Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 46 of 196
Found at i:12632008 original size:17 final size:16
Alignment explanation
Indices: 12631986--12632017 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12631976 GAGAAAAGAA
12631986 AAGAAAATAATAGAAAG
1 AAGAAAATAA-AGAAAG
12632003 AAGAAAATAAAGAAA
1 AAGAAAATAAAGAAA
12632018 AGGGGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (16 bp):
AAGAAAATAAAGAAAG
Found at i:12634932 original size:27 final size:27
Alignment explanation
Indices: 12634902--12634953 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
12634892 AAATATAAGC
12634902 TCTTTAATGGAGAATTTATTTTTCTGT
1 TCTTTAATGGAGAATTTATTTTTCTGT
*
12634929 TCTTTAATGGGGAATTTATTTTTCT
1 TCTTTAATGGAGAATTTATTTTTCT
12634954 TACAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (27 bp):
TCTTTAATGGAGAATTTATTTTTCTGT
Found at i:12635486 original size:2 final size:2
Alignment explanation
Indices: 12635479--12635508 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12635469 AAAACATGAA
12635479 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
12635509 GGTTGTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12641071 original size:12 final size:12
Alignment explanation
Indices: 12641056--12641090 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12641046 TAGGTTTGAA
12641056 AAAATAGAAATG
1 AAAATAGAAATG
*
12641068 AAAATAAAAATG
1 AAAATAGAAATG
*
12641080 AAAATGGAAAT
1 AAAATAGAAAT
12641091 TTGCAATCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (12 bp):
AAAATAGAAATG
Found at i:12641277 original size:26 final size:26
Alignment explanation
Indices: 12641248--12641304 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
12641238 TACCAGGGGC
12641248 AAAATCGTCAAAATTTTACTAAGGGT
1 AAAATCGTCAAAATTTTACTAAGGGT
* *
12641274 AAAATCGTCAAAATTTTGCTAGGGGT
1 AAAATCGTCAAAATTTTACTAAGGGT
12641300 AAAAT
1 AAAAT
12641305 AAGGATGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.30
Consensus pattern (26 bp):
AAAATCGTCAAAATTTTACTAAGGGT
Found at i:12643914 original size:12 final size:12
Alignment explanation
Indices: 12643897--12643921 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12643887 CATCAAATTT
12643897 TTTGTTCTAACA
1 TTTGTTCTAACA
12643909 TTTGTTCTAACA
1 TTTGTTCTAACA
12643921 T
1 T
12643922 AATGTAACTT
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTGTTCTAACA
Found at i:12650824 original size:28 final size:28
Alignment explanation
Indices: 12650792--12650847 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12650782 AGGAAAGAGT
12650792 AAACTTTAATTCAATTCATCAACCTTTC
1 AAACTTTAATTCAATTCATCAACCTTTC
* *
12650820 AAACTTTAATTCAGTTCATCAGCCTTTC
1 AAACTTTAATTCAATTCATCAACCTTTC
12650848 GAATCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
AAACTTTAATTCAATTCATCAACCTTTC
Found at i:12652862 original size:14 final size:14
Alignment explanation
Indices: 12652843--12652872 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12652833 ACTAAGAATA
12652843 TACAAATAAATACT
1 TACAAATAAATACT
12652857 TACAAATAAATACT
1 TACAAATAAATACT
12652871 TA
1 TA
12652873 AGAAACGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
TACAAATAAATACT
Found at i:12656451 original size:73 final size:72
Alignment explanation
Indices: 12656320--12656492 Score: 231
Period size: 73 Copynumber: 2.4 Consensus size: 72
12656310 TGCTCAGGGC
* * * *
12656320 TTTAGCGGCGTTTTTG-GTAAAGTGCCGCAAAAAACCTAAGCCGAATGATGCCGTTTTCTGAACT
1 TTTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAACT
12656384 TTAGGGGA
65 TTAGGGGA
* * *
12656392 TTTAGCGGCGCTTTTGAGAAAGCGTCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAACT
12656457 TTAGGGGA
65 TTAGGGGA
* * *
12656465 TTTAGCGGCATTTTTAAGAAAGCACCGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGC
12656493 TAATGCTCAG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
72 23 0.26
73 64 0.74
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (72 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAACTT
TAGGGGA
Found at i:12656521 original size:186 final size:185
Alignment explanation
Indices: 12656208--12656604 Score: 525
Period size: 186 Copynumber: 2.1 Consensus size: 185
12656198 AAAATAAGCA
*
12656208 TTAGCGGCGTTTTCCAGAAAGCGCCACAAAAAACCTAAGCCCAACGACACCGTTTTCCTAGCTTT
1 TTAGCGGCGTTTT-AAGAAAGCGCCACAAAAAACCTAAGCCCAACGACACCGTTTTCCTAGCTTT
** * *
12656273 CAGGGATTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG-G
65 CAGGGATTTAGCGGCATTTCTAAAAAAGCACCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAG
** * * *
12656337 TAAAGTGCCGC-AAAAAACCTAAGCCGAATGATGCCGTTTTCTGAACTTTAGGGGAT
130 -AAACCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAACTTTAGGAGAT
* *
12656393 TTAGCGGCGCTTTTGAGAAAGCGTCGCA-AAAAAACCTAAGCCCAACGACGCCGTTTT-CTGAGC
1 TTAGCGGCG-TTTTAAGAAAGCG-C-CACAAAAAACCTAAGCCCAACGACACCGTTTTCCT-AGC
* *
12656456 TTT-AGGGGATTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAGGGATTTAGCGGCGTTTT
62 TTTCA-GGGATTTAGCGGCATTTCTAAAAAAGCACCGCTAATGCTCAGGGATTTAGCGGCGTTTT
* * *
12656520 TGAGAAACCGCCGCAAAAAAACCTAAGCCCAACGATGCTGTTTTCTGAGCTTTTGGAGAT
126 TGAGAAACCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAACTTTAGGAGAT
*
12656580 TTAACGGCGTTTTTAAGAAAGCGCC
1 TTAGCGGCG-TTTTAAGAAAGCGCC
12656605 GCTAATGCTC
Statistics
Matches: 186, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
185 21 0.11
186 103 0.55
187 62 0.33
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.26
Consensus pattern (185 bp):
TTAGCGGCGTTTTAAGAAAGCGCCACAAAAAACCTAAGCCCAACGACACCGTTTTCCTAGCTTTC
AGGGATTTAGCGGCATTTCTAAAAAAGCACCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGA
AACCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTGAACTTTAGGAGAT
Found at i:12656593 original size:114 final size:113
Alignment explanation
Indices: 12656388--12657271 Score: 1043
Period size: 114 Copynumber: 7.9 Consensus size: 113
12656378 TGAACTTTAG
* *
12656388 GGGATTTAGCGGCGCTTTTGAGAAAGCGTCGCAAAAAAACCTAAGCCCAACGACGC-CGTTTTCT
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGA-GCTCGTTTTCT
* *
12656452 GAGCTTTAGGGGATTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCA
65 GAGCTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
*
12656502 GGGATTTAGCGGCGTTTTTGAGAAACCGCCGCAAAAAAACCTAAGCCCAACGATGCT-GTTTTCT
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGA-GCTCGTTTTCT
* *
12656566 GAGCTTTTGGAGATTTAACGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
65 GAGC-TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
* * * * * * *
12656616 AGGCTTTAGCGGTGTTTTTGGGAAAGCGCCGTAAAAAAATCAAAGCCCAACTGAG--C--TTTC-
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAAC-GAGCTCGTTTTCT
* *
12656676 -A-----GGGGATTTAGTGGCGTTTTTAAGAAAGCACCGCTAATGCTCA
65 GAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
* * *
12656719 GGGATTTAGCGACATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGA-CGTCATTTTCT
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGAGC-TCGTTTTCT
*
12656783 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCGGCTAATGCTCA
65 GAGCTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
* * * * *
12656833 -AGACTTTAGCGACATTTTTGGGAAAGCACCGCAAAAAAAACCTAAGCCCAACGA-CATCGTTTT
1 GGGA-TTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGAGC-TCGTTTT
* *
12656896 CTGAGCTTTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCACTAATGCTCA
63 CTGAGCTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
* * * * *
12656948 GGGCTTTAGCGGCGTTTTTGGGAAAGCTCCGCAAAAAAATCAAAGCCCAACTGAG--C--TTTC-
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAAC-GAGCTCGTTTTCT
*
12657008 --G----GGGGATTTAGCGGCTTTTTTAAGAAAGCGCCGCTAATGCTCA
65 GAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
12657051 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGA-CATCGTTTTC
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGAGC-TCGTTTTC
* * *
12657115 TAAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGTGCCGCTAATGCTCA
64 TGAGCTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
* * * *
12657166 GGGCTTTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAATGA-CGTCGTTTTCT
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGAGC-TCGTTTTCT
12657230 GAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
65 GAGC-TTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
12657272 AAAATAACCT
Statistics
Matches: 666, Mismatches: 67, Indels: 73
0.83 0.08 0.09
Matches are distributed among these distances:
102 2 0.00
103 150 0.23
104 18 0.03
105 1 0.00
106 4 0.01
107 4 0.01
108 2 0.00
109 1 0.00
110 1 0.00
111 8 0.01
113 3 0.00
114 260 0.39
115 211 0.32
116 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (113 bp):
GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGAGCTCGTTTTCTG
AGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA
Found at i:12656879 original size:115 final size:114
Alignment explanation
Indices: 12656666--12657271 Score: 808
Period size: 115 Copynumber: 5.4 Consensus size: 114
12656656 CAAAGCCCAA
* *
12656666 CTGAGCTTTCAGGGGATTTAGTGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGA-TTTAGCG
1 CTGAGCTTTC-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA-GGACTTTAGCG
* * * *
12656730 ACATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTT
64 GCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTT
* * *
12656781 CTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCGGCTAATGCTCAAGACTTTAGCGAC
1 CTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGC
*
12656846 ATTTTTGGGAAAGCACCGCAAAAAAAACCTAAGCCCAACGACATCGTTTT
66 ATTTTTGGGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACATCGTTTT
* * *
12656896 CTGAGCTTTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGC
1 CTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGC
* * * *
12656961 GTTTTTGGGAAAGCTCCGCAAAAAAATCAAAG-CC--C-A-A-------
66 ATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTT
*
12656998 CTGAGCTTTCGGGGGATTTAGCGGCTTTTTTAAGAAAGCGCCGCTAATGCTCAGGGA-TTTAGCG
1 CTGAGCTTTC-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA-GGACTTTAGCG
* *
12657062 GCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACATCGTTTT
64 GCATTTTTGGGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACATCGTTTT
* * * *
12657114 CTAAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGTGCCGCTAATGCTCAGGGCTTTAGCGGC
1 CTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGC
* *
12657179 ATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACGTCGTTTT
66 ATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTT
*
12657228 CTGAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
1 CTGAGC-TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
12657272 AAAATAACCT
Statistics
Matches: 433, Mismatches: 39, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
102 10 0.02
103 65 0.15
104 13 0.03
105 2 0.00
107 1 0.00
108 1 0.00
109 2 0.00
110 1 0.00
111 1 0.00
113 4 0.01
114 111 0.26
115 213 0.49
116 9 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (114 bp):
CTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGC
ATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTT
Found at i:12657015 original size:332 final size:331
Alignment explanation
Indices: 12656388--12657269 Score: 1356
Period size: 332 Copynumber: 2.7 Consensus size: 331
12656378 TGAACTTTAG
* * *
12656388 GGGATTTAGCGGCGCTTTTGAGAAAGCGTCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTG
* * * *
12656453 AGCTTTAGGGGATTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAGGGA-TTTAGCGGCGT
66 AGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCA-GGACTTTAGCGGCAT
* * * *
12656517 TTTTGAGAAACCGCCGCAAAAAAACCTAAGCCCAACG--ATGCTGTTTTCTGAGCTTTTGGAGAT
130 TTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACAT-C-GTTTTCTGAGCTTTCGGGGAT
* * *
12656580 TTAACGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGGTGTTTTTGGGAAAGCGC
193 TTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
12656645 CGTAAAAAAATCAAAGCCCAACTGAGCTTTCAGGGGATTTAGTGGCGTTTTTAAGAAAGCACCGC
258 CGCAAAAAAATCAAAGCCCAACTGAGCTTTCAGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGC
12656710 TAATGCTCA
323 TAATGCTCA
* * *
12656719 GGGATTTAGCGACATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTTCTG
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTG
* * *
12656784 AGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCGGCTAATGCTCAAGACTTTAGCGACATT
66 AGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGCATT
*
12656849 TTTGGGAAAGCACCGCAAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTTTCGGGGATTT
131 TTTGGGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTTTCGGGGATTT
* * *
12656914 AGCGGTGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCTCCG
195 AGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTTGGGAAAGCGCCG
* * *
12656979 CAAAAAAATCAAAGCCCAACTGAGCTTTCGGGGGATTTAGCGGCTTTTTTAAGAAAGCGCCGCTA
260 CAAAAAAATCAAAGCCCAACTGAGCTTTCAGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTA
12657044 ATGCTCA
325 ATGCTCA
*
12657051 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACATCGTTTTCT
1 GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACGTCGTTTTCT
* * * *
12657116 AAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCAT
65 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGCAT
* * *
12657181 TTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACGTCGTTTTCTGAGCTTTTGGGGGATT
130 TTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGC-TTTCGGGGATT
12657246 TAGCGGCGTTTTTAAGAAAGCGCC
194 TAGCGGCGTTTTTAAGAAAGCGCC
12657270 GCAAAATAAC
Statistics
Matches: 500, Mismatches: 45, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
330 2 0.00
331 127 0.25
332 231 0.46
333 138 0.28
334 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (331 bp):
GGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCGTTTTCTG
AGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGACTTTAGCGGCATT
TTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTTTCGGGGATTTA
GCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGC
AAAAAAATCAAAGCCCAACTGAGCTTTCAGGGGATTTAGCGGCGTTTTTAAGAAAGCACCGCTAA
TGCTCA
Found at i:12657049 original size:218 final size:217
Alignment explanation
Indices: 12656669--12657215 Score: 745
Period size: 218 Copynumber: 2.5 Consensus size: 217
12656659 AGCCCAACTG
* * * * *
12656669 AGCTTTCAGGGGATTTAGTGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGATTTAGCGACAT
1 AGCTTTCA-GGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCAT
* *
12656734 TTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGTCATTTTCTGAGCTTTCGGGGATTT
65 TTTTGGGAAAGCGCCGCAAAAAAACCAAAG-CC--C-A----A----CTGAGCTTTCGGGGATTT
* *
12656799 AGCGGCGTTTTTAAGAAAGCGCGGCTAATGCTCA-AGACTTTAGCGACATTTTTGGGAAAGCACC
118 AGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGAGA-TTTAGCGACATTTTTGAGAAAGCACC
*
12656863 GCAAAAAAAACCTAAGCCCAACGACATCGTTTTCTG
182 GCAAAAAAAACCTAAGCCCAACGACATCGTTTTCTA
* * *
12656899 AGCTTTCGGGGATTTAGCGGTGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTT
1 AGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATT
* * *
12656964 TTTGGGAAAGCTCCGCAAAAAAATCAAAGCCCAACTGAGCTTTCGGGGGATTTAGCGGCTTTTTT
66 TTTGGGAAAGCGCCGCAAAAAAACCAAAGCCCAACTGAGCTTTC-GGGGATTTAGCGGCGTTTTT
* * * *
12657029 AAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAAACCT
130 AAGAAAGCGCCGCTAATGCTCAGAGATTTAGCGACATTTTTGAGAAAGCACCGCAAAAAAAACCT
12657094 AAGCCCAACGACATCGTTTTCTA
195 AAGCCCAACGACATCGTTTTCTA
* *
12657117 AGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGTGCCGCTAATGCTCAGGGCTTTAGCGGCATT
1 AGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATT
*
12657182 TTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAA
66 TTTGGGAAAGCGCCGCAAAAAAACCAAAGCCCAA
12657216 TGACGTCGTT
Statistics
Matches: 287, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
217 10 0.03
218 188 0.66
219 2 0.01
221 1 0.00
225 1 0.00
226 1 0.00
228 2 0.01
229 75 0.26
230 7 0.02
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (217 bp):
AGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCATT
TTTGGGAAAGCGCCGCAAAAAAACCAAAGCCCAACTGAGCTTTCGGGGATTTAGCGGCGTTTTTA
AGAAAGCGCCGCTAATGCTCAGAGATTTAGCGACATTTTTGAGAAAGCACCGCAAAAAAAACCTA
AGCCCAACGACATCGTTTTCTA
Found at i:12657301 original size:74 final size:73
Alignment explanation
Indices: 12657170--12657333 Score: 231
Period size: 74 Copynumber: 2.2 Consensus size: 73
12657160 TGCTCAGGGC
* ** * *
12657170 TTTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAATGACGTCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAACCCAACGACGTCGTTTTCTGAGC-
*
12657235 TTTGGGGGA
65 TTTCGGGGA
* *
12657244 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAATAACCTAAACCCAACGACG-CTGTTTTTTGAGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAACCCAACGACGTC-GTTTTCTGAGC
12657308 TTTCGGGGA
65 TTTCGGGGA
12657317 TTTAGCGGCGTTTTTAA
1 TTTAGCGGCGTTTTTAA
12657334 TAATTTGTCT
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
73 26 0.32
74 55 0.68
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAACCCAACGACGTCGTTTTCTGAGCT
TTCGGGGA
Found at i:12658520 original size:17 final size:17
Alignment explanation
Indices: 12658498--12658535 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
12658488 CGATTGCATG
12658498 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
12658515 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
12658532 TTTC
1 TTTC
12658536 CTTTGAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.66
Consensus pattern (17 bp):
TTTCTATTGCTGTTTAT
Found at i:12659258 original size:22 final size:22
Alignment explanation
Indices: 12659217--12659315 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
12659207 GAAGATGAAA
12659217 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
12659238 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
12659260 CTGGAAATTGTTTTGA-TTGTCT
1 CTGGAAATTGTTTTGATTTGT-T
12659282 GCTGGAAATTGTTTTGA-TTGTCT
1 -CTGGAAATTGTTTTGATTTGT-T
12659305 GCTGGAAATTG
1 -CTGGAAATTG
12659316 AATTTGTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
20 7 0.10
21 4 0.06
22 12 0.18
23 45 0.66
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.49
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:12659324 original size:29 final size:23
Alignment explanation
Indices: 12659243--12659315 Score: 114
Period size: 23 Copynumber: 3.2 Consensus size: 23
12659233 TTGTTTTGAT
12659243 ATTGTTCTTGATTTGT-T-CTGGAA
1 ATTGTT-TTGA-TTGTCTGCTGGAA
12659266 ATTGTTTTGATTGTCTGCTGGAA
1 ATTGTTTTGATTGTCTGCTGGAA
12659289 ATTGTTTTGATTGTCTGCTGGAA
1 ATTGTTTTGATTGTCTGCTGGAA
12659312 ATTG
1 ATTG
12659316 AATTTGTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.08
22 5 0.10
23 39 0.81
ACGTcount: A:0.18, C:0.08, G:0.25, T:0.49
Consensus pattern (23 bp):
ATTGTTTTGATTGTCTGCTGGAA
Found at i:12660545 original size:25 final size:25
Alignment explanation
Indices: 12660511--12660616 Score: 121
Period size: 25 Copynumber: 4.2 Consensus size: 25
12660501 TACATCAATA
12660511 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
12660536 ATTAAAATAAGGAC--TAATCA-ATA
1 ATTAAAATAAGGACTTTAAT-ATTTT
12660559 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
12660584 ATTAAAAATCAA-GACATTTAATATTTT
1 ATT-AAAAT-AAGGAC-TTTAATATTTT
*
12660611 AATAAA
1 ATTAAA
12660617 GAAATTTAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
23 19 0.28
24 2 0.03
25 22 0.32
26 11 0.16
27 15 0.22
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.38
Consensus pattern (25 bp):
ATTAAAATAAGGACTTTAATATTTT
Found at i:12660562 original size:23 final size:23
Alignment explanation
Indices: 12660504--12660573 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
12660494 AAAAAATTAC
12660504 ATCAATAATTAAAATAAGGACTTTA
1 ATCAATAATTAAAATAAGGAC--TA
* *
12660529 AT-ATTTTATTAAAATAAGGACTA
1 ATCA-ATAATTAAAATAAGGACTA
12660552 ATCAATAATTAAAATAAGGACT
1 ATCAATAATTAAAATAAGGACT
12660574 TTAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 20 0.51
24 2 0.05
25 17 0.44
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
ATCAATAATTAAAATAAGGACTA
Found at i:12664312 original size:47 final size:45
Alignment explanation
Indices: 12664261--12664428 Score: 132
Period size: 47 Copynumber: 3.6 Consensus size: 45
12664251 TATTTAATAT
*
12664261 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
12664308 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* * *
12664352 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
12664399 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
12664429 TTTTAATTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.13
46 10 0.11
47 36 0.38
48 9 0.09
49 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:12664334 original size:91 final size:91
Alignment explanation
Indices: 12664187--12664394 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
12664177 TTGATTTTAG
* * *
12664187 TAAATTCATATAAGAACATTTTATTGTTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
12664252 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* * *
12664279 TAAATTCATATAAGAAAAATTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
12664344 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
12664370 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
12664395 GTTATAATTA
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 88 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:12664355 original size:44 final size:43
Alignment explanation
Indices: 12664225--12664369 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 43
12664215 AAGAATTTTA
* *
12664225 TGAAATTATATATCATTATTAAATTATATTTAATATTAATTATT
1 TGAAATTATATATAATTATTAAATTATA-TTAATAATAATTATT
* * * *
12664269 TTAAATTGTATA-AATTCATATAAGA-AAAATTATTATCAATAATT-TT
1 TGAAATTATATATAATT-AT-TAA-ATTATATTA--AT-AATAATTATT
*
12664315 ATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATT
1 -TGAAATTATATATAATTATTAAATTATAT-TAATAATAATTATT
*
12664360 TTAAATTATA
1 TGAAATTATA
12664370 CAAATTCATA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.40
45 10 0.13
46 11 0.14
47 20 0.26
48 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
TGAAATTATATATAATTATTAAATTATATTAATAATAATTATT
Found at i:12664363 original size:26 final size:28
Alignment explanation
Indices: 12664309--12664369 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
12664299 TATTATCAAT
* *
12664309 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
12664337 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
12664363 AATTATA
1 AATTATA
12664370 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:12664576 original size:25 final size:26
Alignment explanation
Indices: 12664544--12664598 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
12664534 TTATTAAATT
*
12664544 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
12664569 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
12664594 A-ATAT
1 ATATAT
12664599 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:12664829 original size:16 final size:16
Alignment explanation
Indices: 12664810--12664861 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
12664800 GATTTGTTAT
* *
12664810 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
12664826 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12664842 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12664858 TACA
1 TACA
12664862 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12664921 original size:16 final size:16
Alignment explanation
Indices: 12664900--12664935 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
12664890 TTTGGTTCGC
12664900 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12664916 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12664932 TGTA
1 TGTA
12664936 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12665188 original size:16 final size:16
Alignment explanation
Indices: 12665151--12665216 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 16
12665141 TTAATCATAT
*
12665151 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12665167 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12665182 TTAAAATATAATT-TAA
1 TTAAAATAT-ATTATAA
*
12665198 -TAAAAT-TCTTAATAA
1 TTAAAATATATT-ATAA
12665213 TTAA
1 TTAA
12665217 TATTCTTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
13 2 0.05
14 4 0.10
15 19 0.45
16 14 0.33
17 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12665280 original size:66 final size:62
Alignment explanation
Indices: 12665196--12665413 Score: 177
Period size: 66 Copynumber: 3.5 Consensus size: 62
12665186 AATATAATTT
* *
12665196 AATAAAATTCTTAATAATTAATATTCTTATATGGATTTACTCAAATCATAATATATGATACTGTA
1 AATAAAATT-TAAATAATTAATATTCATATAT-GATTTACTCAAATCATAATATATGATACT-T-
12665261 A
62 A
* * * * *
12665262 AATATAAA-TTAACATAATTATTATT-AAATAT-A-TTA-T--AAT--TAAAATAT-ATAATTT
1 AATA-AAATTTAA-ATAATTAATATTCATATATGATTTACTCAAATCATAATATATGATACTTA
* * *
12665316 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCATATCATAATATATGATACTATA
1 AATAAAATT-TAAATAATTAATATTCATATATG-ATTTACTCAAATCATAATATATGATACT-TA
12665381 AATGAAAATTTGAAATAATTAATATTCATATAT
1 AAT-AAAATTT-AAATAATTAATATTCATATAT
12665414 TTTATTTAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
53 3 0.03
54 16 0.14
55 7 0.06
56 4 0.03
57 8 0.07
58 3 0.03
59 4 0.03
61 3 0.03
62 3 0.03
63 8 0.07
64 4 0.03
65 11 0.09
66 41 0.35
67 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (62 bp):
AATAAAATTTAAATAATTAATATTCATATATGATTTACTCAAATCATAATATATGATACTTA
Found at i:12665317 original size:14 final size:15
Alignment explanation
Indices: 12665268--12665319 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12665258 GTAAAATATA
12665268 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
12665283 TATTAAATATATTAT
1 AATTAAATATATTAT
12665298 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
12665311 AATTTAATA
1 AATTAAATA
12665320 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:12665354 original size:120 final size:121
Alignment explanation
Indices: 12665149--12665443 Score: 442
Period size: 120 Copynumber: 2.5 Consensus size: 121
12665139 TTTTAATCAT
*
12665149 ATTTAAACATAATTATTATTAAATATATTATAATT-AAA-ATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
12665212 ATTAATATTCTTATATGGATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
12665269 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
12665332 ATTAATATTCTTATATGAATTTACTCATATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * * * *
12665388 ATTTGAA-ATAATTAATATT-CATATATTTTATTTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
12665444 TAAAATAATT
Statistics
Matches: 162, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
118 30 0.19
119 45 0.28
120 85 0.52
121 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:12665632 original size:91 final size:92
Alignment explanation
Indices: 12665459--12665666 Score: 280
Period size: 92 Copynumber: 2.3 Consensus size: 92
12665449 TAATTATAAC
* * * * *
12665459 TAATAAATTATATTTTATGAATTT-TATAATTTAAAATATTAATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATATTAATTATTAAATATAATTTAATAAT
* *
12665523 TAATATTAAATTTCATAAAATTCTTGA
66 GAATATTAAATTTCATAAAATTCTTAA
*
12665550 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAG
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAAT-ATTAATTATTAAATATAATTTAATAA
12665614 TG-ATA-TATAATTTCATAAAATTCTTAA
65 TGAATATTA-AATTTCATAAAATTCTTAA
*
12665641 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
12665667 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
90 2 0.02
91 46 0.44
92 51 0.49
93 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (92 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATATTAATTATTAAATATAATTTAATAAT
GAATATTAAATTTCATAAAATTCTTAA
Found at i:12671600 original size:13 final size:13
Alignment explanation
Indices: 12671582--12671608 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12671572 ATAAATAAAT
12671582 AAATTAATGTAAC
1 AAATTAATGTAAC
12671595 AAATTAATGTAAC
1 AAATTAATGTAAC
12671608 A
1 A
12671609 GATTGACAAT
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:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AAATTAATGTAAC
Found at i:12675431 original size:43 final size:42
Alignment explanation
Indices: 12675364--12675633 Score: 263
Period size: 43 Copynumber: 6.3 Consensus size: 42
12675354 ATGTTATGTT
* * * * *
12675364 TTTAGTGGCGTTTTTGCAAGAAGCGTCACTAAAGGTCTTGATC
1 TTTAGCGGCGTTTGTGGAA-AAGCGCCGCTAAAGGTCTTGATC
* * *
12675407 TTTAGTGGCGTTTGTGGAATAAGCGTCGCTAAAGGTCTTGATA
1 TTTAGCGGCGTTTGTGGAA-AAGCGCCGCTAAAGGTCTTGATC
* *
12675450 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTGAAGGTCTTGATT
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGATC
* * ** *
12675493 TTTAGCGGCGTTAGTGGTAATAGCGCCGCTAAATATCCTGATC
1 TTTAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCTTGATC
* * * * *
12675536 TATAGCGGCGTTTGTGGAAAAGCACCGCTAAAGGTCCTAACC
1 TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGATC
* *
12675578 TATAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGT-TATGATC
1 TTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCT-TGATC
* *
12675621 TATAGTGGCGTTT
1 TTTAGCGGCGTTT
12675634 ATTTCTAAAA
Statistics
Matches: 193, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
42 36 0.19
43 153 0.79
44 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGATC
Found at i:12675523 original size:86 final size:84
Alignment explanation
Indices: 12675392--12675633 Score: 261
Period size: 85 Copynumber: 2.8 Consensus size: 84
12675382 AGAAGCGTCA
* * * *
12675392 CTAAAGGTCTTGATCTTTAGTGGCGTTTGTGGAATAAGCGTCGCTAAAGGTCTTGATATTTAGCG
1 CTAAAGGTCTTGATCTTTAGCGGCGTTTGTGGAAT-AGCGCCGCTAAAGGTCCTGATATATAGCG
*
12675457 GCGTTTGTGGGAAAAGCGCCG
65 GCGTTTGT-GGAAAAGCACCG
* * * ** *
12675478 CTGAAGGTCTTGATTTTTAGCGGCGTTAGTGGTAATAGCGCCGCTAAATATCCTGATCTATAGCG
1 CTAAAGGTCTTGATCTTTAGCGGCGTTTGTGG-AATAGCGCCGCTAAAGGTCCTGATATATAGCG
12675543 GCGTTTGTGGAAAAGCACCG
65 GCGTTTGTGGAAAAGCACCG
* * * * ** * *
12675563 CTAAAGGTCCTAACCTATAGCGGCGTTTGTGGGGAA-AGCGCCGCTAAAGGTTATGATCTATAGT
1 CTAAAGGTCTTGATCTTTAGCGGCGTTTGT--GGAATAGCGCCGCTAAAGGTCCTGATATATAGC
12675627 GGCGTTT
64 GGCGTTT
12675634 ATTTCTAAAA
Statistics
Matches: 130, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
85 64 0.49
86 61 0.47
87 5 0.04
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (84 bp):
CTAAAGGTCTTGATCTTTAGCGGCGTTTGTGGAATAGCGCCGCTAAAGGTCCTGATATATAGCGG
CGTTTGTGGAAAAGCACCG
Found at i:12681108 original size:50 final size:50
Alignment explanation
Indices: 12680993--12681185 Score: 244
Period size: 50 Copynumber: 3.8 Consensus size: 50
12680983 GATAATAATA
* ** * *
12680993 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCAG
* * * ** *
12681044 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
12681094 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
12681144 TGCCAACGCCATGTCCCAGACATGGTCTTACAAT-GGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCT
12681186 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 87 0.72
51 34 0.28
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:12683321 original size:18 final size:18
Alignment explanation
Indices: 12683298--12683336 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12683288 ATGGATCGCT
12683298 TTAGTGGCATGTTCTATC
1 TTAGTGGCATGTTCTATC
*
12683316 TTAGTGGCATGTTCTCTC
1 TTAGTGGCATGTTCTATC
12683334 TTA
1 TTA
12683337 AGAATCGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (18 bp):
TTAGTGGCATGTTCTATC
Found at i:12685529 original size:17 final size:17
Alignment explanation
Indices: 12685507--12685541 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12685497 AATAGGGAAA
12685507 GTAATCTTAG-AAGATTT
1 GTAATC-TAGTAAGATTT
12685524 GTAATCTAGTAAGATTT
1 GTAATCTAGTAAGATTT
12685541 G
1 G
12685542 GTTTTGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
GTAATCTAGTAAGATTT
Found at i:12690196 original size:5 final size:5
Alignment explanation
Indices: 12690186--12690217 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12690176 TTGATGAGTA
12690186 TTTTG TTTTG TTTTG TTTT- TTTT- TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
12690218 TATCTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (5 bp):
TTTTG
Found at i:12692993 original size:32 final size:33
Alignment explanation
Indices: 12692950--12693012 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
12692940 TACATGACTA
* * *
12692950 AGATACGTCTACTTTAAA-ACATTTATTAAACT
1 AGATACATCTACTCTAAATACATTCATTAAACT
12692982 AGATACATCTACTCTAAATACATTCATTAAA
1 AGATACATCTACTCTAAATACATTCATTAAA
12693013 TACAAGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (33 bp):
AGATACATCTACTCTAAATACATTCATTAAACT
Found at i:12695704 original size:67 final size:68
Alignment explanation
Indices: 12695611--12695797 Score: 232
Period size: 67 Copynumber: 2.8 Consensus size: 68
12695601 TTCCATTTTC
* * * * *
12695611 TGTCATAGCCCAACTATGATCCTACACAATATAACCCCTATTTGTTGTCCTAGTGGACTTCA-TT
1 TGTCATAGCCCAACTATGGTCTTACACAATATAACCCCTATTTATTGTCCTAGAGGAATTCATTT
12695675 TAT
66 TAT
* * * *
12695678 TGTCATAGCCCAACTATGGTCTTACACAATATAACCCATGTTTATTGTCTTGGAGGAATTCATTT
1 TGTCATAGCCCAACTATGGTCTTACACAATATAACCCCTATTTATTGTCCTAGAGGAATTCATTT
*
12695743 TGT
66 TAT
* * * *
12695746 TGCCATAGCCCAATTATGGTCTTACACAATATAACCCCAAGTTTATTATCCT
1 TGTCATAGCCCAACTATGGTCTTACACAATATAACCCCTA-TTTATTGTCCT
12695798 GACAGACTTC
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
67 53 0.52
68 39 0.39
69 9 0.09
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (68 bp):
TGTCATAGCCCAACTATGGTCTTACACAATATAACCCCTATTTATTGTCCTAGAGGAATTCATTT
TAT
Found at i:12708676 original size:30 final size:29
Alignment explanation
Indices: 12708656--12708720 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 29
12708646 TTAATATTTC
12708656 ATTCAATTTATTAATTTAAATAATAAAAAA
1 ATTCAATTTATTAATTTAAATAAT-AAAAA
12708686 ATTCAATTTATTAATTTAAATAATAAAAAA
1 ATTCAATTTATTAATTTAAATAAT-AAAAA
12708716 ATTCA
1 ATTCA
12708721 TTTCATGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTCAATTTATTAATTTAAATAATAAAAA
Found at i:12717632 original size:15 final size:15
Alignment explanation
Indices: 12717612--12717665 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
12717602 TGACTACTAG
12717612 ATACATCTATTCTAA
1 ATACATCTATTCTAA
* *
12717627 ATACATTTATTAAACTAG
1 ATACATCTATT---CTAA
*
12717645 ATACATCTACTCTAA
1 ATACATCTATTCTAA
12717660 ATACAT
1 ATACAT
12717666 TCATTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 19 0.61
18 12 0.39
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (15 bp):
ATACATCTATTCTAA
Found at i:12717644 original size:33 final size:33
Alignment explanation
Indices: 12717607--12717673 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
12717597 ATGCATGACT
* *
12717607 ACTAGATACATCTATTCTAAATACATTTATTAA
1 ACTAGATACATCTACTCTAAATACATTCATTAA
12717640 ACTAGATACATCTACTCTAAATACATTCATTAA
1 ACTAGATACATCTACTCTAAATACATTCATTAA
12717673 A
1 A
12717674 TAAAAGTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (33 bp):
ACTAGATACATCTACTCTAAATACATTCATTAA
Found at i:12717650 original size:18 final size:16
Alignment explanation
Indices: 12717606--12717653 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
12717596 CATGCATGAC
12717606 TACTAGATACATCTAT
1 TACTAGATACATCTAT
* *
12717622 T-CTAAATACATTTAT
1 TACTAGATACATCTAT
12717637 TAAACTAGATACATCTA
1 T--ACTAGATACATCTA
12717654 CTCTAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
18 11 0.44
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (16 bp):
TACTAGATACATCTAT
Found at i:12720291 original size:19 final size:19
Alignment explanation
Indices: 12720267--12720304 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12720257 AATAAAATAA
*
12720267 TTTATATTTTTAAATTTTT
1 TTTATAGTTTTAAATTTTT
*
12720286 TTTATAGTTTTGAATTTTT
1 TTTATAGTTTTAAATTTTT
12720305 ATAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTATAGTTTTAAATTTTT
Found at i:12727603 original size:59 final size:60
Alignment explanation
Indices: 12727474--12727603 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 60
12727464 CTATATCGTT
**
12727474 TAGTTGGGTGATCAAATTAAAAAAAATTGATAGTTGGGTGACAAAAAGGAAAAAAGACAA
1 TAGTTGGGTGATCAAATTAAAAAAAATTGATAGTTGAATGACAAAAAGGAAAAAAGACAA
* * * * *
12727534 TAATTAGGTGATCAAGTT-AAAAAAATTGATAGTTGAATGATAATAAA-G-AAAAGGAGCAA
1 TAGTTGGGTGATCAAATTAAAAAAAATTGATAGTTGAATGACAA-AAAGGAAAAAAGA-CAA
12727593 TAGTTGGGTGA
1 TAGTTGGGTGA
12727604 CTTGTATTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 6 0.10
59 35 0.59
60 18 0.31
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.25
Consensus pattern (60 bp):
TAGTTGGGTGATCAAATTAAAAAAAATTGATAGTTGAATGACAAAAAGGAAAAAAGACAA
Found at i:12727944 original size:21 final size:21
Alignment explanation
Indices: 12727920--12727963 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12727910 TGCAGTTTCC
*
12727920 ACAACAGCAGCAGCAGCAACA
1 ACAACAACAGCAGCAGCAACA
12727941 ACAACAACAGCAGCAGCAACA
1 ACAACAACAGCAGCAGCAACA
12727962 AC
1 AC
12727964 CCCTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00
Consensus pattern (21 bp):
ACAACAACAGCAGCAGCAACA
Found at i:12737942 original size:3 final size:3
Alignment explanation
Indices: 12737934--12737961 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12737924 AATGCTTCTG
12737934 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12737962 TGTTTAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12741579 original size:15 final size:15
Alignment explanation
Indices: 12741554--12741589 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
12741544 AATTACTTAA
12741554 TTAACTTAATTAAACT
1 TTAA-TTAATTAAACT
12741570 TTAATTAATTAAACT
1 TTAATTAATTAAACT
12741585 TTAAT
1 TTAAT
12741590 CACAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTAATTAAACT
Found at i:12754865 original size:50 final size:50
Alignment explanation
Indices: 12754750--12754942 Score: 260
Period size: 50 Copynumber: 3.8 Consensus size: 50
12754740 GATAATAACA
* ** * **
12754750 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTAG
* * * **
12754801 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAG
*
12754851 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTTG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAG
*
12754901 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12754943 TTACCCAAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 93 0.74
51 32 0.26
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAG
Found at i:12760963 original size:15 final size:15
Alignment explanation
Indices: 12760943--12760973 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12760933 AAAGACAGTA
12760943 ATTACTAGTACTTTT
1 ATTACTAGTACTTTT
12760958 ATTACTAGTACTTTT
1 ATTACTAGTACTTTT
12760973 A
1 A
12760974 GTCTTCATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTACTAGTACTTTT
Found at i:12765255 original size:55 final size:55
Alignment explanation
Indices: 12765195--12765332 Score: 154
Period size: 54 Copynumber: 2.5 Consensus size: 55
12765185 TTTTTTTTGT
** * *
12765195 GTGCTGGGACACTGA-TGGTTGGCATCCTTGTACTAGATTTGAAAAAAAAATTGGG
1 GTGCTGGGACACT-ATTGGCCGGCACCCTTGTACCAGATTTGAAAAAAAAATTGGG
* *
12765250 GTGCTGGGACACTATTGGCCGGCACCCTTGTACCAGATTT-TAAAAAAAATTTGG
1 GTGCTGGGACACTATTGGCCGGCACCCTTGTACCAGATTTGAAAAAAAAATTGGG
** * * *
12765304 GTGCAAGAACACTAATGGCCGACACCCTT
1 GTGCTGGGACACTATTGGCCGGCACCCTT
12765333 TCAATATATA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
54 37 0.52
55 34 0.48
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (55 bp):
GTGCTGGGACACTATTGGCCGGCACCCTTGTACCAGATTTGAAAAAAAAATTGGG
Found at i:12766029 original size:18 final size:18
Alignment explanation
Indices: 12766006--12766045 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
12765996 GGGTCTGATA
12766006 ATGAAGAGCAGTCCGACC
1 ATGAAGAGCAGTCCGACC
12766024 ATGAAGAGCAGTCCGACC
1 ATGAAGAGCAGTCCGACC
12766042 ATGA
1 ATGA
12766046 TATTGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.25, G:0.28, T:0.12
Consensus pattern (18 bp):
ATGAAGAGCAGTCCGACC
Found at i:12768317 original size:25 final size:26
Alignment explanation
Indices: 12768284--12768342 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
12768274 AGTATTGTTT
*
12768284 AAATTATTCAATTATTATATAGTGTA
1 AAATAATTCAATTATTATATAGTGTA
*
12768310 AAA-AATTCGATTATTATATAGTGTA
1 AAATAATTCAATTATTATATAGTGTA
12768335 AAATAATT
1 AAATAATT
12768343 AAGTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (26 bp):
AAATAATTCAATTATTATATAGTGTA
Found at i:12768470 original size:18 final size:18
Alignment explanation
Indices: 12768447--12768753 Score: 109
Period size: 18 Copynumber: 16.5 Consensus size: 18
12768437 TAATAATTAA
12768447 GAAATGAAACAAAAAATT
1 GAAATGAAACAAAAAATT
* *
12768465 GAAATGAAATAAAAAA-A
1 GAAATGAAACAAAAAATT
* * *
12768482 GAAGTGAAACTAAATATT
1 GAAATGAAACAAAAAATT
*
12768500 GAAATGAAATGAAATGAAA-T
1 GAAATGAAA-CAAA--AAATT
** *
12768520 GAAAT-AAATTAAAAA-G
1 GAAATGAAACAAAAAATT
* ** *
12768536 GAAATGTAATGAAAATTT
1 GAAATGAAACAAAAAATT
* *
12768554 GAAATTAAATGAAATAAATT
1 GAAATGAAA-CAAA-AAATT
*
12768574 AGAAAATGAAATGAAACTAAAAATT
1 -G---A---AATGAAACAAAAAATT
* *
12768599 GAAATGAAATAAATTAAAAAT
1 GAAATGAAA-CAA--AAAATT
**
12768620 GAAATGAAATGAAAAATT
1 GAAATGAAACAAAAAATT
12768638 GAAATG-------AAA-T
1 GAAATGAAACAAAAAATT
*
12768648 GAAAT-AAACTAAAAAAAT
1 GAAATGAAAC-AAAAAATT
*
12768666 GAAATGAAACTAAAAATT
1 GAAATGAAACAAAAAATT
12768684 GAAATGAAATGAACAAAAAATT
1 GAAATG--A--AACAAAAAATT
*
12768706 GAAATGAAATAAATAAAAATT
1 GAAATG-AA-ACA-AAAAATT
12768727 GAAATGAAACAAAAAATT
1 GAAATGAAACAAAAAATT
12768745 GAAATGAAA
1 GAAATGAAA
12768754 TAAATTAAAA
Statistics
Matches: 218, Mismatches: 37, Indels: 68
0.67 0.11 0.21
Matches are distributed among these distances:
10 6 0.03
11 3 0.01
16 8 0.04
17 22 0.10
18 84 0.39
19 15 0.07
20 16 0.07
21 33 0.15
22 16 0.07
24 2 0.01
25 5 0.02
26 2 0.01
27 6 0.03
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.21
Consensus pattern (18 bp):
GAAATGAAACAAAAAATT
Found at i:12768509 original size:5 final size:5
Alignment explanation
Indices: 12768499--12768818 Score: 121
Period size: 5 Copynumber: 61.2 Consensus size: 5
12768489 AACTAAATAT
* * *
12768499 TGAAA TGAAA TGAAA TGAAA TGAAA T-AAA TTAAAAA GGAAA TGTAA TGAAAA
1 TGAAA TGAAA TGAAA TGAAA TGAAA TGAAA -T-GAAA TGAAA TGAAA TG-AAA
* *
12768551 TTTGAAA TTAAA TGAAA T-AAA TTAGAAAA TGAAA TGAAA CTAAAAA TTGAAA
1 --TGAAA TGAAA TGAAA TGAAA -T-G-AAA TGAAA TGAAA -T-GAAA -TGAAA
* *
12768603 TGAAA T-AAA TTAAAAA TGAAA TGAAA TGAAA --AAT TGAAA TGAAA TGAAA
1 TGAAA TGAAA -T-GAAA TGAAA TGAAA TGAAA TGAAA TGAAA TGAAA TGAAA
* *
12768652 T-AAA CT-AAA -AAAA TGAAA TGAAA CTAAAAA TTGAAA TGAAA TGAACA
1 TGAAA -TGAAA TGAAA TGAAA TGAAA -T-GAAA -TGAAA TGAAA TGAA-A
** * *
12768699 AAAAA TTGAAA TGAAA T-AAA TAAAAA TTGAAA TGAAA -CAAA --AAA
1 TGAAA -TGAAA TGAAA TGAAA T-GAAA -TGAAA TGAAA TGAAA TGAAA
* * * *
12768743 TTGAAA TGAAA T-AAA TTAAAAA TGAAA T-AAA TTAAA TTTAAAA TTTAAAA
1 -TGAAA TGAAA TGAAA -T-GAAA TGAAA TGAAA TGAAA --TGAAA --TGAAA
12768793 TTGAAA TGAAA TGAAA TGAAA T-AAA T
1 -TGAAA TGAAA TGAAA TGAAA TGAAA T
12768819 TTATTATTTA
Statistics
Matches: 253, Mismatches: 26, Indels: 73
0.72 0.07 0.21
Matches are distributed among these distances:
3 5 0.02
4 33 0.13
5 144 0.57
6 33 0.13
7 33 0.13
8 5 0.02
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (5 bp):
TGAAA
Found at i:12768526 original size:84 final size:87
Alignment explanation
Indices: 12768441--12768819 Score: 233
Period size: 99 Copynumber: 4.0 Consensus size: 87
12768431 ATAAATTAAT
* *
12768441 AATTAA-GAAATGAAACAAAAAATTGAAATGAAATAAAAAAA-GAAGTGAAACTAAATATTGAAA
1 AATTAATGAAATGAAA-AAAAAATTGAAATGAAATAAAAAAATGAAATGAAACTAAAAATTGAAA
12768504 TGAAATGAAA-TGAAATGAAATA
65 TGAAATGAAATTGAAATGAAATA
*
12768526 AATTAAAAAGGAAATGTAATGAAAATTTGAAATT-AAATGAAATAAATTAGAAAATGAAATGAAA
1 AATT---AATGAAATG-AA--AAAA----AAATTGAAATGAAAT-AA--A-AAAATGAAATGAAA
*
12768590 CTAAAAATTGAAATGAAAT-AAATTAAAAATGAAATGA
52 CTAAAAATTGAAATGAAATGAAATT-GAAATGAAAT-A
* **
12768627 AATGAA--AAATTG-AAATGAAA-TGAAAT-AAACTAAAAAAATGAAATGAAACTAAAAATTGAA
1 AATTAATGAAA-TGAAAAAAAAATTGAAATGAAA-TAAAAAAATGAAATGAAACTAAAAATTGAA
12768687 ATGAAATGAACAAAAAATTGAAATGAAATA
64 ATGAAATG------AAATTGAAATGAAATA
* *
12768717 AATAAAAATTGAAATGAAACAAAAAATTGAAATGAAATAAATTAAAAATGAAAT-AAATTAAATT
1 AAT--TAA-TGAAATGAAA-AAAAAATTGAAATGAAAT-AA--AAAAATGAAATGAAACT--A--
*
12768781 TAAAATTTAAAATTGAAATGAAA-TGAAATGAAATA
55 -AAAA-TTGAAA-TGAAATGAAATTGAAATGAAATA
12768816 AATT
1 AATT
12768820 TATTATTTAA
Statistics
Matches: 233, Mismatches: 13, Indels: 84
0.71 0.04 0.25
Matches are distributed among these distances:
85 37 0.16
86 1 0.00
88 8 0.03
89 14 0.06
90 6 0.03
91 12 0.05
92 8 0.03
93 2 0.01
94 11 0.05
95 13 0.06
96 7 0.03
97 10 0.04
98 14 0.06
99 46 0.20
100 23 0.10
101 5 0.02
104 4 0.02
105 5 0.02
106 7 0.03
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (87 bp):
AATTAATGAAATGAAAAAAAAATTGAAATGAAATAAAAAAATGAAATGAAACTAAAAATTGAAAT
GAAATGAAATTGAAATGAAATA
Found at i:12768564 original size:44 final size:44
Alignment explanation
Indices: 12768509--12768808 Score: 281
Period size: 39 Copynumber: 6.9 Consensus size: 44
12768499 TGAAATGAAA
* * *
12768509 TGAAATGAAATGAAATAAATTAAAAAGGAAATGTAATGAAAATT
1 TGAAATGAAATGAAATAAATTAAAAATGAAATGAAATGAAAAAT
*
12768553 TGAAATTAAATGAAATAAATTAGAAAATGAAATGAAACT-AAAAA-
1 TGAAATGAAATGAAATAAATTA-AAAATGAAATGAAA-TGAAAAAT
12768597 T----TGAAATGAAATAAATTAAAAATGAAATGAAATGAAAAAT
1 TGAAATGAAATGAAATAAATTAAAAATGAAATGAAATGAAAAAT
*
12768637 TGAAATGAAATGAAATAAACTAAAAAAATGAAATGAAACT-AAAAAT
1 TGAAATGAAATGAAATAAA-T-TAAAAATGAAATGAAA-TGAAAAAT
* *
12768683 TGAAATGAAATGAACAAAAAATT-GAAATGAAAT-AAAT-AAAAAT
1 TGAAATGAAATG-A-AATAAATTAAAAATGAAATGAAATGAAAAAT
* * *
12768726 TGAAATGAAA-CAAA-AAATT-GAAATGAAAT-AAATTAAAAA-
1 TGAAATGAAATGAAATAAATTAAAAATGAAATGAAATGAAAAAT
* *
12768765 TGAAAT-AAATTAAATTTAAAATTTAAAATTGAAATGAAATGAAA
1 TGAAATGAAATGAAA--T-AAA-TTAAAAATGAAATGAAATGAAA
12768809 TGAAATAAAT
Statistics
Matches: 220, Mismatches: 14, Indels: 42
0.80 0.05 0.15
Matches are distributed among these distances:
38 4 0.02
39 47 0.21
40 24 0.11
41 1 0.00
43 20 0.09
44 41 0.19
45 34 0.15
46 41 0.19
47 3 0.01
48 5 0.02
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (44 bp):
TGAAATGAAATGAAATAAATTAAAAATGAAATGAAATGAAAAAT
Found at i:12768580 original size:17 final size:17
Alignment explanation
Indices: 12768560--12768778 Score: 105
Period size: 18 Copynumber: 12.1 Consensus size: 17
12768550 ATTTGAAATT
12768560 AAATGAAAT-AAATTAGA
1 AAATGAAATGAAATTA-A
*
12768577 AAATGAAATGAAACTAA
1 AAATGAAATGAAATTAA
12768594 AAATTGAAATGAAATAAATTAA
1 AAA-TGAAATG----AAATTAA
*
12768616 AAATGAAATGAAATGAA
1 AAATGAAATGAAATTAA
*
12768633 AAATTGAAATGAAA-T-G
1 AAA-TGAAATGAAATTAA
12768649 AAAT-AAACT--AA--AA
1 AAATGAAA-TGAAATTAA
*
12768662 AAATGAAATGAAACTAA
1 AAATGAAATGAAATTAA
*
12768679 AAATTGAAATGAAATGAACAAA
1 AAA-TGAAATGAAAT----TAA
12768701 AAATTGAAATGAAATAAATAA
1 AAA-TGAAATGAAAT---TAA
**
12768722 AAATTGAAATGAAACAAA
1 AAA-TGAAATGAAATTAA
12768740 AAATTGAAATGAAATAAATTAA
1 AAA-TGAAATG----AAATTAA
12768762 AAATGAAAT-AAATTAA
1 AAATGAAATGAAATTAA
12768778 A
1 A
12768779 TTTAAAATTT
Statistics
Matches: 165, Mismatches: 14, Indels: 47
0.73 0.06 0.21
Matches are distributed among these distances:
13 7 0.04
14 6 0.04
15 4 0.02
16 11 0.07
17 27 0.16
18 45 0.27
21 31 0.19
22 34 0.21
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.21
Consensus pattern (17 bp):
AAATGAAATGAAATTAA
Found at i:12768619 original size:39 final size:38
Alignment explanation
Indices: 12768458--12768778 Score: 214
Period size: 39 Copynumber: 8.1 Consensus size: 38
12768448 AAATGAAACA
** *
12768458 AAAAATTGAAATGAAATAAAAAAAGAAGTGAAACTAAA-T
1 AAAAA-TGAAATGAAATAAAAATTGAAATGAAA-TAAATT
* *
12768497 ---ATTGAAATGAAAT-GAAA-TGAAATGAAATAAATT
1 AAAAATGAAATGAAATAAAAATTGAAATGAAATAAATT
* * *
12768530 AAAAAGGAAATGTAATGAAAATTTGAAATTAAATGAAATAAATT
1 AAAAATGAAATGAAAT-AAAAATTG-----AAATGAAATAAATT
12768574 AGAAAATGAAATGAAACTAAAAATTGAAATGAAATAAATT
1 A-AAAATGAAATGAAA-TAAAAATTGAAATGAAATAAATT
12768614 AAAAATGAAATGAAATGAAAAATTGAAATGAAATGAAATAAACT
1 AAAAATGAAATGAAAT-AAAAATTGAAATGAAAT-AAAT----T
* **
12768658 AAAAAAATGAAATGAAACTAAAAATTGAAATGAAATGAACA
1 --AAAAATGAAATGAAA-TAAAAATTGAAATGAAATAAATT
*
12768699 AAAAATTGAAATGAAATAAATAAAAATTGAAATGAAA-CAA--
1 AAAAA-TGAAATG----AAATAAAAATTGAAATGAAATAAATT
* *
12768739 AAAATTGAAATGAAAT--AAATTAAAAATGAAATAAATT
1 AAAAATGAAATGAAATAAAAATT-GAAATGAAATAAATT
12768776 AAA
1 AAA
12768779 TTTAAAATTT
Statistics
Matches: 231, Mismatches: 19, Indels: 66
0.73 0.06 0.21
Matches are distributed among these distances:
32 4 0.02
33 14 0.06
34 11 0.05
35 17 0.07
36 11 0.05
37 3 0.01
38 3 0.01
39 45 0.19
40 30 0.13
42 2 0.01
43 17 0.07
44 19 0.08
45 21 0.09
46 33 0.14
47 1 0.00
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.22
Consensus pattern (38 bp):
AAAAATGAAATGAAATAAAAATTGAAATGAAATAAATT
Found at i:12768786 original size:21 final size:21
Alignment explanation
Indices: 12768511--12768786 Score: 218
Period size: 21 Copynumber: 13.2 Consensus size: 21
12768501 AAATGAAATG
12768511 AAATGAAATGAAATAAATTAA
1 AAATGAAATGAAATAAATTAA
* * **
12768532 AAAGGAAATGTAATGAAAATTTG
1 AAATGAAATGAAAT--AAATTAA
*
12768555 AAATTAAATGAAATAAATTAGA
1 AAATGAAATGAAATAAATTA-A
12768577 AAATGAAATGAAACT--A--AA
1 AAATGAAATGAAA-TAAATTAA
*
12768595 AATTGAAATGAAATAAATTAA
1 AAATGAAATGAAATAAATTAA
*
12768616 AAATGAAATGAAATGAAAAATT-G
1 AAATGAAATGAAAT---AAATTAA
*
12768639 AAATGAAATGAAATAAACT-A
1 AAATGAAATGAAATAAATTAA
*
12768659 AAA--AAATGAAATGAAACTAA
1 AAATGAAATGAAAT-AAATTAA
* **
12768679 AAATTGAAATGAAATGAACAAA
1 AAA-TGAAATGAAATAAATTAA
12768701 AAATTGAAATGAAATAAA-TAA
1 AAA-TGAAATGAAATAAATTAA
*
12768722 AAATTGAAATGAAA-CAA--AA
1 AAA-TGAAATGAAATAAATTAA
*
12768741 AATTGAAATGAAATAAATTAA
1 AAATGAAATGAAATAAATTAA
*
12768762 AAATGAAAT-AAATTAAATTTA
1 AAATGAAATGAAA-TAAATTAA
12768783 AAAT
1 AAAT
12768787 TTAAAATTGA
Statistics
Matches: 211, Mismatches: 24, Indels: 40
0.77 0.09 0.15
Matches are distributed among these distances:
17 1 0.00
18 32 0.15
19 13 0.06
20 16 0.08
21 70 0.33
22 34 0.16
23 40 0.19
24 5 0.02
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (21 bp):
AAATGAAATGAAATAAATTAA
Found at i:12769466 original size:20 final size:20
Alignment explanation
Indices: 12769419--12769458 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12769409 GCAATACGGT
*
12769419 CAAATATTCACTAATTTATA
1 CAAATATTCACTAATTGATA
12769439 CAAATATTCACTAATTGATA
1 CAAATATTCACTAATTGATA
12769459 AATATATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (20 bp):
CAAATATTCACTAATTGATA
Found at i:12774919 original size:14 final size:14
Alignment explanation
Indices: 12774900--12774927 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12774890 GAAATGGTGC
12774900 GTGGAAGGGGGGAA
1 GTGGAAGGGGGGAA
12774914 GTGGAAGGGGGGAA
1 GTGGAAGGGGGGAA
12774928 ATTAGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.64, T:0.07
Consensus pattern (14 bp):
GTGGAAGGGGGGAA
Found at i:12780963 original size:17 final size:17
Alignment explanation
Indices: 12780941--12780977 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12780931 AGTTATGTTA
12780941 TATGAAAGGTCAAAAGT
1 TATGAAAGGTCAAAAGT
*
12780958 TATGAAAGGTCAAGAGT
1 TATGAAAGGTCAAAAGT
12780975 TAT
1 TAT
12780978 CTTGTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (17 bp):
TATGAAAGGTCAAAAGT
Found at i:12791604 original size:16 final size:16
Alignment explanation
Indices: 12791583--12791614 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12791573 TCAATTAATC
*
12791583 TAATTAATCTAAAAAT
1 TAATTAAACTAAAAAT
12791599 TAATTAAACTAAAAAT
1 TAATTAAACTAAAAAT
12791615 CAATCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAAACTAAAAAT
Found at i:12793514 original size:192 final size:191
Alignment explanation
Indices: 12793165--12793555 Score: 563
Period size: 192 Copynumber: 2.0 Consensus size: 191
12793155 TGACTTGTTC
* * *
12793165 ATTAGTATCCCCTACTAGAATACTTAAAAAAGCTTATTTCCATCATAGATAACCAGTGCCCAATG
1 ATTAGCATCCCCTACTAGAATACTAAAAAAAGCTTATTTCCATCACAGATAACCAGTGCCCAATG
** *
12793230 GCCGACAAATCCCAAATTTTCCTCCCTCTTTATAATTTCATCCACTCTTATAAGAAAAGTCAGAA
66 GCAAACAAATCCCAAATTTTCCT-CCTCTTTATAACTTCATCCACTCTTATAAGAAAAGTCAGAA
* ** *
12793295 TCCACCAGCCTAAGTTGGTTAATCTTATTAAGATCCACATCCTAATCCATTAATCTTCCCAT
130 TCCACCAACCTAAAATGGTTAATCTTATTAAGATACACATCCTAATCCATTAATCTTCCCAT
* *
12793357 ATTAGCATCCTCTACTAGAATAC-AAAAAAATGCTTATTTCCATCACAGATTACCAGTGCCCAAT
1 ATTAGCATCCCCTACTAGAATACTAAAAAAA-GCTTATTTCCATCACAGATAACCAGTGCCCAAT
* *
12793421 GGTAAACAAATCCCAAAATTTTCGCT-CTCTTTATAACTTCATCCACTCTTATAA-ACACAGTCA
65 GGCAAACAAATCCC-AAATTTTC-CTCCTCTTTATAACTTCATCCACTCTTATAAGA-AAAGTCA
* * *
12793484 GAATCCACCAACCTAAAATGGTTGATCTTATTAATATACACATCCTAATCCATTAATCTTCTCAT
127 GAATCCACCAACCTAAAATGGTTAATCTTATTAAGATACACATCCTAATCCATTAATCTTCCCAT
12793549 ATTAGCA
1 ATTAGCA
12793556 CACTCTGCCA
Statistics
Matches: 178, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
191 7 0.04
192 161 0.90
193 8 0.04
194 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (191 bp):
ATTAGCATCCCCTACTAGAATACTAAAAAAAGCTTATTTCCATCACAGATAACCAGTGCCCAATG
GCAAACAAATCCCAAATTTTCCTCCTCTTTATAACTTCATCCACTCTTATAAGAAAAGTCAGAAT
CCACCAACCTAAAATGGTTAATCTTATTAAGATACACATCCTAATCCATTAATCTTCCCAT
Found at i:12801189 original size:25 final size:25
Alignment explanation
Indices: 12801159--12801209 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
12801149 CTTTCATTCA
12801159 TATAACACTTTAAACACAATCATAT
1 TATAACACTTTAAACACAATCATAT
* **
12801184 TATAACACTTTACATGCAATCATAT
1 TATAACACTTTAAACACAATCATAT
12801209 T
1 T
12801210 TAATGATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (25 bp):
TATAACACTTTAAACACAATCATAT
Found at i:12805155 original size:17 final size:17
Alignment explanation
Indices: 12805130--12805168 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12805120 AAAGCCTCGC
* *
12805130 TCAAAAATTTATTTTAT
1 TCAACAATTTATCTTAT
12805147 TCAACAATTTATCTTAT
1 TCAACAATTTATCTTAT
*
12805164 ACAAC
1 TCAAC
12805169 TATTGGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
TCAACAATTTATCTTAT
Found at i:12806321 original size:28 final size:28
Alignment explanation
Indices: 12806266--12806319 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
12806256 TTTTATAAAT
*
12806266 TTTATATTTTAAACTTTTATTTATTTTA
1 TTTATAATTTAAACTTTTATTTATTTTA
12806294 TTTATAATTTATAA-TTTTA-TTATTTT
1 TTTATAATTTA-AACTTTTATTTATTTT
12806320 TAAATGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 15 0.62
29 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTATAATTTAAACTTTTATTTATTTTA
Found at i:12806557 original size:59 final size:58
Alignment explanation
Indices: 12806485--12806643 Score: 178
Period size: 59 Copynumber: 2.7 Consensus size: 58
12806475 GCCTAGAAAT
** * * * *
12806485 TTTGGTATCACATTAGCTATTTTGGTGTC-GGTTAAAAATTTTAGTATCATGTTAAAAA
1 TTTGGTATCACATTAGAAATATTGGTATCTCGTTAAAAATTTTAGCATCA-GTTAAAAA
*
12806543 TATTGGTATCACATTAGAAATATTGGTATCTCGTTAAAAATTTTGGCATCAGTTAAAAA
1 T-TTGGTATCACATTAGAAATATTGGTATCTCGTTAAAAATTTTAGCATCAGTTAAAAA
** * * *
12806602 TTTGGTAT-TGATTAGAAATAGTGATATCGCGTTAAAAATTTT
1 TTTGGTATCACATTAGAAATATTGGTATCTCGTTAAAAATTTT
12806644 TGTATCGATA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
57 29 0.33
58 8 0.09
59 33 0.38
60 17 0.20
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (58 bp):
TTTGGTATCACATTAGAAATATTGGTATCTCGTTAAAAATTTTAGCATCAGTTAAAAA
Found at i:12806635 original size:57 final size:57
Alignment explanation
Indices: 12806515--12806678 Score: 177
Period size: 57 Copynumber: 2.8 Consensus size: 57
12806505 TTTGGTGTCG
** * * *
12806515 GTTAAAAATTTTAGTATCATGTTAAAAATATTGGTATCACATTAGAAATATTGGTATCTC
1 GTTAAAAATTTTAGTATCA-GTTAAAAAT-TTGGTAT-TGATTAGAAATAGTGATATCGC
* *
12806575 GTTAAAAATTTTGGCATCAGTTAAAAATTTGGTATTGATTAGAAATAGTGATATCGC
1 GTTAAAAATTTTAGTATCAGTTAAAAATTTGGTATTGATTAGAAATAGTGATATCGC
* * *
12806632 GTTAAAAATTTTTGTATC-GATAAAAAATTTGGTCTTGTCATTAGAAA
1 GTTAAAAATTTTAGTATCAG-TTAAAAATTTGGTATTG--ATTAGAAA
12806679 GTTAAAAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
56 1 0.01
57 48 0.53
58 7 0.08
59 17 0.19
60 17 0.19
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (57 bp):
GTTAAAAATTTTAGTATCAGTTAAAAATTTGGTATTGATTAGAAATAGTGATATCGC
Found at i:12806649 original size:20 final size:20
Alignment explanation
Indices: 12806503--12806650 Score: 97
Period size: 20 Copynumber: 7.6 Consensus size: 20
12806493 CACATTAGCT
*
12806503 ATTTTGGTGTCG-GTTAAAA
1 ATTTTGGTATCGCGTTAAAA
* **
12806522 ATTTTAGTATCATGTTAAAA
1 ATTTTGGTATCGCGTTAAAA
* * * *
12806542 ATATTGGTATCACATTAGAA
1 ATTTTGGTATCGCGTTAAAA
* *
12806562 ATATTGGTATCTCGTTAAAA
1 ATTTTGGTATCGCGTTAAAA
* *
12806582 ATTTTGGCATC-AGTTAAAA
1 ATTTTGGTATCGCGTTAAAA
* * *
12806601 A-TTTGGTATTG-ATTAGAA
1 ATTTTGGTATCGCGTTAAAA
** *
12806619 ATAGTGATATCGCGTTAAAA
1 ATTTTGGTATCGCGTTAAAA
*
12806639 ATTTTTGTATCG
1 ATTTTGGTATCG
12806651 ATAAAAAATT
Statistics
Matches: 97, Mismatches: 28, Indels: 7
0.73 0.21 0.05
Matches are distributed among these distances:
18 13 0.13
19 23 0.24
20 61 0.63
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTTTGGTATCGCGTTAAAA
Found at i:12807959 original size:24 final size:24
Alignment explanation
Indices: 12807924--12807971 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12807914 GCAAATTTAC
12807924 TTATCATATCACATGCTTATATGT
1 TTATCATATCACATGCTTATATGT
12807948 TTATCACT-TCACATGCTTATATGT
1 TTATCA-TATCACATGCTTATATGT
12807972 ACCTAGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (24 bp):
TTATCATATCACATGCTTATATGT
Found at i:12808982 original size:20 final size:21
Alignment explanation
Indices: 12808957--12809005 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
12808947 GTATCGATCT
* *
12808957 GGTATCGATGCT-TTTCTTAA
1 GGTATCGATGATATTTCCTAA
*
12808977 GGTATCG-TTATATTTCCTAA
1 GGTATCGATGATATTTCCTAA
12808997 GGTATCGAT
1 GGTATCGAT
12809006 ATTCTTGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.43
Consensus pattern (21 bp):
GGTATCGATGATATTTCCTAA
Found at i:12825718 original size:23 final size:23
Alignment explanation
Indices: 12825663--12825719 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
12825653 TCTACAATAT
* * *
12825663 TCAAATAATATTAAAAATGAAAT
1 TCAAACAATATTAAAAACGAAAG
* *
12825686 TCAAATAATATTAAAAACGACAG
1 TCAAACAATATTAAAAACGAAAG
*
12825709 TGAAACAATAT
1 TCAAACAATAT
12825720 AATAAACAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (23 bp):
TCAAACAATATTAAAAACGAAAG
Found at i:12825760 original size:23 final size:23
Alignment explanation
Indices: 12825710--12825764 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
12825700 AAACGACAGT
*
12825710 GAAACAATATAATAAACAGGTAC
1 GAAACAACATAATAAACAGGTAC
* * * *
12825733 AAAACAACATAATAAATAGTTGC
1 GAAACAACATAATAAACAGGTAC
12825756 GAAACAACA
1 GAAACAACA
12825765 ATAAAATAGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.11, T:0.16
Consensus pattern (23 bp):
GAAACAACATAATAAACAGGTAC
Found at i:12834230 original size:8 final size:8
Alignment explanation
Indices: 12834217--12834243 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12834207 TACAAAGACT
12834217 AAATTATA
1 AAATTATA
12834225 AAATTATA
1 AAATTATA
12834233 AAATTATA
1 AAATTATA
12834241 AAA
1 AAA
12834244 AAAACACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATTATA
Found at i:12844584 original size:13 final size:13
Alignment explanation
Indices: 12844566--12844590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12844556 AGCGTGTGGG
12844566 GCCACACAAGCAA
1 GCCACACAAGCAA
12844579 GCCACACAAGCA
1 GCCACACAAGCA
12844591 TGTAGGCCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.40, G:0.16, T:0.00
Consensus pattern (13 bp):
GCCACACAAGCAA
Found at i:12846230 original size:19 final size:19
Alignment explanation
Indices: 12846191--12846231 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12846181 CCGACTTGAA
*
12846191 GATTAATTTTAATTAATTT
1 GATTAATTTTAATTAACTT
12846210 GATTAA-TTTAATTATACTT
1 GATTAATTTTAATTA-ACTT
12846229 GAT
1 GAT
12846232 CAAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
GATTAATTTTAATTAACTT
Found at i:12847397 original size:18 final size:18
Alignment explanation
Indices: 12847363--12847396 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12847353 TTTAAGAAAT
12847363 TTATATTTTAAATTTTTA
1 TTATATTTTAAATTTTTA
12847381 TTAT-TTTTAAATTTTT
1 TTATATTTTAAATTTTT
12847397 TTAGAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTTAAATTTTTA
Found at i:12855064 original size:25 final size:26
Alignment explanation
Indices: 12855036--12855085 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
12855026 AAACAAAACT
*
12855036 AAAATCTAACCTAAAAA-GAAAAGAG
1 AAAACCTAACCTAAAAATGAAAAGAG
*
12855061 AAAACCTAATCTAAAAATGAAAAGA
1 AAAACCTAACCTAAAAATGAAAAGA
12855086 AAATAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAACCTAACCTAAAAATGAAAAGAG
Found at i:12855816 original size:20 final size:20
Alignment explanation
Indices: 12855791--12855834 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
12855781 TAATAACCTC
12855791 AACATCTTATATAAATTTAT
1 AACATCTTATATAAATTTAT
*
12855811 AACATCTTATATAAATTTGT
1 AACATCTTATATAAATTTAT
12855831 AACA
1 AACA
12855835 AAACTCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.41
Consensus pattern (20 bp):
AACATCTTATATAAATTTAT
Found at i:12860073 original size:24 final size:24
Alignment explanation
Indices: 12860046--12860097 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
12860036 TTAGTAAGTC
12860046 AAATAAACTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
12860070 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12860094 AAAT
1 AAAT
12860098 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12861978 original size:106 final size:106
Alignment explanation
Indices: 12861853--12862064 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
12861843 GAAGAGTACA
12861853 AAAGATGGAGATAAAAACTAAACCCCGAAAACCCAAAAAACAAAGAACCCTCAAACGTAAACACA
1 AAAGATGGAGATAAAAACTAAACCCCGAAAACCCAAAAAACAAAGAACCCTCAAACGTAAACACA
12861918 AAATTCTCTGAATGTGTTATGAGTTCTAATCTAATAGGTGT
66 AAATTCTCTGAATGTGTTATGAGTTCTAATCTAATAGGTGT
*
12861959 AAAGATGGAGATAAAAACTAAACCCCGAAAACCCGAAAAACAAAGAACCCTCAAACGTAAACACA
1 AAAGATGGAGATAAAAACTAAACCCCGAAAACCCAAAAAACAAAGAACCCTCAAACGTAAACACA
*
12862024 AAATTCTCTGAATGTGTTATGAGTTCTAATCTAATGGGTGT
66 AAATTCTCTGAATGTGTTATGAGTTCTAATCTAATAGGTGT
12862065 CTCTTAATTC
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (106 bp):
AAAGATGGAGATAAAAACTAAACCCCGAAAACCCAAAAAACAAAGAACCCTCAAACGTAAACACA
AAATTCTCTGAATGTGTTATGAGTTCTAATCTAATAGGTGT
Found at i:12862145 original size:24 final size:24
Alignment explanation
Indices: 12862118--12862169 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12862108 TTAGTAAGTC
*
12862118 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12862142 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12862166 AAAT
1 AAAT
12862170 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12864903 original size:3 final size:3
Alignment explanation
Indices: 12864895--12864921 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12864885 AAACAAGAAC
12864895 ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT
12864922 GCTTCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ACT
Found at i:12876358 original size:23 final size:23
Alignment explanation
Indices: 12876310--12876358 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
12876300 CCATGTGTCG
* * *
12876310 TTTTCTAAAAATAGACTAAGTTT
1 TTTTCTAAAAATAAACTAAATGT
12876333 TTTTCTAAAAGATAAAC-AAATGT
1 TTTTCTAAAA-ATAAACTAAATGT
12876356 TTT
1 TTT
12876359 AAAATGACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (23 bp):
TTTTCTAAAAATAAACTAAATGT
Found at i:12886206 original size:21 final size:21
Alignment explanation
Indices: 12886180--12886255 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
12886170 TATGGATTAT
*
12886180 GGTTTAAGGGTTGGGGTTAAG
1 GGTTTAGGGGTTGGGGTTAAG
* *
12886201 GGTTTATGGGTTTAGGGTT-AG
1 GGTTTA-GGGGTTGGGGTTAAG
* *
12886222 GGGTTAGGGGTTAGGGGTTATG
1 GGTTTAGGGGTT-GGGGTTAAG
*
12886244 TGTTTAGGGGTT
1 GGTTTAGGGGTT
12886256 TATAGTTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 5 0.12
21 18 0.42
22 20 0.47
ACGTcount: A:0.14, C:0.00, G:0.47, T:0.38
Consensus pattern (21 bp):
GGTTTAGGGGTTGGGGTTAAG
Found at i:12886208 original size:28 final size:29
Alignment explanation
Indices: 12886176--12886233 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
12886166 GACTTATGGA
12886176 TTAT-GGTTTAAGGGTT-GGGGTTAAGGGT
1 TTATGGGTTT-AGGGTTAGGGGTTAAGGGT
*
12886204 TTATGGGTTTAGGGTTAGGGGTTAGGGGT
1 TTATGGGTTTAGGGTTAGGGGTTAAGGGT
12886233 T
1 T
12886234 AGGGGTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.40
Consensus pattern (29 bp):
TTATGGGTTTAGGGTTAGGGGTTAAGGGT
Found at i:12886218 original size:7 final size:7
Alignment explanation
Indices: 12886180--12886257 Score: 52
Period size: 7 Copynumber: 10.9 Consensus size: 7
12886170 TATGGATTAT
12886180 GGTTTAAG
1 GGTTT-AG
*
12886188 GG-TTGG
1 GGTTTAG
*
12886194 GGTTAAG
1 GGTTTAG
12886201 GGTTTATG
1 GGTTTA-G
12886209 GGTTTAG
1 GGTTTAG
12886216 GG-TTAG
1 GGTTTAG
*
12886222 GGGTTAG
1 GGTTTAG
*
12886229 GGGTTAG
1 GGTTTAG
*
12886236 GGGTTATG
1 GGTTTA-G
*
12886244 TGTTTAGG
1 GGTTTA-G
12886252 GGTTTA
1 GGTTTA
12886258 TAGTTAATGT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
6 9 0.16
7 29 0.50
8 20 0.34
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (7 bp):
GGTTTAG
Found at i:12886232 original size:14 final size:14
Alignment explanation
Indices: 12886187--12886255 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
12886177 TATGGTTTAA
12886187 GGGTT-GGGGTTAAG
1 GGGTTAGGGGTT-AG
* *
12886201 GGTTTATGGGTTTA-
1 GGGTTA-GGGGTTAG
12886215 GGGTTAGGGGTTAG
1 GGGTTAGGGGTTAG
12886229 GGGTTAGGGGTTATG
1 GGGTTAGGGGTTA-G
* *
12886244 TGTTTAGGGGTT
1 GGGTTAGGGGTT
12886256 TATAGTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 6 0.13
14 22 0.49
15 12 0.27
16 5 0.11
ACGTcount: A:0.13, C:0.00, G:0.49, T:0.38
Consensus pattern (14 bp):
GGGTTAGGGGTTAG
Found at i:12889711 original size:17 final size:17
Alignment explanation
Indices: 12889691--12889740 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
12889681 TTAATATCTA
12889691 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
12889708 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
12889722 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
12889738 TAT
1 TAT
12889741 TTGTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
16 2 0.07
17 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:12889727 original size:13 final size:13
Alignment explanation
Indices: 12889709--12889736 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12889699 TTCTAAATTT
12889709 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
12889722 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
12889735 AT
1 AT
12889737 TTATTTGTAT
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:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:12889767 original size:15 final size:15
Alignment explanation
Indices: 12889732--12889770 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
12889722 ATAAGTTTTC
*
12889732 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
12889747 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
12889763 TAAATTTA
1 TAAATTTA
12889771 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:12889813 original size:62 final size:61
Alignment explanation
Indices: 12889702--12889850 Score: 174
Period size: 62 Copynumber: 2.4 Consensus size: 61
12889692 ATAAGTTTTC
* *** * *
12889702 TAAATTTATAAGTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGT-GTAT
** *
12889763 TAAATTTACTTCGTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATTTATGTGTAT
1 TAAATTTA-TAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
* *
12889825 TAATTTTATAAGTTTTCTACATAAGT
1 TAAATTTATAAGTTTTCTAAATAAGT
12889851 TACATAATAC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
61 23 0.32
62 49 0.67
63 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.48
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATTTATGTGTAT
Found at i:12890015 original size:21 final size:21
Alignment explanation
Indices: 12889989--12890064 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
12889979 TGTTATAATA
*
12889989 CATAACTTGTATATAAGCTTG
1 CATAACTTATATATAAGCTTG
*
12890010 CATAACTTATATTTAAGCTTG
1 CATAACTTATATATAAGCTTG
* * *
12890031 CATAACTTACATAATAA-TTTA
1 CATAACTTATAT-ATAAGCTTG
12890052 CATAACTTATATA
1 CATAACTTATATA
12890065 ATAACATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
20 1 0.02
21 43 0.91
22 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
CATAACTTATATATAAGCTTG
Found at i:12890142 original size:9 final size:9
Alignment explanation
Indices: 12890114--12890429 Score: 335
Period size: 9 Copynumber: 34.8 Consensus size: 9
12890104 CATATATAGA
12890114 AACTTACAT
1 AACTTACAT
* *
12890123 AAATTAAAT
1 AACTTACAT
12890132 AACTTACAT
1 AACTTACAT
12890141 AACTTACAT
1 AACTTACAT
* *
12890150 AAATTAAAT
1 AACTTACAT
12890159 AACTTACAT
1 AACTTACAT
12890168 AACTTACAT
1 AACTTACAT
*
12890177 AAACTTGCAT
1 -AACTTACAT
* *
12890187 AAATTAAAT
1 AACTTACAT
12890196 AACTTACAT
1 AACTTACAT
12890205 AACTTACAT
1 AACTTACAT
*
12890214 AACCTACAT
1 AACTTACAT
* *
12890223 AAATTAAAT
1 AACTTACAT
12890232 AACTTACAT
1 AACTTACAT
12890241 AACTTACAT
1 AACTTACAT
* *
12890250 AAATTAAAT
1 AACTTACAT
12890259 AACTTACAT
1 AACTTACAT
*
12890268 AAACTTGCAT
1 -AACTTACAT
* *
12890278 AAATTAAAT
1 AACTTACAT
12890287 AACTTACAT
1 AACTTACAT
*
12890296 AACCTACAT
1 AACTTACAT
* *
12890305 AAATTAAAT
1 AACTTACAT
12890314 AACTTACAT
1 AACTTACAT
12890323 AACTTACAT
1 AACTTACAT
* *
12890332 AAATTAAAT
1 AACTTACAT
12890341 AACTTACAT
1 AACTTACAT
* * *
12890350 AAATTCCGT
1 AACTTACAT
*
12890359 GGACTTACAT
1 -AACTTACAT
*
12890369 AACCTACAT
1 AACTTACAT
* *
12890378 AAATTAAAT
1 AACTTACAT
12890387 AACTTACAT
1 AACTTACAT
*
12890396 AACTTACTT
1 AACTTACAT
12890405 AACTTACAT
1 AACTTACAT
* *
12890414 AAATTAAAT
1 AACTTACAT
12890423 AACTTAC
1 AACTTAC
12890430 CCGTGTAAAT
Statistics
Matches: 244, Mismatches: 60, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
9 223 0.91
10 21 0.09
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:12890144 original size:27 final size:27
Alignment explanation
Indices: 12890114--12890429 Score: 378
Period size: 27 Copynumber: 11.9 Consensus size: 27
12890104 CATATATAGA
12890114 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
12890141 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
*
12890168 AACTTAC----A-T--A-AACTTGCAT
1 AACTTACATAAATTAAATAACTTACAT
* * * *
12890187 AAATTAAATAACTTACATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
*
12890214 AACCTACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
12890241 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
*
12890268 AAACTTGCATAAATTAAATAACTTACAT
1 -AACTTACATAAATTAAATAACTTACAT
*
12890296 AACCTACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
12890323 AACTTACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
* * * * * * *
12890350 AAATTCCGTGGACTTACATAACCTACAT
1 AACTTACAT-AAATTAAATAACTTACAT
* * * * *
12890378 AAATTAAATAACTTACATAACTTACTT
1 AACTTACATAAATTAAATAACTTACAT
12890405 AACTTACATAAATTAAATAACTTAC
1 AACTTACATAAATTAAATAACTTAC
12890430 CCGTGTAAAT
Statistics
Matches: 247, Mismatches: 32, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
19 13 0.05
20 1 0.00
22 1 0.00
23 1 0.00
24 1 0.00
26 1 0.00
27 183 0.74
28 46 0.19
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (27 bp):
AACTTACATAAATTAAATAACTTACAT
Found at i:12890222 original size:82 final size:81
Alignment explanation
Indices: 12890114--12890429 Score: 378
Period size: 82 Copynumber: 4.0 Consensus size: 81
12890104 CATATATAGA
12890114 AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTAC----
1 AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAA
*
12890175 A-T--A-AACTTGCAT
66 ATTAAATAACTTACAT
* * * * *
12890187 AAATTAAATAACTTACATAACTTACATAACCTACATAAATTAAATAACTTACATAACTTACATAA
1 AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAA
12890252 ATTAAATAACTTACAT
66 ATTAAATAACTTACAT
* *
12890268 AAACTTGCATAAATTAAATAACTTACATAACCTACATAAATTAAATAACTTACATAACTTACATA
1 -AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATA
12890333 AATTAAATAACTTACAT
65 AATTAAATAACTTACAT
* * * * * * * * * * * *
12890350 AAATTCCGTGGACTTACATAACCTACATAAATTAAATAACTTACATAACTTACTTAACTTACATA
1 AACTTACAT-AAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATA
12890415 AATTAAATAACTTAC
65 AATTAAATAACTTAC
12890430 CCGTGTAAAT
Statistics
Matches: 209, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
73 56 0.27
77 1 0.00
78 1 0.00
80 1 0.00
81 14 0.07
82 136 0.65
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (81 bp):
AACTTACATAAATTAAATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAA
ATTAAATAACTTACAT
Found at i:12892839 original size:21 final size:21
Alignment explanation
Indices: 12892804--12892854 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12892794 CTACAACTTA
* *
12892804 AAGTAGATGCGGCAGAGAGGG
1 AAGTAGAGGCGGCAGAGAGAG
* *
12892825 AAGTAGAGGCTGCAGCGAGAG
1 AAGTAGAGGCGGCAGAGAGAG
*
12892846 AAGCAGAGG
1 AAGTAGAGG
12892855 TTCAAAAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.45, T:0.08
Consensus pattern (21 bp):
AAGTAGAGGCGGCAGAGAGAG
Found at i:12893297 original size:42 final size:41
Alignment explanation
Indices: 12893234--12893394 Score: 234
Period size: 42 Copynumber: 3.9 Consensus size: 41
12893224 GCATTTTTGT
*
12893234 AAAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTA
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTA
*
12893275 GAAAAAAACGCCGCTAATGAACATGTTCTTTAGAGGCGCTT-
1 -AAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTA
*
12893316 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTA
* * * *
12893357 AGGAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCG
1 A-AAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCG
12893395 TTTTTCGTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 38 0.35
41 1 0.01
42 71 0.65
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (41 bp):
AAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTA
Found at i:12893330 original size:82 final size:82
Alignment explanation
Indices: 12893233--12893394 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 82
12893223 GGCATTTTTG
* * *
12893233 TAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGAGGCGCTT-AGAAAAAAACGCCGCTAATGAAC
1 TAAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAG-AAAAAACGCCACTAAAGAAC
12893297 ATGTTCTTTAGAGGCGCT
65 ATGTTCTTTAGAGGCGCT
* * *
12893315 TAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGGAAAAACGCCACTAAAGATCA
1 TAAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAGAAAAAACGCCACTAAAGAACA
*
12893380 TGTTCTTTAGCGGCG
66 TGTTCTTTAGAGGCG
12893395 TTTTTCGTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
82 70 0.97
83 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (82 bp):
TAAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAAGAAAAAACGCCACTAAAGAACA
TGTTCTTTAGAGGCGCT
Found at i:12893811 original size:36 final size:35
Alignment explanation
Indices: 12893771--12893840 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
12893761 ATTTGAAGCA
* * * *
12893771 ATAAATGATTTATTGGTCGATGAAGAGCAGCAAAAT
1 ATAAACGACTTATTGGTCGATAAAGAACAG-AAAAT
12893807 ATAAACGACTTATTGGTCGATAAAGAACAGAAAA
1 ATAAACGACTTATTGGTCGATAAAGAACAGAAAA
12893841 CTCAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (35 bp):
ATAAACGACTTATTGGTCGATAAAGAACAGAAAAT
Found at i:12894443 original size:40 final size:40
Alignment explanation
Indices: 12894388--12894467 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
12894378 TCAATTAGAA
12894388 ATTAATTATTAGAGTATCTACACATGTTAGACCCATACTT
1 ATTAATTATTAGAGTATCTACACATGTTAGACCCATACTT
* *
12894428 ATTAATTATTAGAGTATCTACACATGTTTGGCCCATACTT
1 ATTAATTATTAGAGTATCTACACATGTTAGACCCATACTT
12894468 TATTTAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (40 bp):
ATTAATTATTAGAGTATCTACACATGTTAGACCCATACTT
Found at i:12894680 original size:9 final size:9
Alignment explanation
Indices: 12894666--12894690 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12894656 AAATATATAT
12894666 TATTTTTTA
1 TATTTTTTA
12894675 TATTTTTTA
1 TATTTTTTA
12894684 TATTTTT
1 TATTTTT
12894691 AGAAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TATTTTTTA
Found at i:12901265 original size:14 final size:15
Alignment explanation
Indices: 12901246--12901301 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
12901236 GAGGTTTCCC
12901246 CCCTTT-TTTCTTTT
1 CCCTTTATTTCTTTT
*
12901260 CCCTTTTATTTTTTTCT
1 CCC-TTTATTTCTTT-T
*
12901277 CCCTTTCTTTC-TTT
1 CCCTTTATTTCTTTT
12901291 CCCTTTTATTT
1 CCC-TTTATTT
12901302 TTTCTTCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 7 0.21
15 11 0.32
16 12 0.35
17 4 0.12
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.68
Consensus pattern (15 bp):
CCCTTTATTTCTTTT
Found at i:12901292 original size:31 final size:31
Alignment explanation
Indices: 12901246--12901304 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
12901236 GAGGTTTCCC
12901246 CCCTTTTTTCTTTTCCCTTTTATTTTTTTCT
1 CCCTTTTTTCTTTTCCCTTTTATTTTTTTCT
12901277 CCCTTTCTTTC-TTTCCCTTTTATTTTTT
1 CCCTTT-TTTCTTTTCCCTTTTATTTTTT
12901305 CTTCCCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.69
Consensus pattern (31 bp):
CCCTTTTTTCTTTTCCCTTTTATTTTTTTCT
Found at i:12901305 original size:14 final size:14
Alignment explanation
Indices: 12901246--12901305 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
12901236 GAGGTTTCCC
12901246 CCCTTTT-TTCTTTT
1 CCCTTTTATT-TTTT
12901260 CCCTTTTATTTTTTT
1 CCCTTTTA-TTTTTT
* *
12901275 CTCCCTTTCTTTCTTT
1 C-CCTTTTATTT-TTT
12901291 CCCTTTTATTTTTT
1 CCCTTTTATTTTTT
12901305 C
1 C
12901306 TTCCCAAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.29
15 16 0.42
16 11 0.29
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.68
Consensus pattern (14 bp):
CCCTTTTATTTTTT
Found at i:12903104 original size:27 final size:27
Alignment explanation
Indices: 12903070--12903151 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
12903060 TTTAATTTGG
*
12903070 ATATATTACTTTTCAGTTATTTTTTTA
1 ATATATTACTTTTCACTTATTTTTTTA
* * *
12903097 ATATATTACTTTCCATTTGGTTTTTTATA
1 ATATATTACTTTTCACTT-ATTTTTT-TA
* * *
12903126 ATATGTTATTTTTCACTTATTATTTT
1 ATATATTACTTTTCACTTATTTTTTT
12903152 CAAAATTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
27 17 0.39
28 11 0.25
29 16 0.36
ACGTcount: A:0.24, C:0.09, G:0.05, T:0.62
Consensus pattern (27 bp):
ATATATTACTTTTCACTTATTTTTTTA
Found at i:12908073 original size:11 final size:10
Alignment explanation
Indices: 12908057--12908087 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
12908047 GCAGTTGAAC
12908057 AAAAAAATAA
1 AAAAAAATAA
12908067 AAAAAAATAA
1 AAAAAAATAA
12908077 AAAAAAA-AA
1 AAAAAAATAA
12908086 AA
1 AA
12908088 TTGGGCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:12908084 original size:14 final size:15
Alignment explanation
Indices: 12908060--12908088 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12908050 GTTGAACAAA
12908060 AAAATAAAAAAAAAT
1 AAAATAAAAAAAAAT
12908075 AAAA-AAAAAAAAAT
1 AAAATAAAAAAAAAT
12908089 TGGGCCAAAG
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:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAATAAAAAAAAAT
Found at i:12910226 original size:37 final size:37
Alignment explanation
Indices: 12910176--12910254 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
12910166 TTATTACGAA
* *
12910176 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
12910213 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
12910250 GTCTT
1 GTCTT
12910255 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:12910451 original size:47 final size:47
Alignment explanation
Indices: 12910373--12910766 Score: 673
Period size: 47 Copynumber: 8.4 Consensus size: 47
12910363 CCCTTCGGGA
* * * * * * *
12910373 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12910420 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12910467 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12910514 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12910561 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12910608 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12910654 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12910701 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12910748 CTTATCACATATATACACT
1 CTTATCACATATATACACT
12910767 GTCTTGGCTG
Statistics
Matches: 331, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
46 45 0.14
47 286 0.86
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12910701 original size:187 final size:188
Alignment explanation
Indices: 12910373--12910766 Score: 673
Period size: 187 Copynumber: 2.1 Consensus size: 188
12910363 CCCTTCGGGA
* * * * * *
12910373 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
12910438 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* *
12910503 GGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
12910561 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
12910626 TTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
12910690 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12910748 CTTATCACATATATACACT
1 CTTATCACATATATACACT
12910767 GTCTTGGCTG
Statistics
Matches: 194, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
187 119 0.61
188 75 0.39
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12916232 original size:12 final size:12
Alignment explanation
Indices: 12916209--12916240 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12916199 ATTAAAATTA
12916209 ATTATT-TTACT
1 ATTATTATTACT
12916220 ATTATTATTACT
1 ATTATTATTACT
12916232 ATTATTATT
1 ATTATTATT
12916241 TTCCTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTATTATTACT
Found at i:12921397 original size:36 final size:36
Alignment explanation
Indices: 12921350--12921422 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
12921340 ACGACTCCAC
*
12921350 CTTCAATTGGATTATATGTAGAGATTATTGAATCAT
1 CTTCAATTGGATTATATGTAGAGATTAATGAATCAT
12921386 CTTCAATTGGATTATATGTAGAGATTAATGAATCAT
1 CTTCAATTGGATTATATGTAGAGATTAATGAATCAT
12921422 C
1 C
12921423 ACCCTTGTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (36 bp):
CTTCAATTGGATTATATGTAGAGATTAATGAATCAT
Found at i:12926397 original size:3 final size:3
Alignment explanation
Indices: 12926391--12926420 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12926381 TAGTGATGAT
12926391 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12926421 AGAGTCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12933974 original size:34 final size:34
Alignment explanation
Indices: 12933931--12933995 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
12933921 ATTCATATTA
12933931 ATTATTATTTAATTAATTTTACAATTGTATACAT
1 ATTATTATTTAATTAATTTTACAATTGTATACAT
* * *
12933965 ATTATTATTTAATTGATTTTATAATTTTATA
1 ATTATTATTTAATTAATTTTACAATTGTATA
12933996 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (34 bp):
ATTATTATTTAATTAATTTTACAATTGTATACAT
Found at i:12936326 original size:22 final size:22
Alignment explanation
Indices: 12936300--12936408 Score: 87
Period size: 22 Copynumber: 5.0 Consensus size: 22
12936290 GACACCAATA
12936300 TATGAAAGCCCTTTATGGGACG
1 TATGAAAGCCCTTTATGGGACG
* * *
12936322 TATGAGAGCCCTTAATGGGATG
1 TATGAAAGCCCTTTATGGGACG
* * * *
12936344 CAT-AAGAGCCTTTTATGAGACA
1 TATGAA-AGCCCTTTATGGGACG
* * *
12936366 TATGAAAACCCTTTCTAGGACG
1 TATGAAAGCCCTTTATGGGACG
*
12936388 TAT-AAGAGCTCTTTATGGGAC
1 TATGAA-AGCCCTTTATGGGAC
12936409 ATATTAGAGC
Statistics
Matches: 63, Mismatches: 21, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
21 3 0.05
22 58 0.92
23 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (22 bp):
TATGAAAGCCCTTTATGGGACG
Done.