Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 129 of 325
Found at i:40295789 original size:5 final size:5
Alignment explanation
Indices: 40295788--40295831 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
40295778 CTTTTTTATT
40295788 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTTTAA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTT-A TTTTA TTT
40295832 CTTTTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.11
5 23 0.64
6 8 0.22
7 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:40295803 original size:10 final size:10
Alignment explanation
Indices: 40295788--40295831 Score: 63
Period size: 9 Copynumber: 4.3 Consensus size: 10
40295778 CTTTTTTATT
40295788 TTTTATTTTA
1 TTTTATTTTA
40295798 TTTTA-TTTA
1 TTTTATTTTA
40295807 TTTTATTTTA
1 TTTTATTTTA
40295817 TTTTTAATTTTA
1 -TTTT-ATTTTA
40295829 TTT
1 TTT
40295832 CTTTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.29
10 9 0.29
11 7 0.23
12 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:40295803 original size:26 final size:26
Alignment explanation
Indices: 40295782--40295836 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
40295772 GATTATCTTT
*
40295782 TTTATTTT-TTATTTTATTTTATTTAT
1 TTTATTTTATT-TTTAATTTTATTTAT
*
40295808 TTTATTTTATTTTTAATTTTATTTCT
1 TTTATTTTATTTTTAATTTTATTTAT
40295834 TTT
1 TTT
40295837 GAAAACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTATTTTATTTTTAATTTTATTTAT
Found at i:40305647 original size:25 final size:25
Alignment explanation
Indices: 40305613--40305660 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
40305603 TTGCATCAAA
40305613 GGTCATAATCCAGAAACCTGTAGAG
1 GGTCATAATCCAGAAACCTGTAGAG
*
40305638 GGTCATAATCCAGAAACTTGTAG
1 GGTCATAATCCAGAAACCTGTAG
40305661 CCTTTCCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (25 bp):
GGTCATAATCCAGAAACCTGTAGAG
Found at i:40312014 original size:133 final size:133
Alignment explanation
Indices: 40311704--40312246 Score: 448
Period size: 133 Copynumber: 4.1 Consensus size: 133
40311694 TGGAAAATTT
* * * * * * *
40311704 TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATTTCCCTGAAATTACAGTGAAGTAGGTTAAAA
1 TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAG
* * * ** * * * *
40311769 ATAAACAAATCTT-TCTCCCTGATGTTATAGTGGAGTAGATTGAAGATGGGTTACGAATCTTATC
66 CT--ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AG---CAAATCTTATC
* *
40311833 TCCCCGAAG
125 TCTCTGAAG
* * * * *
40311842 TTGCAATGGAGTAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAATGGAGTAGGTTGAAA
1 TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAATGGAGCAGATT-AAA
* * * * *
40311907 -TTACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTGAATATAGCAAATATTATCTCTCT
65 GCTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCTCT
40311971 GAAG
130 GAAG
* * * * * * * * ** * *
40311975 TTGCAGTAGAGCAGATTAATGCTATAAATCATATTTCCCTAAATTTGTAGA-GGAACAAATTAAA
1 TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACA-ATGGAGCAGATTAAA
* * * *
40312039 GCCACAAGTCTTATCTCCCTGAATTTGCAGTAGAGCAGACTGAAGATAGAAAATCTTATCTCTCT
65 GCTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCTCT
40312104 GAAG
130 GAAG
* ** * * * * *
40312108 TTGCACTAGAGCAGATTAAAGTTATAAACCTTATCTCCTTGAAGTTTCAGTAGAGCAGATTAAAG
1 TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAG
* * * * * *
40312173 CTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAG-TAACAAGTCCTATAC-CTCT
66 CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTAT-CTCTCT
40312236 GAAG
130 GAAG
40312240 TTGCAGT
1 TTGCAGT
40312247 GGGTTAGATT
Statistics
Matches: 327, Mismatches: 72, Indels: 18
0.78 0.17 0.04
Matches are distributed among these distances:
132 26 0.08
133 205 0.63
134 1 0.00
136 9 0.03
137 28 0.09
138 55 0.17
139 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (133 bp):
TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAG
CTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCTCTG
AAG
Found at i:40312097 original size:45 final size:44
Alignment explanation
Indices: 40311704--40312532 Score: 371
Period size: 44 Copynumber: 18.5 Consensus size: 44
40311694 TGGAAAATTT
** * * *
40311704 TTGCAGTAGAGCAGATTAAAGCCACAAACCTTATTTCCCTGAAA
1 TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * * *
40311748 TTACAGT-GAAGTAGGTTAAAAATAAACAAATCTT-TCTCCCTGATG
1 TTGCAGTAG-AGCAGATTAAAGAT--ACAAATCTTATCTCCCTGAAG
** * * * * *
40311793 TTATAGTGGAGTAGATTGAAGATGGGTTACGAATCTTATCTCCCCGAAG
1 TTGCAGTAGAGCAGATT-AA-A---GATACAAATCTTATCTCCCTGAAG
* * * ** *
40311842 TTGCAATGGAGTAGATTAAAGCCACAAACCTTATCTCCCTGAAG
1 TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * * * * *
40311886 TTACAATGGAGTAGGTTGAAA-TTACAAGTCTTATCTCCCTGAAG
1 TTGCAGTAGAGCAGATT-AAAGATACAAATCTTATCTCCCTGAAG
* * * * * * * *
40311930 TTGTAGTGGAGCAAACTGAATATAGCAAATATTATCTCTCTGAAG
1 TTGCAGTAGAGCAGATTAAAGATA-CAAATCTTATCTCCCTGAAG
* * * * * * *
40311975 TTGCAGTAGAGCAGATTAATGCTATAAATCATATTTCCCTAAAT
1 TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * ** * *
40312019 TTGTAG-AGGAACAAATTAAAGCCACAAGTCTTATCTCCCTGAAT
1 TTGCAGTA-GAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * *
40312063 TTGCAGTAGAGCAGACTGAAGATAGAAAATCTTATCTCTCTGAAG
1 TTGCAGTAGAGCAGATTAAAGATA-CAAATCTTATCTCCCTGAAG
* * * * *
40312108 TTGCACTAGAGCAGATTAAAGTTATAAACCTTATCTCCTTGAAG
1 TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * *
40312152 TTTCAGTAGAGCAGATTAAAGCTACAAGTCTTATCTCCTTGAAG
1 TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * * * *
40312196 TTGCAGTGGAGTAGATTGAAG-TAACAAGTCCTATAC-CTCTGAAG
1 TTGCAGTAGAGCAGATTAAAGAT-ACAAATCTTAT-CTCCCTGAAG
* * * * *
40312240 TTGCAGT-GGGTTAGATTAAATCTATCATGGCAAATCTTATGTCCTTGAAG
1 TTGCAGTAGAG-CAGATTAAA--GAT-A---CAAATCTTATCTCCCTGAAG
* * * * *
40312290 TTGTAGTAGAGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAG
1 TTGCAGTAGAGCAGATTAAAGAT-ACAAATCTTATCTCCCTGAAG
** * * *
40312335 TTGCAGTAGAGCAGATTACAA-CCACTAACCTTATCTCCCTAAAG
1 TTGCAGTAGAGCAGATTA-AAGATACAAATCTTATCTCCCTGAAG
* * * * * * * *
40312379 TTACAATGGAGCAGGTTGAAGTTAGAAGTCTTATCTCCCTGAAG
1 TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
* * * * * *
40312423 TTACAGTGGAGCAGACTAAAGATGGCTAACCTTATCTCCCTGAAG
1 TTGCAGTAGAGCAGATTAAAGAT-ACAAATCTTATCTCCCTGAAG
* ** * * * *
40312468 TTGTAGGGGAGCAG-GTAGAAGACATCAAATCTTATTTCCCTGAGG
1 TTGCAGTAGAGCAGATTA-AAGATA-CAAATCTTATCTCCCTGAAG
* * *
40312513 TTGTAGTGGAACAGATTAAA
1 TTGCAGTAGAGCAGATTAAA
40312533 TCTATCAAAG
Statistics
Matches: 588, Mismatches: 164, Indels: 65
0.72 0.20 0.08
Matches are distributed among these distances:
43 9 0.02
44 308 0.52
45 188 0.32
46 15 0.03
47 4 0.01
48 12 0.02
49 23 0.04
50 27 0.05
51 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (44 bp):
TTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTGAAG
Found at i:40312479 original size:89 final size:88
Alignment explanation
Indices: 40312319--40312488 Score: 214
Period size: 89 Copynumber: 1.9 Consensus size: 88
40312309 AGATGGCGAA
* * *
40312319 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTACAACCACTAACCTTATCTCCCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAAACCACTAACCTTATCTCCCTAAAGTTACA
* *
40312384 ATGGAGCAGGTTGAAGTTAGAAG
66 AGGGAGCAGGTAGAAGTTAGAAG
* *** * **
40312407 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGATGGCTAACCTTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAA-ACCACTAACCTTATCTCCCTAAAGTTAC
*
40312472 AGGGGAGCAGGTAGAAG
65 AAGGGAGCAGGTAGAAG
40312489 ACATCAAATC
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
88 32 0.47
89 36 0.53
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAAACCACTAACCTTATCTCCCTAAAGTTACA
AGGGAGCAGGTAGAAGTTAGAAG
Found at i:40314305 original size:3 final size:3
Alignment explanation
Indices: 40314283--40314337 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
40314273 TTAGGTATTC
* * * *
40314283 TAT TAT T-T GTAT TAT CAT TAT TAA TAT TAT TAT CAT TAT TAT TAA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40314328 TAT TAT TAT T
1 TAT TAT TAT T
40314338 TTTAAATTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:40314313 original size:18 final size:18
Alignment explanation
Indices: 40314292--40314333 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
40314282 CTATTATTTG
*
40314292 TATTATCATTATTAATAT
1 TATTATCATTATTAATAA
*
40314310 TATTATCATTATTATTAA
1 TATTATCATTATTAATAA
40314328 TATTAT
1 TATTAT
40314334 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATCATTATTAATAA
Found at i:40314897 original size:18 final size:18
Alignment explanation
Indices: 40314874--40314908 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40314864 TAACTTACGG
40314874 GATGTAATTCTCTTTCTC
1 GATGTAATTCTCTTTCTC
40314892 GATGTAATTCTCTTTCT
1 GATGTAATTCTCTTTCT
40314909 TGATTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (18 bp):
GATGTAATTCTCTTTCTC
Found at i:40318140 original size:25 final size:25
Alignment explanation
Indices: 40318093--40318141 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40318083 TTATATTTGT
**
40318093 TAGTATATCTTGAAACTGCTATAGG
1 TAGTATATCTTGAAACTAATATAGG
*
40318118 TAGTATATGTTGAAACTAATATAG
1 TAGTATATCTTGAAACTAATATAG
40318142 ATAGACTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (25 bp):
TAGTATATCTTGAAACTAATATAGG
Found at i:40328136 original size:28 final size:27
Alignment explanation
Indices: 40328069--40328156 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
40328059 CAATATTTTG
** *
40328069 AAAAATATATAAAAATTTACCATATAT
1 AAAAATATATAAAAATTTAAAATTTAT
* *
40328096 AATATATAAATAAAAATTTATAAATTTAT
1 AA-AAATATATAAAAATTTA-AAATTTAT
* *
40328125 AAAAATATATAAAAGAACTAAAAATTTAT
1 AAAAATATAT-AAA-AATTTAAAATTTAT
40328154 AAA
1 AAA
40328157 TTTACAAGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 2 0.04
28 21 0.44
29 21 0.44
30 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAAATATATAAAAATTTAAAATTTAT
Found at i:40331050 original size:30 final size:31
Alignment explanation
Indices: 40331014--40331080 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
40331004 TTAACAACTT
*
40331014 AATGACTTAAAT-AAAATTTTTGAATAATTC
1 AATGACTTAAATGAAAACTTTTGAATAATTC
*
40331044 AATGACTTAAATGAAAACTTTTGAATAGTTC
1 AATGACTTAAATGAAAACTTTTGAATAATTC
*
40331075 ATTGAC
1 AATGAC
40331081 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (31 bp):
AATGACTTAAATGAAAACTTTTGAATAATTC
Found at i:40335278 original size:25 final size:25
Alignment explanation
Indices: 40335248--40335300 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
40335238 CAAATTAAGA
* *
40335248 TATATATTTTTATTTTTTATTTTATTT
1 TATATA-TTTTAATTTTT-TTTCATTT
40335275 TATATATTTTAATTTTTTTTCATTT
1 TATATATTTTAATTTTTTTTCATTT
40335300 T
1 T
40335301 TTTAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 10 0.42
27 6 0.25
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (25 bp):
TATATATTTTAATTTTTTTTCATTT
Found at i:40335294 original size:19 final size:16
Alignment explanation
Indices: 40335254--40335302 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 16
40335244 AAGATATATA
40335254 TTTTTATTTTTTATTT
1 TTTTTATTTTTTATTT
40335270 TATTTTATATATTTTAATTT
1 T-TTTTAT-T-TTTT-ATTT
40335290 TTTTTCATTTTTT
1 TTTTT-ATTTTTT
40335303 TAAATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.04
17 6 0.21
18 5 0.18
19 9 0.32
20 7 0.25
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTATTTTTTATTT
Found at i:40338446 original size:45 final size:45
Alignment explanation
Indices: 40338397--40338490 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
40338387 GTCAGTGAAG
*
40338397 ATAAAAGCTT-CTAATATGATATGGATAAACCACTAAATGGTGCAA
1 ATAAAAG-TTGCTAATATGATATGGATAAACCAATAAATGGTGCAA
* * * *
40338442 ATAAAAGTTGTTAATATGGTGTGGATAAACCAATAAATGGTGCAG
1 ATAAAAGTTGCTAATATGATATGGATAAACCAATAAATGGTGCAA
40338487 ATAA
1 ATAA
40338491 GCTACTAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 2 0.05
45 41 0.95
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.28
Consensus pattern (45 bp):
ATAAAAGTTGCTAATATGATATGGATAAACCAATAAATGGTGCAA
Found at i:40338639 original size:34 final size:34
Alignment explanation
Indices: 40338575--40338641 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
40338565 GGTAGCAACC
* * *
40338575 AATATGCTTATAACAATTAAATACAGTAGCAAAT
1 AATATGCTTATAAAAATCAAATACAATAGCAAAT
*
40338609 AATATGCTTATAAAAGATCAACT-CAATAGCAAA
1 AATATGCTTATAAAA-ATCAAATACAATAGCAAA
40338642 GGTCTTGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (34 bp):
AATATGCTTATAAAAATCAAATACAATAGCAAAT
Found at i:40338923 original size:28 final size:27
Alignment explanation
Indices: 40338892--40338967 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
40338882 AAAATTCTGT
*
40338892 CAAAACTATAAAATATGAAAAATATGGG
1 CAAAACTATAAAATAT-AAAAATAAGGG
* *
40338920 CAAAATTGTAAAATATAAAAATAAGGG
1 CAAAACTATAAAATATAAAAATAAGGG
* *
40338947 AAAAACTATAAAATTTAAAAA
1 CAAAACTATAAAATATAAAAA
40338968 ATACAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 27 0.66
28 14 0.34
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (27 bp):
CAAAACTATAAAATATAAAAATAAGGG
Found at i:40338951 original size:27 final size:28
Alignment explanation
Indices: 40338900--40338993 Score: 88
Period size: 27 Copynumber: 3.5 Consensus size: 28
40338890 GTCAAAACTA
* * *
40338900 TAAAATATGAAAAATATGGGCAAAATTG
1 TAAAATATAAAAAATAAGGGAAAAATTG
* *
40338928 TAAAATAT-AAAAATAAGGGAAAAACTA
1 TAAAATATAAAAAATAAGGGAAAAATTG
*
40338955 TAAAATTTAAAAAATACA---AAAAATTG
1 TAAAATATAAAAAATA-AGGGAAAAATTG
*
40338981 TAAAATCTAAAAA
1 TAAAATATAAAAA
40338994 TAGGGGATAC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 18 0.32
27 22 0.39
28 15 0.27
29 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (28 bp):
TAAAATATAAAAAATAAGGGAAAAATTG
Found at i:40342253 original size:16 final size:16
Alignment explanation
Indices: 40342229--40342272 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
40342219 TTATGTTTTG
*
40342229 TCATGTATTTTTCG-TA
1 TCATATATTTTT-GATA
40342245 TCATATATTTTTGATTA
1 TCATATATTTTTGA-TA
40342262 TCATATATTTT
1 TCATATATTTT
40342273 GTTAACTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 13 0.52
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.59
Consensus pattern (16 bp):
TCATATATTTTTGATA
Found at i:40343317 original size:132 final size:132
Alignment explanation
Indices: 40342786--40343318 Score: 414
Period size: 132 Copynumber: 4.0 Consensus size: 132
40342776 ATTACTCATT
* * * * * * *
40342786 TAAAAATTCTTAAAAACGAAGGCGATATTCGATATTTGACAATTCGTGGAATCGTGCCCTAACGT
1 TAAAAACTCTTAAAAACGAAGGCAATATTCAATGTTTGACAATTCGGGGAATAGTGCCCTATCGT
* * * * * * *
40342851 GTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCAAATAACCCTTCAAAATTTCACTCATGTCT
66 GCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGAAATTTCACTCATATTT
40342916 TC
131 TC
* * ** **
40342918 TAAAAA-TCCTTTAAAACGAAGGCAATACTCGGTGTTTGATGATTC-GGGAATCA-TGCCCTATC
1 TAAAAACT-CTTAAAAACGAAGGCAATATTCAATGTTTGACAATTCGGGGAAT-AGTGCCCTATC
** * * * **
40342980 GTGCTGGGTTGTGATTTCTCGTTTGGTCAAAACAATCAAATATTCCTT-TAGGTTTTCACTCATT
64 GTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGA-AATTTCACTCA-T
* *
40343044 TTTTTT
127 ATTTTC
* ** * * * * * *
40343050 TAAGAAAACACATT-AAAACGAAGGTGATGTTCAATGTTTGGCAATT-TGAGAATCGTGTCCTAT
1 T-A-AAAACTC-TTAAAAACGAAGGCAATATTCAATGTTTGACAATTCGGGGAATAGTGCCCTAT
* * ** * * ** * *
40343113 CGTGCTGGGTTGCACTTTTTTATTGGTTCGAAACAATTGAAGATCCCTTCGGAAA-TTCACTCAC
63 CGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTC-GAAATTTCACTCAT
40343177 ATTTTC
127 ATTTTC
* * * *
40343183 TAAAAACTCTTAAAAACGAAAGAAATGTTCAATGTTTGGCAATTCGGGGAATAGTGCCCTATCGT
1 TAAAAACTCTTAAAAACGAAGGCAATATTCAATGTTTGACAATTCGGGGAATAGTGCCCTATCGT
* * * * * * *
40343248 GCTAGGTTGCAATCTCCCGTTTGTTCAAAATAATCGAATATCTCTTCGAAATTTCACTCGTATTT
66 GCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGAAATTTCACTCATATTT
40343313 TC
131 TC
40343315 TAAA
1 TAAA
40343319 GTTAAGGCAA
Statistics
Matches: 308, Mismatches: 78, Indels: 30
0.74 0.19 0.07
Matches are distributed among these distances:
130 3 0.01
131 103 0.33
132 109 0.35
133 6 0.02
134 84 0.27
135 2 0.01
136 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (132 bp):
TAAAAACTCTTAAAAACGAAGGCAATATTCAATGTTTGACAATTCGGGGAATAGTGCCCTATCGT
GCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGAAATTTCACTCATATTT
TC
Found at i:40344303 original size:50 final size:49
Alignment explanation
Indices: 40344237--40344397 Score: 180
Period size: 50 Copynumber: 3.2 Consensus size: 49
40344227 GTGTGGCCGT
* *
40344237 GTGGG-CCACACAGGTATGGCCAGGTTAGGCGTGTGGGCCACACGAGCGA
1 GTGGGCCCACACAGGTATGGCCAAGTTAGGCGTATGGGCCACAC-AGCGA
* * * *
40344286 GTGAGCCCACACGGGTATGGCCAAGTTAGACGTATAGGCCACACAGGCGA
1 GTGGGCCCACACAGGTATGGCCAAGTTAGGCGTATGGGCCACACA-GCGA
** * * *
40344336 GTGGGCCCACACAGGTATAACCAAGTTGGGCGTTTGGGCTACACAAGCGA
1 GTGGGCCCACACAGGTATGGCCAAGTTAGGCGTATGGGCCACAC-AGCGA
*
40344386 GTGGGCCTACAC
1 GTGGGCCCACAC
40344398 GGGCATGTCA
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
49 5 0.05
50 87 0.94
51 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.35, T:0.16
Consensus pattern (49 bp):
GTGGGCCCACACAGGTATGGCCAAGTTAGGCGTATGGGCCACACAGCGA
Found at i:40359027 original size:48 final size:49
Alignment explanation
Indices: 40358973--40359073 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 49
40358963 GTATTCTTAA
40358973 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGT-
1 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
40359021 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
1 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
40359070 AAAT
1 AAAT
40359074 CCTTCATGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 48 0.92
49 4 0.08
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (49 bp):
AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
Found at i:40360645 original size:92 final size:91
Alignment explanation
Indices: 40360526--40360698 Score: 242
Period size: 92 Copynumber: 1.9 Consensus size: 91
40360516 ATGCAGTATG
* **
40360526 AACTGCCAGATCAGATAATAGTACGTAGCATAGCTAATGTCCCTATG-GTATGGTGCAATGCGGT
1 AACTGCCAGATCAGATAATAGTACGTAGCATAGCTAATGT-AC-ATGAGTAAAGTGCAATGCGGT
40360590 AATCCGCTATACCGATAGGTCGCAATAA
64 AATCCGCTATACCGATAGGTCGCAATAA
* * *
40360618 AACTGCCAGTTCAG-TCAATGGTACGTAGCGTAGCTAATGTACATGCAGTAAAGTGCAATGCGGT
1 AACTGCCAGATCAGAT-AATAGTACGTAGCATAGCTAATGTACATG-AGTAAAGTGCAATGCGGT
40360682 AATCCGCTATACCGATA
64 AATCCGCTATACCGATA
40360699 TAATGTCACC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
90 3 0.04
91 2 0.03
92 67 0.93
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (91 bp):
AACTGCCAGATCAGATAATAGTACGTAGCATAGCTAATGTACATGAGTAAAGTGCAATGCGGTAA
TCCGCTATACCGATAGGTCGCAATAA
Found at i:40362839 original size:92 final size:90
Alignment explanation
Indices: 40362708--40362880 Score: 222
Period size: 92 Copynumber: 1.9 Consensus size: 90
40362698 ATTAAGCTCC
* * *
40362708 TCTTTTTTTTCACTCAATTGAGCACTTGAATTTTAAAAATGCATAAAAAAGACTATC-AAACTTC
1 TCTTTTTTTTCACTCAATTGAGCACTTGAACTTTAAAAATACATAAAAAAGACCATCAAAACTT-
40362772 ATCAAAAAAAGCAATTAAACCCTTGCT
65 ATC-AAAAAAGCAATTAAACCCTTGCT
* * * * * *
40362799 TCTTCTTTTTTCACTCGATTGGGTACTTGAACTTTCAAAATACATCAAAAAGACCCTCAAAACTT
1 TCTT-TTTTTTCACTCAATTGAGCACTTGAACTTTAAAAATACATAAAAAAGACCATCAAAACTT
*
40362864 TTCAAAAAAGCAATTAA
65 ATCAAAAAAGCAATTAA
40362881 GCCCCTACTC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
91 18 0.26
92 46 0.66
93 6 0.09
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (90 bp):
TCTTTTTTTTCACTCAATTGAGCACTTGAACTTTAAAAATACATAAAAAAGACCATCAAAACTTA
TCAAAAAAGCAATTAAACCCTTGCT
Found at i:40362954 original size:19 final size:19
Alignment explanation
Indices: 40362901--40362960 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
40362891 TTACTAAAAA
*
40362901 TTAGAAAAAATAATAAATT
1 TTAGAAAAAATATTAAATT
*
40362920 TTAGAAAAATTATTAAATT
1 TTAGAAAAAATATTAAATT
*
40362939 TTAGTAAAAAAT-TTAAAAT
1 TTAG-AAAAAATATTAAATT
40362958 TTA
1 TTA
40362961 AAATTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 30 0.83
20 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAGAAAAAATATTAAATT
Found at i:40362979 original size:36 final size:38
Alignment explanation
Indices: 40362895--40362980 Score: 97
Period size: 36 Copynumber: 2.3 Consensus size: 38
40362885 CTACTCTTAC
*
40362895 TAAAAATTAG-AAAAAATAATAAATTTTAGAAAAATTAT
1 TAAAAATTAGTAAAAAATAATAAAATTTA-AAAAATTAT
** * *
40362933 TAAATTTTAGTAAAAAAT-TTAAAATTT-AAAATTTAT
1 TAAAAATTAGTAAAAAATAATAAAATTTAAAAAATTAT
40362969 TAAAAATTAGTA
1 TAAAAATTAGTA
40362981 TTTTTTATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
36 18 0.45
38 15 0.38
39 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (38 bp):
TAAAAATTAGTAAAAAATAATAAAATTTAAAAAATTAT
Found at i:40364775 original size:43 final size:39
Alignment explanation
Indices: 40364727--40364849 Score: 115
Period size: 38 Copynumber: 3.1 Consensus size: 39
40364717 GTTTATCAAA
*
40364727 TAGTCCAACAGTACAAAAACAGTGAACATGTTTAACATGTATT
1 TAGTCCAACAGTA-AAAAACA-T--ACATGCTTAACATGTATT
* *
40364770 TAGTCCAACAGT-AGAAATATACATGCTTAACATGTATT
1 TAGTCCAACAGTAAAAAACATACATGCTTAACATGTATT
* ** * * *
40364808 TAGTTCAACAGT-AGCAATAGACATGCTTAACATGTAAT
1 TAGTCCAACAGTAAAAAACATACATGCTTAACATGTATT
40364846 TAGT
1 TAGT
40364850 TTAATAGTAG
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
38 55 0.75
40 1 0.01
41 5 0.07
43 12 0.16
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (39 bp):
TAGTCCAACAGTAAAAAACATACATGCTTAACATGTATT
Found at i:40364850 original size:38 final size:38
Alignment explanation
Indices: 40364752--40364879 Score: 166
Period size: 38 Copynumber: 3.4 Consensus size: 38
40364742 AAAACAGTGA
* * * *
40364752 ACATGTTTAACATGTATTTAGTCCAACAGTAGAAATAT
1 ACATGCTTAACATGTATTTAGTTCAACAGTAGCAATAG
40364790 ACATGCTTAACATGTATTTAGTTCAACAGTAGCAATAG
1 ACATGCTTAACATGTATTTAGTTCAACAGTAGCAATAG
* * * *
40364828 ACATGCTTAACATGTAATTAGTTTAATAGTAGCAGTAG
1 ACATGCTTAACATGTATTTAGTTCAACAGTAGCAATAG
* *
40364866 GCATGCTGAACATG
1 ACATGCTTAACATG
40364880 CAATCAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 80 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (38 bp):
ACATGCTTAACATGTATTTAGTTCAACAGTAGCAATAG
Found at i:40366522 original size:18 final size:18
Alignment explanation
Indices: 40366509--40366543 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40366499 TTAATTTTCT
*
40366509 AGGTTTTTGGAATTTTTG
1 AGGTTTTAGGAATTTTTG
40366527 AGGTTTTAGGAATTTTT
1 AGGTTTTAGGAATTTTT
40366544 TTGAATTTTC
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:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
AGGTTTTAGGAATTTTTG
Found at i:40367218 original size:17 final size:17
Alignment explanation
Indices: 40367174--40367225 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
40367164 TATGATTCAG
40367174 AATATTAT-AAATATATA
1 AATATTATAAAAT-TATA
* *
40367191 TATATTA-AAAATTGTA
1 AATATTATAAAATTATA
40367207 AATATTATAAAATTATA
1 AATATTATAAAATTATA
40367224 AA
1 AA
40367226 ACAAAGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATTATAAAATTATA
Found at i:40367777 original size:22 final size:22
Alignment explanation
Indices: 40367735--40367777 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40367725 GGTTTTACAA
*
40367735 AGATTTAAATATTTTAATTTTG
1 AGATTTAAATATTCTAATTTTG
*
40367757 AGATATTAAAT-TTCTATTTTT
1 AGAT-TTAAATATTCTAATTTT
40367778 TTTCATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (22 bp):
AGATTTAAATATTCTAATTTTG
Found at i:40368683 original size:3 final size:3
Alignment explanation
Indices: 40368677--40368723 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40368667 TTATTTTTCT
40368677 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40368724 TCTATGTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40369063 original size:21 final size:22
Alignment explanation
Indices: 40369020--40369063 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
40369010 TGAAACGTTT
* *
40369020 GTCTATTTTGGTATAAAACTTTA
1 GTCTATTTT-GTAGAAAAATTTA
40369043 GTCTATTTT-TAGAAAAATTTA
1 GTCTATTTTGTAGAAAAATTTA
40369064 CGAGTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (22 bp):
GTCTATTTTGTAGAAAAATTTA
Found at i:40371514 original size:21 final size:21
Alignment explanation
Indices: 40371490--40371532 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40371480 TCATTTTAGA
40371490 TTAATAC-CTAATTATATTATT
1 TTAATACTCTAATTA-ATTATT
*
40371511 TTAATACTTTAATTAATTATT
1 TTAATACTCTAATTAATTATT
40371532 T
1 T
40371533 ATGATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATACTCTAATTAATTATT
Found at i:40375915 original size:16 final size:17
Alignment explanation
Indices: 40375891--40375924 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40375881 AAAAATTTAC
*
40375891 TATATTTAA-TTTAATT
1 TATAATTAATTTTAATT
40375907 TATAATTAATTTTAATT
1 TATAATTAATTTTAATT
40375924 T
1 T
40375925 GTTACAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATTAATTTTAATT
Found at i:40376083 original size:23 final size:22
Alignment explanation
Indices: 40376052--40376111 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
40376042 ATTCTTTTAA
40376052 TAAATATTTATAAAAAAAATATTT
1 TAAA-ATTTATAAAAAAAATA-TT
* *
40376076 TAAAATTT-TATTAAATAATATT
1 TAAAATTTATA-AAAAAAATATT
*
40376098 TAAAAGTTATAAAA
1 TAAAATTTATAAAA
40376112 TAGTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 13 0.43
23 13 0.43
24 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAATTTATAAAAAAAATATT
Found at i:40383960 original size:18 final size:18
Alignment explanation
Indices: 40383937--40383979 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40383927 ATTCAAGGTG
* *
40383937 TAATTAATTTAATTTTTT
1 TAATTAATTAAATTTATT
40383955 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
40383973 TAATTAA
1 TAATTAA
40383980 AAATATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:40386154 original size:22 final size:21
Alignment explanation
Indices: 40386119--40386192 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
40386109 AAAATGTATC
* *
40386119 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40386140 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40386163 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
40386182 TGC-AATCATAT
1 TACAAATCATAT
40386193 ATAAGATTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40386179 original size:19 final size:19
Alignment explanation
Indices: 40386155--40386245 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
40386145 AATCATATCT
40386155 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40386174 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
40386192 TATAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
40386209 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40386228 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
40386246 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 15 0.22
18 15 0.22
19 37 0.55
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40386209 original size:35 final size:37
Alignment explanation
Indices: 40386157--40386245 Score: 137
Period size: 35 Copynumber: 2.4 Consensus size: 37
40386147 TCATATCTTC
40386157 TAAGATTGCATATCATATCTAAGATTGCA-ATCATATA
1 TAAGATTG-ATATCATATCTAAGATTGCATATCATATA
*
40386194 TAAGATTG-TATCATATCTAAGATTGCATATCATATC
1 TAAGATTGATATCATATCTAAGATTGCATATCATATA
40386230 TAAGATTGCATATCAT
1 TAAGATTG-ATATCAT
40386246 TGAAGATTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 19 0.40
36 15 0.31
37 8 0.17
38 6 0.12
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (37 bp):
TAAGATTGATATCATATCTAAGATTGCATATCATATA
Found at i:40386402 original size:21 final size:20
Alignment explanation
Indices: 40386365--40386403 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40386355 TGGACTTCGG
**
40386365 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
40386385 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
40386404 TCTGGGCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:40386658 original size:45 final size:45
Alignment explanation
Indices: 40386609--40386824 Score: 242
Period size: 45 Copynumber: 4.8 Consensus size: 45
40386599 TGCTATATTT
40386609 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTC
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTC
*
40386654 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGCT-TCTTC
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTC
* * * *
40386698 AATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTT
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTC
* * * * * * *
40386743 GATCTGCT--TCGATGTAA-ACACATGAAGGTCAGATCTGCTATGTCTTC
1 GATCTGCTCCCCG-TCTAATACAGA-G-ACGCCAAATCTG-T-TATCTTC
*
40386790 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATC
40386825 ATCTTGGATC
Statistics
Matches: 140, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
43 6 0.04
44 45 0.32
45 58 0.41
46 1 0.01
47 19 0.14
48 5 0.04
49 6 0.04
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (45 bp):
GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTC
Found at i:40386717 original size:89 final size:91
Alignment explanation
Indices: 40386610--40386824 Score: 269
Period size: 89 Copynumber: 2.4 Consensus size: 91
40386600 GCTATATTTG
* * *
40386610 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCG-TCT-AAT
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCT--CCGATCTAAAC
40386673 ACA-GAGACGCCAAATCTGC-T-TCTTCA
64 ACATGA-ACGCCAAATCTGCATGTCTTCA
* * *
40386699 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTTGATCTGCTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTCCGATCTAAACAC
* * * *
40386764 ATGAAGGTCAGATCTGCTATGTCTTCG
66 ATGAACGCCAAATCTGC-ATGTCTTCA
40386791 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
40386825 ATCTTGGATC
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
87 2 0.02
88 2 0.02
89 64 0.58
90 2 0.02
91 1 0.01
92 39 0.35
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (91 bp):
ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGATCTGCTCCGATCTAAACAC
ATGAACGCCAAATCTGCATGTCTTCA
Found at i:40386893 original size:78 final size:78
Alignment explanation
Indices: 40386764--40387058 Score: 477
Period size: 78 Copynumber: 3.8 Consensus size: 78
40386754 ATGTAAACAC
40386764 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
40386829 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
40386842 ATGAAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
40386906 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
40386920 ATGAAGGTCAGATCTGCTGTGTCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
40386985 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * * *
40386998 ATGAAAGTCAGATCTGCTATGTCTTTGATCTGCTCTCCGTCGAATA-TGTAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAG-AGATGCCAAATC
40387059 TGTTTCTTTG
Statistics
Matches: 201, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
77 3 0.01
78 196 0.98
79 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:40390606 original size:28 final size:28
Alignment explanation
Indices: 40390566--40390621 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
40390556 GGCCGGCCAA
40390566 GTAAGGATTTTCTCCACTAAGTTTATAT
1 GTAAGGATTTTCTCCACTAAGTTTATAT
40390594 GTAAGGATTTTCTCCACTAAGTTTATAT
1 GTAAGGATTTTCTCCACTAAGTTTATAT
40390622 TATTTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (28 bp):
GTAAGGATTTTCTCCACTAAGTTTATAT
Found at i:40398924 original size:13 final size:13
Alignment explanation
Indices: 40398906--40398930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40398896 GCAATAAGGT
40398906 AACAAACATATGC
1 AACAAACATATGC
40398919 AACAAACATATG
1 AACAAACATATG
40398931 TAAAAATAGG
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:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (13 bp):
AACAAACATATGC
Found at i:40399654 original size:16 final size:17
Alignment explanation
Indices: 40399633--40399666 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40399623 GATATGATAC
*
40399633 TAAAAT-TATTAAAAAA
1 TAAAATATATAAAAAAA
40399649 TAAAATATATAAAAAAA
1 TAAAATATATAAAAAAA
40399666 T
1 T
40399667 TCAAGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATATATAAAAAAA
Found at i:40399955 original size:22 final size:21
Alignment explanation
Indices: 40399920--40399995 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
40399910 AAAAGGTATC
* *
40399920 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40399941 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40399964 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
40399983 TGC-AATCATATCT
1 TACAAATCATATCT
40399996 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:40400012 original size:35 final size:37
Alignment explanation
Indices: 40399949--40400046 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
40399939 ATTACAAAAT
40399949 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
40399985 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
40400020 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
40400047 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:40400054 original size:17 final size:19
Alignment explanation
Indices: 40399956--40400046 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
40399946 AATCATATCT
40399956 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40399975 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
40399993 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
40400010 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40400029 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
40400047 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40403675 original size:23 final size:24
Alignment explanation
Indices: 40403644--40403699 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
40403634 ACGTAACTCC
* *
40403644 ATGTGATGCCTT-TGTGGCGTACT
1 ATGTAATGCCTTGTGTGGCATACT
* *
40403667 CTGTAATG-CTTGTGTGGCATATT
1 ATGTAATGCCTTGTGTGGCATACT
40403690 ATGTAATGCC
1 ATGTAATGCC
40403700 CTAGAGGTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.12
23 22 0.85
24 1 0.04
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (24 bp):
ATGTAATGCCTTGTGTGGCATACT
Found at i:40412776 original size:15 final size:15
Alignment explanation
Indices: 40412745--40412784 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
40412735 TGATTAAGAA
*
40412745 TTAATTAA-TTTAGT
1 TTAATTAACTTAAGT
40412759 TTAATTAACTTAAGT
1 TTAATTAACTTAAGT
40412774 TTAATT-ACTTA
1 TTAATTAACTTA
40412785 GCATTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (15 bp):
TTAATTAACTTAAGT
Found at i:40421075 original size:32 final size:32
Alignment explanation
Indices: 40421037--40421098 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
40421027 TTACTGCAGC
40421037 TATTTTTCAAATTTGATTATTTT-TAGTTTTTA
1 TATTTTTCAAATTT-ATTATTTTATAGTTTTTA
* * *
40421069 TATTTTTTATATTTATTTTTTTATAGTTTT
1 TATTTTTCAAATTTATTATTTTATAGTTTT
40421099 AAATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (32 bp):
TATTTTTCAAATTTATTATTTTATAGTTTTTA
Found at i:40421083 original size:22 final size:23
Alignment explanation
Indices: 40421053--40421106 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
40421043 TCAAATTTGA
* *
40421053 TTATTTTTA-GTTTTTATATTTT
1 TTATATTTATGTTTTTATAGTTT
*
40421075 TTATATTTATTTTTTTATAG-TT
1 TTATATTTATGTTTTTATAGTTT
*
40421097 TTAAATTTAT
1 TTATATTTAT
40421107 TATTGATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (23 bp):
TTATATTTATGTTTTTATAGTTT
Found at i:40421088 original size:14 final size:15
Alignment explanation
Indices: 40421065--40421093 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40421055 ATTTTTAGTT
40421065 TTTATATTTTTTATA
1 TTTATATTTTTTATA
40421080 TTTAT-TTTTTTATA
1 TTTATATTTTTTATA
40421094 GTTTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATATTTTTTATA
Found at i:40421107 original size:22 final size:23
Alignment explanation
Indices: 40421063--40421107 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
40421053 TTATTTTTAG
* *
40421063 TTTTTATATTTTTTATATTTATT
1 TTTTTATATGTTTTAAATTTATT
40421086 TTTTTATA-GTTTTAAATTTATT
1 TTTTTATATGTTTTAAATTTATT
40421108 ATTGATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTATATGTTTTAAATTTATT
Found at i:40421502 original size:19 final size:18
Alignment explanation
Indices: 40421478--40421527 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
40421468 ATATTACAAA
40421478 AAAATTATATAAAAA-TAAT
1 AAAATTATA-AAAAACT-AT
*
40421497 AAAATTTTAAAAAACTAT
1 AAAATTATAAAAAACTAT
40421515 AAAAGTTATAAAA
1 AAAA-TTATAAAA
40421528 CATTCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAAACTAT
Found at i:40421887 original size:17 final size:17
Alignment explanation
Indices: 40421876--40421908 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40421866 AATAAATATG
40421876 AAAA-AAATATAAAAAT
1 AAAATAAATATAAAAAT
40421892 AAAATAAATA-AAAAAT
1 AAAATAAATATAAAAAT
40421908 A
1 A
40421909 CAAAGAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAATATAAAAAT
Found at i:40427437 original size:19 final size:19
Alignment explanation
Indices: 40427413--40427451 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40427403 TTAGCAAGAT
40427413 AAATTGTCTTAATTGCATG
1 AAATTGTCTTAATTGCATG
40427432 AAATTGTCTTAATTGCATG
1 AAATTGTCTTAATTGCATG
40427451 A
1 A
40427452 TCTGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (19 bp):
AAATTGTCTTAATTGCATG
Found at i:40437547 original size:17 final size:17
Alignment explanation
Indices: 40437527--40437660 Score: 148
Period size: 17 Copynumber: 7.9 Consensus size: 17
40437517 ATGAAAGTTT
40437527 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
40437544 TTTTT-AAACACG-GAA
1 TTTTTAAAACACGAGAA
* * *
40437559 ATTTCAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
* *
40437577 TTTTTAAAACACGACAT
1 TTTTTAAAACACGAGAA
*
40437594 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
40437611 TTTTTAAAACACGA-AGA
1 TTTTTAAAACACGAGA-A
* *
40437628 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAGAA
40437645 TTTTTAAAAGCACGAG
1 TTTTTAAAA-CACGAG
40437661 GATTATTGAA
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.06
16 8 0.08
17 70 0.73
18 12 0.12
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:40437603 original size:34 final size:33
Alignment explanation
Indices: 40437527--40437659 Score: 169
Period size: 34 Copynumber: 3.9 Consensus size: 33
40437517 ATGAAAGTTT
*
40437527 TTTTTAAAACACGAGAATTTTT-AAACACGGAAA
1 TTTTTGAAACACGAGAATTTTTAAAACAC-GAAA
** * *
40437560 TTTCAGAAACACGAAAATTTTTAAAACACGACAT
1 TTTTTGAAACACGAGAATTTTTAAAACACGA-AA
40437594 TTTTTGAAACACGAGAATTTTTAAAACACGAAGA
1 TTTTTGAAACACGAGAATTTTTAAAACACGAA-A
*
40437628 TTTTTGAAACATGAGAATTTTTAAAAGCACGA
1 TTTTTGAAACACGAGAATTTTTAAAA-CACGA
40437660 GGATTATTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 21 0.24
34 60 0.70
35 5 0.06
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (33 bp):
TTTTTGAAACACGAGAATTTTTAAAACACGAAA
Found at i:40438017 original size:8 final size:8
Alignment explanation
Indices: 40437988--40438046 Score: 68
Period size: 8 Copynumber: 7.4 Consensus size: 8
40437978 ATTGAACCCC
40437988 CTTTTTCTT
1 CTTTTT-TT
*
40437997 CCTTTTTT
1 CTTTTTTT
40438005 C-TTTTTT
1 CTTTTTTT
40438012 CTTTTTTT
1 CTTTTTTT
40438020 C-TTTTTT
1 CTTTTTTT
*
40438027 CCTTTTTT
1 CTTTTTTT
40438035 CTTCTTTTT
1 CTT-TTTTT
40438044 CTT
1 CTT
40438047 CCTTTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 14 0.31
8 18 0.40
9 13 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
CTTTTTTT
Found at i:40438019 original size:15 final size:15
Alignment explanation
Indices: 40437990--40438042 Score: 79
Period size: 15 Copynumber: 3.4 Consensus size: 15
40437980 TGAACCCCCT
40437990 TTTTCTTCCTTTTTTC
1 TTTT-TTCCTTTTTTC
*
40438006 TTTTTTCTTTTTTTC
1 TTTTTTCCTTTTTTC
40438021 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
40438036 TTCTTTT
1 TT-TTTT
40438043 TCTTCCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 26 0.76
16 8 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTCCTTTTTTC
Found at i:40438025 original size:23 final size:23
Alignment explanation
Indices: 40437988--40438059 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
40437978 ATTGAACCCC
*
40437988 CTTTTTCTTCCTTTTTTCTTTTTT
1 CTTTTT-TTCTTTTTTTCTTTTTT
*
40438012 CTTTTTTTCTTTTTTCCTTTTTT
1 CTTTTTTTCTTTTTTTCTTTTTT
**
40438035 CTTCTTTTTCTTCCTTT-TTTTTT
1 CTT-TTTTTCTTTTTTTCTTTTTT
40438058 CT
1 CT
40438060 GCTGGGCTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 26 0.62
24 16 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
CTTTTTTTCTTTTTTTCTTTTTT
Found at i:40438343 original size:3 final size:3
Alignment explanation
Indices: 40438337--40438395 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
40438327 TTCTTTTTTT
40438337 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
40438384 TTC TTC TTC TTC
1 TTC TTC TTC TTC
40438396 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:40438352 original size:10 final size:10
Alignment explanation
Indices: 40438327--40438395 Score: 74
Period size: 10 Copynumber: 7.3 Consensus size: 10
40438317 AAAATTTTTT
* *
40438327 TTCTTTTTTT
1 TTCTTCTTTC
40438337 TTCTTCTTTC
1 TTCTTCTTTC
*
40438347 TTCTTCTCTC
1 TTCTTCTTTC
40438357 -T-TTCTTTC
1 TTCTTCTTTC
40438365 TTCTTC-TTC
1 TTCTTCTTTC
*
40438374 TTCTTCCTTC
1 TTCTTCTTTC
40438384 TTCTTC-TTC
1 TTCTTCTTTC
40438393 TTC
1 TTC
40438396 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
8 6 0.12
9 17 0.33
10 29 0.56
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:40438383 original size:13 final size:13
Alignment explanation
Indices: 40438337--40438392 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
40438327 TTCTTTTTTT
*
40438337 TTCTTCTTTCTTC
1 TTCTTCCTTCTTC
*
40438350 TTCTCTCTTTC-T-
1 TTCT-TCCTTCTTC
40438362 TTCTT-CTTCTTC
1 TTCTTCCTTCTTC
40438374 TTCTTCCTTCTTC
1 TTCTTCCTTCTTC
40438387 TTCTTC
1 TTCTTC
40438393 TTCAAAACCG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 2 0.05
12 9 0.24
13 18 0.47
14 6 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTCCTTCTTC
Found at i:40438819 original size:31 final size:30
Alignment explanation
Indices: 40438765--40438867 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
40438755 ATTTAGGATT
**
40438765 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAAAAAGTTTAGGGGTC
* * *
40438795 TAAGTGAAATTTAAAAAAAAGTTTAAGGGTC
1 AAAATGAAATTT-AAAAAAAGTTTAGGGGTC
** *
40438826 AAAATGAAATTTAGGAAAAGTTTAGGGGTT
1 AAAATGAAATTTAAAAAAAGTTTAGGGGTC
*
40438856 AAAATGCAATTT
1 AAAATGAAATTT
40438868 TTATTTTTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 35 0.58
31 25 0.42
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAAAAAGTTTAGGGGTC
Found at i:40438882 original size:14 final size:15
Alignment explanation
Indices: 40438863--40438897 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
40438853 GTTAAAATGC
40438863 AATTTTTATTTTT-A
1 AATTTTTATTTTTGA
*
40438877 AATTTTTTTTTTTGA
1 AATTTTTATTTTTGA
40438892 AATTTT
1 AATTTT
40438898 GAACATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Found at i:40439285 original size:107 final size:106
Alignment explanation
Indices: 40439139--40439337 Score: 319
Period size: 106 Copynumber: 1.9 Consensus size: 106
40439129 CACGTGAGCC
* * *
40439139 AAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAAAAGGCTCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AAAAGGCTCAA
*
40439203 CTCACCTCTCGCAATATGGGTTGATTTTTTTGAAAAATAGAAA
64 CTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAA
* *
40439246 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
40439311 CACCTCTCGCAATATGAGTTGATTTTT
66 CACCTCTCGCAATATGAGTTGATTTTT
40439338 GAAAACAGAA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
106 39 0.46
107 36 0.42
108 10 0.12
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (106 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAA
Found at i:40439324 original size:54 final size:54
Alignment explanation
Indices: 40439139--40439356 Score: 293
Period size: 54 Copynumber: 4.1 Consensus size: 54
40439129 CACGTGAGCC
* * *
40439139 AAGGCTTAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTG-AA
* * *
40439194 AAGGCTCAACTCACCTCTCGCAATATGGGTTGATTTTTTTGAAAA-ATAGA---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAA
* *
40439246 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGAA
40439300 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAA
40439354 AAG
1 AAG
40439357 TAGAAATTGA
Statistics
Matches: 144, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
50 6 0.04
51 4 0.03
52 36 0.25
53 11 0.08
54 45 0.31
55 30 0.21
56 2 0.01
57 10 0.07
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAA
Found at i:40439354 original size:13 final size:14
Alignment explanation
Indices: 40439336--40439369 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40439326 GAGTTGATTT
40439336 TTGAAAA-CAGAAA
1 TTGAAAAGCAGAAA
*
40439349 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
40439363 TTGAAAA
1 TTGAAAA
40439370 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:40439596 original size:85 final size:87
Alignment explanation
Indices: 40439448--40439697 Score: 285
Period size: 85 Copynumber: 2.8 Consensus size: 87
40439438 AGAAATTAAA
* * * *
40439448 AAAAAAATAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATG
1 AAAAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATG
40439513 AGTTGATTTGAAAAG-TAGAATT-
65 AGTTGATTTGAAAAGATAG-ATTG
** * * * *
40439535 AGTAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGTAATATA
1 AAAAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATG
*
40439598 AGTTGATTTTTGGAAAGCATAGATTG
65 AGTTGA--TTTGAAAAG-ATAGATTG
*
40439624 AAAAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATAT
1 AAAAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATAT
40439688 GAGTTGATTT
64 GAGTTGATTT
40439698 TTGAAAAACA
Statistics
Matches: 135, Mismatches: 18, Indels: 18
0.79 0.11 0.11
Matches are distributed among these distances:
84 3 0.02
85 32 0.24
87 31 0.23
88 3 0.02
89 31 0.23
91 32 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (87 bp):
AAAAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGA
GTTGATTTGAAAAGATAGATTG
Found at i:40439687 original size:91 final size:88
Alignment explanation
Indices: 40439441--40439704 Score: 297
Period size: 91 Copynumber: 3.0 Consensus size: 88
40439431 GAAACACAGA
* * *
40439441 AATTAAAAAAAAAATAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTG
1 AATT-AAAAAAACATA-AA-TTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTG
40439506 CAATATGAGTTGA--TTTGAAAAGTAG
62 CAATATGAGTTGATTTTTGAAAAGTAG
** * * * *
40439531 AATTAGTAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGTAA
1 AATTAAAAAAACATAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAA
* *
40439594 TATAAGTTGATTTTTGGAAAGCATAG
65 TATGAGTTGATTTTTGAAAAG--TAG
40439620 -ATTGAAAAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGC
1 AATT-AAAAAAACATAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGC
40439683 AATATGAGTTGATTTTTGAAAA
63 AATATGAGTTGATTTTTGAAAA
40439705 ACAAAAATTA
Statistics
Matches: 145, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
84 3 0.02
85 32 0.22
87 23 0.16
88 5 0.03
89 34 0.23
90 4 0.03
91 41 0.28
93 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (88 bp):
AATTAAAAAAACATAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAAT
ATGAGTTGATTTTTGAAAAGTAG
Found at i:40439693 original size:176 final size:178
Alignment explanation
Indices: 40439301--40439697 Score: 500
Period size: 185 Copynumber: 2.2 Consensus size: 178
40439291 AGAAATTAAA
* *
40439301 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAAGTAGAAATTG
1 AGGCTCAACTCACCTCTTGCAATATGAGTTGA--TTTGAAAACAGAAATTGAAAAGCAGAAATTG
* * * *
40439366 AAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTTTT
64 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-----TTTTTTG
*
40439431 GAAACACAGAAATTAAAAAAAAAATAGAATTTGAAAAGACCTCAGCGTGTGGCCTG
124 GAAACACAG-AATTAAAAAAAAAATAGAATTTGAAAAGACCTCAGCATGTGGCCTG
* * *
40439487 AGACTCAACTCACCTCTTGCAATATGAGTTGATTTGAAAAGTAG-AATTAGTAAAGCAGAAATTG
1 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTGAAAA-CAGAAATT-GAAAAGCAGAAATTG
* *
40439551 AAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGTAATATAAGTTGA-TTTTTGGAAAG
64 AAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGGAAA-
* * * *
40439615 CATAG-ATTGAAAAAAACATA-AA-TTGAAAATACCTCAGCATGTGAGCC-G
128 CACAGAATTAAAAAAAAAATAGAATTTGAAAAGACCTCAGCATGTG-GCCTG
40439663 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTT
1 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTT
40439698 TTGAAAAACA
Statistics
Matches: 190, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
176 54 0.28
177 5 0.03
178 13 0.07
179 9 0.05
180 4 0.02
184 12 0.06
185 63 0.33
186 30 0.16
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (178 bp):
AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTGAAAACAGAAATTGAAAAGCAGAAATTGAA
AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGGAAACAC
AGAATTAAAAAAAAAATAGAATTTGAAAAGACCTCAGCATGTGGCCTG
Found at i:40439848 original size:123 final size:123
Alignment explanation
Indices: 40439627--40439945 Score: 539
Period size: 123 Copynumber: 2.6 Consensus size: 123
40439617 TAGATTGAAA
* * ** ** *
40439627 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACATAAACTGAAAATACCTCGGC--GTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGT
40439692 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
64 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
40439752 AAAACATAAACTGAAAATACCTTGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTGAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
40439817 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
66 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
40439875 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTGAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
40439940 ATTTTT
66 ATTTTT
40439946 TTTAAAAAAA
Statistics
Matches: 184, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 161 0.88
125 23 0.12
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (123 bp):
AAAACATAAACTGAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
Found at i:40439989 original size:195 final size:193
Alignment explanation
Indices: 40439785--40440337 Score: 975
Period size: 195 Copynumber: 2.8 Consensus size: 193
40439775 GGCGTGCCCC
40439785 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
40439850 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
40439915 AACTCATTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTT
*
40439980 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAAATT-AAAGGCTTAGC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAAC--AAAAATTAAAAGGCTTAAC
40440044 TCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCT
64 TCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCT
40440109 CAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
129 CAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
40440173 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
* *
40440238 ACCTCTCGCAATATGAGTTGATTTTTTTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAG
66 ACCTCTCGCAATATGAG-TCA----ATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAG
40440303 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
126 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
40440338 GAAAAACAAA
Statistics
Matches: 344, Mismatches: 5, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
191 7 0.02
192 29 0.08
193 76 0.22
194 18 0.05
195 134 0.39
196 7 0.02
197 69 0.20
198 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (193 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:40440055 original size:318 final size:313
Alignment explanation
Indices: 40439627--40440654 Score: 1174
Period size: 320 Copynumber: 3.2 Consensus size: 313
40439617 TAGATTGAAA
* * * ** * *
40439627 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACATAAACTAAAAATACCTCA--ACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
40439692 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAC
64 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAC
* * *
40439757 ATAAACTGAAAATACCTTGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
129 ATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
*
40439822 TGAAAAA-CAAAAAT-TAAAAG-G-CTT-A-ACTC-AC-C-TCTCGCAATATGAGTCAATTTAAA
194 TAAAAAATCAAAAATCTAAAAGTGTCTTGAGACTCAACTCTTCTCGCAATATGAGTCAATTT-AA
*** **
40439878 ACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGATT
258 A-A-AAAC--AAAA-A--T-----T---AAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
40439943 TTTTTT
308 TTTTTT
** * ** *
40439949 AAAA-A-AATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
*
40440012 A-TTTTGAAAAACAAAAAAATT-AAAGGCTTAGCTCACCTCTCGCAATATGAGTCAATTTAAAAC
66 ATTTTTGAAAAAC--AAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAC
40440075 ATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
129 ATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TT
* * * * **
40440140 TTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
192 TTTAAAAAA-TCAAAAAT--CTAAAAGTGTCTTGAGACTCAACTC--TTCTCGCAATATGAGTCA
** *
40440205 ATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTT
252 ATTTAAAAAAACAAAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT
**
40440267 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
40440332 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACAT
66 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACAT
40440397 AAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTT
131 AAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA---TTT
* * * * * *
40440462 TTAAAAAATTTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
193 TTAAAAAA--TCAAAA-ATCTAAAAGTGTCTTGAGACTCAACTC--TTCTCGCAATATGAG-TCA
* * * * *
40440527 TTTTGAAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAG-TCA----ATTT
252 ATTTAAAAAAACAAAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT
** *
40440584 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGATGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
40440649 ATTTTT
66 ATTTTT
40440655 TTAAAAAAAT
Statistics
Matches: 632, Mismatches: 48, Indels: 57
0.86 0.07 0.08
Matches are distributed among these distances:
317 84 0.13
318 174 0.28
319 15 0.02
320 178 0.28
321 70 0.11
322 64 0.10
323 1 0.00
325 4 0.01
326 2 0.00
327 3 0.00
328 2 0.00
329 7 0.01
330 2 0.00
331 5 0.01
332 1 0.00
333 1 0.00
334 19 0.03
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (313 bp):
AAAACATAAACTAAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACAT
AAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTA
AAAAATCAAAAATCTAAAAGTGTCTTGAGACTCAACTCTTCTCGCAATATGAGTCAATTTAAAAA
AACAAAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT
Found at i:40440124 original size:69 final size:68
Alignment explanation
Indices: 40440043--40440202 Score: 169
Period size: 70 Copynumber: 2.3 Consensus size: 68
40440033 AAAGGCTTAG
* **
40440043 CTCACCTCTCGCAATATGAGTCA-ATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGG
1 CTCACTTCTCGCAATATGAGTCATATTTAAAA-A-AAACTAAAAATACCTCAACGTGCCCCGAGG
40440107 CTCAA
64 CTCAA
* * * ** * **
40440112 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGAGG
1 CTCACTTCTCGCAATATGAG-TCA-TATTTAAAAAAAACTAAAAATACCTCAACGTGCCCCGAGG
40440177 CTCAA
64 CTCAA
*
40440182 CTCATTTCTCGCAATATGAGT
1 CTCACTTCTCGCAATATGAGT
40440203 TGATTTTGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
69 20 0.26
70 49 0.64
71 1 0.01
72 6 0.08
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (68 bp):
CTCACTTCTCGCAATATGAGTCATATTTAAAAAAAACTAAAAATACCTCAACGTGCCCCGAGGCT
CAA
Found at i:40440381 original size:128 final size:127
Alignment explanation
Indices: 40440104--40440460 Score: 541
Period size: 123 Copynumber: 2.9 Consensus size: 127
40440094 GCGTGCCCCG
* * ** **
40440104 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTT-AAA-A-AATTTAAAAATACCTCAAC
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACATAAACTAAAAATACCTCGGC
* ** *
40440166 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAA
66 GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAA
40440227 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACATAAACTAAAAATACCTCGG
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTAAAACATAAACTAAAAATACCTCGG
40440292 CGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAA
65 CGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAA
* *
40440355 AGGCTTAACTCACCTCTCGCAATATGAG-TCA---ATTTAAAACATAAACTAAAAATACCTCGGC
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACATAAACTAAAAATACCTCGGC
40440416 GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
66 GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
40440461 TTTAAAAAAT
Statistics
Matches: 217, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
123 104 0.48
124 7 0.03
125 3 0.01
126 1 0.00
127 53 0.24
128 49 0.23
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (127 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAACATAAACTAAAAATACCTCGGC
GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAA
Found at i:40440638 original size:69 final size:68
Alignment explanation
Indices: 40440549--40440716 Score: 176
Period size: 70 Copynumber: 2.4 Consensus size: 68
40440539 AAAAATTAAA
* * **
40440549 AGGCTTAACTCACCTCTCGCAATATGAGTCA-ATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTCATATTTAAAA-A-AAACTAAAAATACCTCAACGTG
40440613 CCCCG
64 CCCCG
* * * * *
40440618 ATGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAG-TCA-TATTTAAAAAAAACTAAAAATACCTCAACGTG
* **
40440683 TCTTG
64 CCCCG
*
40440688 AGGCTCAACTCATTTCTCGCAATATGAGT
1 AGGCTCAACTCACTTCTCGCAATATGAGT
40440717 TGATTTTCCT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
69 26 0.32
70 49 0.60
71 1 0.01
72 6 0.07
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (68 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTCATATTTAAAAAAAACTAAAAATACCTCAACGTGCC
CCG
Found at i:40440698 original size:193 final size:193
Alignment explanation
Indices: 40440227--40440723 Score: 834
Period size: 194 Copynumber: 2.6 Consensus size: 193
40440217 AAAAATTAAA
* * * **
40440227 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACATAAACTAAAAATACCTCGG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTT-AAA-A-AAATTAAAAATACCTCAA
* ** *
40440292 CGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAG
63 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAG
40440357 GCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCC
127 GCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCC
40440422 CG
192 CG
* *
40440424 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTGAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTAAAAATACCTCAACGT
40440489 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAAACAAAAATTAAAAGGCT
66 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTG-AAAAACAAAAATTAAAAGGCT
40440554 TAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
130 TAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
*
40440618 ATGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTTTAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTAAAAATACCTCAACGT
40440682 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
66 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
40440724 CCTTGGAAAG
Statistics
Matches: 285, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
193 77 0.27
194 166 0.58
195 1 0.00
196 3 0.01
197 38 0.13
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (193 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTAAAAATACCTCAACGT
GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTT
AACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCG
Found at i:40440717 original size:514 final size:510
Alignment explanation
Indices: 40439662--40440723 Score: 1921
Period size: 514 Copynumber: 2.1 Consensus size: 510
40439652 CATGTGAGCC
** *
40439662 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACT
* *
40439727 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTGAAAATACCTTGGCGTGCCCCGAGGCTC
65 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
40439792 AACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCT
130 AACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCT
*
40439857 CGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCAT
195 CGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCAC
40439922 TTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTC
260 TTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTC
*
40439987 AACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAAATTAAAGGCTTAGCTCACCTCT
325 AACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAAATTAAAGGCTTAACTCACCTCT
40440052 CGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCAC
390 CGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCAC
*
40440117 TTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
455 TTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
40440173 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
* *
40440238 ACCTCTCGCAATATGAGTTGATTTTTTTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAG
66 ACCTCTCGCAATATGAG-TCA----ATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAG
40440303 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
126 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
40440368 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
191 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
*
40440433 TCACTTCTCGCAATATGAGTTGATTTTTTTT-AAAAAATTTGAAAATACCTCAACGTGTCTTGAG
256 TCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGAG
*
40440497 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA-ACAAAAATTAAAAGGCTTAACTCA
321 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAAATT-AAAGGCTTAACTCA
*
40440561 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGATGCTCAA
385 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
40440626 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
450 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
40440687 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
40440724 CCTTGGAAAG
Statistics
Matches: 531, Mismatches: 14, Indels: 9
0.96 0.03 0.02
Matches are distributed among these distances:
510 49 0.09
511 32 0.06
513 8 0.02
514 246 0.46
515 196 0.37
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (510 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCA
ACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTC
GCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACT
TCTCGCAATATGAGTTGATTTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGAGGCTCA
ACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAAAATTAAAGGCTTAACTCACCTCTC
GCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACT
TCTCGCAATATGAGTTGATTTTTTTAAAAAAATTAAAAATACCTCAACGTGTCTT
Found at i:40452492 original size:21 final size:20
Alignment explanation
Indices: 40452440--40452492 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
40452430 AATTTTGAAG
40452440 CACGAAATTTTTTTTAAAAA
1 CACGAAATTTTTTTTAAAAA
* *
40452460 AATGAAAGTTTTTTTT-AAAA
1 CACGAAA-TTTTTTTTAAAAA
40452480 CACGAGAATTTTT
1 CACGA-AATTTTT
40452493 AAACACGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (20 bp):
CACGAAATTTTTTTTAAAAA
Found at i:40452493 original size:17 final size:17
Alignment explanation
Indices: 40452471--40452604 Score: 148
Period size: 17 Copynumber: 7.9 Consensus size: 17
40452461 ATGAAAGTTT
40452471 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
40452488 TTTTT-AAACACG-GAA
1 TTTTTAAAACACGAGAA
* * *
40452503 ATTTCAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
* *
40452521 TTTTTAAAACACGACAT
1 TTTTTAAAACACGAGAA
*
40452538 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
40452555 TTTTTAAAACACGA-AGA
1 TTTTTAAAACACGAGA-A
* *
40452572 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAGAA
40452589 TTTTTAAAAGCACGAG
1 TTTTTAAAA-CACGAG
40452605 GATTATTGAA
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.06
16 8 0.08
17 70 0.73
18 12 0.12
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:40452547 original size:34 final size:33
Alignment explanation
Indices: 40452471--40452603 Score: 169
Period size: 34 Copynumber: 3.9 Consensus size: 33
40452461 ATGAAAGTTT
*
40452471 TTTTTAAAACACGAGAATTTTT-AAACACGGAAA
1 TTTTTGAAACACGAGAATTTTTAAAACAC-GAAA
** * *
40452504 TTTCAGAAACACGAAAATTTTTAAAACACGACAT
1 TTTTTGAAACACGAGAATTTTTAAAACACGA-AA
40452538 TTTTTGAAACACGAGAATTTTTAAAACACGAAGA
1 TTTTTGAAACACGAGAATTTTTAAAACACGAA-A
*
40452572 TTTTTGAAACATGAGAATTTTTAAAAGCACGA
1 TTTTTGAAACACGAGAATTTTTAAAA-CACGA
40452604 GGATTATTGA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
33 21 0.24
34 60 0.70
35 5 0.06
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (33 bp):
TTTTTGAAACACGAGAATTTTTAAAACACGAAA
Found at i:40452953 original size:7 final size:7
Alignment explanation
Indices: 40452941--40452983 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
40452931 CTTTTTCTTC
40452941 CTTTTTT
1 CTTTTTT
40452948 CTTTTTT
1 CTTTTTT
40452955 CTTTTTT
1 CTTTTTT
*
40452962 CTTTTTC
1 CTTTTTT
40452969 CTTTTTT
1 CTTTTTT
40452976 CTTCTTTT
1 CTT-TTTT
40452984 TCTTCCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 29 0.88
8 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
CTTTTTT
Found at i:40453283 original size:3 final size:3
Alignment explanation
Indices: 40453277--40453339 Score: 72
Period size: 3 Copynumber: 19.0 Consensus size: 3
40453267 TTTCTTTTTT
40453277 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC -TTC TTC TTC TTC TT-C TTC
40453325 TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC
40453340 AAAATCGAGC
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
3 37 0.66
4 18 0.32
5 1 0.02
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:40453305 original size:22 final size:20
Alignment explanation
Indices: 40453276--40453338 Score: 92
Period size: 19 Copynumber: 3.1 Consensus size: 20
40453266 TTTTCTTTTT
40453276 TTTCTTCTTTCTTCTTCTCTC
1 TTTCTTCTTTCTTCTTCT-TC
40453297 TTTCTTTCTTTCTTCTTCTTC
1 TTTC-TTCTTTCTTCTTCTTC
*
40453318 TTCCTTC-TTCTTCTTCTTC
1 TTTCTTCTTTCTTCTTCTTC
40453337 TT
1 TT
40453339 CAAAATCGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 14 0.35
20 3 0.08
21 9 0.22
22 14 0.35
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCTTCTTTCTTCTTCTTC
Found at i:40453312 original size:25 final size:23
Alignment explanation
Indices: 40453284--40453339 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
40453274 TTTTTCTTCT
*
40453284 TTCTTCTTCTCTCTTTCTTTCTTTC
1 TTCTTCTTCT-TCCTTCTTTC-TTC
40453309 TTCTTCTTCTTCCTTC-TTCTTC
1 TTCTTCTTCTTCCTTCTTTCTTC
40453331 TTCTTCTTC
1 TTCTTCTTC
40453340 AAAATCGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 12 0.40
23 3 0.10
24 5 0.17
25 10 0.33
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (23 bp):
TTCTTCTTCTTCCTTCTTTCTTC
Found at i:40453339 original size:22 final size:24
Alignment explanation
Indices: 40453276--40453339 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
40453266 TTTTCTTTTT
*
40453276 TTTCTTCTTTCTTCTTCTCTCTTTC
1 TTTCTTC-TTCTTCTTCTCTCCTTC
40453301 TTTCTTTCTTCTTCTTCT-TCCTTC
1 TTTC-TTCTTCTTCTTCTCTCCTTC
40453325 -TTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
40453340 AAAATCGAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 12 0.32
23 3 0.08
24 5 0.14
25 14 0.38
26 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTCTTCTTCTTCTTCTCTCCTTC
Found at i:40453748 original size:30 final size:30
Alignment explanation
Indices: 40453708--40453809 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
40453698 ATTTAGGATT
*
40453708 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
40453738 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
40453768 AAAATAAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
40453798 AAAATGCAATTT
1 AAAATGAAATTT
40453810 TTATTTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:40455993 original size:33 final size:33
Alignment explanation
Indices: 40455956--40456025 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
40455946 TCACCTATTT
40455956 TTTTACTTTGAAAATATATAATTTTTGTATATG
1 TTTTACTTTGAAAATATATAATTTTTGTATATG
40455989 TTTTACTTTGAAAATATATAATTTTTGTATATG
1 TTTTACTTTGAAAATATATAATTTTTGTATATG
40456022 TTTT
1 TTTT
40456026 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (33 bp):
TTTTACTTTGAAAATATATAATTTTTGTATATG
Found at i:40456889 original size:19 final size:20
Alignment explanation
Indices: 40456856--40456974 Score: 57
Period size: 19 Copynumber: 6.5 Consensus size: 20
40456846 GAAATTGAAA
*
40456856 ATAATAATTTTTTAAAAATT
1 ATAATAATTTATTAAAAATT
*
40456876 ATAA-AATTTATTAATAATT
1 ATAATAATTTATTAAAAATT
*
40456895 A-AACCAA-TTA-T-AAAA-T
1 ATAA-TAATTTATTAAAAATT
*
40456911 ATAACTAATGTT-TGAAAAA-T
1 ATAA-TAAT-TTATTAAAAATT
* *
40456931 A-AA-AATAT-TTAAATATT
1 ATAATAATTTATTAAAAATT
40456948 ATAATAA-TTATTAAAAA-T
1 ATAATAATTTATTAAAAATT
*
40456966 ATAAAAATT
1 ATAATAATT
40456975 CTAAAATTCT
Statistics
Matches: 76, Mismatches: 11, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
16 8 0.11
17 13 0.17
18 13 0.17
19 30 0.39
20 12 0.16
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
ATAATAATTTATTAAAAATT
Found at i:40459603 original size:37 final size:37
Alignment explanation
Indices: 40459553--40459631 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40459543 TTATTACGAA
* * *
40459553 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
40459590 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
40459627 GTCTT
1 GTCTT
40459632 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:40459829 original size:47 final size:47
Alignment explanation
Indices: 40459750--40459972 Score: 313
Period size: 47 Copynumber: 4.7 Consensus size: 47
40459740 CCCTTCGGGA
* * * * * *
40459750 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40459797 CCTGTCACATATATACACTTTCACATTTATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40459844 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40459891 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40459938 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
40459973 AGAATCCTAA
Statistics
Matches: 158, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 1 0.01
47 157 0.99
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40462088 original size:19 final size:20
Alignment explanation
Indices: 40462059--40462096 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40462049 AGAGACTAAA
40462059 ATGTATAAATTTTGAAATTG
1 ATGTATAAATTTTGAAATTG
*
40462079 ATGT-TAAATTTTGTAATT
1 ATGTATAAATTTTGAAATT
40462097 ATAGATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (20 bp):
ATGTATAAATTTTGAAATTG
Found at i:40465603 original size:47 final size:47
Alignment explanation
Indices: 40465480--40465604 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 47
40465470 CGATAAGTAT
* * **
40465480 CTATACCATGGCCCGTAGCCAAATCAAGGAAACTTATCCCGGAATAC
1 CTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAATAC
* * * *
40465527 CTATACCATGGCCCTTAGCCAAATTAAGGTAACTCCTCTCAAAATAC
1 CTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAATAC
* * *
40465574 TTATATCATGGCTCGTAGCCAAATCAAGGTA
1 CTATACCATGGCCCGTAGCCAAATCAAGGTA
40465605 TTATTCGCAC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (47 bp):
CTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAATAC
Found at i:40469608 original size:23 final size:23
Alignment explanation
Indices: 40469563--40469610 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40469553 GAGTAAACCA
*
40469563 TTTTATTTTTTTATTTCATTTAG
1 TTTTATTTTTTTATTTCAATTAG
*
40469586 TTTTCTTTTTTTAATTT-AATTAG
1 TTTTATTTTTTT-ATTTCAATTAG
40469609 TT
1 TT
40469611 AAAGTTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTTATTTCAATTAG
Found at i:40474076 original size:27 final size:27
Alignment explanation
Indices: 40474046--40474116 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
40474036 ACACGTCAAG
*
40474046 AAAG-AAAGACCTTTATGGCGAACTCTA
1 AAAGAAAAG-CCTTTATGGAGAACTCTA
*
40474073 AAAGAAAAGCCTTTTTGGAGAACTCT-
1 AAAGAAAAGCCTTTATGGAGAACTCTA
** *
40474099 GGAGAAGAGCCTTTATGG
1 AAAGAAAAGCCTTTATGG
40474117 TGAATTCTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 14 0.38
27 19 0.51
28 4 0.11
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (27 bp):
AAAGAAAAGCCTTTATGGAGAACTCTA
Found at i:40474125 original size:26 final size:26
Alignment explanation
Indices: 40474050--40474125 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
40474040 GTCAAGAAAG
* **
40474050 AAAGACCTTTATGGCGAACTCTAAAAGA
1 AAAG-CCTTTATGGAGAACTCT-GGAGA
*
40474078 AAAGCCTTTTTGGAGAACTCTGGAGA
1 AAAGCCTTTATGGAGAACTCTGGAGA
* * *
40474104 AGAGCCTTTATGGTGAATTCTG
1 AAAGCCTTTATGGAGAACTCTG
40474126 TATGGACTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 21 0.52
27 15 0.38
28 4 0.10
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAGCCTTTATGGAGAACTCTGGAGA
Found at i:40474361 original size:35 final size:35
Alignment explanation
Indices: 40474269--40474353 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 35
40474259 TTCATGATGT
40474269 CACTTCGTAGAGCCAATAGATCATTTTTGTAATAC
1 CACTTCGTAGAGCCAATAGATCATTTTTGTAATAC
** * * *
40474304 TGCTCTAG-AGAGCTAATAGATCATTTTTGTGATAC
1 CACT-TCGTAGAGCCAATAGATCATTTTTGTAATAC
40474339 CACTTCGTAGAGCCA
1 CACTTCGTAGAGCCA
40474354 GTTGATCAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
34 2 0.05
35 35 0.90
36 2 0.05
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (35 bp):
CACTTCGTAGAGCCAATAGATCATTTTTGTAATAC
Found at i:40478509 original size:9 final size:9
Alignment explanation
Indices: 40478495--40478519 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40478485 TTTTATTTTC
40478495 AATTAATTA
1 AATTAATTA
40478504 AATTAATTA
1 AATTAATTA
40478513 AATTAAT
1 AATTAAT
40478520 AATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:40489963 original size:5 final size:6
Alignment explanation
Indices: 40489951--40489975 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40489941 ATAAATTTAA
40489951 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
40489976 CCTTCCTTTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:40490036 original size:14 final size:15
Alignment explanation
Indices: 40490019--40490047 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40490009 TCCTCTCCCA
40490019 TTTCTT-TTTTCTTT
1 TTTCTTCTTTTCTTT
40490033 TTTCTTCTTTTCTTT
1 TTTCTTCTTTTCTTT
40490048 CTATTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTCTTTTCTTT
Found at i:40490645 original size:63 final size:63
Alignment explanation
Indices: 40490566--40490693 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 63
40490556 TGACTTACTG
* * * * * *
40490566 TTGCTATTAGAGACCACATGGGCTAAAGACATGGGCGTGTGCCCAAG-CAATGTGACTCACTAT
1 TTGCTATTAAAAACCACATGGGATAAAGAAATAGGCGTATGCCCAAGCCAA-GTGACTCACTAT
* * *
40490629 TTGCTATTAAAAACCACATGGGATAAAGAAATAGGCGTATGTCCAGGCCGAGTGACTCACTAT
1 TTGCTATTAAAAACCACATGGGATAAAGAAATAGGCGTATGCCCAAGCCAAGTGACTCACTAT
40490692 TT
1 TT
40490694 ACAATTTAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 53 0.96
64 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (63 bp):
TTGCTATTAAAAACCACATGGGATAAAGAAATAGGCGTATGCCCAAGCCAAGTGACTCACTAT
Found at i:40490708 original size:63 final size:63
Alignment explanation
Indices: 40490572--40490709 Score: 143
Period size: 63 Copynumber: 2.2 Consensus size: 63
40490562 ACTGTTGCTA
* * * * * *
40490572 TTAGAGACCACATGGGCTAAAGACATGGGCGTGTGCCCAAGCAATGTGACTCACTATTTGCTAT
1 TTAG-GACCACATGGGATAAAGAAATAGGCGTATGCCCAAGCAATGTGACTCACTATTTACAAT
* ** * * *
40490636 TAAAAACCACATGGGATAAAGAAATAGGCGTATGTCCAGGCCGA-GTGACTCACTATTTACAAT
1 TTAGGACCACATGGGATAAAGAAATAGGCGTATGCCCAAG-CAATGTGACTCACTATTTACAAT
40490699 TTAGGACCACA
1 TTAGGACCACA
40490710 CAGGCAAATG
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
63 54 0.93
64 4 0.07
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (63 bp):
TTAGGACCACATGGGATAAAGAAATAGGCGTATGCCCAAGCAATGTGACTCACTATTTACAAT
Found at i:40512538 original size:34 final size:35
Alignment explanation
Indices: 40512492--40512560 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
40512482 GCATAGTTAA
* **
40512492 AACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGT
1 AACAGTCTTGGGCCTAAGCCCATCACAGTATCAGT
*
40512527 AACAGT-TTGGGCCTTAGCCCATCACAGTATCAGT
1 AACAGTCTTGGGCCTAAGCCCATCACAGTATCAGT
40512561 GTCAGTCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (35 bp):
AACAGTCTTGGGCCTAAGCCCATCACAGTATCAGT
Found at i:40513043 original size:18 final size:17
Alignment explanation
Indices: 40513020--40513053 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40513010 TGTGGCTTGC
40513020 CCGTGTGGGCCCACACAT
1 CCGTGT-GGCCCACACAT
*
40513038 CCGTGTTGCCCACACA
1 CCGTGTGGCCCACACA
40513054 GCCCAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (17 bp):
CCGTGTGGCCCACACAT
Found at i:40516386 original size:20 final size:20
Alignment explanation
Indices: 40516357--40516440 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
40516347 GAATTATTGC
*
40516357 ACTTATGTGCCCCTGTTTGT
1 ACTTACGTGCCCCTGTTTGT
*
40516377 ACTTACGTGCCCCTATTTGT
1 ACTTACGTGCCCCTGTTTGT
* * * *
40516397 ACTT-CGATACCCTTGATTGC
1 ACTTACG-TGCCCCTGTTTGT
*
40516417 ACTTATGTGCCCCTGTTTGT
1 ACTTACGTGCCCCTGTTTGT
40516437 ACTT
1 ACTT
40516441 CGATACCCCT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.04
20 47 0.94
21 1 0.02
ACGTcount: A:0.14, C:0.27, G:0.17, T:0.42
Consensus pattern (20 bp):
ACTTACGTGCCCCTGTTTGT
Found at i:40516436 original size:40 final size:40
Alignment explanation
Indices: 40516377--40516473 Score: 133
Period size: 40 Copynumber: 2.4 Consensus size: 40
40516367 CCCTGTTTGT
* * * *
40516377 ACTTACGTGCCCCTATTTGTACTTCGATACCCTTGATTGC
1 ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
40516417 ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
1 ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
*
40516457 A-TATCTGTGCCCCTGTT
1 ACT-TATGTGCCCCTGTT
40516474 GCACTTTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.02
40 50 0.98
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.37
Consensus pattern (40 bp):
ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
Found at i:40516449 original size:20 final size:20
Alignment explanation
Indices: 40516366--40516451 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
40516356 CACTTATGTG
*
40516366 CCCCTGTTTGTACTTACGTG
1 CCCCTGTTTGTACTTACGTA
*
40516386 CCCCTATTTGTACTT-CGATA
1 CCCCTGTTTGTACTTACG-TA
* * * * *
40516406 CCCTTGATTGCACTTATGTG
1 CCCCTGTTTGTACTTACGTA
40516426 CCCCTGTTTGTACTT-CGATA
1 CCCCTGTTTGTACTTACG-TA
40516446 CCCCTG
1 CCCCTG
40516452 AATGCATATC
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 3 0.06
20 46 0.92
21 1 0.02
ACGTcount: A:0.14, C:0.31, G:0.16, T:0.38
Consensus pattern (20 bp):
CCCCTGTTTGTACTTACGTA
Found at i:40516527 original size:20 final size:20
Alignment explanation
Indices: 40516352--40516527 Score: 55
Period size: 20 Copynumber: 9.0 Consensus size: 20
40516342 TTATTGAATT
40516352 ATTGCACTTAT-GTGCCCCTG
1 ATTGCACTT-TGGTGCCCCTG
* * **
40516372 TTTGTACTTACGTGCCCCT-
1 ATTGCACTTTGGTGCCCCTG
* * * * *
40516391 ATTTGTACTTCGATACCCTTG
1 A-TTGCACTTTGGTGCCCCTG
40516412 ATTGCACTTAT-GTGCCCCTG
1 ATTGCACTT-TGGTGCCCCTG
* * * * *
40516432 TTTGTACTTCGATACCCCTG
1 ATTGCACTTTGGTGCCCCTG
*
40516452 AATGCA-TATCT-GTGCCCCTG
1 ATTGCACT-T-TGGTGCCCCTG
* **
40516472 -TTGCACTTTGATGCCTTTG
1 ATTGCACTTTGGTGCCCCTG
* * *
40516491 ATCG-A--TTCGTGCTCCTG
1 ATTGCACTTTGGTGCCCCTG
40516508 ATTGCACTTTGGTGCCCCTG
1 ATTGCACTTTGGTGCCCCTG
40516528 TTATGCATTT
Statistics
Matches: 105, Mismatches: 38, Indels: 26
0.62 0.22 0.15
Matches are distributed among these distances:
17 10 0.10
18 2 0.02
19 13 0.12
20 79 0.75
21 1 0.01
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTGCACTTTGGTGCCCCTG
Found at i:40520444 original size:32 final size:32
Alignment explanation
Indices: 40520408--40520516 Score: 78
Period size: 32 Copynumber: 3.2 Consensus size: 32
40520398 TTACAACATA
40520408 TAAAGTTCTTATTGAAATAGATTATTGCATTT
1 TAAAGTTCTTATTGAAATAGATTATTGCATTT
* * * * *
40520440 TAAAG-T-TTATACGAGCTTATATGGTTATTTACAACTTA
1 TAAAGTTCTTAT-TGA---AATA-GATTA-TTGC-A-TTT
*
40520478 TAAAGTTCTTATTGAAATAAATTATTGCATTT
1 TAAAGTTCTTATTGAAATAGATTATTGCATTT
40520510 TAAAGTT
1 TAAAGTT
40520517 TATACGAGCT
Statistics
Matches: 56, Mismatches: 11, Indels: 20
0.64 0.13 0.23
Matches are distributed among these distances:
30 4 0.07
31 3 0.05
32 14 0.25
33 1 0.02
34 6 0.11
35 7 0.12
36 6 0.11
37 1 0.02
38 7 0.12
39 3 0.05
40 4 0.07
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (32 bp):
TAAAGTTCTTATTGAAATAGATTATTGCATTT
Found at i:40520502 original size:70 final size:70
Alignment explanation
Indices: 40520388--40520528 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
40520378 AGGCATTGAC
*
40520388 ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAGATTATTGCATTTTAAAGTTTATACG
1 ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
40520453 AGCTT
66 AGCTT
*
40520458 ATATGGTTATTTACAACTTATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
1 ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
40520523 AGCTT
66 AGCTT
40520528 A
1 A
40520529 CTAAGCATTC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (70 bp):
ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
AGCTT
Found at i:40524573 original size:18 final size:18
Alignment explanation
Indices: 40524523--40524573 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
40524513 TCTTCCAGGG
40524523 TTAGGGTTTTTA-TTTTA
1 TTAGGGTTTTTATTTTTA
**
40524540 TTAGGG-TTAGAGTTTTTA
1 TTAGGGTTTTTA-TTTTTA
40524558 TTAGGGTTTTTATTTT
1 TTAGGGTTTTTATTTT
40524574 GGGTTTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
18 15 0.56
19 3 0.11
ACGTcount: A:0.18, C:0.00, G:0.22, T:0.61
Consensus pattern (18 bp):
TTAGGGTTTTTATTTTTA
Found at i:40526251 original size:19 final size:18
Alignment explanation
Indices: 40526223--40526265 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
40526213 TTTAAAAACA
* *
40526223 AGAGACTTGAGAGGGTTTG
1 AGAGAATTGAGAGAG-TTG
40526242 AGAGAATTGAGAGAGTTG
1 AGAGAATTGAGAGAGTTG
40526260 AGAGAA
1 AGAGAA
40526266 GGATGTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.37, C:0.02, G:0.40, T:0.21
Consensus pattern (18 bp):
AGAGAATTGAGAGAGTTG
Found at i:40533555 original size:18 final size:19
Alignment explanation
Indices: 40533532--40533568 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40533522 GTTTCTTTTC
40533532 ACTTTCCCCA-TTTTTCCT
1 ACTTTCCCCACTTTTTCCT
*
40533550 ACTTTCTCCACTTTTTCCT
1 ACTTTCCCCACTTTTTCCT
40533569 TCACGTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.38, G:0.00, T:0.51
Consensus pattern (19 bp):
ACTTTCCCCACTTTTTCCT
Found at i:40536555 original size:47 final size:47
Alignment explanation
Indices: 40536492--40536880 Score: 616
Period size: 47 Copynumber: 8.3 Consensus size: 47
40536482 CCCTTCGGGA
* * * *
40536492 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40536539 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40536586 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40536633 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40536680 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40536727 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40536774 CTTATCACATATATACAGTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40536821 CTTGTCACATATATACAATTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40536868 CTTATCACATATA
1 CTTATCACATATA
40536881 CATATCTTGT
Statistics
Matches: 317, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 317 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.