Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 109 of 186
Found at i:36029620 original size:21 final size:20
Alignment explanation
Indices: 36029596--36029697 Score: 82
Period size: 20 Copynumber: 5.0 Consensus size: 20
36029586 GGCCTGGAGC
36029596 AATTTTGACTTGTTTGAAAAT
1 AATTTTGACTTGTTT-AAAAT
36029617 AATTTTGA-TATG-TTAAAAT
1 AATTTTGACT-TGTTTAAAAT
* * * *
36029636 TATTTTAACTTGATTGAAAT
1 AATTTTGACTTGTTTAAAAT
* *
36029656 CATTTTGACTTGGTTAAAAT
1 AATTTTGACTTGTTTAAAAT
* *
36029676 CATTTTCACTTGATTTTAAAAT
1 AATTTTGACTTG--TTTAAAAT
36029698 TGTTTCAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
19 13 0.19
20 37 0.55
21 10 0.15
22 7 0.10
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (20 bp):
AATTTTGACTTGTTTAAAAT
Found at i:36029641 original size:40 final size:41
Alignment explanation
Indices: 36029597--36029697 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 41
36029587 GCCTGGAGCA
* *
36029597 ATTTTGACTTGTTTGAAAATAATTTTGA-TAT-GTTAAAATT
1 ATTTTAACTTGTTTGAAAATAATTTTGACT-TGGTTAAAATC
* *
36029637 ATTTTAACTTGATTG-AAATCATTTTGACTTGGTTAAAATC
1 ATTTTAACTTGTTTGAAAATAATTTTGACTTGGTTAAAATC
* *
36029677 ATTTTCACTTGATTTTAAAAT
1 ATTTTAACTTG-TTTGAAAAT
36029698 TGTTTCAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
39 12 0.24
40 32 0.64
41 2 0.04
42 4 0.08
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (41 bp):
ATTTTAACTTGTTTGAAAATAATTTTGACTTGGTTAAAATC
Found at i:36041313 original size:16 final size:16
Alignment explanation
Indices: 36041294--36041326 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36041284 AGATGGTACC
*
36041294 GTATGAGGCTTTGTAT
1 GTATAAGGCTTTGTAT
36041310 GTATAAGGCTTTGTAT
1 GTATAAGGCTTTGTAT
36041326 G
1 G
36041327 GTCAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.30, T:0.42
Consensus pattern (16 bp):
GTATAAGGCTTTGTAT
Found at i:36047584 original size:46 final size:47
Alignment explanation
Indices: 36047432--36047637 Score: 194
Period size: 46 Copynumber: 4.4 Consensus size: 47
36047422 TTTGTTTGCT
* * * *
36047432 AGTGTAAGGCATGTCTGGGACATGCATCGGCCAC-ATTAT-AAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTAGAGCC
* * * * *
36047478 AGTGTAAGACCATGTTTGGGACATAGCATCGGCATTGAGACG-AGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGCC
*
36047526 AGTGTAAGACATGTCTGGGACATGCATAGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
* * *
36047572 AGTGTAAGACATGTTTGGGACATGCATC-GACTACGAGATGT---GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGCC
36047616 AGTGTAAGACCATGTCTGGGAC
1 AGTGTAAGA-CATGTCTGGGAC
36047638 TGGCATTGGC
Statistics
Matches: 134, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
44 11 0.08
45 14 0.10
46 58 0.43
47 27 0.20
48 23 0.17
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
Found at i:36047827 original size:47 final size:47
Alignment explanation
Indices: 36047432--36047839 Score: 196
Period size: 47 Copynumber: 8.7 Consensus size: 47
36047422 TTTGTTTGCT
*
36047432 AGTGTAAG-GCATGTCTGGGACAT-GCATCGGCCACATT-AT-AA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G--AC-TTGATGAATGAGCC
* * * *
36047478 AGTGTAAGACCATGTTTGGGACATAGCATCGGCATTGA-GACGA-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGATGA--ATGAGCC
* * *
36047526 AGTGTAAGA-CATGTCTGGGACAT-GCATAGGCCTCGA-G-ATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCAT-CGACTTGATGAATG--AGCC
* * * *
36047572 AGTGTAAGA-CATGTTTGGGACAT-GCATCGAC-T-ACGAGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGA-ATGAGCC
* * * * * **
36047616 AGTGTAAGACCATGTCTGGGAC-TGGCATTGGCATGTAT-AGAGGTGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTG-ATGA-ATGAGCC
* * *
36047663 AGTGTAAGGCCATGTCTTGGACATGGCATCAGTACGGATATG-TG-A-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G-AC---T-TGATGAATGAGCC
* * **
36047713 AGTGTAAGACCATGTCTCGGACATGGCGTCGACCTCT-ATTTTG-AT-AGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGA-CT-TGA---TGAATGAGCC
*
36047762 AGTGTAAGACCATATCTGGGACATGGCATCGACTTGATGAATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAATGAGCC
36047809 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
36047840 GCATTATACC
Statistics
Matches: 288, Mismatches: 39, Indels: 69
0.73 0.10 0.17
Matches are distributed among these distances:
43 2 0.01
44 14 0.05
45 25 0.09
46 55 0.19
47 89 0.31
48 30 0.10
49 38 0.13
50 31 0.11
51 1 0.00
52 1 0.00
54 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAATGAGCC
Found at i:36049366 original size:25 final size:26
Alignment explanation
Indices: 36049311--36049367 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
36049301 TGCTTGTGAG
36049311 AGCATACCAATCTACAGCTCGAATGA
1 AGCATACCAATCTACAGCTCGAATGA
* *
36049337 A-CATACCGAT-TCACAGCTCGTAT-A
1 AGCATACCAATCT-ACAGCTCGAATGA
36049361 AGCATAC
1 AGCATAC
36049368 ATGTACAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.11
25 23 0.85
26 1 0.04
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (26 bp):
AGCATACCAATCTACAGCTCGAATGA
Found at i:36055298 original size:43 final size:42
Alignment explanation
Indices: 36055251--36055408 Score: 115
Period size: 43 Copynumber: 3.7 Consensus size: 42
36055241 AACATAAACA
*
36055251 ATGCCAACGTCCTAGACATGGTCTTACATGTAATCAAACATCG
1 ATGCCAACGTCCTAGACATGGTCTTACACGTAATCAAA-ATCG
* * * * *
36055294 ATGCC-ACTATCCCAGACAGGGTCTTACACGAAATCAGATAT-G
1 ATGCCAAC-GTCCTAGACATGGTCTTACACGTAATCA-AAATCG
* * * * *
36055336 ATGCCGATGTTCC-AGACATGGTCTTACACATAAAACAGAAGTCG
1 ATGCCAACG-TCCTAGACATGGTCTTACACGT-AATCA-AAATCG
* **
36055380 ATGCAAACGTCCTAGATGTGGTCTTACAC
1 ATGCCAACGTCCTAGACATGGTCTTACAC
36055409 AAAATCACAT
Statistics
Matches: 89, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
42 23 0.26
43 44 0.49
44 22 0.25
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCTAGACATGGTCTTACACGTAATCAAAATCG
Found at i:36055887 original size:13 final size:13
Alignment explanation
Indices: 36055869--36055898 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36055859 CTTCACCGAA
36055869 TATTAATGGTTCT
1 TATTAATGGTTCT
36055882 TATTAATGGTTCT
1 TATTAATGGTTCT
36055895 TATT
1 TATT
36055899 CAAGTCCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (13 bp):
TATTAATGGTTCT
Found at i:36060523 original size:26 final size:26
Alignment explanation
Indices: 36060462--36060523 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 26
36060452 TTTGACCCAT
* * **
36060462 AGCTCATGCGAGCAGGCTTATTTCAC
1 AGCTCATGTGAGCAGACCCATTTCAC
* * *
36060488 AACTCGTGTGAGCAGACCCATTTTAC
1 AGCTCATGTGAGCAGACCCATTTCAC
36060514 AGCTCATGTG
1 AGCTCATGTG
36060524 GGCAACGATG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (26 bp):
AGCTCATGTGAGCAGACCCATTTCAC
Found at i:36062144 original size:43 final size:43
Alignment explanation
Indices: 36062094--36062244 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 43
36062084 GATTACCAAG
*
36062094 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
* * *
36062136 ATGGTGATTACATGTAAGACCATGTCTGAGACATTGGTATCGTT
1 AT-GTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
* * * * * * * *
36062180 ATATGGTTTCATGTAAGTCCCTGTTTGGGGCAGTGGCATCGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
*
36062223 ATGTGATAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
36062245 ATCCGAGATA
Statistics
Matches: 87, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
42 2 0.02
43 82 0.94
44 3 0.03
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:36063284 original size:36 final size:36
Alignment explanation
Indices: 36063244--36063316 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
36063234 CGTGTGGCTC
*
36063244 GACCGTGTGTGACACATGGCCTTGGTATATGGCTGT
1 GACCGTGTGTGACACATGGCCTTGGTATACGGCTGT
36063280 GACCGTGTGTGACACATGGCCTTGGTATACGGCTGT
1 GACCGTGTGTGACACATGGCCTTGGTATACGGCTGT
36063316 G
1 G
36063317 TGTCCCCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.16, C:0.21, G:0.34, T:0.29
Consensus pattern (36 bp):
GACCGTGTGTGACACATGGCCTTGGTATACGGCTGT
Found at i:36070046 original size:40 final size:39
Alignment explanation
Indices: 36069959--36070209 Score: 256
Period size: 40 Copynumber: 6.3 Consensus size: 39
36069949 TCTTCGGAAT
* * * *
36069959 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCAGGTC
1 TTAGCCCGGATATATCAACTAGCACAA-TGCCTTCGGGTC
* * * *
36069998 TTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATATCAACTAGCAC-AATGCCTTCGGGTC
36070038 TTAGCCCGGATATATCAACTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATCAACTAGCAC-AATGCCTTCGGGTC
* *
36070078 TTAGCCCGGAAAAAATC-ACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGG-ATATATCAACTAGCACAA-TGCCTTCGGGTC
* ** * *
36070118 TTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATATCAACTAGCAC-AATGCCTTCGGGTC
* *
36070158 TTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAT-ATATCAACTAGCACAA-TGCCTTCGGGTC
36070198 TTAGCCCGGATA
1 TTAGCCCGGATA
36070210 AAATTCAAAT
Statistics
Matches: 177, Mismatches: 27, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
39 11 0.06
40 154 0.87
41 12 0.07
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
TTAGCCCGGATATATCAACTAGCACAATGCCTTCGGGTC
Found at i:36070179 original size:120 final size:120
Alignment explanation
Indices: 36069978--36070213 Score: 402
Period size: 120 Copynumber: 2.0 Consensus size: 120
36069968 TATAACCACA
*
36069978 AGCACAATTGCCTTCAGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 AGCACAATTGCCTTCAGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
* *
36070043 CCGGATATATCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGAAAAAATCACT
66 CCGGATAAATCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAAAAATCACT
*
36070098 AGCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 AGCACAATTGCCTTCAGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
* *
36070163 CCGGATAAAATC-ACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAAAAT
66 CCGGAT-AAATCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAAAAAT
36070214 TCAAATGCTC
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 105 0.96
121 4 0.04
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (120 bp):
AGCACAATTGCCTTCAGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
CCGGATAAATCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAAAAATCACT
Found at i:36078657 original size:40 final size:40
Alignment explanation
Indices: 36078613--36078874 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
36078603 GCTCCTCGTT
* *
36078613 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
36078653 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
36078693 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
36078732 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
36078771 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
36078810 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
36078851 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
36078875 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:36083068 original size:42 final size:43
Alignment explanation
Indices: 36082954--36083092 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 43
36082944 TAAAATATCG
* * * * * *
36082954 TGTAAGACCATGTCTGGTACACAGGCCTCGAT-TTGAGATTTACA
1 TGTAAGACCATGTCTGGGACAGAAGCATTGATACT-AGATTT-CA
*
36082998 TGTAAGACCATGTCTGGGACATAAGCATTG-TATCT-GATTTCA
1 TGTAAGACCATGTCTGGGACAGAAGCATTGATA-CTAGATTTCA
* * * * *
36083040 TGTAAGACCCTGTCTGGGATAGAGGCATTGATACTAAATTACA
1 TGTAAGACCATGTCTGGGACAGAAGCATTGATACTAGATTTCA
36083083 TGTAAGACCA
1 TGTAAGACCA
36083093 CATCCGAGAC
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
42 30 0.38
43 22 0.28
44 25 0.32
45 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGAAGCATTGATACTAGATTTCA
Found at i:36084428 original size:13 final size:13
Alignment explanation
Indices: 36084410--36084437 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36084400 GTCGCTGAAT
36084410 TAGGGTTACGAGG
1 TAGGGTTACGAGG
36084423 TAGGGTTACGAGG
1 TAGGGTTACGAGG
36084436 TA
1 TA
36084438 TCACTGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.43, T:0.25
Consensus pattern (13 bp):
TAGGGTTACGAGG
Found at i:36086609 original size:56 final size:56
Alignment explanation
Indices: 36086548--36086699 Score: 198
Period size: 56 Copynumber: 2.7 Consensus size: 56
36086538 CAGACAGGGT
* * * *
36086548 CTTACTCGTAAACACATATCAGAATCACATATCGATGCCAACGCATGAAACATGGA
1 CTTACTCGCACACATATATCAGAATCACATATCGATGCCAACACATGAAACATGGA
* * * *
36086604 CTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGTGGT
1 CTTACTCGCACACATATATCAGAATCACATATCGATGCCAACACATGAAACATGGA
* *
36086660 CTTACTCGCACACATATATCA-AAGTCACAAATTGATGCCA
1 CTTACTCGCACACATATATCAGAA-TCACATATCGATGCCA
36086700 CATATTCTTC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 2 0.02
56 83 0.98
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (56 bp):
CTTACTCGCACACATATATCAGAATCACATATCGATGCCAACACATGAAACATGGA
Found at i:36093022 original size:56 final size:56
Alignment explanation
Indices: 36092815--36093002 Score: 277
Period size: 56 Copynumber: 3.4 Consensus size: 56
36092805 CAGATAGGGT
* * * * * *
36092815 CTTACTCGTAAACACATATCAGAATCACATATCGATGCCAACGTATGAAATGTGGA
1 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGA
* *
36092871 CTTACTCGCACACATATATCGGAATCACATATTGATGCCAACCTATTAAACGTGGA
1 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGA
* *
36092927 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACATGGT
1 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGA
*
36092983 CTTACTCGCCCACATATATC
1 CTTACTCGCACACATATATC
36093003 AAAGTAACAT
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (56 bp):
CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGA
Found at i:36094069 original size:17 final size:17
Alignment explanation
Indices: 36094047--36094090 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
36094037 CATGGCTTAT
* *
36094047 TATTATTTTATGATATA
1 TATTATTTTATAACATA
*
36094064 TATTATATTATAACATA
1 TATTATTTTATAACATA
*
36094081 TATTAATTTA
1 TATTATTTTA
36094091 ATGTTTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TATTATTTTATAACATA
Found at i:36094867 original size:45 final size:45
Alignment explanation
Indices: 36094805--36094894 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
36094795 CATCAATATC
*
36094805 ATCATTACTTTCTAGATTTCTATCTCTTCCAATTGACCATTTCAT
1 ATCATTACTTTCTAGATTTCTATCTCTTCCAATAGACCATTTCAT
* *
36094850 ATCATTACTTTCTAGATTTCTCTCTCTTTCAATAGACCATTTCAT
1 ATCATTACTTTCTAGATTTCTATCTCTTCCAATAGACCATTTCAT
36094895 CCTTTGTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.47
Consensus pattern (45 bp):
ATCATTACTTTCTAGATTTCTATCTCTTCCAATAGACCATTTCAT
Found at i:36094991 original size:16 final size:17
Alignment explanation
Indices: 36094967--36095000 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36094957 AGTCCCTCAT
36094967 AATTCTTTTCCT-ATTC
1 AATTCTTTTCCTAATTC
*
36094983 AATTTTTTTCCTAATTC
1 AATTCTTTTCCTAATTC
36095000 A
1 A
36095001 TCCATTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTCTTTTCCTAATTC
Found at i:36095092 original size:30 final size:31
Alignment explanation
Indices: 36095039--36095097 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
36095029 CACCCTTAAA
* * *
36095039 ATATTTACACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATCAGCCCTTCAAATTTTTC
36095070 ATATTTACACT-TCAGCCCTTCAAATTTT
1 ATATTTACACTATCAGCCCTTCAAATTTT
36095098 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (31 bp):
ATATTTACACTATCAGCCCTTCAAATTTTTC
Found at i:36095105 original size:30 final size:31
Alignment explanation
Indices: 36095039--36095107 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
36095029 CACCCTTAAA
* * *
36095039 ATATTTACACTATTAGTCCTTCAACTTTTTC
1 ATATTTACACTATCAGCCCTTCAACATTTTC
*
36095070 ATATTTACACT-TCAGCCCTTCAA-ATTTTG
1 ATATTTACACTATCAGCCCTTCAACATTTTC
36095099 AGTATTTAC
1 A-TATTTAC
36095108 TCTTGTGTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 17 0.52
31 11 0.33
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.45
Consensus pattern (31 bp):
ATATTTACACTATCAGCCCTTCAACATTTTC
Found at i:36098798 original size:27 final size:27
Alignment explanation
Indices: 36098758--36098836 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
36098748 TACACGTCAC
* * *
36098758 AATATTGTGACAGAGTCACAAGATACA
1 AATATTGTGGCAGAGACACAAGAAACA
* * *
36098785 GATATTGTGGCAGAGACACCAGAAATA
1 AATATTGTGGCAGAGACACAAGAAACA
* *
36098812 AATATTTGTGGCAGAGCCACCAGAA
1 AATA-TTGTGGCAGAGACACAAGAA
36098837 CGCTTCCTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (27 bp):
AATATTGTGGCAGAGACACAAGAAACA
Found at i:36100118 original size:18 final size:17
Alignment explanation
Indices: 36100067--36100121 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
36100057 ATTTGGCTAT
36100067 AGAG-GAAAAGAAGAAG
1 AGAGAGAAAAGAAGAAG
*
36100083 A-AGAGACAATAGATGAAG
1 AGAGAGA-AA-AGAAGAAG
36100101 AGAGGAGAAAAGAAGAAG
1 AGA-GAGAAAAGAAGAAG
36100119 AGA
1 AGA
36100122 AAAGAATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.06
16 3 0.09
17 2 0.06
18 18 0.56
19 3 0.09
20 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.35, T:0.04
Consensus pattern (17 bp):
AGAGAGAAAAGAAGAAG
Found at i:36100127 original size:18 final size:18
Alignment explanation
Indices: 36100071--36100127 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
36100061 GGCTATAGAG
36100071 GAAAAGAAG-A-AGAAGA
1 GAAAAGAAGAAGAGAAGA
* *
36100087 GACAATAGATGAAGAGAGGA
1 GA-AA-AGAAGAAGAGAAGA
*
36100107 GAAAAGAAGAAGAGAAAA
1 GAAAAGAAGAAGAGAAGA
36100125 GAA
1 GAA
36100128 TGTTAGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 2 0.06
17 2 0.06
18 18 0.56
19 3 0.09
20 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.32, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAAGA
Found at i:36101158 original size:13 final size:13
Alignment explanation
Indices: 36101140--36101164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36101130 TAAACCTACA
36101140 AAATAATAATAAT
1 AAATAATAATAAT
36101153 AAATAATAATAA
1 AAATAATAATAA
36101165 CAATAACATC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:36106480 original size:29 final size:29
Alignment explanation
Indices: 36106438--36106671 Score: 158
Period size: 29 Copynumber: 8.1 Consensus size: 29
36106428 TGTGCTAAAT
* *
36106438 GATGGTCGTAACCATTCCTTTTCATATTC
1 GATGGTCGAAACCATCCCTTTTCATATTC
36106467 GATGGTCGAAACCATCCCTTTTCATATTC
1 GATGGTCGAAACCATCCCTTTTCATATTC
**
36106496 GATGGTCGTCACCATCCCTTTTCATAGTT-
1 GATGGTCGAAACCATCCCTTTTCATA-TTC
* * * *
36106525 TATAGTC-ATCACCATCCCTTTTCATAATC
1 GATGGTCGA-AACCATCCCTTTTCATATTC
* * * * * * *
36106554 GATAGCCGAAGCTAT-CCGTTACATAATC
1 GATGGTCGAAACCATCCCTTTTCATATTC
* *
36106582 GATAG-CGAAAGCTATCCCTTTTCATATTC
1 GATGGTCGAAA-CCATCCCTTTTCATATTC
* *
36106611 GATGGTC-ATCACCACCCCTTTTCATAATT-
1 GATGGTCGA-AACCATCCCTTTTCAT-ATTC
* * * *
36106640 AATGGTCGTCAA-CATCCCTTTTAATAATC
1 GATGGTCG-AAACCATCCCTTTTCATATTC
36106669 GAT
1 GAT
36106672 AGCCCAAGCT
Statistics
Matches: 163, Mismatches: 30, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.02
28 23 0.14
29 127 0.78
30 9 0.06
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (29 bp):
GATGGTCGAAACCATCCCTTTTCATATTC
Found at i:36106539 original size:58 final size:58
Alignment explanation
Indices: 36106438--36106671 Score: 176
Period size: 58 Copynumber: 4.1 Consensus size: 58
36106428 TGTGCTAAAT
* * *
36106438 GATGGTCGTAACCATTCCTTTTCATATTCGATGGTCGAAACCATCCCTTTTCATATTC
1 GATGGTCGTAACCATCCCTTTTCATATTCGATAGTCGAAACCATCCCTTTTCATAATC
* * *
36106496 GATGGTCGTCACCATCCCTTTTCATAGTT-TATAGTC-ATCACCATCCCTTTTCATAATC
1 GATGGTCGTAACCATCCCTTTTCATA-TTCGATAGTCGA-AACCATCCCTTTTCATAATC
* * * * * * * *
36106554 GATAGCCG-AAGCTAT-CCGTTACATAATCGATAG-CGAAAGCTATCCCTTTTCATATTC
1 GATGGTCGTAA-CCATCCCTTTTCATATTCGATAGTCGAAA-CCATCCCTTTTCATAATC
* * * * * * *
36106611 GATGGTCATCACCACCCCTTTTCATAATT-AATGGTCGTCAA-CATCCCTTTTAATAATC
1 GATGGTCGTAACCATCCCTTTTCAT-ATTCGATAGTCG-AAACCATCCCTTTTCATAATC
36106669 GAT
1 GAT
36106672 AGCCCAAGCT
Statistics
Matches: 133, Mismatches: 32, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
56 3 0.02
57 38 0.29
58 84 0.63
59 6 0.05
60 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (58 bp):
GATGGTCGTAACCATCCCTTTTCATATTCGATAGTCGAAACCATCCCTTTTCATAATC
Found at i:36110682 original size:13 final size:13
Alignment explanation
Indices: 36110664--36110690 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36110654 AAGTATATTC
36110664 ATATATGTATATA
1 ATATATGTATATA
36110677 ATATATGTATATA
1 ATATATGTATATA
36110690 A
1 A
36110691 GAATACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATATGTATATA
Found at i:36134538 original size:47 final size:47
Alignment explanation
Indices: 36134487--36135163 Score: 868
Period size: 47 Copynumber: 14.1 Consensus size: 47
36134477 TTAGGATTTT
*
36134487 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
36134534 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGTCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
36134585 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGTCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
36134636 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
36134683 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* *** *
36134730 ATGTGATAAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGTCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
36134781 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
36134828 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
36134875 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
36134922 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
36134969 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGTCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
36135020 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
36135067 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * *
36135114 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
36135161 ATG
1 ATG
36135164 CGAAACGTGT
Statistics
Matches: 558, Mismatches: 60, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
47 380 0.68
49 6 0.01
51 172 0.31
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:36134589 original size:42 final size:43
Alignment explanation
Indices: 36134542--36134641 Score: 103
Period size: 51 Copynumber: 2.2 Consensus size: 43
36134532 CAATGTGATG
*
36134542 AATGTGAACCCGTATATATATGTGTGATAAGGTCGAATGGCCAATGTGA
1 AATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCC------A
*
36134591 TGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGTC-
1 --AATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
36134635 AATGTGA
1 AATGTGA
36134642 TGAATGTGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
42 7 0.15
51 40 0.85
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (43 bp):
AATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
Found at i:36134772 original size:145 final size:141
Alignment explanation
Indices: 36134487--36135163 Score: 870
Period size: 145 Copynumber: 4.7 Consensus size: 141
36134477 TTAGGATTTT
* *
36134487 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAA--
** *
36134552 CGTATATATATGTGTGATAAGG-TCGAATGGCCAATGTGATGAATGTGAACCCGTATATATATGT
64 C--ATGCATATGTGTGATAAGGCT-GAATGGCCAATGTGATGAATGTGAA--C--ATACATATGT
*
36134616 GTGATAAGGCCGAATGGTCA
122 GTGATAAGGCCGAATGGCCA
* *
36134636 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * *
36134701 TGCGTATGTGTGATAAGGCTGAATGGCCAATGTGATAAATGTGAACCCGTATATATATGTGTGAT
66 TGCATATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAA--C--ATACATATGTGTGAT
*
36134766 AAGGCCGAATGGTCA
127 AAGGCCGAATGGCCA
* *
36134781 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * *
36134846 TGCGTATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGGGATAAGG
66 TGCATATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATACATATGTGTGATAAGG
*
36134911 CCAAATGGCCA
131 CCGAATGGCCA
* * *
36134922 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAA--
** * * * *
36134987 CGTATATATATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACATGCGTATGTGTGAT
64 C--ATGCATATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATACATATGTGTGAT
36135052 AAGGCCGAATGGCCA
127 AAGGCCGAATGGCCA
* * *
36135067 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * * *
36135132 TGAATATATGTGGTAAGGCCGAATGGCTAATG
66 TGCATATGTGTGATAAGGCTGAATGGCCAATG
36135164 CGAAACGTGT
Statistics
Matches: 485, Mismatches: 38, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
141 109 0.22
143 3 0.01
145 312 0.64
146 1 0.00
147 1 0.00
149 59 0.12
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (141 bp):
ATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCATATGTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATACATATGTGTGATAAGG
CCGAATGGCCA
Found at i:36135151 original size:239 final size:239
Alignment explanation
Indices: 36134509--36135133 Score: 1034
Period size: 239 Copynumber: 2.6 Consensus size: 239
36134499 TGAACATGCG
* ***
36134509 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGG
1 TATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGG
* ** *
36134574 TCGAATGGCCAATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGTCAATG
62 CCGAATGGCCAATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCAATG
36134639 TGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACATGC
123 TGATGAATGTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACATGC
36134704 GTATGTGTGATAAGGCTGAATGGCCAATGTGATAAATGTGAACCCGTATATA
188 GTATGTGTGATAAGGCTGAATGGCCAATGTGATAAATGTGAACCCGTATATA
* *
36134756 TATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACATGCGTATGTGGGATAAGGCCAA
1 TATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
* * *
36134821 ATGGCCAATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCAATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
36134886 GTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACATGCGTATGTGT
131 GTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACATGCGTATGTGT
*
36134951 GATAAGGCTGAATGGCCAATGTGATGAATGTGAACCCGTATATA
196 GATAAGGCTGAATGGCCAATGTGATAAATGTGAACCCGTATATA
36134995 TATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
1 TATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
* *
36135060 ATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
36135125 GTGAACATG
131 GTGAACATG
36135134 AATATATGTG
Statistics
Matches: 357, Mismatches: 21, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
239 276 0.77
241 1 0.00
243 39 0.11
245 1 0.00
247 40 0.11
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (239 bp):
TATGTGTGATAAGGCCGAATGGTCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
GTGAACATGCGTATGTGGGATAAGGCCAAATGGCCAATGTGATGGATGTGAACATGCGTATGTGT
GATAAGGCTGAATGGCCAATGTGATAAATGTGAACCCGTATATA
Found at i:36135226 original size:46 final size:46
Alignment explanation
Indices: 36135137--36135227 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
36135127 GAACATGAAT
* * * *
36135137 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
36135183 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
36135228 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:36135519 original size:37 final size:37
Alignment explanation
Indices: 36135374--36135518 Score: 218
Period size: 37 Copynumber: 3.9 Consensus size: 37
36135364 GGAAATATAT
36135374 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
36135411 TCCGGGTAAGACCCGATGACTACGTGTTGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
** *
36135448 TTTGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * * *
36135485 TCCGCGTAAGACCCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
36135519 TCGTCTGAGC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:36148552 original size:41 final size:41
Alignment explanation
Indices: 36148477--36148643 Score: 158
Period size: 45 Copynumber: 3.9 Consensus size: 41
36148467 TTTTATCAAA
* * * *
36148477 TCACTGGCATT-CAGCCTGCTAGGTTTAAAACCCGAATTCAT
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATT-AT
* *
36148518 TCACTGGCATT-TTGCCTGCTAGGCTCGAAGCCCGATATTATT
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGCCCGA-ATTA-T
* *
36148560 TCACTGGCATTATAGCCCGCTAGGCTCGAAAGCCCAAATAGTAT
1 TCACTGGCATTATAGCCTGCTAGGCTC-AAAGCCCGAAT--TAT
* *
36148604 CTCACCGGCATTATAGCCTGCTAAGCTCAAAGGCCCGAAT
1 -TCACTGGCATTATAGCCTGCTAGGCTCAAA-GCCCGAAT
36148644 AGTATTGTGC
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
41 30 0.29
42 15 0.14
43 15 0.14
44 11 0.11
45 33 0.32
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACTGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATTAT
Found at i:36149485 original size:47 final size:47
Alignment explanation
Indices: 36149429--36149570 Score: 250
Period size: 47 Copynumber: 3.0 Consensus size: 47
36149419 AAAATTTTCT
* *
36149429 TTAACTAAGTAACTTATCCGGAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
36149476 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
*
36149523 TTAACTAAGTAACTTATCCAGAAATATTAAGAGC-AATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
36149569 TT
1 TT
36149571 TAAATTCAAC
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 14 0.15
47 78 0.85
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
Found at i:36156399 original size:40 final size:40
Alignment explanation
Indices: 36156344--36156481 Score: 199
Period size: 40 Copynumber: 3.5 Consensus size: 40
36156334 CGGATGATAA
*
36156344 CCGGGCTAAGTCCCGAAGGCATTTGTCCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
36156384 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
36156424 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
36156464 CC-GGCTAAATCCTGAAGG
1 CCGGGCTAAGTCCCGAAGG
36156482 TACTTGGTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 16 0.18
40 74 0.82
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:36163047 original size:42 final size:43
Alignment explanation
Indices: 36163001--36163084 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
36162991 AAAGGGTTAG
36163001 TAATAAAATAATGGAAATT-GGAGGGGGTGATGAAAAAAAAAA
1 TAATAAAATAATGGAAATTGGGAGGGGGTGATGAAAAAAAAAA
*
36163043 TAATAAAATAATGGAAATTGGGTGGGGGTGATGAAAAAAAAA
1 TAATAAAATAATGGAAATTGGGAGGGGGTGATGAAAAAAAAA
36163085 GAAAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 19 0.47
43 21 0.52
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.20
Consensus pattern (43 bp):
TAATAAAATAATGGAAATTGGGAGGGGGTGATGAAAAAAAAAA
Found at i:36169558 original size:45 final size:45
Alignment explanation
Indices: 36169494--36169581 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
36169484 GGTCTTGTCT
*
36169494 ACAGAACCTTAAGGTTTAGAGAACTAGAGAATCGGTTAAGAATCG
1 ACAGAACCTTAAGGTTTAGAGAACTAGAGAATCGGTCAAGAATCG
36169539 ACAGAACCTTAAGGTTTAGAGAACTAGAGAATCGGTCAAGAAT
1 ACAGAACCTTAAGGTTTAGAGAACTAGAGAATCGGTCAAGAAT
36169582 GATGGAAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (45 bp):
ACAGAACCTTAAGGTTTAGAGAACTAGAGAATCGGTCAAGAATCG
Found at i:36169913 original size:12 final size:12
Alignment explanation
Indices: 36169896--36169990 Score: 50
Period size: 12 Copynumber: 7.9 Consensus size: 12
36169886 GCCTACTCCT
*
36169896 GCTCCTTGATCA
1 GCTCCTTAATCA
* *
36169908 GCTCCTAAATCT
1 GCTCCTTAATCA
* *
36169920 TCTCCTTTATCA
1 GCTCCTTAATCA
* *
36169932 GCTCCTAAATCC
1 GCTCCTTAATCA
*
36169944 TCTCCCTT-ATCA
1 GCT-CCTTAATCA
* *
36169956 GCTCCTAAATCC
1 GCTCCTTAATCA
*
36169968 TCTCTCTT-ATCA
1 GCTC-CTTAATCA
*
36169980 GCTCCTAAATC
1 GCTCCTTAATC
36169991 TTCTCTTGAC
Statistics
Matches: 57, Mismatches: 22, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
11 5 0.09
12 47 0.82
13 5 0.09
ACGTcount: A:0.21, C:0.37, G:0.06, T:0.36
Consensus pattern (12 bp):
GCTCCTTAATCA
Found at i:36169924 original size:24 final size:23
Alignment explanation
Indices: 36169892--36169995 Score: 145
Period size: 24 Copynumber: 4.3 Consensus size: 23
36169882 GTCGGCCTAC
36169892 TCCTGCTCCTTGATCAGCTCCTAAA
1 TCCT-CTCCTT-ATCAGCTCCTAAA
*
36169917 TCTTCTCCTTTATCAGCTCCTAAA
1 TCCTCTCC-TTATCAGCTCCTAAA
36169941 TCCTCTCCCTTATCAGCTCCTAAA
1 TCCTCT-CCTTATCAGCTCCTAAA
36169965 TCCTCTCTCTTATCAGCTCCTAAA
1 TCCTCTC-CTTATCAGCTCCTAAA
*
36169989 TCTTCTC
1 TCCTCTC
36169996 TTGACAGCCT
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.01
24 65 0.89
25 7 0.10
ACGTcount: A:0.19, C:0.38, G:0.06, T:0.38
Consensus pattern (23 bp):
TCCTCTCCTTATCAGCTCCTAAA
Found at i:36174533 original size:29 final size:28
Alignment explanation
Indices: 36174493--36174560 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
36174483 TACAAAATTA
* *
36174493 CTAATTAAATTAATTAACAT-AAATTAAT
1 CTAATGAAATTAATTAACATGAAA-TAAC
*
36174521 CTAATGGAAATTAATTAACCTGAAATAAC
1 CTAAT-GAAATTAATTAACATGAAATAAC
36174550 CTAATGAAATT
1 CTAATGAAATT
36174561 TCTTATTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.31
29 21 0.60
30 3 0.09
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (28 bp):
CTAATGAAATTAATTAACATGAAATAAC
Found at i:36177151 original size:79 final size:81
Alignment explanation
Indices: 36177015--36177199 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
36177005 TTGAATGATG
*
36177015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
36177079 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
36177094 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
36177156 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* * *
36177174 ACCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
36177200 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.64
80 32 0.35
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:36177206 original size:40 final size:40
Alignment explanation
Indices: 36177015--36177199 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
36177005 TTGAATGATG
* * * *
36177015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
36177055 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
36177095 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
36177134 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
36177175 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
36177200 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:36177221 original size:79 final size:79
Alignment explanation
Indices: 36177068--36177232 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
36177058 GGACTAAGAT
* * **
36177068 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
*
36177133 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
36177147 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTTGAACGAGTTA-C
* *
36177210 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
36177226 CCGAAGG
1 CCGAAGG
36177233 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:36191376 original size:37 final size:37
Alignment explanation
Indices: 36191312--36191387 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
36191302 TTACAAGCCA
36191312 AAATCATTATAAGCCACATCTCATGGCTATAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
36191349 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
36191386 AA
1 AA
36191388 CATCGATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 30 0.86
38 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:36195306 original size:46 final size:47
Alignment explanation
Indices: 36195200--36195321 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
36195190 TGTCTTCGAC
** * *
36195200 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
36195250 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
36195296 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
36195322 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:36204525 original size:34 final size:34
Alignment explanation
Indices: 36204487--36204553 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
36204477 AAGTTTTATG
* **
36204487 TAGAATGAATTTTCATGCAATTTGTGTTTTGGAT
1 TAGAACGAATTTTCACACAATTTGTGTTTTGGAT
36204521 TAGAACGAATTTTCACACAATTTGTGTTTTGGA
1 TAGAACGAATTTTCACACAATTTGTGTTTTGGA
36204554 AAAACACTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (34 bp):
TAGAACGAATTTTCACACAATTTGTGTTTTGGAT
Found at i:36210130 original size:53 final size:53
Alignment explanation
Indices: 36210054--36210154 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 53
36210044 ACTACTATAT
* * * *
36210054 GGCAAGCATCCCATGTAAGACCATACCAAGGCATGGCAATGGTGAGTTCATAA
1 GGCAAGCATACCACGTAAGACCATACCAAGACATGGCAATGGTAAGTTCATAA
* **
36210107 GGCAAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 GGCAAGCATACCACGTAAGACCATACCAAGACATGGCAATGGTAAGTT
36210155 TAAAAAGGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (53 bp):
GGCAAGCATACCACGTAAGACCATACCAAGACATGGCAATGGTAAGTTCATAA
Found at i:36214245 original size:53 final size:53
Alignment explanation
Indices: 36214130--36214271 Score: 149
Period size: 53 Copynumber: 2.6 Consensus size: 53
36214120 AGGAAATCAT
* * * * * * * *
36214130 GTAAGACTATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAAGATCCCAT
1 GTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGCAAAGATACCAC
* * *
36214185 GTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAGGATACCAC
1 GTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAAGATACCAC
* *
36214238 GTAAGACCATGTCAAGACATTGCAATGGTAAGTT
1 GTAAGACCATGCCAAGACATGGCAATGGTAAGTT
36214272 TAAAAAGGAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
53 45 0.62
54 3 0.04
55 24 0.33
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (53 bp):
GTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAAGATACCAC
Found at i:36217124 original size:48 final size:48
Alignment explanation
Indices: 36217071--36217167 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
36217061 ACTTCTCTTT
* * *
36217071 GGCCGAATATCACTAGTCCTTCCTCTCACAATCCTTTTTTGGTTTTTA
1 GGCCGAATATCACTAGTCATTCCTCTCACAATCCCTTTTAGGTTTTTA
36217119 GGCCGAATATCACTAGTCATTCCTCTCACAATCCCTTTTAGGTTTTTA
1 GGCCGAATATCACTAGTCATTCCTCTCACAATCCCTTTTAGGTTTTTA
36217167 G
1 G
36217168 CCTTGCTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (48 bp):
GGCCGAATATCACTAGTCATTCCTCTCACAATCCCTTTTAGGTTTTTA
Found at i:36227029 original size:27 final size:27
Alignment explanation
Indices: 36226998--36227067 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
36226988 TTAAGACCCC
*
36226998 TAGTGTAAAATTATTGAAATACCCTTG
1 TAGTGTAAAATTATTGAAATACCCCTG
**
36227025 TAGTGTAAAATTACCGAAATACCCCTG
1 TAGTGTAAAATTATTGAAATACCCCTG
*
36227052 TA-TGGTAAAATGATTG
1 TAGT-GTAAAATTATTG
36227068 TTTTGCCCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (27 bp):
TAGTGTAAAATTATTGAAATACCCCTG
Found at i:36227481 original size:27 final size:27
Alignment explanation
Indices: 36227418--36227496 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
36227408 TATTTAGCTG
* **
36227418 TGGCTATGTGCCTATCATATTTATTAA
1 TGGCTATGTGCCGATCATATTTACCAA
* * *
36227445 TGACTCTGTGCCGATCATATTTACCCA
1 TGGCTATGTGCCGATCATATTTACCAA
* *
36227472 TGGCTGTGTGCCGATTATA-TTACCA
1 TGGCTATGTGCCGATCATATTTACCA
36227497 TTGTTGATGG
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 5 0.12
27 37 0.88
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (27 bp):
TGGCTATGTGCCGATCATATTTACCAA
Found at i:36229144 original size:24 final size:24
Alignment explanation
Indices: 36228950--36229143 Score: 273
Period size: 24 Copynumber: 8.0 Consensus size: 24
36228940 GCTTTATCAT
*
36228950 ATAACTGGAGGCCT-AGCCCCTTTTA
1 ATAACTGG-GGCATAAG-CCCTTTTA
*
36228975 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
36228999 ATAACTGGGGCATAAGCCCTTCTA
1 ATAACTGGGGCATAAGCCCTTTTA
36229023 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
**
36229047 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTA
36229071 ATAACTGGGGCATAAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
* * *
36229097 ATAACTGGTGCATAAGCTCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
36229121 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
36229144 GCACTTCCTC
Statistics
Matches: 152, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
24 122 0.80
25 10 0.07
26 20 0.13
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:36229218 original size:20 final size:20
Alignment explanation
Indices: 36229193--36229259 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
36229183 TTATGAATAC
36229193 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
36229213 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
36229233 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
36229253 ACCATGT
1 ATCATGT
36229260 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:36229224 original size:11 final size:11
Alignment explanation
Indices: 36229193--36229248 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
36229183 TTATGAATAC
36229193 ATCATGTGCAT
1 ATCATGTGCAT
*
36229204 ATCA--TACAT
1 ATCATGTGCAT
36229213 ATCATGTGCAT
1 ATCATGTGCAT
*
36229224 ATCA--TACAT
1 ATCATGTGCAT
*
36229233 GTCATGTGCAT
1 ATCATGTGCAT
36229244 ATCAT
1 ATCAT
36229249 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:36229626 original size:17 final size:17
Alignment explanation
Indices: 36229604--36229644 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
36229594 TTTTTACAAA
36229604 TGGGCCCGAAAGCCCAT
1 TGGGCCCGAAAGCCCAT
*
36229621 TGGGCCCGAAAGCCTAT
1 TGGGCCCGAAAGCCCAT
36229638 TGGGCCC
1 TGGGCCC
36229645 CACTTCGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.34, G:0.32, T:0.15
Consensus pattern (17 bp):
TGGGCCCGAAAGCCCAT
Found at i:36230595 original size:27 final size:27
Alignment explanation
Indices: 36230470--36230705 Score: 163
Period size: 27 Copynumber: 8.7 Consensus size: 27
36230460 TTCATCCTAC
* * * *
36230470 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
* ** ** *
36230497 AAGGCTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
* * * *
36230524 AATGGTATTTCT-ATAATTTTTAGAAAGT
1 AAGGGTATTT-TGGTAA-TTTTACAAACT
** *
36230552 CAAGGGTATTTCT-GTAATTTTGTAAATT
1 -AAGGGTATTT-TGGTAATTTTACAAACT
*
36230580 AAGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAACT
* * * *
36230607 GAGGGTATTTCGATAATTTCACAAAC-
1 AAGGGTATTTTGGTAATTTTACAAACT
* *
36230633 CAGTGGTATTTCGGTAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTTTACAAACT
*
36230661 AGGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
* *
36230688 AGGGGTATTTTTGTAATT
1 AAGGGTATTTTGGTAATT
36230706 CTATCCTATA
Statistics
Matches: 168, Mismatches: 35, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
26 3 0.02
27 135 0.80
28 16 0.10
29 14 0.08
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAACT
Found at i:36230641 original size:54 final size:54
Alignment explanation
Indices: 36230582--36230738 Score: 165
Period size: 54 Copynumber: 2.9 Consensus size: 54
36230572 TGTAAATTAA
*
36230582 GGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGATAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCGATAATTTCACAAACCAG
* * * * * *
36230636 TGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGATAATTTCACAAACCAG
* * ** * *
36230690 GGGTATTTTTGTAATTCTATCCTA-TAGGGGTATTTCAATAATTTGACAA
1 GGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTCGATAATTTCACAA
36230739 TCGAGGGTAA
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 80 0.95
55 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGATAATTTCACAAACCAG
Found at i:36230761 original size:27 final size:27
Alignment explanation
Indices: 36230737--36230934 Score: 254
Period size: 27 Copynumber: 7.3 Consensus size: 27
36230727 ATAATTTGAC
36230737 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
36230764 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
* * *
36230791 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * *
36230818 AATCAAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
36230845 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * * *
36230872 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* **
36230899 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTGTA
36230926 AATCGAGGG
1 AATCGAGGG
36230935 CATTTCAGTA
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 150 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:36230853 original size:81 final size:81
Alignment explanation
Indices: 36230737--36230934 Score: 308
Period size: 81 Copynumber: 2.4 Consensus size: 81
36230727 ATAATTTGAC
* * *
36230737 AATCGAGGGTAAAATGGTAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAATC-GAGGGTAAAACGGTAATTTTGTAAATCGAGGGT
*
36230801 AAAACGATAATTCTGTA
65 AAAACGATAATTCTATA
* *
36230818 AATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
*
36230883 AAACGGTAATTCTATA
66 AAACGATAATTCTATA
*
36230899 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGG
36230935 CATTTCAGTA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
81 106 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTA
AAACGATAATTCTATA
Found at i:36244772 original size:39 final size:39
Alignment explanation
Indices: 36244683--36244937 Score: 368
Period size: 39 Copynumber: 6.5 Consensus size: 39
36244673 ACAAAGCATA
* * *
36244683 CGGGACTTTAAGCCCGGATATAATACCAGTAC-AAAGCCTT
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
36244723 CGGGACTTAGCCCAGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
36244762 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
36244801 CGGGACTTAGCCCGGATATAACACCAGCACGAATACCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
36244840 CGAGACTTAGCCCGGATATAACACCAGCATGAATTCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
36244879 CGGGACTTAGCCCGGATATAACACCAGCACAAACGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* * *
36244918 CAGGAATTAGCCAGGATATA
1 CGGGACTTAGCCCGGATATA
36244938 TATCTCACAC
Statistics
Matches: 197, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
38 19 0.10
39 172 0.87
40 6 0.03
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:36252426 original size:45 final size:45
Alignment explanation
Indices: 36252321--36252539 Score: 311
Period size: 45 Copynumber: 4.9 Consensus size: 45
36252311 CGAATTCGTC
* * *
36252321 CACCGGCATT-TCGCCTGCTAGGCTCGAAGG-CCG-ATA-TCATTT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCT
*
36252363 CACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
36252408 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* * *
36252453 CACCGGTATCATAGCCTGCTAGGCTCAAAGGCTCGAATAGTATCT
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* * *
36252498 CATCGGCATCATAGCCTGCTAGGCTCAAAGACCCGAATAGTA
1 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
36252540 CCGTACAATA
Statistics
Matches: 163, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
42 10 0.06
43 19 0.12
44 3 0.02
45 130 0.80
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (45 bp):
CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
Found at i:36255077 original size:37 final size:37
Alignment explanation
Indices: 36255027--36255101 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
36255017 AGCATACAAT
*
36255027 GAGTTTACTTTGAGTTATTCGAACTTTCCTGGTATTC
1 GAGTTTACTTTGAGTTATTCGAACTTACCTGGTATTC
*
36255064 GAGTTTACTTTGAGTTATTCGAACTTACTTGGTATTC
1 GAGTTTACTTTGAGTTATTCGAACTTACCTGGTATTC
36255101 G
1 G
36255102 TCTCGTTATC
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:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (37 bp):
GAGTTTACTTTGAGTTATTCGAACTTACCTGGTATTC
Found at i:36255091 original size:20 final size:20
Alignment explanation
Indices: 36255031--36255093 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
36255021 TACAATGAGT
36255031 TTACTTTGAGTTATTCGAAC
1 TTACTTTGAGTTATTCGAAC
* * **
36255051 TTTC-CTG-G-TATTCGAGT
1 TTACTTTGAGTTATTCGAAC
36255068 TTACTTTGAGTTATTCGAAC
1 TTACTTTGAGTTATTCGAAC
36255088 TTACTT
1 TTACTT
36255094 GGTATTCGTC
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 10 0.31
18 3 0.09
19 3 0.09
20 16 0.50
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (20 bp):
TTACTTTGAGTTATTCGAAC
Found at i:36255101 original size:17 final size:17
Alignment explanation
Indices: 36255042--36255101 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
36255032 TACTTTGAGT
* *
36255042 TATTCGAACTTTCCTGG
1 TATTCGAACTTACTTGG
**
36255059 TATTCGAGTTTACTTTGAG
1 TATTCGAACTTAC-TTG-G
36255078 TTATTCGAACTTACTTGG
1 -TATTCGAACTTACTTGG
36255096 TATTCG
1 TATTCG
36255102 TCTCGTTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 16 0.47
18 3 0.09
19 4 0.12
20 11 0.32
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (17 bp):
TATTCGAACTTACTTGG
Found at i:36259267 original size:10 final size:10
Alignment explanation
Indices: 36259252--36259280 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
36259242 CGTTCCTTTC
36259252 GCTCTCCTAT
1 GCTCTCCTAT
36259262 GCTCTCCTAT
1 GCTCTCCTAT
36259272 GCTCTCCTA
1 GCTCTCCTA
36259281 ATTATAAAAC
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:0.10, C:0.41, G:0.10, T:0.38
Consensus pattern (10 bp):
GCTCTCCTAT
Found at i:36262716 original size:46 final size:46
Alignment explanation
Indices: 36262665--36262828 Score: 140
Period size: 46 Copynumber: 3.5 Consensus size: 46
36262655 TGGGCATCCA
36262665 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCTG
1 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCTG
* * * *
36262711 AACTCGTTGAGTTGAGTACGAGTTC-GTGA--GATG-TAACTAGGCATCTG
1 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAAC---G--TCTG
* * * * * *
36262758 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGGATGCCTG
1 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCTG
*
36262804 AGCTCGTTGAGTTGAG-TCTGAGTTC
1 AACTCGTTGAGTTGAGTTC-GAGTTC
36262829 GTTTAAGGGC
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 4 0.04
46 49 0.52
47 27 0.29
48 3 0.03
50 3 0.03
51 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGTCTG
Found at i:36266262 original size:39 final size:38
Alignment explanation
Indices: 36266207--36266282 Score: 125
Period size: 39 Copynumber: 2.0 Consensus size: 38
36266197 CATTGAATGG
36266207 TCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCTGNA
1 TCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCTG-A
* *
36266246 TCATGGTGGTTTGAGGAGTTTATACTGCTCATTCCTG
1 TCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCTG
36266283 CTATCAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.38
Consensus pattern (38 bp):
TCATGGTGGTTCGAGGAGTTTATACTCCTCATTCCTGA
Found at i:36271598 original size:6 final size:6
Alignment explanation
Indices: 36271596--36271639 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
36271586 AATGAAAAAG
*
36271596 AAAATA AAAATA AAAATA AAAATA AGAATA AATAA-A AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AA
36271640 TAGGAGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 2 0.06
6 30 0.88
7 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:36271606 original size:18 final size:17
Alignment explanation
Indices: 36271585--36271639 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
36271575 AATAAAATTG
*
36271585 AAATGAAAAAGAAAATAA
1 AAAT-AAAAAAAAAATAA
36271603 AAATAAAAATAAAAATAA
1 AAATAAAAA-AAAAATAA
*
36271621 GAATAAATAAAAAAATAA
1 AAATAAA-AAAAAAATAA
36271639 A
1 A
36271640 TAGGAGGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.16
18 25 0.78
19 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAATAAAAAAAAAATAA
Found at i:36274098 original size:40 final size:40
Alignment explanation
Indices: 36274004--36274228 Score: 238
Period size: 40 Copynumber: 5.6 Consensus size: 40
36273994 TATTCGAATG
*
36274004 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * * *
36274045 ATAACCAGACTAAGATCCGAAGGCATTCGTGCAAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * * * *
36274085 ATATCCGGGCTAAGACCCGAAGGCTTTTGTGCTGGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
36274125 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * * *
36274165 ATATCCGGGCTAGGTTCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
36274205 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
36274229 CTTGTGCAAG
Statistics
Matches: 150, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.01
40 120 0.80
41 28 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:36274185 original size:80 final size:80
Alignment explanation
Indices: 36274004--36274264 Score: 294
Period size: 80 Copynumber: 3.3 Consensus size: 80
36273994 TATTCGAATG
* * * *
36274004 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCAGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCT-GGTGACTATATCCGGGCTAAGACCCGAAGGC
36274069 ATTCGTGCAAGTTGCT
65 ATTCGTGCAAGTTGCT
* * * *
36274085 ATATCCGGGCTAAGACCCGAAGGCTTTTGTGCTGGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTGGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
36274150 TTTGTGCTAG-TGACT
66 TTCGTGCAAGTTG-CT
* * * * * * * *
36274165 ATATCCGGGCTAGGTTCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTGGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
36274230 TT-GTGCAAGTAGTT
66 TTCGTGCAAGTTGCT
*
36274244 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
36274265 ATTACTTGAG
Statistics
Matches: 150, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
78 12 0.08
79 15 0.10
80 91 0.61
81 32 0.21
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTGGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCAAGTTGCT
Found at i:36274218 original size:120 final size:121
Alignment explanation
Indices: 36274004--36274228 Score: 310
Period size: 120 Copynumber: 1.9 Consensus size: 121
36273994 TATTCGAATG
** *
36274004 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCAGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGTGACTATAACCAGACTAAGATCCGAAGGC
* * *
36274069 ATTCGTGCAAGTTGCTATATCCGGGCTAAGACCCGAAGGCTTTTGTGCTGGCGATT
66 ATTCATGCAAGTTGCCACATCCGGGCTAAGACCCGAAGGCTTTTGTGCTGGCGATT
* * * * *
36274125 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAGGTTCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGTGACTATAACCAGACTAAGATCCGAAGGC
* *
36274189 ATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGC
66 ATTCATGCAAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
36274229 CTTGTGCAAG
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
119 2 0.02
120 57 0.63
121 31 0.34
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (121 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGTGACTATAACCAGACTAAGATCCGAAGGC
ATTCATGCAAGTTGCCACATCCGGGCTAAGACCCGAAGGCTTTTGTGCTGGCGATT
Found at i:36275118 original size:50 final size:49
Alignment explanation
Indices: 36275039--36275142 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 49
36275029 GGAATTAAAT
*
36275039 AGTAAATAAATTATTTAATCGAACCTTGATGAATCTATTTTCATAGGAA
1 AGTAAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATAGGAA
36275088 AGTAGAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATAGGAA
1 AGTA-AATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATAGGAA
36275138 AGTAA
1 AGTAA
36275143 CGAAACGATC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 5 0.09
50 48 0.91
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (49 bp):
AGTAAATAAATTATGTAATCGAACCTTGATGAATCTATTTTCATAGGAA
Found at i:36280966 original size:15 final size:16
Alignment explanation
Indices: 36280940--36280980 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
36280930 CCGTGAGTTG
*
36280940 AAGAAAAGAAAA-CAA
1 AAGAAAAAAAAAGCAA
36280955 AAGAAAAAAAAAAGCAA
1 AAG-AAAAAAAAAGCAA
36280972 AA-AAAAAAA
1 AAGAAAAAAA
36280981 GAATGTGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAGCAA
Found at i:36281022 original size:80 final size:80
Alignment explanation
Indices: 36280889--36281048 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
36280879 GGAGGAGAAA
36280889 CAAAAAAAAAAAGAATGTGTGTGGTTGTTTCCCCCCCATTGCCGTGAGTTGAAGAAAAGAAAACA
1 CAAAAAAAAAAAGAATGTGTGTGGTTGTTTCCCCCCCATTGCCGTGAGTTGAAGAAAAGAAAACA
36280954 AAAGAAAAAAAAAAG
66 AAAGAAAAAAAAAAG
36280969 CAAAAAAAAAAAGAATGTGTGTGGTTGTTTCCCCCCCATTGCCGTGAGTTGAAGAAAAGAAAACA
1 CAAAAAAAAAAAGAATGTGTGTGGTTGTTTCCCCCCCATTGCCGTGAGTTGAAGAAAAGAAAACA
36281034 AAAGAAAAAAAAAAG
66 AAAGAAAAAAAAAAG
36281049 TGTCCATCCT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (80 bp):
CAAAAAAAAAAAGAATGTGTGTGGTTGTTTCCCCCCCATTGCCGTGAGTTGAAGAAAAGAAAACA
AAAGAAAAAAAAAAG
Found at i:36282258 original size:35 final size:35
Alignment explanation
Indices: 36282212--36282280 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
36282202 CTATTGAGCC
36282212 GAAATTTGTAAGTGTGATAAGTGTGTTGTGTTTGT
1 GAAATTTGTAAGTGTGATAAGTGTGTTGTGTTTGT
*
36282247 GAAATTTGTAAGTGTGATAAGTGTTTTGTGTTTG
1 GAAATTTGTAAGTGTGATAAGTGTGTTGTGTTTG
36282281 AGCTTTGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.46
Consensus pattern (35 bp):
GAAATTTGTAAGTGTGATAAGTGTGTTGTGTTTGT
Found at i:36282475 original size:40 final size:40
Alignment explanation
Indices: 36282351--36282575 Score: 265
Period size: 40 Copynumber: 5.6 Consensus size: 40
36282341 TATTCGAATG
* *
36282351 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
36282392 ATAAT-CGGACTAAGATCCGAAAGCATTCGTGCGAGTTG-CT
1 AT-ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* * *
36282432 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
36282472 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
36282512 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
36282552 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
36282576 CTTGTGCAAG
Statistics
Matches: 155, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.02
40 124 0.80
41 26 0.17
42 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:36282531 original size:80 final size:80
Alignment explanation
Indices: 36282351--36282611 Score: 287
Period size: 80 Copynumber: 3.3 Consensus size: 80
36282341 TATTCGAATG
* * * *
36282351 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAAT-CGGACTAAGATCCGAAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTAT-ATCCGGGCTAAGACCCGAAGG
*
36282415 CATTCGTGCGAGTTGCT
64 CATTCGTGCGAGTCGCT
* * * * *
36282432 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
36282497 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * *
36282512 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * *
36282577 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
36282591 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
36282612 ATTACTTGAG
Statistics
Matches: 152, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
78 14 0.09
79 16 0.11
80 91 0.60
81 31 0.20
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:36282568 original size:120 final size:120
Alignment explanation
Indices: 36282351--36282611 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
36282341 TATTCGAATG
* * *
36282351 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAATCGGACTAAGATCCGAAAGC
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAATCGGACTAAGATCCGAAAGC
* * * * *
36282416 ATTCGTGCGAGTTGCTATATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGA-TT
66 ATTCATGCGAGTTGCCACATCCAGGCTAAGACCCGAAGGC-CTTGTGCAAG-GAGTT
* * *
36282472 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTAT-ATCCGGGCTAAG-TCCCGAAG
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAAT-CGGACTAAGAT-CCGAAA
* * * *
36282534 GCATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGTAGTT
64 GCATTCATGCGAGTTG-CCACATCCAGGCTAAGACCCGAAGGCCTTGTGCAAGGAGTT
36282591 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAATCCCGAAG
36282612 ATTACTTGAG
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
118 15 0.12
119 21 0.17
120 53 0.44
121 31 0.26
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (120 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAATCGGACTAAGATCCGAAAGC
ATTCATGCGAGTTGCCACATCCAGGCTAAGACCCGAAGGCCTTGTGCAAGGAGTT
Found at i:36297039 original size:16 final size:17
Alignment explanation
Indices: 36297007--36297041 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
36296997 CGTTACAACA
36297007 TTTGTTTGATGTTTATT
1 TTTGTTTGATGTTTATT
*
36297024 TTTGTTTG-TTTTTATT
1 TTTGTTTGATGTTTATT
36297040 TT
1 TT
36297042 GTAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.09, C:0.00, G:0.14, T:0.77
Consensus pattern (17 bp):
TTTGTTTGATGTTTATT
Found at i:36298373 original size:21 final size:21
Alignment explanation
Indices: 36298349--36298389 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36298339 TCAACATACA
*
36298349 TAGATATAACCACAACAAAGC
1 TAGATACAACCACAACAAAGC
* *
36298370 TAGATACACCCACACCAAAG
1 TAGATACAACCACAACAAAG
36298390 TCCGATGCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.29, G:0.10, T:0.12
Consensus pattern (21 bp):
TAGATACAACCACAACAAAGC
Found at i:36303489 original size:27 final size:27
Alignment explanation
Indices: 36303459--36303636 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
36303449 ATATTGAGTC
* * * *
36303459 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
36303486 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36303513 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
36303541 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
36303568 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
36303595 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36303622 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36303637 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:36303598 original size:82 final size:81
Alignment explanation
Indices: 36303480--36303635 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
36303470 TGCTATATAA
* *
36303480 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
36303545 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
36303562 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
36303626 CACTTAGTGC
65 CACTTAGTGC
36303636 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:36311552 original size:27 final size:27
Alignment explanation
Indices: 36311522--36311699 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
36311512 ATATTGAGTC
* * * *
36311522 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
36311549 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36311576 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
36311604 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
36311631 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
36311658 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
36311685 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
36311700 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:36311661 original size:82 final size:81
Alignment explanation
Indices: 36311543--36311698 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
36311533 TGCTATATAA
* *
36311543 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
36311608 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
36311625 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
36311689 CACTTAGTGC
65 CACTTAGTGC
36311699 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:36317413 original size:22 final size:22
Alignment explanation
Indices: 36317382--36317457 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
36317372 TACGGCCTTT
*
36317382 AGCC-TCCTGTCTACGGCGTTG
1 AGCCATCCTGTCTAAGGCGTTG
* * * *
36317403 AGTCATCCTGTCCATGCCGTTG
1 AGCCATCCTGTCTAAGGCGTTG
*
36317425 AGCCATCCTATCTAAGGCGTTG
1 AGCCATCCTGTCTAAGGCGTTG
*
36317447 AGCCGTCCTGT
1 AGCCATCCTGT
36317458 TGACTTAGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 3 0.07
22 40 0.93
ACGTcount: A:0.14, C:0.32, G:0.25, T:0.29
Consensus pattern (22 bp):
AGCCATCCTGTCTAAGGCGTTG
Found at i:36319629 original size:18 final size:18
Alignment explanation
Indices: 36319601--36319645 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
36319591 ACTATTGTTG
*
36319601 AGAAGGAAGTTGATGCTGT
1 AGAA-GAAGTTGATGCTGA
*
36319620 AGAAGAAGTTGTTGCTGA
1 AGAAGAAGTTGATGCTGA
36319638 AGAAGAAG
1 AGAAGAAG
36319646 AAGTTGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.36, T:0.22
Consensus pattern (18 bp):
AGAAGAAGTTGATGCTGA
Found at i:36319651 original size:18 final size:18
Alignment explanation
Indices: 36319614--36319653 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36319604 AGGAAGTTGA
* **
36319614 TGCTGTAGAAGAAGTTGT
1 TGCTGAAGAAGAAGAAGT
36319632 TGCTGAAGAAGAAGAAGT
1 TGCTGAAGAAGAAGAAGT
36319650 TGCT
1 TGCT
36319654 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (18 bp):
TGCTGAAGAAGAAGAAGT
Found at i:36320123 original size:17 final size:17
Alignment explanation
Indices: 36320103--36320139 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
36320093 ATTAAGTATA
36320103 CATTGTCATTACATTGT
1 CATTGTCATTACATTGT
*
36320120 CATTGTCATTACATTTT
1 CATTGTCATTACATTGT
36320137 CAT
1 CAT
36320140 ATTATTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (17 bp):
CATTGTCATTACATTGT
Found at i:36325987 original size:28 final size:28
Alignment explanation
Indices: 36325919--36326184 Score: 392
Period size: 28 Copynumber: 9.5 Consensus size: 28
36325909 CATGAGATTG
* * *
36325919 GCACTAAGTGTGCGGGTTTAAAT-TGTACA
1 GCACTAAGTGTGCGAGTTTGATTATGT--A
*
36325948 GCACTAAGTGTGCGAGCTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
36325976 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
36326004 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
36326032 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
36326060 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
* *
36326088 GCACTAAGTGCGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
36326116 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
36326144 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATGTA
*
36326171 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
36326185 GACTTAAAAT
Statistics
Matches: 225, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
27 24 0.11
28 179 0.80
29 19 0.08
30 3 0.01
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATGTA
Found at i:36340204 original size:63 final size:63
Alignment explanation
Indices: 36340126--36340251 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
36340116 AACTTTTGAA
36340126 TTTCACATCTAATCTTATGTTTGAATATGTGGAAGGTTTGTTAGCTAATATGAATTATCTGTT
1 TTTCACATCTAATCTTATGTTTGAATATGTGGAAGGTTTGTTAGCTAATATGAATTATCTGTT
36340189 TTTCACATCTAATCTTATGTTTGAATATGTGGAAGGTTTGTTAGCTAATATGAATTATCTGTT
1 TTTCACATCTAATCTTATGTTTGAATATGTGGAAGGTTTGTTAGCTAATATGAATTATCTGTT
36340252 GATATATTCA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (63 bp):
TTTCACATCTAATCTTATGTTTGAATATGTGGAAGGTTTGTTAGCTAATATGAATTATCTGTT
Found at i:36342510 original size:24 final size:25
Alignment explanation
Indices: 36342483--36342534 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
36342473 GCCTAGCCTC
36342483 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
36342507 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
36342532 TTT
1 TTT
36342535 CGGTAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:36342518 original size:25 final size:25
Alignment explanation
Indices: 36342490--36342559 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
36342480 CTCTTTTAAT
*
36342490 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
36342515 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* **
36342540 AACTAGGGCGTAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
36342560 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:36343510 original size:29 final size:28
Alignment explanation
Indices: 36343443--36343524 Score: 96
Period size: 27 Copynumber: 2.9 Consensus size: 28
36343433 ATCTACAAAC
* *
36343443 CAAGGGTATTTCAATAATTTTGTAAACA
1 CAAGGGTATTTCTATAATTTTGTAAAAA
*
36343471 -AATGGTATTTCTATAATTTT-TAAAAA
1 CAAGGGTATTTCTATAATTTTGTAAAAA
*
36343497 GTCAAGGGTATTTCTGTAATTTTGTAAA
1 --CAAGGGTATTTCTATAATTTTGTAAA
36343525 TTAGAGGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 5 0.11
27 18 0.40
29 18 0.40
30 4 0.09
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (28 bp):
CAAGGGTATTTCTATAATTTTGTAAAAA
Found at i:36343552 original size:27 final size:27
Alignment explanation
Indices: 36343526--36343629 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 27
36343516 TTTTGTAAAT
*
36343526 TAGAGGTATTCTGGTAATTCTACAAA-
1 TAGAGGTATTTTGGTAATTCTACAAAC
* * *
36343552 TTGAGGGTATTTCGGTAATTTTACAAAC
1 TAGA-GGTATTTTGGTAATTCTACAAAC
* * *
36343580 CAGTGGTATTTTGGTAATTTTAC-AAC
1 TAGAGGTATTTTGGTAATTCTACAAAC
*
36343606 TAGGGGGTATTTTGGTAATTCTAC
1 TA-GAGGTATTTTGGTAATTCTAC
36343630 CCTATAGGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.11
27 56 0.88
28 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (27 bp):
TAGAGGTATTTTGGTAATTCTACAAAC
Found at i:36343588 original size:54 final size:54
Alignment explanation
Indices: 36343501--36343625 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
36343491 TAAAAAGTCA
* ** ** *
36343501 AGGGTATTTCTGTAATTTTGTAAATTAGAGGTATTCTGGTAATTCTACAAATTG
1 AGGGTATTTCGGTAATTTTACAAACCAGAGGTATTCTGGTAATTCTACAAATAG
* * * *
36343555 AGGGTATTTCGGTAATTTTACAAACCAGTGGTATTTTGGTAATTTTACAACTAG
1 AGGGTATTTCGGTAATTTTACAAACCAGAGGTATTCTGGTAATTCTACAAATAG
* *
36343609 GGGGTATTTTGGTAATT
1 AGGGTATTTCGGTAATT
36343626 CTACCCTATA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (54 bp):
AGGGTATTTCGGTAATTTTACAAACCAGAGGTATTCTGGTAATTCTACAAATAG
Found at i:36343639 original size:27 final size:27
Alignment explanation
Indices: 36343530--36343644 Score: 92
Period size: 27 Copynumber: 4.3 Consensus size: 27
36343520 GTAAATTAGA
* * *
36343530 GGTATTCTGGTAATTCTACAAAT-TGAG
1 GGTATTTTGGTAATTCTACAACTAAG-G
* * * *
36343557 GGTATTTCGGTAATTTTACAAAC-CAGT
1 GGTATTTTGGTAATTCTAC-AACTAAGG
* *
36343584 GGTATTTTGGTAATTTTACAACTAGGG
1 GGTATTTTGGTAATTCTACAACTAAGG
*
36343611 GGTATTTTGGTAATTCTAC-CCTATAGG
1 GGTATTTTGGTAATTCTACAACTA-AGG
36343638 GGTATTT
1 GGTATTT
36343645 CAGTAATTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
26 6 0.08
27 62 0.87
28 3 0.04
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (27 bp):
GGTATTTTGGTAATTCTACAACTAAGG
Found at i:36343676 original size:26 final size:26
Alignment explanation
Indices: 36343645--36343731 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
36343635 AGGGGTATTT
36343645 CAGTAATTT-CACAATCGAAGGTAAAA
1 CAGTAATTTGCA-AATCGAAGGTAAAA
* * *
36343671 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CAGTAA-TTTGCAAATCGAAGGTAAAA
* *
36343698 CAGTAATTCTGTAAATCGAGGGTAAAA
1 CAGTAATT-TGCAAATCGAAGGTAAAA
*
36343725 TAGTAAT
1 CAGTAAT
36343732 CCTATAAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.13
27 45 0.85
28 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (26 bp):
CAGTAATTTGCAAATCGAAGGTAAAA
Found at i:36343694 original size:27 final size:27
Alignment explanation
Indices: 36343657--36343748 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
36343647 GTAATTTCAC
* * *
36343657 AATCGAAGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
36343684 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
36343711 AATCGAGGGTAAAATAGTAATCCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
36343738 AATCGAGGGTA
1 AATCGAGGGTA
36343749 CTTTTGTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:36346018 original size:40 final size:40
Alignment explanation
Indices: 36345963--36346259 Score: 458
Period size: 40 Copynumber: 7.5 Consensus size: 40
36345953 CGGATGATAA
* * *
36345963 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
36346003 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
36346043 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
36346083 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
36346123 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
36346163 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
36346203 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
36346242 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
36346260 TACTTGGCTT
Statistics
Matches: 241, Mismatches: 14, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
38 15 0.06
39 16 0.07
40 210 0.87
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:36349764 original size:24 final size:25
Alignment explanation
Indices: 36349737--36349813 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
36349727 GCCTAGCCTC
*
36349737 TTTTAAT-AACTGGGGTAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
36349761 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* *** * *
36349786 TCTCGGTAAACTGGGGCATAGTCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
36349811 TTT
1 TTT
36349814 AGCACTTCCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 6 0.14
25 38 0.86
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:36349772 original size:25 final size:25
Alignment explanation
Indices: 36349744--36349803 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
36349734 CTCTTTTAAT
* * *
36349744 AACTGGGGTAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTCTCGATA
*
36349769 AACTGGGGCAAAGCCCTTCTCGGTA
1 AACTGGGGCAAAGCCCTTCTCGATA
36349794 AACTGGGGCA
1 AACTGGGGCA
36349804 TAGTCCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTCTCGATA
Found at i:36350724 original size:27 final size:27
Alignment explanation
Indices: 36350694--36350827 Score: 85
Period size: 27 Copynumber: 4.9 Consensus size: 27
36350684 GTAAATCTAC
36350694 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
* *
36350721 AAACCAATGGTATTTCTA-TAATTTTTT
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
36350748 AGAAAGTCAAGGGTATTTTTA-TAATTTTGT
1 --AAA-CCAAGGGTA-TTTCAGTAATTTTGT
** ** **
36350778 AAA-TTAGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTGT
***
36350804 AAATTGAGGGTATTTCAGTAATTT
1 AAACCAAGGGTATTTCAGTAATTT
36350828 CACAAACCAG
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
25 4 0.05
26 16 0.19
27 40 0.47
28 4 0.05
29 3 0.03
30 16 0.19
31 3 0.03
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:36350786 original size:26 final size:27
Alignment explanation
Indices: 36350757--36350879 Score: 85
Period size: 26 Copynumber: 4.6 Consensus size: 27
36350747 TAGAAAGTCA
* **
36350757 AGGGTATTTTTATAATTTTGTAAATT-
1 AGGGTATTTTGATAATTTTACAAATTG
*
36350783 AGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGATAATTTTACAAATTG
* * **
36350810 AGGGTA-TTTCAGTAATTTCACAAA-CC
1 AGGGTATTTTGA-TAATTTTACAAATTG
* *
36350836 AGCGGTATTTTTG-TAATTTTACAACTAG
1 AG-GGTA-TTTTGATAATTTTACAAATTG
*
36350864 -GGGTATTTTGGTAATT
1 AGGGTATTTTGATAATT
36350880 CTACCGTATA
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
25 5 0.07
26 36 0.47
27 32 0.42
29 3 0.04
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (27 bp):
AGGGTATTTTGATAATTTTACAAATTG
Found at i:36350832 original size:27 final size:26
Alignment explanation
Indices: 36350778--36350912 Score: 78
Period size: 27 Copynumber: 5.1 Consensus size: 26
36350768 ATAATTTTGT
** *
36350778 AAATTAGGGTATTTTGGTAATTTTAC
1 AAATTAGGGTATTTCAGTAATTTCAC
36350804 AAATTGAGGGTATTTCAGTAATTTCAC
1 AAATT-AGGGTATTTCAGTAATTTCAC
** ** *
36350831 AAACCAGCGGTATTTTTGTAATTTTAC
1 AAATTAG-GGTATTTCAGTAATTTCAC
* **
36350858 -AACTAGGGGTATTTTGGTAA-TTCTAC
1 AAATTA-GGGTATTTCAGTAATTTC-AC
**
36350884 -CGTATAGGGGTATTTCAGTAATTTCAC
1 AAAT-TA-GGGTATTTCAGTAATTTCAC
36350911 AA
1 AA
36350913 TCGACGGTAA
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
25 2 0.02
26 25 0.29
27 55 0.65
28 3 0.04
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (26 bp):
AAATTAGGGTATTTCAGTAATTTCAC
Found at i:36350874 original size:80 final size:80
Alignment explanation
Indices: 36350759--36350912 Score: 206
Period size: 80 Copynumber: 1.9 Consensus size: 80
36350749 GAAAGTCAAG
* * *
36350759 GGTATTTTTATAATTTTGTAAATTAGGGTATTTTGGTAATTTTA-CAAATTGAGGGTATTTCAGT
1 GGTATTTTTATAATTTTGTAAACTAGGGTATTTTGGTAATTCTACCAAATAG-GGGTATTTCAGT
36350823 AATTTCACAAACCAGC
65 AATTTCACAAACCAGC
* **
36350839 GGTATTTTTGTAA-TTT-TACAACTAGGGGTATTTTGGTAATTCTACCGTATAGGGGTATTTCAG
1 GGTATTTTTATAATTTTGTA-AACTA-GGGTATTTTGGTAATTCTACCAAATAGGGGTATTTCAG
36350902 TAATTTCACAA
64 TAATTTCACAA
36350913 TCGACGGTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 7 0.11
80 52 0.80
81 4 0.06
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (80 bp):
GGTATTTTTATAATTTTGTAAACTAGGGTATTTTGGTAATTCTACCAAATAGGGGTATTTCAGTA
ATTTCACAAACCAGC
Found at i:36350948 original size:27 final size:27
Alignment explanation
Indices: 36350911--36351002 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
36350901 GTAATTTCAC
* * *
36350911 AATCGACGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTCTGTA
*
36350938 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTCTGTA
*
36350965 AATCGAGGGTAAAATAGTAATTCTATA
1 AATCGAGGGTAAAATAGTAATTCTGTA
*
36350992 AATAGAGGGTA
1 AATCGAGGGTA
36351003 CTTTGGTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTCTGTA
Found at i:36350948 original size:80 final size:80
Alignment explanation
Indices: 36350769--36350948 Score: 186
Period size: 80 Copynumber: 2.2 Consensus size: 80
36350759 GGTATTTTTA
* * *
36350769 TAATTTTGTAAATTAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAA
1 TAATTTTGTAAATGAGGGTATTTTGGTAATTCTACAAATAGAGGGTATTTCAGTAATTTCACAAA
*** *
36350834 CCAGCGGTATTTTTG
66 CCAGCGGTAAAATGG
** * **
36350849 TAATTTTACAACT-AGGGGTATTTTGGTAATTCTACCGTATAG-GGGTATTTCAGTAATTTCACA
1 TAATTTTGTAAATGA-GGGTATTTTGGTAATTCTA-CAAATAGAGGGTATTTCAGTAATTTCACA
* *
36350912 ATCGA-CGGTAAAATGG
64 AACCAGCGGTAAAATGG
36350928 TAATTTTGTAAATCGAGGGTA
1 TAATTTTGTAAAT-GAGGGTA
36350949 AAACAGTAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
79 18 0.22
80 57 0.71
81 5 0.06
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (80 bp):
TAATTTTGTAAATGAGGGTATTTTGGTAATTCTACAAATAGAGGGTATTTCAGTAATTTCACAAA
CCAGCGGTAAAATGG
Found at i:36353836 original size:46 final size:46
Alignment explanation
Indices: 36353781--36353897 Score: 180
Period size: 46 Copynumber: 2.5 Consensus size: 46
36353771 GAGTGCTAGA
* * *
36353781 GTAAGACATGTTTGGGACATGCATCAGGCTCGAGACGTAAGCCAGT
1 GTAAGACATGTCTAGGACATGCATCAGCCTCGAGACGTAAGCCAGT
* *
36353827 GTAAGACATGTCTAGGACATGTATCAGCCTCGAGACGTAAGCTAGT
1 GTAAGACATGTCTAGGACATGCATCAGCCTCGAGACGTAAGCCAGT
*
36353873 GTAAGACATATCTAGGACATGCATC
1 GTAAGACATGTCTAGGACATGCATC
36353898 TGCTACGAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (46 bp):
GTAAGACATGTCTAGGACATGCATCAGCCTCGAGACGTAAGCCAGT
Found at i:36353907 original size:46 final size:45
Alignment explanation
Indices: 36353775--36353907 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 45
36353765 TAAGATGAGT
* * *
36353775 GCTAGAGTAAGACATGTTTGGGACATGCATCAGGCTCGAGACGTAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCA-GCTCGAGACGTAA
* *
36353821 GCCAGTGTAAGACATGTCTAGGACATGTATCAGCCTCGAGACGTAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAG-CTCGAGACGTAA
* *
36353867 GCTAGTGTAAGACATATCTAGGACATGCATCTGCTACGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCT-CGAGA
36353908 TATGTCAGTG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
45 3 0.04
46 73 0.96
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.23
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCAGCTCGAGACGTAA
Found at i:36354757 original size:21 final size:20
Alignment explanation
Indices: 36354731--36354770 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
36354721 GATTTAATGG
*
36354731 CTACACATGCGTGTTGCCCTT
1 CTACACAGGCGTG-TGCCCTT
*
36354752 CTACACGGGCGTGTGCCCT
1 CTACACAGGCGTGTGCCCT
36354771 GTTCTAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.35, G:0.25, T:0.28
Consensus pattern (20 bp):
CTACACAGGCGTGTGCCCTT
Found at i:36360401 original size:49 final size:49
Alignment explanation
Indices: 36360344--36360658 Score: 439
Period size: 49 Copynumber: 6.6 Consensus size: 49
36360334 TTAAACCCAT
*
36360344 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
36360393 ATGTGAAAGTG--TATATATGTGAATAGGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTG-ATAAGGCCTAATGGCCGATGTGATGA
*
36360441 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
36360490 ATGTGAAAGTGTATATATATGTGATAAGGCTTAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
**
36360539 ATGTGAAAGTGTATATGCA--TGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
36360586 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAATGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
36360633 ATGTGAAAGTGCATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
36360659 TCCCGAAGGG
Statistics
Matches: 240, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
45 4 0.02
47 88 0.37
48 36 0.15
49 102 0.43
50 10 0.04
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:36360833 original size:37 final size:37
Alignment explanation
Indices: 36360777--36360855 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
36360767 CCGAGCTCTA
* *
36360777 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
36360814 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
36360851 AAGAC
1 AAGAC
36360856 TTCGTAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:36362683 original size:13 final size:13
Alignment explanation
Indices: 36362665--36362689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36362655 CCCCTTACAC
36362665 GGGCGTGTCACAT
1 GGGCGTGTCACAT
36362678 GGGCGTGTCACA
1 GGGCGTGTCACA
36362690 CGATCGTGTC
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
GGGCGTGTCACAT
Found at i:36376542 original size:24 final size:23
Alignment explanation
Indices: 36376509--36376553 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
36376499 TACATCAGTG
36376509 AAAGATTTCTTGA-TTAGAAGCGT
1 AAAGATTTCTTGAGTT-GAAGCGT
36376532 AAAGAGTTTCTTGAGTTGAAGC
1 AAAGA-TTTCTTGAGTTGAAGC
36376554 AGGGCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 13 0.65
25 2 0.10
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (23 bp):
AAAGATTTCTTGAGTTGAAGCGT
Found at i:36380733 original size:11 final size:11
Alignment explanation
Indices: 36380704--36380736 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
36380694 CAAGATAGAA
*
36380704 ATAATTAATTT
1 ATAATTATTTT
36380715 ATAATTATTTT
1 ATAATTATTTT
36380726 ATAATTATTTT
1 ATAATTATTTT
36380737 GAGGTTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATAATTATTTT
Done.