Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 34 of 318
Found at i:12675218 original size:5 final size:5
Alignment explanation
Indices: 12675210--12675236 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12675200 TCTTTAGTTT
12675210 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
12675237 TAAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:12681063 original size:5 final size:5
Alignment explanation
Indices: 12681053--12681081 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12681043 GTTTATGGGT
12681053 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
12681082 GTAAGTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:12684703 original size:27 final size:28
Alignment explanation
Indices: 12684640--12684703 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
12684630 ATAAAATTTA
* *
12684640 AATATAATAAATTGAATATTTAATTTTT
1 AATATAAAAAAGTGAATATTTAATTTTT
* *
12684668 AACAAAAAAAAGTG-ATAATTT-ATTTTT
1 AATATAAAAAAGTGAAT-ATTTAATTTTT
12684695 AATATAAAA
1 AATATAAAA
12684704 GTTTAGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (28 bp):
AATATAAAAAAGTGAATATTTAATTTTT
Found at i:12685828 original size:22 final size:21
Alignment explanation
Indices: 12685803--12685866 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
12685793 ATTTTTTGAA
*
12685803 TTATTTTCTTTCTTTATTTATT
1 TTATTTTATTTCTTTATTT-TT
** *
12685825 TTATAGTATTTCTTTATCTTT
1 TTATTTTATTTCTTTATTTTT
*
12685846 TTATTTTGTTATCTTTATTTT
1 TTATTTTATT-TCTTTATTTT
12685867 CTTAAAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
21 9 0.27
22 24 0.73
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (21 bp):
TTATTTTATTTCTTTATTTTT
Found at i:12686942 original size:17 final size:16
Alignment explanation
Indices: 12686913--12686967 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
12686903 ACAGAGAAAT
*
12686913 ATAATAATAAATAATC
1 ATAATAATAAATAATA
12686929 ATAATAATTAAATAATA
1 ATAATAA-TAAATAATA
* * *
12686946 ATAA-ACTTATTAATA
1 ATAATAATAAATAATA
12686961 ATAATAA
1 ATAATAA
12686968 AAGAGTAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 11 0.34
16 9 0.28
17 12 0.38
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:12688322 original size:230 final size:225
Alignment explanation
Indices: 12687905--12688327 Score: 491
Period size: 230 Copynumber: 1.9 Consensus size: 225
12687895 TCCCCTATGT
* * * *
12687905 CTTAACTGGATCACCAACTCAATTATGAAATTATAAAAATACCTCTTTATTATTATTATTATTAT
1 CTTAACTGGATCACCAAATCAATTATGAAATTACAAAAATACCTCTTTATTATAATTAATATTAT
* * * *
12687970 TATGAAGCTTTTGTGTTTTCGTACTTTTACATCAGCTTTAAATAAAAGAATTCAAAATTACAAAT
66 TATGAAGCTTTTATCTTTTCATACTTTTACATCAGATTTAAATAAAAGAATTCAAAATTACAAAT
* * ** * *
12688035 TTGATGATTGGACACTTGTTCAATTGTCTTAAAATATAAGTTCATTACCACTTTACCTATATTTG
131 TTGAAGATTGGACACATGTTCAATAATATTAAAATACAAGTTCATTACCACTTTACCTATATTTG
12688100 TTAGCTAATACTTGCATAGTTGGTGTCACC
196 TTAGCTAATACTTGCATAGTTGGTGTCACC
* * * *
12688130 CTTAACTGGATCATCAAATTAGTTATGAAATTACATAAATACCTCTTCTTTTAAATTATAATTAA
1 CTTAACTGGATCACCAAATCAATTATGAAATTACAAAAATA-C-C-TC-TTT--ATTATAATTAA
* * *
12688195 TATTATTATGACA-CTTTTATCTTTTCATATTTTTATATCATATTTAAATAAAA-AATT-ACAAA
60 TATTATTATGA-AGCTTTTATCTTTTCATACTTTTACATCAGATTTAAATAAAAGAATTCA-AAA
*
12688257 TTACAAATTT-AAGAATT-GA-ACATGCATTCAATAATATTAAAATACAAGTTCATTACTC-GTT
123 TTACAAATTTGAAG-ATTGGACACATG--TTCAATAATATTAAAATACAAGTTCATTAC-CACTT
12688318 TACCTATATT
184 TACCTATATT
12688328 CATTGTTGAA
Statistics
Matches: 164, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
225 35 0.21
226 1 0.01
227 1 0.01
228 6 0.04
229 8 0.05
230 58 0.35
231 54 0.33
232 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (225 bp):
CTTAACTGGATCACCAAATCAATTATGAAATTACAAAAATACCTCTTTATTATAATTAATATTAT
TATGAAGCTTTTATCTTTTCATACTTTTACATCAGATTTAAATAAAAGAATTCAAAATTACAAAT
TTGAAGATTGGACACATGTTCAATAATATTAAAATACAAGTTCATTACCACTTTACCTATATTTG
TTAGCTAATACTTGCATAGTTGGTGTCACC
Found at i:12710280 original size:43 final size:44
Alignment explanation
Indices: 12710208--12710508 Score: 265
Period size: 43 Copynumber: 7.1 Consensus size: 44
12710198 GATTGAAGTC
* * *
12710208 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * * * *
12710252 AAGATATCAGATCCTATC-TCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * *
12710295 AAGAT-GCAGATCTTGTCTTCCCATATTGGTGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * *
12710338 -AGAAAGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
* * *
12710380 AAGATATC--ATC-TATC-TCC--TATTGGTAG-GAAGT-GATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* *
12710417 AAGAT-GCAGATCTTGTCTTCC-ATATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCG
* * *
12710460 AAGA-AACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
12710503 AAGATA
1 AAGATA
12710509 TCTATCTTAT
Statistics
Matches: 207, Mismatches: 33, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
36 1 0.00
37 14 0.07
38 9 0.04
39 6 0.03
40 6 0.03
41 11 0.05
42 31 0.15
43 107 0.52
44 22 0.11
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
AAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCG
Found at i:12710804 original size:127 final size:121
Alignment explanation
Indices: 12710209--12710862 Score: 881
Period size: 128 Copynumber: 5.4 Consensus size: 121
12710199 ATTGAAGTCA
12710209 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATATCAGATCCTATCTCCT
1 AGAAAGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCG-AGATA-C--AT-CTAT-TCCT
12710274 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGT-GCGAAGTAGATCG
59 ATATTGGTAGGAAGT-GATCGAAGATGCAGATCTTGTCTTCCCATA-TGGTGGCGAAGTAGATCG
12710338 AGAAAGCAGATCTTGTCTTCATGTATTGCGTGAAGTAGATCGAAGATATCATCTATCTCC--TAT
1 AGAAAGCAGATCTTGTCTTCATGTATTGCGTGAAGTAGATCG-AGATA-CATCTAT-TCCTATAT
12710401 TGGTAGGAAGTGATCGAAGATGCAGATCTTGTCTT-CCATATTGGTGGCGAAGTAGATCG
63 TGGTAGGAAGTGATCGAAGATGCAGATCTTGTCTTCCCATA-TGGTGGCGAAGTAGATCG
*
12710460 AAGAAA-CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT--ATCTA-TCTTATAT
1 -AGAAAGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCG-AGATACATCTATTCCTATAT
12710521 T-GT----AGTG-TC--A-ATGCAGATCTTGTCTT-CCATATGGTGGCGAAGTAGATC-
63 TGGTAGGAAGTGATCGAAGATGCAGATCTTGTCTTCCCATATGGTGGCGAAGTAGATCG
* *
12710569 -GAAAGCAGAT-TTGTCTTCATGTATTGCGT-AA-TAGAT-GAAATATATCTATTCCTATATTGG
1 AGAAAGCAGATCTTGTCTTCATGTATTGCGTGAAGTAGATCGAGATACATCTATTCCTATATTGG
12710629 TAGGAAGTGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 TAGGAAGTGATCGAAGATGCAGATCTTGTCTTCCCATA-TGGTGGCGAAGTAGATCG
12710686 AGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAGATACAGTCCTATCTTCCTAT
1 AGAAAGCAGATCTTGTCTTCATGTATT-GCGTGAAGTAGATCGAGATACA-T-CTA--TTCCTAT
12710751 ATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATGGTGGCGAAGTAGATCG
61 ATTGGTAGGAAGT-GATCGAAGATGCAGATCTTGTCTTCCCATATGGTGGCGAAGTAGATCG
12710813 AAGAAAGCAGATC-TGTCTTCATGTATTGCGTGAAGTAGATCGAAGATACA
1 -AGAAAGCAGATCTTGTCTTCATGTATTGCGTGAAGTAGATCG-AGATACA
12710863 ATCCATCCCA
Statistics
Matches: 486, Mismatches: 5, Indels: 70
0.87 0.01 0.12
Matches are distributed among these distances:
102 3 0.01
103 1 0.00
104 10 0.02
105 10 0.02
106 6 0.01
107 19 0.04
108 5 0.01
110 21 0.04
111 23 0.05
112 1 0.00
113 1 0.00
114 18 0.04
115 9 0.02
116 17 0.03
118 12 0.02
119 17 0.03
120 13 0.03
121 12 0.02
122 63 0.13
123 45 0.09
124 1 0.00
125 11 0.02
126 17 0.03
127 59 0.12
128 65 0.13
129 27 0.06
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (121 bp):
AGAAAGCAGATCTTGTCTTCATGTATTGCGTGAAGTAGATCGAGATACATCTATTCCTATATTGG
TAGGAAGTGATCGAAGATGCAGATCTTGTCTTCCCATATGGTGGCGAAGTAGATCG
Found at i:12710806 original size:43 final size:44
Alignment explanation
Indices: 12710617--12710832 Score: 216
Period size: 43 Copynumber: 5.1 Consensus size: 44
12710607 AATATATCTA
* *
12710617 TTCCTATATTGGTAG-GAAGT-GATCGAAGATGCAGATCTTGTC
1 TTCCCATATTGGTGGCGAAGTAGATCGAAGATGCAGATCTTGTC
*
12710659 TTCCCATATTGGTGGCGAAGTAGATCG-AGAAAGCAGATCTTGTC
1 TTCCCATATTGGTGGCGAAGTAGATCGAAG-ATGCAGATCTTGTC
*** * * * * *
12710703 TTCATGTATTGG-CGTGAAGTAGATCG-AGATACAG-TCCTATC
1 TTCCCATATTGGTGGCGAAGTAGATCGAAGATGCAGATCTTGTC
* * *
12710744 TTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTC
1 TTCCCATATTGGTGGCGAAGTAGATCGAAGATGCAGATCTTGTC
*
12710787 TTCCCATA-TGGTGGCGAAGTAGATCGAAGAAAGCAGATC-TGTC
1 TTCCCATATTGGTGGCGAAGTAGATCGAAG-ATGCAGATCTTGTC
12710830 TTC
1 TTC
12710833 ATGTATTGCG
Statistics
Matches: 143, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
41 25 0.17
42 30 0.21
43 53 0.37
44 35 0.24
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (44 bp):
TTCCCATATTGGTGGCGAAGTAGATCGAAGATGCAGATCTTGTC
Found at i:12710806 original size:84 final size:84
Alignment explanation
Indices: 12710631--12710813 Score: 194
Period size: 84 Copynumber: 2.2 Consensus size: 84
12710621 TATATTGGTA
* * * *
12710631 GGAAGT-GATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAGAAAGCAG
1 GGAAGTAGATCG-AGATACAG-TCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAGAAAGCAG
* *
12710695 ATCTTGTCTTCATGTATTGGC
64 ATCTTGTCTTCATATAGTGGC
* * *
12710716 GTGAAGTAGATCGAGATACAGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCGA-AGATGCAG
1 G-GAAGTAGATCGAGATACAGTCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAGA-AAGCAG
*
12710779 ATCTTGTCTTCCCATATGGTGGC
64 ATCTTGTCTT--CATATAGTGGC
12710802 -GAAGTAGATCGA
1 GGAAGTAGATCGA
12710814 AGAAAGCAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
83 1 0.01
84 38 0.46
85 19 0.23
86 20 0.24
87 5 0.06
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (84 bp):
GGAAGTAGATCGAGATACAGTCCTATCTTCCCATATTGGTAGCGAAGTAGATCGAGAAAGCAGAT
CTTGTCTTCATATAGTGGC
Found at i:12722985 original size:41 final size:41
Alignment explanation
Indices: 12722930--12723168 Score: 292
Period size: 41 Copynumber: 5.8 Consensus size: 41
12722920 GAATGTAATA
* *
12722930 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
12722971 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
12723012 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
12723053 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
12723094 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGATACAT--TT
* * *
12723135 CAGGCTTTAAGCCTAGCAGG-TAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCT-TAATGCCGGTGA
12723169 ATCTGTTTAA
Statistics
Matches: 180, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
39 3 0.02
40 8 0.04
41 167 0.93
42 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:12727191 original size:16 final size:15
Alignment explanation
Indices: 12727148--12727199 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
12727138 TAAGGAAAAT
12727148 ATATTTTAA-AATTA
1 ATATTTTAATAATTA
12727162 AT-TTTTAATTTAATTA
1 ATATTTTAA--TAATTA
12727178 ATTATTTTAATAATTCA
1 A-TATTTTAATAATT-A
12727195 ATATT
1 ATATT
12727200 AAAAAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.19
14 2 0.06
16 15 0.47
17 3 0.09
18 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTAATAATTA
Found at i:12733270 original size:60 final size:60
Alignment explanation
Indices: 12733150--12733285 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
12733140 ACCAAACAAG
* *
12733150 ATAAAATTA--AATAATTAAATGATTATTTTATAATTTTCTATCATCATATGATCAAGAA
1 ATAAAATTATTAATAATTAAATGATTATTTTATAATTTTCTATCATCAAATAATCAAGAA
* * * * *
12733208 ATAAATTTATTAATAATTTAATGATTATTTTATAATTATTTTA-CAATTAAATAATTAA-AA
1 ATAAAATTATTAATAATTAAATGATTATTTTATAATT-TTCTATC-ATCAAATAATCAAGAA
12733268 ATAAAATTATTAATAATT
1 ATAAAATTATTAATAATT
12733286 GAGTTATCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 8 0.12
60 45 0.68
61 13 0.20
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (60 bp):
ATAAAATTATTAATAATTAAATGATTATTTTATAATTTTCTATCATCAAATAATCAAGAA
Found at i:12735342 original size:17 final size:18
Alignment explanation
Indices: 12735316--12735349 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12735306 TTTTAAAAAA
12735316 TAAAATACATAAAAATAC
1 TAAAATACATAAAAATAC
*
12735334 TAAAA-ACATTAAAATA
1 TAAAATACATAAAAATA
12735350 AATGTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAATACATAAAAATAC
Found at i:12741963 original size:17 final size:17
Alignment explanation
Indices: 12741941--12741976 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12741931 AACCATCCAT
12741941 TTTTGTTTACAAGTGGG
1 TTTTGTTTACAAGTGGG
12741958 TTTTGTTTACAAGTGGG
1 TTTTGTTTACAAGTGGG
12741975 TT
1 TT
12741977 AGTACACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (17 bp):
TTTTGTTTACAAGTGGG
Found at i:12744809 original size:21 final size:21
Alignment explanation
Indices: 12744783--12744823 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12744773 ATCTGCTCAA
* *
12744783 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
12744804 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
12744824 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:12748835 original size:13 final size:13
Alignment explanation
Indices: 12748819--12748843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12748809 CTTTGCATAT
12748819 TGTCTTCAACAGG
1 TGTCTTCAACAGG
12748832 TGTCTTCAACAG
1 TGTCTTCAACAG
12748844 CTCGCACTTT
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:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:12755518 original size:16 final size:17
Alignment explanation
Indices: 12755497--12755532 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
12755487 ACAAGTAAGA
12755497 TTTAAATATT-TCATTT
1 TTTAAATATTATCATTT
12755513 TTTAAATATTATCATTT
1 TTTAAATATTATCATTT
12755530 TTT
1 TTT
12755533 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAATATTATCATTT
Found at i:12757696 original size:16 final size:17
Alignment explanation
Indices: 12757662--12757699 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12757652 TTTTTTATTT
12757662 AAATTTTAAATAAATTA
1 AAATTTTAAATAAATTA
* *
12757679 AAATTTTAAATTAATAA
1 AAATTTTAAATAAATTA
12757696 AAAT
1 AAAT
12757700 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTTTAAATAAATTA
Found at i:12758755 original size:15 final size:15
Alignment explanation
Indices: 12758735--12758765 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12758725 AAAAAAATAA
12758735 TAATAATTAAATCTT
1 TAATAATTAAATCTT
12758750 TAATAATTAAATCTT
1 TAATAATTAAATCTT
12758765 T
1 T
12758766 TCAAACTTTT
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATAATTAAATCTT
Found at i:12764519 original size:46 final size:49
Alignment explanation
Indices: 12764412--12764533 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 49
12764402 TGTCTTCGAC
** * *
12764412 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCCTATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCCTATATATA-CTAAT
* * *
12764462 AAGGGCTTACATGGCTCATTCCTGTCTCCAAAG-CC-ATATATA-TGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCCTATATATACTAAT
*
12764508 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
12764534 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 26 0.42
48 7 0.11
49 2 0.03
50 27 0.44
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (49 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCCTATATATACTAAT
Found at i:12772098 original size:12 final size:13
Alignment explanation
Indices: 12772083--12772116 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12772073 TAATTGACGG
12772083 TTTAATTAATTT-
1 TTTAATTAATTTA
*
12772095 TTTAAATAATTTA
1 TTTAATTAATTTA
12772108 TTTAATTAA
1 TTTAATTAA
12772117 AATTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAATTAATTTA
Found at i:12781282 original size:27 final size:27
Alignment explanation
Indices: 12781231--12781283 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12781221 TTCTTGAATA
*
12781231 ATTTTAGGTTTATATTTTATCATATTC
1 ATTTTAGGTTTATATTTTATAATATTC
12781258 ATTTCTAGGTTT-TA-TTTATTAATATT
1 ATTT-TAGGTTTATATTTTA-TAATATT
12781284 TCGATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
27 12 0.52
28 7 0.30
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (27 bp):
ATTTTAGGTTTATATTTTATAATATTC
Found at i:12782775 original size:3 final size:3
Alignment explanation
Indices: 12782767--12782791 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12782757 AAGTCAGGGT
12782767 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
12782792 AGTAAGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12792991 original size:21 final size:21
Alignment explanation
Indices: 12792965--12793004 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12792955 TCTGCTCAAG
* *
12792965 CTCCACCTGTTTTGGAGTACA
1 CTCCACCTGCTGTGGAGTACA
12792986 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
12793005 TTGCTCGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTACA
Found at i:12804328 original size:23 final size:24
Alignment explanation
Indices: 12804298--12804346 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
12804288 CCATAAATAA
12804298 TTTTAAAA-AATTGTTTAATATTT
1 TTTTAAAATAATTGTTTAATATTT
* *
12804321 TTTTAAAATTTATTTTTTAATATTT
1 TTTTAAAA-TAATTGTTTAATATTT
12804346 T
1 T
12804347 ACTATATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
25 14 0.64
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAAAATAATTGTTTAATATTT
Found at i:12804798 original size:25 final size:25
Alignment explanation
Indices: 12804769--12804826 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
12804759 AAAATAAATT
*
12804769 TAAAAATTTAAAATATATAATAA-TA
1 TAAAAATTCAAAATATATAA-AACTA
*
12804794 TAAAAAATCAAAATATATAAAACTA
1 TAAAAATTCAAAATATATAAAACTA
*
12804819 GAAAAATT
1 TAAAAATT
12804827 GTTCAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (25 bp):
TAAAAATTCAAAATATATAAAACTA
Found at i:12806989 original size:18 final size:19
Alignment explanation
Indices: 12806962--12806997 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
12806952 GTACCTAAAT
12806962 AGTAATCAGTAACGGTAGC
1 AGTAATCAGTAACGGTAGC
12806981 AGTAA-CAGTAACGGTAG
1 AGTAATCAGTAACGGTAG
12806998 TGCTGAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.19
Consensus pattern (19 bp):
AGTAATCAGTAACGGTAGC
Found at i:12807333 original size:40 final size:40
Alignment explanation
Indices: 12807273--12807359 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
12807263 AATTCATTAC
* * * *
12807273 TTCAGTAATTTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAATAACTTCACAATTCAATGCAGTACACAAAACAATA
* *
12807313 TTCAATAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAATAACTTCACAATTCAATGCAGTACACAAAACAATA
12807353 TTCAATA
1 TTCAATA
12807360 TTCCATAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.31
Consensus pattern (40 bp):
TTCAATAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:12808025 original size:25 final size:23
Alignment explanation
Indices: 12807981--12808064 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
12807971 ATTTTGATTT
*
12807981 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
12808005 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
* * *
12808029 ATATAAATTATAT-TTA-AATATA
1 AT-TTAATTATATAATATCATATA
12808051 A-TTAATTATATAAT
1 ATTTAATTATATAAT
12808065 TAAAACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
20 9 0.18
21 1 0.02
22 6 0.12
24 19 0.39
25 14 0.29
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:12808044 original size:35 final size:35
Alignment explanation
Indices: 12807989--12808068 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
12807979 TTATTTAATA
* * *
12807989 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATAATAAATT
*
12808023 CATATAATATAAATTAT-ATTTAAATATAATTAATT
1 -ATATAATATAAATTATAATTTAAATATAATAAATT
12808058 ATATAAT-TAAA
1 ATATAATATAAA
12808069 ACAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 24 0.60
36 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATAATAAATT
Found at i:12808062 original size:22 final size:22
Alignment explanation
Indices: 12808024--12808068 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12808014 TCATAAATTC
*
12808024 ATATAATATAAATTATATTTAA
1 ATATAATATAAATTATAATTAA
*
12808046 ATATAAT-TAATTATATAATTAA
1 ATATAATATAAAT-TATAATTAA
12808068 A
1 A
12808069 ACAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAATATAAATTATAATTAA
Found at i:12820417 original size:22 final size:21
Alignment explanation
Indices: 12820392--12820441 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
12820382 TGAAAATTAC
*
12820392 TACATAATTGCTAAAACTTATA
1 TACAAAATT-CTAAAACTTATA
* *
12820414 TACAAAATTTTAAAATTTATA
1 TACAAAATTCTAAAACTTATA
*
12820435 TAAAAAA
1 TACAAAA
12820442 ACATAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (21 bp):
TACAAAATTCTAAAACTTATA
Found at i:12820621 original size:16 final size:15
Alignment explanation
Indices: 12820592--12820631 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
12820582 GTTTGATTGT
12820592 ATAATT-TTTTTATA
1 ATAATTATTTTTATA
12820606 ATAATTATTCTTTATA
1 ATAATTATT-TTTATA
12820622 ATAATATATT
1 ATAAT-TATT
12820632 ATTCTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 11 0.48
17 4 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATTATTTTTATA
Found at i:12834852 original size:6 final size:6
Alignment explanation
Indices: 12834832--12834880 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
12834822 CTGTCGCTTC
* * *
12834832 CACTGT CACTG- --CTGT CACTGT CACTAT CACTAT CACTGC CACTGT
1 CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT
12834877 CACT
1 CACT
12834881 AGCACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
6 33 0.92
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (6 bp):
CACTGT
Found at i:12834869 original size:18 final size:18
Alignment explanation
Indices: 12834846--12834886 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12834836 GTCACTGCTG
*
12834846 TCACTGTCACTATCACTA
1 TCACTGCCACTATCACTA
*
12834864 TCACTGCCACTGTCACTA
1 TCACTGCCACTATCACTA
*
12834882 GCACT
1 TCACT
12834887 ATTTGCTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTATCACTA
Found at i:12835272 original size:43 final size:43
Alignment explanation
Indices: 12835211--12835302 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
12835201 CAAGAAACTA
*
12835211 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGCAGAGG
1 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
12835254 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
1 AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
*
12835297 CACCAA
1 AACCAA
12835303 CCAACTTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (43 bp):
AACCAAGAATGAGGTTCCCAGGGTTCTTAACACTTAGAAGAGG
Found at i:12842159 original size:21 final size:23
Alignment explanation
Indices: 12842117--12842161 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
12842107 AAATTGTTAT
*
12842117 AAAAATAAAAAAATAAATTTAAA
1 AAAAATAAAAAAATAAACTTAAA
*
12842140 AAAAAT-ACAAAA-AAACTTAAA
1 AAAAATAAAAAAATAAACTTAAA
12842161 A
1 A
12842162 TTTAAATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAATAAAAAAATAAACTTAAA
Found at i:12842253 original size:19 final size:19
Alignment explanation
Indices: 12842231--12842278 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
12842221 ATTTTAAAAC
12842231 TTTTTAAATA-TTTTTACAA
1 TTTTTAAATAGTTTTTAC-A
*
12842250 TTTTT-TATAGTTTTTACA
1 TTTTTAAATAGTTTTTACA
12842268 TTTTTATAATA
1 TTTTTA-AATA
12842279 ATATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 9 0.38
19 12 0.50
20 3 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTAAATAGTTTTTACA
Found at i:12842342 original size:17 final size:17
Alignment explanation
Indices: 12842320--12842354 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12842310 TATCGTATTT
*
12842320 TTTTTTTGTAAATTTTA
1 TTTTTTTCTAAATTTTA
12842337 TTTTTTTCTAAATTTTA
1 TTTTTTTCTAAATTTTA
12842354 T
1 T
12842355 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTTCTAAATTTTA
Found at i:12848606 original size:46 final size:46
Alignment explanation
Indices: 12848542--12848894 Score: 400
Period size: 46 Copynumber: 7.3 Consensus size: 46
12848532 TGACAAGTGG
* * *
12848542 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* *
12848588 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* * *
12848634 AAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* *
12848686 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* *
12848732 AAGTGGAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCAAGTGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
*
12848784 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* *
12848830 AAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
*
12848882 AGAGTGATAAGTG
1 AAAGTGATAAGTG
12848895 GCTACACTTA
Statistics
Matches: 263, Mismatches: 26, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
46 137 0.52
52 126 0.48
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
Found at i:12848612 original size:52 final size:52
Alignment explanation
Indices: 12848580--12848894 Score: 343
Period size: 52 Copynumber: 6.2 Consensus size: 52
12848570 CTTATCTGAT
* ** **
12848580 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-TAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
12848633 CAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
**
12848685 CAAAGTGATAAGTG----G---TAGCTTTAGCTACACTTATCTGATCAAGTGA
1 C-AAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
12848731 CAAGTGGA-AAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCAAGTGA
1 CAAGT-GATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
12848783 C-----A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
* * ** *
12848829 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
12848881 CAGAGTGATAAGTG
1 CA-AGTGATAAGTG
12848895 GCTACACTTA
Statistics
Matches: 228, Mismatches: 18, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
45 9 0.04
46 74 0.32
49 2 0.01
51 1 0.00
52 114 0.50
53 28 0.12
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (52 bp):
CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:12848647 original size:98 final size:98
Alignment explanation
Indices: 12848517--12848895 Score: 650
Period size: 98 Copynumber: 3.9 Consensus size: 98
12848507 GGATTTGAAT
* *
12848517 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCA
12848582 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
66 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
*
12848615 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCA
12848680 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
66 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
*
12848713 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCA
* **
12848778 AGTGACAAAGTGATAAGTGATAGCTTCGGCTAC
66 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
* * *
12848811 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCA
* *
12848876 AGAGACAGAGTGATAAGTGG
66 AGTGACAAAGTGATAAGTGG
12848896 CTACACTTAT
Statistics
Matches: 268, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 268 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (98 bp):
ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCAGCTATACTTATCTGATCA
AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
Found at i:12848901 original size:37 final size:37
Alignment explanation
Indices: 12848858--12849077 Score: 372
Period size: 37 Copynumber: 6.0 Consensus size: 37
12848848 GATAGCTTTA
* *
12848858 GCTACACTTATCTGATCAAGAGACAGAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12848895 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12848932 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12848969 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12849006 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
12849043 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12849078 ATCATACGTA
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.06
36 4 0.02
37 160 0.91
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:12850408 original size:58 final size:59
Alignment explanation
Indices: 12850331--12850449 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
12850321 CATGTGAACA
12850331 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
12850390 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
12850448 TG
1 TG
12850450 ATTTCGTGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 55 0.92
59 5 0.08
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (59 bp):
TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:12850440 original size:28 final size:28
Alignment explanation
Indices: 12850350--12850440 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
12850340 GTGATTCCGT
12850350 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
12850378 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
12850407 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
12850436 GTAAG
1 GTAAG
12850441 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:12850463 original size:49 final size:49
Alignment explanation
Indices: 12850391--12850533 Score: 223
Period size: 49 Copynumber: 2.9 Consensus size: 49
12850381 AGTGATATGT
* *
12850391 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* * *
12850440 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGTATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
12850489 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
12850534 AGAAAACGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 86 1.00
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:12853746 original size:46 final size:46
Alignment explanation
Indices: 12853682--12854034 Score: 400
Period size: 46 Copynumber: 7.3 Consensus size: 46
12853672 TGACAAGTGG
* *
12853682 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* **
12853728 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* *
12853774 AAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* **
12853826 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* *
12853872 AAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
12853924 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
** *
12853970 AAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
*
12854022 AGAGTGATAAGTG
1 AAAGTGATAAGTG
12854035 GCTACACTTA
Statistics
Matches: 263, Mismatches: 26, Indels: 36
0.81 0.08 0.11
Matches are distributed among these distances:
46 138 0.52
52 125 0.48
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
Found at i:12853752 original size:52 final size:52
Alignment explanation
Indices: 12853720--12854034 Score: 352
Period size: 52 Copynumber: 6.2 Consensus size: 52
12853710 CTTATCTGAT
* ** **
12853720 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-TAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
12853773 CAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
**
12853825 CAAAGTGATAAGTG----G---TAGCTTTAGCTACACTTATCTGATCAAGTGA
1 C-AAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
12853871 CAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 CAAGT-GATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
12853923 C-----A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
* * ** *
12853969 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
12854021 CAGAGTGATAAGTG
1 CA-AGTGATAAGTG
12854035 GCTACACTTA
Statistics
Matches: 228, Mismatches: 18, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
45 9 0.04
46 75 0.33
49 2 0.01
51 1 0.00
52 113 0.50
53 28 0.12
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (52 bp):
CAAGTGATAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:12853787 original size:98 final size:98
Alignment explanation
Indices: 12853657--12854035 Score: 659
Period size: 98 Copynumber: 3.9 Consensus size: 98
12853647 GGATTTGAAT
*
12853657 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
12853722 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
66 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
12853755 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
12853820 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
66 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
*
12853853 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
* **
12853918 AGTGACAAAGTGATAAGTGATAGCTTCGGCTAC
66 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
* ** *
12853951 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
* *
12854016 AGAGACAGAGTGATAAGTGG
66 AGTGACAAAGTGATAAGTGG
12854036 CTACACTTAT
Statistics
Matches: 268, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 268 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (98 bp):
ACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCA
AGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
Found at i:12854041 original size:37 final size:37
Alignment explanation
Indices: 12853998--12854217 Score: 372
Period size: 37 Copynumber: 6.0 Consensus size: 37
12853988 GATAGCTTTA
* *
12853998 GCTACACTTATCTGATCAAGAGACAGAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12854035 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12854072 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12854109 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12854146 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
12854183 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12854218 ATCATACGTA
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.06
36 4 0.02
37 160 0.91
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:12858296 original size:22 final size:22
Alignment explanation
Indices: 12858277--12858319 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12858267 AATGTTTTAT
* *
12858277 TGTTTTTTTGTTACCATTTTGA
1 TGTTGTTTTGCTACCATTTTGA
*
12858299 TGTTGTTTTGCTATCATTTTG
1 TGTTGTTTTGCTACCATTTTG
12858320 TTACTATATT
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:0.12, C:0.09, G:0.16, T:0.63
Consensus pattern (22 bp):
TGTTGTTTTGCTACCATTTTGA
Found at i:12863010 original size:21 final size:21
Alignment explanation
Indices: 12862984--12863036 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12862974 CAGCGGTGGT
*
12862984 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGGTACTGTAGC
*
12863005 GGTGAGATTGGGTACTGTAGC
1 GGTGAGATTAGGTACTGTAGC
*
12863026 AGTGAGATTAG
1 GGTGAGATTAG
12863037 AAACAGCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.38, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGGTACTGTAGC
Found at i:12863172 original size:19 final size:18
Alignment explanation
Indices: 12863148--12863203 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
12863138 TAGAAATTTT
12863148 TAAAATTATTTAACAATTA
1 TAAAATTA-TTAACAATTA
*
12863167 TAAAATTAATAA-ATGATTA
1 TAAAATTATTAACA--ATTA
12863186 -AAAATTATT-ACAATTA
1 TAAAATTATTAACAATTA
12863202 TA
1 TA
12863204 TTTATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 4 0.13
17 3 0.10
18 12 0.39
19 12 0.39
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAATTATTAACAATTA
Found at i:12864188 original size:11 final size:12
Alignment explanation
Indices: 12864158--12864190 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12864148 TTCAGCTTGG
12864158 ATGCTGGTTTGC
1 ATGCTGGTTTGC
*
12864170 ACGCTGGTTTGC
1 ATGCTGGTTTGC
12864182 -TGCTGGTTT
1 ATGCTGGTTT
12864191 CCTATTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.42
Consensus pattern (12 bp):
ATGCTGGTTTGC
Found at i:12870700 original size:120 final size:120
Alignment explanation
Indices: 12870562--12871435 Score: 1475
Period size: 120 Copynumber: 7.3 Consensus size: 120
12870552 TAGAAAAAAT
* * * * *
12870562 ATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTCA
* *
12870627 GTAAATTCATATAAGAATATTGAA-TATTAAGAATTTTATTAAATCATATATTTTA
66 GTAAATTAATATAAGAATATT-AATTATTAAGAATTTTATTAAATTATATATTTTA
* * *
12870682 ATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTT
1 ATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTACAGTATCATATATTATGATTTC
* * * *
12870746 AGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATCTTA
65 AGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
* * *
12870802 ATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTT
1 ATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTACAGTATCATATATTATGATTTC
* *
12870866 AGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTA
65 AGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
*
12870922 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTCA
*
12870987 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
*
12871042 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTCA
12871107 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
*
12871162 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTCA
12871227 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
*
12871282 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTCA
12871347 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
12871402 ATTAAAATATATTTAATAATAATTATGTTTAAAT
1 ATTAAAATATATTTAATAATAATTATG-TTAAAT
12871436 ATGATTAAAT
Statistics
Matches: 734, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
119 3 0.00
120 724 0.99
121 7 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTCA
GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
Found at i:12870927 original size:18 final size:17
Alignment explanation
Indices: 12870899--12870933 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12870889 ATTATTAAGA
*
12870899 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12870916 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12870934 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12871167 original size:18 final size:17
Alignment explanation
Indices: 12871139--12871173 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12871129 ATTATTAAGA
*
12871139 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12871156 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12871174 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12871287 original size:18 final size:17
Alignment explanation
Indices: 12871259--12871293 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12871249 ATTATTAAGA
*
12871259 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12871276 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12871294 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12871407 original size:18 final size:17
Alignment explanation
Indices: 12871379--12871413 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12871369 ATTATTAAGA
*
12871379 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12871396 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12871414 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12871627 original size:44 final size:45
Alignment explanation
Indices: 12871578--12871668 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
12871568 ACCTCTATTC
* * *
12871578 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
12871622 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
12871667 CA
1 CA
12871669 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:12871670 original size:16 final size:16
Alignment explanation
Indices: 12871649--12871717 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
12871639 GATTAGCTAT
12871649 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12871665 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
12871682 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
12871698 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
12871714 TACA
1 TACA
12871718 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12871691 original size:33 final size:32
Alignment explanation
Indices: 12871649--12871717 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
12871639 GATTAGCTAT
12871649 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
12871682 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
12871714 TACA
1 TACA
12871718 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:12877277 original size:2 final size:2
Alignment explanation
Indices: 12877270--12877294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12877260 GTGTTTTCAA
12877270 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
12877295 TCTCATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12878598 original size:298 final size:298
Alignment explanation
Indices: 12878062--12878661 Score: 1200
Period size: 298 Copynumber: 2.0 Consensus size: 298
12878052 TGTGATAAAA
12878062 GACAAATCCTTCTTGACTCAAATGTGTAGTATGGGCAAAAAACTCTAATGCTTCAATGGTGGCAT
1 GACAAATCCTTCTTGACTCAAATGTGTAGTATGGGCAAAAAACTCTAATGCTTCAATGGTGGCAT
12878127 GCATAAAGCATGCAAAGTTGATAGAGCCAACTTACACAATCTCCCGCAAAATGAGAATGTGATGA
66 GCATAAAGCATGCAAAGTTGATAGAGCCAACTTACACAATCTCCCGCAAAATGAGAATGTGATGA
12878192 TGGTTCATACACCTTAAAAAAGGAAACAAATATTTCATAAAGAAAAACTCCATTCATAGCATTTG
131 TGGTTCATACACCTTAAAAAAGGAAACAAATATTTCATAAAGAAAAACTCCATTCATAGCATTTG
12878257 CATCCTATTGTTAATAGTTATCCAATTTCCTCAAAAGTATTATTCATTCCTAAAGAATGAACATT
196 CATCCTATTGTTAATAGTTATCCAATTTCCTCAAAAGTATTATTCATTCCTAAAGAATGAACATT
12878322 ATCTTCAAGAGACCATTTCAATTACAGCTTCTTGCTTG
261 ATCTTCAAGAGACCATTTCAATTACAGCTTCTTGCTTG
12878360 GACAAATCCTTCTTGACTCAAATGTGTAGTATGGGCAAAAAACTCTAATGCTTCAATGGTGGCAT
1 GACAAATCCTTCTTGACTCAAATGTGTAGTATGGGCAAAAAACTCTAATGCTTCAATGGTGGCAT
12878425 GCATAAAGCATGCAAAGTTGATAGAGCCAACTTACACAATCTCCCGCAAAATGAGAATGTGATGA
66 GCATAAAGCATGCAAAGTTGATAGAGCCAACTTACACAATCTCCCGCAAAATGAGAATGTGATGA
12878490 TGGTTCATACACCTTAAAAAAGGAAACAAATATTTCATAAAGAAAAACTCCATTCATAGCATTTG
131 TGGTTCATACACCTTAAAAAAGGAAACAAATATTTCATAAAGAAAAACTCCATTCATAGCATTTG
12878555 CATCCTATTGTTAATAGTTATCCAATTTCCTCAAAAGTATTATTCATTCCTAAAGAATGAACATT
196 CATCCTATTGTTAATAGTTATCCAATTTCCTCAAAAGTATTATTCATTCCTAAAGAATGAACATT
12878620 ATCTTCAAGAGACCATTTCAATTACAGCTTCTTGCTTG
261 ATCTTCAAGAGACCATTTCAATTACAGCTTCTTGCTTG
12878658 GACA
1 GACA
12878662 TGACATCGCA
Statistics
Matches: 302, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
298 302 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (298 bp):
GACAAATCCTTCTTGACTCAAATGTGTAGTATGGGCAAAAAACTCTAATGCTTCAATGGTGGCAT
GCATAAAGCATGCAAAGTTGATAGAGCCAACTTACACAATCTCCCGCAAAATGAGAATGTGATGA
TGGTTCATACACCTTAAAAAAGGAAACAAATATTTCATAAAGAAAAACTCCATTCATAGCATTTG
CATCCTATTGTTAATAGTTATCCAATTTCCTCAAAAGTATTATTCATTCCTAAAGAATGAACATT
ATCTTCAAGAGACCATTTCAATTACAGCTTCTTGCTTG
Found at i:12879566 original size:9 final size:9
Alignment explanation
Indices: 12879545--12879596 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
12879535 GAATTTAAAA
*
12879545 AAAAAAAAG
1 AAAAGAAAG
*
12879554 AAAAGAAAT
1 AAAAGAAAG
* *
12879563 AAAAGGAGG
1 AAAAGAAAG
12879572 AAAAGAAAG
1 AAAAGAAAG
*
12879581 AAGAGAAA-
1 AAAAGAAAG
12879589 AAAAGAAA
1 AAAAGAAA
12879597 AGAATGTAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:12879600 original size:13 final size:13
Alignment explanation
Indices: 12879541--12879600 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
12879531 AAAGGAATTT
*
12879541 AAAAAAAAAAAAG
1 AAAAGAAAAAAAG
12879554 AAAAGAAATAAAAG
1 AAAAGAAA-AAAAG
* *
12879568 -GAGGAAAAGAAAG
1 AAAAGAAAA-AAAG
*
12879581 AAGAGAAAAAAAG
1 AAAAGAAAAAAAG
12879594 AAAAGAA
1 AAAAGAA
12879601 TGTAGAGGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
12 1 0.03
13 26 0.70
14 10 0.27
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:12884145 original size:4 final size:4
Alignment explanation
Indices: 12884136--12884164 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
12884126 GTTCATTTCC
12884136 CTCA CTCA CTCA CTCA CTCA CTCA CTCA C
1 CTCA CTCA CTCA CTCA CTCA CTCA CTCA C
12884165 ACGCACACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (4 bp):
CTCA
Found at i:12889303 original size:23 final size:24
Alignment explanation
Indices: 12889261--12889332 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
12889251 AAAGGGGTCT
12889261 AAATTAAAAAAAATTCATTTCAAG
1 AAATTAAAAAAAATTCATTTCAAG
12889285 AAATTAAAAAAAATT-ATTTCAAG
1 AAATTAAAAAAAATTCATTTCAAG
** *
12889308 AAATTAAAAAATTTTCATTTTAAG
1 AAATTAAAAAAAATTCATTTCAAG
12889332 A
1 A
12889333 GAGACCGAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 21 0.48
24 23 0.52
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTAAAAAAAATTCATTTCAAG
Found at i:12889518 original size:14 final size:15
Alignment explanation
Indices: 12889489--12889518 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12889479 TTTACACTTC
12889489 AAAATATATATATCT
1 AAAATATATATATCT
12889504 AAAATATAT-TATCT
1 AAAATATATATATCT
12889518 A
1 A
12889519 TAACTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATATATATCT
Found at i:12893350 original size:16 final size:16
Alignment explanation
Indices: 12893319--12893352 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12893309 GCGAATTCAT
* *
12893319 ATTTAAATTTATTTTA
1 ATTTAAATTAAATTTA
12893335 ATTTAAATTAAATTTA
1 ATTTAAATTAAATTTA
12893351 AT
1 AT
12893353 CTATACTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATTAAATTTA
Found at i:12900778 original size:18 final size:18
Alignment explanation
Indices: 12900755--12900847 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
12900745 CCCAACTACT
*
12900755 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
12900773 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
12900791 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
*
12900809 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
12900827 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
12900845 GTA
1 GTA
12900848 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:12900812 original size:36 final size:36
Alignment explanation
Indices: 12900755--12900847 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
12900745 CCCAACTACT
*
12900755 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
12900791 GTATACGTGAATAGTATCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
12900827 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
12900848 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:12905444 original size:16 final size:17
Alignment explanation
Indices: 12905418--12905459 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
12905408 TAAGGTTGGG
12905418 TTAGAGTTTTATGGATT
1 TTAGAGTTTTATGGATT
*
12905435 TTAG-GTTTTATGGGTT
1 TTAGAGTTTTATGGATT
12905451 TT-GAGTTTT
1 TTAGAGTTTT
12905460 TTATTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 18 0.78
17 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (17 bp):
TTAGAGTTTTATGGATT
Found at i:12910392 original size:26 final size:25
Alignment explanation
Indices: 12910363--12910423 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
12910353 TATTATTTTT
12910363 ATATAAAAATAAATTTTAAAAATA-TA
1 ATATAAAAATAAA--TTAAAAATATTA
* *
12910389 ATATATCAAATACATTAAAAATATTA
1 ATATA-AAAATAAATTAAAAATATTA
*
12910415 AAATAAAAA
1 ATATAAAAA
12910424 AATTTCAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 12 0.41
26 11 0.38
27 6 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (25 bp):
ATATAAAAATAAATTAAAAATATTA
Found at i:12925744 original size:78 final size:78
Alignment explanation
Indices: 12925657--12925815 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
12925647 ATGCATACTA
12925657 TATACTAAATATTGATTAAATTAGTATTATTCGTTGATCACTTCGCAACTTAATTAAGAAATTAT
1 TATACTAAATATTGATTAAATTAGTATTATTCGTTGATCACTTCGCAACTTAATTAAGAAATTAT
12925722 TAAAATATTTAAT
66 TAAAATATTTAAT
12925735 TATACTAAATATTGATTAAATTAGTATTATTCGTTGATCACTTCGCAACTTAATTAAGAAATTAT
1 TATACTAAATATTGATTAAATTAGTATTATTCGTTGATCACTTCGCAACTTAATTAAGAAATTAT
12925800 TAAAATATTTAAT
66 TAAAATATTTAAT
12925813 TAT
1 TAT
12925816 TGTATAAATT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43
Consensus pattern (78 bp):
TATACTAAATATTGATTAAATTAGTATTATTCGTTGATCACTTCGCAACTTAATTAAGAAATTAT
TAAAATATTTAAT
Found at i:12926736 original size:18 final size:18
Alignment explanation
Indices: 12926701--12926739 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12926691 GAAGGTTGTT
*
12926701 TTTAATATTTTTTAATAA
1 TTTAAAATTTTTTAATAA
12926719 TTTAAAATTATTTT-ATAA
1 TTTAAAATT-TTTTAATAA
12926737 TTT
1 TTT
12926740 TTAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAAATTTTTTAATAA
Found at i:12926746 original size:10 final size:10
Alignment explanation
Indices: 12926699--12926749 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
12926689 TTGAAGGTTG
*
12926699 TTTTTAATAT
1 TTTTTAATAA
12926709 TTTTTAATAA
1 TTTTTAATAA
12926719 --TTTAA-AA
1 TTTTTAATAA
*
12926726 TTATTTTATAA
1 TT-TTTAATAA
12926737 TTTTTAATAA
1 TTTTTAATAA
12926747 TTT
1 TTT
12926750 ACTACTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
7 2 0.06
8 5 0.15
10 23 0.68
11 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:12926749 original size:18 final size:19
Alignment explanation
Indices: 12926700--12926749 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
12926690 TGAAGGTTGT
*
12926700 TTTTAATATTTTTTAATAA
1 TTTTAATAATTTTTAATAA
*
12926719 -TTTAA-AATTATTTTATAA
1 TTTTAATAATT-TTTAATAA
12926737 TTTTTAATAATTT
1 -TTTTAATAATTT
12926750 ACTACTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 3 0.12
18 12 0.48
20 6 0.24
21 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAATAATTTTTAATAA
Found at i:12927760 original size:18 final size:18
Alignment explanation
Indices: 12927737--12927776 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12927727 GAAATATTTA
*
12927737 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
12927755 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
12927773 TTTT
1 TTTT
12927777 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:12931780 original size:19 final size:19
Alignment explanation
Indices: 12931756--12931799 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
12931746 GTTTGCTCTG
*
12931756 CCTTTTCTTCCTTTCTTTT
1 CCTTTTCTACCTTTCTTTT
*
12931775 CCTTTTGTACCTTTCTTTT
1 CCTTTTCTACCTTTCTTTT
12931794 CCTTTT
1 CCTTTT
12931800 GTATTCTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (19 bp):
CCTTTTCTACCTTTCTTTT
Found at i:12931800 original size:19 final size:19
Alignment explanation
Indices: 12931765--12931802 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12931755 GCCTTTTCTT
12931765 CCTTTCTTTTCCTTTTGTA
1 CCTTTCTTTTCCTTTTGTA
12931784 CCTTTCTTTTCCTTTTGTA
1 CCTTTCTTTTCCTTTTGTA
12931803 TTCTATCTAG
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:0.05, C:0.26, G:0.05, T:0.63
Consensus pattern (19 bp):
CCTTTCTTTTCCTTTTGTA
Found at i:12964306 original size:30 final size:29
Alignment explanation
Indices: 12964266--12964335 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
12964256 GTTAATAATT
* *
12964266 TATAAGAATTAGATCAAA-TCAAAATTTCGTA
1 TATAA-AATTAGA-AAAATTCAAAA-TTCATA
*
12964297 TATAAAATTATAAAAATTCAAAATTCATA
1 TATAAAATTAGAAAAATTCAAAATTCATA
12964326 TATAAAATTA
1 TATAAAATTA
12964336 CTATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.51
30 12 0.34
31 5 0.14
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Consensus pattern (29 bp):
TATAAAATTAGAAAAATTCAAAATTCATA
Found at i:12972761 original size:31 final size:31
Alignment explanation
Indices: 12972720--12972780 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
12972710 ATTAATAATT
12972720 TTAAATTAAATATTATAATT-ATTTTTAAATA
1 TTAAATTAAATA-TATAATTGATTTTTAAATA
* * *
12972751 TTAATTTAAATATATATTTGTTTTTTAAAT
1 TTAAATTAAATATATAATTGATTTTTAAAT
12972781 CTCATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TTAAATTAAATATATAATTGATTTTTAAATA
Found at i:12975310 original size:6 final size:6
Alignment explanation
Indices: 12975299--12975323 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12975289 GGAACGGCGG
12975299 ACATGC ACATGC ACATGC ACATGC A
1 ACATGC ACATGC ACATGC ACATGC A
12975324 TTGTACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ACATGC
Found at i:12984737 original size:24 final size:24
Alignment explanation
Indices: 12984705--12984754 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
12984695 AAATGAAGCT
12984705 ATAACAACGTGGCTCATCCATTTC
1 ATAACAACGTGGCTCATCCATTTC
12984729 ATAACAACGTGGCTCATCCATTTC
1 ATAACAACGTGGCTCATCCATTTC
12984753 AT
1 AT
12984755 GACGACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (24 bp):
ATAACAACGTGGCTCATCCATTTC
Found at i:12985190 original size:8 final size:8
Alignment explanation
Indices: 12985171--12985208 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
12985161 GCATGGCATC
12985171 CAATCACTT
1 CAATC-CTT
12985180 CAATCCTT
1 CAATCCTT
12985188 CAATCCTT
1 CAATCCTT
12985196 CAATCCTT
1 CAATCCTT
12985204 CAATC
1 CAATC
12985209 ATATTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 24 0.83
9 5 0.17
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (8 bp):
CAATCCTT
Found at i:12994200 original size:58 final size:58
Alignment explanation
Indices: 12994110--12994223 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 58
12994100 TTTCAAGGTT
12994110 AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
1 AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
**
12994168 AGCCAGTTTCCGTCCATTGATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
1 AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
12994224 AATATCAGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (58 bp):
AGCCAGTTTCCGTCCATCAATAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
Found at i:13004001 original size:18 final size:18
Alignment explanation
Indices: 13003978--13004012 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13003968 TGTTAATATA
13003978 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCCTGATTG
*
13003996 GGAGTAAATCCTTGATT
1 GGAGTAAATCCCTGATT
13004013 AGGATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
GGAGTAAATCCCTGATTG
Found at i:13012766 original size:3 final size:3
Alignment explanation
Indices: 13012758--13012783 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13012748 GTACCCATTT
13012758 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
13012784 TGAGAGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:13013713 original size:23 final size:23
Alignment explanation
Indices: 13013670--13013714 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13013660 AATTAATTTA
*
13013670 TTTTTATATTATATAAGTGTAAT
1 TTTTTATATTATATAAATGTAAT
*
13013693 TTTTTGTA-TATATAATATGTAA
1 TTTTTATATTATATAA-ATGTAA
13013715 ACATAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTTTATATTATATAAATGTAAT
Found at i:13015606 original size:16 final size:16
Alignment explanation
Indices: 13015582--13015614 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13015572 TATAGATAAA
13015582 TTATATTTTAGTCACT
1 TTATATTTTAGTCACT
*
13015598 TTATGTTTTAGTCACT
1 TTATATTTTAGTCACT
13015614 T
1 T
13015615 ACATTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (16 bp):
TTATATTTTAGTCACT
Found at i:13016109 original size:23 final size:23
Alignment explanation
Indices: 13016083--13016127 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
13016073 GAAAGTAAGT
13016083 TTAAA-TAATGTAAAATAAAAAAA
1 TTAAATTAAT-TAAAATAAAAAAA
*
13016106 TTAAATTACTTAAAATAAAAAA
1 TTAAATTAATTAAAATAAAAAA
13016128 TATCTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
TTAAATTAATTAAAATAAAAAAA
Found at i:13021014 original size:32 final size:31
Alignment explanation
Indices: 13020978--13021046 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
13020968 ACAAAAATAC
* *
13020978 AATTTCACCACTTAAATAGTCTATATTTTTAT
1 AATTTCA-AACTTAAATAGTCTATATCTTTAT
* * *
13021010 AATTTTTAAAGTTTAATAGTCTATATCTTTAT
1 AA-TTTCAAACTTAAATAGTCTATATCTTTAT
13021042 AATTT
1 AATTT
13021047 TTAAAGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 3 0.10
32 24 0.77
33 4 0.13
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (31 bp):
AATTTCAAACTTAAATAGTCTATATCTTTAT
Found at i:13021047 original size:32 final size:32
Alignment explanation
Indices: 13020992--13021052 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
13020982 TCACCACTTA
*
13020992 AATAGTCTATATTTTTATAATTTTTAAAGTTT
1 AATAGTCTATATCTTTATAATTTTTAAAGTTT
13021024 AATAGTCTATATCTTTATAATTTTTAAAG
1 AATAGTCTATATCTTTATAATTTTTAAAG
13021053 AATTAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (32 bp):
AATAGTCTATATCTTTATAATTTTTAAAGTTT
Found at i:13027280 original size:3 final size:3
Alignment explanation
Indices: 13027267--13027295 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13027257 AAATAGACAC
13027267 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13027296 CAAGGGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13028003 original size:6 final size:6
Alignment explanation
Indices: 13027962--13028002 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
13027952 TATGTTCCAC
*
13027962 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAA CAACA
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACA
13028003 AGTTTTGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.34, G:0.12, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:13028823 original size:65 final size:65
Alignment explanation
Indices: 13028719--13028853 Score: 252
Period size: 65 Copynumber: 2.1 Consensus size: 65
13028709 TGTGGAACCC
*
13028719 TCTTCTCACGGTATCATAAATAGTTATCATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
1 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
*
13028784 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCTTGAACACAATTATGAACCAACAAA
1 TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
13028849 TCTTC
1 TCTTC
13028854 ATTTATTGAG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (65 bp):
TCTTCTCACGGTATCATAAATAGTTAACATTTTTCCCCCCATGAACACAATTATGAACCAACAAA
Found at i:13029005 original size:2 final size:2
Alignment explanation
Indices: 13028998--13029026 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13028988 TTCACACCCT
13028998 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13029027 TAGAATGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13035144 original size:18 final size:18
Alignment explanation
Indices: 13035121--13035159 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
13035111 CAATTAGTAT
13035121 TTTATAAAAAAATTGTAA
1 TTTATAAAAAAATTGTAA
* * *
13035139 TTTATATAAATATTTTAA
1 TTTATAAAAAAATTGTAA
13035157 TTT
1 TTT
13035160 CAGTAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTATAAAAAAATTGTAA
Found at i:13045165 original size:26 final size:26
Alignment explanation
Indices: 13045135--13045185 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
13045125 TTCAAAGAAT
*
13045135 TTTGATCTCTGTTGAAAAATAATTCA
1 TTTGATATCTGTTGAAAAATAATTCA
*
13045161 TTTGATATCTGTTGACAAATAATTC
1 TTTGATATCTGTTGAAAAATAATTC
13045186 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGAAAAATAATTCA
Found at i:13059277 original size:5 final size:5
Alignment explanation
Indices: 13059267--13059291 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13059257 TTCTCTGTTT
13059267 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
13059292 GCATTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:13060062 original size:21 final size:21
Alignment explanation
Indices: 13060038--13060077 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13060028 ATCTTTTTTA
*
13060038 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
13060059 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
13060078 CATTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:13080124 original size:17 final size:17
Alignment explanation
Indices: 13080072--13080134 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
13080062 TTAATAACAC
13080072 TTTATAATTTTATACAATT
1 TTTATAATTTTA-A-AATT
* *
13080091 TTTAT--TTTATTATATT
1 TTTATAATTT-TAAAATT
13080107 TTTATAATTTTAAAATT
1 TTTATAATTTTAAAATT
*
13080124 TTTAAAATTTT
1 TTTATAATTTT
13080135 TTTCTGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
16 8 0.22
17 19 0.53
18 4 0.11
19 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATAATTTTAAAATT
Found at i:13081783 original size:25 final size:25
Alignment explanation
Indices: 13081754--13081803 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
13081744 CAAATAAGAT
13081754 GATTTTCAGATTCTAAAAGAGAGAA
1 GATTTTCAGATTCTAAAAGAGAGAA
*
13081779 GATTTTCAGATTTTAAAAGAGAGAA
1 GATTTTCAGATTCTAAAAGAGAGAA
13081804 ATACTATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (25 bp):
GATTTTCAGATTCTAAAAGAGAGAA
Found at i:13089667 original size:50 final size:50
Alignment explanation
Indices: 13089608--13089709 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
13089598 TTTGCCAGCT
*
13089608 CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATCTATCCAGTC
* *
13089658 CAACATTAGCATCTGCAAAAACAATTAAAAATATCCACATCTATCCAGTC
1 CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATCTATCCAGTC
13089708 CA
1 CA
13089710 CCTTGTTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (50 bp):
CAACATTAGCATCTACAAAAACAATTAAAAAAATCCACATCTATCCAGTC
Found at i:13094250 original size:137 final size:138
Alignment explanation
Indices: 13094003--13094277 Score: 448
Period size: 137 Copynumber: 2.0 Consensus size: 138
13093993 ACAGCTAAAC
* *
13094003 AAATGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAACAC
1 AAATGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACAC
* *
13094068 TAGCTACAAAAGTAATGTAACAATATCATGTGGTAACAAGTTCACATGAAAGTG-AGATATGAAA
66 TAACTACAAAAGTAATGTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCA-ATATGAAA
*
13094132 GATATGCCA
130 GACATGCCA
* *
13094141 AAATGAAATCATTTATGGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAACAC
1 AAATGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACAC
13094205 TAACTACAAAAGTAACT-TAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
66 TAACTACAAAAGTAA-TGTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
13094269 GACATGCCA
130 GACATGCCA
13094278 TTTTCTGAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
137 86 0.67
138 42 0.33
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (138 bp):
AAATGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACAC
TAACTACAAAAGTAATGTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAAG
ACATGCCA
Found at i:13096782 original size:17 final size:18
Alignment explanation
Indices: 13096762--13096825 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
13096752 AATAATTATG
13096762 TAATTAAAATAAAATT-A
1 TAATTAAAATAAAATTAA
**
13096779 TAATTAACTTAAAATTAA
1 TAATTAAAATAAAATTAA
*
13096797 TAATAATAATAATAACATTAA
1 TAAT--TAA-AATAAAATTAA
13096818 TAATTAAA
1 TAATTAAA
13096826 CCTAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 14 0.37
18 6 0.16
19 3 0.08
20 3 0.08
21 12 0.32
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATTAAAATAAAATTAA
Found at i:13098776 original size:14 final size:15
Alignment explanation
Indices: 13098738--13098798 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
13098728 TTTAATTATT
* *
13098738 TAAAAATTATAAAATA
1 TAAAAATTACAATA-A
*
13098754 TAAATAATTAAAATAA
1 TAAA-AATTACAATAA
*
13098770 T-AAAATTACTATAA
1 TAAAAATTACAATAA
13098784 TAAAAATTACAATAA
1 TAAAAATTACAATAA
13098799 CGGTGCTACC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.26
15 14 0.37
16 6 0.16
17 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTACAATAA
Found at i:13098783 original size:23 final size:23
Alignment explanation
Indices: 13098738--13098790 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
13098728 TTTAATTATT
*
13098738 TAAAAATTATAAAATATAAATAA
1 TAAAAATAATAAAATATAAATAA
* *
13098761 TTAAAATAATAAAAT-TACTATAA
1 TAAAAATAATAAAATATA-AATAA
13098784 TAAAAAT
1 TAAAAAT
13098791 TACAATAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAAATAATAAAATATAAATAA
Found at i:13099612 original size:17 final size:17
Alignment explanation
Indices: 13099590--13099623 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13099580 ATCCACTAAT
*
13099590 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
13099607 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
13099624 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:13104251 original size:17 final size:17
Alignment explanation
Indices: 13104229--13104262 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13104219 ATCCACTAAT
*
13104229 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
13104246 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
13104263 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:13111066 original size:16 final size:15
Alignment explanation
Indices: 13111045--13111074 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13111035 AAAATGTGAA
13111045 AAACAAAAAGAAAAAC
1 AAACAAAAA-AAAAAC
13111061 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
13111075 GCTTACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (15 bp):
AAACAAAAAAAAAAC
Found at i:13117384 original size:15 final size:16
Alignment explanation
Indices: 13117354--13117384 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13117344 TTAAGAAGTT
13117354 AATTTAATTATTAATA
1 AATTTAATTATTAATA
13117370 AATTTAATT-TTAATA
1 AATTTAATTATTAATA
13117385 GCCAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAATTATTAATA
Found at i:13119285 original size:41 final size:41
Alignment explanation
Indices: 13119217--13119498 Score: 307
Period size: 41 Copynumber: 6.9 Consensus size: 41
13119207 GCGTTTGTCT
* * * * * *
13119217 AAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCA
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * *
13119258 AAAACACCACTAAAAACTGGTCAATAGCGGCGTTTTTGGCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* *
13119299 AAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCGCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * * *
13119340 -AAACGCCACTAAAAGCTGATCAATAGCGGCATTTTAATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * * *
13119380 CAAACGCCACTAAAAACTAATCAATTGCGGCGTTTTTATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * *** *
13119421 CAAACGCCACAAAAAACTGATCAATTTTGGCGTTTTTATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
*
13119462 AAAACGCCACTAAAAACT-AACTAATAGCGGCGTTTTT
1 AAAACGCCACTAAAAACTGATC-AATAGCGGCGTTTTT
13119499 GGTCCAAACG
Statistics
Matches: 209, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 36 0.17
41 173 0.83
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
Found at i:13119326 original size:82 final size:81
Alignment explanation
Indices: 13119217--13119510 Score: 338
Period size: 82 Copynumber: 3.6 Consensus size: 81
13119207 GCGTTTGTCT
* * * * *
13119217 AAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCAAAAACACCACTAAAAACTGGTCAA
1 AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGGC-CAAACGCCACTAAAAACTGATCAA
**
13119282 TAGCGGCGTTTTTGGCC
65 TAGCGGCGTTTTTATCC
*** * *
13119299 AAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAAT
1 AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAAT
* *
13119364 AGCGGCATTTTAATCC
66 AGCGGCGTTTTTATCC
* * * ** *
13119380 CAAACGCCACTAAAAACTAATCAATTGCGGCGTTTTTATCCCAAACGCCACAAAAAACTGATCAA
1 AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTT-GGCCAAACGCCACTAAAAACTGATCAA
***
13119445 TTTTGGCGTTTTTATCC
65 TAGCGGCGTTTTTATCC
13119462 AAAACGCCACTAAAAACT-AACTAATAGCGGCGTTTTTGGTCCAAACGCC
1 AAAACGCCACTAAAAACTAAAC-AATAGCGGCGTTTTTGG-CCAAACGCC
13119511 GCAAAAAGTT
Statistics
Matches: 177, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
81 68 0.38
82 109 0.62
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (81 bp):
AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAAT
AGCGGCGTTTTTATCC
Found at i:13119517 original size:122 final size:123
Alignment explanation
Indices: 13119217--13119510 Score: 337
Period size: 122 Copynumber: 2.4 Consensus size: 123
13119207 GCGTTTGTCT
* * **
13119217 AAAACGCCACTAAAAGCTAAACT-ATAGCGGCGTTTTTGG-CAAAAACACCACTAAAAACTGGTC
1 AAAACGCCACTAAAAGCT-AACTAATAGCGGCGTTTTTGGTC-CAAACGCCACTAAAAACTAATC
* * * *
13119280 AATAGCGGCGTTTTTGGCCAAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCGCC
64 AATAGCGGCGTTTTTAGCCAAAACGCCACAAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * **
13119340 -AAACGCCACTAAAAGCTGA-TCAATAGCGGC-ATTTTAATCCCAAACGCCACTAAAAACTAATC
1 AAAACGCCACTAAAAGCTAACT-AATAGCGGCGTTTTTGGT-CCAAACGCCACTAAAAACTAATC
* * * *** *
13119402 AATTGCGGCGTTTTTATCCCAAACGCCACAAAAAACTGATCAATTTTGGCGTTTTTATCC
64 AATAGCGGCGTTTTTAGCCAAAACGCCACAAAAAACTGATCAATAGCGGCGTTTTTAGCC
*
13119462 AAAACGCCACTAAAAACTAACTAATAGCGGCGTTTTTGGTCCAAACGCC
1 AAAACGCCACTAAAAGCTAACTAATAGCGGCGTTTTTGGTCCAAACGCC
13119511 GCAAAAAGTT
Statistics
Matches: 140, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
120 1 0.01
121 5 0.04
122 92 0.66
123 36 0.26
124 6 0.04
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (123 bp):
AAAACGCCACTAAAAGCTAACTAATAGCGGCGTTTTTGGTCCAAACGCCACTAAAAACTAATCAA
TAGCGGCGTTTTTAGCCAAAACGCCACAAAAAACTGATCAATAGCGGCGTTTTTAGCC
Found at i:13125506 original size:23 final size:23
Alignment explanation
Indices: 13125476--13125525 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
13125466 AACATTAATC
13125476 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
13125499 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
13125522 AAAT
1 AAAT
13125526 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:13126071 original size:241 final size:241
Alignment explanation
Indices: 13125648--13126082 Score: 789
Period size: 241 Copynumber: 1.8 Consensus size: 241
13125638 ATGAATTAAT
*
13125648 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACATT
*
13125713 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATTGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATCGAG
* *
13125778 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACATATGATGAATCTTAAAAAATTC
13125843 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
*
13125889 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACATT
* * *
13125954 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATCGAG
*
13126019 CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACGTATGATGAATCTTAAAAAATT
131 CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACATATGATGAATCTTAAAAAATT
13126083 ACTATATTCA
Statistics
Matches: 185, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
241 185 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACATT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACATATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:13126225 original size:9 final size:9
Alignment explanation
Indices: 13126202--13126338 Score: 130
Period size: 9 Copynumber: 14.6 Consensus size: 9
13126192 ATTGATCATT
*
13126202 ACTTAAATA
1 ACTTACATA
*
13126211 AATTACATA
1 ACTTACATA
13126220 ACTTACATA
1 ACTTACATA
* *
13126229 ACTCATATA
1 ACTTACATA
13126238 ACTTACATA
1 ACTTACATA
*
13126247 ATTTACATAACA
1 ACTTACAT---A
13126259 ACTTACATA
1 ACTTACATA
*
13126268 ACTCACATA
1 ACTTACATA
*
13126277 ACTCACATA
1 ACTTACATA
13126286 ACTTACATA
1 ACTTACATA
*
13126295 ATTTACATA
1 ACTTACATA
*
13126304 ACTCACATA
1 ACTTACATA
*
13126313 ACGTACATAACA
1 ACTTACAT---A
13126325 ACTTACATA
1 ACTTACATA
13126334 ACTTA
1 ACTTA
13126339 ACTAATACAT
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
9 89 0.85
12 16 0.15
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Done.