Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 133 of 190
Found at i:39403665 original size:22 final size:22
Alignment explanation
Indices: 39403610--39403667 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
39403600 TCAAATCAAT
39403610 ATTTCT-T-GAATTTTAACAAA
1 ATTTCTCTCGAATTTTAACAAA
* *
39403630 ATTT-TCAACAAATTTTAACAAA
1 ATTTCTC-TCGAATTTTAACAAA
39403652 ATTTCTCTCGAATTTT
1 ATTTCTCTCGAATTTT
39403668 TTGAATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 4 0.13
22 23 0.77
23 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (22 bp):
ATTTCTCTCGAATTTTAACAAA
Found at i:39406335 original size:2 final size:2
Alignment explanation
Indices: 39406328--39406355 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39406318 AAGCCTGATG
39406328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39406356 GCAAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39408823 original size:3 final size:3
Alignment explanation
Indices: 39408815--39408893 Score: 85
Period size: 3 Copynumber: 26.7 Consensus size: 3
39408805 AAACTATCGT
*
39408815 ATA ATA AT- ATG ATAA ATA AT- ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
39408858 ATA ATA ATA ATA ATGA ATG ATA ATA TATA A-A ATA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA AT
39408894 GAAGAAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
2 8 0.12
3 50 0.76
4 8 0.12
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39408853 original size:31 final size:32
Alignment explanation
Indices: 39408815--39408893 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 32
39408805 AAACTATCGT
39408815 ATAATAATATGATAAATAATATAAT-ATAAT-A
1 ATAATAATAT-ATAAATAATATAATAATAATGA
39408846 ATAATAATA-AT-AAT-A-ATAATAATAATGA
1 ATAATAATATATAAATAATATAATAATAATGA
*
39408874 ATGATAATATATAAAATAAT
1 ATAATAATATAT-AAATAAT
39408894 GAAGAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
26 5 0.12
27 6 0.15
28 12 0.30
29 4 0.10
31 12 0.30
32 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (32 bp):
ATAATAATATATAAATAATATAATAATAATGA
Found at i:39409932 original size:20 final size:20
Alignment explanation
Indices: 39409904--39409946 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
39409894 GCTGAAAATG
*
39409904 GGTTGGGGTGCTTTGGGC-TA
1 GGTTGGGGT-ATTTGGGCTTA
*
39409924 GGTTTGGGTATTTGGGCTTA
1 GGTTGGGGTATTTGGGCTTA
39409944 GGT
1 GGT
39409947 AGGTTATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.07, C:0.07, G:0.47, T:0.40
Consensus pattern (20 bp):
GGTTGGGGTATTTGGGCTTA
Found at i:39410347 original size:44 final size:44
Alignment explanation
Indices: 39410239--39410477 Score: 181
Period size: 44 Copynumber: 5.6 Consensus size: 44
39410229 ATTTTGGTCT
* * *** *
39410239 GCTCCACTGCAACTTTAGGGAGATAAGA-C--TGGATGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
* * * *
39410280 GCTCTACTACAACTTTAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
* * *
39410324 GCTCCACTGCAACTTCAGGGAGATAGGAT-TG-GCTTCTT-CTGCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTT-TTAAT-CC
* * *** *
39410367 TGTTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGCGATCT
1 -GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
* *
39410409 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
* *
39410453 GCTCTACTGCAACTTCAGGAAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
39410478 GGATTGGCTT
Statistics
Matches: 153, Mismatches: 33, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
41 50 0.33
42 7 0.05
43 9 0.06
44 87 0.57
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
Found at i:39410389 original size:129 final size:129
Alignment explanation
Indices: 39410241--39410491 Score: 457
Period size: 129 Copynumber: 1.9 Consensus size: 129
39410231 TTTGGTCTGC
* *
39410241 TCCACTGCAACTTTAGGGAGATAAGACTGGATGCGATCTGCTCTACTACAACTTTAGAGAGATAA
1 TCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAA
*
39410306 GATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTCTGCCTGT
66 GATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCTGCCTGT
*
39410370 TCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 TCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAA
*
39410435 GATCTGTGGTTTTAATCCGCTCTACTGCAACTTCAGGAAGATAGGATTGGCTTCTTC
66 GATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTC
39410492 AATCTATTTA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 117 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (129 bp):
TCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAA
GATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCTGCCTGT
Found at i:39410524 original size:129 final size:129
Alignment explanation
Indices: 39410248--39410524 Score: 396
Period size: 129 Copynumber: 2.1 Consensus size: 129
39410238 TGCTCCACTG
* * *
39410248 CAACTTTAGGGAGATAAGACTGGATGCGATCTGCTCTACTACAACTTTAGAGAGATAAGATCTGT
1 CAACTTCAGGGAAATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGT
* ** * * *
39410313 GGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTTCTGCCTGTTCCACTG
66 GGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCAACCTATTCAACTA
* *
39410377 CAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGT
1 CAACTTCAGGGAAATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGT
* * *
39410442 GGTTTTAATCCGCTCTACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCAATCTATTTAACTA
66 GGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCAACCTATTCAACTA
39410506 CAA-TGTC-GGGAAAGTAAGA
1 CAACT-TCAGGGAAA-TAAGA
39410525 TTCACCGTCG
Statistics
Matches: 133, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
128 6 0.05
129 127 0.95
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (129 bp):
CAACTTCAGGGAAATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGT
GGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGGCTTCTTCAACCTATTCAACTA
Found at i:39410572 original size:50 final size:50
Alignment explanation
Indices: 39410518--39410796 Score: 208
Period size: 50 Copynumber: 5.6 Consensus size: 50
39410508 ATGTCGGGAA
* * *
39410518 AGTAAGATTCACCGTCGTAGCTTCAATCTGTTCTGCTGCACCGCCTGGGG
1 AGTAAGATTCACCATTGTAGCTTCAATCTGTTCTGCTGCAACGCCTGGGG
* * * ** * *
39410568 AGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTTAATTGCAATG-TTGGGG
1 AGTAAGATTCACCATTGTAGCTTCAATCTGTTCT-GCTGCAACGCCTGGGG
* * * *
39410617 AAGCAAGATTCACCATTGTAGCTTTAATCTGTTCTGCTGCATCGCCTGGGA
1 -AGTAAGATTCACCATTGTAGCTTCAATCTGTTCTGCTGCAACGCCTGGGG
* * * * *
39410668 AGTAAGATTCACCATTGTGGCTTCAATCT-TT-TGAATTACAATGTC-GGGG
1 AGTAAGATTCACCATTGTAGCTTCAATCTGTTCTG--CTGCAACGCCTGGGG
* * * * * * * *
39410717 AAGTGAGATTCACCATCGTAGCTTCAATCTGTTCCGCTGTATCACTTGGGA
1 -AGTAAGATTCACCATTGTAGCTTCAATCTGTTCTGCTGCAACGCCTGGGG
* * *
39410768 AGTAAGATTCGCCGTTGTGGCTTCAATCT
1 AGTAAGATTCACCATTGTAGCTTCAATCT
39410797 TTTAAATTGC
Statistics
Matches: 173, Mismatches: 46, Indels: 20
0.72 0.19 0.08
Matches are distributed among these distances:
48 2 0.01
49 13 0.08
50 145 0.84
51 12 0.07
52 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
AGTAAGATTCACCATTGTAGCTTCAATCTGTTCTGCTGCAACGCCTGGGG
Found at i:39410663 original size:100 final size:100
Alignment explanation
Indices: 39410488--39411013 Score: 685
Period size: 100 Copynumber: 5.3 Consensus size: 100
39410478 GGATTGGCTT
* * * * *
39410488 CTTCAATCTATTT-AACTACAATGTCGGGAAAGTAAGATTCACCGTCGTAGCTTCAATCTGTTCT
1 CTTCAATCT-TTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCT
* * *
39410552 GCTGCACCGCCTGGGGAGTAAGATTCGCCGTTGTAG
65 GCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
* * ** * *
39410588 CTTCAATCTTTTTAATTGCAATGTTGGGGAAGCAAGATTCACCATTGTAGCTTTAATCTGTTCTG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCTG
* *
39410653 CTGCATCGCCTGGGAAGTAAGATTCACCATTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
* * *
39410688 CTTCAATCTTTTGAATTACAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCTG
* * *
39410753 CTGTATCACTTGGGAAGTAAGATTCGCCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
* * **
39410788 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTTAATCTATTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCTG
* * * *
39410853 ATGTATCGCCTGGAAAGTAAGATTCGTCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
* * ** *
39410888 CTTCAATCTTTTGAATTGCAATGTCAGGGAAGTGAGATTCGTCGTCGTAGCTTCAATCTGTTCTG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCTG
* *
39410953 CTGCATCACCTGAGAAGTAAGATTCGCCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
* *
39410988 CTTTAATCTTTTAAATTTCAATGTCG
1 CTTCAATCTTTTAAATTGCAATGTCG
39411014 AGGAGAACTA
Statistics
Matches: 370, Mismatches: 55, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
99 3 0.01
100 367 0.99
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACCATCGTAGCTTCAATCTGTTCTG
CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
Found at i:39411028 original size:52 final size:52
Alignment explanation
Indices: 39410770--39411698 Score: 253
Period size: 50 Copynumber: 18.5 Consensus size: 52
39410760 ACTTGGGAAG
* *
39410770 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCG-GG-GAAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * * * * * ** * ** *
39410820 TGAGATTCACCATCGTAGCTTTAATCTATTCCAATGT--ATCG-CCTGGA-AAG
1 TAAGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTTCAAT-GTCGAGGAGAAC
* * * *
39410870 TAAGATTCGTCGTTGTGGCTTCAATCTTTTGAATTGCAATGTC-AGG-GAAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * * * * **** * ** ** *
39410920 TGAGATTCGTCGTCGTAGCTTCAATCTGTTCTGCTGC-ATCAC-CTGAGAAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
*
39410970 TAAGATTCGCCGTTGTGGCTTTAATCTTTTAAATTTCAATGTCGAGGAGAAC
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* *
39411022 TAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGA-AGC
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * * *** * ** * *
39411073 -AAGATTCACCGTTGTAGCTTCAATCTATTCTGTTGCACCGCCTG-GG-G-AG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTC-GAGGAGAAC
* * * * * * *
39411122 TAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTACATTATCG-GG-GAAGC
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAA-C
* * **** * ** ** *
39411173 -AAGATTCACCGTTGTAGCTTCAAT-TTGTTTCGCTGCACCG-CCTGG-GAAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTT-TTAAATTTCAATGTCGAGGAGAAC
** * * *
39411222 TAAGATTCATCGTTGTGGCTTCAATCTTTTGAATTACAATGTCG-GG-GAAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * * **** * ** *
39411272 TGAA-ATTCGCCGTCGTAGCTTCAATCTGTTCCGCTACACCACCT-G-GGA-AAG
1 T-AAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCA--ATGTCGAGGAGAAC
* *
39411323 TAAGATTCGCCGTTGTGGGC-TCAATCTTTT-AATTGCAATGTC--GGAGAAA
1 TAAGATTCGCCGTTGT-GGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * * * * ** * * ** * *
39411372 TGAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCGCCTG-GGA-AAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTC-GAGGAGAAC
* *
39411423 TAAGATTCGCCGTTGTGGCTTCAATCTTTT-AATTGCAATGTCGAGGA-AGC
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * * ** * ** * *
39411473 -GAGATTCGCCGTTGTAGCTTCAATCTGTTCCA-CT-ATACCTCTTAGGA-AAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCA-ATGTC-GAGGAGAAC
* * *
39411523 TAAGATCCGCCGTTGTGGCTTCAATCTTTT-AATTGCAATGAC-AGG-GAAAC
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAG-AAC
* * * ** * * * *
39411573 -GAGATTCGCCGTTGTAGCTTCAATCTGTTCCATTGCACTGCCTG-GGA-AAG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTC-GAGGAGAAC
* * *
39411623 TAAGATTCGCCGTTGTAGCTTTAATCTTTT-AATTACAATGTCGAGGA-AAC
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
* * *
39411673 -GAGATTCACCGTTGTAGCTTCAATCT
1 TAAGATTCGCCGTTGTGGCTTCAATCT
39411699 GTTCCACTGC
Statistics
Matches: 644, Mismatches: 187, Indels: 97
0.69 0.20 0.10
Matches are distributed among these distances:
48 8 0.01
49 125 0.19
50 324 0.50
51 128 0.20
52 59 0.09
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (52 bp):
TAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAGAAC
Found at i:39411071 original size:152 final size:152
Alignment explanation
Indices: 39410870--39411156 Score: 414
Period size: 152 Copynumber: 1.9 Consensus size: 152
39410860 GCCTGGAAAG
* ** **
39410870 TAAGATTCGTCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCAGGGAAGTGAGATTCGTCGTCG
1 TAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCAAGATTCACCGTCG
* * *
39410935 TAGCTTCAATCTGTTCTGCTGCATCACCTGAGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTT
66 TAGCTTCAATCTATTCTGCTGCACCACCTGAGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTT
39411000 AAATTTCAATGTCGAGGAGAAC
131 AAATTTCAATGTCGAGGAGAAC
* *
39411022 TAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTTCAATGTC-GAGGAAGCAAGATTCACCGTT
1 TAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAG-GGAAGCAAGATTCACCGTC
* * * * *
39411086 GTAGCTTCAATCTATTCTGTTGCACCGCCTGGGGAGTAAGATTCGCTGTTGTAGCTTTAATCTTT
65 GTAGCTTCAATCTATTCTGCTGCACCACCTGAGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTT
*
39411151 TTAATT
130 TAAATT
39411157 ACATTATCGG
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
151 1 0.01
152 117 0.99
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (152 bp):
TAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCAAGATTCACCGTCG
TAGCTTCAATCTATTCTGCTGCACCACCTGAGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTT
AAATTTCAATGTCGAGGAGAAC
Found at i:39411150 original size:100 final size:100
Alignment explanation
Indices: 39411022--39411954 Score: 1203
Period size: 100 Copynumber: 9.3 Consensus size: 100
39411012 CGAGGAGAAC
* * *
39411022 TAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTTCAATGTCGAGGAAGCAAGATTCACCGTTG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTT-AATTACAATGTCGAGGAAGCGAGATTCACCGTTG
* *** *
39411087 TAGCTTCAATCTATTCTGTTGCACCGCCTGGG-GAG
65 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
* * * * * * *
39411122 TAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTACATTATCGGGGAAGCAAGATTCACCGTTG
1 TAAGATTCGCCGTTGTGGCTTCAATC-TTTTAATTACAATGTCGAGGAAGCGAGATTCACCGTTG
* * *
39411187 TAGCTTCAATTTGTTTCGCTGCACCGCCTGGG-AAG
65 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
** * * * * *
39411222 TAAGATTCATCGTTGTGGCTTCAATCTTTTGAATTACAATGTCGGGGAAGTGAAATTCGCCGTCG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTT-AATTACAATGTCGAGGAAGCGAGATTCACCGTTG
* * *
39411287 TAGCTTCAATCTGTTCCGCTACACCACCTGGGAAAG
65 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
* ** *
39411323 TAAGATTCGCCGTTGTGGGC-TCAATCTTTTAATTGCAATGTCG-GAGAAATGAGATTCACCATT
1 TAAGATTCGCCGTTGT-GGCTTCAATCTTTTAATTACAATGTCGAG-GAAGCGAGATTCACCGTT
39411386 GTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
64 GTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
* *
39411423 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGT
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTACAATGTCGAGGAAGCGAGATTCACCGTTGT
** * * *
39411488 AGCTTCAATCTGTTCCACTATACCTCTTAGGAAAG
66 AGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
* * * * *
39411523 TAAGATCCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGAC-AGGGAAACGAGATTCGCCGTTG
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTACAATGTCGA-GGAAGCGAGATTCACCGTTG
* *
39411587 TAGCTTCAATCTGTTCCATTGCACTGCCTGGGAAAG
65 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
* * *
39411623 TAAGATTCGCCGTTGTAGCTTTAATCTTTTAATTACAATGTCGAGGAAACGAGATTCACCGTTGT
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTACAATGTCGAGGAAGCGAGATTCACCGTTGT
39411688 AGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
66 AGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
* ** * *
39411723 TAAGATCCGCTATTGTGGCTTCAATCTTTTAATTGCAATGTCGAGGAAGCGAGATTTACCGTTGT
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTACAATGTCGAGGAAGCGAGATTCACCGTTGT
*
39411788 AGCTTCAATTTGTTCCACTGCACCGCCTGGGAAAG
66 AGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
** * * * *
39411823 TAAGA-TCTATCATTGTGGCTTCAATCTTTTAATTACAATGTCGGGGAAACGAGATTCACCATTG
1 TAAGATTC-GCCGTTGTGGCTTCAATCTTTTAATTACAATGTCGAGGAAGCGAGATTCACCGTTG
39411887 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
65 TAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
*
39411923 TAAGATTCGCCATTGTGGCTTCAATCTTTTAA
1 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAA
39411955 ATTGCAAACT
Statistics
Matches: 733, Mismatches: 89, Indels: 22
0.87 0.11 0.03
Matches are distributed among these distances:
99 10 0.01
100 685 0.93
101 35 0.05
102 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (100 bp):
TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTACAATGTCGAGGAAGCGAGATTCACCGTTGT
AGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAG
Found at i:39413283 original size:16 final size:18
Alignment explanation
Indices: 39413254--39413290 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
39413244 TGGCCTCTCA
39413254 TTTTCTCTC-TTTTTTCT
1 TTTTCTCTCATTTTTTCT
39413271 TTTTCT-TCATTTTTTCT
1 TTTTCTCTCATTTTTTCT
39413288 TTT
1 TTT
39413291 CTTTTCTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTCTCATTTTTTCT
Found at i:39416846 original size:2 final size:2
Alignment explanation
Indices: 39416839--39416892 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
39416829 ACCGTATAAA
*
39416839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
39416881 AT AT AC AT AT AT
1 AT AT AT AT AT AT
39416893 TCGTGAGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:39417027 original size:3 final size:3
Alignment explanation
Indices: 39417019--39417103 Score: 79
Period size: 3 Copynumber: 29.0 Consensus size: 3
39417009 AAATTATCGT
*
39417019 ATA ATA AT- ATG ATAA ATA A-A ATA ATA AT- ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
39417061 ATA AAA ATG ATA AGA ATA ATA ATA ATA ATA ATGA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
39417104 TATTACAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
2 8 0.12
3 54 0.81
4 5 0.07
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:39417057 original size:31 final size:32
Alignment explanation
Indices: 39417019--39417090 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
39417009 AAATTATCGT
* *
39417019 ATAATAATATGATAAATAA-AATAATAAT-ATA
1 ATAATAATATAATAAA-AATAATAAGAATAATA
*
39417050 ATAATAATATAATAAAAATGATAAGAATAATA
1 ATAATAATATAATAAAAATAATAAGAATAATA
39417082 ATAATAATA
1 ATAATAATA
39417091 ATGAATGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 22 0.61
32 12 0.33
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (32 bp):
ATAATAATATAATAAAAATAATAAGAATAATA
Found at i:39418190 original size:20 final size:20
Alignment explanation
Indices: 39418162--39418204 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
39418152 GCTGAAAATG
*
39418162 GGTTGGGGTGTTTTGGGC-TA
1 GGTTGGGGT-ATTTGGGCTTA
*
39418182 GGTTTGGGTATTTGGGCTTA
1 GGTTGGGGTATTTGGGCTTA
39418202 GGT
1 GGT
39418205 AGGTTATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.07, C:0.05, G:0.47, T:0.42
Consensus pattern (20 bp):
GGTTGGGGTATTTGGGCTTA
Found at i:39422355 original size:19 final size:19
Alignment explanation
Indices: 39422333--39422379 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
39422323 TATTAAATAT
39422333 ATATATTATTTTTAATCAA
1 ATATATTATTTTTAATCAA
*
39422352 ATATA--CTTTTTAATCAA
1 ATATATTATTTTTAATCAA
39422369 ATATATATATT
1 ATATAT-TATT
39422380 AAATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 16 0.70
19 5 0.22
20 2 0.09
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTATTTTTAATCAA
Found at i:39422361 original size:17 final size:17
Alignment explanation
Indices: 39422341--39422373 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39422331 ATATATATTA
39422341 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
39422358 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
39422374 TATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:39422389 original size:17 final size:18
Alignment explanation
Indices: 39422319--39422389 Score: 51
Period size: 17 Copynumber: 4.1 Consensus size: 18
39422309 CGACCCTAAT
39422319 TATATATTAAAT-ATATA
1 TATATATTAAATCATATA
* *
39422336 TATTATTTTTAATCA-A-A
1 TA-TATATTAAATCATATA
* * *
39422353 TATACTTTTTAATCAAATA
1 TATA-TATTAAATCATATA
39422372 TATATATTAAAT-ATATA
1 TATATATTAAATCATATA
39422389 T
1 T
39422390 TTTGGTGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 2 0.05
17 20 0.45
18 16 0.36
19 6 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATATTAAATCATATA
Found at i:39428412 original size:22 final size:21
Alignment explanation
Indices: 39428371--39428411 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
39428361 AATTTTTTAA
*
39428371 TTTAAAAATTCTAAAAATTAT
1 TTTAAAAAATCTAAAAATTAT
39428392 TTTAAAAAAT-T-AAAATTAT
1 TTTAAAAAATCTAAAAATTAT
39428411 T
1 T
39428412 AAAAATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 1 0.05
21 9 0.47
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAAAAATCTAAAAATTAT
Found at i:39428737 original size:36 final size:38
Alignment explanation
Indices: 39428637--39428737 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 38
39428627 CATTTAATTA
* *
39428637 ATTTTTAAAATTTAAAAAAATTAA-AAACTATAAAAACT
1 ATTTTTAAAA-ATAAAAAAATTAATTAACTATAAAAACT
* * * *
39428675 ATTTTTAAAAAT-TAGAAATTATATTAATTAT-GAAA-T
1 ATTTTTAAAAATAAAAAAATTA-ATTAACTATAAAAACT
39428711 ATTTTTAAAAATAAAAAAATTAATTAA
1 ATTTTTAAAAATAAAAAAATTAATTAA
39428738 ATGTTGATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
36 25 0.48
37 12 0.23
38 15 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (38 bp):
ATTTTTAAAAATAAAAAAATTAATTAACTATAAAAACT
Found at i:39429405 original size:9 final size:9
Alignment explanation
Indices: 39429393--39429439 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
39429383 TTTTCAGGTG
*
39429393 ATTCGGTTA
1 ATTCGGGTA
*
39429402 ATTCGGTTA
1 ATTCGGGTA
39429411 A-TCGGGTA
1 ATTCGGGTA
39429419 ATTCGGGTA
1 ATTCGGGTA
*
39429428 ATTTGGGTA
1 ATTCGGGTA
39429437 ATT
1 ATT
39429440 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 7 0.20
9 28 0.80
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (9 bp):
ATTCGGGTA
Found at i:39429420 original size:17 final size:18
Alignment explanation
Indices: 39429393--39429439 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
39429383 TTTTCAGGTG
* *
39429393 ATTCGGTTAATTCGGTTA
1 ATTCGGGTAATTCGGGTA
39429411 A-TCGGGTAATTCGGGTA
1 ATTCGGGTAATTCGGGTA
*
39429428 ATTTGGGTAATT
1 ATTCGGGTAATT
39429440 TTTAACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (18 bp):
ATTCGGGTAATTCGGGTA
Found at i:39440282 original size:42 final size:42
Alignment explanation
Indices: 39440218--39440305 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
39440208 CCTGGTTATA
**
39440218 GCACAAAACCACAGCCAGAAGAGGAAGGGAAGCCTGAGTATG
1 GCACAAAACCACAGCCAGAAGAGGAAGAAAAGCCTGAGTATG
* *
39440260 GCACTAAACCAGAGCCAGAAGAGGAAGAAAAGCCTGAGTATG
1 GCACAAAACCACAGCCAGAAGAGGAAGAAAAGCCTGAGTATG
39440302 GCAC
1 GCAC
39440306 CAAGCAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.41, C:0.22, G:0.30, T:0.08
Consensus pattern (42 bp):
GCACAAAACCACAGCCAGAAGAGGAAGAAAAGCCTGAGTATG
Found at i:39440379 original size:165 final size:165
Alignment explanation
Indices: 39440105--39440611 Score: 960
Period size: 165 Copynumber: 3.1 Consensus size: 165
39440095 TCAACCAACA
39440105 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
1 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
*
39440170 AAGACAAGGAGAAGGCAATGCCTGACGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
66 AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
39440235 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
131 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
* *
39440270 AGAGCCAGAAGAGGAAGAAAAGCCTGAGTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
1 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
39440335 AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
66 AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
39440400 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
131 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
39440435 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
1 ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
* *
39440500 AAGACAAGGAGAAGGCAATGCCTGAGGAGTCAGAGAAGCCTGGTTATAGCACAAAACCACAGCCA
66 AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
*
39440565 GAAGAGGAAGGGAAGCCTGAGTATGGTACTAAACC
131 GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
39440600 ACAGCCAGAAGA
1 ACAGCCAGAAGA
39440612 CAAGGAAAAG
Statistics
Matches: 334, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 334 1.00
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.12
Consensus pattern (165 bp):
ACAGCCAGAAGAGGAAGAAAAGCCTGATTATGGCACCAAGCAAAATTTCTATAAACCAGAGCTAG
AAGACAAGGAGAAGGCAATGCCTGAAGAGTCAGAGAAACCTGGTTATAGCACAAAACCACAGCCA
GAAGAGGAAGGGAAGCCTGAGTATGGCACTAAACC
Found at i:39440405 original size:42 final size:42
Alignment explanation
Indices: 39440366--39440470 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
39440356 CTGAAGAGTC
39440366 AGAGAAACCTG-GTTATAGCACAAAACCACAGCCAGAAGAGGA
1 AGAGAAACCTGAG-TATAGCACAAAACCACAGCCAGAAGAGGA
* * * *
39440408 AGGGAAGCCTGAGTATGGCACTAAACCACAGCCAGAAGAGGA
1 AGAGAAACCTGAGTATAGCACAAAACCACAGCCAGAAGAGGA
* *
39440450 AGA-AAAGCCTGATTATGGCAC
1 AGAGAAA-CCTGAGTATAGCAC
39440471 CAAGCAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.94
43 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.11
Consensus pattern (42 bp):
AGAGAAACCTGAGTATAGCACAAAACCACAGCCAGAAGAGGA
Found at i:39450771 original size:25 final size:25
Alignment explanation
Indices: 39450743--39450791 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39450733 TGTGGCATAT
* *
39450743 TATCTATAAAGCCTTTGTGGTGAAC
1 TATCTATAAAACCCTTGTGGTGAAC
*
39450768 TATCTGTAAAACCCTTGTGGTGAA
1 TATCTATAAAACCCTTGTGGTGAA
39450792 TTCTCTGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (25 bp):
TATCTATAAAACCCTTGTGGTGAAC
Found at i:39453854 original size:50 final size:48
Alignment explanation
Indices: 39453764--39453865 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
39453754 TGTCAAAAGC
* **
39453764 ATATATTTATACTTATCAACCACATGTGTCGAATGCACACATATATAT
1 ATATATATATACTTATCAACCACACATGTCGAATGCACACATATATAT
* * *
39453812 ATATATATATACTTAT-AATCCACACATGTCGAATGCATACACATATTT
1 ATATATATATACTTATCAA-CCACACATGTCGAATGCACACATATATAT
39453860 ATATAT
1 ATATAT
39453866 CCAACAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (48 bp):
ATATATATATACTTATCAACCACACATGTCGAATGCACACATATATAT
Found at i:39454086 original size:41 final size:41
Alignment explanation
Indices: 39454041--39454149 Score: 191
Period size: 41 Copynumber: 2.7 Consensus size: 41
39454031 ATTCACCAGA
39454041 ACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGC
1 ACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGC
* *
39454082 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGC
1 ACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGC
*
39454123 ACTTAGCCTGCTAGGCTTTAAGCCTGA
1 ACTTAGCCTGCTAGGCTTAAAGCCTGA
39454150 ATTGATTCAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (41 bp):
ACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGC
Found at i:39454159 original size:41 final size:40
Alignment explanation
Indices: 39454030--39454179 Score: 171
Period size: 41 Copynumber: 3.7 Consensus size: 40
39454020 AGCATAAACA
* * *
39454030 GATTCACCAGAACTTAGCCTGCTAGGCTTAAAGCCTGATT
1 GATTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
39454070 CAGA-TCACCGGCACTTAGCCTGCTAGGC-TTATAGCCTGATT
1 --GATTCACCGGCACTTAGCCTGCTAGGCTTTA-AGCCTGATT
*
39454111 CAGTTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGAATT
1 GA-TTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTG-ATT
* *
39454153 GATTCACTGGCAATATA-CCTGCTAGGC
1 GATTCACCGGCACT-TAGCCTGCTAGGC
39454180 GCTGAGCCTG
Statistics
Matches: 95, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 81 0.85
42 11 0.12
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
GATTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
Found at i:39454188 original size:82 final size:81
Alignment explanation
Indices: 39454032--39454190 Score: 189
Period size: 82 Copynumber: 1.9 Consensus size: 81
39454022 CATAAACAGA
*
39454032 TTCACCAGAACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 TTCACCAGAACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCACCGGCAATTAGCCTGCTAGG
* *
39454097 CTTATAGCCTGATTCAG
65 CCTAGAGCCTGATTCAG
* * * *
39454114 TTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGAATT-GATTCACTGGCAATATA-CCTGCTA
1 TTCACCAGAACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TCACCGGCAAT-TAGCCTGCTA
39454177 GGCGCT-GAGCCTGA
63 GGC-CTAGAGCCTGA
39454191 ATACTCAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
81 2 0.03
82 58 0.88
83 6 0.09
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (81 bp):
TTCACCAGAACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCACCGGCAATTAGCCTGCTAGGC
CTAGAGCCTGATTCAG
Found at i:39456517 original size:15 final size:15
Alignment explanation
Indices: 39456458--39456511 Score: 108
Period size: 15 Copynumber: 3.6 Consensus size: 15
39456448 ATAGACTTAC
39456458 CTCGAACAGTGAAAA
1 CTCGAACAGTGAAAA
39456473 CTCGAACAGTGAAAA
1 CTCGAACAGTGAAAA
39456488 CTCGAACAGTGAAAA
1 CTCGAACAGTGAAAA
39456503 CTCGAACAG
1 CTCGAACAG
39456512 CAAAAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.13
Consensus pattern (15 bp):
CTCGAACAGTGAAAA
Found at i:39467497 original size:1 final size:1
Alignment explanation
Indices: 39467491--39467568 Score: 57
Period size: 1 Copynumber: 78.0 Consensus size: 1
39467481 TTCTGTTGAG
* * * * * * * * * *
39467491 AAAAAAACAAAAATACAAAAAAAAACAAAAAAACAAAAAAAGAAAACAAGAAAATAAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
39467556 AAAAACAAAAAAA
1 AAAAAAAAAAAAA
39467569 CCTCTACCGG
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.04
Consensus pattern (1 bp):
A
Found at i:39467568 original size:8 final size:8
Alignment explanation
Indices: 39467491--39467569 Score: 74
Period size: 8 Copynumber: 10.0 Consensus size: 8
39467481 TTCTGTTGAG
39467491 AAAAAAAC
1 AAAAAAAC
*
39467499 AAAAATAC
1 AAAAAAAC
39467507 AAAAAAA-
1 AAAAAAAC
39467514 AACAAAAA-
1 AA-AAAAAC
39467522 AACAAAAA-
1 AA-AAAAAC
*
39467530 AAGAAAAC
1 AAAAAAAC
* *
39467538 AAGAAAAT
1 AAAAAAAC
*
39467546 AAAAAAAT
1 AAAAAAAC
39467554 AAAAAAAC
1 AAAAAAAC
39467562 AAAAAAAC
1 AAAAAAAC
39467570 CTCTACCGGG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
7 6 0.10
8 57 0.90
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.04
Consensus pattern (8 bp):
AAAAAAAC
Found at i:39468026 original size:15 final size:16
Alignment explanation
Indices: 39468001--39468041 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
39467991 TACTTCACTT
39468001 GAAAAAGAAACGAAAA-
1 GAAAAAGAAAC-AAAAC
39468017 GAAAAA-AAACAAAAC
1 GAAAAAGAAACAAAAC
39468032 GAAAAAGAAA
1 GAAAAAGAAA
39468042 AAGAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.17
15 10 0.43
16 9 0.39
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (16 bp):
GAAAAAGAAACAAAAC
Found at i:39469027 original size:45 final size:45
Alignment explanation
Indices: 39468962--39469212 Score: 323
Period size: 45 Copynumber: 5.6 Consensus size: 45
39468952 TGAAGTCATC
39468962 ATAGCA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
* *
39469007 GTAGCAGATCTTGTCTTCCTGTATTAGCAGCGAAGTAGA-TCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAG
*
39469052 ATAGCA-AGTCTTGTGTTCCTGTATTGGCAGCGAAGTAGACTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
* * *
39469097 ATAACTGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGA-TCGAAG
1 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAG
*
39469142 ATAGTA-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
1 ATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
* ** *
39469187 ATAACAGATCTTACCTTCATGTATTG
1 ATAGCAGATCTTGTCTTCCTGTATTG
39469213 ATGGCGAAGC
Statistics
Matches: 179, Mismatches: 18, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
44 4 0.02
45 170 0.95
46 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (45 bp):
ATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
Found at i:39469115 original size:90 final size:89
Alignment explanation
Indices: 39468962--39469232 Score: 409
Period size: 90 Copynumber: 3.0 Consensus size: 89
39468952 TGAAGTCATC
* *
39468962 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGGTAGCAGATCTTGTCTTCCT
1 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAGATCTTGTCTTCCT
39469027 GTATTAGCAGCGAAGTAGATCGAAG
66 GTATT-GCAGCGAAGTAGATCGAAG
* *
39469052 ATAGCAAGTCTTGTGTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACTGATCTTGTCTTCCT
1 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAGATCTTGTCTTCCT
*
39469117 GTATTGGCAGAGAAGTAGATCGAAG
66 GTATT-GCAGCGAAGTAGATCGAAG
* ** *
39469142 ATAGTAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAGATCTTACCTTCAT
1 ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAGATCTTGTCTTCCT
*
39469207 GTATTG-ATGGCGAAGCAGATCGAAG
66 GTATTGCA--GCGAAGTAGATCGAAG
39469232 A
1 A
39469233 CACCATAGTT
Statistics
Matches: 165, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
88 1 0.01
89 1 0.01
90 163 0.99
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (89 bp):
ATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAGATCTTGTCTTCCT
GTATTGCAGCGAAGTAGATCGAAG
Found at i:39469413 original size:99 final size:99
Alignment explanation
Indices: 39469253--39469845 Score: 619
Period size: 99 Copynumber: 6.0 Consensus size: 99
39469243 TGCAGCAAAG
** * * *
39469253 AAGATTGAAGCCGCAACGACGAATCTTAC-CTCTCTGGCAGTGCAGTGGAACAGATTGAAGCTAC
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTTC-CTGGGA-TGCAGTGGAACAGATTAAAGCTAC
39469317 AACGGCGAATC-TCGTTCCCCGACATTGCAATTTAA
64 AACGGCGAATCTTCGTTCCCCGACATTGCAATTTAA
* * ** *
39469352 AAGATTGAAGCCGCAACGGTGAATTTTACTTTCCTGGTGATACAGTGGATTAGATTGAAGCTACA
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGG-GATGCAGTGGAACAGATTAAAGCTACA
*
39469417 ACGGTGAATC-TCGTTCCCCGACATTGCAATTTAA
65 ACGGCGAATCTTCGTTCCCCGACATTGCAATTTAA
* * * * * * *
39469451 AATATTGAAGCCGCAATGGCGAATCTTACTTTCCTGGTGGTGCAGTGGAGCAAATTAAAGCTACG
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGG-GATGCAGTGGAACAGATTAAAGCTACA
*
39469516 ACGGCGAATCTTTC-TTCCCCGACATTGCAATTAAA
65 ACGGCGAATC-TTCGTTCCCCGACATTGCAATTTAA
* * *
39469551 AATATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGAAGCTACA
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGG-GATGCAGTGGAACAGATTAAAGCTACA
*
39469616 ACGGCGAATCTT-ATTCCCCGACATTGCAA-TTAA
65 ACGGCGAATCTTCGTTCCCCGACATTGCAATTTAA
** * * * * * * *
39469649 AAGGATTGAAGCAACAACGGCGAATCTCACTTCCCTGGCAGTACAATGGAGCAGATTAAAGCTAC
1 AA-GATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGGA-TGCAGTGGAACAGATTAAAGCTAC
* * * ** *
39469714 GATGGTGAATCTTAC-TTCCCTAATATTGCAATTTAA
64 AACGGCGAATCTT-CGTTCCCCGACATTGCAATTTAA
* *
39469750 AAGATTGAAGCCGCAACGGTGAATCTTAC-TTCCTTGGCAGTGCAGTGGAATAGATTAAAGCTAC
1 AAGATTGAAGCCGCAACGGTGAATCTTACTTTCC-TGGGA-TGCAGTGGAACAGATTAAAGCTAC
* * * * *
39469814 GACTGCGAATCGT-GTTCCCTGACATTGTAATT
64 AACGGCGAATCTTCGTTCCCCGACATTGCAATT
39469846 GAGGTCGTAA
Statistics
Matches: 418, Mismatches: 64, Indels: 24
0.83 0.13 0.05
Matches are distributed among these distances:
98 6 0.01
99 243 0.58
100 161 0.39
101 8 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (99 bp):
AAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGGATGCAGTGGAACAGATTAAAGCTACAA
CGGCGAATCTTCGTTCCCCGACATTGCAATTTAA
Found at i:39469575 original size:50 final size:50
Alignment explanation
Indices: 39469253--39469845 Score: 259
Period size: 50 Copynumber: 11.9 Consensus size: 50
39469243 TGCAGCAAAG
** * * * * * * **
39469253 AAGATTGAAGCCGCAACGACGAATCTTACCTCTCTGGCAGTGCAGTGGAA
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
* * *
39469303 CAGATTGAAGCTACAACGGCGAATC-T-CGTTCCCCGACATTGCAATTTAA
1 AAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCTGACATTGCAATTAAA
** * * * ** * * ** *
39469352 AAGATTGAAGCCGCAACGGTGAATTTTACTTTCCTGGTGA-TACAGTGGAT
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GACATTGCAATTAAA
* * * *
39469402 TAGATTGAAGCTACAACGGTGAATC-T-CGTTCCCCGACATTGCAATTTAA
1 AAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCTGACATTGCAATTAAA
* ** * * **** * * **
39469451 AATATTGAAGCCGCAATGGCGAATCTTACTTTCCTGGTGGTGCAGTGGAGC
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAAT-TAAA
* * * *
39469502 AA-ATTAAAGCTACGACGGCGAATCTTTCTTCCCCGACATTGCAATTAAA
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
* ** * * * * ** *
39469551 AATATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGA-TGCAGTGGAT
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGAC-ATTGCAATTAAA
* *
39469601 CAGATTGAAGCTACAACGGCGAATCTTA-TTCCCCGACATTGCAATTAAA
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
* * * * * * ** *
39469650 AGGATTGAAGCAACAACGGCGAATCTCACTTCCCTGGCAGTACAATGGAG
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
* * * * * * * *
39469700 CAGATTAAAGCTACGATGGTGAATCTTACTTCCCTAATATTGCAATTTAA
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
** * * * * * **
39469750 AAGATTGAAGCCGCAACGGTGAATCTTACTTCCTTGGCAGTGCAGTGGAA
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
* * * * * * *
39469800 TAGATTAAAGCTACGACTGCGAATCGT-GTTCCCTGACATTGTAATT
1 AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATT
39469846 GAGGTCGTAA
Statistics
Matches: 377, Mismatches: 153, Indels: 27
0.68 0.27 0.05
Matches are distributed among these distances:
48 5 0.01
49 114 0.30
50 251 0.67
51 7 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (50 bp):
AAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCAATTAAA
Found at i:39469599 original size:199 final size:199
Alignment explanation
Indices: 39469255--39469845 Score: 746
Period size: 199 Copynumber: 3.0 Consensus size: 199
39469245 CAGCAAAGAA
* * * * *
39469255 GATTGAAGCCGCAACGACGAATCTTAC-CTCTCTGGCAGTGCAGTGGAACAGATTGAAGCTACAA
1 GATTGAAGCCGCAACGGCGAATCTTACTTTC-CTGGCAGTGCAGTGGAGCAGATTAAAGCTACGA
*
39469319 CGGCGAATC--TCGTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGTGAATTTTACT
65 CGGCGAATCTTTC-TTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGTGAATCTTACT
* * *
39469382 TTCCTGGTGATACAGTGGATTAGATTGAAGCTACAACGGTGAATCTCGTTCCCCGACATTGCAAT
129 TTCCTGGCGATGCAGTGGATTAGATTGAAGCTACAACGGCGAATCT-GTTCCCCGACATTGCAAT
39469447 TTAAAA-
193 TTAAAAG
* * ** *
39469453 TATTGAAGCCGCAATGGCGAATCTTACTTTCCTGGTGGTGCAGTGGAGCAAATTAAAGCTACGAC
1 GATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGAC
* *
39469518 GGCGAATCTTTCTTCCCCGACATTGCAATTAAAAATATTGAAGCCGCAACGGTGAATCTTACTTT
66 GGCGAATCTTTCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGTGAATCTTACTTT
* *
39469583 CCTGGCGATGCAGTGGATCAGATTGAAGCTACAACGGCGAATCTTATTCCCCGACATTGCAA-TT
131 CCTGGCGATGCAGTGGATTAGATTGAAGCTACAACGGCGAATC-TGTTCCCCGACATTGCAATTT
39469647 AAAAG
195 AAAAG
** * * * * *
39469652 GATTGAAGCAACAACGGCGAATCTCACTTCCCTGGCAGTACAATGGAGCAGATTAAAGCTACGAT
1 GATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGAC
* * ** *
39469717 GGTGAATCTTACTTCCCTAATATTGCAATTTAAAAGATTGAAGCCGCAACGGTGAATCTTAC-TT
66 GGCGAATCTTTCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGTGAATCTTACTTT
* * * * * *
39469781 CCTTGGC-AGTGCAGTGGAATAGATTAAAGCTACGACTGCGAATCGTGTTCCCTGACATTGTAAT
131 CC-TGGCGA-TGCAGTGGATTAGATTGAAGCTACAACGGCGAATC-TGTTCCCCGACATTGCAAT
39469845 T
193 T
39469846 GAGGTCGTAA
Statistics
Matches: 339, Mismatches: 46, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
198 71 0.21
199 264 0.78
200 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (199 bp):
GATTGAAGCCGCAACGGCGAATCTTACTTTCCTGGCAGTGCAGTGGAGCAGATTAAAGCTACGAC
GGCGAATCTTTCTTCCCCGACATTGCAATTTAAAAGATTGAAGCCGCAACGGTGAATCTTACTTT
CCTGGCGATGCAGTGGATTAGATTGAAGCTACAACGGCGAATCTGTTCCCCGACATTGCAATTTA
AAAG
Found at i:39469929 original size:44 final size:43
Alignment explanation
Indices: 39469861--39470078 Score: 172
Period size: 44 Copynumber: 5.0 Consensus size: 43
39469851 CGTAATGGCG
* * *
39469861 AATCATATCTCACTGAAGTTGCAGTGGAGCGGATTAAAACCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC
* * * * * * *
39469904 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGA-TCACATC-T
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC
* * * * *
39469946 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC
* * ** *
39469989 TAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAAC-C
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AACCAC
* * *
39470034 AATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC
39470077 AA
1 AA
39470079 ATCTCGTCCC
Statistics
Matches: 134, Mismatches: 34, Indels: 14
0.74 0.19 0.08
Matches are distributed among these distances:
41 28 0.21
42 6 0.04
43 10 0.07
44 87 0.65
45 2 0.01
46 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAC
Found at i:39469967 original size:85 final size:85
Alignment explanation
Indices: 39469861--39470078 Score: 233
Period size: 85 Copynumber: 2.5 Consensus size: 85
39469851 CGTAATGGCG
* * *
39469861 AATCATATCTCACTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA-ATCTTATCTCCCTGAAGTTG
* * *
39469926 CAGTAGAGTAGATC-A-CATCT
65 CAGTAGAGTAGA-CAAGAAACC
* * * * * * * *
39469946 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAC-AATCTTATCTCCCTGAAGTTG
*
39470011 CAGTGGAGTAGACAGAAGAAACC
65 CAGTAGAGTAGAC--AAGAAACC
*
39470034 AATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCACAA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAA
39470079 ATCTCGTCCC
Statistics
Matches: 106, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
84 1 0.01
85 64 0.60
86 1 0.01
87 3 0.03
88 37 0.35
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (85 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAATCTTATCTCCCTGAAGTTGC
AGTAGAGTAGACAAGAAACC
Found at i:39475229 original size:28 final size:29
Alignment explanation
Indices: 39475127--39475234 Score: 94
Period size: 30 Copynumber: 3.7 Consensus size: 29
39475117 CATACAAAAT
* * * *
39475127 CAGTCTGGGCCTGAGCCCTATACAGTA-G
1 CAGTGTGGGCCTTAGCCCAATACAGTATA
** *
39475155 CAGTGTGTGGGCCAAAGCCCAATACATTATTA
1 CA--GTGTGGGCCTTAGCCCAATACAGTA-TA
*
39475187 GAGTGTGGGCCTTAGCCCAATACAGTA-A
1 CAGTGTGGGCCTTAGCCCAATACAGTATA
*
39475215 CAGTGTGGGCGTTAGCCCAA
1 CAGTGTGGGCCTTAGCCCAA
39475235 AATAGTAATC
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 21 0.33
30 42 0.66
32 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (29 bp):
CAGTGTGGGCCTTAGCCCAATACAGTATA
Found at i:39475241 original size:28 final size:29
Alignment explanation
Indices: 39475188--39475247 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
39475178 ACATTATTAG
*
39475188 AGTGTGGGCCTTAGCCCAATACAGTAA-C
1 AGTGTGGGCCTTAGCCCAAAACAGTAATC
* *
39475216 AGTGTGGGCGTTAGCCCAAAATAGTAATC
1 AGTGTGGGCCTTAGCCCAAAACAGTAATC
39475245 AGT
1 AGT
39475248 ACAAATGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (29 bp):
AGTGTGGGCCTTAGCCCAAAACAGTAATC
Found at i:39475385 original size:26 final size:26
Alignment explanation
Indices: 39475355--39475456 Score: 143
Period size: 26 Copynumber: 3.9 Consensus size: 26
39475345 CATCAATATT
39475355 GCAGCAAAGCTGCCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAGTAAC
*
39475381 ACAGCAAAGCTGCCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAGTAAC
* * *
39475407 GTAGCAGAGCTGCCAGT-ATCAGTATC
1 GCAGCAAAGCTGCCAGTAAT-AGTAAC
*
39475433 GCAGCAAAGCTGCCAGTAACAGTA
1 GCAGCAAAGCTGCCAGTAATAGTA
39475457 TTTGTGGCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
25 2 0.03
26 63 0.95
27 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTAAC
Found at i:39475481 original size:52 final size:52
Alignment explanation
Indices: 39475382--39475482 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
39475372 AATAGTAACA
* * * *
39475382 CAGCAAAGCTGCCAGTAATAGTAACGTAGCAGAGCTGCCAGTATCAGTATCG
1 CAGCAAAGCTGCCAGTAACAGTAACGTAGCAAAGCTACCAATATCAGTATCG
** *
39475434 CAGCAAAGCTGCCAGTAACAGTATTTGTGGCAAAGCTACCAAT-TCAGTA
1 CAGCAAAGCTGCCAGTAACAGTA-ACGTAGCAAAGCTACCAATATCAGTA
39475483 CATTTCCCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 28 0.68
53 13 0.32
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (52 bp):
CAGCAAAGCTGCCAGTAACAGTAACGTAGCAAAGCTACCAATATCAGTATCG
Found at i:39475724 original size:54 final size:54
Alignment explanation
Indices: 39475666--39476626 Score: 1026
Period size: 54 Copynumber: 17.9 Consensus size: 54
39475656 TATCCTATAG
* * * ** * * * *
39475666 GGGTATTTTGGTCATTCTACCTTTCAAAGGTGTTTCAGTAATTTTACCCATTGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * * *
39475720 GGGTATTTCAGTAATTTTACCCATCAAGGGTATTTTGGTCATTTTACCCTTCGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * *
39475774 GGGTATTTT-GATAATTTTACCCATCAAGGGTATTTTGATAATTTTACCCATCAA
1 GGGTATTTTAG-TAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * *
39475828 GGGTATTTTAGTCATTTTACCCTTTGC-A-GGTATTTCGATAATTTTACCCATCGA
1 GGGTATTTTAGTAATTTTACCC-AT-CAAGGGTATTTCGGTAATTTTACCCATCGA
** * * *
39475882 GGGTATTTCGGTAATTTTA-CCATCGATGGTATTTCGATAATTTTACCCATCGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * * * * *
39475935 GGGCATTTTAGT-ATTTTACCCATCGAGGGTATTTTGGTCATTTTACCCTTTGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * *
39475988 GGGTATTTT-GATAATTTTACCCATCAAGGGTATTTTGATAATTTTACCCATCAA
1 GGGTATTTTAG-TAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * *
39476042 GGGTATTTTAGTCATTTTACCCTTTGC-A-GGTATTTCGATAATTTTACCCATCGA
1 GGGTATTTTAGTAATTTTACCC-AT-CAAGGGTATTTCGGTAATTTTACCCATCGA
** * * *
39476096 GGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCGGTCATTTTACCCATCAA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * * *
39476150 GGGTATTTTAGTAATTTTACCTATCAGGGGTATTTCGGTCATTTTACCCTTCGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* ** * *
39476204 AGGTATTTTAGTAATTTTACCCATTGAGGGTATTTCGATCATTTTACCCATCGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * * * * * *
39476258 GGGCATTTTAGT-ATTTTACCCATCGAGGGTATTTTGGTCATTTTACCCTTTGG
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * *
39476311 GGGTATTTTAGTCATTTTACCCTTC-GGGGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * * *
39476364 TGGTATTTTAGTAATTTTACCCATCGAGGGTATTTAGGTAATTTTACCCTTC-A
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * *** * *
39476417 GGGGTATTTCAGTAATTTTACCCTTCAAGGGTATTTTAATAATTTTACCCTTCAA
1 -GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* ** * * * * *
39476472 GGGTATTTCAGTAATTTTACCTTTCAAAGGTATTTCGATAATTTTATCCTTCGG
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
* * * * *
39476526 GGGTATTTCAGTAATTTTACCCATCGATGGTATTTCGGTCATTCTACCCATCGA
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
39476580 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTAC
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTAC
39476627 GACCCAAACC
Statistics
Matches: 772, Mismatches: 117, Indels: 36
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.00
52 10 0.01
53 168 0.22
54 584 0.76
55 7 0.01
56 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGGTAATTTTACCCATCGA
Found at i:39475728 original size:27 final size:27
Alignment explanation
Indices: 39475698--39476626 Score: 877
Period size: 27 Copynumber: 34.6 Consensus size: 27
39475688 TTCAAAGGTG
*
39475698 TTTCAGTAATTTTACCCATTGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
*
39475725 TTTCAGTAATTTTACCCATCAAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
** * *
39475752 TTTTGGTCATTTTACCCTTCGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39475779 TTT-TGATAATTTTACCCATCAAGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
* *
39475806 TTT-TGATAATTTTACCCATCAAGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
* * * *
39475833 TTTTAGTCATTTTACCCTTTGCA-GGTA
1 TTTCAGTAATTTTACCCATCG-AGGGTA
39475860 TTTC-GATAATTTTACCCATCGAGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
* *
39475887 TTTCGGTAATTTTA-CCATCGATGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
*
39475913 TTTC-GATAATTTTACCCATCGAGGGCA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
*
39475940 TTTTAGT-ATTTTACCCATCGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
** * * *
39475966 TTTTGGTCATTTTACCCTTTGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39475993 TTT-TGATAATTTTACCCATCAAGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
* *
39476020 TTT-TGATAATTTTACCCATCAAGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
* * * *
39476047 TTTTAGTCATTTTACCCTTTGCA-GGTA
1 TTTCAGTAATTTTACCCATCG-AGGGTA
39476074 TTTC-GATAATTTTACCCATCGAGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
* * *
39476101 TTTCGGTCATTTTACCCATCAAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* * *
39476128 TTTCGGTCATTTTACCCATCAAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39476155 TTTTAGTAATTTTACCTATC-AGGGGTA
1 TTTCAGTAATTTTACCCATCGA-GGGTA
* * * *
39476182 TTTCGGTCATTTTACCCTTCGAAGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39476209 TTTTAGTAATTTTACCCATTGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39476236 TTTC-GATCATTTTACCCATCGAGGGCA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
*
39476263 TTTTAGT-ATTTTACCCATCGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
** * * * *
39476289 TTTTGGTCATTTTACCCTTTGGGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* * *
39476316 TTTTAGTCATTTTACCCTTCG-GGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39476342 TTTCGGTAATTTTACCCATCGATGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
*
39476369 TTTTAGTAATTTTACCCATCGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
*
39476396 TTT-AGGTAATTTTACCCTTC-AGGGGTA
1 TTTCA-GTAATTTTACCCATCGA-GGGTA
* *
39476423 TTTCAGTAATTTTACCCTTCAAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* * * *
39476450 TTTTAATAATTTTACCCTTCAAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
** * *
39476477 TTTCAGTAATTTTACCTTTCAAAGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* * *
39476504 TTTC-GATAATTTTATCCTTCGGGGGTA
1 TTTCAG-TAATTTTACCCATCGAGGGTA
*
39476531 TTTCAGTAATTTTACCCATCGATGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* * *
39476558 TTTCGGTCATTCTACCCATCGAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
* *
39476585 TTTTAGTAATTTTACCCATCAAGGGTA
1 TTTCAGTAATTTTACCCATCGAGGGTA
*
39476612 TTTCGGTAATTTTAC
1 TTTCAGTAATTTTAC
39476627 GACCCAAACC
Statistics
Matches: 767, Mismatches: 107, Indels: 56
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.00
26 104 0.14
27 650 0.85
28 12 0.02
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
TTTCAGTAATTTTACCCATCGAGGGTA
Found at i:39481480 original size:22 final size:22
Alignment explanation
Indices: 39481452--39481497 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39481442 AAAGGCAATC
*
39481452 TACAAATTAAATC-TCTTAAGAT
1 TACAAATCAAATCTTC-TAAGAT
39481474 TACAAATCAAATCTTCTAAGAT
1 TACAAATCAAATCTTCTAAGAT
39481496 TA
1 TA
39481498 TAGATCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (22 bp):
TACAAATCAAATCTTCTAAGAT
Found at i:39484169 original size:27 final size:27
Alignment explanation
Indices: 39484108--39484169 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
39484098 AATCTACCTT
* *
39484108 ATTTATTCTTTTAATATAAAAAACTAA
1 ATTTAATCATTTAATATAAAAAACTAA
*
39484135 ATTAAATCATTTAATAATAAAAAGA-T-A
1 ATTTAATCATTTAAT-ATAAAAA-ACTAA
39484162 ATTTAATC
1 ATTTAATC
39484170 TCATTACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 20 0.69
28 8 0.28
29 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (27 bp):
ATTTAATCATTTAATATAAAAAACTAA
Found at i:39486418 original size:7 final size:7
Alignment explanation
Indices: 39486402--39486433 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
39486392 ACAAAATTAA
39486402 ATTTTA-
1 ATTTTAT
39486408 ATTTTAT
1 ATTTTAT
39486415 ATTTTAT
1 ATTTTAT
39486422 ATTTTAT
1 ATTTTAT
39486429 ATTTT
1 ATTTT
39486434 TAATATGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTAT
Found at i:39489164 original size:2 final size:2
Alignment explanation
Indices: 39489159--39489183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39489149 TGTGTGTGTG
39489159 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39489184 CAGAATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39491459 original size:19 final size:19
Alignment explanation
Indices: 39491416--39491453 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39491406 TTAATTTATT
*
39491416 AAATTTTAAAAATTCAAAA
1 AAATTATAAAAATTCAAAA
39491435 AAATTATAAAAATT-AAAA
1 AAATTATAAAAATTCAAAA
39491453 A
1 A
39491454 TTATTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATTATAAAAATTCAAAA
Found at i:39492071 original size:98 final size:98
Alignment explanation
Indices: 39491894--39492072 Score: 286
Period size: 98 Copynumber: 1.8 Consensus size: 98
39491884 GAGTAATATG
* * *
39491894 TGGAAACAATAAGTTGACATGGTATTTCATATGTGTTAATATGTTTATCACATTAAATTTTGGAA
1 TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAATATGTCTATCACATTAAATTTTGGAA
*
39491959 ATAGTTAAACTTAATAAACTTAATATCCAACTT
66 ATAGCTAAACTTAATAAACTTAATATCCAACTT
* * *
39491992 TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAGTATGTCTGTCGCATTAAATTTTGGAA
1 TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAATATGTCTATCACATTAAATTTTGGAA
*
39492057 ATAGCTAAATTTAATA
66 ATAGCTAAACTTAATA
39492073 TTCAATTTTG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 73 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (98 bp):
TGGAAACAATAAGTTGACATGGTATTTCACATGTGATAATATGTCTATCACATTAAATTTTGGAA
ATAGCTAAACTTAATAAACTTAATATCCAACTT
Found at i:39493449 original size:29 final size:29
Alignment explanation
Indices: 39493385--39493461 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
39493375 GTGGTCAGGG
* *
39493385 TTGCTCATACAAGCTGACATTTATGAATC
1 TTGCTCACACAAGCTGACATTTATAAATC
* *
39493414 TT-TTCACACAAGTTGACATTTTATAAAT-
1 TTGCTCACACAAGCTGACA-TTTATAAATC
*
39493442 TTGCTCACACAAGCTAACAT
1 TTGCTCACACAAGCTGACAT
39493462 CGTATCAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 16 0.41
29 23 0.59
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (29 bp):
TTGCTCACACAAGCTGACATTTATAAATC
Found at i:39495865 original size:20 final size:20
Alignment explanation
Indices: 39495840--39495880 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39495830 AGATTTTTGA
39495840 GTTTAGGGTTTACGATGTAG
1 GTTTAGGGTTTACGATGTAG
* * *
39495860 GTTTAGTGTTTTCGATTTAG
1 GTTTAGGGTTTACGATGTAG
39495880 G
1 G
39495881 GTTTGAGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.32, T:0.46
Consensus pattern (20 bp):
GTTTAGGGTTTACGATGTAG
Found at i:39496024 original size:27 final size:27
Alignment explanation
Indices: 39495986--39496039 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
39495976 TATTATTTTG
*
39495986 TGATTAGAGTTTTGAGTTTAGGGTTTA
1 TGATTAGAGTTTAGAGTTTAGGGTTTA
* *
39496013 TGATGTAG-GTTTAGTGTTTTGGGTTTA
1 TGAT-TAGAGTTTAGAGTTTAGGGTTTA
39496040 AGGTTTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (27 bp):
TGATTAGAGTTTAGAGTTTAGGGTTTA
Found at i:39496058 original size:22 final size:21
Alignment explanation
Indices: 39496019--39496069 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
39496009 TTTATGATGT
* *
39496019 AGGTTTAGTGTTTTGGGTTTA
1 AGGTTTAGAGTTTGGGGTTTA
*
39496040 AGGTTTAAGAGTTTGGGGTTTG
1 AGGTTT-AGAGTTTGGGGTTTA
*
39496062 GGGTTTAG
1 AGGTTTAG
39496070 GCCGCTTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (21 bp):
AGGTTTAGAGTTTGGGGTTTA
Found at i:39496579 original size:9 final size:9
Alignment explanation
Indices: 39496541--39496571 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
39496531 ACTCTCTAAG
39496541 ATTTATAAA
1 ATTTATAAA
39496550 ATTTATAAA
1 ATTTATAAA
39496559 ATTTATAAA
1 ATTTATAAA
39496568 ATTT
1 ATTT
39496572 TAACAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTTATAAA
Found at i:39497327 original size:252 final size:240
Alignment explanation
Indices: 39496754--39497383 Score: 598
Period size: 240 Copynumber: 2.6 Consensus size: 240
39496744 TTTCCATTAA
* * ** * * * *
39496754 AAAACGCCACAAAATCTAAATATTAGCGGCGTTTGTTCAGAAAACACTGTAAAAAATATA-TAAA
1 AAAACACCACAAAATCTAAA-AGTAGCGGCACTTGTTC-GTAAACACCGCAAAAAACATATTAAA
* * * ** *
39496818 AAATGAAGCAAAACGGCACCGTTTCATTGACGAGTTAAAGGTTAATGGCGTTTTTTGTCAAAACG
64 AATTAAAG-AAAACGGCACCGCTTCATTGACGAGTTAAAATTTAATGGCG-TTTTTATCAAAACG
* * * *
39496883 CCGCAGAAGTTGTGAAACTAGTGGCGTTTTCGCGTAAGTGCCGCAAATATTATAATATAAAATGA
127 CCGCAAAAGTTGTGAAACTAGTGGCGTTTTCACGTAAGCGCCGCAAATATTAAAATATAAAATGA
* * **
39496948 GGCCGTTTTAATAGTAATAAAAAGTTAATCATTACCGGCGTTTTGATTT
192 GGCCGTTTTAATAATAATAAAAAGTTAATCAGTACCGGCGTTTTGAAGT
** * ** * *
39496997 AAAATGCCACAAAATCTAAAATTAGCGGCGTTTTTTGGTAAACACCGCAAAAAACATATTAAAAA
1 AAAACACCACAAAATCTAAAAGTAGCGGCACTTGTTCGTAAACACCGCAAAAAACATATTAAAAA
* * *
39497062 TTAAACG-AAACGGCACCGCTTCGTTGACGAGTTAAATTTTACTGGCGTTTTTATCAAAACGCCG
66 TTAAA-GAAAACGGCACCGCTTCATTGACGAGTTAAAATTTAATGGCGTTTTTATCAAAACGCCG
* * * * * * ** *
39497126 CAAAAGTTGTGAATCTAGTGGCGTTTTTATGTTAGCGCCGCAAATGTTAAAATATAATATGTTGT
130 CAAAAGTTGTGAAACTAGTGGCGTTTTCACGTAAGCGCCGCAAATATTAAAATATAAAATGAGGC
* * *
39497191 CGTTTTTAACATAAATAATACTAATAGAAATTTAATCCGTAGCGGCGTTTTGAAGT
195 CG-TTTT-A-AT-AAT-A-A-T-A-A-AAAGTTAATCAGTACCGGCGTTTTGAAGT
* * * * *
39497247 AGAACACCAGAAAATCTAAACAGTAGCGGCACTTGTTCGTAAAACGCCGCAAAGAGCATATTAAA
1 AAAACACCACAAAATCTAAA-AGTAGCGGCACTTGTTCGT-AAACACCGCAAAAAACATATTAAA
* * * * *
39497312 AATTTAAGAAAACGGCATCGCTTCATTGGCGAGTTAAAATTTAGTGGCATTTTTTATCAAAACGC
64 AATTAAAGAAAACGGCACCGCTTCATTGACGAGTTAAAATTTAATGGC-GTTTTTATCAAAACGC
39497377 CGCAAAA
128 CGCAAAA
39497384 TTTTAAATGA
Statistics
Matches: 317, Mismatches: 54, Indels: 22
0.81 0.14 0.06
Matches are distributed among these distances:
240 70 0.22
241 56 0.18
242 25 0.08
243 22 0.07
244 2 0.01
245 1 0.00
246 1 0.00
247 1 0.00
248 1 0.00
249 1 0.00
250 39 0.12
251 15 0.05
252 61 0.19
253 22 0.07
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (240 bp):
AAAACACCACAAAATCTAAAAGTAGCGGCACTTGTTCGTAAACACCGCAAAAAACATATTAAAAA
TTAAAGAAAACGGCACCGCTTCATTGACGAGTTAAAATTTAATGGCGTTTTTATCAAAACGCCGC
AAAAGTTGTGAAACTAGTGGCGTTTTCACGTAAGCGCCGCAAATATTAAAATATAAAATGAGGCC
GTTTTAATAATAATAAAAAGTTAATCAGTACCGGCGTTTTGAAGT
Found at i:39498212 original size:16 final size:18
Alignment explanation
Indices: 39498191--39498232 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
39498181 ATGTTAAGCT
39498191 ATGTTAA-ACA-TTTTGA
1 ATGTTAACACAGTTTTGA
*
39498207 ATGTTAAGCATAGTTTTGA
1 ATGTTAA-CACAGTTTTGA
39498226 ATGTTAA
1 ATGTTAA
39498233 GCTATGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (18 bp):
ATGTTAACACAGTTTTGA
Found at i:39499758 original size:42 final size:43
Alignment explanation
Indices: 39499678--39499821 Score: 148
Period size: 42 Copynumber: 3.3 Consensus size: 43
39499668 GAATATTACT
*
39499678 TTTAGCGGCGTTTGTGGAGAAAGTGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTC
* * *
39499721 TTTAGCGGCGTTTGTTG-GTATGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTC
* * ** **
39499763 TTTAGCGGCGGCGTTTGTTGTA-AAAGCGCCGTTAAAGAACATGACC
1 TTTA---GCGGCGTTTG-TGGAGAAAGCGCCGCTAAAGGTCATGTTC
39499809 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
39499822 ATTTCTGTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
42 26 0.31
43 25 0.30
45 10 0.12
46 22 0.27
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTC
Found at i:39501118 original size:19 final size:19
Alignment explanation
Indices: 39501094--39501131 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39501084 CTATGCGTAG
39501094 ATAGTTTGATCCGAGAATT
1 ATAGTTTGATCCGAGAATT
39501113 ATAGTTTGATCCGAGAATT
1 ATAGTTTGATCCGAGAATT
39501132 TATTTGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
ATAGTTTGATCCGAGAATT
Found at i:39503867 original size:27 final size:26
Alignment explanation
Indices: 39503837--39504037 Score: 222
Period size: 27 Copynumber: 7.5 Consensus size: 26
39503827 CCTAAAATAT
* * *
39503837 GTAAAATGACTGAAATACCCCAATAAG
1 GTAAAATGACCGAAATACCCCGAT-GG
39503864 GTAAAATGACCGAAATACCCCCGATGG
1 GTAAAATGACCGAAATA-CCCCGATGG
39503891 GTAAAATGACCGAAATACCCCCGATGG
1 GTAAAATGACCGAAATA-CCCCGATGG
* *
39503918 GTAAAATTATCGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCC-CGATGG
* * *
39503945 GTAAAATTACTGAAATACCCTCGAAGG
1 GTAAAATGACCGAAATACCC-CGATGG
*
39503972 GTAAAATGACCAAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCC-CGATGG
* * * *
39503999 GTAAAATTACCAAAATACCTCTATAGG
1 GTAAAATGACCGAAATACCCCGAT-GG
39504026 GTAAAATGACCG
1 GTAAAATGACCG
39504038 TTATACCCTT
Statistics
Matches: 154, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 6 0.04
27 142 0.92
28 6 0.04
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (26 bp):
GTAAAATGACCGAAATACCCCGATGG
Found at i:39503921 original size:54 final size:54
Alignment explanation
Indices: 39503837--39504046 Score: 253
Period size: 54 Copynumber: 3.9 Consensus size: 54
39503827 CCTAAAATAT
* * * *
39503837 GTAAAATGACTGAAATACCCCAATAAGGTAAAATGACCGAAATACCCCCGATGG
1 GTAAAATGACCGAAATACCCCGATAGGGTAAAATGACCGAAATACCCTCGATGG
* *
39503891 GTAAAATGACCGAAATACCCCCGAT-GGGTAAAATTATCGAAATACCCTCGATGG
1 GTAAAATGACCGAAATA-CCCCGATAGGGTAAAATGACCGAAATACCCTCGATGG
* * *
39503945 GTAAAATTACTGAAATACCCTCGA-AGGGTAAAATGACCAAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCC-CGATAGGGTAAAATGACCGAAATACCCTCGATGG
* * * * **
39503999 GTAAAATTACCAAAATACCTCTATAGGGTAAAATGACCGTTATACCCT
1 GTAAAATGACCGAAATACCCCGATAGGGTAAAATGACCGAAATACCCT
39504047 TAGGAGATGA
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
53 5 0.04
54 123 0.92
55 6 0.04
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (54 bp):
GTAAAATGACCGAAATACCCCGATAGGGTAAAATGACCGAAATACCCTCGATGG
Found at i:39504044 original size:81 final size:81
Alignment explanation
Indices: 39503849--39504046 Score: 254
Period size: 81 Copynumber: 2.4 Consensus size: 81
39503839 AAAATGACTG
* * * * *
39503849 AAATACCCCAATAAGGTAAAATGACCGAAATACCCCCGATGGGTAAAATGACCGAAATACCCCCG
1 AAATACCTCAATAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCCCG
* *
39503914 ATGGGTAAAATTATCG
66 ATGGGTAAAATTACCA
* * * *
39503930 AAATACCCTCGAT-GGGTAAAATTACTGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCTC
1 AAATA-CCTCAATAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCCC
39503994 GATGGGTAAAATTACCA
65 GATGGGTAAAATTACCA
* **
39504011 AAATACCTCTATAGGGTAAAATGACCGTTATACCCT
1 AAATACCTCAATAGGGTAAAATGACCGAAATACCCT
39504047 TAGGAGATGA
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
80 6 0.06
81 88 0.89
82 5 0.05
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (81 bp):
AAATACCTCAATAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCAAAATACCCCCG
ATGGGTAAAATTACCA
Found at i:39504264 original size:26 final size:26
Alignment explanation
Indices: 39504228--39504328 Score: 143
Period size: 26 Copynumber: 3.9 Consensus size: 26
39504218 TTTCCACAAA
39504228 TACTATTACTGGCAGCTTTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCAT
* *
39504254 TACTGA-TACTGGCAGCTCTACTGCAT
1 TACT-ATTACTGGCAGCTTTGCTGCAT
* *
39504280 TACTATTACTGGTAGCTTTGCTG-GT
1 TACTATTACTGGCAGCTTTGCTGCAT
39504305 TACTATTACTGGCAGCTTTGCTGC
1 TACTATTACTGGCAGCTTTGCTGC
39504329 GATATTGGTG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
25 24 0.37
26 40 0.62
27 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCAT
Found at i:39504474 original size:30 final size:30
Alignment explanation
Indices: 39504435--39504514 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
39504425 ACTGCATTTG
*
39504435 CACTATTACTGTATTGGGCTAAGACCCACA
1 CACTGTTACTGTATTGGGCTAAGACCCACA
* * *
39504465 CTCTGTTACTGTATTGGGCTATGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGACCCACA
* *
39504495 CACTGCTACTGTATAGGGCT
1 CACTGTTACTGTATTGGGCT
39504515 CAGGCTTAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (30 bp):
CACTGTTACTGTATTGGGCTAAGACCCACA
Found at i:39506802 original size:27 final size:26
Alignment explanation
Indices: 39506770--39506827 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
39506760 TAGATAATCG
39506770 GAAAGCCCTC-TCTCGAGCCATATAATA
1 GAAAG-CCTCATCT-GAGCCATATAATA
*
39506797 GAAAG-CTCATGTGAGCCATATAATA
1 GAAAGCCTCATCTGAGCCATATAATA
*
39506822 GGAAGC
1 GAAAGC
39506828 TTATCCGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 20 0.74
26 2 0.07
27 5 0.19
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (26 bp):
GAAAGCCTCATCTGAGCCATATAATA
Found at i:39506837 original size:25 final size:25
Alignment explanation
Indices: 39506783--39506837 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
39506773 AGCCCTCTCT
*
39506783 CGAGCCATATAATAGAAAGCTCATG
1 CGAGCCATATAATAGAAAGCTCATC
* * *
39506808 TGAGCCATATAATAGGAAGCTTATC
1 CGAGCCATATAATAGAAAGCTCATC
39506833 CGAGC
1 CGAGC
39506838 TGTATAACGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (25 bp):
CGAGCCATATAATAGAAAGCTCATC
Found at i:39506931 original size:25 final size:25
Alignment explanation
Indices: 39506898--39507039 Score: 105
Period size: 25 Copynumber: 5.6 Consensus size: 25
39506888 AATAACGGGT
*
39506898 AGCTTCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
*
39506923 AGCTCCGAATAGCCA-TATAT-AGGAA
1 AGCTCCGAAGAGCCATTA-ATCAGG-A
* * *
39506948 AG-T-TGAAGCGAGCCAAT-ATCGGGA
1 AGCTCCGAA--GAGCCATTAATCAGGA
* *
39506972 AGCTCCGGAGAGCCATTAATCAAGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * *
39506997 AGCTCACAAAGAGCCTTTAATCGGGA
1 AGCTC-CGAAGAGCCATTAATCAGGA
39507023 AGCTCACGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
39507040 ATATCGGGAC
Statistics
Matches: 90, Mismatches: 17, Indels: 19
0.71 0.13 0.15
Matches are distributed among these distances:
23 3 0.03
24 18 0.20
25 36 0.40
26 33 0.37
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.18
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Found at i:39507045 original size:26 final size:27
Alignment explanation
Indices: 39506883--39507054 Score: 109
Period size: 26 Copynumber: 6.9 Consensus size: 27
39506873 AAACTCATAT
* *
39506883 GAGCCA-ATAA-CGGGTAGCT-TCGAA
1 GAGCCATATAATCGGGAAGCTCACGAA
*
39506907 GAGCCAT-TAATCAGGAAGCTC-CGAA
1 GAGCCATATAATCGGGAAGCTCACGAA
* * * * * * *
39506932 TAGCCATAT-ATAGGAAAGTTGAAG-C
1 GAGCCATATAATCGGGAAGCTCACGAA
*
39506957 GAGCCA-AT-ATCGGGAAGCTC-CGGA
1 GAGCCATATAATCGGGAAGCTCACGAA
** *
39506981 GAGCCAT-TAATCAAGAAGCTCACAAA
1 GAGCCATATAATCGGGAAGCTCACGAA
*
39507007 GAGCC-TTTAATCGGGAAGCTCACGAA
1 GAGCCATATAATCGGGAAGCTCACGAA
*
39507033 GAGCCATAT-ATCGGGACGCTCA
1 GAGCCATATAATCGGGAAGCTCA
39507055 TAAGAGCTGT
Statistics
Matches: 111, Mismatches: 26, Indels: 20
0.71 0.17 0.13
Matches are distributed among these distances:
23 1 0.01
24 26 0.23
25 40 0.36
26 42 0.38
27 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (27 bp):
GAGCCATATAATCGGGAAGCTCACGAA
Found at i:39508079 original size:15 final size:16
Alignment explanation
Indices: 39508054--39508088 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
39508044 GTGGCATGTA
*
39508054 AATAGGTCTAATGGTT
1 AATAGGTCTAATGGTC
39508070 AATA-GTCTAATGGTC
1 AATAGGTCTAATGGTC
39508085 AATA
1 AATA
39508089 TGTTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (16 bp):
AATAGGTCTAATGGTC
Found at i:39512464 original size:25 final size:26
Alignment explanation
Indices: 39512434--39512487 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
39512424 ACAGCTCTTA
39512434 TGAGCTTCCCGATT-A-TGGCTCTTCG
1 TGAGCTTCCCG-TTAATTGGCTCTTCG
* *
39512459 TGAGCTTTCCGTTAATTGGCTCTTTG
1 TGAGCTTCCCGTTAATTGGCTCTTCG
39512485 TGA
1 TGA
39512488 CTTTCCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 11 0.44
26 12 0.48
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (26 bp):
TGAGCTTCCCGTTAATTGGCTCTTCG
Found at i:39512673 original size:25 final size:25
Alignment explanation
Indices: 39512564--39512673 Score: 71
Period size: 25 Copynumber: 4.5 Consensus size: 25
39512554 TTCGGGGTTA
*
39512564 CCCGATAT-TGGCTCACATGAGCTT
1 CCCGTTATATGGCTCACATGAGCTT
* * **
39512588 CCTG-AATATGGCTCTTATGAGCTT
1 CCCGTTATATGGCTCACATGAGCTT
* ** * ** *
39512612 CCCATTATAAAGCCCGGATAAGCTT
1 CCCGTTATATGGCTCACATGAGCTT
* * *
39512637 TCCATTACATGGCTCACATGAGCTT
1 CCCGTTATATGGCTCACATGAGCTT
39512662 CCCGTTATATGG
1 CCCGTTATATGG
39512674 ATCGAGACAG
Statistics
Matches: 60, Mismatches: 24, Indels: 3
0.69 0.28 0.03
Matches are distributed among these distances:
23 2 0.03
24 19 0.32
25 39 0.65
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (25 bp):
CCCGTTATATGGCTCACATGAGCTT
Found at i:39520318 original size:18 final size:18
Alignment explanation
Indices: 39520297--39520332 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39520287 TTTGATATGA
39520297 AAATTGATATTGACAATT
1 AAATTGATATTGACAATT
* *
39520315 AAATTGCTATTGATAATT
1 AAATTGATATTGACAATT
39520333 GATATGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (18 bp):
AAATTGATATTGACAATT
Found at i:39528086 original size:18 final size:19
Alignment explanation
Indices: 39528053--39528092 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
39528043 AACATGTTTC
* *
39528053 TTTTATTTT-ATTTTTTAT
1 TTTTATTTTAAATTTTAAT
39528071 TTTTATTTTAAATTTTAAT
1 TTTTATTTTAAATTTTAAT
39528090 TTT
1 TTT
39528093 CTCATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTTAAATTTTAAT
Found at i:39531762 original size:19 final size:21
Alignment explanation
Indices: 39531720--39531772 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
39531710 ATGCCTTTTT
39531720 TGCATT-CATTTCATGCATCA
1 TGCATTACATTTCATGCATCA
39531740 -GCATTACATTTCAT-CA-CA
1 TGCATTACATTTCATGCATCA
*
39531758 TGCATTAAATTTCAT
1 TGCATTACATTTCAT
39531773 AAAAAGACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 20 0.67
20 8 0.27
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (21 bp):
TGCATTACATTTCATGCATCA
Found at i:39536198 original size:43 final size:43
Alignment explanation
Indices: 39536113--39536279 Score: 205
Period size: 43 Copynumber: 3.9 Consensus size: 43
39536103 CGCTAAAAGT
* * *
39536113 CATGACCTTTAGCGGCGC-TTTCCCACAAACGCCGTTATATAC
1 CATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAATAC
*
39536155 CACGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAATAC
1 CATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAATAC
* * *
39536198 CATGAACTTTAGCGGCGCTTTTGT-CACAAACGCCG-TTAATGAA
1 CATGACCTTTAGCGGCGCTTTT-TCCACAAACGCCGCTAAAT-AC
* *
39536241 CATGACCTTTAGCGGCGTTTTTTATCACAAACGCCGCTA
1 CATGACCTTTAGCGGCGCTTTTT-CCACAAACGCCGCTA
39536280 TAGAACAAAC
Statistics
Matches: 108, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
42 22 0.20
43 73 0.68
44 12 0.11
45 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAATAC
Found at i:39536251 original size:86 final size:86
Alignment explanation
Indices: 39536113--39536279 Score: 239
Period size: 86 Copynumber: 1.9 Consensus size: 86
39536103 CGCTAAAAGT
* *
39536113 CATGACCTTTAGCGGCGCTTTCCCACAAACGCCGTTATATACCACGACCTTTAGCGGCGCTTTTT
1 CATGAACTTTAGCGGCGCTTTCCCACAAACGCCGTTATATAACACGACCTTTAGCGGCGCTTTTT
39536178 -CCACAAACGCCGCTAAATAC
66 ACCACAAACGCCGCTAAATAC
** * *
39536198 CATGAACTTTAGCGGCGCTTTTGTCACAAACGCCGTTA-ATGAACATGACCTTTAGCGGCGTTTT
1 CATGAACTTTAGCGGCGC-TTTCCCACAAACGCCGTTATAT-AACACGACCTTTAGCGGCGCTTT
*
39536262 TTATCACAAACGCCGCTA
64 TTACCACAAACGCCGCTA
39536280 TAGAACAAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 19 0.26
86 39 0.54
87 14 0.19
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (86 bp):
CATGAACTTTAGCGGCGCTTTCCCACAAACGCCGTTATATAACACGACCTTTAGCGGCGCTTTTT
ACCACAAACGCCGCTAAATAC
Found at i:39536294 original size:86 final size:86
Alignment explanation
Indices: 39536117--39536303 Score: 229
Period size: 86 Copynumber: 2.2 Consensus size: 86
39536107 AAAAGTCATG
*
39536117 ACCTTTAGCGGCGC-TTTCCCACAAACGCCGTTATATACCACGACCTTTAGCGGCGCTTTTTCCA
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGTTATATAACACGACCTTTAGCGGCGCTTTTTCCA
* *
39536181 CAAACGCCGCTAAATACCATGA
66 CAAACGCCGCTAAAGAACA-GA
** * * *
39536203 A-CTTTAGCGGCGCTTTTGTCACAAACGCCGTTA-ATGAACATGACCTTTAGCGGCGTTTTTTAT
1 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGTTATAT-AACACGACCTTTAGCGGCGCTTTTT-C
*
39536266 CACAAACGCCGCTATAGAACA-A
64 CACAAACGCCGCTAAAGAACAGA
*
39536288 ACCTTTAGCGACGCTT
1 ACCTTTAGCGGCGCTT
39536304 CTCGCAAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
85 16 0.18
86 53 0.61
87 18 0.21
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (86 bp):
ACCTTTAGCGGCGCTTTTCCCACAAACGCCGTTATATAACACGACCTTTAGCGGCGCTTTTTCCA
CAAACGCCGCTAAAGAACAGA
Found at i:39541493 original size:21 final size:21
Alignment explanation
Indices: 39541469--39541527 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
39541459 AGCCTCAAAT
* *
39541469 CTCTAAACCCTAAATCACTAA
1 CTCTAACCCCTAAACCACTAA
*
39541490 CTCTTAACCCCT-AACCCCTAA
1 CTC-TAACCCCTAAACCACTAA
39541511 CTACTAACCCCTAAACC
1 CT-CTAACCCCTAAACC
39541528 TTATTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (21 bp):
CTCTAACCCCTAAACCACTAA
Found at i:39541763 original size:14 final size:15
Alignment explanation
Indices: 39541743--39541771 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39541733 AAACCAGAAC
39541743 CCCTAA-TCCATAAT
1 CCCTAATTCCATAAT
39541757 CCCTAATTCCATAAT
1 CCCTAATTCCATAAT
39541772 ATATAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (15 bp):
CCCTAATTCCATAAT
Found at i:39542219 original size:41 final size:41
Alignment explanation
Indices: 39542173--39542327 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
39542163 AAATGTTTTT
* * *
39542173 GCGGCGCTTTTTAAAAAACGCCGCTAAAGCACTGAGCATTA
1 GCGGCGCTTTTTAAAAAACACCGCTAAAGCCCGGAGCATTA
* *
39542214 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCGGAGCATTA
1 GCGGCGCTTTTTAAAAAACACCGCTAAAGCCCGGAGCATTA
* *
39542255 GCGGCGCTTCTCAAAAAACACCGCTAAAGCCCGGAGCATTA
1 GCGGCGCTTTTTAAAAAACACCGCTAAAGCCCGGAGCATTA
*
39542296 GCGGCGCTTCTCT-AAAAACACCGCTAAAGCCC
1 GCGGCGCTT-TTTAAAAAACACCGCTAAAGCCC
39542328 CGAAAGGTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTTTTAAAAAACACCGCTAAAGCCCGGAGCATTA
Found at i:39542502 original size:39 final size:40
Alignment explanation
Indices: 39542457--39542534 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
39542447 GCGCTTTCCT
* *
39542457 TAAAGCGCCACTAATGCTCGATCTTTAGC-GCGTTTTTTG
1 TAAAGCGCCACTAATGCTAGATCTTTAGCGGCATTTTTTG
* *
39542496 TAAAGCGCCGCTAATGCTAGATTTTTAGCGGCATTTTTT
1 TAAAGCGCCACTAATGCTAGATCTTTAGCGGCATTTTTT
39542535 ATCCAAACGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
TAAAGCGCCACTAATGCTAGATCTTTAGCGGCATTTTTTG
Found at i:39546742 original size:2 final size:2
Alignment explanation
Indices: 39546737--39546764 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39546727 AAAAAAAAGA
39546737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39546765 TAAGAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39547289 original size:12 final size:11
Alignment explanation
Indices: 39547258--39547287 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39547248 TCCTACTGTC
*
39547258 AACAAACATAA
1 AACAAAAATAA
39547269 AACAAAAATAA
1 AACAAAAATAA
39547280 AACAAAAA
1 AACAAAAA
39547288 ATGGGCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (11 bp):
AACAAAAATAA
Found at i:39552325 original size:20 final size:20
Alignment explanation
Indices: 39552297--39552339 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39552287 AAAAAATTTT
* *
39552297 ATATTTAAAACCATAATAAA
1 ATATATAAAACCAAAATAAA
*
39552317 ATATATAAAACTAAAATAAA
1 ATATATAAAACCAAAATAAA
39552337 ATA
1 ATA
39552340 AAAACACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
ATATATAAAACCAAAATAAA
Found at i:39554444 original size:29 final size:29
Alignment explanation
Indices: 39554405--39554460 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
39554395 GCTAATTAAG
*
39554405 ATTAAGTTTTGCTTAATTAAAGTTTAATAA
1 ATTAAGTTTTGATTAATTAAA-TTTAATAA
39554435 ATTAA-TTTTGATTAATTAAATTTAAT
1 ATTAAGTTTTGATTAATTAAATTTAAT
39554461 CAAAAGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 14 0.56
30 5 0.20
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (29 bp):
ATTAAGTTTTGATTAATTAAATTTAATAA
Found at i:39558359 original size:12 final size:12
Alignment explanation
Indices: 39558343--39558372 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39558333 AGAAACATGG
39558343 AAAGAAAGAGAA
1 AAAGAAAGAGAA
*
39558355 GAAGAAAGAGAA
1 AAAGAAAGAGAA
39558367 AAAGAA
1 AAAGAA
39558373 TTCTCATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:39560056 original size:25 final size:25
Alignment explanation
Indices: 39560028--39560093 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
39560018 AAGCTCCTCT
*
39560028 GAGCTGAATAAT-GGTAAGCTCATAC
1 GAGCTGAAT-ATCGGTAAGCTCATAA
* *
39560053 GAGCTGAGTATCGGTATGCTCATAA
1 GAGCTGAATATCGGTAAGCTCATAA
39560078 GAGCTGAA-ATCGGTAA
1 GAGCTGAATATCGGTAA
39560094 CCCTAATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 9 0.26
25 26 0.74
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (25 bp):
GAGCTGAATATCGGTAAGCTCATAA
Found at i:39567014 original size:25 final size:25
Alignment explanation
Indices: 39566986--39567040 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
39566976 AGCTCCTCTT
* *
39566986 AGCTGAATAACGGTAAGGTCATACG
1 AGCTGAATAACGGTAAGCTCATAAG
* *
39567011 AGCTGAGTATCGGTAAGCTCATAAG
1 AGCTGAATAACGGTAAGCTCATAAG
39567036 AGCTG
1 AGCTG
39567041 GAATCGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (25 bp):
AGCTGAATAACGGTAAGCTCATAAG
Found at i:39573500 original size:12 final size:11
Alignment explanation
Indices: 39573465--39573516 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
39573455 TAGTTACATT
39573465 TTTTATTATTTA
1 TTTTATTA-TTA
39573477 GTTTTATTATTA
1 -TTTTATTATTA
39573489 TTTTATTTATTA
1 TTTTA-TTATTA
* *
39573501 CTTTAGTATTA
1 TTTTATTATTA
39573512 GTTTT
1 -TTTT
39573517 GGTTTTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 10 0.29
12 16 0.47
13 8 0.24
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:39582812 original size:13 final size:13
Alignment explanation
Indices: 39582794--39582824 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39582784 TTCCAGCAAC
39582794 TATGAATTTATTT
1 TATGAATTTATTT
39582807 TATGAATTTATTT
1 TATGAATTTATTT
*
39582820 GATGA
1 TATGA
39582825 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:39582994 original size:50 final size:50
Alignment explanation
Indices: 39582919--39583111 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
39582909 ATTTGGGTAA
39582919 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
39582969 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
39583019 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
39583069 AGAACATCCCATGCAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39583112 TGTTATTATC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 96 0.74
51 33 0.26
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:39595567 original size:12 final size:12
Alignment explanation
Indices: 39595550--39595574 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39595540 ACATACTTAA
39595550 AATAAGAATAAT
1 AATAAGAATAAT
39595562 AATAAGAATAAT
1 AATAAGAATAAT
39595574 A
1 A
39595575 TGAAAAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AATAAGAATAAT
Found at i:39595799 original size:3 final size:3
Alignment explanation
Indices: 39595791--39595819 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39595781 AACTAAAGAA
39595791 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39595820 ACTAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39597607 original size:23 final size:22
Alignment explanation
Indices: 39597531--39597944 Score: 283
Period size: 23 Copynumber: 17.7 Consensus size: 22
39597521 TCTACCCTGT
*
39597531 TTGGACAGCTCTTATACATCAGAAA
1 TTGGACAGC-ATTATACA-CA-AAA
* *
39597556 TT-GAGCAGCATGTATATAC-CAA
1 TTGGA-CAGCAT-TATACACAAAA
39597578 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCA-TTATACACAAAA
* *
39597601 TTTGACAGCATGTATATACAAAA
1 TTGGACAGCAT-TATACACAAAA
* *
39597624 TTGGACAGCATTTATTCACCCAAA
1 TTGGACAGCA-TTATACA-CAAAA
* * * *
39597648 TTGGGCAGCATATATATACCAAT
1 TTGGACAGCAT-TATACACAAAA
39597671 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCA-TTATACACAAAA
* *
39597694 TTTGACAGCATGTATATACAAAA
1 TTGGACAGCAT-TATACACAAAA
* *
39597717 TTGGACAACATTTATTCACCAAAA
1 TTGGACAGCA-TTATACA-CAAAA
* * * *
39597741 TTGGGCAGCATATATATATACCAAT
1 TTGGACAGC--AT-TATACACAAAA
39597766 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCA-TTATACACAAAA
* *
39597789 TTTGACAGCATGTATATACAAAA
1 TTGGACAGCAT-TATACACAAAA
*
39597812 TTGGACAGCATTTATTCACCAAAA
1 TTGGACAGCA-TTATACA-CAAAA
* * * *
39597836 TTGGGCAGCATATATATACCAAT
1 TTGGACAGCAT-TATACACAAAA
39597859 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCA-TTATACACAAAA
* * *
39597882 TTTGACAGGATGTATATACAAAA
1 TTGGACAGCAT-TATACACAAAA
* *
39597905 CTGGACAGCATTTATTCACCAAAA
1 TTGGACAGCA-TTATACA-CAAAA
*
39597929 TTGGGCAGCATATATA
1 TTGGACAGCAT-TATA
39597945 TACCAATTTG
Statistics
Matches: 303, Mismatches: 60, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
22 19 0.06
23 182 0.60
24 74 0.24
25 23 0.08
26 5 0.02
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (22 bp):
TTGGACAGCATTATACACAAAA
Found at i:39597686 original size:93 final size:93
Alignment explanation
Indices: 39597531--39597957 Score: 732
Period size: 93 Copynumber: 4.6 Consensus size: 93
39597521 TCTACCCTGT
* * * *
39597531 TTGGACAGC-TCTTATACATCAGAAATTGAGCAGCATGTATATACCAA-TTGGACAGCACTTATA
1 TTGGACAGCAT-TTATTCACCA-AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATA
39597594 CACAAAATTTGACAGCATGTATATACAAAA
64 CACAAAATTTGACAGCATGTATATACAAAA
*
39597624 TTGGACAGCATTTATTCACCCAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
39597689 CAAAATTTGACAGCATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
*
39597717 TTGGACAACATTTATTCACCAAAATTGGGCAGCATATATATATACCAATTTGGACAGCACTTATA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGC--ATATATATACCAATTTGGACAGCACTTATA
39597782 CACAAAATTTGACAGCATGTATATACAAAA
64 CACAAAATTTGACAGCATGTATATACAAAA
39597812 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
*
39597877 CAAAATTTGACAGGATGTATATACAAAA
66 CAAAATTTGACAGCATGTATATACAAAA
*
39597905 CTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGAC
1 TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGAC
39597958 CATTAAAGCA
Statistics
Matches: 320, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
92 23 0.07
93 204 0.64
94 1 0.00
95 92 0.29
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.28
Consensus pattern (93 bp):
TTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA
CAAAATTTGACAGCATGTATATACAAAA
Found at i:39597785 original size:188 final size:186
Alignment explanation
Indices: 39597553--39597957 Score: 731
Period size: 188 Copynumber: 2.2 Consensus size: 186
39597543 TATACATCAG
* *
39597553 AAATTGAGCAGCATGTATATACCAA-TTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
1 AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
*
39597617 TACAAAATTGGACAGCATTTATTCACCCAAATTGGGCAGCATATATATACCAATTTGGACAGCAC
66 TACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCAC
*
39597682 TTATACACAAAATTTGACAGCATGTATATACAAAATTGGACAACATTTATTCACCA
131 TTATACACAAAATTTGACAGCATGTATATACAAAACTGGACAACATTTATTCACCA
39597738 AAATTGGGCAGCATATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTA
1 AAATTGGGCAGC--ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTA
39597803 TATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGC
64 TATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGC
* *
39597868 ACTTATACACAAAATTTGACAGGATGTATATACAAAACTGGACAGCATTTATTCACCA
129 ACTTATACACAAAATTTGACAGCATGTATATACAAAACTGGACAACATTTATTCACCA
39597926 AAATTGGGCAGCATATATATACCAATTTGGAC
1 AAATTGGGCAGCATATATATACCAATTTGGAC
39597958 CATTAAAGCA
Statistics
Matches: 211, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
185 11 0.05
186 20 0.09
187 12 0.06
188 168 0.80
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (186 bp):
AAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATA
TACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCAATTTGGACAGCAC
TTATACACAAAATTTGACAGCATGTATATACAAAACTGGACAACATTTATTCACCA
Found at i:39598696 original size:28 final size:28
Alignment explanation
Indices: 39598656--39598753 Score: 151
Period size: 28 Copynumber: 3.5 Consensus size: 28
39598646 TTTAATAAGT
* * *
39598656 TCGCACACTTAGTGCTTTGCCATTAACC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
39598684 TCGCACATTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
39598712 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
39598740 TCGCACACTTAGTG
1 TCGCACACTTAGTG
39598754 TCGAAAGTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:39600411 original size:21 final size:20
Alignment explanation
Indices: 39600386--39600437 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
39600376 TTTTTCCTAG
*
39600386 GATGTAAATTGTA-TATAATT
1 GATGTAAATTATATTA-AATT
*
39600406 GAATGTGAATTATATTAAATT
1 G-ATGTAAATTATATTAAATT
39600427 GATGTTAAATT
1 GATG-TAAATT
39600438 CATTCATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
GATGTAAATTATATTAAATT
Found at i:39601048 original size:24 final size:25
Alignment explanation
Indices: 39600995--39601050 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
39600985 TTCCCGATAT
* *
39600995 ATGGCTATTTGGAGCTTCCCAATTA
1 ATGGCTCTTTGGAGCTACCCAATTA
39601020 ATGGCTCTTTGGAGCTACCC-ATTA
1 ATGGCTCTTTGGAGCTACCCAATTA
*
39601044 TTGGCTC
1 ATGGCTC
39601051 GCATGAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (25 bp):
ATGGCTCTTTGGAGCTACCCAATTA
Found at i:39601072 original size:24 final size:25
Alignment explanation
Indices: 39601045--39601100 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
39601035 TACCCATTAT
*
39601045 TGGCTCGCATGAGCTTCTTG-AATA
1 TGGCTCGCATGAGCTTCCTGTAATA
* *
39601069 TGGCTCACATGAGCTTCCTGTTATA
1 TGGCTCGCATGAGCTTCCTGTAATA
39601094 TGGCTCG
1 TGGCTCG
39601101 AGAGAGGGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (25 bp):
TGGCTCGCATGAGCTTCCTGTAATA
Found at i:39608604 original size:26 final size:26
Alignment explanation
Indices: 39608575--39608624 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
39608565 CCGATATATA
* *
39608575 GCTCTTCGTGAGCTTTCTGATTAAAG
1 GCTCTTCGTGAGCTTCCTAATTAAAG
*
39608601 GCTCTTTGTGAGCTTCCTAATTAA
1 GCTCTTCGTGAGCTTCCTAATTAA
39608625 TCACTCTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (26 bp):
GCTCTTCGTGAGCTTCCTAATTAAAG
Found at i:39608712 original size:73 final size:73
Alignment explanation
Indices: 39608611--39608750 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
39608601 GCTCTTTGTG
* * *
39608611 AGCTTCCTAATTAATCACTCTCCGGAGCTTCCCGATA-TGGCTCGCTTGAACTTCCCGATATATG
1 AGCTTCCTAATTAATCACTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCCGA-ATATG
39608675 GCTATCCGA
65 GCTATCCGA
* ** * * * *
39608684 AGCTTCCTGATTAATGGCTCTTCAGAGCTACCCGTTATTGGCTCGCATGAGCTTCCTGAATATGG
1 AGCTTCCTAATTAATCACTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCCGAATATGG
39608749 CT
66 CT
39608751 TTTATGAGCT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 38 0.68
74 18 0.32
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (73 bp):
AGCTTCCTAATTAATCACTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCCGAATATGG
CTATCCGA
Found at i:39608761 original size:73 final size:73
Alignment explanation
Indices: 39608600--39608761 Score: 157
Period size: 73 Copynumber: 2.2 Consensus size: 73
39608590 TCTGATTAAA
* * * *
39608600 GGCTCTTTGTGAGCTTCCTAATTAATCACTCTCCGGAGCTTCCCGATATGGCTCGCTTGAACTTC
1 GGCT-TTTATGAGCTTCCTAATTAATCACTCTCCAGAGCTACCCGATATGGCTCGCATGAACTTC
39608665 CCGATATAT
65 CCGATATAT
* ** * ** * * *
39608674 GGC-TATCCGAAGCTTCCTGATTAATGGCTCTTCAGAGCTACCCGTTATTGGCTCGCATGAGCTT
1 GGCTTTTATG-AGCTTCCTAATTAATCACTCTCCAGAGCTACCCGATA-TGGCTCGCATGAACTT
*
39608738 CCTGA-ATAT
64 CCCGATATAT
39608747 GGCTTTTATGAGCTT
1 GGCTTTTATGAGCTT
39608762 TCCGTTATAC
Statistics
Matches: 69, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
72 3 0.04
73 42 0.61
74 24 0.35
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (73 bp):
GGCTTTTATGAGCTTCCTAATTAATCACTCTCCAGAGCTACCCGATATGGCTCGCATGAACTTCC
CGATATAT
Found at i:39611425 original size:20 final size:20
Alignment explanation
Indices: 39611400--39611445 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39611390 CAAAAAAAAA
* * *
39611400 GTTATATTAAATTTTGTAAT
1 GTTATATCAAAATTTCTAAT
39611420 GTTATATCAAAATTTCTAAT
1 GTTATATCAAAATTTCTAAT
*
39611440 GCTATA
1 GTTATA
39611446 CCAATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (20 bp):
GTTATATCAAAATTTCTAAT
Found at i:39611454 original size:20 final size:20
Alignment explanation
Indices: 39611416--39611471 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
39611406 TTAAATTTTG
* * *
39611416 TAATGTTATATCAAAATTTC
1 TAATGATATACCAATATTTC
* *
39611436 TAATGCTATACCAATATTTT
1 TAATGATATACCAATATTTC
*
39611456 TAAAGATATACCAATA
1 TAATGATATACCAATA
39611472 CTAAAATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.39
Consensus pattern (20 bp):
TAATGATATACCAATATTTC
Found at i:39611511 original size:26 final size:26
Alignment explanation
Indices: 39611443--39611521 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
39611433 TTCTAATGCT
* * * *
39611443 ATACCAATATTTTTAAAGATATACCA
1 ATACTAATATTTCTAACGACATACCA
*
39611469 ATACTAAAATTTCTAACGACATACCA
1 ATACTAATATTTCTAACGACATACCA
39611495 ATACTAATATTTCTAAC-ACTATACCA
1 ATACTAATATTTCTAACGAC-ATACCA
39611521 A
1 A
39611522 AATTTTTATC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 2 0.04
26 44 0.96
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.32
Consensus pattern (26 bp):
ATACTAATATTTCTAACGACATACCA
Found at i:39611526 original size:20 final size:20
Alignment explanation
Indices: 39611503--39611550 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
39611493 CAATACTAAT
39611503 ATTTCTAACACTATACCAAA
1 ATTTCTAACACTATACCAAA
* * * *
39611523 ATTTTTATCACTTTATCAAA
1 ATTTCTAACACTATACCAAA
*
39611543 ATATCTAA
1 ATTTCTAA
39611551 TGGATGAAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTCTAACACTATACCAAA
Found at i:39613676 original size:16 final size:16
Alignment explanation
Indices: 39613655--39613724 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
39613645 TTTGGTTCGC
* *
39613655 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
39613671 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
39613687 TGTAATGGAATAGAAG
1 TGTAATGGAATAGAGG
39613703 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
39613719 TGTAAT
1 TGTAAT
39613725 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:39614254 original size:16 final size:16
Alignment explanation
Indices: 39614211--39614256 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
39614201 ACTATAAAAG
*
39614211 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
39614227 ATTATT-AAATATATT
1 ATAATTAAAATATATT
39614242 ATAATTAAAATATAT
1 ATAATTAAAATATAT
39614257 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:39614263 original size:14 final size:15
Alignment explanation
Indices: 39614211--39614265 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
39614201 ACTATAAAAG
39614211 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
39614227 ATTATTAAATATATT
1 ATAATTAAATATATT
39614242 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
39614255 ATAATTTAATA
1 ATAATTAAATA
39614266 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:39614328 original size:61 final size:61
Alignment explanation
Indices: 39614156--39614336 Score: 151
Period size: 61 Copynumber: 3.0 Consensus size: 61
39614146 NNNNNNNNNN
* * * *
39614156 TAATTAATATTCTTATATGAAATTACTCAAATCATAATATATGATACTATAAAA-GATAATT
1 TAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATCATAA-T
* * * * * * * * * *
39614217 TAA-C-ATAATTATTAT-TAAATATATTATAATTAAAATATATAAT-TTAATAAAATTCTTAA-
1 TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT-ATAAAA-TCATAAT
39614276 TAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAT-ATAAT
1 TAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATCATAAT
39614336 T
1 T
39614337 TCTTGTCAAA
Statistics
Matches: 87, Mismatches: 24, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
58 1 0.01
59 33 0.38
60 17 0.20
61 35 0.40
62 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (61 bp):
TAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATCATAAT
Found at i:39615898 original size:25 final size:25
Alignment explanation
Indices: 39615864--39615915 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
39615854 AAGAATCAGT
39615864 AAACTTAAACAGACGGGACTGGTGA
1 AAACTTAAACAGACGGGACTGGTGA
39615889 AAACTTAAACAGACGGGACTGGTGA
1 AAACTTAAACAGACGGGACTGGTGA
39615914 AA
1 AA
39615916 TATAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (25 bp):
AAACTTAAACAGACGGGACTGGTGA
Found at i:39616265 original size:137 final size:138
Alignment explanation
Indices: 39616016--39616280 Score: 417
Period size: 137 Copynumber: 1.9 Consensus size: 138
39616006 AACTTAAAAT
* * * * *
39616016 TGAAATCAATTATGGAATGTGTTACATTCAAAATAACAATAAACAAAATATGGATATAACACTAG
1 TGAAATCAATTATAGAATGAGTTACATTCAAAATAACAATAAACAAAAGATAGATATAACACTAA
* * *
39616081 CTACAAAAGTAATTTAACAATATCATGTGGTAACAAGTTCACCTGAAAGTG-AGATATGAAAGAT
66 CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGCTCACATGAAAGTGCA-ATATGAAAGAT
39616145 ATGCCCAAA
130 ATGCCCAAA
* *
39616154 TGAAATCATTTATAGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATAGATATAACACTAA
1 TGAAATCAATTATAGAATGAGTTACATTCAAAATAACAATAAACAAAAGATAGATATAACACTAA
39616218 CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGCTCACATGAAAGTGCAATATGAAAGA
66 CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGCTCACATGAAAGTGCAATATGAAAGA
39616281 CATGACATTT
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
137 79 0.68
138 37 0.32
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (138 bp):
TGAAATCAATTATAGAATGAGTTACATTCAAAATAACAATAAACAAAAGATAGATATAACACTAA
CTACAAAAGTAATTTAACAATATCATGTAGTAACAAGCTCACATGAAAGTGCAATATGAAAGATA
TGCCCAAA
Found at i:39617995 original size:5 final size:5
Alignment explanation
Indices: 39617985--39618010 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39617975 GAGATGGAAT
39617985 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
39618011 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Done.