TATAACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTTCACACA
Found at i:41573517 original size:62 final size:61
Alignment explanation
Indices: 41573441--41573562 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 61
41573431 TAAACCATTT
* **
41573441 TAATATGGCTATTATAATCATTTTCAATTCGACAAAGTACGATCTTCAAAACATTTATCTAA
1 TAATATGGCTATTATAATCATCTTCAATAAGACAAAGTACGATCTTCAAAACA-TTATCTAA
41573503 TAATATGGCTATTATAATCATCTTCAATAAGACAAAGTACGATCTTCAAAACATTATCTA
1 TAATATGGCTATTATAATCATCTTCAATAAGACAAAGTACGATCTTCAAAACATTATCTA
41573563 GTCTATACAT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 7 0.12
62 50 0.88
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.35
Consensus pattern (61 bp):
TAATATGGCTATTATAATCATCTTCAATAAGACAAAGTACGATCTTCAAAACATTATCTAA
Found at i:41576334 original size:13 final size:13
Alignment explanation
Indices: 41576316--41576340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41576306 TCAAACTATC
41576316 AAATTTTCACACG
1 AAATTTTCACACG
41576329 AAATTTTCACAC
1 AAATTTTCACAC
41576341 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:41580628 original size:11 final size:11
Alignment explanation
Indices: 41580612--41580661 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
41580602 TTTCAATCTT
41580612 TAACTTGAATC
1 TAACTTGAATC
41580623 TAACTTGACAT-
1 TAACTTGA-ATC
41580634 T--CTTGAATC
1 TAACTTGAATC
41580643 TAACTTGAATC
1 TAACTTGAATC
41580654 TAACTTGA
1 TAACTTGA
41580662 CATTATAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.06
9 6 0.17
11 25 0.71
12 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (11 bp):
TAACTTGAATC
Found at i:41580714 original size:13 final size:13
Alignment explanation
Indices: 41580696--41580725 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41580686 TATTATTGAA
41580696 TCTAACTTGACAT
1 TCTAACTTGACAT
41580709 TCTAACTTGACAT
1 TCTAACTTGACAT
41580722 TCTA
1 TCTA
41580726 GCTCCCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (13 bp):
TCTAACTTGACAT
Found at i:41580728 original size:57 final size:59
Alignment explanation
Indices: 41580636--41580771 Score: 192
Period size: 57 Copynumber: 2.4 Consensus size: 59
41580626 CTTGACATTC
* *
41580636 TTGAATCTAACTTGA-A-TCTAACTTGACATTATAGCTCCCCATTGTC-TCTT-TA-TTA
1 TTGAATCTAACTTGACATTCTAACTTGACATTATAGCTCCCCATT-CCAGCTTCTATTTA
* *
41580691 TTGAATCTAACTTGACATTCTAACTTGACATTCTAGCTCCCCATTCCAGCTTCTATTTC
1 TTGAATCTAACTTGACATTCTAACTTGACATTATAGCTCCCCATTCCAGCTTCTATTTA
41580750 TTGAATCTAACTTGACATTCTA
1 TTGAATCTAACTTGACATTCTA
41580772 GCTCCCCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
55 15 0.21
56 2 0.03
57 29 0.40
58 2 0.03
59 24 0.33
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.40
Consensus pattern (59 bp):
TTGAATCTAACTTGACATTCTAACTTGACATTATAGCTCCCCATTCCAGCTTCTATTTA
Found at i:41581305 original size:30 final size:31
Alignment explanation
Indices: 41581253--41581310 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
41581243 CACCCTTAAA
** *
41581253 TATTTACACTATTAGTCCTTCAACTTTTTCG
1 TATTTACACTATTAACCCTTCAAATTTTTCG
41581284 TATTTACACT-TTAACCCTTCAAATTTT
1 TATTTACACTATTAACCCTTCAAATTTT
41581311 GAGTATTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.26, C:0.22, G:0.03, T:0.48
Consensus pattern (31 bp):
TATTTACACTATTAACCCTTCAAATTTTTCG
Found at i:41581317 original size:30 final size:31
Alignment explanation
Indices: 41581253--41581317 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
41581243 CACCCTTAAA
** * **
41581253 TATTTACACTATTAGTCCTTCAACTTTTTCG
1 TATTTACACTATTAACCCTTCAAATTTTGAG
41581284 TATTTACACT-TTAACCCTTCAAATTTTGAG
1 TATTTACACTATTAACCCTTCAAATTTTGAG
41581314 TATT
1 TATT
41581318 GGGCAACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (31 bp):
TATTTACACTATTAACCCTTCAAATTTTGAG
Found at i:41582524 original size:12 final size:13
Alignment explanation
Indices: 41582507--41582535 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41582497 CTCATACATG
41582507 AATAAATAAA-GC
1 AATAAATAAATGC
41582519 AATAAATAAATGC
1 AATAAATAAATGC
41582532 AATA
1 AATA
41582536 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:41589740 original size:21 final size:21
Alignment explanation
Indices: 41589714--41589764 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
41589704 NNNNNNNNNN
*
41589714 AGATTGCATATATCATATCTA
1 AGATTGCATATATCATATCCA
41589735 AGATTGC--ATATCATATCCA
1 AGATTGCATATATCATATCCA
*
41589754 AGATTGTATAT
1 AGATTGCATAT
41589765 CCTCGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (21 bp):
AGATTGCATATATCATATCCA
Found at i:41590151 original size:44 final size:44
Alignment explanation
Indices: 41590075--41590582 Score: 168
Period size: 44 Copynumber: 11.7 Consensus size: 44
41590065 CTCTAATCCA
* * * * * *
41590075 CTCCACTACAACTT-AGGGAGACAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTACTTAGTCTG
41590118 C-CTCACTGCAACTTCAG-GAGGATAAGACTTGTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGAGA-GATAAGACTTGTTTACTTAGTCTG
* **
41590162 CTCCACTGCAACTTCAGAGAGATAAGACTAG---AC-GCGATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTACTTAG-TCTG
* ** * *
41590203 CT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT--TT-GATCCG
1 CTCCACTGCAACTTCAGAGAGATAAGA--CTTGTTTACTTAG-TCTG
* * * * *** *
41590246 CTCCACTGTAACTTCAGGGAGATAGGA-TTATCGGCTCTAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTACT-TAGTCTG
* * * * ** *
41590290 CTCCATTGCAACTTTAGGGAGATAAGATTTG-CCATCTTCAGTCTA
1 CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTA-CTT-AGTCTG
* * *
41590335 C-CTCACTGCAACTTCA-AGAGGATAAGACTTGCTTGCTGAGTCTG
1 CTC-CACTGCAACTTCAGAGA-GATAAGACTTGTTTACTTAGTCTG
* * *** *
41590379 CTCCACTGCAACTTCAGGGAGATAAGACTAG-AGGC-GA-TCTG
1 CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTACTTAGTCTG
* ** * * *
41590420 CT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT--TTAATCCG
1 CTCCACTGCAACTTCAGAGAGATAAGA--CTTGTTTACTTAGTCTG
* * *** *
41590463 CTCCACTGCAACTTCA-AGGAGATAGGA-TTATCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGA-GAGATAAGACTTGTTTAC-TTAGTCTG
* * ** *
41590507 CTCCACTGCAACTTCCGAGAGATAAGATTTG-CCATCTTCAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTA-CTT-AGTCTG
41590552 C-CCTACTGCAACTTCAG-GAGGATAAGACTTG
1 CTCC-ACTGCAACTTCAGAGA-GATAAGACTTG
41590583 CTGGCTTAAA
Statistics
Matches: 355, Mismatches: 69, Indels: 80
0.70 0.14 0.16
Matches are distributed among these distances:
40 46 0.13
41 14 0.04
42 10 0.03
43 29 0.08
44 185 0.52
45 71 0.20
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGAGAGATAAGACTTGTTTACTTAGTCTG
Found at i:41590493 original size:217 final size:217
Alignment explanation
Indices: 41590112--41590584 Score: 786
Period size: 217 Copynumber: 2.2 Consensus size: 217
41590102 TTGTTTATTT
* *
41590112 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTC
1 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTGAGTCTGCTCCACTGCAACTTC
*
41590177 AGAGAGATAAGACTAGACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGAGAGATAAGACTAGACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
* * * *
41590242 TCCGCTCCACTGTAACTTCAGGGAGATAGGATTATCGGCTCTAATCTGCTCCATTGCAACTTTAG
131 TCCGCTCCACTGCAACTTCAAGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAG
*
41590307 GGAGATAAGATTTGCCATCTTC
196 AGAGATAAGATTTGCCATCTTC
* * *
41590329 AGTCTACCTCACTGCAACTTCAAGAGGATAAGACTTGCTTGCTGAGTCTGCTCCACTGCAACTTC
1 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTGAGTCTGCTCCACTGCAACTTC
* *
41590394 AGGGAGATAAGACTAGAGGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
66 AGAGAGATAAGACTAGACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
* *
41590459 TCCGCTCCACTGCAACTTCAAGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCCG
131 TCCGCTCCACTGCAACTTCAAGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAG
41590524 AGAGATAAGATTTGCCATCTTC
196 AGAGATAAGATTTGCCATCTTC
*
41590546 AATCTGCC-CTACTGCAACTTCAGGAGGATAAGACTTGCT
1 AGTCTGCCTC-ACTGCAACTTCAGGAGGATAAGACTTGCT
41590585 GGCTTAAATC
Statistics
Matches: 237, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
216 1 0.00
217 236 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (217 bp):
AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTGAGTCTGCTCCACTGCAACTTC
AGAGAGATAAGACTAGACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
TCCGCTCCACTGCAACTTCAAGGAGATAGGATTATCGGCTCTAATCTGCTCCACTGCAACTTCAG
AGAGATAAGATTTGCCATCTTC
Done.