Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 165 of 175
Found at i:49669686 original size:21 final size:20
Alignment explanation
Indices: 49669662--49669701 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
49669652 CTTCCTATTA
49669662 TCTAATAAAAAACCTAAAATT
1 TCTAATAAAAAACC-AAAATT
*
49669683 TCTAATAATAAACCAAAAT
1 TCTAATAAAAAACCAAAAT
49669702 CACCTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (20 bp):
TCTAATAAAAAACCAAAATT
Found at i:49670118 original size:232 final size:230
Alignment explanation
Indices: 49669578--49670232 Score: 849
Period size: 232 Copynumber: 2.8 Consensus size: 230
49669568 AATACCAAAG
* *
49669578 TAACAAATAAAAAATGAACCCCATTATTATAAATCAAGTTATTAAATATTTCAAACAAATCTTGA
1 TAACAAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGA
* * * * *
49669643 TATTCGAAACTTCCTATTATCTAATAAAAAACCTAAAATTTCTAATAATAAACCAAAATCAC-CT
66 AATTTGAAACTTCCCATTATCCAAT-AAAAACCTAAGATTTCTAATAATAAACCAAAA-C-CGC-
*
49669707 ATAT-GATTAATTACAAATACTTTTTGACAAGTATTT---A-CG-GAGTCATGTGAACCAAAAAC
127 ATATCGATTAATTACAAATACTTTTTGACAAGTGTTTGCCACCGTGAGTCATGTGAACCAAAAAC
* * * * *
49669766 CTATTAATAAATAAGAATACATTTCAGTAAAAAACTTAT
192 CTATCAATAAATAAGAATACATTCCAATAAAAAACCTAC
* * **
49669805 TAACAAATAAAAACTGAACCTCAATATTATAAATCAAATTATTAAATATTTTGAACAAATCTTGA
1 TAACAAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGA
*
49669870 AATTTGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCGAAACCGCATAT
66 AATTTGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATAT
* *
49669935 CGAATTAGTTACAAATACTTTTTGACAAGTGTTTGCCACCGTGAGTCATGTGAACCTAAAACCTA
131 CG-ATTAATTACAAATACTTTTTGACAAGTGTTTGCCACCGTGAGTCATGTGAACCAAAAACCTA
49670000 TCAATAAATAAGAATACATTCCAAT-AAAAACCTAC
195 TCAATAAATAAGAATACATTCCAATAAAAAACCTAC
* *
49670035 TAACAAATAAAAAAAATAAACCTCATTATTATGAATCAAATTATTAAATATTTCAAACAAATCTT
1 TAACAAAT--AAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTT
* * * * *
49670100 GAAATTTAAAATTTCCCATTATCCAATAAAAACCTAAGATTCCTAATAATAACCCAAAACCGCCT
64 GAAATTTGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCAT
* * * * * * * * * *
49670165 ATCTCATTAATTATATACATTTTTTGACAAGCGTTTGCCACTGTAAGTCACGTGAACCCAAAACC
129 ATC-GATTAATTACAAATACTTTTTGACAAGTGTTTGCCACCGTGAGTCATGTGAACCAAAAACC
49670230 TAT
193 TAT
49670233 GTATTCTCAA
Statistics
Matches: 374, Mismatches: 43, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
224 5 0.01
225 3 0.01
226 59 0.16
227 80 0.21
229 1 0.00
230 18 0.05
231 44 0.12
232 164 0.44
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.31
Consensus pattern (230 bp):
TAACAAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGA
AATTTGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATAT
CGATTAATTACAAATACTTTTTGACAAGTGTTTGCCACCGTGAGTCATGTGAACCAAAAACCTAT
CAATAAATAAGAATACATTCCAATAAAAAACCTAC
Found at i:49674467 original size:15 final size:16
Alignment explanation
Indices: 49674412--49674467 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
49674402 AATGCGTTTT
49674412 AAATTATATAATATATAA
1 AAATTATATAAT-T-TAA
* *
49674430 AAATAATATAATATAA
1 AAATTATATAATTTAA
*
49674446 AGTATTATA-AATTTAA
1 A-AATTATATAATTTAA
49674462 AAATTA
1 AAATTA
49674468 GTTGAGCTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 4 0.13
16 11 0.35
17 5 0.16
18 11 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAATTATATAATTTAA
Found at i:49675072 original size:51 final size:51
Alignment explanation
Indices: 49675017--49675137 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 51
49675007 CGTTGTAAAT
* *
49675017 ATTAACGGGATGTGTAAATGTTACAGG-CTAAATATGTTAAATTAAAATTAA
1 ATTAACAGGATGTGTAAATGTTA-AGGACTAAATATATTAAATTAAAATTAA
* * * *
49675068 ATTAACAGAATGTGTAAATGTTATGGACTAAATTTATTAAATTAAAGTTAA
1 ATTAACAGGATGTGTAAATGTTAAGGACTAAATATATTAAATTAAAATTAA
* *
49675119 ATTGACACGATGTGTAAAT
1 ATTAACAGGATGTGTAAAT
49675138 CTTGTGGACT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
50 2 0.03
51 58 0.97
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.35
Consensus pattern (51 bp):
ATTAACAGGATGTGTAAATGTTAAGGACTAAATATATTAAATTAAAATTAA
Found at i:49675146 original size:51 final size:51
Alignment explanation
Indices: 49675017--49675153 Score: 143
Period size: 51 Copynumber: 2.7 Consensus size: 51
49675007 CGTTGTAAAT
* * * * * *
49675017 ATTAACGGGATGTGTAAATGTTACAGG-CTAAATATGTTAAATTAAAATTAA
1 ATTAACAGAATGTGTAAATCTTA-TGGACTAAATTTATTAAATTAAAATTAA
* *
49675068 ATTAACAGAATGTGTAAATGTTATGGACTAAATTTATTAAATTAAAGTTAA
1 ATTAACAGAATGTGTAAATCTTATGGACTAAATTTATTAAATTAAAATTAA
* * *
49675119 ATTGACACG-ATGTGTAAATCTTGTGGACTGAATTT
1 ATTAACA-GAATGTGTAAATCTTATGGACTAAATTT
49675154 GTTATCATAC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 2 0.03
51 71 0.96
52 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (51 bp):
ATTAACAGAATGTGTAAATCTTATGGACTAAATTTATTAAATTAAAATTAA
Found at i:49676194 original size:21 final size:22
Alignment explanation
Indices: 49676170--49676220 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
49676160 AACATAGCAG
49676170 AAAAAAAT-CAAAAA-TTATAA
1 AAAAAAATCCAAAAATTTATAA
*
49676190 AAAAAATTCCAAAAATTTATGAA
1 AAAAAAATCCAAAAATTTAT-AA
49676213 AAAAAAAT
1 AAAAAAAT
49676221 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 6 0.23
22 4 0.15
23 9 0.35
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAAAATCCAAAAATTTATAA
Found at i:49678989 original size:21 final size:23
Alignment explanation
Indices: 49678953--49678995 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
49678943 TTATTTTGTT
49678953 TTTTTATATATTTGAATGATTTC
1 TTTTTATATATTTGAATGATTTC
*
49678976 TTTTTAT-T-TTTGAATTATTT
1 TTTTTATATATTTGAATGATTT
49678996 TTGTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTTATATATTTGAATGATTTC
Found at i:49682454 original size:20 final size:20
Alignment explanation
Indices: 49682408--49682455 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
49682398 CAAAACACAG
49682408 CAGCAAAACAATAGAAACAA
1 CAGCAAAACAATAGAAACAA
* * *
49682428 CAACAAAACAGTGGAAACAA
1 CAGCAAAACAATAGAAACAA
*
49682448 TAGCAAAA
1 CAGCAAAA
49682456 TATAGCAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (20 bp):
CAGCAAAACAATAGAAACAA
Found at i:49688942 original size:60 final size:60
Alignment explanation
Indices: 49688878--49688990 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
49688868 ACCGAACAAA
* * * *
49688878 CAAAAAGATTAGGCATCAAATTAAGAAAAAG-AGTCAAGTTCATGTACCAAATTGGACACC
1 CAAAAAGATTAAGCACCAAATTAACAAAAAGTA-TCAAGTTCAGGTACCAAATTGGACACC
* * * *
49688938 CAAAAAGTTTAAGTACCAACTTAACAAAAAGTATCAAGTTGAGGTACCAAATT
1 CAAAAAGATTAAGCACCAAATTAACAAAAAGTATCAAGTTCAGGTACCAAATT
49688991 AAGAAAAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 43 0.98
61 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (60 bp):
CAAAAAGATTAAGCACCAAATTAACAAAAAGTATCAAGTTCAGGTACCAAATTGGACACC
Found at i:49688985 original size:31 final size:31
Alignment explanation
Indices: 49688942--49689020 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
49688932 GACACCCAAA
* *
49688942 AAGTTTAAGTACCAACTTAACAAAAAGTATC
1 AAGTTCAAGTACCAAATTAACAAAAAGTATC
* * * *
49688973 AAGTTGAGGTACCAAATTAAGAAAAAGTGTC
1 AAGTTCAAGTACCAAATTAACAAAAAGTATC
*
49689004 CAGTTCAAGTACCAAAT
1 AAGTTCAAGTACCAAAT
49689021 ATTATATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (31 bp):
AAGTTCAAGTACCAAATTAACAAAAAGTATC
Found at i:49689234 original size:29 final size:31
Alignment explanation
Indices: 49689168--49689235 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
49689158 TTTAATGATT
*
49689168 AAAATTTATATAATATAAATTATTACAAAGGA
1 AAAATTTATATAATATAAATTATGACAAA-GA
* *
49689200 ATAAATTTATATAAT-TATATTATGCCAAA-A
1 A-AAATTTATATAATATAAATTATGACAAAGA
49689230 AAAATT
1 AAAATT
49689236 AACACATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 5 0.16
30 2 0.06
32 12 0.38
33 13 0.41
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (31 bp):
AAAATTTATATAATATAAATTATGACAAAGA
Found at i:49692837 original size:31 final size:31
Alignment explanation
Indices: 49692797--49692857 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
49692787 AAATAGTTGC
* *
49692797 TAAATTATTTAAAAATTTTCATTTAAGTCAT
1 TAAACTATTTAAAAATTTTCATTCAAGTCAT
* * *
49692828 TAAACTATTTGAAATTTTTTATTCAAGTCA
1 TAAACTATTTAAAAATTTTCATTCAAGTCA
49692858 CTAGGCTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (31 bp):
TAAACTATTTAAAAATTTTCATTCAAGTCAT
Found at i:49696136 original size:175 final size:175
Alignment explanation
Indices: 49695839--49696241 Score: 639
Period size: 175 Copynumber: 2.3 Consensus size: 175
49695829 ACCTTGATTA
* * *
49695839 TTACCTGCATGCTGAA-GATGGTGGATCTCATAGTTGAACAGGTGGCAAAAGTGTTTCTCTTTCT
1 TTACCTGCATGCT-AAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTTCT
* ** * *
49695903 ACTCTTGTCGGTCATGCCATAGGTGGTGGGATCACAACATTTATAGCATCCGACCTAATTCAGTA
65 ACTCTTGACGGTCATGCCATAGGTGGCAGGATCACAACATTGATAGCATCCAACCTAATTCAGTA
* *
49695968 ACCTTGAGTGTAGTTTATCCTTTGAAATACCATGCTTGTCGGGTTC
130 ACCTTAAGTGTAGTTTATCCTTTGAAATACCATGCTTGTCGGCTTC
49696014 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTTCTA
1 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTTCTA
* *
49696079 CTCTTGACGGTTATGTCC-TAGGTGGCAGGATCGCAACATTGATAGCATCCAACCTAATTCAGTA
66 CTCTTGACGGTCATG-CCATAGGTGGCAGGATCACAACATTGATAGCATCCAACCTAATTCAGTA
* * *
49696143 ACCTTAAGTGTAGTTTATCCTTTGAAATACTATTCTTGTCGGCTTT
130 ACCTTAAGTGTAGTTTATCCTTTGAAATACCATGCTTGTCGGCTTC
49696189 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTG
1 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTG
49696242 GGGGGGGGGG
Statistics
Matches: 211, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
174 2 0.01
175 207 0.98
176 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (175 bp):
TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTTCTA
CTCTTGACGGTCATGCCATAGGTGGCAGGATCACAACATTGATAGCATCCAACCTAATTCAGTAA
CCTTAAGTGTAGTTTATCCTTTGAAATACCATGCTTGTCGGCTTC
Found at i:49699784 original size:28 final size:28
Alignment explanation
Indices: 49699753--49699811 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
49699743 CAAACTGAAC
49699753 TTATATAAAATTTTAAATTTATTTTCAG
1 TTATATAAAATTTTAAATTTATTTTCAG
49699781 TTATATAAAATTTTAAATTTATTTTCAG
1 TTATATAAAATTTTAAATTTATTTTCAG
49699809 TTA
1 TTA
49699812 AACTGATCTT
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:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (28 bp):
TTATATAAAATTTTAAATTTATTTTCAG
Found at i:49702243 original size:45 final size:45
Alignment explanation
Indices: 49702179--49702270 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
49702169 AATATAAACA
* *
49702179 AGAGCTAACTCTTTAAAAGGAATGGTATACCTTGTAAGCAATCAC
1 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
49702224 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
1 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
49702269 AG
1 AG
49702271 TTCTCGGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (45 bp):
AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
Found at i:49703045 original size:14 final size:14
Alignment explanation
Indices: 49703022--49703061 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49703012 TTTAATAATG
49703022 TTAAAAATTATACT
1 TTAAAAATTATACT
* * *
49703036 TTAAATATTAAATT
1 TTAAAAATTATACT
49703050 TTAAAAATTATA
1 TTAAAAATTATA
49703062 GGGTCTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAAATTATACT
Found at i:49713378 original size:19 final size:19
Alignment explanation
Indices: 49713356--49713393 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
49713346 GGAATATTAC
49713356 GAAAATAAGAGAGTGTGAA
1 GAAAATAAGAGAGTGTGAA
49713375 GAAAATAAGAGAGTGTGAA
1 GAAAATAAGAGAGTGTGAA
49713394 ATAAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.16
Consensus pattern (19 bp):
GAAAATAAGAGAGTGTGAA
Found at i:49713401 original size:21 final size:19
Alignment explanation
Indices: 49713357--49713399 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
49713347 GAATATTACG
*
49713357 AAAATAAGAGAGTGTGAAG
1 AAAATAAGAGAGTGTGAAA
49713376 AAAATAAGAGAGTGTGAAA
1 AAAATAAGAGAGTGTGAAA
49713395 TAAAA
1 -AAAA
49713400 ATGTGAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (19 bp):
AAAATAAGAGAGTGTGAAA
Found at i:49713944 original size:13 final size:13
Alignment explanation
Indices: 49713926--49713950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49713916 CGAGGGTCCA
49713926 AGGTCCAAGGTTG
1 AGGTCCAAGGTTG
49713939 AGGTCCAAGGTT
1 AGGTCCAAGGTT
49713951 TAAAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (13 bp):
AGGTCCAAGGTTG
Found at i:49716099 original size:16 final size:16
Alignment explanation
Indices: 49716069--49716098 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49716059 ACCTATAATG
49716069 AGATTAATGTTAAAAC
1 AGATTAATGTTAAAAC
49716085 AGATT-ATGTTAAAA
1 AGATTAATGTTAAAA
49716099 ATTTTGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (16 bp):
AGATTAATGTTAAAAC
Found at i:49735359 original size:24 final size:25
Alignment explanation
Indices: 49735329--49735388 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
49735319 ATGTTTTTTT
49735329 TTATTTTTTTTGTT-AATTTGATCC-
1 TTATTTTTTTTGTTAAATTTGA-CCA
*
49735353 TTA-TTTTTTAGTTAAATTTGACCA
1 TTATTTTTTTTGTTAAATTTGACCA
49735377 TTAATTTTTTTT
1 TT-ATTTTTTTT
49735389 AAAAGTCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 11 0.37
24 12 0.40
25 1 0.03
26 6 0.20
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.65
Consensus pattern (25 bp):
TTATTTTTTTTGTTAAATTTGACCA
Found at i:49735366 original size:23 final size:25
Alignment explanation
Indices: 49735333--49735386 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
49735323 TTTTTTTTAT
*
49735333 TTTTTTTGTT-AATTTGATCC-TT-A
1 TTTTTTAGTTAAATTTGA-CCATTAA
49735356 TTTTTTAGTTAAATTTGACCATTAA
1 TTTTTTAGTTAAATTTGACCATTAA
49735381 TTTTTT
1 TTTTTT
49735387 TTAAAAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 11 0.41
24 9 0.33
25 7 0.26
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (25 bp):
TTTTTTAGTTAAATTTGACCATTAA
Found at i:49749305 original size:52 final size:51
Alignment explanation
Indices: 49749223--49749323 Score: 123
Period size: 52 Copynumber: 2.0 Consensus size: 51
49749213 TAATTCTAAA
* ** *
49749223 TAATTCAACAAATTTAATCTTCAATGTTTATATGCTATGTCAATTTAGTAC
1 TAATTCAACAAATTTAATCATCAACATTTATATGCTATATCAATTTAGTAC
* *
49749274 TAATTCTAACAAATTTAA-CAATCAACATTTATATGTTCTATCAATTTAGT
1 TAATTC-AACAAATTTAATC-ATCAACATTTATATGCTATATCAATTTAGT
49749324 CCAGATACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 7 0.17
52 35 0.83
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.43
Consensus pattern (51 bp):
TAATTCAACAAATTTAATCATCAACATTTATATGCTATATCAATTTAGTAC
Found at i:49762810 original size:39 final size:40
Alignment explanation
Indices: 49762759--49762847 Score: 119
Period size: 39 Copynumber: 2.2 Consensus size: 40
49762749 TAAAATTATA
* * *
49762759 TTTAATACAATAAAATATTTATTGCATTTATTTGT-GT-TT
1 TTTAATATAATAAAATATTTATTACATTTA-TGGTAGTATT
*
49762798 TTTAATATAATAAAATATTTATTATATTTATGGTAGTATT
1 TTTAATATAATAAAATATTTATTACATTTATGGTAGTATT
49762838 TTTAATATAA
1 TTTAATATAA
49762848 ATATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 3 0.07
39 29 0.66
40 12 0.27
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (40 bp):
TTTAATATAATAAAATATTTATTACATTTATGGTAGTATT
Found at i:49763958 original size:17 final size:17
Alignment explanation
Indices: 49763919--49763954 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
49763909 ATAACATCTT
49763919 ATATTTATAATTTTATA
1 ATATTTATAATTTTATA
*
49763936 ATATTTATACTTTT-TA
1 ATATTTATAATTTTATA
49763952 ATA
1 ATA
49763955 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATAATTTTATA
Found at i:49766748 original size:27 final size:29
Alignment explanation
Indices: 49766712--49766783 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 29
49766702 AAAATATACT
*
49766712 TTTTTTAATAACTTTAAT-G-ATTTTAAA
1 TTTTTAAATAACTTTAATAGTATTTTAAA
* * *
49766739 TTTTTAAATAAAATTT-ATAGTTTTTTTAA
1 TTTTTAAAT-AACTTTAATAGTATTTTAAA
49766768 TTTTTAAA-AACTTTAA
1 TTTTTAAATAACTTTAA
49766784 AATTAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
27 15 0.42
28 7 0.19
29 14 0.39
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTTTAAATAACTTTAATAGTATTTTAAA
Found at i:49768054 original size:13 final size:13
Alignment explanation
Indices: 49768036--49768060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49768026 TTTTAAAATA
49768036 TTTTTATTTTTAT
1 TTTTTATTTTTAT
49768049 TTTTTATTTTTA
1 TTTTTATTTTTA
49768061 AAATATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:49769017 original size:2 final size:2
Alignment explanation
Indices: 49769010--49769067 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
49769000 AAATTCAAAA
* *
49769010 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
49769052 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
49769068 TAAAGTTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49770383 original size:17 final size:18
Alignment explanation
Indices: 49770346--49770383 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
49770336 AATAAAAATT
*
49770346 TATTTTCTAATGAAATAA
1 TATTTTATAATGAAATAA
*
49770364 TATTTTATAAT-AATTAA
1 TATTTTATAATGAAATAA
49770381 TAT
1 TAT
49770384 CATATAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTTATAATGAAATAA
Found at i:49770893 original size:17 final size:18
Alignment explanation
Indices: 49770871--49770905 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49770861 AACCCACCGT
49770871 AATTT-GTAATTTTTATA
1 AATTTGGTAATTTTTATA
*
49770888 AATTTGGTGATTTTTATA
1 AATTTGGTAATTTTTATA
49770906 CTAAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
AATTTGGTAATTTTTATA
Found at i:49774958 original size:34 final size:34
Alignment explanation
Indices: 49774915--49774980 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
49774905 TCAACTCTGT
** *
49774915 CATTATATATACATAAGTTATATATGAACACCGG
1 CATTATATATACATAAACTATATATAAACACCGG
49774949 CATTATATATACATAAACTATATATAAACACC
1 CATTATATATACATAAACTATATATAAACACC
49774981 CACACTCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (34 bp):
CATTATATATACATAAACTATATATAAACACCGG
Found at i:49780772 original size:3 final size:3
Alignment explanation
Indices: 49780757--49780831 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
49780747 AATACTAACG
* ** * *
49780757 ATA ATA GTA ATA ATA ATA ACC ATA ATA ATA ATA GTA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
49780804 ATA TTTA A-A ATA ATA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
49780832 CATAAAATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 52 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:49780888 original size:29 final size:28
Alignment explanation
Indices: 49780844--49780934 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
49780834 TAAAATTGCT
49780844 AAAATAT-GGGCTAAATCGAAATAAAACA
1 AAAATATAGGGCTAAATCGAAATAAAA-A
* * *
49780872 AAAATATAGGGCGAAATTGAAAGAAAAA
1 AAAATATAGGGCTAAATCGAAATAAAAA
* *
49780900 TAAAATAAAAGGGACTAAATCAAAATAAAAA
1 -AAAAT-ATAGGG-CTAAATCGAAATAAAAA
49780931 AAAA
1 AAAA
49780935 GAAACTGGGC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 8 0.16
29 21 0.41
30 9 0.18
31 13 0.25
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.15
Consensus pattern (28 bp):
AAAATATAGGGCTAAATCGAAATAAAAA
Found at i:49780955 original size:50 final size:51
Alignment explanation
Indices: 49780901--49781009 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 51
49780891 AAAGAAAAAT
*
49780901 AAAATAAAAGGGACTAAATCAAAATAAAAA-AAAAGAAACTGGGCGAA-TTC
1 AAAATAAAAGGGACTAAATCAAAATAAAAATAAAA-AAACTGAGCGAATTTC
* * * *
49780951 AAAATGAAAGGGACTAAATCGAAGTAAAAATAAAAATACTGAGCGAATTTC
1 AAAATAAAAGGGACTAAATCAAAATAAAAATAAAAAAACTGAGCGAATTTC
49781002 -AAATAAAA
1 AAAATAAAA
49781010 AAAGACTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
50 44 0.86
51 7 0.14
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.17
Consensus pattern (51 bp):
AAAATAAAAGGGACTAAATCAAAATAAAAATAAAAAAACTGAGCGAATTTC
Found at i:49782064 original size:15 final size:16
Alignment explanation
Indices: 49782038--49782067 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49782028 TAGTGTTTAG
49782038 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
49782054 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
49782068 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:49784673 original size:3 final size:3
Alignment explanation
Indices: 49784665--49784728 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
49784655 TCAGATAGTC
49784665 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
49784713 CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT C
49784729 ATCATCATCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:49785906 original size:32 final size:32
Alignment explanation
Indices: 49785870--49785934 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
49785860 CCTTGCTTGC
49785870 ACCTTACATTTGCCCCACATCATTTTACATTT
1 ACCTTACATTTGCCCCACATCATTTTACATTT
49785902 ACCTTACATTTGCCCCACATCATTTTACATTT
1 ACCTTACATTTGCCCCACATCATTTTACATTT
49785934 A
1 A
49785935 TGGTTATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (32 bp):
ACCTTACATTTGCCCCACATCATTTTACATTT
Found at i:49802392 original size:43 final size:42
Alignment explanation
Indices: 49802235--49802396 Score: 145
Period size: 43 Copynumber: 3.8 Consensus size: 42
49802225 TAGGATTCCA
* *
49802235 ATATGTGATTTCGTGTAAGACGACGTCTGGGAC-GTTGGCATC-
1 ATATTTGATTTCGTGTAAGACCACGTCTGGGACAG-T-GCATCG
* * *
49802277 AT-TTTGAGATTTACGTGTAAGACCATGTTTGGGACATTAGCATCG
1 ATATTT--GATTT-CGTGTAAGACCACGTCTGGGACAGT-GCATCG
* *
49802322 -TATATGATTTCGTGTAAGACC-CTGTCTGAGACAGTGTCATCG
1 ATATTTGATTTCGTGTAAGACCAC-GTCTGGGACAGTG-CATCG
*
49802364 ATATTTGATTTCATGTAAGACCACGTCTGGGAC
1 ATATTTGATTTCGTGTAAGACCACGTCTGGGAC
49802397 GTTGGCATTG
Statistics
Matches: 96, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
41 3 0.03
42 27 0.28
43 37 0.39
44 27 0.28
45 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
ATATTTGATTTCGTGTAAGACCACGTCTGGGACAGTGCATCG
Found at i:49811637 original size:44 final size:44
Alignment explanation
Indices: 49811574--49812156 Score: 539
Period size: 44 Copynumber: 13.1 Consensus size: 44
49811564 CATCATGGTG
* **
49811574 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* *
49811618 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAGTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
* * *
49811663 AATCTTATCTCCCTGAAATTGCAATGGAGCAAATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
* * *
49811708 AATCTTATCTCTCTGAAGTTACAGTGGAGCAGATT-AAAACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACA
* * *
49811752 AATCTTATCTCCCTGAAGTTGCAGTGGAACATATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * *
49811796 AGTCTCATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* *
49811840 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
*
49811884 AATATTATCTCCCTGAAGTTGCAGTGGAGC-GAATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTGAAGATA-CA
* * ** * *
49811929 AATCTT-TTTCCCTGAAGTTGAAGTGGAATAGATTAAAGCTACAAGTTACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G----AAGATACA
* * * * **
49811979 AATCTTATCTCCCTGAAATTACAATGGAGCAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * *
49812023 AATC--ATCTCCCTGAAATTGCAGTGGAGGAGATTGAAGATACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * ** * * * * * * *
49812065 AGTCTCATCTCTTTGAAGTTGTAGTAGAGTATATTAAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
* * * * *
49812109 AGTCTAATCTCCCCGAAGTTGCAGTGGAGTAGATTTAAG-TAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CA
49812153 AATC
1 AATC
49812157 CCATACCTCT
Statistics
Matches: 443, Mismatches: 79, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
42 34 0.08
43 2 0.00
44 290 0.65
45 83 0.19
47 1 0.00
50 7 0.02
51 26 0.06
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACA
Found at i:49811884 original size:132 final size:133
Alignment explanation
Indices: 49811574--49812156 Score: 613
Period size: 132 Copynumber: 4.4 Consensus size: 133
49811564 CATCATGGTG
* *
49811574 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
* * * * * * *
49811639 CAGTGGAGCAGATTGAAGATAGTAAATCTTATCTCCCTGAAATTGCAATGGAGCAAATTGAAGAT
66 CAGTGGAGCAGATTGAAGATAGCAAATCTCATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTT
49811704 AGCA
131 A-CA
* * *
49811708 AATCTTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAACTACAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
* * * *
49811773 CAGTGGAACATATTGAAGTTA-CAAGTCTCATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTT
66 CAGTGGAGCAGATTGAAGATAGCAAATCTCATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTT
49811837 ACA
131 ACA
* * * *
49811840 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTTACAAATATTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
* * * **
49811905 CAGTGGAGC-GAATTGAAGATAGCAAATCT-TTTTCCCTGAAGTTGAAGTGGAATAGATTAAAGC
66 CAGTGGAGCAG-ATTGAAGATAGCAAATCTCATCTCCCTGAAGTTGTAGTGGAGCAGATT---G-
*
49811968 TACAAGTTACG
126 ---AAGTTACA
* * * * *
49811979 AATCTTATCTCCCTGAAATTACAATGGAGCAGATTAAAGCCACAAATC--ATCTCCCTGAAATTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
* * * ** * * * *
49812042 CAGTGGAGGAGATTGAAGATA-CGAGTCTCATCTCTTTGAAGTTGTAGTAGAGTATATTAAAGTT
66 CAGTGGAGCAGATTGAAGATAGCAAATCTCATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTT
*
49812106 GCA
131 ACA
* * * * *
49812109 AGTCTAATCTCCCCGAAGTTGCAGTGGAGTAGATTTAAG-TAGCAAATC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAATC
49812157 CCATACCTCT
Statistics
Matches: 372, Mismatches: 65, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
129 1 0.00
130 43 0.12
132 101 0.27
133 42 0.11
134 78 0.21
135 1 0.00
136 5 0.01
137 53 0.14
138 1 0.00
139 47 0.13
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (133 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTGAAGATAGCAAATCTCATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGTT
ACA
Found at i:49812418 original size:28 final size:27
Alignment explanation
Indices: 49812362--49812418 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
49812352 CAAATAATAA
* * *
49812362 AAATAAAATAAAATCCAAAAACAGTCC
1 AAATAAAAAAAAACCCAAAAACAGACC
49812389 AAATACAAAAAAAACCCAAAATACA-ACC
1 AAATA-AAAAAAAACCCAAAA-ACAGACC
49812417 AA
1 AA
49812419 CCCCTAACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 5 0.20
28 17 0.68
29 3 0.12
ACGTcount: A:0.67, C:0.21, G:0.02, T:0.11
Consensus pattern (27 bp):
AAATAAAAAAAAACCCAAAAACAGACC
Found at i:49813593 original size:69 final size:63
Alignment explanation
Indices: 49813506--49813718 Score: 197
Period size: 69 Copynumber: 3.3 Consensus size: 63
49813496 TATATTTGTT
* *
49813506 TTATTTA--TTTATTATTCTTTTACTTTTTAAATACCAAATTTTAATATTATTTATATTTCATC
1 TTATTTATTTTTATTATTCTTTTACATTTTAAATACCAAATTTTAATATTATTTATATTT-AGC
* *
49813568 TATTTATTTATTTGTTCATTATTCTTTTACCTTTTAAATACTTAAA-TTTAATATTATTTATATT
1 ---TTATTTATTT-TT-ATTATTCTTTTACATTTTAAATAC-CAAATTTTAATATTATTTATATT
*
49813632 TGGC
60 TAGC
* * * *
49813636 TTATTTA--TTTATTATCCTTTTACATTTTAAGTACCTAATTTTACTATTATTTATATTT-G-
1 TTATTTATTTTTATTATTCTTTTACATTTTAAATACCAAATTTTAATATTATTTATATTTAGC
49813695 TTATATCTATTTATTTATTATTCT
1 TTAT-T-TA-TT-TTTATTATTCT
49813719 CGATTAACTT
Statistics
Matches: 125, Mismatches: 11, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
59 4 0.03
60 4 0.03
61 41 0.33
62 2 0.02
63 1 0.01
65 24 0.19
67 1 0.01
68 3 0.02
69 42 0.34
70 3 0.02
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (63 bp):
TTATTTATTTTTATTATTCTTTTACATTTTAAATACCAAATTTTAATATTATTTATATTTAGC
Found at i:49813650 original size:61 final size:60
Alignment explanation
Indices: 49813575--49813709 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 60
49813565 ATCTATTTAT
* * * *
49813575 TTATTTGTTCATTATTCTTTTACCTTTTAAATACTTAAATTTAATATTATTTATATTTGGC
1 TTATTTATTTATTATTCTTTTACATTTTAAATAC-TAAATTTAATATTATTTATATTTGTC
* * * *
49813636 TTATTTATTTATTATCCTTTTACATTTTAAGTACCTAATTTTACTATTATTTATATTTGT-
1 TTATTTATTTATTATTCTTTTACATTTTAAATA-CTAAATTTAATATTATTTATATTTGTC
*
49813696 TATATCTATTTATT
1 T-TATTTATTTATT
49813710 TATTATTCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 1 0.02
61 61 0.97
62 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (60 bp):
TTATTTATTTATTATTCTTTTACATTTTAAATACTAAATTTAATATTATTTATATTTGTC
Found at i:49826184 original size:30 final size:30
Alignment explanation
Indices: 49826150--49826209 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
49826140 CTGCTTGGAG
49826150 GAAAAATTGTCATTAGATATACATAAGCTT
1 GAAAAATTGTCATTAGATATACATAAGCTT
49826180 GAAAAATTGTCATTAGATATACATAAGCTT
1 GAAAAATTGTCATTAGATATACATAAGCTT
49826210 CATCCTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (30 bp):
GAAAAATTGTCATTAGATATACATAAGCTT
Found at i:49827998 original size:3 final size:3
Alignment explanation
Indices: 49827990--49828015 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49827980 CACCTACAGA
49827990 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
49828016 AACAGCACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49839200 original size:12 final size:11
Alignment explanation
Indices: 49839183--49839212 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
49839173 TAAAAGAGGG
49839183 ATTAAATCTAA
1 ATTAAATCTAA
49839194 ATCTAAATCTAA
1 AT-TAAATCTAA
49839206 ATTAAAT
1 ATTAAAT
49839213 AATAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTAAATCTAA
Found at i:49839250 original size:21 final size:21
Alignment explanation
Indices: 49839226--49839265 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49839216 AAAAATTAGA
*
49839226 TAAAAATAAGTAAAACAAAAT
1 TAAAAATAAATAAAACAAAAT
**
49839247 TAAATCTAAATAAAACAAA
1 TAAAAATAAATAAAACAAA
49839266 TAAATGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAAAATAAATAAAACAAAAT
Found at i:49839257 original size:25 final size:24
Alignment explanation
Indices: 49839192--49839260 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
49839182 GATTAAATCT
*
49839192 AAATCTAAATCTAAATTAAATAATAA
1 AAAT-TAAATCTAAA-TAAATAAAAA
* ** *
49839218 AAATTAGATAAAAATAAGTAAAACA
1 AAATTAAATCTAAATAAATAAAA-A
49839243 AAATTAAATCTAAATAAA
1 AAATTAAATCTAAATAAA
49839261 ACAAATAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
24 7 0.21
25 22 0.67
26 4 0.12
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (24 bp):
AAATTAAATCTAAATAAATAAAAA
Found at i:49839527 original size:14 final size:14
Alignment explanation
Indices: 49839487--49839532 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
49839477 TCTAAATCTA
49839487 AAATAAATAAT-AT
1 AAATAAATAATAAT
49839500 AAATTAAATAATAAT
1 AAA-TAAATAATAAT
49839515 GAAATAAA-AATAAGT
1 -AAATAAATAATAA-T
49839530 AAA
1 AAA
49839533 ACAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 7 0.24
16 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
AAATAAATAATAAT
Found at i:49839543 original size:21 final size:21
Alignment explanation
Indices: 49839519--49839558 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49839509 AATAATGAAA
*
49839519 TAAAAATAAGTAAAACAAAAT
1 TAAAAATAAATAAAACAAAAT
**
49839540 TAAATCTAAATAAAACAAA
1 TAAAAATAAATAAAACAAA
49839559 TAAATGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAAAATAAATAAAACAAAAT
Found at i:49839628 original size:293 final size:288
Alignment explanation
Indices: 49839064--49839634 Score: 682
Period size: 293 Copynumber: 2.0 Consensus size: 288
49839054 GCTTAAACCG
* * * * *
49839064 AAATTAAATTAAATTTGCAGTATAGTGAGTAGGGTCGATCACACAAAGACTGAACTGGTTAATTT
1 AAATTAAATTAAATTTACAGAATAGTAAGTAGGATCGATCACACAAAGACTGAACTGATTAATTT
* * * * **
49839129 TACGATTTCTTATGACCAAGATTAGACAAATTTTCAAAAATAAATAAAAGAGGGATTAAATCTAA
66 TACAATTTCTTATGACCAAGAGTAGACAAATCTGCAAAAATAAATAAAAGAAAGATTAAATCTAA
** * *
49839194 ATCTAAATCTAAATTAAATAATAAAAATTAGATAAAAATAAGTAAAACAAAATTAAATCTAAATA
131 ATCTAAATAAAAATTAAATAATAAAAATGAAATAAAAATAAGTAAAACAAAATTAAATCTAAATA
*** * * * **
49839259 AAACAAATAAATGAAAACTCTAACCTCAAGTGTGATTTTGACTCCGACTACAAACTGATCTTAGA
196 AAACAAATAAATGAAAACTCTAACCTCAAGCACGATTTTAACTCAGACTACAAACTGACCCGAGA
*
49839324 CAATGGATTTTCTCTTTCGCCTAAATCA
261 CAATAGATTTTCTCTTTCGCCTAAATCA
* ** *
49839352 AAATTAAATTAAATTTACAGAATAGTAAGTAGGATCGATCCCACTGAGATTGAACTGATTAATTT
1 AAATTAAATTAAATTTACAGAATAGTAAGTAGGATCGATCACACAAAGACTGAACTGATTAATTT
* * * * *
49839417 TACAATTTCTTATGGCC-AGAAGTAGACAAATCTGC-TAAATAAAATAAAATAAATATTAGATCT
66 TACAATTTCTTATGACCAAG-AGTAGACAAATCTGCAAAAAT-AAATAAAAGAAAGATTAAATCT
*
49839480 AAATCTAAAATAAATAATATAAATTAAATAATAATGAAATAAAAATAAGTAAAACAAAATTAAAT
129 AAATCT-AAATAAA-AAT-TAAA-T-AATAAAAATGAAATAAAAATAAGTAAAACAAAATTAAAT
* * ** *
49839545 CTAAATAAAACAAATAAATGAAAACTCTAACTTTAAGCACGATTTTAACTCTAG-CTATGAATTG
189 CTAAATAAAACAAATAAATGAAAACTCTAACCTCAAGCACGATTTTAACTC-AGACTACAAACTG
49839609 AGCCCGA-ACAATAGATTTTCTCTTTC
253 A-CCCGAGACAATAGATTTTCTCTTTC
49839635 AATTGATAAA
Statistics
Matches: 235, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
287 6 0.03
288 106 0.45
289 5 0.02
290 3 0.01
291 4 0.02
292 1 0.00
293 107 0.46
294 3 0.01
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (288 bp):
AAATTAAATTAAATTTACAGAATAGTAAGTAGGATCGATCACACAAAGACTGAACTGATTAATTT
TACAATTTCTTATGACCAAGAGTAGACAAATCTGCAAAAATAAATAAAAGAAAGATTAAATCTAA
ATCTAAATAAAAATTAAATAATAAAAATGAAATAAAAATAAGTAAAACAAAATTAAATCTAAATA
AAACAAATAAATGAAAACTCTAACCTCAAGCACGATTTTAACTCAGACTACAAACTGACCCGAGA
CAATAGATTTTCTCTTTCGCCTAAATCA
Found at i:49842418 original size:16 final size:16
Alignment explanation
Indices: 49842393--49842427 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49842383 TTTCTATTGA
*
49842393 TCTGTTCTTCCAATTT
1 TCTGTCCTTCCAATTT
*
49842409 TCTGTCCTTCCTATTT
1 TCTGTCCTTCCAATTT
49842425 TCT
1 TCT
49842428 TTTCACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (16 bp):
TCTGTCCTTCCAATTT
Found at i:49845029 original size:5 final size:5
Alignment explanation
Indices: 49845021--49845050 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
49845011 AAAGTCATAA
*
49845021 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
49845051 GGGGCAGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:49854312 original size:22 final size:22
Alignment explanation
Indices: 49854287--49854379 Score: 73
Period size: 22 Copynumber: 4.3 Consensus size: 22
49854277 TGCACTTTGG
**
49854287 TGCTCTCTATTTAGCACTTCAA
1 TGCTCTCTGCTTAGCACTTCAA
* * **
49854309 TGCTATTTGCTTAGCA--TCTGG
1 TGCTCTCTGCTTAGCACTTC-AA
* *
49854330 TGCTCTCTGCTTGGCACTTCAG
1 TGCTCTCTGCTTAGCACTTCAA
* *
49854352 TGCTCTCTGTTTAGCACTACAA
1 TGCTCTCTGCTTAGCACTTCAA
49854374 TGCTCT
1 TGCTCT
49854380 TTGGTGTGGT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.04
21 13 0.24
22 37 0.69
23 2 0.04
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (22 bp):
TGCTCTCTGCTTAGCACTTCAA
Found at i:49854366 original size:43 final size:43
Alignment explanation
Indices: 49854284--49854367 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
49854274 TTTTGCACTT
* *
49854284 TGGTGCTCTCTATTTAGCACTTCAATGCTATTTGCTTAGCATC
1 TGGTGCTCTCTACTTAGCACTTCAATGCTATCTGCTTAGCATC
* * * * *
49854327 TGGTGCTCTCTGCTTGGCACTTCAGTGCTCTCTGTTTAGCA
1 TGGTGCTCTCTACTTAGCACTTCAATGCTATCTGCTTAGCA
49854368 CTACAATGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.40
Consensus pattern (43 bp):
TGGTGCTCTCTACTTAGCACTTCAATGCTATCTGCTTAGCATC
Found at i:49858675 original size:20 final size:20
Alignment explanation
Indices: 49858641--49858682 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
49858631 AACTATTTAA
** *
49858641 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
49858661 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
49858681 AT
1 AT
49858683 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:49863753 original size:20 final size:20
Alignment explanation
Indices: 49863719--49863760 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
49863709 AACTATTTAA
** *
49863719 ATAATATTATTTGAATACTT
1 ATAATATTAAATGAATAATT
49863739 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
49863759 AT
1 AT
49863761 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:49866468 original size:14 final size:15
Alignment explanation
Indices: 49866440--49866470 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
49866430 CGAATATCAA
49866440 ATTTCTATGTATTTC
1 ATTTCTATGTATTTC
49866455 ATTTCTAT-TATTTC
1 ATTTCTATGTATTTC
49866469 AT
1 AT
49866471 CTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTCTATGTATTTC
Found at i:49867805 original size:31 final size:31
Alignment explanation
Indices: 49867767--49867825 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
49867757 CATTTGAGTT
*
49867767 AATTAAGTTATTCGGATAAACTCGAATAAAA
1 AATTAAGTTATTCAGATAAACTCGAATAAAA
* * *
49867798 AATTAAGTTTTTCAGCTTAACTCGAATA
1 AATTAAGTTATTCAGATAAACTCGAATA
49867826 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
AATTAAGTTATTCAGATAAACTCGAATAAAA
Found at i:49868870 original size:2 final size:2
Alignment explanation
Indices: 49868865--49868889 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49868855 AAAAAAAAAA
49868865 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
49868890 AAAGATGCCA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49872059 original size:13 final size:13
Alignment explanation
Indices: 49872043--49872076 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
49872033 AGCTTTTTTT
*
49872043 TATTTTTAATTAA
1 TATTTATAATTAA
49872056 TATTTATAATTAA
1 TATTTATAATTAA
*
49872069 TATATATA
1 TATTTATA
49872077 TTATTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATAATTAA
Found at i:49886910 original size:55 final size:55
Alignment explanation
Indices: 49886727--49886912 Score: 219
Period size: 55 Copynumber: 3.3 Consensus size: 55
49886717 GGGCAATGGT
* *
49886727 AACAATCGATTCAAAATAAGCAATATTCCAACATAACAATCCATTTAAACATATA
1 AACAATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATA
* * * * *
49886782 AACAATCAATTCAAAAAAAAAGTAGTATTCCATCATAACAATCGATTTAAACATATA
1 AACAATCGATTC--AAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATA
* * * * * *
49886839 AATAATCTATTCAAAAGAAGCAATATTCCAACATGACAATTGATTTAAGCATAAA
1 AACAATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATA
* *
49886894 AACAACCGATTGAAAAGAA
1 AACAATCGATTCAAAAGAA
49886913 TATTCTAGCA
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
55 61 0.56
57 48 0.44
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.25
Consensus pattern (55 bp):
AACAATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATA
Found at i:49900076 original size:33 final size:33
Alignment explanation
Indices: 49900033--49900108 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
49900023 TCATCTCCAT
* **
49900033 AAAAAGTCATACAAAGTCATTTTGGTTACTTTAG
1 AAAAA-TCATACAAAATCATTAGGGTTACTTTAG
49900067 AAAAATCATACAAAATCATTAGGGTTACTTTAG
1 AAAAATCATACAAAATCATTAGGGTTACTTTAG
*
49900100 ATAAA-CATA
1 AAAAATCATA
49900109 AACATTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 4 0.11
33 29 0.76
34 5 0.13
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (33 bp):
AAAAATCATACAAAATCATTAGGGTTACTTTAG
Found at i:49913523 original size:22 final size:22
Alignment explanation
Indices: 49913480--49913551 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
49913470 TATGCACTAA
49913480 TAAACAGAGAGCACAGATGTGC
1 TAAACAGAGAGCACAGATGTGC
* *
49913502 TAAACGGAGAGCACTG-TCGTGC
1 TAAACAGAGAGCACAGAT-GTGC
49913524 TAGTAATCAGAGAGCACCA-ATGTGC
1 TA--AA-CAGAGAGCA-CAGATGTGC
49913549 TAA
1 TAA
49913552 TAATCAGAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 1 0.03
22 20 0.50
23 1 0.03
24 2 0.05
25 14 0.35
26 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.18
Consensus pattern (22 bp):
TAAACAGAGAGCACAGATGTGC
Found at i:49914507 original size:5 final size:5
Alignment explanation
Indices: 49914497--49914532 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
49914487 TGTTTGTTTT
*
49914497 TATAA TATAA TATAA TATAC TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
49914533 TAACTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:49914568 original size:10 final size:10
Alignment explanation
Indices: 49914496--49914568 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
49914486 TTGTTTGTTT
49914496 TTATAATATA
1 TTATAATATA
*
49914506 ATATAATATA
1 TTATAATATA
*
49914516 CTATAATATA
1 TTATAATATA
*
49914526 ATATAAT-TAA
1 TTATAATAT-A
*
49914536 CTTTTAAGTAATA
1 -TTATAA-T-ATA
49914549 TTAT--TATA
1 TTATAATATA
49914557 TTATAATATA
1 TTATAATATA
49914567 TT
1 TT
49914569 TTAACTTTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 7 0.14
9 2 0.04
10 31 0.62
11 4 0.08
12 4 0.08
13 1 0.02
14 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (10 bp):
TTATAATATA
Found at i:49920893 original size:13 final size:13
Alignment explanation
Indices: 49920867--49920931 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
49920857 AGTTCTTCAT
49920867 TGCTTTTG-AAAG
1 TGCTTTTGAAAAG
49920879 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
49920892 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
*
49920905 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
49920918 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
49920931 T
1 T
49920932 TTGGTTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
12 10 0.21
13 35 0.74
14 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:49927381 original size:21 final size:22
Alignment explanation
Indices: 49927352--49927398 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
49927342 CAGAAGGAGT
*
49927352 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
49927374 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
49927395 GAGT
1 GAGT
49927399 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:49932523 original size:18 final size:19
Alignment explanation
Indices: 49932490--49932525 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
49932480 ATAAAAATAA
*
49932490 TTTAAATATTAATAATTTT
1 TTTAAATATAAATAATTTT
49932509 TTTAAAT-TAAATAATTT
1 TTTAAATATAAATAATTT
49932526 AGAATGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAATATAAATAATTTT
Found at i:49932632 original size:16 final size:17
Alignment explanation
Indices: 49932606--49932639 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
49932596 TTTTAGTGAT
*
49932606 TATTTTATTTAGATAAA
1 TATTTTATTTAGAAAAA
49932623 TATTTT-TTTAGAAAAA
1 TATTTTATTTAGAAAAA
49932639 T
1 T
49932640 TAAATTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTTATTTAGAAAAA
Found at i:49937157 original size:32 final size:32
Alignment explanation
Indices: 49937106--49937185 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
49937096 ATCATACATT
* * * *
49937106 TTAAATAAACATAATTATTCAAGTAATATATC
1 TTAAATAAATATAACTATTCAAATAACATATC
* *
49937138 TTAAATAGATATAACTATTCAAATAACATTTC
1 TTAAATAAATATAACTATTCAAATAACATATC
*
49937170 ATAAATAAATATAACT
1 TTAAATAAATATAACT
49937186 CCAAGTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (32 bp):
TTAAATAAATATAACTATTCAAATAACATATC
Found at i:49937862 original size:22 final size:22
Alignment explanation
Indices: 49937834--49937877 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
49937824 CATTTTTAAG
49937834 ATATTTTAGATTTTGATAATCT
1 ATATTTTAGATTTTGATAATCT
49937856 ATATTTTAGATTTTGATAATCT
1 ATATTTTAGATTTTGATAATCT
49937878 TGTAAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (22 bp):
ATATTTTAGATTTTGATAATCT
Found at i:49939537 original size:42 final size:42
Alignment explanation
Indices: 49939435--49939575 Score: 142
Period size: 42 Copynumber: 3.3 Consensus size: 42
49939425 TGTATCATCA
* *
49939435 GATAAACCGAAGTAAATACACTAGCACACATAA-TGCATCATTG
1 GATAAACCGAAGTAAATATACTA--ACACATAAGTGCATCATTC
* *
49939478 GATAAATCGAAGTAAATATACTAACACATAAGTGTATCATTC
1 GATAAACCGAAGTAAATATACTAACACATAAGTGCATCATTC
* * * * **
49939520 GATGAACCAAAGCAAATATATTGGCACATAAGTGCATCA-TC
1 GATAAACCGAAGTAAATATACTAACACATAAGTGCATCATTC
*
49939561 AGATAAACTGAAGTA
1 -GATAAACCGAAGTA
49939576 TAAACCCATA
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
41 10 0.12
42 49 0.61
43 21 0.26
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (42 bp):
GATAAACCGAAGTAAATATACTAACACATAAGTGCATCATTC
Found at i:49950435 original size:13 final size:13
Alignment explanation
Indices: 49950419--49950456 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
49950409 TTTAGTTTTC
49950419 TTTTTATTTTAGAT
1 TTTTTATTTTA-AT
*
49950433 TTTTAATTTTAAT
1 TTTTTATTTTAAT
49950446 TTTTTATTTTA
1 TTTTTATTTTA
49950457 TTTCTAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:49950441 original size:14 final size:12
Alignment explanation
Indices: 49950404--49950456 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
49950394 CCTAAATTAC
49950404 TAATTTTTAGTTT
1 TAATTTTTA-TTT
*
49950417 T-CTTTTTATTT
1 TAATTTTTATTT
49950428 TAGATTTTTAATTT
1 TA-ATTTTT-ATTT
49950442 TAATTTTTTATTT
1 TAA-TTTTTATTT
49950455 TA
1 TA
49950457 TTTCTAAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 4 0.12
12 6 0.18
13 13 0.38
14 11 0.32
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.72
Consensus pattern (12 bp):
TAATTTTTATTT
Found at i:49957673 original size:20 final size:20
Alignment explanation
Indices: 49957628--49957679 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
49957618 ATATTAAAAT
49957628 AAAAAATAAA-AATACTTAA
1 AAAAAATAAATAATACTTAA
*
49957647 AATAAAATAAATAA-AGTTATA
1 AA-AAAATAAATAATACTTA-A
49957668 AAAAAATAAATA
1 AAAAAATAAATA
49957680 CCACATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 5 0.17
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAAATAAATAATACTTAA
Found at i:49958173 original size:19 final size:20
Alignment explanation
Indices: 49958151--49958190 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
49958141 TAGTTTAAAG
49958151 TTTA-TTTTATTTTTAAATA
1 TTTATTTTTATTTTTAAATA
49958170 TTTATTTTTTATTTTTAAATA
1 TTTA-TTTTTATTTTTAAATA
49958191 AAATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTTTTATTTTTAAATA
Found at i:49960657 original size:28 final size:28
Alignment explanation
Indices: 49960624--49960692 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
49960614 ATAAAAAAGC
*
49960624 ATATATATAGATA-TAAAATAATAATATT
1 ATATATATAGATATTAAAATAATAA-AAT
* * **
49960652 TTATATATACATATTTTAATAATAAAAT
1 ATATATATAGATATTAAAATAATAAAAT
49960680 ATATATATAGATA
1 ATATATATAGATA
49960693 GATATGTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 24 0.73
29 9 0.27
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
ATATATATAGATATTAAAATAATAAAAT
Found at i:49960859 original size:3 final size:3
Alignment explanation
Indices: 49960832--49960953 Score: 90
Period size: 3 Copynumber: 40.7 Consensus size: 3
49960822 AAATAAAAAC
* * * * *
49960832 ATA ACA ATA ATA TTA ATA A-A TATA ATA ATA ACA ATA GTA A-A GATG
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA -ATA
*
49960877 ATA ATA ATA ATA ATA A-A TATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
49960922 ATA A-A GAAA ATG ATA ATA ATA TTA AAA ATA AT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT
49960954 GAACAAAATA
Statistics
Matches: 92, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
2 4 0.04
3 85 0.92
4 3 0.03
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:49960861 original size:21 final size:21
Alignment explanation
Indices: 49960823--49960925 Score: 111
Period size: 21 Copynumber: 5.0 Consensus size: 21
49960813 AGTGAATATA
* *
49960823 AATAA-AAACATAACAATAAT
1 AATAATAAATATAATAATAAT
* *
49960843 ATTAATAAATATAATAATAAC
1 AATAATAAATATAATAATAAT
* * *
49960864 AATAGTAAAGATGATAATAAT
1 AATAATAAATATAATAATAAT
*
49960885 AATAATAAATATAATAATAAC
1 AATAATAAATATAATAATAAT
49960906 AATAAT-AATAATAATAATAA
1 AATAATAAAT-ATAATAATAA
49960926 AGAAAATGAT
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.10
21 61 0.90
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (21 bp):
AATAATAAATATAATAATAAT
Found at i:49960952 original size:30 final size:30
Alignment explanation
Indices: 49960874--49960962 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 30
49960864 AATAGTAAAG
*
49960874 ATGATAATAATAATAATAAAT-AT--A-ATA
1 ATGATAATAATAATAA-AAATAATAAACAAA
* * * *
49960901 ATAACAATAATAATAATAATAATAAAGAAA
1 ATGATAATAATAATAAAAATAATAAACAAA
* *
49960931 ATGATAATAATATTAAAAATAATGAACAAA
1 ATGATAATAATAATAAAAATAATAAACAAA
49960961 AT
1 AT
49960963 AGTGAAAATG
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.06
27 16 0.33
29 1 0.02
30 28 0.58
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (30 bp):
ATGATAATAATAATAAAAATAATAAACAAA
Found at i:49970230 original size:17 final size:16
Alignment explanation
Indices: 49970199--49970233 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
49970189 GATACAGGGA
*
49970199 CATTTTCGTAATTTTC
1 CATTTTCCTAATTTTC
49970215 CATTTTCCTCAATTTTC
1 CATTTTCCT-AATTTTC
49970232 CA
1 CA
49970234 CCCAATCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.20, C:0.26, G:0.03, T:0.51
Consensus pattern (16 bp):
CATTTTCCTAATTTTC
Found at i:49971031 original size:14 final size:14
Alignment explanation
Indices: 49971012--49971038 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49971002 TAAGTTTTGC
49971012 AGTTTTTTTAATTT
1 AGTTTTTTTAATTT
49971026 AGTTTTTTTAATT
1 AGTTTTTTTAATT
49971039 AATTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
AGTTTTTTTAATTT
Found at i:49973434 original size:16 final size:16
Alignment explanation
Indices: 49973413--49973445 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49973403 TCCAAGTACC
*
49973413 AAAATTAAATGAAAAA
1 AAAATTAAAAGAAAAA
49973429 AAAATTAAAAGAAAAA
1 AAAATTAAAAGAAAAA
49973445 A
1 A
49973446 GCAATGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATTAAAAGAAAAA
Found at i:49980663 original size:16 final size:15
Alignment explanation
Indices: 49980644--49980691 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
49980634 AATGTGAATA
49980644 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
49980660 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
49980675 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
49980691 A
1 A
49980692 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:49980667 original size:24 final size:24
Alignment explanation
Indices: 49980640--49980695 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
49980630 AAAAAATGTG
*
49980640 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
49980664 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
49980688 AATAATAA
1 AATAATAA
49980696 TAATTAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:49980674 original size:8 final size:8
Alignment explanation
Indices: 49980640--49980691 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
49980630 AAAAAATGTG
*
49980640 AATAATAA
1 AATATTAA
49980648 AATATATAA
1 AATAT-TAA
49980657 AATA-TAA
1 AATATTAA
49980664 AATATTAA
1 AATATTAA
*
49980672 AATATCAA
1 AATATTAA
*
49980680 AATATTAG
1 AATATTAA
49980688 AATA
1 AATA
49980692 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:49980934 original size:28 final size:27
Alignment explanation
Indices: 49980895--49980954 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
49980885 TATAGTTAAG
*
49980895 ATATATACATAAGATAACATGTAAAAAT
1 ATATATAAATAAGATAACAT-TAAAAAT
* * *
49980923 ATATATAAATAATATAATATTAAAGAT
1 ATATATAAATAAGATAACATTAAAAAT
49980950 ATATA
1 ATATA
49980955 CATAAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATATAAATAAGATAACATTAAAAAT
Found at i:49980959 original size:25 final size:25
Alignment explanation
Indices: 49980836--49981056 Score: 122
Period size: 25 Copynumber: 9.0 Consensus size: 25
49980826 TAAATACGTG
* *
49980836 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
49980861 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
49980886 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
49980908 ATAACATGTAAAAATATATATAAATAAT
1 ATAATAT-T--AAAGATATATACATAAT
*
49980936 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * * *
49980961 ATAGTATAAAATATATATATACGTAAT
1 ATAATAT-TAA-AGATATATACATAAT
* *
49980988 ATAGA-ATTTAA-A-ATATACCTAAT
1 ATA-ATATTAAAGATATATACATAAT
* *
49981011 AT-AT-TAAAAGA-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
49981033 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
49981056 A
1 A
49981057 ACAAAAAGGA
Statistics
Matches: 152, Mismatches: 30, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
21 4 0.03
22 27 0.18
23 28 0.18
24 8 0.05
25 45 0.30
26 3 0.02
27 18 0.12
28 19 0.12
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:49981581 original size:30 final size:30
Alignment explanation
Indices: 49981545--49981659 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
49981535 TAGGTACAAG
* *
49981545 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
49981575 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
49981605 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
49981635 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
49981660 TGAGAAAAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:49982419 original size:20 final size:21
Alignment explanation
Indices: 49982394--49982432 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49982384 ATGATGTGAT
49982394 TAAAAATA-AATAAAATTTAG
1 TAAAAATACAATAAAATTTAG
*
49982414 TAAAAATACAATAATATTT
1 TAAAAATACAATAAAATTT
49982433 CATATTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAAAATACAATAAAATTTAG
Found at i:49985744 original size:13 final size:13
Alignment explanation
Indices: 49985724--49985757 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
49985714 TAAAATGTTA
49985724 ATAATTTAATAATT
1 ATAATTTAA-AATT
49985738 A-AATTTAAAATT
1 ATAATTTAAAATT
49985750 ATAATTTA
1 ATAATTTA
49985758 TACCCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 13 0.68
14 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAATTTAAAATT
Found at i:49989955 original size:19 final size:19
Alignment explanation
Indices: 49989928--49989964 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
49989918 GATCCATAAT
*
49989928 TTAATTTAAATTATAAAAA
1 TTAAATTAAATTATAAAAA
49989947 TTAAATTAAATTATAAAA
1 TTAAATTAAATTATAAAA
49989965 TATATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAATTAAATTATAAAAA
Found at i:50000142 original size:21 final size:21
Alignment explanation
Indices: 50000112--50000170 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
50000102 ATAATGTTAC
*
50000112 ATAAATATATACCTATATATAT
1 ATAAACATATA-CTATATATAT
*
50000134 -TAAAGATATA-TATATATAT
1 ATAAACATATACTATATATAT
50000153 ATAAACATATACTA-ATAT
1 ATAAACATATACTATATAT
50000171 CAATACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.27
20 13 0.39
21 11 0.33
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAAACATATACTATATATAT
Found at i:50001123 original size:16 final size:16
Alignment explanation
Indices: 50001102--50001144 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
50001092 AAAAAAAGAA
50001102 AGAAGGGAGAGAGGGG
1 AGAAGGGAGAGAGGGG
*
50001118 AGAAGGAAGAGAGGGG
1 AGAAGGGAGAGAGGGG
50001134 A-AAGGG-GAGAG
1 AGAAGGGAGAGAG
50001145 CTCCGGCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (16 bp):
AGAAGGGAGAGAGGGG
Found at i:50008048 original size:4 final size:4
Alignment explanation
Indices: 50008041--50008084 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
50008031 TATCTATACA
50008041 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50008085 AAATGATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:50008114 original size:15 final size:15
Alignment explanation
Indices: 50008091--50008120 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50008081 TATGAAATGA
50008091 TTTAATCTTCTTCTT
1 TTTAATCTTCTTCTT
*
50008106 TTTAGTCTTCTTCTT
1 TTTAATCTTCTTCTT
50008121 CCCTCTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTAATCTTCTTCTT
Found at i:50014934 original size:41 final size:41
Alignment explanation
Indices: 50014889--50014980 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
50014879 GGCTATGTGC
* * *
50014889 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATACCGGTGAAACAATTCAGACTATACGT
* * * *
50014930 CTAGCAGGCTTAATACCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATACCGGTGAAACAATTCAGACTATACGT
50014971 CTAGCAGGCT
1 CTAGCAGGCT
50014981 AAGAGCCGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATACCGGTGAAACAATTCAGACTATACGT
Found at i:50016962 original size:18 final size:18
Alignment explanation
Indices: 50016936--50016997 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
50016926 GGTGGTAGGG
*
50016936 TTTGGGTTTATTGTTGAT
1 TTTGAGTTTATTGTTGAT
* * * *
50016954 TTTGAGTTT-CTGGTAAGG
1 TTTGAGTTTATTGTTGA-T
*
50016972 TTTGGGTTTATTGTTGAT
1 TTTGAGTTTATTGTTGAT
50016990 TTTGAGTT
1 TTTGAGTT
50016998 CCTTCTTCTG
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
17 4 0.13
18 23 0.74
19 4 0.13
ACGTcount: A:0.13, C:0.02, G:0.29, T:0.56
Consensus pattern (18 bp):
TTTGAGTTTATTGTTGAT
Found at i:50016974 original size:36 final size:36
Alignment explanation
Indices: 50016928--50016997 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
50016918 GAGTTTAAGG
*
50016928 TGGTAGGGTTTGGGTTTATTGTTGATTTTGAGTTTC
1 TGGTAAGGTTTGGGTTTATTGTTGATTTTGAGTTTC
50016964 TGGTAAGGTTTGGGTTTATTGTTGATTTTGAGTT
1 TGGTAAGGTTTGGGTTTATTGTTGATTTTGAGTT
50016998 CCTTCTTCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.13, C:0.01, G:0.33, T:0.53
Consensus pattern (36 bp):
TGGTAAGGTTTGGGTTTATTGTTGATTTTGAGTTTC
Found at i:50023573 original size:33 final size:32
Alignment explanation
Indices: 50023536--50023611 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
50023526 AAATGAGAAT
50023536 AATAATAATAATAATAGT-AGTAAAAATATATAA
1 AATAATAATAATAATAGTGA-TAAAAATAT-TAA
* * * *
50023569 AATAAAAAAAATAATAGTGATAACAGTATTAA
1 AATAATAATAATAATAGTGATAAAAATATTAA
50023601 ACATAATAATA
1 A-ATAATAATA
50023612 GTAGTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 4 0.11
33 30 0.86
34 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.28
Consensus pattern (32 bp):
AATAATAATAATAATAGTGATAAAAATATTAA
Found at i:50025364 original size:22 final size:22
Alignment explanation
Indices: 50025336--50025378 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
50025326 CTCTAATCCT
50025336 CTCAATTTCCTTCCAAAATTCC
1 CTCAATTTCCTTCCAAAATTCC
50025358 CTCAATTTCCTTCCAAAATTC
1 CTCAATTTCCTTCCAAAATTC
50025379 TCTGAAACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCAATTTCCTTCCAAAATTCC
Found at i:50025456 original size:51 final size:50
Alignment explanation
Indices: 50025354--50025456 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
50025344 CCTTCCAAAA
* * **
50025354 TTCCCTCAATTTCCTTCCAAAATTCTCTGAAACCCATATTTAATTTCAAT
1 TTCCCTCAATTTCCTTCAAAAATTCTCTCAAACCCATATTTAAAATCAAT
* * *
50025404 TTCCTCTCAATTTCCTTCAAAAATTTTCTCAAATCCATTTTTTAAAAT-AAT
1 TTCC-CTCAATTTCCTTCAAAAATTCTCTCAAACCCA-TATTTAAAATCAAT
50025455 TT
1 TT
50025457 TAATTTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 33 0.75
52 7 0.16
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.44
Consensus pattern (50 bp):
TTCCCTCAATTTCCTTCAAAAATTCTCTCAAACCCATATTTAAAATCAAT
Found at i:50027673 original size:21 final size:21
Alignment explanation
Indices: 50027649--50027696 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
50027639 GATGCCGAAT
* *
50027649 CGGAAGAACCACAATCACCAC
1 CGGAAGAACAACAACCACCAC
* * *
50027670 CGGAGGAAGAACAACCACCGC
1 CGGAAGAACAACAACCACCAC
50027691 CGGAAG
1 CGGAAG
50027697 CTAGAGAATG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.33, G:0.25, T:0.02
Consensus pattern (21 bp):
CGGAAGAACAACAACCACCAC
Found at i:50027922 original size:29 final size:29
Alignment explanation
Indices: 50027880--50028070 Score: 332
Period size: 29 Copynumber: 6.7 Consensus size: 29
50027870 TATAATAAAA
50027880 TAAAAACCCTAACCCTAACCTAACTTAAT
1 TAAAAACCCTAACCCTAACCTAACTTAAT
50027909 TAAAAACCCTAACCCTAACCTAACTTAAT
1 TAAAAACCCTAACCCTAACCTAACTTAAT
*
50027938 TAAAAACCCTAACTCTAACCTAACTTAAT
1 TAAAAACCCTAACCCTAACCTAACTTAAT
* *
50027967 TAAAAACCCTAACCCTAACCTAA-TAAAA
1 TAAAAACCCTAACCCTAACCTAACTTAAT
*
50027995 TAAAAACCTTAACCCTAACCTAACTTAAT
1 TAAAAACCCTAACCCTAACCTAACTTAAT
50028024 TAAAAACCCTAACCCTAACCTAACTTAAT
1 TAAAAACCCTAACCCTAACCTAACTTAAT
50028053 TAAAAACCCTAA-CCTAAC
1 TAAAAACCCTAACCCTAAC
50028071 ATATTTTGAT
Statistics
Matches: 153, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
28 31 0.20
29 122 0.80
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.24
Consensus pattern (29 bp):
TAAAAACCCTAACCCTAACCTAACTTAAT
Found at i:50028026 original size:86 final size:87
Alignment explanation
Indices: 50027880--50028070 Score: 332
Period size: 86 Copynumber: 2.2 Consensus size: 87
50027870 TATAATAAAA
* *
50027880 TAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
1 TAAAAACCCTAACCCTAACCTAACTAAAATAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
*
50027945 CCTAACTCTAACCTAACTTAAT
66 CCTAACCCTAACCTAACTTAAT
*
50027967 TAAAAACCCTAACCCTAACCTAA-TAAAATAAAAACCTTAACCCTAACCTAACTTAATTAAAAAC
1 TAAAAACCCTAACCCTAACCTAACTAAAATAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
50028031 CCTAACCCTAACCTAACTTAAT
66 CCTAACCCTAACCTAACTTAAT
50028053 TAAAAACCCTAA-CCTAAC
1 TAAAAACCCTAACCCTAAC
50028071 ATATTTTGAT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 6 0.06
86 71 0.71
87 23 0.23
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.24
Consensus pattern (87 bp):
TAAAAACCCTAACCCTAACCTAACTAAAATAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
CCTAACCCTAACCTAACTTAAT
Found at i:50031480 original size:126 final size:126
Alignment explanation
Indices: 50031247--50031600 Score: 622
Period size: 126 Copynumber: 2.8 Consensus size: 126
50031237 CCCAAACTTG
*
50031247 CTACTGTAGCAAAATCGCGTCCACGAAGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
50031312 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAATAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAATAAAAAAATTATTTCTTACATGAC
* * *
50031373 CTGCTGTAGCAAAATCGCGTCCACGAGGGGGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
50031438 TAGAAACGATTTTATACTATTTGCTCAAAAACGTCAGA-AAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCA-ATAAAAAAATTATTTCTTACATGAC
50031499 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
50031564 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
50031601 CTCGAAATAA
Statistics
Matches: 215, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
125 1 0.00
126 212 0.99
127 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAATAAAAAAATTATTTCTTACATGAC
Found at i:50033117 original size:13 final size:13
Alignment explanation
Indices: 50033101--50033125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50033091 TAAATATATA
50033101 TTTTTATTTTTAT
1 TTTTTATTTTTAT
50033114 TTTTTATTTTTA
1 TTTTTATTTTTA
50033126 AAATACTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:50037299 original size:17 final size:17
Alignment explanation
Indices: 50037273--50037306 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
50037263 AGAAGCAAAA
*
50037273 GAAAATGAAAAAGAAAG
1 GAAAAAGAAAAAGAAAG
50037290 GAAAAAGAAAAAGAAAG
1 GAAAAAGAAAAAGAAAG
50037307 TTAAAGAATA
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:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAG
Found at i:50041646 original size:108 final size:108
Alignment explanation
Indices: 50041459--50041868 Score: 628
Period size: 108 Copynumber: 3.8 Consensus size: 108
50041449 AAAATTCAAG
* * * * * *
50041459 AGGATATTTGGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCATGTTCCTCA
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
*
50041522 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
50041565 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
*
50041630 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTCTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
*
50041673 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAACACCTTAGGGCACGTTCCTCG
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
*
50041738 AATTTCTAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
** * * *
50041781 AGGATATTTAGCCGTTTGGTTGAACGAGAAAGA-CAGACACCCAGCACCTTAGGGCATGTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATC-GACACCCAGCACCTTAGGGCACGTTCCTC
* * *
50041845 GAGTTTCCAAACGCTAAATATTGC
65 GAATTTCCAAACGCAAAACATTGC
50041869 ATCAATTAGA
Statistics
Matches: 280, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
106 25 0.09
107 1 0.00
108 254 0.91
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
Found at i:50044167 original size:44 final size:44
Alignment explanation
Indices: 50044117--50044500 Score: 284
Period size: 44 Copynumber: 8.8 Consensus size: 44
50044107 ACTTGATTCG
**
50044117 ATCTGCTCCACTGTAATCTCAATGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
* * * *
50044161 ATCTGCTCCACTGTAACCTCAGGGAGATAAGA-CT-T-GATGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
* * * * *
50044202 ATCTACTCCACTGTAATCTCAAGAAGATAAGATCACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
50044246 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
* * * * *
50044290 ATCTGCTCCACTATAACCTCAGGGAGATAAGATCTGAAAT-TCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTGGCTTCA
* * * * * * * *
50044336 GTCTACTCCACTGTAACCTCAGAGAGATATGA-C-CT-GATGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
* * * * *** *
50044377 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCA
* * ** * *
50044421 ATCCGCTCCACTGTAA-CTTCAGGGAGATAGGAT-AGTGTCTTCG
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCA
* * *
50044464 ATCTGCTCCGCCGTAATCTCAAGGAGATAAGATCTCT
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
50044501 AATATTCACC
Statistics
Matches: 267, Mismatches: 61, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
40 1 0.00
41 62 0.23
42 3 0.01
43 33 0.12
44 135 0.51
45 1 0.00
46 31 0.12
47 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
Found at i:50044195 original size:85 final size:83
Alignment explanation
Indices: 50044100--50044500 Score: 347
Period size: 85 Copynumber: 4.6 Consensus size: 83
50044090 CTGCTTAGGA
*
50044100 AGATAGGACTTGATTCGATCTGCTCCACTGTAATCTCAATGAGATAAGATCTCTGGCTTCAATCT
1 AGATAAGACTTGATTCGATCTGCTCCACTGTAATCTCAA-GAGATAAGATCTCT-GCTTCAATCT
50044165 GCTCCACTGTAACCTCAGGG
64 GCTCCACTGTAACCTCAGGG
* * *
50044185 AGATAAGACTTGATGCGATCTACTCCACTGTAATCTCAAGAAGATAAGATCACTAGCTTCAATCT
1 AGATAAGACTTGATTCGATCTGCTCCACTGTAATCTCAAG-AGATAAGATCTCT-GCTTCAATCT
*
50044250 GCTCCACTGTAATCTCAGGG
64 GCTCCACTGTAACCTCAGGG
* * * * * * *
50044270 AGATAAGATCTCTGGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATCTGAAATTCTTC
1 AGATAAGA-CT-T-GATTCGATCTGCTCCACTGTAATCTCA-AGAGATAAGATCT---CTGCTTC
** * *
50044335 GGTCTACTCCACTGTAACCTCAGAG
59 AATCTGCTCCACTGTAACCTCAGGG
* * * * * * ** *
50044360 AGATATGACCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTAATC
1 AGATAAGACTTGATTCGATCTGCTCCACTGTAATC-TCA-AGAGATAAGATC-TCTGCTTCAATC
* *
50044424 CGCTCCACTGTAACTTCAGGG
63 TGCTCCACTGTAACCTCAGGG
* * * *
50044445 AGATAGGA-TAGTGTCTTCGATCTGCTCCGCCGTAATCTCAAGGAGATAAGATCTCT
1 AGATAAGACT--TG-ATTCGATCTGCTCCACTGTAATCTCAA-GAGATAAGATCTCT
50044501 AATATTCACC
Statistics
Matches: 252, Mismatches: 49, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
84 1 0.00
85 114 0.45
86 8 0.03
87 61 0.24
88 34 0.13
89 2 0.01
90 31 0.12
91 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (83 bp):
AGATAAGACTTGATTCGATCTGCTCCACTGTAATCTCAAGAGATAAGATCTCTGCTTCAATCTGC
TCCACTGTAACCTCAGGG
Found at i:50044407 original size:175 final size:174
Alignment explanation
Indices: 50044166--50044498 Score: 422
Period size: 175 Copynumber: 1.9 Consensus size: 174
50044156 CTTCAATCTG
* *
50044166 CTCCACTGTAACCTCAGGGAGATAAGACTTGATGCGATCTACTCCACTGTAATCTCAAGAAGATA
1 CTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCTACTCCACTGTAATCTCAAGAAGATA
* *
50044231 AGATC-ACTAGCTTCAATCTGCTCCACTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCT
66 AGATCTACTA-CTTCAATCCGCTCCACTGTAACT-TCAGGGAGATAAGAT-ACTGGCTTCAATCT
* *
50044294 GCTCCACTATAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
128 GCTCCACCATAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTA
* *
50044341 CTCCACTGTAACCTCAGAGAGATATGACCTGATGCGATCTACTCTACTGTAA-CTTC-AGAGAGA
1 CTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCTACTCCACTGTAATC-TCAAGA-AGA
** * * * * * *
50044404 TAAGATCTTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTG
64 TAAGATCTACTACTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGATACTGGCTTCAATCTG
* * *
50044469 CTCCGCCGTAATCTCAAGGAGATAAGATCT
129 CTCCACCATAACCTCAAGGAGATAAGATCT
50044499 CTAATATTCA
Statistics
Matches: 135, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
174 40 0.30
175 92 0.68
176 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (174 bp):
CTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCTACTCCACTGTAATCTCAAGAAGATA
AGATCTACTACTTCAATCCGCTCCACTGTAACTTCAGGGAGATAAGATACTGGCTTCAATCTGCT
CCACCATAACCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTA
Found at i:50059226 original size:157 final size:153
Alignment explanation
Indices: 50058663--50059318 Score: 940
Period size: 157 Copynumber: 4.3 Consensus size: 153
50058653 NNNNNNNNNN
*
50058663 TTTTTT-CCAGATTTTATTAATTTC-AAAAATATACTATTTTCGTATTTTATTATTTTATATTAT
1 TTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTAT
* *
50058726 TTTAGTAC--AT-TATGAAATGTATTATTTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAATCC
66 TTTAGTACATATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAA-CC
*
50058788 C-TATTTTGGCC-TTTGTTCGTAT
130 CTTATTTTGGCCATTTGTTCATAT
*
50058810 TTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTTGTATTTTATTATTTTATATTAT
1 TTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTAT
*
50058875 TTTAGTACATATCGTTTGAAATGTATTAATTTAGTGT-TTTTTTATATAAATTTAGTAAAAAACC
66 TTTAGTACATAT-GTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAACC
*
50058939 CTTATTTTGGCCCTTTGTTCATATTTT
130 CTTATTTTGGCCATTTGTTCATA---T
* * *
50058966 TTTTTTCCC-GAATTTTATTACTTTC-AAAAATATA-TTTTTTTGAATTTTATTATTTTATATTA
1 TTTTTTCCCAG-ATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTA
* * * *
50059028 TTTTAGTACATTATATTTGAAATGTATTATTTTAATATGTTTTTTAAATAAATTTAGTAAAAAAC
65 TTTTAGTACA-TATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAAC
50059093 CCTTATTTTGGCCATTTGTTCATATTTT
129 CCTTATTTTGGCCATTTGTTCATA---T
* *
50059121 TCTTTTTCTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA-TTTATATTA
1 T-TTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTA
*
50059185 TTTTAGTACATAATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAATTTAGTAAAAAAC
65 TTTTAGTACAT-ATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAAC
* * *
50059250 CCTTATTTTGGCCATTTATTCGTAA
129 CCTTATTTTGGCCATTTGTTCATAT
50059275 TTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCG
1 TTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCG
50059319 AAAATATAAA
Statistics
Matches: 462, Mismatches: 28, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
147 6 0.01
148 17 0.04
149 46 0.10
151 5 0.01
152 34 0.07
153 71 0.15
154 57 0.12
155 66 0.14
156 46 0.10
157 99 0.21
158 15 0.03
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (153 bp):
TTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTAT
TTTAGTACATATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAACCC
TTATTTTGGCCATTTGTTCATAT
Found at i:50059231 original size:312 final size:301
Alignment explanation
Indices: 50058663--50059320 Score: 986
Period size: 312 Copynumber: 2.1 Consensus size: 301
50058653 NNNNNNNNNN
* * *
50058663 TTTTTTCCAG-ATTTTATTAATTTCAAAAATATACTATTTTCGTATTTTATTATTTTATATTATT
1 TTTTTTCCCGAATTTTATTACTTTCAAAAATATACTATTTTCGAATTTTATTATTTTATATTATT
* *
50058727 TTAGTACATTATGAAATGTATTATTTTAGTGTGTTTTTTAAATAAATTTAGTAAAAAATCCCTAT
66 TTAGTACATTATGAAATGTATTATTTTAATATGTTTTTTAAATAAATTTAGTAAAAAATCCCTAT
* *
50058792 TTTGGCCTTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTTGTAT
131 TTTGGCCTTTGTTCATATTTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
50058857 TTTATTATTTTATATTATTTTAGTACATATCGTTTGAAATGTATTAATTTAGTGTTTTTTTATAT
196 TTTATTATTTTATATTATTTTAGTACATATCGTTTGAAATGTATTAATTTAGTGTTTTTTTATAT
* * *
50058922 AAATTTAGTAAAAAACCCTTATTTTGGCCCTTTGTTCATATTTT
261 AAATTTAGTAAAAAACCCTTATTTTGGCCATTTATTCATA---A
* *
50058966 TTTTTTCCCGAATTTTATTACTTTCAAAAATATA-TTTTTTTGAATTTTATTATTTTATATTATT
1 TTTTTTCCCGAATTTTATTACTTTCAAAAATATACTATTTTCGAATTTTATTATTTTATATTATT
50059030 TTAGTACATTATATTTGAAATGTATTATTTTAATATGTTTTTTAAATAAATTTAGTAAAAAA-CC
66 TTAGTACA-T-TA--TGAAATGTATTATTTTAATATGTTTTTTAAATAAATTTAGTAAAAAATCC
* *
50059094 CTTATTTTGGCCATTTGTTCATATTTTTCTTTTTCTCGGATTTTATTACTTTCAAAAAATATACT
127 C-TATTTTGGCC-TTTGTTCATA---TT-TTTTTCCCAGATTTTATTACTTTCAAAAAATATACT
50059159 ATTTTCGTATTTTATTA-TTTATATTATTTTAGTACATAAT-GTTTGAAATGTATTAATTTAGTG
186 ATTTTCGTATTTTATTATTTTATATTATTTTAGTACAT-ATCGTTTGAAATGTATTAATTTAGTG
*
50059222 TGTTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCATTTATTCGTAA
250 T-TTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCATTTATTCATAA
50059275 TTTTTTCCC-AGATTTTATTACTTTCAAAAAATATACTATTTTCGAA
1 TTTTTTCCCGA-ATTTTATTACTTTC-AAAAATATACTATTTTCGAA
50059321 AATATAAAAA
Statistics
Matches: 322, Mismatches: 17, Indels: 24
0.89 0.05 0.07
Matches are distributed among these distances:
303 44 0.14
304 23 0.07
305 2 0.01
306 3 0.01
307 55 0.17
308 10 0.03
309 23 0.07
310 9 0.03
311 54 0.17
312 99 0.31
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (301 bp):
TTTTTTCCCGAATTTTATTACTTTCAAAAATATACTATTTTCGAATTTTATTATTTTATATTATT
TTAGTACATTATGAAATGTATTATTTTAATATGTTTTTTAAATAAATTTAGTAAAAAATCCCTAT
TTTGGCCTTTGTTCATATTTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTAT
TTTATTATTTTATATTATTTTAGTACATATCGTTTGAAATGTATTAATTTAGTGTTTTTTTATAT
AAATTTAGTAAAAAACCCTTATTTTGGCCATTTATTCATAA
Found at i:50059551 original size:16 final size:15
Alignment explanation
Indices: 50059520--50059561 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
50059510 ACAAAATCAA
*
50059520 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
50059535 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
50059551 ATAAAAATTAA
1 ATAAAAGTTAA
50059562 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:50059738 original size:1 final size:1
Alignment explanation
Indices: 50059732--50059828 Score: 113
Period size: 1 Copynumber: 97.0 Consensus size: 1
50059722 ATCATTACAC
** * * *** * *
50059732 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTATAATACTCATACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50059797 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50059829 TTACGATATT
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.91, C:0.03, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:50059803 original size:60 final size:60
Alignment explanation
Indices: 50059714--50059828 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
50059704 AAACTATAAT
*
50059714 ATTACAATATCATTACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 ATTACAATATCATTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
50059774 ATTATAATACTCA-TACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 ATTACAATA-TCATTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50059829 TTACGATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 49 0.94
61 3 0.06
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.10
Consensus pattern (60 bp):
ATTACAATATCATTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:50059910 original size:19 final size:19
Alignment explanation
Indices: 50059865--50059941 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
50059855 AACAACAAAC
*
50059865 AATATTCATAACAACATTA-
1 AATATTCATAA-AAAATTAT
*
50059884 CA-ATTCATAAAAAATTAT
1 AATATTCATAAAAAATTAT
* *
50059902 AATATTCATAAAAAAGTAA
1 AATATTCATAAAAAATTAT
* *
50059921 AATATTC-TACAAAATTCT
1 AATATTCATAAAAAATTAT
50059939 AAT
1 AAT
50059942 CTAACTATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
17 6 0.13
18 19 0.40
19 22 0.47
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (19 bp):
AATATTCATAAAAAATTAT
Found at i:50060090 original size:17 final size:16
Alignment explanation
Indices: 50060064--50060095 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
50060054 CATTTCCTTT
50060064 TCTTTCTTTCTTCTTC
1 TCTTTCTTTCTTCTTC
50060080 TCTTCTCTTTCTTCTT
1 TCTT-TCTTTCTTCTT
50060096 TTTTTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTTTCTTTCTTCTTC
Done.