Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 166 of 333
Found at i:54564242 original size:73 final size:73
Alignment explanation
Indices: 54564153--54564381 Score: 329
Period size: 73 Copynumber: 3.1 Consensus size: 73
54564143 GATTATAGTA
54564153 ATTT-GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAATGCCTTCGGGACT
1 ATTTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAATGCCTTCGGGACT
54564217 TAACCCGG
66 TAACCCGG
*
54564225 ATTTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
1 ATTTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAATGCCTTCGGGACT
54564290 TAACCCGG
66 TAACCCGG
* *
54564298 ATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTT
1 A-TT--T-A---GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAATGCCTT
*
54564362 CGGG-CTTAGCCCGG
59 CGGGACTTAACCCGG
*
54564376 AATTAG
1 ATTTAG
54564382 TATCTCACAC
Statistics
Matches: 143, Mismatches: 6, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
71 1 0.01
72 4 0.03
73 68 0.48
74 3 0.02
75 1 0.01
76 1 0.01
77 2 0.01
78 10 0.07
79 36 0.25
80 17 0.12
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (73 bp):
ATTTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAATGCCTTCGGGACT
TAACCCGG
Found at i:54564318 original size:113 final size:115
Alignment explanation
Indices: 54564120--54564455 Score: 411
Period size: 113 Copynumber: 2.9 Consensus size: 115
54564110 GCTCCTCGTT
* * *
54564120 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAATTTGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
54564184 GATTTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGATT-TA-GCA
65 GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATACGCA
*
54564233 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
54564298 ATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATTA-TA---CGCA
* * * **
54564352 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
54564415 GATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCGGA
65 GAT-TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
54564456 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 14, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
112 9 0.05
113 87 0.44
114 4 0.02
115 2 0.01
117 13 0.07
118 58 0.29
119 24 0.12
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (115 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATACGCA
Found at i:54564350 original size:39 final size:40
Alignment explanation
Indices: 54564230--54564455 Score: 286
Period size: 39 Copynumber: 5.7 Consensus size: 40
54564220 CCCGGATTTA
* * *
54564230 GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTC
* * *
54564270 GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTC
54564310 GCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTC
54564349 GCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTC
* * *
54564388 ACACAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTA
1 GCACAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TC
54564429 GCAC-AA-GCCTTCGGGACTTAGCCCGGA
1 GCACAAATGCCTTCGGGACTTAGCCCGGA
54564456 CAGCATTCAA
Statistics
Matches: 172, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 87 0.51
40 75 0.44
41 8 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTC
Found at i:54564410 original size:79 final size:78
Alignment explanation
Indices: 54564231--54564455 Score: 278
Period size: 79 Copynumber: 2.8 Consensus size: 78
54564221 CCGGATTTAG
* * *
54564231 CACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 CACAAATGCCTTC-GGACTTAGCCCGGAATTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
54564296 GGATTTAGTAACTCG
64 GGAATTAGTAACTCA
*
54564311 CACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CACAAATGCCTTCGGACTTAGCCCGGAATTAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCG
*
54564375 GAATTAGTATCTCA
65 GAATTAGTAACTCA
* *
54564389 CACAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTAGC
1 CACAAATGCCTTCGGA-CTTAGCCCGGA-ATTAGT-AC-TCGCACAAATGCCTTCGGGACTTAGC
54564451 CCGGA
62 CCGGA
54564456 CAGCATTCAA
Statistics
Matches: 129, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
78 44 0.34
79 63 0.49
80 22 0.17
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CACAAATGCCTTCGGACTTAGCCCGGAATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCA
Found at i:54571085 original size:40 final size:40
Alignment explanation
Indices: 54571025--54571374 Score: 565
Period size: 40 Copynumber: 8.7 Consensus size: 40
54571015 GAGCATTGGA
54571025 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
54571065 ATATAACCGGGCTAAAACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
54571105 ATATGTCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
54571145 ATATAACCGGGCTAAAACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
54571185 ATATGTCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
54571225 ATATAACCGGGCTAAAACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
54571265 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
54571305 ATATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
54571347 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
54571375 ATGTGTTTGC
Statistics
Matches: 285, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
40 247 0.87
42 38 0.13
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:54576165 original size:40 final size:39
Alignment explanation
Indices: 54576121--54576365 Score: 301
Period size: 40 Copynumber: 6.3 Consensus size: 39
54576111 GCTCCTCGTT
* *
54576121 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAATTCGCA
54576161 CAAATGCCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAAT-TCGCA
*
54576201 CAAATGCCTTCGGGACTTAACCCGG---A-T--TTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGTTTAGTAATTCGCA
*
54576234 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAATTCGCA
*
54576274 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAATTCGCA
* *
54576314 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAAT-TCGCA
54576353 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54576366 ATCTTAGTCC
Statistics
Matches: 187, Mismatches: 8, Indels: 21
0.87 0.04 0.10
Matches are distributed among these distances:
33 29 0.16
34 1 0.01
35 1 0.01
36 1 0.01
37 1 0.01
38 2 0.01
39 35 0.19
40 115 0.61
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAATTCGCA
Found at i:54576240 original size:33 final size:33
Alignment explanation
Indices: 54576198--54576304 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
54576188 TTAGTATCTC
54576198 GCACAAATGCCTTCGGGACTTAACCCGGATTTA
1 GCACAAATGCCTTCGGGACTTAACCCGGATTTA
54576231 GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAA
1 GCACAAATGCCTTCGGGACTTAACCCGGA-TT--T-A
54576268 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTTA
1 ---GCACAAATGCCTTCGGGACTTAACCCGGATTTA
54576304 G
1 G
54576305 TAACTCGCAC
Statistics
Matches: 67, Mismatches: 0, Indels: 14
0.83 0.00 0.17
Matches are distributed among these distances:
33 30 0.45
34 2 0.03
36 2 0.03
37 2 0.03
39 2 0.03
40 29 0.43
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (33 bp):
GCACAAATGCCTTCGGGACTTAACCCGGATTTA
Found at i:54576243 original size:73 final size:77
Alignment explanation
Indices: 54576121--54576365 Score: 340
Period size: 73 Copynumber: 3.2 Consensus size: 77
54576111 GCTCCTCGTT
* *
54576121 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATT-TA-TAA--CGCACAAATGCCTTCGGGACTTAACCCG
54576185 GATTTAGTATCTCGCA
62 GATTTAGTATCTCGCA
54576201 CAAATGCCTTCGGGACTTAACCCGGA-TT-T-A-GCACAAATGCCTTCGGGACTTAACCCGGATT
1 CAAATGCCTTCGGGACTTAACCCGGATTTATAACGCACAAATGCCTTCGGGACTTAACCCGGATT
*
54576262 TAGTAACTCGCA
66 TAGTATCTCGCA
*
54576274 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-TAA--CGCACAAATGCCTTCGGGACTTAACCCGG
*
54576338 AATTAGTATCTCGCA
63 ATTTAGTATCTCGCA
54576353 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54576366 ATCTTAGTCC
Statistics
Matches: 151, Mismatches: 6, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
73 68 0.45
74 2 0.01
76 2 0.01
77 2 0.01
79 36 0.24
80 41 0.27
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTATAACGCACAAATGCCTTCGGGACTTAACCCGGATT
TAGTATCTCGCA
Found at i:54576319 original size:113 final size:112
Alignment explanation
Indices: 54576121--54576343 Score: 367
Period size: 113 Copynumber: 2.0 Consensus size: 112
54576111 GCTCCTCGTT
* *
54576121 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
54576186 ATTTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGCA
66 ATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGGAATTAGCA
*
54576234 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
54576298 GATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAG
65 GATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGAATTAG
54576344 TATCTCGCAC
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 14 0.14
113 87 0.84
114 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (112 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGAATTAGCA
Found at i:54576378 original size:79 final size:81
Alignment explanation
Indices: 54576228--54576417 Score: 257
Period size: 79 Copynumber: 2.4 Consensus size: 81
54576218 TAACCCGGAT
* *
54576228 TTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTA
1 TTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTA
54576293 ACCCGGAT-TTAGTAAC
66 ACCCGGATATT-GTAAC
* *
54576309 -TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTT
1 TTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTT
** *
54576371 AGTCCGGATATTGTCAC
65 AACCCGGATATTGTAAC
54576388 TTAGCAC-AA-GCCTTCGGGACTTAGCCCGGA
1 TTAGCACAAATGCCTTCGGGACTTAGCCCGGA
54576418 CAGCATTCAA
Statistics
Matches: 97, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 12 0.12
79 60 0.62
80 25 0.26
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
TTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTA
ACCCGGATATTGTAAC
Found at i:54594650 original size:39 final size:40
Alignment explanation
Indices: 54594582--54594761 Score: 251
Period size: 39 Copynumber: 4.6 Consensus size: 40
54594572 CAACCAAGTA
** * *
54594582 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
* *
54594621 CCTTCGGGACTTAGCTCGGTTATAGT-ACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
54594660 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
54594700 -CTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
54594739 CCTTCAGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
54594762 CATCCGAATA
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 87 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:54594735 original size:79 final size:79
Alignment explanation
Indices: 54594582--54594761 Score: 249
Period size: 79 Copynumber: 2.3 Consensus size: 79
54594572 CAACCAAGTA
** * * * *
54594582 CCTTCGGGGTTTAG-CCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCTCGGTTATAG
1 CCTTCGGGACTTAGCCCGGTTATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGATTATAG
*
54594646 TACTCGCACAATTG
66 TACTCGCACAAATG
54594660 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG-CTTCGGGACTTAGCCCGATTATA
1 CCTTCGGGACTTAGCCCGGTTATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGATTATA
54594723 GTAACTCGCACAAATG
65 GT-ACTCGCACAAATG
*
54594739 CCTTCAGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
54594762 CATCCGAATA
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
78 36 0.40
79 55 0.60
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGTTATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGATTATAG
TACTCGCACAAATG
Found at i:54610157 original size:26 final size:25
Alignment explanation
Indices: 54610128--54610186 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
54610118 ATTTACTAAA
*
54610128 ATACCCTAAGTATG-AAAATTACCATT
1 ATACCCT-AG-ATGCAAAATGACCATT
*
54610154 ATACCCCTAGGTGCAAAATGACCATT
1 ATA-CCCTAGATGCAAAATGACCATT
54610180 ATACCCT
1 ATACCCT
54610187 TAGGGTCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 6 0.21
26 19 0.66
27 4 0.14
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.27
Consensus pattern (25 bp):
ATACCCTAGATGCAAAATGACCATT
Found at i:54610287 original size:28 final size:28
Alignment explanation
Indices: 54610247--54610362 Score: 137
Period size: 28 Copynumber: 4.2 Consensus size: 28
54610237 GGAGGAAGCA
54610247 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* *
54610275 TTCTGGTGGCTCTACCACAAATATTTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
* *
54610303 TTCTGGTGGCCCTGCCACAATTATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
** * * *
54610331 AGCTGGTGACTCTGTCAC-AATATTTG-
1 TTCTGGTGGCTCTGCCACAAATATCTGT
54610357 TTCTGG
1 TTCTGG
54610363 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 4 0.05
27 6 0.08
28 63 0.86
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:54610337 original size:56 final size:54
Alignment explanation
Indices: 54610247--54610362 Score: 151
Period size: 56 Copynumber: 2.1 Consensus size: 54
54610237 GGAGGAAGCA
* ** *
54610247 TTCTGGTGGCTCTGCCACAAATATCTGTTTCTGGTGGCTCTACCACAAATATTTG
1 TTCTGGTGGCCCTGCCACAAATATCTGTAGCTGGTGACTCTACCAC-AATATTTG
* **
54610302 TTTCTGGTGGCCCTGCCACAATTATCTGTAGCTGGTGACTCTGTCACAATATTTG
1 -TTCTGGTGGCCCTGCCACAAATATCTGTAGCTGGTGACTCTACCACAATATTTG
54610357 TTCTGG
1 TTCTGG
54610363 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 6 0.11
55 8 0.15
56 39 0.74
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (54 bp):
TTCTGGTGGCCCTGCCACAAATATCTGTAGCTGGTGACTCTACCACAATATTTG
Found at i:54628927 original size:30 final size:30
Alignment explanation
Indices: 54628893--54628952 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54628883 TTCCCGAGCC
*
54628893 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
54628923 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
54628953 AGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:54629512 original size:34 final size:34
Alignment explanation
Indices: 54629469--54629538 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
54629459 GGGTTACATG
54629469 GTAGCTTGGCTACATAAGTTCTGTAGGCTATTGA
1 GTAGCTTGGCTACATAAGTTCTGTAGGCTATTGA
54629503 GTAGCTTGGCTACATAAGTTCTGTAGGCTATTGA
1 GTAGCTTGGCTACATAAGTTCTGTAGGCTATTGA
54629537 GT
1 GT
54629539 TTGTCTAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (34 bp):
GTAGCTTGGCTACATAAGTTCTGTAGGCTATTGA
Found at i:54632799 original size:29 final size:29
Alignment explanation
Indices: 54632766--54632868 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
54632756 TGAATGTGAA
*
54632766 TGGGCCTAACGGGCCATATAAATATTATT
1 TGGGCCTAATGGGCCATATAAATATTATT
* * *
54632795 TGGGCCTAATGGGCCATATACATGTGATT
1 TGGGCCTAATGGGCCATATAAATATTATT
* *
54632824 TGGGCCTAAATGGGCCATATGAATA-TGTT
1 TGGGCCT-AATGGGCCATATAAATATTATT
*
54632853 TGGGCTTAATGGGCCA
1 TGGGCCTAATGGGCCA
54632869 GATATAGGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 9 0.14
29 40 0.63
30 14 0.22
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATATTATT
Found at i:54635566 original size:79 final size:81
Alignment explanation
Indices: 54635455--54635635 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
54635445 GCTACTCGTT
* * *
54635455 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
54635519 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
54635535 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
54635598 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
54635615 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
54635636 TGGACATCAT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 54 0.62
80 29 0.33
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:54635572 original size:39 final size:40
Alignment explanation
Indices: 54635455--54635635 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
54635445 GCTACTCGTT
*
54635455 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
54635495 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
54635535 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
54635574 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
54635615 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
54635636 TGGACATCAT
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 73 0.60
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:54646997 original size:13 final size:14
Alignment explanation
Indices: 54646979--54647009 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
54646969 TTAGCCGATT
54646979 ACAAATATG-TTTA
1 ACAAATATGCTTTA
54646992 ACAAATATGCTTTA
1 ACAAATATGCTTTA
54647006 ACAA
1 ACAA
54647010 TTGTCCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (14 bp):
ACAAATATGCTTTA
Found at i:54650040 original size:55 final size:56
Alignment explanation
Indices: 54649885--54650074 Score: 274
Period size: 56 Copynumber: 3.4 Consensus size: 56
54649875 TCCCAGACAG
* * *
54649885 GGTCTTACTCACACACATAAATCGGAGTCACATATCGATGCCAATGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGT
*
54649941 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGT
* * * * * *
54649997 GGTCTTA-TTGCACACATATATCGGTGTGACATATTGATACCAACGTATTAAACAT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGT
*
54650052 GGTCTTACTCACACACATATATC
1 GGTCTTACTCGCACACATATATC
54650075 AATGCCATGG
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
55 48 0.40
56 72 0.60
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGGAGTCACATATCGATGCCAACGTATTAAACGT
Found at i:54668571 original size:32 final size:32
Alignment explanation
Indices: 54668535--54668601 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
54668525 TACAACAGAC
54668535 ATTAATTCAATTTTCAATTCAGACTCTTTCTT
1 ATTAATTCAATTTTCAATTCAGACTCTTTCTT
*
54668567 ATTAATTCAATTTTCAATTCAGACTCTTTTTT
1 ATTAATTCAATTTTCAATTCAGACTCTTTCTT
54668599 ATT
1 ATT
54668602 CAACACATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTAATTCAATTTTCAATTCAGACTCTTTCTT
Found at i:54670612 original size:40 final size:40
Alignment explanation
Indices: 54670568--54670656 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
54670558 TGTGCGGCAA
*
54670568 TAAGTGTGCGATTTGAAATAGCTTCGGCTATAAATAGCAC
1 TAAGTGTGCGAATTGAAATAGCTTCGGCTATAAATAGCAC
* ** *
54670608 TAAGTGTGCGAATTGGAATAGCTTCGGCTATATGTGGCAC
1 TAAGTGTGCGAATTGAAATAGCTTCGGCTATAAATAGCAC
54670648 TAAGTGTGC
1 TAAGTGTGC
54670657 AATATTGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (40 bp):
TAAGTGTGCGAATTGAAATAGCTTCGGCTATAAATAGCAC
Found at i:54671117 original size:22 final size:22
Alignment explanation
Indices: 54671087--54671132 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
54671077 ACTGTGTGAA
54671087 ATGTCCTCTGTCTTACAGTGTT
1 ATGTCCTCTGTCTTACAGTGTT
*
54671109 ATGTTCTCTGTCTTACAGTGTT
1 ATGTCCTCTGTCTTACAGTGTT
54671131 AT
1 AT
54671133 AAAGCTAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (22 bp):
ATGTCCTCTGTCTTACAGTGTT
Found at i:54674109 original size:40 final size:40
Alignment explanation
Indices: 54674065--54674370 Score: 431
Period size: 40 Copynumber: 7.7 Consensus size: 40
54674055 GCTCCTCGTT
* *
54674065 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
54674105 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
54674145 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
54674185 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
54674225 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
54674265 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
54674304 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
54674345 CAAA-GCCTTCAGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAACCCGGAT
54674371 ATCATTCAAA
Statistics
Matches: 246, Mismatches: 15, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
38 2 0.01
39 32 0.13
40 199 0.81
41 13 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:54680505 original size:50 final size:50
Alignment explanation
Indices: 54680430--54680529 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
54680420 GATTCATAAA
54680430 GGTTCGTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTT
1 GGTTCGTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTT
54680480 GGTTCGTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTT
1 GGTTCGTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTT
54680530 AGTGATTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (50 bp):
GGTTCGTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTT
Found at i:54680554 original size:50 final size:50
Alignment explanation
Indices: 54680435--54680554 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
54680425 ATAAAGGTTC
* * * **
54680435 GTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTTGGTTC
1 GTTTACATAATCTAATCACTATTTAATTCCATTCCTACTATTTTTAGTGA
* *
54680485 GTTTACATAATTTATTCACTATTTAATTCCATTCCTACTATTTTTAGTGA
1 GTTTACATAATCTAATCACTATTTAATTCCATTCCTACTATTTTTAGTGA
* *
54680535 TTTTCCA-AATCTACATCACT
1 GTTTACATAATCTA-ATCACT
54680555 GCTGCTGTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 5 0.08
50 57 0.92
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (50 bp):
GTTTACATAATCTAATCACTATTTAATTCCATTCCTACTATTTTTAGTGA
Found at i:54681332 original size:40 final size:40
Alignment explanation
Indices: 54681288--54681552 Score: 349
Period size: 40 Copynumber: 6.7 Consensus size: 40
54681278 GCTCCTCGTT
*
54681288 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
54681328 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
54681368 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
54681408 CAACTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
54681448 CCAATGCCTTCAGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
54681487 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
54681528 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54681553 CATCATTCAA
Statistics
Matches: 202, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
38 2 0.01
39 32 0.16
40 155 0.77
41 13 0.06
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:54681539 original size:119 final size:120
Alignment explanation
Indices: 54681288--54681552 Score: 340
Period size: 119 Copynumber: 2.2 Consensus size: 120
54681278 GCTCCTCGTT
* *
54681288 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCG
* * *
54681352 GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
65 GAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
* * * *
54681408 CAACTGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCAGG-CTTAGCCCG
1 CAA-AGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCG
* ** * *
54681471 GAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
65 GAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCA
54681528 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
54681553 CATCATTCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
118 3 0.02
119 68 0.54
120 52 0.42
121 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGG
AATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
Found at i:54681959 original size:18 final size:18
Alignment explanation
Indices: 54681936--54681972 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54681926 AGTCACATAT
54681936 GTACGGAATCATGAATCA
1 GTACGGAATCATGAATCA
54681954 GTACGGAATCATGAATCA
1 GTACGGAATCATGAATCA
54681972 G
1 G
54681973 ACTCAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (18 bp):
GTACGGAATCATGAATCA
Found at i:54684337 original size:29 final size:29
Alignment explanation
Indices: 54684295--54684351 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
54684285 GTTGAGAGAA
54684295 GTTAGCTCTTTAGGACATGTAGTATCTAC
1 GTTAGCTCTTTAGGACATGTAGTATCTAC
*
54684324 GTTAGCTCTTTAGGACATTTAGTATCTA
1 GTTAGCTCTTTAGGACATGTAGTATCTA
54684352 TATCGGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (29 bp):
GTTAGCTCTTTAGGACATGTAGTATCTAC
Found at i:54688131 original size:24 final size:24
Alignment explanation
Indices: 54688099--54688159 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
54688089 AAAATCCAAT
* * *
54688099 GCACTATGTGTGCG-GTTTACTATG
1 GCACTATGTGTGCGAGTGTAAT-TA
54688123 GCACTATGTGTGCGAGTGTAATTA
1 GCACTATGTGTGCGAGTGTAATTA
54688147 GCACTATGTGTGC
1 GCACTATGTGTGC
54688160 AAATACGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGAGTGTAATTA
Found at i:54699254 original size:31 final size:31
Alignment explanation
Indices: 54699205--54699336 Score: 185
Period size: 31 Copynumber: 4.3 Consensus size: 31
54699195 TTAGTCTTGA
* * *
54699205 CATAT-ACTGGGCCGAAGCCTTTCCATAAAC
1 CATATCACTGGGCCAAAGCCTTTTCATAAAT
*
54699235 CATATCACTAGGCCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCAAAGCCTTTTCATAAAT
**
54699266 CATATCACTGGGCTGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCAAAGCCTTTTCATAAAT
* *
54699297 CATATCACTGGGCTAAAGCATTTTCATAAAT
1 CATATCACTGGGCCAAAGCCTTTTCATAAAT
54699328 CATATCACT
1 CATATCACT
54699337 ACCGCACTTC
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 5 0.05
31 87 0.95
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCAAAGCCTTTTCATAAAT
Found at i:54702670 original size:42 final size:42
Alignment explanation
Indices: 54702611--54702723 Score: 160
Period size: 40 Copynumber: 2.7 Consensus size: 42
54702601 ATACTCAAAT
**
54702611 TCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAT-TTTAA
1 TCTCGCACACTAAGTGCC-ATACATAGCCGAAGCTATCTCGAA
*
54702653 TCTCGCACACTAAGTGCCATACATAGCTGAAGCTATCTCGAA
1 TCTCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
*
54702695 --TCGCACACTAAGTGCCATACATAGTCGAA
1 TCTCGCACACTAAGTGCCATACATAGCCGAA
54702724 TTGTCATCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 27 0.42
41 17 0.26
42 21 0.32
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (42 bp):
TCTCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
Found at i:54708980 original size:42 final size:43
Alignment explanation
Indices: 54708878--54709024 Score: 179
Period size: 43 Copynumber: 3.4 Consensus size: 43
54708868 CGCGTCCATT
* * ** *
54708878 ATGAACTCGGACCACTCAACGAGCTCGTATGCTCACATCCATA
1 ATGAACTCGGACCACTCAATGAGCTCGGATGCTCACATATATC
*
54708921 ATGAACTCGAACCACTCAATGAGCTCGGATGCT-ACATATATC
1 ATGAACTCGGACCACTCAATGAGCTCGGATGCTCACATATATC
* * * *
54708963 ATGAACTTGGACCACTCAATAAGTTCGGATTCTCACATATATC
1 ATGAACTCGGACCACTCAATGAGCTCGGATGCTCACATATATC
**
54709006 ACAAACTCGGACCACTCAA
1 ATGAACTCGGACCACTCAA
54709025 CAAGCTCGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 34 0.38
43 55 0.62
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (43 bp):
ATGAACTCGGACCACTCAATGAGCTCGGATGCTCACATATATC
Found at i:54711927 original size:16 final size:16
Alignment explanation
Indices: 54711906--54711953 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 16
54711896 ATATGGTACA
54711906 TAAATCATACATTACT
1 TAAATCATACATTACT
54711922 TAAATCATATAACATTACT
1 TAAATC--AT-ACATTACT
54711941 TAAATCATACATT
1 TAAATCATACATT
54711954 TCATAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.38
17 2 0.07
18 2 0.07
19 14 0.48
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATCATACATTACT
Found at i:54712162 original size:29 final size:29
Alignment explanation
Indices: 54712120--54712182 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
54712110 GTGTGCTAAA
**
54712120 CGATGGTTGAAACCATCCATTTTCATATT
1 CGATGGTCAAAACCATCCATTTTCATATT
*
54712149 CGATGGTCAAAACCATCCCTTTTCATATT
1 CGATGGTCAAAACCATCCATTTTCATATT
*
54712178 TGATG
1 CGATG
54712183 ATCTTAACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (29 bp):
CGATGGTCAAAACCATCCATTTTCATATT
Found at i:54713573 original size:28 final size:28
Alignment explanation
Indices: 54713529--54713584 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
54713519 GGGTACCAAG
* *
54713529 GTAAGTTTGTGTGTAAATAATGGAACGT
1 GTAAGTTTGTGTATAAATAATGCAACGT
54713557 GTAAGTTTGTGTATAAATAATGCAACGT
1 GTAAGTTTGTGTATAAATAATGCAACGT
54713585 TACAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (28 bp):
GTAAGTTTGTGTATAAATAATGCAACGT
Found at i:54713896 original size:48 final size:48
Alignment explanation
Indices: 54713844--54713979 Score: 175
Period size: 48 Copynumber: 2.8 Consensus size: 48
54713834 ATCTATATGT
* *
54713844 GATCCTATATAAGACCATGTCTAGGACATGGCATTGGCATCGATCGAC
1 GATCCTATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATAGAC
* * * *
54713892 GATCCAACGTAAGACCATGTCTAGGACATGGCATTGGCATCGATATAT
1 GATCCTATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATAGAC
* * *
54713940 GATCCTATGTAAGACCATAT-TCGAGATATGGCATTGGCAT
1 GATCCTATGTAAGACCATGTCTAG-GACATGGCATTGGCAT
54713980 TCTACCATGT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
47 2 0.03
48 74 0.97
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (48 bp):
GATCCTATGTAAGACCATGTCTAGGACATGGCATTGGCATCGATAGAC
Found at i:54718757 original size:13 final size:12
Alignment explanation
Indices: 54718741--54718780 Score: 57
Period size: 10 Copynumber: 3.4 Consensus size: 12
54718731 ACGTTTCCCT
54718741 TCTCCTCTCTTC
1 TCTCCTCTCTTC
54718753 T-T-CTCTCTTC
1 TCTCCTCTCTTC
54718763 TTCTCCTCTCTTC
1 -TCTCCTCTCTTC
54718776 TCTCC
1 TCTCC
54718781 CTCCATACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 7 0.28
13 8 0.32
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (12 bp):
TCTCCTCTCTTC
Found at i:54728215 original size:27 final size:27
Alignment explanation
Indices: 54728160--54728271 Score: 138
Period size: 27 Copynumber: 4.2 Consensus size: 27
54728150 TAGCATGACT
* * *
54728160 ACCAGAACAGATAA-TGTGACAGTGTC
1 ACCAGAACAGATAATTGTGGCAGAGCC
54728186 ACCAGAACAGATAATTGTGGCAGAGCC
1 ACCAGAACAGATAATTGTGGCAGAGCC
*
54728213 ACCAGAACAGAT-ATATGTGGCAGTGCC
1 ACCAGAACAGATAAT-TGTGGCAGAGCC
* * *
54728240 ACCAGATCAAATAATTGTGGCATAGCC
1 ACCAGAACAGATAATTGTGGCAGAGCC
54728267 ACCAG
1 ACCAG
54728272 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 16 0.21
27 57 0.76
28 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (27 bp):
ACCAGAACAGATAATTGTGGCAGAGCC
Found at i:54728243 original size:54 final size:53
Alignment explanation
Indices: 54728160--54728271 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 53
54728150 TAGCATGACT
* *
54728160 ACCAGAACAGATAATGTGACAGTGTCACCAGAACAGATAATTGTGGCAGAGCC
1 ACCAGAACAGATAATGTGACAGTGCCACCAGAACAAATAATTGTGGCAGAGCC
* * *
54728213 ACCAGAACAGATATATGTGGCAGTGCCACCAGATCAAATAATTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGACAGTGCCACCAGAACAAATAATTGTGGCAGAGCC
54728267 ACCAG
1 ACCAG
54728272 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 13 0.25
54 40 0.75
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (53 bp):
ACCAGAACAGATAATGTGACAGTGCCACCAGAACAAATAATTGTGGCAGAGCC
Found at i:54728932 original size:27 final size:28
Alignment explanation
Indices: 54728902--54728979 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
54728892 CACTCGATAA
54728902 AGATAATTGTGGCAGAGCCACCAGAAT-
1 AGATAATTGTGGCAGAGCCACCAGAATC
*
54728929 AGAT-ATATGTGGCAGTGCCACCA-AATC
1 AGATAAT-TGTGGCAGAGCCACCAGAATC
* *
54728956 AGATAATTGTAGCATAGCCACCAG
1 AGATAATTGTGGCAGAGCCACCAG
54728980 GACGCTTCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
26 5 0.12
27 36 0.84
28 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (28 bp):
AGATAATTGTGGCAGAGCCACCAGAATC
Found at i:54729963 original size:85 final size:85
Alignment explanation
Indices: 54729820--54729990 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
54729810 GGCCGGCCAT
54729820 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
54729885 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
54729905 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
54729970 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
54729990 G
1 G
54729991 GGAATGGGCA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:54731320 original size:47 final size:47
Alignment explanation
Indices: 54731266--54731813 Score: 764
Period size: 47 Copynumber: 11.6 Consensus size: 47
54731256 TATTTGAATA
* * *
54731266 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
54731313 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
54731360 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
54731409 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
54731456 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
54731505 AATGTGAACA-TGTGTATGTGTGATAAGGCCAAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
54731552 AATGTGAACA-TGCATATCTGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
54731599 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
54731646 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
** *
54731693 AATGTGAACA-TACATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
54731740 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATATGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
54731787 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54731814 TCCCGAAGGG
Statistics
Matches: 468, Mismatches: 27, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 374 0.80
49 92 0.20
50 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:54733762 original size:27 final size:27
Alignment explanation
Indices: 54733732--54733811 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
54733722 CCCACTCGAT
54733732 ACAGATAATTGTGGCAGAGCCACCAGA
1 ACAGATAATTGTGGCAGAGCCACCAGA
* *
54733759 ACAGAT-ATATGTGGTAGTGCCACCAGA
1 ACAGATAAT-TGTGGCAGAGCCACCAGA
** *
54733786 TTAGATAATTGTGGCATAGCCACCAG
1 ACAGATAATTGTGGCAGAGCCACCAG
54733812 GACGCTTCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.05
27 40 0.91
28 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (27 bp):
ACAGATAATTGTGGCAGAGCCACCAGA
Found at i:54733959 original size:26 final size:27
Alignment explanation
Indices: 54733915--54733989 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 27
54733905 CAAAAGTAAC
* *
54733915 CCTAGGGGTATAAT-GGTAATTT-TACA
1 CCTAGGGGTAT-ATCAGTAATTTCCACA
*
54733941 CCTAGGGGTATATCAGTAATTTCCATA
1 CCTAGGGGTATATCAGTAATTTCCACA
*
54733968 CATAGGGGTAT-TCAAGTAATTT
1 CCTAGGGGTATATC-AGTAATTT
54733990 AAATATTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.05
26 20 0.48
27 20 0.48
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (27 bp):
CCTAGGGGTATATCAGTAATTTCCACA
Found at i:54735022 original size:24 final size:24
Alignment explanation
Indices: 54734997--54735084 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
54734987 CCCTAATTAG
*
54734997 CTCCTAAATCCTCTCCCTTATCAG
1 CTCCTAAATCCTCTCCCTTATCAA
54735021 CTCCTAAATCCTCTCCCTTATCAA
1 CTCCTAAATCCTCTCCCTTATCAA
* *
54735045 CTCCTAAATCCTATCTCTTATCAA
1 CTCCTAAATCCTCTCCCTTATCAA
54735069 CTCCTAAATCCTCTCC
1 CTCCTAAATCCTCTCC
54735085 TGATAGACTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.24, C:0.41, G:0.01, T:0.34
Consensus pattern (24 bp):
CTCCTAAATCCTCTCCCTTATCAA
Found at i:54746611 original size:30 final size:30
Alignment explanation
Indices: 54746577--54746637 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54746567 TCCTTAACTC
54746577 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54746607 AAACTTTTGCATATTTACATTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54746637 A
1 A
54746638 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54749542 original size:20 final size:20
Alignment explanation
Indices: 54749517--54749555 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54749507 AGGGACTAAA
* *
54749517 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
54749537 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTCTAAAATTT
54749556 TACAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:54751408 original size:79 final size:79
Alignment explanation
Indices: 54751307--54751464 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
54751297 GCCCAAAACA
54751307 TACATTGAGTGTGGTTCGGGACTAAACCGAGAACTTCTAAAACTTTTGCAACACCTAGAAAATTT
1 TACATTGAGTGTGGTTCGGGACTAAACCGAGAACTTCTAAAACTTTTGCAACACCTAGAAAATTT
54751372 TCTTCTTTTGGAGG
66 TCTTCTTTTGGAGG
54751386 TACATTGAGTGTGGTTCGGGACTAAACCGAGAACTTCTAAAACTTTTGCAACACCTAGAAAATTT
1 TACATTGAGTGTGGTTCGGGACTAAACCGAGAACTTCTAAAACTTTTGCAACACCTAGAAAATTT
*
54751451 TCTTGTTTTGGAGG
66 TCTTCTTTTGGAGG
54751465 GTTTAATAGC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (79 bp):
TACATTGAGTGTGGTTCGGGACTAAACCGAGAACTTCTAAAACTTTTGCAACACCTAGAAAATTT
TCTTCTTTTGGAGG
Found at i:54763208 original size:43 final size:42
Alignment explanation
Indices: 54763151--54763303 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 42
54763141 AATGCCAACG
* *
54763151 TCCCAGAC-GTGGTCTTACATGTAATCAAATATTGATGCC-ACTA
1 TCCCAGACAG-GGTCTTACATGAAATCAAATA-CGATGCCGA-TA
*
54763194 TCCCAGACAGGGTCTTACATGAAATCAAATACGATGCCGATG
1 TCCCAGACAGGGTCTTACATGAAATCAAATACGATGCCGATA
* * *
54763236 TCCCAGACATGGTCTTACACAT-AAATCATAAGT-CGATGCCAACA
1 TCCCAGACAGGGTCTT--ACATGAAATCA-AA-TACGATGCCGATA
*
54763280 TCCCAGAC-GTGGTCTTACACGAAA
1 TCCCAGACAG-GGTCTTACATGAAA
54763304 ACACATATTG
Statistics
Matches: 93, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
42 25 0.27
43 38 0.41
44 29 0.31
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (42 bp):
TCCCAGACAGGGTCTTACATGAAATCAAATACGATGCCGATA
Found at i:54763286 original size:44 final size:42
Alignment explanation
Indices: 54763142--54763299 Score: 135
Period size: 44 Copynumber: 3.7 Consensus size: 42
54763132 AGCTCGTACA
* * ** *
54763142 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCAAATATTG
1 ATGCCAACATCCCAGACATGGTCTTACACATAAATC-AA-ATCG
*
54763185 ATGCC-ACTATCCCAGACAGGGTCTT--ACATGAAATCAAATACG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACAT-AAATCAAAT-CG
* **
54763227 ATGCCGATGTCCCAGACATGGTCTTACACATAAATCATAAGTCG
1 ATGCCAACATCCCAGACATGGTCTTACACATAAATCA-AA-TCG
*
54763271 ATGCCAACATCCCAGACGTGGTCTTACAC
1 ATGCCAACATCCCAGACATGGTCTTACAC
54763300 GAAAACACAT
Statistics
Matches: 93, Mismatches: 13, Indels: 17
0.76 0.11 0.14
Matches are distributed among these distances:
41 4 0.04
42 25 0.27
43 30 0.32
44 33 0.35
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCAACATCCCAGACATGGTCTTACACATAAATCAAATCG
Found at i:54774696 original size:27 final size:27
Alignment explanation
Indices: 54774658--54774879 Score: 204
Period size: 27 Copynumber: 8.3 Consensus size: 27
54774648 TTGGGTTCTT
*
54774658 AATACCCTCGGTTTGTAAAATTACCAA
1 AATACCCTCAGTTTGTAAAATTACCAA
* **
54774685 AATACCCTCGGTTTGTAAAATTACCGT
1 AATACCCTCAGTTTGTAAAATTACCAA
**
54774712 AATACCC-CAAGTTTGTAAAATTATAAA
1 AATACCCTC-AGTTTGTAAAATTACCAA
**
54774739 AATACCCTC-GATTTGTAAAATTACTGA
1 AATACCCTCAG-TTTGTAAAATTACCAA
* **
54774766 AATACCC-CTAATTTGTAAAATTATTAA
1 AATACCCTC-AGTTTGTAAAATTACCAA
*
54774793 AATACCC-CTAATTTGTAAAATTACCAA
1 AATACCCTC-AGTTTGTAAAATTACCAA
* *
54774820 GAT-CCCTCAGTTCGTAAAATTACCAA
1 AATACCCTCAGTTTGTAAAATTACCAA
* * *
54774846 AATACCCTC-GTAGTGTAAAATTATCGA
1 AATACCCTCAGT-TTGTAAAATTACCAA
54774873 AATACCC
1 AATACCC
54774880 ATGTAGGATA
Statistics
Matches: 164, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
26 26 0.16
27 137 0.84
28 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AATACCCTCAGTTTGTAAAATTACCAA
Found at i:54774741 original size:54 final size:54
Alignment explanation
Indices: 54774668--54774879 Score: 238
Period size: 54 Copynumber: 3.9 Consensus size: 54
54774658 AATACCCTCG
* *
54774668 GTTTGTAAAATTACCAAAATACCCTCGGTTTGTAAAATTACCGTAATACCCCAA
1 GTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCCAA
** *
54774722 GTTTGTAAAATTATAAAAATACCCTCGATTTGTAAAATTACTGAAATACCCCTAA
1 GTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCC-AA
** *
54774777 -TTTGTAAAATTATTAAAATACCC-CTAATTTGTAAAATTACC-AAGAT-CCCTC-A
1 GTTTGTAAAATTACCAAAATACCCTC-GATTTGTAAAATTACCGAA-ATACCC-CAA
* * *
54774829 GTTCGTAAAATTACCAAAATACCCTCG-TAGTGTAAAATTATCGAAATACCC
1 GTTTGTAAAATTACCAAAATACCCTCGAT-TTGTAAAATTACCGAAATACCC
54774880 ATGTAGGATA
Statistics
Matches: 135, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
52 2 0.01
53 39 0.29
54 92 0.68
55 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
GTTTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCCAA
Found at i:54775216 original size:26 final size:26
Alignment explanation
Indices: 54775178--54775229 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
54775168 TTTGCCACAT
* *
54775178 TTACTGTTGCTGGCAGCTATGCTGCA
1 TTACTATTACTGGCAGCTATGCTGCA
*
54775204 TTACTATTACTGGCAGCTTTGCTGCA
1 TTACTATTACTGGCAGCTATGCTGCA
54775230 ATATTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
TTACTATTACTGGCAGCTATGCTGCA
Found at i:54775377 original size:28 final size:28
Alignment explanation
Indices: 54775330--54775386 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
54775320 CCTGTTATTG
* *
54775330 ACACTGTTACTGTATTGGGCCTA-GGCCC
1 ACACTGTTACTATATAGGG-CTATGGCCC
*
54775358 ACACTGTTGCTATATAGGGCTATGGCCC
1 ACACTGTTACTATATAGGGCTATGGCCC
54775386 A
1 A
54775387 AACTATACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (28 bp):
ACACTGTTACTATATAGGGCTATGGCCC
Found at i:54786188 original size:37 final size:37
Alignment explanation
Indices: 54786138--54786216 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
54786128 TTATTACGAA
* * *
54786138 GTCTTACTCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
54786175 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
54786212 GTCTT
1 GTCTT
54786217 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:54786413 original size:47 final size:47
Alignment explanation
Indices: 54786335--54786898 Score: 861
Period size: 47 Copynumber: 12.1 Consensus size: 47
54786325 CCCTTCGGGA
* * * * * * *
54786335 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54786382 CCTCTCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54786429 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54786476 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54786523 CTTAT--C----ATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54786564 CTTATCACACATGTACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54786611 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54786658 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54786705 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54786752 CTTATCACACATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54786799 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54786846 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54786895 CTTA
1 CTTA
54786899 CTATCATTTC
Statistics
Matches: 486, Mismatches: 23, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
41 40 0.08
43 1 0.00
45 1 0.00
47 402 0.83
49 42 0.09
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54786529 original size:22 final size:22
Alignment explanation
Indices: 54786504--54786572 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
54786494 TTTCACATTC
54786504 ATCACATCGGCTATTAGGCCTT
1 ATCACATCGGCTATTAGGCCTT
* * *
54786526 ATCATA-C-ACT-TTCA--CATT
1 ATCACATCGGCTATT-AGGCCTT
54786544 CATCACATCGGCTATTAGGCCTT
1 -ATCACATCGGCTATTAGGCCTT
54786567 ATCACA
1 ATCACA
54786573 CATGTACACT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
18 3 0.09
19 7 0.21
20 4 0.12
21 4 0.12
22 13 0.38
23 3 0.09
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (22 bp):
ATCACATCGGCTATTAGGCCTT
Found at i:54793902 original size:23 final size:23
Alignment explanation
Indices: 54793876--54793921 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54793866 TTATGTAACG
54793876 TATGCTCAAAAGAGCTCAACTAT
1 TATGCTCAAAAGAGCTCAACTAT
54793899 TATGCTCAAAAGAGCTCAACTAT
1 TATGCTCAAAAGAGCTCAACTAT
54793922 GATTACCAGT
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:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
TATGCTCAAAAGAGCTCAACTAT
Found at i:54797769 original size:21 final size:21
Alignment explanation
Indices: 54797745--54797788 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
54797735 CATTATTAAT
* *
54797745 CAACACAGGCTGAACAGAGGC
1 CAACACAAGCTAAACAGAGGC
54797766 CAACACAAGCTAAACAGAGGC
1 CAACACAAGCTAAACAGAGGC
54797787 CA
1 CA
54797789 CACGGGCGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.30, G:0.23, T:0.05
Consensus pattern (21 bp):
CAACACAAGCTAAACAGAGGC
Found at i:54798409 original size:16 final size:17
Alignment explanation
Indices: 54798388--54798425 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
54798378 TATTAGTTAA
54798388 ATTATTTTATTTCC-TT
1 ATTATTTTATTTCCATT
54798404 ATTA-TTTATTTCCATT
1 ATTATTTTATTTCCATT
54798420 ATTATT
1 ATTATT
54798426 AATCAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 10 0.50
17 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTTTATTTCCATT
Found at i:54800070 original size:6 final size:6
Alignment explanation
Indices: 54800050--54800108 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
54800040 TTTGAGTCCA
*
54800050 TTTA-T TTTA-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTAGT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
54800096 TTCAGT TTTATT T
1 TTTATT TTTATT T
54800109 CTACTTATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 9 0.18
6 40 0.82
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:54802078 original size:47 final size:47
Alignment explanation
Indices: 54802019--54802140 Score: 226
Period size: 47 Copynumber: 2.6 Consensus size: 47
54802009 GCATTGGCAC
54802019 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
54802066 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
54802113 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
54802141 CCAAGGCATG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:54802240 original size:55 final size:54
Alignment explanation
Indices: 54802127--54802448 Score: 319
Period size: 55 Copynumber: 6.0 Consensus size: 54
54802117 ATAAGGATAT
* * * *
54802127 CATGTAAGACCATGCCAAGGCATGGCAATGATAAGTTCTATAAGGC-AAGGAAAT
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGG-TAC
* * * * *
54802181 CATGTAGGATCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGCAAAGGTAC
* * * *
54802236 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAAGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGGTAC
* * * * *
54802289 CATGTAAGACCATGTCAAGACATGGCATTAATAAGTTAGTATAAGGCATAGGTCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGCAAAGGTAC
* * *
54802344 CATGTAAGACCATGCCAAGGCATGGCATTGGTTAGTTC-ATAAGGC-AAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGG-TAC
* * * * * * * *
54802397 CACGTACGACCATGTCAAGACATGGCAATGGTAAGTTCAAAAAGGAAAAGGT
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGGT
54802449 TCCCGAGTAA
Statistics
Matches: 220, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
52 3 0.01
53 86 0.39
54 38 0.17
55 89 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAAGGTAC
Found at i:54802296 original size:53 final size:53
Alignment explanation
Indices: 54802122--54802435 Score: 313
Period size: 53 Copynumber: 5.8 Consensus size: 53
54802112 GTAAGATAAG
* * * *
54802122 GATATCATGTAAGACCATGCCAAGGCATGGCAATGATAAGTTCTATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC-ATAAGGCAAA
* * * * * *
54802176 GAAATCATGTAGGATCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-C-ATAAGGCAAA
* * * * *
54802231 GGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGCAAA
* * * *
54802284 GATACCATGTAAGACCATGTCAAGACATGGCATTAATAAGTTAGTATAAGGCATA
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT--CATAAGGCAAA
* * * * * *
54802339 GGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTTAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGCAAA
* * * * *
54802392 GATACCACGTACGACCATGTCAAGACATGGCAATGGTAAGTTCA
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCA
54802436 AAAAGGAAAA
Statistics
Matches: 213, Mismatches: 44, Indels: 7
0.81 0.17 0.03
Matches are distributed among these distances:
53 89 0.42
54 36 0.17
55 88 0.41
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGCAAA
Found at i:54802432 original size:108 final size:108
Alignment explanation
Indices: 54802127--54802433 Score: 452
Period size: 108 Copynumber: 2.8 Consensus size: 108
54802117 ATAAGGATAT
* * * * * *
54802127 CATGTAAGACCATGCCAAGGCATGGCAATGATAAGTTCTATAAGGCAAGGAAATCATGTAGGATC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTC-ATAAGGCAAGGATACCATGTAAGACC
*
54802192 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
65 ATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCC
* *
54802236 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAAGATACCATGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCATGTAAGACCA
* * *
54802301 TGTCAAGACATGGCATTAATAAGTTAGTATAAGGCATAGGTCC
66 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCC
* * *
54802344 CATGTAAGACCATGCCAAGGCATGGCATTGGTTAGTTCATAAGGCAAGGATACCACGTACGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCATGTAAGACCA
* *
54802409 TGTCAAGACATGGCAATGGTAAGTT
66 TGTCAAGACATGGCATTGATAAGTT
54802434 CAAAAAGGAA
Statistics
Matches: 179, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
108 144 0.80
109 35 0.20
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (108 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCATGTAAGACCA
TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCC
Found at i:54811654 original size:18 final size:17
Alignment explanation
Indices: 54811619--54811651 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54811609 CTTTTTATTC
54811619 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
54811636 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
54811652 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:54815512 original size:149 final size:150
Alignment explanation
Indices: 54815241--54815515 Score: 374
Period size: 149 Copynumber: 1.8 Consensus size: 150
54815231 CATTACAAAC
* * * * * * *
54815241 AATTTTAACTATTTCAATAATTCTTAATAAAAAGAGAATCCAGTAAAATTAATACTAGCTTACTT
1 AATTTTAACGATTTCAACAATTCTTAATAAAAAGAGAATACAATAAAATTAATACCAACTTACTG
* * *
54815306 TAATGGCAACCATGAATAAAAACAGAACTTGCTCATAACATATGTAGAGCATATTCAACAAACGT
66 CAATGGCAACCATGAATAAAAACAGAACTTGCTCATAACATATGAAGAACATATTCAACAAACGT
54815371 AACAACAGTACTAACATAAT
131 AACAACAGTACTAACATAAT
* *
54815391 AATTTTAACGATTTTAACAATTTTTAATAAAAA-AGAATACAATAAAATTAATACCAACTTACTG
1 AATTTTAACGATTTCAACAATTCTTAATAAAAAGAGAATACAATAAAATTAATACCAACTTACTG
* * * * *
54815455 CAATGGCAACCAT-ATATAAAAATAGATCTTTCTCGTACCATATGAAGAACATATTCAACAA
66 CAATGGCAACCATGA-ATAAAAACAGAACTTGCTCATAACATATGAAGAACATATTCAACAA
54815516 CAACAATAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
148 1 0.01
149 77 0.72
150 29 0.27
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (150 bp):
AATTTTAACGATTTCAACAATTCTTAATAAAAAGAGAATACAATAAAATTAATACCAACTTACTG
CAATGGCAACCATGAATAAAAACAGAACTTGCTCATAACATATGAAGAACATATTCAACAAACGT
AACAACAGTACTAACATAAT
Found at i:54815967 original size:24 final size:24
Alignment explanation
Indices: 54815934--54815986 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
54815924 CTGAAGATAC
*
54815934 AAAATGCAAAATTCTAAGTATTGA
1 AAAATACAAAATTCTAAGTATTGA
54815958 AAAATACAAAATTCTAAGTATTGA
1 AAAATACAAAATTCTAAGTATTGA
54815982 AAAAT
1 AAAAT
54815987 GGTCAAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (24 bp):
AAAATACAAAATTCTAAGTATTGA
Found at i:54816065 original size:20 final size:20
Alignment explanation
Indices: 54816037--54816078 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54816027 GAATTCAAGA
*
54816037 TCATAATAA-TGAAATGTTTT
1 TCATAATAAGT-AAATGGTTT
*
54816057 TCATCATAAGTAAATGGTTT
1 TCATAATAAGTAAATGGTTT
54816077 TC
1 TC
54816079 TATGTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (20 bp):
TCATAATAAGTAAATGGTTT
Found at i:54819477 original size:20 final size:20
Alignment explanation
Indices: 54819452--54819490 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54819442 TAAATTTCAA
*
54819452 ATATAAAATATTCATCAATT
1 ATATAAAATACTCATCAATT
*
54819472 ATATAAAATGCTCATCAAT
1 ATATAAAATACTCATCAAT
54819491 AAACTTCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.36
Consensus pattern (20 bp):
ATATAAAATACTCATCAATT
Found at i:54821990 original size:23 final size:22
Alignment explanation
Indices: 54821951--54821995 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
54821941 GATGATAAGT
* *
54821951 ATTTCTACAAATTATAAGAAAA
1 ATTTCTAAAAATGATAAGAAAA
*
54821973 ATTTCTAGAAAATGATAATAAAA
1 ATTTCTA-AAAATGATAAGAAAA
54821996 GAAAATCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
ATTTCTAAAAATGATAAGAAAA
Found at i:54826956 original size:27 final size:27
Alignment explanation
Indices: 54826873--54826958 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
54826863 AAGAATGGTT
* * *
54826873 GAGGGCTTGTCAGAGGCGGCACCGGTG
1 GAGGGCATGCCAGAGGCGGCACCAGTG
*
54826900 GAAGGCATGCCAGAGGCGGCACCAGTG
1 GAGGGCATGCCAGAGGCGGCACCAGTG
* *
54826927 GAGGGCATGCTAGAGGCGGCACTAGTG
1 GAGGGCATGCCAGAGGCGGCACCAGTG
54826954 GAGGG
1 GAGGG
54826959 GTTGTCAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.47, T:0.12
Consensus pattern (27 bp):
GAGGGCATGCCAGAGGCGGCACCAGTG
Found at i:54826968 original size:27 final size:27
Alignment explanation
Indices: 54826873--54826979 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 27
54826863 AAGAATGGTT
* *
54826873 GAGGGCTTGTCAGAGGCGGCACCGGTG
1 GAGGGCATGTCAGAGGCGGCACCAGTG
* *
54826900 GAAGGCATGCCAGAGGCGGCACCAGTG
1 GAGGGCATGTCAGAGGCGGCACCAGTG
*
54826927 GAGGGCATG-CTAGAGGCGGCACTAGTG
1 GAGGGCATGTC-AGAGGCGGCACCAGTG
** **
54826954 GAGGGGTTGTCAGAGGCAACACCAGT
1 GAGGGCATGTCAGAGGCGGCACCAGT
54826980 TGTGCCTATC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.01
27 65 0.97
28 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.43, T:0.13
Consensus pattern (27 bp):
GAGGGCATGTCAGAGGCGGCACCAGTG
Found at i:54827113 original size:18 final size:19
Alignment explanation
Indices: 54827092--54827127 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54827082 GAGAAGAGAA
54827092 GAGAAGAAAG-AAAGAAAT
1 GAGAAGAAAGAAAAGAAAT
54827110 GAGAAGAAAGAAAAGAAA
1 GAGAAGAAAGAAAAGAAA
54827128 AGGTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (19 bp):
GAGAAGAAAGAAAAGAAAT
Found at i:54827326 original size:27 final size:27
Alignment explanation
Indices: 54827296--54827353 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
54827286 GAATGTTATC
*** *
54827296 TTGTAAAAAATTTTAATATATTTGATA
1 TTGTAAAAAATGACAATAAATTTGATA
* *
54827323 TTGTTAGAAATGACAATAAATTTGATA
1 TTGTAAAAAATGACAATAAATTTGATA
54827350 TTGT
1 TTGT
54827354 TAGAAATGGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (27 bp):
TTGTAAAAAATGACAATAAATTTGATA
Found at i:54827354 original size:27 final size:27
Alignment explanation
Indices: 54827310--54827361 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
54827300 AAAAAATTTT
*
54827310 AATATATTTGATATTGTTAGAAATGAC
1 AATAAATTTGATATTGTTAGAAATGAC
54827337 AATAAATTTGATATTGTTAGAAATG
1 AATAAATTTGATATTGTTAGAAATG
54827362 GACTATTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.40
Consensus pattern (27 bp):
AATAAATTTGATATTGTTAGAAATGAC
Found at i:54828960 original size:126 final size:125
Alignment explanation
Indices: 54828799--54829027 Score: 370
Period size: 126 Copynumber: 1.8 Consensus size: 125
54828789 AGCTTTAAGA
* *
54828799 GGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACTCAGTACATTAGGGCACGATCCTCTG
1 GGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACATTAGGGCACAATCCTCTG
* *
54828864 AATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACCGGTAAAG
66 AATTCTTTAAATACCAAACATTGCCATTATTTT-AAAAATTTTGAGAGTGAACCGGTAAAG
* * *
54828925 GGATATTCTG-ATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACAATCCTTT
1 GGATATTC-GAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACATTAGGGCACAATCCTCT
54828989 GAATTCTTTAAATACCAAACATTGCCATTATTTTAAAAA
65 GAATTCTTTAAATACCAAACATTGCCATTATTTTAAAAA
54829028 CAATTGAGAA
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
125 5 0.05
126 89 0.94
127 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (125 bp):
GGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACATTAGGGCACAATCCTCTG
AATTCTTTAAATACCAAACATTGCCATTATTTTAAAAATTTTGAGAGTGAACCGGTAAAG
Found at i:54830673 original size:17 final size:15
Alignment explanation
Indices: 54830640--54830675 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
54830630 GAGGTTTAGG
54830640 TGGGTTTTGGGGTAT
1 TGGGTTTTGGGGTAT
54830655 TGGGTTATTGGGTGTAT
1 TGGGTT-TTGGG-GTAT
54830672 TGGG
1 TGGG
54830676 CTTAGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.44
Consensus pattern (15 bp):
TGGGTTTTGGGGTAT
Found at i:54831080 original size:85 final size:85
Alignment explanation
Indices: 54830964--54831265 Score: 493
Period size: 85 Copynumber: 3.6 Consensus size: 85
54830954 AGCGAAGATA
** * *
54830964 AGATCTGT-AATTTTAGCCTGTTACCCTACTGCTTAAAGGGTTAAGACGGGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
54831028 CACCACTGCTCGGAGAG-CC
66 CACCACTGCTCGGAGAGCCC
*
54831047 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACTTGCT
1 A-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCT
*
54831112 CCACCACTGTTCGGTA-AGCCC
65 CCACCACTGCTCGG-AGAGCCC
*
54831133 AGATCTATAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
*
54831198 CACCACTGCTCGGTGAGCCC
66 CACCACTGCTCGGAGAGCCC
54831218 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
54831266 TTGTATCTTT
Statistics
Matches: 203, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
83 1 0.00
84 7 0.03
85 191 0.94
86 4 0.02
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
CACCACTGCTCGGAGAGCCC
Found at i:54831339 original size:87 final size:87
Alignment explanation
Indices: 54830963--54831355 Score: 410
Period size: 85 Copynumber: 4.6 Consensus size: 87
54830953 CAGCGAAGAT
* ** * *
54830963 AAGATCTGT-AATTTTAGCCTGTTACCCTACTGCTTAAAGGGTTAAGAC--GGGTCTTCGACCTG
1 AAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAGTCTTCGACCTG
* * *
54831025 CTCCACCACTGCTCGGAGAGCC
66 CTCCACCACTGCTAGGTGAGAC
* * *
54831047 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC--GAGTCTTCGACTTG
1 AAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAGTCTTCGACCTG
* * * *
54831110 CTCCACCACTGTTCGGTAAGCC
66 CTCCACCACTGCTAGGTGAGAC
* * *
54831132 CAGATCTATAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC--GAGTCTTCGACCTG
1 AAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAGTCTTCGACCTG
* *
54831195 CTCCACCACTGCTCGGTGAGCC
66 CTCCACCACTGCTAGGTGAGAC
* * * *
54831217 CAGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTA-TCTTTGATCT
1 AAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTG-AGTCTTCGACCT
* * *
54831281 GCTCCACTATTGCTTAGG-GAGAT
65 GCTCCACCACTGC-TAGGTGAGAC
* * * *
54831304 AAGATCTGT-AATCTTCAGCTTGTTACCCTATTGCTTAGGGAGTTAAAGCTTG
1 AAGATCTGTAAAT-TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTG
54831356 CTGAAATTTT
Statistics
Matches: 274, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
84 8 0.03
85 194 0.71
86 3 0.01
87 65 0.24
88 4 0.01
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (87 bp):
AAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAGTCTTCGACCTG
CTCCACCACTGCTAGGTGAGAC
Found at i:54844586 original size:40 final size:40
Alignment explanation
Indices: 54844527--54844674 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
54844517 GAGCATTGGA
* *
54844527 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
54844567 ATATATCCGGGCTATGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
54844607 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
54844647 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
54844675 ATGTGTTTGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:54850988 original size:79 final size:81
Alignment explanation
Indices: 54850852--54851034 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
54850842 TCGAATGATG
* *
54850852 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
54850916 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
54850931 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
54850993 TTTGTGTGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
54851011 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
54851035 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:54851050 original size:40 final size:40
Alignment explanation
Indices: 54850853--54851036 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
54850843 CGAATGATGT
* * * *
54850853 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
54850893 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
54850933 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
54850971 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
54851012 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54851037 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:54851058 original size:79 final size:79
Alignment explanation
Indices: 54850905--54851069 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
54850895 GGACTAAGAT
* **
54850905 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
54850970 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
54850984 CCGAAGGCATTTGTGTGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
54851047 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
54851063 CCGAAGG
1 CCGAAGG
54851070 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:54857416 original size:21 final size:21
Alignment explanation
Indices: 54857390--54857434 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
54857380 GCTGGCTTAT
*
54857390 CATGTTGTTCT-GTGATTCCAG
1 CATGTTGTTCTCG-GACTCCAG
*
54857411 CATGTTTTTCTCGGACTCCAG
1 CATGTTGTTCTCGGACTCCAG
54857432 CAT
1 CAT
54857435 TTGATCCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTCGGACTCCAG
Found at i:54866459 original size:47 final size:47
Alignment explanation
Indices: 54866408--54866567 Score: 257
Period size: 47 Copynumber: 3.4 Consensus size: 47
54866398 TTGTGATGTG
* *
54866408 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
54866455 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * * *
54866502 AGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
*
54866549 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
54866568 TCCCGAAGGG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 105 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
Found at i:54866742 original size:37 final size:37
Alignment explanation
Indices: 54866686--54866764 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54866676 CCGAGCTCTA
* * *
54866686 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
54866723 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54866760 AAGAC
1 AAGAC
54866765 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54869883 original size:28 final size:28
Alignment explanation
Indices: 54869830--54869913 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
54869820 CACTTTGTGC
54869830 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
54869859 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
54869887 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
54869914 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:54869925 original size:23 final size:24
Alignment explanation
Indices: 54869834--54869927 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
54869824 TTGTGCTATT
54869834 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
54869861 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
54869891 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
54869914 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
54869928 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:54870155 original size:22 final size:23
Alignment explanation
Indices: 54870118--54870162 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
54870108 GCTTTACTGA
54870118 TCAGGCACTTTATGTGTAGTATT
1 TCAGGCACTTTATGTGTAGTATT
*
54870141 TCAGGCAC-TTATGTGTCGTATT
1 TCAGGCACTTTATGTGTAGTATT
54870163 CTGATCAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTAGTATT
Found at i:54872979 original size:19 final size:19
Alignment explanation
Indices: 54872955--54872994 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
54872945 TGCAAGTAAG
54872955 TTCAATTCTTGATTATTTC
1 TTCAATTCTTGATTATTTC
54872974 TTCAATTCTTGATTATTTC
1 TTCAATTCTTGATTATTTC
54872993 TT
1 TT
54872995 GAAATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (19 bp):
TTCAATTCTTGATTATTTC
Found at i:54875296 original size:18 final size:18
Alignment explanation
Indices: 54875273--54875307 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54875263 TAATAGATAT
54875273 ACTTAAAATCAAGTTGGC
1 ACTTAAAATCAAGTTGGC
*
54875291 ACTTAAAATCTAGTTGG
1 ACTTAAAATCAAGTTGG
54875308 ATTGCCACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (18 bp):
ACTTAAAATCAAGTTGGC
Found at i:54876009 original size:33 final size:32
Alignment explanation
Indices: 54875972--54876061 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 32
54875962 GAGCCGGTAG
*
54875972 GAGTGCCATACTGCGGTGGATACGACCTAGGAA
1 GAGTGCAATACTGCGGTGGATACGACC-AGGAA
* *
54876005 GAGTG-AAGTACTGCGATGGATACAGGCCAGGAA
1 GAGTGCAA-TACTGCGGTGGATAC-GACCAGGAA
* *
54876038 GACTGCTATACTGCGGTGGATACG
1 GAGTGCAATACTGCGGTGGATACG
54876062 GGCTCTAGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
32 2 0.04
33 42 0.88
34 4 0.08
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (32 bp):
GAGTGCAATACTGCGGTGGATACGACCAGGAA
Found at i:54876124 original size:33 final size:33
Alignment explanation
Indices: 54876041--54876125 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
54876031 CCAGGAAGAC
* * * * *
54876041 TGCTATACTGCGGTGGATACGGGCTCTAGGGAA
1 TGCTGTACTGCGGTGGATAAGGGCCCGAAGGAA
** *
54876074 TGCTGTACTATGATGGATAAGGGCCCGAAGGAA
1 TGCTGTACTGCGGTGGATAAGGGCCCGAAGGAA
54876107 TGCTGTACTGCGGTGGATA
1 TGCTGTACTGCGGTGGATA
54876126 CGACCCAAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (33 bp):
TGCTGTACTGCGGTGGATAAGGGCCCGAAGGAA
Found at i:54876963 original size:14 final size:14
Alignment explanation
Indices: 54876944--54876978 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
54876934 CAAATTACAT
54876944 GTTAGAATAGTATC
1 GTTAGAATAGTATC
54876958 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
54876972 ATTAGAA
1 GTTAGAA
54876979 ATAAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:54879197 original size:27 final size:27
Alignment explanation
Indices: 54879142--54879206 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
54879132 ATCCATAGTG
*
54879142 GTGCCGCCTCTGCCATCCCCACCACCA
1 GTGCCGCCTCTGCCATCCCCACCAACA
*
54879169 GTGCCGCCTAC-GCCAGT-CCCTCCAACA
1 GTGCCGCCT-CTGCCA-TCCCCACCAACA
*
54879196 GTGCCACCTCT
1 GTGCCGCCTCT
54879207 TCCCTAGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.03
27 29 0.91
28 2 0.06
ACGTcount: A:0.15, C:0.51, G:0.17, T:0.17
Consensus pattern (27 bp):
GTGCCGCCTCTGCCATCCCCACCAACA
Found at i:54879606 original size:21 final size:21
Alignment explanation
Indices: 54879581--54879624 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54879571 TATTAGAATA
*
54879581 TTACATAATT-TATAATTTAAT
1 TTACATAATTAT-TAATATAAT
54879602 TTACATAATTATTAATATAAT
1 TTACATAATTATTAATATAAT
54879623 TT
1 TT
54879625 TATAACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTACATAATTATTAATATAAT
Found at i:54879834 original size:22 final size:22
Alignment explanation
Indices: 54879809--54879853 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54879799 GATGTAATGG
*
54879809 TAAAGTATAT-TACATTTTTAAA
1 TAAA-TATATATACATATTTAAA
*
54879831 TAAATATATATATATATTTAAA
1 TAAATATATATACATATTTAAA
54879853 T
1 T
54879854 TTTAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAATATATATACATATTTAAA
Found at i:54883163 original size:24 final size:24
Alignment explanation
Indices: 54883134--54883179 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54883124 TTTCTATATT
*
54883134 AATTTTAATAATATTTTTTATTCA
1 AATTTTAATAATATTATTTATTCA
54883158 AATTTTAATAATATTATTTATT
1 AATTTTAATAATATTATTTATT
54883180 AATTCAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTTTAATAATATTATTTATTCA
Found at i:54883220 original size:23 final size:24
Alignment explanation
Indices: 54883169--54883221 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
54883159 ATTTTAATAA
* *
54883169 TATTATTTATTAATTCAATGTTAT
1 TATTATTTATTAACTCAATATTAT
54883193 T-TTATTTAATT-ACTCAATATT-T
1 TATTATTT-ATTAACTCAATATTAT
54883215 TATTATT
1 TATTATT
54883222 GCTTTATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 19 0.76
24 4 0.16
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TATTATTTATTAACTCAATATTAT
Found at i:54885959 original size:5 final size:5
Alignment explanation
Indices: 54885949--54885974 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
54885939 CTGTAATTAC
54885949 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
54885975 GATGCTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:54887209 original size:21 final size:21
Alignment explanation
Indices: 54887184--54887223 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54887174 TCACAAAACT
54887184 TATTTATA-TTTTAATTAATCA
1 TATTT-TAGTTTTAATTAATCA
*
54887205 TATTTTAGTTTTAGTTAAT
1 TATTTTAGTTTTAATTAAT
54887224 ATTAATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
TATTTTAGTTTTAATTAATCA
Found at i:54890033 original size:18 final size:18
Alignment explanation
Indices: 54889997--54890035 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54889987 AAGAAATATA
*
54889997 AAAAATACATAATATTTT
1 AAAAATACATAATAATTT
54890015 AAAAATA-ATAATAAATTT
1 AAAAATACATAAT-AATTT
54890033 AAA
1 AAA
54890036 TTTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATACATAATAATTT
Found at i:54890088 original size:24 final size:24
Alignment explanation
Indices: 54890039--54890090 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
54890029 ATTTAAATTT
* *
54890039 TATATTAATATTAAATACATATAA
1 TATATCAATATTAAATAAATATAA
54890063 TATATCAATATTAAATAAA-ATAA
1 TATATCAATATTAAATAAATATAA
54890086 -ATATC
1 TATATC
54890091 TTCCATCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 5 0.19
23 4 0.15
24 17 0.65
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TATATCAATATTAAATAAATATAA
Found at i:54892113 original size:573 final size:577
Alignment explanation
Indices: 54890739--54892118 Score: 1767
Period size: 585 Copynumber: 2.4 Consensus size: 577
54890729 ATTTATTCCA
* * * * * *
54890739 TTTTCTCTTCTGAATAGATCGTGTTCTTCACCTAAGTTATTCAATCGAGAAAGAGATCATGAATA
1 TTTTCTCTTTTGAATCGATCAT-TTTTTCACCTAATTTATTCAATCGAGAAAGAGATTATGAATA
* * * * *
54890804 ACATTAGTGGCTAAATCGCTTA-AGGGAGATTAACAAGTGGATAGGGATGTTATTAATGAAGGAT
65 ACATGAGTGGCTAAATC-CTTAGA-GGAGATTAACGAGTGGATGGGGATGTGATTAATAAAGGAT
* *
54890868 TTAGGGTTTCTTGA-ATGGGAATAGTTAGTATAAATTACGTATGCTTAAACCACTAAGCTTGACA
128 TTAGGGTTTCTTGAGA-GGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGAC-
* * *
54890932 AAGC-TAGAAAGTTATCATAGGCAATACGACCACAAAAACAACAACGATCCACTCAAGCACTGAG
191 AACCTTAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGAG
* * ** ** *
54890996 TAATCTTGATGCCAATCGTTTCCATAATACGAAAGTCAAACTTTTTTTTCAACAAATGAGTGGAC
256 TAATATCGATGCCAATCACTTCCATAATACGAAAGTCAAACGGTTTTTTCAACAAATGAGTAGAC
* * * *
54891061 AATCATTTATACAAGAAAGTGTGTTCGATCCTATCATGACTGTTTACCATGAAATATGAGAGTTG
321 AATCATTTATACAAGAAAGTGGGTTCGATCCCAACATGACTGCTTACCATGAAATATGAGAGTTG
* **
54891126 GTACAGTTCCATCATTGGAACAAATTTTGCGCAACCTCGACTTAACTGGCGGTTAACGTAGTAGT
386 GTACAGTTCCATCATTGGAACAAATTTT------CCTCGACTGAACTGGCGGTTAACCCAGTAGT
* * ** *
54891191 TTATGAATCCTACGCCTCCCTGAAAGATAAGGAGAATTTCTAGCAACGTGGCGAGATGATCTCTC
445 TTATGAAACCTACGCCTCCCTAAAAGATAAGGAGAATCACTAGCAACGTGGCGAGATGATCTCTA
* * ** **
54891256 TTGTGGTTGTTAGGGGAAAAGAGGTGTCGATTGCATCTTGTGATCAAATCCATTATTATTCCATT
510 TAGTGGTTGTTAAGGGAAAAGAGGTGTCGATTGCATCTTGCAATCAAATCCACAATTATTCCATT
54891321 CTC
575 CTC
* *
54891324 TTTTCTCTTTTGAATCGATTATTTTCTTCACCTGATTTATTCAATCGAGAAAGAGATTATGAATA
1 TTTTCTCTTTTGAATCGATCATTTT-TTCACCTAATTTATTCAATCGAGAAAGAGATTATGAATA
* * * * *
54891389 ACATGAGTGGCTAAAACCCTTAGAGGAGATTAATGAGTGGATGAGAATGTGATTAATAGAGGATT
65 ACATGAGTGGCT-AAATCCTTAGAGGAGATTAACGAGTGGATGGGGATGTGATTAATAAAGGATT
* *
54891454 TAGGGTTT-TCGAAGAGGGATTAGTTAGTATGAATTACGTATGCCTAAACCACTAAGCTTGACAA
129 TAGGGTTTCTTG-AGAGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAA
* * *
54891518 CCTTAGGAATTTATCATAGGCAAGATGACCACGAAAACAACAACGATCCACTCAAGCA-TCGAGT
193 CCTTAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACT-GAGT
* * * **** *
54891582 AATATCGATGCCAATCACTTCTATAATACGGAAGTCGAACGGTTTTTTGTTTAAATGAGTAGACG
257 AATATCGATGCCAATCACTTCCATAATACGAAAGTCAAACGGTTTTTTCAACAAATGAGTAGACA
* * * *
54891647 ATCTTTTATACAAGAACA-TGGGTTCGATCCCAACATGACTGCTTGCGATGAAATATGGGAGTTG
322 ATCATTTATACAAGAA-AGTGGGTTCGATCCCAACATGACTGCTTACCATGAAATATGAGAGTTG
* * *
54891711 GTACAGTTCCATCATTGGAACAAA-TTT-CTCGACTGAACTTGTGGTTGACCCAGTAGTTTATGA
386 GTACAGTTCCATCATTGGAACAAATTTTCCTCGACTGAACTGGCGGTTAACCCAGTAGTTTATGA
* * * * **
54891774 AACC-ATGCC-CTCTAAAAGTTAGGGAGAATCACTAGCAGTGTGGCGAGATGATCTCTATAGTGG
451 AACCTACGCCTCCCTAAAAGATAAGGAGAATCACTAGCAACGTGGCGAGATGATCTCTATAGTGG
54891837 TTGTTAAGGGAAAAGAGGTGTCGATTGCA-CTTCGCAATCAAATCCACAATTATT-CATTCTC
516 TTGTTAAGGGAAAAGAGGTGTCGATTGCATCTT-GCAATCAAATCCACAATTATTCCATTCTC
*
54891898 TTTTCTCTTTTGAATCGATCATTTTTTCACCTAATTTATTCAATCGAGAAAGCGATTATGAATAA
1 TTTTCTCTTTTGAATCGATCATTTTTTCACCTAATTTATTCAATCGAGAAAGAGATTATGAATAA
* * * *
54891963 TATGAGTGGCTAAATCCATTAGAGGAGATGAACGAGTGGATGGGGATGTGATTAACAAAAGATTT
66 CATGAGTGGCTAAATCC-TTAGAGGAGATTAACGAGTGGATGGGGATGTGATTAATAAAGGATTT
* * * *
54892028 AGGGTTTCTTGAGAGGGATTAGTTAGTATGCATTATGTATGCTTAAACTACTAGGCTTGACAACC
130 AGGGTTTCTTGAGAGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACC
54892093 TTAGGAAGTTATCATAGGCAAGACGA
195 TTAGGAAGTTATCATAGGCAAGACGA
54892119 GGTCAAGAGA
Statistics
Matches: 690, Mismatches: 94, Indels: 34
0.84 0.11 0.04
Matches are distributed among these distances:
572 5 0.01
573 168 0.24
574 36 0.05
575 89 0.13
576 4 0.01
577 33 0.05
584 11 0.02
585 337 0.49
586 7 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (577 bp):
TTTTCTCTTTTGAATCGATCATTTTTTCACCTAATTTATTCAATCGAGAAAGAGATTATGAATAA
CATGAGTGGCTAAATCCTTAGAGGAGATTAACGAGTGGATGGGGATGTGATTAATAAAGGATTTA
GGGTTTCTTGAGAGGGATTAGTTAGTATGAATTACGTATGCTTAAACCACTAAGCTTGACAACCT
TAGGAAGTTATCATAGGCAAGACGACCACAAAAACAACAACGATCCACTCAAGCACTGAGTAATA
TCGATGCCAATCACTTCCATAATACGAAAGTCAAACGGTTTTTTCAACAAATGAGTAGACAATCA
TTTATACAAGAAAGTGGGTTCGATCCCAACATGACTGCTTACCATGAAATATGAGAGTTGGTACA
GTTCCATCATTGGAACAAATTTTCCTCGACTGAACTGGCGGTTAACCCAGTAGTTTATGAAACCT
ACGCCTCCCTAAAAGATAAGGAGAATCACTAGCAACGTGGCGAGATGATCTCTATAGTGGTTGTT
AAGGGAAAAGAGGTGTCGATTGCATCTTGCAATCAAATCCACAATTATTCCATTCTC
Found at i:54893730 original size:13 final size:13
Alignment explanation
Indices: 54893704--54893742 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
54893694 ACCTAAGTCC
54893704 ATAACAGAAACAG
1 ATAACAGAAACAG
* *
54893717 ATATCAGAATCAG
1 ATAACAGAAACAG
54893730 ATAACAGATAACA
1 ATAACAGA-AACA
54893743 TATCAGATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 18 0.86
14 3 0.14
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (13 bp):
ATAACAGAAACAG
Found at i:54893747 original size:19 final size:19
Alignment explanation
Indices: 54893703--54893750 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
54893693 GACCTAAGTC
* *
54893703 CATAACAGA-AACAGATAT
1 CATATCAGATAACAGATAA
*
54893721 CAGAATCAGATAACAGATAA
1 CA-TATCAGATAACAGATAA
54893741 CATATCAGAT
1 CATATCAGAT
54893751 GTACAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.08
19 12 0.50
20 10 0.42
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (19 bp):
CATATCAGATAACAGATAA
Found at i:54894880 original size:7 final size:7
Alignment explanation
Indices: 54894868--54894910 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
54894858 CCCAACATCC
54894868 CCACTAA
1 CCACTAA
54894875 CCACTAA
1 CCACTAA
54894882 CCACTAA
1 CCACTAA
54894889 CCACTAA
1 CCACTAA
54894896 CCACTAA
1 CCACTAA
54894903 CCACTAA
1 CCACTAA
54894910 C
1 C
54894911 ACCCTTATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.14
Consensus pattern (7 bp):
CCACTAA
Found at i:54899063 original size:17 final size:18
Alignment explanation
Indices: 54899043--54899087 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
54899033 GAGTAGCTAA
54899043 TAAGT-TAGTTAGACTGT
1 TAAGTCTAGTTAGACTGT
*
54899060 TAAGTCTA-TTAGGCTGT
1 TAAGTCTAGTTAGACTGT
54899077 TAAGTCTAGTT
1 TAAGTCTAGTT
54899088 GTTAGTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (18 bp):
TAAGTCTAGTTAGACTGT
Found at i:54902460 original size:53 final size:54
Alignment explanation
Indices: 54902390--54902597 Score: 195
Period size: 53 Copynumber: 3.9 Consensus size: 54
54902380 TTTCCTTTTT
* * * *
54902390 GAACTTACCATTTCCATGTCTTGACATGGCCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * *
54902443 GAACTCACCATTGCCATGCCTTGGCATAGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCATTGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* * * * *
54902497 GTAACTCATCAATGCAATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* ** * * * * *
54902552 GAACTTATAAATGTCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTCACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTT
54902598 ATCTTACAAA
Statistics
Matches: 127, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
52 2 0.02
53 42 0.33
54 39 0.31
55 42 0.33
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
GAACTCACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:54902590 original size:54 final size:53
Alignment explanation
Indices: 54902404--54902597 Score: 194
Period size: 55 Copynumber: 3.6 Consensus size: 53
54902394 TTACCATTTC
* * * * * *
54902404 CATGTCTTGACATGGCCTTACGTGGTATCCTTGCCTTAT-GAACTCACCATTG
1 CATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATG
* * **
54902456 CCATGCCTTGGCATAGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAATG
1 -CATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AACTCATCAATG
* * * *
54902511 CAATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATAAATG
1 C-ATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATG
*
54902565 TCATGCCTTGGCATGGTCTTACATGATATCCTT
1 -CATGCCTTGACATGGTCTTACATGATATCCTT
54902598 ATCTTACAAA
Statistics
Matches: 116, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
52 2 0.02
53 30 0.26
54 40 0.34
55 42 0.36
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
CATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAATG
Found at i:54903026 original size:25 final size:25
Alignment explanation
Indices: 54902997--54903058 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 25
54902987 TAAATAAGAA
54902997 ATAATAATTATAATAAT-TTAATAAT
1 ATAATAATTATAATAATGTTAA-AAT
54903022 ATAATAA-TAT-AT-ATGTTAAAAT
1 ATAATAATTATAATAATGTTAAAAT
*
54903044 AAAATAATTA-AATAA
1 ATAATAATTATAATAA
54903059 AAGAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
22 11 0.34
23 10 0.31
24 4 0.12
25 7 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATAATTATAATAATGTTAAAAT
Found at i:54903030 original size:8 final size:8
Alignment explanation
Indices: 54902997--54903032 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
54902987 TAAATAAGAA
54902997 ATAATAATT
1 ATAATAA-T
54903006 ATAATAAT
1 ATAATAAT
*
54903014 TTAATAAT
1 ATAATAAT
54903022 ATAATAAT
1 ATAATAAT
54903030 ATA
1 ATA
54903033 TATGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAATAAT
Found at i:54903065 original size:9 final size:10
Alignment explanation
Indices: 54903053--54903090 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
54903043 TAAAATAATT
54903053 AAATA-AAAG
1 AAATAGAAAG
54903062 AAATA-AAAG
1 AAATAGAAAG
54903071 AAA-AGAAAG
1 AAATAGAAAG
54903080 AAATAGAAAG
1 AAATAGAAAG
54903090 A
1 A
54903091 GGATAGAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 1 0.04
9 19 0.70
10 7 0.26
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (10 bp):
AAATAGAAAG
Found at i:54904155 original size:6 final size:6
Alignment explanation
Indices: 54904144--54904170 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
54904134 CTATTAATTA
54904144 TGTGAC TGTGAC TGTGAC TGTGAC TGT
1 TGTGAC TGTGAC TGTGAC TGTGAC TGT
54904171 TATACAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (6 bp):
TGTGAC
Found at i:54905239 original size:47 final size:46
Alignment explanation
Indices: 54905176--54905309 Score: 139
Period size: 45 Copynumber: 2.9 Consensus size: 46
54905166 TGTCTTAGTT
** ** *
54905176 CCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATCAATG
1 CCAATGCCATGTCTTGACATGGTCTTACATGGAGTCCTTAA-CAATA
* **
54905223 CCAATGCCATGTCTTGACATGGTCTTACACGG-GATCCTT-ACCTTA
1 CCAATGCCATGTCTTGACATGGTCTTACATGGAG-TCCTTAACAATA
*
54905268 CCAATGCCATGTCTTCACATGGTCTTACATGGTA-TCCTTAAC
1 CCAATGCCATGTCTTGACATGGTCTTACATGG-AGTCCTTAAC
54905310 CGTCAATTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
45 37 0.51
46 4 0.05
47 32 0.44
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (46 bp):
CCAATGCCATGTCTTGACATGGTCTTACATGGAGTCCTTAACAATA
Done.