Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 28 of 195
Found at i:6364856 original size:12 final size:12
Alignment explanation
Indices: 6364836--6364878 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
6364826 GTTCAAAATA
* *
6364836 ATTTTTTTTCTT
1 ATTTATTTTATT
6364848 ATTTATTTTATT
1 ATTTATTTTATT
6364860 A-TTATTATTATT
1 ATTTATT-TTATT
6364872 ATTTATT
1 ATTTATT
6364879 GATTAGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:6365027 original size:91 final size:90
Alignment explanation
Indices: 6364932--6365113 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 90
6364922 TTATTTTTGA
* * *
6364932 TTTTCTT-TAAATAAAATTTCAAAAAAGATATTTTTGAGGAGAAGTTGAAAGTATCAATTTTTCT
1 TTTTCTTAAAAATAAAATTTCAAAAAA-ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCT
6364996 TGAAAATAAGTCTTCAAAAAAATATTT
65 TGAAAATAAGTCTTC-AAAAAATATTT
** * *
6365023 TTTTCTTAAAAATAAGTTTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCGATTTTTCTT
1 TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* *
6365088 GAAAATAAGTTTTCTAAAAATATTT
66 GAAAATAAGTCTTCAAAAAATATTT
6365113 T
1 T
6365114 CGAAAAAAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
90 11 0.14
91 55 0.68
92 15 0.19
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (90 bp):
TTTTCTTAAAAATAAAATTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
GAAAATAAGTCTTCAAAAAATATTT
Found at i:6365028 original size:33 final size:33
Alignment explanation
Indices: 6364989--6365057 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
6364979 AAAGTATCAA
*
6364989 TTTTTCTTGAAAATAAGTCTTCAAAAAAATATT
1 TTTTTCTTAAAAATAAGTCTTCAAAAAAATATT
* *
6365022 TTTTTCTTAAAAATAAGTTTTCTAAAAAATATT
1 TTTTTCTTAAAAATAAGTCTTCAAAAAAATATT
6365055 TTT
1 TTT
6365058 GAGAAAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (33 bp):
TTTTTCTTAAAAATAAGTCTTCAAAAAAATATT
Found at i:6365042 original size:16 final size:16
Alignment explanation
Indices: 6364998--6365052 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
6364988 ATTTTTCTTG
* *
6364998 AAAATAAGTCTTCAAA
1 AAAATAAGTTTTCTAA
** *
6365014 AAAATATTTTTTTCTTA
1 AAAATA-AGTTTTCTAA
6365031 AAAATAAGTTTTCTAA
1 AAAATAAGTTTTCTAA
6365047 AAAATA
1 AAAATA
6365053 TTTTTGAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (16 bp):
AAAATAAGTTTTCTAA
Found at i:6365133 original size:57 final size:57
Alignment explanation
Indices: 6365022--6365261 Score: 272
Period size: 57 Copynumber: 4.2 Consensus size: 57
6365012 AAAAAATATT
* * *
6365022 TTTTTCTTAAAAATAAGTTTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCGA
1 TTTTTCTTGAAAATAAGTTTTCT-AAAAATATTTTTGAAAAAAAGTTGAAAGTATCAA
*
6365080 TTTTTCTTGAAAATAAGTTTTCTAAAAATATTTTCGAAAAAAAGTTGAAAGTATCAA
1 TTTTTCTTGAAAATAAGTTTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAA
* ** *
6365137 -TTTTCTTTGAAAATAA-ATTTCTAAAAATGAATTTTTTGAGGAAAAGTTGAAAGTATAAA
1 TTTTTC-TTGAAAATAAGTTTTCTAAAAAT--A-TTTTTGAAAAAAAGTTGAAAGTATCAA
* * * * *
6365196 TTTTTCTCGAAATAAAAG-TTTCAGAAAAATA-TTTTGAAAAAAAATTAAAAGTATCAA
1 TTTTTCTTGAAA-ATAAGTTTTC-TAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAA
6365253 TTTTTCTTG
1 TTTTTCTTG
6365262 TACAAAAGTA
Statistics
Matches: 156, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
56 16 0.10
57 70 0.45
58 23 0.15
59 29 0.19
60 12 0.08
61 6 0.04
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (57 bp):
TTTTTCTTGAAAATAAGTTTTCTAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAA
Found at i:6370415 original size:21 final size:20
Alignment explanation
Indices: 6370389--6370436 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
6370379 TATTGTAACT
6370389 TTTTTAAAGGTTTTTAATTTA
1 TTTTTAAA-GTTTTTAATTTA
* *
6370410 TTTTTAAATTTTTTACTTTA
1 TTTTTAAAGTTTTTAATTTA
6370430 TTATTTA
1 TT-TTTA
6370437 TTTGATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTTAAAGTTTTTAATTTA
Found at i:6374539 original size:22 final size:23
Alignment explanation
Indices: 6374495--6374539 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6374485 TTCTTTTTTC
* *
6374495 TTTCTTTTTTTGAGATATTCTTT
1 TTTCTATTTTTGAGATATACTTT
6374518 TTTCTATTTTTGAGATA-ACTTT
1 TTTCTATTTTTGAGATATACTTT
6374540 GATATACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTCTATTTTTGAGATATACTTT
Found at i:6381854 original size:75 final size:75
Alignment explanation
Indices: 6381731--6381887 Score: 271
Period size: 75 Copynumber: 2.1 Consensus size: 75
6381721 GTCTCGAAGG
* * * *
6381731 AGGTAGGCAAGAGGTTAGGTGGGGGAGAATGTCATGGACCTAAGAAAGAGTCTTGAATCTCACAT
1 AGGTAGGCAAAAGGTTAGGTGAGGGAGAATATCATGGACCTAAGAAAGAGTCCTGAATCTCACAT
6381796 TGAACATAAT
66 TGAACATAAT
6381806 AGGTAGGCAAAAGGTTAGGTGAGGGAGAATATCATGGACCTAAGAAAGAGTCCTGAATCTCACAT
1 AGGTAGGCAAAAGGTTAGGTGAGGGAGAATATCATGGACCTAAGAAAGAGTCCTGAATCTCACAT
6381871 TGAACATAAT
66 TGAACATAAT
6381881 AGG-AGGC
1 AGGTAGGC
6381888 TCACTAGGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 4 0.05
75 74 0.95
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (75 bp):
AGGTAGGCAAAAGGTTAGGTGAGGGAGAATATCATGGACCTAAGAAAGAGTCCTGAATCTCACAT
TGAACATAAT
Found at i:6383187 original size:14 final size:14
Alignment explanation
Indices: 6383158--6383202 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
6383148 TGTTAAAATT
6383158 ATTTTAAATGTA-TA
1 ATTTTAAAT-TATTA
* *
6383172 ATTTTTAATTTTTA
1 ATTTTAAATTATTA
6383186 ATTTTAAATTATTA
1 ATTTTAAATTATTA
6383200 ATT
1 ATT
6383203 ACAATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 1 0.04
14 25 0.96
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTTAAATTATTA
Found at i:6384212 original size:36 final size:36
Alignment explanation
Indices: 6384172--6384245 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
6384162 TTCCATTATT
* *
6384172 ATTACCATATATCATTATAATAATATAAAATATTAA
1 ATTACCATATACCATTATAATAACATAAAATATTAA
* * *
6384208 ATTACCATATACCATTGTAATAGCATAAAATGTTAA
1 ATTACCATATACCATTATAATAACATAAAATATTAA
6384244 AT
1 AT
6384246 CAATGCGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (36 bp):
ATTACCATATACCATTATAATAACATAAAATATTAA
Found at i:6386824 original size:108 final size:110
Alignment explanation
Indices: 6386632--6386835 Score: 263
Period size: 108 Copynumber: 1.9 Consensus size: 110
6386622 AAATATATTT
* ***
6386632 AATTATTTCACCATTTGGGTCAAATTAAAAGTATTTTTTTATTTTGAATTTCTAAATTCTCTATC
1 AATTATTTCACCATTTGGGTCAAATTAAAAATATTTTTTTATTCAAAATTTCTAAATTCTCTATC
6386697 ATTTGGGCCTATTTAGAAATT-TTATTTATTTATTTTAGATTTTTA
66 ATTTGGGCCTATTTAGAAATTCTT-TTTATTTATTTTAGATTTTTA
* * * * * *
6386742 AATTTTTTTACCATTTGGGTCAATTTAAAAATA-TTTTTT-TTCAAAATTTTTAAATTTTTTA-C
1 AATTATTTCACCATTTGGGTCAAATTAAAAATATTTTTTTATTCAAAATTTCTAAATTCTCTATC
*
6386804 TATTTGGGCCTGTTTAGAAATTCTTTTTATTT
66 -ATTTGGGCCTATTTAGAAATTCTTTTTATTT
6386836 CTCTCTTTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 1 0.01
108 43 0.53
109 8 0.10
110 29 0.36
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (110 bp):
AATTATTTCACCATTTGGGTCAAATTAAAAATATTTTTTTATTCAAAATTTCTAAATTCTCTATC
ATTTGGGCCTATTTAGAAATTCTTTTTATTTATTTTAGATTTTTA
Found at i:6386831 original size:52 final size:53
Alignment explanation
Indices: 6386735--6386836 Score: 127
Period size: 51 Copynumber: 1.9 Consensus size: 53
6386725 TTTATTTTAG
*
6386735 ATTTTTAAATTTTTTTACCATTTGGGTCAATTTAAAAATATTTTT-TTTCAAA
1 ATTTTTAAATTTTTTTACCATTTGGGCCAATTTAAAAATATTTTTATTTCAAA
* ** * *
6386787 ATTTTTAAA-TTTTTTACTATTTGGGCCTGTTTAGAAATTCTTTTTATTTC
1 ATTTTTAAATTTTTTTACCATTTGGGCCAATTTA-AAAATATTTTTATTTC
6386837 TCTCTTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 20 0.48
52 18 0.43
53 4 0.10
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (53 bp):
ATTTTTAAATTTTTTTACCATTTGGGCCAATTTAAAAATATTTTTATTTCAAA
Found at i:6387127 original size:4 final size:4
Alignment explanation
Indices: 6387118--6387168 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
6387108 AAATATTTAA
*
6387118 AAAT AAAT AAAC AAAT AAA- ATAAT CAAAT AAAT AAAT AAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT -AAAT AAAT AAAT AAAT -AAAT AAAT
6387168 A
1 A
6387169 CCAAAATGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 1 0.02
4 32 0.78
5 7 0.17
6 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:6387148 original size:25 final size:25
Alignment explanation
Indices: 6387118--6387165 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
6387108 AAATATTTAA
6387118 AAATAAATAAACAAATAAAATAATC
1 AAATAAATAAACAAATAAAATAATC
*
6387143 AAATAAATAAATAAATAAAATAA
1 AAATAAATAAACAAATAAAATAA
6387166 ATACCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (25 bp):
AAATAAATAAACAAATAAAATAATC
Found at i:6387163 original size:17 final size:18
Alignment explanation
Indices: 6387117--6387168 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
6387107 AAAATATTTA
*
6387117 AAAATAAAT-AAACAAAT
1 AAAATAAATAAAATAAAT
*
6387134 AAAAT-AATCAAATAAAT
1 AAAATAAATAAAATAAAT
6387151 -AAATAAATAAAATAAAT
1 AAAATAAATAAAATAAAT
6387168 A
1 A
6387169 CCAAAATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAATAAAATAAAT
Found at i:6387877 original size:9 final size:9
Alignment explanation
Indices: 6387863--6387897 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
6387853 AACTTCATTT
*
6387863 ATTTTTTTC
1 ATTTTTTTA
6387872 A-TTTTTTA
1 ATTTTTTTA
6387880 ATTTTTTTA
1 ATTTTTTTA
6387889 ATTTTTTTA
1 ATTTTTTTA
6387898 TTAACAGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:6387885 original size:17 final size:17
Alignment explanation
Indices: 6387863--6387895 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6387853 AACTTCATTT
*
6387863 ATTTTTTTCATTTTTTA
1 ATTTTTTTAATTTTTTA
6387880 ATTTTTTTAATTTTTT
1 ATTTTTTTAATTTTTT
6387896 TATTAACAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTTTAATTTTTTA
Found at i:6388159 original size:45 final size:45
Alignment explanation
Indices: 6388092--6388218 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 45
6388082 CACTCACAAC
* * * *
6388092 TTTGAAAAAAACAAATATAGCTCATCTAAATAGAGGCTTAACGATTT
1 TTTGAAAAATA-AATTA-AGCTCATCTTAATAGAGGCTTAACGACTT
*
6388139 TTTGAAAAATAAATTAAGCTCCA-CTTAATAGAGACTTAACGACTT
1 TTTGAAAAATAAATTAAGCT-CATCTTAATAGAGGCTTAACGACTT
* *
6388184 TTTGAAAAATAAATTAAGCTCCTCTTAACAGAGGC
1 TTTGAAAAATAAATTAAGCTCATCTTAATAGAGGC
6388219 ACCATAACTT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
44 1 0.01
45 53 0.76
46 6 0.09
47 10 0.14
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (45 bp):
TTTGAAAAATAAATTAAGCTCATCTTAATAGAGGCTTAACGACTT
Found at i:6388229 original size:45 final size:45
Alignment explanation
Indices: 6388137--6388238 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
6388127 GCTTAACGAT
* ** *
6388137 TTTTTGAAAAATAAATTAAGCTCCACTTAATAGAGACTTAACGAC
1 TTTTTGAAAAATAAATTAAGCTCCACTTAACAGAGACACAACAAC
* * * *
6388182 TTTTTGAAAAATAAATTAAGCTCCTCTTAACAGAGGCACCATAAC
1 TTTTTGAAAAATAAATTAAGCTCCACTTAACAGAGACACAACAAC
6388227 --TTTGAAAAATAA
1 TTTTTGAAAAATAA
6388239 GATGCTAATC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 12 0.24
45 37 0.76
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (45 bp):
TTTTTGAAAAATAAATTAAGCTCCACTTAACAGAGACACAACAAC
Found at i:6388262 original size:41 final size:41
Alignment explanation
Indices: 6388184--6388403 Score: 223
Period size: 41 Copynumber: 5.4 Consensus size: 41
6388174 TTAACGACTT
* * *
6388184 TTTGAAAAATAAATTAAGCTCCTCTTAACAGAGGCACCATAAC
1 TTTGAAAAATAAA--ATGCTCTTCTAAACAGAGGCACCATAAC
* **
6388227 TTTGAAAAATAAGATGCTAATCTAAACAGAGGCACCAT---
1 TTTGAAAAATAAAATGCTCTTCTAAACAGAGGCACCATAAC
**
6388265 TTTGAAAAATAAAACT-CTCTTCTAAACAGAGGCACTGTAAC
1 TTTGAAAAATAAAA-TGCTCTTCTAAACAGAGGCACCATAAC
* *
6388306 TTTAAAAAATAAAATGCTCTTCTAAATAGAGGCACCATAAC
1 TTTGAAAAATAAAATGCTCTTCTAAACAGAGGCACCATAAC
* * * * * *
6388347 TTTTGAAGAATAAAATGCTCCTCTAAATAAAGGCACAACAAC
1 -TTTGAAAAATAAAATGCTCTTCTAAACAGAGGCACCATAAC
*
6388389 TTTAAAAAATAAAAT
1 TTTGAAAAATAAAAT
6388404 CAAGCTCTCT
Statistics
Matches: 149, Mismatches: 22, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
38 31 0.21
39 1 0.01
40 1 0.01
41 69 0.46
42 35 0.23
43 12 0.08
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (41 bp):
TTTGAAAAATAAAATGCTCTTCTAAACAGAGGCACCATAAC
Found at i:6388390 original size:83 final size:79
Alignment explanation
Indices: 6388183--6388403 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 79
6388173 CTTAACGACT
* * * * *
6388183 TTTTGAAAAATAAATTAAGCTCCTCTTAACAGAGGCACCATAACTTTGAAAAATAAGATGCTAAT
1 TTTTGAAAAATAAA--ATGCTCCTCTAAACAGAGGCACAATAACTTTAAAAAATAAAATGCTAAT
6388248 CTAAACAGAGGCACCA
64 CTAAACAGAGGCACCA
* ** **
6388264 TTTTGAAAAATAAAACT-CTCTTCTAAACAGAGGCACTGTAACTTTAAAAAATAAAATGCTCTTC
1 TTTTGAAAAATAAAA-TGCTCCTCTAAACAGAGGCACAATAACTTTAAAAAATAAAATGCTAATC
*
6388328 TAAATAGAGGCACCATAA
65 TAAACAGAGGCACC---A
* * * *
6388346 CTTTTGAAGAATAAAATGCTCCTCTAAATAAAGGCACAACAACTTTAAAAAATAAAAT
1 -TTTTGAAAAATAAAATGCTCCTCTAAACAGAGGCACAATAACTTTAAAAAATAAAAT
6388404 CAAGCTCTCT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
79 53 0.45
81 14 0.12
82 2 0.02
83 48 0.41
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (79 bp):
TTTTGAAAAATAAAATGCTCCTCTAAACAGAGGCACAATAACTTTAAAAAATAAAATGCTAATCT
AAACAGAGGCACCA
Found at i:6388812 original size:107 final size:112
Alignment explanation
Indices: 6388650--6388853 Score: 310
Period size: 107 Copynumber: 1.9 Consensus size: 112
6388640 AAAGATTTTT
* *
6388650 ATTTGAATTTTTAGAGATTCACATCTAAAAGTTTAAAAGTTTTTTATTCGAGTTCAAAGGTTCAC
1 ATTTGAATTTTTAGAGATTCACATCTAAAAGTTTAAAAGCTTTTCATTCGAGTTCAAAGGTTCAC
6388715 ATTTGACAAA-TTTAG-GGTTCACATCCAAAAAGTTTAAGCTATTTC
66 ATTTGACAAATTTTAGAGGTTCACATCCAAAAAGTTTAAGCTATTTC
* * *
6388760 ATTTGAA-TTTTAGAGATTCACATC-CAAAGTTTAAAA-CTTTTCATTTGAGTTCAAAGGTTTAC
1 ATTTGAATTTTTAGAGATTCACATCTAAAAGTTTAAAAGCTTTTCATTCGAGTTCAAAGGTTCAC
* *
6388822 ATTTGACAAATTTTAGAGTTTCACATCTAAAA
66 ATTTGACAAATTTTAGAGGTTCACATCCAAAA
6388854 TCTCAAAGGT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
107 32 0.38
108 16 0.19
109 30 0.35
110 7 0.08
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (112 bp):
ATTTGAATTTTTAGAGATTCACATCTAAAAGTTTAAAAGCTTTTCATTCGAGTTCAAAGGTTCAC
ATTTGACAAATTTTAGAGGTTCACATCCAAAAAGTTTAAGCTATTTC
Found at i:6388920 original size:33 final size:33
Alignment explanation
Indices: 6388878--6388984 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 33
6388868 ATTTGAGTTT
* *
6388878 TTCTTAAAGATTCTCATTTGAAAAACTTAAAGA
1 TTCTCAAAGATTTTCATTTGAAAAACTTAAAGA
* *
6388911 TTCTCAAAGATTTTCATTTAAAAAACTTAAAGC
1 TTCTCAAAGATTTTCATTTGAAAAACTTAAAGA
* * *
6388944 TTCTTAAAGATTTTTATTTGAAAACGTCTTAAAGA
1 TTCTCAAAGATTTTCATTTGAAAA--ACTTAAAGA
6388979 TTCTCA
1 TTCTCA
6388985 TTTAAGACTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
33 50 0.81
35 12 0.19
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (33 bp):
TTCTCAAAGATTTTCATTTGAAAAACTTAAAGA
Found at i:6389056 original size:21 final size:21
Alignment explanation
Indices: 6389003--6389156 Score: 119
Period size: 21 Copynumber: 6.8 Consensus size: 21
6388993 TAAAATATTT
* *
6389003 TCAAAGATTTTCATTTGAAAAC
1 TCAAAGATTCTCATTT-AAGAC
*
6389025 GTCTTAAAGATTCTTATTTAAGAC
1 -TC--AAAGATTCTCATTTAAGAC
6389049 TCAAAGATTCTCATTTGAAGATTTC
1 TCAAAGATTCTCATTT-AAGA---C
*
6389074 TTAAAGATTCTCATTTAAGAC
1 TCAAAGATTCTCATTTAAGAC
* * * *
6389095 TCAAAGGTTTTCATTCAAAAATATC
1 TCAAAGATTCTCATT---TAAGA-C
*
6389120 TTAAAGATTCTCATTTAAGAC
1 TCAAAGATTCTCATTTAAGAC
6389141 TCAAAGATTCTCATTT
1 TCAAAGATTCTCATTT
6389157 GAGGATTCAA
Statistics
Matches: 105, Mismatches: 16, Indels: 22
0.73 0.11 0.15
Matches are distributed among these distances:
21 42 0.40
22 7 0.07
23 4 0.04
24 11 0.10
25 41 0.39
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TCAAAGATTCTCATTTAAGAC
Found at i:6389071 original size:14 final size:13
Alignment explanation
Indices: 6389052--6389093 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
6389042 TTAAGACTCA
6389052 AAGATTCTCATTT
1 AAGATTCTCATTT
*
6389065 GAAGATT-TC-TTA
1 -AAGATTCTCATTT
6389077 AAGATTCTCATTT
1 AAGATTCTCATTT
6389090 AAGA
1 AAGA
6389094 CTCAAAGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 8 0.33
14 6 0.25
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (13 bp):
AAGATTCTCATTT
Found at i:6389076 original size:46 final size:46
Alignment explanation
Indices: 6389003--6389158 Score: 222
Period size: 46 Copynumber: 3.4 Consensus size: 46
6388993 TAAAATATTT
* ** *
6389003 TCAAAGATTTTCATTTGAAAACGTCTTAAAGATTCTTATTTAAGAC
1 TCAAAGATTCTCATTTGAAAATTTCTTAAAGATTCTCATTTAAGAC
*
6389049 TCAAAGATTCTCATTTGAAGATTTCTTAAAGATTCTCATTTAAGAC
1 TCAAAGATTCTCATTTGAAAATTTCTTAAAGATTCTCATTTAAGAC
* * ** *
6389095 TCAAAGGTTTTCATTCAAAAATATCTTAAAGATTCTCATTTAAGAC
1 TCAAAGATTCTCATTTGAAAATTTCTTAAAGATTCTCATTTAAGAC
6389141 TCAAAGATTCTCATTTGA
1 TCAAAGATTCTCATTTGA
6389159 GGATTCAAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 95 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (46 bp):
TCAAAGATTCTCATTTGAAAATTTCTTAAAGATTCTCATTTAAGAC
Found at i:6390291 original size:18 final size:20
Alignment explanation
Indices: 6390259--6390325 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
6390249 CAATTTGAGT
6390259 ATTTTTTTCTCTCA-T-TTTC
1 ATTTTTTT-TCTCATTCTTTC
6390278 ACTTTTTTTT-TCATTCTTTC
1 A-TTTTTTTTCTCATTCTTTC
*
6390298 ATTTTTTTTCTCTTTTCTTTC
1 ATTTTTTTTCTC-ATTCTTTC
6390319 -TTTTTTT
1 ATTTTTTT
6390326 CTTTTTTCCA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 21 0.50
21 7 0.17
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTTTTTCTCATTCTTTC
Found at i:6390304 original size:16 final size:15
Alignment explanation
Indices: 6390283--6390380 Score: 57
Period size: 14 Copynumber: 6.4 Consensus size: 15
6390273 TTTTCACTTT
6390283 TTTTTTCATTCTTTCA
1 TTTTTTCATT-TTTCA
6390299 TTTTTTTTC-TCTTTTC-
1 --TTTTTTCAT-TTTTCA
*
6390315 TTTCTT--TTTTTC-
1 TTTTTTCATTTTTCA
6390327 TTTTTTCCATATTTTCCA
1 TTTTTT-CAT-TTTT-CA
6390345 TTTTTTCTATTTTTCA
1 TTTTTTC-ATTTTTCA
6390361 TTTTTT-ATTTCTT-A
1 TTTTTTCATTT-TTCA
6390375 TTTTTT
1 TTTTTT
6390381 TCTCTTTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 22
0.74 0.02 0.24
Matches are distributed among these distances:
12 10 0.14
13 1 0.01
14 16 0.23
15 3 0.04
16 12 0.17
17 11 0.16
18 16 0.23
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:6390319 original size:25 final size:26
Alignment explanation
Indices: 6390285--6390404 Score: 69
Period size: 25 Copynumber: 4.8 Consensus size: 26
6390275 TTCACTTTTT
*
6390285 TTTTCATTCTTTCATTTTTTTTC-TC
1 TTTTCTTTCTTTCATTTTTTTTCATC
** *
6390310 TTTTCTTTCTTTTTTTCTTTTTTCCATA
1 TTTTCTTTCTTTCATT-TTTTTT-CATC
* *
6390338 TTTTCCATTT-TTTC--TATTTTTCATT
1 TTTT-C-TTTCTTTCATTTTTTTTCATC
*
6390363 TTTTATTTC-TT-A-TTTTTTTC-TC
1 TTTTCTTTCTTTCATTTTTTTTCATC
6390385 TTTT-TTCTCTTTCATTTTTT
1 TTTTCTT-TCTTTCATTTTTT
6390405 CTTGTTTTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
21 2 0.03
22 7 0.09
23 14 0.19
24 1 0.01
25 25 0.34
26 11 0.15
27 2 0.03
28 5 0.07
29 4 0.05
30 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTCTTTCTTTCATTTTTTTTCATC
Found at i:6390341 original size:19 final size:18
Alignment explanation
Indices: 6390281--6390391 Score: 57
Period size: 19 Copynumber: 5.9 Consensus size: 18
6390271 CATTTTCACT
*
6390281 TTTTTTTTCATTCTTT-CA
1 TTTTTTTTC-TTTTTTCCA
* **
6390299 TTTTTTTTCTCTTTTCTT
1 TTTTTTTTCTTTTTTCCA
6390317 TCTTTTTTTCTTTTTTCCA
1 T-TTTTTTTCTTTTTTCCA
* * *
6390336 -TATTTTCCATTTTTTCTA
1 TTTTTTTTC-TTTTTTCCA
*
6390354 TTTTTCATTT-TTTATTTCTTA
1 TTTTT--TTTCTTT-TTTC-CA
6390375 TTTTTTTCTCTTTTTTC
1 TTTTTTT-TCTTTTTTC
6390392 TCTTTCATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
17 10 0.14
18 18 0.25
19 22 0.31
20 9 0.13
21 12 0.17
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTCCA
Found at i:6390393 original size:9 final size:8
Alignment explanation
Indices: 6390301--6390413 Score: 61
Period size: 8 Copynumber: 14.0 Consensus size: 8
6390291 TTCTTTCATT
6390301 TTTTTTCTC
1 TTTTTT-TC
6390310 TTTTCTTTC
1 TTTT-TTTC
6390319 TTTTTTTC
1 TTTTTTTC
*
6390327 TTTTTTCC
1 TTTTTTTC
* *
6390335 ATATTTTCC
1 -TTTTTTTC
*
6390344 ATTTTTTC
1 TTTTTTTC
*
6390352 TATTTTTC
1 TTTTTTTC
*
6390360 ATTTTTT-
1 TTTTTTTC
* * *
6390367 ATTTCTTA
1 TTTTTTTC
6390375 TTTTTTTC
1 TTTTTTTC
6390383 TCTTTTTTC
1 T-TTTTTTC
*
6390392 --TCTTTC
1 TTTTTTTC
*
6390398 ATTTTTTC
1 TTTTTTTC
*
6390406 TTGTTTTC
1 TTTTTTTC
6390414 ATTCATTAGT
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
6 5 0.06
7 6 0.07
8 44 0.54
9 24 0.30
10 2 0.02
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTTTTTC
Found at i:6395300 original size:187 final size:188
Alignment explanation
Indices: 6395071--6395430 Score: 421
Period size: 187 Copynumber: 1.9 Consensus size: 188
6395061 ATAATATGAC
* * * * * * *
6395071 AATTATTTTTCTTGAAATTTTATTTAAATTTTTTCATCATTT-GAGATAAATTTA-A-AGAAATT
1 AATTATTGTTATTGAAACTTTATCTAAATTATTCCATCATTTGGA-ACAAATTTAGATA-AAATT
* * *
6395133 TCTCACCTAGAAA-TTTATTCAAAAATTTACCATTTGAAATTTTAAAAAATCTCATCATTGGATA
64 TCTCACCAAAAAATTTTA-T-AAAAATTTACCATTTAAAATTTTAAAAAATCTCATCATTGGATA
*
6395197 ATT-ATCACATATTTTCAACCAAA-ATTTTA-TTTTATTTTAT-TTTTTATTGAAAATAAATATT
127 ATTAAT-ACATATTCTCAA--AAATATTTTATTTTTATTTTATATTTTTATTGAAAATAAATATT
*
6395258 AATTATTGTTATTGAAACTTTATCTAAATTATTCCATCATTTGGAACAAATTTAGATAAAATTTT
1 AATTATTGTTATTGAAACTTTATCTAAATTATTCCATCATTTGGAACAAATTTAGATAAAATTTC
* * * * * *
6395323 TCATCAAAAAATTTTATAAAAATTTACCATTTAAAATTTTTATAAATTTTATTATTGGATAATTA
66 TCACCAAAAAATTTTATAAAAATTTACCATTTAAAATTTTAAAAAATCTCATCATTGGATAATTA
*
6395388 ATACTTATTCTCAAAAATATTTTATTTTTTATTTTATATTTTT
131 ATACATATTCTCAAAAATATTTTA-TTTTTATTTTATATTTTT
6395431 TAAATTTTTT
Statistics
Matches: 145, Mismatches: 19, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
185 3 0.02
186 6 0.04
187 95 0.66
188 31 0.21
189 10 0.07
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (188 bp):
AATTATTGTTATTGAAACTTTATCTAAATTATTCCATCATTTGGAACAAATTTAGATAAAATTTC
TCACCAAAAAATTTTATAAAAATTTACCATTTAAAATTTTAAAAAATCTCATCATTGGATAATTA
ATACATATTCTCAAAAATATTTTATTTTTATTTTATATTTTTATTGAAAATAAATATT
Found at i:6396676 original size:17 final size:16
Alignment explanation
Indices: 6396656--6396699 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
6396646 ACAATTATTG
*
6396656 ATTTAAATTTAAATTTT
1 ATTTAAATTTAAA-TAT
*
6396673 ATTTTAATTTAAATAT
1 ATTTAAATTTAAATAT
*
6396689 ATCTAAATTTA
1 ATTTAAATTTA
6396700 TTTTTTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAAATTTAAATAT
Found at i:6396828 original size:13 final size:13
Alignment explanation
Indices: 6396812--6396836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6396802 TATGTTAAGT
6396812 ATAGATAAATTAA
1 ATAGATAAATTAA
6396825 ATAGATAAATTA
1 ATAGATAAATTA
6396837 TTTTAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
ATAGATAAATTAA
Found at i:6398915 original size:30 final size:30
Alignment explanation
Indices: 6398860--6398916 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
6398850 ATAATGCATA
6398860 AATTTAATTTTTTAATGATTCAAAATAAAT
1 AATTTAATTTTTTAATGATTCAAAATAAAT
6398890 AATTTATACTTTTTTAAT-ATT-AAAATA
1 AATTTA-A-TTTTTTAATGATTCAAAATA
6398917 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
30 12 0.48
31 4 0.16
32 9 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (30 bp):
AATTTAATTTTTTAATGATTCAAAATAAAT
Found at i:6398920 original size:32 final size:30
Alignment explanation
Indices: 6398860--6398920 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
6398850 ATAATGCATA
*
6398860 AATTTAATTTTTTAATGATTCAAAATAAAT
1 AATTTAATTTTTTAATGATTAAAAATAAAT
6398890 AATTTATACTTTTTTAAT-ATTAAAATATAAA
1 AATTTA-A-TTTTTTAATGATTAAAA-ATAAA
6398921 ATAAAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
31 7 0.26
32 14 0.52
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
AATTTAATTTTTTAATGATTAAAAATAAAT
Found at i:6399242 original size:33 final size:33
Alignment explanation
Indices: 6399199--6399263 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
6399189 AATCACTTTT
* *
6399199 AATTAATTAAATTTATAAATATTGTAAATTTATA
1 AATTAATTAAATTCATAAATAAT-TAAATTTATA
6399233 AATT-ATTAAATTCATAAATAATTAAATTTAT
1 AATTAATTAAATTCATAAATAATTAAATTTAT
6399264 GTAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.31
33 16 0.55
34 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (33 bp):
AATTAATTAAATTCATAAATAATTAAATTTATA
Found at i:6399244 original size:16 final size:16
Alignment explanation
Indices: 6399199--6399263 Score: 78
Period size: 16 Copynumber: 3.9 Consensus size: 16
6399189 AATCACTTTT
6399199 AATTAATTAAATTTATA
1 AATT-ATTAAATTTATA
6399216 AA-TATTGTAAATTTATA
1 AATTA-T-TAAATTTATA
*
6399233 AATTATTAAATTCATA
1 AATTATTAAATTTATA
*
6399249 AATAATTAAATTTAT
1 AATTATTAAATTTAT
6399264 GTAATATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 1 0.02
16 24 0.57
17 15 0.36
18 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTATTAAATTTATA
Found at i:6414560 original size:20 final size:20
Alignment explanation
Indices: 6414523--6414561 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6414513 TTGTAACTTA
** *
6414523 GCTTTGGCTTCTTTGCTGCC
1 GCTTTGGCGGCTTGGCTGCC
6414543 GCTTTGGCGGCTTGGCTGC
1 GCTTTGGCGGCTTGGCTGC
6414562 TATAAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.28, G:0.33, T:0.38
Consensus pattern (20 bp):
GCTTTGGCGGCTTGGCTGCC
Found at i:6416764 original size:13 final size:13
Alignment explanation
Indices: 6416746--6416772 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6416736 ATTAAGGATG
6416746 AACTTTATAACAA
1 AACTTTATAACAA
6416759 AACTTTATAACAA
1 AACTTTATAACAA
6416772 A
1 A
6416773 TGTCATAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AACTTTATAACAA
Found at i:6426731 original size:18 final size:19
Alignment explanation
Indices: 6426695--6426737 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6426685 TAGTTAATTG
*
6426695 TTATTTTTTTTAATTTA-T
1 TTATTTTTTTTAATATATT
6426713 TTATTTATTTTT-ATATATT
1 TTATTT-TTTTTAATATATT
6426732 TTATTT
1 TTATTT
6426738 GTCTTAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
TTATTTTTTTTAATATATT
Found at i:6432821 original size:21 final size:22
Alignment explanation
Indices: 6432796--6432836 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6432786 AAAATGTTGG
*
6432796 AAAAGGTTA-GGAAGAAAAAGA
1 AAAAGGTTAGGGAAAAAAAAGA
6432817 AAAAGGTTAGGGAAAAAAAA
1 AAAAGGTTAGGGAAAAAAAA
6432837 AGTGAGCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (22 bp):
AAAAGGTTAGGGAAAAAAAAGA
Found at i:6435547 original size:27 final size:27
Alignment explanation
Indices: 6435505--6435588 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 27
6435495 TGAGTATAAG
*
6435505 TAAATGATTCGATGAATTTTGGAGTAGT
1 TAAA-GATTCAATGAATTTTGGAGTAGT
* * *
6435533 TAAAGTTTCAATGAATTTT-GAGGAAT
1 TAAAGATTCAATGAATTTTGGAGTAGT
* * *
6435559 CAATGATTCAATGGATTCTTGGAGTAGT
1 TAAAGATTCAATGAATT-TTGGAGTAGT
6435587 TA
1 TA
6435589 TTTTGTTGAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
26 18 0.42
27 15 0.35
28 10 0.23
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (27 bp):
TAAAGATTCAATGAATTTTGGAGTAGT
Found at i:6436409 original size:28 final size:28
Alignment explanation
Indices: 6436369--6436449 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
6436359 TTTGGTTAAG
6436369 AATGATTGTTTGAAATCTTATAAGTGCA
1 AATGATTGTTTGAAATCTTATAAGTGCA
* * * *
6436397 AATGATTGTTTG-AATTTTACAAGGGTA
1 AATGATTGTTTGAAATCTTATAAGTGCA
* *
6436424 AAAGATTGGTTGAAATCTTATAAGTG
1 AATGATTGTTTGAAATCTTATAAGTG
6436450 ATGATTTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
27 21 0.49
28 22 0.51
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (28 bp):
AATGATTGTTTGAAATCTTATAAGTGCA
Found at i:6439166 original size:19 final size:16
Alignment explanation
Indices: 6439127--6439159 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6439117 AACGATTTGA
6439127 ATGATAATGACGATTT
1 ATGATAATGACGATTT
*
6439143 ATGATAATGATGATTT
1 ATGATAATGACGATTT
6439159 A
1 A
6439160 CGATGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (16 bp):
ATGATAATGACGATTT
Found at i:6441487 original size:12 final size:12
Alignment explanation
Indices: 6441470--6441494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6441460 CTTAATATAG
6441470 AAATAATGAAAC
1 AAATAATGAAAC
6441482 AAATAATGAAAC
1 AAATAATGAAAC
6441494 A
1 A
6441495 TAAACTGTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
AAATAATGAAAC
Found at i:6444655 original size:22 final size:22
Alignment explanation
Indices: 6444606--6444656 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6444596 ATACTACGCT
*
6444606 TAAAAAAAAAGAAAAAAATGAA
1 TAAAAAAAAAGAAAAAAATAAA
* * **
6444628 TGAAAAAAAAGAAAGATTTAAA
1 TAAAAAAAAAGAAAAAAATAAA
6444650 TAAAAAA
1 TAAAAAA
6444657 TCTAAAATGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (22 bp):
TAAAAAAAAAGAAAAAAATAAA
Found at i:6445788 original size:44 final size:45
Alignment explanation
Indices: 6445707--6445800 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 45
6445697 GAACCTTTTA
* *
6445707 TAAAATGTTGTTAAGTCTCTATTGAGAGAAGCATTTTATATGTTT
1 TAAAATGTTGTTAAGCCTCAATTGAGAGAAGCATTTTATATGTTT
* * * *
6445752 TAAAA-GTTGTTAAGCCTCAATTGTGTGGAGCTTTTTATATGTTT
1 TAAAATGTTGTTAAGCCTCAATTGAGAGAAGCATTTTATATGTTT
*
6445796 AAAAA
1 TAAAA
6445801 ATTATTGAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 37 0.88
45 5 0.12
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (45 bp):
TAAAATGTTGTTAAGCCTCAATTGAGAGAAGCATTTTATATGTTT
Found at i:6446179 original size:2 final size:2
Alignment explanation
Indices: 6446172--6446203 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6446162 ATAAAAAGAC
6446172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6446204 AACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6446800 original size:24 final size:22
Alignment explanation
Indices: 6446767--6446844 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 22
6446757 TTTAACTTCT
*
6446767 ATGTTATTTTATAATTGATTTTA
1 ATGTTATTTT-TAATTAATTTTA
* *
6446790 ATTGTTATTTTTCAATTTA-GTTA
1 A-TGTTATTTTT-AATTAATTTTA
6446813 ATGTTATTTTTTAATTAA-TTT-
1 ATGTTA-TTTTTAATTAATTTTA
6446834 AT-TTATTTTTA
1 ATGTTATTTTTA
6446845 TATATTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
19 6 0.12
20 3 0.06
21 2 0.04
22 12 0.25
23 11 0.23
24 14 0.29
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.64
Consensus pattern (22 bp):
ATGTTATTTTTAATTAATTTTA
Found at i:6449453 original size:25 final size:26
Alignment explanation
Indices: 6449425--6449474 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
6449415 AAACTTTCAT
*
6449425 TAGAAGACATA-AAGGAAAAAAAAAA
1 TAGAAAACATACAAGGAAAAAAAAAA
6449450 TAGAAAACATACTAAGGAAAAAAAA
1 TAGAAAACATAC-AAGGAAAAAAAA
6449475 GGAAAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
27 12 0.55
ACGTcount: A:0.70, C:0.06, G:0.14, T:0.10
Consensus pattern (26 bp):
TAGAAAACATACAAGGAAAAAAAAAA
Found at i:6466436 original size:15 final size:15
Alignment explanation
Indices: 6466398--6466436 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6466388 TAAAATTAAA
6466398 AATAATAATTATGGT
1 AATAATAATTATGGT
* * *
6466413 GATATTAATTATTGT
1 AATAATAATTATGGT
6466428 AATAATAAT
1 AATAATAAT
6466437 ATTATATGTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (15 bp):
AATAATAATTATGGT
Found at i:6468057 original size:9 final size:9
Alignment explanation
Indices: 6468043--6468069 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6468033 ACCCAAAAAC
6468043 AAGAGTAAA
1 AAGAGTAAA
6468052 AAGAGTAAA
1 AAGAGTAAA
6468061 AAGAGTAAA
1 AAGAGTAAA
6468070 GATAAGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (9 bp):
AAGAGTAAA
Found at i:6468276 original size:2 final size:2
Alignment explanation
Indices: 6468269--6468305 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6468259 TCCTTACGTT
6468269 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6468306 GCGACTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6471364 original size:21 final size:21
Alignment explanation
Indices: 6471338--6471394 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
6471328 GAAAGAAAGT
**
6471338 TTGAAAAGAAGAAGCTGGGGG
1 TTGAAAAGAAGAAGCTGAAGG
*
6471359 TTGAAAGAGAGGAA-CTGAAGG
1 TTGAAA-AGAAGAAGCTGAAGG
*
6471380 TT-AAAAGAAGGAGCT
1 TTGAAAAGAAGAAGCT
6471395 ACGGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 5 0.17
20 5 0.17
21 13 0.45
22 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.37, T:0.16
Consensus pattern (21 bp):
TTGAAAAGAAGAAGCTGAAGG
Found at i:6475539 original size:2 final size:2
Alignment explanation
Indices: 6475532--6475559 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6475522 ATCTGAAGGA
6475532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6475560 GTCAAATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6476163 original size:22 final size:23
Alignment explanation
Indices: 6476138--6476203 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 23
6476128 ATTTGAGATT
*
6476138 TTTAAATT-TTAAAACATATATA
1 TTTAAATTATTAAAAAATATATA
*
6476160 TTTAGATTATTAATAAAAAATATATA
1 TTTA-A--ATTATTAAAAAATATATA
6476186 TTTAAATTATTAAAAAAT
1 TTTAAATTATTAAAAAAT
6476204 TCATTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.11
23 13 0.35
25 4 0.11
26 16 0.43
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTAAATTATTAAAAAATATATA
Found at i:6476177 original size:26 final size:26
Alignment explanation
Indices: 6476147--6476202 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
6476137 TTTTAAATTT
* *
6476147 TAAAACATATATATTTAGATTATTAA
1 TAAAAAATATATATTTAAATTATTAA
6476173 TAAAAAATATATATTTAAATTATTAA
1 TAAAAAATATATATTTAAATTATTAA
6476199 -AAAA
1 TAAAA
6476203 TTCATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAAAAATATATATTTAAATTATTAA
Found at i:6485883 original size:5 final size:5
Alignment explanation
Indices: 6485875--6485922 Score: 53
Period size: 5 Copynumber: 9.0 Consensus size: 5
6485865 ATATAATAAA
6485875 TTATT TTATT TTATT TTATTT TTATTT TTATT TT-TT TAATATT TTATT
1 TTATT TTATT TTATT TTA-TT TTA-TT TTATT TTATT T--TATT TTATT
6485923 GTATGAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 3 0.08
5 21 0.54
6 12 0.31
7 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:6485899 original size:6 final size:6
Alignment explanation
Indices: 6485878--6485909 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6485868 TAATAAATTA
6485878 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
6485910 TTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:6485899 original size:16 final size:15
Alignment explanation
Indices: 6485878--6485922 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
6485868 TAATAAATTA
6485878 TTTTATTTTATTTTAT
1 TTTTATTTTATTTT-T
6485894 TTTTATTTTTATTTTT
1 TTTTA-TTTTATTTTT
*
6485910 TTAATATTTTATT
1 TT-TTATTTTATT
6485923 GTATGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTTTT
Found at i:6485917 original size:17 final size:17
Alignment explanation
Indices: 6485875--6485919 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
6485865 ATATAATAAA
6485875 TTATTT-TA-TTTTATT
1 TTATTTATATTTTTATT
*
6485890 TTATTTTTATTTTTATT
1 TTATTTATATTTTTATT
6485907 TT-TTTAATATTTT
1 TTATTT-ATATTTT
6485920 ATTGTATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 15 0.58
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATTTATATTTTTATT
Found at i:6489799 original size:26 final size:27
Alignment explanation
Indices: 6489743--6489801 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
6489733 AATTAAAACT
* * * *
6489743 AATATATTTTTATTTAAAAAGTATATT
1 AATATATATTTATTAAAAAAGTACATA
*
6489770 AATATATATTTA-TAAAAAATTACATA
1 AATATATATTTATTAAAAAAGTACATA
6489796 AATATA
1 AATATA
6489802 CAAAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
AATATATATTTATTAAAAAAGTACATA
Found at i:6489956 original size:37 final size:38
Alignment explanation
Indices: 6489914--6489986 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
6489904 GAGATAGGGA
6489914 TAAATTTGAAATACCCATAAAATATGGGTAT-AAAATG
1 TAAATTTGAAATACCCATAAAATATGGGTATGAAAATG
* *
6489951 TAAATTTGAAATACCCGTAAGATATGGGTATGAAAA
1 TAAATTTGAAATACCCATAAAATATGGGTATGAAAA
6489987 AAATATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (38 bp):
TAAATTTGAAATACCCATAAAATATGGGTATGAAAATG
Found at i:6500276 original size:152 final size:152
Alignment explanation
Indices: 6500000--6500450 Score: 805
Period size: 152 Copynumber: 3.0 Consensus size: 152
6499990 TTTACCAAGT
* *
6500000 AATTAGTTGTTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* *
6500065 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
6500130 TAAAGAAAAAACAAAATCATCC
131 TAAAGAAAAAACAAAATCATCC
*
6500152 AATTAATTATTGGAAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
6500217 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
6500282 TAAA-AAAAATACAAAATCATCC
131 TAAAGAAAAA-ACAAAATCATCC
6500304 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* *
6500369 CTCACCTCAAGAGTATACAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
*
6500434 TAAAGGAAAAAAAAAAA
131 TAAA-GAAAAAACAAAA
6500451 AGAAAAAAAA
Statistics
Matches: 287, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
151 5 0.02
152 272 0.95
153 5 0.02
154 5 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (152 bp):
AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
TAAAGAAAAAACAAAATCATCC
Found at i:6500468 original size:15 final size:13
Alignment explanation
Indices: 6500439--6500507 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
6500429 TTAATTAAAG
6500439 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
6500452 GAAAAAAAAAATCAA
1 GAAAAAAAAAA--AA
** **
6500467 GATCAAAATCAAA
1 GAAAAAAAAAAAA
6500480 GTCAAATAAAAAAAAA
1 G--AAA-AAAAAAAAA
6500496 -AAAAAAAAAAAA
1 GAAAAAAAAAAAA
6500508 AACCTGGAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
12 9 0.21
13 17 0.40
15 10 0.23
16 7 0.16
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.07
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:6500804 original size:20 final size:20
Alignment explanation
Indices: 6500779--6500827 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
6500769 CGGTGGGATT
* *
6500779 TCGCCGGATTCTGGAAATTC
1 TCGCCGGAATCTGGAAAATC
6500799 TCGCCGGAATCTGGAAAATC
1 TCGCCGGAATCTGGAAAATC
6500819 TCGCCGGAA
1 TCGCCGGAA
6500828 GTTCGCCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (20 bp):
TCGCCGGAATCTGGAAAATC
Found at i:6501016 original size:25 final size:25
Alignment explanation
Indices: 6500969--6501022 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
6500959 AATCTGGAAA
6500969 TTTCCCAGAAATTTCCAGAAAATTT
1 TTTCCCAGAAATTTCCAGAAAATTT
*
6500994 TTTCGCCAGAAATTTCTAG-AAATTT
1 TTTC-CCAGAAATTTCCAGAAAATTT
6501019 TTTC
1 TTTC
6501023 TCACTCCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (25 bp):
TTTCCCAGAAATTTCCAGAAAATTT
Found at i:6501411 original size:14 final size:14
Alignment explanation
Indices: 6501388--6501496 Score: 51
Period size: 14 Copynumber: 7.2 Consensus size: 14
6501378 AAAGAAAAGA
6501388 AAAAATAAATAAAT
1 AAAAATAAATAAAT
6501402 AAATAA-AAATAAAAT
1 AAA-AATAAAT-AAAT
*
6501417 AATAAT-AATATAAT
1 AAAAATAAATA-AAT
*
6501431 AATAAATATATAACTAT
1 AA-AAATAAATAA--AT
*
6501448 ATAAATAAAATACATAT
1 AAAAAT-AAATA-A-AT
** * *
6501465 AAATCTAATCTGAAT
1 AAAAATAA-ATAAAT
6501480 AAAAATAAATAAAT
1 AAAAATAAATAAAT
6501494 AAA
1 AAA
6501497 TAAAGATATA
Statistics
Matches: 70, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
13 1 0.01
14 24 0.34
15 20 0.29
16 10 0.14
17 14 0.20
18 1 0.01
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.28
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:6501422 original size:3 final size:3
Alignment explanation
Indices: 6501403--6501536 Score: 52
Period size: 3 Copynumber: 43.3 Consensus size: 3
6501393 TAAATAAATA
*
6501403 AAT AAA AAT AA- AAT AAT AAT AAT -AT AAT AAT AAAT ATAT AACT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA-T A-AT
* * *
6501450 AAAT AA- AAT ACAT -AT AA- ATCT AAT -CT GAAT AAA AAT AAAT AAAT
1 -AAT AAT AAT A-AT AAT AAT A-AT AAT AAT -AAT AAT AAT -AAT -AAT
6501494 AAAT AA- AGAT -AT ACAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 -AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6501537 CATAGAATAC
Statistics
Matches: 103, Mismatches: 8, Indels: 40
0.68 0.05 0.26
Matches are distributed among these distances:
2 15 0.15
3 57 0.55
4 29 0.28
5 2 0.02
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:6501429 original size:22 final size:22
Alignment explanation
Indices: 6501389--6501459 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
6501379 AAGAAAAGAA
6501389 AAAATAAATAAATAA-ATAAAAAT
1 AAAAT-AAT-AATAATATAAAAAT
*
6501412 AAAATAATAATAATATAATAAT
1 AAAATAATAATAATATAAAAAT
*
6501434 -AAAT-AT-ATAACTATATAAAT
1 AAAATAATAATAA-TATAAAAAT
6501454 AAAATA
1 AAAATA
6501460 CATATAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.10
20 9 0.22
21 13 0.32
22 10 0.24
23 5 0.12
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAATAATAATATAAAAAT
Found at i:6501443 original size:11 final size:12
Alignment explanation
Indices: 6501390--6501440 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
6501380 AGAAAAGAAA
6501390 AAATA-AATAAAT
1 AAATATAAT-AAT
6501402 AAATA-AA-AAT
1 AAATATAATAAT
6501412 AAA-ATAATAAT
1 AAATATAATAAT
6501423 -AATATAATAAT
1 AAATATAATAAT
6501434 AAATATA
1 AAATATA
6501441 TAACTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.03
10 10 0.29
11 11 0.31
12 13 0.37
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:6501529 original size:48 final size:47
Alignment explanation
Indices: 6501388--6501529 Score: 136
Period size: 48 Copynumber: 3.0 Consensus size: 47
6501378 AAAGAAAAGA
*
6501388 AAAAATAAATAAATAAATAAAA-ATAAAATAATAATAAT-ATAATAAT
1 AAAAATAAATAAATAAATAAAATAT-ACATAATAATAATAATAATAAT
* * * *
6501434 AAATATATAACTATATAAAT-AAA-ATACAT-ATAA-ATCTAAT-CTGAAT
1 AAA-A-ATAAATAAATAAATAAAATATACATAATAATA-ATAATAAT-AAT
6501480 AAAAATAAATAAATAAATAAAGATATACATAATAATAATAATAATAAT
1 AAAAATAAATAAATAAATAAA-ATATACATAATAATAATAATAATAAT
6501528 AA
1 AA
6501530 TAAAATACAT
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
44 13 0.17
45 9 0.12
46 15 0.20
47 12 0.16
48 25 0.33
49 2 0.03
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (47 bp):
AAAAATAAATAAATAAATAAAATATACATAATAATAATAATAATAAT
Found at i:6501733 original size:1 final size:1
Alignment explanation
Indices: 6501729--6501840 Score: 62
Period size: 1 Copynumber: 112.0 Consensus size: 1
6501719 CATTTTTTGA
* * * ** ** ** ** *
6501729 TTTTTTTTATTTTTGTTTTTATTTTTTTGATTTTTTTGATTTTTTTGATTTTTTTGATTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * *
6501794 ATTTTTTTGATTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6501841 GCTGAAGCTC
Statistics
Matches: 81, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.07, C:0.00, G:0.09, T:0.84
Consensus pattern (1 bp):
T
Found at i:6501836 original size:9 final size:9
Alignment explanation
Indices: 6501721--6501835 Score: 162
Period size: 9 Copynumber: 12.7 Consensus size: 9
6501711 CAACTCAACA
6501721 TTTTTTGAT
1 TTTTTTGAT
*
6501730 TTTTTTTATTT
1 TTTTTTGA--T
*
6501741 TTGTTTTTAT
1 TT-TTTTGAT
6501751 TTTTTTGAT
1 TTTTTTGAT
6501760 TTTTTTGAT
1 TTTTTTGAT
6501769 TTTTTTGAT
1 TTTTTTGAT
6501778 TTTTTTGAT
1 TTTTTTGAT
6501787 TTTTTTGAT
1 TTTTTTGAT
6501796 TTTTTTGAT
1 TTTTTTGAT
*
6501805 TTTTTTGTT
1 TTTTTTGAT
6501814 TTTTTTG-T
1 TTTTTTGAT
6501822 TTTTTTG-T
1 TTTTTTGAT
6501830 TTTTTT
1 TTTTTT
6501836 TTTTTGCTGA
Statistics
Matches: 100, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
8 15 0.15
9 73 0.73
10 3 0.03
11 3 0.03
12 6 0.06
ACGTcount: A:0.08, C:0.00, G:0.10, T:0.83
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:6501971 original size:41 final size:41
Alignment explanation
Indices: 6501847--6502334 Score: 692
Period size: 41 Copynumber: 12.0 Consensus size: 41
6501837 TTTTGCTGAA
6501847 GCTCCTCTAAACAGA-G-ACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGTAC-C-ACGAC-TTTGAAAAGTAAATT
* * * *
6501888 GCTCCTCTAAACAGAGG--CAATGGACTTTGGAAAGTAACTT
1 GCTCCTCTAAACAGAGGTACCA-CGACTTTGAAAAGTAAATT
*
6501928 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
* *
6501969 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
*
6502010 GCTCCTCTAAACAGAGG--CAACGGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCAC-GACTTTGAAAAGTAAATT
*
6502050 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
*
6502091 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
*
6502132 GCTCCTCTAAACAGAGG--CAACGGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCAC-GACTTTGAAAAGTAAATT
*
6502172 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
*
6502213 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTG-AAAAGTAAATT
6502255 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
* *
6502296 GCTCCTCTAAACAGAGG--CAACGAACTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGTACCACG-ACTTTGAAAAGTAAAT
6502335 ACTCCTAGAC
Statistics
Matches: 414, Mismatches: 20, Indels: 27
0.90 0.04 0.06
Matches are distributed among these distances:
39 15 0.04
40 111 0.27
41 239 0.58
42 49 0.12
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
Found at i:6501982 original size:81 final size:80
Alignment explanation
Indices: 6501847--6502334 Score: 698
Period size: 81 Copynumber: 6.0 Consensus size: 80
6501837 TTTTGCTGAA
6501847 GCTCCTCTAAACAGA-G-ACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAAT
1 GCTCCTCTAAACAGAGGTAC-C-ACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAA-
* * *
6501909 GGACTTTGGAAAGTAACTT
62 CGACTTTGAAAAGTAAATT
* *
6501928 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
6501993 ACTTTGAAAAGTAAATT
64 ACTTTGAAAAGTAAATT
* * *
6502010 GCTCCTCTAAACAGAGG--CAACGGACTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGTACCAC-GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAAC
6502073 GACTTTGAAAAGTAAATT
63 GACTTTGAAAAGTAAATT
*
6502091 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAAC-GA
6502156 CTTTGAAAAGTAAATT
65 CTTTGAAAAGTAAATT
* * *
6502172 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACG
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAACG
6502237 ACTTTGAAAAAGTAAATT
64 ACTTTG-AAAAGTAAATT
6502255 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-A
*
6502320 CTTGGAAAAGTAAAT
65 CTTTGAAAAGTAAAT
6502335 ACTCCTAGAC
Statistics
Matches: 374, Mismatches: 18, Indels: 30
0.89 0.04 0.07
Matches are distributed among these distances:
80 10 0.03
81 207 0.55
82 80 0.21
83 77 0.21
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (80 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
TTTGAAAAGTAAATT
Found at i:6502064 original size:122 final size:122
Alignment explanation
Indices: 6501847--6502334 Score: 786
Period size: 122 Copynumber: 4.0 Consensus size: 122
6501837 TTTTGCTGAA
* * * * *
6501847 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAATGG
1 GCTCCTCTCAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
* *
6501911 ACTTTGGAAAGTAACTTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
65 ACTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
6501969 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
6502034 CTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
66 CTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
*
6502091 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
1 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
6502156 CTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
66 CTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
* *
6502213 GCTCCTCTCAACAGAGGTACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
1 GCTCCTCTCAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGG--CAAC
* * *
6502278 -GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAACGAACTTGGAAAAGTAAAT
63 GGACTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACG-ACTTTGAAAAGTAAAT
6502335 ACTCCTAGAC
Statistics
Matches: 349, Mismatches: 12, Indels: 9
0.94 0.03 0.02
Matches are distributed among these distances:
121 4 0.01
122 265 0.76
123 43 0.12
124 34 0.10
125 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (122 bp):
GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGA
CTTTGAAAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGAAAAGTAAATT
Found at i:6503577 original size:6 final size:6
Alignment explanation
Indices: 6503553--6503592 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
6503543 ATTTTTTCAT
6503553 TTTTTC TTCTTTC --TTTC TTTTTC TTTTTC TTTTT- TTTTTC
1 TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
6503593 ATCATCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.13
5 5 0.17
6 17 0.57
7 4 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:6503586 original size:7 final size:7
Alignment explanation
Indices: 6503526--6503591 Score: 62
Period size: 8 Copynumber: 8.9 Consensus size: 7
6503516 AATTCGGATC
6503526 TCTTTTT
1 TCTTTTT
6503533 TCATTTTT
1 TC-TTTTT
6503541 TCATTTTT
1 TC-TTTTT
6503549 TCATTTTT
1 TC-TTTTT
*
6503557 TCTTCTT
1 TCTTTTT
6503564 TCTTTCTT
1 TCTTT-TT
*
6503572 TTTCTTTT
1 TCT-TTTT
6503580 TCTTTTT
1 TCTTTTT
6503587 T-TTTT
1 TCTTTT
6503592 CATCATCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
6 4 0.08
7 15 0.29
8 31 0.60
9 2 0.04
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:6507625 original size:160 final size:160
Alignment explanation
Indices: 6507233--6507711 Score: 786
Period size: 156 Copynumber: 3.0 Consensus size: 160
6507223 TTAAAATTTT
* * * *
6507233 ACCAAGTAGTTAGTTGTTGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
*
6507298 AAATTCCCTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
* *
6507363 GATTATTTAAAG----AAAAATCAAGATCA
131 GATTAATTAAAGAAAAAAAAATCAAAATCA
*
6507389 ACCAATTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
6507454 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
6507519 GATTAATTAAAGAAAAAAAAATCAAAATCA
131 GATTAATTAAAGAAAAAAAAATCAAAATCA
* *
6507549 GCCAAGTAATTAATTATCGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
* *
6507614 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTC
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTC
**
6507679 GGATTAATTAAAGAAAAAAGAAAAAAAAATCA
130 GGATTAATTAAAGAAAAAA-AAATCAAAATCA
6507711 A
1 A
6507712 GATCAAAATC
Statistics
Matches: 301, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
156 135 0.45
160 114 0.38
161 42 0.14
162 10 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (160 bp):
ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
GATTAATTAAAGAAAAAAAAATCAAAATCA
Found at i:6507746 original size:1 final size:1
Alignment explanation
Indices: 6507742--6507770 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
6507732 AAAAAAATTC
6507742 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6507771 CCTGGAGCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6508544 original size:12 final size:12
Alignment explanation
Indices: 6508527--6508560 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
6508517 CTAGCCCTCC
6508527 AAAATAAAAATT
1 AAAATAAAAATT
6508539 AAAAT-AAAATT
1 AAAATAAAAATT
*
6508550 AAAAAAAAAAT
1 AAAATAAAAAT
6508561 CTAGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:6508805 original size:13 final size:13
Alignment explanation
Indices: 6508787--6508811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6508777 CAAGAGAGAA
6508787 AAAAAATAAAAAT
1 AAAAAATAAAAAT
6508800 AAAAAATAAAAA
1 AAAAAATAAAAA
6508812 ATACGGGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:6508869 original size:20 final size:20
Alignment explanation
Indices: 6508847--6508911 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
6508837 TTGCCCATTT
* *
6508847 GGGCCAGGCCCAAATGATCT
1 GGGCCAGGCCCAATTGATCC
*
6508867 GGGTCAGGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
*
6508887 GGGTCAGGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
6508907 GGGCC
1 GGGCC
6508912 CGGACCTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (20 bp):
GGGCCAGGCCCAATTGATCC
Found at i:6514439 original size:33 final size:33
Alignment explanation
Indices: 6514402--6514467 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
6514392 TTTTATATAG
*
6514402 ACATTTTTAGTAAAAATGTTGATAGAATTTTTA
1 ACATTTTTAGTAAAAATATTGATAGAATTTTTA
6514435 ACATTTTTAGTAAAAATATTGATAGAATTTTTA
1 ACATTTTTAGTAAAAATATTGATAGAATTTTTA
6514468 CTATTGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (33 bp):
ACATTTTTAGTAAAAATATTGATAGAATTTTTA
Found at i:6519785 original size:16 final size:17
Alignment explanation
Indices: 6519764--6519798 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6519754 TTTTTTATAT
6519764 ATTTTTTT-AGAAAAAA
1 ATTTTTTTAAGAAAAAA
6519780 ATTTTTTTAAAGAAAAAA
1 ATTTTTTT-AAGAAAAAA
6519798 A
1 A
6519799 AAATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTTTTTTAAGAAAAAA
Found at i:6528828 original size:3 final size:3
Alignment explanation
Indices: 6528814--6528851 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
6528804 ATATAAAAAA
6528814 ATT ATT -TT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6528852 AGAATGAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:6533943 original size:29 final size:29
Alignment explanation
Indices: 6533908--6533977 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 29
6533898 TACGAAAATT
6533908 TAAATTTAAATTTTTTATTA-TAATTTATA
1 TAAATTTAAATTTTTTATTATTAATTTA-A
6533937 TAAATTT-AATTTTTTATTACTTTAATTTAA
1 TAAATTTAAATTTTTTATTA--TTAATTTAA
6533967 T-AATTTAAATT
1 TAAATTTAAATT
6533978 CAATTGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
28 12 0.32
29 12 0.32
30 6 0.16
31 7 0.19
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TAAATTTAAATTTTTTATTATTAATTTAA
Found at i:6534821 original size:21 final size:22
Alignment explanation
Indices: 6534797--6534842 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
6534787 CCCGAAATTA
*
6534797 ATAAAATATTA-TTTTTAAAAT
1 ATAAAAAATTATTTTTTAAAAT
6534818 ATAAAAAATTATTTTTTAAAAT
1 ATAAAAAATTATTTTTTAAAAT
6534840 ATA
1 ATA
6534843 TATTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAAAATTATTTTTTAAAAT
Found at i:6534876 original size:14 final size:14
Alignment explanation
Indices: 6534835--6534882 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6534825 ATTATTTTTT
*
6534835 AAAATATATATTTA
1 AAAATATATATATA
6534849 AAAATATCAT-TATA
1 AAAATAT-ATATATA
*
6534863 TAAATATATATATA
1 AAAATATATATATA
6534877 CAAAAT
1 -AAAAT
6534883 TAAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 20 0.71
15 6 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATATATATA
Found at i:6535213 original size:3 final size:3
Alignment explanation
Indices: 6535199--6535230 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6535189 TCAGATTTCG
*
6535199 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
6535231 GTTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:6541900 original size:2 final size:2
Alignment explanation
Indices: 6541890--6541939 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
6541880 TATATATATA
* *
6541890 GT GT AT GT GT GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6541932 GT GT GT GT
1 GT GT GT GT
6541940 ATTCCTCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.04, C:0.00, G:0.46, T:0.50
Consensus pattern (2 bp):
GT
Found at i:6542305 original size:38 final size:38
Alignment explanation
Indices: 6542254--6542329 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
6542244 TAGTCTTTTT
6542254 CAACATTTCTGAGTTGTTTTCATCTTTTATTCTTCTCA
1 CAACATTTCTGAGTTGTTTTCATCTTTTATTCTTCTCA
6542292 CAACATTTCTGAGTTGTTTTCATCTTTTATTCTTCTCA
1 CAACATTTCTGAGTTGTTTTCATCTTTTATTCTTCTCA
6542330 TAAACACTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.53
Consensus pattern (38 bp):
CAACATTTCTGAGTTGTTTTCATCTTTTATTCTTCTCA
Found at i:6543094 original size:22 final size:22
Alignment explanation
Indices: 6543066--6543109 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6543056 AACTAGATTT
6543066 TGAAGTTTATTTTTCTTTCATG
1 TGAAGTTTATTTTTCTTTCATG
6543088 TGAAGTTTATTTTTCTTTCATG
1 TGAAGTTTATTTTTCTTTCATG
6543110 CATACTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (22 bp):
TGAAGTTTATTTTTCTTTCATG
Found at i:6544535 original size:22 final size:20
Alignment explanation
Indices: 6544494--6544538 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
6544484 AAATTAAGAT
* *
6544494 AAAAAATAAACTAAATTTTA
1 AAAAAATAAACAAAAATTTA
6544514 AAAAAATAAACCAAAAAATTTA
1 AAAAAATAAA-C-AAAAATTTA
6544536 AAA
1 AAA
6544539 TAACAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAAATAAACAAAAATTTA
Found at i:6548873 original size:163 final size:163
Alignment explanation
Indices: 6548691--6549004 Score: 574
Period size: 163 Copynumber: 1.9 Consensus size: 163
6548681 TACTTTCATT
*
6548691 TTCTTTTCCTTTACTAATATTTATCCAAAAATAACATTAGATTTAGTAAAATGTCATTTCAACTT
1 TTCTTTTCCTTCACTAATATTTATCCAAAAATAACATTAGATTTAGTAAAATGTCATTTCAACTT
6548756 TAGTATTTATTCATTTCCATTAATATTTTAATGTTGTTAAAGAAAAAAATTAGAAGTTTAATAAA
66 TAGTATTTATTCATTTCCATTAATATTTTAATGTTGTTAAAGAAAAAAATTAGAAGTTTAATAAA
6548821 ACTCATTATAATATTAATAAAAATATTTTAATG
131 ACTCATTATAATATTAATAAAAATATTTTAATG
* * * *
6548854 TTCTTTTCCTTCACTAATATTTATCCAAACATGACATTAGGTTTAGTAAAATGTCCTTTCAACTT
1 TTCTTTTCCTTCACTAATATTTATCCAAAAATAACATTAGATTTAGTAAAATGTCATTTCAACTT
*
6548919 TAGTATTTATTCATTTCCATTAATATTTTAATGTTGTTATAGAAAAAAATTAGAAGTTTAATAAA
66 TAGTATTTATTCATTTCCATTAATATTTTAATGTTGTTAAAGAAAAAAATTAGAAGTTTAATAAA
6548984 ACTCATTATAATATTAATAAA
131 ACTCATTATAATATTAATAAA
6549005 TCAAATATTA
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 145 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (163 bp):
TTCTTTTCCTTCACTAATATTTATCCAAAAATAACATTAGATTTAGTAAAATGTCATTTCAACTT
TAGTATTTATTCATTTCCATTAATATTTTAATGTTGTTAAAGAAAAAAATTAGAAGTTTAATAAA
ACTCATTATAATATTAATAAAAATATTTTAATG
Found at i:6551384 original size:17 final size:17
Alignment explanation
Indices: 6551362--6551397 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6551352 AAATGTAAAT
* *
6551362 AACAAATTAATATATTC
1 AACAAATAAATAAATTC
6551379 AACAAATAAATAAATTC
1 AACAAATAAATAAATTC
6551396 AA
1 AA
6551398 TAAGGCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
AACAAATAAATAAATTC
Found at i:6552784 original size:6 final size:6
Alignment explanation
Indices: 6552773--6552810 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
6552763 AACTAAATCA
* *
6552773 AAAAAT AAAAAT AAAAAT AAAAAT -ATAAC AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
6552811 TTTATTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 3 0.11
6 24 0.89
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:6553679 original size:18 final size:17
Alignment explanation
Indices: 6553658--6553700 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
6553648 ATATAGAAAC
6553658 AAAAATTAGAAAAAAATT
1 AAAAATT-GAAAAAAATT
**
6553676 AAAAATTTTAAAAAATT
1 AAAAATTGAAAAAAATT
6553693 AAAGAATT
1 AAA-AATT
6553701 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
AAAAATTGAAAAAAATT
Found at i:6553688 original size:17 final size:18
Alignment explanation
Indices: 6553668--6553702 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6553658 AAAAATTAGA
6553668 AAAAAATTAAA-AATTTT
1 AAAAAATTAAAGAATTTT
6553685 AAAAAATTAAAGAATTTT
1 AAAAAATTAAAGAATTTT
6553703 TTAAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAAAATTAAAGAATTTT
Found at i:6553771 original size:29 final size:27
Alignment explanation
Indices: 6553739--6553802 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
6553729 AATGAACAAT
*
6553739 TAAAAAAATAAAAAATTTAATAAATTTAA
1 TAAAAAAAT-AAAAATATAA-AAATTTAA
*
6553768 TAAAAATATAAAAATATAAAAATTTAA
1 TAAAAAAATAAAAATATAAAAATTTAA
*
6553795 -AATAAAAT
1 TAAAAAAAT
6553803 TTTAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 6 0.19
27 8 0.26
28 9 0.29
29 8 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAAAAAATAAAAATATAAAAATTTAA
Found at i:6553772 original size:27 final size:26
Alignment explanation
Indices: 6553738--6553796 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
6553728 AAATGAACAA
*
6553738 TTAAAAAAATA-AAAAATTTAATAAAT
1 TTAAAAAAATATAAAAATATAA-AAAT
6553764 TTAATAAAAATATAAAAATATAAAAAT
1 TTAA-AAAAATATAAAAATATAAAAAT
6553791 TTAAAA
1 TTAAAA
6553797 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 6 0.20
27 15 0.50
28 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TTAAAAAAATATAAAAATATAAAAAT
Found at i:6553899 original size:20 final size:19
Alignment explanation
Indices: 6553854--6553963 Score: 61
Period size: 18 Copynumber: 5.8 Consensus size: 19
6553844 ATATGATAAG
*
6553854 TAAAAAAATATAGAAATTT
1 TAAAAAAATATAAAAATTT
** *
6553873 TGGAAAAATCTCAAAAATTT
1 TAAAAAAATAT-AAAAATTT
*
6553893 TAAAAAAAATTTACGAAAA--T
1 T-AAAAAAATATA--AAAATTT
*
6553913 T-AAAAAATCTAAAAA-TT
1 TAAAAAAATATAAAAATTT
*
6553930 TAATAAAAATA-AAAAA-AT
1 TAA-AAAAATATAAAAATTT
*
6553948 TCAAAAAATATAAAAA
1 TAAAAAAATATAAAAA
6553964 ATTAAAAAGG
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.06
17 9 0.12
18 23 0.32
19 14 0.19
20 11 0.15
21 7 0.10
22 4 0.06
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (19 bp):
TAAAAAAATATAAAAATTT
Found at i:6553927 original size:9 final size:8
Alignment explanation
Indices: 6553908--6553971 Score: 65
Period size: 9 Copynumber: 7.4 Consensus size: 8
6553898 AAAATTTACG
6553908 AAAATTAA
1 AAAATTAA
6553916 AAAATCTAA
1 AAAAT-TAA
*
6553925 AAATTTAATA
1 AAAATT-A-A
*
6553935 AAAATAAA
1 AAAATTAA
6553943 AAAATTCAA
1 AAAATT-AA
6553952 AAAATATAA
1 AAAAT-TAA
6553961 AAAATTAA
1 AAAATTAA
6553969 AAA
1 AAA
6553972 GGACAGACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
8 18 0.38
9 23 0.49
10 6 0.13
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATTAA
Found at i:6553932 original size:37 final size:36
Alignment explanation
Indices: 6553876--6553971 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
6553866 GAAATTTTGG
**
6553876 AAAAATCTCAAAAATTTTAAAAAAAATTTACGAAAATT-A
1 AAAAATCT-AAAAA-TTTAAAAAAAA--TAAAAAAATTCA
*
6553915 AAAAATCTAAAAATTTAATAAAAATAAAAAAATTCA
1 AAAAATCTAAAAATTTAAAAAAAATAAAAAAATTCA
* *
6553951 AAAAATATAAAAAATTAAAAA
1 AAAAATCTAAAAATTTAAAAA
6553972 GGACAGACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 8 0.16
36 19 0.38
37 10 0.20
38 5 0.10
39 8 0.16
ACGTcount: A:0.69, C:0.05, G:0.01, T:0.25
Consensus pattern (36 bp):
AAAAATCTAAAAATTTAAAAAAAATAAAAAAATTCA
Found at i:6553937 original size:26 final size:26
Alignment explanation
Indices: 6553896--6553971 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
6553886 AAAATTTTAA
*
6553896 AAAAAATTTACGAAAATTAAAAAA-TC
1 AAAAAATTTA-AAAAATTAAAAAATTC
* *
6553922 TAAAAATTTAATAAAAATAAAAAAATTC
1 AAAAAATTT-A-AAAAATTAAAAAATTC
*
6553950 AAAAAATATAAAAAATTAAAAA
1 AAAAAATTTAAAAAATTAAAAA
6553972 GGACAGACTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 19 0.46
27 13 0.32
28 9 0.22
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (26 bp):
AAAAAATTTAAAAAATTAAAAAATTC
Found at i:6553945 original size:19 final size:19
Alignment explanation
Indices: 6553923--6553964 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
6553913 TAAAAAATCT
*
6553923 AAAAATTTAATAAAA-ATAA
1 AAAAATTCAA-AAAATATAA
6553942 AAAAATTCAAAAAATATAA
1 AAAAATTCAAAAAATATAA
6553961 AAAA
1 AAAA
6553965 TTAAAAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATTCAAAAAATATAA
Found at i:6559512 original size:59 final size:57
Alignment explanation
Indices: 6559385--6559674 Score: 422
Period size: 58 Copynumber: 5.0 Consensus size: 57
6559375 TCTTGTGTAG
*
6559385 GAAAAATTGATACTTTTAA-TTTTTCTTCAAAAATATTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTTTTTGAAAATTTATTTTTAA
* * *
6559442 GGAAAATTGATACTTTTAACTTTTTCTCAAAAATTTTTTTTTGAAAATTTATTTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAA-TATTTTTTGAAAATTTA-TTTTTAA
*
6559501 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTG-AAAATTTATTTTTAA
*
6559559 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATCTTTTTTG-AAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTTAA
* *
6559615 GAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTGAAAATTTTGATTTTTA
1 GAAAAATTGATACTTTCAACTTTTTC-TCAAAA-ATATTTTTTGAAAA-TTT-ATTTTTA
6559675 TTTAAAGAAA
Statistics
Matches: 213, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
56 39 0.18
57 30 0.14
58 86 0.40
59 48 0.23
60 3 0.01
61 7 0.03
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.50
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTATTTTTAA
Found at i:6559530 original size:116 final size:113
Alignment explanation
Indices: 6559385--6559674 Score: 438
Period size: 117 Copynumber: 2.5 Consensus size: 113
6559375 TCTTGTGTAG
* *
6559385 GAAAAATTGATACTTTTAA-TTTTTCTTCAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTT-TTCAAAAATATTTTTTGAAAATTTATTTTTAAGAAAAAT
* *
6559449 TGATACTTTTAACTTTTTCTCAAAAATTTTTTTTTGAAAATTTATTTTTTAA
65 TGATACTTTCAACTTTTTCTCAAAAA-TCTTTTTTG-AAATTTA-TTTTTAA
6559501 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAAATTTATTTTTAAGAAAAAT
1 GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTG-AAAATTTATTTTTAAGAAAAAT
6559566 TGATACTTTCAACTTTTTCTCAAAAATCTTTTTTGAAATTTATTTTTAA
65 TGATACTTTCAACTTTTTCTCAAAAATCTTTTTTGAAATTTATTTTTAA
* *
6559615 GAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTGAAAATTTTGATTTTTA
1 GAAAAATTGATACTTTCAACTTTT-TTTCAAAA-ATATTTTTTGAAAA-TTT-ATTTTTA
6559675 TTTAAAGAAA
Statistics
Matches: 162, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
114 31 0.19
115 17 0.10
116 56 0.35
117 58 0.36
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.50
Consensus pattern (113 bp):
GAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTTCTCAAAAATCTTTTTTGAAATTTATTTTTAA
Found at i:6559706 original size:11 final size:11
Alignment explanation
Indices: 6559692--6559735 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
6559682 AAAATCGAAT
6559692 AAAAAAATAAA
1 AAAAAAATAAA
*
6559703 AAAAAAGTAAA
1 AAAAAAATAAA
*
6559714 ACAAAAATAAA
1 AAAAAAATAAA
*
6559725 AATAAAATAAA
1 AAAAAAATAAA
6559736 GATAAAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:6559740 original size:11 final size:11
Alignment explanation
Indices: 6559695--6559742 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
6559685 ATCGAATAAA
6559695 AAAATAAAAA-
1 AAAATAAAAAT
6559705 AAAAGTAAAACA-
1 AAAA-TAAAA-AT
6559717 AAAATAAAAAT
1 AAAATAAAAAT
*
6559728 AAAATAAAGAT
1 AAAATAAAAAT
6559739 AAAA
1 AAAA
6559743 AGAATATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 5 0.15
11 24 0.71
12 5 0.15
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.12
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6559740 original size:17 final size:17
Alignment explanation
Indices: 6559695--6559757 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
6559685 ATCGAATAAA
6559695 AAAATAAAA-AAAAAGT
1 AAAATAAAATAAAAAGT
*
6559711 AAAACAAAAATAAAAA-T
1 AAAA-TAAAATAAAAAGT
6559728 AAAATAAAGATAAAAAG-
1 AAAATAAA-ATAAAAAGT
* *
6559745 AATATTAAATAAA
1 AAAATAAAATAAA
6559758 TCTAATCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 12 0.31
17 22 0.56
18 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAAAAAGT
Found at i:6559742 original size:22 final size:22
Alignment explanation
Indices: 6559694--6559735 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6559684 AATCGAATAA
6559694 AAAAATAAAAAAAAAGTAAAAC
1 AAAAATAAAAAAAAAGTAAAAC
6559716 AAAAATAAAAATAAAA-TAAA
1 AAAAATAAAAA-AAAAGTAAA
6559736 GATAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAAAAAAGTAAAAC
Found at i:6560731 original size:10 final size:10
Alignment explanation
Indices: 6560716--6560829 Score: 61
Period size: 10 Copynumber: 11.9 Consensus size: 10
6560706 TATTACAAAA
6560716 AAATAATAAT
1 AAATAATAAT
*
6560726 AAATAAATTAT
1 AAAT-AATAAT
6560737 AATATAATAAT
1 AA-ATAATAAT
6560748 AAAT-AT-AT
1 AAATAATAAT
*
6560756 AACTATATAA-
1 AAATA-ATAAT
6560766 AAATACAT-AT
1 AAATA-ATAAT
*
6560776 AAATATTAAT
1 AAATAATAAT
*
6560786 AGA-AA-AA-
1 AAATAATAAT
6560793 AAATAAGTAA-
1 AAATAA-TAAT
6560803 AAAT-ATACAT
1 AAATAATA-AT
6560813 --ATAATAAT
1 AAATAATAAT
6560821 AAATAATAA
1 AAATAATAA
6560830 AATACATAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
7 2 0.03
8 15 0.19
9 10 0.12
10 36 0.45
11 15 0.19
12 2 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (10 bp):
AAATAATAAT
Found at i:6560745 original size:19 final size:21
Alignment explanation
Indices: 6560721--6560776 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
6560711 CAAAAAAATA
6560721 ATAATAAATAAAT-TATAA-T
1 ATAATAAATAAATATATAACT
6560740 ATAAT-AATAAATATATAACT
1 ATAATAAATAAATATATAACT
* *
6560760 ATATAAAAATACATATA
1 ATA-ATAAATAAATATA
6560777 AATATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 7 0.23
19 10 0.32
20 4 0.13
21 1 0.03
22 9 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATAAATAAATATATAACT
Found at i:6560763 original size:22 final size:22
Alignment explanation
Indices: 6560718--6560780 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
6560708 TTACAAAAAA
* *
6560718 ATAATAATAAATAAATTATAAT
1 ATAATAATAAATATATAATAAT
6560740 ATAATAATAAATATATAACT-AT
1 ATAATAATAAATATATAA-TAAT
* *
6560762 ATAAAAATACATATA-AATA
1 ATAATAATAAATATATAATA
6560781 TTAATAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 31 0.89
23 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATAATAAATATATAATAAT
Found at i:6560834 original size:24 final size:24
Alignment explanation
Indices: 6560789--6560842 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
6560779 TATTAATAGA
* *
6560789 AAAAAAATAAGTAAAAATATACAT
1 AAAATAATAAATAAAAATATACAT
*
6560813 ATAATAATAAATAATAAA-ATACAT
1 AAAATAATAAATAA-AAATATACAT
6560837 AAAATA
1 AAAATA
6560843 CAAAAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAATAAATAAAAATATACAT
Found at i:6561043 original size:10 final size:10
Alignment explanation
Indices: 6561030--6561085 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
6561020 AACATTGTCA
6561030 TTTTTTGTTT-
1 TTTTTT-TTTG
6561040 TTTTTTCTTTG
1 TTTTTT-TTTG
*
6561051 TTTTTTTGTG
1 TTTTTTTTTG
*
6561061 TTTTTTTATG
1 TTTTTTTTTG
6561071 TTTTTTTTT-
1 TTTTTTTTTG
6561080 TTTTTT
1 TTTTTT
6561086 ACCAAAGCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
9 6 0.15
10 29 0.71
11 6 0.15
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:6561403 original size:42 final size:41
Alignment explanation
Indices: 6561092--6561430 Score: 489
Period size: 41 Copynumber: 8.1 Consensus size: 41
6561082 TTTTACCAAA
* *
6561092 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-ATAAATT
*
6561135 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
* ** * *
6561176 GCTCTTCTAAACAGAGGCATAATGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAATAAATT
*
6561218 GCTCCTCTAAATAGAGGCACCACGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
* *
6561259 GCTCCTCTAAACAAAGGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
*
6561300 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAATAAATT
*
6561342 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA-TAAATT
* *
6561384 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATCAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
*
6561425 ACTCCT
1 GCTCCT
6561431 TGACGATCAT
Statistics
Matches: 266, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
41 124 0.47
42 115 0.43
43 27 0.10
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
Done.