Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 89
Found at i:5410025 original size:4 final size:4
Alignment explanation
Indices: 5409998--5410047 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
5409988 TTCTTTTCTC
*
5409998 TTTA TTCTA -TTA TTT- TTCTA TTTA TTTA -GTA TTTA TTTA TTTA TTTA
1 TTTA TT-TA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5410045 TTT
1 TTT
5410048 TCTCTAACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 6 0.15
4 29 0.74
5 4 0.10
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:5410030 original size:19 final size:19
Alignment explanation
Indices: 5409991--5410044 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5409981 TTTTTCTTTC
* *
5409991 TTTTCTCTTTATTCTATTAT
1 TTTTCTATTTATT-TAGTAT
5410011 TTTTCTATTTATTTAGTAT
1 TTTTCTATTTATTTAGTAT
5410030 TTATT-TATTTATTTA
1 TT-TTCTATTTATTTA
5410045 TTTTCTCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTCTATTTATTTAGTAT
Found at i:5415889 original size:84 final size:83
Alignment explanation
Indices: 5415281--5416139 Score: 676
Period size: 84 Copynumber: 10.4 Consensus size: 83
5415271 TTAAAGACAA
* * * * * *
5415281 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGATCTTTGATTTCGACTACG
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
5415346 CTCAGCTCCAAGGCATAT
66 CTCAGCTCCAAGGCACAT
* * * * * * * * *
5415364 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCAAGTTTGATTACA
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
5415426 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * *
5415445 CA--T--A--ATAACTCAAGGCTAGAAGGGTTATCTGTCACTAAAAAACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAC-CAAAGACCTTCGAGTTCGACTAC
* *
5415504 GTTCAACTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * *
5415523 CATTTGTAGTATAGCAT-AAGTCGAGAAGGGCTATATG---CCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAAC-TCAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTAC
*
5415584 G-TCCAGCTCTAAGGCAC-T
65 GCT-CAGCTCCAAGGCACAT
* * * ** * * *
5415602 CATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAATAAAGACCTTCGAATTCGATTACA
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
*
5415667 CTCAGCTCAAAGGCACAAT
66 CTCAGCTCCAAGGCAC-AT
* * * * * * * *
5415686 -ATTTGCAGCATAGCTGAAGTCGAGAAGGGCTATCTACCAACCAAAGACCTTCAAGTTTGATTAT
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* * *** *
5415750 ACTTAGCTTCGGGGGCATAT
65 GCTCAGC-TCCAAGGCACAT
* *
5415770 CATTTGCATCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
*
5415835 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * ** * * ** * **
5415854 CATTTGCAGCATAGCTTAAGTTAATAAGGGCTATCTG---CCAAAGACCCGCGAGTTCGATTATA
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
5415916 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * *
5415935 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAACTTCAAGTTTGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTAC
* **
5416000 GCTCAGCTCTAAGGCATGT
65 GCTCAGCTCCAAGGCACAT
* * * * *
5416019 CATTTACAACATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
5416084 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * *
5416103 CATTTACAGCATAACTGAAGGCAAGAAGGGCTATCTG
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTG
5416140 TCAATAAAAT
Statistics
Matches: 605, Mismatches: 142, Indels: 57
0.75 0.18 0.07
Matches are distributed among these distances:
75 22 0.04
77 1 0.00
78 14 0.02
79 51 0.08
80 82 0.14
81 50 0.08
82 34 0.06
83 63 0.10
84 199 0.33
85 89 0.15
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:5415954 original size:165 final size:165
Alignment explanation
Indices: 5415281--5416139 Score: 904
Period size: 165 Copynumber: 5.2 Consensus size: 165
5415271 TTAAAGACAA
* * *
5415281 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGATCTTTGATTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
5415345 GCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * *
5415410 CTCAAGTTTGATTACACTCAGCTTCGAGGGCACAT
131 TTCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
* * *
5415445 CA--T--A--ATAACTCAAGGCTAGAAGGGTTATCTGTC-ACTAAAAAACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-CAAAGACCTTCGAGTTCGACTA
* * * * * * *
5415503 CGTTCAACTCCAAGGCACATCATTTGTAGTATAGCATAAGTCGAGAAGGGCTATATGCCAAAGAC
65 CGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * *
5415568 CTTCGAGTTCGA--CTACGTCCAGC-TCTAAGGCAC-T
130 CTTCGAGTTCGATTATAC-T-CAGCTTCGAGGGCACAT
* * * *
5415602 CATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAA-TAAAGACCTTCGAATTCGATTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * *
5415666 ACTCAGCTCAAAGGCACAAT-ATTTGCAGCATAGCTGAAGTCGAGAAGGGCTATCTACCAACCAA
66 GCTCAGCTCCAAGGCA-TATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT----GCCAA
* * * * *
5415730 AGACCTTCAAGTTTGATTATACTTAGCTTCGGGGGCATAT
126 AGACCTTCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
* * * *
5415770 CATTTGCATCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
** *
5415835 GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTTAATAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
**
5415900 CGCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
131 TTCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
* * * * *
5415935 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGAACTTCAAGTTTGACTA
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* * * * * * *
5415999 CGCTCAGCTCTAAGGCATGTCATTTACAACATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
65 CGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AA
* ** * *
5416064 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT
126 AGACCTTCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
* * * *
5416103 CATTTACAGCATAACTGAAGGCAAGAAGGGCTATCTG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG
5416140 TCAATAAAAT
Statistics
Matches: 575, Mismatches: 93, Indels: 50
0.80 0.13 0.07
Matches are distributed among these distances:
157 6 0.01
158 37 0.06
159 89 0.15
160 1 0.00
161 1 0.00
162 62 0.11
163 30 0.05
164 6 0.01
165 137 0.24
166 22 0.04
167 7 0.01
168 89 0.15
169 88 0.15
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (165 bp):
CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
TTCGAGTTCGATTATACTCAGCTTCGAGGGCACAT
Found at i:5416034 original size:249 final size:248
Alignment explanation
Indices: 5415281--5416139 Score: 915
Period size: 249 Copynumber: 3.5 Consensus size: 248
5415271 TTAAAGACAA
* * * * *
5415281 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGATCTTTGATTTCGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
5415345 GCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
* *
5415410 CTCAAGTTTGATTACACTCAGCTTCGAGGGCACATCA--T-A--ATAACTCAAGGCTAGAAGGGT
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTCAGCATAACTCAAGGCTAGAAGGGT
* * * * * *
5415470 TATCTGTCACTAAAA-AACCTTCGAGTTCGACTACGTTCAACTCCAAGGCACAT
196 TATCTGTCACCAAAAGAA-CTTCAAGTTTGACTACGCTCAGCTCCAAGGCATAT
* * * * *
5415523 CATTTGTAGTATAGCAT-AAGTCGAGAAGGGCTATATG----CCAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAAC-TCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * * * * * *
5415583 CG-TCCAGCTCTAAGGCA-CTCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAATAA
65 CGCT-CAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCC---AA
* * * * * * * *
5415646 AGACCTTCGAATTCGATTACACTCAGC-TCAAAGGCACAAT-ATTTGCAGCATAGCTGAAGTCGA
126 AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCAC-ATCATTT-CAGCATAACTCAAGGCTA
* ** * * ** * ***
5415709 GAAGGGCTATCTACCAACC-AAAGACCTTCAAGTTTGATTATACTTAGCTTCGGGGGCATAT
189 GAAGGGTTATCTGTC-ACCAAAAGAACTTCAAGTTTGACTACGCTCAGC-TCCAAGGCATAT
* *
5415770 CATTTGCATCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
5415835 GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTTAATAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
* *
5415900 CGCGAGTTCGATTATACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
131 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT-CAGCATAACTCAAGGCTAGAAGGG
* *
5415965 TTATCTGTCACCAAAAGAACTTCAAGTTTGACTACGCTCAGCTCTAAGGCATGT
195 TTATCTGTCACCAAAAGAACTTCAAGTTTGACTACGCTCAGCTCCAAGGCATAT
* * * * *
5416019 CATTTACAACATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
5416084 GCTCAGCTCCAAGGCACATCATTTACAGCATAACTGAAGGCAAGAAGGGCTATCTG
66 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG
5416140 TCAATAAAAT
Statistics
Matches: 492, Mismatches: 99, Indels: 45
0.77 0.16 0.07
Matches are distributed among these distances:
238 34 0.07
239 33 0.07
240 9 0.02
241 27 0.05
242 29 0.06
243 1 0.00
244 1 0.00
246 41 0.08
247 40 0.08
249 146 0.30
250 62 0.13
251 36 0.07
252 33 0.07
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (248 bp):
CATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTCAGCATAACTCAAGGCTAGAAGGGT
TATCTGTCACCAAAAGAACTTCAAGTTTGACTACGCTCAGCTCCAAGGCATAT
Found at i:5416860 original size:68 final size:70
Alignment explanation
Indices: 5416744--5416874 Score: 187
Period size: 68 Copynumber: 1.9 Consensus size: 70
5416734 TTTTGACAAA
*
5416744 ATATAATATATAATTTTCAGAAAACAATTTTCGAAAATGTATATATTATATAGTTTTTGAAAATG
1 ATATAATATATAATTTTCAGAAAACAATTTTCGAAAATGTATAAATTATATAGTTTTTGAAAATG
5416809 TTTTT
66 TTTTT
* * * *
5416814 ATATAATATATAGTTTTTA-AAAATC-ATTTT-GAAAATTTATAAATTATATAGTTTTTTAAAA
1 ATATAATATATAATTTTCAGAAAA-CAATTTTCGAAAATGTATAAATTATATAGTTTTTGAAAA
5416875 AACATTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 28 0.51
69 9 0.16
70 18 0.33
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (70 bp):
ATATAATATATAATTTTCAGAAAACAATTTTCGAAAATGTATAAATTATATAGTTTTTGAAAATG
TTTTT
Found at i:5416862 original size:38 final size:38
Alignment explanation
Indices: 5416811--5417031 Score: 126
Period size: 38 Copynumber: 5.9 Consensus size: 38
5416801 TGAAAATGTT
5416811 TTTATATAA-TATATAGTTTTTAAAAATCATTTTGAAAA
1 TTTATA-AATTATATAGTTTTTAAAAATCATTTTGAAAA
* *
5416849 TTTATAAATTATATAGTTTTTTAAAAAACATTTTTTTAAAAAAAA
1 TTTATAAATTATATAG-TTTTTAAAAATCA---TTTT---GAAAA
* *
5416894 CTTATATAA-TATATAGGTTTTTTAAAA-CATTTTGAAAA
1 TTTATA-AATTATATA-GTTTTTAAAAATCATTTTGAAAA
* * * * *
5416932 TATATATATTATATACTTTTAAAAAAACA--TT-----
1 TTTATAAATTATATAGTTTTTAAAAATCATTTTGAAAA
* * *
5416963 TTTAAAAACT-TATAGTTTTT-AAAAT-ATTTTGGAAA
1 TTTATAAATTATATAGTTTTTAAAAATCATTTTGAAAA
* *
5416998 TATATATATTATATAGTTTTTAAAAAATCATTTT
1 TTTATAAATTATATAGTTTTT-AAAAATCATTTT
5417032 TTGAAAACAT
Statistics
Matches: 138, Mismatches: 22, Indels: 45
0.67 0.11 0.22
Matches are distributed among these distances:
28 1 0.01
29 4 0.03
30 10 0.07
31 6 0.04
35 6 0.04
36 12 0.09
37 11 0.08
38 34 0.25
39 17 0.12
41 4 0.03
42 4 0.03
44 2 0.01
45 24 0.17
46 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (38 bp):
TTTATAAATTATATAGTTTTTAAAAATCATTTTGAAAA
Found at i:5416884 original size:83 final size:82
Alignment explanation
Indices: 5416812--5416965 Score: 229
Period size: 83 Copynumber: 1.9 Consensus size: 82
5416802 GAAAATGTTT
* * *
5416812 TTATATAATATATA-GTTTTTAAAAATCATTTTGAAAATTTATAAATTATATAGTTTTTTAAAAA
1 TTATATAATATATAGGTTTTTAAAAA-CATTTTGAAAATATATAAATTATATA-CTTTTAAAAAA
*
5416876 ACATTTTTTTAAAAAAAAC
64 ACATTTTTTGAAAAAAAAC
* *
5416895 TTATATAATATATAGGTTTTTTAAAACATTTTGAAAATATATATATTATATACTTTTAAAAAAAC
1 TTATATAATATATAGGTTTTTAAAAACATTTTGAAAATATATAAATTATATACTTTTAAAAAAAC
5416960 ATTTTT
66 ATTTTT
5416966 AAAAACTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 17 0.26
83 38 0.58
84 10 0.15
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (82 bp):
TTATATAATATATAGGTTTTTAAAAACATTTTGAAAATATATAAATTATATACTTTTAAAAAAAC
ATTTTTTGAAAAAAAAC
Found at i:5417031 original size:149 final size:151
Alignment explanation
Indices: 5416764--5417063 Score: 380
Period size: 149 Copynumber: 2.0 Consensus size: 151
5416754 TAATTTTCAG
* * ** ** *
5416764 AAAACAATTTTCGAAAATGTATATATTATATAGTTTTTGAAAATGTTTTTATATAATATATAGTT
1 AAAACAATTTTCGAAAATATATATATTATATACTTTTAAAAAACATTTTTATAAAATATATAGTT
* *
5416829 TTTAAAAATCATTTTGAAAATTTATAAATTATATAGTTTTTTAAAAAACATTTTTTTAAAAAAAA
66 TTTAAAAATCATTTTGAAAATATATAAATTATATAGTTTTTTAAAAAACATTTTTTGAAAAAAAA
5416894 CTTATATAATATATAGGTTTTTT
131 --TATATAATATATAGGTTTTTT
5416917 AAAAC-ATTTT-GAAAATATATATATTATATACTTTTAAAAAAACATTTTTA-AAAACT-TATAG
1 AAAACAATTTTCGAAAATATATATATTATATACTTTT-AAAAAACATTTTTATAAAA-TATATAG
* * *
5416978 TTTTT-AAAAT-ATTTTGGAAATATATATATTATATAG-TTTTTAAAAAATCATTTTTTGAAAAC
64 TTTTTAAAAATCATTTTGAAAATATATAAATTATATAGTTTTTTAAAAAA-CATTTTTTGAAAAA
* *
5417040 ATATATATAATATATAGTTTTTTT
128 AAATATATAATATATAGGTTTTTT
5417064 CAACTAGCCA
Statistics
Matches: 130, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
147 20 0.15
148 11 0.08
149 37 0.28
150 5 0.04
151 36 0.28
152 16 0.12
153 5 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (151 bp):
AAAACAATTTTCGAAAATATATATATTATATACTTTTAAAAAACATTTTTATAAAATATATAGTT
TTTAAAAATCATTTTGAAAATATATAAATTATATAGTTTTTTAAAAAACATTTTTTGAAAAAAAA
TATATAATATATAGGTTTTTT
Found at i:5417033 original size:68 final size:66
Alignment explanation
Indices: 5416912--5417044 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 66
5416902 ATATATAGGT
*
5416912 TTTTTAAAACATTTTGAAAATATATATATTATATACTTTTAAAAAAACATTTTTAAAAACTTATA
1 TTTTTAAAACATTTTGAAAATATATATATTATATACTTTTAAAAAAACATTTTTAAAAACATATA
5416977 G
66 G
* * * * *
5416978 TTTTTAAAATATTTTGGAAATATATATATTATATAGTTTTTAAAAAATCATTTTTTGAAAACATA
1 TTTTTAAAACATTTTGAAAATATATATATTATATA-CTTTTAAAAAAACA-TTTTTAAAAACATA
5417043 TA
64 TA
5417045 TATAATATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 33 0.56
67 12 0.20
68 14 0.24
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (66 bp):
TTTTTAAAACATTTTGAAAATATATATATTATATACTTTTAAAAAAACATTTTTAAAAACATATA
G
Found at i:5417698 original size:23 final size:22
Alignment explanation
Indices: 5417655--5417698 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5417645 TTTATTTCTA
*
5417655 ATTTTGTATATATATTTTTATC
1 ATTTTGTATATATATTATTATC
5417677 ATTTT-TATATATTAATTATTAT
1 ATTTTGTATATA-T-ATTATTAT
5417699 TATTCACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTGTATATATATTATTATC
Found at i:5417859 original size:8 final size:8
Alignment explanation
Indices: 5417815--5417861 Score: 58
Period size: 8 Copynumber: 5.5 Consensus size: 8
5417805 CTTTGATTCA
5417815 TTTTATTT
1 TTTTATTT
*
5417823 GTTTATTT
1 TTTTATTT
5417831 ATTTTATAATT
1 -TTTTAT--TT
5417842 TTTTATTT
1 TTTTATTT
5417850 TTTTATTT
1 TTTTATTT
5417858 TTTT
1 TTTT
5417862 CCTTTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 21 0.62
9 5 0.15
10 6 0.18
11 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTTATTT
Found at i:5424734 original size:23 final size:23
Alignment explanation
Indices: 5424704--5424767 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
5424694 TTTGAATTAT
5424704 AGGGGAACCGATTCCCCCATTGA
1 AGGGGAACCGATTCCCCCATTGA
5424727 AGGGGAACCGATTCCCCCATTGA
1 AGGGGAACCGATTCCCCCATTGA
*
5424750 AGGGGAACCGAATCCCCC
1 AGGGGAACCGATTCCCCC
5424768 TAGGGGAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.14
Consensus pattern (23 bp):
AGGGGAACCGATTCCCCCATTGA
Found at i:5424787 original size:19 final size:19
Alignment explanation
Indices: 5424703--5424775 Score: 56
Period size: 23 Copynumber: 3.4 Consensus size: 19
5424693 TTTTGAATTA
*
5424703 TAGGGGAACCGATTCCCCC
1 TAGGGGAACCGAATCCCCC
*
5424722 ATTGAAGGGGAACCGATTCCCCC
1 --T--AGGGGAACCGAATCCCCC
5424745 ATTGAAGGGGAACCGAATCCCCC
1 --T--AGGGGAACCGAATCCCCC
5424768 TAGGGGAA
1 TAGGGGAA
5424776 TCGATACCCC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
19 7 0.14
21 2 0.04
23 40 0.82
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (19 bp):
TAGGGGAACCGAATCCCCC
Found at i:5428488 original size:55 final size:55
Alignment explanation
Indices: 5428416--5428718 Score: 365
Period size: 55 Copynumber: 5.6 Consensus size: 55
5428406 AATGAATTTT
*
5428416 AAAGAAACTAAGTCTGATTTTTATAAGTTTCTTGATGATTTTTAAATG-GCCTTTC
1 AAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAG-CTTTC
* * * * *
5428471 AAAGAAACTAAGTCTGATTTTCATGACTTTCTTGATTATTTTTAAATGAACTTTT
1 AAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTC
5428526 AAAGAAACTAAGTCTGATTTTCATAAGTTTC-TGAT-ACTTTTTAAATGAGCTTTC
1 AAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGA-TTTTTAAATGAGCTTTC
* * * * *
5428580 AAAGAAACTAAGTCTGATTTTCAGAAGTTTC-T--TGA---TCAAGTGAGTTTTT
1 AAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTC
* * *
5428629 AAAGAAACTAAGTCTGATTTTCAGAAGTTTATTGATGATTTTTAAATGAGGTTTC
1 AAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTC
* *
5428684 AAAGAAATTAAGTCTGCTTTTCAT-AGATTTCTTGA
1 AAAGAAACTAAGTCTGATTTTCATAAG-TTTCTTGA
5428719 CAAAATGAAT
Statistics
Matches: 214, Mismatches: 24, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
49 40 0.19
50 1 0.00
52 4 0.02
53 2 0.01
54 52 0.24
55 115 0.54
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (55 bp):
AAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGCTTTC
Found at i:5428652 original size:49 final size:49
Alignment explanation
Indices: 5428571--5428664 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
5428561 ACTTTTTAAA
*
5428571 TGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCAAG
1 TGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTATTGATCAAG
* *
5428620 TGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTATTGAT
1 TGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTATTGAT
5428665 GATTTTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (49 bp):
TGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTATTGATCAAG
Found at i:5428806 original size:54 final size:54
Alignment explanation
Indices: 5428721--5428960 Score: 270
Period size: 54 Copynumber: 4.4 Consensus size: 54
5428711 TTTCTTGACA
* * * *
5428721 AAATGAA-TTTTAAAGAAGCTAAGCCTCATTTTTAGAGGTTTCTTGATGTGTTC
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTCTTT
* * *
5428774 AAATGGATTTTTAAAGAAGTTAGGCCTGATTTTTAGGGGTTTCTTGATGTCTTT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTCTTT
* * * * *
5428828 AAATGAATTTTGAAAAAAGTTAAGCCTGATTTTTAGGGGTTT-TATGACGTTTTT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT-TGATGTCTTT
* ** *
5428882 AAATGAATTTTTAAAAGAAGCTAAGCCT-AATTTTAGGGGTTTCTTGATAACTGT
1 AAATGAATTTTT-AAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTCTTT
*
5428936 AAATGAATCTTTTTGAAGAAGCTAA
1 AAATGAA--TTTTTAAAGAAGCTAA
5428961 ATTTATCAAG
Statistics
Matches: 158, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
53 7 0.04
54 122 0.77
55 24 0.15
56 5 0.03
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (54 bp):
AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTCTTT
Found at i:5429733 original size:136 final size:136
Alignment explanation
Indices: 5429485--5429739 Score: 411
Period size: 136 Copynumber: 1.9 Consensus size: 136
5429475 GAATTCAAAG
* *
5429485 AGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAATAAATTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAATTCATAATGAGAAGAGCTTGTTC
* * *
5429550 GACCTATCACTCGATTCACGACATTTCGAATCAATGATGCCTCGCTTGAGGGATCAATATTTCAA
66 GACCTATCACTCGATTCACGACATTTCAAATCAATGACGCATCGCTTGAGGGATCAATATTTCAA
5429615 ATGGAA
131 ATGGAA
*
5429621 AGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAATTCATAATGAGAAGAGCTTGTTC
** * * *
5429686 GACCTATCGTTCGATTCACGGCATTTCAAATCAGTGACGCATGGCTTGAGGGAT
66 GACCTATCACTCGATTCACGACATTTCAAATCAATGACGCATCGCTTGAGGGAT
5429740 TAACACTTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
136 108 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (136 bp):
AGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAATTCATAATGAGAAGAGCTTGTTC
GACCTATCACTCGATTCACGACATTTCAAATCAATGACGCATCGCTTGAGGGATCAATATTTCAA
ATGGAA
Found at i:5433653 original size:41 final size:40
Alignment explanation
Indices: 5433607--5433701 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
5433597 AACTTTATGG
5433607 GAGTTTCGAAACT-ATGACCCAA-AGTTTCGATACCCTTGAAA
1 GAGTTTCGAAACTCATGA---AAGAGTTTCGATACCCTTGAAA
* * *
5433648 GAGTTTCGATACTCTTGAAAGAGTTTCGATACTCTTGAAA
1 GAGTTTCGAAACTCATGAAAGAGTTTCGATACCCTTGAAA
*
5433688 GAGTTTCGATACTC
1 GAGTTTCGAAACTC
5433702 TTACCCAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
39 2 0.04
40 32 0.65
41 12 0.24
42 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (40 bp):
GAGTTTCGAAACTCATGAAAGAGTTTCGATACCCTTGAAA
Found at i:5433654 original size:20 final size:20
Alignment explanation
Indices: 5433629--5433703 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
5433619 TATGACCCAA
*
5433629 AGTTTCGATACCCTTGAAAG
1 AGTTTCGATACTCTTGAAAG
5433649 AGTTTCGATACTCTTGAAAG
1 AGTTTCGATACTCTTGAAAG
5433669 AGTTTCGATACTCTTGAAAG
1 AGTTTCGATACTCTTGAAAG
5433689 AGTTTCGATACTCTT
1 AGTTTCGATACTCTT
5433704 ACCCAGAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (20 bp):
AGTTTCGATACTCTTGAAAG
Found at i:5433969 original size:18 final size:18
Alignment explanation
Indices: 5433933--5433975 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5433923 TCTACCATGG
*
5433933 AAATTGCTAAACATGCTT
1 AAATTTCTAAACATGCTT
*
5433951 AACTTTCTAATACAT-CTT
1 AAATTTCTAA-ACATGCTT
5433969 AAATTTC
1 AAATTTC
5433976 CATGATCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (18 bp):
AAATTTCTAAACATGCTT
Found at i:5440942 original size:33 final size:33
Alignment explanation
Indices: 5440900--5440969 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
5440890 AATGTGTAAG
*
5440900 GAAGCATCATCATTCAATTCAGTAGGTCCAGGA
1 GAAGCATCATCATTCAAGTCAGTAGGTCCAGGA
*
5440933 GAAGCATCATCATTCGAGTCAGTAGGTCCAGGA
1 GAAGCATCATCATTCAAGTCAGTAGGTCCAGGA
5440966 GAAG
1 GAAG
5440970 GTTGTGGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (33 bp):
GAAGCATCATCATTCAAGTCAGTAGGTCCAGGA
Found at i:5445222 original size:30 final size:31
Alignment explanation
Indices: 5445146--5445223 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
5445136 CTTGTGAGCT
* *
5445146 TACCCAAGAAAGTTCTCAGGGCCACGAGGCT
1 TACCCAAGAAAGATCTCAGGGCCACGAGGCC
* *
5445177 TACCCAGGAAAGATCTCAGGTCGCA-G-GGCC
1 TACCCAAGAAAGATCTCAGGGC-CACGAGGCC
*
5445207 TACCCAAGAATGATCTC
1 TACCCAAGAAAGATCTC
5445224 GGCGTCATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 18 0.45
31 20 0.50
32 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (31 bp):
TACCCAAGAAAGATCTCAGGGCCACGAGGCC
Found at i:5449464 original size:31 final size:31
Alignment explanation
Indices: 5449377--5449479 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
5449367 GGGCTTATAT
* * *
5449377 GCCTACCCAAGAAAGTTCTCACGGCCA-CGAG
1 GCCTACCCAAGAAAGATCTCAGGGCCATAG-G
*
5449408 GCCTACCCAAGAAAGATCTCAGGGCCGTAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCATAGG
* ** *
5449439 GCCTACCCAAGAATGATCTTGGGGCCATAGA
1 GCCTACCCAAGAAAGATCTCAGGGCCATAGG
5449470 GCCTACCCAA
1 GCCTACCCAA
5449480 AAGTCACATT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 61 0.98
32 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCAGGGCCATAGG
Found at i:5458543 original size:29 final size:30
Alignment explanation
Indices: 5458511--5458569 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
5458501 TTACCCTTTA
5458511 TATTTG-AAGTGGTATTGTAAAACCCATTC
1 TATTTGAAAGTGGTATTGTAAAACCCATTC
*
5458540 TATTTGAAAGTGGTCTTGTAAAACCCATTC
1 TATTTGAAAGTGGTATTGTAAAACCCATTC
5458570 CTCCTAGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (30 bp):
TATTTGAAAGTGGTATTGTAAAACCCATTC
Found at i:5462855 original size:20 final size:20
Alignment explanation
Indices: 5462830--5462883 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5462820 TCAAGAAAAT
* *
5462830 TAAATCCTCTGGGTCGTTTG
1 TAAATCCTCTGGGTCATATG
5462850 TAAATCCTCTGGGTCATATG
1 TAAATCCTCTGGGTCATATG
* *
5462870 TAAAACCTCAGGGT
1 TAAATCCTCTGGGT
5462884 AGGATGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
TAAATCCTCTGGGTCATATG
Found at i:5462876 original size:119 final size:119
Alignment explanation
Indices: 5462725--5463056 Score: 531
Period size: 119 Copynumber: 2.8 Consensus size: 119
5462715 ATTTCCCACA
*
5462725 AATTTATAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGA
* *
5462790 AAGCG-TCTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCTGGGT
66 AAGTGAT-TTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGT
** * * * *
5462844 CGTTTGTAAATCCTCTGGGTCATATGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAAA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGA
5462909 AAGTGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGT
66 AAGTGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGT
* *
5462963 AATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGGAGGATGTTTTTGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAG-
*
5463028 AAAATGATTTTCAAAGTTTCTCATTTAAT
65 AAAGTGATTTTCAAAGTTTCTCATTTAAT
5463057 TCATTTAGAA
Statistics
Matches: 193, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
119 164 0.85
120 29 0.15
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (119 bp):
AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGA
AAGTGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGGGT
Found at i:5462977 original size:20 final size:20
Alignment explanation
Indices: 5462949--5462997 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5462939 TCAAGAAAAT
* *
5462949 TAAATCCTCCGGGTAATTTG
1 TAAAACCTCCGGGTAATCTG
*
5462969 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTAATCTG
5462989 TAAAACCTC
1 TAAAACCTC
5462998 AGGGGAGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
TAAAACCTCCGGGTAATCTG
Found at i:5463146 original size:20 final size:20
Alignment explanation
Indices: 5463121--5463309 Score: 247
Period size: 20 Copynumber: 9.4 Consensus size: 20
5463111 TTTTCCATGA
*
5463121 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCAGGGTC
5463141 ATTTGTAAAGCCTCAGGGTC
1 ATTTGTAAAGCCTCAGGGTC
* *
5463161 ATTTGTGAAGCCT-ATGGGTA
1 ATTTGTAAAGCCTCA-GGGTC
* *
5463181 ATTTGTAAAGCCTCCGGATC
1 ATTTGTAAAGCCTCAGGGTC
*
5463201 ATTTATAAAGCCTCAGGGTC
1 ATTTGTAAAGCCTCAGGGTC
* *
5463221 ATTCGTAAAACCTCAGGGTC
1 ATTTGTAAAGCCTCAGGGTC
*
5463241 ATTTGTAAAGCCTCAGAGTC
1 ATTTGTAAAGCCTCAGGGTC
5463261 ATTTGTAAAGCCTCAGGGTC
1 ATTTGTAAAGCCTCAGGGTC
* *
5463281 ATTTGTAAAGTCTCCA-AGTC
1 ATTTGTAAAGCCT-CAGGGTC
5463301 ATTTGTAAA
1 ATTTGTAAA
5463310 ACTTTTAGGT
Statistics
Matches: 147, Mismatches: 19, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 144 0.98
21 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
ATTTGTAAAGCCTCAGGGTC
Found at i:5463324 original size:20 final size:20
Alignment explanation
Indices: 5463301--5463355 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5463291 TCTCCAAGTC
*
5463301 ATTTGTAAAACTTTTAGGTA
1 ATTTGTAAAACCTTTAGGTA
*
5463321 ATTTGTAAAACCTTTGGGTA
1 ATTTGTAAAACCTTTAGGTA
* *
5463341 ATTTATAAATCCTTT
1 ATTTGTAAAACCTTT
5463356 GGGTCATCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTTGTAAAACCTTTAGGTA
Found at i:5463525 original size:47 final size:46
Alignment explanation
Indices: 5463467--5463575 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 46
5463457 TTCACTTAAT
* *
5463467 AGTAGTGAAACAGATTCTTTTCAAGTCATATAC-AACCTTCACGAAAG
1 AGTAGTGAAACAAATTCTTTTCAAGTCA-AT-CTAACCTCCACGAAAG
* *
5463514 AGTAGTGAAACAAATTCTTTTCAAGTCAATCTAATCTCCACGGAAG
1 AGTAGTGAAACAAATTCTTTTCAAGTCAATCTAACCTCCACGAAAG
*
5463560 AGTAGTGGAAGCAAAT
1 AGTAGT-GAAACAAAT
5463576 CAACATTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 1 0.02
46 19 0.35
47 35 0.64
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (46 bp):
AGTAGTGAAACAAATTCTTTTCAAGTCAATCTAACCTCCACGAAAG
Found at i:5463672 original size:35 final size:35
Alignment explanation
Indices: 5463623--5463727 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
5463613 CAGATTTTTC
*
5463623 AATTCAATTCAACCTTCACGGAAGAGTAGTGAAGT
1 AATTCAATTCAACCTTCACAGAAGAGTAGTGAAGT
* *
5463658 AATTCGATTTAACCTTCACAGAAGAGTAGTGAAGT
1 AATTCAATTCAACCTTCACAGAAGAGTAGTGAAGT
* * *
5463693 CGA-TCAAATTCAGCCTTCACAAAAGAGTAGTGAAG
1 -AATTC-AATTCAACCTTCACAGAAGAGTAGTGAAG
5463728 CAAGATCAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
35 34 0.57
36 26 0.43
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (35 bp):
AATTCAATTCAACCTTCACAGAAGAGTAGTGAAGT
Found at i:5471670 original size:30 final size:30
Alignment explanation
Indices: 5471628--5471756 Score: 125
Period size: 30 Copynumber: 4.3 Consensus size: 30
5471618 ATAAGTATTT
5471628 GAAA-TTATAAGGACCAAAATAATAAAAACA
1 GAAACTTA-AAGGACCAAAATAATAAAAACA
* * * * *
5471658 TAAACTCAAAGGATCAAAATAGTACAAACA
1 GAAACTTAAAGGACCAAAATAATAAAAACA
* * * **
5471688 GGAATTTAAAGGACTAAAATGGTAAAAACA
1 GAAACTTAAAGGACCAAAATAATAAAAACA
* * *
5471718 GAAACTTAAAGGGCTAAAATAATAAAAATA
1 GAAACTTAAAGGACCAAAATAATAAAAACA
5471748 GAAACTTAA
1 GAAACTTAA
5471757 GGGTCTAAAT
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
30 77 0.97
31 2 0.03
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (30 bp):
GAAACTTAAAGGACCAAAATAATAAAAACA
Found at i:5471765 original size:30 final size:30
Alignment explanation
Indices: 5471638--5471819 Score: 118
Period size: 30 Copynumber: 6.1 Consensus size: 30
5471628 GAAATTATAA
* * * *
5471638 GGACCAAAATAATAAAAACATAAACTCAAA
1 GGACTAAAATAATAAAAACAGAAACTTAAG
* * * * *
5471668 GGA-TCAAAATAGTACAAACAGGAATTTAAA
1 GGACT-AAAATAATAAAAACAGAAACTTAAG
**
5471698 GGACTAAAATGGTAAAAACAGAAACTTAAAG
1 GGACTAAAATAATAAAAACAGAAACTT-AAG
*
5471729 GG-CTAAAATAATAAAAATAGAAACTTAAG
1 GGACTAAAATAATAAAAACAGAAACTTAAG
* ** * * * * *
5471758 GGTCT-AAATAGCAAATACATATATTTAAA
1 GGACTAAAATAATAAAAACAGAAACTTAAG
* * *
5471787 GGACTAAAATAACAAAAATAGACACTTAAG
1 GGACTAAAATAATAAAAACAGAAACTTAAG
5471817 GGA
1 GGA
5471820 ATAGCAAAAA
Statistics
Matches: 116, Mismatches: 31, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
29 25 0.22
30 86 0.74
31 5 0.04
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.19
Consensus pattern (30 bp):
GGACTAAAATAATAAAAACAGAAACTTAAG
Found at i:5471853 original size:30 final size:30
Alignment explanation
Indices: 5471819--5471895 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
5471809 CACTTAAGGG
*
5471819 AATAGCAAAAACAGAAAATTAAACGACCAA
1 AATAGCACAAACAGAAAATTAAACGACCAA
* * * **
5471849 AATAGCACAAACATAAATTTAAAGGATTAA
1 AATAGCACAAACAGAAAATTAAACGACCAA
*
5471879 AATAGCTCAAACAGAAA
1 AATAGCACAAACAGAAA
5471896 CCTAAAGGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.60, C:0.14, G:0.10, T:0.16
Consensus pattern (30 bp):
AATAGCACAAACAGAAAATTAAACGACCAA
Found at i:5471902 original size:30 final size:31
Alignment explanation
Indices: 5471819--5471909 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 31
5471809 CACTTAAGGG
* ** * *
5471819 AATAGCAAAAACAGAAAATTAAACGAC-CAA
1 AATAGCACAAACAGAAACCTAAAGGACTTAA
* **
5471849 AATAGCACAAACATAAATTTAAAGGA-TTAA
1 AATAGCACAAACAGAAACCTAAAGGACTTAA
*
5471879 AATAGCTCAAACAGAAACCTAAAGGACTTAA
1 AATAGCACAAACAGAAACCTAAAGGACTTAA
5471910 CCAGTAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.16
Consensus pattern (31 bp):
AATAGCACAAACAGAAACCTAAAGGACTTAA
Found at i:5472586 original size:49 final size:49
Alignment explanation
Indices: 5472514--5472620 Score: 171
Period size: 49 Copynumber: 2.2 Consensus size: 49
5472504 AGCAAAACAC
*
5472514 TCCCAAAATGCTCATCTCTTCACCCTCTACTCCAATCTAAAGTCACATA
1 TCCCAAAACGCTCATCTCTTCACCCTCTACTCCAATCTAAAGTCACATA
* *
5472563 TCCCAAAACGCTTC-TCTCTTCACCCTCTATTCCAATCTAAAGTCATATA
1 TCCCAAAACGC-TCATCTCTTCACCCTCTACTCCAATCTAAAGTCACATA
5472612 TCCCAAAAC
1 TCCCAAAAC
5472621 CCAAACCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 52 0.96
50 2 0.04
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (49 bp):
TCCCAAAACGCTCATCTCTTCACCCTCTACTCCAATCTAAAGTCACATA
Found at i:5475045 original size:20 final size:20
Alignment explanation
Indices: 5475020--5475058 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5475010 CTTACAATAC
*
5475020 AACCATCAAATTTTTAGTCT
1 AACCATCAAATTATTAGTCT
5475040 AACCATCAAATTATTAGTC
1 AACCATCAAATTATTAGTC
5475059 CGTGTTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (20 bp):
AACCATCAAATTATTAGTCT
Found at i:5477084 original size:16 final size:16
Alignment explanation
Indices: 5477063--5477094 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5477053 TAGACATGTT
*
5477063 TTCAACATGACTTGTA
1 TTCAACATGACCTGTA
5477079 TTCAACATGACCTGTA
1 TTCAACATGACCTGTA
5477095 AATGATCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (16 bp):
TTCAACATGACCTGTA
Found at i:5477259 original size:21 final size:20
Alignment explanation
Indices: 5477230--5477289 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 20
5477220 TTTCAAATGT
5477230 TATAA-TAAAATATTAATTA
1 TATAATTAAAATATTAATTA
* *
5477249 TAGTAATTAAATTAATAA--A
1 TA-TAATTAAAATATTAATTA
* *
5477268 TATACTTAATATATTAATTA
1 TATAATTAAAATATTAATTA
5477288 TA
1 TA
5477290 ATTATTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 11 0.35
19 5 0.16
20 6 0.19
21 9 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TATAATTAAAATATTAATTA
Found at i:5477300 original size:30 final size:30
Alignment explanation
Indices: 5477232--5477314 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
5477222 TCAAATGTTA
*
5477232 TAATAAA-ATA-TTAATTATAGTAATTAAAT
1 TAATAAATATACTTAA-TATATTAATTAAAT
5477261 TAATAAATATACTTAATATATTAATTATAAT
1 TAATAAATATACTTAATATATTAATTA-AAT
* * *
5477292 T-ATTAATATGCTTTATAT-TTAAT
1 TAATAAATATACTTAATATATTAAT
5477315 ATTTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 12 0.26
30 27 0.57
31 8 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TAATAAATATACTTAATATATTAATTAAAT
Found at i:5477319 original size:13 final size:13
Alignment explanation
Indices: 5477303--5477381 Score: 63
Period size: 13 Copynumber: 5.6 Consensus size: 13
5477293 ATTAATATGC
5477303 TTTATATTTAATA
1 TTTATATTTAATA
5477316 TTTATATTTATATA
1 TTTATATTTA-ATA
5477330 CTTTAATACTTT-ATA
1 -TTT-ATA-TTTAATA
*
5477345 TTTAATACTT-ATA
1 TTT-ATATTTAATA
5477358 TTATATAGTTTAATA
1 TT-TATA-TTTAATA
5477373 CTTTATATT
1 -TTTATATT
5477382 ATATACATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
13 20 0.36
14 15 0.27
15 13 0.23
16 5 0.09
17 3 0.05
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.58
Consensus pattern (13 bp):
TTTATATTTAATA
Found at i:5477322 original size:22 final size:22
Alignment explanation
Indices: 5477305--5477453 Score: 93
Period size: 22 Copynumber: 6.9 Consensus size: 22
5477295 TAATATGCTT
5477305 TATA-TTTAATATTTATATTTA
1 TATACTTTAATATTTATATTTA
5477326 TATACTTTAATACTTTATATTTA
1 TATACTTTAATA-TTTATATTTA
5477349 -ATAC-TT-ATATTATATAGTTTA
1 TATACTTTAATATT-TATA-TTTA
*
5477370 -ATACTTT-ATATTATATACATTA
1 TATACTTTAATATT-TATA-TTTA
* * *
5477392 -GTAC-TTATGTAGTTATGTATTT-
1 TATACTTTA-ATA-TT-TATATTTA
* *
5477414 TATA-TTTAATACTTGTATTTA
1 TATACTTTAATATTTATATTTA
*
5477435 TATACTTTAATACTTATAT
1 TATACTTTAATATTTATAT
5477454 CCAAACATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.02
20 14 0.13
21 21 0.20
22 44 0.42
23 19 0.18
24 6 0.06
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (22 bp):
TATACTTTAATATTTATATTTA
Found at i:5477338 original size:8 final size:7
Alignment explanation
Indices: 5477306--5477381 Score: 54
Period size: 7 Copynumber: 10.7 Consensus size: 7
5477296 AATATGCTTT
5477306 ATATTTA
1 ATATTTA
5477313 ATATTT-
1 ATATTTA
5477319 ATATTTA
1 ATATTTA
5477326 TATACTTTA
1 -ATA-TTTA
5477335 ATACTTT-
1 ATA-TTTA
5477342 ATATTTA
1 ATATTTA
*
5477349 ATACTT-
1 ATATTTA
5477355 ATA-TTA
1 ATATTTA
5477361 TATAGTTTA
1 -ATA-TTTA
5477370 ATACTTT-
1 ATA-TTTA
5477377 ATATT
1 ATATT
5477382 ATATACATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
5 2 0.03
6 14 0.24
7 20 0.34
8 16 0.27
9 7 0.12
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:5477397 original size:43 final size:42
Alignment explanation
Indices: 5477313--5477399 Score: 99
Period size: 43 Copynumber: 2.0 Consensus size: 42
5477303 TTTATATTTA
*
5477313 ATATTTATATTTATATACTTTAATACTTTATATTTAATACTT
1 ATATTTATATTTATATACTTTAATACTTTATAATTAATACTT
*
5477355 ATATTATATAGTTTA-ATACTTT-ATA-TTATATACATTAGTACTT
1 ATATT-TATA-TTTATATACTTTAATACTT-TATA-ATTAATACTT
5477398 AT
1 AT
5477400 GTAGTTATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
41 2 0.05
42 12 0.31
43 21 0.54
44 4 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (42 bp):
ATATTTATATTTATATACTTTAATACTTTATAATTAATACTT
Found at i:5481884 original size:240 final size:239
Alignment explanation
Indices: 5481461--5482020 Score: 811
Period size: 240 Copynumber: 2.4 Consensus size: 239
5481451 AATCACCAAG
*
5481461 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGC-CGGATGAGTTCTTCTCATTATGA
1 GTTGAACAA-TTCTTCTCATTATGAACTTCTTCTCCTTC-CTCGGATGAGTTCTTCTCATTATGA
* * *
5481525 ACTCTCAACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTGATGCTAATCCA
64 ACTCTCCACTGGAAATGTTGATCCCCCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTAATCCA
*
5481590 ACTCCTTATGTGAGGGACTGGTGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACGAGCA
129 ACTCCTTATGTGAGGGACTGCTGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACGAGCA
* *
5481655 AAAGTCGGTGATGTTCCAATTCCTTATGCGATGGAAA-CAAGCTAAA
194 AAAGTCGGTGATGTTCCAACTCCTTATACGAT-GAAAGCAAGCTAAA
5481701 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTTCCTCGGATGAGTTCTTCTCATTATGAA
1 GTTGAAC-AATTCTTCTCATTATGAACTTCTTCTCCTTCCTCGGATGAGTTCTTCTCATTATGAA
* * * * *
5481766 CTCTCCACTGGAAATGTTGATCCCCCTCCTTCTGTGATGATTGATCTAAGGTAATGTTGATCCAT
65 CTCTCCACTGGAAATGTTGATCCCCCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTAATCCAA
5481831 CTCCTTATGTGAGGGACTAGCT-AAATGATTATGCTGATCCAACTCCTTATGTGATGGACGAGCA
130 CTCCTTATGTGAGGGACT-GCTGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACGAGCA
*
5481895 AAAGTCGGTGTTGTTCCAACTCCTTATACGATGAAAGCAAGCTAAA
194 AAAGTCGGTGATGTTCCAACTCCTTATACGATGAAAGCAAGCTAAA
* * *
5481941 ---G-----TTCTTCTCATTATGAACTTCTTTTCCCTT-ATCGGATGAGTTATTCTCATTATGAA
1 GTTGAACAATTCTTCTCATTATGAACTTCTTCT-CCTTCCTCGGATGAGTTCTTCTCATTATGAA
* * *
5481997 ATATCCACTGGAAAGGTTGATCCC
65 CTCTCCACTGGAAATGTTGATCCC
5482021 TCGAGTGAGG
Statistics
Matches: 296, Mismatches: 19, Indels: 19
0.89 0.06 0.06
Matches are distributed among these distances:
231 68 0.23
232 4 0.01
237 1 0.00
239 5 0.02
240 214 0.72
241 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (239 bp):
GTTGAACAATTCTTCTCATTATGAACTTCTTCTCCTTCCTCGGATGAGTTCTTCTCATTATGAAC
TCTCCACTGGAAATGTTGATCCCCCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTAATCCAAC
TCCTTATGTGAGGGACTGCTGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACGAGCAAA
AGTCGGTGATGTTCCAACTCCTTATACGATGAAAGCAAGCTAAA
Found at i:5482319 original size:139 final size:139
Alignment explanation
Indices: 5481939--5482435 Score: 825
Period size: 139 Copynumber: 3.6 Consensus size: 139
5481929 AAGCAAGCTA
* * * * *
5481939 AAGTTCTTCTCATTATGAACTTCTTTTCCCTTATCGGATGAGTTATTCTCATTATGAAATATCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
* *
5482004 CTGGAAAGGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGACGAATCGAGCTA
66 CTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA
5482069 AGGTTGAAC
131 AGGTTGAAC
* *
5482078 AAGATCTTCTCATTATGAACTTGTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTCTCC
* * *
5482143 ACTGGAAATGTTGATCCCTCGAGTGAGGTGTTACTGATTCAACTCCATATGTGATGAATTGAGTT
65 ACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCT
5482208 AAGGTTGAAC
130 AAGGTTGAAC
5482218 AAGTTCTTCTCATTATGAACTTCTTC-CCCTTCATCGGATGAGTTCTTCTCATTATGAACTCTCC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCC-TCATCGGATGAGTTCTTCTCATTATGAACTCTCC
* *
5482282 ATTGGAAATGTTGTTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCT
65 ACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCT
5482347 AAGGTTGAAC
130 AAGGTTGAAC
5482357 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
* *
5482422 TTGGAAGTGTTGAT
66 CTGGAAATGTTGAT
5482436 TGGTTTTCCC
Statistics
Matches: 334, Mismatches: 21, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
139 206 0.62
140 128 0.38
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (139 bp):
AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
CTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA
AGGTTGAAC
Found at i:5483287 original size:54 final size:52
Alignment explanation
Indices: 5483168--5483338 Score: 182
Period size: 54 Copynumber: 3.2 Consensus size: 52
5483158 ATTTACAGTT
** * ***
5483168 ATCAAGAAACCCCTAAAATTAGGCTTAGCTTCTTTCAAAAATTCA-AAAAAAA
1 ATCAAGAAACCCCTAAAATTAGGCTTAATTTCTTT-GAAAATTCATTTGAAAA
* **
5483220 ATCAAAAAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAA
1 ATCAAGAAACCCCT-AAAATTAGGCTTAATTTCTTTGAAAATTCATTTGAAAA
**
5483273 CATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAATGTTCATTTAAGAAAA
1 -ATCAAGAAACCCCT-AAAATTAGGCTTAATTTCTTTGAAAATTCATTT--GAAAA
5483329 ATCAAGAAAC
1 ATCAAGAAAC
5483339 TTCCGAAAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
52 21 0.21
53 21 0.21
54 42 0.42
55 10 0.10
56 5 0.05
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (52 bp):
ATCAAGAAACCCCTAAAATTAGGCTTAATTTCTTTGAAAATTCATTTGAAAA
Found at i:5485300 original size:22 final size:22
Alignment explanation
Indices: 5485259--5485321 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
5485249 GATCTGTCTA
*
5485259 TTTCTTTTTTTTAATATTTTT-T-
1 TTTCTTTTTTCT-AT-TTTTTCTC
*
5485281 TTCCTTTTCTTCTATTTTTTCTC
1 TTTCTTTT-TTCTATTTTTTCTC
5485304 TTTCTTTTTTCTATTTTT
1 TTTCTTTTTTCTATTTTT
5485322 CTGTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 5 0.14
22 20 0.57
23 10 0.29
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTTTTTTCTATTTTTTCTC
Found at i:5485330 original size:17 final size:16
Alignment explanation
Indices: 5485259--5485367 Score: 50
Period size: 17 Copynumber: 6.8 Consensus size: 16
5485249 GATCTGTCTA
*
5485259 TTTCTTTTTTT-TAAT
1 TTTCTTTTTTTCTATT
* *
5485274 ATT-TTTTTTCCT-TT
1 TTTCTTTTTTTCTATT
*
5485288 TCTTCTATTTTTTC--TC
1 T-TTCT-TTTTTTCTATT
5485304 TTTC-TTTTTTCTATT
1 TTTCTTTTTTTCTATT
*
5485319 TTTCTGTTTTTTTTATGT
1 TTTCT-TTTTTTCTAT-T
* * *
5485337 GTTTCTCTTTTTTTTCTC
1 -TTTCT-TTTTTTCTATT
5485355 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
5485368 CTTTCTTTGT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
13 7 0.10
14 7 0.10
15 13 0.18
16 10 0.14
17 20 0.28
18 1 0.01
19 14 0.19
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTTCTATT
Found at i:5485332 original size:19 final size:19
Alignment explanation
Indices: 5485261--5485353 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 19
5485251 TCTGTCTATT
* *
5485261 TCTTTTTTTTAATATTTTTTT
1 TCTTTTTTTT-CTA-TTTTTC
* *
5485282 TCCTTTTCTTCTATTTTTTC
1 TCTTTTTTTTCTA-TTTTTC
5485302 TCTTTCTTTTTTCTATTTTTC
1 TC-TT-TTTTTTCTATTTTTC
* * * *
5485323 TGTTTTTTTTATGTGTTTC
1 TCTTTTTTTTCTATTTTTC
5485342 TCTTTTTTTTCT
1 TCTTTTTTTTCT
5485354 CTTTCTTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 22 0.38
20 12 0.21
21 16 0.28
22 8 0.14
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.76
Consensus pattern (19 bp):
TCTTTTTTTTCTATTTTTC
Found at i:5485354 original size:11 final size:12
Alignment explanation
Indices: 5485338--5485375 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
5485328 TTTTTATGTG
5485338 TTTCTCTTT-TT
1 TTTCTCTTTCTT
5485349 TTTCTCTTTCTTTT
1 TTTCTCTTTC--TT
5485363 TTTCTCTTTCTT
1 TTTCTCTTTCTT
5485375 T
1 T
5485376 GTTTGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 3 0.12
14 12 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTCTTTCTT
Found at i:5486799 original size:21 final size:23
Alignment explanation
Indices: 5486758--5486808 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
5486748 ATGCACATGC
5486758 AAATG-AAAATATACAAAAATGG
1 AAATGCAAAATATACAAAAATGG
* *
5486780 GAATGCAAAA-ATAC-AAAATGT
1 AAATGCAAAATATACAAAAATGG
5486801 AAATGCAA
1 AAATGCAA
5486809 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.18
Consensus pattern (23 bp):
AAATGCAAAATATACAAAAATGG
Found at i:5501309 original size:128 final size:128
Alignment explanation
Indices: 5501081--5501419 Score: 660
Period size: 128 Copynumber: 2.6 Consensus size: 128
5501071 CATTGACAAA
*
5501081 TTATCATTGTCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
5501146 TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
66 TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
*
5501209 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGAGACACTAGATATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
5501274 TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
66 TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
5501337 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
1 TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
5501402 TCACTATTCACATGAAGG
66 TCACTATTCACATGAAGG
5501420 GGGAATCGGT
Statistics
Matches: 208, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 208 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (128 bp):
TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATT
TCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATG
Found at i:5501828 original size:15 final size:15
Alignment explanation
Indices: 5501791--5501820 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5501781 TCATTATATC
5501791 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
5501806 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
5501821 TATATGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
AAAATGTTTTCAACA
Found at i:5501971 original size:34 final size:33
Alignment explanation
Indices: 5501933--5502039 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
5501923 TAAGTTGAAA
*
5501933 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATAT
* * *
5501967 TTTAAATTTAATTTTCGAATAATATTATTTTTATT
1 TTT-AATTTAAATTTCGAATAATATAATTTATA-T
* *
5502002 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
5502035 TTTAA
1 TTTAA
5502040 AAACATTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
33 5 0.08
34 50 0.81
35 7 0.11
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (33 bp):
TTTAATTTAAATTTCGAATAATATAATTTATAT
Found at i:5502650 original size:21 final size:21
Alignment explanation
Indices: 5502559--5502652 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
5502549 TATGGTATAA
* * *
5502559 AACCCTGTGGGCTTGGCATGT
1 AACCCTGCGGGCTCGGAATGT
* *
5502580 AA-CCTGGTGGGCTAGGAATGT
1 AACCCT-GCGGGCTCGGAATGT
5502601 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGT
5502622 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGT
5502643 AACCCTGCGG
1 AACCCTGCGG
5502653 AGATGGCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
AACCCTGCGGGCTCGGAATGT
Found at i:5502676 original size:42 final size:41
Alignment explanation
Indices: 5502572--5502676 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 41
5502562 CCTGTGGGCT
*
5502572 TGGCATGTAACCTGGTGGGCTAGGAATGTAACCCTGCGGGC
1 TGGCATGTAACCTGGTGGGCTAGGAATGTAACCCTGCGGGA
* * *
5502613 TCGGAATGTAACCCT-GCGGGCTCGGAATGTAACCCTGCGGAGA
1 T-GGCATGTAA-CCTGGTGGGCTAGGAATGTAACCCTGCGG-GA
* *
5502656 TGGCATATAAACTGGTGGGCT
1 TGGCATGTAACCTGGTGGGCT
5502677 TGGCATATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
41 3 0.06
42 44 0.85
43 5 0.10
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (41 bp):
TGGCATGTAACCTGGTGGGCTAGGAATGTAACCCTGCGGGA
Found at i:5502682 original size:21 final size:21
Alignment explanation
Indices: 5502656--5502703 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5502646 CCTGCGGAGA
*
5502656 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
5502677 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
5502698 GGGCAT
1 TGGCAT
5502704 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:5504470 original size:34 final size:31
Alignment explanation
Indices: 5504427--5504515 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
5504417 TTAATAATTC
*
5504427 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
5504461 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
5504492 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
5504516 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:5504492 original size:31 final size:33
Alignment explanation
Indices: 5504427--5504506 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
5504417 TTAATAATTC
* *
5504427 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
5504461 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
5504492 TATAAAATATAATAA
1 TA-AAAAAATAATAA
5504507 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:5504808 original size:50 final size:50
Alignment explanation
Indices: 5504709--5504811 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 50
5504699 GCATTTAATG
* * * * *
5504709 GAAGGCGCGTCCCCGGGGATGCGCTTTCCACACGTGGCAGTCGAGTCAGT
1 GAAGGCGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGCCAACTCAGT
5504759 GAAGGCGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGCCAACTCAGT
1 GAAGGCGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGCCAACTCAGT
5504809 GAA
1 GAA
5504812 AACACGGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.19, C:0.32, G:0.33, T:0.16
Consensus pattern (50 bp):
GAAGGCGCGTCCCCGGGGATGCGCCTTCCACACGTGACAGCCAACTCAGT
Found at i:5509597 original size:3 final size:3
Alignment explanation
Indices: 5509589--5509655 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
5509579 CTGTAAAATA
*
5509589 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5509637 AAT AAT AAT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
5509656 GTAAAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5510104 original size:138 final size:138
Alignment explanation
Indices: 5509856--5510542 Score: 912
Period size: 138 Copynumber: 5.0 Consensus size: 138
5509846 AGGTAAATTT
* * * * * *
5509856 TGGAGATAACACGGTTCTTAC-ATGATGAGGAAATCTGGTTATCTAAGGGTGATGGTGCTCCTAC
1 TGGAGATAACACGGTTCCTACGA-GATGAGGAAGTCTGGCTATCTAAGGATGACGCTGCTCCTAC
* * * * * * *
5509920 ATGATGAGGAGATCTAGTCAGTAGATAACACTGTTCCTACATGATGAGGACATCTGGCCATCTTT
65 GTGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
5509985 AGGGATAAA
130 AGGGATAAA
* * * *
5509994 TGGAGATAACACGGTTCCTACGAGATGAAGAAGTCTGACTATCTAAGGATGACGTTGCTCCTACA
1 TGGAGATAACACGGTTCCTACGAGATGAGGAAGTCTGGCTATCTAAGGATGACGCTGCTCCTACG
* * * *
5510059 TGATGATGAGATCTGGTTGGTGGATGACATTGTTCCTACGTGATGAGGATGTCTGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
*
5510124 GGGATAAT
131 GGGATAAA
* * * *
5510132 TGGAGATAAAACGATTCCTACGCGATGAGGAAGTCTCGCTATCTAAGGATGACGCTGCTCCTACG
1 TGGAGATAACACGGTTCCTACGAGATGAGGAAGTCTGGCTATCTAAGGATGACGCTGCTCCTACG
* * *
5510197 TGATGAGGAGATCTGATCGGTGGATGACACTGTTCCTACGTGATGACGACATCTGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
5510262 GGGATAAA
131 GGGATAAA
* *
5510270 TGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATAACGCTGCTCCTACG
1 TGGAGATAACACGGTTCCTACGAGATGAGGAAGTCTGGCTATCTAAGGATGACGCTGCTCCTACG
* * * * * * *
5510335 TGATGAGGAGATATGGTTGGTGGATTACATTGTTCCTACGTGATGATGATGTATGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
5510400 GGGATAAA
131 GGGATAAA
* * * * *
5510408 TGAAGATAACACGGTTTCTA--AGATGAGGATGTCTGGCTATATAAGGATGACGCTGCTCCAACG
1 TGGAGATAACACGGTTCCTACGAGATGAGGAAGTCTGGCTATCTAAGGATGACGCTGCTCCTACG
* * * * *
5510471 TGATAAGAAGATCTGGTCGGTGAATGAAACTGCTCCTACGTGATGAGGACGTCTGGCCATCTTTA
66 TGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
5510536 GGGATAA
131 GGGATAA
5510543 TTTGTTTCAA
Statistics
Matches: 481, Mismatches: 67, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
136 98 0.20
138 382 0.79
139 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (138 bp):
TGGAGATAACACGGTTCCTACGAGATGAGGAAGTCTGGCTATCTAAGGATGACGCTGCTCCTACG
TGATGAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTA
GGGATAAA
Found at i:5510651 original size:66 final size:65
Alignment explanation
Indices: 5510545--5510866 Score: 468
Period size: 65 Copynumber: 4.9 Consensus size: 65
5510535 AGGGATAATT
* *
5510545 TGTTTCAAGAGAAACTGTCTCAGGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTGT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT-T
5510610 A
65 A
* *
5510611 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
** *
5510676 T-TCTTC-AGTAGAAGTTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACACTCTCAAAGGT
1 TGT-TTCAAG-AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT
5510739 TA
64 TA
* * * *
5510741 TTTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATTTATTTCAACGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * * *
5510806 TCTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG
5510867 TGAGATCACT
Statistics
Matches: 230, Mismatches: 22, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
64 3 0.01
65 165 0.72
66 62 0.27
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:5510668 original size:36 final size:36
Alignment explanation
Indices: 5510541--5510669 Score: 117
Period size: 36 Copynumber: 3.8 Consensus size: 36
5510531 CTTTAGGGAT
** * *
5510541 AATTTGTTTCAAGAGAAACTGTCTCAGGAGAGACAA
1 AATTTGTTTCAAGAGAAACAATCTCAAGAAAGACAA
* *
5510577 AATTTGTTTCAAGGGAAACAATCTC---AAAG---T
1 AATTTGTTTCAAGAGAAACAATCTCAAGAAAGACAA
** * **
5510607 TGTATGTTTCAAGAGAAACTGTCTCAAGAAAGACAA
1 AATTTGTTTCAAGAGAAACAATCTCAAGAAAGACAA
5510643 AATTTGTTTCAAGAGAAACAATCTCAA
1 AATTTGTTTCAAGAGAAACAATCTCAA
5510670 AGGTTATTCT
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
30 19 0.27
33 7 0.10
36 44 0.63
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (36 bp):
AATTTGTTTCAAGAGAAACAATCTCAAGAAAGACAA
Found at i:5511792 original size:3 final size:3
Alignment explanation
Indices: 5511780--5511826 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
5511770 TTTTGATCCT
* *
5511780 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA TTT ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5511827 GTAAAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5512221 original size:20 final size:20
Alignment explanation
Indices: 5512196--5512240 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5512186 GATGAGGAAG
5512196 TCTGCCTATCTAAGGATGAC
1 TCTGCCTATCTAAGGATGAC
5512216 TCTGCCTATCTAAGGATGAC
1 TCTGCCTATCTAAGGATGAC
*
5512236 GCTGC
1 TCTGC
5512241 TCCTACGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (20 bp):
TCTGCCTATCTAAGGATGAC
Found at i:5512352 original size:158 final size:156
Alignment explanation
Indices: 5512066--5512378 Score: 437
Period size: 158 Copynumber: 2.0 Consensus size: 156
5512056 GAAATCTGGT
* * * * *
5512066 TATCTAAGGGTGATGCTGCTCATACGTGATGAGGAGATTTGGTCGGTGGAATACTGTTGCTACAT
1 TATCTAAGGATGACGCTGCTCATACGTGATGAGGAGATATGGTCGGTGGAACACTGTTCCTACAT
* * * *
5512131 GATGAGGATGTATGGCCACCTTTAGGGATAAATGGAGATAACACGGTTCCTACGTGATGAGGAAG
66 GATGAGGACGTATGGCCACCTTTAGGGATAAATAGAGATAACACGATTCCTACGCGATGAGGAAG
*
5512196 TCTGCCTATCTAAGGATGACTCTGCC
131 TCTGCCTATCTAAGGATGACGCTGCC
* *
5512222 TATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTTTTCCTAC
1 TATCTAAGGATGACGCTGCTCATACGTGATGAGGAGATATGGTCGGTGGA--ACACTGTTCCTAC
* * * ** *
5512287 GTGATGAGGGCGTCTGGCCATTTTTAGGGATAAATATAGATAACACGATTCCTACGCGATGAGGA
64 ATGATGAGGACGTATGGCCACCTTTAGGGATAAATAGAGATAACACGATTCCTACGCGATGAGGA
*
5512352 AGTCTGGCTATCTAAGGATGACGCTGC
129 AGTCTGCCTATCTAAGGATGACGCTGC
5512379 TCCTACGTGA
Statistics
Matches: 136, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
156 46 0.34
158 90 0.66
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.28
Consensus pattern (156 bp):
TATCTAAGGATGACGCTGCTCATACGTGATGAGGAGATATGGTCGGTGGAACACTGTTCCTACAT
GATGAGGACGTATGGCCACCTTTAGGGATAAATAGAGATAACACGATTCCTACGCGATGAGGAAG
TCTGCCTATCTAAGGATGACGCTGCC
Found at i:5512469 original size:138 final size:138
Alignment explanation
Indices: 5512216--5512595 Score: 526
Period size: 138 Copynumber: 2.8 Consensus size: 138
5512206 TAAGGATGAC
*
5512216 TCTGCCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTTT
1 TCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTTT
* * * * *
5512281 TCCTACGTGATGAGGGCGTCTGGCCATTTTTAGGGATAAATATAGATAACACGATTCCTACGCGA
66 TCTTACGTGATGAGGACGTCTGGCCATCTTTAGGGATAAATAGAGATAACACGATTCCTACACGA
*
5512346 TGAGGAAG
131 TGAGAAAG
* * **
5512354 TCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAAGAGATGTGGTCGGTGGATGACACAGT
1 TCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTTT
* * * * *
5512419 TCTTACATGATGAGGACGTCTGGCCATCTTTAGGGATAAATGGAGATAACATGGTTCCTATACGA
66 TCTTACGTGATGAGGACGTCTGGCCATCTTTAGGGATAAATAGAGATAACACGATTCCTACACGA
5512484 TGAGAAAG
131 TGAGAAAG
* * * ** * * *
5512492 TTTGGCTATCTACGAATGACGCTGCTCCTACACGATGAGGAGATCTGGTCGATGGTTGACACTTT
1 TCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTTT
* *
5512557 TCTAACGTGATGAGGACATCTGGCCATCTTTAGGGATAA
66 TCTTACGTGATGAGGACGTCTGGCCATCTTTAGGGATAA
5512596 TTTATTTCAA
Statistics
Matches: 212, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 212 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (138 bp):
TCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTTT
TCTTACGTGATGAGGACGTCTGGCCATCTTTAGGGATAAATAGAGATAACACGATTCCTACACGA
TGAGAAAG
Found at i:5512710 original size:66 final size:65
Alignment explanation
Indices: 5512602--5512740 Score: 199
Period size: 66 Copynumber: 2.1 Consensus size: 65
5512592 ATAATTTATT
* * *
5512602 TCAAGAAAAATTGCCTCAAGAGAGACAAAACTTGTTTTAAGGGAAACAATCTCAAA-GTTGTATG
1 TCAAGAGAAACTGCCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATG-T-TATG
5512666 TC
64 TC
* * *
5512668 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTATGTT
1 TCAAGAGAAACTGCCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATGTTATGTC
5512733 TCAAGAGA
1 TCAAGAGA
5512741 GACAAAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 13 0.20
66 52 0.79
67 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (65 bp):
TCAAGAGAAACTGCCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAATGTTATGTC
Found at i:5512721 original size:36 final size:36
Alignment explanation
Indices: 5512616--5512722 Score: 84
Period size: 36 Copynumber: 3.1 Consensus size: 36
5512606 GAAAAATTGC
* *
5512616 CTCAAGAGAGACAAAACTTGTTTTAAGGGAAACAAT
1 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAT
* * * * **
5512652 CTCAA-AGTTG------TATGTCTCAAGAGAAACTGT
1 CTCAAGAG-AGACAAAATTTGTTTCAAGGGAAACAAT
5512682 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAT
1 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAT
5512718 CTCAA
1 CTCAA
5512723 ATGTTATGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 16
0.62 0.18 0.20
Matches are distributed among these distances:
30 19 0.39
31 2 0.04
35 2 0.04
36 26 0.53
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (36 bp):
CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAT
Found at i:5512742 original size:50 final size:50
Alignment explanation
Indices: 5512683--5512790 Score: 189
Period size: 50 Copynumber: 2.2 Consensus size: 50
5512673 AGAAACTGTC
*
5512683 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTATGTT
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
*
5512733 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACACTCTCAAAGGTTATGTT
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
*
5512783 TTAAGAGA
1 TCAAGAGA
5512791 AACTATCTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (50 bp):
TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
Found at i:5512808 original size:65 final size:65
Alignment explanation
Indices: 5512733--5512969 Score: 384
Period size: 65 Copynumber: 3.6 Consensus size: 65
5512723 ATGTTATGTT
* * *
5512733 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACACTCTCAAAGGTTATGTTTTAAGAGAAACTATC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTTTCAAGAGAAACTGTC
*
5512798 TCAAGAGAGACAAATTTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTTTCAAGAGAAACTGTC
* * *
5512863 TCAAGAGAGACACAATTTGTTTAAAGGGAAATAATCTCAAAGGTTATGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTTTCAAGAGAAACTGTC
* * *
5512928 TCAAGTGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAG
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG
5512970 TGAGATCAAT
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 158 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (65 bp):
TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTTTCAAGAGAAACTGTC
Found at i:5512820 original size:115 final size:116
Alignment explanation
Indices: 5512617--5512855 Score: 390
Period size: 115 Copynumber: 2.1 Consensus size: 116
5512607 AAAAATTGCC
* * *
5512617 TCAAGAGAGACAAAACTTGTTTTAAGGGAAACAATCTCAAAGTTGTATGTCTCAAGAGAAACTGT
1 TCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTGTATGTCTCAAGAGAAACTAT
*
5512682 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAATGTTATGTT
66 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
* * * *
5512733 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACACTCTCAAAGGT-TATGTTTTAAGAGAAACTAT
1 TCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTGTATGTCTCAAGAGAAACTAT
*
5512797 CTCAAGAGAGACAAATTTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
66 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
5512848 TCAAGAGA
1 TCAAGAGA
5512856 AACTGTCTCA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
115 74 0.65
116 40 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (116 bp):
TCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTGTATGTCTCAAGAGAAACTAT
CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATGTT
Found at i:5512829 original size:36 final size:35
Alignment explanation
Indices: 5512779--5512996 Score: 147
Period size: 36 Copynumber: 6.4 Consensus size: 35
5512769 TCAAAGGTTA
*
5512779 TGTTTTAAGAGAAACTATCTCAAGAGAGACAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAC-AATTT
* * *
5512815 TGTTTCAAGGGAAACAATCTCAA-AG-G----TTA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAATTT
* *
5512844 TGTTTCAAGAGAAACTGTCTCAAGAGAGACACAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACA-ATTT
* * *
5512880 TGTTTAAAGGGAAA-TAATCTCAA-AG-G----TTA
1 TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAATTT
* * **
5512909 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAACT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAC-AATTT
* *
5512945 TGTTTCAAGAGAAACAATCTCAAAGTGAGATCAATTT
1 TGTTTCAAGAGAAACTATCTC-AAGAGAGA-CAATTT
*
5512982 TGTTTCAAGTGAAAC
1 TGTTTCAAGAGAAAC
5512997 AATTTCAAAA
Statistics
Matches: 138, Mismatches: 26, Indels: 35
0.69 0.13 0.18
Matches are distributed among these distances:
29 41 0.30
30 4 0.03
31 2 0.01
34 2 0.01
35 5 0.04
36 58 0.42
37 25 0.18
38 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAATTT
Found at i:5512864 original size:29 final size:29
Alignment explanation
Indices: 5512815--5512931 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 29
5512805 AGACAAATTT
* *
5512815 TGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTATCTCAAAGGTTA
*
5512844 TGTTTCAAGAGAAACTGTCTCAAGAGAGACACAATT-
1 TGTTTCAAGAGAAACTATCTCAA-AG-G------TTA
* *
5512880 TGTTTAAAGGGAAA-TAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACT-ATCTCAAAGGTTA
*
5512909 TGTTTCAAGAGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTATCTCAA
5512932 GTGAGACAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
28 2 0.03
29 38 0.56
30 3 0.04
31 1 0.01
34 1 0.01
35 3 0.04
36 18 0.26
37 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (29 bp):
TGTTTCAAGAGAAACTATCTCAAAGGTTA
Found at i:5512985 original size:37 final size:37
Alignment explanation
Indices: 5512909--5513005 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
5512899 TCAAAGGTTA
**
5512909 TGTTTCAAGAGAAACTGTCTC-AAGTGAGACAAAACT
1 TGTTTCAAGAGAAACAATCTCAAAGTGAGACAAAACT
**
5512945 TGTTTCAAGAGAAACAATCTCAAAGTGAGATC-AATTT
1 TGTTTCAAGAGAAACAATCTCAAAGTGAGA-CAAAACT
* *
5512982 TGTTTCAAGTGAAACAATTTCAAA
1 TGTTTCAAGAGAAACAATCTCAAA
5513006 ATCTGTGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
36 19 0.36
37 33 0.62
38 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGAGAAACAATCTCAAAGTGAGACAAAACT
Found at i:5513133 original size:88 final size:92
Alignment explanation
Indices: 5512917--5513150 Score: 268
Period size: 88 Copynumber: 2.6 Consensus size: 92
5512907 TATGTTTCAA
* * *
5512917 GAGAA-ACTGTCTCAAGTGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGTGAGATCAATT
1 GAGAACACTGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAACAATCTC-AAGTGAGATCAATT
5512981 TTGTTTCAAGTGAAACAATTTCAAAATCTGT
65 TTGTTT-AA--GAAACAATTTCAAAATCTGT
* * * * * *
5513012 GAAAACA-TGTCTCAAGAGAGGCGAACTTCGTTTTGAA-AGAAACAATCTCAAGTGAGATCAGTT
1 GAGAACACTGTCTCAAGTGAGACGAAATTTGTTTT-AAGAGAAACAATCTCAAGTGAGATCAATT
5513075 TTGTTT-A-AAA-AATTTCAAAAT-T-T
65 TTGTTTAAGAAACAATTTCAAAATCTGT
*
5513098 GCAGAACACTGTCTCAAGTGAGACGAAATTTGTTTTAAGAAAAACAATCTCAA
1 G-AGAACACTGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAACAATCTCAA
5513151 AAGCTTATAG
Statistics
Matches: 119, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
86 2 0.02
87 8 0.07
88 47 0.39
89 3 0.03
92 1 0.01
94 19 0.16
95 36 0.30
96 3 0.03
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (92 bp):
GAGAACACTGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAACAATCTCAAGTGAGATCAATTT
TGTTTAAGAAACAATTTCAAAATCTGT
Found at i:5514373 original size:138 final size:137
Alignment explanation
Indices: 5514156--5514704 Score: 581
Period size: 138 Copynumber: 4.0 Consensus size: 137
5514146 TAAATTTTGG
* * * * * ** *
5514156 AGATAACAC-AGTTCCTACGTGATGAGAAAATCTAGTTATCTAAGGGTCTTGCTA-CTCCTACGT
1 AGATAACACGA-TTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATGATG--AGCTCCTACAT
* * * *
5514219 GATGAGGAGATCTGGTCGGTGGATGACACTATTGCTACGTGATGAGGACGTTTGGCCATATTTAG
63 GATGAGGAGATCTGGTCGGTGGATGACACTATTCCTACGTGATGAGGACGTCTGACCATCTTTAG
5514284 GGATAAATGA
128 GGATAAATGA
* * *
5514294 AGATAACACGATTCCTACGCGAAT-AGGAAGTATGTCTATCTAAGGATGATGCAGCTCCTACATG
1 AGATAACACGATTCCTACGTG-ATGAGGAAGTCTGGCTATCTAAGGATGATG-AGCTCCTACATG
* * *
5514358 ATGAGGAGATTTGGTCGGTGGATGACACTATTCATACGTGATGAGGACGTCTGCCCATCTTTAGG
64 ATGAGGAGATCTGGTCGGTGGATGACACTATTCCTACGTGATGAGGACGTCTGACCATCTTTAGG
5514423 GATAAAT-A
129 GATAAATGA
* * *
5514431 GAGATAACACTATTCCTACATGATGAGAAAGTCTGGCTATCTAAGGATGATGATGCTCCTA-AGT
1 -AGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATGATGA-GCTCCTACA-T
* *
5514495 GATGAGGAGATCTGGTCGGTGGATGACA-TAGTTCCTATGTGATAAGGACGTCTGACCATCTTTA
63 GATGAGGAGATCTGGTCGGTGGATGACACTA-TTCCTACGTGATGAGGACGTCTGACCATCTTTA
*
5514559 GGGATAAAATGG
127 GGGAT-AAATGA
* * * * * * * * * * *
5514571 AGAAAACATGGTTCCTAGGTGATGATGAATTCTGGCTATCGAAGGATGACGTTGTTCCTATATGA
1 AGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATGATG-AGCTCCTACATGA
* * * * *
5514636 TGAGGAGATCTGGTTGGTGGATGACACTTTTCCTACGTGATGAGGACATCTAGA-TATATTTAGG
65 TGAGGAGATCTGGTCGGTGGATGACACTATTCCTACGTGATGAGGACGTCT-GACCATCTTTAGG
5514700 GATAA
129 GATAA
5514705 TTTGTTTCAA
Statistics
Matches: 347, Mismatches: 50, Indels: 28
0.82 0.12 0.07
Matches are distributed among these distances:
137 8 0.02
138 224 0.65
139 111 0.32
140 4 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (137 bp):
AGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGATGATGAGCTCCTACATGAT
GAGGAGATCTGGTCGGTGGATGACACTATTCCTACGTGATGAGGACGTCTGACCATCTTTAGGGA
TAAATGA
Found at i:5514872 original size:65 final size:65
Alignment explanation
Indices: 5514707--5515026 Score: 509
Period size: 65 Copynumber: 4.9 Consensus size: 65
5514697 AGGGATAATT
* * * * *
5514707 TGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTAGTTTCAAGGGAAACAATATCAAAGTTGT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT-T
5514772 A
65 A
*
5514773 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
*
5514838 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
*
5514903 TGTTTTAAGAGAAACTGTCTCAAGAGAG--AAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * * *
5514966 TGTTTCAAGAGAAACTTTCTCAAGAGAGGCAAAACTTGTTTCAAGAGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG
5515027 TGAGATCAAT
Statistics
Matches: 239, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
63 61 0.26
65 121 0.51
66 57 0.24
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:5514976 original size:128 final size:130
Alignment explanation
Indices: 5514707--5515026 Score: 536
Period size: 128 Copynumber: 2.5 Consensus size: 130
5514697 AGGGATAATT
* * * *
5514707 TGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAACTAGTTTCAAGGGAAACAATATCAAAGTTGT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTGT
5514772 ATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT
66 ATGTTTTAAGAGAAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT
5514837 A
130 A
* *
5514838 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT-T
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTGT
5514902 ATGTTTTAAGAGAAACTGTCTCAAGAGAG-AAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
66 ATGTTTTAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * *
5514966 TGTTTCAAGAGAAACTTTCTCAAGAGAGGCAAAACTTGTTTCAAGAGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAG
5515027 TGAGATCAAT
Statistics
Matches: 178, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
128 91 0.51
130 30 0.17
131 57 0.32
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (130 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTGT
ATGTTTTAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:5514988 original size:29 final size:29
Alignment explanation
Indices: 5514874--5514980 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 29
5514864 AGATAAAATT
*
5514874 TGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
* **
5514903 TGTTTTAAGAGAAACTGTCTCAAGAGAGAAAATT-
1 TGTTTCAAGAGAAACAATCTCAA-AG-G----TTA
*
5514937 TGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
5514966 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
5514981 TTTCTCAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.03
29 33 0.53
30 2 0.03
31 1 0.02
32 1 0.02
33 2 0.03
34 19 0.31
35 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (29 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTA
Found at i:5515177 original size:88 final size:91
Alignment explanation
Indices: 5515011--5515207 Score: 278
Period size: 88 Copynumber: 2.2 Consensus size: 91
5515001 TTGTTTCAAG
*
5515011 AGAAACAATCTCAAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGAAAACC
1 AGAAACAATCTC-AAGTGAGATCAATTTTGTTTC-A---AAACAATTTCAAAATTTGAGAAAACC
*
5515076 TGTCTCAAGTGAGACGAACTTTGTTTTGA-A
61 TGTCTCAAGTGAGACGAAATTTGTTTTGAGA
*
5515106 AGAAACAATCTCAAGTGAGATTAATTTTGTTTC-AAA-AATTTCAAAATTTGCAGAAAACC-GTC
1 AGAAACAATCTCAAGTGAGATCAATTTTGTTTCAAAACAATTTCAAAATTTG-AGAAAACCTGTC
5515168 TCAAGTGAGACGAAATTTGTTTTGAGA
65 TCAAGTGAGACGAAATTTGTTTTGAGA
5515195 A-AAACAATCTCAA
1 AGAAACAATCTCAA
5515208 AAGTTTATAG
Statistics
Matches: 97, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
88 53 0.55
89 12 0.12
94 20 0.21
95 12 0.12
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (91 bp):
AGAAACAATCTCAAGTGAGATCAATTTTGTTTCAAAACAATTTCAAAATTTGAGAAAACCTGTCT
CAAGTGAGACGAAATTTGTTTTGAGA
Found at i:5515984 original size:3 final size:3
Alignment explanation
Indices: 5515978--5516032 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
5515968 ATATTATTAA
* * * *
5515978 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AGT GAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5516026 AAT AAT A
1 AAT AAT A
5516033 GTAAAAAGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5516003 original size:18 final size:18
Alignment explanation
Indices: 5515980--5516036 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
5515970 ATTATTAAAA
5515980 TAATAATAATAATAATAG
1 TAATAATAATAATAATAG
5515998 TAATAATAATAATAATAG
1 TAATAATAATAATAATAG
* *
5516016 TGATAAAAATAATAATAG
1 TAATAATAATAATAATAG
5516034 TAA
1 TAA
5516037 AAAGTGTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAATAG
Found at i:5516491 original size:138 final size:138
Alignment explanation
Indices: 5516237--5516780 Score: 650
Period size: 138 Copynumber: 3.9 Consensus size: 138
5516227 AATTTTTGGG
** * * * * * *
5516237 GATAACAC-AGTTCCTACATGATGAGTAAATCTGGTTATCTAAGGGTGATGA-TGCTCCTACATG
1 GATAACACGA-TTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGA-CACTGCTTCTACATG
* * * * * * *
5516300 ATGAGGAGATTTGGAT-GGTAGATGAAAATGTTTCTACGTGATGA-GAAAGTCTGGCCATCTTTA
64 ATAAGGAGATCTGG-TCGGTGGATGACACTGTTCCTACGTGATGAGGACA-TCTGGCCATCTTTA
*
5516363 GGGATAAATAGA
127 GGGATAAATGGA
* * *
5516375 GATAACACGATTCCTATGCGATGAGGAAGTCTGGCTATCTAAGGATGACACGGCTTCTACGTGAT
1 GATAACACGATTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTTCTACATGAT
* * * * *
5516440 GAGGAGATCTGGCCGGTGGATGACATTGTTCCTACGTGATGAGGATATCTGGCCATCTTTTGGGA
66 AAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCCATCTTTAGGGA
5516505 TAAATGGA
131 TAAATGGA
* * *
5516513 GATAACAC-AGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGAGATTGCTTCTACGTGA
1 GATAACACGA-TTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTTCTACATGA
* *
5516577 TAAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGACGAGGACGTCTGGCCAT-TATTAGG
65 TAAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCCATCT-TTAGG
5516641 GATAAATGGA
129 GATAAATGGA
* * ** *
5516651 GATAACACGGTTCCTACGCGATGAGGAAGTCTGACTATCTAAGGATGATGCTGCTCCTACATGAT
1 GATAACACGATTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTTCTACATGAT
* * * *
5516716 AAGGAGATCTGTTTGGTGGATTACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTTAGGGA
66 AAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCCATCTTTAGGGA
5516781 CAATTTGTTT
Statistics
Matches: 356, Mismatches: 42, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
137 3 0.01
138 348 0.98
139 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (138 bp):
GATAACACGATTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACACTGCTTCTACATGAT
AAGGAGATCTGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCCATCTTTAGGGA
TAAATGGA
Found at i:5516736 original size:276 final size:276
Alignment explanation
Indices: 5516237--5516780 Score: 725
Period size: 276 Copynumber: 2.0 Consensus size: 276
5516227 AATTTTTGGG
* * * *
5516237 GATAACACAGTTCCTACATGATGAGTAAATCTGGTTATCTAAGGGTGATGATGCTCCTACATGAT
1 GATAACACAGTTCCTACACGATGAGGAAATCTGGCTATCTAAGGATGATGATGCTCCTACATGAT
* * * *
5516302 GAGGAGATTTGGATGGTAGATGAAAATGTTTCTACGTGATGAGAAAGTCTGGCCATCTTTAGGGA
66 AAGGAGATCTGGATGGTAGATGAAAATGTTCCTACGTGACGAGAAAGTCTGGCCATCTTTAGGGA
* * *
5516367 TAAATAGAGATAACACGATTCCTATGCGATGAGGAAGTCTGGCTATCTAAGGATGACACGGCTTC
131 TAAATAGAGATAACACGATTCCTACGCGATGAGGAAGTCTGACTATCTAAGGATGACACGGCTCC
* * * *
5516432 TACGTGATGAGGAGATCTGGCCGGTGGATGACATTGTTCCTACGTGATGAGGATATCTGGCCATC
196 TACATGATAAGGAGATCTGGCCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCCATC
*
5516497 TTTTGGGATAAATGGA
261 TTTAGGGATAAATGGA
* * * *
5516513 GATAACACAGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGA-GATTGCTTCTACGTGA
1 GATAACACAGTTCCTACACGATGAGGAAATCTGGCTATCTAAGGATGATGA-TGCTCCTACATGA
* * * * *
5516577 TAAGGAGATCTGG-TCGGTGGATGACACTGTTCCTACGTGACGAGGACGTCTGGCCAT-TATTAG
65 TAAGGAGATCTGGAT-GGTAGATGAAAATGTTCCTACGTGACGAGAAAGTCTGGCCATCT-TTAG
* * ** *
5516640 GGATAAATGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGACTATCTAAGGATGATGCTGC
128 GGATAAATAGAGATAACACGATTCCTACGCGATGAGGAAGTCTGACTATCTAAGGATGACACGGC
*** * *
5516705 TCCTACATGATAAGGAGATCTGTTTGGTGGATTACACTGTTCCTACGTGATGAGGACGTCTGGCC
193 TCCTACATGATAAGGAGATCTGGCCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCC
5516770 ATCTTTAGGGA
258 ATCTTTAGGGA
5516781 CAATTTGTTT
Statistics
Matches: 230, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
275 4 0.02
276 226 0.98
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (276 bp):
GATAACACAGTTCCTACACGATGAGGAAATCTGGCTATCTAAGGATGATGATGCTCCTACATGAT
AAGGAGATCTGGATGGTAGATGAAAATGTTCCTACGTGACGAGAAAGTCTGGCCATCTTTAGGGA
TAAATAGAGATAACACGATTCCTACGCGATGAGGAAGTCTGACTATCTAAGGATGACACGGCTCC
TACATGATAAGGAGATCTGGCCGGTGGATGACACTGTTCCTACGTGATGAGGACATCTGGCCATC
TTTAGGGATAAATGGA
Found at i:5516909 original size:36 final size:36
Alignment explanation
Indices: 5516852--5517207 Score: 178
Period size: 36 Copynumber: 10.6 Consensus size: 36
5516842 TAAAGTTGTA
**
5516852 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAATATT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
* *
5516888 TGTTTCAGGGGAAACAATCTCAA-AG-G-T--TA--
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
* * *
5516917 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
**
5516953 TACTTC-AGTAGAAACAATCTCAA-AG-G-T--TA--
1 TGTTTCAAG-AGAAACAATCTCAAGAGAGATAATATT
** * * *
5516982 TGTTTCAAGAGAAACTCTCTCTAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
*
5517018 TGTTTCAAGGGAAACAATCTCAA-AG-G-T--TA--
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
* ** * *
5517047 TGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
* *
5517083 TGTTTCAAGGGAAATAATCTCAA-AG-G-T--TA--
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
*** * * * *
5517112 TGTTTCAAGAGAAATTGTCTCAACAGAGACAAAACT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
* *
5517148 TGTTTCAAGAGAAACAATATCAAAGTGAGATCAAT-TT
1 TGTTTCAAGAGAAACAATCTC-AAGAGAGAT-AATATT
* *
5517185 TGTTTCAAGTGAAACAATTTCAA
1 TGTTTCAAGAGAAACAATCTCAA
5517208 AATCTGTAAA
Statistics
Matches: 234, Mismatches: 54, Indels: 64
0.66 0.15 0.18
Matches are distributed among these distances:
29 75 0.32
30 10 0.04
31 9 0.04
33 1 0.00
34 8 0.03
35 10 0.04
36 93 0.40
37 26 0.11
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAATCTCAAGAGAGATAATATT
Found at i:5516930 original size:29 final size:29
Alignment explanation
Indices: 5516888--5517125 Score: 104
Period size: 29 Copynumber: 7.5 Consensus size: 29
5516878 AGATAATATT
* *
5516888 TGTTTCAGGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
* **
5516917 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACAATCTCAA-AG-G---TTA
*
5516951 TTTACTTC-AGTAGAAACAATCTCAAAGGTTA
1 TGT--TTCAAG-AGAAACAATCTCAAAGGTTA
** *
5516982 TGTTTCAAGAGAAACTCTCTCTAGAGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTC-A-A-AG-----GTTA
*
5517018 TGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
* **
5517047 TGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAA-AG-G------TTA
* *
5517083 TGTTTCAAGGGAAATAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
5517112 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
5517126 TTGTCTCAAC
Statistics
Matches: 157, Mismatches: 25, Indels: 54
0.67 0.11 0.23
Matches are distributed among these distances:
28 4 0.03
29 66 0.42
30 7 0.04
31 6 0.04
32 2 0.01
33 2 0.01
34 6 0.04
35 7 0.04
36 53 0.34
37 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (29 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTA
Found at i:5516960 original size:65 final size:65
Alignment explanation
Indices: 5516786--5517172 Score: 560
Period size: 65 Copynumber: 5.9 Consensus size: 65
5516776 AGGGACAATT
* * * * *
5516786 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCATGGGAAACAATCTTAAAGTTGT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT-T
5516851 A
65 A
* * *
5516852 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAATATTTGTTTCAGGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* ** *
5516917 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTACTTC-AGTAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GGAAACAATCTCAAAGGTT
5516981 A
65 A
* *
5516982 TGTTTCAAGAGAAACTCTCTCTAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* *
5517047 TGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * * * *
5517112 TGTTTCAAGAGAAATTGTCTCAACAGAGACAAAACTTGTTTCAAGAGAAACAATATCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG
5517173 TGAGATCAAT
Statistics
Matches: 289, Mismatches: 30, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
64 1 0.00
65 230 0.80
66 58 0.20
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:5517625 original size:19 final size:20
Alignment explanation
Indices: 5517603--5517641 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5517593 TTAGATCTCT
*
5517603 CTCTGTGTT-TTCTTTTTTC
1 CTCTGTGTTCTTCATTTTTC
*
5517622 CTCTGTTTTCTTCATTTTTC
1 CTCTGTGTTCTTCATTTTTC
5517642 TTCGAATCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.03, C:0.23, G:0.08, T:0.67
Consensus pattern (20 bp):
CTCTGTGTTCTTCATTTTTC
Found at i:5518138 original size:3 final size:3
Alignment explanation
Indices: 5518132--5518198 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
5518122 ATAATATATT
5518132 TAA TAA T-A TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5518178 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
5518199 ATAAAATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5518138 original size:12 final size:11
Alignment explanation
Indices: 5518121--5518202 Score: 103
Period size: 12 Copynumber: 7.2 Consensus size: 11
5518111 CTGTAAAATA
*
5518121 AATAATATATTT
1 AATAATATA-AT
5518133 AATAATATAAT
1 AATAATATAAT
*
5518144 AATAATAAAAT
1 AATAATATAAT
5518155 AATAATAATAAT
1 AATAAT-ATAAT
5518167 AATAATAATAAT
1 AATAAT-ATAAT
5518179 AATAATAATAAT
1 AATAAT-ATAAT
5518191 AATAATA-AAT
1 AATAATATAAT
5518201 AA
1 AA
5518203 AATTAAAAGT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
10 5 0.08
11 18 0.27
12 43 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATATAAT
Found at i:5518652 original size:138 final size:139
Alignment explanation
Indices: 5518404--5518951 Score: 651
Period size: 138 Copynumber: 4.0 Consensus size: 139
5518394 AGGTAAATTT
* * * * * * * *
5518404 TGGAGATAACACAGTTCCTACATGATGAGGAAATCTGGTTATCTAAGGGTGACGCTACTCCTATG
1 TGGAGATAACACAATTCCTACACGATGAGGAAGTATGGCTATCTAAGGATGACGCTGCTCCTACG
* * * * *
5518469 TGATGAGGAGATTTGGTC-AGTGGATGACACTCTTCTTATGTGATGAGGTCGTCTGGCCATCTTT
66 TGATGAGGAGATCTGGTCGAGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
*
5518533 ATGGATAAA
131 AGGGATAAA
** *
5518542 TGGAGATAACACGGTTCCTACACGATGAGGAAGTATGGCTATCTAAGGATGACACTGCTCCTACG
1 TGGAGATAACACAATTCCTACACGATGAGGAAGTATGGCTATCTAAGGATGACGCTGCTCCTACG
* *
5518607 TGATTAGGAGATCTGGTCGA-TGGATGAGACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
66 TGATGAGGAGATCTGGTCGAGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
5518671 AGGGATAAA
131 AGGGATAAA
* ** * * *
5518680 TAGAGATAACATTATTCCTAAAAGATGAGGAAGTTTGGCTATCTAAGGATGACGCTGCTCCTACG
1 TGGAGATAACACAATTCCTACACGATGAGGAAGTATGGCTATCTAAGGATGACGCTGCTCCTACG
* * * * * * *
5518745 TGATTAGGAGATATGGTCG-GTGGATGACACAGTTCTTACGTGATGAGGGCATCTGGCCATATTT
66 TGATGAGGAGATCTGGTCGAGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
*
5518809 AGGAATAAA
131 AGGGATAAA
* * ** * * *
5518818 TGGAGATAACACAATTCCTACTCAATGAGGAAGTATGATTGTCTAAGGATGACGTTGCT-CTACA
1 TGGAGATAACACAATTCCTACACGATGAGGAAGTATGGCTATCTAAGGATGACGCTGCTCCTACG
* * * *
5518882 TGATGAAGAGATCTGGT-TAGTGGATGACAATGTTCCTACGTGATGAGGAC--CTAGCCATCTTT
66 TGATGAGGAGATCTGGTCGAGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
5518944 AGGGATAA
131 AGGGATAA
5518952 TTTGTTTCAA
Statistics
Matches: 350, Mismatches: 57, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
135 17 0.05
137 45 0.13
138 287 0.82
139 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (139 bp):
TGGAGATAACACAATTCCTACACGATGAGGAAGTATGGCTATCTAAGGATGACGCTGCTCCTACG
TGATGAGGAGATCTGGTCGAGTGGATGACACTGTTCCTACGTGATGAGGACGTCTGGCCATCTTT
AGGGATAAA
Found at i:5519135 original size:36 final size:34
Alignment explanation
Indices: 5519026--5519264 Score: 95
Period size: 36 Copynumber: 7.3 Consensus size: 34
5519016 TGCATGTTGT
*
5519026 AAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTC
1 AAGAGAAACTGTCTCAAGA-AG-CAAAATTTGTTTC
* ** * *
5519062 AAGGGAAACAATCTC-A-AAG----GTTATGCTTC
1 AAGAGAAACTGTCTCAAGAAGCAAAATT-TGTTTC
5519091 AAGAGAAACTGTCTCAAGATAGACAAAATTTGTTTC
1 AAGAGAAACTGTCTCAAGA-AG-CAAAATTTGTTTC
* ** *
5519127 AAGGGAAACAATCTC-A-AAG----GTTAT-TTTC
1 AAGAGAAACTGTCTCAAGAAGCAAAATT-TGTTTC
5519155 AAGAGAAACTGTCTCAAGAGAGTCAAAATTTGTTTC
1 AAGAGAAACTGTCTCAAGA-AG-CAAAATTTGTTTC
* ** *
5519191 AAGGGAAACAATCTC-A-AAG----GTTATGTTTC
1 AAGAGAAACTGTCTCAAGAAGCAAAATT-TGTTTC
*
5519220 AAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTT-
1 AAGAGAAACTGTCTCAAGA-AG-CAAAATTTGTTTC
5519255 AAGGAGAAAC
1 AA-GAGAAAC
5519265 AATCTCAAAG
Statistics
Matches: 146, Mismatches: 28, Indels: 58
0.63 0.12 0.25
Matches are distributed among these distances:
28 22 0.15
29 37 0.25
30 3 0.02
31 4 0.03
32 4 0.03
33 6 0.04
34 3 0.02
35 6 0.04
36 58 0.40
37 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (34 bp):
AAGAGAAACTGTCTCAAGAAGCAAAATTTGTTTC
Found at i:5519155 original size:28 final size:29
Alignment explanation
Indices: 5519121--5519228 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 29
5519111 AGACAAAATT
*
5519121 TGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
** *
5519150 T-TTTCAAGAGAAACTGTCTCAAGAGAGTCAAAATT
1 TGTTTCAAGAGAAACAATCTCAA-AG-GT-----TA
*
5519185 TGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTA
5519214 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
5519229 TGTCTCAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
28 18 0.29
29 18 0.29
30 2 0.03
34 2 0.03
35 4 0.06
36 18 0.29
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (29 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTA
Found at i:5519189 original size:64 final size:65
Alignment explanation
Indices: 5518954--5519274 Score: 488
Period size: 65 Copynumber: 4.9 Consensus size: 65
5518944 AGGGATAATT
* * * * *
5518954 TGTTTCAAAAGAAACTGTCTCAAGAAAGACTAAATTTATTTCAGGGGAAACAATCTCAAA-GTTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT-
5519018 CA
65 -A
*
5519020 TGTTGT-AAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT
1 TGTT-TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT
5519084 A
65 A
* *
5519085 TGCTTCAAGAGAAACTGTCTCAAGATAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
*
5519150 T-TTTCAAGAGAAACTGTCTCAAGAGAGTCAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
*
5519214 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTT-AAGGAGAAACAATCTCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG-GAAACAATCTCAAAG
5519275 TGAGATCAAT
Statistics
Matches: 236, Mismatches: 14, Indels: 11
0.90 0.05 0.04
Matches are distributed among these distances:
64 66 0.28
65 114 0.48
66 52 0.22
67 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:5519205 original size:129 final size:131
Alignment explanation
Indices: 5518957--5519274 Score: 484
Period size: 129 Copynumber: 2.4 Consensus size: 131
5518947 GATAATTTGT
* * * *
5518957 TTCAAAAGAAACTGTCTCAAGAAAGACTAAATTTATTTCAGGGGAAACAATCTCAAA-GTTGCAT
1 TTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT-CAT
5519021 GTTGTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTAT
65 GTTGTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTAT
5519086 GC
130 GC
*
5519088 TTCAAGAGAAACTGTCTCAAGATAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTT-AT-
1 TTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTCATG
* *
5519151 TT-TCAAGAGAAACTGTCTCAAGAGAGTCAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTAT
66 TTGT-AAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTAT
*
5519215 GT
130 GC
* *
5519217 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTT-AAGGAGAAACAATCTCAAAG
1 TTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGG-GAAACAATCTCAAAG
5519275 TGAGATCAAT
Statistics
Matches: 174, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
128 5 0.03
129 112 0.64
130 2 0.01
131 52 0.30
132 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (131 bp):
TTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTCATG
TTGTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTATG
C
Found at i:5519439 original size:88 final size:92
Alignment explanation
Indices: 5519259--5519452 Score: 220
Period size: 88 Copynumber: 2.1 Consensus size: 92
5519249 TTGTTTAAGG
5519259 AGAAACAATCTCAAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATATGTGAAAATA
1 AGAAACAATCTCAAAGTGAGATCAATTTTGTTT--A-TGAAACAATTTCAAAATATGTGAAAATA
* * *
5519324 TGTCTCAAGCGAGATGAACTTCATTTTGAA
63 CGTCTCAAGCGAGACGAAATTCATTTTGAA
* * *
5519354 AGAAATAATCTC-AAGTGAGATCAATTTTGTTT-T-AAA-AATTTCAAAATTTGT-AGAAATCCG
1 AGAAACAATCTCAAAGTGAGATCAATTTTGTTTATGAAACAATTTCAAAATATGTGA-AAATACG
* **
5519414 TCTCAAGTGAGACGAAATTTGTTTTGAGA
65 TCTCAAGCGAGACGAAATTCATTTTGA-A
5519443 A-AAACAATCT
1 AGAAACAATCT
5519453 TAAAAGCTTA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
87 1 0.01
88 49 0.56
89 5 0.06
90 1 0.01
94 20 0.23
95 11 0.13
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (92 bp):
AGAAACAATCTCAAAGTGAGATCAATTTTGTTTATGAAACAATTTCAAAATATGTGAAAATACGT
CTCAAGCGAGACGAAATTCATTTTGAA
Found at i:5521926 original size:24 final size:23
Alignment explanation
Indices: 5521872--5521932 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
5521862 TTCTTGTATT
5521872 ATTTTTTTTCTTTTTCTTCTTTG
1 ATTTTTTTTCTTTTTCTTCTTTG
* *
5521895 ATTATTTTTGCTCTTTT-TTCTTTTC
1 ATT-TTTTTTCT-TTTTCTTC-TTTG
*
5521920 TTTTTTTTTCTTT
1 ATTTTTTTTCTTT
5521933 GCTCTTATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 5 0.16
24 17 0.55
25 9 0.29
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (23 bp):
ATTTTTTTTCTTTTTCTTCTTTG
Found at i:5521933 original size:29 final size:32
Alignment explanation
Indices: 5521875--5521938 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 32
5521865 TTGTATTATT
5521875 TTTTTTCTTTTTCTTCTTTGATTATTTTTGCTC
1 TTTTTTCTTTTTCTTCTTT-ATTATTTTTGCTC
5521908 TTTTTTC-TTTTCTT-TTT-TT-TTCTTTGCTC
1 TTTTTTCTTTTTCTTCTTTATTATT-TTTGCTC
5521937 TT
1 TT
5521939 ATCCTTGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 2 0.07
29 11 0.37
31 3 0.10
32 7 0.23
33 7 0.23
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.77
Consensus pattern (32 bp):
TTTTTTCTTTTTCTTCTTTATTATTTTTGCTC
Found at i:5526528 original size:44 final size:44
Alignment explanation
Indices: 5526456--5526559 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
5526446 TACACTACAG
* *
5526456 AGTGTATCGATGCACATACAAGACATGCATCAGTGC-ACTTTCAT
1 AGTGTATCGATGCATATACAAGACATGCATCAGTACAAC-TTCAT
* ** *
5526500 AGTGTATCGATGCATATTCAAGGGATGCATCGGTACAACTTCAT
1 AGTGTATCGATGCATATACAAGACATGCATCAGTACAACTTCAT
*
5526544 AGTTTATCGATGCATA
1 AGTGTATCGATGCATA
5526560 GTGCACAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 50 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCATATACAAGACATGCATCAGTACAACTTCAT
Found at i:5531933 original size:19 final size:19
Alignment explanation
Indices: 5531909--5531953 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5531899 AGTTGACCTA
5531909 GTGCATCGGTACACTTGGG
1 GTGCATCGGTACACTTGGG
5531928 GTGCATCGGTACACTTGGG
1 GTGCATCGGTACACTTGGG
5531947 GTGCATC
1 GTGCATC
5531954 TGTGCATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.22, G:0.36, T:0.27
Consensus pattern (19 bp):
GTGCATCGGTACACTTGGG
Found at i:5533329 original size:17 final size:17
Alignment explanation
Indices: 5533307--5533341 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5533297 AATATAACAC
* *
5533307 CTACCCGATCATGGTAT
1 CTACCCAATCATGCTAT
5533324 CTACCCAATCATGCTAT
1 CTACCCAATCATGCTAT
5533341 C
1 C
5533342 ATTAGATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (17 bp):
CTACCCAATCATGCTAT
Found at i:5536751 original size:20 final size:20
Alignment explanation
Indices: 5536726--5536767 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
5536716 TCATTTCATT
5536726 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
*
5536746 TAAAGGTCTTAACCTTTGAA
1 TAAAGGTCTTAACCTTTCAA
5536766 TA
1 TA
5536768 CAAATTCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:5541880 original size:23 final size:23
Alignment explanation
Indices: 5541832--5541881 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5541822 ATCATGACTA
*
5541832 TTCATGAAAAATAATTAAGTCTT
1 TTCATGAAAAATAATTAAGTCAT
**
5541855 TTCATGAAAAATAATTATTTCAT
1 TTCATGAAAAATAATTAAGTCAT
5541878 TTCA
1 TTCA
5541882 CCCCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:5541980 original size:21 final size:21
Alignment explanation
Indices: 5541962--5542003 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5541952 TCATTTCATT
5541962 TAAAGGTCTTAA-CTTTTCAA
1 TAAAGGTCTTAACCTTTTCAA
5541982 TAAAGGTCTTAACCTTTT-AA
1 TAAAGGTCTTAACCTTTTCAA
5542002 TA
1 TA
5542004 CAAATTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
TAAAGGTCTTAACCTTTTCAA
Found at i:5545243 original size:23 final size:22
Alignment explanation
Indices: 5545207--5545258 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
5545197 CACCTAAGTG
*
5545207 CCACATA-TTTGTCCCGAATGA
1 CCACATAGTTTGTCCCGAAGGA
*
5545228 CCACATAGGTTTGTCCTGAAGGA
1 CCACATA-GTTTGTCCCGAAGGA
5545251 CCACATAG
1 CCACATAG
5545259 AACTCTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 19 0.70
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (22 bp):
CCACATAGTTTGTCCCGAAGGA
Found at i:5545488 original size:17 final size:17
Alignment explanation
Indices: 5545468--5545501 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5545458 ATTACACTTC
5545468 ATATAAAACATAATAAA
1 ATATAAAACATAATAAA
* *
5545485 ATATTAAATATAATAAA
1 ATATAAAACATAATAAA
5545502 TAAACAGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATAAAACATAATAAA
Found at i:5545823 original size:20 final size:20
Alignment explanation
Indices: 5545785--5545840 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
5545775 TTCAGGCTGA
* *
5545785 ATAGTATCGATACCCCTCTT
1 ATAGTACCGATACCACTCTT
*
5545805 ATAGTACCGATACTACTCTT
1 ATAGTACCGATACCACTCTT
*
5545825 CTAGGGTACCGATACC
1 ATA--GTACCGATACC
5545841 CACTTCGGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 19 0.66
22 10 0.34
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (20 bp):
ATAGTACCGATACCACTCTT
Found at i:5546504 original size:3 final size:3
Alignment explanation
Indices: 5546492--5546534 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
5546482 GGAGTCACGC
*
5546492 GAA G-A GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5546535 TAAGTGAGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:5554428 original size:21 final size:20
Alignment explanation
Indices: 5554400--5554438 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5554390 CTTTGTAGGA
*
5554400 ATTTATGGCATCGACAAAAG
1 ATTTATGGCATCCACAAAAG
*
5554420 ATTTCATGGCTTCCACAAA
1 ATTT-ATGGCATCCACAAA
5554439 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCATCCACAAAAG
Found at i:5559928 original size:15 final size:15
Alignment explanation
Indices: 5559910--5559939 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5559900 CAAAGGAGGG
5559910 CATCATAAAGAAAAA
1 CATCATAAAGAAAAA
5559925 CATCATAAAGAAAAA
1 CATCATAAAGAAAAA
5559940 GATCCCTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (15 bp):
CATCATAAAGAAAAA
Found at i:5564066 original size:21 final size:22
Alignment explanation
Indices: 5564041--5564091 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
5564031 CACCAAAGTT
*
5564041 CCACATA-TTTATCCCGAATGA
1 CCACATAGTTTATCCCAAATGA
* *
5564062 TCACATAGGTTTGTCCCAAATGA
1 CCACATA-GTTTATCCCAAATGA
5564085 CCACATA
1 CCACATA
5564092 CAACCCTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.25
23 18 0.75
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (22 bp):
CCACATAGTTTATCCCAAATGA
Found at i:5567209 original size:17 final size:17
Alignment explanation
Indices: 5567187--5567229 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
5567177 AGTTATAATC
5567187 CAATTCCTCCTTAAAAT
1 CAATTCCTCCTTAAAAT
5567204 CAATTCCTCCTTAAAAT
1 CAATTCCTCCTTAAAAT
5567221 CAATTCCTC
1 CAATTCCTC
5567230 AAACTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (17 bp):
CAATTCCTCCTTAAAAT
Found at i:5572092 original size:2 final size:2
Alignment explanation
Indices: 5572083--5572271 Score: 88
Period size: 2 Copynumber: 107.5 Consensus size: 2
5572073 AATATAAAAA
*
5572083 AT AT -T AT AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5572119 A- AA AA AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5572154 AT AT AT AT A- AT -T A- AT AT A- AA AT AT -T AA AA AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5572190 AT AT AT A- AT -T A- AT AT A- AA AA AT AT A- AA AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
5572226 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT CG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5572267 AT AT A
1 AT AT A
5572272 ATCGGGGCGG
Statistics
Matches: 149, Mismatches: 12, Indels: 52
0.70 0.06 0.24
Matches are distributed among these distances:
1 26 0.17
2 123 0.83
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5572092 original size:25 final size:25
Alignment explanation
Indices: 5572064--5572230 Score: 130
Period size: 22 Copynumber: 7.2 Consensus size: 25
5572054 GGGTTTGTAT
5572064 TATATAATTAATATAAAAAA-TAT-
1 TATATAATTAATATAAAAAATTATA
* *
5572087 TATAT-ATT-ATATATATAATTA-A
1 TATATAATTAATATAAAAAATTATA
*
5572109 TATA-AAAT-ATA-AAAAATATTATA
1 TATATAATTAATATAAAAA-ATTATA
*
5572132 TATATAATTAATATAAAATATTATA
1 TATATAATTAATATAAAAAATTATA
*
5572157 TATATAATTAATATAAAATATTA-A
1 TATATAATTAATATAAAAAATTATA
* * *
5572181 -AAAT-ATT-ATATATATAATTA-A
1 TATATAATTAATATAAAAAATTATA
* *
5572202 TATA-AA-AAATATAAAATATTATA
1 TATATAATTAATATAAAAAATTATA
5572225 TATATA
1 TATATA
5572231 TATATATATA
Statistics
Matches: 115, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
21 22 0.19
22 34 0.30
23 18 0.16
24 5 0.04
25 32 0.28
26 4 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TATATAATTAATATAAAAAATTATA
Found at i:5572102 original size:34 final size:34
Alignment explanation
Indices: 5572064--5572230 Score: 210
Period size: 34 Copynumber: 5.2 Consensus size: 34
5572054 GGGTTTGTAT
* *
5572064 TATATAATTAATATAAAAAATATTATATATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
5572098 TATATAATTAATAT--AAAATATAAAA-A--ATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
**
5572127 T-TAT-A-T-ATATAATTAATATAAAATATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
*
5572157 TATATAATTAATATAAAATATTA-AAAATATTATA
1 TATATAATTAATATAAAA-AATATAAAATATTATA
5572191 TATATAATTAATATAAAAAATATAAAATATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
5572225 TATATA
1 TATATA
5572231 TATATATATA
Statistics
Matches: 114, Mismatches: 8, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.04
26 1 0.01
27 10 0.09
28 4 0.04
29 4 0.04
30 4 0.04
31 4 0.04
32 10 0.09
33 4 0.04
34 66 0.58
35 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TATATAATTAATATAAAAAATATAAAATATTATA
Found at i:5572158 original size:59 final size:59
Alignment explanation
Indices: 5572090--5572208 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
5572080 AAAATATTAT
5572090 ATATTATATATATAATTAATATAAAATATAAAAAATATTATATATATAATTAATATAAA
1 ATATTATATATATAATTAATATAAAATATAAAAAATATTATATATATAATTAATATAAA
*
5572149 ATATTATATATATAATTAATATAAAATATTAAAAATATTATATATATAATTAATATAAA
1 ATATTATATATATAATTAATATAAAATATAAAAAATATTATATATATAATTAATATAAA
5572208 A
1 A
5572209 AATATAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (59 bp):
ATATTATATATATAATTAATATAAAATATAAAAAATATTATATATATAATTAATATAAA
Done.