Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 134 of 410
Found at i:40497352 original size:40 final size:40
Alignment explanation
Indices: 40497259--40497409 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
40497249 AAATTGAATG
* * * * *
40497259 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
40497298 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
40497338 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* *
40497378 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
40497410 AAATCGTGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
39 32 0.33
40 62 0.65
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:40497424 original size:40 final size:38
Alignment explanation
Indices: 40497255--40497426 Score: 161
Period size: 40 Copynumber: 4.4 Consensus size: 38
40497245 TGAGAAATTG
* *
40497255 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-A
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * *
40497294 AAT-TATATCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
40497331 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
40497371 AGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 A-ATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
40497411 AATCGTGATATCCGGG
1 AAT-GT-ATATCCGGG
40497427 TAAAGTCCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
36 2 0.02
37 4 0.04
38 2 0.02
39 26 0.24
40 74 0.68
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:40499301 original size:20 final size:20
Alignment explanation
Indices: 40499276--40499320 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
40499266 CGAAAAATAA
*
40499276 TTTCTGAAAAATTACTTACT
1 TTTCTGAAAAATGACTTACT
*
40499296 TTTCTGGAAAATGACTTACT
1 TTTCTGAAAAATGACTTACT
40499316 TTTCT
1 TTTCT
40499321 AGTGTTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTCTGAAAAATGACTTACT
Found at i:40503112 original size:53 final size:54
Alignment explanation
Indices: 40503023--40503235 Score: 245
Period size: 55 Copynumber: 3.9 Consensus size: 54
40503013 TATGTGGTAT
* * *
40503023 CCTTTTGAAACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
* * *
40503077 CCTTATG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTG
* * * * * *
40503130 CCTTATAGTAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTA
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
40503185 CCTTA-GAAACCTTACCAATTGCCATGCCTT-AGCATGGTCTTACATGGTATC
1 CCTTATGAAA-CTTACCAA-TGCCATGCCTTGA-CATGGTCTTACATGGTATC
40503236 ATTAAACCCT
Statistics
Matches: 133, Mismatches: 19, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 47 0.35
54 15 0.11
55 67 0.50
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.35
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTG
Found at i:40503183 original size:108 final size:110
Alignment explanation
Indices: 40503031--40503231 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
40503021 ATCCTTTTGA
* * *
40503031 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTACCTTA-GAAACCTCACCAA
*
40503094 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
40503139 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTACCTTAGAAACCTCACCAAT
40503204 TGCCATGCCTTAGCATGGTCTTACATGG
66 TGCCATGCCTTAGCATGGTCTTACATGG
40503232 TATCATTAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.58
109 7 0.08
110 27 0.33
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTACCTTAGAAACCTCACCAAT
TGCCATGCCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:40508482 original size:16 final size:16
Alignment explanation
Indices: 40508461--40508491 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40508451 GACAACATGA
*
40508461 TTGAATATGATTAGTT
1 TTGAATATGAATAGTT
40508477 TTGAATATGAATAGT
1 TTGAATATGAATAGT
40508492 AAATGACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (16 bp):
TTGAATATGAATAGTT
Found at i:40511794 original size:21 final size:22
Alignment explanation
Indices: 40511768--40511822 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
40511758 TCACACTCAA
40511768 ATGCATCCACAACCAAG-CCAG
1 ATGCATCCACAACCAAGACCAG
* *
40511789 ATGCATCCAC-ACCAGGATCAG
1 ATGCATCCACAACCAAGACCAG
*
40511810 ATGCAACCACAAC
1 ATGCATCCACAAC
40511823 ACTCTTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.17
21 22 0.76
22 2 0.07
ACGTcount: A:0.38, C:0.36, G:0.15, T:0.11
Consensus pattern (22 bp):
ATGCATCCACAACCAAGACCAG
Found at i:40521640 original size:52 final size:47
Alignment explanation
Indices: 40521516--40521640 Score: 126
Period size: 47 Copynumber: 2.6 Consensus size: 47
40521506 TCAAGGTAGG
* * *
40521516 AAATAAAGTCATGCATTATGTAACTCTCATGTTAAATTTTGAATCAT
1 AAATTAAGTCATGCATTATGTAACTCTCATGTTAAAGTTTGAATAAT
* * *
40521563 AAATTATGACATGCTTTATGTAACTCTCATGTTAGTTAAAGTTT-ACATAATT
1 AAATTAAGTCATGCATTATGTAACTCTCA---T-GTTAAAGTTTGA-ATAA-T
*
40521615 AAATTAAGTCATGCATTAAGTAACTC
1 AAATTAAGTCATGCATTATGTAACTC
40521641 ATCTGTTCAT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
47 25 0.40
50 2 0.03
51 12 0.19
52 23 0.37
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (47 bp):
AAATTAAGTCATGCATTATGTAACTCTCATGTTAAAGTTTGAATAAT
Found at i:40523761 original size:21 final size:19
Alignment explanation
Indices: 40523697--40523751 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 19
40523687 TAATGAGAGA
*
40523697 AAATGAGCGAAAAATAAAAG
1 AAATGAGAGAAAAA-AAAAG
40523717 AAATTGAGAGAAGAAAAAAAG
1 AAA-TGAGAGAA-AAAAAAAG
40523738 AAATGAGAGAAAAA
1 AAATGAGAGAAAAA
40523752 GAAATTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 15 0.47
22 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.22, T:0.09
Consensus pattern (19 bp):
AAATGAGAGAAAAAAAAAG
Found at i:40523764 original size:16 final size:16
Alignment explanation
Indices: 40523732--40523790 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
40523722 GAGAGAAGAA
*
40523732 AAAAAGAAA-TGAGAG
1 AAAAAGAAATTGAAAG
40523747 AAAAAGAAATTGAAAG
1 AAAAAGAAATTGAAAG
*
40523763 AAAAAGAGAGCTTGAAAG
1 AAAAAGA-A-ATTGAAAG
40523781 AAAAGAGAAA
1 AAAA-AGAAA
40523791 GAAAAAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.24
16 12 0.32
17 1 0.03
18 12 0.32
19 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.08
Consensus pattern (16 bp):
AAAAAGAAATTGAAAG
Found at i:40525800 original size:50 final size:52
Alignment explanation
Indices: 40525735--40525833 Score: 157
Period size: 50 Copynumber: 1.9 Consensus size: 52
40525725 TGAATAAAGT
* *
40525735 CATGCATTATTTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATTATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATAATTAAATTATGA
*
40525785 CATGCTTTATGTAACTCTCATGTTAGTTAAAGTTTGCATAATTAAATTA
1 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATAATTAAATTA
40525834 AGTCATGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 26 0.59
51 11 0.25
52 7 0.16
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (52 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTGCATAATTAAATTATGA
Found at i:40532871 original size:12 final size:12
Alignment explanation
Indices: 40532854--40532878 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40532844 CTTACTTACT
40532854 TTTCTTCCTTAG
1 TTTCTTCCTTAG
40532866 TTTCTTCCTTAG
1 TTTCTTCCTTAG
40532878 T
1 T
40532879 AAACATACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTCTTCCTTAG
Found at i:40540670 original size:47 final size:47
Alignment explanation
Indices: 40540619--40540812 Score: 262
Period size: 47 Copynumber: 4.1 Consensus size: 47
40540609 TTAGGATATT
** * *
40540619 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40540666 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40540713 ATGTGATGAATGTGAGCATGCATATGTGTCATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
40540760 ATATGGTGAATATGAACATGCATATACGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40540807 ATGTGA
1 ATGTGA
40540813 AATATGTATG
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 128 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40540719 original size:22 final size:22
Alignment explanation
Indices: 40540648--40540719 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
40540638 GTATATATGA
40540648 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
40540670 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
40540695 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
40540717 GAT
1 GAT
40540720 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:40540937 original size:98 final size:98
Alignment explanation
Indices: 40540777--40541064 Score: 510
Period size: 98 Copynumber: 2.9 Consensus size: 98
40540767 GAATATGAAC
*
40540777 ATGCATATACGTGGTAAAGCCGAATGG-CTAATGTG-AA-ATATGTATGAGATATGTATATGTGG
1 ATGCATAT--GTGGTAAAGCCGAATGGTC-AATGTGAAATATATATATGAGATATGTATATGTGG
40540839 TAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
63 TAAAGCCGAATGGCTAATGTGAAATATGTATGAGAT
40540875 ATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAA
1 ATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAA
40540940 AGCCGAATGGCTAATGTGAAATATGTATGAGAT
66 AGCCGAATGGCTAATGTGAAATATGTATGAGAT
40540973 ATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAA
1 ATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAA
*
40541038 AGCCGAATGGCTAGTGTGAAATATGTA
66 AGCCGAATGGCTAATGTGAAATATGTA
40541065 GGCGATGTGC
Statistics
Matches: 185, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
96 23 0.12
97 3 0.02
98 159 0.86
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (98 bp):
ATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATATGTATGAGAT
Found at i:40541080 original size:50 final size:48
Alignment explanation
Indices: 40540782--40541064 Score: 444
Period size: 48 Copynumber: 5.8 Consensus size: 48
40540772 TGAACATGCA
*
40540782 TATACGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
40540830 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
40540878 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
40540928 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
40540976 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
*
40541026 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
40541065 GGCGATGTGC
Statistics
Matches: 217, Mismatches: 10, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
47 2 0.01
48 122 0.56
49 8 0.04
50 83 0.38
51 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:40541292 original size:37 final size:37
Alignment explanation
Indices: 40541200--40541318 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
40541190 ACATGAAACT
*
40541200 TGGAGATTATGTCCGGGTAAGACCCGACGACTACGTG
1 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
*
40541237 TGTG-GAGTATGTCCGGGTAAGACCCGATGACTACGTG
1 TG-GAGATTATGTCCGGGTAAGACCCGATGACTACGTG
* ** * *
40541274 TGGAGATTTTGTATGGGTAAGACCCGATAACTTCGTG
1 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
40541311 TGGAGATT
1 TGGAGATT
40541319 TCGTCTGAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
36 1 0.01
37 70 0.97
38 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.27
Consensus pattern (37 bp):
TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
Found at i:40542641 original size:40 final size:40
Alignment explanation
Indices: 40542586--40543055 Score: 755
Period size: 40 Copynumber: 11.8 Consensus size: 40
40542576 GAGAATTGAG
40542586 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
40542626 AGTGATATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
40542665 AGTGATGTATCCGGACTAAGTCCCGAAGAGCACTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40542705 AGTGATATATTCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
40542745 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
40542785 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
40542825 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
40542865 AGTGATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
40542905 AGTGATGTATCCAGACTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
40542945 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
40542985 AGTGATGTATCCGGGCTAAGTTCCGAA-AGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
40543024 AGTGATATATCCGTGCTAAATCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
40543056 ATCATGCTGG
Statistics
Matches: 398, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
39 72 0.18
40 326 0.82
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:40547016 original size:47 final size:47
Alignment explanation
Indices: 40546960--40547153 Score: 244
Period size: 47 Copynumber: 4.1 Consensus size: 47
40546950 TTAGGATTTT
** * *
40546960 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40547007 ATGTCATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40547054 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * ** * * *
40547101 ATGTGGTGAATATGAACATGCATATACATGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40547148 ATGTGA
1 ATGTGA
40547154 AATATGTATA
Statistics
Matches: 125, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 125 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40547281 original size:98 final size:96
Alignment explanation
Indices: 40547129--40547307 Score: 306
Period size: 98 Copynumber: 1.8 Consensus size: 96
40547119 TGCATATACA
*
40547129 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATAAGATATGTATATGTGGTAAAGCCGAATGGC
1 TGGTAAAGCCGAATGGCTAATGTGAAATATATATAAGATATGTATATGTGGTAAAGCCGAATGGC
40547194 TAATGTGAAATATGTATGAGATATGCATATG
66 TAATGTGAAATATGTATGAGATATGCATATG
40547225 TGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAAT
1 TGGTAAAGCCGAATGGCT-AATGTGAAATATATATA--AGATATGTATATGTGGTAAAGCCGAAT
*
40547289 GGCTAGTGTGAAATATGTA
63 GGCTAATGTGAAATATGTA
40547308 GGCGATGTGT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
95 1 0.01
96 32 0.41
98 45 0.58
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (96 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATATATAAGATATGTATATGTGGTAAAGCCGAATGGC
TAATGTGAAATATGTATGAGATATGCATATG
Found at i:40547323 original size:50 final size:48
Alignment explanation
Indices: 40547129--40547307 Score: 288
Period size: 48 Copynumber: 3.7 Consensus size: 48
40547119 TGCATATACA
40547129 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATAAGATATGTATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATAAGATATGTATATG
* *
40547177 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATG
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATAAGATATGTATATG
*
40547225 TGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATGTATATG
1 TGGTAAAGCCGAATGGCT-AATGTGAAATATGTATA--AGATATGTATATG
*
40547275 TGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TGGTAAAGCCGAATGGCTAATGTGAAATATGTA
40547308 GGCGATGTGT
Statistics
Matches: 120, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
47 1 0.01
48 77 0.64
50 41 0.34
51 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (48 bp):
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATAAGATATGTATATG
Found at i:40547562 original size:37 final size:37
Alignment explanation
Indices: 40547443--40547561 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
40547433 ACATGAAACT
*
40547443 TGGAGATTATGTCTGGGTAAGACCCGATGACTACGTG
1 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
* * *
40547480 TGGGGAGTATGTCCGGGTAAGACCCGATGACTACATG
1 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
* * * *
40547517 TGGAGATTTTGTCCGGGTAAGACCCGATAATTTCGTG
1 TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
40547554 TGGAGATT
1 TGGAGATT
40547562 TCGTCTGAGC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.28
Consensus pattern (37 bp):
TGGAGATTATGTCCGGGTAAGACCCGATGACTACGTG
Found at i:40552396 original size:40 final size:40
Alignment explanation
Indices: 40552351--40552516 Score: 167
Period size: 39 Copynumber: 4.2 Consensus size: 40
40552341 CGGAATATAA
40552351 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40552391 CCGGATAGAATAACTCGCACGAATG-CTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40552430 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
40552470 CCGGATATAATTTCCAGCA-TAATTTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40552509 CCGGATAT
1 CCGGATAT
40552517 CATTCAATTT
Statistics
Matches: 102, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
39 55 0.54
40 47 0.46
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40552499 original size:79 final size:79
Alignment explanation
Indices: 40552367--40552516 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 79
40552357 ATAATCACGT
* *
40552367 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCTTCGGGTCTTAGCCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCTTCGGGGCTTAGCCC
40552432 GGATATAGCCACTA
66 GGATATAGCCACTA
* * ** * *
40552446 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTTCTTCGGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCTTCGGGGCTTAGC
40552509 CCGGATAT
64 CCGGATAT
40552517 CATTCAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 3 0.05
79 58 0.95
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCTTCGGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40560509 original size:79 final size:81
Alignment explanation
Indices: 40560408--40560592 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
40560398 ACGACTCGCT
** * *
40560408 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTT-GGGATCCTAACCC
* *
40560471 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* * * **
40560488 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTTGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTGGGATCCTAACCCGG
*
40560552 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
40560568 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40560593 CATCATTCGA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 52 0.58
80 34 0.38
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTGGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:40560592 original size:40 final size:40
Alignment explanation
Indices: 40560401--40560592 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
40560391 GGATATAACG
* ** * *
40560401 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
40560441 ACTCGCACAAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
40560481 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* * * * *
40560520 ACTCGCACGAATGCCTT-TGGATCCTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
40560560 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
40560593 CATCATTCGA
Statistics
Matches: 124, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
38 2 0.02
39 30 0.24
40 82 0.66
41 10 0.08
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:40567628 original size:6 final size:6
Alignment explanation
Indices: 40567610--40567691 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
40567600 AAGAAACATT
*
40567610 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
40567659 ATCAGT ATCAGGTA GT-AGA ATCAAA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
40567692 ATGAATGCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.07
6 48 0.80
7 6 0.10
8 2 0.03
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:40567631 original size:18 final size:18
Alignment explanation
Indices: 40567610--40567691 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 18
40567600 AAGAAACATT
40567610 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
40567628 ATCAGAATCAGAATCAG-
1 ATCAGAATCAGAATCAGA
* *
40567645 GTGACAGAATCAGAATCAGT
1 AT--CAGAATCAGAATCAGA
* *
40567665 ATCAGGTAGT-AGAATCAAA
1 ATCA-G-AATCAGAATCAGA
40567684 ATCAGAAT
1 ATCAGAAT
40567692 ATGAATGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
17 3 0.06
18 18 0.35
19 28 0.54
20 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:40567655 original size:25 final size:25
Alignment explanation
Indices: 40567624--40567691 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
40567614 GAACTAGAAT
40567624 CAGAATCAGAATCAGAATCAGGT-G
1 CAGAATCAGAATCAGAATCAGGTAG
*
40567648 ACAGAATCAGAATCAGTATCAGGTAG
1 -CAGAATCAGAATCAGAATCAGGTAG
* *
40567674 TAGAATCAAAATCAGAAT
1 CAGAATCAGAATCAGAAT
40567692 ATGAATGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAG
Found at i:40567846 original size:27 final size:26
Alignment explanation
Indices: 40567809--40567909 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
40567799 AGCATGGCTG
*
40567809 CCAGAACAGATATTGT-GCTAGAGTCA
1 CCAGAACAGATATTGTGGC-AGAGACA
*
40567835 CCAGATACAGATATTTTGGCAGAGACA
1 CCAGA-ACAGATATTGTGGCAGAGACA
* * *
40567862 CTAGAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCAGAGACA
*
40567889 CCAGAATCAGATAATGTGGCA
1 CCAGAA-CAGATATTGTGGCA
40567910 AAGCCACTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
26 12 0.19
27 43 0.68
28 8 0.13
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGACA
Found at i:40568528 original size:27 final size:27
Alignment explanation
Indices: 40568480--40568747 Score: 313
Period size: 27 Copynumber: 10.3 Consensus size: 27
40568470 GGGGCAAAAT
* * *
40568480 GGTAATTTTACCCCAC-GAGGGTATCTC
1 GGTAATTCTACCCTACAG-GGGTATTTC
*
40568507 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40568534 GATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
40568561 AGTAATTCTACCTTAGAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40568588 GATAATTCTACCCTACA--GG------
1 GGTAATTCTACCCTACAGGGGTATTTC
40568607 GGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40568633 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
40568660 AATAATTCTATCCTACAGGGGTGTTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40568687 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
40568714 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
40568741 GGTAATT
1 GGTAATT
40568748 TCACAAATCA
Statistics
Matches: 208, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.08
20 2 0.01
25 2 0.01
26 17 0.08
27 170 0.82
28 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:40568614 original size:19 final size:19
Alignment explanation
Indices: 40568590--40568626 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40568580 GGTATTTCGA
40568590 TAATTCTACCCTACAGGGG
1 TAATTCTACCCTACAGGGG
40568609 TAATTCTACCCTACAGGG
1 TAATTCTACCCTACAGGG
40568627 TATTTCGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (19 bp):
TAATTCTACCCTACAGGGG
Found at i:40568658 original size:126 final size:127
Alignment explanation
Indices: 40568480--40568736 Score: 385
Period size: 126 Copynumber: 2.0 Consensus size: 127
40568470 GGGGCAAAAT
* * * *
40568480 GGTAATTTTACCCCACGAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGATAATTCTA-
1 GGTAATTCTACCCCACGAGGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTAT
* *
40568544 CCTTACAGGGGTATTTC-AGTAATTCTACCTTAGAGGGGTATTTCGATAATTCTACCCTACAGG
66 CC-TACAGGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGG
* *
40568607 GGTAATTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTAT
1 GGTAATTCTACCCCACGAGGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTAT
* *
40568671 CCTACAGGGGTGTTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGG
66 CCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGG
40568733 GGTA
1 GGTA
40568737 TTTCGGTAAT
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
126 101 0.86
127 17 0.14
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (127 bp):
GGTAATTCTACCCCACGAGGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTAT
CCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGG
Found at i:40568680 original size:99 final size:100
Alignment explanation
Indices: 40568507--40568709 Score: 320
Period size: 99 Copynumber: 2.0 Consensus size: 100
40568497 AGGGTATCTC
* * * *
40568507 GGTAATTCTACCCTATAGGGGTATTTCGATAATTCTACCTTACAGGGGTATTTCAGTAATTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAAGGGTATTTCAATAATTCTAC
*
40568572 CTTAGAGGGGTATTTCGATAATTCTACCCTACAGG
66 CTTACAGGGGTATTTCGATAATTCTACCCTACAGG
*
40568607 GGTAATTCTACCCTACA-GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTAT
1 GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAAGGGTATTTCAATAATTCTA-
*
40568671 CC-TACAGGGGTGTTTCGATAATTCTACCCTACAGG
65 CCTTACAGGGGTATTTCGATAATTCTACCCTACAGG
40568706 GGTA
1 GGTA
40568710 TTTCGGTAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 77 0.81
100 18 0.19
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (100 bp):
GGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAAGGGTATTTCAATAATTCTAC
CTTACAGGGGTATTTCGATAATTCTACCCTACAGG
Found at i:40568774 original size:81 final size:80
Alignment explanation
Indices: 40568607--40568774 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 80
40568597 ACCCTACAGG
40568607 GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTATC
1 GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTATC
** * *
40568672 CTACAGGGGTGTTTC
66 AAACAAGGGTATTTC
* * **
40568687 GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATT-TCA
1 GGTAATTCTACCCTACA-GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCT-A
*
40568751 -CAAATCAAGGGTATTTT
64 TCAAA-CAAGGGTATTTC
40568768 GGTAATT
1 GGTAATT
40568775 TTATAAACCA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
80 19 0.25
81 56 0.75
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (80 bp):
GGTAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAATAATTCTATC
AAACAAGGGTATTTC
Found at i:40568794 original size:27 final size:27
Alignment explanation
Indices: 40568732--40568894 Score: 100
Period size: 27 Copynumber: 6.2 Consensus size: 27
40568722 TACCCTACAG
* * * *
40568732 GGGTATTTCGGTAATTTCACAAATCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
*
40568759 GGGTATTTTGGTAATTTTATAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
** ***
40568786 GGGTATTTTGG----TTTATTGATTGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*
40568809 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
** * * *
40568836 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** * * *
40568863 GGGTAAAATGGTAATTCTGTAAATCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
40568890 GGGTA
1 GGGTA
40568895 AAACGATAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
23 17 0.16
27 87 0.84
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:40568878 original size:54 final size:54
Alignment explanation
Indices: 40568817--40568934 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
40568807 GAGGGTATTT
* *** * *
40568817 TGGTAATTTTGTAAACCAAGGGTATTTC-AGTAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAACCAAGGGTAAAACGA-TAATTCTGTAAATCGAGAGTAAAA
*
40568871 TGGTAATTCTGTAAATCAAGGGTAAAACGATAATTCTGTAAATCGAGAGTAAAA
1 TGGTAATTCTGTAAACCAAGGGTAAAACGATAATTCTGTAAATCGAGAGTAAAA
40568925 TGGTAATTCT
1 TGGTAATTCT
40568935 ATCTTATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 55 0.98
55 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (54 bp):
TGGTAATTCTGTAAACCAAGGGTAAAACGATAATTCTGTAAATCGAGAGTAAAA
Found at i:40568895 original size:27 final size:27
Alignment explanation
Indices: 40568846--40568934 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
40568836 GGGTATTTCA
*
40568846 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40568873 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40568900 ATAATTCTGTAAATCGAGAGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40568927 GTAATTCT
1 GTAATTCT
40568935 ATCTTATTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40568969 original size:27 final size:27
Alignment explanation
Indices: 40568939--40569033 Score: 120
Period size: 27 Copynumber: 3.5 Consensus size: 27
40568929 AATTCTATCT
*
40568939 TATTTCGGTAATTTTACAAATCGAGGA
1 TATTTCGGTAATTTTACAAATCGAGGG
* * *
40568966 TATTTGGGTAATTTTATAAATCGGGGG
1 TATTTCGGTAATTTTACAAATCGAGGG
*
40568993 TACTTT-GGTAATTTTACAAGTCGAGGG
1 TA-TTTCGGTAATTTTACAAATCGAGGG
*
40569020 TATTTCAGTAATTT
1 TATTTCGGTAATTT
40569034 GGTAAACTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.05
27 52 0.90
28 3 0.05
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.41
Consensus pattern (27 bp):
TATTTCGGTAATTTTACAAATCGAGGG
Found at i:40571472 original size:35 final size:35
Alignment explanation
Indices: 40571432--40571608 Score: 214
Period size: 35 Copynumber: 5.1 Consensus size: 35
40571422 AAAAACATCA
* *
40571432 AATGCTCACAAGAGCTAGTCCAACCATAACACACC
1 AATGCTCATAAGAGCTAGTCCAACCAAAACACACC
* * *
40571467 AATGCTCATAAGATCTAGTCCAACTAAAACACGCC
1 AATGCTCATAAGAGCTAGTCCAACCAAAACACACC
*
40571502 AATGTTCATAAGAGCTAGTCCAACCAAAACACGA-C
1 AATGCTCATAAGAGCTAGTCCAACCAAAACAC-ACC
* * *
40571537 AATTCCCATAAGAGCTAGTCCAA-CAGAAACACGCC
1 AATGCTCATAAGAGCTAGTCCAACCA-AAACACACC
* **
40571572 AATGCTTATAAGAGCTAGTCCAACTGAAACACACC
1 AATGCTCATAAGAGCTAGTCCAACCAAAACACACC
40571607 AA
1 AA
40571609 ACAAAGAGTA
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
34 2 0.02
35 117 0.98
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.17
Consensus pattern (35 bp):
AATGCTCATAAGAGCTAGTCCAACCAAAACACACC
Found at i:40573407 original size:16 final size:15
Alignment explanation
Indices: 40573386--40573415 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40573376 AAAATGTAAG
40573386 TTAATATAACATGTTA
1 TTAATATAA-ATGTTA
40573402 TTAATATAAATGTT
1 TTAATATAAATGTT
40573416 TTTTTCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (15 bp):
TTAATATAAATGTTA
Found at i:40577566 original size:36 final size:36
Alignment explanation
Indices: 40577517--40577590 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
40577507 GCCCTCATAC
40577517 CATCATGGATTCACGAGTAGCAAGCTCTATTCATGA
1 CATCATGGATTCACGAGTAGCAAGCTCTATTCATGA
* *
40577553 CATCATGGGTTCACGAGTAGCAAGCTCTATTCGTGA
1 CATCATGGATTCACGAGTAGCAAGCTCTATTCATGA
40577589 CA
1 CA
40577591 AACGCCCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (36 bp):
CATCATGGATTCACGAGTAGCAAGCTCTATTCATGA
Found at i:40579557 original size:21 final size:21
Alignment explanation
Indices: 40579522--40579564 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40579512 TGTTGTAAAT
*
40579522 TGAAAGTTTTTGATAGA-AAG
1 TGAAAGTTATTGATAGATAAG
40579542 TGAAAGATTATTGATAGATAAG
1 TGAAAG-TTATTGATAGATAAG
40579564 T
1 T
40579565 CACTTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (21 bp):
TGAAAGTTATTGATAGATAAG
Found at i:40580283 original size:33 final size:33
Alignment explanation
Indices: 40580246--40580493 Score: 187
Period size: 33 Copynumber: 7.6 Consensus size: 33
40580236 TACCCAAATG
**
40580246 GTACAACTTGAAAAGGTTATGTACACTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* **
40580279 GTAC-ACTTGAAAAGGAAAGGTATGCTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* * *
40580311 ATACCA-TATGAAAAGGAAAGGTACACTTTGTGT
1 GTACAACT-TGAAAAGGAAATGTACACTTTGTGT
* * * * *
40580344 ATACCACTTGAAAAGGAAAGGTACACTATATGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
** * *
40580377 GTAC-ACTTGAAAAGGTTATGTGCACTTTGAGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* ** ** * *
40580409 GTAAAAAATGAAAAGGGTATGTACACTTCGCGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
* * * * * *
40580442 GTACCACTTGAAAAGGGAATTTACACCTCGAGT
1 GTACAACTTGAAAAGGAAATGTACACTTTGTGT
*
40580475 GTACAACTAGAAAAGGAAA
1 GTACAACTTGAAAAGGAAA
40580494 AGTCCATCAG
Statistics
Matches: 175, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
32 51 0.29
33 123 0.70
34 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (33 bp):
GTACAACTTGAAAAGGAAATGTACACTTTGTGT
Found at i:40580323 original size:65 final size:65
Alignment explanation
Indices: 40580246--40580411 Score: 194
Period size: 65 Copynumber: 2.5 Consensus size: 65
40580236 TACCCAAATG
**
40580246 GTACAACTTGAAAAGGTTATGTACACTTTGTGTGTA-CACTTGAAAAGGAAAGGTATGCT-T-TG
1 GTAC-ACTTGAAAAGGTTATGTACACTTTGTGTGTACCACTTGAAAAGGAAAGGTACACTATATG
40580308 T
65 T
* ** * *
40580309 GTATACCATATGAAAAGGAAAGGTACACTTTGTGTATACCACTTGAAAAGGAAAGGTACACTATA
1 GTACA-C-T-TGAAAAGGTTATGTACACTTTGTGTGTACCACTTGAAAAGGAAAGGTACACTATA
40580374 TGT
63 TGT
* *
40580377 GTACACTTGAAAAGGTTATGTGCACTTTGAGTGTA
1 GTACACTTGAAAAGGTTATGTACACTTTGTGTGTA
40580412 AAAAATGAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.05
64 1 0.01
65 46 0.55
66 22 0.27
67 2 0.02
68 7 0.08
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (65 bp):
GTACACTTGAAAAGGTTATGTACACTTTGTGTGTACCACTTGAAAAGGAAAGGTACACTATATGT
Found at i:40580405 original size:98 final size:98
Alignment explanation
Indices: 40580251--40580457 Score: 216
Period size: 98 Copynumber: 2.1 Consensus size: 98
40580241 AAATGGTACA
** * * * ** * **
40580251 ACTTGAAAAGGTTATGTACACTTTGTGTGTACACTTGAAAAGGAAAGGTATGCTTTGTGTATACC
1 ACTTGAAAAGGAAAGGTACACTATATGTGTACACTTGAAAAGGAAAGGTACACTTTGAGTATAAA
* * *
40580316 ATATGAAAAGGAAAGGTACACTTTGTGTATACC
66 AAATGAAAAGGAAAGGTACACTTCGCGTATACC
** * * *
40580349 ACTTGAAAAGGAAAGGTACACTATATGTGTACACTTGAAAAGGTTATGTGCACTTTGAGTGTAAA
1 ACTTGAAAAGGAAAGGTACACTATATGTGTACACTTGAAAAGGAAAGGTACACTTTGAGTATAAA
** * *
40580414 AAATGAAAAGGGTATGTACACTTCGCGTGTACC
66 AAATGAAAAGGAAAGGTACACTTCGCGTATACC
40580447 ACTTGAAAAGG
1 ACTTGAAAAGG
40580458 GAATTTACAC
Statistics
Matches: 87, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (98 bp):
ACTTGAAAAGGAAAGGTACACTATATGTGTACACTTGAAAAGGAAAGGTACACTTTGAGTATAAA
AAATGAAAAGGAAAGGTACACTTCGCGTATACC
Found at i:40588025 original size:40 final size:40
Alignment explanation
Indices: 40587980--40588109 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
40587970 CGGAATACAA
40587980 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
40588020 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
40588060 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
40588100 CCGGATATAA
1 CCGGATATAA
40588110 TTTCCAGCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:40591075 original size:33 final size:33
Alignment explanation
Indices: 40591027--40591173 Score: 251
Period size: 33 Copynumber: 4.5 Consensus size: 33
40591017 TGTGTACACT
*
40591027 TGAAAATGAAAGGTATACTTTGTGTATACCATA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATA
*
40591060 TGAAAAGGAAGGGTATACTTTGTGTATACCATA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATA
40591093 TGAAAAGGAAAGGTATACTTTGTGTATACCATA
1 TGAAAAGGAAAGGTATACTTTGTGTATACCATA
40591126 TGAAAAGGAAAGGTATACTTTGTGTATACCACT-
1 TGAAAAGGAAAGGTATACTTTGTGTATACCA-TA
*
40591159 TGAAAGGGAAAGGTA
1 TGAAAAGGAAAGGTA
40591174 CACTATATGT
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
33 108 0.99
34 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (33 bp):
TGAAAAGGAAAGGTATACTTTGTGTATACCATA
Found at i:40591227 original size:33 final size:32
Alignment explanation
Indices: 40591182--40591297 Score: 126
Period size: 33 Copynumber: 3.6 Consensus size: 32
40591172 TACACTATAT
*
40591182 GTGTAC-ACTTGAAAAGGTTATGTGCACTTTGA
1 GTGTACAACTTGAAAAGG-TATGTGCACTTCGA
* * *
40591214 GTGTACAAATTGAAAAGAGTATGTACACTTCGT
1 GTGTACAACTTGAAAAG-GTATGTGCACTTCGA
* * *
40591247 GTGTACCACTTGAAAAGGGAATGTGCACCTCGA
1 GTGTACAACTTGAAAA-GGTATGTGCACTTCGA
*
40591280 GTGTACAACTAGAAAAGG
1 GTGTACAACTTGAAAAGG
40591298 AAAAGTCCAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
32 8 0.12
33 59 0.86
34 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (32 bp):
GTGTACAACTTGAAAAGGTATGTGCACTTCGA
Found at i:40600160 original size:44 final size:42
Alignment explanation
Indices: 40600088--40600190 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 42
40600078 ATATGTGTTA
* * * * * *
40600088 TCGTGTAAGACCACGTCTAGGACGTTGGCATCGATTTGTGATT
1 TCGTGTAAGACCATGTCCAAGACATTGGCATC-ATATATGATT
40600131 TACGTGTAAGACCATGTCCAAGACATTGGCATCATATATGATT
1 T-CGTGTAAGACCATGTCCAAGACATTGGCATCATATATGATT
*
40600174 TCGTGTAAGACCCTGTC
1 TCGTGTAAGACCATGTC
40600191 TGGGATAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 15 0.29
43 10 0.19
44 27 0.52
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCCAAGACATTGGCATCATATATGATT
Found at i:40605541 original size:48 final size:48
Alignment explanation
Indices: 40605482--40605655 Score: 217
Period size: 48 Copynumber: 3.6 Consensus size: 48
40605472 TGATATGTGT
* * * *
40605482 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGAGATGCAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACATGCAA
* * *
40605530 GCCAGTGTAAGACATGCCTGGGACATGCATCGGCATTGAGACAAG--A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACATGCAA
* * *
40605576 GCTAGTGTAAGACATGTCTGGCACATGCATCGGCATTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACATGCAA
* *
40605624 GCTAGTGTAAGACTTGTCTAGGACATGGCATC
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATC
40605656 AGCTTGTTGT
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
46 40 0.37
48 62 0.58
49 5 0.05
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACATGCAA
Found at i:40605648 original size:94 final size:95
Alignment explanation
Indices: 40605482--40605655 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 95
40605472 TGATATGTGT
* * * *
40605482 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGAGATGCAAGCCAGTGTAAGACATGC
1 GCTAGTGTAAGACATGTCTGGCACATGCATCGGCATCGAGAGATACAAGCCAGTGTAAGACATGC
*
40605547 CTGGGACAT-GCATCGGCATTGAGACAAGA
66 CTAGGACATGGCATCGGCATTGAGACAAGA
* * * * *
40605576 GCTAGTGTAAGACATGTCTGGCACATGCATCGGCATTGAGATATACAAGCTAGTGTAAGACTTGT
1 GCTAGTGTAAGACATGTCTGGCACATGCATCGGCATCGAGAGATACAAGCCAGTGTAAGACATGC
40605641 CTAGGACATGGCATC
66 CTAGGACATGGCATC
40605656 AGCTTGTTGT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
94 64 0.93
95 5 0.07
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (95 bp):
GCTAGTGTAAGACATGTCTGGCACATGCATCGGCATCGAGAGATACAAGCCAGTGTAAGACATGC
CTAGGACATGGCATCGGCATTGAGACAAGA
Found at i:40612902 original size:29 final size:29
Alignment explanation
Indices: 40612870--40613001 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
40612860 ATAGTGAATC
40612870 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
40612899 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
40612929 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
40612958 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
40612987 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40613002 GTACAATTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:40613011 original size:59 final size:59
Alignment explanation
Indices: 40612870--40613001 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
40612860 ATAGTGAATC
40612870 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
* *
40612929 CGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
40612987 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40613002 GTACAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 24 0.34
59 47 0.66
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:40620761 original size:29 final size:29
Alignment explanation
Indices: 40620729--40620860 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
40620719 ATAGTGAATC
40620729 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
40620758 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
40620788 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
40620817 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
40620846 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40620861 GTACAATTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:40620870 original size:59 final size:59
Alignment explanation
Indices: 40620729--40620860 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
40620719 ATAGTGAATC
40620729 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
* *
40620788 CGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
40620846 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40620861 GTACAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 24 0.34
59 47 0.66
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:40622609 original size:27 final size:28
Alignment explanation
Indices: 40622553--40622620 Score: 129
Period size: 27 Copynumber: 2.5 Consensus size: 28
40622543 AAATTTGTAC
40622553 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
40622581 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
40622608 AGCACTAAGTGTG
1 AGCACTAAGTGTG
40622621 TGGACTCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:40622633 original size:27 final size:27
Alignment explanation
Indices: 40622553--40622634 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
40622543 AAATTTGTAC
* * *
40622553 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
* * *
40622581 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
40622608 AGCACTAAGTGTGTG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
40622635 GTTTTGAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 31 0.63
28 17 0.35
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:40629892 original size:27 final size:28
Alignment explanation
Indices: 40629836--40629903 Score: 129
Period size: 27 Copynumber: 2.5 Consensus size: 28
40629826 AAATTTGTAC
40629836 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
40629864 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
40629891 AGCACTAAGTGTG
1 AGCACTAAGTGTG
40629904 TGGACTCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:40629916 original size:27 final size:27
Alignment explanation
Indices: 40629836--40629917 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
40629826 AAATTTGTAC
* * *
40629836 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
* * *
40629864 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
40629891 AGCACTAAGTGTGTG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
40629918 GTTTTGAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 31 0.63
28 17 0.35
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:40635027 original size:30 final size:30
Alignment explanation
Indices: 40634991--40635121 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
40634981 GACAAGATTG
* * * * *
40634991 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
40635021 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
40635049 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40635079 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40635108 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40635122 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:40635082 original size:58 final size:58
Alignment explanation
Indices: 40634991--40635121 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
40634981 GACAAGATTG
* * * * * *
40634991 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
40635049 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
40635108 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40635122 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:40643047 original size:40 final size:40
Alignment explanation
Indices: 40642990--40643175 Score: 220
Period size: 40 Copynumber: 4.7 Consensus size: 40
40642980 TCGAATGATG
* * *
40642990 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
40643030 TCCGGACTAAGAT-CCGAAGGCATTTATGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40643070 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40643110 TCCGGGA-TAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCC-GGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
40643151 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGACTAAGTCCCGAAGGCATTTG
40643176 AACGAGTGCT
Statistics
Matches: 131, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40647850 original size:40 final size:39
Alignment explanation
Indices: 40647705--40647859 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 39
40647695 GATAAATGGA
** *
40647705 CTAAGTCCCGAAGGCATTTGCACTAGTGACTAGT-TCCGGG
1 CTAAGTCCCGAAGGCATTTGTGCGAGT-ACTA-TATCCGGG
*
40647745 CTAAGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGG
1 CTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGG
40647785 CTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGG
1 CTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCCGGG
* * * * *
40647825 CTATGCCCCGAAGGTATTCGAGCGAGTAGCTATAT
1 CTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAT
40647860 TCGGTGTACT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 97 0.96
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
CTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGG
Found at i:40649395 original size:28 final size:27
Alignment explanation
Indices: 40649332--40649401 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40649322 ATAGTGAGTC
*
40649332 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
40649359 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
40649387 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40649402 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40658372 original size:22 final size:22
Alignment explanation
Indices: 40658347--40658388 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40658337 CGATGGATGC
*
40658347 GTATTGAGTTA-TAATATGTAAT
1 GTATT-AGTTAGTAAAATGTAAT
40658369 GTATTAGTTAGTAAAATGTA
1 GTATTAGTTAGTAAAATGTA
40658389 TGCCATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (22 bp):
GTATTAGTTAGTAAAATGTAAT
Found at i:40659128 original size:40 final size:40
Alignment explanation
Indices: 40659073--40659327 Score: 336
Period size: 40 Copynumber: 6.4 Consensus size: 40
40659063 ATGATAACCA
* * *
40659073 GGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCG
**
40659113 GGCTAAGTCTTGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
40659153 GTCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* *
40659193 AGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
40659233 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* * * *
40659273 GGCTATGTCCCGAAGGTATTCGAGCGAG-TAGCTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG
* *
40659312 GGTTAAATCCCGAAGG
1 GGCTAAGTCCCGAAGG
40659328 TACTTGGCTT
Statistics
Matches: 192, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 16 0.08
40 176 0.92
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:40661587 original size:43 final size:43
Alignment explanation
Indices: 40661538--40661683 Score: 129
Period size: 43 Copynumber: 3.3 Consensus size: 43
40661528 TTTGAAGATA
40661538 TTATTTTATTTTAATTTAATCACAATAAATATTTTGTCTACTT
1 TTATTTTATTTTAATTTAATCACAATAAATATTTTGTCTACTT
** * *
40661581 TTATTTTAATTTTAATTT-A-C-CTAATTAAATTAAATTGTATTAAAAATT
1 TTATTTT-ATTTTAATTTAATCAC-AA-TAAA-TATTTTGT-CT---ACTT
* *
40661629 TTATTTTATTTTATTTTAATCAGGAA-AAATATTTTGTCTACTT
1 TTATTTTATTTTAATTTAATCA-CAATAAATATTTTGTCTACTT
40661672 TTATTTTATTTT
1 TTATTTTATTTT
40661684 TAAATTACCT
Statistics
Matches: 81, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 27 0.33
44 16 0.20
45 1 0.01
46 1 0.01
47 15 0.19
48 14 0.17
49 1 0.01
50 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (43 bp):
TTATTTTATTTTAATTTAATCACAATAAATATTTTGTCTACTT
Found at i:40661632 original size:48 final size:47
Alignment explanation
Indices: 40661579--40661728 Score: 132
Period size: 48 Copynumber: 3.2 Consensus size: 47
40661569 TTTTGTCTAC
40661579 TTTTATTTTAATTTTAATTTACCTAATTAAATTAAATTGTATTAAAAA
1 TTTTATTTTAATTTTAATTTACCTAATTAAATTAAATTGTATT-AAAA
* * * ** ** *
40661627 TTTTATTTT-ATTTTATTTTA-ATCAGGAAA--AATATT-T-TGTCTAC
1 TTTTATTTTAATTTTAATTTACCTAATTAAATTAA-ATTGTAT-TAAAA
* *
40661670 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAA
1 TTTTATTTTAATTTTAATTTACCTAATTAAATTAAATTGTA-TTAAAA
40661718 TTTTATTTTAA
1 TTTTATTTTAA
40661729 ATATTTTATT
Statistics
Matches: 74, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
43 11 0.15
44 12 0.16
45 8 0.11
46 8 0.11
47 13 0.18
48 21 0.28
49 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (47 bp):
TTTTATTTTAATTTTAATTTACCTAATTAAATTAAATTGTATTAAAA
Found at i:40661639 original size:91 final size:91
Alignment explanation
Indices: 40661538--40661727 Score: 319
Period size: 91 Copynumber: 2.1 Consensus size: 91
40661528 TTTGAAGATA
*
40661538 TTATTTTATTTTAATTTAATCA-CAATAAATATTTTGTCTACTTTTATTTTAATTTTAATTTACC
1 TTATTTTATTTTAATTTAATCAGCAA-AAATATTTTGTCTACTTTTATTTTAATTTTAAATTACC
40661602 TAATTAAATTAAATTGTATTAAAAATT
65 TAATTAAATTAAATTGTATTAAAAATT
* * *
40661629 TTATTTTATTTTATTTTAATCAGGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACCT
1 TTATTTTATTTTAATTTAATCAGCAAAAATATTTTGTCTACTTTTATTTTAATTTTAAATTACCT
*
40661694 AATTAAATTAAATTGTATTTAAAATT
66 AATTAAATTAAATTGTATTAAAAATT
40661720 TTATTTTA
1 TTATTTTA
40661728 AATATTTTAT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 91 0.98
92 2 0.02
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (91 bp):
TTATTTTATTTTAATTTAATCAGCAAAAATATTTTGTCTACTTTTATTTTAATTTTAAATTACCT
AATTAAATTAAATTGTATTAAAAATT
Found at i:40661729 original size:105 final size:102
Alignment explanation
Indices: 40661497--40661806 Score: 383
Period size: 105 Copynumber: 3.1 Consensus size: 102
40661487 TTAACCTTAT
* * * * *
40661497 TAATTAAATTAAATTGTAATTAAAGTTTTATTTTGAAGATATTATTTTATTTTAATTTAATCACA
1 TAATTAAATTAAATTGT-ATTAAA-TTTTATTTTAAAAATTTTATTTTATTTTATTTTAATCAGA
* *
40661562 ATAAATATTTTGTCTACTTTTATTTTAATTTTAATTTACC
64 A-AAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
40661602 TAATTAAATTAAATTG----------TA--TTAAAAATTTTATTTTATTTTATTTTAATCAGGAA
1 TAATTAAATTAAATTGTATTAAATTTTATTTTAAAAATTTTATTTTATTTTATTTTAATCA-GAA
40661655 AAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
65 AAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
*
40661693 TAATTAAATTAAATTGTATTTAAAATTTTATTTTAAATATTTTATTTTATTTTATTTTAATCACG
1 TAATTAAATTAAATTGTA-TT-AAATTTTATTTTAAAAATTTTATTTTATTTTATTTTAATCA-G
**
40661758 AAAAATATTTTCACTACTTTTATTTTATTTTTAAATTACC
63 AAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
40661798 TAATTAAAT
1 TAATTAAAT
40661807 AATCATTCTT
Statistics
Matches: 179, Mismatches: 11, Indels: 30
0.81 0.05 0.14
Matches are distributed among these distances:
91 79 0.44
92 2 0.01
93 2 0.01
103 2 0.01
105 94 0.53
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (102 bp):
TAATTAAATTAAATTGTATTAAATTTTATTTTAAAAATTTTATTTTATTTTATTTTAATCAGAAA
AATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
Found at i:40661736 original size:14 final size:13
Alignment explanation
Indices: 40661711--40661752 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 13
40661701 TTAAATTGTA
40661711 TTTAAAATTTTAT
1 TTTAAAATTTTAT
40661724 TTTAAATATTTTAT
1 TTTAAA-ATTTTAT
40661738 TTT---ATTTTAT
1 TTTAAAATTTTAT
40661748 TTTAA
1 TTTAA
40661753 TCACGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.38
13 6 0.23
14 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTAAAATTTTAT
Found at i:40661948 original size:27 final size:27
Alignment explanation
Indices: 40661910--40662012 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 27
40661900 TATATCATAT
40661910 CTTACATAATTTACATAAGATAAATAA
1 CTTACATAATTTACATAAGATAAATAA
** *
40661937 CTTACATAATTTACATAACTTACATAA
1 CTTACATAATTTACATAAGATAAATAA
* * * *
40661964 CTTACATAA-TGACGT---AT-CATAT
1 CTTACATAATTTACATAAGATAAATAA
40661986 CTTACATAATTTACATAAGATAAATAA
1 CTTACATAATTTACATAAGATAAATAA
40662013 TTATATGTAC
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
22 13 0.22
23 5 0.08
26 6 0.10
27 36 0.60
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.35
Consensus pattern (27 bp):
CTTACATAATTTACATAAGATAAATAA
Found at i:40661954 original size:18 final size:18
Alignment explanation
Indices: 40661905--40662003 Score: 81
Period size: 18 Copynumber: 5.3 Consensus size: 18
40661895 CAATATATAT
*
40661905 CATATCTTACATAATTTA
1 CATAACTTACATAATTTA
** * *
40661923 CATAAGATAAATAACTTA
1 CATAACTTACATAATTTA
* *
40661941 CATAATTTACATAACTTA
1 CATAACTTACATAATTTA
*
40661959 CATAACTTACATAATGACGTA
1 CATAACTTACATAAT---TTA
*
40661980 TCATATCTTACATAATTTA
1 -CATAACTTACATAATTTA
40661999 CATAA
1 CATAA
40662004 GATAAATAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
18 45 0.71
19 2 0.03
21 2 0.03
22 14 0.22
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.36
Consensus pattern (18 bp):
CATAACTTACATAATTTA
Found at i:40662003 original size:9 final size:9
Alignment explanation
Indices: 40661905--40661972 Score: 82
Period size: 9 Copynumber: 7.6 Consensus size: 9
40661895 CAATATATAT
*
40661905 CATATCTTA
1 CATAACTTA
*
40661914 CATAATTTA
1 CATAACTTA
**
40661923 CATAAGATA
1 CATAACTTA
*
40661932 AATAACTTA
1 CATAACTTA
*
40661941 CATAATTTA
1 CATAACTTA
40661950 CATAACTTA
1 CATAACTTA
40661959 CATAACTTA
1 CATAACTTA
40661968 CATAA
1 CATAA
40661973 TGACGTATCA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:40663285 original size:14 final size:14
Alignment explanation
Indices: 40663260--40663302 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
40663250 TTCTAAATAT
40663260 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
40663273 TTATAATTGTTTAA
1 TTATAATTGTTTAA
40663287 TTATAATTGTTTAA
1 TTATAATTGTTTAA
40663301 TT
1 TT
40663303 CAATTCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 6 0.21
14 23 0.79
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:40663765 original size:21 final size:21
Alignment explanation
Indices: 40663719--40663768 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40663709 TTAGAGCGGA
* *
40663719 GGCAGCAAAGAGGGAGGCAGT
1 GGCAGCAGAGAGGGAGGCAGC
* *
40663740 AGCAGCAGCGAGGGAGGCAGC
1 GGCAGCAGAGAGGGAGGCAGC
40663761 GGCAGCAG
1 GGCAGCAG
40663769 TGATGGCAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.48, T:0.02
Consensus pattern (21 bp):
GGCAGCAGAGAGGGAGGCAGC
Found at i:40668145 original size:20 final size:18
Alignment explanation
Indices: 40668110--40668149 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
40668100 CAATTTAAAA
*
40668110 AATTATAAAATATTATTT
1 AATTATAAAAAATTATTT
40668128 AATTATTAAAAAAGTTATTT
1 AATTA-TAAAAAA-TTATTT
40668148 AA
1 AA
40668150 ATCTTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTATAAAAAATTATTT
Found at i:40669006 original size:13 final size:13
Alignment explanation
Indices: 40668984--40669031 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
40668974 AATTCAAGTC
40668984 AATAATTATTGATA
1 AATAA-TATTGATA
*
40668998 AATAATATTGACCA
1 AATAATATTGA-TA
*
40669012 AAAACATATTGATA
1 AATA-ATATTGATA
40669026 AATAAT
1 AATAAT
40669032 GACTCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 8 0.29
14 13 0.46
15 7 0.25
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (13 bp):
AATAATATTGATA
Found at i:40673386 original size:3 final size:3
Alignment explanation
Indices: 40673378--40673434 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
40673368 TGTCTTGGAA
40673378 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40673426 AAT AAT AAT
1 AAT AAT AAT
40673435 TGATGTTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40674375 original size:24 final size:24
Alignment explanation
Indices: 40674346--40674453 Score: 153
Period size: 24 Copynumber: 4.5 Consensus size: 24
40674336 ATTGACTTCG
* *
40674346 GCACTATGTGTGCGAATTTGAATA
1 GCACTATGTGTGCGAACTTGTATA
* *
40674370 GCACTATGTGTGCGAAATTGTATG
1 GCACTATGTGTGCGAACTTGTATA
* *
40674394 GCAATATGTGTGCGGACTTGTATA
1 GCACTATGTGTGCGAACTTGTATA
*
40674418 GCACTATGTGTGCGGACTTGTATA
1 GCACTATGTGTGCGAACTTGTATA
40674442 GCACTATGTGTG
1 GCACTATGTGTG
40674454 TGGATTTAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (24 bp):
GCACTATGTGTGCGAACTTGTATA
Found at i:40682504 original size:23 final size:24
Alignment explanation
Indices: 40682450--40682532 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
40682440 ATTGACTTCG
* * *
40682450 GCACTATGTATGCGAATTTGAATA
1 GCACTATGTGTGCGAAATTGTATA
*
40682474 GCACTATGTGTG-GAAATTGTATG
1 GCACTATGTGTGCGAAATTGTATA
* *
40682497 GCACTATGTGTGCGGACTTGTATA
1 GCACTATGTGTGCGAAATTGTATA
40682521 GCACTATGTGTG
1 GCACTATGTGTG
40682533 TGGATTTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.39
24 31 0.61
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGAAATTGTATA
Found at i:40683828 original size:2 final size:2
Alignment explanation
Indices: 40683821--40683846 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40683811 TACTTTAATG
40683821 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
40683847 GAGTATGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40684199 original size:16 final size:16
Alignment explanation
Indices: 40684178--40684208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40684168 CTATGCATGC
*
40684178 AAAATATAAAAGACAG
1 AAAATAAAAAAGACAG
40684194 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
40684209 CAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGACAG
Found at i:40689196 original size:46 final size:46
Alignment explanation
Indices: 40689055--40689177 Score: 201
Period size: 46 Copynumber: 2.7 Consensus size: 46
40689045 CTGCCCCTAG
* * *
40689055 GTGAACTCAGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCATAA
*
40689101 GTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCATAA
*
40689147 GTGAACTCGGACTCAACTCAATGAGTTCGGA
1 GTGAACTCGGACTCAACTCAACGAGTTCGGA
40689178 TGCTCAACCA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
GTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCATAA
Found at i:40691191 original size:39 final size:39
Alignment explanation
Indices: 40691146--40691246 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
40691136 ATCGGGATCT
* * * *
40691146 GAAGCCCAAAGTCTAGCTGAAGTACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
40691185 GAAGCCCGAAGGATAACTGGAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
40691224 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
40691247 TCACCAGAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:40707551 original size:40 final size:40
Alignment explanation
Indices: 40707496--40707754 Score: 425
Period size: 40 Copynumber: 6.5 Consensus size: 40
40707486 TTCGGATGAC
40707496 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
40707536 ATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* *
40707575 ATCCGGGCTAAGCCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* *
40707615 ATCTGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
40707655 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
40707695 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
40707735 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
40707755 TACTTGGGTT
Statistics
Matches: 209, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
39 53 0.25
40 154 0.74
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:40711172 original size:195 final size:194
Alignment explanation
Indices: 40710841--40711230 Score: 719
Period size: 195 Copynumber: 2.0 Consensus size: 194
40710831 CTCTCTGTGC
40710841 ACCCTTAGTTTAGTTAATTAGTTTAGATAAACAAATCCCTTAATTTTTAGGCTAGATAATAAAAA
1 ACCCTTAGTTTAGTTAATTAGTTTAGATAAACAAATCCCTTAATTTTTAGGCTAGATAATAAAAA
*
40710906 AAAGTAATTACTAGTACTATTGGTTCCTTTGGGTTTGACAATCTGGTCTTGCTAAAGCTATACTA
66 AAAGTAATTACTAGTACTATTGGTTCCTTTGGGTTCGACAATCTGGTCTTGCTAAAGCTATACTA
40710971 CTGTTCGATAGGTACACTTGCCTTCA-TCGTGATAATAGTTAGTTTCAAGAACGATTAGTTATAA
131 CTGTTCGATAGGTACACTTGCCTTCATTC-TGATAATAGTTAGTTTCAAGAACGATTAGTTATAA
40711035 ACCCTTAGTTTAGTTAATTAGTTTAGATAAACAAATCCCTTAATTTTTAGGCTAGATAATAAAAA
1 ACCCTTAGTTTAGTTAATTAGTTTAGATAAACAAATCCCTTAATTTTTAGGCTAGATAATAAAAA
* *
40711100 GAAAGTAATTACTAGTACTCTTGGTTCCTTTGGGTTCGACAATCTGGTTTTGCTAAAGCTATACT
66 -AAAGTAATTACTAGTACTATTGGTTCCTTTGGGTTCGACAATCTGGTCTTGCTAAAGCTATACT
*
40711165 ACTGTTCGATAGGTACACTTGCCTTCATTCTGATAATAGTTAGTTTTAAGAACGATTAGTTATAA
130 ACTGTTCGATAGGTACACTTGCCTTCATTCTGATAATAGTTAGTTTCAAGAACGATTAGTTATAA
40711230 A
1 A
40711231 TTTTTAAACC
Statistics
Matches: 190, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
194 65 0.34
195 123 0.65
196 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (194 bp):
ACCCTTAGTTTAGTTAATTAGTTTAGATAAACAAATCCCTTAATTTTTAGGCTAGATAATAAAAA
AAAGTAATTACTAGTACTATTGGTTCCTTTGGGTTCGACAATCTGGTCTTGCTAAAGCTATACTA
CTGTTCGATAGGTACACTTGCCTTCATTCTGATAATAGTTAGTTTCAAGAACGATTAGTTATAA
Found at i:40720530 original size:30 final size:30
Alignment explanation
Indices: 40720475--40720605 Score: 164
Period size: 30 Copynumber: 4.5 Consensus size: 30
40720465 ATAGTGAATC
*
40720475 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
40720504 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
40720534 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * *
40720562 CGCACACTTAGTGCTGTACAATTTTAAAC-
1 CGCACACTTAGTGCTATATAATTTTCAACT
40720591 CTGCACACTTAGTGC
1 C-GCACACTTAGTGC
40720606 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 47 0.51
31 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:40720585 original size:58 final size:57
Alignment explanation
Indices: 40720474--40720605 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 57
40720464 TATAGTGAAT
* * * * *
40720474 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAG
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAA
*
40720532 CTCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAA
1 C-CGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAA
40720590 CCTGCACACTTAGTGC
1 CC-GCACACTTAGTGC
40720606 CAATCTTGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 3 0.05
58 42 0.65
59 20 0.31
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAA
Found at i:40724672 original size:40 final size:40
Alignment explanation
Indices: 40724627--40724793 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40724617 CGGAATATAA
40724627 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40724667 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40724707 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40724747 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40724786 CCGGATAT
1 CCGGATAT
40724794 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40724777 original size:80 final size:79
Alignment explanation
Indices: 40724627--40724793 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
40724617 CGGAATATAA
* *
40724627 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
40724692 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
40724707 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
40724769 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
40724786 CCGGATAT
1 CCGGATAT
40724794 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:40725641 original size:17 final size:19
Alignment explanation
Indices: 40725618--40725663 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40725608 AAGAAGCATG
40725618 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40725636 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40725654 AATCATGCTC
1 AATCATGCTC
40725664 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40732732 original size:39 final size:40
Alignment explanation
Indices: 40732626--40732791 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
40732616 CGGAATATAA
*
40732626 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAATTGCCTTCGGGTCTTAGC
* * * *
40732666 CCGGATAGAATAACTCGCACGAA-TGCCTTC-GGCCTTAGC
1 CCGGATATAATCACTAGCAC-AATTGCCTTCGGGTCTTAGC
* *
40732705 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAATTGCCTTCGGGTCTTAGC
** * * *
40732745 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAATTGCCTTCGGGTCTTAGC
40732784 CCGGATAT
1 CCGGATAT
40732792 CATTCAATTT
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 45 0.42
40 57 0.54
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAATTGCCTTCGGGTCTTAGC
Found at i:40733639 original size:17 final size:19
Alignment explanation
Indices: 40733616--40733661 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40733606 AAGAAGCATG
40733616 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40733634 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40733652 AATCATGCTC
1 AATCATGCTC
40733662 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40734437 original size:39 final size:39
Alignment explanation
Indices: 40734393--40734521 Score: 143
Period size: 40 Copynumber: 3.3 Consensus size: 39
40734383 TCGGAAATAA
40734393 CCGGATATAACACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40734432 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40734472 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACACTAGCACAAATGCCTTCGGGTCTTAGC
40734512 CCGGATATAA
1 CCGGATATAA
40734522 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
39 10 0.14
40 62 0.86
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40734536 original size:40 final size:40
Alignment explanation
Indices: 40734408--40734557 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
40734398 TATAACACGT
* * *
40734408 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
40734448 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
40734488 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
40734528 GCATAATTGTCTTCGGG--TTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
40734558 CATTCAATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
38 12 0.13
39 2 0.02
40 74 0.82
41 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:40734542 original size:80 final size:78
Alignment explanation
Indices: 40734408--40734555 Score: 192
Period size: 80 Copynumber: 1.9 Consensus size: 78
40734398 TATAACACGT
*
40734408 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGG--TTAGCC
40734473 CGGATGTAGCCACTA
64 CGGATGTAGCCACTA
* * * * *
40734488 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGTTAGCC
40734551 CGGAT
64 CGGAT
40734556 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
78 11 0.18
79 3 0.05
80 46 0.77
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (78 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTTAGCCCG
GATGTAGCCACTA
Found at i:40744250 original size:40 final size:39
Alignment explanation
Indices: 40744205--40744334 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
40744195 CGGAATATAA
40744205 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
40744245 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40744285 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
40744325 CCGGATATAA
1 CCGGATATAA
40744335 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:40744349 original size:40 final size:40
Alignment explanation
Indices: 40744221--40744372 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
40744211 ATAACCATGT
* * *
40744221 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
40744261 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
40744301 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
40744341 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
40744373 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:40744355 original size:80 final size:80
Alignment explanation
Indices: 40744221--40744370 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
40744211 ATAACCATGT
*
40744221 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
40744285 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
40744301 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
40744364 CCCGGAT
64 CCCGGAT
40744371 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:40752269 original size:40 final size:40
Alignment explanation
Indices: 40752224--40752310 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
40752214 CGGAATATAA
* *
40752224 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAAC
* * *
40752264 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAAC
40752304 CCGGATA
1 CCGGATA
40752311 AATTTCCAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:40757940 original size:13 final size:13
Alignment explanation
Indices: 40757932--40757956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40757922 TGAAATTAAT
40757932 AATAAAAATAAAA
1 AATAAAAATAAAA
40757945 AATAAAAATAAA
1 AATAAAAATAAA
40757957 CTTTCTAAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:40760061 original size:55 final size:55
Alignment explanation
Indices: 40760002--40760108 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 55
40759992 AAAATTTGAC
** *
40760002 AGGTTCGACCACGGGTGTTCGACACCGGCGTGTCGCACGCCCGTGCTATTTTATT
1 AGGTTCGACCACGGGTCCTCCACACCGGCGTGTCGCACGCCCGTGCTATTTTATT
* * * * * * *
40760057 AGGTTCGTCCATGGTTCCTCCATACGGGCGTGTCGCACGCCTGTGTTATTTT
1 AGGTTCGACCACGGGTCCTCCACACCGGCGTGTCGCACGCCCGTGCTATTTT
40760109 GGCAGGCTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.31
Consensus pattern (55 bp):
AGGTTCGACCACGGGTCCTCCACACCGGCGTGTCGCACGCCCGTGCTATTTTATT
Found at i:40765797 original size:19 final size:20
Alignment explanation
Indices: 40765758--40765795 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40765748 AGTAGAGTTG
*
40765758 TTATTCTTAGAAAATAAAAT
1 TTATACTTAGAAAATAAAAT
*
40765778 TTATACTTAGAAATTAAA
1 TTATACTTAGAAAATAAA
40765796 TTCTCACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
TTATACTTAGAAAATAAAAT
Found at i:40768120 original size:20 final size:21
Alignment explanation
Indices: 40768095--40768133 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40768085 CCCAATGTAC
40768095 TTTTCATATACA-CATATAAT
1 TTTTCATATACATCATATAAT
*
40768115 TTTTCATTTACATCATATA
1 TTTTCATATACATCATATA
40768134 TGATTTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTCATATACATCATATAAT
Found at i:40768360 original size:43 final size:42
Alignment explanation
Indices: 40768305--40768471 Score: 178
Period size: 43 Copynumber: 4.0 Consensus size: 42
40768295 ATATCGTACA
*
40768305 ATGCCAACATCCCAGACGTGGTCTTACATGCTATCACATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACG-TATCACATATCG
* * *
40768348 ATGCC-ACTATCCCAGACAG-GGTCTTGCACGAATCAAATA-CG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGTATCACATATCG
* * ** *
40768389 ATGTCGATGTCCCAGACATGGTCTTACACGTGATCACATATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGT-ATCACATATCG
* *
40768432 ATGCCAACATCCAAGACGTGGTCTTACACGAATCACATAT
1 ATGCCAACATCCCAGACGTGGTCTTACACGTATCACATAT
40768472 AGGAAATCTT
Statistics
Matches: 100, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
41 24 0.24
42 26 0.26
43 49 0.49
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGTATCACATATCG
Found at i:40771602 original size:37 final size:37
Alignment explanation
Indices: 40771549--40771634 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
40771539 TTATTACGAA
40771549 GTCTTACCCGGACATAATCTCCACACATAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACATAGTCATCGG
* *
40771586 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACATAGTCATCGG
*
40771623 GTCTCACCCGGA
1 GTCTTACCCGGA
40771635 ACATTTTCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACATAGTCATCGG
Found at i:40771790 original size:49 final size:49
Alignment explanation
Indices: 40771735--40772092 Score: 591
Period size: 49 Copynumber: 7.4 Consensus size: 49
40771725 TTTTACATTA
*
40771735 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
40771784 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
40771833 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
40771882 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
40771931 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
40771980 GCCATTAGGCCTTATCACATAT--ATACACTTTCACATTCATCACATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * * *
40772027 GCCA-TACGGCCTTATCACACAT--ATGCACTTTCACATTCATCACATTG
1 GCCATTA-GGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
40772074 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
40772093 CATATATGTA
Statistics
Matches: 301, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
46 2 0.01
47 82 0.27
48 1 0.00
49 216 0.72
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:40780175 original size:50 final size:49
Alignment explanation
Indices: 40780114--40780253 Score: 172
Period size: 49 Copynumber: 2.8 Consensus size: 49
40780104 TATGAGGTAG
** **
40780114 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCA
* * * * *
40780164 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCGGATAATTTGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCA
* *
40780213 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40780254 GCTTTGGCTA
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 39 0.51
50 37 0.49
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCA
Found at i:40780238 original size:49 final size:50
Alignment explanation
Indices: 40780108--40780253 Score: 177
Period size: 50 Copynumber: 2.9 Consensus size: 50
40780098 ATCTATTATG
* ** **
40780108 AGGTAGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTT
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
40780158 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCGGATAATT
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
40780208 -TGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40780254 GCTTTGGCTA
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
49 39 0.49
50 41 0.51
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (50 bp):
AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:40784134 original size:13 final size:13
Alignment explanation
Indices: 40784116--40784140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40784106 TATGGTCTAC
40784116 GATTTCGCGAAAT
1 GATTTCGCGAAAT
40784129 GATTTCGCGAAA
1 GATTTCGCGAAA
40784141 ATTTTGTTAA
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:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
GATTTCGCGAAAT
Found at i:40785606 original size:50 final size:49
Alignment explanation
Indices: 40785481--40785668 Score: 225
Period size: 50 Copynumber: 3.8 Consensus size: 49
40785471 TGAGGCCACA
* * * *
40785481 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCACG
* ** *
40785532 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
* * *
40785582 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* *
40785630 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40785669 GCTTTGGCTA
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
48 39 0.33
50 45 0.38
51 34 0.29
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:40785686 original size:101 final size:101
Alignment explanation
Indices: 40785481--40785672 Score: 273
Period size: 98 Copynumber: 1.9 Consensus size: 101
40785471 TGAGGCCACA
* * *
40785481 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAACTTCGATCACATGTGTAGTACTAAG
* * *
40785546 TGCAGGCTACTACGTGTATCAGATGGTTAGGTCATG
66 TGCAGGCTACTACGCGTACCAGATGCTTAGGTCATG
* *
40785582 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-G-TCGCATGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAACTTCGATCACATGTGTAGTACTAAG
*
40785644 TGCAGGCTACTATGCGTACCAGATAGCTT
66 TGCAGGCTACTACGCGTACCAGAT-GCTT
40785673 TGGCTATAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 38 0.47
99 4 0.05
100 2 0.02
101 37 0.46
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAACTTCGATCACATGTGTAGTACTAAG
TGCAGGCTACTACGCGTACCAGATGCTTAGGTCATG
Found at i:40789497 original size:27 final size:27
Alignment explanation
Indices: 40789460--40789519 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
40789450 GGTCATTAAG
40789460 ACCCC-AGTTTGTAAAAGTACCAAAAT
1 ACCCCTAGTTTGTAAAAGTACCAAAAT
* * *
40789486 ACCCCTAGTTTGTAAAATTACCGAATT
1 ACCCCTAGTTTGTAAAAGTACCAAAAT
40789513 ACCCCTA
1 ACCCCTA
40789520 TAAGGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (27 bp):
ACCCCTAGTTTGTAAAAGTACCAAAAT
Found at i:40792888 original size:193 final size:193
Alignment explanation
Indices: 40792559--40792932 Score: 543
Period size: 193 Copynumber: 1.9 Consensus size: 193
40792549 CTAAACATAG
* * * *
40792559 TGTAACATCCCTAACCTCCATCTGTAGTCAGAATAGGGTTTCAGAGTATTACCGAAACTTTAAGA
1 TGTAACACCCCTAACCTCCATCTATAGTCAGAATAGGGTTTCAGAGCAATACCGAAACTTTAAGA
** * *
40792624 ATGTTTTACAAATAATCTATGTAAATTACTATTCATTAACCGAGATCATTCAAAACATCCCTGAA
66 ACATTTTACAAATAATCTATGTAAATTACTATTCATTAACCAAGATCATTAAAAACATCCCTGAA
* * * * * *
40792689 TTGGACCTTGAAGGCCTAATACGAGCATTAGAGTCGAGTC-GAGACTTAATCGGGCACTCCAAA
131 TTGGACCCTCAAGGCCCAATACAAGCACTAAAGTCGAGTCAG-GACTTAATCGGGCACTCCAAA
* * *
40792752 TGTAACACCCCTAACCTGCATCTATCGTCAGAATAGGGTTTCAGAGCAATACCGAAACTTTCAGA
1 TGTAACACCCCTAACCTCCATCTATAGTCAGAATAGGGTTTCAGAGCAATACCGAAACTTTAAGA
* * * *
40792817 ACATTTTACAAATAATTTATGTAAATTACTATTTATTAACCAAGATCATTAAAAACGTCCCTTAA
66 ACATTTTACAAATAATCTATGTAAATTACTATTCATTAACCAAGATCATTAAAAACATCCCTGAA
40792882 TTGGACCCTCAAGGCCCAATACAAGCACTAAAGTCGAGTCAGGACTTAATC
131 TTGGACCCTCAAGGCCCAATACAAGCACTAAAGTCGAGTCAGGACTTAATC
40792933 AAGAACTCTA
Statistics
Matches: 159, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
193 158 0.99
194 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (193 bp):
TGTAACACCCCTAACCTCCATCTATAGTCAGAATAGGGTTTCAGAGCAATACCGAAACTTTAAGA
ACATTTTACAAATAATCTATGTAAATTACTATTCATTAACCAAGATCATTAAAAACATCCCTGAA
TTGGACCCTCAAGGCCCAATACAAGCACTAAAGTCGAGTCAGGACTTAATCGGGCACTCCAAA
Found at i:40794712 original size:13 final size:13
Alignment explanation
Indices: 40794694--40794718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40794684 GATATTATAT
40794694 GTGTGAAAATTTC
1 GTGTGAAAATTTC
40794707 GTGTGAAAATTT
1 GTGTGAAAATTT
40794719 TATTGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:40795982 original size:43 final size:44
Alignment explanation
Indices: 40795824--40795987 Score: 162
Period size: 43 Copynumber: 3.8 Consensus size: 44
40795814 ATAGGATTCT
* *
40795824 GATATGTGA-TTTCATGTAAGACCACGTCTGGGAC-GTTGGAATC
1 GATATGTGAGTTACATGTAAGACCACGTCTGGGACAG-TGGCATC
* * * * *
40795867 GATTTTTGATTTACATGTAAGACCATGTTTGGGACA-TCGGCATC
1 GATATGTGAGTTACATGTAAGACCACGTCTGGGACAGT-GGCATC
* **
40795911 G-TATATGAGTT-TGTGTAAGACC-CTGTCTGGGACAGTGGCATC
1 GATATGTGAGTTACATGTAAGACCAC-GTCTGGGACAGTGGCATC
40795953 GATATGTGA-TTACATGTAAGACCACGTCTGGGACA
1 GATATGTGAGTTACATGTAAGACCACGTCTGGGACA
40795988 TTAGCGTTGT
Statistics
Matches: 97, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
42 27 0.28
43 41 0.42
44 29 0.30
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (44 bp):
GATATGTGAGTTACATGTAAGACCACGTCTGGGACAGTGGCATC
Found at i:40799244 original size:79 final size:81
Alignment explanation
Indices: 40799135--40799317 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
40799125 TACTCGTTCA
* *
40799135 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
40799198 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
40799215 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
40799278 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
40799294 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40799318 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:40799317 original size:40 final size:40
Alignment explanation
Indices: 40799114--40799317 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
40799104 CGGAATTTAA
** *
40799114 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40799154 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40799194 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40799233 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40799273 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40799313 CCGGA
1 CCGGA
40799318 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.