Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 43 of 328
Found at i:12478874 original size:19 final size:18
Alignment explanation
Indices: 12478838--12478874 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12478828 TTGATATGAT
*
12478838 ATTAAAATTATTAAAAAA
1 ATTAAAATTATAAAAAAA
12478856 ATTAAAATATATAAAAAAA
1 ATTAAAAT-TATAAAAAAA
12478875 TCAGGGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATTAAAATTATAAAAAAA
Found at i:12479166 original size:21 final size:22
Alignment explanation
Indices: 12479142--12479184 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12479132 AAATTAAATC
12479142 TCTAAGATTACA-ATCATATCT
1 TCTAAGATTACATATCATATCT
*
12479163 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACATATCATATCT
12479185 ATGATTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (22 bp):
TCTAAGATTACATATCATATCT
Found at i:12479190 original size:19 final size:19
Alignment explanation
Indices: 12479163--12479199 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12479153 AATCATATCT
12479163 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12479182 TCTATGATTGCATATCAT
1 TCTAAGATTGCATATCAT
12479200 TGAAGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12479350 original size:21 final size:21
Alignment explanation
Indices: 12479326--12479366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12479316 CGTTTATTTT
*
12479326 TTTATT-TTTCTTTTTTTTGGG
1 TTTATTATTT-TTGTTTTTGGG
12479347 TTTATTATTTTTGTTTTTGG
1 TTTATTATTTTTGTTTTTGG
12479367 ACTTATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.07, C:0.02, G:0.15, T:0.76
Consensus pattern (21 bp):
TTTATTATTTTTGTTTTTGGG
Found at i:12489011 original size:4 final size:4
Alignment explanation
Indices: 12489002--12489027 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12488992 ACACAAGTGT
12489002 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
12489028 TGTACGTACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:12491200 original size:18 final size:18
Alignment explanation
Indices: 12491177--12491211 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
12491167 AAAATTTAAG
12491177 TCCAATGAATCTACTTCT
1 TCCAATGAATCTACTTCT
12491195 TCCAATGAATCTACTTC
1 TCCAATGAATCTACTTC
12491212 CATATACACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (18 bp):
TCCAATGAATCTACTTCT
Found at i:12491408 original size:2 final size:2
Alignment explanation
Indices: 12491368--12491394 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12491358 CTCACTTTCC
12491368 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 A
12491395 GATGAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12492179 original size:2 final size:2
Alignment explanation
Indices: 12492160--12492193 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12492150 CCAAAAATGA
* *
12492160 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12492194 TAAAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12492518 original size:12 final size:12
Alignment explanation
Indices: 12492501--12492525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12492491 GATTCATGGG
12492501 TTCTTTTTTTTT
1 TTCTTTTTTTTT
12492513 TTCTTTTTTTTT
1 TTCTTTTTTTTT
12492525 T
1 T
12492526 GGAAATTTTA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:12495557 original size:22 final size:22
Alignment explanation
Indices: 12495532--12495577 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12495522 TGCATAAGAA
12495532 TATATCACATACCTGGCCAACT
1 TATATCACATACCTGGCCAACT
12495554 TATATCACATACCTGGCCAACT
1 TATATCACATACCTGGCCAACT
12495576 TA
1 TA
12495578 ATGCATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (22 bp):
TATATCACATACCTGGCCAACT
Found at i:12495860 original size:26 final size:26
Alignment explanation
Indices: 12495831--12495890 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
12495821 TCCCTTTGAA
* * *
12495831 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
12495857 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
12495885 TCATTC
1 TCATTC
12495891 TCAATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:12495876 original size:28 final size:28
Alignment explanation
Indices: 12495845--12495907 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
12495835 TCGATATTTT
12495845 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
12495873 GCACACTAAGTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
12495901 GTACACT
1 GCACACT
12495908 GAGTACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:12500932 original size:57 final size:57
Alignment explanation
Indices: 12500841--12501196 Score: 599
Period size: 57 Copynumber: 6.2 Consensus size: 57
12500831 GATCTCATTT
* * *
12500841 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* *
12500900 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAATCA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
12500957 CACACACAGTGCCTCAACAA-CGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
*
12501013 CACACACAGTGCCTCAACAACCGATCTCGTACACACAGTGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
12501070 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTAC-GAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
12501126 CACACACAGTGCCTCAACAACTGATCTCACACACACAGTGCTCGGTTACGGAACTCA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
12501183 CACACACAGTGCCT
1 CACACACAGTGCCT
12501197 ATGTTCACTT
Statistics
Matches: 283, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
56 108 0.38
57 168 0.59
59 7 0.02
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:12501009 original size:113 final size:114
Alignment explanation
Indices: 12500840--12501196 Score: 610
Period size: 113 Copynumber: 3.1 Consensus size: 114
12500830 TGATCTCATT
** * * *
12500840 TCACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCGCACAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
*
12500905 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAA
66 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
12500954 TCACACACACAGTGCCTCAACAA-CGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
*
12501018 ACAGTGCCTCAACAACCGATCTCGTACACACAGTGCTCGGTTACGGAAC
66 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
*
12501067 TCGCACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTAC-GAACTCGCACAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
* *
12501131 ACAGTGCCTCAACAACTGATCTCACACACACAGTGCTCGGTTACGGAAC
66 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
12501180 TCACACACACAGTGCCT
1 TCACACACACAGTGCCT
12501197 ATGTTCACTT
Statistics
Matches: 230, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
113 182 0.79
114 48 0.21
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (114 bp):
TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
Found at i:12501161 original size:170 final size:170
Alignment explanation
Indices: 12500840--12501196 Score: 608
Period size: 170 Copynumber: 2.1 Consensus size: 170
12500830 TGATCTCATT
** * * *
12500840 TCACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCGCACAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
12500905 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAATCACACACACAGTGCC
66 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAATCACACACACAGTGCC
*
12500970 TCAACAACGATCTCGCACACACAGTGCTCGGTTACGGAAC
131 TCAACAACGATCTCACACACACAGTGCTCGGTTACGGAAC
* *
12501010 TCGCACACACAGTGCCTCAACAACCGATCTCGTACACACAGTGCTCGGTTACGGAACTCGCACAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
* *
12501075 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTAC-GAACTCGCACACACAGTGCC
66 ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAATCACACACACAGTGCC
12501139 TCAACAACTGATCTCACACACACAGTGCTCGGTTACGGAAC
131 TCAACAAC-GATCTCACACACACAGTGCTCGGTTACGGAAC
12501180 TCACACACACAGTGCCT
1 TCACACACACAGTGCCT
12501197 ATGTTCACTT
Statistics
Matches: 175, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
169 26 0.15
170 149 0.85
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (170 bp):
TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGCACAC
ACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAATCACACACACAGTGCC
TCAACAACGATCTCACACACACAGTGCTCGGTTACGGAAC
Found at i:12503137 original size:26 final size:26
Alignment explanation
Indices: 12503108--12503167 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
12503098 TCCCTTTGAA
* * *
12503108 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
12503134 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
12503162 TCATTC
1 TCATTC
12503168 TCAATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:12503153 original size:28 final size:28
Alignment explanation
Indices: 12503122--12503184 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
12503112 TCGATATTTT
12503122 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
12503150 GCACACTAAGTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
12503178 GTACACT
1 GCACACT
12503185 GAGTACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:12506414 original size:39 final size:39
Alignment explanation
Indices: 12506346--12506488 Score: 214
Period size: 39 Copynumber: 3.6 Consensus size: 39
12506336 TAACTTACGA
* *
12506346 ACCTTAAGTCTGAATTATAATTCCAGCATATAGCCTGCGG
1 ACCTTAAGTCCGGA-TATAATTCCAGCATATAGCCTGCGG
*
12506386 ACCTTAAGTCCGGATATATTTCCAGCATATAGCCTGCGG
1 ACCTTAAGTCCGGATATAATTCCAGCATATAGCCTGCGG
* *
12506425 ACCTTAAGTCTGAATATAATTCCAGCATATAGCCTGCGG
1 ACCTTAAGTCCGGATATAATTCCAGCATATAGCCTGCGG
*
12506464 ACCTTAAGTTCGGATTATAATTCCA
1 ACCTTAAGTCCGGA-TATAATTCCA
12506489 AATATCATGC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 71 0.76
40 22 0.24
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (39 bp):
ACCTTAAGTCCGGATATAATTCCAGCATATAGCCTGCGG
Found at i:12506471 original size:78 final size:79
Alignment explanation
Indices: 12506310--12506488 Score: 252
Period size: 79 Copynumber: 2.3 Consensus size: 79
12506300 CTTCGGAACT
* * * *
12506310 TTAAGCCCGGATATATTTCTAGCACGTAACTTACGAACCTTAAGTCTGAATTATAATTCCAGCAT
1 TTAAGTCCGGATATATTTCCAGCACATAACCTACGAACCTTAAGTCTGAATTATAATTCCAGCAT
12506375 ATAGCCTGCGGACC
66 ATAGCCTGCGGACC
* * * *
12506389 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTTAAGTCTGAA-TATAATTCCAGCAT
1 TTAAGTCCGGATATATTTCCAGCACATAACCTACGAACCTTAAGTCTGAATTATAATTCCAGCAT
12506453 ATAGCCTGCGGACC
66 ATAGCCTGCGGACC
* *
12506467 TTAAGTTCGGATTATAATTCCA
1 TTAAGTCCGGA-TATATTTCCA
12506489 AATATCATGC
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 38 0.43
79 51 0.57
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (79 bp):
TTAAGTCCGGATATATTTCCAGCACATAACCTACGAACCTTAAGTCTGAATTATAATTCCAGCAT
ATAGCCTGCGGACC
Found at i:12513048 original size:2 final size:2
Alignment explanation
Indices: 12513041--12513078 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12513031 TTAAAACACA
12513041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12513079 TGTTTTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12514878 original size:17 final size:17
Alignment explanation
Indices: 12514852--12514897 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
12514842 GGCCAATCTG
*
12514852 GGCGTGTGGGCC-ACAC
1 GGCGTATGGGCCTACAC
12514868 GAGCGTATGGGCCTACAC
1 G-GCGTATGGGCCTACAC
12514886 GGACGTATGGGC
1 GG-CGTATGGGC
12514898 TCATGTATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
18 14 0.54
ACGTcount: A:0.17, C:0.26, G:0.41, T:0.15
Consensus pattern (17 bp):
GGCGTATGGGCCTACAC
Found at i:12517204 original size:122 final size:121
Alignment explanation
Indices: 12516979--12517221 Score: 396
Period size: 122 Copynumber: 2.0 Consensus size: 121
12516969 GATTATTTGA
* *
12516979 TTCTGACTTTGTTTCTGTAAGGACTTAAGTTCGAATCTGTATCTATTCTGCATACGAGAATTTTG
1 TTCTGACTTTGTTTCTGTAAGGACTTAAGTCCGAATCTGTATCTATTCTGCATACGAGAATTTTA
* * *
12517044 TGTTTATTTGTATGACTATCTCTGTTGGGTTACACACTGAGTTTACGAAGACTCAC
66 TGTTTATTTGCATGACTATCTCTATTGGGTTACACACTGAGTTTACGAAAACTCAC
* *
12517100 TTCTGACATTTGTTTCTGTAAGGACTTACGTCCGAATCTGTATCTGTTCTGCATACGAGAATTTT
1 TTCTGAC-TTTGTTTCTGTAAGGACTTAAGTCCGAATCTGTATCTATTCTGCATACGAGAATTTT
* *
12517165 ATGTTTGTTTGCATGACTATCTCTATTGGGTTACGCACTGAGTTTACGAAAACTCAC
65 ATGTTTATTTGCATGACTATCTCTATTGGGTTACACACTGAGTTTACGAAAACTCAC
12517222 ATCTATTTGT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
121 7 0.06
122 105 0.94
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (121 bp):
TTCTGACTTTGTTTCTGTAAGGACTTAAGTCCGAATCTGTATCTATTCTGCATACGAGAATTTTA
TGTTTATTTGCATGACTATCTCTATTGGGTTACACACTGAGTTTACGAAAACTCAC
Found at i:12517986 original size:20 final size:20
Alignment explanation
Indices: 12517945--12517988 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12517935 AGTTAGAAAC
* *
12517945 TGAAACTTCTAAAATATTTT
1 TGAAAATTCTAAAATATATT
12517965 TGAAAATTCTAATAA-ATATT
1 TGAAAATTCTAA-AATATATT
12517985 TGAA
1 TGAA
12517989 GTATAACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (20 bp):
TGAAAATTCTAAAATATATT
Found at i:12526931 original size:2 final size:2
Alignment explanation
Indices: 12526924--12526951 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12526914 ATAATCTCAA
12526924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12526952 GTATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12529733 original size:2 final size:2
Alignment explanation
Indices: 12529726--12529752 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12529716 AAAATAAAAG
12529726 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12529753 GACAAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12532855 original size:23 final size:23
Alignment explanation
Indices: 12532769--12532856 Score: 59
Period size: 23 Copynumber: 3.6 Consensus size: 23
12532759 CATCTTTTGA
* *
12532769 CCAAAACAACAAAAACCCAGAAA
1 CCAAAACATCAAAAACCCAGAAT
* * *
12532792 CCAAAACATCTAAAGATCAAGAATT
1 CCAAAACATC-AAAAACCCAGAA-T
* * *
12532817 AGACTAAAATACCAAAAACCCAGAAT
1 ---CCAAAACATCAAAAACCCAGAAT
12532843 CCAAAACATCAAAA
1 CCAAAACATCAAAA
12532857 TAAGATAATA
Statistics
Matches: 46, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
23 20 0.43
24 9 0.20
26 1 0.02
27 9 0.20
28 7 0.15
ACGTcount: A:0.59, C:0.25, G:0.06, T:0.10
Consensus pattern (23 bp):
CCAAAACATCAAAAACCCAGAAT
Found at i:12535802 original size:31 final size:31
Alignment explanation
Indices: 12535764--12535827 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
12535754 CCTTTTCATA
12535764 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
12535795 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
12535826 TT
1 TT
12535828 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:12536068 original size:24 final size:24
Alignment explanation
Indices: 12536017--12536135 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
12536007 GCTTTATCAT
*
12536017 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
12536042 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
12536066 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
12536089 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
12536113 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12536136 TCACTTCCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 23 0.27
24 51 0.59
25 12 0.14
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12536096 original size:47 final size:48
Alignment explanation
Indices: 12536017--12536135 Score: 161
Period size: 47 Copynumber: 2.5 Consensus size: 48
12536007 GCTTTATCAT
*
12536017 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
12536066 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
*
12536113 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12536136 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 43 0.67
48 9 0.14
49 12 0.19
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:12536211 original size:20 final size:20
Alignment explanation
Indices: 12536186--12536245 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
12536176 TATGATTACC
12536186 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
12536206 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
12536226 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
12536246 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:12536216 original size:11 final size:11
Alignment explanation
Indices: 12536186--12536240 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
12536176 TATGATTACC
12536186 TCATGTGCATA
1 TCATGTGCATA
*
12536197 TCA--TACATA
1 TCATGTGCATA
12536206 TCATGTGCATA
1 TCATGTGCATA
* *
12536217 TCA--TACATT
1 TCATGTGCATA
12536226 TCATGTGCATA
1 TCATGTGCATA
12536237 TCAT
1 TCAT
12536241 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:12536320 original size:25 final size:25
Alignment explanation
Indices: 12536288--12536335 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12536278 ATACATAAAC
* * *
12536288 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12536313 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12536336 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12543880 original size:30 final size:31
Alignment explanation
Indices: 12543844--12543906 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
12543834 CCTTTTCATA
12543844 TTTCATATTTCATAATACT-GGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
12543874 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
12543905 TT
1 TT
12543907 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:12544148 original size:24 final size:24
Alignment explanation
Indices: 12544097--12544214 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
12544087 GCTTTATCAT
*
12544097 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
12544122 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
12544146 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
12544169 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
12544192 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12544215 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
22 16 0.19
23 12 0.14
24 45 0.53
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12544185 original size:46 final size:48
Alignment explanation
Indices: 12544097--12544214 Score: 161
Period size: 46 Copynumber: 2.5 Consensus size: 48
12544087 GCTTTATCAT
*
12544097 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
12544146 ATAACTGGGGCATAAGCCCTTTT-ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
12544192 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12544215 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
46 37 0.58
47 6 0.09
48 9 0.14
49 12 0.19
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:12544295 original size:11 final size:11
Alignment explanation
Indices: 12544265--12544318 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
12544255 TATGATTACC
12544265 TCATGTGCATA
1 TCATGTGCATA
*
12544276 TCA--TACATA
1 TCATGTGCATA
12544285 TCATGTGCATA
1 TCATGTGCATA
*
12544296 TCA--TACAT-
1 TCATGTGCATA
12544304 TCATGTGCATA
1 TCATGTGCATA
12544315 TCAT
1 TCAT
12544319 ACATACCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 3 0.09
9 12 0.35
10 4 0.12
11 15 0.44
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:12544309 original size:19 final size:20
Alignment explanation
Indices: 12544265--12544323 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
12544255 TATGATTACC
12544265 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
12544285 TCATGTGCATATCATACAT-
1 TCATGTGCATATCATACATA
12544304 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
12544324 CCATATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:12544398 original size:25 final size:25
Alignment explanation
Indices: 12544366--12544413 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12544356 ATACATAAAC
* * *
12544366 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
12544391 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
12544414 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:12546356 original size:3 final size:3
Alignment explanation
Indices: 12546348--12546396 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
12546338 TGTATTTTCA
* *
12546348 TAT TAT TAT TAT TAT AAT TAT TAT TAT ATAT TAT T-G TAT TAT CTAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT
12546394 TAT
1 TAT
12546397 ATGTAACACA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 32 0.82
4 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:12546387 original size:15 final size:15
Alignment explanation
Indices: 12546337--12546401 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
12546327 TTAAATTTTC
*
12546337 TTGTATTTTCATATTA
1 TTGTATTAT-ATATTA
*
12546353 TTATTATTATA-ATTA
1 TT-GTATTATATATTA
12546368 -T-TATTATATATTA
1 TTGTATTATATATTA
*
12546381 TTGTATTATCTATTA
1 TTGTATTATATATTA
12546396 TATGTA
1 T-TGTA
12546402 ACACATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
12 7 0.17
13 4 0.10
14 2 0.05
15 16 0.39
16 7 0.17
17 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (15 bp):
TTGTATTATATATTA
Found at i:12559148 original size:71 final size:71
Alignment explanation
Indices: 12559027--12559160 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 71
12559017 GTTTTCCAAG
* * *
12559027 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTAT
12559092 GTTTCA
66 GTTTCA
* * * * *
12559098 AAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTT
12559161 CTGCTTTTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:12559200 original size:160 final size:160
Alignment explanation
Indices: 12558936--12559322 Score: 704
Period size: 160 Copynumber: 2.4 Consensus size: 160
12558926 TTGTTTTTTC
*
12558936 CAAAAATCAACTCATATTGCGAGAAGTGAGTAGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
12559001 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
12559066 GACACATTGAGGTAATTTCAATTTATGTTT
131 GACACATTGAGGTAATTTCAATTTATGTTT
*
12559096 CAAAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
12559161 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
*
12559226 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACATTGAGGTAATTTCAATTTATGTTT
* * *
12559256 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GCGGCACGCTAATGTATTTTCAAAT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAG-GGCACGCTGAGGTATTTTCAATT
12559320 TCT
65 TCT
12559323 ATTTTCAAAA
Statistics
Matches: 219, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
159 1 0.00
160 218 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (160 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
GACACATTGAGGTAATTTCAATTTATGTTT
Found at i:12559316 original size:71 final size:72
Alignment explanation
Indices: 12559187--12559362 Score: 230
Period size: 71 Copynumber: 2.5 Consensus size: 72
12559177 GTTTTCCAAG
* * *
12559187 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC-AATT-T
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAAATTCT
12559250 ATGTTTCA
66 AT-TTTCA
* ** * * *
12559258 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGCGGCACGCTAATGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAAATTCT
12559323 ATTTTCA
66 ATTTTCA
* *
12559330 AAAGTCAATTCATATTGCGAGAGGTGAGTTGAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
12559363 TCTTTTTAAC
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 49 0.54
72 39 0.43
73 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (72 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTAAGGTAATTTCAAATTCT
ATTTTCA
Found at i:12559541 original size:68 final size:66
Alignment explanation
Indices: 12559401--12559574 Score: 181
Period size: 68 Copynumber: 2.6 Consensus size: 66
12559391 TTTTTTTAAT
* ** *
12559401 TTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGTTTTTCGAAATCT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCACTTTTC-AAATCC
12559466 AC
65 AC
* * * * *
12559468 TTTTCAAATTATTAACTCATGTTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTACTTTT-AATTT
1 TTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTTTCACTTTTCAA-AT
12559532 CCA-
63 CCAC
* **
12559535 TGTTTCAAAAATCAACCCATATTGCGAGAAATGAGTTGAG
1 T-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
12559575 TCTCTGTTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
67 36 0.40
68 40 0.45
69 13 0.15
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (66 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCACTTTTCAAATCCA
C
Found at i:12561455 original size:3 final size:3
Alignment explanation
Indices: 12561447--12561481 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
12561437 TGTATTTTCA
*
12561447 TAT TAT TAT TAT TAT AAT TAT TAT TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
12561482 GTATATTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12566812 original size:2 final size:2
Alignment explanation
Indices: 12566805--12566844 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12566795 TGTTTTTGTA
12566805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12566845 TATGTGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12570233 original size:63 final size:62
Alignment explanation
Indices: 12570155--12570288 Score: 153
Period size: 62 Copynumber: 2.1 Consensus size: 62
12570145 ACATCCTGCC
* * * * *
12570155 ACACGGCCTGGGCACAAGCCCATGTGCCTTGGTTGTATGGTTTT-TAAGTACAAACAGTGAGTT
1 ACACGGCCTAGGCACAAGCCCATGT-CCCTAGCTGTATGGTTTTAT-ACTACAAACAGTGAGTT
* * * * *
12570218 ACATGGCCTAGGCACACGCTCGTGTCCCTAGCTGTGTGGTTTTATACTACAAACAGTGAGTT
1 ACACGGCCTAGGCACAAGCCCATGTCCCTAGCTGTATGGTTTTATACTACAAACAGTGAGTT
12570280 ACACGGCCT
1 ACACGGCCT
12570289 GGAAACAAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
62 38 0.64
63 21 0.36
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (62 bp):
ACACGGCCTAGGCACAAGCCCATGTCCCTAGCTGTATGGTTTTATACTACAAACAGTGAGTT
Found at i:12576101 original size:15 final size:15
Alignment explanation
Indices: 12576081--12576110 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12576071 AAAATGTCAA
12576081 GTATCGATACCTTAG
1 GTATCGATACCTTAG
*
12576096 GTATCGATACTTTAG
1 GTATCGATACCTTAG
12576111 TGCCAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (15 bp):
GTATCGATACCTTAG
Found at i:12581858 original size:25 final size:28
Alignment explanation
Indices: 12581794--12581859 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
12581784 TGTTATTTAT
*
12581794 TTATTTATTTTAAACTTTTTTTCATACA
1 TTATTTATTTTAAACTTGTTTTCATACA
*
12581822 TTATTTATTTTAAA-TTGTTTT-AT-TA
1 TTATTTATTTTAAACTTGTTTTCATACA
*
12581847 TTATTTACTTTAA
1 TTATTTATTTTAA
12581860 GTTTTTCACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.37
26 2 0.06
27 6 0.17
28 14 0.40
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.64
Consensus pattern (28 bp):
TTATTTATTTTAAACTTGTTTTCATACA
Found at i:12582177 original size:24 final size:26
Alignment explanation
Indices: 12582141--12582192 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
12582131 ACATTATTTT
12582141 ATTGTTTTGTATATTAATGATTTTAA
1 ATTGTTTTGTATATTAATGATTTTAA
* *
12582167 ATTG-TTT-TATATTATTTATTTTAA
1 ATTGTTTTGTATATTAATGATTTTAA
12582191 AT
1 AT
12582193 CGCTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 3 0.12
26 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
ATTGTTTTGTATATTAATGATTTTAA
Found at i:12583674 original size:6 final size:6
Alignment explanation
Indices: 12583665--12583704 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
12583655 CTATATCTAT
12583665 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
12583705 ATTTTTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:12583710 original size:18 final size:18
Alignment explanation
Indices: 12583665--12583709 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
12583655 CTATATCTAT
*
12583665 TTTTGCTTTTGCTTTTGC
1 TTTTACTTTTGCTTTTGC
*
12583683 TTTTGCTTTTGCTTTTGC
1 TTTTACTTTTGCTTTTGC
12583701 TTTTA-TTTT
1 TTTTACTTTT
12583710 TCTTATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.02, C:0.13, G:0.13, T:0.71
Consensus pattern (18 bp):
TTTTACTTTTGCTTTTGC
Found at i:12584258 original size:19 final size:19
Alignment explanation
Indices: 12584217--12584260 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12584207 TTTTTTTTTT
*
12584217 TGCATTCATTTCATGCATT
1 TGCATTCATTTCATGCATA
*
12584236 TGCATTGCATTTCAT-CGTA
1 TGCATT-CATTTCATGCATA
12584255 TGCATT
1 TGCATT
12584261 AAATTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (19 bp):
TGCATTCATTTCATGCATA
Found at i:12587369 original size:39 final size:39
Alignment explanation
Indices: 12587315--12587392 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
12587305 CTTCTTAATT
12587315 GCATTTGCTATCCTTGATTAACTTAATTGCTTCGAGCTA
1 GCATTTGCTATCCTTGATTAACTTAATTGCTTCGAGCTA
12587354 GCATTTGCTATCCTTGATTAACTTAATTGCTTCGAGCTA
1 GCATTTGCTATCCTTGATTAACTTAATTGCTTCGAGCTA
12587393 TTCTTCTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (39 bp):
GCATTTGCTATCCTTGATTAACTTAATTGCTTCGAGCTA
Found at i:12588490 original size:133 final size:133
Alignment explanation
Indices: 12588252--12588657 Score: 487
Period size: 133 Copynumber: 3.1 Consensus size: 133
12588242 CGGTGTATTC
* * * *
12588252 ATAGATCTTATCTCCATGAGTTAGTAATGGAGCAGATCGAAGACGGTGAATCTTATCTCCCTGAA
1 ATAGATCTTATCTCCATGAGGTAGTAACGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAG
12588317 GT-GACAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTAAGCAGCAGTGGAGCAAGCTGAA
66 GTAG-CAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTAAGCAGCAGTGGAGCAAGCTGAA
12588381 GATT
130 GATT
* * * * * *
12588385 ATAGATCTTATCTCTATGAGGTAGCAACGGAACAGATCAAAGACGACAAATCTTATCTCCCTGAG
1 ATAGATCTTATCTCCATGAGGTAGTAACGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAG
* *
12588450 GTAGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTGAGCAGCAGTGGAGCAGGCTGAAG
66 GTAGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTAAGCAGCAGTGGAGCAAGCTGAAG
12588515 ATT
131 ATT
* * * * * * * *
12588518 ACAGTTCTTATCTCCCT-AAGCAGTAGCGGAGCAGATCGAATATGGCGAATCTTATCTTCCC-GA
1 ATAGATCTTATCTCCATGAGGTAGTAACGGAGCAGATCGAAGACGGCGAATCTTATC-TCCCTGA
* * * * * * * *
12588581 GGTAGTAGGGGAGCAGATTTAAGCCACCAGTCTTATCTTCCTGAAGTAGCAAG-GGAGCAAACTG
65 GGTAGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCT-AAGCAGC-AGTGGAGCAAGCTG
12588645 AAGATT
128 AAGATT
*
12588651 GTAGATC
1 ATAGATC
12588658 CCATCTCCCT
Statistics
Matches: 230, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
132 67 0.29
133 160 0.70
134 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (133 bp):
ATAGATCTTATCTCCATGAGGTAGTAACGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAG
GTAGCAAGGGAGCAGATTTAAGCCACTAGCCTTGTCTCCCTAAGCAGCAGTGGAGCAAGCTGAAG
ATT
Found at i:12588671 original size:45 final size:45
Alignment explanation
Indices: 12588615--12588725 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
12588605 CACCAGTCTT
* *
12588615 ATCTTCCTGAAGTAGCAAG-GGAGCAAACTGAAGATTGTAGATCCC
1 ATCTCCCTGAAGTAGCAAGTGGAGCAAACTGAAG-TTGAAGATCCC
* **
12588660 ATCTCCCTGAAGTAGC-AGTGGAGCAAATTGAAGTTGAAGATCTT
1 ATCTCCCTGAAGTAGCAAGTGGAGCAAACTGAAGTTGAAGATCCC
* *
12588704 ATCTCCTTGAAGTTGCAA-TGGA
1 ATCTCCCTGAAGTAGCAAGTGGA
12588726 ATAGATCAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
44 28 0.49
45 29 0.51
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (45 bp):
ATCTCCCTGAAGTAGCAAGTGGAGCAAACTGAAGTTGAAGATCCC
Found at i:12591438 original size:5 final size:5
Alignment explanation
Indices: 12591430--12591459 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
12591420 GCCCAACCCA
*
12591430 AAAAC AAAAC AAAAC AAAAC AAAAA AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
12591460 CCTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:12592535 original size:3 final size:3
Alignment explanation
Indices: 12592527--12592739 Score: 173
Period size: 3 Copynumber: 70.0 Consensus size: 3
12592517 ATCATTTTAC
12592527 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * **
12592575 TTA TTA TGA CTA TTA TTA TTA CTA CTA CTA TTA TTT TTA TTA ACA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
12592622 TTA TTA TTA TTA TTA TTT TTA -CA ATA TTA TTA TT- TCCTA TT- TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA
* ** * *
12592666 TTA TATA TTA TTA TTG TTA TTA ACA TATA TTA TTA ATA TTAA TGTA CTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A T-TA TTA
*
12592715 TTA TTT TCTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
12592740 CTAATATCAC
Statistics
Matches: 170, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
2 5 0.03
3 152 0.89
4 11 0.06
5 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12594606 original size:3 final size:3
Alignment explanation
Indices: 12594598--12595310 Score: 405
Period size: 3 Copynumber: 238.0 Consensus size: 3
12594588 TTCAAAATTT
* *
12594598 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
12594646 TAA T-A TAT TGA TAA TAA TAAA TAA TAA -AA GGAA TAA AAA TAA TAG
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA TAA TAA TAA
* * * * * **
12594691 TAC TAA TAA GAA TAT TAA CAA TAG TAA TAA TAA CGA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
12594736 TAC TAA TATA TACA TGAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TA-A T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12594784 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * * *
12594830 TTAA TGA CAA TAA T-A TACGT TAA TAA TGA TAA TAA TAA TATG TAA -AA
1 -TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * * * * * *
12594877 AAA GGGAA TAA TTA TAG T-A TAG TAA GAA TAA TAA TAA GAA TAA TAG
1 TAA --TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
12594923 TAG TAG TAA TAAA TAA -AA GGTAA TAG TAA TAA AAA TAA AAA TAA AAA
1 TAA TAA TAA T-AA TAA TAA --TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
12594970 TAA TAG TAA TAA TGA TAA TAA TAA TAA TAG TAA TAA -AA CAGA GAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * ** * * * * * *
12595015 -AA AAA AACA TAA CGA TAA GAG CAA TAA TAA TAA TTA TTA TAA TAG
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
12595060 TAA TAA T-A TAA -AA TTAA TGA T-A TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * ** * *
12595102 GCA -AA TAA GT-A TGAA -AA GAA -AA T-A TAA CCA TAG TAA TAA TAG
1 TAA TAA TAA -TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
12595144 T-A TAG TAA TAA TAA TAG TAA GAA TAA TAA TGA TAA T-A TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
12595190 TAG TAA T-A TAA CAA TAA -AA -AA TAA TAG TAA TGAA -AA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*** *
12595232 TAA CGG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12595280 TAA TAA T-A TAA TAA TAAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA
12595311 AGCAGCAAAA
Statistics
Matches: 544, Mismatches: 120, Indels: 92
0.72 0.16 0.12
Matches are distributed among these distances:
2 46 0.08
3 451 0.83
4 38 0.07
5 9 0.02
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:12596897 original size:12 final size:12
Alignment explanation
Indices: 12596877--12596911 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12596867 TATGTTGGAT
12596877 AAAATTAAAATA
1 AAAATTAAAATA
* *
12596889 AAAAATAAATTA
1 AAAATTAAAATA
12596901 AAAATTAAAAT
1 AAAATTAAAAT
12596912 GATTTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATTAAAATA
Found at i:12597582 original size:27 final size:27
Alignment explanation
Indices: 12597552--12597605 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
12597542 GAAAACATTT
*
12597552 CTTATAGAATTATAAAAAGCTTTTAAA
1 CTTATAGAATCATAAAAAGCTTTTAAA
12597579 CTTATAGAATCATAAAAAGCTTTTAAA
1 CTTATAGAATCATAAAAAGCTTTTAAA
12597606 ATATAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (27 bp):
CTTATAGAATCATAAAAAGCTTTTAAA
Found at i:12601560 original size:5 final size:5
Alignment explanation
Indices: 12601550--12601581 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12601540 TTTAGTATAT
12601550 TATTA TATTA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
12601582 AAACTAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:12601570 original size:15 final size:14
Alignment explanation
Indices: 12601545--12601581 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
12601535 TTATGTTTAG
12601545 TATAT-TATTATAT
1 TATATATATTATAT
12601558 TATATTATATTATAT
1 TATA-TATATTATAT
12601573 TATATATAT
1 TATATATAT
12601582 AAACTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 6 0.27
15 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATATATTATAT
Found at i:12602870 original size:15 final size:15
Alignment explanation
Indices: 12602850--12602906 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
12602840 CGATGAATTT
12602850 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
12602865 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
12602880 ATTGAATTTATATTG
1 ATTGAATTTATATTG
12602895 ATTGAA-TTATAT
1 ATTGAATTTATAT
12602907 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:12603379 original size:42 final size:42
Alignment explanation
Indices: 12603279--12603382 Score: 154
Period size: 42 Copynumber: 2.4 Consensus size: 42
12603269 TTTATCGATT
*
12603279 AGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTGTC
1 AGGCACTTTATGTGTCG--TGTCAGGCACCTCGTGTGTCGTGTC
* **
12603323 AGGCACCTCGTGTGTCGTGTCAGGCACCTCGTGTGTCGTGTC
1 AGGCACTTTATGTGTCGTGTCAGGCACCTCGTGTGTCGTGTC
12603365 AGGCACTTTATGTGTCGT
1 AGGCACTTTATGTGTCGT
12603383 ATACTGATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
42 39 0.74
44 14 0.26
ACGTcount: A:0.12, C:0.24, G:0.30, T:0.34
Consensus pattern (42 bp):
AGGCACTTTATGTGTCGTGTCAGGCACCTCGTGTGTCGTGTC
Found at i:12603382 original size:21 final size:21
Alignment explanation
Indices: 12603300--12603370 Score: 142
Period size: 21 Copynumber: 3.4 Consensus size: 21
12603290 GTGTCGTATT
12603300 TCAGGCACCTCGTGTGTCGTG
1 TCAGGCACCTCGTGTGTCGTG
12603321 TCAGGCACCTCGTGTGTCGTG
1 TCAGGCACCTCGTGTGTCGTG
12603342 TCAGGCACCTCGTGTGTCGTG
1 TCAGGCACCTCGTGTGTCGTG
12603363 TCAGGCAC
1 TCAGGCAC
12603371 TTTATGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.11, C:0.30, G:0.32, T:0.27
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTG
Found at i:12607927 original size:5 final size:5
Alignment explanation
Indices: 12607917--12607953 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
12607907 TTTAGTATAT
12607917 TATTA TATTA TATTA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
12607954 AAACTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:12609235 original size:15 final size:15
Alignment explanation
Indices: 12609215--12609271 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
12609205 CGATGAATTT
12609215 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
12609230 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
12609245 ATTGAATTTATATTG
1 ATTGAATTTATATTG
12609260 ATTGAA-TTATAT
1 ATTGAATTTATAT
12609272 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:12609673 original size:23 final size:23
Alignment explanation
Indices: 12609643--12609727 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 23
12609633 GCTTTATCGA
12609643 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
12609666 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATT
* *
12609687 TCAGGCAC-CT-CGTGT-GT-TT
1 TCAGGCACTTTATGTGTCGTATT
*
12609706 TTAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
12609728 ACTGATCAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 2 0.04
19 11 0.23
20 1 0.02
21 12 0.26
22 2 0.04
23 19 0.40
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:12609690 original size:21 final size:22
Alignment explanation
Indices: 12609655--12609703 Score: 82
Period size: 21 Copynumber: 2.2 Consensus size: 22
12609645 AGGCACTTTA
12609655 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
12609678 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
12609699 TGTGT
1 TGTGT
12609704 TTTTAGGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.65
23 9 0.35
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:12612819 original size:17 final size:17
Alignment explanation
Indices: 12612797--12612832 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12612787 TCTCTATTTT
12612797 TACACATAGAATAACTA
1 TACACATAGAATAACTA
12612814 TACACATAGAATAACTA
1 TACACATAGAATAACTA
12612831 TA
1 TA
12612833 ACACTCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (17 bp):
TACACATAGAATAACTA
Found at i:12615233 original size:17 final size:18
Alignment explanation
Indices: 12615205--12615242 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
12615195 ATAGAAGATA
*
12615205 TTATTTAGTTTTATTTAT
1 TTATTTAGTTTTATTAAT
12615223 TTATTTA-TTTTATTAAT
1 TTATTTAGTTTTATTAAT
12615240 TTA
1 TTA
12615243 GGTTAAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTATTTAGTTTTATTAAT
Found at i:12617841 original size:18 final size:18
Alignment explanation
Indices: 12617814--12617859 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12617804 ACCAGTACCT
*
12617814 GACACAAGTCGAAG-CCAC
1 GACACTAGTCG-AGCCCAC
*
12617832 GACACTAGTCGTGCCCAC
1 GACACTAGTCGAGCCCAC
12617850 GACACTAGTC
1 GACACTAGTC
12617860 AGGATAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.13
Consensus pattern (18 bp):
GACACTAGTCGAGCCCAC
Found at i:12621208 original size:19 final size:19
Alignment explanation
Indices: 12621180--12621218 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
12621170 AGAGCGAAAG
12621180 AAACGAG-AAACGGGCCAA
1 AAACGAGAAAACGGGCCAA
*
12621198 AAACAGAGAAAATGGGCCAA
1 AAAC-GAGAAAACGGGCCAA
12621218 A
1 A
12621219 GTACGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.54, C:0.18, G:0.26, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAACGGGCCAA
Found at i:12624430 original size:19 final size:19
Alignment explanation
Indices: 12624402--12624440 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
12624392 AGAGCGAAAG
12624402 AAACGAG-AAACAGGCCAA
1 AAACGAGAAAACAGGCCAA
*
12624420 AAACAGAGAAAATAGGCCAA
1 AAAC-GAGAAAACAGGCCAA
12624440 A
1 A
12624441 GTACAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.59, C:0.18, G:0.21, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAACAGGCCAA
Found at i:12625888 original size:13 final size:13
Alignment explanation
Indices: 12625870--12625897 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12625860 GGTTGTTTAT
12625870 TAAACTAATTAAC
1 TAAACTAATTAAC
12625883 TAAACTAATTAAC
1 TAAACTAATTAAC
12625896 TA
1 TA
12625898 TTGAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12634295 original size:13 final size:13
Alignment explanation
Indices: 12634277--12634305 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12634267 GGTTGTTTAT
12634277 TAAACTAATTAAC
1 TAAACTAATTAAC
12634290 TAAACTAATTAAC
1 TAAACTAATTAAC
12634303 TAA
1 TAA
12634306 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12644009 original size:39 final size:39
Alignment explanation
Indices: 12643950--12644050 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
12643940 ATCGTGATCT
** *
12643950 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACA
1 GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACA
*
12643989 GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACA
* *
12644028 GAAGCCCAAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTAAAGC
12644051 TCATCAGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACA
Found at i:12648583 original size:38 final size:35
Alignment explanation
Indices: 12648524--12648641 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
12648514 TCAATCATGC
*
12648524 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
12648563 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
12648594 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
12648625 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
12648642 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:12648585 original size:31 final size:31
Alignment explanation
Indices: 12648547--12648641 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
12648537 CCTTTTCATA
*
12648547 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12648578 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12648609 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
12648640 TT
1 TT
12648642 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:12648897 original size:23 final size:24
Alignment explanation
Indices: 12648833--12648949 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
12648823 GCTTTATCAT
*
12648833 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
12648858 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
12648882 ATAA-TGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
12648904 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
12648927 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12648950 TCACTTCCTC
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
22 20 0.24
23 23 0.28
24 28 0.34
25 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:12648936 original size:46 final size:48
Alignment explanation
Indices: 12648833--12648949 Score: 152
Period size: 46 Copynumber: 2.5 Consensus size: 48
12648823 GCTTTATCAT
*
12648833 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
12648882 ATAA-TGGGGCATAAGCCCTTTT-ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
12648927 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
12648950 TCACTTCCTC
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
45 18 0.29
46 24 0.39
47 9 0.15
48 7 0.11
49 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:12649025 original size:20 final size:20
Alignment explanation
Indices: 12649000--12649038 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12648990 TATGATTACC
12649000 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATT
12649020 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
12649039 ACCATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
TCATGTGCATATCATACATT
Found at i:12649112 original size:25 final size:25
Alignment explanation
Indices: 12649080--12649128 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12649070 TCATACATAA
* * *
12649080 ACCTAGGGGTATAATGGTCATTTTT
1 ACCTAGGGGCAAAACGGTCATTTTT
12649105 ACCTAGGGGCAAAACGGTCATTTT
1 ACCTAGGGGCAAAACGGTCATTTT
12649129 CATGGTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
ACCTAGGGGCAAAACGGTCATTTTT
Found at i:12660714 original size:27 final size:28
Alignment explanation
Indices: 12660657--12660726 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
12660647 AAATTTGTAC
**
12660657 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
12660685 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
12660712 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
12660727 GACTCACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:12675383 original size:11 final size:11
Alignment explanation
Indices: 12675369--12675409 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
12675359 TATTTTCTCC
12675369 CTATTTTGCTA
1 CTATTTTGCTA
*
12675380 CTATTTTACTA
1 CTATTTTGCTA
* *
12675391 TTATGTTGCTA
1 CTATTTTGCTA
12675402 CTATTTTG
1 CTATTTTG
12675410 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:12675510 original size:30 final size:30
Alignment explanation
Indices: 12675450--12675510 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12675440 ATTTTATTGT
* * *
12675450 TAATTTTTTTATTATTTTAAAGATATTTGC
1 TAATTTTGTTATTATTTTAAAGACACTTGC
* *
12675480 TAATTTTGTTATTATTTTAGAGGCACTTGC
1 TAATTTTGTTATTATTTTAAAGACACTTGC
12675510 T
1 T
12675511 TGTTAAGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACACTTGC
Found at i:12675664 original size:12 final size:12
Alignment explanation
Indices: 12675635--12675666 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
12675625 ATATATTTTG
12675635 AAATT-ATATAA
1 AAATTAATATAA
12675646 AAA-TAATATAA
1 AAATTAATATAA
12675657 AAATTAATAT
1 AAATTAATAT
12675667 GGCGGGCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 12 0.63
12 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:12700010 original size:22 final size:22
Alignment explanation
Indices: 12699971--12700012 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12699961 TAGAAGAAGG
*
12699971 AAAAAAATAAAAAGAAAGAAAC
1 AAAAAAATAAAAAAAAAGAAAC
12699993 AAAAAAA-AAAAGAAAAAGAA
1 AAAAAAATAAAA-AAAAAGAA
12700013 GAATGGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (22 bp):
AAAAAAATAAAAAAAAAGAAAC
Found at i:12705102 original size:12 final size:13
Alignment explanation
Indices: 12705087--12705116 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12705077 AAATTCCTTT
12705087 TAATA-TAAAAAA
1 TAATATTAAAAAA
12705099 TAATATTAAAAAA
1 TAATATTAAAAAA
12705112 TAATA
1 TAATA
12705117 CGAGTGGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAATATTAAAAAA
Found at i:12707259 original size:23 final size:24
Alignment explanation
Indices: 12707206--12707259 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
12707196 AAATTGTGAA
* *
12707206 TTTAATTTTTTTACTTTAATTATC
1 TTTAACTTTTTGACTTTAATTATC
12707230 TTT-ACTTTTTGA-TTTAATTAAT-
1 TTTAACTTTTTGACTTTAATT-ATC
12707252 TTTAACTT
1 TTTAACTT
12707260 CTTAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 10 0.38
23 13 0.50
24 3 0.12
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTAACTTTTTGACTTTAATTATC
Found at i:12710492 original size:13 final size:13
Alignment explanation
Indices: 12710476--12710509 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12710466 TAAATTATAA
*
12710476 ATTATTATTAACT
1 ATTATTATTAAAT
12710489 ATTATTATTAAAT
1 ATTATTATTAAAT
*
12710502 AATATTAT
1 ATTATTAT
12710510 ATATATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATTATTAAAT
Found at i:12711073 original size:21 final size:21
Alignment explanation
Indices: 12711025--12711133 Score: 128
Period size: 21 Copynumber: 5.1 Consensus size: 21
12711015 GGCTTTACTG
* *
12711025 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
12711046 ATTTCAGGCACCTTGTGTGTCGT
1 A--TCAGGCACCTTGTGTGTCGT
*
12711069 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
*
12711090 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
* * * *
12711111 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
12711132 AT
1 AT
12711134 ATTGATCAGG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
21 58 0.75
23 19 0.25
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.37
Consensus pattern (21 bp):
ATCAGGCACCTTGTGTGTCGT
Found at i:12717346 original size:12 final size:12
Alignment explanation
Indices: 12717329--12717367 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12717319 TAAATTATAA
12717329 ATTATTATTAAT
1 ATTATTATTAAT
12717341 ATTATTATTAAAT
1 ATTATTATT-AAT
* *
12717354 AATATTATAAAT
1 ATTATTATTAAT
12717366 AT
1 AT
12717368 ATATAGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:12717377 original size:13 final size:12
Alignment explanation
Indices: 12717318--12717371 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
12717308 TTATTGATTT
12717318 ATAA-ATTATAA
1 ATAATATTATAA
*
12717329 AT--TATTATTA
1 ATAATATTATAA
*
12717339 ATATTATTATTAA
1 ATAATATTA-TAA
12717352 ATAATATTATAA
1 ATAATATTATAA
12717364 ATATATAT
1 ATA-ATAT
12717372 AGTAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 2 0.06
12 11 0.31
13 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAATATTATAA
Found at i:12717924 original size:21 final size:21
Alignment explanation
Indices: 12717889--12717984 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
12717879 AGGCACTTTA
12717889 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
12717912 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
12717933 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * * **
12717954 TGTGTCGTTTTAGGCACTTTA
1 TGTGTCGTATCAGGCACCTCG
12717975 TGTGTCGTAT
1 TGTGTCGTAT
12717985 ACTGATCAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 58 0.87
23 9 0.13
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:12717959 original size:42 final size:42
Alignment explanation
Indices: 12717876--12717984 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 42
12717866 GGCTTTACTG
* *
12717876 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTA--TCAGGCACCTCGTGTGTCGT
*
12717920 ATCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
* * * *
12717962 TTTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
12717985 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 38 0.67
44 19 0.33
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.36
Consensus pattern (42 bp):
ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
Found at i:12723911 original size:13 final size:13
Alignment explanation
Indices: 12723893--12723918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12723883 GAATATTGCA
12723893 TGAAAAATTTTAT
1 TGAAAAATTTTAT
12723906 TGAAAAATTTTAT
1 TGAAAAATTTTAT
12723919 CAATTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TGAAAAATTTTAT
Found at i:12725112 original size:34 final size:33
Alignment explanation
Indices: 12725074--12725137 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
12725064 GTATTGAAGG
* * *
12725074 AAAGGTATACTTTGTGTATACCACTTGAAAAGAA
1 AAAGGTACACTATATGTATA-CACTTGAAAAGAA
*
12725108 AAAGGTACACTATATGTGTACACTTGAAAA
1 AAAGGTACACTATATGTATACACTTGAAAA
12725138 TGTTATATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 10 0.38
34 16 0.62
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (33 bp):
AAAGGTACACTATATGTATACACTTGAAAAGAA
Found at i:12727318 original size:30 final size:31
Alignment explanation
Indices: 12727283--12727353 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 31
12727273 AGCATTGCAG
12727283 AATATG-A-AAGGGAGTTTGTTCGGTTAAGCC
1 AATATGCAGAAGGG-GTTTGTTCGGTTAAGCC
*
12727313 AATATGCTAGTGAATGGGTTTGTTCGGTTAAGCC
1 AATATGC-A--GAAGGGGTTTGTTCGGTTAAGCC
12727347 AATATGC
1 AATATGC
12727354 TAGTGAATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 6 0.17
32 1 0.03
34 24 0.69
35 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (31 bp):
AATATGCAGAAGGGGTTTGTTCGGTTAAGCC
Found at i:12727335 original size:34 final size:34
Alignment explanation
Indices: 12727296--12727365 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
12727286 ATGAAAGGGA
12727296 GTTTGTTCGGTTAAGCCAATATGCTAGTGAATGG
1 GTTTGTTCGGTTAAGCCAATATGCTAGTGAATGG
12727330 GTTTGTTCGGTTAAGCCAATATGCTAGTGAATGG
1 GTTTGTTCGGTTAAGCCAATATGCTAGTGAATGG
12727364 GT
1 GT
12727366 CTAAACAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (34 bp):
GTTTGTTCGGTTAAGCCAATATGCTAGTGAATGG
Found at i:12754907 original size:29 final size:28
Alignment explanation
Indices: 12754873--12754976 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 28
12754863 GTGACAAGAT
12754873 TGGCACTAAGTGTGCAAGCTTGAAATATA
1 TGGCACTAAGTGTGCAAGCTT-AAATATA
12754902 TGGCACTAAGTGTGCGAA-CTTAAATTATA
1 TGGCACTAAGTGTGC-AAGCTTAAA-TATA
* * *
12754931 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCAAGCTTAAAT-ATA
12754960 TGGCACTAAGTGTGCAA
1 TGGCACTAAGTGTGCAA
12754977 AATCGATTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.08
29 59 0.89
30 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCAAGCTTAAATATA
Found at i:12763017 original size:29 final size:28
Alignment explanation
Indices: 12762983--12763086 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 28
12762973 GTGACAAGAT
12762983 TGGCACTAAGTGTGCAAGCTTGAAATATA
1 TGGCACTAAGTGTGCAAGCTT-AAATATA
12763012 TGGCACTAAGTGTGCGAA-CTTAAATTATA
1 TGGCACTAAGTGTGC-AAGCTTAAA-TATA
* * *
12763041 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCAAGCTTAAAT-ATA
12763070 TGGCACTAAGTGTGCAA
1 TGGCACTAAGTGTGCAA
12763087 AATCGATTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.08
29 59 0.89
30 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCAAGCTTAAATATA
Found at i:12768579 original size:17 final size:17
Alignment explanation
Indices: 12768552--12768585 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12768542 CGACCAATTG
12768552 GGCCGTGTGGGCCACACA
1 GGCCGTGTGGGCC-CACA
12768570 GGCC-TGTGGGCCCACA
1 GGCCGTGTGGGCCCACA
12768586 TGGGTGAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.15, C:0.35, G:0.38, T:0.12
Consensus pattern (17 bp):
GGCCGTGTGGGCCCACA
Found at i:12775437 original size:17 final size:16
Alignment explanation
Indices: 12775396--12775440 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
12775386 TATCTATTTT
12775396 TTCTTTCTTGTTTTTGC
1 TTCTTT-TTGTTTTTGC
12775413 -TC--TTTGTTTTCTGC
1 TTCTTTTTGTTTT-TGC
12775427 TTCTTTTTGTTTTT
1 TTCTTTTTGTTTTT
12775441 TTTGCTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
13 7 0.29
14 4 0.17
15 2 0.08
16 3 0.12
17 8 0.33
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (16 bp):
TTCTTTTTGTTTTTGC
Found at i:12775446 original size:19 final size:20
Alignment explanation
Indices: 12775419--12775458 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12775409 TTGCTCTTTG
12775419 TTTTCTGCTTCTT-TTTGTT
1 TTTTCTGCTTCTTGTTTGTT
* *
12775438 TTTTTTGCTTGTTGTTTGTT
1 TTTTCTGCTTCTTGTTTGTT
12775458 T
1 T
12775459 GTTTGTCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (20 bp):
TTTTCTGCTTCTTGTTTGTT
Found at i:12776208 original size:3 final size:3
Alignment explanation
Indices: 12776200--12776234 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12776190 ATAAAAATGA
12776200 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12776235 AATGAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12776598 original size:13 final size:14
Alignment explanation
Indices: 12776567--12776597 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12776557 AAATGAAAGT
*
12776567 AAAATTACAAGGAA
1 AAAATTAAAAGGAA
12776581 AAAATTAAAAGGAA
1 AAAATTAAAAGGAA
12776595 AAA
1 AAA
12776598 TATAGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAATTAAAAGGAA
Found at i:12780071 original size:21 final size:21
Alignment explanation
Indices: 12780045--12780086 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12780035 AAAGAAGAAG
12780045 CCCTTTTT-AGCCATTTTTTAA
1 CCCTTTTTGA-CCATTTTTTAA
*
12780066 CCCTTTTTGACCCTTTTTTAA
1 CCCTTTTTGACCATTTTTTAA
12780087 AGTAAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.26, G:0.05, T:0.52
Consensus pattern (21 bp):
CCCTTTTTGACCATTTTTTAA
Found at i:12782919 original size:15 final size:15
Alignment explanation
Indices: 12782901--12782952 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
12782891 ATACACTAAT
*
12782901 ATAATAATAGCTATA
1 ATAATAATAGCAATA
*
12782916 ATAATACTAGCAATA
1 ATAATAATAGCAATA
* * *
12782931 GTAATAATTTGTAATA
1 ATAATAA-TAGCAATA
12782947 ATAATA
1 ATAATA
12782953 TATACACAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (15 bp):
ATAATAATAGCAATA
Found at i:12783024 original size:2 final size:2
Alignment explanation
Indices: 12782975--12783005 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12782965 GATATTTAAA
*
12782975 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12783006 ATAGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12783646 original size:18 final size:18
Alignment explanation
Indices: 12783625--12783662 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
12783615 TTGGGGTAAG
12783625 TTTTTCTTT-TTCTTTTTT
1 TTTTTCTTTATT-TTTTTT
12783643 TTTTTCTTTATTTTTTTT
1 TTTTTCTTTATTTTTTTT
12783661 TT
1 TT
12783663 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTCTTTATTTTTTTT
Found at i:12784687 original size:73 final size:74
Alignment explanation
Indices: 12784572--12784849 Score: 359
Period size: 73 Copynumber: 3.8 Consensus size: 74
12784562 AAGATAGAAT
* * * *
12784572 TTGAAAATACCTTAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATT
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
12784637 TAATGGGAA
66 TAATGGGAA
* * *
12784646 TTGAAATTACCTCAGCGTG-CCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGGTTTTAGATT
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
12784710 TAATGGGAA
66 TAATGGGAA
* * *
12784719 TTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA--
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
*
12784782 AACAT--GAA
66 TA-ATGGGAA
* * * ***
12784790 TTGAAATTACCCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
12784850 CTTGGAAACA
Statistics
Matches: 184, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
71 55 0.30
72 1 0.01
73 70 0.38
74 58 0.32
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (74 bp):
TTGAAATTACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATT
TAATGGGAA
Found at i:12784761 original size:147 final size:145
Alignment explanation
Indices: 12784572--12785241 Score: 420
Period size: 159 Copynumber: 4.4 Consensus size: 145
12784562 AAGATAGAAT
*
12784572 TTGAAAATACCTTAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATT
1 TTGAAAATACCTCAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGA--
* * * * *
12784637 TA-ATGGGAATTGAAATTACCTCAGCGTG-CCCAAGGTTCAACTCACTTCTCGCAATATGAGTTG
64 AACAT--GAATTGAAATTACCCCAACGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
12784700 GTTTTAGATTTAATGGGAA
127 ATTTTAGATTTAATGGGAA
* * * * * *
12784719 TTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
***
12784784 CATGAATTGAAATTACCCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
66 CATGAATTGAAATTACCCCAACGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
** * *
12784849 TCTTGGAAACATGAACTAAAAAGCAGAAA
129 T-TT------A-G-A-TTTAATG--GGAA
*** * * *
12784878 TTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
* * *** *
12784943 CATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTT
66 CATGAATTGAAATTACCCCAACGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
* * *
12785008 TCTTGGAAAACATGAATTAAAAAGTAGAAA
129 T-TT-------A-G-ATT--TAA-TGGGAA
* * * * *
12785038 TTGAAAATACCTCAGCGTGCC-CTGAGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTTATT
1 TTGAAAATACCTCAGCGTGCCAC-AAGGCTCAACTCACCTCTCGCAATATGAGTCGA-TTTTA-G
* * * * * * * * *
12785102 TAATAGGAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGC
63 AAACATGAATTGAAATTACCCCAACGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * *
12785167 TTTTTGA--AACAT--AAA
128 TTTTAGATTTA-ATGGGAA
* * * ***
12785182 TTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG-CTGATTTT
1 TTGAAAATACCTCAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTC-GATTTT
12785242 CTTGGAAAAC
Statistics
Matches: 444, Mismatches: 53, Indels: 56
0.80 0.10 0.10
Matches are distributed among these distances:
143 4 0.01
144 70 0.16
145 31 0.07
146 5 0.01
147 59 0.13
148 2 0.00
150 1 0.00
151 1 0.00
154 1 0.00
155 1 0.00
156 1 0.00
157 4 0.01
159 132 0.30
160 69 0.16
161 7 0.02
162 56 0.13
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (145 bp):
TTGAAAATACCTCAGCGTGCCACAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTAGAAA
CATGAATTGAAATTACCCCAACGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TAGATTTAATGGGAA
Found at i:12784832 original size:71 final size:71
Alignment explanation
Indices: 12784527--12784849 Score: 334
Period size: 73 Copynumber: 4.5 Consensus size: 71
12784517 AATTAAAAGA
* * * *
12784527 CTCAACTCACCTCTCGTAATATGAATTGACTCTTTAAGAT--A--GAATTTGAAAATACCTTAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TTT-AGATAAATGGAA-TTGAAATTACCTCAGC
12784588 GTGCCACAAGG
62 GTGCC-CAAGG
* *
12784599 CTCAACTCACCTCTCGCAATATGAGTCGATTTTAGATTTAATGGGAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGA-TAAAT-GGAATTGAAATTACCTCAGCGT
12784664 GCCCAAGG
64 GCCCAAGG
* * * *
12784672 TTCAACTCACTTCTCGCAATATGAGTTGGTTTTAGATTTAATGGGAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGA-TAAAT-GGAATTGAAATTACCTCAGCGT
12784737 GCCCCAAGG
64 G-CCCAAGG
* * * * *
12784746 TTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA-AACAT-GAATTGAAATTACCCCAACGTG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATAA-ATGGAATTGAAATTACCTCAGCGTG
***
12784809 TCTTGAGG
65 -CCCAAGG
12784817 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
12784850 CTTGGAAACA
Statistics
Matches: 223, Mismatches: 20, Indels: 17
0.86 0.08 0.07
Matches are distributed among these distances:
69 3 0.01
70 4 0.02
71 56 0.25
72 28 0.13
73 69 0.31
74 60 0.27
75 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (71 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTAGATAAATGGAATTGAAATTACCTCAGCGTGC
CCAAGG
Found at i:12784991 original size:71 final size:71
Alignment explanation
Indices: 12784875--12785241 Score: 279
Period size: 71 Copynumber: 4.9 Consensus size: 71
12784865 TAAAAAGCAG
* * *
12784875 AAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
12784940 AAACAT
66 AAACAT
* *
12784946 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTCT
1 AAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTT-T
12785011 TGGAAAACAT
64 T-G-AAACAT
* * ** * ** * * * * * *
12785021 GAATTAAAAAGTAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTTGCAATA
1 AAATTGAAAA-T---ACCTCAACGTGCCT-TGAG-G--CTCA-ACTC-A--C-C-TCTCGCAATA
* *
12785086 TGAGTTGATTTTT-ATTTA-AT
52 TGAGCTGATTTTTGA--AACAT
* * ** *
12785106 AGGAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTTT
1 A--AATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
12785171 TGAAACAT
64 TGAAACAT
* *
12785179 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
12785242 CTTGGAAAAC
Statistics
Matches: 226, Mismatches: 46, Indels: 48
0.71 0.14 0.15
Matches are distributed among these distances:
71 111 0.49
72 4 0.02
73 25 0.11
74 3 0.01
75 14 0.06
76 1 0.00
77 1 0.00
78 3 0.01
79 10 0.04
80 2 0.01
81 2 0.01
82 2 0.01
83 9 0.04
84 4 0.02
85 3 0.01
86 2 0.01
87 10 0.04
88 4 0.02
89 16 0.07
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (71 bp):
AAATTGAAAATACCTCAACGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
AAACAT
Found at i:12785006 original size:159 final size:160
Alignment explanation
Indices: 12784717--12785170 Score: 698
Period size: 159 Copynumber: 2.8 Consensus size: 160
12784707 ATTTAATGGG
* ** *
12784717 AATTGAAATTACCTCAGCGTGCCCCAAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
* * *
12784782 AACATGAATTGAAATTACCCCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
12784847 TTTCTTGG-AAACATGAACTAAAAAGCAGA
131 TTTCTTGGAAAACATGAACTAAAAAGCAGA
*
12784876 AATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
12784941 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
* *
12785006 TTTCTTGGAAAACATGAATTAAAAAGTAGA
131 TTTCTTGGAAAACATGAACTAAAAAGCAGA
*
12785036 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTT-A
1 AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
* * * **
12785100 TTTA-ATAGGAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGC
66 --AACATA--AATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGC
*
12785164 TGCTTTT
127 TGATTTT
12785171 TGAAACATAA
Statistics
Matches: 272, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
159 131 0.48
160 83 0.31
161 1 0.00
162 57 0.21
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (160 bp):
AATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTCTTGGAAAACATGAACTAAAAAGCAGA
Found at i:12785128 original size:73 final size:71
Alignment explanation
Indices: 12785035--12785241 Score: 274
Period size: 73 Copynumber: 2.9 Consensus size: 71
12785025 TAAAAAGTAG
* * * *
12785035 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTT-
1 AAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
*
12785099 ATTTA-AT
66 A--AACAT
* *
12785106 AGGAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTTT
1 A--AATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
12785171 TGAAACAT
64 TGAAACAT
* * *
12785179 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
12785242 CTTGGAAAAC
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
71 58 0.48
72 1 0.01
73 60 0.50
74 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (71 bp):
AAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
AAACAT
Found at i:12785128 original size:233 final size:233
Alignment explanation
Indices: 12784876--12785331 Score: 831
Period size: 233 Copynumber: 2.0 Consensus size: 233
12784866 AAAAAGCAGA
** * *
12784876 AATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
12784941 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
12785006 TTTCTTGGAAAACATGAATTAAAAAGTAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
131 TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
*
12785071 TCACTTCTTGCAATATGAGTTGATTTTTATTTAATAGG
196 TCACTTCTCGCAATATGAGTTGATTTTTATTTAATAGG
* *
12785109 AATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGCTTTTTGA
1 AATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
12785174 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
66 AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
*
12785239 TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGGAAATACCTCAGCGTGCCCTGAGGCTCAAC
131 TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
12785304 TCACTTCTCGCAATATGAGTTGATTTTT
196 TCACTTCTCGCAATATGAGTTGATTTTT
12785332 GGAAAAAAAC
Statistics
Matches: 214, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
233 214 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (233 bp):
AATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGA
AACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
TTTCTTGGAAAACATGAATTAAAAAGCAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAAC
TCACTTCTCGCAATATGAGTTGATTTTTATTTAATAGG
Found at i:12797575 original size:15 final size:15
Alignment explanation
Indices: 12797557--12797610 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
12797547 AAATATACAC
*
12797557 TAATAATAATAGCTA
1 TAATAATAATAGCAA
*
12797572 TAATAATACTAGCAA
1 TAATAATAATAGCAA
* * *
12797587 TAGTAATAATTGGAAA
1 TAATAATAA-TAGCAA
12797603 TAATAATA
1 TAATAATA
12797611 TATACACAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 20 0.65
16 11 0.35
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (15 bp):
TAATAATAATAGCAA
Done.