Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 140 of 141
Found at i:42356846 original size:20 final size:21
Alignment explanation
Indices: 42356818--42356862 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
42356808 TTTAAAGAAT
*
42356818 TTTATTTTTTATTTTTATGTT
1 TTTATTTTTTATTTTTATCTT
42356839 TTTA-TTTTTATTTTTATCTT
1 TTTATTTTTTATTTTTATCTT
42356859 TTTA
1 TTTA
42356863 AAAATACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTATTTTTTATTTTTATCTT
Found at i:42356862 original size:14 final size:13
Alignment explanation
Indices: 42356817--42356853 Score: 65
Period size: 14 Copynumber: 2.8 Consensus size: 13
42356807 GTTTAAAGAA
42356817 TTTTATTTTTTAT
1 TTTTATTTTTTAT
42356830 TTTTATGTTTTTAT
1 TTTTAT-TTTTTAT
42356844 TTTTATTTTT
1 TTTTATTTTT
42356854 ATCTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:42358810 original size:50 final size:50
Alignment explanation
Indices: 42358676--42358870 Score: 259
Period size: 50 Copynumber: 3.9 Consensus size: 50
42358666 AGCCAAGGCT
* * * * * **
42358676 ATCTGGTACACATGGTAGCCTGCACTTAGTACTACACATGCGACC-AATT
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
* * * *
42358725 ATC-CAGTATACTTAGTAGCCTGCACTTAGTACTACACACGTGACCTAGCC
1 ATCTGA-TACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
*
42358775 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCTAACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
42358825 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT
42358871 CACAATAGAT
Statistics
Matches: 127, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
49 37 0.29
50 89 0.70
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACC
Found at i:42359146 original size:27 final size:27
Alignment explanation
Indices: 42359116--42359169 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
42359106 TCATACAACC
* *
42359116 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
42359143 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
42359170 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:42364554 original size:46 final size:46
Alignment explanation
Indices: 42364501--42364808 Score: 202
Period size: 50 Copynumber: 6.5 Consensus size: 46
42364491 TTTGTGTGCT
42364501 AGTGTAAGA-CATGTCTGGGACATGCATTAGCCATATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATTAGCCATA-TATGAGAGCC
** * * *
42364547 AGTGTAAGACCATGTCTGGGACATGGCATT-GGAATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATTAGCCA-T-ATATGAGAGCC
* *
42364595 AGTGTAAGA-CATG-CTGGGACATGCATCAGCC-TCGAGATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGCATTAGCCAT--ATATG-AGAGCC
* * * * * * **
42364640 AATGTAAGA-CATGCCTGGGACATGCA-TCGGC-TACATGATGTGTT
1 AGTGTAAGACCATGTCTGGGACATGCATTAGCCATATATGA-GAGCC
* * *
42364684 AGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATTAGC-C--ATATATGAGAGCC
* * * *
42364734 AGTGTAATACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATTAGC-C--ATATATGAGAGCC
*
42364784 AGTGTAATACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
42364809 GCATCGGCAT
Statistics
Matches: 218, Mismatches: 27, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
42 1 0.00
43 4 0.02
44 10 0.05
45 40 0.18
46 35 0.16
47 22 0.10
48 23 0.11
49 2 0.01
50 76 0.35
51 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATTAGCCATATATGAGAGCC
Found at i:42364746 original size:50 final size:50
Alignment explanation
Indices: 42364684--42364817 Score: 250
Period size: 50 Copynumber: 2.7 Consensus size: 50
42364674 ATGATGTGTT
*
42364684 AGTGTAAGACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
1 AGTGTAATACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
42364734 AGTGTAATACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
1 AGTGTAATACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
*
42364784 AGTGTAATACCATGTCTGGGACATGGCATCGGCA
1 AGTGTAATACCATGTCTGGGACATGGCATTGGCA
42364818 TTATACCCAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (50 bp):
AGTGTAATACCATGTCTGGGACATGGCATTGGCACGGATATGTGAGAGTC
Found at i:42369693 original size:14 final size:14
Alignment explanation
Indices: 42369671--42369700 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42369661 TTTGTCATGG
42369671 TAACCAAATACATA
1 TAACCAAATACATA
*
42369685 TAACTAAATACATA
1 TAACCAAATACATA
42369699 TA
1 TA
42369701 TTTCATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (14 bp):
TAACCAAATACATA
Found at i:42380881 original size:28 final size:28
Alignment explanation
Indices: 42380818--42381083 Score: 453
Period size: 28 Copynumber: 9.5 Consensus size: 28
42380808 ATATTGAGTC
*
42380818 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
42380845 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
42380873 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
42380901 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
42380929 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
42380957 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
42380985 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
42381013 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
42381041 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
42381070 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42381084 CAATCTCATG
Statistics
Matches: 228, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.10
28 187 0.82
29 19 0.08
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42385989 original size:27 final size:26
Alignment explanation
Indices: 42385941--42386000 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42385931 GCGAGGCTGC
*
42385941 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
42385968 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
42385994 CAGATAT
1 CAGATAT
42386001 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42386045 original size:71 final size:67
Alignment explanation
Indices: 42385968--42386109 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
42385958 TCACCAGATA
* * *
42385968 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
42386033 GGCTGC
62 GGCTGC
* *
42386039 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
42386104 GC
66 GC
42386106 CAGA
1 CAGA
42386110 ACGCTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 41 0.62
71 25 0.38
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:42386087 original size:27 final size:26
Alignment explanation
Indices: 42386039--42386090 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42386029 GCGAGGCTGC
*
42386039 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
42386065 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
42386091 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42393101 original size:28 final size:28
Alignment explanation
Indices: 42393069--42393196 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
42393059 ATAGTAAGTC
*
42393069 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
42393097 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
42393126 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
42393154 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
42393183 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42393197 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42393159 original size:57 final size:57
Alignment explanation
Indices: 42393068--42393196 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
42393058 TATAGTAAGT
*
42393068 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
42393125 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
42393182 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42393197 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:42401671 original size:28 final size:28
Alignment explanation
Indices: 42401639--42401735 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
42401629 GATGTCTCAT
*
42401639 ACACTAAGTACCATACTCAATATCTTTC
1 ACACTAAGTGCCATACTCAATATCTTTC
* * *
42401667 ACACTAAGTGTCATTCTCAATAT-TTTGT
1 ACACTAAGTGCCATACTCAATATCTTT-C
**
42401695 ACACTAAGTGCCATACTCGAA-ATCTCAC
1 ACACTAAGTGCCATACTC-AATATCTTTC
42401723 ACACTAAGTGCCA
1 ACACTAAGTGCCA
42401736 CGAAACTATC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
27 3 0.05
28 51 0.89
29 3 0.05
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (28 bp):
ACACTAAGTGCCATACTCAATATCTTTC
Found at i:42415063 original size:37 final size:37
Alignment explanation
Indices: 42415003--42415077 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
42414993 ACCAAAGGAC
* *
42415003 TTAGAACCTTACCGGCTCTTTGGATTCTCTACTTTTT
1 TTAGAACCTTACCAGCTCCTTGGATTCTCTACTTTTT
42415040 TTAGAACCTTACCAGCTCCTTGGATTCTCTACTTTTT
1 TTAGAACCTTACCAGCTCCTTGGATTCTCTACTTTTT
42415077 T
1 T
42415078 GACTAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.12, T:0.45
Consensus pattern (37 bp):
TTAGAACCTTACCAGCTCCTTGGATTCTCTACTTTTT
Found at i:42415852 original size:14 final size:15
Alignment explanation
Indices: 42415833--42415862 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42415823 TGACATAATG
42415833 AGTATGTAG-TTCTA
1 AGTATGTAGTTTCTA
42415847 AGTATGTAGTTTCTA
1 AGTATGTAGTTTCTA
42415862 A
1 A
42415863 TTCTTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (15 bp):
AGTATGTAGTTTCTA
Found at i:42418176 original size:19 final size:19
Alignment explanation
Indices: 42418152--42418189 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42418142 ATATGTAAGG
*
42418152 TTTTTATTTTTGTTTTTAT
1 TTTTTATTTTTCTTTTTAT
42418171 TTTTTATTTTTCTTTTTAT
1 TTTTTATTTTTCTTTTTAT
42418190 CTTGATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTTCTTTTTAT
Found at i:42419264 original size:22 final size:22
Alignment explanation
Indices: 42419217--42419264 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
42419207 TATTTTACTT
* * **
42419217 ATTTAGCAAAATAATTTCACCT
1 ATTTAGCAAAATAAATCCACAG
42419239 ATTTAGCAAAATAAATCCACAG
1 ATTTAGCAAAATAAATCCACAG
42419261 ATTT
1 ATTT
42419265 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (22 bp):
ATTTAGCAAAATAAATCCACAG
Found at i:42419273 original size:7 final size:7
Alignment explanation
Indices: 42419261--42419285 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42419251 AAATCCACAG
42419261 ATTTTAA
1 ATTTTAA
42419268 ATTTTAA
1 ATTTTAA
42419275 ATTTTAA
1 ATTTTAA
42419282 ATTT
1 ATTT
42419286 ATATAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:42428200 original size:32 final size:32
Alignment explanation
Indices: 42428159--42428222 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
42428149 AAATATACAT
42428159 GTATTATATTAAATTGCCTATTTGATAAGAAA
1 GTATTATATTAAATTGCCTATTTGATAAGAAA
*
42428191 GTATTATATTAAATTTCCTATTTGATAAGAAA
1 GTATTATATTAAATTGCCTATTTGATAAGAAA
42428223 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (32 bp):
GTATTATATTAAATTGCCTATTTGATAAGAAA
Found at i:42428715 original size:40 final size:40
Alignment explanation
Indices: 42428661--42428811 Score: 180
Period size: 40 Copynumber: 3.7 Consensus size: 40
42428651 CTCGATATAT
*
42428661 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* *
42428701 TATATATCCAGGTTAAATCCCGCAAGCTTCGTGTTGGTCATA
1 TATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGT-A-A
* * *
42428743 TATATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGT-A
1 TATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* *
42428782 -CTATATCCAGGCTTAAAGTTCCGCAGGCTT
1 TATATATCCAGG-TTAAA-TCCCGCAGGCTT
42428812 TGAGCTAGTA
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
38 9 0.09
39 6 0.06
40 46 0.48
41 1 0.01
42 34 0.35
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (40 bp):
TATATATCCAGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
Found at i:42428747 original size:42 final size:40
Alignment explanation
Indices: 42428661--42428787 Score: 182
Period size: 40 Copynumber: 3.1 Consensus size: 40
42428651 CTCGATATAT
42428661 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * *
42428701 TATATATCCAGGTTAAATCCCGCAAGCTTCGTGTTGGTCATA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT-A-A
* * *
42428743 TATATATCCGGGTTAAATCCCGCAGGCTTAGTACTGGTAC
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
42428783 TATAT
1 TATAT
42428788 CCAGGCTTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
40 40 0.53
41 2 0.03
42 34 0.45
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (40 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
Found at i:42441325 original size:47 final size:47
Alignment explanation
Indices: 42441247--42441657 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
42441237 CCCTTCGGGA
* * * * * *
42441247 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42441294 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441341 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441388 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441435 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441482 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441529 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441576 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42441623 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
42441658 AGAATCCTAA
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42442997 original size:53 final size:53
Alignment explanation
Indices: 42442917--42443023 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
42442907 CATCTTTTCA
* **
42442917 ATCTCTCCTTGAGCAATTTGGCATTTTCATATGAGAACATTTGGAATTCTTCT
1 ATCTCTCCTTGAACAATTTGAAATTTTCATATGAGAACATTTGGAATTCTTCT
42442970 ATCTCTCCTTGAACAATTTGAAATTTTCATATGAGAACATTTGGAATTCTTCT
1 ATCTCTCCTTGAACAATTTGAAATTTTCATATGAGAACATTTGGAATTCTTCT
42443023 A
1 A
42443024 ACTCATCAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (53 bp):
ATCTCTCCTTGAACAATTTGAAATTTTCATATGAGAACATTTGGAATTCTTCT
Found at i:42455258 original size:13 final size:13
Alignment explanation
Indices: 42455240--42455264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42455230 TGTGGGTGCA
42455240 CACGGTCGTGTCG
1 CACGGTCGTGTCG
42455253 CACGGTCGTGTC
1 CACGGTCGTGTC
42455265 CGGCGTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CACGGTCGTGTCG
Found at i:42457241 original size:13 final size:13
Alignment explanation
Indices: 42457223--42457247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42457213 TGTGGGTGCA
42457223 CACGGTCGTGTCG
1 CACGGTCGTGTCG
42457236 CACGGTCGTGTC
1 CACGGTCGTGTC
42457248 CGGCGTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CACGGTCGTGTCG
Found at i:42466957 original size:40 final size:41
Alignment explanation
Indices: 42466902--42467001 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
42466892 CTATCTCGGT
*
42466902 ATCGCACACTTAGTGCCACATATAGCCGAAGCTAT-TCCAA
1 ATCGCACACTAAGTGCCACATATAGCCGAAGCTATCTCCAA
* * * * *
42466942 CTCGCACACTGAGTGCTATATATATAGCCGAAGCTATCTCGAA
1 ATCGCACACTAAGTGC--CACATATAGCCGAAGCTATCTCCAA
42466985 AT-GCACACTAAGTGCCA
1 ATCGCACACTAAGTGCCA
42467002 AACATAGTCG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
40 15 0.31
42 29 0.59
43 5 0.10
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (41 bp):
ATCGCACACTAAGTGCCACATATAGCCGAAGCTATCTCCAA
Found at i:42469094 original size:8 final size:8
Alignment explanation
Indices: 42469081--42469112 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
42469071 CTAGATCGGC
42469081 AAAAGCCG
1 AAAAGCCG
42469089 AAAAGCCG
1 AAAAGCCG
*
42469097 AAATGCCG
1 AAAAGCCG
42469105 AAAAGCCG
1 AAAAGCCG
42469113 GTATTTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:42469569 original size:27 final size:26
Alignment explanation
Indices: 42469529--42469667 Score: 161
Period size: 27 Copynumber: 5.2 Consensus size: 26
42469519 AGGAAGCGTC
* *
42469529 CTGGTGGCTATGCCACAATTATCTAAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
42469556 CTGGTGGCTCTGCCACATATATCTGAT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
42469583 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
42469610 CTGGTGGCTCTACCACGATTATTTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
42469638 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
42469664 CTGG
1 CTGG
42469668 CAGTCATGCT
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.07
27 75 0.77
28 16 0.16
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:42475539 original size:40 final size:40
Alignment explanation
Indices: 42475476--42475686 Score: 311
Period size: 40 Copynumber: 5.3 Consensus size: 40
42475466 ATTCGGATTG
*
42475476 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGATTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
42475515 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42475555 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42475595 ATAACCGGGCTAAGTCCTGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
42475635 ATAACCGGGCTAAGTCCCGAAGACATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
*
42475675 ATATCC-GGCTAA
1 ATAACCGGGCTAA
42475687 ACCCTGAAGG
Statistics
Matches: 158, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 21 0.13
40 137 0.87
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:42488998 original size:16 final size:16
Alignment explanation
Indices: 42488979--42489013 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42488969 CTTTCCCCCA
42488979 TCTAATTTCGA-ATTCC
1 TCTAATTTC-ATATTCC
42488995 TCTAATTTCATATTCC
1 TCTAATTTCATATTCC
42489011 TCT
1 TCT
42489014 TTTCTTGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.23, C:0.26, G:0.03, T:0.49
Consensus pattern (16 bp):
TCTAATTTCATATTCC
Found at i:42491859 original size:33 final size:34
Alignment explanation
Indices: 42491766--42491863 Score: 94
Period size: 34 Copynumber: 2.9 Consensus size: 34
42491756 GTTTCAGCTA
* * *
42491766 GGGCCTTAGCCCATTTCAAAATCAGAAACAGTGT
1 GGGCCTAAGCCCATTTCAGAATCAGTAACAGTGT
* * **
42491800 GGGTCTAAGCCAATTTCAGTAA-CAGTATTAGTG-
1 GGGCCTAAGCCCATTTCAG-AATCAGTAACAGTGT
*
42491833 GGGCCTAAGCCCATTACAGAATCAGT-ACAGT
1 GGGCCTAAGCCCATTTCAGAATCAGTAACAGT
42491864 ATGCAATCAA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
32 5 0.10
33 20 0.40
34 23 0.46
35 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (34 bp):
GGGCCTAAGCCCATTTCAGAATCAGTAACAGTGT
Found at i:42505422 original size:10 final size:10
Alignment explanation
Indices: 42505407--42505435 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
42505397 ATTATCACTT
42505407 AAACAATTTC
1 AAACAATTTC
42505417 AAACAATTTC
1 AAACAATTTC
42505427 AAACAATTT
1 AAACAATTT
42505436 AATTCACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (10 bp):
AAACAATTTC
Found at i:42509075 original size:27 final size:27
Alignment explanation
Indices: 42509021--42509131 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
42509011 AGCATGGCTG
* *
42509021 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
42509047 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
42509074 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
42509101 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
42509128 CCAG
1 CCAG
42509132 GACGCTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.19
27 61 0.79
28 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:42510596 original size:24 final size:24
Alignment explanation
Indices: 42510569--42510644 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
42510559 CTCTAATCAG
42510569 CTCCCTTATCAGCTCCTAAATCCT
1 CTCCCTTATCAGCTCCTAAATCCT
*
42510593 CTCCCTTATTAGCTCCTAAATCCT
1 CTCCCTTATCAGCTCCTAAATCCT
* *
42510617 CTCCCTTATCAGCTCCCAAATCTT
1 CTCCCTTATCAGCTCCTAAATCCT
42510641 CTCC
1 CTCC
42510645 TGACAGCCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.20, C:0.42, G:0.04, T:0.34
Consensus pattern (24 bp):
CTCCCTTATCAGCTCCTAAATCCT
Found at i:42516225 original size:30 final size:29
Alignment explanation
Indices: 42516189--42516252 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
42516179 ATGAATCGAA
42516189 AGCTTTGACACTAAGTGTGCGATTTAAACT
1 AGCTTTGACACTAAGTGTGCGATTT-AACT
*
42516219 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGACACTAAGTGTGCGATTTAACT
42516248 AGCTT
1 AGCTT
42516253 CAGCTACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (29 bp):
AGCTTTGACACTAAGTGTGCGATTTAACT
Found at i:42525750 original size:46 final size:46
Alignment explanation
Indices: 42525692--42525903 Score: 390
Period size: 46 Copynumber: 4.6 Consensus size: 46
42525682 CATAAGCGAA
* *
42525692 AACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTG
1 AACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTG
42525738 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
42525784 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
42525830 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
42525876 AACTCGGACTCAACTCAACGAGTTCGGA
1 AACTCGGACTCAACTCAACGAGTTCGGA
42525904 TGCTCAACCA
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
45 2 0.01
46 161 0.99
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTG
Found at i:42528249 original size:46 final size:45
Alignment explanation
Indices: 42528105--42528272 Score: 180
Period size: 46 Copynumber: 3.6 Consensus size: 45
42528095 TTTGTGTGCT
42528105 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCAC-TTGATGAGAGCC
* * *
42528151 AGTGTATGACCATGTCTGGGACATGGCATCGACA-TTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGCCACTT--GATGAGAGCC
* *
42528199 AGTGTAAGATATGTCTGGGACGTGCATCGGCCACTTGATGCA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCACTTGATG-AGAGCC
* *
42528245 AGTGTAAGGCATGTCTAGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
42528273 TACTTCATGA
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
45 2 0.02
46 44 0.43
47 33 0.32
48 23 0.23
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCCACTTGATGAGAGCC
Found at i:42534416 original size:46 final size:46
Alignment explanation
Indices: 42534349--42534523 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
42534339 TGTAACCCGC
* * * *
42534349 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42534395 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42534441 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42534487 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42534524 TGCTCAACCA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42536486 original size:45 final size:45
Alignment explanation
Indices: 42536417--42536503 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
42536407 CATACTTTCA
*
42536417 CACCAGCATTATACCCTGTTAGGCTCAAAGGCCCGAATAGTATAT
1 CACCAGCATTATACCCTGCTAGGCTCAAAGGCCCGAATAGTATAT
* *
42536462 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
1 CACCAGCATTATACCCTGCTAGGCTCAAAGGCCCGAATAGTA
42536504 CTGTACGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CACCAGCATTATACCCTGCTAGGCTCAAAGGCCCGAATAGTATAT
Found at i:42537287 original size:25 final size:25
Alignment explanation
Indices: 42537253--42537357 Score: 122
Period size: 25 Copynumber: 4.2 Consensus size: 25
42537243 AAGTACTTTA
* *
42537253 AAATTTAACCGAAAATATTAAGAGC
1 AAATTTAACCGAAATTATTAAGAAC
*
42537278 AAATTTAACC-AGGATTATTAAGAAC
1 AAATTTAACCGA-AATTATTAAGAAC
* * *
42537303 AACTTTAACCGGAATTATTAAGAGC
1 AAATTTAACCGAAATTATTAAGAAC
* *
42537328 AAATTTAACCGGAACTATTAAGAAC
1 AAATTTAACCGAAATTATTAAGAAC
42537353 AAATT
1 AAATT
42537358 AAGAAGCTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
24 1 0.01
25 67 0.99
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (25 bp):
AAATTTAACCGAAATTATTAAGAAC
Found at i:42537322 original size:50 final size:50
Alignment explanation
Indices: 42537256--42537354 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
42537246 TACTTTAAAA
*
42537256 TTTAACCGAAAATATTAAGAGCAAATTTAACCAGG-ATTATTAAGAACAAC
1 TTTAACCGAAAATATTAAGAGCAAATTTAACC-GGAACTATTAAGAACAAC
* *
42537306 TTTAACCGGAATTATTAAGAGCAAATTTAACCGGAACTATTAAGAACAA
1 TTTAACCGAAAATATTAAGAGCAAATTTAACCGGAACTATTAAGAACAA
42537355 ATTAAGAAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 2 0.04
50 43 0.96
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (50 bp):
TTTAACCGAAAATATTAAGAGCAAATTTAACCGGAACTATTAAGAACAAC
Found at i:42545332 original size:26 final size:27
Alignment explanation
Indices: 42545303--42545362 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
42545293 CCACATATAT
*
42545303 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
42545329 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
42545356 ATATCTG
1 ATATCTG
42545363 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:42547535 original size:35 final size:35
Alignment explanation
Indices: 42547484--42547552 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
42547474 GTTCTGGCAG
*
42547484 CCTCGCTGCAATCTGGTGGCCTCGCCACATATATC
1 CCTCACTGCAATCTGGTGGCCTCGCCACATATATC
*
42547519 CCTCACTGCAATCTGGTGGCTTCGCCACATATAT
1 CCTCACTGCAATCTGGTGGCCTCGCCACATATAT
42547553 ATATATCTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.28
Consensus pattern (35 bp):
CCTCACTGCAATCTGGTGGCCTCGCCACATATATC
Found at i:42547579 original size:33 final size:32
Alignment explanation
Indices: 42547530--42547593 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
42547520 CTCACTGCAA
* *
42547530 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
42547563 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
42547594 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:42547607 original size:27 final size:26
Alignment explanation
Indices: 42547555--42547614 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42547545 ACATATATAT
*
42547555 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
42547581 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
42547608 ATATCTG
1 ATATCTG
42547615 GCAACCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:42554646 original size:40 final size:39
Alignment explanation
Indices: 42554548--42554810 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
42554538 TCCTCGTTCA
* * * *
42554548 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
42554587 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
42554626 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
42554666 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
42554706 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
42554746 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
42554787 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42554811 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:42554770 original size:120 final size:119
Alignment explanation
Indices: 42554548--42554810 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
42554538 TCCTCGTTCA
* * *
42554548 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
42554613 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
42554666 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
42554731 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
42554787 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42554811 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:42554819 original size:41 final size:41
Alignment explanation
Indices: 42554742--42554819 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42554732 TTTGTATCTC
* * *
42554742 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42554783 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42554820 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42562594 original size:40 final size:40
Alignment explanation
Indices: 42562494--42562665 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
42562484 GCTCCTCGTT
* * *
42562494 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
42562534 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
42562573 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
42562613 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
42562653 CAAATGCCTTCGG
1 CAAATGCCTTCGG
42562666 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:42562678 original size:80 final size:79
Alignment explanation
Indices: 42562494--42562718 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
42562484 GCTCCTCGTT
* * * * *
42562494 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
42562558 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * *
42562573 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
** *
42562638 AATTT-GTATCTCGCA
64 AATTTAACAACTCGCA
* * * * *
42562653 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
42562717 GA
63 GA
42562719 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 68 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAACAACTCGCA
Found at i:42562727 original size:41 final size:41
Alignment explanation
Indices: 42562650--42562727 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42562640 TTTGTATCTC
* * *
42562650 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42562691 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42562728 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42577499 original size:48 final size:48
Alignment explanation
Indices: 42577428--42577522 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
42577418 AAAATTGTGA
42577428 CAGCCCAAAGTTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAAT
1 CAGCCCAAAGTTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAAT
*
42577476 CAGCCCAAAGTTGACCCTAGTCGGGAAGTGGTTTTGGGACCGCTAAA
1 CAGCCCAAAGTTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAA
42577523 CCGAGTCACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.21
Consensus pattern (48 bp):
CAGCCCAAAGTTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAAT
Found at i:42592560 original size:40 final size:39
Alignment explanation
Indices: 42592509--42592781 Score: 170
Period size: 39 Copynumber: 6.9 Consensus size: 39
42592499 GAATTCAATC
*
42592509 ACCAACACAAAGCCTACAGGA-CTTGAAGCCCGGATATAGT
1 ACCAGCACAAAGCCTAC-GGACCTT-AAGCCCGGATATAGT
* * *
42592549 ACCAGTACAAAGCCTGCGGACCTTAAGTCCGGATATAGT
1 ACCAGCACAAAGCCTACGGACCTTAAGCCCGGATATAGT
* * * * * *
42592588 ACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAAT
1 ACCAGCACAAAGCCTACGGACCTTAAGCCCGGATATAGT
* * ** * * * * *
42592627 TCTAGCATGAAGCCTGCGGGTCTTTAAGCCCGAATATAAT
1 ACCAGCACAAAGCCTAC-GGACCTTAAGCCCGGATATAGT
* * * * * * *
42592667 TCCAGCACGAAGCCTGCGGACCTTAAGTCCAGATACAAT
1 ACCAGCACAAAGCCTACGGACCTTAAGCCCGGATATAGT
* ** * * * *
42592706 TCCAGCATGAAGCCTGCGGACCTTAAGTCCGGATACAAT
1 ACCAGCACAAAGCCTACGGACCTTAAGCCCGGATATAGT
* ** * *
42592745 TCCAGCATGAAGCCTGCGGACCTTAAGTCCGGATATA
1 ACCAGCACAAAGCCTACGGACCTTAAGCCCGGATATA
42592782 CATCAAATAT
Statistics
Matches: 202, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
39 154 0.76
40 48 0.24
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.20
Consensus pattern (39 bp):
ACCAGCACAAAGCCTACGGACCTTAAGCCCGGATATAGT
Found at i:42592585 original size:39 final size:39
Alignment explanation
Indices: 42592538--42592781 Score: 308
Period size: 39 Copynumber: 6.2 Consensus size: 39
42592528 GACTTGAAGC
* * * *
42592538 CCGGATATAGTACCAGTACAAAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
* * *
42592577 CCGGATATAGTACCAGCACGAAGCCTGCGGATCTTAAGT
1 CCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
* * * * * *
42592616 CCGGATACAATTCTAGCATGAAGCCTGCGGGTCTTTAAGC
1 CCGGATATAATTCCAGCACGAAGCCTGC-GGACCTTAAGT
*
42592656 CCGAATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
* * *
42592695 CCAGATACAATTCCAGCATGAAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
* *
42592734 CCGGATACAATTCCAGCATGAAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
42592773 CCGGATATA
1 CCGGATATA
42592782 CATCAAATAT
Statistics
Matches: 179, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
39 148 0.83
40 31 0.17
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGT
Found at i:42592672 original size:79 final size:78
Alignment explanation
Indices: 42592558--42592779 Score: 336
Period size: 79 Copynumber: 2.8 Consensus size: 78
42592548 TACCAGTACA
* * *
42592558 AAGCCTGCGGACCTTAAGTCCGGATATAGTACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATA
1 AAGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA
*
42592623 CAATTCTAGCATG
66 CAATTCCAGCATG
* * * * *
42592636 AAGCCTGCGGGTCTTTAAGCCCGAATATAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCAGAT
1 AAGCCTGC-GGACCTTAAGTCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGGAT
42592701 ACAATTCCAGCATG
65 ACAATTCCAGCATG
* *
42592715 AAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGCATGAAGCCTGCGGACCTTAAGTCCGGATA
1 AAGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA
42592780 TACATCAAAT
Statistics
Matches: 127, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 58 0.46
79 69 0.54
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21
Consensus pattern (78 bp):
AAGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA
CAATTCCAGCATG
Found at i:42592731 original size:118 final size:118
Alignment explanation
Indices: 42592534--42592763 Score: 352
Period size: 118 Copynumber: 1.9 Consensus size: 118
42592524 ACAGGACTTG
* * * * * *
42592534 AAGCCCGGATATAGTACCAGTACAAAGCCTGCGGACCTTAAGTCCGGATATAGTACCAGCACGAA
1 AAGCCCGAATATAATACCAGCACAAAGCCTGCGGACCTTAAGTCCAGATACAATACCAGCACGAA
* *
42592599 GCCTGCGGATCTTAAGTCCGGATACAATTCTAGCATGAAGCCTGCGGGTCTTT
66 GCCTGCGGACCTTAAGTCCGGATACAATTCCAGCATGAAGCCTGCGGGTCTTT
* * * *
42592652 AAGCCCGAATATAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCAGATACAATTCCAGCATGAA
1 AAGCCCGAATATAATACCAGCACAAAGCCTGCGGACCTTAAGTCCAGATACAATACCAGCACGAA
42592717 GCCTGCGGACCTTAAGTCCGGATACAATTCCAGCATGAAGCCTGCGG
66 GCCTGCGGACCTTAAGTCCGGATACAATTCCAGCATGAAGCCTGCGG
42592764 ACCTTAAGTC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 100 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.20
Consensus pattern (118 bp):
AAGCCCGAATATAATACCAGCACAAAGCCTGCGGACCTTAAGTCCAGATACAATACCAGCACGAA
GCCTGCGGACCTTAAGTCCGGATACAATTCCAGCATGAAGCCTGCGGGTCTTT
Found at i:42596028 original size:27 final size:27
Alignment explanation
Indices: 42595997--42596174 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42595987 TAAATTGTAC
42595997 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42596024 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42596050 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42596078 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42596106 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42596133 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42596160 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42596175 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42596111 original size:82 final size:81
Alignment explanation
Indices: 42595998--42596153 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42595988 AAATTGTACA
* *
42595998 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42596062 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42596079 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42596144 TGCGAGTTGA
65 TGCGAATTGA
42596154 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42596165 original size:82 final size:81
Alignment explanation
Indices: 42595994--42596174 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42595984 GATTAAATTG
* *
42595994 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42596059 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42596075 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42596139 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42596157 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42596175 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42600200 original size:43 final size:43
Alignment explanation
Indices: 42600063--42600224 Score: 147
Period size: 43 Copynumber: 3.8 Consensus size: 43
42600053 ATCTTGTACA
* * ** *
42600063 ATGCCAACGTCCCAAATGTGGTCTTACATGT-AATCAAATATAG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAAATCAAATA-CG
* *
42600106 ATGCC-ACTATCCCAGACAG-GGTCTTACAC-GAAATCAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACATAAATCAAATACG
* *
42600148 ATGCTAACGTCCTAGAC-TGGTCTTACACATAAATCATAAGT-CG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAAATCA-AA-TACG
42600191 ATGCCAACGTCCCAGACGTGGTCTTACACTATAA
1 ATGCCAACGTCCCAGACGTGGTCTTACAC-ATAA
42600225 CACATATCGA
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
41 10 0.10
42 20 0.21
43 50 0.52
44 13 0.13
45 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACATAAATCAAATACG
Found at i:42607567 original size:42 final size:42
Alignment explanation
Indices: 42607502--42607700 Score: 226
Period size: 42 Copynumber: 4.7 Consensus size: 42
42607492 AGCTTGTACA
*
42607502 ATGCCAACGTCCCAGACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAACATCCCAGA-AGTGGTCTTACACGAAATCAAATACG
*
42607544 ATGCCAACATCCCAGAAGTGGTCTTACACGTAATCAAATATCG
1 ATGCCAACATCCCAGAAGTGGTCTTACACGAAATCAAATA-CG
* *
42607587 ATGCC-ACTATCCCAAATAG-GGTTTTACACGAAATCAAATACG
1 ATGCCAAC-ATCCCAGA-AGTGGTCTTACACGAAATCAAATACG
* *
42607629 ATGCCAACATCCCAGACGTGGTCTTACACGTAAATCATAAGT-TG
1 ATGCCAACATCCCAGAAGTGGTCTTACACG-AAATCA-AA-TACG
* * *
42607673 ATGCCAACGTCCTAGATGTGGTCTTACA
1 ATGCCAACATCCCAGAAGTGGTCTTACA
42607701 TGATAACACA
Statistics
Matches: 136, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
41 3 0.02
42 61 0.45
43 41 0.30
44 30 0.22
45 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAACATCCCAGAAGTGGTCTTACACGAAATCAAATACG
Found at i:42612180 original size:55 final size:54
Alignment explanation
Indices: 42612028--42612241 Score: 225
Period size: 55 Copynumber: 4.0 Consensus size: 54
42612018 TTACTCGGGA
* * * * * * *
42612028 ACCTTTTCCTTTTTGAACTTACCATTGACATGTCTTGGCATGGTCTTACGTGGT
1 ACCTTTTCCTTATAGAACTCATCAATGCCATGTCTTGGCATGGTCTTACATGGT
* * * * * *
42612082 ATCC-TTGCCTTAT-GAACTCACCAATGCGATGCCCTGGCATGGTCTTACATGGG
1 A-CCTTTTCCTTATAGAACTCATCAATGCCATGTCTTGGCATGGTCTTACATGGT
* *
42612135 ACCTTTTCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGAT
1 ACCTTTTCCTTATAG-AACTCATCAATGCCATGTCTTGGCATGGTCTTACATGGT
** * *
42612190 TTCTTTTCCATATAGAACTTATCAATGCCATGTCTTGGCATGGTCTTACATG
1 ACCTTTTCCTTATAGAACTCATCAATGCCATGTCTTGGCATGGTCTTACATG
42612242 ATATCCTTAT
Statistics
Matches: 133, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
52 2 0.02
53 41 0.31
54 44 0.33
55 46 0.35
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
ACCTTTTCCTTATAGAACTCATCAATGCCATGTCTTGGCATGGTCTTACATGGT
Found at i:42612236 original size:54 final size:54
Alignment explanation
Indices: 42612030--42612246 Score: 229
Period size: 54 Copynumber: 4.0 Consensus size: 54
42612020 ACTCGGGAAC
* * * * * * *
42612030 CTTTTCCTTTTTGAACTTACCATTGACATGTCTTGGCATGGTCTTACGTGGTAT
1 CTTTTCCTTATAGAACTCACCAATGCCATGTCTTGGCATGGTCTTACATGATAT
* * * * * ** *
42612084 CCTTGCCTTAT-GAACTCACCAATGCGATGCCCTGGCATGGTCTTACATGGGAC
1 CTTTTCCTTATAGAACTCACCAATGCCATGTCTTGGCATGGTCTTACATGATAT
* * *
42612137 CTTTTCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTT
1 CTTTTCCTTATAG-AACTCACCAATGCCATGTCTTGGCATGGTCTTACATGATAT
* * *
42612192 CTTTTCCATATAGAACTTATCAATGCCATGTCTTGGCATGGTCTTACATGATAT
1 CTTTTCCTTATAGAACTCACCAATGCCATGTCTTGGCATGGTCTTACATGATAT
42612246 C
1 C
42612247 CTTATCTTAC
Statistics
Matches: 134, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
53 42 0.31
54 48 0.36
55 44 0.33
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (54 bp):
CTTTTCCTTATAGAACTCACCAATGCCATGTCTTGGCATGGTCTTACATGATAT
Found at i:42612284 original size:47 final size:47
Alignment explanation
Indices: 42612228--42612349 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
42612218 CATGTCTTGG
* *
42612228 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
42612275 CATGGTCTTACATGGTATCCTTGTCTTATCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
42612322 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
42612350 GTGCCAATGC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:42612439 original size:47 final size:48
Alignment explanation
Indices: 42612321--42612440 Score: 120
Period size: 47 Copynumber: 2.5 Consensus size: 48
42612311 CATGTTCCAA
* *
42612321 ACATGGTCTTACATGGTATCCTT-GTCTTAGTGCCAATGCCACATCTTG
1 ACATGGTCTTACATGGTATCCTTAATC-TAATGCCAATGCCACATCTTG
** * * ** *
42612369 ATGTGGTCTTACATGG-AGACCTTAATC-AATGCCGATGCCATGTGTTG
1 ACATGGTCTTACATGGTA-TCCTTAATCTAATGCCAATGCCACATCTTG
42612416 ACATGGTCTTACATGGTATCCTTAA
1 ACATGGTCTTACATGGTATCCTTAA
42612441 CCGTCAATTC
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
47 36 0.63
48 19 0.33
49 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (48 bp):
ACATGGTCTTACATGGTATCCTTAATCTAATGCCAATGCCACATCTTG
Found at i:42620952 original size:65 final size:65
Alignment explanation
Indices: 42620848--42621119 Score: 508
Period size: 65 Copynumber: 4.2 Consensus size: 65
42620838 AGTTGTAGCA
*
42620848 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTTAAACATGCATTC
1 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTC
*
42620913 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTTAAACATGCATTC
1 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTC
*
42620978 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACACGCATTC
1 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTC
*
42621043 AGGTCAACCTTATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTCAAACATGCATTC
1 AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTC
42621108 AGGTCAACCTTA
1 AGGTCAACCTTA
42621120 ACCCTAGGGG
Statistics
Matches: 203, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 203 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (65 bp):
AGGTCAACCTTATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACATGCATTC
Found at i:42621178 original size:27 final size:26
Alignment explanation
Indices: 42621121--42621178 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
42621111 TCAACCTTAA
* *
42621121 CCCTAGGGGTATATCAGTAATTTTGC
1 CCCTAGGGGTAAATCAGTAATTTTCC
* *
42621147 TCCTAGGGGTAAATCTGTAAATTTTCC
1 CCCTAGGGGTAAATCAGT-AATTTTCC
42621174 CCCTA
1 CCCTA
42621179 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (26 bp):
CCCTAGGGGTAAATCAGTAATTTTCC
Found at i:42622195 original size:48 final size:48
Alignment explanation
Indices: 42622124--42622218 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
42622114 ACTCGAATCC
42622124 AGGAGATCTAAAGTTTCGGCTATAAGTCCCTAAATCTATGGTATTTCT
1 AGGAGATCTAAAGTTTCGGCTATAAGTCCCTAAATCTATGGTATTTCT
42622172 AGGAGATCTAAAGTTTCGGCTATAAGTCCCTAAATCTATGGTATTTC
1 AGGAGATCTAAAGTTTCGGCTATAAGTCCCTAAATCTATGGTATTTC
42622219 AGTTTTTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (48 bp):
AGGAGATCTAAAGTTTCGGCTATAAGTCCCTAAATCTATGGTATTTCT
Found at i:42622706 original size:170 final size:170
Alignment explanation
Indices: 42622424--42622763 Score: 671
Period size: 170 Copynumber: 2.0 Consensus size: 170
42622414 GGTTTTGTGA
*
42622424 AGGATGGGATTGACAGAGGAGGTGAGTAGAATGGTAGGAATGTTTTGGCTAGAGAAGAAAATAAG
1 AGGATGGGATTGACAGAGGAGGTGAGTAGAATGGTAGGAATGTTTTGCCTAGAGAAGAAAATAAG
42622489 GAGAAAAAGAAAATAGAAGAATTCGGCACTCAGGAGATCTAACTTTGCGTTTTTCTACTTTTTGG
66 GAGAAAAAGAAAATAGAAGAATTCGGCACTCAGGAGATCTAACTTTGCGTTTTTCTACTTTTTGG
42622554 GATACTGAGAAGAGAATAGAATGAAAGGGAAGGATCTAGG
131 GATACTGAGAAGAGAATAGAATGAAAGGGAAGGATCTAGG
42622594 AGGATGGGATTGACAGAGGAGGTGAGTAGAATGGTAGGAATGTTTTGCCTAGAGAAGAAAATAAG
1 AGGATGGGATTGACAGAGGAGGTGAGTAGAATGGTAGGAATGTTTTGCCTAGAGAAGAAAATAAG
42622659 GAGAAAAAGAAAATAGAAGAATTCGGCACTCAGGAGATCTAACTTTGCGTTTTTCTACTTTTTGG
66 GAGAAAAAGAAAATAGAAGAATTCGGCACTCAGGAGATCTAACTTTGCGTTTTTCTACTTTTTGG
42622724 GATACTGAGAAGAGAATAGAATGAAAGGGAAGGATCTAGG
131 GATACTGAGAAGAGAATAGAATGAAAGGGAAGGATCTAGG
42622764 TGGCTAACCC
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 169 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.24
Consensus pattern (170 bp):
AGGATGGGATTGACAGAGGAGGTGAGTAGAATGGTAGGAATGTTTTGCCTAGAGAAGAAAATAAG
GAGAAAAAGAAAATAGAAGAATTCGGCACTCAGGAGATCTAACTTTGCGTTTTTCTACTTTTTGG
GATACTGAGAAGAGAATAGAATGAAAGGGAAGGATCTAGG
Found at i:42630093 original size:65 final size:65
Alignment explanation
Indices: 42629989--42630119 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
42629979 AGTCCCATGC
*
42629989 ATCAGATAATAATAACATGGCATGCAGTAAATAGTAACAGTCAAACACGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTCAAACACGCATTCAGGTCAACCTT
*
42630054 ATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTCAAACATGCATTCAGGTCAACCTT
1 ATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTCAAACACGCATTCAGGTCAACCTT
42630119 A
1 A
42630120 ACCCTAGGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (65 bp):
ATCAGATAATAATAACATGGAATGCAGTAAATAGTAACAGTCAAACACGCATTCAGGTCAACCTT
Found at i:42630178 original size:27 final size:26
Alignment explanation
Indices: 42630121--42630178 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
42630111 TCAACCTTAA
* *
42630121 CCCTAGGGGTATATCAGTAATTTTGC
1 CCCTAGGGGTAAATCAGTAATTTTCC
* *
42630147 TCCTAGGGGTAAATCTGTAAATTTTCC
1 CCCTAGGGGTAAATCAGT-AATTTTCC
42630174 CCCTA
1 CCCTA
42630179 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (26 bp):
CCCTAGGGGTAAATCAGTAATTTTCC
Found at i:42633818 original size:20 final size:20
Alignment explanation
Indices: 42633772--42633819 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
42633762 AGTAAGCTCG
*
42633772 GTTGAGCTCACACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
42633792 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
42633812 GTTGAGCT
1 GTTGAGCT
42633820 AGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:42636987 original size:54 final size:54
Alignment explanation
Indices: 42636803--42636999 Score: 254
Period size: 55 Copynumber: 3.6 Consensus size: 54
42636793 AAATTACCAT
* * * * *
42636803 TGCCATGTCTTGGCATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTAATCAA
** *
42636856 TGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATAGTAACTAATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCC-TTGCCTTATAG-AACTAATCAA
* * * *
42636911 TGCCATGTCTTGGCATGGTCTTACATGATTTCGTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTAATCAA
42636965 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTT
42637000 ATCTTGCCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.02
53 35 0.28
54 42 0.34
55 44 0.35
56 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAGAACTAATCAA
Found at i:42637033 original size:47 final size:47
Alignment explanation
Indices: 42636978--42637099 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 47
42636968 CATGCCTTGG
* * *
42636978 CATGGTCTTACATGATATCCTTATCTTGCCAAATGCCATGTTCCGAA
1 CATGGTCTTACATGATATCCTTATCTTACCAAATACCATGTTCCAAA
* * *
42637025 CATGGTCTTACATGGTATCCTTGTTTTACCAAATACCATGTTCCAAA
1 CATGGTCTTACATGATATCCTTATCTTACCAAATACCATGTTCCAAA
* * *
42637072 CATGGTCTTACATGGTTTCCTTGTCTTA
1 CATGGTCTTACATGATATCCTTATCTTA
42637100 GTTCCAATGC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (47 bp):
CATGGTCTTACATGATATCCTTATCTTACCAAATACCATGTTCCAAA
Found at i:42637305 original size:44 final size:44
Alignment explanation
Indices: 42637239--42637322 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
42637229 TCCTTAATCG
* *
42637239 TCAATTCCTCCTTAAATTCCATGTTATGAA-CATGGACTTTTCTA
1 TCAATTCCTCCTTAAATTCCATGGTA-CAACCATGGACTTTTCTA
* *
42637283 TCAATT-CTTCTTTAATTGCCATGGTACAACCATGGACTTT
1 TCAATTCCTCCTTAAATT-CCATGGTACAACCATGGACTTT
42637323 GAGATATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 11 0.32
44 23 0.68
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (44 bp):
TCAATTCCTCCTTAAATTCCATGGTACAACCATGGACTTTTCTA
Found at i:42640299 original size:11 final size:11
Alignment explanation
Indices: 42640279--42640307 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42640269 ACCCAATTCA
42640279 TTTC-CTCACT
1 TTTCTCTCACT
42640289 TTTCTCTCACT
1 TTTCTCTCACT
42640300 TTTCTCTC
1 TTTCTCTC
42640308 TTCATTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTCTCTCACT
Found at i:42642150 original size:43 final size:41
Alignment explanation
Indices: 42642095--42642252 Score: 126
Period size: 43 Copynumber: 3.8 Consensus size: 41
42642085 ATATCGAATA
* * * **
42642095 ATGCCAATGTCCCAAACATGGTCTTATATGCTATCTCATATCG
1 ATGCCACTGTCCCAAACATGGTCTTACATG-AATCAAATA-CG
*
42642138 ATGCCACTGTCCCAAACAGGGTCTTACATGAATCAAATACG
1 ATGCCACTGTCCCAAACATGGTCTTACATGAATCAAATACG
* * *
42642179 ATGCC-CATGTCCCAGACATGGTCTTACTCAT-AACCACATATCG
1 ATGCCAC-TGTCCCAAACATGGTCTTA--CATGAATCAAATA-CG
* *
42642222 ATGCCAAC-GTCCC-GACGTGGTCTTACATGAA
1 ATGCC-ACTGTCCCAAACATGGTCTTACATGAA
42642253 AACACATATA
Statistics
Matches: 97, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
40 4 0.04
41 26 0.27
42 24 0.25
43 42 0.43
45 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (41 bp):
ATGCCACTGTCCCAAACATGGTCTTACATGAATCAAATACG
Found at i:42642302 original size:45 final size:45
Alignment explanation
Indices: 42642132--42642395 Score: 258
Period size: 45 Copynumber: 6.0 Consensus size: 45
42642122 ATGCTATCTC
* * *
42642132 ATATCGATGCC-ACTGTCCCAAACAG-GGTCTTACATG-AATCA-A-
1 ATATCGATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACAT
* * * * * *
42642174 ATA-CGATGCCCATGTCCCAGACATGGTCTTACTC-ATAAC-CAC
1 ATATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAT
*
42642216 ATATCGATGCCAACGTCCC-GACGTGGTCTTACATGAAAACACAT
1 ATATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAT
* *
42642260 ATATCGATGCCAACGTCCCAGATGTGGTCTTACACAAAAACACAT
1 ATATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAT
* * * *
42642305 ATATCGATGCCAACGTCCCTGCCGGGGTCTTACATGAAAACACAT
1 ATATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAT
* * * * *
42642350 ATATTGATGCCAACGTCCTAAATGTGGTCGTACACGAAAACACAT
1 ATATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAT
42642395 A
1 A
42642396 GCATAATCCT
Statistics
Matches: 181, Mismatches: 32, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
41 26 0.14
42 19 0.10
43 17 0.09
44 21 0.12
45 98 0.54
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (45 bp):
ATATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAT
Found at i:42642359 original size:90 final size:89
Alignment explanation
Indices: 42642216--42642395 Score: 288
Period size: 90 Copynumber: 2.0 Consensus size: 89
42642206 TCATAACCAC
* *
42642216 ATATCGATGCCAACGTCCCGACGTGGTCTTACATGAAAACACATATATCGATGCCAACGTCCCAG
1 ATATCGATGCCAACGTCCCGACGGGGTCTTACATGAAAACACATATATCGATGCCAACGTCCCAA
*
42642281 ATGTGGTCTTACACAAAAACACAT
66 ATGTGGTCGTACACAAAAACACAT
* * *
42642305 ATATCGATGCCAACGTCCCTGCCGGGGTCTTACATGAAAACACATATATTGATGCCAACGTCCTA
1 ATATCGATGCCAACGTCCC-GACGGGGTCTTACATGAAAACACATATATCGATGCCAACGTCCCA
*
42642370 AATGTGGTCGTACACGAAAACACAT
65 AATGTGGTCGTACACAAAAACACAT
42642395 A
1 A
42642396 GCATAATCCT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 19 0.23
90 64 0.77
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (89 bp):
ATATCGATGCCAACGTCCCGACGGGGTCTTACATGAAAACACATATATCGATGCCAACGTCCCAA
ATGTGGTCGTACACAAAAACACAT
Found at i:42644171 original size:47 final size:47
Alignment explanation
Indices: 42644120--42644337 Score: 382
Period size: 47 Copynumber: 4.6 Consensus size: 47
42644110 AGATGACAGT
** * * *
42644120 CAGTGTAAGACCATGTAAGGGACATGGCATTGACTTCAGATATGAGC
1 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
42644167 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
1 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
42644214 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
1 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
42644261 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
1 CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
*
42644308 CAGTGTAAGACCATGTCTGGGACATGGCAT
1 CAGTGTAAGACCATGTCTGGGACACGGCAT
42644338 CGACACCTTA
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 165 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (47 bp):
CAGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGC
Found at i:42644218 original size:94 final size:94
Alignment explanation
Indices: 42644029--42644337 Score: 391
Period size: 94 Copynumber: 3.3 Consensus size: 94
42644019 GACGAAAGAT
* ** * *
42644029 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CCTCGAGACGTAAGCGAGTGTAAGA-CATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCAT-GGACTTC-AGATATGAGCCAGTGTAAGACCATGTC
* * *
42644090 TGGGACA-TGCATCGG--TTACGAGATGA-CAGTC
64 TGGGACACGGCAT-GGACTT--GAGAT-ATGAGCC
** *
42644121 AGTGTAAGACCATGTAAGGGACATGGCATTGACTTCAGATATGAGCCAGTGTAAGACCATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATGGACTTCAGATATGAGCCAGTGTAAGACCATGTCTG
42644186 GGACACGGCATGGACTTGAGATATGAGCC
66 GGACACGGCATGGACTTGAGATATGAGCC
* *
42644215 AGTGTAAGACCATGTCTGGGACACGGCATGGACTTGAGATATGAGCCAGTGTAAGACCATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATGGACTTCAGATATGAGCCAGTGTAAGACCATGTCTG
42644280 GGACACGGCATGGACTTGAGATATGAGCC
66 GGACACGGCATGGACTTGAGATATGAGCC
42644309 AGTGTAAGACCATGTCTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
42644338 CGACACCTTA
Statistics
Matches: 192, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
92 9 0.05
93 30 0.16
94 147 0.77
95 4 0.02
96 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (94 bp):
AGTGTAAGACCATGTCTGGGACATGGCATGGACTTCAGATATGAGCCAGTGTAAGACCATGTCTG
GGACACGGCATGGACTTGAGATATGAGCC
Found at i:42650317 original size:40 final size:40
Alignment explanation
Indices: 42650273--42650536 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
42650263 GCTCCTCGTT
* *
42650273 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
42650313 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42650353 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42650393 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
42650433 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42650472 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
42650513 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42650537 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42652743 original size:40 final size:40
Alignment explanation
Indices: 42652695--42652773 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
42652685 TTTCTGTTCG
*
42652695 GCATCCTTAATCAAATCAACTCTGAAAATTTTACTTTCAA
1 GCATCCTTAATCAAATCAACTCCGAAAATTTTACTTTCAA
42652735 GCATCCTTAATCAAATCAACTCCGAAAATTTTACTTTCA
1 GCATCCTTAATCAAATCAACTCCGAAAATTTTACTTTCA
42652774 CCGAGCTCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (40 bp):
GCATCCTTAATCAAATCAACTCCGAAAATTTTACTTTCAA
Found at i:42655804 original size:256 final size:256
Alignment explanation
Indices: 42655344--42655852 Score: 991
Period size: 256 Copynumber: 2.0 Consensus size: 256
42655334 ATCAAGTTCT
*
42655344 CCGGGAAACAGGAACCTCGAATTTCTAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAA
1 CCGGAAAACAGGAACCTCGAATTTCTAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAA
*
42655409 CGACCCAAGGGGTTTGACACCCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGA
66 CGACCCAAGGGATTTGACACCCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGA
42655474 TGCTAAGGTTTCACATATGTAAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTAT
131 TGCTAAGGTTTCACATATGTAAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTAT
42655539 CAAAGAGAGTAAAAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGCCG
196 CAAAGAGAGTAAAAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGCCG
*
42655600 CCGGAAAACAGGAACCTTGAATTTCTAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAA
1 CCGGAAAACAGGAACCTCGAATTTCTAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAA
42655665 CGACCCAAGGGATTTGACACCCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGA
66 CGACCCAAGGGATTTGACACCCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGA
42655730 TGCTAAGGTTTCACATATGTAAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTAT
131 TGCTAAGGTTTCACATATGTAAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTAT
42655795 CAAAGAGAGTAAAAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACG
196 CAAAGAGAGTAAAAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACG
42655853 TATAGCATAA
Statistics
Matches: 250, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
256 250 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (256 bp):
CCGGAAAACAGGAACCTCGAATTTCTAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAA
CGACCCAAGGGATTTGACACCCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGA
TGCTAAGGTTTCACATATGTAAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTAT
CAAAGAGAGTAAAAGTACCGGTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGCCG
Found at i:42658643 original size:40 final size:40
Alignment explanation
Indices: 42658599--42658862 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
42658589 GCTCCTCGTT
* *
42658599 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
42658639 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42658679 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42658719 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
42658759 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42658798 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
42658839 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42658863 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42671266 original size:27 final size:27
Alignment explanation
Indices: 42671165--42671271 Score: 137
Period size: 27 Copynumber: 3.9 Consensus size: 27
42671155 AGGAAGCGTC
* *
42671165 CTGGTGGCTATGCCACAATAATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
42671192 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
42671219 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
42671247 CTGGTGACTCTGTCACATTATCTGT
1 CTGGTGGCTCTGCCACATTATCTGT
42671272 TTTGGTAGCC
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
26 2 0.03
27 53 0.74
28 17 0.24
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:42671269 original size:54 final size:54
Alignment explanation
Indices: 42671165--42671277 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
42671155 AGGAAGCGTC
*
42671165 CTGGTGGCTATGCCACAATAATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATAATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
42671219 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATAATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
*
42671273 TTGGT
1 CTGGT
42671278 AGCCATGCTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATAATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:42674870 original size:51 final size:51
Alignment explanation
Indices: 42674815--42674912 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
42674805 ACCTTATAAC
42674815 ATGTAACACATCCATAATGAACTCAAACC-TCTCAACGAGCTCAGATGTTAG
1 ATGTAACACATCCATAATGAACTCAAACCAT-TCAACGAGCTCAGATGTTAG
* * * ** *
42674866 ATGTATCGCATCCATTATGAACTCGGACCATTCAACGAGCTCGGATG
1 ATGTAACACATCCATAATGAACTCAAACCATTCAACGAGCTCAGATG
42674913 CTCACATCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 39 0.98
52 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (51 bp):
ATGTAACACATCCATAATGAACTCAAACCATTCAACGAGCTCAGATGTTAG
Found at i:42675040 original size:43 final size:43
Alignment explanation
Indices: 42674884--42675039 Score: 152
Period size: 43 Copynumber: 3.7 Consensus size: 43
42674874 CATCCATTAT
* * * ** ** *
42674884 GAACTCGGACCATTCAACGAGCTCGGATGCTCACATCCAAAAT
1 GAACTCGGACCACTCAACGAGCTCGAATGCTTACATATATCAC
* * *
42674927 GAACTCAGACCACTCAAGGAGCTCGGATGC-TACATATATCAC
1 GAACTCGGACCACTCAACGAGCTCGAATGCTTACATATATCAC
* * * *
42674969 GAACTTGGACCACTCAACAAGTTCGAATTCTTACATATATCAC
1 GAACTCGGACCACTCAACGAGCTCGAATGCTTACATATATCAC
* *
42675012 GAACTCGGACCATTCAATGAGCTCGAAT
1 GAACTCGGACCACTCAACGAGCTCGAAT
42675040 TTCTTAATTC
Statistics
Matches: 91, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 29 0.32
43 62 0.68
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
GAACTCGGACCACTCAACGAGCTCGAATGCTTACATATATCAC
Found at i:42683006 original size:29 final size:30
Alignment explanation
Indices: 42682959--42683016 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
42682949 TTTAATGAGA
42682959 TTGATAGCAGGAATAAGGAGTATAAACTCC
1 TTGATAGCAGGAATAAGGAGTATAAACTCC
*
42682989 TTGA-AGCAGGAATGAGGAGTATAAACTC
1 TTGATAGCAGGAATAAGGAGTATAAACTC
42683017 TTCGAACCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (30 bp):
TTGATAGCAGGAATAAGGAGTATAAACTCC
Found at i:42690400 original size:18 final size:20
Alignment explanation
Indices: 42690358--42690394 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42690348 ATATTTTATG
*
42690358 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
42690377 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
42690395 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:42698579 original size:30 final size:30
Alignment explanation
Indices: 42698545--42698605 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
42698535 TTCCCGAGCC
42698545 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
42698575 TAGGGGCAAAATTGTAATTTTGTAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
42698605 T
1 T
42698606 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:42700093 original size:39 final size:38
Alignment explanation
Indices: 42699985--42700168 Score: 174
Period size: 39 Copynumber: 4.7 Consensus size: 38
42699975 ATTATATTAT
** * *
42699985 CAGCACAAAGCCTGCGGGACTTTAA-CCCGGATACATTTC
1 CAGCAC-AAGCCTGC-GGACCCTAAGTCCGGATACAATTC
* * * * *
42700024 CAGCACGAAGCCTGTGGGA-CTTTAGCCCGGATACATTTC
1 CAGCAC-AAGCCTG-CGGACCCTAAGTCCGGATACAATTC
* *
42700063 CAGCACGAAGCCTGCGGACCCTAAGTCCGGATATAATCC
1 CAGCAC-AAGCCTGCGGACCCTAAGTCCGGATACAATTC
* *
42700102 CAGCACATAGCCTGCAGACCCTAAGTCCGGATATAATTC
1 CAGCACA-AGCCTGCGGACCCTAAGTCCGGATACAATTC
42700141 CAGCACATAGCCTGCGGACCCTAAGTCC
1 CAGCACA-AGCCTGCGGACCCTAAGTCC
42700169 AAATACACAT
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
38 7 0.06
39 120 0.94
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (38 bp):
CAGCACAAGCCTGCGGACCCTAAGTCCGGATACAATTC
Found at i:42703669 original size:4 final size:4
Alignment explanation
Indices: 42703660--42703698 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
42703650 TAGTTCCGTT
42703660 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTT- TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
42703699 AAGCTCCTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:42705677 original size:46 final size:46
Alignment explanation
Indices: 42705619--42705791 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
42705609 TTGGGCATCG
*
42705619 GAACTCGATGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCC
*** * * * *
42705665 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GCGTCC
* * * *
42705712 GAGCTCATCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTC-C
*
42705758 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42705792 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
45 1 0.01
46 66 0.65
47 35 0.34
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCC
Found at i:42714288 original size:27 final size:27
Alignment explanation
Indices: 42714247--42714300 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
42714237 TGTCATGTGA
* *
42714247 AATTGAATGGCAAATTATTCTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
42714274 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
42714301 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:42714717 original size:99 final size:99
Alignment explanation
Indices: 42714546--42714741 Score: 320
Period size: 99 Copynumber: 2.0 Consensus size: 99
42714536 ATCTATTGTG
*
42714546 AGGTCACATGTGTAGTACTAAGTGCACGCCACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCACATGTGTAGTACTAAGTGCACGCCACTACGTGTACCGGATAATTCGTCGCATGTGTAGT
* * *
42714611 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 ACTAAGTGCAAGCTACTACGCGTACCAGATGGTT
* * *
42714645 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTCGTCGCATGTGTAGT
1 AGGTCACATGTGTAGTACTAAGTGCACGCCACTACGTGTACCGGATAATTCGTCGCATGTGTAGT
*
42714710 ACTAAGTGCAAGCTACTATGCGTACCAGATGG
66 ACTAAGTGCAAGCTACTACGCGTACCAGATGG
42714742 CCTTGTCTAC
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (99 bp):
AGGTCACATGTGTAGTACTAAGTGCACGCCACTACGTGTACCGGATAATTCGTCGCATGTGTAGT
ACTAAGTGCAAGCTACTACGCGTACCAGATGGTT
Found at i:42714735 original size:49 final size:49
Alignment explanation
Indices: 42714547--42714727 Score: 254
Period size: 49 Copynumber: 3.7 Consensus size: 49
42714537 TCTATTGTGA
* * *
42714547 GGTCACATGTGTAGTACTAAGTGCACGCCACTACGTGTACCGGATAATT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * **
42714596 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
42714645 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* *
42714695 CGTCGCATGTGTAGTACTAAGTGCAAGCTACTA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
42714728 TGCGTACCAG
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
49 71 0.62
50 43 0.38
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:42720097 original size:12 final size:13
Alignment explanation
Indices: 42720069--42720101 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42720059 TTATTTCTTT
42720069 TTCTCCATCTACC
1 TTCTCCATCTACC
*
42720082 TTCTCC-TCTTCC
1 TTCTCCATCTACC
42720094 TTCTCCAT
1 TTCTCCAT
42720102 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:42721201 original size:28 final size:28
Alignment explanation
Indices: 42721169--42721233 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
42721159 ATTTACTAGA
*
42721169 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
42721197 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
42721225 ATACCCCTA
1 ATACCCCTA
42721234 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:42721398 original size:27 final size:27
Alignment explanation
Indices: 42721339--42721428 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
42721329 AGGAAGCGTC
42721339 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* * *
42721367 TTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
42721394 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
42721423 CTGGTG
1 CTGGTG
42721429 ACTCTGTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 22 0.42
28 24 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:42721439 original size:29 final size:28
Alignment explanation
Indices: 42721349--42721439 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
42721339 CTGGTGGCTA
* * * *
42721349 TGCCACAAATTATCTGTTTTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
42721377 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
42721404 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
42721433 TGTCACA
1 TGCCACA
42721440 TTTTCTGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.43
28 15 0.28
29 15 0.28
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:42721447 original size:55 final size:56
Alignment explanation
Indices: 42721339--42721453 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
42721329 AGGAAGCGTC
* * *
42721339 CTGGTGGCTATGCCACAAATTATCTGTTTTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
42721394 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
42721450 CTGG
1 CTGG
42721454 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:42721914 original size:19 final size:19
Alignment explanation
Indices: 42721892--42721930 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42721882 TTTAATTATT
* *
42721892 TTTTATCGTTTTGTTTTAC
1 TTTTATCATTTTATTTTAC
*
42721911 TTTTATTATTTTATTTTAC
1 TTTTATCATTTTATTTTAC
42721930 T
1 T
42721931 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTATCATTTTATTTTAC
Found at i:42725446 original size:101 final size:99
Alignment explanation
Indices: 42725247--42725447 Score: 258
Period size: 99 Copynumber: 2.0 Consensus size: 99
42725237 TATGTAGCCA
* * * * * *
42725247 AACTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTGCACG
1 AACTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTACACA
*
42725312 TAGTAGCCTGCACTTAGTACTACACACGTGACCT
66 TAGTAGCCTGCACTTAGTACTACACACGCGACCT
* * * * *
42725346 AACTATCTGATACACTTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCATGTACG
1 AACTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCAGGTACA
* *
42725411 CATAGTAGCCTGGACTTAGTACTACACATGCGACCT
64 CATAGTAGCCTGCACTTAGTACTACACACGCGACCT
42725447 A
1 A
42725448 GCTACATATA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 42 0.49
100 3 0.03
101 41 0.48
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (99 bp):
AACTATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCAGGTACACA
TAGTAGCCTGCACTTAGTACTACACACGCGACCT
Found at i:42725548 original size:67 final size:64
Alignment explanation
Indices: 42725434--42725591 Score: 167
Period size: 67 Copynumber: 2.4 Consensus size: 64
42725424 ACTTAGTACT
* *
42725434 ACACATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATAG-ATC
1 ACACATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACATAGCACC
* ** * *
42725497 ACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTAC-ACATGATGTGCACTTAG
1 ACACATGCGACCTAGCTACAT-AT-A--TCCCGTAGCTCTCTTGT-CTACATGATGTACACATAG
42725561 CACC
61 CACC
* *
42725565 ATACATGTGACCTAGCTACATACTATC
1 ACACATGCGACCTAGCTACATA-TATC
42725592 TGAATCATCC
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 20 0.26
64 2 0.03
65 3 0.04
67 31 0.40
68 22 0.28
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (64 bp):
ACACATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACATAGCACC
Found at i:42726287 original size:30 final size:30
Alignment explanation
Indices: 42726251--42726311 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
42726241 TCCTTAACTC
42726251 AAACTTTGGAAAT-TTTACAATTTTGCCCCT
1 AAACTTT-GAAATATTTACAATTTTGCCCCT
* * *
42726281 AAACTTTTACATATTTACACTTTTGCCCCT
1 AAACTTTGAAATATTTACAATTTTGCCCCT
42726311 A
1 A
42726312 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTGAAATATTTACAATTTTGCCCCT
Found at i:42729492 original size:46 final size:48
Alignment explanation
Indices: 42729261--42729622 Score: 283
Period size: 46 Copynumber: 7.7 Consensus size: 48
42729251 GGGTATAATA
* * **
42729261 CCGATGCCATGTCCTAGACATGGTCTTACACTGGC-T-CATCCATCAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACAT-CTTGTAG
* * * *
42729308 TCGATGCAATGTCCCAGACATGGTCTTACACTGACTATCAAAT-TTG-AGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-T-ACATCTTGTA-G
* *
42729357 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATTCGT-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TT-ACATCTT-GTAG
*
42729407 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC--ACATCTTGTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTTGTAG
* *
42729453 CCGATG-CATGTCCCAGACAT-GTCTTACATTGGCTTACATCTCG-AGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTTGTA-G
* * **
42729499 CCGAAG-CATGTCCCAGACAT-GTCTTACACTAGC--AC-TCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATC-T-TGTA-G
* * ** *
42729545 CAGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CCTAATGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACATCTTGTAG
*
42729593 CTGATG-CATGTCCCAGACAT-GTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
42729623 AGCTCACACA
Statistics
Matches: 260, Mismatches: 33, Indels: 45
0.77 0.10 0.13
Matches are distributed among these distances:
43 2 0.01
44 14 0.05
45 17 0.07
46 67 0.26
47 59 0.23
48 19 0.07
49 40 0.15
50 38 0.15
51 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATCTTGTAG
Found at i:42729573 original size:94 final size:92
Alignment explanation
Indices: 42729263--42729625 Score: 307
Period size: 94 Copynumber: 3.9 Consensus size: 92
42729253 GTATAATACC
* * ** *
42729263 GATGCCATGTCCTAGACATGGTCTTACACTGGC-T-CATCCATCAAGTCGATGCAATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACAT-AATCGGGCCGATGC-ATGTCCCAGA
* * *
42729326 CATGGTCTTACACT-G-ACTATCAAATTTGAGGCC
64 CAT-GTCTTACACTAGCAC-ATC----TTCAAGCA
* * *
42729359 GATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCACATATTCGTGCCGATGCCATGTCCCAG
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TT-ACATAATCGGGCCGATG-CATGTCCCAG
** *
42729424 ACATGGTCTTACACT-GACACATCTTGTAGCC
63 ACAT-GTCTTACACTAG-CACATCTTCAAGCA
* * *
42729455 GATG-CATGTCCCAGACAT-GTCTTACATTGGCTTACAT-CTCGAGGCCGAAGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATAATCG-GGCCGATGCATGTCCCAGAC
42729517 ATGTCTTACACTAGCAC-TCGTCTCAATGCA
65 ATGTCTTACACTAGCACATC-T-TCAA-GCA
* *
42729547 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CCTAAT-GTGGCTGATGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-TACATAATCG-GGCCGATGCATGTCCCAGA
42729610 CATGTCTTACACTAGC
64 CATGTCTTACACTAGC
42729626 TCACACAAAT
Statistics
Matches: 228, Mismatches: 23, Indels: 34
0.80 0.08 0.12
Matches are distributed among these distances:
89 2 0.01
90 14 0.06
91 20 0.09
92 16 0.07
93 16 0.07
94 60 0.26
95 16 0.07
96 41 0.18
98 1 0.00
99 33 0.14
100 7 0.03
101 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (92 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTTACATAATCGGGCCGATGCATGTCCCAGACA
TGTCTTACACTAGCACATCTTCAAGCA
Found at i:42735891 original size:229 final size:229
Alignment explanation
Indices: 42735622--42736079 Score: 898
Period size: 229 Copynumber: 2.0 Consensus size: 229
42735612 AAATTTATCG
42735622 AAGTAATAGGTTTGTCTTACGTTATCTATCCAAAGAGAGAAGATTCATTTTGACTGAGAAAGGTA
1 AAGTAATAGGTTTGTCTTACGTTATCTATCCAAAGAGAGAAGATTCATTTTGACTGAGAAAGGTA
42735687 AACCCAATCCTCAATTGTCTTCTCTTCATATTCGTCAAGGTAAGTCATCTGAAAAATTTCAAATA
66 AACCCAATCCTCAATTGTCTTCTCTTCATATTCGTCAAGGTAAGTCATCTGAAAAATTTCAAATA
42735752 TCTTTGCTCACTTCGATTGAAGTTGAAAATTCCATTGATTGGTTGTTTGGAAATTATTTATACTT
131 TCTTTGCTCACTTCGATTGAAGTTGAAAATTCCATTGATTGGTTGTTTGGAAATTATTTATACTT
42735817 TGATGTGATGGATTTTTCCTTTTGGAATTGTGAT
196 TGATGTGATGGATTTTTCCTTTTGGAATTGTGAT
42735851 AAGTAATAGGTTTGTCTTACGTTATCTATCCAAAGAGAGAAGATTCATTTTGACTGAGAAAGGTA
1 AAGTAATAGGTTTGTCTTACGTTATCTATCCAAAGAGAGAAGATTCATTTTGACTGAGAAAGGTA
* *
42735916 AACCCAATCCTCAATTTTCTTCTCTTCATATTCGTCAAGGTAAGTCATCTGAAAATTTTCAAATA
66 AACCCAATCCTCAATTGTCTTCTCTTCATATTCGTCAAGGTAAGTCATCTGAAAAATTTCAAATA
42735981 TCTTTGCTCACTTCGATTGAAGTTGAAAATTCCATTGATTGGTTGTTTGGAAATTATTTATACTT
131 TCTTTGCTCACTTCGATTGAAGTTGAAAATTCCATTGATTGGTTGTTTGGAAATTATTTATACTT
42736046 TGATGTGATGGATTTTTCCTTTTGGAATTGTGAT
196 TGATGTGATGGATTTTTCCTTTTGGAATTGTGAT
42736080 GATGTGATTA
Statistics
Matches: 227, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 227 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (229 bp):
AAGTAATAGGTTTGTCTTACGTTATCTATCCAAAGAGAGAAGATTCATTTTGACTGAGAAAGGTA
AACCCAATCCTCAATTGTCTTCTCTTCATATTCGTCAAGGTAAGTCATCTGAAAAATTTCAAATA
TCTTTGCTCACTTCGATTGAAGTTGAAAATTCCATTGATTGGTTGTTTGGAAATTATTTATACTT
TGATGTGATGGATTTTTCCTTTTGGAATTGTGAT
Found at i:42736912 original size:30 final size:30
Alignment explanation
Indices: 42736878--42736974 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
42736868 AGCTCACTCC
42736878 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
42736908 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
42736938 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
42736968 TAGCTCA
1 TAGCTCA
42736975 TTTTACTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:42740605 original size:21 final size:21
Alignment explanation
Indices: 42740579--42740641 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
42740569 TTGGTATTTG
*
42740579 GGAATTAGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
42740600 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
42740621 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
42740642 ATGGTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:42743131 original size:10 final size:10
Alignment explanation
Indices: 42743116--42743153 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
42743106 GCTCGTTTCC
*
42743116 AGCTCACTCG
1 AGCTCAATCG
42743126 AGCTCAAGTC-
1 AGCTCAA-TCG
42743136 AGCTCAATCG
1 AGCTCAATCG
42743146 AGCTCAAT
1 AGCTCAAT
42743154 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:42743140 original size:20 final size:20
Alignment explanation
Indices: 42743115--42743152 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42743105 AGCTCGTTTC
*
42743115 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
42743135 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
42743153 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:42743159 original size:20 final size:20
Alignment explanation
Indices: 42743116--42743176 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
42743106 GCTCGTTTCC
* * *
42743116 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
42743136 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
42743156 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
42743176 A
1 A
42743177 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:42743170 original size:11 final size:10
Alignment explanation
Indices: 42743126--42743172 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
42743116 AGCTCACTCG
*
42743126 AGCTCAAGTC
1 AGCTCAATTC
42743136 AGCTCAA-TC
1 AGCTCAATTC
*
42743145 GAGCTCAATTT
1 -AGCTCAATTC
42743156 AGCTACAATTC
1 AGCT-CAATTC
42743167 AGCTCA
1 AGCTCA
42743173 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:42744655 original size:33 final size:33
Alignment explanation
Indices: 42744618--42744683 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
42744608 AGTTTAACTT
*
42744618 ACAATTGTTTCATATTTCCCCTGTGTTGTTGTC
1 ACAATTGTTTCATATTCCCCCTGTGTTGTTGTC
42744651 ACAATTGTTTCATATTCCCCCTGTGTTGTTGTC
1 ACAATTGTTTCATATTCCCCCTGTGTTGTTGTC
42744684 TATCAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (33 bp):
ACAATTGTTTCATATTCCCCCTGTGTTGTTGTC
Found at i:42752504 original size:11 final size:10
Alignment explanation
Indices: 42752476--42752503 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
42752466 ATATACTTCG
42752476 ATTTTTTTGA
1 ATTTTTTTGA
42752486 ATTTTTTTGA
1 ATTTTTTTGA
42752496 ATTTTTTT
1 ATTTTTTT
42752504 TTCAAATTTC
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:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:42753968 original size:20 final size:19
Alignment explanation
Indices: 42753945--42754009 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
42753935 AAGCTCAAAC
42753945 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
42753965 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
42753985 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
42754005 GAGCT
1 GAGCT
42754010 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Done.