Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 140 of 297
Found at i:48174628 original size:86 final size:88
Alignment explanation
Indices: 48174494--48174693 Score: 341
Period size: 86 Copynumber: 2.3 Consensus size: 88
48174484 TTTTTTGTAC
* *
48174494 TTGAACTTTCAAAATACATCAAAAAAGCCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTAC
1 TTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAACCTTTTAAAAAAAAGCAATTAAGCCCCTAC
48174559 -TTTTTTTTCACTCAATTGGGT-
66 TTTTTTTTTCACTCAATTGGGTA
*
48174580 TTGAACTTTCAAAATGCATCAAAAAAGCCTTCAAACCTTTTAAAAAAAAGCAATTAAGCCCCTAC
1 TTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAACCTTTTAAAAAAAAGCAATTAAGCCCCTAC
48174645 TTTTTTTTTCACTCAATTGGGTA
66 TTTTTTTTTCACTCAATTGGGTA
*
48174668 CTTAAACTTTCAAAATGCATCAAAAA
1 -TTGAACTTTCAAAATGCATCAAAAA
48174694 GACCATCAAC
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
86 62 0.58
87 21 0.20
89 24 0.22
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (88 bp):
TTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAACCTTTTAAAAAAAAGCAATTAAGCCCCTAC
TTTTTTTTTCACTCAATTGGGTA
Found at i:48174853 original size:19 final size:19
Alignment explanation
Indices: 48174824--48174874 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
48174814 AATAAAAATT
*
48174824 AAAATATTAAAAATTAGAAA
1 AAAATA-TAAAAATCAGAAA
*
48174844 AAAATAT-AAAATCATAAA
1 AAAATATAAAAATCAGAAA
48174862 AAATATATAAAAA
1 AAA-ATATAAAAA
48174875 ATTGTGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.44
19 5 0.19
20 10 0.37
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATATAAAAATCAGAAA
Found at i:48174884 original size:19 final size:19
Alignment explanation
Indices: 48174861--48174912 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
48174851 AAAATCATAA
48174861 AAAATATATAAAAAATTGT
1 AAAATATATAAAAAATTGT
* *
48174880 GAAAT-TTTATAAAAATTGT
1 AAAATATATA-AAAAATTGT
*
48174899 AAAAAATTATAAAA
1 AAAATA-TATAAAA
48174913 TATAAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
18 3 0.12
19 16 0.64
20 3 0.12
21 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAATATATAAAAAATTGT
Found at i:48174905 original size:10 final size:10
Alignment explanation
Indices: 48174832--48174912 Score: 60
Period size: 10 Copynumber: 8.3 Consensus size: 10
48174822 TTAAAATATT
*
48174832 AAAAATTAGA
1 AAAAATTATA
48174842 AAAAA--ATA
1 AAAAATTATA
* *
48174850 TAAAATCATA
1 AAAAATTATA
48174860 AAAAATATATA
1 AAAAAT-TATA
* *
48174871 AAAAATTGTG
1 AAAAATTATA
**
48174881 AAATTTTAT-
1 AAAAATTATA
*
48174890 AAAAATTGTA
1 AAAAATTATA
48174900 AAAAATTATA
1 AAAAATTATA
48174910 AAA
1 AAA
48174913 TATAAAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
8 6 0.11
9 6 0.11
10 33 0.61
11 9 0.17
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:48174925 original size:17 final size:18
Alignment explanation
Indices: 48174793--48174928 Score: 62
Period size: 17 Copynumber: 7.3 Consensus size: 18
48174783 CAATAAAAGC
48174793 TATAAATATTATCAAAATTT
1 TATAAA-ATTAT-AAAATTT
* *
48174813 TAATAAAAAT-TAAAATAT
1 T-ATAAAATTATAAAATTT
* ***
48174831 TA-AAAATTAGAAAAAAA
1 TATAAAATTATAAAATTT
* *
48174848 TATAAAATCATAAAAAATATA
1 TATAAAAT--TATAAAAT-TT
* * *
48174869 TAAAAAATTGTGAAATTT
1 TATAAAATTATAAAATTT
* **
48174887 TATAAAAATTGTAAAAAAT
1 TAT-AAAATTATAAAATTT
48174906 TATAAAA-TATAAAATTT
1 TATAAAATTATAAAATTT
48174923 TATAAA
1 TATAAA
48174929 GTCGTAAGAA
Statistics
Matches: 88, Mismatches: 21, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.06
17 21 0.24
18 19 0.22
19 21 0.24
20 9 0.10
21 13 0.15
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (18 bp):
TATAAAATTATAAAATTT
Found at i:48178720 original size:47 final size:47
Alignment explanation
Indices: 48178659--48178772 Score: 135
Period size: 47 Copynumber: 2.4 Consensus size: 47
48178649 GCAATACCAT
* * *
48178659 AGACACGGTTTTACACTAGCTAAAATCTC-AAGTCGATGCCATGTCCC
1 AGACATGGTCTTACACTAGCTAAAATCTCGAAGCCGATG-CATGTCCC
** *
48178706 AGACATGGTCTTACACT-GACTATCATCTCGTAGCCGATGCATGTCCC
1 AGACATGGTCTTACACTAG-CTAAAATCTCGAAGCCGATGCATGTCCC
48178753 AGACAT-GTCTTACACTAGCT
1 AGACATGGTCTTACACTAGCT
48178773 CACACACGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
46 13 0.22
47 38 0.66
48 7 0.12
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (47 bp):
AGACATGGTCTTACACTAGCTAAAATCTCGAAGCCGATGCATGTCCC
Found at i:48179092 original size:190 final size:190
Alignment explanation
Indices: 48178769--48179149 Score: 762
Period size: 190 Copynumber: 2.0 Consensus size: 190
48178759 GTCTTACACT
48178769 AGCTCACACACGAATGACCCAAATGTCATGGCATGAATATCTGGTTTATTTCCTAAGGTTTCAAC
1 AGCTCACACACGAATGACCCAAATGTCATGGCATGAATATCTGGTTTATTTCCTAAGGTTTCAAC
48178834 GGGAATTCTACTATCTCATTTATCATTATACATTCTCAATTTCACAATCAAGCAACCCATGCTAT
66 GGGAATTCTACTATCTCATTTATCATTATACATTCTCAATTTCACAATCAAGCAACCCATGCTAT
48178899 AATAATTCAAGCACATATAATTAACAATGTAGTGATATTATTTACATACAACTTACCTCG
131 AATAATTCAAGCACATATAATTAACAATGTAGTGATATTATTTACATACAACTTACCTCG
48178959 AGCTCACACACGAATGACCCAAATGTCATGGCATGAATATCTGGTTTATTTCCTAAGGTTTCAAC
1 AGCTCACACACGAATGACCCAAATGTCATGGCATGAATATCTGGTTTATTTCCTAAGGTTTCAAC
48179024 GGGAATTCTACTATCTCATTTATCATTATACATTCTCAATTTCACAATCAAGCAACCCATGCTAT
66 GGGAATTCTACTATCTCATTTATCATTATACATTCTCAATTTCACAATCAAGCAACCCATGCTAT
48179089 AATAATTCAAGCACATATAATTAACAATGTAGTGATATTATTTACATACAACTTACCTCG
131 AATAATTCAAGCACATATAATTAACAATGTAGTGATATTATTTACATACAACTTACCTCG
48179149 A
1 A
48179150 ATTACAAAAT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 191 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (190 bp):
AGCTCACACACGAATGACCCAAATGTCATGGCATGAATATCTGGTTTATTTCCTAAGGTTTCAAC
GGGAATTCTACTATCTCATTTATCATTATACATTCTCAATTTCACAATCAAGCAACCCATGCTAT
AATAATTCAAGCACATATAATTAACAATGTAGTGATATTATTTACATACAACTTACCTCG
Found at i:48179554 original size:13 final size:13
Alignment explanation
Indices: 48179538--48179603 Score: 98
Period size: 13 Copynumber: 5.1 Consensus size: 13
48179528 TTTAAACCAA
48179538 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
48179551 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
48179564 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
48179577 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
48179590 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
48179603 A
1 A
48179604 TTGCCAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
12 5 0.10
13 38 0.79
14 5 0.10
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:48182103 original size:68 final size:69
Alignment explanation
Indices: 48182020--48182178 Score: 212
Period size: 74 Copynumber: 2.2 Consensus size: 69
48182010 TAGAGTTAAG
** * *
48182020 TTCAATTTTAGGTGGTGG-AGAAGTAGAATCACTGCTAGCCATTAAGGACGATGGTGATAGTTTC
1 TTCAATTTTAGGTGGTGGTAGAAGTAGAATCACCACCAGCCATTAAGAACGATGGTGATAGTTTC
48182084 AACA
66 AACA
* *
48182088 TTCAATTTTAAGTGGTGATGGTTTAGAAGTAGAATCGCCACCAGCCATTAAGAACGATGGTGATA
1 TTCAATTTT-A--GGTGGTGG--TAGAAGTAGAATCACCACCAGCCATTAAGAACGATGGTGATA
48182153 GTTTCAACA
61 GTTTCAACA
48182162 TTCAATTTTAGGTGGTG
1 TTCAATTTTAGGTGGTG
48182179 ATGGTTTAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
68 9 0.12
69 1 0.01
71 13 0.17
73 1 0.01
74 54 0.69
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (69 bp):
TTCAATTTTAGGTGGTGGTAGAAGTAGAATCACCACCAGCCATTAAGAACGATGGTGATAGTTTC
AACA
Found at i:48182138 original size:74 final size:73
Alignment explanation
Indices: 48182038--48182214 Score: 266
Period size: 74 Copynumber: 2.4 Consensus size: 73
48182028 TAGGTGGTGG
** * *
48182038 AGAAGTAGAATCACTGCTAGCCATTAAGGACGATGGTGATAGTTTCAACATTCAATTTTAAGTGG
1 AGAAGTAGAATC-CCACCAGCCATTAAGAACGATGGTGATAGTTTCAACATTCAATTTTAAGTGG
48182103 TGATGGTTT
65 TGATGGTTT
*
48182112 AGAAGTAGAATCGCCACCAGCCATTAAGAACGATGGTGATAGTTTCAACATTCAATTTTAGGTGG
1 AGAAGTAGAATC-CCACCAGCCATTAAGAACGATGGTGATAGTTTCAACATTCAATTTTAAGTGG
48182177 TGATGGTTT
65 TGATGGTTT
* *
48182186 AGAATTAGAAT-CCACCAGCCATTGAGAAC
1 AGAAGTAGAATCCCACCAGCCATTAAGAAC
48182215 AATGAACTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
72 17 0.18
74 78 0.82
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (73 bp):
AGAAGTAGAATCCCACCAGCCATTAAGAACGATGGTGATAGTTTCAACATTCAATTTTAAGTGGT
GATGGTTT
Found at i:48195237 original size:24 final size:24
Alignment explanation
Indices: 48195210--48195257 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
48195200 GATGGAGACA
48195210 AAGACAAAGACGAAGGCGAAGGTC
1 AAGACAAAGACGAAGGCGAAGGTC
** *
48195234 AAGATGAAGATGAAGGCGAAGGTC
1 AAGACAAAGACGAAGGCGAAGGTC
48195258 GAGATGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.35, T:0.08
Consensus pattern (24 bp):
AAGACAAAGACGAAGGCGAAGGTC
Found at i:48195262 original size:24 final size:24
Alignment explanation
Indices: 48195216--48195270 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
48195206 GACAAAGACA
*
48195216 AAGACGAAGGCGAAGGTCAAGATG
1 AAGATGAAGGCGAAGGTCAAGATG
*
48195240 AAGATGAAGGCGAAGGTCGAGATG
1 AAGATGAAGGCGAAGGTCAAGATG
48195264 AAGATGA
1 AAGATGA
48195271 GTACGAGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.38, T:0.11
Consensus pattern (24 bp):
AAGATGAAGGCGAAGGTCAAGATG
Found at i:48195283 original size:24 final size:24
Alignment explanation
Indices: 48195216--48195291 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
48195206 GACAAAGACA
* * *
48195216 AAGACGAAGGCGAAGGTCAAGATG
1 AAGATGAAGACGAAGGTCGAGATG
*
48195240 AAGATGAAGGCGAAGGTCGAGATG
1 AAGATGAAGACGAAGGTCGAGATG
*
48195264 AAGATG-AGTACG-AGGATCGAGGTG
1 AAGATGAAG-ACGAAGG-TCGAGATG
48195288 AAGA
1 AAGA
48195292 CGAAAAAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.11
24 41 0.89
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.12
Consensus pattern (24 bp):
AAGATGAAGACGAAGGTCGAGATG
Found at i:48210190 original size:25 final size:25
Alignment explanation
Indices: 48210158--48210207 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
48210148 ATTTAAAATA
48210158 AATTTCAATAGGAAAGTAATTACAT
1 AATTTCAATAGGAAAGTAATTACAT
48210183 AATTTCAATAGGAAAGTAATTACAT
1 AATTTCAATAGGAAAGTAATTACAT
48210208 GCCCAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (25 bp):
AATTTCAATAGGAAAGTAATTACAT
Found at i:48211936 original size:20 final size:21
Alignment explanation
Indices: 48211899--48211939 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
48211889 CTAATGGGAC
*
48211899 AAGTGACATGGCCGGTTAACT
1 AAGTGACATGGCCAGTTAACT
48211920 AAGTGAC-TGGCCAGTTAACT
1 AAGTGACATGGCCAGTTAACT
48211940 TGCCACGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
AAGTGACATGGCCAGTTAACT
Found at i:48212073 original size:30 final size:30
Alignment explanation
Indices: 48212009--48212080 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
48211999 AGAAAAGTTG
* *
48212009 GATTGAGATTAAGGAAAAAAAGAAAAGATT
1 GATTGAGATTAAGGAAAAAAAGAAAAAATC
*
48212039 GATTGAGATTAA-TAAGAAGAAA-AAAAAATC
1 GATTGAGATTAAGGAA-AA-AAAGAAAAAATC
*
48212069 GATTGGGATTAA
1 GATTGAGATTAA
48212081 CATTTTAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.06
30 31 0.86
31 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.22, T:0.22
Consensus pattern (30 bp):
GATTGAGATTAAGGAAAAAAAGAAAAAATC
Found at i:48219627 original size:45 final size:44
Alignment explanation
Indices: 48219587--48219732 Score: 156
Period size: 45 Copynumber: 3.4 Consensus size: 44
48219577 TATGTGTTCT
* *
48219587 CGTGTAAGACTATGTCTGGGACGTTGGCATCGATATATGTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATC-ATATATGTGATTA
48219632 CGTGTAAGACCATGTCTGGGACATTGGCATCATAT-T-TGATT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCATATATGTGATTA
* * * * * * *
48219673 CGTTTAAGACCCTATTTAGGATAGTGGCATCA-ATATGTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCATATATGTGATTA
* *
48219716 CATGTAAGACCACGTCT
1 CGTGTAAGACCATGTCT
48219733 AGGATGTTGG
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
40 2 0.02
41 26 0.31
42 10 0.12
43 12 0.14
44 4 0.05
45 29 0.35
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCATATATGTGATTA
Found at i:48219949 original size:18 final size:19
Alignment explanation
Indices: 48219915--48219952 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
48219905 GATGCAAATT
48219915 ATATATGATGTAAATGAAA
1 ATATATGATGTAAATGAAA
*
48219934 ATATATG-TGTATATGAAA
1 ATATATGATGTAAATGAAA
48219952 A
1 A
48219953 GTACACTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (19 bp):
ATATATGATGTAAATGAAA
Found at i:48228556 original size:66 final size:68
Alignment explanation
Indices: 48228427--48228556 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 68
48228417 GGGATGTATC
*
48228427 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC-T-AGAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
48228492 AGGACA
63 AGGACA
* *
48228498 CCATGTAGACAAGAGAGCTA-T-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACTAGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
48228557 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
69 1 0.02
71 20 0.36
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (68 bp):
CCATGTAGACAAGAGAGCTACTAGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGG
ACA
Found at i:48230292 original size:25 final size:25
Alignment explanation
Indices: 48230263--48230312 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
48230253 CCTTATAACA
* * *
48230263 TGAAAATGACCGTTTTGCCCCTAGG
1 TGAAAATGACCATTATACCCCTAGG
48230288 TGAAAATGACCATTATACCCCTAGG
1 TGAAAATGACCATTATACCCCTAGG
48230313 GTTTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (25 bp):
TGAAAATGACCATTATACCCCTAGG
Found at i:48230724 original size:31 final size:31
Alignment explanation
Indices: 48230686--48230749 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
48230676 CGTTTACAGT
*
48230686 AAAGGCTTCGGCGCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
48230717 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
48230748 AA
1 AA
48230750 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:48236977 original size:25 final size:25
Alignment explanation
Indices: 48236948--48236995 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
48236938 TTATAACATG
* * *
48236948 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
48236973 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
48236996 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:48237079 original size:11 final size:11
Alignment explanation
Indices: 48237043--48237098 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
48237033 CATGGTATGT
48237043 ATGATATGCAC
1 ATGATATGCAC
* *
48237054 ATGACATG--T
1 ATGATATGCAC
48237063 ATGATATGCAC
1 ATGATATGCAC
*
48237074 ATGATATG--T
1 ATGATATGCAC
48237083 ATGATATGCAC
1 ATGATATGCAC
48237094 ATGAT
1 ATGAT
48237099 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:48237098 original size:20 final size:20
Alignment explanation
Indices: 48237032--48237098 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
48237022 ATTTTGATAA
*
48237032 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
48237052 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
48237072 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
48237092 ACATGAT
1 ACATGAT
48237099 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:48237181 original size:25 final size:24
Alignment explanation
Indices: 48237149--48237195 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
48237139 AGGAAGTGAA
*
48237149 AAAGGGCTTATGCC-CCAGTTATTC
1 AAAGGGC-TAGGCCTCCAGTTATTC
48237173 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
48237196 ATGATAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTC
Found at i:48237424 original size:31 final size:31
Alignment explanation
Indices: 48237389--48237452 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
48237379 CGTTTACAGT
48237389 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
48237420 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
48237451 AA
1 AA
48237453 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:48242741 original size:40 final size:40
Alignment explanation
Indices: 48242677--48242813 Score: 202
Period size: 40 Copynumber: 3.4 Consensus size: 40
48242667 ACTCGACATC
** * *
48242677 TCGCACACTAAGTGCTGTACATAGCCGAAGCTATCTTAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
* *
48242717 TCGCACACTATGTGCCATATATAGCCGAAGGTATCTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
*
48242757 TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
*
48242797 TCACACACTAAGTGCCA
1 TCGCACACTAAGTGCCA
48242814 CAAATAACTG
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
Found at i:48243331 original size:20 final size:20
Alignment explanation
Indices: 48243279--48243321 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
48243269 AAAAGCTATT
*
48243279 AATCTAACATTAAACCATCCA
1 AATCTATCA-TAAACCATCCA
48243300 AATCTATCATAAACCAT-CA
1 AATCTATCATAAACCATCCA
48243319 AAT
1 AAT
48243322 TACTCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
AATCTATCATAAACCATCCA
Found at i:48252467 original size:24 final size:24
Alignment explanation
Indices: 48252439--48252524 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
48252429 AGGAAATTCA
*
48252439 CACACATAGTGCGATGCTAA-CCTG
1 CACACATAGTGCCATGCTAATCC-G
* *
48252463 CACACATAGTGCCTTGCTAATCCA
1 CACACATAGTGCCATGCTAATCCG
* * *
48252487 CACACGTAGTGCCATTCAAATCCG
1 CACACATAGTGCCATGCTAATCCG
48252511 CACACATAGTGCCA
1 CACACATAGTGCCA
48252525 ATGTCATTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 50 0.96
25 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (24 bp):
CACACATAGTGCCATGCTAATCCG
Found at i:48253112 original size:2 final size:2
Alignment explanation
Indices: 48253105--48253139 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48253095 CTTCAATAAA
48253105 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
48253140 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48253885 original size:17 final size:17
Alignment explanation
Indices: 48253863--48253896 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48253853 CCCCACTTAA
*
48253863 TATATTATAACTTATTT
1 TATATTATAACATATTT
48253880 TATATTATAACATATTT
1 TATATTATAACATATTT
48253897 CAAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:48268817 original size:39 final size:40
Alignment explanation
Indices: 48268722--48268983 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
48268712 TTGAATGATG
*
48268722 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
48268760 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
48268801 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
48268840 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
48268879 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
48268918 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
48268957 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
48268984 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:48276594 original size:24 final size:23
Alignment explanation
Indices: 48276566--48276611 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
48276556 GAAGGGAAAG
48276566 AGGTGAGTTTGGAAAA-CTCAGTNA
1 AGGTGAGTTT-GAAAAGCTCAGT-A
48276590 AGGTGAGTTTGAAAAGCTCAGT
1 AGGTGAGTTTGAAAAGCTCAGT
48276612 GTGTAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.26
Consensus pattern (23 bp):
AGGTGAGTTTGAAAAGCTCAGTA
Found at i:48279187 original size:47 final size:47
Alignment explanation
Indices: 48279136--48280688 Score: 2607
Period size: 47 Copynumber: 32.7 Consensus size: 47
48279126 TTAGGATTCT
* * *
48279136 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
48279183 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48279231 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48279279 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48279327 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48279375 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48279423 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48279471 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
*
48279519 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279566 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279613 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279660 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279707 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279754 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279801 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279848 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279895 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279942 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48279989 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48280036 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48280083 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48280130 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48280177 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
48280224 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
48280271 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48280319 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48280367 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48280415 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48280463 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48280511 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
48280559 ATGTGATGAATGTGAAAGTGTATATATATGTGATAA-GCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
* * * *
48280607 ATGTGATGAATGTGAAAGTGTATATATGTGA-CAGGGCTGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCG
* * *
48280654 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
48280689 TCCCGAAGGG
Statistics
Matches: 1480, Mismatches: 17, Indels: 17
0.98 0.01 0.01
Matches are distributed among these distances:
45 1 0.00
46 29 0.02
47 784 0.53
48 640 0.43
49 26 0.02
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:48280876 original size:37 final size:37
Alignment explanation
Indices: 48280807--48280885 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
48280797 CCGAGCTCTA
* *
48280807 AAGACCCGATGACTACATGTAGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACATGTAGGGATTATGTCCGGGT
* *
48280844 AAGACCCGATAACTTCGTGT-GGAGATTATGTCCGGGT
1 AAGACCCGATAACTACATGTAGG-GATTATGTCCGGGT
48280881 AAGAC
1 AAGAC
48280886 TTCATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACATGTAGGGATTATGTCCGGGT
Found at i:48291943 original size:13 final size:13
Alignment explanation
Indices: 48291925--48291949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48291915 GAATTTACAT
48291925 GTATGAAAATTTC
1 GTATGAAAATTTC
48291938 GTATGAAAATTT
1 GTATGAAAATTT
48291950 GTTTGTTTGT
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:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
GTATGAAAATTTC
Found at i:48293386 original size:34 final size:35
Alignment explanation
Indices: 48293340--48293426 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
48293330 AGGTAAGTAT
48293340 ATGT-AAGCTTATATTGAACTTGAT-TATTCGATTAC
1 ATGTGAAG-TTATATTGAACTT-ATATATTCGATTAC
* **
48293375 ATGTGAA-TTATATTGAACTTATATATTCGGTTTT
1 ATGTGAAGTTATATTGAACTTATATATTCGATTAC
*
48293409 ATGTGAAGTTATTTTGAA
1 ATGTGAAGTTATATTGAA
48293427 TGTGCATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.04
34 28 0.62
35 13 0.29
36 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (35 bp):
ATGTGAAGTTATATTGAACTTATATATTCGATTAC
Found at i:48296839 original size:18 final size:18
Alignment explanation
Indices: 48296818--48296861 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
48296808 ACTTTTTCTT
48296818 CTTCAGCAACAACTTCCG
1 CTTCAGCAACAACTTCCG
**
48296836 CTTC-GACAACAACTTCTT
1 CTTCAG-CAACAACTTCCG
48296854 CTTCAGCA
1 CTTCAGCA
48296862 GCATCAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.27
Consensus pattern (18 bp):
CTTCAGCAACAACTTCCG
Found at i:48306460 original size:19 final size:19
Alignment explanation
Indices: 48306411--48306462 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
48306401 GTAATTGAAC
* *
48306411 TTGAAAATTGGACTTGAGA
1 TTGAAAATTGGGCCTGAGA
*
48306430 TCGAAAATTGGGCCTGAGA
1 TTGAAAATTGGGCCTGAGA
48306449 TTGAAAATTGGGCC
1 TTGAAAATTGGGCC
48306463 CAAGAACCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (19 bp):
TTGAAAATTGGGCCTGAGA
Found at i:48307055 original size:29 final size:29
Alignment explanation
Indices: 48307019--48307077 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
48307009 TGTGCACAAA
* * *
48307019 GGATGTCTTTTTTCTACTGTGTCGTGTAG
1 GGATGTCTTTTTGCTACCGTGCCGTGTAG
*
48307048 GGATGTCTTTTTGCTGCCGTGCCGTGTAG
1 GGATGTCTTTTTGCTACCGTGCCGTGTAG
48307077 G
1 G
48307078 TGGTCGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.08, C:0.17, G:0.32, T:0.42
Consensus pattern (29 bp):
GGATGTCTTTTTGCTACCGTGCCGTGTAG
Found at i:48311614 original size:21 final size:21
Alignment explanation
Indices: 48311590--48311631 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
48311580 ATATCGACTA
48311590 AAGCCAGTCATGTTCCAGATG
1 AAGCCAGTCATGTTCCAGATG
48311611 AAGCCAGTCATGTTCCAGATG
1 AAGCCAGTCATGTTCCAGATG
48311632 CTTCAGACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
AAGCCAGTCATGTTCCAGATG
Found at i:48311911 original size:19 final size:19
Alignment explanation
Indices: 48311887--48311924 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48311877 TAAGAATGCT
48311887 AAGTTGAGGAACGAGATCA
1 AAGTTGAGGAACGAGATCA
48311906 AAGTTGAGGAACGAGATCA
1 AAGTTGAGGAACGAGATCA
48311925 CTTCTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.16
Consensus pattern (19 bp):
AAGTTGAGGAACGAGATCA
Found at i:48327354 original size:76 final size:76
Alignment explanation
Indices: 48327205--48327356 Score: 187
Period size: 76 Copynumber: 2.0 Consensus size: 76
48327195 TGTGAGTGGG
* * * *
48327205 CTACCCCTAACGCCTTCTATGAAAAATTTAGTCTGGGTCATCGTGGATCGATTAACCAAAACCGC
1 CTACCCCTAACGCCTTCTAAGAAAAATTCAGTCTGGGCCATCGTGGATCGATTAACCAAAACCAC
* *
48327270 TCATTTCATAC
66 CCACTTCATAC
* * * * * * *
48327281 CTACCCCTCACGCCTTCTAAGAAAGATTCAGTGTGGGCCATCGTGGATCGGTTGACCAAATCTAC
1 CTACCCCTAACGCCTTCTAAGAAAAATTCAGTCTGGGCCATCGTGGATCGATTAACCAAAACCAC
48327346 CCACTTCATAC
66 CCACTTCATAC
48327357 TGGTTTGTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (76 bp):
CTACCCCTAACGCCTTCTAAGAAAAATTCAGTCTGGGCCATCGTGGATCGATTAACCAAAACCAC
CCACTTCATAC
Found at i:48333542 original size:29 final size:28
Alignment explanation
Indices: 48333506--48333583 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
48333496 TCATGAGATT
48333506 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
48333536 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
*
48333563 TGGCACTAAGTATGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
48333584 GATTATTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.12
29 34 0.81
30 3 0.07
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:48333801 original size:174 final size:174
Alignment explanation
Indices: 48333536--48333863 Score: 584
Period size: 174 Copynumber: 1.9 Consensus size: 174
48333526 AAATTGTACA
**
48333536 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTATGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTATGCCCGGTTGATTATTAAGCACTATG
* *
48333601 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
48333666 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * *
48333710 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCCCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTATGCCCGGTTGATTATTAAGCACTATG
*
48333775 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
48333840 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
48333864 ACCTTGAGTT
Statistics
Matches: 146, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 146 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTATGCCCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:48334309 original size:69 final size:69
Alignment explanation
Indices: 48334198--48334332 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 69
48334188 ATATACTCAT
* *
48334198 TCGGTGTTTGCTTGTCACCTATTCTAGGTTTCTTGGACTCGTCTCTTTTTGCGTGATCGTGCCGT
1 TCGGTGTTTCCTTGTCACCTATTCTAGGTTTCTTGGACTCGTCTCTTTTTGCGTGATCGGGCCGT
48334263 CGAC
66 CGAC
48334267 TCGGTGTTTCCTTGTCACCTATTCTAGGTTTCTTGGACTCGTCTCTTTTTGCGTGATCGGGCCGT
1 TCGGTGTTTCCTTGTCACCTATTCTAGGTTTCTTGGACTCGTCTCTTTTTGCGTGATCGGGCCGT
48334332 C
66 C
48334333 ATCGAAGTCA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.08, C:0.25, G:0.24, T:0.42
Consensus pattern (69 bp):
TCGGTGTTTCCTTGTCACCTATTCTAGGTTTCTTGGACTCGTCTCTTTTTGCGTGATCGGGCCGT
CGAC
Found at i:48339216 original size:43 final size:42
Alignment explanation
Indices: 48339168--48339292 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 42
48339158 GATTTCTAAC
48339168 ATGTGTTCTTGTGTAAGACCATGTCTGGGACGTTGGCATCAAT
1 ATGTGTTC-TGTGTAAGACCATGTCTGGGACGTTGGCATCAAT
* * ** *
48339211 ATGTGTTCTCGTATAAGACCCTGTCTAAGACAG-TGGCATCGAT
1 ATGTGTTCT-GTGTAAGACCATGTCTGGGAC-GTTGGCATCAAT
* *
48339254 ATGTGATTAC-ATGTAAGACCACGTCTGGGACGTTGGCAT
1 ATGTG-TT-CTGTGTAAGACCATGTCTGGGACGTTGGCAT
48339293 TGTACGATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
42 2 0.03
43 60 0.91
44 3 0.05
45 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
ATGTGTTCTGTGTAAGACCATGTCTGGGACGTTGGCATCAAT
Found at i:48342658 original size:40 final size:40
Alignment explanation
Indices: 48342588--48342845 Score: 337
Period size: 40 Copynumber: 6.5 Consensus size: 40
48342578 AAACCAAGTA
* * *
48342588 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
48342627 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
48342667 CCTTCGGGACTTAGCCTGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
48342707 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
48342747 CCTTCGAGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCG-GGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* ** * *
48342787 CCTTCGGGGCTTAGCCCGGA-ATTAGTCGCTAGAACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
48342827 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
48342846 TTATCATCCG
Statistics
Matches: 202, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
39 17 0.08
40 183 0.91
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:48346370 original size:12 final size:12
Alignment explanation
Indices: 48346353--48346377 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48346343 GAGAATTGGA
48346353 GTAATTACACAT
1 GTAATTACACAT
48346365 GTAATTACACAT
1 GTAATTACACAT
48346377 G
1 G
48346378 AACACAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (12 bp):
GTAATTACACAT
Found at i:48346642 original size:14 final size:15
Alignment explanation
Indices: 48346614--48346642 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48346604 TTATAAAAAA
48346614 TTATAAAACATTTAT
1 TTATAAAACATTTAT
48346629 TTATAAAA-ATTTAT
1 TTATAAAACATTTAT
48346643 GACCATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATAAAACATTTAT
Found at i:48367283 original size:21 final size:22
Alignment explanation
Indices: 48367257--48367310 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
48367247 AAAATAGGCC
48367257 ACACGCTCGTGT-GGAAGGGTA
1 ACACGCTCGTGTGGGAAGGGTA
48367278 ACACGCTCGTGTGGGAAGGGTA
1 ACACGCTCGTGTGGGAAGGGTA
*
48367300 ACACGTTCGTG
1 ACACGCTCGTG
48367311 CCCCACACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.20
Consensus pattern (22 bp):
ACACGCTCGTGTGGGAAGGGTA
Found at i:48368434 original size:47 final size:47
Alignment explanation
Indices: 48368373--48368542 Score: 159
Period size: 47 Copynumber: 3.6 Consensus size: 47
48368363 TTAAGTGCCG
*
48368373 ATGCCATGTCCCAGACATAGTCTTACACTAGCTCAT-AGCT-TAAGTCA
1 ATGCCATGTCCCAGACAT-GTCTTACACTAGCT-ATCAGCTCTAAGCCA
* * ** *
48368420 ATGCCATGTCCCAGACATGGTCTTACACTAACTATCATCTCTTGGCCG
1 ATGCCATGTCCCAGACAT-GTCTTACACTAGCTATCAGCTCTAAGCCA
** * *
48368468 ATG-CATGTCCCAGACATGTCTTACACTAGCCCTCATCTC-AATGCCG
1 ATGCCATGTCCCAGACATGTCTTACACTAGCTATCAGCTCTAA-GCCA
* *
48368514 ATGCCATGTCCCGGATATGGTCTTACACT
1 ATGCCATGTCCCAGACAT-GTCTTACACT
48368543 GGCTTACACG
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
46 28 0.27
47 60 0.58
48 16 0.15
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGTCTTACACTAGCTATCAGCTCTAAGCCA
Found at i:48368534 original size:94 final size:94
Alignment explanation
Indices: 48368369--48368542 Score: 246
Period size: 94 Copynumber: 1.8 Consensus size: 94
48368359 TGGGTTAAGT
* *
48368369 GCCGATGCCATGTCCCAGACATAGTCTTACACTAGCTCATAGCTTAAGTCAATGCCATGTCCCAG
1 GCCGATGCCATGTCCCAGACATAGTCTTACACTAGCTCATA-CTCAAGCCAATGCCATGTCCCAG
48368434 ACATGGTCTTACACTAACTATCATCTCTTG
65 ACATGGTCTTACACTAACTATCATCTCTTG
*
48368464 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCCCTCAT-CTCAATGCCGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATAGTCTTACACTAG--CTCATACTCAA-GCCAATGCCATGTCCC
* *
48368526 GGATATGGTCTTACACT
63 AGACATGGTCTTACACT
48368543 GGCTTACACG
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
93 16 0.23
94 43 0.61
95 12 0.17
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAGACATAGTCTTACACTAGCTCATACTCAAGCCAATGCCATGTCCCAGA
CATGGTCTTACACTAACTATCATCTCTTG
Found at i:48371209 original size:34 final size:34
Alignment explanation
Indices: 48371165--48371236 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
48371155 GCATTAATGT
* *
48371165 TACTATTACTGTATTGGGCTGA-GGCCC-ACACTGA
1 TACTAATACTGTAATGGGCT-ACGGCCCTA-ACTGA
48371199 TACTAATACTGTAATGGGCTACGGCCCTAACTGA
1 TACTAATACTGTAATGGGCTACGGCCCTAACTGA
48371233 TACT
1 TACT
48371237 GGACTGTCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 1 0.03
34 32 0.94
35 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (34 bp):
TACTAATACTGTAATGGGCTACGGCCCTAACTGA
Found at i:48381664 original size:46 final size:46
Alignment explanation
Indices: 48381597--48381767 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 46
48381587 TGATATGTGT
*
48381597 GCTAGTATAAGACATGTCTGGGACATGCATCAACCACAGTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGA
* * * *
48381643 GCTAGTGTAAGACACGTCTGGGACATGCATCAGCCTCGAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCAC-AG-TA-TGAGA
* * * * * *
48381691 GCCAGTGTAAGACATGTATAGGACATGCATC-AGCATTGAG-ACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCA--CAGTATGAGA
*
48381737 GCTAGTGTAGGACATGTCTGGGACATGCATC
1 GCTAGTGTAAGACATGTCTGGGACATGCATC
48381768 GAGGTTGCGA
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 62 0.62
47 3 0.03
48 32 0.32
49 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAACCACAGTATGAGA
Found at i:48381780 original size:94 final size:94
Alignment explanation
Indices: 48381639--48381811 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
48381629 ACCACAGTAT
**
48381639 GAGAGCTAGTGTAAGACACGTCTGGGACATGCATCAGCCTCGAGATATTTAAGCCAGTGTAAGAC
1 GAGAGCTAGTGTAAGACACGTCTGGGACATGCATCAGCCTCGAGATATACAAGCCAGTGTAAGAC
48381704 ATGTATAGGACATGCATCAGCATTGAGAC
66 ATGTATAGGACATGCATCAGCATTGAGAC
* * * * * *
48381733 GAGAGCTAGTGTAGGACATGTCTGGGACATGCATCGAG-GTTGCGATATACAAGCTAGTGTAAGA
1 GAGAGCTAGTGTAAGACACGTCTGGGACATGCATC-AGCCTCGAGATATACAAGCCAGTGTAAGA
* * *
48381797 CCTGTCTGGGACATG
65 CATGTATAGGACATG
48381812 GTGTTAGCTT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
94 65 0.97
95 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (94 bp):
GAGAGCTAGTGTAAGACACGTCTGGGACATGCATCAGCCTCGAGATATACAAGCCAGTGTAAGAC
ATGTATAGGACATGCATCAGCATTGAGAC
Found at i:48381803 original size:48 final size:47
Alignment explanation
Indices: 48381597--48381811 Score: 188
Period size: 48 Copynumber: 4.6 Consensus size: 47
48381587 TGATATGTGT
* * * *
48381597 GCTAGTATAAGACATGTCTGGGACATGCATCAACCA--CAG-TATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-AGCATTGAGATAT-AAA
* * * *
48381643 GCTAGTGTAAGACACGTCTGGGACATGCATCAGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATA-TAAA
* * * ** *
48381691 GCCAGTGTAAGACATGTATAGGACATGCATCAGCATTGAGA-CGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATATAAA
* * *
48381737 GCTAGTGTAGGACATGTCTGGGACATGCATCGAG-GTTGCGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-AGCATTGAGATATA-AA
*
48381785 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
48381812 GTGTTAGCTT
Statistics
Matches: 134, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
45 2 0.01
46 62 0.46
47 5 0.04
48 64 0.48
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGATATAAA
Found at i:48381936 original size:49 final size:49
Alignment explanation
Indices: 48381831--48381949 Score: 150
Period size: 49 Copynumber: 2.4 Consensus size: 49
48381821 TGTTGTGTGT
* *
48381831 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATAGCATCGACACCGATAGATGAAAGC
* * * *
48381880 TAGTGTAAGACCTGTCTGGGACATAGCATCGGC-CTCGCTATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATAGCATCGACAC-CGATAGATGAAAGC
*
48381929 CATTGTAAGACCATGTCTGGG
1 CAGTGTAAGACC-TGTCTGGG
48381950 GCGTCGGTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.02
49 51 0.85
50 8 0.13
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATAGCATCGACACCGATAGATGAAAGC
Found at i:48387105 original size:40 final size:40
Alignment explanation
Indices: 48387046--48387233 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
48387036 GAGCATTGGA
48387046 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
*
48387086 ATATATCCGGGCTATGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
* * *
48387126 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
* *
48387166 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
* *
48387206 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
48387234 ATGTGTTTGC
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
Found at i:48402623 original size:71 final size:71
Alignment explanation
Indices: 48402507--48402648 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
48402497 ACTCAGGAAC
48402507 TTGAAACGCCACTGAGAAGGGTTCCCCACAATTGCGATGTCCTGCTCGACCATGACCATAGCTAC
1 TTGAAACGCCACTGAGAAGGGTTCCCCACAATTGCGATGTCCTGCTCGACCATGACCATAGCTAC
48402572 CACCAG
66 CACCAG
*
48402578 TTGAAACGCCACTGAGAAGTGTTCCCCACAATTGCGATGTCCTGCTCGACCATGACCATAGCTAC
1 TTGAAACGCCACTGAGAAGGGTTCCCCACAATTGCGATGTCCTGCTCGACCATGACCATAGCTAC
48402643 CACCAG
66 CACCAG
48402649 ATATAATATT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (71 bp):
TTGAAACGCCACTGAGAAGGGTTCCCCACAATTGCGATGTCCTGCTCGACCATGACCATAGCTAC
CACCAG
Found at i:48409645 original size:47 final size:47
Alignment explanation
Indices: 48409574--48409703 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
48409564 ACAATAGATA
** * * * *
48409574 AGTACCTATACCATAACCCATAGCCAAATTAAGGTAACTTATCCCG-G
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCAT-CAGTG
* *
48409621 AGTACCTATACCATGGCCTGTAGCCAAATCAAGGTAACTCCTCAGTG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCAGTG
*
48409668 AATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
48409704 TTATTCATAC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 2 0.03
47 70 0.97
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCAGTG
Found at i:48416371 original size:27 final size:27
Alignment explanation
Indices: 48416340--48416517 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
48416330 TAAATTGTAC
48416340 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * ** *
48416367 TGCACTAAGTGTGTGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
48416393 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
48416421 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
48416449 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
48416476 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
48416503 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
48416518 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 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:48416454 original size:82 final size:81
Alignment explanation
Indices: 48416341--48416496 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
48416331 AAATTGTACA
* * *
48416341 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGTGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
48416405 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
48416422 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
48416487 TGCGAGTTGA
65 TGCGAATTGA
48416497 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:48416508 original size:82 final size:81
Alignment explanation
Indices: 48416337--48416517 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
48416327 GATTAAATTG
* * *
48416337 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGTGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
48416402 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
48416418 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
48416482 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
48416500 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
48416518 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:48427297 original size:14 final size:14
Alignment explanation
Indices: 48427278--48427323 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
48427268 TGAGACTTTT
48427278 TAAAAAAATCAAAA
1 TAAAAAAATCAAAA
48427292 TAAAAAAAT--AAA
1 TAAAAAAATCAAAA
48427304 TCAAAAAAATCAAAA
1 T-AAAAAAATCAAAA
48427319 -AAAAA
1 TAAAAA
48427324 GAAGAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.14
13 13 0.45
14 9 0.31
15 3 0.10
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (14 bp):
TAAAAAAATCAAAA
Found at i:48427315 original size:9 final size:9
Alignment explanation
Indices: 48427279--48427321 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
48427269 GAGACTTTTT
48427279 AAAAAAATC
1 AAAAAAATC
48427288 AAAATAAA--
1 AAAA-AAATC
48427296 AAAATAAATC
1 AAAA-AAATC
48427306 AAAAAAATC
1 AAAAAAATC
48427315 AAAAAAA
1 AAAAAAA
48427322 AAGAAGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.26
9 16 0.52
10 7 0.23
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:48428537 original size:64 final size:64
Alignment explanation
Indices: 48428462--48428781 Score: 577
Period size: 64 Copynumber: 5.0 Consensus size: 64
48428452 TCATTCATAA
* * **
48428462 CACATCCAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
48428526 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
48428590 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
48428654 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
* * *
48428718 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAACATCCTAATTATTTGGCATAAGCAT
1 CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
48428782 GATACATGAA
Statistics
Matches: 249, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 249 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAGGCGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:48429167 original size:44 final size:45
Alignment explanation
Indices: 48429095--48429194 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 45
48429085 AGTCACCAGC
* * *
48429095 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTCAATATACAAG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATACAAGAT
* **
48429139 CTTATCTCCCTGAGGTTGCAGTGGAGCAGACTAAAGATTGAAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATACAAGAT
48429184 CTTATCTCCCT
1 CTTATCTCCCT
48429195 AAGCAGTAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 37 0.76
45 12 0.24
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATACAAGAT
Found at i:48429345 original size:176 final size:176
Alignment explanation
Indices: 48429136--48429612 Score: 652
Period size: 176 Copynumber: 2.7 Consensus size: 176
48429126 TCAATATACA
* * * ** *
48429136 AGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAG
1 AGTCTTATATTCCTGAGGTAGCAAAGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAG
48429201 TAGAGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGATTTTACCA
66 TAGAGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGATTTTACCA
* *
48429266 CTGGCCTTATCTCTCT-AAGGTAGCAAGAGAGCAGGTTGGCAATTGT
131 CTGACCTTACCTCTCTGAA-GTAGCAAGAGAGCAGGTTGGCAATTGT
* * * * **
48429312 AGTCTTATTTTCTTGAGGTAGCAAAGAAGCAGACTGAAA-ATTGAAGATTTTATATCTTTAAGCA
1 AGTCTTATATTCCTGAGGTAGCAAAGAAGCAGACT-AAAGATTGAAGATCTTATCTCCCTAAGCA
* * * * *
48429376 GTAGGGGAGCAGATCGAAGATGGTGAATCTTATCTCTATGTATCGGAAATGGAGCAGATTTTACC
65 GTAGAGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGATTTTACC
*
48429441 ACTGACCTTACCTCTCTGAAGTAGCAAGAGAGCAGGTTGGCGATTGT
130 ACTGACCTTACCTCTCTGAAGTAGCAAGAGAGCAGGTTGGCAATTGT
* * * * *
48429488 AGTCTTATATTCCTGATGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAGGTAG
1 AGTCTTATATTCCTGAGGTAGCAAAGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAG
* * * * *
48429553 TTGCGGAGCAGATTGAGGATGGCGAATCTTATCTCCATGTATTGGCAATGGGGCAGATTT
66 TAGAGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGATTT
48429613 AAGTCACCAG
Statistics
Matches: 259, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
175 2 0.01
176 252 0.97
177 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (176 bp):
AGTCTTATATTCCTGAGGTAGCAAAGAAGCAGACTAAAGATTGAAGATCTTATCTCCCTAAGCAG
TAGAGGAGCAGATCGAAGATGGCGAATCTTATCTCCATGTATTGGCAATGGAGCAGATTTTACCA
CTGACCTTACCTCTCTGAAGTAGCAAGAGAGCAGGTTGGCAATTGT
Found at i:48432033 original size:371 final size:371
Alignment explanation
Indices: 48431350--48432062 Score: 1347
Period size: 371 Copynumber: 1.9 Consensus size: 371
48431340 GTTGCTCACA
* *
48431350 GAATTTGGTTGTTTTGGATTAATTATATTTAATTATTCATTTCATATTTTAGTTAAATAAGGTTT
1 GAATTTGGTTATTTTGGATTAATTATATTTAATTATTCATTTCATATTTTAGTTAAATAAGGTTC
*
48431415 TGTTATCTTTATTCACCAAGTACTGTATTTAATGCATGTATATTATCCCATGATCGTTATTTTTT
66 TGTTATCTTCATTCACCAAGTACTGTATTTAATGCATGTATATTATCCCATGATCGTTATTTTTT
*
48431480 CTTTTGGTTTATAAAATGTTGCTTTATGGTCTTCAATTCTTTAAAATCAATTATTCCATTTTGTT
131 CTTTTGGTTTATAAAATGTTGCTTTATGGTCTTCAACTCTTTAAAATCAATTATTCCATTTTGTT
48431545 TAAAATAAAATCAATACATTTTGAGATAATTTACAATCATTTATTTAAACTTCTTTGTTAAAAAC
196 TAAAATAAAATCAATACATTTTGAGATAATTTACAATCATTTATTTAAACTTCTTTGTTAAAAAC
48431610 AAGGCAATATTCAATATTTAGGAATTCGAGAAAACGTGCCCTACCATGCTGGGTACGATTTTTCG
261 AAGGCAATATTCAATATTTAGGAATTCGAGAAAACGTGCCCTACCATGCTGGGTACGATTTTTCG
48431675 TTGGACTGAATATCTAGTAAATCAATTGTTGCTCACCCATGCTTGT
326 TTGGACTGAATATCTAGTAAATCAATTGTTGCTCACCCATGCTTGT
48431721 GAATTTGGTTATTTTGGATTAATTATATTTAATTATTCGA-TTCATATTTTAGTTAAATAAGGTT
1 GAATTTGGTTATTTTGGATTAATTATATTTAATTATTC-ATTTCATATTTTAGTTAAATAAGGTT
* *
48431785 CTGTTATCTTCATTCACCAAGTACTGTATTTTATGCATGTATATTATCCCATGATTGTTATTTTT
65 CTGTTATCTTCATTCACCAAGTACTGTATTTAATGCATGTATATTATCCCATGATCGTTATTTTT
*
48431850 TCTTTTGGTTTATAAAATGTTGCTTTATGGTCTTCAACTCTTTAAAATTAATTATTCCATTTTGT
130 TCTTTTGGTTTATAAAATGTTGCTTTATGGTCTTCAACTCTTTAAAATCAATTATTCCATTTTGT
48431915 TTAAAATAAAATCAATACATTTTGAGATAATTTACAATCATTTATTTAAACTTCTTTGTTAAAAA
195 TTAAAATAAAATCAATACATTTTGAGATAATTTACAATCATTTATTTAAACTTCTTTGTTAAAAA
48431980 CAAGGCAATATTCAATATTTAGGAATTCGAGAAAACGTGCCCTACCATGCTGGGTACGATTTTTC
260 CAAGGCAATATTCAATATTTAGGAATTCGAGAAAACGTGCCCTACCATGCTGGGTACGATTTTTC
48432045 GTTGGACTGAATATCTAG
325 GTTGGACTGAATATCTAG
48432063 ATATCCTTTT
Statistics
Matches: 334, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
371 333 1.00
372 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (371 bp):
GAATTTGGTTATTTTGGATTAATTATATTTAATTATTCATTTCATATTTTAGTTAAATAAGGTTC
TGTTATCTTCATTCACCAAGTACTGTATTTAATGCATGTATATTATCCCATGATCGTTATTTTTT
CTTTTGGTTTATAAAATGTTGCTTTATGGTCTTCAACTCTTTAAAATCAATTATTCCATTTTGTT
TAAAATAAAATCAATACATTTTGAGATAATTTACAATCATTTATTTAAACTTCTTTGTTAAAAAC
AAGGCAATATTCAATATTTAGGAATTCGAGAAAACGTGCCCTACCATGCTGGGTACGATTTTTCG
TTGGACTGAATATCTAGTAAATCAATTGTTGCTCACCCATGCTTGT
Found at i:48442122 original size:28 final size:26
Alignment explanation
Indices: 48442075--48442129 Score: 60
Period size: 28 Copynumber: 2.0 Consensus size: 26
48442065 TTGCTTTTAG
48442075 ATCAAGATGAGCCTAGGACTTATCAAGA
1 ATCAAGATGAGCCTAGGAC-TAT-AAGA
48442103 ATCAATGATGAGCAC-A-GACTATAAGA
1 ATCAA-GATGAGC-CTAGGACTATAAGA
48442129 A
1 A
48442130 ATGGCTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
26 5 0.20
27 3 0.12
28 8 0.32
29 8 0.32
30 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (26 bp):
ATCAAGATGAGCCTAGGACTATAAGA
Found at i:48448138 original size:50 final size:50
Alignment explanation
Indices: 48448078--48448175 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
48448068 AAATTGTGGA
* *
48448078 CTCAGTTTACCTTTTTGAACAAATCTCAATACCTTTCTCCATGGAGATGC
1 CTCAGCTTACCGTTTTGAACAAATCTCAATACCTTTCTCCATGGAGATGC
*
48448128 CTCAGCTTACCGTTTTGAACAAATCTCAATATCTTTCTCCATGGAGAT
1 CTCAGCTTACCGTTTTGAACAAATCTCAATACCTTTCTCCATGGAGAT
48448176 ACTTTCAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (50 bp):
CTCAGCTTACCGTTTTGAACAAATCTCAATACCTTTCTCCATGGAGATGC
Found at i:48452322 original size:14 final size:14
Alignment explanation
Indices: 48452299--48452337 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
48452289 GGGCCTCTTC
*
48452299 TCAGCTTTCTAACA
1 TCAGCCTTCTAACA
*
48452313 TCAGCCTTCTGACA
1 TCAGCCTTCTAACA
48452327 TCAGCCTTCTA
1 TCAGCCTTCTA
48452338 CTACTACTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (14 bp):
TCAGCCTTCTAACA
Found at i:48458887 original size:27 final size:27
Alignment explanation
Indices: 48458857--48458951 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
48458847 AATTGTACAA
* *
48458857 CACTAAGTGTGCGATTTGACTATGTTG
1 CACTAAGTGTGCGAATTGACTATGATG
* *
48458884 CACTAAGTGTGCGAAATGAATATGATG
1 CACTAAGTGTGCGAATTGACTATGATG
* **
48458911 CACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGAATTGACTATGATG
48458938 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
48458952 TGTAGAGTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (27 bp):
CACTAAGTGTGCGAATTGACTATGATG
Found at i:48459485 original size:28 final size:28
Alignment explanation
Indices: 48459428--48459747 Score: 556
Period size: 28 Copynumber: 11.5 Consensus size: 28
48459418 TAAATTGTGC
*
48459428 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459455 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459483 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459511 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459539 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459567 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459595 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459623 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48459651 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
48459679 AGCACTAAGTGTGCGAG-TTGATTACGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* * *
48459706 GGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
48459733 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
48459748 GGCTCAATAT
Statistics
Matches: 284, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
27 61 0.21
28 223 0.79
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:48468374 original size:3 final size:3
Alignment explanation
Indices: 48468366--48468393 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48468356 TTCTAGCTAA
48468366 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
48468394 TATACTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:48469534 original size:21 final size:20
Alignment explanation
Indices: 48469496--48469532 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48469486 ATTTTTTTTT
48469496 AAATTCAAAATATTTATAAA
1 AAATTCAAAATATTTATAAA
*
48469516 AAATTCTAAA-ATTTATA
1 AAATTCAAAATATTTATA
48469533 TATATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTCAAAATATTTATAAA
Found at i:48472495 original size:40 final size:39
Alignment explanation
Indices: 48472397--48472619 Score: 250
Period size: 40 Copynumber: 5.6 Consensus size: 39
48472387 TCCTCGTTCA
* * * * *
48472397 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
48472436 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
48472475 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
*
48472515 GAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
48472555 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
48472596 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
48472620 CAGCATTCAA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 37 0.23
40 116 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:48478795 original size:40 final size:40
Alignment explanation
Indices: 48478747--48478853 Score: 187
Period size: 40 Copynumber: 2.7 Consensus size: 40
48478737 ACAAACACAT
* *
48478747 TTGCCTTCGGGTCATAACCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
48478787 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
48478827 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
48478854 ATCCAATGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:48483842 original size:41 final size:41
Alignment explanation
Indices: 48483727--48483876 Score: 212
Period size: 41 Copynumber: 3.7 Consensus size: 41
48483717 CGCTGACTCA
* * *
48483727 AAAAGCCTTTCGAGACCAAGCTCGGATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
* * * * * *
48483768 GAAGGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
48483808 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
48483849 AAAAGCCCTTCGAGACCAAGCTCGGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
48483877 TAAACCCCAA
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
40 32 0.34
41 61 0.66
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
Found at i:48486492 original size:17 final size:17
Alignment explanation
Indices: 48486472--48486530 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
48486462 ATTTCTCCTT
48486472 TTTCTTTCTTTCTTTCC
1 TTTCTTTCTTTCTTTCC
* * *
48486489 TTTCTTTGTTTCGTCCC
1 TTTCTTTCTTTCTTTCC
** *
48486506 CCTCTTTCTTTCTTTTC
1 TTTCTTTCTTTCTTTCC
48486523 TATTCTTT
1 T-TTCTTT
48486531 TTCTTTTGTT
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTCC
Found at i:48486590 original size:5 final size:5
Alignment explanation
Indices: 48486580--48486704 Score: 250
Period size: 5 Copynumber: 25.0 Consensus size: 5
48486570 ATTATTAAAC
48486580 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
48486630 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
48486680 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
48486705 CTAAGTAATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 120 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:48492647 original size:20 final size:20
Alignment explanation
Indices: 48492624--48492673 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
48492614 AAATCCAAAT
48492624 TAAAATACTAAAATTCAAGA
1 TAAAATACTAAAATTCAAGA
* *
48492644 TAAAAT-CTTGAAATTTAAGA
1 TAAAATAC-TAAAATTCAAGA
48492664 TAAGAATACT
1 TAA-AATACT
48492674 GATGTGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 4 0.16
22 1 0.04
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (20 bp):
TAAAATACTAAAATTCAAGA
Found at i:48495816 original size:52 final size:52
Alignment explanation
Indices: 48495754--48495853 Score: 200
Period size: 52 Copynumber: 1.9 Consensus size: 52
48495744 AATTATATAT
48495754 TAAAAAGAAACCTGCTCTCAAAGGCATTTAGATATGTGTCTAAATCAATCAG
1 TAAAAAGAAACCTGCTCTCAAAGGCATTTAGATATGTGTCTAAATCAATCAG
48495806 TAAAAAGAAACCTGCTCTCAAAGGCATTTAGATATGTGTCTAAATCAA
1 TAAAAAGAAACCTGCTCTCAAAGGCATTTAGATATGTGTCTAAATCAA
48495854 CTATAACTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (52 bp):
TAAAAAGAAACCTGCTCTCAAAGGCATTTAGATATGTGTCTAAATCAATCAG
Found at i:48495998 original size:30 final size:31
Alignment explanation
Indices: 48495942--48496016 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
48495932 TAGTAATGAT
* *
48495942 AAAATTATATTTTAATTTTCTTAAAAATAATA
1 AAAATT-TAATTTAATTCTCTTAAAAATAATA
*
48495974 AAAATTTAATTTAATTCT-TTAAAAATTATA
1 AAAATTTAATTTAATTCTCTTAAAAATAATA
* *
48496004 AAGATATAATTTA
1 AAAATTTAATTTA
48496017 TTGAAATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 22 0.58
31 10 0.26
32 6 0.16
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (31 bp):
AAAATTTAATTTAATTCTCTTAAAAATAATA
Found at i:48501150 original size:15 final size:15
Alignment explanation
Indices: 48501127--48501160 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48501117 CCTAAATTTG
*
48501127 AATAATAATTATCTT
1 AATAATAATTATCCT
*
48501142 AATATTAATTATCCT
1 AATAATAATTATCCT
48501157 AATA
1 AATA
48501161 GAATAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAATAATTATCCT
Found at i:48505849 original size:20 final size:20
Alignment explanation
Indices: 48505816--48505853 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48505806 TATCATCATC
* *
48505816 TTCTTGCATTTCATATACTA
1 TTCTTCCATGTCATATACTA
48505836 TTCTTCCATGTCATATAC
1 TTCTTCCATGTCATATAC
48505854 AGTATTCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCTTCCATGTCATATACTA
Found at i:48507683 original size:27 final size:27
Alignment explanation
Indices: 48507645--48507702 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
48507635 TCAAAAGTAA
*
48507645 ACTCATTCTGAACTTATTTAGGTTACC
1 ACTCACTCTGAACTTATTTAGGTTACC
*
48507672 ACTCACTCTGAACTTGTTTAGGTTACC
1 ACTCACTCTGAACTTATTTAGGTTACC
48507699 ACTC
1 ACTC
48507703 GCTATATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (27 bp):
ACTCACTCTGAACTTATTTAGGTTACC
Found at i:48512335 original size:49 final size:49
Alignment explanation
Indices: 48512276--48512402 Score: 184
Period size: 49 Copynumber: 2.6 Consensus size: 49
48512266 ACATCGAGGC
*
48512276 CGATGACATGTCCTAGACAGGTCTTACACTGGCTCTCACTTATCTGTGT
1 CGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCACTTATCTGTGT
* *
48512325 TGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTTATCTGTGT
1 CGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCACTTATCTGTGT
* *
48512374 CGATGCCGTTGTCCCT-GACAGGTCATACA
1 CGATGCC-ATGT-CCTAGACAGGTCTTACA
48512403 TTGACAGACA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
49 52 0.75
50 15 0.22
51 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (49 bp):
CGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCACTTATCTGTGT
Found at i:48516260 original size:12 final size:12
Alignment explanation
Indices: 48516220--48516263 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
48516210 ATCCCACCCC
48516220 AAAATAGATACA
1 AAAATAGATACA
* *
48516232 GAAAACAAATACAA
1 -AAAATAGATAC-A
48516246 AAAATAGATACA
1 AAAATAGATACA
48516258 AAAATA
1 AAAATA
48516264 ACAGATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 7 0.27
13 18 0.69
14 1 0.04
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAATAGATACA
Found at i:48529293 original size:13 final size:13
Alignment explanation
Indices: 48529275--48529319 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
48529265 AGCACATAGG
48529275 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
48529288 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
48529301 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
*
48529314 CATGTG
1 CGTGTG
48529320 ACTTCAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.02, C:0.22, G:0.44, T:0.31
Consensus pattern (13 bp):
CGTGTGGCTTGGC
Found at i:48536648 original size:13 final size:13
Alignment explanation
Indices: 48536624--48536671 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
48536614 CTTAATTAAG
48536624 ATAAATAAATAAAA
1 ATAAA-AAATAAAA
*
48536638 AGT-GAAAATAAAA
1 A-TAAAAAATAAAA
48536651 ATAAAAAATAAAAA
1 ATAAAAAAT-AAAA
48536665 ATAAAAA
1 ATAAAAA
48536672 GTTTTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 1 0.03
13 14 0.48
14 13 0.45
15 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:48536657 original size:7 final size:7
Alignment explanation
Indices: 48536624--48536671 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
48536614 CTTAATTAAG
48536624 ATAAATAA
1 ATAAA-AA
48536632 ATAAAAA
1 ATAAAAA
* *
48536639 GT-GAAA
1 ATAAAAA
48536645 AT-AAAA
1 ATAAAAA
48536651 ATAAAAA
1 ATAAAAA
48536658 ATAAAAA
1 ATAAAAA
48536665 ATAAAAA
1 ATAAAAA
48536672 GTTTTTAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 9 0.26
7 21 0.60
8 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:48542210 original size:3 final size:3
Alignment explanation
Indices: 48542204--48542259 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
48542194 TAAGATTTTG
* * *
48542204 TTA TTA TTA TTA TTAA TTA TTA GTA -TA GTC TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48542248 TTA TTA TTA TTA
1 TTA TTA TTA TTA
48542260 ATTTTAAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:48545543 original size:27 final size:27
Alignment explanation
Indices: 48545503--48545589 Score: 106
Period size: 27 Copynumber: 3.2 Consensus size: 27
48545493 AGGAAGCGTC
*
48545503 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
48545530 CTGGTGGCTCTGCCAC-GTATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
48545557 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
*
48545584 CCGGTG
1 CTGGTG
48545590 ACTTCGTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.14
27 44 0.86
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:48549245 original size:16 final size:17
Alignment explanation
Indices: 48549214--48549246 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48549204 CCCCATAGAT
48549214 ATCAAACATACAGAATA
1 ATCAAACATACAGAATA
*
48549231 ATCAATCAT-CAGAATA
1 ATCAAACATACAGAATA
48549247 CAGTCTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (17 bp):
ATCAAACATACAGAATA
Found at i:48557495 original size:17 final size:17
Alignment explanation
Indices: 48557473--48557506 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
48557463 TTAACTTTTG
48557473 CCTAAATACCAATTTAA
1 CCTAAATACCAATTTAA
48557490 CCTAAATACCAATTTAA
1 CCTAAATACCAATTTAA
48557507 TCTCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (17 bp):
CCTAAATACCAATTTAA
Found at i:48558008 original size:25 final size:23
Alignment explanation
Indices: 48557975--48558034 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
48557965 TTTTATTTAG
*
48557975 TTTAGTTATAA-TATAATATAATAT
1 TTTAATTATAAGTA-AATAT-ATAT
*
48557999 TCTTATTTATTAAGTAAATATATAT
1 T-TTAATTA-TAAGTAAATATATAT
48558024 TTTAATTATAA
1 TTTAATTATAA
48558035 AAATCTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 3 0.10
24 7 0.23
25 11 0.35
26 8 0.26
27 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTAATTATAAGTAAATATATAT
Found at i:48560977 original size:43 final size:43
Alignment explanation
Indices: 48560819--48560977 Score: 114
Period size: 43 Copynumber: 3.7 Consensus size: 43
48560809 TGTACAATGC
*** *
48560819 CAACGTCCCAGATGTGGTCTTACATGTAATC-GAATATCGATG-
1 CAACGTCCCAGATGTGGTCTTACACAAAATCTCAA-ATCGATGT
** * *
48560861 CCTCTGTCCCAGATAG-GGTCTTACATAAAA--TCAAATATGATGT
1 CAAC-GTCCCAGAT-GTGGTCTTACACAAAATCTCAAAT-CGATGT
* * ** *
48560904 CGATGT-CCAGACATGGTTTTACACATAAATCTCAAATCGATGT
1 CAACGTCCCAGATGTGGTCTTACACA-AAATCTCAAATCGATGT
48560947 CAACGTCCCAGATGTGGTCTTACACAAAATC
1 CAACGTCCCAGATGTGGTCTTACACAAAATC
48560978 ACATATCGGA
Statistics
Matches: 88, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
41 16 0.18
42 13 0.15
43 36 0.41
44 23 0.26
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
CAACGTCCCAGATGTGGTCTTACACAAAATCTCAAATCGATGT
Found at i:48571535 original size:40 final size:40
Alignment explanation
Indices: 48571491--48571794 Score: 459
Period size: 40 Copynumber: 7.6 Consensus size: 40
48571481 AAGTGAATAT
* * * * **
48571491 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
*
48571531 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
48571571 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
48571611 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
48571651 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
48571691 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
48571731 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
48571770 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
48571795 TGAACGAGGA
Statistics
Matches: 251, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 35 0.14
40 216 0.86
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:48571589 original size:80 final size:80
Alignment explanation
Indices: 48571452--48571794 Score: 458
Period size: 80 Copynumber: 4.3 Consensus size: 80
48571442 TTGAATGCTG
* * * * * * * *
48571452 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
* *
48571515 TTGTGCGAGATACTAAA
64 TCGTGCGAGTTACTAAA
48571532 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
**
48571597 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
*
48571612 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
**
48571677 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* *
48571692 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATT-
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
48571756 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* * *
48571771 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
48571795 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 20, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
79 34 0.14
80 201 0.83
81 6 0.02
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
GTGCGAGTTACTAAA
Found at i:48571665 original size:120 final size:119
Alignment explanation
Indices: 48571452--48571794 Score: 476
Period size: 120 Copynumber: 2.9 Consensus size: 119
48571442 TTGAATGCTG
* * * * * *
48571452 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGG-C
* *
48571514 TTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
62 ATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
48571572 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATT-
** *
48571637 GTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
48571692 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTG
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTG
* * * *
48571757 TGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
66 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
48571795 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
119 37 0.18
120 156 0.78
121 8 0.04
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTG
TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:48579599 original size:40 final size:39
Alignment explanation
Indices: 48579568--48579777 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
48579558 GGACTAAGAT
* *
48579568 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
48579608 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
48579648 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
48579688 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
48579728 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
48579767 CCGAAGGCATT
1 CCGAAGGCATT
48579778 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:48579731 original size:120 final size:120
Alignment explanation
Indices: 48579515--48579777 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
48579505 TTGAATGCTG
* *
48579515 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
48579579 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
48579635 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
48579698 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
48579754 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
48579778 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:48579797 original size:79 final size:80
Alignment explanation
Indices: 48579516--48579812 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
48579506 TGAATGCTGT
* ** * * * **
48579516 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
48579579 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
48579596 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
48579660 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
48579676 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
48579740 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
48579755 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
48579813 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:48589123 original size:48 final size:48
Alignment explanation
Indices: 48589052--48589380 Score: 345
Period size: 48 Copynumber: 6.9 Consensus size: 48
48589042 AACGTGATCA
* * *
48589052 CGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATTGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
* * * * *
48589100 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCATATATCGAGGA
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
* * * * *
48589148 CGATGCCATGTCTCAAACATGGTCTTACATTGGCTCACATATTGAGGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
* * * * * *
48589196 CGATGCCATGTCCCAGACATGGTCTTACTCTAGCTCTCATATCAATGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
* * *
48589244 CGATGCCATGTTCCAAACATAGTCTTACACCAGCTCACATATCGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
* * * * * * * *
48589292 CAATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCACATCAATGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
* * *
48589340 CGATGCCATGTTCCAAAGATGGTTTTACACCT-GCTCACATA
1 CGATGCCATGTCCCAAACATGGTCTTACA-CTAGCTCACATA
48589381 ACCCTAGTAT
Statistics
Matches: 228, Mismatches: 52, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
48 226 0.99
49 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATATCGAGGC
Found at i:48589215 original size:96 final size:96
Alignment explanation
Indices: 48589051--48589380 Score: 425
Period size: 96 Copynumber: 3.4 Consensus size: 96
48589041 TAACGTGATC
*
48589051 ACGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATTGAGGCCGATGCCATGTCCCAG
1 ACGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAG
* *
48589116 ACATGGTCTTATACTGGCTCAT-ATATCGAGG
66 ACATGGTCTTATACTAGCTC-TCATATCAAGG
* * *
48589147 ACGATGCCATG-TCTCAAACATGGTCTTACATTGGCTCACATATTGAGGTCGATGCCATGTCCCA
1 ACGATGCCATGTTC-CAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCA
*
48589211 GACATGGTCTTACT-CTAGCTCTCATATCAATG
65 GACATGGTCTTA-TACTAGCTCTCATATCAAGG
* * * * * *
48589243 TCGATGCCATGTTCCAAACATAGTCTTACACCAGCTCACATATCGAGGCCAATGCCATGTCCTAG
1 ACGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAG
* * *
48589308 ACATGGTCTTACACTAGCTCTCACATCAATG
66 ACATGGTCTTATACTAGCTCTCATATCAAGG
* * *
48589339 TCGATGCCATGTTCCAAAGATGGTTTTACACCT-GCTCACATA
1 ACGATGCCATGTTCCAAACATGGTCTTACA-CTAGCTCACATA
48589381 ACCCTAGTAT
Statistics
Matches: 206, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
95 3 0.01
96 199 0.97
97 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (96 bp):
ACGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATTGAGGCCGATGCCATGTCCCAG
ACATGGTCTTATACTAGCTCTCATATCAAGG
Found at i:48593443 original size:43 final size:43
Alignment explanation
Indices: 48593319--48593443 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
48593309 AGAAAGCTCG
* * *
48593319 TACAATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCAAA
1 TACAATGCCGATGTCCCAGACATGGTCTTACATGTAAATCAAA
* * *
48593361 TATCAATGCCTG-TGTCCTAGACAGGGTCTTACACG-AAATCAAA
1 TA-CAATGCC-GATGTCCCAGACATGGTCTTACATGTAAATCAAA
*
48593404 TACAATGCCGATGCCCCAGACATGGTCTTACATGTAAATC
1 TACAATGCCGATGTCCCAGACATGGTCTTACATGTAAATC
48593444 TCAAATCGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 28 0.41
43 39 0.57
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
TACAATGCCGATGTCCCAGACATGGTCTTACATGTAAATCAAA
Found at i:48599658 original size:5 final size:5
Alignment explanation
Indices: 48599650--48599678 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
48599640 TTAGTTTAGT
48599650 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
48599679 CTAATATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:48603335 original size:44 final size:44
Alignment explanation
Indices: 48603279--48603366 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
48603269 TGACACAAAA
* *
48603279 TCAAATACGATGCTGACGTCCTAGACATGGTCTTACACGTAAATC
1 TCAAATACGATGCTAACGTCCCAGACATGGTCTTACACG-AAATC
* * *
48603324 TCAAAT-CGATGCTAATGTCCCAGACGTGTTCTTACACGAAATC
1 TCAAATACGATGCTAACGTCCCAGACATGGTCTTACACGAAATC
48603367 ACATATCGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 5 0.13
44 27 0.71
45 6 0.16
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
TCAAATACGATGCTAACGTCCCAGACATGGTCTTACACGAAATC
Found at i:48608366 original size:16 final size:16
Alignment explanation
Indices: 48608340--48608372 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48608330 ATATTAAGCA
48608340 AAGTGTCGATTGAGTAT
1 AAGTGTCGATTGA-TAT
48608357 AAGT-TCGATTGATAT
1 AAGTGTCGATTGATAT
48608372 A
1 A
48608373 GATATTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
AAGTGTCGATTGATAT
Found at i:48611730 original size:19 final size:19
Alignment explanation
Indices: 48611697--48611739 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
48611687 AAACATGGGT
48611697 TTTTACAATGAAAAACCTAA
1 TTTTACAATGAAAAA-CTAA
* *
48611717 TTTTA-AATGGAAAATTAA
1 TTTTACAATGAAAAACTAA
48611735 TTTTA
1 TTTTA
48611740 TATTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (19 bp):
TTTTACAATGAAAAACTAA
Found at i:48624332 original size:495 final size:498
Alignment explanation
Indices: 48623389--48624395 Score: 1385
Period size: 495 Copynumber: 2.0 Consensus size: 498
48623379 CCTCCATAAA
* * * * * *
48623389 ATCGTCTGTATATAGTCCCACGGCAGCTCCAAATTCTAGAACACTTAACTGCAGTACTAGACCGC
1 ATCGTCTATATAGAATCCCAAGACAGCTCCAAATTCTAGAACACTCAACTGCAGTACTAGACCGC
* * *
48623454 CAAGGCAGAATTGGACTGTTTCTAGGTCATCGTACTCTGCCATAACCGTTTGCAACTGAAACGTC
66 CAAGGCAAAATTGGACTGTTCCTAGGTCATCGTACTCTGCCATAACCGTTTGCAACTGAAACATC
* * * *
48623519 GAGTATAGTTCCAAAGTGAACTCTAGATACGTCGGCTTGATGATACCAAAGAAGCGGTCCCACAG
131 GAGCATAGTTCCAAAGTGAACTCCAGATACGTCAGCTCGATGATACCAAAGAAGCGGT----C--
* * *
48623584 AGCAGTGGCGAGGAGGGCCCAAACTGAATCAGCTAGGTGGACCTGTTCTAATGCAGCCCAATCGA
190 -G-AGT-G-GAGGAGGGCCCAAACTGAATCAGCTAGGTGGACCTGCTCTAATACAGCCCAATCAA
* * ** *
48623649 CGCAACGACCCACACCAAGAGGTCGGGTACGTAGAATTTGAAATAATTCTTCCTGGGGCCCTGGT
251 CGCAACGACCCACACAAAGAGGTCGGGTACGTAGAATCTGAAATAATTCTTCCTCAGGCCCTAGT
* * * *
48623714 GGAAATTGGAGGAATTAATGGCGGATCTCAGTGGTGGCACTCGAGGACGTCGCACCTGATCCCTT
316 GGAAATTGGAGGAATGAATGGCGAATCTCAGTGGTGGCACTCGAGGAAGTCCCACCTGATCCCTT
* * *
48623779 TCGCTTTTTAGAGGTGGGGACAGAAGTTTTCTTTCCTCAAGTGTTTGTCATGATGTACCTGAAAG
381 TCGCTTTTTAGAGCTGGGGACAGAAATTTTCTTTCCTCAAGTGTTTGTCATGATGTACCAGAAAG
*
48623844 ACAAAACATTTCAATATGAATAGAATCGACATAATTAAAACTTAACCAAAGAC
446 ACAAAACATTTCAATATGAATAGAATCGACATAATTAAAACTTAACCAAAAAC
* * * *
48623897 ATCGTCTATATAGAATCCCAAGACAGGTCCAAATTCTGGGACACTCAACTGCCGTACTAGACCGC
1 ATCGTCTATATAGAATCCCAAGACAGCTCCAAATTCTAGAACACTCAACTGCAGTACTAGACCGC
* * * * * *
48623962 CAAGGTAAAATTGGACTGTTCCTGGGTCGTTGTACTCTGCCATAACCGTTTGCGAGTGAAACATC
66 CAAGGCAAAATTGGACTGTTCCTAGGTCATCGTACTCTGCCATAACCGTTTGCAACTGAAACATC
* * *
48624027 GAGCATAGTTCTAAAGTGAACTCCAGATACGTCAGCTCGATTATATCAAAGAAGCGGT-G-GT-G
131 GAGCATAGTTCCAAAGTGAACTCCAGATACGTCAGCTCGATGATACCAAAGAAGCGGTCGAGTGG
* * * * * *
48624089 AGGAGGGCTCGAACTGAATCAGCTAGGTGGACCTGCTCTAATACGGCCTAATCAATGCAACGGCC
196 AGGAGGGCCCAAACTGAATCAGCTAGGTGGACCTGCTCTAATACAGCCCAATCAACGCAACGACC
48624154 CACACTAAAG-GGTCGGGTACGTAGAATCTGAAATAATTCTTCCTCAGGCCCTAGTGGAAATTGG
261 CACAC-AAAGAGGTCGGGTACGTAGAATCTGAAATAATTCTTCCTCAGGCCCTAGTGGAAATTGG
* *
48624218 AGGAATGGATGGCGAATCTCAGTGGTGGCACTTGAGGAAGTCCCACCTGATCCCTTTCG-TTTTG
325 AGGAATGAATGGCGAATCTCAGTGGTGGCACTCGAGGAAGTCCCACCTGATCCCTTTCGCTTTT-
*
48624282 TAGAGCTGGGGACAGAAATTTTCTTTCCTCAAGTGTTTGTCATGATGTACCAGAAAGATAAAACA
389 TAGAGCTGGGGACAGAAATTTTCTTTCCTCAAGTGTTTGTCATGATGTACCAGAAAGACAAAACA
* * *
48624347 TTTCAATATGAATAGAATCGGCATAATTAACACTTAATCAAAAAC
454 TTTCAATATGAATAGAATCGACATAATTAAAACTTAACCAAAAAC
48624392 ATCG
1 ATCG
48624396 AGAAGCTTAG
Statistics
Matches: 443, Mismatches: 54, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
494 4 0.01
495 271 0.61
496 3 0.01
498 2 0.00
500 1 0.00
508 162 0.37
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (498 bp):
ATCGTCTATATAGAATCCCAAGACAGCTCCAAATTCTAGAACACTCAACTGCAGTACTAGACCGC
CAAGGCAAAATTGGACTGTTCCTAGGTCATCGTACTCTGCCATAACCGTTTGCAACTGAAACATC
GAGCATAGTTCCAAAGTGAACTCCAGATACGTCAGCTCGATGATACCAAAGAAGCGGTCGAGTGG
AGGAGGGCCCAAACTGAATCAGCTAGGTGGACCTGCTCTAATACAGCCCAATCAACGCAACGACC
CACACAAAGAGGTCGGGTACGTAGAATCTGAAATAATTCTTCCTCAGGCCCTAGTGGAAATTGGA
GGAATGAATGGCGAATCTCAGTGGTGGCACTCGAGGAAGTCCCACCTGATCCCTTTCGCTTTTTA
GAGCTGGGGACAGAAATTTTCTTTCCTCAAGTGTTTGTCATGATGTACCAGAAAGACAAAACATT
TCAATATGAATAGAATCGACATAATTAAAACTTAACCAAAAAC
Found at i:48625594 original size:13 final size:13
Alignment explanation
Indices: 48625576--48625600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48625566 GACCATGTAA
48625576 CTTCCACGGCCGC
1 CTTCCACGGCCGC
48625589 CTTCCACGGCCG
1 CTTCCACGGCCG
48625601 TGGTGATTTA
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:0.08, C:0.52, G:0.24, T:0.16
Consensus pattern (13 bp):
CTTCCACGGCCGC
Found at i:48630784 original size:19 final size:19
Alignment explanation
Indices: 48630760--48630799 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
48630750 ACAAAACAAG
48630760 AGATATCATTCCTCATTTT
1 AGATATCATTCCTCATTTT
48630779 AGATATCATTCCTCATTTT
1 AGATATCATTCCTCATTTT
48630798 AG
1 AG
48630800 CCGTTTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (19 bp):
AGATATCATTCCTCATTTT
Found at i:48630939 original size:40 final size:40
Alignment explanation
Indices: 48630884--48630963 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
48630874 GGTAATAAGT
*
48630884 TCAACCACTGTTTAGTCTTATTCCTCAATGAAAAGGGAAA
1 TCAACCACTATTTAGTCTTATTCCTCAATGAAAAGGGAAA
48630924 TCAACCACTATTTAGTCTTATTCCTCAATGAAAAGGGAAA
1 TCAACCACTATTTAGTCTTATTCCTCAATGAAAAGGGAAA
48630964 AACCAAAGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (40 bp):
TCAACCACTATTTAGTCTTATTCCTCAATGAAAAGGGAAA
Found at i:48632357 original size:51 final size:49
Alignment explanation
Indices: 48632233--48632374 Score: 187
Period size: 49 Copynumber: 2.9 Consensus size: 49
48632223 TAGCCAAAGC
*
48632233 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
* * * *
48632282 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG-ATCGAAGT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-T
* *
48632333 TATCGGGTACGCATAGTAGCCTGCACTTAGCACTACACATGC
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGC
48632375 GACCTCATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
49 38 0.47
50 4 0.05
51 38 0.47
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (49 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
Found at i:48650461 original size:16 final size:18
Alignment explanation
Indices: 48650434--48650466 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48650424 TAGAATTAGG
48650434 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
48650451 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
48650467 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:48652928 original size:19 final size:19
Alignment explanation
Indices: 48652904--48652940 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48652894 ATATCATCAA
*
48652904 AGTAGAAAAGAGAAAGGAG
1 AGTAGAAAAAAGAAAGGAG
48652923 AGTAGAAAAAAGAAAGGA
1 AGTAGAAAAAAGAAAGGA
48652941 AAGGACGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.05
Consensus pattern (19 bp):
AGTAGAAAAAAGAAAGGAG
Found at i:48654467 original size:17 final size:17
Alignment explanation
Indices: 48654428--48654469 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
48654418 CAGCAAATGA
48654428 ATTTAAACTTAAAAAAT
1 ATTTAAACTTAAAAAAT
* *
48654445 AATTAAAGTTAAAAAA-
1 ATTTAAACTTAAAAAAT
48654461 ATTTTAAAC
1 A-TTTAAAC
48654470 CCCTAACTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTTAAACTTAAAAAAT
Done.