Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 325 of 373
Found at i:109189093 original size:15 final size:15
Alignment explanation
Indices: 109189069--109189103 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
109189059 TAATATTTTA
109189069 ATTA-ATTTTTAAAT
1 ATTATATTTTTAAAT
*
109189083 ATTATATTTTTAATT
1 ATTATATTTTTAAAT
109189098 ATTATA
1 ATTATA
109189104 ATTAGCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATATTTTTAAAT
Found at i:109196989 original size:31 final size:31
Alignment explanation
Indices: 109196951--109197068 Score: 155
Period size: 31 Copynumber: 3.8 Consensus size: 31
109196941 ACAAATGACA
* * *
109196951 AGTGAAAAGTGGTAGCTTCTGCTACCTGGTC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
109196982 AGTGAAAAGTGGTAGCTCCGGTTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
109197013 AGTGAAAAATGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* * *
109197044 AGTGAATAGTTGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
109197069 AAGTGACAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:109197172 original size:47 final size:46
Alignment explanation
Indices: 109197086--109197258 Score: 130
Period size: 47 Copynumber: 3.7 Consensus size: 46
109197076 AAGTGATTTC
* * ** * * *
109197086 CGTATAATACCATATTTGGGATATAACATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
109197132 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * * * * *
109197179 CGTGTACGACCATAGCTGGGTTATGGCATCGATATGTGATATGTGATTA
1 CGTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATATGA-TA
* * * *
109197228 CATGTAAGACCATAGCTGGGCTATGGCATCA
1 CGTATAAGACCATATCTGGGATATGGCATCA
109197259 TTATGTGAAG
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
46 26 0.25
47 38 0.37
48 12 0.12
49 28 0.27
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:109197245 original size:49 final size:47
Alignment explanation
Indices: 109197137--109197266 Score: 163
Period size: 49 Copynumber: 2.7 Consensus size: 47
109197127 TGCTACTGTA
* * * *
109197137 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGATATGGCATCATATGTGATATGTGATTCATG
* *
109197183 TACGACCATAGCTGGGTTATGGCATCGATATGTGATATGTGATTACATG
1 TAAGACCATAGCTGGGATATGGCATC-ATATGTGATATGTGATT-CATG
*
109197232 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGATATGGCATCA-TATGTGA
109197267 AGGTGTAAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
46 23 0.32
47 1 0.01
48 14 0.19
49 34 0.47
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (47 bp):
TAAGACCATAGCTGGGATATGGCATCATATGTGATATGTGATTCATG
Found at i:109198773 original size:13 final size:13
Alignment explanation
Indices: 109198755--109198781 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
109198745 TCCAGCGAAT
109198755 TCTAACTCCATAA
1 TCTAACTCCATAA
109198768 TCTAACTCCATAA
1 TCTAACTCCATAA
109198781 T
1 T
109198782 TTCCAACCAA
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:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (13 bp):
TCTAACTCCATAA
Found at i:109200226 original size:30 final size:30
Alignment explanation
Indices: 109200190--109200249 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
109200180 ACTTAACAAT
109200190 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
109200220 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
109200250 TAATAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:109200307 original size:22 final size:22
Alignment explanation
Indices: 109200282--109200324 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
109200272 TATTCAAACA
109200282 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
** *
109200304 ATAATAGTAAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
109200325 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:109202007 original size:74 final size:73
Alignment explanation
Indices: 109201880--109202104 Score: 310
Period size: 74 Copynumber: 3.0 Consensus size: 73
109201870 TGGTCCCCCC
* * * *
109201880 AAGGTTTAA-ATTTTTTGCAATTTAGCCCTTTATAGAGATACTAT-GACCCTCCCAAAAATATAA
1 AAGGTTTAAGA-TTTTTGCAATTT-CCCCTTTGTATATATACTATAG-CCCTCCCAAAAATATAA
109201943 GTAGGCCCTCT
63 GTAGGCCCTCT
* *
109201954 AAGGTTTAAGATTTTTGCAATTTTCCCGTTTGTATATATACTATAGCCTTCCCAAAAATATAAGT
1 AAGGTTTAAGATTTTTGCAA-TTTCCCCTTTGTATATATACTATAGCCCTCCCAAAAATATAAGT
109202019 AGGCCCTCT
65 AGGCCCTCT
* *
109202028 AAGGTTTAAGATTTTTGCAATTTCCCCCTTTGAATATATACTATAACCCTCCCAAAAATATAAGT
1 AAGGTTTAAGATTTTTGCAATTT-CCCCTTTGTATATATACTATAGCCCTCCCAAAAATATAAGT
109202093 AGGCCTCTCT
65 AGGCC-CTCT
109202103 AA
1 AA
109202105 TATTTTTATA
Statistics
Matches: 136, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
73 3 0.02
74 122 0.90
75 11 0.08
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (73 bp):
AAGGTTTAAGATTTTTGCAATTTCCCCTTTGTATATATACTATAGCCCTCCCAAAAATATAAGTA
GGCCCTCT
Found at i:109202144 original size:13 final size:12
Alignment explanation
Indices: 109202112--109202136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
109202102 TAATATTTTT
109202112 ATAATATTAAAA
1 ATAATATTAAAA
109202124 ATAATATTAAAA
1 ATAATATTAAAA
109202136 A
1 A
109202137 ATATTATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATATTAAAA
Found at i:109202234 original size:24 final size:25
Alignment explanation
Indices: 109202207--109202257 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
109202197 AACTTTTGAA
**
109202207 TAATATTTTTGTT-AAATAATAATT
1 TAATATTTTACTTAAAATAATAATT
109202231 TAATATTTTACTTAAAATAATAATT
1 TAATATTTTACTTAAAATAATAATT
109202256 TA
1 TA
109202258 TAAGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TAATATTTTACTTAAAATAATAATT
Found at i:109205014 original size:20 final size:23
Alignment explanation
Indices: 109204977--109205020 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
109204967 CATAGAAAAC
109204977 AATTTTAGTGTTAGTAAAATTAA
1 AATTTTAGTGTTAGTAAAATTAA
109205000 AATTTTA-TG-TA-TAAAATTAA
1 AATTTTAGTGTTAGTAAAATTAA
109205020 A
1 A
109205021 TTAAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 2 0.10
23 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
AATTTTAGTGTTAGTAAAATTAA
Found at i:109205035 original size:25 final size:25
Alignment explanation
Indices: 109204993--109205043 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
109204983 AGTGTTAGTA
* *
109204993 AAATTAAAATTTTATGTATAAAATT
1 AAATTAAAAATTCATGTATAAAATT
* *
109205018 AAATTAAAAATTCGTGTATAATATT
1 AAATTAAAAATTCATGTATAAAATT
109205043 A
1 A
109205044 CATATTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (25 bp):
AAATTAAAAATTCATGTATAAAATT
Found at i:109229722 original size:29 final size:29
Alignment explanation
Indices: 109229680--109229736 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
109229670 GTAATAATAC
109229680 AAATTCCACCATCTTTTTTCCAAGCATAT
1 AAATTCCACCATCTTTTTTCCAAGCATAT
109229709 AAATTCCACCATCTTTTTTCCAAGCATA
1 AAATTCCACCATCTTTTTTCCAAGCATA
109229737 CCCTTCTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATTCCACCATCTTTTTTCCAAGCATAT
Found at i:109237323 original size:69 final size:69
Alignment explanation
Indices: 109237210--109237348 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
109237200 GATAGGAAAA
*
109237210 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTCCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTCCAGCAGGTTTTGTAGTGGTGGTAGG
109237275 GCTG
66 GCTG
*
109237279 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTCCAGCAGGTTTTGTAGTGGTGGTAGG
109237344 GCTG
66 GCTG
109237348 A
1 A
109237349 TAGAGTCTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTCCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:109251328 original size:54 final size:55
Alignment explanation
Indices: 109251258--109251366 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 55
109251248 GTGAAAATAA
*
109251258 TTTTCAAGTTCAAGGATTAACTTGAATAAAAATAATCAAGTATAAAAACTATCAC
1 TTTTCAAGTTCAAGGATTAACTTGAATAAAAATAATCAAATATAAAAACTATCAC
* *
109251313 TTTT-AAGTTCGAGGATTAACTTGGATAAAAATAATCAAATATAAAAACTATCAC
1 TTTTCAAGTTCAAGGATTAACTTGAATAAAAATAATCAAATATAAAAACTATCAC
109251367 CAAGTTTAGC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 47 0.92
55 4 0.08
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (55 bp):
TTTTCAAGTTCAAGGATTAACTTGAATAAAAATAATCAAATATAAAAACTATCAC
Found at i:109255602 original size:15 final size:17
Alignment explanation
Indices: 109255571--109255603 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
109255561 CTCTACTTAT
109255571 TTTAATTATATAATTTA
1 TTTAATTATATAATTTA
109255588 TTTAATTA-A-AATTTA
1 TTTAATTATATAATTTA
109255603 T
1 T
109255604 AATTTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATTATATAATTTA
Found at i:109256190 original size:19 final size:19
Alignment explanation
Indices: 109256168--109256217 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
109256158 TGACTTATTG
**
109256168 ATTAAATTGGAATTAAAAA
1 ATTAAATTAAAATTAAAAA
*
109256187 ATTAATTTAAAATTAAAAA
1 ATTAAATTAAAATTAAAAA
* *
109256206 AGTAAAATAAAA
1 ATTAAATTAAAA
109256218 AATACATCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (19 bp):
ATTAAATTAAAATTAAAAA
Found at i:109256848 original size:3 final size:3
Alignment explanation
Indices: 109256842--109257146 Score: 126
Period size: 3 Copynumber: 101.0 Consensus size: 3
109256832 AAAGCTGCTG
* * *
109256842 CTT CTT CTT CTT C-T CTTT CTC CTT C-T CATT CTC CTT CTT C-T CCT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT C-TT CTT CTT CTT CTT CTT
* * * * * * * * *
109256886 CCT CCT CCT CCT CCT CTT CCT CCT CCTT CTT TTT CTC CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT
* * * *
109256932 CTT CTT CTT TTT CCTT CTT CTT CTT CTT CTT CCT CCT CATT CTT CTC
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT
* * * *
109256979 CTT C-T CCT CTTT CTT C-T CTT -TCT CATT CTC CTT CTT CTC CTT CTC
1 CTT CTT CTT C-TT CTT CTT CTT CT-T C-TT CTT CTT CTT CTT CTT CTT
* * * *
109257024 CTC CTT C-T CCT CCT CTT -TT -TT CCTT CTT CTT CTT CTT CTT ATT
1 CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT
* * ** * * * * *
109257067 CGTC CTC CCC CTC CTC CTC CTT CTT CTT CTT TTT CTT TTT CCTT -TT
1 C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT
*
109257113 CCTC CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
109257147 TAATTCAACT
Statistics
Matches: 244, Mismatches: 37, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
2 19 0.08
3 203 0.83
4 21 0.09
5 1 0.00
ACGTcount: A:0.01, C:0.42, G:0.00, T:0.57
Consensus pattern (3 bp):
CTT
Found at i:109260340 original size:37 final size:40
Alignment explanation
Indices: 109260244--109260341 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
109260234 AACACACCAG
* * ** *
109260244 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCAGATAAACCAAAGTAATAA
* *
109260284 TTTGACACCCAGTGTCTCATCAGCTAAACCAAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCAGATAAACCAAAGTAATAA
109260322 -TTGACACCCAGTGCCTCATC
1 TTTGACACCCAGTGCCTCATC
109260342 GAATTAATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.38
38 2 0.04
39 1 0.02
40 28 0.56
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCAGATAAACCAAAGTAATAA
Found at i:109261291 original size:11 final size:10
Alignment explanation
Indices: 109261275--109261343 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 10
109261265 GTCTTTCTCC
109261275 TTTTCTTTCCT
1 TTTTCTTT-CT
109261286 TTTTCTTTCT
1 TTTTCTTTCT
*
109261296 TTTTCCCTTCT
1 TTTT-CTTTCT
* *
109261307 GTTTCATTTAT
1 TTTTC-TTTCT
109261318 TCTTTCTTTCT
1 T-TTTCTTTCT
*
109261329 TTCT-TTTCT
1 TTTTCTTTCT
*
109261338 ATTTCT
1 TTTTCT
109261344 ATTTCTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
9 7 0.16
10 10 0.22
11 24 0.53
12 4 0.09
ACGTcount: A:0.04, C:0.23, G:0.01, T:0.71
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:109265891 original size:15 final size:13
Alignment explanation
Indices: 109265858--109265882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109265848 ACAAACACTA
109265858 AAATTTTCACACG
1 AAATTTTCACACG
109265871 AAATTTTCACAC
1 AAATTTTCACAC
109265883 ATATAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:109279932 original size:25 final size:25
Alignment explanation
Indices: 109279904--109279970 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
109279894 CCGATTTATG
109279904 GCTCGCATAAGCTTCCCAATATACA
1 GCTCGCATAAGCTTCCCAATATACA
*
109279929 GCTCG-ATTGAA-CTTCCCATTATACA
1 GCTCGCA-T-AAGCTTCCCAATATACA
* *
109279954 GCTCACATGAGCTTCCC
1 GCTCGCATAAGCTTCCC
109279971 GTTTACATGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 30 0.86
26 3 0.09
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (25 bp):
GCTCGCATAAGCTTCCCAATATACA
Found at i:109288633 original size:11 final size:11
Alignment explanation
Indices: 109288613--109288656 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
109288603 AGATAAATGT
*
109288613 TATTTAATTAA
1 TATTTTATTAA
109288624 TATTTTATTAA
1 TATTTTATTAA
* *
109288635 GACTTTTAGTAA
1 TA-TTTTATTAA
109288647 TATTTTATTA
1 TATTTTATTA
109288657 TTAAATGACT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:109289918 original size:19 final size:19
Alignment explanation
Indices: 109289896--109289933 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
109289886 ATTAAGAATG
109289896 GAAGATATAATTATACTAA
1 GAAGATATAATTATACTAA
109289915 GAAGATATAATTATACTAA
1 GAAGATATAATTATACTAA
109289934 ATAGTGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (19 bp):
GAAGATATAATTATACTAA
Found at i:109290122 original size:22 final size:22
Alignment explanation
Indices: 109290097--109290168 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
109290087 ACTGTTTCAT
*
109290097 ACTTCGGTGTTTATCGTTTTGC
1 ACTTCGGTGCTTATCGTTTTGC
* *
109290119 ACTTCGGAGCTTA-CTATTTTGC
1 ACTTCGGTGCTTATC-GTTTTGC
* *
109290141 ACTTCGATGCTTAGT-GATTTGC
1 ACTTCGGTGCTTA-TCGTTTTGC
109290163 ACTTCG
1 ACTTCG
109290169 ATGCATACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (22 bp):
ACTTCGGTGCTTATCGTTTTGC
Found at i:109290169 original size:22 final size:22
Alignment explanation
Indices: 109290113--109290182 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
109290103 GTGTTTATCG
109290113 TTTTGCACTTCGGA-GCTTACTA
1 TTTTGCACTTC-GATGCTTACTA
*
109290135 TTTTGCACTTCGATGCTTAGTGA
1 TTTTGCACTTCGATGCTTACT-A
*
109290158 -TTTGCACTTCGATGCATACTA
1 TTTTGCACTTCGATGCTTACTA
109290179 TTTT
1 TTTT
109290183 ATTAGTGTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.07
22 38 0.90
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (22 bp):
TTTTGCACTTCGATGCTTACTA
Found at i:109301942 original size:43 final size:44
Alignment explanation
Indices: 109301884--109301972 Score: 162
Period size: 43 Copynumber: 2.0 Consensus size: 44
109301874 TTCATATACA
109301884 TATATTACATAAAAAAATATTAGCAACCTAACGCACGGGGAAAT
1 TATATTACATAAAAAAATATTAGCAACCTAACGCACGGGGAAAT
*
109301928 TATATTACAT-AAAAAATATTAGCAACCTATCGCACGGGGAAAT
1 TATATTACATAAAAAAATATTAGCAACCTAACGCACGGGGAAAT
109301971 TA
1 TA
109301973 GAAAATTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 34 0.77
44 10 0.23
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (44 bp):
TATATTACATAAAAAAATATTAGCAACCTAACGCACGGGGAAAT
Found at i:109302846 original size:3 final size:3
Alignment explanation
Indices: 109302827--109302880 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
109302817 AATGTAAGAG
* * * * *
109302827 AAT AAT AA- AAG ATT AAT AAT AAT TAT AAT AGT AAA AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
109302874 AAT AAT A
1 AAT AAT A
109302881 GCTAAGTGGG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:109302986 original size:15 final size:15
Alignment explanation
Indices: 109302966--109302996 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109302956 AAAAAATATA
109302966 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
109302981 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
109302996 A
1 A
109302997 GAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAAAT
Found at i:109303300 original size:3 final size:3
Alignment explanation
Indices: 109303294--109303427 Score: 112
Period size: 3 Copynumber: 44.7 Consensus size: 3
109303284 ATAGTTGTAG
* * * * * * *
109303294 TAA TAA TAA TAG TAA GAA AAA TAG TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
109303341 T-A TAA CAA -AA GAA TAA TAA TAA TAA TAG TAA TGGAGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T--A-A TAA TAA TAA
* *
109303387 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAC TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
109303428 TAAATAAAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
2 6 0.06
3 94 0.90
4 1 0.01
5 1 0.01
6 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:109303338 original size:20 final size:21
Alignment explanation
Indices: 109303299--109303338 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
109303289 TGTAGTAATA
*
109303299 ATAATAGTAAGAAAAATAGTG
1 ATAATAGTAACAAAAATAGTG
*
109303320 ATAATA-TAACAATAATAGT
1 ATAATAGTAACAAAAATAGT
109303339 AATATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAATAGTAACAAAAATAGTG
Found at i:109303433 original size:12 final size:13
Alignment explanation
Indices: 109303352--109303441 Score: 89
Period size: 12 Copynumber: 6.9 Consensus size: 13
109303342 ATAACAAAAG
109303352 AATAATAATA-AT
1 AATAATAATATAT
* *
109303364 AATAGTAATGGAGAT
1 AATAATAAT--ATAT
109303379 AATAATAATA-AT
1 AATAATAATATAT
109303391 AATAATAATA-AT
1 AATAATAATATAT
109303403 AATAATAATGATACT
1 AATAATAAT-ATA-T
109303418 AATAATAATATA-
1 AATAATAATATAT
*
109303430 AATAAAAATATA
1 AATAATAATATA
109303442 AACAACAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
12 42 0.61
13 2 0.03
14 5 0.07
15 20 0.29
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (13 bp):
AATAATAATATAT
Found at i:109303587 original size:9 final size:9
Alignment explanation
Indices: 109303573--109303597 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
109303563 AAATATAAAA
109303573 GAAAAGGAC
1 GAAAAGGAC
109303582 GAAAAGGAC
1 GAAAAGGAC
109303591 GAAAAGG
1 GAAAAGG
109303598 GGCTAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.36, T:0.00
Consensus pattern (9 bp):
GAAAAGGAC
Found at i:109304585 original size:33 final size:33
Alignment explanation
Indices: 109304538--109304606 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
109304528 AGTGTCAGAC
109304538 GCGTGGAGCATGGTGACCAAGGCTGAGGGGCAT
1 GCGTGGAGCATGGTGACCAAGGCTGAGGGGCAT
* * * *
109304571 GCGTGGGGCGTGGTGGCCAAGGCTGAGGGGTAT
1 GCGTGGAGCATGGTGACCAAGGCTGAGGGGCAT
109304604 GCG
1 GCG
109304607 GCAGCTGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.16, C:0.17, G:0.51, T:0.16
Consensus pattern (33 bp):
GCGTGGAGCATGGTGACCAAGGCTGAGGGGCAT
Found at i:109305469 original size:87 final size:88
Alignment explanation
Indices: 109305378--109305621 Score: 311
Period size: 87 Copynumber: 2.8 Consensus size: 88
109305368 TGAATTCAAC
* * *
109305378 CTGTTACCCTACTGCTTAGGG-GTTTAAGGTCTGT-AATTTCAGCTTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGTG-TTAAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGG
109305441 GGGTTAAAGCCCATCACGT-TCT-AT
65 GGGTTAAAGCCC-T-ACGTCTCTGAT
*
109305465 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTT-AGCCTGTTACTCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGG
* * *
109305529 GGTTAAGGCCCTTCGTCTTTGAT
66 GGTTAAAGCCCTACGTCTCTGAT
** * *
109305552 CTGTTTCCCTACTGCTTAGGGTGACAAGATCTGTGAA-TTCAACCTGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGG
*
109305616 GTTTAA
66 GGTTAA
109305622 GGTCTGTAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
85 3 0.02
86 5 0.04
87 125 0.90
88 6 0.04
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (88 bp):
CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTTCAGCCTGTTACCCTACTGCTTAGGG
GGTTAAAGCCCTACGTCTCTGAT
Found at i:109305469 original size:130 final size:131
Alignment explanation
Indices: 109305282--109305536 Score: 370
Period size: 130 Copynumber: 2.0 Consensus size: 131
109305272 AGGATATTTG
* * *
109305282 ATTTCTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCATCGCCTTCGATCTGTTTCCCTAC
1 ATTTCTAGCCTGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTAC
* * *
109305347 TGGTTAGGGT-TATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTG
66 TGCTTAGGGTGT-TAAGATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTG
109305411 TA
130 TA
* * * *
109305413 ATTTC-AGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACGTTCTATCTGTTTCCCTAC
1 ATTTCTAGCCTGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTAC
* * *
109305477 TGCTTAGGGTGTTAAGATCTGTAAATTTAGCCTGTTACTCTACTGCTTAGGGGGTTAAGG
66 TGCTTAGGGTGTTAAGATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGG
109305537 CCCTTCGTCT
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
130 104 0.95
131 6 0.05
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (131 bp):
ATTTCTAGCCTGTTACCCTACTACTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTAC
TGCTTAGGGTGTTAAGATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGT
A
Found at i:109305662 original size:217 final size:217
Alignment explanation
Indices: 109305287--109305968 Score: 1037
Period size: 217 Copynumber: 3.1 Consensus size: 217
109305277 ATTTGATTTC
* * * * * *
109305287 TAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTCATCGCCTTCGATCTGTTTCCCTACTGGTT
1 TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTT
* *
109305352 AGGGTTATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAATTT
66 AGGGTGATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATT
* * *
109305417 CAGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACGTTCTATCTGTTTCCCTACTGCTT
131 CGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTT
109305482 AGGGTGTTAAGATCTGTAAATT
196 AGGGTGTTAAGATCTGTAAATT
*
109305504 TAGCCTGTTACTCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTT
1 TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTT
*
109305569 AGGGTGACAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATT
66 AGGGTGATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATT
*
109305634 CGGATTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTT
131 CGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTT
109305699 AGGGTGTTAAGATCTGTAAATT
196 AGGGTGTTAAGATCTGTAAATT
*
109305721 TAGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTT
1 TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTT
* *
109305786 AGGGTGATAAGATCTGTGAATTCAACCTGTTACCCTACTACTTAGGGGTTTAAAGTCTGTAAATT
66 AGGGTGATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATT
* * *** * *
109305851 CGGCTTGTTACCCTACTGCTTAGGGGG-TCAAGACCCTTTGTCTTCGATTTG-CTCCACTACTGC
131 CGGCTTGTTACCCTACTGCTTAGGGGGTTAAAG-CCCATCACCTTCGATCTGTTTCC-CTACTGC
* * *
109305914 TTAGGGAGATAAGATCTG-CAATT
194 TTAGGGTGTTAAGATCTGTAAATT
** * * *
109305937 CGGTCTGTTACCCTACTACTTAGGGGTTTAAG
1 TAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
109305969 ATCTGTAAAT
Statistics
Matches: 427, Mismatches: 36, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
216 37 0.09
217 390 0.91
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (217 bp):
TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTT
AGGGTGATAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATT
CGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTT
AGGGTGTTAAGATCTGTAAATT
Found at i:109305686 original size:87 final size:86
Alignment explanation
Indices: 109305595--109305840 Score: 305
Period size: 87 Copynumber: 2.8 Consensus size: 86
109305585 TGAATTCAAC
* * *
109305595 CTGTTACCCTACTGCTTAGGG-GTTTAAGGTCTGTAAATTCGGATTGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTGCTTAGGGTG-TTAAGATCTGTAAATTC-GACTGTTACCCTACTGCTTAGGG
109305659 GGTTAAAGCCCATCACCTTCGAT
64 GGTTAAAGCCCATCACCTTCGAT
* * *
109305682 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGAGG
1 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAA-TTCGACTGTTACCCTACTGCTTAGGGG
* * ** *
109305747 GTTAAGGCCCTTCGTCTTTGAT
65 GTTAAAGCCCATCACCTTCGAT
* * * *
109305769 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTGAATTCAACCTGTTACCCTACTACTTAGGGG
1 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTCGA-CTGTTACCCTACTGCTTAGGGG
*
109305834 TTTAAAG
65 GTTAAAG
109305841 TCTGTAAATT
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
86 2 0.01
87 131 0.96
88 3 0.02
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (86 bp):
CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTCGACTGTTACCCTACTGCTTAGGGGG
TTAAAGCCCATCACCTTCGAT
Found at i:109305753 original size:130 final size:129
Alignment explanation
Indices: 109305465--109305753 Score: 398
Period size: 130 Copynumber: 2.2 Consensus size: 129
109305455 CACGTTCTAT
* * * * *
109305465 CTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTTAGCCTGTTACTCTACTGCTTAGGGG
1 CTGTTACCCTACTGCTTAGGG-GTTAAGGTCTGTAAATTCAGACTGTTACCCTACTGCTTAGGGG
* * ** * *
109305530 GTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTTAGGGTGACAAGATCTGTGAATTCAAC
65 GTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGTGACAAGATCTGTAAATTCAAC
* *
109305595 CTGTTACCCTACTGCTTAGGGGTTTAAGGTCTGTAAATTCGGATTGTTACCCTACTGCTTAGGGG
1 CTGTTACCCTACTGCTTAGGGG-TTAAGGTCTGTAAATTCAGACTGTTACCCTACTGCTTAGGGG
** * *
109305660 GTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGTGTTAAGATCTGTAAATTTAGC
65 GTTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGTGACAAGATCTGTAAATTCAAC
109305725 CTGTTACCCTACTGCTTAGAGGGTTAAGG
1 CTGTTACCCTACTGCTTAG-GGGTTAAGG
109305754 CCCTTCGTCT
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
129 1 0.01
130 136 0.97
131 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (129 bp):
CTGTTACCCTACTGCTTAGGGGTTAAGGTCTGTAAATTCAGACTGTTACCCTACTGCTTAGGGGG
TTAAAGCCCATCACCTTCGATCTGTTTCCCTACTGCTTAGGGTGACAAGATCTGTAAATTCAAC
Found at i:109305816 original size:130 final size:128
Alignment explanation
Indices: 109305549--109306013 Score: 460
Period size: 130 Copynumber: 3.6 Consensus size: 128
109305539 CTTCGTCTTT
* * ** * *
109305549 GATCTGTTTCCCTACTGCTTA-GGGTGACAAGATCTGTGAATTCAACCTGTTACCCTACTGCTTA
1 GATCTGTTACCCTACTACTTAGGGGT-TTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTA
* * * * * * * **
109305613 GGGGTTTAAGG-TC-TGTAAATTCGGATTGTTACCCTACTGCTTAGGGGGTTAA-AGCCCATCAC
65 GGGGGTTAAGGCCCTTGT--CTTC-GATTGTTTCCCTACTGCTTAGGGAGATAAGA-TCTGTCA-
*
109305675 CTTC
125 ATTC
* * *
109305679 GATCTGTTTCCCTACTGCTTA-GGGTGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTA
1 GATCTGTTACCCTACTACTTAGGGGT-TTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTA
* * * *
109305743 GAGGGTTAAGGCCCTTCGTCTTTGATCTGTTTCCCTACTGCTTAGGGTGATAAGATCTGTGAATT
65 GGGGGTTAAGGCCCTT-GTCTTCGAT-TGTTTCCCTACTGCTTAGGGAGATAAGATCTGTCAATT
109305808 C
128 C
* * * *
109305809 AACCTGTTACCCTACTACTTAGGGGTTTAA-AGTCTGTAAATTCGGCTTGTTACCCTACTGCTTA
1 GATCTGTTACCCTACTACTTAGGGGTTTAAGA-TCTGTAAATTCAGCCTGTTACCCTACTGCTTA
* * *
109305873 GGGGGTCAAGACCCTTTGTCTTCGATT-TGCTCCACTACTGCTTAGGGAGATAAGATCTG-CAAT
65 GGGGGTTAAGGCCC-TTGTCTTCGATTGT-TTCC-CTACTGCTTAGGGAGATAAGATCTGTCAAT
109305936 TC
127 TC
* * *
109305938 GGTCTGTTACCCTACTACTTAGGGGTTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGGTTAG
1 GATCTGTTACCCTACTACTTAGGGGTTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAG
109306003 GGGGTTAAGGC
66 GGGGTTAAGGC
109306014 TTGTGGATTC
Statistics
Matches: 283, Mismatches: 41, Indels: 23
0.82 0.12 0.07
Matches are distributed among these distances:
128 1 0.00
129 75 0.27
130 168 0.59
131 35 0.12
132 2 0.01
133 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (128 bp):
GATCTGTTACCCTACTACTTAGGGGTTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAG
GGGGTTAAGGCCCTTGTCTTCGATTGTTTCCCTACTGCTTAGGGAGATAAGATCTGTCAATTC
Found at i:109306185 original size:64 final size:64
Alignment explanation
Indices: 109306084--109306211 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
109306074 TCATGTATCT
109306084 ATGCTTATGCCAAATAATTAAGATGCAATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAAGATGCAATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
* * * *
109306148 ATGCTTATGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATGCAATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
109306212 TTATGAATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAAGATGCAATGATTGAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:109307882 original size:7 final size:7
Alignment explanation
Indices: 109307870--109307895 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
109307860 TTTGGGTCTC
109307870 TTTTTCT
1 TTTTTCT
109307877 TTTTTCT
1 TTTTTCT
109307884 TTTTTCT
1 TTTTTCT
109307891 TTTTT
1 TTTTT
109307896 TTTGCCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:109312642 original size:24 final size:25
Alignment explanation
Indices: 109312602--109312656 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
109312592 AATGTAAGAG
109312602 AATAATA--AAAAATTAATAATAAT
1 AATAATAGTAAAAATTAATAATAAT
* *
109312625 TATAATAGTAAAAA-TAATAATAGT
1 AATAATAGTAAAAATTAATAATAAT
109312649 AATAATAG
1 AATAATAG
109312657 CTAAGTGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 16 0.59
25 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (25 bp):
AATAATAGTAAAAATTAATAATAAT
Found at i:109312646 original size:15 final size:15
Alignment explanation
Indices: 109312626--109312655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109312616 AATAATAATT
109312626 ATAATAGTAAAAATA
1 ATAATAGTAAAAATA
*
109312641 ATAATAGTAATAATA
1 ATAATAGTAAAAATA
109312656 GCTAAGTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAATAGTAAAAATA
Found at i:109312759 original size:15 final size:15
Alignment explanation
Indices: 109312741--109312771 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109312731 AAAAATATTA
109312741 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
109312756 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
109312771 A
1 A
109312772 GAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAAAT
Found at i:109313313 original size:26 final size:26
Alignment explanation
Indices: 109313284--109313391 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
109313274 TGGTACAAAT
*
109313284 TGATAGTGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
109313310 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109313336 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
109313362 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
109313388 TGAT
1 TGAT
109313392 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:109316143 original size:9 final size:9
Alignment explanation
Indices: 109316122--109316277 Score: 61
Period size: 9 Copynumber: 17.4 Consensus size: 9
109316112 ATAAAAAGAA
109316122 AATA-TAAT
1 AATAGTAAT
*
109316130 CATAGTAAT
1 AATAGTAAT
**
109316139 AATAGTTGT
1 AATAGTAAT
* *
109316148 AGTAATAAT
1 AATAGTAAT
*
109316157 AATAGTAAGAAA
1 AATAGT---AAT
*
109316169 AATAGTGAT
1 AATAGTAAT
*
109316178 AATA-TAAC
1 AATAGTAAT
* *
109316186 AATAATAGT
1 AATAGTAAT
*
109316195 AATA-TAAC
1 AATAGTAAT
*
109316203 AAAAG-AAT
1 AATAGTAAT
*
109316211 AATAATAAT
1 AATAGTAAT
109316220 AATAGTAAT
1 AATAGTAAT
**
109316229 -GGAGATAAT
1 AATAG-TAAT
*
109316238 AATAATAAT
1 AATAGTAAT
*
109316247 AATAATAAT
1 AATAGTAAT
*
109316256 AATAATAAT
1 AATAGTAAT
* *
109316265 GATACTAAT
1 AATAGTAAT
109316274 AATA
1 AATA
109316278 ATATAAATAA
Statistics
Matches: 107, Mismatches: 32, Indels: 17
0.69 0.21 0.11
Matches are distributed among these distances:
8 21 0.20
9 77 0.72
10 1 0.01
12 8 0.07
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.30
Consensus pattern (9 bp):
AATAGTAAT
Found at i:109316156 original size:3 final size:3
Alignment explanation
Indices: 109316150--109316280 Score: 106
Period size: 3 Copynumber: 43.7 Consensus size: 3
109316140 ATAGTTGTAG
* * * * * * *
109316150 TAA TAA TAA TAG TAA GAA AAA TAG TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
109316197 T-A TAA CAA -AA GAA TAA TAA TAA TAA TAG TAA TGGAGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T--A-A TAA TAA TAA
* *
109316243 TAA TAA TAA TAA TAA TAA TAA TGA TAC TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
109316281 TAAATAAAAA
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
2 6 0.06
3 91 0.90
4 1 0.01
5 1 0.01
6 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:109316194 original size:20 final size:21
Alignment explanation
Indices: 109316155--109316194 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
109316145 TGTAGTAATA
*
109316155 ATAATAGTAAGAAAAATAGTG
1 ATAATAGTAACAAAAATAGTG
*
109316176 ATAATA-TAACAATAATAGT
1 ATAATAGTAACAAAAATAGT
109316195 AATATAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAATAGTAACAAAAATAGTG
Found at i:109316286 original size:12 final size:13
Alignment explanation
Indices: 109316208--109316294 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 13
109316198 ATAACAAAAG
109316208 AATAATAATA-AT
1 AATAATAATATAT
* *
109316220 AATAGTAATGGAGAT
1 AATAATAAT--ATAT
109316235 AATAATAATA-AT
1 AATAATAATATAT
109316247 AATAATAATA-AT
1 AATAATAATATAT
* *
109316259 AATAATGATA-CT
1 AATAATAATATAT
109316271 AATAATAATATA-
1 AATAATAATATAT
*
109316283 AATAAAAATATA
1 AATAATAATATA
109316295 AACAACAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
12 52 0.81
13 1 0.02
14 1 0.02
15 10 0.16
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (13 bp):
AATAATAATATAT
Found at i:109317425 original size:33 final size:33
Alignment explanation
Indices: 109317381--109317449 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
109317371 AGTGTCAGAC
109317381 GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
1 GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
* * *
109317414 GCGTGGGGCGTGGTGGCCAAGGCTGAGGGGTAT
1 GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
109317447 GCG
1 GCG
109317450 GCGGCTGAAG
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:0.14, C:0.17, G:0.52, T:0.16
Consensus pattern (33 bp):
GCGTGGAGCGTGGTGACCAAGGCTGAGGGGCAT
Found at i:109318120 original size:13 final size:13
Alignment explanation
Indices: 109318102--109318127 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
109318092 TTGCAAAAAT
109318102 TACTCCATTTGTC
1 TACTCCATTTGTC
109318115 TACTCCATTTGTC
1 TACTCCATTTGTC
109318128 ACATGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
TACTCCATTTGTC
Found at i:109318640 original size:13 final size:13
Alignment explanation
Indices: 109318617--109318660 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
109318607 AAATAAACAA
109318617 TTAATAGAATCAG
1 TTAATAGAATCAG
109318630 TTAATCA-AATCAG
1 TTAAT-AGAATCAG
*
109318643 TTAATAGAATCAA
1 TTAATAGAATCAG
109318656 TTAAT
1 TTAAT
109318661 TAAACCAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (13 bp):
TTAATAGAATCAG
Found at i:109319698 original size:19 final size:19
Alignment explanation
Indices: 109319674--109319712 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
109319664 ATCTAAAATG
109319674 ATAAAATATGTATCCTTCA
1 ATAAAATATGTATCCTTCA
*
109319693 ATAAAATATTTATCCTTCA
1 ATAAAATATGTATCCTTCA
109319712 A
1 A
109319713 CTCTTATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAAAATATGTATCCTTCA
Found at i:109321105 original size:37 final size:37
Alignment explanation
Indices: 109321057--109321193 Score: 145
Period size: 37 Copynumber: 3.7 Consensus size: 37
109321047 TCTATCGAGC
*
109321057 CAAATCTTACTGTTATACTGAATGAAGCTCAATCGAA
1 CAAATCTTACTGTTATACTGAATGAAGCTTAATCGAA
* * *
109321094 CAAATCATACTGTTATACTGAATGGAGCTTAA-CTAA
1 CAAATCTTACTGTTATACTGAATGAAGCTTAATCGAA
** *
109321130 GCAAATCTTACCATTATACTGAAT-AATGTTTAATCGAGA
1 -CAAATCTTACTGTTATACTGAATGAA-GCTTAATCGA-A
* *
109321169 -AAATTTTACTGTTATACTGAGTGAA
1 CAAATCTTACTGTTATACTGAATGAA
109321194 TTTCAAACGA
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
36 4 0.05
37 72 0.89
38 4 0.05
39 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (37 bp):
CAAATCTTACTGTTATACTGAATGAAGCTTAATCGAA
Found at i:109325779 original size:40 final size:40
Alignment explanation
Indices: 109325732--109325811 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
109325722 TCATTTTGGA
109325732 CAAAACCAGATTCATTTCAAAATAATTTCATTTCTTCATT
1 CAAAACCAGATTCATTTCAAAATAATTTCATTTCTTCATT
109325772 CAAAACCAGATTCATTTCAAAATAATTTCATTTCTTCATT
1 CAAAACCAGATTCATTTCAAAATAATTTCATTTCTTCATT
109325812 TACATTTTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (40 bp):
CAAAACCAGATTCATTTCAAAATAATTTCATTTCTTCATT
Found at i:109325865 original size:19 final size:19
Alignment explanation
Indices: 109325829--109325866 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
109325819 TGGAGAAAAC
**
109325829 CATAATCATTTCTGAATGT
1 CATAATCATTTCCAAATGT
109325848 CATAATCATTTCCAAATGT
1 CATAATCATTTCCAAATGT
109325867 TTCTCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (19 bp):
CATAATCATTTCCAAATGT
Found at i:109333376 original size:42 final size:42
Alignment explanation
Indices: 109333312--109333463 Score: 153
Period size: 42 Copynumber: 3.6 Consensus size: 42
109333302 TCGAGACTAT
* * *
109333312 GTGTAAGACCATATATGAGATATGGAATCATTATGAGAATTC
1 GTGTAAGACCATATCTGGGATATGGAATCAATATGAGAATTC
* *
109333354 GTGTAAGACCATATCTGGGATATGGCATCAATATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGAATCAATATGAGAATTC
* * ** * * *
109333396 GTGTAAGACCATAGCTGGGCTATTGGCGTCGATACGAG-ATCCC
1 GTGTAAGACCATATCTGGGATA-TGGAATCAATATGAGAAT-TC
**
109333439 ACGTAAGACCATATCTGGGATATGG
1 GTGTAAGACCATATCTGGGATATGG
109333464 CATTGGTGTG
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 61 0.66
43 31 0.34
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGAATCAATATGAGAATTC
Found at i:109334953 original size:14 final size:14
Alignment explanation
Indices: 109334934--109334968 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
109334924 TTGTTTCACT
109334934 GAAAATGACTTTTG
1 GAAAATGACTTTTG
*
109334948 GAAAATGATTTTTG
1 GAAAATGACTTTTG
109334962 GAAAATG
1 GAAAATG
109334969 GATTACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (14 bp):
GAAAATGACTTTTG
Found at i:109335538 original size:16 final size:16
Alignment explanation
Indices: 109335507--109335543 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
109335497 ATGTTAAGAA
109335507 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
109335523 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
109335539 TATTA
1 TATTA
109335544 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:109335603 original size:16 final size:16
Alignment explanation
Indices: 109335557--109335606 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
109335547 TAAAATTGAA
109335557 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
109335574 A-A--AATAATAAATT
1 ATATTAATAATTTATT
109335587 ATATTAATAATTTATT
1 ATATTAATAATTTATT
109335603 ATAT
1 ATAT
109335607 GACTACATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:109338378 original size:241 final size:239
Alignment explanation
Indices: 109337955--109338435 Score: 890
Period size: 241 Copynumber: 2.0 Consensus size: 239
109337945 GGCGAGGAAG
109337955 ATTGGAAGTAGATGGACAAGCAACAATATGGAATACGAAACACAATGAATAAACTAATCAAAATC
1 ATTGGAAGTAGATGGACAAGCAACAATATGGAATACGAAACACAATGAATAAACTAATCAAAATC
109338020 AAAGAGACAGCTATAAAACCAATAGCTACATTTCAGTCTTGGTTAAACTTTAAACAACAAATAAA
66 AAAGAGACAGCTATAAAACCAATAGCTACATTTCAGTCTTGGTTAAACTTTAAACAACAAATAAA
*
109338085 CTGCCTAGGATGTTACTGTTAGTAATAGATACCAAACATATTCCCATAATATGACTATTACCTAG
131 CTGCCTAGGATGTTACTGGTAGTAATAGATACCAAACATATTCCCATAATATGAC--TTACCTAG
*
109338150 AGACCAAATAACCCTAAGTCACTTGCTCACTCACCAGGTTCAAACT
194 AGACCAAATAACCCTAAATCACTTGCTCACTCACCAGGTTCAAACT
*
109338196 ATTGGAAGTAGATGGACAAGCAGCAATATGGAATACGAAACACAATGAATAAACTAATCAAAATC
1 ATTGGAAGTAGATGGACAAGCAACAATATGGAATACGAAACACAATGAATAAACTAATCAAAATC
109338261 AAAGAGACAGCTATAAAACCAATAGCTACATTTCAGTCTTGGTTAAACTTTAAACAACAAATAAA
66 AAAGAGACAGCTATAAAACCAATAGCTACATTTCAGTCTTGGTTAAACTTTAAACAACAAATAAA
* *
109338326 CTGCCTAGGATGTTACTGGTAGTAATAGATACCAAACATATTCCTATAATATGACTTACCTAGGG
131 CTGCCTAGGATGTTACTGGTAGTAATAGATACCAAACATATTCCCATAATATGACTTACCTAGAG
*
109338391 AGCAAATAACCCTAAATCACTTGCTCACTCACCAGGTTCAAACT
196 ACCAAATAACCCTAAATCACTTGCTCACTCACCAGGTTCAAACT
109338435 A
1 A
109338436 ATGAAGATTA
Statistics
Matches: 234, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
239 52 0.22
241 182 0.78
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (239 bp):
ATTGGAAGTAGATGGACAAGCAACAATATGGAATACGAAACACAATGAATAAACTAATCAAAATC
AAAGAGACAGCTATAAAACCAATAGCTACATTTCAGTCTTGGTTAAACTTTAAACAACAAATAAA
CTGCCTAGGATGTTACTGGTAGTAATAGATACCAAACATATTCCCATAATATGACTTACCTAGAG
ACCAAATAACCCTAAATCACTTGCTCACTCACCAGGTTCAAACT
Found at i:109341555 original size:18 final size:18
Alignment explanation
Indices: 109341522--109341560 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
109341512 ATTACAAAAA
*
109341522 AAATTTAAAATAATTTTT
1 AAATTTAAAATAATTTAT
109341540 AAATTTCAAAAT-ATTTAT
1 AAATTT-AAAATAATTTAT
109341558 AAA
1 AAA
109341561 AAATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTAAAATAATTTAT
Found at i:109341566 original size:21 final size:22
Alignment explanation
Indices: 109341540--109341586 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
109341530 AATAATTTTT
*
109341540 AAATTTCAAAA-TATTTATAAA
1 AAATTTCAAAATTATATATAAA
109341561 AAATTTCAAAATTTATATATAAA
1 AAATTTCAAAA-TTATATATAAA
109341584 AAA
1 AAA
109341587 GTTATGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTTCAAAATTATATATAAA
Found at i:109344582 original size:42 final size:42
Alignment explanation
Indices: 109344523--109344608 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
109344513 CTATGCAAAA
109344523 ACGTCGATTTGACATCTTACAAGAAGCTAAGCCAAGAATTCT
1 ACGTCGATTTGACATCTTACAAGAAGCTAAGCCAAGAATTCT
109344565 ACGTCGATTTGACATCTTACAAGAAGCTAAGCCAAGAATTCT
1 ACGTCGATTTGACATCTTACAAGAAGCTAAGCCAAGAATTCT
109344607 AC
1 AC
109344609 ATTGCTAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (42 bp):
ACGTCGATTTGACATCTTACAAGAAGCTAAGCCAAGAATTCT
Found at i:109348835 original size:25 final size:26
Alignment explanation
Indices: 109348800--109348873 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
109348790 GAAGCTTTGG
109348800 AGAGCCATTAA-CGGGAAGCTCACAA
1 AGAGCCATTAATCGGGAAGCTCACAA
* * * *
109348825 AGAGCCTTTAATCTGGAAGCTCTCGA
1 AGAGCCATTAATCGGGAAGCTCACAA
*
109348851 AGAGCCA-TATATCGGGATGCTCA
1 AGAGCCATTA-ATCGGGAAGCTCA
109348874 TAAGAGTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 12 0.31
26 27 0.69
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATCGGGAAGCTCACAA
Found at i:109350762 original size:21 final size:22
Alignment explanation
Indices: 109350710--109350762 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
109350700 AAATAAAGTC
*
109350710 CATGTA-CAAATATCATCATCT
1 CATGTATCATATATCATCATCT
* *
109350731 CATGTTTTCATATATCAT-ATGT
1 CATG-TATCATATATCATCATCT
109350753 CATGTATCAT
1 CATGTATCAT
109350763 CATTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (22 bp):
CATGTATCATATATCATCATCT
Found at i:109353519 original size:27 final size:27
Alignment explanation
Indices: 109353488--109353579 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
109353478 CATGATTTTA
*
109353488 CACTTTGGTGCCTCTTATTTTGTTATG
1 CACTTTGGTGCCTCCTATTTTGTTATG
109353515 CACTTTGGTGCCTCCTATTTTGTTATG
1 CACTTTGGTGCCTCCTATTTTGTTATG
*** * *
109353542 CACTTCATTGCCTCCTGTTCTGTTATG
1 CACTTTGGTGCCTCCTATTTTGTTATG
*
109353569 CACATTGGTGC
1 CACTTTGGTGC
109353580 TTGTGTTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (27 bp):
CACTTTGGTGCCTCCTATTTTGTTATG
Found at i:109354189 original size:17 final size:18
Alignment explanation
Indices: 109354166--109354215 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
109354156 TAAGGAGATA
109354166 AAAAATAAATAAATAACG
1 AAAAATAAATAAATAACG
* *
109354184 -AAAATACATAAAT-AGG
1 AAAAATAAATAAATAACG
*
109354200 AAAAATAAACAAATAA
1 AAAAATAAATAAATAA
109354216 ATTAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 23 0.88
18 1 0.04
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (18 bp):
AAAAATAAATAAATAACG
Found at i:109355527 original size:21 final size:22
Alignment explanation
Indices: 109355501--109355557 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
109355491 ATATTGGACT
*
109355501 TTGTCTTGAGACATAAAC-CCC
1 TTGTCTTGAGACATAAACTCAC
* * *
109355522 TTGTCTCGAGACACACACTCAC
1 TTGTCTTGAGACATAAACTCAC
109355544 TTGTCTTGAGACAT
1 TTGTCTTGAGACAT
109355558 GATAAATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (22 bp):
TTGTCTTGAGACATAAACTCAC
Found at i:109357925 original size:43 final size:43
Alignment explanation
Indices: 109357858--109357971 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 43
109357848 TTATTTCGGA
* * *
109357858 AAACGTCGCTATAGAGCATGATCTTTAGCGGCGCTTTCCCTAC
1 AAACGTCGCTATAGAACATGATCTTTAGCAGCGCTTTCACTAC
* * * * *
109357901 AAACGTTGCTATAGAACATAATCTTAAGCAGCGCTTTTATTAC
1 AAACGTCGCTATAGAACATGATCTTTAGCAGCGCTTTCACTAC
* *
109357944 AAACGTCGCTAAAGAACATGATTTTTAG
1 AAACGTCGCTATAGAACATGATCTTTAG
109357972 TGACCTTTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
AAACGTCGCTATAGAACATGATCTTTAGCAGCGCTTTCACTAC
Found at i:109358524 original size:66 final size:66
Alignment explanation
Indices: 109358397--109358530 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
109358387 ATTTTAAAGC
* * * * * *
109358397 TGTAGCTAGAGTTCGTCATATTTTTTTGTTGCCTCTGCTGCCCTTGTTGTTGCATCTGCTTTAAG
1 TGTAGCTAGAGTTCATCATATTTTTTTGTAGCCTCTGCTGCCCTCGATGCTGCATCAGCTTTAAG
109358462 T
66 T
* * * *
109358463 TGTAGCTGGAGTTCATCATATTTTCTTTG-AGCCTCTGCTTCTCTCGATGCTGCCTCAGCTTTAA
1 TGTAGCTAGAGTTCATCATATTTT-TTTGTAGCCTCTGCTGCCCTCGATGCTGCATCAGCTTTAA
109358527 GT
65 GT
109358529 TG
1 TG
109358531 AGCAATTTGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (66 bp):
TGTAGCTAGAGTTCATCATATTTTTTTGTAGCCTCTGCTGCCCTCGATGCTGCATCAGCTTTAAG
T
Found at i:109363077 original size:21 final size:20
Alignment explanation
Indices: 109363044--109363110 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
109363034 GTGTTTTGAA
109363044 CACACGGCAGTGTCTGGTGGG
1 CACACGGC-GTGTCTGGTGGG
* ** *
109363065 CACACGGGCGTGTGTTTTGGA
1 CACAC-GGCGTGTCTGGTGGG
* *
109363086 CACACAGCCGTGTTTGGTGGG
1 CACAC-GGCGTGTCTGGTGGG
109363107 CACA
1 CACA
109363111 TGAGAGTGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.16, C:0.24, G:0.37, T:0.22
Consensus pattern (20 bp):
CACACGGCGTGTCTGGTGGG
Found at i:109363090 original size:42 final size:42
Alignment explanation
Indices: 109363031--109363110 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
109363021 CTCACGCGGA
*
109363031 CGTGTGTTTTGAACACACGGCAGTGTCTGGTGGGCACACGGG
1 CGTGTGTTTTGAACACACAGCAGTGTCTGGTGGGCACACGGG
* * *
109363073 CGTGTGTTTTGGACACACAGCCGTGTTTGGTGGGCACA
1 CGTGTGTTTTGAACACACAGCAGTGTCTGGTGGGCACA
109363111 TGAGAGTGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.16, C:0.21, G:0.36, T:0.26
Consensus pattern (42 bp):
CGTGTGTTTTGAACACACAGCAGTGTCTGGTGGGCACACGGG
Found at i:109363120 original size:42 final size:42
Alignment explanation
Indices: 109363032--109363120 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
109363022 TCACGCGGAC
* * *
109363032 GTGTGTTTTGAACACACGGCAGTGTCTGGTGGGCACACGGGC
1 GTGTGTTTTGAACACACAGCAGTGTCTGGTGGGCACACGAGA
* * * *
109363074 GTGTGTTTTGGACACACAGCCGTGTTTGGTGGGCACATGAGA
1 GTGTGTTTTGAACACACAGCAGTGTCTGGTGGGCACACGAGA
109363116 GTGTG
1 GTGTG
109363121 AGTCCCTCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.17, C:0.18, G:0.38, T:0.27
Consensus pattern (42 bp):
GTGTGTTTTGAACACACAGCAGTGTCTGGTGGGCACACGAGA
Found at i:109368567 original size:21 final size:23
Alignment explanation
Indices: 109368536--109368578 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
109368526 ATCCTCCTGG
109368536 CGCCACGCACC-CCCCGTACACA
1 CGCCACGCACCACCCCGTACACA
*
109368558 CGCCA-GCACCACCCTGTACAC
1 CGCCACGCACCACCCCGTACAC
109368579 CTCGAGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.56, G:0.14, T:0.07
Consensus pattern (23 bp):
CGCCACGCACCACCCCGTACACA
Found at i:109370743 original size:130 final size:130
Alignment explanation
Indices: 109370510--109370875 Score: 509
Period size: 130 Copynumber: 2.8 Consensus size: 130
109370500 ATTCTTCAAT
*
109370510 ACGAAGATGAAATTTGATGTTCGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT
1 ACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT
* * *
109370575 CGCATTTGCTCAAAATAATCGAATTTCCCTTCGAAATTTCATTCATATCTTTTAAAATCCCTTAA
66 CGCATTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATATCTTTTAAAATCCCTAAA
* * *
109370640 ACGAAGATGAGATTTGATGTTTGGCAATTCGCGAAACCGTGCCCTAACGTGTTGGGTTGCAATTT
1 ACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT
* * * * *
109370705 TGCATTTGCTCAAAATAATCGAATATCACTTTAAAATTTCGTTCATGTCTTTTAAAATCCCTAAA
66 CGCATTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATATCTTTTAAAATCCCTAAA
** * * * * *
109370770 ACGAAGGCGATATGTGATATTTGGCAATTCGCGGGATCGTGCCCTAACGTGTTGGGTAGCAATTT
1 ACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT
* * * *
109370835 CCCGA-TTGTTTAAAATAATCAAATATCCCTTCAAAATTTCA
66 CGC-ATTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCA
109370876 CTCGGGTCTT
Statistics
Matches: 206, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 205 1.00
131 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (130 bp):
ACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTT
CGCATTTGCTCAAAATAATCGAATATCCCTTCAAAATTTCATTCATATCTTTTAAAATCCCTAAA
Found at i:109370935 original size:130 final size:127
Alignment explanation
Indices: 109370527--109370987 Score: 442
Period size: 130 Copynumber: 3.5 Consensus size: 127
109370517 TGAAATTTGA
*
109370527 TGTTCGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATA
1 TGTTTGGCAATTCGCGG-ATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATA
* * * * *
109370592 ATCGAATTTCCCTTCGAAATTTCATTCATATCTTTTAAAATCCCTT-AAACGAAGATGAGATTTG
65 ATCGAATATCCCTTCAAAATTTCATTCATGTCTTTTAAAAT-CCTTAAAACGAAG--GCGATATG
*
109370656 A
127 G
* * *
109370657 TGTTTGGCAATTCGCGAAACCGTGCCCTAACGTGTTGGGTTGCAATTTTGCATTTGCTCAAAATA
1 TGTTTGGCAATTCGCG-GATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATA
* * * *
109370722 ATCGAATATCACTTTAAAATTTCGTTCATGTCTTTTAAAATCCCTAAAACGAAGGCGATATGTG
65 ATCGAATATCCCTTCAAAATTTCATTCATGTCTTTTAAAATCCTTAAAACGAAGGCGATATG-G
* * * * *
109370786 ATATTTGGCAATTCGCGGGATCGTGCCCTAACGTGTTGGGTAGCAATTTCCCGA-TTGTTTAAAA
1 -TGTTTGGCAATTCGC-GGATCGTGCCCTAACGTGTTGGGTTGCAATTTCGC-ATTTGCTCAAAA
* * ** * * *
109370850 TAATCAAATATCCCTTCAAAATTTCACTCGGGTCTTCTAAAAATCCTTTAAAATGAAGGCAATAC
63 TAATCGAATATCCCTTCAAAATTTCATTCATGTCTT-TTAAAATCC-TTAAAACGAAGGCGATA-
109370915 TCGG
125 T-GG
* * * * * ** * * * *
109370919 TGTTTGACAATTCG-GGAATCATGCCTTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACA
1 TGTTTGGCAATTCGCGG-ATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATA
109370983 ATCGA
65 ATCGA
109370988 GTATTCATTT
Statistics
Matches: 272, Mismatches: 47, Indels: 23
0.80 0.14 0.07
Matches are distributed among these distances:
128 6 0.02
129 3 0.01
130 185 0.68
131 49 0.18
132 26 0.10
133 2 0.01
134 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (127 bp):
TGTTTGGCAATTCGCGGATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAAATAA
TCGAATATCCCTTCAAAATTTCATTCATGTCTTTTAAAATCCTTAAAACGAAGGCGATATGG
Found at i:109376021 original size:3 final size:3
Alignment explanation
Indices: 109376013--109376043 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
109376003 CGATTAAAAA
*
109376013 ATC ATC ATC ATC ATC ATC ATC ATC AAC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
109376044 AGTACAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:109382300 original size:12 final size:12
Alignment explanation
Indices: 109382285--109382328 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
109382275 TTTCATTTCA
*
109382285 TCCTCATCTTCC
1 TCCTCCTCTTCC
109382297 TCCTCCTCTTCC
1 TCCTCCTCTTCC
*
109382309 TCCTCCTCCTCC
1 TCCTCCTCTTCC
109382321 TCCTCCTC
1 TCCTCCTC
109382329 CTCTTCTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (12 bp):
TCCTCCTCTTCC
Found at i:109382302 original size:3 final size:3
Alignment explanation
Indices: 109382294--109382331 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
109382284 ATCCTCATCT
*
109382294 TCC TCC TCC TCT TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
109382332 TTCTTGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
TCC
Found at i:109385894 original size:18 final size:18
Alignment explanation
Indices: 109385871--109385937 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 18
109385861 TTCATAGATA
109385871 AGTAAAACTAAAACTCTT
1 AGTAAAACTAAAACTCTT
* *
109385889 AGTAAAACCTGATATAA-TAGATA
1 AGTAAAA-CT-A-A-AACT--CTT
109385912 AGTAAAACTAAAACTCTT
1 AGTAAAACTAAAACTCTT
109385930 AGTAAAAC
1 AGTAAAAC
109385938 CTGATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
18 16 0.42
19 4 0.11
20 3 0.08
21 3 0.08
22 4 0.11
23 8 0.21
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.25
Consensus pattern (18 bp):
AGTAAAACTAAAACTCTT
Found at i:109385921 original size:41 final size:42
Alignment explanation
Indices: 109385864--109385967 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 42
109385854 TCTTTATTTC
109385864 ATAGATAAGTAAAACTAAAACTCTTAGTAAAACCTG-ATATA
1 ATAGATAAGTAAAACTAAAACTCTTAGTAAAACCTGAATATA
109385905 ATAGATAAGTAAAACTAAAACTCTTAGTAAAACCTGATATATA
1 ATAGATAAGTAAAACTAAAACTCTTAGTAAAACCTGA-ATATA
* *
109385948 ATAAATAAATAAAACTAAAA
1 ATAGATAAGTAAAACTAAAA
109385968 ACTCCTATTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
41 36 0.61
43 23 0.39
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.26
Consensus pattern (42 bp):
ATAGATAAGTAAAACTAAAACTCTTAGTAAAACCTGAATATA
Found at i:109391863 original size:43 final size:44
Alignment explanation
Indices: 109391816--109391919 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 44
109391806 ATGAATTAAA
* * *
109391816 AATTAAATTAAAATAGAAGTTGTGATAATTATACATT-TAAAAT
1 AATTAAATTAAAATAAAAGTTGTGATAATTACACATTAAAAAAT
109391859 AATTATAATGT--AATAAAAGTTGTGATAATTACACATTAAAAAAT
1 AATTA-AAT-TAAAATAAAAGTTGTGATAATTACACATTAAAAAAT
109391903 AATTAAAATTTAAAATA
1 AATT-AAA-TTAAAATA
109391920 CAATTATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
43 29 0.57
44 15 0.29
45 3 0.06
46 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (44 bp):
AATTAAATTAAAATAAAAGTTGTGATAATTACACATTAAAAAAT
Found at i:109391936 original size:20 final size:21
Alignment explanation
Indices: 109391911--109391959 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
109391901 ATAATTAAAA
*
109391911 TTTAAAATACAAT-TATTAAT
1 TTTAAAATAAAATGTATTAAT
*
109391931 TTTAAAA-AAAATGTGTTAAT
1 TTTAAAATAAAATGTATTAAT
*
109391951 TTAAAAATA
1 TTTAAAATA
109391960 GAGTTATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 19 0.79
21 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
TTTAAAATAAAATGTATTAAT
Found at i:109399898 original size:26 final size:28
Alignment explanation
Indices: 109399868--109399928 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
109399858 TATATTAATA
* * *
109399868 AAATATATAT-TACT-TAATATTTAAGT
1 AAATATATATATAATATAATAATAAAGT
109399894 AAATATATATATAATATAATAATAAAGT
1 AAATATATATATAATATAATAATAAAGT
109399922 AAATATA
1 AAATATA
109399929 AAATAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 3 0.10
28 17 0.57
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (28 bp):
AAATATATATATAATATAATAATAAAGT
Found at i:109399949 original size:24 final size:25
Alignment explanation
Indices: 109399889--109399950 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
109399879 ACTTAATATT
* *
109399889 TAAGTAAAT-ATATATATAATATAA
1 TAAGTAAATGAAATATAAAATATAA
109399913 TAA-TAAA-GTAAATATAAAATA-AA
1 TAAGTAAATG-AAATATAAAATATAA
109399936 TAAGTAAATGAAATA
1 TAAGTAAATGAAATA
109399951 AATAAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 9 0.28
24 22 0.69
25 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (25 bp):
TAAGTAAATGAAATATAAAATATAA
Found at i:109400111 original size:61 final size:61
Alignment explanation
Indices: 109400046--109400166 Score: 206
Period size: 61 Copynumber: 2.0 Consensus size: 61
109400036 GATATATTTA
* * *
109400046 AAGTCATACTAGAATTCTCGACTAAAAAGATAAAAGATAAAGTTGACGAGGAATAGCTCGG
1 AAGTCATACTAGAATTCTCGACTAAAAAGACAAAAGATAAAGTCGACGAGGAATACCTCGG
*
109400107 AAGTCATACTAGAATTCTCGACTAAAAAGGCAAAAGATAAAGTCGACGAGGAATACCTCG
1 AAGTCATACTAGAATTCTCGACTAAAAAGACAAAAGATAAAGTCGACGAGGAATACCTCG
109400167 AAATTTCCAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.20
Consensus pattern (61 bp):
AAGTCATACTAGAATTCTCGACTAAAAAGACAAAAGATAAAGTCGACGAGGAATACCTCGG
Found at i:109400527 original size:37 final size:37
Alignment explanation
Indices: 109400485--109400578 Score: 170
Period size: 37 Copynumber: 2.5 Consensus size: 37
109400475 ACTTCGAGTT
*
109400485 GATGAGACACTGGGTGCCAATTTACTTCGGTTTAGCC
1 GATGAGACACTGGGTGCCAATTTACTTCGATTTAGCC
109400522 GATGAGACACTGGGTGCCAATTTACTTCGATTTAGCC
1 GATGAGACACTGGGTGCCAATTTACTTCGATTTAGCC
*
109400559 GATGAGACACTAGGTGCCAA
1 GATGAGACACTGGGTGCCAA
109400579 ACTGGTGTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (37 bp):
GATGAGACACTGGGTGCCAATTTACTTCGATTTAGCC
Found at i:109400815 original size:16 final size:17
Alignment explanation
Indices: 109400764--109400834 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 17
109400754 TTATATACTC
*
109400764 ATGAATTGA-GTATGGT
1 ATGAATTGATGTATTGT
* *
109400780 ATGAAATGATGTATT-C
1 ATGAATTGATGTATTGT
109400796 ATGAATTGA-GTATTGT
1 ATGAATTGATGTATTGT
109400812 ATG-ATTGATGTCATTGT
1 ATGAATTGATGT-ATTGT
*
109400829 ACGAAT
1 ATGAAT
109400835 AAATATGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 10 0.23
16 21 0.48
17 11 0.25
18 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.39
Consensus pattern (17 bp):
ATGAATTGATGTATTGT
Found at i:109403541 original size:25 final size:25
Alignment explanation
Indices: 109403486--109403541 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
109403476 TTTAATATTA
109403486 ATAA-TTTATTATTAAAATTTTAAAT
1 ATAATTTTATTATTAAAA-TTTAAAT
109403511 AT-ATTTTATTATTAAAA-TTAAAT
1 ATAATTTTATTATTAAAATTTAAAT
109403534 CATAATTT
1 -ATAATTT
109403542 ATAAGTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.21
24 3 0.11
25 19 0.68
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTTTATTATTAAAATTTAAAT
Found at i:109412869 original size:17 final size:15
Alignment explanation
Indices: 109412830--109412870 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
109412820 ATAATTCATA
109412830 AATATATTATTTATT
1 AATATATTATTTATT
*
109412845 AATATATTA-TAATT
1 AATATATTATTTATT
109412859 AATATATTATTT
1 AATATATTATTT
109412871 TTTGGTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATATTATTTATT
Found at i:109413034 original size:32 final size:32
Alignment explanation
Indices: 109412989--109413053 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
109412979 TTTAGATCAA
*
109412989 AAATGAATCTAAACAGA-TGGTTATCTAAATTC
1 AAATGAATCTAAACA-ACTAGTTATCTAAATTC
* * *
109413021 AAATGCATTTAAACAACTATTTATCTAAATTC
1 AAATGAATCTAAACAACTAGTTATCTAAATTC
109413053 A
1 A
109413054 TTATAAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (32 bp):
AAATGAATCTAAACAACTAGTTATCTAAATTC
Found at i:109413536 original size:21 final size:22
Alignment explanation
Indices: 109413510--109413568 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
109413500 GTTTTAAGAA
*
109413510 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
109413531 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
109413553 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
109413569 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:109413583 original size:26 final size:24
Alignment explanation
Indices: 109413539--109413588 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
109413529 ATTTGTTTTA
*
109413539 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
109413563 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
109413589 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:109415248 original size:13 final size:13
Alignment explanation
Indices: 109415230--109415254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109415220 TATTAGGATT
109415230 ATTTAATTTTAAG
1 ATTTAATTTTAAG
109415243 ATTTAATTTTAA
1 ATTTAATTTTAA
109415255 TTATCTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTAATTTTAAG
Found at i:109421658 original size:6 final size:6
Alignment explanation
Indices: 109421647--109421674 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
109421637 AGGCAACCCA
109421647 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
109421675 ATTTTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:109421675 original size:22 final size:22
Alignment explanation
Indices: 109421650--109421696 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
109421640 CAACCCAATT
109421650 TTTATTTTTAT-TT-TTATTTTTA
1 TTTA-TTTTATCTTATTA-TTTTA
109421672 TTTATTTTATCTTATTATTTTA
1 TTTATTTTATCTTATTATTTTA
109421694 TTT
1 TTT
109421697 TATTCAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
22 14 0.61
23 3 0.13
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTATTTTATCTTATTATTTTA
Found at i:109423181 original size:15 final size:15
Alignment explanation
Indices: 109423161--109423190 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109423151 CATTTTATTT
*
109423161 ATATTAGGATAATTA
1 ATATTAAGATAATTA
109423176 ATATTAAGATAATTA
1 ATATTAAGATAATTA
109423191 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:109423218 original size:27 final size:26
Alignment explanation
Indices: 109423157--109423219 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
109423147 ACTCCATTTT
109423157 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * *
109423184 ATAATTATTAGGATTATTTAATTTTAAG
1 AT-TTTATTAGGA-TAATTAATATTAAG
109423212 ATTTTATT
1 ATTTTATT
109423220 TTAATTATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:109438496 original size:60 final size:60
Alignment explanation
Indices: 109438398--109438512 Score: 194
Period size: 60 Copynumber: 1.9 Consensus size: 60
109438388 TGATACTGCG
109438398 AGCTCCCTTAACTGTCCTCTCACTGTACATCTCATGTGTATCCATCTAGTGGGGTCTGGA
1 AGCTCCCTTAACTGTCCTCTCACTGTACATCTCATGTGTATCCATCTAGTGGGGTCTGGA
* * **
109438458 AGCTCCCTTAACTTTCCTCTCATTGTACATCTTGTGTGTATCCATCTAGTGGGGT
1 AGCTCCCTTAACTGTCCTCTCACTGTACATCTCATGTGTATCCATCTAGTGGGGT
109438513 TTAGTCGGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (60 bp):
AGCTCCCTTAACTGTCCTCTCACTGTACATCTCATGTGTATCCATCTAGTGGGGTCTGGA
Found at i:109443273 original size:20 final size:19
Alignment explanation
Indices: 109443222--109443275 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
109443212 GGCCCGTTAG
*
109443222 AAAAAAACC-AGAAATTAA
1 AAAAAAACCAATAAATTAA
**
109443240 AAAAACAAAAAATAAATTAA
1 AAAAA-AACCAATAAATTAA
109443260 AATAAAAACCAATAAA
1 AA-AAAAACCAATAAA
109443276 AGTTCATCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 5 0.18
19 2 0.07
20 18 0.64
21 3 0.11
ACGTcount: A:0.76, C:0.09, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAAAAACCAATAAATTAA
Found at i:109444737 original size:14 final size:14
Alignment explanation
Indices: 109444718--109444746 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
109444708 ATATATATAT
109444718 ATAATTCATGATAA
1 ATAATTCATGATAA
109444732 ATAATTCATGATAA
1 ATAATTCATGATAA
109444746 A
1 A
109444747 GTTAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
ATAATTCATGATAA
Found at i:109444983 original size:30 final size:31
Alignment explanation
Indices: 109444949--109445008 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
109444939 CATGTTATTT
*
109444949 TATACAT-ATAAT-TTCTTTTAAATCTATTAG
1 TATACATAATAATGTT-TTTAAAATCTATTAG
*
109444979 TATACATAATTATGTTTTTAAAATCTATTA
1 TATACATAATAATGTTTTTAAAATCTATTA
109445009 CATATACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 17 0.65
32 2 0.08
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.50
Consensus pattern (31 bp):
TATACATAATAATGTTTTTAAAATCTATTAG
Found at i:109453588 original size:44 final size:44
Alignment explanation
Indices: 109453528--109453982 Score: 350
Period size: 44 Copynumber: 10.1 Consensus size: 44
109453518 TTGAATATAG
* * *
109453528 CAAATTTTATCT-CCTGAAGATGCAGTGGAGC-GAAATAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAGCTA
* * * * * * *
109453571 CAAATCTCATATCCCTGAAGTTGTAGTAGATCGGATTAGAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
*
109453615 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-CAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTA
* * *
109453659 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTTAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
*
109453703 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* *
109453747 CAAATCTTATCTCGCTGAAGTTGCAGTGGAGTAGATTGAAA--TGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCT-A
* * * * * * *
109453791 CAAATCATATATCACTGAAGTTGCAATGG-GTTAAATTAAATCTACCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCT---A
* * *
109453838 CAGCGAATCTTATTTCCCTGAAGTTGCAGTGAAACAGATTAAAGCTACAAGTTA
1 CA---AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG---C----TA
* ** *
109453892 CAAATCTTATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
* * * * *
109453936 CGAATCTCATCTCCTTGAAGTTACAGCGGAGTC-GATTGAAA-CTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATT-AAAGCTA
109453980 CAA
1 CAA
109453983 TTCCTATACC
Statistics
Matches: 333, Mismatches: 55, Indels: 47
0.77 0.13 0.11
Matches are distributed among these distances:
43 16 0.05
44 238 0.71
45 9 0.03
47 3 0.01
48 1 0.00
50 29 0.09
51 32 0.10
53 1 0.00
54 3 0.01
57 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA
Found at i:109453746 original size:132 final size:131
Alignment explanation
Indices: 109453528--109454001 Score: 398
Period size: 132 Copynumber: 3.5 Consensus size: 131
109453518 TTGAATATAG
* * * * *
109453528 CAAATTTTATCTCCTGAAGATGCAGTGGAG-CGAAATAAAGCTACAAATCTCATATCCCTGAAGT
1 CAAATCTTATCTCCTGAAGTTGCAGTGGAGTAG-ATTAAAGCTACAAATCTTATATCCCTGAAGT
* * * *
109453592 TGTAGTAGATCGGATT-AGAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA
65 TGCAGTGGAACAGATTGA-AGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA
109453656 CAA
129 CAA
* *
109453659 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTTAAGCTACAAATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCC-TGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATATCCCTGAAGT
* * * *
109453724 TGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCGCTGAAGTTGCAGTGGAGTAGATTGAAAT
65 TGCAGTGGAACAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAC
*
109453789 GA
130 AA
* * * * * *
109453791 CAAATCATATATCACTGAAGTTGCAATGG-GTTAAATTAAATCTACCACAGCGAATCTTATTTCC
1 CAAATCTTATCTC-CTGAAGTTGCAGTGGAG-TAGATTAAAGCT---ACA---AATCTTATATCC
* * * **
109453855 CTGAAGTTGCAGTGAAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCTTGAAGTTATAGTG
58 CTGAAGTTGCAGTGGAACAGATT---G----AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTG
* *
109453920 GAGCAGATTGAAGCTA
116 GAGCAGATTGAAACAA
* * * * * * * * *
109453936 CGAATCTCATCTCCTTGAAGTTACAGCGGAGTCGATTGAAA-CTACAATTCCTATACCCCTAAAG
1 CAAATCTTATCTCC-TGAAGTTGCAGTGGAGTAGATT-AAAGCTACAAATCTTATATCCCTGAAG
109454000 TT
64 TT
109454002 ATAATGGGTT
Statistics
Matches: 275, Mismatches: 47, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
131 14 0.05
132 132 0.48
133 3 0.01
135 3 0.01
138 32 0.12
139 15 0.05
141 1 0.00
142 3 0.01
144 1 0.00
145 67 0.24
146 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (131 bp):
CAAATCTTATCTCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATATCCCTGAAGTT
GCAGTGGAACAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACA
A
Found at i:109460499 original size:23 final size:23
Alignment explanation
Indices: 109460473--109460520 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
109460463 AAAACTTAAT
109460473 AATAATTGTTGATAAAGTGATAA
1 AATAATTGTTGATAAAGTGATAA
* * * *
109460496 AATATTTGTTTATAAATTTATAA
1 AATAATTGTTGATAAAGTGATAA
109460519 AA
1 AA
109460521 CACCTGCTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (23 bp):
AATAATTGTTGATAAAGTGATAA
Found at i:109461121 original size:20 final size:18
Alignment explanation
Indices: 109461079--109461133 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 18
109461069 TTTATTTGTC
**
109461079 AAAATTAT-AAATTTATT
1 AAAATTATAAAATTTAAA
109461096 AAAATTATCAAAATGTTAAA
1 AAAATTAT-AAAAT-TTAAA
109461116 AAAATTATAAAATTTAAA
1 AAAATTATAAAATTTAAA
109461134 CTATCAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 9 0.27
20 11 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATTATAAAATTTAAA
Found at i:109461127 original size:8 final size:8
Alignment explanation
Indices: 109461079--109461166 Score: 54
Period size: 8 Copynumber: 10.5 Consensus size: 8
109461069 TTTATTTGTC
109461079 AAAATTAT
1 AAAATTAT
*
109461087 AAATTTATT
1 AAAATTA-T
109461096 AAAATTAT
1 AAAATTAT
*
109461104 CAAAATGTTAAA
1 -AAAA--TT-AT
109461116 AAAATTAT
1 AAAATTAT
109461124 AAAATT-T
1 AAAATTAT
*
109461131 -AAACTAT
1 AAAATTAT
*
109461138 CAAACTTAT
1 -AAAATTAT
*
109461147 AAAATTAG
1 AAAATTAT
*
109461155 AAAATAAT
1 AAAATTAT
109461163 AAAA
1 AAAA
109461167 ATATTTAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
6 4 0.07
7 2 0.03
8 30 0.49
9 18 0.30
11 6 0.10
12 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Found at i:109467612 original size:20 final size:21
Alignment explanation
Indices: 109467584--109467637 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
109467574 GAAAGAAAAA
*
109467584 AGAAAAAGAAAAAGA-GAAGG
1 AGAAGAAGAAAAAGAGGAAGG
* *
109467604 AGAAGAAGAAGAAGAGGGAGG
1 AGAAGAAGAAAAAGAGGAAGG
*
109467625 -GAAGAAAAAAAAG
1 AGAAGAAGAAAAAG
109467638 GTAATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
AGAAGAAGAAAAAGAGGAAGG
Found at i:109468263 original size:146 final size:145
Alignment explanation
Indices: 109468078--109469371 Score: 1722
Period size: 146 Copynumber: 9.1 Consensus size: 145
109468068 AAAAAATCCA
* * *
109468078 AAAATAAAATAAAAAAGGCCAAAATTAGAGTTTTTTACTAAATTAATATAAATATACTAAAATAA
1 AAAATAAAA-AAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAA-AAACTAAAATAA
*
109468143 TACATATGAAACATTATGTACTAAAATAATA-AAAAAATAAAATACGAAAATAGTATATTTTGAA
64 TACATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
109468207 AAATAAAATCCGAAAAT
129 AAATAAAATCCGAAAAT
* *
109468224 AAAATAAAAAATAAACGGCCAAAATCAAAATTTTTTACTAAATTAATATAAAAAAACTAAAATAA
1 AAAATAAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAAAACTAAAATAA
* *
109468289 TACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACAAAAATAGTATATTTTAA
64 TACATATGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAA
*
109468354 AAAATAAAATCCGAAAAC
128 AAAATAAAATCCGAAAAT
*
109468372 AAAAT---AAAAAA--GCCAAAATCACA-TATTTTTACTAAATTAATATAAAAAAACTAAAATAA
1 AAAATAAAAAAAAACGGCCAAAATCAGAGT-TTTTTACTAAATTAATAT-AAAAAACTAAAATAA
* *
109468431 TAC--ATGAAACATTATGTACTAAAATAATATAAAAAACAAAATACG---A-A-TATATCTTAAA
64 TACATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAA
109468489 AAATAAAATCCGAAAAT
129 AAATAAAATCCGAAAAT
* *
109468506 --AA-AAATAAAAAGGGCCAAAATCAGAGTTTTTT--TAAATTAATATAAAAAACTAAAATAATA
1 AAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACTAAAATAATA
* * *
109468566 C--ATGAAACATTATGTACTAAAATAATATAAAAAAATAAAATACAAAAATAATAAATTTTAAAA
66 CATATGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAA
*
109468629 AATAAAATCTGAAAAT
130 AATAAAATCCGAAAAT
* * *
109468645 -AAA-AATAAAAAA-TGCCAAAATCAGAGTTTTTTTCTAAATTAATATAAAAAACTAAAATAATA
1 AAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACTAAAATAATA
* * * *
109468707 CATTTGAAACATTATGTACTAAAATAATATAAAAGAATAAAATACCAAAAGAGCATATTTTAAAA
66 CATATGAAACATTATGTACTAAAATAATATAAAA-AATAAAATACGAAAATAGTATATTTTAAAA
* *
109468772 AATAAAATCTGAAAAC
130 AATAAAATCCGAAAAT
* * * *
109468788 AAAAT-AAATAAAACGGCCAAAATCACAGATTTTTACTAAATTAGTATAAAAAAACTAAAATAAT
1 AAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAAAACTAAAATAAT
* *
109468852 AC--ATGAAACATTATTTACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTT-AAA
65 ACATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAA
*
109468914 AA-AAAATCCAAAAAT
130 AATAAAATCCGAAAAT
* * *
109468929 -AAA-AAATAAAAAGGGCC-AAATCAGAGTTTTTTTTCTAAATTAATATAAAAAACTAAAATAAT
1 AAAATAAAAAAAAACGGCCAAAATCAGAG-TTTTTTACTAAATTAATATAAAAAACTAAAATAAT
* *
109468991 AC--ATGAAACATTATGTACTAAAATAATATAAAAAACAAAATACGAAAATAGTATATATTAAAA
65 ACATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAA
109469054 AATAAAATCCGAAAAT
130 AATAAAATCCGAAAAT
*
109469070 AAAATAAAAAATAAACGGCCAAAATCAGAGTTTTTTATTAAATTAATATAAAAAACTAAAATAAT
1 AAAATAAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACTAAAATAAT
* * * *
109469135 ACATTTGGAATATTATGTACTAAAATAATATAAAAAATAAAATATGAAAATAGTATATTTTAAAA
65 ACATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAA
* *
109469200 AGTAAAATCCAAAAAT
130 AATAAAATCCGAAAAT
* * * *
109469216 AAAATAAAAAAACAAACGGTCAAAATCGGAGTTTTTTATTAAATTAATATAAAAAATACAAAAAT
1 AAAAT-AAAAAA-AAACGGCCAAAATCAGAGTTTTTTACTAAATTAATAT-AAAAA-ACTAAAAT
* * *
109469281 AATACATTTGAAACATTATGTACTAAAATAATAT-AAAAATAAAAAACGAAAATAATATATTTTA
62 AATACATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTA
109469345 AAAAATAAAATCCGAAAAT
127 AAAAATAAAATCCGAAAAT
109469364 AAAATAAA
1 AAAATAAA
109469372 TACCAAAATA
Statistics
Matches: 1025, Mismatches: 83, Indels: 79
0.86 0.07 0.07
Matches are distributed among these distances:
132 2 0.00
133 45 0.04
134 55 0.05
135 1 0.00
136 17 0.02
137 2 0.00
138 1 0.00
139 136 0.13
140 69 0.07
141 52 0.05
142 60 0.06
143 93 0.09
144 83 0.08
145 42 0.04
146 175 0.17
147 47 0.05
148 106 0.10
149 39 0.04
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (145 bp):
AAAATAAAAAAAAACGGCCAAAATCAGAGTTTTTTACTAAATTAATATAAAAAACTAAAATAATA
CATATGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAA
ATAAAATCCGAAAAT
Found at i:109468602 original size:13 final size:13
Alignment explanation
Indices: 109468584--109468618 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
109468574 ATTATGTACT
109468584 AAAATAATATAAA
1 AAAATAATATAAA
* *
109468597 AAAATAAAATACA
1 AAAATAATATAAA
109468610 AAAATAATA
1 AAAATAATA
109468619 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATATAAA
Found at i:109469077 original size:25 final size:25
Alignment explanation
Indices: 109469010--109469084 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 25
109469000 ATTATGTACT
* *
109469010 AAAATAATATAAAAAACAAAATACG
1 AAAATAAAATAAAAAATAAAATACG
*
109469035 AAAATAGTATATATTAAAAAATAAAATCCG
1 AAAATA--A-A-A-TAAAAAATAAAATACG
109469065 AAAATAAAATAAAAAATAAA
1 AAAATAAAATAAAAAATAAA
109469085 CGGCCAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
25 17 0.40
26 1 0.02
27 2 0.05
28 1 0.02
29 1 0.02
30 20 0.48
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (25 bp):
AAAATAAAATAAAAAATAAAATACG
Found at i:109475758 original size:78 final size:78
Alignment explanation
Indices: 109475662--109475818 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
109475652 TAACACTAAA
*
109475662 CAAACTATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
1 CAAAATATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
109475727 ACAAAAAAATTAC
66 ACAAAAAAATTAC
109475740 CAAAATATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
1 CAAAATATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
*
109475805 ACAAATAAATTAC
66 ACAAAAAAATTAC
109475818 C
1 C
109475819 TTTTCTTTTC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (78 bp):
CAAAATATATAATACTAACAAAATAATTTTTTCTTATCATAATCTATTTTATTTAAAAAATAACA
ACAAAAAAATTAC
Found at i:109475846 original size:22 final size:22
Alignment explanation
Indices: 109475820--109475861 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
109475810 TAAATTACCT
109475820 TTTCTTTTCTTTCT-TCTTCTCC
1 TTTC-TTTCTTTCTATCTTCTCC
109475842 TTTCTTTCTTTCTATCTTCT
1 TTTCTTTCTTTCTATCTTCT
109475862 TCTTCTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTCTTTCTATCTTCTCC
Found at i:109479444 original size:43 final size:43
Alignment explanation
Indices: 109479382--109479469 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
109479372 AAATCTCAAC
* *
109479382 TTTAAAATTAACCTGAACGACAACGTTTCCTAACTTTGACTAA
1 TTTAAAATTAACCTAAACGACAACGTTTCCTAACTTAGACTAA
*
109479425 TTTAAAATTAACCTAAACGACAACGTTTCGTAACTTAGACTAA
1 TTTAAAATTAACCTAAACGACAACGTTTCCTAACTTAGACTAA
109479468 TT
1 TT
109479470 GACTTGGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (43 bp):
TTTAAAATTAACCTAAACGACAACGTTTCCTAACTTAGACTAA
Found at i:109479778 original size:16 final size:17
Alignment explanation
Indices: 109479747--109479780 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
109479737 TCTCCACCCA
*
109479747 CCTCAACTCTCCTCCTC
1 CCTCAAATCTCCTCCTC
109479764 CCTCAAATC-CCTCCTC
1 CCTCAAATCTCCTCCTC
109479780 C
1 C
109479781 TTTCCCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.59, G:0.00, T:0.26
Consensus pattern (17 bp):
CCTCAAATCTCCTCCTC
Found at i:109483559 original size:88 final size:88
Alignment explanation
Indices: 109483410--109483586 Score: 345
Period size: 88 Copynumber: 2.0 Consensus size: 88
109483400 GGGTATCATA
*
109483410 GAAAATGATGTTAGGTAAGCTGCGTGGTCTTTTTCTTTTTTCGGCATTTCATAGATCTTTCTTCC
1 GAAAATGATGTTAGGTAAGCTGCGTGGTCCTTTTCTTTTTTCGGCATTTCATAGATCTTTCTTCC
109483475 AGTGTAAGAAGTAATTCACCTAT
66 AGTGTAAGAAGTAATTCACCTAT
109483498 GAAAATGATGTTAGGTAAGCTGCGTGGTCCTTTTCTTTTTTCGGCATTTCATAGATCTTTCTTCC
1 GAAAATGATGTTAGGTAAGCTGCGTGGTCCTTTTCTTTTTTCGGCATTTCATAGATCTTTCTTCC
109483563 AGTGTAAGAAGTAATTCACCTAT
66 AGTGTAAGAAGTAATTCACCTAT
109483586 G
1 G
109483587 TTACAGAGCT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (88 bp):
GAAAATGATGTTAGGTAAGCTGCGTGGTCCTTTTCTTTTTTCGGCATTTCATAGATCTTTCTTCC
AGTGTAAGAAGTAATTCACCTAT
Found at i:109484268 original size:35 final size:35
Alignment explanation
Indices: 109484222--109484303 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
109484212 GTATAAAAGT
* *
109484222 TATTTGAACCATTAAAACTTTTTAAGAAATCAGGG
1 TATTTAAACCATTAAAACTTTTTAAGAAATCAAGG
* *
109484257 TATTTAAACCATTGAAACTTTTTAAGAAATCAAGT
1 TATTTAAACCATTAAAACTTTTTAAGAAATCAAGG
109484292 TATTTAAACCAT
1 TATTTAAACCAT
109484304 GAGAATATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (35 bp):
TATTTAAACCATTAAAACTTTTTAAGAAATCAAGG
Found at i:109484440 original size:5 final size:5
Alignment explanation
Indices: 109484432--109484457 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
109484422 ATAAATTTAA
109484432 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
109484458 CTTTTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Done.