Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 79 of 206
Found at i:22528842 original size:58 final size:58
Alignment explanation
Indices: 22528774--22528970 Score: 209
Period size: 58 Copynumber: 3.3 Consensus size: 58
22528764 ATCCAATTTA
* *
22528774 ATTGAGGAAAGGAGGTCAAAATTTGTTTATGTGGAAAGCTGCTTTTCGATCATGATCT
1 ATTGAAGAAAGGAGGTCAAAATTTGTTTATGTGGAAAGCTACTTTTCGATCATGATCT
*** * ** * * * *
22528832 ATTGAAGAAAGGAGGTCAAAGCATACCATTTTTGAAGAAAGCCACCTTTCAATCCA--ATTT
1 ATTGAAGAAAGGAGGTCAAA--AT-TTGTTTATGTGGAAAGCTACTTTTCGAT-CATGATCT
*
22528892 AATTGAGGAAAGGAGGTCAAAATTTGTTTATGTGGAAAGCTACTTTTCGATCATGATCT
1 -ATTGAAGAAAGGAGGTCAAAATTTGTTTATGTGGAAAGCTACTTTTCGATCATGATCT
*
22528951 ATTAAAGAAAGGAGGTCAAA
1 ATTGAAGAAAGGAGGTCAAA
22528971 GCTTGTTTTA
Statistics
Matches: 107, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
57 2 0.02
58 56 0.52
59 5 0.05
60 5 0.05
61 37 0.35
62 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (58 bp):
ATTGAAGAAAGGAGGTCAAAATTTGTTTATGTGGAAAGCTACTTTTCGATCATGATCT
Found at i:22528903 original size:61 final size:60
Alignment explanation
Indices: 22528734--22528912 Score: 168
Period size: 61 Copynumber: 3.0 Consensus size: 60
22528724 TAACGAATAT
* * *
22528734 CATACCATTTTTGCAGAAAGTCACCTTCCGATCCAATTTAATTGAGGAAAGGAGGTCAAA
1 CATACCATTTTTGAAGAAAGCCACCTTTCGATCCAATTTAATTGAGGAAAGGAGGTCAAA
*** * ** ** * * *
22528794 -AT-TTGTTTATGTGGAAAGCTGCTTTTCGAT-CATGATCT-ATTGAAGAAAGGAGGTCAAA
1 CATACCATTTTTGAAGAAAGCCACCTTTCGATCCA--ATTTAATTGAGGAAAGGAGGTCAAA
*
22528852 GCATACCATTTTTGAAGAAAGCCACCTTTCAATCCAATTTAATTGAGGAAAGGAGGTCAAA
1 -CATACCATTTTTGAAGAAAGCCACCTTTCGATCCAATTTAATTGAGGAAAGGAGGTCAAA
22528913 ATTTGTTTAT
Statistics
Matches: 87, Mismatches: 25, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
57 2 0.02
58 36 0.41
59 5 0.06
60 5 0.06
61 37 0.43
62 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (60 bp):
CATACCATTTTTGAAGAAAGCCACCTTTCGATCCAATTTAATTGAGGAAAGGAGGTCAAA
Found at i:22528945 original size:119 final size:119
Alignment explanation
Indices: 22528734--22528972 Score: 424
Period size: 119 Copynumber: 2.0 Consensus size: 119
22528724 TAACGAATAT
* * *
22528734 CATACCATTTTTGCAGAAAGTCACCTTCCGATCCAATTTAATTGAGGAAAGGAGGTCAAAATTTG
1 CATACCATTTTTGAAGAAAGCCACCTTCCAATCCAATTTAATTGAGGAAAGGAGGTCAAAATTTG
* *
22528799 TTTATGTGGAAAGCTGCTTTTCGATCATGATCTATTGAAGAAAGGAGGTCAAAG
66 TTTATGTGGAAAGCTACTTTTCGATCATGATCTATTAAAGAAAGGAGGTCAAAG
*
22528853 CATACCATTTTTGAAGAAAGCCACCTTTCAATCCAATTTAATTGAGGAAAGGAGGTCAAAATTTG
1 CATACCATTTTTGAAGAAAGCCACCTTCCAATCCAATTTAATTGAGGAAAGGAGGTCAAAATTTG
22528918 TTTATGTGGAAAGCTACTTTTCGATCATGATCTATTAAAGAAAGGAGGTCAAAG
66 TTTATGTGGAAAGCTACTTTTCGATCATGATCTATTAAAGAAAGGAGGTCAAAG
22528972 C
1 C
22528973 TTGTTTTAAG
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 114 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (119 bp):
CATACCATTTTTGAAGAAAGCCACCTTCCAATCCAATTTAATTGAGGAAAGGAGGTCAAAATTTG
TTTATGTGGAAAGCTACTTTTCGATCATGATCTATTAAAGAAAGGAGGTCAAAG
Found at i:22544870 original size:41 final size:41
Alignment explanation
Indices: 22544729--22544886 Score: 120
Period size: 42 Copynumber: 3.8 Consensus size: 41
22544719 AACATAGCTC
* * * * ** *
22544729 CTAAGCACGAGCCTAAATTGTTAATCCAAAATGCTAATGCTC
1 CTAAGCATGAGCTTAAACTGTTCATCCAAAA-AATAATGCTT
** * * ** *
22544771 CTAAATATGAGCTTAAACTATTCAGCCTAAACGATGATGCTT
1 CTAAGCATGAGCTTAAACTGTTCATCC-AAAAAATAATGCTT
* *
22544813 CTAAGCACGAGTTTAAACTGTTCATCCAAAAAATAATG-TT
1 CTAAGCATGAGCTTAAACTGTTCATCCAAAAAATAATGCTT
**
22544853 CTTAAGCATGAGCTTAAACTGCACATCCAAAAAA
1 C-TAAGCATGAGCTTAAACTGTTCATCCAAAAAA
22544887 ATATAAATGG
Statistics
Matches: 89, Mismatches: 25, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
40 3 0.03
41 36 0.40
42 47 0.53
43 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (41 bp):
CTAAGCATGAGCTTAAACTGTTCATCCAAAAAATAATGCTT
Found at i:22545709 original size:148 final size:148
Alignment explanation
Indices: 22545441--22545735 Score: 502
Period size: 148 Copynumber: 2.0 Consensus size: 148
22545431 TGATTAATTG
22545441 ATTATTTAACTGAGTGCTTAATTATCGGCCATTCAGTGTTTCTCCAAGTATGCTAAGTTCTCAGT
1 ATTATTTAACTGAGTGCTTAATTATCGGCCATTCAGTGTTTCTCCAAGTATGCTAAGTTCTCAGT
* **
22545506 ATACTAGGATTGACAACCCTAGTAGAATAATTAGATAGATGAGCTTGAAAGGGTATTCTGTTGT-
66 ATACTAGGATTGACAACCCTAGTAGAATAATTAGATAGATGAGATCAAAAGGGTATTCTGTTGTG
22545570 TGAAGTCTTTGGTAAACTA
131 T-AAGTCTTTGGTAAACTA
* * * * *
22545589 ATTATTTAATTGAGTGCTTATTTATCGGCCATTCAGTGTTTGTTCAAGTGTGCTAAGTTCTCAGT
1 ATTATTTAACTGAGTGCTTAATTATCGGCCATTCAGTGTTTCTCCAAGTATGCTAAGTTCTCAGT
22545654 ATACTAGGATTGACAACCCTAGTAGAATAATTAGATAGATGAGATCAAAAGGGTATTCTGTTGTG
66 ATACTAGGATTGACAACCCTAGTAGAATAATTAGATAGATGAGATCAAAAGGGTATTCTGTTGTG
22545719 TAAGTCTTTGGTAAACT
131 TAAGTCTTTGGTAAACT
22545736 TATGCTGAGT
Statistics
Matches: 138, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
148 137 0.99
149 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (148 bp):
ATTATTTAACTGAGTGCTTAATTATCGGCCATTCAGTGTTTCTCCAAGTATGCTAAGTTCTCAGT
ATACTAGGATTGACAACCCTAGTAGAATAATTAGATAGATGAGATCAAAAGGGTATTCTGTTGTG
TAAGTCTTTGGTAAACTA
Found at i:22552597 original size:2 final size:2
Alignment explanation
Indices: 22552592--22552618 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22552582 TAATCAGTTC
22552592 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22552619 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22555003 original size:13 final size:13
Alignment explanation
Indices: 22554985--22555050 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
22554975 TAGATTTTTC
22554985 CTAAATATTATCA
1 CTAAATATTATCA
22554998 CTAAATA--ATC-
1 CTAAATATTATCA
22555008 CTAAATATTATCA
1 CTAAATATTATCA
*
22555021 CTAAATA--AT-T
1 CTAAATATTATCA
*
22555031 CTAAATATTATTA
1 CTAAATATTATCA
22555044 CTAAATA
1 CTAAATA
22555051 ATTCAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 14 0.31
11 5 0.11
12 5 0.11
13 21 0.47
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:22555013 original size:10 final size:11
Alignment explanation
Indices: 22554983--22555038 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 11
22554973 GCTAGATTTT
22554983 TCCTAAATATTA
1 TCCTAAATA-TA
22554995 TCACTAAATA-A
1 TC-CTAAATATA
22555006 TCCTAAATATTA
1 TCCTAAATA-TA
22555018 TCACTAAATA-A
1 TC-CTAAATATA
*
22555029 TTCTAAATAT
1 TCCTAAATAT
22555039 TATTACTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
10 14 0.37
11 5 0.13
12 5 0.13
13 14 0.37
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (11 bp):
TCCTAAATATA
Found at i:22555053 original size:23 final size:23
Alignment explanation
Indices: 22554985--22555059 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
22554975 TAGATTTTTC
*
22554985 CTAAATATTATCACTAAATAATC
1 CTAAATATTATCACTAAATAATT
22555008 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
22555031 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
22555054 CAAAAT
1 CTAAAT
22555060 TTAAAAATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:22557862 original size:15 final size:17
Alignment explanation
Indices: 22557842--22557879 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
22557832 ATAAATAAAT
22557842 AATAAAA-G-AAACAAA
1 AATAAAAGGAAAACAAA
22557857 AATAAAAGGAAAACAAA
1 AATAAAAGGAAAACAAA
22557874 AA-AAAA
1 AATAAAA
22557880 CACAACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (17 bp):
AATAAAAGGAAAACAAA
Found at i:22558672 original size:40 final size:40
Alignment explanation
Indices: 22558628--22558840 Score: 205
Period size: 40 Copynumber: 5.2 Consensus size: 40
22558618 GTCTTTGTTC
* *
22558628 GCTCCGCTACTGCTTAGGGAGATAAGACTTGACGCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCT
* * * ** *
22558668 GCTCCACTATTGCTTAGGGAGATAAGATATGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCGATCT
* *
22558710 GCTTCTCTACTGCTTAGGGAGATAAGACTTGATGCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCT
* * ** *
22558750 GCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCGATCT
* *
22558792 GCTTCTCTACTGCTTAGGGAGATAAGACTTGATGCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCT
22558832 GCTCCACTA
1 GCTCCACTA
22558841 TTGNNNNNNN
Statistics
Matches: 133, Mismatches: 32, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
39 6 0.05
40 62 0.47
41 6 0.05
42 54 0.41
43 5 0.04
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (40 bp):
GCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCT
Found at i:22558734 original size:42 final size:42
Alignment explanation
Indices: 22558678--22558818 Score: 180
Period size: 42 Copynumber: 3.4 Consensus size: 42
22558668 GCTCCACTAT
*
22558678 TGCTTAGGGAGATAAGATATGTGGTTTTGTCCGCTTCTCTAC
1 TGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTTCTCTAC
* ** * * * *
22558720 TGCTTAGGGAGATAAGA-CT-T-GATGCGATCTGCTCCACTAT
1 TGCTTAGGGAGATAAGATCTGTGGTTTTG-TCCGCTTCTCTAC
22558760 TGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTTCTCTAC
1 TGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTTCTCTAC
22558802 TGCTTAGGGAGATAAGA
1 TGCTTAGGGAGATAAGA
22558819 CTTGATGCGA
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
39 3 0.04
40 27 0.34
41 3 0.04
42 44 0.55
43 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (42 bp):
TGCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTTCTCTAC
Found at i:22558741 original size:82 final size:82
Alignment explanation
Indices: 22558634--22558843 Score: 402
Period size: 82 Copynumber: 2.6 Consensus size: 82
22558624 GTTCGCTCCG
*
22558634 CTACTGCTTAGGGAGATAAGACTTGACGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATATG
1 CTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATATG
22558699 TGGTTTTGTCCGCTTCT
66 TGGTTTTGTCCGCTTCT
*
22558716 CTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTG
1 CTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATATG
22558781 TGGTTTTGTCCGCTTCT
66 TGGTTTTGTCCGCTTCT
22558798 CTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTG
1 CTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTG
22558844 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 126 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (82 bp):
CTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAAGATATG
TGGTTTTGTCCGCTTCT
Found at i:22559884 original size:40 final size:40
Alignment explanation
Indices: 22559829--22560251 Score: 519
Period size: 40 Copynumber: 10.4 Consensus size: 40
22559819 NNNNNNNNNN
22559829 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
1 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
* *
22559869 GCTTAGGGAGATAAGATCTGTGGTTCTG-TCTGCTCCACTACT
1 GCTTAGGGAGATAAGA-CT-TGATGC-GATCTGCTCCACTACT
22559911 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
1 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
* *
22559951 GCTTAGGGAGATAAGACTTGATGCGATCCGCTCCACTATT
1 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
* **** * *
22559991 GCTTAGGGAGATAAGATCTGTGGTTTTTTCCGCTCCGCTACT
1 GCTTAGGGAGATAAGA-CT-TGATGCGATCTGCTCCACTACT
* *
22560033 GCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTATT
1 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
* * *
22560073 GCTTAGGGAGATAAGATCTGTGGTTCG-TCCGCTCCACTACT
1 GCTTAGGGAGATAAGA-CT-TGATGCGATCTGCTCCACTACT
* *
22560114 GCTTAGGGAGATAAGATTTGATGCGATCTGCTCCACTATT
1 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
* ** * *
22560154 GCTTAGGGAGATAAGATCTGTGGTTTTG-TCCGCTCCGCTACT
1 GCTTAGGGAGATAAGA-CT-T-GATGCGATCTGCTCCACTACT
*
22560196 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATT
1 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
22560236 GCTTAGGGAGATAAGA
1 GCTTAGGGAGATAAGA
22560252 TCTGTGTCTT
Statistics
Matches: 325, Mismatches: 45, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
39 9 0.03
40 174 0.54
41 41 0.13
42 97 0.30
43 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
GCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACT
Found at i:22559966 original size:82 final size:81
Alignment explanation
Indices: 22559829--22560257 Score: 598
Period size: 82 Copynumber: 5.3 Consensus size: 81
22559819 NNNNNNNNNN
* * *
22559829 GCTTAGGGAGATAAGA-CT-TGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG
1 GCTTAGGGAGATAAGATCTGTGATTCG-TCCGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGA
* *
22559892 TTCTG-TCTGCTCCACTACT
63 TGC-GATCTGCTCCACTATT
* *
22559911 GCTTAGGGAGATAAGA-CT-TGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATG
1 GCTTAGGGAGATAAGATCTGTGATTCG-TCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATG
*
22559974 CGATCCGCTCCACTATT
65 CGATCTGCTCCACTATT
* ** * *
22559991 GCTTAGGGAGATAAGATCTGTGGTTTTTTCCGCTCCGCTACTGCTTAAGGAGATAAGACTTGATG
1 GCTTAGGGAGATAAGATCTGT-GATTCGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATG
22560056 CGATCTGCTCCACTATT
65 CGATCTGCTCCACTATT
* *
22560073 GCTTAGGGAGATAAGATCTGTGGTTCGTCCGCTCCACTACTGCTTAGGGAGATAAGATTTGATGC
1 GCTTAGGGAGATAAGATCTGTGATTCGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGC
22560138 GATCTGCTCCACTATT
66 GATCTGCTCCACTATT
* * *
22560154 GCTTAGGGAGATAAGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATG
1 GCTTAGGGAGATAAGATCTGT-GATTCGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATG
22560219 CGATCTGCTCCACTATT
65 CGATCTGCTCCACTATT
22560236 GCTTAGGGAGATAAGATCTGTG
1 GCTTAGGGAGATAAGATCTGTG
22560258 TCTTCGATCC
Statistics
Matches: 320, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
79 1 0.00
80 32 0.10
81 80 0.25
82 205 0.64
83 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (81 bp):
GCTTAGGGAGATAAGATCTGTGATTCGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGC
GATCTGCTCCACTATT
Found at i:22560149 original size:163 final size:164
Alignment explanation
Indices: 22559858--22560257 Score: 646
Period size: 163 Copynumber: 2.4 Consensus size: 164
22559848 GATGCGATCT
* * * *
22559858 GCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTG-TCTGCTCCACTACTGCTTAGGGAGA
1 GCTCCGCTACTGCTTAGGGAGATAAGA-CT-TGATGC-GATCTGCTCCACTATTGCTTAGGGAGA
*
22559922 TAAGA-CT-TGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCC
63 TAAGATCTGTGATGCGATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCC
*
22559985 ACTATTGCTTAGGGAGATAAGATCTGTGGTTTTTTCC
128 ACTATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCC
*
22560022 GCTCCGCTACTGCTTAAGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAA
1 GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAA
* * * *
22560087 GATCTGTGGTTCG-TCCGCTCCACTACTGCTTAGGGAGATAAGATTTGATGCGATCTGCTCCACT
66 GATCTGTGATGCGATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCACT
22560151 ATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCC
131 ATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCC
22560185 GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAA
1 GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAA
22560250 GATCTGTG
66 GATCTGTG
22560258 TCTTCGATCC
Statistics
Matches: 221, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
161 1 0.00
162 33 0.15
163 157 0.71
164 30 0.14
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (164 bp):
GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATAA
GATCTGTGATGCGATCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCACT
ATTGCTTAGGGAGATAAGATCTGTGGTTTTGTCC
Found at i:22565421 original size:20 final size:20
Alignment explanation
Indices: 22565396--22565438 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
22565386 TCTATGTATG
22565396 GCATATCATCGGTGACTGAT
1 GCATATCATCGGTGACTGAT
22565416 GCATATCATCGGTGACTGAT
1 GCATATCATCGGTGACTGAT
22565436 GCA
1 GCA
22565439 ATGATGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCATATCATCGGTGACTGAT
Found at i:22567063 original size:12 final size:12
Alignment explanation
Indices: 22567046--22567079 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
22567036 GAAATCTCTC
*
22567046 TGTGTTGGTCCT
1 TGTGTTGGGCCT
22567058 TGTGTTGGGCCT
1 TGTGTTGGGCCT
22567070 TGTGTTGGGC
1 TGTGTTGGGC
22567080 TCCTGCCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.41, T:0.44
Consensus pattern (12 bp):
TGTGTTGGGCCT
Found at i:22573232 original size:15 final size:17
Alignment explanation
Indices: 22573212--22573249 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
22573202 ATAAATAAAT
22573212 AATAAAA-G-AAACAAA
1 AATAAAAGGAAAACAAA
22573227 AATAAAAGGAAAACAAA
1 AATAAAAGGAAAACAAA
22573244 AA-AAAA
1 AATAAAA
22573250 CACAACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (17 bp):
AATAAAAGGAAAACAAA
Found at i:22586349 original size:13 final size:13
Alignment explanation
Indices: 22586331--22586373 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
22586321 TAAATTTTTT
22586331 CTAAATATTATCA
1 CTAAATATTATCA
22586344 CTAAATA--ATC-
1 CTAAATATTATCA
22586354 CTAAATATTATCA
1 CTAAATATTATCA
22586367 CTAAATA
1 CTAAATA
22586374 ATTAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:22586359 original size:23 final size:23
Alignment explanation
Indices: 22586331--22586375 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
22586321 TAAATTTTTT
22586331 CTAAATATTATCACTAAATAATC
1 CTAAATATTATCACTAAATAATC
22586354 CTAAATATTATCACTAAATAAT
1 CTAAATATTATCACTAAATAAT
22586376 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATC
Found at i:22586382 original size:23 final size:23
Alignment explanation
Indices: 22586333--22586382 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
22586323 AATTTTTTCT
**
22586333 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCAA
*
22586356 AAATATTATCACTAAATAATTAA
1 AAATATTATCACTAAATAATCAA
22586379 AAAT
1 AAAT
22586383 TTAAAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCAA
Found at i:22587491 original size:23 final size:23
Alignment explanation
Indices: 22587456--22587508 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
22587446 TGATTTATTG
22587456 TAGCAC-ATCGGTGCAATTCATCC
1 TAGCACTAT-GGTGCAATTCATCC
* * *
22587479 TGGCACTATGGTGCTATTCATTC
1 TAGCACTATGGTGCAATTCATCC
22587502 TAGCACT
1 TAGCACT
22587509 TTTCTGTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (23 bp):
TAGCACTATGGTGCAATTCATCC
Found at i:22589930 original size:45 final size:44
Alignment explanation
Indices: 22589860--22590280 Score: 169
Period size: 44 Copynumber: 9.7 Consensus size: 44
22589850 TACTGCATCT
* * * *
22589860 TCTACTCCACTGCAA-TATCATGGAGATAGGATTTGCTTTCTTGGG
1 TCTACTCCACTGCAACT-TCAGGGAGATAAGATTCGCTTTCTT-GA
* * *
22589905 TCTACTCCACTGCAACTTCAGGGAGATAAGACTCG-ATGC--GA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCTTTCTTGA
* * * * *
22589946 TCTAC-ACTCTGCAACTTCAGAGAGATAAGATTCGATATT-TTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCT-TTCTTGA
** * * * * * *
22589989 TCCGCTTCACAGCAATTTCAGGGAGATAGGATTTGCTTTCTTGGG
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCTTTCTT-GA
* * ** *
22590034 TCTGCTCCACTGCAACTTCTA-GGAGATAAGA--CCCGAT-GTGA
1 TCTACTCCACTGCAACTTC-AGGGAGATAAGATTCGCTTTCTTGA
* * *
22590075 TCTACTCTACTGCAACTTCAGAGAGATAAGA-TCTG-TGATT-TTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTC-GCT--TTCTTGA
** * * * * *
22590119 TCCGCTCCACTGCAACTTCAGAGAGATATGATT--ATTGGTTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCTT--TCTTGA
* ** *
22590163 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCTTTCTTGA
* * * *
22590207 GTCTGC-CTCACTGCAACTTTA-GGAGGATAAGACTT-GATTACTT-A
1 -TCTACTC-CACTGCAACTTCAGGGA-GATAAGA-TTCGCTTTCTTGA
* *
22590251 GTCTGCTCCACAGCAACTTCAGGGAGATAA
1 -TCTACTCCACTGCAACTTCAGGGAGATAA
22590281 ATCTAGATGC
Statistics
Matches: 285, Mismatches: 64, Indels: 55
0.71 0.16 0.14
Matches are distributed among these distances:
40 26 0.09
41 34 0.12
42 3 0.01
43 10 0.04
44 122 0.43
45 86 0.30
46 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCTTTCTTGA
Found at i:22590135 original size:44 final size:44
Alignment explanation
Indices: 22589954--22590407 Score: 226
Period size: 44 Copynumber: 10.4 Consensus size: 44
22589944 GATCTACACT
* *
22589954 CTGCAACTTCAGAGAGATAAGAT-TCGAT-ATTTTAATCCGCTTCA
1 CTGCAACTTCAGAGAGATAAGATCT-G-TGATTTTAATCTGCTCCA
* * * * * **
22589998 CAGCAATTTCAGGGAGATAGGAT-T-TGCTTTCTTGGGTCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCTGTG-ATT-TT-AATCTGCTCCA
** * * * *
22590043 CTGCAACTTCTAG-GAGATAAGA-C-CCGA-TGTGATCTACTCTA
1 CTGCAACTTC-AGAGAGATAAGATCTGTGATTTTAATCTGCTCCA
*
22590084 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCA
* * *
22590128 CTGCAACTTCAGAGAGATATGAT-TATTGGTTTTAATCTGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCT-GTGATTTTAATCTGCTCCA
* ** * *
22590172 CTGCAACTTCAGGGAGATAAGAT-TCGCCATCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGAGAGATAAGATCT-GTGAT-TTTAATCTGCTC-CA
* *
22590217 CTGCAACTTTAG-GAGGATAAGA-CT-TGATTACTTAGTCTGCTCCA
1 CTGCAACTTCAGAGA-GATAAGATCTGTGATT--TTAATCTGCTCCA
* * * *** *
22590261 CAGCAACTTCAGGGAGATAA-ATCT-AGA-TGCGATCTGCT-CT
1 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCA
* * **
22590301 CTGTAACTTCAGAGAGATAAAATCTGTGATTTTAATCCACTCCA
1 CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCA
* * * * ** **
22590345 CTGTAACTTCAGGGAGATAGGAT-TATTGGCTTTAATCTATTCCA
1 CTGCAACTTCAGAGAGATAAGATCT-GTGATTTTAATCTGCTCCA
* *
22590389 CTACAACTTCAGGGAGATA
1 CTGCAACTTCAGAGAGATA
22590408 GGATTATTGG
Statistics
Matches: 314, Mismatches: 70, Indels: 52
0.72 0.16 0.12
Matches are distributed among these distances:
40 20 0.06
41 38 0.12
42 5 0.02
43 17 0.05
44 176 0.56
45 56 0.18
46 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
CTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCTGCTCCA
Found at i:22590171 original size:129 final size:129
Alignment explanation
Indices: 22589882--22590193 Score: 393
Period size: 129 Copynumber: 2.4 Consensus size: 129
22589872 CAATATCATG
* ** * *
22589882 GAGATAGGATTTGCTTTCTTGGGTCTACTCCACTGCAACTTCAGGGAGATAAGACTCGATGCGAT
1 GAGATAGGATTTGCGTTCTTGAATCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGAT
* * *
22589947 CTACACTCTGCAACTTCAGAGAGATAAGATTCGATATTTTAATCCGCTTCACAGCAATTTCAGG
66 CTACACTCTGCAACTTCAGAGAGATAAGATTCGATATTTTAATCCGCTCCACAGCAACTTCAGA
* ** *
22590011 GAGATAGGATTTGCTTTCTTGGGTCTGCTCCACTGCAACTTCTA-GGAGATAAGACCCGATGTGA
1 GAGATAGGATTTGCGTTCTTGAATCTGCTCCACTGCAACTTC-AGGGAGATAAGACCCGATGCGA
* *
22590075 TCTACTCTACTGCAACTTCAGAGAGATAAGA-TCTG-TGATTTTAATCCGCTCCACTGCAACTTC
65 TCTACACT-CTGCAACTTCAGAGAGATAAGATTC-GAT-ATTTTAATCCGCTCCACAGCAACTTC
22590138 AGA
127 AGA
*
22590141 GAGATATGATTATTG-GTT-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 GAGATAGGA-T-TTGCGTTCTTGAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
22590194 TTCGCCATCT
Statistics
Matches: 164, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
128 1 0.01
129 98 0.60
130 59 0.36
131 3 0.02
132 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (129 bp):
GAGATAGGATTTGCGTTCTTGAATCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGAT
CTACACTCTGCAACTTCAGAGAGATAAGATTCGATATTTTAATCCGCTCCACAGCAACTTCAGA
Found at i:22590408 original size:44 final size:44
Alignment explanation
Indices: 22590331--22590456 Score: 153
Period size: 44 Copynumber: 2.9 Consensus size: 44
22590321 AATCTGTGAT
**
22590331 TTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTATTGGC
1 TTTAATCCACTCCACTACAACTTCAGGGAGATAGGATTATTGGC
* *
22590375 TTTAATCTATTCCACTACAACTTCAGGGAGATAGGATTATTGGC
1 TTTAATCCACTCCACTACAACTTCAGGGAGATAGGATTATTGGC
* * * ** * *
22590419 TTCAAACCGCTTTACTGCAACTTCAGGGAGATAAGATT
1 TTTAATCCACTCCACTACAACTTCAGGGAGATAGGATT
22590457 TGCCATCTTC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (44 bp):
TTTAATCCACTCCACTACAACTTCAGGGAGATAGGATTATTGGC
Found at i:22590863 original size:44 final size:42
Alignment explanation
Indices: 22590808--22591172 Score: 276
Period size: 44 Copynumber: 8.7 Consensus size: 42
22590798 TGCTATTTTC
* *
22590808 AACCTACTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGA-CT-CAATCTTT
* * *
22590852 AATCTATTCCACTGCTG-CCAAGGGAGATAGAATTCTCAATCTTC
1 AACCTATTCCACTGCTGACC-AGGGAGATAGGA--CTCAATCTTT
*
22590896 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGA--CTCAATCTTT
* * *
22590940 AACCTATTCGACAGCT-ATCTAGGGAGATAGGA-T---TCTTT
1 AACCTATTCCACTGCTGA-CCAGGGAGATAGGACTCAATCTTT
* * *
22590978 AATCTATTTCACTGCTG--C----AGATA-G---CATTCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGACTCAATCTTT
* * * * * *
22591010 AATCTATTTCACTGCTGCCCAGAGAGATAGAATTCTCAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGA--CTCAATCTTT
* *
22591054 AACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATATTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGA-CT-CAATCTTT
* * * *
22591098 AACCTATTCCATTGCTGTCCAGAGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGA--CTCAATCTTT
22591142 AACCTATTCCACTGCTGACCAGGGAGATAGG
1 AACCTATTCCACTGCTGACCAGGGAGATAGG
22591173 GCTGGGGTCA
Statistics
Matches: 262, Mismatches: 37, Indels: 44
0.76 0.11 0.13
Matches are distributed among these distances:
31 1 0.00
32 27 0.10
34 1 0.00
38 22 0.08
43 5 0.02
44 201 0.77
45 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (42 bp):
AACCTATTCCACTGCTGACCAGGGAGATAGGACTCAATCTTT
Found at i:22590964 original size:88 final size:87
Alignment explanation
Indices: 22590805--22591172 Score: 365
Period size: 88 Copynumber: 4.4 Consensus size: 87
22590795 ATCTGCTATT
* * * *
22590805 TTCAACCTACTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATC-ACAATCTTTAACCTATTCCACTGCTGC
* *
22590870 CAAGGGAGATAGAATTCTCAATC
65 CCAGAGAGATAGAATTCTCAATC
* * **
22590893 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCGACAGCTAT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TCACAATCTTTAACCTATTCCACTGCTGC
* * *
22590958 CTAGGGAGATAGGA-T-TC--T-
65 CCAGAGAGATAGAATTCTCAATC
* * * * *
22590976 TT-AATCTATTTCACTGCTG--C----AGATA-G----CATTCTTTAATCTATTTCACTGCTGCC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATCACAATCTTTAACCTATTCCACTGCTGCC
22591029 CAGAGAGATAGAATTCTCAATC
66 CAGAGAGATAGAATTCTCAATC
* * * *
22591051 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTTACAATATTTAACCTATTCCATTGCTGT
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TCACAATCTTTAACCTATTCCACTGCTGC
* *
22591116 CCAGAGAGATAGGATTCACAATC
65 CCAGAGAGATAGAATTCTCAATC
*
22591139 TTTAACCTATTCCACTGCTGACCAGGGAGATAGG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGG
22591173 GCTGGGGTCA
Statistics
Matches: 228, Mismatches: 33, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
70 30 0.13
71 1 0.00
72 2 0.01
74 1 0.00
75 3 0.01
76 20 0.09
78 1 0.00
80 1 0.00
82 20 0.09
83 3 0.01
84 1 0.00
86 2 0.01
87 1 0.00
88 141 0.62
89 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (87 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATCACAATCTTTAACCTATTCCACTGCTGCC
CAGAGAGATAGAATTCTCAATC
Found at i:22591007 original size:32 final size:32
Alignment explanation
Indices: 22590964--22591027 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
22590954 CTATCTAGGG
*
22590964 AGATAGGATTCTTTAATCTATTTCACTGCTGC
1 AGATAGCATTCTTTAATCTATTTCACTGCTGC
22590996 AGATAGCATTCTTTAATCTATTTCACTGCTGC
1 AGATAGCATTCTTTAATCTATTTCACTGCTGC
22591028 CCAGAGAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (32 bp):
AGATAGCATTCTTTAATCTATTTCACTGCTGC
Found at i:22591231 original size:88 final size:88
Alignment explanation
Indices: 22591172--22591577 Score: 573
Period size: 88 Copynumber: 4.6 Consensus size: 88
22591162 AGGGAGATAG
* * * * *
22591172 GGCTGGGGTCATCAATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTAC
1 GGCTGGTGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTAC
*
22591237 TCCGCTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * * *
22591260 GACTGGTGTCTTTGATCTACTTCGTTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAGCCTAC
1 GGCTGGTGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTAC
22591325 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
22591348 GGCTGGTGTCTTCGATATGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTTTTTTTAGCCTGC
1 GGCTGGTGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTAC
22591413 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
22591436 GGCTGGTGT-ATTCAATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTG
1 GGCTGGTGTCA-TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTA
** *
22591500 CTCTACTACAACCCAGGGAGGCAA
65 CTCCGCTGCAACCCAGGGAGGCAA
22591524 GGCTGGTGT-ATTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
1 GGCTGGTGTCA-TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT
22591578 CTTCACTAAT
Statistics
Matches: 287, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
88 287 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCATCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTAC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:22591346 original size:44 final size:44
Alignment explanation
Indices: 22591205--22591348 Score: 132
Period size: 44 Copynumber: 3.3 Consensus size: 44
22591195 GTTGTCGGTG
* *
22591205 CAGGAAGGCAAGATCTACTATTTTTAACCTACTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGCAACC
* * * * * * * **
22591249 CAAGG-AGGCAAGA-CTGGTGTCTTT-GATCTACTTCGTTGTCGATG
1 C-AGGAAGGCAAGATCTGCTATTTTTAG-CCTACTCCGCTG-CAACC
22591293 CAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGCAACC
*
22591337 CAGGGAGGCAAG
1 CAGGAAGGCAAG
22591349 GCTGGTGTCT
Statistics
Matches: 73, Mismatches: 21, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
43 19 0.26
44 33 0.45
45 20 0.27
46 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGCAACC
Found at i:22591462 original size:43 final size:43
Alignment explanation
Indices: 22591327--22591462 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 43
22591317 TAGCCTACTC
* * *
22591327 CGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATATGCTT
1 CGCTGCAACCCAGGGAGGCAAGGCTGGTGTATTCAATCTGCTT
**** * * * * * * * ** *
22591370 CGCTGTCGGTGCAAGAAGGCAAGATCTGCTTTTTTTAGCCTGCTC
1 CGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTATTCAATCTGCTT
22591415 CGCTGCAACCCAGGGAGGCAAGGCTGGTGTATTCAATCTGCTT
1 CGCTGCAACCCAGGGAGGCAAGGCTGGTGTATTCAATCTGCTT
22591458 CGCTG
1 CGCTG
22591463 TTGGTGCAGG
Statistics
Matches: 61, Mismatches: 30, Indels: 4
0.64 0.32 0.04
Matches are distributed among these distances:
43 23 0.38
44 22 0.36
45 16 0.26
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (43 bp):
CGCTGCAACCCAGGGAGGCAAGGCTGGTGTATTCAATCTGCTT
Found at i:22591566 original size:44 final size:44
Alignment explanation
Indices: 22591337--22591568 Score: 105
Period size: 44 Copynumber: 5.3 Consensus size: 44
22591327 CGCTGCAACC
* * *
22591337 CAGGGAGGCAAGGCTGGTGTCTTCGATATGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTATTCGATCTGCTTCGCTGTCGGTG
* * * * ** * * ****
22591381 CAAGAAGGCAAGATCTGCT-TTTTTTAGCCTGCTCCGCTG-CAACC
1 CAGGAAGGCAAG-GCTGGTGTATTCGA-TCTGCTTCGCTGTCGGTG
* * *
22591425 CAGGGAGGCAAGGCTGGTGTATTCAATCTGCTTCGCTGTTGGTG
1 CAGGAAGGCAAGGCTGGTGTATTCGATCTGCTTCGCTGTCGGTG
* * * ** * * * ****
22591469 CAGGAAGGCAAGATCTGCTAT-TTTTAGCCTGC-TCTACT-ACAACC
1 CAGGAAGGCAAG-GCTGGTGTATTCGA-TCTGCTTC-GCTGTCGGTG
*
22591513 CAGGGAGGCAAGGCTGGTGTATTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGGTGTATTCGATCTGCTTCGCTGTCGGTG
22591557 CAGGAAGGCAAG
1 CAGGAAGGCAAG
22591569 ATCTGCTATC
Statistics
Matches: 122, Mismatches: 56, Indels: 20
0.62 0.28 0.10
Matches are distributed among these distances:
43 25 0.20
44 73 0.60
45 24 0.20
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTGTATTCGATCTGCTTCGCTGTCGGTG
Found at i:22592834 original size:17 final size:18
Alignment explanation
Indices: 22592812--22592846 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
22592802 TTGGCCTCTC
22592812 CATTTTTCTT-TTCTTTT
1 CATTTTTCTTATTCTTTT
22592829 CATTTTTCTTATTCTTTT
1 CATTTTTCTTATTCTTTT
22592847 TATCACTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (18 bp):
CATTTTTCTTATTCTTTT
Found at i:22603354 original size:50 final size:49
Alignment explanation
Indices: 22603286--22603412 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 49
22603276 TATTTTTCTT
* * *
22603286 TAATTAATTTAAGTTAATTAAGAGATAAAATAATATTTTTATATTAT-TAC
1 TAATTAAATTAAATTAATTAAGAGATAAAATAA-ATTATTATATTATCT-C
* * * *
22603336 TAATTAAATTAAAATAATTAAGTGATAATATTAAATTATTATTTTATCTC
1 TAATTAAATTAAATTAATTAAGAGATAA-AATAAATTATTATATTATCTC
22603386 TAATT-AATTAAATTAA-TAAGAGATAAA
1 TAATTAAATTAAATTAATTAAGAGATAAA
22603413 GACTAAATAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
47 1 0.02
48 9 0.14
49 10 0.15
50 41 0.62
51 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (49 bp):
TAATTAAATTAAATTAATTAAGAGATAAAATAAATTATTATATTATCTC
Found at i:22607501 original size:3 final size:3
Alignment explanation
Indices: 22607493--22607525 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
22607483 ATCTCAGTTC
22607493 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
22607526 TCACCTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:22609601 original size:12 final size:12
Alignment explanation
Indices: 22609584--22609614 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
22609574 ATATTAAGAT
22609584 GGTTAAAAATAA
1 GGTTAAAAATAA
22609596 GGTTAAAAATAA
1 GGTTAAAAATAA
*
22609608 AGTTAAA
1 GGTTAAA
22609615 TAATTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (12 bp):
GGTTAAAAATAA
Found at i:22612321 original size:3 final size:3
Alignment explanation
Indices: 22612313--22612343 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
22612303 TCTACTTTTC
*
22612313 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
22612344 TGCATTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:22612333 original size:15 final size:16
Alignment explanation
Indices: 22612307--22612340 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
22612297 GGTTGGTCTA
22612307 CTTTTCTCTTCTTCTT
1 CTTTTCTCTTCTTCTT
22612323 CTTTT-TCTTCTTCTT
1 CTTTTCTCTTCTTCTT
22612338 CTT
1 CTT
22612341 CTTTGCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
CTTTTCTCTTCTTCTT
Found at i:22614702 original size:2 final size:2
Alignment explanation
Indices: 22614697--22614731 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22614687 CCAAAAAATA
22614697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22614732 CAGTGGAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22617383 original size:21 final size:21
Alignment explanation
Indices: 22617357--22617398 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
22617347 TTTATCAACA
*
22617357 AAAATGGAGAGATGAGAAGAG
1 AAAATGGAAAGATGAGAAGAG
*
22617378 AAAATGGAAAGGTGAGAAGAG
1 AAAATGGAAAGATGAGAAGAG
22617399 GGTGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.10
Consensus pattern (21 bp):
AAAATGGAAAGATGAGAAGAG
Found at i:22617543 original size:22 final size:22
Alignment explanation
Indices: 22617508--22617549 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
22617498 TCGGGTCGGG
22617508 TTATTATATAATAAAATATATT
1 TTATTATATAATAAAATATATT
* * *
22617530 TTATTTTATTATAATATATA
1 TTATTATATAATAAAATATA
22617550 ACAATTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATATAATAAAATATATT
Found at i:22624280 original size:8 final size:8
Alignment explanation
Indices: 22624267--22624291 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
22624257 TTAGAAATGG
22624267 AAAACTAT
1 AAAACTAT
22624275 AAAACTAT
1 AAAACTAT
22624283 AAAACTAT
1 AAAACTAT
22624291 A
1 A
22624292 TTGGTGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAACTAT
Found at i:22629788 original size:17 final size:18
Alignment explanation
Indices: 22629756--22629792 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
22629746 CCTTGTGGTT
*
22629756 CACCCGTGTCGGCCCACA
1 CACCCGCGTCGGCCCACA
22629774 CACCCGCGT-GGCCCACA
1 CACCCGCGTCGGCCCACA
22629791 CA
1 CA
22629793 ACCCATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.19, C:0.51, G:0.22, T:0.08
Consensus pattern (18 bp):
CACCCGCGTCGGCCCACA
Found at i:22640777 original size:18 final size:18
Alignment explanation
Indices: 22640751--22640785 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22640741 TAGATGTGCA
*
22640751 CATTAAATGTAGATATGT
1 CATTAAATGGAGATATGT
*
22640769 CATTGAATGGAGATATG
1 CATTAAATGGAGATATG
22640786 ATATGTTGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (18 bp):
CATTAAATGGAGATATGT
Found at i:22641609 original size:15 final size:15
Alignment explanation
Indices: 22641589--22641617 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22641579 GTGTTTTTAA
22641589 CTAAACTTTTGGTAT
1 CTAAACTTTTGGTAT
22641604 CTAAACTTTTGGTA
1 CTAAACTTTTGGTA
22641618 CCCTATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
CTAAACTTTTGGTAT
Found at i:22644731 original size:18 final size:18
Alignment explanation
Indices: 22644708--22644743 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
22644698 GGGCTTAGAC
22644708 CTTTTAAAGAATTTTATT
1 CTTTTAAAGAATTTTATT
*
22644726 CTTTTAGAGAATTTTATT
1 CTTTTAAAGAATTTTATT
22644744 ATTGTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
CTTTTAAAGAATTTTATT
Found at i:22648020 original size:54 final size:54
Alignment explanation
Indices: 22647953--22648058 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 54
22647943 ATGGTTACAC
* * *
22647953 TCCTGGCAAACTACCCCATTTTTCCTATCCTAGT-GAACTATCCCATGTTTACCG
1 TCCTGGCAAACTACCCCAGTTTTACTATCCGAGTAG-ACTATCCCATGTTTACCG
** * *
22648007 TCCTGGCGGACTACCCCAGTTTTACTATTCGGGTAGACTATCCCATGTTTAC
1 TCCTGGCAAACTACCCCAGTTTTACTATCCGAGTAGACTATCCCATGTTTAC
22648059 TATCATGGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (54 bp):
TCCTGGCAAACTACCCCAGTTTTACTATCCGAGTAGACTATCCCATGTTTACCG
Found at i:22648068 original size:27 final size:26
Alignment explanation
Indices: 22647989--22648069 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
22647979 ATCCTAGTGA
** **
22647989 ACTATCCCATGTTTACCGTCCTGGCGG
1 ACTATCCCATGTTTACTAT-CTGGTAG
* *
22648016 ACTACCCCA-GTTTTACTATTCGGGTAG
1 ACTATCCCATG-TTTACTA-TCTGGTAG
22648043 ACTATCCCATGTTTACTATCATGGTAG
1 ACTATCCCATGTTTACTATC-TGGTAG
22648070 GCTACCTCGT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
26 3 0.07
27 37 0.88
28 2 0.05
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (26 bp):
ACTATCCCATGTTTACTATCTGGTAG
Found at i:22648329 original size:67 final size:67
Alignment explanation
Indices: 22648239--22648588 Score: 382
Period size: 67 Copynumber: 5.2 Consensus size: 67
22648229 AGATATAGTA
* * * * * * * *
22648239 TTACACATCATACTCTATTTTTAATGTCTTGGAAAACTCTCTATGTTGTCATAACCAAGCTATGG
1 TTACACATCATACCCCATGTTTAATGTCCTAGAAGACTCTCTATGTTGTCATAGCCGAGCTATGG
22648304 TC
66 TC
* * *
22648306 TTACACATCATACCCCATGTTTAATATCCT-GACGGACTCTCTATGTTGTCATCGCCGAGCTATG
1 TTACACATCATACCCCATGTTTAATGTCCTAGA-AGACTCTCTATGTTGTCATAGCCGAGCTATG
22648370 GTC
65 GTC
* * ** * *
22648373 TTACACATCATACCCTATGTTTAATGTCCTGGTGGACTCTCTATGTTGCCATAGCCGAGCTATTG
1 TTACACATCATACCCCATGTTTAATGTCCTAGAAGACTCTCTATGTTGTCATAGCCGAGCTATGG
22648438 TC
66 TC
* * * * ** *
22648440 TTGCACATCATACCTCATGTTTAATGTCCTAGCAA-ACTCTCTTTGTTGCCATAGATGAGTTATG
1 TTACACATCATACCCCATGTTTAATGTCCTAG-AAGACTCTCTATGTTGTCATAGCCGAGCTATG
*
22648504 GTT
65 GTC
* * * *
22648507 TTACACATCAAACCCCATGTTTAATGTCCTAGCAGACTCTCTATGTT-TCCATAGCTGAGCTATA
1 TTACACATCATACCCCATGTTTAATGTCCTAGAAGACTCTCTATGTTGT-CATAGCCGAGCTATG
22648571 GTC
65 GTC
*
22648574 TTACACATTATACCC
1 TTACACATCATACCC
22648589 TATTGCAGCC
Statistics
Matches: 238, Mismatches: 40, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
66 3 0.01
67 234 0.98
68 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (67 bp):
TTACACATCATACCCCATGTTTAATGTCCTAGAAGACTCTCTATGTTGTCATAGCCGAGCTATGG
TC
Found at i:22651504 original size:7 final size:7
Alignment explanation
Indices: 22651492--22651524 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
22651482 AAAATAACTG
22651492 TTTTTTC
1 TTTTTTC
22651499 TTTTTTC
1 TTTTTTC
22651506 -TTTTTC
1 TTTTTTC
22651512 -TTTTTC
1 TTTTTTC
22651518 TTTTTTC
1 TTTTTTC
22651525 AGAAAACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:22651509 original size:6 final size:6
Alignment explanation
Indices: 22651493--22651522 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
22651483 AAATAACTGT
22651493 TTTTTC TTTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTT
22651523 TCAGAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:22660862 original size:15 final size:17
Alignment explanation
Indices: 22660842--22660874 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22660832 GGAATTTCAC
22660842 AAATAG-CT-AAAGAAA
1 AAATAGTCTAAAAGAAA
22660857 AAATAGTCTAAAAGAAA
1 AAATAGTCTAAAAGAAA
22660874 A
1 A
22660875 GCAAACAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATAGTCTAAAAGAAA
Found at i:22664395 original size:20 final size:20
Alignment explanation
Indices: 22664370--22664414 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
22664360 GAAAAATACA
*
22664370 AAAAAAATCAAAGTTATTT-T
1 AAAAAAATCAAA-ATATTTAT
*
22664390 AAAAAATTCAAAATATTTAT
1 AAAAAAATCAAAATATTTAT
22664410 AAAAA
1 AAAAA
22664415 TTCTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAAAATCAAAATATTTAT
Found at i:22664426 original size:18 final size:19
Alignment explanation
Indices: 22664386--22664430 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
22664376 ATCAAAGTTA
22664386 TTTTA-AAAAATTCAAAAT
1 TTTTATAAAAATTCAAAAT
* *
22664404 ATTTATAAAAATTC-TAAT
1 TTTTATAAAAATTCAAAAT
22664422 TTTTATAAA
1 TTTTATAAA
22664431 TCTTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTATAAAAATTCAAAAT
Found at i:22664453 original size:16 final size:17
Alignment explanation
Indices: 22664434--22664474 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
22664424 TTATAAATCT
22664434 TTTAAAAATTAAAA-TA
1 TTTAAAAATTAAAATTA
22664450 TTTAAAAA-TAAAATTA
1 TTTAAAAATTAAAATTA
*
22664466 TATAAAAAT
1 TTTAAAAAT
22664475 GTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTAAAAATTAAAATTA
Found at i:22664453 original size:27 final size:28
Alignment explanation
Indices: 22664399--22664459 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
22664389 TAAAAAATTC
** *
22664399 AAAATATTTATAAAAATTCTAATTTTTA
1 AAAATATTTATAAAAATTAAAATATTTA
* *
22664427 TAAATCTTT-TAAAAATTAAAATATTTA
1 AAAATATTTATAAAAATTAAAATATTTA
22664454 AAAATA
1 AAAATA
22664460 AAATTATATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATATTTATAAAAATTAAAATATTTA
Found at i:22666183 original size:3 final size:3
Alignment explanation
Indices: 22666175--22666203 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
22666165 TTTGGGACCA
22666175 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
22666204 ATTACCAGCA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:22670538 original size:27 final size:27
Alignment explanation
Indices: 22670508--22670566 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
22670498 AAAGATTGTT
*
22670508 AGAACTCTTCTAAAAG-AAAACTCAAAG
1 AGAACTCTT-GAAAAGAAAAACTCAAAG
* *
22670535 AGAAATTCTTGAAGAGAAAAACTCAAAG
1 AG-AACTCTTGAAAAGAAAAACTCAAAG
22670563 AGAA
1 AGAA
22670567 TTTTATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.17
Consensus pattern (27 bp):
AGAACTCTTGAAAAGAAAAACTCAAAG
Found at i:22670563 original size:14 final size:14
Alignment explanation
Indices: 22670524--22670566 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
22670514 CTTCTAAAAG
22670524 AAAACTCAAAGAGA
1 AAAACTCAAAGAGA
** **
22670538 AATTCTTGAAGAGA
1 AAAACTCAAAGAGA
22670552 AAAACTCAAAGAGA
1 AAAACTCAAAGAGA
22670566 A
1 A
22670567 TTTTATTAAC
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (14 bp):
AAAACTCAAAGAGA
Found at i:22671624 original size:2 final size:2
Alignment explanation
Indices: 22671619--22671649 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22671609 TGTCAAATTC
*
22671619 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22671650 AAGCACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22672249 original size:34 final size:32
Alignment explanation
Indices: 22672197--22672297 Score: 103
Period size: 35 Copynumber: 2.9 Consensus size: 32
22672187 ATGCTCAAAA
*
22672197 TGGACAGCATTTATACATGCAAAGCAACCACATT
1 TGGACAACATTTA-ACATGCAAA-CAACCACATT
*
22672231 TGGACAACATTATAACATGTAAAAACAACCACATT
1 TGGACAACATT-TAACATG--CAAACAACCACATT
* *
22672266 TGGACATCATTGTAATATGCGAAACAACCACA
1 TGGACAACATT-TAACATGC-AAACAACCACA
22672298 CTTTAATACC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
34 26 0.46
35 28 0.49
36 3 0.05
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.23
Consensus pattern (32 bp):
TGGACAACATTTAACATGCAAACAACCACATT
Found at i:22679578 original size:21 final size:21
Alignment explanation
Indices: 22679534--22679578 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22679524 TAATGGATAT
**
22679534 TATATACATATAATACTTTAA
1 TATATACATATAATAAGTTAA
22679555 TATATACATAT-ATAAGTT-A
1 TATATACATATAATAAGTTAA
22679574 TATAT
1 TATAT
22679579 TATGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 11 0.50
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATACATATAATAAGTTAA
Found at i:22689623 original size:38 final size:38
Alignment explanation
Indices: 22689572--22689647 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
22689562 TTAGGGCTTG
22689572 GTACAACAAATTGATTGTAAAACTTTAAGTACTTGTAT
1 GTACAACAAATTGATTGTAAAACTTTAAGTACTTGTAT
22689610 GTACAACAAATTGATTGTAAAACTTTAAGTACTTGTAT
1 GTACAACAAATTGATTGTAAAACTTTAAGTACTTGTAT
22689648 AATAGGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (38 bp):
GTACAACAAATTGATTGTAAAACTTTAAGTACTTGTAT
Found at i:22692186 original size:74 final size:74
Alignment explanation
Indices: 22692100--22692244 Score: 175
Period size: 74 Copynumber: 2.0 Consensus size: 74
22692090 AAACTTCTTA
* * * *
22692100 TTTATCATATAAATTCATTTAATAAAAACCTTTTAATAGAATCAAAATTCTT-ATTTATAAATAT
1 TTTATCAAATAAATTAATTTAATAAAAACATTTTAATAAAATCAAAATT-TTGATTTATAAATAT
22692164 GATAAATATT
65 GATAAATATT
* * ** * * *
22692174 TTTATCAAATAAATTAATTTCATCAAATTATTTTATTAAAATTAAAATTTTGATTTATACATATG
1 TTTATCAAATAAATTAATTTAATAAAAACATTTTAATAAAATCAAAATTTTGATTTATAAATATG
22692239 ATAAAT
66 ATAAAT
22692245 TTTATAAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 2 0.03
74 57 0.97
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (74 bp):
TTTATCAAATAAATTAATTTAATAAAAACATTTTAATAAAATCAAAATTTTGATTTATAAATATG
ATAAATATT
Found at i:22692705 original size:26 final size:24
Alignment explanation
Indices: 22692670--22692738 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 24
22692660 TTGAATGTTA
*
22692670 TAATAAAATACTATAAAA-TATAGG
1 TAATAAAATACTATAAAATTAT-CG
22692694 TATCATAAAATACTATAAAATTATCG
1 TA--ATAAAATACTATAAAATTATCG
22692720 TAATTAAAATACTATAAAA
1 TAA-TAAAATACTATAAAA
22692739 AGGCTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (24 bp):
TAATAAAATACTATAAAATTATCG
Found at i:22694121 original size:30 final size:31
Alignment explanation
Indices: 22694086--22694153 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
22694076 TTAACTAAAA
*
22694086 AAAAGTTACAATTTGA-TCATTGAACTATTC
1 AAAAGTTACAATTTAAGTCATTGAACTATTC
* ***
22694116 GAAAGTTTTTATTTAAGTCATTGAACTATTC
1 AAAAGTTACAATTTAAGTCATTGAACTATTC
22694147 AAAAGTT
1 AAAAGTT
22694154 TTTATTTAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (31 bp):
AAAAGTTACAATTTAAGTCATTGAACTATTC
Found at i:22694140 original size:31 final size:31
Alignment explanation
Indices: 22694102--22694166 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
22694092 TACAATTTGA
*
22694102 TCATTGAACTATTCGAAAGTTTTTATTTAAG
1 TCATTGAACTATTCAAAAGTTTTTATTTAAG
22694133 TCATTGAACTATTCAAAAGTTTTTATTTAAG
1 TCATTGAACTATTCAAAAGTTTTTATTTAAG
22694164 TCA
1 TCA
22694167 ATAGCTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (31 bp):
TCATTGAACTATTCAAAAGTTTTTATTTAAG
Found at i:22697124 original size:30 final size:30
Alignment explanation
Indices: 22697085--22697146 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
22697075 AAATTATTTT
22697085 TTATATTTTA-AATAAAAATTAAATAAAAAA
1 TTATATTTTATAATAAAAATTAAA-AAAAAA
* * **
22697115 TTATTTTTTATATTTTAAATTAAAAAAAAA
1 TTATATTTTATAATAAAAATTAAAAAAAAA
22697145 TT
1 TT
22697147 TGATTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATATTTTATAATAAAAATTAAAAAAAAA
Found at i:22708059 original size:18 final size:18
Alignment explanation
Indices: 22708006--22708059 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
22707996 ACAATAAAAA
*
22708006 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAAATGAAT
* *
22708024 AACGATTTGTAAATGAAT
1 AACGTTTTGAAAATGAAT
* *
22708042 AATGTTTTGAAAACGAAT
1 AACGTTTTGAAAATGAAT
22708060 GACACAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.35
Consensus pattern (18 bp):
AACGTTTTGAAAATGAAT
Found at i:22714580 original size:17 final size:17
Alignment explanation
Indices: 22714550--22714588 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
22714540 CAGATAATGT
* *
22714550 AAATTTAAATATTAAAA
1 AAATTGAAAAATTAAAA
22714567 AAATTGAAAAATTAAAA
1 AAATTGAAAAATTAAAA
*
22714584 TAATT
1 AAATT
22714589 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATTGAAAAATTAAAA
Found at i:22715755 original size:25 final size:27
Alignment explanation
Indices: 22715723--22715785 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
22715713 CGACCTTTCA
*
22715723 AAATTTTT-AACAT-TTAACCGAACCG
1 AAATTTTTAAAAATATTAACCGAACCG
22715748 AAATTTTTTCAAAAATAATTAACCGAACCG
1 AAA-TTTTT-AAAAAT-ATTAACCGAACCG
22715778 AAATTTTT
1 AAATTTTT
22715786 TCGGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.09
26 5 0.16
28 4 0.12
29 5 0.16
30 15 0.47
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (27 bp):
AAATTTTTAAAAATATTAACCGAACCG
Found at i:22715862 original size:9 final size:9
Alignment explanation
Indices: 22715848--22715905 Score: 98
Period size: 9 Copynumber: 6.4 Consensus size: 9
22715838 TTTGGTTAAA
22715848 AATTAACCG
1 AATTAACCG
22715857 AATTAACCG
1 AATTAACCG
22715866 AATTAACCG
1 AATTAACCG
* *
22715875 GATTACCCG
1 AATTAACCG
22715884 AATTAACCG
1 AATTAACCG
22715893 AATTAACCG
1 AATTAACCG
22715902 AATT
1 AATT
22715906 GAATTACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:22721611 original size:15 final size:15
Alignment explanation
Indices: 22721593--22721623 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22721583 TGGCGTAGTT
*
22721593 GGTAGTGGCAGAGGA
1 GGTAGCGGCAGAGGA
22721608 GGTAGCGGCAGAGGA
1 GGTAGCGGCAGAGGA
22721623 G
1 G
22721624 TGGTTGATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.55, T:0.10
Consensus pattern (15 bp):
GGTAGCGGCAGAGGA
Found at i:22721865 original size:21 final size:21
Alignment explanation
Indices: 22721822--22721865 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22721812 ATTTCTTCAA
* *
22721822 CTCTTTCACTTTAGTAGAATT
1 CTCTTTCACTTCAGCAGAATT
*
22721843 CTCTTTCACTTCAGCAGATTT
1 CTCTTTCACTTCAGCAGAATT
22721864 CT
1 CT
22721866 TCATCAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (21 bp):
CTCTTTCACTTCAGCAGAATT
Found at i:22724529 original size:16 final size:17
Alignment explanation
Indices: 22724493--22724529 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
22724483 GCTATATTTA
*
22724493 ATTTTTGATATGTTTTT
1 ATTTTTGATATGTTTTC
22724510 ATTTTTGATATG-TTTC
1 ATTTTTGATATGTTTTC
22724526 ATTT
1 ATTT
22724530 AAAACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.68
Consensus pattern (17 bp):
ATTTTTGATATGTTTTC
Found at i:22724693 original size:47 final size:47
Alignment explanation
Indices: 22724619--22724710 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
22724609 GTCTTCAAAC
22724619 AATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAATTAAAA
1 AATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAATTAAAA
*
22724666 AATGTTTTATATTACTTATATTTTTTGATTAAAAATTATAATTAA
1 AATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAATTAA
22724711 CACTACAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (47 bp):
AATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAATTAAAA
Found at i:22726994 original size:50 final size:50
Alignment explanation
Indices: 22726877--22727168 Score: 253
Period size: 50 Copynumber: 5.7 Consensus size: 50
22726867 GAATATAACA
* * * * ** * * * *
22726877 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGAGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * **
22726926 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * ** * *
22726976 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * *
22727026 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
** *
22727076 TGCCAACGTTATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
* * *
22727132 TGCCAATGCCATGTCTCAGACATGGTTTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
22727169 TCTCATCCTC
Statistics
Matches: 199, Mismatches: 37, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
49 37 0.19
50 128 0.64
53 1 0.01
56 33 0.17
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:22728429 original size:14 final size:14
Alignment explanation
Indices: 22728410--22728450 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
22728400 TAAATTATTT
22728410 ATTATTTTTATTAA
1 ATTATTTTTATTAA
*
22728424 ATTATTTTTAAT-A
1 ATTATTTTTATTAA
*
22728437 A-TAATTTTATTAA
1 ATTATTTTTATTAA
22728450 A
1 A
22728451 ATTTAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTTTATTAA
Found at i:22728652 original size:16 final size:16
Alignment explanation
Indices: 22728626--22728691 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
22728616 TACTGATTGT
22728626 AGCTCTATTCCATTAG
1 AGCTCTATTCCATTAG
* *
22728642 AGTTTTATTCCATTAG
1 AGCTCTATTCCATTAG
*
22728658 AGCTCTATTCCGTTAG
1 AGCTCTATTCCATTAG
* *
22728674 AACTCTATTCTATTAG
1 AGCTCTATTCCATTAG
22728690 AG
1 AG
22728692 TGAACCAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (16 bp):
AGCTCTATTCCATTAG
Found at i:22729802 original size:39 final size:39
Alignment explanation
Indices: 22729759--22729837 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
22729749 GGTACCTGAG
22729759 CTTAACTTTTTGGTTCAAATTGTTACTTGAACTTGGATT
1 CTTAACTTTTTGGTTCAAATTGTTACTTGAACTTGGATT
22729798 CTTAACTTTTTGGTTCAAATTGTTACTTGAACTTGGATT
1 CTTAACTTTTTGGTTCAAATTGTTACTTGAACTTGGATT
22729837 C
1 C
22729838 ATAGTTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (39 bp):
CTTAACTTTTTGGTTCAAATTGTTACTTGAACTTGGATT
Found at i:22736571 original size:7 final size:7
Alignment explanation
Indices: 22736559--22736591 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
22736549 TAGAAAAAAC
22736559 AAACTTT
1 AAACTTT
22736566 AAACTTT
1 AAACTTT
22736573 AAACTTT
1 AAACTTT
22736580 AAA-TTT
1 AAACTTT
22736586 ATAACT
1 A-AACT
22736592 CACTAATAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 19 0.79
8 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AAACTTT
Found at i:22738971 original size:16 final size:17
Alignment explanation
Indices: 22738940--22738972 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22738930 ATGGTAGTTG
*
22738940 AATTGCTTTGCTTTCAT
1 AATTGCTTTACTTTCAT
22738957 AATTG-TTTACTTTCAT
1 AATTGCTTTACTTTCAT
22738973 GTGGAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (17 bp):
AATTGCTTTACTTTCAT
Found at i:22745018 original size:42 final size:41
Alignment explanation
Indices: 22744967--22745068 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 41
22744957 CAATTTTTAT
***
22744967 TATTTATAACAAATTAAAGAGTTATTAATTTAAAATTCTATA
1 TATTTATAACAAATTAAA-ACAAATTAATTTAAAATTCTATA
22745009 TATTTATAACAAATTAATAACAAATTAATTTAAAATTCTATA
1 TATTTATAACAAATTAA-AACAAATTAATTTAAAATTCTATA
22745051 TATTTATAACAAATTAAA
1 TATTTATAACAAATTAAA
22745069 TAACAGCAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.02
42 54 0.96
43 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (41 bp):
TATTTATAACAAATTAAAACAAATTAATTTAAAATTCTATA
Found at i:22747571 original size:22 final size:22
Alignment explanation
Indices: 22747546--22747610 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
22747536 CTTCTAAATA
22747546 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
* *
22747568 TGTT-AT-GA-AA-TTA-AATA
1 TGTTGATGGACAATTTATATTT
22747585 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
22747607 TGTT
1 TGTT
22747611 ATGAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 4 0.12
21 5 0.15
22 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (22 bp):
TGTTGATGGACAATTTATATTT
Found at i:22747579 original size:19 final size:19
Alignment explanation
Indices: 22747557--22747618 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
22747547 GTTGATGGAC
22747557 AATTTATATTTTGTTATGA
1 AATTTATATTTTGTTATGA
* *
22747576 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
22747595 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
22747615 AATT
1 AATT
22747619 AAATATGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 8 0.24
20 4 0.12
21 5 0.15
22 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (19 bp):
AATTTATATTTTGTTATGA
Found at i:22747583 original size:39 final size:39
Alignment explanation
Indices: 22747540--22747633 Score: 188
Period size: 39 Copynumber: 2.4 Consensus size: 39
22747530 GCTTTCCTTC
22747540 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
22747579 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
22747618 TAAATATGTTGATGGA
1 TAAATATGTTGATGGA
22747634 TTAATGTATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (39 bp):
TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
Found at i:22747652 original size:39 final size:38
Alignment explanation
Indices: 22747540--22747652 Score: 102
Period size: 39 Copynumber: 2.9 Consensus size: 38
22747530 GCTTTCCTTC
* ***
22747540 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATGTATA-TAAATTATGAAAT
* ***
22747579 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATGTATA-TAAATTATGAAAT
*
22747618 TAAATATGTTGATGGATTAATGTATGA-AAATTATG
1 TAAATATGTTGATGGA-CAATGTAT-ATAAATTATG
22747653 GTTTGTTGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 60 0.90
40 6 0.09
41 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (38 bp):
TAAATATGTTGATGGACAATGTATATAAATTATGAAAT
Found at i:22751851 original size:6 final size:6
Alignment explanation
Indices: 22751832--22751864 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
22751822 TCTAAATGAA
22751832 TTCATT TCTCATT TTCATT TTCATT TTCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TT
22751865 GAGAAAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCATT
Found at i:22752311 original size:19 final size:19
Alignment explanation
Indices: 22752287--22752326 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
22752277 GATTCTATTT
22752287 TATCTTACTGTAACCATTA
1 TATCTTACTGTAACCATTA
*
22752306 TATCTTATTGTAACCATTA
1 TATCTTACTGTAACCATTA
22752325 TA
1 TA
22752327 ACTTCATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (19 bp):
TATCTTACTGTAACCATTA
Found at i:22756584 original size:13 final size:13
Alignment explanation
Indices: 22756566--22756590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22756556 TGTGTGAATC
22756566 AATTTCATATATT
1 AATTTCATATATT
22756579 AATTTCATATAT
1 AATTTCATATAT
22756591 GTTCTCTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTCATATATT
Found at i:22758342 original size:17 final size:17
Alignment explanation
Indices: 22758320--22758360 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
22758310 AGATCTCTGA
22758320 CGAGCTTCCAAATCGAT
1 CGAGCTTCCAAATCGAT
22758337 CGAGCTTCCAAATCGAT
1 CGAGCTTCCAAATCGAT
*
22758354 TGAGCTT
1 CGAGCTT
22758361 TCGATAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (17 bp):
CGAGCTTCCAAATCGAT
Found at i:22763002 original size:40 final size:40
Alignment explanation
Indices: 22762950--22763145 Score: 313
Period size: 40 Copynumber: 4.9 Consensus size: 40
22762940 GCTTTCAGAA
* * *
22762950 GTACCGAAGTACAATCAGGGGCATGTATGTGCATTTAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
*
22762990 GTACTGAAGTAC-AACAGGGGCACGTATGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* * *
22763029 GTACCAAAGTACAAACAGGGGCTCTTATGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
22763069 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
*
22763109 GTACCGAAGTACAAATAGGGGCACGTATGTGCATTCA
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
22763146 TATAGTAATT
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 34 0.24
40 109 0.76
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (40 bp):
GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
Found at i:22763029 original size:20 final size:20
Alignment explanation
Indices: 22762964--22763145 Score: 77
Period size: 20 Copynumber: 9.2 Consensus size: 20
22762954 CGAAGTACAA
*
22762964 TCAGGGGCATGTATGTGCAT
1 TCAGGGGCACGTATGTGCAT
* * * *
22762984 TTAGGGGTAC-TGAAGTACA-
1 TCAGGGGCACGT-ATGTGCAT
*
22763003 ACAGGGGCACGTATGTGCAT
1 TCAGGGGCACGTATGTGCAT
* ** * * *
22763023 TCAGGGGTACCAAAGTACAA
1 TCAGGGGCACGTATGTGCAT
* * *
22763043 ACAGGGGCTCTTATGTGCAT
1 TCAGGGGCACGTATGTGCAT
* * * *
22763063 TCAGGGGTACCG-AAGTACAA
1 TCAGGGGCA-CGTATGTGCAT
*
22763083 ACAGGGGCACGTATGTGCAT
1 TCAGGGGCACGTATGTGCAT
* * * *
22763103 TCAGGGGTACCG-AAGTACAAA
1 TCAGGGGCA-CGTATGTGC-AT
22763124 T-AGGGGCACGTATGTGCAT
1 TCAGGGGCACGTATGTGCAT
22763143 TCA
1 TCA
22763146 TATAGTAATT
Statistics
Matches: 107, Mismatches: 46, Indels: 18
0.63 0.27 0.11
Matches are distributed among these distances:
19 19 0.18
20 83 0.78
21 5 0.05
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (20 bp):
TCAGGGGCACGTATGTGCAT
Found at i:22787052 original size:58 final size:55
Alignment explanation
Indices: 22786933--22787052 Score: 125
Period size: 57 Copynumber: 2.1 Consensus size: 55
22786923 AATTCCTTGT
* ** *
22786933 TCATTTCTAAATGAATTCATTTCTCATTTTCATTTCCATTTTGAGAAAACCACAT
1 TCATTTCCAAATGAATTCATTTCTCATTTTCATTTCCATACTGAGAAAACCACAA
* * * *
22786988 TTATTTCCAAATG-ATTCCATTTTCTCCATTTTCATTTTCATACTGTAGAAAATCATAA
1 TCATTTCCAAATGAATT-CA-TTTCT-CATTTTCATTTCCATACTG-AGAAAACCACAA
22787046 TCATTTC
1 TCATTTC
22787053 TGAATGTTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
54 3 0.06
55 13 0.25
56 5 0.10
57 16 0.31
58 15 0.29
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (55 bp):
TCATTTCCAAATGAATTCATTTCTCATTTTCATTTCCATACTGAGAAAACCACAA
Found at i:22788986 original size:78 final size:78
Alignment explanation
Indices: 22788898--22789044 Score: 224
Period size: 78 Copynumber: 1.9 Consensus size: 78
22788888 CTTTATTTTA
*
22788898 TTTTTAAATAGGATACTTGTAAGACACTTGGTAAG-CCTATAAATAGGCACTTAGTAAGTCCATA
1 TTTTTAAATAGGATACTTGTAAGACACTTGGTAAGTCC-ATAAATAGACACTTAGTAAGTCCATA
22788962 GATATCAAATACAT
65 GATATCAAATACAT
* * * * *
22788976 TTTTTTAATAGGATACTTGTAAGACATTTGGTAAGTCCATAGATAGACACTTAGTAATTCTATAG
1 TTTTTAAATAGGATACTTGTAAGACACTTGGTAAGTCCATAAATAGACACTTAGTAAGTCCATAG
22789041 ATAT
66 ATAT
22789045 TCAATAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
78 60 0.97
79 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (78 bp):
TTTTTAAATAGGATACTTGTAAGACACTTGGTAAGTCCATAAATAGACACTTAGTAAGTCCATAG
ATATCAAATACAT
Found at i:22789032 original size:23 final size:23
Alignment explanation
Indices: 22788997--22789043 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
22788987 GATACTTGTA
* *
22788997 AGACATTTGGTAAGTCCATAGAT
1 AGACACTTAGTAAGTCCATAGAT
* *
22789020 AGACACTTAGTAATTCTATAGAT
1 AGACACTTAGTAAGTCCATAGAT
22789043 A
1 A
22789044 TTCAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (23 bp):
AGACACTTAGTAAGTCCATAGAT
Found at i:22789563 original size:30 final size:30
Alignment explanation
Indices: 22789529--22789590 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
22789519 AACACTCAAA
*
22789529 CAAGAAAATTGATCAAGTAAAATCAAGCAT
1 CAAGAAAATTGATAAAGTAAAATCAAGCAT
22789559 CAAGAAAATTGATAAAGTAAAATCAAGCAT
1 CAAGAAAATTGATAAAGTAAAATCAAGCAT
22789589 CA
1 CA
22789591 CTGTTATGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (30 bp):
CAAGAAAATTGATAAAGTAAAATCAAGCAT
Found at i:22790930 original size:152 final size:154
Alignment explanation
Indices: 22790744--22791048 Score: 515
Period size: 152 Copynumber: 2.0 Consensus size: 154
22790734 TGAAGATGTT
22790744 TTTATATAGACTAGCTAACTATATCAAAATAAAACTCCTAAATACAATAAAACTCTAATTAATCT
1 TTTATATAGACTAGCTAACTATATCAAAATAAAACTCCTAAATACAATAAAACTCTAATTAATCT
*
22790809 AAATAATAAGTAGTTTTAGTGAAACTAAACTCGCTTGTTGCTTAAGAAACAT-AAACTTCT-AAC
66 AAATAAGAAGTAGTTTTAGTGAAACTAAACTCGCTTGTTGCTTAAGAAACATAAAACTTCTAAAC
* *
22790872 AATTCAAAATATTGAAAAATATCC
131 AATTCAAAATACTAAAAAATATCC
* * * *
22790896 TTTATATAGACTAGCTAATTATATCAAAGTAAAACTCCTAAGTATAATAAAACTCTAATTAATCT
1 TTTATATAGACTAGCTAACTATATCAAAATAAAACTCCTAAATACAATAAAACTCTAATTAATCT
* *
22790961 AAATAAGAAGTAGTTTTAGTGAAACTAAATTCTCTTGTTGCTTAAGAAACATAAAACTTCTAAAC
66 AAATAAGAAGTAGTTTTAGTGAAACTAAACTCGCTTGTTGCTTAAGAAACATAAAACTTCTAAAC
22791026 AATTCAAAATACTAAAAAATATC
131 AATTCAAAATACTAAAAAATATC
22791049 TTAAATTTTA
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
152 110 0.77
153 8 0.06
154 24 0.17
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (154 bp):
TTTATATAGACTAGCTAACTATATCAAAATAAAACTCCTAAATACAATAAAACTCTAATTAATCT
AAATAAGAAGTAGTTTTAGTGAAACTAAACTCGCTTGTTGCTTAAGAAACATAAAACTTCTAAAC
AATTCAAAATACTAAAAAATATCC
Found at i:22792568 original size:15 final size:16
Alignment explanation
Indices: 22792539--22792570 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22792529 TTGATAGTTA
22792539 TTTTATGAAATATAAT
1 TTTTATGAAATATAAT
22792555 TTTTATGAAA-ATAAT
1 TTTTATGAAATATAAT
22792570 T
1 T
22792571 ATGTAACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTATGAAATATAAT
Found at i:22798141 original size:228 final size:225
Alignment explanation
Indices: 22797735--22798450 Score: 615
Period size: 228 Copynumber: 3.1 Consensus size: 225
22797725 AAAAACAAGT
* * * * *
22797735 ATTAGCGGCG-TTTACTAAAAGCGCCGCAAAATATGACAACCAAAACGCAGAGTATGGTCTAGAT
1 ATTAGCGGCGCTTTATTAGAAGCGCCGCAAAATAT-ACAACCAAAACGCAGAGTTTGGTAT-GAC
* * ***
22797799 GTATATTAGGATTAGTGGCGC-TTACAGACAAACGCCGCTAAAG-AGTACTATTAGCGGCGCGCA
64 GTATATTAGAATTAGTGGCGCTTTA-AG-CAAACGCCGCAAAAGTA-TACTATTAGCGGCGCTTT
* * * * * * * *** *
22797862 ATCAGAAGCGCCGCTATATATCTTAATCAAAACTCAGCGTTTTGGTCTTGATGTACAATATAATT
126 CTTAGAAGCGCCGCAATATATATTAA-CGAAACGCTGCGTTTAAATCTTGATGTACAATAGAATT
* *
22797927 ACTGGCGCTT-ATAATAAAACGCCGCTAAA-TATCAGC
190 ACTGGCG-TTCAGAAGAAAACGCCGCTAAATTAT-AGC
* *
22797963 ATTAGCGGCGCTTT-TGGT-TAAGCGCCGCAATATATACAGACCAAAACGCAGAGTTTGGTAATG
1 ATTAGCGGCGCTTTAT--TAGAAGCGCCGCAAAATATACA-ACCAAAACGCAGAGTTTGGT-ATG
* * * *
22798026 AGGTATATTAGAATTAGTGGCGCTTTATGGAAACGCCGCAAAAGTATACTATTAGCGTCGCTTTC
62 ACGTATATTAGAATTAGTGGCGCTTTAAGCAAACGCCGCAAAAGTATACTATTAGCGGCGCTTTC
* * * *
22798091 TTAGAAGCGCCGCAATATATATTAACGGAAACGCTGCGTTTAAATCTTGATGTATACTGGAGTTA
127 TTAGAAGCGCCGCAATATATATTAAC-GAAACGCTGCGTTTAAATCTTGATGTACAATAGAATTA
* * * **
22798156 GTGGCGTTCAGGAGAAATCGCCGCTAAATTATATT
191 CTGGCGTTCAGAAGAAAACGCCGCTAAATTATAGC
* * * * * * *
22798191 ATTAGCGGCGCTTTATTAGAAGCGCCGCAAGATATATTAACCTAAACGCTGCGTTTAGATCTTGA
1 ATTAGCGGCGCTTTATTAGAAGCGCCGCAAAATATA-CAACCAAAACGCAGAGTTT-GGT-ATGA
** * *
22798256 CGTATACTT-GAATTAGTGGCGCTTTCCGTAAACGCCGCAAAAGTATACTATTAGTGGCGCTTTC
63 CGTATA-TTAGAATTAGTGGCGCTTTAAGCAAACGCCGCAAAAGTATACTATTAGCGGCGCTTTC
* ** * * * * *
22798320 TTATAAGCGCCGCAATATATAAGACCGAAACGCTGCGTTTAAATCTTGATGTATACTGGAATTAG
127 TTAGAAGCGCCGCAATATATATTAACGAAACGCTGCGTTTAAATCTTGATGTACAATAGAATTAC
* * * **
22798385 TGGCGTTCACG-AGAAATCACCGCTAAATCATATT
192 TGGCGTTCA-GAAGAAAACGCCGCTAAATTATAGC
* *
22798419 ATTAGCGGCGC-TTATTTGTTAGCGCCGCAAAA
1 ATTAGCGGCGCTTTATTAG-AAGCGCCGCAAAA
22798451 GATCTTCACC
Statistics
Matches: 410, Mismatches: 61, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
227 10 0.02
228 244 0.60
229 149 0.36
230 7 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (225 bp):
ATTAGCGGCGCTTTATTAGAAGCGCCGCAAAATATACAACCAAAACGCAGAGTTTGGTATGACGT
ATATTAGAATTAGTGGCGCTTTAAGCAAACGCCGCAAAAGTATACTATTAGCGGCGCTTTCTTAG
AAGCGCCGCAATATATATTAACGAAACGCTGCGTTTAAATCTTGATGTACAATAGAATTACTGGC
GTTCAGAAGAAAACGCCGCTAAATTATAGC
Found at i:22798203 original size:115 final size:114
Alignment explanation
Indices: 22798036--22798431 Score: 498
Period size: 115 Copynumber: 3.5 Consensus size: 114
22798026 AGGTATATTA
* * *
22798036 GAATTAGTGGCGCTTTATG-GAAACGCCGCAAAAGTATACTATTAGCGTCGCTTTCTTAGAAGCG
1 GAATTAGTGGCG-TTCACGAGAAACGCCGCAAAAGTATACTATTAGCGGCGCTTTCTTAGAAGCG
*
22798100 CCGCAATATATATTAACGGAAACGCTGCGTTTAAATCTTGATGTATACTG
65 CCGCAATATATATTAACCGAAACGCTGCGTTTAAATCTTGATGTATACTG
* * * * * *
22798150 GAGTTAGTGGCGTTCAGGAGAAATCGCCGCTAAATTATATTATTAGCGGCGCTTTATTAGAAGCG
1 GAATTAGTGGCGTTCACGAGAAA-CGCCGCAAAAGTATACTATTAGCGGCGCTTTCTTAGAAGCG
* * * * *
22798215 CCGCAAGATATATTAACCTAAACGCTGCGTTTAGATCTTGACGTATACTT
65 CCGCAATATATATTAACCGAAACGCTGCGTTTAAATCTTGATGTATACTG
* * *
22798265 GAATTAGTGGCGCTTTC-CG-TAAACGCCGCAAAAGTATACTATTAGTGGCGCTTTCTTATAAGC
1 GAATTAGTGGCG--TTCACGAGAAACGCCGCAAAAGTATACTATTAGCGGCGCTTTCTTAGAAGC
22798328 GCCGCAATATATA--AGACCGAAACGCTGCGTTTAAATCTTGATGTATACTG
64 GCCGCAATATATATTA-ACCGAAACGCTGCGTTTAAATCTTGATGTATACTG
* * *
22798378 GAATTAGTGGCGTTCACGAGAAATCACCGCTAAA-TCATATTATTAGCGGCGCTT
1 GAATTAGTGGCGTTCACGAGAAA-CGCCGCAAAAGT-ATACTATTAGCGGCGCTT
22798432 ATTTGTTAGC
Statistics
Matches: 240, Mismatches: 33, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
111 3 0.01
112 3 0.01
113 51 0.21
114 85 0.35
115 94 0.39
116 1 0.00
117 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (114 bp):
GAATTAGTGGCGTTCACGAGAAACGCCGCAAAAGTATACTATTAGCGGCGCTTTCTTAGAAGCGC
CGCAATATATATTAACCGAAACGCTGCGTTTAAATCTTGATGTATACTG
Found at i:22798813 original size:7 final size:7
Alignment explanation
Indices: 22798798--22798856 Score: 82
Period size: 7 Copynumber: 8.3 Consensus size: 7
22798788 CGATTATGGT
*
22798798 GTTTTGG
1 GTTTAGG
22798805 GTTTAGG
1 GTTTAGG
22798812 GTTTAGG
1 GTTTAGG
22798819 AGTTTAGG
1 -GTTTAGG
*
22798827 GTTTAAG
1 GTTTAGG
22798834 GTTTAGG
1 GTTTAGG
*
22798841 GTTTGGG
1 GTTTAGG
22798848 GTTTAGG
1 GTTTAGG
22798855 GT
1 GT
22798857 GCTTAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 39 0.85
8 7 0.15
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:22798828 original size:22 final size:21
Alignment explanation
Indices: 22798798--22798856 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 21
22798788 CGATTATGGT
*
22798798 GTTTTGGGTTTAGGGTTTAGG
1 GTTTAGGGTTTAGGGTTTAGG
*
22798819 AGTTTAGGGTTTAAGGTTTAGG
1 -GTTTAGGGTTTAGGGTTTAGG
*
22798841 GTTTGGGGTTTAGGGT
1 GTTTAGGGTTTAGGGT
22798857 GCTTAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTTTAGG
Found at i:22801879 original size:34 final size:36
Alignment explanation
Indices: 22801801--22801880 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 36
22801791 AATTTTTTAT
* **
22801801 TTTATTTTACTCACGAATTAAATATTAAATATTTTA
1 TTTATTTTAATCACGAATTAAATATTAAATATTAAA
* * *
22801837 TTTTTTTTAATCACGAA-T-ATTTTTAAATATTAAA
1 TTTATTTTAATCACGAATTAAATATTAAATATTAAA
22801871 TTTATTTTAA
1 TTTATTTTAA
22801881 AGTTCAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
34 21 0.57
35 1 0.03
36 15 0.41
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (36 bp):
TTTATTTTAATCACGAATTAAATATTAAATATTAAA
Found at i:22801915 original size:18 final size:17
Alignment explanation
Indices: 22801887--22801936 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
22801877 TTAAAGTTCA
*
22801887 AATTTCATATCTTACGT
1 AATTTCATATCTTACAT
22801904 AATTTACATATCTTACAT
1 AATTT-CATATCTTACAT
*
22801922 AA-TTCATAACTTACA
1 AATTTCATATCTTACA
22801937 CAACTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 13 0.43
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTCATATCTTACAT
Found at i:22802318 original size:9 final size:9
Alignment explanation
Indices: 22802304--22802398 Score: 85
Period size: 9 Copynumber: 11.2 Consensus size: 9
22802294 TACATAATAA
22802304 TACATAACT
1 TACATAACT
22802313 TACATAA--
1 TACATAACT
* *
22802320 GACATAACG
1 TACATAACT
*
22802329 TACATAAGT
1 TACATAACT
*
22802338 TTCATAA--
1 TACATAACT
*
22802345 TACACAACT
1 TACATAACT
*
22802354 TACACAACT
1 TACATAACT
*
22802363 TACACAACT
1 TACATAACT
22802372 TACATAACT
1 TACATAACT
22802381 TACATAA--
1 TACATAACT
22802388 TACATAACT
1 TACATAACT
22802397 TA
1 TA
22802399 TTCCTAAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
7 18 0.25
9 54 0.75
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.28
Consensus pattern (9 bp):
TACATAACT
Found at i:22802357 original size:25 final size:25
Alignment explanation
Indices: 22802304--22802366 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
22802294 TACATAATAA
*
22802304 TACATAACTTACATAAGACATAACG
1 TACATAACTTACATAAGACACAACG
* * * *
22802329 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAAGACACAACG
*
22802354 TACACAACTTACA
1 TACATAACTTACA
22802367 CAACTTACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (25 bp):
TACATAACTTACATAAGACACAACG
Found at i:22802393 original size:16 final size:17
Alignment explanation
Indices: 22802293--22802398 Score: 85
Period size: 16 Copynumber: 6.2 Consensus size: 17
22802283 TACATACATA
22802293 TTACATAATAATACATAAC
1 TTACATAAT--TACATAAC
*
22802312 TTACATAA-GACATAAC
1 TTACATAATTACATAAC
* *
22802328 GTACATAAGTTTCATAA-
1 TTACATAA-TTACATAAC
* *
22802345 -TACACAACTTACACAAC
1 TTACATAA-TTACATAAC
*
22802362 TTACACAACTTACATAAC
1 TTACATAA-TTACATAAC
22802380 TTACATAA-TACATAAC
1 TTACATAATTACATAAC
22802396 TTA
1 TTA
22802399 TTCCTAAATC
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
16 37 0.51
18 28 0.38
19 8 0.11
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (17 bp):
TTACATAATTACATAAC
Found at i:22807874 original size:21 final size:21
Alignment explanation
Indices: 22807850--22807918 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
22807840 CAGCAACTTA
*
22807850 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAG
*
22807871 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCGACAGCGAGAG
*
22807892 AAGCAGAGGCCG-CAGCAAGAG
1 AAGCAGAGG-CGACAGCGAGAG
22807913 AAGCAG
1 AAGCAG
22807919 CGAGAGAAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.41, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAG
Found at i:22807918 original size:12 final size:12
Alignment explanation
Indices: 22807903--22807942 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
22807893 AGCAGAGGCC
22807903 GCAGCAAGAGAA
1 GCAGCAAGAGAA
*
22807915 GCAGCGAGAGAA
1 GCAGCAAGAGAA
*
22807927 GCAGCAATAGAA
1 GCAGCAAGAGAA
22807939 GCAG
1 GCAG
22807943 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.45, C:0.17, G:0.35, T:0.03
Consensus pattern (12 bp):
GCAGCAAGAGAA
Found at i:22808452 original size:43 final size:42
Alignment explanation
Indices: 22808405--22808631 Score: 316
Period size: 43 Copynumber: 5.3 Consensus size: 42
22808395 TTTCCTTCCA
* *
22808405 AAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTTTTTTAT
1 AAGCGCCGCT-AAAGAGCATGATCTTTAGCGGCGTTTTTTTCT
*
22808448 AAGCGCCGCTAAAGAGCATGATCTTTAGGGGCG--TTTTTCT
1 AAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTTTTTCT
* *
22808488 AAGCGCCGCTAAAGAGCGTGATCTTTAG-GCGCATTTGTTTTCT
1 AAGCGCCGCTAAAGAGCATGATCTTTAGCG-GCGTTT-TTTTCT
22808531 AAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTGTTTTCT
1 AAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTT-TTTTCT
*
22808574 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTACGT
1 AAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTTTTT-C-T
*
22808618 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
22808632 TTAGTGACGT
Statistics
Matches: 168, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.01
40 35 0.21
42 26 0.15
43 91 0.54
44 15 0.09
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTTTTTCT
Found at i:22808539 original size:83 final size:84
Alignment explanation
Indices: 22808405--22808631 Score: 325
Period size: 83 Copynumber: 2.7 Consensus size: 84
22808395 TTTCCTTCCA
*
22808405 AAGCGCCGCTAAAAGAACATGATCTTTAGCGGCGTTTTTTTATAAGCGCCGCTAAAGAGCATGAT
1 AAGCGCCGCT-AAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAGCATGAT
*
22808470 CTTTAGGGGCG-T-TTTTCT
65 CTTTAGCGGCGTTGTTTTCT
* * *
22808488 AAGCGCCGCTAAAGAGCGTGATCTTTAG-GCGCATTTGTTTTCTAAGCGCCGCTAAAGAGCATGA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCG-GCGTTT-TTTTCTAAGCGCCGCTAAAGAGCATGA
22808552 TCTTTAGCGGCGTTTGTTTTCT
64 TCTTTAGCGGCG-TTGTTTTCT
*
22808574 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTACGTAAGCGCCGCAAAAG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-C-TAAGCGCCGCTAAAG
22808632 TTAGTGACGT
Statistics
Matches: 127, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
81 1 0.01
82 21 0.17
83 47 0.37
85 5 0.04
86 38 0.30
87 15 0.12
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAGCATGATC
TTTAGCGGCGTTGTTTTCT
Found at i:22808728 original size:21 final size:21
Alignment explanation
Indices: 22808702--22808744 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22808692 TTAGTGGCGT
* *
22808702 TAAAAAGCGCCGCTAAAGACC
1 TAAAAAACGCCGCTAAAAACC
22808723 TAAAAAACGCCGCTAAAAACC
1 TAAAAAACGCCGCTAAAAACC
22808744 T
1 T
22808745 GTTCTGCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.14, T:0.12
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAAACC
Found at i:22815536 original size:30 final size:30
Alignment explanation
Indices: 22815500--22815560 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
22815490 AAGTACGTTT
22815500 TAAGCAGTGGCAGTGTTAGTGAGTGTTGAG
1 TAAGCAGTGGCAGTGTTAGTGAGTGTTGAG
22815530 TAAGCAGTGGCAGTGTTAGTGAGTGTTGAG
1 TAAGCAGTGGCAGTGTTAGTGAGTGTTGAG
22815560 T
1 T
22815561 GCATCAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.31
Consensus pattern (30 bp):
TAAGCAGTGGCAGTGTTAGTGAGTGTTGAG
Found at i:22817326 original size:20 final size:20
Alignment explanation
Indices: 22817301--22817339 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22817291 TCTGTGCTTG
22817301 TTGGGTGTATTCAATCATAC
1 TTGGGTGTATTCAATCATAC
22817321 TTGGGTGTATTCAATCATA
1 TTGGGTGTATTCAATCATA
22817340 AGCATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGGGTGTATTCAATCATAC
Found at i:22822719 original size:29 final size:29
Alignment explanation
Indices: 22822693--22822763 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
22822683 TCAAGTTATA
22822693 TTTTAGTCACTTATGTTTGAAATGTTACG
1 TTTTAGTCACTTATGTTTGAAATGTTACG
* * *
22822722 TTTTAATTACTTATGTTTGAAATTTTACG
1 TTTTAGTCACTTATGTTTGAAATGTTACG
22822751 TTTTAGTCACTTA
1 TTTTAGTCACTTA
22822764 CGTTATCGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (29 bp):
TTTTAGTCACTTATGTTTGAAATGTTACG
Found at i:22826201 original size:54 final size:54
Alignment explanation
Indices: 22826091--22826203 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
22826081 GTTGTAGTCC
* * * **
22826091 GTGTGCCAGATCGTGTAACTCTCTAACTTGTGACACACGGTCGTGTCACAGGCT
1 GTGTGCCAGATCGTGTAACACGCTAACTTATGACACACGGTCGTGTCACAAACT
* * *
22826145 GTGTGCTAGGTCGTGTAACACGCTAACTTAAT-ACACACGGTCGTGTCTCAAACT
1 GTGTGCCAGATCGTGTAACACGCTAACTT-ATGACACACGGTCGTGTCACAAACT
22826199 GTGTG
1 GTGTG
22826204 TGGCACACGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
54 49 0.98
55 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (54 bp):
GTGTGCCAGATCGTGTAACACGCTAACTTATGACACACGGTCGTGTCACAAACT
Found at i:22841142 original size:17 final size:17
Alignment explanation
Indices: 22841122--22841154 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22841112 TAGAATTTGG
22841122 TTGAGAAAA-TAATTTAA
1 TTGA-AAAATTAATTTAA
22841139 TTGAAAAATTAATTTA
1 TTGAAAAATTAATTTA
22841155 GTTACTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TTGAAAAATTAATTTAA
Done.