Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 90 of 362
Found at i:28722976 original size:23 final size:25
Alignment explanation
Indices: 28722935--28722988 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
28722925 CTTTAACTTG
*
28722935 TATTATATACTTATCTTTATTTATA
1 TATTATATAATTATCTTTATTTATA
28722960 TATTA-ATAATTA-CTTTATTTATA
1 TATTATATAATTATCTTTATTTATA
*
28722983 TTTTAT
1 TATTAT
28722989 TATTACCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 15 0.58
24 6 0.23
25 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTATATAATTATCTTTATTTATA
Found at i:28723095 original size:13 final size:14
Alignment explanation
Indices: 28723077--28723118 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
28723067 TGTACTTAAC
28723077 TTATATTTATAT-A
1 TTATATTTATATAA
28723090 TTATATGTTATATAA
1 TTATAT-TTATATAA
28723105 TTAT-TTTATTATAA
1 TTATATTTA-TATAA
28723119 AAATCCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATATTTATATAA
Found at i:28723256 original size:18 final size:20
Alignment explanation
Indices: 28723206--28723271 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 20
28723196 AATTATAAAT
* * *
28723206 TTTTGTTATTATATATTATA
1 TTTTATTATTAAATATCATA
28723226 TATTGTA-TATTAAATA-C-TA
1 T-TT-TATTATTAAATATCATA
28723245 TTTTATTATTAAATATCATA
1 TTTTATTATTAAATATCATA
28723265 TTTTATT
1 TTTTATT
28723272 TGTATTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 2 0.05
18 11 0.29
19 4 0.11
20 10 0.26
21 10 0.26
22 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTATTATTAAATATCATA
Found at i:28731924 original size:15 final size:14
Alignment explanation
Indices: 28731903--28731941 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
28731893 TTTTTTATAT
28731903 ATTATTTATTTCAA
1 ATTATTTATTTCAA
* *
28731917 ATTTATTTTTTTCAT
1 A-TTATTTATTTCAA
28731932 ATTATTTATT
1 ATTATTTATT
28731942 CTAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTATTTCAA
Found at i:28731971 original size:25 final size:26
Alignment explanation
Indices: 28731933--28731981 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
28731923 TTTTTTCATA
*
28731933 TTATTTATTCTAAA-TATTTTATACG
1 TTATTTATTCTAAACCATTTTATACG
28731958 TTATTTATGT-TAAACCATTTTATA
1 TTATTTAT-TCTAAACCATTTTATA
28731982 TATTATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (26 bp):
TTATTTATTCTAAACCATTTTATACG
Found at i:28731987 original size:26 final size:24
Alignment explanation
Indices: 28731872--28731993 Score: 91
Period size: 26 Copynumber: 4.6 Consensus size: 24
28731862 AGTCATATAC
*
28731872 ATATATTTTTCTATTTAAATATTTTTT
1 ATATATTATT-TATTTAAATA--TTTT
28731899 ATATATTATTTATTTCAAATTTATTTTT
1 ATATATTATTTATTT-AAA--TA-TTTT
*
28731927 TTCATATTATTTATTCTAAATATTTT
1 AT-ATATTATTTATT-TAAATATTTT
** *
28731953 ATACGTTATTTATGTTAAACCATTTT
1 ATATATTATTTAT-TTAAA-TATTTT
*
28731979 ATATATTATCTATTT
1 ATATATTATTTATTT
28731994 TAAGTTTTAT
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
25 15 0.19
26 26 0.33
27 14 0.18
28 6 0.08
29 17 0.22
30 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.61
Consensus pattern (24 bp):
ATATATTATTTATTTAAATATTTT
Found at i:28732233 original size:46 final size:46
Alignment explanation
Indices: 28732175--28732267 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 46
28732165 ACTTTCTATG
* *
28732175 TTTTCTTTTAAATTGTTATATATACT-ATTCATTTTA-AGTTGTATTA
1 TTTTATTTTAAATTATTATATATACTAATT-ATTTTAGA-TTGTATTA
* *
28732221 TTTTATTTTAAATTATTATGTATATTAATTATTTTAGATTGTATTA
1 TTTTATTTTAAATTATTATATATACTAATTATTTTAGATTGTATTA
28732267 T
1 T
28732268 ACTATTCCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 37 0.90
47 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.60
Consensus pattern (46 bp):
TTTTATTTTAAATTATTATATATACTAATTATTTTAGATTGTATTA
Found at i:28732353 original size:22 final size:21
Alignment explanation
Indices: 28732323--28732364 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
28732313 TTTTTTATGT
28732323 ATTACTTATTTAAAATTGTCTC
1 ATTACTTATTTAAAA-TGTCTC
* *
28732345 ATTATTTATTTTAAATGTCT
1 ATTACTTATTTAAAATGTCT
28732365 TTGTGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTACTTATTTAAAATGTCTC
Found at i:28736774 original size:14 final size:14
Alignment explanation
Indices: 28736755--28736854 Score: 53
Period size: 14 Copynumber: 7.0 Consensus size: 14
28736745 TAAAATATTT
28736755 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
*
28736769 TTTTCTCTCTTTATT-
1 TTTTCT-T-TTTTTTC
* *
28736784 TTTCCTTATTTTTC
1 TTTTCTTTTTTTTC
28736798 -TTTCTTTCTTTTTC
1 TTTTCTTT-TTTTTC
* *
28736812 TATCTTATTTTTTTCC
1 T-T-TTCTTTTTTTTC
* * *
28736828 TATTCTTCTTCTTC
1 TTTTCTTTTTTTTC
*
28736842 TTAT-TTTTTTTTC
1 TTTTCTTTTTTTTC
28736855 CACAAAAACT
Statistics
Matches: 62, Mismatches: 17, Indels: 15
0.66 0.18 0.16
Matches are distributed among these distances:
13 16 0.26
14 23 0.37
15 6 0.10
16 12 0.19
17 5 0.08
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:28736785 original size:28 final size:28
Alignment explanation
Indices: 28736753--28736808 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
28736743 TTTAAAATAT
* *
28736753 TTTTTTCTTTTTTTTCTTTTCTCTCTTTA
1 TTTTTCCTTATTTTTC-TTTCTCTCTTTA
*
28736782 TTTTTCCTTATTTTTCTTTCTTTCTTT
1 TTTTTCCTTATTTTTCTTTCTCTCTTT
28736809 TTCTATCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTTCCTTATTTTTCTTTCTCTCTTTA
Found at i:28736798 original size:38 final size:39
Alignment explanation
Indices: 28736754--28736843 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
28736744 TTAAAATATT
* *
28736754 TTTTTCTTTTTTTTC-TTTTCTCTCTT-TATTTTTCCTTA
1 TTTTTCTTTTCTTTCTTTTTCTATCTTATATTTTTCC-TA
*
28736792 TTTTTC-TTTCTTTCTTTTTCTATCTTATTTTTTTCCTA
1 TTTTTCTTTTCTTTCTTTTTCTATCTTATATTTTTCCTA
*
28736830 TTCTTCTTCTTCTT
1 TTTTTCTT-TTCTT
28736844 ATTTTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
37 7 0.16
38 23 0.52
39 9 0.20
40 5 0.11
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (39 bp):
TTTTTCTTTTCTTTCTTTTTCTATCTTATATTTTTCCTA
Found at i:28736852 original size:27 final size:26
Alignment explanation
Indices: 28736788--28736852 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
28736778 TTTATTTTTC
*
28736788 CTTATTTTTCTTTCTTTCTTTTTCTAT
1 CTTATTTTT-TTTCTTTCTTCTTCTAT
*
28736815 CTTATTTTTTTCCTATTCTTCTTCT-T
1 CTTATTTTTTTTCT-TTCTTCTTCTAT
28736841 CTTATTTTTTTT
1 CTTATTTTTTTT
28736853 TCCACAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.47
27 18 0.53
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (26 bp):
CTTATTTTTTTTCTTTCTTCTTCTAT
Found at i:28743770 original size:40 final size:40
Alignment explanation
Indices: 28743743--28743888 Score: 222
Period size: 40 Copynumber: 3.6 Consensus size: 40
28743733 AGATATGGTC
28743743 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGACA-TAGTA
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTA
* *
28743783 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAAATTAGTA
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* * *
28743823 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAATC
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28743863 ACTAGCACAAATGTCTTCGGGACTTA
1 ACTAGCACAAATGCCTTCGGGACTTA
28743889 ACCCCGTTAG
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 97 0.99
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:28754713 original size:40 final size:40
Alignment explanation
Indices: 28754667--28754850 Score: 244
Period size: 40 Copynumber: 4.6 Consensus size: 40
28754657 CTCGCACAAG
* * *
28754667 GCCTTCGGGTCTTGGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
28754707 GCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
28754747 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
28754787 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
28754827 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
28754851 CATTCGAATA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 122 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:28754765 original size:80 final size:79
Alignment explanation
Indices: 28754631--28754850 Score: 257
Period size: 80 Copynumber: 2.8 Consensus size: 79
28754621 ACCCAAGTAT
* * * * * * *
28754631 CTTCGGGATTTAGCTGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTGGCCCGGATATGGTC
1 CTTCGGGACTTAGCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG-C
*
28754695 -ACTAGCATAAATGC
65 AACTAGCACAAATGC
* *
28754709 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGC
1 CTTCGGGACTTAG-CCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGC
*
28754774 AACTCGCACAAATGC
65 AACTAGCACAAATGC
* * *
28754789 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGA-CTTAG-CCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT
28754851 CATTCGAATA
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
78 12 0.10
79 20 0.16
80 90 0.74
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCGGATATAATCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGCA
ACTAGCACAAATGC
Found at i:28757295 original size:18 final size:18
Alignment explanation
Indices: 28757272--28757310 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28757262 GTCTTAGTAC
*
28757272 ATGTTTAGAGTGTTATAT
1 ATGTTTAGAGTATTATAT
*
28757290 ATGTTTATAGTATTATAT
1 ATGTTTAGAGTATTATAT
28757308 ATG
1 ATG
28757311 GTTTTAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (18 bp):
ATGTTTAGAGTATTATAT
Found at i:28761347 original size:64 final size:64
Alignment explanation
Indices: 28761273--28761406 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 64
28761263 TAATATTTCT
* * *
28761273 ATATTTCTATCATGATTTTTAATAAATTTATTTATTGATATAATATGTCTCATCTAATAGACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATAGACAA
* *
28761337 ATATTTCTATCACGATTTTTGATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATAGACAA
28761401 ATATTT
1 ATATTT
28761407 AATAAAATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (64 bp):
ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATAGACAA
Found at i:28761419 original size:64 final size:64
Alignment explanation
Indices: 28761286--28761420 Score: 184
Period size: 64 Copynumber: 2.1 Consensus size: 64
28761276 TTTCTATCAT
* * * * *
28761286 GATTTTTAATAAATTTATTTATTGATATAATATGTCTCATCTAATAGACAAATATTTCTATCAC
1 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATAGACAAATATTTATATAAA
* *
28761350 GATTTTTGATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAAATATTTA-ATAAA
1 GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATAGACAAATATTTATATAAA
28761413 -ATATTTTA
1 GAT-TTTTA
28761421 TATAGTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
62 2 0.03
63 7 0.11
64 53 0.85
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (64 bp):
GATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATAGACAAATATTTATATAAA
Found at i:28761481 original size:24 final size:24
Alignment explanation
Indices: 28761454--28761524 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
28761444 ATTATTATTG
*
28761454 AAATATTCTCTTCCGTTTTATCAC
1 AAATATTATCTTCCGTTTTATCAC
*
28761478 AAATTTTAT-TGTCCGTTTTATCAC
1 AAATATTATCT-TCCGTTTTATCAC
* *
28761502 AAATATTATCGTCTGTTTTATCA
1 AAATATTATCTTCCGTTTTATCA
28761525 TTTAAGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (24 bp):
AAATATTATCTTCCGTTTTATCAC
Found at i:28761967 original size:241 final size:241
Alignment explanation
Indices: 28761566--28762217 Score: 1154
Period size: 241 Copynumber: 2.7 Consensus size: 241
28761556 ATACCTTTTT
* * *
28761566 AAGTTCTATCGAGCTCATTTACTATTG-A-A-T--TTACCATGTAGCTTGCTTATCCCTTAAAAT
1 AAGTTCTATCGAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGTTTGTCCATTAAAAT
*
28761626 TACAACAATAGCTGACATTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
66 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
* *
28761691 CTGGAAACCTAACGGGTTGTCTTATATCAAGCTGTAAGATATAATGGATCCTCCCTAAGTGTAAC
131 CTGGAAACCTAACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAAGTGTAAC
*
28761756 AACGCCATGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAA
196 AACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAA
28761802 AAGTTCTATCGAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGTTTGTCCATTAAAAT
1 AAGTTCTATCGAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGTTTGTCCATTAAAAT
*
28761867 TACAATAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
66 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
* *
28761932 CTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGTAAC
131 CTGGAAACCTAACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAAGTGTAAC
28761997 AACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAA
196 AACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAA
*
28762043 AAGTTCTATCAAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGTTTGTCCATTAAAAT
1 AAGTTCTATCGAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGTTTGTCCATTAAAAT
28762108 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
66 TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
*
28762173 CTGGAAGCCTAAC-GGTTGCCTTATATCGAGCTGTAAGATATAATG
131 CTGGAAACCTAACGGGTTGCCTTATATCGAGCTGTAAGATATAATG
28762218 AATCAAATTT
Statistics
Matches: 397, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
236 27 0.07
237 1 0.00
238 1 0.00
239 1 0.00
240 32 0.08
241 335 0.84
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (241 bp):
AAGTTCTATCGAGCTCATTTACTATTGAATATTCATTACCATGTAGCTTGTTTGTCCATTAAAAT
TACAACAATAGCTGACCTTCTCTCCAACCTTTTTTTAAATATTTTAAAGATTCAAAGTATATAGG
CTGGAAACCTAACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAAGTGTAAC
AACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAA
Found at i:28767135 original size:17 final size:16
Alignment explanation
Indices: 28767098--28767137 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
28767088 TATTATGAAT
28767098 TTATTAATTCTTTCAA
1 TTATTAATTCTTTCAA
* *
28767114 ATATTAATTACTTTCTA
1 TTATTAATT-CTTTCAA
28767131 TTATTAA
1 TTATTAA
28767138 ATAATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTAATTCTTTCAA
Found at i:28768075 original size:33 final size:33
Alignment explanation
Indices: 28768033--28768114 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 33
28768023 TTAGAATTAA
* *
28768033 TGTTTTTGGTTGTATTTTTTATGCTAAATTTGT
1 TGTTTTTGGTTGCATTTTTTATACTAAATTTGT
*
28768066 TGTTTTTGGTTGCA--TTTTATACTATATTTGT
1 TGTTTTTGGTTGCATTTTTTATACTAAATTTGT
* *
28768097 TGTATTTGGTTGGATTTT
1 TGTTTTTGGTTGCATTTT
28768115 AATGCAGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 27 0.64
33 15 0.36
ACGTcount: A:0.15, C:0.04, G:0.20, T:0.62
Consensus pattern (33 bp):
TGTTTTTGGTTGCATTTTTTATACTAAATTTGT
Found at i:28768243 original size:43 final size:43
Alignment explanation
Indices: 28768185--28768305 Score: 161
Period size: 43 Copynumber: 2.8 Consensus size: 43
28768175 CGTTTGTGGG
* *
28768185 AAAAGCGCCGCTAAAAGCAGTGACTTTTAGCGGCGCTTTACCC
1 AAAAACGCCGCTAAAAGCCGTGACTTTTAGCGGCGCTTTACCC
* * * * *
28768228 ACAAACGCTGTTAAAAGCCGTGACTTTTAGCAGCGCTTTGCCC
1 AAAAACGCCGCTAAAAGCCGTGACTTTTAGCGGCGCTTTACCC
* *
28768271 AAAAACGCCGCTAAAATCCTTGACTTTTAGCGGCG
1 AAAAACGCCGCTAAAAGCCGTGACTTTTAGCGGCG
28768306 TTTTTTCAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAAGCCGTGACTTTTAGCGGCGCTTTACCC
Found at i:28769293 original size:27 final size:28
Alignment explanation
Indices: 28769241--28769299 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
28769231 ATCAAATTTA
* *
28769241 ATAACTAACAAAAATATTTC-ATAAAAT
1 ATAACTAACAAAAATATTACAAAAAAAT
*
28769268 ATAACTAACTAAAAT-TTAACAAAAAAAT
1 ATAACTAACAAAAATATT-ACAAAAAAAT
28769296 ATAA
1 ATAA
28769300 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 15 0.56
28 10 0.37
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (28 bp):
ATAACTAACAAAAATATTACAAAAAAAT
Found at i:28778463 original size:18 final size:18
Alignment explanation
Indices: 28778430--28778481 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
28778420 ATTGCATATA
*
28778430 AAAAAAT-TAAAGTTTAC
1 AAAAAATATAAAATTTAC
* *
28778447 AATAAAA-ATAATATTTAT
1 AA-AAAATATAAAATTTAC
28778465 AAAAAATATAAAATTTA
1 AAAAAATATAAAATTTA
28778482 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAAATATAAAATTTAC
Found at i:28779019 original size:37 final size:37
Alignment explanation
Indices: 28778978--28779056 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
28778968 ATATAATATT
28778978 ATATGTTCTTATAGTTTATTATAATTATAAGGCTCAA
1 ATATGTTCTTATAGTTTATTATAATTATAAGGCTCAA
28779015 ATATGTTCTTATAGTTTATTATAATTATAAGGCTCAA
1 ATATGTTCTTATAGTTTATTATAATTATAAGGCTCAA
28779052 ATATG
1 ATATG
28779057 CATTTATTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (37 bp):
ATATGTTCTTATAGTTTATTATAATTATAAGGCTCAA
Found at i:28779306 original size:18 final size:19
Alignment explanation
Indices: 28779285--28779320 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28779275 AATACATAAA
28779285 AAATT-TAAAATATAAAAT
1 AAATTATAAAATATAAAAT
*
28779303 AAATTATAAATTATAAAA
1 AAATTATAAAATATAAAA
28779321 ATATATGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTATAAAATATAAAAT
Found at i:28781167 original size:27 final size:27
Alignment explanation
Indices: 28781129--28781524 Score: 356
Period size: 27 Copynumber: 14.6 Consensus size: 27
28781119 TTAGTTTACC
* * *
28781129 AAATTACTAAAATGCCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
28781156 AAATTACTAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
28781183 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
28781210 AAATTACCAAAATA-CCTCTAGTTTGTG
1 AAATTACCAAAATACCCTCGA-TTTGTA
* * *
28781237 AAATTACCAAAATACCTTTGATTTGTG
1 AAATTACCAAAATACCCTCGATTTGTA
** *
28781264 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
28781291 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
** *
28781318 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **
28781345 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
*
28781372 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
28781399 AAATTACCAAAATACCC-CTAATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
28781426 AAATTACCAAAATACCTTC-AGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
** * *
28781453 AAATTACTGAAATGCCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
** * * *
28781480 AAATTACTGACATGCCCTCGACTTGTAA
1 AAATTACCAAAATACCCTCGATTTGT-A
*
28781508 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
28781525 CTAATTTACA
Statistics
Matches: 309, Mismatches: 49, Indels: 21
0.82 0.13 0.06
Matches are distributed among these distances:
26 5 0.02
27 285 0.92
28 19 0.06
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:28781593 original size:27 final size:27
Alignment explanation
Indices: 28781563--28781731 Score: 196
Period size: 27 Copynumber: 6.3 Consensus size: 27
28781553 CGATTTACAA
* * *
28781563 AATTATTGAAATACCCATGTAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
28781590 AATTACCGAAATACCCCTGTAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
28781617 AATTACTAAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
28781644 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
28781671 AATTACTGAAATACCCCTGTAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
28781698 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
28781725 AATTACT
1 AATTACT
28781732 ATTTTGCTTC
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 121 0.98
28 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:28781723 original size:81 final size:81
Alignment explanation
Indices: 28781561--28781729 Score: 221
Period size: 81 Copynumber: 2.1 Consensus size: 81
28781551 CTCGATTTAC
* * *
28781561 AAAATTATTGAAATACCCATGTAGGATAGAATTACCGAAATACCCCTGTAGGATAGAATTACTAA
1 AAAATTATCGAAATACCCATGTAGGATAGAATTACCGAAATACCCCTGTAGGATAAAATTACCAA
28781626 AATACCCCTATAGGGT
66 AATACCCCTATAGGGT
* * * * * *
28781642 AGAATTATCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAAAATTACCGA
1 AAAATTATCGAAATACCCATGTAGGATAGAATTACCGAAATACCCCTGTAGGATAAAATTACCAA
* * * *
28781707 GATACCCTTGTGGGGT
66 AATACCCCTATAGGGT
28781723 AAAATTA
1 AAAATTA
28781730 CTATTTTGCT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 74 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (81 bp):
AAAATTATCGAAATACCCATGTAGGATAGAATTACCGAAATACCCCTGTAGGATAAAATTACCAA
AATACCCCTATAGGGT
Found at i:28782012 original size:24 final size:25
Alignment explanation
Indices: 28781937--28782005 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
28781927 GGAAGTGCTG
* *
28781937 AAAGGGCTTTGCCCCAGTTTACCGA
1 AAAGGGCTTTGCCCCAGTTTATCAA
*
28781962 AAGGGGCTTTGCCCCAGTTTATCAA
1 AAAGGGCTTTGCCCCAGTTTATCAA
28781987 AAAGGGCTTTGCCCCAGTT
1 AAAGGGCTTTGCCCCAGTT
28782006 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTATCAA
Found at i:28782018 original size:24 final size:25
Alignment explanation
Indices: 28781937--28782018 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
28781927 GGAAGTGCTG
* *
28781937 AAAG-GGCTTTGCCCCAGTTTACCG
1 AAAGAGGCTTTGCCCCAGTTTATCA
*
28781961 AAAGGGGCTTTGCCCCAGTTTATCA
1 AAAGAGGCTTTGCCCCAGTTTATCA
*
28781986 AAA-AGGGCTTTGCCCCAG-TTATTA
1 AAAGA-GGCTTTGCCCCAGTTTATCA
28782010 AAAGAGGCT
1 AAAGAGGCT
28782019 AGGCCTTCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
24 16 0.31
25 35 0.69
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAGAGGCTTTGCCCCAGTTTATCA
Found at i:28790983 original size:12 final size:12
Alignment explanation
Indices: 28790966--28790992 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28790956 TCCGAAGTAT
28790966 ATATATATATAC
1 ATATATATATAC
28790978 ATATATATATAC
1 ATATATATATAC
28790990 ATA
1 ATA
28790993 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:28791523 original size:27 final size:28
Alignment explanation
Indices: 28791439--28791536 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
28791429 CATGAGATTG
* * * *
28791439 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
28791468 ACACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
28791496 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28791523 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28791537 GACTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 24 0.39
28 21 0.34
29 17 0.27
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28791547 original size:27 final size:27
Alignment explanation
Indices: 28791469--28791549 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
28791459 AATTGTACAA
* *
28791469 CACTAAGTGTGCGAGTTTGATTATATAG
1 CACTAAGTGTGCGA-CTTGAATATATAG
* *
28791497 CACTAAGTGTGCGAGTTGATTATATAG
1 CACTAAGTGTGCGACTTGAATATATAG
*
28791524 CACTGAGTGTGCGGACTT-AATATATA
1 CACTAAGTGTGC-GACTTGAATATATA
28791550 CTTTTGAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
27 30 0.62
28 18 0.38
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
CACTAAGTGTGCGACTTGAATATATAG
Found at i:28797611 original size:42 final size:42
Alignment explanation
Indices: 28797564--28797672 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
28797554 TGAGATTACA
28797564 TGTAAGACCATGTCTGGGACATTGACAT-TGTATTGCAATTAT-
1 TGTAAGACCATGTCTGGGACATTGACATAT-TA-TGCAATTATG
* *
28797606 TGTAAGACCATGTCTGGGACATTGGCATCATTATGCGATTATG
1 TGTAAGACCATGTCTGGGACATTGACAT-ATTATGCAATTATG
*
28797649 TGTAAGACCATGTCTAGGACATTG
1 TGTAAGACCATGTCTGGGACATTG
28797673 GCATCGTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
42 35 0.57
43 25 0.41
44 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGACATATTATGCAATTATG
Found at i:28797669 original size:43 final size:43
Alignment explanation
Indices: 28797564--28797761 Score: 192
Period size: 43 Copynumber: 4.7 Consensus size: 43
28797554 TGAGATTACA
* *
28797564 TGTAAGACCATGTCTGGGACATTGACAT--TGTATTGCAATTAT-
1 TGTAAGACCATGTCTGGGACATTGGCATCAT-TA-TGCGATTATG
28797606 TGTAAGACCATGTCTGGGACATTGGCATCATTATGCGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCATTATGCGATTATG
* * *
28797649 TGTAAGACCATGTCTAGGACATTGGCATCGTTATTCGATT-TAG
1 TGTAAGACCATGTCTGGGACATTGGCATCATTATGCGATTAT-G
* * * * * *
28797692 TGTAAGACCTTGTCGGGGATAGTGGCATCGA-TATGTGATAATG
1 TGTAAGACCATGTCTGGGACATTGGCATC-ATTATGCGATTATG
* * *
28797735 TGTAAGATCATATCTGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
28797762 TGTACGAGCT
Statistics
Matches: 132, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
42 42 0.32
43 88 0.67
44 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCATTATGCGATTATG
Found at i:28797738 original size:86 final size:85
Alignment explanation
Indices: 28797564--28797741 Score: 216
Period size: 86 Copynumber: 2.1 Consensus size: 85
28797554 TGAGATTACA
* * * * *
28797564 TGTAAGACCATGTCTGGGACATTGACATTGTATTGCAATTATTGTAAGACCATGTCTGGGACATT
1 TGTAAGACCATGTCTAGGACATTGACATCGTATTGCAATTAGTGTAAGACCATGTCGGGGACAGT
*
28797629 GGCATCATTATGCGATTATG
66 GGCATCATTATGCGATAATG
* * * *
28797649 TGTAAGACCATGTCTAGGACATTGGCATCGTTATT-CGATTTAGTGTAAGACCTTGTCGGGGATA
1 TGTAAGACCATGTCTAGGACATTGACATCG-TATTGC-AATTAGTGTAAGACCATGTCGGGGACA
*
28797713 GTGGCATCGA-TATGTGATAATG
64 GTGGCATC-ATTATGCGATAATG
28797735 TGTAAGA
1 TGTAAGA
28797742 TCATATCTGG
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
85 28 0.35
86 50 0.63
87 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (85 bp):
TGTAAGACCATGTCTAGGACATTGACATCGTATTGCAATTAGTGTAAGACCATGTCGGGGACAGT
GGCATCATTATGCGATAATG
Found at i:28803955 original size:54 final size:54
Alignment explanation
Indices: 28803750--28803956 Score: 211
Period size: 55 Copynumber: 3.9 Consensus size: 54
28803740 TTCCTTTTTA
* * * *
28803750 AACTTACCATTTCCATGTCTTGACATGGTCTTAC-TGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATAG
* * * * * * *
28803802 AAGTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATAG
** * * * * *
28803856 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTACCTTGTAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATAG
* *
28803911 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTTA
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTA
28803957 AACCCTAGTT
Statistics
Matches: 124, Mismatches: 28, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
52 29 0.23
53 15 0.12
54 39 0.31
55 41 0.33
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATAG
Found at i:28808849 original size:9 final size:9
Alignment explanation
Indices: 28808835--28808868 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
28808825 TTCTCATAAG
28808835 AGCTTACTA
1 AGCTTACTA
28808844 AGCTTACTA
1 AGCTTACTA
*
28808853 AGCTTAAT-
1 AGCTTACTA
28808861 AGCTTACT
1 AGCTTACT
28808869 TTGTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (9 bp):
AGCTTACTA
Found at i:28810987 original size:26 final size:25
Alignment explanation
Indices: 28810952--28811012 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
28810942 TTTACCCAAT
*
28810952 TAAAATTTTTGACAATTTTACGCTCGA
1 TAAAA-TTTTGACAATGTTA-GCTCGA
** *
28810979 TAAAATTTTGATGATGTTATCTCGA
1 TAAAATTTTGACAATGTTAGCTCGA
28811004 TAAAATTTT
1 TAAAATTTT
28811013 AAGAAAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 14 0.47
26 11 0.37
27 5 0.17
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (25 bp):
TAAAATTTTGACAATGTTAGCTCGA
Found at i:28813561 original size:21 final size:21
Alignment explanation
Indices: 28813521--28813562 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28813511 TATTTAAATA
28813521 AAGTTTTCAATATTTATTTAT
1 AAGTTTTCAATATTTATTTAT
*
28813542 AAGTCTTTCATTATTT-TTTAT
1 AAGT-TTTCAATATTTATTTAT
28813563 TCCACCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
AAGTTTTCAATATTTATTTAT
Found at i:28851099 original size:40 final size:41
Alignment explanation
Indices: 28851043--28851224 Score: 228
Period size: 40 Copynumber: 4.5 Consensus size: 41
28851033 AATTCAAATA
*
28851043 TATATATGGCACTTAGTGTGCGATTC-AAGAAAGCTTCAGC
1 TATATATGGCACTTAGTGTGCGATTCGAAGAAAGCTTCGGC
* **
28851083 TATATATGGCATTTAGTGTGTAATTC-AAGAAAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATTCGAAGAAAGCTTCGGC
* * *
28851123 TATATATGACACTTAGTGTGCGATTCGAA-ATAGCTTTGGC
1 TATATATGGCACTTAGTGTGCGATTCGAAGAAAGCTTCGGC
** *
28851163 TATATATGGCACTTAGTGTGCGAGACTG-AGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATTC-GAAGAAAGCTTCGGC
*
28851204 TATATAAGGCACTTAGTGTGC
1 TATATATGGCACTTAGTGTGC
28851225 AAAATTATAA
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
40 91 0.73
41 33 0.27
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (41 bp):
TATATATGGCACTTAGTGTGCGATTCGAAGAAAGCTTCGGC
Found at i:28851179 original size:80 final size:80
Alignment explanation
Indices: 28851043--28851266 Score: 249
Period size: 80 Copynumber: 2.8 Consensus size: 80
28851033 AATTCAAATA
* * *
28851043 TATATATGGCACTTAGTGTGCGATTCAAGAAAGCTTCA-GCTATATATGGCATTTAGTGTG-TA-
1 TATATATGGCACTTAGTGTGCGATTCAA-ATAGCTT-AGGCTATATATGGCACTTAGTGTGCGAG
*
28851105 ATTCAAGAAAGCTTCGGC
64 ACT-AAGAAAGCTTCGGC
* *
28851123 TATATATGACACTTAGTGTGCGATTCGAAATAGCTTTGGCTATATATGGCACTTAGTGTGCGAGA
1 TATATATGGCACTTAGTGTGCGATTC-AAATAGCTTAGGCTATATATGGCACTTAGTGTGCGAGA
* *
28851188 CTGAGATAGCTTCGGC
65 CTAAGAAAGCTTCGGC
* * *
28851204 TATATAAGGCACTTAGTGTGCAAAATT-ATAATAGCTTAGGCTATGTATTGGCACTTAGTGTGC
1 TATATATGGCACTTAGTGTGC--GATTCA-AATAGCTTAGGCTATATA-TGGCACTTAGTGTGC
28851267 AAGATATCAA
Statistics
Matches: 123, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
80 52 0.42
81 35 0.28
82 18 0.15
83 18 0.15
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (80 bp):
TATATATGGCACTTAGTGTGCGATTCAAATAGCTTAGGCTATATATGGCACTTAGTGTGCGAGAC
TAAGAAAGCTTCGGC
Found at i:28851209 original size:41 final size:41
Alignment explanation
Indices: 28851043--28851266 Score: 222
Period size: 40 Copynumber: 5.5 Consensus size: 41
28851033 AATTCAAATA
* * *
28851043 TATATATGGCACTTAGTGTGCGATTC-AAGAAAGCTTCAGC
1 TATATATGGCACTTAGTGTGCGATACTAAGATAGCTTCGGC
* ** * *
28851083 TATATATGGCATTTAGTGTGTAATTC-AAGAAAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATACTAAGATAGCTTCGGC
* * * *
28851123 TATATATGACACTTAGTGTGCGATTCGAA-ATAGCTTTGGC
1 TATATATGGCACTTAGTGTGCGATACTAAGATAGCTTCGGC
* *
28851163 TATATATGGCACTTAGTGTGCGAGACTGAGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATACTAAGATAGCTTCGGC
* * * * *
28851204 TATATAAGGCACTTAGTGTGCAAAATTATA-ATAGCTTAGGC
1 TATATATGGCACTTAGTGTGCGATACTA-AGATAGCTTCGGC
*
28851245 TATGTATTGGCACTTAGTGTGC
1 TATATA-TGGCACTTAGTGTGC
28851267 AAGATATCAA
Statistics
Matches: 156, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 91 0.58
41 50 0.32
42 15 0.10
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (41 bp):
TATATATGGCACTTAGTGTGCGATACTAAGATAGCTTCGGC
Found at i:28855083 original size:30 final size:30
Alignment explanation
Indices: 28855049--28855109 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28855039 TCCTTAACTC
28855049 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28855079 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28855109 A
1 A
28855110 GGCTCAGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:28864881 original size:23 final size:23
Alignment explanation
Indices: 28864837--28864881 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28864827 TTATATCCAT
* * *
28864837 ACCAAAATCATGCCTAATCATAA
1 ACCAAAATCATACCAAAACATAA
*
28864860 ACCAAAGTCATACCAAAACATA
1 ACCAAAATCATACCAAAACATA
28864882 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.27, G:0.04, T:0.18
Consensus pattern (23 bp):
ACCAAAATCATACCAAAACATAA
Found at i:28870195 original size:40 final size:40
Alignment explanation
Indices: 28870054--28870182 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 40
28870044 TAACTCATTC
* *
28870054 AATGCCTTCGGCACTTAACCCGGATTTAA-AACTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* * *
28870092 GATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
28870132 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
28870172 AATACCTTCGG
1 AATGCCTTCGG
28870183 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 25 0.32
39 8 0.10
40 45 0.58
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:28870220 original size:80 final size:78
Alignment explanation
Indices: 28870057--28870234 Score: 195
Period size: 79 Copynumber: 2.3 Consensus size: 78
28870047 CTCATTCAAT
* * * *
28870057 GCCTTCGGCACTTAACCCGGATTTAAAACTCGCACGATGCCTTCGGGACTTAACCCGGAATTAGT
1 GCCTTCGGGACTTAACCCGGAATTAAAACTCGCACAATACCTTCGGGACTTAACCCGGAATTAGT
*
28870122 ATCTCGCACAAAG
66 ATCTAGCACAAAG
**
28870135 GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGG-ATA
1 GCCTTCGGGACTTAACCCGGAATTAA-AACTCGCAC-AATACCTTCGGGA-CTTAACCCGGAAT-
28870198 TAGTCA-CTTAGCACAAA-
62 TAGT-ATC-TAGCACAAAG
*
28870215 GCCTTC-GGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
28870235 CAGCATTCAA
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
78 24 0.28
79 27 0.31
80 26 0.30
81 9 0.10
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (78 bp):
GCCTTCGGGACTTAACCCGGAATTAAAACTCGCACAATACCTTCGGGACTTAACCCGGAATTAGT
ATCTAGCACAAAG
Found at i:28877956 original size:40 final size:40
Alignment explanation
Indices: 28877778--28877996 Score: 200
Period size: 40 Copynumber: 5.5 Consensus size: 40
28877768 CTCGTTCAAG
* * ***
28877778 TGCCTTCGGGACATAGCCCGG--TTAATAACTCATTC-AA
1 TGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
* *
28877815 TGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAA
* *
28877855 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
*
28877895 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
* ** * * *
28877935 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA
1 TGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACAAA
*
28877976 -GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
28877997 CAGCATTCAA
Statistics
Matches: 151, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
37 19 0.13
39 14 0.09
40 107 0.71
41 11 0.07
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
Found at i:28885675 original size:39 final size:39
Alignment explanation
Indices: 28885610--28885716 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 39
28885600 TAGCTCCTCG
* * *
28885610 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATA-AAACTCA
* * *
28885650 TTCAATGCCTTCGGCACTTAACCCGGATTTTAAAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAAAACTCA
**
28885689 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
28885717 ATTAGTATCT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 24 0.43
40 32 0.57
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (39 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAAAACTCA
Found at i:28885749 original size:80 final size:80
Alignment explanation
Indices: 28885656--28885836 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
28885646 CTCATTCAAT
* * * *
28885656 GCCTTCGGCACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
*
28885718 TTAGT-A-TCTCGCACAAA
64 -TAGTCACT-TAGCACAAA
**
28885735 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
28885800 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
28885816 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
28885837 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 7 0.08
80 70 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:28885796 original size:40 final size:40
Alignment explanation
Indices: 28885653--28885836 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
28885643 TAACTCATTC
* * *
28885653 AATGCCTTCGGCACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
28885693 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
28885733 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
28885773 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
28885814 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28885837 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 102 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:28889888 original size:41 final size:41
Alignment explanation
Indices: 28889803--28890025 Score: 254
Period size: 41 Copynumber: 5.5 Consensus size: 41
28889793 TAATTATACC
* *
28889803 TGAATTGCACATACGTGCCCCTA-TTGTACTTTAGTACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCA
*
28889843 TGAATTGCACATATGTGCCCCTATTTGTA-TTTCGGTACCCA
1 TGAATTGCACATACGTGCCCCTATTTGTACTTT-GGTACCCA
* * * * * * *
28889884 TGAATTACAAATACGTGACCTTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCA
* * *
28889925 TGAATTGCACATACATG-CCTTTTTTGTACTTTGGTACCCA
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCA
* * *
28889965 TGAATTGCACATACATGCCCCTGTTTGTACTTTGATACCCA
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCA
* *
28890006 TGAATAGCACTTACGTGCCC
1 TGAATTGCACATACGTGCCC
28890026 TTGTTCCCAC
Statistics
Matches: 156, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
40 62 0.40
41 92 0.59
42 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCA
Found at i:28889964 original size:81 final size:81
Alignment explanation
Indices: 28889826--28890026 Score: 233
Period size: 81 Copynumber: 2.5 Consensus size: 81
28889816 CGTGCCCCTA
* * *
28889826 TTGTACTTTAGTACCCTTGAATTGCACATATGTGCCCCTATTTGTATTTCGGTACCCATGAATTA
1 TTGTACTTTGGTACCCATGAATTGCACATACGTG-CCCTATTTGTATTTCGGTACCCATGAATTA
* *
28889891 CAAATACGTGACCTTGT
65 CAAATACATGACCCTGT
* * * * * *
28889908 TTGTACTTCGGTACCCCTGAATTGCACATACATGCCTTTTTTGTACTTT-GGTACCCATGAATTG
1 TTGTACTTTGGTACCCATGAATTGCACATACGTGCCCTATTTGTA-TTTCGGTACCCATGAATTA
* *
28889972 CACATACATGCCCCTGT
65 CAAATACATGACCCTGT
* * *
28889989 TTGTACTTTGATACCCATGAATAGCACTTACGTGCCCT
1 TTGTACTTTGGTACCCATGAATTGCACATACGTGCCCT
28890027 TGTTCCCACT
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
81 67 0.68
82 32 0.32
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (81 bp):
TTGTACTTTGGTACCCATGAATTGCACATACGTGCCCTATTTGTATTTCGGTACCCATGAATTAC
AAATACATGACCCTGT
Found at i:28899246 original size:79 final size:81
Alignment explanation
Indices: 28899137--28899319 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
28899127 TACTCGTTCA
* *
28899137 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
28899200 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
28899217 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
28899280 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
28899296 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28899320 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:28899319 original size:40 final size:40
Alignment explanation
Indices: 28899116--28899319 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
28899106 CGGAATTTAA
** *
28899116 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28899156 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28899196 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28899235 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28899275 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28899315 CCGGA
1 CCGGA
28899320 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28907312 original size:79 final size:81
Alignment explanation
Indices: 28907199--28907381 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
28907189 TACTCGTTCA
* *
28907199 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
28907262 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
28907279 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
28907342 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
28907358 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28907382 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:28907381 original size:40 final size:40
Alignment explanation
Indices: 28907178--28907381 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
28907168 TCGAATTTAA
** *
28907178 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28907218 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28907258 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28907297 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28907337 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28907377 CCGGA
1 CCGGA
28907382 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28909916 original size:45 final size:45
Alignment explanation
Indices: 28909847--28909936 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
28909837 TCCTATACGG
* *
28909847 GGCAATAGAAATAGGTATTGTTCCTTGCATCAACTCAATAGCAAA
1 GGCAATAGAAATAGGTATTGTTCCTGGCATCAACTCAATACCAAA
* *
28909892 GGCAATAGAAATAGGTGTTTTTCCTGGCATCAACTCAATACCAAA
1 GGCAATAGAAATAGGTATTGTTCCTGGCATCAACTCAATACCAAA
28909937 CTCTACTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (45 bp):
GGCAATAGAAATAGGTATTGTTCCTGGCATCAACTCAATACCAAA
Found at i:28918727 original size:694 final size:693
Alignment explanation
Indices: 28916654--28918715 Score: 3761
Period size: 693 Copynumber: 3.0 Consensus size: 693
28916644 ATTGTATGAT
*
28916654 AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTGTTTTGATATCCCAGGATACTGATT
1 AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTATTTTGATATCCCAGGATACTGATT
*
28916719 CAAGATAAGCTCTTATTCAGAAGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
66 CAAGATAAGCTCTTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
* * * * *
28916784 AGAGTTGATTGCTCGCCTAGAGATAGGGTGACAAGATTTTGCCGGATTAGGGTGAAACCTAATAG
131 GGAGTTGATTGCGCGCCTAGAGATAGGATGACAAGATTTTACCGAATTAGGGTGAAACCTAATAG
* * * *
28916849 GGGATCTATAGATCGAGTTAATGCAACCCTAGAGTGTTAATTAGAGAAAAGTCTTAATTATTCAA
196 GGGATCCATAGATCGAGTTAATGTAACCCTAGAGTGTTAATTAGAGAACAGTCTCAATTATTCAA
*
28916914 TCTAGGGATTAGACGTTATTAGTCTTGAACAAGGATAATAACATAACTTAGGGATCTCTACGGAA
261 TCTAGGGATTAGACGTTATTAGTCTTGAATAAGGATAATAACATAACTTAGGGATCTCTACGGAA
* *
28916979 CAAGTTAAATGAATAAATCGTCCGATTCAGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTT
326 CAAGTTAAATGAATAAATCGTCCAATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTT
*
28917044 CCTTAGGT-ATTGTCTTAATTCAATTGTTTTCCAAAAGTAATCCCCCAATTCTACTTTATGTTAA
391 CCTTAGGTAATTGTCTTAATTCAATTATTTTCCAAAAGTAATCCCCCAATTCTACTTTATGTTAA
28917108 TTTTTAATTTAGATAATTAGTTAGTTAAAACAAAACCCCCTTATTTTTAGGCTAGATAATAAAAA
456 TTTTTAATTTAGATAATTAGTTAGTTAAAACAAAACCCCCTTATTTTTAGGCTAGATAATAAAAA
*
28917173 GACAGTCATTACTAGTGCTTTTAGTTCCTTTGGATTCGACAATCTGATCTTGCTAAAACTATACT
521 GACAGTCATTACTAGTGCTTTTAGTTCCTTTGGATTCGACAATCCGATCTTGCTAAAACTATACT
28917238 ACTGTTCGATAGGTACACTTGCCTACATCATGATAATATTTCATTTCAAGAAAGATTCATTATAA
586 ACTGTTCGATAGGTACACTTGCCTACATCATGATAATATTTCATTTCAAGAAAGATTCATTATAA
28917303 ATATTTAAAACCCGTCACACGAAAATTGCAATCAAGTTTTTGC
651 ATATTTAAAACCCGTCACACGAAAATTGCAATCAAGTTTTTGC
28917346 AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTATTTTGATATCCCAGGATACTGATT
1 AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTATTTTGATATCCCAGGATACTGATT
28917411 CAAGATAAGCTCTTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
66 CAAGATAAGCTCTTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
28917476 GGAGTTGATTGCGCGCCTAGAGATAGGATGACAAGATTTTACCGAATTAGGGTGAAACCTAATAG
131 GGAGTTGATTGCGCGCCTAGAGATAGGATGACAAGATTTTACCGAATTAGGGTGAAACCTAATAG
28917541 GGGATCCATAGATCGAGTTAATGTAACCCTAGAGTGTTAATTAGAGAACAGTCTCAATTATTCAA
196 GGGATCCATAGATCGAGTTAATGTAACCCTAGAGTGTTAATTAGAGAACAGTCTCAATTATTCAA
28917606 TCTAGGGATTAGACGTTATTAGTCTTGAATAAGGATAATAACATAACTTAGGGATCTCTACGGAA
261 TCTAGGGATTAGACGTTATTAGTCTTGAATAAGGATAATAACATAACTTAGGGATCTCTACGGAA
28917671 CAAGTTAAATGAATAAATCGTCCAATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTT
326 CAAGTTAAATGAATAAATCGTCCAATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTT
*
28917736 CCTTAGGTAATTGTCTTAATTCAATTATTTTCTAAAAGTAATCCCCCAATTCTACTTTATGTTAA
391 CCTTAGGTAATTGTCTTAATTCAATTATTTTCCAAAAGTAATCCCCCAATTCTACTTTATGTTAA
28917801 TTTTTAATTTAGATAATTAGTTAGTTAAAACAAAACCCCCTTATTTTTAGGCTAGATAATAAAAA
456 TTTTTAATTTAGATAATTAGTTAGTTAAAACAAAACCCCCTTATTTTTAGGCTAGATAATAAAAA
28917866 GACAGTCATTACTAGTGCTTTTAGTTCCTTTGGATTCGACAATCCGATCTTGCTAAAACTATACT
521 GACAGTCATTACTAGTGCTTTTAGTTCCTTTGGATTCGACAATCCGATCTTGCTAAAACTATACT
28917931 ACTGTTCGATAGGTACACTTGCCTACATCATGATAATATTTCATTTCAAGAAAGATTCATTATAA
586 ACTGTTCGATAGGTACACTTGCCTACATCATGATAATATTTCATTTCAAGAAAGATTCATTATAA
28917996 ATATTTAAAACCCGTCACACGAAAATTGCAATCAAGTTTTTGC
651 ATATTTAAAACCCGTCACACGAAAATTGCAATCAAGTTTTTGC
28918039 AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTATTTTGATATCCCAGGATACTGATT
1 AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTATTTTGATATCCCAGGATACTGATT
28918104 CAAGATAAGCTCTTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
66 CAAGATAAGCTCTTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
28918169 GGAGTTGATTGCGCGCCTAGAGATAGGATGACAAGATTTTACCGAATTAGGGTGAAACCTAATAG
131 GGAGTTGATTGCGCGCCTAGAGATAGGATGACAAGATTTTACCGAATTAGGGTGAAACCTAATA-
28918234 GGGGATCCATAGATCGAGTTAATGTAACCCTAGAGTGTTAATTAGAGAACAGTCTCAATTATTCA
195 GGGGATCCATAGATCGAGTTAATGTAACCCTAGAGTGTTAATTAGAGAACAGTCTCAATTATTCA
28918299 ATCTAGGGATTAGACGTTATTAGTCTTGAATAAGGATAATAACATAACTTAGGGATCTCTACGGA
260 ATCTAGGGATTAGACGTTATTAGTCTTGAATAAGGATAATAACATAACTTAGGGATCTCTACGGA
28918364 ACAAGTTAAATGAATAAATCGTCCAATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTT
325 ACAAGTTAAATGAATAAATCGTCCAATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTT
*
28918429 TCCTTAGGTAATTGTCTTAATTCAATTATTTTCCAAAAGTAATCCCCCAATTCTACTTTCT-TTG
390 TCCTTAGGTAATTGTCTTAATTCAATTATTTTCCAAAAGTAATCCCCCAATTCTACTTTATGTT-
** * * *
28918493 AATTCGTAGTTTAGATAATTACTTAGTTAAAACAAAACCCCTTTATTTTTAGGCTAGATAATAAA
454 AATTTTTAATTTAGATAATTAGTTAGTTAAAACAAAACCCCCTTATTTTTAGGCTAGATAATAAA
* * * *
28918558 AAGACAATCATTACTAGTACTTTTAGTTCCTTTGGGTTCGACAATCCGGTCTTGCTAAAACTATA
519 AAGACAGTCATTACTAGTGCTTTTAGTTCCTTTGGATTCGACAATCCGATCTTGCTAAAACTATA
* * * * *
28918623 CTACTGTTCGATAGGTTCACTTTCCTACATCGTGATAATAGTT-AGTTTCAAGAACGATTCATTA
584 CTACTGTTCGATAGGTACACTTGCCTACATCATGATAATATTTCA-TTTCAAGAAAGATTCATTA
* * *
28918687 TAAATTTTTAAAACCTGTCATACGAAAAT
648 TAAATATTTAAAACCCGTCACACGAAAAT
28918716 CGTGATCAAG
Statistics
Matches: 1330, Mismatches: 36, Indels: 6
0.97 0.03 0.00
Matches are distributed among these distances:
692 384 0.29
693 488 0.37
694 458 0.34
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (693 bp):
AAATATTTAACTTGTTCTTAATTATGTGTTCTTAATTCTTATTTTGATATCCCAGGATACTGATT
CAAGATAAGCTCTTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGTCATAATTAAGC
GGAGTTGATTGCGCGCCTAGAGATAGGATGACAAGATTTTACCGAATTAGGGTGAAACCTAATAG
GGGATCCATAGATCGAGTTAATGTAACCCTAGAGTGTTAATTAGAGAACAGTCTCAATTATTCAA
TCTAGGGATTAGACGTTATTAGTCTTGAATAAGGATAATAACATAACTTAGGGATCTCTACGGAA
CAAGTTAAATGAATAAATCGTCCAATTCGGAGCCAGAATAACAAGTAAAGTCTAGGTGGATTTTT
CCTTAGGTAATTGTCTTAATTCAATTATTTTCCAAAAGTAATCCCCCAATTCTACTTTATGTTAA
TTTTTAATTTAGATAATTAGTTAGTTAAAACAAAACCCCCTTATTTTTAGGCTAGATAATAAAAA
GACAGTCATTACTAGTGCTTTTAGTTCCTTTGGATTCGACAATCCGATCTTGCTAAAACTATACT
ACTGTTCGATAGGTACACTTGCCTACATCATGATAATATTTCATTTCAAGAAAGATTCATTATAA
ATATTTAAAACCCGTCACACGAAAATTGCAATCAAGTTTTTGC
Found at i:28948643 original size:46 final size:45
Alignment explanation
Indices: 28948542--28948635 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 45
28948532 TGTAACCCGC
* * *
28948542 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-ATGCGCAA
*
28948588 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAA
28948632 CCAT
1 CCAT
28948636 CCTAGTGACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 9 0.20
46 35 0.80
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAA
Found at i:28960162 original size:40 final size:40
Alignment explanation
Indices: 28960118--28960305 Score: 290
Period size: 40 Copynumber: 4.7 Consensus size: 40
28960108 GCTACTAGCT
28960118 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28960158 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
28960198 CAAATGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* ** * *
28960238 CAAATGCCTTTGGG-CTTAGCCC-GAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
28960277 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
28960306 CAATCCGAAT
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
38 3 0.02
39 31 0.23
40 100 0.74
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28969388 original size:57 final size:57
Alignment explanation
Indices: 28969319--28969439 Score: 233
Period size: 57 Copynumber: 2.1 Consensus size: 57
28969309 CGTGCTTAAA
*
28969319 GCCGTGTGAAAATAGGGCAAAGATTTTCCCAAACACGGGCTACGATAAAATGCCATG
1 GCCGTGTAAAAATAGGGCAAAGATTTTCCCAAACACGGGCTACGATAAAATGCCATG
28969376 GCCGTGTAAAAATAGGGCAAAGATTTTCCCAAACACGGGCTACGATAAAATGCCATG
1 GCCGTGTAAAAATAGGGCAAAGATTTTCCCAAACACGGGCTACGATAAAATGCCATG
28969433 GCCGTGT
1 GCCGTGT
28969440 GACATGGCCG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (57 bp):
GCCGTGTAAAAATAGGGCAAAGATTTTCCCAAACACGGGCTACGATAAAATGCCATG
Found at i:28969506 original size:55 final size:55
Alignment explanation
Indices: 28969447--28969572 Score: 139
Period size: 55 Copynumber: 2.3 Consensus size: 55
28969437 TGTGACATGG
* * *
28969447 CCGTGGTCGAACCTGTCAAAACAACACGGGCGTGCGACATTCCCGTGTGGAAG-AA
1 CCGTGGTCGAACCTGTCAAAACAACACGAGCGTGCGACATGCCCGTGT-CAAGCAA
* * * * * *
28969502 CCGTGGGT-GAACCTATTAAAACAGCACGAGCGTGTGACATGCCCGTGTCTAGCAC
1 CCGT-GGTCGAACCTGTCAAAACAACACGAGCGTGCGACATGCCCGTGTCAAGCAA
28969557 CCGTGGTCGAACCTGT
1 CCGTGGTCGAACCTGT
28969573 TAGATTGACA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
54 5 0.09
55 50 0.86
56 3 0.05
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.19
Consensus pattern (55 bp):
CCGTGGTCGAACCTGTCAAAACAACACGAGCGTGCGACATGCCCGTGTCAAGCAA
Found at i:28990548 original size:20 final size:20
Alignment explanation
Indices: 28990523--28990563 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28990513 GGGCAAAAGT
28990523 GTAAAATGTGGAACTTTAGG
1 GTAAAATGTGGAACTTTAGG
28990543 GTAAAATGTGGAACTTTAGG
1 GTAAAATGTGGAACTTTAGG
28990563 G
1 G
28990564 GCAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (20 bp):
GTAAAATGTGGAACTTTAGG
Found at i:28990573 original size:22 final size:20
Alignment explanation
Indices: 28990525--28990573 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
28990515 GCAAAAGTGT
*
28990525 AAAATGTGGAACTTTAGGGT
1 AAAATGTGGAACTTTAGGGA
28990545 AAAATGTGGAACTTTAGGGGCA
1 AAAATGTGGAACTTTA-GGG-A
28990567 AAAATGT
1 AAAATGT
28990574 AATTTTACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.27
Consensus pattern (20 bp):
AAAATGTGGAACTTTAGGGA
Found at i:28990990 original size:48 final size:48
Alignment explanation
Indices: 28990934--28991116 Score: 161
Period size: 48 Copynumber: 3.8 Consensus size: 48
28990924 ACATGTGAGT
* * * **
28990934 ATAA-AGATCCCGTGTAAGACCATATCTGGGATATGACATTGGCATTG
1 ATAAGAGATCCCATATAAGACCATATCTGGGATATGGCATTGGCACCG
* ** * * *
28990981 ATAAGAGATCCCATATAAGATCACGTCTAGGACATGGCATCGGCACCG
1 ATAAGAGATCCCATATAAGACCATATCTGGGATATGGCATTGGCACCG
* * * * *
28991029 GTATGAGATCTCATGTAAGACCATATCTGGGATATGGCATTGGCAGCG
1 ATAAGAGATCCCATATAAGACCATATCTGGGATATGGCATTGGCACCG
* * * * * *
28991077 ATATGAGGTCCCGTATAAGACCATGTCTAGGACATGGCAT
1 ATAAGAGATCCCATATAAGACCATATCTGGGATATGGCAT
28991117 CAACACCATT
Statistics
Matches: 105, Mismatches: 30, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
47 4 0.04
48 101 0.96
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (48 bp):
ATAAGAGATCCCATATAAGACCATATCTGGGATATGGCATTGGCACCG
Found at i:28991070 original size:96 final size:96
Alignment explanation
Indices: 28990946--28991207 Score: 277
Period size: 96 Copynumber: 2.8 Consensus size: 96
28990936 AAAGATCCCG
** *
28990946 TGTAAGACCATATCTGGGATATGACATTGGCATTGATAAGAGATCCCATATAAGATCACGTCTAG
1 TGTAAGACCATATCTGGGATATGACATTGGCAGCGATAAGAGATCCCATATAAGACCACGTCTAG
** *
28991011 GACATGGCATCGGCACCGGTATGAGA-TCTCA
66 GACATGGCATCAACACCAGTATGAGACT-TCA
* * * * *
28991042 TGTAAGACCATATCTGGGATATGGCATTGGCAGCGATATGAGGTCCCGTATAAGACCATGTCTAG
1 TGTAAGACCATATCTGGGATATGACATTGGCAGCGATAAGAGATCCCATATAAGACCACGTCTAG
* *
28991107 GACATGGCATCAACACCATTATGAGACTTCG
66 GACATGGCATCAACACCAGTATGAGACTTCA
* * ** * * *
28991138 TGTAAGACCATAGT-TGGG--CT---ATTGGCATCGATGTGAGATCTCATGTAAGACCACGTCTG
1 TGTAAGACCATA-TCTGGGATATGACATTGGCAGCGATAAGAGATCCCATATAAGACCACGTCTA
28991197 GGACATGGCAT
65 GGACATGGCAT
28991208 TGGCATCTTT
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
91 42 0.30
94 1 0.01
96 97 0.68
97 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (96 bp):
TGTAAGACCATATCTGGGATATGACATTGGCAGCGATAAGAGATCCCATATAAGACCACGTCTAG
GACATGGCATCAACACCAGTATGAGACTTCA
Found at i:28991130 original size:48 final size:47
Alignment explanation
Indices: 28990985--28991132 Score: 143
Period size: 48 Copynumber: 3.1 Consensus size: 47
28990975 GCATTGATAA
* * *
28990985 GAGATCCCATATAAGATCACGTCTAGGACATGGCATCGGCACCGGTAT
1 GAGATCCCATATAAGACCATGTCTAGGACATGGCATCGGCACC-ATAT
* * * * * * *
28991033 GAGATCTCATGTAAGACCATATCTGGGATATGGCATTGGCAGCGATAT
1 GAGATCCCATATAAGACCATGTCTAGGACATGGCATCGGCA-CCATAT
* * **
28991081 GAGGTCCCGTATAAGACCATGTCTAGGACATGGCATCAACACCATTAT
1 GAGATCCCATATAAGACCATGTCTAGGACATGGCATCGGCACCA-TAT
28991129 GAGA
1 GAGA
28991133 CTTCGTGTAA
Statistics
Matches: 76, Mismatches: 22, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
47 2 0.03
48 73 0.96
49 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (47 bp):
GAGATCCCATATAAGACCATGTCTAGGACATGGCATCGGCACCATAT
Found at i:28997457 original size:18 final size:18
Alignment explanation
Indices: 28997434--28997494 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
28997424 ATATGGGGCA
28997434 TCCGAGTTCGTTGAGTGG
1 TCCGAGTTCGTTGAGTGG
**
28997452 TCCGAGTTCG--GAAG-CA
1 TCCGAGTTCGTTG-AGTGG
28997468 TCCGAGCTT-GTTGAGTGG
1 TCCGAG-TTCGTTGAGTGG
28997486 TCCGAGTTC
1 TCCGAGTTC
28997495 ATAATGGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 8 0.24
17 8 0.24
18 17 0.52
ACGTcount: A:0.15, C:0.21, G:0.34, T:0.30
Consensus pattern (18 bp):
TCCGAGTTCGTTGAGTGG
Found at i:29009014 original size:40 final size:40
Alignment explanation
Indices: 29008930--29009113 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
29008920 TTGAATGCTG
* * * *
29008930 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
29008969 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
29009010 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
29009050 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
29009090 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29009114 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:29009067 original size:80 final size:81
Alignment explanation
Indices: 29008930--29009110 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
29008920 TTGAATGCTG
* * *
29008930 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
29008994 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
29009010 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
29009071 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
29009090 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
29009111 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:29009134 original size:39 final size:38
Alignment explanation
Indices: 29009011--29009160 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
29009001 GTTATTAATT
* ** * *
29009011 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
29009051 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
29009090 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
29009130 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
29009161 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:29016868 original size:40 final size:40
Alignment explanation
Indices: 29016784--29016967 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
29016774 TTGAATGCTG
* * * *
29016784 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
29016823 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
29016864 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
29016904 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
29016944 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29016968 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:29016921 original size:80 final size:81
Alignment explanation
Indices: 29016784--29016964 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
29016774 TTGAATGCTG
* * *
29016784 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
29016848 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
29016864 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
29016925 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
29016944 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
29016965 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:29016988 original size:39 final size:38
Alignment explanation
Indices: 29016865--29017014 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
29016855 GTTATTAATT
* ** * *
29016865 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
29016905 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
29016944 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
29016984 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
29017015 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:29019535 original size:23 final size:23
Alignment explanation
Indices: 29019509--29019621 Score: 124
Period size: 23 Copynumber: 4.9 Consensus size: 23
29019499 TAACTCATAT
29019509 GAGCTTACTGTTTCAGCTC-ATCA
1 GAGCTTACTGTTTCAGCTCAAT-A
* *
29019532 GAGCTTATTGATTCAGCTCGAA-A
1 GAGCTTACTGTTTCAGCTC-AATA
*
29019555 GAGCTTACT-ATTCAGCTCAATA
1 GAGCTTACTGTTTCAGCTCAATA
*
29019577 GAGCTTACCGTTTTCAGCTCAATA
1 GAGCTTACTG-TTTCAGCTCAATA
*
29019601 GAGCTTACTATTATCAGCTCA
1 GAGCTTACTGTT-TCAGCTCA
29019622 TGAAAAGCTT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.03
22 18 0.23
23 28 0.36
24 28 0.36
25 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (23 bp):
GAGCTTACTGTTTCAGCTCAATA
Found at i:29021831 original size:18 final size:19
Alignment explanation
Indices: 29021791--29021833 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
29021781 CAGGCTAAAG
29021791 ACACGGGCGTGTCTGAGCC
1 ACACGGGCGTGTCTGAGCC
*
29021810 ACACGGGCGTGTGTGA-CC
1 ACACGGGCGTGTCTGAGCC
29021828 ACACGG
1 ACACGG
29021834 CTACCCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.19, C:0.30, G:0.37, T:0.14
Consensus pattern (19 bp):
ACACGGGCGTGTCTGAGCC
Found at i:29026449 original size:48 final size:48
Alignment explanation
Indices: 29026389--29026553 Score: 195
Period size: 48 Copynumber: 3.4 Consensus size: 48
29026379 ATGTGAGTAT
* *
29026389 TGAGATATCGTATAAGACCATATTTGGGATATGACATTGACATCAATA
1 TGAGATCTCGTATAAGACCATATTTGGGATATGGCATTGACATCAATA
* * ** * * * *
29026437 AGAGATCCCGTATAAGACCACGTCTGGGACATGGCATCGACATCAGTA
1 TGAGATCTCGTATAAGACCATATTTGGGATATGGCATTGACATCAATA
* * * *
29026485 TGAGATCTCATGTAAGACCATATTTGGGATATGGCATTGGCATCGATA
1 TGAGATCTCGTATAAGACCATATTTGGGATATGGCATTGACATCAATA
*
29026533 TGAGGTCTCGTATAAGACCAT
1 TGAGATCTCGTATAAGACCAT
29026554 GCCTGGGACA
Statistics
Matches: 92, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (48 bp):
TGAGATCTCGTATAAGACCATATTTGGGATATGGCATTGACATCAATA
Found at i:29026560 original size:96 final size:96
Alignment explanation
Indices: 29026401--29026602 Score: 273
Period size: 96 Copynumber: 2.1 Consensus size: 96
29026391 AGATATCGTA
*
29026401 TAAGACCATATTTGGGATATGACATTGACATCAATAAGAGATCCCGTATAAGACCACGTCTGGGA
1 TAAGACCATATTTGGGATATGACATTGACATCAATAAGAGATCCCGTATAAGACCACGCCTGGGA
29026466 CATGGCATCGACATCAG-TATGAGA-TCTCATG
66 CATGGCATCGACA-CAGTTATGAGACT-TCATG
* * * * * * *
29026497 TAAGACCATATTTGGGATATGGCATTGGCATCGATATGAGGTCTCGTATAAGACCATGCCTGGGA
1 TAAGACCATATTTGGGATATGACATTGACATCAATAAGAGATCCCGTATAAGACCACGCCTGGGA
** *
29026562 CATGGCATCGGTACCGTTATGAGACTTCATG
66 CATGGCATCGACACAGTTATGAGACTTCATG
29026593 TAAGACCATA
1 TAAGACCATA
29026603 GCTGGGCTGT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 2 0.02
96 90 0.97
97 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (96 bp):
TAAGACCATATTTGGGATATGACATTGACATCAATAAGAGATCCCGTATAAGACCACGCCTGGGA
CATGGCATCGACACAGTTATGAGACTTCATG
Found at i:29026597 original size:48 final size:47
Alignment explanation
Indices: 29026449--29026601 Score: 146
Period size: 48 Copynumber: 3.2 Consensus size: 47
29026439 AGATCCCGTA
* * *
29026449 TAAGACCACGTCTGGGACATGGCATCGACATCAGTATGAGATCTCATG
1 TAAGACCATGTCTGGGACATGGCATCGGCA-CCGTATGAGATCTCATG
* * * * * * * *
29026497 TAAGACCATATTTGGGATATGGCATTGGCATCGATATGAGGTCTCGTA
1 TAAGACCATGTCTGGGACATGGCATCGGCACCG-TATGAGATCTCATG
* *
29026545 TAAGACCATGCCTGGGACATGGCATCGGTACCGTTATGAGA-CTTCATG
1 TAAGACCATGTCTGGGACATGGCATCGGCACCG-TATGAGATC-TCATG
29026593 TAAGACCAT
1 TAAGACCAT
29026602 AGCTGGGCTG
Statistics
Matches: 81, Mismatches: 22, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
47 2 0.02
48 79 0.98
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGGCATCGGCACCGTATGAGATCTCATG
Found at i:29029652 original size:27 final size:27
Alignment explanation
Indices: 29029614--29029698 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
29029604 TCGGTCATTA
*
29029614 TACACTACAAGGATATTTTGGTAATTT
1 TACACTACAAGGGTATTTTGGTAATTT
*
29029641 TACACTGCAAGGGTATTTTGGTAATTT
1 TACACTACAAGGGTATTTTGGTAATTT
*
29029668 TACACTACAAGGGTATTTTGATAATTT
1 TACACTACAAGGGTATTTTGGTAATTT
29029695 TACA
1 TACA
29029699 AATCGGGGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (27 bp):
TACACTACAAGGGTATTTTGGTAATTT
Found at i:29029708 original size:27 final size:27
Alignment explanation
Indices: 29029627--29029963 Score: 339
Period size: 27 Copynumber: 12.5 Consensus size: 27
29029617 ACTACAAGGA
* * *
29029627 TATTTTGGTAATTTTAC-ACTGCAAGGG
1 TATTTTGATAATTTTACAAAT-CGAGGG
* * *
29029654 TATTTTGGTAATTTTAC-ACTACAAGGG
1 TATTTTGATAATTTTACAAAT-CGAGGG
*
29029681 TATTTTGATAATTTTACAAATCGGGGG
1 TATTTTGATAATTTTACAAATCGAGGG
* *
29029708 T-GTTTCAGTAATTTTACAAATCGAGGG
1 TATTTTGA-TAATTTTACAAATCGAGGG
*
29029735 TA-TTTCAGTAATTTTACAAATCGAGGG
1 TATTTTGA-TAATTTTACAAATCGAGGG
29029762 TATTTTGATAATTTTACAAATC-AGGG
1 TATTTTGATAATTTTACAAATCGAGGG
* *
29029788 TATTTCGATAATTTTATAAATCGAGGG
1 TATTTTGATAATTTTACAAATCGAGGG
*
29029815 TATTTCGATAATTTTACAAATCGAGGG
1 TATTTTGATAATTTTACAAATCGAGGG
* **
29029842 CATTTCAATAATTTTACAAATCGAGGG
1 TATTTTGATAATTTTACAAATCGAGGG
* *
29029869 AATTTTGCTAATTTTACAAA-CTG-GGG
1 TATTTTGATAATTTTACAAATC-GAGGG
*
29029895 ATATTTCGATAATTTTACAAA-CTGAGGG
1 -TATTTTGATAATTTTACAAATC-GAGGG
* * * *
29029923 TACTTTGGTAACTTTCCAAATCGAGGG
1 TATTTTGATAATTTTACAAATCGAGGG
*
29029950 TATTTCGATAATTT
1 TATTTTGATAATTT
29029964 CTCTTTATTT
Statistics
Matches: 271, Mismatches: 30, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
26 32 0.12
27 229 0.85
28 10 0.04
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (27 bp):
TATTTTGATAATTTTACAAATCGAGGG
Found at i:29030329 original size:28 final size:28
Alignment explanation
Indices: 29030298--29030372 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
29030288 TCTCGTCCAC
29030298 ATGGCCCATCAGGCCCAACCACATTCAT
1 ATGGCCCATCAGGCCCAACCACATTCAT
* *
29030326 ATGGCCTATCAGGCCCAATCACATTCAT
1 ATGGCCCATCAGGCCCAACCACATTCAT
29030354 ATGGCCCATCAGGCCCAAC
1 ATGGCCCATCAGGCCCAAC
29030373 TACTTCCCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (28 bp):
ATGGCCCATCAGGCCCAACCACATTCAT
Found at i:29063090 original size:35 final size:35
Alignment explanation
Indices: 29063044--29063112 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
29063034 TAACCTTAAT
29063044 GAAATAATTATACAAACATTATATTCATGTCCTTG
1 GAAATAATTATACAAACATTATATTCATGTCCTTG
29063079 GAAATAATTATACAAACATTATATTCATGTCCTT
1 GAAATAATTATACAAACATTATATTCATGTCCTT
29063113 AACCGTCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (35 bp):
GAAATAATTATACAAACATTATATTCATGTCCTTG
Found at i:29068665 original size:14 final size:15
Alignment explanation
Indices: 29068630--29068666 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
29068620 AAATATGATC
29068630 CATTCATTCCCTCATT
1 CATTCA-TCCCTCATT
29068646 CA-TCATCCCTCA-T
1 CATTCATCCCTCATT
29068659 CATTCATC
1 CATTCATC
29068667 ATTATCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 12 0.60
15 3 0.15
16 2 0.10
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.38
Consensus pattern (15 bp):
CATTCATCCCTCATT
Found at i:29071905 original size:40 final size:40
Alignment explanation
Indices: 29071860--29071941 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
29071850 TACAGATATG
*
29071860 TTCGACGACA-AATCAATTATATATGGCACTTAGTGTGCGA
1 TTCGAC-ACAGAATCAACTATATATGGCACTTAGTGTGCGA
* ** *
29071900 TTCGACATAGCTTCGACTATATATGGCACTTAGTGTGCGA
1 TTCGACACAGAATCAACTATATATGGCACTTAGTGTGCGA
29071940 TT
1 TT
29071942 TAAGATAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 34 0.94
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (40 bp):
TTCGACACAGAATCAACTATATATGGCACTTAGTGTGCGA
Found at i:29071950 original size:40 final size:40
Alignment explanation
Indices: 29071877--29071979 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 40
29071867 ACAAATCAAT
*
29071877 TATATATGGCACTTAGTGTGCGATTCGACATAGCTTCGAC
1 TATATATGGCACTTAGTGTGCGATTCAACATAGCTTCGAC
* * *
29071917 TATATATGGCACTTAGTGTGCGATTTAAGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATTCAACATAGCTTCGAC
* **
29071957 TATGTACAGCACTTAGTGTGCGA
1 TATATATGGCACTTAGTGTGCGA
29071980 GATATCGAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGATTCAACATAGCTTCGAC
Found at i:29072009 original size:28 final size:28
Alignment explanation
Indices: 29071965--29072061 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 28
29071955 GCTATGTACA
29071965 GCACTTAGTGTGCGAGATATCGAGTGTG
1 GCACTTAGTGTGCGAGATATCGAGTGTG
29071993 GCACTTAGTGT-CTGAGATATCGAGTGTG
1 GCACTTAGTGTGC-GAGATATCGAGTGTG
* * * *
29072021 GCACTTAGTGCGCGAGATATTGAGTATA
1 GCACTTAGTGTGCGAGATATCGAGTGTG
*
29072049 ACACTTAGTGTGC
1 GCACTTAGTGTGC
29072062 AAGGCTTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 1 0.02
28 59 0.97
29 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (28 bp):
GCACTTAGTGTGCGAGATATCGAGTGTG
Found at i:29078876 original size:40 final size:40
Alignment explanation
Indices: 29078817--29079010 Score: 309
Period size: 40 Copynumber: 4.9 Consensus size: 40
29078807 GATATAGCTT
* *
29078817 CTCGCTCAAATGCCATCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
29078857 CTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* * *
29078897 CTCGCACAATTGCCTTCGGGACTTGGCCTGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
29078937 CTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
*
29078977 CTCGCACAAATGCCTTCGAG-CTTAGCCCGGTTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
29079011 CAATCCGAAT
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.09
40 130 0.91
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
Found at i:29078930 original size:80 final size:80
Alignment explanation
Indices: 29078790--29079010 Score: 313
Period size: 80 Copynumber: 2.8 Consensus size: 80
29078780 AAACTAAGTA
** * * *
29078790 CCTTCGGGGTTTAG-CCGGATATAGCT-TCTCGCTCAAATGCCATCGGGACTTAGCCCGGTTATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATA
*
29078853 GTAACTCGCACAATTG
65 GTAACTCGCACAAATG
* * * *
29078869 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTGGCCTGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
29078934 TAACTCGCACAAATG
66 TAACTCGCACAAATG
*
29078949 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
29079011 CAATCCGAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 25 0.20
80 100 0.80
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG
Found at i:29086345 original size:40 final size:40
Alignment explanation
Indices: 29086301--29086414 Score: 185
Period size: 40 Copynumber: 2.9 Consensus size: 40
29086291 GATATAGCTT
* *
29086301 CTCGCTCAAATGCCTTCGGGACTTAGTCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
* *
29086341 CTCGCACAATTGCTTTCGGGACTTAGCCCGGTTATAGTAA
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
29086381 CTCGCACAAATGCCTTCGGG-CTTAGCCCGGTTAT
1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
29086415 CAATCCGAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 14 0.21
40 54 0.79
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
Found at i:29091709 original size:40 final size:39
Alignment explanation
Indices: 29091665--29091767 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 39
29091655 AAAAATCAAT
29091665 TATATATGCCACTTAGTGTGCGATTCAACATAGCTTCGGC
1 TATATATG-CACTTAGTGTGCGATTCAACATAGCTTCGGC
* *
29091705 TATATATGGCACTTAGTGTGCGATTTAAGATAGCTTCGGC
1 TATATAT-GCACTTAGTGTGCGATTCAACATAGCTTCGGC
*
29091745 TACGTACA-GCACTTAGTGTGCGA
1 TA--TATATGCACTTAGTGTGCGA
29091768 GATATCGAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
40 53 0.93
41 1 0.02
42 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (39 bp):
TATATATGCACTTAGTGTGCGATTCAACATAGCTTCGGC
Found at i:29091797 original size:28 final size:28
Alignment explanation
Indices: 29091753--29091824 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
29091743 GCTACGTACA
* *
29091753 GCACTTAGTGTGCGAGATATCGAGTGTG
1 GCACTTAGTGTGCGAGATATCAAGTATG
*
29091781 GCACTTAGTGTGTGAGATATCAAGTATG
1 GCACTTAGTGTGCGAGATATCAAGTATG
**
29091809 AAACTTAGTGTGCGAG
1 GCACTTAGTGTGCGAG
29091825 GCTTTGAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (28 bp):
GCACTTAGTGTGCGAGATATCAAGTATG
Found at i:29098609 original size:16 final size:16
Alignment explanation
Indices: 29098590--29098621 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29098580 AAGAATGCTA
29098590 ATGAGTAAGTTATGCG
1 ATGAGTAAGTTATGCG
29098606 ATGAGTAAGTTATGCG
1 ATGAGTAAGTTATGCG
29098622 TAAGATACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (16 bp):
ATGAGTAAGTTATGCG
Found at i:29100144 original size:40 final size:40
Alignment explanation
Indices: 29100046--29100270 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
29100036 GCTCCTCGTT
* * * *
29100046 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
29100086 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
29100125 CGAATGCCTTCGGGTCTTAACCCGGATTTAGTACCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
29100165 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
29100205 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
29100246 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
29100271 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 39 0.25
40 103 0.66
41 15 0.10
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29100279 original size:41 final size:41
Alignment explanation
Indices: 29100202--29100279 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29100192 TTTGTATCTC
* * *
29100202 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29100243 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29100280 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:29105394 original size:39 final size:39
Alignment explanation
Indices: 29105190--29105412 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
29105180 TTGAATGCTG
* * * * * *
29105190 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
29105230 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
29105270 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
29105310 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
29105350 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
29105389 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29105413 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:29105432 original size:79 final size:80
Alignment explanation
Indices: 29105270--29105447 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
29105260 AGATACAAGT
* * * *
29105270 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
29105335 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
29105350 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
29105414 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
29105429 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
29105448 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:29114296 original size:18 final size:18
Alignment explanation
Indices: 29114273--29114309 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29114263 GGCCATTTGT
29114273 TAATTAGATGGACAAATA
1 TAATTAGATGGACAAATA
29114291 TAATTAGATGGACAAATA
1 TAATTAGATGGACAAATA
29114309 T
1 T
29114310 GGACATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (18 bp):
TAATTAGATGGACAAATA
Found at i:29120346 original size:28 final size:29
Alignment explanation
Indices: 29120236--29120348 Score: 115
Period size: 29 Copynumber: 4.0 Consensus size: 29
29120226 GTGAGCATGA
* **
29120236 ATATGAATGTGA-CTGGGCCTAGCGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
29120264 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
29120293 ATAT-ACAGGTTATTTGGGCATAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
29120322 ATATGAATATGA-TTGGGCTTAATGGGC
1 ATATGAATGTGATTTGGGCCTAATGGGC
29120349 TAGATACAGG
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
28 26 0.37
29 44 0.62
30 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:29124643 original size:29 final size:28
Alignment explanation
Indices: 29124610--29124701 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 28
29124600 TGGGCCAAGC
29124610 GGGCCATATAAATGTGATTTGGGTCTAAT
1 GGGCCATATAAATGTGATTTGGG-CTAAT
29124639 GGGCCATATACAA-GTGATTTGGGCCTAAT
1 GGGCCATATA-AATGTGATTTGGG-CTAAT
* *
29124668 GGGCCATATGAATATGA-TTGGGCTTAAT
1 GGGCCATATAAATGTGATTTGGGC-TAAT
29124696 GGGCCA
1 GGGCCA
29124702 GATACAGGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
27 1 0.02
28 17 0.30
29 37 0.65
30 2 0.04
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
GGGCCATATAAATGTGATTTGGGCTAAT
Found at i:29131684 original size:33 final size:31
Alignment explanation
Indices: 29131603--29131688 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
29131593 AACCCTTCCT
* *
29131603 GCATTAAATCCAACCAAAAATAGAAAATATA
1 GCATAAAATCCAACCAAAAACAGAAAATATA
* * *
29131634 GCATGAAATCCAACCAAAAACAGCAAATGTA
1 GCATAAAATCCAACCAAAAACAGAAAATATA
*
29131665 GCATAAAAAATACAACCAAAAACA
1 GCAT--AAAATCCAACCAAAAACA
29131689 TTAAATCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 31 0.66
33 16 0.34
ACGTcount: A:0.58, C:0.20, G:0.08, T:0.14
Consensus pattern (31 bp):
GCATAAAATCCAACCAAAAACAGAAAATATA
Found at i:29131945 original size:21 final size:21
Alignment explanation
Indices: 29131921--29131981 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
29131911 TCTGCTACCA
*
29131921 TTGCTGTTACC-TCTGCCTCCC
1 TTGCTGCTACCAT-TGCCTCCC
29131942 TTGCTGCTACCATTGCCTCCC
1 TTGCTGCTACCATTGCCTCCC
* * * *
29131963 TCGCTACTGCCACTGCCTC
1 TTGCTGCTACCATTGCCTC
29131982 TGTCTCTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.08, C:0.44, G:0.15, T:0.33
Consensus pattern (21 bp):
TTGCTGCTACCATTGCCTCCC
Found at i:29137436 original size:9 final size:9
Alignment explanation
Indices: 29137422--29137544 Score: 156
Period size: 9 Copynumber: 13.7 Consensus size: 9
29137412 TAAGTATAAT
29137422 TAAGTTATG
1 TAAGTTATG
*
29137431 TAAGTTCTG
1 TAAGTTATG
29137440 TAAGTTATG
1 TAAGTTATG
*
29137449 TGAGTTATG
1 TAAGTTATG
*
29137458 TAGGTTATG
1 TAAGTTATG
*
29137467 TAAGTTATA
1 TAAGTTATG
29137476 TAAGTTATG
1 TAAGTTATG
**
29137485 TGGGTTATG
1 TAAGTTATG
* *
29137494 TTAGTTTTG
1 TAAGTTATG
*
29137503 TGAGTTATG
1 TAAGTTATG
29137512 TAAGTTATG
1 TAAGTTATG
*
29137521 TAAGTTATA
1 TAAGTTATG
29137530 TAAGTTATG
1 TAAGTTATG
29137539 TAAGTT
1 TAAGTT
29137545 CAAGTATATA
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 96 1.00
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29137848 original size:13 final size:15
Alignment explanation
Indices: 29137814--29137874 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
29137804 CAGATGGAAA
29137814 AAAAAAT-TTTAATT
1 AAAAAATATTTAATT
*
29137828 AAATAATATTT-A-T
1 AAAAAATATTTAATT
29137841 AAAAAATATATTAATT
1 AAAAAATAT-TTAATT
* * *
29137857 TAATAATATTTAAAT
1 AAAAAATATTTAATT
29137872 AAA
1 AAA
29137875 TTAATCCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.24
14 9 0.24
15 11 0.30
16 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAATATTTAATT
Found at i:29137854 original size:29 final size:29
Alignment explanation
Indices: 29137812--29137868 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
29137802 ATCAGATGGA
*
29137812 AAAAAAAATTTTAATTAAATAATATTTAT
1 AAAAAAAATATTAATTAAATAATATTTAT
* *
29137841 AAAAAATATATTAATTTAATAATATTTA
1 AAAAAAAATATTAATTAAATAATATTTA
29137869 AATAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAAAAAATATTAATTAAATAATATTTAT
Found at i:29137869 original size:15 final size:15
Alignment explanation
Indices: 29137821--29137918 Score: 61
Period size: 16 Copynumber: 6.9 Consensus size: 15
29137811 AAAAAAAAAT
29137821 TTTAATTAAATAATA
1 TTTAATTAAATAATA
*
29137836 TTT-A-TAAAAAATA
1 TTTAATTAAATAATA
*
29137849 TATTAATTTAATAATA
1 T-TTAATTAAATAATA
29137865 --T--TTAAATAA-A
1 TTTAATTAAATAATA
* *
29137875 -TTAATCCAAATTATA
1 TTTAAT-TAAATAATA
29137890 -TTAATTAAATAATA
1 TTTAATTAAATAATA
*
29137904 TTTAAATAAAATAAT
1 TTT-AATTAAATAAT
29137919 CCAAATTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
10 1 0.02
11 8 0.12
13 11 0.17
14 15 0.23
15 12 0.19
16 17 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAATTAAATAATA
Found at i:29137893 original size:39 final size:39
Alignment explanation
Indices: 29137847--29137937 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
29137837 TTATAAAAAA
* *
29137847 TATATTAATTTAATAATATTTAAATAAATTAATCCAAAT
1 TATATTAATTAAATAATATTTAAATAAAATAATCCAAAT
29137886 TATATTAATTAAATAATATTTAAATAAAATAATCCAAAT
1 TATATTAATTAAATAATATTTAAATAAAATAATCCAAAT
29137925 TATATTAATTAAA
1 TATATTAATTAAA
29137938 ATAAGATTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (39 bp):
TATATTAATTAAATAATATTTAAATAAAATAATCCAAAT
Found at i:29137895 original size:19 final size:19
Alignment explanation
Indices: 29137873--29137936 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
29137863 TATTTAAATA
29137873 AATTAATCCAAATTATATT
1 AATTAATCCAAATTATATT
* *
29137892 AATTAAAT--AATATTTAAATA
1 AATT-AATCCAA-A-TTATATT
*
29137912 AAATAATCCAAATTATATT
1 AATTAATCCAAATTATATT
29137931 AATTAA
1 AATTAA
29137937 AATAAGATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 2 0.06
19 18 0.53
20 12 0.35
21 2 0.06
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAATCCAAATTATATT
Found at i:29138717 original size:67 final size:67
Alignment explanation
Indices: 29138609--29138746 Score: 267
Period size: 67 Copynumber: 2.1 Consensus size: 67
29138599 CATACACCTG
29138609 CATTTTATGATGTAAAGCATGCTAGTTGCTACTCCAATGGCTAATCTTAGTTGTCTATGTGGTTT
1 CATTTTATGATGTAAAGCATGCTAGTTGCTACTCCAATGGCTAATCTTAGTTGTCTATGTGGTTT
29138674 GC
66 GC
*
29138676 CATTTTATGATGTAAAGCATGCTAGTTGCTATTCCAATGGCTAATCTTAGTTGTCTATGTGGTTT
1 CATTTTATGATGTAAAGCATGCTAGTTGCTACTCCAATGGCTAATCTTAGTTGTCTATGTGGTTT
29138741 GC
66 GC
29138743 CATT
1 CATT
29138747 ATAAATTGAG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (67 bp):
CATTTTATGATGTAAAGCATGCTAGTTGCTACTCCAATGGCTAATCTTAGTTGTCTATGTGGTTT
GC
Found at i:29141692 original size:26 final size:26
Alignment explanation
Indices: 29141657--29141776 Score: 197
Period size: 26 Copynumber: 4.6 Consensus size: 26
29141647 AAGAATGAGA
*
29141657 TAAAATTTGAAATATTGAAAATTATT
1 TAAAATTTGAAATCTTGAAAATTATT
29141683 TAAAATTTGAAATCTTGAAAATTATT
1 TAAAATTTGAAATCTTGAAAATTATT
29141709 TAAAATTTGAAATCTTGAAAATTATT
1 TAAAATTTGAAATCTTGAAAATTATT
* *
29141735 TAAAATTTTAATTCTTGAAAATTATT
1 TAAAATTTGAAATCTTGAAAATTATT
29141761 CT-AAATTTGAAATCTT
1 -TAAAATTTGAAATCTT
29141777 TAAATTTTGA
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 87 0.99
27 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (26 bp):
TAAAATTTGAAATCTTGAAAATTATT
Found at i:29141826 original size:7 final size:7
Alignment explanation
Indices: 29141814--29141847 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
29141804 ATTAAAAAAC
29141814 AACCCCT
1 AACCCCT
29141821 AACCCCT
1 AACCCCT
*
29141828 AACCCTT
1 AACCCCT
29141835 AAACCCCT
1 -AACCCCT
29141843 AACCC
1 AACCC
29141848 TTGTCCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.32, C:0.53, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCCCT
Found at i:29141841 original size:15 final size:15
Alignment explanation
Indices: 29141821--29141849 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29141811 AACAACCCCT
29141821 AACCCCTAACCCTTA
1 AACCCCTAACCCTTA
29141836 AACCCCTAACCCTT
1 AACCCCTAACCCTT
29141850 GTCCCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCCTAACCCTTA
Found at i:29141899 original size:7 final size:7
Alignment explanation
Indices: 29141887--29141930 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
29141877 CATATCCTAT
29141887 TAAACCC
1 TAAACCC
29141894 TAAACCC
1 TAAACCC
29141901 TAAACCCC
1 TAAA-CCC
*
29141909 TAACCCC
1 TAAACCC
29141916 T-AACCC
1 TAAACCC
29141922 TATAACCC
1 TA-AACCC
29141930 T
1 T
29141931 TCTCTCCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 5 0.16
7 15 0.47
8 12 0.38
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:29141974 original size:14 final size:15
Alignment explanation
Indices: 29141947--29141979 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29141937 CTATCCTATT
29141947 AACCATAAACCCTTA
1 AACCATAAACCCTTA
29141962 AACCATAAA-CCTTA
1 AACCATAAACCCTTA
29141976 AACC
1 AACC
29141980 TTACATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (15 bp):
AACCATAAACCCTTA
Found at i:29142041 original size:15 final size:15
Alignment explanation
Indices: 29142003--29142051 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
29141993 CTTAAACCAC
*
29142003 AAACC-ATAACCCCT
1 AAACCAATAATCCCT
*
29142017 AAACCCATAATCCCT
1 AAACCAATAATCCCT
* *
29142032 AAATCAATAATCCAT
1 AAACCAATAATCCCT
29142047 AAACC
1 AAACC
29142052 TTAAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACCAATAATCCCT
Found at i:29149848 original size:13 final size:14
Alignment explanation
Indices: 29149832--29149860 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29149822 GAGAGCCATC
29149832 AGCAAAGG-AGCAA
1 AGCAAAGGAAGCAA
29149845 AGCAAAGGAAGCAA
1 AGCAAAGGAAGCAA
29149859 AG
1 AG
29149861 AAGCATTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.14, G:0.31, T:0.00
Consensus pattern (14 bp):
AGCAAAGGAAGCAA
Found at i:29155575 original size:17 final size:17
Alignment explanation
Indices: 29155553--29155588 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29155543 GAATAACTAG
29155553 CATTTAGGCATACATAA
1 CATTTAGGCATACATAA
29155570 CATTTAGGCATACATAA
1 CATTTAGGCATACATAA
29155587 CA
1 CA
29155589 CCATGTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (17 bp):
CATTTAGGCATACATAA
Done.