Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 161 of 259
Found at i:52608006 original size:98 final size:97
Alignment explanation
Indices: 52607882--52608061 Score: 254
Period size: 98 Copynumber: 1.8 Consensus size: 97
52607872 TTCACATGTT
* *
52607882 TCAGTGTAAGACCTATCTGGGACATGGCATCGACATCGATGGATGAGAGCCAATGTAAGAGC-TG
1 TCAGTGTAAGACCTATCTGGGACATGGCATCGACATAGAT-G-TGAGAGCCAATGTAAGACCATG
*
52607946 TCTGGGACATGGCATCGGCGTCGATATATGAAAG
64 TCTGGAACATGGCATCGGCGTCGATATATGAAAG
* * * * * *
52607980 TCAGTGTAAGACCTGTCTGGGACATGGCATTGACTTAGATGTGTGAGCCAGTGTAAGACCATGTT
1 TCAGTGTAAGACCTATCTGGGACATGGCATCGACATAGATGTGAGAGCCAATGTAAGACCATGTC
52608045 TGGAACATGGCATCGGC
66 TGGAACATGGCATCGGC
52608062 ATTGTACCCT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
96 16 0.22
97 20 0.28
98 36 0.50
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (97 bp):
TCAGTGTAAGACCTATCTGGGACATGGCATCGACATAGATGTGAGAGCCAATGTAAGACCATGTC
TGGAACATGGCATCGGCGTCGATATATGAAAG
Found at i:52612224 original size:5 final size:5
Alignment explanation
Indices: 52612214--52612238 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52612204 TATAAAATCA
52612214 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
52612239 TTATTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:52616096 original size:16 final size:16
Alignment explanation
Indices: 52616075--52616108 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52616065 ACAGTCTTCT
52616075 TTCTTCCATACCTTTC
1 TTCTTCCATACCTTTC
**
52616091 TTCTTCTGTACCTTTC
1 TTCTTCCATACCTTTC
52616107 TT
1 TT
52616109 TACCAAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.32, G:0.03, T:0.56
Consensus pattern (16 bp):
TTCTTCCATACCTTTC
Found at i:52626316 original size:18 final size:18
Alignment explanation
Indices: 52626293--52626331 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52626283 CTTGAACTTT
* *
52626293 ATTTTTGGATGATTTTTA
1 ATTTTTGCATGAGTTTTA
*
52626311 ATTTTTGCATTAGTTTTA
1 ATTTTTGCATGAGTTTTA
52626329 ATT
1 ATT
52626332 ACTTAGGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.62
Consensus pattern (18 bp):
ATTTTTGCATGAGTTTTA
Found at i:52628157 original size:40 final size:40
Alignment explanation
Indices: 52628059--52628321 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
52628049 TCCTCGTTCA
* * * * *
52628059 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52628098 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52628138 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52628178 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52628218 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
52628258 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52628298 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52628322 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52628330 original size:41 final size:41
Alignment explanation
Indices: 52628253--52628330 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
52628243 TTAGTATCTC
* * *
52628253 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
52628294 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
52628331 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:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:52635215 original size:40 final size:40
Alignment explanation
Indices: 52634992--52635201 Score: 314
Period size: 40 Copynumber: 5.3 Consensus size: 40
52634982 TCCTCGTTCA
* * * * *
52634992 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52635031 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52635071 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52635111 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52635151 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
52635191 AAGGCCTTCGG
1 AATGCCTTCGG
52635202 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:52635238 original size:80 final size:80
Alignment explanation
Indices: 52634995--52635254 Score: 265
Period size: 80 Copynumber: 3.3 Consensus size: 80
52634985 TCGTTCAAAT
* * * * * * * *
52634995 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* * *
52635059 ACAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * *
52635074 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
52635139 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * **
52635154 GCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
* *
52635218 ATTCACTTAGCAC-AAA
65 AATAAC-TAGCACGAAA
* *
52635234 GCCTTCGGAACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
52635255 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:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:52635238 original size:120 final size:118
Alignment explanation
Indices: 52634990--52635254 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 118
52634980 GCTCCTCGTT
* * *
52634990 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGA
* * * *
52635055 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 TTTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
* * * *
52635109 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGG
** * ** * *
52635174 ATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
64 ATTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCA
*
52635230 CAAAGCCTTCGGAACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
52635255 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:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGAT
TTAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATAATAACTAGCA
Found at i:52635263 original size:41 final size:41
Alignment explanation
Indices: 52635186--52635263 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
52635176 TTAGTATCTC
* * * *
52635186 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
52635227 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
52635264 ATTAATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:52637113 original size:24 final size:25
Alignment explanation
Indices: 52637055--52637113 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
52637045 CTCAAGTATA
* *
52637055 TTTTATTTTCATGTTTATTTCTTGT
1 TTTTATTTTTATGTTTATTTCTAGT
52637080 TTTT-TGTTTTA-GTTTATTT-TCAGT
1 TTTTAT-TTTTATGTTTATTTCT-AGT
52637104 TTTTATTTTT
1 TTTTATTTTT
52637114 GGGTAGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 1 0.03
24 19 0.66
25 9 0.31
ACGTcount: A:0.12, C:0.05, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTTATTTTTATGTTTATTTCTAGT
Found at i:52644530 original size:33 final size:33
Alignment explanation
Indices: 52644493--52644559 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
52644483 TTTTTAAAAA
52644493 ATAATTTTTAATTCTTTTATTTAAAGATAATAT
1 ATAATTTTTAATTCTTTTATTTAAAGATAATAT
52644526 ATAATTTTTAATTCTTTTATTTAAAGATAATAT
1 ATAATTTTTAATTCTTTTATTTAAAGATAATAT
52644559 A
1 A
52644560 AAAGTGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (33 bp):
ATAATTTTTAATTCTTTTATTTAAAGATAATAT
Found at i:52644644 original size:28 final size:28
Alignment explanation
Indices: 52644608--52644666 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
52644598 AATTATAATT
52644608 TAAAAGAATGAATATCTTTATAATTTCA
1 TAAAAGAATGAATATCTTTATAATTTCA
52644636 TAAAAGAATGAATATCTTTATAATTTCA
1 TAAAAGAATGAATATCTTTATAATTTCA
52644664 TAA
1 TAA
52644667 TTAAGTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAAAGAATGAATATCTTTATAATTTCA
Found at i:52644906 original size:3 final size:3
Alignment explanation
Indices: 52644898--52644924 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52644888 ACTATAGGCA
52644898 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
52644925 AAAAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52645599 original size:18 final size:17
Alignment explanation
Indices: 52645559--52645601 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
52645549 CGATTAGATC
52645559 ATTAA-TTTTTTATATA
1 ATTAATTTTTTTATATA
* *
52645575 CTTAATTTTTTTATCTA
1 ATTAATTTTTTTATATA
52645592 ATTCAATTTT
1 ATT-AATTTT
52645602 AACAACTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.18
17 12 0.55
18 6 0.27
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTAATTTTTTTATATA
Found at i:52646952 original size:5 final size:5
Alignment explanation
Indices: 52646942--52646972 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
52646932 AATTATAAAA
52646942 TATTT TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
52646973 TTAACTCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:52649829 original size:21 final size:22
Alignment explanation
Indices: 52649763--52649842 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
52649753 CCCGAATCAG
*
52649763 CTATTTTGTTATTGT-TTCGCTA
1 CTATTTTGTTATTATATT-GCTA
* * *
52649785 CTATTTTATTTTTATTTTGCTA
1 CTATTTTGTTATTATATTGCTA
*
52649807 CTA-TTTGTTATTATATTGTTA
1 CTATTTTGTTATTATATTGCTA
*
52649828 CTATTTTGTTGTTAT
1 CTATTTTGTTATTAT
52649843 TGTTTTGATA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.35
22 29 0.60
23 2 0.04
ACGTcount: A:0.17, C:0.09, G:0.10, T:0.64
Consensus pattern (22 bp):
CTATTTTGTTATTATATTGCTA
Found at i:52649843 original size:11 final size:11
Alignment explanation
Indices: 52649764--52649843 Score: 54
Period size: 11 Copynumber: 7.4 Consensus size: 11
52649754 CCGAATCAGC
52649764 TATTTTGTTAT
1 TATTTTGTTAT
* * * *
52649775 TGTTTCGCTAC
1 TATTTTGTTAT
* *
52649786 TATTTTATTTT
1 TATTTTGTTAT
* *
52649797 TATTTTGCTAC
1 TATTTTGTTAT
52649808 TA-TTTGTTAT
1 TATTTTGTTAT
* *
52649818 TATATTGTTAC
1 TATTTTGTTAT
*
52649829 TATTTTGTTGT
1 TATTTTGTTAT
52649840 TATT
1 TATT
52649844 GTTTTGATAT
Statistics
Matches: 47, Mismatches: 21, Indels: 2
0.67 0.30 0.03
Matches are distributed among these distances:
10 8 0.17
11 39 0.83
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:52650550 original size:26 final size:26
Alignment explanation
Indices: 52650490--52650551 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
52650480 TAAAATGAAC
52650490 ATTTATGTTTTTTTATTCATTTCTACT
1 ATTTAT-TTTTTTTATTCATTTCTACT
*
52650517 CTTT-TTTTTTTATGATTC-TTTCTA-T
1 ATTTATTTTTTT-T-ATTCATTTCTACT
52650542 ATTTATTTTT
1 ATTTATTTTT
52650552 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 10 0.33
26 13 0.43
27 7 0.23
ACGTcount: A:0.16, C:0.10, G:0.03, T:0.71
Consensus pattern (26 bp):
ATTTATTTTTTTTATTCATTTCTACT
Found at i:52652740 original size:6 final size:6
Alignment explanation
Indices: 52652729--52652892 Score: 72
Period size: 6 Copynumber: 27.5 Consensus size: 6
52652719 AAGAAAAGCT
* * *
52652729 ATAATA ATAATA GTAATT ATAATA A-AAGTA ATAATA ATAA-A TATAACA
1 ATAATA ATAATA ATAATA ATAATA ATAA-TA ATAATA ATAATA -ATAATA
* * * * * *
52652777 ATAGTA ATATTA GTGATA A-AA-A ATAATA GCT-ATA AAAATA A-ACATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA -ATAATA ATAATA ATA-ATA
** * * * * *
52652823 ATAACC ATGACA ATAAAGA ATAATA GTAATA ATAATA ATAATA ATAAAA
1 ATAATA ATAATA AT-AATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
52652872 ATAA-A AGTAATA TTAATA ATA
1 ATAATA A-TAATA ATAATA ATA
52652893 TATTGTATTA
Statistics
Matches: 118, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
4 2 0.02
5 9 0.08
6 97 0.82
7 10 0.08
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.29
Consensus pattern (6 bp):
ATAATA
Found at i:52652752 original size:15 final size:15
Alignment explanation
Indices: 52652729--52652890 Score: 66
Period size: 15 Copynumber: 10.7 Consensus size: 15
52652719 AAGAAAAGCT
*
52652729 ATAATAATAATAGTA
1 ATAATAATAAAAGTA
*
52652744 ATTATAATAAAAGTA
1 ATAATAATAAAAGTA
52652759 ATAATAATAAATA-TA
1 ATAATAATAAA-AGTA
* * * *
52652774 ACAATAGTAATATTA
1 ATAATAATAAAAGTA
* *
52652789 GTGATAA-AAAA-TA
1 ATAATAATAAAAGTA
* *
52652802 ATAGCT-ATAAAAATA
1 ATA-ATAATAAAAGTA
* *
52652817 A-ACATAATAACCATGACA
1 ATA-ATAATAA--AAG-TA
* *
52652835 ATAAAGAATAATAGTA
1 AT-AATAATAAAAGTA
52652851 ATAATAATAATAA-TA
1 ATAATAATAA-AAGTA
*
52652866 ATAAAAATAAAAGTA
1 ATAATAATAAAAGTA
*
52652881 ATATTAATAA
1 ATAATAATAA
52652891 TATATTGTAT
Statistics
Matches: 106, Mismatches: 28, Indels: 26
0.66 0.17 0.16
Matches are distributed among these distances:
13 4 0.04
14 13 0.12
15 73 0.69
16 5 0.05
17 2 0.02
18 2 0.02
19 6 0.06
20 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (15 bp):
ATAATAATAAAAGTA
Found at i:52652893 original size:9 final size:9
Alignment explanation
Indices: 52652729--52652892 Score: 72
Period size: 9 Copynumber: 18.3 Consensus size: 9
52652719 AAGAAAAGCT
52652729 ATAATAATA
1 ATAATAATA
* *
52652738 ATAGTAATT
1 ATAATAATA
52652747 ATAATAA-A
1 ATAATAATA
52652755 AGTAATAATA
1 A-TAATAATA
52652765 ATAA-ATATA
1 ATAATA-ATA
* *
52652774 ACAATAGTA
1 ATAATAATA
* * *
52652783 ATATTAGTG
1 ATAATAATA
52652792 ATAA-AA-A
1 ATAATAATA
*
52652799 ATAATAGCT-
1 ATAATA-ATA
*
52652808 ATAAAAATA
1 ATAATAATA
52652817 A-ACATAATA
1 ATA-ATAATA
** * *
52652826 ACCATGACA
1 ATAATAATA
*
52652835 ATAAAGAATA
1 AT-AATAATA
*
52652845 ATAGTAATA
1 ATAATAATA
52652854 ATAATAATA
1 ATAATAATA
*
52652863 ATAATAAAA
1 ATAATAATA
52652872 ATAA-AAGTA
1 ATAATAA-TA
*
52652881 ATATTAATA
1 ATAATAATA
52652890 ATA
1 ATA
52652893 TATTGTATTA
Statistics
Matches: 112, Mismatches: 30, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
7 4 0.04
8 8 0.07
9 90 0.80
10 10 0.09
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.29
Consensus pattern (9 bp):
ATAATAATA
Found at i:52653120 original size:143 final size:145
Alignment explanation
Indices: 52652973--52653251 Score: 329
Period size: 149 Copynumber: 1.9 Consensus size: 145
52652963 AGTAATAAAG
* *
52652973 TAATAAATAAACAT-AAAAAGGAAA-GT-GTATAATATAATAATATTAAAATAAGGTAAT-T-AA
1 TAAT-AATAAA-ATAAAAAAGCAAATGTAGTATAATA-AA-AATATTAAAATAAAGTAATATAAA
* * * * *
52653033 AAATATTACGA-TATAAATACATATATATATGCATATTTAATAAAAATATACACTAATAT-TAAT
62 AAATAATACGAGTATAAAAACATATACATATACATATATAATAAAAA-ATACACTAATATATAAT
52653096 AATAATAATGATAATAGTAA
126 AATAATAATGATAATAGTAA
*
52653116 TAATATTAAAATACAAAAAGCAAATGTAGTATAATAAAAATATTAAAATAAAGTAATAATAAAAA
1 TAATAATAAAATA-AAAAAGCAAATGTAGTATAATAAAAATATTAAAATAAAGTAAT-AT-AAAA
* *
52653181 AATAATACTATGTATAAAAATATATACATATACATATATAATAAAAAATACACTAATATATAATA
63 AATAATACGA-GTATAAAAACATATACATATACATATATAATAAAAAATACACTAATATATAATA
*
52653246 CTAATA
127 ATAATA
52653252 CTAACACATT
Statistics
Matches: 114, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
141 2 0.02
142 5 0.04
143 31 0.27
144 4 0.04
145 9 0.08
147 11 0.10
148 12 0.11
149 40 0.35
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (145 bp):
TAATAATAAAATAAAAAAGCAAATGTAGTATAATAAAAATATTAAAATAAAGTAATATAAAAAAT
AATACGAGTATAAAAACATATACATATACATATATAATAAAAAATACACTAATATATAATAATAA
TAATGATAATAGTAA
Found at i:52653426 original size:22 final size:21
Alignment explanation
Indices: 52653371--52653426 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
52653361 ATTAACAAAA
52653371 TAATAATAATAATAAGTTAAAG
1 TAATAATAAT-ATAAGTTAAAG
* **
52653393 TAATAATAATATATGTTAATT
1 TAATAATAATATAAGTTAAAG
52653414 TAATACATAATAT
1 TAATA-ATAATAT
52653427 GGAAAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TAATAATAATATAAGTTAAAG
Found at i:52654277 original size:24 final size:24
Alignment explanation
Indices: 52654231--52654279 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52654221 TAATTTCATT
* *
52654231 AAAAATAAACATACATCTCTCTAA
1 AAAAAAAAACATACATCTATCTAA
* *
52654255 AAAAAAAAACATACCTGTATCTAA
1 AAAAAAAAACATACATCTATCTAA
52654279 A
1 A
52654280 TCTCATCACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAAAAAAACATACATCTATCTAA
Found at i:52656629 original size:28 final size:28
Alignment explanation
Indices: 52656589--52656645 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
52656579 CATGTTTTTC
52656589 CCTTGAGGATCATATCTCTATTGAATAT
1 CCTTGAGGATCATATCTCTATTGAATAT
52656617 CCTTGAGGATCATATCTCTATTGAATAT
1 CCTTGAGGATCATATCTCTATTGAATAT
52656645 C
1 C
52656646 TTTAAAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (28 bp):
CCTTGAGGATCATATCTCTATTGAATAT
Found at i:52664460 original size:91 final size:91
Alignment explanation
Indices: 52664297--52664563 Score: 358
Period size: 91 Copynumber: 2.9 Consensus size: 91
52664287 CTCGTATAAT
* * * * *
52664297 AATAATACACAAATTGATAATTTAAATACCACATTAAATATTTTCAAAGTATAAGTACCACATTG
1 AATAATACACAAATTGATAGTTTAAGTACCACATTAGATATTTTCAAAGTATAAGAACCACATTA
*
52664362 GATATTTTATAAAAATACAAGTAACA
66 GACATTTTATAAAAATACAAGTAACA
* *
52664388 TATAATACACAAATTGATAGTTTAAGTACCACATTAGATATTTTTAAAGTATAAGAACCACATTA
1 AATAATACACAAATTGATAGTTTAAGTACCACATTAGATATTTTCAAAGTATAAGAACCACATTA
* *
52664453 GACATTTTATGAAAGA-ACAAGTACCA
66 GACATTTTAT-AAAAATACAAGTAACA
* * * * * *
52664479 AATAATACATAAATTGATAGTTTAAGTATCATATTAGACATTTTCAAAGTA-CAGATACTACATT
1 AATAATACACAAATTGATAGTTTAAGTACCACATTAGATATTTTCAAAGTATAAGA-ACCACATT
52664543 AGACATTTTATAAAAATACAA
65 AGACATTTTATAAAAATACAA
52664564 TTACAAAATG
Statistics
Matches: 154, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
90 7 0.05
91 143 0.93
92 4 0.03
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (91 bp):
AATAATACACAAATTGATAGTTTAAGTACCACATTAGATATTTTCAAAGTATAAGAACCACATTA
GACATTTTATAAAAATACAAGTAACA
Found at i:52665756 original size:67 final size:67
Alignment explanation
Indices: 52665637--52665768 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 67
52665627 TCGAACTAGA
* *
52665637 GCATTCAAAGATACATGTCTGACTAAATACATTCAATCACTCGGGAACTTTTTTTCATGTATCTT
1 GCATTCAAAGATACATGTCCGACTAAATACATTCAATCACTCGCGAACTTTTTTTCATGTATCTT
52665702 GG
66 GG
* * * * *
52665704 GCATTCACAGATACGTGTCCGACTAAATATATTCAATTAC-C-CGAACTTTTTTTCATGTATTTT
1 GCATTCAAAGATACATGTCCGACTAAATACATTCAATCACTCGCGAACTTTTTTTCATGTATCTT
52665767 GG
66 GG
52665769 AGGACTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 22 0.38
66 1 0.02
67 35 0.60
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (67 bp):
GCATTCAAAGATACATGTCCGACTAAATACATTCAATCACTCGCGAACTTTTTTTCATGTATCTT
GG
Found at i:52672248 original size:25 final size:25
Alignment explanation
Indices: 52672219--52672269 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
52672209 CAAAGGAAAA
**
52672219 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
*
52672244 TCCTAATAGAATTCTTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
52672269 T
1 T
52672270 TTATAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:52677461 original size:2 final size:2
Alignment explanation
Indices: 52677454--52677478 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52677444 ATTCAATGAT
52677454 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52677479 TTCTACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52682158 original size:31 final size:31
Alignment explanation
Indices: 52682090--52682299 Score: 296
Period size: 31 Copynumber: 6.8 Consensus size: 31
52682080 ATAAATGACA
*
52682090 AGTGAAAAGTGGTAGTTTCGGCTACCTGAT-
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
52682120 AGTGAAAAGTGGTAGTTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
** *
52682151 AGTGAAAAGTGGTAGCTTTTGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
52682182 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
52682213 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
52682244 AGTGAAAAATGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
52682275 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
52682300 AAGTGACAAG
Statistics
Matches: 163, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
30 30 0.18
31 133 0.82
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:52682403 original size:47 final size:46
Alignment explanation
Indices: 52682317--52682434 Score: 146
Period size: 47 Copynumber: 2.5 Consensus size: 46
52682307 AAGTGATTTC
* * *
52682317 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
52682363 CTGTATAAGACCATATCTGGGATATGGCATCATTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
52682410 CGTGTAAGACCATAGCTGGGCTATG
1 CGTATAAGACCATATCTGGGATATG
52682435 ACATTGATAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 22 0.35
47 40 0.65
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:52684185 original size:21 final size:21
Alignment explanation
Indices: 52684159--52684213 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
52684149 TGTAGGCTGC
* *
52684159 ACAGAAGCACATAAGTGCTAA
1 ACAGAAACACATAAGGGCTAA
* *
52684180 ACAGAAACCCATAAGGGTTAA
1 ACAGAAACACATAAGGGCTAA
* *
52684201 ACAAAAACTCATA
1 ACAGAAACACATA
52684214 TGAGTTGACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (21 bp):
ACAGAAACACATAAGGGCTAA
Found at i:52691461 original size:24 final size:22
Alignment explanation
Indices: 52691418--52691461 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
52691408 TGAGTTTTTG
*
52691418 TTTTTAATTTTAATATTTTTAT
1 TTTTTAATTTTAATAATTTTAT
52691440 TTTTTAAATTTTTAATAATTTT
1 TTTTT-AA-TTTTAATAATTTT
52691462 TAACCGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTAATTTTAATAATTTTAT
Found at i:52691834 original size:13 final size:13
Alignment explanation
Indices: 52691816--52691847 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
52691806 AAAGTGATGG
52691816 TTTATCAAAGAAC
1 TTTATCAAAGAAC
52691829 TTTATCAAAGAAC
1 TTTATCAAAGAAC
52691842 TTTATC
1 TTTATC
52691848 TTGAAATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (13 bp):
TTTATCAAAGAAC
Found at i:52692211 original size:20 final size:19
Alignment explanation
Indices: 52692186--52692257 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
52692176 TAATTACAAA
52692186 TTTATAACATATAGTTTAAT
1 TTTATAACAT-TAGTTTAAT
*
52692206 TTTATAAACATTTTA-TTTTAT
1 TTTAT-AACA--TTAGTTTAAT
* *
52692227 TTTATTACATTAGCTTAAT
1 TTTATAACATTAGTTTAAT
*
52692246 TTTATAATATTA
1 TTTATAACATTA
52692258 ACAAACATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
18 3 0.07
19 14 0.33
20 8 0.19
21 14 0.33
22 2 0.05
23 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTATAACATTAGTTTAAT
Found at i:52693418 original size:16 final size:16
Alignment explanation
Indices: 52693372--52693420 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
52693362 TTAAAAAATA
52693372 TTTATAT-TATTTTAA-
1 TTTATATAT-TTTTAAT
*
52693387 TTTA-ATATTTAATAAT
1 TTTATATATTT-TTAAT
52693403 TTTATATATTTTTAAT
1 TTTATATATTTTTAAT
52693419 TT
1 TT
52693421 ATTGATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 10 0.36
17 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATATTTTTAAT
Found at i:52693421 original size:15 final size:15
Alignment explanation
Indices: 52693371--52693422 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
52693361 TTTAAAAAAT
52693371 ATTTATAT-TATTTTA
1 ATTTATATAT-TTTTA
*
52693386 ATTTA-ATATTTAATA
1 ATTTATATATTT-TTA
52693401 ATTTTATATATTTTTA
1 A-TTTATATATTTTTA
52693417 ATTTAT
1 ATTTAT
52693423 TGATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 14 0.45
16 7 0.23
17 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTATATATTTTTA
Found at i:52696361 original size:16 final size:16
Alignment explanation
Indices: 52696340--52696405 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
52696330 GATTGATATT
52696340 GAAATGAAAAATATGA
1 GAAATGAAAAATATGA
52696356 GAAATG---AATATGA
1 GAAATGAAAAATATGA
*
52696369 G--ATGAGAAAATATTA
1 GAAATGA-AAAATATGA
*
52696384 -AAATGACAAATATGA
1 GAAATGAAAAATATGA
52696399 GAAATGA
1 GAAATGA
52696406 TTATGAGATG
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
11 3 0.08
13 8 0.20
15 13 0.32
16 16 0.40
ACGTcount: A:0.58, C:0.02, G:0.20, T:0.21
Consensus pattern (16 bp):
GAAATGAAAAATATGA
Found at i:52696396 original size:43 final size:43
Alignment explanation
Indices: 52696335--52696420 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
52696325 TATGTGATTG
*
52696335 ATATTGAAATGAAAAATATGAGAAATGAATATGAGATGAGAAA
1 ATATTAAAATGAAAAATATGAGAAATGAATATGAGATGAGAAA
* *
52696378 ATATTAAAATGACAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTAAAATGAAAAATATGAGAAATGAATATGAGATGAGAAA
52696421 TGAAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.55, C:0.01, G:0.20, T:0.24
Consensus pattern (43 bp):
ATATTAAAATGAAAAATATGAGAAATGAATATGAGATGAGAAA
Found at i:52705088 original size:175 final size:176
Alignment explanation
Indices: 52704807--52705126 Score: 456
Period size: 176 Copynumber: 1.8 Consensus size: 176
52704797 TAGATCTTCA
*
52704807 ATCTTCAATCTTCAGTCTGCTTTCTTGCTGCCTCAGGAAGATAAGACTAAAATCGCTAACCTGCT
1 ATCTTCAATCTTCAGTCTGCTTTCTTGCTGCCTCAGAAAGATAAGACTAAAATCGCTAACCTGCT
* * *
52704872 CTCTTGCTACCTCAGAGAGATAAGGCTAGTGGCTAAAATCTGCTCC-AT-TACTG-TACATGGAG
66 CTCTTGCTACCTCAGAGAGATAAGACTAGAGGCTAAAATCTGCTCCAATGT-C-GATACATAGAG
*
52704934 ATAAGTTTTGCCATCTTCGATCTGCTCTACTACTACTTAGAGAGATAAG
129 ATAAGATTTGCC-TCTTCGATCTGCTCTACTACTACTTAGAGAGATAAG
* *
52704983 ATCTTCAA-CTTTCAGTCTGCTTTCTTGCTAG-CTCAGAAAGATAAGACT-CAATC-TTCAACCT
1 ATCTTCAATC-TTCAGTCTGCTTTCTTGCT-GCCTCAGAAAGATAAGACTAAAATCGCT-AACCT
* *
52705044 GCTCTCTTGCTACCTCAGAGAGATAAGACTTGAGGCTTAAATCTGCTCCAATGTCGATACATAGA
63 GCTCTCTTGCTACCTCAGAGAGATAAGACTAGAGGCTAAAATCTGCTCCAATGTCGATACATAGA
52705109 GATAAGATTTGCCTCTTC
128 GATAAGATTTGCCTCTTC
52705127 CAATATTCAA
Statistics
Matches: 129, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
174 1 0.01
175 61 0.47
176 65 0.50
177 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (176 bp):
ATCTTCAATCTTCAGTCTGCTTTCTTGCTGCCTCAGAAAGATAAGACTAAAATCGCTAACCTGCT
CTCTTGCTACCTCAGAGAGATAAGACTAGAGGCTAAAATCTGCTCCAATGTCGATACATAGAGAT
AAGATTTGCCTCTTCGATCTGCTCTACTACTACTTAGAGAGATAAG
Found at i:52705113 original size:176 final size:179
Alignment explanation
Indices: 52704721--52705126 Score: 483
Period size: 175 Copynumber: 2.3 Consensus size: 179
52704711 GGACTGGTGA
* * * * *
52704721 CTTAAATCTTCTCCATTGTCGATACATGGGGATAAGATTCGTCATCCTT-GATCTGCTCCACAAC
1 CTTAAATCTGCTCCAATGTCGATACATGGAGATAAGATTTGCCAT-CTTCGATCTGCTCCACAAC
* *
52704785 TACTTAGGGAAATAGATCTTCAATCTTCAATCTTCAGTCTGCTTTCTTGCTGCCTCAGGAAGATA
65 TACTTAGAGAAATAGATCTTCAA---TC-ATCTTCAGTCTGCTTTCTTGCTGCCTCAGAAAGATA
* *
52704850 AGACTAAAATCGCTAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTGG
126 AGACTAAAATCGCTAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACTAGAGG
* * * *
52704904 CTAAAATCTGCTCC-AT-TACTG-TACATGGAGATAAGTTTTGCCATCTTCGATCTGCTCTACTA
1 CTTAAATCTGCTCCAATGT-C-GATACATGGAGATAAGATTTGCCATCTTCGATCTGCTCCACAA
*
52704966 CTACTTAGAGAGATAAGATCTTCAA-C-T-TTCAGTCTGCTTTCTTGCTAG-CTCAGAAAGATAA
64 CTACTTAGAGAAAT-AGATCTTCAATCATCTTCAGTCTGCTTTCTTGCT-GCCTCAGAAAGATAA
* * *
52705027 GACT-CAATC-TTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACTTGAGG
127 GACTAAAATCGCT-AACCTGCTCTCTTGCTACCTCAGAGAGATAAGACTAGAGG
*
52705079 CTTAAATCTGCTCCAATGTCGATACATAGAGATAAGATTTGCC-TCTTC
1 CTTAAATCTGCTCCAATGTCGATACATGGAGATAAGATTTGCCATCTTC
52705127 CAATATTCAA
Statistics
Matches: 194, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
174 1 0.01
175 60 0.31
176 57 0.29
177 3 0.02
179 1 0.01
181 4 0.02
182 45 0.23
183 23 0.12
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (179 bp):
CTTAAATCTGCTCCAATGTCGATACATGGAGATAAGATTTGCCATCTTCGATCTGCTCCACAACT
ACTTAGAGAAATAGATCTTCAATCATCTTCAGTCTGCTTTCTTGCTGCCTCAGAAAGATAAGACT
AAAATCGCTAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACTAGAGG
Found at i:52705233 original size:147 final size:147
Alignment explanation
Indices: 52705000--52705274 Score: 394
Period size: 147 Copynumber: 1.9 Consensus size: 147
52704990 ACTTTCAGTC
*
52705000 TGCTTTCTTGCTAGCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGA
1 TGCTTCCTTGCTAGCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGA
* * * *
52705065 GATAAGACTTGAGGCTTAAATCTGCTCCAATG-TCGATACATAGAGATAAGATTTGCC-TCTTCC
66 GAGAAGACTAGAGGCTAAAATCTGCTCCAATGCTCG-TACATAGAGATAAGATTCGCCATCTTCC
52705128 AATATTCAATCTTCAATT
130 AATATTCAATCTTCAATT
* *
52705146 TGCTTCCTTGCTA-CTTCAGGAAGATAAGACTACCATCTTCAACCTGCTCTCTTGCTACCTCAGA
1 TGCTTCCTTGCTAGC-TCAGAAAGATAAGACT-CAATCTTCAACCTGCTCTCTTGCTACCTCAGA
* * * * *
52705210 GAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTGTACATGGAGATAAGATTCGCCATCTTC
64 GAGAGAAGACTAGAGGCTAAAATCTGCTCCAATGCTCGTACATAGAGATAAGATTCGCCATCTTC
52705275 GATCTGCTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
145 1 0.01
146 27 0.24
147 78 0.69
148 7 0.06
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (147 bp):
TGCTTCCTTGCTAGCTCAGAAAGATAAGACTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGA
GAGAAGACTAGAGGCTAAAATCTGCTCCAATGCTCGTACATAGAGATAAGATTCGCCATCTTCCA
ATATTCAATCTTCAATT
Found at i:52705478 original size:175 final size:175
Alignment explanation
Indices: 52705132--52706027 Score: 836
Period size: 175 Copynumber: 5.1 Consensus size: 175
52705122 TCTTCCAATA
* * *
52705132 TTCAATCTTCAATTTGCTTCCTTGCTA-CTTCAGGAAGATAAGACTACCA-TCTTCAACCTGCTC
1 TTCAATCTTCAGTCTGCTTCCTTGCTACCTT-AGGAAGATAAGA--ATCATTCTTCAACCTGCTC
* * ***
52705195 TCTTGCTACCTCAGAGAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTGTACATGGAGATA
63 TCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGATA
*
52705260 AGATTCGCCATCTTCGATCTGCTT-CACTACTGCTTAGGGAGATAAGATC
128 AGATT-GACATCTTCGATCTG-TTCCACTACTGCTTAGGGAGATAAGATC
* * *
52705309 TTCAATCTCCAGTCTGCTTCCTTGATACCTTAGAAAGATAAGAATCATTCTTCAACCTGCTCTCT
1 TTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGAATCATTCTTCAACCTGCTCTCT
* * * * *
52705374 TGCTACCTCAGAGAGATAAGGCTGGTGG-TAAAATATACTTCATTGTCAATATATGGAGATAAGA
66 TGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGATAAGA
* * * * *
52705438 TTTATAGTCTTTGGTCTGTTCCACTACTGTTTAGGGAGATAAGA-C
131 TTGACA-TCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATC
* * * *
52705483 ATTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTTAACCTACTCTC
1 -TTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGAATCATTCTTCAACCTGCTCTC
* * * **
52705548 TTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCTATTTCTGATACATGGAGATAAG
65 TTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGATAAG
* *
52705613 ATTTACCAGCTTCGATCTG--CC-CTACTGCAACTTCAGGGAGATAAGATC
130 ATTGA-CATCTTCGATCTGTTCCACTACTG---CTT-AGGGAGATAAGATC
* * * * ***
52705661 TTCAATCTTCAATCTGCTTCCTTGCTA-CTTCGGGAAGATAAGACTACAATAGCCAACCTGCTCT
1 TTCAATCTTCAGTCTGCTTCCTTGCTACCTT-AGGAAGATAAGAAT-CATTCTTCAACCTGCTCT
* * *
52705725 CTTGCTACCAT-AGAGAGAT-AGG-TCAGTGGCTAAAATCTGCTCCA-TGCCGATACATGAAGAT
64 CTTGCTACC-TCAGAGAGATAAGGCT-GGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGAT
* * *
52705786 AAGATTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATC
127 AAGATT-GACATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATC
* * * * * * * * *
52705836 TTCAATCTTCAGTCTGC-TCCACTGCAACCTCA-AAGAGATAAGACTTGTATAC-TGAGCCTGCT
1 TTCAATCTTCAGTCTGCTTCC-TTGCTACCTTAGGA-AGATAAGA-AT-CATTCTTCAACCTGCT
* * * * * * * * *
52705898 C-CACTGCAACTTCAGGGAGATAAAGCTGGTGACTTAAATCTACTCCATTGCCAGTACATGGAGA
62 CTC-TTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGA
* * * * *
52705962 TAAGATTCGTCATCTTTGGTCTGTTCCACTACTGCTTAGGGAAATAAGACC
126 TAAGATT-GACATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATC
*
52706013 TGCAATCTTCAGTCT
1 TTCAATCTTCAGTCT
52706028 ACTCCACTGC
Statistics
Matches: 593, Mismatches: 97, Indels: 58
0.79 0.13 0.08
Matches are distributed among these distances:
173 6 0.01
174 12 0.02
175 212 0.36
176 143 0.24
177 178 0.30
178 35 0.06
179 7 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (175 bp):
TTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGAATCATTCTTCAACCTGCTCTCT
TGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCAATACATGGAGATAAGA
TTGACATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATC
Found at i:52705788 original size:352 final size:351
Alignment explanation
Indices: 52705131--52705853 Score: 885
Period size: 352 Copynumber: 2.1 Consensus size: 351
52705121 CTCTTCCAAT
* * * *
52705131 ATTCAATCTTCAATTTGCTTCCTTGCTACTTCAGGAAGATAAGACTACCATCTTCAACCTGCTCT
1 ATTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTA-CATCTTCAACCTACTCT
52705196 CTTGCTACCTCAGAGAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTGTACATGGAGATAA
65 CTTGCTACCTCAGAGAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTGTACATGGAGATAA
* * *
52705261 GATTCGCCATCTTCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTTCAATCTCCAGTCTGC
130 GATTCACCAGCTTCGATCTGC-TCACTACTGCTTAGGGAGATAAGATCTTCAATCTCCAATCTGC
* ***
52705326 TTCCTTGATACCTTAGAAAGATAAGAATCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGAT
194 TTCCTTGATACCTTAGAAAGATAAGAATCAATAGCCAACCTGCTCTCTTGCTACCTCAGAGAGAT
* * * * * * * * *
52705391 AAGGCTGGTGGTAAAATATACTTCATTGTCAATATATGGAGATAAGATT-TATAGTCTTTGGTCT
259 AAGGCTAGTGGTAAAATATACTCCATTGCCAATACATGAAGATAAGATTCGACA-TCTTCGATCT
* *
52705455 GTTCCACTACTGTTTAGGGAGATAAGA-C
323 GCTCCACTACTGCTTAGGGAGATAAGATC
*
52705483 ATTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT-CATTCTTTAACCTACTCT
1 ATTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACA-TCTTCAACCTACTCT
* * * * *
52705547 CTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCTATTTC-TGATACATGGAGATA
65 CTTGCTACCTCAGAGAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTG-TACATGGAGATA
* *
52705611 AGATTTACCAGCTTCGATCTGC-C-CTACTGCAACTTCAGGGAGATAAGATCTTCAATCTTCAAT
129 AGATTCACCAGCTTCGATCTGCTCACTACTG---CTT-AGGGAGATAAGATCTTCAATCTCCAAT
* * * *
52705674 CTGCTTCCTTGCTA-CTTCGGGAAGATAAGACTACAATAGCCAACCTGCTCTCTTGCTACCAT-A
190 CTGCTTCCTTGATACCTT-AGAAAGATAAGAAT-CAATAGCCAACCTGCTCTCTTGCTACC-TCA
* * * *
52705737 GAGAGAT-AGG-TCAGTGGCTAAAATCTGCTCCA-TGCCGATACATGAAGATAAGATTCGCCATC
252 GAGAGATAAGGCT-AGTGG-TAAAATATACTCCATTGCCAATACATGAAGATAAGATTCGACATC
*
52705799 TTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATC
315 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
52705836 -TTCAATCTTCAGTCTGCT
1 ATTCAATCTTCAGTCTGCT
52705854 CCACTGCAAC
Statistics
Matches: 319, Mismatches: 39, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
348 6 0.02
349 1 0.00
350 4 0.01
351 95 0.30
352 168 0.53
353 44 0.14
354 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (351 bp):
ATTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACATCTTCAACCTACTCTC
TTGCTACCTCAGAGAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTGTACATGGAGATAAG
ATTCACCAGCTTCGATCTGCTCACTACTGCTTAGGGAGATAAGATCTTCAATCTCCAATCTGCTT
CCTTGATACCTTAGAAAGATAAGAATCAATAGCCAACCTGCTCTCTTGCTACCTCAGAGAGATAA
GGCTAGTGGTAAAATATACTCCATTGCCAATACATGAAGATAAGATTCGACATCTTCGATCTGCT
CCACTACTGCTTAGGGAGATAAGATC
Found at i:52706021 original size:352 final size:351
Alignment explanation
Indices: 52705131--52706023 Score: 866
Period size: 352 Copynumber: 2.5 Consensus size: 351
52705121 CTCTTCCAAT
* * * * * * * *
52705131 ATTCAATCTTCAATTTGCTTCCTTGCTACTTCAGGAAGATAAGACTACCAT-CTTCAACCTGCTC
1 ATTCAATCTTCAGTCTGCTTCCCTGCAACCTCAAGAAGATAAGACT--CATACTTGAACCTACTC
* * * * * * * *
52705195 TCTTGCTACCTCAGAGAGAGAAGGCTAGTGGCTAAAATCTGCTCCATTGCTTGTACATGGAGATA
64 TCCTGCAACCTCAGAGAGATAAAGCTGGTGACTTAAATCTGCTCCATTGCCTGTACATGGAGATA
* *
52705260 AGATTCGCCATCTTCGATCTGCTT-CACTACTGCTTAGGGAGATAAGATCTTCAATCTCCAGTCT
129 AGATTCGCCATCTTCGATCTG-TTCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAATCT
* ***
52705324 GCTTCCTTGATACCTTAGAAAGATAAGAATCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAG
193 GCTTCCTTGATACCTTAGAAAGATAAGAATCAATAGCCAACCTGCTCTCTTGCTACCTCAGAGAG
* * * * * * * * *
52705389 ATAAGGCTGGTGGTAAAATATACTTCATTGTCAATATATGGAGATAAGATTTATAGTCTTTGGTC
258 ATAAGGCTAGTGGTAAAATATACTCCATTGCCAATACATGAAGATAAGATTGACAGTCTTCGATC
* *
52705454 TGTTCCACTACTGTTTAGGGAGATAAGAC
323 TGCTCCACTACTGCTTAGGGAGATAAGAC
* * * * *
52705483 ATTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTTAACCTACTCTC
1 ATTCAATCTTCAGTCTGCTTCCCTGCAACCTCAAGAAGATAAGACTCATACTTGAACCTACTCTC
* * * * * *
52705548 TTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCTATT-TCTGATACATGGAGATAA
66 CTGCAACCTCAGAGAGATAAAGCTGGTGACTTAAATCTGCTCCATTGCCTG-TACATGGAGATAA
** *
52705612 GATTTACCAGCTTCGATCTG--CC-CTACTGCAACTTCAGGGAGATAAGATCTTCAATCTTCAAT
130 GATTCGCCATCTTCGATCTGTTCCACTACTG---CTT-AGGGAGATAAGATCTTCAATCTTCAAT
* * * *
52705674 CTGCTTCCTTGCTA-CTTCGGGAAGATAAGACTACAATAGCCAACCTGCTCTCTTGCTACCAT-A
191 CTGCTTCCTTGATACCTT-AGAAAGATAAGAAT-CAATAGCCAACCTGCTCTCTTGCTACC-TCA
* * * *
52705737 GAGAGAT-AGG-TCAGTGGCTAAAATCTGCTCCA-TGCCGATACATGAAGATAAGATTCGCCA-T
253 GAGAGATAAGGCT-AGTGG-TAAAATATACTCCATTGCCAATACATGAAGATAAGATT-GACAGT
*
52705798 CTTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATC
315 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA-C
* * *
52705836 -TTCAATCTTCAGTCTGC-TCCACTGCAACCTCAA-AGAGATAAGACTTGTATAC-TGAGCCTGC
1 ATTCAATCTTCAGTCTGCTTCC-CTGCAACCTCAAGA-AGATAAGAC-T-CATACTTGAACCTAC
* * * *
52705897 TC-CACTGCAACTTCAGGGAGATAAAGCTGGTGACTTAAATCTACTCCATTGCCAGTACATGGAG
62 TCTC-CTGCAACCTCAGAGAGATAAAGCTGGTGACTTAAATCTGCTCCATTGCCTGTACATGGAG
* * * * * *
52705961 ATAAGATTCGTCATCTTTGGTCTGTTCCACTACTGCTTAGGGAAATAAGACCTGCAATCTTCA
126 ATAAGATTCGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCA
52706024 GTCTACTCCA
Statistics
Matches: 451, Mismatches: 67, Indels: 46
0.80 0.12 0.08
Matches are distributed among these distances:
348 6 0.01
349 1 0.00
350 5 0.01
351 96 0.21
352 208 0.46
353 121 0.27
354 6 0.01
355 2 0.00
356 6 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (351 bp):
ATTCAATCTTCAGTCTGCTTCCCTGCAACCTCAAGAAGATAAGACTCATACTTGAACCTACTCTC
CTGCAACCTCAGAGAGATAAAGCTGGTGACTTAAATCTGCTCCATTGCCTGTACATGGAGATAAG
ATTCGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAATCTGCT
TCCTTGATACCTTAGAAAGATAAGAATCAATAGCCAACCTGCTCTCTTGCTACCTCAGAGAGATA
AGGCTAGTGGTAAAATATACTCCATTGCCAATACATGAAGATAAGATTGACAGTCTTCGATCTGC
TCCACTACTGCTTAGGGAGATAAGAC
Found at i:52706344 original size:64 final size:63
Alignment explanation
Indices: 52706235--52706360 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 63
52706225 TCATGTATCT
52706235 TGCTTATGTCAAATAATTAGGTACTATGATCAAAATGAATCAAATGCACCTAACTAGATGTGA
1 TGCTTATGTCAAATAATTAGGTACTATGATCAAAATGAATCAAATGCACCTAACTAGATGTGA
* ** * *
52706298 TGCTTATGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTGGATGTG
1 TGCTTATGTCAAATAATTAGG-TACTATGATCAAAATGAATCAAATGCACCTAACTAGATGTG
52706361 TTATGAACGA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
63 21 0.37
64 36 0.63
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (63 bp):
TGCTTATGTCAAATAATTAGGTACTATGATCAAAATGAATCAAATGCACCTAACTAGATGTGA
Found at i:52707481 original size:9 final size:9
Alignment explanation
Indices: 52707469--52707498 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
52707459 CTTTCTTTTT
52707469 TTTTTTTGA
1 TTTTTTTGA
52707478 TTTTTTTGA
1 TTTTTTTGA
52707487 TTTTTTTGA
1 TTTTTTTGA
52707496 TTT
1 TTT
52707499 CCATTACGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:52708094 original size:23 final size:23
Alignment explanation
Indices: 52708037--52708094 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
52708027 TCACTATGAC
* * *
52708037 CTTTGTTCTTTTCTTTTCTTTTC
1 CTTTTTTCTTTTCTTTTCTTGTA
52708060 CTTTTCTT-TTTTCTATTT-TTGTA
1 CTTTT-TTCTTTTCT-TTTCTTGTA
52708083 CTTTTTTCTTTT
1 CTTTTTTCTTTT
52708095 TGTATGCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.07
23 22 0.76
24 5 0.17
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (23 bp):
CTTTTTTCTTTTCTTTTCTTGTA
Found at i:52714332 original size:47 final size:47
Alignment explanation
Indices: 52714278--52714507 Score: 336
Period size: 47 Copynumber: 4.9 Consensus size: 47
52714268 TTAGGATTTT
** * * *
52714278 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
52714325 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
52714372 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
52714419 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
52714466 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAAT
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAAT
52714508 TGCTAATGCG
Statistics
Matches: 170, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 167 0.98
48 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:52714425 original size:22 final size:22
Alignment explanation
Indices: 52714354--52714425 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
52714344 GCATATATGA
52714354 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
52714376 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
52714401 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
52714423 GAT
1 GAT
52714426 GAATGTGAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:52714472 original size:22 final size:22
Alignment explanation
Indices: 52714397--52714472 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
52714387 ACATGCATAT
*
52714397 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
52714419 ATGTGATGAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
52714443 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
52714466 ATGTGAT
1 ATGTGAT
52714473 GAACGTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:52714559 original size:46 final size:46
Alignment explanation
Indices: 52714489--52714625 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
52714479 GGAAGTGTAT
*
52714489 ATATGTGGTAAAGCCGAATTGCTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* *
52714535 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * * *
52714581 ATATGTGGTAATGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
52714626 TGTATATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.27
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:52716164 original size:40 final size:40
Alignment explanation
Indices: 52716114--52716348 Score: 389
Period size: 40 Copynumber: 5.9 Consensus size: 40
52716104 TTTTATATGG
52716114 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
*
52716154 TCCAGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
52716194 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
** *
52716234 TCTTGGCTAAGTCCCGAAGAGCATACGTGTTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
* * *
52716274 TCCGGGCTAAGTCTCGAAGAGCATTCGTACTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
* *
52716314 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTG
1 TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTG
52716349 ATGTGTATTC
Statistics
Matches: 181, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTATA
Found at i:52716562 original size:25 final size:25
Alignment explanation
Indices: 52716512--52716564 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
52716502 TGTGTAACAA
* *
52716512 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
52716537 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
52716562 CAA
1 CAA
52716565 GTTCTTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:52720391 original size:25 final size:25
Alignment explanation
Indices: 52720316--52720513 Score: 147
Period size: 25 Copynumber: 8.3 Consensus size: 25
52720306 CGAATGGCAA
52720316 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * * *
52720341 ATGAGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
52720363 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* *
52720388 ATGTGAT-AAGGCTG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
52720410 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
* * *
52720435 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-TGAACAT-GCATAT
*
52720457 ATGTGATGAATGTGAACATGCATAA
1 ATGTGATGAATGTGAACATGCATAT
52720482 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
52720507 ATGTGAT
1 ATGTGAT
52720514 AAGGCAGAAT
Statistics
Matches: 133, Mismatches: 19, Indels: 42
0.69 0.10 0.22
Matches are distributed among these distances:
22 24 0.18
23 27 0.20
24 27 0.20
25 55 0.41
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (25 bp):
ATGTGATGAATGTGAACATGCATAT
Found at i:52720416 original size:22 final size:22
Alignment explanation
Indices: 52720345--52720463 Score: 66
Period size: 22 Copynumber: 5.1 Consensus size: 22
52720335 GCATATATGA
*
52720345 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
* *
52720367 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCTG-A-ATGGC-CA-ATGT
52720392 GATAAGGCTGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
* *
52720414 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCTG-A-ATGGC-CA-ATGT
*
52720439 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
52720461 GAT
1 GAT
52720464 GAATGTGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
22 20 0.27
23 18 0.25
24 18 0.25
25 17 0.23
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
GATAAGGCTGAATGGCCAATGT
Found at i:52720486 original size:47 final size:47
Alignment explanation
Indices: 52720269--52720488 Score: 377
Period size: 47 Copynumber: 4.7 Consensus size: 47
52720259 TTAGGATTTT
* * * *
52720269 ATGTGATGAATGTGAATATGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
52720316 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
52720363 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
52720410 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
52720457 ATGTGATGAATGTGAACATGCATAAATGTGAT
1 ATGTGATGAATGTGAACATGCATATATGTGAT
52720489 GAATGTGAAC
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 166 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:52720497 original size:119 final size:119
Alignment explanation
Indices: 52720362--52720578 Score: 346
Period size: 119 Copynumber: 1.8 Consensus size: 119
52720352 CCGAATGGCC
* *
52720362 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCAATGTGATGAATGT-GAA
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGAA
* *
52720426 CATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATA
66 -ATGCATATATGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAACATGCATA
52720481 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGAA
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGAA
* * * *
52720546 GTGTATATATGTGGTAAAGCCAAATGGCTAATG
66 ATGCATATATGTGATAAAGCCAAATGGCCAATG
52720579 CGAAATGTGT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 86 0.97
120 3 0.03
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (119 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGAA
ATGCATATATGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAACATGCATA
Found at i:52720558 original size:72 final size:72
Alignment explanation
Indices: 52720409--52720542 Score: 250
Period size: 72 Copynumber: 1.9 Consensus size: 72
52720399 CTGAATGGCC
* *
52720409 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAAC
52720474 ATGCATA
66 ATGCATA
52720481 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTG
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTG
52720543 GAAGTGTATA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (72 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAAC
ATGCATA
Found at i:52720572 original size:47 final size:47
Alignment explanation
Indices: 52720481--52720578 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
52720471 AACATGCATA
* *
52720481 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCC
1 AATGTGATGAACGTGAACATGCATATATGTGATAAGCCAGAATGGCC
* * * *
52720528 AATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCA-AATGGCT
1 AATGTGATGAACGT-GAACATGCATATATGTGAT-AAGCCAGAATGGCC
52720575 AATG
1 AATG
52720579 CGAAATGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
47 35 0.81
48 8 0.19
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.27
Consensus pattern (47 bp):
AATGTGATGAACGTGAACATGCATATATGTGATAAGCCAGAATGGCC
Found at i:52720608 original size:46 final size:46
Alignment explanation
Indices: 52720552--52720688 Score: 211
Period size: 46 Copynumber: 3.0 Consensus size: 46
52720542 GGAAGTGTAT
52720552 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
* * *
52720598 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
52720644 ATATGTGGTAAAGCCAAATGGATAATGTGAGATTTGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATG
52720689 TGTATATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:52721943 original size:38 final size:34
Alignment explanation
Indices: 52721885--52721967 Score: 85
Period size: 37 Copynumber: 2.3 Consensus size: 34
52721875 ACAATTGATT
* *
52721885 TAATAATACATAAAAAATGAATAAATAATATACAA
1 TAATAATATATAAAAAATGAA-AAATAAAATACAA
*
52721920 TAATAATATATAAAATAATATGAAAAGTAAAATACAA
1 TAATAATATAT-AAA-AA-ATGAAAAATAAAATACAA
*
52721957 CACATAATATA
1 TA-ATAATATA
52721968 CAAAGCAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 10 0.25
36 3 0.08
37 14 0.35
38 13 0.32
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.27
Consensus pattern (34 bp):
TAATAATATATAAAAAATGAAAAATAAAATACAA
Found at i:52726028 original size:46 final size:46
Alignment explanation
Indices: 52725975--52726111 Score: 220
Period size: 46 Copynumber: 3.0 Consensus size: 46
52725965 TATATATACA
* * * *
52725975 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
52726021 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
52726067 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
52726112 ATACACTTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:52726155 original size:22 final size:22
Alignment explanation
Indices: 52726129--52726203 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
52726119 TCCACGTTCG
52726129 TCACATTGGCCATTCTGCCTTA
1 TCACATTGGCCATTCTGCCTTA
*
52726151 TCACATATATG-CATGT-T-CACATTCA
1 TCACAT-T-GGCCAT-TCTGC-C-TT-A
*
52726176 TCACATTGGCCATTCGGCCTTA
1 TCACATTGGCCATTCTGCCTTA
52726198 TCACAT
1 TCACAT
52726204 ATATGCATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 18
0.66 0.05 0.29
Matches are distributed among these distances:
22 14 0.34
23 10 0.24
24 9 0.22
25 8 0.20
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (22 bp):
TCACATTGGCCATTCTGCCTTA
Found at i:52726156 original size:47 final size:47
Alignment explanation
Indices: 52726085--52726463 Score: 589
Period size: 47 Copynumber: 8.1 Consensus size: 47
52726075 ACACATTTCG
* * * * * * *
52726085 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCGTCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
*
52726132 CATTGGCCATTCTGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
52726179 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52726226 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52726273 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52726320 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
52726367 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * * **
52726414 CATTTGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
52726461 CAT
1 CAT
52726464 AAAATCCTAA
Statistics
Matches: 315, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
46 1 0.00
47 314 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:52726273 original size:25 final size:25
Alignment explanation
Indices: 52726244--52726368 Score: 76
Period size: 23 Copynumber: 5.2 Consensus size: 25
52726234 ATTCGGCCTT
52726244 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
52726269 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
52726291 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
52726316 AT--CACAT-TGGCCA--TTCGGCCTT-
1 ATCACACATAT-G-CATGTTC-ACATTC
52726338 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
52726363 ATCACA
1 ATCACA
52726369 TTGGCCATTC
Statistics
Matches: 74, Mismatches: 8, Indels: 36
0.63 0.07 0.31
Matches are distributed among these distances:
22 12 0.16
23 22 0.30
24 22 0.30
25 18 0.24
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (25 bp):
ATCACACATATGCATGTTCACATTC
Found at i:52729325 original size:39 final size:39
Alignment explanation
Indices: 52729269--52729412 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
52729259 CCAACATAAT
*
52729269 TGCCTTCGGGATTTAGCCCGGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
* *
52729308 TGCCTTCGGGACATAGCCCGGATATAACACCAGCGCGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
* *
52729347 TGCCTTCGGAACTTAGCCCGGATATAACACCAGTACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
52729386 TGCCTTCGGGACTTAGCCCGGATATAA
1 TGCCTTCGGGACTTAGCCCGGATATAA
52729413 ATCTCACACA
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (39 bp):
TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
Found at i:52732730 original size:34 final size:34
Alignment explanation
Indices: 52732687--52732753 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
52732677 AGATCGTTGT
52732687 ACATTTTCGTACTACCCGGGTGAACTGACATTCG
1 ACATTTTCGTACTACCCGGGTGAACTGACATTCG
52732721 ACATTTTCGTACTACCCGGGTGAACTGACATTC
1 ACATTTTCGTACTACCCGGGTGAACTGACATTC
52732754 AGCTACTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (34 bp):
ACATTTTCGTACTACCCGGGTGAACTGACATTCG
Found at i:52737332 original size:39 final size:39
Alignment explanation
Indices: 52737277--52737459 Score: 321
Period size: 39 Copynumber: 4.7 Consensus size: 39
52737267 CCAACATAAT
*
52737277 TGCCTTCGGGACTTAGCCTGGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
*
52737316 TGCCTTCGGGATTTAGCCCGGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
* *
52737355 TGCCTTCGGGACATAGCCCGGATATAACACCAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
*
52737394 TGCCTTCGGAACTTAGCCCGGATATAACACCAGCACGAA
1 TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
52737433 TGCCTTCGGGACTTAGCCCGGATATAA
1 TGCCTTCGGGACTTAGCCCGGATATAA
52737460 ATCTCACACA
Statistics
Matches: 135, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 135 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (39 bp):
TGCCTTCGGGACTTAGCCCGGATATAACACCAGCACGAA
Found at i:52746618 original size:24 final size:24
Alignment explanation
Indices: 52746591--52746643 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
52746581 TTTAATGAAT
* * * *
52746591 TAGTTTGCACATACTTGATAAAGC
1 TAGTTCGCACATACATGACAAAAC
*
52746615 TAGTTCGCATATACATGACAAAAC
1 TAGTTCGCACATACATGACAAAAC
52746639 TAGTT
1 TAGTT
52746644 AGCGCATGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (24 bp):
TAGTTCGCACATACATGACAAAAC
Found at i:52750181 original size:41 final size:42
Alignment explanation
Indices: 52750135--52750216 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
52750125 TTGGTACCTG
52750135 AACTTAACAC-TTTTTCTTAATTTGGAACTTAAACTTGACAA
1 AACTTAACACTTTTTTCTTAATTTGGAACTTAAACTTGACAA
* *
52750176 AACTTAACACTTTTTTCTTATTTTGGTACTTAAACTTGACA
1 AACTTAACACTTTTTTCTTAATTTGGAACTTAAACTTGACA
52750217 CTTTTTCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 10 0.26
42 28 0.74
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (42 bp):
AACTTAACACTTTTTTCTTAATTTGGAACTTAAACTTGACAA
Found at i:52750233 original size:31 final size:32
Alignment explanation
Indices: 52750175--52750243 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
52750165 AAACTTGACA
* **
52750175 AAACTTAACACTTTTTTCTTATTTTGGTACTT
1 AAACTTAACACTTTTTTCATAAGTTGGTACTT
*
52750207 AAACTTGACAC-TTTTTCATAAGTTGGTACTT
1 AAACTTAACACTTTTTTCATAAGTTGGTACTT
52750238 AAACTT
1 AAACTT
52750244 TTTGGGGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (32 bp):
AAACTTAACACTTTTTTCATAAGTTGGTACTT
Found at i:52751701 original size:21 final size:22
Alignment explanation
Indices: 52751668--52751709 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
52751658 AAAAATGAAT
*
52751668 TTTTTCGTGTAAAAACTCAAGC
1 TTTTTCGTATAAAAACTCAAGC
*
52751690 TTTTTC-TATAAAATCTCAAG
1 TTTTTCGTATAAAAACTCAAG
52751710 TAACTCCCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTTTCGTATAAAAACTCAAGC
Found at i:52754895 original size:21 final size:22
Alignment explanation
Indices: 52754871--52754911 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52754861 TAAATCTCTG
* *
52754871 GGGTTTAAGG-TCTAGATTTTA
1 GGGTTCAAGGTTCAAGATTTTA
52754892 GGGTTCAAGGTTCAAGATTT
1 GGGTTCAAGGTTCAAGATTT
52754912 AAGGTCGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.39
Consensus pattern (22 bp):
GGGTTCAAGGTTCAAGATTTTA
Found at i:52754912 original size:21 final size:21
Alignment explanation
Indices: 52754871--52754942 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 21
52754861 TAAATCTCTG
* *
52754871 GGGTTTAAGG-TCTAGATTTTA
1 GGGTTCAAGGTTCAAGA-TTTA
52754892 GGGTTCAAGGTTCAAGATTTA
1 GGGTTCAAGGTTCAAGATTTA
* *
52754913 AGG-TCGAGAGTTCAATG-TTTA
1 GGGTTCAAG-GTTCAA-GATTTA
*
52754934 GGGTCCAAG
1 GGGTTCAAG
52754943 ATTTAAGGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.10
21 27 0.68
22 9 0.22
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.33
Consensus pattern (21 bp):
GGGTTCAAGGTTCAAGATTTA
Found at i:52754975 original size:21 final size:22
Alignment explanation
Indices: 52754919--52754975 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
52754909 TTTAAGGTCG
*
52754919 AGAGTTCAATGTTT-AGGGTCCA
1 AGAGTT-AAGGTTTAAGGGTCCA
*
52754941 AGATTTAAGG-TTAAGGGTCCA
1 AGAGTTAAGGTTTAAGGGTCCA
*
52754962 A-AGTTGAGGTTTAA
1 AGAGTTAAGGTTTAA
52754976 AAAAATTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 8 0.28
21 16 0.55
22 5 0.17
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGTTAAGGTTTAAGGGTCCA
Found at i:52759418 original size:19 final size:21
Alignment explanation
Indices: 52759380--52759423 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
52759370 TAAAATATAA
* *
52759380 ATTTTGAATTTTTTATAAA-T
1 ATTTTAAATTTTTGATAAATT
52759400 ATTTTAAATTTTTGA-AAATT
1 ATTTTAAATTTTTGATAAATT
52759420 ATTT
1 ATTT
52759424 CGATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTAAATTTTTGATAAATT
Found at i:52769907 original size:37 final size:37
Alignment explanation
Indices: 52769866--52769938 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
52769856 AAAACGGTAA
52769866 GATTTACTC-AGTTAAGCTCCATTCAGTATAATAGTAT
1 GATTTACTCGA-TTAAGCTCCATTCAGTATAATAGTAT
* * **
52769903 GATTTGCTCGATTGAGCTTTATTCAGTATAATAGTA
1 GATTTACTCGATTAAGCTCCATTCAGTATAATAGTA
52769939 AGAGTTGGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (37 bp):
GATTTACTCGATTAAGCTCCATTCAGTATAATAGTAT
Found at i:52772823 original size:30 final size:30
Alignment explanation
Indices: 52772789--52772851 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
52772779 ACTTAACAAG
*
52772789 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
52772819 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
52772849 CAA
1 CAA
52772852 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:52774818 original size:24 final size:25
Alignment explanation
Indices: 52774786--52774834 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
52774776 ATGTATGAAA
*
52774786 TGAATGATTTT-TTGAATAATTTAG
1 TGAATGATTTTAGTGAATAATTTAG
52774810 TGAATGATTTTAAGTGAATAATTTA
1 TGAATGATTTT-AGTGAATAATTTA
52774835 AAGTAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TGAATGATTTTAGTGAATAATTTAG
Found at i:52774827 original size:14 final size:14
Alignment explanation
Indices: 52774798--52774838 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
52774788 AATGATTTTT
52774798 TGAATAATTT--AG
1 TGAATAATTTAAAG
* *
52774810 TGAATGATTTTAAG
1 TGAATAATTTAAAG
52774824 TGAATAATTTAAAG
1 TGAATAATTTAAAG
52774838 T
1 T
52774839 AAGAAAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.38
14 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (14 bp):
TGAATAATTTAAAG
Found at i:52776029 original size:21 final size:21
Alignment explanation
Indices: 52776004--52776071 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
52775994 ACAATATATC
52776004 GATACATGC-AAGAAATGTATT
1 GATACAT-CTAAGAAATGTATT
* ***
52776025 GATACCTCTAAGGTGTGTATT
1 GATACATCTAAGAAATGTATT
*
52776046 GATACATCTAAGAAATGTATC
1 GATACATCTAAGAAATGTATT
52776067 GATAC
1 GATAC
52776072 CTTACCCACA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
GATACATCTAAGAAATGTATT
Found at i:52778697 original size:28 final size:28
Alignment explanation
Indices: 52778657--52778713 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
52778647 TTCACTCATA
*
52778657 GGAATGAAGTTACCTGTTGGAATTAGTC
1 GGAATAAAGTTACCTGTTGGAATTAGTC
52778685 GGAATAAAGTTACCTGTTGGAATTAGTC
1 GGAATAAAGTTACCTGTTGGAATTAGTC
52778713 G
1 G
52778714 CTACAAGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (28 bp):
GGAATAAAGTTACCTGTTGGAATTAGTC
Found at i:52781130 original size:69 final size:69
Alignment explanation
Indices: 52781019--52781157 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
52781009 TTGTCTGGAA
* *
52781019 AGGATAAAACATGAAAGTTGTTTATATTGGCACTCATGAGCCTCTCCCCATTGGGTATATTCTAA
1 AGGATAAAACATGAAAGCTGTTTATATTGGCACTCATGAGCCTCTCACCATTGGGTATATTCTAA
52781084 TATC
66 TATC
*
52781088 AGGATAAAACATGAAAGCTGTTTGTATTGGCACTCATGAGCCTCTCACCATTGGGTATATTCTAA
1 AGGATAAAACATGAAAGCTGTTTATATTGGCACTCATGAGCCTCTCACCATTGGGTATATTCTAA
52781153 TATC
66 TATC
52781157 A
1 A
52781158 CCTAGCAGAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (69 bp):
AGGATAAAACATGAAAGCTGTTTATATTGGCACTCATGAGCCTCTCACCATTGGGTATATTCTAA
TATC
Found at i:52794168 original size:25 final size:25
Alignment explanation
Indices: 52794136--52794188 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
52794126 ATCTATAAAG
*
52794136 AACTCCACTTCTTTATCCGATAGTA
1 AACTCCACTTCTCTATCCGATAGTA
* *
52794161 AACTCCACTTCTCTATCCGGTGGTA
1 AACTCCACTTCTCTATCCGATAGTA
52794186 AAC
1 AAC
52794189 CAGGTAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.32
Consensus pattern (25 bp):
AACTCCACTTCTCTATCCGATAGTA
Found at i:52799097 original size:30 final size:31
Alignment explanation
Indices: 52799040--52799097 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
52799030 TTGGGATGGA
* *
52799040 AAGGAAGTAAAAGTTTTGGGGGGAAAGTGGG
1 AAGGAAGTAAAAGTTTTGAGGGAAAAGTGGG
*
52799071 AAGG-AGTAAAAGTTTTTAGGGAAAAGT
1 AAGGAAGTAAAAGTTTTGAGGGAAAAGT
52799098 AAAAAGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
AAGGAAGTAAAAGTTTTGAGGGAAAAGTGGG
Found at i:52800348 original size:17 final size:17
Alignment explanation
Indices: 52800322--52800355 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52800312 TTTGCACTTT
*
52800322 CCATTTATGAATCTAAA
1 CCATTCATGAATCTAAA
52800339 CCATTCATGAATCTAAA
1 CCATTCATGAATCTAAA
52800356 GAATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (17 bp):
CCATTCATGAATCTAAA
Found at i:52810489 original size:23 final size:22
Alignment explanation
Indices: 52810462--52810526 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
52810452 AACAAAATTT
*
52810462 TAATATTTTATATTTATCTCAAA
1 TAATATTTTATATTTAT-TAAAA
*
52810485 TAATATATTATATTT-TTAAAA
1 TAATATTTTATATTTATTAAAA
52810506 TAA-ATTTT-TATTTATTTAAAA
1 TAATATTTTATATTTA-TTAAAA
52810527 ATAAGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 13 0.35
22 1 0.03
23 14 0.38
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTTTATATTTATTAAAA
Found at i:52812086 original size:20 final size:20
Alignment explanation
Indices: 52812063--52812101 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52812053 AAACTTTCTT
* *
52812063 GTTTTAAGTAGTTATTTCAA
1 GTTTTAAATAATTATTTCAA
52812083 GTTTTAAATAATTATTTCA
1 GTTTTAAATAATTATTTCA
52812102 TATATCACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (20 bp):
GTTTTAAATAATTATTTCAA
Found at i:52816182 original size:13 final size:13
Alignment explanation
Indices: 52816164--52816206 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
52816154 AATTTTAAAT
52816164 TATTTAGTGATAA
1 TATTTAGTGATAA
*
52816177 TATTTA--GA-AT
1 TATTTAGTGATAA
52816187 TATTTAGTGATAA
1 TATTTAGTGATAA
52816200 TATTTAG
1 TATTTAG
52816207 AAAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:52816187 original size:23 final size:23
Alignment explanation
Indices: 52816157--52816208 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
52816147 TAGTTTAAAT
52816157 TTTA-AATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
52816179 TTTAGAATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
52816202 TTTAGAA
1 TTTAGAA
52816209 AAAATCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (23 bp):
TTTAGAATTATTTAGTGATAATA
Found at i:52817179 original size:5 final size:6
Alignment explanation
Indices: 52817161--52817185 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52817151 TTTAAACCCC
52817161 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
52817186 CAGCATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:52819484 original size:24 final size:24
Alignment explanation
Indices: 52819457--52819505 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
52819447 ATGTACAAAG
*
52819457 ATTGATGTTCGTAGTGGAACCCTC
1 ATTGATGTTCGTAGTAGAACCCTC
52819481 ATTGATGTTCGTAGTAGAACCCTC
1 ATTGATGTTCGTAGTAGAACCCTC
52819505 A
1 A
52819506 CTATGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
ATTGATGTTCGTAGTAGAACCCTC
Found at i:52822891 original size:13 final size:13
Alignment explanation
Indices: 52822873--52822927 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
52822863 AATTTTGAAT
52822873 TATTTAGTGATAA
1 TATTTAGTGATAA
*
52822886 TATTTAGTAATAA
1 TATTTAGTGATAA
52822899 TATTTAG-GAT--
1 TATTTAGTGATAA
* *
52822909 TATTTAATTATAA
1 TATTTAGTGATAA
52822922 TATTTA
1 TATTTA
52822928 AAAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 25 0.71
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:52824983 original size:30 final size:30
Alignment explanation
Indices: 52824911--52824995 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
52824901 GGATGTGGAG
* * * * * *
52824911 CTTCTACAGGCGACAGTGCAGGTGATGGCA
1 CTTCTACGGGTGACGGTGCCGGTGACGACA
*
52824941 CTTCTACGGGTGACGGTGCTGGTGACGACA
1 CTTCTACGGGTGACGGTGCCGGTGACGACA
*
52824971 CTTCTA-GTGGTGATGGTGCCGGTGA
1 CTTCTACG-GGTGACGGTGCCGGTGA
52824996 TTTGATTCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 1 0.02
30 45 0.98
ACGTcount: A:0.18, C:0.21, G:0.36, T:0.25
Consensus pattern (30 bp):
CTTCTACGGGTGACGGTGCCGGTGACGACA
Found at i:52827553 original size:30 final size:30
Alignment explanation
Indices: 52827517--52827601 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
52827507 GGATGTGGAG
* *
52827517 CTTCTACAGGCGATGGTGCAGGTGAGGGCA
1 CTTCTACAGGTGATGGTGCAGGTGAGGACA
* * *
52827547 CTTCTACAGGTGACGGTGCTGGTGATGACA
1 CTTCTACAGGTGATGGTGCAGGTGAGGACA
** *
52827577 CTTGGACAGGTGATGGTGCCGGTGA
1 CTTCTACAGGTGATGGTGCAGGTGA
52827602 TGGAGATGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.24
Consensus pattern (30 bp):
CTTCTACAGGTGATGGTGCAGGTGAGGACA
Found at i:52829696 original size:10 final size:11
Alignment explanation
Indices: 52829677--52829701 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52829667 GATAAATACG
52829677 AAAACAAAAAA
1 AAAACAAAAAA
52829688 AAAACAAAAAA
1 AAAACAAAAAA
52829699 AAA
1 AAA
52829702 GAACATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:52829964 original size:20 final size:21
Alignment explanation
Indices: 52829936--52829975 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
52829926 CTCTTTTCTC
52829936 TTTTCTCTTTT-TGTTTTTTTG
1 TTTTCTCTTTTCT-TTTTTTTG
52829957 TTTT-TCTTTTCTTTTTTTT
1 TTTTCTCTTTTCTTTTTTTT
52829976 AAATACAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (21 bp):
TTTTCTCTTTTCTTTTTTTTG
Found at i:52830568 original size:7 final size:7
Alignment explanation
Indices: 52830548--52830581 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
52830538 TTTATTGCGT
52830548 TTTATTA
1 TTTATTA
52830555 GTTTATTA
1 -TTTATTA
52830563 TTTATTA
1 TTTATTA
*
52830570 TTTATAA
1 TTTATTA
52830577 TTTAT
1 TTTAT
52830582 ACCCCTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (7 bp):
TTTATTA
Found at i:52830686 original size:19 final size:19
Alignment explanation
Indices: 52830664--52830713 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
52830654 TACAAACTAT
*
52830664 TTTATTATTTATTTATTTA
1 TTTATTACTTATTTATTTA
*
52830683 TTTATTACTTCTTTATTT-
1 TTTATTACTTATTTATTTA
52830701 TTATATATACTTA
1 TT-TAT-TACTTA
52830714 AAAATTAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 2 0.08
19 19 0.73
20 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTACTTATTTATTTA
Found at i:52830775 original size:26 final size:27
Alignment explanation
Indices: 52830741--52830792 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
52830731 ATTCTTTTGT
*
52830741 TTGTGCATTTTTA-TTTATTTATTATTA
1 TTGTGCATTATTATTTTATTT-TTATTA
52830768 TTGT-CATTATTATTTTATTTTTATT
1 TTGTGCATTATTATTTTATTTTTATT
52830793 CTTTTGTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (27 bp):
TTGTGCATTATTATTTTATTTTTATTA
Found at i:52830787 original size:31 final size:29
Alignment explanation
Indices: 52830749--52830826 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 29
52830739 GTTTGTGCAT
52830749 TTTTATTTATTTATTATTATTG-TCATTATTA
1 TTTTA-TTATTTATT-TTATTGTTC-TTATTA
*
52830780 TTTTATT-TTTATTCTT-TTGTTCTTGTTA
1 TTTTATTATTTATT-TTATTGTTCTTATTA
*
52830808 TTTTATTATTTCTTTTATT
1 TTTTATTATTTATTTTATT
52830827 ATTTTTGGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 17 0.41
29 17 0.41
30 2 0.05
31 5 0.12
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (29 bp):
TTTTATTATTTATTTTATTGTTCTTATTA
Found at i:52834536 original size:19 final size:20
Alignment explanation
Indices: 52834500--52834539 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
52834490 CAATGTCGTA
*
52834500 TATGTAAAATATATTTGTTT
1 TATGTAAAATAGATTTGTTT
52834520 TATGTAAAA-AGATTTGTTT
1 TATGTAAAATAGATTTGTTT
52834539 T
1 T
52834540 GTAGTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (20 bp):
TATGTAAAATAGATTTGTTT
Found at i:52835910 original size:28 final size:29
Alignment explanation
Indices: 52835865--52835920 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
52835855 TAACCAGCCA
* * *
52835865 TCAAGGCCCATCAAGGAAAGAA-TCTAAC
1 TCAAGGCCAAACAAGGAAAAAACTCTAAC
*
52835893 TCAAGGCCAAACATGGAAAAAACTCTAA
1 TCAAGGCCAAACAAGGAAAAAACTCTAA
52835921 TTCACACTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.14
Consensus pattern (29 bp):
TCAAGGCCAAACAAGGAAAAAACTCTAAC
Found at i:52842753 original size:44 final size:44
Alignment explanation
Indices: 52842705--52842867 Score: 157
Period size: 44 Copynumber: 3.7 Consensus size: 44
52842695 AATCTTCCTA
* * * * *
52842705 AAGTTGCAGTAGAGTAAATTGAAGCCACAAGTCTTATCTCTCTG
1 AAGTTACAGTAGAGCAAATTGAAGCTACAAGTCTTTTTTCTCTG
* * *
52842749 AAGTTACAGTAGAGCAGATTGAGGCTACAAGT-TTTTTTCCCTG
1 AAGTTACAGTAGAGCAAATTGAAGCTACAAGTCTTTTTTCTCTG
** * * * *
52842792 AAGTTGTAGTGGAACAAATTGAAGTTACAAATCTTTTTTCTCTG
1 AAGTTACAGTAGAGCAAATTGAAGCTACAAGTCTTTTTTCTCTG
* * * *
52842836 AAGTTACAGTGGAACAGATTAAAGCTACAAGT
1 AAGTTACAGTAGAGCAAATTGAAGCTACAAGT
52842868 GACAAATCTT
Statistics
Matches: 95, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
43 32 0.34
44 63 0.66
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (44 bp):
AAGTTACAGTAGAGCAAATTGAAGCTACAAGTCTTTTTTCTCTG
Found at i:52842897 original size:51 final size:51
Alignment explanation
Indices: 52842813--52842918 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
52842803 GAACAAATTG
* * * * *
52842813 AAGTTACAAATCTTTTTTCTCTGAAGTTACAGTGGAACAGATTA-AAGCTAC
1 AAGTGACAAATCTTATCTCCCTAAAGTTACAGTGGAACAGA-TACAAGCTAC
* * *
52842864 AAGTGACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATACAAGTTAC
1 AAGTGACAAATCTTATCTCCCTAAAGTTACAGTGGAACAGATACAAGCTAC
52842915 AAGT
1 AAGT
52842919 CTTATCTCCC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.04
51 44 0.96
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (51 bp):
AAGTGACAAATCTTATCTCCCTAAAGTTACAGTGGAACAGATACAAGCTAC
Found at i:52842924 original size:44 final size:44
Alignment explanation
Indices: 52842861--52842949 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
52842851 AGATTAAAGC
* *
52842861 TACAAGTGACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
1 TACAAGTGACAAATCTTATCTCCCTAAAGTTACAGTAGAGCAGA
* * * *
52842905 TACAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTAGAGTAGA
1 TACAAGTGACAAATCTTATCTCCCTAAAGTTACAGTAGAGCAGA
52842949 T
1 T
52842950 TGAAACTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
TACAAGTGACAAATCTTATCTCCCTAAAGTTACAGTAGAGCAGA
Found at i:52842994 original size:42 final size:42
Alignment explanation
Indices: 52842931--52843034 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
52842921 TATCTCCCTG
52842931 AAGTTACAGTAGAGTAGATTGAAACTAAATCCTATACCTCTA
1 AAGTTACAGTAGAGTAGATTGAAACTAAATCCTATACCTCTA
* * *
52842973 AAGTTTCAGTAGAGTATATTGAAACTAAATCTTATACCTCTA
1 AAGTTACAGTAGAGTAGATTGAAACTAAATCCTATACCTCTA
*
52843015 AAGTTGCAGTAG-GTCAGATT
1 AAGTTACAGTAGAGT-AGATT
52843035 AAATCTACCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 2 0.04
42 54 0.96
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (42 bp):
AAGTTACAGTAGAGTAGATTGAAACTAAATCCTATACCTCTA
Found at i:52843128 original size:44 final size:43
Alignment explanation
Indices: 52843055--52843161 Score: 101
Period size: 44 Copynumber: 2.4 Consensus size: 43
52843045 TGGCGAATCT
* ** * *
52843055 TATCTCCCTGAAGTGGCAGTGGAGCAGATT-AAAGCTTCGACTTTC
1 TATCT-CCTGAAGTTGCAGCAGAGCAGATTGAAA-CTAC-ACTTCC
*
52843100 -ATCTCCTTGAAGTTGCAGCAGAGTAGATTGAAACTACACTTCC
1 TATCTCC-TGAAGTTGCAGCAGAGCAGATTGAAACTACACTTCC
52843143 TATACTCCTGAAGTTGCAG
1 TAT-CTCCTGAAGTTGCAG
52843162 TGGGTTAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
43 7 0.13
44 38 0.73
45 7 0.13
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (43 bp):
TATCTCCTGAAGTTGCAGCAGAGCAGATTGAAACTACACTTCC
Found at i:52844847 original size:11 final size:11
Alignment explanation
Indices: 52844831--52844889 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
52844821 ATTATTGTCA
52844831 TTATTATTTTT
1 TTATTATTTTT
52844842 TTATTATTCTTT
1 TTATTATT-TTT
*
52844854 TT-TTCTTGTTATT
1 TTATT-AT-TT-TT
52844867 TTATTATTTCTT
1 TTATTATTT-TT
52844879 TTATTATTTTT
1 TTATTATTTTT
52844890 GGCACTTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 12 0.30
12 20 0.50
13 6 0.15
14 2 0.05
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (11 bp):
TTATTATTTTT
Found at i:52844854 original size:14 final size:14
Alignment explanation
Indices: 52844811--52844874 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
52844801 TGCGTTTCTA
52844811 TTTATTTATTATTATT
1 TTTA-TTATTATT-TT
* *
52844827 GTCATTATTATTTT
1 TTTATTATTATTTT
*
52844841 TTTATTATTCTTTT
1 TTTATTATTATTTT
* *
52844855 TTTCTTGTTATTTT
1 TTTATTATTATTTT
*
52844869 ATTATT
1 TTTATT
52844875 TCTTTTATTA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 28 0.74
15 8 0.21
16 2 0.05
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATTATTATTTT
Found at i:52846791 original size:43 final size:43
Alignment explanation
Indices: 52846721--52846827 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 43
52846711 TGTGATTTTG
* * * ** * * *
52846721 TGTAAGACCATGTCTAGGACACTGGCATCGGTATGAGATTACG
1 TGTAAGACCATATCTGGGATAGAGGCATCGATATGAGATAACA
* * *
52846764 TGTAAGACCCTATCTGGGATAGAGGCATCGATTTGTGATAACA
1 TGTAAGACCATATCTGGGATAGAGGCATCGATATGAGATAACA
*
52846807 TGTAAGACTATATCTGGGATA
1 TGTAAGACCATATCTGGGATA
52846828 TGGCATTGTA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGATAGAGGCATCGATATGAGATAACA
Found at i:52849453 original size:40 final size:41
Alignment explanation
Indices: 52849403--52849520 Score: 134
Period size: 40 Copynumber: 2.9 Consensus size: 41
52849393 TTAGCGGTGA
52849403 TTTTAGAAAAACGTCGCTATAGATCGACCATTAGTGGCG-TT
1 TTTTA-AAAAACGTCGCTATAGATCGACCATTAGTGGCGCTT
* * * **
52849444 TTTTAAAAAACGCCGCTATGGGTCGACCATTAGCAGCGCTT
1 TTTTAAAAAACGTCGCTATAGATCGACCATTAGTGGCGCTT
* *
52849485 TCTT-AAAAACGTAGCTATA-AGTCGACCATTAGTGGC
1 TTTTAAAAAACGTCGCTATAGA-TCGACCATTAGTGGC
52849521 ACATTTTGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
40 53 0.84
41 10 0.16
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
TTTTAAAAAACGTCGCTATAGATCGACCATTAGTGGCGCTT
Found at i:52849533 original size:40 final size:39
Alignment explanation
Indices: 52849402--52849534 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 39
52849392 ATTAGCGGTG
*
52849402 ATTTTAGAAAAACGTCGCTATAGATCGACCATTAGTGGCGT
1 ATTTT-GAAAAACGTCGCTATAG-TCGACCATTAGTGGCGC
* * * * **
52849443 TTTTTAAAAAACGCCGCTATGGGTCGACCATTAGCAGCGC
1 ATTTTGAAAAACGTCGCTAT-AGTCGACCATTAGTGGCGC
* * *
52849483 -TTTCTTAAAAACGTAGCTATAAGTCGACCATTAGTGGCAC
1 ATTT-TGAAAAACGTCGCTAT-AGTCGACCATTAGTGGCGC
52849523 ATTTTGAAAAAC
1 ATTTTGAAAAAC
52849535 ACCGCAAAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
39 3 0.04
40 62 0.85
41 8 0.11
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (39 bp):
ATTTTGAAAAACGTCGCTATAGTCGACCATTAGTGGCGC
Found at i:52849862 original size:14 final size:14
Alignment explanation
Indices: 52849840--52850040 Score: 81
Period size: 14 Copynumber: 14.4 Consensus size: 14
52849830 TCAATTATCA
*
52849840 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
52849854 TTATGGTTTAGGGT
1 TTATGGTTTAGGGT
* *
52849868 ATATGATTTAGGGT
1 TTATGGTTTAGGGT
* *
52849882 TTAAGCTTTAGGAGT
1 TTATGGTTTAGG-GT
*
52849897 TACTAT--TTTAAGGT
1 T--TATGGTTTAGGGT
*
52849911 TTATGGATTATGGGT
1 TTATGGTTTA-GGGT
* * *
52849926 TTAGGGATTATGGT
1 TTATGGTTTAGGGT
* *
52849940 TTATGATTTAAGG-
1 TTATGGTTTAGGGT
***
52849953 TT-TGG-CCGGGGT
1 TTATGGTTTAGGGT
* *
52849965 TTAAGGTTTAGGGG
1 TTATGGTTTAGGGT
* * *
52849979 TTAAGGGTAAGGG-
1 TTATGGTTTAGGGT
* *
52849992 TTAGGGTTTTAAGGT
1 TTATGG-TTTAGGGT
* * *
52850007 TTATAGTTTATGTT
1 TTATGGTTTAGGGT
*
52850021 TTATGATTTAGGGT
1 TTATGGTTTAGGGT
52850035 TTATGG
1 TTATGG
52850041 GATATGGGTT
Statistics
Matches: 135, Mismatches: 41, Indels: 22
0.68 0.21 0.11
Matches are distributed among these distances:
11 2 0.01
12 7 0.05
13 9 0.07
14 91 0.67
15 24 0.18
17 2 0.01
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:52849928 original size:15 final size:14
Alignment explanation
Indices: 52849908--52849944 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
52849898 ACTATTTTAA
52849908 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
52849922 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
52849937 GGTTTATG
1 GGTTTATG
52849945 ATTTAAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:52850030 original size:21 final size:21
Alignment explanation
Indices: 52849997--52850039 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52849987 AAGGGTTAGG
* *
52849997 GTTTTAAGGTTTATAGTTTAT
1 GTTTTAAGATTTAGAGTTTAT
* *
52850018 GTTTTATGATTTAGGGTTTAT
1 GTTTTAAGATTTAGAGTTTAT
52850039 G
1 G
52850040 GGATATGGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (21 bp):
GTTTTAAGATTTAGAGTTTAT
Found at i:52850917 original size:28 final size:28
Alignment explanation
Indices: 52850877--52850940 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
52850867 AAACGGCGTC
52850877 GTTTTGATATAATCGCCACTAATTTTTA
1 GTTTTGATATAATCGCCACTAATTTTTA
52850905 GTTTTGATATAATCGCCACTAATTTTTA
1 GTTTTGATATAATCGCCACTAATTTTTA
52850933 GTTTTGAT
1 GTTTTGAT
52850941 TGAAACAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (28 bp):
GTTTTGATATAATCGCCACTAATTTTTA
Found at i:52851061 original size:72 final size:73
Alignment explanation
Indices: 52850957--52851106 Score: 178
Period size: 72 Copynumber: 2.1 Consensus size: 73
52850947 AAGGCTGTTT
* * *
52850957 TATTTCTCTCCCCCCAATTTCCTCTTCTTTCCCGATTTCATTTTCTTTCTCAGCCATTCTTAGCC
1 TATTTCTCTCCCCCCAATTTCCTCTTCTTTCCCAATTTCATTTTCTTTCTCAGCCATTCTCAACC
52851022 TGTTCCTC
66 TGTTCCTC
* * * * * *
52851030 TATTTCTCT-CCCCC-GTTTCCCTTTTCTTTCCCAATTTCCTTTTTTTTCTCGGCCTTTCTCAAC
1 TATTTCTCTCCCCCCAATTT-CCTCTTCTTTCCCAATTTCATTTTCTTTCTCAGCCATTCTCAAC
* *
52851093 TTGTTCTTC
65 CTGTTCCTC
52851102 TATTT
1 TATTT
52851107 TTTACCCGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
71 3 0.05
72 53 0.82
73 9 0.14
ACGTcount: A:0.09, C:0.35, G:0.05, T:0.51
Consensus pattern (73 bp):
TATTTCTCTCCCCCCAATTTCCTCTTCTTTCCCAATTTCATTTTCTTTCTCAGCCATTCTCAACC
TGTTCCTC
Done.