Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 163 of 210
Found at i:54737122 original size:13 final size:13
Alignment explanation
Indices: 54737106--54737131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54737096 TATAATAAAA
54737106 TAAAATAATATTT
1 TAAAATAATATTT
54737119 TAAAATAATATTT
1 TAAAATAATATTT
54737132 AATGAATTTG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATAATATTT
Found at i:54737231 original size:23 final size:22
Alignment explanation
Indices: 54737201--54737247 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
54737191 AATATATTAA
54737201 AAGCAAAT-TCGAAAATAATATT
1 AAGCAAATAT-GAAAATAATATT
*
54737223 AAGCTAAATATTAAAATAATATT
1 AAGC-AAATATGAAAATAATATT
54737246 AA
1 AA
54737248 AAACGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 17 0.77
24 1 0.05
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (22 bp):
AAGCAAATATGAAAATAATATT
Found at i:54739171 original size:44 final size:44
Alignment explanation
Indices: 54739034--54739449 Score: 333
Period size: 44 Copynumber: 9.7 Consensus size: 44
54739024 TTTGGTCTAT
* * * *
54739034 TCCACTGTAATCTCAGGGAGATAAGA-CA-T-GATGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
* * * ** * *
54739075 TCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTTATTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATTACTAGATTCAATCTGC
* * * *
54739118 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATATGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
* * *
54739162 TCCATTGTAATCTCAGGGAGATAAGATT--T-GATACGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
* * * * ** * *
54739203 TCTACTGTAA-CTTTAGAGAGATAAGA-TCCTTTATTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATTACTAGATTCAATCTGC
* *
54739246 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
* * *
54739290 TCCACTGTAATCTCAGGGAGATAAGA--CCT-GATACGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
* * * *
54739331 TCTACTGTAA-CTTTAGAGAGATAAGATT-CTTTA-ATTTAATCTGC
1 TCCACTGTAATC-TCAGGGAGATAAGATTAC--TAGATTCAATCTGC
* *
54739375 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
*
54739419 TCCACTGTAATCTCAGGGAGATAGGATTACT
1 TCCACTGTAATCTCAGGGAGATAAGATTACT
54739450 TGCTTCAGTC
Statistics
Matches: 293, Mismatches: 62, Indels: 37
0.75 0.16 0.09
Matches are distributed among these distances:
40 4 0.01
41 81 0.28
42 6 0.02
43 56 0.19
44 144 0.49
45 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATTACTAGATTCAATCTGC
Found at i:54739378 original size:85 final size:86
Alignment explanation
Indices: 54739034--54739446 Score: 335
Period size: 85 Copynumber: 4.8 Consensus size: 86
54739024 TTTGGTCTAT
* * * *
54739034 TCCACTGTAATCTCAGGGAGATAAGA-CATGATGCGATCTACTCTACTGTAA-CTTCAGAGAGAT
1 TCCACTGTAATCTCAGGGAGATAAGATCCTGATTCGATCTGCTCCACTGTAATC-TCAGAGAGAT
* * *
54739097 AAGATCCTTT-ATTTAATCCGC
65 AAGATTCTTTAATTCAATCTGC
* * * * * *
54739118 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATATGCTCCATTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAAGA-TCCT-GATTCGATCTGCTCCACTGTAATCTCAGAGAGA
* * *
54739183 TAAGA---TTTGATACGATCTGC
64 TAAGATTCTTTAATTCAATCTGC
* * * * ** * *
54739203 TCTACTGTAA-CTTTAGAGAGATAAGATCCTTTATTTAATCCGCTCCACTGTAATCTCAGGGAGA
1 TCCACTGTAATC-TCAGGGAGATAAGATCC-TGATTCGATCTGCTCCACTGTAATCTCAGAGAGA
* *
54739267 TAGGATTAC--TAGCTTCAATCTGC
64 TAAGATT-CTTTA-ATTCAATCTGC
* * *
54739290 TCCACTGTAATCTCAGGGAGATAAGA-CCTGATACGATCTGCTCTACTGTAA-CTTTAGAGAGAT
1 TCCACTGTAATCTCAGGGAGATAAGATCCTGATTCGATCTGCTCCACTGTAATC-TCAGAGAGAT
*
54739353 AAGATTCTTTAATTTAATCTGC
65 AAGATTCTTTAATTCAATCTGC
* * * * *
54739375 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAAGA-TCCT-GATTCGATCTGCTCCACTGTAATCTCAGAGAGA
*
54739440 TAGGATT
64 TAAGATT
54739447 ACTTGCTTCA
Statistics
Matches: 255, Mismatches: 54, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
84 63 0.25
85 92 0.36
86 6 0.02
87 60 0.24
88 33 0.13
89 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (86 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCTGATTCGATCTGCTCCACTGTAATCTCAGAGAGATA
AGATTCTTTAATTCAATCTGC
Found at i:54739430 original size:129 final size:128
Alignment explanation
Indices: 54739034--54739441 Score: 708
Period size: 128 Copynumber: 3.2 Consensus size: 128
54739024 TTTGGTCTAT
* * *
54739034 TCCACTGTAATCTCAGGGAGATAAGACATGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAAGACATGATACGATCTGCTCTACTGTAACTTTAGAGAGATAA
* *
54739099 GATCCTTTATTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATATGC
66 GATCCTTTATTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
* **
54739162 TCCATTGTAATCTCAGGGAGATAAGATTTGATACGATCTGCTCTACTGTAACTTTAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAAGACATGATACGATCTGCTCTACTGTAACTTTAGAGAGATAA
54739227 GATCCTTTATTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
66 GATCCTTTATTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
*
54739290 TCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCTGCTCTACTGTAACTTTAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAAGACATGATACGATCTGCTCTACTGTAACTTTAGAGAGATAA
* *
54739355 GATTCTTTAATTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
66 GATCCTTT-ATTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
54739419 TCCACTGTAATCTCAGGGAGATA
1 TCCACTGTAATCTCAGGGAGATA
54739442 GGATTACTTG
Statistics
Matches: 266, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
128 189 0.71
129 77 0.29
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (128 bp):
TCCACTGTAATCTCAGGGAGATAAGACATGATACGATCTGCTCTACTGTAACTTTAGAGAGATAA
GATCCTTTATTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
Found at i:54741505 original size:14 final size:14
Alignment explanation
Indices: 54741486--54741515 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54741476 TTCCTATTGG
54741486 CCGCCTCCACTGCA
1 CCGCCTCCACTGCA
54741500 CCGCCTCCACTGCA
1 CCGCCTCCACTGCA
54741514 CC
1 CC
54741516 ATTCATTTTT
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:0.13, C:0.60, G:0.13, T:0.13
Consensus pattern (14 bp):
CCGCCTCCACTGCA
Found at i:54758283 original size:40 final size:40
Alignment explanation
Indices: 54758216--54758313 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 40
54758206 AATTATTGAA
* ** * *
54758216 TGAATGCACATATGTGCCCCTATTTGTACTTCGGTACTCC
1 TGAATGCACATACGTGCCAATAATTGTACTTCGGTACCCC
*
54758256 TGCATGCACATACGTGCCAATAATTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCAATAATTGTACTTCGGTACCCC
* *
54758296 TGAATGCACTTACATGCC
1 TGAATGCACATACGTGCC
54758314 TTTGCATATA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (40 bp):
TGAATGCACATACGTGCCAATAATTGTACTTCGGTACCCC
Found at i:54770447 original size:23 final size:25
Alignment explanation
Indices: 54770402--54770451 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
54770392 TGCATGAATA
*
54770402 ATAATAATAATAATGCAAGTAACAAT
1 ATAATAATAACAAT-CAAGTAACAAT
54770428 ATAATAATAACAAT-AA-TAACAAT
1 ATAATAATAACAATCAAGTAACAAT
54770451 A
1 A
54770452 ACGATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
26 13 0.57
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (25 bp):
ATAATAATAACAATCAAGTAACAAT
Found at i:54772455 original size:44 final size:44
Alignment explanation
Indices: 54772361--54772644 Score: 171
Period size: 44 Copynumber: 6.3 Consensus size: 44
54772351 TTTTAATCCA
* * * * * * ** *
54772361 CTCCACTGCAACTTTAGGGAGATAGGATTAGTAACTTTAGTCTT
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAACCTG
*
54772405 CTCCACTGCAACTTCAAGGAGATAAGACTTGTATCTTCAACCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAACCTG
* * * * *
54772449 CCCCACTACAACTTC-AGGGGTACAAGGTTTGT-TACTTCAACCTG
1 CTCCACTGCAACTTCAAGGAG-ATAAGATTTGTAT-CTTCAACCTG
* * * * ** * *
54772493 CTCTACTGTAAC-TCTAGAGAGATAAGGTTTGTGGCTTTAATCTG
1 CTCCACTGCAACTTCAAG-GAGATAAGATTTGTATCTTCAACCTG
* *
54772537 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCCTGTCTTCAATCTG
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTA-----TCTTCAACCTG
* * * *
54772586 CTCCACTGCAAATTC-AGAGAGATAAGATTGGTTTATTTTTAACCTG
1 CTCCACTGCAACTTCAAG-GAGATAAGATT--TGTATCTTCAACCTG
*
54772632 CTCCACTACAACT
1 CTCCACTGCAACT
54772645 ACTCCACTAC
Statistics
Matches: 185, Mismatches: 41, Indels: 26
0.73 0.16 0.10
Matches are distributed among these distances:
43 7 0.04
44 116 0.63
45 5 0.03
46 19 0.10
48 1 0.01
49 34 0.18
51 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAACCTG
Found at i:54772651 original size:14 final size:14
Alignment explanation
Indices: 54772632--54772658 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54772622 TTTTAACCTG
54772632 CTCCACTACAACTA
1 CTCCACTACAACTA
54772646 CTCCACTACAACT
1 CTCCACTACAACT
54772659 TCAGGGAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (14 bp):
CTCCACTACAACTA
Found at i:54781740 original size:6 final size:6
Alignment explanation
Indices: 54781729--54781760 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
54781719 AATAAATATA
54781729 TATTTT TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TA
54781761 AAATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:54784854 original size:14 final size:14
Alignment explanation
Indices: 54784835--54784867 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54784825 CTGGCCCACC
54784835 TATATTAATT-TTTT
1 TATATT-ATTATTTT
54784849 TATATTATTATTTT
1 TATATTATTATTTT
54784863 TATAT
1 TATAT
54784868 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATTATTATTTT
Found at i:54784938 original size:24 final size:24
Alignment explanation
Indices: 54784906--54784951 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54784896 CAAACACACT
*
54784906 AAAACATTAAAAGAAATGTTTTCC
1 AAAAAATTAAAAGAAATGTTTTCC
*
54784930 AAAAAATTAAAAGAAATTTTTT
1 AAAAAATTAAAAGAAATGTTTT
54784952 AAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (24 bp):
AAAAAATTAAAAGAAATGTTTTCC
Found at i:54786138 original size:14 final size:14
Alignment explanation
Indices: 54786119--54786151 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54786109 CTGGCCCACC
54786119 TATATTAATT-TTTT
1 TATATT-ATTATTTT
54786133 TATATTATTATTTT
1 TATATTATTATTTT
54786147 TATAT
1 TATAT
54786152 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATTATTATTTT
Found at i:54789111 original size:17 final size:17
Alignment explanation
Indices: 54789089--54789126 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54789079 GAAACCCTAG
54789089 CTTTTTCTACTTTCTTT
1 CTTTTTCTACTTTCTTT
* *
54789106 CTTTTTTTATTTTCTTT
1 CTTTTTCTACTTTCTTT
54789123 CTTT
1 CTTT
54789127 CCTTCTCTGT
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:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTTTCTACTTTCTTT
Found at i:54789548 original size:17 final size:17
Alignment explanation
Indices: 54789526--54789563 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54789516 GAAACCCTAG
54789526 CTTTTTCTACTTTCTTT
1 CTTTTTCTACTTTCTTT
* *
54789543 CTTTTTTTATTTTCTTT
1 CTTTTTCTACTTTCTTT
54789560 CTTT
1 CTTT
54789564 CCTTCTCTGT
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:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTTTCTACTTTCTTT
Found at i:54789677 original size:437 final size:437
Alignment explanation
Indices: 54788863--54789736 Score: 1739
Period size: 437 Copynumber: 2.0 Consensus size: 437
54788853 AAAATTTATA
54788863 CTTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATTAATCTAGTCTCTAATA
1 CTTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATTAATCTAGTCTCTAATA
54788928 CTCAAATTATTCAATATAGAAAACATTTAAAAACTCAATAATTTCTAAAATTTAGACATGGGTCA
66 CTCAAATTATTCAATATAGAAAACATTTAAAAACTCAATAATTTCTAAAATTTAGACATGGGTCA
54788993 GGTAGTATTTAATGCCAGGATTCTAAAAACATAAAAATTACAAGAAAAGTGACTAAATTGACTAA
131 GGTAGTATTTAATGCCAGGATTCTAAAAACATAAAAATTACAAGAAAAGTGACTAAATTGACTAA
54789058 CCAATTAAGCTTTGAACAATTGAAACCCTAGCTTTTTCTACTTTCTTTCTTTTTTTATTTTCTTT
196 CCAATTAAGCTTTGAACAATTGAAACCCTAGCTTTTTCTACTTTCTTTCTTTTTTTATTTTCTTT
54789123 CTTTCCTTCTCTGTTTTCGTTTCAATTTGTTTCTTTTTCTATTTCTTTTTCATTTTATTTGTGTT
261 CTTTCCTTCTCTGTTTTCGTTTCAATTTGTTTCTTTTTCTATTTCTTTTTCATTTTATTTGTGTT
54789188 GTTTTATTATTATTTCATTTACTTATTATCATAATAATATAATATATATACTTAAATATTAAGTA
326 GTTTTATTATTATTTCATTTACTTATTATCATAATAATATAATATATATACTTAAATATTAAGTA
54789253 AGTATAATTTATAAATAAATATATGTATATAAATTTTACACATGGCT
391 AGTATAATTTATAAATAAATATATGTATATAAATTTTACACATGGCT
54789300 CTTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATTAATCTAGTCTCTAATA
1 CTTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATTAATCTAGTCTCTAATA
54789365 CTCAAATTATTCAATATAGAAAACATTTAAAAACTCAATAATTTCTAAAATTTAGACATGGGTCA
66 CTCAAATTATTCAATATAGAAAACATTTAAAAACTCAATAATTTCTAAAATTTAGACATGGGTCA
54789430 GGTAGTATTTAATGCCAGGATTCTAAAAACATAAAAATTACAAGAAAAGTGACTAAATTGACTAA
131 GGTAGTATTTAATGCCAGGATTCTAAAAACATAAAAATTACAAGAAAAGTGACTAAATTGACTAA
*
54789495 CCAATTGAGCTTTGAACAATTGAAACCCTAGCTTTTTCTACTTTCTTTCTTTTTTTATTTTCTTT
196 CCAATTAAGCTTTGAACAATTGAAACCCTAGCTTTTTCTACTTTCTTTCTTTTTTTATTTTCTTT
54789560 CTTTCCTTCTCTGTTTTCGTTTCAATTTGTTTCTTTTTCTATTTCTTTTTCATTTTATTTGTGTT
261 CTTTCCTTCTCTGTTTTCGTTTCAATTTGTTTCTTTTTCTATTTCTTTTTCATTTTATTTGTGTT
54789625 GTTTTATTATTATTTCATTTACTTATTATCATAATAATATAATATATATACTTAAATATTAAGTA
326 GTTTTATTATTATTTCATTTACTTATTATCATAATAATATAATATATATACTTAAATATTAAGTA
54789690 AGTATAATTTATAAATAAATATATGTATATAAATTTTACACATGGCT
391 AGTATAATTTATAAATAAATATATGTATATAAATTTTACACATGGCT
54789737 TCACCAACAC
Statistics
Matches: 436, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
437 436 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (437 bp):
CTTTATTCTACAATTCAATCCTTTTTCATTTCTAACTTAAAAATCTATTAATCTAGTCTCTAATA
CTCAAATTATTCAATATAGAAAACATTTAAAAACTCAATAATTTCTAAAATTTAGACATGGGTCA
GGTAGTATTTAATGCCAGGATTCTAAAAACATAAAAATTACAAGAAAAGTGACTAAATTGACTAA
CCAATTAAGCTTTGAACAATTGAAACCCTAGCTTTTTCTACTTTCTTTCTTTTTTTATTTTCTTT
CTTTCCTTCTCTGTTTTCGTTTCAATTTGTTTCTTTTTCTATTTCTTTTTCATTTTATTTGTGTT
GTTTTATTATTATTTCATTTACTTATTATCATAATAATATAATATATATACTTAAATATTAAGTA
AGTATAATTTATAAATAAATATATGTATATAAATTTTACACATGGCT
Found at i:54798986 original size:36 final size:36
Alignment explanation
Indices: 54798940--54799014 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
54798930 ATGTTCATGA
* *
54798940 TTTACGAACTTACTAAGCATTATATGCTTATGTTGT
1 TTTACAAACTTACTAAGCATTATATGCTTACGTTGT
54798976 TTTACAAACTTACTAAGCATTATATGCTTACGTTGT
1 TTTACAAACTTACTAAGCATTATATGCTTACGTTGT
54799012 TTT
1 TTT
54799015 CTTTCCTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTACAAACTTACTAAGCATTATATGCTTACGTTGT
Found at i:54801864 original size:27 final size:27
Alignment explanation
Indices: 54801807--54801984 Score: 97
Period size: 27 Copynumber: 6.4 Consensus size: 27
54801797 TTAGGTTGCA
* * * *
54801807 CCACGAAGGTGTTCCTTTTCAGATATAG
1 CCACGAAGG-CTTCCTTTACAGAGATTG
*
54801835 CCACGAAGGCTTCCTTTACAAAGATTG
1 CCACGAAGGCTTCCTTTACAGAGATTG
* * *
54801862 CCACAAAGACTTTCCTTTCCAGAG-TTG
1 CCACGAAGGC-TTCCTTTACAGAGATTG
* * * * * ** *
54801889 ACACCAAGGCATCCTCTCCTTAGGTTGCG
1 CCACGAAGGCTTCCTTTACAGAGATT--G
* * * *
54801918 CCACGAAGGCATTCCTTTTCAAATATAG
1 CCACGAAGGC-TTCCTTTACAGAGATTG
* *
54801946 CCACGAAGGCTTCATTTACGGAGATTG
1 CCACGAAGGCTTCCTTTACAGAGATTG
*
54801973 CCACAAAGGCTT
1 CCACGAAGGCTT
54801985 TCCTGTCTAG
Statistics
Matches: 112, Mismatches: 33, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
26 9 0.08
27 55 0.49
28 31 0.28
29 9 0.08
30 8 0.07
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (27 bp):
CCACGAAGGCTTCCTTTACAGAGATTG
Found at i:54801944 original size:111 final size:111
Alignment explanation
Indices: 54801748--54801998 Score: 385
Period size: 111 Copynumber: 2.3 Consensus size: 111
54801738 TCGTTTGTAT
* *
54801748 TTGCCACAAGGGCTTTCCTTTACAGAGTTGACACCAAGGCATCCTATCCTTAGGTTGCACCACGA
1 TTGCCACAAAGGCTTTCCTTTCCAGAGTTGACACCAAGGCATCCTATCCTTAGGTTGCACCACGA
** * *
54801813 AGGTGTTCCTTTTCAGATATAGCCACGAAGGCTTCCTTTACAAAGA
66 AGGCATTCCTTTTCAAATATAGCCACGAAGGCTTCATTTACAAAGA
* * *
54801859 TTGCCACAAAGACTTTCCTTTCCAGAGTTGACACCAAGGCATCCTCTCCTTAGGTTGCGCCACGA
1 TTGCCACAAAGGCTTTCCTTTCCAGAGTTGACACCAAGGCATCCTATCCTTAGGTTGCACCACGA
**
54801924 AGGCATTCCTTTTCAAATATAGCCACGAAGGCTTCATTTACGGAGA
66 AGGCATTCCTTTTCAAATATAGCCACGAAGGCTTCATTTACAAAGA
* *
54801970 TTGCCACAAAGGCTTTCCTGTCTAGAGTT
1 TTGCCACAAAGGCTTTCCTTTCCAGAGTT
54801999 TGCTACAAAG
Statistics
Matches: 126, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 126 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (111 bp):
TTGCCACAAAGGCTTTCCTTTCCAGAGTTGACACCAAGGCATCCTATCCTTAGGTTGCACCACGA
AGGCATTCCTTTTCAAATATAGCCACGAAGGCTTCATTTACAAAGA
Found at i:54802010 original size:28 final size:28
Alignment explanation
Indices: 54801970--54802044 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
54801960 TTTACGGAGA
*
54801970 TTGCCACAAAGGCTTTCCTGTCTAGAGT
1 TTGCTACAAAGGCTTTCCTGTCTAGAGT
*
54801998 TTGCTACAAAGGCTTTCTTGTCTAGAGT
1 TTGCTACAAAGGCTTTCCTGTCTAGAGT
*
54802026 TTACTACAAAGGCTTTCCT
1 TTGCTACAAAGGCTTTCCT
54802045 TTGACAGAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (28 bp):
TTGCTACAAAGGCTTTCCTGTCTAGAGT
Found at i:54802064 original size:29 final size:29
Alignment explanation
Indices: 54802031--54802187 Score: 94
Period size: 29 Copynumber: 5.6 Consensus size: 29
54802021 AGAGTTTACT
* * *
54802031 ACAAAGGCTTTCCTTTGACAGAGATCGCC
1 ACAAAGGCTTACCTTTAACAGAGTTCGCC
* * * * *
54802060 ACAAAGTCTGACCTTTCACAGA-TTTGGC
1 ACAAAGGCTTACCTTTAACAGAGTTCGCC
*
54802088 ACAAAGGCGTT--CTTTAATAG-GTTCGCC
1 ACAAAGGC-TTACCTTTAACAGAGTTCGCC
* **
54802115 ACAAAGGCTTACCTTT-TCAGAGTTTTTCC
1 ACAAAGGCTTACCTTTAACAGAG-TTCGCC
* * * *
54802144 A-TAAGGGTTGTCCTTTAACAG-GTTTGCC
1 ACAAAGGCTT-ACCTTTAACAGAGTTCGCC
54802172 ACAAAGGCTTACCTTT
1 ACAAAGGCTTACCTTT
54802188 CTAGATTTTT
Statistics
Matches: 94, Mismatches: 25, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
26 2 0.02
27 21 0.22
28 32 0.34
29 36 0.38
30 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (29 bp):
ACAAAGGCTTACCTTTAACAGAGTTCGCC
Found at i:54802228 original size:57 final size:57
Alignment explanation
Indices: 54802112--54802239 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 57
54802102 TAATAGGTTC
* * * * **
54802112 GCCACAAAGGCTTACCTTTTCAGAGTTTTTCCATAAGGGTTGTCCTTTAACAGGTTT
1 GCCACAAAGGCTTACCTTTTCAGAGTTTTTCCACAAAGGTCGTCCTTAAACAGAATT
*
54802169 GCCACAAAGGCTTACC-TTTCTAGATTTTTTCCACAAAGG-CGTCCTTAAACAGAAATT
1 GCCACAAAGGCTTACCTTTTC-AGAGTTTTTCCACAAAGGTCGTCCTTAAACAG-AATT
54802226 GCCACAAAAGGCTT
1 GCCAC-AAAGGCTT
54802240 TTCTTTTCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
56 15 0.25
57 38 0.62
58 8 0.13
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (57 bp):
GCCACAAAGGCTTACCTTTTCAGAGTTTTTCCACAAAGGTCGTCCTTAAACAGAATT
Found at i:54802514 original size:53 final size:53
Alignment explanation
Indices: 54802359--54802515 Score: 180
Period size: 53 Copynumber: 3.1 Consensus size: 53
54802349 ATTTAATTTG
*
54802359 TTTCCATATGATGCAATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
1 TTTCCATATGATGTAATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
** * * * *
54802412 TTTTAATATGATGTCAT-A-CTA--A-TTACGGTCTTATATGATATGGTCTTC
1 TTTCCATATGATGTAATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
* * * *
54802460 TTTCCTTATGATGTTATAACCCACCAGTTATGGTCTTACACGATATGGTTTTC
1 TTTCCATATGATGTAATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
54802513 TTT
1 TTT
54802516 AGTGCCATGG
Statistics
Matches: 83, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
48 37 0.45
49 2 0.02
50 2 0.02
51 2 0.02
52 2 0.02
53 38 0.46
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (53 bp):
TTTCCATATGATGTAATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
Found at i:54804257 original size:3 final size:3
Alignment explanation
Indices: 54804249--54804277 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54804239 TACTTTATTG
54804249 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
54804278 TCCATCCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:54805269 original size:51 final size:50
Alignment explanation
Indices: 54805214--54805398 Score: 212
Period size: 51 Copynumber: 3.7 Consensus size: 50
54805204 CCGATTTACA
* * *
54805214 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCATCCGGTACACG
** * ** *
54805265 TAGTAGCCTGCACATAGTACTACACACGTGATTGA-AGCTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATCCGGTACACG
* * *
54805316 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTCCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-TCCGGTACACG
54805366 TAGTAGCCTGCACATAGTACTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC
54805399 TAGCAATTTC
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 41 0.37
51 67 0.61
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATATCATCCGGTACACG
Found at i:54805391 original size:101 final size:101
Alignment explanation
Indices: 54805212--54805396 Score: 309
Period size: 101 Copynumber: 1.8 Consensus size: 101
54805202 ACCCGATTTA
* *
54805212 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TATCATCCGATACACGTAGTAGCCTGCA
54805277 CATAGTACTACACACGTGATTGAAGCTATCCGGTATG
65 CATAGTACTACACACGTGATTGAAGCTATCCGGTATG
* *
54805314 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTCCACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATATCA-TCCGATACACGTAGTAGCCTGCA
54805378 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
54805397 CCTAGCAATT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.51
102 34 0.44
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATATCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATTGAAGCTATCCGGTATG
Found at i:54813671 original size:22 final size:21
Alignment explanation
Indices: 54813622--54813673 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
54813612 AATAATTATG
*
54813622 TTAA-ATTATATTTTATAGTA
1 TTAATATTATATTTTATAATA
54813642 TTATATATTATGATTTTAGTAAT-
1 TTA-ATATTAT-ATTTTA-TAATA
54813665 TTAATATTA
1 TTAATATTA
54813674 AGAATATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTAATATTATATTTTATAATA
Found at i:54813963 original size:16 final size:16
Alignment explanation
Indices: 54813942--54813974 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54813932 TTGATTTGTT
*
54813942 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
54813958 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
54813974 A
1 A
54813975 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:54825373 original size:89 final size:90
Alignment explanation
Indices: 54825262--54825441 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 90
54825252 ATAAAATATT
54825262 ATAAAATTTAATAAACTATTTTGGGTTTTTTACAATAATATTATAAAAAAACAAAAATTTACCAA
1 ATAAAATTTAATAAACTATTTTGGGTTTTTTACAATAATATTATAAAAAAACAAAAATTTACCAA
54825327 AATATTATAACTTTTTTTATTTACC
66 AATATTATAACTTTTTTTATTTACC
54825352 ATAAAATTT-ATAAACTATTTTGGGTTTTTTACAATAATATTATAAAAAAACAAAAATTTACCAA
1 ATAAAATTTAATAAACTATTTTGGGTTTTTTACAATAATATTATAAAAAAACAAAAATTTACCAA
54825416 AATATTATAACTTTTTTTATTTACC
66 AATATTATAACTTTTTTTATTTACC
54825441 A
1 A
54825442 AAATATATAA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 81 0.90
90 9 0.10
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (90 bp):
ATAAAATTTAATAAACTATTTTGGGTTTTTTACAATAATATTATAAAAAAACAAAAATTTACCAA
AATATTATAACTTTTTTTATTTACC
Found at i:54825460 original size:26 final size:26
Alignment explanation
Indices: 54825431--54825482 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
54825421 TATAACTTTT
54825431 TTTATTTACCAAAATATATAAAAAAA
1 TTTATTTACCAAAATATATAAAAAAA
54825457 TTTATTTACCAAAATATATAAAAAAA
1 TTTATTTACCAAAATATATAAAAAAA
54825483 CAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (26 bp):
TTTATTTACCAAAATATATAAAAAAA
Found at i:54825488 original size:89 final size:87
Alignment explanation
Indices: 54825306--54825492 Score: 202
Period size: 89 Copynumber: 2.2 Consensus size: 87
54825296 ATAATATTAT
* ** *
54825306 AAAAAAACAAAAATTTACCAAAATATTATAACTTTTTTTATTTACCATAAAATTTATAAACTATT
1 AAAAAAACAAAAATTTACCAAAATATTATAACTTTTTTTATTTACCA-AAAATATATAAAAAAAT
* *** * ** *
54825371 TTGGGTTTTTTACAATAATATTAT
65 TT-GATTTACCAAAATAATAAAAC
54825395 AAAAAAACAAAAATTTACCAAAATATTATAACTTTTTTTATTTACC-AAAATATATAAAAAAATT
1 AAAAAAACAAAAATTTACCAAAATATTATAACTTTTTTTATTTACCAAAAATATATAAAAAAATT
54825459 T-ATTTACCAAAATATATAAAA-
66 TGATTTACCAAAATA-ATAAAAC
*
54825480 AAACAAA-AAAAAT
1 AAAAAAACAAAAAT
54825493 CAGATTGATG
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
84 6 0.07
85 14 0.16
86 4 0.05
87 15 0.18
89 46 0.54
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (87 bp):
AAAAAAACAAAAATTTACCAAAATATTATAACTTTTTTTATTTACCAAAAATATATAAAAAAATT
TGATTTACCAAAATAATAAAAC
Found at i:54825560 original size:27 final size:27
Alignment explanation
Indices: 54825530--54825623 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
54825520 CGCCAATGGT
* *
54825530 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
54825557 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
54825584 ATTGGCGGCACCAATGGTGCC-ATACTA
1 ATTGGCGGCACCAATGGTGCCAATAC-C
54825611 ATTGGCGGCACCA
1 ATTGGCGGCACCA
54825624 CTCGTATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
26 3 0.05
27 58 0.95
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:54825727 original size:10 final size:11
Alignment explanation
Indices: 54825705--54825742 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
54825695 GTTGCTGCGG
*
54825705 AAAAGAAGAGA
1 AAAAGAGGAGA
54825716 AAAAGAGG-GA
1 AAAAGAGGAGA
54825726 AAAAGAGGAGA
1 AAAAGAGGAGA
54825737 AAAAGA
1 AAAAGA
54825743 AGGTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAAAGAGGAGA
Found at i:54825806 original size:19 final size:21
Alignment explanation
Indices: 54825768--54825806 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
54825758 AATAATTGAT
*
54825768 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
54825789 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
54825807 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:54825868 original size:3 final size:3
Alignment explanation
Indices: 54825852--54825886 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
54825842 AAAATAATAG
*
54825852 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54825887 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:54825891 original size:3 final size:3
Alignment explanation
Indices: 54825885--54825925 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
54825875 ATTATTATTA
*
54825885 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTC TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
54825926 AGTATTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.29, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:54829016 original size:18 final size:18
Alignment explanation
Indices: 54828993--54829047 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
54828983 TCCCTCTTCT
54828993 TCTTCTTCTTTTTTTTTC
1 TCTTCTTCTTTTTTTTTC
* **
54829011 TCTTCTCCTTTCCTTTTC
1 TCTTCTTCTTTTTTTTTC
*
54829029 T-TTCCTTCTTTTTCTTTC
1 TCTT-CTTCTTTTTTTTTC
54829047 T
1 T
54829048 TTCATCTCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTCTTCTTTTTTTTTC
Found at i:54829016 original size:24 final size:24
Alignment explanation
Indices: 54828986--54829082 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 24
54828976 TCTTCCTTCC
*
54828986 CTCTTCTTCTTCTTCTTTTTTTTT
1 CTCTTCTTCTTCTTCTTTTTCTTT
* *
54829010 CTCTTC-TCCT-TTCCTTTTCTTT
1 CTCTTCTTCTTCTTCTTTTTCTTT
* * *
54829032 C-CTTCTTTTTCTT-TCTTTC-AT
1 CTCTTCTTCTTCTTCTTTTTCTTT
*
54829053 CTCCT-TTCTTTCTT-TTTTTCTTT
1 CTCTTCTTC-TTCTTCTTTTTCTTT
54829076 CT-TTCTT
1 CTCTTCTT
54829083 TCTTTCCCTC
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
21 8 0.15
22 30 0.56
23 10 0.19
24 6 0.11
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (24 bp):
CTCTTCTTCTTCTTCTTTTTCTTT
Found at i:54829046 original size:4 final size:4
Alignment explanation
Indices: 54829025--54829088 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
54829015 CTCCTTTCCT
* * *
54829025 TTTC TTTC CTTC -TT- TTTC TTTC TTTC ATCTCC TTTC TTTC TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -T-TTC TTTC TTTC TTTC TTTC
54829073 TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC
54829089 CCTCTCCTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
3 4 0.08
4 43 0.84
5 2 0.04
6 2 0.04
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:54829889 original size:22 final size:22
Alignment explanation
Indices: 54829831--54829889 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
54829821 GAATGGTATC
54829831 TACAAATCAAATCTCTAAGATT
1 TACAAATCAAATCTCTAAGATT
*
54829853 TACAAAATCATATCTCCTAAGA-T
1 TAC-AAATCAAATCT-CTAAGATT
*
54829876 TACATATCAAATCT
1 TACAAATCAAATCT
54829890 ACGATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 12 0.38
23 14 0.44
24 6 0.19
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
TACAAATCAAATCTCTAAGATT
Found at i:54835005 original size:22 final size:22
Alignment explanation
Indices: 54834978--54835031 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
54834968 CGAATGGTAT
54834978 CAAATCAAATC-TCTAAGATTA
1 CAAATCAAATCTTCTAAGATTA
*
54834999 CAAAATCATATCTTCTAAGATTA
1 C-AAATCAAATCTTCTAAGATTA
*
54835022 CATATCAAAT
1 CAAATCAAAT
54835032 ATACGATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 11 0.39
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (22 bp):
CAAATCAAATCTTCTAAGATTA
Found at i:54842787 original size:20 final size:19
Alignment explanation
Indices: 54842743--54842794 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
54842733 AATATATGTT
54842743 TATTT-AATATATTATAAA
1 TATTTAAATATATTATAAA
* *
54842761 T-TATAAATATATTTTAAA
1 TATTTAAATATATTATAAA
*
54842779 TAATTTAAAAATATTA
1 T-ATTTAAATATATTA
54842795 AATTAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 14 0.54
20 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTTAAATATATTATAAA
Found at i:54845670 original size:16 final size:16
Alignment explanation
Indices: 54845645--54845690 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
54845635 TTGATTTGCT
*
54845645 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
*
54845661 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
54845677 ATTACGCCTCTATT
1 ATTACGCCTCTATT
54845691 TCAATACAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:54847232 original size:6 final size:6
Alignment explanation
Indices: 54847221--54847550 Score: 660
Period size: 6 Copynumber: 55.0 Consensus size: 6
54847211 ATTAATATAT
54847221 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847269 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847317 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847365 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847413 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847461 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847509 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA
54847551 GTTTCATCAA
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 324 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:54848918 original size:12 final size:12
Alignment explanation
Indices: 54848903--54848940 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
54848893 TGAAAAGTTT
54848903 AATAATAATATA
1 AATAATAATATA
54848915 AATAATAATATA
1 AATAATAATATA
* *
54848927 TATAATGATATA
1 AATAATAATATA
54848939 AA
1 AA
54848941 AGTTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
AATAATAATATA
Found at i:54848927 original size:43 final size:42
Alignment explanation
Indices: 54848867--54848962 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 42
54848857 TACATTAGTC
54848867 TAAATAAGTAATATATATATAT-ATAATGAAAAGTTTAATAATAATA
1 TAAATAA-TAATATATATA-ATGAT-AT-AAAAGTTTAATAA-AATA
*
54848913 TAAATAATAATATATATAATGATATAAAAGTTTAATAACATA
1 TAAATAATAATATATATAATGATATAAAAGTTTAATAAAATA
54848955 T-AATAATA
1 TAAATAATA
54848963 TGTATAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
41 7 0.15
42 4 0.08
43 13 0.27
44 4 0.08
45 13 0.27
46 7 0.15
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (42 bp):
TAAATAATAATATATATAATGATATAAAAGTTTAATAAAATA
Found at i:54850384 original size:26 final size:25
Alignment explanation
Indices: 54850345--54850393 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
54850335 CTTATATCCG
*
54850345 AATCAAATAGAAGAGA-AAAAATCAA
1 AATCAAATAAAAGA-ATAAAAATCAA
54850370 AATCAAAATAAAAGAATAAAAATC
1 AATC-AAATAAAAGAATAAAAATC
54850394 CATCCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.14
Consensus pattern (25 bp):
AATCAAATAAAAGAATAAAAATCAA
Found at i:54857529 original size:15 final size:14
Alignment explanation
Indices: 54857509--54857551 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 14
54857499 TATTTTAAAT
54857509 TTTTTAAAAATTATA
1 TTTTTAAAAATTA-A
54857524 TTTTTAAAATAATTAA
1 TTTTT-AAA-AATTAA
54857540 TATTTTAAAAAT
1 T-TTTTAAAAAT
54857552 AAAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.32
16 8 0.32
17 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTTAAAAATTAA
Found at i:54857544 original size:18 final size:18
Alignment explanation
Indices: 54857503--54857553 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
54857493 AAAAAATATT
*
54857503 TTAA-ATTTTTTAAA-AA
1 TTAATATTTTTAAAATAA
54857519 TT-ATATTTTTAAAATAA
1 TTAATATTTTTAAAATAA
*
54857536 TTAATATTTTAAAAATAA
1 TTAATATTTTTAAAATAA
54857554 AAATATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 11 0.37
17 4 0.13
18 14 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATATTTTTAAAATAA
Found at i:54857558 original size:17 final size:18
Alignment explanation
Indices: 54857521--54857559 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54857511 TTTAAAAATT
* *
54857521 ATATTTTTAAAATAATTA
1 ATATTTTAAAAATAATAA
54857539 ATATTTTAAAAATAA-AA
1 ATATTTTAAAAATAATAA
54857556 ATAT
1 ATAT
54857560 AAGATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTTAAAAATAATAA
Found at i:54866461 original size:6 final size:6
Alignment explanation
Indices: 54866450--54866477 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
54866440 GAGCAGCACT
54866450 AATGCA AATGCA AATGCA AATGCA AATG
1 AATGCA AATGCA AATGCA AATGCA AATG
54866478 AAGAGGTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
AATGCA
Found at i:54866946 original size:111 final size:111
Alignment explanation
Indices: 54866724--54866997 Score: 351
Period size: 111 Copynumber: 2.5 Consensus size: 111
54866714 ACAGGCAGCG
* * *
54866724 TTACGGACAACGAAAATGC-AGTTCGGAATGAGAATAACGCTT-TCCAGAACTT---GAACAACA
1 TTACCGACAACGAAAATGCAAG-TCAGAATGAGAATAATGCTTCT-CAGAACTTAAAGAACAACA
* * * **
54866784 ATAACAATGAGAATGCAGGCCAAAATGAGAATGATGCTGCTCAGAGCA
64 ACAACAATGAGAATGCAGACCAAAATAAGAAAAATGCTGCTCAGAGCA
* * *
54866832 TTACTGACAACAAAAATGCAAGTCAGAATGAGAATGATGCTTCTCAGAACTTAAAGAACAACAAC
1 TTACCGACAACGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAACTTAAAGAACAACAAC
* * *
54866897 AACAATGAGAGTGCAGACCGAAATAAGAAAAATGCTGCTGAGAGCA
66 AACAATGAGAATGCAGACCAAAATAAGAAAAATGCTGCTCAGAGCA
* *
54866943 TTACCGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAGAACTTAAA
1 TTACCGACAACGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAACTTAAA
54866998 CAACGACGGA
Statistics
Matches: 143, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
108 42 0.29
109 3 0.02
111 98 0.69
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (111 bp):
TTACCGACAACGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAACTTAAAGAACAACAAC
AACAATGAGAATGCAGACCAAAATAAGAAAAATGCTGCTCAGAGCA
Found at i:54867064 original size:111 final size:109
Alignment explanation
Indices: 54866724--54867050 Score: 333
Period size: 111 Copynumber: 3.0 Consensus size: 109
54866714 ACAGGCAGCG
* * * * * * *
54866724 TTACGGACAACGAAAATGCAGTTCGGAATGAGAATAACGCTTTCCAGAACTTGAACAACAATAAC
1 TTACCGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAGAACTTAAACAAC-ACAAC
* * *
54866789 AATGAGAATGCAGGCCAAAATGAG--AATGATGCTGCTCAGAGCA
65 AATGAGAATGCAAGACAGAATGAGAAAATGATGCTGCTCAGAGCA
* * * * *
54866832 TTACTGACAACAAAAATGCAAGTCAGAATGAGAATGATGCTTCTCAGAACTTAAAGAACAACAAC
1 TTACCGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAGAACTT--A-AACAAC-AC
* * * *
54866897 AACAATGAGAGTGC-AGACCGAAATAAGAAAA--ATGCTGCTGAGAGCA
62 AACAATGAGAATGCAAGACAG-AATGAGAAAATGATGCTGCTCAGAGCA
*
54866943 TTACCGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAGAACTTAAACAACGACGGA
1 TTACCGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAGAACTTAAACAAC-AC-AA
* *
54867008 -AATGAGAATGCAAGACAGAATGAGAACAATGATCCTGTTCAGA
64 CAATGAGAATGCAAGACAGAATGAGAA-AATGATGCTGCTCAGA
54867051 TCAACACCAA
Statistics
Matches: 177, Mismatches: 31, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
108 68 0.38
109 9 0.05
110 2 0.01
111 96 0.54
113 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (109 bp):
TTACCGACAACGAAAATGCAGGTCAGAATGAGAATAATGCTTCCCAGAACTTAAACAACACAACA
ATGAGAATGCAAGACAGAATGAGAAAATGATGCTGCTCAGAGCA
Found at i:54868821 original size:89 final size:88
Alignment explanation
Indices: 54868641--54868805 Score: 215
Period size: 89 Copynumber: 1.8 Consensus size: 88
54868631 TAAAACTATA
* * * * *
54868641 AAAAGTGATTATCAAAATATCCTTTTTTAATTATTTTTTTAATTTAATATTTCAATTATTAGACT
1 AAAAGTGATTATAAAAATATCCTTTTTAAATTAATTATTTAATTTAATATTTCAATTATTAAACT
*
54868706 TTTAATCTTGATCTAAAATTACT
66 TTTAATATTGATCTAAAATTACT
* *
54868729 AAAAGTGATTGTTAAAAATATCC-TTTTAAATTAAATTATTTAATTTAATATTTTTAATTATTAA
1 AAAAGTGATT-ATAAAAATATCCTTTTTAAATT-AATTATTTAATTTAATA-TTTCAATTATTAA
54868793 ACTTTTCAATATT
63 ACTTTT-AATATT
54868806 ATTAAATTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
88 18 0.28
89 25 0.38
90 17 0.26
91 5 0.08
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (88 bp):
AAAAGTGATTATAAAAATATCCTTTTTAAATTAATTATTTAATTTAATATTTCAATTATTAAACT
TTTAATATTGATCTAAAATTACT
Found at i:54869095 original size:18 final size:19
Alignment explanation
Indices: 54869072--54869115 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
54869062 TTTAGAAATT
*
54869072 ATTTTTATCGT-ATTAATA
1 ATTTTTATAGTAATTAATA
*
54869090 ATTTTTGTAGTAATTAATA
1 ATTTTTATAGTAATTAATA
*
54869109 TTTTTTA
1 ATTTTTA
54869116 AATTATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (19 bp):
ATTTTTATAGTAATTAATA
Found at i:54878389 original size:132 final size:132
Alignment explanation
Indices: 54878141--54879014 Score: 1428
Period size: 132 Copynumber: 6.6 Consensus size: 132
54878131 GAGACAAGGC
*
54878141 TAAATCTGCTT-CCACTATCTTAGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
*
54878205 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGTTTGGTGG
66 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
54878270 CT
131 CT
* * * *
54878272 TAAATTTGCTTCCCACTATCTTAGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
* * *
54878337 TAGGGATATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAGGGAGACAAGGCTTGATGG
66 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
54878402 CT
131 CT
*
54878404 TAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
* * * * *
54878469 TAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTGAGAGAGACAAGGTTTGGCGG
66 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
54878534 CT
131 CT
54878536 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
* * * *
54878601 TAGGGAGATAATATCTATAATCTTCAACCTTCTCCGCTGCTGCTTAGGGAGACAAGGTTTGGTGG
66 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
54878666 CT
131 CT
*
54878668 TAAATCTGCTTCCCACTATCTTGGAAATATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
* *
54878733 TAGGGAGATAAGATCTACATTCTTCAACCTTCTCCACT-CTTGCTCAGGGAGACAAGGCTTGGTG
66 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGC-TGCTCAGGGAGACAAGGCTTGGTG
54878797 GCT
130 GCT
* * * * * *
54878800 TAAATTTGCTTCCTACTATTTTGGAAAGATAAGTTTCACCGTCTTTGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
* *
54878865 TAGGGAGATAAGATCTACATTCTTCAACCTTCTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGG
66 TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
54878930 CT
131 CT
* * *
54878932 TAAATCTGCTTCCCATTATTTTGGAAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCT
1 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
54878997 TAGGGAGATAAGATCTAC
66 TAGGGAGATAAGATCTAC
54879015 TGGTTACCGA
Statistics
Matches: 697, Mismatches: 43, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
131 11 0.02
132 685 0.98
133 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
TAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGG
CT
Found at i:54878538 original size:264 final size:264
Alignment explanation
Indices: 54877933--54879014 Score: 1736
Period size: 264 Copynumber: 4.1 Consensus size: 264
54877923 GTCGACTTTA
* ** *
54877933 ATCTGCTCCACTGCAACTTAAGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
54877998 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
54878063 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
*
54878128 AGGGAGAC-A------A-GGC-TAAATCTGCTT-CCACTATCTTAGAAAGATAAGATTCGCCGTC
196 AGGGAGACAAGGCTTGATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
54878183 TTCG
261 TTCG
54878187 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
* * * * *
54878252 GGAGACAAGGTTTGGTGGCTTAAATTTGCTTCCCACTATCTTAGAAAGATAAGATTTGTCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
* *
54878317 CGATCTGCTCCACTACTGCTTAGGGATATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTA
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
*
54878382 AGGGAGACAAGGCTTGATGGCTTAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
196 AGGGAGACAAGGCTTGATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
54878447 TTCG
261 TTCG
* *
54878451 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTGAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
* * *
54878516 AGAGACAAGGTTTGGCGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
* * *
54878581 CGATCTGCTCCACTACTGCTTAGGGAGATAATATCTATAATCTTCAACCTTCTCCGCTGCTGCTT
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
* * *
54878646 AGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAATATAAGATTCGCCGTC
196 AGGGAGACAAGGCTTGATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
54878711 TTCG
261 TTCG
* *
54878715 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACATTCTTCAACCTTCTCCACT-CTTGCTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGC-TGCTCA
* * * * *
54878779 GGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCCTACTATTTTGGAAAGATAAGTTTCACCGTCT
65 GGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCT
* * *
54878844 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACATTCTTCAACCTTCTCCACTGCTGCT
130 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCT
* * *
54878909 CAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCATTATTTTGGAAAGATAAGATTCGCCGT
195 CAGGGAGACAAGGCTTGATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGT
*
54878974 CTTTG
260 CTTCG
54878979 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
54879015 TGGTTACCGA
Statistics
Matches: 765, Mismatches: 52, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
254 192 0.25
255 1 0.00
261 1 0.00
262 3 0.00
263 11 0.01
264 557 0.73
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (264 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
AGGGAGACAAGGCTTGATGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
TTCG
Found at i:54878746 original size:396 final size:394
Alignment explanation
Indices: 54877933--54879014 Score: 1759
Period size: 396 Copynumber: 2.8 Consensus size: 394
54877923 GTCGACTTTA
* ** *
54877933 ATCTGCTCCACTGCAACTTAAGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
54877998 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
54878063 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
*
54878128 AGGGAGACAA------GGC-TAAATCTGCTT-CCACTATCTTAGAAAGATAAGATTCGCCGTCTT
196 AGGGAGACAAGGTTGGGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
54878185 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
261 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
* * *
54878250 AGGGAGACAAGGTTTGGTGGCTTAAATTTGCTTCCCACTATCTTAGAAAGATAAGATTTGTCGTC
326 AGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCCGTC
54878315 TTCG
391 TTCG
* *
54878319 ATCTGCTCCACTACTGCTTAGGGATATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTAAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
* *
54878384 GGAGACAAGGCTTGATGGCTTAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
66 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
* *
54878449 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTG
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
*
54878514 AGAGAGACAAGGTTTGGCGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
196 AGGGAGACAAGG-TTGG-GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
* *
54878579 TTCGATCTGCTCCACTACTGCTTAGGGAGATAATATCTATAATCTTCAACCTTCTCCGCTGCTGC
259 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGC
* * *
54878644 TTAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAATATAAGATTCGCCG
324 TCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCCG
54878709 TCTTCG
389 TCTTCG
* *
54878715 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACATTCTTCAACCTTCTCCACT-CTTGCTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGC-TGCTCA
* * * * *
54878779 GGGAGACAAGGCTTGGTGGCTTAAATTTGCTTCCTACTATTTTGGAAAGATAAGTTTCACCGTCT
65 GGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCT
* * *
54878844 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACATTCTTCAACCTTCTCCACTGCTGCT
130 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCT
* *
54878909 CAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCATTATTTTGGAAAGATAAGATTCGCCGT
195 CAGGGAGACAAGG-TTGG-GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGT
*
54878974 CTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
258 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
54879015 TGGTTACCGA
Statistics
Matches: 641, Mismatches: 44, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
386 194 0.30
394 3 0.00
395 12 0.02
396 432 0.67
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (394 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
AGGGAGACAAGGTTGGGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
AGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCCGTC
TTCG
Found at i:54891116 original size:24 final size:25
Alignment explanation
Indices: 54891088--54891144 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
54891078 ATATACATAT
54891088 AAATAT-GAAAATACTCATTAAAAA
1 AAATATAGAAAATACTCATTAAAAA
* *
54891112 AAATATAGGAAAATATTCGTTAAAAA
1 AAATATA-GAAAATACTCATTAAAAA
*
54891138 ATATATA
1 AAATATA
54891145 TATATGTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
26 22 0.79
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (25 bp):
AAATATAGAAAATACTCATTAAAAA
Found at i:54891125 original size:26 final size:26
Alignment explanation
Indices: 54891094--54891144 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
54891084 ATATAAATAT
54891094 GAAAATACTCATTAAAAAAAATATAG
1 GAAAATACTCATTAAAAAAAATATAG
* * *
54891120 GAAAATATTCGTTAAAAAATATATA
1 GAAAATACTCATTAAAAAAAATATA
54891145 TATATGTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (26 bp):
GAAAATACTCATTAAAAAAAATATAG
Found at i:54905617 original size:16 final size:16
Alignment explanation
Indices: 54905596--54905626 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54905586 TACATATATA
54905596 AAATATAAGTAAATAG
1 AAATATAAGTAAATAG
*
54905612 AAATATAATTAAATA
1 AAATATAAGTAAATA
54905627 TAATAATAAA
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:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATATAAGTAAATAG
Found at i:54907287 original size:84 final size:84
Alignment explanation
Indices: 54907189--54907381 Score: 232
Period size: 85 Copynumber: 2.3 Consensus size: 84
54907179 TTCTGTCTAC
* *
54907189 TCCACTGCAGCTTCAGGGAGATAAGACTAT-ACGCGATCTGCTCT-CTGCAACTTCAGAGAGATA
1 TCCACTGCAACTTCAGGGAGAT-AGAAT-TGACGCGATCTGCTCTACTGCAACTTCAGAGAGATA
54907252 AGATCT-ATGGTTTTAATTCAT
64 AGATCTGA-GGTTTTAATTCAT
* * *
54907273 TCCATTGCAACTTCAGGGAGATAGAATTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 TCCACTGCAACTTCAGGGAGATAGAATT-GACGCGATCTGCTCTACTGCAACTTCAGAGAGATAA
* *
54907338 GATCTGAGGTTTTAA-CCTAC
65 GATCTGAGGTTTTAATTC-AT
* *
54907358 TCTACTACAACTTCAGGGAGATAG
1 TCCACTGCAACTTCAGGGAGATAG
54907382 GATTATTGGC
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
82 1 0.01
83 4 0.04
84 33 0.35
85 55 0.59
86 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (84 bp):
TCCACTGCAACTTCAGGGAGATAGAATTGACGCGATCTGCTCTACTGCAACTTCAGAGAGATAAG
ATCTGAGGTTTTAATTCAT
Found at i:54907570 original size:100 final size:100
Alignment explanation
Indices: 54907436--54907947 Score: 808
Period size: 100 Copynumber: 5.1 Consensus size: 100
54907426 GATTCGCCAT
*
54907436 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* *
54907501 CTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGA
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * *
54907536 CTTTAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* *
54907601 TTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
*
54907636 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCTGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* ** * *
54907701 CTACACTACTAGGGAAGTAAGATTCGCCGTTATGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* *
54907736 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCATAACTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* *
54907801 CTACACCGCCAGGGAAGTAAGATTCGTCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * * *
54907836 CTTCAATCTATTTAACTGCAACGTCAGGGAAACAAGATTCGCCATTGTGGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
*
54907901 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGCGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
54907936 CTTCAATCTATT
1 CTTCAATCTATT
54907948 CCATTGTAAT
Statistics
Matches: 377, Mismatches: 35, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 377 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
Found at i:54907950 original size:50 final size:50
Alignment explanation
Indices: 54907469--54907950 Score: 415
Period size: 50 Copynumber: 9.6 Consensus size: 50
54907459 TCGGGGAAAC
** * *
54907469 AAGATTCGCCGTCATAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* * * ** ** * **
54907519 AAGATTCACCGTTGTGACTTTAATCTATTTAACTGCAATGTCAGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* * * * *
54907569 AAGATTCACCGTCGTAGCTTCAATCTGTTCCATTGCACCGCCAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* ** ** * * **
54907619 AAGATTCACCGTTGTGGCTTCAATCTATTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* * * * * ** *
54907669 AAGATTCGCTGTCGTAGCTTCAATCTGTTCCACTACACTACTAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* ** ** * * **
54907719 AAGATTCGCCGTTATGGCTTCAATCTATTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
** ** * *
54907769 AAGATTCGCCGTCATAACTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* ** * * **
54907819 AAGATTCGTCGTTGTGGCTTCAATCTATTTAACTGCAACGTCAGGGAAAC
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
* *
54907869 AAGATTCGCCATTGTGGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
*
54907919 AAGATTCGCCGTTGCGGCTTCAATCTATTCCA
1 AAGATTCGCCGTTGTGGCTTCAATCTATTCCA
54907951 TTGTAATACC
Statistics
Matches: 325, Mismatches: 107, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 325 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
Found at i:54920586 original size:14 final size:14
Alignment explanation
Indices: 54920567--54920593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54920557 ATTTTTCTGT
54920567 TTTATTTATTATTA
1 TTTATTTATTATTA
54920581 TTTATTTATTATT
1 TTTATTTATTATT
54920594 TGTTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:54920591 original size:11 final size:11
Alignment explanation
Indices: 54920568--54920600 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54920558 TTTTTCTGTT
54920568 TTATTTA-TTA
1 TTATTTATTTA
54920578 TTATTTATTTA
1 TTATTTATTTA
*
54920589 TTATTTGTTTA
1 TTATTTATTTA
54920600 T
1 T
54920601 AATATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:54921716 original size:15 final size:17
Alignment explanation
Indices: 54921683--54921721 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
54921673 ATTAAAAGGT
54921683 TAAA-TAAGTAAATAAA
1 TAAAGTAAGTAAATAAA
54921699 TAAAGTAAGT-AA-AAA
1 TAAAGTAAGTAAATAAA
54921714 TAAAGTAA
1 TAAAGTAA
54921722 AACAAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.50
16 6 0.27
17 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (17 bp):
TAAAGTAAGTAAATAAA
Found at i:54922515 original size:30 final size:29
Alignment explanation
Indices: 54922488--54922836 Score: 190
Period size: 30 Copynumber: 11.7 Consensus size: 29
54922478 GTCATCAACC
54922488 AATGAAAAGGGATAGCTTCGACTATCAA-
1 AATGAAAAGGGATAGCTTCGACTATCAAT
* * *
54922516 AATTTGGAAAGGGATATCTTCGGCTATCAAAT
1 AA--TGAAAAGGGATAGCTTCGACTATC-AAT
* * * *
54922548 TATGAAAAGGGATAG-TGACGACCATCAAC
1 AATGAAAAGGGATAGCT-TCGACTATCAAT
* * * *
54922577 AATGAAAATGGATGATG-AT-GACCATCAAC
1 AATGAAAAGGGAT-A-GCTTCGACTATCAAT
* * *
54922606 AATGAAAAGGGAT-GATGACGACCATCGAAT
1 AATGAAAAGGGATAGCT-TCGACTATC-AAT
* * *
54922636 TATGAAAAGGGATGGCTTCAACTATCAAATT
1 AATGAAAAGGGATAGCTTCGACTATC-AA-T
* *
54922667 ATTATGAGAAGGGATAGCTTCGGCTATCGAAT
1 A--ATGAAAAGGGATAGCTTCGACTATC-AAT
* *
54922699 TATGAAAAGGGATAGCTTCGGCTATCAAAT
1 AATGAAAAGGGATAGCTTCGACTATC-AAT
* * * *
54922729 TATGAAAAGGGATAG-TGACGACCATCAAC
1 AATGAAAAGGGATAGCT-TCGACTATCAAT
* * *
54922758 AATGAAAAGGGAT-GGTGACGACCATCGAAT
1 AATGAAAAGGGATAGCT-TCGACTATC-AAT
* * * *
54922788 TATGAAAAGGGATGGCTTTGACTATCAAA
1 AATGAAAAGGGATAGCTTCGACTATCAAT
*
54922817 ATATGGAAAGGGATAGCTTC
1 A-ATGAAAAGGGATAGCTTC
54922837 AGCTATCGAA
Statistics
Matches: 252, Mismatches: 49, Indels: 38
0.74 0.14 0.11
Matches are distributed among these distances:
26 1 0.00
28 3 0.01
29 71 0.28
30 144 0.57
31 8 0.03
32 2 0.01
33 23 0.09
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.23
Consensus pattern (29 bp):
AATGAAAAGGGATAGCTTCGACTATCAAT
Found at i:54930214 original size:30 final size:29
Alignment explanation
Indices: 54930180--54930480 Score: 196
Period size: 30 Copynumber: 10.1 Consensus size: 29
54930170 ATATCAATGG
54930180 AAAGGGATAGCTTCGACTATCGAATTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
* * * **
54930210 AAAGGGATGGTGACGACCATC-AACAATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* * * * * *
54930239 AAAGGCATGGTGACAACCATTGAATTATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* *
54930269 AAAGGGATGGCTTCGGCTATCAAATTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
* *
54930299 AAAGGGATGGCTTTGGCTATCGAATTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
*
54930329 AAAGGGATAGCTTC-AGCTATCAAATTATGA
1 AAAGGGAT-GCTTCGA-CTATCGAATTATGA
* * * *
54930359 AAAGGGATGGTGACGACCATC-AATAATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* * * * *
54930388 AAAGTGATGGTGACGACCATCAAATTATGA
1 AAAGGGATGCT-TCGACTATCGAATTATGA
* *
54930418 AAAGGGATGGCTTCGACTAT-GAAAATATGG
1 AAAGGGAT-GCTTCGACTATCG-AATTATGA
* * *
54930448 AAAGGGATAACTTCGGCTATCGAACTATGA
1 AAAGGGAT-GCTTCGACTATCGAATTATGA
54930478 AAA
1 AAA
54930481 CGGGTGGTAA
Statistics
Matches: 219, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
29 55 0.25
30 158 0.72
31 6 0.03
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (29 bp):
AAAGGGATGCTTCGACTATCGAATTATGA
Found at i:54930329 original size:60 final size:60
Alignment explanation
Indices: 54930180--54930480 Score: 249
Period size: 60 Copynumber: 5.0 Consensus size: 60
54930170 ATATCAATGG
* * * * *
54930180 AAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGAT-GGTGACGACCATCAACA--ATGA
1 AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCT-TCGGCTATCAA-ATTATGA
* * * * * *
54930239 AAAGGCATGG-TGACAACCATTGAATTATGAAAAGGGATGGCTTCGGCTATCAAATTATGA
1 AAAGGGATGGCT-TCGACTATCGAATTATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
* * *
54930299 AAAGGGATGGCTTTGGCTATCGAATTATGAAAAGGGATAGCTTCAGCTATCAAATTATGA
1 AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
* * * * * * * *
54930359 AAAGGGATGG-TGACGACCATC-AATAATGAAAAGTGAT-GGTGACGACCATCAAATTATGA
1 AAAGGGATGGCT-TCGACTATCGAATTATGAAAAGGGATAGCT-TCGGCTATCAAATTATGA
* * * * *
54930418 AAAGGGATGGCTTCGACTAT-GAAAATATGGAAAGGGATAACTTCGGCTATCGAACTATGA
1 AAAGGGATGGCTTCGACTATCG-AATTATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
54930478 AAA
1 AAA
54930481 CGGGTGGTAA
Statistics
Matches: 188, Mismatches: 43, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
58 4 0.02
59 83 0.44
60 99 0.53
61 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (60 bp):
AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
Found at i:54930391 original size:119 final size:119
Alignment explanation
Indices: 54930180--54930494 Score: 329
Period size: 119 Copynumber: 2.6 Consensus size: 119
54930170 ATATCAATGG
* * * *
54930180 AAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGAT-G-GTGACGACCATCAACA-ATGAAAA
1 AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCA-G-CTATCAA-ATATGAAAA
* * * * * *
54930242 GGCATGGTGACAACCATTGAATTATGAAAAGGGATGGCT-TCGGCTATCAAATTATGA
63 GGGATGGTGACAACCATTCAATAATGAAAAGGGATGG-TGACGACCATCAAATTATGA
* *
54930299 AAAGGGATGGCTTTGGCTATCGAATTATGAAAAGGGATAGCTTCAGCTATCAAATTATGAAAAGG
1 AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCAGCTATCAAA-TATGAAAAGG
* *
54930364 GATGGTGACGACCA-TCAATAATGAAAAGTGATGGTGACGACCATCAAATTATGA
65 GATGGTGACAACCATTCAATAATGAAAAGGGATGGTGACGACCATCAAATTATGA
* * * * *
54930418 AAAGGGATGGCTTCGACTAT-GAAAATATGGAAAGGGATAACTTCGGCTATCGAACTATGAAAAC
1 AAAGGGATGGCTTCGACTATCG-AATTATGAAAAGGGATAGCTTCAGCTATC-AAATATGAAAA-
*
54930482 GGG-TGGTAACAAC
63 GGGATGGTGACAAC
54930495 TATCGTGATT
Statistics
Matches: 165, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
118 3 0.02
119 132 0.80
120 28 0.17
121 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.23
Consensus pattern (119 bp):
AAAGGGATGGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCAGCTATCAAATATGAAAAGGG
ATGGTGACAACCATTCAATAATGAAAAGGGATGGTGACGACCATCAAATTATGA
Found at i:54930452 original size:149 final size:149
Alignment explanation
Indices: 54930180--54930480 Score: 453
Period size: 149 Copynumber: 2.0 Consensus size: 149
54930170 ATATCAATGG
*
54930180 AAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAAAGGC
1 AAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAAAGGC
** * * **
54930245 ATGGTGACAACCATTGAATTATGAAAAGGGATGGCTTCGGCTATCAAATTATGAAAAGGGATGGC
66 ATGGTGACAACCATCAAATTATGAAAAGGGATGGCTTCGACTATCAAAATATGAAAAGGGATAAC
* *
54930310 TTTGGCTATCGAATTATGA
131 TTCGGCTATCGAACTATGA
*
54930329 AAAGGGATAGCTTC-AGCTATCAAATTATGAAAAGGGATGGTGACGACCATCAATAATGAAAAGT
1 AAAGGGATAGCTTCGA-CTATCAAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAAAG-
* * *
54930393 G-ATGGTGACGACCATCAAATTATGAAAAGGGATGGCTTCGACTATGAAAATATGGAAAGGGATA
64 GCATGGTGACAACCATCAAATTATGAAAAGGGATGGCTTCGACTATCAAAATATGAAAAGGGATA
54930457 ACTTCGGCTATCGAACTATGA
129 ACTTCGGCTATCGAACTATGA
54930478 AAA
1 AAA
54930481 CGGGTGGTAA
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
148 1 0.01
149 135 0.99
150 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (149 bp):
AAAGGGATAGCTTCGACTATCAAATTATGAAAAGGGATGGTGACGACCATCAACAATGAAAAGGC
ATGGTGACAACCATCAAATTATGAAAAGGGATGGCTTCGACTATCAAAATATGAAAAGGGATAAC
TTCGGCTATCGAACTATGA
Found at i:54935193 original size:25 final size:25
Alignment explanation
Indices: 54935165--54935225 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
54935155 CCACAGCTTG
* *
54935165 TGAGAGCATACCGATTTATATCTCA
1 TGAGAGCATACCAATTTATAGCTCA
* *
54935190 TGAGAGCATATCAATTTATAGCTCG
1 TGAGAGCATACCAATTTATAGCTCA
54935215 TGAGAGCATAC
1 TGAGAGCATAC
54935226 TGATCTACAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (25 bp):
TGAGAGCATACCAATTTATAGCTCA
Found at i:54935237 original size:25 final size:25
Alignment explanation
Indices: 54935157--54935250 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 25
54935147 CAGATACTCC
* *
54935157 ACAGCTTGTGAGAGCATACCGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* * * *
54935182 ATATCTCATGAGAGCATA-TCAATTT
1 ACAGCTCGTGAGAGCATACT-GATTT
* *
54935207 ATAGCTCGTGAGAGCATACTGATCT
1 ACAGCTCGTGAGAGCATACTGATTT
* *
54935232 ACAGCTCGAGTGAGCATAC
1 ACAGCTCGTGAGAGCATAC
54935251 AAAATCACAA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
25 53 0.98
26 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACTGATTT
Found at i:54942275 original size:8 final size:8
Alignment explanation
Indices: 54942262--54942287 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
54942252 AAGTTAAGAA
54942262 AAATTGCG
1 AAATTGCG
54942270 AAATTGCG
1 AAATTGCG
54942278 AAATTGCG
1 AAATTGCG
54942286 AA
1 AA
54942288 TTTTCCCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (8 bp):
AAATTGCG
Found at i:54944399 original size:11 final size:11
Alignment explanation
Indices: 54944383--54944407 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54944373 TTACCAACAC
54944383 AATTCATATAT
1 AATTCATATAT
54944394 AATTCATATAT
1 AATTCATATAT
54944405 AAT
1 AAT
54944408 AACTCGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTCATATAT
Found at i:54948601 original size:7 final size:7
Alignment explanation
Indices: 54948583--54948613 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
54948573 TTTACCACTC
54948583 TAATTCCA
1 TAATT-CA
54948591 TAATTCA
1 TAATTCA
54948598 TAATTCA
1 TAATTCA
54948605 TAATTCA
1 TAATTCA
54948612 TA
1 TA
54948614 CCTTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATTCA
Found at i:54949087 original size:38 final size:38
Alignment explanation
Indices: 54949045--54949120 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
54949035 ATAACATGAG
*
54949045 TTGCATTGTAATGCCATGAATCTCATGAGTAACACAAA
1 TTGCATTGTAATGCCACGAATCTCATGAGTAACACAAA
* *
54949083 TTGCATTGTAGTGCCACGAATGTCATGAGTAACACAAA
1 TTGCATTGTAATGCCACGAATCTCATGAGTAACACAAA
54949121 AAACATGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (38 bp):
TTGCATTGTAATGCCACGAATCTCATGAGTAACACAAA
Found at i:54955602 original size:17 final size:16
Alignment explanation
Indices: 54955577--54955624 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
54955567 ACATACGTAA
*
54955577 CTCTTTTTTCTTTCTTT
1 CTCTCTTTTCTTT-TTT
54955594 CTCTCTTTTCCTTTTTT
1 CTCTCTTTT-CTTTTTT
54955611 CT-TCTTATTCTTTT
1 CTCTCTT-TTCTTTT
54955625 ATCAAGTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.32
17 15 0.54
18 4 0.14
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (16 bp):
CTCTCTTTTCTTTTTT
Found at i:54956366 original size:19 final size:20
Alignment explanation
Indices: 54956342--54956390 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
54956332 CTTACATGCC
54956342 AAAGTGAAAAATTT-ATTTT
1 AAAGTGAAAAATTTAATTTT
54956361 AAAGTG-AAAATTTAATTTT
1 AAAGTGAAAAATTTAATTTT
54956380 AAAGTGGAAAA
1 AAAGT-GAAAA
54956391 GTGATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.26
19 16 0.59
20 1 0.04
21 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (20 bp):
AAAGTGAAAAATTTAATTTT
Found at i:54956399 original size:20 final size:19
Alignment explanation
Indices: 54956342--54956398 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
54956332 CTTACATGCC
* **
54956342 AAAGTGAAAAATTTATTTT
1 AAAGTGAAAAGTGAATTTT
* *
54956361 AAAGTGAAAATTTAATTTT
1 AAAGTGAAAAGTGAATTTT
54956380 AAAGTGGAAAAGTG-ATTTT
1 AAAGT-GAAAAGTGAATTTT
54956399 TGTGGCCATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.39
Consensus pattern (19 bp):
AAAGTGAAAAGTGAATTTT
Found at i:54959900 original size:39 final size:39
Alignment explanation
Indices: 54959780--54959893 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
54959770 TCTAACCACC
* * *
54959780 TAACATACAAGCATATATCACAGTACTCAAATAATCACA
1 TAACATTCAAGCATATATCACAATACTCATATAATCACA
* * *
54959819 TAACATTTAAGCATAAATCCCAATACTCATATAATCACA
1 TAACATTCAAGCATATATCACAATACTCATATAATCACA
* *
54959858 TAACATTCAAACATATATCACAATACTCATTTAATC
1 TAACATTCAAGCATATATCACAATACTCATATAATC
54959894 GTATAACTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (39 bp):
TAACATTCAAGCATATATCACAATACTCATATAATCACA
Found at i:54969602 original size:21 final size:21
Alignment explanation
Indices: 54969578--54969621 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
54969568 TCCTTTTTCA
54969578 TAACATTCTTAGTTGTTTATT
1 TAACATTCTTAGTTGTTTATT
54969599 TAACATTCTTAGTTGTTTATT
1 TAACATTCTTAGTTGTTTATT
54969620 TA
1 TA
54969622 CTCGTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (21 bp):
TAACATTCTTAGTTGTTTATT
Found at i:54988678 original size:2 final size:2
Alignment explanation
Indices: 54988671--54988697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54988661 TGAGTAGTTT
54988671 TA 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 T
54988698 TATGTTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54994742 original size:27 final size:27
Alignment explanation
Indices: 54994699--54994919 Score: 293
Period size: 27 Copynumber: 8.3 Consensus size: 27
54994689 AGAGGTCGAT
* *
54994699 AAATTACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54994726 GAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54994753 AAATGACTGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
54994780 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
54994807 GAATGACCGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
54994833 GAATGATCGAAATA-CCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
54994859 AAATGACTGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
54994886 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
54994913 GAATGAC
1 AAATGAC
54994920 TGTTATACCC
Statistics
Matches: 168, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 46 0.27
27 122 0.73
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:54994891 original size:106 final size:108
Alignment explanation
Indices: 54994704--54994919 Score: 355
Period size: 106 Copynumber: 2.0 Consensus size: 108
54994694 TCGATAAATT
*
54994704 ACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAGGGTAAAATGACTGAAATACC
1 ACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACTGAAATACC
*
54994769 CCCATAAGGTAAAATGACCGAAATACCCCTATAGGGTAGAATG
66 CCCATAAGGTAAAATGACCGAAATACCCCCATAGGGTAGAATG
* *
54994812 ACCGAAATA-CCCCATAGGGTAGAATGATCGAAATACCC-CATAAGGTAAAATGACTGAAATACC
1 ACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACTGAAATACC
* * *
54994875 CTCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATG
66 CCCATAAGGTAAAATGACCGAAATACCCCCATAGGGTAGAATG
54994918 AC
1 AC
54994920 TGTTATACCC
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 65 0.64
107 27 0.27
108 9 0.09
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (108 bp):
ACCGAAATACCCCCATAAGGTAGAATGACCGAAATACCCTCATAAGGTAAAATGACTGAAATACC
CCCATAAGGTAAAATGACCGAAATACCCCCATAGGGTAGAATG
Found at i:54996513 original size:51 final size:50
Alignment explanation
Indices: 54996371--54996555 Score: 187
Period size: 51 Copynumber: 3.7 Consensus size: 50
54996361 TGAAAGTGAT
* * * *
54996371 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGCACCAGA-ATGATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GTTA
* * *
54996421 GGTCGCATGTGTAGTACTATGTGCAGGATACT--GTGCATACCGGATAGTTCC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTG--TACCGGATAGTT-A
* * * *
54996472 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGTAA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTA
* *
54996522 TGGTCACATGTGTAGTACTACGTACAGGCTACTA
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTA
54996556 TGTGAATCGA
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
48 3 0.03
50 36 0.33
51 68 0.62
53 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTA
Found at i:54996617 original size:45 final size:45
Alignment explanation
Indices: 54996566--54996653 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
54996556 TGTGAATCGA
* * * * *
54996566 ACATCATTGATTAGTAATGTGGTTGTTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCCACCAG
54996611 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCCACC
54996654 GAGTATCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCCACCAG
Found at i:55002050 original size:51 final size:51
Alignment explanation
Indices: 55001921--55002081 Score: 164
Period size: 51 Copynumber: 3.2 Consensus size: 51
55001911 AAAGTGATGG
* * * * * *
55001921 TCACGTGTTTAGTACTATTTGCAGGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACGTGTGTAGTACTATATGCAGGCTACTATGTGTACCAGATAGT-TTCGA
* * * * *
55001971 TCGCATCTGTAGTACTATATGCAAGCTACTATGTGTACCGGATAGTTTCGA
1 TCACGTGTGTAGTACTATATGCAGGCTACTATGTGTACCAGATAGTTTCGA
* * *
55002022 TCACGTGTGTAGTACTATGTGCAGGCTACTTTGCGTACCAGATAGTTTCGA
1 TCACGTGTGTAGTACTATATGCAGGCTACTATGTGTACCAGATAGTTTCGA
*
55002073 TCATGTGTG
1 TCACGTGTG
55002082 ATTAATAAGG
Statistics
Matches: 89, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
50 34 0.38
51 54 0.61
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATATGCAGGCTACTATGTGTACCAGATAGTTTCGA
Found at i:55007110 original size:6 final size:6
Alignment explanation
Indices: 55007101--55007125 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55007091 AAAAAGACTC
55007101 AGTGGA AGTGGA AGTGGA AGTGGA A
1 AGTGGA AGTGGA AGTGGA AGTGGA A
55007126 TAAACTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
AGTGGA
Found at i:55016608 original size:15 final size:16
Alignment explanation
Indices: 55016579--55016608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55016569 CAAACATGTT
55016579 TTAACACATTATCAAA
1 TTAACACATTATCAAA
55016595 TTAACACA-TATCAA
1 TTAACACATTATCAA
55016609 CAATGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:55028811 original size:22 final size:21
Alignment explanation
Indices: 55028786--55028827 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
55028776 TTTGTGATTC
*
55028786 ATTGGTTGTGAATTAAGCATGA
1 ATTGGATGTGAATTAA-CATGA
*
55028808 ATTGGATGTTAATTAACATG
1 ATTGGATGTGAATTAACATG
55028828 CTGTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (21 bp):
ATTGGATGTGAATTAACATGA
Found at i:55036417 original size:35 final size:34
Alignment explanation
Indices: 55036378--55036456 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
55036368 CGTCTTTCAA
* *
55036378 GGTGTCGCCTTGAAGGACCCATATACCATTTACAC
1 GGTGTCGCCCTGAAGAACCCATATA-CATTTACAC
* * * *
55036413 GGTGTTGCCCTGAAGAACCTATGTACGTTTACAC
1 GGTGTCGCCCTGAAGAACCCATATACATTTACAC
55036447 GGTGTCGCCC
1 GGTGTCGCCC
55036457 CTAAGAATCT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 17 0.46
35 20 0.54
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (34 bp):
GGTGTCGCCCTGAAGAACCCATATACATTTACAC
Found at i:55042963 original size:16 final size:18
Alignment explanation
Indices: 55042937--55042969 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55042927 TTAAACTAAC
55042937 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
55042954 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
55042970 CCCAATTCTA
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:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:55043040 original size:73 final size:74
Alignment explanation
Indices: 55042945--55043092 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 74
55042935 ACTAAATTAA
55042945 TTTCTCAATTAAATAATTTTCTCAACCCAATTCTAATTCCGTTCAAATAATAGCAACTTTACCAC
1 TTTCTCAATTAAATAATTTTCTCAACCCAATTCTAATTCCGTTCAAATAATAGCAACTTTACCAC
55043010 AATAGAATC
66 AATAGAATC
55043019 TTTCTCAATT-AATAATTTTCTCAACCCAATTCTAATTCCGTTCAAATAATAGCAACTTTACCAC
1 TTTCTCAATTAAATAATTTTCTCAACCCAATTCTAATTCCGTTCAAATAATAGCAACTTTACCAC
55043083 AATAGAATC
66 AATAGAATC
55043092 T
1 T
55043093 ATGAAGAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 64 0.86
74 10 0.14
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (74 bp):
TTTCTCAATTAAATAATTTTCTCAACCCAATTCTAATTCCGTTCAAATAATAGCAACTTTACCAC
AATAGAATC
Found at i:55047441 original size:10 final size:11
Alignment explanation
Indices: 55047415--55047454 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
55047405 AGGCCTTATT
55047415 TTAC-TTTTAG
1 TTACTTTTTAG
55047425 TTA-TTTTTA-
1 TTACTTTTTAG
55047434 TTACTTTTTAG
1 TTACTTTTTAG
*
55047445 ATACTTTTTA
1 TTACTTTTTA
55047455 TTTGATGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 3 0.12
10 14 0.54
11 9 0.35
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (11 bp):
TTACTTTTTAG
Found at i:55056698 original size:97 final size:97
Alignment explanation
Indices: 55056528--55056749 Score: 294
Period size: 97 Copynumber: 2.3 Consensus size: 97
55056518 AAATTAAAGT
* * * * *
55056528 ATTTAGTTAAAATAAAAGTAT-TAGTAATAATATCAAAGGAAAAAAAATCTTATTTTCAAGCTTA
1 ATTTAGTTAAAATAAAAATATATAGTAATAATATCAAAGCAAAAAAAATCTCATTTTCAAGATGA
* *
55056592 TGTATAAACTTGGGAATGTCTACTTCTTCATA
66 TGTATAAACTTGGGAATCTCTACTTCTTCAGA
* *
55056624 ATTTGGTTAAAATAAAAATAGTATAGTAATAATA-CTAAA-CAAAAAAAATCTCGTTTTCAAGAT
1 ATTTAGTTAAAATAAAAATA-TATAGTAATAATATC-AAAGCAAAAAAAATCTCATTTTCAAGAT
*
55056687 GATGTATAAACTTGGGAATCTCTACTTCTTGAGA
64 GATGTATAAACTTGGGAATCTCTACTTCTTCAGA
55056721 ATTTAGTT-AAATAAAAATAT-TA-TAATAAT
1 ATTTAGTTAAAATAAAAATATATAGTAATAAT
55056750 GATATGATAT
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
93 7 0.06
94 2 0.02
95 1 0.01
96 29 0.26
97 59 0.53
98 14 0.12
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (97 bp):
ATTTAGTTAAAATAAAAATATATAGTAATAATATCAAAGCAAAAAAAATCTCATTTTCAAGATGA
TGTATAAACTTGGGAATCTCTACTTCTTCAGA
Found at i:55057418 original size:26 final size:24
Alignment explanation
Indices: 55057367--55057416 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
55057357 GTTAAAACTC
*
55057367 TTCTAAAAGAAAAATAAAGAGAAA
1 TTCTAAAAAAAAAATAAAGAGAAA
55057391 TTCTAAAAAAAGAAACTCAAAGAGAA
1 TTCTAAAAAAA-AAA-T-AAAGAGAA
55057417 TTTTATTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 3 0.14
26 1 0.05
27 8 0.36
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (24 bp):
TTCTAAAAAAAAAATAAAGAGAAA
Found at i:55058488 original size:14 final size:14
Alignment explanation
Indices: 55058466--55058535 Score: 90
Period size: 14 Copynumber: 5.1 Consensus size: 14
55058456 TAATTTTTGC
*
55058466 GGTGGTTAGTTTAT
1 GGTGATTAGTTTAT
55058480 GGTGATTAGTTTAT
1 GGTGATTAGTTTAT
55058494 GGTGATTAGTTTAT
1 GGTGATTAGTTTAT
**
55058508 GGTGATT--TTTGC
1 GGTGATTAGTTTAT
*
55058520 GGTGGTTAGTTTAT
1 GGTGATTAGTTTAT
55058534 GG
1 GG
55058536 GATAAGGCGG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.19
14 39 0.81
ACGTcount: A:0.16, C:0.01, G:0.34, T:0.49
Consensus pattern (14 bp):
GGTGATTAGTTTAT
Found at i:55058505 original size:28 final size:26
Alignment explanation
Indices: 55058458--55058567 Score: 116
Period size: 28 Copynumber: 4.2 Consensus size: 26
55058448 ACTTGTGCTA
*
55058458 ATTTTTGCGGTGGTTAGTTTATGGTG
1 ATTTTTACGGTGGTTAGTTTATGGTG
* *
55058484 ATTAGTTTATGGTGATTAGTTTATGGTG
1 ATT--TTTACGGTGGTTAGTTTATGGTG
*
55058512 ATTTTTGCGGTGGTTAGTTTATGG-G
1 ATTTTTACGGTGGTTAGTTTATGGTG
****
55058537 A-TAAGGCGGTGGTTAGTTTATGGTG
1 ATTTTTACGGTGGTTAGTTTATGGTG
55058562 ATTTTT
1 ATTTTT
55058568 GTTATTGCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 19 0.28
25 4 0.06
26 22 0.32
28 23 0.34
ACGTcount: A:0.16, C:0.03, G:0.33, T:0.48
Consensus pattern (26 bp):
ATTTTTACGGTGGTTAGTTTATGGTG
Found at i:55059578 original size:5 final size:5
Alignment explanation
Indices: 55059556--55059598 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
55059546 TAGAATTACT
55059556 TAATA T-ATA TAA-A TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
55059599 CTATATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.22
5 28 0.78
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:55061920 original size:12 final size:12
Alignment explanation
Indices: 55061903--55061927 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55061893 AAATTGGGGC
55061903 TGAATTTTAAAA
1 TGAATTTTAAAA
55061915 TGAATTTTAAAA
1 TGAATTTTAAAA
55061927 T
1 T
55061928 CCAGAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (12 bp):
TGAATTTTAAAA
Found at i:55063747 original size:19 final size:19
Alignment explanation
Indices: 55063723--55063763 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
55063713 ATGAATTACA
*
55063723 TTAATACTCTTTTTATATT
1 TTAATACCCTTTTTATATT
55063742 TTAATACCCTTTTTATATT
1 TTAATACCCTTTTTATATT
55063761 TTA
1 TTA
55063764 CTCAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATACCCTTTTTATATT
Found at i:55069262 original size:23 final size:22
Alignment explanation
Indices: 55069236--55069279 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
55069226 GGATTTACAT
*
55069236 AATCCTCTAAGATTACAAAATCA
1 AATCCTATAAGATTA-AAAATCA
*
55069259 AATCTTATAAGATTAAAAATC
1 AATCCTATAAGATTAAAAATC
55069280 TTCTATGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.30
Consensus pattern (22 bp):
AATCCTATAAGATTAAAAATCA
Found at i:55069993 original size:7 final size:7
Alignment explanation
Indices: 55069983--55070013 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
55069973 AAAAAAAATC
55069983 AATATCA
1 AATATCA
55069990 AATATCA
1 AATATCA
55069997 AATATCA
1 AATATCA
55070004 AATATCA
1 AATATCA
55070011 AAT
1 AAT
55070014 GGAAGTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
AATATCA
Found at i:55081567 original size:20 final size:20
Alignment explanation
Indices: 55081542--55081581 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55081532 CATTCAAGTT
55081542 CAATAACGAGATCAAAGGCC
1 CAATAACGAGATCAAAGGCC
55081562 CAATAACGAGATCAAAGGCC
1 CAATAACGAGATCAAAGGCC
55081582 GGACAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.20, T:0.10
Consensus pattern (20 bp):
CAATAACGAGATCAAAGGCC
Found at i:55093220 original size:7 final size:7
Alignment explanation
Indices: 55093201--55093245 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
55093191 AAAACTGATG
*
55093201 ATAATGT
1 ATAATAT
55093208 ATAATAT
1 ATAATAT
*
55093215 AGAATAT
1 ATAATAT
55093222 ATAATAT
1 ATAATAT
55093229 ATAATAT
1 ATAATAT
55093236 ATAATAT
1 ATAATAT
55093243 ATA
1 ATA
55093246 TGCTTCAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:55093531 original size:180 final size:181
Alignment explanation
Indices: 55093216--55093578 Score: 719
Period size: 180 Copynumber: 2.0 Consensus size: 181
55093206 GTATAATATA
55093216 GAATATATAATATATAATATATAATATATATGCTTCAGTTATATTAACAATTGAATTCCGTATAA
1 GAATATATAATATATAATATATAATATATATGCTTCAGTTATATTAACAATTGAATTCCGTATAA
55093281 TATGAATGTGTCGAATGATTAGTGCTATAATGTTATTTTATGAGTTTTGGTGGATTGTTATATTT
66 TATGAATGTGTCGAATGATTAGTGCTATAATGTTATTTTATGAGTTTTGGTGGATTGTTATATTT
55093346 GATTCTAATATTTAATATCTATTAAATCAATTAAAAAGAATAATGTTTTTG
131 GATTCTAATATTTAATATCTATTAAATCAATTAAAAAGAATAATGTTTTTG
55093397 GAATATATAATA-ATAATATATAATATATATGCTTCAGTTATATTAACAATTGAATTCCGTATAA
1 GAATATATAATATATAATATATAATATATATGCTTCAGTTATATTAACAATTGAATTCCGTATAA
55093461 TATGAATGTGTCGAATGATTAGTGCTATAATGTTATTTTATGAGTTTTGGTGGATTGTTATATTT
66 TATGAATGTGTCGAATGATTAGTGCTATAATGTTATTTTATGAGTTTTGGTGGATTGTTATATTT
55093526 GATTCTAATATTTAATATCTATTAAATCAATTAAAAAGAATAATGTTTTTG
131 GATTCTAATATTTAATATCTATTAAATCAATTAAAAAGAATAATGTTTTTG
55093577 GA
1 GA
55093579 TTTTTATTGC
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 170 0.93
181 12 0.07
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (181 bp):
GAATATATAATATATAATATATAATATATATGCTTCAGTTATATTAACAATTGAATTCCGTATAA
TATGAATGTGTCGAATGATTAGTGCTATAATGTTATTTTATGAGTTTTGGTGGATTGTTATATTT
GATTCTAATATTTAATATCTATTAAATCAATTAAAAAGAATAATGTTTTTG
Found at i:55094885 original size:38 final size:39
Alignment explanation
Indices: 55094827--55094903 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
55094817 ATGTATTGCC
55094827 AAATACAATGCTAAATTAACTTCAGCTACCTTAGAAGAA
1 AAATACAATGCTAAATTAACTTCAGCTACCTTAGAAGAA
55094866 AAATACAATG-TAAATTAACTTCAGCTACCTTAGAAGAA
1 AAATACAATGCTAAATTAACTTCAGCTACCTTAGAAGAA
55094904 TAAACATGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 28 0.74
39 10 0.26
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (39 bp):
AAATACAATGCTAAATTAACTTCAGCTACCTTAGAAGAA
Found at i:55100623 original size:2 final size:2
Alignment explanation
Indices: 55100616--55100652 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
55100606 TCCATATAAT
*
55100616 AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
55100653 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:55104141 original size:45 final size:45
Alignment explanation
Indices: 55104092--55104185 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
55104082 AACAGATACT
* *
55104092 CGGTGG-ATCCAGCACATAGCAACCACCTTATTAATTAATGATGTC
1 CGGTGGAAT-CAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
55104137 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
55104182 CGGT
1 CGGT
55104186 TCACATAGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:55104267 original size:51 final size:50
Alignment explanation
Indices: 55104191--55104365 Score: 190
Period size: 51 Copynumber: 3.5 Consensus size: 50
55104181 TCGGTTCACA
** *
55104191 TAGTAGCCTATACATGGTACTACACATGAGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGAGACCA-TACCATCCGATACACG
* * * * * * *
55104242 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACACA
1 TAGTAGCCTGCACATAGTACTACACATGAGA-CCATACCATCCGATACACG
* * * *
55104293 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGAGACCATACCATCCGA-TACACG
55104343 TAGTAGCCTGCACATAGTACTAC
1 TAGTAGCCTGCACATAGTACTAC
55104366 GCACATGACC
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
49 4 0.04
50 29 0.28
51 67 0.66
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGAGACCATACCATCCGATACACG
Found at i:55104319 original size:26 final size:26
Alignment explanation
Indices: 55104287--55104365 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
55104277 AACTATCCGG
55104287 TACACATAGTAGCCTGCACATAGTAC
1 TACACATAGTAGCCTGCACATAGTAC
* ** *
55104313 TACACAT-G-CGACCT--ATCATTCTAG
1 TACACATAGTAG-CCTGCA-CATAGTAC
*
55104337 TACACGTAGTAGCCTGCACATAGTAC
1 TACACATAGTAGCCTGCACATAGTAC
55104363 TAC
1 TAC
55104366 GCACATGACC
Statistics
Matches: 38, Mismatches: 9, Indels: 12
0.64 0.15 0.20
Matches are distributed among these distances:
23 1 0.03
24 12 0.32
25 8 0.21
26 16 0.42
27 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACATAGTAC
Found at i:55104363 original size:101 final size:101
Alignment explanation
Indices: 55104182--55104365 Score: 271
Period size: 102 Copynumber: 1.8 Consensus size: 101
55104172 CAATGATGTT
* * *
55104182 CGGTTCACATAGTAGCCTATACATGGTACTACACATGAGACCATTACCATCCGATACACGTAGTA
1 CGGTACACATAGTAGCCTACACATAGTACTACACATGAGACCA-TACCATCCGATACACGTAGTA
55104247 GCCTGCACATAGTACTACACACGTGATCGAAACTATC
65 GCCTGCACATAGTACTACACACGTGATCGAAACTATC
* * * * *
55104284 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTAGTACACGTAGTA
1 CGGTACACATAGTAGCCTACACATAGTACTACACATGAGACCATACCATCCGA-TACACGTAGTA
55104348 GCCTGCACATAGTACTAC
65 GCCTGCACATAGTACTAC
55104366 GCACATGACC
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
100 7 0.10
101 29 0.40
102 37 0.51
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CGGTACACATAGTAGCCTACACATAGTACTACACATGAGACCATACCATCCGATACACGTAGTAG
CCTGCACATAGTACTACACACGTGATCGAAACTATC
Found at i:55106003 original size:11 final size:11
Alignment explanation
Indices: 55105989--55106014 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55105979 AATTTTTGGG
55105989 AAAAACAAAAT
1 AAAAACAAAAT
55106000 AAAAACAAAAT
1 AAAAACAAAAT
55106011 AAAA
1 AAAA
55106015 TCTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAACAAAAT
Found at i:55107061 original size:17 final size:17
Alignment explanation
Indices: 55107026--55107062 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55107016 TTGGAAAGTG
**
55107026 AAATAATAAAATATGAT
1 AAATAATAAAATAACAT
55107043 AAATAATAAAATAACAT
1 AAATAATAAAATAACAT
55107060 AAA
1 AAA
55107063 ATATCATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAATAAAATAACAT
Found at i:55108112 original size:24 final size:23
Alignment explanation
Indices: 55108084--55108176 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 23
55108074 TTCCCAATTA
*
55108084 ATTGGCTCTCTGGAGCTTCTCTAT
1 ATTGGCTCTCTGAAGCTTC-CTAT
* *
55108108 ATTGGCTCGCTTGAACCTTCCTGAT
1 ATTGGCTCTC-TGAAGCTTCCT-AT
* *
55108133 ATTGGCTCATATG-AGCTTCCCATT
1 ATTGGCTC-TCTGAAGCTTCCTA-T
*
55108157 AATGGCTCTCTGAAGCTTCC
1 ATTGGCTCTCTGAAGCTTCC
55108177 CGATACATGG
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 4 0.07
24 32 0.58
25 19 0.35
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (23 bp):
ATTGGCTCTCTGAAGCTTCCTAT
Found at i:55108163 original size:49 final size:50
Alignment explanation
Indices: 55108105--55108214 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 50
55108095 GGAGCTTCTC
* * * *
55108105 TATATTGGCTCGCTTGAACCTTCCTGATA-TTGGCTCATATGAGCTTCCCAT
1 TATA-TGGCTCGC-TGAACCTTCCCGATACATGGCTCACATGAGCTACCCAT
* *
55108156 TA-ATGGCTCTCTGAAGCTTCCCGATACATGGCTCACATGAGCTACCCAT
1 TATATGGCTCGCTGAACCTTCCCGATACATGGCTCACATGAGCTACCCAT
55108205 TATATGGCTC
1 TATATGGCTC
55108215 CTCCCAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
48 13 0.25
49 28 0.55
50 8 0.16
51 2 0.04
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (50 bp):
TATATGGCTCGCTGAACCTTCCCGATACATGGCTCACATGAGCTACCCAT
Found at i:55108177 original size:24 final size:25
Alignment explanation
Indices: 55108135--55108214 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
55108125 TTCCTGATAT
*
55108135 TGGCTCATATGAGCTTCCCATTA-A
1 TGGCTCACATGAGCTTCCCATTACA
*
55108159 TGGCTCTC-TGAAGCTTCCCGA-TACA
1 TGGCTCACATG-AGCTTCCC-ATTACA
* *
55108184 TGGCTCACATGAGCTACCCATTATA
1 TGGCTCACATGAGCTTCCCATTACA
55108209 TGGCTC
1 TGGCTC
55108215 CTCCCAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 17 0.37
25 25 0.54
26 2 0.04
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCATTACA
Done.