Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 184 of 335
Found at i:55395555 original size:13 final size:13
Alignment explanation
Indices: 55395534--55395570 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
55395524 TTTTATTATT
*
55395534 ATTTGGCCTATGA
1 ATTTAGCCTATGA
*
55395547 ATTTAGCCTATGT
1 ATTTAGCCTATGA
55395560 ATTTAGCCTAT
1 ATTTAGCCTAT
55395571 AAATAGACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (13 bp):
ATTTAGCCTATGA
Found at i:55396248 original size:2 final size:2
Alignment explanation
Indices: 55396241--55396271 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55396231 TAGTATAGAA
55396241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55396272 AGTTTGGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55396473 original size:15 final size:14
Alignment explanation
Indices: 55396450--55396498 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
55396440 CTAATTAATC
55396450 TTAAATTTTTGTTAA
1 TTAAATTTTT-TTAA
* *
55396465 TTAAGTTTTAATTAA
1 TTAAATTTT-TTTAA
55396480 TTAAATTTGTTTTAA
1 TTAAATTT-TTTTAA
55396495 TTAA
1 TTAA
55396499 GATTAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
TTAAATTTTTTTAA
Found at i:55396486 original size:30 final size:31
Alignment explanation
Indices: 55396441--55396499 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
55396431 AACCTTTGTC
55396441 TAATTAATCTTAAATTT-TTGTTAATTAAGTTT
1 TAATTAA-CTTAAATTTGTT-TTAATTAAGTTT
55396473 TAATTAA-TTAAATTTGTTTTAATTAAG
1 TAATTAACTTAAATTTGTTTTAATTAAG
55396500 ATTAAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 17 0.65
31 2 0.08
32 7 0.27
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (31 bp):
TAATTAACTTAAATTTGTTTTAATTAAGTTT
Found at i:55398289 original size:14 final size:14
Alignment explanation
Indices: 55398271--55398304 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55398261 AATATTTTTA
55398271 AAAAATAAAAAATTC
1 AAAAAT-AAAAATTC
*
55398286 AAAAATTAAAATTC
1 AAAAATAAAAATTC
55398300 AAAAA
1 AAAAA
55398305 GAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATAAAAATTC
Found at i:55399907 original size:21 final size:21
Alignment explanation
Indices: 55399864--55399913 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
55399854 AGCTTTTATC
* * *
55399864 TTAGGGTAACTTCTTGGTGAG
1 TTAGGGCAACTTCTTGATAAG
55399885 TTAGGGCAACTTCTTGATAAG
1 TTAGGGCAACTTCTTGATAAG
*
55399906 TTGGGGCA
1 TTAGGGCA
55399914 GCCACTTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (21 bp):
TTAGGGCAACTTCTTGATAAG
Found at i:55401486 original size:92 final size:91
Alignment explanation
Indices: 55401330--55401498 Score: 311
Period size: 92 Copynumber: 1.8 Consensus size: 91
55401320 CGCCCTAAGT
*
55401330 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
55401395 GAGTTCGGATGCCTAGTTACATTCAC
66 GAGTTCGGATGCCTAGTTACATTCAC
*
55401421 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55401486 CGAGTTCGGATGC
65 CGAGTTCGGATGC
55401499 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 27 0.36
92 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTCAC
Found at i:55401495 original size:46 final size:45
Alignment explanation
Indices: 55401325--55401494 Score: 220
Period size: 46 Copynumber: 3.7 Consensus size: 45
55401315 TAACCCGCCC
* *
55401325 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCA
* *
55401370 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCA
* *
55401416 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATCCA
55401462 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
55401495 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 34 0.32
46 62 0.58
47 2 0.02
48 4 0.04
49 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCA
Found at i:55401514 original size:46 final size:46
Alignment explanation
Indices: 55401327--55401514 Score: 151
Period size: 46 Copynumber: 4.1 Consensus size: 46
55401317 ACCCGCCCTA
* * * *
55401327 AGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T
*
55401371 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT
* * * * *
55401419 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT
55401464 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
55401510 AGTGA
1 AGTGA
55401515 CATGTCACTT
Statistics
Matches: 116, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
44 9 0.08
45 32 0.28
46 65 0.56
47 1 0.01
48 4 0.03
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:55401951 original size:30 final size:30
Alignment explanation
Indices: 55401917--55401976 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
55401907 ATTTAATACG
55401917 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
55401947 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
55401977 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:55408339 original size:46 final size:46
Alignment explanation
Indices: 55408272--55408397 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
55408262 AACCCGCCCC
* * * *
55408272 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
55408318 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
55408364 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55408398 TGCTCAACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:55408416 original size:46 final size:45
Alignment explanation
Indices: 55408274--55408416 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
55408264 CCCGCCCCTA
* * ** * *
55408274 AGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
*** *
55408319 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
55408365 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCT
55408412 AGTGA
1 AGTGA
55408417 CATGTCACTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
46 81 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCT
Found at i:55408853 original size:30 final size:30
Alignment explanation
Indices: 55408819--55408878 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
55408809 ATTTAATACG
55408819 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
55408849 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
55408879 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:55412736 original size:35 final size:35
Alignment explanation
Indices: 55412696--55412762 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
55412686 AGACAATAAT
55412696 AAAGAAATCCAAACCTGCCATACACTTTAATAACC
1 AAAGAAATCCAAACCTGCCATACACTTTAATAACC
* * *
55412731 AAAGAAATCTAAACTTGTCATACACTTTAATA
1 AAAGAAATCCAAACCTGCCATACACTTTAATA
55412763 CAAACAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.25
Consensus pattern (35 bp):
AAAGAAATCCAAACCTGCCATACACTTTAATAACC
Found at i:55414835 original size:80 final size:80
Alignment explanation
Indices: 55414751--55414899 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
55414741 TATGGTAACC
* * * *
55414751 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
55414815 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
55414831 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
55414896 CCGG
66 CCGG
55414900 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:55414841 original size:40 final size:38
Alignment explanation
Indices: 55414792--55414899 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
55414782 ATCACGATTT
*
55414792 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
55414832 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
55414872 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
55414900 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:55422941 original size:79 final size:80
Alignment explanation
Indices: 55422858--55423005 Score: 174
Period size: 80 Copynumber: 1.9 Consensus size: 80
55422848 TATGGTAACC
* * * *
55422858 CGCACCAAGGCCTAC-GGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
55422921 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
55422937 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
55423002 CCGG
66 CCGG
55423006 TTATAATTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
79 13 0.23
80 43 0.77
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:55422947 original size:40 final size:38
Alignment explanation
Indices: 55422898--55423005 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
55422888 ATCACGATTT
*
55422898 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
55422938 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
55422978 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
55423006 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:55430879 original size:40 final size:40
Alignment explanation
Indices: 55430834--55431000 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
55430824 CGGAATATAA
55430834 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
55430874 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
55430914 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55430954 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55430993 CCGGATAT
1 CCGGATAT
55431001 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55430984 original size:80 final size:79
Alignment explanation
Indices: 55430834--55431000 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
55430824 CGGAATATAA
* *
55430834 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
55430899 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
55430914 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
55430976 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
55430993 CCGGATAT
1 CCGGATAT
55431001 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:55431849 original size:17 final size:19
Alignment explanation
Indices: 55431826--55431871 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
55431816 AAGAAGCATG
55431826 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
55431844 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
55431862 AATCATGCTC
1 AATCATGCTC
55431872 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:55433200 original size:30 final size:30
Alignment explanation
Indices: 55433164--55433370 Score: 178
Period size: 30 Copynumber: 6.9 Consensus size: 30
55433154 AAGAAACATT
* *
55433164 ATCAGAATT-GGAACCAAAATGAGAATCAGA
1 ATCAGAATTAGGAA-CAGAATCAGAATCAGA
* *
55433194 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGGAACAGAATCAGAATCAGA
*
55433224 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATTAGGAACAGAATCAGAATCAGA
*
55433254 ATCAGAATTAGGTGACAGAATCAGAATCAGA
1 ATCAGAATTAGG-AACAGAATCAGAATCAGA
*
55433285 ATCAGTAA-CA-GAATCAGAATCAGAATCAGTA
1 ATCAG-AATTAGGAA-CAGAATCAGAATCAG-A
* * *
55433316 A-CAGAATCA-GAATCAGAATCAGTATTAGTA
1 ATCAGAATTAGGAA-CAGAATCAGAATCAG-A
*
55433346 A-CAGAATCA-GAATCAGAATCAGAAT
1 ATCAGAATTAGGAA-CAGAATCAGAAT
55433371 TACGTGACAG
Statistics
Matches: 157, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.03
30 122 0.78
31 29 0.18
32 2 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (30 bp):
ATCAGAATTAGGAACAGAATCAGAATCAGA
Found at i:55433305 original size:109 final size:109
Alignment explanation
Indices: 55433185--55433395 Score: 395
Period size: 109 Copynumber: 1.9 Consensus size: 109
55433175 AACCAAAATG
55433185 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
* *
55433250 CAGAATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGTAAC
66 CAGAATCAGAATTACGTGACAGAATCAGAACCAGAATCAGTAAC
*
55433294 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
55433359 CAGAATCAGAATTACGTGACAGAATCAGAACCAGAAT
66 CAGAATCAGAATTACGTGACAGAATCAGAACCAGAAT
55433396 GTGAATGCAA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 99 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (109 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
CAGAATCAGAATTACGTGACAGAATCAGAACCAGAATCAGTAAC
Found at i:55433388 original size:6 final size:6
Alignment explanation
Indices: 55433185--55433370 Score: 206
Period size: 6 Copynumber: 30.8 Consensus size: 6
55433175 AACCAAAATG
*
55433185 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
55433233 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
55433282 AGAATC AGTAA-C AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC
* *
55433330 AGAATC AGTATT AGTAA-C AGAATC AGAATC AGAATC AGAAT
1 AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAAT
55433371 TACGTGACAG
Statistics
Matches: 155, Mismatches: 10, Indels: 30
0.79 0.05 0.15
Matches are distributed among these distances:
5 12 0.08
6 131 0.85
7 10 0.06
8 2 0.01
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:55433569 original size:27 final size:26
Alignment explanation
Indices: 55433528--55433628 Score: 121
Period size: 27 Copynumber: 3.8 Consensus size: 26
55433518 CTCAGTTATT
* *
55433528 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
55433555 AGATATTGTGGCAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
*
55433581 AGATATTTGTGGCATAGCCACCAGAAAC
1 AGATA-TTGTGGCAGAGCCACCAG-AAC
* * *
55433609 ATATAATGTGGCAAAGCCAC
1 AGATATTGTGGCAGAGCCAC
55433629 TTAACAGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 7 0.11
27 52 0.79
28 7 0.11
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:55433814 original size:22 final size:22
Alignment explanation
Indices: 55433786--55433850 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
55433776 GCAAATACTT
*
55433786 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
55433808 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
55433830 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
55433851 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:55434333 original size:27 final size:27
Alignment explanation
Indices: 55434275--55434585 Score: 329
Period size: 27 Copynumber: 11.3 Consensus size: 27
55434265 AAGGGCAAAA
* * * *
55434275 TGGTAATTTTACCCCACA-AGGTATCT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
55434301 TGGTAATTCCACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
55434328 TAGTAATTCTACCTTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
*
55434355 TAGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
55434382 CGGTAATTCTACCCTACAGGGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
55434409 CGATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
55434436 CTGTATTTCTGTATTTCTACCCTATAGGGGTATTT
1 -TG-------GTAATTCTACCCTACAGGGGTATTT
* *
55434471 CGGTAATTCTACCCTACA-GGGTATTG
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
55434497 CGATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
55434524 CGGTAATTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
55434551 CGGTAATTCTACCCTGCAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
55434578 TGGTAATT
1 TGGTAATT
55434586 TTATTGATCG
Statistics
Matches: 244, Mismatches: 31, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
26 39 0.16
27 181 0.74
28 1 0.00
34 1 0.00
35 22 0.09
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAGGGGTATTT
Found at i:55434541 original size:115 final size:116
Alignment explanation
Indices: 55434334--55434560 Score: 357
Period size: 115 Copynumber: 2.0 Consensus size: 116
55434324 ATTTTAGTAA
* * * *
55434334 TTCTACCTTATAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTAC
1 TTCTACCCTATAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTAC
* * *
55434399 AGGGGTATTGCGATAATTCTACCCTACAGGGGTATTTCTGTATTTCTGTAT
66 AGGGGTATTGCGATAATTCTACCCTACAAGGGTATTTCGGTAATTCTGTAT
*
55434450 TTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACA-GGGTATTGCGATAATTCTACCCTAC
1 TTCTACCCTATAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTAC
* *
55434514 AGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCT
66 AGGGGTATTGCGATAATTCTACCCTACAAGGGTATTTCGGTAATTCT
55434561 ACCCTGCAGG
Statistics
Matches: 101, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
115 65 0.64
116 36 0.36
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (116 bp):
TTCTACCCTATAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTAC
AGGGGTATTGCGATAATTCTACCCTACAAGGGTATTTCGGTAATTCTGTAT
Found at i:55434571 original size:142 final size:143
Alignment explanation
Indices: 55434311--55434577 Score: 412
Period size: 142 Copynumber: 1.9 Consensus size: 143
55434301 TGGTAATTCC
* * * **
55434311 ACCCTACAGGGGTATTTTAGTAATTCTACCTTATAGGGGTATTTTAGTAATTCTACCCTACAGGG
1 ACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTCGAGTAATTCTACCCTACAGGG
*
55434376 GTATTTCGGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTACAGGGGTATTTCTGTA
66 GTATTTCGGTAATTCTACCCTACAAGGGTATTGCGATAATTCTACCCTACAGGGGTATTTCTGTA
55434441 TTTCTGTATTTCT
131 TTTCTGTATTTCT
* *
55434454 ACCCTATAGGGGTATTTCGGTAATTCTACCCTACA-GGGTATTGCGA-TAATTCTACCCTACAGG
1 ACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATT-CGAGTAATTCTACCCTACAGG
* * *
55434517 GGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTGCAGGGGTATTT
65 GGTATTTCGGTAATTCTACCCTACAAGGGTATTGCGATAATTCTACCCTACAGGGGTATTT
55434578 TGGTAATTTT
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
142 81 0.72
143 31 0.28
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (143 bp):
ACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTCGAGTAATTCTACCCTACAGGG
GTATTTCGGTAATTCTACCCTACAAGGGTATTGCGATAATTCTACCCTACAGGGGTATTTCTGTA
TTTCTGTATTTCT
Found at i:55434600 original size:27 final size:27
Alignment explanation
Indices: 55434570--55434919 Score: 175
Period size: 27 Copynumber: 13.1 Consensus size: 27
55434560 TACCCTGCAG
* **
55434570 GGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
* **
55434597 GGGTATTTCAGTAATTTTGCAAA-CTGA
1 GGGTATTTCGGTAATTTTATAAATC-GA
*
55434624 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
* * *
55434651 GGATATTTGGGTAATTTTATAAACCG-
1 GGGTATTTCGGTAATTTTATAAATCGA
* * *
55434677 GGGTACTTT-GGTAATTTTACAACTGGA
1 GGGTA-TTTCGGTAATTTTATAAATCGA
** *
55434704 -GGTATTTTAGTAATTTCAT-AATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
** *
55434729 GGGTAAAAT-GGTAATTTTGTAAA-CTGA
1 GGGT-ATTTCGGTAATTTTATAAATC-GA
** *
55434756 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
*** * * *
55434783 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTATTTCGGTAATTTTATAAATCGA
** *
55434810 GGGTAAAAT-GGTAATTCTATAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** *
55434837 GGGTAAAAT-GGTAATTTTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
** * *
55434864 GGGTGA-AACGGTAATTCTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTATAAATCGA
* *
55434891 GGGTACTTT-GGTAATTTTACAAATTGA
1 GGGTA-TTTCGGTAATTTTATAAATCGA
55434918 GG
1 GG
55434920 ACATTTTAGT
Statistics
Matches: 264, Mismatches: 44, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
25 7 0.03
26 47 0.18
27 205 0.78
28 5 0.02
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTATAAATCGA
Found at i:55434605 original size:54 final size:53
Alignment explanation
Indices: 55434438--55434585 Score: 208
Period size: 53 Copynumber: 2.8 Consensus size: 53
55434428 GGGTATTTCT
* * *
55434438 GTATTTCTGTATTTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTAC-AGG
1 GTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA-CCTACAAGG
* *
55434491 GTATTGCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGG
1 GTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA-CCTACAAGG
* *
55434545 GTATTTCGGTAATTCTACCCTGCAGGGGTATTTTGGTAATT
1 GTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATT
55434586 TTATTGATCG
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
53 45 0.53
54 40 0.47
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (53 bp):
GTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTACAAGG
Found at i:55434611 original size:54 final size:53
Alignment explanation
Indices: 55434438--55434612 Score: 194
Period size: 54 Copynumber: 3.3 Consensus size: 53
55434428 GGGTATTTCT
* * *
55434438 GTATTTCTGTATTTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTAC-AGG
1 GTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTA-CCTACAAGG
*
55434491 GTATTGC-GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGG
1 GTATTTCAG-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTA-CCTACAAGG
* * * * * *
55434545 GTATTTCGGTAATTCTACCCTGCAGGGGTATTTTGGTAATTTTA-TTGATCGAGG
1 GTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCT-A-CAAGG
55434599 GTATTTCAGTAATT
1 GTATTTCAGTAATT
55434613 TTGCAAACTG
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
52 2 0.02
53 46 0.43
54 58 0.54
55 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (53 bp):
GTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTACAAGG
Found at i:55434906 original size:81 final size:81
Alignment explanation
Indices: 55434723--55434895 Score: 294
Period size: 81 Copynumber: 2.1 Consensus size: 81
55434713 GTAATTTCAT
* *
55434723 AATCGAGGGTAAAATGGTAATTTTGTAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
55434788 AAACAGTAATTCTGTA
66 AAACAGTAATTCTGTA
55434804 AATCGAGGGTAAAATGGTAATTCTATAAA-TCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAACT-GAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
* *
55434868 GAAACGGTAATTCTGTA
65 AAAACAGTAATTCTGTA
55434885 AATCGAGGGTA
1 AATCGAGGGTA
55434896 CTTTGGTAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 1 0.01
81 86 0.99
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAACTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
AAACAGTAATTCTGTA
Found at i:55434908 original size:54 final size:54
Alignment explanation
Indices: 55434723--55434895 Score: 267
Period size: 54 Copynumber: 3.2 Consensus size: 54
55434713 GTAATTTCAT
*
55434723 AATCGAGGGTAAAATGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTCTGTA
** * *
55434777 AATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTA
* *
55434831 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTGAAACGGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTA
55434885 AATCGAGGGTA
1 AATCGAGGGTA
55434896 CTTTGGTAAT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 106 0.99
55 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (54 bp):
AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTA
Found at i:55434932 original size:81 final size:81
Alignment explanation
Indices: 55434723--55434940 Score: 231
Period size: 81 Copynumber: 2.7 Consensus size: 81
55434713 GTAATTTCAT
* ** ** *
55434723 AATCGAGGGTAAAATGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTACAAATC-GAGGACAAAATAGTAATTTTGTAAATCGAGGGT
55434787 AAAACAGTAATTCTGTA
65 AAAACAGTAATTCTGTA
* ** * *
55434804 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGACAAAATAGTAATTTTGTAAATCGAGGGTA
*
55434869 AAACGGTAATTCTGTA
66 AAACAGTAATTCTGTA
*** * * *** *
55434885 AATCGAGGGTACTTTGGTAATTTTACAAATTGAGGACATTTTAGTAATTTGGTAAA
1 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGACAAAATAGTAATTTTGTAAA
55434941 CTAAAGTATT
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
81 118 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGACAAAATAGTAATTTTGTAAATCGAGGGTA
AAACAGTAATTCTGTA
Found at i:55436019 original size:32 final size:32
Alignment explanation
Indices: 55435976--55436045 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
55435966 CACGGCTTAC
* **
55435976 AGCCATCAGTAGCGGTAATTTGATTGGCACAA
1 AGCCATCAGTAGCGGTAATATGATCCGCACAA
* * *
55436008 AGCCATTAGTAGCTGTAATATGATCCGCACAC
1 AGCCATCAGTAGCGGTAATATGATCCGCACAA
55436040 AGCCAT
1 AGCCAT
55436046 GGGTAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (32 bp):
AGCCATCAGTAGCGGTAATATGATCCGCACAA
Found at i:55436160 original size:22 final size:22
Alignment explanation
Indices: 55436115--55436176 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
55436105 AATACGATTA
** * *
55436115 GCACAAAGCCATAAACAAGATG
1 GCACAAAGCCATAATTAGGTTG
*
55436137 GCACAAAGCCATATTTAGGTTG
1 GCACAAAGCCATAATTAGGTTG
*
55436159 GCACAGAGCCATAATTAG
1 GCACAAAGCCATAATTAG
55436177 ATTAAGCGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (22 bp):
GCACAAAGCCATAATTAGGTTG
Found at i:55439344 original size:40 final size:40
Alignment explanation
Indices: 55439277--55439444 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
55439267 AAATTGAATG
* * * * *
55439277 ATATCCGGGCTAAGCCCCAAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
55439317 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
55439357 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
55439397 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
55439437 ATATCCGG
1 ATATCCGG
55439445 TTATATTCCG
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.03
40 99 0.95
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:55440992 original size:43 final size:42
Alignment explanation
Indices: 55440939--55441076 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 42
55440929 CGTAAGATCG
* *
55440939 TGTCAGGGACACAGGCCTCGATTGAGATTTACGTATAAAACCA
1 TGTCTGGGACACAGGCCTCGATTGAGA-TTACGTATAAGACCA
* ** *
55440982 TGTCTGGGACATCA-GCATCGTATCT--GATT-CGTGCAAGACCT
1 TGTCTGGGACA-CAGGCCTCG-AT-TGAGATTACGTATAAGACCA
55441023 TGTCTGGGACACAGGCCTCGATTGAGAGTTACGTATAAGACCA
1 TGTCTGGGACACAGGCCTCGATTGAGA-TTACGTATAAGACCA
55441066 TGTCTGGGACA
1 TGTCTGGGACA
55441077 TCGGCATCGT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
39 1 0.01
40 4 0.05
41 26 0.34
42 4 0.05
43 37 0.48
44 4 0.05
45 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (42 bp):
TGTCTGGGACACAGGCCTCGATTGAGATTACGTATAAGACCA
Found at i:55441085 original size:84 final size:85
Alignment explanation
Indices: 55440939--55441129 Score: 294
Period size: 84 Copynumber: 2.3 Consensus size: 85
55440929 CGTAAGATCG
* *
55440939 TGTCAGGGACACAGGCCTCGATTGAGATTTACGTATAAAACCATGTCTGGGACATCAGCATCGTA
1 TGTCTGGGACACAGGCCTCGATTGAGAGTTACGTATAAAACCATGTCTGGGACATCAGCATCGTA
*
55441004 TCTGA-TTCGTGCAAGACCT
66 TCTGATTTCGTGCAAGACCC
* *
55441023 TGTCTGGGACACAGGCCTCGATTGAGAGTTACGTATAAGACCATGTCTGGGACATCGGCATCGTA
1 TGTCTGGGACACAGGCCTCGATTGAGAGTTACGTATAAAACCATGTCTGGGACATCAGCATCGTA
*
55441088 TCTGATTTCGTGTAAGACCC
66 TCTGATTTCGTGCAAGACCC
* * *
55441108 TGTATGGGACAGAGGCATCGAT
1 TGTCTGGGACACAGGCCTCGAT
55441130 ATTGAATTAC
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 66 0.68
85 31 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (85 bp):
TGTCTGGGACACAGGCCTCGATTGAGAGTTACGTATAAAACCATGTCTGGGACATCAGCATCGTA
TCTGATTTCGTGCAAGACCC
Found at i:55441116 original size:42 final size:41
Alignment explanation
Indices: 55440967--55441159 Score: 160
Period size: 42 Copynumber: 4.6 Consensus size: 41
55440957 CGATTGAGAT
* * *
55440967 TTACGTATAAAACCATGTCTGGGACATCAGCATCGTATCTGA
1 TTACGTGTAAGACCATGTCTGGGACATCGGCATCGTAT-TGA
* * *
55441009 TT-CGTGCAAGACCTTGTCTGGGACA-CAGGCCTCG-ATTGAGA
1 TTACGTGTAAGACCATGTCTGGGACATC-GGCATCGTATT--GA
*
55441050 GTTACGTATAAGACCATGTCTGGGACATCGGCATCGTATCTGA
1 -TTACGTGTAAGACCATGTCTGGGACATCGGCATCGTAT-TGA
* * * **
55441093 TTTCGTGTAAGACCCTGTATGGGACAGAGGCATCGATATTGAA
1 TTACGTGTAAGACCATGTCTGGGACATCGGCATCG-TATTG-A
* *
55441136 TTAC-TGTAAGACCACGTCCGGGAC
1 TTACGTGTAAGACCATGTCTGGGAC
55441160 GTCGACATTG
Statistics
Matches: 120, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 26 0.22
42 51 0.43
43 35 0.29
44 3 0.03
45 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (41 bp):
TTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATTGA
Found at i:55442382 original size:27 final size:27
Alignment explanation
Indices: 55442352--55442453 Score: 118
Period size: 27 Copynumber: 3.8 Consensus size: 27
55442342 GCCCAACAGG
*
55442352 GGTATTTCGGTAATTTTACACTAC-AAA
1 GGTATTTCGGTAATTTTACAAT-CGAAA
*
55442379 GGTATTTCGGTAATTTTACAATCGAAG
1 GGTATTTCGGTAATTTTACAATCGAAA
* *
55442406 GGTATTTCGATAATTTTACAGATTG-AA
1 GGTATTTCGGTAATTTTACA-ATCGAAA
* *
55442433 GGTATTTCAGTACTTTTACAA
1 GGTATTTCGGTAATTTTACAA
55442454 ACCAGGGGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
26 2 0.03
27 60 0.92
28 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (27 bp):
GGTATTTCGGTAATTTTACAATCGAAA
Found at i:55442435 original size:54 final size:54
Alignment explanation
Indices: 55442351--55442453 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
55442341 TGCCCAACAG
* * *
55442351 GGGTATTTCGGTAATTTTACACTACAAAGGTATTTCGGTAATTTTACAATCGAA
1 GGGTATTTCGATAATTTTACAATACAAAGGTATTTCAGTAATTTTACAATCGAA
** *
55442405 GGGTATTTCGATAATTTTACAGAT-TGAAGGTATTTCAGTACTTTTACAA
1 GGGTATTTCGATAATTTTACA-ATACAAAGGTATTTCAGTAATTTTACAA
55442454 ACCAGGGGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (54 bp):
GGGTATTTCGATAATTTTACAATACAAAGGTATTTCAGTAATTTTACAATCGAA
Found at i:55447501 original size:16 final size:16
Alignment explanation
Indices: 55447480--55447512 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55447470 ACACTTAACC
*
55447480 AAAAATTCTAAGCACA
1 AAAAATGCTAAGCACA
55447496 AAAAATGCTAAGCACA
1 AAAAATGCTAAGCACA
55447512 A
1 A
55447513 GGAGACCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAAATGCTAAGCACA
Found at i:55450045 original size:28 final size:28
Alignment explanation
Indices: 55449985--55450058 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
55449975 ATACATGTAT
* *
55449985 ATGGCCCACTAGGCCCAATCTCTTTCAT
1 ATGGCCCATTAGGCCCAATCTCTTTCAC
*
55450013 ATGGCCCATTAGGCCCAATCT-TATTTAC
1 ATGGCCCATTAGGCCCAATCTCT-TTCAC
* *
55450041 GTGGCCTATTAGGCCCAA
1 ATGGCCCATTAGGCCCAA
55450059 ATCACATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (28 bp):
ATGGCCCATTAGGCCCAATCTCTTTCAC
Found at i:55456949 original size:24 final size:24
Alignment explanation
Indices: 55456917--55457006 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
55456907 TATTGATATA
55456917 TCAACTCGTAAGAGCTTACTATTT
1 TCAACTCGTAAGAGCTTACTATTT
**
55456941 TCAACTCGTTGGAGCTTACTA-TT
1 TCAACTCGTAAGAGCTTACTATTT
* * *
55456964 TCAACTCATAAAAGCTTACTGTTT
1 TCAACTCGTAAGAGCTTACTATTT
* *
55456988 TCAGCTCGTTAGAGCTTAC
1 TCAACTCGTAAGAGCTTAC
55457007 CGTTTCAGCT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 18 0.33
24 36 0.67
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (24 bp):
TCAACTCGTAAGAGCTTACTATTT
Found at i:55457016 original size:23 final size:23
Alignment explanation
Indices: 55456917--55457032 Score: 99
Period size: 24 Copynumber: 5.0 Consensus size: 23
55456907 TATTGATATA
*
55456917 TCAACTCGTAAGAGCTTACTATTT
1 TCAACTCGTAAGAGCTTACT-GTT
** *
55456941 TCAACTCGTTGGAGCTTACTATT
1 TCAACTCGTAAGAGCTTACTGTT
* *
55456964 TCAACTCATAAAAGCTTACTGTTT
1 TCAACTCGTAAGAGCTTACTG-TT
* * *
55456988 TCAGCTCGTTAGAGCTTACCGTT
1 TCAACTCGTAAGAGCTTACTGTT
* *
55457011 TCAGCTCAATAA-AGCTTACTGT
1 TCAACTC-GTAAGAGCTTACTGT
55457033 CCATCAACTC
Statistics
Matches: 74, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
23 36 0.49
24 38 0.51
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (23 bp):
TCAACTCGTAAGAGCTTACTGTT
Found at i:55457031 original size:47 final size:47
Alignment explanation
Indices: 55456917--55457032 Score: 144
Period size: 47 Copynumber: 2.5 Consensus size: 47
55456907 TATTGATATA
* * * * *
55456917 TCAACTCGTAAGAGCTTACTATTTTCAACTCGTTGGAGCTTACTATT
1 TCAACTCATAAAAGCTTACTGTTTTCAACTCGTTAGAGCTTACCATT
* *
55456964 TCAACTCATAAAAGCTTACTGTTTTCAGCTCGTTAGAGCTTACCGTT
1 TCAACTCATAAAAGCTTACTGTTTTCAACTCGTTAGAGCTTACCATT
*
55457011 TCAGCTCA-ATAAAGCTTACTGT
1 TCAACTCATA-AAAGCTTACTGT
55457033 CCATCAACTC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 1 0.02
47 59 0.98
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (47 bp):
TCAACTCATAAAAGCTTACTGTTTTCAACTCGTTAGAGCTTACCATT
Found at i:55461740 original size:39 final size:39
Alignment explanation
Indices: 55461622--55461804 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
55461612 TCGTTCAAAC
* * ** * **
55461622 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
55461662 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* *
55461702 GCCTTCGGGCTTAGCCCGGATATCATAACTCACCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55461741 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55461780 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
55461805 CTCGAACATT
Statistics
Matches: 124, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 86 0.69
40 38 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:55469154 original size:39 final size:39
Alignment explanation
Indices: 55469036--55469217 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
55469026 TCGTTCAAAC
* * ** * **
55469036 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
55469076 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
55469116 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55469155 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55469194 GCCTTC-GGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
55469218 CTCGAACATT
Statistics
Matches: 125, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
38 18 0.14
39 69 0.55
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:55472654 original size:20 final size:19
Alignment explanation
Indices: 55472629--55472678 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
55472619 AAGTTTATGT
55472629 TAAGTAAATGAAATGGAAA
1 TAAGTAAATGAAATGGAAA
* * *
55472648 GTAAGTAAAGGGAATGGTAA
1 -TAAGTAAATGAAATGGAAA
55472668 TAAAGTAAATG
1 T-AAGTAAATG
55472679 GAGTGGTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.22
Consensus pattern (19 bp):
TAAGTAAATGAAATGGAAA
Found at i:55472685 original size:20 final size:21
Alignment explanation
Indices: 55472650--55472691 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
55472640 AATGGAAAGT
55472650 AAGTAAAGGGAATGGTA-ATA
1 AAGTAAAGGGAATGGTACATA
* *
55472670 AAGTAAATGGAGTGGTACATA
1 AAGTAAAGGGAATGGTACATA
55472691 A
1 A
55472692 TTTATGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (21 bp):
AAGTAAAGGGAATGGTACATA
Found at i:55477365 original size:24 final size:24
Alignment explanation
Indices: 55477330--55477406 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
55477320 AGACTCACCG
*
55477330 CAGCTCGAATGAGCTTACTATTCT
1 CAGCTCGTATGAGCTTACTATTCT
*
55477354 CAGCTCGTATGAACTTACTATT-T
1 CAGCTCGTATGAGCTTACTATTCT
*
55477377 -AGCTCGTCA-GAGCTTACTGTTCAT
1 CAGCTCGT-ATGAGCTTACTATTC-T
55477401 CAGCTC
1 CAGCTC
55477407 AGGAGAAGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 17 0.38
23 2 0.04
24 21 0.47
25 5 0.11
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACTATTCT
Found at i:55484247 original size:18 final size:18
Alignment explanation
Indices: 55484224--55484261 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55484214 TTTCTAGCTT
55484224 AGTCTCGAATCGTTTCTA
1 AGTCTCGAATCGTTTCTA
55484242 AGTCTCGAATCGTTTCTA
1 AGTCTCGAATCGTTTCTA
55484260 AG
1 AG
55484262 GTATTTCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (18 bp):
AGTCTCGAATCGTTTCTA
Found at i:55487610 original size:46 final size:46
Alignment explanation
Indices: 55487543--55487801 Score: 215
Period size: 46 Copynumber: 5.6 Consensus size: 46
55487533 CTCATAGCTA
* * *
55487543 ATGCATGTCCCAAACATGTCTTACATTGGCTTACGTCTCGAGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCG
* * *
55487589 ATGCATGCCCCAGACATGTCTTACACTGGCTCT-CATAAT-GTGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCT-TACAT-CTCGAGGCCG
* * * *
55487635 ATGCATGTCCCAGACATGTCTTACACTGGCACTA-ATCTCAATGTCG
1 ATGCATGTCCCAGACATGTCTTACACTGGC-TTACATCTCGAGGCCG
* * * * *
55487681 ATGCATGTCCTAGACATGTCTTACACTGGCACT-CATCTCAATGCCA
1 ATGCATGTCCCAGACATGTCTTACACTGGC-TTACATCTCGAGGCCG
* * * **
55487727 ATGCCATGTCCCATACATGGTCTTACACTGGCTCT-CATAAT-GTGGATG
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCG
*
55487775 ATGCATGTCCTAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
55487802 AGCTCACACA
Statistics
Matches: 175, Mismatches: 28, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.01
46 126 0.72
47 26 0.15
48 21 0.12
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCG
Found at i:55487778 original size:140 final size:138
Alignment explanation
Indices: 55487543--55487801 Score: 367
Period size: 140 Copynumber: 1.9 Consensus size: 138
55487533 CTCATAGCTA
* * * * *
55487543 ATGCATGTCCCAAACATGTCTTACATTGGCTTACGTCTCGAGGCCGATGCATGCCCCAGACATGT
1 ATGCATGTCCCAAACATGTCTTACACTGGCCTACATCTCAAGGCCAATGCATGCCCCAGACATGT
*
55487608 CTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTGGCACTAATCT
66 CTTACACTGGCTCTCATAATGTGGACGATGCATGTCCCAGACATGTCTTACACTGGCACTAATCT
55487673 CAATGTCG
131 CAATGTCG
* * * * *
55487681 ATGCATGTCCTAGACATGTCTTACACTGGCACT-CATCTCAATGCCAATGCCATGTCCCATACAT
1 ATGCATGTCCCAAACATGTCTTACACTGGC-CTACATCTCAAGGCCAATG-CATGCCCCAGACAT
* *
55487745 GGTCTTACACTGGCTCTCATAATGTGGATGATGCATGTCCTAGACATGTCTTACACT
64 -GTCTTACACTGGCTCTCATAATGTGGACGATGCATGTCCCAGACATGTCTTACACT
55487802 AGCTCACACA
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
138 39 0.37
139 13 0.12
140 53 0.50
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (138 bp):
ATGCATGTCCCAAACATGTCTTACACTGGCCTACATCTCAAGGCCAATGCATGCCCCAGACATGT
CTTACACTGGCTCTCATAATGTGGACGATGCATGTCCCAGACATGTCTTACACTGGCACTAATCT
CAATGTCG
Found at i:55487784 original size:94 final size:90
Alignment explanation
Indices: 55487542--55487801 Score: 244
Period size: 92 Copynumber: 2.8 Consensus size: 90
55487532 TCTCATAGCT
* * * * * * *
55487542 AATGCATGTCCCAAACATGTCTTACATTGGCTTACGT--CTCGAGGCCGATGCATGCCCCAGACA
1 AATGCATGTCCCAGACATGTCTTACACTGGC--AC-TAACTCAATGTCGATGCATGTCCTAGACA
*
55487605 TGTCTTACACTGGCTCTCATAATGTGGCC
63 TGTCTTACACTGGCACTCATAA-GTGGCC
*
55487634 GATGCATGTCCCAGACATGTCTTACACTGGCACTAATCTCAATGTCGATGCATGTCCTAGACATG
1 AATGCATGTCCCAGACATGTCTTACACTGGCACTAA-CTCAATGTCGATGCATGTCCTAGACATG
55487699 TCTTACACTGGCACTCATCTCAA-T-GCC
65 TCTTACACTGGCACTCA--T-AAGTGGCC
* * * *
55487726 AATGCCATGTCCCATACATGGTCTTACACTGGCTCTCA-T-AATGTGGATGATGCATGTCCTAGA
1 AATG-CATGTCCCAGACAT-GTCTTACACTGGCACTAACTCAATGT---CGATGCATGTCCTAGA
55487789 CATGTCTTACACT
61 CATGTCTTACACT
55487802 AGCTCACACA
Statistics
Matches: 143, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
89 1 0.01
90 2 0.01
91 5 0.03
92 74 0.52
93 14 0.10
94 45 0.31
95 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (90 bp):
AATGCATGTCCCAGACATGTCTTACACTGGCACTAACTCAATGTCGATGCATGTCCTAGACATGT
CTTACACTGGCACTCATAAGTGGCC
Found at i:55495844 original size:15 final size:15
Alignment explanation
Indices: 55495812--55495840 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55495802 ATTTTCTATG
55495812 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
55495827 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
55495841 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:55496358 original size:15 final size:15
Alignment explanation
Indices: 55496338--55496368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55496328 AAATATGAAA
55496338 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
55496353 GATATGTTTTGTATT
1 GATATGTTTTGGATT
55496368 G
1 G
55496369 GAATTTTTGA
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:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:55496980 original size:45 final size:45
Alignment explanation
Indices: 55496918--55497139 Score: 291
Period size: 45 Copynumber: 4.9 Consensus size: 45
55496908 TAGGATTCCG
* **
55496918 ATATGTGTTTTTGTGTAAGACCACGTTTGGGACGTTGGCATTGAT
1 ATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCAAT
* * *
55496963 ATATGTGTTTTCATGTAAGACCATGTCTGGGACGTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCAAT
* *
55497008 ATATGTGGTTACGTGTAAGACCACGTTTGGGACGTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCAAT
* **
55497053 ATATGTGTTTTCCTGTAAGACCACGTTTGGGGGGTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCAAT
* * * * * *
55497098 ATATGTGGTTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 ATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCATC
55497140 GTATTTGATT
Statistics
Matches: 152, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 152 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTTTGGGACGTTGGCATCAAT
Found at i:55497071 original size:90 final size:90
Alignment explanation
Indices: 55496930--55497168 Score: 324
Period size: 90 Copynumber: 2.7 Consensus size: 90
55496920 ATGTGTTTTT
** *
55496930 GTGTAAGACCACGTTTGGGACGTTGGCATTGATATATGTGTTTTCATGTAAGACCATGTCTGGGA
1 GTGTAAGACCACGTTTGGGACGTTGGCATCAATATATGTGTTTTCATGTAAGACCACGTCTGGGA
55496995 CGTTGGCATCAATATATGTGGTTAC
66 CGTTGGCATCAATATATGTGGTTAC
* * *
55497020 GTGTAAGACCACGTTTGGGACGTTGGCATCAATATATGTGTTTTCCTGTAAGACCACGTTTGGGG
1 GTGTAAGACCACGTTTGGGACGTTGGCATCAATATATGTGTTTTCATGTAAGACCACGTCTGGGA
*
55497085 GGTTGGCATCAATATATGTGGTTAC
66 CGTTGGCATCAATATATGTGGTTAC
* * * * * * *
55497110 GTGTAAGACCATGTCTGGGACATCGGCATC-GTAT-T-TG-ATTCATGTAAGACCCCGTCTGG
1 GTGTAAGACCACGTTTGGGACGTTGGCATCAATATATGTGTTTTCATGTAAGACCACGTCTGG
55497169 AACAGTGGCG
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
86 18 0.14
87 2 0.02
88 1 0.01
89 3 0.02
90 109 0.82
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (90 bp):
GTGTAAGACCACGTTTGGGACGTTGGCATCAATATATGTGTTTTCATGTAAGACCACGTCTGGGA
CGTTGGCATCAATATATGTGGTTAC
Found at i:55497577 original size:24 final size:24
Alignment explanation
Indices: 55497550--55497598 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55497540 AATTGAATGA
55497550 TAGTTTGTTAATGTATATATATGT
1 TAGTTTGTTAATGTATATATATGT
55497574 TAGTTTGTTAATGTATATATATGT
1 TAGTTTGTTAATGTATATATATGT
55497598 T
1 T
55497599 CATTCGGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (24 bp):
TAGTTTGTTAATGTATATATATGT
Found at i:55500336 original size:49 final size:46
Alignment explanation
Indices: 55500264--55500386 Score: 133
Period size: 49 Copynumber: 2.6 Consensus size: 46
55500254 ATGTGAGAGC
* * *
55500264 CAGTGTAAGACCATGCCTGGGACATGTCATCT-ACCTCGATTTTGAT-AGT
1 CAGTGTAAGACCATG-CTTGGACATGGCAT-TGA-CTCGA--TGGATGAGT
*
55500313 CAGTGTAAGACCATGTCTTGGACATGGCATTGACTTGATGGATGAGT
1 CAGTGTAAGACCATG-CTTGGACATGGCATTGACTCGATGGATGAGT
55500360 CAGTGTAAGACCATGCTTGGGACATGG
1 CAGTGTAAGACCATGCTT-GGACATGG
55500387 TATCGGTATT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
46 7 0.11
47 26 0.39
48 5 0.08
49 28 0.42
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
CAGTGTAAGACCATGCTTGGACATGGCATTGACTCGATGGATGAGT
Found at i:55500383 original size:47 final size:48
Alignment explanation
Indices: 55500264--55500386 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 48
55500254 ATGTGAGAGC
* * *
55500264 CAGTGTAAGACCATGCCTGGGACATGTCATCTACCTCGATTTTGATAGT
1 CAGTGTAAGACCATGCTTGGGACATGGCATCTACCTCGA-TTGGATAGT
*
55500313 CAGTGTAAGACCATGTCTT-GGACATGGCAT-TGA-CTTGA-TGGATGAGT
1 CAGTGTAAGACCATG-CTTGGGACATGGCATCT-ACCTCGATTGGAT-AGT
55500360 CAGTGTAAGACCATGCTTGGGACATGG
1 CAGTGTAAGACCATGCTTGGGACATGG
55500387 TATCGGTATT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
46 7 0.11
47 26 0.39
48 5 0.08
49 26 0.39
50 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (48 bp):
CAGTGTAAGACCATGCTTGGGACATGGCATCTACCTCGATTGGATAGT
Found at i:55507679 original size:27 final size:27
Alignment explanation
Indices: 55507649--55507731 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
55507639 GACCCCCTTG
* *
55507649 GTGGTAAAATGATTGTATTGCCCCTAT
1 GTGGTAAAATGACTGTTTTGCCCCTAT
* *
55507676 GTGGTAAAATGACTATTTTGCCCTTAT
1 GTGGTAAAATGACTGTTTTGCCCCTAT
* * *
55507703 ATGCTAAAGTGACTGTTTTGCCCCTAT
1 GTGGTAAAATGACTGTTTTGCCCCTAT
55507730 GT
1 GT
55507732 AATGTAAGTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
GTGGTAAAATGACTGTTTTGCCCCTAT
Found at i:55509521 original size:44 final size:43
Alignment explanation
Indices: 55509449--55509575 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 43
55509439 TATTAATCTG
* * **
55509449 AATTATCGTGTAAGACCGTGTCTAGGACACAGGCATCGATTTCA
1 AATT-TCGTGTAAGACCATGTCTGGGACACAGGCATCGATAACA
*
55509493 AATTTACGTGTAAGACCATGTCTGGGACATC-GGCATCG-TAACT
1 AATTT-CGTGTAAGACCATGTCTGGGACA-CAGGCATCGATAACA
* * * *
55509536 GATTTCGTATAAGACCCTGTCTGGGACAGAGGCATCGATA
1 AATTTCGTGTAAGACCATGTCTGGGACACAGGCATCGATA
55509576 CTGAATTACA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
42 28 0.40
43 9 0.13
44 32 0.46
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (43 bp):
AATTTCGTGTAAGACCATGTCTGGGACACAGGCATCGATAACA
Found at i:55509579 original size:42 final size:42
Alignment explanation
Indices: 55509454--55509605 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 42
55509444 ATCTGAATTA
* * * **
55509454 TCGTGTAAGACCGTGTCTAGGACACAGGCATCGATTTCAAATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCGA-TACTGATT
55509497 TACGTGTAAGACCATGTCTGGGACATC-GGCATCG-TAACTGATT
1 T-CGTGTAAGACCATGTCTGGGACA-CAGGCATCGAT-ACTGATT
* * *
55509540 TCGTATAAGACCCTGTCTGGGACAGAGGCATCGATACTGAATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCGATACTG-ATT
* * **
55509583 ACATGTAAGACCACATCTGGGAC
1 TCGTGTAAGACCATGTCTGGGAC
55509606 GTTGGCATTA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
42 33 0.37
43 27 0.30
44 28 0.31
45 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACACAGGCATCGATACTGATT
Found at i:55514420 original size:40 final size:39
Alignment explanation
Indices: 55514376--55514600 Score: 281
Period size: 40 Copynumber: 5.7 Consensus size: 39
55514366 GCCACTAGCT
*
55514376 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
55514416 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
55514455 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
55514495 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
55514535 CGAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
55514575 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
55514601 TATCATCGGA
Statistics
Matches: 165, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 39 0.24
40 126 0.76
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:55516937 original size:15 final size:15
Alignment explanation
Indices: 55516917--55516948 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55516907 ATGCATAAGG
55516917 TATTGGTCTCGGCAC
1 TATTGGTCTCGGCAC
55516932 TATTGGTCTCGGCAC
1 TATTGGTCTCGGCAC
55516947 TA
1 TA
55516949 AGTGTGCGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (15 bp):
TATTGGTCTCGGCAC
Found at i:55517111 original size:59 final size:58
Alignment explanation
Indices: 55517015--55517146 Score: 246
Period size: 59 Copynumber: 2.3 Consensus size: 58
55517005 AAAATTGTAC
55517015 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
*
55517073 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATAT
55517132 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55517147 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 23 0.32
59 49 0.68
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (58 bp):
AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:55517135 original size:88 final size:89
Alignment explanation
Indices: 55516985--55517146 Score: 263
Period size: 88 Copynumber: 1.8 Consensus size: 89
55516975 GACAAGATTG
* * *
55516985 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
55517050 AAGTGTGCGAGCTGAAAATATATA
66 AAGTGTGCGAGCTGAAAATATATA
* * *
55517074 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
55517138 AAGTGTGCG
66 AAGTGTGCG
55517147 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 52 0.78
89 15 0.22
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (89 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT
AAGTGTGCGAGCTGAAAATATATA
Found at i:55517158 original size:29 final size:29
Alignment explanation
Indices: 55517015--55517146 Score: 246
Period size: 29 Copynumber: 4.5 Consensus size: 29
55517005 AAAATTGTAC
*
55517015 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
55517044 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
55517073 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
55517103 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
55517132 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55517147 GATTCACTAT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:55520371 original size:47 final size:47
Alignment explanation
Indices: 55520305--55520736 Score: 641
Period size: 47 Copynumber: 9.1 Consensus size: 47
55520295 TATCACAGTT
* * *
55520305 ATACACTTCCAC-TTCCATCACATTGACCATTCGGCCTTATCATATAT
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCATATAC
* *
55520352 ATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAC
55520399 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAT--CATATAC
* * *
55520448 ATACACCTTCACATTCATCACATTGGCCATTCAGCCTTATCATATAT
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAC
* *
55520495 ATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAC
55520542 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAT--CATATAC
* *
55520591 ATACACCTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAT
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAC
* *
55520638 ATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAC
* * *
55520685 ATACACCTTCACATTCATTACATTGGCCATTCAGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAT--CATATAC
55520734 ATA
1 ATA
55520737 TCTTGTACAT
Statistics
Matches: 350, Mismatches: 28, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
47 250 0.71
48 2 0.01
49 98 0.28
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCATATAC
Found at i:55520489 original size:96 final size:96
Alignment explanation
Indices: 55520305--55520736 Score: 653
Period size: 96 Copynumber: 4.5 Consensus size: 96
55520295 TATCACAGTT
* * * *
55520305 ATACACTTCCAC-TTCCATCACATTGACCATTCGGCCTTAT--CATATATATATACTTTCACATT
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATT
55520367 CATCACATTGGCCATTCGGCCTTATCACATAC
65 CATCACATTGGCCATTCGGCCTTATCACATAC
*
55520399 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACCTTCACATTC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTC
* * *
55520464 ATCACATTGGCCATTCAGCCTTATCATATAT
66 ATCACATTGGCCATTCGGCCTTATCACATAC
*
55520495 ATATACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATTC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTC
55520558 ATCACATTGGCCATTCGGCCTTATCACATATAC
66 ATCACATTGGCCATTCGGCCTTATCAC--ATAC
* * *
55520591 ATACACCTTCACATTCATCACATTGGCCATTCGGCCTTAT--CATATATATATACTTTCACATTC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTC
55520654 ATCACATTGGCCATTCGGCCTTATCACATAC
66 ATCACATTGGCCATTCGGCCTTATCACATAC
* * *
55520685 ATACACCTTCACATTCATTACATTGGCCATTCAGCCTTATCACATATACATA
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATA
55520737 TCTTGTACAT
Statistics
Matches: 309, Mismatches: 20, Indels: 16
0.90 0.06 0.05
Matches are distributed among these distances:
94 122 0.39
95 2 0.01
96 185 0.60
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (96 bp):
ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTC
ATCACATTGGCCATTCGGCCTTATCACATAC
Found at i:55520563 original size:143 final size:143
Alignment explanation
Indices: 55520320--55520736 Score: 789
Period size: 143 Copynumber: 2.9 Consensus size: 143
55520310 CTTCCACTTC
*
55520320 CATCACATTGACCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
55520385 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
55520450 ACACCTTCACATT
131 ACACCTTCACATT
*
55520463 CATCACATTGGCCATTCAGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
55520528 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
55520593 ACACCTTCACATT
131 ACACCTTCACATT
55520606 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
1 CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
* * *
55520671 GCCTTATCACATACATACACCTTCACATTCATTACATTGGCCATTCAGCCTTATCACATATACAT
66 GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
55520736 A
131 A
55520737 TCTTGTACAT
Statistics
Matches: 268, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 268 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (143 bp):
CATCACATTGGCCATTCGGCCTTATCATATATATATACTTTCACATTCATCACATTGGCCATTCG
GCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAT
ACACCTTCACATT
Found at i:55532120 original size:15 final size:15
Alignment explanation
Indices: 55532100--55532131 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55532090 GGAAAGCAAT
55532100 GATAGCCTTAGAAGG
1 GATAGCCTTAGAAGG
55532115 GATAGCCTTAGAAGG
1 GATAGCCTTAGAAGG
55532130 GA
1 GA
55532132 CCCATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.19
Consensus pattern (15 bp):
GATAGCCTTAGAAGG
Found at i:55534325 original size:31 final size:31
Alignment explanation
Indices: 55534287--55534350 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
55534277 CCTTTTCATA
55534287 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
55534318 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
55534349 TT
1 TT
55534351 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:55534599 original size:24 final size:25
Alignment explanation
Indices: 55534559--55534666 Score: 114
Period size: 25 Copynumber: 4.4 Consensus size: 25
55534549 CTGGAAGCCT
*
55534559 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTAATAAACTAGGGCAAA
* *
55534583 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTAGGGCAAA
*
55534608 AGCCCTTTTAATAAATTAGGGCAAA
1 AGCCCTTTTAATAAACTAGGGCAAA
** *
55534633 AGCCCTTTTCGGTAAACTAGGGC-AT
1 AGCCCTTTT-AATAAACTAGGGCAAA
55534658 AGCCCTTTT
1 AGCCCTTTT
55534667 TACACTTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
23 7 0.10
24 13 0.18
25 43 0.59
26 10 0.14
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTAGGGCAAA
Found at i:55534737 original size:20 final size:20
Alignment explanation
Indices: 55534714--55534760 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
55534704 TTATGAATGC
55534714 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
55534734 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
55534754 ATCATGT
1 ATCATGT
55534761 ATATCAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:55541124 original size:18 final size:18
Alignment explanation
Indices: 55541101--55541135 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55541091 CCTACACCCT
55541101 TCCGCGACCACGTCCACA
1 TCCGCGACCACGTCCACA
* *
55541119 TCCGCGGCCTCGTCCAC
1 TCCGCGACCACGTCCAC
55541136 GAGCTCCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.51, G:0.20, T:0.14
Consensus pattern (18 bp):
TCCGCGACCACGTCCACA
Found at i:55542464 original size:31 final size:31
Alignment explanation
Indices: 55542426--55542489 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
55542416 CCTTTTCATA
55542426 TTTCATATTTCATAACACTGGGCCGAAACCT
1 TTTCATATTTCATAACACTGGGCCGAAACCT
** *
55542457 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAACCT
55542488 TT
1 TT
55542490 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAACCT
Found at i:55542738 original size:24 final size:25
Alignment explanation
Indices: 55542698--55542780 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 25
55542688 CTGGAGGCCT
55542698 AGCCTCTTTTAAT-AACT-GGG-ACAA
1 AGCC-CTTTTAATAAACTAGGGCA-AA
*
55542722 AGCCCTTTTGATAAACTAGGGCAAA
1 AGCCCTTTTAATAAACTAGGGCAAA
55542747 AGCCCTTTTAATAAACTAGGGCAAA
1 AGCCCTTTTAATAAACTAGGGCAAA
*
55542772 AGCCTTTTT
1 AGCCCTTTT
55542781 CGGTAAACTG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
23 7 0.13
24 8 0.15
25 37 0.70
26 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTAGGGCAAA
Found at i:55542794 original size:26 final size:25
Alignment explanation
Indices: 55542720--55542805 Score: 111
Period size: 25 Copynumber: 3.4 Consensus size: 25
55542710 TAACTGGGAC
55542720 AAAGCCCTTTTGATAAACTAGGGCA
1 AAAGCCCTTTTGATAAACTAGGGCA
*
55542745 AAAGCCCTTTTAATAAACTAGGGCA
1 AAAGCCCTTTTGATAAACTAGGGCA
* * *
55542770 AAAGCCTTTTTCGGTAAACTGGGGC-
1 AAAGCCCTTTT-GATAAACTAGGGCA
*
55542795 ATAGCCCTTTT
1 AAAGCCCTTTT
55542806 TGCACTTCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
25 43 0.81
26 10 0.19
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (25 bp):
AAAGCCCTTTTGATAAACTAGGGCA
Found at i:55542801 original size:50 final size:47
Alignment explanation
Indices: 55542686--55542805 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 47
55542676 TTTATCATAT
*
55542686 AACTGGAGGCCTAGCCTCTTTTAATAACTGGGACAAAGCCCTTTTGATA
1 AACTGG-GGCATAGCC-CTTTTAATAACTGGGACAAAGCCCTTTTGATA
* * * *
55542735 AACTAGGGCAAAAGCCCTTTTAATAAACTAGGG-CAAAAGCCTTTTTCGGTA
1 AACTGGGGC-ATAGCCCTTTTAAT-AACT-GGGAC-AAAGCCCTTTT-GATA
55542786 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCATAGCCCTTTT
55542806 TGCACTTCCT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
48 11 0.19
49 14 0.24
50 23 0.39
51 11 0.19
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
AACTGGGGCATAGCCCTTTTAATAACTGGGACAAAGCCCTTTTGATA
Found at i:55542876 original size:20 final size:20
Alignment explanation
Indices: 55542853--55542899 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
55542843 TTATGAATAC
55542853 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
55542873 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
55542893 ATCATGT
1 ATCATGT
55542900 ATATCAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:55545966 original size:19 final size:19
Alignment explanation
Indices: 55545942--55545982 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
55545932 TGTGGTCCTT
*
55545942 ATTTCAACATCAAAATTTA
1 ATTTCAACATCAAAATTAA
**
55545961 ATTTCAATTTCAAAATTAA
1 ATTTCAACATCAAAATTAA
55545980 ATT
1 ATT
55545983 AGTATTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTCAACATCAAAATTAA
Found at i:55547577 original size:13 final size:13
Alignment explanation
Indices: 55547559--55547585 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55547549 GTGATATAGG
55547559 TGATATCTAAATA
1 TGATATCTAAATA
55547572 TGATATCTAAATA
1 TGATATCTAAATA
55547585 T
1 T
55547586 TTAAGATATT
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:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TGATATCTAAATA
Found at i:55552293 original size:11 final size:11
Alignment explanation
Indices: 55552263--55552308 Score: 51
Period size: 10 Copynumber: 4.2 Consensus size: 11
55552253 GATAATATGA
55552263 ATAAACTTTTT
1 ATAAACTTTTT
*
55552274 A-AAAGTTTTT
1 ATAAACTTTTT
55552284 ATAAACTTTTT
1 ATAAACTTTTT
55552295 A-AAATTCTTTTT
1 ATAAA--CTTTTT
55552307 AT
1 AT
55552309 TAATTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 12 0.41
11 10 0.34
12 7 0.24
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (11 bp):
ATAAACTTTTT
Found at i:55553098 original size:30 final size:29
Alignment explanation
Indices: 55553057--55553120 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
55553047 ATTCAACATC
55553057 ATTTTAGTTGAAATCGTAATAT-TATAA-T
1 ATTTTAGTTGAAATC-TAATATGTATAATT
* *
55553085 ATTTTCAGTTTGAATTCTATTATGTATAATT
1 ATTTT-AG-TTGAAATCTAATATGTATAATT
55553116 ATTTT
1 ATTTT
55553121 TTCAGATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.17
29 7 0.23
30 12 0.40
31 6 0.20
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (29 bp):
ATTTTAGTTGAAATCTAATATGTATAATT
Found at i:55554534 original size:31 final size:31
Alignment explanation
Indices: 55554499--55554575 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
55554489 ACTATTAAAA
* *
55554499 TAGTCACTTTTGTTTCTCTGATATTATAGTT
1 TAGTCACTTATGTTTCTCTGATATTACAGTT
* * *
55554530 TAGTCACTAATGTTTCTCTGATGTTACATTT
1 TAGTCACTTATGTTTCTCTGATATTACAGTT
55554561 TAGTCACTTATGTTT
1 TAGTCACTTATGTTT
55554576 GAAATGTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.14, G:0.13, T:0.52
Consensus pattern (31 bp):
TAGTCACTTATGTTTCTCTGATATTACAGTT
Found at i:55555808 original size:23 final size:25
Alignment explanation
Indices: 55555780--55555827 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
55555770 AATTTTTATA
55555780 TTTTAATTTAATA-TAATA-TAATT
1 TTTTAATTTAATATTAATATTAATT
*
55555803 TTTTAATTTTATATTAATATTAATT
1 TTTTAATTTAATATTAATATTAATT
55555828 AATTCAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 5 0.23
25 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTAATTTAATATTAATATTAATT
Found at i:55560433 original size:31 final size:31
Alignment explanation
Indices: 55560395--55560536 Score: 114
Period size: 31 Copynumber: 4.6 Consensus size: 31
55560385 TAAGAAGTCA
* *
55560395 TTATTTGAGCAATTTTGAAAAGTTTTAGCCC
1 TTATTTGAACAATTTTGAAAAGGTTTAGCCC
* * * * *
55560426 TTATTTGATCACTTTCGAAAAGGTTTGGCCT
1 TTATTTGAACAATTTTGAAAAGGTTTAGCCC
**
55560457 TTATTTGAAC-ATTTTGAAAAGGTTTA-ATC
1 TTATTTGAACAATTTTGAAAAGGTTTAGCCC
* *
55560486 TTCATTTGAAC-ATTTTAATAAATG-TTAGACCC
1 TT-ATTTGAACAATTTTGA-AAAGGTTTAG-CCC
*
55560518 TTATTT-AACCATTTTGAAA
1 TTATTTGAACAATTTTGAAA
55560537 TATTTGATCT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
29 2 0.02
30 35 0.40
31 48 0.55
32 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (31 bp):
TTATTTGAACAATTTTGAAAAGGTTTAGCCC
Found at i:55562396 original size:27 final size:28
Alignment explanation
Indices: 55562342--55562395 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
55562332 AAAATGATTG
55562342 AAAAATTTCTCCATAAGTAGCTTTTTTA
1 AAAAATTTCTCCATAAGTAGCTTTTTTA
55562370 AAAAATTTCTCCATAAGTAGCTTTTT
1 AAAAATTTCTCCATAAGTAGCTTTTT
55562396 ATCTACTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (28 bp):
AAAAATTTCTCCATAAGTAGCTTTTTTA
Found at i:55562633 original size:13 final size:14
Alignment explanation
Indices: 55562610--55562638 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55562600 AATAAATGAA
55562610 ATATTTAAATTTTT
1 ATATTTAAATTTTT
55562624 ATATTT-AATTTTT
1 ATATTTAAATTTTT
55562637 AT
1 AT
55562639 CTAAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTAAATTTTT
Found at i:55562982 original size:13 final size:13
Alignment explanation
Indices: 55562964--55562990 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55562954 TTGGAGAGGG
55562964 ACTGAAGTTGGCT
1 ACTGAAGTTGGCT
55562977 ACTGAAGTTGGCT
1 ACTGAAGTTGGCT
55562990 A
1 A
55562991 AGGAGTTGGG
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:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (13 bp):
ACTGAAGTTGGCT
Found at i:55563471 original size:16 final size:16
Alignment explanation
Indices: 55563437--55563483 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
55563427 AAATGTTTTG
55563437 ATATAATT-TAATATAAA
1 ATATAATTAT-AT-TAAA
55563454 ATATAATTATATTAAA
1 ATATAATTATATTAAA
* *
55563470 ATATGATTAAATTA
1 ATATAATTATATTA
55563484 TTCTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 16 0.59
17 10 0.37
18 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATAATTATATTAAA
Found at i:55563621 original size:16 final size:16
Alignment explanation
Indices: 55563600--55563653 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
55563590 TAAATTATTG
55563600 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
** **
55563616 ATTACAGTTCTATTAT
1 ATTACAACTCTATTCC
*
55563632 ATTATAACTCTATTCC
1 ATTACAACTCTATTCC
*
55563648 GTTACA
1 ATTACA
55563654 TTTCAAAATT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:55563905 original size:11 final size:11
Alignment explanation
Indices: 55563891--55563922 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
55563881 GAAAAGGAGC
55563891 AAAAAAAGAAA
1 AAAAAAAGAAA
55563902 AAAAAAAG-AA
1 AAAAAAAGAAA
55563912 AAAAAAAGAAA
1 AAAAAAAGAAA
55563923 CAGTAGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:55564081 original size:13 final size:13
Alignment explanation
Indices: 55564059--55564088 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55564049 TTTCATTTAA
55564059 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
55564072 AAAAAGAAAAAAG
1 AAAAAAAAAAAAG
55564085 AAAA
1 AAAA
55564089 GGTGTTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:55567489 original size:39 final size:39
Alignment explanation
Indices: 55567428--55567586 Score: 257
Period size: 39 Copynumber: 4.1 Consensus size: 39
55567418 AATTATATTA
* *
55567428 CCAGCACAAAGCCTGC-GGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
* *
55567466 CCTGCACGAAGCCTACGGGACTTTAGCCTGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
55567505 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
* *
55567544 TCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
55567583 CCAG
1 CCAG
55567587 TATCTTGCAT
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
38 13 0.12
39 98 0.88
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (39 bp):
CCAGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
Found at i:55570889 original size:2 final size:2
Alignment explanation
Indices: 55570882--55570929 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
55570872 TATAGGCATG
55570882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55570924 TA TA TA
1 TA TA TA
55570930 ATAACTTGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55571502 original size:22 final size:24
Alignment explanation
Indices: 55571477--55571520 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
55571467 ATTTTAATTT
55571477 ATAATTCA-TAAAA-ATAAAAACA
1 ATAATTCATTAAAACATAAAAACA
*
55571499 ATAATTTATTAAAACATAAAAA
1 ATAATTCATTAAAACATAAAAA
55571521 ATAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAATTCATTAAAACATAAAAACA
Found at i:55571908 original size:20 final size:21
Alignment explanation
Indices: 55571868--55571911 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
55571858 TAATGAACTT
55571868 TAAATTTTTATGATATAAAAA
1 TAAATTTTTATGATATAAAAA
55571889 TAAATATTTTAT-AT-TAAAAA
1 TAAAT-TTTTATGATATAAAAA
55571909 TAA
1 TAA
55571912 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATTTTTATGATATAAAAA
Found at i:55574516 original size:40 final size:40
Alignment explanation
Indices: 55574457--55574598 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
55574447 AAATTGAATG
* * *
55574457 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
55574497 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
55574537 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
55574577 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
55574599 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:55574622 original size:40 final size:40
Alignment explanation
Indices: 55574495--55574624 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
55574485 ATGCTGGAAA
* * *
55574495 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * **
55574535 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
55574575 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
55574615 TTATATCCGG
1 TTATATCCGG
55574625 TTATATTCCG
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:55576380 original size:29 final size:29
Alignment explanation
Indices: 55576337--55576393 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
55576327 TGTTTTTTGG
*
55576337 TTGGTTTGCTAACTAACCGAAAAACTTAC
1 TTGGTTTGCTAACTAACCAAAAAACTTAC
*
55576366 TTGGTTTGCTGACTAACCAAAAAACTTA
1 TTGGTTTGCTAACTAACCAAAAAACTTA
55576394 GGTAACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (29 bp):
TTGGTTTGCTAACTAACCAAAAAACTTAC
Found at i:55580112 original size:2 final size:2
Alignment explanation
Indices: 55580105--55580147 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
55580095 TTTCCAATGT
*
55580105 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
55580148 AATTACATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55582043 original size:40 final size:40
Alignment explanation
Indices: 55581999--55582079 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
55581989 TCACAAGTTT
* *
55581999 TGTACTTTTTGAAAATTTAGCCCTTCATATTTACAAATTC
1 TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
55582039 TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
1 TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
55582079 T
1 T
55582080 ATCAATTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (40 bp):
TGTACTTTTTGAAAATTTAACCCTCCATATTTACAAATTC
Found at i:55590315 original size:49 final size:50
Alignment explanation
Indices: 55590214--55590335 Score: 144
Period size: 49 Copynumber: 2.5 Consensus size: 50
55590204 TCGTGCTAGT
* *
55590214 GTAAGA-CATGTCTGGGACAT-GCATCAGCACGTATACACGAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCAGCACGTATACACGAGAGCCAGC
* ** *
55590262 GTAAGACCATGTCTGGGACATGGCATCAGCCTCG-ATGGA-GATAGCCAGC
1 GTAAGACCATGTCTGGGACATGGCATCAG-CACGTATACACGAGAGCCAGC
*
55590311 GTAAGACCATGTCTGGGATATGGCA
1 GTAAGACCATGTCTGGGACATGGCA
55590336 GTGGCAACTT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
48 6 0.09
49 45 0.70
50 10 0.16
51 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATCAGCACGTATACACGAGAGCCAGC
Found at i:55596837 original size:26 final size:26
Alignment explanation
Indices: 55596801--55596852 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55596791 TCTTATTTCT
55596801 TCACCAAAATTATCAGAAAAAATGGA
1 TCACCAAAATTATCAGAAAAAATGGA
55596827 TCACCAAAATTATCAGAAAAAATGGA
1 TCACCAAAATTATCAGAAAAAATGGA
55596853 GTTTTGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (26 bp):
TCACCAAAATTATCAGAAAAAATGGA
Found at i:55597306 original size:30 final size:30
Alignment explanation
Indices: 55597249--55597306 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
55597239 CTTTCGAGCA
* **
55597249 TAGGGGTAAAATGGTCATTTTGTCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
55597279 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
55597307 ATGTAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:55599222 original size:30 final size:30
Alignment explanation
Indices: 55599181--55599248 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
55599171 TCGATTAGAA
*
55599181 GCCCATGTACTGCCACACGGCCTACCACAC
1 GCCCGTGTACTGCCACACGGCCTACCACAC
* *
55599211 GCCCGTGTACTGCCACATGGCCTACCATAC
1 GCCCGTGTACTGCCACACGGCCTACCACAC
*
55599241 GGCCGTGT
1 GCCCGTGT
55599249 GGCATCAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.19, C:0.41, G:0.22, T:0.18
Consensus pattern (30 bp):
GCCCGTGTACTGCCACACGGCCTACCACAC
Found at i:55603797 original size:47 final size:47
Alignment explanation
Indices: 55603743--55603842 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
55603733 TTAGGATTTT
* * *
55603743 ATGTGATGAATGTGAGCGTGTATATATGAGAT-AAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAAGG-CGAATGGCCA
* * * *
55603790 ATGTGATGATTGTGAACATGCATATATGTGGTAAAGGCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAAGGCGAATGGCCA
55603837 ATGTGA
1 ATGTGA
55603843 AATATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 41 0.91
48 4 0.09
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAAGGCGAATGGCCA
Found at i:55603966 original size:50 final size:50
Alignment explanation
Indices: 55603812--55603947 Score: 254
Period size: 50 Copynumber: 2.7 Consensus size: 50
55603802 TGAACATGCA
*
55603812 TATATGTGGTAAAGGCGAATGGCTAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
55603862 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
*
55603912 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
55603948 GTAGGCGATG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (50 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
Found at i:55604205 original size:37 final size:37
Alignment explanation
Indices: 55604097--55604205 Score: 175
Period size: 37 Copynumber: 2.9 Consensus size: 37
55604087 GGAAATATAT
* *
55604097 TCCGGGTAAGGCCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
55604134 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
55604171 TCCGGGTAAGACCCGATAACCT-CGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGA-CTACGTGTGGAGATTT
55604206 CGTCTGAGCT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 66 0.97
38 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:55607531 original size:39 final size:40
Alignment explanation
Indices: 55607422--55607548 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
55607412 TCACTCAAAG
*
55607422 GCCTTCGGGAC-AAACCCCGG-TTATAGTAACTCGCACGAAT
1 GCCTTCGGGACTTAA-CCCGGATT-TAGTAACTCGCACGAAT
* *
55607462 GCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCACAAAT
1 GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACGAAT
* *
55607502 GCCTTCGGG-CTTAACCCGGATTTATTAACTCGCACGAAC
1 GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACGAAT
55607541 GCCTTCGG
1 GCCTTCGG
55607549 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
39 34 0.43
40 41 0.52
41 4 0.05
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACGAAT
Found at i:55615144 original size:40 final size:40
Alignment explanation
Indices: 55615045--55615267 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
55615035 TAACGGGGTC
55615045 AAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
55615085 AAGT-CCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
55615124 AAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTACA-TCCGGGCT
* *
55615164 AAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
* * * * * * *
55615204 AAGACCCGAAGACATTTGTGCTAGTGACCATATCCGGACT
1 AAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
* * *
55615244 AAGACCCGACGGC-CTTGTGCGAGT
1 AAGTCCCGAAGGCATTTGTGCGAGT
55615268 GGTTATATCC
Statistics
Matches: 168, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 49 0.29
40 118 0.70
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
AAGTCCCGAAGGCATTTGTGCGAGTTACTACATCCGGGCT
Found at i:55618280 original size:42 final size:42
Alignment explanation
Indices: 55618215--55618369 Score: 204
Period size: 42 Copynumber: 3.7 Consensus size: 42
55618205 GGTTACTAGT
* *
55618215 GTGTAAGACCATATCTGGTATATGGCATCTATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTC
*
55618257 GTGTAAGACCATATTTGGGATATGGCATCAATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTC
* * *
55618299 GTGTAAGACCATAGCTGGGCTATTGGCATCGATATGAGA-TTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCAATATGAGACTT-C
* **
55618342 ATGTAAGATTATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
55618370 TGGTACGGTA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
42 66 0.67
43 33 0.33
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTC
Found at i:55618361 original size:85 final size:84
Alignment explanation
Indices: 55618215--55618369 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 84
55618205 GGTTACTAGT
* * * *
55618215 GTGTAAGACCATATCTGGTATATGGCATCTATATGAGACTTCGTGTAAGACCATATTTGGGATAT
1 GTGTAAGACCATAGCTGGTATATGGCATCGATATGAGACTTCATGTAAGACCATATCTGGGATAT
55618280 GGCATCAATATGAGACTTC
66 GGCATCAATATGAGACTTC
**
55618299 GTGTAAGACCATAGCTGGGCTAT-TGGCATCGATATGAGA-TTACATGTAAGATTATATCTGGGA
1 GTGTAAGACCATAGCT-GG-TATATGGCATCGATATGAGACTT-CATGTAAGACCATATCTGGGA
55618362 TATGGCAT
63 TATGGCAT
55618370 TGGTACGGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
84 17 0.27
85 42 0.68
86 3 0.05
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (84 bp):
GTGTAAGACCATAGCTGGTATATGGCATCGATATGAGACTTCATGTAAGACCATATCTGGGATAT
GGCATCAATATGAGACTTC
Found at i:55622738 original size:26 final size:26
Alignment explanation
Indices: 55622709--55622762 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
55622699 TCCGTTGCAT
55622709 GTTAGTAAAGTTGAAAATAGTTGAAG
1 GTTAGTAAAGTTGAAAATAGTTGAAG
55622735 GTTAGTAAAGTTGAAAATAGTTGAAG
1 GTTAGTAAAGTTGAAAATAGTTGAAG
55622761 GT
1 GT
55622763 GTTATTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (26 bp):
GTTAGTAAAGTTGAAAATAGTTGAAG
Done.