Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 158 of 332
Found at i:52034262 original size:40 final size:40
Alignment explanation
Indices: 52034157--52034371 Score: 264
Period size: 40 Copynumber: 5.5 Consensus size: 40
52034147 CGGATGATAA
* * *
52034157 CCGGGCTAAGTCCCGAAGGCATCTGTGCAAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
52034197 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52034236 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
* * *
52034276 CTGGGCTAAGTCCCGATGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52034316 CCGGGCTAAGTCCTGAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
52034355 CC-GGCTAA-ACCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52034372 TACTTGGTTG
Statistics
Matches: 155, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
37 7 0.05
38 8 0.05
39 45 0.29
40 93 0.60
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52042152 original size:40 final size:39
Alignment explanation
Indices: 52042008--52042163 Score: 154
Period size: 39 Copynumber: 4.0 Consensus size: 39
52041998 TTTGAATATG
* * *
52042008 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-ATA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAA
* ** * * *
52042047 TCCGGACTAAGATCGAATGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
52042086 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
52042125 TCTGGGTTAAGTCCCGAAGGCAATTGTGCGACTTACTAA
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA
52042164 GGCATTTGAA
Statistics
Matches: 95, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
38 10 0.11
39 60 0.63
40 25 0.26
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52045257 original size:19 final size:20
Alignment explanation
Indices: 52045220--52045257 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52045210 ATAAGGTGGT
52045220 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
52045240 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
52045258 GGTGGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:52047262 original size:39 final size:39
Alignment explanation
Indices: 52047218--52047294 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
52047208 TATATTCGAC
52047218 CAAATAAGTAAAATATGTACAAGATGTTATATTATGATA
1 CAAATAAGTAAAATATGTACAAGATGTTATATTATGATA
52047257 CAAATAAGTAAAATATGTACAAGATGTTATATTATGAT
1 CAAATAAGTAAAATATGTACAAGATGTTATATTATGAT
52047295 TCTTGAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (39 bp):
CAAATAAGTAAAATATGTACAAGATGTTATATTATGATA
Found at i:52047292 original size:19 final size:19
Alignment explanation
Indices: 52047231--52047292 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
52047221 ATAAGTAAAA
52047231 TATGTACAAGATGTTATAT
1 TATGTACAAGATGTTATAT
* *
52047250 TATGATACAA-ATAAG-TAAAA
1 TATG-TACAAGAT--GTTATAT
52047270 TATGTACAAGATGTTATAT
1 TATGTACAAGATGTTATAT
52047289 TATG
1 TATG
52047293 ATTCTTGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 14 0.41
21 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (19 bp):
TATGTACAAGATGTTATAT
Found at i:52054394 original size:22 final size:22
Alignment explanation
Indices: 52054369--52054444 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
52054359 AGATATGTAT
52054369 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
52054391 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
52054415 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
52054438 ATGTGAT
1 ATGTGAT
52054445 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:52054419 original size:25 final size:25
Alignment explanation
Indices: 52054391--52054468 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
52054381 CGAATGGCCA
52054391 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * ***
52054416 ATGTGAT-AAGGCCG-AA-TGGCCA-
1 ATGTGATGAATG-TGAAAGTGTATAT
52054438 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
52054463 ATGTGA
1 ATGTGA
52054469 CAAGGCCTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 14 0.37
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:52054419 original size:47 final size:47
Alignment explanation
Indices: 52054366--52054660 Score: 491
Period size: 47 Copynumber: 6.3 Consensus size: 47
52054356 ACAAGATATG
52054366 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
52054413 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
52054460 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
52054507 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
52054554 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
52054601 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
52054648 TAAATGTGATAAG
1 TATATGTGATAAG
52054661 TCCCGAAGGG
Statistics
Matches: 230, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 230 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:52063882 original size:48 final size:48
Alignment explanation
Indices: 52063826--52064010 Score: 235
Period size: 48 Copynumber: 3.9 Consensus size: 48
52063816 GACATGGTAG
* * * *
52063826 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGCACATATA
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
** ** *
52063874 GATGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGATCGTAGATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * *
52063922 GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATCTCATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * *
52063970 GATGCCAAAGCCATGTCCTAGACATGGTCTTATATGGGATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
52064011 GTACACAACC
Statistics
Matches: 116, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 116 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:52063993 original size:96 final size:96
Alignment explanation
Indices: 52063826--52064013 Score: 286
Period size: 96 Copynumber: 2.0 Consensus size: 96
52063816 GACATGGTAG
* * *
52063826 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGCACATATAGATGCCAATGCCATGTC
1 GATGCCAATGCCATATCCCAAACATGGTCTTACATGGGAGCACATATAGATGCCAAAGCCATGTC
*
52063891 CCAGACATGGTCTTATGTGGGATCGTAGATC
66 CCAGACATGGTCTTATATGGGATCGTAGATC
* * * * *
52063922 GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATCTCATATCGATGCCAAAGCCATGTC
1 GATGCCAATGCCATATCCCAAACATGGTCTTACATGGGAGCACATATAGATGCCAAAGCCATGTC
*
52063987 CTAGACATGGTCTTATATGGGATCGTA
66 CCAGACATGGTCTTATATGGGATCGTA
52064014 CACAACCCTA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (96 bp):
GATGCCAATGCCATATCCCAAACATGGTCTTACATGGGAGCACATATAGATGCCAAAGCCATGTC
CCAGACATGGTCTTATATGGGATCGTAGATC
Found at i:52068210 original size:39 final size:41
Alignment explanation
Indices: 52068109--52068292 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
52068099 TTGAATGATG
* *
52068109 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
52068149 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
52068189 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
52068228 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
52068267 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52068293 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:52068245 original size:79 final size:80
Alignment explanation
Indices: 52068109--52068292 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
52068099 TTGAATGATG
*
52068109 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
52068173 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
52068188 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
52068250 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
52068267 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52068293 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:52068315 original size:78 final size:79
Alignment explanation
Indices: 52068162--52068325 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
52068152 GGACTAAGAT
* **
52068162 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
52068227 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
52068241 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
52068303 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
52068319 CCGAAGG
1 CCGAAGG
52068326 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:52076098 original size:40 final size:39
Alignment explanation
Indices: 52076015--52076198 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 39
52076005 TTGAATGATG
* * * *
52076015 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
52076054 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
52076094 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
52076133 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
52076174 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
52076199 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 45 0.36
40 70 0.56
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52076150 original size:79 final size:80
Alignment explanation
Indices: 52076015--52076198 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 80
52076005 TTGAATGATG
* * *
52076015 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
52076079 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
52076093 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
52076156 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
52076173 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
52076199 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 67 0.74
80 22 0.24
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:52076220 original size:79 final size:79
Alignment explanation
Indices: 52076067--52076231 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
52076057 GGACTAAGAT
* * **
52076067 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
52076132 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
52076146 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
52076209 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
52076225 CCGAAGG
1 CCGAAGG
52076232 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:52082623 original size:48 final size:48
Alignment explanation
Indices: 52082529--52082626 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
52082519 CACATGGTAG
* * * * *
52082529 GATGCCAATGCCATATCTCGGATATAGTTTTACATGTGATCACATATC
1 GATGCCAATGCCATATCCCAGACATAGTATTACATGGGATCACATATC
* * * *
52082577 GATGCCAATGCCATGTCCCAGACATGGTATTACGTGGGATCTCATATC
1 GATGCCAATGCCATATCCCAGACATAGTATTACATGGGATCACATATC
52082625 GA
1 GA
52082627 AGCCGGTAGC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATAGTATTACATGGGATCACATATC
Found at i:52086979 original size:40 final size:40
Alignment explanation
Indices: 52086930--52087070 Score: 212
Period size: 40 Copynumber: 3.5 Consensus size: 40
52086920 CGGATGTAAC
* *
52086930 AACCAGCACGAATGCCTTCGAGACTTAACTCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
52086970 AACCCGCACGAATGCTTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
52087010 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
52087050 AACTAGCAC-AATTGCCTTCGG
1 AACCAGCACGAA-TGCCTTCGG
52087071 ATCTTAGTCC
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 2 0.02
40 91 0.98
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:52089572 original size:20 final size:20
Alignment explanation
Indices: 52089547--52089585 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52089537 GAAAGGCACT
52089547 GGCGTACCCCAAGGTACACG
1 GGCGTACCCCAAGGTACACG
*
52089567 GGCGTACCCCGAGGTACAC
1 GGCGTACCCCAAGGTACAC
52089586 AGGTGTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.36, G:0.31, T:0.10
Consensus pattern (20 bp):
GGCGTACCCCAAGGTACACG
Found at i:52114397 original size:43 final size:43
Alignment explanation
Indices: 52114348--52114543 Score: 277
Period size: 43 Copynumber: 4.6 Consensus size: 43
52114338 CGTCCAAAAT
** * * *
52114348 GTGGTCTTACATGTAACCTCATATCGATGCCACTGTCCCAGAC
1 GTGGTCTTACACATAATCACATATCGATGCCAATGTCCCAGAC
* * **
52114391 AG-GGTCTTACTCATAAACACATATCGATGCCAACATCCCAGAC
1 -GTGGTCTTACACATAATCACATATCGATGCCAATGTCCCAGAC
*
52114434 GTGGTCTTACACATAATCACATACCGATGCCAATGTCCCAGAC
1 GTGGTCTTACACATAATCACATATCGATGCCAATGTCCCAGAC
52114477 GTGGTCTTACACATAATCACATATCGATGCCAATGTCCCAGAC
1 GTGGTCTTACACATAATCACATATCGATGCCAATGTCCCAGAC
*
52114520 ATGGTCTTACACATAATCACATAT
1 GTGGTCTTACACATAATCACATAT
52114544 TGATATCACA
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
42 1 0.01
43 134 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (43 bp):
GTGGTCTTACACATAATCACATATCGATGCCAATGTCCCAGAC
Found at i:52120555 original size:16 final size:16
Alignment explanation
Indices: 52120534--52120576 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
52120524 GTAGATAGGC
52120534 AAAAGCCGAAATG-TCG
1 AAAAGCCGAAATGCT-G
52120550 AAAAGCCGAAATGCTG
1 AAAAGCCGAAATGCTG
*
52120566 AAAAGCTGAAA
1 AAAAGCCGAAA
52120577 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (16 bp):
AAAAGCCGAAATGCTG
Found at i:52120875 original size:29 final size:29
Alignment explanation
Indices: 52120788--52120875 Score: 142
Period size: 29 Copynumber: 3.1 Consensus size: 29
52120778 GTGAGCATGA
*
52120788 ATAT-AATGTTATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
52120816 ACATAAATGTGATTTGGGCCTAAAGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
52120845 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
52120874 AT
1 AT
52120876 GTGAATATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 3 0.06
29 51 0.94
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:52124406 original size:43 final size:43
Alignment explanation
Indices: 52124351--52124567 Score: 276
Period size: 43 Copynumber: 5.0 Consensus size: 43
52124341 ATATCGTACA
** * *
52124351 ATGCCAACGTCCCAGACGTGGTCTTACATGTAACCTCATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
* * *
52124394 ATGCC-ACTGTCCCAGACAG-GGTCTTACTCATAAACACATATAG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACATAATCACATATCG
* * * * *
52124437 ATGCCTACATCCCAGATGTGGTATTACACATAATCACATACCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
*
52124480 ATGCCAACGTCCTAGACGTGGTCTTACACATAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
*
52124523 ATGCCAACGTCCCAGACATGGTCTTACACATAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
52124566 AT
1 AT
52124568 ATCACATATA
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.02
43 143 0.96
44 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACATAATCACATATCG
Found at i:52129685 original size:15 final size:15
Alignment explanation
Indices: 52129662--52129707 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
52129652 ATTATGATAT
52129662 TGTATCTTGGATTTC
1 TGTATCTTGGATTTC
*
52129677 TGTACCTTGGATTTC
1 TGTATCTTGGATTTC
*
52129692 TATATCTTGGATTTC
1 TGTATCTTGGATTTC
52129707 T
1 T
52129708 TTGTCCTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52
Consensus pattern (15 bp):
TGTATCTTGGATTTC
Found at i:52129717 original size:15 final size:15
Alignment explanation
Indices: 52129664--52129727 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
52129654 TATGATATTG
* *
52129664 TATCTTGGATTTCTG
1 TATCCTGGATTTCTT
*
52129679 TA-CCTTGGATTTCTA
1 TATCC-TGGATTTCTT
*
52129694 TATCTTGGATTTCTT
1 TATCCTGGATTTCTT
* *
52129709 TGTCCTGGACTTCTT
1 TATCCTGGATTTCTT
52129724 TATC
1 TATC
52129728 TCGATTTTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 1 0.03
15 37 0.95
16 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.52
Consensus pattern (15 bp):
TATCCTGGATTTCTT
Found at i:52129728 original size:30 final size:30
Alignment explanation
Indices: 52129664--52129728 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
52129654 TATGATATTG
*
52129664 TATCTTGGATTTCTGTACCTTGGATTTCTA
1 TATCTTGGATTTCTGTACCTTGGACTTCTA
*
52129694 TATCTTGGATTTCTTTGT-CC-TGGACTTCTT
1 TATCTTGGATTTC--TGTACCTTGGACTTCTA
52129724 TATCT
1 TATCT
52129729 CGATTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 26 0.84
31 2 0.06
32 3 0.10
ACGTcount: A:0.14, C:0.18, G:0.15, T:0.52
Consensus pattern (30 bp):
TATCTTGGATTTCTGTACCTTGGACTTCTA
Found at i:52133217 original size:6 final size:6
Alignment explanation
Indices: 52133206--52133239 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
52133196 ATGAATAAAC
*
52133206 TTATGT TTATGT TTATGT TTATGA TTATGT TTAT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTAT
52133240 TATGCCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (6 bp):
TTATGT
Found at i:52135151 original size:47 final size:47
Alignment explanation
Indices: 52135064--52135305 Score: 403
Period size: 47 Copynumber: 5.1 Consensus size: 47
52135054 CCCTTCGGGA
* * * * * * *
52135064 CTTATCACCTTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52135111 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52135158 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52135205 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52135252 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52135299 CTTATCA
1 CTTATCA
52135306 TCATTTCATA
Statistics
Matches: 184, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 184 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52147694 original size:27 final size:27
Alignment explanation
Indices: 52147664--52147724 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
52147654 TAAGAATAGT
*
52147664 GAAATTACTTGA-ATACCCCTATGTATA
1 GAAATTAC-TGATATACCCCTAGGTATA
*
52147691 GAAATTACTGATATACCCCTAGGTGTA
1 GAAATTACTGATATACCCCTAGGTATA
52147718 -AAATTAC
1 GAAATTAC
52147725 CATTATACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (27 bp):
GAAATTACTGATATACCCCTAGGTATA
Found at i:52147731 original size:26 final size:27
Alignment explanation
Indices: 52147676--52147738 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
52147666 AATTACTTGA
* *
52147676 ATACCCCTATGTATAGAAATTACTGAT
1 ATACCCCTAGGTATAGAAATTACTCAT
*
52147703 ATACCCCTAGGTGTA-AAATTAC-CATT
1 ATACCCCTAGGTATAGAAATTACTCA-T
52147729 ATA-CCCTAGG
1 ATACCCCTAGG
52147739 GTTACTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 8 0.25
26 11 0.34
27 13 0.41
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (27 bp):
ATACCCCTAGGTATAGAAATTACTCAT
Found at i:52147883 original size:27 final size:28
Alignment explanation
Indices: 52147841--52147907 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
52147831 GACGAAATGT
52147841 TCTGGTGGCTAC-GCCACAATTATCTG-A
1 TCTGGTGGCT-CTGCCACAATTATCTGTA
*
52147868 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAATTATCTGTA
*
52147896 TCTGGTGACTCT
1 TCTGGTGGCTCT
52147908 ATCACACTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 1 0.03
27 23 0.64
28 12 0.33
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.34
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAATTATCTGTA
Found at i:52147918 original size:27 final size:28
Alignment explanation
Indices: 52147861--52147926 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
52147851 ACGCCACAAT
* * *
52147861 TATCTG-ATCTGGTGGCTCTGCCACGAT
1 TATCTGTATCTGGTGACTCTACCACGAC
*
52147888 TATCTGTATCTGGTGACTCTATCAC-AC
1 TATCTGTATCTGGTGACTCTACCACGAC
52147915 TATCTGT-TCTGG
1 TATCTGTATCTGG
52147927 CAGCCATGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.15
27 14 0.41
28 15 0.44
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (28 bp):
TATCTGTATCTGGTGACTCTACCACGAC
Found at i:52160912 original size:24 final size:25
Alignment explanation
Indices: 52160879--52160931 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
52160869 CTATTAGAAT
52160879 AAATCCTATCTCAATTTCATCCATC
1 AAATCCTATCTCAATTTCATCCATC
52160904 AAAT-CTATCTCAATTTCATCCATC
1 AAATCCTATCTCAATTTCATCCATC
52160928 AAAT
1 AAAT
52160932 AAATAGATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATCCTATCTCAATTTCATCCATC
Found at i:52161808 original size:23 final size:23
Alignment explanation
Indices: 52161782--52161825 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
52161772 TGGGCATTTG
*
52161782 ATACCTTTAACAATTAGAATTCA
1 ATACATTTAACAATTAGAATTCA
52161805 ATACATTTAACAATTAGAATT
1 ATACATTTAACAATTAGAATT
52161826 TAACTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (23 bp):
ATACATTTAACAATTAGAATTCA
Found at i:52163827 original size:35 final size:35
Alignment explanation
Indices: 52163756--52163828 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
52163746 TATAACATTG
* ** * **
52163756 CATATGGCCAAATATGCACATTCAAAATAATTTCA
1 CATATGACCAAATACACAAATTCAAAATAAACTCA
*
52163791 CATATGACCAAATACACAAATTCAATATAAACTCA
1 CATATGACCAAATACACAAATTCAAAATAAACTCA
52163826 CAT
1 CAT
52163829 GTAATCTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.26
Consensus pattern (35 bp):
CATATGACCAAATACACAAATTCAAAATAAACTCA
Found at i:52164026 original size:39 final size:42
Alignment explanation
Indices: 52163983--52164077 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
52163973 CGGTATAAAA
*
52163983 CCTGCTAGGCATAA-GCCTGA-A-TTACTCACCAGCACAAAG
1 CCTGCTAGGCACAAGGCCTGATATTTACTCACCAGCACAAAG
* * * * * *
52164022 CCTGCTAGACCCAAGGTCTGATATTTATTCACCGGCACTAAG
1 CCTGCTAGGCACAAGGCCTGATATTTACTCACCAGCACAAAG
52164064 CCTGCTAGGCACAA
1 CCTGCTAGGCACAA
52164078 AGCCCGATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 11 0.25
40 5 0.11
41 1 0.02
42 27 0.61
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (42 bp):
CCTGCTAGGCACAAGGCCTGATATTTACTCACCAGCACAAAG
Found at i:52167190 original size:48 final size:48
Alignment explanation
Indices: 52167133--52167357 Score: 192
Period size: 48 Copynumber: 4.8 Consensus size: 48
52167123 ATGGTAAGAC
* * * * *
52167133 GCCAATGCCATATCTCGGATATGGTCTTACATGGGATCACATATCGAT
1 GCCAATGCCATGTCCCAGACATGGTCATACATGGGATCACATATCGAT
* *** **
52167181 GCCAATGCCATGTCCCAGACATGGTCCTACATGGGATTGTAGGTCGAT
1 GCCAATGCCATGTCCCAGACATGGTCATACATGGGATCACATATCGAT
* *
52167229 GCCAACGCCATGTCCCAGACATGGTCATGCATGGGATCACATATCGAT
1 GCCAATGCCATGTCCCAGACATGGTCATACATGGGATCACATATCGAT
* * * ** *
52167277 GCCGAT---A-G-CCCAG-CTATGGTCTTACACGAAATTACATATCGAT
1 GCCAATGCCATGTCCCAGAC-ATGGTCATACATGGGATCACATATCGAT
* * **
52167320 GCCAAAGCCATGTCCCAAACATGGTTTTACATGGGATC
1 GCCAATGCCATGTCCCAGACATGGTCATACATGGGATC
52167358 GTACATAACC
Statistics
Matches: 136, Mismatches: 34, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
42 1 0.01
43 31 0.23
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 99 0.73
49 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (48 bp):
GCCAATGCCATGTCCCAGACATGGTCATACATGGGATCACATATCGAT
Found at i:52170109 original size:31 final size:33
Alignment explanation
Indices: 52170054--52170118 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
52170044 TTTAGGTCAC
* *
52170054 AACCCATAACAAAATCAATTGGGCCT-AGCCCA
1 AACCAATAACAAAATCAAGTGGGCCTAAGCCCA
*
52170086 AACCAATAACAGAA-CAAGTGGGCCTAAGCCCA
1 AACCAATAACAAAATCAAGTGGGCCTAAGCCCA
52170118 A
1 A
52170119 TACAGTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.43, C:0.29, G:0.15, T:0.12
Consensus pattern (33 bp):
AACCAATAACAAAATCAAGTGGGCCTAAGCCCA
Found at i:52170957 original size:27 final size:26
Alignment explanation
Indices: 52170912--52171133 Score: 142
Period size: 27 Copynumber: 8.2 Consensus size: 26
52170902 ATTTTATCCT
* *
52170912 ACAAGGGTATTT-TAGTAATTTTACACT
1 ACAAGGGTATTTCGA-TAATTTTACA-A
52170939 ACAAGGGTATTTCGATAATTTTACAA
1 ACAAGGGTATTTCGATAATTTTACAA
** * * *
52170965 ACTGGGGGTATTTTGGTAATTTTATAA
1 AC-AAGGGTATTTCGATAATTTTACAA
**** * * *
52170992 TTTGGGGGTATTTTGGGTAATTTTATAA
1 -ACAAGGGTA-TTTCGATAATTTTACAA
*
52171020 ACTAGGGTATTTC-AGTAATTTTACAA
1 ACAAGGGTATTTCGA-TAATTTTACAA
*
52171046 ACCGAGGGTATTTCGATAATTTTACAA
1 A-CAAGGGTATTTCGATAATTTTACAA
* * *
52171073 TTCAAGGGTATTTTGGTAATTTTACAA
1 -ACAAGGGTATTTCGATAATTTTACAA
* * *
52171100 ACTAGGGGTATTTCGGTAATTTTATAA
1 AC-AAGGGTATTTCGATAATTTTACAA
52171127 ATCAAGG
1 A-CAAGG
52171134 TCTTAAAGAC
Statistics
Matches: 158, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
26 17 0.11
27 122 0.77
28 19 0.12
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (26 bp):
ACAAGGGTATTTCGATAATTTTACAA
Found at i:52170960 original size:54 final size:53
Alignment explanation
Indices: 52170902--52171133 Score: 184
Period size: 54 Copynumber: 4.3 Consensus size: 53
52170892 CAAAACAGTC
** *
52170902 ATTTTATCCTACAAGGGTATTTTAGTAATTTTACACTACAAGGGTATTTCGATA
1 ATTTTATCAAACAAGGGTATTTTAGTAATTTTACA-AACAAGGGTATTTCGATA
** * * **** * *
52170956 ATTTTA-CAAACTGGGGGTATTTTGGTAATTTTATAATTTGGGGGTATTTTGGGTA
1 ATTTTATCAAAC-AAGGGTATTTTAGTAATTTTACAA-ACAAGGGTA-TTTCGATA
* * *
52171011 ATTTTAT-AAACTAGGGTATTTCAGTAATTTTACAAACCGAGGGTATTTCGATA
1 ATTTTATCAAACAAGGGTATTTTAGTAATTTTACAAA-CAAGGGTATTTCGATA
* * * *
52171064 ATTTTA-CAATTCAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTA
1 ATTTTATCAA-ACAAGGGTATTTTAGTAATTTTACAAAC-AAGGGTATTTCGATA
52171118 ATTTTAT-AAATCAAGG
1 ATTTTATCAAA-CAAGG
52171134 TCTTAAAGAC
Statistics
Matches: 137, Mismatches: 31, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
53 18 0.13
54 103 0.75
55 16 0.12
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (53 bp):
ATTTTATCAAACAAGGGTATTTTAGTAATTTTACAAACAAGGGTATTTCGATA
Found at i:52171039 original size:81 final size:79
Alignment explanation
Indices: 52170913--52171123 Score: 260
Period size: 81 Copynumber: 2.6 Consensus size: 79
52170903 TTTTATCCTA
* * * * *
52170913 CAAGGGTATTTTAGTAATTTTACACTACAAGGGTATTTCGATAATTTTACAAACTGGGGGTATTT
1 CAAGGGTATTTTGGTAATTTTACA-AACTAGGGTATTTCG-TAATTTTACAAACCGAGGGTATTT
* * *
52170978 TGGTAATTTTATAATT
64 CGATAATTTTACAATT
*** *
52170994 TGGGGGTATTTTGGGTAATTTTATAAACTAGGGTATTTCAGTAATTTTACAAACCGAGGGTATTT
1 CAAGGGTATTTT-GGTAATTTTACAAACTAGGGTATTTC-GTAATTTTACAAACCGAGGGTATTT
52171059 CGATAATTTTACAATT
64 CGATAATTTTACAATT
52171075 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTTA
1 CAAGGGTATTTTGGTAATTTTACAAACTA-GGGTATTTC-GTAATTTTA
52171124 TAAATCAAGG
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
80 16 0.15
81 83 0.75
82 11 0.10
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (79 bp):
CAAGGGTATTTTGGTAATTTTACAAACTAGGGTATTTCGTAATTTTACAAACCGAGGGTATTTCG
ATAATTTTACAATT
Found at i:52174915 original size:22 final size:22
Alignment explanation
Indices: 52174887--52174950 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
52174877 TAAATACGTT
* *
52174887 TGGCACAAAGCCATAGTCAGGA
1 TGGCACAGAGCCATAATCAGGA
** * *
52174909 TGGCACAGAGCCATTTTTAGGT
1 TGGCACAGAGCCATAATCAGGA
52174931 TGGCACAGAGCCATAATCAG
1 TGGCACAGAGCCATAATCAG
52174951 ATTACGTGGC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (22 bp):
TGGCACAGAGCCATAATCAGGA
Found at i:52175337 original size:27 final size:25
Alignment explanation
Indices: 52175304--52175552 Score: 198
Period size: 27 Copynumber: 9.4 Consensus size: 25
52175294 CAAAATAGTC
*
52175304 ATTTTACCATACAGGGGTATTTCAGTA
1 ATTTTA-CAAACAGGGGTATTTC-GTA
*
52175331 ATTTTAC--ACAAGGGTATTTCAGTA
1 ATTTTACAAACAGGGGTATTTC-GTA
*
52175355 ATTTTACAAACTGGGGGTATTTCGATA
1 ATTTTACAAAC-AGGGGTATTTCG-TA
*** *
52175382 ATTTTACAATTTGGGGTATTTTGGGTA
1 ATTTTACAAACAGGGGTA-TTT-CGTA
* *
52175409 ATTTTACAAACTGGGGTATTTCAATA
1 ATTTTACAAACAGGGGTATTTC-GTA
*
52175435 ATTTTACAAACCGAGGGTATTTCGATA
1 ATTTTACAAACAG-GGGTATTTCG-TA
52175462 ATTTTACAAATCAGGGGTATTTCGATA
1 ATTTTACAAA-CAGGGGTATTTCG-TA
* * * *
52175489 ATTTTATAATTC-GAAGGTATTTTGGTA
1 ATTTTACAA-ACAG-GGGTA-TTTCGTA
52175516 ATTTTACAAACCAGGGGTATTTCGGTA
1 ATTTTACAAA-CAGGGGTATTTC-GTA
52175543 ATTTTACAAA
1 ATTTTACAAA
52175553 TTAGAGTCTT
Statistics
Matches: 184, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
24 23 0.12
26 31 0.17
27 122 0.66
28 8 0.04
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (25 bp):
ATTTTACAAACAGGGGTATTTCGTA
Found at i:52175453 original size:54 final size:54
Alignment explanation
Indices: 52175315--52175553 Score: 265
Period size: 54 Copynumber: 4.5 Consensus size: 54
52175305 TTTTACCATA
* *
52175315 CAGGGGTATTTC-AGTAATTTTAC--A-CAAGGGTATTTCAGTAATTTTACAAAC
1 CAGGGGTATTTCGA-TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAAC
** * * *
52175366 TGGGGGTATTTCGATAATTTTACAATTTG-GGGTATTTTGGGTAATTTTACAAA-
1 CAGGGGTATTTCGATAATTTTACAAATCGAGGGTA-TTTCGGTAATTTTACAAAC
* * * * *
52175419 CTGGGGTATTTCAATAATTTTACAAACCGAGGGTATTTCGATAATTTTACAAAT
1 CAGGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAAC
* * * *
52175473 CAGGGGTATTTCGATAATTTTATAATTCGAAGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAAC
*
52175527 CAGGGGTATTTCGGTAATTTTACAAAT
1 CAGGGGTATTTCGATAATTTTACAAAT
52175554 TAGAGTCTTA
Statistics
Matches: 154, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
51 19 0.12
52 1 0.01
53 44 0.29
54 90 0.58
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (54 bp):
CAGGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAAC
Found at i:52175934 original size:239 final size:238
Alignment explanation
Indices: 52175516--52175998 Score: 770
Period size: 239 Copynumber: 2.0 Consensus size: 238
52175506 TATTTTGGTA
** *
52175516 ATTTTACAAACCAGGGGTATTTCGGTAATTTTACAAATTAGAGTCTTAAAGACCTAACAGAAGGT
1 ATTTTACAAACCAGGGGTATTTCGGTAATTTTACAAACAAGAGTCTTAAAGACCCAACAGAAGGT
* *
52175581 CCACCGTCACCTCAGCAACTTAAGTAACTTAAACAAACATAACGATGCAAGTGGGCCTAAGGCTT
66 CCACCGTCACCTCAGCAACTTAAGTAACCTAAACAAACATAACGATGCAAGTGGACCTAAGGCTT
*
52175646 ATTACTCAGCCCAAGTGGGCCCAAACGCTCGTGTGGCCCATTTAGCCTAAATTTAGATATGGCTA
131 ATTACTCAGCCCAAGTGGGCCCAAACGCTCGTGTGGCCCATTTAGCCTAAATTTAGATACGGCTA
*
52175711 TGTGTACACCATAGCCTAGTTAATTAATAGCCACTTATCATAG
196 TGTGTACACCATAGCCCAGTTAATTAATAGCCACTTATCATAG
*
52175754 ATTTTACAAACTAGGGGTATTTCGGTAATTTTACAAACCAAG-GTCTTAAAGACCCAACAGAAGG
1 ATTTTACAAACCAGGGGTATTTCGGTAATTTTACAAA-CAAGAGTCTTAAAGACCCAACAGAAGG
* * * *
52175818 TCCACCGTCACCTCGAGCGACTTAAGTGACCTAAACAGACATAACGGTGCAAGTGGACCTAAGGC
65 TCCACCGTCACCTC-AGCAACTTAAGTAACCTAAACAAACATAACGATGCAAGTGGACCTAAGGC
* *
52175883 TTATTACTCGGCCCAAGTGGGCCCAGACGCTCGTGTGGCCCATTTAGCCTAAATTTAGATACGGC
129 TTATTACTCAGCCCAAGTGGGCCCAAACGCTCGTGTGGCCCATTTAGCCTAAATTTAGATACGGC
* * * * *
52175948 TATGTGTACACTATAGCCCGGTTCATTAATAGTCACTTATCGTAG
194 TATGTGTACACCATAGCCCAGTTAATTAATAGCCACTTATCATAG
52175993 ATTTTA
1 ATTTTA
52175999 TCTGTGTGGG
Statistics
Matches: 224, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
238 71 0.32
239 153 0.68
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (238 bp):
ATTTTACAAACCAGGGGTATTTCGGTAATTTTACAAACAAGAGTCTTAAAGACCCAACAGAAGGT
CCACCGTCACCTCAGCAACTTAAGTAACCTAAACAAACATAACGATGCAAGTGGACCTAAGGCTT
ATTACTCAGCCCAAGTGGGCCCAAACGCTCGTGTGGCCCATTTAGCCTAAATTTAGATACGGCTA
TGTGTACACCATAGCCCAGTTAATTAATAGCCACTTATCATAG
Found at i:52178580 original size:21 final size:22
Alignment explanation
Indices: 52178540--52178580 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52178530 TTCCAAATAA
* *
52178540 AACATTATATCATTTCTAATTC
1 AACATTATATCAATTATAATTC
52178562 AACATT-TATCAATTATAAT
1 AACATTATATCAATTATAAT
52178581 CGGGCATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (22 bp):
AACATTATATCAATTATAATTC
Found at i:52179831 original size:15 final size:16
Alignment explanation
Indices: 52179804--52179833 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52179794 AGATATTCCA
52179804 ATTTAGTCCCATTTTT
1 ATTTAGTCCCATTTTT
52179820 ATTTAG-CCCATTTT
1 ATTTAGTCCCATTTT
52179834 GGCAATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTAGTCCCATTTTT
Found at i:52180571 original size:42 final size:42
Alignment explanation
Indices: 52180524--52180618 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
52180514 ATGGCCTCTA
* *
52180524 ACACGGGCGTGTCTTTGGCCGTGTGAGGCACACGACCGAGCC
1 ACACGGGCGTGTCTTTGGCCATGTGAGACACACGACCGAGCC
** * * *
52180566 ACACGGATGTGTCTTTGGCCATGTGAGACACACGGCTGAGCT
1 ACACGGGCGTGTCTTTGGCCATGTGAGACACACGACCGAGCC
52180608 ACACGGGCGTG
1 ACACGGGCGTG
52180619 CGTCCCCTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.19, C:0.27, G:0.35, T:0.19
Consensus pattern (42 bp):
ACACGGGCGTGTCTTTGGCCATGTGAGACACACGACCGAGCC
Found at i:52187665 original size:5 final size:5
Alignment explanation
Indices: 52187655--52187697 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
52187645 TTGTGTGTTC
52187655 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
52187698 TCACATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:52189039 original size:43 final size:45
Alignment explanation
Indices: 52188989--52189146 Score: 209
Period size: 45 Copynumber: 3.6 Consensus size: 45
52188979 TGGCGTTTCA
* *
52188989 CCTGCTAGGCTCGAA-GCCCG-ATA-TCATTTCACCGACATTATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCACCGACATTATAG
*
52189032 CCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCACC-AGCATTATAA
1 CCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCACCGA-CATTATAG
* *
52189077 CCTACTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATTATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGACATTATAG
52189122 CCTGCTAGGCTCAAAGGCCCGAATA
1 CCTGCTAGGCTCAAAGGCCCGAATA
52189147 ATACTATGCG
Statistics
Matches: 102, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
43 12 0.12
44 11 0.11
45 78 0.76
46 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGACATTATAG
Found at i:52190009 original size:47 final size:47
Alignment explanation
Indices: 52189957--52190099 Score: 277
Period size: 47 Copynumber: 3.0 Consensus size: 47
52189947 AAAATTTTCT
52189957 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
52190004 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
*
52190051 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
52190098 TT
1 TT
52190100 TAAATTCAAC
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.29
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGGAAATATTAAGGGCAAATTTAACAAGC
Found at i:52196733 original size:45 final size:45
Alignment explanation
Indices: 52196634--52196762 Score: 199
Period size: 45 Copynumber: 2.9 Consensus size: 45
52196624 CGATATCATT
*
52196634 TCACCGGCATTATAGCCAGCTA-GCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATC
* *
52196678 TCACCGGCATTATAACCTGCTAGGCTCAAAGGCCTGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
52196723 TCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
52196763 ATACTGTGCG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 23 0.30
45 54 0.70
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:52197631 original size:47 final size:47
Alignment explanation
Indices: 52197571--52197666 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
52197561 AAAATTTTCT
*
52197571 TTAACTAACTAACTTATCCAGAAATATTAAGGGCAAATTTAACAAGC
1 TTAACTAACTAACTTATCCAGAAATATTAAGAGCAAATTTAACAAGC
* *
52197618 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAACTAACTTATCCAGAAATATTAAGAGCAAATTTAACAAGC
52197665 TT
1 TT
52197667 TAAATTCAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (47 bp):
TTAACTAACTAACTTATCCAGAAATATTAAGAGCAAATTTAACAAGC
Found at i:52201296 original size:43 final size:44
Alignment explanation
Indices: 52201248--52201330 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
52201238 GGAACGTTGA
*
52201248 CTTCGATTTGAAATAT-CATGTAAGACCGTGTCTGGGACACAAG
1 CTTCGATTTGAAATATACATGTAAGACCATGTCTGGGACACAAG
* * *
52201291 CTTCGATTTGAGATTTACGTGTAAGACCATGTCTGGGACA
1 CTTCGATTTGAAATATACATGTAAGACCATGTCTGGGACA
52201331 TCGGCATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 14 0.40
44 21 0.60
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
CTTCGATTTGAAATATACATGTAAGACCATGTCTGGGACACAAG
Found at i:52201414 original size:43 final size:42
Alignment explanation
Indices: 52201250--52201413 Score: 120
Period size: 43 Copynumber: 3.8 Consensus size: 42
52201240 AACGTTGACT
* ** * *
52201250 TCGATTTGAAATATCATGTAAGACCGTGTCTGGGACACAAGCT
1 TCGATTTGAATTA-CATGTAAGACCACGTCTGGGACACAGGCA
* *
52201293 TCGATTTGAGATTTACGTGTAAGACCATGTCTGGGACATC-GGCA
1 TCGATTTGA-A-TTACATGTAAGACCACGTCTGGGACA-CAGGCA
*** * *
52201337 TC-ATATCTG-ATTTTGTGTAAGACC-CTGTCTGGGATAGAGGCA
1 TCGAT-T-TGAATTACATGTAAGACCAC-GTCTGGGACACAGGCA
52201379 TCGATATTGAATTACATGTAAGACCACGTCTGGGA
1 TCGAT-TTGAATTACATGTAAGACCACGTCTGGGA
52201414 TGTTGGCATT
Statistics
Matches: 98, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 29 0.30
43 36 0.37
44 28 0.29
45 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
TCGATTTGAATTACATGTAAGACCACGTCTGGGACACAGGCA
Found at i:52204509 original size:43 final size:42
Alignment explanation
Indices: 52204405--52204524 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 42
52204395 AGGGTCACTA
* *
52204405 AGATTACGTGTAAGACCATACCTGGGATATGGCATCGAAATG
1 AGATTACGTGTAAGACCATACCTGCGATATGGCATCGAAACG
* *
52204447 AGACTT-CGTGTAA-AGCCATAGCT-CGACTATTGGCATCGATACG
1 AGA-TTACGTGTAAGA-CCATACCTGCGA-TA-TGGCATCGAAACG
* *
52204490 AGATTACATGTAAGACCATATCTTG-GATATGGCAT
1 AGATTACGTGTAAGACCATA-CCTGCGATATGGCAT
52204525 TGGTATGTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
41 3 0.05
42 27 0.43
43 29 0.46
44 4 0.06
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATACCTGCGATATGGCATCGAAACG
Found at i:52220934 original size:40 final size:40
Alignment explanation
Indices: 52220879--52221089 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
52220869 ATTTGAATGA
*
52220879 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
52220919 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
52220959 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
52220999 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
52221039 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
52221079 TATCC-GGCTAA
1 TATCCGGGCTAA
52221090 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:52229106 original size:40 final size:40
Alignment explanation
Indices: 52229051--52229261 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
52229041 ATTTGAATGA
*
52229051 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
52229091 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
52229131 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
52229171 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
52229211 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
52229251 TATCC-GGCTAA
1 TATCCGGGCTAA
52229262 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:52241618 original size:43 final size:43
Alignment explanation
Indices: 52241461--52241617 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 43
52241451 TGTGTTATCG
* *
52241461 TGTAAGACCACGTATGGGACGTTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTACA
* * * * * *
52241505 TGTAAGACCATGCCTGGGACATTGGCATCG-TATTTAATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
** * *
52241547 TGTAAGACCTTGTCTGGGATAG-TGGCATTGATATTTGATTACA
1 TGTAAGACCACGTCTGGGA-CGTTGGCATCGATATTTGATTACA
52241590 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
52241618 TATATGAGCT
Statistics
Matches: 90, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
42 29 0.32
43 35 0.39
44 26 0.29
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTACA
Found at i:52248043 original size:27 final size:27
Alignment explanation
Indices: 52248009--52248212 Score: 234
Period size: 27 Copynumber: 7.6 Consensus size: 27
52247999 TAAATTGTAC
*
52248009 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
52248036 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * **
52248063 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
*
52248089 ATGCACTAAGTGTGCGAATTGACCATGT
1 A-GCACTAAGTGTGCGAATTGACTATGT
*
52248117 GGCACTAAGTGTGCGAGATTGA-TCATGT
1 AGCACTAAGTGTGCGA-ATTGACT-ATGT
* *
52248145 AGCACTAAGTGTGCG-ATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
52248171 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
52248198 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52248213 GACTCAATAT
Statistics
Matches: 154, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
26 23 0.15
27 108 0.70
28 23 0.15
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:52251135 original size:24 final size:25
Alignment explanation
Indices: 52251108--52251164 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
52251098 ATGAGTGATA
*
52251108 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
52251132 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
52251156 AAAAAAGAA
1 AAAAAAGAA
52251165 TTTGTTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 13 0.46
24 7 0.25
25 8 0.29
ACGTcount: A:0.63, C:0.04, G:0.23, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:52264245 original size:7 final size:7
Alignment explanation
Indices: 52264235--52264273 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
52264225 CAAAAATAAA
52264235 AATCTTC
1 AATCTTC
52264242 AATCTTC
1 AATCTTC
*
52264249 GATCTTC
1 AATCTTC
52264256 AATCTTC
1 AATCTTC
52264263 AATCTTC
1 AATCTTC
52264270 AATC
1 AATC
52264274 AAATACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (7 bp):
AATCTTC
Found at i:52267462 original size:29 final size:29
Alignment explanation
Indices: 52267424--52267487 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
52267414 CCAAATTAAA
52267424 CACCCCACTAAACCGA-CTACTAACTCCAT
1 CACCCCACTAAACC-ATCTACTAACTCCAT
* *
52267453 CACCCTACTAAACCATCTACTACCTCCAT
1 CACCCCACTAAACCATCTACTAACTCCAT
52267482 CACCCC
1 CACCCC
52267488 CACACCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.31, C:0.48, G:0.02, T:0.19
Consensus pattern (29 bp):
CACCCCACTAAACCATCTACTAACTCCAT
Found at i:52267494 original size:37 final size:37
Alignment explanation
Indices: 52267453--52267524 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
52267443 CTAACTCCAT
*
52267453 CACCCTACTAAACCATCTACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
52267490 CACCCTACTAAACCATCCACTACCTCCATCACCCC
1 CACCCTACTAAACCATCCACTACCTCCATCACCCC
52267525 TACTAACTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (37 bp):
CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
Found at i:52267948 original size:11 final size:11
Alignment explanation
Indices: 52267928--52267961 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
52267918 ATGTTTCATA
52267928 TTATTATATTAT
1 TTATT-TATTAT
52267940 TTATTTATTAT
1 TTATTTATTAT
*
52267951 ATATTTATTAT
1 TTATTTATTAT
52267962 GTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:52267949 original size:16 final size:15
Alignment explanation
Indices: 52267928--52267959 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52267918 ATGTTTCATA
52267928 TTATTATATTATTTAT
1 TTATTATA-TATTTAT
52267944 TTATTATATATTTAT
1 TTATTATATATTTAT
52267959 T
1 T
52267960 ATGTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATATATTTAT
Found at i:52270553 original size:21 final size:23
Alignment explanation
Indices: 52270516--52270561 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
52270506 TTTATTAATG
52270516 TTTTATAATATTATTTTTAAAAA
1 TTTTATAATATTATTTTTAAAAA
*
52270539 TTTTA-AATA-TATTTTTTAAAA
1 TTTTATAATATTATTTTTAAAAA
52270560 TT
1 TT
52270562 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 4 0.18
23 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATAATATTATTTTTAAAAA
Found at i:52270563 original size:34 final size:34
Alignment explanation
Indices: 52270516--52270631 Score: 122
Period size: 34 Copynumber: 3.6 Consensus size: 34
52270506 TTTATTAATG
* *
52270516 TTTTATAATATTATTTTTAAAAATTTTAAATATA
1 TTTTTTAAAATTATTTTTAAAAATTTTAAATATA
*
52270550 TTTTTTAAAATTATTTTTTAAAA-TTTAAATATTA
1 TTTTTTAAAATTATTTTTAAAAATTTTAAATA-TA
52270584 TTTTTT--AA--A-TTTT--AAATTTTAAATATA
1 TTTTTTAAAATTATTTTTAAAAATTTTAAATATA
* *
52270611 GTTTTTGAAATTATTTTTAAA
1 TTTTTTAAAATTATTTTTAAA
52270632 TATATTCAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
27 10 0.14
28 8 0.12
29 6 0.09
30 1 0.01
31 1 0.01
32 6 0.09
33 8 0.12
34 29 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TTTTTTAAAATTATTTTTAAAAATTTTAAATATA
Found at i:52270585 original size:21 final size:21
Alignment explanation
Indices: 52270553--52270600 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
52270543 AAATATATTT
52270553 TTTAAA-ATTATTTTTTAAAA
1 TTTAAATATTATTTTTTAAAA
*
52270573 TTTAAATATTATTTTTTAAAT
1 TTTAAATATTATTTTTTAAAA
52270594 TTTAAAT
1 TTTAAAT
52270601 TTTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAAATATTATTTTTTAAAA
Found at i:52270592 original size:14 final size:14
Alignment explanation
Indices: 52270539--52270634 Score: 63
Period size: 13 Copynumber: 7.7 Consensus size: 14
52270529 TTTTTAAAAA
52270539 TTTTAAATA-TATT
1 TTTTAAATATTATT
52270552 TTTTAAA-ATTATT
1 TTTTAAATATTATT
52270565 TTTT-AA-A--A--
1 TTTTAAATATTATT
52270573 -TTTAAATATTATT
1 TTTTAAATATTATT
* **
52270586 TTTTAAATTTTAAA
1 TTTTAAATATTATT
*
52270600 TTTTAAATA-TAGT
1 TTTTAAATATTATT
*
52270613 TTTTGAA-ATTA-T
1 TTTTAAATATTATT
52270625 TTTTAAATAT
1 TTTTAAATAT
52270635 ATTCAAACTT
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
7 3 0.05
8 2 0.03
9 1 0.02
10 1 0.02
11 1 0.02
12 12 0.18
13 27 0.42
14 18 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTAAATATTATT
Found at i:52270596 original size:7 final size:7
Alignment explanation
Indices: 52270565--52270607 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
52270555 TAAAATTATT
52270565 TTTTAAA
1 TTTTAAA
*
52270572 ATTTAAA
1 TTTTAAA
* **
52270579 TATTATT
1 TTTTAAA
52270586 TTTTAAA
1 TTTTAAA
52270593 TTTTAAA
1 TTTTAAA
52270600 TTTTAAA
1 TTTTAAA
52270607 T
1 T
52270608 ATAGTTTTTG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTAAA
Found at i:52270597 original size:28 final size:28
Alignment explanation
Indices: 52270565--52270622 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
52270555 TAAAATTATT
*
52270565 TTTTAAAATTTAAATATTA-TTTTTTAAA
1 TTTTAAAATTTAAATA-TAGTTTTTGAAA
*
52270593 TTTTAAATTTTAAATATAGTTTTTGAAA
1 TTTTAAAATTTAAATATAGTTTTTGAAA
52270621 TT
1 TT
52270623 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTAAAATTTAAATATAGTTTTTGAAA
Found at i:52270627 original size:12 final size:12
Alignment explanation
Indices: 52270516--52270637 Score: 64
Period size: 14 Copynumber: 10.1 Consensus size: 12
52270506 TTTATTAATG
52270516 TTTTATAATATTAT
1 TTTTA-AATA-TAT
52270530 TTTTAAA-A-A-
1 TTTTAAATATAT
52270539 TTTTAAATATATT
1 TTTTAAATATA-T
52270552 TTTTAAA-ATTAT
1 TTTTAAATA-TAT
*
52270564 TTTTTAA-A-A-
1 TTTTAAATATAT
52270573 -TTTAAATATTATT
1 TTTTAAATA-TA-T
* *
52270586 TTTTAAATTTTAAA
1 TTTTAAA-TAT-AT
52270600 TTTTAAATATAGT
1 TTTTAAATATA-T
52270613 TTTTGAAAT-TAT
1 TTTT-AAATATAT
52270625 TTTTAAATATAT
1 TTTTAAATATAT
52270637 T
1 T
52270638 CAAACTTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
8 5 0.06
9 8 0.09
10 3 0.03
11 6 0.07
12 20 0.23
13 19 0.22
14 23 0.27
15 2 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTTAAATATAT
Found at i:52270836 original size:36 final size:36
Alignment explanation
Indices: 52270789--52270859 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
52270779 TATTTTATTT
52270789 TGGCTCCACCTCTTGATTCTCTAGCATATATAGAAA
1 TGGCTCCACCTCTTGATTCTCTAGCATATATAGAAA
*
52270825 TGGCTCCACCTCTTGATTCTCTAGTATATATAGAA
1 TGGCTCCACCTCTTGATTCTCTAGCATATATAGAA
52270860 TGGTGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (36 bp):
TGGCTCCACCTCTTGATTCTCTAGCATATATAGAAA
Found at i:52273593 original size:18 final size:19
Alignment explanation
Indices: 52273561--52273605 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
52273551 AAAGTCATAG
52273561 TTTTTTTAACAAATAAAT-
1 TTTTTTTAACAAATAAATC
*
52273579 TATTTTTTAA-TAATAAATC
1 T-TTTTTTAACAAATAAATC
52273598 TTTTTTTA
1 TTTTTTTA
52273606 TATTTTTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTTAACAAATAAATC
Found at i:52273936 original size:6 final size:6
Alignment explanation
Indices: 52273872--52273920 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
52273862 ATTATAAAAT
* *
52273872 AAATTA AAATAGA AAA-AA GAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
52273920 A
1 A
52273921 GGACAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 3 0.08
6 31 0.82
7 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:52273955 original size:23 final size:21
Alignment explanation
Indices: 52273925--52273974 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
52273915 AATAAAGGAC
*
52273925 AAAAAAATAAAATATTATTTTTA
1 AAAAAAATAAAATA-TA-ATTTA
*
52273948 AAAAAAATTAAATATAATTTA
1 AAAAAAATAAAATATAATTTA
52273969 AAAAAA
1 AAAAAA
52273975 TGTTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAAATAAAATATAATTTA
Found at i:52274017 original size:15 final size:15
Alignment explanation
Indices: 52273997--52274054 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
52273987 TTTAAAAATA
52273997 ATTTAAAAATTTTAT
1 ATTTAAAAATTTTAT
*
52274012 ATTTAAAAA-TTTGT
1 ATTTAAAAATTTTAT
* *
52274026 ATTTAAAAAATTTAA
1 ATTTAAAAATTTTAT
*
52274041 ATTTAAAATTTTTA
1 ATTTAAAAATTTTA
52274055 AAAATAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 13 0.35
15 24 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTAAAAATTTTAT
Found at i:52274057 original size:22 final size:23
Alignment explanation
Indices: 52274032--52274101 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
52274022 TTGTATTTAA
* *
52274032 AAAATTTAA-ATTTAAAATTTTT
1 AAAATATAATATTTAAAAATTTT
*
52274054 AAAA-ATAATTTTTAAAAATTTT
1 AAAATATAATATTTAAAAATTTT
* *
52274076 AAAATATACAT-TTTAAATATTAT
1 AAAATATA-ATATTTAAAAATTTT
52274099 AAA
1 AAA
52274102 CCAAATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
22 19 0.47
23 16 0.40
24 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATAATATTTAAAAATTTT
Found at i:52274063 original size:13 final size:13
Alignment explanation
Indices: 52274047--52274072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52274037 TTAAATTTAA
52274047 AATTTTTAAAAAT
1 AATTTTTAAAAAT
52274060 AATTTTTAAAAAT
1 AATTTTTAAAAAT
52274073 TTTAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:52274071 original size:23 final size:24
Alignment explanation
Indices: 52274042--52274089 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
52274032 AAAATTTAAA
*
52274042 TTTAAAATTTTTAAAA-ATA-ATT
1 TTTAAAAATTTTAAAATATACATT
52274064 TTTAAAAATTTTAAAATATACATT
1 TTTAAAAATTTTAAAATATACATT
52274088 TT
1 TT
52274090 AAATATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 3 0.13
24 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAAAATTTTAAAATATACATT
Found at i:52274215 original size:22 final size:21
Alignment explanation
Indices: 52274181--52274266 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 21
52274171 ATTATGAATG
52274181 ATATTT-AAATTTTAAATATAT
1 ATATTTAAAATTTTAAA-ATAT
*
52274202 ATATTTAAAATTTTAAAAAAT
1 ATATTTAAAATTTTAAAATAT
*
52274223 AATATTATAAAAAATTTAAAATAT
1 -ATATT-T-AAAATTTTAAAATAT
*
52274247 ACATTTAAAATATTATAAAA
1 ATATTTAAAAT-TT-TAAAA
52274267 CCAATAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
21 13 0.24
22 18 0.33
23 10 0.19
24 13 0.24
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTTAAAATTTTAAAATAT
Found at i:52274293 original size:12 final size:11
Alignment explanation
Indices: 52274263--52274311 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
52274253 AAAATATTAT
*
52274263 AAAACCAATAA
1 AAAACAAATAA
*
52274274 TAAACAAATAA
1 AAAACAAATAA
52274285 AAAAGCAAATAA
1 AAAA-CAAATAA
**
52274297 AGGACAAATAA
1 AAAACAAATAA
52274308 AAAA
1 AAAA
52274312 ACTAAAATAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAACAAATAA
Found at i:52274318 original size:32 final size:34
Alignment explanation
Indices: 52274272--52274348 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
52274262 TAAAACCAAT
*
52274272 AATAAACAAATAAAAAAGCAAATAAAG-G-AC-A
1 AATAAAAAAATAAAAAAGCAAATAAAGAGAACAA
* *
52274303 AATAAAAAAACTAAAATAGTAAATAAAGAAGAACAA
1 AATAAAAAAA-TAAAAAAGCAAATAAAG-AGAACAA
52274339 AATAAAAAAA
1 AATAAAAAAA
52274349 AACGAAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 9 0.24
32 15 0.39
34 1 0.03
35 2 0.05
36 11 0.29
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (34 bp):
AATAAAAAAATAAAAAAGCAAATAAAGAGAACAA
Found at i:52274326 original size:21 final size:22
Alignment explanation
Indices: 52274302--52274342 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52274292 AATAAAGGAC
52274302 AAATAAA-AA-AACTAAAATAGT
1 AAATAAAGAAGAAC-AAAATAGT
52274323 AAATAAAGAAGAACAAAATA
1 AAATAAAGAAGAACAAAATA
52274343 AAAAAAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATAAAGAAGAACAAAATAGT
Found at i:52277251 original size:101 final size:101
Alignment explanation
Indices: 52277074--52277425 Score: 395
Period size: 101 Copynumber: 3.5 Consensus size: 101
52277064 AATTGATGGA
* *
52277074 TAAGACCTTGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTATGACATTTTAG
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTAGGCTATGACATTTTAG
* *
52277139 TGAAAAGACCATAATTGGGTTATGGCACCGTGAGCG
66 TGAAAAGACCATAACTGGGTTACGGCACCGTGAGCG
*
52277175 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTAGGCTATGGCATTTTAG
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTAGGCTATGACATTTTAG
*
52277240 TGAAAATACCATAACTGGGTTACGGCACCGTGAGCG
66 TGAAAAGACCATAACTGGGTTACGGCACCGTGAGCG
* * * * * *
52277276 TAAGACCATGATTGGACCATGGTTGTATATATATAAGTGTGTAAGACCATAACTGGGCTATGACA
1 TAAGACCATGGTTGGACCAT-G--GCA-ATATTTAA--ATGTAAGACCATAGCTAGGCTATGACA
* * * * * *** *
52277341 TCTGA-AGATAAGACCATAACTGGGTTATGGCACTACGAGTG
60 TTTTAGTGAAAAGACCATAACTGGGTTACGGCACCGTGAGCG
* * * **
52277382 TAAGACCATGGTAGGGCCACGGCAATA--TATGTGTAAGACCATAG
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAG
52277426 TTGGACTATG
Statistics
Matches: 215, Mismatches: 30, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
98 13 0.06
100 2 0.01
101 114 0.53
102 4 0.02
103 2 0.01
104 2 0.01
105 8 0.04
106 44 0.20
107 26 0.12
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTAGGCTATGACATTTTAG
TGAAAAGACCATAACTGGGTTACGGCACCGTGAGCG
Found at i:52284007 original size:12 final size:12
Alignment explanation
Indices: 52283990--52284014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52283980 TTGTAAATTA
52283990 AACAAATAAAAT
1 AACAAATAAAAT
52284002 AACAAATAAAAT
1 AACAAATAAAAT
52284014 A
1 A
52284015 GTTTCTAGCA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AACAAATAAAAT
Found at i:52286358 original size:24 final size:24
Alignment explanation
Indices: 52286300--52286349 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
52286290 GAATAAAGAA
52286300 TAATGATACATGAGTCAAAATATT
1 TAATGATACATGAGTCAAAATATT
*
52286324 TAATGATACATGAGTCAAGATATT
1 TAATGATACATGAGTCAAAATATT
52286348 TA
1 TA
52286350 GTGTAACATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (24 bp):
TAATGATACATGAGTCAAAATATT
Found at i:52291759 original size:21 final size:23
Alignment explanation
Indices: 52291724--52291766 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
52291714 CCAAAACAGT
*
52291724 ATAAATGATAGGAAAAC-TAAAG
1 ATAAATGACAGGAAAACATAAAG
52291746 ATAAAT-ACAGGAAAACATAAA
1 ATAAATGACAGGAAAACATAAA
52291767 AAACAGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (23 bp):
ATAAATGACAGGAAAACATAAAG
Found at i:52294609 original size:23 final size:21
Alignment explanation
Indices: 52294578--52294632 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
52294568 AGAGAGAATC
52294578 AAAAATAAAGAGTAA-ACAAAAG
1 AAAAATAAA-AG-AACACAAAAG
*
52294600 AAAAATTAAAAGAACATAAAAG
1 AAAAA-TAAAAGAACACAAAAG
52294622 AAAAAATAAAA
1 -AAAAATAAAA
52294633 TTGCTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
22 18 0.62
23 9 0.31
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAGAACACAAAAG
Found at i:52296803 original size:46 final size:46
Alignment explanation
Indices: 52296750--52296925 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
52296740 TATTTGGGCA
** *
52296750 TCCGAACTCGTTGAGTTGAGTTTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
52296796 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--A--CG
* * *
52296843 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
52296889 CCCGAGCTCGTTGAGTTGAGCCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52296926 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 2 0.02
46 57 0.55
47 25 0.24
48 2 0.02
50 5 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:52296899 original size:93 final size:93
Alignment explanation
Indices: 52296746--52296916 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
52296736 GGGATATTTG
* * * *
52296746 GGCATCCGAACTCGTTGAGTTGAGTTTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
*
52296811 TTGAGTCCGAGTTTGTGAGATGTAACTA
66 TTGAGCCCGAGTTTGTGAGATGTAACTA
* *
52296839 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
52296904 TTGAGCCCGAGTT
66 TTGAGCCCGAGTT
52296917 CACTTATGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGCCCGAGTTTGTGAGATGTAACTA
Found at i:52298537 original size:126 final size:125
Alignment explanation
Indices: 52298300--52298577 Score: 352
Period size: 126 Copynumber: 2.2 Consensus size: 125
52298290 TAAATATACA
* * * *
52298300 AAAAAAGCTTCCAACTGGATGC--TTTTTTATTACAATTGATTTTGAAAAATAATTTTGAGAAGA
1 AAAAAAGCTCCCAGCTGGAAGCTTTTTTTTATTACAATTGATTCTGAAAAATAATTTTGAGAAGA
52298363 TGGTTCTAAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACT-
66 T-GTTCTAAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACTG
* * *
52298423 AAAAAAGGCTCCTAGTTGGAAGCTTTTTTTTTTGTACAATTGATTCTGAAAAAATAATTTTGAGA
1 AAAAAA-GCTCCCAGCTGGAAGCTTTTTTTTAT-TACAATTGATTCTG-AAAAATAATTTTGAGA
* * * *
52298488 TAG-T-TT-TGAAAAAATAGGTTAAAAAACGCTTCAATCAGGATGCACTGTCAGCAAAAGTACTG
63 -AGATGTTCT-AAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACTG
*
52298550 AAAAAAGTTCCCAGCTGGAAGCTTTTTT
1 AAAAAAGCTCCCAGCTGGAAGCTTTTTT
52298578 CAGTAGTGCT
Statistics
Matches: 133, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
123 6 0.05
124 11 0.08
125 1 0.01
126 77 0.58
127 19 0.14
128 17 0.13
129 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (125 bp):
AAAAAAGCTCCCAGCTGGAAGCTTTTTTTTATTACAATTGATTCTGAAAAATAATTTTGAGAAGA
TGTTCTAAAAAATAGGTTAAAAAACGCTTCAAGCAAGATACAATGTCAGCAAAAGTACTG
Found at i:52301788 original size:59 final size:59
Alignment explanation
Indices: 52301685--52301851 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 59
52301675 TAGTTCCTAA
* ****** * * *
52301685 TTTATTAAATGAAACTATATAAAAATAATTTGTATTGTCGTATTCAAAAGAACTTCTAT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAACAACATATAT
* * *
52301744 TTTATTAAATGACACAATATAAAAATAATTTGTACAAAAATATTCAGAACAACATATTT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAACAACATATAT
** * * *
52301803 TTTATTAAATGAAACAATATAAAAGCAGTTTGTACAAATATATTAAAAA
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAA
52301852 AATCAATGCA
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 88 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (59 bp):
TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAACAACATATAT
Found at i:52302142 original size:21 final size:21
Alignment explanation
Indices: 52302099--52302151 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
52302089 TACAAGGCAC
**
52302099 ACATGCCCGTGTGGTCAAGGG
1 ACATGCCCGTGTGACCAAGGG
52302120 ACATGCCCGTGTGACCATA-GG
1 ACATGCCCGTGTGACCA-AGGG
*
52302141 ACAAGCCCGTG
1 ACATGCCCGTG
52302152 CTACAGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (21 bp):
ACATGCCCGTGTGACCAAGGG
Found at i:52302989 original size:26 final size:26
Alignment explanation
Indices: 52302960--52303021 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 26
52302950 ATTTCATACT
52302960 TAAAACATTTATATAATTCACACAAA
1 TAAAACATTTATATAATTCACACAAA
52302986 TAAAAACATTTATATAATTCACACAAA
1 T-AAAACATTTATATAATTCACACAAA
*
52303013 TACAACATT
1 TAAAACATT
52303022 GAATTCAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAACATTTATATAATTCACACAAA
Found at i:52302992 original size:27 final size:27
Alignment explanation
Indices: 52302961--52303014 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
52302951 TTTCATACTT
52302961 AAAACATTTATATAATTCACACAAATA
1 AAAACATTTATATAATTCACACAAATA
52302988 AAAACATTTATATAATTCACACAAATA
1 AAAACATTTATATAATTCACACAAATA
52303015 CAACATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAACATTTATATAATTCACACAAATA
Found at i:52307304 original size:46 final size:44
Alignment explanation
Indices: 52307200--52307307 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52307190 TGTCTTTGAC
** * * *
52307200 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52307244 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52307290 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52307308 TTTTTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52311922 original size:17 final size:17
Alignment explanation
Indices: 52311900--52311932 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52311890 GAAATATATA
52311900 AGGGTTAGGATACACAT
1 AGGGTTAGGATACACAT
52311917 AGGGTTAGGATACACA
1 AGGGTTAGGATACACA
52311933 CCTGGCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (17 bp):
AGGGTTAGGATACACAT
Found at i:52320350 original size:20 final size:20
Alignment explanation
Indices: 52320311--52320351 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52320301 GACCATTTGC
* *
52320311 TAATTTCAAATAACACATAT
1 TAATTTCAAATAAAAAATAT
*
52320331 TAATTTCTAATAAAAAATAT
1 TAATTTCAAATAAAAAATAT
52320351 T
1 T
52320352 TTGCGAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTCAAATAAAAAATAT
Found at i:52322326 original size:3 final size:3
Alignment explanation
Indices: 52322318--52322366 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
52322308 ATGGTTTGAA
* * *
52322318 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52322366 A
1 A
52322367 TTAACATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52322542 original size:3 final size:3
Alignment explanation
Indices: 52322529--52322630 Score: 100
Period size: 3 Copynumber: 34.3 Consensus size: 3
52322519 TTAATTAGTT
*
52322529 TAA TAA T-A TAA TAA TAA TAA -AA TAAA GAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * * * * * *
52322573 TAA TAG TAA TAG TAA TAG TAA TAG TAA TAG TAG TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
52322621 TAA TAT TAA T
1 TAA TAA TAA T
52322631 TAATTTAATA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
2 4 0.05
3 76 0.93
4 2 0.02
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52324141 original size:52 final size:52
Alignment explanation
Indices: 52324037--52324142 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
52324027 GGTGTAGGAT
* * * * * *
52324037 TTGTGGCTTTAATCTGCTCTACTGCAACGTCAGGGAGATAAGATTGGTTATC
1 TTGTAGCTTTAATCTGCTCTACTACAACGTCAGGGAAATAAAATTCGCTATC
* * *
52324089 TTGTAGCTTTAATCTGTTCTACTATAACTTCAGGGAAATAAAATTCGCTATC
1 TTGTAGCTTTAATCTGCTCTACTACAACGTCAGGGAAATAAAATTCGCTATC
52324141 TT
1 TT
52324143 TAATCTGCTC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (52 bp):
TTGTAGCTTTAATCTGCTCTACTACAACGTCAGGGAAATAAAATTCGCTATC
Found at i:52324257 original size:94 final size:94
Alignment explanation
Indices: 52324140--52324367 Score: 237
Period size: 94 Copynumber: 2.4 Consensus size: 94
52324130 AATTCGCTAT
* ** * ** * *
52324140 CTTTAATCTGCTCCACTGTAACTTCAAGAAGATAAGATTTACCATGGTAAATTTGATCCGACCTA
1 CTTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTACCATAATAAATTTAATCCGACCCA
* *
52324205 CTGTAACTTC-AGAGGTAT-AGAAATTGTGA
66 CTGCAACTTCAAG-GGTATGAG-AATTGTAA
* * *** * *
52324234 CTTTAATCTACTCCATTACAACTTCAAGGAGATGAGATTCGTCATAATAACTTTAATCCGTCCCA
1 CTTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTACCATAATAAATTTAATCCGACCCA
*
52324299 CTGCAACTTCAAGGGTATGAGATTTGTAA
66 CTGCAACTTCAAGGGTATGAGAATTGTAA
*
52324328 CTTCAATCTACTCCACTACAACTTC-AGTGAGATAAGATTT
1 CTTTAATCTACTCCACTACAACTTCAAG-GAGATAAGATTT
52324368 GGTATTTTTA
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
93 2 0.02
94 103 0.94
95 4 0.04
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (94 bp):
CTTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTACCATAATAAATTTAATCCGACCCA
CTGCAACTTCAAGGGTATGAGAATTGTAA
Found at i:52324486 original size:133 final size:133
Alignment explanation
Indices: 52324347--52324590 Score: 326
Period size: 133 Copynumber: 1.8 Consensus size: 133
52324337 ACTCCACTAC
* * * *
52324347 AACTTCAGTGAGATAAGATTTGGTATTTTTAATCTACTCCACTGCGACTTCAGGGAGATAAGACT
1 AACTTCAGAGAGATAAGATTTGCTATTTTTAATCTACTCCACTGCAACTCCAGGGAGATAAGACT
* * * * *
52324412 TGTGACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTTTAGCTTTAATCTGCTCTAC
66 TATGACTTCAACCTACTCCACTACAACTTCAAGGAGATAAGATTTTTAGCTTTAATCTGCTCTAC
52324477 AGT
131 AGT
* * * ** *
52324480 AACTTCAGAGAGATAAGATTTTCTATTTTTAGTCTGCTCCACTGCAACTCCTTGGAGATAAGATT
1 AACTTCAGAGAGATAAGATTTGCTATTTTTAATCTACTCCACTGCAACTCCAGGGAGATAAGACT
* * *
52324545 TATGGCTTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTT
66 TATGACTTCAACCTACTCCACTACAACTTCAAGGAGATAAGATTTT
52324591 CCATGATAAC
Statistics
Matches: 93, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
133 93 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (133 bp):
AACTTCAGAGAGATAAGATTTGCTATTTTTAATCTACTCCACTGCAACTCCAGGGAGATAAGACT
TATGACTTCAACCTACTCCACTACAACTTCAAGGAGATAAGATTTTTAGCTTTAATCTGCTCTAC
AGT
Found at i:52324517 original size:89 final size:89
Alignment explanation
Indices: 52324338--52324591 Score: 228
Period size: 89 Copynumber: 2.9 Consensus size: 89
52324328 CTTCAATCTA
* * * * ** * * *
52324338 CTCCACTACAACTTCAGTGAGATAAGATTTGGTATTTTTAATCTACTCCACTGCGACTTCAGGGA
1 CTCCACTGCAACTCCAGGGAGATAAGATTT-ATAGCTTTAATCTACTCCACTACAACTTCAAGGA
* * * * **
52324403 GATAAGACTTGT-GA-CTTCAACCTG
65 GATAAGA-TTTTCTATTTTTAGTCTG
* * * * * *
52324427 CTCCACTGCAACTTCAGGGAGATAAGGTTTTTAGCTTTAATCTGCTCTAC-AGTAACTTC-AGAG
1 CTCCACTGCAACTCCAGGGAGATAAGATTTATAGCTTTAATCTACTCCACTA-CAACTTCAAG-G
52324490 AGATAAGATTTTCTATTTTTAGTCTG
64 AGATAAGATTTTCTATTTTTAGTCTG
** *
52324516 CTCCACTGCAACTCCTTGGAGATAAGATTTATGGCTTTAATCTACTCCACTACAACTTCAAGGAG
1 CTCCACTGCAACTCCAGGGAGATAAGATTTATAGCTTTAATCTACTCCACTACAACTTCAAGGAG
52324581 ATAAGATTTTC
66 ATAAGATTTTC
52324592 CATGATAACT
Statistics
Matches: 132, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
87 4 0.03
88 30 0.23
89 95 0.72
90 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (89 bp):
CTCCACTGCAACTCCAGGGAGATAAGATTTATAGCTTTAATCTACTCCACTACAACTTCAAGGAG
ATAAGATTTTCTATTTTTAGTCTG
Found at i:52324652 original size:94 final size:94
Alignment explanation
Indices: 52324538--52324737 Score: 249
Period size: 94 Copynumber: 2.1 Consensus size: 94
52324528 TCCTTGGAGA
* *
52324538 TAAGATTTATGGCTTTAATCTACTCCACTACAACT-TCAAGGAGATAAGATTTTCCATGATAACT
1 TAAGATTTATGGCTTCAATCTACTCCACTACAACTCT-AAGGAGATAAGATTTGCCATGATAACT
* **
52324602 TCGATCTGTCCCACTGCAATTTTAGGGGTG
65 TCAATCCATCCCACTGCAATTTTAGGGGTG
* * * * *
52324632 TAAGATTTGTGGCTTCAATCTGCTCCACTGCAACTCTAGGGAGATAAGATTTGCCATGATAGCTT
1 TAAGATTTATGGCTTCAATCTACTCCACTACAACTCTAAGGAGATAAGATTTGCCATGATAACTT
* * *
52324697 CAATCCATCCCACTGTAATTTCAAGGGTG
66 CAATCCATCCCACTGCAATTTTAGGGGTG
* *
52324726 CAGGATTTATGG
1 TAAGATTTATGG
52324738 TTTTTTTGAT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 88 0.99
95 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (94 bp):
TAAGATTTATGGCTTCAATCTACTCCACTACAACTCTAAGGAGATAAGATTTGCCATGATAACTT
CAATCCATCCCACTGCAATTTTAGGGGTG
Found at i:52324680 original size:44 final size:44
Alignment explanation
Indices: 52324296--52324684 Score: 264
Period size: 44 Copynumber: 8.7 Consensus size: 44
52324286 TTAATCCGTC
* * *
52324296 CCACTGCAACTTCAAGGG-TATGAGATTTGTAACTTCAATCTACT
1 CCACTGCAACTTC-AGGGAGATAAGATTTGTAACTTCAATCTGCT
* * ** * *
52324340 CCACTACAACTTCAGTGAGATAAGATTTGGTATTTTTAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTT-GTAACTTCAATCTGCT
* * * *
52324385 CCACTGCGACTTCAGGGAGATAAGACTTGTGACTTCAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * * *
52324429 CCACTGCAACTTCAGGGAGATAAGGTTTTTAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * * * * ** * *
52324473 CTACAGTAACTTCAGAGAGATAAGATTTTCTATTTTTAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTCAATCTGCT
* ** * ** * *
52324518 CCACTGCAACTCCTTGGAGATAAGATTTATGGCTTTAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * *
52324562 CCACTACAACTTCAAGGAGATAAGATTTTCCATGATAACTTCGATCTG-T
1 CCACTGCAACTTCAGGGAGATAAGA--TT---TG-TAACTTCAATCTGCT
* * * **
52324611 CCCACTGCAATTTTAGGG-GTGTAAGATTTGTGGCTTCAATCTGCT
1 -CCACTGCAACTTCAGGGAG-ATAAGATTTGTAACTTCAATCTGCT
52324656 CCACTGCAAC-TCTAGGGAGATAAGATTTG
1 CCACTGCAACTTC-AGGGAGATAAGATTTG
52324685 CCATGATAGC
Statistics
Matches: 263, Mismatches: 68, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
43 4 0.02
44 152 0.58
45 74 0.28
46 2 0.01
48 2 0.01
49 3 0.01
50 26 0.10
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
Found at i:52328027 original size:247 final size:246
Alignment explanation
Indices: 52327585--52328078 Score: 835
Period size: 247 Copynumber: 2.0 Consensus size: 246
52327575 ATCTTGAAAG
52327585 GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
1 GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
* * * *
52327650 TATATATGCTTAGGTTATTTACTTCATTTTCCTTATTCTTTGGGTTGATCTTTTGATGCTTTCTC
66 TATATATGCTCAGGTTATTTACTTCATTTTCCTTATTCTTCGGGTTGATCTTTTAATGCTTTCCC
*
52327715 CTGCATCTATCTTCCCACTTCTTATTGTGTTTTCAATCATCTCACCAAACATTACTATATCTGAG
131 CTGCATCTATCTTCCCACTTCTTATTCTGTTTTCAATCATCTCACCAAACATTACTATATCTGAG
* *
52327780 AAGCTTCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTCAGA
196 AACCTCCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTCAGA
* * * *
52327831 GCCTTGATAGCTAGTGGTTACGGCCCTCGGCTGACCTACAATGACTGATTTGGAATACCCTTTAT
1 GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
*
52327896 TATATATGCTCAGGTTATTTACTTCATTTTCCTTGTTCTTCGAGGTTGATCTTTTAATGCTTTCC
66 TATATATGCTCAGGTTATTTACTTCATTTTCCTTATTCTTCG-GGTTGATCTTTTAATGCTTTCC
* *
52327961 CCTGCATCTATCTTCCTACTTCTTATTCTGTTTTCAATCATCTCGCCAAACATTACTATATCTGA
130 CCTGCATCTATCTTCCCACTTCTTATTCTGTTTTCAATCATCTCACCAAACATTACTATATCTGA
* *
52328026 GAACCTCCTCGTAGCGCTTCCCAACATATGGTTAATGAATGGGGCTTTTAGA
195 GAACCTCCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTCAGA
52328078 G
1 G
52328079 TGTTGATGAA
Statistics
Matches: 231, Mismatches: 16, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
246 100 0.43
247 131 0.57
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (246 bp):
GCCTTGATAGCTAGTGGTTACGGCCCCCGGCTAACCTACAATGACCGATTTAGAATACCCTTTAT
TATATATGCTCAGGTTATTTACTTCATTTTCCTTATTCTTCGGGTTGATCTTTTAATGCTTTCCC
CTGCATCTATCTTCCCACTTCTTATTCTGTTTTCAATCATCTCACCAAACATTACTATATCTGAG
AACCTCCTCGTAGCGCTTCCCAACATATGGGTAATGAATGGGGCTTTCAGA
Found at i:52329157 original size:19 final size:20
Alignment explanation
Indices: 52329126--52329179 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
52329116 GGGTTTTTTG
* *
52329126 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGCA
*
52329145 TGCAATGTAATGCAAATGCA
1 TGAAATGTAATGCAAATGCA
52329165 TGAAATG-AATGCAAA
1 TGAAATGTAATGCAAA
52329180 AAGAGGGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGCA
Found at i:52331155 original size:3 final size:3
Alignment explanation
Indices: 52331147--52331192 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
52331137 ATGGTTTGAA
52331147 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52331193 TTAACATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:52331327 original size:3 final size:3
Alignment explanation
Indices: 52331319--52331505 Score: 146
Period size: 3 Copynumber: 62.0 Consensus size: 3
52331309 AAAAATGATG
* *
52331319 TAA TAA TAA TGA TAA TAA -AA TAAA GAA TAA TAA TACA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A -TAA TAA TAA
* * * * * * *
52331366 TAG TAG TAG TAA -AGA CAA TAA T-A TAA TAA GAA TGA TGA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
52331410 TAC TAA TAC TAA TAA TAA TAG TAA TAA TAG TAA TAA TAG TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
52331458 TAA TAA TAA GAA TAA TAG TAA TAA TAA TAG TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52331506 AATTAATTAA
Statistics
Matches: 148, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
2 5 0.03
3 136 0.92
4 5 0.03
5 2 0.01
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:52334585 original size:30 final size:30
Alignment explanation
Indices: 52334512--52334586 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
52334502 TCATGATCAT
**
52334512 GATCAGATCTTGGTATTTCAGTTAGGAAAG
1 GATCAGATCTTGGTAAATCAGTTAGGAAAG
* *
52334542 GATCAAATATTGGTAAATCAGTTAGGAAAG
1 GATCAGATCTTGGTAAATCAGTTAGGAAAG
*
52334572 GATCTGATCTTGGTA
1 GATCAGATCTTGGTA
52334587 TAACTATTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.32
Consensus pattern (30 bp):
GATCAGATCTTGGTAAATCAGTTAGGAAAG
Found at i:52339440 original size:6 final size:6
Alignment explanation
Indices: 52339429--52339456 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52339419 ATCTACATGC
52339429 ATATTG ATATTG ATATTG ATATTG ATAT
1 ATATTG ATATTG ATATTG ATATTG ATAT
52339457 CTTAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (6 bp):
ATATTG
Found at i:52341291 original size:26 final size:26
Alignment explanation
Indices: 52341223--52341297 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
52341213 AAAGCTCCGG
*
52341223 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCGGGAAGCTCACAA
* * *
52341249 AGAGCCTTTAATCGGGAAGCTTACGA
1 AGAGCCATTAATCGGGAAGCTCACAA
*
52341275 AGAGCCATATAAT-GGGATGCTCA
1 AGAGCCAT-TAATCGGGAAGCTCA
52341298 TAAGAGCTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATCGGGAAGCTCACAA
Found at i:52346329 original size:29 final size:29
Alignment explanation
Indices: 52346287--52346345 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52346277 TGAAAGATTA
52346287 CCTTTCTGTTAGTGTATTTGAGTATATTT
1 CCTTTCTGTTAGTGTATTTGAGTATATTT
52346316 CCTTTCTGTTAGTGTATTTGAGTATATTT
1 CCTTTCTGTTAGTGTATTTGAGTATATTT
52346345 C
1 C
52346346 ATATGCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (29 bp):
CCTTTCTGTTAGTGTATTTGAGTATATTT
Found at i:52358240 original size:23 final size:23
Alignment explanation
Indices: 52358209--52358257 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
52358199 AATGATAGCC
*
52358209 AATCCATACCCAGAATAACATCA
1 AATCAATACCCAGAATAACATCA
*
52358232 AATCAATACTCAGAATAACATCA
1 AATCAATACCCAGAATAACATCA
52358255 AAT
1 AAT
52358258 TCCCAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.24, G:0.04, T:0.20
Consensus pattern (23 bp):
AATCAATACCCAGAATAACATCA
Found at i:52358613 original size:23 final size:23
Alignment explanation
Indices: 52358587--52358632 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
52358577 GAACAATAGT
52358587 GTATTTTGCTCTCGTACGAGTAA
1 GTATTTTGCTCTCGTACGAGTAA
52358610 GTATTTTGCTCTCGTACGAGTAA
1 GTATTTTGCTCTCGTACGAGTAA
52358633 TCCTAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (23 bp):
GTATTTTGCTCTCGTACGAGTAA
Found at i:52363372 original size:29 final size:29
Alignment explanation
Indices: 52363328--52363403 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
52363318 TTATGCTTCC
52363328 AATCTTTATATCTTTTTACCTTTAAAATTT
1 AATCTTTATAT-TTTTTACCTTTAAAATTT
* * * **
52363358 AGTCTTTCTATTTTTAATTTTTAAAATTT
1 AATCTTTATATTTTTTACCTTTAAAATTT
*
52363387 AATCTTTTTAATTTTTT
1 AATCTTTAT-ATTTTTT
52363404 TATTTAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.28, C:0.09, G:0.01, T:0.62
Consensus pattern (29 bp):
AATCTTTATATTTTTTACCTTTAAAATTT
Found at i:52368336 original size:3 final size:3
Alignment explanation
Indices: 52368328--52368386 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
52368318 AAATTAAGTT
52368328 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52368376 TTA TTA TTA TT
1 TTA TTA TTA TT
52368387 CTGTTTTTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.