Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 127 of 320
Found at i:41456318 original size:43 final size:43
Alignment explanation
Indices: 41456204--41456337 Score: 152
Period size: 43 Copynumber: 3.2 Consensus size: 43
41456194 TCACACATAT
**
41456204 CATA-CAATGCCAACGTCCCAGACGTGGTCTTACGTGTAATCA
1 CATATCAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCA
* * *
41456246 CATAT-TATGCC-ACTTCCCAAACAG-GGTCTTACACGTAATCA
1 CATATCAATGCCAACGTCCCAGAC-GTGGTCTTACACGTAATCA
* *
41456287 CTTATCAATGCCAACGTCCCAGACGTGGTCTTACACG-AGAACA
1 CATATCAATGCCAACGTCCCAGACGTGGTCTTACACGTA-ATCA
41456330 CATATCAA
1 CATATCAA
41456338 AAATCCTATG
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
41 28 0.37
42 17 0.23
43 30 0.40
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
CATATCAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCA
Found at i:41471170 original size:27 final size:26
Alignment explanation
Indices: 41471139--41471316 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
41471129 TAAATTGTAC
41471139 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
41471166 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
41471192 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
41471220 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
41471248 GGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
41471275 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
41471302 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41471317 GACTCGATAT
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 104 0.79
28 26 0.20
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:41471255 original size:82 final size:81
Alignment explanation
Indices: 41471140--41471295 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41471130 AAATTGTACA
*
41471140 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
41471204 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
41471221 GCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
41471286 TGCGAGTTGA
65 TGCGAATTGA
41471296 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41471307 original size:82 final size:81
Alignment explanation
Indices: 41471136--41471316 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41471126 GATTAAATTG
*
41471136 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
41471201 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
41471217 TGCGGCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
41471281 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41471299 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41471317 GACTCGATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41475483 original size:15 final size:15
Alignment explanation
Indices: 41475459--41475490 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41475449 GTCTTATAAC
*
41475459 AAGTTGAATAACAAT
1 AAGTTAAATAACAAT
41475474 AAGTTAAATAACAAT
1 AAGTTAAATAACAAT
41475489 AA
1 AA
41475491 CACATACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (15 bp):
AAGTTAAATAACAAT
Found at i:41479412 original size:44 final size:42
Alignment explanation
Indices: 41479359--41479484 Score: 114
Period size: 44 Copynumber: 3.0 Consensus size: 42
41479349 ATCTAAATTA
*
41479359 TTGTGTAAGACCGTGTCTGGGACACAGGCATCGAAT-TGAAATT
1 TTGTGTAAGACCATGTCTGGGACACAGGCATCGAATCTG--ATT
* * *
41479402 TATGTGTAAGACCATGTCTTGGATATCA-GCATCGTATCTGATT
1 T-TGTGTAAGACCATGTCTGGGACA-CAGGCATCGAATCTGATT
* * * *
41479445 TCGTATAAGACCCTGTCTGGGACAGAGGCATC-AATACTGA
1 TTGTGTAAGACCATGTCTGGGACACAGGCATCGAAT-CTGA
41479485 ATTACATGTA
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
41 3 0.04
42 27 0.40
43 5 0.07
44 28 0.42
45 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TTGTGTAAGACCATGTCTGGGACACAGGCATCGAATCTGATT
Found at i:41484887 original size:37 final size:37
Alignment explanation
Indices: 41484837--41484915 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
41484827 TTATTACGAA
* *
41484837 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTTATCAG
*
41484874 GTCTTACCCGGACAAAATTCCCACACGTAGTTATCAG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTTATCAG
41484911 GTCTT
1 GTCTT
41484916 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTTATCAG
Found at i:41485112 original size:47 final size:47
Alignment explanation
Indices: 41485034--41485622 Score: 928
Period size: 47 Copynumber: 12.4 Consensus size: 47
41485024 CCCTTCGGGA
* * * * * * *
41485034 CTTATCACATTTATGCACTTTCACGTCCATCACGTTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
41485081 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41485128 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41485175 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTATGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41485222 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41485269 CTTGTCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41485316 CTTATCACATACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACAT--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
41485365 CTTATCACATACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACAT--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
41485414 CTTATCACATACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACAT--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41485463 CTTACCACATATATACACTTTCACATTCATCACTTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41485510 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41485557 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41485604 CTTATCACATATATACACT
1 CTTATCACATATATACACT
41485623 GTCTTGGCTG
Statistics
Matches: 510, Mismatches: 29, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
46 2 0.00
47 364 0.71
49 144 0.28
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41485603 original size:288 final size:284
Alignment explanation
Indices: 41485034--41485622 Score: 986
Period size: 288 Copynumber: 2.1 Consensus size: 284
41485024 CCCTTCGGGA
* * * * * * * * *
41485034 CTTATCACATTTATGCACTTTCACGTCCATCACGTTGGCCACTCA-GCCCTGTCACAT--ATATA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATACATATA
41485096 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
** *
41485161 ATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTATGCCTTA
130 ATCGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
41485226 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTGTCACACATATACACTTTC
195 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTC
41485291 ACATTCATCACATCGGCCATTAGGC
260 ACATTCATCACATCGGCCATTAGGC
41485316 CTTATCACATACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATACATAT
1 CTTATCACAT--ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATACATAT
41485381 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATACATATACACTTTCACATTCAT
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT--ATATACACTTTCACATTCAT
*
41485446 CACATCGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACTTCGGCTATTAGGCC
127 CACATCGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCC
41485511 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT
192 TTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACT
41485576 TTCACATTCATCACATCGGCCATTAGGC
257 TTCACATTCATCACATCGGCCATTAGGC
41485604 CTTATCACATATATACACT
1 CTTATCACATATATACACT
41485623 GTCTTGGCTG
Statistics
Matches: 286, Mismatches: 14, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
282 10 0.03
283 2 0.01
284 35 0.12
286 56 0.20
288 183 0.64
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (284 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATACATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTACCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
CACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCA
CATTCATCACATCGGCCATTAGGC
Found at i:41502913 original size:41 final size:40
Alignment explanation
Indices: 41502827--41502926 Score: 137
Period size: 41 Copynumber: 2.5 Consensus size: 40
41502817 AAATTAGCTA
* * *
41502827 TATATATGGTACCTAGTGTGCGATTCGACATAGCTTCGAC
1 TATATATGGCACTTAGTGTGCGAATCGACATAGCTTCGAC
* * *
41502867 TATATATGGCACTTAGTGTGTGAGATCGAGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGA-ATCGACATAGCTTCGAC
41502908 TATATATGGCACTTAGTGT
1 TATATATGGCACTTAGTGT
41502927 ATGATTTGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 20 0.38
41 33 0.62
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGAATCGACATAGCTTCGAC
Found at i:41503727 original size:24 final size:24
Alignment explanation
Indices: 41503699--41503760 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 24
41503689 TGTTTATGGC
41503699 TAAATTGGATG-TTTATTTATATTA
1 TAAATTGG-TGTTTTATTTATATTA
41503723 TAAATTGGTGTCATTTTATTTATATTA
1 TAAATTGGTG---TTTTATTTATATTA
41503750 TAAATTGGTGT
1 TAAATTGGTGT
41503761 CATTTTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 2 0.06
24 9 0.26
27 23 0.68
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.53
Consensus pattern (24 bp):
TAAATTGGTGTTTTATTTATATTA
Found at i:41503744 original size:27 final size:27
Alignment explanation
Indices: 41503710--41503766 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
41503700 AAATTGGATG
41503710 TTTATTTATATTATAAATTGGTGTCAT
1 TTTATTTATATTATAAATTGGTGTCAT
41503737 TTTATTTATATTATAAATTGGTGTCAT
1 TTTATTTATATTATAAATTGGTGTCAT
41503764 TTT
1 TTT
41503767 GGTTGTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.58
Consensus pattern (27 bp):
TTTATTTATATTATAAATTGGTGTCAT
Found at i:41507540 original size:28 final size:28
Alignment explanation
Indices: 41507500--41507556 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41507490 GAATCTAAGT
41507500 TAGAAAAATATTTTAAAATTATTTTCTG
1 TAGAAAAATATTTTAAAATTATTTTCTG
41507528 TAGAAAAATATTTTAAAATTATTTTCTG
1 TAGAAAAATATTTTAAAATTATTTTCTG
41507556 T
1 T
41507557 GTTTATTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (28 bp):
TAGAAAAATATTTTAAAATTATTTTCTG
Found at i:41509953 original size:27 final size:27
Alignment explanation
Indices: 41509919--41510118 Score: 276
Period size: 27 Copynumber: 7.4 Consensus size: 27
41509909 TGGATAAGTT
* *
41509919 GTAGAATTATCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
41509946 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
41509973 GTAGAATTATTGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
41510000 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
41510027 ATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
41510054 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
41510081 GTAGAATTACCGCGATACCCTTGT-GTG
1 GTAGAATTACCGAAATACCCCTGTAG-G
*
41510108 GTAAAATTACC
1 GTAGAATTACC
41510119 ATTTTGCCCC
Statistics
Matches: 154, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 1 0.01
27 153 0.99
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:41510941 original size:71 final size:69
Alignment explanation
Indices: 41510750--41510962 Score: 259
Period size: 71 Copynumber: 3.1 Consensus size: 69
41510740 GAGGAAGTGT
* * * * *
41510750 TCTGGCAGCCTCACTGCAATCTGGTGGCCTCGCCAC--ATATATCTATTCTAGTGACTTCGTCAC
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTTGCCACATATATATATATTCTGGTGACTTCGTCAC
41510813 AATA
66 AATA
* *
41510817 TCTGACAGCCTTGCTGCAATCTGGTGGCTTTGCCACATATATATATCCATTCTGGTGACTTCGTC
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTTGCCACATATATATAT--ATTCTGGTGACTTCGTC
41510882 ACAATA
64 ACAATA
* * * * * *
41510888 TCTGGCAGCCTCGCTGCAATATAGTGGCTTTGCCACATATATATATATGTTCTGGTGGCCTAGCC
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTTGCCACATATATATATA--TTCTGGTGACTTCGTC
41510953 ACAATA
64 ACAATA
41510959 TCTG
1 TCTG
41510963 TATCTGGTGA
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
67 31 0.25
69 8 0.06
71 86 0.69
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (69 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCTTTGCCACATATATATATATTCTGGTGACTTCGTCAC
AATA
Found at i:41516921 original size:27 final size:27
Alignment explanation
Indices: 41516888--41517059 Score: 186
Period size: 27 Copynumber: 6.4 Consensus size: 27
41516878 TCGATAAGTT
* *
41516888 GTAGAATTACCGAAATACCCCTATAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
41516915 GTAGAATTACCAAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
41516942 GTAGAACTT-TTGAAATACTCCTGTAGG
1 GTAGAA-TTACCGAAATACCCCTGTAGG
* * * *
41516969 ATAGAAATACCAAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
41516996 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
41517023 GTAGAATTACTG-AATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
41517049 GTAAAATTACC
1 GTAGAATTACC
41517060 ATTTTGCCCC
Statistics
Matches: 120, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
26 22 0.18
27 96 0.80
28 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:41517853 original size:27 final size:26
Alignment explanation
Indices: 41517801--41517859 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
41517791 CCACATATAT
*
41517801 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
41517827 ATATCTGTATCTGGTGACTTTGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
41517854 ATATCT
1 ATATCT
41517860 CGCAGCCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:41522865 original size:27 final size:27
Alignment explanation
Indices: 41522835--41523012 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
41522825 ATATTGAGTC
* * * *
41522835 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41522862 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41522889 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** *
41522917 CGCACACTTAGTGCCGCA-AGGTCAATT
1 CGCACACTTAGTGCTACATA-GTCAAAT
* **
41522944 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
* *
41522971 CGCACACTCAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41522998 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41523013 GTACAATTGA
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41522974 original size:82 final size:81
Alignment explanation
Indices: 41522856--41523011 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
41522846 TGCTATATAA
* * *
41522856 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTCAGTGCAACATAGTCAAA-TCGCA
41522921 CACTTAGTGCCGCAAGG
65 CACTTAGTGCCGCAAGG
* * **
41522938 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTCAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTCAGTGCAACATAGTCAAATCGCA
41523002 CACTTAGTGC
65 CACTTAGTGC
41523012 TGTACAATTG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTCAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCAAGG
Found at i:41530915 original size:27 final size:27
Alignment explanation
Indices: 41530885--41531062 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41530875 ATATTGAGTC
* * * *
41530885 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41530912 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41530939 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41530967 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41530994 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41531021 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41531048 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41531063 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41531024 original size:82 final size:81
Alignment explanation
Indices: 41530906--41531061 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41530896 TGCTATATAA
* *
41530906 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41530971 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41530988 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41531052 CACTTAGTGC
65 CACTTAGTGC
41531062 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41534341 original size:39 final size:40
Alignment explanation
Indices: 41534296--41534464 Score: 220
Period size: 39 Copynumber: 4.3 Consensus size: 40
41534286 GCTCCTCGTT
* * *
41534296 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
41534336 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
41534375 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* *
41534415 CAAA-GCCTTCGGG-CTTAACCCGGATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
41534452 CAAATGCCTTCGG
1 CAAATGCCTTCGG
41534465 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
37 14 0.12
38 22 0.19
39 43 0.37
40 38 0.32
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:41534399 original size:79 final size:77
Alignment explanation
Indices: 41534296--41534464 Score: 221
Period size: 79 Copynumber: 2.2 Consensus size: 77
41534286 GCTCCTCGTT
* * *
41534296 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAAGCCTTCGGG-CATAACCCGGA
41534361 TTTAACAACTCGCA
65 TTT-ACAACTCGCA
* * * * *
41534375 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGCCTTCGGGCTTAACCCGGAT
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAAGCCTTCGGGCATAACCCGGAT
** *
41534440 TTGTATCTCGCA
66 TTACAACTCGCA
41534452 CAAATGCCTTCGG
1 CAAATGCCTTCGG
41534465 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 19 0.24
78 13 0.17
79 46 0.59
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAAGCCTTCGGGCATAACCCGGAT
TTACAACTCGCA
Found at i:41534526 original size:41 final size:41
Alignment explanation
Indices: 41534449--41534526 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41534439 TTTGTATCTC
* * *
41534449 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41534490 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41534527 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41542250 original size:40 final size:39
Alignment explanation
Indices: 41542152--41542319 Score: 205
Period size: 40 Copynumber: 4.3 Consensus size: 39
41542142 TCCTCGTTCA
* * *
41542152 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
**
41542191 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* *
41542230 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
* * *
41542270 AA-GCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 AATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCAC
41542308 AAATGCCTTCGG
1 -AATGCCTTCGG
41542320 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
38 30 0.26
39 42 0.37
40 43 0.37
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCAC
Found at i:41542253 original size:79 final size:78
Alignment explanation
Indices: 41542150--41542319 Score: 216
Period size: 79 Copynumber: 2.2 Consensus size: 78
41542140 GCTCCTCGTT
* *
41542150 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAA-GCCTTCGGGACATAACCCGGA
41542214 ATTTAACAACTCGCA
65 ATTT-ACAACTCGCA
* * * * * *
41542229 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAGCCTTCGGGGCTTAACCCGGAA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGCCTTCGGGACATAACCCGGAA
** *
41542294 TTTGTATCTCGCA
66 TTTACAACTCGCA
41542307 CAAATGCCTTCGG
1 CAAATGCCTTCGG
41542320 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
78 37 0.47
79 41 0.53
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGCCTTCGGGACATAACCCGGAA
TTTACAACTCGCA
Found at i:41542332 original size:78 final size:79
Alignment explanation
Indices: 41542150--41542333 Score: 221
Period size: 78 Copynumber: 2.3 Consensus size: 79
41542140 GCTCCTCGTT
* *
41542150 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
41542215 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * * * * *
41542229 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAA-GCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
** *
41542293 ATTT-GTATCTCGCA
65 ATTTAACAACTCGCA
*
41542307 CAAATGCCTTC-GGATCTTAGTCCGGAT
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT
41542334 ATATTCACTT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
77 3 0.03
78 45 0.51
79 41 0.46
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
TTTAACAACTCGCA
Found at i:41542380 original size:40 final size:41
Alignment explanation
Indices: 41542304--41542380 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
41542294 TTTGTATCTC
* * *
41542304 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41542345 GCACAAA-GCCTTCGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACA-CATTCA
41542381 ANNNNNNNNN
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 11 0.34
40 14 0.44
41 7 0.22
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41556094 original size:40 final size:40
Alignment explanation
Indices: 41556037--41556252 Score: 278
Period size: 40 Copynumber: 5.5 Consensus size: 40
41556027 CGGATGATAA
*
41556037 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
* *
41556077 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
* *
41556117 CCGGGCTAAGTCCC-AAGGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAA-GGCATTTGTGCGAGTTACTACAT
* *
41556157 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
* * *
41556197 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTACAT
* *
41556236 CC-GGTTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAG
41556253 TTACTTGGCT
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
38 14 0.09
39 17 0.11
40 127 0.79
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
Found at i:41569855 original size:34 final size:34
Alignment explanation
Indices: 41569769--41569856 Score: 122
Period size: 34 Copynumber: 2.6 Consensus size: 34
41569759 GTACTGAATT
* * * *
41569769 GGGCTAAGTCCCGCACTAATATTGCTACTGATAT
1 GGGCTAAGGCCCACACTGATATTGCTACTGATAA
41569803 GGGCTAAGGCCCACACTGATATTGCTACTGATAA
1 GGGCTAAGGCCCACACTGATATTGCTACTGATAA
* *
41569837 GGGCTTAGGCCCAGACTGAT
1 GGGCTAAGGCCCACACTGAT
41569857 CAACACTGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (34 bp):
GGGCTAAGGCCCACACTGATATTGCTACTGATAA
Found at i:41572163 original size:27 final size:27
Alignment explanation
Indices: 41572133--41572285 Score: 207
Period size: 27 Copynumber: 5.7 Consensus size: 27
41572123 ACCCAAATAT
*
41572133 CCTCAATTTATAAAATTACCGTTTTAC
1 CCTCGATTTATAAAATTACCGTTTTAC
* *
41572160 CCTCGATTTACAAAATTACAGTTTTAC
1 CCTCGATTTATAAAATTACCGTTTTAC
* *
41572187 CTTCGATTTATAAAATTACCATTTTAC
1 CCTCGATTTATAAAATTACCGTTTTAC
* *
41572214 CCTCGATTTATAGAATTATCGTTTTAC
1 CCTCGATTTATAAAATTACCGTTTTAC
* *
41572241 CCTCGATTTATAGAATTACCATTTTAC
1 CCTCGATTTATAAAATTACCGTTTTAC
* *
41572268 CCTCAATTTACAAAATTA
1 CCTCGATTTATAAAATTA
41572286 TTAATACACC
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.41
Consensus pattern (27 bp):
CCTCGATTTATAAAATTACCGTTTTAC
Found at i:41572196 original size:54 final size:54
Alignment explanation
Indices: 41572133--41572286 Score: 229
Period size: 54 Copynumber: 2.9 Consensus size: 54
41572123 ACCCAAATAT
* *
41572133 CCTCAATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTA-CAGTTTTAC
1 CCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTATC-GTTTTAC
* * *
41572187 CTTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTATCGTTTTAC
1 CCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTAC
* *
41572241 CCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAAAATTAT
1 CCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTAT
41572287 TAATACACCA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 88 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (54 bp):
CCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTATCGTTTTAC
Found at i:41572201 original size:81 final size:81
Alignment explanation
Indices: 41572112--41572282 Score: 202
Period size: 81 Copynumber: 2.1 Consensus size: 81
41572102 GTACCCCTGG
*
41572112 TTTATAAAACTACCCA-AATATCCTCAATTTATAAAATTACCGTTTTACCCTCGATTTACAAAAT
1 TTTATAAAACTA-CCATAATACCCTCAATTTATAAAATTACCGTTTTACCCTCGATTTACAAAAT
* *
41572176 TA-CAGTTTTACCTTCGA
65 TACCA-TTTTACCCTCAA
* ** * * * * *
41572193 TTTATAAAATTACCATTTTACCCTCGATTTATAGAATTATCGTTTTACCCTCGATTTATAGAATT
1 TTTATAAAACTACCATAATACCCTCAATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATT
41572258 ACCATTTTACCCTCAA
66 ACCATTTTACCCTCAA
*
41572274 TTTACAAAA
1 TTTATAAAA
41572283 TTATTAATAC
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
80 3 0.04
81 71 0.93
82 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (81 bp):
TTTATAAAACTACCATAATACCCTCAATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATT
ACCATTTTACCCTCAA
Found at i:41572323 original size:81 final size:81
Alignment explanation
Indices: 41572238--41572430 Score: 219
Period size: 81 Copynumber: 2.4 Consensus size: 81
41572228 ATTATCGTTT
* *** * *
41572238 TACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAAAATTATTAATACACCATTGGTT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTCAATTTACAAAATTACTAAAACACCATTGGTT
41572303 TACAAAATTACCAAAA
66 TACAAAATTACCAAAA
* * ** * *
41572319 TACCCTCGA-TTAGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACTAAAATACCCTTGGT
1 TACCCTCGATTTA-TAAAATTACCAAAATACCCTCAATTTACAAAATTACTAAAACACCATTGGT
**
41572383 TTGTAAAATTACCAAAA
65 TTACAAAATTACCAAAA
* *
41572400 TACCCTTGATTTATAAAA-TACCGAAATACCC
1 TACCCTCGATTTATAAAATTACCAAAATACCC
41572431 CTATAGGGTA
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
80 15 0.16
81 76 0.81
82 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (81 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCTCAATTTACAAAATTACTAAAACACCATTGGTT
TACAAAATTACCAAAA
Found at i:41572432 original size:27 final size:27
Alignment explanation
Indices: 41572089--41572430 Score: 181
Period size: 27 Copynumber: 12.7 Consensus size: 27
41572079 CCCCCAGTTG
* * *
41572089 TAAAATTACCAAAGTACCCCTGGTTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* * * **
41572116 TAAAACTACCCAAATATCCTCAATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
**** *
41572143 TAAAATTACCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* ***
41572170 CAAAATTA-CAGTTTTA-CCTTCGATTTA
1 TAAAATTACCA-AAATACCCTT-GATTTA
*** *
41572197 TAAAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* * **** *
41572224 TAGAATTATCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* *** **
41572251 TAGAATTACCATTTTACCCTCAATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* ** * * * *
41572278 CAAAATTATTAATACACCATTGGTTTA
1 TAAAATTACCAAAATACCCTTGATTTA
* *
41572305 CAAAATTACCAAAATACCCTCGA-TTA
1 TAAAATTACCAAAATACCCTTGATTTA
*
41572331 GTAAAATTACCAAAATACCCTT-AGTTTG
1 -TAAAATTACCAAAATACCCTTGA-TTTA
* * *
41572359 TAAAATTACTAAAATACCCTTGGTTTG
1 TAAAATTACCAAAATACCCTTGATTTA
41572386 TAAAATTACCAAAATACCCTTGATTTA
1 TAAAATTACCAAAATACCCTTGATTTA
*
41572413 TAAAA-TACCGAAATACCC
1 TAAAATTACCAAAATACCC
41572431 CTATAGGGTA
Statistics
Matches: 254, Mismatches: 53, Indels: 17
0.78 0.16 0.05
Matches are distributed among these distances:
26 20 0.08
27 227 0.89
28 7 0.03
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.35
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTTGATTTA
Found at i:41572453 original size:27 final size:27
Alignment explanation
Indices: 41572422--41572662 Score: 299
Period size: 27 Copynumber: 8.9 Consensus size: 27
41572412 ATAAAATACC
*
41572422 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* * * *
41572449 AAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACT
41572476 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
41572503 GAAATACCCCTGTAAGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACT
*
41572530 GAAATACCCCTATAGGGTTA-AATTACT
1 GAAATACCCCTGTAGGG-TAGAATTACT
*
41572557 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
41572584 GAAATACCCTTGTAGGGTAGAAATA-T
1 GAAATACCCCTGTAGGGTAGAATTACT
41572610 CGAAATACCCCTGTAGGGTAGAATTA-T
1 -GAAATACCCCTGTAGGGTAGAATTACT
* * * *
41572637 CGAGATACCCATGTGGGGTAAAATTA
1 -GAAATACCCCTGTAGGGTAGAATTA
41572663 TCATTTTTCC
Statistics
Matches: 186, Mismatches: 25, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 182 0.98
28 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACT
Found at i:41572481 original size:80 final size:80
Alignment explanation
Indices: 41572306--41572484 Score: 206
Period size: 80 Copynumber: 2.2 Consensus size: 80
41572296 ATTGGTTTAC
*
41572306 AAAATTACCAAAATACCCTCGATTAGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACTAA
1 AAAATTACCAAAATACCCTCGATTAGTAAAATTACCAAAATACCCTTAG-TGGTAAAATTACTAA
**
41572371 AATACCCTTGGTTTGT
65 AATACCCTTGGTGGGT
* * *
41572387 AAAATTACCAAAATACCCTTGATTTA-TAAAA-TACCGAAATACCCCTATAG-GGTAGAATTACT
1 AAAATTACCAAAATACCCTCGA-TTAGTAAAATTACCAAAATA-CCCT-TAGTGGTAAAATTACT
41572449 AAAATACCCTT-GTAGGGT
63 AAAATACCCTTGGT-GGGT
*
41572467 AGAAA-TACCGAAATACCC
1 A-AAATTACCAAAATACCC
41572485 CTGTAGGGTA
Statistics
Matches: 86, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
79 2 0.02
80 45 0.52
81 33 0.38
82 6 0.07
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.28
Consensus pattern (80 bp):
AAAATTACCAAAATACCCTCGATTAGTAAAATTACCAAAATACCCTTAGTGGTAAAATTACTAAA
ATACCCTTGGTGGGT
Found at i:41572486 original size:54 final size:54
Alignment explanation
Indices: 41572418--41572646 Score: 336
Period size: 54 Copynumber: 4.2 Consensus size: 54
41572408 ATTTATAAAA
* * *
41572418 TACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAAT
* *
41572472 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAAT
41572526 TACCGAAATACCCCTATAGGGTTA-AATTACTGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTATAGGG-TAGAATTACTGAAATACCCCTGTAGGGTAGAAT
* * *
41572580 TACCGAAATACCCTTGTAGGGTAGAAATA-TCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTATAGGGTAGAATTACT-GAAATACCCCTGTAGGGTAGAAT
* *
41572634 TATCGAGATACCC
1 TACCGAAATACCC
41572647 ATGTGGGGTA
Statistics
Matches: 160, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
53 3 0.02
54 155 0.97
55 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (54 bp):
TACCGAAATACCCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAAT
Found at i:41576380 original size:40 final size:40
Alignment explanation
Indices: 41576144--41576399 Score: 376
Period size: 40 Copynumber: 6.4 Consensus size: 40
41576134 GATGATAACG
*
41576144 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
*
41576184 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
* *
41576224 GGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATTTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
41576264 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
**
41576304 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
41576344 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
41576384 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
41576400 TACTTGGTTT
Statistics
Matches: 201, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 16 0.08
40 185 0.92
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:41585022 original size:40 final size:40
Alignment explanation
Indices: 41584945--41585126 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
41584935 AAACCAAGTA
** * *
41584945 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
41584984 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
41585024 TCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41585064 CCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
41585104 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
41585127 CATCCGACTA
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 13 0.10
40 119 0.90
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:41591530 original size:43 final size:43
Alignment explanation
Indices: 41591331--41591528 Score: 216
Period size: 43 Copynumber: 4.6 Consensus size: 43
41591321 TAATTTTTTA
* *
41591331 AAAGGTCATGATTTTTAGTGGCGTTTGTGGGAAAAGCGTCGCT
1 AAAGGTCATGATTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
** * * *
41591374 AAAGGTTGTGTTTTTTAGCGGCGTTGGTGGGAAAAGCGTCGCT
1 AAAGGTCATGATTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* * * * *
41591417 AAAGGTCGTGTTTTTTAGCGGCATTAGTGGGAAAAGCGCCACT
1 AAAGGTCATGATTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
** * * * *
41591460 AAAGGTCATGACCTTTAGCGACATTTTTGGTAAAAGCGCCGCT
1 AAAGGTCATGATTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* *
41591503 AAAGATCATGACTTTTAGCGGCGTTT
1 AAAGGTCATGATTTTTAGCGGCGTTT
41591529 TTTTCATAAA
Statistics
Matches: 132, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 132 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (43 bp):
AAAGGTCATGATTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
Found at i:41597158 original size:47 final size:47
Alignment explanation
Indices: 41597022--41597160 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 47
41597012 GCCCCTAAGT
* * * *
41597022 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA--TAAGT
1 GAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCATCCATCTCAGC
* *
41597068 GAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCATCTCAGC
41597115 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATCTCA
1 GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATCCATCTCA
41597161 ACTAGTTCGG
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
43 1 0.01
44 3 0.04
45 2 0.03
46 28 0.36
47 36 0.47
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCATCTCAGC
Found at i:41597628 original size:30 final size:30
Alignment explanation
Indices: 41597594--41597653 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
41597584 ATTTAATACG
*
41597594 AACTTTAGAAAAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAAGTACACTTTTGCCCCTA
* * *
41597624 AACTTTTGCATAAGTACACTTTTGCCCCTA
1 AACTTTAGAAAAAGTACACTTTTGCCCCTA
41597654 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (30 bp):
AACTTTAGAAAAAGTACACTTTTGCCCCTA
Found at i:41608523 original size:24 final size:25
Alignment explanation
Indices: 41608490--41608542 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
41608480 GGCCTAGCCT
41608490 TTTTTAAT-AACTAGGGC-AATGCCC
1 TTTTTAATAAACTAGGGCAAAT-CCC
* *
41608514 TTTTTGATAAACTGGGGCAAATCCC
1 TTTTTAATAAACTAGGGCAAATCCC
41608539 TTTT
1 TTTT
41608543 CAGTAAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 15 0.60
26 3 0.12
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (25 bp):
TTTTTAATAAACTAGGGCAAATCCC
Found at i:41614614 original size:17 final size:17
Alignment explanation
Indices: 41614594--41614635 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
41614584 AATTCCATAT
*
41614594 CTATTTGATACCTATAG
1 CTATTAGATACCTATAG
41614611 CTATTAGATACCTATAG
1 CTATTAGATACCTATAG
41614628 CTATTAGA
1 CTATTAGA
41614636 ATCCAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (17 bp):
CTATTAGATACCTATAG
Found at i:41617840 original size:33 final size:33
Alignment explanation
Indices: 41617802--41617901 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
41617792 TTCATACATA
41617802 TTTCATATGTCCACATATGTTCATATACTTACC
1 TTTCATATGTCCACATATGTTCATATACTTACC
* *
41617835 TTTCAT-TCT-CA-ATCATG---ATATACATT-TC
1 TTTCATATGTCCACAT-ATGTTCATATAC-TTACC
***
41617863 AAACATATGTCCACATATGTTCATATACTTACC
1 TTTCATATGTCCACATATGTTCATATACTTACC
41617896 TTTCAT
1 TTTCAT
41617902 TCTCAATCAT
Statistics
Matches: 48, Mismatches: 10, Indels: 18
0.63 0.13 0.24
Matches are distributed among these distances:
28 10 0.21
29 4 0.08
30 7 0.15
31 7 0.15
32 4 0.08
33 16 0.33
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (33 bp):
TTTCATATGTCCACATATGTTCATATACTTACC
Found at i:41617876 original size:61 final size:61
Alignment explanation
Indices: 41617805--41617930 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
41617795 ATACATATTT
41617805 CATATGTCCACATATGTTCATATACTTACCTTTCATTCTCAATCATGATATACATTTCAAA
1 CATATGTCCACATATGTTCATATACTTACCTTTCATTCTCAATCATGATATACATTTCAAA
41617866 CATATGTCCACATATGTTCATATACTTACCTTTCATTCTCAATCATGATATACATTTCAAA
1 CATATGTCCACATATGTTCATATACTTACCTTTCATTCTCAATCATGATATACATTTCAAA
41617927 CATA
1 CATA
41617931 CCTGAATCGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (61 bp):
CATATGTCCACATATGTTCATATACTTACCTTTCATTCTCAATCATGATATACATTTCAAA
Found at i:41618112 original size:44 final size:42
Alignment explanation
Indices: 41618052--41618154 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
41618042 TCCCAGACGT
* * *
41618052 GGTCCTACATGTAATCAAATATCGTTGCC-ACTGTCCCAAACAA
1 GGTCTTACATGAAATCAAATA-CGATGCCGA-TGTCCCAAACAA
* *
41618095 GGTCTTTACATGAAATCAAATACGATGCCGATGTCCCAGACAT
1 GGTC-TTACATGAAATCAAATACGATGCCGATGTCCCAAACAA
41618138 GGTCTTACATGTAAATC
1 GGTCTTACATG-AAATC
41618155 TCGAATCGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
42 7 0.13
43 29 0.56
44 16 0.31
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
GGTCTTACATGAAATCAAATACGATGCCGATGTCCCAAACAA
Found at i:41618130 original size:43 final size:43
Alignment explanation
Indices: 41618052--41618206 Score: 120
Period size: 44 Copynumber: 3.6 Consensus size: 43
41618042 TCCCAGACGT
* * *
41618052 GGTCCTACATGTAATCAAATATCGTTGCCACTGTCCCAAACAA
1 GGTCTTACATGAAATCAAATATCGATGCCACTGTCCCAAACAA
* *
41618095 GGTCTTTACATGAAATCAAATA-CGATGCCGA-TGTCCCAGACAT
1 GGTC-TTACATGAAATCAAATATCGATGCC-ACTGTCCCAAACAA
** * * **
41618138 GGTCTTACATGTAAATCTCGA-ATCGATACCAAC-GTCCCAGACTT
1 GGTCTTACATG-AAATC-AAATATCGATGCC-ACTGTCCCAAACAA
* *
41618182 GGTCTTACACGAAATCACATATCGA
1 GGTCTTACATGAAATCAAATATCGA
41618207 AAATCCTATG
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
42 8 0.09
43 40 0.43
44 44 0.48
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
GGTCTTACATGAAATCAAATATCGATGCCACTGTCCCAAACAA
Found at i:41630784 original size:69 final size:66
Alignment explanation
Indices: 41630707--41630855 Score: 167
Period size: 67 Copynumber: 2.2 Consensus size: 66
41630697 CATCATGTGT
* * * *
41630707 ACAAGAGAGCTACAAGACATCATGATGTAGCTAGGGTCGCATGGGTGATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC-AG-CAT-AT-ATGTAGCTA-GGTCGCATGCGTGATACCAGTGAAGGACACC
41630770 ATGTAG
61 ATGTAG
* * *
41630776 ACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
41630841 AG
65 AG
41630843 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
41630856 GAGATAAACT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
64 15 0.21
65 9 0.13
66 4 0.06
67 27 0.39
68 2 0.03
69 13 0.19
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:41654179 original size:29 final size:29
Alignment explanation
Indices: 41654117--41654191 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
41654107 AATTATATTC
* * *
41654117 ATATGGCTCATGAGGCCCAAATCACCTGT
1 ATATGGCCCATTAGGCCCAAATCACATGT
*
41654146 ATATGGCCCATTAGGCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
* *
41654175 TTATGGCCCGTTAGGCC
1 ATATGGCCCATTAGGCC
41654192 TAGCCACATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:41654446 original size:8 final size:8
Alignment explanation
Indices: 41654415--41654466 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
41654405 GTAGCCAAAC
41654415 TTTCGGCT
1 TTTCGGCT
*
41654423 TTTCGACAT
1 TTTCGGC-T
41654432 TTT-GGCT
1 TTTCGGCT
41654439 TTTCGGCT
1 TTTCGGCT
* *
41654447 TTTCAGCA
1 TTTCGGCT
*
41654455 TTTCGGTT
1 TTTCGGCT
41654463 TTTC
1 TTTC
41654467 AGTATTTCGC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
7 4 0.11
8 27 0.77
9 4 0.11
ACGTcount: A:0.08, C:0.21, G:0.19, T:0.52
Consensus pattern (8 bp):
TTTCGGCT
Found at i:41654456 original size:24 final size:24
Alignment explanation
Indices: 41654415--41654466 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
41654405 GTAGCCAAAC
*
41654415 TTTCGGCTTTTCGACATTTTGGCT
1 TTTCGGCTTTTCGACATTTCGGCT
*
41654439 TTTCGGCTTTTC-AGCATTTCGGTT
1 TTTCGGCTTTTCGA-CATTTCGGCT
41654463 TTTC
1 TTTC
41654467 AGTATTTCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.08, C:0.21, G:0.19, T:0.52
Consensus pattern (24 bp):
TTTCGGCTTTTCGACATTTCGGCT
Found at i:41654458 original size:16 final size:16
Alignment explanation
Indices: 41654439--41654481 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
41654429 CATTTTGGCT
41654439 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
* *
41654455 TTTCGGTTTTTCAGTA
1 TTTCGGCTTTTCAGCA
*
41654471 TTTCGCCTTTT
1 TTTCGGCTTTT
41654482 GCCGATACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.53
Consensus pattern (16 bp):
TTTCGGCTTTTCAGCA
Found at i:41655711 original size:16 final size:16
Alignment explanation
Indices: 41655690--41655723 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41655680 AGAAAATTCA
41655690 GGATTTCAGGATTCTT
1 GGATTTCAGGATTCTT
*
41655706 GGATTTCAGGATTTTT
1 GGATTTCAGGATTCTT
41655722 GG
1 GG
41655724 GGCGTTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.29, T:0.44
Consensus pattern (16 bp):
GGATTTCAGGATTCTT
Found at i:41665955 original size:57 final size:56
Alignment explanation
Indices: 41665894--41666011 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 56
41665884 CACATACCTA
* *
41665894 TATATGGCCCACTAGACCC-AATTATATTCACATGGCCCATTAGACCCAAATCATAAT
1 TATATGGCCCACTAGACCCAAATCACATTCACATGG-CCATTAGACCCAAATCA-AAT
** * * * *
41665951 TATATGGCCCTTTAGGCCCAAATCACATTTATATGGCCATTAGACCCAAATCACAT
1 TATATGGCCCACTAGACCCAAATCACATTCACATGGCCATTAGACCCAAATCAAAT
41666007 TATAT
1 TATAT
41666012 TCATGCTCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
56 7 0.13
57 33 0.63
58 12 0.23
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (56 bp):
TATATGGCCCACTAGACCCAAATCACATTCACATGGCCATTAGACCCAAATCAAAT
Found at i:41666002 original size:28 final size:29
Alignment explanation
Indices: 41665894--41666011 Score: 134
Period size: 29 Copynumber: 4.2 Consensus size: 29
41665884 CACATACCTA
* * *
41665894 TATATGGCCCACTAGACCC-AATTATATT
1 TATATGGCCCATTAGACCCAAATCACATT
* * * *
41665922 CACATGGCCCATTAGACCCAAATCATAAT
1 TATATGGCCCATTAGACCCAAATCACATT
* *
41665951 TATATGGCCCTTTAGGCCCAAATCACATT
1 TATATGGCCCATTAGACCCAAATCACATT
41665980 TATATGG-CCATTAGACCCAAATCACA-T
1 TATATGGCCCATTAGACCCAAATCACATT
41666007 TATAT
1 TATAT
41666012 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.08
28 33 0.43
29 37 0.49
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGACCCAAATCACATT
Found at i:41666250 original size:8 final size:8
Alignment explanation
Indices: 41666223--41666265 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
41666213 ATAGCCAAAC
*
41666223 TTTCAGCT
1 TTTCGGCT
* *
41666231 TTTCGACA
1 TTTCGGCT
41666239 TTTCGGCT
1 TTTCGGCT
41666247 TTTCGGCT
1 TTTCGGCT
*
41666255 TTTCGACT
1 TTTCGGCT
41666263 TTT
1 TTT
41666266 TCCGATCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.09, C:0.23, G:0.16, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:41680748 original size:76 final size:76
Alignment explanation
Indices: 41680622--41680774 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
41680612 CTATATTTCT
* *
41680622 CAATAGATTTATTCAAGATCCTCCTTTTGTTTCATTATTTCAATAAAAATATTACATGCAAAATC
1 CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTACATGCAAAATC
41680687 GTTGTCGACCA
66 GTTGTCGACCA
*
41680698 CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTGCATGCAAAATC
1 CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTACATGCAAAATC
41680763 GTTGTCGACCA
66 GTTGTCGACCA
41680774 C
1 C
41680775 TTTTATTATT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (76 bp):
CAATAGATTTATTCAAGATCCTCATTTTATTTCATTATTTCAATAAAAATATTACATGCAAAATC
GTTGTCGACCA
Found at i:41691055 original size:27 final size:27
Alignment explanation
Indices: 41691024--41691201 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41691014 TAAATTGTAC
41691024 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41691051 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41691077 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41691105 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41691133 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41691160 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41691187 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41691202 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41691138 original size:82 final size:81
Alignment explanation
Indices: 41691025--41691180 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41691015 AAATTGTACA
* *
41691025 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41691089 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41691106 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41691171 TGCGAGTTGA
65 TGCGAATTGA
41691181 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41691192 original size:82 final size:81
Alignment explanation
Indices: 41691021--41691201 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41691011 GATTAAATTG
* *
41691021 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41691086 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41691102 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41691166 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41691184 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41691202 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41698969 original size:27 final size:27
Alignment explanation
Indices: 41698938--41699115 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41698928 TAAATTGTAC
41698938 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41698965 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41698991 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41699019 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41699047 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41699074 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41699101 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41699116 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41699052 original size:82 final size:81
Alignment explanation
Indices: 41698939--41699094 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41698929 AAATTGTACA
* *
41698939 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41699003 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41699020 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41699085 TGCGAGTTGA
65 TGCGAATTGA
41699095 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41699106 original size:82 final size:81
Alignment explanation
Indices: 41698935--41699115 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41698925 GATTAAATTG
* *
41698935 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41699000 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41699016 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41699080 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41699098 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41699116 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41701455 original size:33 final size:33
Alignment explanation
Indices: 41701412--41701481 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
41701402 GGCTAGCCAA
* *
41701412 TATAAGGGCTTAAATGGTATACTTATTCTTTTG
1 TATAAAGGCTTAAATGGTATAATTATTCTTTTG
*
41701445 TATAAAGGCTTAAATTGTATAATTATTCTTTTG
1 TATAAAGGCTTAAATGGTATAATTATTCTTTTG
41701478 TATA
1 TATA
41701482 TGGCCATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (33 bp):
TATAAAGGCTTAAATGGTATAATTATTCTTTTG
Found at i:41703372 original size:117 final size:116
Alignment explanation
Indices: 41703160--41703377 Score: 328
Period size: 117 Copynumber: 1.9 Consensus size: 116
41703150 GTTTTGTGGC
* *
41703160 TAAAGATGAATTGACGGATAAAACTATAATTGAGTTATCGCACTATAAACGTAAGACCATGGTTG
1 TAAAGATGAATTGACGGATAAAACCATAACTGAGTTATCGCACTATAAACGTAAGACCATGGTTG
*
41703225 GACCATGTCAATATTTATATGTAAGACCATAATTGGGTTATGACATTAATG
66 GACCATGGCAATATTTATATGTAAGACCATAATTGGGTTATGACATTAATG
* * * *
41703276 TAAAGGATGAATTGACGGATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTT
1 TAAA-GATGAATTGACGGATAAAACCATAACTGAGTTATCGCACTATAAACGTAAGACCATGGTT
* * * *
41703341 GGACCATGGCAGTGTTTATATGTAAGGCCATAGTTGG
65 GGACCATGGCAATATTTATATGTAAGACCATAATTGG
41703378 ACTATGGCAT
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
116 4 0.04
117 86 0.96
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (116 bp):
TAAAGATGAATTGACGGATAAAACCATAACTGAGTTATCGCACTATAAACGTAAGACCATGGTTG
GACCATGGCAATATTTATATGTAAGACCATAATTGGGTTATGACATTAATG
Found at i:41708166 original size:20 final size:20
Alignment explanation
Indices: 41708141--41708180 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41708131 TAAATATTTT
41708141 TTTCTATGAAAATTGAGTAA
1 TTTCTATGAAAATTGAGTAA
41708161 TTTCTATGAAAATTGAGTAA
1 TTTCTATGAAAATTGAGTAA
41708181 AATTTAAGTA
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:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTCTATGAAAATTGAGTAA
Found at i:41719543 original size:39 final size:40
Alignment explanation
Indices: 41719448--41719709 Score: 301
Period size: 39 Copynumber: 6.7 Consensus size: 40
41719438 TTGAATGATG
*
41719448 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGA-TAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
41719486 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATATTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
41719527 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
41719566 TCCAGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
41719605 TCCGGGCTAAG-CCCGAAGGCAGTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
41719644 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
41719683 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41719710 AACGAGGAGC
Statistics
Matches: 196, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
39 126 0.64
40 57 0.29
41 12 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41719742 original size:79 final size:79
Alignment explanation
Indices: 41719500--41719734 Score: 221
Period size: 78 Copynumber: 3.0 Consensus size: 79
41719490 GGACTAAGAT
* * * ** *
41719500 CCGAAGGCATTTGTGCGAGATATTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCAAGAT-ACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCAGTTGAACGAG-TGACTA
* * * *
41719564 ATTCCAGGCT-AAGC
65 AATCCGGGTTAAATC
* ** *
41719578 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCAGTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCAGTTGAACGAGTGACTAA
*
41719643 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41719657 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAGTTGAACGAGTGA-
*
41719719 CTATATCC-GGTTAAAT
62 CTAAATCCGGGTTAAAT
41719735 TTCGAAGGTA
Statistics
Matches: 135, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 69 0.51
79 41 0.30
80 24 0.18
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCAGTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:41727566 original size:39 final size:39
Alignment explanation
Indices: 41727470--41727731 Score: 311
Period size: 39 Copynumber: 6.6 Consensus size: 39
41727460 TTGAATGATG
*
41727470 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
41727508 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
* *
41727549 TCCGGGCTAAGCTCGAAGGCATTTGTGCAAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
41727588 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
41727627 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
41727666 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
41727705 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
41727732 AACGAGGAGC
Statistics
Matches: 198, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
39 128 0.65
40 58 0.29
41 11 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:41727762 original size:79 final size:79
Alignment explanation
Indices: 41727522--41727762 Score: 233
Period size: 78 Copynumber: 3.1 Consensus size: 79
41727512 GGACTAAGAT
* * ** *
41727522 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCTCGAAGGCATTTGTGCAAGAT-ACTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TGACTA
* * * *
41727586 ATTCCGGGCT-AAGC
65 AATCCGAGTTAAATC
* ** *
41727600 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
* *
41727665 ATCCGGGTTAAGTC
66 ATCCGAGTTAAATC
*
41727679 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
41727741 CTATATCC-AGTTAAATT
62 CTAAATCCGAGTTAAATC
41727758 CCGAA
1 CCGAA
41727763 AGTACGTGAT
Statistics
Matches: 142, Mismatches: 15, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
77 1 0.01
78 71 0.50
79 45 0.32
80 25 0.18
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGAGTTAAATC
Found at i:41740932 original size:67 final size:67
Alignment explanation
Indices: 41740823--41741009 Score: 248
Period size: 67 Copynumber: 2.8 Consensus size: 67
41740813 ATGGGCTGTA
* * * * * **
41740823 ATGGGGTACAATGTGTAAAACTATAGCTCGGCTATGGTAACATAGAGAGTTTGCCAAGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAAGACATTAA
41740888 AC
66 AC
* *
41740890 ATGGGATATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTCCACCAAGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAAGACATTAA
41740955 AC
66 AC
* * * * *
41740957 ATGGGGTATGATGTGTAAGACCATATCTCGACTATGACATCATATAGAGTTCA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCA
41741010 TCGAGGCAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 104 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (67 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTTCACCAAGACATTAA
AC
Found at i:41746401 original size:16 final size:16
Alignment explanation
Indices: 41746376--41746408 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41746366 TATTCTTATG
*
41746376 TTTTATGACATGATGA
1 TTTTAAGACATGATGA
41746392 TTTTAAGACATGATGA
1 TTTTAAGACATGATGA
41746408 T
1 T
41746409 CATTTTTCCC
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:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (16 bp):
TTTTAAGACATGATGA
Found at i:41755860 original size:38 final size:38
Alignment explanation
Indices: 41755796--41755870 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
41755786 AATCCGAGTT
*
41755796 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
41755834 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
41755871 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:41755983 original size:40 final size:40
Alignment explanation
Indices: 41755924--41756145 Score: 365
Period size: 40 Copynumber: 5.6 Consensus size: 40
41755914 AGGTCTCGAC
41755924 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
41755963 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
41756003 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
41756043 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
41756083 GATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
41756123 GTTGTATCCGGACTAAGTTCCGA
1 GATGTATCCGGGCTAAGTCCCGA
41756146 CCGGACTAAG
Statistics
Matches: 169, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 4 0.02
40 165 0.98
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:41756151 original size:16 final size:16
Alignment explanation
Indices: 41756130--41756161 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41756120 AGTGTTGTAT
41756130 CCGGACTAAGTTCCGA
1 CCGGACTAAGTTCCGA
41756146 CCGGACTAAGTTCCGA
1 CCGGACTAAGTTCCGA
41756162 AGAGCATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (16 bp):
CCGGACTAAGTTCCGA
Found at i:41756206 original size:40 final size:40
Alignment explanation
Indices: 41756146--41756247 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
41756136 TAAGTTCCGA
*
41756146 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
* * *
41756186 CCGTGCTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
* *
41756226 CCGGGCTAGGTCCCGAAGAGCA
1 CCGGGCTAAGTTCCGAAGAGCA
41756248 ATCATGCTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
Found at i:41756214 original size:96 final size:96
Alignment explanation
Indices: 41756050--41756229 Score: 315
Period size: 96 Copynumber: 1.9 Consensus size: 96
41756040 AGTGATGTAT
41756050 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCCGAAGAGCATTC
1 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCCGAAGAGCATTC
*
41756115 GTGCTAGTGTTGTATCCGGACTAAGTTCCGA
66 GTGCTAGTGTTATATCCGGACTAAGTTCCGA
* * *
41756146 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAGTTCCGAAGAGCATTC
1 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCCGAAGAGCATTC
*
41756211 GTGCTGGTGTTATATCCGG
66 GTGCTAGTGTTATATCCGG
41756230 GCTAGGTCCC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (96 bp):
CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCCGAAGAGCATTC
GTGCTAGTGTTATATCCGGACTAAGTTCCGA
Found at i:41756256 original size:40 final size:40
Alignment explanation
Indices: 41756146--41756260 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
41756136 TAAGTTCCGA
* * *
41756146 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATAT
* * *
41756186 CCGTGCTAAGTTCCGAAGAGCATTCGTGCTGGTGTTATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATAT
* * *
41756226 CCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
41756261 CGTGTATTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATAT
Found at i:41761345 original size:11 final size:11
Alignment explanation
Indices: 41761329--41761359 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
41761319 GCTCTCTTGT
41761329 ACACATAGTGA
1 ACACATAGTGA
41761340 ACACATAGTGA
1 ACACATAGTGA
*
41761351 ACACTTAGT
1 ACACATAGT
41761360 ACTACCCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (11 bp):
ACACATAGTGA
Found at i:41773496 original size:14 final size:14
Alignment explanation
Indices: 41773452--41773500 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
41773442 CTATGGAGGA
41773452 AAAGAAGA-AAAAG
1 AAAGAAGAGAAAAG
* *
41773465 AAA-AAGTTGAAGAG
1 AAAGAAG-AGAAAAG
41773479 -AAGAAGAGAAAAG
1 AAAGAAGAGAAAAG
41773492 AAAGAAGAG
1 AAAGAAGAG
41773501 GAGAATGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
12 3 0.11
13 10 0.36
14 15 0.54
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (14 bp):
AAAGAAGAGAAAAG
Found at i:41803051 original size:3 final size:3
Alignment explanation
Indices: 41803043--41803074 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
41803033 TGAAAGCAAG
*
41803043 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41803075 AAACAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41803064 original size:12 final size:12
Alignment explanation
Indices: 41803047--41803087 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
41803037 AGCAAGAATA
41803047 ATAATAATAATG
1 ATAATAATAATG
*
41803059 ATAATAATAATA
1 ATAATAATAATG
* *
41803071 ATAAAAACAATG
1 ATAATAATAATG
41803083 ATAAT
1 ATAAT
41803088 GATATATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:41803560 original size:25 final size:26
Alignment explanation
Indices: 41803517--41803567 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
41803507 ATAATATGGT
41803517 TATTAAGAAAATACATACAATATATAA
1 TATTAAG-AAATACATACAATATATAA
*
41803544 TATTAAG-AATATATACAATATATA
1 TATTAAGAAATACATACAATATATA
41803568 TGGTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.70
27 7 0.30
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (26 bp):
TATTAAGAAATACATACAATATATAA
Found at i:41803960 original size:23 final size:22
Alignment explanation
Indices: 41803923--41803976 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
41803913 ATAGTATAAG
*
41803923 AAATATATAACTAAT-GACATT
1 AAATATATAACTAATAGACATA
*
41803944 AAATATATATACATAATAGATATA
1 AAATATATA-AC-TAATAGACATA
41803968 AAATATATA
1 AAATATATA
41803977 CAATATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 4 0.14
24 13 0.46
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATATATAACTAATAGACATA
Found at i:41803991 original size:24 final size:23
Alignment explanation
Indices: 41803923--41803978 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
41803913 ATAGTATAAG
41803923 AAATATATA-AC-TAATGACAT-T
1 AAATATATATACATAAT-ACATAT
*
41803944 AAATATATATACATAATAGATAT
1 AAATATATATACATAATACATAT
41803967 AAA-ATATATACA
1 AAATATATATACA
41803979 ATATATACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 9 0.29
22 14 0.45
23 8 0.26
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATATATATACATAATACATAT
Found at i:41804208 original size:3 final size:3
Alignment explanation
Indices: 41804200--41804257 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
41804190 ATAACAACCC
41804200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41804248 ATA ATA ATA A
1 ATA ATA ATA A
41804258 GAAGATAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41804984 original size:18 final size:18
Alignment explanation
Indices: 41804963--41804997 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41804953 ATTTTTTTAA
41804963 AAAAATAGAAA-AATAAAT
1 AAAAAT-GAAATAATAAAT
41804981 AAAAATGAAATAATAAA
1 AAAAATGAAATAATAAA
41804998 AGTAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAATGAAATAATAAAT
Found at i:41807581 original size:22 final size:21
Alignment explanation
Indices: 41807525--41807567 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41807515 TATCAAATAC
41807525 ATATATATACATGTACCGAAA
1 ATATATATACATGTACCGAAA
41807546 ATATATATACATGTACCGAAA
1 ATATATATACATGTACCGAAA
41807567 A
1 A
41807568 ATAATCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (21 bp):
ATATATATACATGTACCGAAA
Found at i:41831927 original size:3 final size:3
Alignment explanation
Indices: 41831919--41831951 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41831909 TGCTAAAATC
41831919 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41831952 CCAATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41833489 original size:19 final size:19
Alignment explanation
Indices: 41833448--41833491 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
41833438 TGCCACGTTT
*
41833448 AAAAATTAAAAAAATAATT
1 AAAAATTAAAAAAATAATC
*
41833467 AAAAATCTAAAAAAATCA-C
1 AAAAAT-TAAAAAAATAATC
41833486 AAAAAT
1 AAAAAT
41833492 ATGAAAACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAAATTAAAAAAATAATC
Found at i:41833490 original size:20 final size:19
Alignment explanation
Indices: 41833448--41833490 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
41833438 TGCCACGTTT
**
41833448 AAAAATTAAAAAAATAATT
1 AAAAATTAAAAAAATAACA
*
41833467 AAAAATCTAAAAAAATCACA
1 AAAAAT-TAAAAAAATAACA
41833487 AAAA
1 AAAA
41833491 TATGAAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAATTAAAAAAATAACA
Found at i:41842174 original size:35 final size:35
Alignment explanation
Indices: 41842112--41842225 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 35
41842102 AATCCCTTCA
* * * *
41842112 AAACACACCAACTGGTCACAAGAGCTAGTCCTACCG
1 AAACACGCCAA-TGCTCATAAGAGCTAGTCCAACCG
*
41842148 AAACACGCCAATGCTCATAATAGCTAGTCCAACCG
1 AAACACGCCAATGCTCATAAGAGCTAGTCCAACCG
* *
41842183 AAACACGCCAATGCTCATAAGAGATAGTCCAACTG
1 AAACACGCCAATGCTCATAAGAGCTAGTCCAACCG
41842218 AAACACGC
1 AAACACGC
41842226 TAAACAGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 60 0.86
36 10 0.14
ACGTcount: A:0.39, C:0.31, G:0.16, T:0.15
Consensus pattern (35 bp):
AAACACGCCAATGCTCATAAGAGCTAGTCCAACCG
Found at i:41844107 original size:35 final size:35
Alignment explanation
Indices: 41844059--41844192 Score: 126
Period size: 35 Copynumber: 3.8 Consensus size: 35
41844049 GCCACGATTC
** *
41844059 ACAACTCAGTATGGTTAATACCATACCTATGTTTT
1 ACAACTCAGTATGGAAAATACCATACCTATGTATT
*
41844094 ACAACTC-GATATGGGAAATACCATACCTATGTATT
1 ACAACTCAG-TATGGAAAATACCATACCTATGTATT
* * * ** *
41844129 ATAACTCAGTTTGGAGAATACCATACCTACATATC
1 ACAACTCAGTATGGAAAATACCATACCTATGTATT
* * * *
41844164 ATAGCTTAGTATGGAATATACCATACCTA
1 ACAACTCAGTATGGAAAATACCATACCTA
41844193 CATGTCATAA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
34 1 0.01
35 80 0.98
36 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (35 bp):
ACAACTCAGTATGGAAAATACCATACCTATGTATT
Found at i:41846022 original size:16 final size:16
Alignment explanation
Indices: 41846001--41846036 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41845991 AATTTACCAC
41846001 TTAAGTCCTTACTTAT
1 TTAAGTCCTTACTTAT
*
41846017 TTAAGTCCTTCCTTAT
1 TTAAGTCCTTACTTAT
41846033 TTAA
1 TTAA
41846037 CTTTCAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAGTCCTTACTTAT
Found at i:41848039 original size:30 final size:30
Alignment explanation
Indices: 41848003--41848227 Score: 183
Period size: 30 Copynumber: 7.5 Consensus size: 30
41847993 GTTACCACCA
*
41848003 CTTTTCATAGTTCGATAGTCGATGCTATCC
1 CTTTTCATAGTTCGATAGTCGAAGCTATCC
* * *
41848033 CTTTTCATATTTTGAT-GATC-ATCA-CCATCC
1 CTTTTCATAGTTCGATAG-TCGA--AGCTATCC
* * * *
41848063 CTTTTCACAGTT-GATGGTCGTCA-CCATCC
1 CTTTTCATAGTTCGATAGTCG-AAGCTATCC
* * * * *
41848092 CCTTTCATAATTTGATAGCCGAAGCTACCC
1 CTTTTCATAGTTCGATAGTCGAAGCTATCC
* *
41848122 CTTTTCATAATTCGATAGTCGAAGGTATCC
1 CTTTTCATAGTTCGATAGTCGAAGCTATCC
*
41848152 CTTTTCATAGTTTGATAG-CTGAAGCTATCC
1 CTTTTCATAGTTCGATAGTC-GAAGCTATCC
* * * *
41848182 CTTTTAATAGTTCGATAGCCGAAGTTATAC
1 CTTTTCATAGTTCGATAGTCGAAGCTATCC
41848212 CTTTTCATAGTTCGAT
1 CTTTTCATAGTTCGAT
41848228 GGTCATGTAA
Statistics
Matches: 157, Mismatches: 28, Indels: 20
0.77 0.14 0.10
Matches are distributed among these distances:
29 25 0.16
30 131 0.83
31 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (30 bp):
CTTTTCATAGTTCGATAGTCGAAGCTATCC
Found at i:41848086 original size:29 final size:30
Alignment explanation
Indices: 41848029--41848098 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
41848019 AGTCGATGCT
* *
41848029 ATCCCTTTTCATATTTTGATGATCATCACC
1 ATCCCTTTTCACATGTTGATGATCATCACC
* *
41848059 ATCCCTTTTCACA-GTTGATGGTCGTCACC
1 ATCCCTTTTCACATGTTGATGATCATCACC
*
41848088 ATCCCCTTTCA
1 ATCCCTTTTCA
41848099 TAATTTGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.20, C:0.31, G:0.10, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCACATGTTGATGATCATCACC
Found at i:41850709 original size:25 final size:27
Alignment explanation
Indices: 41850672--41850724 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
41850662 TCAAACATGC
41850672 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
41850698 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
41850724 A
1 A
41850725 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:41852243 original size:32 final size:32
Alignment explanation
Indices: 41852206--41852270 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41852196 AATGCTTACC
41852206 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
41852238 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
41852270 A
1 A
41852271 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:41854516 original size:28 final size:28
Alignment explanation
Indices: 41854300--41854509 Score: 314
Period size: 28 Copynumber: 7.5 Consensus size: 28
41854290 ATATTAAGTC
* *
41854300 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41854327 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41854355 TGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41854383 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
41854411 CCCGCACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41854439 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
41854467 CGCACACTTAGTGCTACACAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
41854495 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41854510 GTACAATTTA
Statistics
Matches: 170, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
27 22 0.13
28 148 0.87
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:41862040 original size:40 final size:40
Alignment explanation
Indices: 41862010--41862179 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
41862000 GGACTAAGAT
* *
41862010 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
41862050 CCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
41862090 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
41862130 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
41862169 CCGAAGGCATT
1 CCGAAGGCATT
41862180 TGAACGAGGA
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 33 0.28
40 83 0.72
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:41862106 original size:80 final size:79
Alignment explanation
Indices: 41861957--41862179 Score: 232
Period size: 80 Copynumber: 2.8 Consensus size: 79
41861947 TTGAATGCTG
* * * ** * * * * *
41861957 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
41862021 TGTGCGAGATACTAAA
64 CGTGCGAGATACTAAA
* * *
41862037 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
41862102 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
41862117 TCCGGGTTACGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
41862180 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 35 0.29
80 81 0.68
81 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAA
Found at i:41862199 original size:79 final size:80
Alignment explanation
Indices: 41862032--41862214 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
41862022 GTGCGAGATA
* * *
41862032 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
41862097 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
41862112 TTAAATCCGGGTTACGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
41862176 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
41862191 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
41862215 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:41865903 original size:28 final size:28
Alignment explanation
Indices: 41865659--41865896 Score: 379
Period size: 28 Copynumber: 8.5 Consensus size: 28
41865649 ATATTAAGTC
* *
41865659 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41865686 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
41865714 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41865742 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41865770 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
41865798 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
41865826 CGCACACTTAGTGCTACACAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
41865854 CGCACACTTAGTGCTACACAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
41865882 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41865897 GTACAATTTA
Statistics
Matches: 204, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
27 22 0.11
28 182 0.89
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:41875218 original size:32 final size:32
Alignment explanation
Indices: 41875181--41875241 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
41875171 CTTACCATGC
41875181 CCATCATCCATTAACTATTAAAATGCTAATGT
1 CCATCATCCATTAACTATTAAAATGCTAATGT
41875213 CCATCATCCATTAACTATTAAAATGCTAA
1 CCATCATCCATTAACTATTAAAATGCTAA
41875242 AATGCATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (32 bp):
CCATCATCCATTAACTATTAAAATGCTAATGT
Found at i:41878835 original size:44 final size:44
Alignment explanation
Indices: 41878785--41878871 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
41878775 ATTAGTTTAT
41878785 TAAATTAACTTTAATGAAATAATATAAAAATCATATAACACAAC
1 TAAATTAACTTTAATGAAATAATATAAAAATCATATAACACAAC
41878829 TAAATTAACTTTAATGAAATAATATAAAAATCATATAACACAA
1 TAAATTAACTTTAATGAAATAATATAAAAATCATATAACACAA
41878872 GTCTATTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (44 bp):
TAAATTAACTTTAATGAAATAATATAAAAATCATATAACACAAC
Found at i:41879992 original size:30 final size:30
Alignment explanation
Indices: 41879956--41880029 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
41879946 CAGGTCGTCA
***
41879956 CTATCCCTTTTCATAATTTGATAGTTGAAG
1 CTATCCCTTTTCATAATTTGATAGCAAAAG
41879986 CTATCCCTTTTCATAATTTGATAGCAAAAG
1 CTATCCCTTTTCATAATTTGATAGCAAAAG
41880016 CTATCCCTTTTCAT
1 CTATCCCTTTTCAT
41880030 TGGTCGATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (30 bp):
CTATCCCTTTTCATAATTTGATAGCAAAAG
Found at i:41890621 original size:23 final size:22
Alignment explanation
Indices: 41890570--41890621 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41890560 CCTCGTCTTT
*
41890570 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41890592 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41890615 TTCTTTT
1 TTCTTTT
41890622 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41896593 original size:21 final size:20
Alignment explanation
Indices: 41896569--41896613 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
41896559 ATACATAACA
41896569 ATAGGAATAAAAAGTATATAC
1 ATAGGAATAAAAA-TATATAC
* * *
41896590 ATAGTATTAAAAATATGTAC
1 ATAGGAATAAAAATATATAC
41896610 ATAG
1 ATAG
41896614 TATAGCGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.29
Consensus pattern (20 bp):
ATAGGAATAAAAATATATAC
Found at i:41896610 original size:20 final size:21
Alignment explanation
Indices: 41896576--41896616 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
41896566 ACAATAGGAA
41896576 TAAAAAGTATATACATAGTAT
1 TAAAAAGTATATACATAGTAT
*
41896597 TAAAAA-TATGTACATAGTAT
1 TAAAAAGTATATACATAGTAT
41896617 AGCGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (21 bp):
TAAAAAGTATATACATAGTAT
Found at i:41896624 original size:25 final size:25
Alignment explanation
Indices: 41896596--41896643 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41896586 ATACATAGTA
** *
41896596 TTAAAAATATGTACATAGTATAGCG
1 TTAAAAATACATACATAATATAGCG
41896621 TTAAAAATACATACATAATATAG
1 TTAAAAATACATACATAATATAG
41896644 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGCG
Found at i:41896684 original size:24 final size:24
Alignment explanation
Indices: 41896624--41896730 Score: 76
Period size: 24 Copynumber: 4.3 Consensus size: 24
41896614 TATAGCGTTA
* * *
41896624 AAAATACATACATAATATAGTTATT
1 AAAATATATACATAAGATA-ATATT
41896649 AAAAAATATATACATAAGATAATATGT
1 --AAAATATATACATAAGATAATAT-T
* * *
41896676 -AAATATATATATAATATAGTATT
1 AAAATATATACATAAGATAATATT
*
41896699 AAAAATATATACAT--GATATATATA
1 -AAAATATATACATAAGATA-ATATT
41896723 AAAATATA
1 AAAATATA
41896731 ATATTTAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
23 12 0.18
24 22 0.33
25 11 0.17
26 3 0.05
27 18 0.27
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (24 bp):
AAAATATATACATAAGATAATATT
Found at i:41896759 original size:37 final size:37
Alignment explanation
Indices: 41896678--41896767 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 37
41896668 TAATATGTAA
* * *
41896678 ATATATAT-ATAATATAGTATTAAAAATATATACATG
1 ATATATATAAAAATATAATATTAAAAATATATACACG
*
41896714 ATATATATAAAAATATAATATTTAAAAGATATATATACG
1 ATATATATAAAAATATAATA-TTAAAA-ATATATACACG
41896753 TAATATATATAAAAA
1 --ATATATATAAAAA
41896768 ATGTATACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
36 8 0.18
37 9 0.20
38 6 0.13
39 9 0.20
41 13 0.29
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (37 bp):
ATATATATAAAAATATAATATTAAAAATATATACACG
Found at i:41896774 original size:24 final size:24
Alignment explanation
Indices: 41896747--41896809 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
41896737 AAAAGATATA
*
41896747 TATACGTAATATATA-TAAAAAAT
1 TATACATAATATATATTAAAAAAT
*
41896770 GTATACATAATATAGTATTAAAATAT
1 -TATACATAATATA-TATTAAAAAAT
41896796 T-TACATAATATATA
1 TATACATAATATATA
41896810 CATATTAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 2 0.06
24 23 0.66
25 3 0.09
26 7 0.20
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (24 bp):
TATACATAATATATATTAAAAAAT
Found at i:41896879 original size:21 final size:20
Alignment explanation
Indices: 41896850--41896903 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
41896840 TAATACTACA
*
41896850 TAAATATATACATATATATAT
1 TAAACATATACATATATA-AT
*
41896871 TAAAGATATATACATATATAAT
1 T-AA-ACATATACATATATAAT
*
41896893 AAAACATATAC
1 TAAACATATAC
41896904 TAATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 4 0.14
23 15 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAACATATACATATATAAT
Found at i:41896918 original size:3 final size:3
Alignment explanation
Indices: 41896904--41896994 Score: 53
Period size: 3 Copynumber: 30.0 Consensus size: 3
41896894 AAACATATAC
* * * *
41896904 TAA TAT TAA TAA TAA TAA GAA TAA GAA TAA T-A TAAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* * * *
41896949 -ATA TAA TAA TAT TAAA TAA TAT TAA AAA TAA TTAA T-T TAA TAA TAA
1 TA-A TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
41896995 AGAAATGGAA
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
2 4 0.06
3 53 0.82
4 8 0.12
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:41896969 original size:18 final size:18
Alignment explanation
Indices: 41896867--41896970 Score: 51
Period size: 18 Copynumber: 5.8 Consensus size: 18
41896857 ATACATATAT
*
41896867 ATATTAAAGATATATACATA
1 ATATTAAATA-ATATA-ATA
* *
41896887 TATAATAAA-ACATATACTA
1 -ATATTAAATA-ATATAATA
*
41896906 ATATT-AATAATAATAAGA
1 ATATTAAATAAT-ATAATA
41896924 ATA--AGAATAATATAAATA
1 ATATTA-AATAATAT-AATA
*
41896942 ATAGT--A-AATATAATA
1 ATATTAAATAATATAATA
41896957 ATATTAAATAATAT
1 ATATTAAATAATAT
41896971 TAAAAATAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.12
16 5 0.08
17 8 0.12
18 29 0.45
19 2 0.03
20 6 0.09
21 7 0.11
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.34
Consensus pattern (18 bp):
ATATTAAATAATATAATA
Found at i:41896990 original size:34 final size:34
Alignment explanation
Indices: 41896929--41896993 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
41896919 TAAGAATAAG
*
41896929 AATAATATAAATAATAGTAAATATAATAATATTA
1 AATAATATAAATAATAATAAATATAATAATATTA
* *
41896963 AATAATATTAAA-AATAATTAATTTAATAATA
1 AATAATA-TAAATAATAATAAATATAATAATA
41896994 AAGAAATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (34 bp):
AATAATATAAATAATAATAAATATAATAATATTA
Found at i:41898644 original size:44 final size:44
Alignment explanation
Indices: 41898548--41898693 Score: 154
Period size: 44 Copynumber: 3.3 Consensus size: 44
41898538 ATCTGTTTTT
* *
41898548 CTGCAACTTCA-GAGAGATGAGATCTAGTATCTTCAATCTGCTCCG
1 CTGCAACTTCAGGA-AGATGA-ATCTTGTATCTTCAATCTGCTCCA
* * * *
41898593 CTACAACTTCAGGAAGATGAAACTTGTAACTTCAACCTGCTCCA
1 CTGCAACTTCAGGAAGATGAATCTTGTATCTTCAATCTGCTCCA
* * *
41898637 CTGCAACTTCAGGGAGGCA-GAATC-TGTATCTTCGATCAGCTCCA
1 CTGCAACTTCA-GGAAG-ATGAATCTTGTATCTTCAATCTGCTCCA
41898681 CTGCAACTTCAGG
1 CTGCAACTTCAGG
41898694 GAGGAAAAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
43 2 0.02
44 56 0.66
45 24 0.28
46 3 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (44 bp):
CTGCAACTTCAGGAAGATGAATCTTGTATCTTCAATCTGCTCCA
Done.