Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 146 of 203
Found at i:46442125 original size:19 final size:19
Alignment explanation
Indices: 46442101--46442141 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
46442091 AAAGACTAAT
46442101 CATGAGATGATTGTAATAA
1 CATGAGATGATTGTAATAA
*
46442120 CATGAGATGATTGTAATCA
1 CATGAGATGATTGTAATAA
46442139 CAT
1 CAT
46442142 ACTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (19 bp):
CATGAGATGATTGTAATAA
Found at i:46446263 original size:27 final size:27
Alignment explanation
Indices: 46446233--46446410 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
46446223 ATATTGAGTC
* * * *
46446233 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
46446260 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
46446287 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
46446315 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
46446342 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
46446369 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
46446396 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
46446411 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:46446372 original size:82 final size:81
Alignment explanation
Indices: 46446254--46446409 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
46446244 TGCTATATAA
* *
46446254 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
46446319 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
46446336 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
46446400 CACTTAGTGC
65 CACTTAGTGC
46446410 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:46456943 original size:9 final size:9
Alignment explanation
Indices: 46456929--46456953 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46456919 TGAACTTTGT
46456929 TGTTGTTGA
1 TGTTGTTGA
46456938 TGTTGTTGA
1 TGTTGTTGA
46456947 TGTTGTT
1 TGTTGTT
46456954 CTATTGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (9 bp):
TGTTGTTGA
Found at i:46457373 original size:104 final size:103
Alignment explanation
Indices: 46457179--46457380 Score: 230
Period size: 104 Copynumber: 2.0 Consensus size: 103
46457169 CGTTTTGATC
* * * * * *
46457179 TATTGGCGTTGTGGCGAGATATTGATTAATGAAATTCTGGCATTATGGCGGGATGTTGATTGGAT
1 TATTGGCGTTGTGGCGAGATATTGATAAATGAAATTCTGGCATTATGGCGAGACGTTAATTGAAA
* ** *
46457244 GAATTATTGGGGTTGTGCAGAATGTTAATTGAAAAAAT
66 AAAACATTGGGGTTATGCAGAATGTTAATTGAAAAAAT
* *
46457282 TATTGGCGTTGTGGTTG-GATGATTGATAAATGAAGTTCTGGCATTATGGCGAGACG-TAATTGA
1 TATTGGCGTTGTGG-CGAGAT-ATTGATAAATGAAATTCTGGCATTATGGCGAGACGTTAATTGA
*
46457345 AAAAAACATTGGTGTTATGGC-GAGATGTTAATTGAA
64 AAAAAACATTGGGGTTAT-GCAGA-ATGTTAATTGAA
46457381 GGAGGACTAG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
103 36 0.44
104 46 0.56
ACGTcount: A:0.29, C:0.06, G:0.30, T:0.35
Consensus pattern (103 bp):
TATTGGCGTTGTGGCGAGATATTGATAAATGAAATTCTGGCATTATGGCGAGACGTTAATTGAAA
AAAACATTGGGGTTATGCAGAATGTTAATTGAAAAAAT
Found at i:46463497 original size:12 final size:12
Alignment explanation
Indices: 46463480--46463504 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46463470 ATGATTGTGA
46463480 TTGTTTGAGATT
1 TTGTTTGAGATT
46463492 TTGTTTGAGATT
1 TTGTTTGAGATT
46463504 T
1 T
46463505 CATAATCAAA
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:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTGTTTGAGATT
Found at i:46469879 original size:44 final size:42
Alignment explanation
Indices: 46469824--46470074 Score: 268
Period size: 44 Copynumber: 5.7 Consensus size: 42
46469814 TGGTATTTTT
* *
46469824 AACCTACTCCACTGCTGCTCAGGGAGATAAGGTTCACGATCTTC
1 AACCTATTCCACTGCTGC-CAGGGAGAT-AGGTTCACAATCTTC
* **
46469868 AACCTATTCCACTGCTAACCAGGGAGATAGGACCTACAATCTTC
1 AACCTATTCCACTGCT-GCCAGGGAGATAGGTTC-ACAATCTTC
* * *
46469912 AATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTC
1 AACCTATTCCACTGCTG-CCAGGGAGATAG-GTTCACAATCTTC
* **
46469956 AACCTATTCCACTGCTAACCAGGGAGATAGGACCTACAATCTTC
1 AACCTATTCCACTGCT-GCCAGGGAGATAGGTTC-ACAATCTTC
* * *
46470000 AATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTC
1 AACCTATTCCACTGCTG-CCAGGGAGATAG-GTTCACAATCTTC
*
46470044 AACCTATTCCACTACTGACCAGGGAGATAGG
1 AACCTATTCCACTGCTG-CCAGGGAGATAGG
46470075 GCTGGGGTCA
Statistics
Matches: 172, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
43 5 0.03
44 164 0.95
45 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
AACCTATTCCACTGCTGCCAGGGAGATAGGTTCACAATCTTC
Found at i:46469935 original size:88 final size:88
Alignment explanation
Indices: 46469831--46470074 Score: 418
Period size: 88 Copynumber: 2.8 Consensus size: 88
46469821 TTTAACCTAC
* * * *
46469831 TCCACTGCTGCTCAGGGAGATA-AGGTTCACGATCTTCAACCTATTCCACTGCTAACCAGGGAGA
1 TCCACTGCTGCCCAGGGAGATAGA-ATTCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGA
46469895 TAGGACCTACAATCTTCAATCTAT
65 TAGGACCTACAATCTTCAATCTAT
46469919 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGAT
46469984 AGGACCTACAATCTTCAATCTAT
66 AGGACCTACAATCTTCAATCTAT
* *
46470007 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTACTGACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGAT
46470072 AGG
66 AGG
46470075 GCTGGGGTCA
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
88 148 0.99
89 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (88 bp):
TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGAT
AGGACCTACAATCTTCAATCTAT
Found at i:46469971 original size:132 final size:132
Alignment explanation
Indices: 46469824--46470073 Score: 335
Period size: 132 Copynumber: 1.9 Consensus size: 132
46469814 TGGTATTTTT
* ** *
46469824 AACCTACTCCACTGCT-GCTCAGGGAGATAAGGTTC-ACGATCTTCAACCTATTCCACTGCTAAC
1 AACCTACTCCACTGCTAAC-CAGGGAGAT-AGGACCTACAATCTTCAACCTATTCCACTGCTAAC
* * * *
46469887 CAGGGAGATAGGA-CCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAA
64 CAGGGAGATAGAATCCT-CAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGAATTCTCAA
46469951 TCTTC
128 TCTTC
* * **
46469956 AACCTATTCCACTGCTAACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCA
1 AACCTACTCCACTGCTAACCAGGGAGATAGGACCTACAATCTTCAACCTATTCCACTGCTAACCA
*
46470021 GGGAGATAGAATTCTCAATCTTCAACCTATTCCACTACTGACCAGGGAGATAG
66 GGGAGATAGAATCCTCAATCTTCAACCTATTCCACTACTGACCAGGGAGATAG
46470074 GGCTGGGGTC
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
131 4 0.04
132 95 0.93
133 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (132 bp):
AACCTACTCCACTGCTAACCAGGGAGATAGGACCTACAATCTTCAACCTATTCCACTGCTAACCA
GGGAGATAGAATCCTCAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGAATTCTCAATCT
TC
Found at i:46470257 original size:88 final size:87
Alignment explanation
Indices: 46470074--46470485 Score: 518
Period size: 88 Copynumber: 4.7 Consensus size: 87
46470064 AGGGAGATAG
* * * * * * *
46470074 GGCTGGGGTCATCAATCTACTTCGCTGTCGGTGCAGGAAGACAAGATTTACTATTTTTTAACCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAG-CAAGATCTGCTA-TTTTTAACCTG
* *
46470139 CTCCGTTGCAACCCAGGAAGGCAA
64 CTCCGCTGCAACCCAGGGAGGCAA
* * *
46470163 GGCTGGTGTCTTCAATCTGCTTCGGTGTCGGTGCATGAAAGCAAGATTTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCA-GAAAGCAAGATCTGCTATTTTTAACCTGC
*
46470228 TCCGCTACAACCCAGGGAGGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
* *
46470251 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCA-GAAAGCAAGATCTGCTATTTTTAACCTGC
46470316 TCCGCTGCAACCCAGGGAGGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
* * * * * *
46470339 GGCAGGTGTCTTTGATCTGCTTCACTGTCGGCGCAGGAAGACAAGATCTGTTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAG-CAAGATCTGCTATTTTTAACCTGC
*
46470404 TCCACTGCAACCCAGGGAGGCAA
65 TCCGCTGCAACCCAGGGAGGCAA
* * * * * *
46470427 GGCTGGTGTCTTTGATCTACTTTGCTGTTGGTGCAGGAAGGCCAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCA-GAAAGCAAGATCTGCTATTTTTA
46470486 CTGATCTGCT
Statistics
Matches: 287, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
87 3 0.01
88 235 0.82
89 45 0.16
90 4 0.01
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (87 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAAAGCAAGATCTGCTATTTTTAACCTGCT
CCGCTGCAACCCAGGGAGGCAA
Found at i:46470327 original size:176 final size:176
Alignment explanation
Indices: 46470074--46470485 Score: 574
Period size: 176 Copynumber: 2.3 Consensus size: 176
46470064 AGGGAGATAG
* * * * * *
46470074 GGCTGGGGTCATCAATCTACTTCGCTGTCGGTGCAGGAAGACAAGATTTACTATTTTTTAACCTG
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTTAACCTG
* * ** *
46470139 CTCCGTTGCAACCCAGGAAGGCAAGGCTGGTGTCTTCAATCTGCTTCGGTGTCGGTGCATGAAAG
65 CTCCGCTGCAACCCAGGAAGGCAAGGCAGGTGTCTTCAATCTGCTTCACTGTCGGCGCA-GAAAG
* *
46470204 -CAAGATTTGCTATTTTTAACCTGCTCCGCTACAACCCAGGGAGGCAA
129 ACAAGATCTGCTATTTTTAACCTGCTCCACTACAACCCAGGGAGGCAA
* *
46470251 GGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* ** *
46470316 TCCGCTGCAACCCAGGGAGGCAAGGCAGGTGTCTTTGATCTGCTTCACTGTCGGCGCAGGAAGAC
66 TCCGCTGCAACCCAGGAAGGCAAGGCAGGTGTCTTCAATCTGCTTCACTGTCGGCGCAGAAAGAC
* *
46470381 AAGATCTGTTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAA
131 AAGATCTGCTATTTTTAACCTGCTCCACTACAACCCAGGGAGGCAA
* * * *
46470427 GGCTGGTGTCTTTGATCTACTTTGCTGTTGGTGCAGGAAGGCCAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
46470486 CTGATCTGCT
Statistics
Matches: 207, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
175 4 0.02
176 158 0.76
177 45 0.22
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (176 bp):
GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGAAGGCAAGGCAGGTGTCTTCAATCTGCTTCACTGTCGGCGCAGAAAGAC
AAGATCTGCTATTTTTAACCTGCTCCACTACAACCCAGGGAGGCAA
Found at i:46470337 original size:44 final size:44
Alignment explanation
Indices: 46470203--46470427 Score: 139
Period size: 44 Copynumber: 5.1 Consensus size: 44
46470193 GTGCATGAAA
* * *
46470203 GCAAGATTTGCTATTTTTAACCTGCTCCGCTACAACCCAGGGAG
1 GCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAG
* * * * ** * * **** *
46470247 GCAAG-GCTGGTGTCTTCGATCTGCTTCACTGTCGGTGCAGGAAG
1 GCAAGATCTGCTATTTTTAACCTGCTCCACTG-CAACCCAGGGAG
*
46470291 GCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAG
1 GCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAG
* * * * * * * * ** * *
46470335 GCAAG-GCAGGTGTCTTTGATCTGCTTCACTGTCGGCGCAGGAAG
1 GCAAGATCTGCTATTTTTAACCTGCTCCACTG-CAACCCAGGGAG
* *
46470379 ACAAGATCTGTTATTTTTAACCTGCTCCACTGCAACCCAGGGAG
1 GCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAG
46470423 GCAAG
1 GCAAG
46470428 GCTGGTGTCT
Statistics
Matches: 120, Mismatches: 57, Indels: 8
0.65 0.31 0.04
Matches are distributed among these distances:
43 32 0.27
44 53 0.44
45 35 0.29
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (44 bp):
GCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAG
Found at i:46471706 original size:6 final size:6
Alignment explanation
Indices: 46471691--46471728 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
46471681 GGCCTCTCTA
46471691 TTTTTC -TTTTC -TTTT- TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
46471729 ATCACTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 13 0.43
6 17 0.57
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:46471736 original size:22 final size:21
Alignment explanation
Indices: 46471691--46471736 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
46471681 GGCCTCTCTA
* **
46471691 TTTTTCTTTTCTTTTTTTTTC
1 TTTTTCTTTTCTTTTTATCAC
46471712 TTTTTCTTTTTCTTTTTATCAC
1 TTTTTC-TTTTCTTTTTATCAC
46471734 TTT
1 TTT
46471737 CATTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTTCTTTTTATCAC
Found at i:46478298 original size:18 final size:19
Alignment explanation
Indices: 46478277--46478313 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
46478267 ACGTGGAAAG
*
46478277 TGTATATGTGT-TATAAAA
1 TGTATATGTATATATAAAA
46478295 TGTATATGTATATATAAAA
1 TGTATATGTATATATAAAA
46478314 AATATAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
TGTATATGTATATATAAAA
Found at i:46480974 original size:13 final size:13
Alignment explanation
Indices: 46480944--46481087 Score: 141
Period size: 13 Copynumber: 10.8 Consensus size: 13
46480934 TGAAAATGAA
*
46480944 TATATGAAAATAGA
1 TATATG-AAATAGT
*
46480958 TATATGAAATGGT
1 TATATGAAATAGT
46480971 TATATG-AATCAGT
1 TATATGAAAT-AGT
*
46480984 TATATGAAAATAGA
1 TATATG-AAATAGT
*
46480998 TATATGAAATGGT
1 TATATGAAATAGT
46481011 TATATG-AATCAGT
1 TATATGAAAT-AGT
*
46481024 TATATGAAAATAGA
1 TATATG-AAATAGT
46481038 TATATGAAATAGT
1 TATATGAAATAGT
*
46481051 TATATG-AATCGGT
1 TATATGAAAT-AGT
*
46481064 TATATGGAAATAGA
1 TATAT-GAAATAGT
46481078 TATATGAAAT
1 TATATGAAAT
46481088 GAAACATTGG
Statistics
Matches: 109, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
12 9 0.08
13 62 0.57
14 29 0.27
15 9 0.08
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (13 bp):
TATATGAAATAGT
Found at i:46480974 original size:27 final size:27
Alignment explanation
Indices: 46480944--46481058 Score: 130
Period size: 27 Copynumber: 4.3 Consensus size: 27
46480934 TGAAAATGAA
*
46480944 TATATGAAAATAGATATATGAAATGGT
1 TATATGAAAATAGATATATGAAATAGT
* *
46480971 TATATG--AATCAGTTATATGAAAATAGA
1 TATATGAAAAT-AGATATATG-AAATAGT
* *
46480998 TATATG-AAATGGTTATATG-AATCAGT
1 TATATGAAAATAGATATATGAAAT-AGT
46481024 TATATGAAAATAGATATATGAAATAGT
1 TATATGAAAATAGATATATGAAATAGT
46481051 TATATGAA
1 TATATGAA
46481059 TCGGTTATAT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
25 6 0.08
26 16 0.21
27 47 0.63
28 6 0.08
ACGTcount: A:0.47, C:0.02, G:0.17, T:0.35
Consensus pattern (27 bp):
TATATGAAAATAGATATATGAAATAGT
Found at i:46480999 original size:40 final size:40
Alignment explanation
Indices: 46480944--46481088 Score: 263
Period size: 40 Copynumber: 3.6 Consensus size: 40
46480934 TGAAAATGAA
46480944 TATATGAAAATAGATATATGAAATGGTTATATGAATCAGT
1 TATATGAAAATAGATATATGAAATGGTTATATGAATCAGT
46480984 TATATGAAAATAGATATATGAAATGGTTATATGAATCAGT
1 TATATGAAAATAGATATATGAAATGGTTATATGAATCAGT
* *
46481024 TATATGAAAATAGATATATGAAATAGTTATATGAATCGGT
1 TATATGAAAATAGATATATGAAATGGTTATATGAATCAGT
*
46481064 TATATGGAAATAGATATATGAAATG
1 TATATGAAAATAGATATATGAAATG
46481089 AAACATTGGA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (40 bp):
TATATGAAAATAGATATATGAAATGGTTATATGAATCAGT
Found at i:46481073 original size:27 final size:25
Alignment explanation
Indices: 46480952--46481085 Score: 126
Period size: 27 Copynumber: 5.1 Consensus size: 25
46480942 AATATATGAA
* *
46480952 AATAGATATATGAAATGGTTATATG
1 AATAGTTATATGAAATAGTTATATG
*
46480977 AATCAGTTATATGAAAATAGATATATG
1 AAT-AGTTATATG-AAATAGTTATATG
*
46481004 AAATGGTTATATG-AATCAGTTATATG
1 -AATAGTTATATGAAAT-AGTTATATG
*
46481030 AAAATAGATATATGAAATAGTTATATG
1 --AATAGTTATATGAAATAGTTATATG
* *
46481057 AATCGGTTATATGGAAATAGATATATG
1 AAT-AGTTATAT-GAAATAGTTATATG
46481084 AA
1 AA
46481086 ATGAAACATT
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
25 9 0.10
26 22 0.24
27 54 0.59
28 6 0.07
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (25 bp):
AATAGTTATATGAAATAGTTATATG
Found at i:46482658 original size:21 final size:22
Alignment explanation
Indices: 46482634--46482679 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
46482624 CATAAAGCTA
*
46482634 ATACTCTCCAA-CACACCAAAT
1 ATACCCTCCAAGCACACCAAAT
*
46482655 ATACCCTTCAAGCACACCAAAT
1 ATACCCTCCAAGCACACCAAAT
46482677 ATA
1 ATA
46482680 TATACCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (22 bp):
ATACCCTCCAAGCACACCAAAT
Found at i:46486117 original size:19 final size:18
Alignment explanation
Indices: 46486081--46486121 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
46486071 TAACATTGAA
46486081 TTTT-AAAAATTTTATAT
1 TTTTAAAAAATTTTATAT
*
46486098 TTTTAAAAAATATTTTTAT
1 TTTTAAAAAAT-TTTATAT
46486117 TTTTA
1 TTTTA
46486122 TTTTTGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAAAAATTTTATAT
Found at i:46486424 original size:7 final size:7
Alignment explanation
Indices: 46486381--46486428 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 7
46486371 AATTGAACAA
46486381 AATTTTAT
1 AATTTT-T
46486389 AATTTTAT
1 AATTTT-T
46486397 AATTTTT
1 AATTTTT
46486404 AATATTTT
1 AAT-TTTT
*
46486412 CTATTTTT
1 -AATTTTT
46486420 AATTTTT
1 AATTTTT
46486427 AA
1 AA
46486429 CAATCTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 12 0.33
8 22 0.61
9 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (7 bp):
AATTTTT
Found at i:46486608 original size:26 final size:27
Alignment explanation
Indices: 46486579--46486633 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
46486569 ATTTTTTATC
46486579 TCTAAAT-TTTTTA-TATTTCATATATT
1 TCTAAATATTTTTATTATTTCATA-ATT
*
46486605 TCTAAATCATTTTTATTTTTTCATAATT
1 TCTAAAT-ATTTTTATTATTTCATAATT
46486633 T
1 T
46486634 TTTGTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 7 0.28
28 10 0.40
29 8 0.32
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (27 bp):
TCTAAATATTTTTATTATTTCATAATT
Found at i:46491568 original size:15 final size:15
Alignment explanation
Indices: 46491548--46491589 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
46491538 TTAGGTAAGA
46491548 TTATTTAATATT-TAG
1 TTATTTAAT-TTATAG
*
46491563 TTATTTAATTTATAT
1 TTATTTAATTTATAG
46491578 TTATTTAATTTA
1 TTATTTAATTTA
46491590 ACTGGGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTATTTAATTTATAG
Found at i:46491579 original size:19 final size:21
Alignment explanation
Indices: 46491550--46491590 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
46491540 AGGTAAGATT
46491550 ATTTAATATTTAGTT-ATTTA
1 ATTTAATATTTAGTTAATTTA
*
46491570 ATTT-ATATTTATTTAATTTA
1 ATTTAATATTTAGTTAATTTA
46491590 A
1 A
46491591 CTGGGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTAATATTTAGTTAATTTA
Found at i:46500443 original size:26 final size:25
Alignment explanation
Indices: 46500405--46500477 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 25
46500395 CATACCTATG
46500405 TTACCCTTAGTAAAATTTTGA-AGATT
1 TTACCCTT-GTAAAATTTTGACAG-TT
46500431 TTACCTCTTGTAAAATTTTGACAGTT
1 TTACC-CTTGTAAAATTTTGACAGTT
46500457 TTACCCCTTGTAAAATTTTGA
1 TTA-CCCTTGTAAAATTTTGA
46500478 GAAAATATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
26 37 0.84
27 7 0.16
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (25 bp):
TTACCCTTGTAAAATTTTGACAGTT
Found at i:46512029 original size:25 final size:25
Alignment explanation
Indices: 46511990--46512071 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
46511980 CAGACACACC
46511990 ACAGCTCGTACGAGCTTATCGATTT
1 ACAGCTCGTACGAGCTTATCGATTT
*
46512015 ACAGCTCGCTA-GAGCTTACCGATTCT
1 ACAGCTCG-TACGAGCTTATCGATT-T
* *
46512041 -C-GACTTGTATGAGCTTATCGATTT
1 ACAG-CTCGTACGAGCTTATCGATTT
*
46512065 ATAGCTC
1 ACAGCTC
46512072 ATGAGAGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.09
25 38 0.83
26 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (25 bp):
ACAGCTCGTACGAGCTTATCGATTT
Found at i:46512101 original size:50 final size:49
Alignment explanation
Indices: 46511992--46512104 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 49
46511982 GACACACCAC
* * *
46511992 AGCTCGTACGAGCTTATCGATTTACAGCTCGCTAGAGCTTACCGATTCT
1 AGCTCGTATGAGCTTATCGATTTACAGCTCGATAGAGCATACCGATTCT
* * * *
46512041 CGACTTGTATGAGCTTATCGATTTATAGCTC-ATGAGAGCATACGGATTCAT
1 AG-CTCGTATGAGCTTATCGATTTACAGCTCGAT-AGAGCATACCGATTC-T
46512092 AGCTCGTATGAGC
1 AGCTCGTATGAGC
46512105 ATACATGTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
49 2 0.04
50 48 0.92
51 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (49 bp):
AGCTCGTATGAGCTTATCGATTTACAGCTCGATAGAGCATACCGATTCT
Found at i:46513157 original size:24 final size:22
Alignment explanation
Indices: 46513121--46513168 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
46513111 ATACTACATG
* *
46513121 TTTAATGCTTAATTTTGCTTGT
1 TTTAATGCTTAATATGGCTTGT
46513143 TTTAGATGCATTAATATGGCTTGT
1 TTTA-ATGC-TTAATATGGCTTGT
46513167 TT
1 TT
46513169 ACATGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 4 0.18
24 14 0.64
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.54
Consensus pattern (22 bp):
TTTAATGCTTAATATGGCTTGT
Found at i:46513169 original size:23 final size:22
Alignment explanation
Indices: 46513119--46513175 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
46513109 ATATACTACA
* *
46513119 TGTTTAATGC-TTAATTTTGCT
1 TGTTTAATGCATTAATATGGCT
46513140 TGTTTTAGATGCATTAATATGGCT
1 TG-TTTA-ATGCATTAATATGGCT
46513164 TGTTTACATGCA
1 TGTTTA-ATGCA
46513176 CAATGTTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.07
22 4 0.13
23 13 0.43
24 11 0.37
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.49
Consensus pattern (22 bp):
TGTTTAATGCATTAATATGGCT
Found at i:46515816 original size:21 final size:20
Alignment explanation
Indices: 46515792--46515834 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
46515782 GCTCCTACCG
46515792 AGTTAAAAGAGTTAAAAGCAT
1 AGTTAAAAGAGTTAAAAG-AT
* *
46515813 AGTTACAAGAGTTGAAAGAT
1 AGTTAAAAGAGTTAAAAGAT
46515833 AG
1 AG
46515835 GGGTTTGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (20 bp):
AGTTAAAAGAGTTAAAAGAT
Found at i:46517337 original size:25 final size:25
Alignment explanation
Indices: 46517300--46517366 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
46517290 GACACACCAT
* *
46517300 AGCTCGTATGAGCTTACCGATTTAC
1 AGCTCGTATGAGCATACCGATTCAC
*
46517325 AGCTCGTGA-GAGCATACCGATTCAT
1 AGCTCGT-ATGAGCATACCGATTCAC
46517350 AGCTCGT-TCGAGCATAC
1 AGCTCGTAT-GAGCATAC
46517367 ATGTACAGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (25 bp):
AGCTCGTATGAGCATACCGATTCAC
Found at i:46518610 original size:12 final size:12
Alignment explanation
Indices: 46518593--46518622 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46518583 TCAAGCTATT
46518593 ACACGGCCTAGC
1 ACACGGCCTAGC
*
46518605 ACACGGCCTGGC
1 ACACGGCCTAGC
46518617 ACACGG
1 ACACGG
46518623 ACGTGTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:46519534 original size:26 final size:26
Alignment explanation
Indices: 46519503--46519565 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
46519493 TATTTTACAC
*
46519503 CTAGTAAAATTTTGACGATTTTACCAT
1 CTAGTAAAATTTTGACGACTTTACC-T
*
46519530 C-AGT-AAATTTTGATGACTTTACCT
1 CTAGTAAAATTTTGACGACTTTACCT
46519554 CTAGTAAAATTT
1 CTAGTAAAATTT
46519566 CTAGAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 2 0.06
25 20 0.62
26 9 0.28
27 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (26 bp):
CTAGTAAAATTTTGACGACTTTACCT
Found at i:46522443 original size:25 final size:26
Alignment explanation
Indices: 46522397--46522450 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
46522387 TACCCAAATA
46522397 TGATAGTTTTCATTGTTAAAAACTAG
1 TGATAGTTTTCATTGTTAAAAACTAG
*
46522423 TGATATTTTTCATTGTTAAAAACTAG
1 TGATAGTTTTCATTGTTAAAAACTAG
46522449 TG
1 TG
46522451 GTAGAGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (26 bp):
TGATAGTTTTCATTGTTAAAAACTAG
Found at i:46524125 original size:16 final size:15
Alignment explanation
Indices: 46524065--46524124 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
46524055 AAGTGCAGAT
*
46524065 TTTTTGAGTTCAATT
1 TTTTTGAGTTCAATA
**
46524080 TTTTTTTGTTCAA-A
1 TTTTTGAGTTCAATA
*
46524094 TTTTATCATGTTCAAGTA
1 TTTT-TGA-GTTCAA-TA
46524112 TTTTTGAGTTCAA
1 TTTTTGAGTTCAA
46524125 GCTTATTCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.11
15 12 0.34
16 12 0.34
17 2 0.06
18 5 0.14
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTTTGAGTTCAATA
Found at i:46536908 original size:106 final size:106
Alignment explanation
Indices: 46536718--46536967 Score: 392
Period size: 106 Copynumber: 2.4 Consensus size: 106
46536708 CTATACAAGT
*
46536718 ACTGATATTATAAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTTCTTTGAGTTAGCTGATTTA
1 ACTGATATTATAAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTTCTTTGAGTTAGCTAATTTA
* * * *
46536783 ATATCGCAACTCTTGAAATAGTTTGATGACCTACGTTCACA
66 AGATCGCAACTCCTAAAATAGTTCGATGACCTACGTTCACA
* * *
46536824 ACTGGTATTATAAGGGTTAGCCGATTTAAGATCGCAACCTAAGTTTCTTTGAGTTAGCTAATTTA
1 ACTGATATTATAAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTTCTTTGAGTTAGCTAATTTA
46536889 AGATCGCAACTCCTAAAATAGTTCGATGACCTACGTTCACA
66 AGATCGCAACTCCTAAAATAGTTCGATGACCTACGTTCACA
** * *
46536930 GTTGATATTATAAAGGTTAGTTGATTTAAGATTGCAAC
1 ACTGATATTATAAAGGTTAGCTGATTTAAGATCGCAAC
46536968 TTGTAAAACA
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 129 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (106 bp):
ACTGATATTATAAAGGTTAGCTGATTTAAGATCGCAACCTAAGTTTCTTTGAGTTAGCTAATTTA
AGATCGCAACTCCTAAAATAGTTCGATGACCTACGTTCACA
Found at i:46536987 original size:69 final size:69
Alignment explanation
Indices: 46536876--46537053 Score: 248
Period size: 69 Copynumber: 2.6 Consensus size: 69
46536866 GTTTCTTTGA
* * ** *
46536876 GTTAGCTAATTTAAGATCGCAACTCCTAAAATAGTTCGATGACCTACGTTCACAGTTGATATTAT
1 GTTAGCTGATTTAAGATCGCAACTCCTAAAACAACTCGATGACCTACGTTCACAGCTGATATTAT
46536941 AAAG
66 AAAG
* * **
46536945 GTTAGTTGATTTAAGATTGCAACTTGTAAAACAACTCGATGACCTACGTTCACAGCTGATATTAT
1 GTTAGCTGATTTAAGATCGCAACTCCTAAAACAACTCGATGACCTACGTTCACAGCTGATATTAT
46537010 AAAG
66 AAAG
* * *
46537014 GTTAGCTGATTTAATATCGTAACTCCTAAAACTACTCGAT
1 GTTAGCTGATTTAAGATCGCAACTCCTAAAACAACTCGAT
46537054 CACATCTGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 93 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (69 bp):
GTTAGCTGATTTAAGATCGCAACTCCTAAAACAACTCGATGACCTACGTTCACAGCTGATATTAT
AAAG
Found at i:46541008 original size:54 final size:54
Alignment explanation
Indices: 46540926--46541056 Score: 262
Period size: 54 Copynumber: 2.4 Consensus size: 54
46540916 TAGGGTCTAA
46540926 ATTTAGCCTGGACTGGTAATCCCAACAATACTCTATGAGTTTATATTACAGGTG
1 ATTTAGCCTGGACTGGTAATCCCAACAATACTCTATGAGTTTATATTACAGGTG
46540980 ATTTAGCCTGGACTGGTAATCCCAACAATACTCTATGAGTTTATATTACAGGTG
1 ATTTAGCCTGGACTGGTAATCCCAACAATACTCTATGAGTTTATATTACAGGTG
46541034 ATTTAGCCTGGACTGGTAATCCC
1 ATTTAGCCTGGACTGGTAATCCC
46541057 GCTGTAAGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
ATTTAGCCTGGACTGGTAATCCCAACAATACTCTATGAGTTTATATTACAGGTG
Found at i:46548835 original size:57 final size:57
Alignment explanation
Indices: 46548750--46548870 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 57
46548740 GCAGAAATGG
*
46548750 TGAAAATGGAGAAATGGGAAACATTTGGAAATGAA-TAAGGTTTTCTCCAAAATGAAAA
1 TGAAAAGGGAGAAATGGGAAACATTTGGAAATGAAGTAA--TTTTCTCCAAAATGAAAA
*
46548808 TGAAAAGGGAGAAA-GGGAAATATTTGGAAATGAATGTAATTTTCTCCAAAATGAAAA
1 TGAAAAGGGAGAAATGGGAAACATTTGGAAATGAA-GTAATTTTCTCCAAAATGAAAA
46548865 TGAAAA
1 TGAAAA
46548871 ATGAAAATGA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
57 43 0.73
58 13 0.22
59 3 0.05
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (57 bp):
TGAAAAGGGAGAAATGGGAAACATTTGGAAATGAAGTAATTTTCTCCAAAATGAAAA
Found at i:46548873 original size:13 final size:13
Alignment explanation
Indices: 46548855--46548880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46548845 AATTTTCTCC
46548855 AAAATGAAAATGA
1 AAAATGAAAATGA
46548868 AAAATGAAAATGA
1 AAAATGAAAATGA
46548881 CCTGGAAATG
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:46550759 original size:41 final size:41
Alignment explanation
Indices: 46550707--46550811 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
46550697 GGCTCTATGT
** *
46550707 GCCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTAT
1 GCCTAGCAGGCTTGATGCCGGTGAAATAAATCAGACTTTAA
* * * * *
46550748 GTCTAGCAGGCTTCATGCCGGTGTATTAAATCAGGCTTTAA
1 GCCTAGCAGGCTTGATGCCGGTGAAATAAATCAGACTTTAA
46550789 GCCTAGCAGGCTTTG-TGCCGGTG
1 GCCTAGCAGGC-TTGATGCCGGTG
46550812 TATCATTTCA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 51 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (41 bp):
GCCTAGCAGGCTTGATGCCGGTGAAATAAATCAGACTTTAA
Found at i:46550834 original size:41 final size:40
Alignment explanation
Indices: 46550706--46550835 Score: 93
Period size: 41 Copynumber: 3.2 Consensus size: 40
46550696 AGGCTCTATG
* *
46550706 TGCCTAGCAGGC-TTGATGCCGGTGAAATATTTC-AGACTTTA
1 TGCCTAGCAGGCTTTG-TGCCGGTG-TATATTTCAAGA-TATA
* ** ** * * *
46550747 TGTCTAGCAGGCTTCATGCCGGTGTATTAAATCAGGCTTTA
1 TGCCTAGCAGGCTTTGTGCCGGTGTA-TATTTCAAGATATA
* *
46550788 AGCCTAGCAGGCTTTGTGCCGGTGTATCATTTCAAGATATG
1 TGCCTAGCAGGCTTTGTGCCGGTGTAT-ATTTCAAGATATA
46550829 TGCCTAG
1 TGCCTAG
46550836 TGATTTCTAT
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
40 2 0.03
41 62 0.94
42 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (40 bp):
TGCCTAGCAGGCTTTGTGCCGGTGTATATTTCAAGATATA
Found at i:46551644 original size:94 final size:94
Alignment explanation
Indices: 46551483--46551668 Score: 372
Period size: 94 Copynumber: 2.0 Consensus size: 94
46551473 TATGTGTGGA
46551483 AGTTATATGTGACATGTTGGAATAGTAGTAAAGTGAATATATAATATGAACTATAAATGGAAGTG
1 AGTTATATGTGACATGTTGGAATAGTAGTAAAGTGAATATATAATATGAACTATAAATGGAAGTG
46551548 TATTTTTAGATGTCAATGATGAGTTACCT
66 TATTTTTAGATGTCAATGATGAGTTACCT
46551577 AGTTATATGTGACATGTTGGAATAGTAGTAAAGTGAATATATAATATGAACTATAAATGGAAGTG
1 AGTTATATGTGACATGTTGGAATAGTAGTAAAGTGAATATATAATATGAACTATAAATGGAAGTG
46551642 TATTTTTAGATGTCAATGATGAGTTAC
66 TATTTTTAGATGTCAATGATGAGTTAC
46551669 TTAAGTATTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (94 bp):
AGTTATATGTGACATGTTGGAATAGTAGTAAAGTGAATATATAATATGAACTATAAATGGAAGTG
TATTTTTAGATGTCAATGATGAGTTACCT
Found at i:46552829 original size:34 final size:34
Alignment explanation
Indices: 46552786--46552859 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
46552776 TTCTAAATAC
* *
46552786 ACCAAATTGCACATAAGTGCATTCATCCCTCACA
1 ACCAAATTGCACATAAGTGCATCCATCCCACACA
*
46552820 ACCAAATTGCACATAAGTGTATCCATCCCACACA
1 ACCAAATTGCACATAAGTGCATCCATCCCACACA
46552854 ACCAAA
1 ACCAAA
46552860 GAGCACTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.32, G:0.08, T:0.20
Consensus pattern (34 bp):
ACCAAATTGCACATAAGTGCATCCATCCCACACA
Found at i:46552872 original size:34 final size:34
Alignment explanation
Indices: 46552794--46552873 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
46552784 ACACCAAATT
* * **
46552794 GCACATAAGTGCATTCATCCCTCACAACCAAATT
1 GCACATAAGTGCATCCATCCCACACAACCAAAGA
*
46552828 GCACATAAGTGTATCCATCCCACACAACCAAAGA
1 GCACATAAGTGCATCCATCCCACACAACCAAAGA
46552862 GCAC-TAAAGTGC
1 GCACAT-AAGTGC
46552874 TAAGCTAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (34 bp):
GCACATAAGTGCATCCATCCCACACAACCAAAGA
Found at i:46560863 original size:43 final size:43
Alignment explanation
Indices: 46560797--46560924 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 43
46560787 AGTTCGTACA
*
46560797 ATGCCA-TCGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCACT-GTCCCAGACGTGGTCTTACACGTAATCACATATCG
* *
46560840 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAATCAGATATTG
1 ATGCCACTGTCCCAGAC-GTGGTCTTACACGTAATCACATATCG
* *
46560883 ATGCCGAC-GTCCCAGACGTGGTCTTACACGAAAACACATATC
1 ATGCC-ACTGTCCCAGACGTGGTCTTACACGTAATCACATATC
46560925 AGAGTCCTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
42 1 0.01
43 69 0.93
44 4 0.05
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:46562085 original size:14 final size:15
Alignment explanation
Indices: 46562066--46562094 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
46562056 TCACAAAACT
46562066 TTCACACAT-ATAAA
1 TTCACACATAATAAA
46562080 TTCACACATAATAAA
1 TTCACACATAATAAA
46562095 CATAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:46563347 original size:24 final size:23
Alignment explanation
Indices: 46563308--46563352 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
46563298 TATATTATTT
46563308 GTTAAATTTTTATATTTAATATAG
1 GTTAAATTTTTATA-TTAATATAG
46563332 GTTAAA-TTTTATTATTAATAT
1 GTTAAATTTTTA-TATTAATAT
46563353 CTATGTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (23 bp):
GTTAAATTTTTATATTAATATAG
Found at i:46564160 original size:9 final size:9
Alignment explanation
Indices: 46564119--46564174 Score: 58
Period size: 9 Copynumber: 5.8 Consensus size: 9
46564109 TAATTTAGCA
46564119 TTTTATATAT
1 TTTTA-ATAT
*
46564129 TTTTAAAGATT
1 TTTT-AATA-T
*
46564140 TTTTAGTAAT
1 TTTTAAT-AT
46564150 TTTTAATAT
1 TTTTAATAT
46564159 TTTTAATAT
1 TTTTAATAT
46564168 TTTTAAT
1 TTTTAAT
46564175 GTATATTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 18 0.46
10 14 0.36
11 7 0.18
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTAATAT
Found at i:46567365 original size:27 final size:27
Alignment explanation
Indices: 46567335--46567422 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 27
46567325 AGAGGTGGTG
*
46567335 CCTATCTGGTAGGCGTCACTGGTGACT
1 CCTATCTGGTAGGCGCCACTGGTGACT
* *
46567362 CCTATCTGCTAGGTGCCACTGGTGACT
1 CCTATCTGGTAGGCGCCACTGGTGACT
* * *
46567389 CTTATCTGGTAGGCACCACTGGTGACA
1 CCTATCTGGTAGGCGCCACTGGTGACT
46567416 CCTATCT
1 CCTATCT
46567423 CATAAGCGGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (27 bp):
CCTATCTGGTAGGCGCCACTGGTGACT
Found at i:46570762 original size:76 final size:77
Alignment explanation
Indices: 46570677--46570841 Score: 260
Period size: 77 Copynumber: 2.2 Consensus size: 77
46570667 TTAAGTAAAT
* * * * * *
46570677 AATACAAAGTTTATTATTTAAATTGTAAAAAAAA-CCCTAAAATTAATAATTGAAGTGGCAAAAA
1 AATACAAAGTTAATTATTTAAATTGAAAAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAA
46570741 AGTCATTACATA
66 AGTCATTACATA
46570753 AATACAAAGTTAATTATTTAAATTGAAAAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAA
1 AATACAAAGTTAATTATTTAAATTGAAAAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAA
46570818 AGTCATTACATA
66 AGTCATTACATA
*
46570830 AATATAAAGTTA
1 AATACAAAGTTA
46570842 TTTAAATTAC
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 32 0.40
77 49 0.60
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (77 bp):
AATACAAAGTTAATTATTTAAATTGAAAAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAA
AGTCATTACATA
Found at i:46571072 original size:33 final size:33
Alignment explanation
Indices: 46571029--46571108 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
46571019 CTTGAGCTAG
* *
46571029 GAGGAATGGAGTACAGCAGCGGATACGGGCCGA
1 GAGGAGTGGAGTACAGCAGCAGATACGGGCCGA
* * * * *
46571062 GAGGAGTGGAGTACGGCGGTAGATATGGGCCGG
1 GAGGAGTGGAGTACAGCAGCAGATACGGGCCGA
*
46571095 GAGGAGTAGAGTAC
1 GAGGAGTGGAGTAC
46571109 TGAGGTGGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.14, G:0.46, T:0.12
Consensus pattern (33 bp):
GAGGAGTGGAGTACAGCAGCAGATACGGGCCGA
Found at i:46573189 original size:158 final size:157
Alignment explanation
Indices: 46572902--46573191 Score: 510
Period size: 158 Copynumber: 1.8 Consensus size: 157
46572892 TTAGAAATAG
*
46572902 AAAACAACATTAAATATCTCATAATTTCCCATAATTTACCTACAATAAAAAAATTTATGTTAGTT
1 AAAACAACAGTAAATATCTCATAATTTCCCATAATTTACCTACAATAAAAAAATTTATGTTAGTT
* * *
46572967 TACAATAATAATATAATTAAAATAAATATAAACTATCTAAATATAAAAAACATACGACTAAAAAA
66 TACAATAACAATATAATTAAAATAAATATAAACTATCTAAACATAAAAAACATACGAATAAAAAA
46573032 ATAATAGTAATAGAAACATACATGTAA
131 ATAATAGTAATAGAAACATACATGTAA
* *
46573059 AAAACCACAGTAAATATCTCATAATTTCTCATATATTTACCTACAATAAAAAAATTTATGTTAGT
1 AAAACAACAGTAAATATCTCATAATTTCCCATA-ATTTACCTACAATAAAAAAATTTATGTTAGT
46573124 TTACAATAACAATATAATTAAAATAAATATAAACTATCTAAACATAAAAAA-ATACGAATAAAAA
65 TTACAATAACAATATAATTAAAATAAATATAAACTATCTAAACATAAAAAACATACGAATAAAAA
46573188 AATA
130 AATA
46573192 GAAACATACC
Statistics
Matches: 126, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
157 46 0.37
158 80 0.63
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (157 bp):
AAAACAACAGTAAATATCTCATAATTTCCCATAATTTACCTACAATAAAAAAATTTATGTTAGTT
TACAATAACAATATAATTAAAATAAATATAAACTATCTAAACATAAAAAACATACGAATAAAAAA
ATAATAGTAATAGAAACATACATGTAA
Found at i:46573321 original size:16 final size:17
Alignment explanation
Indices: 46573302--46573337 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
46573292 AAAATCAAAT
46573302 AAAATTACATT-ATAAA
1 AAAATTACATTAATAAA
46573318 AAAATTACATTAATAAA
1 AAAATTACATTAATAAA
46573335 AAA
1 AAA
46573338 TCACAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATTACATTAATAAA
Found at i:46573366 original size:23 final size:21
Alignment explanation
Indices: 46573324--46573366 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
46573314 TAAAAAAATT
*
46573324 ACATTAATAAAAAATCACAAA
1 ACATTAATAAAAAATAACAAA
*
46573345 ACATTAAACTAAACAATAACAA
1 ACATT-AA-TAAAAAATAACAA
46573367 TTTATATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (21 bp):
ACATTAATAAAAAATAACAAA
Found at i:46574185 original size:71 final size:71
Alignment explanation
Indices: 46574102--46574254 Score: 306
Period size: 71 Copynumber: 2.2 Consensus size: 71
46574092 ATTGGTATTC
46574102 ATGGTTTTGTTTGTATGTTTTCCCCGATTGCATGTTTGTATTGCCATAGCAGCTTTTGTTGTTTC
1 ATGGTTTTGTTTGTATGTTTTCCCCGATTGCATGTTTGTATTGCCATAGCAGCTTTTGTTGTTTC
46574167 CTTTGT
66 CTTTGT
46574173 ATGGTTTTGTTTGTATGTTTTCCCCGATTGCATGTTTGTATTGCCATAGCAGCTTTTGTTGTTTC
1 ATGGTTTTGTTTGTATGTTTTCCCCGATTGCATGTTTGTATTGCCATAGCAGCTTTTGTTGTTTC
46574238 CTTTGT
66 CTTTGT
46574244 ATGGTTTTGTT
1 ATGGTTTTGTT
46574255 GGTAAATAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.11, C:0.14, G:0.22, T:0.53
Consensus pattern (71 bp):
ATGGTTTTGTTTGTATGTTTTCCCCGATTGCATGTTTGTATTGCCATAGCAGCTTTTGTTGTTTC
CTTTGT
Found at i:46576595 original size:92 final size:91
Alignment explanation
Indices: 46576448--46576655 Score: 355
Period size: 92 Copynumber: 2.3 Consensus size: 91
46576438 ATGATTTTAG
* *
46576448 TAAATTCATATAAGAACATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
46576513 TTTAA-AATTTAATTATTTTAAATTATA
66 TTTAATAA--TAATTATTTTAAATTATA
*
46576540 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
46576605 TTTAATAATAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
*
46576631 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
46576656 GTTATAATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
91 42 0.38
92 67 0.60
93 2 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATA
Found at i:46576747 original size:59 final size:58
Alignment explanation
Indices: 46576682--46576870 Score: 163
Period size: 59 Copynumber: 3.2 Consensus size: 58
46576672 ATTTTATTAA
46576682 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTATATTTTATAGT
* * ** * *
46576741 ATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTA-TT-AA-GA-ATTTTATTA-
1 ATCATATATT-TTA-ATTA--AAA-T-ATAT-TTAATATTAATTATTTAAATTATATTTTA-TAG
*
46576801 A
58 T
* * *
46576802 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATATTTTATAGT
46576861 ATCATATATT
1 ATCATATATT
46576871 ATGATTTGAG
Statistics
Matches: 98, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
54 9 0.09
55 4 0.04
56 3 0.03
57 5 0.05
58 2 0.02
59 28 0.29
60 4 0.04
61 18 0.18
62 3 0.03
63 5 0.05
64 1 0.01
65 6 0.06
66 10 0.10
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATATTTTATAGT
Found at i:46576801 original size:120 final size:120
Alignment explanation
Indices: 46576671--46576966 Score: 531
Period size: 120 Copynumber: 2.5 Consensus size: 120
46576661 AATTATTTTA
* *
46576671 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* *
46576735 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
46576791 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
46576856 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
46576911 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
46576967 ATATGATTAA
Statistics
Matches: 170, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
120 168 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:46576809 original size:61 final size:61
Alignment explanation
Indices: 46576744--46576931 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
46576734 TTATAGTATC
*
46576744 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
46576805 ATATATTTTAATTAAAATATATTTA-ATAATAAT-TATG-TTAAATT-A-TATTTTA-CAGTATC
1 ATATATTATGATTTAAGTAAATTCATATAAGAATAT-TGATT--ATTAAGAATTTTATTA-AATT
*
46576864 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
46576925 ATATATT
1 ATATATT
46576932 TTAATTATAA
Statistics
Matches: 93, Mismatches: 24, Indels: 20
0.68 0.18 0.15
Matches are distributed among these distances:
58 1 0.01
59 32 0.34
60 20 0.22
61 39 0.42
62 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:46576820 original size:18 final size:17
Alignment explanation
Indices: 46576792--46576826 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
46576782 ATTATTAAGA
*
46576792 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
46576809 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
46576827 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:46576928 original size:59 final size:59
Alignment explanation
Indices: 46576745--46576928 Score: 164
Period size: 54 Copynumber: 3.1 Consensus size: 59
46576735 TATAGTATCA
*
46576745 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
* * ** * * * *
46576804 TATA-TAT--TTTAATTAAAAT-ATAT-TTAATAATAATTATGTTA-AATTATATTTTACAGTAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTAT-TAAGAATT-T-TATTA-A--AT
*
46576863 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
46576924 TATAT
1 TATAT
46576929 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
54 14 0.15
55 7 0.08
56 13 0.14
57 1 0.01
58 3 0.03
59 11 0.12
61 6 0.06
62 3 0.03
63 1 0.01
64 13 0.14
65 7 0.08
66 14 0.15
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
Found at i:46576951 original size:15 final size:15
Alignment explanation
Indices: 46576916--46576957 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46576906 TTAAGAATTT
*
46576916 TATTAAATTAT-ATA
1 TATTTAATTATAATA
46576930 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
46576944 TATTTAATAATAAT
1 TATTTAATTATAAT
46576958 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:46577201 original size:16 final size:16
Alignment explanation
Indices: 46577180--46577212 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
46577170 TTGATTTGTT
46577180 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
46577196 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
46577212 A
1 A
46577213 ATATAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:46577333 original size:76 final size:78
Alignment explanation
Indices: 46577252--46577411 Score: 209
Period size: 80 Copynumber: 2.1 Consensus size: 78
46577242 TTTAAAAAAA
* * * * *
46577252 TTTACATTACTAAAAAATCA-CAAA-AC-ACTGAACACTAACAATTTATAACCTAATCATAAATT
1 TTTACATTAATAAAAAATCATAAAATACAACTAAACAC-AACAAATTATAACATAATCATAAATT
46577314 ACAAACAAAATAAT
65 ACAAACAAAATAAT
*
46577328 TTTACATTAATAAAAAATCATAAAATACTAAACTAAACACAACAAATTATAACATAATCCTAAAT
1 TTTACATTAATAAAAAATCATAAAATAC--AACTAAACACAACAAATTATAACATAATCATAAAT
*
46577393 TACTAACAAAATAAT
64 TACAAACAAAATAAT
46577408 TTTA
1 TTTA
46577412 AAACAATTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
76 19 0.26
77 3 0.04
78 2 0.03
80 40 0.56
81 8 0.11
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (78 bp):
TTTACATTAATAAAAAATCATAAAATACAACTAAACACAACAAATTATAACATAATCATAAATTA
CAAACAAAATAAT
Found at i:46577613 original size:18 final size:18
Alignment explanation
Indices: 46577574--46577619 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
46577564 AATACATACC
*
46577574 TTCTCCTTCTCCTTCTCC
1 TTCTCCTTCTCCTTCTCA
*
46577592 TTCTCCTTCTCCTTCTTA
1 TTCTCCTTCTCCTTCTCA
*
46577610 TTCTTCTTCT
1 TTCTCCTTCT
46577620 TCTTTTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (18 bp):
TTCTCCTTCTCCTTCTCA
Found at i:46577623 original size:6 final size:6
Alignment explanation
Indices: 46577572--46577607 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
46577562 ATAATACATA
46577572 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
46577608 TATTCTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CCTTCT
Found at i:46578352 original size:60 final size:58
Alignment explanation
Indices: 46578239--46578421 Score: 163
Period size: 60 Copynumber: 3.1 Consensus size: 58
46578229 CTTTCAGGTT
** ** * * *
46578239 TTCAATGA-CTAACTTGGA-CAAAAAAAAGTTCAAGTCATAATACGTGAAGAATTGTCAAA
1 TTCAA-GACCTAACTTGGACCAAAAAAAAGTTCAAG-CCCAATGTGAGAACAATTG-CAAG
** * *
46578298 TTCAAGGTCTAACTTGGACCAAAAAAAAGTTCATGACCCAATGTGGGAACAATTGCTAAG
1 TTCAAGACCTAACTTGGACCAAAAAAAAGTTCAAG-CCCAATGTGAGAACAATTGC-AAG
* * *
46578358 TTCAAGACCTAACTTAGACTAAAAAAAAGTTCAAGCCTCAATGTGAAAACAATTGCCAAG
1 TTCAAGACCTAACTTGGACCAAAAAAAAGTTCAAGCC-CAATGTGAGAACAATTG-CAAG
46578418 TTCA
1 TTCA
46578422 GGGCTTATCT
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
58 1 0.01
59 18 0.18
60 82 0.80
61 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (58 bp):
TTCAAGACCTAACTTGGACCAAAAAAAAGTTCAAGCCCAATGTGAGAACAATTGCAAG
Found at i:46582507 original size:44 final size:44
Alignment explanation
Indices: 46582413--46582515 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
46582403 TTTGCTTTCA
* *
46582413 GCTGTGGATACACAACAAGTACCCGCAAATGGAATCTACCATTG
1 GCTGTGGATTCACAGCAAGTACCCGCAAATGGAATCTACCATTG
* * *
46582457 GCTGTGGATTCACAGCAA-TACCCTGTAGATGGAATCTGCC-TCTG
1 GCTGTGGATTCACAGCAAGTACCC-GCAAATGGAATCTACCAT-TG
*
46582501 GTTGTGGATTCACAG
1 GCTGTGGATTCACAG
46582516 TGGTTTGCAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
43 6 0.12
44 45 0.88
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
GCTGTGGATTCACAGCAAGTACCCGCAAATGGAATCTACCATTG
Found at i:46586130 original size:21 final size:21
Alignment explanation
Indices: 46586091--46586130 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46586081 AAATGGCACA
***
46586091 ATATTTTTATTTTTTATAATT
1 ATATTTTTATTTAAAATAATT
46586112 ATATTTTTATTTAAAATAA
1 ATATTTTTATTTAAAATAA
46586131 AAGCAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTTTATTTAAAATAATT
Found at i:46591536 original size:28 final size:28
Alignment explanation
Indices: 46591505--46591580 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
46591495 ATTCCATGCT
*
46591505 TTTAATTTTATTAAATTACATCAAAGCA
1 TTTAATTTTATTAAATTACATCAAAGAA
*
46591533 TTTAATTTTGTTAAATTACATCAAAGAA
1 TTTAATTTTATTAAATTACATCAAAGAA
*
46591561 TTTAATTTTATAAAATTACA
1 TTTAATTTTATTAAATTACA
46591581 CTAGTCCCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (28 bp):
TTTAATTTTATTAAATTACATCAAAGAA
Found at i:46592236 original size:91 final size:91
Alignment explanation
Indices: 46591950--46592433 Score: 402
Period size: 98 Copynumber: 5.0 Consensus size: 91
46591940 GCAGTTTTTT
* * * *
46591950 TTATAATTATTTTGTTAGTAATTTAGGATTATGTTATAAATTGCTGT-GTTTAGTTTAGTATTTT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG-T-TAG--T-GTTTTGTATTTT
* * * *
46592014 GTGATTTCTTATTAATGTAAAATTATTT--TG
61 GTGATTTTTTAGTAATGT-AATTTTTTTAATG
* * * *
46592044 TGA-A-TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTATTTTGTGTTTTATGAT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTATTTTGTGAT
* * *
46592107 ATTTTAGTAATATAATTTTTTAAAAAAATAATT
66 TTTTTAGTAATGTAATTTTTT-------TAATG
*
46592140 TTATAGTTATTTTATTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTATTTTGTGAT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTATTTTGTGAT
*
46592205 TTATTAGTAATGTAATTTTTTTAATG
66 TTTTTAGTAATGTAATTTTTTTAATG
* * * *
46592231 TTATAGTTATTTTGTTAGTAATTTATGATTAGTTTATAATTTGTTACTGTTTAGTTTAGGGTTTT
1 TTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTT--TGTA---TTTT
*
46592296 GTGATTTTTTAGTAATGTAATTTTTTTTAAAG
61 GTGATTTTTTAGTAATGTAA-TTTTTTTAATG
* **
46592328 ATAATTTTATAGTTTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTCAGTTTAG
1 -TTATAGT-TA--TTTTGTTAGTAATTTATGATTAGG-T-TATAAATTGTTAGTG-T---TTT-G
*
46592393 TATTTTGTGATTTTTTTATTAATGTAAATTTTTTATAATG
55 TATTTTGTGA-TTTTTTAGTAATGT-AATTTTTT-TAATG
46592433 T
1 T
46592434 AATTTTATTT
Statistics
Matches: 319, Mismatches: 39, Indels: 54
0.77 0.09 0.13
Matches are distributed among these distances:
87 6 0.02
88 22 0.07
89 1 0.00
90 1 0.00
91 54 0.17
92 35 0.11
93 4 0.01
94 3 0.01
96 26 0.08
97 11 0.03
98 77 0.24
99 2 0.01
101 23 0.07
102 1 0.00
103 21 0.07
104 21 0.07
105 7 0.02
106 2 0.01
107 2 0.01
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.56
Consensus pattern (91 bp):
TTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTATTTTGTGAT
TTTTTAGTAATGTAATTTTTTTAATG
Found at i:46592399 original size:103 final size:97
Alignment explanation
Indices: 46592051--46592441 Score: 411
Period size: 98 Copynumber: 4.0 Consensus size: 97
46592041 TTGTGAATTA
* * * *
46592051 TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTA--GTATTTTGTGTTTTATGATATTTTAG
1 TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTATTTAGTATTTTGTGATTTTTTAG
* * *
46592114 TAATATAATTTTTTAAAAAAATAATTTTATAGTT
66 TAATGTAATTTTTT-ATAAAGTAATTTTATAG-T
* *
46592148 ATTTTATTAGTAATTTATGATTAGGTTATAAATTGTTAGTGT-TTT-GTATTTTGTGATTTATTA
1 -TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTATTTAGTATTTTGTGATTTTTTA
* * **
46592211 GTAATGTAATTTTTT-TAATGTTATAGT-TA--
65 GTAATGTAATTTTTTATAAAGTAATTTTATAGT
* * * **
46592240 TTTTGTTAGTAATTTATGATTAGTTTATAATTTGTTACTGTTTAGTTTAGGGTTTTGTGATTTTT
1 TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTA--GTGTA-TTTAGTATTTTGTGATTTTT
*
46592305 TAGTAATGTAATTTTTTTTAAAGATAATTTTATAGT
63 TAGTAATGTAATTTTTTATAAAG-TAATTTTATAGT
46592341 TTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTCAGTTTAGTATTTTGTGATTT
1 TTTTGTTAGTAATTTATGATTAGG-T-TATAAATTGTTAGTG-T-A-TTTAGTATTTTGTGA-TT
* *
46592406 TTTTATTAATGTAAATTTTTTATAATGTAATTTTAT
60 TTTTAGTAATGT-AATTTTTTATAAAGTAATTTTAT
46592442 TTGTTTTTTT
Statistics
Matches: 244, Mismatches: 31, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
91 34 0.14
93 3 0.01
95 5 0.02
96 36 0.15
97 4 0.02
98 68 0.28
99 5 0.02
100 2 0.01
101 25 0.10
102 2 0.01
103 26 0.11
104 22 0.09
105 12 0.05
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.57
Consensus pattern (97 bp):
TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTATTTAGTATTTTGTGATTTTTTAG
TAATGTAATTTTTTATAAAGTAATTTTATAGT
Found at i:46592426 original size:17 final size:15
Alignment explanation
Indices: 46592404--46592439 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
46592394 ATTTTGTGAT
46592404 TTTTTTATTAATGTAAA
1 TTTTTTA-TAATGT-AA
46592421 TTTTTTATAATGTAA
1 TTTTTTATAATGTAA
46592436 TTTT
1 TTTT
46592440 ATTTGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTTATAATGTAA
Found at i:46599219 original size:25 final size:24
Alignment explanation
Indices: 46599189--46599241 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
46599179 AAAATGCCAG
46599189 ATTTTAA-CGAAAACTATCCTGATTT
1 ATTTTAAGCGAAAA-TATCCT-ATTT
* *
46599214 ATTTTAAGTGAAAATATCCTTTTT
1 ATTTTAAGCGAAAATATCCTATTT
46599238 ATTT
1 ATTT
46599242 AATTTGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTTAAGCGAAAATATCCTATTT
Found at i:46605066 original size:20 final size:20
Alignment explanation
Indices: 46605008--46605064 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 20
46604998 ATATTTTCCC
46605008 ATAAAAAT-GATAAAAAA--T
1 ATAAAAATAGA-AAAAAATTT
46605026 A-AAAAATAGAAAAAAATTT
1 ATAAAAATAGAAAAAAATTT
*
46605045 ATAAAAATAGGAAAGAAATT
1 ATAAAAATA-GAAAAAAATT
46605065 ATTTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 12 0.36
18 3 0.09
19 2 0.06
20 7 0.21
21 9 0.27
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (20 bp):
ATAAAAATAGAAAAAAATTT
Found at i:46605113 original size:31 final size:31
Alignment explanation
Indices: 46605075--46605149 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
46605065 ATTTTTTATT
* *
46605075 AAAATTAATATAAACTTACAAAAT-TTATAAA
1 AAAATTAATAAAAACTTA-AAAATATCATAAA
*
46605106 AAAATTAATAAAAACTTATAAATATCATAAA
1 AAAATTAATAAAAACTTAAAAATATCATAAA
46605137 AAAATCTAATAAA
1 AAAAT-TAATAAA
46605150 TTCTAATAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.10
31 28 0.72
32 7 0.18
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (31 bp):
AAAATTAATAAAAACTTAAAAATATCATAAA
Found at i:46605237 original size:21 final size:20
Alignment explanation
Indices: 46605213--46605267 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
46605203 AAATTTTAGG
46605213 AAAAACATATAAAAAATTCTT
1 AAAAACATATAAAAAATT-TT
* * *
46605234 AAAAACCTATGAAAAATTAT
1 AAAAACATATAAAAAATTTT
46605254 AAAAA-AT-TAAAAAA
1 AAAAACATATAAAAAA
46605268 ATTATTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 1 0.03
20 6 0.21
21 16 0.55
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAACATATAAAAAATTTT
Found at i:46605266 original size:9 final size:10
Alignment explanation
Indices: 46605220--46605316 Score: 58
Period size: 10 Copynumber: 9.9 Consensus size: 10
46605210 AGGAAAAACA
46605220 TATAAAAAAT
1 TATAAAAAAT
* **
46605230 TCTTAAAAACC
1 T-ATAAAAAAT
*
46605241 TATGAAAAAT
1 TATAAAAAAT
46605251 TATAAAAAAT
1 TATAAAAAAT
46605261 TA-AAAAAAT
1 TATAAAAAAT
* *
46605270 TATTAAATA-
1 TATAAAAAAT
*
46605279 TAT-TAAAAT
1 TATAAAAAAT
* * *
46605288 TGATATATACT
1 T-ATAAAAAAT
46605299 TAT-AAAAAT
1 TATAAAAAAT
46605308 TATAAAAAA
1 TATAAAAAA
46605317 CCATAAAACC
Statistics
Matches: 64, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
8 3 0.05
9 19 0.30
10 30 0.47
11 12 0.19
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:46605267 original size:19 final size:21
Alignment explanation
Indices: 46605245--46605286 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
46605235 AAAACCTATG
46605245 AAAAATTA-TAAA-AAATTAA
1 AAAAATTATTAAATAAATTAA
*
46605264 AAAAATTATTAAATATATTAA
1 AAAAATTATTAAATAAATTAA
46605285 AA
1 AA
46605287 TTGATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATTATTAAATAAATTAA
Found at i:46605925 original size:23 final size:21
Alignment explanation
Indices: 46605875--46605929 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
46605865 GTTTATCTAA
* *
46605875 TTTTTAATAATTTTTAAGATT
1 TTTTTTATAATTTTTAAGAAT
46605896 TTATTTTATAAGTTTTTAAGAAAT
1 TT-TTTTATAA-TTTTTAAG-AAT
46605920 TTTTTTATAA
1 TTTTTTATAA
46605930 AAATTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 16 0.55
24 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTTTATAATTTTTAAGAAT
Found at i:46605936 original size:25 final size:22
Alignment explanation
Indices: 46605875--46605945 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
46605865 GTTTATCTAA
*
46605875 TTTTTAATAATTTTTAAGATTT
1 TTTTTAAAAATTTTTAAGATTT
* *
46605897 TATTTTATAAGTTTTTAAGAAATTT
1 T-TTTTAAAAATTTTTAAG--ATTT
* *
46605922 TTTTATAAAAATTTTGAATATTT
1 TTTT-TAAAAATTTTTAAGATTT
46605945 T
1 T
46605946 AAATGTGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
22 1 0.03
23 19 0.50
24 3 0.08
25 15 0.39
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (22 bp):
TTTTTAAAAATTTTTAAGATTT
Found at i:46605981 original size:19 final size:20
Alignment explanation
Indices: 46605953--46606006 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
46605943 TTTAAATGTG
46605953 TTTTATTAATTT-TATAAAAT
1 TTTTATTAATTTAT-TAAAAT
46605973 TTTTA-TAATTTATTAAAA-
1 TTTTATTAATTTATTAAAAT
46605991 -TTTATTAGATTTATTA
1 TTTTATTA-ATTTATTA
46606007 TATGTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.13
18 2 0.06
19 19 0.61
20 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATTAATTTATTAAAAT
Found at i:46606034 original size:21 final size:21
Alignment explanation
Indices: 46606004--46606054 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
46605994 ATTAGATTTA
* *
46606004 TTATATGTTTTTTTATAATAT
1 TTATAAGTTTTTTTAAAATAT
* *
46606025 TTAT-AGGTTTTTTAAAATTT
1 TTATAAGTTTTTTTAAAATAT
46606045 TTATAAGTTT
1 TTATAAGTTT
46606055 ATATGAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (21 bp):
TTATAAGTTTTTTTAAAATAT
Found at i:46606065 original size:28 final size:28
Alignment explanation
Indices: 46606034--46606132 Score: 76
Period size: 26 Copynumber: 3.5 Consensus size: 28
46606024 TTTATAGGTT
*
46606034 TTTTAAAATTTTTATAAGTTTATATGAA
1 TTTTAAAATTTTTATAAGTTTATATAAA
** *
46606062 TTTTATTATTTTTA-ATGTTTA-ATAAA
1 TTTTAAAATTTTTATAAGTTTATATAAA
* * * * * *
46606088 TATTATATTTTTTATAATTTTATAATTAT
1 TTTTAAAATTTTTATAAGTTTAT-ATAAA
46606117 TTTTAATAATTTTTAT
1 TTTTAA-AATTTTTAT
46606133 GAGAAAATAT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
26 15 0.28
27 11 0.21
28 12 0.23
29 7 0.13
30 8 0.15
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTAAAATTTTTATAAGTTTATATAAA
Found at i:46606108 original size:9 final size:9
Alignment explanation
Indices: 46605953--46606132 Score: 62
Period size: 9 Copynumber: 18.7 Consensus size: 9
46605943 TTTAAATGTG
46605953 TTTTATTAAT
1 TTTTA-TAAT
*
46605963 TTTATAAAAT
1 TTT-TATAAT
46605973 TTTTATAAT
1 TTTTATAAT
*
46605982 TTATTAAAAT
1 TT-TTATAAT
*
46605992 TTATTA-GAT
1 TT-TTATAAT
*
46606001 TTATTATATGTTT
1 TT-TTATA---AT
46606014 TTTTATAAT
1 TTTTATAAT
* *
46606023 ATTTATAGGTT
1 TTTTATA--AT
*
46606034 TTTTAAAAT
1 TTTTATAAT
46606043 TTTTATAAGT
1 TTTTATAA-T
*
46606053 TTATATGAA-
1 TTTTAT-AAT
*
46606062 TTTTATTA-
1 TTTTATAAT
46606070 TTTT-TAAT
1 TTTTATAAT
* *
46606078 GTTTAATAAA
1 -TTTTATAAT
* *
46606088 TATTATATT
1 TTTTATAAT
46606097 TTTTATAAT
1 TTTTATAAT
*
46606106 TTTATAATTAT
1 TTT-T-ATAAT
46606117 TTTTAATAAT
1 TTTT-ATAAT
46606127 TTTTAT
1 TTTTAT
46606133 GAGAAAATAT
Statistics
Matches: 128, Mismatches: 27, Indels: 31
0.69 0.15 0.17
Matches are distributed among these distances:
7 2 0.02
8 5 0.04
9 55 0.43
10 41 0.32
11 17 0.13
12 5 0.04
13 3 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:46606268 original size:12 final size:12
Alignment explanation
Indices: 46606251--46606275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46606241 CTTAATAAAT
46606251 TTTTTTATTAAC
1 TTTTTTATTAAC
46606263 TTTTTTATTAAC
1 TTTTTTATTAAC
46606275 T
1 T
46606276 GCAGAAACTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTATTAAC
Found at i:46608729 original size:29 final size:28
Alignment explanation
Indices: 46608677--46608731 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
46608667 AAATGAAAAT
* * *
46608677 TTATTTAGAAAGTTAGGTAGTTTTTAGA
1 TTATTTAGAAAGTAAGATAATTTTTAGA
46608705 TTATTTAGAAAAGTAAGATAATTTTTA
1 TTATTTAG-AAAGTAAGATAATTTTTA
46608732 AAAGTTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.45
Consensus pattern (28 bp):
TTATTTAGAAAGTAAGATAATTTTTAGA
Found at i:46616184 original size:14 final size:14
Alignment explanation
Indices: 46616161--46616200 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
46616151 ACAGAAAAGT
*
46616161 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
46616175 AAATCATTTTACGG
1 AAAACATTTTACAG
46616189 AAAACATTTTAC
1 AAAACATTTTAC
46616201 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:46616186 original size:34 final size:35
Alignment explanation
Indices: 46616126--46616192 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
46616116 CAAACACCAG
* *
46616126 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
46616161 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
46616193 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:46617576 original size:116 final size:116
Alignment explanation
Indices: 46617419--46617646 Score: 429
Period size: 116 Copynumber: 2.0 Consensus size: 116
46617409 GAAGGGATTC
*
46617419 AATCTGTCAATTTTAGTTTTTGGTGAAAATTAAAATATGGGGTCATCATCAGTAATAACCCTAGA
1 AATCTGTCAATTTTAGTTTTTGGTGAAAATTAAAATATGGGGTCATCATCAGTAATAACCCCAGA
46617484 AGATGTGTTGGAACCATTGATGAATGATGGAACCATTGATGCTCTCAAGTT
66 AGATGTGTTGGAACCATTGATGAATGATGGAACCATTGATGCTCTCAAGTT
46617535 AATCTGTCAATTTTAGTTTTTGGTGAAAATTAAAATATGGGGTCATCATCAGTAATAACCCCAGA
1 AATCTGTCAATTTTAGTTTTTGGTGAAAATTAAAATATGGGGTCATCATCAGTAATAACCCCAGA
**
46617600 AGATGTGTTGGAGTCATTGATGAATGATGGAACCATTGATGCTCTCA
66 AGATGTGTTGGAACCATTGATGAATGATGGAACCATTGATGCTCTCA
46617647 GGTTGAAGAT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 109 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (116 bp):
AATCTGTCAATTTTAGTTTTTGGTGAAAATTAAAATATGGGGTCATCATCAGTAATAACCCCAGA
AGATGTGTTGGAACCATTGATGAATGATGGAACCATTGATGCTCTCAAGTT
Found at i:46619773 original size:34 final size:34
Alignment explanation
Indices: 46619730--46619802 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
46619720 AAAGTATGTA
*
46619730 ATGTGGTTATTAGATTGGGTTTTCAAATATGATT
1 ATGTTGTTATTAGATTGGGTTTTCAAATATGATT
46619764 ATGTTGTTATTAGATTGGGTTTTCAAATATGATT
1 ATGTTGTTATTAGATTGGGTTTTCAAATATGATT
46619798 ATGTT
1 ATGTT
46619803 AACATTTTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (34 bp):
ATGTTGTTATTAGATTGGGTTTTCAAATATGATT
Found at i:46620119 original size:120 final size:119
Alignment explanation
Indices: 46619980--46620213 Score: 441
Period size: 120 Copynumber: 2.0 Consensus size: 119
46619970 TGAAATAAAA
46619980 AAATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAA
1 AAATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAA
*
46620045 GAATTTTATTAAATTATATATTTTTATTAAATTATGTTTAATAATAATTATTTT
66 GAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
46620099 AAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTA
1 AAATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTA
*
46620164 ATAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATT
65 AGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATT
46620214 CTGTTAAACT
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 7 0.06
120 105 0.94
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (119 bp):
AAATTATTTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAA
GAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTT
Found at i:46620189 original size:18 final size:18
Alignment explanation
Indices: 46620155--46620201 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
46620145 ATAAGAATAT
46620155 TTAATATTA-ATAATTTTA
1 TTAA-ATTATATAATTTTA
*
46620173 TTAAATTATATATTTTTA
1 TTAAATTATATAATTTTA
46620191 TTAAATTATAT
1 TTAAATTATAT
46620202 TTAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTATATAATTTTA
Found at i:46620452 original size:16 final size:16
Alignment explanation
Indices: 46620431--46620470 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
46620421 AATTGAATTA
46620431 CTATTAC-GCCTCTATT
1 CTATTACAG-CTCTATT
46620447 CTATTACAGCTCTATT
1 CTATTACAGCTCTATT
*
46620463 CCATTACA
1 CTATTACA
46620471 ACGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (16 bp):
CTATTACAGCTCTATT
Found at i:46626239 original size:11 final size:11
Alignment explanation
Indices: 46626220--46626267 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
46626210 AAGTCATTTT
*
46626220 AAATTTTAAAA
1 AAATATTAAAA
46626231 AAATATTAAAA
1 AAATATTAAAA
*
46626242 AAAGTATGAACAA
1 AAA-TATTAA-AA
46626255 AATATATTAAAA
1 AA-ATATTAAAA
46626267 A
1 A
46626268 GTTATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 13 0.42
12 8 0.26
13 9 0.29
14 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (11 bp):
AAATATTAAAA
Found at i:46628595 original size:34 final size:34
Alignment explanation
Indices: 46628554--46628624 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
46628544 TCATGTATAA
*
46628554 TTGTTAAAGATTATTTTTTTGAGTTGATTTTGAT
1 TTGTTAAAGATTATTTATTTGAGTTGATTTTGAT
46628588 TTGTTAAAGATTATTTATTTGAGTTGATTTTGAT
1 TTGTTAAAGATTATTTATTTGAGTTGATTTTGAT
46628622 TTG
1 TTG
46628625 GAAACATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (34 bp):
TTGTTAAAGATTATTTATTTGAGTTGATTTTGAT
Found at i:46644510 original size:22 final size:22
Alignment explanation
Indices: 46644482--46644524 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
46644472 AGCTGATAAA
*
46644482 CAGTAAGCTCTATTGAGCTGAG
1 CAGTAAGCTCTATCGAGCTGAG
46644504 CAGTAAGCTCTATCGAGCTGA
1 CAGTAAGCTCTATCGAGCTGA
46644525 AACGGTAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
CAGTAAGCTCTATCGAGCTGAG
Found at i:46644536 original size:23 final size:23
Alignment explanation
Indices: 46644456--46644559 Score: 95
Period size: 23 Copynumber: 4.4 Consensus size: 23
46644446 GAGCCATGAT
46644456 CGGTAAGCTC-ATCCCGAGCTGATAAA
1 CGGTAAGCTCTAT--CGAGCTG--AAA
* * *
46644482 CAGTAAGCTCTATTGAGCTG-AG
1 CGGTAAGCTCTATCGAGCTGAAA
*
46644504 CAGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
** *
46644527 CGGTAAGCTCCGTAGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
46644550 CGGTAAGCTC
1 CGGTAAGCTC
46644560 ATACAAGCTG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
22 20 0.30
23 30 0.45
25 6 0.09
26 9 0.13
27 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (23 bp):
CGGTAAGCTCTATCGAGCTGAAA
Found at i:46649482 original size:52 final size:48
Alignment explanation
Indices: 46649463--46649665 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
46649453 TGACAAGTGG
* *
46649463 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
46649509 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
46649561 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
46649607 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
46649653 AAAGTGATAAGTG
1 AAAGTGATAAGTG
46649666 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:46649517 original size:98 final size:98
Alignment explanation
Indices: 46649397--46649665 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
46649387 TTTGAGTACT
*
46649397 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
46649462 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
46649495 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
46649560 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
46649593 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
46649658 GATAAGTG
65 GAAAAGTG
46649666 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:46649673 original size:37 final size:37
Alignment explanation
Indices: 46649629--46649774 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
46649619 GATAGCTTTA
*
46649629 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
46649666 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
46649703 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
46649740 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
46649775 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:46651628 original size:13 final size:13
Alignment explanation
Indices: 46651612--46651636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46651602 CAAGTATTCA
46651612 ACCCAACCCAATT
1 ACCCAACCCAATT
46651625 ACCCAACCCAAT
1 ACCCAACCCAAT
46651637 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:46651757 original size:9 final size:9
Alignment explanation
Indices: 46651739--46651805 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
46651729 GTAGTGATTC
46651739 AATTCGGTT
1 AATTCGGTT
*
46651748 AATTCAGTT
1 AATTCGGTT
* *
46651757 AATTTGGGT
1 AATTCGGTT
* *
46651766 AATCCGATT
1 AATTCGGTT
*
46651775 AATTCGGGT
1 AATTCGGTT
46651784 AATTCGGTT
1 AATTCGGTT
46651793 AATTCGGTT
1 AATTCGGTT
46651802 AATT
1 AATT
46651806 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:46653398 original size:9 final size:9
Alignment explanation
Indices: 46653381--46653417 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46653371 TGAGTTTTCG
46653381 AATTCGAAT
1 AATTCGAAT
*
46653390 AACTCGAAT
1 AATTCGAAT
46653399 AATTCGAAT
1 AATTCGAAT
46653408 AATTCGAAT
1 AATTCGAAT
46653417 A
1 A
46653418 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:46654204 original size:5 final size:5
Alignment explanation
Indices: 46654194--46654219 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46654184 CTCGAAAATT
46654194 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
46654220 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:46655346 original size:251 final size:251
Alignment explanation
Indices: 46654903--46655409 Score: 1005
Period size: 251 Copynumber: 2.0 Consensus size: 251
46654893 ATGGACCTAG
46654903 ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
1 ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
46654968 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
66 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
46655033 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
131 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
46655098 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
196 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
*
46655154 ATTAAGACTTTGTTATAATCGTCAATGTCCTGAAACTTAACCAAAAAATATCCATTAATGATATC
1 ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
46655219 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
66 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
46655284 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
131 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
46655349 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
196 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
46655405 ATTAA
1 ATTAA
46655410 TTCAAAATCA
Statistics
Matches: 255, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 255 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (251 bp):
ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
Found at i:46656409 original size:5 final size:5
Alignment explanation
Indices: 46656399--46656424 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46656389 CTCGAAAATT
46656399 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
46656425 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:46657551 original size:251 final size:251
Alignment explanation
Indices: 46657108--46657614 Score: 1005
Period size: 251 Copynumber: 2.0 Consensus size: 251
46657098 ATGGACCTAG
46657108 ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
1 ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
46657173 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
66 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
46657238 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
131 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
46657303 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
196 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
*
46657359 ATTAAGACTTTGTTATAATCGTCAATGTCCTGAAACTTAACCAAAAAATATCCATTAATGATATC
1 ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
46657424 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
66 CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
46657489 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
131 CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
46657554 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
196 ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
46657610 ATTAA
1 ATTAA
46657615 TTCAAAATCA
Statistics
Matches: 255, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 255 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (251 bp):
ATTAAGACTTTGTTATAATCGTCAATGTCCTAAAACTTAACCAAAAAATATCCATTAATGATATC
CATTAGATGAAAAGATTTTGCAGGTTTCTAGAGATTAAGGATACAGTTGTGAAGCACGTTGTAGC
CAATGTTGCGCCCTAACAGCTTGTGAATGACCGTCAACTCCATCTCTTTAAACAGTATGTCCTTA
ATACAATCCGAGAAGGCGATTGCCGGAATCCCATGGACGTATTCACATCTCCTTCC
Found at i:46658770 original size:5 final size:5
Alignment explanation
Indices: 46658762--46658787 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46658752 GAGATGGAAT
46658762 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
46658788 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:46658787 original size:26 final size:26
Alignment explanation
Indices: 46658736--46658787 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
46658726 TGAAGTTTTC
* * *
46658736 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
46658762 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
46658788 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:46659171 original size:9 final size:9
Alignment explanation
Indices: 46659157--46659185 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
46659147 TAAACAATTC
46659157 AATAATATA
1 AATAATATA
46659166 AATAATATA
1 AATAATATA
46659175 AATAATATA
1 AATAATATA
46659184 AA
1 AA
46659186 ATGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:46659736 original size:9 final size:9
Alignment explanation
Indices: 46659722--46659758 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46659712 TATAGTTTGA
46659722 TATTCGAAT
1 TATTCGAAT
46659731 TATTCGAAT
1 TATTCGAAT
*
46659740 TATTCGAGT
1 TATTCGAAT
46659749 TATTCGAAT
1 TATTCGAAT
46659758 T
1 T
46659759 TGGAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:46661351 original size:43 final size:43
Alignment explanation
Indices: 46661290--46661406 Score: 225
Period size: 43 Copynumber: 2.7 Consensus size: 43
46661280 TCTTTAGTAT
*
46661290 TTGAGCTACTAGATCTAGTTTCATTGACATCCGAGCAAATAGC
1 TTGAGTTACTAGATCTAGTTTCATTGACATCCGAGCAAATAGC
46661333 TTGAGTTACTAGATCTAGTTTCATTGACATCCGAGCAAATAGC
1 TTGAGTTACTAGATCTAGTTTCATTGACATCCGAGCAAATAGC
46661376 TTGAGTTACTAGATCTAGTTTCATTGACATC
1 TTGAGTTACTAGATCTAGTTTCATTGACATC
46661407 ACCTAATGTG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (43 bp):
TTGAGTTACTAGATCTAGTTTCATTGACATCCGAGCAAATAGC
Found at i:46667899 original size:2 final size:2
Alignment explanation
Indices: 46667892--46667924 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46667882 CAAACTCATA
46667892 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46667925 AACACACCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46671142 original size:20 final size:20
Alignment explanation
Indices: 46671094--46671145 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
46671084 ACAAAAATTA
* *
46671094 AAAAAATCAAAATATTTTTT
1 AAAAATTCAAAATATTTTAT
*
46671114 TAAAATTCAAAATA-TTTAT
1 AAAAATTCAAAATATTTTAT
46671133 AAAAATTTCAAAA
1 AAAAA-TTCAAAA
46671146 AAAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTCAAAATATTTTAT
Found at i:46698787 original size:185 final size:184
Alignment explanation
Indices: 46698467--46698815 Score: 565
Period size: 185 Copynumber: 1.9 Consensus size: 184
46698457 ATATTAATTT
*
46698467 CACAATAAAGTTTGAGTGCAAATATCACACAAGACAAAAAGACTGCAGTCATGCAAACCGGACAC
1 CACAATAAAGTTTGAGTGCAAATATCACACAAGACAAAAAGACTGCAGTAATGCAAACCGGACAC
* *
46698532 TGCCTTCCTGAGATAAACATGCATGTTGTTGAACATTAAGCTACATTTTCAGAAAAGCCATACCA
66 TGCCTTCCTGAGATAAACATGAATGTAGTTGAACATTAAGCTACATTTTCAGAAAAGCCATACCA
46698597 ACACCAGCTACAAAGTTTTTTAGTGTTCTCATGTACTAAAACAGAAAAATATAA
131 ACACCAGCTACAAAGTTTTTTAGTGTTCTCATGTACTAAAACAGAAAAATATAA
* * *
46698651 CACAATAAGAGTTTGAGTGCAAATATTACACAAGACAAAAGGACTGCAGTAATGCAAACTGGACA
1 CACAATAA-AGTTTGAGTGCAAATATCACACAAGACAAAAAGACTGCAGTAATGCAAACCGGACA
** * *
46698716 CTGCCTTCCTGAGATAAACATGAAT-TAAGTTGAACATTAAGCTATGTTTTCGGAAAAGTCATAC
65 CTGCCTTCCTGAGATAAACATGAATGT-AGTTGAACATTAAGCTACATTTTCAGAAAAGCCATAC
* *
46698780 CAACACCAGCTACTAAGTTTTTTGGTGTTCTCATGT
129 CAACACCAGCTACAAAGTTTTTTAGTGTTCTCATGT
46698816 GCTATGGCAT
Statistics
Matches: 151, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
184 9 0.06
185 142 0.94
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (184 bp):
CACAATAAAGTTTGAGTGCAAATATCACACAAGACAAAAAGACTGCAGTAATGCAAACCGGACAC
TGCCTTCCTGAGATAAACATGAATGTAGTTGAACATTAAGCTACATTTTCAGAAAAGCCATACCA
ACACCAGCTACAAAGTTTTTTAGTGTTCTCATGTACTAAAACAGAAAAATATAA
Found at i:46702486 original size:19 final size:20
Alignment explanation
Indices: 46702452--46702498 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
46702442 TACCAGATAC
*
46702452 AAACAAAATGGCCATCACAT
1 AAACAAAATAGCCATCACAT
46702472 AAACAAAA-AGCCATCACAT
1 AAACAAAATAGCCATCACAT
*
46702491 AATCAAAA
1 AAACAAAA
46702499 CCAATACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.57, C:0.23, G:0.06, T:0.13
Consensus pattern (20 bp):
AAACAAAATAGCCATCACAT
Found at i:46707548 original size:14 final size:14
Alignment explanation
Indices: 46707529--46707556 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46707519 GAAATAGGCC
46707529 TAAGCCTTCCAACT
1 TAAGCCTTCCAACT
46707543 TAAGCCTTCCAACT
1 TAAGCCTTCCAACT
46707557 ATACCACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
TAAGCCTTCCAACT
Done.