Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 183 of 199
Found at i:53273510 original size:18 final size:17
Alignment explanation
Indices: 53273457--53273511 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 17
53273447 TGAATAAATT
53273457 ACTCATCTTAGTTAATTA
1 ACTCATCTTAGTTAA-TA
*
53273475 AGTTCATCTTAGTTAATA
1 A-CTCATCTTAGTTAATA
53273493 ACTCATCTTAGATTAATA
1 ACTCATCTTAG-TTAATA
53273511 A
1 A
53273512 ATGAGTTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.27
18 11 0.33
19 13 0.39
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (17 bp):
ACTCATCTTAGTTAATA
Found at i:53277079 original size:38 final size:38
Alignment explanation
Indices: 53277028--53277104 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
53277018 CCTCCTCCAA
53277028 CACACGCTCGGATGGGGTTTACCACAATCCCTATAGAC
1 CACACGCTCGGATGGGGTTTACCACAATCCCTATAGAC
*
53277066 CACACGCTTGGATGGGGTTTACCACAATCCCTATAGAC
1 CACACGCTCGGATGGGGTTTACCACAATCCCTATAGAC
53277104 C
1 C
53277105 TGGATCCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (38 bp):
CACACGCTCGGATGGGGTTTACCACAATCCCTATAGAC
Found at i:53280124 original size:109 final size:109
Alignment explanation
Indices: 53279933--53280146 Score: 419
Period size: 109 Copynumber: 2.0 Consensus size: 109
53279923 TCATTTGAAT
53279933 AAAACTTAACAACCAAATATTACCACATCAACGACAAAGAAATTATTCTCTTACCTGACACCAAA
1 AAAACTTAACAACCAAATATTACCACATCAACGACAAAGAAATTATTCTCTTACCTGACACCAAA
53279998 ATTGGAACACGCAAAAAGAATTTGAGCAATGGAAGCACACATTC
66 ATTGGAACACGCAAAAAGAATTTGAGCAATGGAAGCACACATTC
*
53280042 AAAACTTAACAACCAAATATTACCACATCAACGACAAAGAGATTATTCTCTTACCTGACACCAAA
1 AAAACTTAACAACCAAATATTACCACATCAACGACAAAGAAATTATTCTCTTACCTGACACCAAA
53280107 ATTGGAACACGCAAAAAGAATTTGAGCAATGGAAGCACAC
66 ATTGGAACACGCAAAAAGAATTTGAGCAATGGAAGCACAC
53280147 CACACCCACA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.20
Consensus pattern (109 bp):
AAAACTTAACAACCAAATATTACCACATCAACGACAAAGAAATTATTCTCTTACCTGACACCAAA
ATTGGAACACGCAAAAAGAATTTGAGCAATGGAAGCACACATTC
Found at i:53282700 original size:42 final size:41
Alignment explanation
Indices: 53282641--53282742 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 41
53282631 GTCCACATGA
* *
53282641 CAGACACACGGGTGTGTGACTTGGCCATGTAAGACACACGGC
1 CAGACACACGGGTGTGTGACTTAGCCACGTAAGACACAC-GC
* * *
53282683 CAGACACACGAGTGTGTGACTTAGCCGCGTAAGGCACACGC
1 CAGACACACGGGTGTGTGACTTAGCCACGTAAGACACACGC
53282724 CTAG-CACACGGGTGTGTGA
1 C-AGACACACGGGTGTGTGA
53282743 GGCCATTTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 17 0.32
42 36 0.68
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.17
Consensus pattern (41 bp):
CAGACACACGGGTGTGTGACTTAGCCACGTAAGACACACGC
Found at i:53284274 original size:22 final size:21
Alignment explanation
Indices: 53284241--53284281 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
53284231 TGTTTATATA
53284241 TAAATATATATTCTTTATAAATT
1 TAAATATATA-T-TTTATAAATT
53284264 TAAAT-TATATTTTATAAA
1 TAAATATATATTTTATAAA
53284282 ATTATATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 4 0.22
23 5 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATATATATTTTATAAATT
Found at i:53284638 original size:21 final size:21
Alignment explanation
Indices: 53284612--53284652 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53284602 ATGGATAAAA
53284612 TTTAAGATTTAATATTTAGAT
1 TTTAAGATTTAATATTTAGAT
* * *
53284633 TTTAAGGTTTAGTCTTTAGA
1 TTTAAGATTTAATATTTAGA
53284653 GTCTATAGAT
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:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (21 bp):
TTTAAGATTTAATATTTAGAT
Found at i:53286029 original size:22 final size:22
Alignment explanation
Indices: 53285973--53286021 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
53285963 ATATCCAAAC
53285973 AATAACAA-CAAAATAGTAGCAA
1 AATAA-AAGCAAAATAGTAGCAA
* *
53285995 CATAAAAGCAAAATGGTAGCAA
1 AATAAAAGCAAAATAGTAGCAA
53286017 AATAA
1 AATAA
53286022 GGAGAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.14
Consensus pattern (22 bp):
AATAAAAGCAAAATAGTAGCAA
Found at i:53288763 original size:26 final size:26
Alignment explanation
Indices: 53288734--53288784 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
53288724 TATTAACAAC
*
53288734 AATAAAACATGTTTGAACCCCACATT
1 AATAAAACATGTTTCAACCCCACATT
*
53288760 AATAAAACATGTTTCAACCTCACAT
1 AATAAAACATGTTTCAACCCCACAT
53288785 GGTCCAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (26 bp):
AATAAAACATGTTTCAACCCCACATT
Found at i:53289469 original size:20 final size:21
Alignment explanation
Indices: 53289434--53289472 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
53289424 TAATACATAT
*
53289434 TTAAATAATTATAATTTGATA
1 TTAAATAATAATAATTTGATA
53289455 TTAAA-AATAATAATTTGA
1 TTAAATAATAATAATTTGA
53289473 ATTTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAAATAATAATAATTTGATA
Found at i:53307256 original size:26 final size:26
Alignment explanation
Indices: 53307189--53307257 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
53307179 CATTCTGACC
* *
53307189 CACAGCTCTTGTGAGCAGGCCCATTT
1 CACAGCTCTTGTGAGTAGGCACATTT
*
53307215 CATAGCTCTTGTGAGTAGGCACATTT
1 CACAGCTCTTGTGAGTAGGCACATTT
*
53307241 CACAGCTCGTGTGAGTA
1 CACAGCTCTTGTGAGTA
53307258 ATAATGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (26 bp):
CACAGCTCTTGTGAGTAGGCACATTT
Found at i:53308629 original size:18 final size:18
Alignment explanation
Indices: 53308606--53308641 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53308596 TGTGTGACCC
53308606 TTGCAGTTCAATTTTTCT
1 TTGCAGTTCAATTTTTCT
53308624 TTGCAGTTCAATTTTTCT
1 TTGCAGTTCAATTTTTCT
53308642 AACTTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (18 bp):
TTGCAGTTCAATTTTTCT
Found at i:53312390 original size:13 final size:13
Alignment explanation
Indices: 53312374--53312399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53312364 TAAAAAGGAT
53312374 ATAAAAAATAAAA
1 ATAAAAAATAAAA
53312387 ATAAAAAATAAAA
1 ATAAAAAATAAAA
53312400 TGGACAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:53315099 original size:50 final size:50
Alignment explanation
Indices: 53314994--53315126 Score: 140
Period size: 50 Copynumber: 2.7 Consensus size: 50
53314984 TCATTAAGAT
* * *** *
53314994 TATGAGAGGTCCCATGTAAGACCATGTCTAGGACGTAGCGTTGACACCGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCACGGACACCAA
* ** * *
53315044 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCACGGGCACCAA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCACGGACACCAA
** *
53315094 TATGAGAACTCCCATGTAAGACCATATCTGGGA
1 TATGAGAGGTCCCATGTAAGACCATGTCTGGGA
53315127 TATGACATTG
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.20
Consensus pattern (50 bp):
TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCACGGACACCAA
Found at i:53317653 original size:16 final size:16
Alignment explanation
Indices: 53317622--53317652 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53317612 ATAACTATTT
53317622 CTTGTCATATAAAAAA
1 CTTGTCATATAAAAAA
53317638 CTTGT-ATATAAAAAA
1 CTTGTCATATAAAAAA
53317653 ATATTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
CTTGTCATATAAAAAA
Found at i:53320903 original size:13 final size:13
Alignment explanation
Indices: 53320887--53320911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53320877 ATGGAAGGCA
53320887 GAAATTTTATTAG
1 GAAATTTTATTAG
53320900 GAAATTTTATTA
1 GAAATTTTATTA
53320912 TGTACAGTAA
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
GAAATTTTATTAG
Found at i:53322917 original size:16 final size:16
Alignment explanation
Indices: 53322896--53322945 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
53322886 TCGGGTTCGA
53322896 TTTCAAGGATCTTTTG
1 TTTCAAGGATCTTTTG
53322912 TTTCAAGGATCTTTTG
1 TTTCAAGGATCTTTTG
53322928 TTTCAAGGATCTTTTG
1 TTTCAAGGATCTTTTG
53322944 TT
1 TT
53322946 AGTCCAACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCAAGGATCTTTTG
Found at i:53323561 original size:43 final size:43
Alignment explanation
Indices: 53323500--53323605 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 43
53323490 TCACAAATGT
*
53323500 CGCTATAGAACATGATCTTTAACGACGCTTTTACTAAAAACGC
1 CGCTATAGAACATGATCTTTAACGAAGCTTTTACTAAAAACGC
* * * * *
53323543 CGCTATAGAACATAATCTTTAGCGAATCTTTTACTACAAATGC
1 CGCTATAGAACATGATCTTTAACGAAGCTTTTACTAAAAACGC
*
53323586 CGCTAAAGAACATGATCTTT
1 CGCTATAGAACATGATCTTT
53323606 TGCATCGTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (43 bp):
CGCTATAGAACATGATCTTTAACGAAGCTTTTACTAAAAACGC
Found at i:53323732 original size:43 final size:43
Alignment explanation
Indices: 53323656--53323773 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
53323646 TCCTACAAGT
* * * * * *
53323656 GCCGTTAAAGATCATATTCTACAACAGCATTTGTAGGAAAAGC
1 GCCGCTAAAAATCATGTTCTACAGCGGCGTTTGTAGGAAAAGC
** * *
53323699 GTTGCTAAATATCATGTTCTACAGCGGCGTTTGTATGAAAAGC
1 GCCGCTAAAAATCATGTTCTACAGCGGCGTTTGTAGGAAAAGC
* *
53323742 GCCGCTAAAAATCATGTTCTATAGTGGCGTTT
1 GCCGCTAAAAATCATGTTCTACAGCGGCGTTT
53323774 TCCCACATAA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
GCCGCTAAAAATCATGTTCTACAGCGGCGTTTGTAGGAAAAGC
Found at i:53324032 original size:17 final size:18
Alignment explanation
Indices: 53323997--53324032 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53323987 TTGAATTTTT
*
53323997 TTTAAAATATATGAAATA
1 TTTAAAAAATATGAAATA
53324015 TTTAAAAAATAT-AAATA
1 TTTAAAAAATATGAAATA
53324032 T
1 T
53324033 AAAATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TTTAAAAAATATGAAATA
Found at i:53331935 original size:51 final size:51
Alignment explanation
Indices: 53331766--53331956 Score: 185
Period size: 51 Copynumber: 3.8 Consensus size: 51
53331756 TGAAAGTGAA
* * *
53331766 AGTGAT-GGTCACATGTGTAGTATTTTGTGCAGGCTACTACGTGTACGAG-
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGGT
* * * * *** *
53331815 AGTGATAGGTCGCAGGTGTAGTACTATGTGTAGGCTACTATGCACACCGGAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGGT
* * *
53331867 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGGT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGGT
*
53331918 AGTGAT-GGTCACATGTGTAGTAATATGTGCAGGCTACTA
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTA
53331957 TGTGAACCGG
Statistics
Matches: 110, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
49 6 0.05
50 31 0.28
51 69 0.63
52 3 0.03
53 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (51 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGGT
Found at i:53331966 original size:102 final size:101
Alignment explanation
Indices: 53331774--53331958 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
53331764 AAAGTGATGG
* * * *
53331774 TCACATGTGTAGTATTTTGTGCAGGCTACTACGTGTACGAGAGTGATAGGTCGCAGGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGAGAGTGATAGGTCACAGGTGTAGTAA
*
53331839 TATGTGTAGGCTACTATGCACACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCACACCGGATAGCTTCGA
* * *
53331875 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGGTAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGAG-AGTGATAGGTCACAGGTGTAGT
53331939 AATATGTGCAGGCTACTATG
64 AATATGTGCAGGCTACTATG
53331959 TGAACCGGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 34 0.46
102 34 0.46
103 6 0.08
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGAGAGTGATAGGTCACAGGTGTAGTAA
TATGTGCAGGCTACTATGCACACCGGATAGCTTCGA
Found at i:53332034 original size:46 final size:43
Alignment explanation
Indices: 53331962--53332060 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
53331952 TACTATGTGA
*
53331962 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
53332005 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
53332051 ACCGTGTATC
1 ACCG-GTATC
53332061 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 27 0.56
47 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:53332205 original size:16 final size:16
Alignment explanation
Indices: 53332184--53332215 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53332174 TGATTGAATG
*
53332184 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
53332200 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
53332216 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:53344053 original size:14 final size:13
Alignment explanation
Indices: 53344020--53344053 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
53344010 ATAAAAAACT
53344020 AAAAAAGGAGGAA
1 AAAAAAGGAGGAA
53344033 AAGAAAAGGAGGAGA
1 AA-AAAAGGAGGA-A
53344048 AAAAAA
1 AAAAAA
53344054 CTTCATGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 14 0.74
15 3 0.16
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAAAAGGAGGAA
Found at i:53345787 original size:34 final size:33
Alignment explanation
Indices: 53345732--53345826 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 33
53345722 AATGATTGGT
* **
53345732 TGTCCATTGAGGTGC-CTGAACAGCCTTGTTGTTG
1 TGTCCATTGATGTGCAC-GAACAGCCTTG-TACTG
* * *
53345766 TGTCTATTGATGTGCACGAACAACCCTGTACTG
1 TGTCCATTGATGTGCACGAACAGCCTTGTACTG
* *
53345799 TGTCCATTGGTGTGCATGAACAGCCTTG
1 TGTCCATTGATGTGCACGAACAGCCTTG
53345827 AGTTGAATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
33 26 0.53
34 22 0.45
35 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (33 bp):
TGTCCATTGATGTGCACGAACAGCCTTGTACTG
Found at i:53351750 original size:15 final size:14
Alignment explanation
Indices: 53351729--53351767 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
53351719 AGAAGTCCTT
*
53351729 TTTATTTTTATTTT
1 TTTATTTTTATTTC
53351743 TGTTATTTTTATTTC
1 T-TTATTTTTATTTC
53351758 TTTATTTTTA
1 TTTATTTTTA
53351768 AGAACAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTATTTTTATTTC
Found at i:53358012 original size:27 final size:29
Alignment explanation
Indices: 53357964--53358017 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
53357954 TCTATATTTT
* * *
53357964 GGGATTTAATTCTATTATAAGGTCTTTGA
1 GGGATTAAATTCTATTAAAAGGGCTTTGA
53357993 GGGATTAAATT-T-TTAAAAGGGCTTT
1 GGGATTAAATTCTATTAAAAGGGCTTT
53358018 AGATTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 1 0.05
29 10 0.45
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.43
Consensus pattern (29 bp):
GGGATTAAATTCTATTAAAAGGGCTTTGA
Found at i:53365163 original size:7 final size:7
Alignment explanation
Indices: 53365151--53365181 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
53365141 ATTAAAAGTA
53365151 GTCCAAG
1 GTCCAAG
53365158 GTCCAAG
1 GTCCAAG
53365165 GTCCAAG
1 GTCCAAG
53365172 GTCCAAG
1 GTCCAAG
53365179 GTC
1 GTC
53365182 ATTCTCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCCAAG
Found at i:53367242 original size:13 final size:14
Alignment explanation
Indices: 53367211--53367247 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
53367201 GAAGATATTT
53367211 AAAT-AATAATTAAA
1 AAATAAATAATT-AA
53367225 AAATAAATAATT-A
1 AAATAAATAATTAA
53367238 AAATAAATAA
1 AAATAAATAA
53367248 ATAATGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 4 0.18
15 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATAAATAATTAA
Found at i:53368641 original size:85 final size:85
Alignment explanation
Indices: 53368497--53368729 Score: 335
Period size: 85 Copynumber: 2.8 Consensus size: 85
53368487 CCGTTACTCA
* * *
53368497 GTGGATTCAGCACTTAGCAACCACC-TTAAATTCAGTGATATGGGGAATTAGCACATAGCAACCA
1 GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCA
53368561 CTTTCACAATCAAAGATACG
66 CTTTCACAATCAAAGATACG
* * *
53368581 GTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGTACATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCA
*
53368646 CTTTCACAATCAAATATACG
66 CTTTCACAATCAAAGATACG
* * * * *
53368666 GTGGAATCAACACTTAGCAACCACCTTTAGAA-TCAATAATTCGGGGAATCAGCACTTAGCAACC
1 GTGGAATCAGCACTTAGCAACCACCTTTA-AATTCAGTGATACGGGGAATCAGCACATAGCAACC
53368730 CCTCGGAGAA
Statistics
Matches: 133, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
84 24 0.18
85 108 0.81
86 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (85 bp):
GTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCA
CTTTCACAATCAAAGATACG
Found at i:53368642 original size:42 final size:42
Alignment explanation
Indices: 53368503--53368729 Score: 239
Period size: 43 Copynumber: 5.4 Consensus size: 42
53368493 CTCAGTGGAT
* *
53368503 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATATGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAA-TCAATGATACGGGGAA
* * *
53368544 TTAGCACATAGCAACCA-CTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG-GGAA
* * *
53368587 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
* *
53368629 TCAGTACATAGCAACC-CCTTTCACAATCAAAT-ATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATC-AATGATACGG-GGAA
* * * *
53368672 TCAACACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
53368714 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
53368730 CCTCGGAGAA
Statistics
Matches: 154, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 22 0.14
42 60 0.39
43 62 0.40
44 9 0.06
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTACAATCAATGATACGGGGAA
Found at i:53368735 original size:26 final size:26
Alignment explanation
Indices: 53368706--53368758 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53368696 AATCAATAAT
*
53368706 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGAGAATCAGCACTTAGCAACCCC
** *
53368732 TCGGAGAATTTGCACTTAGCGACCCC
1 TCGGAGAATCAGCACTTAGCAACCCC
53368758 T
1 T
53368759 TTTTATCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.21
Consensus pattern (26 bp):
TCGGAGAATCAGCACTTAGCAACCCC
Found at i:53370265 original size:50 final size:50
Alignment explanation
Indices: 53370206--53370307 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
53370196 ACAGTTCAGT
53370206 AACGTATGTTGATAATCAATAACTCTTTATTCAACTCAGGCTGAATCATA
1 AACGTATGTTGATAATCAATAACTCTTTATTCAACTCAGGCTGAATCATA
53370256 AACGTATGTTGATAATCAATAACTCTTTATTCAACTCAGGCTGAATCATA
1 AACGTATGTTGATAATCAATAACTCTTTATTCAACTCAGGCTGAATCATA
53370306 AA
1 AA
53370308 TGATGTTTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (50 bp):
AACGTATGTTGATAATCAATAACTCTTTATTCAACTCAGGCTGAATCATA
Found at i:53372122 original size:41 final size:42
Alignment explanation
Indices: 53372043--53372123 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
53372033 CGTTTTCTCT
**
53372043 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
*
53372085 ATGCCATAG-CCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGTCCAACTATGGTCTTACACA-TATGCACATAT
53372124 CACACCAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (42 bp):
ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
Found at i:53372570 original size:26 final size:26
Alignment explanation
Indices: 53372534--53372588 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
53372524 CAACAAAAAC
*
53372534 TTTTTTTTTAACTTATGATCATCTTT
1 TTTTTTTTTAACTTATGATCATCTCT
53372560 TTTTTTTTTAACTTATGATCATCTCT
1 TTTTTTTTTAACTTATGATCATCTCT
53372586 TTT
1 TTT
53372589 CATACATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.13, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTTTTTTAACTTATGATCATCTCT
Found at i:53374770 original size:43 final size:43
Alignment explanation
Indices: 53374667--53374900 Score: 214
Period size: 43 Copynumber: 5.5 Consensus size: 43
53374657 TCCGTTACTT
* **
53374667 GGTGGATTCAACACTTAGCAACCACC-TTA-AATTCAGTGATAC
1 GGTGGAATCAACACTTAGCAACCACCTTTACAA-TCAAAGATAC
* * *
53374709 -GAGGAATCAGCACATAGCAACC-CCTTTCACAATCAAAGATAC
1 GGTGGAATCAACACTTAGCAACCACCTTT-ACAATCAAAGATAC
* * ** *
53374751 GGTGGAATCAACACTTAGCAACCACCTTTATATTCAGTGATAT
1 GGTGGAATCAACACTTAGCAACCACCTTTACAATCAAAGATAC
* * * *
53374794 GG-GGAATCAGCACATAGCAAAC-CCTTTCACAATCAAATATAC
1 GGTGGAATCAACACTTAGCAACCACCTTT-ACAATCAAAGATAC
* * *
53374836 GGTGGAATCAGCACTTAGCAACCACCTTTAGAATC-AAGAATTC
1 GGTGGAATCAACACTTAGCAACCACCTTTACAATCAAAG-ATAC
53374879 GG-GGAATCAACACTTAGCAACC
1 GGTGGAATCAACACTTAGCAACC
53374901 CCTCGGGGAA
Statistics
Matches: 154, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
40 2 0.01
41 25 0.16
42 57 0.37
43 60 0.39
44 10 0.06
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (43 bp):
GGTGGAATCAACACTTAGCAACCACCTTTACAATCAAAGATAC
Found at i:53374811 original size:85 final size:85
Alignment explanation
Indices: 53374667--53374865 Score: 328
Period size: 85 Copynumber: 2.4 Consensus size: 85
53374657 TCCGTTACTT
* *
53374667 GGTGGATTCAACACTTAGCAACCACC-TTAAATTCAGTGATACGAGGAATCAGCACATAGCAACC
1 GGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGAGGAATCAGCACATAGCAAAC
53374731 CCTTTCACAATCAAAGATAC
66 CCTTTCACAATCAAAGATAC
* * *
53374751 GGTGGAATCAACACTTAGCAACCACCTTTATATTCAGTGATATGGGGAATCAGCACATAGCAAAC
1 GGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGAGGAATCAGCACATAGCAAAC
*
53374816 CCTTTCACAATCAAATATAC
66 CCTTTCACAATCAAAGATAC
*
53374836 GGTGGAATCAGCACTTAGCAACCACCTTTA
1 GGTGGAATCAACACTTAGCAACCACCTTTA
53374866 GAATCAAGAA
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 25 0.23
85 82 0.77
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (85 bp):
GGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGAGGAATCAGCACATAGCAAAC
CCTTTCACAATCAAAGATAC
Found at i:53374883 original size:85 final size:84
Alignment explanation
Indices: 53374667--53374903 Score: 318
Period size: 85 Copynumber: 2.8 Consensus size: 84
53374657 TCCGTTACTT
* * *
53374667 GGTGGATTCAACACTTAGCAACCACC-TTAAATTCAGTGATACGAGGAATCAGCACATAGCAACC
1 GGTGGAATCAACACTTAGCAACCACCTTTAAA-TCAGTGATTCGGGGAATCAGCACATAGCAACC
53374731 CCTTTCACAATCAAAGATAC
65 CCTTTCACAATCAAAGATAC
* *
53374751 GGTGGAATCAACACTTAGCAACCACCTTTATATTCAGTGATAT-GGGGAATCAGCACATAGCAAA
1 GGTGGAATCAACACTTAGCAACCACCTTTA-AATCAGTGAT-TCGGGGAATCAGCACATAGCAAC
*
53374815 CCCTTTCACAATCAAATATAC
64 CCCTTTCACAATCAAAGATAC
* * * *
53374836 GGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAAG-AATTCGGGGAATCAACACTTAGCAAC
1 GGTGGAATCAACACTTAGCAACCACCTTTA-AATC-AGTGATTCGGGGAATCAGCACATAGCAAC
53374900 CCCT
64 CCCT
53374904 CGGGGAATCT
Statistics
Matches: 135, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
84 26 0.19
85 106 0.79
86 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (84 bp):
GGTGGAATCAACACTTAGCAACCACCTTTAAATCAGTGATTCGGGGAATCAGCACATAGCAACCC
CTTTCACAATCAAAGATAC
Found at i:53374906 original size:26 final size:26
Alignment explanation
Indices: 53374877--53374929 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
53374867 AATCAAGAAT
53374877 TCGGGGAATCAACACTTAGCAACCCC
1 TCGGGGAATCAACACTTAGCAACCCC
** *
53374903 TCGGGGAATCTGCACTTAGCGACCCC
1 TCGGGGAATCAACACTTAGCAACCCC
53374929 T
1 T
53374930 TTTTATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.19
Consensus pattern (26 bp):
TCGGGGAATCAACACTTAGCAACCCC
Found at i:53375300 original size:30 final size:30
Alignment explanation
Indices: 53375266--53375323 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53375256 TCTTTAACTC
*
53375266 AAACTTTTGGAAAATTACAATTTTGCCCTT
1 AAACTTTTGCAAAATTACAATTTTGCCCTT
* * *
53375296 AAACTTTTGCATATTTACACTTTTGCCC
1 AAACTTTTGCAAAATTACAATTTTGCCC
53375324 CAAAGCTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCTT
Found at i:53380647 original size:28 final size:28
Alignment explanation
Indices: 53380611--53380666 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
53380601 CAGTATCAGT
* *
53380611 ACAGTGTGGACCCCAGCCCATTATAGTA
1 ACAGTGTGGACCCAAGCCCAATATAGTA
* *
53380639 ACAGTGTGGGCCTAAGCCCAATATAGTA
1 ACAGTGTGGACCCAAGCCCAATATAGTA
53380667 TCATATGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (28 bp):
ACAGTGTGGACCCAAGCCCAATATAGTA
Found at i:53381082 original size:27 final size:27
Alignment explanation
Indices: 53381059--53381109 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
53381049 TTCTACCTTT
53381059 CGGGGGTATTTCAGTAATTTTACCCTA
1 CGGGGGTATTTCAGTAATTTTACCCTA
*
53381086 CGGGGGTATTTCGGTAA-TTTACCC
1 CGGGGGTATTTCAGTAATTTTACCC
53381110 ACTGAGTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (27 bp):
CGGGGGTATTTCAGTAATTTTACCCTA
Found at i:53381106 original size:26 final size:26
Alignment explanation
Indices: 53381062--53381262 Score: 237
Period size: 26 Copynumber: 7.7 Consensus size: 26
53381052 TACCTTTCGG
*
53381062 GGGTATTTC-AGTAATTTTACCC-TACGG
1 GGGTATTTCGA-TAA-TTTACCCAT-CGA
*
53381089 GGGTATTTCGGTAATTTACCCA-CTGA
1 GGGTATTTCGATAATTTACCCATC-GA
*
53381115 GTGTATTTCGATAATTTACCCATCGA
1 GGGTATTTCGATAATTTACCCATCGA
* * *
53381141 AGGTATTTTGGTAATTTACCCATCGA
1 GGGTATTTCGATAATTTACCCATCGA
* * *
53381167 GGGTATTTCAATTATTTACCCATCGT
1 GGGTATTTCGATAATTTACCCATCGA
53381193 GGGTATTTCGATAATTTACCCATCGA
1 GGGTATTTCGATAATTTACCCATCGA
* * *
53381219 GGGTTTTTCGGTAATATACCCATCGA
1 GGGTATTTCGATAATTTACCCATCGA
53381245 GGGTATTTCGATAATTTA
1 GGGTATTTCGATAATTTA
53381263 GGCCCATTAC
Statistics
Matches: 147, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
25 1 0.01
26 133 0.90
27 13 0.09
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (26 bp):
GGGTATTTCGATAATTTACCCATCGA
Found at i:53388455 original size:27 final size:26
Alignment explanation
Indices: 53388391--53388455 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
53388381 CAGCATAGCT
53388391 ACCAGATCAGTATATGTGGCAAAACC
1 ACCAGATCAGTATATGTGGCAAAACC
* * *
53388417 ACCAGTAACAGTAGT-TGTGGCAGAGCC
1 ACCAG-ATCAGTA-TATGTGGCAAAACC
53388444 ACCAGCATCAGT
1 ACCAG-ATCAGT
53388456 GCTTCCTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 5 0.16
27 26 0.81
28 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (26 bp):
ACCAGATCAGTATATGTGGCAAAACC
Found at i:53388646 original size:27 final size:27
Alignment explanation
Indices: 53388625--53388708 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 27
53388615 ACAGTCATTC
*
53388625 TACCCTTCGGGGGTATTTCAGTAATAT
1 TACCCTTCAGGGGTATTTCAGTAATAT
* **
53388652 TACCCTTTAGGGGTATTTTGGTAATA-
1 TACCCTTCAGGGGTATTTCAGTAATAT
* **
53388678 TACCCATTGA-GGGTATTTTGGTAAT-T
1 TACCC-TTCAGGGGTATTTCAGTAATAT
53388704 TACCC
1 TACCC
53388709 ATCGAGGTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 25 0.50
27 25 0.50
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (27 bp):
TACCCTTCAGGGGTATTTCAGTAATAT
Found at i:53388691 original size:26 final size:26
Alignment explanation
Indices: 53388662--53388838 Score: 255
Period size: 26 Copynumber: 6.8 Consensus size: 26
53388652 TACCCTTTAG
* * *
53388662 GGGTATTTTGGTAATATACCCATTGA
1 GGGTATTTTGATAATTTACCCATCGA
*
53388688 GGGTATTTTGGTAATTTACCCATCGA
1 GGGTATTTTGATAATTTACCCATCGA
* *
53388714 GGTTATTTTGGTAATTTACCCATCGA
1 GGGTATTTTGATAATTTACCCATCGA
* *
53388740 GGTTATTTCGATAATTTACCCATCGA
1 GGGTATTTTGATAATTTACCCATCGA
*
53388766 GGGTATTTTGATAATTTACCCATAGA
1 GGGTATTTTGATAATTTACCCATCGA
* *
53388792 GGGTATTTCGATAATTTACCCATCCA
1 GGGTATTTTGATAATTTACCCATCGA
53388818 GGGTATTTTGATAATTTACCC
1 GGGTATTTTGATAATTTACCC
53388839 CCGTTACGGC
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 139 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (26 bp):
GGGTATTTTGATAATTTACCCATCGA
Found at i:53390970 original size:22 final size:22
Alignment explanation
Indices: 53390942--53390984 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
53390932 TTTATTGTTC
53390942 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
53390964 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
53390985 TGGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:53393503 original size:30 final size:30
Alignment explanation
Indices: 53393405--53393503 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
53393395 TGTGTATACA
*
53393405 ATATAT-TATATATATTAGT-GGG-TGT-T
1 ATATATATATATATATAAGTGGGGTTGTGT
*
53393431 ATATATATA-ATATATAAATAGGGAAGTTG-GT
1 ATATATATATATATATAAGT-GGG--GTTGTGT
* *
53393462 AATATACATATATATATGAGTGGGGTTGTGT
1 -ATATATATATATATATAAGTGGGGTTGTGT
53393493 ATATATATATA
1 ATATATATATA
53393504 CGTGGGTGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
26 14 0.25
27 2 0.04
28 2 0.04
30 15 0.26
31 5 0.09
32 11 0.19
33 8 0.14
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.41
Consensus pattern (30 bp):
ATATATATATATATATAAGTGGGGTTGTGT
Found at i:53396565 original size:15 final size:15
Alignment explanation
Indices: 53396545--53396574 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53396535 AAACAGTCCA
53396545 ATGAACAAAACAAAC
1 ATGAACAAAACAAAC
53396560 ATGAACAAAACAAAC
1 ATGAACAAAACAAAC
53396575 GAACCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
ATGAACAAAACAAAC
Found at i:53403587 original size:28 final size:28
Alignment explanation
Indices: 53403547--53403602 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
53403537 CTATTGCCAC
*
53403547 ATCACTTAGTCTTTTTCTTTCTTAAGAA
1 ATCACTTAGTCTTTTTCTTTCTAAAGAA
53403575 ATCACTTAGTCTTTTTCTTTCTAAAGAA
1 ATCACTTAGTCTTTTTCTTTCTAAAGAA
53403603 GTATTTATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (28 bp):
ATCACTTAGTCTTTTTCTTTCTAAAGAA
Found at i:53412018 original size:23 final size:23
Alignment explanation
Indices: 53411956--53412384 Score: 255
Period size: 23 Copynumber: 18.5 Consensus size: 23
53411946 ATATATATAT
*
53411956 ATATATATACAAAATTGGACAGC
1 ATATATATCCAAAATTGGACAGC
* * *
53411979 ATTTATACACCAAAATTTGACAGC
1 ATATATA-TCCAAAATTGGACAGC
* *
53412003 ATGTATATCCAAAATTAGACAGC
1 ATATATATCCAAAATTGGACAGC
* *
53412026 ATTTAT-TCACCAAAATTGGGCAGC
1 ATATATAT--CCAAAATTGGACAGC
*
53412050 ATATATATACC-AATTTGGACAGC
1 ATATATAT-CCAAAATTGGACAGC
* *
53412073 ACT-TATA-CACAAAATTTGACGGC
1 A-TATATATC-CAAAATTGGACAGC
* *
53412096 ATGTATATACAAAATTGGACAGC
1 ATATATATCCAAAATTGGACAGC
* *
53412119 ATTTAT-TCACCAAAATTGGGCAGC
1 ATATATAT--CCAAAATTGGACAGC
*
53412143 ATATATATACC-AATTTGG-CAGC
1 ATATATAT-CCAAAATTGGACAGC
*
53412165 ACT-TATA-CACAAAATTGGGCAGC
1 A-TATATATC-CAAAATTGGACAGC
*
53412188 ATATATATACC-AATTTGGACAGC
1 ATATATAT-CCAAAATTGGACAGC
*
53412211 ACT-TATA-CACAAAATTTGACAGC
1 A-TATATATC-CAAAATTGGACAGC
*
53412234 ATGTATA-CACAAAATTGGACAGC
1 ATATATATC-CAAAATTGGACAGC
* **
53412257 ATTTAT-TCACCAAAATTGGGTAGC
1 ATATATAT--CCAAAATTGGACAGC
*
53412281 ATATATATACC-AATTTGGACAGC
1 ATATATAT-CCAAAATTGGACAGC
* * *
53412304 AGATATA--CACAATTTGACAGC
1 ATATATATCCAAAATTGGACAGC
* *
53412325 ACATATATACAAAATTGGACAGC
1 ATATATATCCAAAATTGGACAGC
* **
53412348 ATTTAT-TCACCAAAATTGGGTAGC
1 ATATATAT--CCAAAATTGGACAGC
53412372 ATATATATACCAA
1 ATATATAT-CCAA
53412385 TTTGAGTAGC
Statistics
Matches: 323, Mismatches: 50, Indels: 65
0.74 0.11 0.15
Matches are distributed among these distances:
20 2 0.01
21 18 0.06
22 23 0.07
23 168 0.52
24 106 0.33
25 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (23 bp):
ATATATATCCAAAATTGGACAGC
Found at i:53412222 original size:138 final size:138
Alignment explanation
Indices: 53411959--53412364 Score: 566
Period size: 138 Copynumber: 2.9 Consensus size: 138
53411949 TATATATATA
* * * * * *
53411959 TATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGCATGTATAT-CCAAAATTAGAC
1 TATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACC--AATTTGGC
* *
53412023 AGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAAT
64 AGCACTTATACA-CAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAAT
*
53412088 TTGACGGCATG
128 TTGACAGCATG
53412099 TATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGCAG
1 TATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGCAG
53412164 CACTTATACACAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTG
66 CACTTATACACAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTG
53412229 ACAGCATG
131 ACAGCATG
* *
53412237 TATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGTAGCATATATATACCAATTTGGACA
1 TATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGG-CA
** * * * * * * *
53412302 GCAGATATACAC--AATTTGACAGCACATATATACAAAATTGGACAGCATTTATTCACCAAAATT
65 GCACTTATACACAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA-CAAAATT
53412365 GGGTAGCATA
Statistics
Matches: 243, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
137 36 0.15
138 129 0.53
139 28 0.12
140 48 0.20
141 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (138 bp):
TATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGCAG
CACTTATACACAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTG
ACAGCATG
Found at i:53412289 original size:93 final size:94
Alignment explanation
Indices: 53411956--53412388 Score: 504
Period size: 93 Copynumber: 4.7 Consensus size: 94
53411946 ATATATATAT
* * * * *
53411956 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGCATGTATAT-CCAAAATTA
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGGCAGCATATATATACC-AATTTG
* *
53412020 GACAGCATTTATTCACCAAAATTGGGCAGC
65 GACAGCATTTATACACCAAAATTGGACAGC
* * * * * * * * *
53412050 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGACGGCATGTATATACAAAATTGG
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGGCAGCATATATATACCAATTTGG
* *
53412114 ACAGCATTTATTCACCAAAATTGGGCAGC
66 ACAGCATTTATACACCAAAATTGGACAGC
* * *
53412143 ATATATATACCAATTTGG-CAGCACTTATACA-CAAAATTGGGCAGCATATATATACCAATTTGG
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGGCAGCATATATATACCAATTTGG
* *
53412206 ACAGCACTTATACA-CAAAATTTGACAGC
66 ACAGCATTTATACACCAAAATTGGACAGC
* * * *
53412234 ATGTATACACAAAATTGGACAGCATTTATTCACCAAAATTGGGTAGCATATATATACCAATTTGG
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGGCAGCATATATATACCAATTTGG
** *
53412299 ACAGCAGATATACA-C--AATTTGACAGC
66 ACAGCATTTATACACCAAAATTGGACAGC
* * *
53412325 ACATATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGTAGCATATATATACCAATTTG
1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGGCAGCATATATATACCAATTTG
53412389 AGTAGCATTT
Statistics
Matches: 308, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
91 98 0.32
92 62 0.20
93 118 0.38
94 30 0.10
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (94 bp):
ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGGCAGCATATATATACCAATTTGG
ACAGCATTTATACACCAAAATTGGACAGC
Found at i:53413165 original size:28 final size:28
Alignment explanation
Indices: 53413133--53413286 Score: 227
Period size: 28 Copynumber: 5.5 Consensus size: 28
53413123 TTTAATAATT
** * *
53413133 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
53413161 TCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
53413189 TCGCACACTTAGTGATTTACAATGAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
53413217 TCGCACACTTAGTGATTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
53413245 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
53413273 TCGCACACTTAGTG
1 TCGCACACTTAGTG
53413287 TCGAAAGTCA
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 115 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:53418933 original size:15 final size:16
Alignment explanation
Indices: 53418908--53418937 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53418898 ATAATCAAAC
53418908 TTTATTCATACTTAAA
1 TTTATTCATACTTAAA
53418924 TTTA-TCATACTTAA
1 TTTATTCATACTTAA
53418938 CAAAATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTATTCATACTTAAA
Found at i:53420640 original size:33 final size:33
Alignment explanation
Indices: 53420594--53420747 Score: 115
Period size: 33 Copynumber: 4.6 Consensus size: 33
53420584 CATATAAAGG
**
53420594 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
53420627 GGTTGCTAAGTGCTGATTCCACCGCATCTGCAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-AT-T-C-AT-T---GGT
*
53420669 GGTTGCTAAGTGCT-ATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
** *
53420695 GGTTGCTGTGTGCTGATTCCCTGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
53420728 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
53420748 ACCGTATTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 32
0.69 0.07 0.23
Matches are distributed among these distances:
26 12 0.13
27 8 0.08
31 2 0.02
32 3 0.03
33 37 0.39
34 3 0.03
35 2 0.02
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 2 0.02
41 5 0.05
42 16 0.17
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:53420765 original size:101 final size:103
Alignment explanation
Indices: 53420590--53420854 Score: 435
Period size: 101 Copynumber: 2.6 Consensus size: 103
53420580 ATTGCATATA
53420590 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
53420655 TGCAATGTG-AAGGGGGTTGCTAAGTGCT-ATTCCCCC
66 TGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * *
53420691 AAGGGGTTGCTGTGTGCTGATTCCCTGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
* * *
53420756 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTTCTCC
66 TGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
53420794 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCAGAATCCACCG
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
53420855 ATAACGGTTA
Statistics
Matches: 152, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
101 69 0.45
102 19 0.12
103 64 0.42
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
TGAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:53445790 original size:3 final size:3
Alignment explanation
Indices: 53445775--53445825 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
53445765 ATATGTGTAG
*
53445775 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53445823 TAA
1 TAA
53445826 ATATAACATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53454090 original size:23 final size:22
Alignment explanation
Indices: 53454064--53454114 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
53454054 TAAAATTTAA
*
53454064 AAAATTATAAATTAATAAATGAT
1 AAAATTACAAATTAA-AAATGAT
**
53454087 AAAATTACATTTTAAAAATGAT
1 AAAATTACAAATTAAAAATGAT
53454109 AAAATT
1 AAAATT
53454115 GTGAGCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAATTACAAATTAAAAATGAT
Found at i:53460554 original size:16 final size:16
Alignment explanation
Indices: 53460533--53460564 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53460523 ACCCAAAATT
*
53460533 TTTTTTTTCCTTTTTC
1 TTTTTTCTCCTTTTTC
53460549 TTTTTTCTCCTTTTTC
1 TTTTTTCTCCTTTTTC
53460565 GTATATCAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTCTCCTTTTTC
Found at i:53461804 original size:16 final size:16
Alignment explanation
Indices: 53461773--53461804 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53461763 ACTGATATAC
*
53461773 GAAAAAGGAGAAAAAA
1 GAAAAAGGAAAAAAAA
53461789 GAAAAAGGAAAAAAAA
1 GAAAAAGGAAAAAAAA
53461805 AATTGGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
GAAAAAGGAAAAAAAA
Found at i:53461894 original size:108 final size:109
Alignment explanation
Indices: 53461782--53462014 Score: 282
Period size: 110 Copynumber: 2.1 Consensus size: 109
53461772 CGAAAAAGGA
53461782 GAAAAAAG-AAAAAGGAAAAAAAAAATT-GGTGCTGGCCTG-CAATGGCCGGCACCCAA-CACTA
1 GAAAAAAGTAAAAA--AAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCCGGCA-CCAAGCAC-A
* * *
53461843 A-TAAAAAAATTTACTTTTTT-TCTTATTAAAATCA-AGTATCAGTATAC
62 ATTAAAAAAAATT-CTTTTTTGTCGTATCAAAATCAGA-TATCAGTATAC
* ** *
53461890 GAAAAAAGTAAAAAAAAAATAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAAGTACAATTT
1 GAAAAAAGTAAAAAAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCCGGCACCAAGCACAA-TT
*
53461955 AAAAAAAATTCTTTTTTGTCGTATCAGAATCAGATATCAGTATAC
65 AAAAAAAATTCTTTTTTGTCGTATCAAAATCAGATATCAGTATAC
53462000 GAAAAAAGTAAAAAA
1 GAAAAAAGTAAAAAA
53462015 TATTTTTTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
107 9 0.08
108 26 0.24
109 26 0.24
110 47 0.43
111 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (109 bp):
GAAAAAAGTAAAAAAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCCGGCACCAAGCACAATTA
AAAAAAATTCTTTTTTGTCGTATCAAAATCAGATATCAGTATAC
Found at i:53462002 original size:110 final size:105
Alignment explanation
Indices: 53461809--53462051 Score: 296
Period size: 110 Copynumber: 2.3 Consensus size: 105
53461799 AAAAAAAATT
* * *
53461809 GGTGCTGGCCTG-CAATGGCCGGCACCCAACACTAATAAAAAAATTTACTTTTTTTCTTATTAAA
1 GGTGCTGGCCTGTCAATGGCCGGCA-CCAACACTAATAAAAAAAATTACTTTTTTTCGTATCAAA
53461873 ATCAAGTATCAGTATACGAAAAAAGTAAAAAAAAAATAATTTTG
65 ATCAAGTATCAGTATACGAAAAAAGT--AAAAAAAAT-ATTTTG
*
53461917 GGTGCTGGCCTGTCAATGGCCGGCACCAAGTAC-AATTTAAAAAAAATT-CTTTTTTGTCGTATC
1 GGTGCTGGCCTGTCAATGGCCGGCACCAA-CACTAA--TAAAAAAAATTACTTTTTT-TCGTATC
* * * *
53461980 AGAATC-AGATATCAGTATACGAAAAAAGTAAAAAATATTTTTTT
62 AAAATCAAG-TATCAGTATACGAAAAAAGTAAAAAAAATATTTTG
*
53462024 TGTGCTGGCCTGTCAATGGCCGGCACCA
1 GGTGCTGGCCTGTCAATGGCCGGCACCA
53462052 CCTTGTAATG
Statistics
Matches: 120, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
107 31 0.26
108 26 0.22
109 23 0.19
110 40 0.33
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (105 bp):
GGTGCTGGCCTGTCAATGGCCGGCACCAACACTAATAAAAAAAATTACTTTTTTTCGTATCAAAA
TCAAGTATCAGTATACGAAAAAAGTAAAAAAAATATTTTG
Found at i:53465771 original size:13 final size:13
Alignment explanation
Indices: 53465755--53465785 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
53465745 CTCCTCACAC
53465755 GAATACATTATTT
1 GAATACATTATTT
53465768 GAATACATTATTT
1 GAATACATTATTT
53465781 GAATA
1 GAATA
53465786 ACGAATCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (13 bp):
GAATACATTATTT
Found at i:53475193 original size:12 final size:12
Alignment explanation
Indices: 53475176--53475202 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53475166 AGCGTGTGAG
53475176 ACATGAACTCAA
1 ACATGAACTCAA
53475188 ACATGAACTCAA
1 ACATGAACTCAA
53475200 ACA
1 ACA
53475203 GGTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
ACATGAACTCAA
Found at i:53476572 original size:2 final size:2
Alignment explanation
Indices: 53476565--53476611 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
53476555 CAAGAAGTTA
53476565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53476607 AT AT A
1 AT AT A
53476612 AAACACAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53481247 original size:26 final size:27
Alignment explanation
Indices: 53481217--53481280 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
53481207 GCGAGCCATT
*
53481217 TCGGGAAGCTCACAAAGAGCC-TTTAA
1 TCGGGAAGCTCACAAAGAGCCATATAA
*
53481243 TCGGGAAGCTCACGAAGAGCCATATAA
1 TCGGGAAGCTCACAAAGAGCCATATAA
*
53481270 T-GGGATGCTCA
1 TCGGGAAGCTCA
53481281 TAAGAGCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 29 0.85
27 5 0.15
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (27 bp):
TCGGGAAGCTCACAAAGAGCCATATAA
Found at i:53483847 original size:18 final size:19
Alignment explanation
Indices: 53483824--53483878 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
53483814 GAACAAGAAC
53483824 TTGAGAAAATTGAGAGAG-
1 TTGAGAAAATTGAGAGAGA
*
53483842 TTGAGAGAATT-AGGAGAGA
1 TTGAGAAAATTGA-GAGAGA
53483861 TT-AGAAATAATTGAGAGA
1 TTGAG-AA-AATTGAGAGA
53483879 ATAGGATGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 1 0.03
18 17 0.57
19 3 0.10
20 8 0.27
21 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (19 bp):
TTGAGAAAATTGAGAGAGA
Found at i:53484490 original size:23 final size:23
Alignment explanation
Indices: 53484460--53484504 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
53484450 CCGATTTGCT
*
53484460 CCCTCTGTTTCTTTTCTTTTCTG
1 CCCTCTGTTTATTTTCTTTTCTG
53484483 CCCTCTGTTTATTTTCTTTTCT
1 CCCTCTGTTTATTTTCTTTTCT
53484505 TTTCTTCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.02, C:0.29, G:0.07, T:0.62
Consensus pattern (23 bp):
CCCTCTGTTTATTTTCTTTTCTG
Found at i:53484519 original size:61 final size:61
Alignment explanation
Indices: 53484446--53484608 Score: 236
Period size: 66 Copynumber: 2.6 Consensus size: 61
53484436 CCTTCTAGCC
53484446 TCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
1 TCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
* *
53484507 TCTTCCGATTTGCTCCCTCCGTTTATTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTT
1 TCTGCCGATTTGCTCCCT-C---T-GTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTT
53484572 T
61 T
* * *
53484573 TCTGCCAATTTGCTTCCTTTGTTTCTTTTCTTTTCT
1 TCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCT
53484609 TTTCTACACA
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
61 32 0.36
62 2 0.02
65 1 0.01
66 55 0.61
ACGTcount: A:0.04, C:0.27, G:0.09, T:0.60
Consensus pattern (61 bp):
TCTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTT
Found at i:53484552 original size:28 final size:28
Alignment explanation
Indices: 53484521--53484578 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
53484511 CCGATTTGCT
53484521 CCCTCCGTTTATTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
*
53484549 CCCTCTGTTTATTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
53484577 CC
1 CC
53484579 AATTTGCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.03, C:0.29, G:0.07, T:0.60
Consensus pattern (28 bp):
CCCTCCGTTTATTTTCTTTTCTTTTCTG
Found at i:53484558 original size:66 final size:66
Alignment explanation
Indices: 53484467--53484613 Score: 240
Period size: 66 Copynumber: 2.2 Consensus size: 66
53484457 GCTCCCTCTG
* *
53484467 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTTCCGATTTGCTCCCTCCGTTTA
1 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGCCAATTTGCTCCCTCCGTTTA
53484532 T
66 T
* ** *
53484533 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGCCAATTTGCTTCCTTTGTTTC
1 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGCCAATTTGCTCCCTCCGTTTA
53484598 T
66 T
53484599 TTTCTTTTCTTTTCT
1 TTTCTTTTCTTTTCT
53484614 ACACATTTAC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 75 1.00
ACGTcount: A:0.04, C:0.25, G:0.07, T:0.64
Consensus pattern (66 bp):
TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGCCAATTTGCTCCCTCCGTTTA
T
Found at i:53484631 original size:66 final size:66
Alignment explanation
Indices: 53484467--53484631 Score: 154
Period size: 66 Copynumber: 2.5 Consensus size: 66
53484457 GCTCCCTCTG
* * ** * * *
53484467 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTTCCGATTTGCTCCCTCCGTTTA
1 TTTCTTTTCTTTTCTACCATCTGTCCAGTTTCTTTTCTTTTCTGCCAATTTGCTCCCTCCGTTTA
53484532 T
66 T
* * ** * * ** *
53484533 TTTCTTTTCTTTTCTGCCCTCTGTTTATTTTCTTTTCTTTTCTGCCAATTTGCTTCCTTTGTTTC
1 TTTCTTTTCTTTTCTACCATCTGTCCAGTTTCTTTTCTTTTCTGCCAATTTGCTCCCTCCGTTTA
53484598 T
66 T
53484599 TTTCTTTTCTTTTCTACACAT-T-TACCAGTTTCT
1 TTTCTTTTCTTTTCTAC-CATCTGT-CCAGTTTCT
53484632 GCTGATTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 83 0.97
67 2 0.02
ACGTcount: A:0.07, C:0.25, G:0.07, T:0.61
Consensus pattern (66 bp):
TTTCTTTTCTTTTCTACCATCTGTCCAGTTTCTTTTCTTTTCTGCCAATTTGCTCCCTCCGTTTA
T
Found at i:53487715 original size:15 final size:15
Alignment explanation
Indices: 53487680--53487731 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
53487670 TTAAGAATTT
*
53487680 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53487694 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53487708 TATTTAATAATAAT-
1 TATTTAATTATAATA
53487722 TATGTTAATT
1 TAT-TTAATT
53487732 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53487816 original size:119 final size:120
Alignment explanation
Indices: 53487555--53487966 Score: 711
Period size: 120 Copynumber: 3.4 Consensus size: 120
53487545 AATTATTTTA
* * * * *
53487555 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
* * *
53487619 TATAGTGTAATATATTATGATTTGAGTGAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
53487675 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTTTATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
53487740 ATAGTATCATATATTATGA-TTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
53487794 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
53487859 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
53487914 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
53487967 TAAATATTAT
Statistics
Matches: 278, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
119 116 0.42
120 160 0.58
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:53487822 original size:66 final size:66
Alignment explanation
Indices: 53487752--53487942 Score: 171
Period size: 60 Copynumber: 3.1 Consensus size: 66
53487742 AGTATCATAT
53487752 ATTATGATTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTT
1 ATTATGATTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTT
53487817 A
66 A
* * * * * *
53487818 ATTAT-A---A-TATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-T--AGTATCATA-
1 ATTATGATTGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTAAATTAT-ATAT
53487870 --T-
63 TTTA
*
53487871 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGA-TTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
53487936 TA
65 TA
53487938 ATTAT
1 ATTAT
53487943 AATATATTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 39
0.64 0.09 0.27
Matches are distributed among these distances:
53 5 0.05
54 2 0.02
56 4 0.04
57 3 0.03
58 2 0.02
59 15 0.16
60 25 0.27
61 15 0.16
62 2 0.02
63 3 0.03
64 4 0.04
65 1 0.01
66 6 0.07
67 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (66 bp):
ATTATGATTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTT
A
Found at i:53487834 original size:15 final size:15
Alignment explanation
Indices: 53487799--53487850 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
53487789 TTAAGAATTT
*
53487799 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53487813 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53487827 TATTTAATAATAAT-
1 TATTTAATTATAATA
53487841 TATGTTAATT
1 TAT-TTAATT
53487851 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53487949 original size:16 final size:16
Alignment explanation
Indices: 53487928--53487969 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53487918 TTATTAAATT
*
53487928 ATATATTTTAATTATA
1 ATATATTTTAATAATA
53487944 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
53487959 AT-TATGTTTAA
1 ATATAT-TTTAA
53487970 ATATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:53487954 original size:15 final size:15
Alignment explanation
Indices: 53487919--53487960 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
53487909 TTAAGAATTT
*
53487919 TATTAAATTAT-ATA
1 TATTTAATTATAATA
53487933 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
53487947 TATTTAATAATAAT
1 TATTTAATTATAAT
53487961 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:53488140 original size:39 final size:40
Alignment explanation
Indices: 53488097--53488201 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 40
53488087 TTCCATTATG
53488097 CTATTACACCTCTATTCCATTCAACCAAACACA-AGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACA-ATAGATTTA
* * *
53488136 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACAATAGATTTA
53488181 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
53488202 ACGCCTCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 15 0.27
40 5 0.09
43 1 0.02
44 17 0.31
45 17 0.31
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACAATAGATTTA
Found at i:53488195 original size:45 final size:44
Alignment explanation
Indices: 53488095--53488203 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
53488085 TTTTCCATTA
53488095 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * *
53488134 TACTATTACGCCTCTATTCCATTACATTCAACCAAACA-ATTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACA-AGA-T
53488179 TGCTATTACACCTCTATTCCATTAC
1 TGCTATTACACCTCTATTCCATTAC
53488204 GCCTCTATTC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
43 1 0.02
44 16 0.28
45 24 0.41
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:53488208 original size:16 final size:16
Alignment explanation
Indices: 53488183--53488231 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
53488173 TTGATTTGCT
*
53488183 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
53488199 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
53488215 ATTACGCCTATATTCC
1 ATTACGCCTCTATTCC
53488231 A
1 A
53488232 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53488879 original size:35 final size:37
Alignment explanation
Indices: 53488834--53488906 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
53488824 TAAACATTAA
*
53488834 AAAATTATTTTAAAAATAAAAAAT-AAAAATAT-TTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAATATATTT
*
53488869 AAAAGTATTTTAAAATTAAAAAATAAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAAATATATTT
53488906 A
1 A
53488907 TTATATTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 22 0.65
36 8 0.24
37 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (37 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAAATATATTT
Found at i:53492548 original size:20 final size:21
Alignment explanation
Indices: 53492515--53492553 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
53492505 GGAGAAATAG
53492515 AAAAGAATGAAAAA-AAAATT
1 AAAAGAATGAAAAAGAAAATT
53492535 AAAAGAAT-ATAAAAGAAAA
1 AAAAGAATGA-AAAAGAAAA
53492554 AATTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAAGAATGAAAAAGAAAATT
Found at i:53498931 original size:9 final size:9
Alignment explanation
Indices: 53498913--53498950 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
53498903 TGGCACTGGA
*
53498913 GACGAGGAT
1 GACGACGAT
*
53498922 GACGATGAT
1 GACGACGAT
53498931 GACGACGAT
1 GACGACGAT
53498940 GACGACGAT
1 GACGACGAT
53498949 GA
1 GA
53498951 TGAGGGTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.37, T:0.13
Consensus pattern (9 bp):
GACGACGAT
Found at i:53498978 original size:15 final size:15
Alignment explanation
Indices: 53498958--53498999 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
53498948 TGATGAGGGT
*
53498958 GAGGAAGAGGAAGAA
1 GAGGAAGAAGAAGAA
* *
53498973 GAGGAAGAAGATGAG
1 GAGGAAGAAGAAGAA
53498988 GAGGAAGAAGAA
1 GAGGAAGAAGAA
53499000 CTTCAGCCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.02
Consensus pattern (15 bp):
GAGGAAGAAGAAGAA
Found at i:53504306 original size:30 final size:28
Alignment explanation
Indices: 53504264--53504329 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
53504254 GAATATATAA
53504264 TAAATATATTTTTTAAAAATTTTTTAATTT
1 TAAA-ATATTTTTT-AAAATTTTTTAATTT
** * *
53504294 TAAAATACTTTTTTTTATTTTTTTATTTT
1 TAAAATA-TTTTTTAAAATTTTTTAATTT
53504323 TAAAATA
1 TAAAATA
53504330 AATTTTTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TAAAATATTTTTTAAAATTTTTTAATTT
Found at i:53505760 original size:9 final size:9
Alignment explanation
Indices: 53505746--53505770 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53505736 TATTATAAAA
53505746 TAATTATAT
1 TAATTATAT
53505755 TAATTATAT
1 TAATTATAT
53505764 TAATTAT
1 TAATTAT
53505771 CTATACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATTATAT
Found at i:53522812 original size:46 final size:45
Alignment explanation
Indices: 53522760--53522957 Score: 245
Period size: 46 Copynumber: 4.6 Consensus size: 45
53522750 TTTGAGTACT
* *
53522760 TCTGATCAAGTGACAAAGTGATAAGTGATAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
**
53522806 TCTGATCAAGAAACAAAGTGATAA---GT-G----GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
53522843 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
53522889 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
53522934 TCTGATC-AGGGAC-AAGTGATAAGT
1 TCTGATCAAGTGACAAAGTGATAAGT
53522958 AATCATACGT
Statistics
Matches: 134, Mismatches: 9, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
37 31 0.23
40 2 0.01
41 1 0.01
42 1 0.01
43 12 0.09
44 5 0.04
45 20 0.15
46 62 0.46
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:53522840 original size:37 final size:37
Alignment explanation
Indices: 53522796--53522870 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
53522786 GATAGTTTTA
53522796 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
** *
53522833 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
53522870 G
1 G
53522871 TAGCCTTAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:53522905 original size:83 final size:83
Alignment explanation
Indices: 53522760--53522916 Score: 260
Period size: 83 Copynumber: 1.9 Consensus size: 83
53522750 TTTGAGTACT
**
53522760 TCTGATCAAGTGACAAAGTGATAAGTGATAGTTTTAGCTACACTTATCTGATCAAGAAACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTATCTGATCAAGAAACAAAGT
53522825 GATAAGTGGCTACACTTA
66 GATAAGTGGCTACACTTA
* * **
53522843 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTATCTGATCAAGAAACAAAGT
53522908 GATAAGTGG
66 GATAAGTGG
53522917 TAGCCTAGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (83 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTTAGCTACACTTATCTGATCAAGAAACAAAGT
GATAAGTGGCTACACTTA
Found at i:53529980 original size:9 final size:9
Alignment explanation
Indices: 53529966--53529994 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
53529956 CCTATATTGG
53529966 TCATTCTCA
1 TCATTCTCA
53529975 TCATTCTCA
1 TCATTCTCA
53529984 TCATTCTCA
1 TCATTCTCA
53529993 TC
1 TC
53529995 CCGCTACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (9 bp):
TCATTCTCA
Found at i:53531329 original size:30 final size:30
Alignment explanation
Indices: 53531290--53531362 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
53531280 ACTTAAAGGG
53531290 TTGTAATTTTATTGATTTTTTTA-AAAAAAAA
1 TTGT-ATTTTATT-ATTTTTTTAGAAAAAAAA
* * *
53531321 TTGTATTTTCTTTTTTTTTTAGTAAAAAAA
1 TTGTATTTTATTATTTTTTTAGAAAAAAAA
*
53531351 TAGTATTTTATT
1 TTGTATTTTATT
53531363 TTAAAAACCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 8 0.22
30 24 0.67
31 4 0.11
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (30 bp):
TTGTATTTTATTATTTTTTTAGAAAAAAAA
Found at i:53535499 original size:9 final size:9
Alignment explanation
Indices: 53535487--53535550 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
53535477 TTTAATTAAT
53535487 TTTTAAAAA
1 TTTTAAAAA
53535496 TTTTAAAAA
1 TTTTAAAAA
**
53535505 TTCAAAAAA
1 TTTTAAAAA
*
53535514 TTATAAAACCA
1 TTTTAAAA--A
*
53535525 TTTTTAAAA
1 TTTTAAAAA
53535534 -TTTAAAAA
1 TTTTAAAAA
53535542 TTGTTAAAA
1 TT-TTAAAA
53535551 TTATTAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.16
9 24 0.55
10 6 0.14
11 7 0.16
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:53544778 original size:58 final size:58
Alignment explanation
Indices: 53544655--53544811 Score: 251
Period size: 59 Copynumber: 2.7 Consensus size: 58
53544645 AAAGTTGCTA
*
53544655 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAACTACCAGCATGTCAAGGATTAAATT
1 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAAGTACCAGCATGTCAAGGATTAAATT
* * * *
53544713 TGTTTTGGCACTAAAAGTAAACCACAAGCCACAAGAACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-CAACCGCAAGCCACAAGTACCAGCATGTCAAGGATTAAATT
*
53544772 TGTTTGGGCACTAAAAGCAACCGCAAGCCACAAGTACCAG
1 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAAGTACCAG
53544812 TCCAACCCCT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 37 0.42
59 52 0.58
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGCAACCGCAAGCCACAAGTACCAGCATGTCAAGGATTAAATT
Found at i:53547052 original size:15 final size:15
Alignment explanation
Indices: 53547032--53547061 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53547022 GGCAATCACT
53547032 CATTCTTAAAACCAA
1 CATTCTTAAAACCAA
*
53547047 CATTCTTAATACCAA
1 CATTCTTAAAACCAA
53547062 AGAGTCAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (15 bp):
CATTCTTAAAACCAA
Found at i:53547217 original size:20 final size:20
Alignment explanation
Indices: 53547192--53547231 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53547182 ATCAGTGTAA
53547192 ACCCACGACAGTTATTGGTT
1 ACCCACGACAGTTATTGGTT
53547212 ACCCACGACAGTTATTGGTT
1 ACCCACGACAGTTATTGGTT
53547232 GGGCTGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (20 bp):
ACCCACGACAGTTATTGGTT
Found at i:53549222 original size:3 final size:3
Alignment explanation
Indices: 53549214--53549297 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
53549204 AGAGAAATAG
53549214 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
53549262 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
53549298 TGGAAGGAGC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:53558280 original size:4 final size:4
Alignment explanation
Indices: 53558271--53558301 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
53558261 GTATTTTGTT
*
53558271 TTTA TTTA TTTG TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
53558302 TTGTCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:53558691 original size:2 final size:2
Alignment explanation
Indices: 53558684--53558708 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53558674 TGGATTCGGG
53558684 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
53558709 ACTATAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53565841 original size:15 final size:15
Alignment explanation
Indices: 53565821--53565850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53565811 TTAATTTATA
*
53565821 TATTTAAATTAATAT
1 TATTTAAAATAATAT
53565836 TATTTAAAATAATAT
1 TATTTAAAATAATAT
53565851 AACAAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTAAAATAATAT
Found at i:53567316 original size:15 final size:15
Alignment explanation
Indices: 53567292--53567325 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53567282 CAAAATCTTA
53567292 AAATTCTATAAAACT
1 AAATTCTATAAAACT
53567307 CAAATT-TATAAAACT
1 -AAATTCTATAAAACT
53567322 AAAT
1 AAAT
53567326 ACAATATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 9 0.50
16 5 0.28
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATTCTATAAAACT
Found at i:53567900 original size:68 final size:68
Alignment explanation
Indices: 53567820--53567952 Score: 248
Period size: 68 Copynumber: 2.0 Consensus size: 68
53567810 ACTTTTCACA
*
53567820 GATCCTTATATGATTTACATATCTTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
1 GATCCTTATATGATCTACATATCTTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
53567885 ACG
66 ACG
*
53567888 GATCCTTATATGATCTACATATCTTATGTATGAGATATGAAATCACAAAAAGATATAAGCTCACT
1 GATCCTTATATGATCTACATATCTTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
53567953 TCATGAAGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (68 bp):
GATCCTTATATGATCTACATATCTTATATATGAGATATGAAATCACAAAAAGATATAAGCTCACT
ACG
Found at i:53569832 original size:14 final size:14
Alignment explanation
Indices: 53569813--53569846 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53569803 CAACAATATA
53569813 ATTTTAGTAAATGT
1 ATTTTAGTAAATGT
*
53569827 ATTTTAGTAACTGT
1 ATTTTAGTAAATGT
53569841 ACTTTT
1 A-TTTT
53569847 TAAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (14 bp):
ATTTTAGTAAATGT
Found at i:53574047 original size:21 final size:21
Alignment explanation
Indices: 53574021--53574079 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
53574011 TTTTTGCCCT
53574021 GAACCTTGAACTTCAAACCCC
1 GAACCTTGAACTTCAAACCCC
* * *
53574042 GAACCTTAAACTTGAAACCCT
1 GAACCTTGAACTTCAAACCCC
*
53574063 AAACCTTGAAC-TCAAAC
1 GAACCTTGAACTTCAAAC
53574080 TCCAAACTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.39, C:0.32, G:0.08, T:0.20
Consensus pattern (21 bp):
GAACCTTGAACTTCAAACCCC
Found at i:53589722 original size:2 final size:2
Alignment explanation
Indices: 53589715--53589759 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
53589705 TTGATATCTA
53589715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53589757 AT A
1 AT A
53589760 CTACTTACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53591063 original size:2 final size:2
Alignment explanation
Indices: 53591056--53591098 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53591046 AAATATCCTG
53591056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53591098 A
1 A
53591099 GTTAGAACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53595443 original size:19 final size:19
Alignment explanation
Indices: 53595415--53595451 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53595405 TGATCCAATC
53595415 AAAAAATT-AATAAAAAAT
1 AAAAAATTAAATAAAAAAT
53595433 AAAAAATTTAAATAAAAAA
1 AAAAAA-TTAAATAAAAAA
53595452 AACTTGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAAATTAAATAAAAAAT
Found at i:53600375 original size:25 final size:25
Alignment explanation
Indices: 53600347--53600460 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 25
53600337 CTTATGAGTA
*
53600347 TCCCGATACTTGGCTCTCACGAGCT
1 TCCCGATAATTGGCTCTCACGAGCT
*
53600372 TCCC-ATTATTTGGCTCTC-CGGAGCT
1 TCCCGA-TAATTGGCTCTCAC-GAGCT
* * * *
53600397 TCTCGATAATAGGCTCTTATGAGCT
1 TCCCGATAATTGGCTCTCACGAGCT
* * * *
53600422 TCTCGATTAA-AGGTTCTC-CGAACT
1 TCCCGA-TAATTGGCTCTCACGAGCT
53600446 GTCCCGATAATTGGC
1 -TCCCGATAATTGGC
53600461 ATGCAATAGC
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
24 9 0.13
25 56 0.81
26 4 0.06
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.32
Consensus pattern (25 bp):
TCCCGATAATTGGCTCTCACGAGCT
Found at i:53600485 original size:25 final size:25
Alignment explanation
Indices: 53600468--53600542 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
53600458 GGCATGCAAT
53600468 AGCTTCCCATTACATGGCTCACATG
1 AGCTTCCCATTACATGGCTCACATG
* * * *
53600493 AGCTTCCCGTTATATGGCTCAAAAG
1 AGCTTCCCATTACATGGCTCACATG
*
53600518 AGCTTCCCGATTACAT-GCTCGCATG
1 AGCTTCCC-ATTACATGGCTCACATG
53600543 GGCATACCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 35 0.88
26 5 0.12
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (25 bp):
AGCTTCCCATTACATGGCTCACATG
Found at i:53602229 original size:25 final size:24
Alignment explanation
Indices: 53602126--53602233 Score: 74
Period size: 25 Copynumber: 4.4 Consensus size: 24
53602116 GAACATAAAT
* *
53602126 GGGAAGCTCATAAGAGGCCATAATC
1 GGGAAGCTCATAAGA-ACCATTATC
* * * * *
53602151 GAGAAGTTCA-AGCGAGCCAATATC
1 GGGAAGCTCATA-AGAACCATTATC
* * *
53602175 GGGAAGCTCTTGAGAACCATTAAAC
1 GGGAAGCTCATAAGAACCATT-ATC
*
53602200 AGGAAGCTCATAAGAACCTATTATC
1 GGGAAGCTCATAAGAACC-ATTATC
53602225 GGGAAGCTC
1 GGGAAGCTC
53602234 CAGAGAGCCA
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
24 21 0.34
25 37 0.61
26 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (24 bp):
GGGAAGCTCATAAGAACCATTATC
Found at i:53602382 original size:25 final size:24
Alignment explanation
Indices: 53602354--53602412 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
53602344 AACCATATAA
*
53602354 CGGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAG-CAAATAT
** *
53602379 CGGGATTCTCATGAGAGCTAATAT
1 CGGGAAGCTCATGAGAGCAAATAT
*
53602403 CGGGACGCTC
1 CGGGAAGCTC
53602413 TTTTGAGCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (24 bp):
CGGGAAGCTCATGAGAGCAAATAT
Found at i:53602555 original size:13 final size:13
Alignment explanation
Indices: 53602537--53602562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53602527 ATATGTGATC
53602537 GATAATTATACAT
1 GATAATTATACAT
53602550 GATAATTATACAT
1 GATAATTATACAT
53602563 TTCAAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
GATAATTATACAT
Found at i:53610459 original size:16 final size:16
Alignment explanation
Indices: 53610438--53610469 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53610428 TGAAAAAGTA
53610438 AATTAAAATTCAACTG
1 AATTAAAATTCAACTG
53610454 AATTAAAATTCAACTG
1 AATTAAAATTCAACTG
53610470 GTGAATGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
AATTAAAATTCAACTG
Found at i:53627225 original size:43 final size:42
Alignment explanation
Indices: 53627159--53627329 Score: 172
Period size: 43 Copynumber: 4.0 Consensus size: 42
53627149 ATAGGATTTC
53627159 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
53627202 CGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGTCAT
1 CGA-TTGTGATTACGTGTAAGACCACGTCTGGGACGTTGG-CAT
* * *
53627246 CGTATT-TGATT-CGTTTAATACTC-TGTCTGGGACAG-TGGCAT
1 CG-ATTGTGATTACGTGTAAGAC-CACGTCTGGGAC-GTTGGCAT
*
53627287 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGAT-TGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
53627330 TGTACGAGTC
Statistics
Matches: 107, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
40 2 0.02
41 6 0.06
42 28 0.26
43 59 0.55
44 11 0.10
45 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (42 bp):
CGATTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:53629702 original size:25 final size:25
Alignment explanation
Indices: 53629641--53629752 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 25
53629631 TCACATGTAT
*
53629641 GCTCCTACGAGC-G-ATAATCGGTAA
1 GCTCATACGAGCTGAAT-ATCGGTAA
* * *
53629665 ACTCCTCCGAGCTGAATATCGGTAA
1 GCTCATACGAGCTGAATATCGGTAA
* * *
53629690 GCTCATACAAGCTGAGTATCGATAA
1 GCTCATACGAGCTGAATATCGGTAA
* *
53629715 GCTC-TCACGAGCT-ACAAATTGGTAA
1 GCTCAT-ACGAGCTGA-ATATCGGTAA
53629740 GCTCATACGAGCT
1 GCTCATACGAGCT
53629753 ACGGTGAGTC
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
24 12 0.17
25 55 0.79
26 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAATATCGGTAA
Found at i:53635687 original size:6 final size:6
Alignment explanation
Indices: 53635676--53635704 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53635666 TTATGTTTTA
53635676 TTATTT TTATTT TTATTT TTATTT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTATT
53635705 ATATATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:53636462 original size:2 final size:2
Alignment explanation
Indices: 53636455--53636485 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53636445 ATGCCTTTGA
*
53636455 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53636486 AATTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53637255 original size:4 final size:4
Alignment explanation
Indices: 53637246--53637276 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
53637236 ATATGTTTTG
53637246 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
53637277 TTTTGGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:53637607 original size:2 final size:2
Alignment explanation
Indices: 53637591--53637632 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
53637581 GGATTCAAGG
* *
53637591 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53637633 CATACGACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Done.