Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 161 of 235
Found at i:54357150 original size:16 final size:16
Alignment explanation
Indices: 54357125--54357156 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54357115 ATGTGATCCA
54357125 AAAATCATATTTTTGC
1 AAAATCATATTTTTGC
*
54357141 AAAATTATATTTTTGC
1 AAAATCATATTTTTGC
54357157 CCCTAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
AAAATCATATTTTTGC
Found at i:54358610 original size:20 final size:19
Alignment explanation
Indices: 54358565--54358610 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
54358555 ATACTCACAA
54358565 ATTA-ATTAAATAAATAAC
1 ATTATATTAAATAAATAAC
* *
54358583 ATTTTATTAAAGTAAATAAT
1 ATTATATTAAA-TAAATAAC
54358603 ATTATATT
1 ATTATATT
54358611 TCAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 3 0.13
19 6 0.26
20 14 0.61
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTATATTAAATAAATAAC
Found at i:54364262 original size:117 final size:117
Alignment explanation
Indices: 54364056--54364291 Score: 445
Period size: 117 Copynumber: 2.0 Consensus size: 117
54364046 TACTTAGTAG
*
54364056 TGTTTGTGATTTAATTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGCTTTTCAAGCATA
1 TGTTTGTAATTTAATTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGCTTTTCAAGCATA
54364121 ACTATTTCATAGTTTCTTATTTTGGTAATTGGTTTGAGGGAGGACCCATGCA
66 ACTATTTCATAGTTTCTTATTTTGGTAATTGGTTTGAGGGAGGACCCATGCA
* *
54364173 TGTTTGTAATTTAGTTCGTAGCCATGATTTTCTTGGATGACTAGTTTTGGAGCTTTTCAAGCATA
1 TGTTTGTAATTTAATTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGCTTTTCAAGCATA
54364238 ACTATTTCATAGTTTCTTATTTTGGTAATTGGTTTGAGGGAGGACCCATGCA
66 ACTATTTCATAGTTTCTTATTTTGGTAATTGGTTTGAGGGAGGACCCATGCA
54364290 TG
1 TG
54364292 ATTATAATGA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (117 bp):
TGTTTGTAATTTAATTCGTAGCCATGATTTTCTTGGATGACTAGTGTTGGAGCTTTTCAAGCATA
ACTATTTCATAGTTTCTTATTTTGGTAATTGGTTTGAGGGAGGACCCATGCA
Found at i:54367060 original size:31 final size:31
Alignment explanation
Indices: 54367022--54367085 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
54367012 CTCGTCACAC
54367022 GTTATGTTCATTTACAACCGTACATTTAGGA
1 GTTATGTTCATTTACAACCGTACATTTAGGA
54367053 GTTATGTTCATTTACAACCGTACATTTAGGA
1 GTTATGTTCATTTACAACCGTACATTTAGGA
54367084 GT
1 GT
54367086 GAGCAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (31 bp):
GTTATGTTCATTTACAACCGTACATTTAGGA
Found at i:54377032 original size:18 final size:18
Alignment explanation
Indices: 54376998--54377347 Score: 194
Period size: 18 Copynumber: 19.1 Consensus size: 18
54376988 TCATTAACAA
* *
54376998 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAATTAT
* *
54377015 TCAGTAACAGTCACTTAT
1 TCAGTAACAATCAATTAT
*
54377033 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* *
54377051 TCAATAATAA-CAAATTAT
1 TCAGTAACAATC-AATTAT
*
54377069 TCAGTATCAATCAATTGATCGGTT
1 TCAGTAACAATCAATT-A-----T
54377093 ATCCAGTAACAATCAATTAT
1 -T-CAGTAACAATCAATTAT
*
54377113 TTAGTAA-AATC-ATATAT
1 TCAGTAACAATCAAT-TAT
* * *
54377130 TCAATAGCAATTAAGTTAT
1 TCAGTAACAATCAA-TTAT
* *
54377149 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
*
54377167 TTAGTAA-AATC-ATATAT
1 TCAGTAACAATCAAT-TAT
* * *
54377184 TCAATAGCAATTAAGTTAT
1 TCAGTAACAATCAA-TTAT
* * *
54377203 TCAGTAACAGTTATTTAT
1 TCAGTAACAATCAATTAT
* *
54377221 TCAGTGACAATCAGTTAT
1 TCAGTAACAATCAATTAT
**
54377239 TCAGTAATGATCAATTAT
1 TCAGTAACAATCAATTAT
* * *
54377257 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTAT
* *
54377275 TCAGTAACAGTCTATTA-
1 TCAGTAACAATCAATTAT
54377292 TCTAGTAACAGA-CAATTAT
1 TC-AGTAACA-ATCAATTAT
* * *
54377311 TCGGTAATAGTCAATTAT
1 TCAGTAACAATCAATTAT
* *
54377329 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTAT
54377347 T
1 T
54377348 TTATACCTTT
Statistics
Matches: 253, Mismatches: 57, Indels: 45
0.71 0.16 0.13
Matches are distributed among these distances:
16 4 0.02
17 28 0.11
18 169 0.67
19 32 0.13
20 3 0.01
24 1 0.00
25 2 0.01
26 14 0.06
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (18 bp):
TCAGTAACAATCAATTAT
Found at i:54377221 original size:54 final size:54
Alignment explanation
Indices: 54377090--54377213 Score: 230
Period size: 54 Copynumber: 2.3 Consensus size: 54
54377080 CAATTGATCG
*
54377090 GTTATCCAGTAACAATCAATTATTTAGTAAAATCATATATTCAATAGCAATTAA
1 GTTATCCAGTAACAGTCAATTATTTAGTAAAATCATATATTCAATAGCAATTAA
54377144 GTTATCCAGTAACAGTCAATTATTTAGTAAAATCATATATTCAATAGCAATTAA
1 GTTATCCAGTAACAGTCAATTATTTAGTAAAATCATATATTCAATAGCAATTAA
*
54377198 GTTATTCAGTAACAGT
1 GTTATCCAGTAACAGT
54377214 TATTTATTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (54 bp):
GTTATCCAGTAACAGTCAATTATTTAGTAAAATCATATATTCAATAGCAATTAA
Found at i:54377603 original size:45 final size:45
Alignment explanation
Indices: 54377516--54377625 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
54377506 TCTGGAACAG
* * *
54377516 TAACAGTAATAGTAACAGTATTCAACACATAAAGCGCTGAATCGA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGCGCCGAATCGA
* * * *
54377561 TAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGG
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGCGCCGAATCGA
*
54377606 TAACAGTAACGGTAACAGTA
1 TAACAGTAACAGTAACAGTA
54377626 ACAGTAGTCG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGCGCCGAATCGA
Found at i:54377616 original size:51 final size:48
Alignment explanation
Indices: 54377510--54377648 Score: 142
Period size: 45 Copynumber: 2.9 Consensus size: 48
54377500 AACAAATCTG
* * * * *
54377510 GAACAGTAACAGTAATAGTAACAGTATTCAACACATAAAGCGCTGAATC
1 GAACAGTAACGGTAACAGTAACAGTATTCGACACA-AAAGTGCCGAATC
54377559 G---A-TAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
1 GAACAGTAACGGTAACAGTAACAGTATTCGACACA-AAAGTGCCGAATC
* * *
54377604 GGTAACAGTAACGGTAACAGTAACAGTAGTCGGCACATAAGTGCC
1 -G-AACAGTAACGGTAACAGTAACAGTATTCGACACAAAAGTGCC
54377649 TGATCAGTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
45 37 0.49
46 2 0.03
49 1 0.01
50 8 0.11
51 27 0.36
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (48 bp):
GAACAGTAACGGTAACAGTAACAGTATTCGACACAAAAGTGCCGAATC
Found at i:54377620 original size:12 final size:12
Alignment explanation
Indices: 54377603--54377627 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54377593 AGTGCCGAAT
54377603 CGGTAACAGTAA
1 CGGTAACAGTAA
54377615 CGGTAACAGTAA
1 CGGTAACAGTAA
54377627 C
1 C
54377628 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:54379368 original size:5 final size:5
Alignment explanation
Indices: 54379358--54379420 Score: 117
Period size: 5 Copynumber: 12.4 Consensus size: 5
54379348 TTACTTATTT
54379358 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
54379408 ATATA ATAATA AT
1 ATATA AT-ATA AT
54379421 TTCTTATATT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 52 0.91
6 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:54379547 original size:21 final size:22
Alignment explanation
Indices: 54379508--54379560 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
54379498 CATACAATTG
*
54379508 TTAAAATAATATTATAATATCA
1 TTAAAATAATATTACAATATCA
*
54379530 TTAATATAA-ATTACAATAT-A
1 TTAAAATAATATTACAATATCA
*
54379550 ATAAAATAATA
1 TTAAAATAATA
54379561 ATATAGTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 10 0.38
22 8 0.31
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAAATAATATTACAATATCA
Found at i:54383994 original size:18 final size:18
Alignment explanation
Indices: 54383962--54384257 Score: 121
Period size: 18 Copynumber: 16.1 Consensus size: 18
54383952 TCATTAACAA
*
54383962 TCAG-AACAATTATTTAT
1 TCAGTAACAATCATTTAT
*
54383979 TCAGTAACAGTCATTTAT
1 TCAGTAACAATCATTTAT
* *
54383997 TCGGTAACAATCAATTAT
1 TCAGTAACAATCATTTAT
* * * *
54384015 TCAATAATAACCAATTAT
1 TCAGTAACAATCATTTAT
* *
54384033 TTAGTATCAATCAATTGATCGGTTAT
1 TCAG--T-AA-CAA-TCAT---TTAT
* * * *
54384059 CCAGTAATAGTCAATTAT
1 TCAGTAACAATCATTTAT
* **
54384077 TTAGTAA-AATCAGATAT
1 TCAGTAACAATCATTTAT
* ** * *
54384094 TCAATAGTAATTAAGTTAT
1 TCAGTAACAA-TCATTTAT
* *
54384113 TCAGTAACAGTCATCTAT
1 TCAGTAACAATCATTTAT
* *
54384131 TCAGTGACAATCAGTTAT
1 TCAGTAACAATCATTTAT
** *
54384149 TCAGTAATGATCAATTAT
1 TCAGTAACAATCATTTAT
* * *
54384167 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCATTTAT
*
54384185 TCAGTAACAGTC-TATTAT
1 TCAGTAACAATCAT-TTAT
* * *
54384203 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCATTTAT
* *
54384221 TCAGTAACAGTCAATTAT
1 TCAGTAACAATCATTTAT
* *
54384239 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCATTTAT
54384257 T
1 T
54384258 TTATTCCTTT
Statistics
Matches: 208, Mismatches: 58, Indels: 25
0.71 0.20 0.09
Matches are distributed among these distances:
17 15 0.07
18 163 0.78
19 12 0.06
20 1 0.00
21 4 0.02
22 3 0.01
23 3 0.01
24 1 0.00
26 6 0.03
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (18 bp):
TCAGTAACAATCATTTAT
Found at i:54384015 original size:36 final size:36
Alignment explanation
Indices: 54383962--54384245 Score: 171
Period size: 36 Copynumber: 7.7 Consensus size: 36
54383952 TCATTAACAA
* * *
54383962 TCAG-AACAATTATTTATTCAGTAACAGTCATTTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAATTAT
* * * **
54383997 TCGGTAACAATCAATTATTCAATAATAACCAATTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAATTAT
* * *
54384033 TTAGTATCAATCAATTGATCGGTTATCCAGTAATAGTCAATTAT
1 TCAGTAACAATCAATT-A-----T-T-CAGTAACAGTCAATTAT
* * ** * *
54384077 TTAGTAA-AATCAGA-TATTCAATAGTAATTAAGTTAT
1 TCAGTAACAATCA-ATTATTCAGTAACAGTCAA-TTAT
* * * *
54384113 TCAGTAACAGTC-ATCTATTCAGTGACAATCAGTTAT
1 TCAGTAACAATCAAT-TATTCAGTAACAGTCAATTAT
** * * *
54384149 TCAGTAATGATCAATTATTCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAATTAT
* * *
54384185 TCAGTAACAGTCTATTATCCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAATTAT
*
54384221 TCAGTAACAGTCAATTATTCAGTAA
1 TCAGTAACAATCAATTATTCAGTAA
54384246 TAATCAGTTA
Statistics
Matches: 191, Mismatches: 43, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
35 13 0.07
36 130 0.68
37 18 0.09
42 2 0.01
43 7 0.04
44 21 0.11
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (36 bp):
TCAGTAACAATCAATTATTCAGTAACAGTCAATTAT
Found at i:54384112 original size:54 final size:54
Alignment explanation
Indices: 54384054--54384257 Score: 164
Period size: 54 Copynumber: 3.8 Consensus size: 54
54384044 CAATTGATCG
* * * *
54384054 GTTATCCAGTAATAGTCAATTATTTAGTAAAATCAGATATTCAATAGTAATTAA
1 GTTATTCAGTAATAGTCAATTATTCAGTAAAATCAGATATTCAATAATAATCAA
* * * * *
54384108 GTTATTCAGTAACAGTC-ATCTATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 GTTATTCAGTAATAGTCAAT-TATTCAGT-AAAATCAGATATTCAATAATAATCAA
* * * * * * * *
54384163 -TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-TTATCCAGTAACAGTCAA
1 GTTATTCAGTAATAGTCAATTATTCAGTAA-AATC-AGATATTCAATAATAATCAA
* *
54384217 -TTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 GTTATTCAGTAATAGTCAATTATTCAGTAA-AATCAGATATT
54384258 TTATTCCTTT
Statistics
Matches: 120, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
53 4 0.03
54 94 0.78
55 22 0.18
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (54 bp):
GTTATTCAGTAATAGTCAATTATTCAGTAAAATCAGATATTCAATAATAATCAA
Found at i:54384190 original size:72 final size:72
Alignment explanation
Indices: 54384055--54384257 Score: 225
Period size: 72 Copynumber: 2.8 Consensus size: 72
54384045 AATTGATCGG
* * * * * * *
54384055 TTATCCAGTAATAGTCAATTATTTAGTAA-AATCAGA-TATTCAATAGTAATTAAGTTATTCAGT
1 TTATCCAGTAACAATCAATTATTCAGTAACAGTCA-ATTATTCAGTAATAA-TCAGTTATTCAGT
54384118 AACAGTC-A
64 AACAGTCTA
* * * * *
54384126 TCTATTCAGTGACAATCAGTTATTCAGTAA-TGATCAATTATTCAGTAATATTCAGTTATTCAGT
1 T-TATCCAGTAACAATCAATTATTCAGTAACAG-TCAATTATTCAGTAATAATCAGTTATTCAGT
54384190 AACAGTCTA
64 AACAGTCTA
*
54384199 TTATCCAGTAACAGTCAATTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TTATCCAGTAACAATCAATTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
54384258 TTATTCCTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
71 1 0.01
72 92 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (72 bp):
TTATCCAGTAACAATCAATTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATTCAGTAA
CAGTCTA
Found at i:54384257 original size:36 final size:36
Alignment explanation
Indices: 54384055--54384257 Score: 189
Period size: 36 Copynumber: 5.6 Consensus size: 36
54384045 AATTGATCGG
* * * * *
54384055 TTATCCAGTAATAGTCAATTATTTAGTAA-AATCAGA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCA-A
* * *
54384091 -TATTCAATAGTAATTAAGTTATTCAGTAACAGTC-A
1 TTATTCAGTAATAA-TCAGTTATTCAGTAACAGTCAA
* * *
54384126 TCTATTCAGTGACAATCAGTTATTCAGTAA-TGATCAA
1 T-TATTCAGTAATAATCAGTTATTCAGTAACAG-TCAA
* *
54384163 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCAA
* * * *
54384199 TTATCCAGTAACAGTCAATTATTCAGTAACAGTCAA
1 TTATTCAGTAATAATCAGTTATTCAGTAACAGTCAA
54384235 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAATAATCAGTTATT
54384258 TTATTCCTTT
Statistics
Matches: 132, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
35 11 0.08
36 106 0.80
37 15 0.11
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (36 bp):
TTATTCAGTAATAATCAGTTATTCAGTAACAGTCAA
Found at i:54384484 original size:45 final size:45
Alignment explanation
Indices: 54384428--54384537 Score: 175
Period size: 45 Copynumber: 2.4 Consensus size: 45
54384418 TCCAGAACAG
* *
54384428 TAACAGTAACAGTAATAGTATTCAACACACAAAGTGCTGAATCGA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
* *
54384473 TAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
*
54384518 TAACAGTAACGGTAACAGTA
1 TAACAGTAACAGTAACAGTA
54384538 ACAGTAGTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGA
Found at i:54384528 original size:51 final size:49
Alignment explanation
Indices: 54384422--54384565 Score: 163
Period size: 45 Copynumber: 3.0 Consensus size: 49
54384412 AACAAATCCA
* * * *
54384422 GAACAGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGCTGAATC
1 GAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
54384471 G---A-TAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
1 GAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
* * * *
54384516 GATAACAGTAACGGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTAATC
1 G--AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
54384566 AGTAAGCCGG
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
45 40 0.49
46 1 0.01
49 1 0.01
50 12 0.15
51 27 0.33
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.19
Consensus pattern (49 bp):
GAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
Found at i:54386292 original size:7 final size:7
Alignment explanation
Indices: 54386280--54386330 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
54386270 TTTACTTATT
54386280 TATATAA
1 TATATAA
54386287 TATAT-A
1 TATATAA
54386293 -ATATAA
1 TATATAA
54386299 TATATAA
1 TATATAA
54386306 TATA-ATA
1 TATATA-A
54386313 TAATATAA
1 T-ATATAA
54386321 TA-ATAA
1 TATATAA
54386327 TATA
1 TATA
54386331 ATATAATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
5 4 0.11
6 9 0.24
7 19 0.50
8 5 0.13
9 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:54386296 original size:5 final size:5
Alignment explanation
Indices: 54386288--54386338 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
54386278 TTTATATAAT
54386288 ATATA ATATAA TATATA ATATA ATATA ATATA ATAATA ATATA ATATA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
54386336 ATA
1 ATA
54386339 ACAATTCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 32 0.74
6 7 0.16
7 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:54386298 original size:12 final size:12
Alignment explanation
Indices: 54386281--54386335 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
54386271 TTACTTATTT
54386281 ATATAATATATA
1 ATATAATATATA
54386293 ATATAATATATA
1 ATATAATATATA
54386305 ATAT-A-ATATA
1 ATATAATATATA
54386315 ATATAATA-ATA
1 ATATAATATATA
54386326 ATATAATATA
1 ATATAATATA
54386336 ATAACAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.22
11 13 0.32
12 18 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATAATATATA
Found at i:54386325 original size:3 final size:3
Alignment explanation
Indices: 54386283--54386339 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
54386273 ACTTATTTAT
54386283 ATA ATA TATA AT- ATA ATA TATA AT- ATA AT- ATA AT- ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
54386326 AT- ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA A
54386340 CAATTCTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
2 12 0.26
3 28 0.61
4 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:54387647 original size:43 final size:43
Alignment explanation
Indices: 54387586--54387726 Score: 196
Period size: 43 Copynumber: 3.3 Consensus size: 43
54387576 ATTTGAAAAG
* * * *
54387586 ACGCCGCTAATGATCAGGACCTTTAGCGGCGCTTTTCCAACAA
1 ACGCCGCTAAAGGTCAGGACCTTTAGCGACGCTTTTCCCACAA
* *
54387629 ACGCCGCTAAAGGTCAGGACCTTTCGCGACGC-TTTCCCACAG
1 ACGCCGCTAAAGGTCAGGACCTTTAGCGACGCTTTTCCCACAA
* *
54387671 ACG-CTCTAAAGGTTAGGACCTTTAGCGACGCTTTTCCCACAA
1 ACGCCGCTAAAGGTCAGGACCTTTAGCGACGCTTTTCCCACAA
54387713 ACGCCGCTAAAGGT
1 ACGCCGCTAAAGGT
54387727 TATAAAAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 25 0.29
42 23 0.27
43 37 0.44
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (43 bp):
ACGCCGCTAAAGGTCAGGACCTTTAGCGACGCTTTTCCCACAA
Found at i:54387749 original size:16 final size:17
Alignment explanation
Indices: 54387728--54387760 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54387718 GCTAAAGGTT
*
54387728 ATAAAA-ATTTTAAAAA
1 ATAAAATATTATAAAAA
54387744 ATAAAATATTATAAAAA
1 ATAAAATATTATAAAAA
54387761 TGTCCTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATATTATAAAAA
Found at i:54388400 original size:12 final size:12
Alignment explanation
Indices: 54388383--54388415 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
54388373 TTGAAGAACC
54388383 ATTAATCATGTT
1 ATTAATCATGTT
54388395 ATTAATCATGTT
1 ATTAATCATGTT
54388407 ATTAATCAT
1 ATTAATCAT
54388416 ATATGCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
ATTAATCATGTT
Found at i:54391987 original size:15 final size:15
Alignment explanation
Indices: 54391940--54391988 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
54391930 CCCCTATCAC
*
54391940 CACCTCTTCCACCAC
1 CACCTCTTCCACCAT
* *
54391955 CTCCTCTTCC-TC-T
1 CACCTCTTCCACCAT
54391968 C-CCTCTTCCACCAT
1 CACCTCTTCCACCAT
54391982 CACCTCT
1 CACCTCT
54391989 GCCCCTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 3 0.11
15 14 0.52
ACGTcount: A:0.12, C:0.57, G:0.00, T:0.31
Consensus pattern (15 bp):
CACCTCTTCCACCAT
Found at i:54392475 original size:23 final size:23
Alignment explanation
Indices: 54392456--54392518 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
54392446 TAAAAAATGC
54392456 TAATACAATTACATATAAAATTT
1 TAATACAATTACATATAAAATTT
*
54392479 TAATA-AATATAAAT-TAAAAATTT
1 TAATACAAT-TACATAT-AAAATTT
54392502 TAATACAATTACATATA
1 TAATACAATTACATATA
54392519 TAGGATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATACAATTACATATAAAATTT
Found at i:54392538 original size:46 final size:46
Alignment explanation
Indices: 54392456--54392545 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
54392446 TAAAAAATGC
*
54392456 TAATACAATTACATATAAAATTTTAATAAATATAAATTAAAAATTT
1 TAATACAATTACATATAAAATATTAATAAATATAAATTAAAAATTT
* *
54392502 TAATACAATTACATATATAGGATATTAA-ATAT-TAAATTAAAAAT
1 TAATACAATTACATATA-A-AATATTAATAAATATAAATTAAAAAT
54392546 AATATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 29 0.74
47 4 0.10
48 6 0.15
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (46 bp):
TAATACAATTACATATAAAATATTAATAAATATAAATTAAAAATTT
Found at i:54392819 original size:17 final size:17
Alignment explanation
Indices: 54392774--54392819 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
54392764 CGAGCATGAG
*
54392774 AAAAA-GAAAACATTTC
1 AAAAAGGAAAACGTTTC
54392790 AAAAAGGAAAACGTTTC
1 AAAAAGGAAAACGTTTC
54392807 AAAAAGGAAAACG
1 AAAAAGGAAAACG
54392820 ACCCCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 5 0.18
17 23 0.82
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.13
Consensus pattern (17 bp):
AAAAAGGAAAACGTTTC
Found at i:54393713 original size:7 final size:7
Alignment explanation
Indices: 54393701--54393805 Score: 63
Period size: 7 Copynumber: 14.7 Consensus size: 7
54393691 ACTAATTAAT
54393701 CTAAACC
1 CTAAACC
54393708 CTAAACC
1 CTAAACC
*
54393715 TCTTAACCC
1 -C-TAAACC
*
54393724 CT-ATCC
1 CTAAACC
*
54393730 CATAAACA
1 C-TAAACC
*
54393738 CTAAACT
1 CTAAACC
54393745 CTAAACC
1 CTAAACC
*
54393752 CTTAACC
1 CTAAACC
*
54393759 CCAAACC
1 CTAAACC
*
54393766 CTTACACC
1 C-TAAACC
* *
54393774 TTAAACT
1 CTAAACC
54393781 CT-AACC
1 CTAAACC
54393787 CT-AACAC
1 CTAAAC-C
54393794 CTAAACC
1 CTAAACC
54393801 CTAAA
1 CTAAA
54393806 TCATAATCCT
Statistics
Matches: 75, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
6 12 0.16
7 46 0.61
8 12 0.16
9 5 0.07
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:54393779 original size:36 final size:36
Alignment explanation
Indices: 54393701--54393802 Score: 102
Period size: 36 Copynumber: 2.8 Consensus size: 36
54393691 ACTAATTAAT
* * * *
54393701 CTAAACCCTAAACCTCTTAACCCCTATCCCATAAACA
1 CTAAACTCTAAACC-CTTAACCCCAAACCCTTAAACA
*
54393738 CTAAACTCTAAACCCTTAACCCCAAACCCTTACAC-
1 CTAAACTCTAAACCCTTAACCCCAAACCCTTAAACA
*
54393773 CTTAAACTCT-AACCC-TAACACCTAAACCCT
1 C-TAAACTCTAAACCCTTAAC-CCCAAACCCT
54393803 AAATCATAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.07
35 15 0.26
36 25 0.44
37 13 0.23
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (36 bp):
CTAAACTCTAAACCCTTAACCCCAAACCCTTAAACA
Found at i:54394059 original size:40 final size:41
Alignment explanation
Indices: 54393864--54394098 Score: 312
Period size: 41 Copynumber: 5.8 Consensus size: 41
54393854 AACTCCTAAA
* ** **
54393864 GCCGCTAATGCTCTGGTCATTAGCGGCGTTTTTTCGTAAGC
1 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
* * * **
54393905 GCCGCTAATGCTTTGGTCATTAGCGGCGTTTTTCCGTAAGC
1 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
*
54393946 GCCGCTAATGCTCTGGTCTTTAGCGGCATTTTACCAAAAGC
1 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
*
54393987 GCTGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
1 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
* *
54394028 GCCGCTAATGCTC-AGTCTTTAGCGGCATTTTACCAAAAGC
1 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
* *
54394068 GTCGCTAATGCTC-AGTCTTTAGCGGCGTTTT
1 GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTT
54394099 TTACTAAAAC
Statistics
Matches: 179, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
40 54 0.30
41 125 0.70
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
GCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGC
Found at i:54394121 original size:81 final size:81
Alignment explanation
Indices: 54393901--54394140 Score: 252
Period size: 81 Copynumber: 3.0 Consensus size: 81
54393891 GTTTTTTCGT
* * * * * ** ** *
54393901 AAGCGCCGCTAATGCTTTGGTCATTAGCGGCGTTTTTCCGTAAGCGCCGCTAATGCTCTGGTCTT
1 AAGCGCTGCTAATGCTCTAGTCTTTAGCGGCGTTTTACCAAAAGCAACGCTAATGCTC-AGTCTT
54393966 TAGCGGCATTTTACCAA
65 TAGCGGCATTTTACCAA
* **
54393983 AAGCGCTGCTAATGCTCTGGTCTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCAGTCTTT
1 AAGCGCTGCTAATGCTCTAGTCTTTAGCGGCGTTTTACCAAAAGCAACGCTAATGCTCAGTCTTT
54394048 AGCGGCATTTTACCAA
66 AGCGGCATTTTACCAA
* ** * *
54394064 AAGCG-TCGCTAATGCTC-AGTCTTTAGCGGCGTTTTTTACTAAAA-CAACGCTGTTGCTCTGTT
1 AAGCGCT-GCTAATGCTCTAGTCTTTAGCGGCG--TTTTACCAAAAGCAACGCTAATGCTCAGTC
*
54394126 TTTAGCGGCGTTTTA
63 TTTAGCGGCATTTTA
54394141 TAAAGCCCTA
Statistics
Matches: 139, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
80 14 0.10
81 63 0.45
82 62 0.45
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (81 bp):
AAGCGCTGCTAATGCTCTAGTCTTTAGCGGCGTTTTACCAAAAGCAACGCTAATGCTCAGTCTTT
AGCGGCATTTTACCAA
Found at i:54394305 original size:20 final size:21
Alignment explanation
Indices: 54394273--54394314 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
54394263 CTAAACCGAT
*
54394273 AACTTAGGAAAATTTTTGAAA
1 AACTTAGGAAAATTTTTCAAA
54394294 AACTTA-GAAAATTTTTCAAA
1 AACTTAGGAAAATTTTTCAAA
54394314 A
1 A
54394315 TACAGGGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AACTTAGGAAAATTTTTCAAA
Found at i:54398439 original size:13 final size:13
Alignment explanation
Indices: 54398421--54398448 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54398411 GGTACCTTGG
54398421 AGAATTTCTATCA
1 AGAATTTCTATCA
54398434 AGAATTTCTATCA
1 AGAATTTCTATCA
54398447 AG
1 AG
54398449 GATTCTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (13 bp):
AGAATTTCTATCA
Found at i:54401154 original size:40 final size:40
Alignment explanation
Indices: 54401108--54401289 Score: 265
Period size: 40 Copynumber: 4.5 Consensus size: 40
54401098 TTATACTCTT
* * *
54401108 TGTTTGGTGTGTTTTGGTTGGATCAGCTCTTATAAGCTTC
1 TGTTTGGTGTGTTTCGGTTGGATCAGATCTTATGAGCTTC
* ** *
54401148 TATTTGGCATGTTTCGGTTCGATCAGATCTTATGAGCTTC
1 TGTTTGGTGTGTTTCGGTTGGATCAGATCTTATGAGCTTC
*
54401188 TGTTTGGTGTGTTTCGGTTGGATCAAATCTTATGAGCTTC
1 TGTTTGGTGTGTTTCGGTTGGATCAGATCTTATGAGCTTC
* *
54401228 TGTTTGGTGTGTTTCAGTTGGATCAGCTCTTATGAGCTTC
1 TGTTTGGTGTGTTTCGGTTGGATCAGATCTTATGAGCTTC
*
54401268 TGTATGGTGTGTTTCGGTTGGA
1 TGTTTGGTGTGTTTCGGTTGGA
54401290 CTAGATTTCC
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 125 1.00
ACGTcount: A:0.14, C:0.13, G:0.28, T:0.45
Consensus pattern (40 bp):
TGTTTGGTGTGTTTCGGTTGGATCAGATCTTATGAGCTTC
Found at i:54406718 original size:20 final size:20
Alignment explanation
Indices: 54406685--54406729 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54406675 AGCACATGTA
* * *
54406685 TTCATAAAATTTTATAATTT
1 TTCATAAAAGTTTACAACTT
*
54406705 TTCATCAAAGTTTACAACTT
1 TTCATAAAAGTTTACAACTT
54406725 TTCAT
1 TTCAT
54406730 TTTAGTCCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAAGTTTACAACTT
Found at i:54413733 original size:40 final size:40
Alignment explanation
Indices: 54413678--54413846 Score: 277
Period size: 40 Copynumber: 4.2 Consensus size: 40
54413668 CGGATGATAA
* * * *
54413678 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
54413718 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54413758 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54413798 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54413838 CCGGGCTAA
1 CCGGGCTAA
54413847 TGAATAAATT
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
40 121 0.99
41 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54420011 original size:40 final size:40
Alignment explanation
Indices: 54419956--54420263 Score: 336
Period size: 40 Copynumber: 7.5 Consensus size: 40
54419946 CGGATGATAA
* * * *
54419956 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAATGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-T
*
54419996 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
*
54420036 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
54420076 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACTATAT
* *
54420116 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGNATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGAC----T------ATAT
** * *
54420166 CCGGGCTCGGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
*
54420206 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT-AGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATAT
* *
54420246 TC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54420264 TACTTGGTTT
Statistics
Matches: 238, Mismatches: 16, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
39 17 0.07
40 180 0.76
41 2 0.01
44 1 0.00
46 1 0.00
50 37 0.16
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:54420089 original size:80 final size:80
Alignment explanation
Indices: 54419956--54420263 Score: 370
Period size: 80 Copynumber: 3.7 Consensus size: 80
54419946 CGGATGATAA
* * * * *
54419956 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAATGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT
54420020 GTGCGAGTTACTATAT
65 GTGCGAGTTACTATAT
54420036 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
54420101 TGCGAGTTGCTATAT
66 TGCGAGTTACTATAT
* **
54420116 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGNATATCCGGGCTCGGTCCCG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC----T------ATATCCGGGCTAAGTCCCG
*
54420181 AAGGCATTTGTGTGAGTTACTATAT
56 AAGGCATTTGTGCGAGTTACTATAT
* * *
54420206 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATTC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
54420264 TACTTGGTTT
Statistics
Matches: 199, Mismatches: 17, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
79 13 0.07
80 111 0.56
81 1 0.01
84 1 0.01
86 1 0.01
89 2 0.01
90 70 0.35
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:54420187 original size:50 final size:49
Alignment explanation
Indices: 54420112--54420210 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 49
54420102 GCGAGTTGCT
54420112 ATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
1 ATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
* *
54420161 NATATCCGGGCTCGGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGG
1 -ATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
54420211 CTAAGTCCCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.27
Consensus pattern (49 bp):
ATATCCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGG
Found at i:54420225 original size:90 final size:89
Alignment explanation
Indices: 54420072--54420245 Score: 269
Period size: 90 Copynumber: 1.9 Consensus size: 89
54420062 GCGAGTTACT
* *
54420072 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAGGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
*
54420137 TTTGTGCGAGTTA-CTATATCCGGG
66 TTTGAGCGAG-TAGCTATATCCGGG
** *
54420161 NATATCCGGGCTCGGTCCCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCGAAGGC
1 -ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGC
54420226 ATTTGAGCGAGTAGCTATAT
65 ATTTGAGCGAGTAGCTATAT
54420246 TCGGCTAAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 2 0.03
90 75 0.97
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (89 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGAGCGAGTAGCTATATCCGGG
Found at i:54425883 original size:20 final size:18
Alignment explanation
Indices: 54425849--54425895 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
54425839 TTCCTCAAGC
54425849 AAACGAAAAATAAAATAA
1 AAACGAAAAATAAAATAA
*
54425867 AAACGAAGAAGATAAAATTA
1 AAACGAA-AA-ATAAAATAA
*
54425887 AAACTAAAA
1 AAACGAAAA
54425896 GAAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 14 0.56
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.13
Consensus pattern (18 bp):
AAACGAAAAATAAAATAA
Found at i:54430567 original size:46 final size:48
Alignment explanation
Indices: 54430454--54430578 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 48
54430444 ACATCAAAGT
* * * * *
54430454 CGATGCTATGTCCCGGATAGGTCTTACACTGACTTTCATATATCGAGGC
1 CGATGC-ATGTCCCAGACATGTCTTACACTGACTCTCATAAATCGAGGC
* * *
54430503 CGATGCCGTGTCCCAGACATGTCTTACACTGGCTCTCA-AAAT-GTGGC
1 CGATG-CATGTCCCAGACATGTCTTACACTGACTCTCATAAATCGAGGC
54430550 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
54430579 AGCACACATA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
46 23 0.35
47 9 0.14
48 3 0.05
49 30 0.45
50 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (48 bp):
CGATGCATGTCCCAGACATGTCTTACACTGACTCTCATAAATCGAGGC
Found at i:54432863 original size:11 final size:12
Alignment explanation
Indices: 54432847--54432883 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
54432837 AGGTTTCTAG
54432847 AAGAGTTTGAA-
1 AAGAGTTTGAAT
54432858 AAGAGTTTGAAT
1 AAGAGTTTGAAT
54432870 AAG-GTTTGAAT
1 AAGAGTTTGAAT
54432881 AAG
1 AAG
54432884 TTGTTGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (12 bp):
AAGAGTTTGAAT
Found at i:54434361 original size:27 final size:27
Alignment explanation
Indices: 54434312--54434370 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
54434302 CCCTATTTGA
* *
54434312 AAAATTACCCAAATAACATTGTAGTGT
1 AAAATTACCCAAATAACACTGTAGGGT
* * *
54434339 AAAATTACCGAAATACCCCTGTAGGGT
1 AAAATTACCCAAATAACACTGTAGGGT
54434366 AAAAT
1 AAAAT
54434371 GACTGTTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (27 bp):
AAAATTACCCAAATAACACTGTAGGGT
Found at i:54434752 original size:22 final size:22
Alignment explanation
Indices: 54434718--54434797 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
54434708 GCCGCTTAAT
*
54434718 CTGATTATGGCTCTGTGCCAAC
1 CTGAATATGGCTCTGTGCCAAC
* * **
54434740 CTGAATATTGCTCTGTGCTATG
1 CTGAATATGGCTCTGTGCCAAC
* * *
54434762 CTGATTATGACTCTGTACCAAC
1 CTGAATATGGCTCTGTGCCAAC
*
54434784 CTAAATATGGCTCT
1 CTGAATATGGCTCT
54434798 ATGCTATGTT
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (22 bp):
CTGAATATGGCTCTGTGCCAAC
Found at i:54434768 original size:44 final size:44
Alignment explanation
Indices: 54434718--54434823 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 44
54434708 GCCGCTTAAT
* * * *
54434718 CTGATTATGGCTCTGTGCCAACCTGAATATTGCTCTGTGCTATG
1 CTGATTATGGCTCTGTACCAACCTAAATATGGCTCTATGCTATG
*
54434762 CTGATTATGACTCTGTACCAACCTAAATATGGCTCTATGCTATG
1 CTGATTATGGCTCTGTACCAACCTAAATATGGCTCTATGCTATG
* * *
54434806 TTAATTATGGCTTTGTAC
1 CTGATTATGGCTCTGTAC
54434824 AAATCGTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (44 bp):
CTGATTATGGCTCTGTACCAACCTAAATATGGCTCTATGCTATG
Found at i:54452685 original size:66 final size:67
Alignment explanation
Indices: 54452556--54452685 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
54452546 GGGATGTATC
*
54452556 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
54452621 AGGACA
62 AGGACA
* *
54452627 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
54452686 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
71 21 0.38
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:54456985 original size:13 final size:13
Alignment explanation
Indices: 54456967--54456996 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54456957 ATAACATTTT
*
54456967 ATTTCAAATATTC
1 ATTTCAAATATCC
54456980 ATTTCAAATATCC
1 ATTTCAAATATCC
54456993 ATTT
1 ATTT
54456997 TCACATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTCAAATATCC
Found at i:54457478 original size:24 final size:24
Alignment explanation
Indices: 54457433--54457502 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
54457423 ACATTGATAT
* ** * *
54457433 AATGGTTTCCTTTTTTATCTTTTC
1 AATGGTATCCTTTTCAACCTTTAC
*
54457457 AATGGTATCCTTTTCGACCTTTAC
1 AATGGTATCCTTTTCAACCTTTAC
* *
54457481 ATTGGTAACCTTTTCAACCTTT
1 AATGGTATCCTTTTCAACCTTT
54457503 CCATTGTGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (24 bp):
AATGGTATCCTTTTCAACCTTTAC
Found at i:54457507 original size:24 final size:24
Alignment explanation
Indices: 54457459--54457508 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
54457449 ATCTTTTCAA
* *
54457459 TGGTATCCTTTTCGACCTTTACAT
1 TGGTAACCTTTTCAACCTTTACAT
*
54457483 TGGTAACCTTTTCAACCTTTCCAT
1 TGGTAACCTTTTCAACCTTTACAT
54457507 TG
1 TG
54457509 TGTCAGGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.44
Consensus pattern (24 bp):
TGGTAACCTTTTCAACCTTTACAT
Found at i:54460413 original size:10 final size:10
Alignment explanation
Indices: 54460393--54460486 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 10
54460383 TTTTTTACTA
54460393 TATTATTATAT
1 TATT-TTATAT
54460404 TATTTTATAT
1 TATTTTATAT
* *
54460414 TCTATTATA-
1 TATTTTATAT
54460423 TA-TTTATAT
1 TATTTTATAT
*
54460432 TATTATTACA-
1 TATT-TTATAT
54460442 TA--TTAT-T
1 TATTTTATAT
*
54460449 TATTTTGTAT
1 TATTTTATAT
54460459 TA-TTTATAT
1 TATTTTATAT
54460468 ATATTATTAT-T
1 -TATT-TTATAT
*
54460479 TATATTAT
1 TATTTTAT
54460487 TATTTCAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 22
0.67 0.09 0.23
Matches are distributed among these distances:
7 5 0.08
8 5 0.08
9 16 0.25
10 24 0.38
11 10 0.16
12 4 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (10 bp):
TATTTTATAT
Found at i:54460421 original size:20 final size:18
Alignment explanation
Indices: 54460396--54460484 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 18
54460386 TTTACTATAT
54460396 TATTATATTATTTTATATTC
1 TATTATA-TA-TTTATATTC
*
54460416 TATTATATATTTATATTAT
1 TATTATATATTTATATT-C
* *
54460435 TATTACATATTATTTATT-
1 TATTATATATT-TATATTC
*
54460453 T-TGTAT-TATTTATA-TA
1 TAT-TATATATTTATATTC
54460469 TATTAT-TATTTATATT
1 TATTATATATTTATATT
54460485 ATTATTTCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
15 1 0.02
16 15 0.26
17 7 0.12
18 11 0.19
19 12 0.21
20 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTATATATTTATATTC
Found at i:54460431 original size:36 final size:36
Alignment explanation
Indices: 54460391--54460486 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 36
54460381 TGTTTTTTAC
54460391 TATATTATTATATTATTTTATATTCTATTATATATTTA
1 TATATTATTATATTATTTTATATTCTATTATATA--TA
* * *
54460429 TATTATTATTACATATTA-TTTATTTTGTATTATTTATA
1 TA-TATTATT--ATATTATTTTATATTCTATTATATATA
*
54460467 TATATTATTAT-TTATATTAT
1 TATATTATTATATTATTTTAT
54460487 TATTTCAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
34 3 0.06
35 6 0.12
37 7 0.14
38 6 0.12
39 7 0.14
40 15 0.30
41 6 0.12
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (36 bp):
TATATTATTATATTATTTTATATTCTATTATATATA
Found at i:54463075 original size:205 final size:205
Alignment explanation
Indices: 54462716--54463295 Score: 901
Period size: 205 Copynumber: 2.8 Consensus size: 205
54462706 ATAGGCCGCA
* *
54462716 ACATAGTAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAATATGATTTGGCATCCTTGT
1 ACATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGT
* * *
54462781 GCTTACAATGAGCGAATCGAAGACATAACTGATTTGGCTTTCATGTGTTTACGATGAAGCAAATC
66 GCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
* *
54462846 TAAGATGATTTGGCATTTCTGTATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGATG
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACG
54462911 GGGAGCAGAT
196 GGGAGCAGAT
* *
54462921 ACATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCCAAGATGATTTGGTATCCTTGT
1 ACATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGT
* *
54462986 GCTTACAAGGAGCGAATCGAATACATAGCTGATTTGGCTTTCACGTGTTTACAATGAAGCAAATC
66 GCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
* *
54463051 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGACG
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACG
54463116 GGGAGCAGAT
196 GGGAGCAGAT
* * ** * * * *
54463126 ACGTAGCAGACCTCGGCTTTAGATAATTT-CACTGAAGTAAGATCCAAGATGATTTGGCATTCTT
1 ACATAGCAGATCTCACCTTCAGAT-GTTTATACTGAAG-AAGATCCAAGATGATTTGGCATCCTT
* * * * *
54463190 GTGCTTACATGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTGATGATGAAGCAAA
64 GTGCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAA
54463255 TCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAAT
129 TCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAAT
54463296 TGAAGAAGCA
Statistics
Matches: 343, Mismatches: 30, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
205 218 0.64
206 125 0.36
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (205 bp):
ACATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGT
GCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACG
GGGAGCAGAT
Found at i:54465124 original size:20 final size:20
Alignment explanation
Indices: 54465096--54465153 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
54465086 TTTTTTGACA
54465096 TATTCATATT-TTTTACTATAT-
1 TATT-ATATTATTTTA-TAT-TC
54465117 TATTATATTATTTTATATTC
1 TATTATATTATTTTATATTC
54465137 TATTATA-TA-TTTATATT
1 TATTATATTATTTTATATT
54465154 ATTATTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.23
19 3 0.09
20 15 0.43
21 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATATTATTTTATATTC
Found at i:54465180 original size:14 final size:13
Alignment explanation
Indices: 54465119--54465219 Score: 89
Period size: 14 Copynumber: 7.5 Consensus size: 13
54465109 TACTATATTA
54465119 TTATATTATTTTAT
1 TTATATTA-TTTAT
* *
54465133 ATTCTATTATATAT
1 -TTATATTATTTAT
54465147 TTATATTA-TTAT
1 TTATATTATTTAT
*
54465159 TACATATTATTTATT
1 T-TATATTATTTA-T
*
54465174 TTGTATTATTTAT
1 TTATATTATTTAT
*
54465187 ATATATTA-TTAT
1 TTATATTATTTAT
*
54465199 TTATATTATTATTT
1 TTATATTATT-TAT
54465213 TTATATT
1 TTATATT
54465220 TAAATATTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.21
13 21 0.30
14 25 0.36
15 9 0.13
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (13 bp):
TTATATTATTTAT
Found at i:54465182 original size:40 final size:38
Alignment explanation
Indices: 54465114--54465213 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 38
54465104 TTTTTTACTA
* *
54465114 TATTATTATATTATTTTATATTCTATTATATATTTATAT
1 TATTATTATATTA-TTTATTTTCTATTATATATATATAT
* *
54465153 TATTATTACATATTATTTATTTTGTATTATTTATATATAT
1 TATTATT--ATATTATTTATTTTCTATTATATATATATAT
54465193 TATTATTTATATTA-TTATTTT
1 TATTA-TTATATTATTTATTTT
54465214 TATATTTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 7 0.13
39 13 0.24
40 26 0.48
41 8 0.15
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (38 bp):
TATTATTATATTATTTATTTTCTATTATATATATATAT
Found at i:54465216 original size:18 final size:18
Alignment explanation
Indices: 54465112--54465216 Score: 62
Period size: 18 Copynumber: 5.9 Consensus size: 18
54465102 TATTTTTTAC
*
54465112 TATATTATTA-TATTATTT
1 TATATTATTATTTTTA-TT
* *
54465130 TATATT-CTATTATATATT
1 TATATTATTATT-TTTATT
**
54465148 TATATTATTA-TTACATAT
1 TATATTATTATTTTTAT-T
54465166 TAT-TTATT-TTGTATTATT
1 TATATTATTATT-T-TTATT
*
54465184 TATA-TA-TATTATTATT
1 TATATTATTATTTTTATT
54465200 TATATTATTATTTTTAT
1 TATATTATTATTTTTAT
54465217 ATTTAAATAT
Statistics
Matches: 67, Mismatches: 9, Indels: 22
0.68 0.09 0.22
Matches are distributed among these distances:
16 9 0.13
17 15 0.22
18 37 0.55
19 6 0.09
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (18 bp):
TATATTATTATTTTTATT
Found at i:54469415 original size:46 final size:46
Alignment explanation
Indices: 54469363--54469454 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
54469353 AGTTCAGGCC
*
54469363 CGAGCTCCTTACAGAATTAATTTGGCTTTAGCCTATTCAAATACAA
1 CGAGCTCCTTACAGAATTAATTTGGCTTTAGCCCATTCAAATACAA
54469409 CGAGCTCCTTACAGAATTAATTTGGCTTTAGCCCATTCAAATACAA
1 CGAGCTCCTTACAGAATTAATTTGGCTTTAGCCCATTCAAATACAA
54469455 TCTCAGAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (46 bp):
CGAGCTCCTTACAGAATTAATTTGGCTTTAGCCCATTCAAATACAA
Found at i:54473848 original size:37 final size:37
Alignment explanation
Indices: 54473797--54473983 Score: 266
Period size: 37 Copynumber: 5.1 Consensus size: 37
54473787 CTTTAGCTCA
* * * * *
54473797 GACAAAATCTCCACATGAAGTTATCGGGTCTTACCCA
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
54473834 AACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
54473871 GACATACTCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
* * *
54473908 GGCATACTCTCCACACATAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
54473945 GACATAATCTCCACACGTAGTCATCGGGTCTCACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
54473982 GA
1 GA
54473984 ATATATTTCC
Statistics
Matches: 136, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 136 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (37 bp):
GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:54474267 original size:47 final size:47
Alignment explanation
Indices: 54474189--54474616 Score: 631
Period size: 47 Copynumber: 9.1 Consensus size: 47
54474179 ATATATATTT
* * * *
54474189 CACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * * *
54474236 CACATTGGCCATTTGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
54474283 CACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* *
54474330 CACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * *
54474377 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
54474424 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* *
54474471 CACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * * *
54474518 CACATTGGCCATTTGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* ** *
54474565 CACATTGGCCATTCGGCCTTATCACATATATACACATTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
54474612 CACAT
1 CACAT
54474617 AAAATCCTAA
Statistics
Matches: 343, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 343 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
Found at i:54474359 original size:141 final size:141
Alignment explanation
Indices: 54474188--54474617 Score: 770
Period size: 141 Copynumber: 3.0 Consensus size: 141
54474178 TATATATATT
* * * *
54474188 TCACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
1 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
*
54474253 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGACCTTATCACATATATGCAT
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
54474318 GTTCACATTCA
131 GTTCACATTCA
* *
54474329 CCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
1 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
54474394 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
54474459 GTTCACATTCA
131 GTTCACATTCA
54474470 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
1 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
* *
54474535 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
*
54474600 ATTCACATTCA
131 GTTCACATTCA
54474611 TCACATA
1 TCACATA
54474618 AAATCCTAAA
Statistics
Matches: 277, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 277 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (141 bp):
TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTTGGC
CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
GTTCACATTCA
Found at i:54475630 original size:57 final size:57
Alignment explanation
Indices: 54475542--54475656 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
54475532 TTCCAAGTCC
54475542 AAACACTTATGAACTTACCATTTGAGTTTAAGACATATCATGGCCACATCATATCTT
1 AAACACTTATGAACTTACCATTTGAGTTTAAGACATATCATGGCCACATCATATCTT
54475599 AAACACTTATGAACTTACCATTTGAGTTTAAGACATATCATGGCCACATCATATCTT
1 AAACACTTATGAACTTACCATTTGAGTTTAAGACATATCATGGCCACATCATATCTT
54475656 A
1 A
54475657 TTAAATCAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (57 bp):
AAACACTTATGAACTTACCATTTGAGTTTAAGACATATCATGGCCACATCATATCTT
Found at i:54479143 original size:40 final size:41
Alignment explanation
Indices: 54479077--54479212 Score: 206
Period size: 40 Copynumber: 3.4 Consensus size: 41
54479067 CGGATGATAA
* *
54479077 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATAT
* * *
54479117 CTGGGCAAAGCCCCGAAGGCATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATAT
54479157 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATAT
54479197 CCGGGCTAAGTCCCGA
1 CCGGGCTAAGTCCCGA
54479213 NNNNNNNNNN
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.02
40 85 0.98
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATAT
Found at i:54486611 original size:46 final size:44
Alignment explanation
Indices: 54486547--54486661 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
54486537 ACAGGACAGA
* * * * *
54486547 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGTCATGTAAGTCCATATT--AAATATAGCATTAGAG
* *
54486593 ACAGGATTGAGTCATGTAAGTCCATATTATATATAGCATTAGAG
1 ACAGGAATGAGTCATGTAAGTCCATATTAAATATAGCATTAGAG
* *
54486637 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGTCATGTAAGTCCAT
54486662 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (44 bp):
ACAGGAATGAGTCATGTAAGTCCATATTAAATATAGCATTAGAG
Found at i:54496020 original size:75 final size:74
Alignment explanation
Indices: 54495936--54496086 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 74
54495926 TTAAGTCTCA
*
54495936 TAAGCTTTGGAAATTAATTGGTAATGTTTTGGGTCAAAATTGGTGATTTTGGGGGTGATTTTTAG
1 TAAGCTTTGGAAATTAATTGGTAATGTTTTGGGTCAAAATTGGTGACTTT-GGGGTGATTTTTAG
54496001 GTCCTGACAT
65 GTCCTGACAT
*
54496011 TAAGCTTTGGAAATTAATTGGTAATGTTTTGGGTCAAATTTGGTGACTTTGGGGTGATTTTTAGG
1 TAAGCTTTGGAAATTAATTGGTAATGTTTTGGGTCAAAATTGGTGACTTTGGGGTGATTTTTAGG
*
54496076 TCCTGGCAT
66 TCCTGACAT
54496085 TA
1 TA
54496087 GGGATGACTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 25 0.34
75 48 0.66
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (74 bp):
TAAGCTTTGGAAATTAATTGGTAATGTTTTGGGTCAAAATTGGTGACTTTGGGGTGATTTTTAGG
TCCTGACAT
Found at i:54497561 original size:49 final size:49
Alignment explanation
Indices: 54497508--54497729 Score: 291
Period size: 49 Copynumber: 4.5 Consensus size: 49
54497498 TACGCATAGC
*
54497508 AGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGT
1 AGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACGTAGT
* ** * * *
54497557 AGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACATGTAGT
1 AGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACGTAGT
* * * * *
54497607 AGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGT
1 AGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACGTAGT
*
54497658 AGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGT
1 AGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACGTAGT
*
54497707 AGCCTACACTTAGTACTACACAC
1 AGCCTGCACTTAGTACTACACAC
54497730 ATGACCTCAC
Statistics
Matches: 147, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
49 63 0.43
50 47 0.32
51 37 0.25
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
AGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACGTAGT
Found at i:54497670 original size:101 final size:98
Alignment explanation
Indices: 54497508--54497729 Score: 291
Period size: 101 Copynumber: 2.2 Consensus size: 98
54497498 TACGCATAGC
* *
54497508 AGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTAGTAC
1 AGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTAGTAC
* * *
54497573 TACACACGTGACCTAACCATCTGATACATGTAGT
66 TACACACGCGACC-AACCATCCGATACACGTAGT
* * * *
54497607 AGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACTTAGT
1 AGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACTTAGT
* ** *
54497672 ACTACACATGCGACCAATTATCCGGTACACGTAGT
64 ACTACACACGCGACCAACCATCCGATACACGTAGT
*
54497707 AGCCTACACTTAGTACTACACAC
1 AGCCTGCACTTAGTACTACACAC
54497730 ATGACCTCAC
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
99 25 0.23
100 40 0.37
101 42 0.39
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (98 bp):
AGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTAGTAC
TACACACGCGACCAACCATCCGATACACGTAGT
Found at i:54510902 original size:21 final size:20
Alignment explanation
Indices: 54510834--54510901 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
54510824 ATAAAGTTTG
54510834 GAATTTTT-ATAAA-TATTTT
1 GAATTTTTGA-AAATTATTTT
*
54510853 AAATTTTTGAAAATTATTTTT
1 GAATTTTTGAAAATTA-TTTT
54510874 GAATTTTTGAAAATTATTTT
1 GAATTTTTGAAAATTATTTT
54510894 GAATTTTT
1 GAATTTTT
54510902 TTTTTTTGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 10 0.23
20 15 0.34
21 19 0.43
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
GAATTTTTGAAAATTATTTT
Found at i:54518978 original size:14 final size:14
Alignment explanation
Indices: 54518956--54518995 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
54518946 TTCTTTCTTT
54518956 TTCTATCAATTCTA
1 TTCTATCAATTCTA
*
54518970 TTCTCTCAATTCTA
1 TTCTATCAATTCTA
*
54518984 TTC-ATCTATTCT
1 TTCTATCAATTCT
54518996 CTCAATTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCTATCAATTCTA
Found at i:54520617 original size:42 final size:43
Alignment explanation
Indices: 54520565--54520645 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
54520555 TTTTGATTTA
* *
54520565 CGTGTAAGACCATGTCTGGGACATTAGCATCG-TATATGTGTT
1 CGTGTAAGACCATATCTGGGACAGTAGCATCGATATATGTGTT
* *
54520607 CGTGTAAGACCCTATCTGGGACAGTGGCATCGATATATG
1 CGTGTAAGACCATATCTGGGACAGTAGCATCGATATATG
54520646 ATTACATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCATATCTGGGACAGTAGCATCGATATATGTGTT
Found at i:54521505 original size:30 final size:30
Alignment explanation
Indices: 54521469--54521525 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
54521459 TTCCCGAGCC
54521469 TAGGGGCAAAACTGTAAATATGCAAAAGTT
1 TAGGGGCAAAACTGTAAATATGCAAAAGTT
* * *
54521499 TAGGGGCAAAATTGTAATTTTGCAAAA
1 TAGGGGCAAAACTGTAAATATGCAAAA
54521526 TTTTGAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAACTGTAAATATGCAAAAGTT
Found at i:54522343 original size:64 final size:64
Alignment explanation
Indices: 54522264--54522447 Score: 212
Period size: 67 Copynumber: 2.8 Consensus size: 64
54522254 AGACATTATG
* * *
54522264 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * *
54522328 ATGTAGCTAGGTCGCATGGGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
54522393 AA
63 AA
* * *
54522395 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
54522448 CGAACTATAT
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 26 0.26
66 22 0.22
67 33 0.33
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:54532983 original size:43 final size:43
Alignment explanation
Indices: 54532870--54532984 Score: 101
Period size: 44 Copynumber: 2.6 Consensus size: 43
54532860 TGTGTTATCG
* ***
54532870 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTCTGTTTTTTG
1 TGTAAGA-CACGTCTGGGACGTTGGCATCGACTTCTGTATTACA
* * *
54532914 TGTAAGACCCTGTCTGGGATAG-TGGCATCGA-TATTTG-ATTACA
1 TGTAAGACAC-GTCTGGGA-CGTTGGCATCGACT-TCTGTATTACA
54532957 TGTAAGACTACGTCTGGGACGTTGGCAT
1 TGTAAGAC-ACGTCTGGGACGTTGGCAT
54532985 TGTACGAGCT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
42 1 0.02
43 27 0.47
44 28 0.49
45 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (43 bp):
TGTAAGACACGTCTGGGACGTTGGCATCGACTTCTGTATTACA
Found at i:54534122 original size:29 final size:28
Alignment explanation
Indices: 54534078--54534167 Score: 126
Period size: 29 Copynumber: 3.1 Consensus size: 28
54534068 TGAGCATGAC
* *
54534078 TATAAATGTGAATTGGGCTTGATGGGCCA
1 TATAAATGTG-ATTGGGCCTAATGGGCCA
54534107 TATAAATGTGATTTGGGCCTAATGGGCCA
1 TATAAATGTGA-TTGGGCCTAATGGGCCA
* *
54534136 TATAAATGTGATTGGGCCTAGTGGGCTA
1 TATAAATGTGATTGGGCCTAATGGGCCA
54534164 TATA
1 TATA
54534168 CAGGTATGTG
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
28 20 0.36
29 36 0.64
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.32
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAATGGGCCA
Found at i:54537761 original size:27 final size:27
Alignment explanation
Indices: 54537730--54538097 Score: 357
Period size: 27 Copynumber: 13.7 Consensus size: 27
54537720 TTAGTTTACC
* ** *
54537730 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * * *
54537757 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
** * *
54537784 AAATTACTGAAATACCGTT-GATTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
54537810 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * * * *
54537837 AAATTATCGAAATA-CCATCGATTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * **
54537863 AAATTACTAAAAT-GCCTTCAATTTGTA
1 AAATTACCAAAATACCCTT-GGTTTGTA
* **
54537890 AAATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
54537917 AAGTTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
**
54537944 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTGTA
*
54537971 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
**
54537998 AAATTACCAAAATA-CCTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTGTA
* * *
54538024 AAGTTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
54538051 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTGTA
54538078 AAATTACCAAAATACCCTTG
1 AAATTACCAAAATACCCTTG
54538098 TAGGGTAGAA
Statistics
Matches: 271, Mismatches: 65, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
26 63 0.23
27 205 0.76
28 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTGTA
Found at i:54537850 original size:80 final size:79
Alignment explanation
Indices: 54537730--54538093 Score: 349
Period size: 80 Copynumber: 4.5 Consensus size: 79
54537720 TTAGTTTACC
* * * * **
54537730 AAATTACCAAAGTACCCCCGGTTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTACTGAA
1 AAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATA-CCTCGATTTGTAAAATTACCAAA
*
54537795 ATACCGTTGATTGTA
65 ATACCCTTGATTGTA
* * * * *
54537810 AAATTACTAAAATACCCTCGATTTGTAAAATTATCGAAATACCATCGA-TTGTAAAATTACTAAA
1 AAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATACC-TCGATTTGTAAAATTACCAAA
* *
54537874 AT-GCCTTCAATTTGTA
65 ATACCCTT-GA-TTGTA
* * ** * * *
54537890 AAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATACCTCGA-TTTGTAAAATTACCAAA
*
54537955 ATACCCTTGGTT-TACA
65 ATACCCTTGATTGT--A
* * ** *
54537971 AAATTACCAAAATACCC-CTGGTTTGTAAAATTACCAAAATACCTTGGTTTACAAAGTTACCAAA
1 AAATTACCAAAATACCCTC-GGTTTGTAAAATTACCAAAATACCTCGATTTGTAAAATTACCAAA
* *
54538035 ATACCCCTAGTTTGTA
65 ATA-CCCTTGATTGTA
*
54538051 AAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACC
1 AAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATACC
54538094 CTTGTAGGGT
Statistics
Matches: 231, Mismatches: 41, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
78 3 0.01
79 23 0.10
80 138 0.60
81 62 0.27
82 5 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (79 bp):
AAATTACCAAAATACCCTCGGTTTGTAAAATTACCAAAATACCTCGATTTGTAAAATTACCAAAA
TACCCTTGATTGTA
Found at i:54538109 original size:27 final size:27
Alignment explanation
Indices: 54538052--54538221 Score: 180
Period size: 27 Copynumber: 6.3 Consensus size: 27
54538042 TAGTTTGTAA
** *
54538052 AATTACCAAAATACCCTTGGT-TTGTAA
1 AATTACCAAAATACCCTT-GTAGGGTAG
54538079 AATTACCAAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCTTGTAGGGTAG
* *
54538106 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCAAAATACCCTTGTAGGGTAG
*
54538133 AATCACCAAAATACCCTTGTAGGGTAG
1 AATTACCAAAATACCCTTGTAGGGTAG
* * * *
54538160 AAATACCGAAATACCCCTGTAGGATAG
1 AATTACCAAAATACCCTTGTAGGGTAG
* * * * * *
54538187 AATTATCGAGATAACCTTGTGGGGTAA
1 AATTACCAAAATACCCTTGTAGGGTAG
54538214 AATTACCA
1 AATTACCA
54538222 TTTTGCCCCT
Statistics
Matches: 119, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 2 0.02
27 117 0.98
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGTAGGGTAG
Found at i:54538110 original size:107 final size:108
Alignment explanation
Indices: 54537887--54538120 Score: 382
Period size: 107 Copynumber: 2.2 Consensus size: 108
54537877 CCTTCAATTT
54537887 GTAAAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTAAAATTACC
1 GTAAAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTAAAATTACC
**
54537952 AAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTT
66 AAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTGG
54537995 GTAAAATTACCAAAATACC-TTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTAAAATTACC
1 GTAAAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTAAAATTACC
** *
54538059 AAAATACCCTTGGTTTGTAAAATTACCAAAATA-CCCTTGTAGG
66 AAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGT-GG
* *
54538102 GTAGAATTACCGAAATACC
1 GTAAAATTACCAAAATACC
54538121 CCTGTAGGGT
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
106 6 0.05
107 93 0.79
108 19 0.16
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (108 bp):
GTAAAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTAAAATTACC
AAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTGG
Found at i:54538121 original size:54 final size:54
Alignment explanation
Indices: 54537730--54538094 Score: 377
Period size: 53 Copynumber: 6.8 Consensus size: 54
54537720 TTAGTTTACC
* ** * * * *
54537730 AAATTACCAAAGTACCCCCGGTTTATAAAATTACCCAAATA-TCCTCGATTTGTA
1 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAG-TTTGTA
** * * * *
54537784 AAATTACTGAAATACCGTTGATTGT--AAAATTACTAAAATA-CCCTCGATTTGTA
1 AAATTACCAAAATACCCTTGGTT-TACAAAATTACCAAAATACCCCTAG-TTTGTA
* * * * * * * * *
54537837 AAATTATCGAAATACCATCGATTGT--AAAATTACTAAAAT-GCCTTCAATTTGTA
1 AAATTACCAAAATACCCTTGGTT-TACAAAATTACCAAAATACCCCT-AGTTTGTA
* *
54537890 AAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTA
*
54537944 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTA
*
54537998 AAATTACCAAAATA-CCTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTA
**
54538051 AAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC
1 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCC
54538095 TTGTAGGGTA
Statistics
Matches: 269, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
52 1 0.00
53 138 0.51
54 126 0.47
55 4 0.01
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTAGTTTGTA
Found at i:54538147 original size:81 final size:81
Alignment explanation
Indices: 54537887--54538191 Score: 237
Period size: 81 Copynumber: 3.8 Consensus size: 81
54537877 CCTTCAATTT
* * ** * * ** *
54537887 GTAAAATTACCAAAATACCTTTGGTTTACAAAGTTACCAAAATACCCCTAGTTTG-TAAAATTAC
1 GTAAAATCACCAAAATACCCTTGGTTTGTAAAATTACCAAAATA-CCCTTGTAGGATAGAATTAC
* * **
54537951 CAAAATACCCTTGGTTT
65 CAAAATACCCCTAGTGG
** * * ** *
54537968 ACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATA-CCTTG--GTTTACAAAGTTA
1 GTAAAATCACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTGTAGGATA-GAA-TTA
**
54538030 CCAAAATACCCCTAGTTT
64 CCAAAATACCCCTAGTGG
* *
54538048 GTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTGTAGGGTAGAATTACC
1 GTAAAATCACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTGTAGGATAGAATTACC
*
54538113 GAAATACCCCT-GTAGG
66 AAAATACCCCTAGT-GG
* ** * *
54538129 GTAGAATCACCAAAATACCCTT-GTAGGGTAGAAA-TACCGAAATACCCCTGTAGGATAGAATTA
1 GTAAAATCACCAAAATACCCTTGGT-TTGTA-AAATTACCAAAATACCCTTGTAGGATAGAATTA
54538192 TCGAGATAAC
Statistics
Matches: 187, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
78 2 0.01
79 7 0.04
80 64 0.34
81 106 0.57
82 5 0.03
83 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (81 bp):
GTAAAATCACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTGTAGGATAGAATTACC
AAAATACCCCTAGTGG
Found at i:54538212 original size:81 final size:81
Alignment explanation
Indices: 54538048--54538221 Score: 199
Period size: 81 Copynumber: 2.1 Consensus size: 81
54538038 CCCCTAGTTT
* ** * *
54538048 GTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTGTAGGGTAGAATTACC
1 GTAAAATCACCAAAATACCCTTGGTGGGTAAAATTACCAAAATACCCCTGTAGGATAGAATTACC
*
54538113 GAAATACCCCTGTAGG
66 GAAATAACCCTGTAGG
* *
54538129 GTAGAATCACCAAAATACCCTT-GTAGGGTAGAAA-TACCGAAATACCCCTGTAGGATAGAATTA
1 GTAAAATCACCAAAATACCCTTGGT-GGGTA-AAATTACCAAAATACCCCTGTAGGATAGAATTA
* * * *
54538192 TCGAGATAACCTTGTGGG
64 CCGAAATAACCCTGTAGG
*
54538210 GTAAAATTACCA
1 GTAAAATCACCA
54538222 TTTTGCCCCT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 2 0.03
81 72 0.94
82 3 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (81 bp):
GTAAAATCACCAAAATACCCTTGGTGGGTAAAATTACCAAAATACCCCTGTAGGATAGAATTACC
GAAATAACCCTGTAGG
Found at i:54538459 original size:25 final size:25
Alignment explanation
Indices: 54538425--54538494 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
54538415 AGGAAGTGCT
*
54538425 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
54538450 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
54538475 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54538495 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:54538507 original size:24 final size:24
Alignment explanation
Indices: 54538424--54538507 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 24
54538414 GAGGAAGTGC
*
54538424 TAAAAGGGCTTTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
54538449 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
54538473 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
54538497 TAAAAGAGGCT
1 TAAAAG-GGCT
54538508 AGGCCTCCAG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 40 0.75
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:54538518 original size:50 final size:50
Alignment explanation
Indices: 54538425--54538519 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
54538415 AGGAAGTGCT
**
54538425 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
**
54538475 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
54538520 ATATGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 24 0.62
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:54541018 original size:21 final size:21
Alignment explanation
Indices: 54540976--54541019 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54540966 TTGGCCGAAT
*
54540976 ATCTATTATTCCCCTTTTCCA
1 ATCTATTATTCCCCTTTGCCA
*
54540997 ATCTATT-TTCCTCTTTGGCCA
1 ATCTATTATTCCCCTTT-GCCA
54541018 AT
1 AT
54541020 TACTTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.18, C:0.30, G:0.05, T:0.48
Consensus pattern (21 bp):
ATCTATTATTCCCCTTTGCCA
Found at i:54542577 original size:46 final size:46
Alignment explanation
Indices: 54542412--54542581 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 46
54542402 AACCCACCCC
* * * * * * *
54542412 TAAGTGAACTCGGAATCAACTCAACAAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA
* * * *
54542458 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTTGCATCCA
* *
54542506 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA
54542551 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
54542582 GGAAGCTCAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 3 0.03
46 53 0.53
47 26 0.26
48 2 0.02
49 3 0.03
50 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA
Found at i:54542603 original size:46 final size:45
Alignment explanation
Indices: 54542462--54542603 Score: 121
Period size: 46 Copynumber: 3.1 Consensus size: 45
54542452 CATCCATAAA
*
54542462 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGAAGCTC-A---ACCATCT-AG
* * ** * *
54542509 CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCAT-AAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGA-AGCT-CAACCATCTAG
54542555 TGAACTCGGACTCAACTCAACGAGTTCGGAAGCTCAACCATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGAAGCTCAACCAT-CTAG
54542601 TGA
1 TGA
54542604 CATGTCACTT
Statistics
Matches: 75, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
44 6 0.08
45 3 0.04
46 33 0.44
47 31 0.41
49 1 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGAAGCTCAACCATCTAG
Found at i:54545660 original size:29 final size:29
Alignment explanation
Indices: 54545624--54545680 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
54545614 AAATAAATAT
54545624 GGAAAGGGTTTTTCAACGATATCATATTG
1 GGAAAGGGTTTTTCAACGATATCATATTG
54545653 GGAAAGGGTTTTTCAACGATATCATATT
1 GGAAAGGGTTTTTCAACGATATCATATT
54545681 TTGCAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (29 bp):
GGAAAGGGTTTTTCAACGATATCATATTG
Found at i:54546086 original size:95 final size:95
Alignment explanation
Indices: 54545923--54546112 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
54545913 CTTTCTGAAA
*
54545923 TTAAGCAGTCATATGTACTTCTAAGGATAAATGCACACATAGAATGTCCGGAAAATGTCATAGTA
1 TTAAGCAGTCATATGTACTTCTAAGGATAAATGCACACATAGAATGTCCAGAAAATGTCATAGTA
54545988 ACTACCCGACTATAACCATTGTACTCAACC
66 ACTACCCGACTATAACCATTGTACTCAACC
54546018 TTAAGCAGTCATATGTACTTCTAAGGATAAATGCACACATAGAATGTCCAGAAAATGTCATAGTA
1 TTAAGCAGTCATATGTACTTCTAAGGATAAATGCACACATAGAATGTCCAGAAAATGTCATAGTA
54546083 ACTACCCGACTATAACCATTGTACTCAACC
66 ACTACCCGACTATAACCATTGTACTCAACC
54546113 ATCAATATAA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (95 bp):
TTAAGCAGTCATATGTACTTCTAAGGATAAATGCACACATAGAATGTCCAGAAAATGTCATAGTA
ACTACCCGACTATAACCATTGTACTCAACC
Found at i:54548211 original size:24 final size:24
Alignment explanation
Indices: 54548182--54548230 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
54548172 AATCATACAT
54548182 AAAGTTATATCAACTTCTTTATAA
1 AAAGTTATATCAACTTCTTTATAA
54548206 AAAGTTATATCAACTTCTTTATAA
1 AAAGTTATATCAACTTCTTTATAA
54548230 A
1 A
54548231 CACTTCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (24 bp):
AAAGTTATATCAACTTCTTTATAA
Found at i:54558535 original size:36 final size:36
Alignment explanation
Indices: 54558485--54558556 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
54558475 TCCAAAACTC
54558485 TTAACATGAACTGGGACAGAGCGTCGTCCCCCGCAG
1 TTAACATGAACTGGGACAGAGCGTCGTCCCCCGCAG
** * *
54558521 TTAACATGGCCTGGGATAGAGTGTCGTCCCCCGCAG
1 TTAACATGAACTGGGACAGAGCGTCGTCCCCCGCAG
54558557 CCCGATCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.19
Consensus pattern (36 bp):
TTAACATGAACTGGGACAGAGCGTCGTCCCCCGCAG
Found at i:54563192 original size:43 final size:43
Alignment explanation
Indices: 54563140--54563223 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
54563130 AAATTGATTA
54563140 ACAACGCCAATGTCCCAGACATGATCTTACACGTAAGCACAAT
1 ACAACGCCAATGTCCCAGACATGATCTTACACGTAAGCACAAT
* * * * * *
54563183 ACAATGCCAATGTCCTAGACATGGTTTTACATGTAATCACA
1 ACAACGCCAATGTCCCAGACATGATCTTACACGTAAGCACA
54563224 TCTCGATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (43 bp):
ACAACGCCAATGTCCCAGACATGATCTTACACGTAAGCACAAT
Found at i:54566546 original size:35 final size:35
Alignment explanation
Indices: 54566517--54566586 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
54566507 ATACATCACA
*
54566517 AAACAT-ATTTCATAACTACTAGTCTATACATGCC
1 AAACATCAATTCATAACTACTAGTCTATACATGCC
* *
54566551 ATACTTCAATTCATAACTACTAGTCTATACATGCC
1 AAACATCAATTCATAACTACTAGTCTATACATGCC
54566586 A
1 A
54566587 TACTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 4 0.12
35 28 0.88
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (35 bp):
AAACATCAATTCATAACTACTAGTCTATACATGCC
Found at i:54566587 original size:35 final size:35
Alignment explanation
Indices: 54566525--54566591 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
54566515 CAAAACATAT
54566525 TTCATAACTACTAGTCTATACATGCCATACTTCAA
1 TTCATAACTACTAGTCTATACATGCCATACTTCAA
54566560 TTCATAACTACTAGTCTATACATGCCATACTT
1 TTCATAACTACTAGTCTATACATGCCATACTT
54566592 TAAATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (35 bp):
TTCATAACTACTAGTCTATACATGCCATACTTCAA
Found at i:54567109 original size:30 final size:30
Alignment explanation
Indices: 54567073--54567134 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
54567063 CAAATAGCTG
*
54567073 AAGCTAGTTTAAATCACATACTTAGTGCCA
1 AAGCTAGTTTAAATCACACACTTAGTGCCA
*
54567103 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCACACACTTAGTGCCA
54567133 AA
1 AA
54567135 ACTTCCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (30 bp):
AAGCTAGTTTAAATCACACACTTAGTGCCA
Found at i:54568993 original size:40 final size:40
Alignment explanation
Indices: 54568811--54569033 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
54568801 TCCTCGTTCA
* * * * *
54568811 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
54568850 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
54568890 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
54568930 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
54568970 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
54569010 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54569034 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:54569042 original size:41 final size:41
Alignment explanation
Indices: 54568965--54569042 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54568955 TTAGTATCTC
* * *
54568965 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54569006 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54569043 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:54579668 original size:18 final size:18
Alignment explanation
Indices: 54579647--54579690 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
54579637 ATATTTTCTT
*
54579647 ATTATAAAATAAAATTTG-
1 ATTATAAAAGAAAA-TTGC
54579665 ATTATTAAAAGAAAATTGC
1 ATTA-TAAAAGAAAATTGC
54579684 ATTATAA
1 ATTATAA
54579691 TATTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (18 bp):
ATTATAAAAGAAAATTGC
Found at i:54583208 original size:24 final size:24
Alignment explanation
Indices: 54583176--54583250 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
54583166 AAAGCTGTTA
*
54583176 GGAGAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
54583200 GGAGAGGATTTAGGAGCTGATAGG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
54583224 GGAGAGGATTTATGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
54583248 GGA
1 GGA
54583251 CAACAGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.31, C:0.03, G:0.43, T:0.24
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:54584266 original size:16 final size:15
Alignment explanation
Indices: 54584241--54584271 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
54584231 CTAGATCGGC
54584241 GAAAGCCGAAAAGTT
1 GAAAGCCGAAAAGTT
54584256 GAAATGCCGAAAAGTT
1 GAAA-GCCGAAAAGTT
54584272 AGTATTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.13, G:0.26, T:0.16
Consensus pattern (15 bp):
GAAAGCCGAAAAGTT
Found at i:54591063 original size:24 final size:24
Alignment explanation
Indices: 54591036--54591136 Score: 166
Period size: 24 Copynumber: 4.2 Consensus size: 24
54591026 AAGGCTATCA
*
54591036 GGAGAGGATTTAGGAGCTAATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
54591060 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
54591084 GGAGAGGATTTATGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
54591108 GGAGAGGATTTAGGAGTTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
54591132 GGAGA
1 GGAGA
54591137 ACGGTGTTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.34, C:0.03, G:0.41, T:0.23
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:54594903 original size:13 final size:13
Alignment explanation
Indices: 54594885--54594910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54594875 TAATGGAAAA
54594885 CCATTATGTGTTT
1 CCATTATGTGTTT
54594898 CCATTATGTGTTT
1 CCATTATGTGTTT
54594911 TGTAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CCATTATGTGTTT
Found at i:54597427 original size:23 final size:22
Alignment explanation
Indices: 54597395--54597506 Score: 118
Period size: 23 Copynumber: 5.0 Consensus size: 22
54597385 TGAGCTGATG
*
54597395 AACAGTAAGCTCTATTGACCTGA
1 AACAGTAAGCTCTATTGAGCT-A
* *
54597418 AACGGTAAGCTCTATTAAGCTA
1 AACAGTAAGCTCTATTGAGCTA
54597440 AACAGTAAGCTCT-TTCGAGCTA
1 AACAGTAAGCTCTATT-GAGCTA
* * *
54597462 AACTGGTAAACTCTAATGAGCTAA
1 AAC-AGTAAGCTCTATTGAGCT-A
*
54597486 AACAGTAAGCTCTTTTGAGCT
1 AACAGTAAGCTCTATTGAGCT
54597507 GTAGTGAGTC
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.03
22 21 0.29
23 45 0.62
24 5 0.07
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (22 bp):
AACAGTAAGCTCTATTGAGCTA
Found at i:54597470 original size:45 final size:45
Alignment explanation
Indices: 54597395--54597507 Score: 140
Period size: 45 Copynumber: 2.5 Consensus size: 45
54597385 TGAGCTGATG
* * *
54597395 AACAGTAAGCTCTATTGACCTGAAACGGTAAGCTCTATTAAGCT-A
1 AACAGTAAGCTCT-TTGAGCTGAAACGGTAAACTCTAATAAGCTAA
*
54597440 AACAGTAAGCTCTTTCGAGCT-AAACTGGTAAACTCTAATGAGCTAA
1 AACAGTAAGCTCTTT-GAGCTGAAAC-GGTAAACTCTAATAAGCTAA
54597486 AACAGTAAGCTCTTTTGAGCTG
1 AACAGTAAGCTC-TTTGAGCTG
54597508 TAGTGAGTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
44 6 0.10
45 32 0.54
46 18 0.31
47 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (45 bp):
AACAGTAAGCTCTTTGAGCTGAAACGGTAAACTCTAATAAGCTAA
Found at i:54601954 original size:42 final size:43
Alignment explanation
Indices: 54601897--54602007 Score: 129
Period size: 42 Copynumber: 2.6 Consensus size: 43
54601887 TCGACTTATG
*
54601897 ATTTATGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATTT
1 ATTTACGTGTAAGACCATGTCTGGGACAGT-GGCATCGATATTT
* * *
54601939 GGTTT-CGTGTAAGACCCTATCTGGGACAGTGGCATCGATATTT
1 -ATTTACGTGTAAGACCATGTCTGGGACAGTGGCATCGATATTT
* *
54601982 ATTTACTTGTAAGACCACGTCTGGGA
1 ATTTACGTGTAAGACCATGTCTGGGA
54602008 TGTTGGAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.54
43 26 0.46
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
ATTTACGTGTAAGACCATGTCTGGGACAGTGGCATCGATATTT
Found at i:54602777 original size:10 final size:10
Alignment explanation
Indices: 54602738--54602780 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
54602728 TTGTGTATCA
*
54602738 TATGTTTTGG
1 TATGATTTGG
54602748 TATGATTTTGG
1 TATGA-TTTGG
54602759 CTCATGATTTGG
1 -T-ATGATTTGG
54602771 TATGATTTGG
1 TATGATTTGG
54602781 AATGGTGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 13 0.45
11 6 0.21
12 6 0.21
13 4 0.14
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (10 bp):
TATGATTTGG
Found at i:54621570 original size:40 final size:39
Alignment explanation
Indices: 54621506--54621717 Score: 228
Period size: 40 Copynumber: 5.3 Consensus size: 39
54621496 TCTTCGGAAT
* * *
54621506 TTAG-CCGGATATAACCACAAGCACAAATGCCCTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
*
54621545 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
54621585 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCAGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
54621625 TTATCCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * * *
54621665 TTGGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
*
54621705 TTAGCCTGGATAT
1 TTAGCCCGGATAT
54621718 CATTCAAATG
Statistics
Matches: 142, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
39 10 0.07
40 125 0.88
41 7 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:54621633 original size:80 final size:80
Alignment explanation
Indices: 54621506--54621717 Score: 309
Period size: 80 Copynumber: 2.7 Consensus size: 80
54621496 TCTTCGGAAT
* * * * * *
54621506 TTAG-CCGGATATAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
54621570 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * *
54621585 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCAGGTCTTATCCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
54621650 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * *
54621665 TTGGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCTGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
54621718 CATTCAAATG
Statistics
Matches: 117, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 4 0.03
80 113 0.97
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:54628646 original size:15 final size:16
Alignment explanation
Indices: 54628628--54628665 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54628618 AATTGGAAAG
54628628 ATGAAAAGTT-ATTAA
1 ATGAAAAGTTAATTAA
* *
54628643 ATGACAATTTAATTAA
1 ATGAAAAGTTAATTAA
54628659 ATGAAAA
1 ATGAAAA
54628666 ACAAAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (16 bp):
ATGAAAAGTTAATTAA
Found at i:54631426 original size:47 final size:48
Alignment explanation
Indices: 54631311--54631444 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 48
54631301 AGGAATGTGA
* * * *
54631311 GAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGAT
1 GAGCCAGTGTAAGACTATGTCTGGGACATGGCATC-GACTCGA-TTCGAT
* * *
54631361 -AGTCAGTGTAAGACTATGTCTGGGACATGGCATCGACTTGA-TGGAT
1 GAGCCAGTGTAAGACTATGTCTGGGACATGGCATCGACTCGATTCGAT
*
54631407 GAGCCAGTGTAAGACTATGTCTGTGACATGGCATCGAC
1 GAGCCAGTGTAAGACTATGTCTGGGACATGGCATCGAC
54631445 ATTATACCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 4 0.05
47 35 0.47
48 5 0.07
49 30 0.41
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (48 bp):
GAGCCAGTGTAAGACTATGTCTGGGACATGGCATCGACTCGATTCGAT
Found at i:54632436 original size:12 final size:12
Alignment explanation
Indices: 54632419--54632448 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
54632409 GTTTTTAGAA
54632419 ACGGGCTAAGAC
1 ACGGGCTAAGAC
54632431 ACGGGCTAAGAC
1 ACGGGCTAAGAC
54632443 ACGGGC
1 ACGGGC
54632449 ATGTCATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.37, T:0.07
Consensus pattern (12 bp):
ACGGGCTAAGAC
Found at i:54632651 original size:21 final size:21
Alignment explanation
Indices: 54632625--54632684 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
54632615 GTCATAATGG
*
54632625 CACACGGGTGTGT-TGCCCTTC
1 CACACGGGCGTGTGT-CCCTTC
54632646 CACACGGGCGTGTGTCCCTTC
1 CACACGGGCGTGTGTCCCTTC
* *
54632667 CAGACGGTCGTGTG-CCCT
1 CACACGGGCGTGTGTCCCT
54632685 ATTTCAAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.11
21 30 0.86
22 1 0.03
ACGTcount: A:0.10, C:0.35, G:0.30, T:0.25
Consensus pattern (21 bp):
CACACGGGCGTGTGTCCCTTC
Found at i:54643899 original size:44 final size:44
Alignment explanation
Indices: 54643833--54643974 Score: 132
Period size: 42 Copynumber: 3.3 Consensus size: 44
54643823 TCTAAGATAT
* * *
54643833 CGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTTCAGATTTA
1 CGTGTAAGACCATGTCTAGGACACAGGCATCGATTTCAGATTTA
* *
54643877 CGTGTAAGACCATGTCTAGGACATCA-ACATCG-TATCTA-ATTT-
1 CGTGTAAGACCATGTCTAGGACA-CAGGCATCGATTTC-AGATTTA
* * * * *
54643919 CGTGTAAGACCCTGTCTAGGACAAAGGCATCGA-TACTGAATTA
1 CGTGTAAGACCATGTCTAGGACACAGGCATCGATTTCAGATTTA
*
54643962 CATGTAAGACCAT
1 CGTGTAAGACCAT
54643975 ATCTGAGACG
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 31 0.40
43 18 0.23
44 26 0.33
45 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTAGGACACAGGCATCGATTTCAGATTTA
Found at i:54646210 original size:48 final size:49
Alignment explanation
Indices: 54646135--54646229 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 49
54646125 TGTAAGACTT
* *
54646135 AGTAAATATGCACGGAAGTGCGTATCTACAGAAG-TATCATGTGCAATC
1 AGTAAACATGCACGGAAGTGCGGATCTACAGAAGCTATCATGTGCAATC
* *
54646183 AGTAAACATGCACGGGAGTGTGGATCTACAGAAGCTATCATGTGCAA
1 AGTAAACATGCACGGAAGTGCGGATCTACAGAAGCTATCATGTGCAA
54646230 GAGGTTTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 30 0.71
49 12 0.29
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (49 bp):
AGTAAACATGCACGGAAGTGCGGATCTACAGAAGCTATCATGTGCAATC
Found at i:54655393 original size:24 final size:24
Alignment explanation
Indices: 54655366--54655418 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
54655356 AAGGCTGTCA
54655366 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
54655390 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
54655414 GGAGA
1 GGAGA
54655419 ACGGTGTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.43, T:0.21
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:54656930 original size:27 final size:26
Alignment explanation
Indices: 54656862--54656962 Score: 112
Period size: 27 Copynumber: 3.8 Consensus size: 26
54656852 CTGGTGGTTA
** *
54656862 TGCCACAATTATCTCATCTAGTGGCAC
1 TGCCAC-ATTATCTGTTCTGGTGGCAC
*
54656889 TGCCACATATATCTGTTCTGGTGGCTC
1 TGCCACAT-TATCTGTTCTGGTGGCAC
*
54656916 TGCCACAATTATCTGTTCTGGTGACAC
1 TGCCAC-ATTATCTGTTCTGGTGGCAC
* *
54656943 TGTCACATTATTTGTTCTGG
1 TGCCACATTATCTGTTCTGG
54656963 CAGTCATGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
26 15 0.23
27 47 0.73
28 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (26 bp):
TGCCACATTATCTGTTCTGGTGGCAC
Found at i:54656944 original size:54 final size:53
Alignment explanation
Indices: 54656852--54656962 Score: 141
Period size: 54 Copynumber: 2.1 Consensus size: 53
54656842 AGGAAGCGTC
* *
54656852 CTGGTGGTTATGCCACAATTATCTCATCTAGTGGCACTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTCATCTAGTGACACTGCCACAT-TATCTGTT
* ** * * *
54656906 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACACTGTCACATTATTTGTT
1 CTGGTGGCTATGCCACAATTATCTCATCTAGTGACACTGCCACATTATCTGTT
54656959 CTGG
1 CTGG
54656963 CAGTCATGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 11 0.22
54 38 0.78
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTCATCTAGTGACACTGCCACATTATCTGTT
Done.