Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 46 of 378
Found at i:11440069 original size:16 final size:17
Alignment explanation
Indices: 11440034--11440076 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
11440024 AATCCTTTTA
11440034 ATTATTT-TTTTATAAT
1 ATTATTTATTTTATAAT
11440050 -TTATTTATTTTA-AAT
1 ATTATTTATTTTATAAT
11440065 ATTATTTATTTT
1 ATTATTTATTTT
11440077 TACTATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTATTTATTTTATAAT
Found at i:11440188 original size:22 final size:19
Alignment explanation
Indices: 11440153--11440251 Score: 76
Period size: 21 Copynumber: 4.9 Consensus size: 19
11440143 TATCATTTAT
11440153 ATTTTATTATATATTATATC
1 ATTTTATTATATATTAT-TC
11440173 ATTTTACTATATATATTATTC
1 ATTTTA-T-TATATATTATTC
* *
11440194 ATTATATTAT-TTTTATTC
1 ATTTTATTATATATTATTC
11440212 TATTATATATTATATTATT-TTGC
1 -ATT-T-TATTATA-TATTATT-C
* *
11440235 TTTTTATTATTTATTAT
1 ATTTTATTATATATTAT
11440252 GTATAATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
18 7 0.11
19 10 0.16
20 14 0.22
21 15 0.23
22 14 0.22
23 4 0.06
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (19 bp):
ATTTTATTATATATTATTC
Found at i:11440197 original size:29 final size:32
Alignment explanation
Indices: 11440157--11440226 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 32
11440147 ATTTATATTT
11440157 TATTATATATTATATCA-TTTTA-CTA-TATA
1 TATTATATATTATATCATTTTTATCTATTATA
*
11440186 TATTAT-TCATTATATTATTTTTATTCTATTATA
1 TATTATAT-ATTATATCATTTTTA-TCTATTATA
11440219 TATTATAT
1 TATTATAT
11440227 TATTTTGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 1 0.03
29 14 0.41
30 5 0.15
32 3 0.09
33 10 0.29
34 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTATATATTATATCATTTTTATCTATTATA
Found at i:11440222 original size:12 final size:12
Alignment explanation
Indices: 11440115--11440229 Score: 58
Period size: 12 Copynumber: 10.2 Consensus size: 12
11440105 AAAATTATTA
11440115 TATATATTAT-T
1 TATATATTATAT
11440126 T-T-TATT-TAT
1 TATATATTATAT
11440135 GTATA-ATTTATCAT
1 -TATATA-TTAT-AT
*
11440149 T-TATATTTTAT
1 TATATATTATAT
11440160 TATATATTATAT
1 TATATATTATAT
*
11440172 CAT-T-TTACTA-
1 TATATATTA-TAT
11440182 TATATATTAT-T
1 TATATATTATAT
*
11440193 CATTATATTAT-T
1 TA-TATATTATAT
*
11440205 T-T-TATTCTAT
1 TATATATTATAT
11440215 TATATATTATAT
1 TATATATTATAT
11440227 TAT
1 TAT
11440230 TTTGCTTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 33
0.66 0.07 0.28
Matches are distributed among these distances:
8 1 0.01
9 10 0.13
10 10 0.13
11 13 0.16
12 40 0.51
13 3 0.04
14 2 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (12 bp):
TATATATTATAT
Found at i:11440228 original size:26 final size:25
Alignment explanation
Indices: 11440108--11440251 Score: 116
Period size: 26 Copynumber: 5.5 Consensus size: 25
11440098 ATGTAAAAAA
11440108 ATTAT-TATATATATTATTTTTATTT
1 ATTATATAT-TATATTATTTTTATTT
* *
11440133 ATGTATA-ATT-TATCATTTATATTTT
1 AT-TATATATTATATTATTTTTA-TTT
*
11440158 ATTATATATTATATCATTTTACTATATAT
1 ATTATATATTATATTATTTT--TAT-T-T
11440187 ATTAT-TCATTATATTATTTTTATTCT
1 ATTATAT-ATTATATTATTTTTATT-T
*
11440213 ATTATATATTATATTATTTTGCTTTTT
1 ATTATATATTATATTATTTT--TATTT
*
11440240 ATTATTTATTAT
1 ATTATATATTAT
11440252 GTATAATTTT
Statistics
Matches: 99, Mismatches: 7, Indels: 24
0.76 0.05 0.18
Matches are distributed among these distances:
24 13 0.13
25 11 0.11
26 33 0.33
27 17 0.17
28 7 0.07
29 18 0.18
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (25 bp):
ATTATATATTATATTATTTTTATTT
Found at i:11440247 original size:7 final size:7
Alignment explanation
Indices: 11440108--11440251 Score: 50
Period size: 7 Copynumber: 19.7 Consensus size: 7
11440098 ATGTAAAAAA
11440108 ATTA-TT
1 ATTATTT
11440114 ATATATATT
1 AT-TAT-TT
11440123 ATT-TTT
1 ATTATTT
*
11440129 ATTTATGT
1 A-TTATTT
*
11440137 ATAATTT
1 ATTATTT
*
11440144 ATCATTT
1 ATTATTT
11440151 A-TATTTT
1 ATTA-TTT
*
11440158 ATTATAT
1 ATTATTT
*
11440165 ATTATATC
1 ATTAT-TT
11440173 ATT-TTACT
1 ATTATT--T
11440181 ATATATATT
1 AT-TAT-TT
11440190 ATTCATTAT
1 ATT-ATT-T
11440199 ATTATTT
1 ATTATTT
11440206 -TTATTCT
1 ATTATT-T
*
11440213 ATTATAT
1 ATTATTT
11440220 ATTATATT
1 ATTAT-TT
*
11440228 ATT-TTG
1 ATTATTT
*
11440234 CTT-TTT
1 ATTATTT
11440240 ATTATTT
1 ATTATTT
11440247 ATTAT
1 ATTAT
11440252 GTATAATTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 37
0.67 0.10 0.24
Matches are distributed among these distances:
6 19 0.18
7 45 0.43
8 24 0.23
9 14 0.13
10 1 0.01
11 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (7 bp):
ATTATTT
Found at i:11440261 original size:55 final size:54
Alignment explanation
Indices: 11440110--11440261 Score: 139
Period size: 55 Copynumber: 2.8 Consensus size: 54
11440100 GTAAAAAAAT
* * * * * *
11440110 TATTATAT-ATATTA-TTTTTATTTATGTATAATTTATCATTTATATTTTATTATA
1 TATTATATCATTTTACTTTTTA-TTATTTATTA-TTATAATTTTTATTCTATTATA
* * *
11440164 TATTATATCATTTTACTATATATATTATTCATTA-TATTATTTTTATTCTATTATA
1 TATTATATCATTTTACT-T-TTTATTATTTATTATTATAATTTTTATTCTATTATA
* *
11440219 TATTATATTATTTTGCTTTTTATTATTTATTATGTATAATTTT
1 TATTATATCATTTTACTTTTTATTATTTATTAT-TATAATTTT
11440262 AAAAATTCTA
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
53 12 0.15
54 9 0.11
55 46 0.58
56 1 0.01
57 8 0.10
58 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (54 bp):
TATTATATCATTTTACTTTTTATTATTTATTATTATAATTTTTATTCTATTATA
Found at i:11440519 original size:14 final size:14
Alignment explanation
Indices: 11440500--11440535 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11440490 ACCACATTTA
11440500 TTGTATTTAGTTTT
1 TTGTATTTAGTTTT
*
11440514 TTGTATTTATTTTT
1 TTGTATTTAGTTTT
*
11440528 TTATATTT
1 TTGTATTT
11440536 TATATGTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (14 bp):
TTGTATTTAGTTTT
Found at i:11440528 original size:13 final size:13
Alignment explanation
Indices: 11440495--11440528 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
11440485 TTTTTACCAC
*
11440495 ATTTATTGTATTT
1 ATTTTTTGTATTT
11440508 AGTTTTTTGTATTT
1 A-TTTTTTGTATTT
11440522 ATTTTTT
1 ATTTTTT
11440529 TATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (13 bp):
ATTTTTTGTATTT
Found at i:11447714 original size:12 final size:12
Alignment explanation
Indices: 11447697--11447728 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11447687 TTTTAAAGAT
11447697 TTTTCAGAGTAA
1 TTTTCAGAGTAA
*
11447709 TTTTCATAGTAA
1 TTTTCAGAGTAA
11447721 TTTTCAGA
1 TTTTCAGA
11447729 ACACTCTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (12 bp):
TTTTCAGAGTAA
Found at i:11452636 original size:90 final size:90
Alignment explanation
Indices: 11452372--11452964 Score: 910
Period size: 90 Copynumber: 6.7 Consensus size: 90
11452362 ATCGAGGAAG
* *
11452372 CAGATTTGGTGTTTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
* * * *
11452437 TTACATCAAATCAGTTTGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * * *
11452462 CAGATTTAGCGTCTCTG---TA-ACGGGGAACAAATCAAAGATAGTAGATTTGACA--CGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
*
11452521 TTACATCGAAGCATATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * *
11452546 CAGATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAATAGATCTGATATTCATGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
*
11452611 TTACATCGAAGCAGATCAAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* *
11452636 CAGATTTGGCGTCTCTATATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGC
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
* *
11452701 TTACATTGAAGCAAATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
*
11452726 CAGATTTGGTGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
* *
11452791 TTGCATCGAAGTAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
11452816 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
11452881 TTACATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* *
11452906 CAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCAAAGATAGTAGATCTGACATTC
1 CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTC
11452965 ATCTCTGTAT
Statistics
Matches: 453, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
84 43 0.09
86 29 0.06
87 4 0.01
88 26 0.06
90 351 0.77
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (90 bp):
CAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGT
TTACATCGAAGCAGATCGAAGATGA
Found at i:11452975 original size:49 final size:49
Alignment explanation
Indices: 11452917--11453013 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
11452907 AGATTTGGCG
*
11452917 TCTCTGTATTAGACGGGGAGTAGATCAAAGATAGTAGATCTGACATTCA
1 TCTCTGTATTAGACGGGGAGCAGATCAAAGATAGTAGATCTGACATTCA
*
11452966 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTC
1 TCTCTGTATTAGACGGGGAGCAGATCAAAGATAGTAGATCTGACATTC
11453014 GTGTGTTTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (49 bp):
TCTCTGTATTAGACGGGGAGCAGATCAAAGATAGTAGATCTGACATTCA
Found at i:11452998 original size:229 final size:229
Alignment explanation
Indices: 11452737--11453193 Score: 824
Period size: 229 Copynumber: 2.0 Consensus size: 229
11452727 AGATTTGGTG
*
11452737 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTGCATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
* * *
11452802 TAGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATC
66 CAGATCGAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
*
11452867 TGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACG
131 TGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
*
11452932 GGGAGTAGATCAAAGATAGTAGATCTGACATTCA
196 GGGAGCAGATCAAAGATAGTAGATCTGACATTCA
11452966 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
*
11453031 CAGATCGAAGATGACAGATTTGGTGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
66 CAGATCGAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
* *
11453096 TGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGATAAATTTGGCGTCTCTGTATTAGACG
131 TGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
*
11453161 GGGAGCAGATCGAAGATAGTAGATCTGACATTC
196 GGGAGCAGATCAAAGATAGTAGATCTGACATTC
11453194 GTGTGTTTAC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
229 218 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (229 bp):
TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
CAGATCGAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
TGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
GGGAGCAGATCAAAGATAGTAGATCTGACATTCA
Found at i:11453081 original size:90 final size:90
Alignment explanation
Indices: 11452966--11453510 Score: 798
Period size: 90 Copynumber: 6.1 Consensus size: 90
11452956 CTGACATTCA
11452966 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
*
11453031 CAGATCGAAGATGACAGATTTGGTG
66 CAGATCGAAGATGACAGATTTGGCG
* *
11453056 TCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
* * *
11453121 TAGATCGAAGATGATAAATTTGGCG
66 CAGATCGAAGATGACAGATTTGGCG
11453146 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
* * *
11453211 TAGATCGAAGATGATAAATTTGGCG
66 CAGATCGAAGATGACAGATTTGGCG
* * * *
11453236 TCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTCGTGTGTTTACATCAAAT
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
* * *
11453301 CAAATCAAAGATGACAGATTTGGTG
66 CAGATCGAAGATGACAGATTTGGCG
* *
11453326 TCTCTGTATTAGACGGGGAACAGATCAAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
*
11453391 TAGATCGAAGATGAC-----TGGCG
66 CAGATCGAAGATGACAGATTTGGCG
* * *
11453411 TCTCTGTATTAGACGGGGAGCA-AGTCGAAGATAGCAGATCTAACATTTGTGTGTTTACATCGAA
1 TCTCTGTATTAGACGGGGAGCAGA-TCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAA
*
11453475 GCAGATCAAAGAT-AGCAGATTTGGCG
65 GCAGATCGAAGATGA-CAGATTTGGCG
* *
11453501 TATTTGTATT
1 TCTCTGTATT
11453511 TGATAAGGAG
Statistics
Matches: 411, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
84 2 0.00
85 73 0.18
90 336 0.82
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (90 bp):
TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
CAGATCGAAGATGACAGATTTGGCG
Found at i:11453234 original size:319 final size:319
Alignment explanation
Indices: 11452647--11453283 Score: 1130
Period size: 319 Copynumber: 2.0 Consensus size: 319
11452637 AGATTTGGCG
*
11452647 TCTCTATATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGCTTACATTGAAG
1 TCTCTATATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGCTTACATCGAAG
* *
11452712 CAAATCGAAGATGACAGATTTGGTGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATC
66 CAAATCGAAGATGACAGATTTGGTGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
* *
11452777 TGACATTCGTGTGTTTGCATCGAAGTAGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACG
131 TGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
11452842 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGAC
196 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGAC
* * * *
11452907 AGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCAAAGATAGTAGATCTGACATTCA
261 AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCAAAGATAGTAGATCTAACATTCA
* *
11452966 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTATATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGCTTACATCGAAG
*
11453031 CAGATCGAAGATGACAGATTTGGTGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
66 CAAATCGAAGATGACAGATTTGGTGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
*
11453096 TGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGATAAATTTGGCGTCTCTGTATTAGACG
131 TGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
* *
11453161 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGAT
196 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGAC
*
11453226 AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTC
261 AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCAAAGATAGTAGATCTAACATTC
11453284 GTGTGTTTAC
Statistics
Matches: 302, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
319 302 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (319 bp):
TCTCTATATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGCTTACATCGAAG
CAAATCGAAGATGACAGATTTGGTGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
TGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGAC
AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCAAAGATAGTAGATCTAACATTCA
Found at i:11453316 original size:409 final size:409
Alignment explanation
Indices: 11452557--11453373 Score: 1400
Period size: 409 Copynumber: 2.0 Consensus size: 409
11452547 AGATTTGGCG
*
11452557 TCTCTGTATTAGACAGGGAGCAGATCGAAGATAATAGATCTGATATTCATGTGTTTACATCGAAG
1 TCTCTGTATTAGACAGGGAGCAGATCGAAGATAATAGATCTGACATTCATGTGTTTACATCGAAG
*
11452622 CAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAGCAGATCGAAGATAGTAGATC
66 CAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
* * *
11452687 TGACATTCGTGTGCTTACATTGAAGCAAATCGAAGATGACAGATTTGGTGTCTCTGTATTAGACG
131 TGACATTCGTGTGCTTACATCGAAGCAAATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
*
11452752 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTGCATCGAAGTAGATCGAAGATGAC
196 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGAC
* * *
11452817 AGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTT
261 AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTCGTGTGTT
* * * **
11452882 TACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGTAGATCAAAG
326 TACATCAAAGCAAATCAAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAG
11452947 ATAGTAGATCTGACATTCA
391 ATAGTAGATCTGACATTCA
* * *
11452966 TCTCTGTATTAGACGGGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAG
1 TCTCTGTATTAGACAGGGAGCAGATCGAAGATAATAGATCTGACATTCATGTGTTTACATCGAAG
* *
11453031 CAGATCGAAGATGACAGATTTGGTGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
66 CAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
* * * *
11453096 TGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGATAAATTTGGCGTCTCTGTATTAGACG
131 TGACATTCGTGTGCTTACATCGAAGCAAATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
*
11453161 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGAT
196 GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGAC
11453226 AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTCGTGTGTT
261 AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTCGTGTGTT
* *
11453291 TACATCAAATCAAATCAAAGATGACAGATTTGGTGTCTCTGTATTAGACGGGGAACAGATCAAAG
326 TACATCAAAGCAAATCAAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAG
11453356 ATAGTAGATCTGACATTC
391 ATAGTAGATCTGACATTC
11453374 GTGTGTTTAC
Statistics
Matches: 382, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
409 382 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (409 bp):
TCTCTGTATTAGACAGGGAGCAGATCGAAGATAATAGATCTGACATTCATGTGTTTACATCGAAG
CAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACGGGGAACAGATCGAAGATAGTAGATC
TGACATTCGTGTGCTTACATCGAAGCAAATCGAAGATGACAAATTTGGCGTCTCTGTATTAGACG
GGGAGCAGATCGAAGATAGTAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGAC
AAATTTGGCGTCTCTGTATTAGACAGGGAGCAGATCGAAGATAGTAGATCTAACATTCGTGTGTT
TACATCAAAGCAAATCAAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAACAGATCAAAG
ATAGTAGATCTGACATTCA
Found at i:11455093 original size:12 final size:12
Alignment explanation
Indices: 11455078--11455221 Score: 97
Period size: 12 Copynumber: 12.0 Consensus size: 12
11455068 TATTTAAAAA
11455078 ATTATTATATAT
1 ATTATTATATAT
* *
11455090 ATTATTTTTATTT
1 ATTA-TTATATAT
11455103 ATGTATTATTTATCAT
1 AT-TATTA--TAT-AT
11455119 ATTATT-TATAT
1 ATTATTATATAT
*
11455130 TTTATTATATAT
1 ATTATTATATAT
*
11455142 TTTATT-TATAT
1 ATTATTATATAT
11455153 ATT-TTAT-TAT
1 ATTATTATATAT
11455163 A-TATTATATCAT
1 ATTATTATAT-AT
* *
11455175 TTTACTATATAT
1 ATTATTATATAT
11455187 ATTATTCAT-TAT
1 ATTATT-ATATAT
*
11455199 ATTATT-TTTAT
1 ATTATTATATAT
11455210 -TCTATTATATAT
1 AT-TATTATATAT
11455222 TATATTATTT
Statistics
Matches: 106, Mismatches: 11, Indels: 30
0.72 0.07 0.20
Matches are distributed among these distances:
9 1 0.01
10 12 0.11
11 23 0.22
12 39 0.37
13 19 0.18
14 2 0.02
15 7 0.07
16 3 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:11455114 original size:15 final size:14
Alignment explanation
Indices: 11455078--11455248 Score: 93
Period size: 12 Copynumber: 12.6 Consensus size: 14
11455068 TATTTAAAAA
11455078 ATTATTATATATATT
1 ATTATT-TATATATT
*
11455093 ATT-TTTATTTATGT
1 ATTATTTATATAT-T
*
11455107 ATTATTTAT-CA-T
1 ATTATTTATATATT
11455119 ATTA-TT-TATATT
1 ATTATTTATATATT
11455131 -TTA-TTATATATT
1 ATTATTTATATATT
11455143 -TTATTTATATATT
1 ATTATTTATATATT
11455156 -TTA-TTATATATT
1 ATTATTTATATATT
11455168 ATATCATTTTACTATATAT
1 AT-T-A-TTTA-TATAT-T
*
11455187 ATTATTCATTATATT
1 ATTATTTA-TATATT
*
11455202 ATT-TTTAT-T-CT
1 ATTATTTATATATT
*
11455213 ATTATATATTATATT
1 ATTATTTA-TATATT
* *
11455228 ATT-TTTCT-TTTT
1 ATTATTTATATATT
11455240 ATTATTTAT
1 ATTATTTAT
11455249 TATGTATAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 38
0.71 0.07 0.22
Matches are distributed among these distances:
10 1 0.01
11 12 0.10
12 34 0.27
13 26 0.21
14 14 0.11
15 17 0.14
16 8 0.06
17 4 0.03
18 6 0.05
19 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (14 bp):
ATTATTTATATATT
Found at i:11455127 original size:23 final size:22
Alignment explanation
Indices: 11455029--11455229 Score: 100
Period size: 23 Copynumber: 9.2 Consensus size: 22
11455019 TTTTAAATAT
*
11455029 TTTATATATTATTTAT-TTTTA
1 TTTATATATTATTTATATATTA
* * *
11455050 CTATAAACATTATTTATATA-T-
1 -TTTATATATTATTTATATATTA
* * *
11455071 TTAAAAAATTA-TTATATA-TA
1 TTTATATATTATTTATATATTA
* *
11455091 -TTAT-TTTTATTTATGTATTA
1 TTTATATATTATTTATATATTA
*
11455111 TTTATCATATTATTTATATTTTA
1 TTTAT-ATATTATTTATATATTA
* *
11455134 TTATATATTTTATTTATATATTT
1 TT-TATATATTATTTATATATTA
*
11455157 TATTATATATTA--TATCATTTTA
1 T-TTATATATTATTTAT-ATATTA
* *
11455179 CTATATATATTATTCATTATATTA
1 -TTTATATATTATTTA-TATATTA
*
11455203 TTT-T-TATTCTATTATATATTA
1 TTTATATATTAT-TTATATATTA
11455224 TATTAT
1 T-TTAT
11455230 TTTTCTTTTT
Statistics
Matches: 135, Mismatches: 27, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
18 3 0.02
19 16 0.12
20 10 0.07
21 20 0.15
22 32 0.24
23 43 0.32
24 10 0.07
25 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATATATTATTTATATATTA
Found at i:11455167 original size:46 final size:45
Alignment explanation
Indices: 11455095--11455205 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 45
11455085 TATATATTAT
* *
11455095 TTTTATTTATGTATTATTTATCATATTATTTAT-ATTTTATTATATA
1 TTTTATTTATATATTATTTATCATATTA--TATCATTTTACTATATA
*
11455141 TTTTATTTATATATTTTATTAT-ATATTATATCATTTTACTATATA
1 TTTTATTTATATATTAT-TTATCATATTATATCATTTTACTATATA
* *
11455186 TATTATTCATTATATTATTT
1 TTTTATTTA-TATATTATTT
11455206 TTATTCTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
44 3 0.05
45 21 0.38
46 28 0.50
47 4 0.07
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.64
Consensus pattern (45 bp):
TTTTATTTATATATTATTTATCATATTATATCATTTTACTATATA
Found at i:11455168 original size:32 final size:33
Alignment explanation
Indices: 11455087--11455232 Score: 73
Period size: 31 Copynumber: 4.5 Consensus size: 33
11455077 AATTATTATA
* *
11455087 TATATTATT-TTTA-TTTATGTAT-TA-TTTAT
1 TATATTATTATATATTTTATTTATATATTTTAT
*
11455116 CATATTATT-TATATTTTA-TTATATATTTTAT
1 TATATTATTATATATTTTATTTATATATTTTAT
* *
11455147 T-TATATATT-T-TATTATATATTATATCATTTTAC
1 TATAT-TATTATATATTTTAT-TTATAT-ATTTTAT
* *
11455180 TATATATATTATTCATTATATTATTT-T-TATTCTAT
1 TATAT-TATTA-T-A-TATTTTATTTATATATTTTAT
11455215 TATA-TATTATATTATTTT
1 TATATTATTATA-TATTTT
11455233 TCTTTTTATT
Statistics
Matches: 93, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
29 14 0.15
30 15 0.16
31 17 0.18
32 7 0.08
33 12 0.13
34 8 0.09
35 9 0.10
36 2 0.02
37 1 0.01
38 2 0.02
39 6 0.06
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (33 bp):
TATATTATTATATATTTTATTTATATATTTTAT
Found at i:11455521 original size:14 final size:14
Alignment explanation
Indices: 11455499--11455534 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11455489 ACCACATTTA
11455499 TTATATTTAGTTTT
1 TTATATTTAGTTTT
* *
11455513 TTGTATTTATTTTT
1 TTATATTTAGTTTT
11455527 TTATATTT
1 TTATATTT
11455535 TATATGTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (14 bp):
TTATATTTAGTTTT
Found at i:11455589 original size:11 final size:11
Alignment explanation
Indices: 11455554--11455600 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
11455544 ATAACTTGTT
*
11455554 TATTTATTTTTG
1 TATTTA-TTTAG
11455566 TATCTT-TTT-G
1 TAT-TTATTTAG
11455576 TATTTATTTAG
1 TATTTATTTAG
11455587 TATTTATTTAG
1 TATTTATTTAG
11455598 TAT
1 TAT
11455601 GTTAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.06
10 7 0.22
11 18 0.56
12 3 0.09
13 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (11 bp):
TATTTATTTAG
Found at i:11456555 original size:34 final size:34
Alignment explanation
Indices: 11456512--11456600 Score: 126
Period size: 34 Copynumber: 2.6 Consensus size: 34
11456502 GTAATATGAT
*
11456512 ATGCTTATAACAAATCAATACAGTA-ACAATTAAA
1 ATGCTTATAACAAATCAATACAATAGA-AATTAAA
*
11456546 ATGCTTATAACAAATCAATACAATAGAAATTAAT
1 ATGCTTATAACAAATCAATACAATAGAAATTAAA
* *
11456580 ATGCTTATGACAGATCAATAC
1 ATGCTTATAACAAATCAATAC
11456601 TATATCAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 49 0.98
35 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (34 bp):
ATGCTTATAACAAATCAATACAATAGAAATTAAA
Found at i:11461699 original size:15 final size:15
Alignment explanation
Indices: 11461664--11461705 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11461654 AAAATATTAA
11461664 AATATA-TAAT-TTT
1 AATATATTAATATTT
*
11461677 ATTAATATTAATATTT
1 AAT-ATATTAATATTT
11461693 AATATATTAATAT
1 AATATATTAATAT
11461706 AAGTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 2 0.08
14 3 0.12
15 14 0.58
16 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATATTAATATTT
Found at i:11462997 original size:19 final size:18
Alignment explanation
Indices: 11462973--11463111 Score: 67
Period size: 19 Copynumber: 7.3 Consensus size: 18
11462963 TTTGATATTT
11462973 TTTTTATATTATTTATATA
1 TTTTTATATTATTTATA-A
11462992 TTTTTATGATT-TTTATAA
1 TTTTTAT-ATTATTTATAA
11463010 GTTTTT-T-TTAATTT-TAAA
1 -TTTTTATATT-ATTTAT-AA
11463028 TATTTGT-TATTAATTTGATAA
1 T-TTT-TATATT-ATTT-ATAA
*
11463049 ATTTT-TATTATTTATTAGA
1 TTTTTATATTATTTA-TA-A
* *
11463068 TTTTTTAGAATATTTATAA
1 -TTTTTATATTATTTATAA
11463087 GTTTTTATGATT-TTTATAA
1 -TTTTTAT-ATTATTTATAA
*
11463106 ATTTTA
1 TTTTTA
11463112 AGTTTATAAG
Statistics
Matches: 97, Mismatches: 8, Indels: 31
0.71 0.06 0.23
Matches are distributed among these distances:
16 2 0.02
17 3 0.03
18 21 0.22
19 40 0.41
20 21 0.22
21 9 0.09
22 1 0.01
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTTATATTATTTATAA
Found at i:11463024 original size:9 final size:9
Alignment explanation
Indices: 11462973--11463163 Score: 72
Period size: 9 Copynumber: 20.7 Consensus size: 9
11462963 TTTGATATTT
11462973 TTTTTAT-A
1 TTTTTATAA
11462981 TTATTTATATA
1 TT-TTTATA-A
*
11462992 TTTTTATGA
1 TTTTTATAA
11463001 TTTTTATAA
1 TTTTTATAA
*
11463010 GTTTTTTTTAA
1 --TTTTTATAA
*
11463021 -TTTTAAATA
1 TTTTTATA-A
11463030 TTTGTTATTAA
1 TTT-TTA-TAA
*
11463041 -TTTGATAAA
1 TTTTTAT-AA
*
11463050 TTTTTATTA
1 TTTTTATAA
* *
11463059 TTTATTAGAT
1 TTT-TTATAA
*
11463069 TTTTTAGAA
1 TTTTTATAA
*
11463078 TATTTATAA
1 TTTTTATAA
*
11463087 GTTTTTATGA
1 -TTTTTATAA
11463097 TTTTTATAA
1 TTTTTATAA
* *
11463106 ATTTTA-AG
1 TTTTTATAA
* *
11463114 TTTATAAGAA
1 TTT-TTATAA
*
11463124 TTTTAATAA
1 TTTTTATAA
11463133 -TTTT-TAA
1 TTTTTATAA
*
11463140 TGTTTA-ATA
1 TTTTTATA-A
*
11463149 TTTTTATGA
1 TTTTTATAA
11463158 TTTTTA
1 TTTTTA
11463164 ATGATTTTTT
Statistics
Matches: 136, Mismatches: 28, Indels: 37
0.68 0.14 0.18
Matches are distributed among these distances:
7 3 0.02
8 18 0.13
9 68 0.50
10 31 0.23
11 15 0.11
12 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11463059 original size:22 final size:20
Alignment explanation
Indices: 11463017--11463060 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
11463007 TAAGTTTTTT
*
11463017 TTAATTTTAAATATTTGTTA
1 TTAATTTTAAATATTTATTA
*
11463037 TTAATTTGATAAATTTTTATTA
1 TTAATTT--TAAATATTTATTA
11463059 TT
1 TT
11463061 TATTAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTAATTTTAAATATTTATTA
Found at i:11463127 original size:26 final size:26
Alignment explanation
Indices: 11463070--11463145 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
11463060 TTATTAGATT
* * * *
11463070 TTTTAGAATATTTATAAGTTTTTATGAT
1 TTTTATAA-ATTT-TAAGTTTATAAGAA
11463098 TTTTATAAATTTTAAGTTTATAAGAA
1 TTTTATAAATTTTAAGTTTATAAGAA
*
11463124 TTTTAATAATTTTTAATGTTTA
1 TTTT-ATAAATTTTAA-GTTTA
11463146 ATATTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.37
27 14 0.34
28 12 0.29
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (26 bp):
TTTTATAAATTTTAAGTTTATAAGAA
Found at i:11463167 original size:10 final size:10
Alignment explanation
Indices: 11463088--11463172 Score: 55
Period size: 9 Copynumber: 9.5 Consensus size: 10
11463078 TATTTATAAG
11463088 TTTTT-ATGA
1 TTTTTAATGA
*
11463097 TTTTT-ATAA
1 TTTTTAATGA
*
11463106 ATTTTAA-G-
1 TTTTTAATGA
*
11463114 TTTATAA-GA
1 TTTTTAATGA
* *
11463123 ATTTTAATAA
1 TTTTTAATGA
11463133 TTTTTAATG-
1 TTTTTAATGA
11463142 --TTTAAT-A
1 TTTTTAATGA
11463149 TTTTT-ATGA
1 TTTTTAATGA
11463158 TTTTTAATGA
1 TTTTTAATGA
11463168 TTTTT
1 TTTTT
11463173 TTATAAGTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
7 6 0.10
8 8 0.14
9 26 0.45
10 18 0.31
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (10 bp):
TTTTTAATGA
Found at i:11463197 original size:22 final size:21
Alignment explanation
Indices: 11463149--11463195 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
11463139 ATGTTTAATA
*
11463149 TTTTTATGATTTTTAATGATT
1 TTTTTATAATTTTTAATGATT
11463170 TTTTTATAAGTTTTTAA-GATT
1 TTTTTATAA-TTTTTAATGATT
11463191 TTTTT
1 TTTTT
11463196 TACGTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (21 bp):
TTTTTATAATTTTTAATGATT
Found at i:11463288 original size:37 final size:36
Alignment explanation
Indices: 11463203--11463337 Score: 123
Period size: 37 Copynumber: 3.7 Consensus size: 36
11463193 TTTTACGTTA
11463203 TTATA-CAATTTTGAATATGTTTTATTAAT-TTTATAAT
1 TTATATCAATTTT-AATAT-TTTTA-TAATATTTATAAT
* * *
11463240 TGATTTGAATTTTAATATTTTTATAATATTTATAAGT
1 TTATATCAATTTTAATATTTTTATAATATTTATAA-T
* *
11463277 TTATATCAATTTTAATTTTTTTA-AATATTTAACAAT
1 TTATATCAATTTTAATATTTTTATAATATTT-ATAAT
* * *
11463313 TTTTATGATTTTTTAATATTTTTAT
1 TTATATCA-ATTTTAATATTTTTAT
11463338 GAGATAATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
35 4 0.05
36 26 0.32
37 44 0.55
38 6 0.08
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.59
Consensus pattern (36 bp):
TTATATCAATTTTAATATTTTTATAATATTTATAAT
Found at i:11475230 original size:35 final size:35
Alignment explanation
Indices: 11475203--11475368 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
11475193 CATGGCAAAG
*
11475203 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
11475238 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
11475273 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
11475313 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
11475348 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
11475369 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:11475322 original size:75 final size:75
Alignment explanation
Indices: 11475203--11475373 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
11475193 CATGGCAAAG
** *
11475203 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
11475262 CCATACTGAGC
65 CCATACCGAGC
11475273 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
11475338 CATACCGAGT
66 CATACCGAGC
**
11475348 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
11475374 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:11482689 original size:35 final size:35
Alignment explanation
Indices: 11482662--11482827 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
11482652 CATGGCAAAG
*
11482662 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
11482697 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
11482732 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
11482772 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
11482807 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
11482828 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:11482781 original size:75 final size:75
Alignment explanation
Indices: 11482662--11482832 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
11482652 CATGGCAAAG
** *
11482662 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
11482721 CCATACTGAGC
65 CCATACCGAGC
11482732 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
11482797 CATACCGAGT
66 CATACCGAGC
**
11482807 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
11482833 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:11491148 original size:10 final size:10
Alignment explanation
Indices: 11491118--11491156 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
11491108 TTAAATTCTA
11491118 AAAGATAAAT
1 AAAGATAAAT
*
11491128 AAGGATAAAT
1 AAAGATAAAT
*
11491138 AAAGATCAAT
1 AAAGATAAAT
*
11491148 AGAGATAAA
1 AAAGATAAA
11491157 AGCTAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.64, C:0.03, G:0.15, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:11491446 original size:11 final size:11
Alignment explanation
Indices: 11491430--11491459 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11491420 TCATACTCAA
11491430 AATAAATATAT
1 AATAAATATAT
11491441 AATAAATATAT
1 AATAAATATAT
11491452 AA-AAATAT
1 AATAAATAT
11491460 GTCATTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAATATAT
Found at i:11491948 original size:14 final size:14
Alignment explanation
Indices: 11491929--11491988 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
11491919 GTATATCATC
11491929 ATTTAAATCCACTA
1 ATTTAAATCCACTA
11491943 ATTTAAATCCAC--
1 ATTTAAATCCACTA
* *
11491955 ATGTGTATAT-CA-TC
1 AT-T-TAAATCCACTA
11491969 ATTTAAATCCACTA
1 ATTTAAATCCACTA
11491983 ATTTAA
1 ATTTAA
11491989 CTCTCATGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
12 6 0.16
13 6 0.16
14 25 0.68
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.38
Consensus pattern (14 bp):
ATTTAAATCCACTA
Found at i:11492004 original size:40 final size:40
Alignment explanation
Indices: 11491909--11491988 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
11491899 AATTAAACTT
11491909 ATCCACATGTGTATATCATCATTTAAATCCACTAATTTAA
1 ATCCACATGTGTATATCATCATTTAAATCCACTAATTTAA
11491949 ATCCACATGTGTATATCATCATTTAAATCCACTAATTTAA
1 ATCCACATGTGTATATCATCATTTAAATCCACTAATTTAA
11491989 CTCTCATGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (40 bp):
ATCCACATGTGTATATCATCATTTAAATCCACTAATTTAA
Found at i:11492988 original size:17 final size:18
Alignment explanation
Indices: 11492966--11492999 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11492956 CAAGAATAGT
11492966 AAGCAT-AAAATAGTTTC
1 AAGCATGAAAATAGTTTC
11492983 AAGCATGAAAATAGTTT
1 AAGCATGAAAATAGTTT
11493000 AGCACATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (18 bp):
AAGCATGAAAATAGTTTC
Found at i:11493279 original size:21 final size:21
Alignment explanation
Indices: 11493254--11493295 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11493244 TACTCGTGTA
11493254 ATTTCCTTTCTGAATTTTTTT
1 ATTTCCTTTCTGAATTTTTTT
*
11493275 ATTTCTTTTCTGAATTTTTTT
1 ATTTCCTTTCTGAATTTTTTT
11493296 CTTTTTGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (21 bp):
ATTTCCTTTCTGAATTTTTTT
Found at i:11495285 original size:52 final size:51
Alignment explanation
Indices: 11495200--11495332 Score: 182
Period size: 51 Copynumber: 2.6 Consensus size: 51
11495190 ATGTCACTAG
*
11495200 TGACT-CAAGTGTGGTACTATGTGAAGGCTACTTTGTGAAGAAAGATAGCTT
1 TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTT
* *
11495251 TG-GTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGGTAGCTT
1 TGACT-ACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
*
11495302 TGACTACAACG-GTGGTACTATGTGTAGGCCA
1 TGACTACAA-GTGTGGTACTATGTGAAGGCCA
11495333 TCGGGTATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
50 1 0.01
51 36 0.49
52 36 0.49
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (51 bp):
TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTT
Found at i:11495321 original size:51 final size:52
Alignment explanation
Indices: 11495205--11495332 Score: 181
Period size: 52 Copynumber: 2.5 Consensus size: 52
11495195 ACTAGTGACT
* *
11495205 CAAGTGTGGTACTATGTGAAGGCTACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGCTCA
*
11495257 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGACT-A
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTG-CTCA
*
11495308 CAACG-GTGGTACTATGTGTAGGCCA
1 CAA-GTGTGGTACTATGTGAAGGCCA
11495333 TCGGGTATCC
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
51 34 0.49
52 36 0.51
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGCTCA
Found at i:11498842 original size:28 final size:28
Alignment explanation
Indices: 11498802--11498858 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
11498792 TATTTTAGCC
11498802 TAAATTTCCAATCCCCAGGATGTCTCGG
1 TAAATTTCCAATCCCCAGGATGTCTCGG
11498830 TAAATTTCCAATCCCCAGGATGTCTCGG
1 TAAATTTCCAATCCCCAGGATGTCTCGG
11498858 T
1 T
11498859 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (28 bp):
TAAATTTCCAATCCCCAGGATGTCTCGG
Found at i:11499223 original size:13 final size:13
Alignment explanation
Indices: 11499207--11499232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11499197 ATTTCGTTAC
11499207 TGTATTCTTTTAA
1 TGTATTCTTTTAA
11499220 TGTATTCTTTTAA
1 TGTATTCTTTTAA
11499233 AAGTTTCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TGTATTCTTTTAA
Found at i:11502958 original size:4 final size:4
Alignment explanation
Indices: 11502949--11502994 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
11502939 ATACACAAAA
*
11502949 TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
11502995 AACCTTATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:11511106 original size:4 final size:4
Alignment explanation
Indices: 11511097--11511163 Score: 125
Period size: 4 Copynumber: 16.8 Consensus size: 4
11511087 TGATAAGGTC
*
11511097 TACA TACA TACA TACA TACA TATA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
11511145 TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TAC
11511164 GTAATTTGTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:11521044 original size:2 final size:2
Alignment explanation
Indices: 11520989--11521024 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11520979 CCTATACTAC
11520989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11521025 ATGATTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11525895 original size:31 final size:31
Alignment explanation
Indices: 11525860--11525933 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
11525850 ATATAGGAAT
* *
11525860 AATTACCAAGTTCATGCTCTAATATGAAAAC
1 AATTACCAAGTTCAGGCTCCAATATGAAAAC
* * *
11525891 AATTACCTAGGTCAGGCTCCAATATGGAAAC
1 AATTACCAAGTTCAGGCTCCAATATGAAAAC
*
11525922 AATTACTAAGTT
1 AATTACCAAGTT
11525934 AAGCCTTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (31 bp):
AATTACCAAGTTCAGGCTCCAATATGAAAAC
Found at i:11529170 original size:26 final size:26
Alignment explanation
Indices: 11529116--11529169 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
11529106 TTATTATTTT
* *
11529116 AAATATATATAATATAAATTTATATA
1 AAATATATACAATATAAAATTATATA
11529142 AAATATATACAAT-TAAAATTATATA
1 AAATATATACAATATAAAATTATATA
11529167 AAA
1 AAA
11529170 AGCTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATATATACAATATAAAATTATATA
Found at i:11529227 original size:17 final size:18
Alignment explanation
Indices: 11529205--11529250 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
11529195 TAAAAATTAT
11529205 AATTTATAAATTAAT-AA
1 AATTTATAAATTAATAAA
* *
11529222 AATTTACAAATTTATAAA
1 AATTTATAAATTAATAAA
*
11529240 AATATATAAAT
1 AATTTATAAAT
11529251 ATATAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTTATAAATTAATAAA
Found at i:11529289 original size:25 final size:26
Alignment explanation
Indices: 11529186--11529299 Score: 78
Period size: 25 Copynumber: 4.5 Consensus size: 26
11529176 TAATATTTTG
* *
11529186 AAAAATATATAAAAAT-TATAATTTAT
1 AAAAATATATAAATATATA-AATATAT
* * * *
11529212 -AAATTA-ATAAAATTTACAAATTTAT
1 AAAAATATAT-AAATATATAAATATAT
*
11529237 AAAAATATATAAATATATAAA-AGAAT
1 AAAAATATATAAATATATAAATA-TAT
*
11529263 AAAAAT-TATAAATGTATAAATATAT
1 AAAAATATATAAATATATAAATATAT
*
11529288 -AAAATATCTAAA
1 AAAAATATATAAA
11529300 AAGCACAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
24 7 0.10
25 36 0.52
26 24 0.35
27 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAAATATATAAATATATAAATATAT
Found at i:11529302 original size:43 final size:43
Alignment explanation
Indices: 11529188--11529300 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
11529178 ATATTTTGAA
* * ** *
11529188 AAATATATAAAAAT-TAT-AATTTATAAATTAATAAAATTTAC
1 AAATGTATAAAAATATATAAATATATAAAAGAATAAAAATTAC
* *
11529229 AAATTTATAAAAATATATAAATATATAAAAGAATAAAAATTAT
1 AAATGTATAAAAATATATAAATATATAAAAGAATAAAAATTAC
* *
11529272 AAATGTATAAATATATA-AAATATCTAAAA
1 AAATGTATAAAAATATATAAATATATAAAA
11529301 AGCACAATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 13 0.21
42 14 0.23
43 34 0.56
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (43 bp):
AAATGTATAAAAATATATAAATATATAAAAGAATAAAAATTAC
Found at i:11530429 original size:5 final size:5
Alignment explanation
Indices: 11530419--11530444 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11530409 ATATTTTACA
11530419 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
11530445 ATTGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:11531099 original size:95 final size:95
Alignment explanation
Indices: 11530986--11531176 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
11530976 CAGGTGCCTA
11530986 ATCTATCTAACACTCAGATGGATGATTGCAATACCCTCTCCCCAAAATAACCTCACTTACAAGGC
1 ATCTATCTAACACTCAGATGGATGATTGCAATACCCTCTCCCCAAAATAACCTCACTTACAAGGC
11531051 GGATAATCTCTCCAAAAGAATATCTAGAAT
66 GGATAATCTCTCCAAAAGAATATCTAGAAT
*
11531081 ATCTATCTAACACTCAGATGGATGATTGCAATACCCTCTCCCCAAAATAACCTCACTTACAAGGT
1 ATCTATCTAACACTCAGATGGATGATTGCAATACCCTCTCCCCAAAATAACCTCACTTACAAGGC
11531146 GGATAATCTCTCCAAAAGAATATCTAGAAT
66 GGATAATCTCTCCAAAAGAATATCTAGAAT
11531176 A
1 A
11531177 ATAACCTGAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (95 bp):
ATCTATCTAACACTCAGATGGATGATTGCAATACCCTCTCCCCAAAATAACCTCACTTACAAGGC
GGATAATCTCTCCAAAAGAATATCTAGAAT
Found at i:11533410 original size:43 final size:41
Alignment explanation
Indices: 11533354--11533509 Score: 172
Period size: 43 Copynumber: 3.7 Consensus size: 41
11533344 ATATCGTACA
11533354 ATGCCAATGTCCCAGACGTGGTCTTACATGCAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACA--CAATCACATATCG
* * *
11533397 ATGCCACTATCCCAGACAG-GGTCTTACACAAATCAAATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACAC-AATCACATATCG
* * * *
11533438 GTGACAATGTCCCAGACATGGTCTTACACATAATCACATATTG
1 ATGCCAATGTCCCAGACGTGGTCTTACAC--AATCACATATCG
*
11533481 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAATGTCCCAGACGTGGTCTTACAC
11533510 GAGAACACAT
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 26 0.28
42 16 0.17
43 50 0.54
44 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACAATCACATATCG
Found at i:11533696 original size:2 final size:2
Alignment explanation
Indices: 11533652--11533680 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11533642 CGGTTTTTTC
11533652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11533681 CATTTCAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11541445 original size:2 final size:2
Alignment explanation
Indices: 11541438--11541465 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11541428 CTATAAAATC
11541438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11541466 GATTTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11541744 original size:18 final size:18
Alignment explanation
Indices: 11541721--11541755 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11541711 TAATTTTAAA
*
11541721 AAATTTTATATTAAAATC
1 AAATTTAATATTAAAATC
*
11541739 AAATTTAATATTTAAAT
1 AAATTTAATATTAAAAT
11541756 TAAACGAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTTAATATTAAAATC
Found at i:11544894 original size:18 final size:17
Alignment explanation
Indices: 11544868--11544916 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
11544858 AATTATTGGG
*
11544868 AAATTTAAAAAATCATA
1 AAATATAAAAAATCATA
* *
11544885 AAAGTGTAAAAAATTCTTA
1 AAA-TATAAAAAA-TCATA
11544904 AAATATAAAAAAT
1 AAATATAAAAAAT
11544917 ATTTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 16 0.59
19 7 0.26
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (17 bp):
AAATATAAAAAATCATA
Found at i:11548698 original size:75 final size:75
Alignment explanation
Indices: 11548579--11548749 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
11548569 CATGGCAAAG
** *
11548579 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
11548638 CCATACTGAGC
65 CCATACCGAGC
11548649 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
11548714 CATACCGAGT
66 CATACCGAGC
***
11548724 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
11548750 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:11548717 original size:35 final size:35
Alignment explanation
Indices: 11548582--11548747 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
11548572 GGCAAAGTGT
* **
11548582 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
11548617 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
11548652 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
11548692 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
11548727 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
11548748 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:11556195 original size:75 final size:75
Alignment explanation
Indices: 11556076--11556246 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
11556066 CATGGCAAAG
** *
11556076 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
11556135 CCATACTGAGC
65 CCATACCGAGC
11556146 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
11556211 CATACCGAGT
66 CATACCGAGC
***
11556221 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
11556247 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:11556214 original size:35 final size:35
Alignment explanation
Indices: 11556079--11556244 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
11556069 GGCAAAGTGT
* **
11556079 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
11556114 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
11556149 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
11556189 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
11556224 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
11556245 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:11558175 original size:21 final size:21
Alignment explanation
Indices: 11558149--11558188 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11558139 CAAAACAACG
*
11558149 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTGACTTTTAACTTGA
11558170 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
11558189 TAGATAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTGA
Found at i:11558422 original size:3 final size:3
Alignment explanation
Indices: 11558414--11558456 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
11558404 GTTTTGAAGT
11558414 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11558457 GATATTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11558540 original size:9 final size:9
Alignment explanation
Indices: 11558526--11558577 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
11558516 TTTTATAAAA
11558526 TTTTTAATT
1 TTTTTAATT
11558535 TTTTTAA-T
1 TTTTTAATT
*
11558543 TTTTCAATT
1 TTTTTAATT
11558552 TTTTTATATAT
1 TTTTTA-AT-T
*
11558563 ATTTTAGATT
1 TTTTTA-ATT
11558573 TTTTT
1 TTTTT
11558578 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.20
9 13 0.37
10 7 0.20
11 8 0.23
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTAATT
Found at i:11562658 original size:100 final size:100
Alignment explanation
Indices: 11562466--11562658 Score: 221
Period size: 100 Copynumber: 1.9 Consensus size: 100
11562456 TTATAGAGAA
*
11562466 TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAATATGCAAGATCAAATTTAACATCA
1 TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAATATGCAAGATCAAATATAACATCA
* *
11562531 CCTAAGTACTTACTCATATGGCTGAATATACAAAT
66 CATAAGTACTTACTCATATGGCCGAATATACAAAT
* *** * * *
11562566 TCAAATATAATATCACTTTTGTGCATACCT-TCATGGTCAAATATTCAAGATTC-AATATAACGT
1 TCAAAGATAATATCACAAATGTGCATACCTAT-ATGGCCAAATATGCAAGA-TCAAATATAACAT
* * *
11562629 TACATATGTACTTAC-CTATGTGGCCGAATA
64 CACATAAGTACTTACTC-ATATGGCCGAATA
11562659 AATACAAGAT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
99 2 0.03
100 73 0.95
101 2 0.03
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (100 bp):
TCAAAGATAATATCACAAATGTGCATACCTATATGGCCAAATATGCAAGATCAAATATAACATCA
CATAAGTACTTACTCATATGGCCGAATATACAAAT
Found at i:11563816 original size:23 final size:22
Alignment explanation
Indices: 11563790--11563843 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
11563780 TTAATTTATG
*
11563790 TTATAATATATAC-ATATTATTA
1 TTATAATATA-ACTATAATATTA
* *
11563812 CTTATATTATAACTTTAATATTA
1 -TTATAATATAACTATAATATTA
11563835 TTATAATAT
1 TTATAATAT
11563844 TATTTCCACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAATATAACTATAATATTA
Found at i:11568913 original size:3 final size:3
Alignment explanation
Indices: 11568905--11568942 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
11568895 TCACGTGTCA
*
11568905 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
11568943 TTTTAGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11568985 original size:2 final size:2
Alignment explanation
Indices: 11568973--11569008 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11568963 AATAAAATCA
11568973 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11569009 AATTTTAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11570188 original size:2 final size:2
Alignment explanation
Indices: 11570183--11570220 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11570173 TTCTTCTTTT
11570183 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11570221 ATTTTGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11572291 original size:2 final size:2
Alignment explanation
Indices: 11572284--11572308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11572274 TGGCTTTCTT
11572284 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
11572309 TTTCTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11584029 original size:13 final size:13
Alignment explanation
Indices: 11584011--11584035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11584001 CTAATTGGCT
11584011 TAGAAAAAAATTC
1 TAGAAAAAAATTC
11584024 TAGAAAAAAATT
1 TAGAAAAAAATT
11584036 TTAAATAGAT
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:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
TAGAAAAAAATTC
Found at i:11586525 original size:35 final size:33
Alignment explanation
Indices: 11586478--11586546 Score: 77
Period size: 35 Copynumber: 2.0 Consensus size: 33
11586468 TTGAACTGTG
* *
11586478 GCATGAGATTTTAAATTTTGGACATTGAATAATTT
1 GCATGAGATTTTAAATTATGG--ATTAAATAATTT
*
11586513 GCATG-GATTTTTATATTATGGATTAAATAATTT
1 GCATGAGA-TTTTAAATTATGGATTAAATAATTT
11586546 G
1 G
11586547 ACATTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 12 0.40
34 2 0.07
35 16 0.53
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.45
Consensus pattern (33 bp):
GCATGAGATTTTAAATTATGGATTAAATAATTT
Found at i:11587038 original size:16 final size:16
Alignment explanation
Indices: 11587019--11587049 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11587009 TTGTAGATTG
11587019 TGAAAACTATAGACTT
1 TGAAAACTATAGACTT
*
11587035 TGAAAACTCTAGACT
1 TGAAAACTATAGACT
11587050 CTGTAGTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (16 bp):
TGAAAACTATAGACTT
Found at i:11587927 original size:18 final size:20
Alignment explanation
Indices: 11587887--11587928 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
11587877 TCTCTCAACA
*
11587887 AAAATTACAAAATAATTTTT
1 AAAATTACAAAATAATTTAT
11587907 AAAATT-CAAAAT-ATTTAT
1 AAAATTACAAAATAATTTAT
11587925 AAAA
1 AAAA
11587929 ATCCCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTACAAAATAATTTAT
Found at i:11587929 original size:19 final size:19
Alignment explanation
Indices: 11587886--11587943 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
11587876 CTCTCTCAAC
11587886 AAAAATTACAAAATAATTT-T
1 AAAAATT-CAAAAT-ATTTAT
*
11587906 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
* *
11587925 AAAAATCCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
11587943 A
1 A
11587944 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 11 0.33
19 16 0.48
20 6 0.18
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:11587972 original size:20 final size:20
Alignment explanation
Indices: 11587943--11587983 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11587933 CAAAATTTAT
11587943 ATTTT-AAAAAAGTTTATAAA
1 ATTTTAAAAAAAG-TTATAAA
*
11587963 ATTTTTAAAAAAGTTATAAA
1 ATTTTAAAAAAAGTTATAAA
11587983 A
1 A
11587984 AATATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAAAAGTTATAAA
Found at i:11587984 original size:21 final size:21
Alignment explanation
Indices: 11587944--11587983 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11587934 AAAATTTATA
11587944 TTTTAAAAAAGTTTATAAAAT
1 TTTTAAAAAAGTTTATAAAAT
11587965 TTTTAAAAAAG-TTATAAAA
1 TTTTAAAAAAGTTTATAAAA
11587984 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTAAAAAAGTTTATAAAAT
Found at i:11596597 original size:21 final size:21
Alignment explanation
Indices: 11596571--11596647 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
11596561 CAGAAGCTTG
*
11596571 AAAGCTAAACAGAAGCTCGTA
1 AAAGCTTAACAGAAGCTCGTA
11596592 AAAGCTTAACAGAAGCTCGTA
1 AAAGCTTAACAGAAGCTCGTA
*
11596613 AGAGCTTAACAGAAGCTCGTA
1 AAAGCTTAACAGAAGCTCGTA
** *
11596634 GGAGCTGAACAGAA
1 AAAGCTTAACAGAA
11596648 AGTAAAACAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (21 bp):
AAAGCTTAACAGAAGCTCGTA
Found at i:11596628 original size:42 final size:40
Alignment explanation
Indices: 11596560--11596647 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 40
11596550 GAATACATTG
* *
11596560 ACAGAAGCTTGAAAGCTAAACAGAAGCTCGTAAAAGCTTA
1 ACAGAAGCTCGAAAGCTAAACAGAAGCTCGTAAAAGCTGA
* **
11596600 ACAGAAGCTCGTAAGAGCTTAACAGAAGCTCGTAGGAGCTGA
1 ACAGAAGCTCG-AA-AGCTAAACAGAAGCTCGTAAAAGCTGA
11596642 ACAGAA
1 ACAGAA
11596648 AGTAAAACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 10 0.24
41 2 0.05
42 29 0.71
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (40 bp):
ACAGAAGCTCGAAAGCTAAACAGAAGCTCGTAAAAGCTGA
Found at i:11596807 original size:17 final size:17
Alignment explanation
Indices: 11596787--11596824 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11596777 TATTAAATTC
*
11596787 AATAATATATTTCCAAT
1 AATAATATAATTCCAAT
*
11596804 AATAATTTAATTCCAAT
1 AATAATATAATTCCAAT
11596821 AATA
1 AATA
11596825 TAACATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATATAATTCCAAT
Found at i:11599953 original size:29 final size:30
Alignment explanation
Indices: 11599906--11599973 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
11599896 TGGCCCAAGA
* *
11599906 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
11599936 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
11599966 GCAAATAT
1 GTAAATAT
11599974 TTTAAGGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:11600229 original size:24 final size:21
Alignment explanation
Indices: 11600201--11600268 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
11600191 ACAAAAAAGA
*
11600201 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCCAAGTCACTTC---TCTT
*
11600225 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
**
11600246 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
11600267 TT
1 TT
11600269 AAGAATTATG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
21 26 0.63
24 15 0.37
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGTCCAAGTCACTTCTCTT
Found at i:11600247 original size:21 final size:21
Alignment explanation
Indices: 11600221--11600268 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
11600211 TCACTTCGTT
11600221 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
11600242 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
11600263 TCTTTT
1 TCTTTT
11600269 AAGAATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.10, C:0.23, G:0.10, T:0.56
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:11600505 original size:2 final size:2
Alignment explanation
Indices: 11600498--11600531 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11600488 ATTTTATTTA
11600498 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
11600532 GTAAGGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11602415 original size:46 final size:46
Alignment explanation
Indices: 11602363--11602572 Score: 341
Period size: 46 Copynumber: 4.6 Consensus size: 46
11602353 AGTGTGCTCT
11602363 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
11602409 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
11602455 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
11602501 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
11602547 ATGACA-GAAAATGAATAAGACCATGG
1 CTGATATG-AAATGTGTAAGACCATGG
11602573 CAACGTGATA
Statistics
Matches: 158, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
45 1 0.01
46 157 0.99
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:11602572 original size:30 final size:30
Alignment explanation
Indices: 11602536--11602602 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
11602526 GTTGAAAGAT
11602536 ACCATGGCAACATGACA-GAAAATGAATAAG
1 ACCATGGCAACATGACATG-AAATGAATAAG
* *
11602566 ACCATGGCAACGTGATATGAAATGAATAAG
1 ACCATGGCAACATGACATGAAATGAATAAG
11602596 ACCATGG
1 ACCATGG
11602603 TTGAAAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (30 bp):
ACCATGGCAACATGACATGAAATGAATAAG
Found at i:11602580 original size:76 final size:76
Alignment explanation
Indices: 11602490--11602646 Score: 305
Period size: 76 Copynumber: 2.1 Consensus size: 76
11602480 GTTGAAAGAT
11602490 ACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
1 ACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
11602555 AAATGAATAAG
66 AAATGAATAAG
11602566 ACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
1 ACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
*
11602631 AAATGAGTAAG
66 AAATGAATAAG
11602642 ACCAT
1 ACCAT
11602647 AGTTGAAAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (76 bp):
ACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
AAATGAATAAG
Found at i:11602615 original size:122 final size:121
Alignment explanation
Indices: 11602444--11602689 Score: 341
Period size: 122 Copynumber: 2.0 Consensus size: 121
11602434 GTTGAAAGAT
** * *
11602444 ACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATG
1 ACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-G
* * * *
11602509 -AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAATAAG
65 AAAATGAATAAGACCATAGTTGAAAAACACCATGGCAACATGACA-AAAATAAATAAG
*
11602566 ACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
1 ACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
* * * * *
11602631 AAATGAGTAAGACCATAGTTGAAAAACACTATGGCATCATGTCAAAGATAAATAAG
66 AAATGAATAAGACCATAGTTGAAAAACACCATGGCAACATGACAAAAATAAATAAG
11602687 ACC
1 ACC
11602690 GTGGATGGGA
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
121 14 0.13
122 95 0.87
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (121 bp):
ACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
AAATGAATAAGACCATAGTTGAAAAACACCATGGCAACATGACAAAAATAAATAAG
Found at i:11602616 original size:46 final size:46
Alignment explanation
Indices: 11602566--11602689 Score: 126
Period size: 46 Copynumber: 2.7 Consensus size: 46
11602556 AATGAATAAG
* * *
11602566 ACCATGGCAACGTGATATG-AAATGAATAAGACCATGGTTGAAAGAT
1 ACCATGGCAACATGACA-GAAAATGAATAAGACCATAGTTGAAAGAT
* * *
11602612 ACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAAAC
1 ACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGAT
* * * * *
11602658 ACTATGGCATCATGTCA-AAGATAAATAAGACC
1 ACCATGGCAACATGACAGAAAATGAATAAGACC
11602690 GTGGATGGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
45 13 0.20
46 52 0.80
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.19
Consensus pattern (46 bp):
ACCATGGCAACATGACAGAAAATGAATAAGACCATAGTTGAAAGAT
Found at i:11602973 original size:16 final size:17
Alignment explanation
Indices: 11602952--11602984 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11602942 ATGATGGAGC
11602952 ATGAAAT-ATTGATATA
1 ATGAAATAATTGATATA
11602968 ATGAAATAATTGATATA
1 ATGAAATAATTGATATA
11602985 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATAATTGATATA
Found at i:11609410 original size:47 final size:48
Alignment explanation
Indices: 11609293--11609417 Score: 162
Period size: 48 Copynumber: 2.6 Consensus size: 48
11609283 GTGCGAATGA
* *** *
11609293 TACCTTGATTTGGCTAGGGGCCATGGTATAGGTATTTCAGAGAGGAGT
1 TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAGAGAGAAGT
*
11609341 TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAG-GATAAGT
1 TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAGAGAGAAGT
* **
11609388 TACCTTGATTTGGTTACAGGCCATGGTATA
1 TACCTTGATTTGGCTAGGGGCCATGGTATA
11609418 AGTACTTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 32 0.47
48 36 0.53
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (48 bp):
TACCTTGATTTGGCTAGGGGCCATGGTATAGATACAGCAGAGAGAAGT
Found at i:11610197 original size:23 final size:22
Alignment explanation
Indices: 11610157--11610201 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
11610147 GAATTGTGCA
*
11610157 TATTGATGATGATTTTGGCTACC
1 TATTGATGATGATATTGG-TACC
11610180 TATTGTATGATGA-ATTGGTACC
1 TATTG-ATGATGATATTGGTACC
11610202 AGTTTGGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.42
Consensus pattern (22 bp):
TATTGATGATGATATTGGTACC
Found at i:11611309 original size:39 final size:39
Alignment explanation
Indices: 11611130--11611306 Score: 228
Period size: 39 Copynumber: 4.5 Consensus size: 39
11611120 CATTTTTGTT
11611130 AGTATTGTGATATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTG--ATATATGCTTGAATGTTATGTGATTATATG
* * *
11611171 AGTATTGTGAGATATGTTTGAATGTTATGTGATTATATA
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * * *
11611210 AATATTGAGATATATGCTTGAACGTTATGTAATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * *
11611249 AGTATTTTGATATATGCTTAAATATTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
11611288 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
11611307 AAAAGTTAAC
Statistics
Matches: 116, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
39 107 0.92
41 9 0.08
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.46
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:11611618 original size:30 final size:30
Alignment explanation
Indices: 11611582--11611641 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
11611572 TCGTAGGTGT
11611582 TATTGTTGTTTGTTTTCGTTTTGGGAATAA
1 TATTGTTGTTTGTTTTCGTTTTGGGAATAA
11611612 TATTGTTGTTTGTTTTCGTTTTGGGAATAA
1 TATTGTTGTTTGTTTTCGTTTTGGGAATAA
11611642 GGCAATGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (30 bp):
TATTGTTGTTTGTTTTCGTTTTGGGAATAA
Found at i:11612744 original size:22 final size:22
Alignment explanation
Indices: 11612718--11612762 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11612708 AGATCAACAC
11612718 AAATAT-AATCACATACATATCA
1 AAATATCAATCACAT-CATATCA
**
11612740 AAATATCAATTTCATCATATCA
1 AAATATCAATCACATCATATCA
11612762 A
1 A
11612763 TCATCATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATCAATCACATCATATCA
Found at i:11612959 original size:22 final size:22
Alignment explanation
Indices: 11612934--11612976 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11612924 AAACCACAAC
*
11612934 TGATCTGTAGATAAACTGCCAT
1 TGATCTGCAGATAAACTGCCAT
*
11612956 TGATTTGCAGATAAACTGCCA
1 TGATCTGCAGATAAACTGCCA
11612977 CTAATAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
TGATCTGCAGATAAACTGCCAT
Found at i:11613061 original size:73 final size:73
Alignment explanation
Indices: 11612919--11613176 Score: 399
Period size: 73 Copynumber: 3.5 Consensus size: 73
11612909 ACATCGTTTA
* * * *
11612919 TGGACAAACCACAACTGATCTGTAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAA
1 TGGACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAA
11612984 CACTGATG
66 CACTGATG
* *
11612992 TGAACAAGCCACCACTGGTTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAA
1 TGGACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAA
11613057 CACTGATG
66 CACTGATG
*
11613065 TGGACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAATTGCCACTAATAA
1 TGGACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAA
*
11613130 CACTAATG
66 CACTGATG
* * * * *
11613138 TGGACAAGCCACCACTAAATTGCAAATATACTACCATTG
1 TGGACAAGCCACCACTGATTTGCAGATAAACTGCCATTG
11613177 CTTCCACCTT
Statistics
Matches: 170, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 170 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (73 bp):
TGGACAAGCCACCACTGATTTGCAGATAAACTGCCATTGATTTGCAGATAAACTGCCACTAATAA
CACTGATG
Found at i:11613105 original size:22 final size:22
Alignment explanation
Indices: 11613080--11613122 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11613070 AAGCCACCAC
11613080 TGATTTGCAGATAAACTGCCAT
1 TGATTTGCAGATAAACTGCCAT
*
11613102 TGATTTGCAGATAAATTGCCA
1 TGATTTGCAGATAAACTGCCA
11613123 CTAATAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (22 bp):
TGATTTGCAGATAAACTGCCAT
Found at i:11619079 original size:145 final size:147
Alignment explanation
Indices: 11618802--11619085 Score: 464
Period size: 145 Copynumber: 1.9 Consensus size: 147
11618792 AACAGGAAAG
*
11618802 AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAAGCATGGTAGGCA
1 AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAACCATGGTAGGCA
* * *
11618867 AAGGAATGAGTGGTCGGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAGAGAGCA
66 AAGGAATGAGTGGTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAAAGAACA
11618932 GGGGAGAGGCTGATGAA
131 GGGGAGAGGCTGATGAA
* * **
11618949 AGGATGGGAGAAATAAGATGCATATGC-AATTAGAAGAAATCATAATCGAAAACCATGGTAGGCA
1 AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAACCATGGTAGGCA
* *
11619013 AAGGAATGAGT-GTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGTAACAGGCAAAAGAACA
66 AAGGAATGAGTGGTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAAAGAACA
11619077 GGGGAGAGG
131 GGGGAGAGG
11619086 TTTTAGACTT
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
145 57 0.45
146 44 0.35
147 26 0.20
ACGTcount: A:0.45, C:0.10, G:0.31, T:0.14
Consensus pattern (147 bp):
AGGATGCGAGAAATAAGATGCATATGCAAACTAGAAGAAATCATAATAAAAAACCATGGTAGGCA
AAGGAATGAGTGGTCAGGGTTTAAGGAAGAACTGAGAACAGAAGAAAGAAACAGACAAAAGAACA
GGGGAGAGGCTGATGAA
Found at i:11621870 original size:15 final size:14
Alignment explanation
Indices: 11621845--11621884 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
11621835 AAAAGTGTTA
11621845 AAAAAATATTTTCT
1 AAAAAATATTTTCT
* *
11621859 GAAAAATAATTTCT
1 AAAAAATATTTTCT
11621873 AAAAAATGATTT
1 AAAAAAT-ATTT
11621885 ACTTTTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAAAATATTTTCT
Found at i:11621997 original size:18 final size:18
Alignment explanation
Indices: 11621971--11622013 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
11621961 AAAATTTATT
*
11621971 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
11621989 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
11622007 TTTATAT
1 TTTATAT
11622014 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:11627725 original size:21 final size:21
Alignment explanation
Indices: 11627688--11627750 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
11627678 TGATCAGAAT
*
11627688 ACGACACATAA-GTGCCTGAA
1 ACGACACACAAGGTGCCTGAA
* **
11627708 ACGACACACGAGGTGCCTGCT
1 ACGACACACAAGGTGCCTGAA
*
11627729 GCGACACACAAGGTGCCTGAA
1 ACGACACACAAGGTGCCTGAA
11627750 A
1 A
11627751 TATGACACAT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.33, C:0.29, G:0.25, T:0.13
Consensus pattern (21 bp):
ACGACACACAAGGTGCCTGAA
Found at i:11628005 original size:28 final size:29
Alignment explanation
Indices: 11627973--11628028 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
11627963 AAACACACAG
* *
11627973 TATAATCC-TCCCAAACACACCATAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
11628001 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCCATCCAAAACACACCAGAATA
11628029 GCACAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:11633242 original size:22 final size:22
Alignment explanation
Indices: 11633212--11633254 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11633202 TTCAAATATG
11633212 TAAAATAATATACTGTTTTATT
1 TAAAATAATATACTGTTTTATT
*
11633234 TAAACTAATATACTGTTTTAT
1 TAAAATAATATACTGTTTTAT
11633255 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATAATATACTGTTTTATT
Found at i:11633638 original size:2 final size:2
Alignment explanation
Indices: 11633633--11633765 Score: 266
Period size: 2 Copynumber: 66.5 Consensus size: 2
11633623 CTCTCTCTTT
11633633 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11633675 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11633717 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11633759 CA CA CA C
1 CA CA CA C
11633766 TTCTTCCCTA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 131 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11635797 original size:23 final size:23
Alignment explanation
Indices: 11635741--11635797 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
11635731 GCTGTACCTT
11635741 AGAAAGAGATATTTGCCTTTGCCTG
1 AGAAAGAG--ATTTGCCTTTGCCTG
*
11635766 -GTAATGAGATTTGCCTTTGCCTG
1 AG-AAAGAGATTTGCCTTTGCCTG
11635789 AGAAAGAGA
1 AGAAAGAGA
11635798 GAAAAAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 21 0.75
24 2 0.07
25 5 0.18
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (23 bp):
AGAAAGAGATTTGCCTTTGCCTG
Found at i:11645443 original size:22 final size:24
Alignment explanation
Indices: 11645401--11645444 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
11645391 TAACTAAGTT
11645401 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
11645425 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
11645445 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:11646489 original size:5 final size:5
Alignment explanation
Indices: 11646479--11646530 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
11646469 AATCTGTTTC
*
11646479 ATAAT ATAAT ATAAT ATAATT ATAAT ATAAT -CAAT -TAAT AGTAAT AT-AT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
11646528 ATA
1 ATA
11646531 CCTAAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 10 0.24
5 21 0.51
6 10 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:11646504 original size:16 final size:15
Alignment explanation
Indices: 11646479--11646530 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
11646469 AATCTGTTTC
11646479 ATAATATAATATAAT
1 ATAATATAATATAAT
11646494 ATAATTATAATATAAT
1 ATAA-TATAATATAAT
*
11646510 -CAAT-TAATAGTAAT
1 ATAATATAATA-TAAT
11646524 AT-ATATA
1 ATAATATA
11646531 CCTAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 8 0.26
16 11 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATATAATATAAT
Found at i:11651863 original size:28 final size:27
Alignment explanation
Indices: 11651795--11651939 Score: 121
Period size: 28 Copynumber: 5.2 Consensus size: 27
11651785 TGGTGAATTA
** *
11651795 TGAAAAGAATATACTTTGTGGCGAACTC
1 TGAAAAGAATAGCCTGTGTGGCGAAC-C
* *
11651823 CGAAAAGAATAGCCTCTGTGGCGAACC
1 TGAAAAGAATAGCCTGTGTGGCGAACC
* **
11651850 ATGAAAAGAATAGCCTATGTACCGAA-C
1 -TGAAAAGAATAGCCTGTGTGGCGAACC
* * *
11651877 TGTAAAAATAATAGCCTGTGAGGCAAACTC
1 TG--AAAAGAATAGCCTGTGTGGCGAAC-C
*
11651907 TGAAAAGAATAGCTTGTGTGGCGAACTC
1 TGAAAAGAATAGCCTGTGTGGCGAAC-C
11651935 TGAAA
1 TGAAA
11651940 GGGATGCCTT
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 87 0.93
30 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (27 bp):
TGAAAAGAATAGCCTGTGTGGCGAACC
Found at i:11651876 original size:56 final size:56
Alignment explanation
Indices: 11651771--11651919 Score: 129
Period size: 56 Copynumber: 2.7 Consensus size: 56
11651761 CATGACAATT
* * * ** ** * ** *
11651771 AAGAATAGCCTTTATGGTGAATTATGAAAAGAATATACTTTGTGGCGAACTCCGAA
1 AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTCCAAA
**
11651827 AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTGTAAA
1 AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTCCAAA
* * * *
11651883 AATAATAGCCTGTGAGGCAAACTC-TGAAAAGAATAGC
1 AAGAATAGCCTCTGTGGCGAAC-CATGAAAAGAATAGC
11651920 TTGTGTGGCG
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
56 74 0.99
57 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (56 bp):
AAGAATAGCCTCTGTGGCGAACCATGAAAAGAATAGCCTATGTACCGAACTCCAAA
Found at i:11651932 original size:56 final size:55
Alignment explanation
Indices: 11651794--11651934 Score: 140
Period size: 56 Copynumber: 2.5 Consensus size: 55
11651784 ATGGTGAATT
* * * *
11651794 ATGAAAAGAATATACTTTGTGGCGAACTCCGAAAAGAATAGCCTCTGTGGCGAACC
1 ATGAAAAGAATA-GCTTTGTGGCGAACTCCAAAAAGAATAGCCTCTGAGGCAAACC
* ** ** * *
11651850 ATGAAAAGAATAGCCTATGTACCGAACTGTAAAAATAATAGCCTGTGAGGCAAACTC
1 ATGAAAAGAATAG-CTTTGTGGCGAACTCCAAAAAGAATAGCCTCTGAGGCAAAC-C
11651907 -TGAAAAGAATAGCTTGTGTGGCGAACTC
1 ATGAAAAGAATAGCTT-TGTGGCGAACTC
11651935 TGAAAGGGAT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
55 2 0.03
56 64 0.96
57 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (55 bp):
ATGAAAAGAATAGCTTTGTGGCGAACTCCAAAAAGAATAGCCTCTGAGGCAAACC
Found at i:11653745 original size:34 final size:34
Alignment explanation
Indices: 11653702--11653823 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 34
11653692 ACATATATGA
*
11653702 ATATCATATCAGAATGTCATATTACCAGAAACAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
* * *
11653736 ATATCATATCAAAATGTCGTATTTCTAGAAACAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
* * * *
11653770 ATA-CTAGATTAGAATGTCATATTTTCATAAACAT
1 ATATC-ATATCAGAATGTCATATTTCCAGAAACAT
11653804 AT-T--TGATCAGAATGTCATAT
1 ATATCAT-ATCAGAATGTCATAT
11653824 CAAATCAAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
32 14 0.19
33 1 0.01
34 57 0.79
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTTCCAGAAACAT
Found at i:11654674 original size:30 final size:30
Alignment explanation
Indices: 11654638--11654700 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
11654628 ATTTATTTTA
11654638 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
11654668 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
11654698 TTG
1 TTG
11654701 ATTGTTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:11666343 original size:2 final size:2
Alignment explanation
Indices: 11666331--11666361 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11666321 AGGATTAATA
*
11666331 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11666362 ATCACACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11667972 original size:23 final size:23
Alignment explanation
Indices: 11667945--11667991 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
11667935 CATCATCATC
11667945 AAAAATT-TAAATAAATTTATAAA
1 AAAAATTGTAAA-AAATTTATAAA
*
11667968 AAAAATTGTAAACAATTTATAAA
1 AAAAATTGTAAAAAATTTATAAA
11667991 A
1 A
11667992 TATAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAAATTGTAAAAAATTTATAAA
Done.