Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 118 of 205
Found at i:35502643 original size:13 final size:13
Alignment explanation
Indices: 35502625--35502653 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35502615 GCCCAAACTT
35502625 AATTACCCAACCC
1 AATTACCCAACCC
35502638 AATTACCCAACCC
1 AATTACCCAACCC
35502651 AAT
1 AAT
35502654 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (13 bp):
AATTACCCAACCC
Found at i:35502833 original size:9 final size:9
Alignment explanation
Indices: 35502820--35502879 Score: 102
Period size: 9 Copynumber: 6.7 Consensus size: 9
35502810 GTATTTTTCA
35502820 GTAATTCGG
1 GTAATTCGG
*
35502829 TTAATTCGG
1 GTAATTCGG
*
35502838 TTAATTCGG
1 GTAATTCGG
35502847 GTAATTCGG
1 GTAATTCGG
35502856 GTAATTCGG
1 GTAATTCGG
35502865 GTAATTCGG
1 GTAATTCGG
35502874 GTAATT
1 GTAATT
35502880 TTTAACCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (9 bp):
GTAATTCGG
Found at i:35503056 original size:12 final size:12
Alignment explanation
Indices: 35503039--35503063 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35503029 AGTAATTTCG
35503039 GGTCGGTTAACC
1 GGTCGGTTAACC
35503051 GGTCGGTTAACC
1 GGTCGGTTAACC
35503063 G
1 G
35503064 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:35503420 original size:22 final size:23
Alignment explanation
Indices: 35503395--35503447 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
35503385 AAGGAACTTG
*
35503395 AATTGATATATAA-TAACTA-GAA
1 AATT-ATATAGAATTAACTATGAA
*
35503417 AATTATTTAGAATTAACTATGAA
1 AATTATATAGAATTAACTATGAA
35503440 AATGTATA
1 AAT-TATA
35503448 AATATTAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 6 0.24
24 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (23 bp):
AATTATATAGAATTAACTATGAA
Found at i:35508150 original size:14 final size:14
Alignment explanation
Indices: 35508131--35508161 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
35508121 ACAAATATCC
35508131 CAGATAAGAGTACA
1 CAGATAAGAGTACA
35508145 CAGATAAGAGTACA
1 CAGATAAGAGTACA
35508159 CAG
1 CAG
35508162 TCAATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (14 bp):
CAGATAAGAGTACA
Found at i:35508941 original size:21 final size:21
Alignment explanation
Indices: 35508911--35508964 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
35508901 GCCATGTGCC
*
35508911 CGACCGTGTGCAA-GGTCTACA
1 CGACTGTGTG-AAGGGTCTACA
*
35508932 CGGCTGTGTGAAGGGTCTACA
1 CGACTGTGTGAAGGGTCTACA
35508953 CGACTGTGTGAA
1 CGACTGTGTGAA
35508965 AGAGGGACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (21 bp):
CGACTGTGTGAAGGGTCTACA
Found at i:35512089 original size:38 final size:38
Alignment explanation
Indices: 35512047--35512139 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 38
35512037 ACCACTCCGA
* *
35512047 CCACCCTACACACCACAATTGGACTAT-AGTA-AGCCCAT
1 CCACCCTACACACCACAATAGGACCATGA-TAGA-CCCAT
*
35512085 CCACCCTACACACCA-TATAGGACCATGATAGACCCAT
1 CCACCCTACACACCACAATAGGACCATGATAGACCCAT
35512122 CCACCCTACACACCACAA
1 CCACCCTACACACCACAA
35512140 ATGTGGAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
37 30 0.62
38 18 0.38
ACGTcount: A:0.35, C:0.41, G:0.09, T:0.15
Consensus pattern (38 bp):
CCACCCTACACACCACAATAGGACCATGATAGACCCAT
Found at i:35512654 original size:21 final size:21
Alignment explanation
Indices: 35512613--35512654 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
35512603 GGAGAGTCTA
* *
35512613 GGTCGTGTGAAGGGTCTACAT
1 GGTCGTGTGAAGAGACTACAT
35512634 GGTCGTGTGAAAGAGAC-ACAT
1 GGTCGTGTG-AAGAGACTACAT
35512655 TACCGTGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (21 bp):
GGTCGTGTGAAGAGACTACAT
Found at i:35512661 original size:21 final size:21
Alignment explanation
Indices: 35512637--35512685 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
35512627 TCTACATGGT
*
35512637 CGTGTGAAAGAGACACATTAC
1 CGTGTGAAAGAGACACATGAC
** *
35512658 CGTGTGGTAGAGACACATGCC
1 CGTGTGAAAGAGACACATGAC
35512679 CGTGTGA
1 CGTGTGA
35512686 GTAGCCTATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (21 bp):
CGTGTGAAAGAGACACATGAC
Found at i:35516178 original size:40 final size:40
Alignment explanation
Indices: 35516081--35516261 Score: 165
Period size: 40 Copynumber: 4.5 Consensus size: 40
35516071 TTGAATGCTG
* * * *
35516081 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
35516121 TCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
35516161 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAA
* **
35516201 TCCGGGTTAAGTCCCGAAGGCA-TTGTATGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
35516241 -CCAGGCTATGTCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCA
35516262 CATAAATTGT
Statistics
Matches: 117, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
39 29 0.25
40 80 0.68
41 8 0.07
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:35517372 original size:19 final size:18
Alignment explanation
Indices: 35517348--35517386 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35517338 ATTGCGTGTT
*
35517348 TGAATAGAAATAAAATAAA
1 TGAATAGAAA-AAAAGAAA
*
35517367 TGAATAGGAAAAAAGAAA
1 TGAATAGAAAAAAAGAAA
35517385 TG
1 TG
35517387 GGAAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (18 bp):
TGAATAGAAAAAAAGAAA
Found at i:35525366 original size:37 final size:37
Alignment explanation
Indices: 35525324--35525394 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
35525314 GTAAGACTTG
35525324 TAGTTGTGTATATATTTGGTATTATGACTCTTGTCTA
1 TAGTTGTGTATATATTTGGTATTATGACTCTTGTCTA
35525361 TAGTTGTGTATATATTTGGTATTATGACTCTTGT
1 TAGTTGTGTATATATTTGGTATTATGACTCTTGT
35525395 ATGTATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.21, C:0.07, G:0.20, T:0.52
Consensus pattern (37 bp):
TAGTTGTGTATATATTTGGTATTATGACTCTTGTCTA
Found at i:35535073 original size:27 final size:27
Alignment explanation
Indices: 35535033--35535285 Score: 219
Period size: 27 Copynumber: 9.4 Consensus size: 27
35535023 GATTCGTGGG
* * *
35535033 AAAATGATTGAAATACCCTCAAAAGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
35535060 AAAATGACTAAAATACCC-CTGAAGGAT
1 AAAATGACTGAAATACCCTC-GAAGGGT
*
35535087 AAAATGACTGAAATACCC-CTGAAGGGG
1 AAAATGACTGAAATACCCTC-GAAGGGT
* * ** * *
35535114 AAATTTACCAAAATACCCCCAAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* * *
35535141 AGAATAATTGAAATA-CCTCTGAAGGGT
1 AAAATGACTGAAATACCCTC-GAAGGGT
** *
35535168 AAAATGACCAAAATACCCTTGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
35535195 AAAATGACCGAAATACCCCCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
35535222 AAAAT-AATCGAAATACTCTCGAAGGGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
*
35535249 AAAATGACTGAAATACCCT-TATAGGGT
1 AAAATGACTGAAATACCCTCGA-AGGGT
35535276 AAAATGACTG
1 AAAATGACTG
35535286 TGATACCCCT
Statistics
Matches: 181, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
26 6 0.03
27 169 0.93
28 6 0.03
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.20
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTCGAAGGGT
Found at i:35535165 original size:81 final size:81
Alignment explanation
Indices: 35535043--35535283 Score: 279
Period size: 81 Copynumber: 3.0 Consensus size: 81
35535033 AAAATGATTG
* * * * * * *
35535043 AAATACCCTCAAAAGGTAAAATGACTAAAATACCCCTGAAGGATAAAATGACTGAAATACCCCTG
1 AAATACCCCCAAAGGGTAAAATAATTGAAATACCTCTGAAGGGTAAAATGACTGAAATACCCCTG
* *
35535108 AAGGGGAAATTTACCA
66 AAGGGGAAAATGACCA
* ** *
35535124 AAATACCCCCAAAGGGTAGAATAATTGAAATACCTCTGAAGGGTAAAATGACCAAAATACCCTTG
1 AAATACCCCCAAAGGGTAAAATAATTGAAATACCTCTGAAGGGTAAAATGACTGAAATACCCCTG
* *
35535189 AAGGGTAAAATGACCG
66 AAGGGGAAAATGACCA
* *
35535205 AAATACCCCCGAAGGGTAAAATAATCGAAATA-CTCTCGAAGGGTAAAATGACTGAAATA-CCCT
1 AAATACCCCCAAAGGGTAAAATAATTGAAATACCTCT-GAAGGGTAAAATGACTGAAATACCCCT
* *
35535268 TATAGGGTAAAATGAC
65 GA-AGGGGAAAATGAC
35535284 TGTGATACCC
Statistics
Matches: 136, Mismatches: 22, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
80 8 0.06
81 128 0.94
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (81 bp):
AAATACCCCCAAAGGGTAAAATAATTGAAATACCTCTGAAGGGTAAAATGACTGAAATACCCCTG
AAGGGGAAAATGACCA
Found at i:35535676 original size:28 final size:28
Alignment explanation
Indices: 35535636--35535698 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
35535626 CACTATACTG
* **
35535636 GTTACTATATTGGGCTAAGGCCTGCACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
35535664 GTTACTGTTTTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
35535692 G-TACTGT
1 GTTACTGT
35535699 GACTGTATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.33
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:35538713 original size:28 final size:28
Alignment explanation
Indices: 35538671--35538732 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
35538661 TATACAGTCG
* * *
35538671 CAGT-ACAATGTGGGCTTTAGCCCAAAA
1 CAGTAACAATGCGGGCCTTAACCCAAAA
* *
35538698 TAGTAACAATGCGGGCCTTAACCCAATA
1 CAGTAACAATGCGGGCCTTAACCCAAAA
35538726 CAGTAAC
1 CAGTAAC
35538733 CAGTACAGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (28 bp):
CAGTAACAATGCGGGCCTTAACCCAAAA
Found at i:35539132 original size:27 final size:27
Alignment explanation
Indices: 35539074--35539253 Score: 177
Period size: 27 Copynumber: 6.7 Consensus size: 27
35539064 TCATCTCCTA
** *
35539074 GGGGTATCACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTTTG
*
35539101 AGGGTATTTCAGTCATTTTA-CCTTTCG
1 GGGGTATTTCAGTCATTTTACCCTTT-G
** *
35539128 GGGGTATTTTGGTCATTTTACCCTTTA
1 GGGGTATTTCAGTCATTTTACCCTTTG
** *
35539155 GGGGTATTTCCTTTA-TTT-CCCTTTCG
1 GGGGTATTTCAGTCATTTTACCCTTT-G
* *
35539181 GGGGTATTTTAGTCATTTTACCCTTCG
1 GGGGTATTTCAGTCATTTTACCCTTTG
**
35539208 AAGGTATTTCAGTCATTTTACCCTTTG
1 GGGGTATTTCAGTCATTTTACCCTTTG
* *
35539235 AGGGTATTTCGGTCATTTT
1 GGGGTATTTCAGTCATTTT
35539254 TCTACGAATT
Statistics
Matches: 124, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
25 6 0.05
26 18 0.15
27 90 0.73
28 10 0.08
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTTTG
Found at i:35539196 original size:53 final size:54
Alignment explanation
Indices: 35539084--35539253 Score: 202
Period size: 54 Copynumber: 3.2 Consensus size: 54
35539074 GGGGTATCAC
*
35539084 AGTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCTTTCGGGGGTATTTT
1 AGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCTTTCGGGGGTATTTT
* ** * *
35539138 GGTCATTTTACCCTTT-AGGGGTATTTCCTTTA-TTTCCCTTTCGGGGGTATTTT
1 AGTCATTTTACCCTTTGA-GGGTATTTCAGTCATTTTACCTTTCGGGGGTATTTT
* * * *
35539191 AGTCATTTTACCCTTCGAAGGTATTTCAGTCATTTTACCCTTT-GAGGGTATTTC
1 AGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTA-CCTTTCGGGGGTATTTT
*
35539245 GGTCATTTT
1 AGTCATTTT
35539254 TCTACGAATT
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
53 45 0.47
54 46 0.48
55 5 0.05
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.46
Consensus pattern (54 bp):
AGTCATTTTACCCTTTGAGGGTATTTCAGTCATTTTACCTTTCGGGGGTATTTT
Found at i:35542262 original size:21 final size:21
Alignment explanation
Indices: 35542236--35542280 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
35542226 AACTTGCAGC
35542236 TCAGCCAACAAGCTACCATCA
1 TCAGCCAACAAGCTACCATCA
*
35542257 TCAGCCAATAAGCTACCATCA
1 TCAGCCAACAAGCTACCATCA
35542278 TCA
1 TCA
35542281 AACAAGCTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.36, G:0.09, T:0.18
Consensus pattern (21 bp):
TCAGCCAACAAGCTACCATCA
Found at i:35542287 original size:18 final size:19
Alignment explanation
Indices: 35542241--35542288 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
35542231 GCAGCTCAGC
35542241 CAACAAGCTACCATCATCA
1 CAACAAGCTACCATCATCA
*
35542260 GCCAATAAGCTACCATCATCA
1 --CAACAAGCTACCATCATCA
35542281 -AACAAGCT
1 CAACAAGCT
35542289 GAGATGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
21 18 0.72
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (19 bp):
CAACAAGCTACCATCATCA
Found at i:35558381 original size:25 final size:25
Alignment explanation
Indices: 35558345--35558396 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
35558335 TCTGAGTAGG
*
35558345 GTCACACACCCGTGTGCCAGGCCGT
1 GTCACACACCCGTGTGCCAGGCAGT
*
35558370 GTCACACGCCCGTGTGCCAGGCAGT
1 GTCACACACCCGTGTGCCAGGCAGT
35558395 GT
1 GT
35558397 GCTACCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.15, C:0.37, G:0.31, T:0.17
Consensus pattern (25 bp):
GTCACACACCCGTGTGCCAGGCAGT
Found at i:35559484 original size:35 final size:35
Alignment explanation
Indices: 35559416--35559578 Score: 148
Period size: 35 Copynumber: 4.6 Consensus size: 35
35559406 AGTACATCGA
* * *
35559416 TAATCCAACCGAAATACACCAAATGCTCATAAGAGC
1 TAATCCATCCGAAACACACC-AATGCTCGTAAGAGC
* *
35559452 CAATCCATCCGAAACACACCAATGCTCGTAAGAGT
1 TAATCCATCCGAAACACACCAATGCTCGTAAGAGC
* * * * *
35559487 TAATCCCTCCAAAACACACCGATGCTCAG-AACAGT
1 TAATCCATCCGAAACACACCAATGCTC-GTAAGAGC
* * * *
35559522 TAATCCCTCCTAAACATACCAATGCTCGAAAGAGC
1 TAATCCATCCGAAACACACCAATGCTCGTAAGAGC
* * *
35559557 TAGTCCAACTGAAACACACCAA
1 TAATCCATCCGAAACACACCAA
35559579 AACAAATAGT
Statistics
Matches: 104, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
34 1 0.01
35 85 0.82
36 18 0.17
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (35 bp):
TAATCCATCCGAAACACACCAATGCTCGTAAGAGC
Found at i:35572052 original size:13 final size:13
Alignment explanation
Indices: 35572034--35572068 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
35572024 GCATGTCTCT
*
35572034 CACATGGCTTAGC
1 CACATGGCCTAGC
35572047 CACATGGCCTAGC
1 CACATGGCCTAGC
*
35572060 CACACGGCC
1 CACATGGCC
35572069 GTGTGATCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.14
Consensus pattern (13 bp):
CACATGGCCTAGC
Found at i:35579455 original size:44 final size:44
Alignment explanation
Indices: 35579392--35579615 Score: 151
Period size: 44 Copynumber: 4.8 Consensus size: 44
35579382 GATTTGTTGT
* * *
35579392 CTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTGG
* * *
35579436 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-----C-----TGGTGG
* *** * ** * * * *
35579490 CTTTAATCAATTCCACTACAACGCCAGGGAAATAAGATTCGCTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-GGTGG
*
35579535 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTGG
* * * *
35579579 CTTCACTCTGCACCACTGCAAGTTCAGGAAGATAAGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
35579616 TCCGCCATAA
Statistics
Matches: 133, Mismatches: 36, Indels: 22
0.70 0.19 0.12
Matches are distributed among these distances:
44 70 0.53
45 30 0.23
49 1 0.01
54 32 0.24
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTGG
Found at i:35579459 original size:143 final size:143
Alignment explanation
Indices: 35579260--35579677 Score: 611
Period size: 143 Copynumber: 2.9 Consensus size: 143
35579250 TCAATATACC
* * ** * * * *
35579260 CCACTGCAACTTCAGGGGGATAAGATTTGGTAACTTCAACCTACTCCACTGTAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGA-CTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGA
* ** * *
35579325 TAAGGTTTGCCATAATTTGTAGCTTTAATTTGTTCCACTGCAATGCCAGGGAAATAAGATTTGTT
65 TAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGTT
35579390 GTCTTCAGTCTGCT
130 GTCTTCAGTCTGCT
* *
35579404 CCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAT
** * * *
35579469 AAGATCCGCCATAATTTGTAGCTTTAATCAATTCCACTACAACGCCAGGGAAATAAGATTCGCTG
66 AAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGTTG
35579534 TCTTCAGTCTGCT
131 TCTTCAGTCTGCT
* * *
35579547 CCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCACTCTGCACCACTGCAAGTTCAGGAAGAT
1 CCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAT
*
35579612 AAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCGTTG
66 AAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGTTG
35579677 T
131 T
35579678 AATGACTTCA
Statistics
Matches: 243, Mismatches: 31, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
143 221 0.91
144 22 0.09
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (143 bp):
CCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGAT
AAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAGATTCGTTG
TCTTCAGTCTGCT
Found at i:35581443 original size:1 final size:1
Alignment explanation
Indices: 35581433--35581558 Score: 54
Period size: 1 Copynumber: 126.0 Consensus size: 1
35581423 CCGGTAGAGG
* * * * * * * ** * * * *
35581433 TTTTTATTTTTTTGTTTTTTGTTTTTCTGTTCTTTGTTTAGTTTTTTGTTTTTTGTTCTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * *
35581498 TTTTGTTTTTTTTTTTTGTTTTTTGTTTTTTGTTTTGTCTTTTTTGTTATTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35581559 CTTTCCTCTA
Statistics
Matches: 82, Mismatches: 43, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (1 bp):
T
Found at i:35581483 original size:34 final size:32
Alignment explanation
Indices: 35581435--35581558 Score: 125
Period size: 31 Copynumber: 4.0 Consensus size: 32
35581425 GGTAGAGGTT
*
35581435 TTTATTTTTTTGTTTTTTGTTTTTCTGTTCTTTG
1 TTTAGTTTTTTGTTTTTTGTTTTT-TGTT-TTTG
*
35581469 TTTAGTTTTTTGTTTTTTGTTCTTTG-TTTT-
1 TTTAGTTTTTTGTTTTTTGTTTTTTGTTTTTG
35581499 TTT-GTTTTTT-TTTTTTGTTTTTTGTTTTTTG
1 TTTAGTTTTTTGTTTTTTGTTTTTTG-TTTTTG
* * * *
35581530 TTTTG-TCTTT-TTTGTTATTTTTTGTTTTT
1 TTTAGTTTTTTGTTTTTTGTTTTTTGTTTTT
35581559 CTTTCCTCTA
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.16
29 7 0.09
30 12 0.15
31 22 0.28
32 2 0.03
33 2 0.03
34 22 0.28
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.82
Consensus pattern (32 bp):
TTTAGTTTTTTGTTTTTTGTTTTTTGTTTTTG
Found at i:35581489 original size:41 final size:38
Alignment explanation
Indices: 35581440--35581558 Score: 156
Period size: 35 Copynumber: 3.1 Consensus size: 38
35581430 AGGTTTTTAT
35581440 TTTTTTGTTTTTTGTTTTTCTGTTCTTTGTTTAGTTTTTTG
1 TTTTTTGTTTTTTGTTTTTCT-TT-TTTGTTTA-TTTTTTG
* *
35581481 TTTTTTGTTCTTTGTTTTT-TTGTTT-TTT-TTTTTTG
1 TTTTTTGTTTTTTGTTTTTCTTTTTTGTTTATTTTTTG
35581516 TTTTTTGTTTTTTGTTTTGTCTTTTTTG-TTATTTTTTG
1 TTTTTTGTTTTTTGTTTT-TCTTTTTTGTTTATTTTTTG
35581554 TTTTT
1 TTTTT
35581559 CTTTCCTCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
35 24 0.34
36 1 0.01
37 10 0.14
38 15 0.21
39 1 0.01
40 1 0.01
41 18 0.26
ACGTcount: A:0.02, C:0.03, G:0.13, T:0.82
Consensus pattern (38 bp):
TTTTTTGTTTTTTGTTTTTCTTTTTTGTTTATTTTTTG
Found at i:35581505 original size:49 final size:49
Alignment explanation
Indices: 35581443--35581563 Score: 140
Period size: 49 Copynumber: 2.4 Consensus size: 49
35581433 TTTTTATTTT
* *
35581443 TTTG-TTTTTTGTTTTTCTGTTCTTTG-TTTAGTTTTTTGTTTTTTGTTC
1 TTTGTTTTTTTGTTTTTCT-TTCTTTGTTTTAGTTTTTTGTTTTGTCTTC
* * *
35581491 TTTGTTTTTTTGTTTTT-TTTTTTTGTTTTTTGTTTTTTGTTTTGTCTTT
1 TTTGTTTTTTTGTTTTTCTTTCTTTG-TTTTAGTTTTTTGTTTTGTCTTC
35581540 TTTGTTATTTTTTGTTTTTCTTTC
1 TTTG-T-TTTTTTGTTTTTCTTTC
35581564 CTCTACTACT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 6 0.10
48 5 0.08
49 34 0.56
50 1 0.02
51 12 0.20
52 3 0.05
ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81
Consensus pattern (49 bp):
TTTGTTTTTTTGTTTTTCTTTCTTTGTTTTAGTTTTTTGTTTTGTCTTC
Found at i:35581558 original size:7 final size:7
Alignment explanation
Indices: 35581440--35581550 Score: 129
Period size: 7 Copynumber: 15.9 Consensus size: 7
35581430 AGGTTTTTAT
35581440 TTTTTTG
1 TTTTTTG
35581447 TTTTTTG
1 TTTTTTG
35581454 TTTTTCTG
1 TTTTT-TG
*
35581462 TTCTTTG
1 TTTTTTG
*
35581469 --TTTAG
1 TTTTTTG
35581474 TTTTTTG
1 TTTTTTG
35581481 TTTTTTG
1 TTTTTTG
*
35581488 TTCTTTG
1 TTTTTTG
35581495 TTTTTTTG
1 -TTTTTTG
35581503 TTTTTT-
1 TTTTTTG
35581509 TTTTTTG
1 TTTTTTG
35581516 TTTTTTG
1 TTTTTTG
35581523 TTTTTTG
1 TTTTTTG
* *
35581530 TTTTGTC
1 TTTTTTG
35581537 TTTTTTG
1 TTTTTTG
35581544 TTATTTT
1 TT-TTTT
35581551 TTGTTTTTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
5 3 0.03
6 6 0.07
7 63 0.72
8 16 0.18
ACGTcount: A:0.02, C:0.04, G:0.13, T:0.82
Consensus pattern (7 bp):
TTTTTTG
Found at i:35589716 original size:12 final size:14
Alignment explanation
Indices: 35589687--35589718 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
35589677 GTTTGGGATA
35589687 GGGTTTGGTAATTT
1 GGGTTTGGTAATTT
35589701 GGGTTT-GTAA-TT
1 GGGTTTGGTAATTT
35589713 GGGTTT
1 GGGTTT
35589719 TTTGTATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (14 bp):
GGGTTTGGTAATTT
Found at i:35592962 original size:13 final size:14
Alignment explanation
Indices: 35592944--35592972 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35592934 AAAAATGAAC
35592944 AAAATGA-ATAGGA
1 AAAATGACATAGGA
35592957 AAAATGACATAGGA
1 AAAATGACATAGGA
35592971 AA
1 AA
35592973 TATTCAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.14
Consensus pattern (14 bp):
AAAATGACATAGGA
Found at i:35594086 original size:27 final size:27
Alignment explanation
Indices: 35594029--35594089 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
35594019 GGCATCCTTT
* *
35594029 GATAGTCTGATGGGACAATAATCACAG
1 GATAGTCTGATGGGACAATAAACACAA
* *
35594056 GATAGTCT-ATTGGGACACTAAACATAA
1 GATAGTCTGA-TGGGACAATAAACACAA
35594083 GATAGTC
1 GATAGTC
35594090 CACCGGGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (27 bp):
GATAGTCTGATGGGACAATAAACACAA
Found at i:35598097 original size:13 final size:14
Alignment explanation
Indices: 35598079--35598120 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
35598069 GCTAGGGAGG
35598079 TTTTGACAATAA-A
1 TTTTGACAATAATA
*
35598092 TTTTGAAAATAATA
1 TTTTGACAATAATA
*
35598106 TTTTCACAATTAATA
1 TTTTGACAA-TAATA
35598121 AGATAAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 8 0.33
15 5 0.21
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (14 bp):
TTTTGACAATAATA
Found at i:35604915 original size:12 final size:12
Alignment explanation
Indices: 35604898--35604923 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35604888 AGGATATGCA
35604898 ATCTTAGATATG
1 ATCTTAGATATG
35604910 ATCTTAGATATG
1 ATCTTAGATATG
35604922 AT
1 AT
35604924 ATTGCAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:35604950 original size:19 final size:20
Alignment explanation
Indices: 35604910--35604979 Score: 88
Period size: 20 Copynumber: 3.4 Consensus size: 20
35604900 CTTAGATATG
35604910 ATCTTAGATATGATATTGCA
1 ATCTTAGATATGATATTGCA
35604930 ATCTTAGATATGATA-TGCA
1 ATCTTAGATATGATATTGCA
* *
35604949 ATCTTAGAAGATATGATTTTGTA
1 ATCTT---AGATATGATATTGCA
35604972 ATCTTAGA
1 ATCTTAGA
35604980 GATTTAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.20
20 18 0.41
22 9 0.20
23 8 0.18
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (20 bp):
ATCTTAGATATGATATTGCA
Found at i:35604982 original size:22 final size:22
Alignment explanation
Indices: 35604915--35604982 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
35604905 ATATGATCTT
*
35604915 AGATATGATATTGCAATCTT--
1 AGATATGATTTTGCAATCTTAG
*
35604935 AGATATGA-TATGCAATCTTAG
1 AGATATGATTTTGCAATCTTAG
*
35604956 AAGATATGATTTTGTAATCTTAG
1 -AGATATGATTTTGCAATCTTAG
35604979 AGAT
1 AGAT
35604983 TTAATTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 9 0.22
20 8 0.20
22 12 0.30
23 11 0.28
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATTTTGCAATCTTAG
Found at i:35605271 original size:20 final size:20
Alignment explanation
Indices: 35605246--35605316 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
35605236 CGATTTAGTC
35605246 TTTTATTATTTATTATTTAT
1 TTTTATTATTTATTATTTAT
*
35605266 TTTTATTAAATTTGA-T-TTTCT
1 TTTTATT--ATTT-ATTATTTAT
* *
35605287 TGTTATTACGTTATTA-TTAT
1 TTTTATTA-TTTATTATTTAT
35605307 TTTTATTATT
1 TTTTATTATT
35605317 ATCATTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
19 3 0.08
20 20 0.51
21 10 0.26
22 5 0.13
23 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTATTATTTATTATTTAT
Found at i:35605305 original size:3 final size:3
Alignment explanation
Indices: 35605297--35605335 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
35605287 TGTTATTACG
* * *
35605297 TTA TTA TTA TTT TTA TTA TTA TCA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35605336 CCATATATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:35605490 original size:17 final size:17
Alignment explanation
Indices: 35605470--35605504 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35605460 TATATGCATA
*
35605470 TATATACATTTACATTT
1 TATATACATATACATTT
35605487 TATATACATATACATTT
1 TATATACATATACATTT
35605504 T
1 T
35605505 TTATTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATACATATACATTT
Found at i:35605605 original size:19 final size:18
Alignment explanation
Indices: 35605581--35605629 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
35605571 GTATGTTTTC
35605581 TTATATTAT-TCTTCATAAA
1 TTATATTATAT-TTC-TAAA
35605600 TTATATATATATTTCTAAA
1 TTATAT-TATATTTCTAAA
35605619 TTA-ATTA-ATTT
1 TTATATTATATTT
35605630 TAATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 2 0.07
19 13 0.46
20 6 0.21
21 1 0.04
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATTATATTTCTAAA
Found at i:35605701 original size:32 final size:32
Alignment explanation
Indices: 35605642--35605725 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
35605632 ATATATGTAA
35605642 TTATTATTTGTTTATATATATAAATATATATG
1 TTATTATTTGTTTATATATATAAATATATATG
* * *
35605674 TTATTATCTTTTTTATA-ATCTATATATATATG
1 TTATTAT-TTGTTTATATATATAAATATATATG
*
35605706 -TATATAATT-TTTATATATAT
1 TTAT-TATTTGTTTATATATAT
35605726 GTACATGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 6 0.14
31 8 0.18
32 22 0.50
33 8 0.18
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (32 bp):
TTATTATTTGTTTATATATATAAATATATATG
Found at i:35605711 original size:21 final size:21
Alignment explanation
Indices: 35605687--35605728 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35605677 TTATCTTTTT
35605687 TATAATCTATATATATATGTA
1 TATAATCTATATATATATGTA
* *
35605708 TATAATTTTTATATATATGTA
1 TATAATCTATATATATATGTA
35605729 CATGTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (21 bp):
TATAATCTATATATATATGTA
Found at i:35610979 original size:44 final size:44
Alignment explanation
Indices: 35610907--35611442 Score: 458
Period size: 44 Copynumber: 12.2 Consensus size: 44
35610897 GGAGGTCCTA
* *
35610907 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGATGCAGATCTTG
* * * *
35610950 TCTTCCCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAG-ATGCAGATCTTG
* * ** * * *
35610995 TCTTCATGTATTGG-CATGAAGTAGATTC-AAGATAGTAGATCCTA
1 TCTTCCTATATTGGTCGCGAAGTAGA-TCGAAGAT-GCAGATCTTG
* *
35611039 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGATGCAGATCTTG
* * * * * * * *
35611082 TCTTCCCATTTTGGTGGCGGAGTATATCGAAGAAAGTAGATTTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAG-ATGCAGATCTTG
* * * * *
35611127 TCTTCATGTATTGG-CGTGAAGCAGATCGAAGATAGCAGATCCTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGAT-GCAGATCTTG
* *
35611171 TCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGATGCAGATCTTG
* * * *
35611215 TCTTCCTATACTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAG-ATGCAGATCTTG
* * ** ** *
35611260 TCTTCATGTATTGG-CATGAAGTAGATCGAAGATAGCAGGCCATG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGAT-GCAGATCTTG
** * *
35611304 TCTTCCTATATTGGT-AAGAAGTGGATCGAAGATGTAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGATGCAGATCTTG
* * * *
35611347 TCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAG-ATGCAGATCTTG
* * **
35611392 TCTTCATGTATTGG-CATGAAGTAGATCGAAGATAGCAGATCTTG
1 TCTTCCTATATTGGTCGCGAAGTAGATCGAAGAT-GCAGATCTTG
35611436 TCTTCCT
1 TCTTCCT
35611443 GCACTGACAG
Statistics
Matches: 386, Mismatches: 91, Indels: 31
0.76 0.18 0.06
Matches are distributed among these distances:
43 61 0.16
44 225 0.58
45 100 0.26
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (44 bp):
TCTTCCTATATTGGTCGCGAAGTAGATCGAAGATGCAGATCTTG
Found at i:35611128 original size:132 final size:132
Alignment explanation
Indices: 35610890--35611442 Score: 876
Period size: 132 Copynumber: 4.2 Consensus size: 132
35610880 GCAGATCAGT
* * *
35610890 GAAGATAGGAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
35610955 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
35611020 TTC
131 -TC
* *
35611023 -AAGATAGTAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
** * * * * * *
35611087 CCATTTTGGTGGCGGAGTATATCGAAGAAAGTAGATTTTGTCTTCATGTATTGGCGTGAAGCAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
35611152 TC
131 TC
35611154 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
35611219 CCTATACTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
65 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
35611284 ATC
130 ATC
* * *
35611287 GAAGATAGCAG-GCCATGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGTAGATCTTGTCTT
1 GAAGATAGCAGATCC-TGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTT
35611351 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
65 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
35611416 ATC
130 ATC
*
35611419 GAAGATAGCAGATCTTGTCTTCCT
1 GAAGATAGCAGATCCTGTCTTCCT
35611443 GCACTGACAG
Statistics
Matches: 389, Mismatches: 27, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
131 2 0.01
132 269 0.69
133 118 0.30
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (132 bp):
GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
TC
Found at i:35611397 original size:265 final size:264
Alignment explanation
Indices: 35610890--35611442 Score: 876
Period size: 265 Copynumber: 2.1 Consensus size: 264
35610880 GCAGATCAGT
* * *
35610890 GAAGATAGGAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
35610955 CCATATTGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
* * *
35611020 TTCAAGATAGTAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCT
131 TTCAAGATAGCAGAGCCTATCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCT
** * * * * *
35611085 TCCCATTTTGGTGGCGGAGTATATCGAAGAAAGTAGATTTTGTCTTCATGTATTGGCGTGAAGCA
196 TCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGCA
35611150 GATC
261 GATC
35611154 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
35611219 CCTATACTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
65 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAG
* *
35611284 A-TCGAAGATAGCAG-GCCATGTCTTCCTATATTGGTAAGAAGTGGATCGAAGATGTAGATCTTG
130 ATTC-AAGATAGCAGAGCC-TATCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTG
35611347 TCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAA
193 TCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAA
*
35611412 GTAGATC
258 GCAGATC
*
35611419 GAAGATAGCAGATCTTGTCTTCCT
1 GAAGATAGCAGATCCTGTCTTCCT
35611443 GCACTGACAG
Statistics
Matches: 265, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
264 35 0.13
265 230 0.87
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (264 bp):
GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
TTCAAGATAGCAGAGCCTATCTTCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCT
TCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGCA
GATC
Found at i:35611534 original size:88 final size:88
Alignment explanation
Indices: 35611423--35611652 Score: 334
Period size: 88 Copynumber: 2.6 Consensus size: 88
35611413 TAGATCGAAG
* *
35611423 ATAGCAGATCTTGTCTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
35611488 GGTTGCAGCGGCGCAAGCTAAAA
66 GGTTGCAGCGGAGCAAGCTAAAA
* * *
35611511 ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGTAGATCAAAGACACCAGCCTTGCCTCCTTG
1 ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* *
35611576 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAAGCTAAAA
* * * * * *
35611599 ATAGCAAATCCTACCTTCCTGCACCGACAGCGAAGCAGATCGATGACCCCAGCC
1 ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCC
35611653 CTATCTCCCT
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 126 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAAGCTAAAA
Found at i:35611548 original size:265 final size:262
Alignment explanation
Indices: 35610979--35611556 Score: 610
Period size: 265 Copynumber: 2.2 Consensus size: 262
35610969 GAGTAGATCG
* * * * * * * *
35610979 AAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATTC-AAGATAGTAGATCC-TATCT
1 AAGAAAGCAGATCTTGCCTTCATGCACTGACACGAAGTAGA-TCAAAGATAGCAG-GCCATGTCT
* ** * *
35611042 TCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATTTTGGTGGCGGAGTAT
64 TCCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAG
* * *
35611107 ATCGAAGAAAGTAGATTTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGATCCTGT
129 ATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGCAGATCGAAGATAGCAGATCCTGT
* * ** ** ** * * * * *
35611172 CTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCCTATACTGGTGGCGAAG
194 CTTCCTACACTGACAGCGAAGCAGATCGAAGAACCAGACCTTGCCTCCCTAGACTGGCGGCGAAG
35611237 TGGATC
259 T-GA-C
* * * * * *
35611243 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAGGCCATGTCTT
1 -AAGAAAGCAGATCTTGCCTTCATGCACTGACACGAAGTAGATCAAAGATAGCAGGCCATGTCTT
*
35611308 CCTATATTGGTAAGAAGTGGATCGAAGATGTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
65 CCTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
* *
35611373 TCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCAGATCTTGTC
130 TCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGCAGATCGAAGATAGCAGATCCTGTC
* * * **
35611438 TTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGTTGCAGCGGCGC
195 TTCCTACACTGACAGCGAAGCAGATCGAAGA-ACCAGACCTTGCCTCCCTAGACTG--GCGGCG-
35611502 AAGCT-A-
256 AAG-TGAC
*
35611508 AA-AATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGTAGATCAAAGA
1 AAGAA-AGCAGATCTTGCCTTCATGCACTGACA-CGAAGTAGATCAAAGA
35611557 CACCAGCCTT
Statistics
Matches: 265, Mismatches: 39, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
263 2 0.01
264 28 0.11
265 222 0.84
266 3 0.01
267 6 0.02
268 3 0.01
269 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (262 bp):
AAGAAAGCAGATCTTGCCTTCATGCACTGACACGAAGTAGATCAAAGATAGCAGGCCATGTCTTC
CTATATTGGTAAGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
CGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGCAGATCGAAGATAGCAGATCCTGTCT
TCCTACACTGACAGCGAAGCAGATCGAAGAACCAGACCTTGCCTCCCTAGACTGGCGGCGAAGTG
AC
Found at i:35611682 original size:88 final size:88
Alignment explanation
Indices: 35611437--35611682 Score: 242
Period size: 88 Copynumber: 2.8 Consensus size: 88
35611427 CAGATCTTGT
* * * * * * **
35611437 CTTCCTGCACTGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGCGC
1 CTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCCTACCTCCCTGGGTAGCAGCGGAAC
* * * * *
35611502 AAGCTAAAAATAGCAGATCTTGC
66 AGGTTAAAAATAGCAAATCCTAC
* * * * * * *
35611525 CTTCCTGCACTGACAGCGAAGTAGATCAAAGACACCAGCCTTGCCTCCTTGGGTTGCAGCGGAGC
1 CTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCCTACCTCCCTGGGTAGCAGCGGAAC
35611590 AGGTTAAAAATAGCAAATCCTAC
66 AGGTTAAAAATAGCAAATCCTAC
* * * * *
35611613 CTTCCTGCACCGACAGCGAAGCAGATCGATGACCCCAGCCCTATCTCCCT-GGTCAGCAGTGGAA
1 CTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCCTACCTCCCTGGGT-AGCAGCGGAA
*
35611677 TAGGTT
65 CAGGTT
35611683 GAAGATTGAG
Statistics
Matches: 134, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
87 3 0.02
88 131 0.98
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (88 bp):
CTTCCTGCACCGACAGCGAAGCAGATCAAAGACACCAGCCCTACCTCCCTGGGTAGCAGCGGAAC
AGGTTAAAAATAGCAAATCCTAC
Found at i:35611718 original size:44 final size:44
Alignment explanation
Indices: 35611652--35611817 Score: 190
Period size: 44 Copynumber: 3.8 Consensus size: 44
35611642 TGACCCCAGC
* *
35611652 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * * *
35611696 TCTATCTCCTTGGGCAGTAGTGGAATAGATTGAAGATTGTTG-GT
1 CCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAAGATTG-TGAAT
* *
35611740 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAATATTGTGAAT
1 CCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * * *
35611784 GCTATCTCCCTGAGAAGTAGTGGAGTAGGTTGAA
1 CCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAA
35611818 AATAGCAAAT
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.02
44 97 0.97
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (44 bp):
CCTATCTCCCTGGGCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:35611767 original size:88 final size:88
Alignment explanation
Indices: 35611652--35611817 Score: 260
Period size: 88 Copynumber: 1.9 Consensus size: 88
35611642 TGACCCCAGC
* * * *
35611652 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCTTGGGCAGTAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATGCTATCTCCCTGAGAAGTAGT
35611717 GGAATAGATTGAAGATTGTTGGT
66 GGAATAGATTGAAGATTGTTGGT
* *
35611740 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAATATTGTGAATGCTATCTCCCTGAGAAGTAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATGCTATCTCCCTGAGAAGTAGT
* *
35611805 GGAGTAGGTTGAA
66 GGAATAGATTGAA
35611818 AATAGCAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (88 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATGCTATCTCCCTGAGAAGTAGT
GGAATAGATTGAAGATTGTTGGT
Found at i:35612637 original size:22 final size:23
Alignment explanation
Indices: 35612609--35612653 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35612599 ATGCAATATT
35612609 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
35612631 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
35612654 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:35612936 original size:7 final size:7
Alignment explanation
Indices: 35612924--35612953 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
35612914 TTAGTCTTTT
35612924 TTATTTA
1 TTATTTA
35612931 TTATTTA
1 TTATTTA
35612938 TTATTTA
1 TTATTTA
35612945 TTA-TTA
1 TTATTTA
35612951 TTA
1 TTA
35612954 AATTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:35612941 original size:3 final size:3
Alignment explanation
Indices: 35612928--35613024 Score: 67
Period size: 3 Copynumber: 33.0 Consensus size: 3
35612918 TCTTTTTTAT
* * * *
35612928 TTA TTA TTTA TTA TTTA TTA TTA TTA -AA TT- TGA TT- TTC TTG TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
35612972 TTA -AA TAA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35613019 TTA TTA
1 TTA TTA
35613025 CTATATATAC
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
2 5 0.07
3 63 0.85
4 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:35612941 original size:14 final size:13
Alignment explanation
Indices: 35612924--35613023 Score: 55
Period size: 14 Copynumber: 7.4 Consensus size: 13
35612914 TTAGTCTTTT
35612924 TTATTTATTATTTA
1 TTATTTATTA-TTA
35612938 TTATTTATTATTA
1 TTATTTATTATTA
*
35612951 TTAAATTTGATT-TTC
1 TT--ATTT-ATTATTA
* *
35612966 TT-GTTATTAAATAA
1 TTATTTATT--ATTA
*
35612980 TTA-TTATTGTTA
1 TTATTTATTATTA
35612992 TTATTATCATTATTA
1 TTATT-T-ATTATTA
*
35613007 TTA-TTATAATTA
1 TTATTTATTATTA
35613019 TTATT
1 TTATT
35613024 ACTATATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 23
0.68 0.08 0.23
Matches are distributed among these distances:
11 3 0.04
12 16 0.24
13 8 0.12
14 20 0.30
15 17 0.25
16 3 0.04
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:35613185 original size:17 final size:17
Alignment explanation
Indices: 35613154--35613197 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
35613144 CATAACTTTT
*
35613154 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
35613170 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
35613187 ATATACATTTT
1 ATATACATTTT
35613198 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:35613311 original size:39 final size:38
Alignment explanation
Indices: 35613210--35613311 Score: 96
Period size: 39 Copynumber: 2.6 Consensus size: 38
35613200 ATTTCCTAAC
* * *
35613210 TTTTATATGCATATATATACTTTTATATTTTTTTGATAAA
1 TTTTATAT--ATATATATATTTTTATATTTTGTTCATAAA
* ** * *
35613250 TATGTATATACGTATGTTTTTTTATATTATTGTTCATAAA
1 T-TTTATATATATATATATTTTTATATT-TTGTTCATAAA
35613290 TTTTATATATATATATATTTTT
1 TTTTATATATATATATATTTTT
35613312 CTAAGTTAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
39 30 0.64
40 11 0.23
41 6 0.13
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (38 bp):
TTTTATATATATATATATTTTTATATTTTGTTCATAAA
Found at i:35613391 original size:30 final size:30
Alignment explanation
Indices: 35613357--35613413 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35613347 TATTTGTTTA
*
35613357 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATGTATATAAT-TTTTTTATAATC
35613387 TATATATATGTATATAATTTTTTTATA
1 TATATATATGTATATAATTTTTTTATA
35613414 TATGTACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (30 bp):
TATATATATGTATATAATTTTTTTATAATC
Found at i:35621685 original size:12 final size:12
Alignment explanation
Indices: 35621668--35621693 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35621658 CGTTTGCCAC
35621668 CAAATCACTGAA
1 CAAATCACTGAA
35621680 CAAATCACTGAA
1 CAAATCACTGAA
35621692 CA
1 CA
35621694 TAACAGGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
CAAATCACTGAA
Found at i:35625888 original size:170 final size:167
Alignment explanation
Indices: 35625565--35625895 Score: 423
Period size: 170 Copynumber: 2.0 Consensus size: 167
35625555 CTTCATTTTC
* * *
35625565 TTCTTAACGGCAAATTGTCTAGTTCACTGATGATGCATAAAAATATACGGTGTCACTTTATTTTG
1 TTCTTAACGACAAATTATCTAGTTCACTGATAATGCATAAAAATATACGGTGTCACTTTATTTTG
* * * * * *
35625630 TTTTTGGTAAATTAAAATATGGAAAACTTTACCTCCAAGAAAGCACTAATGTTGGAGAATCTTAG
66 ATTTTAGTAAATAAAAATATGAAAAACTTCACCTCCAAAAAAGCACTAATGTTGGAGAATCTTAG
35625695 GCTACCTAGTCAAAGTTGAGGCCCAAAACCATTTTTGAT
131 G--ACCTAGTCAAAGTTGAGGCCCAAAACCATTTTTGAT
* * * * *
35625734 TTCTCTAACGACAAATTATTTAGTTCATTGATAATGCATAAAATTATAGGGTGTCACTCTATTTT
1 TTCT-TAACGACAAATTATCTAGTTCACTGATAATGCATAAAAATATACGGTGTCACT-T-TATT
** *
35625799 ACTTGATTTTAGTGGATAAAAATATTAAAAACTTCACCTCCAAAAAAGCACTAATGTTGGAGAAT
63 --TTGATTTTAGTAAATAAAAATATGAAAAACTTCACCTCCAAAAAAGCACTAATGTTGGAGAAT
*
35625864 TTTAGG-CC-AGTCAAAGTTGAGGCCCAAAACCA
126 CTTAGGACCTAGTCAAAGTTGAGGCCCAAAACCA
35625896 CATCTGGTTC
Statistics
Matches: 139, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
169 4 0.03
170 70 0.50
171 3 0.02
172 3 0.02
174 59 0.42
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (167 bp):
TTCTTAACGACAAATTATCTAGTTCACTGATAATGCATAAAAATATACGGTGTCACTTTATTTTG
ATTTTAGTAAATAAAAATATGAAAAACTTCACCTCCAAAAAAGCACTAATGTTGGAGAATCTTAG
GACCTAGTCAAAGTTGAGGCCCAAAACCATTTTTGAT
Found at i:35631481 original size:2 final size:2
Alignment explanation
Indices: 35631474--35631519 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35631464 GAAAAAGGAA
35631474 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35631516 AG AG
1 AG AG
35631520 GGCACGGAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35632190 original size:21 final size:21
Alignment explanation
Indices: 35632166--35632245 Score: 106
Period size: 21 Copynumber: 3.6 Consensus size: 21
35632156 ACTTACATGG
35632166 TTATTAATAATAAAATAATTT
1 TTATTAATAATAAAATAATTT
35632187 TTATTAATAATAAAATAATTT
1 TTATTAATAATAAAATAATTT
*
35632208 TTATAAATAATAAATATCAATTT
1 TTATTAATAATAAA-AT-AATTT
35632231 GTTAAATTAATAATA
1 -TT--ATTAATAATA
35632246 TTTTATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
21 34 0.65
22 2 0.04
23 5 0.10
24 2 0.04
26 9 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
TTATTAATAATAAAATAATTT
Found at i:35633770 original size:15 final size:15
Alignment explanation
Indices: 35633711--35633771 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
35633701 TAATATTAAC
*
35633711 AATAAAAGTAATACT
1 AATAAAAGTAATAGT
*
35633726 AATAATAA-TATTAGT
1 AATAA-AAGTAATAGT
*
35633741 AATAACAAAAATAATAGT
1 AAT---AAAAGTAATAGT
35633759 AATAAAAGTAATA
1 AATAAAAGTAATA
35633772 AAGATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 22 0.59
16 2 0.05
17 2 0.05
18 11 0.30
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
AATAAAAGTAATAGT
Found at i:35633771 original size:18 final size:18
Alignment explanation
Indices: 35633707--35633781 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 18
35633697 GTGATAATAT
* *
35633707 TAACAATAA-AAGTAATAC
1 TAACAATAATAA-TAGTAA
* *
35633725 TAATAATAATATTAGTAA
1 TAACAATAATAATAGTAA
*
35633743 TAACAAAAATAATAGTAA
1 TAACAATAATAATAGTAA
35633761 TAA-AAGTAATAA-AGATAA
1 TAACAA-TAATAATAG-TAA
35633779 TAA
1 TAA
35633782 TACTATAGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.09
18 41 0.89
19 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.27
Consensus pattern (18 bp):
TAACAATAATAATAGTAA
Found at i:35633861 original size:15 final size:15
Alignment explanation
Indices: 35633806--35633861 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
35633796 CGACGTTAAT
*
35633806 AATAATAATATTAAA
1 AATAATAATAATAAA
* *
35633821 AATAAAAATAACAAA
1 AATAATAATAATAAA
* *
35633836 ACTACTAATAATAAA
1 AATAATAATAATAAA
*
35633851 AATAATGATAA
1 AATAATAATAA
35633862 AATAGCAAAG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:35635059 original size:50 final size:50
Alignment explanation
Indices: 35634992--35635258 Score: 250
Period size: 50 Copynumber: 5.3 Consensus size: 50
35634982 AACTCGTAAG
** * * *
35634992 TTTAATCTGTTTGACTGTGATGTC-GGCGAAGCAAGATTCACCGTTGTGTC
1 TTTAATCTGTTCCACTGTAATGTCAGG-GAAGTAAGATTCACCGTTGTGGC
* ** * * *
35635042 TTCAATCTGTTCCACTGTACCGCCTGGGAAGTAAGATTCACCATTGTGGC
1 TTTAATCTGTTCCACTGTAATGTCAGGGAAGTAAGATTCACCGTTGTGGC
* * ** * *
35635092 TTTATTCTTTTTAACTATAATGTCAGGGAAGTAAGATTCGCCGTTGTGGC
1 TTTAATCTGTTCCACTGTAATGTCAGGGAAGTAAGATTCACCGTTGTGGC
* * * *
35635142 TTTAATCTGTTCCACTGCACTG-CATGGGAAGTAAGATTCACTGTTGTAGC
1 TTTAATCTGTTCCACTGTAATGTCA-GGGAAGTAAGATTCACCGTTGTGGC
* ** * * * *
35635192 TTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGC
1 TTTAATCTGTTCCACTGTAATGTCAGGGAAGTAAGATTCACCGTTGTGGC
35635242 TTTAATCTGTTCCACTG
1 TTTAATCTGTTCCACTG
35635259 CATCGCCTGG
Statistics
Matches: 170, Mismatches: 44, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
49 2 0.01
50 165 0.97
51 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (50 bp):
TTTAATCTGTTCCACTGTAATGTCAGGGAAGTAAGATTCACCGTTGTGGC
Found at i:35635194 original size:100 final size:99
Alignment explanation
Indices: 35635011--35635275 Score: 361
Period size: 100 Copynumber: 2.6 Consensus size: 99
35635001 TTTGACTGTG
* * * *
35635011 ATGTCGGCGAAGCAAGATTCACCGTTGTGTCTTCAATCTGTTCCACTGTACCGCCTGGGAAGTAA
1 ATGTCGG-GAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
* * *
35635076 GATTCACCATTGTGGCTTTATTCTTTTTAACTATA
65 GATTCACCATTGTAGCTTTAATCTTTTTAACTACA
* * *
35635111 ATGTCAGGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCATGGGAAGTAA
1 ATGTC-GGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
** *
35635176 GATTCACTGTTGTAGCTTTAATCTTTTTAACTGCA
65 GATTCACCATTGTAGCTTTAATCTTTTTAACTACA
*
35635211 ATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA-TCGCCTGGGAAGTA
1 ATGTC-GGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACT-GCCTGGGAAGTA
35635275 A
64 A
35635276 AACTGGTATT
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
99 1 0.01
100 142 0.98
101 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
ATGTCGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAAG
ATTCACCATTGTAGCTTTAATCTTTTTAACTACA
Found at i:35636137 original size:42 final size:42
Alignment explanation
Indices: 35636054--35636137 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
35636044 AGTATAGCAA
**
35636054 GATCACCACATGCCCCAATATAATCAAAATTCGAGTTGCTCT
1 GATCACCACATGCCCCAATATAATCAAAATTCGAGCCGCTCT
* * * * *
35636096 GATCACCTCATGCCCCATTTTAATCAATATTTGAGCCGCTCT
1 GATCACCACATGCCCCAATATAATCAAAATTCGAGCCGCTCT
35636138 TTTTTGGATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.30
Consensus pattern (42 bp):
GATCACCACATGCCCCAATATAATCAAAATTCGAGCCGCTCT
Found at i:35637131 original size:21 final size:21
Alignment explanation
Indices: 35637089--35637137 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35637079 CCTTGGCCTC
*
35637089 TCCTTTTCTTTTTTTCTTTTT
1 TCCTTTTCTTTTTTTCTGTTT
35637110 TCCTTTTCTCTTTTTT-TGTTT
1 TCCTTTTCT-TTTTTTCTGTTT
*
35637131 TCATTTT
1 TCCTTTT
35637138 GACTTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (21 bp):
TCCTTTTCTTTTTTTCTGTTT
Found at i:35637132 original size:15 final size:15
Alignment explanation
Indices: 35637092--35637125 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35637082 TGGCCTCTCC
* *
35637092 TTTTCTTTTTTTCTT
1 TTTTCCTTTTCTCTT
35637107 TTTTCCTTTTCTCTT
1 TTTTCCTTTTCTCTT
35637122 TTTT
1 TTTT
35637126 TGTTTTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCCTTTTCTCTT
Found at i:35637137 original size:6 final size:6
Alignment explanation
Indices: 35637123--35637161 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
35637113 TTTTCTCTTT
* *
35637123 TTTTG- TTTTCA TTTTGA CTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
35637162 TCTTCTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:35642162 original size:3 final size:3
Alignment explanation
Indices: 35642147--35642312 Score: 56
Period size: 3 Copynumber: 56.0 Consensus size: 3
35642137 GATAGCAGTG
* * * *
35642147 ATA ATA TTA ATA ATA A-A AGTA ATA CTA ATA ATA ATA TTA GTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
35642192 ACA AAA ATA ATA GTA ATA A-A AGTA ACA A-A GATA ATA ATA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA
* * * ** * * * * *
35642236 GTA ATG ATG ACG TTA ATA ATA ATA ATA CTA AAA ATA AAA ATA A-A AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
35642283 ACTA CTA ATA ATA AAA ATA ATT ATA A-A ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35642313 GCAAAGATAT
Statistics
Matches: 117, Mismatches: 36, Indels: 20
0.68 0.21 0.12
Matches are distributed among these distances:
2 10 0.09
3 101 0.86
4 6 0.05
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:35642202 original size:27 final size:26
Alignment explanation
Indices: 35642172--35642240 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
35642162 AAAGTAATAC
35642172 TAATAATAATATTAGTAATAACAAAAA
1 TAATAATAATA-TAGTAATAACAAAAA
* *
35642199 TAATAGTAATA-A--AAGTAACAAAGA
1 TAATAATAATATAGTAA-TAACAAAAA
*
35642223 TAATAATACTATAGTAAT
1 TAATAATAATATAGTAAT
35642241 GATGACGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.06
24 17 0.50
25 2 0.06
26 1 0.03
27 12 0.35
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.29
Consensus pattern (26 bp):
TAATAATAATATAGTAATAACAAAAA
Found at i:35643480 original size:50 final size:50
Alignment explanation
Indices: 35643426--35643684 Score: 257
Period size: 50 Copynumber: 5.2 Consensus size: 50
35643416 TGTGATGTCG
* * * **
35643426 GGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTGTTCCACTGCACCGCCT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAATGCCT
* * * * ** ** * *
35643476 GGGAAGTAAGATTCACCATTGTGGCTTTATTCTTTTTAACTATAATGTCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAATGCCT
* * *
35643526 GGGAAGTAAGATTCGCTGTTGTGGCTTTAATCTGTTCCACTGCAGTGCAT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAATGCCT
* * * ** * *
35643576 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAATGCCT
* * * *
35643626 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATTGCCT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAATGCCT
35643676 GGGAAGTAA
1 GGGAAGTAA
35643685 AATTGGTATT
Statistics
Matches: 161, Mismatches: 48, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 161 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAATGCCT
Found at i:35643603 original size:100 final size:100
Alignment explanation
Indices: 35643420--35643684 Score: 368
Period size: 100 Copynumber: 2.6 Consensus size: 100
35643410 TTTGACTGTG
* * *
35643420 ATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
* * *
35643485 GATTCACCATTGTGGCTTTATTCTTTTTAACTATA
66 GATTCACCATTGTAGCTTTAATCTTTTTAACTACA
* * * * *
35643520 ATGTCAGGGAAGTAAGATTCGCTGTTGTGGCTTTAATCTGTTCCACTGCAGTGCATGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
* ** *
35643585 GATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCA
66 GATTCACCATTGTAGCTTTAATCTTTTTAACTACA
* * *
35643620 ATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATTGCCTGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
35643685 AATTGGTATT
Statistics
Matches: 143, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 143 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (100 bp):
ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
GATTCACCATTGTAGCTTTAATCTTTTTAACTACA
Found at i:35644963 original size:14 final size:14
Alignment explanation
Indices: 35644944--35644978 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35644934 ACCCTCTCCA
*
35644944 TCATTTTGTATTTT
1 TCATTTTCTATTTT
*
35644958 TCATTTTCTCTTTT
1 TCATTTTCTATTTT
35644972 TCATTTT
1 TCATTTT
35644979 TCACATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.71
Consensus pattern (14 bp):
TCATTTTCTATTTT
Found at i:35650759 original size:14 final size:15
Alignment explanation
Indices: 35650740--35650769 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
35650730 AGGCACACAC
35650740 ACAAAAAA-AAAAAA
1 ACAAAAAACAAAAAA
35650754 ACAAAAAACAAAAAA
1 ACAAAAAACAAAAAA
35650769 A
1 A
35650770 TGAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAAACAAAAAA
Found at i:35651894 original size:18 final size:18
Alignment explanation
Indices: 35651871--35651908 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
35651861 CCTTACTAAC
35651871 GTTTATATATTTTATTGG
1 GTTTATATATTTTATTGG
35651889 GTTTATATATTTTATTGG
1 GTTTATATATTTTATTGG
35651907 GT
1 GT
35651909 AAATTATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (18 bp):
GTTTATATATTTTATTGG
Found at i:35660946 original size:17 final size:17
Alignment explanation
Indices: 35660909--35660950 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
35660899 TTTAAATATC
*
35660909 AAAATTCAATAAATTAAT
1 AAAATT-AATAAATAAAT
*
35660927 AAAATTAATGAATAAAT
1 AAAATTAATAAATAAAT
35660944 AAAATTA
1 AAAATTA
35660951 TGACCTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATTAATAAATAAAT
Found at i:35672377 original size:23 final size:24
Alignment explanation
Indices: 35672346--35672396 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
35672336 ACTTTGAAAA
35672346 CATGATTGAGTAGTTAAGTTTTAG
1 CATGATTGAGTAGTTAAGTTTTAG
35672370 CATG-TTGAGTAGTTAAGTTTTAG
1 CATGATTGAGTAGTTAAGTTTTAG
35672393 CATG
1 CATG
35672397 CCTTGCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (24 bp):
CATGATTGAGTAGTTAAGTTTTAG
Found at i:35676222 original size:48 final size:47
Alignment explanation
Indices: 35676170--35676302 Score: 176
Period size: 47 Copynumber: 2.8 Consensus size: 47
35676160 TGATTTGTAC
* *
35676170 AAAAATGAACAGCATTTAAGCACCAATTTGGACAACATTAATATGCTA
1 AAAAATGAACAGCATTTAAACAAC-ATTTGGACAACATTAATATGCTA
* * * * * *
35676218 AAAAACGAACAGCATTTAACCAACATTCGAACAACATCAGTATGCTA
1 AAAAATGAACAGCATTTAAACAACATTTGGACAACATTAATATGCTA
*
35676265 AAAAATGGACAGCATTTAAACAACATTTGGACAACATT
1 AAAAATGAACAGCATTTAAACAACATTTGGACAACATT
35676303 TAATCAACAT
Statistics
Matches: 72, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 51 0.71
48 21 0.29
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.23
Consensus pattern (47 bp):
AAAAATGAACAGCATTTAAACAACATTTGGACAACATTAATATGCTA
Found at i:35676302 original size:22 final size:22
Alignment explanation
Indices: 35676270--35676507 Score: 120
Period size: 22 Copynumber: 10.5 Consensus size: 22
35676260 TGCTAAAAAA
35676270 TGGACAGCATTTAAACAACATT
1 TGGACAGCATTTAAACAACATT
* *
35676292 TGGACAACATTTAATCAACATT
1 TGGACAGCATTTAAACAACATT
* * ** **
35676314 CGGACATCATTAGTATGCTAA-AAA
1 TGGACAGCATT--TAAAC-AACATT
*
35676338 TGGACAGTATTTAAACAACATT
1 TGGACAGCATTTAAACAACATT
** * *
35676360 CAGACAACATTTAACCAACATT
1 TGGACAGCATTTAAACAACATT
* ** * **
35676382 TGGACAACATTAGTATGCTAAAAAA
1 TGGACAGCATT--TAAAC-AACATT
*
35676407 TGGACAGCATTTAAACAACAGT
1 TGGACAGCATTTAAACAACATT
* * *
35676429 CGGACAGCATTTAACCAATATT
1 TGGACAGCATTTAAACAACATT
* * **
35676451 TGGACAGCA-TTAGCATGCTAAAAAA
1 TGGACAGCATTTA--A-AC-AACATT
35676476 TGGACAGCATTTAAACAACATT
1 TGGACAGCATTTAAACAACATT
*
35676498 CGGACAGCAT
1 TGGACAGCAT
35676508 CTTGTCATAA
Statistics
Matches: 157, Mismatches: 47, Indels: 24
0.69 0.21 0.11
Matches are distributed among these distances:
21 5 0.03
22 100 0.64
23 5 0.03
24 17 0.11
25 27 0.17
26 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (22 bp):
TGGACAGCATTTAAACAACATT
Found at i:35676368 original size:11 final size:11
Alignment explanation
Indices: 35676346--35676392 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
35676336 AATGGACAGT
*
35676346 ATTTAAACAAC
1 ATTTAGACAAC
*
35676357 ATTCAGACAAC
1 ATTTAGACAAC
35676368 ATTTA-ACCAAC
1 ATTTAGA-CAAC
*
35676379 ATTTGGACAAC
1 ATTTAGACAAC
35676390 ATT
1 ATT
35676393 AGTATGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 1 0.03
11 28 0.93
12 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (11 bp):
ATTTAGACAAC
Found at i:35676504 original size:69 final size:69
Alignment explanation
Indices: 35676226--35676507 Score: 422
Period size: 69 Copynumber: 4.1 Consensus size: 69
35676216 TAAAAAACGA
* *
35676226 ACAGCATTTAACCAACATTCGAACAACATCAGTATGCTAAAAAATGGACAGCATTTAAACAACAT
1 ACAGCATTTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAACAT
*
35676291 TTGG
66 TCGG
* * * *
35676295 ACAACATTTAATCAACATTCGGACATCATTAGTATGCT-AAAAATGGACAGTATTTAAACAACAT
1 ACAGCATTTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAACAT
*
35676359 TCAG
66 TCGG
* * *
35676363 ACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAACAG
1 ACAGCATTTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAACAT
35676428 TCGG
66 TCGG
* * * *
35676432 ACAGCATTTAACCAATATTTGGACAGCATTAGCATGCTAAAAAATGGACAGCATTTAAACAACAT
1 ACAGCATTTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAACAT
35676497 TCGG
66 TCGG
35676501 ACAGCAT
1 ACAGCAT
35676508 CTTGTCATAA
Statistics
Matches: 193, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 62 0.32
69 131 0.68
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (69 bp):
ACAGCATTTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAACAT
TCGG
Found at i:35677216 original size:42 final size:42
Alignment explanation
Indices: 35677149--35677228 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
35677139 TATAATATAT
*
35677149 CGATGCCACTATCCCAGACAGGGTCTTACACGAAATCATCTA
1 CGATGCCACTATCCCAAACAGGGTCTTACACGAAATCATCTA
* * *
35677191 CGATGCCAGTGTCCCAAACATGGTCTTACACGAAATCA
1 CGATGCCACTATCCCAAACAGGGTCTTACACGAAATCA
35677229 CACCTTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (42 bp):
CGATGCCACTATCCCAAACAGGGTCTTACACGAAATCATCTA
Found at i:35685460 original size:5 final size:5
Alignment explanation
Indices: 35685450--35685474 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35685440 TCTTTTTCTA
35685450 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
35685475 TATAAGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:35699826 original size:29 final size:29
Alignment explanation
Indices: 35699772--35699830 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
35699762 AGCCCATATA
*
35699772 TTTCACAATTTCTCACATTTGACCCACAAT
1 TTTCACAATTTCTCACATTTAACCCA-AAT
*
35699802 TTTCAC-ATTTCTCA-TTTTAACCCCAAAT
1 TTTCACAATTTCTCACATTTAA-CCCAAAT
35699830 T
1 T
35699831 GACATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 8 0.31
29 12 0.46
30 6 0.23
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.41
Consensus pattern (29 bp):
TTTCACAATTTCTCACATTTAACCCAAAT
Found at i:35715103 original size:25 final size:25
Alignment explanation
Indices: 35715046--35715097 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
35715036 CTCATGAGTG
* *
35715046 TCCTGATATTTGGTTCTTACGAGCT
1 TCCTGTTATATGGTTCTTACGAGCT
* *
35715071 TCCTGTTATATGGTTTTTCCGAGCT
1 TCCTGTTATATGGTTCTTACGAGCT
35715096 TC
1 TC
35715098 TCGTTAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (25 bp):
TCCTGTTATATGGTTCTTACGAGCT
Found at i:35725931 original size:32 final size:34
Alignment explanation
Indices: 35725862--35725931 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
35725852 ATTTATTTGA
*
35725862 AATTTTATATAATTTAATAAAATTATTTGAATGT
1 AATTTTATATAATTTAATAAAATTATTTGAATAT
35725896 AATTTTA-AT-ATTTAAATAAAAATTA-TT-AATAT
1 AATTTTATATAATTT-AAT-AAAATTATTTGAATAT
35725928 AATT
1 AATT
35725932 AAAATAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
32 12 0.36
33 7 0.21
34 14 0.42
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
AATTTTATATAATTTAATAAAATTATTTGAATAT
Found at i:35725953 original size:24 final size:25
Alignment explanation
Indices: 35725901--35725955 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
35725891 AATGTAATTT
*
35725901 TAAT-ATTTAAATAAAAATTATTAA
1 TAATAATTAAAATAAAAATTATTAA
* *
35725925 T-ATAATTAAAAT-AAAATTGTTTA
1 TAATAATTAAAATAAAAATTATTAA
35725948 TAATAATT
1 TAATAATT
35725956 TTAAAACCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATAATTAAAATAAAAATTATTAA
Found at i:35732281 original size:30 final size:31
Alignment explanation
Indices: 35732232--35732289 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
35732222 ATTATTGAAC
*
35732232 TATTCAAAAGTTTTCATTTAAGTCATTAAAT
1 TATTCAAAAGTTTTCATTTAAATCATTAAAT
* *
35732263 TATTCGAAA-TTTTTATTTAAATCATTA
1 TATTCAAAAGTTTTCATTTAAATCATTA
35732290 GGCTGCTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAATCATTAAAT
Found at i:35733085 original size:30 final size:29
Alignment explanation
Indices: 35733022--35733085 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
35733012 GTTTAATGTA
* * *
35733022 CAATTTTATACATGAACTTTGATTTTGTG
1 CAATTTTATACATAAAATTTGATTTTGTC
35733051 CAATTTTATACATAAAAATTTGA-TTTGATC
1 CAATTTTATACAT-AAAATTTGATTTTG-TC
35733081 CAATT
1 CAATT
35733086 CTCACAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (29 bp):
CAATTTTATACATAAAATTTGATTTTGTC
Found at i:35733243 original size:31 final size:31
Alignment explanation
Indices: 35733208--35733330 Score: 94
Period size: 31 Copynumber: 4.1 Consensus size: 31
35733198 ATGTGTATGA
*
35733208 TTGAATAACAATCAAAGTTTCATGTATATAT
1 TTGAACAACAATCAAAGTTTCATGTATATAT
* * * *
35733239 TTGAACCACAATCAAAGTTTTATGTGTATAA
1 TTGAACAACAATCAAAGTTTCATGTATATAT
* * *
35733270 TTGTACCA-AATCAAAGTTT-ATATATCA-AT
1 TTGAACAACAATCAAAGTTTCATGTAT-ATAT
* **
35733299 TTGCACATTGAATCAAAG-TTCATGTATA-AT
1 TTGAACA-ACAATCAAAGTTTCATGTATATAT
35733329 TT
1 TT
35733331 TAAAATTTAT
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
29 10 0.13
30 19 0.25
31 46 0.61
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (31 bp):
TTGAACAACAATCAAAGTTTCATGTATATAT
Found at i:35733284 original size:30 final size:31
Alignment explanation
Indices: 35733215--35733288 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
35733205 TGATTGAATA
*
35733215 ACAATCAAAGTTTCATGTATATATTTGAACC
1 ACAATCAAAGTTTCATGTATATAATTGAACC
* * *
35733246 ACAATCAAAGTTTTATGTGTATAATTGTACC
1 ACAATCAAAGTTTCATGTATATAATTGAACC
35733277 A-AATCAAAGTTT
1 ACAATCAAAGTTT
35733289 ATATATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (31 bp):
ACAATCAAAGTTTCATGTATATAATTGAACC
Found at i:35739003 original size:15 final size:15
Alignment explanation
Indices: 35738983--35739014 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35738973 CATTTCACTA
*
35738983 TTATGTCTTTTATAT
1 TTATGTATTTTATAT
35738998 TTATGTATTTTATAT
1 TTATGTATTTTATAT
35739013 TT
1 TT
35739015 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATTTTATAT
Found at i:35740739 original size:12 final size:12
Alignment explanation
Indices: 35740722--35740769 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
35740712 TTTTAATAAG
35740722 ATTTAATATTAA
1 ATTTAATATTAA
35740734 ATTTAATCA-TAA
1 ATTTAAT-ATTAA
35740746 ATATT-ATATT-A
1 AT-TTAATATTAA
35740757 ATTTAATATTAA
1 ATTTAATATTAA
35740769 A
1 A
35740770 GTAATTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.06
11 9 0.29
12 17 0.55
13 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:35742933 original size:26 final size:27
Alignment explanation
Indices: 35742897--35742969 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
35742887 TATTTTCTTG
*
35742897 AAATTTTACCAGGGGTAAAATTG-TTA
1 AAATTTTACCAGGGGTAAAATTGATCA
35742923 AAATTTTACCAGGGGTAAAA-TGATCA
1 AAATTTTACCAGGGGTAAAATTGATCA
***
35742949 AAATTTTGTTAGGGGTAAAAT
1 AAATTTTACCAGGGGTAAAAT
35742970 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 2 0.05
26 39 0.95
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (27 bp):
AAATTTTACCAGGGGTAAAATTGATCA
Found at i:35752785 original size:29 final size:28
Alignment explanation
Indices: 35752753--35752814 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
35752743 AAAAAGTCGT
*
35752753 TTTTTTCAAAATTTACTGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** *
35752782 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
35752810 TTTTT
1 TTTTT
35752815 CGCGAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:35760924 original size:3 final size:3
Alignment explanation
Indices: 35760916--35760951 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35760906 GTTTTCTCCC
35760916 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35760952 GTTGTTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35762164 original size:74 final size:74
Alignment explanation
Indices: 35762038--35762198 Score: 286
Period size: 74 Copynumber: 2.2 Consensus size: 74
35762028 TGACCAAATT
* *
35762038 AACTAAAAAATATTTGAGTGGCCAAAATAGATCATTATTTAGAGTGACTAACAAGATAGTTGACC
1 AACTAAAAAATATCTGAGTGCCCAAAATAGATCATTATTTAGAGTGACTAACAAGATAGTTGACC
35762103 CTATTTAAA
66 CTATTTAAA
*
35762112 AACTCAAAAATATCTGAGTGCCCAAAATAGATCATTATTTAGAGTGACTAACAAGATAGTTGACC
1 AACTAAAAAATATCTGAGTGCCCAAAATAGATCATTATTTAGAGTGACTAACAAGATAGTTGACC
35762177 CTATTTAAA
66 CTATTTAAA
*
35762186 AATTAAAAAATAT
1 AACTAAAAAATAT
35762199 ATATGACATG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 82 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (74 bp):
AACTAAAAAATATCTGAGTGCCCAAAATAGATCATTATTTAGAGTGACTAACAAGATAGTTGACC
CTATTTAAA
Found at i:35771399 original size:17 final size:17
Alignment explanation
Indices: 35771377--35771409 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35771367 AATGGATCAT
35771377 GGTTTATCTTTAGTTCC
1 GGTTTATCTTTAGTTCC
35771394 GGTTTATCTTTAGTTC
1 GGTTTATCTTTAGTTC
35771410 TCAATTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (17 bp):
GGTTTATCTTTAGTTCC
Found at i:35772225 original size:43 final size:43
Alignment explanation
Indices: 35772128--35772226 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
35772118 TAGCTCTCTC
*
35772128 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAGCGTGG
1 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
*** *
35772171 TTATGGTTACCATTAGTGTTG-CTTAATTGGACATTTAACGTTG
1 TTATAACTACCATTAGTG-TGCCTTAATTGGACATTTAACGTGG
35772214 TTATAACTACCAT
1 TTATAACTACCAT
35772227 CAAACTTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 45 0.96
44 2 0.04
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (43 bp):
TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
Found at i:35772845 original size:21 final size:20
Alignment explanation
Indices: 35772821--35772888 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
35772811 TTATAACTAC
35772821 CATTAGTGTGCCTTAATTGGA
1 CATTAGTGTG-CTTAATTGGA
* *
35772842 CATTTAGCGTGGTTATAATT--A
1 CA-TTAGTGT-GCT-TAATTGGA
35772863 CCATTAGTGTTGCTTAATTGGA
1 -CATTAGTG-TGCTTAATTGGA
35772885 CATT
1 CATT
35772889 TAACGTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
20 5 0.14
21 14 0.39
22 11 0.31
23 6 0.17
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTAGTGTGCTTAATTGGA
Found at i:35772848 original size:22 final size:21
Alignment explanation
Indices: 35772823--35772890 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
35772813 ATAACTACCA
35772823 TTAGTGTGCCTTAATTGGACAT
1 TTAGTGTG-CTTAATTGGACAT
* *
35772845 TTAGCGTGGTTATAATT--ACCA-
1 TTAGTGT-GCT-TAATTGGA-CAT
35772866 TTAGTGTTGCTTAATTGGACAT
1 TTAGTG-TGCTTAATTGGACAT
35772888 TTA
1 TTA
35772891 ACGTTGTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
20 5 0.14
21 10 0.29
22 14 0.40
23 6 0.17
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (21 bp):
TTAGTGTGCTTAATTGGACAT
Found at i:35772872 original size:43 final size:43
Alignment explanation
Indices: 35772811--35772909 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
35772801 TAGCTCTCTC
*
35772811 TTATAACTACCATTAGTG-TGCCTTAATTGGACATTTAGCGTGG
1 TTATAACTACCATTAGTGTTG-CTTAATTGGACATTTAACGTGG
* *
35772854 TTATAATTACCATTAGTGTTGCTTAATTGGACATTTAACGTTG
1 TTATAACTACCATTAGTGTTGCTTAATTGGACATTTAACGTGG
35772897 TTATAACTACCAT
1 TTATAACTACCAT
35772910 CAAACTTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 49 0.96
44 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.40
Consensus pattern (43 bp):
TTATAACTACCATTAGTGTTGCTTAATTGGACATTTAACGTGG
Found at i:35773534 original size:54 final size:54
Alignment explanation
Indices: 35773462--35773624 Score: 148
Period size: 54 Copynumber: 3.1 Consensus size: 54
35773452 TATTATTAAG
* *
35773462 AATTTTATGAAATT-ATATATCATTATTAAATTATATTTAAT-ATAAATTATTTTA
1 AATTATATCAAATTCATATAT-ATTATTAAATTATATTTAATAAT-AATTATTTTA
* *
35773516 AATTATA-CAAATTCATATA-A-CA--AAATT-TA-TTAGTAATAATTATTTTA
1 AATTATATCAAATTCATATATATTATTAAATTATATTTAATAATAATTATTTTA
* * * * *
35773563 AATTTTATTAAA-TCATATATTTTAATTAAAATATATTTAATAATAATTATTTCA
1 AATTATATCAAATTCATATATATT-ATTAAATTATATTTAATAATAATTATTTTA
35773617 AATTATAT
1 AATTATAT
35773625 TTTATAGTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
47 27 0.31
48 7 0.08
49 5 0.06
50 1 0.01
51 1 0.01
52 5 0.06
53 7 0.08
54 34 0.39
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (54 bp):
AATTATATCAAATTCATATATATTATTAAATTATATTTAATAATAATTATTTTA
Found at i:35773691 original size:15 final size:16
Alignment explanation
Indices: 35773663--35773692 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35773653 TAAATTCATA
35773663 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
35773679 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
35773693 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:35773693 original size:120 final size:120
Alignment explanation
Indices: 35773563--35773889 Score: 611
Period size: 120 Copynumber: 2.7 Consensus size: 120
35773553 AATTATTTTA
*
35773563 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
35773628 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
35773683 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
35773748 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
35773803 AAATTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
35773867 TATAGTATCATATATTATGATTT
65 TATAGTATCATATATTATGATTT
35773890 AATTAAAATA
Statistics
Matches: 203, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
120 201 0.99
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:35773694 original size:130 final size:127
Alignment explanation
Indices: 35773524--35773889 Score: 521
Period size: 120 Copynumber: 3.0 Consensus size: 127
35773514 TAAATTATAC
* * * *
35773524 AAATTCATATAACAAAATTTATTAGTAATAATTATTTTAAATTTTATTAAATCATATATTTTAAT
1 AAATTCATATAAGAATATTTATTATTAAGAATT-TTTTAAA-TTTATTAAAT-ATATATTTTAAT
35773589 TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
63 TAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
*
35773654 AAATTCATATAAGAATATTTATTATTAAGAA--TTTT--A-TTA--AATTATATATTTTAATTAA
1 AAATTCATATAAGAATATTTATTATTAAGAATTTTTTAAATTTATTAAATATATATTTTAATTAA
35773712 AATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
66 AATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
*
35773774 AAATTCATATAAGAATATTGATTATTAAG--------AAATTTATTAAATTATATATTTTAATTA
1 AAATTCATATAAGAATATTTATTATTAAGAATTTTTTAAATTTATTAAA-TATATATTTTAATTA
35773831 AAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATATTATGATTT
65 AAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATGATTT
35773890 AATTAAAATA
Statistics
Matches: 222, Mismatches: 7, Indels: 24
0.88 0.03 0.09
Matches are distributed among these distances:
116 1 0.00
117 3 0.01
119 2 0.01
120 176 0.79
121 5 0.02
123 3 0.01
125 1 0.00
127 4 0.02
130 27 0.12
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (127 bp):
AAATTCATATAAGAATATTTATTATTAAGAATTTTTTAAATTTATTAAATATATATTTTAATTAA
AATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGT
Found at i:35773701 original size:61 final size:61
Alignment explanation
Indices: 35773636--35773823 Score: 188
Period size: 61 Copynumber: 3.1 Consensus size: 61
35773626 TTATAGTATC
35773636 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATT
* * ** * * * * * * * *
35773697 ATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCA-AATT-A-TATTTTA-TAGTATC
1 ATATATTATGATTTTAGTAAATTCATATAAGAA-TATTT-ATTATTAAGAATTTTATTA-AATT
* *
35773756 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAAATTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATT
35773817 ATATATT
1 ATATATT
35773824 TTAATTAAAA
Statistics
Matches: 93, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
58 3 0.03
59 33 0.35
60 14 0.15
61 40 0.43
62 3 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATT
Found at i:35773712 original size:18 final size:17
Alignment explanation
Indices: 35773684--35773718 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35773674 ATTATTAAGA
*
35773684 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35773701 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35773719 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35780231 original size:14 final size:15
Alignment explanation
Indices: 35780209--35780285 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
35780199 CAATCAAACA
35780209 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
35780223 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
35780238 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
35780258 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
**
35780272 CTGGAAAA-CATTTT
1 CCAGAAAATCATTTT
35780286 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:35780250 original size:20 final size:20
Alignment explanation
Indices: 35780225--35780264 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35780215 AATATTTTCC
*
35780225 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
35780245 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
35780265 TCATTTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:35780700 original size:18 final size:16
Alignment explanation
Indices: 35780690--35780734 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
35780680 TTTGAGTTGA
35780690 GAAAATTATTTAATTG
1 GAAAATTATTTAATTG
*
35780706 GAAAATTAATTAATT-
1 GAAAATTATTTAATTG
35780721 -AAAATTAATTTAAT
1 GAAAATT-ATTTAAT
35780735 AAATAATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (16 bp):
GAAAATTATTTAATTG
Found at i:35786359 original size:20 final size:20
Alignment explanation
Indices: 35786321--35786359 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35786311 TATAGTTGAA
*
35786321 ATAGTATTTTATGCTTTTTC
1 ATAGTATTTTATGATTTTTC
35786341 ATAGT-TTTTATGATATTTT
1 ATAGTATTTTATGAT-TTTT
35786360 GATACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (20 bp):
ATAGTATTTTATGATTTTTC
Found at i:35787695 original size:9 final size:9
Alignment explanation
Indices: 35787678--35787714 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
35787668 TGAGTTTTCG
35787678 AATTCGAAT
1 AATTCGAAT
*
35787687 AACTCGAAT
1 AATTCGAAT
*
35787696 AATTCAAAT
1 AATTCGAAT
35787705 AATTCGAAT
1 AATTCGAAT
35787714 A
1 A
35787715 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35787968 original size:30 final size:31
Alignment explanation
Indices: 35787934--35787993 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
35787924 AAACCTTTTA
*
35787934 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCATCCCAC
* *
35787964 TTTTCCCCTAAAACTTTTATTCCCATCCCA
1 TTTTCCCCCAAAACTTTTACTCCCATCCCA
35787994 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCATCCCAC
Found at i:35792445 original size:12 final size:13
Alignment explanation
Indices: 35792430--35792458 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35792420 TTTTATAAGA
35792430 AAATAAAT-AAAT
1 AAATAAATAAAAT
35792442 AAATAAATAAAAT
1 AAATAAATAAAAT
35792455 AAAT
1 AAAT
35792459 CAAACACGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:35795757 original size:40 final size:40
Alignment explanation
Indices: 35795666--35795888 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
35795656 TCCTCGTTCA
* * * * *
35795666 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
35795705 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGTACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
35795745 AATGCCTTCGGGACTTAGCCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
35795785 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
** * * * *
35795825 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
35795865 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
35795889 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
39 35 0.23
40 112 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:35795820 original size:80 final size:79
Alignment explanation
Indices: 35795664--35795888 Score: 263
Period size: 80 Copynumber: 2.8 Consensus size: 79
35795654 GCTCCTCGTT
* * * * *
35795664 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACGTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
* *
35795729 TTTAACAACTCGTA
66 ATTAACAACTCGCA
* *
35795743 CGAATGCCTTCGGGACTTAGCCCGGCTTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
*
35795808 AATTAATAACTCGCA
65 AATTAACAACTCGCA
* * * * * * *
35795823 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG
35795887 GA
64 GA
35795889 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
79 39 0.31
80 81 0.65
81 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
ATTAACAACTCGCA
Done.