Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 156 of 295
Found at i:49103577 original size:46 final size:46
Alignment explanation
Indices: 49103521--49103689 Score: 161
Period size: 46 Copynumber: 3.7 Consensus size: 46
49103511 TGGTTGAGCA
49103521 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
49103567 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* * * *
49103612 CATCTGAACTTGTTGAGTTGAGTCC-AGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * *
49103659 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
49103690 TTAGGGGCGG
Statistics
Matches: 98, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 19 0.19
46 39 0.40
47 22 0.22
49 4 0.04
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:49103676 original size:92 final size:93
Alignment explanation
Indices: 49103518--49103687 Score: 270
Period size: 92 Copynumber: 1.8 Consensus size: 93
49103508 GGATGGTTGA
* *
49103518 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
49103583 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
49103611 GCATCTGAACTTGTTGAGTTGAGTCC-AGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
*
49103675 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
49103688 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 46 0.66
93 24 0.34
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:49111227 original size:46 final size:46
Alignment explanation
Indices: 49111105--49111229 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
49111095 GGTTGAGCAT
* * *
49111105 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
49111151 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
49111197 CCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
49111230 GGGGCGGGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:49115038 original size:22 final size:21
Alignment explanation
Indices: 49115008--49115073 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
49114998 TATAAATTAA
49115008 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
49115030 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
49115051 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
49115070 ATCT
1 ATCT
49115074 AATATTGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:49115060 original size:19 final size:19
Alignment explanation
Indices: 49115025--49115086 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
49115015 AGATTACAAG
49115025 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
49115046 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
*
49115065 ATCATATCTAATATTGCAT
1 ATCATATCTAAGATTGCAT
49115084 ATC
1 ATC
49115087 CTTAAAGATT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 31 0.77
20 1 0.03
21 8 0.20
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:49115792 original size:16 final size:16
Alignment explanation
Indices: 49115723--49115790 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
49115713 TTTGGTTCGC
49115723 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49115739 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
49115755 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
49115771 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
49115787 TGTA
1 TGTA
49115791 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:49115822 original size:45 final size:44
Alignment explanation
Indices: 49115771--49115865 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
49115761 GGATTAGAGG
* * *
49115771 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
49115816 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
49115860 TGTAAT
1 TGTAAT
49115866 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:49116048 original size:18 final size:17
Alignment explanation
Indices: 49116027--49116061 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49116017 TTATTATTTA
*
49116027 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
49116045 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49116062 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49116055 original size:28 final size:27
Alignment explanation
Indices: 49115985--49116057 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
49115975 TTTATTATCA
*
49115985 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
49116013 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
49116040 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
49116058 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:49116195 original size:18 final size:17
Alignment explanation
Indices: 49116174--49116208 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49116164 TTATTATTAA
*
49116174 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
49116192 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49116209 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49116220 original size:147 final size:149
Alignment explanation
Indices: 49115946--49116220 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
49115936 ATGATTATTG
*
49115946 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
49116011 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
49116076 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
49116095 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
49116158 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
49116221 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:49116254 original size:61 final size:61
Alignment explanation
Indices: 49116189--49116376 Score: 185
Period size: 61 Copynumber: 3.1 Consensus size: 61
49116179 TTTTAATTAA
49116189 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * ** * * *
49116250 AATATATGATACTGTAA-AATATAAATTAA-AA-TAATAATTATTAAAT--ATATTA-T--AATT
1 AATATAT-A-A-TTTAATAAAAT-TCTTAATAATTAAT-ATTCTTATATGAAT-TTACTCAAATC
*
49116307 AA
60 AT
*
49116309 AATATATAATTTAATAAAATTCTTAATAATTAATAGTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
49116370 AATATAT
1 AATATAT
49116377 GATACTATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 8 0.08
57 14 0.15
58 8 0.08
59 14 0.15
61 21 0.22
62 8 0.08
63 15 0.16
64 8 0.08
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:49116296 original size:120 final size:120
Alignment explanation
Indices: 49116152--49116449 Score: 492
Period size: 120 Copynumber: 2.5 Consensus size: 120
49116142 ATTTAATCAT
*
49116152 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
49116217 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
65 ATTAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
49116274 A-TTAAAATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
49116338 TTAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 TTAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
49116393 ATTTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
49116450 TAAAATAATT
Statistics
Matches: 166, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
119 3 0.02
120 154 0.93
121 8 0.05
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (120 bp):
ATTTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:49116313 original size:16 final size:16
Alignment explanation
Indices: 49116273--49116318 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
49116263 GTAAAATATA
49116273 AATTAAAATA-ATAAT
1 AATTAAAATATATAAT
* *
49116288 TATT-AAATATATTAT
1 AATTAAAATATATAAT
49116303 AATTAAAATATATAAT
1 AATTAAAATATATAAT
49116319 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
14 5 0.20
15 10 0.40
16 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAAAATATATAAT
Found at i:49116460 original size:54 final size:54
Alignment explanation
Indices: 49116267--49116460 Score: 144
Period size: 54 Copynumber: 3.4 Consensus size: 54
49116257 GATACTGTAA
* *
49116267 AATATAAA-TTAAAATAA-TAATTATTAAATATATTATAATTAAAATATATAATTT
1 AATA-AAATTTAAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTT
* * * *
49116321 AATAAAATTCT-TAATAATTAATAGTCT-TATATGAATTTACTCAAATCATAATATATGATACTA
1 AATAAAATT-TAAAATAATTAATA-T-TAAATAT--ATTT--T--AATTAAAATATATGAT--T-
49116384 T
54 T
* *
49116385 AAAAGAAAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTT
1 --AATAAAATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTT
49116441 AATAAAATTTAAAATAATTA
1 AATAAAATTTAAAATAATTA
49116461 TAACTAATAA
Statistics
Matches: 109, Mismatches: 13, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
53 3 0.03
54 30 0.28
55 9 0.08
56 2 0.02
57 4 0.04
59 15 0.14
61 14 0.13
63 5 0.05
64 2 0.02
65 6 0.06
66 19 0.17
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (54 bp):
AATAAAATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTT
Found at i:49117187 original size:16 final size:16
Alignment explanation
Indices: 49117166--49117201 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
49117156 TAAGAAATCA
49117166 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
49117182 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
49117198 CAGC
1 CAGC
49117202 TCCTGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (16 bp):
CAGCCATGTACTCCTG
Found at i:49124067 original size:40 final size:40
Alignment explanation
Indices: 49123977--49124197 Score: 227
Period size: 40 Copynumber: 5.5 Consensus size: 40
49123967 CTCAAGTAAT
* * * *
49123977 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
49124015 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
49124055 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
49124095 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
49124135 CTTC-GAATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
49124176 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
49124198 CATTCGAATA
Statistics
Matches: 148, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
38 11 0.07
39 17 0.11
40 91 0.61
41 27 0.18
42 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:49124846 original size:38 final size:38
Alignment explanation
Indices: 49124793--49124955 Score: 308
Period size: 38 Copynumber: 4.3 Consensus size: 38
49124783 TGCTTACCTA
*
49124793 TGGCCGAACACACACATCAACTTATGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
49124831 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
*
49124869 TGGCCGAACATACACATCAACTCATGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
49124907 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
49124945 TGGCCGAACAT
1 TGGCCGAACAT
49124956 GCATGTCTAT
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 122 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (38 bp):
TGGCCGAACATACACATCAACTTATGTACTCATTCATG
Found at i:49130002 original size:6 final size:6
Alignment explanation
Indices: 49129993--49130048 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
49129983 ATATATATGA
* * *
49129993 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAC TTTAAT TTTAAT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT
*
49130041 TTTAAT TT
1 TTTGAT TT
49130049 CTGCTACTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (6 bp):
TTTGAT
Found at i:49130662 original size:10 final size:10
Alignment explanation
Indices: 49130647--49130671 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49130637 TATTTTACAA
49130647 ATTTATATAT
1 ATTTATATAT
49130657 ATTTATATAT
1 ATTTATATAT
49130667 ATTTA
1 ATTTA
49130672 ATTTTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTATATAT
Found at i:49130783 original size:99 final size:99
Alignment explanation
Indices: 49130673--49130878 Score: 353
Period size: 99 Copynumber: 2.1 Consensus size: 99
49130663 ATATATTTAA
*
49130673 TTTTTAGAATTTATAAAGTAATTTTTATTTTCAAAACATATGAATTCCATGTGGGACTTTTTTAT
1 TTTTTA-AATTTATAAAGTAATTTTTATTTTCAAAACATATGAATTCCATGTGGGACTTTTTGAT
*
49130738 TGAAGTGCCACGTA-G-TACATTCTTATTTAACTGAT
65 TGAAGTG--ACATATGATACATTCTTATTTAACTGAT
49130773 TTTTTAAATTTATAAAGTAATTTTTATTTTCAAAACATATGAATTCCATGTGGGACTTTTTGATT
1 TTTTTAAATTTATAAAGTAATTTTTATTTTCAAAACATATGAATTCCATGTGGGACTTTTTGATT
49130838 GAAGTGACATATGATACATTCTTATTTAACTGAT
66 GAAGTGACATATGATACATTCTTATTTAACTGAT
49130872 TTTTTAA
1 TTTTTAA
49130879 TAATTGTGAA
Statistics
Matches: 102, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
97 4 0.04
98 1 0.01
99 91 0.89
100 6 0.06
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (99 bp):
TTTTTAAATTTATAAAGTAATTTTTATTTTCAAAACATATGAATTCCATGTGGGACTTTTTGATT
GAAGTGACATATGATACATTCTTATTTAACTGAT
Found at i:49130906 original size:99 final size:98
Alignment explanation
Indices: 49130704--49130906 Score: 257
Period size: 99 Copynumber: 2.1 Consensus size: 98
49130694 TTTTTATTTT
* *
49130704 CAAAACATATGAATTCCATGTGGGACTTTTTTATTGAAGTGCCACGTAGTACATTCTTATTTAAC
1 CAAAACATATGAATTCCATGTGGGACTTTTTGATTGAAGTG-CACATAGTACATTCTTATTTAAC
* * * ** **
49130769 TGATTTTTTAAATTTATAAAGTAATTTTTATTTT
65 TGATTTTTTAAAATTATAAACTAATATCAATTAA
49130803 CAAAACATATGAATTCCATGTGGGACTTTTTGATTGAAGTG-ACATATGATACATTCTTATTTAA
1 CAAAACATATGAATTCCATGTGGGACTTTTTGATTGAAGTGCACATA-G-TACATTCTTATTTAA
* *
49130867 CTGATTTTTTAATAATTGTGAACTAA-ATCAATTAA
64 CTGATTTTTTAA-AATTATAAACTAATATCAATTAA
49130902 CAAAA
1 CAAAA
49130907 TGTAATTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
97 4 0.04
98 1 0.01
99 76 0.84
100 9 0.10
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (98 bp):
CAAAACATATGAATTCCATGTGGGACTTTTTGATTGAAGTGCACATAGTACATTCTTATTTAACT
GATTTTTTAAAATTATAAACTAATATCAATTAA
Found at i:49133485 original size:30 final size:30
Alignment explanation
Indices: 49133449--49133508 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
49133439 TAACAACACC
49133449 GGGTAGTCTTCCCATCCCCTACTGACTAGA
1 GGGTAGTCTTCCCATCCCCTACTGACTAGA
49133479 GGGTAGTCTTCCCATCCCCTACTGACTAGA
1 GGGTAGTCTTCCCATCCCCTACTGACTAGA
49133509 CAAGGCTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (30 bp):
GGGTAGTCTTCCCATCCCCTACTGACTAGA
Found at i:49143258 original size:21 final size:21
Alignment explanation
Indices: 49143232--49143283 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
49143222 AAATGACAGT
* * *
49143232 GAAACAACATCAAAATGGTAG
1 GAAACAACAGCAAAATAGTAA
*
49143253 GAAACAATAGCAAAATAGTAA
1 GAAACAACAGCAAAATAGTAA
*
49143274 TAAACAACAG
1 GAAACAACAG
49143284 TGAAAAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.58, C:0.13, G:0.15, T:0.13
Consensus pattern (21 bp):
GAAACAACAGCAAAATAGTAA
Found at i:49144147 original size:23 final size:24
Alignment explanation
Indices: 49144101--49144148 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
49144091 AAATATTAAA
*
49144101 ATATATAATTTTATAACTTTATTT
1 ATATATAATTTTATAACTTAATTT
49144125 ATATAT-ATTTTATAA-TTAAATTT
1 ATATATAATTTTATAACTT-AATTT
49144148 A
1 A
49144149 AATAAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 14 0.64
24 6 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATATAATTTTATAACTTAATTT
Found at i:49145631 original size:28 final size:28
Alignment explanation
Indices: 49145591--49145647 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
49145581 AAACCGTAAC
49145591 ACTAAAGAATATATATATTAGATGTAGA
1 ACTAAAGAATATATATATTAGATGTAGA
49145619 ACTAAAGAATATATATATTAGATGTAGA
1 ACTAAAGAATATATATATTAGATGTAGA
49145647 A
1 A
49145648 AAATAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.32
Consensus pattern (28 bp):
ACTAAAGAATATATATATTAGATGTAGA
Found at i:49156469 original size:49 final size:49
Alignment explanation
Indices: 49156298--49156522 Score: 270
Period size: 49 Copynumber: 4.5 Consensus size: 49
49156288 TGAGGTCGCA
* * * * *
49156298 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACG
* * * ** *
49156349 TGTGTAGTACTAAGTGCAGGCTACTACGTATATCAGATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
49156399 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* * ***
49156448 TGTGTAGTACTAAGTGTAGGCTACTAAGTGTACCGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
*
49156497 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
49156523 TGCGTACCAG
Statistics
Matches: 150, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 75 0.50
50 43 0.29
51 32 0.21
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:49156472 original size:99 final size:100
Alignment explanation
Indices: 49156297--49156530 Score: 301
Period size: 99 Copynumber: 2.4 Consensus size: 100
49156287 GTGAGGTCGC
* *
49156297 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACGTGTGTAGTACTAA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGAAAACTGTGATCACGTGTGTAGTACTAA
* * **
49156362 GTGCAGGCTACTACGTATATCAGATGGTTAGGTCAT
66 GTGCAGGCTACTAAGTATACCAGATAATT-GGTCAT
* * * *
49156398 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACGTGTGTAGTACTAA
1 ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGAAAACTGTGATCACGTGTGTAGTACTAA
* * * *
49156461 GTGTAGGCTACTAAGTGTACCGGATAATTGGTCGT
66 GTGCAGGCTACTAAGTATACCAGATAATTGGTCAT
* *
49156496 ATGTGTAGTACTATGTGCAGGCTACTATGCGTACC
1 ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACC
49156531 AGATAGCTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 36 0.31
99 42 0.37
100 1 0.01
101 36 0.31
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (100 bp):
ATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGAAAACTGTGATCACGTGTGTAGTACTAA
GTGCAGGCTACTAAGTATACCAGATAATTGGTCAT
Found at i:49164581 original size:18 final size:18
Alignment explanation
Indices: 49164550--49164619 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
49164540 TTGGGTCCTG
49164550 TGGG-CCACACGGGCGTA
1 TGGGTCCACACGGGCGTA
* *
49164567 TGGGTCCATACGGGCGTG
1 TGGGTCCACACGGGCGTA
49164585 TGGGTCCACACGGGCGTA
1 TGGGTCCACACGGGCGTA
*
49164603 TGGGTCCACACAGGCGT
1 TGGGTCCACACGGGCGT
49164620 GTGAGCCCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 4 0.09
18 43 0.91
ACGTcount: A:0.16, C:0.27, G:0.40, T:0.17
Consensus pattern (18 bp):
TGGGTCCACACGGGCGTA
Found at i:49164595 original size:36 final size:35
Alignment explanation
Indices: 49164548--49164622 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 35
49164538 TTTTGGGTCC
* *
49164548 TGTGGGCCACACGGGCGTATGGGTCCATACGGGCG
1 TGTGGGCCACACGGGCGTATGGGTCCACACAGGCG
49164583 TGTGGGTCCACACGGGCGTATGGGTCCACACAGGCG
1 TGTGGG-CCACACGGGCGTATGGGTCCACACAGGCG
49164619 TGTG
1 TGTG
49164623 AGCCCATCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.15, C:0.25, G:0.41, T:0.19
Consensus pattern (35 bp):
TGTGGGCCACACGGGCGTATGGGTCCACACAGGCG
Found at i:49170412 original size:21 final size:21
Alignment explanation
Indices: 49170346--49170412 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
49170336 GTCTAGGCCG
*
49170346 TGTGGAGGCC-TACATGCCCA
1 TGTGGAGGCCACACATGCCCA
*
49170366 TGTGAAGGCCACACATGCCCA
1 TGTGGAGGCCACACATGCCCA
** *
49170387 TGTGGAGGGGACACATGCCCG
1 TGTGGAGGCCACACATGCCCA
49170408 TGTGG
1 TGTGG
49170413 TTAGCCCGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 9 0.22
21 31 0.77
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
TGTGGAGGCCACACATGCCCA
Found at i:49174888 original size:6 final size:6
Alignment explanation
Indices: 49174877--49174909 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
49174867 ATCTTGTGTC
49174877 AAAAAG AAAAAG AAAAA- AAAAAG AAAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAA
49174910 GAGATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:49174897 original size:11 final size:11
Alignment explanation
Indices: 49174877--49174911 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
49174867 ATCTTGTGTC
49174877 AAAAAGAAAAAG
1 AAAAA-AAAAAG
49174889 AAAAAAAAAAG
1 AAAAAAAAAAG
*
49174900 AAAAAAGAAAG
1 AAAAAAAAAAG
49174911 A
1 A
49174912 GATGATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:49175721 original size:61 final size:58
Alignment explanation
Indices: 49175645--49175781 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 58
49175635 TTATTATGTA
* *
49175645 ATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATATAATTTAAT--AAA-AAAAATAAATAATTTAATAAC
* *
49175706 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAACAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAATAAATAATTTAATAAC
49175764 ATTCTTAATATAATTATT
1 ATT-TTAATATAATTATT
49175782 TTTATATTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
58 20 0.29
59 17 0.24
61 32 0.46
62 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAATAAATAATTTAATAAC
Found at i:49180818 original size:5 final size:5
Alignment explanation
Indices: 49180810--49180853 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
49180800 AGCATATCAT
* *
49180810 ATATC ATATC AAATC ATATC ATATC ATATC GATTTTC ATATC AT
1 ATATC ATATC ATATC ATATC ATATC ATATC -A-TATC ATATC AT
49180854 GTCGTAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 28 0.85
6 2 0.06
7 3 0.09
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:49182847 original size:15 final size:15
Alignment explanation
Indices: 49182827--49182883 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
49182817 CGATGAATTT
49182827 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
49182842 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
49182857 ATTGAATTTATATTG
1 ATTGAATTTATATTG
49182872 ATTGAA-TTATAT
1 ATTGAATTTATAT
49182884 AATATACATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:49183285 original size:23 final size:23
Alignment explanation
Indices: 49183267--49183364 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 23
49183257 AGGCACTTTA
49183267 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
49183290 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
49183311 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
49183334 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
49183355 TGTGTCGTAT
1 TGTGTCGTAT
49183365 ACTGATCAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
21 36 0.52
22 4 0.06
23 29 0.42
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:49183317 original size:44 final size:44
Alignment explanation
Indices: 49183254--49183364 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
49183244 GACTTTATCG
* *
49183254 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
*
49183298 ATCAGGCACCTCGTGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
* * * *
49183342 TTTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
49183365 ACTGATCAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (44 bp):
ATCAGGCACCTCATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
Found at i:49188831 original size:15 final size:15
Alignment explanation
Indices: 49188811--49188867 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
49188801 CGATGAATTT
49188811 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
49188826 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
49188841 ATTGAATTTATATTG
1 ATTGAATTTATATTG
49188856 ATTGAA-TTATAT
1 ATTGAATTTATAT
49188868 AATATACATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:49189269 original size:23 final size:23
Alignment explanation
Indices: 49189251--49189348 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 23
49189241 AGGCACTTTA
49189251 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
49189274 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
49189295 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
49189318 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
49189339 TGTGTCGTAT
1 TGTGTCGTAT
49189349 ACTGATCAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
21 36 0.52
22 4 0.06
23 29 0.42
ACGTcount: A:0.13, C:0.22, G:0.27, T:0.38
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:49189300 original size:44 final size:44
Alignment explanation
Indices: 49189238--49189348 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
49189228 GGCTTTATCA
* *
49189238 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
*
49189282 ATCAGGCACCTCGTGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
* * * *
49189326 TTTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
49189349 ACTGATCAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (44 bp):
ATCAGGCACCTCATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
Found at i:49192307 original size:35 final size:35
Alignment explanation
Indices: 49192261--49192381 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 35
49192251 CAAGGTTCCT
*
49192261 TATATCATCACATATGGCCAAATATACAAGTATAA
1 TATAACATCACATATGGCCAAATATACAAGTATAA
* * * * * *
49192296 TAAAACATCACATGTAGTCAAATATTCAAGTTTAA
1 TATAACATCACATATGGCCAAATATACAAGTATAA
* * * *
49192331 TATAACATCATATGTGGCCAAAGATACAAGTACAA
1 TATAACATCACATATGGCCAAATATACAAGTATAA
* *
49192366 TATATCATCATATATG
1 TATAACATCACATATG
49192382 TACATACCTA
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.30
Consensus pattern (35 bp):
TATAACATCACATATGGCCAAATATACAAGTATAA
Found at i:49198706 original size:30 final size:29
Alignment explanation
Indices: 49198650--49198710 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
49198640 ATCCAAGATG
49198650 ACTTGACTCGAGCCTTCTTGCAAAGACCAT
1 ACTTGACTCGAGCCTTC-TGCAAAGACCAT
*
49198680 ACTTGACTCGAGCCCTTC-GACGAAGACCAT
1 ACTTGACTCGAG-CCTTCTG-CAAAGACCAT
49198710 A
1 A
49198711 GCACCCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 22 0.79
31 5 0.18
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (29 bp):
ACTTGACTCGAGCCTTCTGCAAAGACCAT
Found at i:49199704 original size:22 final size:22
Alignment explanation
Indices: 49199679--49199727 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
49199669 ATAACAGAAT
* *
49199679 ATATCATAGCATATCAGATTTC
1 ATATCAGAGCATATCAGATATC
* *
49199701 ATATCGGAGCATATCATATATC
1 ATATCAGAGCATATCAGATATC
49199723 ATATC
1 ATATC
49199728 GTATCGTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
ATATCAGAGCATATCAGATATC
Found at i:49199718 original size:27 final size:27
Alignment explanation
Indices: 49199683--49199759 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 27
49199673 CAGAATATAT
*
49199683 CATAGCATATCAGATTTCATATCGGAG
1 CATATCATATCAGATTTCATATCGGAG
* * * * *
49199710 CATATCATAT-ATCATATCGTATCGTAT
1 CATATCATATCA-GATTTCATATCGGAG
* *
49199737 CATATCATATCTGTTTTCATATC
1 CATATCATATCAGATTTCATATC
49199760 ATGTTGTAGC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (27 bp):
CATATCATATCAGATTTCATATCGGAG
Found at i:49199728 original size:22 final size:22
Alignment explanation
Indices: 49199686--49199728 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
49199676 AATATATCAT
*
49199686 AGCATATCAGATTTCATATCGG
1 AGCATATCAGATATCATATCGG
*
49199708 AGCATATCATATATCATATCG
1 AGCATATCAGATATCATATCG
49199729 TATCGTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
AGCATATCAGATATCATATCGG
Found at i:49199737 original size:15 final size:15
Alignment explanation
Indices: 49199719--49199794 Score: 53
Period size: 15 Copynumber: 4.8 Consensus size: 15
49199709 GCATATCATA
*
49199719 TATCATATCGTATCG
1 TATCATATCATATCG
49199734 TATCATATCATATCTG
1 TATCATATCATATC-G
* * *
49199750 TTTTCATATCATGTTG
1 -TATCATATCATATCG
* * *
49199766 TAGCATGTTTCATATCT
1 TATCA--TATCATATCG
49199783 TATCATATCATA
1 TATCATATCATA
49199795 ACTCATGCCA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
15 22 0.49
16 2 0.04
17 21 0.47
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (15 bp):
TATCATATCATATCG
Found at i:49199828 original size:22 final size:22
Alignment explanation
Indices: 49199775--49199830 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
49199765 GTAGCATGTT
* *
49199775 TCATATCTTATCATATCATAAC
1 TCATATCATGTCATATCATAAC
** *
49199797 TCATGCCATGTCATATCATATC
1 TCATATCATGTCATATCATAAC
49199819 TCATATCATGTC
1 TCATATCATGTC
49199831 CTACCCCAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.39
Consensus pattern (22 bp):
TCATATCATGTCATATCATAAC
Found at i:49200937 original size:16 final size:17
Alignment explanation
Indices: 49200906--49200938 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49200896 AAAAAAACTC
*
49200906 AAAGAAAAGTGAAAGAA
1 AAAGAAAAGAGAAAGAA
49200923 AAAGAAAA-AGAAAGAA
1 AAAGAAAAGAGAAAGAA
49200939 CAAAAGGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGAGAAAGAA
Found at i:49202968 original size:19 final size:20
Alignment explanation
Indices: 49202944--49202988 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
49202934 TTGAGATGGA
49202944 ATGATATTCAACTTTGTGG-
1 ATGATATTCAACTTTGTGGT
* *
49202963 ATGATATTTAACTTTTTGGT
1 ATGATATTCAACTTTGTGGT
49202983 ATGATA
1 ATGATA
49202989 GGGACATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (20 bp):
ATGATATTCAACTTTGTGGT
Found at i:49209028 original size:191 final size:191
Alignment explanation
Indices: 49208686--49209066 Score: 591
Period size: 191 Copynumber: 2.0 Consensus size: 191
49208676 ATAATCTCTC
* * *
49208686 TTACATGAAATAGTCATACCTTTTTCCCTCCTATGACTAAGTTGTCTCCACTTCAAACGAGTCGA
1 TTACACGAAATAGTCATACCTTTTTCCCTCCTATGACCAAGTTGTCTCCACTTCAAACGAGTCCA
* *** * *
49208751 GTTTAACTCTTTAACAGATGTGGGACGTCTGGTTTCACCGGTCACCGTTGATCCTTCCAAAACAT
66 GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
* * * *
49208816 AAAGACTTTTAATATTTTTACCTTTCATAGAAAAGAAGAGCCTCATGAGATACCTTAATGT
131 AAAGACTTTCAATACTTTTACCTTTCATAAAAAAGAAGAGCCTCATAAGATACCTTAATGT
* **
49208877 TTACACGAAATAGTCATACCTTTTTCTCTCCTATGACCAAGTTGTCTCTGCTTCAAACGAGTCCA
1 TTACACGAAATAGTCATACCTTTTTCCCTCCTATGACCAAGTTGTCTCCACTTCAAACGAGTCCA
49208942 GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
66 GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
* * *
49209007 AAAGACTTTCAATCCTTTTACCTTTTATAAAAAAGAAGAGCCTTATAAGATACCTTAATG
131 AAAGACTTTCAATACTTTTACCTTTCATAAAAAAGAAGAGCCTCATAAGATACCTTAATG
49209067 CCGCTTGAAT
Statistics
Matches: 171, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
191 171 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (191 bp):
TTACACGAAATAGTCATACCTTTTTCCCTCCTATGACCAAGTTGTCTCCACTTCAAACGAGTCCA
GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
AAAGACTTTCAATACTTTTACCTTTCATAAAAAAGAAGAGCCTCATAAGATACCTTAATGT
Found at i:49215304 original size:7 final size:7
Alignment explanation
Indices: 49215292--49215316 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49215282 AGTCGTTTCA
49215292 TATTTAG
1 TATTTAG
49215299 TATTTAG
1 TATTTAG
49215306 TATTTAG
1 TATTTAG
49215313 TATT
1 TATT
49215317 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:49215879 original size:30 final size:30
Alignment explanation
Indices: 49215815--49215879 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
49215805 AACGACACAG
* * * * *
49215815 GCCCATCAACAGCGGCTACACAATCGCCGG
1 GCCCATCAACAACGCCCACACAATCACCGA
*
49215845 GCCCATCAACAACGCCCACACAATCATCGA
1 GCCCATCAACAACGCCCACACAATCACCGA
49215875 GCCCA
1 GCCCA
49215880 ATGCCTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.43, G:0.17, T:0.09
Consensus pattern (30 bp):
GCCCATCAACAACGCCCACACAATCACCGA
Found at i:49219244 original size:46 final size:46
Alignment explanation
Indices: 49219066--49219323 Score: 156
Period size: 46 Copynumber: 5.5 Consensus size: 46
49219056 TTTGTGCGCT
* * * * *
49219066 AGTGTAAGA-AATGTCCGGGACATGCATTGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGA-GATGA-AGCC
** * * * * * *
49219112 AGTGTAAGACCATGTCTAAGACATGGCAACGAC-ATTGTGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTA-CGAGATGA-AGCC
* *
49219160 AGTGTAAGA-CATGTATGGGGCATGCATCGGCCT-CGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CTACGAGATG-AAGCC
* * *
49219206 AGTGTAAGA-CATGTCTGGGACATGCATTGGCTATGAGATG-AGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGAAGCC
* * *
49219250 AGTGTAAGACCACGTTTGGGACATGACATCAGC-ACGGAGATGCGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATG-CATCGGCTAC-GAGAT--GA-AGCC
49219300 AGTGTAAGACCATGTCT-GGACATG
1 AGTGTAAGACCATGTCTGGGACATG
49219324 GCGTTAGACT
Statistics
Matches: 162, Mismatches: 35, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
44 12 0.07
45 16 0.10
46 64 0.40
47 23 0.14
48 22 0.14
49 7 0.04
50 18 0.11
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGAAGCC
Found at i:49220916 original size:30 final size:30
Alignment explanation
Indices: 49220880--49220948 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
49220870 ATGGGGCAGA
49220880 CCGTGTGTCACACACGGCCTAGACACATGC
1 CCGTGTGTCACACACGGCCTAGACACATGC
*
49220910 CCGTGTGTCACACATGGCCTAGACACATGC
1 CCGTGTGTCACACACGGCCTAGACACATGC
49220940 CCGTGTGTC
1 CCGTGTGTC
49220949 CAACCTTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (30 bp):
CCGTGTGTCACACACGGCCTAGACACATGC
Found at i:49222145 original size:45 final size:45
Alignment explanation
Indices: 49222081--49222167 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
49222071 CCAAAACATG
*
49222081 TGTCACATATATTACGAACTCAGACCACAACTCAATGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
* * *
49222126 TGTCATATATATCATGAACTCAGATCACAACTCAATGAGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
49222168 AGATTACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
Found at i:49230773 original size:44 final size:41
Alignment explanation
Indices: 49230676--49230775 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 41
49230666 CAATTGTATT
*
49230676 TGGCACTAAGTGTGCGATTCAAAATAGCTTCGGCTATATGA
1 TGGCACTAAGTGTGCGATCCAAAATAGCTTCGGCTATATGA
* * *
49230717 -GGCACTAAGTGTGCGATACCGAGATAGCTTCGGTTA-ATTGAGA
1 TGGCACTAAGTGTGCGAT-CCAAAATAGCTTCGGCTATA-T--GA
49230760 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
49230776 GAATCGTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
40 18 0.36
41 15 0.30
43 2 0.04
44 15 0.30
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGATCCAAAATAGCTTCGGCTATATGA
Found at i:49233195 original size:126 final size:125
Alignment explanation
Indices: 49232970--49233469 Score: 673
Period size: 125 Copynumber: 4.0 Consensus size: 125
49232960 GGCCAATTAT
* * * * * *
49232970 GAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTTAGACATTTTGCTGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATA-ATTTTGCTGACAGTGCATC
* *
49233035 CTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTGAAAATTATTTTTTCAA
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
**
49233096 GAACTACTGTAGAAAAAGAGCGTTTACGTAGGAGCTTTTTCCTATAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTT-CTATAATTTTGCTGACAGTGCATC
* * * * * *
49233161 CTGCTTGAGGCATTTTTGACACTATTTGTTCAG-AACTTCTTCTCATAATTATCTTTTCAT
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* * ** * *
49233221 GAACTAATTTAGAAAAAGAGCGTCCACGT-GGTAGCTTTTTTCCCTAATTTTGCTGACAATACAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGG-AGC-TTTTTCTATAATTTTGCTGACAGTGCAT
* * *
49233285 CCTGCTTGAAGCGTTTTTGGCACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTT-AG
64 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* *
49233346 GAACTACTGTAGAAAAAGAGCGTCCAAGTAGGAGCTTTTTCTATATTTTTGCTGACAGTGCATCC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATAATTTTGCTGACAGTGCATCC
* **
49233411 TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACGCCTTCTCAAAATTATTTTTTCA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCA
49233470 GTGTAAAAAT
Statistics
Matches: 323, Mismatches: 45, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
124 79 0.24
125 130 0.40
126 111 0.34
127 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
Found at i:49233552 original size:30 final size:29
Alignment explanation
Indices: 49233520--49233642 Score: 120
Period size: 29 Copynumber: 4.0 Consensus size: 29
49233510 GTTATTTTTA
*
49233520 AAAAAACTAAACCCTAATTTAATTTATTT
1 AAAAACCTAAACCCTAATTTAATTTATTT
*
49233549 AAAACCCTAGAACCCTAATTTAGTTAATTTATTT
1 AAAAACCTA-AACCCTAA--T--TTAATTTATTT
* *
49233583 AAAAATCGTAAACCCCAATTTAATTTATTT
1 AAAAA-CCTAAACCCTAATTTAATTTATTT
* * * *
49233613 AAAACCCCAAACCCTAATTTACTTAATTT
1 AAAAACCTAAACCCTAATTTAATTTATTT
49233642 A
1 A
49233643 TTTTAAAATC
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
29 27 0.35
30 23 0.30
32 2 0.03
34 22 0.29
35 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAACCTAAACCCTAATTTAATTTATTT
Found at i:49233581 original size:34 final size:32
Alignment explanation
Indices: 49233526--49233669 Score: 138
Period size: 34 Copynumber: 4.5 Consensus size: 32
49233516 TTTAAAAAAA
49233526 CTAAACCCTAA--T-TTAATTTATTTAAAACC
1 CTAAACCCTAATTTATTAATTTATTTAAAACC
*
49233555 CTAGAACCCTAATTTAGTTAATTTATTTAAAAATC
1 CTA-AACCCTAATTTA-TTAATTTATTT-AAAACC
* *
49233590 GTAAACCCCAA--T-TTAATTTATTTAAAACC
1 CTAAACCCTAATTTATTAATTTATTTAAAACC
* *
49233619 CCAAACCCTAATTTACTTAATTTATTTTAAAATC
1 CTAAACCCTAATTTA-TTAATTTA-TTTAAAACC
**
49233653 CTAAATTCTAATTTATT
1 CTAAACCCTAATTTATT
49233670 TAAAACCCTA
Statistics
Matches: 93, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
29 16 0.17
30 19 0.20
31 1 0.01
32 2 0.02
33 10 0.11
34 38 0.41
35 7 0.08
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (32 bp):
CTAAACCCTAATTTATTAATTTATTTAAAACC
Found at i:49233639 original size:63 final size:64
Alignment explanation
Indices: 49233516--49233657 Score: 214
Period size: 64 Copynumber: 2.2 Consensus size: 64
49233506 CAATGTTATT
** * * *
49233516 TTTAAAAAAACTAAACCCTAATTTAATTTATTTAAAACCCTAGAACCCTAATTTAGTTAATTTA
1 TTTAAAAATCCTAAACCCCAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
*
49233580 TTTAAAAATCGTAAACCCCAATTTAATTTATTTAAAACCCCA-AACCCTAATTTACTTAATTTA
1 TTTAAAAATCCTAAACCCCAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
*
49233643 TTTTAAAATCCTAAA
1 TTTAAAAATCCTAAA
49233658 TTCTAATTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 33 0.47
64 37 0.53
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (64 bp):
TTTAAAAATCCTAAACCCCAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
Found at i:49233665 original size:25 final size:23
Alignment explanation
Indices: 49233635--49233692 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
49233625 CCTAATTTAC
*
49233635 TTAATTTATTTTAAAATCCTAAAT
1 TTAATTTATTTTAAAACCCT-AAT
49233659 TCTAATTTA-TTTAAAACCCTAAT
1 T-TAATTTATTTTAAAACCCTAAT
49233682 TTAATTTATTT
1 TTAATTTATTT
49233693 GAAACCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 7 0.23
23 6 0.19
24 11 0.35
25 7 0.23
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTATTTTAAAACCCTAAT
Found at i:49233666 original size:63 final size:64
Alignment explanation
Indices: 49233516--49233671 Score: 217
Period size: 63 Copynumber: 2.5 Consensus size: 64
49233506 CAATGTTATT
** * *
49233516 TTTAAAAAAACTAAACCCTAATTTAATTTATTTAAAACCCTAGAACCCTAATTTAGTTAATTTA
1 TTTAAAAATCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
* *
49233580 TTTAAAAATCGTAAACCCCAATTTAATTTATTTAAAACCCCA-AACCCTAATTTACTTAATTTA
1 TTTAAAAATCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
* **
49233643 TTTTAAAATCCTAAATTCTAATTT-ATTTA
1 TTTAAAAATCCTAAACCCTAATTTAATTTA
49233672 AAACCCTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 5 0.06
63 39 0.48
64 37 0.46
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.40
Consensus pattern (64 bp):
TTTAAAAATCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
Found at i:49233689 original size:22 final size:23
Alignment explanation
Indices: 49233635--49233703 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
49233625 CCTAATTTAC
*
49233635 TTAATTTATTTTAAAATCCTAAAT
1 TTAATTTA-TTTAAAACCCTAAAT
49233659 TCTAATTTATTTAAAACCCT-AAT
1 T-TAATTTATTTAAAACCCTAAAT
* *
49233682 TTAATTTATTTGAAACCTTAAA
1 TTAATTTATTTAAAACCCTAAA
49233704 AACCCTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 16 0.40
23 6 0.15
24 11 0.28
25 7 0.17
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (23 bp):
TTAATTTATTTAAAACCCTAAAT
Found at i:49236572 original size:48 final size:48
Alignment explanation
Indices: 49236514--49236666 Score: 209
Period size: 48 Copynumber: 3.2 Consensus size: 48
49236504 TAGCCGGGCT
* * *
49236514 ATTGGTATCGATATGTGATCCCATGTAAGACTATGTCTAGGACATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
** **
49236562 ATTGGCATCGACCTACGATCCCATGTAAGACCATGT-TCGGGACATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCT-GGGACATGGC
* *
49236610 ATTGGCATCGATATGTGATCCCATGTAAGACCATATCTGGGATATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
49236658 ATTGGCATC
1 ATTGGCATC
49236667 CTACCATATG
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
47 1 0.01
48 88 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (48 bp):
ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
Found at i:49238936 original size:41 final size:40
Alignment explanation
Indices: 49238891--49239048 Score: 176
Period size: 41 Copynumber: 3.9 Consensus size: 40
49238881 GATTCTTAGT
*
49238891 ACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTAGACC
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGA-C
* * * * *
49238932 ACTGGCTCGAAGGCCCTTCGGAACTAAGTTCGG-TTATGAC
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTA-GAC
* * *
49238972 ACTGGCTCTAAAGCCCTTCGAAACTAAGTTCGGTTATTAG-C
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGG--ATTAGAC
*
49239013 ACTGGCTCAAAGGCCCTTCGAAACCAAGCTCGGATT
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATT
49239049 TAAACCCTGA
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.03
40 34 0.34
41 59 0.59
42 1 0.01
43 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGAC
Found at i:49253155 original size:48 final size:48
Alignment explanation
Indices: 49253084--49253223 Score: 190
Period size: 48 Copynumber: 2.9 Consensus size: 48
49253074 TAGGGTTATG
*
49253084 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACC
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACA
* *
49253132 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGATA
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACA
** * * * **
49253180 TGTGATCCCATGTAAGACCATATCCGGGATATGGAATTGGCATC
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATC
49253224 CTACCATGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (48 bp):
TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACA
Found at i:49262362 original size:44 final size:43
Alignment explanation
Indices: 49262314--49262470 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
49262304 TGTGTTATCG
* * *
49262314 TGTAAGACCACTTATGGGACATTGGCATCA-ACTTATGATTTACG
1 TGTAAGACCACTTCTAGGACATTGGCATCATA-TT-TGATTTACA
* * *
49262358 TGTAAGACCACTTTTGGGACATTGGCATTATATTTGATTT-CA
1 TGTAAGACCACTTCTAGGACATTGGCATCATATTTGATTTACA
*
49262400 TGTAAGACC-CTGTCTAGGACAGTGGCATCGATATTTGA-TTACA
1 TGTAAGACCACT-TCTAGGACATTGGCATC-ATATTTGATTTACA
*
49262443 TGTAAGACCACGTCTAGGACATTGGCAT
1 TGTAAGACCACTTCTAGGACATTGGCAT
49262471 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.02
42 25 0.25
43 40 0.40
44 31 0.31
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACTTCTAGGACATTGGCATCATATTTGATTTACA
Found at i:49262633 original size:21 final size:21
Alignment explanation
Indices: 49262607--49262650 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49262597 GAGGATAAGG
49262607 TAAGTACAAAGCATATGTATA
1 TAAGTACAAAGCATATGTATA
49262628 TAAGTACAAAGCATATGTATA
1 TAAGTACAAAGCATATGTATA
49262649 TA
1 TA
49262651 TGTGAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.30
Consensus pattern (21 bp):
TAAGTACAAAGCATATGTATA
Found at i:49263236 original size:9 final size:9
Alignment explanation
Indices: 49263222--49263250 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
49263212 AGATTGAATG
49263222 ATGGATATT
1 ATGGATATT
49263231 ATGGATATT
1 ATGGATATT
49263240 ATGGATATT
1 ATGGATATT
49263249 AT
1 AT
49263251 TCAGTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
ATGGATATT
Found at i:49273014 original size:129 final size:129
Alignment explanation
Indices: 49272784--49273034 Score: 344
Period size: 129 Copynumber: 1.9 Consensus size: 129
49272774 CGCTAAACTG
* * * * * **
49272784 ATTAGTGATAGACTGAAAGTCCCTTCTGATAGGCAGAAGTCTTACATAGATCTGAAATGTTGTGA
1 ATTAGTGATAAACTAAAAGTCCCTTCTGATAAGCAAAAGTCTTACACAGATCTGAAACATTGTGA
* *
49272849 CATCAAGTTTTAGGTTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGGAA-AAAGTGAAATTT
66 CATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCA-CTTGGGAAGAAAGTGAAATTT
* * * *
49272913 ATTAGTGATAAACTAAAAG-CTGCTTGTGATAAGCAAAAGTCTTACGCAGATTTGAAACATTGTG
1 ATTAGTGATAAACTAAAAGTC-CCTTCTGATAAGCAAAAGTCTTACACAGATCTGAAACATTGTG
*
49272977 ACATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCACTTTGGAAGAAAGT
65 ACATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCACTTGGGAAGAAAGT
49273035 TCTAATATTC
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
128 8 0.08
129 98 0.92
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (129 bp):
ATTAGTGATAAACTAAAAGTCCCTTCTGATAAGCAAAAGTCTTACACAGATCTGAAACATTGTGA
CATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCACTTGGGAAGAAAGTGAAATTT
Found at i:49282159 original size:27 final size:27
Alignment explanation
Indices: 49282097--49282467 Score: 251
Period size: 27 Copynumber: 13.8 Consensus size: 27
49282087 CCAAACTATT
* * *
49282097 TAAAATTATCGAAATACCCCCA-TTTG
1 TAAAATTACCGAAATACCCCTAGATTG
* ** *
49282123 AAAAATTACCGAAATACCTTTAGATTA
1 TAAAATTACCGAAATACCCCTAGATTG
* *
49282150 TAAAATTACCAAAATA-CCCTCAGTTTG
1 TAAAATTACCGAAATACCCCT-AGATTG
* * * *
49282177 TAAAATCACTGAAA-AACCCTCGAATTG
1 TAAAATTACCGAAATACCCCTAG-ATTG
** *
49282204 TAAAATTATTGAAATA-CCCTAGTTTG
1 TAAAATTACCGAAATACCCCTAGATTG
* ** *
49282230 TAAAATTATCGAAATACCTTTAGATTA
1 TAAAATTACCGAAATACCCCTAGATTG
*
49282257 TAAAATTACCAAAATACCCCT-GATTTG
1 TAAAATTACCGAAATACCCCTAGA-TTG
* * * *
49282284 TAAAATCACCAAAATACCCTTGGATTG
1 TAAAATTACCGAAATACCCCTAGATTG
*
49282311 TAAAATTATCGAAATACCCCT-GATTTG
1 TAAAATTACCGAAATACCCCTAGA-TTG
* *
49282338 TAAAATTACCAAAAT-GCCCTCAGATTG
1 TAAAATTACCGAAATACCCCT-AGATTG
** *
49282365 TAAAATTAATGAAAGACTCCC--GATTTG
1 TAAAATTACCGAAATAC-CCCTAGA-TTG
* * *
49282392 TAAAATTACCAAAATACCCC-CGATTTA
1 TAAAATTACCGAAATACCCCTAGA-TTG
* * *
49282419 TAAAATTACTGAAATA-CCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTAG-ATTG
49282446 TAAAATTACCGAAATACCCCTA
1 TAAAATTACCGAAATACCCCTA
49282468 TAGGGTAAAA
Statistics
Matches: 269, Mismatches: 58, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
26 55 0.20
27 201 0.75
28 10 0.04
29 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTAGATTG
Found at i:49282349 original size:54 final size:54
Alignment explanation
Indices: 49282097--49282464 Score: 317
Period size: 54 Copynumber: 6.9 Consensus size: 54
49282087 CCAAACTATT
* * * * *
49282097 TAAAATTATCGAAATACCCC-CATTTGAAAAATTACCGAAATACCTTTAGATTA
1 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
* * * * * *
49282150 TAAAATTACCAAAATA-CCCTCAGTTTGTAAAATCACTGAAAA-ACCCTC-GAATTG
1 TAAAATTATCGAAATACCCCTGA-TTTGTAAAATTAC-CAAAATACCCTCAG-ATTA
* * * * *
49282204 TAAAATTATTGAAATA-CCCT-AGTTTGTAAAATTATCGAAATACCTTTAGATTA
1 TAAAATTATCGAAATACCCCTGA-TTTGTAAAATTACCAAAATACCCTCAGATTA
* * * ** *
49282257 TAAAATTACCAAAATACCCCTGATTTGTAAAATCACCAAAATACCCTTGGATTG
1 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
* *
49282311 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATGCCCTCAGATTG
1 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
* *
49282365 TAAAATTAAT-GAAAGACTCCC-GATTTGTAAAATTACCAAAATACCC-CCGATTTA
1 TAAAATT-ATCGAAATAC-CCCTGATTTGTAAAATTACCAAAATACCCTCAGA-TTA
* * *
49282419 TAAAATTA-CTGAAATACCCTTG-TAGTGTAAAATTACCGAAATACCC
1 TAAAATTATC-GAAATACCCCTGAT-TTGTAAAATTACCAAAATACCC
49282465 CTATAGGGTA
Statistics
Matches: 258, Mismatches: 42, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
52 6 0.02
53 57 0.22
54 186 0.72
55 9 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (54 bp):
TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
Found at i:49282475 original size:27 final size:27
Alignment explanation
Indices: 49282419--49282478 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
49282409 CCCCGATTTA
* * * *
49282419 TAAAATTACTGAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTATAGGG
49282446 TAAAATTACCGAAATACCCCTATAGGG
1 TAAAATTACCGAAATACCCCTATAGGG
49282473 TAAAAT
1 TAAAAT
49282479 GAATGTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTATAGGG
Found at i:49282981 original size:27 final size:27
Alignment explanation
Indices: 49282923--49282984 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
49282913 CTATGTACCT
* * *
49282923 ATCATATTTATCGATGACTCTGTGTCG
1 ATCATATTTACCCATGACTCTGTGTAG
*
49282950 ATCATATTTACCCATGACTGTGTGCTAG
1 ATCATATTTACCCATGACTCTGTG-TAG
49282978 -TCATATT
1 ATCATATT
49282985 ACCGTCACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (27 bp):
ATCATATTTACCCATGACTCTGTGTAG
Found at i:49283323 original size:27 final size:27
Alignment explanation
Indices: 49283264--49283323 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
49283254 AGATGCGCTA
* ** *
49283264 GGCCCAATTGATTCTGTTATGGGCTGT
1 GGCCCAAATGATAATGTAATGGGCTGT
* *
49283291 GACCCAAATGATAATGTAATGGGCTTT
1 GGCCCAAATGATAATGTAATGGGCTGT
49283318 GGCCCA
1 GGCCCA
49283324 CTTATGCTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (27 bp):
GGCCCAAATGATAATGTAATGGGCTGT
Found at i:49284032 original size:20 final size:20
Alignment explanation
Indices: 49284007--49284055 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
49283997 CAGCCTGTGG
49284007 TATCGATATCGCTT-TAAAAA
1 TATCGATA-CGCTTATAAAAA
**
49284027 TATCGATACTTTTATAAAAA
1 TATCGATACGCTTATAAAAA
49284047 TATCGATAC
1 TATCGATAC
49284056 TTGTGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (20 bp):
TATCGATACGCTTATAAAAA
Found at i:49284056 original size:20 final size:21
Alignment explanation
Indices: 49284021--49284075 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
49284011 GATATCGCTT
*
49284021 TAAAAATATCGATACTT-TTA
1 TAAAAATATCGATACTTGTGA
49284041 TAAAAATATCGATACTTGTGA
1 TAAAAATATCGATACTTGTGA
*
49284062 -AAAAATATCAATAC
1 TAAAAATATCGATAC
49284076 CAATATGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (21 bp):
TAAAAATATCGATACTTGTGA
Found at i:49291231 original size:41 final size:41
Alignment explanation
Indices: 49291185--49291264 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
49291175 GTGATTCCTT
49291185 AGGACAAGATTGATATCTAGCACACAAGCATACATTAAATA
1 AGGACAAGATTGATATCTAGCACACAAGCATACATTAAATA
*
49291226 AGGACAATATTGATATCTAGCACACAAGCATACATTAAA
1 AGGACAAGATTGATATCTAGCACACAAGCATACATTAAA
49291265 CATAATCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (41 bp):
AGGACAAGATTGATATCTAGCACACAAGCATACATTAAATA
Found at i:49293925 original size:22 final size:22
Alignment explanation
Indices: 49293876--49293948 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
49293866 ATAGCTCGTA
*
49293876 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTG-TTCAGCTCAAT
* *
49293899 GGAGCTTACTGTTCAGCTCAAC
1 AGAGCTTACTGTTCAGCTCAAT
*
49293921 AGAGCTTACCATTTTCAGCTCAAT
1 AGAGCTTA-C-TGTTCAGCTCAAT
49293945 AGAG
1 AGAG
49293949 ACTATTGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.38
23 11 0.26
24 15 0.36
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:49304020 original size:22 final size:23
Alignment explanation
Indices: 49303974--49304020 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
49303964 CATTGGAGCC
*
49303974 TACTGATTCAGCTCGAAAGAGCT
1 TACTGATTCAGCTCGAAAGAACT
49303997 TACT-ATTCAGCTC-AACAGAACT
1 TACTGATTCAGCTCGAA-AGAACT
49304019 TA
1 TA
49304021 GCGTTTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 16 0.73
23 4 0.18
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (23 bp):
TACTGATTCAGCTCGAAAGAACT
Found at i:49314394 original size:22 final size:22
Alignment explanation
Indices: 49314355--49314465 Score: 136
Period size: 22 Copynumber: 5.0 Consensus size: 22
49314345 GAGTCATGGT
* *
49314355 CGGTAAGCTCCT-TCGAGCAGAA
1 CGGTAAGCT-CTATTGAGCTGAA
*
49314377 CAGTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTATTGAGCTG-AA
49314400 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
49314422 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
* *
49314444 CGATAAGCT-TCAATGAGCTGAA
1 CGGTAAGCTCT-ATTGAGCTGAA
49314466 ACATAAGCTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.04
22 56 0.70
23 21 0.26
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (22 bp):
CGGTAAGCTCTATTGAGCTGAA
Found at i:49314406 original size:45 final size:44
Alignment explanation
Indices: 49314355--49314452 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
49314345 GAGTCATGGT
49314355 CGGTAAGCTCCT-TCGAGCAGAACAGTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCT-CTATCGAGCAGAACAGTAAGCTCTATTGAGCTG-AA
* * *
49314400 CGGTAAGCTCTATTGAGCTGAACGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATCGAGCAGAACAGTAAGCTCTATTGAGCTGAA
*
49314444 CGATAAGCT
1 CGGTAAGCT
49314453 TCAATGAGCT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
44 12 0.25
45 36 0.75
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
CGGTAAGCTCTATCGAGCAGAACAGTAAGCTCTATTGAGCTGAA
Found at i:49324054 original size:40 final size:41
Alignment explanation
Indices: 49324010--49324104 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 41
49324000 AGCGATTCTG
* *
49324010 ACTTGTTTTAAAATCATTTT-GA-TGTGTTAAAATGATTTTA
1 ACTTGTTTTAAAATCATTTTGGATTG-GTTAAAATCAATTTA
* * * *
49324050 ACTTG-ATTGAAATCATTTTGGCTTGGTTAAAATCAATTTC
1 ACTTGTTTTAAAATCATTTTGGATTGGTTAAAATCAATTTA
49324090 ACTTGATTTTAAAAT
1 ACTTG-TTTTAAAAT
49324105 TGTTTCAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
39 12 0.28
40 23 0.53
41 2 0.05
42 6 0.14
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (41 bp):
ACTTGTTTTAAAATCATTTTGGATTGGTTAAAATCAATTTA
Found at i:49324067 original size:20 final size:20
Alignment explanation
Indices: 49324017--49324097 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
49324007 CTGACTTGTT
*
49324017 TTAAAATCATTTTGA-TGTG-
1 TTAAAATCATTTTAACT-TGA
*
49324036 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
* ** *
49324056 TTGAAATCATTTTGGCTTGG
1 TTAAAATCATTTTAACTTGA
* *
49324076 TTAAAATCAATTTCACTTGA
1 TTAAAATCATTTTAACTTGA
49324096 TT
1 TT
49324098 TTAAAATTGT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
19 15 0.31
20 33 0.69
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.46
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:49328729 original size:48 final size:46
Alignment explanation
Indices: 49328660--49328780 Score: 127
Period size: 48 Copynumber: 2.6 Consensus size: 46
49328650 TGTCTTCGAC
** * * *
49328660 ATGGACTTACATGAATTATTCCTGTCTCC-AATGCCATATATATATAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAT-CCATATAGAT-GAT
* * *
49328707 AATGGGCTTACATGGCTCATTCCTATCTCCAAATCCATATAGCTGAT
1 -ATGGACTTACATGGCTCATTCCTGTCTCCAAATCCATATAGATGAT
*
49328754 ATGGACTTACATGGCTCATTTCTGTCT
1 ATGGACTTACATGGCTCATTCCTGTCT
49328781 TGTCCTGTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
46 24 0.39
47 2 0.03
48 32 0.52
49 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAATCCATATAGATGAT
Found at i:49333403 original size:13 final size:13
Alignment explanation
Indices: 49333373--49333411 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
49333363 AAATATATAC
* *
49333373 AAAATATTAAATT
1 AAAATATAAAAAT
*
49333386 CAAATATAAAAAT
1 AAAATATAAAAAT
49333399 AAAATATAAAAAT
1 AAAATATAAAAAT
49333412 TAAACAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATATAAAAAT
Found at i:49333604 original size:17 final size:18
Alignment explanation
Indices: 49333584--49333622 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
49333574 TTTAATAAAA
49333584 AAATAAAATTT-AGAGAG
1 AAATAAAATTTAAGAGAG
*
49333601 AAATAAAATTTAAGTGAG
1 AAATAAAATTTAAGAGAG
49333619 AAAT
1 AAAT
49333623 TAAGAGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (18 bp):
AAATAAAATTTAAGAGAG
Found at i:49341633 original size:91 final size:90
Alignment explanation
Indices: 49341514--49341690 Score: 264
Period size: 91 Copynumber: 2.0 Consensus size: 90
49341504 ATAAATTCCC
* *
49341514 TAAAAATATTTCAAGAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCTTTT
1 TAAAAATATTTCAAAAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCATTT
49341579 AATTGTTTAGCTAAATCCACTTTCT
66 AATTGTTTAGCTAAATCCACTTTCT
* * ** *
49341604 TAAAAATATTTCAAAAAAAGCTATTTTAAATGAAACAAACATATATTTGGCTTTTTCTTTTCATT
1 TAAAAATATTTC-AAAAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCATT
* *
49341669 TAATTGTTTAGTTAAATTCACT
65 TAATTGTTTAGCTAAATCCACT
49341691 AAACAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 12 0.16
91 65 0.84
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (90 bp):
TAAAAATATTTCAAAAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCATTT
AATTGTTTAGCTAAATCCACTTTCT
Found at i:49346083 original size:16 final size:16
Alignment explanation
Indices: 49346059--49346089 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49346049 GAGAAGAAAT
49346059 TATGAGTTTTGAGAAG
1 TATGAGTTTTGAGAAG
*
49346075 TATGGGTTTTGAGAA
1 TATGAGTTTTGAGAA
49346090 AAAGAATAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (16 bp):
TATGAGTTTTGAGAAG
Found at i:49349670 original size:26 final size:26
Alignment explanation
Indices: 49349641--49349690 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
49349631 CACCAATATT
* *
49349641 GCAGCAGAGCTGCCAGTAACAGTAAC
1 GCAGCAAAGCTACCAGTAACAGTAAC
* *
49349667 GCAGCAAAGTTACCAGTATCAGTA
1 GCAGCAAAGCTACCAGTAACAGTA
49349691 TATGGCACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (26 bp):
GCAGCAAAGCTACCAGTAACAGTAAC
Found at i:49349718 original size:20 final size:20
Alignment explanation
Indices: 49349694--49349771 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
49349684 ATCAGTATAT
*
49349694 GGCACAAAGCCATCAATAGT
1 GGCACAAAGCCATCAATAGC
49349714 GGCACAAAGCCATCAATAGC
1 GGCACAAAGCCATCAATAGC
49349734 GGCACAAAGCCATCAATAGC
1 GGCACAAAGCCATCAATAGC
*
49349754 GGCACAAAGCCATAAATA
1 GGCACAAAGCCATCAATA
49349772 TCACAGTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.42, C:0.27, G:0.19, T:0.12
Consensus pattern (20 bp):
GGCACAAAGCCATCAATAGC
Found at i:49350089 original size:27 final size:27
Alignment explanation
Indices: 49350059--49350123 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
49350049 GGGTAAAATA
*
49350059 GTCATTTTATCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
*
49350086 GTCAGTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
49350113 GTCATTTTACC
1 GTCATTTTACC
49350124 TGCCTTAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Found at i:49353657 original size:20 final size:20
Alignment explanation
Indices: 49353603--49353700 Score: 81
Period size: 20 Copynumber: 4.9 Consensus size: 20
49353593 ATCAATATAT
*
49353603 GGCACAAAGCCA-CGAGTAGC
1 GGCACAAAGCCATC-AGTAGA
* *
49353623 GGCTCAAAGCTATCAGTAGA
1 GGCACAAAGCCATCAGTAGA
* * *
49353643 GGCACAATGCCATCAATAGT
1 GGCACAAAGCCATCAGTAGA
* * *
49353663 GGCACAAAGACATCAATAGC
1 GGCACAAAGCCATCAGTAGA
* *
49353683 GACACAAAGCCATAAGTA
1 GGCACAAAGCCATCAGTA
49353701 TCGCAACAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 61 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (20 bp):
GGCACAAAGCCATCAGTAGA
Found at i:49360690 original size:22 final size:22
Alignment explanation
Indices: 49360663--49360720 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
49360653 TCTCCGATTA
49360663 TTAGCACATTAATGCTCT-TCGT
1 TTAGCACATTAATGCTCTCT-GT
**
49360685 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTAATGCTCTCTGT
* *
49360707 ATAGCATATTAATG
1 TTAGCACATTAATG
49360721 ATCCCTATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAATGCTCTCTGT
Found at i:49364644 original size:42 final size:43
Alignment explanation
Indices: 49364572--49364674 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 43
49364562 TATGATTTAC
* *
49364572 GTGTAAGACCATGTCTGGGACTTCGACATCG-TATTTGATTTT
1 GTGTAAGACCATGTCTGGAACGTCGACATCGATATTTGATTTT
* * **
49364614 GTGTAAGACCCTGTCTGGAACAGT-GGCATCGATATTTGATTAC
1 GTGTAAGACCATGTCTGGAAC-GTCGACATCGATATTTGATTTT
* *
49364657 ATGTAAGACCACGTCTGG
1 GTGTAAGACCATGTCTGG
49364675 GATGTTGGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
42 25 0.50
43 25 0.50
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGAACGTCGACATCGATATTTGATTTT
Found at i:49364684 original size:43 final size:44
Alignment explanation
Indices: 49364515--49364685 Score: 133
Period size: 43 Copynumber: 4.0 Consensus size: 44
49364505 CATAGGATCT
* * * *
49364515 GATATGTGATTTCGTGTAAGACCACGTTTGGGAC-ATTGGCAT-
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACTGTTGGCATC
* * * *
49364557 TA-ACTTATGATTTACGTGTAAGACCATGTCTGGGACT-TCGACATC
1 GATA-TT-TGA-TTACGTGTAAGACCACGTCTGGGACTGTTGGCATC
** * *
49364602 G-TATTTGATTTTGTGTAAGACC-CTGTCTGGAACAG-TGGCATC
1 GATATTTGATTACGTGTAAGACCAC-GTCTGGGACTGTTGGCATC
*
49364644 GATATTTGATTACATGTAAGACCACGTCTGGGA-TGTTGGCAT
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACTGTTGGCAT
49364686 TGTATGATCT
Statistics
Matches: 98, Mismatches: 20, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
41 1 0.01
42 29 0.30
43 37 0.38
44 30 0.31
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (44 bp):
GATATTTGATTACGTGTAAGACCACGTCTGGGACTGTTGGCATC
Found at i:49368121 original size:141 final size:142
Alignment explanation
Indices: 49367865--49368137 Score: 340
Period size: 141 Copynumber: 1.9 Consensus size: 142
49367855 TCTCACATCT
**
49367865 AAGTCGATGCCATGTCCCAGACAGGTCGTACACTAACTTTCATACATCGAGGCTGATGCCATGTC
1 AAGTCGATGCCATGTCCCAGACAGGTCGTACACTAACTTTCATACATCGAGGCCAATGCCATGTC
* ** * **
49367930 CCAGACAAGTCTTACACTGGCTCTTGTTTATCTGTGTCGATGCCATGTCCCAGACAGGTCTTACA
66 CCAAACAAGTCTTACACTGGCTCTCATCTATCAATGTCGATGCCATGTCCCAGACAGGTCTTACA
49367995 CTGAAACACCTC
131 CTGAAACACCTC
* * * *
49368007 AAGTCGATGCCATGTCCCAGACAGGTCTTACACT-AGTTTGCATATC-TTGA-GCCAATGTCATG
1 AAGTCGATGCCATGTCCCAGACAGGTCGTACACTAACTTT-CATA-CATCGAGGCCAATGCCATG
* * *
49368069 TCCCAAATAGGTCTTACA-TAGGCTCTCATCTATCAATG-CTGTTGCCATGTCCCAGACAGGTCT
64 TCCCAAACAAGTCTTACACT-GGCTCTCATCTATCAATGTC-GATGCCATGTCCCAGACAGGTCT
49368132 TACACT
127 TACACT
49368138 AGCACGCACA
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
140 2 0.02
141 69 0.62
142 40 0.36
143 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (142 bp):
AAGTCGATGCCATGTCCCAGACAGGTCGTACACTAACTTTCATACATCGAGGCCAATGCCATGTC
CCAAACAAGTCTTACACTGGCTCTCATCTATCAATGTCGATGCCATGTCCCAGACAGGTCTTACA
CTGAAACACCTC
Found at i:49371714 original size:21 final size:21
Alignment explanation
Indices: 49371688--49371743 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
49371678 AGCAGCGGTG
*
49371688 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
49371709 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
*
49371730 ACGGTGAGATTAGA
1 GCGGTGAGATTAGA
49371744 AACAATGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:49374783 original size:49 final size:47
Alignment explanation
Indices: 49374673--49374798 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 47
49374663 ATAGGGTACG
* * *
49374673 ATGTCGACGCCATGTTCCAAACATGGTCTTACGCTGGCTCTCACATCT
1 ATGTCGATGCCATGTCCCAAACA-GGTCTTACACTGGCTCTCACATCT
* **
49374721 AAGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCGTTTATCT
1 ATGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTC--ACATCT
*
49374770 ATGTCGATGCCATGTCCCAAACAGTTCTT
1 ATGTCGATGCCATGTCCCAAACAGGTCTT
49374799 GTAATGGCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 17 0.25
48 20 0.29
49 31 0.46
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.30
Consensus pattern (47 bp):
ATGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCACATCT
Found at i:49375650 original size:29 final size:30
Alignment explanation
Indices: 49375613--49375669 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
49375603 CCGAGCCTTG
*
49375613 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
49375642 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
49375670 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:49375899 original size:13 final size:13
Alignment explanation
Indices: 49375881--49375912 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49375871 TTTCCAGCAA
49375881 TTATGAATTTATT
1 TTATGAATTTATT
49375894 TTATGAATTTATT
1 TTATGAATTTATT
*
49375907 TGATGA
1 TTATGA
49375913 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:49376136 original size:49 final size:50
Alignment explanation
Indices: 49376007--49376247 Score: 306
Period size: 49 Copynumber: 4.7 Consensus size: 50
49375997 ATTTGGGTAA
* * *
49376007 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
49376063 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
*
49376113 AGAGGT-CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
49376162 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
49376212 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
49376248 TTTGGCATGT
Statistics
Matches: 168, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
49 48 0.29
50 46 0.27
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:49376191 original size:99 final size:104
Alignment explanation
Indices: 49376011--49376247 Score: 342
Period size: 99 Copynumber: 2.3 Consensus size: 104
49376001 GGGTAAAGAG
* *
49376011 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCCTGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCATCC---AGATCATGAGAGGTCCCCTAT
* *
49376076 AAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGAG-AG
63 AAGACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAAC
* *
49376117 GT-CCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC-GA-GATGAGAGGTCCCCTATAAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCATCCAGATCATGAGAGGTCCCCTATAAG
49376178 ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
49376217 ATCCCATGTAAGACCATGTCTGGGACATGGC
1 ATCCCATGTAAGACCATGTCTGGGACATGGC
49376248 TTTGGCATGT
Statistics
Matches: 121, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
98 1 0.01
99 51 0.42
100 4 0.03
101 28 0.23
104 2 0.02
105 34 0.28
106 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (104 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCATCCAGATCATGAGAGGTCCCCTATAAG
ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
Found at i:49387528 original size:26 final size:26
Alignment explanation
Indices: 49387490--49387542 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
49387480 ATATAAATGC
* *
49387490 ATCCCCAATGATCATTTCTTGTACTA
1 ATCCCCAAGGATCATTTCTTCTACTA
49387516 ATCCCCAAGGATCATTTCTTCTACTA
1 ATCCCCAAGGATCATTTCTTCTACTA
49387542 A
1 A
49387543 CATGGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (26 bp):
ATCCCCAAGGATCATTTCTTCTACTA
Found at i:49388525 original size:3 final size:3
Alignment explanation
Indices: 49388519--49388556 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
49388509 CACAACAATT
49388519 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
49388557 TTGTCAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:49389807 original size:5 final size:5
Alignment explanation
Indices: 49389794--49389865 Score: 74
Period size: 5 Copynumber: 14.4 Consensus size: 5
49389784 TTTCATATTG
* * *
49389794 TATCA TATCT TATCA TATCA TAACA TATCA TATCA TACCA TATCGA -ATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATC-A TATCA
* * *
49389844 TAGCA TATCT TATCA TGTCA TA
1 TATCA TATCA TATCA TATCA TA
49389866 GAATGTCCTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
4 1 0.02
5 51 0.96
6 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (5 bp):
TATCA
Found at i:49393615 original size:80 final size:82
Alignment explanation
Indices: 49393470--49393654 Score: 222
Period size: 80 Copynumber: 2.3 Consensus size: 82
49393460 GCTCCTCGTT
* * *
49393470 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
49393534 GAT-TTAGTAAC-TCGCA
66 GATATT-GTAACTTAGCA
* **
49393550 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
*
49393613 GGATATTGTCACTTAGCA
65 GGATATTGTAACTTAGCA
*
49393631 C-AA-GACTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
49393655 CAGCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
79 22 0.24
80 60 0.66
81 9 0.10
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GATATTGTAACTTAGCA
Found at i:49393616 original size:40 final size:40
Alignment explanation
Indices: 49393470--49393602 Score: 214
Period size: 40 Copynumber: 3.3 Consensus size: 40
49393460 GCTCCTCGTT
* * * *
49393470 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
49393510 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
49393550 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
49393590 CAAATGCCTTCGG
1 CAAATGCCTTCGG
49393603 ATCTTAGTCC
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 86 0.98
41 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:49395450 original size:16 final size:16
Alignment explanation
Indices: 49395429--49395459 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49395419 TTCAGACTTG
49395429 AATTTTCTCAAGCTTT
1 AATTTTCTCAAGCTTT
*
49395445 AATTTTTTCAAGCTT
1 AATTTTCTCAAGCTT
49395460 GGATTAGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTTCTCAAGCTTT
Found at i:49402580 original size:7 final size:7
Alignment explanation
Indices: 49402568--49402728 Score: 122
Period size: 7 Copynumber: 23.7 Consensus size: 7
49402558 TACTTAGTAT
*
49402568 TCAATCC
1 TCAATTC
*
49402575 TCAATCC
1 TCAATTC
*
49402582 TAAATTC
1 TCAATTC
49402589 TCAATTC
1 TCAATTC
*
49402596 TCAATTT
1 TCAATTC
*
49402603 TCAATCC
1 TCAATTC
*
49402610 TCAATTT
1 TCAATTC
49402617 TC-A-T-
1 TCAATTC
*
49402621 TCAATTG
1 TCAATTC
49402628 TCAATTC
1 TCAATTC
49402635 TCAATTC
1 TCAATTC
49402642 TCAA-TC
1 TCAATTC
49402648 TTCAA-TC
1 -TCAATTC
49402655 -CAATTC
1 TCAATTC
49402661 TCAATTC
1 TCAATTC
*
49402668 TGAA-TC
1 TCAATTC
*
49402674 ATCAATCC
1 -TCAATTC
*
49402682 TTAATTC
1 TCAATTC
49402689 TCAATTC
1 TCAATTC
*
49402696 TGAA-TC
1 TCAATTC
*
49402702 ATCAATCC
1 -TCAATTC
*
49402710 TTAATTC
1 TCAATTC
49402717 TCAATTC
1 TCAATTC
49402724 TCAAT
1 TCAAT
49402729 CATCAATCAT
Statistics
Matches: 123, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
4 2 0.02
5 5 0.04
6 10 0.08
7 104 0.85
8 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.02, T:0.40
Consensus pattern (7 bp):
TCAATTC
Found at i:49402591 original size:14 final size:14
Alignment explanation
Indices: 49402568--49402749 Score: 124
Period size: 14 Copynumber: 13.4 Consensus size: 14
49402558 TACTTAGTAT
*
49402568 TCAATCCTCAATCC
1 TCAATTCTCAATCC
* *
49402582 TAAATTCTCAATTC
1 TCAATTCTCAATCC
*
49402596 TCAATTTTCAATCC
1 TCAATTCTCAATCC
*
49402610 TCAATTTTC-AT--
1 TCAATTCTCAATCC
* *
49402621 TCAATTGTCAATTC
1 TCAATTCTCAATCC
*
49402635 TCAATTCTCAATCT
1 TCAATTCTCAATCC
*
49402649 TCAA-TC-CAATTC
1 TCAATTCTCAATCC
* *
49402661 TCAATTCTGAATCA
1 TCAATTCTCAATCC
* * *
49402675 TCAATCCTTAATTC
1 TCAATTCTCAATCC
* *
49402689 TCAATTCTGAATCA
1 TCAATTCTCAATCC
* * *
49402703 TCAATCCTTAATTC
1 TCAATTCTCAATCC
*
49402717 TCAATTCTCAATCA
1 TCAATTCTCAATCC
*
49402731 TCAA-TCATCAATCA
1 TCAATTC-TCAATCC
49402745 TCAAT
1 TCAAT
49402750 CATCAATTTT
Statistics
Matches: 130, Mismatches: 31, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
11 8 0.06
12 10 0.08
13 8 0.06
14 104 0.80
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (14 bp):
TCAATTCTCAATCC
Found at i:49402632 original size:32 final size:33
Alignment explanation
Indices: 49402568--49402764 Score: 140
Period size: 35 Copynumber: 6.0 Consensus size: 33
49402558 TACTTAGTAT
* * *
49402568 TCAATCCTCAATCCTAAATTCTCAATTCTCAATTT
1 TCAATCCTCAATCTTCAA-T-TCAATTCTCAATTC
* *
49402603 TCAATCCTCAATTTTC-ATTCAATTGTCAATTC
1 TCAATCCTCAATCTTCAATTCAATTCTCAATTC
* *
49402635 TCAATTCTCAATCTTCAATCCAATTCTCAATTC
1 TCAATCCTCAATCTTCAATTCAATTCTCAATTC
* *
49402668 TGAATCATCAATC--C--TT-AATTCTCAATTC
1 TCAATCCTCAATCTTCAATTCAATTCTCAATTC
* *
49402696 TGAATCATCAATCCTT-AATTCTCAATTCTCAA-TC
1 TCAATCCTCAAT-CTTCAA-T-TCAATTCTCAATTC
* * *
49402730 ATCAATCATCAATCATCAATCATCAATTTTCAATT
1 -TCAATCCTCAATCTTCAAT--TCAATTCTCAATT
49402765 ATTTTTTAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
28 24 0.18
29 2 0.02
31 1 0.01
32 26 0.20
33 26 0.20
34 7 0.05
35 45 0.34
36 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.02, T:0.40
Consensus pattern (33 bp):
TCAATCCTCAATCTTCAATTCAATTCTCAATTC
Found at i:49402696 original size:28 final size:28
Alignment explanation
Indices: 49402630--49402736 Score: 173
Period size: 28 Copynumber: 3.9 Consensus size: 28
49402620 TTCAATTGTC
*
49402630 AATTCTCAATTCTCAATCTTCAATCC--
1 AATTCTCAATTCTCAATCATCAATCCTT
*
49402656 AATTCTCAATTCTGAATCATCAATCCTT
1 AATTCTCAATTCTCAATCATCAATCCTT
*
49402684 AATTCTCAATTCTGAATCATCAATCCTT
1 AATTCTCAATTCTCAATCATCAATCCTT
49402712 AATTCTCAATTCTCAATCATCAATC
1 AATTCTCAATTCTCAATCATCAATC
49402737 ATCAATCATC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 24 0.32
28 52 0.68
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTCTCAATTCTCAATCATCAATCCTT
Found at i:49402734 original size:7 final size:7
Alignment explanation
Indices: 49402698--49402756 Score: 68
Period size: 7 Copynumber: 8.4 Consensus size: 7
49402688 CTCAATTCTG
49402698 AATCATC
1 AATCATC
* *
49402705 AATCCTT
1 AATCATC
49402712 AATTC-TC
1 AA-TCATC
49402719 AATTC-TC
1 AA-TCATC
49402726 AATCATC
1 AATCATC
49402733 AATCATC
1 AATCATC
49402740 AATCATC
1 AATCATC
49402747 AATCATC
1 AATCATC
49402754 AAT
1 AAT
49402757 TTTCAATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
6 2 0.04
7 43 0.91
8 2 0.04
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (7 bp):
AATCATC
Found at i:49402749 original size:28 final size:28
Alignment explanation
Indices: 49402569--49402742 Score: 147
Period size: 28 Copynumber: 6.6 Consensus size: 28
49402559 ACTTAGTATT
* *
49402569 CAATCCTCAATCCTAAATTCTCAATTCT
1 CAATCATCAATCCTCAATTCTCAATTCT
** *
49402597 CAATTTTCAATCCTCAATTTTC-A-T-T
1 CAATCATCAATCCTCAATTCTCAATTCT
** *
49402622 CAATTGTCAATTCTCAATTCTCAA---T
1 CAATCATCAATCCTCAATTCTCAATTCT
49402647 C--T--TCAAT-C-CAATTCTCAATTCT
1 CAATCATCAATCCTCAATTCTCAATTCT
* *
49402669 GAATCATCAATCCTTAATTCTCAATTCT
1 CAATCATCAATCCTCAATTCTCAATTCT
* *
49402697 GAATCATCAATCCTTAATTCTCAATTCT
1 CAATCATCAATCCTCAATTCTCAATTCT
*
49402725 CAATCATCAATCATCAAT
1 CAATCATCAATCCTCAAT
49402743 CATCAATCAT
Statistics
Matches: 124, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.08
20 1 0.01
21 5 0.04
22 1 0.01
23 1 0.01
24 1 0.01
25 22 0.18
26 7 0.06
27 2 0.02
28 74 0.60
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (28 bp):
CAATCATCAATCCTCAATTCTCAATTCT
Found at i:49402762 original size:21 final size:21
Alignment explanation
Indices: 49402689--49402763 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
49402679 TCCTTAATTC
* *
49402689 TCAATTCTGAATCATCAATCC
1 TCAATTCTCAATCATCAATCA
*
49402710 TTAATTCTCAATTC-TCAATCA
1 TCAATTCTCAA-TCATCAATCA
49402731 TCAA-TCATCAATCATCAATCA
1 TCAATTC-TCAATCATCAATCA
*
49402752 TCAATTTTCAAT
1 TCAATTCTCAAT
49402764 TATTTTTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
20 4 0.09
21 38 0.84
22 3 0.07
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.37
Consensus pattern (21 bp):
TCAATTCTCAATCATCAATCA
Found at i:49402825 original size:20 final size:20
Alignment explanation
Indices: 49402787--49402825 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49402777 CTTTTTCTGA
*
49402787 ATTTTATTCTCTTAGATTTT
1 ATTTTATTCTCTTAAATTTT
49402807 ATTTTATTC-CTTATAATTT
1 ATTTTATTCTCTTA-AATTT
49402826 GTAAAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTTATTCTCTTAAATTTT
Found at i:49414335 original size:13 final size:13
Alignment explanation
Indices: 49414296--49414327 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49414286 TGGTTCCCTC
49414296 TTATGGGCGTGTG
1 TTATGGGCGTGTG
*
49414309 CTATGGGCGTGTG
1 TTATGGGCGTGTG
49414322 TTATGG
1 TTATGG
49414328 CTGTGTGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.44, T:0.38
Consensus pattern (13 bp):
TTATGGGCGTGTG
Found at i:49415526 original size:18 final size:20
Alignment explanation
Indices: 49415503--49415544 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
49415493 AGCAAGATGA
49415503 AAATAATATT-AA-TAAAC-T
1 AAATAA-ATTGAATTAAACAT
49415521 AAATAAATTGAATTAAACAT
1 AAATAAATTGAATTAAACAT
49415541 AAAT
1 AAAT
49415545 CTACTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 5 0.24
20 5 0.24
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AAATAAATTGAATTAAACAT
Done.