Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 155 of 218
Found at i:47125578 original size:16 final size:16
Alignment explanation
Indices: 47125559--47125591 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
47125549 GATTTGATAA
47125559 TATGTCTTTTTGCATT
1 TATGTCTTTTTGCATT
*
47125575 TATGTCTTTTTGTATT
1 TATGTCTTTTTGCATT
47125591 T
1 T
47125592 TGTATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.67
Consensus pattern (16 bp):
TATGTCTTTTTGCATT
Found at i:47125594 original size:7 final size:7
Alignment explanation
Indices: 47125582--47125611 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
47125572 ATTTATGTCT
47125582 TTTTGTA
1 TTTTGTA
47125589 TTTTGTA
1 TTTTGTA
47125596 TTTTGTA
1 TTTTGTA
47125603 TTTTGTA
1 TTTTGTA
47125610 TT
1 TT
47125612 CAGCATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (7 bp):
TTTTGTA
Found at i:47126117 original size:8 final size:8
Alignment explanation
Indices: 47126104--47126155 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
47126094 GTTGAACTAG
47126104 ATTTTATA
1 ATTTTATA
47126112 ATTTTATA
1 ATTTTATA
47126120 ATTTTATA
1 ATTTTATA
47126128 ATTTT-TAA
1 ATTTTAT-A
47126136 ATGTTTATGA
1 AT-TTTAT-A
*
47126146 ATTTTTTA
1 ATTTTATA
47126154 AT
1 AT
47126156 AATTGACTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 1 0.03
8 27 0.69
9 7 0.18
10 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (8 bp):
ATTTTATA
Found at i:47128078 original size:39 final size:39
Alignment explanation
Indices: 47128032--47128116 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
47128022 ATAGAAATAT
*
47128032 GGTGATTATTCGAGCTATATGCTTAGCAGGCTGTGTGCC
1 GGTGATTATTCGAGCTATATGCCTAGCAGGCTGTGTGCC
* *
47128071 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
1 GGTGATTATTCGAGCTATATGCCTAGCAGGCTGTGTGCC
47128110 GGTGATT
1 GGTGATT
47128117 GACTCATACT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.33
Consensus pattern (39 bp):
GGTGATTATTCGAGCTATATGCCTAGCAGGCTGTGTGCC
Found at i:47130172 original size:25 final size:24
Alignment explanation
Indices: 47130121--47130212 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 24
47130111 ACACACCACA
* *
47130121 GCTCTTATGAGCATCCCGATATTTG
1 GCTCTTATGAGCTTCCCGAT-TATG
*
47130146 GCTCTTACGAGCTTCCCGATTGATG
1 GCTCTTATGAGCTTCCCGATT-ATG
* * *
47130171 GCTATTTTGAACTTCCCGATTTATG
1 GCTCTTATGAGCTTCCCGA-TTATG
*
47130196 GCT-TGCATGAGCTTCCC
1 GCTCT-TATGAGCTTCCC
47130213 AATATACAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 2 0.04
25 50 0.93
26 2 0.04
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGATTATG
Found at i:47130299 original size:25 final size:25
Alignment explanation
Indices: 47130228--47130299 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
47130218 ACAACTCGAT
*
47130228 AGAGCTTCCCGTTACTTAGCTCACA
1 AGAGCTTCCCGTTACATAGCTCACA
* * * * *
47130253 TGAGCTTCCTGTTATATGGCTCAGA
1 AGAGCTTCCCGTTACATAGCTCACA
47130278 AGAGCTTCCCGTTTACAT-GCTC
1 AGAGCTTCCCG-TTACATAGCTC
47130300 GTATGAGCAC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 32 0.86
26 5 0.14
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (25 bp):
AGAGCTTCCCGTTACATAGCTCACA
Found at i:47130433 original size:21 final size:22
Alignment explanation
Indices: 47130400--47130441 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
47130390 CAATGGGCAA
*
47130400 AGTTCTGATATGAGA-TATTATG
1 AGTTCTGAAATGA-ACTATTATG
47130422 AGTT-TGAAATGAACTATTAT
1 AGTTCTGAAATGAACTATTAT
47130442 CCATATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 1 0.06
21 13 0.72
22 4 0.22
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (22 bp):
AGTTCTGAAATGAACTATTATG
Found at i:47131178 original size:42 final size:42
Alignment explanation
Indices: 47131110--47131222 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 42
47131100 TATTTTTGTC
* * *
47131110 CACACGGGCAAAGACACAGGCATGTGTCTCAGTCGTGTGTGA
1 CACACGGGCAGAGACACGGGCGTGTGTCTCAGTCGTGTGTGA
* *
47131152 CACACGAGCAGAGACACGGGCGTGTGTCTCAGTCTTGTGTGA
1 CACACGGGCAGAGACACGGGCGTGTGTCTCAGTCGTGTGTGA
* *
47131194 CACACGGGCAAGTGACACGGCCGTGTGTC
1 CACACGGGC-AGAGACACGGGCGTGTGTC
47131223 CCCTGTATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
42 45 0.73
43 17 0.27
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19
Consensus pattern (42 bp):
CACACGGGCAGAGACACGGGCGTGTGTCTCAGTCGTGTGTGA
Found at i:47154401 original size:18 final size:18
Alignment explanation
Indices: 47154378--47154415 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
47154368 TGTTAGGTGC
*
47154378 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
47154396 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
47154414 GT
1 GT
47154416 TTCATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:47154691 original size:21 final size:21
Alignment explanation
Indices: 47154667--47154711 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
47154657 CCCACAACCA
47154667 GAACAACCACAACCCCCGCCG
1 GAACAACCACAACCCCCGCCG
47154688 GAACAACCACAACCCCCGCCG
1 GAACAACCACAACCCCCGCCG
47154709 GAA
1 GAA
47154712 GCTGAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.49, G:0.16, T:0.00
Consensus pattern (21 bp):
GAACAACCACAACCCCCGCCG
Found at i:47158286 original size:126 final size:126
Alignment explanation
Indices: 47157951--47158347 Score: 593
Period size: 126 Copynumber: 3.2 Consensus size: 126
47157941 TAAGGCCAAA
*
47157951 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
47158016 ATCCTGCTTGAAGCGTTTTTGACACTA-TTTTTTCAGAACCGTCTTTTCAAAATTATTTTTT
66 ATCCTACTTGAAGCGTTTTTGACACTACTTTTTT-AGAACCGTCTTCTCAAAATTATTTTTT
* * * ** *
47158077 CAAGAACCACTGTAGAAAAAGAGTGTTCATGTGGTAGC-TTTTTCAGTAATTTTGCTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
47158141 ATCCTACTTGAAGTGTTTTTGAAACTACTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTACTTGAAGCGTTTTTGACACTACTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
*
47158202 CAAGAACTATTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
47158267 ATCCTACTTCAAGCGTTTTTGACATTACCTTTTTAGAACCGTCTTCTCAAAATTAATTTTT
66 ATCCTACTTGAAGCGTTTTTGACACTACTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
* *
47158328 C-TGAAACTATTGTAGAAAAA
1 CAAG-AACTACTGTAGAAAAA
47158348 AAACAAAATT
Statistics
Matches: 243, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
125 107 0.44
126 136 0.56
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (126 bp):
CAAGAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCCTACTTGAAGCGTTTTTGACACTACTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:47158451 original size:34 final size:33
Alignment explanation
Indices: 47158420--47158534 Score: 144
Period size: 34 Copynumber: 3.5 Consensus size: 33
47158410 TTAAAAAAAA
47158420 CTAAACCCTAATTTAATTAATTTTCTTAAAAACT
1 CTAAACCCTAATTTAATTAATTTT-TTAAAAACT
* * *
47158454 CTAAACCCTCATTTAATTAATTTATTT-TAAACC
1 CTAAACCCTAATTTAATTAATTT-TTTAAAAACT
*
47158487 CTTAAAACCTAATTTAATT-ATTTTTTAAAAACT
1 C-TAAACCCTAATTTAATTAATTTTTTAAAAACT
*
47158520 CTAAACTCTAATTTA
1 CTAAACCCTAATTTA
47158535 TTTTTTAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
32 15 0.22
33 14 0.20
34 39 0.57
35 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (33 bp):
CTAAACCCTAATTTAATTAATTTTTTAAAAACT
Found at i:47158625 original size:22 final size:23
Alignment explanation
Indices: 47158586--47158631 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
47158576 TTATTTTAAC
*
47158586 AAAACCCTAACACTAC-AACCCT
1 AAAACCCTAACACCACAAACCCT
47158608 AAAACCCTAA-ACCCACAAACCCT
1 AAAACCCTAACA-CCACAAACCCT
47158631 A
1 A
47158632 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 13 0.62
23 7 0.33
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (23 bp):
AAAACCCTAACACCACAAACCCT
Found at i:47160061 original size:111 final size:111
Alignment explanation
Indices: 47159867--47160088 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
47159857 TTAATTTATT
47159867 TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTTATTAATTAA
1 TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTTATTAATTAA
47159932 TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA
66 TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA
*
47159978 TCAACAAAGCCCCTTAAAATTAATTATTTGATGGTCATCATTCCTTAATTTTTTTTATTAATTAA
1 TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTTATTAATTAA
47160043 TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA
66 TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA
47160089 CAAACTGAAT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.46
Consensus pattern (111 bp):
TCAACAAAGCCCCTTAAAATTAATTATTTAATGGTCATCATTCCTTAATTTTTTTTATTAATTAA
TGTTCAGTGATACAAATCTGTTTCTTATTACATTTTATATAATGTA
Found at i:47165960 original size:21 final size:21
Alignment explanation
Indices: 47165934--47166005 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
47165924 ATTGTAGGAA
47165934 AATAATTATTGAGTGAAGAAT
1 AATAATTATTGAGTGAAGAAT
* * **
47165955 AATAATTGAAT-ATTGTTGGAA-
1 AATAATT-ATTGAGTG-AAGAAT
*
47165976 AATAATTATTGAGTGATGAAT
1 AATAATTATTGAGTGAAGAAT
*
47165997 GATAATTAT
1 AATAATTAT
47166006 ATCTCTTGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
20 5 0.13
21 28 0.74
22 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (21 bp):
AATAATTATTGAGTGAAGAAT
Found at i:47165983 original size:42 final size:42
Alignment explanation
Indices: 47165924--47166003 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
47165914 CATGTAGGGG
47165924 ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATTGAAT
1 ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATTGAAT
* * *
47165966 ATTGTTGGAAAATAATTATTGAGTGATGAATGATAATT
1 ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATT
47166004 ATATCTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (42 bp):
ATTGTAGGAAAATAATTATTGAGTGAAGAATAATAATTGAAT
Found at i:47174000 original size:16 final size:16
Alignment explanation
Indices: 47173979--47174016 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
47173969 TTATTTAAAA
**
47173979 AAATATTATTTATTTT
1 AAATATTATTTACATT
47173995 AAATATTATTTACATT
1 AAATATTATTTACATT
47174011 AAATAT
1 AAATAT
47174017 ATTAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTATTTACATT
Found at i:47176812 original size:18 final size:19
Alignment explanation
Indices: 47176785--47176849 Score: 51
Period size: 21 Copynumber: 3.3 Consensus size: 19
47176775 AGTAAATAAT
*
47176785 TAATAGTAAAGTA-AGTAA
1 TAATAATAAAGTACAGTAA
* * *
47176803 TAATAATAAATATAATACTAA
1 TAATAATAAA-GT-ACAGTAA
47176824 TAATAATAATAGTAGCAGTAA
1 TAATAATAA-AGTA-CAGTAA
47176845 TAATA
1 TAATA
47176850 TAATAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 9 0.25
19 1 0.03
20 2 0.06
21 23 0.64
22 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (19 bp):
TAATAATAAAGTACAGTAA
Found at i:47178632 original size:87 final size:87
Alignment explanation
Indices: 47178541--47178961 Score: 307
Period size: 87 Copynumber: 4.8 Consensus size: 87
47178531 GCCGTCTTCG
* *
47178541 ATCTGCTCCACTACTTCTTAGGGAGATAGGATCTAACATCTTTAG-CCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATC-TTAGACCTGCTCCACTACTGCTTA
**
47178605 GGGAGATAGGACTGGTGGCTTAA
65 GGGAGATAGGACTGCCGGCTTAA
* * * * * *
47178628 ATCTGCTTCACTACTGCTTAGGAAGAT-GAGAT-TCGCCGTCTTCGATCTGCTCCACTACTGCTT
1 ATCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-ACCATCTTAGACCTGCTCCACTACTGCTT
* * * ** **
47178691 AGGGAGATAAGATTTACCATCTTCG
64 AGGGAGATAGGA-CTGCCGGCTTAA
* * * ***** * * * *
47178716 ACCTGCTCCACTACTGCTTAGAGAGAGAGGA-CTGGTGGCTTAAATCTACTTCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTAGACCTGCTCCACTACTGCTTAG
* * * **
47178780 GAAGAT-GAGATTCGCCGTCTTCG
66 GGAGATAG-GACT-GCCGGCTTAA
* *
47178803 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTAGACCTGCTCCACTACTGCTTAG
**
47178868 GGAGATAGGACTGGTGGCTTAA
66 GGAGATAGGACTGCCGGCTTAA
* * * * * * * *
47178890 ATCTACTTCACTACTGCTTAGGAAGAT-GAGAT-TCGCCGTCTTCGATCTGCTCCACTATTGCTT
1 ATCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-ACCATCTTAGACCTGCTCCACTACTGCTT
47178953 AGGGAGATA
64 AGGGAGATA
47178962 AGATCTACCA
Statistics
Matches: 260, Mismatches: 62, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
86 8 0.03
87 190 0.73
88 60 0.23
89 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTAGACCTGCTCCACTACTGCTTAG
GGAGATAGGACTGCCGGCTTAA
Found at i:47178692 original size:131 final size:131
Alignment explanation
Indices: 47178456--47178989 Score: 926
Period size: 131 Copynumber: 4.1 Consensus size: 131
47178446 TTTTTTCAGT
* * * *
47178456 CTGCTCCGCTACTGCTTAGGGAGATAAGACTGGTGGCTTAAATCTGCTTCACTACTACTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
* * * *
47178521 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTTCTTAGGGAGATAGGATCTAACATCTT-TA
66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
47178585 GC
131 -C
*
47178587 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
*
47178652 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTACCATCTTCGA
66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
47178717 C
131 C
* *
47178718 CTGCTCCACTACTGCTTAGAGAGAGAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
47178783 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
47178848 C
131 C
47178849 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
*
47178914 GATGAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTACCATCTTCGA
66 GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
47178979 C
131 C
*
47178980 CTGTTCCACT
1 CTGCTCCACT
47178990 GTAACCTTAG
Statistics
Matches: 386, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
131 385 1.00
132 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
GATGAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
C
Found at i:47178716 original size:175 final size:175
Alignment explanation
Indices: 47178497--47178874 Score: 402
Period size: 175 Copynumber: 2.2 Consensus size: 175
47178487 GGTGGCTTAA
* * * * * * * *
47178497 ATCTGCTTCACTACTACTTAGGAAGATGAGATTCGCCGTCTTCGATCTGCTCCACTACTTCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCACCATCTTCGACCTGCTCCACTACTGCTTAG
* * * * * * * **
47178562 GGAGATAGGATCTAACATCTTTAGCCTGCTCCACTACTGCTTAGGGAGAT-AGGACT-GGTGGCT
66 AGAGAGAGGA-CTAACAGCTTAAACCTACTCCACTACTGCTTAGGAAGATGA-GACTCGCCGGCT
* * * *
47178625 TAAATCTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCG
129 TAAATCTGCTCCACTACTGCTTAGGAAGATAAGATCT-ACCATCTTCG
*
47178672 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTTACCATCTTCGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCACCATCTTCGACCTGCTCCACTACTGCTTAG
**** * * * * *
47178737 AGAGAGAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATGAGATTCGCCGTCTTC
66 AGAGAGAGGACTAACAGCTTAAACCTACTCCACTACTGCTTAGGAAGATGAGACTCGCCGGCTTA
* *
47178802 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCG
131 AATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACCATCTTCG
*
47178847 ACCTGCTCCACTACTGCTTAGGGAGATA
1 ATCTGCTCCACTACTGCTTAGGGAGATA
47178875 GGACTGGTGG
Statistics
Matches: 166, Mismatches: 34, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
174 31 0.19
175 134 0.81
176 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.30
Consensus pattern (175 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATTCACCATCTTCGACCTGCTCCACTACTGCTTAG
AGAGAGAGGACTAACAGCTTAAACCTACTCCACTACTGCTTAGGAAGATGAGACTCGCCGGCTTA
AATCTGCTCCACTACTGCTTAGGAAGATAAGATCTACCATCTTCG
Found at i:47178976 original size:44 final size:44
Alignment explanation
Indices: 47178455--47179012 Score: 427
Period size: 44 Copynumber: 12.8 Consensus size: 44
47178445 TTTTTTTCAG
* ** * **
47178455 TCTGCTCCGCTACTGCTTAGGGAGATAAGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * * *
47178498 TCTGCTTCACTACTACTTAGGAAGATGAGAT-TCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA
* * ** * *
47178542 TCTGCTCCACTACTTCTTAGGGAGATAGGATCTAACATCTT-TA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * ** * **
47178585 GCCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * *
47178629 TCTGCTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA
* * *
47178673 TCTGCTCCACTACTGCTTAGGGAGATAAGATTTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * * * ** * **
47178717 CCTGCTCCACTACTGCTTAGAGAGAGAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * * *
47178760 TCTACTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA
* *
47178804 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * ** * **
47178848 CCTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* * * *
47178891 TCTACTTCACTACTGCTTAGGAAGATGAGAT-TCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GCCGTCTTCGA
* * *
47178935 TCTGCTCCACTATTGCTTAGGGAGATAAGATCTACCATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
* *
47178979 CCTGTTCCACTGTAAC--CTTAGGGAGATAAGATCT
1 TCTGCTCCAC--T-ACTGCTTAGGGAGATAAGATCT
47179013 AAAATTCTTC
Statistics
Matches: 395, Mismatches: 103, Indels: 32
0.75 0.19 0.06
Matches are distributed among these distances:
43 117 0.30
44 254 0.64
45 22 0.06
46 1 0.00
47 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (44 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCCGTCTTCGA
Found at i:47179007 original size:45 final size:45
Alignment explanation
Indices: 47178953--47179369 Score: 294
Period size: 46 Copynumber: 9.3 Consensus size: 45
47178943 ACTATTGCTT
* ** ** *
47178953 AGGGAGATAAGATCTACCA-TCTTCGACCTGTTCCACTGTAACCTT
1 AGGGAGATAAGATCTA-AATTCTTCGGTCTACTCCACTGTAACCTC
47178998 AGGGAGATAAGATCTAAAATTCTTCGGTCTACTCCACTGTAACCTC
1 AGGGAGATAAGATCT-AAATTCTTCGGTCTACTCCACTGTAACCTC
*
47179044 AAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTC
1 AGGGAGATAAGATCT-AAATTCTTCGGTCTACTCCACTGTAACCTC
** ** ** * *
47179090 AGGGAGATAAGATCCTTTATT-TT-AATCCGCTCCACTGTAGCTTC
1 AGGGAGATAAGAT-CTAAATTCTTCGGTCTACTCCACTGTAACCTC
* * * * ** *
47179134 AGGGAGATAGGAT-T-ACTAGCTCCAATCTGCTCCACTGTAACCTC
1 AGGGAGATAAGATCTAAAT-TCTTCGGTCTACTCCACTGTAACCTC
* * *
47179178 AGGGAGATAAGATCTGAAATTCTTTGGTCTACTCCACAGTAATCTC
1 AGGGAGATAAGATCT-AAATTCTTCGGTCTACTCCACTGTAACCTC
** * *** * *
47179224 AGGGAGATAAGA-CTTGCA-TATTCAACCTGCTCCACTGTAACTTC
1 AGGGAGATAAGATC-TAAATTCTTCGGTCTACTCCACTGTAACCTC
* ** * * * * * *
47179268 AGGGAGATAAGGT-T-TGTGGCTTTGATCTGCTCCTCTGTAATCTC
1 AGGGAGATAAGATCTAAAT-TCTTCGGTCTACTCCACTGTAACCTC
* *
47179312 AGGGAGATAAGATCTGAAATTTTTCGGTCTACTGCACTGTAACCTC
1 AGGGAGATAAGATCT-AAATTCTTCGGTCTACTCCACTGTAACCTC
47179358 AGGGAGATAAGA
1 AGGGAGATAAGA
47179370 CTTGCATATT
Statistics
Matches: 288, Mismatches: 68, Indels: 31
0.74 0.18 0.08
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 2 0.01
44 115 0.40
45 22 0.08
46 142 0.49
47 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (45 bp):
AGGGAGATAAGATCTAAATTCTTCGGTCTACTCCACTGTAACCTC
Found at i:47179039 original size:46 final size:46
Alignment explanation
Indices: 47178928--47179597 Score: 350
Period size: 44 Copynumber: 15.0 Consensus size: 46
47178918 AGATTCGCCG
* ** * **
47178928 TCTTCGATCTGCTCCACTAT-TGCTTAGGGAGATAAGATCTACCA-
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * *
47178972 TCTTCGACCTGTTCCACTGTAACCTTAGGGAGATAAGATCTAAAAT
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * *
47179018 TCTTCGGTCTACTCCACTGTAACCTCAAGGAGATAAGATCTGAAAT
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * **
47179064 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGATCCT-TTAT
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTAAAAT
* * * * * **
47179110 T-TT-AATCCGCTCCACTGTAGCTTCAGGGAGATAGGAT-TACTA-
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * *
47179152 GCTCCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * * * ***
47179198 TCTTTGGTCTACTCCACAGTAATCTCAGGGAGATAAGA-CTTGCA-
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * * * **
47179242 TATTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGT-T--TGT
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * * *
47179285 GGCTTTGATCTGCTCCTCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * * ***
47179332 TTTTCGGTCTACTGCACTGTAACCTCAGGGAGATAAGA-CTTGCA-
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * * * * **
47179376 TATTCAACCTAC-CCTACTGTAACTTCAGGGAGATAAGGT-T--TGT
1 TCTTCGATCTGCTCC-ACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * * *
47179419 GGCTTCGATCTGCTCCTCTGTAATCTCAGGGAAATAAGATCTGAAAT
1 -TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * ***
47179466 TCTTCGACCTGCTCCAC--T-ACTGCTTAGGGAGATAGGA--TAGTGT
1 TCTTCGATCTGCTCCACTGTAAC--CTCAGGGAGATAAGATCTAAAAT
* * * *
47179509 CCTT-GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT---CT
1 TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
* * * *
47179551 GGCGTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 -TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
47179598 ATTCACTGAT
Statistics
Matches: 468, Mismatches: 124, Indels: 65
0.71 0.19 0.10
Matches are distributed among these distances:
42 12 0.03
43 25 0.05
44 224 0.48
45 48 0.10
46 154 0.33
47 5 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTTCGATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTAAAAT
Found at i:47179194 original size:134 final size:134
Alignment explanation
Indices: 47179029--47179597 Score: 638
Period size: 134 Copynumber: 4.3 Consensus size: 134
47179019 CTTCGGTCTA
*
47179029 CTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGG
* * * * *
47179094 AGATAAGATCCTT-TAT-TTTAATCC-GCTCCACTGTAGCTTCAGGGAGAT-AGGATTACTAGCT
66 AGATAAGA--CTTGCATATTCAA-CCTGCTCCACTGTAACTTCAGGGAGATAAGG-TTTCTGGCT
*
47179155 CCAATCTG
127 TCAATCTG
* * *
47179163 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTACTCCACAGTAATCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGG
* **
47179228 AGATAAGACTTGCATATTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTTGA
66 AGATAAGACTTGCATATTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTCTGGCTTCAA
47179293 TCTG
131 TCTG
* * * *
47179297 CTCCTCTGTAATCTCAGGGAGATAAGATCTGAAATTTTTCGGTCTACTGCACTGTAACCTCAGGG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGG
* * *
47179362 AGATAAGACTTGCATATTCAACCTAC-CCTACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCG
66 AGATAAGACTTGCATATTCAACCTGCTCC-ACTGTAACTTCAGGGAGATAAGGTTTCTGGCTTCA
47179426 ATCTG
130 ATCTG
* * * ** * *
47179431 CTCCTCTGTAATCTCAGGGAAATAAGATCTGAAATTCTTCGACCTGCTCCAC--T-ACTGCTTAG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAAC--CTCAG
* * ** * * * * * * *
47179493 GGAGATAGGA-TAGTGTCCTT-GATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCG
64 GGAGATAAGACTTGCAT-ATTCAACCTGCTCCACTGTAACT-TCAGGGAGATAAGGTTTCTGGCT
47179555 TCAATCTG
127 TCAATCTG
47179563 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
47179598 ATTCACTGAT
Statistics
Matches: 379, Mismatches: 46, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
131 3 0.01
132 75 0.20
133 23 0.06
134 275 0.73
135 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (134 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGG
AGATAAGACTTGCATATTCAACCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTCTGGCTTCAA
TCTG
Found at i:47180834 original size:7 final size:7
Alignment explanation
Indices: 47180822--47180873 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
47180812 GCCTCTCCAT
47180822 TTTTTCA
1 TTTTTCA
47180829 TTTTTCA
1 TTTTTCA
47180836 -TTTT-A
1 TTTTTCA
47180841 TTTTTTCA
1 -TTTTTCA
*
47180849 ATTTTCA
1 TTTTTCA
*
47180856 -TTCTCA
1 TTTTTCA
47180862 TTTTTCA
1 TTTTTCA
47180869 TTTTT
1 TTTTT
47180874 TCAGAGTGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 1 0.03
6 9 0.24
7 27 0.71
8 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCA
Found at i:47180843 original size:20 final size:21
Alignment explanation
Indices: 47180819--47180873 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
47180809 TTAGCCTCTC
47180819 CATTTTTTCATTTTTCATT-T
1 CATTTTTTCATTTTTCATTCT
* *
47180839 TATTTTTTCAATTTTCATTCT
1 CATTTTTTCATTTTTCATTCT
47180860 CA-TTTTTCATTTTT
1 CATTTTTTCATTTTT
47180874 TCAGAGTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.16, C:0.15, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTTCATTTTTCATTCT
Found at i:47186549 original size:18 final size:19
Alignment explanation
Indices: 47186522--47186586 Score: 51
Period size: 21 Copynumber: 3.3 Consensus size: 19
47186512 AGTAAATAAT
*
47186522 TAATAGTAAAGTA-AGTAA
1 TAATAATAAAGTACAGTAA
* * *
47186540 TAATAATAAATATAATACTAA
1 TAATAATAAA-GT-ACAGTAA
47186561 TAATAATAATAGTAGCAGTAA
1 TAATAATAA-AGTA-CAGTAA
47186582 TAATA
1 TAATA
47186587 TAATAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 9 0.25
19 1 0.03
20 2 0.06
21 23 0.64
22 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (19 bp):
TAATAATAAAGTACAGTAA
Found at i:47190472 original size:91 final size:89
Alignment explanation
Indices: 47190329--47190551 Score: 281
Period size: 91 Copynumber: 2.5 Consensus size: 89
47190319 TTAAGGGTAT
* * * *
47190329 AAAAAGCCCTTAAACTTTTTCAAAAAAAGCAATTAAGCCCTTCCTTTTTTTTTAT-ATTCAATTG
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTT-TCACTCAATTG
47190393 AGCACTTAAACTTTCAAAATACT-TC
65 AGCACTTAAACTTTCAAAAT-CTATC
*
47190418 AAAAATGCCCTCAAACTTCTTCAAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTTCACTCAATT
1 AAAAA-GCCCTCAAACTTTTTC-AAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTTCACTCAATT
* * * *
47190483 GGGTACTTGAACTTTCAAAATGTATC
64 GAGCACTTAAACTTTCAAAATCTATC
* *
47190509 AAAAAGACCCTCAAAATTTTTC-AAAAAATCAATTAAGCCCCTG
1 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTG
47190552 TTCTTATTAA
Statistics
Matches: 117, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
89 25 0.21
90 17 0.15
91 75 0.64
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.33
Consensus pattern (89 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTTTTTTTCACTCAATTGA
GCACTTAAACTTTCAAAATCTATC
Found at i:47190602 original size:19 final size:19
Alignment explanation
Indices: 47190580--47190624 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
47190570 AAAAAATTAG
*
47190580 AAAATATTAAATTTTAGA-A
1 AAAATATTAAATATTA-ATA
47190599 AAAATATTAAATATTAATA
1 AAAATATTAAATATTAATA
47190618 AAAATAT
1 AAAATAT
47190625 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATATTAAATATTAATA
Found at i:47190927 original size:10 final size:10
Alignment explanation
Indices: 47190912--47190977 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
47190902 TTCTTACGAC
47190912 TTTATAAAAT
1 TTTATAAAAT
*
47190922 TTTATAATAT
1 TTTATAAAAT
*
47190932 TATTAT--ATT
1 T-TTATAAAAT
*
47190941 TTTAT-ATAT
1 TTTATAAAAT
47190950 TTTAT-AAAT
1 TTTATAAAAT
* *
47190959 TTTTTACAAT
1 TTTATAAAAT
47190969 TTTATAAAA
1 TTTATAAAA
47190978 AAAATACAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
8 4 0.09
9 15 0.35
10 20 0.47
11 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:47190960 original size:19 final size:19
Alignment explanation
Indices: 47190912--47190976 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
47190902 TTCTTACGAC
*
47190912 TTTATAAAATTTTATAATAT
1 TTTATAAATTTTTAT-ATAT
47190932 TATTAT--ATTTTTATATAT
1 T-TTATAAATTTTTATATAT
*
47190950 TTTATAAATTTTT-TACAAT
1 TTTATAAATTTTTATA-TAT
47190969 TTTATAAA
1 TTTATAAA
47190977 AAAAATACAG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 4 0.10
18 7 0.18
19 23 0.59
20 1 0.03
21 4 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATAAATTTTTATATAT
Found at i:47191003 original size:10 final size:10
Alignment explanation
Indices: 47190988--47191039 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
47190978 AAAATACAGT
47190988 TTTTTTTATA
1 TTTTTTTATA
47190998 TTTTTTTACTA
1 TTTTTTTA-TA
47191009 --TTTTTATA
1 TTTTTTTATA
*
47191017 TTTTTTTCTA
1 TTTTTTTATA
* *
47191027 ATTTTTAATA
1 TTTTTTTATA
47191037 TTT
1 TTT
47191040 GAATTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 24 0.71
11 2 0.06
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:47191014 original size:19 final size:19
Alignment explanation
Indices: 47190990--47191039 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
47190980 AATACAGTTT
47190990 TTTTTATATTTTTTTACT-A
1 TTTTTATATTTTTTT-CTAA
47191009 TTTTTATATTTTTTTCTAA
1 TTTTTATATTTTTTTCTAA
47191028 TTTTTAATATTT
1 TTTTT-ATATTT
47191040 GAATTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.07
19 21 0.72
20 6 0.21
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATATTTTTTTCTAA
Found at i:47193335 original size:20 final size:18
Alignment explanation
Indices: 47193310--47193348 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47193300 GAGCTTCGGT
47193310 TTTAATAATACAACATATTA
1 TTTAAT-ATACAA-ATATTA
*
47193330 TTTAATTTACAAATATTA
1 TTTAATATACAAATATTA
47193348 T
1 T
47193349 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAATATACAAATATTA
Found at i:47193356 original size:19 final size:19
Alignment explanation
Indices: 47193318--47193357 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
47193308 GTTTTAATAA
*
47193318 TACAACATATTATTTAATT
1 TACAACATATTATATAATT
47193337 TACAA-ATATTATATATATT
1 TACAACATATTATATA-ATT
47193356 TA
1 TA
47193358 AGCAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
TACAACATATTATATAATT
Found at i:47193702 original size:19 final size:19
Alignment explanation
Indices: 47193667--47193704 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
47193657 AATATAAAAC
*
47193667 TTTTAACAATAACATATTA
1 TTTTAACAAGAACATATTA
47193686 TTTTAACACAGAA-ATATTA
1 TTTTAACA-AGAACATATTA
47193705 AACTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTTAACAAGAACATATTA
Found at i:47196739 original size:23 final size:23
Alignment explanation
Indices: 47196675--47196740 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
47196665 TCGTTGGCCA
*
47196675 AGTATAAATCATTT-GTAATAAA-T
1 AGTATAAATAATTTAGT--TAAATT
**
47196698 AGTAT--ATAATTTAACTAAATT
1 AGTATAAATAATTTAGTTAAATT
47196719 AGTATAAATAATTTAGTTAAAT
1 AGTATAAATAATTTAGTTAAAT
47196741 ATTTAGTAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 4 0.12
21 12 0.35
23 18 0.53
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (23 bp):
AGTATAAATAATTTAGTTAAATT
Found at i:47196746 original size:12 final size:14
Alignment explanation
Indices: 47196717--47196748 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
47196707 TTTAACTAAA
47196717 TTAGTATAAATAAT
1 TTAGTATAAATAAT
47196731 TTAGT-TAAAT-AT
1 TTAGTATAAATAAT
47196743 TTAGTA
1 TTAGTA
47196749 AGGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 5 0.29
14 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TTAGTATAAATAAT
Found at i:47206909 original size:29 final size:29
Alignment explanation
Indices: 47206876--47206944 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
47206866 AAACCTTATT
47206876 GTTGCGGAAAC-T-TAATTTTAAACAATTGA
1 GTTGCGGAAACATGTAA-TTTAAA-AATTGA
* * *
47206905 TTTGCGAAAACATGTTATTTAAAAATTGA
1 GTTGCGGAAACATGTAATTTAAAAATTGA
47206934 GTTGCGGAAAC
1 GTTGCGGAAAC
47206945 GTAGCGTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 24 0.73
30 7 0.21
31 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (29 bp):
GTTGCGGAAACATGTAATTTAAAAATTGA
Found at i:47207683 original size:32 final size:32
Alignment explanation
Indices: 47207628--47207766 Score: 181
Period size: 32 Copynumber: 4.4 Consensus size: 32
47207618 GAATGGCTAC
* *
47207628 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
47207659 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
47207691 CAGCCATCAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
47207723 AAGCCATTAGTAACGGTAATATGACCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
47207755 AAGCCATCAGTA
1 AAGCCATCAGTA
47207767 GCATCACAAC
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 10 0.11
32 83 0.89
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:47207969 original size:24 final size:24
Alignment explanation
Indices: 47207941--47208013 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
47207931 GCTCAGAATT
* *
47207941 AGTCATGCAAATCGCAGACAAATC
1 AGTCATACAAATCACAGACAAATC
* * *
47207965 AGTCATACTAATTACAGACAATTC
1 AGTCATACAAATCACAGACAAATC
** * *
47207989 AGTCATTTACATCACGGACAAATC
1 AGTCATACAAATCACAGACAAATC
47208013 A
1 A
47208014 ACTATTTACA
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (24 bp):
AGTCATACAAATCACAGACAAATC
Found at i:47208084 original size:27 final size:27
Alignment explanation
Indices: 47208054--47208157 Score: 109
Period size: 27 Copynumber: 3.9 Consensus size: 27
47208044 TTTACCCTCT
47208054 AGGGGCATTACAGTCATTTTACCTTAC
1 AGGGGCATTACAGTCATTTTACCTTAC
* * * *
47208081 AGGGGCATTGCGGTCATTTAACCTTAT
1 AGGGGCATTACAGTCATTTTACCTTAC
* * * *
47208108 GGGGGTATTACAGTTATTTTACCCTAC
1 AGGGGCATTACAGTCATTTTACCTTAC
* * *
47208135 AAGAGCATTATAGTCATTTTACC
1 AGGGGCATTACAGTCATTTTACC
47208158 ATATGAGGGT
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
AGGGGCATTACAGTCATTTTACCTTAC
Found at i:47208151 original size:54 final size:54
Alignment explanation
Indices: 47208055--47208187 Score: 131
Period size: 54 Copynumber: 2.5 Consensus size: 54
47208045 TTACCCTCTA
* * * * * * *
47208055 GGGGCATTACAGTCATTTTACCTTACAGGGGCATTGCGGTCATTTAACCTTATG
1 GGGGTATTACAGTCATTTTACCCTACAAGAGCATTACAGTCATTTAACCATATG
* * *
47208109 GGGGTATTACAGTTATTTTACCCTACAAGAGCATTATAGTCATTTTACCATATG
1 GGGGTATTACAGTCATTTTACCCTACAAGAGCATTACAGTCATTTAACCATATG
* * ***
47208163 AGGGTTTTTTGGTCATTTTACCCTA
1 GGGGTATTACAGTCATTTTACCCTA
47208188 AAAGGGTATT
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (54 bp):
GGGGTATTACAGTCATTTTACCCTACAAGAGCATTACAGTCATTTAACCATATG
Found at i:47208203 original size:27 final size:27
Alignment explanation
Indices: 47208056--47208231 Score: 102
Period size: 27 Copynumber: 6.5 Consensus size: 27
47208046 TACCCTCTAG
* * *
47208056 GGGCATTACAGTCATTTTACCTTACAG
1 GGGCATTACGGTCATTTTACCTTAAAA
* * ***
47208083 GGGCATTGCGGTCATTTAACCTTATGG
1 GGGCATTACGGTCATTTTACCTTAAAA
* * * * *
47208110 GGGTATTACAGTTATTTTACCCTACAA
1 GGGCATTACGGTCATTTTACCTTAAAA
* ** * **
47208137 GAGCATTATAGTCATTTTACCATATGA
1 GGGCATTACGGTCATTTTACCTTAAAA
** ** *
47208164 GGGTTTTTTGGTCATTTTACCCTAAAA
1 GGGCATTACGGTCATTTTACCTTAAAA
* *
47208191 GGGTATTACGGTCGTTTTACCTTATAAA
1 GGGCATTACGGTCATTTTACCTTA-AAA
47208219 -GGCATTACGGTCA
1 GGGCATTACGGTCA
47208232 AACTACAACA
Statistics
Matches: 112, Mismatches: 36, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
27 109 0.97
28 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (27 bp):
GGGCATTACGGTCATTTTACCTTAAAA
Found at i:47209899 original size:51 final size:51
Alignment explanation
Indices: 47209811--47210151 Score: 279
Period size: 51 Copynumber: 6.7 Consensus size: 51
47209801 TGTCGATGAA
* * * *
47209811 CACGTGTGTAGTACTGTGTGTGGAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTAC--TATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * * * **
47209864 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCTA-AAAGCTTCGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATT-G-GT
* * * * *
47209915 CACGTGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTA-CGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATTGGT
* * * * * *
47209966 TACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA--TATTGGT
* *
47210017 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGATAAATA-TTGGT
* * * *
47210067 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ACTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
*
47210116 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
47210152 TCGAATGATA
Statistics
Matches: 231, Mismatches: 45, Indels: 28
0.76 0.15 0.09
Matches are distributed among these distances:
49 38 0.16
50 53 0.23
51 123 0.53
52 4 0.02
53 13 0.06
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:47209989 original size:102 final size:101
Alignment explanation
Indices: 47209811--47210154 Score: 385
Period size: 102 Copynumber: 3.4 Consensus size: 101
47209801 TGTCGATGAA
* * * *
47209811 CACGTGTGTAGTACTGTGTGTGGAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAG
1 CACGTATGTAGTAC--TATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAG
47209875 TACTAAGTGAAGGCTACTATGTGTACCTAAAAGCTTCGAG
63 TACTAAGTGAAGGCTACTATGTGTACCTAAAAGCTT-GAG
* * * * *
47209915 CACGTGTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTACGGTTACATGTGTAGTAC
1 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
* * *
47209980 TAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTGTACCTAAAAGC-TTGAG
* * * *
47210016 TCACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGT
1 -CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGT
* * * * *
47210079 ACTATGTGAAGGCTACTACGTGAACTGTAAAA-C-TGAT
64 ACTAAGTGAAGGCTACTATGTGTAC-CTAAAAGCTTGAG
47210116 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCG
47210155 AATGATAAAA
Statistics
Matches: 206, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
99 36 0.17
100 2 0.01
101 38 0.18
102 113 0.55
103 3 0.01
104 14 0.07
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (101 bp):
CACGTATGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCTAAAAGCTTGAG
Found at i:47217455 original size:36 final size:35
Alignment explanation
Indices: 47217398--47217626 Score: 161
Period size: 36 Copynumber: 6.6 Consensus size: 35
47217388 CTTAGACGTA
*
47217398 TCTATTCCAA-TTTTTTTAAGGTTGCCTTAGAAGTG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGAAG-G
** *
47217433 TCTATCTTAACTTTTTTTAAGGTTGTCTTAGATAAGG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAG--AAGG
*
47217470 TTTATCCCAAC-TTTTTTAAGGTTGCCTTAG-A--
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGAAGG
* *
47217501 -CGA-CCCAAATTTTTTTAAAGGTTGCCTTAGATAAGG
1 TCTATCCCAACTTTTTTT-AAGGTTGCCTTAG--AAGG
* * * * * *
47217537 TTTATCCCAGC-CTTTTTAAGTTTGTCTTAGACGGG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGA-AGG
* * *
47217572 TCTATCCCAAC-CTTTTTAAGATTGCCTTAGATGAG
1 TCTATCCCAACTTTTTTTAAGGTTGCCTTAGAAG-G
* *
47217607 TTTATCCCAACCTTTTTTAA
1 TCTATCCCAACTTTTTTTAA
47217627 ATGTCGGTAT
Statistics
Matches: 153, Mismatches: 26, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
29 5 0.03
30 7 0.05
31 13 0.08
33 1 0.01
34 3 0.02
35 47 0.31
36 55 0.36
37 15 0.10
38 7 0.05
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (35 bp):
TCTATCCCAACTTTTTTTAAGGTTGCCTTAGAAGG
Found at i:47217532 original size:67 final size:66
Alignment explanation
Indices: 47217444--47217623 Score: 202
Period size: 67 Copynumber: 2.7 Consensus size: 66
47217434 CTATCTTAAC
* *
47217444 TTTTTTTAAGGTTGTCTTAGATAAGGTTTATCCCAACTTTTTTAAGGTTGCCTTAGACGACCCAA
1 TTTTTTTAAGGTTGCCTTAGATAAGGTTTATCCCAACCTTTTTAAGGTTGCCTTAGACGACCCAA
47217509 A
66 A
* * *
47217510 TTTTTTTAAAGGTTGCCTTAGATAAGGTTTATCCCAGCCTTTTTAAGTTTGTCTTAGACGGGTCT
1 TTTTTTT-AAGGTTGCCTTAGATAAGGTTTATCCCAACCTTTTTAAGGTTGCCTTAGAC--G---
47217575 ATCCC-AA
60 A-CCCAAA
** * *
47217582 CCTTTTTAAGATTGCCTTAGATGA-GTTTATCCCAACCTTTTT
1 TTTTTTTAAGGTTGCCTTAGATAAGGTTTATCCCAACCTTTTT
47217624 TAAATGTCGG
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
66 7 0.07
67 46 0.47
69 1 0.01
70 17 0.18
71 15 0.15
72 8 0.08
73 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (66 bp):
TTTTTTTAAGGTTGCCTTAGATAAGGTTTATCCCAACCTTTTTAAGGTTGCCTTAGACGACCCAA
A
Found at i:47217580 original size:35 final size:35
Alignment explanation
Indices: 47217387--47217623 Score: 126
Period size: 35 Copynumber: 6.8 Consensus size: 35
47217377 GAAAAAATTA
* ** *
47217387 CCTTAGACGTA-TCTATTCCAATTTTTTTAAGGTTG
1 CCTTAGACG-AGTCTATCCCAACCTTTTTAAGATTG
* * ** * *
47217422 CCTTAGAAGTGTCTATCTTAACTTTTTTTAAGGTTG
1 CCTTAGACGAGTCTATCCCAAC-CTTTTTAAGATTG
* ** * * *
47217458 TCTTAGATAAGGTTTATCCCAACTTTTTTAAGGTTG
1 CCTTAGACGA-GTCTATCCCAACCTTTTTAAGATTG
* ** *
47217494 CCTTAGACGA--C---CCAAATTTTTTTAAAGGTTG
1 CCTTAGACGAGTCTATCCCAACCTTTTT-AAGATTG
** * * *
47217525 CCTTAGATAAGGTTTATCCCAGCCTTTTTAAGTTTG
1 CCTTAGACGA-GTCTATCCCAACCTTTTTAAGATTG
* *
47217561 TCTTAGACGGGTCTATCCCAACCTTTTTAAGATTG
1 CCTTAGACGAGTCTATCCCAACCTTTTTAAGATTG
* *
47217596 CCTTAGATGAGTTTATCCCAACCTTTTT
1 CCTTAGACGAGTCTATCCCAACCTTTTT
47217624 TAAATGTCGG
Statistics
Matches: 154, Mismatches: 38, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
30 10 0.06
31 15 0.10
35 61 0.40
36 51 0.33
37 17 0.11
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.42
Consensus pattern (35 bp):
CCTTAGACGAGTCTATCCCAACCTTTTTAAGATTG
Found at i:47221629 original size:18 final size:18
Alignment explanation
Indices: 47221595--47221628 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47221585 AATTGGTTAT
*
47221595 TTTTATTATTTTATTTTA
1 TTTTATTATTTGATTTTA
47221613 TTTTATT-TTTGATTTT
1 TTTTATTATTTGATTTT
47221629 TGGTAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTATTTGATTTTA
Found at i:47222546 original size:21 final size:21
Alignment explanation
Indices: 47222502--47222570 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
47222492 TACCTCAGTT
* *
47222502 ACACAAGCGTGTCTCTCA-ACC
1 ACACGAGCGTGTCTCTTAGA-C
*
47222523 ACAC-AGCTGTGTCTCTTAGGC
1 ACACGAGC-GTGTCTCTTAGAC
*
47222544 ACACGGGCGTGTCTCTTAGAC
1 ACACGAGCGTGTCTCTTAGAC
47222565 ACACGA
1 ACACGA
47222571 CCATGTATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.08
21 35 0.88
22 2 0.05
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (21 bp):
ACACGAGCGTGTCTCTTAGAC
Found at i:47229931 original size:18 final size:18
Alignment explanation
Indices: 47229908--47229944 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47229898 CGGTTGATGG
* *
47229908 TTTATTTATTCATGTAAT
1 TTTATTAATTCATCTAAT
47229926 TTTATTAATTCATCTAAT
1 TTTATTAATTCATCTAAT
47229944 T
1 T
47229945 GGACAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTATTAATTCATCTAAT
Found at i:47234413 original size:51 final size:51
Alignment explanation
Indices: 47234068--47234415 Score: 323
Period size: 51 Copynumber: 6.9 Consensus size: 51
47234058 CTATTATCAT
* * *
47234068 TCGATACACGTTGTAGCCTTCACATAGTACTACACACGTGATCAATT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* * * * * *
47234119 -CGGTTCACGTAATAGCCTTCACATAGTACTATACATGTGATCAAGT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* ** *
47234169 -CGATTCACGTAGTAGCCTTCACATAGTACTACATACGTGAGTA-AAGCTTT-
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA--TTTA
* * * * *
47234219 TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * * * *
47234270 TCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA-AAGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA
* * ** * * *
47234321 TCGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
*
47234372 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
47234416 ACACTTTCAC
Statistics
Matches: 237, Mismatches: 52, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.00
50 82 0.35
51 152 0.64
52 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (51 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
Found at i:47234413 original size:102 final size:102
Alignment explanation
Indices: 47234068--47234416 Score: 454
Period size: 102 Copynumber: 3.4 Consensus size: 102
47234058 CTATTATCAT
* * * * * * * *
47234068 TCGATACACGTTGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTTTTACGGTTCACGTAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * * *
47234131 TAGCCTTCACATAGTACTATACATGTGATCAAGT-TTTA
65 TAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTA
* * ** *
47234169 -CGATTCACGTAGTAGCCTTCACATAGTACTACATACGTGAGTAAAGCTTTTCGATACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
*
47234233 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* * * *
47234270 TCAATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACATATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
47234335 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
47234372 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
47234417 CACTTTCACT
Statistics
Matches: 218, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
100 39 0.18
101 40 0.18
102 139 0.64
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
Found at i:47235665 original size:41 final size:41
Alignment explanation
Indices: 47235608--47235758 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
47235598 TTAGCAACCC
* * *
47235608 TCGGGGAATCAGCACTTAGCAACCCCTTTTTGATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT
47235649 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT
* *
47235690 TCGGGGAATTTGCACTTGGCAACCCCTTTTCGATCAATGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT
* * *
47235731 TCGGGTAATCTGCACTTAGTAACGCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
47235759 ACATTCAATG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTCGATCAATGAT
Found at i:47235667 original size:66 final size:67
Alignment explanation
Indices: 47235545--47235673 Score: 172
Period size: 66 Copynumber: 1.9 Consensus size: 67
47235535 AGGATACGGT
**
47235545 GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTTTGGGAATCAGCACTTAGCAACCCTC
1 GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTCGGGGAATCAGCACTTAGCAACCCTC
47235610 GG
66 GG
* * * * *
47235612 GGAATCAGCACTTAGCAACC-CCTTTTTG-ATCAGTGATTCGGGGAATCTGCACTTAGCAACCC
1 GGAATCAGCACTTAGCAACCACC-TTTAGAATAAATAATTCGGGGAATCAGCACTTAGCAACCC
47235674 CTTTTCGATC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 30 0.56
67 24 0.44
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (67 bp):
GGAATCAGCACTTAGCAACCACCTTTAGAATAAATAATTCGGGGAATCAGCACTTAGCAACCCTC
GG
Found at i:47241909 original size:9 final size:9
Alignment explanation
Indices: 47241892--47241928 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
47241882 TATAGTTTGA
47241892 TATTCGAAT
1 TATTCGAAT
*
47241901 TATTTGAAT
1 TATTCGAAT
*
47241910 TATTCGAGT
1 TATTCGAAT
47241919 TATTCGAAT
1 TATTCGAAT
47241928 T
1 T
47241929 CAAAAACTCA
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:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:47241999 original size:9 final size:9
Alignment explanation
Indices: 47241982--47242012 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
47241972 TTGAGTTGAT
47241982 TCGAATAAC
1 TCGAATAAC
*
47241991 TCGATTAAC
1 TCGAATAAC
47242000 TCGAATAAC
1 TCGAATAAC
47242009 TCGA
1 TCGA
47242013 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:47243630 original size:15 final size:13
Alignment explanation
Indices: 47243612--47243645 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
47243602 TCTTCTTCTC
47243612 CTTTTTCTTTTGGTT
1 CTTTTTCTTTT--TT
47243627 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
47243640 CTTTTT
1 CTTTTT
47243646 AATAACTCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
15 11 0.58
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:47246615 original size:21 final size:20
Alignment explanation
Indices: 47246595--47246645 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
47246585 CCTCCATTCT
47246595 TTCTTTTTTATTATT-TTTTC
1 TTCTTTTTTATT-TTATTTTC
47246615 TCTCATTCTTTTATTTTATTTTC
1 T-TC-TT-TTTTATTTTATTTTC
47246638 -TCTTTTTT
1 TTCTTTTTT
47246646 CTTTCCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
19 4 0.15
20 3 0.11
21 4 0.15
22 4 0.15
23 12 0.44
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCTTTTTTATTTTATTTTC
Found at i:47247373 original size:62 final size:61
Alignment explanation
Indices: 47247219--47247383 Score: 186
Period size: 62 Copynumber: 2.7 Consensus size: 61
47247209 CTGAATTTGA
* * * *
47247219 GGCACACGGGCTAGGGACACGGGCGTGTGTCTAGGTCATGTAACTCACTGTTTGTATTTCT
1 GGCACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTGTATTTCT
* * ** * * *
47247280 GGCAACACAAGCCAGGGACACCCGCGTGTGTCCAGGCCGTGTAACTTATTGTTTGTATTTCT
1 GGC-ACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTGTATTTCT
* * *
47247342 GGTCACACAGGCTAGGGACATAGGTGCGTGTCTAGGCCGTGT
1 GG-CACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGT
47247384 GAGGGTATTG
Statistics
Matches: 84, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
61 3 0.04
62 80 0.95
63 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (61 bp):
GGCACACAGGCTAGGGACACAGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTGTATTTCT
Found at i:47252004 original size:23 final size:23
Alignment explanation
Indices: 47251953--47251997 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
47251943 ACCAAAATAA
47251953 TAAATTATTGCAACGGTAGTGAC
1 TAAATTATTGCAACGGTAGTGAC
*
47251976 TAAATTATT-CTAACGGTTGTGA
1 TAAATTATTGC-AACGGTAGTGA
47251998 TCAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (23 bp):
TAAATTATTGCAACGGTAGTGAC
Found at i:47257642 original size:21 final size:20
Alignment explanation
Indices: 47257588--47257658 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
47257578 GTATATCATG
47257588 TATGTTATGTATATTACTATT
1 TATG-TATGTATATTACTATT
*
47257609 TATGTATGTATATTAGGTATGT
1 TATGTATGTATATTA-CTAT-T
*
47257631 TATGTA-GTATATTACTGTT
1 TATGTATGTATATTACTATT
47257650 TATGTATGT
1 TATGTATGT
47257659 TATGTATTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.16
20 15 0.34
21 15 0.34
22 7 0.16
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.54
Consensus pattern (20 bp):
TATGTATGTATATTACTATT
Found at i:47257649 original size:18 final size:19
Alignment explanation
Indices: 47257576--47257658 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 19
47257566 TGTCAAAAAA
*
47257576 ATGTATATCA-TG-TATGTT
1 ATGTATATTACTGTTATG-T
*
47257594 ATGTATATTACTATTTATGT
1 ATGTATATTACT-GTTATGT
*
47257614 ATGTATATTAGGTATGTTATGT
1 ATGTATATTA---CTGTTATGT
47257636 A-GTATATTACTGTTTATGT
1 ATGTATATTACTG-TTATGT
47257655 ATGT
1 ATGT
47257659 TATGTATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
18 11 0.21
19 8 0.15
20 13 0.25
21 12 0.23
22 7 0.13
23 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.52
Consensus pattern (19 bp):
ATGTATATTACTGTTATGT
Found at i:47257653 original size:41 final size:38
Alignment explanation
Indices: 47257576--47257658 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 38
47257566 TGTCAAAAAA
*
47257576 ATGTATATCATGTATGTTATGTATATTACTATTTATGT
1 ATGTATATCAGGTATGTTATGTATATTACTATTTATGT
* *
47257614 ATGTATATTAGGTATGTTATGTAGTATATTACTGTTTATGT
1 ATGTATATCAGGTATGTTA--T-GTATATTACTATTTATGT
47257655 ATGT
1 ATGT
47257659 TATGTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 17 0.44
40 1 0.03
41 21 0.54
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.52
Consensus pattern (38 bp):
ATGTATATCAGGTATGTTATGTATATTACTATTTATGT
Found at i:47257657 original size:28 final size:28
Alignment explanation
Indices: 47257625--47257721 Score: 124
Period size: 28 Copynumber: 3.4 Consensus size: 28
47257615 TGTATATTAG
47257625 GTATGTTATGTAGTATATTACTGTTTAT
1 GTATGTTATGTAGTATATTACTGTTTAT
* * *
47257653 GTATGTTATGTATTATATTATTGTTAAT
1 GTATGTTATGTAGTATATTACTGTTTAT
* *
47257681 GTATTTTATGTATGT-TATGTAGTGTTTAT
1 GTATGTTATGTA-GTATAT-TACTGTTTAT
47257710 GTATGTTATGTA
1 GTATGTTATGTA
47257722 TATTACCATT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
28 39 0.66
29 20 0.34
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.56
Consensus pattern (28 bp):
GTATGTTATGTAGTATATTACTGTTTAT
Found at i:47257663 original size:9 final size:9
Alignment explanation
Indices: 47257585--47257722 Score: 99
Period size: 9 Copynumber: 14.7 Consensus size: 9
47257575 AATGTATATC
47257585 ATGTATGTT
1 ATGTATGTT
*
47257594 ATGTATATT
1 ATGTATGTT
*
47257603 A-CTAT-TT
1 ATGTATGTT
47257610 ATGTATGTAT
1 ATGTATGT-T
47257620 ATTAGGTATGTT
1 A-T--GTATGTT
47257632 ATGTA-GTAT
1 ATGTATGT-T
47257641 AT-TACTGTTT
1 ATGTA-TG-TT
47257651 ATGTATGTT
1 ATGTATGTT
47257660 ATGTAT-TAT
1 ATGTATGT-T
47257669 AT-TATTGTT
1 ATGTA-TGTT
*
47257678 AATGTATTTT
1 -ATGTATGTT
47257688 ATGTATGTT
1 ATGTATGTT
47257697 ATGTAGTGTTT
1 ATGTA-TG-TT
47257708 ATGTATGTT
1 ATGTATGTT
47257717 ATGTAT
1 ATGTAT
47257723 ATTACCATTT
Statistics
Matches: 106, Mismatches: 5, Indels: 36
0.72 0.03 0.24
Matches are distributed among these distances:
7 3 0.03
8 13 0.12
9 50 0.47
10 18 0.17
11 14 0.13
12 2 0.02
13 6 0.06
ACGTcount: A:0.26, C:0.01, G:0.17, T:0.55
Consensus pattern (9 bp):
ATGTATGTT
Found at i:47258181 original size:18 final size:18
Alignment explanation
Indices: 47258145--47258182 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47258135 GGGGAACCAC
*
47258145 ATTGTAATGAAGAATTTA
1 ATTGTAATGAAGAAGTTA
47258163 ATTGTAATG-AGAGAGTTA
1 ATTGTAATGAAGA-AGTTA
47258181 AT
1 AT
47258183 AGTAGGGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (18 bp):
ATTGTAATGAAGAAGTTA
Found at i:47263195 original size:25 final size:25
Alignment explanation
Indices: 47263167--47263255 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
47263157 TGGCTCGTAT
*
47263167 GAGCTTCCTGATAATTGGCTCTCCG
1 GAGCTTCCCGATAATTGGCTCTCCG
**
47263192 GAGCTTCCCGATAATTGGCTCTCAT
1 GAGCTTCCCGATAATTGGCTCTCCG
* * *
47263217 GAGCTT--C-TTGATTAGCTCTCCG
1 GAGCTTCCCGATAATTGGCTCTCCG
47263239 GAGCTTCCCGAT-ATTGG
1 GAGCTTCCCGATAATTGG
47263256 ATCATATGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
22 16 0.31
23 1 0.02
24 5 0.10
25 29 0.57
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGATAATTGGCTCTCCG
Found at i:47263245 original size:47 final size:46
Alignment explanation
Indices: 47263184--47263276 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 46
47263174 CTGATAATTG
*
47263184 GCTCTCCGGAGCTTCCCGATAATTGGCTC-TCATGAGC-TTCTTGATTA
1 GCTCTCCGGAGCTTCCCGAT-ATTGGATCAT-ATGAGCTTTC-TGATTA
47263231 GCTCTCCGGAGCTTCCCGATATTGGATCATATGAGCTTTCTGATTA
1 GCTCTCCGGAGCTTCCCGATATTGGATCATATGAGCTTTCTGATTA
47263277 TGGTTCTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
46 19 0.44
47 24 0.56
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (46 bp):
GCTCTCCGGAGCTTCCCGATATTGGATCATATGAGCTTTCTGATTA
Found at i:47263275 original size:46 final size:47
Alignment explanation
Indices: 47263184--47263276 Score: 138
Period size: 46 Copynumber: 2.0 Consensus size: 47
47263174 CTGATAATTG
*
47263184 GCTCTCCGGAGCTTCCCGATAATTGGCTCTCATGAGCTTCTTGATTA
1 GCTCTCCGGAGCTTCCCGATAATTGGATCTCATGAGCTTCTTGATTA
47263231 GCTCTCCGGAGCTTCCCGAT-ATTGGATCAT-ATGAGCTT-TCTGATTA
1 GCTCTCCGGAGCTTCCCGATAATTGGATC-TCATGAGCTTCT-TGATTA
47263277 TGGTTCTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 1 0.02
46 21 0.49
47 21 0.49
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (47 bp):
GCTCTCCGGAGCTTCCCGATAATTGGATCTCATGAGCTTCTTGATTA
Found at i:47266891 original size:21 final size:21
Alignment explanation
Indices: 47266867--47266906 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47266857 GAGAAAAATG
* *
47266867 AAAGAGATAGCAGCGAAAACA
1 AAAGAGATAGAAGAGAAAACA
47266888 AAAGAGATAGAAGAGAAAA
1 AAAGAGATAGAAGAGAAAA
47266907 AGGTTGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.25, T:0.05
Consensus pattern (21 bp):
AAAGAGATAGAAGAGAAAACA
Found at i:47267371 original size:29 final size:29
Alignment explanation
Indices: 47267339--47267396 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
47267329 ACCAATAAAA
*
47267339 GCCCTTTTTTTCAA-AATTTACCGAAATGG
1 GCCCATTTTTT-AATAATTTACCGAAATGG
* *
47267368 GCCCATTTTTTAATTATTTACCGGAATGG
1 GCCCATTTTTTAATAATTTACCGAAATGG
47267397 TCATTTTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (29 bp):
GCCCATTTTTTAATAATTTACCGAAATGG
Found at i:47267644 original size:22 final size:22
Alignment explanation
Indices: 47267607--47267721 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
47267597 CACGAACAAA
47267607 TCCTCTCTAATATTCCTTCTCAAT
1 TCCTCTC-AAT-TTCCTTCTCAAT
47267631 TCCTCTCAATTTCCTTC-CAAAT
1 TCCTCTCAATTTCCTTCTC-AAT
* * *
47267653 TTCTCTCAATTTCCTTATAAAAT
1 TCCTCTCAATTTCCTTCT-CAAT
*
47267676 TCTCTCAAACTCATATTTCATT-TCAATT
1 TC-CT----CTCA-ATTTCCTTCTCAA-T
47267704 TCCTCTCAATTTCCTTCT
1 TCCTCTCAATTTCCTTCT
47267722 AAAATTATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
21 1 0.01
22 32 0.44
23 12 0.16
24 9 0.12
27 4 0.05
28 8 0.11
29 7 0.10
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.46
Consensus pattern (22 bp):
TCCTCTCAATTTCCTTCTCAAT
Found at i:47267710 original size:51 final size:50
Alignment explanation
Indices: 47267650--47267777 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 50
47267640 TTTCCTTCCA
* *
47267650 AATTTCTCTCAATTTCCTTATAAAATTCTCTCAAA-CTCATATTTCATTTC
1 AATTTCTCTCAATTTCCTTATAAAATTATCTCAAATCT-ATATTTAATTTC
* *
47267700 AATTTCCTCTCAATTTCCTTCTAAAATTATTTCAAATCTATATTTAATTTC
1 AATTT-CTCTCAATTTCCTTATAAAATTATCTCAAATCTATATTTAATTTC
* *
47267751 AATTTTCTCTAAATTTCCGTTTTAAAA
1 AA-TTTCTCTCAATTTCC-TTATAAAA
47267778 ATAATTTTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
50 5 0.07
51 51 0.75
52 12 0.18
ACGTcount: A:0.31, C:0.20, G:0.01, T:0.48
Consensus pattern (50 bp):
AATTTCTCTCAATTTCCTTATAAAATTATCTCAAATCTATATTTAATTTC
Found at i:47269599 original size:18 final size:19
Alignment explanation
Indices: 47269573--47269612 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
47269563 AGGTGCGTTT
*
47269573 CCTAGCCCTTATATGTA-C
1 CCTAACCCTTATATGTATC
47269591 CCTAACCCTTATATGTATC
1 CCTAACCCTTATATGTATC
47269610 CCT
1 CCT
47269613 TTTCGAGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (19 bp):
CCTAACCCTTATATGTATC
Found at i:47270029 original size:25 final size:25
Alignment explanation
Indices: 47270000--47270257 Score: 224
Period size: 25 Copynumber: 10.7 Consensus size: 25
47269990 TATTTAAATA
*
47270000 TTATTTGATGCAATAAAATTGAAGT
1 TTATTTGATGTAATAAAATTGAAGT
*
47270025 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATTGAAGT
* *
47270050 TTATTTAATGTAATAAAATAT-AAAT
1 TTATTTGATGTAATAAAAT-TGAAGT
**
47270075 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATTGAAGT
*
47270094 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATTGAAGT
47270120 TTATTTGATGTAATAAAATAT-AAGT
1 TTATTTGATGTAATAAAAT-TGAAGT
* *
47270145 TTATTGGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATTGAAGT
* *
47270170 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATTGAAGT
**
47270195 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATTGAAGT
*
47270214 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATTGAAGT
47270240 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
47270258 ACTCTAACCT
Statistics
Matches: 189, Mismatches: 22, Indels: 44
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.01
20 11 0.06
21 15 0.08
22 2 0.01
23 2 0.01
24 16 0.08
25 139 0.74
26 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATTGAAGT
Found at i:47270213 original size:120 final size:120
Alignment explanation
Indices: 47270000--47270257 Score: 464
Period size: 120 Copynumber: 2.1 Consensus size: 120
47269990 TATTTAAATA
* *
47270000 TTATTTGATGCAATAAAATTGAAGTTTATTTGATGTAATAAAATAGAAGTTTATTTAATGTAATA
1 TTATTTGATGTAATAAAATTGAAGTTTATTGGATGTAATAAAATAGAAGTTTATTTAATGTAATA
*
47270065 AAATATAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGT
66 AAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGT
*
47270120 TTATTTGATGTAATAAAATAT-AAGTTTATTGGATGTAATAAAATAGAAGTTTATTTGATGTAAT
1 TTATTTGATGTAATAAAAT-TGAAGTTTATTGGATGTAATAAAATAGAAGTTTATTTAATGTAAT
47270184 AAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGT
65 AAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGT
47270240 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
47270258 ACTCTAACCT
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 132 0.99
121 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (120 bp):
TTATTTGATGTAATAAAATTGAAGTTTATTGGATGTAATAAAATAGAAGTTTATTTAATGTAATA
AAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGT
Found at i:47270283 original size:13 final size:13
Alignment explanation
Indices: 47270265--47270308 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
47270255 AAAACTCTAA
47270265 CCTAATTAAATAC
1 CCTAATTAAATAC
47270278 CCTAATTAAATAC
1 CCTAATTAAATAC
* *
47270291 CATAATTAAAAAC
1 CCTAATTAAATAC
47270304 CCTAA
1 CCTAA
47270309 CCCTAATCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (13 bp):
CCTAATTAAATAC
Found at i:47270352 original size:13 final size:13
Alignment explanation
Indices: 47270334--47270439 Score: 87
Period size: 13 Copynumber: 8.5 Consensus size: 13
47270324 TAACCTAAAT
47270334 TAATTCAAAACCC
1 TAATTCAAAACCC
47270347 TAATTCAAAACCC
1 TAATTCAAAACCC
*
47270360 TAATTAAAAACCC
1 TAATTCAAAACCC
* **
47270373 TAA-CCCTAACCC
1 TAATTCAAAACCC
* * *
47270385 TAA-CCTAAA--T
1 TAATTCAAAACCC
*
47270395 TAATTCAAAAACC
1 TAATTCAAAACCC
47270408 TAATT-AAATACCC
1 TAATTCAAA-ACCC
*
47270421 TAATTAAAAACCC
1 TAATTCAAAACCC
47270434 TAATTC
1 TAATTC
47270440 TAACCTAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
10 3 0.04
11 4 0.05
12 15 0.20
13 50 0.67
14 3 0.04
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25
Consensus pattern (13 bp):
TAATTCAAAACCC
Found at i:47270364 original size:67 final size:61
Alignment explanation
Indices: 47270267--47270436 Score: 236
Period size: 61 Copynumber: 2.7 Consensus size: 61
47270257 AACTCTAACC
*
47270267 TAATT-AAATACCCTAATTAAATACCATAATTAAAAACCCTAACCCTAATCCTAACCCTAACCTA
1 TAATTCAAA-ACCCTAATTAAATACCCTAATTAAAAACCCTAA--C----CCTAACCCTAACCTA
47270331 AAT
59 AAT
47270334 TAATTCAAAACCCTAATTCAAA-ACCCTAATTAAAAACCCTAACCCTAACCCTAACCTAAAT
1 TAATTCAAAACCCTAATT-AAATACCCTAATTAAAAACCCTAACCCTAACCCTAACCTAAAT
*
47270395 TAATTCAAAAACCTAATTAAATACCCTAATTAAAAACCCTAA
1 TAATTCAAAACCCTAATTAAATACCCTAATTAAAAACCCTAA
47270437 TTCTAACCTA
Statistics
Matches: 98, Mismatches: 2, Indels: 12
0.88 0.02 0.11
Matches are distributed among these distances:
60 3 0.03
61 55 0.56
65 1 0.01
67 33 0.34
68 6 0.06
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (61 bp):
TAATTCAAAACCCTAATTAAATACCCTAATTAAAAACCCTAACCCTAACCCTAACCTAAAT
Found at i:47270433 original size:55 final size:57
Alignment explanation
Indices: 47270316--47270461 Score: 183
Period size: 61 Copynumber: 2.5 Consensus size: 57
47270306 TAACCCTAAT
*
47270316 CCTAACCCTAACCTAAATTAATTCAAAACCCTAATTCAAAACCCTAATTAAAAACCCTAAC
1 CCTAACCCTAACCTAAATTAATTCAAAAACCTAATTCAAAACCCTAATT-AAAA--C-AAC
47270377 CCTAACCCTAACCTAAATTAATTCAAAAACCTAATT-AAATACCCTAATT-AAA-AAC
1 CCTAACCCTAACCTAAATTAATTCAAAAACCTAATTCAAA-ACCCTAATTAAAACAAC
** *
47270432 CCTAATTCTAACCTAATTTAATT-AAAAACC
1 CCTAACCCTAACCTAAATTAATTCAAAAACC
47270462 CTAAAAACCC
Statistics
Matches: 80, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
54 7 0.09
55 23 0.29
59 3 0.04
60 3 0.04
61 44 0.55
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (57 bp):
CCTAACCCTAACCTAAATTAATTCAAAAACCTAATTCAAAACCCTAATTAAAACAAC
Found at i:47270471 original size:87 final size:87
Alignment explanation
Indices: 47270360--47271058 Score: 990
Period size: 87 Copynumber: 8.2 Consensus size: 87
47270350 TTCAAAACCC
* * *
47270360 TAATTAAAAACCCTAACCCTAACCCTAA-CCTAAATTAATTCAAAAA-CCTAA-TTAAATACCCT
1 TAATTAAAAACCCTAA---AAACCCTAATCCTAATTTAATT-AAAAACCCTAACCT-AA-ACCCT
* **
47270422 AATTAAAAACCCTAATTCTAACCTAATT
60 AATTAAATACCCTAACCCTAACCTAATT
47270450 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
*
47270515 ATACCTTAACCCTAACCTAATT
66 ATACCCTAACCCTAACCTAATT
47270537 TAA-T--------TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
*
47270593 ATACTCTAACCCTAACCTAATT
66 ATACCCTAACCCTAACCTAATT
47270615 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATT-A
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
47270679 A-A---T-ACCCTAACCTAATT
66 ATACCCTAACCCTAACCTAATT
* *
47270696 TAATTAAAAACCCTAAAAACTCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCTTAATTAA
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
*
47270761 ATACCCTAACCCTAATCTAATT
66 ATACCCTAACCCTAACCTAATT
*
47270783 TAATTAAAAACCCTAAAAACCTTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
*
47270848 ATACCCTAACCCTAATCTAATT
66 ATACCCTAACCCTAACCTAATT
*
47270870 TAATTAAAAACCCTAAAAACCCTTATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
47270935 ATACCCTAACCCTAACCTAATT
66 ATACCCTAACCCTAACCTAATT
* *
47270957 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAGACCCTAACCCT-AA-CCTAATTT
1 TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAA-CCTAAACCCTAATTA
* ** * *
47271020 AAT-TCAAAACCTTAACCTAAAT
65 AATACCCTAACCCTAACCTAATT
*
47271042 TATTTAAAAACCCTAAA
1 TAATTAAAAACCCTAAA
47271059 CTAAGTTAAC
Statistics
Matches: 563, Mismatches: 27, Indels: 43
0.89 0.04 0.07
Matches are distributed among these distances:
78 75 0.13
79 1 0.00
81 75 0.13
82 3 0.01
83 1 0.00
85 31 0.06
86 14 0.02
87 325 0.58
88 21 0.04
89 1 0.00
90 16 0.03
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (87 bp):
TAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAA
ATACCCTAACCCTAACCTAATT
Found at i:47270503 original size:38 final size:31
Alignment explanation
Indices: 47270421--47271030 Score: 423
Period size: 29 Copynumber: 21.4 Consensus size: 31
47270411 TTAAATACCC
**
47270421 TAATTAAAAACCCT-AATTCTAA-CCTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
47270450 TAATTAAAAACCCTAAAAACCCTAATCCTAATT
1 TAATTAAAAACCCT--AAACCCTAATCCTAATT
* *
47270483 TAATTAAAAACCCT-AA-CCTAAACC----C
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
* *
47270508 TAATTAAATA-CCTTAACCCTAA-CCTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
47270537 TAATT---AA----AAACCCTAATCCTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
* *
47270561 TAATTAAAAACCCT-AA-CCTAAACC----C
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
* *
47270586 TAATTAAATACTCT-AACCCTAA-CCTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
47270615 TAATTAAAAACCCTAAAAACCCTAATCCTAATT
1 TAATTAAAAACCCT--AAACCCTAATCCTAATT
* *
47270648 TAATTAAAAACCCT-AA-CCTAAACC----C
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270673 TAATTAAATACCCT-AA--C-----CTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270696 TAATTAAAAACCCTAAAAACTCTAATCCTAATT
1 TAATTAAAAACCCT--AAACCCTAATCCTAATT
*
47270729 TAATTAAAAACCCT-AA-CCTAAACC----T
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270754 TAATTAAATACCCT-AACCCTAAT-CTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270783 TAATTAAAAACCCTAAAAACCTTAATCCTAATT
1 TAATTAAAAACCCT--AAACCCTAATCCTAATT
* *
47270816 TAATTAAAAACCCT-AA-CCTAAACC----C
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270841 TAATTAAATACCCT-AACCCTAAT-CTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270870 TAATTAAAAACCCTAAAAACCCTTATCCTAATT
1 TAATTAAAAACCCT--AAACCCTAATCCTAATT
* *
47270903 TAATTAAAAACCCT-AA-CCTAAACC----C
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47270928 TAATTAAATACCCT-AACCCTAA-CCTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
47270957 TAATTAAAAACCCTAAAAACCCTAATCCTAATT
1 TAATTAAAAACCCT--AAACCCTAATCCTAATT
*
47270990 TAATTAAAGACCCT-AACCCTAA-CCTAATT
1 TAATTAAAAACCCTAAACCCTAATCCTAATT
*
47271019 TAATTCAAAACC
1 TAATTAAAAACC
47271031 TTAACCTAAA
Statistics
Matches: 470, Mismatches: 43, Indels: 136
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.00
23 21 0.04
24 16 0.03
25 94 0.20
26 28 0.06
27 2 0.00
28 1 0.00
29 127 0.27
30 20 0.04
32 38 0.08
33 122 0.26
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (31 bp):
TAATTAAAAACCCTAAACCCTAATCCTAATT
Found at i:47270511 original size:25 final size:24
Alignment explanation
Indices: 47270463--47270614 Score: 112
Period size: 24 Copynumber: 6.0 Consensus size: 24
47270453 TTAAAAACCC
**
47270463 TAAAAACCCTAATCCTAA-TTTAAT
1 TAAAAACCCTAA-CCTAACCCTAAT
47270487 TAAAAACCCTAACCTAAACCCTAAT
1 TAAAAACCCTAACCT-AACCCTAAT
* * *
47270512 TAAATACCTTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAA-CCTAACC----CTAAT
**
47270541 TAAAAACCCTAATCCTAA-TTTAAT
1 TAAAAACCCTAA-CCTAACCCTAAT
47270565 TAAAAACCCTAACCTAAACCCTAAT
1 TAAAAACCCTAACCT-AACCCTAAT
* *
47270590 TAAATACTCTAACCCTAA-CCTAAT
1 TAAAAACCCTAA-CCTAACCCTAAT
47270614 T
1 T
47270615 TAATTAAAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
23 6 0.06
24 40 0.38
25 34 0.32
26 6 0.06
29 19 0.18
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAAAACCCTAACCTAACCCTAAT
Found at i:47270676 original size:25 final size:23
Alignment explanation
Indices: 47270628--47270782 Score: 103
Period size: 25 Copynumber: 6.0 Consensus size: 23
47270618 TTAAAAACCC
**
47270628 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAA-CCTAACCTAAT
47270652 TAAAAACCCTAACCTAAACCCTAAT
1 TAAAAACCCTAACCT-AA-CCTAAT
* **
47270677 TAAATACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAACCTAAT
47270700 TAAAAACCCTAAAAACTCTAATCCTAATTTAAT
1 TAAAAACCCT---AAC-CTAA-CCT-A----AT
47270733 TAAAAACCCTAACCTAAACCTTAAT
1 TAAAAACCCTAACCT-AACC-TAAT
* *
47270758 TAAATACCCTAACCCTAATCTAAT
1 TAAAAACCCTAA-CCTAACCTAAT
47270782 T
1 T
47270783 TAATTAAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 30
0.73 0.07 0.21
Matches are distributed among these distances:
23 16 0.15
24 21 0.20
25 34 0.32
26 6 0.06
27 4 0.04
28 1 0.01
29 6 0.06
30 6 0.06
33 12 0.11
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAAACCCTAACCTAACCTAAT
Found at i:47270785 original size:25 final size:23
Alignment explanation
Indices: 47270709--47270782 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
47270699 TTAAAAACCC
* *
47270709 TAAAAACTCTAATCCTAATTTAAT
1 TAAAAACCCTAA-CCTAATCTAAT
*
47270733 TAAAAACCCTAACCTAAACCTTAAT
1 TAAAAACCCTAACCT-AATC-TAAT
*
47270758 TAAATACCCTAACCCTAATCTAAT
1 TAAAAACCCTAA-CCTAATCTAAT
47270782 T
1 T
47270783 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 3 0.07
24 18 0.43
25 18 0.43
26 3 0.07
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATCTAAT
Found at i:47270859 original size:255 final size:255
Alignment explanation
Indices: 47270541--47271058 Score: 730
Period size: 255 Copynumber: 2.0 Consensus size: 255
47270531 CTAATTTAAT
47270541 TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAAATACTC-TAACCC
1 TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAA-CCTAATTAAATAC-CATAACCC
47270605 TAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAA
64 TAACCTAATTTAATTAAAAACCCT--AAA-CCTAATCCTAATTTAATTAAAAACCCTAACCTAAA
*
47270670 CCCTAATT-AA-A---T-ACCCTAACCTAATTTAATTAAAAACCCTAAAAACTCTAATCCTAATT
126 CCCTAATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATT
* *
47270729 TAATTAAAAACCCTAACCTAAACCTTAATTAAATACCCTAACCCTAATCTAATTTAATTAAAAAC
191 TAATTAAAAACCCTAACCTAAACCCTAATTAAATA--CTAACCCTAACCTAATTTAATTAAAAAC
47270794 CC
254 CC
* *
47270796 TAAAAACCTTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTAATTAAATACCCTAACCCT
1 TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAA-CCTAATTAAATACCATAACCCT
* *
47270861 AATCTAATTTAATTAAAAACCCTAAAAACCCTTATCCTAATTTAATTAAAAACCCTAACCTAAAC
65 AACCTAATTTAATTAAAAACCCT--AAA-CCTAATCCTAATTTAATTAAAAACCCTAACCTAAAC
47270926 CCTAATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTT
127 CCTAATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTT
* * * * * * *
47270991 AATTAAAGACCCTAACCCT-AA-CCTAATTTAATTCAAAACCTTAACCTAAATTATTTAAAAACC
192 AATTAAAAACCCTAA-CCTAAACCCTAATTAAATAC-TAACCCTAACCTAATTTAATTAAAAACC
47271054 C
255 C
47271055 TAAA
1 TAAA
47271059 CTAAGTTAAC
Statistics
Matches: 241, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
254 1 0.00
255 132 0.55
256 2 0.01
257 1 0.00
258 1 0.00
259 28 0.12
260 10 0.04
261 63 0.26
262 3 0.01
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.28
Consensus pattern (255 bp):
TAAAAACCCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCTAATTAAATACCATAACCCTA
ACCTAATTTAATTAAAAACCCTAAACCTAATCCTAATTTAATTAAAAACCCTAACCTAAACCCTA
ATTAAATACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAAACCCTAATCCTAATTTAATT
AAAAACCCTAACCTAAACCCTAATTAAATACTAACCCTAACCTAATTTAATTAAAAACCC
Found at i:47270872 original size:25 final size:23
Alignment explanation
Indices: 47270796--47270869 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
47270786 TTAAAAACCC
* *
47270796 TAAAAACCTTAATCCTAATTTAAT
1 TAAAAACCCTAA-CCTAATCTAAT
*
47270820 TAAAAACCCTAACCTAAACCCTAAT
1 TAAAAACCCTAACCT-AA-TCTAAT
*
47270845 TAAATACCCTAACCCTAATCTAAT
1 TAAAAACCCTAA-CCTAATCTAAT
47270869 T
1 T
47270870 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 3 0.07
24 19 0.45
25 17 0.40
26 3 0.07
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATCTAAT
Found at i:47270951 original size:25 final size:24
Alignment explanation
Indices: 47270903--47270956 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
47270893 TATCCTAATT
47270903 TAATTAAAAACCCTAACCTAAACCC
1 TAATTAAAAACCCTAACCTAAA-CC
*
47270928 TAATTAAATACCCTAACCCT-AACC
1 TAATTAAAAACCCTAA-CCTAAACC
47270952 TAATT
1 TAATT
47270957 TAATTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.26
25 17 0.63
26 3 0.11
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (24 bp):
TAATTAAAAACCCTAACCTAAACC
Found at i:47270997 original size:24 final size:24
Alignment explanation
Indices: 47270970--47271057 Score: 79
Period size: 29 Copynumber: 3.5 Consensus size: 24
47270960 TTAAAAACCC
47270970 TAAAAACCCTAATCCTAATTTAAT
1 TAAAAACCCTAATCCTAATTTAAT
*
47270994 TAAAGACCCTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAA---T--CCTAATTTAAT
* * * *
47271023 TCAAAACCTTAA-CCTAAATTATT
1 TAAAAACCCTAATCCTAATTTAAT
47271046 TAAAAACCCTAA
1 TAAAAACCCTAA
47271058 ACTAAGTTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
23 19 0.37
24 11 0.22
27 1 0.02
29 20 0.39
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (24 bp):
TAAAAACCCTAATCCTAATTTAAT
Found at i:47271035 original size:23 final size:23
Alignment explanation
Indices: 47271004--47271067 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
47270994 TAAAGACCCT
* *
47271004 AACCCTAACCTAATTTAATTCAA
1 AACCCTAACCTAAATTAATTAAA
* *
47271027 AACCTTAACCTAAATTATTTAAA
1 AACCCTAACCTAAATTAATTAAA
* *
47271050 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAAATTAA
47271068 CAATGTTACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:47271220 original size:116 final size:116
Alignment explanation
Indices: 47271064--47271288 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 116
47271054 CTAAACTAAG
**
47271064 TTAACAATGTTACATTCATGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* * *
47271129 T-AATTT-TACATAATTTGATAGTTTTACTAACCATTAACACAATTTGTTGAC
66 TAAATTTATAC-T-ATTTGATAATTTTAATAACAATTAACACAATTTGTTGAC
* * *
47271180 TTAATAATTTTACATTCACATAATGTTAGATTTGGTAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
47271245 TAAATTTATACTATTTGATAATTTTAATAACAATTAATACAATT
66 TAAATTTATACTATTTGATAATTTTAATAACAATTAACACAATT
47271289 ATCAATTAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 89 0.91
117 6 0.06
118 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
TTAACAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAAATTTATACTATTTGATAATTTTAATAACAATTAACACAATTTGTTGAC
Found at i:47274610 original size:126 final size:125
Alignment explanation
Indices: 47274315--47274667 Score: 501
Period size: 126 Copynumber: 2.8 Consensus size: 125
47274305 CCCAAACATG
* *
47274315 CTACTGTAGCAAAATCGCGTCCACGATGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * *** * *
47274380 TAGAA-CTGATTTTACACTATTTGCTTAGAAACATCAACTCAAAATTATTTTTTCCGGGAT
66 TAGAAGC-GATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCGGGAC
* * *
47274440 CTACTGTAGCAAAAGCGCGTCCATGAGGGCGCGATATCACAAATTTTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
47274505 TACAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCGGGAC
* * *
47274566 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGGGATTTCATAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
47274631 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
47274668 CTCGAAATTA
Statistics
Matches: 201, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
125 92 0.46
126 109 0.54
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCGGGAC
Found at i:47277239 original size:39 final size:39
Alignment explanation
Indices: 47277185--47277264 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
47277175 GTATAATTTA
47277185 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
*
47277224 GAACTTTTGTTTGCATTCCTCATCCTTATCTTAGCTTTG
1 GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
47277263 GA
1 GA
47277265 CTTCTCATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (39 bp):
GAACTTTTGTTTGCATTCCTCATCCTCATCTTAGCTTTG
Found at i:47278752 original size:16 final size:16
Alignment explanation
Indices: 47278731--47278762 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47278721 GCGAGGAATG
47278731 GCTTAGTAGGAGCCTA
1 GCTTAGTAGGAGCCTA
*
47278747 GCTTAGTAGGTGCCTA
1 GCTTAGTAGGAGCCTA
47278763 AATAGGTACC
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:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (16 bp):
GCTTAGTAGGAGCCTA
Found at i:47279212 original size:22 final size:22
Alignment explanation
Indices: 47279187--47279233 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
47279177 TCAGCTCTAT
*
47279187 CTTCCTTTCCATATCTCTTAAC
1 CTTCCTTTACATATCTCTTAAC
*
47279209 CTTCCTTTATATATCTCTTAAC
1 CTTCCTTTACATATCTCTTAAC
47279231 CTT
1 CTT
47279234 GGCTCTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTCCTTTACATATCTCTTAAC
Found at i:47286193 original size:11 final size:11
Alignment explanation
Indices: 47286179--47286210 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
47286169 TTATATATTC
47286179 TTTAAATTTTT
1 TTTAAATTTTT
47286190 TTTAAATTTTT
1 TTTAAATTTTT
*
47286201 TTAAAATTTT
1 TTTAAATTTT
47286211 CTAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTAAATTTTT
Found at i:47288843 original size:10 final size:10
Alignment explanation
Indices: 47288828--47288855 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
47288818 TGCCCCTAAT
47288828 TTATAAAAAA
1 TTATAAAAAA
47288838 TTATAAAAAA
1 TTATAAAAAA
47288848 TTATAAAA
1 TTATAAAA
47288856 TATATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:47289250 original size:21 final size:21
Alignment explanation
Indices: 47289226--47289266 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47289216 TTTCTAATTT
* * *
47289226 TTAATATTTTATATTTTTTTA
1 TTAAAATTTAATAATTTTTTA
47289247 TTAAAATTTAATAATTTTTT
1 TTAAAATTTAATAATTTTTT
47289267 GTCACATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTAAAATTTAATAATTTTTTA
Found at i:47289492 original size:89 final size:86
Alignment explanation
Indices: 47289363--47289592 Score: 238
Period size: 89 Copynumber: 2.7 Consensus size: 86
47289353 TAACGGTTAA
* * * *
47289363 AGGGCATTTTTGATACATTTTGATAGTTTAAGTACCCAATTGAGTGTAAAAAAAAAAGCAGGGGC
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAAA--A-GGGC
* *
47289428 CTAATTACTTATCT-TGAAAAAGTTT
62 CTAATGACTT-TCTCTGAAAAAATTT
* *
47289453 -GGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG---AAAAAAAAGGGCTTTA
1 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAAGGGCCTAA
* *
47289514 TGGCTTTTTCTGAAAAAATTT
66 TGACTTTCTCTGAAAAAATTT
* * *
47289535 GAGGGCCTCTTTT-ATGCATTTTGAAAGTTCAAGTATCTAATTGAGTGCAAAAAAAAAA
1 -AGGGCCT-TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAA
47289593 CTTAATTGTT
Statistics
Matches: 121, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
81 2 0.02
82 20 0.17
83 1 0.01
84 38 0.31
85 11 0.09
87 8 0.07
89 41 0.34
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (86 bp):
AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAAAGGGCCTAA
TGACTTTCTCTGAAAAAATTT
Found at i:47289606 original size:84 final size:83
Alignment explanation
Indices: 47289453--47289620 Score: 223
Period size: 84 Copynumber: 2.0 Consensus size: 83
47289443 GAAAAAGTTT
** *
47289453 GGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGGGCTTTATGGC
1 GGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGAACTTAATGGC
*
47289518 TTTTTCTGAAAAAATTTGA
66 TTTTT-TGAAAAAATATGA
* * *
47289537 GGGCCTCTTTT-ATGCATTTTGAAAGTTCAAGTATCTAATTGAGTGCAAAAAAAA-AACTTAATT
1 GGGCCT-TTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAAGAACTTAATG
*
47289600 GTTTTTTTGAAAAAATATGA
64 GCTTTTTTGAAAAAATATGA
47289620 G
1 G
47289621 AACTTTTTAC
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
83 13 0.18
84 49 0.66
85 12 0.16
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (83 bp):
GGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAGAACTTAATGGC
TTTTTTGAAAAAATATGA
Found at i:47291172 original size:248 final size:247
Alignment explanation
Indices: 47290727--47291608 Score: 1229
Period size: 248 Copynumber: 3.6 Consensus size: 247
47290717 AAATAATAAT
* * *
47290727 AATAACATACAATAGATAATGAACT-TATGGTTTGAAACTAGTTAACAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
*** * * * * *
47290791 TACGATGTTAAAATTGAAAATTTTAGGTTAAAAATGGTTATCATGGCGTTGGCATCAATCTTGAG
66 TACGATGTTAAAA-TGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAG
*
47290856 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCCCTAT
130 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCTCTAT
*
47290921 CACATGTGTATGCGTGTAAAAACAAAAATTTGTGAACACAAATGTGTGTTTAAA
195 CACATGCGTATGCGTGTAAAAACAAAAATTT-TGAACACAAATGTGTGTTTAAA
* *
47290975 AATAGCATACAATAGATAATGAAACT-TATGGTTTGAAAATAATTAATAATAACACATGAAATAT
1 AATAACATACAATAGATAATGAAA-TATATGGTTTGAAACTAATTAATAATAACACATGAAATAT
47291039 GTACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAG
65 GTACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAG
* *
47291104 TGGATGTCGAGTTAAATTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCTTTAT
130 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCTCTAT
* * **
47291169 CACATGCGTATGTGGGTGGAAACAACAAATTTTGAACACAAATGTGTGTTTAAA
195 CACATGCGTATGCGTGTAAAAACAA-AAATTTTGAACACAAATGTGTGTTTAAA
*
47291223 AATAACATACAATAGATAATGAAATGTATGGTTTGAAACTAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
* * * *
47291288 TATGATGTTAAAATG-AAAAAA-A-ATTAAATTTTTTTTATCATGATGTTGTCATCAATCTTGAG
66 TACGATGTTAAAATGAAAAAAATAGATTAAA-ATTGTTTATCATGGTGTTGTCATCAATCTTGAG
* ** *
47291350 TTGATGTCGAGTTAACTTATGTTACCAACTCAATCAAACACATTAATATATACTAGAAT-TCCTA
130 TGGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCT-CTA
* * * * * * *
47291414 TCACACGCATATGCGTATGGATATA-AAAAATTTTGAACACAAATCTGTGTTCAAA
194 TCACATGCGTATGCG--TGTAAAAACAAAAATTTTGAACACAAATGTGTGTTTAAA
* *
47291469 TATAACATACAATAGATAACGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
1 AATAACATACAATAGATAATGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
* * * * *
47291534 TACAATGTTAAAATAAAAAAAAATAGATTAAAATTGTTTAACATGGTTTTGTCATCAATCTTAAG
66 TACGATGTTAAAAT-GAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAG
*
47291599 TTGATGTCGA
130 TGGATGTCGA
47291609 TTATACACAC
Statistics
Matches: 568, Mismatches: 55, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
245 7 0.01
246 199 0.35
247 9 0.02
248 253 0.45
249 94 0.17
250 6 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (247 bp):
AATAACATACAATAGATAATGAAATATATGGTTTGAAACTAATTAATAATAACACATGAAATATG
TACGATGTTAAAATGAAAAAAATAGATTAAAATTGTTTATCATGGTGTTGTCATCAATCTTGAGT
GGATGTCGAGTTAACTTATGACACCAACTCAATCAAATACATTAATATATACTAGAATCTCTATC
ACATGCGTATGCGTGTAAAAACAAAAATTTTGAACACAAATGTGTGTTTAAA
Found at i:47303208 original size:49 final size:50
Alignment explanation
Indices: 47303147--47303311 Score: 142
Period size: 49 Copynumber: 3.3 Consensus size: 50
47303137 AAGTTGATCT
*
47303147 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGTAGCTCCAAA
1 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGAAGCTCCAAA
* * * * * * *
47303197 GAGCAAT-TAACGGGAAGCAC-CAGATAGCCATATAACAGGCAG-TTCAAGC
1 GAGCAATATAACGGGAAGCTCACAAAGAGCCA-ATAACGGGAAGCTCCAA-A
* ** *
47303246 GAGC-A-CTAACGGGAAGCTCACAAAGAGCCTTTAATCGGGAAGCTCACGAA
1 GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAA-CGGGAAGCTC-CAAA
*
47303296 GAGCCATATAACGGGA
1 GAGCAATATAACGGGA
47303312 CGCTTATAAG
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
48 28 0.32
49 37 0.42
50 12 0.14
51 3 0.03
52 8 0.09
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (50 bp):
GAGCAATATAACGGGAAGCTCACAAAGAGCCAATAACGGGAAGCTCCAAA
Found at i:47303310 original size:26 final size:26
Alignment explanation
Indices: 47303147--47303311 Score: 139
Period size: 24 Copynumber: 6.6 Consensus size: 26
47303137 AAGTTGATCT
*
47303147 GAGCAATATAACGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
*
47303173 GAGCCA-ATAACGGGTAGCTC-CAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* * *
47303197 GAGCAAT-TAACGGGAAGCAC-CAGA
1 GAGCCATATAACGGGAAGCTCACAAA
* * * * **
47303221 TAGCCATATAACAGGCAGTTCA-AGC
1 GAGCCATATAACGGGAAGCTCACAAA
*
47303246 GAG-CA-CTAACGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* *
47303270 GAGCC-TTTAATCGGGAAGCTCACGAA
1 GAGCCATATAA-CGGGAAGCTCACAAA
47303296 GAGCCATATAACGGGA
1 GAGCCATATAACGGGA
47303312 CGCTTATAAG
Statistics
Matches: 108, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
23 11 0.10
24 34 0.31
25 30 0.28
26 29 0.27
27 4 0.04
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACAAA
Found at i:47307276 original size:18 final size:19
Alignment explanation
Indices: 47307245--47307287 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
47307235 TATTTTTATC
*
47307245 ATAAAAAATCATTAAAAATT
1 ATAAAAAA-CATTAAAAATA
47307265 ATAAAAAA-ATTAAAAATA
1 ATAAAAAACATTAAAAATA
47307283 ATAAA
1 ATAAA
47307288 TTTGATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
20 8 0.36
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAAACATTAAAAATA
Found at i:47307422 original size:10 final size:10
Alignment explanation
Indices: 47307409--47307475 Score: 59
Period size: 10 Copynumber: 7.0 Consensus size: 10
47307399 ATTTAAAGTT
47307409 TTATAAAAAA
1 TTATAAAAAA
*
47307419 TTATAAAAAC
1 TTATAAAAAA
47307429 TTAT-AAAAA
1 TTATAAAAAA
47307438 -TATAAAAAA
1 TTATAAAAAA
* **
47307447 TT-CAAAATT
1 TTATAAAAAA
*
47307456 TTCTAAAAAA
1 TTATAAAAAA
*
47307466 ATATAAAAAA
1 TTATAAAAAA
47307476 AAATTATAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
8 3 0.07
9 15 0.34
10 26 0.59
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:47307432 original size:20 final size:18
Alignment explanation
Indices: 47307409--47307445 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
47307399 ATTTAAAGTT
47307409 TTATAAAAAATTATAAAAAC
1 TTAT-AAAAA-TATAAAAAC
47307429 TTATAAAAATATAAAAA
1 TTATAAAAATATAAAAA
47307446 ATTCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TTATAAAAATATAAAAAC
Found at i:47307441 original size:49 final size:47
Alignment explanation
Indices: 47307314--47307474 Score: 159
Period size: 49 Copynumber: 3.3 Consensus size: 47
47307304 CGAACTTACA
* *
47307314 AAAAAATTATAAAAATTATTAAAACATCAT-CAAAATTTATAGTTATTAT
1 AAAAAATTATAAAAATTA-TAAAACAT-ATAAAAAATTTAAAGTT-TTAT
47307363 AAAAAAATTAT-AAAATTA-ACAAAGCATATAAAACATATTTAAAGTTTTAT
1 -AAAAAATTATAAAAATTATA-AAA-CATATAAAA-A-ATTTAAAGTTTTAT
* * *
47307413 AAAAAATTATAAAAACTTATAAAA-ATATAAAAAATTCAAAATTTTCT
1 AAAAAATTATAAAAA-TTATAAAACATATAAAAAATTTAAAGTTTTAT
*
47307460 AAAAAAATATAAAAA
1 AAAAAATTATAAAAA
47307475 AAAATTATAA
Statistics
Matches: 97, Mismatches: 6, Indels: 19
0.80 0.05 0.16
Matches are distributed among these distances:
47 26 0.27
48 6 0.06
49 30 0.31
50 19 0.20
51 15 0.15
52 1 0.01
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.32
Consensus pattern (47 bp):
AAAAAATTATAAAAATTATAAAACATATAAAAAATTTAAAGTTTTAT
Found at i:47309997 original size:19 final size:21
Alignment explanation
Indices: 47309968--47310008 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
47309958 GTCCCTTGGA
47309968 ACCCAAAAATTATA-GTTTTG
1 ACCCAAAAATTATATGTTTTG
*
47309988 ACCC-AAAATTTTATGTTTTG
1 ACCCAAAAATTATATGTTTTG
47310008 A
1 A
47310009 TCAATTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
ACCCAAAAATTATATGTTTTG
Found at i:47311369 original size:52 final size:52
Alignment explanation
Indices: 47311263--47311434 Score: 214
Period size: 50 Copynumber: 3.4 Consensus size: 52
47311253 ATGATGCTTA
* * *
47311263 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAA-TGAACA-AATGAGTTACTT
1 AATGCATGACTTAATTTAATGATGCAAACTTAAACT-AACATGA-GAGTTACAT
47311312 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
* *
47311364 AATGCATGTCATAATTT-ATGATGCAAACTT-AACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
* *
47311414 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
47311435 CAGAACACAT
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
49 13 0.12
50 37 0.34
51 25 0.23
52 31 0.29
53 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (52 bp):
AATGCATGACTTAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
Found at i:47313658 original size:19 final size:18
Alignment explanation
Indices: 47313621--47313656 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47313611 AAAAATTGTC
*
47313621 TTGTGTCGTTTTCATATA
1 TTGTGTCCTTTTCATATA
47313639 TTGTGTCCTTTT-ATATA
1 TTGTGTCCTTTTCATATA
47313656 T
1 T
47313657 ATATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58
Consensus pattern (18 bp):
TTGTGTCCTTTTCATATA
Found at i:47316291 original size:40 final size:40
Alignment explanation
Indices: 47316230--47316311 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
47316220 TGTTGAGGAG
*
47316230 ATTGCTTCAAACCGTACAAAGACTTTTGTAAGAGACAAAC
1 ATTGCTTCAAACCATACAAAGACTTTTGTAAGAGACAAAC
* *
47316270 ATTGCTTCAAACCATATAAAGACTTTTGTAAGAGACAGAC
1 ATTGCTTCAAACCATACAAAGACTTTTGTAAGAGACAAAC
47316310 AT
1 AT
47316312 AATATTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (40 bp):
ATTGCTTCAAACCATACAAAGACTTTTGTAAGAGACAAAC
Found at i:47320162 original size:19 final size:19
Alignment explanation
Indices: 47320137--47320209 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
47320127 GAACAAATGC
47320137 AAAATTATTAAAAAAT-TT
1 AAAATTATTAAAAAATATT
*
47320155 AGAAATTA-TAAAGAATATT
1 A-AAATTATTAAAAAATATT
47320174 AATAATTATTGAAAAAATATTT
1 AA-AATTATT-AAAAAATA-TT
47320196 AAAA-TATATAAAAA
1 AAAATTAT-TAAAAA
47320210 CTAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 9 0.20
19 14 0.30
20 9 0.20
21 10 0.22
22 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
AAAATTATTAAAAAATATT
Found at i:47320233 original size:14 final size:15
Alignment explanation
Indices: 47320214--47320242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47320204 TAAAAACTAA
47320214 AAAAAT-ATATTATG
1 AAAAATAATATTATG
47320228 AAAAATAATATTATG
1 AAAAATAATATTATG
47320243 TGGTTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AAAAATAATATTATG
Found at i:47321669 original size:21 final size:21
Alignment explanation
Indices: 47321645--47321686 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
47321635 CCTGTGATAC
47321645 CTATTACTTTGGTTTGAGTTT
1 CTATTACTTTGGTTTGAGTTT
47321666 CTATTACTTTGGTTTGAGTTT
1 CTATTACTTTGGTTTGAGTTT
47321687 TAGGTTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.19, T:0.57
Consensus pattern (21 bp):
CTATTACTTTGGTTTGAGTTT
Found at i:47348163 original size:21 final size:21
Alignment explanation
Indices: 47348137--47348178 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47348127 CAAACAATCA
*
47348137 CAAAAAATATTAATACCTTTT
1 CAAAAAATATCAATACCTTTT
* *
47348158 CAAAAAGTATCGATACCTTTT
1 CAAAAAATATCAATACCTTTT
47348179 ACTAGGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
CAAAAAATATCAATACCTTTT
Found at i:47353115 original size:51 final size:50
Alignment explanation
Indices: 47352990--47353177 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
47352980 TATCATTCGA
* * * *
47352990 TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTCGG
1 TACACATAGTAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGG
* ** *
47353040 TTCATGTAGTAGCCTACACATAGTACCACACACGTGACCAAAGCCTTCCGG
1 TACACATAGTAGCCTACACATAGTACTACACACGTGACCAAA-CCTTCCGG
* * * *
47353091 TACACATAGTAGCCTACACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACATAGTAGCCTACACATAGTACTACACACGTGACCA-AACCT-TCCGG
* * *
47353142 TACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TACACATAGTAGCCTACACATAGTACTACACACGTG
47353178 TTTATAGGCA
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 36 0.31
51 77 0.67
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (50 bp):
TACACATAGTAGCCTACACATAGTACTACACACGTGACCAAACCTTCCGG
Found at i:47353121 original size:12 final size:13
Alignment explanation
Indices: 47353091--47353123 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
47353081 AGCCTTCCGG
47353091 TACACATAGTAGCC
1 TACACATAGTA-CC
47353105 TACACATAGTA-C
1 TACACATAGTACC
47353117 TACACAT
1 TACACAT
47353124 GTGACCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Done.