Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 163 of 344
Found at i:54425941 original size:45 final size:44
Alignment explanation
Indices: 54425877--54426001 Score: 146
Period size: 45 Copynumber: 2.8 Consensus size: 44
54425867 CTAGGAATTA
*
54425877 AGAAATACGAACTTGTTGAGTTGGTCCGAGTTCAT-GATATATGTG
1 AGAAAT-CGAACTTGTTGAGTTGGTCCAAGTTCATAG-TATATGTG
*
54425922 AGAAATCTGAACTTGTTGAGTTGGTCCAAGTTCGTAGTATATGTG
1 AGAAATC-GAACTTGTTGAGTTGGTCCAAGTTCATAGTATATGTG
* * *
54425967 A-AGCATCCGAGCTCGTTGAGTTGGTCCAAGTTCAT
1 AGA-AAT-CGAACTTGTTGAGTTGGTCCAAGTTCAT
54426002 TATGGATGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
44 2 0.03
45 66 0.94
46 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (44 bp):
AGAAATCGAACTTGTTGAGTTGGTCCAAGTTCATAGTATATGTG
Found at i:54444340 original size:18 final size:18
Alignment explanation
Indices: 54444317--54444354 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
54444307 AGGCTTGGCT
54444317 AATAAGGAAATTT-GATAA
1 AATAAGG-AATTTCGATAA
54444335 AATAAGGAATTTCGATAA
1 AATAAGGAATTTCGATAA
54444353 AA
1 AA
54444355 ATCAACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.55, C:0.03, G:0.16, T:0.26
Consensus pattern (18 bp):
AATAAGGAATTTCGATAA
Found at i:54446130 original size:19 final size:19
Alignment explanation
Indices: 54446106--54446152 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
54446096 TCTCGTATGG
54446106 CATAGGCTCTAGCTGGAGC
1 CATAGGCTCTAGCTGGAGC
54446125 CATAGGCTCTAGCTGGAGC
1 CATAGGCTCTAGCTGGAGC
*
54446144 CCTAGGCTC
1 CATAGGCTC
54446153 AGATCGCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (19 bp):
CATAGGCTCTAGCTGGAGC
Found at i:54454226 original size:61 final size:62
Alignment explanation
Indices: 54454115--54454247 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 62
54454105 GTGACGACAC
* * *
54454115 GGCCGTGTGAACAACAAAAGCCAGGTCGTGCGCGAGACACGGTCGAGTGATGGCCAGAGTGT
1 GGCCGTGTGAACAACAAAAGCCAGGTCGTGCGCGAGACACAGCCGAGTGATAGCCAGAGTGT
* * * *
54454177 GGCCATGTGAACAA-AAAGGTCAGGTCGTGCGCGAGACACAGCCGTGTGATAGCCAGAGTGT
1 GGCCGTGTGAACAACAAAAGCCAGGTCGTGCGCGAGACACAGCCGAGTGATAGCCAGAGTGT
54454238 GGCCGTGTGA
1 GGCCGTGTGA
54454248 GCCACACGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
61 50 0.79
62 13 0.21
ACGTcount: A:0.26, C:0.22, G:0.37, T:0.16
Consensus pattern (62 bp):
GGCCGTGTGAACAACAAAAGCCAGGTCGTGCGCGAGACACAGCCGAGTGATAGCCAGAGTGT
Found at i:54457121 original size:46 final size:46
Alignment explanation
Indices: 54457054--54457222 Score: 196
Period size: 46 Copynumber: 3.7 Consensus size: 46
54457044 CGCCCCTAAG
* * *
54457054 TGAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTAGCATCCATAAA
* * * * **
54457100 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACG-TTAGCATCCAT-AAA
* * * *
54457147 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACGTTAGCATCCATAAA
54457193 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
54457223 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
46 64 0.64
47 36 0.36
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACGTTAGCATCCATAAA
Found at i:54457164 original size:93 final size:93
Alignment explanation
Indices: 54457055--54457225 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54457045 GCCCCTAAGT
*
54457055 GAACTCGAACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54457120 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
54457148 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54457213 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54457226 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54478227 original size:46 final size:45
Alignment explanation
Indices: 54478160--54478324 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 45
54478150 CGCCCCTAAG
*
54478160 TGAACTCGGACTCAACTCAACGAGGTCAGGCTTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCAGGCTTT-GCATCCATAAA
* * *
54478206 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTC--A-GGCT--TTGCATCCATAAA
* *
54478253 CGAACTCGGACTCAACTCAACGAGTTC-GGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCAGG-C-TTTGCATCCATAAA
54478299 TGAACTC-GACTCAACTCAACGAGTTC
1 TGAACTCGGACTCAACTCAACGAGTTC
54478325 GGATGCTCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 21 0.21
46 32 0.32
47 27 0.27
48 2 0.02
49 4 0.04
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCAGGCTTTGCATCCATAAA
Found at i:54478276 original size:93 final size:92
Alignment explanation
Indices: 54478161--54478330 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 92
54478151 GCCCCTAAGT
54478161 GAACTCGGACTCAACTCAACGAGGTCAGG-C-TTTCGCATCCATAAATGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGGTC-GGACATTT-GCATCCATAAATGAACTC-GACTCAACTC
54478224 AACGAGTTCGGATGCCTAGTTACATCTCAC
63 AACGAGTTCGGATGCCTAGTTACATCTCAC
* *
54478254 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGGTCGGACATTTGCATCCATAAATGAACTCGACTCAACTCAAC
54478319 GAGTTCGGATGC
66 GAGTTCGGATGC
54478331 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
92 27 0.37
93 43 0.59
94 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGGTCGGACATTTGCATCCATAAATGAACTCGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54478346 original size:45 final size:45
Alignment explanation
Indices: 54478158--54478346 Score: 131
Period size: 46 Copynumber: 4.1 Consensus size: 45
54478148 CCCGCCCCTA
* * * * * *
54478158 AGTGAACTCGGACTCAACTCAACGAGGTCAGGCTTTCGCATCCAT-A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGCTCAACCATCT
*
54478204 AATGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * *
54478251 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
54478297 AGTGAACTC-GACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
54478342 AGTGA
1 AGTGA
54478347 CATGTCACTT
Statistics
Matches: 114, Mismatches: 14, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
43 9 0.08
44 4 0.04
45 29 0.25
46 36 0.32
47 31 0.27
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:54481259 original size:64 final size:64
Alignment explanation
Indices: 54481178--54481361 Score: 183
Period size: 67 Copynumber: 2.8 Consensus size: 64
54481168 AGACATTATG
* *
54481178 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAAACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAAACAAGAGAGCTACGAGATAA
* * * * * * *
54481242 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAAACAAGAGAGCTACGAGAT
54481307 AA
63 AA
* * * * **
54481309 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGTGTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAAACAAGAGAGC
54481362 CGAACTATAT
Statistics
Matches: 96, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
63 19 0.20
64 21 0.22
65 8 0.08
66 16 0.17
67 30 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAAACAAGAGAGCTACGAGATAA
Found at i:54484160 original size:30 final size:31
Alignment explanation
Indices: 54484124--54484186 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
54484114 ACTTATTTTA
*
54484124 TTGTTAA-TTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTTATTATTATTTTAAAGACAT
*
54484154 TTGTTAATTTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTTATTATTATTTTAAAGACAT
54484185 TT
1 TT
54484187 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTATTATTATTTTAAAGACAT
Found at i:54484293 original size:18 final size:18
Alignment explanation
Indices: 54484270--54484309 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
54484260 GAAATATTTA
*
54484270 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
54484288 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
54484306 TTTT
1 TTTT
54484310 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:54484341 original size:12 final size:12
Alignment explanation
Indices: 54484311--54484343 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
54484301 TATATTTTTT
54484311 AAAATT-ATATA
1 AAAATTAATATA
54484322 AAAA-TAATATA
1 AAAATTAATATA
54484333 AAAATTAATAT
1 AAAATTAATAT
54484344 GGGTGGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:54487572 original size:39 final size:40
Alignment explanation
Indices: 54487368--54487590 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
54487358 TTGAATGCTG
* * * * * *
54487368 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
54487408 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
54487448 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
54487488 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
54487528 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
54487567 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54487591 TGAATGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:54487610 original size:79 final size:80
Alignment explanation
Indices: 54487443--54487625 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
54487433 GTGCGAGATA
* * *
54487443 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
54487508 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
54487523 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
54487587 CATTTGAATGAGGAG
66 CATTCGAACGAGGAG
* *
54487602 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
54487626 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:54495468 original size:39 final size:40
Alignment explanation
Indices: 54495264--54495486 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
54495254 TTGAATGCTG
* * * * * *
54495264 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * * *
54495304 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCCAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
54495344 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
54495384 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
54495424 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
54495463 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54495487 TGAACGAGGA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 35 0.22
40 117 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:54495506 original size:79 final size:80
Alignment explanation
Indices: 54495339--54495521 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
54495329 GTGCCAGATA
* * *
54495339 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
54495404 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
54495419 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
54495483 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
54495498 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
54495522 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:54496845 original size:2 final size:2
Alignment explanation
Indices: 54496840--54496868 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54496830 TATATAGATA
54496840 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
54496869 CTCCAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:54498848 original size:62 final size:62
Alignment explanation
Indices: 54498751--54499036 Score: 371
Period size: 62 Copynumber: 4.6 Consensus size: 62
54498741 GTGCGGGGTT
* *
54498751 CACACGGCCAAGGACACGGGCGTATGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAAC
1 CACACGGCCAAGGACACGGGCATGTGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAAC
* *
54498813 CACACGGCCAGGGACACAGGCATGTGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAA-
1 CACACGGCCAAGGACACGGGCATGTGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAAC
* * *
54498874 C-CATGGCCAAGGACACGGGCATGTTCCC-GGTCCGTGTAACTCACTGTTTGTGCTTAAAAAC
1 CACACGGCCAAGGACACGGGCATGTGCCCAGG-CCATGTAACTCACTGTTTGTGCTTAAAAAC
* * ** * * * *
54498935 CACATGGCTAAGGACACAAGCTTGTGCCCAGGTCACGTAACTCACTATTTGTGCTTAAAAAC
1 CACACGGCCAAGGACACGGGCATGTGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAAC
* * *
54498997 CACACTGCCAAGGCACACGGGCGTGTGCCAAGGCCATGTA
1 CACACGGCCAAGG-ACACGGGCATGTGCCCAGGCCATGTA
54499037 GTAGGATATT
Statistics
Matches: 192, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
59 2 0.01
60 51 0.27
61 2 0.01
62 115 0.60
63 22 0.11
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (62 bp):
CACACGGCCAAGGACACGGGCATGTGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAAC
Found at i:54498932 original size:122 final size:122
Alignment explanation
Indices: 54498756--54499036 Score: 368
Period size: 122 Copynumber: 2.3 Consensus size: 122
54498746 GGGTTCACAC
*
54498756 GGCCAAGGACACGGGCGTATGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAACCACACGGC
1 GGCCAAGGACACGGGCATATGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAACCACACGGC
* * * *
54498821 CAGGGACACAGGCATGTGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAACCAT
66 CAAGGACACAAGCATGTGCCCAGGCCACGTAACTCACTATTTGTGCTTAAAAACCAT
* * * *
54498878 GGCCAAGGACACGGGCATGTTCCC-GGTCCGTGTAACTCACTGTTTGTGCTTAAAAACCACATGG
1 GGCCAAGGACACGGGCATATGCCCAGG-CCATGTAACTCACTGTTTGTGCTTAAAAACCACACGG
* * *
54498942 CTAAGGACACAAGCTTGTGCCCAGGTCACGTAACTCACTATTTGTGCTTAAAAACCACACT
65 CCAAGGACACAAGCATGTGCCCAGGCCACGTAACTCACTATTTGTGCTTAAAAA-C-CA-T
* * *
54499003 -GCCAAGGCACACGGGCGTGTGCCAAGGCCATGTA
1 GGCCAAGG-ACACGGGCATATGCCCAGGCCATGTA
54499037 GTAGGATATT
Statistics
Matches: 137, Mismatches: 16, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
121 2 0.01
122 103 0.75
123 1 0.01
124 9 0.07
125 20 0.15
126 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.21
Consensus pattern (122 bp):
GGCCAAGGACACGGGCATATGCCCAGGCCATGTAACTCACTGTTTGTGCTTAAAAACCACACGGC
CAAGGACACAAGCATGTGCCCAGGCCACGTAACTCACTATTTGTGCTTAAAAACCAT
Found at i:54500936 original size:46 final size:46
Alignment explanation
Indices: 54500865--54500981 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
54500855 GTGTCGATGC
* *
54500865 CATGTCCCAGATATAGTCTTACACTGAC-TATCATCTC-ATAGCCGACG
1 CATGTCCCAGACAT-GTCTTACACTGACTTA-CATCTCGAGA-CCGACG
* *
54500912 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGACCGATG
1 CATGTCCCAGACATGTCTTACACTGACTTACATCTCGAGACCGACG
* *
54500958 CATGTCCAAGACATGTATTACACT
1 CATGTCCCAGACATGTCTTACACT
54500982 AGCACTCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
46 45 0.73
47 17 0.27
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTTACATCTCGAGACCGACG
Found at i:54503443 original size:52 final size:53
Alignment explanation
Indices: 54503270--54503472 Score: 149
Period size: 54 Copynumber: 3.8 Consensus size: 53
54503260 AGGGTTTAAG
* * * * * * * *
54503270 GATACCAAGTAAGACCATACCAA-AGCATGGCATTGTTAAGTTTTACAAGGCAAG
1 GATACCACGTAAGACCATGCCAAGA-CATGGAAATGGTAAG-TTCATAAGGCAAA
* * * * * * * * *
54503324 GAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGCAAA
1 GATACCACGTAAGACCATGCCAAGACATGGAAATGGT-AAGTTC-ATAAGGCAAA
* * * * * *
54503379 GATCCCATGTAAGACCATGCCAAG-GATGGCAATGGTGAGTTCATAAGGCAAG
1 GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATAAGGCAAA
54503431 GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTT
1 GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTT
54503473 TAAAAAGGAA
Statistics
Matches: 118, Mismatches: 27, Indels: 9
0.77 0.18 0.06
Matches are distributed among these distances:
52 31 0.26
53 17 0.14
54 39 0.33
55 31 0.26
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.20
Consensus pattern (53 bp):
GATACCACGTAAGACCATGCCAAGACATGGAAATGGTAAGTTCATAAGGCAAA
Found at i:54517696 original size:40 final size:40
Alignment explanation
Indices: 54517473--54517682 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
54517463 TCCTCGTTCA
* * * * *
54517473 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
54517512 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
54517552 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
54517592 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
54517632 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
54517672 AAGGCCTTCGG
1 AATGCCTTCGG
54517683 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:54517719 original size:80 final size:80
Alignment explanation
Indices: 54517476--54517735 Score: 265
Period size: 80 Copynumber: 3.3 Consensus size: 80
54517466 TCGTTCAAAT
* * * * * * * *
54517476 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* * *
54517540 ACAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * *
54517555 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
54517620 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * **
54517635 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
* **
54517699 ATTCGCTTAGCAC-AAA
65 AATAAC-TAGCACGAAA
*
54517715 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
54517736 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 34 0.22
80 119 0.75
81 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:54517719 original size:120 final size:118
Alignment explanation
Indices: 54517471--54517735 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 118
54517461 GCTCCTCGTT
* * *
54517471 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
* * * *
54517536 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * *
54517590 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGG
** * ** * **
54517655 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCGCTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
54517711 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
54517736 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
119 35 0.29
120 81 0.67
121 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:54525645 original size:40 final size:40
Alignment explanation
Indices: 54525422--54525631 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
54525412 TCCTCGTTCA
* * * * *
54525422 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
54525461 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
54525501 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
54525541 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
54525581 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
54525621 AAGGCCTTCGG
1 AATGCCTTCGG
54525632 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.21
40 125 0.79
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:54525668 original size:80 final size:80
Alignment explanation
Indices: 54525425--54525684 Score: 265
Period size: 80 Copynumber: 3.3 Consensus size: 80
54525415 TCGTTCAAAT
* * * * * * * *
54525425 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* * *
54525489 ACAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * *
54525504 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
54525569 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * **
54525584 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
* **
54525648 ATTCGCTTAGCAC-AAA
65 AATAAC-TAGCACGAAA
*
54525664 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
54525685 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 34 0.22
80 119 0.75
81 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:54525668 original size:120 final size:118
Alignment explanation
Indices: 54525420--54525684 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 118
54525410 GCTCCTCGTT
* * *
54525420 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
* * * *
54525485 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * *
54525539 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGG
** * ** * **
54525604 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCGCTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
54525660 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
54525685 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
119 35 0.29
120 81 0.67
121 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:54529932 original size:261 final size:261
Alignment explanation
Indices: 54529468--54529987 Score: 968
Period size: 261 Copynumber: 2.0 Consensus size: 261
54529458 TAAGTAATCT
*
54529468 TTATTGATTTTCTGTAAGTTTTGGTTTCGTTGAATGTTGATGTCGAATTTTTCGACGTAGGTACT
1 TTATTGATTTTCTGTAAGTTTTGGTTTCGTAGAATGTTGATGTCGAATTTTTCGACGTAGGTACT
*
54529533 TTGAGTATAATTGTGCATTGCTGTTGATAAACTTGATTGATTGAGTTATTGAATGATCGTTTTAG
66 TTGAGTATAATTGTGCATTGCTGTTGATAAACTTGATTGATTGAGTTATTGAATGAACGTTTTAG
* *
54529598 GCTTTAGAACTTCTATTCATTATCACTACTTTGAAATCGTTATAGGTGCGTATCGAAAACCTTAG
131 GCTTCAGAACTTCTATTCATTATCACTACTTTGAAATCGTTATAGGTGCGTATCAAAAACCTTAG
54529663 ATTTTGCAAGTTTTGTTGTCAAAAATAGTGGTTGTCAACCTCATATGGCCAGGCGCCGTGTGAAT
196 ATTTTGCAAGTTTTGTTGTCAAAAATAGTGGTTGTCAACCTCATATGGCCAGGCGCCGTGTGAAT
54529728 G
261 G
54529729 TTATTGATTTTCTGTAAGTTTTGGTTTCGTAGAATGTTGATGTCGAATTTTTCGACGTAGGTACT
1 TTATTGATTTTCTGTAAGTTTTGGTTTCGTAGAATGTTGATGTCGAATTTTTCGACGTAGGTACT
* *
54529794 TTGAGTATAATTGTTCATTGTTGTTGATAAACTTGATTGATTGAGTTATTGAATGAACGTTTTAG
66 TTGAGTATAATTGTGCATTGCTGTTGATAAACTTGATTGATTGAGTTATTGAATGAACGTTTTAG
54529859 GCTTCAGAACTTCTATTCATTATCACTACTTTGAAATCGTTATAGGTGCGTATCAAAAACCTTAG
131 GCTTCAGAACTTCTATTCATTATCACTACTTTGAAATCGTTATAGGTGCGTATCAAAAACCTTAG
* *
54529924 ATTTTGCAAGTTTTGTTGTCAAAAATAGTGGTTGTCAACCTCATATGGCCAGGTGCTGTGTGAA
196 ATTTTGCAAGTTTTGTTGTCAAAAATAGTGGTTGTCAACCTCATATGGCCAGGCGCCGTGTGAA
54529988 CGGCCATGTA
Statistics
Matches: 251, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
261 251 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (261 bp):
TTATTGATTTTCTGTAAGTTTTGGTTTCGTAGAATGTTGATGTCGAATTTTTCGACGTAGGTACT
TTGAGTATAATTGTGCATTGCTGTTGATAAACTTGATTGATTGAGTTATTGAATGAACGTTTTAG
GCTTCAGAACTTCTATTCATTATCACTACTTTGAAATCGTTATAGGTGCGTATCAAAAACCTTAG
ATTTTGCAAGTTTTGTTGTCAAAAATAGTGGTTGTCAACCTCATATGGCCAGGCGCCGTGTGAAT
G
Found at i:54536489 original size:21 final size:22
Alignment explanation
Indices: 54536463--54536509 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
54536453 CTCTGCTCAA
*
54536463 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
54536484 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
54536506 ACTC
1 ACTC
54536510 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:54541522 original size:18 final size:17
Alignment explanation
Indices: 54541495--54541533 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54541485 TTTCTCTACT
*
54541495 TTTTGATTTTCTTCACAC
1 TTTTGATTTT-TGCACAC
*
54541513 TTTTGGTTTTTGCACAC
1 TTTTGATTTTTGCACAC
54541530 TTTT
1 TTTT
54541534 TTCTGTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.13, C:0.18, G:0.10, T:0.59
Consensus pattern (17 bp):
TTTTGATTTTTGCACAC
Found at i:54541534 original size:18 final size:19
Alignment explanation
Indices: 54541492--54541534 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
54541482 TATTTTCTCT
*
54541492 ACTTTTTGATTTTCTTCAC
1 ACTTTTTGATTTTCTGCAC
*
54541511 AC-TTTTGGTTTT-TGCAC
1 ACTTTTTGATTTTCTGCAC
54541528 ACTTTTT
1 ACTTTTT
54541535 TCTGTCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.14, C:0.19, G:0.09, T:0.58
Consensus pattern (19 bp):
ACTTTTTGATTTTCTGCAC
Found at i:54544709 original size:25 final size:26
Alignment explanation
Indices: 54544652--54544710 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 26
54544642 AAAGATGATT
*
54544652 GATTTCCAAAATAAAAGAAGTTACAGATT
1 GATTTCCAAAATAAAAGAAGTT--A-ATG
54544681 GATTTCCAAAATAAAAGAAGTT-ATG
1 GATTTCCAAAATAAAAGAAGTTAATG
54544706 GATTT
1 GATTT
54544711 TTCCATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 7 0.24
29 22 0.76
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (26 bp):
GATTTCCAAAATAAAAGAAGTTAATG
Found at i:54544709 original size:29 final size:29
Alignment explanation
Indices: 54544648--54544703 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
54544638 TTTAAAAGAT
54544648 GATTGATTTCCAAAATAAAAGAAGTTACA
1 GATTGATTTCCAAAATAAAAGAAGTTACA
54544677 GATTGATTTCCAAAATAAAAGAAGTTA
1 GATTGATTTCCAAAATAAAAGAAGTTA
54544704 TGGATTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (29 bp):
GATTGATTTCCAAAATAAAAGAAGTTACA
Found at i:54553753 original size:93 final size:93
Alignment explanation
Indices: 54553641--54553811 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
54553631 GCCCATAAGT
* *
54553641 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54553706 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
54553734 GAACTCGGACTCAACTCAACGAGTTCGGACATTGGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
54553799 CGAGTTTGGATGC
66 CGAGCTCGGATGC
54553812 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:54553804 original size:46 final size:45
Alignment explanation
Indices: 54553633--54553802 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 45
54553623 TGTAACCCGC
* *
54553633 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTGGCAT
*
54553679 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-A-TGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTGGC-A--T
* *** *
54553725 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTGGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTGGCAT
*
54553772 CCATAGGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
54553803 TTTGGATGCT
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 2 0.02
44 1 0.01
45 2 0.02
46 62 0.60
47 32 0.31
49 2 0.02
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTGGCAT
Found at i:54555774 original size:18 final size:18
Alignment explanation
Indices: 54555731--54555779 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
54555721 TTCTCTTTTT
*
54555731 AAATAAAAAC-AAATAAA
1 AAATAAAAACAAAACAAA
* *
54555748 ATATTAAAACAAAACAAA
1 AAATAAAAACAAAACAAA
*
54555766 AAATAAAAATAAAA
1 AAATAAAAACAAAA
54555780 ACCAATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (18 bp):
AAATAAAAACAAAACAAA
Found at i:54567798 original size:7 final size:7
Alignment explanation
Indices: 54567788--54567813 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54567778 TTACTATATC
54567788 ATATAAT
1 ATATAAT
54567795 ATATAAT
1 ATATAAT
54567802 ATATAAT
1 ATATAAT
54567809 ATATA
1 ATATA
54567814 TTAATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:54572870 original size:23 final size:24
Alignment explanation
Indices: 54572834--54572878 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
54572824 CAAAAATTGA
54572834 TTCAATATAGAAAGAAAAAATAAT
1 TTCAATATAGAAAGAAAAAATAAT
* *
54572858 TTCAATA-ATAAAGAGAAAATA
1 TTCAATATAGAAAGAAAAAATA
54572879 TTTTGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.24
Consensus pattern (24 bp):
TTCAATATAGAAAGAAAAAATAAT
Found at i:54573039 original size:21 final size:21
Alignment explanation
Indices: 54573015--54573055 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
54573005 ATTCTATTGG
54573015 AATTTTGGGAAGGACAAAGAT
1 AATTTTGGGAAGGACAAAGAT
54573036 AATTTTGGGAAGGACAAAGA
1 AATTTTGGGAAGGACAAAGA
54573056 GATGAATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.29, T:0.22
Consensus pattern (21 bp):
AATTTTGGGAAGGACAAAGAT
Found at i:54575412 original size:17 final size:17
Alignment explanation
Indices: 54575390--54575424 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54575380 ATCTAATGTG
*
54575390 TTTGTGTTGTATTGGAT
1 TTTGTGTTGTAATGGAT
*
54575407 TTTGTGTTTTAATGGAT
1 TTTGTGTTGTAATGGAT
54575424 T
1 T
54575425 GATGAGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (17 bp):
TTTGTGTTGTAATGGAT
Found at i:54578135 original size:22 final size:22
Alignment explanation
Indices: 54578102--54578149 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
54578092 TGGGAAACTA
54578102 CATCTGATTCTGATCTATTCTT
1 CATCTGATTCTGATCTATTCTT
* *
54578124 CATCT-ATATCTGATTTTTTCTT
1 CATCTGAT-TCTGATCTATTCTT
54578146 CATC
1 CATC
54578150 GTATTTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (22 bp):
CATCTGATTCTGATCTATTCTT
Found at i:54579657 original size:25 final size:24
Alignment explanation
Indices: 54579622--54579677 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
54579612 CATCTCAACC
54579622 CTTTTCATCTCTTCACTT-CTCTTTCA
1 CTTTTC-TCTCTTCA-TTGCTC-TTCA
54579648 CTTTTCTCTCTTCATTGCTCTTCA
1 CTTTTCTCTCTTCATTGCTCTTCA
54579672 -TTTTCT
1 CTTTTCT
54579678 TCCCCATTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 11 0.38
26 6 0.21
ACGTcount: A:0.09, C:0.32, G:0.02, T:0.57
Consensus pattern (24 bp):
CTTTTCTCTCTTCATTGCTCTTCA
Found at i:54580503 original size:58 final size:58
Alignment explanation
Indices: 54580413--54580528 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
54580403 ACAAAGAGAT
*
54580413 ATAGTCAAGAGATAAATGGATTTTCGAAGCTAAGTATATTCATAAGCTAGCAAATTAC
1 ATAGTCAAGAGATAAAAGGATTTTCGAAGCTAAGTATATTCATAAGCTAGCAAATTAC
* * *
54580471 ATAGTCAAGAGATAAAAGGATTTTTGGAGCTAAGTATATTCATAAGTTAGCAAATTAC
1 ATAGTCAAGAGATAAAAGGATTTTCGAAGCTAAGTATATTCATAAGCTAGCAAATTAC
54580529 CGTGTTGTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.30
Consensus pattern (58 bp):
ATAGTCAAGAGATAAAAGGATTTTCGAAGCTAAGTATATTCATAAGCTAGCAAATTAC
Found at i:54581429 original size:54 final size:54
Alignment explanation
Indices: 54581347--54581454 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
54581337 GCAGAAAGAT
54581347 TCCTCATAAAGTATTTCCTACCTAGCAAGAATGCTAAGTTGAGTAATGATATCA
1 TCCTCATAAAGTATTTCCTACCTAGCAAGAATGCTAAGTTGAGTAATGATATCA
54581401 TCCTCATAAAGTATTTCCTACCTAGCAAGAATGCTAAGTTGAGTAATGATATCA
1 TCCTCATAAAGTATTTCCTACCTAGCAAGAATGCTAAGTTGAGTAATGATATCA
54581455 CTGTTTTCCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (54 bp):
TCCTCATAAAGTATTTCCTACCTAGCAAGAATGCTAAGTTGAGTAATGATATCA
Found at i:54589192 original size:10 final size:11
Alignment explanation
Indices: 54589167--54589200 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
54589157 AAATGTTCAT
54589167 AAAAAAAGATAC
1 AAAAAAAGA-AC
54589179 AAAAAAAGAA-
1 AAAAAAAGAAC
54589189 AAAAAAAGAAC
1 AAAAAAAGAAC
54589200 A
1 A
54589201 TATGTACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 2 0.10
12 9 0.43
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAC
Found at i:54592250 original size:246 final size:247
Alignment explanation
Indices: 54591813--54592298 Score: 785
Period size: 246 Copynumber: 2.0 Consensus size: 247
54591803 AGTTCATGGT
54591813 GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
1 GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
* ***
54591878 ATTTATGGACTATGATAAGAGTGTGTGGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
66 ATTTATGGACTATGATAACAGTGTACAGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
* * *
54591943 TAGCTCTTTAGAGGGAGTAAGTGTTTCTAGCCTTGGTTGACAAGGCAAATATAGCGAAAGAAGTG
131 TAGCTCTTCAGAGGGAGCAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
* * *
54592008 AAGCGCACTGAGTGTGAGAGGAGAGACCAAGAGAGAGG-TCAAGTTTCTGCA
196 AAGCACACTGAATGTGAGAGAAGAGACCAAGAGAGAGGTTCAAGTTTCTGCA
* * * *
54592059 GAGATAATTTTAGCCATGTATGATGCCAAGTTTTTGAGATTGAGCGGATATACTTGTGCTTTGGT
1 GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
* * *
54592124 ATTTATGGACTATGATAACAGTGTACAGTTTGAAGAAGGTTTGTGTTATAATCTATGGGTTTTGA
66 ATTTATGGACTATGATAACAGTGTACAGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
* *
54592189 TAGCTCTTCAGAGGGAGCGAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGTGAAAGAAGTG
131 TAGCTCTTCAGAGGGAGCAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
*
54592254 AAGCATACTGAATGTGAGAGAAGAGACCAAGAGAGAGGTTCAAGT
196 AAGCACACTGAATGTGAGAGAAGAGACCAAGAGAGAGGTTCAAGT
54592299 AAGATTAAGA
Statistics
Matches: 219, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
246 213 0.97
247 6 0.03
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (247 bp):
GAGATAATTTTAGCCATGTATGAGGCCAAGTTTCTGAAATTGAGCAGATATACTTGTGCTTTGGT
ATTTATGGACTATGATAACAGTGTACAGTTTCAAGAAGGTTTGTGTTATAATCTATGAGTTATGA
TAGCTCTTCAGAGGGAGCAAGTGTTTCTAGCCTTGGTTGACAAGGCAAAGATAGCGAAAGAAGTG
AAGCACACTGAATGTGAGAGAAGAGACCAAGAGAGAGGTTCAAGTTTCTGCA
Found at i:54595759 original size:46 final size:46
Alignment explanation
Indices: 54595706--54595836 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 46
54595696 GGGTTATTGT
* *
54595706 GAGCTAGTGTAAGACTTGTCTGGGACATGCATCGGCCACATTATG-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTAAGAA
54595752 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG--CATTAAGACAA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCCATTAAG--AA
* *
54595800 GTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
54595837 TCGAGATGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
45 6 0.08
46 21 0.28
47 26 0.35
48 21 0.28
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAAGAA
Found at i:54602006 original size:3 final size:3
Alignment explanation
Indices: 54601998--54602031 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54601988 GTTAGCTTTG
54601998 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
54602032 CTTTTGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:54602044 original size:15 final size:15
Alignment explanation
Indices: 54601957--54602056 Score: 53
Period size: 15 Copynumber: 6.5 Consensus size: 15
54601947 TTGAACATTA
**
54601957 TTCTTTTTCTTTATT
1 TTCTTTTTCTTCCTT
*
54601972 TTCTTGTT-TTCCTT
1 TTCTTTTTCTTCCTT
*
54601986 TTGTTAGCTTTGCTT-CTT
1 TTCTT---TTT-CTTCCTT
*
54602004 CTTCTTCTTCTT-CTT
1 -TTCTTTTTCTTCCTT
*
54602019 CTTCTTCTTCTTCCTT
1 -TTCTTTTTCTTCCTT
* *
54602035 TTGTTTTTCTTTCTT
1 TTCTTTTTCTTCCTT
54602050 TTCTTTT
1 TTCTTTT
54602057 GATTTCTCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
14 8 0.12
15 43 0.64
16 5 0.07
17 2 0.03
18 3 0.04
19 6 0.09
ACGTcount: A:0.02, C:0.22, G:0.05, T:0.71
Consensus pattern (15 bp):
TTCTTTTTCTTCCTT
Found at i:54616674 original size:24 final size:25
Alignment explanation
Indices: 54616634--54616683 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
54616624 AAGGAATTCG
*
54616634 CACACACACGTGCCTC-TAATCATT
1 CACACACAAGTGCCTCTTAATCATT
*
54616658 CACACACATAGTG-CTCTTATTCATT
1 CACACACA-AGTGCCTCTTAATCATT
54616683 C
1 C
54616684 GTTATTACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.28, C:0.34, G:0.08, T:0.30
Consensus pattern (25 bp):
CACACACAAGTGCCTCTTAATCATT
Found at i:54616937 original size:40 final size:40
Alignment explanation
Indices: 54616832--54617147 Score: 380
Period size: 40 Copynumber: 8.1 Consensus size: 40
54616822 CTAGGCATGA
* * * *
54616832 AGCCCGAATACACGTCACCAGCATGATTGCTCTTC-GGACCT
1 AGCCCGGATACA--TCACTAGCATGAATGCTCTTCGGGACTT
* * * **
54616873 AG-CC-GATATAACACCAGCATGAATGCTCTTCGGGGTTT
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
* * * *
54616911 AGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
54616951 A-CCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
* *
54616990 AGTCCGAATACATCACTAGCATGAATGCTCTTCGGGACTT
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
* *
54617030 AGCCCGGGTACATCACTAG-ACGAATGCTCTTC-GGAC-T
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
*
54617067 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTT
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
*
54617107 AGCCCGGATACATCACTAGCACG-ATGCTCTTCGGGA-TT
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
54617145 AGC
1 AGC
54617148 TGGTATCGTC
Statistics
Matches: 239, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
37 38 0.16
38 26 0.11
39 67 0.28
40 106 0.44
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
Found at i:54617107 original size:77 final size:79
Alignment explanation
Indices: 54616832--54617140 Score: 371
Period size: 77 Copynumber: 3.9 Consensus size: 79
54616822 CTAGGCATGA
* * * * * * * *
54616832 AGCCCGAATACACGTCACCAGCATGATTGCTCTTCGG-ACCTAG-CC-GATATAACACCAGCATG
1 AGCCCGGATACA--TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACG
**
54616894 AATGCTCTTCGGGGTTT
64 AATGCTCTTC-GGACTT
* * * *
54616911 AGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTA-CCCGGATACATCACTAGCATGAA
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
54616975 TGCTCTTCGGGACTT
66 TGCTCTTC-GGACTT
* * * *
54616990 AGTCCGAATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGGTACATCACTAG-ACGAA
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
54617054 TGCTCTTCGGAC-T
66 TGCTCTTCGGACTT
54617067 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACG-A
1 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
54617131 TGCTCTTCGG
66 TGCTCTTCGG
54617141 GATTAGCTGG
Statistics
Matches: 201, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
77 87 0.43
78 13 0.06
79 85 0.42
80 16 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
AGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
TGCTCTTCGGACTT
Found at i:54619450 original size:47 final size:46
Alignment explanation
Indices: 54619372--54619862 Score: 674
Period size: 47 Copynumber: 10.6 Consensus size: 46
54619362 CCCTTCGGGA
* * * * *
54619372 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGC
* *
54619419 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
* *
54619466 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
54619513 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
* *
54619560 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
*
54619607 CTTATCACATATATACAATTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
54619654 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTA-GC
*
54619703 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATT-AGC
54619752 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
54619799 CTT-T-ACATAT-TACA-TTTCACA-T--TCACATC-GCCATTAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGC
* *
54619837 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
54619863 CACAATTATC
Statistics
Matches: 411, Mismatches: 23, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
38 5 0.01
39 8 0.02
40 13 0.03
41 3 0.01
42 7 0.02
43 7 0.02
44 4 0.01
45 6 0.01
46 4 0.01
47 261 0.64
49 92 0.22
50 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (46 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGC
Found at i:54624379 original size:37 final size:37
Alignment explanation
Indices: 54624306--54624380 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
54624296 ATACGGAAAG
* * *
54624306 ACAATTTATATTAGTAGACGAAACTAATCATGTCCTT
1 ACAACTTATATTAATAGACGAAACTAATCATATCCTT
* **
54624343 ACAACTTATATTAATAGATGAAACTAATTGTATCCTT
1 ACAACTTATATTAATAGACGAAACTAATCATATCCTT
54624380 A
1 A
54624381 GTCAAATCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (37 bp):
ACAACTTATATTAATAGACGAAACTAATCATATCCTT
Found at i:54625332 original size:57 final size:57
Alignment explanation
Indices: 54625271--54625413 Score: 142
Period size: 57 Copynumber: 2.5 Consensus size: 57
54625261 GAAGTGATAC
* * *
54625271 TGGTTTTCACTATAATGAAAATAAAAATGGAGAAATGAAAACATTTGGAAATTATTA
1 TGGTTTTCACGAAAATGAAAATAAAAATAGAGAAATGAAAACATTTGGAAATTATTA
* * * * * * * * *
54625328 TGGTTTTCTCGAAAATGGAAATGAAAATAGAGATATGGAATCATTTGGAAATGAATG
1 TGGTTTTCACGAAAATGAAAATAAAAATAGAGAAATGAAAACATTTGGAAATTATTA
** *
54625385 TGGTTTTTTCCAAAATGAAAATGAAAAAT
1 TGGTTTTCACGAAAATGAAAAT-AAAAAT
54625414 GAAAAAAATG
Statistics
Matches: 69, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
57 64 0.93
58 5 0.07
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (57 bp):
TGGTTTTCACGAAAATGAAAATAAAAATAGAGAAATGAAAACATTTGGAAATTATTA
Found at i:54628766 original size:47 final size:47
Alignment explanation
Indices: 54628704--54628794 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
54628694 GGTAACCTAG
* * *
54628704 GATGGTAGCTTATATGTACATTGAGTCATC-TTTCCTAGGCAACCTGA
1 GATGGTAGATTATATGTACACTGAGTCATCGATTCC-AGGCAACCTGA
54628751 GATGGTAGATTATATGTACACTGAGTCATCGATTCCAGGCAACC
1 GATGGTAGATTATATGTACACTGAGTCATCGATTCCAGGCAACC
54628795 CAGGGTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 36 0.90
48 4 0.10
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (47 bp):
GATGGTAGATTATATGTACACTGAGTCATCGATTCCAGGCAACCTGA
Found at i:54632530 original size:40 final size:40
Alignment explanation
Indices: 54632430--54632601 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
54632420 GCTCCTCGTT
* * *
54632430 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
54632470 C-AATGCCTTCGGGACATAACCCAGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
54632509 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
54632549 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
54632589 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54632602 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54632614 original size:80 final size:79
Alignment explanation
Indices: 54632430--54632654 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
54632420 GCTCCTCGTT
* * * * * *
54632430 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCAG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
54632494 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
54632509 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
54632574 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
54632589 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
54632653 GA
63 GA
54632655 CATCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 68 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:54632638 original size:40 final size:42
Alignment explanation
Indices: 54632586--54632663 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
54632576 TTTGTATCTC
* *
54632586 GCACAAATGCCTTC-GGATCTTAGTCCGGATAT-ATTCACTTA
1 GCACAAATGCCTTCGGGA-CTTAGCCCGGACATCATTCACTTA
54632627 GCACAAA-GCCTTCGGGACTTAGCCCGGACATCATTCA
1 GCACAAATGCCTTCGGGACTTAGCCCGGACATCATTCA
54632664 ATTAATCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 18 0.55
41 15 0.45
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (42 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGACATCATTCACTTA
Found at i:54639822 original size:39 final size:40
Alignment explanation
Indices: 54639777--54639948 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
54639767 GCTCCTCGTT
* * *
54639777 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
54639817 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
54639856 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
54639896 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
54639936 CAAATGCCTTCGG
1 CAAATGCCTTCGG
54639949 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:54639877 original size:40 final size:39
Alignment explanation
Indices: 54639779--54640001 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
54639769 TCCTCGTTCA
* * * *
54639779 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
54639818 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
54639857 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
54639897 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
54639937 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
54639978 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54640002 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:54639961 original size:80 final size:79
Alignment explanation
Indices: 54639777--54640001 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
54639767 GCTCCTCGTT
* * * * *
54639777 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
54639841 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
54639856 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
54639921 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
54639936 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
54640000 GA
63 GA
54640002 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:54640010 original size:41 final size:41
Alignment explanation
Indices: 54639933--54640010 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54639923 TTTGTATCTC
* * *
54639933 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54639974 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54640011 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54641738 original size:24 final size:24
Alignment explanation
Indices: 54641710--54641772 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
54641700 AATTGTATAA
54641710 GATAGTGAAATGCATAAATTAG-T
1 GATAGTGAAATGCATAAATTAGCT
*
54641733 GCATAG-G-AATGTCATATATTAGCT
1 G-ATAGTGAAATG-CATAAATTAGCT
*
54641757 GAAAGTGAAATGCATA
1 GATAGTGAAATGCATA
54641773 TGTTTGGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 4 0.12
23 14 0.42
24 11 0.33
25 4 0.12
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (24 bp):
GATAGTGAAATGCATAAATTAGCT
Found at i:54643296 original size:37 final size:37
Alignment explanation
Indices: 54643246--54643359 Score: 158
Period size: 37 Copynumber: 3.1 Consensus size: 37
54643236 ACCTTTAGCT
* * *
54643246 CAGACGAAATCTCCACACAAAGTTATCGGGTCTTACC
1 CAGACAAAATCTCCACACATAGTCATCGGGTCTTACC
*
54643283 CAGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CAGACAAAATCTCCACACATAGTCATCGGGTCTTACC
* * *
54643320 CGGACATAATCTCCACACATAGTCATC-GGTCTTACT
1 CAGACAAAATCTCCACACATAGTCATCGGGTCTTACC
54643356 CAGA
1 CAGA
54643360 ATATATTTCC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 11 0.16
37 57 0.84
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.23
Consensus pattern (37 bp):
CAGACAAAATCTCCACACATAGTCATCGGGTCTTACC
Found at i:54643634 original size:48 final size:48
Alignment explanation
Indices: 54643505--54643689 Score: 307
Period size: 48 Copynumber: 3.8 Consensus size: 48
54643495 GCACATCGCC
*
54643505 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * * *
54643553 TATATATATCTCACATTAACCATTCAGCTTTACCACATATGCATATCTCA
1 TACATAT-T-TCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
54643603 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
54643651 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
54643690 TGCATGTTCA
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
48 82 0.65
49 2 0.02
50 42 0.33
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:54643694 original size:98 final size:98
Alignment explanation
Indices: 54643505--54643688 Score: 318
Period size: 98 Copynumber: 1.9 Consensus size: 98
54643495 GCACATCGCC
*
54643505 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATCTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATCTCACATT
54643570 AACCATTCAGCTTTACCACATATGCATATCTCA
66 AACCATTCAGCTTTACCACATATGCATATCTCA
*
54643603 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT-T-TCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATCTCACATT
* *
54643666 AGCCATTCGGCTTTACCACATAT
66 AACCATTCAGCTTTACCACATAT
54643689 ATGCATGTTC
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 28 0.34
97 1 0.01
98 53 0.65
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (98 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATCTCACATT
AACCATTCAGCTTTACCACATATGCATATCTCA
Found at i:54643733 original size:47 final size:47
Alignment explanation
Indices: 54643659--54643852 Score: 316
Period size: 47 Copynumber: 4.1 Consensus size: 47
54643649 CATACATATT
* * * *
54643659 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
54643706 CCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
54643753 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
54643800 TCACATTGGCCATTCCGCCTTATCTCATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
54643847 TCACAT
1 TCACAT
54643853 AAAATCCTAA
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 137 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:54643746 original size:25 final size:25
Alignment explanation
Indices: 54643727--54643853 Score: 92
Period size: 25 Copynumber: 5.3 Consensus size: 25
54643717 ATTCAGCCTT
54643727 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
* * *
54643752 ATCACAT-T-GGCCA--TTCGGCCTT-
1 ATCACATATATG-CATGTTC-ACATTC
54643774 ATCACATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
* * * *
54643799 ATCACAT-T-GGCCAT-TCCGCCTT-
1 ATCACATATATG-CATGTTCACATTC
*
54643821 ATCTCATATATGCATGTTCACATTC
1 ATCACATATATGCATGTTCACATTC
54643846 ATCACATA
1 ATCACATA
54643854 AAATCCTAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 24
0.65 0.14 0.21
Matches are distributed among these distances:
22 16 0.22
23 17 0.23
24 17 0.23
25 24 0.32
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (25 bp):
ATCACATATATGCATGTTCACATTC
Found at i:54643884 original size:94 final size:91
Alignment explanation
Indices: 54643685--54643873 Score: 231
Period size: 94 Copynumber: 2.1 Consensus size: 91
54643675 GCTTTACCAC
*
54643685 ATATATGCATGTTCATATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
1 ATATATGCATGTTCACATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
** * * *
54643750 TCATCACATTGGCCATTCGGCCTTATCAC
66 TCATCACATT-GAAAAT--GCCTAATCAA
* * *
54643779 ATATATGCATGTTCACATTCATCACATTGGCCATTCCGCCTTATCTCATATATGCATGTTCACAT
1 ATATATGCATGTTCACATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
54643844 TCATCACA-T-AAAAT-CCTAAATCAAA
66 TCATCACATTGAAAATGCCT-AATC-AA
54643869 ATATA
1 ATATA
54643874 AATTTTCATG
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
88 3 0.04
89 3 0.04
90 6 0.07
91 2 0.02
93 1 0.01
94 69 0.82
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.34
Consensus pattern (91 bp):
ATATATGCATGTTCACATTCACCACATTGGCCATTCAGCCTTATCACATATATGCATGTTCACAT
TCATCACATTGAAAATGCCTAATCAA
Found at i:54648478 original size:50 final size:50
Alignment explanation
Indices: 54648409--54648962 Score: 434
Period size: 50 Copynumber: 11.0 Consensus size: 50
54648399 TAAGATGATT
*
54648409 TTAGGTCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * ** * *
54648459 TTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCA-ACAAC
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGA-TAG
* * * * * *
54648510 TTCA-ATCACGTGTGTAGTACTAAGTGGAGGCTACTACTTGTATCAAATGG
1 TT-AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * *
54648560 TTAGGTCACGTGTGTAGTACTAAGAGCAGGCTAATACGTGTACTAGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * * * * * *
54648610 TTAGGTCGCATGTATAGTACTAAGTGCAGGCTACTATGCGTACCCGACAAC
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
** * * * ** * *
54648661 TTCAAATCACGTGTGTAGTACTAAGCGCAGGCTATTATGCATACCCA-ACAAC
1 TT-AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGA-TAG
* *
54648713 TTCA-ATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAG
1 TT-AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * * * * *
54648763 TTAGGTCACATGTGTAGTAATAAGTGCAGGCTACTATGCGTACCTGACAAC
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
* * * * ** * ** *
54648814 TTCGATCACGTGTTTAGTACAAAGTATAGGCTACTACATGTGTCAGATGG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * *
54648864 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTATTTCGTGTACCAAAT-T
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * * *
54648913 TTTGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGAGTACCAGATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
54648963 CTTCGGTTAC
Statistics
Matches: 387, Mismatches: 105, Indels: 24
0.75 0.20 0.05
Matches are distributed among these distances:
49 42 0.11
50 194 0.50
51 107 0.28
52 42 0.11
53 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (50 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
Found at i:54648545 original size:101 final size:101
Alignment explanation
Indices: 54648414--54648896 Score: 513
Period size: 101 Copynumber: 4.8 Consensus size: 101
54648404 TGATTTTAGG
* * *
54648414 TCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
54648479 TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
66 TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
* * * * *
54648515 TCACGTGTGTAGTACTAAGTGGAGGCTACTACTTGTATCAAATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
* * * ** * * * *
54648580 TAAGAGCAGGCTAATACGTGTA-CTAGA-TAGTT-AGG
66 TAAGTGCAGGCTACTATGCATACCCA-ACAACTTCA-A
* * * * * * * * **
54648615 TCGCATGTATAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAAATCACGTGTGTAGT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAGTT-AGGTCACGTGTGTAGT
* *
54648680 ACTAAGCGCAGGCTATTATGCATACCCAACAACTTCAA
64 ACTAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
* * *
54648718 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAGTTAGGTCACATGTGTAGTAA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
* ** *
54648783 TAAGTGCAGGCTACTATGCGTACCTGACAACTTCGA
66 TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
* * ** * ** *
54648819 TCACGTGTTTAGTACAAAGTATAGGCTACTACATGTGTCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
54648884 TAAGTGCAGGCTA
66 TAAGTGCAGGCTA
54648897 TTTCGTGTAC
Statistics
Matches: 306, Mismatches: 69, Indels: 14
0.79 0.18 0.04
Matches are distributed among these distances:
99 1 0.00
100 37 0.12
101 190 0.62
102 37 0.12
103 40 0.13
104 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTAC
TAAGTGCAGGCTACTATGCATACCCAACAACTTCAA
Found at i:54649181 original size:16 final size:15
Alignment explanation
Indices: 54649160--54649189 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54649150 GAATGGAGTA
54649160 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
54649176 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
54649190 AAAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:54653938 original size:2 final size:2
Alignment explanation
Indices: 54653931--54653956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54653921 TATGATATGC
54653931 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54653957 TCTATGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54655523 original size:50 final size:50
Alignment explanation
Indices: 54655459--54655809 Score: 357
Period size: 50 Copynumber: 7.0 Consensus size: 50
54655449 TAAGATGGTT
* *
54655459 TTAGGTCACATGTGTAGTACTAAGTGTAGGGTACTACGTGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
** * * * * *
54655509 TTAGGTTGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAAC
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
* * * * * * *
54655560 TTCA-ATCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAAC
1 TT-AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
* *
54655611 TTCA-ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
1 TT-AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * *
54655661 TTAGGTCACATGTGTAGTACTAAGTCCAGGCTGCTACGTGTATCAGATGG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
** * * * *
54655711 TTAGGTCATGTGTGTAGTACTAAGTGCAAGCTATTACGTGTACCGGATTG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * *
54655761 TT-GGTCGCATGTGTAGTACTAAGTGTAGGCTACTAGGCGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
54655810 CTTCTGTTAC
Statistics
Matches: 255, Mismatches: 43, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
49 38 0.15
50 126 0.49
51 90 0.35
52 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
Found at i:54655584 original size:51 final size:51
Alignment explanation
Indices: 54655519--54655646 Score: 256
Period size: 51 Copynumber: 2.5 Consensus size: 51
54655509 TTAGGTTGCA
54655519 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACG
54655570 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACG
54655621 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
54655647 CGTGTACCAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACG
Found at i:54656028 original size:16 final size:15
Alignment explanation
Indices: 54656007--54656036 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54655997 GAATGGAGTA
54656007 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
54656023 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
54656037 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:54660009 original size:3 final size:3
Alignment explanation
Indices: 54659996--54660027 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
54659986 AATTTGGATG
*
54659996 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54660028 TCGTATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:54661489 original size:8 final size:8
Alignment explanation
Indices: 54661472--54661507 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
54661462 CTAGATCAGC
54661472 AAAAGCCG
1 AAAAGCCG
*
54661480 AAAAGTCG
1 AAAAGCCG
54661488 AAAAGCCG
1 AAAAGCCG
*
54661496 AAATGCCG
1 AAAAGCCG
54661504 AAAA
1 AAAA
54661508 ACCGGCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.53, C:0.19, G:0.22, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:54661789 original size:27 final size:27
Alignment explanation
Indices: 54661759--54661820 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
54661749 ATTTACTAAA
*
54661759 ATACCCCTAAGTATG-AAAATTACTATT
1 ATACCCCTAAG-ATGCAAAATTACCATT
* * *
54661786 ATA-CCTTTAGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCATT
54661812 ATACCCCTA
1 ATACCCCTA
54661821 GGGTTAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
25 2 0.07
26 19 0.70
27 6 0.22
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCATT
Found at i:54661964 original size:27 final size:27
Alignment explanation
Indices: 54661926--54662031 Score: 142
Period size: 27 Copynumber: 3.9 Consensus size: 27
54661916 GAGGAAGCGT
54661926 TCTGGTGGCTCTACCACAAATATCTG-A
1 TCTGGTGGCTCTACCAC-AATATCTGTA
* *
54661953 TCTGGTGGCTCTGCCACAAATATCTGTT
1 TCTGGTGGCTCTACCAC-AATATCTGTA
*
54661981 TCTAGTGGCTCTACCACAATATCTGTA
1 TCTGGTGGCTCTACCACAATATCTGTA
* *
54662008 TCTGGTGACTCTATCACAATATCT
1 TCTGGTGGCTCTACCACAATATCT
54662032 ATTCTGGCAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
27 55 0.79
28 15 0.21
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTACCACAATATCTGTA
Found at i:54662026 original size:55 final size:54
Alignment explanation
Indices: 54661925--54662031 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 54
54661915 GGAGGAAGCG
* * *
54661925 TTCTGGTGGCTCTACCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTAGTGGCTCTACCACAAATATCTGATCTGGTGACTCTACCAC-AATATCTGT
*
54661980 TTCTAGTGGCTCTACCAC-AATATCTGTATCTGGTGACTCTATCACAATATCT
1 TTCTAGTGGCTCTACCACAAATATCTG-ATCTGGTGACTCTACCACAATATCT
54662032 ATTCTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
54 15 0.32
55 32 0.68
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
TTCTAGTGGCTCTACCACAAATATCTGATCTGGTGACTCTACCACAATATCTGT
Found at i:54675027 original size:20 final size:21
Alignment explanation
Indices: 54674990--54675028 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
54674980 TAAAATAGAT
54674990 TAAATAATAATTTGGAAAAAA
1 TAAATAATAATTTGGAAAAAA
* *
54675011 TAAA-AATATTTTTGAAAA
1 TAAATAATAATTTGGAAAA
54675029 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (21 bp):
TAAATAATAATTTGGAAAAAA
Found at i:54679330 original size:29 final size:29
Alignment explanation
Indices: 54679217--54679327 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
54679207 ACATACATGC
*
54679217 ATATGGCCCACTTA-GCCC-AATCTCATTT
1 ATATGGCCCA-TTAGGCCCAAATCACATTT
* * * * *
54679245 ATATGGCCCATCAGGCCCTATTCATATTC
1 ATATGGCCCATTAGGCCCAAATCACATTT
* *
54679274 ATATGGCCCATTACGCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACATTT
*
54679303 ATATGGCCCGTTAGGCCCAAATCAC
1 ATATGGCCCATTAGGCCCAAATCAC
54679328 CTTATATTCA
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
27 2 0.03
28 14 0.21
29 51 0.76
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATTT
Found at i:54681637 original size:47 final size:47
Alignment explanation
Indices: 54681529--54681659 Score: 137
Period size: 47 Copynumber: 2.8 Consensus size: 47
54681519 GACACATCTC
*
54681529 GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAA
1 GTAGCCGATGCATGT-CCAGACATGTCTTACACTAGCTCTCGTATCAA
* *
54681577 -TA-CCGATGCCATGTCCAAGACATGGTCTTACACTGGCT-T-TTAT-AA
1 GTAGCCGATG-CATGTCC-AGACAT-GTCTTACACTAGCTCTCGTATCAA
*
54681622 TGTAGCCGATGCATGTACCAGACATATCTTACACTAGC
1 -GTAGCCGATGCATGT-CCAGACATGTCTTACACTAGC
54681660 CCACAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
45 2 0.03
46 21 0.30
47 27 0.38
48 21 0.30
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (47 bp):
GTAGCCGATGCATGTCCAGACATGTCTTACACTAGCTCTCGTATCAA
Found at i:54682574 original size:10 final size:9
Alignment explanation
Indices: 54682551--54682575 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54682541 TCAAGGATCC
54682551 CAAAAACAT
1 CAAAAACAT
54682560 CAAAAACAT
1 CAAAAACAT
54682569 CAAAAAC
1 CAAAAAC
54682576 CAACACCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (9 bp):
CAAAAACAT
Found at i:54688040 original size:46 final size:46
Alignment explanation
Indices: 54687984--54688154 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 46
54687974 CACTGAAACA
54687984 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGAG
* * * * * *
54688030 GCCAATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
* * *
54688076 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAG
* *
54688124 GCCGATGCATGTCCCAAACATGTCTTGCACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
54688155 AGCCCACAAT
Statistics
Matches: 103, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
46 52 0.50
47 27 0.26
48 23 0.22
49 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
Found at i:54688155 original size:94 final size:92
Alignment explanation
Indices: 54687984--54688157 Score: 235
Period size: 94 Copynumber: 1.9 Consensus size: 92
54687974 CACTGAAACA
* * *
54687984 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAATGCATGTCCTAGAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCAATGCATGTCCCAAAC
54688049 ATGTCTTACACTAGCTCTCGTCTCAAT
66 ATGTCTTACACTAGCTCTCGTCTCAAT
* * *
54688076 GCCGATGCCATGTCCCAGACATGGTCTTACATTGGCTCT-CATAAT-GTGGCCGATGCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-ATCGAGGCCAATGCATGTCCC
*
54688139 AAACATGTCTTGCACTAGC
62 AAACATGTCTTACACTAGC
54688158 CCACAATAGC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
92 7 0.10
93 14 0.20
94 48 0.68
95 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCAATGCATGTCCCAAAC
ATGTCTTACACTAGCTCTCGTCTCAAT
Found at i:54688832 original size:20 final size:21
Alignment explanation
Indices: 54688807--54688846 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54688797 ACAATTTCAA
54688807 TTATTTCAC-ACATTCACAAC
1 TTATTTCACAACATTCACAAC
* *
54688827 TTATTTTACAACTTTCACAA
1 TTATTTCACAACATTCACAA
54688847 AATGGTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATTTCACAACATTCACAAC
Found at i:54689050 original size:10 final size:9
Alignment explanation
Indices: 54689026--54689051 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54689016 TTCAAGGATC
54689026 TCAAAAACA
1 TCAAAAACA
54689035 TCAAAAACA
1 TCAAAAACA
54689044 TCAAAAAC
1 TCAAAAAC
54689052 CAACACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (9 bp):
TCAAAAACA
Found at i:54692113 original size:30 final size:30
Alignment explanation
Indices: 54692055--54692113 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
54692045 ATTTTCGAGC
**
54692055 CTAGAGGCAAAATGGTCATTTTGTCAAAGT
1 CTAGAGGCAAAATGGTCATTTTACCAAAGT
* *
54692085 CTAGGGGCAAAATGGTCGTTTTACCAAAG
1 CTAGAGGCAAAATGGTCATTTTACCAAAG
54692114 ATATGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (30 bp):
CTAGAGGCAAAATGGTCATTTTACCAAAGT
Found at i:54692591 original size:46 final size:46
Alignment explanation
Indices: 54692458--54692676 Score: 175
Period size: 46 Copynumber: 4.7 Consensus size: 46
54692448 TTGTGTGAGG
*
54692458 TAGTGTAGGACATGTCTGGGACATGGCATCGGCATTGA-GACGA-GT-GC
1 TAGTGTAAGACATGTCTGGGACATGGCATCGGC--T-ACGA-GATGTAGC
* * *
54692505 TGGTGTAAGACATGTTTGGGACAT-GCATCGGCCT-CAAGATGTAAGC
1 TAGTGTAAGACATGTCTGGGACATGGCATCGG-CTACGAGATGT-AGC
* *
54692551 CAGTGTAAGACATGTCTGGGACAT-GCATCGGCTACGAGATGT-GT
1 TAGTGTAAGACATGTCTGGGACATGGCATCGGCTACGAGATGTAGC
* *
54692595 TAGTATAAGACCATGTCTGGGACATGGCATCGGC-ACAGATATGCTAGAAC
1 TAGTGTAAGA-CATGTCTGGGACATGGCATCGGCTAC-GAGATG-TAG--C
* * *
54692645 TTGTGTGAGACCATGTCTGTGACATGGCATCG
1 TAGTGTAAGA-CATGTCTGGGACATGGCATCG
54692677 ACACCTGACC
Statistics
Matches: 142, Mismatches: 17, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
43 2 0.01
44 12 0.08
45 19 0.13
46 57 0.40
47 23 0.16
48 1 0.01
50 28 0.20
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (46 bp):
TAGTGTAAGACATGTCTGGGACATGGCATCGGCTACGAGATGTAGC
Found at i:54695178 original size:47 final size:46
Alignment explanation
Indices: 54695055--54695180 Score: 141
Period size: 46 Copynumber: 2.7 Consensus size: 46
54695045 TGTAACCCGC
* * *
54695055 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCCTTTACAT
* *
54695101 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--GCCT--TTACAT
*
54695151 -C-TCA-CGAACTCGGACTCAACTCAACGAGCT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCT
54695181 TAGAACTCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
46 35 0.50
47 24 0.34
48 5 0.07
49 1 0.01
50 5 0.07
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCCTTTACAT
Found at i:54699073 original size:16 final size:15
Alignment explanation
Indices: 54699047--54699083 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
54699037 TATGAATCGG
*
54699047 CAAAAGCCGAAATGC
1 CAAAAGCCGAAAAGC
54699062 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
54699078 CAAAAG
1 CAAAAG
54699084 TTTGGCTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.51, C:0.24, G:0.19, T:0.05
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:54699341 original size:29 final size:28
Alignment explanation
Indices: 54699308--54699392 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
54699298 AATGTGACTG
*
54699308 GGCCTAACGAGCCATATAAATCTGATTTA
1 GGCCTAA-GAGCCATATAAATATGATTTA
* * ** *
54699337 GGCCTAATAGGCCATATACAGGTGATTTG
1 GGCCTAAGA-GCCATATAAATATGATTTA
* *
54699366 GGCCTAATGGGCCATATGAATATGATT
1 GGCCTAA-GAGCCATATAAATATGATT
54699393 GGGCTTAATG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.02
29 42 0.98
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (28 bp):
GGCCTAAGAGCCATATAAATATGATTTA
Found at i:54702365 original size:14 final size:14
Alignment explanation
Indices: 54702346--54702373 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54702336 CGCCCCAAAA
54702346 ACTGTATCATCTAC
1 ACTGTATCATCTAC
54702360 ACTGTATCATCTAC
1 ACTGTATCATCTAC
54702374 TCTAACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
ACTGTATCATCTAC
Found at i:54727919 original size:35 final size:35
Alignment explanation
Indices: 54727848--54727930 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
54727838 CAAGGTTCAT
54727848 TATATCATCACATATCGCCAAACATACAAGTACAA
1 TATATCATCACATATCGCCAAACATACAAGTACAA
* *
54727883 TATATCATCATATAT-GACCAAATATACAAGCT-CAA
1 TATATCATCACATATCG-CCAAACATACAAG-TACAA
* *
54727918 TAAAACATCACAT
1 TATATCATCACAT
54727931 GTAGTCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 39 0.95
36 1 0.02
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (35 bp):
TATATCATCACATATCGCCAAACATACAAGTACAA
Found at i:54727940 original size:35 final size:35
Alignment explanation
Indices: 54727901--54727967 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
54727891 CATATATGAC
54727901 CAAATATACAAGCTCAATAAAACATCACATGTAGT
1 CAAATATACAAGCTCAATAAAACATCACATGTAGT
* * * *
54727936 CAAATATTCAAGTTTAATATAACATCACATGT
1 CAAATATACAAGCTCAATAAAACATCACATGT
54727968 GACAGCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.28
Consensus pattern (35 bp):
CAAATATACAAGCTCAATAAAACATCACATGTAGT
Found at i:54728347 original size:56 final size:56
Alignment explanation
Indices: 54728261--54728380 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
54728251 ACAAGGGATG
*
54728261 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATAGAAAAATAAAATAAGAAGC
*
54728317 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATAGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATAGAAAAATAAAATAAGAAGC
54728373 ATGGGCAA
1 ATGGGCAA
54728381 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATAGAAAAATAAAATAAGAAGC
Found at i:54729771 original size:40 final size:40
Alignment explanation
Indices: 54729508--54729772 Score: 331
Period size: 40 Copynumber: 6.7 Consensus size: 40
54729498 TCGAATGATG
* * * * *
54729508 TCCGGGCTAAGTCCCGAAGG-TTTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
54729548 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54729588 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54729627 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54729667 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54729707 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54729748 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54729773 AACGAGTAGC
Statistics
Matches: 202, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
39 34 0.17
40 158 0.78
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54729779 original size:120 final size:118
Alignment explanation
Indices: 54729561--54729805 Score: 314
Period size: 120 Copynumber: 2.1 Consensus size: 118
54729551 GGACTAAGAT
* *
54729561 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
* ** *
54729626 ATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAGTC
66 ATCCGGGCTAAGTCCCGAAGGCATTGGAACGAG-TAGCTAAATCC-GGTTAAATC
* * * *
54729680 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTA
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
* * * *
54729745 TAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATT
65 -AATCCGGGCTAAGTCCCGAAGGCATTGGAACGAGTAGCTAAATCCGGTTAAATC
54729799 CCGAAGG
1 CCGAAGG
54729806 TACGTGATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
119 50 0.46
120 57 0.52
121 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (118 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
ATCCGGGCTAAGTCCCGAAGGCATTGGAACGAGTAGCTAAATCCGGTTAAATC
Found at i:54737519 original size:40 final size:40
Alignment explanation
Indices: 54737435--54737629 Score: 216
Period size: 40 Copynumber: 4.9 Consensus size: 40
54737425 TCGAATGATG
* * * * * *
54737435 TCCGGGCTAAGTCCCGAAGG-TTTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAA
* * * *
54737475 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTGGTGCGAGTTACTAAA
54737515 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAA
* * *
54737554 TCTGGGTTAAGTCCCGAAGGCATTGGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAA
* *
54737594 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTAC
54737630 GTTAAGTCCC
Statistics
Matches: 133, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 33 0.25
40 92 0.69
41 8 0.06
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAA
Found at i:54737637 original size:31 final size:31
Alignment explanation
Indices: 54737599--54737660 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
54737589 CTAAATCCGG
54737599 GTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 GTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
* *
54737630 GTTAAGTCCCGATGGCATTTGTGTGAGTTAC
1 GTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
54737661 TATAACCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (31 bp):
GTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
Found at i:54737684 original size:71 final size:71
Alignment explanation
Indices: 54737559--54737690 Score: 203
Period size: 71 Copynumber: 1.9 Consensus size: 71
54737549 CTAAATCTGG
*
54737559 GTTAAGTCCCGAAGGCATTGGTGTGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTTAAGTCCCGAAGGCATTGGTGTGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCG
54737624 AGTTAC
66 AGTTAC
* * * *
54737630 GTTAAGTCCCGATGGCATTTGTGTGAGTTACTATAA-CCGGGCTATGTCCTGAAGGCATTTG
1 GTTAAGTCCCGAAGGCATTGGTGTGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTG
54737691 AACGAGTAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 53 0.96
72 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (71 bp):
GTTAAGTCCCGAAGGCATTGGTGTGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCG
AGTTAC
Found at i:54741659 original size:27 final size:27
Alignment explanation
Indices: 54741628--54741805 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54741618 TAAATTGTAC
54741628 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54741655 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
54741681 ATGCACTAAGTGTGCGATTTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54741709 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54741737 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
54741764 AGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54741791 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54741806 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54741769 original size:82 final size:81
Alignment explanation
Indices: 54741629--54741784 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
54741619 AAATTGTACA
* * *
54741629 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
*
54741694 GCGATTTGACCATGCG
66 GCGAGTTGACCATGCG
** *
54741710 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAAT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
54741774 GTGCGAGTTGA
64 GTGCGAGTTGA
54741785 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAGTTGACCATGCG
Found at i:54741796 original size:82 final size:81
Alignment explanation
Indices: 54741625--54741805 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
54741615 GATTAAATTG
* *
54741625 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
* *
54741690 GTGTGCGATTTGACCA
66 ATGTGCGAGTTGACCA
* * ** *
54741706 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
**
54741770 AAATGTGCGAGTTGATTA
64 AAATGTGCGAGTTGACCA
* *
54741788 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54741806 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
ATGTGCGAGTTGACCA
Found at i:54747610 original size:26 final size:26
Alignment explanation
Indices: 54747580--54747631 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
54747570 AATTTTTGGA
54747580 AAACGTTTTCGTTGCGGAAGTTTTGC
1 AAACGTTTTCGTTGCGGAAGTTTTGC
54747606 AAACGTTTTCGTTGCGGAAGTTTTGC
1 AAACGTTTTCGTTGCGGAAGTTTTGC
54747632 TTTGTTGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (26 bp):
AAACGTTTTCGTTGCGGAAGTTTTGC
Found at i:54748238 original size:28 final size:28
Alignment explanation
Indices: 54748194--54748309 Score: 155
Period size: 28 Copynumber: 4.2 Consensus size: 28
54748184 AGTATGGCTG
* * *
54748194 CCAG-AACAGA-AATTGTGACAGAGTCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
* * *
54748220 CTAGATACAGATATTTGTGGCAGGGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
*
54748248 CCAGAAACAGATATTTGTGGCAAAGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
54748276 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
54748304 CCAGAA
1 CCAGAA
54748310 CGCTTCCTCC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 3 0.04
27 5 0.06
28 69 0.90
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGAAACAGATATTTGTGGCAGAGCCA
Found at i:54753244 original size:59 final size:59
Alignment explanation
Indices: 54753152--54753271 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
54753142 AATGTTATAC
*
54753152 TTTAACATAAATAAGTTACCTTAGCCGAATACTAATATTTCTCATTCAGCATAATATTA
1 TTTAACACAAATAAGTTACCTTAGCCGAATACTAATATTTCTCATTCAGCATAATATTA
* * *
54753211 TTTAACACAAATAATTTACCTTGGCCGAATACTAATATTTCTCATTTAGCATAATATTA
1 TTTAACACAAATAAGTTACCTTAGCCGAATACTAATATTTCTCATTCAGCATAATATTA
54753270 TT
1 TT
54753272 CAACTTTTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.39
Consensus pattern (59 bp):
TTTAACACAAATAAGTTACCTTAGCCGAATACTAATATTTCTCATTCAGCATAATATTA
Found at i:54753565 original size:35 final size:35
Alignment explanation
Indices: 54753488--54753649 Score: 157
Period size: 35 Copynumber: 4.6 Consensus size: 35
54753478 AATACTCAAG
* *
54753488 GTTCATTATATCATCACATATCG-CCAAACATACAA
1 GTTCAATATATCATCACATAT-GACCAAATATACAA
* *
54753523 GTACAATATATCATCATATATGACCAAATATACAA
1 GTTCAATATATCATCACATATGACCAAATATACAA
* * * * * * *
54753558 GCTCAATAAAACATCACATGT-AGTCAGATATTCAA
1 GTTCAATATATCATCACATATGA-CCAAATATACAA
* * * *
54753593 GTTTAATATAACATCACATGTGGCCAAATATACAA
1 GTTCAATATATCATCACATATGACCAAATATACAA
54753628 GTTCAATATATCATCACATATG
1 GTTCAATATATCATCACATATG
54753650 TACATACCTA
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
34 2 0.02
35 99 0.98
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (35 bp):
GTTCAATATATCATCACATATGACCAAATATACAA
Found at i:54757578 original size:42 final size:42
Alignment explanation
Indices: 54757531--54757622 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
54757521 TGCCCCTTAG
* ** *
54757531 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
54757573 GCCCATTTCAATATGACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
54757615 GCCCATTT
1 GCCCATTT
54757623 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:54757830 original size:25 final size:26
Alignment explanation
Indices: 54757770--54757839 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
54757760 CTCTTTTAAC
* * *
54757770 AACTGGGGCAAAACCC-TTTCTGATA
1 AACTGGGGCAGAGCCCTTTTCAGATA
54757795 AACTGGGGCAGAGCCCTTTTCAG-TA
1 AACTGGGGCAGAGCCCTTTTCAGATA
*
54757820 AACTGGGGCAGAGCCTTTTT
1 AACTGGGGCAGAGCCCTTTT
54757840 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 35 0.88
26 5 0.12
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAGAGCCCTTTTCAGATA
Found at i:54758785 original size:27 final size:27
Alignment explanation
Indices: 54758755--54758806 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
54758745 ATAAATCTAC
*
54758755 AAACCAAGGGTATTTCAATAATTTTGT
1 AAACCAAGGGTATTCCAATAATTTTGT
* *
54758782 AAACCAATGGTATTCCTATAATTTT
1 AAACCAAGGGTATTCCAATAATTTT
54758807 TTTAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (27 bp):
AAACCAAGGGTATTCCAATAATTTTGT
Found at i:54758851 original size:27 final size:27
Alignment explanation
Indices: 54758821--54758916 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
54758811 AAAAGTCAAT
* **
54758821 GGTATTTTTGTAATTTTGTAAATT-AGG
1 GGTATTTTGGTAATTTTACAAATTGA-G
54758848 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTGGTAATTTTACAAATTGAG
* **
54758875 GGTATTTCGGTAATTTCT-CAAA-CCAG
1 GGTATTTTGGTAATTT-TACAAATTGAG
54758901 TGGTATTTTGGTAATT
1 -GGTATTTTGGTAATT
54758917 CTATCCTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.03
27 55 0.93
28 2 0.03
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAATTGAG
Found at i:54759049 original size:27 final size:27
Alignment explanation
Indices: 54758948--54759053 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
54758938 ATAATTTCAC
**
54758948 AATCGAGGGTAAAACAGTAATTTTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
* *
54758975 AATTGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
* * *
54759002 AATCGAGGGTAAAACGATAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
***
54759029 AATCGAGGGTACTTTGGTAATTTTA
1 AATCGAGGGTAAAATGGTAATTTTA
54759054 CAAGTCAAGG
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTATA
Found at i:54759065 original size:54 final size:53
Alignment explanation
Indices: 54758939--54759066 Score: 143
Period size: 54 Copynumber: 2.4 Consensus size: 53
54758929 GGTATTTCAA
* * *
54758939 TAATTTCACAATCGAGGGTAAAACAGTAATTTTATAAATTGAGGGTAAAATGG
1 TAATTTTACAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGG
***
54758992 TAATTTTGTA-AATCGAGGGTAAAAC-GATAATTCTATAAATCGAGGGTACTTTGG
1 TAA-TTT-TACAATCGAGGGTAAAACAG-TAATTCTATAAATCGAGGGTAAAATGG
*
54759046 TAATTTTACAAGTCAAGGGTA
1 TAATTTTACAA-TCGAGGGTA
54759067 TTTCAGTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
52 2 0.03
53 9 0.14
54 51 0.81
55 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (53 bp):
TAATTTTACAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGG
Found at i:54761430 original size:42 final size:42
Alignment explanation
Indices: 54761383--54761474 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
54761373 TGGCCCTTAG
* ** *
54761383 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
*
54761425 GCCCATTTCAATATGACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
54761467 GCCCATTT
1 GCCCATTT
54761475 GGGGAGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:54761687 original size:25 final size:25
Alignment explanation
Indices: 54761622--54761690 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
54761612 CTCTTTTAAT
* * *
54761622 AACTGGGGCAAAACCCTTTCTGATA
1 AACTGGGGCAGAGCCCTTTCCGATA
* *
54761647 AACTGGGGTAGAGCCCTTTCCGGTA
1 AACTGGGGCAGAGCCCTTTCCGATA
*
54761672 AACTGGGGCAGCGCCCTTT
1 AACTGGGGCAGAGCCCTTT
54761691 TAGCACTTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (25 bp):
AACTGGGGCAGAGCCCTTTCCGATA
Done.