Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 176 of 226
Found at i:53871433 original size:45 final size:45
Alignment explanation
Indices: 53871366--53871454 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
53871356 TAGTTGGGAG
53871366 GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTAA
1 GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTAA
* * *
53871411 GAGTTTTTGCTGTTAGCTGAGTTCACCTACAATAGCAGTTTCTA
1 GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTA
53871455 CTCCAGTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (45 bp):
GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTAA
Found at i:53872374 original size:5 final size:5
Alignment explanation
Indices: 53872366--53872392 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
53872356 ATTTGGGTGG
53872366 TTTGT TTTGT TTTGT TTTGT TTTGT TT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TT
53872393 ATAACGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTGT
Found at i:53874882 original size:36 final size:36
Alignment explanation
Indices: 53874835--53874908 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
53874825 AAACGAAATG
53874835 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
1 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
53874871 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
1 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
53874907 TA
1 TA
53874909 CACAACAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (36 bp):
TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
Found at i:53884576 original size:27 final size:27
Alignment explanation
Indices: 53884390--53884565 Score: 255
Period size: 27 Copynumber: 6.5 Consensus size: 27
53884380 ATAGATACCT
*
53884390 ATAGGGTAAAATGACTGAAATACCCTC
1 ATAGGGTAAAATGACTGAAATACCCCC
*
53884417 ATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
** * *
53884444 ATAGATTAAAGTGA-TCGAAATACCCTC
1 ATAGGGTAAAATGACT-GAAATACCCCC
*
53884471 ATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
*
53884498 ATAGGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
*
53884525 ATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
53884552 ATAGGGTAAAATGA
1 ATAGGGTAAAATGA
53884566 TTGTTATACC
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 130 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:53884589 original size:54 final size:53
Alignment explanation
Indices: 53884390--53884591 Score: 255
Period size: 54 Copynumber: 3.7 Consensus size: 53
53884380 ATAGATACCT
*
53884390 ATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCT-ATAGGGTAAAATGACTGAAATACCCCC
** * *
53884444 ATAGATTAAAGTGA-TCGAAATACCCTCATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCCT-ATAGGGTAAAATGACTGAAATACCCCC
*
53884498 ATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATA-CCCTATAGGGTAAAATGACTGAAATACCCCC
* **
53884552 ATAGGGTAAAATGATTGTTATACCCT-TAGGAGATAAAATG
1 ATAGGGTAAAATGACTGAAATACCCTATAGG-G-TAAAATG
53884592 GCTGTTATGG
Statistics
Matches: 130, Mismatches: 13, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
52 4 0.03
53 6 0.05
54 115 0.88
55 5 0.04
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (53 bp):
ATAGGGTAAAATGACTGAAATACCCTATAGGGTAAAATGACTGAAATACCCCC
Found at i:53884589 original size:81 final size:79
Alignment explanation
Indices: 53884390--53884591 Score: 251
Period size: 81 Copynumber: 2.5 Consensus size: 79
53884380 ATAGATACCT
* * *
53884390 ATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGACTAAAATACCCCCATAGATTAAAG
1 ATAGGGTAAAATGATTGAAATACCCT--TAGGGTAAAATGACTAAAATACCCCCATAGAGTAAAA
* *
53884455 TGATCGAAATACCCTC
64 TGACCGAAATACCCCC
* * * *
53884471 ATAGGGTAAAATGATTGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAA
1 ATAGGGTAAAATGATTGAAATA--CCCTTAGGGTAAAATGACTAAAATACCCCCATAGAGTAAAA
53884536 TGACCGAAATACCCCC
64 TGACCGAAATACCCCC
**
53884552 ATAGGGTAAAATGATTGTTATACCCTTAGGAGATAAAATG
1 ATAGGGTAAAATGATTGAAATACCCTTAGG-G-TAAAATG
53884592 GCTGTTATGG
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
79 7 0.07
80 1 0.01
81 94 0.90
83 3 0.03
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (79 bp):
ATAGGGTAAAATGATTGAAATACCCTTAGGGTAAAATGACTAAAATACCCCCATAGAGTAAAATG
ACCGAAATACCCCC
Found at i:53884867 original size:26 final size:26
Alignment explanation
Indices: 53884800--53884876 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
53884790 TGTGCCACAT
*
53884800 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTTGCAGCTTTGCTGCG
*
53884826 ATACTGA-TA-TTGGCAGCTCTGCTGCG
1 ATACT-ATTACTT-GCAGCTTTGCTGCG
* *
53884852 ATGCTATTACTTGCAGTTTTGCTGC
1 ATACTATTACTTGCAGCTTTGCTGC
53884877 AATATTGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 2 0.05
26 37 0.88
27 3 0.07
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.36
Consensus pattern (26 bp):
ATACTATTACTTGCAGCTTTGCTGCG
Found at i:53898736 original size:29 final size:29
Alignment explanation
Indices: 53898677--53898745 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
53898667 CAGTTGAACA
53898677 TAAATTTTAAAAATAAAAAATAGAGTAAT
1 TAAATTTTAAAAATAAAAAATAGAGTAAT
* *
53898706 TAAATTTCTATAAATAAAAAA-ATA-TATAT
1 TAAATTT-TAAAAATAAAAAATAGAGTA-AT
53898735 TAAATTTTAAA
1 TAAATTTTAAA
53898746 TTTACTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.14
29 18 0.51
30 12 0.34
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAATTTTAAAAATAAAAAATAGAGTAAT
Found at i:53898882 original size:3 final size:3
Alignment explanation
Indices: 53898869--53898907 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
53898859 TAAAATGAAT
53898869 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53898908 TGCAGTAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:53899576 original size:29 final size:29
Alignment explanation
Indices: 53899543--53899598 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
53899533 CTCAAAGGAA
*
53899543 TTTTAGAATATTTTCACATGTGTCATTAT
1 TTTTAGAATATTTTCAAATGTGTCATTAT
* * *
53899572 TTTTAGATTTTTTTTAAATGTGTCATT
1 TTTTAGAATATTTTCAAATGTGTCATT
53899599 TTACTCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (29 bp):
TTTTAGAATATTTTCAAATGTGTCATTAT
Found at i:53902583 original size:25 final size:25
Alignment explanation
Indices: 53902536--53902584 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
53902526 GTTCACTTTT
*
53902536 TTACAAAAATAATATAAACAATTAA
1 TTACAAAAATAATATAAAAAATTAA
*
53902561 TTACAAAAATAGGTA-AAAAAATTA
1 TTACAAAAATA-ATATAAAAAATTA
53902585 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
TTACAAAAATAATATAAAAAATTAA
Found at i:53906773 original size:24 final size:24
Alignment explanation
Indices: 53906746--53906797 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
53906736 TTTCTAGGAG
* **
53906746 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
53906770 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
53906794 ATTT
1 ATTT
53906798 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:53910201 original size:16 final size:16
Alignment explanation
Indices: 53910180--53910211 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53910170 AAATTGTACC
53910180 TAAGTCAGAAGGGGCA
1 TAAGTCAGAAGGGGCA
53910196 TAAGTCAGAAGGGGCA
1 TAAGTCAGAAGGGGCA
53910212 CATTGAGGAA
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:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (16 bp):
TAAGTCAGAAGGGGCA
Found at i:53911215 original size:24 final size:24
Alignment explanation
Indices: 53911153--53911204 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
53911143 TTTCTAGAAG
* **
53911153 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGTATTTATTAACATAATAT
53911177 ATTTAGTATTTATTAACATAATAT
1 ATTTAGTATTTATTAACATAATAT
53911201 ATTT
1 ATTT
53911205 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Found at i:53911849 original size:31 final size:31
Alignment explanation
Indices: 53911813--53911873 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
53911803 TTCATTTAAT
53911813 GGCTTTTCAAATATATGAAAATTTTGAATAC
1 GGCTTTTCAAATATATGAAAATTTTGAATAC
53911844 GGCTTTTCAAATATATGAAAATTTTGAATA
1 GGCTTTTCAAATATATGAAAATTTTGAATA
53911874 TATTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (31 bp):
GGCTTTTCAAATATATGAAAATTTTGAATAC
Found at i:53940699 original size:14 final size:15
Alignment explanation
Indices: 53940675--53940703 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53940665 TTTTTCTGTT
53940675 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
53940690 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
53940704 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:53942844 original size:23 final size:23
Alignment explanation
Indices: 53942817--53942987 Score: 114
Period size: 23 Copynumber: 7.3 Consensus size: 23
53942807 ATGAGTTGAA
53942817 CCAATTTGTTACAAATATGCTGT
1 CCAATTTGTTACAAATATGCTGT
* * * **
53942840 CCAATTTTGATGCTTAA-ATGCTAC
1 CCAA-TTTGTTAC-AAATATGCTGT
*
53942864 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACAAATATGCTGT
* * * *
53942887 CCAATTTTGATGCTTAA-ATGCTGC
1 CCAA-TTTGTTAC-AAATATGCTGT
*
53942911 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACAAATATGCTGT
* ** *
53942934 CCAATTTTGATGATTAA-ATGCTGC
1 CCAA-TTTG-TTACAAATATGCTGT
*
53942958 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTACAAATATGCTGT
*
53942981 CTAATTT
1 CCAATTT
53942988 TGATGCTTAA
Statistics
Matches: 107, Mismatches: 32, Indels: 18
0.68 0.20 0.11
Matches are distributed among these distances:
22 5 0.05
23 51 0.48
24 45 0.42
25 6 0.06
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (23 bp):
CCAATTTGTTACAAATATGCTGT
Found at i:53942860 original size:24 final size:24
Alignment explanation
Indices: 53942833--53943011 Score: 166
Period size: 24 Copynumber: 7.6 Consensus size: 24
53942823 TGTTACAAAT
*
53942833 ATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGCCCAATTTTGATGCTTAA
* * * * *
53942857 ATGCTACCCAA-TTTGTTACATAT
1 ATGCTGCCCAATTTTGATGCTTAA
*
53942880 ATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGCCCAATTTTGATGCTTAA
* * * *
53942904 ATGCTGCCCAA-TTTGTTACATAT
1 ATGCTGCCCAATTTTGATGCTTAA
* *
53942927 ATGCTGTCCAATTTTGATGATTAA
1 ATGCTGCCCAATTTTGATGCTTAA
* * * *
53942951 ATGCTGCCCAA-TTTGTTACATAT
1 ATGCTGCCCAATTTTGATGCTTAA
* *
53942974 ATGCTGTCTAATTTTGATGCTTAA
1 ATGCTGCCCAATTTTGATGCTTAA
53942998 ATGCTGCCCAATTT
1 ATGCTGCCCAATTT
53943012 GTTGCATATA
Statistics
Matches: 115, Mismatches: 37, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
23 51 0.44
24 64 0.56
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (24 bp):
ATGCTGCCCAATTTTGATGCTTAA
Found at i:53943047 original size:47 final size:47
Alignment explanation
Indices: 53942817--53943036 Score: 377
Period size: 47 Copynumber: 4.7 Consensus size: 47
53942807 ATGAGTTGAA
* *
53942817 CCAATTTGTTACAAATATGCTGTCCAATTTTGATGCTTAAATGCTAC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
53942864 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
53942911 CCAATTTGTTACATATATGCTGTCCAATTTTGATGATTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
53942958 CCAATTTGTTACATATATGCTGTCTAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
* * *
53943005 CCAATTTGTTGCATATATGCTATCCAGTTTTG
1 CCAATTTGTTACATATATGCTGTCCAATTTTG
53943037 GTGTAAAAAT
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 164 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:53943068 original size:94 final size:94
Alignment explanation
Indices: 53942817--53943078 Score: 328
Period size: 94 Copynumber: 2.8 Consensus size: 94
53942807 ATGAGTTGAA
* * * * * **
53942817 CCAATTTGTTACAAATATGCTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
1 CCAATTTGTTACATATATGCTATCCAATTTTGATGATAAAATGCTGCCCAAACTGTTACATATAT
53942882 GCTGTCCAATTTTGATGCTTAAATGCTGC
66 GCTGTCCAATTTTGATGCTTAAATGCTGC
* * **
53942911 CCAATTTGTTACATATATGCTGTCCAATTTTGATGATTAAATGCTGCCCAATTTGTTACATATAT
1 CCAATTTGTTACATATATGCTATCCAATTTTGATGATAAAATGCTGCCCAAACTGTTACATATAT
*
53942976 GCTGTCTAATTTTGATGCTTAAATGCTGC
66 GCTGTCCAATTTTGATGCTTAAATGCTGC
* * * * * **
53943005 CCAATTTGTTGCATATATGCTATCCAGTTTTGGTG-TAAAAATGTTGCTCAAACTGTTGTATATA
1 CCAATTTGTTACATATATGCTATCCAATTTTGATGAT-AAAATGCTGCCCAAACTGTTACATATA
*
53943069 TGCTGCCCAA
65 TGCTGTCCAA
53943079 ATTGATGTAT
Statistics
Matches: 150, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
93 1 0.01
94 149 0.99
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (94 bp):
CCAATTTGTTACATATATGCTATCCAATTTTGATGATAAAATGCTGCCCAAACTGTTACATATAT
GCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:53943071 original size:141 final size:141
Alignment explanation
Indices: 53942817--53943078 Score: 373
Period size: 141 Copynumber: 1.9 Consensus size: 141
53942807 ATGAGTTGAA
53942817 CCAATTTGTTACAAATATGCTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
1 CCAATTTGTTACAAATATGCTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
* * ** *
53942882 GCTGTCCAATTTTGATGCTTAAATGCTGCCCAATTTGTTACATATATGCTGTCCAATTTTGATGA
66 GCTATCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATATATGCTGCCCAATTTTGATGA
53942947 TTAAATGCTGC
131 TTAAATGCTGC
* * * *
53942958 CCAATTTGTTACATATATGCTGTCTAATTTTGATGCTTAAATGCTGCCCAATTTGTTGCATATAT
1 CCAATTTGTTACAAATATGCTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
* * * * **
53943023 GCTATCCAGTTTTGGTG-TAAAAATGTTGCTCAAACTGTTGTATATATGCTGCCCAA
66 GCTATCCAATTTTGATGCT-AAAATGCTGCCCAAACTGTTACATATATGCTGCCCAA
53943079 ATTGATGTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
140 1 0.01
141 104 0.99
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (141 bp):
CCAATTTGTTACAAATATGCTGTCCAATTTTGATGCTTAAATGCTACCCAATTTGTTACATATAT
GCTATCCAATTTTGATGCTAAAATGCTGCCCAAACTGTTACATATATGCTGCCCAATTTTGATGA
TTAAATGCTGC
Found at i:53943079 original size:23 final size:23
Alignment explanation
Indices: 53943053--53943102 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
53943043 AAATGTTGCT
*
53943053 CAAACTGTTGTATATATGCTGCC
1 CAAACTGATGTATATATGCTGCC
* * *
53943076 CAAATTGATGTATTTATGCTGTC
1 CAAACTGATGTATATATGCTGCC
53943099 CAAA
1 CAAA
53943103 TTTTGGTGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (23 bp):
CAAACTGATGTATATATGCTGCC
Found at i:53943103 original size:23 final size:23
Alignment explanation
Indices: 53943061--53943104 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53943051 CTCAAACTGT
53943061 TGTATATATGCTGCCCAAATTGA
1 TGTATATATGCTGCCCAAATTGA
* *
53943084 TGTATTTATGCTGTCCAAATT
1 TGTATATATGCTGCCCAAATT
53943105 TTGGTGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (23 bp):
TGTATATATGCTGCCCAAATTGA
Found at i:53943143 original size:71 final size:73
Alignment explanation
Indices: 53942995--53943174 Score: 192
Period size: 71 Copynumber: 2.5 Consensus size: 73
53942985 TTTTGATGCT
* * * * *
53942995 TAAATGCTGCCCAATTTGTTGCATATATGCTATCC-AGTTTTGGTGTAAAAATGTTGCTCAAACT
1 TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAAACT
53943059 GTTGTATA
66 GTTGTATA
* * *
53943067 T--ATGCTGCCCAAATTGATGTATTTATGCTGTCCAAATTTTGGTGTGAAAATGTTG-TCTAA-T
1 TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAAACT
53943128 -TTGGTATA
66 GTT-GTATA
** * * *
53943136 TAAATGCTGTTCAAATTTATGTATAAAAGCTGTCCAAAT
1 TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAAT
53943175 ATGGTAGATT
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
68 2 0.02
69 7 0.08
70 31 0.34
71 49 0.54
72 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (73 bp):
TAAATGCTGCCCAAATTGATGTATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAAACT
GTTGTATA
Found at i:53949521 original size:25 final size:25
Alignment explanation
Indices: 53949493--53949546 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
53949483 CTTGTGATCA
53949493 TTTTTGAACCAA-TATTCTTTCAGTC
1 TTTTTGAA-CAATTATTCTTTCAGTC
* *
53949518 TTTTTGAATAATTATTCTTTCATTC
1 TTTTTGAACAATTATTCTTTCAGTC
53949543 TTTT
1 TTTT
53949547 GGATTTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.22, C:0.15, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTTTGAACAATTATTCTTTCAGTC
Found at i:53950683 original size:13 final size:13
Alignment explanation
Indices: 53950667--53950759 Score: 57
Period size: 13 Copynumber: 7.3 Consensus size: 13
53950657 AATCACAATC
*
53950667 AAAATCAAAAAAG
1 AAAATAAAAAAAG
* **
53950680 AAAAGAAAAATTG
1 AAAATAAAAAAAG
*
53950693 AAATTAAAAAAAG
1 AAAATAAAAAAAG
* *
53950706 -TAATAAAAAAAC
1 AAAATAAAAAAAG
* *
53950718 AAAATCAAAAAAT
1 AAAATAAAAAAAG
* *
53950731 AAAA-AAAAGAAC
1 AAAATAAAAAAAG
53950743 AAAA-AAAAGAAAG
1 AAAATAAAA-AAAG
53950756 AAAA
1 AAAA
53950760 AAAGAAGAAA
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
12 22 0.37
13 37 0.63
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (13 bp):
AAAATAAAAAAAG
Found at i:53950688 original size:12 final size:11
Alignment explanation
Indices: 53950673--53950771 Score: 65
Period size: 12 Copynumber: 8.3 Consensus size: 11
53950663 AATCAAAATC
53950673 AAAAAAGAAAA
1 AAAAAAGAAAA
*
53950684 GAAAAATTGAAATTA
1 -AAAAA-AGAAA--A
*
53950699 AAAAAAGTAATA
1 AAAAAAG-AAAA
*
53950711 AAAAAACAAAA
1 AAAAAAGAAAA
* *
53950722 TCAAAAA-ATAA
1 -AAAAAAGAAAA
53950733 AAAAAAGAACAA
1 AAAAAAGAA-AA
53950745 AAAAAAGAAAGA
1 AAAAAAGAAA-A
53950757 AAAAAAGAAGAA
1 AAAAAAGAA-AA
53950769 AAA
1 AAA
53950772 GTCAAAATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
10 5 0.07
11 8 0.12
12 42 0.61
13 6 0.09
14 7 0.10
15 1 0.01
ACGTcount: A:0.80, C:0.03, G:0.09, T:0.08
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:53950734 original size:19 final size:19
Alignment explanation
Indices: 53950707--53950748 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
53950697 TAAAAAAAGT
*
53950707 AATAAAAAAACAAAATCAAAA
1 AATAAAAAAA-AGAA-CAAAA
53950728 AATAAAAAAAAGAACAAAA
1 AATAAAAAAAAGAACAAAA
53950747 AA
1 AA
53950749 AAGAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.83, C:0.07, G:0.02, T:0.07
Consensus pattern (19 bp):
AATAAAAAAAAGAACAAAA
Found at i:53950761 original size:33 final size:34
Alignment explanation
Indices: 53950693--53950773 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
53950683 AGAAAAATTG
* * **
53950693 AAATTAAAAAAAGTAATAAAAAAACAAAATCAAA
1 AAATAAAAAAAAGTAACAAAAAAACAAAAGAAAA
53950727 AAATAAAAAAAAG-AACAAAAAAA-AGAAAGAAAA
1 AAATAAAAAAAAGTAACAAAAAAACA-AAAGAAAA
* *
53950760 AAAGAAGAAAAAGT
1 AAATAAAAAAAAGT
53950774 CAAAATCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 1 0.03
33 26 0.67
34 12 0.31
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.09
Consensus pattern (34 bp):
AAATAAAAAAAAGTAACAAAAAAACAAAAGAAAA
Found at i:53953080 original size:28 final size:28
Alignment explanation
Indices: 53952990--53953142 Score: 220
Period size: 28 Copynumber: 5.5 Consensus size: 28
53952980 ATATTAAGTC
*
53952990 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53953017 CGCACACTTAGTGCTACATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53953044 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
53953072 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
53953100 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53953129 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53953143 CAATCTCATG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 46 0.40
28 50 0.43
29 19 0.17
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53953093 original size:55 final size:56
Alignment explanation
Indices: 53952990--53953142 Score: 220
Period size: 55 Copynumber: 2.8 Consensus size: 56
53952980 ATATTAAGTC
*
53952990 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
* *
53953044 TGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
* * * *
53953100 CGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATATAA-TCAAACTCGCACACTTAGTGC
53953143 CAATCTCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
54 21 0.24
55 26 0.30
56 22 0.25
57 19 0.22
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (56 bp):
CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:53956387 original size:44 final size:44
Alignment explanation
Indices: 53956337--53957162 Score: 179
Period size: 44 Copynumber: 19.0 Consensus size: 44
53956327 CAATGAAATT
*
53956337 ACAGATCTTATCTCCCTAAGTCGTAGTGGAGCAGATCGAAGATG
1 ACAGATCTTATCTCCCTAAGTCGTAGTGGAGCAGATCGAAGATA
* ** **
53956381 GCAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATTAAAGCCA
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
** * * * * ** * *
53956425 GTA-ATCCTATCTCTCTGAAGTTGCAGTGGAGTGGAT-TAAAATA
1 ACAGATCTTATCTCCCT-AAGTCGTAGTGGAGCAGATCGAAGATA
* * *** * * *
53956468 AAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--CAT-
1 ACAGATCTTATCTCCCT-AAGTCGTAGTGGAGCAGATCGAAGATA
* * *** * *
53956510 -CAGGTCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGA-A
1 ACAGATCTTATCTCCCT-AAGTCGTAGTGGAGCAGATCGAAGATA
* *
53956553 GCAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAGATC
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
* * *
53956597 ACAAATCTTATCTCCCTAAG-CAGTAGTGGAACAGATTG-A-A-A
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
* * * * * *
53956638 CCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAG-TGTAT-TAAAATA
1 ACAG--ATCTTATCTCCCT-AAGTCGTAGTGGAGCAG-ATCGAAGATA
* * * * * *
53956684 AAAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCG--CAT-
1 ACAGATCTTATCTCCCT-AAGTCGTAGTGGAGCAGATCGAAGATA
* * * * * * * *
53956726 A-AGGTCTTATCACTCTGAGGTTGTAGCGGAGCAGACCGAAGAATT
1 ACAGATCTTATCTCCCT-AAGTCGTAGTGGAGCAGATCGAAG-ATA
* *
53956771 ACAGATATTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAGATG
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
* * * * * * *
53956815 ACA-AGCCTTATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAAGATT
1 ACAGA-TCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
** * * * * * * * * *
53956859 GTAGACCTTATCTCCTTGAG-CAGCAGTGGAGTAGGTTGGAGATT
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
** * * * * * * *
53956903 GTAGACCTTATCTCCCTTAG-CAGCT-GTGGAGTAGGTTGAAAATT
1 ACAGATCTTATCTCCCTAAGTC-G-TAGTGGAGCAGATCGAAGATA
* * *
53956947 ACAGATCTTATCTCCCTAAGTAGTAGTGAAGCAGATCGAAG-TCC
1 ACAGATCTTATCTCCCTAAGTCGTAGTGGAGCAGATCGAAGAT-A
* * * * * * * * * *
53956991 CCAG-CCTTGTCTCCCTGAG-CAGCAGTGGAGTAGGTTGAAAATT
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
* * *
53957034 ACAGATTTTATCTCCCTAAG-CAGTAGTGGACCAGATCGAAG-TCT
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGAT-A
* * * * * * * * * *
53957078 CCAG-CCTTGTCTCCCTGAG-CAGCAGTGGAGTAGGTTGAAAATT
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATA
* *
53957121 ACAGATCTGATCTCCCTAAG-CAGTAGTGGAGTAGATCGAAGA
1 ACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGA
53957163 CCACAGCCTT
Statistics
Matches: 593, Mismatches: 150, Indels: 78
0.72 0.18 0.10
Matches are distributed among these distances:
41 62 0.10
42 2 0.00
43 115 0.19
44 377 0.64
45 23 0.04
46 14 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ACAGATCTTATCTCCCTAAGTCGTAGTGGAGCAGATCGAAGATA
Found at i:53956715 original size:216 final size:217
Alignment explanation
Indices: 53956336--53956844 Score: 790
Period size: 216 Copynumber: 2.3 Consensus size: 217
53956326 TCAATGAAAT
* *
53956336 TACAGATCTTATCTCCCTAAGTC-GTAGTGGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAA
1 TACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAA
* *
53956400 GCAGTAGTGGAGCAGATTAAAGCCAGTAATCCTATCTCTCTGAAGTTGCAGTGGAGTGGATTAAA
65 GCAGTAGTGGAACAGATTAAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
* *
53956465 ATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGG
130 ATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATAAGGTCTTATCACCCTGAGG
53956530 TTACAGCGGAGCAGACCGAAGAA
195 TTACAGCGGAGCAGACCGAAGAA
* *
53956553 -GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATCACAAATCTTATCTCCCTAAG
1 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAAG
* *
53956617 CAGTAGTGGAACAGATTGAAA-CCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGTGTATTAAA
66 CAGTAGTGGAACAGATT-AAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
** *
53956681 ATAAAAGATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATCGCATAAGGTCTTATCACTCTGAGG
130 ATAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATAAGGTCTTATCACCCTGAGG
**
53956746 TTGTAGCGGAGCAGACCGAAGAA
195 TTACAGCGGAGCAGACCGAAGAA
* ** *
53956769 TTACAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAGCCTTATCTCCCTGA
1 -TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAA
*
53956834 GCAGCAGTGGA
65 GCAGTAGTGGA
53956845 GTAGGTTGAA
Statistics
Matches: 266, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
215 1 0.00
216 195 0.73
217 3 0.01
218 67 0.25
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (217 bp):
TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAATCTTATCTCCCTAAG
CAGTAGTGGAACAGATTAAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAA
TAAAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATAAGGTCTTATCACCCTGAGGT
TACAGCGGAGCAGACCGAAGAA
Found at i:53957025 original size:87 final size:87
Alignment explanation
Indices: 53956767--53957218 Score: 546
Period size: 87 Copynumber: 5.2 Consensus size: 87
53956757 CAGACCGAAG
* ** * *
53956767 AATTACAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAAGCCTTATCTCCCT
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG-TCCCCAGCCTTGTCTCCCT
53956832 GAGCAGCAGTGGAGTAGGTTGAA
65 GAGCAGCAGTGGAGTAGGTTGAA
* ** * * * * * * * * *** *
53956855 GATTGTAGACCTTATCTCCTTGAGCAGCAGTGGAGTAGGTTGGAGAT-TGTAGACCTTATCTCCC
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG-TCCCCAG-CCTTGTCTCCC
* *
53956919 TTAGCAGCTGTGGAGTAGGTTGAA
64 TGAGCAGCAGTGGAGTAGGTTGAA
* *
53956943 AATTACAGATCTTATCTCCCTAAGTAGTAGTGAAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
53957008 AGCAGCAGTGGAGTAGGTTGAA
66 AGCAGCAGTGGAGTAGGTTGAA
* * *
53957030 AATTACAGATTTTATCTCCCTAAGCAGTAGTGGACCAGATCGAAGTCTCCAGCCTTGTCTCCCTG
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
53957095 AGCAGCAGTGGAGTAGGTTGAA
66 AGCAGCAGTGGAGTAGGTTGAA
* * * * *
53957117 AATTACAGATCTGATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACCACAGCCTTGTCTCCATG
1 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
* *
53957182 AGTAGCAGTAGAGTAGGTTGAA
66 AGCAGCAGTGGAGTAGGTTGAA
* *
53957204 AATAACAAATCTTAT
1 AATTACAGATCTTAT
53957219 ATTCCTGTAT
Statistics
Matches: 308, Mismatches: 54, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
87 206 0.67
88 102 0.33
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTG
AGCAGCAGTGGAGTAGGTTGAA
Found at i:53957517 original size:50 final size:50
Alignment explanation
Indices: 53957375--53957507 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
53957365 GTAGAGGAAC
* * *
53957375 AGATTGAAGCTACAACAG-CGAATTTTGCTTCCCCGACATTGCAATTAATA
1 AGATTGAAGCTACAA-AGACGAATCTTGTTTCCCCAACATTGCAATTAATA
* *
53957425 AGATTGAAGCTACAACGACGAATCTTGTTTCCCCAACATTGCAGTTAAATA
1 AGATTGAAGCTACAAAGACGAATCTTGTTTCCCCAACATTGCAATT-AATA
* **
53957476 A-ATTTAAGCTACAAAGGTGAATCTTGTTTCCC
1 AGATTGAAGCTACAAAGACGAATCTTGTTTCCC
53957508 TGGCATTGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 66 0.92
51 5 0.07
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (50 bp):
AGATTGAAGCTACAAAGACGAATCTTGTTTCCCCAACATTGCAATTAATA
Found at i:53959315 original size:9 final size:9
Alignment explanation
Indices: 53959278--53959334 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
53959268 TGGTATTATC
*
53959278 ATTATTATT
1 ATTACTATT
53959287 ATTACTACTT
1 ATTACTA-TT
*
53959297 -TTATTATT
1 ATTACTATT
*
53959305 ATTAATATT
1 ATTACTATT
53959314 ATTACTATT
1 ATTACTATT
* *
53959323 GTTGCTATT
1 ATTACTATT
53959332 ATT
1 ATT
53959335 GATAATATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 2 0.05
9 35 0.90
10 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.60
Consensus pattern (9 bp):
ATTACTATT
Found at i:53959331 original size:27 final size:27
Alignment explanation
Indices: 53959278--53959344 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
53959268 TGGTATTATC
* *
53959278 ATTATTATTATTACTACTTTTATTATT
1 ATTAATATTATTACTACTTTTACTATT
*
53959305 ATTAATATTATTACTA-TTGTTGCTATT
1 ATTAATATTATTACTACTT-TTACTATT
* *
53959332 ATTGATAATATTA
1 ATTAATATTATTA
53959345 GTCACTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (27 bp):
ATTAATATTATTACTACTTTTACTATT
Found at i:53959334 original size:3 final size:3
Alignment explanation
Indices: 53959271--53959322 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
53959261 ATTGTGTTGG
* * *
53959271 TAT TAT CAT TAT TAT TAT TAC TACT T-T TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
53959316 TAC TAT T
1 TAT TAT T
53959323 GTTGCTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.92
4 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:53962595 original size:68 final size:67
Alignment explanation
Indices: 53962495--53962776 Score: 274
Period size: 68 Copynumber: 4.3 Consensus size: 67
53962485 AGGAGTTTGT
*
53962495 TAGGACATTAAACATGGGTTCATAATGTGTAAGACCGTAGCTC-GACTATGGCAACATATGGAGT
1 TAGGACATTAAACAT-GGTTCATAATGTGTAAGACCGTAGCTCAG-CTATGGCAACATATGGAAT
*
53962559 CTAC
64 CTGC
* ** * *
53962563 TAGGACATTAAACATAGGTTCATAATATGTAAGATTGTAGCTCAGCGATGACAACATATGGAATC
1 TAGGACATTAAACAT-GGTTCATAATGTGTAAGACCGTAGCTCAGCTATGGCAACATATGGAATC
53962628 --C
65 TGC
* ** * *
53962629 ---G--ATTAAACATGGCTTCATAATCTGTAAGGTCGTAGCTTAGCTATGGAAACATATGGAATC
1 TAGGACATTAAACATGG-TTCATAATGTGTAAGACCGTAGCTCAGCTATGGCAACATATGGAATC
53962689 TGC
65 TGC
* * ** * * * *
53962692 CAAGTTATTAAGCATGAGTTCATAATGTGTAAGACTGTAGCTCAGCTATGGCAACATATAGAGTC
1 TAGGACATTAAACATG-GTTCATAATGTGTAAGACCGTAGCTCAGCTATGGCAACATATGGAATC
53962757 TGC
65 TGC
*
53962760 TAGGACATTAAATATGG
1 TAGGACATTAAACATGG
53962777 GACCATATTG
Statistics
Matches: 175, Mismatches: 29, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
60 2 0.01
61 49 0.28
63 2 0.01
66 2 0.01
67 1 0.01
68 117 0.67
69 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (67 bp):
TAGGACATTAAACATGGTTCATAATGTGTAAGACCGTAGCTCAGCTATGGCAACATATGGAATCT
GC
Found at i:53962664 original size:61 final size:61
Alignment explanation
Indices: 53962569--53962688 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
53962559 CTACTAGGAC
*
53962569 ATTAAACATAGGTTCATAATATGTAAGATTGTAGCTCAGCGAT-GACAACATATGGAATCCG
1 ATTAAACATAGGTTCATAATATGTAAGATCGTAGCTCAGCGATGGA-AACATATGGAATCCG
* * * *
53962630 ATTAAACAT-GGCTTCATAATCTGTAAGGTCGTAGCTTAGCTATGGAAACATATGGAATC
1 ATTAAACATAGG-TTCATAATATGTAAGATCGTAGCTCAGCGATGGAAACATATGGAATC
53962689 TGCCAAGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 2 0.04
61 48 0.92
62 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (61 bp):
ATTAAACATAGGTTCATAATATGTAAGATCGTAGCTCAGCGATGGAAACATATGGAATCCG
Found at i:53962731 original size:129 final size:129
Alignment explanation
Indices: 53962501--53962750 Score: 315
Period size: 129 Copynumber: 1.9 Consensus size: 129
53962491 TTGTTAGGAC
* * * * * * *
53962501 ATTAAACATGGGTTCATAATGTGTAAGACCGTAGCTCGACTATGGCAACATATGGAGTCTACTAG
1 ATTAAACATGGCTTCATAATCTGTAAGACCGTAGCTAGACTATGGAAACATATGGAATCTACCAA
*
53962566 GACATTAAACATAGGTTCATAATATGTAAGATTGTAGCTCAGCGATGACAACATATGGAATCCG
66 GACATTAAACATAGGTTCATAATATGTAAGACTGTAGCTCAGCGATGACAACATATGGAATCCG
** *
53962630 ATTAAACATGGCTTCATAATCTGTAAGGTCGTAGCTTAG-CTATGGAAACATATGGAATCTGCCA
1 ATTAAACATGGCTTCATAATCTGTAAGACCGTAGC-TAGACTATGGAAACATATGGAATCTACCA
** * * * *
53962694 AGTTATTAAGCAT-GAGTTCATAATGTGTAAGACTGTAGCTCAGCTATGGCAACATAT
65 AGACATTAAACATAG-GTTCATAATATGTAAGACTGTAGCTCAGCGATGACAACATAT
53962751 AGAGTCTGCT
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
128 1 0.01
129 99 0.97
130 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (129 bp):
ATTAAACATGGCTTCATAATCTGTAAGACCGTAGCTAGACTATGGAAACATATGGAATCTACCAA
GACATTAAACATAGGTTCATAATATGTAAGACTGTAGCTCAGCGATGACAACATATGGAATCCG
Found at i:53967300 original size:26 final size:25
Alignment explanation
Indices: 53967159--53967323 Score: 132
Period size: 26 Copynumber: 6.4 Consensus size: 25
53967149 CGGGATGTAC
* * * *
53967159 TTTAGCAGGCCTTAAGTCGATGTTTG
1 TTTAGCAGGCTTTGAG-CGATGATTA
*
53967185 TTTAGCAGGCTTTGAGCCGATGTTTA
1 TTTAGCAGGCTTTGAG-CGATGATTA
* * *
53967211 TTTAACAGCCTTTGAGCAAGTGATTA
1 TTTAGCAGGCTTTGAGCGA-TGATTA
* ** *
53967237 TTTAGCAGGCCTTGAGCTGGCGCTTA
1 TTTAGCAGGCTTTGAGC-GATGATTA
*
53967263 TCTAGCAGGCTTTGAGTCGATGATTA
1 TTTAGCAGGCTTTGAG-CGATGATTA
* * *
53967289 TTTAGCAAGCTTTGAGCCAGTAATTA
1 TTTAGCAGGCTTTGAGCGA-TGATTA
53967315 TTTAGCAGG
1 TTTAGCAGG
53967324 TACTATGTAC
Statistics
Matches: 110, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
25 4 0.04
26 105 0.95
27 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.35
Consensus pattern (25 bp):
TTTAGCAGGCTTTGAGCGATGATTA
Found at i:53969888 original size:349 final size:349
Alignment explanation
Indices: 53969249--53969948 Score: 1391
Period size: 349 Copynumber: 2.0 Consensus size: 349
53969239 GTATTTATGG
53969249 CATGGAATTGAATTGTTTTGTTAAGTGAATTATGGTGCCAATGAATGGCATATTGGTTAAGCTTA
1 CATGGAATTGAATTGTTTTGTTAAGTGAATTATGGTGCCAATGAATGGCATATTGGTTAAGCTTA
53969314 TAGGATGATTGATTTAGCATGTTTTGGAGTGTGTTAGAACGTGTTTTAGTCATATGAATGTGTGT
66 TAGGATGATTGATTTAGCATGTTTTGGAGTGTGTTAGAACGTGTTTTAGTCATATGAATGTGTGT
53969379 GGAAATGGTTTGGTTTGGTGCCCGAGTAATTATGTTTGAATTGGCTTGCATTAGGGTTTATTTAG
131 GGAAATGGTTTGGTTTGGTGCCCGAGTAATTATGTTTGAATTGGCTTGCATTAGGGTTTATTTAG
53969444 GGAGCACACGGCCTGGGACACAAGCTGTCACATAGCTGTGTGCCACACATGGCCACACAACACAG
196 GGAGCACACGGCCTGGGACACAAGCTGTCACATAGCTGTGTGCCACACATGGCCACACAACACAG
53969509 CTGTGTGTCCATTAAATTTTAAGTGGAGGATGAACCACACGGTCACAGAGAGTTACACGGCATGG
261 CTGTGTGTCCATTAAATTTTAAGTGGAGGATGAACCACACGGTCACAGAGAGTTACACGGCATGG
53969574 CAACACGGCCATGTGACCCTATTT
326 CAACACGGCCATGTGACCCTATTT
53969598 CATGGAATTGAATTGTTTTGTTAAGTGAATTATGGTGCCAATGAATGGCATATTGGTTAAGCTTA
1 CATGGAATTGAATTGTTTTGTTAAGTGAATTATGGTGCCAATGAATGGCATATTGGTTAAGCTTA
53969663 TAGGATGATTGATTTAGCATGTTTTGGAGTGTGTTAGAACGTGTTTTAGTCATATGAATGTGTGT
66 TAGGATGATTGATTTAGCATGTTTTGGAGTGTGTTAGAACGTGTTTTAGTCATATGAATGTGTGT
53969728 GGAAATGGTTTGGTTTGGTGCCCGAGTAATTATGTTTGAATTGGCTTGCATTAGGGTTTATTTAG
131 GGAAATGGTTTGGTTTGGTGCCCGAGTAATTATGTTTGAATTGGCTTGCATTAGGGTTTATTTAG
*
53969793 GGAGCACACGGCCTGGGATACAAGCTGTCACATAGCTGTGTGCCACACATGGCCACACAACACAG
196 GGAGCACACGGCCTGGGACACAAGCTGTCACATAGCTGTGTGCCACACATGGCCACACAACACAG
53969858 CTGTGTGTCCATTAAATTTTAAGTGGAGGATGAACCACACGGTCACAGAGAGTTACACGGCATGG
261 CTGTGTGTCCATTAAATTTTAAGTGGAGGATGAACCACACGGTCACAGAGAGTTACACGGCATGG
53969923 CAACACGGCCATGTGACCCTATTT
326 CAACACGGCCATGTGACCCTATTT
53969947 CA
1 CA
53969949 AATACCCACA
Statistics
Matches: 350, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
349 350 1.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (349 bp):
CATGGAATTGAATTGTTTTGTTAAGTGAATTATGGTGCCAATGAATGGCATATTGGTTAAGCTTA
TAGGATGATTGATTTAGCATGTTTTGGAGTGTGTTAGAACGTGTTTTAGTCATATGAATGTGTGT
GGAAATGGTTTGGTTTGGTGCCCGAGTAATTATGTTTGAATTGGCTTGCATTAGGGTTTATTTAG
GGAGCACACGGCCTGGGACACAAGCTGTCACATAGCTGTGTGCCACACATGGCCACACAACACAG
CTGTGTGTCCATTAAATTTTAAGTGGAGGATGAACCACACGGTCACAGAGAGTTACACGGCATGG
CAACACGGCCATGTGACCCTATTT
Found at i:53973903 original size:8 final size:9
Alignment explanation
Indices: 53973885--53974001 Score: 62
Period size: 9 Copynumber: 12.7 Consensus size: 9
53973875 ATTGTTTTAG
53973885 AAAATTTTT
1 AAAATTTTT
53973894 AAAA-TTTT
1 AAAATTTTT
*
53973902 AAATTTCTTT
1 AAAATT-TTT
*
53973912 ATATATTTTTT
1 A-A-AATTTTT
*
53973923 AGAATTTTT
1 AAAATTTTT
** *
53973932 AAAAAATAT
1 AAAATTTTT
53973941 -AAA-TTTT
1 AAAATTTTT
*
53973948 AAAATTGTT
1 AAAATTTTT
53973957 ATAAATATTTT
1 A-AAAT-TTTT
53973968 -AAATTTTT
1 AAAATTTTT
53973976 AAAATTATTT
1 AAAATT-TTT
**
53973986 TGAATTTTT
1 AAAATTTTT
53973995 GAAAATT
1 -AAAATT
53974002 ATTTTGAATT
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
7 2 0.02
8 17 0.21
9 32 0.39
10 19 0.23
11 8 0.10
12 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (9 bp):
AAAATTTTT
Found at i:53973929 original size:10 final size:9
Alignment explanation
Indices: 53973889--53974015 Score: 53
Period size: 9 Copynumber: 13.6 Consensus size: 9
53973879 TTTTAGAAAA
53973889 TTTTTAAA-
1 TTTTTAAAT
*
53973897 ATTTTAAAT
1 TTTTTAAAT
53973906 TTCTTTATATAT
1 TT-TTTA-A-AT
53973918 TTTTTAGAA-
1 TTTTTA-AAT
*
53973927 TTTTTAAAA
1 TTTTTAAAT
** *
53973936 AATATAAA-
1 TTTTTAAAT
*
53973944 TTTTAAAAT
1 TTTTTAAAT
*
53973953 TGTTATAAAT
1 T-TTTTAAAT
*
53973963 ATTTTAAAT
1 TTTTTAAAT
*
53973972 TTTTAAAAT
1 TTTTTAAAT
*
53973981 TATTTTGAAT
1 T-TTTTAAAT
*
53973991 TTTTGAAAAT
1 TTTT-TAAAT
*
53974001 TATTTTGAAT
1 T-TTTTAAAT
53974011 TTTTT
1 TTTTT
53974016 TTTATAATTT
Statistics
Matches: 87, Mismatches: 22, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
8 13 0.15
9 35 0.40
10 26 0.30
11 9 0.10
12 4 0.05
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:53973984 original size:19 final size:19
Alignment explanation
Indices: 53973943--53974014 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
53973933 AAAAATATAA
*
53973943 ATTTTAAAATTGTTATAAA-T
1 ATTTT-AAATTTTTA-AAATT
53973963 ATTTTAAATTTTTAAAATT
1 ATTTTAAATTTTTAAAATT
*
53973982 ATTTTGAATTTTTGAAAATT
1 ATTTTAAATTTTT-AAAATT
*
53974002 ATTTTGAATTTTT
1 ATTTTAAATTTTT
53974015 TTTTATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.06
19 21 0.44
20 24 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAATT
Found at i:53973999 original size:20 final size:19
Alignment explanation
Indices: 53973962--53974014 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 19
53973952 TTGTTATAAA
*
53973962 TATTTTAAATTTTTAAAAT
1 TATTTTGAATTTTTAAAAT
53973981 TATTTTGAATTTTTGAAAAT
1 TATTTTGAATTTTT-AAAAT
53974001 TATTTTGAATTTTT
1 TATTTTGAATTTTT
53974015 TTTTATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTTTGAATTTTTAAAAT
Found at i:53977527 original size:19 final size:19
Alignment explanation
Indices: 53977500--53977542 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
53977490 ATCGAAGACC
*
53977500 AATTCGGGACAAAACAT-AA
1 AATTTGGGACAAAAC-TGAA
53977519 AATTTGGGACAAAACTGAA
1 AATTTGGGACAAAACTGAA
53977538 AATTT
1 AATTT
53977543 TCAAATCAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (19 bp):
AATTTGGGACAAAACTGAA
Found at i:53982890 original size:51 final size:51
Alignment explanation
Indices: 53982835--53983272 Score: 420
Period size: 51 Copynumber: 8.6 Consensus size: 51
53982825 TATCGAAGAA
** * * *
53982835 CACATGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATATA-TTATGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTT-TGGT
* * * * *
53982886 CACATGTGTAGTACTAAGTAAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
* ** * * *
53982937 CACGTGTGTAGTACTGCGTGAAGGCTACTAAGTGAATCGATAAA-TGATGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACT-TTGGT
* * * *
53982988 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
* * * * *
53983039 CACGTGTGTAGTAC-AGTGTGAAGGCTACTACGTGAATCGATAAA-TGATGGT
1 CACATGTGTAGTACTA-AGTGAAGGCTACTATGTGAACCGATAAACT-TTGGT
* * * *
53983090 CACATGTGTAGTACTAAGTGAAGGCTACGATGTGTACCGAGAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
** ** * * *
53983141 CATGTGTGTAGTACTGTGTGAAGGCTACTAAGTGAATCGATAAA-TGATGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACT-TTGGT
* *
53983192 CACATGTGTAGTACTAAGTGAAGGTTACTATGTGTACCGA-AAAGCTTTGGT
1 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAA-CTTTGGT
* *
53983243 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACATGTGTAGTACTAAGTGAAGGCTACTA
53983273 CGTGTATAGA
Statistics
Matches: 305, Mismatches: 72, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
50 7 0.02
51 292 0.96
52 6 0.02
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGAAGGCTACTATGTGAACCGATAAACTTTGGT
Found at i:53983315 original size:102 final size:102
Alignment explanation
Indices: 53982839--53983276 Score: 759
Period size: 102 Copynumber: 4.3 Consensus size: 102
53982829 GAAGAACACA
* *
53982839 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATATATTATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
*
53982904 TAAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
* *
53982941 TGTGTAGTACTGCGTGAAGGCTACTAAGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
53983006 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
*
53983043 TGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
* *
53983108 TGAAGGCTACGATGTGTACCGAGAAGCTTTGGTCATG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
*
53983145 TGTGTAGTACTGTGTGAAGGCTACTAAGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
* * *
53983210 TGAAGGTTACTATGTGTACCGAAAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
*
53983247 TGTGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTG
53983277 TATAGAATGA
Statistics
Matches: 318, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 318 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (102 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
TGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACG
Found at i:53983543 original size:37 final size:38
Alignment explanation
Indices: 53983474--53983546 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
53983464 ATATGTGGAA
* **
53983474 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
*
53983512 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAA
53983547 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:53983820 original size:21 final size:21
Alignment explanation
Indices: 53983791--53983841 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
53983781 TGATTTTGGG
*
53983791 AAATCATTAAAAATTGTAAAA
1 AAATAATTAAAAATTGTAAAA
*
53983812 AAATAATTAAAAATTTTAAAA
1 AAATAATTAAAAATTGTAAAA
53983833 AAATAATTA
1 AAATAATTA
53983842 TGAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATAATTAAAAATTGTAAAA
Found at i:53988335 original size:39 final size:39
Alignment explanation
Indices: 53988198--53988332 Score: 216
Period size: 39 Copynumber: 3.5 Consensus size: 39
53988188 ATTCACTTTT
* *
53988198 AAGCATATATCACATTACACATATAATCGCATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
*
53988237 AAGCATATATCACAATACACATATAACCACATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
* * *
53988276 AAGCATATATCACAACACTCATCTAATCACATAACATTC
1 AAGCATATATCACAATACACATATAATCACATAACATTC
53988315 AAGCATATATCACAATAC
1 AAGCATATATCACAATAC
53988333 TCAAAAACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (39 bp):
AAGCATATATCACAATACACATATAATCACATAACATTC
Found at i:53993161 original size:51 final size:49
Alignment explanation
Indices: 53993097--53993237 Score: 146
Period size: 45 Copynumber: 2.9 Consensus size: 49
53993087 ATCAGTAACG
* *
53993097 GTAACAATGTTCGACACACAAAGTGCCGAATCGGTAACGGTAACAATAACA
1 GTAACAGTATTCGACACACAAAGTGCCGAATC-GTAAC-GTAACAATAACA
** *
53993148 GTAACAGTATTCGACACACAAAGTATCGAATC---A-GTAACAGTAACA
1 GTAACAGTATTCGACACACAAAGTGCCGAATCGTAACGTAACAATAACA
* * *
53993193 GTAACAGTATTCAACACACAAAGTGCTGGATCTGTAACAGTAACA
1 GTAACAGTATTCGACACACAAAGTGCCGAATC-GTAAC-GTAACA
53993238 GTAGTCGGCA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
45 38 0.51
47 1 0.01
49 1 0.01
51 34 0.46
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.20
Consensus pattern (49 bp):
GTAACAGTATTCGACACACAAAGTGCCGAATCGTAACGTAACAATAACA
Found at i:53993238 original size:45 final size:45
Alignment explanation
Indices: 53993136--53993240 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
53993126 ATCGGTAACG
* *
53993136 GTAACAATAACAGTAACAGTATTCGACACACAAAGTATCGAATCA
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCA
* * *
53993181 GTAACAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGGATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATC-GAATCA
53993226 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
53993241 GTCGGCACAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.02
45 53 0.98
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCA
Found at i:53993238 original size:51 final size:49
Alignment explanation
Indices: 53993078--53993240 Score: 174
Period size: 51 Copynumber: 3.3 Consensus size: 49
53993068 AAACACACCA
* * * *
53993078 GTAACAGTAATCAGTAACGGTAACAATGTTCGACACACAAAGTGCCGAATC
1 GTAACAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCTG-ATC
* *
53993129 GGTAACGGTAACAATAACAGTAACAGTATTCGACACACAAA--G-T-ATC
1 -GTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGATC
*
53993175 G-AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGGATC
1 GTAA-CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCT-GATC
53993225 TGTAACAGTAACAGTA
1 -GTAACAGTAACAGTA
53993241 GTCGGCACAT
Statistics
Matches: 94, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
44 2 0.02
45 34 0.36
46 3 0.03
47 1 0.01
48 1 0.01
49 1 0.01
50 3 0.03
51 38 0.40
52 11 0.12
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (49 bp):
GTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGATC
Found at i:53993528 original size:39 final size:40
Alignment explanation
Indices: 53993444--53993529 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 40
53993434 TTTATTACTT
* * * *
53993444 CAGTAATTTCATAATTCAATGCATTATACATAACAATATT
1 CAGTATTTTCATAATTCAATGCAGTATACAAAACAATATC
*
53993484 CAGTATTTTCATAATTCACT-CAGTACT-CAAAACAATATC
1 CAGTATTTTCATAATTCAATGCAGTA-TACAAAACAATATC
53993523 CAGTATT
1 CAGTATT
53993530 CCCTAATTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 21 0.52
40 19 0.47
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.36
Consensus pattern (40 bp):
CAGTATTTTCATAATTCAATGCAGTATACAAAACAATATC
Found at i:53993648 original size:18 final size:19
Alignment explanation
Indices: 53993609--53993649 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
53993599 ATATCAATCA
*
53993609 TCAATTTCAATATTCCAGT
1 TCAATTTCAATATTCCAAT
53993628 TCAA-TTCAATGATT-CAAT
1 TCAATTTCAAT-ATTCCAAT
53993646 TCAA
1 TCAA
53993650 ACCATTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.39
Consensus pattern (19 bp):
TCAATTTCAATATTCCAAT
Found at i:53993668 original size:26 final size:25
Alignment explanation
Indices: 53993639--53993688 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53993629 CAATTCAATG
53993639 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
53993665 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
53993689 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:53994480 original size:13 final size:13
Alignment explanation
Indices: 53994462--53994502 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
53994452 CTCAAACTTC
53994462 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
53994475 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
* *
53994488 TC-CTTCTTTCCT
1 TCTTTTCTTTCTT
53994500 TCT
1 TCT
53994503 CTGTTTCGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:53994712 original size:8 final size:8
Alignment explanation
Indices: 53994701--53994763 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
53994691 ATTTATTTAA
53994701 AATATAAT
1 AATATAAT
53994709 AATATAAT
1 AATATAAT
53994717 AATATAAT
1 AATATAAT
53994725 AATATAAT
1 AATATAAT
* *
53994733 -ATAATTTAC
1 AAT-A-TAAT
53994742 AATATAAT
1 AATATAAT
*
53994750 AAAATAAT
1 AATATAAT
53994758 AATATA
1 AATATA
53994764 CTTCAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 2 0.04
8 39 0.85
9 3 0.07
10 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATAAT
Found at i:53995696 original size:48 final size:48
Alignment explanation
Indices: 53995639--53995736 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
53995629 TATTCACTTG
* *
53995639 TGACGTTCAAATTATGGTATTCCTTAATCCTAAGTGGATGGCAGGCTA
1 TGACGTTCAAATTATGGTATACCTTAATCCTAAGTGGATGACAGGCTA
53995687 TGACGTTCAAATTATGGTATACCTTAATCCTAAGTGGATGACAGGCTA
1 TGACGTTCAAATTATGGTATACCTTAATCCTAAGTGGATGACAGGCTA
53995735 TG
1 TG
53995737 TATGCATGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (48 bp):
TGACGTTCAAATTATGGTATACCTTAATCCTAAGTGGATGACAGGCTA
Found at i:54001509 original size:29 final size:31
Alignment explanation
Indices: 54001444--54001509 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
54001434 AAATGATCAT
* * *
54001444 TAAACTATTGACTTCATTCTATTTTGTTCAC
1 TAAACTATTAACTTCATTCGATTTAGTTCAC
* *
54001475 TCAACTATTAATTTC-TTCGATTTAG-TCAC
1 TAAACTATTAACTTCATTCGATTTAGTTCAC
54001504 TAAACT
1 TAAACT
54001510 TTTCAAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 9 0.31
30 8 0.28
31 12 0.41
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (31 bp):
TAAACTATTAACTTCATTCGATTTAGTTCAC
Found at i:54002095 original size:12 final size:12
Alignment explanation
Indices: 54002078--54002103 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54002068 CACCACTTAT
54002078 AATAATTGTTGA
1 AATAATTGTTGA
54002090 AATAATTGTTGA
1 AATAATTGTTGA
54002102 AA
1 AA
54002104 AACATGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (12 bp):
AATAATTGTTGA
Found at i:54003425 original size:6 final size:6
Alignment explanation
Indices: 54003414--54003444 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
54003404 ATTACCAACA
*
54003414 ATAATT ATAATT ATAATT ATAATC ATAATT A
1 ATAATT ATAATT ATAATT ATAATT ATAATT A
54003445 ATATACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
ATAATT
Found at i:54010357 original size:27 final size:26
Alignment explanation
Indices: 54010327--54010393 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
54010317 AGATCACCAC
54010327 AAAGGCTTCTATTTCATAGATT-TCTAT
1 AAAGGCTTCTATTTC-TAGATTGTC-AT
54010354 AAAGGCTT-TCATTTTCTAGATTGTCAT
1 AAAGGCTTCT-A-TTTCTAGATTGTCAT
*
54010381 AAAGGTTTC-ATTT
1 AAAGGCTTCTATTT
54010394 TCTGGCGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 24 0.69
28 6 0.17
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (26 bp):
AAAGGCTTCTATTTCTAGATTGTCAT
Found at i:54010396 original size:26 final size:27
Alignment explanation
Indices: 54010338--54010396 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
54010328 AAGGCTTCTA
54010338 TTTCATAGATTTCTATAAAGGCTTTCAT
1 TTTC-TAGATTTCTATAAAGGCTTTCAT
54010366 TTTCTAGATTGTC-ATAAAGG-TTTCAT
1 TTTCTAGATT-TCTATAAAGGCTTTCAT
54010392 TTTCT
1 TTTCT
54010397 GGCGTATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.37
27 13 0.43
28 6 0.20
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (27 bp):
TTTCTAGATTTCTATAAAGGCTTTCAT
Found at i:54015899 original size:39 final size:39
Alignment explanation
Indices: 54015829--54016001 Score: 159
Period size: 45 Copynumber: 4.2 Consensus size: 39
54015819 ATTTGCCGGC
* * *
54015829 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
54015867 TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
* *
54015906 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTAC---T---GATTCGGCACTTTATGTGTCGAATACTGTTACTG
* * *
54015951 TTACTGTTATCGATTCGGCACTTTGTGTATCGAATACTGTTACCG
1 TTAC-----T-GATTCGGCACTTTATGTGTCGAATACTGTTACTG
54015996 TTACTG
1 TTACTG
54016002 TTACAGATTT
Statistics
Matches: 116, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
38 14 0.12
39 26 0.22
40 1 0.01
42 1 0.01
45 72 0.62
47 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTATGTGTCGAATACTGTTACTG
Found at i:54015924 original size:45 final size:45
Alignment explanation
Indices: 54015856--54016055 Score: 283
Period size: 45 Copynumber: 4.4 Consensus size: 45
54015846 ATGTGCCGAC
* *
54015856 TACTGTTACTGTTACTGATTCGGCACTTTATGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
*
54015901 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* *
54015946 TACTGTTACTGTTATCGATTCGGCACTTTGTGTATCGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * ** *
54015991 TACCGTTACTGTTACAGATTTAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
54016036 TACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACCGATT
54016056 ACTGTATACT
Statistics
Matches: 138, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 138 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:54018126 original size:15 final size:15
Alignment explanation
Indices: 54018106--54018160 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
54018096 CCTTAATTAA
54018106 TTAATTAAAACTTAT
1 TTAATTAAAACTTAT
**
54018121 TTAATTAATCCTTAAT
1 TTAATTAAAACTT-AT
* *
54018137 CATAATTAAATCTTAT
1 -TTAATTAAAACTTAT
54018153 TTAATTAA
1 TTAATTAA
54018161 TCATTAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 18 0.56
16 4 0.12
17 10 0.31
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTAAAACTTAT
Found at i:54018152 original size:32 final size:32
Alignment explanation
Indices: 54018107--54018177 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
54018097 CTTAATTAAT
*
54018107 TAATTAAAACTTATTTAATTAATCCTTAATCA
1 TAATTAAAACTTATTTAATTAATCATTAATCA
* *
54018139 TAATTAAATCTTATTTAATTAATCATTAATTA
1 TAATTAAAACTTATTTAATTAATCATTAATCA
*
54018171 CAATTAA
1 TAATTAA
54018178 CCAAACTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (32 bp):
TAATTAAAACTTATTTAATTAATCATTAATCA
Found at i:54020207 original size:45 final size:45
Alignment explanation
Indices: 54020183--54020352 Score: 250
Period size: 45 Copynumber: 3.8 Consensus size: 45
54020173 AACAAGATGT
* * *
54020183 CATAGTGTCTTTTAACTATGGTCTTATTCATTTTCGGTATAGTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGGTATAGTGC
54020228 CATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGGTATAGTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGGTATAGTGC
* **
54020273 CATAGTGTCTTTCAAATATGGTCTTATTTATTTCCGGTATAGTGC
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGGTATAGTGC
* * * *
54020318 CATAATGTCTTTCAACTAAGGTCTTAATCATTTTT
1 CATAGTGTCTTTCAACTATGGTCTTATTTATTTTT
54020353 CAAGCCAATT
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 112 1.00
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46
Consensus pattern (45 bp):
CATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGGTATAGTGC
Found at i:54033863 original size:15 final size:15
Alignment explanation
Indices: 54033843--54033877 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
54033833 ATAATCTGAG
54033843 TGTCTCTTTAGTTCT
1 TGTCTCTTTAGTTCT
54033858 TGTCTCTTTAGTTCT
1 TGTCTCTTTAGTTCT
54033873 TGTCT
1 TGTCT
54033878 TGTTAAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.06, C:0.20, G:0.14, T:0.60
Consensus pattern (15 bp):
TGTCTCTTTAGTTCT
Found at i:54036095 original size:29 final size:29
Alignment explanation
Indices: 54036040--54036095 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
54036030 ACCATATATT
*
54036040 ACGTTTGTAGGTTTAGTATGCAGTGTATA
1 ACGTTTGTAGGTTTAGTATACAGTGTATA
*
54036069 ACGTTTGTAGGTATT-GTATACATTGTA
1 ACGTTTGTAGGT-TTAGTATACAGTGTA
54036096 CGTTATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (29 bp):
ACGTTTGTAGGTTTAGTATACAGTGTATA
Found at i:54036882 original size:29 final size:30
Alignment explanation
Indices: 54036849--54036920 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
54036839 AAATCAAAAT
* *
54036849 TTCATGTATAAAATTGCACA-AAATTAAAG
1 TTCATGTATAAAATTACACATAAACTAAAG
* *
54036878 TTCATGTATAAAATTATACATTAAACTAATG
1 TTCATGTATAAAATTACACA-TAAACTAAAG
54036909 TTCATGTATAAA
1 TTCATGTATAAA
54036921 TTTGAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 18 0.49
31 19 0.51
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (30 bp):
TTCATGTATAAAATTACACATAAACTAAAG
Found at i:54040725 original size:3 final size:3
Alignment explanation
Indices: 54040711--54040783 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
54040701 ATAGCAAACA
* *
54040711 AAG AAT AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
54040759 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
54040784 CTTGTTTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:54043970 original size:80 final size:80
Alignment explanation
Indices: 54043886--54044104 Score: 233
Period size: 80 Copynumber: 2.7 Consensus size: 80
54043876 ATCGATATTT
* *
54043886 AGCCTACTAAGCACTAAGCTTGATAGATTCACTGGCACAAAGCCTACTAGGCATAAAGCCCAATA
1 AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCTACTAGGCATAAAGCCCAATA
* * **
54043951 AGTTCACCGGTACAA
66 ACTACACCGACACAA
** * * * * *
54043966 AGCCTGTTAATCATTAAGCTTGATAAATTCACTAGCACAAAGTCTGA-TAGGCACAAAGCCCGAT
1 AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCT-ACTAGGCATAAAGCCCAAT
54044030 AACTACACCGACACAA
65 AACTACACCGACACAA
* * * * *** *
54044046 AACCTACTAGGCACTAAGCTTTATAAATTCACCAGCATGGAGCCTGCTAGGCATAAAGC
1 AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCTACTAGGCATAAAGC
54044105 TTGCTAAGCA
Statistics
Matches: 110, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
80 109 0.99
81 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (80 bp):
AGCCTACTAAGCACTAAGCTTGATAAATTCACTAGCACAAAGCCTACTAGGCATAAAGCCCAATA
ACTACACCGACACAA
Found at i:54057455 original size:17 final size:17
Alignment explanation
Indices: 54057429--54057475 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
54057419 GTTAAATCAT
* *
54057429 CAATAATAAATCAAGAG
1 CAATACTAAATCAAAAG
54057446 CAATACTAAATGCAAAAG
1 CAATACTAAAT-CAAAAG
54057464 CAA-ACCTAAATC
1 CAATA-CTAAATC
54057476 CATAACCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.55, C:0.19, G:0.09, T:0.17
Consensus pattern (17 bp):
CAATACTAAATCAAAAG
Found at i:54059611 original size:21 final size:21
Alignment explanation
Indices: 54059587--54059627 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54059577 ATTTTCTAAC
54059587 TTAATCTTA-ATTATTAATTAG
1 TTAATC-TAGATTATTAATTAG
*
54059608 TTAATCTAGATTGTTAATTA
1 TTAATCTAGATTATTAATTA
54059628 AATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
TTAATCTAGATTATTAATTAG
Found at i:54060392 original size:23 final size:23
Alignment explanation
Indices: 54060342--54060392 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
54060332 TAAGAATATT
*
54060342 ATAAATTATAAAAATTAAATAAA
1 ATAAATTATAAAAAATAAATAAA
*
54060365 TTAAATTTATAAAAAATAAA-AAA
1 ATAAA-TTATAAAAAATAAATAAA
54060388 ATAAA
1 ATAAA
54060393 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAATTATAAAAAATAAATAAA
Found at i:54060831 original size:30 final size:29
Alignment explanation
Indices: 54060795--54060885 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
54060785 TTATCTAATT
54060795 TTTTTATTTTTATTTTAAATATATATTCTC
1 TTTTTATTTTTATTTTAAATATATATT-TC
*
54060825 TTTTTATTTTCA-TTT---TATATA-TTC
1 TTTTTATTTTTATTTTAAATATATATTTC
54060849 TTTTTATTTTTATTTTAAATTTATATATATTC
1 TTTTTATTTTTATTTTAAA--TATATAT-TTC
54060881 TTTTT
1 TTTTT
54060886 TTAAAGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
24 13 0.25
25 4 0.08
26 6 0.12
29 3 0.06
30 17 0.33
32 8 0.16
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTATTTTTATTTTAAATATATATTTC
Found at i:54060855 original size:13 final size:13
Alignment explanation
Indices: 54060814--54060855 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
54060804 TTATTTTAAA
54060814 TATATATTCTCTTT
1 TATATATTCT-TTT
* *
54060828 T-TATTTTCATTT
1 TATATATTCTTTT
54060840 TATATATTCTTTT
1 TATATATTCTTTT
54060853 TAT
1 TAT
54060856 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 4 0.17
13 18 0.78
14 1 0.04
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATATTCTTTT
Found at i:54060863 original size:24 final size:24
Alignment explanation
Indices: 54060782--54060865 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
54060772 ATTATTTGAA
*
54060782 ATTTTATCTAATT-TTTTTATTTTT
1 ATTTTATAT-ATTCTTTTTATTTTT
*
54060806 ATTTTAAATATATATTCTCTTTTTATTTTC
1 A-TTT---TATATA-T-TCTTTTTATTTTT
54060836 ATTTTATATATTCTTTTTATTTTT
1 ATTTTATATATTCTTTTTATTTTT
54060860 ATTTTA
1 ATTTTA
54060866 AATTTATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
24 19 0.38
25 4 0.08
26 6 0.12
27 1 0.02
28 5 0.10
29 4 0.08
30 11 0.22
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTTATATATTCTTTTTATTTTT
Found at i:54060881 original size:32 final size:30
Alignment explanation
Indices: 54060781--54060885 Score: 98
Period size: 32 Copynumber: 3.6 Consensus size: 30
54060771 AATTATTTGA
*
54060781 AATTTTATCTAATT-TTTTTATTTTTATTTT
1 AATTTTATAT-ATTCTTTTTATTTTTATTTT
* *
54060811 AA--ATATATATTC----TCTTTTTATTTT
1 AATTTTATATATTCTTTTTATTTTTATTTT
*
54060835 CATTTTATATATTCTTTTTATTTTTATTTT
1 AATTTTATATATTCTTTTTATTTTTATTTT
54060865 AAATTTATATATATTCTTTTT
1 -AATTT-TATATATTCTTTTT
54060886 TTAAAGTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
24 12 0.20
26 9 0.15
27 3 0.05
28 4 0.07
30 13 0.22
31 4 0.07
32 14 0.24
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (30 bp):
AATTTTATATATTCTTTTTATTTTTATTTT
Found at i:54060887 original size:23 final size:23
Alignment explanation
Indices: 54060853--54060902 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
54060843 ATATTCTTTT
54060853 TATTTTTATTTTAAA-TTTATATA
1 TATTTTTATTTTAAAGTTT-TATA
54060876 TATTCTTT-TTTTAAAGTTTTATA
1 TATT-TTTATTTTAAAGTTTTATA
54060899 -ATTT
1 TATTT
54060903 ATATATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.04
22 3 0.12
23 15 0.60
24 6 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTTATTTTAAAGTTTTATA
Found at i:54060902 original size:32 final size:31
Alignment explanation
Indices: 54060813--54060919 Score: 93
Period size: 32 Copynumber: 3.6 Consensus size: 31
54060803 TTTATTTTAA
* *
54060813 ATATATATTCTCTT-TTT--ATTTT-CATTT
1 ATATATATTCTTTTATTTAAATTTTAAATTT
**
54060840 -TATATATTCTTTTTATTTTTATTTTAAATTT
1 ATATATATTC-TTTTATTTAAATTTTAAATTT
54060871 ATATATATTCTTTT-TTTAAAGTTTTATAATTT
1 ATATATATTCTTTTATTTAAA-TTTTA-AATTT
*
54060903 ATATAT-TTCTTATATTT
1 ATATATATTCTTTTATTT
54060920 TTTGACAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
26 9 0.14
27 3 0.05
28 3 0.05
30 9 0.14
31 19 0.29
32 23 0.35
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (31 bp):
ATATATATTCTTTTATTTAAATTTTAAATTT
Found at i:54060908 original size:30 final size:31
Alignment explanation
Indices: 54060836--54060909 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
54060826 TTTTATTTTC
**
54060836 ATTTTATATATTCTTTTTATTTTTATTTTAA
1 ATTTTATATATTCTTTTTATTTAAATTTTAA
54060867 ATTTATATATATTC-TTTT-TTTAAAGTTTTATA
1 ATTT-TATATATTCTTTTTATTTAAA-TTTTA-A
54060899 A-TTTATATATT
1 ATTTTATATATT
54060910 TCTTATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 12 0.32
31 15 0.39
32 11 0.29
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (31 bp):
ATTTTATATATTCTTTTTATTTAAATTTTAA
Found at i:54061411 original size:59 final size:55
Alignment explanation
Indices: 54061300--54061427 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 55
54061290 TACACTAATC
* *
54061300 GTCACCTAACTATTAGTATTTTTTTTGTGACTCAATTATGAAAAGTTACAAAATG
1 GTCACCTAACTATTAGTATTTTTTTTGTCACTCAACTATGAAAAGTTACAAAATG
* *
54061355 GTCACTTAACTATTAGTAAATTTATTTTTTGGTCACTCAACTATG-AAAGTTACAAAATT
1 GTCACCTAACTATTAGT--A-TT-TTTTTT-GTCACTCAACTATGAAAAGTTACAAAATG
*
54061414 GTCACCCAACTATT
1 GTCACCTAACTATT
54061428 CAATTTTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
55 16 0.26
57 1 0.02
58 2 0.03
59 31 0.50
60 12 0.19
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (55 bp):
GTCACCTAACTATTAGTATTTTTTTTGTCACTCAACTATGAAAAGTTACAAAATG
Found at i:54061443 original size:60 final size:60
Alignment explanation
Indices: 54061316--54061448 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 60
54061306 TAACTATTAG
* * * ** *
54061316 TATTTTTTTTGTGACTCAATTATGAAAAGTTACAAAATGGTCACTTAACTATTAGTAAATT
1 TATTTTTTTGGTCACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATTA-CAAATT
* *
54061377 TA-TTTTTTGGTCACTCAACTATG-AAAGTTACAAAATTGTCACCCAACTATT-CAATTT
1 TATTTTTTTGGTCACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATTACAAATT
54061434 TATCTTTTTT-GTCAC
1 TAT-TTTTTTGGTCAC
54061449 AAGAGGGGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
57 6 0.10
58 5 0.08
59 31 0.50
60 18 0.29
61 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (60 bp):
TATTTTTTTGGTCACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATTACAAATT
Found at i:54064874 original size:25 final size:24
Alignment explanation
Indices: 54064837--54064909 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
54064827 CTCTCTCTCT
54064837 TGAGCCATATAACGAGAAGCTCATG
1 TGAGCCAT-TAACGAGAAGCTCATG
54064862 TGAGCCATGTAACG-GAAAGCTCATG
1 TGAGCCAT-TAACGAG-AAGCTCATG
*
54064887 AGAGCCATTAAC-AGGAAGCTCAT
1 TGAGCCATTAACGA-GAAGCTCAT
54064910 AAGAGGTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 13 0.30
25 30 0.70
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
TGAGCCATTAACGAGAAGCTCATG
Found at i:54064905 original size:24 final size:24
Alignment explanation
Indices: 54064838--54065031 Score: 124
Period size: 24 Copynumber: 7.8 Consensus size: 24
54064828 TCTCTCTCTT
* *
54064838 GAGCCATATAACGAGAAGCTCATGT
1 GAGCCAT-TAACGGGAAGCTCATGA
*
54064863 GAGCCATGTAACGGAAAGCTCATGA
1 GAGCCAT-TAACGGGAAGCTCATGA
* *
54064888 GAGCCATTAACAGGAAGCTCATAA
1 GAGCCATTAACGGGAAGCTCATGA
** *** * * *
54064912 GAGGTA-TAATCAAAAAGTTCAAGC
1 GAGCCATTAA-CGGGAAGCTCATGA
*
54064936 GAGCCATTATCGGGAAGCTGCA-GA
1 GAGCCATTAACGGGAAGCT-CATGA
*
54064960 GAGCCATTATCGGGAAGCTCCA-GA
1 GAGCCATTAACGGGAAGCT-CATGA
*
54064984 GAGCCATTAATTGGGAAGCTCATGAAA
1 GAGCCATTAA-CGGGAAGCTCATG--A
* *
54065011 GAGTCTTTAATCGGGAAGCTC
1 GAGCCATTAA-CGGGAAGCTC
54065032 CGAAAAGCCA
Statistics
Matches: 133, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
23 3 0.02
24 70 0.53
25 41 0.31
27 19 0.14
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCATGA
Found at i:54065038 original size:27 final size:26
Alignment explanation
Indices: 54064936--54065042 Score: 107
Period size: 24 Copynumber: 4.3 Consensus size: 26
54064926 AAGTTCAAGC
* *
54064936 GAGCCATT-ATCGGGAAGCTGC-AGA
1 GAGCCATTAATCGGGAAGCTCCGAAA
*
54064960 GAGCCATT-ATCGGGAAGCTCC-AGA
1 GAGCCATTAATCGGGAAGCTCCGAAA
* *
54064984 GAGCCATTAATTGGGAAGCTCATGAAA
1 GAGCCATTAATCGGGAAGCTC-CGAAA
* *
54065011 GAGTCTTTAATCGGGAAGCTCCGAAA
1 GAGCCATTAATCGGGAAGCTCCGAAA
54065037 -AGCCAT
1 GAGCCAT
54065043 ATATCAGGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
24 31 0.44
25 15 0.21
26 4 0.06
27 20 0.29
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.20
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCTCCGAAA
Found at i:54088176 original size:8 final size:8
Alignment explanation
Indices: 54088165--54088209 Score: 69
Period size: 7 Copynumber: 6.0 Consensus size: 8
54088155 ATTTCTGGTC
54088165 TTAGGGTT
1 TTAGGGTT
54088173 TTAGGG-T
1 TTAGGGTT
54088180 TTAGGGTT
1 TTAGGGTT
54088188 TT-GGGTT
1 TTAGGGTT
54088195 TT-GGGTT
1 TTAGGGTT
54088202 TTAGGGTT
1 TTAGGGTT
54088210 AGTGAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.60
8 14 0.40
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (8 bp):
TTAGGGTT
Found at i:54088185 original size:15 final size:15
Alignment explanation
Indices: 54088165--54088209 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
54088155 ATTTCTGGTC
54088165 TTAGGGTTTTAGGGT
1 TTAGGGTTTTAGGGT
54088180 TTAGGGTTTT-GGGT
1 TTAGGGTTTTAGGGT
*
54088194 TTTGGGTTTTAGGGT
1 TTAGGGTTTTAGGGT
54088209 T
1 T
54088210 AGTGAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (15 bp):
TTAGGGTTTTAGGGT
Found at i:54088194 original size:22 final size:22
Alignment explanation
Indices: 54088168--54088209 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
54088158 TCTGGTCTTA
54088168 GGGTTTTAGGG-TTTAGGGTTTT
1 GGGTTTT-GGGTTTTAGGGTTTT
54088190 GGGTTTTGGGTTTTAGGGTT
1 GGGTTTTGGGTTTTAGGGTT
54088210 AGTGAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (22 bp):
GGGTTTTGGGTTTTAGGGTTTT
Found at i:54092607 original size:27 final size:27
Alignment explanation
Indices: 54092577--54092660 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
54092567 AAAGGCATTC
*
54092577 CTTTTAGAGTTCGCCACTAATGTTATT
1 CTTTTAGAGTTCGCCACTAAGGTTATT
* * *
54092604 CTTTTAGGGTTCTCAACTAAGGTTATT
1 CTTTTAGAGTTCGCCACTAAGGTTATT
* * * *
54092631 CTTCTAGAGTTTGCCACAAAGGCTATT
1 CTTTTAGAGTTCGCCACTAAGGTTATT
54092658 CTT
1 CTT
54092661 AGTTGTCGTG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.42
Consensus pattern (27 bp):
CTTTTAGAGTTCGCCACTAAGGTTATT
Found at i:54108024 original size:12 final size:12
Alignment explanation
Indices: 54108007--54108033 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54107997 ACAAGGGATA
54108007 GTATACCATTTG
1 GTATACCATTTG
54108019 GTATACCATTTG
1 GTATACCATTTG
54108031 GTA
1 GTA
54108034 CCTAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (12 bp):
GTATACCATTTG
Found at i:54108083 original size:28 final size:27
Alignment explanation
Indices: 54108026--54108084 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
54108016 TTGGTATACC
*
54108026 ATTTGGTACCTAATATTTTAATATTTA
1 ATTTGGTACCTAATATTTTAATATTCA
*
54108053 ATTTGGTACTTGAATATTTTAATGA-TCA
1 ATTTGGTACCT-AATATTTTAAT-ATTCA
54108081 ATTT
1 ATTT
54108085 AGTATCTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 10 0.36
28 17 0.61
29 1 0.04
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (27 bp):
ATTTGGTACCTAATATTTTAATATTCA
Found at i:54118163 original size:22 final size:19
Alignment explanation
Indices: 54118138--54118179 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
54118128 TGATAATCAT
54118138 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
54118160 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
54118179 T
1 T
54118180 CAACTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:54118239 original size:16 final size:17
Alignment explanation
Indices: 54118218--54118252 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54118208 AAATTTGATC
54118218 ATATTT-TATTTAATAA
1 ATATTTATATTTAATAA
*
54118234 ATATTTATTTTTAATAA
1 ATATTTATATTTAATAA
54118251 AT
1 AT
54118253 TAATAGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTATATTTAATAA
Found at i:54118705 original size:22 final size:21
Alignment explanation
Indices: 54118675--54118715 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54118665 GAGTTTCACA
*
54118675 ATGTCTAATTACAGTCTCTAAC
1 ATGTCTAA-TAAAGTCTCTAAC
*
54118697 ATGTGTAATAAAGTCTCTA
1 ATGTCTAATAAAGTCTCTA
54118716 CCAAGCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCTAATAAAGTCTCTAAC
Found at i:54122986 original size:6 final size:6
Alignment explanation
Indices: 54122954--54122998 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
54122944 TAAGTCTAAG
* * * *
54122954 AAAATA ACAATA AACATA AGAAGA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
54122999 CAAATAAACT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:54144998 original size:62 final size:61
Alignment explanation
Indices: 54144902--54145025 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 61
54144892 TCAGAAAATG
*
54144902 ACCAATACAAAATAATTTAATACAAACTCAACCATTTCTGTCATGCACATGGCAGACAACA
1 ACCAATACAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATGGCAGACAACA
*
54144963 ACCAATACAAAAATAATTTAATACAAACACAACCATTTTTGTCATGCACATGGCAGACAACA
1 ACCAATAC-AAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATGGCAGACAACA
54145025 A
1 A
54145026 TAGACAATAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 8 0.13
62 52 0.87
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (61 bp):
ACCAATACAAAATAATTTAATACAAACACAACCATTTCTGTCATGCACATGGCAGACAACA
Found at i:54145290 original size:6 final size:6
Alignment explanation
Indices: 54145281--54145506 Score: 174
Period size: 6 Copynumber: 37.7 Consensus size: 6
54145271 AAATAACCTT
*
54145281 AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCA
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG
* * * *
54145329 AAATCG AAATCG AAATCG AAATCG AAATCA AAATCA AAATCA AAATCA
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG
* * * * * * *
54145377 AAATCA AAATCA AAATTG AAATC- AAAGTCA AAATCA AAATCAG TGAGT-G
1 AAATCG AAATCG AAATCG AAATCG AAA-TCG AAATCG AAATC-G -AAATCG
** * * * * * *
54145426 -TTTCA AAATTG AAATCA AAATCA AAATCG AAATCA AAAT-T AGAATC-
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG A-AATCG
* *
54145472 ATAATCG AAATCA AAATTG AAATCG AAATCG AAAT
1 A-AATCG AAATCG AAATCG AAATCG AAATCG AAAT
54145507 AACCCTAAAT
Statistics
Matches: 185, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
4 1 0.01
5 4 0.02
6 174 0.94
7 4 0.02
8 2 0.01
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (6 bp):
AAATCG
Found at i:54145304 original size:18 final size:18
Alignment explanation
Indices: 54145281--54145506 Score: 196
Period size: 18 Copynumber: 12.9 Consensus size: 18
54145271 AAATAACCTT
*
54145281 AAATCGAAATCGAAATCG
1 AAATCGAAATCAAAATCG
*
54145299 AAATCGAAATCGAAATCG
1 AAATCGAAATCAAAATCG
54145317 AAATCGAAATCAAAATCG
1 AAATCGAAATCAAAATCG
*
54145335 AAATCGAAATCGAAATCG
1 AAATCGAAATCAAAATCG
* *
54145353 AAATCAAAATCAAAATCA
1 AAATCGAAATCAAAATCG
* *
54145371 AAATCAAAATCAAAATCA
1 AAATCGAAATCAAAATCG
* * *
54145389 AAATTGAAATCAAAGTCA
1 AAATCGAAATCAAAATCG
* *
54145407 AAATCAAAATC--AGT-G
1 AAATCGAAATCAAAATCG
* ** *
54145422 -AGT-G-TTTCAAAATTG
1 AAATCGAAATCAAAATCG
*
54145437 AAATCAAAATCAAAATCG
1 AAATCGAAATCAAAATCG
* * *
54145455 AAATCAAAATTAGAATC-
1 AAATCGAAATCAAAATCG
*
54145472 ATAATCGAAATCAAAATTG
1 A-AATCGAAATCAAAATCG
*
54145491 AAATCGAAATCGAAAT
1 AAATCGAAATCAAAAT
54145507 AACCCTAAAT
Statistics
Matches: 172, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
12 2 0.01
14 4 0.02
15 1 0.01
16 5 0.03
17 1 0.01
18 158 0.92
19 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATCGAAATCAAAATCG
Found at i:54145532 original size:16 final size:16
Alignment explanation
Indices: 54145513--54145543 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54145503 AAATAACCCT
54145513 AAATAACCCTAAATTG
1 AAATAACCCTAAATTG
54145529 AAATAACCCTAAATT
1 AAATAACCCTAAATT
54145544 CAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAACCCTAAATTG
Found at i:54146963 original size:50 final size:50
Alignment explanation
Indices: 54146838--54147135 Score: 353
Period size: 50 Copynumber: 5.8 Consensus size: 50
54146828 ATTTGGGTAA
* * * *
54146838 AGAGATCCCATGTAAGACTATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
54146894 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
54146944 AGAGGTCTCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
54146994 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* ** * * * * *
54147044 AAAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATAGGCACCTATATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
54147094 AGAACTCTCATGTAAGACCATATCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
54147136 GTACAAGAAA
Statistics
Matches: 214, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
50 171 0.80
53 3 0.01
55 1 0.00
56 39 0.18
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:54154019 original size:22 final size:20
Alignment explanation
Indices: 54153983--54154031 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
54153973 ATTTATCTTT
*
54153983 AATAAAAATAAATAAATAGTTG
1 AATAAAAAGAAATAAATA--TG
* *
54154005 AATAAAAAGATATAATTATG
1 AATAAAAAGAAATAAATATG
54154025 AATAAAA
1 AATAAAA
54154032 TCAAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (20 bp):
AATAAAAAGAAATAAATATG
Found at i:54154065 original size:19 final size:18
Alignment explanation
Indices: 54153989--54154068 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 18
54153979 CTTTAATAAA
*
54153989 AATAAATAAAT-AGT-TG
1 AATAAATAAATAATTATG
*
54154005 AATAAAAAGATATAATTATG
1 AATAAATA-A-ATAATTATG
*
54154025 AATAAAATCAA-AA-TAT-
1 AAT-AAATAAATAATTATG
54154041 AA-AAATAAATAATTATG
1 AATAAATAAATAATTATG
54154058 AATGAAATAAA
1 AAT-AAATAAA
54154069 CAAATAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 12 0.24
17 6 0.12
18 4 0.08
19 10 0.20
20 6 0.12
21 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (18 bp):
AATAAATAAATAATTATG
Found at i:54154076 original size:33 final size:33
Alignment explanation
Indices: 54154005--54154076 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
54153995 TAAATAGTTG
*
54154005 AATAAAAAGATATAATTATGAATAAAATCAAAA
1 AATAAAAAGAAATAATTATGAATAAAATCAAAA
* * *
54154038 TATAAAAATAAATAATTATGAATGAAAT-AAACA
1 AATAAAAAGAAATAATTATGAATAAAATCAAA-A
54154071 AATAAA
1 AATAAA
54154077 TGAATGAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (33 bp):
AATAAAAAGAAATAATTATGAATAAAATCAAAA
Found at i:54200075 original size:24 final size:23
Alignment explanation
Indices: 54200039--54200086 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
54200029 TCATACTTCT
*
54200039 ATTTTTTTTTATAAATTTATATG
1 ATTTTTTGTTATAAATTTATATG
* *
54200062 ATTTATTTGTTATAATTTTGTATG
1 ATTT-TTTGTTATAAATTTATATG
54200086 A
1 A
54200087 ATTCTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.62
Consensus pattern (23 bp):
ATTTTTTGTTATAAATTTATATG
Found at i:54206485 original size:10 final size:10
Alignment explanation
Indices: 54206472--54206533 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
54206462 TTGTAATTTC
*
54206472 TAAATTTTTA
1 TAAATTTTAA
54206482 TAAAATTTTAA
1 T-AAATTTTAA
*
54206493 TAAATTTTTA
1 TAAATTTTAA
54206503 TAAAATTTTAA
1 T-AAATTTTAA
54206514 TAAATTTTAA
1 TAAATTTTAA
*
54206524 TAAAATTTAA
1 TAAATTTTAA
54206534 AAACTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
10 28 0.61
11 18 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TAAATTTTAA
Found at i:54206489 original size:11 final size:11
Alignment explanation
Indices: 54206473--54206531 Score: 86
Period size: 11 Copynumber: 5.5 Consensus size: 11
54206463 TGTAATTTCT
*
54206473 AAATTTTTATA
1 AAATTTTAATA
54206484 AAATTTTAAT-
1 AAATTTTAATA
*
54206494 AAATTTTTATA
1 AAATTTTAATA
54206505 AAATTTTAAT-
1 AAATTTTAATA
54206515 AAATTTTAATA
1 AAATTTTAATA
54206526 AAATTT
1 AAATTT
54206532 AAAAACTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
10 19 0.44
11 24 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTTAATA
Found at i:54206542 original size:21 final size:21
Alignment explanation
Indices: 54206472--54206531 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
54206462 TTGTAATTTC
54206472 TAAATTTTTATAAAATTTTAA
1 TAAATTTTTATAAAATTTTAA
54206493 TAAATTTTTATAAAATTTTAA
1 TAAATTTTTATAAAATTTTAA
*
54206514 TAAATTTTAATAAAATTT
1 TAAATTTTTATAAAATTT
54206532 AAAAACTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATTTTTATAAAATTTTAA
Found at i:54207172 original size:43 final size:42
Alignment explanation
Indices: 54207065--54207377 Score: 373
Period size: 42 Copynumber: 7.4 Consensus size: 42
54207055 ACGTCGCTAA
* *
54207065 CTTTTGCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCGCTAAAGATCATGTT
*
54207109 TTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
54207151 CTTTAGCGGCGCTTAGAAAAAAACACCGCTAGAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* *
54207193 CTTTAGCGGCGCTTAGAAACAAACGCTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
54207235 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAAAAAACGCCGCTAAAGATCATGTT
* ** * * *
54207278 CTTTAGCGGCGCTTTGGAGGAAAACACCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
* **
54207321 CTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGA-TCA-TGTT
*
54207363 CTTTAGCGGTGCTTA
1 CTTTAGCGGCGCTTA
54207378 TTTCACAAAC
Statistics
Matches: 237, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.01
42 153 0.65
43 68 0.29
44 14 0.06
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:54207833 original size:21 final size:21
Alignment explanation
Indices: 54207809--54207856 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
54207799 GCTTCTATTG
* *
54207809 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
* *
54207830 CTGCTCCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCAGCCT
54207851 CTGCTT
1 CTGCTT
54207857 TAAGTTGCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.46, G:0.19, T:0.33
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCT
Found at i:54213249 original size:9 final size:9
Alignment explanation
Indices: 54213235--54213485 Score: 176
Period size: 9 Copynumber: 29.8 Consensus size: 9
54213225 AACTTATTTA
54213235 TTATGTAAG
1 TTATGTAAG
54213244 TTATGTAAG
1 TTATGTAAG
*
54213253 TTGTGTAAG
1 TTATGTAAG
54213262 TTATGTAAG
1 TTATGTAAG
*
54213271 CTATGTAAG
1 TTATGTAAG
*
54213280 TTGTGT-A-
1 TTATGTAAG
* *
54213287 TTATGCAAC
1 TTATGTAAG
54213296 TTATGTAAG
1 TTATGTAAG
*
54213305 TTGTGT-A-
1 TTATGTAAG
54213312 TTATGTAAG
1 TTATGTAAG
*
54213321 TTATGTCAG
1 TTATGTAAG
*
54213330 TTGTGT-A-
1 TTATGTAAG
* *
54213337 TTATGAAAC
1 TTATGTAAG
54213346 TTATGTAAG
1 TTATGTAAG
*
54213355 TTATGT--C
1 TTATGTAAG
*
54213362 TTTTGTAAG
1 TTATGTAAG
* *
54213371 TGATGTAAA
1 TTATGTAAG
*
54213380 ATATGT-A-
1 TTATGTAAG
54213387 TTATGTAAG
1 TTATGTAAG
*
54213396 TTATGTCAG
1 TTATGTAAG
*
54213405 TTGTGT-A-
1 TTATGTAAG
*
54213412 TTATGTAAA
1 TTATGTAAG
54213421 TTATGT-A-
1 TTATGTAAG
54213428 TTATGTAAG
1 TTATGTAAG
*
54213437 TTATGTAAT
1 TTATGTAAG
*
54213446 TTGTGT-A-
1 TTATGTAAG
*
54213453 TTATGTAAC
1 TTATGTAAG
* *
54213462 TTATTTAAT
1 TTATGTAAG
54213471 TTATGTAAG
1 TTATGTAAG
54213480 -TATGTA
1 TTATGTA
54213486 TTATTATGTA
Statistics
Matches: 190, Mismatches: 36, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
7 39 0.21
8 20 0.11
9 131 0.69
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:54213300 original size:25 final size:25
Alignment explanation
Indices: 54213233--54213532 Score: 243
Period size: 25 Copynumber: 11.9 Consensus size: 25
54213223 ATAACTTATT
54213233 TATTATGTAAGTTATGTAAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTG
*
54213258 TAAGTTATGTAAGCTATGTAAGTTGTG
1 T-A-TTATGTAAGTTATGTAAGTTGTG
* *
54213285 TATTATGCAACTTATGTAAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTG
*
54213310 TATTATGTAAGTTATGTCAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTG
* * *
54213335 TATTATGAAACTTATGTAAGTTATG
1 TATTATGTAAGTTATGTAAGTTGTG
* * * ** *
54213360 TCTTTTGTAAGTGATGTAAAATATG
1 TATTATGTAAGTTATGTAAGTTGTG
*
54213385 TATTATGTAAGTTATGTCAGTTGTG
1 TATTATGTAAGTTATGTAAGTTGTG
* *
54213410 TATTATGTAAATTATGT-A-TTATG
1 TATTATGTAAGTTATGTAAGTTGTG
* * *
54213433 TAAGTTATGTAATTTGTGT-A-TTATG
1 T-A-TTATGTAAGTTATGTAAGTTGTG
* * *
54213458 TAACTTATTTAATTTATGTAAGTATGTAT
1 T-A-TTATGTAAGTTATGTAAGT-TGT-G
* * *
54213487 TATTATGTAATTTAT-TATGTAG-G
1 TATTATGTAAGTTATGTAAGTTGTG
*
54213510 ATATTATCTAAGTTATGTAAGTT
1 -TATTATGTAAGTTATGTAAGTT
54213533 TTTTTTTGGT
Statistics
Matches: 223, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
23 5 0.02
24 15 0.07
25 156 0.70
26 7 0.03
27 36 0.16
28 3 0.01
29 1 0.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (25 bp):
TATTATGTAAGTTATGTAAGTTGTG
Found at i:54213315 original size:16 final size:16
Alignment explanation
Indices: 54213296--54213443 Score: 106
Period size: 16 Copynumber: 9.0 Consensus size: 16
54213286 ATTATGCAAC
*
54213296 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
54213312 TTATGTAAGTTATGTCA
1 TTATGTAAGTTATGT-A
* *
54213329 GTTGTGT-A-TTATGAAA
1 -TTATGTAAGTTATG-TA
*
54213345 CTTATGTAAGTTATGTC
1 -TTATGTAAGTTATGTA
* *
54213362 TTTTGTAAGTGATGTAAA
1 TTATGTAAGTTATGT--A
*
54213380 ATATGT-A-TTATGTAA
1 TTATGTAAGTTATGT-A
* *
54213395 GTTATGTCAGTTGTGTA
1 -TTATGTAAGTTATGTA
*
54213412 TTATGTAAATTATGTA
1 TTATGTAAGTTATGTA
54213428 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
54213444 ATTTGTGTAT
Statistics
Matches: 103, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
15 2 0.02
16 76 0.74
17 6 0.06
18 19 0.18
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:54213325 original size:34 final size:36
Alignment explanation
Indices: 54213236--54213325 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 36
54213226 ACTTATTTAT
* * *
54213236 TATGTAAGTTATGTAAGTTGTGTAAGTTATGTAAGC
1 TATGTAAGTTATGTAAGTTATGCAACTTATGTAAGC
* *
54213272 TATGTAAGTTGTGT-A-TTATGCAACTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGCAACTTATGTAAGC
*
54213306 TGTGT-A-TTATGTAAGTTATG
1 TATGTAAGTTATGTAAGTTATG
54213326 TCAGTTGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 5 0.11
33 2 0.04
34 24 0.53
35 1 0.02
36 13 0.29
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.44
Consensus pattern (36 bp):
TATGTAAGTTATGTAAGTTATGCAACTTATGTAAGC
Done.