Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_pilon, whole genome shotgun sequence
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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 39
Found at i:5450989 original size:26 final size:26
Alignment explanation
Indices: 5450892--5450991 Score: 100
Period size: 26 Copynumber: 3.9 Consensus size: 26
5450882 GTATTTTGCT
* *
5450892 TGAA-GAAAAAA-GAAGAAGAAAAAA
1 TGAATGAAAAAATGAAAAAAAAAAAA
*
5450916 TGAGAAGAAAAAATGAAAAAAATAAAAA
1 TGA-ATGAAAAAATGAAAAAAA-AAAAA
* * *
5450944 -AAATAAAAAAAT-AATAAAAAAAAA
1 TGAATGAAAAAATGAAAAAAAAAAAA
5450968 TGAATGAAAAAATGAAAAAAAAAA
1 TGAATGAAAAAATGAAAAAAAAAA
5450992 TGAAGGTTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
24 8 0.13
25 17 0.28
26 24 0.39
27 7 0.11
28 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (26 bp):
TGAATGAAAAAATGAAAAAAAAAAAA
Found at i:5450993 original size:12 final size:12
Alignment explanation
Indices: 5450897--5450995 Score: 83
Period size: 13 Copynumber: 7.8 Consensus size: 12
5450887 TTGCTTGAAG
5450897 AAAAAA-GAAGAA
1 AAAAAATGAA-AA
*
5450909 GAAAAAATGAGAAG
1 -AAAAAATGA-AAA
5450923 AAAAAATGAAAA
1 AAAAAATGAAAA
**
5450935 AAATAAAAAAAATA
1 AAA-AAATGAAA-A
*
5450949 AAAAAATAATAAA
1 AAAAAATGA-AAA
**
5450962 AAAAAATGAATG
1 AAAAAATGAAAA
5450974 AAAAAATGAAAA
1 AAAAAATGAAAA
5450986 AAAAAATGAA
1 AAAAAATGAA
5450996 GGTTCAAGAT
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
12 26 0.37
13 35 0.49
14 9 0.13
15 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:5452059 original size:55 final size:55
Alignment explanation
Indices: 5451989--5452492 Score: 755
Period size: 55 Copynumber: 9.1 Consensus size: 55
5451979 AGGTTTCCCA
* *
5451989 ACGATTGTTGAAGATTGTTCAAGTCTCATACTCTCTAAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
5452044 ACGTTTGTTGAAGATTTTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
5452099 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
5452154 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
5452209 ACGTTTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGAC
5452265 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
5452320 ACG-TTCGTTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATATGGAGCAGGC
1 ACGATT-GTTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGAC
* *
5452376 ACGATTATTG-AGAATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGAC
1 ACGATTGTTGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * ** *
5452431 ATGATTATCG-AGAATCGTTTGAGTCTTGTACTCTCTGGAA-AAATGGGGAGCAGAC
1 ACGATTGTTGAAG-ATTGTTCGAGTCTCATACTCTCT-GAAGAAATAGGGAGCAGAC
5452486 ACGATTG
1 ACGATTG
5452493 ACAAATATTT
Statistics
Matches: 416, Mismatches: 27, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
54 2 0.00
55 312 0.75
56 100 0.24
57 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:5452309 original size:111 final size:111
Alignment explanation
Indices: 5451989--5452492 Score: 759
Period size: 111 Copynumber: 4.6 Consensus size: 111
5451979 AGGTTTCCCA
* * *
5451989 ACGATTGTTGAAGATTGTTCAAGTCTCATACTCTCTAAAG-AAATAGGGAGCAGACACGTTTGTT
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTT
*
5452053 GAAGATTTTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
66 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
5452099 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTGTT
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTT
*
5452163 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGAC
66 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
5452209 ACGTTTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTT
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTT
5452274 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
66 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
5452320 ACG-TTCGTTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATATGGAGCAGGCACGATTAT
1 ACGATT-GTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGT
*
5452384 TG-AGAATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGAC
65 TGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * ** * *
5452431 ATGATTATCG-AGAATCGTTTGAGTCTTGTACTCTCTGGA-AAAATGGGGAGCAGACACGATTG
1 ACGATTGTTGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTG
5452493 ACAAATATTT
Statistics
Matches: 364, Mismatches: 25, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
110 169 0.46
111 193 0.53
112 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (111 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTT
GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:5452338 original size:166 final size:165
Alignment explanation
Indices: 5451989--5452492 Score: 759
Period size: 166 Copynumber: 3.0 Consensus size: 165
5451979 AGGTTTCCCA
* *
5451989 ACGATTGTTGAAGATTGTTCAAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGTTTGTTG
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATA-GGAGCAGACACGTTTGTTG
*
5452054 AAGATTTTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTGTTGAAGATTGTT
65 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
5452118 CGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
130 CGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
5452154 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGACACGTTTGTTG
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAG-GAGCAGACACGTTTGTTG
5452219 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
65 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
5452284 CGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
130 CGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
5452320 ACG-TTCGTTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATATGGAGCAGGCACGATTAT
1 ACGATT-GTTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATA-GGAGCAGACACGTTTGT
* * *
5452384 TG-AGAATTGTTCGAGTCTCATACTCTCTGAA-AAAATAGGGAGCAGACATGATTATCG-AGAAT
63 TGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAG-AT
* * ** *
5452446 CGTTTGAGTCTTGTACTCTCTGGAA-AAATGGGGAGCAGAC
126 TGTTCGAGTCTCATACTCTCT-GAAGAAATAGGGAGCAGAC
5452486 ACGATTG
1 ACGATTG
5452493 ACAAATATTT
Statistics
Matches: 315, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
164 1 0.00
165 94 0.30
166 168 0.53
167 51 0.16
168 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (165 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGAGCAGACACGTTTGTTGA
AGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATTGTTC
GAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:5453894 original size:25 final size:23
Alignment explanation
Indices: 5453866--5453913 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
5453856 TCTTAGACGG
*
5453866 TGGCCGTGGAGATCTTTGGGTTTTC
1 TGGCCGTGGAG-GCTTT-GGTTTTC
*
5453891 TGGCGGTGGAGGCTTTGGTTTTC
1 TGGCCGTGGAGGCTTTGGTTTTC
5453914 GGGGTTGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 10 0.48
ACGTcount: A:0.06, C:0.15, G:0.40, T:0.40
Consensus pattern (23 bp):
TGGCCGTGGAGGCTTTGGTTTTC
Found at i:5458164 original size:35 final size:35
Alignment explanation
Indices: 5458118--5458213 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
5458108 AACACATTCA
* **
5458118 TCAATTATATTCTAAACCCCAAATTCTAAAATGTT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
*
5458153 TCAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
* * **
5458188 TCAATTACATACCCAACCCCAAATTC
1 TCAATTATATTCTAAACCCCAAATTC
5458214 ATAATTCATT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.41, C:0.26, G:0.01, T:0.32
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCCAAAATACT
Found at i:5458875 original size:148 final size:148
Alignment explanation
Indices: 5458696--5458987 Score: 512
Period size: 148 Copynumber: 2.0 Consensus size: 148
5458686 AAAAAATTAA
* *
5458696 ATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTCAAAA
1 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAAA
*
5458761 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTG
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
5458826 TTTTATAAACTGAACTGG
131 TTTTATAAACTGAACTGG
5458844 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAAA
1 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAAA
* * * * *
5458909 ATTCAATTCAATTCGACTTGATTTGAATTTTATAAATTCAAATCGAAAATATTTCGAGTTAATTA
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
5458974 TTTTATAAACTGAA
131 TTTTATAAACTGAA
5458988 TTGAGTATTT
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
148 136 1.00
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.38
Consensus pattern (148 bp):
ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTCAAAA
ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
TTTTATAAACTGAACTGG
Found at i:5459824 original size:2 final size:2
Alignment explanation
Indices: 5459817--5459847 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5459807 TTATTTTATC
5459817 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 A
5459848 AATCTGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5473083 original size:23 final size:23
Alignment explanation
Indices: 5473054--5473257 Score: 277
Period size: 23 Copynumber: 8.9 Consensus size: 23
5473044 AGACGAATTA
5473054 AAGAAGGAGAAATGAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
5473077 AAGAAGGAGAAATGAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
5473100 AAGAAGGAGAAATGAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
5473123 AAGAAGGAGAAATGAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
* *
5473146 AAGAAGAAGAAATGGGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
* * **
5473169 AAAAAGAAGAAACAAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
* *
5473192 AA-AAGAAGAAACGAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
* * *
5473214 AAAAAGAAGAAACGAGTTTATGG
1 AAGAAGGAGAAATGAGTTTATGG
*
5473237 AAGAA-GAGCAATTGAGTTTAT
1 AAGAAGGAG-AAATGAGTTTAT
5473258 AGATGAAGAA
Statistics
Matches: 168, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
22 23 0.14
23 145 0.86
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (23 bp):
AAGAAGGAGAAATGAGTTTATGG
Found at i:5481998 original size:51 final size:51
Alignment explanation
Indices: 5481922--5482019 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
5481912 TACAATGGGC
5481922 TCATTTTTCTCACTACTTTTTCTCTCAGACGAATGGAAGAAGAAGAATAAA
1 TCATTTTTCTCACTACTTTTTCTCTCAGACGAATGGAAGAAGAAGAATAAA
* *
5481973 TCATTTTTCTCACTACTTTTTCTCTCAGACGAATTGAAGAAGGAGAA
1 TCATTTTTCTCACTACTTTTTCTCTCAGACGAATGGAAGAAGAAGAA
5482020 ATGAGTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (51 bp):
TCATTTTTCTCACTACTTTTTCTCTCAGACGAATGGAAGAAGAAGAATAAA
Found at i:5482038 original size:23 final size:23
Alignment explanation
Indices: 5482008--5482205 Score: 209
Period size: 23 Copynumber: 8.4 Consensus size: 23
5481998 CAGACGAATT
*
5482008 GAAGAAGGAGAAATGAGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
* *
5482031 GAAGAAGGAGAAATGAGTTTATA
1 GAAGAAGAAGAAATGAGTTTATG
* *
5482054 GAAGTAGAAGAAATGTGTTTATGG
1 GAAGAAGAAGAAATGAGTTTAT-G
*
5482078 AAGAAGAAGAAGAAATGGGTTTATG
1 --GAAGAAGAAGAAATGAGTTTATG
* *
5482103 GAAAAAGAAGAAACGAGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
* *
5482126 GAAAAAGAAGAAATTAGTTTATG
1 GAAGAAGAAGAAATGAGTTTATG
* *
5482149 GAAGAAG-AGCAAGTGAGTTTATA
1 GAAGAAGAAG-AAATGAGTTTATG
**
5482172 GAAGAAGAAGAATAAAATGTTTATG
1 GAAGAAGAAGAA-ATGA-GTTTATG
5482197 GAAGAAGAA
1 GAAGAAGAA
5482206 TAATAATTCA
Statistics
Matches: 148, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.01
23 107 0.72
24 3 0.02
25 16 0.11
26 20 0.14
ACGTcount: A:0.48, C:0.01, G:0.29, T:0.22
Consensus pattern (23 bp):
GAAGAAGAAGAAATGAGTTTATG
Found at i:5482092 original size:72 final size:72
Alignment explanation
Indices: 5482008--5482156 Score: 210
Period size: 72 Copynumber: 2.1 Consensus size: 72
5481998 CAGACGAATT
* * * * **
5482008 GAAGAAGGAGAAATGAGTTTATGGAAGAAGGAGAAATGAGTTTATAGAAGTAGAAGAAATGT-GT
1 GAAGAAGAAGAAATGAGTTTATGGAAAAAGAAGAAACGAGTTTATAGAAAAAGAAGAAAT-TAGT
5482072 TTATGGAA
65 TTATGGAA
* *
5482080 GAAGAAGAAGAAATGGGTTTATGGAAAAAGAAGAAACGAGTTTATGGAAAAAGAAGAAATTAGTT
1 GAAGAAGAAGAAATGAGTTTATGGAAAAAGAAGAAACGAGTTTATAGAAAAAGAAGAAATTAGTT
5482145 TATGGAA
66 TATGGAA
5482152 GAAGA
1 GAAGA
5482157 GCAAGTGAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.01
72 67 0.99
ACGTcount: A:0.48, C:0.01, G:0.30, T:0.21
Consensus pattern (72 bp):
GAAGAAGAAGAAATGAGTTTATGGAAAAAGAAGAAACGAGTTTATAGAAAAAGAAGAAATTAGTT
TATGGAA
Found at i:5482183 original size:72 final size:67
Alignment explanation
Indices: 5482008--5482205 Score: 200
Period size: 72 Copynumber: 2.8 Consensus size: 67
5481998 CAGACGAATT
* * * *
5482008 GAAGAAGGAGAAATGAGTTTATGGAAGAAGGAGAAATGAGTTTATAGAAGTAGAAGAAATGTGTT
1 GAAGAA-GAGAAGTGAGTTTATGGAAGAAGAAGAAA-GAGTTTATGGAAGAAGAAGAAATGTGTT
5482073 TATG
64 TATG
* * *
5482077 GAAGAAGAAGAAGAAATGGGTTTATGGAAAAAGAAGAAACGAGTTTATGGAAAAAGAAGAAAT-T
1 GAAGAAG-AGAAG---TGAGTTTATGGAAGAAGAAGAAA-GAGTTTATGGAAGAAGAAGAAATGT
5482141 AGTTTATG
61 -GTTTATG
* *
5482149 GAAGAAGAGCAAGTGAGTTTATAGAAGAAGAAGAATAAAATGTTTATGGAAGAAGAA
1 GAAGAAGAG-AAGTGAGTTTATGGAAGAAGAAG-A-AAGA-GTTTATGGAAGAAGAA
5482206 TAATAATTCA
Statistics
Matches: 107, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
68 1 0.01
69 27 0.25
70 2 0.02
71 20 0.19
72 57 0.53
ACGTcount: A:0.48, C:0.01, G:0.29, T:0.22
Consensus pattern (67 bp):
GAAGAAGAGAAGTGAGTTTATGGAAGAAGAAGAAAGAGTTTATGGAAGAAGAAGAAATGTGTTTA
TG
Found at i:5492014 original size:16 final size:16
Alignment explanation
Indices: 5491966--5492016 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 16
5491956 TTTAATTATA
5491966 TATTAATAAAATAAAAAT
1 TATTAATAAAAT--AAAT
*
5491984 T-TCATATAAAA-AAAT
1 TATTA-ATAAAATAAAT
5491999 TATTAATAAAATAAAT
1 TATTAATAAAATAAAT
5492015 TA
1 TA
5492017 GAGTGATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.39
16 8 0.29
17 2 0.07
18 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAATAAAATAAAT
Found at i:5492785 original size:20 final size:20
Alignment explanation
Indices: 5492762--5492852 Score: 146
Period size: 20 Copynumber: 4.5 Consensus size: 20
5492752 ACCCAATTTC
*
5492762 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAAAAGT
5492782 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGT
* *
5492802 CAAATTTGCAACACAGAAGT
1 CAAATTCGCAACACAAAAGT
*
5492822 CAAATTCGCAACACAAAAAT
1 CAAATTCGCAACACAAAAGT
5492842 CAAATTCGCAA
1 CAAATTCGCAA
5492853 AGTGCGTTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACACAAAAGT
Found at i:5492790 original size:40 final size:40
Alignment explanation
Indices: 5492762--5492852 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
5492752 ACCCAATTTC
5492762 CAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
* *
5492802 CAAATTTGCAACACAGAAGTCAAATTCGCAACACAAAAAT
1 CAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
5492842 CAAATTCGCAA
1 CAAATTCGCAA
5492853 AGTGCGTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.16
Consensus pattern (40 bp):
CAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
Found at i:5493213 original size:20 final size:20
Alignment explanation
Indices: 5493185--5493252 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
5493175 CTTAAATTCA
*
5493185 CAACACGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
* *
5493205 CAACGCGAAAATAAAAAGCG
1 CAACGCGAAAATGAAAATCG
5493225 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
5493245 CAACGCGA
1 CAACGCGA
5493253 TTTTCATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.51, C:0.22, G:0.19, T:0.07
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:5493272 original size:20 final size:20
Alignment explanation
Indices: 5493249--5493309 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
5493239 AAATCGCAAC
*
5493249 GCGATTTTCATGTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
5493269 GCGATTTTAATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5493289 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5493309 G
1 G
5493310 TGAATTTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:5493323 original size:20 final size:20
Alignment explanation
Indices: 5493249--5493323 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
5493239 AAATCGCAAC
* *
5493249 GCGATTTTCATGTTCGCGTT
1 GCGATTTTAATTTTCGCGTT
5493269 GCGATTTTAATTTTCGCGTT
1 GCGATTTTAATTTTCGCGTT
*
5493289 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAATTTTCGCGTT
* * *
5493309 GTGAATTTAAGTTTC
1 GCGATTTTAATTTTC
5493324 AGAAACTACT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.15, C:0.16, G:0.21, T:0.48
Consensus pattern (20 bp):
GCGATTTTAATTTTCGCGTT
Found at i:5495617 original size:24 final size:24
Alignment explanation
Indices: 5495590--5495643 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5495580 CTGAAACATC
5495590 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
5495614 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
5495638 ATCAAA
1 ATCAAA
5495644 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5495657 original size:24 final size:24
Alignment explanation
Indices: 5495590--5495657 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
5495580 CTGAAACATC
* * *
5495590 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
5495614 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
5495638 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
5495658 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:5496600 original size:19 final size:20
Alignment explanation
Indices: 5496577--5496726 Score: 155
Period size: 19 Copynumber: 7.7 Consensus size: 20
5496567 ACTAAAACCT
* *
5496577 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
5496596 GTTGCAAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
*
5496616 GTTGCGAATTTGAAA-TCCA
1 GTTGCGAATTTGAAATTCGA
5496635 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
5496654 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
5496673 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTC-GA
* ** * *
5496694 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGA
5496714 GTTGCGAATTTGA
1 GTTGCGAATTTGA
5496727 CTTATGTGTT
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
19 64 0.57
20 35 0.31
21 14 0.12
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:5496676 original size:57 final size:58
Alignment explanation
Indices: 5496577--5496693 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 58
5496567 ACTAAAACCT
*
5496577 GTTGCGAAATTAAATTCGTGTTGCAAATTCGAAAATCGAGTTGCGAATTTGAAATCCA
1 GTTGCGAAATTAAATTCGAGTTGCAAATTCGAAAATCGAGTTGCGAATTTGAAATCCA
* * * * *
5496635 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCA
1 GTTGCGAAATT-AAATTCGAGTTGCAAATTCGAAAATCGAGTTGCGAATTTGAAATCCA
5496692 GT
1 GT
5496694 GTTGTGAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 21 0.40
58 25 0.48
59 6 0.12
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.34
Consensus pattern (58 bp):
GTTGCGAAATTAAATTCGAGTTGCAAATTCGAAAATCGAGTTGCGAATTTGAAATCCA
Found at i:5496717 original size:20 final size:20
Alignment explanation
Indices: 5496673--5496756 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
5496663 TTGAAATTCA
* **
5496673 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTTTGT
*
5496694 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
5496714 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
5496734 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
5496754 GTT
1 GTT
5496757 ACGATTTACA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
20 45 0.80
21 11 0.20
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.48
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:5496736 original size:40 final size:41
Alignment explanation
Indices: 5496635--5496756 Score: 146
Period size: 40 Copynumber: 3.1 Consensus size: 41
5496625 TTGAAATCCA
** **
5496635 GTTGCGAATTTGAAATTCA--GTTGCGAATTTGA-AATTCA
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTTTGT
*
5496673 GTTGCGAATTTGAAATTCAGTGTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTTTGT
*
5496714 GTTGCGAATTTG-ACTT-ATGTGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCA-GTGTTGCGAATTTGACTTTTGT
5496754 GTT
1 GTT
5496757 ACGATTTACA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
38 19 0.26
39 1 0.01
40 39 0.53
41 14 0.19
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTTTTGT
Found at i:5496784 original size:20 final size:20
Alignment explanation
Indices: 5496758--5496841 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
5496748 TTTTGTGTTA
5496758 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
* *
5496778 AGATTTACAAATTCACGTTG
1 CGATTTACAAATTCGCGTTG
*
5496798 CGATTTTCCAAATTCGCGTTG
1 CGA-TTTACAAATTCGCGTTG
* *
5496819 CGATTTACATATTCGTGTTG
1 CGATTTACAAATTCGCGTTG
5496839 CGA
1 CGA
5496842 ATTTGGAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 37 0.67
21 18 0.33
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:5500939 original size:18 final size:18
Alignment explanation
Indices: 5500916--5500965 Score: 91
Period size: 18 Copynumber: 2.7 Consensus size: 18
5500906 CTACACTCCT
5500916 GCAACAAACAACAATGAA
1 GCAACAAACAACAATGAA
5500934 GCAACAAACAACAATGAA
1 GCAACAAACAACAATGAA
5500952 GCAACAAAACAACA
1 GCAAC-AAACAACA
5500966 TCATTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.62, C:0.24, G:0.10, T:0.04
Consensus pattern (18 bp):
GCAACAAACAACAATGAA
Found at i:5509430 original size:30 final size:31
Alignment explanation
Indices: 5509396--5509462 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
5509386 AATGGAGCCA
** *
5509396 TTAGACATTGTTATCATTTT-GCCACTCACG
1 TTAGACATTAATATCATTTTAGCCACCCACG
*
5509426 TTAGACATTAATGTCATTTTAGCCACCCACG
1 TTAGACATTAATATCATTTTAGCCACCCACG
5509457 TTAGAC
1 TTAGAC
5509463 TTCAATGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (31 bp):
TTAGACATTAATATCATTTTAGCCACCCACG
Found at i:5509457 original size:31 final size:31
Alignment explanation
Indices: 5509409--5509477 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
5509399 GACATTGTTA
*
5509409 TCATTTT-GCCACTCACGTTAGACATT-AATG
1 TCATTTTAGCCACCCACGTTAGAC-TTCAATG
5509439 TCATTTTAGCCACCCACGTTAGACTTCAATG
1 TCATTTTAGCCACCCACGTTAGACTTCAATG
*
5509470 TCAATTTA
1 TCATTTTA
5509478 ATCACTCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 9 0.26
31 26 0.74
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.36
Consensus pattern (31 bp):
TCATTTTAGCCACCCACGTTAGACTTCAATG
Found at i:5509585 original size:113 final size:112
Alignment explanation
Indices: 5509384--5509607 Score: 295
Period size: 113 Copynumber: 2.0 Consensus size: 112
5509374 ATTTGAAATG
* *
5509384 ATAATGGAGCCATTAGACATTGTTATCATTTTGCCACTCACGTTAGACATTAATGTCATTTTAGC
1 ATAATGAAGCCATTAGACATTGTTATCATTTTGCCACCCACGTTAGACATTAATGTCATTTTAGC
* * *
5509449 CACCCACGTTAGACTTCAATGTCAATTTAATCACTCATGTTAAATTA
66 CACCCACATCAAACTTCAATGTCAATTTAATCACTCATGTTAAATTA
* * *
5509496 ATAATGAAGCCATTAGACATTGTTATCATTTTAGTCACCCATGTTAGACTTTAATGTCATTTTAG
1 ATAATGAAGCCATTAGACATTGTTATCATTTT-GCCACCCACGTTAGACATTAATGTCATTTTAG
* * *** * * *
5509561 TCACTCACATCAAACTTTGTTGTCATTTTAATCATTCATGTTGAATT
65 CCACCCACATCAAACTTCAATGTCAATTTAATCACTCATGTTAAATT
5509608 GGTATAACAA
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
112 31 0.33
113 64 0.67
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (112 bp):
ATAATGAAGCCATTAGACATTGTTATCATTTTGCCACCCACGTTAGACATTAATGTCATTTTAGC
CACCCACATCAAACTTCAATGTCAATTTAATCACTCATGTTAAATTA
Found at i:5515945 original size:43 final size:43
Alignment explanation
Indices: 5515897--5515982 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
5515887 TTAAATCTCG
* *
5515897 TATTTTTTATTCTTTAATTTTCTAAAGAAATTTTAATAAAAAT
1 TATTTTTTATTCTTTAAGTTACTAAAGAAATTTTAATAAAAAT
** *
5515940 TATTTTTTATTCTTTAAGTTACTAAATTAATTTTAATGAAAAT
1 TATTTTTTATTCTTTAAGTTACTAAAGAAATTTTAATAAAAAT
5515983 ATTAAAAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (43 bp):
TATTTTTTATTCTTTAAGTTACTAAAGAAATTTTAATAAAAAT
Found at i:5519920 original size:17 final size:17
Alignment explanation
Indices: 5519877--5519924 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
5519867 TAAAAAAATA
5519877 AATAAATATATTATT-T
1 AATAAATATATTATTAT
5519893 AATAAA-ATATTATTAT
1 AATAAATATATTATTAT
* *
5519909 TATAAATGTATTATTA
1 AATAAATATATTATTA
5519925 ATCTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.29
16 12 0.43
17 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AATAAATATATTATTAT
Found at i:5520209 original size:16 final size:17
Alignment explanation
Indices: 5520178--5520210 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5520168 TATAACAATA
5520178 TTAAATAGATAAAATTT
1 TTAAATAGATAAAATTT
*
5520195 TTAAATATA-AAAATTT
1 TTAAATAGATAAAATTT
5520211 AAATTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATAGATAAAATTT
Found at i:5524018 original size:3 final size:3
Alignment explanation
Indices: 5524010--5524035 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5524000 CGTTAACCCC
5524010 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
5524036 CTCACACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:5529426 original size:5 final size:5
Alignment explanation
Indices: 5529416--5529442 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5529406 TACAATTAAT
5529416 AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AA
5529443 AAAGTGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:5529999 original size:20 final size:19
Alignment explanation
Indices: 5529960--5530001 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5529950 TTTCTTTGAT
5529960 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
5529979 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
5529999 ATT
1 ATT
5530002 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:5530112 original size:120 final size:120
Alignment explanation
Indices: 5529869--5530105 Score: 313
Period size: 120 Copynumber: 2.0 Consensus size: 120
5529859 AATATATATT
* * * *
5529869 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAG
* *
5529932 GTACCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
**
5529987 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* ** * *
5530052 GTTATTTTAAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAAC
65 GGTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
5530105 A
1 A
5530106 GGATTAAAAT
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 19 0.18
119 27 0.26
120 39 0.38
121 18 0.17
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAG
GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:5530757 original size:11 final size:11
Alignment explanation
Indices: 5530738--5530770 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5530728 CTCTCTCATT
5530738 TTCTTTCTCTC
1 TTCTTTCTCTC
*
5530749 TTTTTTCTCTC
1 TTCTTTCTCTC
5530760 TTCTTTCTCTC
1 TTCTTTCTCTC
5530771 AAATGAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTCTTTCTCTC
Found at i:5531569 original size:3 final size:3
Alignment explanation
Indices: 5531552--5531617 Score: 89
Period size: 3 Copynumber: 21.0 Consensus size: 3
5531542 TTTGGGCCTG
5531552 TAA TAA -AA TTAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
5531599 TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA
5531618 AAAACCAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.03
3 45 0.78
4 11 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5532083 original size:113 final size:113
Alignment explanation
Indices: 5531954--5532631 Score: 1016
Period size: 113 Copynumber: 6.0 Consensus size: 113
5531944 ATAGAGTTAT
* *
5531954 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
5532019 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* * *
5532067 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCCTTCTTTAGACGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
5532132 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
5532180 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * **
5532245 ATTATGAACTTTCTCTGGAAATGATGATCCATTGAATGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* * * * * *
5532293 ACAAAAAGTTGAACAAGTTTTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * **
5532358 ATTATGAACTTGAC-CTGGCAATGCTGATCCATCGGGTGATGAATTAAA
66 ATTATGAACTT-TCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
* * * *
5532406 GTAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
5532471 ATTATGAAATTTCTCTTGAAATGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
*
5532519 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
5532584 ATTATGAACTTTCTCTGGAAAATCTGATCCATCGAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
5532632 ATCTTTGCTA
Statistics
Matches: 508, Mismatches: 55, Indels: 4
0.90 0.10 0.01
Matches are distributed among these distances:
112 1 0.00
113 506 1.00
114 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
Found at i:5541540 original size:15 final size:15
Alignment explanation
Indices: 5541517--5541548 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5541507 TGCAATGAAT
5541517 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
5541532 AATGCATGTATGCAA
1 AATGAATGTATGCAA
5541547 AA
1 AA
5541549 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:5545502 original size:20 final size:19
Alignment explanation
Indices: 5545463--5545504 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5545453 TTTCTTTGAT
5545463 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
5545482 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
5545502 ATT
1 ATT
5545505 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:5545615 original size:120 final size:120
Alignment explanation
Indices: 5545372--5545608 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 120
5545362 AATATATATT
* * * *
5545372 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
* *
5545435 GTACCTTAAGACAACTATTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAACTACTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
**
5545490 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCA
* ** ** * *
5545555 GTTATTTTAAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAAC
65 GGTACCTTAAGACAACTACTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
5545608 A
1 A
5545609 TGATTAAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 19 0.19
119 27 0.27
120 37 0.37
121 18 0.18
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAG
GTACCTTAAGACAACTACTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:5545636 original size:20 final size:20
Alignment explanation
Indices: 5545601--5545640 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5545591 TAAATAAATA
*
5545601 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
5545622 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
5545641 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:5546272 original size:13 final size:13
Alignment explanation
Indices: 5546246--5546288 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5546236 GAAGGGCCAG
5546246 CTCTCTCATTTTCT
1 CTCTCTC-TTTTCT
*
5546260 TTCTCTCTTTTCT
1 CTCTCTCTTTTCT
5546273 CTCTCT-TCTTTCT
1 CTCTCTCT-TTTCT
5546286 CTC
1 CTC
5546289 AAATGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 19 0.73
14 6 0.23
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.60
Consensus pattern (13 bp):
CTCTCTCTTTTCT
Found at i:5547090 original size:3 final size:3
Alignment explanation
Indices: 5547073--5547125 Score: 72
Period size: 3 Copynumber: 17.0 Consensus size: 3
5547063 TTTAGGCCTG
5547073 TAA TAA -AA TTAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA
5547120 TAA TAA
1 TAA TAA
5547126 AAAACCAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.04
3 36 0.78
4 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5547110 original size:13 final size:13
Alignment explanation
Indices: 5547073--5547125 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
5547063 TTTAGGCCTG
*
5547073 TAATAA-AATTAA
1 TAATAATAAATAA
5547085 TAATAAT-AATAA
1 TAATAATAAATAA
5547097 TAATAATAAATAA
1 TAATAATAAATAA
5547110 TAATAATAAATAA
1 TAATAATAAATAA
5547123 TAA
1 TAA
5547126 AAAACCAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
12 17 0.45
13 21 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:5551025 original size:60 final size:60
Alignment explanation
Indices: 5550901--5551013 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
5550891 AGGATCATAG
* * * *
5550901 TTTAAGGATGAAATTATAATATTTAAAAGTTTAAGTACTAATTAAAAATGAATGCAATAA
1 TTTAAGAAGGAAATTAAAATATTTAAAAATTTAAGTACTAATTAAAAATGAATGCAATAA
*
5550961 TTTAAGAAGGAAATTAAAATATTTAAAAATTTAAAG-ACTAATTTAAAATGAAT
1 TTTAAGAAGGAAATTAAAATATTTAAAAATTT-AAGTACTAATTAAAAATGAAT
5551014 TTTATAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.35
Consensus pattern (60 bp):
TTTAAGAAGGAAATTAAAATATTTAAAAATTTAAGTACTAATTAAAAATGAATGCAATAA
Found at i:5551633 original size:16 final size:16
Alignment explanation
Indices: 5551598--5551640 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5551588 TTCATCTTTA
*
5551598 ATATTATATATCAACAT
1 ATATTAT-TAACAACAT
*
5551615 ATATTATTAACATCAT
1 ATATTATTAACAACAT
*
5551631 ATATAATTAA
1 ATATTATTAA
5551641 TATATGAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTATTAACAACAT
Found at i:5552149 original size:23 final size:23
Alignment explanation
Indices: 5552119--5552163 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5552109 TTAAACAACC
* *
5552119 AAAAACGTGTCATAGAGGCAGAG
1 AAAAACGTGTCAAAAAGGCAGAG
5552142 AAAAACGTGTCAAAAAGGCAGA
1 AAAAACGTGTCAAAAAGGCAGA
5552164 ATAATACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.27, T:0.11
Consensus pattern (23 bp):
AAAAACGTGTCAAAAAGGCAGAG
Found at i:5552172 original size:23 final size:23
Alignment explanation
Indices: 5552120--5552188 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
5552110 TAAACAACCA
* *
5552120 AAAACGTGTCATAGAGGCAGAGA-
1 AAAACGTGTCAAAAAGGCAGA-AT
5552143 AAAACGTGTCAAAAAGGCAGAAT
1 AAAACGTGTCAAAAAGGCAGAAT
* *
5552166 AATACGT-TCCAAAAAAGCAGAAT
1 AAAACGTGT-CAAAAAGGCAGAAT
5552189 TATTAAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.05
23 38 0.95
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.14
Consensus pattern (23 bp):
AAAACGTGTCAAAAAGGCAGAAT
Found at i:5552350 original size:18 final size:19
Alignment explanation
Indices: 5552327--5552363 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5552317 AACTAACAGC
5552327 GGCTA-TGGAAAAGAGAGA
1 GGCTATTGGAAAAGAGAGA
5552345 GGCTATTGGAAAAGAGAGA
1 GGCTATTGGAAAAGAGAGA
5552364 AAACGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.43, C:0.05, G:0.38, T:0.14
Consensus pattern (19 bp):
GGCTATTGGAAAAGAGAGA
Found at i:5553011 original size:16 final size:16
Alignment explanation
Indices: 5552992--5553025 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5552982 TTTTACGATC
*
5552992 AATTAATTATTATATA
1 AATTAAATATTATATA
*
5553008 AATTAAATATTTTATA
1 AATTAAATATTATATA
5553024 AA
1 AA
5553026 ATAGTTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAATATTATATA
Found at i:5555128 original size:5 final size:5
Alignment explanation
Indices: 5555120--5555145 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5555110 AAAATCAAAT
5555120 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
5555146 ACAATGAATA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:5556417 original size:35 final size:35
Alignment explanation
Indices: 5556358--5556425 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
5556348 GTTTCAAAGA
*
5556358 TGGTATCAATACCATCCTTAAGGTATCGGTACCCT
1 TGGTATCAATACCATCCTTAAGGTATCGATACCCT
* * * *
5556393 TGGTATCGATACTATTCTTCAGGTATCGATACC
1 TGGTATCAATACCATCCTTAAGGTATCGATACC
5556426 TCATGAATGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (35 bp):
TGGTATCAATACCATCCTTAAGGTATCGATACCCT
Found at i:5558603 original size:42 final size:42
Alignment explanation
Indices: 5558549--5558686 Score: 95
Period size: 42 Copynumber: 3.3 Consensus size: 42
5558539 ATGTTGCGGC
5558549 ATTTAT-TGAAAAAATGTCACTATAGATGAACCCTATTATGGA
1 ATTTATAT-AAAAAATGTCACTATAGATGAACCCTATTATGGA
* * * * * *
5558591 ATTTATAT-AAAAATGTCGCTAAAG-T-ACTACTCTGTTACGGT
1 ATTTATATAAAAAATGTCACTATAGATGA--ACCCTATTATGGA
* * ** * * *
5558632 GTTTATTTGGAAAATGCCACTATAGATGAACCCTATTGTGGC
1 ATTTATATAAAAAATGTCACTATAGATGAACCCTATTATGGA
*
5558674 ATTTGTATAAAAA
1 ATTTATATAAAAA
5558687 CTCCGCTAAA
Statistics
Matches: 68, Mismatches: 22, Indels: 12
0.67 0.22 0.12
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 29 0.43
42 34 0.50
43 2 0.03
44 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (42 bp):
ATTTATATAAAAAATGTCACTATAGATGAACCCTATTATGGA
Found at i:5558637 original size:83 final size:83
Alignment explanation
Indices: 5558509--5558864 Score: 390
Period size: 83 Copynumber: 4.3 Consensus size: 83
5558499 TATTATTGCG
* * * * *
5558509 TTTGTATAAAAACGCCGCTAAAGTATTATTATGTTGCGGCATTTATTGAAAAAATGTCACTATAG
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTATTGAAAAAATGCCACTATAG
5558574 ATGAACCCTATTATGGAA
66 ATGAACCCTATTATGGAA
* * * * * *
5558592 TTTATATAAAAATGTCGCTAAAGTACTACTCTGTTACGGTGTTTATTTG-GAAAATGCCACTATA
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTA-TTGAAAAAATGCCACTATA
* *
5558656 GATGAACCCTATTGTGGCA
65 GATGAACCCTATTATGGAA
* * * ** *
5558675 TTTGTATAAAAACTCCGCTAAAGTACTACTCTGTTGTGGCGTTTGTTGAAAAAATATCACTATAT
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTATTGAAAAAATGCCACTATAG
* ** **
5558740 ATGAATCCTATTACAGTG
66 ATGAACCCTATTATGGAA
* * * *
5558758 TTTGTATAAAAACACCGCTAAAGTACTACTCTGTTGTGGCTTTTGTTGAAAAAATGCCACTATAG
1 TTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTATTGAAAAAATGCCACTATAG
* ***
5558823 ATGAACCCTATTACGTCG
66 ATGAACCCTATTATGGAA
* *
5558841 TTTATATGAAAACGCCGCTAAAGT
1 TTTGTATAAAAACGCCGCTAAAGT
5558865 TATCATTTTG
Statistics
Matches: 228, Mismatches: 43, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
82 3 0.01
83 222 0.97
84 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (83 bp):
TTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTATTGAAAAAATGCCACTATAG
ATGAACCCTATTATGGAA
Found at i:5558727 original size:41 final size:41
Alignment explanation
Indices: 5558667--5558803 Score: 100
Period size: 41 Copynumber: 3.3 Consensus size: 41
5558657 ATGAACCCTA
*
5558667 TTGTGGCATTTGTATAAAAACTCCGCTAAAGTACTACTCTG
1 TTGTGGCGTTTGTATAAAAACTCCGCTAAAGTACTACTCTG
* * * * * *
5558708 TTGTGGCGTTTGT-TGAAAAAATATCACTATA-TA-TGAATCCTA
1 TTGTGGCGTTTGTAT-AAAAACT-CCGCTAAAGTACT-ACT-CTG
*** * *
5558750 TTACAGTGTTTGTATAAAAACACCGCTAAAGTACTACTCTG
1 TTGTGGCGTTTGTATAAAAACTCCGCTAAAGTACTACTCTG
*
5558791 TTGTGGCTTTTGT
1 TTGTGGCGTTTGT
5558804 TGAAAAAATG
Statistics
Matches: 66, Mismatches: 23, Indels: 14
0.64 0.22 0.14
Matches are distributed among these distances:
40 2 0.03
41 37 0.56
42 25 0.38
43 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (41 bp):
TTGTGGCGTTTGTATAAAAACTCCGCTAAAGTACTACTCTG
Found at i:5559174 original size:62 final size:62
Alignment explanation
Indices: 5559108--5559329 Score: 426
Period size: 62 Copynumber: 3.6 Consensus size: 62
5559098 GAGGGTGATA
5559108 TTTGAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
1 TTTGAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
5559170 TTTGAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
1 TTTGAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
*
5559232 TTTAAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
1 TTTGAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
*
5559294 TTCGAATAAATAAACCTTAGAATCTATCATGGAAGA
1 TTTGAATAAATAAACCTTAGAATCTATCATGGAAGA
5559330 AATTAATAAG
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 157 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (62 bp):
TTTGAATAAATAAACCTTAGAATCTATCATGGAAGAGACTTAAGAAATTAATAAGAAAAGAC
Found at i:5560407 original size:28 final size:28
Alignment explanation
Indices: 5560367--5560420 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
5560357 GTCCTAGTTT
5560367 TTAAGTTAAAATC-TCGATCCCAACCCGA
1 TTAAGTTAAAATCAT-GATCCCAACCCGA
*
5560395 TTAAGTTAAAATCATGATCCCGACCC
1 TTAAGTTAAAATCATGATCCCAACCC
5560421 AACTCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (28 bp):
TTAAGTTAAAATCATGATCCCAACCCGA
Found at i:5565243 original size:2 final size:2
Alignment explanation
Indices: 5565238--5565270 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5565228 ATCACACATC
5565238 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5565271 TGTATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5565427 original size:18 final size:17
Alignment explanation
Indices: 5565404--5565440 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5565394 TAGATTTTTG
*
5565404 TCCCGAATGACCACTATA
1 TCCCGAAGGACCAC-ATA
5565422 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
5565439 TC
1 TC
5565441 ACATATGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.32, C:0.35, G:0.14, T:0.19
Consensus pattern (17 bp):
TCCCGAAGGACCACATA
Found at i:5565467 original size:18 final size:18
Alignment explanation
Indices: 5565444--5565479 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5565434 ACATATCACA
5565444 TATGTCCCGAAAGACCAC
1 TATGTCCCGAAAGACCAC
*
5565462 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAAGACCAC
5565480 GTAGAACCCT
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:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAAGACCAC
Found at i:5565800 original size:2 final size:2
Alignment explanation
Indices: 5565788--5565864 Score: 138
Period size: 2 Copynumber: 39.0 Consensus size: 2
5565778 TTCATATTAA
*
5565788 AT AT AT CT 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 AT AT AT AT
5565829 AT AT AT AT 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 AT AT AT AT
5565865 GAAACTTATA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5565988 original size:17 final size:18
Alignment explanation
Indices: 5565963--5566012 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
5565953 CACTTCTATT
*
5565963 ATTTCATTTATATAC-TA
1 ATTTAATTTATATACTTA
*
5565980 ATTTAATTTATTTACTTA
1 ATTTAATTTATATACTTA
*
5565998 ATTCAATTTCATATA
1 ATTTAATTT-ATATA
5566013 TTCCCTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.48
18 10 0.37
19 4 0.15
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATTTATATACTTA
Found at i:5566005 original size:18 final size:17
Alignment explanation
Indices: 5565968--5566012 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5565958 CTATTATTTC
*
5565968 ATTTATATACTAATTTA
1 ATTTATATACTAATTCA
*
5565985 ATTTATTTACTTAATTCA
1 ATTTATATAC-TAATTCA
5566003 ATTTCATATA
1 ATTT-ATATA
5566013 TTCCCTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 10 0.43
19 4 0.17
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATACTAATTCA
Found at i:5567085 original size:21 final size:22
Alignment explanation
Indices: 5567061--5567113 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
5567051 GTTTTCCCCC
5567061 GGTATCGATACCCTCCA-CATA-
1 GGTATCGATA-CCTCCACCATAT
*
5567082 GGTATCGATACCTCTACCATAT
1 GGTATCGATACCTCCACCATAT
5567104 GGTATCGATA
1 GGTATCGATA
5567114 TTGTTTATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.17
21 14 0.48
22 10 0.34
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCTCCACCATAT
Found at i:5568800 original size:19 final size:20
Alignment explanation
Indices: 5568771--5568808 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5568761 CAGAAATTGT
5568771 TGAAGGTGCATCGATGCACA
1 TGAAGGTGCATCGATGCACA
5568791 TGAA-GTGCATCGATGCAC
1 TGAAGGTGCATCGATGCAC
5568809 TCCTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCACA
Found at i:5568927 original size:63 final size:64
Alignment explanation
Indices: 5568796--5568937 Score: 153
Period size: 63 Copynumber: 2.2 Consensus size: 64
5568786 GCACATGAAG
* * *
5568796 TGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGAACAAGTAG
1 TGCATCGATGCACTCCCTTAAAATAAAAACATCGAATGCCATCAGTGTACCGATGAACAAGTAA
* ** ** ** *
5568860 TGCATCGATGCAC-CCCTTAATATTCAAACATCGAATGGGATTTGTGTACCGAT-ACACAGGTAA
1 TGCATCGATGCACTCCCTTAAAATAAAAACATCGAATGCCATCAGTGTACCGATGA-ACAAGTAA
*
5568923 TGCATCGATACACTC
1 TGCATCGATGCACTC
5568938 ATTAACCTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
62 1 0.02
63 49 0.77
64 14 0.22
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCACTCCCTTAAAATAAAAACATCGAATGCCATCAGTGTACCGATGAACAAGTAA
Found at i:5569558 original size:18 final size:18
Alignment explanation
Indices: 5569535--5569599 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
5569525 GGACACATTC
5569535 AGTGGTCTTTCGGGATGT
1 AGTGGTCTTTCGGGATGT
* *
5569553 AGTGGTCCTTCGGGATATAT
1 AGTGGTCTTTCGGG--ATGT
*
5569573 CCAGTGGTCTTTCGGGACGT
1 --AGTGGTCTTTCGGGATGT
5569593 AGTGGTC
1 AGTGGTC
5569600 CTTTGGGACA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
18 20 0.53
20 5 0.13
22 13 0.34
ACGTcount: A:0.14, C:0.17, G:0.35, T:0.34
Consensus pattern (18 bp):
AGTGGTCTTTCGGGATGT
Found at i:5569578 original size:40 final size:40
Alignment explanation
Indices: 5569469--5569649 Score: 218
Period size: 40 Copynumber: 4.4 Consensus size: 40
5569459 GGACATATCC
* * *
5569469 AGTGGTCCTTCGGGACACATTCAGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGACACATCCAGTGGTCTTTCGGG--ATGT
*
5569511 CCAGTGGTCCTTCGGGACACATTCAGTGGTCTTTCGGGATGT
1 --AGTGGTCCTTCGGGACACATCCAGTGGTCTTTCGGGATGT
* * *
5569553 AGTGGTCCTTCGGGATATATCCAGTGGTCTTTCGGGACGT
1 AGTGGTCCTTCGGGACACATCCAGTGGTCTTTCGGGATGT
* * * *
5569593 AGTGGTCCTTTGGGACATATCCAATGGTCTTTAGGGATGT
1 AGTGGTCCTTCGGGACACATCCAGTGGTCTTTCGGGATGT
*
5569633 AATGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
5569650 AATATTCACT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 86 0.69
42 3 0.02
44 35 0.28
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACACATCCAGTGGTCTTTCGGGATGT
Found at i:5569587 original size:62 final size:63
Alignment explanation
Indices: 5569446--5569590 Score: 195
Period size: 62 Copynumber: 2.3 Consensus size: 63
5569436 TCGAGGGTTA
*
5569446 CAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGGACACATTCAGTGGTCCTTCGGGACATAT
1 CAGTGGTCCTTCGGGACACATCCAGTGGTCCTTCGGG--A-ATTCAGTGGTCCTTCGGGACATAT
5569511 C
63 C
* * *
5569512 CAGTGGTCCTTCGGGACACATTCAGTGGTCTTTCGGG-ATGT-AGTGGTCCTTCGGGATATATC
1 CAGTGGTCCTTCGGGACACATCCAGTGGTCCTTCGGGAAT-TCAGTGGTCCTTCGGGACATATC
*
5569574 CAGTGGTCTTTCGGGAC
1 CAGTGGTCCTTCGGGAC
5569591 GTAGTGGTCC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
62 38 0.52
63 1 0.01
66 34 0.47
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.30
Consensus pattern (63 bp):
CAGTGGTCCTTCGGGACACATCCAGTGGTCCTTCGGGAATTCAGTGGTCCTTCGGGACATATC
Found at i:5569621 original size:62 final size:64
Alignment explanation
Indices: 5569446--5569613 Score: 172
Period size: 62 Copynumber: 2.7 Consensus size: 64
5569436 TCGAGGGTTA
* * * *
5569446 CAGTGGTCCTTCGGG-ACATATCCAGTGGTCCTTCGGGACACATTCAGTGGTCCTTCGGGACATA
1 CAGTGGTCCTTCGGGAACA-GT-CAGTGGTCCTTTGGGACATA-TCAGTGGTCCTTCGGGATATA
5569510 TC
63 TC
* *
5569512 CAGTGGTCCTTCGGGACACATTCAGTGGT-CTTTCGGG--ATGT-AGTGGTCCTTCGGGATATAT
1 CAGTGGTCCTTCGGGA-ACAGTCAGTGGTCCTTT-GGGACATATCAGTGGTCCTTCGGGATATAT
5569573 C
64 C
*
5569574 CAGTGGTCTTTCGGG-AC-GT-AGTGGTCCTTTGGGACATATC
1 CAGTGGTCCTTCGGGAACAGTCAGTGGTCCTTTGGGACATATC
5569614 CAATGGTCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
58 9 0.10
59 5 0.06
60 5 0.06
62 34 0.39
63 1 0.01
64 1 0.01
65 3 0.03
66 25 0.29
67 1 0.01
68 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (64 bp):
CAGTGGTCCTTCGGGAACAGTCAGTGGTCCTTTGGGACATATCAGTGGTCCTTCGGGATATATC
Found at i:5569629 original size:22 final size:22
Alignment explanation
Indices: 5569446--5569621 Score: 197
Period size: 22 Copynumber: 8.4 Consensus size: 22
5569436 TCGAGGGTTA
5569446 CAGTGGTCCTTCGGGACATATC
1 CAGTGGTCCTTCGGGACATATC
* *
5569468 CAGTGGTCCTTCGGGACACATT
1 CAGTGGTCCTTCGGGACATATC
5569490 CAGTGGTCCTTCGGGACATATC
1 CAGTGGTCCTTCGGGACATATC
* *
5569512 CAGTGGTCCTTCGGGACACATT
1 CAGTGGTCCTTCGGGACATATC
* *
5569534 CAGTGGTCTTTCGGG--ATGT-
1 CAGTGGTCCTTCGGGACATATC
*
5569553 -AGTGGTCCTTCGGGATATATC
1 CAGTGGTCCTTCGGGACATATC
* *
5569574 CAGTGGTCTTTCGGGAC--GT-
1 CAGTGGTCCTTCGGGACATATC
*
5569593 -AGTGGTCCTTTGGGACATATC
1 CAGTGGTCCTTCGGGACATATC
*
5569614 CAATGGTC
1 CAGTGGTC
5569622 TTTAGGGATG
Statistics
Matches: 128, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
18 27 0.21
20 7 0.05
22 94 0.73
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (22 bp):
CAGTGGTCCTTCGGGACATATC
Found at i:5569647 original size:18 final size:18
Alignment explanation
Indices: 5569537--5569647 Score: 60
Period size: 18 Copynumber: 5.7 Consensus size: 18
5569527 ACACATTCAG
* *
5569537 TGGTCTTTCGGGATGTAG
1 TGGTCCTTCGGGATGTAA
*
5569555 TGGTCCTTCGGGATATATCCA
1 TGGTCCTTCGGGATGTA---A
* * *
5569576 GTGGTCTTTCGGGACGTAG
1 -TGGTCCTTCGGGATGTAA
* *
5569595 TGGTCCTTTGGGACATATCCAA
1 TGGTCCTTCGGG--ATGT--AA
* *
5569617 TGGTCTTTAGGGATGTAA
1 TGGTCCTTCGGGATGTAA
5569635 TGGTCCTTCGGGA
1 TGGTCCTTCGGGA
5569648 CAAATATTCA
Statistics
Matches: 68, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
18 38 0.56
20 5 0.07
22 25 0.37
ACGTcount: A:0.16, C:0.17, G:0.32, T:0.34
Consensus pattern (18 bp):
TGGTCCTTCGGGATGTAA
Found at i:5575869 original size:63 final size:62
Alignment explanation
Indices: 5575778--5575937 Score: 162
Period size: 61 Copynumber: 2.6 Consensus size: 62
5575768 TTGAAGGTGC
* * * *
5575778 ATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGT
1 ATCGATGCACAGGTAGTGCATCGATGCAC-CCCTTAAAAT-AAAACATCGAATGCCATCAGTGT
* * ** ** **
5575842 ATCGACGCACA-GTAGTGCATCGATGCACCCCTTAATATTCAACATCGAATGGGATTTGTGT
1 ATCGATGCACAGGTAGTGCATCGATGCACCCCTTAAAATAAAACATCGAATGCCATCAGTGT
* *
5575903 ACCGATGC-CAGGTAGTGCATCGATGCACCCGTTAA
1 ATCGATGCACAGGTAGTGCATCGATGCACCCCTTAA
5575938 GGGATGCATC
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
60 2 0.02
61 46 0.57
62 8 0.10
63 15 0.19
64 10 0.12
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (62 bp):
ATCGATGCACAGGTAGTGCATCGATGCACCCCTTAAAATAAAACATCGAATGCCATCAGTGT
Found at i:5576502 original size:22 final size:22
Alignment explanation
Indices: 5576474--5576534 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
5576464 TCGAGGGTTA
*
5576474 CAGTGGTCCTTCGGGATATATC
1 CAGTGGTCCTTCGGGATACATC
* * *
5576496 CAGTGGTCATTCGGGACACATT
1 CAGTGGTCCTTCGGGATACATC
*
5576518 CAGTGGTCCTTCCGGAT
1 CAGTGGTCCTTCGGGAT
5576535 GTAGTGTTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (22 bp):
CAGTGGTCCTTCGGGATACATC
Found at i:5576563 original size:40 final size:40
Alignment explanation
Indices: 5576497--5576633 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 40
5576487 GGATATATCC
* * *
5576497 AGTGGTCATTCGGGACACATTC-AGTGGTCCTTCCGGATGT
1 AGTGGTCCTTCGGGACATA-TCAAGTGGTCCTTACGGATGT
* * *
5576537 AGTGTTCCTTCGGGACATATCAAGTGGTCTTTAGGGATGT
1 AGTGGTCCTTCGGGACATATCAAGTGGTCCTTACGGATGT
* * * *
5576577 AGTGGTCCTTTGGGACATATCCAA-TGGTCTTTAGGGACGT
1 AGTGGTCCTTCGGGACATAT-CAAGTGGTCCTTACGGATGT
* *
5576617 AATGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
5576634 AATATTCACT
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.02
40 78 0.94
41 3 0.04
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.31
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACATATCAAGTGGTCCTTACGGATGT
Found at i:5576573 original size:22 final size:22
Alignment explanation
Indices: 5576548--5576614 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
5576538 GTGTTCCTTC
5576548 GGGACATATCAAGTGGTCTTTA
1 GGGACATATCAAGTGGTCTTTA
*
5576570 GGG--ATGT--AGTGGTCCTTT-
1 GGGACATATCAAGTGGT-CTTTA
5576588 GGGACATATCCAA-TGGTCTTTA
1 GGGACATAT-CAAGTGGTCTTTA
5576610 GGGAC
1 GGGAC
5576615 GTAATGGTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
18 9 0.25
19 4 0.11
20 6 0.17
21 4 0.11
22 12 0.33
23 1 0.03
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.31
Consensus pattern (22 bp):
GGGACATATCAAGTGGTCTTTA
Found at i:5580645 original size:166 final size:168
Alignment explanation
Indices: 5580457--5580791 Score: 640
Period size: 166 Copynumber: 2.0 Consensus size: 168
5580447 TCCTAGTCTT
5580457 TAGGCAAATAGAATTCCTGTTTTTTAGGAAAATAAAACAATCAAAAGTTTGTTTAGATTATCATA
1 TAGGCAAATAGAATTCCTGTTTTTTAGGAAAATAAAACAATCAAAAGTTTGTTTAGATTATCATA
5580522 ATCTCCGGAATATTTTTTAGATTTTATCTTAAACTCTTGTTGTATAAATAGATTGTTTTAGTTAT
66 ATCTCCGGAATATTTTTTAGATTTTATCTTAAACTCTTGTTGTATAAATAGATTGTTTTAGTTAT
5580587 TG-ATAAATGTGTGA-TTCAGCAAGTTTTCTC-TATTTC
131 TGAATAAATGTGTGATTTCAGCAAGTTTT-TCATATTTC
5580623 TAGGCAAATAGAATTCCTGTTTTTTAGGAAAATAAAACAATCAAAAGTTTGTTTAGATTATCATA
1 TAGGCAAATAGAATTCCTGTTTTTTAGGAAAATAAAACAATCAAAAGTTTGTTTAGATTATCATA
5580688 ATCTCCGGAATATTTTTTAGATTTTATCTTAAACTCTTGTTGTATAAATAGATTGTTTTAGTTAT
66 ATCTCCGGAATATTTTTTAGATTTTATCTTAAACTCTTGTTGTATAAATAGATTGTTTTAGTTAT
5580753 TGAATAAATGTGTGATTTCAGCAAGTTTTTCATATTTC
131 TGAATAAATGTGTGATTTCAGCAAGTTTTTCATATTTC
5580791 T
1 T
5580792 TTCTTGTTTT
Statistics
Matches: 166, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
166 132 0.80
167 14 0.08
168 20 0.12
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (168 bp):
TAGGCAAATAGAATTCCTGTTTTTTAGGAAAATAAAACAATCAAAAGTTTGTTTAGATTATCATA
ATCTCCGGAATATTTTTTAGATTTTATCTTAAACTCTTGTTGTATAAATAGATTGTTTTAGTTAT
TGAATAAATGTGTGATTTCAGCAAGTTTTTCATATTTC
Found at i:5581559 original size:26 final size:26
Alignment explanation
Indices: 5581530--5581587 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
5581520 TTGCTCATAT
5581530 TTCTCCTAATCTTACTCTCACATCCC
1 TTCTCCTAATCTTACTCTCACATCCC
5581556 TTCTCCTAATCTTACTCTCACATCCC
1 TTCTCCTAATCTTACTCTCACATCCC
5581582 TTCTCC
1 TTCTCC
5581588 GAACCTAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (26 bp):
TTCTCCTAATCTTACTCTCACATCCC
Found at i:5588044 original size:110 final size:105
Alignment explanation
Indices: 5587843--5588057 Score: 385
Period size: 110 Copynumber: 2.0 Consensus size: 105
5587833 AAGAGCAATG
5587843 TTGAGGGACGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCATCAATACCGTTATTTGGTAAATC
1 TTGAGGGACGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCATCAATACCGTTATTTGGTAAATC
5587908 GAGCTCCATCAACTGCAATAGAGCTGAATACACCAATGGA
66 GAGCTCCATCAACTGCAATAGAGCTGAATACACCAATGGA
5587948 TTGAGGGACGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCAGTCAATACCGCCTGTTATTTGGT
1 TTGAGGGACGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCA-TCAATA---CC-GTTATTTGGT
5588013 AAATCGAGCTCCATCAACTGCAATAGAGCTGAATACACCAATGGA
61 AAATCGAGCTCCATCAACTGCAATAGAGCTGAATACACCAATGGA
5588058 GATGTGGACT
Statistics
Matches: 105, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
105 42 0.40
106 6 0.06
109 2 0.02
110 55 0.52
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (105 bp):
TTGAGGGACGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCATCAATACCGTTATTTGGTAAATC
GAGCTCCATCAACTGCAATAGAGCTGAATACACCAATGGA
Found at i:5591992 original size:23 final size:24
Alignment explanation
Indices: 5591961--5592006 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
5591951 CAACATACAT
**
5591961 TAAAAATTATTATTT-TAAAATAA
1 TAAAAATTAAAATTTATAAAATAA
*
5591984 TAAATATTAAAATTTATAAAATA
1 TAAAAATTAAAATTTATAAAATA
5592007 TCAGTATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAAAATTAAAATTTATAAAATAA
Found at i:5599843 original size:12 final size:12
Alignment explanation
Indices: 5599826--5599859 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5599816 GAAAATAAAG
5599826 AAAACTTAATGT
1 AAAACTTAATGT
*
5599838 AAAACTTGATGT
1 AAAACTTAATGT
5599850 AAAAC-TAATG
1 AAAACTTAATG
5599860 ACCCTAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:5607532 original size:10 final size:10
Alignment explanation
Indices: 5607517--5607541 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5607507 TTATATGTTC
5607517 GTTCATTTAT
1 GTTCATTTAT
5607527 GTTCATTTAT
1 GTTCATTTAT
5607537 GTTCA
1 GTTCA
5607542 AACAGAGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:5607920 original size:16 final size:16
Alignment explanation
Indices: 5607899--5607930 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5607889 CAAAAAAATG
5607899 GTTCGTTTATGTTCGT
1 GTTCGTTTATGTTCGT
5607915 GTTCGTTTATGTTCGT
1 GTTCGTTTATGTTCGT
5607931 TTATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
GTTCGTTTATGTTCGT
Found at i:5609318 original size:16 final size:16
Alignment explanation
Indices: 5609305--5609347 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
5609295 TGAACTGATC
*
5609305 TGATATTTACCTGACT
1 TGATAATTACCTGACT
5609321 TGATAATTACCTGACT
1 TGATAATTACCTGACT
5609337 TGATAATTACC
1 TGATAATTACC
5609348 CGATTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (16 bp):
TGATAATTACCTGACT
Found at i:5609676 original size:6 final size:6
Alignment explanation
Indices: 5609635--5611292 Score: 591
Period size: 6 Copynumber: 278.3 Consensus size: 6
5609625 TTAATGTATG
* **
5609635 TATA-A TATATA T-TATA TATACA TGCATA -AGTATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TA-TATA TATATA TATATA
* * * * ** *
5609681 TGTGT- TGTATG TAT-TA TA-ATA TAT-TA TATATA CTGCA-A TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA -TATATA TATATA
* * * * * * * *
5609725 TATATG TATATG TATATG TAT-TG T-TATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5609771 TATGTA TATGTA TATGTA TATGTA TATATA TGTATA GTATATT TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA -TATATA TATATA
* * * * * * * *
5609820 TATATG TATATA TGTATA TGTATG TATATG TATATG TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5609868 TATGTA TATGT- TATGTA TATGTA TATGTA T-TATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * *
5609914 TGTATA T-TATA GTATATGA TATGTA TATGTA TATGTA TAGTATA TGTATA
1 TATATA TATATA -TATAT-A TATATA TATATA TATATA TA-TATA TATATA
* * * * * * * * *
5609964 TGTATG TATATG TATGTA TATGTA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
5610012 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TTTATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5610060 TA-ATGA TGTATA TGTATA TGTATA GTATATG TATATG TA-ATG TATATG
1 TATAT-A TATATA TATATA TATATA -TATATA TATATA TATATA TATATA
* * * * * * * *
5610108 TATATG TATATG TATATG TATAT- TGTATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5610155 TATGTA TATGATA TGTATA TATGTA T-TGTA TATGTA TGTATA TGTAT-
1 TATATA TAT-ATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
5610202 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTAT- TGTGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5610249 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA T-TGATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TAT-ATA TATATA
* * * * *
5610297 TATATG TATAGTA TATGTA TATGTA T-TGTA TATGTA TAT-TA TAGTATA
1 TATATA TATA-TA TATATA TATATA TATATA TATATA TATATA TA-TATA
* * * * * * * *
5610345 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATG TATAGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATA-TA TATATA
* * * * * * * * * *
5610394 TATGTA TATGTA TGTATA TGTATG TGTATA TGTATA TGTATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5610442 T-TATG TATATG TATATG TATATG TATATG TATATG TATATG TATAGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATA-TA
* * * * * * * *
5610490 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5610538 TATATA GTATCTA TATGTA TATGTA TATGTA TGTATA TGTATG TATATG
1 TATATA -TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5610587 TATATG TATATG TATATG TATATG TATATA TGTATG TATATG TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5610635 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TCTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* ** * * * * * *
5610683 TGTATA GGTATA TGTA-A TTTATA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5610730 TGTATA TGTATA TGTATA TATATA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
5610778 TATGTA TATGTA TATGTA TATGTA TGTATA TGTATA TGTATA TGTATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5610826 TAT-TA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5610873 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5610921 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
5610969 TATGTA TATGTA TATGTA TATGTA TGTATC TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * * *
5611017 TGTATA T-TGTA TATGTA TATGTA TGTATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5611064 TATATG TATATG TATATG TATATG TATATG TATAGTA TATGTA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATA-TA TATATA TATATA
* * * * * * *
5611113 TGTATA T-TATA TATGTA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * *
5611160 TGTATA TGTATA T-TATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5611207 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
5611255 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TA
5611293 ATGTATAAGT
Statistics
Matches: 1490, Mismatches: 119, Indels: 87
0.88 0.07 0.05
Matches are distributed among these distances:
4 1 0.00
5 108 0.07
6 1327 0.89
7 53 0.04
8 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:5609734 original size:12 final size:12
Alignment explanation
Indices: 5609719--5611291 Score: 2375
Period size: 12 Copynumber: 135.4 Consensus size: 12
5609709 TATACTGCAA
5609719 TATATGTATATG
1 TATATGTATATG
5609731 TATATGTATATG
1 TATATGTATATG
5609743 TAT-TGT-TATG
1 TATATGTATATG
5609753 TATATGTATATG
1 TATATGTATATG
5609765 TATATG--TATG
1 TATATGTATATG
5609775 TATATGTATATG
1 TATATGTATATG
5609787 TATATGTATA--
1 TATATGTATATG
5609797 TATATGTATA-G
1 TATATGTATATG
*
5609808 TATATTTATATG
1 TATATGTATATG
5609820 TATATGTATATATG
1 TATATG--TATATG
5609834 TATATG--TATG
1 TATATGTATATG
5609844 TATATGTATATG
1 TATATGTATATG
5609856 --TATGTATATG
1 TATATGTATATG
5609866 TATATGTATATG
1 TATATGTATATG
5609878 T-TATGTATATG
1 TATATGTATATG
5609889 TATATG--TAT-
1 TATATGTATATG
5609898 TATATGTATATG
1 TATATGTATATG
5609910 TATATGTATAT-
1 TATATGTATATG
5609921 TATA-GTATATG
1 TATATGTATATG
5609932 -ATATGTATATG
1 TATATGTATATG
5609943 TATATGTATA-G
1 TATATGTATATG
5609954 TATATGTATATG
1 TATATGTATATG
5609966 --TATGTATATG
1 TATATGTATATG
5609976 --TATGTATATG
1 TATATGTATATG
5609986 --TATGTATATG
1 TATATGTATATG
5609996 TATATGTATATG
1 TATATGTATATG
5610008 TATATGTATATG
1 TATATGTATATG
5610020 TATATGTATATG
1 TATATGTATATG
5610032 TATATGTATATG
1 TATATGTATATG
5610044 TATATGTATAT-
1 TATATGTATATG
5610055 T-TATGTAATGATG
1 TATATGT-AT-ATG
5610068 TATATGTATATG
1 TATATGTATATG
5610080 TATA-GTATATG
1 TATATGTATATG
5610091 TATATGTA-ATG
1 TATATGTATATG
5610102 TATATGTATATG
1 TATATGTATATG
5610114 TATATGTATATG
1 TATATGTATATG
*
5610126 TATAT-TGTATG
1 TATATGTATATG
5610137 TATATGTATATG
1 TATATGTATATG
5610149 TATATG--TATG
1 TATATGTATATG
5610159 TATATG-ATATG
1 TATATGTATATG
5610170 TATATATGTAT-TG
1 --TATATGTATATG
5610183 TATATG--TATG
1 TATATGTATATG
5610193 TATATGTAT-TG
1 TATATGTATATG
5610204 TATATGTATATG
1 TATATGTATATG
5610216 TATATGTATATG
1 TATATGTATATG
5610228 TATATGTATATG
1 TATATGTATATG
*
5610240 TATTGTGTATATG
1 TA-TATGTATATG
5610253 TATATGTATATG
1 TATATGTATATG
5610265 TATATGTATATG
1 TATATGTATATG
5610277 TATATGTATTGATG
1 TATATGTA-T-ATG
5610291 TATATGTATATG
1 TATATGTATATG
5610303 TATA-GTATATG
1 TATATGTATATG
5610314 TATATGTAT-TG
1 TATATGTATATG
5610325 TATATGTATAT-
1 TATATGTATATG
5610336 TATA-GTATATG
1 TATATGTATATG
5610347 TATATGTATATG
1 TATATGTATATG
5610359 TATATGTATATG
1 TATATGTATATG
5610371 TATATG--TATG
1 TATATGTATATG
5610381 TATA-GTATATG
1 TATATGTATATG
5610392 TATATGTATATG
1 TATATGTATATG
5610404 --TATGTATATG
1 TATATGTATATG
*
5610414 TATGTGTATATG
1 TATATGTATATG
5610426 TATATG--TATG
1 TATATGTATATG
5610436 TATATGT-TATG
1 TATATGTATATG
5610447 TATATGTATATG
1 TATATGTATATG
5610459 TATATGTATATG
1 TATATGTATATG
5610471 TATATGTATATG
1 TATATGTATATG
5610483 TATA-GTATATG
1 TATATGTATATG
5610494 TATATGTATATG
1 TATATGTATATG
5610506 TATATGTATATG
1 TATATGTATATG
5610518 TATATGTATATG
1 TATATGTATATG
*
5610530 TATATGTATATA
1 TATATGTATATG
*
5610542 TAGTATCTATATG
1 TA-TATGTATATG
5610555 TATATGTATATG
1 TATATGTATATG
5610567 --TATGTATATG
1 TATATGTATATG
5610577 --TATGTATATG
1 TATATGTATATG
5610587 TATATGTATATG
1 TATATGTATATG
5610599 TATATGTATATG
1 TATATGTATATG
* *
5610611 TATATATGTATG
1 TATATGTATATG
5610623 TATATG--TATG
1 TATATGTATATG
5610633 TATATGTATATG
1 TATATGTATATG
5610645 TATATGTATATG
1 TATATGTATATG
5610657 TATATGTATATG
1 TATATGTATATG
*
5610669 --TATCTATATG
1 TATATGTATATG
*
5610679 TATATGTATAGG
1 TATATGTATATG
*
5610691 TATATGTA-ATT
1 TATATGTATATG
5610702 TATATGTATATG
1 TATATGTATATG
5610714 TATATGTATATG
1 TATATGTATATG
5610726 TATATGTATATG
1 TATATGTATATG
*
5610738 TATATGTATATATA
1 TATATG--TATATG
5610752 TATATGTATATG
1 TATATGTATATG
5610764 TATATGTATATG
1 TATATGTATATG
5610776 TATATGTATATG
1 TATATGTATATG
5610788 TATATGTATATG
1 TATATGTATATG
5610800 --TATGTATATG
1 TATATGTATATG
5610810 TATATGTATATG
1 TATATGTATATG
5610822 TATGTAT-TATATG
1 TA--TATGTATATG
5610835 TATATGTATATG
1 TATATGTATATG
5610847 TATATGTATATG
1 TATATGTATATG
5610859 TATATGTATATG
1 TATATGTATATG
5610871 TATATGTATATG
1 TATATGTATATG
5610883 TATATGTATATG
1 TATATGTATATG
5610895 TATATGTATATG
1 TATATGTATATG
5610907 TATATGTATATG
1 TATATGTATATG
5610919 TATATGTATATG
1 TATATGTATATG
5610931 TATATGTATATG
1 TATATGTATATG
5610943 TATATGTATATG
1 TATATGTATATG
5610955 TATATGTATATG
1 TATATGTATATG
5610967 TATATGTATATG
1 TATATGTATATG
5610979 TATATGTATATG
1 TATATGTATATG
*
5610991 --TATGTATCTG
1 TATATGTATATG
5611001 TATATGTATATG
1 TATATGTATATG
5611013 TATATGTATATTG
1 TATATGTATA-TG
5611026 TATATGTATATG
1 TATATGTATATG
5611038 TATGTATGTATATG
1 TA--TATGTATATG
5611052 TATATGTATATG
1 TATATGTATATG
5611064 TATATGTATATG
1 TATATGTATATG
5611076 TATATGTATATG
1 TATATGTATATG
5611088 TATATGTATA-G
1 TATATGTATATG
5611099 TATATG--TATG
1 TATATGTATATG
5611109 TATATGTATAT-
1 TATATGTATATG
* *
5611120 TATATATGTATG
1 TATATGTATATG
5611132 TATATGTATATG
1 TATATGTATATG
5611144 TATATGTATATG
1 TATATGTATATG
5611156 TATATGTATATG
1 TATATGTATATG
5611168 TATAT-TATATG
1 TATATGTATATG
5611179 TATATGTATATG
1 TATATGTATATG
5611191 TATATGTATATG
1 TATATGTATATG
5611203 TATATGTATATG
1 TATATGTATATG
5611215 TATATGTATATG
1 TATATGTATATG
5611227 TATATGTATATG
1 TATATGTATATG
5611239 TATATGTATATG
1 TATATGTATATG
5611251 TATATGTATATG
1 TATATGTATATG
5611263 TATATGTATATG
1 TATATGTATATG
5611275 TATATGTATATG
1 TATATGTATATG
5611287 TATAT
1 TATAT
5611292 AATGTATAAG
Statistics
Matches: 1455, Mismatches: 29, Indels: 154
0.89 0.02 0.09
Matches are distributed among these distances:
9 10 0.01
10 211 0.15
11 206 0.14
12 918 0.63
13 54 0.04
14 56 0.04
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (12 bp):
TATATGTATATG
Found at i:5609740 original size:18 final size:18
Alignment explanation
Indices: 5609719--5611291 Score: 2375
Period size: 18 Copynumber: 90.3 Consensus size: 18
5609709 TATACTGCAA
5609719 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5609737 TATATGTAT-TGT-TATG
1 TATATGTATATGTATATG
5609753 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5609771 --TATGTATATGTATATG
1 TATATGTATATGTATATG
5609787 TATATGTATA--TATATG
1 TATATGTATATGTATATG
*
5609803 TATA-GTATATTTATATG
1 TATATGTATATGTATATG
5609820 TATATGTATATATGTATATG
1 TATATG--TATATGTATATG
5609840 --TATGTATATGTATATG
1 TATATGTATATGTATATG
5609856 --TATGTATATGTATATG
1 TATATGTATATGTATATG
5609872 TATATGT-TATGTATATG
1 TATATGTATATGTATATG
5609889 TATATG--TAT-TATATG
1 TATATGTATATGTATATG
5609904 TATATGTATATGTATAT-
1 TATATGTATATGTATATG
5609921 TATA-GTATATG-ATATG
1 TATATGTATATGTATATG
5609937 TATATGTATATGTATA-G
1 TATATGTATATGTATATG
5609954 TATATGTATATG--TATG
1 TATATGTATATGTATATG
5609970 TATATG--TATGTATATG
1 TATATGTATATGTATATG
5609986 --TATGTATATGTATATG
1 TATATGTATATGTATATG
5610002 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610020 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610038 TATATGTATATGTATAT-
1 TATATGTATATGTATATG
5610055 T-TATGTAATGATGTATATG
1 TATATGT-AT-ATGTATATG
5610074 TATATGTATA-GTATATG
1 TATATGTATATGTATATG
5610091 TATATGTA-ATGTATATG
1 TATATGTATATGTATATG
5610108 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610126 TATAT-TGTATGTATATG
1 TATATGTATATGTATATG
5610143 TATATGTATATG--TATG
1 TATATGTATATGTATATG
5610159 TATATG-ATATGTATATATG
1 TATATGTATATG--TATATG
5610178 TAT-TGTATATG--TATG
1 TATATGTATATGTATATG
5610193 TATATGTAT-TGTATATG
1 TATATGTATATGTATATG
5610210 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610228 TATATGTATATGTATTGTG
1 TATATGTATATGTA-TATG
5610247 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610265 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610283 TATTGATGTATATGTATATG
1 TA-T-ATGTATATGTATATG
5610303 TATA-GTATATGTATATG
1 TATATGTATATGTATATG
5610320 TAT-TGTATATGTATAT-
1 TATATGTATATGTATATG
5610336 TATA-GTATATGTATATG
1 TATATGTATATGTATATG
5610353 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610371 TATATG--TATGTATA-G
1 TATATGTATATGTATATG
5610386 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610404 --TATGTATATGTATGTG
1 TATATGTATATGTATATG
5610420 TATATGTATATG--TATG
1 TATATGTATATGTATATG
5610436 TATATGT-TATGTATATG
1 TATATGTATATGTATATG
5610453 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610471 TATATGTATATGTATA-G
1 TATATGTATATGTATATG
5610488 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610506 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610524 TATATGTATATGTATATA
1 TATATGTATATGTATATG
*
5610542 TAGTATCTATATGTATATG
1 TA-TATGTATATGTATATG
5610561 TATATG--TATGTATATG
1 TATATGTATATGTATATG
5610577 --TATGTATATGTATATG
1 TATATGTATATGTATATG
5610593 TATATGTATATGTATATG
1 TATATGTATATGTATATG
* *
5610611 TATATATGTATGTATATG
1 TATATGTATATGTATATG
5610629 --TATGTATATGTATATG
1 TATATGTATATGTATATG
5610645 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610663 TATATG--TATCTATATG
1 TATATGTATATGTATATG
*
5610679 TATATGTATAGGTATATG
1 TATATGTATATGTATATG
*
5610697 TA-ATTTATATGTATATG
1 TATATGTATATGTATATG
5610714 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610732 TATATGTATATGTATATATA
1 TATATGTATATG--TATATG
5610752 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610770 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610788 TATATGTATATG--TATG
1 TATATGTATATGTATATG
5610804 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610822 TATGTAT-TATATGTATATG
1 TA--TATGTATATGTATATG
5610841 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610859 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610877 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610895 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610913 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610931 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610949 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5610967 TATATGTATATGTATATG
1 TATATGTATATGTATATG
*
5610985 TATATG--TATGTATCTG
1 TATATGTATATGTATATG
5611001 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611019 TATATTGTATATGTATATG
1 TATA-TGTATATGTATATG
5611038 TATGTATGTATATGTATATG
1 TA--TATGTATATGTATATG
5611058 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611076 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611094 TATA-GTATATG--TATG
1 TATATGTATATGTATATG
*
5611109 TATATGTATAT-TATATA
1 TATATGTATATGTATATG
*
5611126 TGTATGTATATGTATATG
1 TATATGTATATGTATATG
5611144 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611162 TATATGTATAT-TATATG
1 TATATGTATATGTATATG
5611179 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611197 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611215 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611233 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611251 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611269 TATATGTATATGTATATG
1 TATATGTATATGTATATG
5611287 TATAT
1 TATAT
5611292 AATGTATAAG
Statistics
Matches: 1443, Mismatches: 29, Indels: 166
0.88 0.02 0.10
Matches are distributed among these distances:
14 12 0.01
15 56 0.04
16 257 0.18
17 244 0.17
18 723 0.50
19 80 0.06
20 69 0.05
21 2 0.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TATATGTATATGTATATG
Found at i:5621308 original size:28 final size:29
Alignment explanation
Indices: 5621257--5621325 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
5621247 AATTATTGTT
* *
5621257 TTTAATTTTT-TTAATGGAAGAAATAAT-
1 TTTAATTTTTATTAATGAAAAAAATAATC
5621284 TCTTAATTTTTATTAAT-AAAAAAATAATC
1 T-TTAATTTTTATTAATGAAAAAAATAATC
5621313 TTTAATTTTTATT
1 TTTAATTTTTATT
5621326 TATTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 30 0.81
29 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTAATTTTTATTAATGAAAAAAATAATC
Found at i:5623496 original size:5 final size:5
Alignment explanation
Indices: 5623486--5623532 Score: 85
Period size: 5 Copynumber: 9.2 Consensus size: 5
5623476 TTAATGACAT
5623486 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA T
5623533 GTATGTATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 36 0.88
6 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:5631830 original size:26 final size:26
Alignment explanation
Indices: 5631794--5631935 Score: 186
Period size: 26 Copynumber: 5.5 Consensus size: 26
5631784 TAAAAAATGA
5631794 TTTTTGAAAACATATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
* *
5631820 TTTTTGAAAACAT-TTTGAA-A-ACA-
1 TTTTTGAAAACATATAT-AATATATAG
5631843 -TTTTGAAAACATATATATAATATATAG
1 TTTTTGAAAAC--ATATATAATATATAG
5631870 TTTTTGAAAACATATATAATATATAG
1 TTTTTGAAAACATATATAATATATAG
*
5631896 TTTTTAAAAACATATATTAATATATAG
1 TTTTTGAAAACATATA-TAATATATAG
5631923 TTTTTGAAAACAT
1 TTTTTGAAAACAT
5631936 TTTGAAAATA
Statistics
Matches: 101, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.10
24 6 0.06
25 6 0.06
26 47 0.47
27 22 0.22
28 10 0.10
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATAG
Found at i:5631837 original size:11 final size:11
Alignment explanation
Indices: 5631821--5631854 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
5631811 AATATATAGT
5631821 TTTTGAAAACA
1 TTTTGAAAACA
5631832 TTTTGAAAACA
1 TTTTGAAAACA
5631843 TTTTGAAAACA
1 TTTTGAAAACA
5631854 T
1 T
5631855 ATATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:5631839 original size:37 final size:37
Alignment explanation
Indices: 5631795--5632171 Score: 330
Period size: 36 Copynumber: 10.5 Consensus size: 37
5631785 AAAAAATGAT
*
5631795 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * * * * * *
5631832 TTTTGAAAACAT-TTTGAAAACATA-TATAT-AATATATA
1 TTTTGAAAATATATAT-AATATATAGTTTTTGAA-A-ACA
*
5631869 GTTTTTGAAAACATATATAATATATAGTTTTT---AA-A
1 --TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
5631904 -----AACATATAT-TAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
5631935 TTTTGAAAATATATATAATATATAG-TTTTGAAAAAA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
5631971 ATTTGAAAATATATATAATATATAG-TTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
5632007 TTTTGAAAAGATATATATAATATATAGTTTTTGAAAACA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACA
* *
5632046 ATTTGAAAATATATATATAATATATAGTTTTTTTAAAACA
1 TTTTG-AAA-ATATATATAATATATAG-TTTTTGAAAACA
* *
5632086 TTTT-TAAATATATATAATATATAG-TTTTGAAAACGT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAAC-A
* *
5632122 TTTTG-AAA-GTATAT-ATATA-A-TTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
5632154 TTTTAGAAAATATATATA
1 TTTT-GAAAATATATATA
5632172 TAATATACAT
Statistics
Matches: 284, Mismatches: 28, Indels: 57
0.77 0.08 0.15
Matches are distributed among these distances:
27 15 0.05
28 7 0.02
30 2 0.01
31 1 0.00
32 4 0.01
33 12 0.04
34 8 0.03
35 22 0.08
36 70 0.25
37 51 0.18
38 19 0.07
39 54 0.19
40 19 0.07
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:5632152 original size:33 final size:33
Alignment explanation
Indices: 5632060--5632173 Score: 115
Period size: 33 Copynumber: 3.3 Consensus size: 33
5632050 GAAAATATAT
* * *
5632060 ATATAATATATAGTTTTTTTAAAACATTTTT-AA
1 ATAT-ATATATAGATTTTTGAAAACGTTTTTGAA
*
5632093 ATATATATAATATATAGTTTTGAAAACGTTTTTGAA
1 ATATATAT-ATAGAT--TTTTGAAAACGTTTTTGAA
*
5632129 AGTATATATATA-ATTTTTGAAAACGTTTTAGAAA
1 A-TATATATATAGATTTTTGAAAACGTTTTTG-AA
5632163 ATATATATATA
1 ATATATATATA
5632174 ATATACATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
32 4 0.06
33 34 0.49
34 3 0.04
35 16 0.23
36 6 0.09
37 7 0.10
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (33 bp):
ATATATATATAGATTTTTGAAAACGTTTTTGAA
Found at i:5632173 original size:76 final size:75
Alignment explanation
Indices: 5631941--5632178 Score: 204
Period size: 76 Copynumber: 3.1 Consensus size: 75
5631931 AACATTTTGA
*
5631941 AAATATATATAATATATAGTTTTGAAAAAAATTTGAAAATATATATAATATATAGTTTTGAAAAC
1 AAATATATATAATATATAGTTTTGAAAACAATTTGAAAATATATAT-ATA-AT--TTTTGAAAAC
5632006 ATTTT-G--AA-A-
62 ATTTTAGAAAATAT
* * * ****
5632015 AGATATATATAATATATAGTTTTTGAAAACAATTTGAAAATATATATATAATATAT--AGTTTTT
1 AAATATATATAATATATAG-TTTTGAAAACAATTTGAAAATATATATATAATTTTTGAAAACATT
*
5632078 TTA-AAACATTTTT
65 TTAGAAA-A--TAT
** * *
5632091 AAATATATATAATATATAGTTTTGAAAACGTTTTTGAAAGTATATATATAATTTTTGAAAACGTT
1 AAATATATATAATATATAGTTTTGAAAAC-AATTTGAAAATATATATATAATTTTTGAAAACATT
5632156 TTAGAAAATAT
65 TTAGAAAATAT
*
5632167 ATATATAATATA
1 AAATAT-ATATA
5632179 CATTTAAAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
69 5 0.04
71 3 0.02
72 1 0.01
73 2 0.02
74 21 0.16
75 36 0.28
76 46 0.36
77 5 0.04
78 7 0.05
79 3 0.02
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (75 bp):
AAATATATATAATATATAGTTTTGAAAACAATTTGAAAATATATATATAATTTTTGAAAACATTT
TAGAAAATAT
Found at i:5632234 original size:4 final size:4
Alignment explanation
Indices: 5632225--5632272 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
5632215 TATTATTTTC
*
5632225 ATTT ATTT A-TT ATTT ATTT ATTT -TTCGT TTTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT--T ATTT ATTT ATTT ATTT ATTT
5632273 TGTTTTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
3 5 0.13
4 31 0.79
5 1 0.03
6 2 0.05
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:5632245 original size:25 final size:24
Alignment explanation
Indices: 5632230--5632279 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
5632220 TTTTCATTTA
5632230 TTTA-TTATTTATTTATTTTTCGTT
1 TTTATTTATTTATTTA-TTTTCGTT
5632254 TTTATTTATTTATTTATTTT-GTT
1 TTTATTTATTTATTTATTTTCGTT
5632277 TTT
1 TTT
5632280 TTCAGAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 6 0.24
24 8 0.32
25 11 0.44
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTATTTATTTATTTATTTTCGTT
Found at i:5633496 original size:15 final size:14
Alignment explanation
Indices: 5633476--5633509 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5633466 TTGTTTTTGT
*
5633476 TTTTTTTATTATTTA
1 TTTTTTTA-AATTTA
5633491 TTTTTTTAAATTTA
1 TTTTTTTAAATTTA
5633505 TTTTT
1 TTTTT
5633510 GATCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTAAATTTA
Found at i:5633504 original size:21 final size:21
Alignment explanation
Indices: 5633480--5633519 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5633470 TTTTGTTTTT
*
5633480 TTTATTATTT-ATTTTTTTAAA
1 TTTATT-TTTGATCTTTTTAAA
5633501 TTTATTTTTGATCTTTTTA
1 TTTATTTTTGATCTTTTTA
5633520 GGACAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATTTTTGATCTTTTTAAA
Found at i:5635273 original size:31 final size:31
Alignment explanation
Indices: 5635214--5635276 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5635204 TACAATACAA
*
5635214 TCCCCCAATATTTAGTCCATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATGG
** *
5635245 TCCCCCAACATTTAGTCTGTTTGTAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATGG
5635276 T
1 T
5635277 TCCCGACCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTGCAATATGG
Found at i:5637533 original size:24 final size:24
Alignment explanation
Indices: 5637506--5637553 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5637496 ACATAAAAAA
5637506 AACTACGAAACAAAGGAGTTGAAT
1 AACTACGAAACAAAGGAGTTGAAT
*
5637530 AACTACGAAACAAATGAGTTGAAT
1 AACTACGAAACAAAGGAGTTGAAT
5637554 TGGTTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (24 bp):
AACTACGAAACAAAGGAGTTGAAT
Found at i:5639505 original size:15 final size:16
Alignment explanation
Indices: 5639485--5639516 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5639475 CACAATCGCG
5639485 CAGGATTCCGGG-GCA
1 CAGGATTCCGGGAGCA
5639500 CAGGATTCCGGGAGCA
1 CAGGATTCCGGGAGCA
5639516 C
1 C
5639517 CGTGGTCGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.22, C:0.28, G:0.38, T:0.12
Consensus pattern (16 bp):
CAGGATTCCGGGAGCA
Found at i:5648250 original size:2 final size:2
Alignment explanation
Indices: 5648243--5648268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5648233 CCCTTATCTC
5648243 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
5648269 GAAAAGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5650509 original size:2 final size:2
Alignment explanation
Indices: 5650502--5650538 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5650492 TTATTCTTAT
5650502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5650539 TAATCATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5650605 original size:2 final size:2
Alignment explanation
Indices: 5650598--5650628 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5650588 ATTCTATCGT
5650598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5650629 TCTTTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5650710 original size:16 final size:16
Alignment explanation
Indices: 5650653--5650715 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
5650643 TCATATATCA
5650653 TTATTATTTATATATAT
1 TTATTATTT-TATATAT
*
5650670 TT-TTCTTATTATA-A-
1 TTATTATT-TTATATAT
*
5650684 TTA-TATGTTATATAT
1 TTATTATTTTATATAT
5650699 TTATTATTTTATATAT
1 TTATTATTTTATATAT
5650715 T
1 T
5650716 CATTTTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 4 0.11
16 20 0.54
17 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTATTTTATATAT
Found at i:5650738 original size:15 final size:15
Alignment explanation
Indices: 5650718--5650749 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5650708 TATATATTCA
*
5650718 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
5650733 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
5650748 TT
1 TT
5650750 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:5650766 original size:20 final size:20
Alignment explanation
Indices: 5650719--5650772 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
5650709 ATATATTCAT
*
5650719 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTGTATC
5650740 TTCTATTTTTATTTTTGTAT-
1 TT-TATTTTTATTTTTGTATC
*
5650760 TGTTATTGTTATT
1 T-TTATTTTTATT
5650773 ATCTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 16 0.55
22 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTTTTGTATC
Found at i:5661371 original size:18 final size:17
Alignment explanation
Indices: 5661362--5661400 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
5661352 AAAAATTGAA
5661362 AAAAAAGAAAAAAGAAC
1 AAAAAAGAAAAAAGAAC
*
5661379 AAAAAAG-AGAAAGAAC
1 AAAAAAGAAAAAAGAAC
5661395 AAAAAA
1 AAAAAA
5661401 TAAGGTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAC
Found at i:5662620 original size:110 final size:110
Alignment explanation
Indices: 5662418--5662624 Score: 324
Period size: 110 Copynumber: 1.9 Consensus size: 110
5662408 GCTTCCCAGT
* *
5662418 TTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
5662483 CAACGAAGGGGCGACTGATTGTTAACAAACAACTTTTTAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCA
* * * *
5662528 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTTAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
5662593 CAGCGAAGGGGCGGCTGACTGTCAACAAACAA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAA
5662625 TTTCCAGAGC
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCA
Found at i:5664188 original size:19 final size:19
Alignment explanation
Indices: 5664136--5664190 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5664126 TTTATATATA
* *
5664136 TATATACTTTTAATTCTTTT
1 TATATA-TTTTTATTATTTT
**
5664156 TCATATATCATTATTATTTT
1 T-ATATATTTTTATTATTTT
5664176 TATATATTTTTATTA
1 TATATATTTTTATTA
5664191 CTATAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.43
20 11 0.39
21 5 0.18
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATATTTTTATTATTTT
Found at i:5664330 original size:33 final size:31
Alignment explanation
Indices: 5664257--5664336 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
5664247 TTTTATCTTC
5664257 TATTTTTATTTTTGTATTGTTATTGTTATTA
1 TATTTTTATTTTTGTATTGTTATTGTTATTA
*
5664288 TCTTCTTTATTTTATGTATT-TTATT-TATATATA
1 TATT-TTTATTTT-TGTATTGTTATTGT-TAT-TA
*
5664321 TATATTTTATATTTGT
1 TAT-TTTTATTTTTGT
5664337 TTTTGTGCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
31 4 0.10
32 19 0.46
33 17 0.41
34 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (31 bp):
TATTTTTATTTTTGTATTGTTATTGTTATTA
Found at i:5667648 original size:20 final size:20
Alignment explanation
Indices: 5667623--5667684 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
5667613 TGGTTTTAAA
5667623 AAATAATTTAAATTATAATT
1 AAATAATTTAAATTATAATT
* * *
5667643 AAATAATATAATAGTATTA-T
1 AAATAATTTAA-ATTATAATT
5667663 AAAT-ATTTACAATTA-AATT
1 AAATAATTTA-AATTATAATT
5667682 AAA
1 AAA
5667685 CAAAAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.03
19 11 0.33
20 16 0.48
21 5 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATAATTTAAATTATAATT
Found at i:5669583 original size:2 final size:2
Alignment explanation
Indices: 5669576--5669608 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5669566 ATTAAAAAGT
5669576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5669609 TTGGTTGTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5669736 original size:3 final size:3
Alignment explanation
Indices: 5669728--5669866 Score: 271
Period size: 3 Copynumber: 46.7 Consensus size: 3
5669718 TTTTGTTTGG
5669728 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5669776 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5669824 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5669867 AGGTTTTTGA
Statistics
Matches: 135, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.01
3 133 0.99
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5672755 original size:2 final size:2
Alignment explanation
Indices: 5672748--5672777 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5672738 TTCATATTAA
5672748 AT 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 AT
5672778 TCATTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5679303 original size:260 final size:258
Alignment explanation
Indices: 5678838--5679548 Score: 904
Period size: 260 Copynumber: 2.7 Consensus size: 258
5678828 TTATATAATT
* * * *
5678838 TGAAAAATGAGAAAACAATTTTCAAAGTTTCTAATTTAATGTTTTAACAAAATAAAATCTTTGAA
1 TGAAAAATGAGAAAACAATTTTCAAAGTTTCTCATTTAATGTTTTCA-AAAATGAAATTTTTGAA
*
5678903 AAGTAAAAAAGCTATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTC
65 AAGTAAAAAA-CGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTC
* * * * * *
5678968 GAGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCATTCGAGTCATCTGTTAGCCTTTCGAG
129 GAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTGTCAGTCTTTCGAG
* * * * * *
5679033 CAATATGATAAGTCCTTCGGGCCATCCATAAGACCTTTAGACAGTATGTTTTCATATAATGTTT-
194 CAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGACAGGATGTTCTCACATAAT-TTTA
*
5679097 G
258 A
*
5679098 TGAAAAATGAGAAAAGCAATTTTCAAAGTTTCTCATCTAATGTTTTCAGAAAATGAAATTTTTGA
1 TGAAAAATGAGAAAA-CAATTTTCAAAGTTTCTCATTTAATGTTTTCA-AAAATGAAATTTTTGA
* * * *
5679163 AAAGTAAAAAACGGTTTCCAAAGTTTCTTACCCAGTAAAATATTTCCAAAATTGGTAAGTCCTTC
64 AAAGTAAAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTC
* * * ** *
5679228 GAGTCATCAATCAGTCTTTCGAGCATGATGATTGTATCTTTTGGGTTATCTGTCAGTCTTTCGAG
129 GAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTGTCAGTCTTTCGAG
* * * *
5679293 CAAGATGATAAGTTCTTCAGGCCATCTATAAGACCTTCGGACAGGATGTTCTCACATGATTTTCA
194 CAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGACAGGATGTTCTCACATAATTTT-A
5679358 A
258 A
** * * *
5679359 AAAAATATATGAGAAAACGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAATGAAATTTTTGA
1 TGAAA-A-ATGAGAAAACAATTTTCAAAGTTTCTCATTTAATGTTTTCAAAAATGAAATTTTTGA
* * * *
5679424 AAAGTAAGAAA-GTAATTTCCAAAGTTTCTTACCTATTAAACTACTTCCAAAATTGGCAAGTCAT
64 AAAGTAAAAAACG--ATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCAT
* * * *
5679488 TCGGGCTATCAGTAAGTTTTTCGAGCATGGTGATTAAATCTTTCGGGTTATCTGTCAGTCT
127 TCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTGTCAGTCT
5679549 CACTTGAGAC
Statistics
Matches: 386, Mismatches: 58, Indels: 12
0.85 0.13 0.03
Matches are distributed among these distances:
259 3 0.01
260 168 0.44
261 83 0.22
262 123 0.32
263 9 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (258 bp):
TGAAAAATGAGAAAACAATTTTCAAAGTTTCTCATTTAATGTTTTCAAAAATGAAATTTTTGAAA
AGTAAAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCGA
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTGTCAGTCTTTCGAGCA
AGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGACAGGATGTTCTCACATAATTTTAA
Done.