Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 24 of 438
Found at i:6187430 original size:17 final size:17
Alignment explanation
Indices: 6187408--6187442 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6187398 TTGATATGAT
6187408 ACTAAAAT-TATTAAAAA
1 ACTAAAATATA-TAAAAA
6187425 ACTAAAATATATAAAAA
1 ACTAAAATATATAAAAA
6187442 A
1 A
6187443 AATCAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ACTAAAATATATAAAAA
Found at i:6187443 original size:18 final size:17
Alignment explanation
Indices: 6187408--6187443 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6187398 TTGATATGAT
*
6187408 ACTAAAATTATTAAAAA
1 ACTAAAATTATAAAAAA
6187425 ACTAAAATATATAAAAAA
1 ACTAAAAT-TATAAAAAA
6187443 A
1 A
6187444 ATCAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
ACTAAAATTATAAAAAA
Found at i:6187734 original size:22 final size:21
Alignment explanation
Indices: 6187699--6187774 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
6187689 AAAAGGTATC
* *
6187699 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
6187720 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
6187743 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
6187762 TGC-AATCATATCT
1 TACAAATCATATCT
6187775 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:6187759 original size:19 final size:19
Alignment explanation
Indices: 6187735--6187825 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
6187725 AATCATATCT
6187735 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
6187754 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
6187772 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
6187789 TCTAAGATTTCATATCATA
1 TCTAAGATTGCATATCATA
6187808 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
6187826 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 16 0.24
19 36 0.54
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:6190774 original size:19 final size:19
Alignment explanation
Indices: 6190750--6190795 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
6190740 AATGCCTCTT
6190750 TTTGCATT-CATTTCATTCA
1 TTTGCATTGCATTTCA-TCA
6190769 TTTGCATTGCATTTCATCA
1 TTTGCATTGCATTTCATCA
*
6190788 TATGCATT
1 TTTGCATT
6190796 AAATTTCACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.50
Consensus pattern (19 bp):
TTTGCATTGCATTTCATCA
Found at i:6190801 original size:19 final size:20
Alignment explanation
Indices: 6190759--6190803 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
6190749 TTTTGCATTC
* **
6190759 ATTTCATTCATTTGCATTGC
1 ATTTCATTCATATGCATTAA
6190779 ATTTCA-TCATATGCATTAA
1 ATTTCATTCATATGCATTAA
6190798 ATTTCA
1 ATTTCA
6190804 CGAAAGGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTTCATTCATATGCATTAA
Found at i:6190956 original size:24 final size:24
Alignment explanation
Indices: 6190928--6190979 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
6190918 TAGAAAGATT
*
6190928 AGAACAGATGTAAA-AGAAAATGCA
1 AGAACAGATGCAAACA-AAAATGCA
*
6190952 AGAACAGATGCAAACACAAATGCA
1 AGAACAGATGCAAACAAAAATGCA
6190976 AGAA
1 AGAA
6190980 TTGTTGGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.58, C:0.13, G:0.19, T:0.10
Consensus pattern (24 bp):
AGAACAGATGCAAACAAAAATGCA
Found at i:6191268 original size:82 final size:82
Alignment explanation
Indices: 6191114--6191278 Score: 208
Period size: 82 Copynumber: 2.0 Consensus size: 82
6191104 GGAATGACAA
* * *
6191114 TGAAGATCCTCTCTACCCCTTGGTTTCACCCCGGCAAATGCTCAAACGCAATACGAGATGTACAC
1 TGAAGATCCTCTCTACCCCTTGGTTTCACCCCGACAAATGCTCAAACGCAACACGAGACGTACAC
*
6191179 GCAAAGGCCATCCGTTAC
66 G-AAAGGCCATCCATTAC
* * *
6191197 TGAAGATCCTCTCTACCCC-TGGTTTCACCCCGATAAATGCTCAAATGCAACCCGAGACGCATAC
1 TGAAGATCCTCTCTACCCCTTGGTTTCACCCCGACAAATGCTCAAACGCAACACGAGACG--TAC
* *
6191261 ATG-AAGGCCGTCCATTAC
64 ACGAAAGGCCATCCATTAC
6191279 AATCAGGCCC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
82 47 0.66
83 19 0.27
84 5 0.07
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.22
Consensus pattern (82 bp):
TGAAGATCCTCTCTACCCCTTGGTTTCACCCCGACAAATGCTCAAACGCAACACGAGACGTACAC
GAAAGGCCATCCATTAC
Found at i:6222271 original size:18 final size:17
Alignment explanation
Indices: 6222248--6222288 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
6222238 TTTTGTGACT
6222248 AAAAAAG-AGAGAGAGAGA
1 AAAAAAGAAGA-AGA-AGA
6222266 AAAAAAGAAGAAGAAGA
1 AAAAAAGAAGAAGAAGA
6222283 AAAAAA
1 AAAAAA
6222289 TGGAGAGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 10 0.45
19 3 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAGAAGAAGA
Found at i:6223605 original size:133 final size:133
Alignment explanation
Indices: 6223118--6223703 Score: 698
Period size: 132 Copynumber: 4.4 Consensus size: 133
6223108 GTGAATTCAC
* * * * *
6223118 AGATCTTATCTCTATGAGGCAGCAA-GGAACAGATCGAAGATGACAAATCTTATCT-TTCTGAGG
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGACAAATCTTATCTCCT-TGAGG
* * * *
6223181 TAGCAAATGAGCAGATTCAAGCCACTAGCCTTGTCTCACTGAGTAGGAGTGGAGCAGGCTGAAGA
65 CAGCAAAGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGTAGGAGTGGAGCAGGCTAAAGA
6223246 TT-T
130 TTGT
* * * *** * * * *
6223249 AGATCTTATCTCCATAAGGTAGCAATAGAGCAGATTGAAGACGGTGAATCTTATCTCCGTAAAGT
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGACAAATCTTATCTCCTTGAGGC
* * *
6223314 AGCAAAGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGCAGGAATAGAGCAGGCTAAAGA-
66 AGCAAAGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGTAGGAGTGGAGCAGGCTAAAGAT
*
6223378 TAT
131 TGT
* * * *
6223381 AGACCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGGCGAATCTTATCTCCCTGAGGC
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGACAAATCTTATCTCCTTGAGGC
* **
6223446 AGCAAAAAGAGCAGATTCAAGCCACTAGCCTTGTCTCTTTGAGTAGGAGTGGAGCAGGCTAAAGA
66 AGC-AAAGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGTAGGAGTGGAGCAGGCTAAAGA
6223511 TTGT
130 TTGT
* * *
6223515 AGATCTTATCTCCATGAGGTAGTAATGGAGCAGATCGAAGATGACAAATCTTATCTTCTTGAGGC
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGACAAATCTTATCTCCTTGAGGC
* * * * *
6223580 AGCAAGGGAACAGAGTCAAGCCACTAGCCTTGTCTCCCTGAGTAGGAGTGGAGCAAGCTGAAGAT
66 AGCAAAGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGTAGGAGTGGAGCAGGCTAAAGAT
6223645 TGT
131 TGT
* * * * * * * *
6223648 AGATCTTATCTCCCT-AAGTAGCAGTAGAGTAGATTGAAG-CCACAAGTCTTATCTCC
1 AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGACAAATCTTATCTCC
6223704 CTGAAGTTGC
Statistics
Matches: 388, Mismatches: 62, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
131 36 0.09
132 163 0.42
133 126 0.32
134 63 0.16
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (133 bp):
AGATCTTATCTCCATGAGGTAGCAATGGAGCAGATCGAAGACGACAAATCTTATCTCCTTGAGGC
AGCAAAGGAGCAGATTCAAGCCACTAGCCTTGTCTCCCTGAGTAGGAGTGGAGCAGGCTAAAGAT
TGT
Found at i:6223822 original size:176 final size:176
Alignment explanation
Indices: 6223607--6223972 Score: 552
Period size: 176 Copynumber: 2.1 Consensus size: 176
6223597 AAGCCACTAG
* * *
6223607 CCTTGTCTCCCTGAGTAGGAGTGGAGCAAGCTGAAGATTGTAGATCTTATCTCCCTAAGTAGCAG
1 CCTTGTCTCCCTGAGCAAGAGTGGAGCAAGCTAAAGATTGTAGATCTTATCTCCCTAAGTAGCAG
* * *
6223672 TAGAGTAGATTGAAGCCACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGAAGATCGAAGCCCCAA
66 TAGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGAAGATCGAAGCCACAA
* *
6223737 TCCTTATCTCTATGAAGTTGCAGTAGAGCAGGATAAAAGTTACAAA
131 TCCTTATCTCTATAAAGTTGCAGTAGAGCAGGATAAAAGTCACAAA
* *
6223783 CCTTGTCTCCCTGAGCAAGAGTGGAGCAGGCTAAAGATTGTAGATCTTATCTCCCTAAGTAGTAG
1 CCTTGTCTCCCTGAGCAAGAGTGGAGCAAGCTAAAGATTGTAGATCTTATCTCCCTAAGTAGCAG
* ** *
6223848 TGGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCTGATCGAAGTCACAA
66 TAGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGAAGATCGAAGCCACAA
* ** *
6223913 TCCTTATCTCTCTAAAGTTGTTGTAGAGCAGGATAAAAGTCATAAA
131 TCCTTATCTCTATAAAGTTGCAGTAGAGCAGGATAAAAGTCACAAA
* *
6223959 CCTTATTTCCCTGA
1 CCTTGTCTCCCTGA
6223973 AGTTGCAGTG
Statistics
Matches: 170, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
176 170 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (176 bp):
CCTTGTCTCCCTGAGCAAGAGTGGAGCAAGCTAAAGATTGTAGATCTTATCTCCCTAAGTAGCAG
TAGAGCAGATTGAAGCCACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGAAGATCGAAGCCACAA
TCCTTATCTCTATAAAGTTGCAGTAGAGCAGGATAAAAGTCACAAA
Found at i:6223894 original size:44 final size:43
Alignment explanation
Indices: 6223651--6223987 Score: 167
Period size: 44 Copynumber: 7.7 Consensus size: 43
6223641 AGATTGTAGA
* * *
6223651 TCTTATCTCCCTAAGTAGCAGTAGAGTAGATTGAAGCCACAAG
1 TCTTATCTCCCTAAGTTGCAGTGGAGCAGATTGAAGCCACAAG
* * *
6223694 TCTTATCTCCCTGAAGTTGCAGTGGAGAAGATCGAAGCCCCAA-
1 TCTTATCTCCCT-AAGTTGCAGTGGAGCAGATTGAAGCCACAAG
** * ** ** *
6223737 TCCTTATCTCTATGAAGTTGCAGTAGAGCAGGATAAAAGTTACAAA
1 T-CTTATCTCCCT-AAGTTGCAGTGGAGCA-GATTGAAGCCACAAG
* * * ** ** * *****
6223783 CCTTGTCTCCCTGAGCAAG-AGTGGAGCAGGCTAAAGATTGTAG
1 TCTTATCTCCCTAAG-TTGCAGTGGAGCAGATTGAAGCCACAAG
* *
6223826 ATCTTATCTCCCTAAGTAGTAGTGGAGCAGATTGAAGCCACAAG
1 -TCTTATCTCCCTAAGTTGCAGTGGAGCAGATTGAAGCCACAAG
* * *
6223870 TCTTATCTCCCTAAAGTTGCAGTGGAGCTGATCGAAGTCACAA-
1 TCTTATCTCCCT-AAGTTGCAGTGGAGCAGATTGAAGCCACAAG
* ** * ** * * *
6223913 TCCTTATCTCTCTAAAGTTGTTGTAGAGCAGGATAAAAGTCATAAA
1 T-CTTATCTCCCT-AAGTTGCAGTGGAGCA-GATTGAAGCCACAAG
* *
6223959 CCTTATTTCCCTGAAGTTGCAGTGGAGCA
1 TCTTATCTCCCT-AAGTTGCAGTGGAGCA
6223988 AGTTGAAATT
Statistics
Matches: 221, Mismatches: 62, Indels: 20
0.73 0.20 0.07
Matches are distributed among these distances:
43 35 0.16
44 135 0.61
45 51 0.23
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTAAGTTGCAGTGGAGCAGATTGAAGCCACAAG
Found at i:6225851 original size:26 final size:26
Alignment explanation
Indices: 6225798--6225959 Score: 141
Period size: 26 Copynumber: 6.2 Consensus size: 26
6225788 AAAATAGTTT
* * ** *
6225798 TATTACTTACTTTAAATTGTCATATA
1 TATTATTTATTTTAAATTGTTTTGTA
*
6225824 TATCATTTATTTTAAATTGTTTTGTA
1 TATTATTTATTTTAAATTGTTTTGTA
*
6225850 TATTATTTATTTTAAATTATTTTGTA
1 TATTATTTATTTTAAATTGTTTTGTA
* *
6225876 TATTGTTTATTTCAAATTGTTTAT-TACA
1 TATTATTTATTTTAAATTGTTT-TGT--A
*
6225904 TATTATTTATTTTAAATT-ATTT-TA
1 TATTATTTATTTTAAATTGTTTTGTA
* * * **
6225928 CATTATTTACTTTAAGTTGTTTTACA
1 TATTATTTATTTTAAATTGTTTTGTA
6225954 TATTAT
1 TATTAT
6225960 CTTGTTCCAT
Statistics
Matches: 111, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
24 16 0.14
25 3 0.03
26 72 0.65
27 3 0.03
28 17 0.15
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (26 bp):
TATTATTTATTTTAAATTGTTTTGTA
Found at i:6225870 original size:14 final size:14
Alignment explanation
Indices: 6225828--6225925 Score: 69
Period size: 14 Copynumber: 7.3 Consensus size: 14
6225818 CATATATATC
6225828 ATTTATTTTAAATT
1 ATTTATTTTAAATT
* * *
6225842 -GTT-TTGTATATT
1 ATTTATTTTAAATT
6225854 ATTTATTTTAAATT
1 ATTTATTTTAAATT
* *
6225868 A-TT-TTGTATATT
1 ATTTATTTTAAATT
* *
6225880 GTTTATTTCAAATT
1 ATTTATTTTAAATT
* ** *
6225894 GTTTATTACATATT
1 ATTTATTTTAAATT
6225908 ATTTATTTTAAATT
1 ATTTATTTTAAATT
6225922 ATTT
1 ATTT
6225926 TACATTATTT
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
12 14 0.23
13 8 0.13
14 40 0.65
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (14 bp):
ATTTATTTTAAATT
Found at i:6227634 original size:23 final size:23
Alignment explanation
Indices: 6227608--6227670 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
6227598 AATGTCAACT
*
6227608 TTTAACAAAGTTAACATTTACTG
1 TTTAACAAAGTTAATATTTACTG
* *
6227631 TTT-A-AAAGATATTATTTACTG
1 TTTAACAAAGTTAATATTTACTG
*
6227652 TTTAACAATGTTAATATTT
1 TTTAACAAAGTTAATATTT
6227671 CAAAAAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.53
22 2 0.06
23 13 0.41
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (23 bp):
TTTAACAAAGTTAATATTTACTG
Found at i:6227824 original size:19 final size:20
Alignment explanation
Indices: 6227800--6227842 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6227790 TATTTAATTC
6227800 TTTTTAATAA-TA-TAAAAAG
1 TTTTT-ATAACTATTAAAAAG
*
6227819 TTTTTATAACTATTTAAAAG
1 TTTTTATAACTATTAAAAAG
6227839 TTTT
1 TTTT
6227843 CATTTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 7 0.33
20 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTTTATAACTATTAAAAAG
Found at i:6229977 original size:31 final size:30
Alignment explanation
Indices: 6229920--6229978 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
6229910 GTAAATACTC
* * * *
6229920 AAAATTTGATGGATTAAAGTGTAAATATGA
1 AAAACTTGAAGGACTAAAGTGCAAATATGA
6229950 AAAACTTGAAGGACTAATAGTGCAAATAT
1 AAAACTTGAAGGACTAA-AGTGCAAATAT
6229979 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAACTTGAAGGACTAAAGTGCAAATATGA
Found at i:6230237 original size:29 final size:31
Alignment explanation
Indices: 6230189--6230252 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
6230179 TTTATAGTTA
*
6230189 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
6230220 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
6230249 TTTA
1 TTTA
6230253 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:6230241 original size:8 final size:8
Alignment explanation
Indices: 6230230--6230254 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6230220 TTTAATAAGA
6230230 TATTTTAT
1 TATTTTAT
6230238 TATTTTAT
1 TATTTTAT
6230246 TATTTTAT
1 TATTTTAT
6230254 T
1 T
6230255 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:6234683 original size:14 final size:15
Alignment explanation
Indices: 6234650--6234682 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
6234640 TGAATAGTTC
6234650 TTTTCTCTTAATCAT
1 TTTTCTCTTAATCAT
6234665 TTTTCTCTTAATCAT
1 TTTTCTCTTAATCAT
6234680 TTT
1 TTT
6234683 CAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTCTCTTAATCAT
Found at i:6235739 original size:18 final size:18
Alignment explanation
Indices: 6235679--6235757 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
6235669 TTAAAATCAT
* *
6235679 TAAAATTGTAAAAAAATA
1 TAAAATTATAAAAAATTA
*
6235697 TAAAATTTTATAAAAATTCA
1 TAAAATTATA-AAAAATT-A
6235717 TAAAAAATTAT--AAAATTA
1 T--AAAATTATAAAAAATTA
*
6235735 TAAAATTACAAAAACA-TA
1 TAAAATTATAAAAA-ATTA
6235753 TAAAA
1 TAAAA
6235758 GTGAAAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
16 7 0.14
18 21 0.42
19 13 0.26
20 2 0.04
22 7 0.14
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (18 bp):
TAAAATTATAAAAAATTA
Found at i:6238036 original size:25 final size:25
Alignment explanation
Indices: 6238008--6238058 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6237998 AATTTATAAC
6238008 GAATGTTTCAAAATATGCCCAATTG
1 GAATGTTTCAAAATATGCCCAATTG
6238033 GAATGTTTCAAAATATGCCCAATTG
1 GAATGTTTCAAAATATGCCCAATTG
6238058 G
1 G
6238059 CTAACTGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (25 bp):
GAATGTTTCAAAATATGCCCAATTG
Found at i:6239934 original size:29 final size:29
Alignment explanation
Indices: 6239892--6239951 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6239882 AATATCCAGC
*
6239892 ACTTTAATCCAAAATCAAGTTAAAAACTA
1 ACTTAAATCCAAAATCAAGTTAAAAACTA
6239921 ACTTAAATCCAAAATCAAGTTAAAAACTA
1 ACTTAAATCCAAAATCAAGTTAAAAACTA
6239950 AC
1 AC
6239952 AGTCCAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.25
Consensus pattern (29 bp):
ACTTAAATCCAAAATCAAGTTAAAAACTA
Found at i:6247756 original size:23 final size:23
Alignment explanation
Indices: 6247726--6247829 Score: 81
Period size: 23 Copynumber: 4.6 Consensus size: 23
6247716 TCAACTCGTA
6247726 AGAGCTTACTATTTCAGCTCATT
1 AGAGCTTACTATTTCAGCTCATT
**
6247749 AGAGCTTACCGTTTCAGCT--TGT
1 AGAGCTTACTATTTCAGCTCAT-T
* * *
6247771 ATGAGTTTACTA-ATAAGCTCGA-T
1 A-GAGCTTACTATTTCAGCTC-ATT
** *
6247794 AGAGCTTACCGTTTCAGCTCAAT
1 AGAGCTTACTATTTCAGCTCATT
6247817 AGAGCTTACTATT
1 AGAGCTTACTATT
6247830 CATTAGCTCA
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
21 1 0.02
22 15 0.25
23 44 0.73
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (23 bp):
AGAGCTTACTATTTCAGCTCATT
Found at i:6247826 original size:45 final size:45
Alignment explanation
Indices: 6247726--6247853 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
6247716 TCAACTCGTA
* * **
6247726 AGAGCTTACTATTTCAGCTCATTAGAGCTTACCGTTTCAGCTTGT
1 AGAGCTTACTATATAAGCTCATTAGAGCTTACCGTTTCAGCTAAT
*
6247771 ATGAGTTTACTA-ATAAGCTCGA-TAGAGCTTACCGTTTCAGCTCAAT
1 A-GAGCTTACTATATAAGCTC-ATTAGAGCTTACCGTTTCAGCT-AAT
* *
6247817 AGAGCTTACTATTCATTAGCTCATAAGGAGCTTACCG
1 AGAGCTTACTA-T-ATAAGCTCATTA-GAGCTTACCG
6247854 ACCATAGCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
45 36 0.54
46 12 0.18
47 1 0.01
48 8 0.12
49 10 0.15
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (45 bp):
AGAGCTTACTATATAAGCTCATTAGAGCTTACCGTTTCAGCTAAT
Found at i:6256233 original size:3 final size:3
Alignment explanation
Indices: 6256225--6256263 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6256215 AAAAGAAAAT
6256225 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6256264 GGTTTAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6259768 original size:38 final size:38
Alignment explanation
Indices: 6259720--6259852 Score: 203
Period size: 38 Copynumber: 3.5 Consensus size: 38
6259710 GGCTCAAAGG
* * * *
6259720 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
6259758 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
* *
6259796 CCCGGATATATTACCAGCACGAAGCCTACGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
*
6259834 CCCGGATATAATTCCAGCA
1 CCCGGATATAATACCAGCA
6259853 TATAGCCCGC
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 87 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTACGGGATTTAA
Found at i:6266836 original size:33 final size:33
Alignment explanation
Indices: 6266715--6266835 Score: 143
Period size: 33 Copynumber: 3.7 Consensus size: 33
6266705 AGTTTGCATG
* * *
6266715 CATATAGGCTCACATAATCCTAGGGTTCGCATA
1 CATACAGGCTCGCATAATCCTAGGGTTCACATA
* *
6266748 CATACAGGCTCGCATAATTCTAGGGTTCACATG
1 CATACAGGCTCGCATAATCCTAGGGTTCACATA
* * * *
6266781 CATACAAGCTCACATAATCCTATGGTTCATATA
1 CATACAGGCTCGCATAATCCTAGGGTTCACATA
* *
6266814 CATCCAGGCTTGCATAATCCTA
1 CATACAGGCTCGCATAATCCTA
6266836 TATGATTTTA
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (33 bp):
CATACAGGCTCGCATAATCCTAGGGTTCACATA
Found at i:6268177 original size:26 final size:27
Alignment explanation
Indices: 6268147--6268202 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
6268137 TGATTTGTAA
*
6268147 TAAA-TTTTTTTTCTCTCCTATTTTGT
1 TAAATTTTTTTTTCTCTCCCATTTTGT
6268173 TAAATTTTTTTTTCTCTCCCATTTTGT
1 TAAATTTTTTTTTCTCTCCCATTTTGT
6268200 TAA
1 TAA
6268203 CAAACTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.62
Consensus pattern (27 bp):
TAAATTTTTTTTTCTCTCCCATTTTGT
Found at i:6268898 original size:18 final size:18
Alignment explanation
Indices: 6268877--6268936 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
6268867 CTTTTTGCAC
*
6268877 TTTTATATTTTTTTTAAT
1 TTTTATATTTTTTATAAT
6268895 TTTTA-ATATTTTTATAAT
1 TTTTATAT-TTTTTATAAT
*
6268913 CTTTTATGATTTTCTATAAT
1 -TTTTAT-ATTTTTTATAAT
6268933 TTTT
1 TTTT
6268937 TATACTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.06
18 14 0.39
19 9 0.25
20 9 0.25
21 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTATATTTTTTATAAT
Found at i:6268918 original size:10 final size:9
Alignment explanation
Indices: 6268877--6268936 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
6268867 CTTTTTGCAC
*
6268877 TTTTATATT
1 TTTTATAAT
*
6268886 TTTTTTAAT
1 TTTTATAAT
6268895 TTTTA-ATAT
1 TTTTATA-AT
6268904 TTTTATAAT
1 TTTTATAAT
*
6268913 CTTTTATGAT
1 -TTTTATAAT
6268923 TTTCTATAAT
1 TTT-TATAAT
6268933 TTTT
1 TTTT
6268937 TATACTTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 1 0.02
9 24 0.57
10 17 0.40
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTTATAAT
Found at i:6268940 original size:10 final size:10
Alignment explanation
Indices: 6268877--6268940 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
6268867 CTTTTTGCAC
6268877 TTTTAT-ATT
1 TTTTATAATT
*
6268886 TTTTTTAATT
1 TTTTATAATT
*
6268896 TTTAAT-A-T
1 TTTTATAATT
*
6268904 TTTTATAATC
1 TTTTATAATT
*
6268914 TTTTATGATT
1 TTTTATAATT
*
6268924 TTCTATAATT
1 TTTTATAATT
6268934 TTTTATA
1 TTTTATA
6268941 CTTCTTTTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
8 6 0.14
9 7 0.17
10 29 0.69
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:6268945 original size:18 final size:18
Alignment explanation
Indices: 6268877--6268945 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
6268867 CTTTTTGCAC
* *
6268877 TTTTATATTTTTTTTAATT
1 TTTTATA-TTTCTATAATT
* * *
6268896 TTTAATATTTTTATAATC
1 TTTTATATTTCTATAATT
6268914 TTTTATGATTTTCTATAATT
1 TTTTAT-A-TTTCTATAATT
*
6268934 TTTTATACTTCT
1 TTTTATATTTCT
6268946 TTTTAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
18 18 0.44
19 8 0.20
20 15 0.37
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTATATTTCTATAATT
Found at i:6269145 original size:21 final size:20
Alignment explanation
Indices: 6269108--6269146 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6269098 TTTAAACTTT
*
6269108 TTTTTTGTAATTTTATATAA
1 TTTTTTGCAATTTTATATAA
*
6269128 TTTTTTGCACTTTCTATAT
1 TTTTTTGCAATTT-TATAT
6269147 TTTTATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTTGCAATTTTATATAA
Found at i:6269236 original size:25 final size:25
Alignment explanation
Indices: 6269192--6269248 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
6269182 AAATTTCATA
*
6269192 TTTTTTAATTCATACCATTTTTA-AT
1 TTTTTTAATTCATA-CATTTATATAT
6269217 TTTTTTAATTTTCATA-ATTTATATAT
1 TTTTTTAA--TTCATACATTTATATAT
6269243 TTTTTT
1 TTTTTT
6269249 CTCATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 14 0.50
26 8 0.29
27 6 0.21
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTTAATTCATACATTTATATAT
Found at i:6269321 original size:18 final size:18
Alignment explanation
Indices: 6269295--6269351 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
6269285 TATATTATTC
*
6269295 TTTTGTAATTTTTAATAT
1 TTTTATAATTTTTAATAT
*
6269313 TTTTATAATATTTAATAGT
1 TTTTATAATTTTTAATA-T
* *
6269332 TTTTAATTATTTTAAATAT
1 TTTT-ATAATTTTTAATAT
6269351 T
1 T
6269352 AAACTCTAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.47
19 7 0.22
20 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTAATAT
Found at i:6270453 original size:51 final size:51
Alignment explanation
Indices: 6270378--6270480 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
6270368 CTCCTTTTTC
*
6270378 TCTTCTTTTTTGACGTTTTTGTTTTGACTAAATTATTTGTGTAATCACTAT
1 TCTTCTTTTTTGACGTTTTTGTTTTGACTAAATTATTTGGGTAATCACTAT
*
6270429 TCTTCTTTTTTGACGTTTTTGTTTTGAGTAAATTATTTGGGTAATCACTAT
1 TCTTCTTTTTTGACGTTTTTGTTTTGACTAAATTATTTGGGTAATCACTAT
6270480 T
1 T
6270481 GTACAAAAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (51 bp):
TCTTCTTTTTTGACGTTTTTGTTTTGACTAAATTATTTGGGTAATCACTAT
Found at i:6271076 original size:25 final size:23
Alignment explanation
Indices: 6271048--6271093 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
6271038 ATTAATACTA
*
6271048 ATATTTATATTAATTAAAAATAAGT
1 ATATTAATATTAA--AAAAATAAGT
6271073 ATATTAATATTAAAAAAATAA
1 ATATTAATATTAAAAAAATAA
6271094 AAATATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATTAATATTAAAAAAATAAGT
Found at i:6273710 original size:16 final size:16
Alignment explanation
Indices: 6273685--6273723 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
6273675 GTTATGAAAA
6273685 TTTTAAATTTGA-ATAT
1 TTTTAAATTT-ATATAT
*
6273701 TTTTATATTTATATAT
1 TTTTAAATTTATATAT
6273717 TTTTAAA
1 TTTTAAA
6273724 ATAACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTATATAT
Found at i:6273875 original size:29 final size:29
Alignment explanation
Indices: 6273843--6273902 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6273833 TTGGCTCAAA
*
6273843 GTAAGGTTAATAATATTACATGTGCAACT
1 GTAAAGTTAATAATATTACATGTGCAACT
6273872 GTAAAGTTAATAATATTACATGTGCAACT
1 GTAAAGTTAATAATATTACATGTGCAACT
6273901 GT
1 GT
6273903 GTTAATAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (29 bp):
GTAAAGTTAATAATATTACATGTGCAACT
Found at i:6273906 original size:26 final size:27
Alignment explanation
Indices: 6273848--6273910 Score: 101
Period size: 29 Copynumber: 2.3 Consensus size: 27
6273838 TCAAAGTAAG
6273848 GTTAATAATATTACATGTGCAACTGTAAA
1 GTTAATAATATTACATGTGCAACTGT--A
6273877 GTTAATAATATTACATGTGCAACTGT-
1 GTTAATAATATTACATGTGCAACTGTA
6273903 GTTAATAA
1 GTTAATAA
6273911 ACATGTGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 8 0.24
29 26 0.76
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (27 bp):
GTTAATAATATTACATGTGCAACTGTA
Found at i:6281529 original size:14 final size:14
Alignment explanation
Indices: 6281494--6281521 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6281484 TATAAAATTA
6281494 AAATTTATTTTTAT
1 AAATTTATTTTTAT
6281508 AAATTTATTTTTAT
1 AAATTTATTTTTAT
6281522 CTTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AAATTTATTTTTAT
Found at i:6281836 original size:26 final size:26
Alignment explanation
Indices: 6281806--6281857 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
6281796 GTGAAATGTA
* * *
6281806 AAAATTTTATTACATGACGTGGGCTC
1 AAAATATTATTAAATGACATGGGCTC
6281832 AAAATATTATTAAATGACATGGGCTC
1 AAAATATTATTAAATGACATGGGCTC
6281858 CGCAACTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (26 bp):
AAAATATTATTAAATGACATGGGCTC
Found at i:6283510 original size:16 final size:17
Alignment explanation
Indices: 6283479--6283512 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6283469 GTCCTCAAAA
6283479 TTATTATTTTAGAATTT
1 TTATTATTTTAGAATTT
*
6283496 TTATTTTTTTA-AATTT
1 TTATTATTTTAGAATTT
6283512 T
1 T
6283513 CATATATTCC
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTATTATTTTAGAATTT
Found at i:6286130 original size:28 final size:27
Alignment explanation
Indices: 6286078--6286190 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 27
6286068 CTATTCAGAA
* *
6286078 ATCAGTGTTAA-CTAGGCCTTAGCCCAT
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
*
6286105 ATCAGTATTAATCTGGGCCATAGCCCCT
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
*
6286133 -TACAGTAATAGAGTATACTGGGCCTAGCCCAT
1 AT-CAGT-AT-TA--AT-CTGGGCCTAGCCCAT
*
6286165 ATCAGTATCAATCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCC-TAGCCC
6286191 TATTACAAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
27 18 0.26
28 25 0.36
29 2 0.03
30 2 0.03
31 2 0.03
32 13 0.19
33 8 0.11
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (27 bp):
ATCAGTATTAATCTGGGCCTAGCCCAT
Found at i:6286215 original size:60 final size:60
Alignment explanation
Indices: 6286092--6286226 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
6286082 GTGTTAACTA
* * *
6286092 GGCCTTAGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTAATAGAGTATACTG
1 GGCC-TAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTAAGAGAGTATACTG
* * *
6286153 GGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-CGAGA-TATATTG
1 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTAAGAGAGTATACTG
*
6286213 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
6286227 TAACATAGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
60 51 0.78
61 11 0.17
62 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (60 bp):
GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTAAGAGAGTATACTG
Found at i:6288435 original size:19 final size:18
Alignment explanation
Indices: 6288398--6288441 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
6288388 ATACATACAG
6288398 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
6288415 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
6288434 TACTAATT
1 TAATAATT
6288442 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:6290403 original size:28 final size:27
Alignment explanation
Indices: 6290367--6290465 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 27
6290357 GTGTTAACTA
* *
6290367 GGCCTTAGCCCATATTAGTATTAATCTG
1 GGCC-TAGCCCATATCAGTATCAATCTG
* *
6290395 GGCCATAGCCCCT-TACAGTAATAGAGTATACTG
1 GGCC-TAGCCCATAT-CAGT-AT-CA--AT-CTG
6290428 GGCCTAGCCCATATCAGTATCAATCTG
1 GGCCTAGCCCATATCAGTATCAATCTG
6290455 GGCCGTAGCCC
1 GGCC-TAGCCC
6290466 TATTACAAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
27 8 0.14
28 22 0.39
29 2 0.04
30 2 0.04
31 2 0.04
32 13 0.23
33 8 0.14
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (27 bp):
GGCCTAGCCCATATCAGTATCAATCTG
Found at i:6290490 original size:60 final size:60
Alignment explanation
Indices: 6290367--6290501 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
6290357 GTGTTAACTA
* * * *
6290367 GGCCTTAGCCCATATTAGTATTAATCTGGGCCATAGCCCCTTACAGTAATAGAGTATACTG
1 GGCC-TAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTAAGAGAGTATACTG
* * *
6290428 GGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-CGAGA-TATATTG
1 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTAAGAGAGTATACTG
*
6290488 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
6290502 TAACATAGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
60 50 0.78
61 11 0.17
62 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (60 bp):
GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTAAGAGAGTATACTG
Found at i:6290603 original size:22 final size:22
Alignment explanation
Indices: 6290575--6290616 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6290565 CATGATAACC
6290575 CCATCCAACCCTACACTTCCCT
1 CCATCCAACCCTACACTTCCCT
*
6290597 CCATCCATCCCTACACTTCC
1 CCATCCAACCCTACACTTCC
6290617 TGTGGGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.55, G:0.00, T:0.24
Consensus pattern (22 bp):
CCATCCAACCCTACACTTCCCT
Found at i:6292717 original size:19 final size:18
Alignment explanation
Indices: 6292680--6292723 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
6292670 ATACATACAG
6292680 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
6292697 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
6292716 TACTAATT
1 TAATAATT
6292724 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:6293036 original size:3 final size:3
Alignment explanation
Indices: 6293030--6293060 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6293020 AAACATATAC
*
6293030 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6293061 GTTGGGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6293128 original size:2 final size:2
Alignment explanation
Indices: 6293121--6293150 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6293111 AAAACATTAC
6293121 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6293151 CATAAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6293179 original size:3 final size:3
Alignment explanation
Indices: 6293165--6293222 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
6293155 AAGTATACTC
6293165 TAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
6293211 TAA TAA AAA TAA
1 TAA TAA TAA TAA
6293223 ATAAATAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6293226 original size:4 final size:4
Alignment explanation
Indices: 6293217--6293275 Score: 95
Period size: 4 Copynumber: 15.2 Consensus size: 4
6293207 ATAATAATAA
6293217 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
6293264 AAA- AAAG AAAT A
1 AAAT AAAT AAAT A
6293276 CACATAATAG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
3 6 0.12
4 46 0.88
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:6293254 original size:15 final size:15
Alignment explanation
Indices: 6293179--6293275 Score: 104
Period size: 12 Copynumber: 7.0 Consensus size: 15
6293169 ACATAATAAT
6293179 AATAAT-AAT-AAT-
1 AATAATAAATAAATA
6293191 AATAAT-AAT-AAT-
1 AATAATAAATAAATA
6293203 AATAAT-AAT-AATA
1 AATAATAAATAAATA
6293216 AA-AATAAATAAATA
1 AATAATAAATAAATA
6293230 AATAAATAAATAAATA
1 AAT-AATAAATAAATA
6293246 AATAATAAATAAATA
1 AATAATAAATAAATA
* *
6293261 AATAAAAAAGAAATA
1 AATAATAAATAAATA
6293276 CACATAATAG
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
12 27 0.35
13 5 0.06
14 6 0.08
15 25 0.32
16 15 0.19
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:6299677 original size:33 final size:33
Alignment explanation
Indices: 6299639--6299722 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
6299629 AGGATATCTG
*
6299639 TGCGAGCCTATATATATGTGAACCCTAGGATTA
1 TGCGAGCCTATATGTATGTGAACCCTAGGATTA
*
6299672 TGCGAGCCTATATGTATGTGGACCCTAGGATTA
1 TGCGAGCCTATATGTATGTGAACCCTAGGATTA
* *
6299705 TGCAAGTCTATATGTATG
1 TGCGAGCCTATATGTATG
6299723 CAAACCTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (33 bp):
TGCGAGCCTATATGTATGTGAACCCTAGGATTA
Found at i:6302006 original size:23 final size:23
Alignment explanation
Indices: 6301980--6302041 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 23
6301970 AATTTTAAAT
6301980 TTTAATAAATTTAATATTTATTA
1 TTTAATAAATTTAATATTTATTA
6302003 TTTAA-AAA--T-ATCATTTATTA
1 TTTAATAAATTTAAT-ATTTATTA
6302023 TTTAAT-AATGTTAATATTT
1 TTTAATAAAT-TTAATATTT
6302042 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
19 2 0.06
20 16 0.48
22 3 0.09
23 10 0.30
24 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAATAAATTTAATATTTATTA
Found at i:6305012 original size:51 final size:51
Alignment explanation
Indices: 6304954--6305055 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
6304944 CCACGTTCTC
*
6304954 CTGCATTAACAATAATACTCATCCAATCAAGCTAAAACTTAATCCATAACA
1 CTGCATTAACAATAATACTCATCCAATCAAGCTAAAACTTAATCCACAACA
*
6305005 CTGCATTAACAATACTACTCATCCAATCAAGCTAAAACTTAATCCACAACA
1 CTGCATTAACAATAATACTCATCCAATCAAGCTAAAACTTAATCCACAACA
6305056 TCATAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.27, G:0.04, T:0.25
Consensus pattern (51 bp):
CTGCATTAACAATAATACTCATCCAATCAAGCTAAAACTTAATCCACAACA
Found at i:6305600 original size:30 final size:30
Alignment explanation
Indices: 6305561--6305619 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
6305551 CTTAACAAGA
*
6305561 AAATACCTTTAAAATAATAACAAAATTAAC
1 AAATACCTTTAAAACAATAACAAAATTAAC
* *
6305591 AAATGCCTTTAAAACAATAATAAAATTAA
1 AAATACCTTTAAAACAATAACAAAATTAA
6305620 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (30 bp):
AAATACCTTTAAAACAATAACAAAATTAAC
Found at i:6305698 original size:11 final size:11
Alignment explanation
Indices: 6305660--6305699 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
6305650 CAATAACAAT
6305660 AAAATAGTAGC
1 AAAATAGTAGC
* * *
6305671 AACATAATAGT
1 AAAATAGTAGC
6305682 AAAATAGTAGC
1 AAAATAGTAGC
6305693 AAAATAG
1 AAAATAG
6305700 GGAGAAAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:6306118 original size:19 final size:17
Alignment explanation
Indices: 6306085--6306155 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
6306075 AAAACTTTCC
6306085 ATTAATAAATTATAAAACA
1 ATTAA-AAATTATAAAA-A
6306104 ATTAAAAATTA-ATAAAA
1 ATTAAAAATTATA-AAAA
*
6306121 TTTACAAAATTTATAAAAA
1 ATTA-AAAA-TTATAAAAA
6306140 ATATAAAAATTATAAA
1 AT-TAAAAATTATAAA
6306156 GCAAACTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.11
18 20 0.44
19 17 0.38
20 3 0.07
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAAAAATTATAAAAA
Found at i:6306149 original size:8 final size:9
Alignment explanation
Indices: 6306091--6306155 Score: 60
Period size: 9 Copynumber: 7.1 Consensus size: 9
6306081 TTCCATTAAT
6306091 AAATTATAA
1 AAATTATAA
*
6306100 AACAAT-TAA
1 AA-ATTATAA
6306109 AAATTAATAA
1 AAATT-ATAA
* *
6306119 AATTTACAA
1 AAATTATAA
*
6306128 AATTTATAA
1 AAATTATAA
*
6306137 AAAATATAA
1 AAATTATAA
6306146 AAATTATAA
1 AAATTATAA
6306155 A
1 A
6306156 GCAAACTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 2 0.04
9 34 0.76
10 9 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:6306423 original size:15 final size:16
Alignment explanation
Indices: 6306403--6306435 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6306393 TATATATTTT
6306403 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
6306418 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
6306435 T
1 T
6306436 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:6306520 original size:22 final size:22
Alignment explanation
Indices: 6306481--6306539 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
6306471 GTTTTAAGAA
*
6306481 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
6306502 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
6306524 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
6306540 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:6306556 original size:26 final size:24
Alignment explanation
Indices: 6306510--6306557 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
6306500 ATTTGTTTTA
*
6306510 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
6306534 ATATTTGATTTATTATATTTTTAA
1 ATATTT-ATTT-TTATATTTTTAA
6306558 TTTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:6315931 original size:20 final size:19
Alignment explanation
Indices: 6315896--6315949 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
6315886 ACTTAAAATC
6315896 ATTA-AAAAT-TTAAAAAA
1 ATTATAAAATATTAAAAAA
6315913 ATTATAAAATATTATAAAAA
1 ATTATAAAATATTA-AAAAA
* *
6315933 ATCATAAAATAATAAAA
1 ATTATAAAATATTAAAA
6315950 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.12
18 5 0.16
19 6 0.19
20 17 0.53
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTATAAAATATTAAAAAA
Found at i:6315957 original size:16 final size:15
Alignment explanation
Indices: 6315938--6315980 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
6315928 AAAAAATCAT
*
6315938 AAAATAATAAAATTAA
1 AAAATAATAAAAAT-A
6315954 AAAATAA-AAAAATA
1 AAAATAATAAAAATA
6315968 AAAATATATAAAA
1 AAAATA-ATAAAA
6315981 GTGAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 11 0.46
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAATAAAAATA
Found at i:6323483 original size:13 final size:13
Alignment explanation
Indices: 6323465--6323489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6323455 CTAACCCAAA
6323465 TAGACTGCCCCAG
1 TAGACTGCCCCAG
6323478 TAGACTGCCCCA
1 TAGACTGCCCCA
6323490 ACGAACTCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.40, G:0.20, T:0.16
Consensus pattern (13 bp):
TAGACTGCCCCAG
Found at i:6328903 original size:22 final size:22
Alignment explanation
Indices: 6328878--6328929 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
6328868 TGGACAAGCC
*
6328878 ACCACATAATTGCTGATAAACA
1 ACCACATAATTGCAGATAAACA
6328900 ACCACATAATTGCAGATAAACA
1 ACCACATAATTGCAGATAAACA
6328922 ACCACATA
1 ACCACATA
6328930 TCTTCCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.19
Consensus pattern (22 bp):
ACCACATAATTGCAGATAAACA
Found at i:6329185 original size:18 final size:19
Alignment explanation
Indices: 6329155--6329191 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6329145 TTTTCACAAA
*
6329155 CATCACAATCACATAATAT
1 CATCACAATCACACAATAT
6329174 CATCAC-ATCACACAATAT
1 CATCACAATCACACAATAT
6329192 ACTTTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (19 bp):
CATCACAATCACACAATAT
Found at i:6330482 original size:39 final size:38
Alignment explanation
Indices: 6330434--6330523 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 38
6330424 TTAAATTTGA
6330434 TATTAAGATAATCACTTTAATATTAAATT-AATA-AAATAC
1 TATTAAGATAAT-ACTTTAA-ATTAAATTAAATATAAAT-C
*
6330473 TATTAAGATAA-ATTTTAAATTAAATTAAATATTAAATC
1 TATTAAGATAATACTTTAAATTAAATTAAATA-TAAATC
*
6330511 TATTAAAATAATA
1 TATTAAGATAATA
6330524 ATATTTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
36 8 0.18
37 10 0.22
38 11 0.24
39 16 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (38 bp):
TATTAAGATAATACTTTAAATTAAATTAAATATAAATC
Found at i:6330491 original size:68 final size:67
Alignment explanation
Indices: 6330382--6330507 Score: 164
Period size: 68 Copynumber: 1.9 Consensus size: 67
6330372 TGTGACAAAA
* * **
6330382 TTTAATATTAAATCTTATTAAATTAATAAGATAAACATTAAATTAAATTTGATATTAAGATAATC
1 TTTAATATTAAATCTAATAAAATTAATAAGATAAACATTAAATTAAATTAAATATTAAGATAATC
6330447 AC
66 AC
* **
6330449 TTTAATATTAAAT-TAATAAAATACTATTAAGATAAATTTTAAATTAAATTAAATATTAA
1 TTTAATATTAAATCTAATAAAAT--TAATAAGATAAACATTAAATTAAATTAAATATTAA
6330508 ATCTATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 7 0.14
67 13 0.26
68 30 0.60
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (67 bp):
TTTAATATTAAATCTAATAAAATTAATAAGATAAACATTAAATTAAATTAAATATTAAGATAATC
AC
Found at i:6330515 original size:57 final size:57
Alignment explanation
Indices: 6330383--6330524 Score: 134
Period size: 57 Copynumber: 2.5 Consensus size: 57
6330373 GTGACAAAAT
*
6330383 TTAATATTAAATCTTATTAAATTAATAAGATAAACATTAAATTAAATTTGATATTAAGA
1 TTAATATTAAATC-TATTAAATTAATAAGATAAACATTAAATTAAATTTGAAATTAA-A
* * *
6330442 -TAATCACTTTAA--TATTAAATTAATAA-A-ATACTATTAAGA-TAAATTTTAAATTAAA
1 TTAAT-A-TTAAATCTATTAAATTAATAAGATAAAC-ATTAA-ATTAAATTTGAAATTAAA
*
6330497 TTAAATATTAAATCTATTAAAATAATAA
1 TT-AATATTAAATCTATTAAATTAATAA
6330525 TATTTTTGGA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
55 8 0.12
56 21 0.30
57 31 0.45
58 4 0.06
59 1 0.01
60 4 0.06
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (57 bp):
TTAATATTAAATCTATTAAATTAATAAGATAAACATTAAATTAAATTTGAAATTAAA
Found at i:6333299 original size:19 final size:19
Alignment explanation
Indices: 6333275--6333314 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6333265 TTTTCATCAT
*
6333275 AATAAAATAAAA-TAATAAA
1 AATAAAACAAAACT-ATAAA
6333294 AATAAAACAAAACTATAAA
1 AATAAAACAAAACTATAAA
6333313 AA
1 AA
6333315 AAATAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AATAAAACAAAACTATAAA
Found at i:6333802 original size:55 final size:56
Alignment explanation
Indices: 6333737--6333851 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 56
6333727 AGCATGGCTG
* * *
6333737 CCAGATACAGA-AAATGTGACA-GAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACATG-GCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* *
6333793 CCAGA-ACAGATATACGTGGCATGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACATGGCCACCAGAACAGATAATTTGTGGCATAGCCA
6333848 CCAG
1 CCAG
6333852 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 20 0.39
57 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACATGGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:6333848 original size:28 final size:27
Alignment explanation
Indices: 6333762--6333851 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
6333752 GTGACAGAGT
*
6333762 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
**
6333791 CACCAGAACAGAT-ATACGTGGCATGGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
6333818 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
6333846 CACCAG
1 CACCAG
6333852 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 1 0.02
27 22 0.42
28 23 0.43
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:6334005 original size:28 final size:28
Alignment explanation
Indices: 6333964--6334018 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
6333954 CCTTAGAGGT
*
6333964 ATAAAGGTCATTTTGCACACATAGGGGC
1 ATAAAGGTAATTTTGCACACATAGGGGC
* *
6333992 ATAATGGTAATTTTGCATACATAGGGG
1 ATAAAGGTAATTTTGCACACATAGGGG
6334019 TATTCTAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (28 bp):
ATAAAGGTAATTTTGCACACATAGGGGC
Found at i:6346155 original size:97 final size:97
Alignment explanation
Indices: 6345989--6346182 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
6345979 ACCATATCAT
6345989 ATTGAACTTCTCAAACCATTCATCCACACATTAAAGGGACTTAAACTTCACCTAAACAACCAAAA
1 ATTGAACTTCTCAAACCATTCATCCACACATTAAAGGGACTTAAACTTCACCTAAACAACCAAAA
6346054 CAACCAATATGTCATTCAAAGGCACCACAATA
66 CAACCAATATGTCATTCAAAGGCACCACAATA
6346086 ATTGAACTTCTCAAACCATTCATCCACACATTAAAGGGACTTAAACTTCACCTAAACAACCAAAA
1 ATTGAACTTCTCAAACCATTCATCCACACATTAAAGGGACTTAAACTTCACCTAAACAACCAAAA
6346151 CAACCAATATGTCATTCAAAGGCACCACAATA
66 CAACCAATATGTCATTCAAAGGCACCACAATA
6346183 TATATACCAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (97 bp):
ATTGAACTTCTCAAACCATTCATCCACACATTAAAGGGACTTAAACTTCACCTAAACAACCAAAA
CAACCAATATGTCATTCAAAGGCACCACAATA
Found at i:6346764 original size:38 final size:38
Alignment explanation
Indices: 6346708--6346836 Score: 161
Period size: 38 Copynumber: 3.4 Consensus size: 38
6346698 TCACTAATAA
* *
6346708 TAAGACTGAATAACACCGGCACTAATCCTACTAGGCAC
1 TAAGCCTGAATAACACCGGCACTAATCCTGCTAGGCAC
* *
6346746 TAAGCCTGAATAACACCGGCACTAAGT-TTGCTATGCAC
1 TAAGCCTGAATAACACCGGCACTAA-TCCTGCTAGGCAC
* * *
6346784 TAAGCCTAAATAACACCGACACTAAGCCTGCTAGGCAC
1 TAAGCCTGAATAACACCGGCACTAATCCTGCTAGGCAC
* *
6346822 TAAGCTTGAGTAACA
1 TAAGCCTGAATAACA
6346837 GTATGGTTCA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
38 76 0.99
39 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (38 bp):
TAAGCCTGAATAACACCGGCACTAATCCTGCTAGGCAC
Found at i:6347734 original size:38 final size:38
Alignment explanation
Indices: 6347691--6347767 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
6347681 TTTCCATAGC
6347691 CATTTAACCCTTTTAACTAATAAATTTCAACTTTTACG
1 CATTTAACCCTTTTAACTAATAAATTTCAACTTTTACG
6347729 CATTTAACCCTTTTAACTAATAAATTTCAACTTTTACG
1 CATTTAACCCTTTTAACTAATAAATTTCAACTTTTACG
6347767 C
1 C
6347768 CTTTTACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.42
Consensus pattern (38 bp):
CATTTAACCCTTTTAACTAATAAATTTCAACTTTTACG
Found at i:6348657 original size:33 final size:33
Alignment explanation
Indices: 6348598--6348728 Score: 111
Period size: 33 Copynumber: 4.0 Consensus size: 33
6348588 TATAGGCTTT
* *
6348598 CATAATCCTGGGGTGT-GCAAACATACAGGCTTG
1 CATAATCCTGGGGT-TCGCATACATACAGGCTCG
* * *
6348631 CATAATCCTGGGGTTCGCATATATACAGTCTCA
1 CATAATCCTGGGGTTCGCATACATACAGGCTCG
* * * *
6348664 CATAATTCTAGGATTCACATACATACAGGCTCG
1 CATAATCCTGGGGTTCGCATACATACAGGCTCG
* ** * * *
6348697 CATAGTCCTATGGTTTGTATACATATAGGCTC
1 CATAATCCTGGGGTTCGCATACATACAGGCTC
6348729 ATATAGTCCT
Statistics
Matches: 77, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
32 1 0.01
33 76 0.99
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (33 bp):
CATAATCCTGGGGTTCGCATACATACAGGCTCG
Found at i:6349798 original size:7 final size:7
Alignment explanation
Indices: 6349786--6349817 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
6349776 ACATCCATAA
6349786 AATAAAT
1 AATAAAT
6349793 AATAAAT
1 AATAAAT
6349800 AATAAAT
1 AATAAAT
6349807 AATAAAT
1 AATAAAT
6349814 AATA
1 AATA
6349818 GTTTCTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:6350093 original size:32 final size:32
Alignment explanation
Indices: 6350057--6350133 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 32
6350047 GTAACAACTT
6350057 TTCTCTCTCTCCCCTATTTAGTTTTAAAAAAC
1 TTCTCTCTCTCCCCTATTTAGTTTTAAAAAAC
6350089 TTCTCTCTCT--CCTATTTAGTTTTAAAAAAC
1 TTCTCTCTCTCCCCTATTTAGTTTTAAAAAAC
*
6350119 TT-TCTTTTCTCCCCT
1 TTCTC-TCTCTCCCCT
6350134 TCTGTAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 2 0.05
30 26 0.63
32 13 0.32
ACGTcount: A:0.21, C:0.29, G:0.03, T:0.48
Consensus pattern (32 bp):
TTCTCTCTCTCCCCTATTTAGTTTTAAAAAAC
Found at i:6350846 original size:10 final size:10
Alignment explanation
Indices: 6350831--6350872 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
6350821 AAATATTTTT
6350831 ATTTT-TATA
1 ATTTTCTATA
*
6350840 ATCTTT-TATG
1 AT-TTTCTATA
6350850 ATTTTCTATA
1 ATTTTCTATA
6350860 ATTTTCTATA
1 ATTTTCTATA
6350870 ATT
1 ATT
6350873 GTTTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (10 bp):
ATTTTCTATA
Found at i:6351138 original size:9 final size:9
Alignment explanation
Indices: 6351126--6351189 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
6351116 ATATTTTAAA
6351126 AATTTTCAT
1 AATTTTCAT
6351135 AATTTT--T
1 AATTTTCAT
6351142 AA--TTCAT
1 AATTTTCAT
6351149 ACCATTTT--T
1 A--ATTTTCAT
**
6351158 AATTTTTTT
1 AATTTTCAT
6351167 AATTTTCAT
1 AATTTTCAT
6351176 AATTTTCAT
1 AATTTTCAT
6351185 AATTT
1 AATTT
6351190 ATATATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
5 2 0.04
7 10 0.22
9 31 0.69
11 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (9 bp):
AATTTTCAT
Found at i:6351145 original size:16 final size:16
Alignment explanation
Indices: 6351126--6351189 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 16
6351116 ATATTTTAAA
6351126 AATTTTCATAATTTTT
1 AATTTTCATAATTTTT
6351142 AA--TTCATACCATTTTT
1 AATTTTCATA--ATTTTT
**
6351158 AATTTTTTTAATTTTCAT
1 AATTTTCATAATTTT--T
6351176 AATTTTCATAATTT
1 AATTTTCATAATTT
6351190 ATATATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.16
16 15 0.39
18 17 0.45
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTCATAATTTTT
Found at i:6351155 original size:25 final size:24
Alignment explanation
Indices: 6351126--6351189 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
6351116 ATATTTTAAA
6351126 AATTTTCATAATTTTTAA-TTCAT
1 AATTTTCATAATTTTTAATTTCAT
6351149 ACCATTTT--TAATTTTTTTAATTTTCAT
1 A--ATTTTCATAA--TTTTTAA-TTTCAT
6351176 AATTTTCATAATTT
1 AATTTTCATAATTT
6351190 ATATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
23 4 0.12
25 20 0.61
27 9 0.27
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTTTCATAATTTTTAATTTCAT
Found at i:6351280 original size:19 final size:18
Alignment explanation
Indices: 6351256--6351308 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
6351246 TCTTCTGTAA
6351256 TTTTTAATATTTTTAT-G
1 TTTTTAATATTTTTATAG
*
6351273 ATTTTTTATGATTTTTAATAG
1 -TTTTTAAT-ATTTTT-ATAG
*
6351294 TTTTTAATAATTTTA
1 TTTTTAATATTTTTA
6351309 AATATAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 8 0.28
19 11 0.38
20 9 0.31
21 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTTAATATTTTTATAG
Found at i:6351312 original size:10 final size:10
Alignment explanation
Indices: 6351253--6351312 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 10
6351243 TATTCTTCTG
6351253 TAATTTTTAA
1 TAATTTTTAA
6351263 T-ATTTTT-A
1 TAATTTTTAA
* *
6351271 TGATTTTTTA
1 TAATTTTTAA
*
6351281 TGATTTTTAA
1 TAATTTTTAA
*
6351291 TAGTTTTTAA
1 TAATTTTTAA
*
6351301 TAATTTTAAA
1 TAATTTTTAA
6351311 TA
1 TA
6351313 TAAAACTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
8 2 0.05
9 12 0.28
10 29 0.67
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:6355356 original size:21 final size:20
Alignment explanation
Indices: 6355308--6355365 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
6355298 CATGTAACTT
* *
6355308 TGTCACACGGGCGTGTGTCTC
1 TGTCACAC-GACGTGTGCCTC
* *
6355329 AGCCACACGACCGTGTGCCTC
1 TGTCACACGA-CGTGTGCCTC
6355350 TGTCACACAGACGTGT
1 TGTCACAC-GACGTGT
6355366 CACTCTTCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (20 bp):
TGTCACACGACGTGTGCCTC
Found at i:6358092 original size:20 final size:20
Alignment explanation
Indices: 6358069--6358108 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6358059 TGGGTGTGTT
6358069 AGTTTACCTTTGGGTCTCGG
1 AGTTTACCTTTGGGTCTCGG
6358089 AGTTTACCTTTGGGTCTCGG
1 AGTTTACCTTTGGGTCTCGG
6358109 GTTCAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.30, T:0.40
Consensus pattern (20 bp):
AGTTTACCTTTGGGTCTCGG
Found at i:6358263 original size:32 final size:33
Alignment explanation
Indices: 6358210--6358277 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
6358200 ATTTTATTTT
6358210 ATTTTAATTTGAAAAATAAGAAGCTATCCCAAA
1 ATTTTAATTTGAAAAATAAGAAGCTATCCCAAA
*
6358243 ATTTTAATTTG-AAAATAAGAAGTTATCCCAAA
1 ATTTTAATTTGAAAAATAAGAAGCTATCCCAAA
6358275 ATT
1 ATT
6358278 GCTTTCATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (33 bp):
ATTTTAATTTGAAAAATAAGAAGCTATCCCAAA
Found at i:6360119 original size:41 final size:41
Alignment explanation
Indices: 6360061--6360239 Score: 243
Period size: 41 Copynumber: 4.4 Consensus size: 41
6360051 ATAATTGGGT
* * *
6360061 CTGCTCACACAAGCTGTCAGTCAAGACGTAGCTACATGGTG
1 CTGCTCACACAAGCTGTCAGTCAAGACGTAGCAACACGATG
* * *
6360102 TTGCTCACACAAGCTGTCAGTCAAGACGTAGCTACA-TAGTG
1 CTGCTCACACAAGCTGTCAGTCAAGACGTAGCAACACGA-TG
* *
6360143 CTGCTCACACAAGTTGTCAGTCAAGACGTATCAACACGATG
1 CTGCTCACACAAGCTGTCAGTCAAGACGTAGCAACACGATG
* * *
6360184 CTGCTCACACAAGTTGTCAGTCAAGACATATCAACACGATG
1 CTGCTCACACAAGCTGTCAGTCAAGACGTAGCAACACGATG
6360225 CTGCTCACACAAGCT
1 CTGCTCACACAAGCT
6360240 ACAAAGTAAC
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 125 0.99
42 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (41 bp):
CTGCTCACACAAGCTGTCAGTCAAGACGTAGCAACACGATG
Found at i:6361472 original size:34 final size:34
Alignment explanation
Indices: 6361429--6361495 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
6361419 GCATTACCGG
6361429 ACTAAAAACACATATAACTGTACTATTTTCATAT
1 ACTAAAAACACATATAACTGTACTATTTTCATAT
6361463 ACTAAAAACACATATAACTGTACTATTTTCATA
1 ACTAAAAACACATATAACTGTACTATTTTCATA
6361496 CATTCGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (34 bp):
ACTAAAAACACATATAACTGTACTATTTTCATAT
Found at i:6362351 original size:10 final size:10
Alignment explanation
Indices: 6362336--6362367 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
6362326 ATATAATACC
6362336 TACCAAAACA
1 TACCAAAACA
6362346 TACCAAAACA
1 TACCAAAACA
6362356 TACCAAAACA
1 TACCAAAACA
6362366 TA
1 TA
6362368 ATATCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.12
Consensus pattern (10 bp):
TACCAAAACA
Found at i:6362898 original size:20 final size:20
Alignment explanation
Indices: 6362873--6362910 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6362863 CAATAGCTAG
*
6362873 TCCATATAAATAGTATTTCA
1 TCCATATAAACAGTATTTCA
6362893 TCCATATAAACAGTATTT
1 TCCATATAAACAGTATTT
6362911 ATGCCCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (20 bp):
TCCATATAAACAGTATTTCA
Found at i:6363116 original size:47 final size:47
Alignment explanation
Indices: 6363063--6363160 Score: 142
Period size: 47 Copynumber: 2.1 Consensus size: 47
6363053 CTCTATTGAA
* *
6363063 CTGAAACGGTAAGCTATGACGAGCTAAAAACAATAAACTCTTATGAG
1 CTGAAACAGTAAGCTATAACGAGCTAAAAACAATAAACTCTTATGAG
* * * *
6363110 CTGAAACAGTAAGCTCTAACGAGCTGAAAACAGTAAGCTCTTATGAG
1 CTGAAACAGTAAGCTATAACGAGCTAAAAACAATAAACTCTTATGAG
6363157 CTGA
1 CTGA
6363161 TTTATTGGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (47 bp):
CTGAAACAGTAAGCTATAACGAGCTAAAAACAATAAACTCTTATGAG
Found at i:6363159 original size:24 final size:24
Alignment explanation
Indices: 6363045--6363160 Score: 112
Period size: 24 Copynumber: 4.9 Consensus size: 24
6363035 AAGCTGATGG
*
6363045 ACAGTAAGCTC-TATTGAACTG-AA
1 ACAGTAAGCTCTTA-TGAGCTGAAA
* * * * *
6363068 ACGGTAAGCTATGACGAGCTAAAA
1 ACAGTAAGCTCTTATGAGCTGAAA
* *
6363092 ACAATAAACTCTTATGAGCTG-AA
1 ACAGTAAGCTCTTATGAGCTGAAA
* *
6363115 ACAGTAAGCTCTAACGAGCTGAAA
1 ACAGTAAGCTCTTATGAGCTGAAA
6363139 ACAGTAAGCTCTTATGAGCTGA
1 ACAGTAAGCTCTTATGAGCTGA
6363161 TTTATTGGTA
Statistics
Matches: 71, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
23 32 0.45
24 39 0.55
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (24 bp):
ACAGTAAGCTCTTATGAGCTGAAA
Found at i:6363771 original size:10 final size:9
Alignment explanation
Indices: 6363747--6363772 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6363737 AAATTAATCC
6363747 CATTTTTGA
1 CATTTTTGA
6363756 CATTTTTGA
1 CATTTTTGA
6363765 CATTTTTG
1 CATTTTTG
6363773 TCAAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (9 bp):
CATTTTTGA
Found at i:6378160 original size:20 final size:20
Alignment explanation
Indices: 6378135--6378172 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6378125 CGGGTTTATC
*
6378135 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
6378155 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
6378173 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:6379834 original size:28 final size:28
Alignment explanation
Indices: 6379802--6379870 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
6379792 GCGTAGATCA
6379802 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
6379830 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
6379858 CGATA-TACCCCTA
1 CGAAATTACCCCTA
6379871 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:6383433 original size:20 final size:20
Alignment explanation
Indices: 6383410--6383450 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6383400 AAACAGTAGC
6383410 TCATCAATATAAACAATATT
1 TCATCAATATAAACAATATT
* *
6383430 TCATCCATATAAACAGTATT
1 TCATCAATATAAACAATATT
6383450 T
1 T
6383451 ATGCCCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (20 bp):
TCATCAATATAAACAATATT
Found at i:6383602 original size:25 final size:23
Alignment explanation
Indices: 6383542--6383614 Score: 60
Period size: 26 Copynumber: 3.0 Consensus size: 23
6383532 ATCATTTTCT
6383542 GCTCTTTCGAGCTATGAACAGTAA
1 GCTCTTT-GAGCTATGAACAGTAA
* *
6383566 GCTCCTCCTGAGCTGATGGACAGTAA
1 GCT-CT-TTGAGCT-ATGAACAGTAA
6383592 GCTCTATTGAG-T-TGAAACAGTAA
1 GCTCT-TTGAGCTATG-AACAGTAA
6383615 ACTCCAACGA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 2 0.05
23 7 0.17
24 4 0.10
25 13 0.32
26 14 0.35
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (23 bp):
GCTCTTTGAGCTATGAACAGTAA
Found at i:6388262 original size:18 final size:18
Alignment explanation
Indices: 6388236--6388272 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6388226 ATTTCTCTCC
*
6388236 CCCGGTTCCCTTTTCTTT
1 CCCGATTCCCTTTTCTTT
*
6388254 CCCGATTCCTTTTTCTTT
1 CCCGATTCCCTTTTCTTT
6388272 C
1 C
6388273 TCAGCCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.38, G:0.08, T:0.51
Consensus pattern (18 bp):
CCCGATTCCCTTTTCTTT
Found at i:6389618 original size:26 final size:25
Alignment explanation
Indices: 6389589--6389694 Score: 158
Period size: 26 Copynumber: 4.1 Consensus size: 25
6389579 TGGTACAAAT
6389589 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTC-A
6389615 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
6389641 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
6389667 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
6389693 TG
1 TG
6389695 CTAAGAATTT
Statistics
Matches: 77, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
26 74 0.96
27 3 0.04
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:6391358 original size:27 final size:27
Alignment explanation
Indices: 6391317--6391429 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
6391307 GAGGAAGCGT
*
6391317 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
6391344 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
6391371 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
6391399 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
6391425 TCTGG
1 TCTGG
6391430 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:6391422 original size:54 final size:54
Alignment explanation
Indices: 6391315--6391429 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6391305 TGGAGGAAGC
*
6391315 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
6391369 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
6391423 GTTCTGG
1 GTTCTGG
6391430 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:6394339 original size:66 final size:65
Alignment explanation
Indices: 6394208--6394341 Score: 153
Period size: 66 Copynumber: 2.0 Consensus size: 65
6394198 GCAAATTGCT
* * * * *
6394208 CAACTTAAAGTGGAGGCAGCATCGAGAGAAGCAAAGGCTCAAAGAATATATGAAGAACTCTAGCT
1 CAACTTAAAGCGGAGGCAGCAACGAGAGAAGCAAAGGC-CAAAGAAAATATGAAGAACCCCAGCT
6394273 A
65 A
* * * *
6394274 CAACTTAAAGCGGAGGCAGCAACGAGGGAAGCAGAGG-CAAGCAGAAAATATGACGGACCCCAGC
1 CAACTTAAAGCGGAGGCAGCAACGAGAGAAGCAAAGGCCAA--AGAAAATATGAAGAACCCCAGC
6394338 TA
64 TA
6394340 CA
1 CA
6394342 GCTTCAGAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
64 3 0.05
66 54 0.95
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (65 bp):
CAACTTAAAGCGGAGGCAGCAACGAGAGAAGCAAAGGCCAAAGAAAATATGAAGAACCCCAGCTA
Found at i:6394705 original size:43 final size:43
Alignment explanation
Indices: 6394656--6394742 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
6394646 GAACATAACT
6394656 TTTAGCGGCGTTTATGGGGAAAACACCGCTAACA-GTCATGTTC
1 TTTAGCGGCGTTTATGGGGAAAACACCGCTAA-AGGTCATGTTC
* * *
6394699 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTATGGGGAAAACACCGCTAAAGGTCATGTTC
6394742 T
1 T
6394743 ATAGTGGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTATGGGGAAAACACCGCTAAAGGTCATGTTC
Found at i:6395337 original size:90 final size:90
Alignment explanation
Indices: 6395232--6395398 Score: 298
Period size: 90 Copynumber: 1.9 Consensus size: 90
6395222 TTCCGTATAC
* * * *
6395232 AATGTTTCCAATGATTACAGCTATAATGTTATTGTATGAGTCTTGGTGGATTGTTATATATGATT
1 AATGTTTCCAATGATTACAACTACAATGTTATTGTATGAGTCTTGGTGGATTGTTATATATAAAT
6395297 GAAATATTTAATTCCATATACTATG
66 GAAATATTTAATTCCATATACTATG
6395322 AATGTTTCCAATGATTACAACTACAATGTTATTGTATGAGTCTTGGTGGATTGTTATATATAAAT
1 AATGTTTCCAATGATTACAACTACAATGTTATTGTATGAGTCTTGGTGGATTGTTATATATAAAT
6395387 GAAATATTTAAT
66 GAAATATTTAAT
6395399 AATTCCATTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (90 bp):
AATGTTTCCAATGATTACAACTACAATGTTATTGTATGAGTCTTGGTGGATTGTTATATATAAAT
GAAATATTTAATTCCATATACTATG
Found at i:6396678 original size:68 final size:68
Alignment explanation
Indices: 6396602--6396728 Score: 254
Period size: 68 Copynumber: 1.9 Consensus size: 68
6396592 AGGAGTGTCC
6396602 AATATCTTGATATGAGATTTACCTTTATTCAAATTATTTTGGTTTAAATTTGAAATATTCAAATT
1 AATATCTTGATATGAGATTTACCTTTATTCAAATTATTTTGGTTTAAATTTGAAATATTCAAATT
6396667 TGA
66 TGA
6396670 AATATCTTGATATGAGATTTACCTTTATTCAAATTATTTTGGTTTAAATTTGAAATATT
1 AATATCTTGATATGAGATTTACCTTTATTCAAATTATTTTGGTTTAAATTTGAAATATT
6396729 GAAACAAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (68 bp):
AATATCTTGATATGAGATTTACCTTTATTCAAATTATTTTGGTTTAAATTTGAAATATTCAAATT
TGA
Found at i:6397372 original size:16 final size:16
Alignment explanation
Indices: 6397339--6397379 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
6397329 TTATTTAATC
6397339 ATTTATATTTTATTTTT
1 ATTTAT-TTTTATTTTT
6397356 A-TTATTTTTATTATTT
1 ATTTATTTTTATT-TTT
6397372 ATTTATTT
1 ATTTATTT
6397380 CTCTTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 7 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTATTTTTATTTTT
Found at i:6403459 original size:27 final size:28
Alignment explanation
Indices: 6403422--6403900 Score: 470
Period size: 27 Copynumber: 17.7 Consensus size: 28
6403412 TACCAAAGTA
6403422 CTCACGATTTACAGAATTACCGTTTTACC
1 CTCA-GATTTACAGAATTACCGTTTTACC
* *
6403451 CTCAG-TTTATAGAATTACTGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
** * *
6403478 CTC-GATTTGTAAAATTACTGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
6403505 CTC-GATTTACAGAATTACCGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
**
6403532 CTCAG-TTTACAGAATTACTATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
*
6403559 CTC-GATTTACAGAATTACCATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
***
6403586 CTCAG-TTTACAGAATTATTATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* *
6403613 CT-TGATTTACAGAATTACTGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* * *
6403640 TTC-GATTTATAGAATTACCATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
** *
6403667 CTC-GATTTGTAAAATTACCGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* **
6403694 TTCAG-TTTACAGAATTACTATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* *
6403721 CTC-GATATATAGAATTACCGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* *
6403748 CCCA-ATTTACATAATTACCGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* * * *
6403775 C-CTGATTTACATAATTATCATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* *
6403802 CT-GGATTTACAGAATTACCATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* **
6403829 CTC-GATTTATAGAATTACTATTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* *
6403856 CT-TGATTTACAGAATTACTGTTTTACC
1 CTCAGATTTACAGAATTACCGTTTTACC
* *
6403883 CT-TGATTTACAAAATTAC
1 CTCAGATTTACAGAATTAC
6403901 TAAAATACCC
Statistics
Matches: 387, Mismatches: 50, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.01
27 374 0.97
28 4 0.01
29 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.41
Consensus pattern (28 bp):
CTCAGATTTACAGAATTACCGTTTTACC
Found at i:6403484 original size:54 final size:54
Alignment explanation
Indices: 6403426--6403900 Score: 528
Period size: 54 Copynumber: 8.8 Consensus size: 54
6403416 AAAGTACTCA
** * *
6403426 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTATTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
** * *
6403480 CGATTTGTAAAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
*
6403534 C-AGTTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCATTTTACCCT
1 CGA-TTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * * *
6403588 C-AGTTTACAGAATTATTATTTTACCCTTGATTTACAGAATTACTGTTTTACCTT
1 CGA-TTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * ** * *
6403642 CGATTTATAGAATTACCATTTTACCCTCGATTTGTAAAATTACCGTTTTACCTT
1 CGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * *
6403696 C-AGTTTACAGAATTACTATTTTACCCTCGATATATAGAATTACCGTTTTACCCC
1 CGA-TTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * ** * * *
6403750 CAATTTACATAATTACCGTTTTACCC-CTGATTTACATAATTATCATTTTACCCT
1 CGATTTACAGAATTACTATTTTACCCTC-GATTTACAGAATTACCGTTTTACCCT
* * * **
6403804 GGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * * *
6403858 TGATTTACAGAATTACTGTTTTACCCTTGATTTACAAAATTAC
1 CGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTAC
6403901 TAAAATACCC
Statistics
Matches: 360, Mismatches: 54, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
53 3 0.01
54 353 0.98
55 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (54 bp):
CGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
Found at i:6403911 original size:81 final size:82
Alignment explanation
Indices: 6403426--6403900 Score: 570
Period size: 81 Copynumber: 5.9 Consensus size: 82
6403416 AAAGTACTCA
* * ** *
6403426 CGATTTACAGAATTACCGTTTTACCC-TCAGTTTATAGAATTACTGTTTTACCCTCGATTTGTAA
1 CGATTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAG
**
6403490 AATTACTGTTTTACCCT
66 AATTACCATTTTACCCT
6403507 CGATTTACAGAATTACCGTTTTACCC-TCAGTTTACAGAATTACTATTTTACCCTCGATTTACAG
1 CGATTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAG
6403571 AATTACCATTTTACCCT
66 AATTACCATTTTACCCT
*** * * * *
6403588 C-AGTTTACAGAATTATTATTTTACCCTTGA-TTTACAGAATTACTGTTTTACCTTCGATTTATA
1 CGA-TTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACTATTTTACCCTCGATTTACA
6403651 GAATTACCATTTTACCCT
65 GAATTACCATTTTACCCT
** * * *
6403669 CGATTTGTAAAATTACCGTTTTA-CCTTCAGTTTACAGAATTACTATTTTACCCTCGATATATAG
1 CGATTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAG
* *
6403733 AATTACCGTTTTACCCC
66 AATTACCATTTTACCCT
* * * * * *
6403750 CAATTTACATAATTACCGTTTTACCCCTGA-TTTACATAATTA-TCATTTTACCCTGGATTTACA
1 CGATTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACT-ATTTTACCCTCGATTTACA
6403813 GAATTACCATTTTACCCT
65 GAATTACCATTTTACCCT
* ** * * * *
6403831 CGATTTATAGAATTACTATTTTACCCTTGA-TTTACAGAATTACTGTTTTACCCTTGATTTACAA
1 CGATTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAG
6403895 AATTAC
66 AATTAC
6403901 TAAAATACCC
Statistics
Matches: 339, Mismatches: 48, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
80 7 0.02
81 324 0.96
82 8 0.02
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (82 bp):
CGATTTACAGAATTACCGTTTTACCCTTCAGTTTACAGAATTACTATTTTACCCTCGATTTACAG
AATTACCATTTTACCCT
Found at i:6405241 original size:9 final size:9
Alignment explanation
Indices: 6405229--6405305 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
6405219 TTTGATAAAC
6405229 ATGATATGT
1 ATGATATGT
*
6405238 ATGATATGCAC
1 ATGATATG--T
6405249 ATGATATGT
1 ATGATATGT
*
6405258 ATGATATGCAC
1 ATGATATG--T
*
6405269 ATGACATGT
1 ATGATATGT
*
6405278 ATGATATGCAC
1 ATGATATG--T
6405289 ATGATATGT
1 ATGATATGT
6405298 ATGATATG
1 ATGATATG
6405306 CACACGATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:6405252 original size:20 final size:20
Alignment explanation
Indices: 6405227--6405317 Score: 164
Period size: 20 Copynumber: 4.5 Consensus size: 20
6405217 ATTTTGATAA
6405227 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
6405247 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
6405267 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
6405287 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
6405307 ACACGATATGT
1 ACATGATATGT
6405318 TCATAAATGC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:6405254 original size:11 final size:11
Alignment explanation
Indices: 6405238--6405316 Score: 71
Period size: 11 Copynumber: 7.7 Consensus size: 11
6405228 CATGATATGT
6405238 ATGATATGCAC
1 ATGATATGCAC
*
6405249 ATGATATG--T
1 ATGATATGCAC
6405258 ATGATATGCAC
1 ATGATATGCAC
* *
6405269 ATGACATG--T
1 ATGATATGCAC
6405278 ATGATATGCAC
1 ATGATATGCAC
*
6405289 ATGATATG--T
1 ATGATATGCAC
6405298 ATGATATGCAC
1 ATGATATGCAC
*
6405309 ACGATATG
1 ATGATATG
6405317 TTCATAAATG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
9 23 0.43
11 30 0.57
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:6405420 original size:24 final size:23
Alignment explanation
Indices: 6405364--6405530 Score: 219
Period size: 24 Copynumber: 7.0 Consensus size: 23
6405354 GAGGAAGTGA
6405364 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
6405387 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
6405410 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
* *
6405434 CAAAAGGTCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
6405458 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
6405481 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
6405506 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
6405530 A
1 A
6405531 TGATAAAGCA
Statistics
Matches: 128, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
23 42 0.33
24 75 0.59
25 11 0.09
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Done.