Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold424
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: 897778
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 4 of 6
Found at i:498074 original size:174 final size:176
Alignment explanation
Indices: 497596--498079 Score: 618
Period size: 174 Copynumber: 2.8 Consensus size: 176
497586 GATGATAAAG
* * *
497596 GTGCCAATATGCTGATTCAAGG-CAGTGACATTGGTCTTAAAGATGAAGGTGCTAATATGTTAAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGTTGAT
* * *
497660 TCAAGGCCAACGATATTGGGTTTGTGCCAA-GTGTTGATTCAAGGCCAGCGACCTTGGTCTTAAA
66 TCAAGGCCAACGATATTGGGCTTGTGCCAATGTGTTGATTCAAGACCAGCGACATTGGTCTTAAA
* * * * *
497724 GATAAAGGTGCCAATATGTTGATTCAAGGCCAGCGACATTAGGCTT
131 GATGAAGGTGCCAATATGCTAATTCAACGCCAGCAACATTAGGCTT
* * *
497770 ATGCCAATATGCTGATTCAAGGCCAACGACATTGGCCTTAAAGATGAAGGTGCCAATATGTTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGTTGAT
* * * * *
497835 TCAAGGCCAGCAATATTGGGCTTGTGCTAATGTGTTGATTCAA-AGCCAACAACATTGGTCTTAA
66 TCAAGGCCAACGATATTGGGCTTGTGCCAATGTGTTGATTCAAGA-CCAGCGACATTGGTCTTAA
* * *
497899 AGATGAAGGTGCC-A-ATGCTAATTCAACGCTAGCAATATTGGGCTT
130 AGATGAAGGTGCCAATATGCTAATTCAACGCCAGCAACATTAGGCTT
* * * * *
497944 GTGCCAATGTGATTATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGTTGAT
* * * * * * *
498009 TCAAGGCCAACGATTTTAGGCTTGTGCCAATTTGCTGATTCAAGACTAGCGACATTAGACTTAAA
66 TCAAGGCCAACGATATTGGGCTTGTGCCAATGTGTTGATTCAAGACCAGCGACATTGGTCTTAAA
498074 GATGAA
131 GATGAA
498080 AAGAATGCCA
Statistics
Matches: 264, Mismatches: 42, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
174 159 0.60
175 65 0.25
176 40 0.15
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (176 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGTTGAT
TCAAGGCCAACGATATTGGGCTTGTGCCAATGTGTTGATTCAAGACCAGCGACATTGGTCTTAAA
GATGAAGGTGCCAATATGCTAATTCAACGCCAGCAACATTAGGCTT
Found at i:498074 original size:262 final size:265
Alignment explanation
Indices: 497623--498108 Score: 696
Period size: 262 Copynumber: 1.8 Consensus size: 265
497613 CAAGGCAGTG
* * * *
497623 ACATTGGTCTTAAAGATGAAGGTGCTAATATGTTAATTCAAGGCCAACGATATTGGGTTTGTGCC
1 ACATTGGTCTTAAAGATGAAGGTGCTAATATGCTAATTCAACGCCAACAATATTGGGCTTGTGCC
* *
497688 AAGTGTTGATTCAAGGCCAGCGACCTTGGTCTTAAAGATAAAGGTGCCAATATGTTGATTCAAGG
66 AAGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGG
* * * *
497753 CCAGCGACATTAGGCTTATGCCAATATGCTGATTCAAGGCCAACGACATTGGCCTTAAAGATG-A
131 CCAACGACATTAGGCTTATGCCAATATGCTGATTCAAGACCAACGACATTAGACTTAAAGATGAA
* *
497817 AG-GTGCCAATATGTTGATTCAAGGCCAGCAATATTGGGCTTGTGCTAATGTGTTGATTCAAAGC
196 AGAATGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTGTGCTAATGTGTTGATTCAAAGC
497881 CAACA
261 CAACA
* * *
497886 ACATTGGTCTTAAAGATGAAGGTGC-CA-ATGCTAATTCAACGCTAGCAATATTGGGCTTGTGCC
1 ACATTGGTCTTAAAGATGAAGGTGCTAATATGCTAATTCAACGCCAACAATATTGGGCTTGTGCC
497949 AATGTGATT-ATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAA-GTGCCAATATGCTGATTCA
66 AA-GTG-TTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-AAAGGTGCCAATATGCTGATTCA
** * * * *
498012 AGGCCAACGATTTTAGGCTTGTGCCAATTTGCTGATTCAAGACTAGCGACATTAGACTTAAAGAT
128 AGGCCAACGACATTAGGCTTATGCCAATATGCTGATTCAAGACCAACGACATTAGACTTAAAGAT
*
498077 GAAAAGAATGCCAATGTGCTGATTCAAGGCCA
193 G-AAAGAATGCCAATATGCTGATTCAAGGCCA
498109 ACGACATTGG
Statistics
Matches: 195, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
261 32 0.16
262 108 0.55
263 30 0.15
264 3 0.02
265 22 0.11
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (265 bp):
ACATTGGTCTTAAAGATGAAGGTGCTAATATGCTAATTCAACGCCAACAATATTGGGCTTGTGCC
AAGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGG
CCAACGACATTAGGCTTATGCCAATATGCTGATTCAAGACCAACGACATTAGACTTAAAGATGAA
AGAATGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTGTGCTAATGTGTTGATTCAAAGC
CAACA
Found at i:498114 original size:52 final size:52
Alignment explanation
Indices: 498033--498157 Score: 144
Period size: 52 Copynumber: 2.4 Consensus size: 52
498023 TTTAGGCTTG
* * * *
498033 TGCCAATTTGCTGATTCAAGACTAGCGACATTAGACTTAAAGAT-GAAAAGAA
1 TGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGGAAAAG-A
* * * * *
498085 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGGTGGTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGGAAAAGA
*
498137 TGCCAATATGCTGATTTAAGG
1 TGCCAATATGCTGATTCAAGG
498158 TTAGTGATGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
52 57 0.92
53 5 0.08
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGGAAAAGA
Found at i:498247 original size:31 final size:32
Alignment explanation
Indices: 498208--498282 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
498198 CCAACGACAT
*
498208 TGGG-TTTAG-AAGGGTTGCCACTGACTTATG
1 TGGGCTTTAGAAAGGGTTGCCACAGACTTATG
* *
498238 TGGGCTTTAGAAAAGGGTTGCCACAGAGTTGTG
1 TGGGCTTTAG-AAAGGGTTGCCACAGACTTATG
498271 TGGGCTTT-GAAA
1 TGGGCTTTAGAAA
498283 AGAAAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.10
31 8 0.21
32 1 0.03
33 26 0.67
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.31
Consensus pattern (32 bp):
TGGGCTTTAGAAAGGGTTGCCACAGACTTATG
Found at i:498256 original size:33 final size:32
Alignment explanation
Indices: 498217--498284 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
498207 TTGGGTTTAG
*
498217 AAGGGTTGCCACTGACTTATGTGGGCTTTAGAA
1 AAGGGTTGCCACAGACTTATGTGGGCTTT-GAA
* *
498250 AAGGGTTGCCACAGAGTTGTGTGGGCTTTGAA
1 AAGGGTTGCCACAGACTTATGTGGGCTTTGAA
498282 AAG
1 AAG
498285 AAAAAAGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.28
Consensus pattern (32 bp):
AAGGGTTGCCACAGACTTATGTGGGCTTTGAA
Found at i:498356 original size:33 final size:33
Alignment explanation
Indices: 498312--498897 Score: 381
Period size: 27 Copynumber: 18.6 Consensus size: 33
498302 TTGTGGACTT
*
498312 AAAAGGGTGCCACGGAGTTGTAGG-CTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGT-GGACTTAAAAGG
* * * * *
498345 GAAAAGATGCCACGGAGATATGGATTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* ** *
498378 AAAAAGGTGCCGCATAGATGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
498411 AAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGG
1 AAAAA-GGTGCCACGGAGTTGTGGACTTAAAAGG
* * * *
498445 -AAAAGGTCCCACAGAGTTGTGGGCTTAAAAGAAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG---G
*
498480 AAAAAGGGTGCCACGGAGTTATGGACTTAAAAGG
1 AAAAA-GGTGCCACGGAGTTGTGGACTTAAAAGG
* *
498514 -AAAAGGTGCCACGGAGTTATGGGCTTTGAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGG
* ** * *
498547 AAAAATGTGCCA-TAAGTTATGGACTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* *
498579 -AAAAGGTGCCACAGAGTTGTGGACTTAAACGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
498611 ----A--TGTCACGGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
498638 AAAAA-GTGCCACAGAGTTGTAGACTCAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
498670 ----A--TACCATGGAGTTGTAGACTTAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
498696 -----GGTGCCATGGAGTTGTGGACTTAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
498723 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
** *
498755 ----A-GTGCCATAGAGTTATGGACTTAAAA-G
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * *
498782 -----GGTACCACAGAGTTGTGGGCTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
*
498810 AAAAAGAGTGCTA-GTGAGTTGTGGACTTAAAAGG
1 AAAAAG-GTGCCACG-GAGTTGTGGACTTAAAAGG
* *
498844 AAAAGGGGTGCCATGGAGTTGTAGG-CTTTGAAAA-G
1 AAAA-AGGTGCCACGGAGTTGT-GGAC-TT-AAAAGG
498879 AAAAAGGTGCCACGGAGTT
1 AAAAAGGTGCCACGGAGTT
498898 ATGAAAGGGT
Statistics
Matches: 447, Mismatches: 68, Indels: 75
0.76 0.12 0.13
Matches are distributed among these distances:
26 1 0.00
27 110 0.25
28 3 0.01
29 1 0.00
31 15 0.03
32 110 0.25
33 76 0.17
34 89 0.20
35 11 0.02
36 8 0.02
37 23 0.05
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.21
Consensus pattern (33 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:498387 original size:66 final size:65
Alignment explanation
Indices: 498312--498657 Score: 300
Period size: 66 Copynumber: 5.3 Consensus size: 65
498302 TTGTGGACTT
* * * *
498312 AAAAGGGTGCCACGGAGTTGTAGGCTTAAAAGGGAAAA-GATGCCACGGAGATATGGATTTAAAA
1 AAAA-GGTGCCACAGAGTTGT-GGCTTAAAAGGAAAAAGGATGCCACGGAGTTATGGACTTAAAA
498376 GG
64 GG
* * * * * *
498378 AAAAAGGTGCCGCATAGATGTGGACTTAAAAGGAAAAAGGGTGCCATGGAGTTGTGGACTTAAAA
1 -AAAAGGTGCCACAGAGTTGTGG-CTTAAAAGGAAAAAGGATGCCACGGAGTTATGGACTTAAAA
498443 GG
64 GG
* * *
498445 AAAAGGTCCCACAGAGTTGTGGGCTTAAAAGAAAAAAAAAGGGTGCCACGGAGTTATGGACTTAA
1 AAAAGGTGCCACAGAGTTGT-GGCTTAAAAG---GAAAAAGGATGCCACGGAGTTATGGACTTAA
498510 AAGG
62 AAGG
* * * **
498514 AAAAGGTGCCACGGAGTTATGGGCTTTGAAAA-GAAAAATG-TGCCA-TAAGTTATGGACTTAAA
1 AAAAGGTGCCACAGAGTTGT-GGC-TT-AAAAGGAAAAAGGATGCCACGGAGTTATGGACTTAAA
*
498576 AAG
63 AGG
* * *
498579 AAAAGGTGCCACAGAGTTGTGGACTT-------AAACGGATGTCACGGAGTTGTGGACTTAAAAG
1 AAAAGGTGCCACAGAGTTGTGG-CTTAAAAGGAAAAAGGATGCCACGGAGTTATGGACTTAAAAG
498637 G
65 G
*
498638 AAAAAGTGCCACAGAGTTGT
1 AAAAGGTGCCACAGAGTTGT
498658 AGACTCAAAA
Statistics
Matches: 233, Mismatches: 35, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.02
58 4 0.02
59 35 0.15
64 4 0.02
65 38 0.16
66 54 0.23
67 35 0.15
69 53 0.23
70 2 0.01
71 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (65 bp):
AAAAGGTGCCACAGAGTTGTGGCTTAAAAGGAAAAAGGATGCCACGGAGTTATGGACTTAAAAGG
Found at i:498506 original size:69 final size:69
Alignment explanation
Indices: 498352--498607 Score: 276
Period size: 69 Copynumber: 3.8 Consensus size: 69
498342 AGGGAAAAGA
* * * * * *
498352 TGCCACGGAGATATGGATTTAAAAGGAAAAAGGTGCCGCATAGATGTGGACTTAAAAG---GAAA
1 TGCCACGGAGTTATGGACTTAAAAGG-AAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAAA
498414 AAGGG
65 AAGGG
* * * *
498419 TGCCATGGAGTTGTGGACTTAAAAGGAAAAGGTCCCACAGAGTTGTGGGCTTAAAAGAAAAAAAA
1 TGCCACGGAGTTATGGACTTAAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAAAA
498484 AGGG
66 AGGG
* * * *
498488 TGCCACGGAGTTATGGACTTAAAAGGAAAAGGTGCCACGGAGTTATGGGCTT---TGAAAAGAAA
1 TGCCACGGAGTTATGGACTTAAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAAA-AAA
*
498550 AA-TG
65 AAGGG
** *
498554 TGCCA-TAAGTTATGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAA
1 TGCCACGGAGTTATGGACTTAAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAA
498608 CGGATGTCAC
Statistics
Matches: 159, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
65 40 0.25
66 37 0.23
67 27 0.17
69 55 0.35
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (69 bp):
TGCCACGGAGTTATGGACTTAAAAGGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAAAA
AGGG
Found at i:498681 original size:59 final size:59
Alignment explanation
Indices: 498561--498815 Score: 188
Period size: 59 Copynumber: 4.4 Consensus size: 59
498551 ATGTGCCATA
* * * * * * **
498561 AGTTATGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAACGGATGTCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTTGTAGACTCAAAAGGATACCACGG
*
498620 AGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTTGTAGACTCAAAAGGATACCATGG
1 AGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTTGTAGACTCAAAAGGATACCACGG
* ** * * * *
498679 AGTTGTAGACTTAAAAGG-----GTGCCATGGAGTTGTGGACTTAAAAGAAAAAGGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTTGTAGACTCAAAAG-----GATACCACGG
* * * * * *
498738 AGTTGTGGACTTAAAA-G----AGTGCCATAGAGTTATGGACTTAAAAGGGTACCACAG
1 AGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTTGTAGACTCAAAAGGATACCACGG
*
498792 AGTTGTGGGCTTAAAAGGAAAAAG
1 AGTTGTGGACTTAAAAGGAAAAAG
498816 AGTGCTAGTG
Statistics
Matches: 162, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
54 45 0.28
55 1 0.01
58 1 0.01
59 115 0.71
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.22
Consensus pattern (59 bp):
AGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTTGTAGACTCAAAAGGATACCACGG
Found at i:498708 original size:86 final size:86
Alignment explanation
Indices: 498591--498815 Score: 292
Period size: 86 Copynumber: 2.6 Consensus size: 86
498581 AAGGTGCCAC
* * *
498591 AGAGTTGTGGACTTAAACGGATGTCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTT
1 AGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTT
498656 GTAGACTCAAAAG-GATACCAT
66 GTAGACTCAAAAGAG-TACCAT
* * * *
498677 GGAGTTGTAGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAA-GAAAAAGGTGCCACGGAGT
1 AGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA-GTGCCACAGAGT
* * *
498741 TGTGGACTTAAAAGAGTGCCAT
65 TGTAGACTCAAAAGAGTACCAT
* * * *
498763 AGAGTTATGGACTTAAAAGGGTACCACAGAGTTGTGGGCTTAAAAGGAAAAAG
1 AGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAG
498816 AGTGCTAGTG
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
85 6 0.05
86 106 0.89
87 7 0.06
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (86 bp):
AGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGTGCCACAGAGTT
GTAGACTCAAAAGAGTACCAT
Found at i:498971 original size:29 final size:29
Alignment explanation
Indices: 498939--498994 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
498929 AAGGGAATGA
* *
498939 TGCCACGGAGTCGTGGACATTTGGAAGGG
1 TGCCACAGAGTCATGGACATTTGGAAGGG
* *
498968 TGCCACAGAGTCATGGGCTTTTGGAAG
1 TGCCACAGAGTCATGGACATTTGGAAG
498995 AAAAGGATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.23
Consensus pattern (29 bp):
TGCCACAGAGTCATGGACATTTGGAAGGG
Found at i:499039 original size:30 final size:31
Alignment explanation
Indices: 498968--499105 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 31
498958 TTTGGAAGGG
* *
498968 TGCCACAGAGTCATGGGCTTTTGGAAGAAA-AGGA
1 TGCCACTGAGTCATGGAC-TTT--AAGAAAGA-GA
*
499002 TGTCACTGAGTCATGGACTTTAA-AAAGAGA
1 TGCCACTGAGTCATGGACTTTAAGAAAGAGA
* *
499032 TGCCACTGAGTCGTGGAC-ATAGAGAAA-AGA
1 TGCCACTGAGTCATGGACTTTA-AGAAAGAGA
*
499062 TGCCACTGAGTCATGGACTTTGAAGAAAAAGGA
1 TGCCACTGAGTCATGGACTTT-AAGAAAGA-GA
*
499095 TGTCACTGAGT
1 TGCCACTGAGT
499106 AGTAGACTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
29 2 0.02
30 42 0.48
31 12 0.14
32 2 0.02
33 15 0.17
34 15 0.17
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.22
Consensus pattern (31 bp):
TGCCACTGAGTCATGGACTTTAAGAAAGAGA
Found at i:499096 original size:93 final size:93
Alignment explanation
Indices: 498937--499105 Score: 236
Period size: 93 Copynumber: 1.8 Consensus size: 93
498927 AAAAGGGAAT
* * * *
498937 GATGCCACGGAGTCGTGGACATTTGGAAGGGTGCCACAGAGTCATGGGCTTTTGGAAGAAAAGGA
1 GATGCCACGGAGTCGTGGACATTAGGAAAGATGCCACAGAGTCATGGACTTTTGGAAGAAAAGGA
499002 TGTCACTGAGTCATGGACTTTAAAAAGA
66 TGTCACTGAGTCATGGACTTTAAAAAGA
* *
499030 GATGCCACTGAGTCGTGGACA-TAGAGAAAAGATGCCACTGAGTCATGGAC-TTT-GAAGAAAAA
1 GATGCCACGGAGTCGTGGACATTAG-G-AAAGATGCCACAGAGTCATGGACTTTTGGAAG-AAAA
499092 GGATGTCACTGAGT
63 GGATGTCACTGAGT
499106 AGTAGACTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
92 6 0.09
93 42 0.63
94 19 0.28
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (93 bp):
GATGCCACGGAGTCGTGGACATTAGGAAAGATGCCACAGAGTCATGGACTTTTGGAAGAAAAGGA
TGTCACTGAGTCATGGACTTTAAAAAGA
Found at i:499114 original size:93 final size:93
Alignment explanation
Indices: 498937--499140 Score: 231
Period size: 93 Copynumber: 2.2 Consensus size: 93
498927 AAAAGGGAAT
* * * *
498937 GATGCCACGGAGTCGTGGACATTTGGAAGGGTGCCACAGAGTCATGGGCTTTTGGAAGAAAAGGA
1 GATGCCACGGAGTCGTGGACATTAGGAAAGATGCCACAGAGTCATGGACTTTTGGAAGAAAAGGA
*
499002 TGTCACTGAGTCATGGACTTTAAAAAGA
66 TGTCACTGAGTCATAGACTTTAAAAAGA
* *
499030 GATGCCACTGAGTCGTGGACA-TAGAGAAAAGATGCCACTGAGTCATGGAC-TTT-GAAGAAAAA
1 GATGCCACGGAGTCGTGGACATTAG-G-AAAGATGCCACAGAGTCATGGACTTTTGGAAG-AAAA
*
499092 GGATGTCACTGAGT-AGTAGACTTTTAGGAAAG-
63 GGATGTCACTGAGTCA-TAGAC-TTTA-AAAAGA
*
499124 G-TGCCATGGAGTCGTGG
1 GATGCCACGGAGTCGTGG
499141 GCTTTTAGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
92 7 0.07
93 60 0.63
94 24 0.25
95 4 0.04
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (93 bp):
GATGCCACGGAGTCGTGGACATTAGGAAAGATGCCACAGAGTCATGGACTTTTGGAAGAAAAGGA
TGTCACTGAGTCATAGACTTTAAAAAGA
Found at i:499136 original size:63 final size:62
Alignment explanation
Indices: 498993--499112 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 62
498983 GGCTTTTGGA
* * * *
498993 AGAAAAGGATGTCACTGAGTCATGGACTTTAA-AAAGA-GATGCCACTGAGTCGTGGACATAG
1 AGAAAA-GATGCCACTGAGTCATGGACTTTAAGAAAAAGGATGCCACTGAGTAGTAGACATAG
*
499054 AGAAAAGATGCCACTGAGTCATGGACTTTGAAGAAAAAGGATGTCACTGAGTAGTAGAC
1 AGAAAAGATGCCACTGAGTCATGGACTTT-AAGAAAAAGGATGCCACTGAGTAGTAGAC
499113 TTTTAGGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 22 0.43
61 8 0.16
62 4 0.08
63 17 0.33
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (62 bp):
AGAAAAGATGCCACTGAGTCATGGACTTTAAGAAAAAGGATGCCACTGAGTAGTAGACATAG
Found at i:500414 original size:17 final size:15
Alignment explanation
Indices: 500394--500453 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
500384 GATTTTGCCC
*
500394 TTTTTCTTTTTTTGTG
1 TTTTT-TTTTTTTTTG
* *
500410 TTTTTTATGTCTTTTG
1 TTTTTT-TTTTTTTTG
500426 TTTTGTTTTTTGTTTTG
1 TTTT-TTTTTT-TTTTG
500443 TTTTTTTTTTT
1 TTTTTTTTTTT
500454 GCTTTTGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 2 0.06
16 23 0.64
17 11 0.31
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:500438 original size:12 final size:12
Alignment explanation
Indices: 500403--500459 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
500393 CTTTTTCTTT
*
500403 TTTTGTGTTTT-
1 TTTTGTTTTTTG
* *
500414 TTATGTCTTTTG
1 TTTTGTTTTTTG
500426 TTTTGTTTTTTG
1 TTTTGTTTTTTG
*
500438 TTTTGTTTTTTT
1 TTTTGTTTTTTG
500450 TTTTGCTTTT
1 TTTTG-TTTT
500460 GACAGTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.23
12 26 0.67
13 4 0.10
ACGTcount: A:0.02, C:0.04, G:0.14, T:0.81
Consensus pattern (12 bp):
TTTTGTTTTTTG
Found at i:507420 original size:20 final size:20
Alignment explanation
Indices: 507395--507445 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
507385 AAATTCCTAG
*
507395 ATGTATTGATACA-ATGATCA
1 ATGTATCGATACATAT-ATCA
*
507415 ATGTATCGATACATATATTA
1 ATGTATCGATACATATATCA
507435 ATGTATCGATA
1 ATGTATCGATA
507446 TATCTCCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATATATCA
Found at i:511627 original size:13 final size:13
Alignment explanation
Indices: 511609--511633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
511599 TAAAGATTAG
511609 TGTATCGATACAA
1 TGTATCGATACAA
511622 TGTATCGATACA
1 TGTATCGATACA
511634 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:511712 original size:13 final size:13
Alignment explanation
Indices: 511694--511720 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
511684 TACAAAACTT
511694 ATGTATCGATACA
1 ATGTATCGATACA
511707 ATGTATCGATACA
1 ATGTATCGATACA
511720 A
1 A
511721 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:511717 original size:32 final size:33
Alignment explanation
Indices: 511676--511740 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
511666 TAGCTTAAAT
*
511676 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCAATACAA
*
511708 TGTATCGATACAACACTTTATGTATCAATACAA
1 TGTATCGATACAAAACTTTATGTATCAATACAA
511741 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCAATACAA
Found at i:512465 original size:55 final size:54
Alignment explanation
Indices: 512398--512702 Score: 226
Period size: 55 Copynumber: 5.4 Consensus size: 54
512388 ACCAATACGT
* *
512398 TGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGATGTCAATGTGC
1 TGATTCAAGGCCAACTATATTGGGTT-AAAGATGAGAAAAAGGATGTCAATGTGC
* * ** *
512453 TGATTCAAGGCCAGCTACATTGAACTTAAAGATGAG-AAAA--ATGCCAATGTGC
1 TGATTCAAGGCCAACTATATTG-GGTTAAAGATGAGAAAAAGGATGTCAATGTGC
* * *
512505 TGATTCAAGGCCAACAATATGGGGTTTTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATA
1 TGATTCAAGGCCAACTATATTGGG--TTAAAGATG-A---GA-AAAAG-GAT---G-T--CAATG
*
512570 TGT
52 TGC
* *
512573 TGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGC
1 TGATTCAAGGCCAACTATATTGGG-TTAAAGATGAGAAAAAGGATGTCAATGTGC
* * ** * *
512628 TGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAAGG-TGCCAATATGC
1 TGATTCAAGGCCAACTATATTG-GGTTAAAGATGAGAAAAAGGATGTCAATGTGC
*
512680 TGATTCAAGGCCAGCTATATTGG
1 TGATTCAAGGCCAACTATATTGG
512703 ACTTAAAGGT
Statistics
Matches: 199, Mismatches: 32, Indels: 42
0.73 0.12 0.15
Matches are distributed among these distances:
52 59 0.30
53 15 0.08
54 6 0.03
55 60 0.30
56 2 0.01
57 2 0.01
58 1 0.01
59 4 0.02
61 3 0.02
62 7 0.04
63 2 0.01
65 1 0.01
66 1 0.01
67 9 0.05
68 27 0.14
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (54 bp):
TGATTCAAGGCCAACTATATTGGGTTAAAGATGAGAAAAAGGATGTCAATGTGC
Found at i:512622 original size:175 final size:175
Alignment explanation
Indices: 512376--512692 Score: 550
Period size: 175 Copynumber: 1.8 Consensus size: 175
512366 GAGGATGAAG
512376 AGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGG
1 AGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGG
*
512441 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAGAAAA-ATGCCAATGTGC
66 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-GAAAAGATGCCAATATGC
512505 TGATTCAAGGCCAACAATATGGGGTTTTAAAGATGAAGGTGAGAAA
130 TGATTCAAGGCCAACAATATGGGGTTTTAAAGATGAAGGTGAGAAA
* *
512551 AGTGATAAAGATG-CCAATATGTTGATTCACGGCCAACGATATTGGGCTT-AAAGATGAGAAAAA
1 AGTGATAAA-AGGACCAATACGTTGATTCACGGCCAACGATATTGGG-TTCAAAGATGAGAAAAA
*
512614 GGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATG
64 GGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGATGCCAATATG
512679 CTGATTCAAGGCCA
129 CTGATTCAAGGCCA
512693 GCTATATTGG
Statistics
Matches: 135, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
174 5 0.04
175 126 0.93
176 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (175 bp):
AGTGATAAAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGG
ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGATGCCAATATGCT
GATTCAAGGCCAACAATATGGGGTTTTAAAGATGAAGGTGAGAAA
Found at i:512725 original size:43 final size:43
Alignment explanation
Indices: 512664--513120 Score: 547
Period size: 43 Copynumber: 10.1 Consensus size: 43
512654 TAAAGATGGA
*
512664 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
512707 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
512750 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * **
512799 AAAGGTGCTAATGTATTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
512842 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
512891 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
512934 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
512983 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
513026 AAAGATGAAGGTGCCAATATGCTG-TTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
513074 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
513117 AAAG
1 AAAG
513121 ATGAAGGTGC
Statistics
Matches: 359, Mismatches: 30, Indels: 50
0.82 0.07 0.11
Matches are distributed among these distances:
42 16 0.04
43 178 0.50
44 5 0.01
45 1 0.00
46 2 0.01
47 2 0.01
48 27 0.08
49 128 0.36
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:512795 original size:92 final size:92
Alignment explanation
Indices: 512611--513159 Score: 902
Period size: 92 Copynumber: 5.9 Consensus size: 92
512601 AAGATGAGAA
* * *
512611 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
*
512676 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
512707 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
512772 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* **
512799 AAAGGTGCTAATGTATTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
512864 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
512891 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
512956 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
512983 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
513048 TG-TTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
513074 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* * *
513139 TGTTTTAATGCCAGCGATATT
66 TGATTCAAGGCCAGCGATATT
513160 AGGCTTAGAA
Statistics
Matches: 436, Mismatches: 16, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
91 90 0.21
92 300 0.69
95 41 0.09
96 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:512803 original size:22 final size:22
Alignment explanation
Indices: 512778--512845 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
512768 ATGCTGATTC
512778 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* *
512800 AAGG--TGCTAATGTATT-GA-TTC
1 AAGGCCAGCT-A--TATTGGACTTA
*
512821 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
512843 AAG
1 AAG
512846 AAGAAGGTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
20 6 0.18
21 9 0.26
22 12 0.35
23 7 0.21
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:513304 original size:33 final size:33
Alignment explanation
Indices: 513166--513339 Score: 268
Period size: 32 Copynumber: 5.4 Consensus size: 33
513156 TATTAGGCTT
*
513166 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
513199 AG-AGGGTTGCCACCGACTTGTGTAGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
513230 AGAAGGGTTGCCACCGACTTGTGTGGGC-TTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
513262 AGAAGGGTTGCCACCGATTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
513295 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
513328 AG-AGGG-TGCCAC
1 AGAAGGGTTGCCAC
513340 GGAGTCGTGG
Statistics
Matches: 130, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
31 11 0.08
32 81 0.62
33 38 0.29
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:513369 original size:34 final size:34
Alignment explanation
Indices: 513330--513555 Score: 280
Period size: 34 Copynumber: 6.7 Consensus size: 34
513320 GGCTTTAGAG
* *
513330 AGGGTGCCACGGAGTCGTGGACTTAAAAGGAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
* **
513364 AGGGTGCCACGGAGTTGTGGGCTTTCAA--AAAA
1 AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
*
513396 A-GGTGCCACGGAGTTATGGACTTAGAAGGAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
*
513429 AGTGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
* * * *
513463 AGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
1 AGGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAA
*
513498 A-GGTGCCACGAAGTTGTGGACTTAGAAGGAAAA
1 AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
* * *
513531 AGAGTGCCACGGAGTTATGGGCTTA
1 AGGGTGCCACGGAGTTGTGGACTTA
513556 AACGGGTGAG
Statistics
Matches: 164, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
31 22 0.13
32 5 0.03
33 16 0.10
34 110 0.67
35 11 0.07
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.19
Consensus pattern (34 bp):
AGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
Found at i:513441 original size:99 final size:101
Alignment explanation
Indices: 513333--513545 Score: 340
Period size: 99 Copynumber: 2.1 Consensus size: 101
513323 TTTAGAGAGG
* *
513333 GTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTT-CAA-AAAA
1 GTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* *
513396 AGGTGCCACGGAGTTATGGACTTAGAAGGAAAAAGT
66 AGGTGCCACGAAGTTATGGACTTAGAAGGAAAAAGA
* *
513432 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
1 GTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAA
*
513497 AAGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGA
65 AAGGTGCCACGAAGTTATGGACTTAGAAGGAAAAAGA
513534 GTGCCACGGAGT
1 GTGCCACGGAGT
513546 TATGGGCTTA
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
99 53 0.51
101 2 0.02
102 49 0.47
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.19
Consensus pattern (101 bp):
GTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
AGGTGCCACGAAGTTATGGACTTAGAAGGAAAAAGA
Found at i:515019 original size:14 final size:14
Alignment explanation
Indices: 515002--515037 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
514992 CTTTTTGTTG
515002 TTTTTTTTTCTTCT
1 TTTTTTTTTCTTCT
515016 TTTTTTTTTCTTCT
1 TTTTTTTTTCTTCT
515030 TTTTTTTT
1 TTTTTTTT
515038 GTTTATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTCT
Found at i:526767 original size:27 final size:27
Alignment explanation
Indices: 526729--526802 Score: 148
Period size: 27 Copynumber: 2.7 Consensus size: 27
526719 TTTGGTTGAA
526729 AATGGGGTTGGAGTGTCCCCTCGGAGG
1 AATGGGGTTGGAGTGTCCCCTCGGAGG
526756 AATGGGGTTGGAGTGTCCCCTCGGAGG
1 AATGGGGTTGGAGTGTCCCCTCGGAGG
526783 AATGGGGTTGGAGTGTCCCC
1 AATGGGGTTGGAGTGTCCCC
526803 GATGAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.43, T:0.23
Consensus pattern (27 bp):
AATGGGGTTGGAGTGTCCCCTCGGAGG
Found at i:529041 original size:13 final size:13
Alignment explanation
Indices: 529023--529047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
529013 CAAAGATCAG
529023 TGTATCGATACAA
1 TGTATCGATACAA
529036 TGTATCGATACA
1 TGTATCGATACA
529048 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:529126 original size:13 final size:13
Alignment explanation
Indices: 529108--529134 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
529098 TACAAAACTT
529108 ATGTATCGATACA
1 ATGTATCGATACA
529121 ATGTATCGATACA
1 ATGTATCGATACA
529134 A
1 A
529135 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:529127 original size:32 final size:33
Alignment explanation
Indices: 529090--529154 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
529080 TAGCTTAAAT
529090 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
*
529122 TGTATCGATACAACACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
529155 ATCGTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:531102 original size:57 final size:58
Alignment explanation
Indices: 531006--531121 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 58
530996 AACAATAGGC
* ***
531006 CCATAAATATATGCAAATTAGGCTCCACTCTTCTTGGACATGTGAATTAGGCTCCAAG
1 CCATAAATATATGCAAATTAGGCTCCACTCTCCTTGGACATACAAATTAGGCTCCAAG
* * *
531064 CCATGAATATATGCAAATT-GGCTTCACTCTCCTTGGACATACAAATTGGGCTCCAAG
1 CCATAAATATATGCAAATTAGGCTCCACTCTCCTTGGACATACAAATTAGGCTCCAAG
531121 C
1 C
531122 TTTATTCTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 33 0.65
58 18 0.35
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (58 bp):
CCATAAATATATGCAAATTAGGCTCCACTCTCCTTGGACATACAAATTAGGCTCCAAG
Found at i:539529 original size:21 final size:21
Alignment explanation
Indices: 539491--539530 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
539481 ATCAAATCTT
* *
539491 CTTCAAATTTCTTAATTTTCA
1 CTTCAAAATACTTAATTTTCA
*
539512 CTTCAAAATACTTCATTTT
1 CTTCAAAATACTTAATTTT
539531 TCCTCAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (21 bp):
CTTCAAAATACTTAATTTTCA
Found at i:539839 original size:20 final size:20
Alignment explanation
Indices: 539814--539862 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
539804 GCAGCCACCT
539814 CCAGGTCGCGATCGACACTC
1 CCAGGTCGCGATCGACACTC
539834 CCAGGTCGCGATCGACACTC
1 CCAGGTCGCGATCGACACTC
539854 CCAGGTCGC
1 CCAGGTCGC
539863 AACTGGGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.41, G:0.27, T:0.14
Consensus pattern (20 bp):
CCAGGTCGCGATCGACACTC
Found at i:550762 original size:19 final size:19
Alignment explanation
Indices: 550738--550798 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
550728 ACAGTAAATT
550738 TATCGATACATAAGTTTTG
1 TATCGATACATAAGTTTTG
550757 TATCGATAC--AA----TG
1 TATCGATACATAAGTTTTG
*
550770 TAGCGATACATAAGTTTTG
1 TATCGATACATAAGTTTTG
550789 TATCGATACA
1 TATCGATACA
550799 ATACCCTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 20 0.59
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (19 bp):
TATCGATACATAAGTTTTG
Found at i:555949 original size:477 final size:475
Alignment explanation
Indices: 554564--556140 Score: 1931
Period size: 477 Copynumber: 3.3 Consensus size: 475
554554 AACACATTCT
* * * * ** *
554564 CTTAAATAAGACAAGCATCGATTCTCATAACAATATCCATTCTTTTCATTATTGGGAACCAAAAG
1 CTTAAATAAGACAAGCATCAATTCTCATAACAGTCTCCATTCTTTTAAAGATTGGGAACCAAAAA
* * *
554629 CACATTCACTTCATTAGGATACATGACATTAATGCTTTGGTGTTACAAGAAAAGCTTTTCTTTCC
66 CACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTCC
* * *
554694 ACTATTTTTGATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACAAATCC
131 ACCATTTTTGATAGAATCAAAGTTTGTCTCTAAAATAAGAC-AACATGAATAGTCATAAAAATCC
* * * * * *
554759 CCATTCTTTTTAGGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACACGATATTGATGCT
195 CCATTCTTTTCAAGATTAAGCACCATAAACATAGTATTCTCATTAGGATACACGATATTGATGTT
** * *
554824 TTGGTTTCGCAAGAAAGGGTTTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCATGCTTCAAATG
260 TTGGTTTCGCAAGAAAGGCATTTTTCCTACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATG
* * *
554889 AGACAAACATGGATTCCT-GTAATGATCTTCGTTCATTTTGTGATTAGGAACTATAAACACATTC
325 AGACAAACATGGATT-CTACTAATGATCTTCGCTCATTTTGTGATTAGGCACTATAAACACATTC
* * * * *
554953 T-TCTCATTAGGATAAATAATATTGACGATAATTCTTTTGCATGAAAATCTTTTCTTTG-CC--T
389 TCT-TCATTAGGACAAATGATGTTGATGAT-TTTCTTTTGCATGAAAATCTTTTCTTTGCCCTAT
* * * *
555014 TAT--TTAAAATTAAAGTTCATCC
452 TTTCCTTTAAATCAAAGTTCATAC
* * * * * * * *
555036 CTTGAATAAAACCAGCATCAATTCTCGTAATAGTCTCTATTCTTTTCAAGATTGGGAACCAAAAG
1 CTTAAATAAGACAAGCATCAATTCTCATAACAGTCTCCATTCTTTTAAAGATTGGGAACCAAAAA
* * * * *
555101 CGCATTTCCTTCATAAGGACATATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTCC
66 CACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTCC
* ** * * ** ** **
555166 ACCGTTTTTGATAGAATCAAAGTTCATCCCTCAAAGGAGACAACCATGGAAT-GTGGTAACCATC
131 ACCATTTTTGATAGAATCAAAGTTTGTCTCTAAAATAAGACAA-CAT-GAATAGTCATAAAAATC
* *** * ** * * * *
555230 TCCA-TCTACACACGATT-AGTGCCATAAATAT-GATATCCCCATTACGATACACGATATTGATG
194 CCCATTCTTTTCAAGATTAAGCACCATAAACATAG-TATTCTCATTAGGATACACGATATTGATG
*
555292 TTTTGGTTTCGCAAGAAAGGTATTTTT-CTCACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAA
258 TTTTGGTTTCGCAAGAAAGGCATTTTTCCT-ACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAA
* *
555356 ATGAGACAAACATGGATTCTACTAATGATCTTCACTCATTTTGTGATTAGACACTATAAACACAT
322 ATGAGACAAACATGGATTCTACTAATGATCTTCGCTCATTTTGTGATTAGGCACTATAAACACAT
* * *
555421 TCTCCTCATTAGGACAAATGATGTTGATGATTTTATTTTGCATGCAAATCTTTTCTTTGCCCTAT
387 TCTCTTCATTAGGACAAATGATGTTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTGCCCTAT
555486 TTTCCTTTAAATCAAAGTTCATAC
452 TTTCCTTTAAATCAAAGTTCATAC
*
555510 CTTAAATAAGACAAGCATCAATTCTCATAACTGTCTCCATTC-TTTAAGAGATTGGGAACCAAAA
1 CTTAAATAAGACAAGCATCAATTCTCATAACAGTCTCCATTCTTTTAA-AGATTGGGAACCAAAA
* *
555574 ACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAAAAAACCTTTTCTTTC
65 ACACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTC
* * **
555639 CACCATTTTTTATAGAATCAAAGTTTGTCTCTAAAATAAGACAGACATGAATACTCATAGTAATC
130 CACCATTTTTGATAGAATCAAAGTTTGTCTCTAAAATAAGACA-ACATGAATAGTCATAAAAATC
* *
555704 CCCATTCTTTTCAAGATTAAGCACCATAAACATAGTTTTCTTATTAGGATACACGATATTGATGT
194 CCCATTCTTTTCAAGATTAAGCACCATAAACATAGTATTCTCATTAGGATACACGATATTGATGT
* * * * *
555769 TTTGGTTTCACAAGAAAGGCATTTTTCCTA-AAACTTTTTGCAAAGTCTAAAATTCGTGCCTCAA
259 TTTGGTTTCGCAAGAAAGGCATTTTTCCTACCAA-TTTTTGTAAAGTCT-AAGTTCATGCCTCAA
* *
555833 ATGAGACAAACATAGATTCTACTAATGATCTTCGCTCATTTTGTGATTAGGCACTATAAACAAAT
322 ATGAGACAAACATGGATTCTACTAATGATCTTCGCTCATTTTGTGATTAGGCACTATAAACACAT
** * * *
555898 TCTCTTTGTTAGGACAAATGATGTTGATGATTTTCTTTTGCATGGAAATCTTTTCATTACCCTAT
387 TCTCTTCATTAGGACAAATGATGTTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTGCCCTAT
*
555963 TTTCCTTTAAATCAAAGTTTATAC
452 TTTCCTTTAAATCAAAGTTCATAC
** * * *
555987 CTTAAATAAGACAAGCATCAATTCTTGTAACAGTCTCGATTCTTTAAAAGTTTGGGAACCAAAAA
1 CTTAAATAAGACAAGCATCAATTCTCATAACAGTCTCCATTCTTTTAAAGATTGGGAACCAAAAA
* * * * * * *
556052 CACATTCCTTTCTTTAGGATAAAAGACATCGATGCTTTGGTGTCGCAAGAAAAGCTTTTCATTCC
66 CACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTCC
** *
556117 ACTGTTTTTTATAGAATCAAAGTT
131 ACCATTTTTGATAGAATCAAAGTT
556141 CGTCCCTCAA
Statistics
Matches: 937, Mismatches: 147, Indels: 37
0.84 0.13 0.03
Matches are distributed among these distances:
469 29 0.03
470 175 0.19
471 10 0.01
472 160 0.17
473 12 0.01
474 171 0.18
475 12 0.01
476 74 0.08
477 290 0.31
478 4 0.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (475 bp):
CTTAAATAAGACAAGCATCAATTCTCATAACAGTCTCCATTCTTTTAAAGATTGGGAACCAAAAA
CACATTCCCTTCATTAGGATACATGACATTGATGCTTTGGTGTCACAAGAAAAGCTTTTCTTTCC
ACCATTTTTGATAGAATCAAAGTTTGTCTCTAAAATAAGACAACATGAATAGTCATAAAAATCCC
CATTCTTTTCAAGATTAAGCACCATAAACATAGTATTCTCATTAGGATACACGATATTGATGTTT
TGGTTTCGCAAGAAAGGCATTTTTCCTACCAATTTTTGTAAAGTCTAAGTTCATGCCTCAAATGA
GACAAACATGGATTCTACTAATGATCTTCGCTCATTTTGTGATTAGGCACTATAAACACATTCTC
TTCATTAGGACAAATGATGTTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTGCCCTATTTTC
CTTTAAATCAAAGTTCATAC
Found at i:557088 original size:159 final size:159
Alignment explanation
Indices: 556925--557230 Score: 393
Period size: 159 Copynumber: 1.9 Consensus size: 159
556915 TTCGTGCCTC
* * * *** * * *
556925 AAATGAGATAAACATAGATTCTAGTAATGATCTTTTTTCATTTTGTGATTAGGTACTCAT-ATCA
1 AAATGAGACAAACATAGATTCTACTAATAATCTTCACTCATTCTGTGATTAGGCACT-ATAAACA
* * * * *
556989 CATTCTCCTTATTAGGATAAA-GGATACTAATGATTTTCTTTTGCATGGAAATCTTTTCTTTA-C
65 CATTCTCCTCATTAGGATAAATGGA-ACTAATAATTTTCTATTACAAGGAAATCTTTTCTTTATC
557052 CTTATTTTCCATAAAATCAAAATTCATTCCTT
129 C-TATTTTCCATAAAATCAAAATTCATTCCTT
*
557084 AAATGAGACAAACATGGATTCTACTAATAATCTTCACTCATTCTGTGATTAGGCACTATAAACAC
1 AAATGAGACAAACATAGATTCTACTAATAATCTTCACTCATTCTGTGATTAGGCACTATAAACAC
* * *
557149 ATTCTCCTCATTAGGATAAATGGAATTGATAATTTTCTATTACAAGGAGATCTTTTCTTTATCCT
66 ATTCTCCTCATTAGGATAAATGGAACTAATAATTTTCTATTACAAGGAAATCTTTTCTTTATCCT
*
557214 ATTTTCCTTAAAATCAA
131 ATTTTCCATAAAATCAA
557231 TGTTCATCCT
Statistics
Matches: 125, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
158 2 0.02
159 118 0.94
160 5 0.04
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (159 bp):
AAATGAGACAAACATAGATTCTACTAATAATCTTCACTCATTCTGTGATTAGGCACTATAAACAC
ATTCTCCTCATTAGGATAAATGGAACTAATAATTTTCTATTACAAGGAAATCTTTTCTTTATCCT
ATTTTCCATAAAATCAAAATTCATTCCTT
Found at i:557847 original size:15 final size:15
Alignment explanation
Indices: 557827--557871 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
557817 ATTTCGCCAA
557827 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
557842 ATCCACCACCTAATA
1 ATCCACCACAAAATC
*
557857 ACCCACCACAAAATC
1 ATCCACCACAAAATC
557872 GTTGATACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.13
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:565141 original size:26 final size:26
Alignment explanation
Indices: 565090--565162 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
565080 AAAAAAATGG
*
565090 TTGTCAAAAAAT-TATCGTCAAGAACTT
1 TTGTCAAGAAATGT-TCGTCAAGAAC-T
565117 TTGTCAAG-AATGTTCGTC-AGAAACT
1 TTGTCAAGAAATGTTCGTCAAG-AACT
*
565142 TTGTCAAGAAATTTTCGTCAA
1 TTGTCAAGAAATGTTCGTCAA
565163 TATGACCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 11 0.28
26 20 0.50
27 9 0.22
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (26 bp):
TTGTCAAGAAATGTTCGTCAAGAACT
Found at i:565219 original size:28 final size:27
Alignment explanation
Indices: 565179--565243 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 27
565169 CTTTTTTTCA
565179 AAAGCCCACAAGTTAATGGCACCCCTT
1 AAAGCCCACAAGTTAATGGCACCCCTT
* * *
565206 CAAAGCCCATAAGTTAGTGGTACCCCTT
1 -AAAGCCCACAAGTTAATGGCACCCCTT
565234 AAAGCCCACA
1 AAAGCCCACA
565244 CAAGTCGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAGCCCACAAGTTAATGGCACCCCTT
Found at i:565299 original size:28 final size:27
Alignment explanation
Indices: 565264--565602 Score: 345
Period size: 28 Copynumber: 12.0 Consensus size: 27
565254 GTAATCTCTC
565264 TCAAAGCCCACAAGTCAGTGGCATCCTT
1 TCAAAGCCCACAAGTCAGTGGCA-CCTT
*
565292 TCAAAGCCCACAAGTTAGTGGCACCTT
1 TCAAAGCCCACAAGTCAGTGGCACCTT
* * * *
565319 CTCAAAGCCCATAAGTCAGTGGTATCTCC
1 -TCAAAGCCCACAAGTCAGTGGCACCT-T
*
565348 TCAAAGCCCACAAGTCAGTGGCACTTTT
1 TCAAAGCCCACAAGTCAGTGGCAC-CTT
* * * *
565376 TTAAAACCCACAAGTCTGTGGTACCTT
1 TCAAAGCCCACAAGTCAGTGGCACCTT
* *
565403 CTCAAAGCCCACATGTCAGTAGCATCCTT
1 -TCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
565432 TCAAAGCCCACAAGTCAGTGGTACTATT
1 TCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
565460 TCAAAACCCATAAGTCAGTGGCACCTT
1 TCAAAGCCCACAAGTCAGTGGCACCTT
*
565487 TCAAAGCCCACAAGTCAGTAGCACCCCTT
1 TCAAAGCCCACAAGTCAGTGGCA--CCTT
* *
565516 TCAAAGTCCACAAGTTAGTGGCACCTCTT
1 TCAAAGCCCACAAGTCAGTGGCA-C-CTT
* *
565545 TCAAAGCCCACAAGTCAGTAGCATTCTT
1 TCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
565573 TCAAAGCCTACACAAGTCGGTGGCAACTT
1 TCAAAGCC--CACAAGTCAGTGGCACCTT
565602 T
1 T
565603 TTGTAAAGCC
Statistics
Matches: 256, Mismatches: 44, Indels: 21
0.80 0.14 0.07
Matches are distributed among these distances:
27 29 0.11
28 158 0.62
29 56 0.22
30 13 0.05
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (27 bp):
TCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:565335 original size:56 final size:56
Alignment explanation
Indices: 565174--565589 Score: 337
Period size: 56 Copynumber: 7.3 Consensus size: 56
565164 ATGACCTTTT
* * * * *
565174 TTTCAAAAGCCCACAAGTTAATGGCACC-CCTTCAAAGCCCATAAGTTAGTGGTACCC
1 TTTC-AAAGCCCACAAGTTAGTGGCACCTTC-TCAAAGCCCACAAGTCAGTGGTATCC
* * * *
565231 CTT-AAAGCCCACACAAGTCGATAGT--AATCTCTCTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAG-CC-CACAAGT---TAGTGGCACCT-TCTCAAAGCCCACAAGTCAGTGGTATCC
*
565290 TTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCATAAGTCAGTGGTAT-C
1 TTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTATCC
* * * * * * *
565345 TCCTCAAAGCCCACAAGTCAGTGGCACTTTTTTAAAACCCACAAGTCTGTGGTA-CC
1 T-TTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTATCC
* * * *
565401 TTCTCAAAGCCCACATGTCAGTAGCATCCTT-TCAAAGCCCACAAGTCAGTGGTA-CTA
1 TT-TCAAAGCCCACAAGTTAGTGGCA-CCTTCTCAAAGCCCACAAGTCAGTGGTATC-C
* * * * * *
565458 TTTCAAAACCCATAAGTCAGTGGCACCTT-TCAAAGCCCACAAGTCAGTAGCACCCC
1 TTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTA-TCC
* * * * *
565514 TTTCAAAGTCCACAAGTTAGTGGCACCTCTTTCAAAGCCCACAAGTCAGTAGCATTC
1 TTTCAAAGCCCACAAGTTAGTGGCACCT-TCTCAAAGCCCACAAGTCAGTGGTATCC
565571 TTTCAAAGCCTACACAAGT
1 TTTCAAAGCC--CACAAGT
565590 CGGTGGCAAC
Statistics
Matches: 294, Mismatches: 44, Indels: 40
0.78 0.12 0.11
Matches are distributed among these distances:
55 35 0.12
56 157 0.53
57 29 0.10
58 32 0.11
59 33 0.11
60 8 0.03
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (56 bp):
TTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTATCC
Found at i:565386 original size:84 final size:85
Alignment explanation
Indices: 565179--565590 Score: 390
Period size: 84 Copynumber: 4.8 Consensus size: 85
565169 CTTTTTTTCA
* * * * * * * * *
565179 AAAGCCCACAAGTTAATGGCACCCCTTCAAAGCCCATAAGTTAGTGGTACC-CCTTAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGTTAGTGGCACCTTCTCAAAG-CC-C
*
565243 ACAAGTC-GATAGTAATCTCTCTC
64 ACAAGTCAG-TAG-CATCTCTCTC
*
565266 AAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACT-CTTTCAAAACCCACAAGTTAGTGGCACCTTCTCAAAGCCCA
* * *
565330 TAAGTCAGTGGTATCTC-CTC
65 CAAGTCAGTAGCATCTCTCTC
* * *
565350 AAAGCCCACAAGTCAGTGGCACTTTTTTAAAACCCACAAGTCT-GTGGTACCTTCTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGT-TAGTGGCACCTTCTCAAAGCCCA
* *
565414 CATGTCAGTAGCATC-CTTTC
65 CAAGTCAGTAGCATCTCTCTC
* * * *
565434 AAAGCCCACAAGTCAGTGGTACTATTTCAAAACCCATAAGTCAGTGGCACCTT-TCAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGTTAGTGGCACCTTCTCAAAGCCCAC
* * *
565498 AAGTCAGTAGCACCCCTTTC
66 AAGTCAGTAGCATCTCTCTC
* * * * * *
565518 AAAGTCCACAAGTTAGTGGCACCTCTTTCAAAGCCCACAAGTCAGTAGCATTCTT-TCAAAGCCT
1 AAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAACCCACAAGTTAGTGGCA-CCTTCTCAAAGCC-
565582 ACACAAGTC
63 -CACAAGTC
565591 GGTGGCAACT
Statistics
Matches: 277, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
83 24 0.09
84 141 0.51
85 31 0.11
86 20 0.07
87 47 0.17
88 14 0.05
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (85 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTCAAAACCCACAAGTTAGTGGCACCTTCTCAAAGCCCAC
AAGTCAGTAGCATCTCTCTC
Found at i:566660 original size:20 final size:20
Alignment explanation
Indices: 566635--566711 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
566625 TTTTACCTAG
*
566635 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * *
566655 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
566675 ATATATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
566695 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
566712 GTTCTTTTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:568915 original size:161 final size:161
Alignment explanation
Indices: 568663--568975 Score: 403
Period size: 161 Copynumber: 1.9 Consensus size: 161
568653 GGATACTCTA
* * * ** *
568663 ACCTTATTCTAATGAAAATTCAAATTTTCCTTTGCATAATTTTGACTTTGGGGAAACTTCATCCT
1 ACCTTATTCTAATGAAAATTCAAATTTTCCTTCGCATAATTTTAACCTTAAGGAAACTCCATCCT
** ** *
568728 TGCTATTCTAAGGGGATACACCAACCC-GTTCTAAAAAAAAATCAAATTTTTCCTTGTATAATTT
66 CACTATTCTAAGAAGATACACCAACCCTGTTCT-AAAAAAAATCAAATTTTTCCTCGTATAATTT
*
568792 CGTCCTTGGGGAAACTCCATCCCTACCATTCC
130 CGTCATTGGGGAAACTCCATCCCTACCATTCC
* * * *
568824 ACCTTGTTCTAATGAAAATTCAAGTTTTTCTTCGCATAATTTTAACCTTAAGGAAGCTCCATCCT
1 ACCTTATTCTAATGAAAATTCAAATTTTCCTTCGCATAATTTTAACCTTAAGGAAACTCCATCCT
* * * * * * *
568889 CATTATTCTGAGAAGATACTCCAACCCTGTTCTAACAAAATTTAAATTTTTCCTCGTATAATTTT
66 CACTATTCTAAGAAGATACACCAACCCTGTTCTAAAAAAAATCAAATTTTTCCTCGTATAATTTC
568954 GTCATTGGGGAAACTCCATCCC
131 GTCATTGGGGAAACTCCATCCC
568976 CATTTCTCTA
Statistics
Matches: 128, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
161 123 0.96
162 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (161 bp):
ACCTTATTCTAATGAAAATTCAAATTTTCCTTCGCATAATTTTAACCTTAAGGAAACTCCATCCT
CACTATTCTAAGAAGATACACCAACCCTGTTCTAAAAAAAATCAAATTTTTCCTCGTATAATTTC
GTCATTGGGGAAACTCCATCCCTACCATTCC
Found at i:569062 original size:88 final size:87
Alignment explanation
Indices: 568859--569089 Score: 232
Period size: 88 Copynumber: 2.6 Consensus size: 87
568849 TTTTCTTCGC
* * * * * ** ** **
568859 ATAATTTTAACCTTAAGGAAGCTCCATCCTCATTATTCTGAGAAGATACTCCAACCCTGTTCTAA
1 ATAATTTTATCATTAGGGAAACTCCATCCCCATTATTCCAAGGGGATACTCCAACCCCATTCTAA
* * *
568924 CAAAATTTAAATTTTTCCTCGT
66 CAAAATTCAAAATTTTCCTCAT
* * * *
568946 ATAATTTTGTCATTGGGGAAACTCCATCCCCATT-TCTCTAAGGGGATACTTCAACCCCATTCTA
1 ATAATTTTATCATTAGGGAAACTCCATCCCCATTAT-TCCAAGGGGATACTCCAACCCCATTCTA
*
569010 ACAAAAATTCAAAATTTTCTTTCAT
65 AC-AAAATTCAAAATTTTC-CTCAT
* *
569035 ATAA-TTTATCCTTAGGGAAACTTCATCCCCATTATTCCAAGGGGATACTCCAACC
1 ATAATTTTATCATTAGGGAAACTCCATCCCCATTATTCCAAGGGGATACTCCAACC
569090 TCGTTTTTCA
Statistics
Matches: 117, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
86 1 0.01
87 51 0.44
88 57 0.49
89 8 0.07
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (87 bp):
ATAATTTTATCATTAGGGAAACTCCATCCCCATTATTCCAAGGGGATACTCCAACCCCATTCTAA
CAAAATTCAAAATTTTCCTCAT
Found at i:570837 original size:16 final size:16
Alignment explanation
Indices: 570798--570841 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
570788 TTAAATTTAT
570798 AATTAAATAAATTTAAA
1 AATTAAA-AAATTTAAA
* *
570815 ATTTTAAAAATTTTAAA
1 A-ATTAAAAAATTTAAA
570832 AATTAAAAAA
1 AATTAAAAAA
570842 CAATTATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTAAAAAATTTAAA
Found at i:570901 original size:147 final size:150
Alignment explanation
Indices: 570693--570965 Score: 444
Period size: 147 Copynumber: 1.8 Consensus size: 150
570683 CTCGATCCTT
**
570693 AACAATTATCATAAATTATTCATATCTTTTTATATGTACTACGATTAATATTCAATAACTTAAAT
1 AACAATTATCATAAATTATTCATATCTTTTTATATGTACTAAAATTAATATTCAATAACTTAAAT
570758 CTAAACAATTATCATAAATATAATTTAAAATTAAATTT-ATAATTAAAT-AAATT-TAAAATTTT
66 CTAAACAATTATCATAAATATAATTTAAAATTAAATTTAATAATTAAATAAAATTATAAAATTTT
570820 AAAAATTTTAAAAATTAAAA
131 AAAAATTTTAAAAATTAAAA
* * * *
570840 AACAATTATCATAAATTGTTCATCTCTTTTTATATGTACTAAAATTCATATTCAATTACTTAAAT
1 AACAATTATCATAAATTATTCATATCTTTTTATATGTACTAAAATTAATATTCAATAACTTAAAT
* * *
570905 CTAAAGAATTATCATAAATATAATTTAATATTAATTTTAATAATTAAATAAAATTATAAAA
66 CTAAACAATTATCATAAATATAATTTAAAATTAAATTTAATAATTAAATAAAATTATAAAA
570966 AAAACTTAAT
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
147 94 0.82
148 10 0.09
149 5 0.04
150 5 0.04
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (150 bp):
AACAATTATCATAAATTATTCATATCTTTTTATATGTACTAAAATTAATATTCAATAACTTAAAT
CTAAACAATTATCATAAATATAATTTAAAATTAAATTTAATAATTAAATAAAATTATAAAATTTT
AAAAATTTTAAAAATTAAAA
Found at i:571525 original size:33 final size:33
Alignment explanation
Indices: 571479--571574 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
571469 CAACCAGATG
571479 TATCGATACATTATGCTTTGTATCGATACATTA
1 TATCGATACATTATGCTTTGTATCGATACATTA
* * *
571512 TATCGATAAATTATGCTTTGTATGGATACATTG
1 TATCGATACATTATGCTTTGTATCGATACATTA
*
571545 TATCGATACATGT-T-CATTGTATCGATACAT
1 TATCGATACAT-TATGCTTTGTATCGATACAT
571575 GGACAATTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 14 0.25
33 41 0.73
34 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TATCGATACATTATGCTTTGTATCGATACATTA
Found at i:571585 original size:20 final size:19
Alignment explanation
Indices: 571539--571595 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
571529 TTGTATGGAT
*
571539 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
571558 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
571577 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
571596 AAATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:571668 original size:33 final size:33
Alignment explanation
Indices: 571624--571692 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
571614 CTACCACTGT
*
571624 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
* *
571657 TTGTATTGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
571690 TTG
1 TTG
571693 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:573952 original size:20 final size:20
Alignment explanation
Indices: 573906--573953 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
573896 AGATGATATT
573906 AAAAAATTAGATAATGAAAA
1 AAAAAATTAGATAATGAAAA
* *
573926 AATAAATTAGCTAA-GAAAA
1 AAAAAATTAGATAATGAAAA
573945 ACAAAAATT
1 A-AAAAATT
573954 TGCATGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAAAATTAGATAATGAAAA
Found at i:579132 original size:22 final size:22
Alignment explanation
Indices: 579107--579148 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
579097 TTTTTAAAGA
*
579107 TTTGACAAAAGGTGAGAAATGC
1 TTTGACAAAAGGGGAGAAATGC
*
579129 TTTGATAAAAGGGGAGAAAT
1 TTTGACAAAAGGGGAGAAAT
579149 ATGCTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (22 bp):
TTTGACAAAAGGGGAGAAATGC
Found at i:579753 original size:19 final size:20
Alignment explanation
Indices: 579729--579782 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
579719 ACATCATCCT
**
579729 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
579748 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
579768 TTGTATCGATACATG
1 TTGTATCGATACATG
579783 AACTTAGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:579848 original size:13 final size:13
Alignment explanation
Indices: 579827--579879 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
579817 CAATACATGG
*
579827 TACAATGTATCGA
1 TACATTGTATCGA
579840 TACATTGTATCGA
1 TACATTGTATCGA
579853 TACA-TGT-T-G-
1 TACATTGTATCGA
579862 -A-ATTGTATCGA
1 TACATTGTATCGA
579873 TACATTG
1 TACATTG
579880 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 4 0.12
9 1 0.03
10 2 0.06
11 1 0.03
12 4 0.12
13 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:579856 original size:33 final size:33
Alignment explanation
Indices: 579811--579879 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
579801 CTACCACTAT
579811 TTGTATCAATACATGGT-ACAATGTATCGATACA
1 TTGTATCAATACATGGTGA-AATGTATCGATACA
* * *
579844 TTGTATCGATACATGTTGAATTGTATCGATACA
1 TTGTATCAATACATGGTGAAATGTATCGATACA
579877 TTG
1 TTG
579880 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCAATACATGGTGAAATGTATCGATACA
Found at i:584222 original size:51 final size:51
Alignment explanation
Indices: 584162--584281 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 51
584152 TCAAAAATAA
* * *
584162 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAAAAATAAGGT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTTAAAAATAAAGT
* * **
584213 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTTAAAAATAAAGT
584264 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
584282 TCAGAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTTAAAAATAAAGT
Found at i:584298 original size:28 final size:28
Alignment explanation
Indices: 584264--584365 Score: 170
Period size: 28 Copynumber: 3.6 Consensus size: 28
584254 GAAATAAAGT
* *
584264 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTAGAGTATCCCC-GATGAAATAA
584292 CGGGGTTAGAGTATCCCCGATGAAATAA
1 CGGGGTTAGAGTATCCCCGATGAAATAA
584320 CGGGGTTAGAGTATCCCCGATGAAATAA
1 CGGGGTTAGAGTATCCCCGATGAAATAA
584348 CGGGGTTAGAGTATCCCC
1 CGGGGTTAGAGTATCCCC
584366 AATTATGAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
27 1 0.01
28 70 0.99
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (28 bp):
CGGGGTTAGAGTATCCCCGATGAAATAA
Found at i:584377 original size:186 final size:186
Alignment explanation
Indices: 584156--584498 Score: 445
Period size: 186 Copynumber: 1.8 Consensus size: 186
584146 ATCCTCTCAA
* * * ** * * *
584156 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAAAAATAAGGTCGGGGTTG
1 AAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCGATGCTTTAAAAATAAAATCAGAGTTA
* * * **
584221 GAGTATCCCCGATTGT-GAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCA
66 AAGTATCCCCGATTATGGA-AAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCA
* *
584285 GAAATAACGGGGTTAGAGTATCCCCGATGAAATAACGGGGTTAGAGTATCCCCGATG
130 GAAATAACGGGATTAAAGTATCCCCGATGAAATAACGGGGTTAGAGTATCCCCGATG
* * **
584342 AAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAATCAGAGTTA
1 AAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCGATGCTTTAAAAATAAAATCAGAGTTA
** * * **
584407 AAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTTGG
66 AAGTATCCCCGATTATGGAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAG
584472 AAATAACGGGATTAAAGTATCCCCGAT
131 AAATAACGGGATTAAAGTATCCCCGAT
584499 AGTGGACAAT
Statistics
Matches: 131, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
186 129 0.98
187 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (186 bp):
AAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCGATGCTTTAAAAATAAAATCAGAGTTA
AAGTATCCCCGATTATGGAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAG
AAATAACGGGATTAAAGTATCCCCGATGAAATAACGGGGTTAGAGTATCCCCGATG
Found at i:584463 original size:51 final size:51
Alignment explanation
Indices: 584348--584466 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
584338 GATGAAATAA
* *
584348 CGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAAT
1 CGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAAC
* * * * *
584399 CAGAGTTAAAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAAC
1 CGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAAC
*
584450 CGGGGTTGGAGTATCCC
1 CGGGGTTAGAGTATCCC
584467 TTTGGAAATA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (51 bp):
CGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAAC
Found at i:584491 original size:130 final size:130
Alignment explanation
Indices: 584341--584657 Score: 404
Period size: 130 Copynumber: 2.4 Consensus size: 130
584331 TATCCCCGAT
* * * *
584341 GAAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATTGATGTTTTGGAAATAAAATCAGAGTT
1 GAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACCAGAGTG
* * * *
584406 AAAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCC-CTTT
66 AAAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCTC-TC
584470 G
130 G
* * * * * * * *
584471 GAAATAACGGGATTAAAGTATCCCCGA-TAGTGGACAATCGGTGTTTTGAAAATAAAACCGGGGT
1 GAAATAACGGGGTTAGAGTATCCCCGATTA-TGAAAAATTGGTGTTTTGGAAATAAAACCAGAGT
** * *
584535 GGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAACTGAGGTTGGAGTATCCTCTC
65 GAAAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCTCTC
584600 G
130 G
* *
584601 GAAATAACGGGGTTAGAGTATCCCCGATTATAAAAAATTGGTGTTTTGGAAAAAAAA
1 GAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAA
584658 ACATGAATGA
Statistics
Matches: 156, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
129 2 0.01
130 151 0.97
131 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (130 bp):
GAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACCAGAGTG
AAAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCTCTCG
Found at i:587085 original size:20 final size:20
Alignment explanation
Indices: 587060--587114 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
587050 GTAAACCCAG
*
587060 AATGTATCGATCCAATGAAC
1 AATGTATCGATACAATGAAC
*
587080 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATGAAC
587100 AATGTATCGATACAA
1 AATGTATCGATACAA
587115 ATTGTGAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:587810 original size:41 final size:40
Alignment explanation
Indices: 587682--587810 Score: 118
Period size: 41 Copynumber: 3.1 Consensus size: 40
587672 TTAGGAGGGG
* ** *
587682 AAAGAAATGGAAGAGGTGTCCCACTTTTTGAGGACAAAGG-A
1 AAAGAAAAGGAA-A-GTGTCCTGCTTCTTGAGGACAAAGGAA
* * * *
587723 AAAGAGAATGAAA-TAGGTCTTGCTCCTTGAGGACAAAGGAA
1 AAAGAAAAGGAAAGT--GTCCTGCTTCTTGAGGACAAAGGAA
587764 GAAAGAAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAA
1 -AAAGAAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAG-GAA
587806 AAAGA
1 AAAGA
587811 GTACGTCCTG
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
38 1 0.01
40 19 0.27
41 35 0.50
42 14 0.20
43 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.19
Consensus pattern (40 bp):
AAAGAAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGGAA
Found at i:587917 original size:42 final size:42
Alignment explanation
Indices: 587810--587922 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 42
587800 AGTGAAAAAG
*
587810 AGTACGTCCTGCTTTTCAAGGACAAAGAAAAAAAGGAAAACGAA
1 AGTACGTCCTGCTTTT-AAGGACAAA-AGAAAAAGGAAAACGAA
* * * *
587854 A-TGCGTCATGCTATTTGAGGACAAAAGAAAAAGGAAAA-TAA
1 AGTACGTCCTGCT-TTTAAGGACAAAAGAAAAAGGAAAACGAA
*
587895 AGTACGTCCTACTCTTTAAGGACAAAAG
1 AGTACGTCCTGCT-TTTAAGGACAAAAG
587923 GGAAAAGAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.05
42 33 0.58
43 17 0.30
44 4 0.07
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.19
Consensus pattern (42 bp):
AGTACGTCCTGCTTTTAAGGACAAAAGAAAAAGGAAAACGAA
Found at i:587955 original size:45 final size:38
Alignment explanation
Indices: 587900--587994 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 38
587890 AATAAAGTAC
*
587900 GTCCTACTCTTTAAGGACAAAAGGGAAAAGAAGGGAATGAAGTGT
1 GTCCTGCTCTTTAAGGAC-AAA-GGAAAA-AA-GGAA--AAG-GT
*
587945 GTCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAAAGGT
1 GTCCTGCTCTTTAAGGACAAAGGAAAAAAGGAAAAGGT
587983 GTCCTGCTCTTT
1 GTCCTGCTCTTT
587995 GAGGCCTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
38 14 0.29
39 3 0.06
41 4 0.08
42 2 0.04
43 6 0.12
44 3 0.06
45 16 0.33
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (38 bp):
GTCCTGCTCTTTAAGGACAAAGGAAAAAAGGAAAAGGT
Found at i:587994 original size:38 final size:44
Alignment explanation
Indices: 587900--587998 Score: 129
Period size: 38 Copynumber: 2.4 Consensus size: 44
587890 AATAAAGTAC
* *
587900 GTCCTACTCTTTAAGGACAAAAGGGAAAAGAAGGGAATGAAGTGT
1 GTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAA-GAAGTGT
587945 GTCCTGCTCTTTGAGGAC-AAA-GGAAAA-AA-GGAA-AAG-GT
1 GTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAAGAAGTGT
587983 GTCCTGCTCTTTGAGG
1 GTCCTGCTCTTTGAGG
587999 CCTAAAAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
38 18 0.35
39 3 0.06
41 4 0.08
42 2 0.04
43 6 0.12
44 3 0.06
45 16 0.31
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.22
Consensus pattern (44 bp):
GTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAAGAAGTGT
Found at i:588041 original size:61 final size:60
Alignment explanation
Indices: 587970--588335 Score: 363
Period size: 61 Copynumber: 6.1 Consensus size: 60
587960 GACAAAGGAA
* * *
587970 AAAAGGAAAAGGTGTCCTGCTCTTTGAGGCCTAAAAAGTGCCACCAACTCGTGTGGGCTTT
1 AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * ** *
588031 GAAAAGAAAAGACGTCCTGCTCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
1 -AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * ** * * * *
588092 GCAAAGAGAAA-GCATCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAGTGGTCTTT
1 -AAAAGA-AAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
* **
588153 AAAAGGAGAAA-GCATCCCACTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAA-GA-AAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
*
588214 ----G-AAAGGCGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT
1 AAAAGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
588269 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAATACCACCAACTTGTGTGAGCTTT
1 AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTTGTGTGGGCTTT
588331 AAAAG
1 AAAAG
588336 GCATCCTACT
Statistics
Matches: 260, Mismatches: 31, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
54 3 0.01
55 45 0.17
56 1 0.00
60 4 0.02
61 173 0.67
62 34 0.13
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (60 bp):
AAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:588206 original size:122 final size:116
Alignment explanation
Indices: 587975--588356 Score: 446
Period size: 122 Copynumber: 3.2 Consensus size: 116
587965 AGGAAAAAAG
** * * **
587975 GAAAAGGTGTCCTGCTCTTTGAGGCCTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAA
1 GAAAAGGCATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAA
* * **
588039 AAGACGTCCTGCTCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT
65 AAG-CGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* * *
588092 GCAAAGAGAAAGCATCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTCGAGTGGTCTTTAAAA
1 G-AAA-AG---GCATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTCGTGTGGGCTTTAAAA
* **
588157 GGAGAAAGCATCCCACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
61 GGA-AAAGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* * * *
588214 G-AAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
1 GAAAAGGCATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAA
* *
588278 AGGCGTCCTGCTCTTTGAGGACTAGAAAAATACCACCAACTTGTGTGAGCTTT
66 A-GCGTCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTT
*
588331 -AAAAGGCATCCTACTTTTTGAGGACT
1 GAAAAGGCATCCTACTCTTTGAGGACT
588357 AAAGGGCGAA
Statistics
Matches: 224, Mismatches: 31, Indels: 20
0.81 0.11 0.07
Matches are distributed among these distances:
115 3 0.01
116 70 0.31
117 48 0.21
118 3 0.01
119 4 0.02
120 2 0.01
121 4 0.02
122 86 0.38
123 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (116 bp):
GAAAAGGCATCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAA
AGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:588245 original size:55 final size:55
Alignment explanation
Indices: 588172--588356 Score: 235
Period size: 55 Copynumber: 3.2 Consensus size: 55
588162 AAGCATCCCA
*
588172 CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
588227 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTG
1 CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTG
* * * * * *
588288 CTCTTTGAGGACTAGAAAAATACCACCAACTTGTGTGAGCTTTAAAAGGCATCCTA
1 CTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
*
588344 CTTTTTGAGGACT
1 CTCTTTGAGGACT
588357 AAAGGGCGAA
Statistics
Matches: 115, Mismatches: 8, Indels: 13
0.85 0.06 0.10
Matches are distributed among these distances:
55 41 0.36
56 22 0.19
60 1 0.01
61 25 0.22
62 26 0.23
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (55 bp):
CTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTG
Found at i:588629 original size:107 final size:108
Alignment explanation
Indices: 588370--588673 Score: 398
Period size: 107 Copynumber: 2.7 Consensus size: 108
588360 GGGCGAAAAG
*
588370 AGAGAGCGTCCTGCTCTTTGAGGACCGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAA
1 AGAG-GCGTCCTGCTCTTTGAGGACTGA-AAGTGCCACCAACTTGTGTGGGCTTT-----GA-AA
* *** *
588435 GGCGTCCTGCTCTTTGAGAACTGGGAAGTGCCACCAACTTGTGTGGGCTTTA
58 GGCGTCCTGCTCTTTGAGGACTAAAAAATGCCACC-ACTTGTGTGGGCTTTA
* *
588487 AGAGGCGTCCTGCTCTTTGAAGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
1 AGAGGCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
*
588552 TACTCTTTGAGGACTAAAAAATGCCA-C-CTTGTGTGGGCTTTGA
65 TGCTCTTTGAGGACTAAAAAATGCCACCACTTGTGTGGGCTTT-A
588595 A-AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
1 AGAGGCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
588659 TGCTCTTTGAGGACT
65 TGCTCTTTGAGGACT
588674 GAAGGGTGAA
Statistics
Matches: 172, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
106 4 0.02
107 84 0.49
108 2 0.01
109 1 0.01
110 29 0.17
111 2 0.01
116 44 0.26
117 6 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (108 bp):
AGAGGCGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCT
GCTCTTTGAGGACTAAAAAATGCCACCACTTGTGTGGGCTTTA
Found at i:588675 original size:55 final size:54
Alignment explanation
Indices: 588375--588676 Score: 396
Period size: 55 Copynumber: 5.4 Consensus size: 54
588365 AAAAGAGAGA
*
588375 GCGTCCTGCTCTTTGAGGACCGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGA-AAGTGCCACCAACTTGTGTGGGCTTT-----GA-AAG
* *
588436 GCGTCCTGCTCTTTGAGAACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-AAGAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AG
* *
588491 GCGTCCTGCTCTTTGAAGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * *
588546 GCGTCCTACTCTTTGAGGACTAAAAAATGCCA-C--CTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
588598 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAG
588653 GCGTCCTGCTCTTTGAGGACTGAA
1 GCGTCCTGCTCTTTGAGGACTGAA
588677 GGGTGAAAGG
Statistics
Matches: 220, Mismatches: 14, Indels: 20
0.87 0.06 0.08
Matches are distributed among these distances:
51 3 0.01
52 44 0.20
53 1 0.00
54 2 0.01
55 122 0.55
56 2 0.01
61 45 0.20
62 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (54 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:588725 original size:94 final size:96
Alignment explanation
Indices: 588598--588789 Score: 255
Period size: 94 Copynumber: 2.0 Consensus size: 96
588588 GCTTTGAAAG
* *
588598 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-G-AAAGGCGTCCTG
1 GCGTCCTGCTCCTTGAGGACTGAAAGGTCCCACCAACTTGTGTGGGCTTTAGAAAAGGCGTCCTG
* **
588661 CTCTTTGAGGACTGAAGGGTGAAAGGAGAGA
66 CTCTTTGAGGACTAAAAAGTGAAAGGAGAGA
*
588692 GCGTTCTGCTCCTTGAGGACT-AGAAGGTCCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCG
1 GCGTCCTGCTCCTTGAGGACTGA-AAGGTCCCACCAACTTGTGTGGGCTTT----AGAAAAGGCG
*
588756 TCTTGCTCTTTGAGGACTAAAAAGTGAAAGGAGA
61 TCCTGCTCTTTGAGGACTAAAAAGTGAAAGGAGA
588790 AAGTTTAGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
93 1 0.01
94 45 0.54
99 1 0.01
100 37 0.44
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (96 bp):
GCGTCCTGCTCCTTGAGGACTGAAAGGTCCCACCAACTTGTGTGGGCTTTAGAAAAGGCGTCCTG
CTCTTTGAGGACTAAAAAGTGAAAGGAGAGA
Found at i:589768 original size:1 final size:1
Alignment explanation
Indices: 589762--589809 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
589752 CTTTTCTCTC
* * * * *
589762 TTTTTTTCTTTTTTTATTTTTTTGTTTTTTTTCTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
589810 AAAAAATGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.04, G:0.04, T:0.90
Consensus pattern (1 bp):
T
Found at i:589776 original size:25 final size:25
Alignment explanation
Indices: 589748--589808 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
589738 AAGCAGGCTC
*
589748 TTTTCTTTTCTCT-CTTTTTTTCTTT
1 TTTTATTTT-TCTGCTTTTTTTCTTT
* *
589773 TTTTATTTTTTTGTTTTTTTTCTTT
1 TTTTATTTTTCTGCTTTTTTTCTTT
*
589798 TGTTTTTTTTT
1 T-TTTATTTTT
589809 TAAAAAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.07
25 20 0.67
26 8 0.27
ACGTcount: A:0.02, C:0.10, G:0.03, T:0.85
Consensus pattern (25 bp):
TTTTATTTTTCTGCTTTTTTTCTTT
Found at i:589781 original size:14 final size:13
Alignment explanation
Indices: 589762--589807 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
589752 CTTTTCTCTC
589762 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
* *
589775 TTATTTT-TTTGT
1 TTTTTTTCTTTTT
589787 TTTTTTTCTTTTGT
1 TTTTTTTCTTTT-T
589801 TTTTTTT
1 TTTTTTT
589808 TTAAAAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 9 0.33
14 8 0.30
ACGTcount: A:0.02, C:0.04, G:0.04, T:0.89
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:589809 original size:25 final size:25
Alignment explanation
Indices: 589762--589809 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
589752 CTTTTCTCTC
589762 TTTTTTTCTTTTTTTATTTTTTTGT
1 TTTTTTTCTTTTTTTATTTTTTTGT
589787 TTTTTTTCTTTTGTTT-TTTTTTT
1 TTTTTTTCTTTT-TTTATTTTTTT
589810 AAAAAATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.02, C:0.04, G:0.04, T:0.90
Consensus pattern (25 bp):
TTTTTTTCTTTTTTTATTTTTTTGT
Found at i:602388 original size:51 final size:51
Alignment explanation
Indices: 602293--602410 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
602283 AAAAATAACG
** * *
602293 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATGCTTTAAAAATAAGGCCA
1 GGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTTAAAAATAAAGCCA
* * ** * *
602344 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGTCG
1 GGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTTAAAAATAAAGCCA
602395 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
602411 TTAGAAATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATCAATACTTTAAAAATAAAGCCA
Found at i:602431 original size:28 final size:27
Alignment explanation
Indices: 602393--602467 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 27
602383 GAAATAAAGT
602393 CGGGGTTGGAGTATCCCC-TTAGAAATAA
1 CGGGGTTGGAGTATCCCCATT--AAATAA
*
602421 CGGGGTCGGAGTATCCCCGATTAAATAA
1 CGGGGTTGGAGTATCCCC-ATTAAATAA
*
602449 CGGGGTTAGAGTATCCCCA
1 CGGGGTTGGAGTATCCCCA
602468 ATTGTGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.02
28 39 0.93
30 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATTAAATAA
Found at i:602517 original size:51 final size:51
Alignment explanation
Indices: 602457--602565 Score: 166
Period size: 51 Copynumber: 2.1 Consensus size: 51
602447 AACGGGGTTA
*
602457 GAGTATCCCCAATTGTGAAAAATTGATGTTTT-GAAAATAAAATCAGAGTTG
1 GAGTATCCCCAATTATGAAAAATTGATGTTTTAG-AAATAAAATCAGAGTTG
* * *
602508 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTG
1 GAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAATCAGAGTTG
602559 GAGTATC
1 GAGTATC
602566 TCCTTGGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (51 bp):
GAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAATCAGAGTTG
Found at i:602559 original size:158 final size:158
Alignment explanation
Indices: 602285--602599 Score: 450
Period size: 158 Copynumber: 2.0 Consensus size: 158
602275 ATCCCCTCAA
* * ** *
602285 AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGCTTTAAAAATAAGGCCAGGGTTG
1 AAATAACGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGCTTTAAAAATAAAACCAGAGTTG
* * * *
602350 GAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTTAG
66 GAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTAG
* *
602415 AAATAACGGGGTCGGAGTATCCCCGATT
131 AAATAACAGGGTCAGAGTATCCCCGATT
* * *
602443 AAATAACGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGTTTTGAAAATAAAATCAGAGTTG
1 AAATAACGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGCTTTAAAAATAAAACCAGAGTTG
** * * *
602508 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTTGG
66 GAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTAG
*
602573 AAATAACAGGGTTAGAGTATCCCCGAT
131 AAATAACAGGGTCAGAGTATCCCCGAT
602600 GGTGGAAAAT
Statistics
Matches: 137, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 137 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (158 bp):
AAATAACGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGCTTTAAAAATAAAACCAGAGTTG
GAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTAG
AAATAACAGGGTCAGAGTATCCCCGATT
Found at i:602609 original size:130 final size:130
Alignment explanation
Indices: 602443--602752 Score: 449
Period size: 130 Copynumber: 2.4 Consensus size: 130
602433 ATCCCCGATT
*
602443 AAATAACGGGGTTAGAGTATCCCCAATTGTGAAAAATTGATGTTTTGAAAATAAAATCAGAGTTG
1 AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAATCAGAGTTG
* * * * *
602508 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTTGG
66 AAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTTAG
* * * ** * *
602573 AAATAACAGGGTTAGAGTATCCCCGATGGTGGAAAATCAATGTTTTGGAAATAAAATCAGGGTTG
1 AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAATCAGAGTTG
* * *
602638 AAGTATCCTCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTTAG
66 AAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTTAG
* * *
602703 AAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGAAA
1 AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAA
602753 GTTAAAACAT
Statistics
Matches: 155, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
130 155 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (130 bp):
AAATAACGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAATCAGAGTTG
AAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTTAG
Found at i:602643 original size:51 final size:50
Alignment explanation
Indices: 602577--602698 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 50
602567 CCTTGGAAAT
*
602577 AACAGGGTT-AGAGTATCCCCGATGGTGGAAAATCAATGTTTTGGAAATAA
1 AACAGGGTTGA-AGTATCCCCGATGGTGGAAAATCAATGTTTTAGAAATAA
* * **
602627 AATCAGGGTTGAAGTATCCTCGATTGTGGAAAATTGATGTTTTAGAAATAA
1 AA-CAGGGTTGAAGTATCCCCGATGGTGGAAAATCAATGTTTTAGAAATAA
* *
602678 AACCGAGGTTGGAGTATCCCC
1 AACAG-GGTTGAAGTATCCCC
602699 TTAGAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
50 4 0.07
51 56 0.92
52 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (50 bp):
AACAGGGTTGAAGTATCCCCGATGGTGGAAAATCAATGTTTTAGAAATAA
Found at i:605135 original size:20 final size:20
Alignment explanation
Indices: 605108--605162 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
605098 AAAATGCCTG
*
605108 AATGTATCGATACATTGCAA-
1 AATGTATCGATACAATG-AAC
* *
605128 ATTGTATCAATACAATGAAC
1 AATGTATCGATACAATGAAC
605148 AATGTATCGATACAA
1 AATGTATCGATACAA
605163 ATTGTGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:606339 original size:21 final size:22
Alignment explanation
Indices: 606298--606351 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
606288 TTTATTGTTC
606298 ATTAAT-TAAAAATTATTTAAAT
1 ATTAATATAAAAATTA-TTAAAT
606320 -TTAATATAAAAATGTA-TAAAT
1 ATTAATATAAAAAT-TATTAAAT
606341 ATTAATATAAA
1 ATTAATATAAA
606352 GAGCTTACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.34
22 17 0.59
23 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTAATATAAAAATTATTAAAT
Found at i:607114 original size:48 final size:48
Alignment explanation
Indices: 607020--607114 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
607010 ATTTTATTTA
* * * *
607020 TAATTAAATTATATTAATTAAGAGATAAAAATATAAAAGAATTGTTTC
1 TAATTAAATTAAATTAATTAAAAGATAAAAAGATAAAAGAAGTGTTTC
* *
607068 TAATTAAATTAAATTAATTAAAAGATAAATAAGA-AAGATAAGTGTTT
1 TAATTAAATTAAATTAATTAAAAGATAAA-AAGATAAAAGAAGTGTTT
607115 TTAAAGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 37 0.93
49 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (48 bp):
TAATTAAATTAAATTAATTAAAAGATAAAAAGATAAAAGAAGTGTTTC
Found at i:610049 original size:13 final size:13
Alignment explanation
Indices: 610031--610056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
610021 AATTTTTTTG
610031 TGTATCGATACAT
1 TGTATCGATACAT
610044 TGTATCGATACAT
1 TGTATCGATACAT
610057 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:610151 original size:20 final size:20
Alignment explanation
Indices: 610105--610181 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
610095 TTCCCAATGA
***
610105 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
610126 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
610146 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
610166 TGTGTATCGATACATT
1 CATGTATCGATACATT
610182 TAAGGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:612620 original size:13 final size:13
Alignment explanation
Indices: 612602--612639 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
612592 ATAATCCCCC
612602 TGTATCGATACAG
1 TGTATCGATACAG
*
612615 TGTATCGATACAT
1 TGTATCGATACAG
612628 TGTATCGATACA
1 TGTATCGATACA
612640 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:614741 original size:15 final size:15
Alignment explanation
Indices: 614721--614751 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
614711 ATTTCGTTTG
*
614721 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
614736 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
614751 G
1 G
614752 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:618828 original size:13 final size:13
Alignment explanation
Indices: 618810--618835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
618800 AATTTTTTTG
618810 TGTATCGATACAT
1 TGTATCGATACAT
618823 TGTATCGATACAT
1 TGTATCGATACAT
618836 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:618930 original size:20 final size:20
Alignment explanation
Indices: 618884--618960 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
618874 TTCCCAATGA
***
618884 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
618905 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
618925 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
618945 TGTGTATCGATACATT
1 CATGTATCGATACATT
618961 TAAGGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:619282 original size:26 final size:26
Alignment explanation
Indices: 619253--619308 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
619243 CTAGAATTTT
*
619253 TCTTGGGATGGATATAAGAAAATGAA
1 TCTTGGGATGGATATAAGAAAATAAA
619279 TCTTGGGATGGATATAAGAAAATAAA
1 TCTTGGGATGGATATAAGAAAATAAA
619305 TCTT
1 TCTT
619309 ACTCGGATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.30
Consensus pattern (26 bp):
TCTTGGGATGGATATAAGAAAATAAA
Found at i:620525 original size:35 final size:34
Alignment explanation
Indices: 620464--620545 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
620454 ATATCATCGA
* *
620464 TTCAGATCAAGTCTCAATGACTTTTGAAGCAAAT
1 TTCAGATCAAGTCTCAATGACCTTTGAAACAAAT
*
620498 TTCATGATCAAGTCTCTA-GAACCTTTGAAACAAAT
1 TTCA-GATCAAGTCTCAATG-ACCTTTGAAACAAAT
* *
620533 TTTAGACCAAGTC
1 TTCAGATCAAGTC
620546 ATTTAAAGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 13 0.32
35 28 0.68
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (34 bp):
TTCAGATCAAGTCTCAATGACCTTTGAAACAAAT
Found at i:621340 original size:13 final size:13
Alignment explanation
Indices: 621322--621347 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
621312 TACAGCAAGT
621322 ATGTATCGATACA
1 ATGTATCGATACA
621335 ATGTATCGATACA
1 ATGTATCGATACA
621348 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:623596 original size:21 final size:22
Alignment explanation
Indices: 623558--623604 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
623548 TTGCAAGTTG
* *
623558 AAATAAAGAAGTTGGCTAATAA
1 AAATAAAGAAGTTAGCTAAGAA
*
623580 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAGAA
623601 AAAT
1 AAAT
623605 GAAAACTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAAGAA
Found at i:625426 original size:15 final size:15
Alignment explanation
Indices: 625406--625436 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
625396 TAAAAATGTC
*
625406 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
625421 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
625436 C
1 C
625437 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:627532 original size:13 final size:13
Alignment explanation
Indices: 627514--627550 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
627504 ACATTTTTCT
627514 TTGTATCGATACA
1 TTGTATCGATACA
627527 TTGTATCGATACA
1 TTGTATCGATACA
627540 TTGTATCGATA
1 TTGTATCGATA
627551 TAGGGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:629343 original size:12 final size:12
Alignment explanation
Indices: 629326--629350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
629316 AAGGGGGAGA
629326 GAAAATAGATAT
1 GAAAATAGATAT
629338 GAAAATAGATAT
1 GAAAATAGATAT
629350 G
1 G
629351 TGCAAATAAA
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:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAAATAGATAT
Found at i:630130 original size:13 final size:13
Alignment explanation
Indices: 630112--630137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
630102 TACAGCAAGT
630112 ATGTATCGATACA
1 ATGTATCGATACA
630125 ATGTATCGATACA
1 ATGTATCGATACA
630138 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:647024 original size:3 final size:3
Alignment explanation
Indices: 647016--647043 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
647006 AATTTTGTGT
647016 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
647044 AGTTTGCATA
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:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:650711 original size:80 final size:80
Alignment explanation
Indices: 650621--650769 Score: 289
Period size: 80 Copynumber: 1.9 Consensus size: 80
650611 ACAAACTTAA
*
650621 GCAGAACATAATAGGATAAAAAAAATCCAAATTAGGAAGCTACATTCTAATATAAATTCCAAATA
1 GCAGAACATAATAGGATAAAAAAAATCCAAATTAAGAAGCTACATTCTAATATAAATTCCAAATA
650686 TCAATTAAAAATTAG
66 TCAATTAAAAATTAG
650701 GCAGAACATAATAGGATAAAAAAAATCCAAATTAAGAAGCTACATTCTAATATAAATTCCAAATA
1 GCAGAACATAATAGGATAAAAAAAATCCAAATTAAGAAGCTACATTCTAATATAAATTCCAAATA
650766 TCAA
66 TCAA
650770 ATATAACCAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.24
Consensus pattern (80 bp):
GCAGAACATAATAGGATAAAAAAAATCCAAATTAAGAAGCTACATTCTAATATAAATTCCAAATA
TCAATTAAAAATTAG
Found at i:651086 original size:28 final size:28
Alignment explanation
Indices: 651054--651110 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
651044 AGGCTTTCCT
651054 CCTTAAAATATCATTGCTCAAATTTTTC
1 CCTTAAAATATCATTGCTCAAATTTTTC
*
651082 CCTTAAAATATTATTGCTCAAATTTTTC
1 CCTTAAAATATCATTGCTCAAATTTTTC
651110 C
1 C
651111 GACACCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (28 bp):
CCTTAAAATATCATTGCTCAAATTTTTC
Found at i:655134 original size:3 final size:3
Alignment explanation
Indices: 655126--655153 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
655116 TACGTACATA
655126 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
655154 GTTGTTGTTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:655158 original size:3 final size:3
Alignment explanation
Indices: 655152--655179 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
655142 ATTATTATTA
655152 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
655180 GTAGATTGAG
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:655509 original size:18 final size:18
Alignment explanation
Indices: 655486--655525 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
655476 GGTAAAGTAT
655486 TAGCTGTATGCATGGTAA
1 TAGCTGTATGCATGGTAA
655504 TAGCTGTATGCATGGTAA
1 TAGCTGTATGCATGGTAA
655522 TAGC
1 TAGC
655526 ATGCAGCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (18 bp):
TAGCTGTATGCATGGTAA
Found at i:656244 original size:97 final size:100
Alignment explanation
Indices: 656120--656305 Score: 245
Period size: 97 Copynumber: 1.9 Consensus size: 100
656110 TATGAAATAT
* * * * *
656120 TTACGTGAATAAAGAATTCAGGTTTAATAAGAAAATTATTTC-ACGTTTTAA-TCTAA-AAAAA-
1 TTACGTGAAAAAAGAATTCAAGATTAATAAGAAAATTA-CTCAACATTTTAATTCTAATAAAAAT
*
656181 ATCATTAATTAATTAAGAACATAATGGTCCATACTA
65 ATCATTAATTAATTAAAAACATAATGGTCCATACTA
* * * *
656217 TTACGTTAAAAAAGAATTCAAGATTAATAATAAAATTACTCAATATTTTAATTTTAATAAAAATA
1 TTACGTGAAAAAAGAATTCAAGATTAATAAGAAAATTACTCAACATTTTAATTCTAATAAAAATA
656282 TCATTAATTAATTAAAAACATAAT
66 TCATTAATTAATTAAAAACATAAT
656306 AATCAATACT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
96 2 0.03
97 40 0.53
98 4 0.05
99 5 0.07
100 24 0.32
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (100 bp):
TTACGTGAAAAAAGAATTCAAGATTAATAAGAAAATTACTCAACATTTTAATTCTAATAAAAATA
TCATTAATTAATTAAAAACATAATGGTCCATACTA
Found at i:660011 original size:33 final size:32
Alignment explanation
Indices: 659974--660087 Score: 88
Period size: 32 Copynumber: 3.5 Consensus size: 32
659964 TATTAAATTT
* *
659974 GGGTTTGGGTTAGTTTCAGGTTCAGATTTTCTC
1 GGGTTTGGGTT-CTTTCAGGTTCAGACTTTCTC
* * * *
660007 GGGTTAGGGTTCTTTTAGGTTCGGGCTTTCTC
1 GGGTTTGGGTTCTTTCAGGTTCAGACTTTCTC
* * * *
660039 GGGTTTTGGCTT-TCTCGGGTTCAGGCTATT-TC
1 GGG-TTTGGGTTCTTTCAGGTTCAGACT-TTCTC
*
660071 GGGTTTGAGTTCTTTCA
1 GGGTTTGGGTTCTTTCA
660088 AGTTTGGGTT
Statistics
Matches: 62, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
31 6 0.10
32 38 0.61
33 18 0.29
ACGTcount: A:0.09, C:0.15, G:0.32, T:0.45
Consensus pattern (32 bp):
GGGTTTGGGTTCTTTCAGGTTCAGACTTTCTC
Found at i:660043 original size:16 final size:16
Alignment explanation
Indices: 660024--660075 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
660014 GGTTCTTTTA
*
660024 GGTTCGGGCTTTCTCG
1 GGTTCAGGCTTTCTCG
**
660040 GGTTTTGGCTTTCTCG
1 GGTTCAGGCTTTCTCG
660056 GGTTCAGGCTATT-TCG
1 GGTTCAGGCT-TTCTCG
660072 GGTT
1 GGTT
660076 TGAGTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 29 0.94
17 2 0.06
ACGTcount: A:0.04, C:0.19, G:0.35, T:0.42
Consensus pattern (16 bp):
GGTTCAGGCTTTCTCG
Found at i:663528 original size:20 final size:20
Alignment explanation
Indices: 663503--663559 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
663493 AACAAAAGAT
*
663503 AGAATGTATCGATACGTTGA
1 AGAATGTATCGATACATTGA
663523 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
663543 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
663560 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:666068 original size:21 final size:21
Alignment explanation
Indices: 666027--666110 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
666017 ACACTAAAAT
* **
666027 TAAAAA-TATATTAAATATTA
1 TAAAAATTATATGAAACGTTA
666047 TAAAAATTATATGAAGA-GTTA
1 TAAAAATTATATGAA-ACGTTA
* *
666068 TCAAAATTATATCAAACGTTA
1 TAAAAATTATATGAAACGTTA
* *
666089 AACAAAATTATATGGAACGTTA
1 TA-AAAATTATATGAAACGTTA
666111 AGCATTCTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.13
21 27 0.52
22 18 0.35
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (21 bp):
TAAAAATTATATGAAACGTTA
Found at i:666094 original size:22 final size:22
Alignment explanation
Indices: 666069--666111 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
666059 GAAGAGTTAT
666069 CAAAATTATATCAAACGTTAAA
1 CAAAATTATATCAAACGTTAAA
**
666091 CAAAATTATATGGAACGTTAA
1 CAAAATTATATCAAACGTTAA
666112 GCATTCTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (22 bp):
CAAAATTATATCAAACGTTAAA
Found at i:667167 original size:19 final size:18
Alignment explanation
Indices: 667142--667206 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
667132 ATTTCAACGA
667142 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
667160 TGTTGTATCGATAC---A-
1 T-TTGTATCGATACATAAG
667175 -TTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
667192 TTTTGTATCGATACA
1 -TTTGTATCGATACA
667207 ATGTACAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 12 0.30
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:667179 original size:32 final size:32
Alignment explanation
Indices: 667143--667211 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
667133 TTTCAACGAT
667143 TTGTATCGATACATAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCGATACA
*
667175 TTGTATCGATACATAAGTTTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCGATACA
*
667207 ATGTA
1 TTGTA
667212 CAGTTACGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (32 bp):
TTGTATCGATACATAAGTGTTGTATCGATACA
Found at i:667180 original size:13 final size:13
Alignment explanation
Indices: 667162--667188 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
667152 TACATAAGTG
667162 TTGTATCGATACA
1 TTGTATCGATACA
667175 TTGTATCGATACA
1 TTGTATCGATACA
667188 T
1 T
667189 AAGTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:667277 original size:13 final size:13
Alignment explanation
Indices: 667259--667283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
667249 ATTGCTCAAA
667259 TGTATCGATACAT
1 TGTATCGATACAT
667272 TGTATCGATACA
1 TGTATCGATACA
667284 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:667336 original size:52 final size:52
Alignment explanation
Indices: 667292--667420 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
667282 CACTGATCTT
667292 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
667344 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
667396 TGTATCGATACATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
667421 TCATATTTAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:681295 original size:20 final size:19
Alignment explanation
Indices: 681271--681325 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
681261 CGTCCTCTAC
681271 AAAAAAAAAAAACAAACAA
1 AAAAAAAAAAAACAAACAA
*
681290 ACAAAACAAAAAAA-AAAGAA
1 A-AAAA-AAAAAAACAAACAA
* *
681310 AAAAAACAACAACAAA
1 AAAAAAAAAAAACAAA
681326 AAGGGTTCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.17
19 8 0.27
20 10 0.33
21 7 0.23
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAACAAACAA
Done.