Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 104 of 211
Found at i:28868068 original size:3 final size:3
Alignment explanation
Indices: 28868060--28868089 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28868050 TTTTCTACTG
*
28868060 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28868090 CTCTTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28877038 original size:21 final size:22
Alignment explanation
Indices: 28876990--28877040 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
28876980 TTAATTATTG
28876990 TTAAAAAT-TTTAAAATATATA
1 TTAAAAATATTTAAAATATATA
*
28877011 TT-TAAATATTT-AAATATACT-
1 TTAAAAATATTTAAAATATA-TA
28877031 TTAAAAATAT
1 TTAAAAATAT
28877041 ATTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAAATATTTAAAATATATA
Found at i:28883175 original size:45 final size:45
Alignment explanation
Indices: 28883111--28883353 Score: 281
Period size: 45 Copynumber: 5.4 Consensus size: 45
28883101 GATCAGAGTG
* * *
28883111 TGCCATGGTATCTTTCAACCATGGTCTTATTTACTCTCGTCTTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGA
*
28883156 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGG
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGA
* * * *
28883201 TGCCGTGGTGTCTTTCAACCATTGTCATATTTATTCTCGTCTTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGA
* * * * * *
28883246 TGCCAGAGTGTCTTTCAAACATGGTCTTATTCATTTTCCGTCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCT-CGTCTTGA
* * ** *
28883292 TGCCACAGTGTCTTTCAACCATGGTCTTATTCATT-TAATTTGTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCT-TGA
*
28883337 TGCCATAGCGTCTTTCA
1 TGCCATAGTGTCTTTCA
28883354 GTTGTGGTCT
Statistics
Matches: 168, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
44 1 0.01
45 128 0.76
46 39 0.23
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGA
Found at i:28891060 original size:40 final size:41
Alignment explanation
Indices: 28891000--28891198 Score: 127
Period size: 40 Copynumber: 4.7 Consensus size: 41
28890990 GTAGCTTCAG
* * *
28891000 TCTGCTGCACTTCTGTTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGCGA
* ***
28891040 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATGCGA
** * *** * * *
28891083 TCCACTCTACTACAAATTCAGGGAGATAGGA-TTGGTTTTTCTTCTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGG-----ATGC-GA
*
28891129 TCTGCTCCACTACTGCTTAAGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGCGA
*
28891169 TCTGCTCCACTACTGCATAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
28891199 TCTGTGGTTT
Statistics
Matches: 118, Mismatches: 29, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
39 1 0.01
40 57 0.48
41 5 0.04
42 2 0.02
43 15 0.13
44 11 0.09
45 11 0.09
46 16 0.14
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATGCGA
Found at i:28891177 original size:129 final size:128
Alignment explanation
Indices: 28890949--28891287 Score: 511
Period size: 129 Copynumber: 2.6 Consensus size: 128
28890939 ATGATATATC
* * ** * * *
28890949 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTAG--TAGCTTCAGTCTGCTGCACTT
1 GTTTTAATCCGCT-CACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTA
* *
28891012 CTGTTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG
65 CTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTG
* * *
28891076 GTTTTAATCCACTCTACTACAAATTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTA
1 GTTTTAATCCGCTC-ACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTA
*
28891141 CTGCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTG
65 CTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTG
*
28891205 GTTTTAATCCGCTACAGTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTA
1 GTTTTAATCCGCT-CACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTA
28891270 CTGCTTAGGGAGATAAGA
65 CTGCTTAGGGAGATAAGA
28891288 TATATGGTTT
Statistics
Matches: 190, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
126 1 0.01
127 35 0.18
129 153 0.81
130 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (128 bp):
GTTTTAATCCGCTCACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTAC
TGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATCTGTG
Found at i:28891262 original size:89 final size:89
Alignment explanation
Indices: 28891169--28891376 Score: 353
Period size: 89 Copynumber: 2.3 Consensus size: 89
28891159 CTTGATGCGA
* * * *
28891169 TCTGCTCCACTACTGCATAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTACACTGCAACTTCAGG
28891234 GAGATAGGATTGGTTTTTCTTCTG
66 GAGATAGGATTGGTTTTTCTTCTG
* * *
28891258 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATTCGCTCCACTGGAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTACACTGCAACTTCAGG
28891323 GAGATAGGATTGGTTTTTCTTCTG
66 GAGATAGGATTGGTTTTTCTTCTG
28891347 TCTGCTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
28891377 CTTGATGCGA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 112 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (89 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTACACTGCAACTTCAGG
GAGATAGGATTGGTTTTTCTTCTG
Found at i:28891274 original size:218 final size:218
Alignment explanation
Indices: 28891040--28891505 Score: 824
Period size: 218 Copynumber: 2.1 Consensus size: 218
28891030 CTTGATGCGA
* * *
28891040 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCACTCTACTACAAATTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCACTCCACTACAAATTCAGG
28891105 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAAGGAGATAAGACTTGATGCGAT
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAAGGAGATAAGACTTGATGCGAT
28891170 CTGCTCCACTACTGCATAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGGG
131 CTGCTCCACTACTGCATAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGGG
28891235 AGATAGGATTGGTTTTTCTTCTG
196 AGATAGGATTGGTTTTTCTTCTG
* * ** *
28891258 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATTCGCTCCACTGGAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCACTCCACTACAAATTCAGG
*
28891323 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGAT
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAAGGAGATAAGACTTGATGCGAT
**
28891388 CTGCTCCACTACTGTTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGGG
131 CTGCTCCACTACTGCATAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGGG
28891453 AGATAGGATTGGTTTTTCTTCTG
196 AGATAGGATTGGTTTTTCTTCTG
*
28891476 TCTGCTCTACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
28891506 CTTGATGCGA
Statistics
Matches: 236, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 236 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (218 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCACTCCACTACAAATTCAGG
GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAAGGAGATAAGACTTGATGCGAT
CTGCTCCACTACTGCATAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGGG
AGATAGGATTGGTTTTTCTTCTG
Found at i:28891391 original size:129 final size:129
Alignment explanation
Indices: 28891258--28892108 Score: 1405
Period size: 129 Copynumber: 6.6 Consensus size: 129
28891248 TTTTCTTCTG
* * * *
28891258 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATTCGCTCCACTGGAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
28891323 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * *
28891387 TCTGCTCCACTACTGTTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
*
28891452 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCTACTACTGCTTAGGGAGATAAGACTTGATGCGA
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * *
28891516 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
28891581 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* *
28891645 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTTCACTGCAACTTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
* * * *
28891710 GAGATATGATTGGTTTTTTTTCTGCCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGCGA
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* *
28891774 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAAATTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
* * *
28891839 GAGATAGGATTGGTTTTTCTTCTGTCTGCTTCACTACTACTTAAGGAGATAAGACTTGATGCGA
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
28891903 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
* * ** * * *
28891968 AAAATAGGATTGGTTTTTCTTCTACCTGCTCTACTACTGCTCAGGGAGATAAGACTTGATACGA
66 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
** *
28892032 TCTGCTCCACTACTGCACAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
28892097 GAGATAGGATTG
66 GAGATAGGATTG
28892109 ATTTCTTTCA
Statistics
Matches: 672, Mismatches: 50, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 672 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (129 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGG
GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:28891407 original size:40 final size:41
Alignment explanation
Indices: 28891347--28892061 Score: 265
Period size: 40 Copynumber: 16.7 Consensus size: 41
28891337 TTTTCTTCTG
*
28891347 TCTGCTCCACTACTGCTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
* * **
28891387 TCTGCTCCACTACTGTTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATTCGA
* * * * ** * *
28891430 TCCGCTACAGTGCAACTTCAGGGAGATAGGA-TTGGTTTTTCTTCTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGG-----ATTC-GA
* *
28891476 TCTGCTCTACTACTGCTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
* **
28891516 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATTCGA
**** * *
28891559 T-TCGCTCCACTGGAACTTCAGGGAGATAGGA-TTGGTTTTTCTTCTG-
1 TCT-GCTCCACTACTGCTT-AGGGAGATAAGACTTGG-----ATTC-GA
*
28891605 TCTGCTCCACTACTGCTTAGGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
* **
28891645 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATTCGA
* * * ** * *
28891688 TCCGCTTCACTGCAACTTTAGGGAGATATGA-TTGGTTTTTTTTCTG-
1 TCTGCTCCACTACTGC-TTAGGGAGATAAGACTTGG-----ATTC-GA
* * *
28891734 CCTGCTCCACTACTGCTTAGAGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
* **
28891774 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATTCGA
* * *** * * *
28891817 TCCGCTCCACTGCAAATTCAAGGAGATAGGA-TTGGTTTTTCTTCTG-
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGG-----ATTC-GA
* * * *
28891863 TCTGCTTCACTACTACTTAAGGAGATAAGACTT-GATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
* **
28891903 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGGATTCGA
* * ** * * * * * *
28891946 TCCGCTCCACTGCAACTTCAAGAAAATAGGA-TTGGTTTTTCTTCTA
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGG-----ATTCGA
* * * *
28891992 CCTGCTCTACTACTGCTCAGGGAGATAAGACTT-GATACGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
**
28892032 TCTGCTCCACTACTGCACAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
28892062 TCTGTGGTTT
Statistics
Matches: 488, Mismatches: 127, Indels: 120
0.66 0.17 0.16
Matches are distributed among these distances:
39 4 0.01
40 181 0.37
41 25 0.05
42 11 0.02
43 76 0.16
44 53 0.11
45 58 0.12
46 79 0.16
47 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (41 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGGATTCGA
Found at i:28891413 original size:258 final size:251
Alignment explanation
Indices: 28891129--28892108 Score: 1001
Period size: 258 Copynumber: 3.8 Consensus size: 251
28891119 TTTTCTTCTG
*
28891129 TCTGCTCCACTACTGCTTAAGGAGATAAGACT-TGATGCGATCTGCTCCACTACTGC-ATAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTCTG-TG-GATCTGCTCCACTACTGCAATAGGGA
* * * * * * *
28891192 GATAAGATCTGTGGTTTTAATCCGCTACAGTGCAACTTCAGGGAGATAGGA-TTGGTTTTTCTTC
64 GATAAGAT-TGTGTTTTTAATCCGCTACACTACTACTT-AGGGAGATAAGACTT-G-----ATGC
*
28891256 TG-TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATTCGCTCCACTGGAACTTC
121 -GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTC
28891320 AGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGC
185 AGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGC
28891385 GA
250 GA
* * * ** *
28891387 TCTGCTCCACTACTGTTTAGGGAGATAAGA-TCTGTGGTTTTAATCCGCTACAGTGCAACTTCAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTCTGTGGATCTGCTCCACTAC--TGCAA--T-AG
* ** *
28891451 GGAGATAGGATTG-GTTTTTCTTCTGTCTGCT-CTACTACTGCTTAGGGAGATAAGACTTGATGC
61 GGAGATAAGATTGTGTTTTTAATC---C-GCTAC-ACTACTACTTAGGGAGATAAGACTTGATGC
28891514 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCA
121 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCA
28891579 GGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCG
186 GGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCG
28891644 A
251 A
* * ** *
28891645 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTGTGGTTTTAATCCGCTTCACTGCAACTTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTCTGTGGATCTGCTCCAC-T-ACTGCAA---TAG
* * ** * * *
28891709 GGAGATATGATTGGTTTTTTTTCTGCCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGCGA
61 GGAGATAAGATT-GTGTTTTTAAT-CC-GCTACACTACTACTTAGGGAGATAAGACTTGATGCGA
* * * * *
28891774 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAAATTCAAG
123 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCAGG
* * *
28891839 GAGATAGGATTGGTTTTTCTTCTGTCTGCTTCACTACTACTTAAGGAGATAAGACTTGATGCGA
188 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * ** * *
28891903 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTGTGGTTTTAATCCGCTCCACTGCAACTTCAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTCTGTGGATCTGCTCCACT--ACTGCAA--T-AG
* * * ** * * *
28891967 GAAAATAGGATTG-GTTTTTCTTCTACCTGCT-CTACTACTGCTCAGGGAGATAAGACTTGATAC
61 GGAGATAAGATTGTG-TTTT-TAAT-CC-GCTAC-ACTACTACTTAGGGAGATAAGACTTGATGC
** * * *
28892030 GATCTGCTCCACTACTGCACAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCA
121 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCA
*
28892095 AGGAGATAGGATTG
186 GGGAGATAGGATTG
28892109 ATTTCTTTCA
Statistics
Matches: 649, Mismatches: 47, Indels: 52
0.87 0.06 0.07
Matches are distributed among these distances:
256 10 0.02
257 13 0.02
258 564 0.87
259 6 0.01
260 15 0.02
261 4 0.01
262 12 0.02
263 14 0.02
264 11 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (251 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTCTGTGGATCTGCTCCACTACTGCAATAGGGAGA
TAAGATTGTGTTTTTAATCCGCTACACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTCC
ACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCAGGGAGATAGG
ATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:28891522 original size:387 final size:383
Alignment explanation
Indices: 28891129--28892108 Score: 1163
Period size: 387 Copynumber: 2.5 Consensus size: 383
28891119 TTTTCTTCTG
* *
28891129 TCTGCTCCACTACTGCTTAAGGAGATAAGA-CT-T-GATGCGA-TCTGCTCCACT-ACTGCATAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGATGCAATTC-GCTCCACTGACTGC--AG
* * *
28891189 GGAGATAAGATCTGTGGTTTTAATC-C-GCTACAGTGCAACTTCAGGGAGATAGGA-TTGGTTTT
63 GGAGATAAGAT-TG-GGTTTTAATCTCTGCTACACTACAACTT-AGGGAGATAAGACTT-G----
* * * *
28891251 TCTTCTG-TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATTCGCTCCACTGGA
120 -ATGC-GATCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTCCACTGCA
* *
28891315 ACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTT
183 ACTTCAGGGAGATAGGATTGGTTTTTCTTCTGCCTGCTCCACTACTGCTTAGAGAGATAAGACTT
* *
28891380 GATGCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTACAGTGCAA
248 GATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTACACTGCAA
* * * *
28891445 CTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGC-TCTACTACTGCTTAGGGAGATAAGACTT
313 ATTCAAGGAGATAGGATTGGTTTTTCTTCTGTCTGCTTC-ACTACTACTTAAGGAGATAAGACTT
28891509 GATGCGA
377 GATGCGA
* ** *
28891516 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGTTTTAATTCGCTCCACTGGAACTTCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGATGCAATTCGCTCCACT-G-ACTGCAGG
* * ** * **
28891581 GAGATAGGATTGGTTTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGAT
64 GAGATAAGATTGGGTTTTAATC--TCTGCTACACTACAACTTAGGGAGATAAGACTTGATGCGAT
* * * *
28891646 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTTCACTGCAACTTTAGGG
127 CTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTCCACTGCAACTTCAGGG
* *
28891711 AGATATGATTGGTTTTTTTTCTGCCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGCGATC
192 AGATAGGATTGGTTTTTCTTCTGCCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGCGATC
*
28891776 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAAATTCAAGGA
257 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTACACTGCAAATTCAAGGA
28891841 GATAGGATTGGTTTTTCTTCTGTCTGCTTCACTACTACTTAAGGAGATAAGACTTGATGCGA
322 GATAGGATTGGTTTTTCTTCTGTCTGCTTCACTACTACTTAAGGAGATAAGACTTGATGCGA
* * ** * * *
28891903 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGATGCAATTCGCTCCACTG--ACTGCAGG
* * * * ** ** * *
28891968 AAAATAGGATTGGTTTTTCTTCTACCTGCT-CTACTACTGCTCAGGGAGATAAGACTTGATACGA
64 GAGATAAGATTGGGTTTTAATCT--CTGCTAC-ACTACAACTTAGGGAGATAAGACTTGATGCGA
** * * *
28892032 TCTGCTCCACTACTGCACAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAG
126 TCTGCTCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTCCACTGCAACTTCAGG
28892097 GAGATAGGATTG
191 GAGATAGGATTG
28892109 ATTTCTTTCA
Statistics
Matches: 527, Mismatches: 48, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
385 1 0.00
386 3 0.01
387 455 0.86
388 4 0.01
389 8 0.02
390 13 0.02
391 14 0.03
392 13 0.02
393 16 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (383 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTATGGATGCAATTCGCTCCACTGACTGCAGGGA
GATAAGATTGGGTTTTAATCTCTGCTACACTACAACTTAGGGAGATAAGACTTGATGCGATCTGC
TCCACTACTGCTTAGGGAGATAAGATATATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
AGGATTGGTTTTTCTTCTGCCTGCTCCACTACTGCTTAGAGAGATAAGACTTGATGCGATCTGCT
CCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAATCCGCTACACTGCAAATTCAAGGAGATA
GGATTGGTTTTTCTTCTGTCTGCTTCACTACTACTTAAGGAGATAAGACTTGATGCGA
Found at i:28891634 original size:347 final size:345
Alignment explanation
Indices: 28890941--28891634 Score: 1138
Period size: 347 Copynumber: 2.0 Consensus size: 345
28890931 AAAGGTATAT
*
28890941 GATATATCGTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCTGCT
1 GATATATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCTGCT
* * *
28891006 GCACTTCTGTTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
66 CCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
28891071 CTGTGGTTTTAATCCACTCTACTACAAATTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTC
131 CTGTGGTTTTAATCCACTCTACTACAAATTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTC
28891136 CACTACTGCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATC
196 CACTACTGCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATC
* *
28891201 TGTGGTTTTAATCCGCTACAGTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCC
261 TATGGTTTTAATCCGCTACACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCC
28891266 ACTACTGCTTAGGGAGATAA
326 ACTACTGCTTAGGGAGATAA
* * * * ** *
28891286 GATATATGGTTTTAATTCGCTCCACTGGAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTG
1 GATATATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAG--TAGCTTCAGTCTG
*
28891351 CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGTTTAGGGAGATAAG
64 CTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAG
* * * *
28891416 ATCTGTGGTTTTAATCCGCTAC-AGTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTG
129 ATCTGTGGTTTTAATCCACT-CTACTACAAATTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTG
* * *
28891480 CTCTACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAG
193 CTCCACTACTGCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAG
* * *
28891545 ATCTATGGTTTTAATTCGCTCCACTGGAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGC
258 ATCTATGGTTTTAATCCGCTACACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGC
28891610 TCCACTACTGCTTAGGGAGATAA
323 TCCACTACTGCTTAGGGAGATAA
28891633 GA
1 GA
28891635 CTTGATGCGA
Statistics
Matches: 322, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
345 45 0.14
347 276 0.86
348 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (345 bp):
GATATATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCTGCT
CCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
CTGTGGTTTTAATCCACTCTACTACAAATTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTC
CACTACTGCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCATAGGGAGATAAGATC
TATGGTTTTAATCCGCTACACTGCAACTTCAGGGAGATAGGATTGGTTTTTCTTCTGTCTGCTCC
ACTACTGCTTAGGGAGATAA
Found at i:28892202 original size:50 final size:50
Alignment explanation
Indices: 28892142--28892950 Score: 508
Period size: 50 Copynumber: 16.3 Consensus size: 50
28892132 GTCGGGGAAC
*
28892142 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * *
28892192 AAGATTCACCGTTG-CGACTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
1 AAGATTCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * ** * * ** * * ** **
28892242 AAGATTTGCCATTGCGGCTTCAGTCTTTTTAATTGCAATTTCAGGGAAAC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * * * *
28892292 AAGATTTGTCGTGGTAGTTTCAATTTGTTCCACTGCACCGTCAGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * ** * * * * *
28892342 AACATTCACCGTTGTGGCTTCAATCT-TTGTAATTGCAATGTCAGAGAA-C
1 AAGATTCGCCGTTGTAGCTTCAATCTGTT-CCACTGCACTGCCAGGGAAGT
* *
28892391 AAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCAGTGCCAGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
*** * ** * * * * *
28892441 AAGATTCGCCGTTCCGGCTTCAATCTTTTTAATTACAATGTCAGGGAAAT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* ** *
28892491 GAA-ATTCACCGTCATAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
1 -AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * * * ** * * ** *
28892541 AAAATTCACTGTTGCAGCTTCAATATTTTTAATTGCAATGTTAGGGAA-C
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* *
28892590 AAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCA-TCACCAGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACT-GCCAGGGAAGT
** * * *
28892640 AAGATTCGCCGTTGCGGCTTCAATCT-TT-AACTATG-A-TG-TAGGGAAAT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC--TGCACTGCCAGGGAAGT
* ** *
28892687 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCACTAAGGG-AGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGC-CAGGGAAGT
** * * ** * * * **
28892737 AAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCAATGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * *
28892787 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGGAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * ** * * * ** *
28892837 AAGATTCACCGTTGCAACTTCAATCTTTTTAATTGTAATGTTAGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * *
28892887 AAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
*
28892937 AAGATTCACCGTTG
1 AAGATTCGCCGTTG
28892951 CGACTTCAAT
Statistics
Matches: 553, Mismatches: 188, Indels: 36
0.71 0.24 0.05
Matches are distributed among these distances:
47 32 0.06
48 6 0.01
49 80 0.14
50 428 0.77
51 7 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
Found at i:28892296 original size:100 final size:100
Alignment explanation
Indices: 28892142--28892968 Score: 936
Period size: 100 Copynumber: 8.3 Consensus size: 100
28892132 GTCGGGGAAC
** * ** * * * ** *
28892142 AAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATTCACCGTTG-
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
*
28892206 CGACTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
66 AG-CTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
** * * * * * *
28892242 AAGATTTGCCATTGCGGCTTCAGTCTTTTTAATTGCAATTTCAGGGAAACAAGATTTGTCGTGGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
* * *
28892307 AGTTTCAATTTGTTCCACTGCACCGTCAGGGAAGT
66 AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* * * * *
28892342 AACATTCACCGTTGTGGCTTCAATCTTTGTAATTGCAATGTCAGAG-AACAAGATTCGTCGTTGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
**
28892406 AGCTTCAATCTGTTCCACTGCAGTGCCAGGGAAGT
66 AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* * * * * **
28892441 AAGATTCGCCGTTCCGGCTTCAATCTTTTTAATTACAATGTCAGGGAAATGAA-ATTCACCGTCA
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAA-CAAGATTCGCCGTTG
28892505 TAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
65 TAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* * * * *
28892541 AAAATTCACTGTTGCAGCTTCAATATTTTTAATTGCAATGTTAGGG-AACAAGATTCGCCGTTGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
* * *
28892605 AGCTTCAATCTGATCCACTGCATCACCAGGGAAGT
66 AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* * *
28892640 AAGATTCGCCGTTGCGGCTTCAATC--TTTAACTATG--ATGT-AGGGAAATAAGATTCACCGTT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAA-T-TGCAATGTCAGGGAAACAAGATTCGCCGTT
* *
28892700 GTAGCTTCAATCTGTTCCACTGCACCACTAAGGG-AGT
64 GTAGCTTCAATCTGTTCCACTGCACCGC-CAGGGAAGT
* * ** **
28892737 AAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCAATGAAGTAAGATTCGCCGTTGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
* * *
28892802 AGCTTCAATCTATTCCACTGCACCGCTAGGGGAGT
66 AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
** * * * *
28892837 AAGATTCACCGTTGCAACTTCAATCTTTTTAATTGTAATGTTAGGGAAGCAAGATTCGCCATTGT
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
*
28892902 AGCTTCAATCTGTTCCACTGCACCGCCAAGGAAGT
66 AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
*
28892937 AAGATTCACCGTTGCGACTTCAATCTTTTTAA
1 AAGATTCACCGTTGCGGCTTCAATCTTTTTAA
28892969 CCATAATGCC
Statistics
Matches: 612, Mismatches: 101, Indels: 28
0.83 0.14 0.04
Matches are distributed among these distances:
96 4 0.01
97 78 0.13
98 8 0.01
99 163 0.27
100 356 0.58
101 3 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (100 bp):
AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAAGATTCGCCGTTGT
AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
Found at i:28892436 original size:199 final size:198
Alignment explanation
Indices: 28892192--28892968 Score: 949
Period size: 199 Copynumber: 3.9 Consensus size: 198
28892182 CCAGGGAAGT
* * * *
28892192 AAGATTCACCGTTG-CGACTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTTGCCATTG
1 AAGATTCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
* * *** * * *
28892256 CGGCTTCAGTCTTTTTAATTGCAATTTCAGGGAAACAAGATTTGTCGTGGTAGTTTCAATTTGTT
65 CGGCTTCAATCTTTTTAATTGCAATGT-AGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTT
* * * * *
28892321 CCACTGCACCGTCAGGGAAGTAACATTCACCGTTGTGGCTTCAATCTTTGTAATTGCAATGTCAG
129 CCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATATTTTTAATTGCAATGTCAG
28892386 AGAAC
194 AGAAC
* ** *
28892391 AAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCAGTGCCAGGGAAGTAAGATTCGCCGTTCC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
* * **
28892456 GGCTTCAATCTTTTTAATTACAATGTCAGGGAAATGAA-ATTCACCGTCATAGCTTCAATCTGTT
66 GGCTTCAATCTTTTTAATTGCAATGT-AGGGAAA-CAAGATTCACCGTTGTAGCTTCAATCTGTT
* * * *
28892520 CCACTGCACCGCCAGGGAAGTAAAATTCACTGTTGCAGCTTCAATATTTTTAATTGCAATGTTAG
129 CCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATATTTTTAATTGCAATGTCAG
*
28892585 GGAAC
194 AGAAC
* * *
28892590 AAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCACCAGGGAAGTAAGATTCGCCGTTGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
*
28892655 GGCTTCAATC--TTTAACTATG--ATGTAGGGAAATAAGATTCACCGTTGTAGCTTCAATCTGTT
66 GGCTTCAATCTTTTTAA-T-TGCAATGTAGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTT
* * *
28892716 CCACTGCACCACTAAGGG-AGTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCAATGTCA
129 CCACTGCACCGC-CAGGGAAGTAAGATTCACCGTTGCGGCTTCAATATTTTTAATTGCAATGTCA
*
28892780 -ATGAAGT
193 GA-GAA-C
* * * *
28892787 AAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGGAGTAAGATTCACCGTTGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
** * * * *
28892852 AACTTCAATCTTTTTAATTGTAATGTTAGGGAAGCAAGATTCGCCATTGTAGCTTCAATCTGTTC
66 GGCTTCAATCTTTTTAATTGCAATG-TAGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTC
* * *
28892917 CACTGCACCGCCAAGGAAGTAAGATTCACCGTTGCGACTTCAATCTTTTTAA
130 CACTGCACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATATTTTTAA
28892969 CCATAATGCC
Statistics
Matches: 498, Mismatches: 66, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
195 2 0.00
196 86 0.17
197 81 0.16
198 2 0.00
199 247 0.50
200 80 0.16
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (198 bp):
AAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
GGCTTCAATCTTTTTAATTGCAATGTAGGGAAACAAGATTCACCGTTGTAGCTTCAATCTGTTCC
ACTGCACCGCCAGGGAAGTAAGATTCACCGTTGCGGCTTCAATATTTTTAATTGCAATGTCAGAG
AAC
Found at i:28902911 original size:29 final size:26
Alignment explanation
Indices: 28902889--28902938 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
28902879 TATTTAACAC
28902889 TAAGAATT-TTATTAAATTATATTTAA
1 TAAGAATTATT-TTAAATTATATTTAA
*
28902915 TAATAATTATTTTAAATTATATTT
1 TAAGAATTATTTTAAATTATATTT
28902939 TATAGTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TAAGAATTATTTTAAATTATATTTAA
Found at i:28902915 original size:105 final size:101
Alignment explanation
Indices: 28902694--28903030 Score: 516
Period size: 105 Copynumber: 3.3 Consensus size: 101
28902684 AAGTAGATTA
28902694 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
28902759 AAATTCATATAAGAATATTTAATACTAAGATTTTTAT
66 AAATTCATATAAGAATATTTAA-ACTAAGATTTTTAT
*
28902796 TAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAAT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTT-A-
* *
28902861 TATAAATTCATATAAGAATATTTAACACTAAGAATTTTAT
64 -GTAAATTCATATAAGAATATTTAA-ACTAAGATTTTTAT
*
28902901 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTGTATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
*** * *
28902966 AAATTCATAT-ATTTTA-TTAAATTATATATTTTTAT
66 AAATTCATATAAGAATATTTAAACTA-AGATTTTTAT
*
28903001 TAAATTATATTTAATAATAATTATATTAAA
1 TAAATTATATTTAATAATAATTATTTTAAA
28903031 ATATGATTAA
Statistics
Matches: 217, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
99 3 0.01
100 41 0.19
101 3 0.01
102 72 0.33
103 1 0.00
104 1 0.00
105 96 0.44
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (101 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
AAATTCATATAAGAATATTTAAACTAAGATTTTTAT
Found at i:28902981 original size:18 final size:17
Alignment explanation
Indices: 28902958--28903010 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
28902948 GTATATTATG
*
28902958 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
28902976 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
28902993 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
28903011 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:28903257 original size:46 final size:44
Alignment explanation
Indices: 28903169--28903261 Score: 141
Period size: 46 Copynumber: 2.1 Consensus size: 44
28903159 TTACAACATT
* *
28903169 ATTCCATTCAACTAAACAGAAGAATACTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATACTATTACGCCTCTATTCC
*
28903213 ATTCCATTCAACCAAACAAAAGGATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAA-GAATA-CTATTACGCCTCTATTCC
28903259 ATT
1 ATT
28903262 ACAGCGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.30
Consensus pattern (44 bp):
ATTCCATTCAACCAAACAAAAGAATACTATTACGCCTCTATTCC
Found at i:28913276 original size:41 final size:41
Alignment explanation
Indices: 28913219--28913324 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
28913209 AATGAGATAA
* *
28913219 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
28913260 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
28913301 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
28913325 AATTGCCAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:28932753 original size:23 final size:22
Alignment explanation
Indices: 28932727--28932779 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
28932717 TTGAGAGTGA
*
28932727 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
28932750 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
28932772 AAAAGAAA
1 AAAAGAAA
28932780 AAGACGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:28951736 original size:19 final size:19
Alignment explanation
Indices: 28951712--28951750 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28951702 GTTCGTATGG
28951712 TTAAACTTTAAAGTTTATA
1 TTAAACTTTAAAGTTTATA
28951731 TTAAACTTTAAAGTTTATA
1 TTAAACTTTAAAGTTTATA
28951750 T
1 T
28951751 ATATGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
TTAAACTTTAAAGTTTATA
Found at i:28952082 original size:42 final size:43
Alignment explanation
Indices: 28952012--28952139 Score: 172
Period size: 42 Copynumber: 3.0 Consensus size: 43
28952002 TGAGTTTTCG
* * * *
28952012 TTCAACCCTTACGGGTTT-TCGTTCAGCTCTTTTGAGCTTCTGT
1 TTCAACCCTTATGGGTTTCT-TTTTAGCTCTTATGAGCTTCTGT
* *
28952055 TT-AACCCTTATGGGTTTCTTTTTAGCTCTTACGAGCTT-TTT
1 TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
28952096 TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
1 TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
28952139 T
1 T
28952140 CAGCCTTCGG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 4 0.05
42 64 0.86
43 6 0.08
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.48
Consensus pattern (43 bp):
TTCAACCCTTATGGGTTTCTTTTTAGCTCTTATGAGCTTCTGT
Found at i:28952136 original size:21 final size:21
Alignment explanation
Indices: 28952036--28952136 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
28952026 GTTTTCGTTC
* *
28952036 AGCTCTTTTGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTTTTT
* * * *
28952057 AACCCTTATGGGTTTCTTTTT
1 AGCTCTTATGAGCTTCTTTTT
*
28952078 AGCTCTTACGAGCTT-TTTTT
1 AGCTCTTATGAGCTTCTTTTT
* * * *
28952098 CAACCCTTATGGGTTTCTTTTT
1 -AGCTCTTATGAGCTTCTTTTT
28952120 AGCTCTTATGAGCTTCT
1 AGCTCTTATGAGCTTCT
28952137 GTTCAGCCTT
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 5 0.09
21 48 0.83
22 5 0.09
ACGTcount: A:0.14, C:0.21, G:0.16, T:0.50
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTTTTT
Found at i:28953724 original size:25 final size:23
Alignment explanation
Indices: 28953675--28953724 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
28953665 CATACTTCCA
**
28953675 GAACATAAAAAAATTAGAATTTT
1 GAACATAAAAAAATTAGAAAATT
*
28953698 GAACATAATAAAAGCTTAGAAAATT
1 GAACATAA-AAAA-ATTAGAAAATT
28953723 GA
1 GA
28953725 GTAATAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (23 bp):
GAACATAAAAAAATTAGAAAATT
Found at i:28959114 original size:70 final size:72
Alignment explanation
Indices: 28959000--28959150 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
28958990 GGGGAATCAT
* *
28959000 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28959064 GATATCG
66 GATATCG
***
28959071 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28959135 GATATCG
66 GATATCG
28959142 CACTTAGCA
1 CACTTAGCA
28959151 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:28959254 original size:104 final size:103
Alignment explanation
Indices: 28959070--28959292 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
28959060 AATGGATATC
28959070 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
28959135 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
28959173 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
28959238 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
28959277 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
28959293 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:28959654 original size:29 final size:29
Alignment explanation
Indices: 28959621--28959684 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
28959611 TAATCCACCA
28959621 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
28959650 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
28959680 CCCAA
1 CCCAA
28959685 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:28959658 original size:30 final size:30
Alignment explanation
Indices: 28959628--28959684 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28959618 CCACCCAACT
28959628 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
28959657 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
28959685 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:28965036 original size:103 final size:104
Alignment explanation
Indices: 28964854--28965041 Score: 299
Period size: 103 Copynumber: 1.8 Consensus size: 104
28964844 NNNNNNNNNC
* *
28964854 CAACCCCCTTTCACATTTCAAAGATATGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGA
1 CAACCCCCTTTCACATTTCAAAGATATGGTGGATATCGCACATAGCACCACCAATAAACCGGGGA
**
28964919 ATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAG
66 ATCAGCACACAGCAACCCCTCGGGGGAATCAGCACATAG
* *
28964958 CAACCCCCTTTCACATTTCAAAGATAT-GTGGATCA-CGCACATAGCACCACCCATAAATCGGGG
1 CAACCCCCTTTCACATTTCAAAGATATGGTGGAT-ATCGCACATAGCACCACCAATAAACCGGGG
28965021 AATCAGCACACAGCAACCCCT
65 AATCAGCACACAGCAACCCCT
28965042 TTTATATACA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
103 49 0.64
104 28 0.36
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.19
Consensus pattern (104 bp):
CAACCCCCTTTCACATTTCAAAGATATGGTGGATATCGCACATAGCACCACCAATAAACCGGGGA
ATCAGCACACAGCAACCCCTCGGGGGAATCAGCACATAG
Found at i:28965397 original size:29 final size:30
Alignment explanation
Indices: 28965373--28965428 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
28965363 CACCCAAATT
28965373 TTTTG-AAAATTACAATTTTG-CCCCAAAC
1 TTTTGCAAAATTACAATTTTGTCCCCAAAC
* *
28965401 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGTCCCCAA
28965429 GCTCGGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGTCCCCAAAC
Found at i:28972197 original size:70 final size:72
Alignment explanation
Indices: 28972083--28972233 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
28972073 GGGGAATCAT
* *
28972083 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28972147 GATATCG
66 GATATCG
***
28972154 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
28972218 GATATCG
66 GATATCG
28972225 CACTTAGCA
1 CACTTAGCA
28972234 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:28972264 original size:103 final size:102
Alignment explanation
Indices: 28972153--28972373 Score: 347
Period size: 103 Copynumber: 2.2 Consensus size: 102
28972143 AATGGATATC
28972153 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGT
* *
28972217 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
65 GGATCA-CGCACATAGCACCACCAATAAACC-GGGAATCA
28972256 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTG
* *
28972321 GATCACGCACATAGCACCACCCATAAATCGGGAATCA
66 GATCACGCACATAGCACCACCAATAAACCGGGAATCA
**
28972358 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
28972374 TTTATATACA
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
102 22 0.20
103 67 0.61
104 21 0.19
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (102 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTG
GATCACGCACATAGCACCACCAATAAACCGGGAATCA
Found at i:28972278 original size:27 final size:27
Alignment explanation
Indices: 28972247--28972298 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
28972237 CCAATGAACC
*
28972247 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
28972274 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
28972299 TTCACATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:28972735 original size:29 final size:29
Alignment explanation
Indices: 28972702--28972765 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
28972692 TAATCCACCA
28972702 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
28972731 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
28972761 CCCAA
1 CCCAA
28972766 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:28972739 original size:30 final size:30
Alignment explanation
Indices: 28972709--28972765 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28972699 CCACCCAACT
28972709 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
28972738 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
28972766 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:28978434 original size:21 final size:22
Alignment explanation
Indices: 28978391--28978434 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28978381 ATTCATGACA
*
28978391 GAAACGAAGAGAAACACTTACC
1 GAAACGAAGAGAAACACTAACC
* *
28978413 GAAACGAAGCG-AGCACTAACC
1 GAAACGAAGAGAAACACTAACC
28978434 G
1 G
28978435 CATGCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.25, G:0.23, T:0.07
Consensus pattern (22 bp):
GAAACGAAGAGAAACACTAACC
Found at i:28982888 original size:17 final size:17
Alignment explanation
Indices: 28982866--28982898 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28982856 TATAGCTTCC
28982866 TTTGAAAGCTT-TAAAAA
1 TTTGAAA-CTTCTAAAAA
28982883 TTTGAAACTTCTAAAA
1 TTTGAAACTTCTAAAA
28982899 GAAGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
TTTGAAACTTCTAAAAA
Found at i:28991444 original size:43 final size:42
Alignment explanation
Indices: 28991355--28991480 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 42
28991345 AGCTCGTACA
* *
28991355 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATACTG
1 ATGCC-ACGTCCCAGACGTGGTCTTACACGTAAACACATACTG
*
28991398 ATGCCACCGTCCCAGACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCA-CGTCCCAGAC-GTGGTCTTACACGTAAACACATACT-G
* * *
28991441 ATGCCGACATCCCAAACGTGGTCTTACACGAAAACACATA
1 ATGCC-ACGTCCCAGACGTGGTCTTACACGTAAACACATA
28991481 TCGGAGTCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 64 0.90
44 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGTGGTCTTACACGTAAACACATACTG
Found at i:28993653 original size:21 final size:21
Alignment explanation
Indices: 28993629--28993673 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
28993619 AGATAGGGAG
28993629 TGACACTTACAATTTCATTAT
1 TGACACTTACAATTTCATTAT
*
28993650 TGACACTTACAATTTTATTAT
1 TGACACTTACAATTTCATTAT
28993671 TGA
1 TGA
28993674 TAAAGGTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (21 bp):
TGACACTTACAATTTCATTAT
Found at i:28995489 original size:31 final size:31
Alignment explanation
Indices: 28995396--28995491 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
28995386 GGCAAATTAC
*
28995396 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
28995427 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
28995459 AAGAGTAATTGAATTCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
28995490 AA
1 AA
28995492 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:28998648 original size:9 final size:9
Alignment explanation
Indices: 28998636--28998736 Score: 81
Period size: 9 Copynumber: 11.7 Consensus size: 9
28998626 TTTTTTTTGC
28998636 GCTTTTTTT
1 GCTTTTTTT
28998645 GC-TTTTTT
1 GCTTTTTTT
28998653 G--TTTTTT
1 GCTTTTTTT
**
28998660 --TTTTTGC
1 GCTTTTTTT
*
28998667 GCTTTTTACT
1 GCTTTTT-TT
28998677 -CTTTTTTT
1 GCTTTTTTT
*
28998685 GCGCTTTTTT
1 GC-TTTTTTT
28998695 GCTTTTTTT
1 GCTTTTTTT
28998704 G-TTTTTTT
1 GCTTTTTTT
*
28998712 GCTGTTTTT
1 GCTTTTTTT
28998721 GCTTTTTTTT
1 GC-TTTTTTT
28998731 GCTTTT
1 GCTTTT
28998737 ATTTAAAGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
7 10 0.13
8 16 0.21
9 33 0.44
10 16 0.21
ACGTcount: A:0.01, C:0.12, G:0.13, T:0.74
Consensus pattern (9 bp):
GCTTTTTTT
Found at i:28998681 original size:31 final size:31
Alignment explanation
Indices: 28998624--28998683 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
28998614 GGTAGGCAAC
*
28998624 TTTTTTTTTTGCGCTTTTTTTGCTTTTTTGT
1 TTTTTTTTTTGCGCTTTTTCTGCTTTTTTGT
28998655 TTTTTTTTTTGCGCTTTTTACT-CTTTTTT
1 TTTTTTTTTTGCGCTTTTT-CTGCTTTTTT
28998684 TGCGCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.02, C:0.12, G:0.10, T:0.77
Consensus pattern (31 bp):
TTTTTTTTTTGCGCTTTTTCTGCTTTTTTGT
Found at i:28998702 original size:10 final size:10
Alignment explanation
Indices: 28998626--28998736 Score: 81
Period size: 10 Copynumber: 11.4 Consensus size: 10
28998616 TAGGCAACTT
28998626 TTTTTTTTGC
1 TTTTTTTTGC
*
28998636 GCTTTTTTTGC
1 -TTTTTTTTGC
*
28998647 TTTTTTGTT-T
1 TTTTTT-TTGC
28998657 TTTTTTTTGC
1 TTTTTTTTGC
** *
28998667 -GCTTTTTAC
1 TTTTTTTTGC
28998676 TCTTTTTTTGC
1 T-TTTTTTTGC
**
28998687 GCTTTTTTGC
1 TTTTTTTTGC
28998697 -TTTTTTTG-
1 TTTTTTTTGC
28998705 -TTTTTTTGC
1 TTTTTTTTGC
*
28998714 -TGTTTTTGC
1 TTTTTTTTGC
28998723 TTTTTTTTGC
1 TTTTTTTTGC
28998733 TTTT
1 TTTT
28998737 ATTTAAAGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
8 8 0.10
9 23 0.29
10 31 0.39
11 17 0.22
ACGTcount: A:0.01, C:0.12, G:0.13, T:0.75
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:28999377 original size:31 final size:31
Alignment explanation
Indices: 28999284--28999379 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
28999274 GGCAAATTAC
*
28999284 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
28999315 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
28999347 AAGAGTAATTGAATTCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
28999378 AA
1 AA
28999380 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:29001332 original size:15 final size:15
Alignment explanation
Indices: 29001309--29001338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29001299 AATCGCTTGA
*
29001309 ACATTCTTTGTGAAT
1 ACATGCTTTGTGAAT
29001324 ACATGCTTTGTGAAT
1 ACATGCTTTGTGAAT
29001339 GCAACACAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (15 bp):
ACATGCTTTGTGAAT
Found at i:29001671 original size:88 final size:90
Alignment explanation
Indices: 29001439--29001671 Score: 231
Period size: 90 Copynumber: 2.6 Consensus size: 90
29001429 CTCGAGTTTT
* ** * ** * *
29001439 TGGATAAACCAAAAATGTTGCAGGTTAATACGTTGCCAAATGGTTGTGAATACACAACATATTTG
1 TGGATGAACCAACGATGTTGCAGATTAATACACTGCCAGATGGTTGTGAATACACAACATATTCG
* * * * *
29001504 CAAATAAGAGCTTCTAGATATTGGA
66 CAAATAAGAACTGCCAGAAAGTGGA
* * * *
29001529 TGGATGAACCAACGATGTTGCAGGTTAATACACTACTAGATGGTTGTGAGTACACAACATATTCG
1 TGGATGAACCAACGATGTTGCAGATTAATACACTGCCAGATGGTTGTGAATACACAACATATTCG
*
29001594 -AAGATAAGAACTGCCA-AAAGTGGG
66 CAA-ATAAGAACTGCCAGAAAGTGGA
* * *
29001618 TGGATGAACC-AC-CTGTTTTCAGATTTATACACTGCCAGATGGTTGTGAATACAC
1 TGGATGAACCAACGATG-TTGCAGATTAATACACTGCCAGATGGTTGTGAATACAC
29001672 CATAGGGTTG
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
87 2 0.02
88 34 0.29
89 17 0.14
90 65 0.55
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (90 bp):
TGGATGAACCAACGATGTTGCAGATTAATACACTGCCAGATGGTTGTGAATACACAACATATTCG
CAAATAAGAACTGCCAGAAAGTGGA
Found at i:29003935 original size:21 final size:21
Alignment explanation
Indices: 29003919--29003972 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
29003909 ATGAGGGTCT
*
29003919 ACACTCCCATGTGGAGGCTAC
1 ACACGCCCATGTGGAGGCTAC
* *
29003940 ACACGCCCATGTGAAGGCCAC
1 ACACGCCCATGTGGAGGCTAC
*
29003961 ATACGCCCATGT
1 ACACGCCCATGT
29003973 AAACAGCCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17
Consensus pattern (21 bp):
ACACGCCCATGTGGAGGCTAC
Found at i:29018710 original size:17 final size:17
Alignment explanation
Indices: 29018688--29018720 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29018678 TTATACTACA
29018688 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
29018705 AAATATTTTTTATTAA
1 AAATATTTATTATTAA
29018721 AACATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:29018791 original size:18 final size:19
Alignment explanation
Indices: 29018768--29018803 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29018758 ATATTATTTT
*
29018768 TAAAATTTAT-TATTAAAA
1 TAAAATTGATATATTAAAA
29018786 TAAAATTGATATATTAAA
1 TAAAATTGATATATTAAA
29018804 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTGATATATTAAAA
Found at i:29018836 original size:31 final size:30
Alignment explanation
Indices: 29018767--29018843 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
29018757 AATATTATTT
29018767 TTAAAATTTATTATTAAAATAAAATTGATA
1 TTAAAATTTATTATTAAAATAAAATTGATA
*
29018797 TATTAAA-TTATTTATTAAAATAATGAATT-ATA
1 T-TAAAATTTA-TTATTAAAATAA--AATTGATA
29018829 TTAAAATTTTATTAT
1 TTAAAA-TTTATTAT
29018844 ATGATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 4 0.10
31 20 0.51
32 8 0.21
33 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAAAATTTATTATTAAAATAAAATTGATA
Found at i:29018940 original size:17 final size:18
Alignment explanation
Indices: 29018913--29018946 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29018903 TATATTAATA
*
29018913 TTTTAATAAATTTAAATG
1 TTTTAATAAATATAAATG
29018931 TTTTAA-AAATATAAAT
1 TTTTAATAAATATAAAT
29018947 AAAAATTATT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTTAATAAATATAAATG
Found at i:29025617 original size:23 final size:23
Alignment explanation
Indices: 29025591--29025640 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
29025581 TTAATATTTA
29025591 TATTTGACTATTT-TATATATGTT
1 TATTT-ACTATTTGTATATATGTT
* * *
29025614 TATTTATTGTTTGTATATTTGTT
1 TATTTACTATTTGTATATATGTT
29025637 TATT
1 TATT
29025641 ATTCATGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (23 bp):
TATTTACTATTTGTATATATGTT
Found at i:29029930 original size:40 final size:40
Alignment explanation
Indices: 29029797--29029936 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
29029787 AACTTTGAGT
* * *
29029797 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATATATT
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGGAT-TATC
* * * *
29029838 CGATGAGGCATTGTGTGTC-AA-T-TTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGGATTATC
* *
29029875 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGGATTATC
* * *
29029915 CGATGAGGTAGTGGGTGCCAAA
1 CGATGAGGCACTGGGTGTCAAA
29029937 CTGGATTGTA
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
37 18 0.23
38 12 0.15
39 2 0.03
40 32 0.41
41 15 0.19
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (40 bp):
CGATGAGGCACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:29056705 original size:23 final size:23
Alignment explanation
Indices: 29056662--29056708 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29056652 TTTAGTAATA
*
29056662 AATATTTTATAGAATAAAATATG
1 AATATTTTATAAAATAAAATATG
*
29056685 AATATTTTATTAAAAT-TAATATG
1 AATATTTTA-TAAAATAAAATATG
29056708 A
1 A
29056709 GTTTTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
AATATTTTATAAAATAAAATATG
Found at i:29060215 original size:2 final size:2
Alignment explanation
Indices: 29060208--29060242 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29060198 AGAAAACTAG
*
29060208 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29060243 TACAAGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29064029 original size:44 final size:43
Alignment explanation
Indices: 29063965--29064461 Score: 238
Period size: 44 Copynumber: 11.4 Consensus size: 43
29063955 AAGTAGCCTT
*
29063965 ACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTGCTCC
1 ACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTCC
* * * *
29064009 ACTGCAACTTCAGGGAGATAAGACTAGATGC--GATCTGCT-C
1 ACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTCC
* * * ** *
29064049 TCTACAACTTCAGAGAGATAAGATCCAAGATT--TTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGA--CTTG-TTACTTAATCTGCTCC
* * * * * * *
29064093 CCTGAAACTTCAGGGAAATAGGA-TTATTGGCTTTAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGTT-AC-TTAATCTGCTCC
* ** * *
29064137 ACTGCAACTTCGGGGAGATAAGGTTTGTCATCTTCAGTCTGC-CTC
1 ACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC-C
* *
29064182 ACTGCAACTTCA-GGAGGATAAGACCTGCTTACTTAGTCTGCTCC
1 ACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTCC
* * **
29064226 ACTGCAACTTCAAGGAGATAAGACTAG--A-TGGGATCTGC-CC
1 ACTGCAACTTCAGGGAGATAAGACTTGTTACT-TAATCTGCTCC
* * ** ** *
29064266 TCTGCAACTTCAGAGAGATAAGATCCAAGATT--TTAATCCACTCT
1 ACTGCAACTTCAGGGAGATAAGA--CTTG-TTACTTAATCTGCTCC
* * * * * *
29064310 ACTACAACTTCAGGGAAATAGGA-TTATTGGCTTTAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGTT-AC-TTAATCTGCTCC
* ** *
29064354 ACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-CTC
1 ACTGCAACTTCAGGGAGATAAGACTTGTTA-CTT-AATCTGCTC-C
*
29064399 GCTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAATCTGCTCC
1 ACTGCAACTTCAGGGA-GATAAGACTTG-TTACTTAATCTGCTCC
29064443 ACTGCAACTTCAGGGAGAT
1 ACTGCAACTTCAGGGAGAT
29064462 GAGATTATTG
Statistics
Matches: 335, Mismatches: 80, Indels: 76
0.68 0.16 0.15
Matches are distributed among these distances:
40 48 0.14
41 12 0.04
42 6 0.02
43 13 0.04
44 177 0.53
45 76 0.23
46 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
ACTGCAACTTCAGGGAGATAAGACTTGTTACTTAATCTGCTCC
Found at i:29064340 original size:217 final size:217
Alignment explanation
Indices: 29063960--29064461 Score: 853
Period size: 217 Copynumber: 2.3 Consensus size: 217
29063950 TCTTCAAGTA
* *
29063960 GCCTTACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
29064025 GATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCGC
66 GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
* *
29064090 TCCCCTGAAACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCGGGGAGA
131 TCCACTGAAACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
* *
29064155 TAAGGTTTGTCATCTTCAGTCT
196 TAAGATTTGCCATCTTCAGTCT
* *
29064177 GCCTCACTGCAACTTCAGGAGGATAAGACCTGCTTACTTAGTCTGCTCCACTGCAACTTCAAGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
* *
29064242 GATAAGACTAGATGGGATCTGCCCTCTGCAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
66 GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
*
29064307 TCTACT-ACAACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAG
131 TCCACTGA-AACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAG
29064371 ATAAGATTTGCCATCTTCAGTCT
195 ATAAGATTTGCCATCTTCAGTCT
* *
29064394 GCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTACTTAATCTGCTCCACTGCAACTTCAGGGA
1 GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
29064459 GAT
66 GAT
29064462 GAGATTATTG
Statistics
Matches: 267, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
216 1 0.00
217 266 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
GCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTAGATGCGATCTGCCCTCTACAACTTCAGAGAGATAAGATCCAAGATTTTAATCCAC
TCCACTGAAACTTCAGGGAAATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGA
TAAGATTTGCCATCTTCAGTCT
Found at i:29077957 original size:3 final size:3
Alignment explanation
Indices: 29077949--29077974 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29077939 CTGTTAAACT
29077949 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
29077975 GGTGTTTATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29086712 original size:2 final size:2
Alignment explanation
Indices: 29086701--29086739 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
29086691 ACGGTCTAAA
29086701 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29086740 CAATGTACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29087343 original size:21 final size:22
Alignment explanation
Indices: 29087310--29087352 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
29087300 CAAATTTCAG
*
29087310 AAATTGATATTT-ATTTTTTAA
1 AAATTGATATTTAATTATTTAA
* *
29087331 AAATTTATTTTTAATTATTTAA
1 AAATTGATATTTAATTATTTAA
29087353 TTTAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATTGATATTTAATTATTTAA
Found at i:29090850 original size:94 final size:94
Alignment explanation
Indices: 29090716--29090925 Score: 251
Period size: 94 Copynumber: 2.2 Consensus size: 94
29090706 TATTTTTAAG
* * * * *
29090716 GCTCGTTGATTTACGATCACAGTCTAAGTTCATTGATTTACAATTATGAACAAGTTT-TCCTGAG
1 GCTCGCTGATTTACAATCATAGCCTAAGTTCATTGATTTACAATCATGAA-AAGTTTCTCCTGAG
29090780 TTTGCTGACTTACAATCACAACTCCAAATA
65 TTTGCTGACTTACAATCACAACTCCAAATA
* * * * *
29090810 GCTCGGTGATTTACAATCATAGCCTAAGTTTATTGATTTACGATCATGAATAGTTTCTCTTGAGT
1 GCTCGCTGATTTACAATCATAGCCTAAGTTCATTGATTTACAATCATGAAAAGTTTCTCCTGAGT
* * **
29090875 TTGTTGATTTATTATCACAACTCCAAATA
66 TTGCTGACTTACAATCACAACTCCAAATA
* * *
29090904 ACTCACTAATTTACAATCATAG
1 GCTCGCTGATTTACAATCATAG
29090926 TTGATATTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
93 5 0.05
94 93 0.95
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (94 bp):
GCTCGCTGATTTACAATCATAGCCTAAGTTCATTGATTTACAATCATGAAAAGTTTCTCCTGAGT
TTGCTGACTTACAATCACAACTCCAAATA
Found at i:29090975 original size:27 final size:27
Alignment explanation
Indices: 29090945--29091048 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
29090935 TTAAGGCTTT
29090945 TTGATTTACGATCACAACCTAAGTTCA
1 TTGATTTACGATCACAACCTAAGTTCA
* *
29090972 TTGATTAACGATCATGAACAATTTCTCCTAAGTTCG
1 TTGATTTACGATC----ACAA-----CCTAAGTTCA
* *
29091008 CTGATTTACGATCACAACCTAAATTCA
1 TTGATTTACGATCACAACCTAAGTTCA
*
29091035 TTAATTTACGATCA
1 TTGATTTACGATCA
29091049 TGAATAATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
27 32 0.53
31 4 0.07
32 4 0.07
36 20 0.33
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (27 bp):
TTGATTTACGATCACAACCTAAGTTCA
Found at i:29091085 original size:63 final size:63
Alignment explanation
Indices: 29090946--29091088 Score: 164
Period size: 63 Copynumber: 2.3 Consensus size: 63
29090936 TAAGGCTTTT
* * * * *
29090946 TGATTTACGATCACAACCTAAGTTCATTGATTAACGATCATGAACAATTTCTCCTAAGTTCGC
1 TGATTCACAATCACAACCTAAATTCATTAATTAACGATCATGAACAATTTCTCCTAAGTTAGC
* * * * *
29091009 TGATTTACGATCACAACCTAAATTCATTAATTTACGATCATGAATAATATT-TCCTGAGTTAG-
1 TGATTCACAATCACAACCTAAATTCATTAATTAACGATCATGAACAAT-TTCTCCTAAGTTAGC
29091071 TGGATTCACAATCACAAC
1 T-GATTCACAATCACAAC
29091089 TTAGGTACGA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
62 1 0.01
63 67 0.96
64 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (63 bp):
TGATTCACAATCACAACCTAAATTCATTAATTAACGATCATGAACAATTTCTCCTAAGTTAGC
Found at i:29098675 original size:16 final size:16
Alignment explanation
Indices: 29098656--29098689 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29098646 TGAAATGAAT
*
29098656 ATGTGTAAATATGATA
1 ATGTGCAAATATGATA
29098672 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
29098688 AT
1 AT
29098690 TGGATATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:29102903 original size:83 final size:85
Alignment explanation
Indices: 29102802--29102969 Score: 277
Period size: 85 Copynumber: 2.0 Consensus size: 85
29102792 AAGGGGATGT
* **
29102802 GGATGAAGGGAGCTCTACATGTAGCAACAGA-G-GTGAGTTTAAGGCTAGCAATGGAGAAAAGAG
1 GGATGAAGGGAGCTCTACATGTAGCAACAGAGGTGTGAGTTTAAGGCTAACAATAAAGAAAAGAG
29102865 GAACTGGTAAGTCTCTTTAC
66 GAACTGGTAAGTCTCTTTAC
**
29102885 GGATGAAGGGAGCTCTACATGTAGCAGTAGAGGTGTGAGTTTAAGGCTAACAATAAAGAAAAGAG
1 GGATGAAGGGAGCTCTACATGTAGCAACAGAGGTGTGAGTTTAAGGCTAACAATAAAGAAAAGAG
29102950 GAACTGGTAAGTCTCTTTAC
66 GAACTGGTAAGTCTCTTTAC
29102970 CTCCCTCTAT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 29 0.37
84 1 0.01
85 48 0.62
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (85 bp):
GGATGAAGGGAGCTCTACATGTAGCAACAGAGGTGTGAGTTTAAGGCTAACAATAAAGAAAAGAG
GAACTGGTAAGTCTCTTTAC
Found at i:29114009 original size:62 final size:57
Alignment explanation
Indices: 29113922--29114034 Score: 138
Period size: 62 Copynumber: 1.9 Consensus size: 57
29113912 TATATATACA
*
29113922 TTTTTTATAATATATATATACACACACTTTTCCA-AATTATTATAAATATATTTTCTGCAT
1 TTTTTTATAATACATATATACACACA-TTTT-CATAA-T-TTATAAATATATTTTCTGCAT
* *
29113982 TTTTCTTATATATACATATATATACACATTTTCATAATTTATTAATATATTTT
1 TTTT-TTATA-ATACATATATACACACATTTTCATAATTTATAAATATATTTT
29114035 ACTTGTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
59 14 0.30
60 7 0.15
61 11 0.23
62 15 0.32
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (57 bp):
TTTTTTATAATACATATATACACACATTTTCATAATTTATAAATATATTTTCTGCAT
Found at i:29114203 original size:19 final size:20
Alignment explanation
Indices: 29114168--29114212 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
29114158 TCATGTTTAT
29114168 ATATTTTATATAATATATAC
1 ATATTTTATATAATATATAC
* *
29114188 ATATTTTGTAAATATATATAC
1 ATATTTTATATA-ATATATAC
29114209 ATAT
1 ATAT
29114213 AATTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATTTTATATAATATATAC
Found at i:29117707 original size:13 final size:13
Alignment explanation
Indices: 29117689--29117713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29117679 TATTTTAATA
29117689 TTATTTTGTGTGT
1 TTATTTTGTGTGT
29117702 TTATTTTGTGTG
1 TTATTTTGTGTG
29117714 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:29118867 original size:41 final size:41
Alignment explanation
Indices: 29118822--29118922 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 41
29118812 GCTTAGCGCT
*
29118822 TAGCAGGCTTATTGCCGGTAAAACACTTCAGACTAAATGTC
1 TAGCAGGCTTAATGCCGGTAAAACACTTCAGACTAAATGTC
* * * *
29118863 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTAAAACACTTCAGACTAAATGTC
29118904 TAGCAGGC-TAAGTGCCGGT
1 TAGCAGGCTTAA-TGCCGGT
29118923 GTACTGAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 3 0.06
41 51 0.94
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTAAAACACTTCAGACTAAATGTC
Found at i:29125186 original size:15 final size:15
Alignment explanation
Indices: 29125157--29125200 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29125147 AAAGATGTGA
29125157 AAAAATG-AAAA-GG
1 AAAAATGAAAAATGG
29125170 AAAAATGAAAAATGG
1 AAAAATGAAAAATGG
29125185 AAAAA-GTAAAAATGG
1 AAAAATG-AAAAATGG
29125200 A
1 A
29125201 GAGGCTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 16 0.57
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (15 bp):
AAAAATGAAAAATGG
Found at i:29126569 original size:88 final size:88
Alignment explanation
Indices: 29126460--29126771 Score: 482
Period size: 88 Copynumber: 3.5 Consensus size: 88
29126450 CTGAAGATAG
* *
29126460 CAGATCTTGCCTTCCTATACTGACAGAGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
*
29126525 GTAGTGAAGTAGGTTGAAAATGA
66 GTAGTGGAGTAGGTTGAAAATGA
*
29126548 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGTA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
29126613 GTAGTGGAGTAGGTTGAAAATGA
66 GTAGTGGAGTAGGTTGAAAATGA
* * * *
29126636 CAGATATTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTATCTCCTTGGGCA
1 CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
*
29126701 ATAGTGGAGTAGGTTGAAAAT-A
66 GTAGTGGAGTAGGTTGAAAATGA
* * * * *
29126723 GCAAATCTTGCCTTCTTGTACTGGCAGCGAAGTAGATCGAAGACACCAG
1 -CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAG
29126772 TCTTATCACC
Statistics
Matches: 208, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 1 0.00
88 207 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTGGGCA
GTAGTGGAGTAGGTTGAAAATGA
Found at i:29126864 original size:50 final size:50
Alignment explanation
Indices: 29126800--29127274 Score: 355
Period size: 50 Copynumber: 9.5 Consensus size: 50
29126790 GCAATTAAAA
* *
29126800 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
* *** * * * * ** **
29126850 AGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
*
29126900 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
* * * * *** * * * * ** **
29126950 AGATTAAAGTCACAACAGCGGATCTGGTTTCCCCGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
*
29127000 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
* * *** * ** **
29127050 AGATTGAAGTCATAACGGCAGATCTGGTTTCGCCGATAGC-GT--AATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTC-CC--TGGCGGTGCAATGGAGC
*
29127100 AGATTGAAGCCACAATGGCAGATCTTACTTCCCTGGCGGTGCAGA-GGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCA-ATGGAGC
* * *** * * * * ** **
29127150 AGATTGAAGTCACAACGGTAGATCTGGTTTCCCCGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
* *
29127200 AGATTGAAGCCACAACGGCAGATCTTACTTCCTTGGCGGTGTAATGGAGC
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
* *
29127250 AGATTGAAGTCACAACGGCGGATCT
1 AGATTGAAGCCACAACGGCAGATCT
29127275 GGTTTCCCCG
Statistics
Matches: 306, Mismatches: 111, Indels: 16
0.71 0.26 0.04
Matches are distributed among these distances:
47 3 0.01
48 2 0.01
49 3 0.01
50 290 0.95
51 3 0.01
52 2 0.01
53 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGCAATGGAGC
Found at i:29126960 original size:100 final size:100
Alignment explanation
Indices: 29126784--29127323 Score: 902
Period size: 100 Copynumber: 5.4 Consensus size: 100
29126774 TTATCACCTT
* * *
29126784 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
29126849 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
66 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
29126884 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
* * *
29126949 CAGATTAAAGTCACAACAGCGGATCTGGTTTCCCC
66 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
29126984 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
* *
29127049 CAGATTGAAGTCATAACGGCAGATCTGGTTTCGCC
66 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
* * * *
29127084 GATAGCGTAATTAAAAAGATTGAAGCCACAATGGCAGATCTTACTTCCCTGGCGGTGCAGA-GGA
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTA-ATGGA
*
29127148 GCAGATTGAAGTCACAACGGTAGATCTGGTTTCCCC
65 GCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
*
29127184 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCTTGGCGGTGTAATGGAG
1 GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
*
29127249 CAGATTGAAGTCACAACGGCGGATCTGGTTTCCCC
66 CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
* *
29127284 GACAACGCAATTAAAAAAGATTAAAGCCACAACGGCAGAT
1 GACAGCGCAATT-AAAAAGATTGAAGCCACAACGGCAGAT
29127324 TTTTACCTCC
Statistics
Matches: 410, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
99 1 0.00
100 382 0.93
101 27 0.07
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (100 bp):
GACAGCGCAATTAAAAAGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGCGGTGTAATGGAG
CAGATTGAAGTCACAACGGCAGATCTGGTTTCCCC
Found at i:29129210 original size:64 final size:64
Alignment explanation
Indices: 29129083--29129214 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 64
29129073 TTTTATAAAT
*
29129083 ATATATATACACACACTTTTCCAAATTATTATAAATATATTTTCTGCATTTTTCTTATATATAC
1 ATATATATACACACACTTTTCCAAATTATTATAAATATATTTTCTGCATATTTCTTATATATAC
* * *
29129147 ATATATATATACACA-TTTT-CATAA-T-TTATTAATATATTTTACTTGTATATTT-TTATACCT
1 ATATATATACACACACTTTTCCA-AATTATTATAAATATATTTT-C-TGCATATTTCTTATA--T
29129207 ATAC
61 ATAC
29129211 ATAT
1 ATAT
29129215 TTTATTATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
61 14 0.24
62 9 0.15
63 13 0.22
64 23 0.39
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (64 bp):
ATATATATACACACACTTTTCCAAATTATTATAAATATATTTTCTGCATATTTCTTATATATAC
Found at i:29129327 original size:10 final size:9
Alignment explanation
Indices: 29129304--29129340 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
29129294 TTTTCCCGTA
29129304 TTATATAAT
1 TTATATAAT
*
29129313 TTATATATGT
1 TTATATA-AT
29129323 TTATATAAT
1 TTATATAAT
29129332 TTATATAAT
1 TTATATAAT
29129341 ATATTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
TTATATAAT
Found at i:29129379 original size:21 final size:22
Alignment explanation
Indices: 29129325--29129380 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
29129315 ATATATGTTT
* *
29129325 ATATAATTTATATAATATATTC
1 ATATAATTTAAATAATATATAC
*
29129347 ATAT-TTTGTAAAT-ATATATAC
1 ATATAATT-TAAATAATATATAC
29129368 ATATAATTTAAAT
1 ATATAATTTAAAT
29129381 TAAAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATAATTTAAATAATATATAC
Found at i:29131719 original size:19 final size:21
Alignment explanation
Indices: 29131681--29131720 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
29131671 CTTGTTTTGA
*
29131681 TTAAATAAATTATTTAAAATT
1 TTAAATAAATTATATAAAATT
29131702 TTAAA-AAA-TATATAAAATT
1 TTAAATAAATTATATAAAATT
29131721 GATTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 3 0.17
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATAAATTATATAAAATT
Found at i:29133778 original size:125 final size:124
Alignment explanation
Indices: 29133499--29133770 Score: 408
Period size: 125 Copynumber: 2.2 Consensus size: 124
29133489 TTATTTCGAG
* **
29133499 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCACTGATACCAGGATGCTATCAGAGAAGAAATTGT
*
29133563 GAAATCGTGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGTCAGAAATAATTTTTT
65 GAAATCGCGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGTCAGAAATAATTTTTT
*
29133623 TTGACGTTTTCTAAGCAAATAGTATAAAATCACTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCACTGATACCAGGATGCTATCA-GAGAAGAAATTG
*
29133687 TGAAATCGCGCCCTCGTGGACGCGATTTC-GCTACAGTTGGTCATGT-AGGAAATAATTATTTT
64 TGAAATCGCGCCCTCGTGGACGCCATTTCGGC-ACAGTTGGTCATGTCA-GAAATAATT-TTTT
29133749 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTGAGCAAATAGT
29133771 GTCAAATCGT
Statistics
Matches: 135, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
124 10 0.07
125 114 0.84
126 11 0.08
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCACTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGTCAGAAATAATTTTTT
Found at i:29136931 original size:28 final size:28
Alignment explanation
Indices: 29136899--29137597 Score: 796
Period size: 28 Copynumber: 23.9 Consensus size: 28
29136889 GATTATCAAA
29136899 TTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
* **
29136927 TTAGGGTTAGGGTTTTTAATTTAATTAAA
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
*
29136956 TTAGGATAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAGG
29136989 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
*
29137018 TTAGGCTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
29137046 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
29137075 TTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
* * **
29137103 TTATGTTAGGGTTTTTAATTTAATTAAA
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
*
29137131 TTAGGATAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAGG
29137164 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
* *
29137193 TTAGGTTAGAGTTTTTAATTTAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
* **
29137221 TTAGGGTTTAGGGTTTTTAATTTAATTAAA
1 TTA-GG-TTAGGGTTTTTAATTAAATTAGG
*
29137251 TTAGGATAGGGTTTTTAATTAAATCAAATTAGG
1 TTAGGTTAGGGTTTTTAA-T---T-AAATTAGG
*
29137284 TTAGGGTTAGAGTTTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
29137313 TTAGGTTAGGGTTTTTAATT-AA--A--
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
*
29137336 TTAGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
*
29137364 TTAGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
* **
29137392 TTAGGGCTTAGGGTTTTTAATTTAATTAAA
1 TTA-GG-TTAGGGTTTTTAATTAAATTAGG
*
29137422 TTAGGATAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAGG
*
29137455 TTAGGGTTAGGATTTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
29137484 TTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
29137512 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGTTAGGG--TTT--TT-AATTAAATTAGG
* **
29137545 TTAGGGTTAGGGTTTTTAATTTAATTAAA
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
29137574 TTAGGTTAGGGTTTTTAATTAAAT
1 TTAGGTTAGGGTTTTTAATTAAAT
29137598 CAAATAATAT
Statistics
Matches: 583, Mismatches: 47, Indels: 82
0.82 0.07 0.12
Matches are distributed among these distances:
23 20 0.03
24 2 0.00
25 1 0.00
26 1 0.00
27 2 0.00
28 238 0.41
29 129 0.22
30 68 0.12
32 21 0.04
33 60 0.10
34 41 0.07
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (28 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGG
Found at i:29136966 original size:57 final size:57
Alignment explanation
Indices: 29136896--29137602 Score: 829
Period size: 62 Copynumber: 12.1 Consensus size: 57
29136886 TAAGATTATC
*
29136896 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTTAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
*
29136953 AAATTAGGATAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
** *
29137015 AGGTTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
** * *
29137072 AGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTA-TGTTAGGGTTTTTAATTTAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
*
29137128 AAATTAGGATAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
** * * *
29137190 AGGTTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTAGGGTTTTTAATTTAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATT
* *
29137248 AAATTAGGATAGGGTTTTTAATTAAATCAAATTAGGTTAGGGTTAGAGTTTTTAATTAAATT
1 AAATTAGGTTAGGGTTTTTAA-T---T-AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
**
29137310 AGGTTAGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
* * *
29137361 AAGTTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGCTTAGGGTTTTTAATTTAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATT
* *
29137419 AAATTAGGATAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAAATT
1 AAATTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
**
29137481 AGGTTAGGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGTTTTTAATTAAATT
1 AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
* ** *
29137537 AAATTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATC
1 -AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
29137599 AAAT
1 AAAT
29137603 AATATCAAAA
Statistics
Matches: 568, Mismatches: 47, Indels: 70
0.83 0.07 0.10
Matches are distributed among these distances:
51 43 0.08
52 5 0.01
54 2 0.00
56 57 0.10
57 120 0.21
58 77 0.14
59 5 0.01
60 14 0.02
61 23 0.04
62 192 0.34
63 30 0.05
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (57 bp):
AAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT
Found at i:29137587 original size:62 final size:61
Alignment explanation
Indices: 29136899--29137602 Score: 698
Period size: 57 Copynumber: 11.9 Consensus size: 61
29136889 GATTATCAAA
**
29136899 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTTAATTAAATTAGG
*
29136961 --A---TAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGTT--TTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTT---TTTAATTTAATTAAATTAGG
* **
29137018 TTAGGCTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG---TT--TTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTTAATTAAATTAGG
** *
29137075 TTAGGTTAGGGTTTTTAATTAAATTAGGTTATGTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
*
29137136 --A---TAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGTT--TTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTT---TTTAATTTAATTAAATTAGG
* * **
29137193 TTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTA-GG-TTAGGGTTTTTAATTTAATTAAATTAGG
* *
29137256 --A---TAGGGTTTTTAATTAAATCAAATTAGGTTAGGGTTAGAGTT--TTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTT---TTTAATTTAATTAAATTAGG
*
29137313 TTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTAGGG---TT--TTTAATTAAATTAAG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
* **
29137364 TTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGCTTAGGGTTTTTAATTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTA-GG-TTAGGGTTTTTAATTTAATTAAATTAGG
*** *
29137427 --A---TAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTA-ATTTAATTAAATTAGG
** *
29137484 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
* * *
29137545 TTAGGGTTAGGGTTTTTAATTTAATTAAATTAGGTTAGGGTTTTTAATTAAATCAAAT
1 TTA-GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTTAATTAAAT
29137603 AATATCAAAA
Statistics
Matches: 544, Mismatches: 45, Indels: 106
0.78 0.06 0.15
Matches are distributed among these distances:
51 27 0.05
53 3 0.01
55 2 0.00
56 74 0.14
57 153 0.28
58 50 0.09
59 13 0.02
60 4 0.01
61 38 0.07
62 133 0.24
63 39 0.07
64 8 0.01
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (61 bp):
TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTTAATTAAATTAGG
Found at i:29139760 original size:14 final size:15
Alignment explanation
Indices: 29139743--29139776 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29139733 AATATTTATC
29139743 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
29139757 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
29139772 TAAAA
1 TAAAA
29139777 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:29139925 original size:28 final size:28
Alignment explanation
Indices: 29139874--29139930 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
29139864 TTGAAAATAT
* *
29139874 TAAAAATTTTAAAATTATTTTTAAAAAA
1 TAAAAATTTTAAAAGTATTCTTAAAAAA
29139902 TAAAAATATTTAAAAGT-TTCTTAAAAAA
1 TAAAAAT-TTTAAAAGTATTCTTAAAAAA
29139930 T
1 T
29139931 GAAATTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (28 bp):
TAAAAATTTTAAAAGTATTCTTAAAAAA
Found at i:29140008 original size:21 final size:21
Alignment explanation
Indices: 29139964--29140012 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
29139954 TAATATGGAG
*
29139964 TTGAGAGATTTTTTGAAGGAAAT
1 TTGAG-GA-TTTTGGAAGGAAAT
29139987 TGTGAGGATTTTGGAAGG-AAT
1 T-TGAGGATTTTGGAAGGAAAT
29140008 TTGAG
1 TTGAG
29140013 AGTTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 9 0.38
23 3 0.12
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.37
Consensus pattern (21 bp):
TTGAGGATTTTGGAAGGAAAT
Found at i:29140044 original size:22 final size:22
Alignment explanation
Indices: 29140019--29140065 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
29140009 TGAGAGTTTA
*
29140019 AGAGAATTTTGGAAGGAATTTG
1 AGAGAATTTTGGAAGGAAATTG
* *
29140041 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
29140063 AGA
1 AGA
29140066 TGGGATTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:29140050 original size:52 final size:52
Alignment explanation
Indices: 29139967--29140065 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
29139957 TATGGAGTTG
* * * * *
29139967 AGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
* * *
29140019 AGAGAATTTTGGAAGGAATTTGAGAGAATTTTTGAATGAAATTGAGA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGA
29140066 TGGGATTTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.34
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTTA
Found at i:29144840 original size:25 final size:25
Alignment explanation
Indices: 29144810--29144877 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
29144800 CGGTAAACAA
29144810 TAAGCTC-TTCTGAGCTGAATAACGG
1 TAAGCTCTTTC-GAGCTGAATAACGG
*
29144835 TAAGCTCTTTCGAGCTGCATAACGG
1 TAAGCTCTTTCGAGCTGAATAACGG
* *
29144860 TAAGCTCATACGAGCTGA
1 TAAGCTCTTTCGAGCTGA
29144878 TTATTGATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 35 0.92
26 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (25 bp):
TAAGCTCTTTCGAGCTGAATAACGG
Found at i:29147069 original size:7 final size:7
Alignment explanation
Indices: 29147057--29147086 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
29147047 TAATGTGTTA
29147057 ATGTGAT
1 ATGTGAT
29147064 ATGTGAT
1 ATGTGAT
*
29147071 ATATGAT
1 ATGTGAT
29147078 ATGTGAT
1 ATGTGAT
29147085 AT
1 AT
29147087 ATGTTGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (7 bp):
ATGTGAT
Found at i:29147079 original size:14 final size:14
Alignment explanation
Indices: 29147060--29147089 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29147050 TGTGTTAATG
29147060 TGATATGTGATATA
1 TGATATGTGATATA
29147074 TGATATGTGATATA
1 TGATATGTGATATA
29147088 TG
1 TG
29147090 TTGTGTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (14 bp):
TGATATGTGATATA
Found at i:29151506 original size:58 final size:58
Alignment explanation
Indices: 29151416--29151536 Score: 233
Period size: 58 Copynumber: 2.1 Consensus size: 58
29151406 TTACATTGTG
*
29151416 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGGATTTTCATCTAAT
1 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
29151474 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
1 TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
29151532 TAATA
1 TAATA
29151537 CATGAACCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (58 bp):
TAATAAAGTAGAGATAATCACTTAGTTCAACTAGTAAGAACATGAATTTTCATCTAAT
Found at i:29152159 original size:16 final size:16
Alignment explanation
Indices: 29152116--29152168 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
29152106 TTACCCTATA
29152116 AAAAATAAT-AATTTT
1 AAAAATAATAAATTTT
* *
29152131 AGTATATAA-AAATTTT
1 A-AAAATAATAAATTTT
29152147 AAAAATAATAAA--TT
1 AAAAATAATAAATTTT
29152161 AAAAATAA
1 AAAAATAA
29152169 CCAAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 10 0.32
15 6 0.19
16 15 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAAATAATAAATTTT
Found at i:29152165 original size:15 final size:15
Alignment explanation
Indices: 29152145--29152179 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
29152135 TATAAAAATT
*
29152145 TTAAAAATAA-TAAA
1 TTAAAAATAACCAAA
29152159 TTAAAAATAACCAAA
1 TTAAAAATAACCAAA
29152174 TTAAAA
1 TTAAAA
29152180 TAGTCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TTAAAAATAACCAAA
Found at i:29154723 original size:29 final size:29
Alignment explanation
Indices: 29154690--29154762 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
29154680 AAATTGCATT
*
29154690 ATTATATTAATTATGTTAT-AAAAATAATA
1 ATTATATTAATTAT-ATATGAAAAATAATA
**
29154719 ATTATATTAATTATATATGTTAAATAATA
1 ATTATATTAATTATATATGAAAAATAATA
*
29154748 ATTATA-TATTTATAT
1 ATTATATTAATTATAT
29154763 TAAATCACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 11 0.28
29 28 0.72
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTATATTAATTATATATGAAAAATAATA
Found at i:29155329 original size:12 final size:12
Alignment explanation
Indices: 29155314--29155347 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29155304 CTTAGGCTTT
29155314 ATAATAATAACA
1 ATAATAATAACA
* *
29155326 ATAACAACAACA
1 ATAATAATAACA
29155338 ATAATAATAA
1 ATAATAATAA
29155348 GAGTACTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:29156767 original size:27 final size:27
Alignment explanation
Indices: 29156712--29156802 Score: 157
Period size: 27 Copynumber: 3.4 Consensus size: 27
29156702 AATAAAAATA
*
29156712 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAA-ATTTTTTTATTT
29156740 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
29156767 ACCAAAATATTAT-AATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
29156793 ACCAAAATAT
1 ACCAAAATAT
29156803 ACCAAAAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 23 0.37
27 24 0.39
28 15 0.24
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:29157144 original size:19 final size:19
Alignment explanation
Indices: 29157120--29157186 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 19
29157110 ATAGATAAAA
*
29157120 TATTTTAATTTAACAACTC
1 TATTTTAATTTAATAACTC
* *
29157139 TATTTTAATGTAATAA-AC
1 TATTTTAATTTAATAACTC
* *
29157157 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAACTC
29157176 TATTTTAATTT
1 TATTTTAATTT
29157187 TAAAAAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (19 bp):
TATTTTAATTTAATAACTC
Found at i:29157365 original size:82 final size:82
Alignment explanation
Indices: 29157270--29157434 Score: 330
Period size: 82 Copynumber: 2.0 Consensus size: 82
29157260 AAAAGGAAAA
29157270 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
29157335 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
29157352 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
29157417 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
29157434 A
1 A
29157435 TTTTAATTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (82 bp):
AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:29157542 original size:18 final size:19
Alignment explanation
Indices: 29157503--29157561 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
29157493 ATTTTATATT
29157503 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
29157522 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
29157540 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
29157559 TTA
1 TTA
29157562 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:29158272 original size:27 final size:27
Alignment explanation
Indices: 29158242--29158305 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
29158232 TTTTTTTGGT
*
29158242 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
29158269 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
29158296 ATATTTTGGT
1 ATATTTTGGT
29158306 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:29159859 original size:54 final size:54
Alignment explanation
Indices: 29159742--29159865 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 54
29159732 AAGCTTTAAG
* * * * *
29159742 TCAGTGAGTTACACGGCCTAGCACACGGCCTGGCACATGGGCATGTGTGACAAC
1 TCAGTGAGTTACACGACCTAGCACACGACCTGGAACACGGGCATGTGGGACAAC
* * * *
29159796 TCAGAGAGTTACACGACCTAGCACACGACCTGGAACACGGGCTTGTGGGGCTAC
1 TCAGTGAGTTACACGACCTAGCACACGACCTGGAACACGGGCATGTGGGACAAC
*
29159850 TTAGTGAGTTACACGA
1 TCAGTGAGTTACACGA
29159866 GTGAGGACAC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (54 bp):
TCAGTGAGTTACACGACCTAGCACACGACCTGGAACACGGGCATGTGGGACAAC
Found at i:29163530 original size:16 final size:16
Alignment explanation
Indices: 29163491--29163530 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29163481 CTTACTCCTT
*
29163491 CCCAATTGAAACCCAG
1 CCCAATTTAAACCCAG
*
29163507 CCCAATTTAAATCCAG
1 CCCAATTTAAACCCAG
29163523 CCCAATTT
1 CCCAATTT
29163531 TTTCTTAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (16 bp):
CCCAATTTAAACCCAG
Found at i:29164683 original size:9 final size:9
Alignment explanation
Indices: 29164665--29164745 Score: 90
Period size: 9 Copynumber: 8.6 Consensus size: 9
29164655 TGTAGTGATT
*
29164665 TAATTTGGG
1 TAATTCGGG
29164674 TAATTCGGG
1 TAATTCGGG
*
29164683 TAATTTGGG
1 TAATTCGGG
29164692 TAATTTTCGGG
1 TAA--TTCGGG
29164703 TAATTCGGG
1 TAATTCGGG
* *
29164712 TAATTTGAG
1 TAATTCGGG
29164721 TAATTTTCGGG
1 TAA--TTCGGG
29164732 TAATTCGGG
1 TAATTCGGG
29164741 TAATT
1 TAATT
29164746 TTTAACAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 46 0.75
11 15 0.25
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.42
Consensus pattern (9 bp):
TAATTCGGG
Found at i:29164702 original size:20 final size:18
Alignment explanation
Indices: 29164665--29164746 Score: 101
Period size: 20 Copynumber: 4.3 Consensus size: 18
29164655 TGTAGTGATT
29164665 TAATTTGGGTAATTCGGG
1 TAATTTGGGTAATTCGGG
29164683 TAATTTGGGTAATTTTCGGG
1 TAATTTGGGTAA--TTCGGG
* * *
29164703 TAATTCGGGTAATTTGAG
1 TAATTTGGGTAATTCGGG
29164721 TAATTTTCGGGTAATTCGGG
1 TAA-TTT-GGGTAATTCGGG
29164741 TAATTT
1 TAATTT
29164747 TTAACAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
18 19 0.35
19 5 0.09
20 30 0.56
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (18 bp):
TAATTTGGGTAATTCGGG
Found at i:29164705 original size:29 final size:29
Alignment explanation
Indices: 29164671--29164746 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
29164661 GATTTAATTT
*
29164671 GGGTAATTCGGGTAATTTGGGTAATTTTC
1 GGGTAATTCGGGTAATTTGAGTAATTTTC
29164700 GGGTAATTCGGGTAATTTGAGTAATTTTC
1 GGGTAATTCGGGTAATTTGAGTAATTTTC
29164729 GGGTAATTCGGGTAATTT
1 GGGTAATTCGGGTAATTT
29164747 TTAACAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (29 bp):
GGGTAATTCGGGTAATTTGAGTAATTTTC
Found at i:29164788 original size:9 final size:9
Alignment explanation
Indices: 29164774--29164800 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
29164764 ACACATACTT
29164774 TTCGGTTAA
1 TTCGGTTAA
29164783 TTCGGTTAA
1 TTCGGTTAA
29164792 TTCGGTTAA
1 TTCGGTTAA
29164801 CGACCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:29169251 original size:21 final size:21
Alignment explanation
Indices: 29169225--29169431 Score: 132
Period size: 21 Copynumber: 9.9 Consensus size: 21
29169215 GAACAGAGTA
* * *
29169225 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTGAACAGAAACT
* * * *
29169246 CATAAGGGTTGAACGGAAGCT
1 CATAAGAGCTGAACAGAAACT
29169267 CATAAGAGCTGAAC-GAAAGCT
1 CATAAGAGCTGAACAGAAA-CT
** *
29169288 CATAAGAGCTGAATGGAAGCT
1 CATAAGAGCTGAACAGAAACT
*
29169309 CATAAGAGCTGAACAGAAACC
1 CATAAGAGCTGAACAGAAACT
* * * *
29169330 CATAAGGGTTAAACAGAAGCT
1 CATAAGAGCTGAACAGAAACT
* *
29169351 CGTAAGAGCTGAACAGAAACC
1 CATAAGAGCTGAACAGAAACT
* * * * * *
29169372 CATCAGGGTTAAATAGAAGCT
1 CATAAGAGCTGAACAGAAACT
29169393 CA-ATAGAGCTGAAC-GAAAACT
1 CATA-AGAGCTGAACAG-AAACT
* * *
29169414 CATATGAGTTAAACAGAA
1 CATAAGAGCTGAACAGAA
29169432 GCTTGTGAGA
Statistics
Matches: 137, Mismatches: 43, Indels: 12
0.71 0.22 0.06
Matches are distributed among these distances:
20 4 0.03
21 128 0.93
22 5 0.04
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
CATAAGAGCTGAACAGAAACT
Found at i:29169391 original size:84 final size:84
Alignment explanation
Indices: 29169225--29169452 Score: 255
Period size: 84 Copynumber: 2.7 Consensus size: 84
29169215 GAACAGAGTA
* * * * * *
29169225 CATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTGAACGAAAGCTCA
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACGAAAGCCCA
* *
29169290 TAAGAGCTGAATGGAAGCT
66 TAAGAGCTAAATAGAAGCT
29169309 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACAGAAA-CCC
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAAC-GAAAGCCC
* * *
29169373 ATCAGGGTTAAATAGAAGCT
65 ATAAGAGCTAAATAGAAGCT
* * * * * *
29169393 CA-ATAGAGCTGAAC-GAAAACTCATATGAGTTAAACAGAAGCTTGTGAGAGCTAAACGAAA
1 CATA-AGAGCTGAACAG-AAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACGAAA
29169453 AGTAAACATG
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
83 6 0.05
84 114 0.92
85 4 0.03
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (84 bp):
CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCGTAAGAGCTGAACGAAAGCCCA
TAAGAGCTAAATAGAAGCT
Found at i:29169425 original size:42 final size:42
Alignment explanation
Indices: 29169225--29169434 Score: 219
Period size: 42 Copynumber: 5.0 Consensus size: 42
29169215 GAACAGAGTA
* * * * *
29169225 CATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
* * * **
29169267 CATAAGAGCTGAAC-GAAAGCTCATAAGAGCTGAATGGAAGCT
1 CATAAGAGCTGAACAGAAA-CCCATAAGAGTTAAACAGAAGCT
*
29169309 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
* * * *
29169351 CGTAAGAGCTGAACAGAAACCCATCAGGGTTAAATAGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
* *
29169393 CA-ATAGAGCTGAAC-GAAAACTCATATGAGTTAAACAGAAGCT
1 CATA-AGAGCTGAACAG-AAACCCATAAGAGTTAAACAGAAGCT
29169435 TGTGAGAGCT
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 6 0.04
42 133 0.93
43 4 0.03
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (42 bp):
CATAAGAGCTGAACAGAAACCCATAAGAGTTAAACAGAAGCT
Found at i:29171612 original size:24 final size:25
Alignment explanation
Indices: 29171558--29171614 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
29171548 ATAAATTATT
* * *
29171558 AATATTAATTACTTAGAAATATTTA
1 AATATTAATTAATTACAAATATTAA
*
29171583 AA-ATTAATTAATT-CATATATTAA
1 AATATTAATTAATTACAAATATTAA
29171606 AATATTAAT
1 AATATTAAT
29171615 AATAAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.33
24 16 0.59
25 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AATATTAATTAATTACAAATATTAA
Found at i:29176673 original size:41 final size:41
Alignment explanation
Indices: 29176607--29176697 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
29176597 CTTACCTTTT
* *
29176607 GGGGCTTTAGCGGCGATTTTAAAAAAGTGTCGCTAATGCTC
1 GGGGCTTTAGCGGCGATTTTAAAAAAGCGCCGCTAATGCTC
* * *
29176648 GGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTG
1 GGGGCTTTAGCGGCGATTTTAAAAAAGCGCCGCTAATGCTC
*
29176689 GGGGATTTA
1 GGGGCTTTA
29176698 AAAGCACCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (41 bp):
GGGGCTTTAGCGGCGATTTTAAAAAAGCGCCGCTAATGCTC
Found at i:29176708 original size:27 final size:27
Alignment explanation
Indices: 29176670--29176724 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
29176660 GCGTTTTTGA
*
29176670 AAAAGCGCCGCTAATGCTGGGGGATTT
1 AAAAGCACCGCTAATGCTGGGGGATTT
*
29176697 AAAAGCACCGCTAATGCTGGGGGCTTT
1 AAAAGCACCGCTAATGCTGGGGGATTT
29176724 A
1 A
29176725 GCGGCGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (27 bp):
AAAAGCACCGCTAATGCTGGGGGATTT
Found at i:29177424 original size:15 final size:14
Alignment explanation
Indices: 29177407--29177455 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
29177397 CATATTTTAA
*
29177407 GGTTTAGGGAGTAT
1 GGTTTAGGGATTAT
*
29177421 AGGTGTAGGGATTAT
1 -GGTTTAGGGATTAT
*
29177436 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
29177450 GGTTTA
1 GGTTTA
29177456 ATGGTGGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:29177491 original size:15 final size:15
Alignment explanation
Indices: 29177471--29177500 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29177461 GGAGATTTAA
29177471 AGTTTAGGGGTTAGG
1 AGTTTAGGGGTTAGG
*
29177486 AGTTTAGTGGTTAGG
1 AGTTTAGGGGTTAGG
29177501 CATATTATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (15 bp):
AGTTTAGGGGTTAGG
Found at i:29177586 original size:289 final size:289
Alignment explanation
Indices: 29177262--29177917 Score: 903
Period size: 289 Copynumber: 2.3 Consensus size: 289
29177252 GATTTTGGGT
* * *
29177262 GTTTAGATTAAAT-TTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAACAGATAA
1 GTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTATTATATAATTGTAAAAGAGATAA
* * *
29177326 TAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTTAAGATTTAAAGCCGGTTTA
66 TAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAAGCAGGTTTA
* * *
29177391 GGAGTTCATATTTTAAGGTTTAGGGAGTATAGG-TGTAGGGATTATGGATTAGGGATTATGGTTT
131 AGAGTGCATATTTTAAGGTTTAAGGAGTAT-GGATGTAGGGATTATGGATTAGGGATTATGGTTT
* * * *
29177455 AATGG-TGGAGATTTAAAGTTTAGGGGTTAGGAGTT-TAGTGGTTAGGCATATTATGGG-TTAAA
195 AAGGGCTAG-GATTTAAAGTTTA-GGGTTAGGAGTTATAGTAGTTAAG-A-ATTA-GGGATTAAA
** * * *
29177517 AG-TCAGGGATT-TGGGGTCGGGTCAGGGTTTTGG
255 AGTTCAGGGATTCAAGGGTCGAGTCAAGGTTTTGA
29177550 GTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTATTATATAATTGTAAAAGAGATAA
1 GTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTATTATATAATTGTAAAAGAGATAA
* * *
29177615 TAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATTATTAATTTAAGATTTAAGGCATGTTTA
66 TAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAAGCAGGTTTA
*
29177680 AGAGTGCATATTTTAAGGTTTAAGGAGTATGGATTTAGGGATTATGGATTAGGGATTATGGTTTA
131 AGAGTGCATATTTTAAGGTTTAAGGAGTATGGATGTAGGGATTATGGATTAGGGATTATGGTTTA
* * * *
29177745 AGGGCTAGGATTTAAGGTTTAGGGTTAGGGGTTAGACGATAGTAGTTAAGAGTTAGGGATTCAAA
196 AGGGCTAGGATTTAAAGTTTAGGGTTAGGAGTT-----ATAGTAGTTAAGAATTAGGGATTAAAA
* *
29177810 GTTTAGGGATTCAAGGGTCGAGTTAAGGTTTTGA
256 GTTCAGGGATTCAAGGGTCGAGTCAAGGTTTTGA
29177844 GTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTATTATATAATTGTAAAAGAGATA
1 GTTTAGATTAATTA-TTTTTTAATTTATATTTTAAATATGTTATTATATAATTGTAAAAGAGATA
29177909 ATAATAAAT
65 ATAATAAAT
29177918 CAAATATATT
Statistics
Matches: 327, Mismatches: 28, Indels: 19
0.87 0.07 0.05
Matches are distributed among these distances:
288 25 0.08
289 181 0.55
290 2 0.01
291 3 0.01
292 9 0.03
293 9 0.03
294 39 0.12
295 59 0.18
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.42
Consensus pattern (289 bp):
GTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTATTATATAATTGTAAAAGAGATAA
TAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAAGCAGGTTTA
AGAGTGCATATTTTAAGGTTTAAGGAGTATGGATGTAGGGATTATGGATTAGGGATTATGGTTTA
AGGGCTAGGATTTAAAGTTTAGGGTTAGGAGTTATAGTAGTTAAGAATTAGGGATTAAAAGTTCA
GGGATTCAAGGGTCGAGTCAAGGTTTTGA
Found at i:29177748 original size:15 final size:14
Alignment explanation
Indices: 29177696--29177744 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
29177686 CATATTTTAA
* *
29177696 GGTTTAAGGAGTAT
1 GGTTTAGGGATTAT
29177710 GGATTTAGGGATTAT
1 GG-TTTAGGGATTAT
*
29177725 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
29177739 GGTTTA
1 GGTTTA
29177745 AGGGCTAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.39
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:29177763 original size:21 final size:22
Alignment explanation
Indices: 29177691--29177774 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 22
29177681 GAGTGCATAT
*
29177691 TTTAAGGTTTAAGGAG-TATGGA
1 TTTAAGGTTTAAGG-GTTAGGGA
* * * *
29177713 TTTAGGGATTATGGATTAGGGA
1 TTTAAGGTTTAAGGGTTAGGGA
* *
29177735 -TTATGGTTTAAGGGCTA-GGA
1 TTTAAGGTTTAAGGGTTAGGGA
29177755 TTTAAGGTTT-AGGGTTAGGG
1 TTTAAGGTTTAAGGGTTAGGG
29177775 GTTAGACGAT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 9 0.19
21 22 0.47
22 16 0.34
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.37
Consensus pattern (22 bp):
TTTAAGGTTTAAGGGTTAGGGA
Found at i:29182106 original size:43 final size:43
Alignment explanation
Indices: 29182021--29182111 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
29182011 CTTTGAGTTC
* * * * *
29182021 ATTA-CAAGATTTCCTTGATTAAGTAAGTGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATGATATCTTTT
* *
29182063 ATTACCAAGATTTACTTGATTAAGAAAATGCATGGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATGATATCTTTT
29182106 ATTACC
1 ATTACC
29182112 TTGCAATGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 4 0.10
43 37 0.90
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATGATATCTTTT
Found at i:29182524 original size:43 final size:43
Alignment explanation
Indices: 29182476--29182766 Score: 291
Period size: 43 Copynumber: 6.8 Consensus size: 43
29182466 AGGTTATGTT
* ** * * *
29182476 TTTAGCGGCGTTTTTGCGAGAAGCGCTGCTAAAGGCCACGATC
1 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
29182519 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
1 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
* * * *
29182562 TTTAGCGGTGTTTGTGATAAAAGTGCTGCGAAAGGTCAAGATA
1 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
* *
29182605 TTTAGCGGCGTTTGTGATAAAAGTGCCGCTAAAGGTCATA-ATC
1 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCA-AGATC
* * * * * *
29182648 TTTAGCGGTGTTCGTGAGAAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
* * ** * * * * *
29182691 TTTAGCAGCGTTCGTGGGAAAAGCACCGCTGAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
*
29182734 TTTAGCGGCGTTT-TCGA-AAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGT-GATAAAAGCGCTGCTAAAG
29182767 ATCATGTTCT
Statistics
Matches: 215, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
42 15 0.07
43 199 0.93
44 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCAAGATC
Found at i:29191006 original size:20 final size:20
Alignment explanation
Indices: 29190962--29190999 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29190952 ATAGATTGCA
*
29190962 GTTAAAAATTTAATAAATAG
1 GTTAAAAAGTTAATAAATAG
29190982 GTTAAAAAGTTAATAAAT
1 GTTAAAAAGTTAATAAAT
29191000 TTTTTAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (20 bp):
GTTAAAAAGTTAATAAATAG
Done.