Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 151 of 207
Found at i:46332018 original size:18 final size:17
Alignment explanation
Indices: 46331985--46332018 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
46331975 AAATATGACG
*
46331985 TAAAAATTTAAAAAATC
1 TAAAAAATTAAAAAATC
46332002 TAAAAAATTATAAAAAT
1 TAAAAAATTA-AAAAAT
46332019 TTCTCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATTAAAAAATC
Found at i:46332053 original size:23 final size:22
Alignment explanation
Indices: 46332011--46332052 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
46332001 CTAAAAAATT
*
46332011 ATAAAAATTTCTCAAATTTTAA
1 ATAAAAAATTCTCAAATTTTAA
46332033 ATAAAAAATTCT-AAACTTTT
1 ATAAAAAATTCTCAAA-TTTT
46332053 TTAATGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAAAAATTCTCAAATTTTAA
Found at i:46332391 original size:24 final size:24
Alignment explanation
Indices: 46332364--46332411 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
46332354 AAATTAGTAA
46332364 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
46332388 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
46332412 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:46334357 original size:24 final size:24
Alignment explanation
Indices: 46334330--46334377 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
46334320 AAATTAGTAA
46334330 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
46334354 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
46334378 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:46337007 original size:24 final size:23
Alignment explanation
Indices: 46336969--46337021 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
46336959 TGAAATAAAA
* *
46336969 TAAAAATAGTGATAATCATATATT
1 TAAAAATAATGATAATCAT-TAAT
* *
46336993 TAAAAATAATTATAATTATTAAT
1 TAAAAATAATGATAATCATTAAT
46337016 TAAAAA
1 TAAAAA
46337022 ACTATGCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
TAAAAATAATGATAATCATTAAT
Found at i:46340286 original size:22 final size:22
Alignment explanation
Indices: 46340260--46340331 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
46340250 TTCTAAATCT
46340260 ATTTAGAACCACTTTAGATATA
1 ATTTAGAACCACTTTAGATATA
* * * * *
46340282 ATTTATACAGCACATTACATATG
1 ATTTAGA-ACCACTTTAGATATA
46340305 ATTTAGAACCACTTTAGATATA
1 ATTTAGAACCACTTTAGATATA
46340327 ATTTA
1 ATTTA
46340332 TACAGCACAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 22 0.56
23 17 0.44
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
ATTTAGAACCACTTTAGATATA
Found at i:46340308 original size:23 final size:23
Alignment explanation
Indices: 46340277--46340348 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
46340267 ACCACTTTAG
46340277 ATATAATTTATACAGCACATTAC
1 ATATAATTTATACAGCACATTAC
* * * * *
46340300 ATATGATTTAGA-ACCACTTTAG
1 ATATAATTTATACAGCACATTAC
46340322 ATATAATTTATACAGCACATTAC
1 ATATAATTTATACAGCACATTAC
46340345 ATAT
1 ATAT
46340349 GCTAATTGGC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 17 0.45
23 21 0.55
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (23 bp):
ATATAATTTATACAGCACATTAC
Found at i:46340315 original size:45 final size:45
Alignment explanation
Indices: 46340260--46340349 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
46340250 TTCTAAATCT
46340260 ATTTAGAACCACTTTAGATATAATTTATACAGCACATTACATATG
1 ATTTAGAACCACTTTAGATATAATTTATACAGCACATTACATATG
46340305 ATTTAGAACCACTTTAGATATAATTTATACAGCACATTACATATG
1 ATTTAGAACCACTTTAGATATAATTTATACAGCACATTACATATG
46340350 CTAATTGGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (45 bp):
ATTTAGAACCACTTTAGATATAATTTATACAGCACATTACATATG
Found at i:46346899 original size:11 final size:12
Alignment explanation
Indices: 46346881--46346909 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
46346871 GCATTAAGGT
46346881 TATTTTATTTTA
1 TATTTTATTTTA
46346893 T-TTTTATTTTA
1 TATTTTATTTTA
46346904 TATTTT
1 TATTTT
46346910 TGATGTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:46347736 original size:17 final size:17
Alignment explanation
Indices: 46347714--46347761 Score: 78
Period size: 18 Copynumber: 2.8 Consensus size: 17
46347704 TCATCATGTT
46347714 AAAATAATTTTTTTGTC
1 AAAATAATTTTTTTGTC
46347731 AAAATAAATTTTTTTGTC
1 AAAAT-AATTTTTTTGTC
*
46347749 AAAATAGTTTTTT
1 AAAATAATTTTTT
46347762 AAAAAGTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
AAAATAATTTTTTTGTC
Found at i:46353525 original size:50 final size:50
Alignment explanation
Indices: 46353407--46353902 Score: 449
Period size: 50 Copynumber: 9.7 Consensus size: 50
46353397 GGATGAGATA
* *
46353407 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTC
*
46353463 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * *
46353513 TCATGTAAGACCATGTCTAGGACATGTCGTTGGCACTGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
** * * * * * **
46353563 CCCCGTAAGACTATGTCTGGGACATGGCATAGACACCTATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * *
46353613 CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-GATGAGAGGTC
* *
46353669 CCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGATGAGAAGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* *
46353719 TCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
** * * * * **
46353769 CCCCGTAAGACCATGTATGGGATATGGCA-TGGACACCTATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATGAGAGGTC
* * * * * * * **
46353819 CCATGTATGACCATATCTGGGATATGACATTGGCA--GTACAAGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTC
* * *
46353868 CCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
46353903 TGTTATATTC
Statistics
Matches: 362, Mismatches: 69, Indels: 25
0.79 0.15 0.05
Matches are distributed among these distances:
49 38 0.10
50 236 0.65
51 6 0.02
53 3 0.01
55 3 0.01
56 76 0.21
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:46353675 original size:156 final size:150
Alignment explanation
Indices: 46353411--46353853 Score: 402
Period size: 156 Copynumber: 2.9 Consensus size: 150
46353401 GAGATACCAT
* ** * *
46353411 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCA-TAG-A-CACCGAGATGA-G-AA-CTCCCATGTAAGACCA
* * * * *
46353476 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAAGACCATGTCTAGGACATGTC
60 TGTCTGGGATATGGCATTGGCACAGAGATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGC
* * * *
46353541 GTTGGCACTGAGATGAGAGGTCCCCC
125 ATTGGCACCGAGATGAGAAGTCCCAC
* * *
46353567 GTAAGACTATGTCTGGGACATGGCATAGACACCTATATGAGAACTCCCATGTAAGACCATGTCTG
1 GTAAGACCATGTCTGGGACATGGCATAGACACCGAGATGAGAACTCCCATGTAAGACCATGTCTG
* * *
46353632 GGATATGGCATTGGCATCATTAAGATTATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGC
66 GGATATGGCATTGGCA-C----AGA-GATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGC
* *
46353697 ATTGGCACCGAGATGAGAAGTCTCAT
125 ATTGGCACCGAGATGAGAAGTCCCAC
* * * ** ** *
46353723 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATG
1 GTAAGACCATGTCTGGGACATGGCATAGACACCGAGATGAGAACTCCCATGTAAGACCATGTCTG
** * ** * * * * *
46353788 GGATATGGCA-TGGACACCTATATGAGAACTCCCATGTATGACCATATCTGGGATATGACATTGG
66 GGATATGGCATTGG-CACAGAGATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGG
46353852 CA
130 CA
46353854 GTACAAGAAA
Statistics
Matches: 238, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
150 74 0.31
151 4 0.02
152 1 0.00
153 6 0.03
154 1 0.00
155 8 0.03
156 144 0.61
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (150 bp):
GTAAGACCATGTCTGGGACATGGCATAGACACCGAGATGAGAACTCCCATGTAAGACCATGTCTG
GGATATGGCATTGGCACAGAGATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGC
ACCGAGATGAGAAGTCCCAC
Found at i:46353762 original size:206 final size:206
Alignment explanation
Indices: 46353407--46353853 Score: 750
Period size: 206 Copynumber: 2.2 Consensus size: 206
46353397 GGATGAGATA
* *
46353407 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAAAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAAAGGTCCCATGTAAG
* *
46353472 ACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATGTAAGACCATGTCTAGGACA
66 ACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTAGGACA
* * * *
46353537 TGTCGTTGGCACTGAGATGAGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATAGACACCTA
131 TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATAGACACCTA
46353602 TATGAGAACTC
196 TATGAGAACTC
*
46353613 CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAGAGGTCCCATGTAAG
1 CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAAAGGTCCCATGTAAG
* *
46353678 ACCATGTTTGGGACATGGCATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTGGGACA
66 ACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTAGGACA
* *
46353743 TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGATATGGCATGGACACCTA
131 TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATAGACACCTA
46353808 TATGAGAACTC
196 TATGAGAACTC
* * *
46353819 CCATGTATGACCATATCTGGGATATGACATTGGCA
1 CCATGTAAGACCATGTCTGGGATATGGCATTGGCA
46353854 GTACAAGAAA
Statistics
Matches: 225, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
206 225 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (206 bp):
CCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTAAGATTATGAAAGGTCCCATGTAAG
ACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCTCATGTAAGACCATGTCTAGGACA
TGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATAGACACCTA
TATGAGAACTC
Found at i:46356225 original size:30 final size:30
Alignment explanation
Indices: 46356160--46356245 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
46356150 CACGAGAATA
* **
46356160 AGTTGCTCACACAAGCTGACAATATTTCAG
1 AGTTGCTCACACAAGCTGACATTATAACAG
* *
46356190 GGTTGCTCACACAAGCTGACATTGTAACAG
1 AGTTGCTCACACAAGCTGACATTATAACAG
* *
46356220 AGTTGCTTACATAAGCTGACATTATA
1 AGTTGCTCACACAAGCTGACATTATA
46356246 TCGAGATTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (30 bp):
AGTTGCTCACACAAGCTGACATTATAACAG
Found at i:46361551 original size:11 final size:11
Alignment explanation
Indices: 46361535--46361560 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46361525 ATACCAAATG
46361535 TAAAAAATAAA
1 TAAAAAATAAA
46361546 TAAAAAATAAA
1 TAAAAAATAAA
46361557 TAAA
1 TAAA
46361561 TGGCAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:46362504 original size:16 final size:16
Alignment explanation
Indices: 46362483--46362515 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46362473 TTTAAAAGAT
46362483 TTGAAA-GAAAACTCAA
1 TTGAAATGAAAA-TCAA
46362499 TTGAAATGAAAATCAA
1 TTGAAATGAAAATCAA
46362515 T
1 T
46362516 GCCGAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (16 bp):
TTGAAATGAAAATCAA
Found at i:46369654 original size:17 final size:18
Alignment explanation
Indices: 46369634--46369681 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
46369624 AATTTAGTTC
*
46369634 ATTTTTTTATTTTTC-TT
1 ATTTATTTATTTTTCGTT
*
46369651 ATTTATTTA-ATTTCGTT
1 ATTTATTTATTTTTCGTT
46369668 ATTTATTTATTTTT
1 ATTTATTTATTTTT
46369682 ATCACATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 19 0.73
18 3 0.12
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (18 bp):
ATTTATTTATTTTTCGTT
Found at i:46372622 original size:50 final size:50
Alignment explanation
Indices: 46372523--46372710 Score: 169
Period size: 50 Copynumber: 3.6 Consensus size: 50
46372513 AAAGAGATCC
*
46372523 CATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCA---AG---ATGAGAGGTCT
* * * *
46372579 CATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCT
** * * ** * **
46372629 CCCGTAAGACCATGTCTGGGACATGTCATGGGCACTTATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCT
* * *
46372679 CATGTAAGACCCTATCTGGGATATGACATTGG
1 CATGTAAGACCATGTCTGGGACATGACATTGG
46372711 TAGTTCAAGA
Statistics
Matches: 108, Mismatches: 24, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
50 73 0.68
53 2 0.02
56 33 0.31
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCT
Found at i:46377501 original size:35 final size:35
Alignment explanation
Indices: 46377402--46377502 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 35
46377392 ATTTATTGAT
* * * *
46377402 ATTCTGATTCGCATGTTGAGCATGCTATTATTCTG
1 ATTCTGATTCGCATGTTAAGCATGCCATTGTTCTA
* * * *
46377437 ATTCTGATTCACTTGTTAAGCTTGTCATTGTTCTA
1 ATTCTGATTCGCATGTTAAGCATGCCATTGTTCTA
* *
46377472 ATTCTGATTCGCATATTAAACATGCCATTGT
1 ATTCTGATTCGCATGTTAAGCATGCCATTGT
46377503 GATAAATCGT
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.44
Consensus pattern (35 bp):
ATTCTGATTCGCATGTTAAGCATGCCATTGTTCTA
Found at i:46378848 original size:11 final size:11
Alignment explanation
Indices: 46378819--46378851 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
46378809 AGTGAAAAAG
46378819 AAAAGTGAG-A
1 AAAAGTGAGAA
46378829 AAAAGTGAGAA
1 AAAAGTGAGAA
*
46378840 AAAAATGAGAA
1 AAAAGTGAGAA
46378851 A
1 A
46378852 TTCCAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (11 bp):
AAAAGTGAGAA
Found at i:46379080 original size:101 final size:102
Alignment explanation
Indices: 46378960--46379144 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
46378950 AAAGTGATGG
* *
46378960 TCACGTGTGTAGTAGTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
46379023 ACTATGTGCAGGCTACTATGCGTATCGAATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTATCGAATAGCTTCGA
* *
46379061 TCACGTGTGTAGTACTATGTGCAGGCTACTTCGTGTATCAGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
* *
46379126 TTATGTGTAGGCTACTATG
66 CTATGTGCAGGCTACTATG
46379145 TGAACCAGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 39 0.51
102 33 0.43
103 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTATCGAATAGCTTCGA
Found at i:46379081 original size:51 final size:50
Alignment explanation
Indices: 46378960--46379142 Score: 172
Period size: 51 Copynumber: 3.6 Consensus size: 50
46378950 AAAGTGATGG
* * *
46378960 TCACGTGTGTAGTAGTATGTGCAGGCTACTACGTGTACCAGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAATGATAGA
* * * * * *
46379010 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATC-GAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAAT-G-ATAGA
* * * *
46379061 TCACGTGTGTAGTACTATGTGCAGGCTACTTCGTGTATCAGATAGTGAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGA-A-TGATAGA
* * *
46379112 TCACATGTGTAGTATTATGTGTAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
46379143 TGTGAACCAG
Statistics
Matches: 108, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
49 4 0.04
50 34 0.31
51 64 0.59
52 3 0.03
53 2 0.02
54 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAATGATAGA
Found at i:46379239 original size:46 final size:44
Alignment explanation
Indices: 46379153--46379240 Score: 106
Period size: 46 Copynumber: 2.0 Consensus size: 44
46379143 TGTGAACCAG
* *
46379153 TATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCCACCGGA
1 TATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCCACCGGA
* *
46379197 TATCATTGATTAGAAAGGATGGTTGCTGTGTGCTAAAT-CCACCG
1 TATCATTAATTA-AAAGG-TGGTTGCTATGTGCT-AATCCCACCG
46379241 TGTATCTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 11 0.30
45 4 0.11
46 20 0.54
47 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (44 bp):
TATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCCACCGGA
Found at i:46383406 original size:21 final size:21
Alignment explanation
Indices: 46383372--46383413 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
46383362 ATTAGCATCA
46383372 ATTATAACAACTCAAAACATG
1 ATTATAACAACTCAAAACATG
46383393 ATTA-AACAAGCTCAAAACATG
1 ATTATAACAA-CTCAAAACATG
46383414 TCACATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.21
Consensus pattern (21 bp):
ATTATAACAACTCAAAACATG
Found at i:46387355 original size:3 final size:3
Alignment explanation
Indices: 46387340--46387390 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
46387330 TGTCCATGGA
*
46387340 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46387388 AAT
1 AAT
46387391 GGAAAATAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46390361 original size:22 final size:22
Alignment explanation
Indices: 46390329--46390371 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
46390319 TACACACGCA
*
46390329 AATATTTTTTAAAAAATATTTT
1 AATATTATTTAAAAAATATTTT
*
46390351 AATATTATTTAAAATATATTT
1 AATATTATTTAAAAAATATTT
46390372 CATTATCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTATTTAAAAAATATTTT
Found at i:46395687 original size:57 final size:57
Alignment explanation
Indices: 46395593--46395752 Score: 248
Period size: 57 Copynumber: 2.8 Consensus size: 57
46395583 GCATGTAACA
* *
46395593 CTTAGAGACAACTCTCACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
1 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
* * * * *
46395650 CTTAGAGACAGCTCGCACTTCACCAGTTTGTATCTCCATCTCTGTTCACATGCAATG
1 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
*
46395707 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTTAGTT
1 CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTT
46395753 TCCAAGCTCT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.29
Consensus pattern (57 bp):
CTTAGAGACAGCTCACACTTCACCAGTTCGCAACTCCATCTCAGTTCACATGCAATG
Found at i:46400779 original size:99 final size:102
Alignment explanation
Indices: 46400615--46400819 Score: 308
Period size: 99 Copynumber: 2.0 Consensus size: 102
46400605 ATCAACAAAT
* * *
46400615 ATTTTAAAATTTTTAAAATATATATTATTATAAAGTACATAAAAATTAAGAACAAAAACAAGAAG
1 ATTTTAAAATTTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAG
46400680 TACACGT-GGTTGCCATGCGGGCAGCCATATTTAAAA
66 TACACGTAGGTTGCCATGCGGGCAGCCATATTTAAAA
* *
46400716 ATTTT-AAA-TTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAATAAAAACATGAAG
1 ATTTTAAAATTTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAG
* * * *
46400779 TACATGTAGGTTGCCATGCGGGCTGTCATATTTCAAA
66 TACACGTAGGTTGCCATGCGGGCAGCCATATTTAAAA
46400816 ATTT
1 ATTT
46400820 AATGTTTTAG
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
99 56 0.60
100 33 0.35
101 5 0.05
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (102 bp):
ATTTTAAAATTTTTAAAAAATATATAATTATAAAGTACATAAAAATTAAAAACAAAAACAAGAAG
TACACGTAGGTTGCCATGCGGGCAGCCATATTTAAAA
Found at i:46400898 original size:31 final size:31
Alignment explanation
Indices: 46400860--46400922 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
46400850 ATAATTCAAT
*
46400860 TCTTTTTT-AAAGATTGATGGTCAAATTTAAC
1 TCTTTTTTAAAAGATTGA-GATCAAATTTAAC
*
46400891 TCTTTTTTAAAAGCTTGAGATCAAATTTAAC
1 TCTTTTTTAAAAGATTGAGATCAAATTTAAC
46400922 T
1 T
46400923 AAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
TCTTTTTTAAAAGATTGAGATCAAATTTAAC
Found at i:46406526 original size:78 final size:77
Alignment explanation
Indices: 46406294--46406530 Score: 379
Period size: 75 Copynumber: 3.1 Consensus size: 77
46406284 TTTAAATACA
* *
46406294 AAGTTGACTATTTAAATTGTAAAAAAAAACAACATAAAATTGATAAATAAAATGACAACAAATTC
1 AAGTTGACTATTTAAATTG-AAAAAAAAA-ATCATAAAATTGATAAATAAAATGGCAACAAATTC
46406359 ATTACATAAATATG
64 ATTACATAAATATG
46406373 AAGTTGACTATTTAAATTG--AAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCAT
1 AAGTTGACTATTTAAATTGAAAAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCAT
46406436 TACATAAATATG
66 TACATAAATATG
* * * *
46406448 AAGTTGACTATTTAAATCGAAAAAAATAAATCATAAAATTGATAAATAAAATGGGAAAAAAATCA
1 AAGTTGACTATTTAAATTGAAAAAAA-AAATCATAAAATTGATAAATAAAATGGCAACAAATTCA
46406513 TTACATAAATATG
65 TTACATAAATATG
46406526 AAGTT
1 AAGTT
46406531 ATTTATATTA
Statistics
Matches: 149, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
75 65 0.44
76 7 0.05
77 5 0.03
78 53 0.36
79 19 0.13
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (77 bp):
AAGTTGACTATTTAAATTGAAAAAAAAAATCATAAAATTGATAAATAAAATGGCAACAAATTCAT
TACATAAATATG
Found at i:46406756 original size:33 final size:33
Alignment explanation
Indices: 46406714--46406777 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
46406704 ATGAACTTGA
*
46406714 GCCGGGAGAAGTGGTGTACGACGGTGGATACGG
1 GCCGGGAGAAGTGGAGTACGACGGTGGATACGG
46406747 GCCGGGAGAAGTGGAGTACGACGGTGGATAC
1 GCCGGGAGAAGTGGAGTACGACGGTGGATAC
46406778 AGGTTGGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.16, G:0.47, T:0.14
Consensus pattern (33 bp):
GCCGGGAGAAGTGGAGTACGACGGTGGATACGG
Found at i:46406793 original size:33 final size:33
Alignment explanation
Indices: 46406714--46406798 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
46406704 ATGAACTTGA
* * *
46406714 GCCGGGAGAAGTGGTGTACGACGGTGGATACGG
1 GCCGGAAGAAGTGGAGTACGACGGTGGATACAG
*
46406747 GCCGGGAGAAGTGGAGTACGACGGTGGATACAG
1 GCCGGAAGAAGTGGAGTACGACGGTGGATACAG
** *
46406780 GTTGGAAGGAGTGGAGTAC
1 GCCGGAAGAAGTGGAGTAC
46406799 TGAGTTGGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.25, C:0.13, G:0.47, T:0.15
Consensus pattern (33 bp):
GCCGGAAGAAGTGGAGTACGACGGTGGATACAG
Found at i:46407920 original size:31 final size:31
Alignment explanation
Indices: 46407882--46407945 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
46407872 TGCAAATTGG
46407882 ATAATAGGGGTAAGTACATCAAGTGGACCGT
1 ATAATAGGGGTAAGTACATCAAGTGGACCGT
46407913 ATAATAGGGGTAAGTACATCAAGTGGACCGT
1 ATAATAGGGGTAAGTACATCAAGTGGACCGT
46407944 AT
1 AT
46407946 TGCCGTTTGC
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:0.36, C:0.12, G:0.28, T:0.23
Consensus pattern (31 bp):
ATAATAGGGGTAAGTACATCAAGTGGACCGT
Found at i:46409225 original size:30 final size:29
Alignment explanation
Indices: 46409186--46409242 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
46409176 ATAAACACTA
* *
46409186 AACATAAACAATTTATAAATAATAATTAAT
1 AACAAAAACAATTTATAAACAA-AATTAAT
46409216 AACAAAAACAATTTATAAACAAAATTA
1 AACAAAAACAATTTATAAACAAAATTA
46409243 TTTACTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (29 bp):
AACAAAAACAATTTATAAACAAAATTAAT
Found at i:46409292 original size:23 final size:23
Alignment explanation
Indices: 46409264--46409332 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 23
46409254 AATACTTACC
*
46409264 TTTTCTTTCTTTCTTCTTCTTCT
1 TTTTCTTTCTTTCTTCTTCTCCT
* *
46409287 TTTTCTTTTTTTTTTCTTCTCCT
1 TTTTCTTTCTTTCTTCTTCTCCT
46409310 TTCTCTCCTTTCTTTCTCTCTTC
1 TT-T-T-CTTTCTTTCT-TCTTC
46409333 CGGTGCACCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 22 0.59
24 1 0.03
25 1 0.03
26 8 0.22
27 5 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTTCTTTCTTCTTCTCCT
Found at i:46410882 original size:27 final size:26
Alignment explanation
Indices: 46410812--46410889 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 26
46410802 GCATTTTGAC
*
46410812 CCCTAAACTTTTCCTAAATTTCATTTGA
1 CCCTAAAC-TTT-CTAAATTTCATTAGA
46410840 CCCTTAAACTTT-TAAATTTCACTTAGA
1 CCC-TAAACTTTCTAAATTTCA-TTAGA
46410867 CCCT-AACTTTCATAAATTTCATT
1 CCCTAAACTTTC-TAAATTTCATT
46410890 TTAATCCTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
25 6 0.13
26 12 0.27
27 16 0.36
28 6 0.13
29 5 0.11
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (26 bp):
CCCTAAACTTTCTAAATTTCATTAGA
Found at i:46411438 original size:12 final size:11
Alignment explanation
Indices: 46411416--46411499 Score: 70
Period size: 12 Copynumber: 7.8 Consensus size: 11
46411406 AGAAGAGGAG
46411416 AAAAAGAAAGA
1 AAAAAGAAAGA
46411427 AAAAAGAGAAGA
1 AAAAAGA-AAGA
*
46411439 AAAGAGAGAAGA
1 AAAAAGA-AAGA
*
46411451 AAAGAGAAAG-
1 AAAAAGAAAGA
46411461 -AAAAG-AAGA
1 AAAAAGAAAGA
*
46411470 AAAAAG-GAGA
1 AAAAAGAAAGA
*
46411480 AAAAA-ATAGA
1 AAAAAGAAAGA
46411490 AAAGAAGAAA
1 AAA-AAGAAA
46411500 ATAAAATAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
8 3 0.05
9 4 0.06
10 19 0.31
11 12 0.19
12 24 0.39
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:46411474 original size:10 final size:10
Alignment explanation
Indices: 46411416--46411498 Score: 64
Period size: 10 Copynumber: 7.8 Consensus size: 10
46411406 AGAAGAGGAG
46411416 AAAAAGAAAGA
1 AAAAAG-AAGA
46411427 AAAAAG-AGA
1 AAAAAGAAGA
46411436 AGAAAAGAGAGA
1 A-AAAAGA-AGA
46411448 AGAAAAG-AGAA
1 A-AAAAGAAG-A
46411459 AGAAAAGAAGA
1 A-AAAAGAAGA
*
46411470 AAAAAGGAGA
1 AAAAAGAAGA
46411480 AAAAA-ATAGA
1 AAAAAGA-AGA
46411490 AAAGAAGAA
1 AAA-AAGAA
46411499 AATAAAATAA
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
9 4 0.06
10 26 0.42
11 19 0.31
12 13 0.21
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:46411490 original size:28 final size:31
Alignment explanation
Indices: 46411424--46411500 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 31
46411414 AGAAAAAGAA
46411424 AGAAA-AAAGAGAAGAAAAGAGAGAAGAAAAG
1 AGAAAGAAA-AGAAGAAAAGAGAGAAGAAAAG
*
46411455 AGAAAGAAAAGAAGAAAA-A-AGGAGAAAA-
1 AGAAAGAAAAGAAGAAAAGAGAGAAGAAAAG
46411483 A-AATAGAAAAGAAGAAAA
1 AGAA-AGAAAAGAAGAAAA
46411501 TAAAATAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 2 0.05
28 15 0.35
29 8 0.19
30 1 0.02
31 14 0.33
32 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (31 bp):
AGAAAGAAAAGAAGAAAAGAGAGAAGAAAAG
Found at i:46411510 original size:28 final size:28
Alignment explanation
Indices: 46411433--46411515 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
46411423 AAGAAAAAAG
46411433 AGAAGAAAAGAGAGAAGAAAAGAGAA-AGAAA
1 AGAAGAAAA-A-AGAAGAAAA-A-AATAGAAA
*
46411464 AGAAGAAAAAAGGAGAAAAAAATAGAAA
1 AGAAGAAAAAAGAAGAAAAAAATAGAAA
*
46411492 AGAAGAAAATAA-AATAAAAAAATA
1 AGAAGAAAA-AAGAAGAAAAAAATA
46411516 AAAGATAAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
27 2 0.04
28 25 0.53
29 10 0.21
30 1 0.02
31 9 0.19
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (28 bp):
AGAAGAAAAAAGAAGAAAAAAATAGAAA
Found at i:46411658 original size:20 final size:22
Alignment explanation
Indices: 46411635--46411678 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
46411625 AAAAAAGCAC
46411635 AAAAGAAG-AGAAAGAAGCAGAAA
1 AAAAGAAGAAGAAAGAAGCAG--A
46411658 AAAAGAAGAAGAAAGAAGCAG
1 AAAAGAAGAAGAAAGAAGCAG
46411679 CAGCCTCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.68, C:0.05, G:0.27, T:0.00
Consensus pattern (22 bp):
AAAAGAAGAAGAAAGAAGCAGA
Found at i:46412512 original size:17 final size:19
Alignment explanation
Indices: 46412472--46412512 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
46412462 TCGTTGTCAA
*
46412472 AAAAATTCTCCTTGTTTTC
1 AAAAATTCTCCTTATTTTC
*
46412491 GAAAATT-T-CTTATTTTC
1 AAAAATTCTCCTTATTTTC
46412508 AAAAA
1 AAAAA
46412513 GTCGTGTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 12 0.63
18 1 0.05
19 6 0.32
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
AAAAATTCTCCTTATTTTC
Found at i:46412715 original size:19 final size:17
Alignment explanation
Indices: 46412669--46412716 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
46412659 TCGTGTTTCG
*
46412669 TATTTTAACAAAAAATT
1 TATTTTAAAAAAAAATT
46412686 TATTTTCAAAAAACAAATT
1 TATTTT-AAAAAA-AAATT
*
46412705 CTGTTTTAAAAA
1 -TATTTTAAAAA
46412717 TTCTCGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 10 0.38
20 5 0.19
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (17 bp):
TATTTTAAAAAAAAATT
Found at i:46424830 original size:125 final size:123
Alignment explanation
Indices: 46424404--46424844 Score: 737
Period size: 123 Copynumber: 3.6 Consensus size: 123
46424394 ATTTTTTTAA
46424404 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
46424469 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
46424527 GAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTA-TTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
*
46424591 TGTTTTAAA-TCACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTTGTTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAA-TTTTTG-TTTTTC
46424650 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
46424715 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* ** * * *
46424773 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTTTCA-T
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-GCAC--GCCGAGGTATTTTTAGT
46424836 TTATGTTTT
63 TTATGTTTT
46424845 TTTTCAATCA
Statistics
Matches: 301, Mismatches: 10, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
121 35 0.12
122 27 0.09
123 156 0.52
124 35 0.12
125 48 0.16
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (123 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:46425036 original size:72 final size:72
Alignment explanation
Indices: 46424856--46427196 Score: 4001
Period size: 72 Copynumber: 32.6 Consensus size: 72
46424846 TTTCAATCAT
* * ** *
46424856 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGTTGAGGTAATTTTC
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAA-TTTC
46424921 AATTTCTG
65 AATTTCTG
*
46424929 CTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
*
46424994 AATTTTTG
65 AATTTCTG
46425002 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425067 ATTT-TG
66 ATTTCTG
* * *
46425073 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGT-ATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425137 ATTTCTG
66 ATTTCTG
46425144 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425209 ATTTCTG
66 ATTTCTG
*
46425216 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGT-ATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46425280 ATTTTTG
66 ATTTCTG
46425287 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
*
46425352 AATTTTTG
65 AATTTCTG
46425360 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46425425 ATTTTTG
66 ATTTCTG
* * *
46425432 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425497 ATTTCTG
66 ATTTCTG
*
46425504 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTTAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425569 ATTTCTG
66 ATTTCTG
* *
46425576 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46425641 ATTTTTG
66 ATTTCTG
46425648 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTTGAGGTAATTTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
46425712 AATTT-TG
65 AATTTCTG
46425719 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425784 ATTT-TG
66 ATTTCTG
*
46425790 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACA--TCTGAGGTAATTTC
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT-TGAGGTAATTTC
46425853 AATTTCTG
65 AATTTCTG
46425861 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46425926 ATTTCTG
66 ATTTCTG
* *
46425933 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46425998 ATTTTTG
66 ATTTCTG
46426005 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
46426070 AATTT-TG
65 AATTTCTG
* * *
46426077 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46426142 ATTTCTG
66 ATTTCTG
46426149 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46426214 ATTTCTG
66 ATTTCTG
* *
46426221 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46426286 ATTTTTG
66 ATTTCTG
46426293 CTTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTTGAGGTAA-TTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
*
46426356 AATTTTTG
65 AATTTCTG
46426364 -TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46426428 ATTTTTG
66 ATTTCTG
* *
46426435 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACATGCTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46426499 ATTTCTG
66 ATTTCTG
46426506 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46426571 ATTTCTG
66 ATTTCTG
* *
46426578 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46426643 ATTTTTG
66 ATTTCTG
*
46426650 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTAAGGTAATTTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
46426715 AATTTCTG
65 AATTTCTG
* * * *
46426723 TTTTCAAAATTTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46426788 ATTTCTG
66 ATTTCTG
46426795 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46426860 ATTTTTG
66 ATTTCTG
* * *
46426867 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46426932 ATTTCTG
66 ATTTCTG
* *
46426939 TTTTCAAAATTC-ACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
*
46427003 ATTTTTG
66 ATTTCTG
46427010 CTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
46427075 AATTTCTG
65 AATTTCTG
*
46427083 TTTTCAAAATTTAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTCA
1 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
46427147 ATTTCTG
66 ATTTCTG
* **
46427154 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 -TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
46427197 TTAATTTCTG
Statistics
Matches: 2157, Mismatches: 89, Indels: 44
0.94 0.04 0.02
Matches are distributed among these distances:
69 27 0.01
70 102 0.05
71 475 0.22
72 1213 0.56
73 286 0.13
74 54 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (72 bp):
TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
ATTTCTG
Found at i:46427278 original size:54 final size:54
Alignment explanation
Indices: 46427146--46427414 Score: 452
Period size: 55 Copynumber: 5.0 Consensus size: 54
46427136 GAGGTATTTC
46427146 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
46427199 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
46427253 AATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* *
46427307 AATTTCTATTTTTCAAAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* *
46427362 GCAAATTCTG-TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1 --AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
46427415 GGTTCACGTG
Statistics
Matches: 204, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
53 50 0.25
54 68 0.33
55 75 0.37
56 5 0.02
57 6 0.03
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (54 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:46427681 original size:15 final size:16
Alignment explanation
Indices: 46427655--46427691 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
46427645 GTTAATTTTC
46427655 AAAATTTCAAAAAAAA
1 AAAATTTCAAAAAAAA
*
46427671 AAAATTT-AAAAAATA
1 AAAATTTCAAAAAAAA
46427686 AAAATT
1 AAAATT
46427692 GCATTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATTTCAAAAAAAA
Found at i:46427727 original size:30 final size:30
Alignment explanation
Indices: 46427687--46427788 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
46427677 TAAAAAATAA
* * *
46427687 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCTTAAAC-TTTCATT
*
46427717 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCTTAAACTTTCATT
* *
46427747 AAATTTCACTTAGACCCTTAAACTTTCATT
1 AAATTTCATTTTGACCCTTAAACTTTCATT
46427777 AAATTTCATTTT
1 AAATTTCATTTT
46427789 AATCCTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 4 0.06
30 59 0.94
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTGACCCTTAAACTTTCATT
Found at i:46428244 original size:14 final size:15
Alignment explanation
Indices: 46428218--46428257 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
46428208 ATCAAATAAA
46428218 GAAAAGAGAAGAGAG
1 GAAAAGAGAAGAGAG
*
46428233 GAAAAG-GAAGAGTG
1 GAAAAGAGAAGAGAG
46428247 G--AAGAGAAGAG
1 GAAAAGAGAAGAG
46428258 CCCGTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 6 0.26
14 8 0.35
15 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (15 bp):
GAAAAGAGAAGAGAG
Found at i:46428358 original size:11 final size:11
Alignment explanation
Indices: 46428334--46428392 Score: 68
Period size: 12 Copynumber: 5.2 Consensus size: 11
46428324 CGGCCCGAAG
46428334 AAGAGGAAGAAA
1 AAGA-GAAGAAA
46428346 AAGA-AAGGAAAA
1 AAGAGAA-G-AAA
46428358 AAGAGAAGAAA
1 AAGAGAAGAAA
46428369 AAGAGAAAGAAA
1 AAGAG-AAGAAA
46428381 AAGA-AAGAAA
1 AAGAGAAGAAA
46428391 AA
1 AA
46428393 AAGGAGAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.23
11 9 0.21
12 22 0.51
13 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAGAGAAGAAA
Found at i:46428369 original size:10 final size:11
Alignment explanation
Indices: 46428334--46428391 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
46428324 CGGCCCGAAG
*
46428334 AAGAGGAAGAA
1 AAGAGAAAGAA
46428345 AA-AGAAAGGAA
1 AAGAGAAA-GAA
*
46428356 AAAAGAGAAGAAA
1 AAGAGA-AAG-AA
46428369 AAGAGAAAGAA
1 AAGAGAAAGAA
46428380 AA-AGAAAGAA
1 AAGAGAAAGAA
46428390 AA
1 AA
46428392 AAAGGAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 14 0.34
11 11 0.27
12 7 0.17
13 9 0.22
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAGAAAGAA
Found at i:46428379 original size:35 final size:35
Alignment explanation
Indices: 46428334--46428424 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
46428324 CGGCCCGAAG
* *
46428334 AAGAGGAAGAAAAAGAAAGGAAAAAA-GAGAAGAAA
1 AAGAGAAAGAAAAAGAAAGAAAAAAAGGAG-AGAAA
46428369 AAGAGAAAGAAAAAGAAAGAAAAAAAGGAGAGAAA
1 AAGAGAAAGAAAAAGAAAGAAAAAAAGGAGAGAAA
* *
46428404 AA-A-ATAGAAAAGGAAAGAAAA
1 AAGAGAAAGAAAAAGAAAGAAAA
46428425 TAAAATAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 16 0.31
34 1 0.02
35 31 0.61
36 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (35 bp):
AAGAGAAAGAAAAAGAAAGAAAAAAAGGAGAGAAA
Found at i:46428393 original size:11 final size:11
Alignment explanation
Indices: 46428343--46428424 Score: 71
Period size: 12 Copynumber: 7.3 Consensus size: 11
46428333 GAAGAGGAAG
46428343 AAAAAGAAAGGA
1 AAAAAGAAA-GA
46428355 AAAAAGAGAAGA
1 AAAAAGA-AAGA
46428367 AAAAGAGAAAG-
1 AAAA-AGAAAGA
46428378 AAAAAGAAAGAA
1 AAAAAGAAAG-A
*
46428390 AAAAAGGAGAGA
1 AAAAA-GAAAGA
*
46428402 AAAAA-ATAG-
1 AAAAAGAAAGA
*
46428411 AAAAGGAAAGA
1 AAAAAGAAAGA
46428422 AAA
1 AAA
46428425 TAAAATAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
9 4 0.07
10 12 0.20
11 7 0.12
12 27 0.46
13 9 0.15
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:46428393 original size:23 final size:23
Alignment explanation
Indices: 46428355--46428437 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
46428345 AAAGAAAGGA
*
46428355 AAAAAGAGAAGAAAAAGA-GAAAG
1 AAAAAGA-AAGAAAAAAAGGAAAG
*
46428378 AAAAAGAAAGAAAAAAAGGAGAG
1 AAAAAGAAAGAAAAAAAGGAAAG
46428401 AAAAA-AATAG---AAAAGGAAAG
1 AAAAAGAA-AGAAAAAAAGGAAAG
*
46428421 AAAATA-AAATAAAAAAA
1 AAAA-AGAAAGAAAAAAA
46428438 TAAAAAGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 14 0.28
21 3 0.06
22 11 0.22
23 22 0.44
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAAGAAAGAAAAAAAGGAAAG
Found at i:46428429 original size:22 final size:20
Alignment explanation
Indices: 46428366--46428436 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 20
46428356 AAAAGAGAAG
*
46428366 AAAAAGAGAAAGAAAAAGAAAGAA
1 AAAAAG-GAAAG-AAAA-AAA-TA
*
46428390 AAAAAGGAGAGAAAAAAATA
1 AAAAAGGAAAGAAAAAAATA
*
46428410 GAAAAGGAAAGAAAATAAAATA
1 AAAAAGGAAAG-AAA-AAAATA
46428432 AAAAA
1 AAAAA
46428437 ATAAAAAGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 10 0.25
21 6 0.15
22 14 0.35
23 4 0.10
24 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (20 bp):
AAAAAGGAAAGAAAAAAATA
Found at i:46428585 original size:24 final size:24
Alignment explanation
Indices: 46428558--46428613 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
46428548 AGCAAAAAAA
46428558 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
*
46428582 AAGCAGAAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
46428606 AAGCAGCA
1 AAGCAGCA
46428614 GGCCTCCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.66, C:0.09, G:0.25, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:46428779 original size:12 final size:13
Alignment explanation
Indices: 46428751--46428784 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
46428741 ATCCAGCAAA
46428751 AAAAAAAGAAAGAG
1 AAAAAAA-AAAGAG
46428765 AAAAAAAAAAG-G
1 AAAAAAAAAAGAG
46428777 AAAAAAAA
1 AAAAAAAA
46428785 GGCCCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 4 0.20
14 7 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:46429278 original size:18 final size:17
Alignment explanation
Indices: 46429231--46429292 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
46429221 TAAAGAAAAA
*
46429231 TCGTGTTTCAAAAATTT
1 TCGTGTTTCCAAAATTT
*
46429248 TCATGTCTT-CAAAATTT
1 TCGTGT-TTCCAAAATTT
*
46429265 TCCGTGTTTCCAAATATAT
1 T-CGTGTTTCCAAA-ATTT
46429284 TCGTGTTTC
1 TCGTGTTTC
46429293 TTTCTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.41
18 18 0.49
19 4 0.11
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCCAAAATTT
Found at i:46429332 original size:17 final size:17
Alignment explanation
Indices: 46429312--46429637 Score: 87
Period size: 17 Copynumber: 18.8 Consensus size: 17
46429302 AAAAAAAATC
46429312 CGTGTTTCAAAAATTCT
1 CGTGTTTCAAAAATTCT
** **
46429329 CGTGAAT-AAAAA-AAT
1 CGTGTTTCAAAAATTCT
*
46429344 CGTGTTTTCAAAAATTCC
1 CGTG-TTTCAAAAATTCT
* **
46429362 CGTGTTTTAAAAA-AAT
1 CGTGTTTCAAAAATTCT
* *
46429378 CGTTTTTTAAAAAAATTTCT
1 CG-TGTTT-CAAAAA-TTCT
*
46429398 CGTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTCT
* *
46429415 CGTGTTTTCAAAATTTTT
1 CGTG-TTTCAAAAATTCT
***
46429433 CGTGTCAAAAAAATTCT
1 CGTGTTTCAAAAATTCT
* * *
46429450 CCTGTATCGAAAATT-T
1 CGTGTTTCAAAAATTCT
* * * *
46429466 CCTTATTTTCAAAATTTTT
1 -CGT-GTTTCAAAAATTCT
* *
46429485 CGTGTTTTCAAAAAATAT
1 CGTG-TTTCAAAAATTCT
* *
46429503 TGTGTTTCGAAAA-TCTT
1 CGTGTTTCAAAAATTC-T
* * *
46429520 TGTGTTTTTAAAAATTTT
1 CGTG-TTTCAAAAATTCT
*
46429538 GGTGTTTCAAAAATT-T
1 CGTGTTTCAAAAATTCT
*
46429554 CCGCGTTTCTAAAAATTC-
1 -CGTGTTTC-AAAAATTCT
* *
46429572 AGATGATTT-AAAAAATCTT
1 CG-TG-TTTCAAAAATTC-T
46429591 CGTGCTTTCAAAAACTTC-
1 CGTG-TTTCAAAAA-TTCT
* * *
46429609 GGTGTTTC-TAAATTTT
1 CGTGTTTCAAAAATTCT
*
46429625 CATGTTTCAAAAA
1 CGTGTTTCAAAAA
46429638 AAAATCCTCG
Statistics
Matches: 220, Mismatches: 63, Indels: 52
0.66 0.19 0.16
Matches are distributed among these distances:
15 7 0.03
16 20 0.09
17 93 0.42
18 80 0.36
19 15 0.07
20 5 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAAATTCT
Found at i:46429344 original size:33 final size:33
Alignment explanation
Indices: 46429303--46429391 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
46429293 TTTCTTTTAA
*
46429303 AAAAAAATCCGTG-TTTCAAAAATTCTCGTGAAT
1 AAAAAAAT-CGTGTTTTCAAAAATTCCCGTGAAT
**
46429336 AAAAAAATCGTGTTTTCAAAAATTCCCGTGTTTT
1 AAAAAAATCGTGTTTTCAAAAATTCCCGTG-AAT
* *
46429370 AAAAAAATCGTTTTTTAAAAAA
1 AAAAAAATCGTGTTTTCAAAAA
46429392 ATTTCTCGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 4 0.08
33 24 0.49
34 21 0.43
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (33 bp):
AAAAAAATCGTGTTTTCAAAAATTCCCGTGAAT
Found at i:46429356 original size:16 final size:16
Alignment explanation
Indices: 46429335--46429393 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
46429325 TTCTCGTGAA
46429335 TAAAAAAATCGTGTTT
1 TAAAAAAATCGTGTTT
* *
46429351 TCAAAAATTCCCGTGTTT
1 TAAAAAAAT--CGTGTTT
*
46429369 TAAAAAAATCGTTTTT
1 TAAAAAAATCGTGTTT
46429385 TAAAAAAAT
1 TAAAAAAAT
46429394 TTCTCGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 22 0.61
18 14 0.39
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (16 bp):
TAAAAAAATCGTGTTT
Found at i:46429357 original size:18 final size:17
Alignment explanation
Indices: 46429336--46429392 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
46429326 TCTCGTGAAT
46429336 AAAAAAATCGTGTTTT-
1 AAAAAAATCGTGTTTTA
* *
46429352 CAAAAATTCCCGTGTTTT-
1 AAAAAAAT--CGTGTTTTA
*
46429370 AAAAAAATCGTTTTTTA
1 AAAAAAATCGTGTTTTA
46429387 AAAAAA
1 AAAAAA
46429393 TTTCTCGTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 13 0.39
17 6 0.18
18 14 0.42
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (17 bp):
AAAAAAATCGTGTTTTA
Found at i:46429409 original size:18 final size:17
Alignment explanation
Indices: 46429388--46429637 Score: 134
Period size: 18 Copynumber: 14.3 Consensus size: 17
46429378 CGTTTTTTAA
46429388 AAAAATTTCTCGTGTTTC
1 AAAAATTT-TCGTGTTTC
46429406 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* ***
46429424 AAAATTTTTCGTGTCAA
1 AAAAATTTTCGTGTTTC
* * *
46429441 AAAAATTCTCCTGTATC
1 AAAAATTTTCGTGTTTC
* * * *
46429458 GAAAATTTCCTTATTTTC
1 AAAAATTTTCGT-GTTTC
*
46429476 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
46429494 AAAAAATATT-GTGTTTC
1 -AAAAATTTTCGTGTTTC
* *
46429511 GAAAATCTTT-GTGTTTTT
1 AAAAAT-TTTCGTG-TTTC
*
46429529 AAAAATTTTGGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
46429546 AAAAATTTCCGCGTTTC
1 AAAAATTTTCGTGTTTC
*
46429563 TAAAAA--TTCAGATGATTTA
1 -AAAAATTTTC-G-TG-TTTC
*
46429582 AAAAATCTTCGTGCTTTC
1 AAAAATTTTCGTG-TTTC
*
46429600 AAAAA-CTTCGGTGTTTC
1 AAAAATTTTC-GTGTTTC
* *
46429617 -TAAATTTTCATGTTTC
1 AAAAATTTTCGTGTTTC
46429633 AAAAA
1 AAAAA
46429638 AAAATCCTCG
Statistics
Matches: 176, Mismatches: 40, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
16 16 0.09
17 69 0.39
18 77 0.44
19 11 0.06
20 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:46429428 original size:35 final size:35
Alignment explanation
Indices: 46429343--46429553 Score: 117
Period size: 35 Copynumber: 6.0 Consensus size: 35
46429333 AATAAAAAAA
* * * **
46429343 TCGTGTTTTCAAAAATTCCCGTGTTTTAAAAA-AA
1 TCGTGTTTTCAAAATTTCTCGTGTTTCAAAAATTT
* *
46429377 TCGTTTTTTAAAAAAATTTCTCGTGTTTCAAAAATTT
1 TCGTGTTTT--CAAAATTTCTCGTGTTTCAAAAATTT
* *** *
46429414 TCGTGTTTTCAAAATTTTTCGTGTCAAAAAAATTC
1 TCGTGTTTTCAAAATTTCTCGTGTTTCAAAAATTT
* * * * *
46429449 TCCTG-TATCGAAAATTTC-CTTATTTTCAAAATTTT
1 TCGTGTTTTC-AAAATTTCTCGT-GTTTCAAAAATTT
** * * *
46429484 TCGTGTTTTCAAAAAATATTGTGTTTCGAAAATCTT
1 TCGTGTTTTCAAAATTTCTCGTGTTTCAAAAAT-TT
* *
46429520 T-GTGTTTTTAAAAATTT-TGGTGTTTCAAAAATTT
1 TCGTG-TTTTCAAAATTTCTCGTGTTTCAAAAATTT
46429554 CCGCGTTTCT
Statistics
Matches: 129, Mismatches: 39, Indels: 18
0.69 0.21 0.10
Matches are distributed among these distances:
34 15 0.12
35 71 0.55
36 35 0.27
37 8 0.06
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (35 bp):
TCGTGTTTTCAAAATTTCTCGTGTTTCAAAAATTT
Found at i:46429465 original size:52 final size:53
Alignment explanation
Indices: 46429386--46429489 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 53
46429376 ATCGTTTTTT
* * * *
46429386 AAAAAAATTTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTTCGTGTC
1 AAAAAAATTTCTCCTGTATCAAAAATTTCCGTATTTTCAAAATTTTTCGTGTC
* *
46429439 AAAAAAA-TTCTCCTGTATCGAAAATTTCCTTATTTTCAAAATTTTTCGTGT
1 AAAAAAATTTCTCCTGTATCAAAAATTTCCGTATTTTCAAAATTTTTCGTGT
46429490 TTTCAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
52 38 0.84
53 7 0.16
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (53 bp):
AAAAAAATTTCTCCTGTATCAAAAATTTCCGTATTTTCAAAATTTTTCGTGTC
Found at i:46429708 original size:16 final size:17
Alignment explanation
Indices: 46429687--46429722 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
46429677 TTTCAAAAAC
*
46429687 AAATTTTC-TGTTTTAA
1 AAATTTTCGTGTTTCAA
46429703 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
46429720 AAA
1 AAA
46429723 GAAGATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:46429815 original size:17 final size:16
Alignment explanation
Indices: 46429795--46429848 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
46429785 TTTTAAAAAA
46429795 AAAATTTTTGTGTTTCT
1 AAAATTTTTGTGTTT-T
* *
46429812 AAAATTCTTGTATTTT
1 AAAATTTTTGTGTTTT
*
46429828 AAAATTTTCGTGTTTT
1 AAAATTTTTGTGTTTT
46429844 CAAAA
1 -AAAA
46429849 AAAGAAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (16 bp):
AAAATTTTTGTGTTTT
Found at i:46429843 original size:16 final size:15
Alignment explanation
Indices: 46429795--46429848 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
46429785 TTTTAAAAAA
46429795 AAAATTTTTGTGTTTCT
1 AAAA-TTTTGTGTTT-T
*
46429812 AAAATTCTTGTATTTT
1 AAAATT-TTGTGTTTT
46429828 AAAATTTTCGTGTTTT
1 AAAATTTT-GTGTTTT
46429844 CAAAA
1 -AAAA
46429849 AAAGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 15 0.47
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (15 bp):
AAAATTTTGTGTTTT
Found at i:46431595 original size:29 final size:29
Alignment explanation
Indices: 46431481--46431658 Score: 128
Period size: 29 Copynumber: 6.0 Consensus size: 29
46431471 TTTGCATGAT
46431481 CATATAGGCTCGCATGTACCTAGGGTTCACATGG
1 CATATAGGCTCGCATGTACCTAGGGTT--C---G
* *
46431515 CATATAGGCAT-GCATGCT-CTTAGGGATCG
1 CATATAGGC-TCGCATG-TACCTAGGGTTCG
* * * **
46431544 CATAAAGGCTCGTAAGTTTCTAGGGTTCG
1 CATATAGGCTCGCATGTACCTAGGGTTCG
* *
46431573 CACATAGGCTCGCATGTACCTAGGGTTCA
1 CATATAGGCTCGCATGTACCTAGGGTTCG
* * * *
46431602 CATGTAGGGTCGCATGTACCTAAGGTTCA
1 CATATAGGCTCGCATGTACCTAGGGTTCG
* *
46431631 CATATAGGCTCACAT-AATCCTAGGGTTC
1 CATATAGGCTCGCATGTA-CCTAGGGTTC
46431659 TTATATAATC
Statistics
Matches: 115, Mismatches: 24, Indels: 15
0.75 0.16 0.10
Matches are distributed among these distances:
28 3 0.03
29 88 0.77
32 1 0.01
34 21 0.18
35 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (29 bp):
CATATAGGCTCGCATGTACCTAGGGTTCG
Found at i:46431702 original size:36 final size:36
Alignment explanation
Indices: 46431661--46431737 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
46431651 TAGGGTTCTT
* * * *
46431661 ATATAATCAACATATGGTTCGCATAACATGACTTGC
1 ATATAATAAACACATGGTTCACATAACATGACTCGC
* *
46431697 ATATAATAAACACATGGTTCACATATCATGGCTCGC
1 ATATAATAAACACATGGTTCACATAACATGACTCGC
46431733 ATATA
1 ATATA
46431738 GATTCAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (36 bp):
ATATAATAAACACATGGTTCACATAACATGACTCGC
Found at i:46433070 original size:31 final size:30
Alignment explanation
Indices: 46433035--46433112 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
46433025 ATGCTCAAAT
*
46433035 CAATTCAACAATGTATATTC-ATATA-CGAA
1 CAATTCAACAATGTATA-TCGATATACCCAA
** *
46433064 TCCAATTCAGGAATGAATATCGATATACCCAA
1 --CAATTCAACAATGTATATCGATATACCCAA
46433096 CAATTCAACAATGTATA
1 CAATTCAACAATGTATA
46433113 ACTATTCACG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
30 16 0.42
31 19 0.50
32 3 0.08
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (30 bp):
CAATTCAACAATGTATATCGATATACCCAA
Found at i:46433348 original size:184 final size:184
Alignment explanation
Indices: 46433080--46433594 Score: 766
Period size: 184 Copynumber: 2.8 Consensus size: 184
46433070 TCAGGAATGA
* * * * *
46433080 ATATCGATATACCCAACAATTCAACAATGTATAACTATTCACGAATCAAGATCGGCAATATATAA
1 ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
*
46433145 TCAGACACAAATCAAATTCAGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
66 TCAAACACAAATCAAATTCAGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
46433210 AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
131 AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
46433264 ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
1 ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
* *
46433329 TCATACACAAATTAAATTCAGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
66 TCAAACACAAATCAAATTCAGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
* ** *
46433394 AGTACGAATTAATTTTAGTAATGTACAACCCTGTATGAATCAAGTCAGCAACTT
131 AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
* * ** *
46433448 ATATCCATATACCAAATAATTC-GACAATGTATAACCATACACGAATCAAGTTCGATAATGTATA
1 ATATCCATATACCAAACAATTCAG-CAATGTATAACCATACACGAATCAAGATCGGCAATATATA
* * * * * *
46433512 ATCAAATACAAATCCAATTCGGCATCCTATATACAT-AACAAATTCAATATCGCCAATATATAAC
65 ATCAAACACAAATCAAATTCAGCATCCTATATTCATAAAC-AATTCACTATCGACAATATATAAC
*
46433576 CATGTAC-AAGTTAATTTCA
129 CAAGTACGAA-TTAATTTCA
46433595 GAAAGGTAAA
Statistics
Matches: 302, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
183 6 0.02
184 296 0.98
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (184 bp):
ATATCCATATACCAAACAATTCAGCAATGTATAACCATACACGAATCAAGATCGGCAATATATAA
TCAAACACAAATCAAATTCAGCATCCTATATTCATAAACAATTCACTATCGACAATATATAACCA
AGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAGCAACTT
Found at i:46433507 original size:91 final size:91
Alignment explanation
Indices: 46433193--46433509 Score: 257
Period size: 91 Copynumber: 3.5 Consensus size: 91
46433183 CAATTCACTA
* * * *
46433193 TCGACAATATATAACCAAGTACGAATTAATTTCAACAATGTACAACCCTGTACGAATCAAGTCAG
1 TCGACAATATATAACCAAGCACGAATCAAGTTCGACAATGTACAACCCTGTACGAATCAAGTCAG
*
46433258 CAACTTATATCCATATACCAAACAAT
66 CAACTTATATCCATATACCAAATAAT
* * * * * * * ** * * *
46433284 TC-AGCAATGTATAACCATA-CACGAATCAAGATCGGCAATATATAATCATACACAAATTAAATT
1 TCGA-CAATATATAACCA-AGCACGAATCAAGTTCGACAATGTACAACCCTGTACGAA-TCAAGT
* * * * * *
46433347 CAGCATCCTATATTCATA-AACAATTCACT
63 CAGCAACTTATATCCATATACCAAAT-AAT
* * ** * *
46433376 ATCGACAATATATAACCAAGTACGAATTAA-TTTTAGTAATGTACAACCCTGTATGAATCAAGTC
1 -TCGACAATATATAACCAAGCACGAATCAAGTTCGA-CAATGTACAACCCTGTACGAATCAAGTC
46433440 AGCAACTTATATCCATATACCAAATAAT
64 AGCAACTTATATCCATATACCAAATAAT
* *
46433468 TCGACAATGTATAACCATA-CACGAATCAAGTTCGATAATGTA
1 TCGACAATATATAACCA-AGCACGAATCAAGTTCGACAATGTA
46433510 TAATCAAATA
Statistics
Matches: 163, Mismatches: 52, Indels: 22
0.69 0.22 0.09
Matches are distributed among these distances:
90 1 0.01
91 73 0.45
92 49 0.30
93 39 0.24
94 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (91 bp):
TCGACAATATATAACCAAGCACGAATCAAGTTCGACAATGTACAACCCTGTACGAATCAAGTCAG
CAACTTATATCCATATACCAAATAAT
Found at i:46448126 original size:16 final size:16
Alignment explanation
Indices: 46448101--46448131 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46448091 AACAAAAATA
*
46448101 TTTACGGAAACAATTG
1 TTTACAGAAACAATTG
46448117 TTTACAGAAACAATT
1 TTTACAGAAACAATT
46448132 TTTTTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
TTTACAGAAACAATTG
Found at i:46452215 original size:102 final size:101
Alignment explanation
Indices: 46452036--46452240 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 101
46452026 TCTTTTCTTT
46452036 TTAGGTCTGCATATGATTTTTTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATTT
1 TTAGGTCTGCATATGATTTTTTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATTT
* * *
46452101 TTTCTTCGGTTTCTTGTACAAACTCAGGACCCATTA
66 TGTCTTCAGTTTCCTGTACAAACTCAGGACCCATTA
46452137 TTAGGTCTGCATATGATTTTTGTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
1 TTAGGTCTGCATATGATTTTT-TCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATT
*
46452202 TTGTCTTCAGTTTCCTGTACTAACTCAGGACCCATTA
65 TTGTCTTCAGTTTCCTGTACAAACTCAGGACCCATTA
46452239 TT
1 TT
46452241 TTTCTTTCTT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 21 0.21
102 78 0.79
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (101 bp):
TTAGGTCTGCATATGATTTTTTCTGTTAGAAGTTGTTTTTAACCTCTCTTGAATTACTCAAATTT
TGTCTTCAGTTTCCTGTACAAACTCAGGACCCATTA
Found at i:46456109 original size:42 final size:43
Alignment explanation
Indices: 46456046--46456142 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
46456036 TTACGATTTA
* * *
46456046 CATGTAAGACCATGTCTGGGACATTGGCATC-ATATAAGAGTT
1 CATGTAAGACCATGCCGGGGACAGTGGCATCGATATAAGAGTT
* * ** *
46456088 CGTGTAAGACCCTGCCGGGGACAGTGGCATCGATATTTGATTT
1 CATGTAAGACCATGCCGGGGACAGTGGCATCGATATAAGAGTT
46456131 CATGTAAGACCA
1 CATGTAAGACCA
46456143 CGTCTGGGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 26 0.59
43 18 0.41
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (43 bp):
CATGTAAGACCATGCCGGGGACAGTGGCATCGATATAAGAGTT
Found at i:46456152 original size:43 final size:43
Alignment explanation
Indices: 46455989--46456160 Score: 127
Period size: 43 Copynumber: 4.0 Consensus size: 43
46455979 CATAGGATTC
* * * * * **
46455989 CGATATGTGATTACGTGTAAGACCACGTTTGGCACTTTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACAGTGGCAT
* * * *
46456032 TGAT-TTACGATTTACATGTAAGACCATGTCTGGGACATTGGCAT
1 CGATATT-TGATTT-CATGTAAGACCACGTCTGGGACAGTGGCAT
** * * * *
46456076 C-ATATAAGAGTTCGTGTAAGACC-CTGCCGGGGACAGTGGCAT
1 CGATATTTGATTTCATGTAAGACCAC-GTCTGGGACAGTGGCAT
46456118 CGATATTTGATTTCATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACAG-TGGCAT
46456161 TGAATGAGCT
Statistics
Matches: 98, Mismatches: 24, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
42 27 0.28
43 44 0.45
44 27 0.28
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
CGATATTTGATTTCATGTAAGACCACGTCTGGGACAGTGGCAT
Found at i:46460180 original size:16 final size:15
Alignment explanation
Indices: 46460149--46460188 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
46460139 TTAAAAATCA
*
46460149 ATTTTTAACTTAAAAT
1 ATTTTTAA-ATAAAAT
46460165 ATATTTTAAATAAAAT
1 AT-TTTTAAATAAAAT
46460181 ATTTTTAA
1 ATTTTTAA
46460189 TGACATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAATAAAAT
Found at i:46460185 original size:32 final size:31
Alignment explanation
Indices: 46460117--46460188 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 31
46460107 TATTTAGTAC
* *
46460117 TTTTTAAACTTAAAATGTATTTTTAAAAATCAA
1 TTTTT-AACTTAAAATATATTTTAAAAAAT-AA
46460150 TTTTTAACTTAAAATATATTTTAAATAAA-ATA
1 TTTTTAACTTAAAATATATTTTAAA-AAATA-A
46460182 TTTTTAA
1 TTTTTAA
46460189 TGACATTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 26 0.74
33 8 0.23
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (31 bp):
TTTTTAACTTAAAATATATTTTAAAAAATAA
Found at i:46460580 original size:63 final size:61
Alignment explanation
Indices: 46460477--46460596 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 61
46460467 ATGTGATATC
*
46460477 TGTATTTTAAAAATGTCCAATGACTGTACCTGAACTATCAATATGTATTTTATTATGATGCA
1 TGTATTTTAAAAATGTCCAATGA-TGTACCTGAACTATCAATATATATTTTATTATGATGCA
* *
46460539 TGTACTTTTATAAAATGTCCAATG-TGGTACTTGAACTATCAATATATGTTTTATTATG
1 TGTA-TTTTA-AAAATGTCCAATGAT-GTACCTGAACTATCAATATATATTTTATTATG
46460597 GTACCGTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
62 5 0.10
63 34 0.65
64 13 0.25
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (61 bp):
TGTATTTTAAAAATGTCCAATGATGTACCTGAACTATCAATATATATTTTATTATGATGCA
Found at i:46460798 original size:30 final size:31
Alignment explanation
Indices: 46460719--46460802 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
46460709 AAAATCAAAT
* *
46460719 TTAATTAAAAAAGACAAATAACTAAACATATGG
1 TTAA-TAAAAAA-ATAAATAACTAAAAATATGG
*
46460752 CTAATAAAAAAGAAATAAATAA-TAAAAATATGG
1 TTAAT--AAAA-AAATAAATAACTAAAAATATGG
46460785 TTAATAAAAAAATAAATA
1 TTAATAAAAAAATAAATA
46460803 TAATACCATC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
30 9 0.20
31 4 0.09
32 1 0.02
33 17 0.39
34 11 0.25
35 2 0.05
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (31 bp):
TTAATAAAAAAATAAATAACTAAAAATATGG
Found at i:46461396 original size:20 final size:20
Alignment explanation
Indices: 46461351--46461398 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
46461341 TTTTTATATA
46461351 GTTATTA-TGAATTTATTAT
1 GTTATTATTGAATTTATTAT
*
46461370 GTAATTATTGAATTTATTAT
1 GTTATTATTGAATTTATTAT
*
46461390 TTTATTATT
1 GTTATTATT
46461399 TTAACCATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
GTTATTATTGAATTTATTAT
Found at i:46466770 original size:3 final size:3
Alignment explanation
Indices: 46466762--46466787 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46466752 TGTAGTCTCT
46466762 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
46466788 GATTTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:46469628 original size:27 final size:26
Alignment explanation
Indices: 46469594--46469701 Score: 90
Period size: 27 Copynumber: 4.0 Consensus size: 26
46469584 TTTCCACTTA
46469594 TAAGATAGTCCTGACAGACTTCCCATT
1 TAAGATAGTCCTGACAGACTTCCCA-T
* **
46469621 TAAGATAGTCCTAACAGACTTTTACAT
1 TAAGATAGTCCTGACAGAC-TTCCCAT
* * *
46469648 TAAGACAGTCTTGACGGACTTCCACAT
1 TAAGATAGTCCTGACAGACTTCC-CAT
* * * **
46469675 TAAAATCGTCCTTATGGACTTCCCAT
1 TAAGATAGTCCTGACAGACTTCCCAT
46469701 T
1 T
46469702 TATCAGATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
26 6 0.09
27 54 0.84
28 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (26 bp):
TAAGATAGTCCTGACAGACTTCCCAT
Found at i:46471317 original size:29 final size:27
Alignment explanation
Indices: 46471299--46471368 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
46471289 ATATTAAGTC
46471299 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
46471326 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
46471354 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
46471369 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:46471362 original size:28 final size:28
Alignment explanation
Indices: 46471299--46471396 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
46471289 ATATTAAGTC
*
46471299 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
46471326 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
46471354 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
46471383 CGCACACTTAGTGC
1 CGCACACTTAGTGC
46471397 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:46476126 original size:143 final size:144
Alignment explanation
Indices: 46475868--46476161 Score: 518
Period size: 143 Copynumber: 2.0 Consensus size: 144
46475858 GATATGGTTG
* * *
46475868 ATCAAGATAGGATTTGTCCTTCCTACATAATGGGAGCAATATCTTAGGCCTCTTGATTGAGTGAG
1 ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGCAATATCTTAGGCCTCTAGATGGAGTGAG
46475933 ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTA-TTTTTTTATTAT
66 ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTAT
46475997 AGTCTACACAGAAT
131 AGTCTACACAGAAT
* *
46476011 ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGGAATATTTTAGGCCTCTAGATGGAGTGAG
1 ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGCAATATCTTAGGCCTCTAGATGGAGTGAG
* *
46476076 ACTAGAAATGGATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTGT
66 ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTAT
46476141 AGTCTACACAGAAT
131 AGTCTACACAGAAT
46476155 ATCAAGA
1 ATCAAGA
46476162 AATATGAGAT
Statistics
Matches: 143, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 111 0.78
144 32 0.22
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (144 bp):
ATCAAGATAGGATTTGTCCCTCCTACATAATGGGAGCAATATCTTAGGCCTCTAGATGGAGTGAG
ACTAGAAATGCATGGCCATGCTCGAATAAGTTGATATGAGATATCACACTTATTTTTTTTATTAT
AGTCTACACAGAAT
Found at i:46484279 original size:39 final size:39
Alignment explanation
Indices: 46484225--46484303 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
46484215 AAAGTTCAAG
46484225 ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
1 ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
*
46484264 ATAATTTCGTTGTTCATTCTTTGACTGAGTGGATTATGT
1 ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
46484303 A
1 A
46484304 GAGGCTGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (39 bp):
ATAATTTCGTTGTTCATTCTTTGACTAAGTGGATTATGT
Found at i:46495338 original size:25 final size:25
Alignment explanation
Indices: 46495310--46495365 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
46495300 CTTTCAAGTG
* *
46495310 AATTCGCCACAGAGGCTTTCCATGA
1 AATTCACCACAAAGGCTTTCCATGA
* * *
46495335 AATTCACCATAAAGGTTTTTCATGA
1 AATTCACCACAAAGGCTTTCCATGA
46495360 AATTCA
1 AATTCA
46495366 TGTTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (25 bp):
AATTCACCACAAAGGCTTTCCATGA
Found at i:46496237 original size:16 final size:17
Alignment explanation
Indices: 46496216--46496251 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
46496206 TCAATCATCC
46496216 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
46496232 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
46496249 CTC
1 CTC
46496252 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:46502595 original size:7 final size:7
Alignment explanation
Indices: 46502583--46502612 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
46502573 ACTTTTTCAA
46502583 TCATCCC
1 TCATCCC
46502590 TCATCCC
1 TCATCCC
46502597 TCATCCC
1 TCATCCC
46502604 TCATCCC
1 TCATCCC
46502611 TC
1 TC
46502613 TCATCTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.57, G:0.00, T:0.30
Consensus pattern (7 bp):
TCATCCC
Found at i:46508529 original size:81 final size:81
Alignment explanation
Indices: 46508393--46508591 Score: 218
Period size: 81 Copynumber: 2.5 Consensus size: 81
46508383 GGAAAGGATG
* * * * * * *
46508393 CCTATGTGGCTCAAGATGAAAGGAACGTCTTTATGGTGAATCATGAAAAGGTAGTCTTTGTGGCA
1 CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGCGAATCATGAAAAGGTAGTCTCTATGGCA
46508458 AACCCTGCAATAATAA
66 AACCCTGCAATAATAA
* * * ** *
46508474 CCTATATGGCACAATATGAAAGGAACGCCTTTGTGGCGAATTATGAAGGGGTAGTCTCTATGGCG
1 CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGCGAATCATGAAAAGGTAGTCTCTATGGCA
* *
46508539 AACCCTGCAATGATCA
66 AACCCTGCAATAATAA
* * * * *
46508555 CCTTTGTGACAAAAAATGAAAGGAATGCATTTGTGGC
1 CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGC
46508592 AAACTCCATA
Statistics
Matches: 97, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 97 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (81 bp):
CCTATGTGGCACAAAATGAAAGGAACGCCTTTGTGGCGAATCATGAAAAGGTAGTCTCTATGGCA
AACCCTGCAATAATAA
Found at i:46510963 original size:10 final size:10
Alignment explanation
Indices: 46510945--46510992 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
46510935 CATATCTGTC
* *
46510945 AAAAATAATG
1 AAAATTAATT
46510955 AAAATTAATT
1 AAAATTAATT
*
46510965 AAAATTTGATAT
1 AAAA-TTAAT-T
46510977 AAAATTAATT
1 AAAATTAATT
46510987 AAAATT
1 AAAATT
46510993 CAACATGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 19 0.59
11 8 0.25
12 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
AAAATTAATT
Found at i:46512940 original size:29 final size:30
Alignment explanation
Indices: 46512880--46512940 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
46512870 GCCTTTTAAA
*** **
46512880 AATATTTACAAAAAGAGACATTTAATTTTT
1 AATATTTACAAAAAGAGACAACCAAAATTT
46512910 AATATTTACAAAAAGAG-CAACCAAAATTT
1 AATATTTACAAAAAGAGACAACCAAAATTT
46512939 AA
1 AA
46512941 AAATAATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACCAAAATTT
Found at i:46523748 original size:20 final size:20
Alignment explanation
Indices: 46523723--46523770 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
46523713 TATCATCATA
46523723 ACAGATACCCTTCTTGACAT
1 ACAGATACCCTTCTTGACAT
46523743 ACAGATACCCTTCTTGACAT
1 ACAGATACCCTTCTTGACAT
46523763 ACAGATAC
1 ACAGATAC
46523771 ACATCTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.27
Consensus pattern (20 bp):
ACAGATACCCTTCTTGACAT
Found at i:46540370 original size:14 final size:14
Alignment explanation
Indices: 46540348--46540385 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
46540338 TCAAAAAAAT
* *
46540348 AAATCATTTTTCAG
1 AAATTATTTTCCAG
46540362 AAATTATTTTCCAG
1 AAATTATTTTCCAG
46540376 AAATTATTTT
1 AAATTATTTT
46540386 ATTGACAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:46541202 original size:9 final size:9
Alignment explanation
Indices: 46541188--46541215 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
46541178 TTTTGTTACA
46541188 ACAATTAAT
1 ACAATTAAT
46541197 ACAATTAAT
1 ACAATTAAT
46541206 ACAATTAAT
1 ACAATTAAT
46541215 A
1 A
46541216 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:46541237 original size:68 final size:68
Alignment explanation
Indices: 46541158--46541358 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 68
46541148 TCAAGTTTGT
*
46541158 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
46541223 AAA
66 AAA
46541226 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
46541282 AAA
66 AAA
46541285 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
46541348 AAT
66 AAA
46541351 TTTACTAA
1 TTTACTAA
46541359 CAATTAATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 20
0.85 0.01 0.14
Matches are distributed among these distances:
59 56 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 32 0.26
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:46541368 original size:16 final size:16
Alignment explanation
Indices: 46541347--46541388 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
46541337 AATAATTTGA
*
46541347 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
46541363 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
46541379 TAGTTTTAAT
1 TAATTTTAAT
46541389 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:46541372 original size:22 final size:23
Alignment explanation
Indices: 46541362--46541417 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
46541352 TTACTAACAA
* * *
46541362 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
46541384 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
46541407 TTAATTTTAAT
1 TTAATTTTAAT
46541418 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:46541614 original size:6 final size:6
Alignment explanation
Indices: 46541605--46541635 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
46541595 TGAAAGTGAA
46541605 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT G
1 GGAAAT GGAAAT GGAAAT GGAAAT GGAAAT G
46541636 TAAACATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GGAAAT
Found at i:46544106 original size:29 final size:28
Alignment explanation
Indices: 46544073--46544128 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
46544063 CTTTGCTCCT
46544073 AATAATGTTA-CTTCCAAGATTTGAAACCC
1 AATAATGTTACCTT-CAAGATTT-AAACCC
*
46544102 AATAATGTTACCTTCAATATTTAAACC
1 AATAATGTTACCTTCAAGATTTAAACC
46544129 TATATTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 17 0.68
30 3 0.12
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (28 bp):
AATAATGTTACCTTCAAGATTTAAACCC
Found at i:46544340 original size:14 final size:14
Alignment explanation
Indices: 46544303--46544346 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
46544293 GAATTTAAAT
46544303 ATAAATATAATTACA
1 ATAAATATAATTA-A
*
46544318 ATAAATATATTTAA
1 ATAAATATAATTAA
*
46544332 ATAACTATAATTAA
1 ATAAATATAATTAA
46544346 A
1 A
46544347 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAATATAATTAA
Found at i:46544387 original size:25 final size:25
Alignment explanation
Indices: 46544307--46544390 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
46544297 TTAAATATAA
* *
46544307 ATATAATTACAATAAATATATTTAAAT
1 ATATAATTA-AATTAATA-ATTAAAAT
** *
46544334 AACTATAATTAAAATTAATTTTTATAAT
1 -A-TATAATT-AAATTAATAATTAAAAT
46544362 ATATAATTAAATTAATAATTAAAAT
1 ATATAATTAAATTAATAATTAAAAT
46544387 ATAT
1 ATAT
46544391 TTAACCTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
25 18 0.39
26 7 0.15
27 1 0.02
28 6 0.13
29 13 0.28
30 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATAATTAAATTAATAATTAAAAT
Found at i:46545602 original size:38 final size:38
Alignment explanation
Indices: 46545558--46545640 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
46545548 TTCATATTTT
** *
46545558 AAATAAAAAAACAAAAATTTTTAAAATTTATATT-TAAA
1 AAATAAAAAAAC-AAAATTTTTAAAATAAAAATTATAAA
* * *
46545596 AAATAAAAAAGCATATTTTTTAAAATAAAAATTATAAA
1 AAATAAAAAAACAAAATTTTTAAAATAAAAATTATAAA
46545634 AAATAAA
1 AAATAAA
46545641 CTCTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 16 0.42
38 22 0.58
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (38 bp):
AAATAAAAAAACAAAATTTTTAAAATAAAAATTATAAA
Found at i:46545667 original size:30 final size:30
Alignment explanation
Indices: 46545614--46545680 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
46545604 AAGCATATTT
46545614 TTTAAAA-TAAAAATTATAAAAAATAAACTC
1 TTTAAAATTAAAAATTATAAAAAATAAA-TC
* *
46545644 TTTAAAATTCAAAAA-TAT-AAAAATTAATT
1 TTTAAAATT-AAAAATTATAAAAAATAAATC
46545673 TTTAAAAT
1 TTTAAAAT
46545681 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 9 0.27
30 15 0.45
31 4 0.12
32 5 0.15
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (30 bp):
TTTAAAATTAAAAATTATAAAAAATAAATC
Found at i:46545689 original size:31 final size:33
Alignment explanation
Indices: 46545620--46545689 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 33
46545610 ATTTTTTAAA
46545620 ATAAAAATTATAAAAAATAAACTCTTTAAAATT
1 ATAAAAATTATAAAAAATAAACTCTTTAAAATT
* * *
46545653 -CAAAAA-TAT-AAAAATTAA-TTTTTAAAATAT
1 ATAAAAATTATAAAAAATAAACTCTTTAAAAT-T
46545683 ATAAAAA
1 ATAAAAA
46545690 AATTCTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 9 0.29
30 9 0.29
31 8 0.26
32 5 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (33 bp):
ATAAAAATTATAAAAAATAAACTCTTTAAAATT
Found at i:46545904 original size:24 final size:24
Alignment explanation
Indices: 46545852--46545905 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
46545842 CCAGTAATTA
46545852 AAAAAATTTTCCACATTATTCCAG
1 AAAAAATTTTCCACATTATTCCAG
* * * * *
46545876 TAAAATTTTTTCATATTATTCCGG
1 AAAAAATTTTCCACATTATTCCAG
46545900 AAAAAA
1 AAAAAA
46545906 AGCCAATAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.37
Consensus pattern (24 bp):
AAAAAATTTTCCACATTATTCCAG
Found at i:46547205 original size:17 final size:18
Alignment explanation
Indices: 46547183--46547221 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
46547173 AGAAGGGAAA
46547183 AAGATA-AAAAGAAAAAG-
1 AAGATAGAAAA-AAAAAGC
46547200 AAGATAGAAAAAAAAAGC
1 AAGATAGAAAAAAAAAGC
46547218 AAGA
1 AAGA
46547222 AGTTAGGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (18 bp):
AAGATAGAAAAAAAAAGC
Found at i:46552918 original size:3 final size:3
Alignment explanation
Indices: 46552910--46552936 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
46552900 GGAGAAGGGA
46552910 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
46552937 ATTGTTGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:46562609 original size:5 final size:5
Alignment explanation
Indices: 46562599--46562629 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
46562589 TAAGAGGCAT
46562599 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA A
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA A
46562630 CATACAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (5 bp):
ATCTA
Found at i:46571118 original size:43 final size:42
Alignment explanation
Indices: 46571068--46571205 Score: 145
Period size: 43 Copynumber: 3.3 Consensus size: 42
46571058 TATCCCGGAT
* * * *
46571068 ATGGTCTTACATGTTAACACATTTTGATGCCACTGTACCAGAC
1 ATGGTCTTACACGTT-ACTCATTTTGATGCCAATGTCCCAGAC
* * * *
46571111 AGGGTCTTATACG--ACTCATATATGATGCCAATATCCCAGAC
1 ATGGTCTTACACGTTACTCAT-TTTGATGCCAATGTCCCAGAC
* *
46571152 ATGGTCTTACACGTTCTCTCATTTCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTT-ACTCATTTTGATGCCAATGTCCCAGAC
46571195 ATGGTCTTACA
1 ATGGTCTTACA
46571206 TGAAATCACA
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
40 5 0.06
41 28 0.36
43 39 0.51
44 5 0.06
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGGTCTTACACGTTACTCATTTTGATGCCAATGTCCCAGAC
Found at i:46573425 original size:14 final size:15
Alignment explanation
Indices: 46573390--46573427 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
46573380 GTAGCTTGTT
*
46573390 CGGTTC-ACTAGATT
1 CGGTTCAACTAGATG
46573404 CGGTTCAACTA-ATG
1 CGGTTCAACTAGATG
46573418 CGGTTCAACT
1 CGGTTCAACT
46573428 GAACCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (15 bp):
CGGTTCAACTAGATG
Found at i:46579574 original size:12 final size:12
Alignment explanation
Indices: 46579557--46579587 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
46579547 TAAAACCAAG
46579557 CATATATCACTT
1 CATATATCACTT
46579569 CATATATCACTT
1 CATATATCACTT
46579581 CATATAT
1 CATATAT
46579588 ATCACTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (12 bp):
CATATATCACTT
Found at i:46579587 original size:14 final size:13
Alignment explanation
Indices: 46579558--46579597 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 13
46579548 AAAACCAAGC
46579558 ATATATCACTTC-
1 ATATATCACTTCA
46579570 ATATATCACTTCA
1 ATATATCACTTCA
46579583 TATATATCACTTCA
1 -ATATATCACTTCA
46579597 A
1 A
46579598 ACATTACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.46
13 1 0.04
14 13 0.50
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATCACTTCA
Found at i:46584532 original size:17 final size:16
Alignment explanation
Indices: 46584497--46584555 Score: 86
Period size: 15 Copynumber: 3.8 Consensus size: 16
46584487 TATAGTCTCA
*
46584497 TATAGTGTCACAA-TC
1 TATAGTTTCACAAGTC
46584512 TATAGTTTTCACAAGTC
1 TATAG-TTTCACAAGTC
46584529 TATAGTTTCA-AAGTC
1 TATAGTTTCACAAGTC
46584544 TATAGTTTCACA
1 TATAGTTTCACA
46584556 TCTAAACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
15 20 0.50
16 13 0.32
17 7 0.17
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (16 bp):
TATAGTTTCACAAGTC
Found at i:46585580 original size:22 final size:21
Alignment explanation
Indices: 46585531--46585581 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
46585521 TGGATAAGCC
*
46585531 ACCACATAATTGCCGATAACG
1 ACCACATAATTGCCAATAACG
*
46585552 ACCACATAATTG-CAATTAAACT
1 ACCACATAATTGCCAA-T-AACG
46585574 ACCACATA
1 ACCACATA
46585582 GCTTCCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 11 0.42
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (21 bp):
ACCACATAATTGCCAATAACG
Found at i:46596576 original size:67 final size:67
Alignment explanation
Indices: 46596466--46596606 Score: 255
Period size: 67 Copynumber: 2.1 Consensus size: 67
46596456 ATACTATGGA
*
46596466 TTAGGGATTAATTGTGAAAATAAGCTTGTTTTAGTTTTAGGGACTAAATTAAACAAATTGAAAAA
1 TTAGGGATTAATTGTGAAAATAAGCTTGTTTCAGTTTTAGGGACTAAATTAAACAAATTGAAAAA
46596531 CT
66 CT
* *
46596533 TTAGGGATTATTTGTGAAAATAAGCTTGTTTCAGTTTTTGGGACTAAATTAAACAAATTGAAAAA
1 TTAGGGATTAATTGTGAAAATAAGCTTGTTTCAGTTTTAGGGACTAAATTAAACAAATTGAAAAA
46596598 CT
66 CT
46596600 TTAGGGA
1 TTAGGGA
46596607 AATTATGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.36
Consensus pattern (67 bp):
TTAGGGATTAATTGTGAAAATAAGCTTGTTTCAGTTTTAGGGACTAAATTAAACAAATTGAAAAA
CT
Found at i:46605757 original size:34 final size:34
Alignment explanation
Indices: 46605719--46605791 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
46605709 CACATTCAAG
* *
46605719 CCAATATTGGACGTTATGTCACCACATGGGAGAT
1 CCAATATTGGACATTATGTCACCACATGGGAGAC
46605753 CCAATATTGGACATTATGTCACCACATGGGAGAC
1 CCAATATTGGACATTATGTCACCACATGGGAGAC
46605787 CCAAT
1 CCAAT
46605792 GTCGCAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (34 bp):
CCAATATTGGACATTATGTCACCACATGGGAGAC
Found at i:46611074 original size:17 final size:17
Alignment explanation
Indices: 46611029--46611076 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
46611019 CATTGTCCCC
*
46611029 AATGCATTGAC-ATGAA
1 AATGCAATGACAATGAA
* * *
46611045 TATGTAATTACAATGAA
1 AATGCAATGACAATGAA
46611062 AATGCAATGACAATG
1 AATGCAATGACAATG
46611077 TATACTTATC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (17 bp):
AATGCAATGACAATGAA
Done.