Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold294.1
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: 1351009
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 40239 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:403094 original size:89 final size:90
Alignment explanation
Indices: 402986--403201 Score: 230
Period size: 90 Copynumber: 2.4 Consensus size: 90
402976 TAAATTACAG
* *
402986 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAG-TTACA-AGTCTTATCTC-CTTGAAGT
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGATTACAGA-TCTTATCTCTC-TGAAGT
403048 TGCAGTAGAGCAGACTGAAAATAGCAA
64 TGCAGTAGAGCAGACTGAAAATAGCAA
* * *
403075 ATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAG----ATTACAGATCTTATCTCTCTGAA
* *
403140 GTTGCAGTAGAGCAGA-T-CAAA-A-CAG
62 GTTGCAGTAGAGCAGACTGAAAATAGCAA
* * * *
403165 ATCTTGTCTCCCTGAAGTTGTAGTGGAACAGATCGAA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAA
403202 AACGGTAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
89 33 0.31
90 34 0.31
91 1 0.01
92 3 0.03
93 1 0.01
94 34 0.31
95 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (90 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAGATTACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGCAGACTGAAAATAGCAA
Found at i:403180 original size:41 final size:41
Alignment explanation
Indices: 403120--403242 Score: 122
Period size: 41 Copynumber: 2.9 Consensus size: 41
403110 AAGCTAAATT
* *
403120 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC-AAA
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* *
403161 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAACAGATCGAAA
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* * *
403203 ACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGAT
1 AC---AGATCTTGTCTCCCTGAAGTTGCAGTG-AGCAGAT
403243 TCAAGCCATC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 33 0.49
42 5 0.07
44 1 0.01
45 28 0.42
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
ACAGATCTTGTCTCCCTGAAGTTGCAGTGAGCAGATCGAAA
Found at i:403294 original size:224 final size:224
Alignment explanation
Indices: 403062--403560 Score: 820
Period size: 224 Copynumber: 2.2 Consensus size: 224
403052 GTAGAGCAGA
*
403062 CTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
1 CTGAAAATAGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
**
403127 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTGTAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
*
403192 ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCATCAAGC
131 ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGC
* *
403257 CTTAATCCCCAAAGCAGTAGGGTAATAGG
196 CTTAACCCCCAAAGCAATAGGGTAATAGG
* * *
403286 TTGAAAATAGCAAATTTTATATCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
1 CTGAAAATAGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
403351 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
* *
403416 ACAGATCGAAGACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGT
131 ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGC
*
403481 CTTAACCCCCTAAGCAATAGGGTAATAGG
196 CTTAACCCCCAAAGCAATAGGGTAATAGG
* * * * * *
403510 CCGAAAATCA-CTAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAG
1 CTGAAAAT-AGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAG
403561 ACAACGGATC
Statistics
Matches: 253, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
224 252 1.00
225 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (224 bp):
CTGAAAATAGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGC
CTTAACCCCCAAAGCAATAGGGTAATAGG
Found at i:403404 original size:41 final size:41
Alignment explanation
Indices: 403344--403466 Score: 113
Period size: 41 Copynumber: 2.9 Consensus size: 41
403334 AAGCTAAATT
* *
403344 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC-AAA
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* * *
403385 ACAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAG
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* * *
403427 ACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGAT
1 AC---AGATCTTGTCTCCCTGAAGTTGCAGTG-AGCAGAT
403467 TCAAGCCACC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 33 0.50
42 4 0.06
44 1 0.02
45 28 0.42
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (41 bp):
ACAGATCTTGTCTCCCTGAAGTTGCAGTGAGCAGATCGAAA
Found at i:405124 original size:24 final size:24
Alignment explanation
Indices: 405087--405149 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
405077 TCATGTACAC
*
405087 ATTATT-TATATTATTTTCA-TGATT
1 ATTATTGTAT-TTATTTTCACT-ACT
* *
405111 ATTATTGTGTTTATTTTTACTACT
1 ATTATTGTATTTATTTTCACTACT
405135 ATTATTGTATTTATT
1 ATTATTGTATTTATT
405150 ATTAGTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.63
Consensus pattern (24 bp):
ATTATTGTATTTATTTTCACTACT
Found at i:405164 original size:24 final size:24
Alignment explanation
Indices: 405108--405164 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
405098 TATTTTCATG
* *
405108 ATTATTATTGTGTTTATTTTTACT
1 ATTATTATTGTATTTATTATTACT
* *
405132 ACTATTATTGTATTTATTATTAGT
1 ATTATTATTGTATTTATTATTACT
*
405156 ATTAGTATT
1 ATTATTATT
405165 ATAATTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (24 bp):
ATTATTATTGTATTTATTATTACT
Found at i:405291 original size:14 final size:14
Alignment explanation
Indices: 405272--405307 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
405262 TATTTTTAAC
405272 ATATATATGTATAT
1 ATATATATGTATAT
*
405286 ATATATATGTATGT
1 ATATATATGTATAT
405300 ATATATAT
1 ATATATAT
405308 ATTTATGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:405377 original size:2 final size:2
Alignment explanation
Indices: 405370--405450 Score: 55
Period size: 2 Copynumber: 42.5 Consensus size: 2
405360 GTGTATGTAT
* * *
405370 TA TA TA TA TT TT TA -A TA CTA TA T- TA TG TA TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
405409 TA TA TA TA TA TA TA TA TA TT TA T- TA TA TT TT TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
405450 T
1 T
405451 TTTTAATATC
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
1 5 0.08
2 56 0.89
3 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (2 bp):
TA
Found at i:405467 original size:25 final size:24
Alignment explanation
Indices: 405372--405491 Score: 97
Period size: 25 Copynumber: 5.0 Consensus size: 24
405362 GTATGTATTA
405372 TATATATTT-TTAATACTATATTATG
1 TATATATTTATT-ATA-TATATTATG
*
405397 TATATATTATATTATATATA-TATA
1 TATATATT-TATTATATATATTATG
*
405421 TATATATTTATTATAT-TTTTATG
1 TATATATTTATTATATATATTATG
*
405444 TATATATTT-TTAATATCACATTAT-
1 TATATATTTATT-ATAT-ATATTATG
* * *
405468 TCATATGTTTTTTTTATATATTAT
1 T-ATATATTTATTATATATATTAT
405492 CCCATGTAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.04
23 24 0.30
24 18 0.23
25 26 0.33
26 6 0.08
27 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (24 bp):
TATATATTTATTATATATATTATG
Found at i:407648 original size:45 final size:44
Alignment explanation
Indices: 407588--407885 Score: 244
Period size: 49 Copynumber: 6.6 Consensus size: 44
407578 ACCATCCTAG
*
407588 CTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CAAATCTTAT
* * * *
407633 TTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAG----A-TACAAATCTTAT
* * * * *
407682 CTCTCTGAAGTTGCAGTAGAGCAG-GTCGAAGTTACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATACAAATCTTAT
* * *
407726 CTCCTTGAAGTTGCAGTAGAGCAGACTGAAAATAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CAAATCTTAT
* * *
407771 TTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAG----A-TACAAATCTTAT
* * * * *
407820 CTCTCTGAAGTTGCAGTAGAGCAGA-TCAA-A-ACAGATCTTGT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAATCTTAT
* *
407861 CTCCCTGAAGTTGTAGTGGAACAGA
1 CTCCCTGAAGTTGCAGTGGAGCAGA
407886 TCGAAAACGG
Statistics
Matches: 206, Mismatches: 34, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
41 31 0.15
43 1 0.00
44 37 0.18
45 63 0.31
48 4 0.02
49 66 0.32
50 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAATCTTAT
Found at i:407763 original size:138 final size:138
Alignment explanation
Indices: 407595--407843 Score: 471
Period size: 138 Copynumber: 1.8 Consensus size: 138
407585 TAGCTCCCTA
* *
407595 AAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT
1 AAGTTGCAGTAGAGCAGACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT
407660 GAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTA
66 GAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTA
407725 TCTCCTTG
131 TCTCCTTG
*
407733 AAGTTGCAGTAGAGCAGACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATT
1 AAGTTGCAGTAGAGCAGACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT
407798 GAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
66 GAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
407844 ATCAAAACAG
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 108 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (138 bp):
AAGTTGCAGTAGAGCAGACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT
GAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTA
TCTCCTTG
Found at i:407785 original size:89 final size:90
Alignment explanation
Indices: 407588--407890 Score: 239
Period size: 94 Copynumber: 3.3 Consensus size: 90
407578 ACCATCCTAG
* * * * * *
407588 CTCCCTAAAGTTGCAGTGGAGCAGA-CTGAAGA-TAGCAAATCTTATTTCCCTGAAGTTGCAGTG
1 CTCCCTGAAGTTGCAGTAGAGCAGATC-GAAGATTA-CAGATCTTATCTCTCTGAAGTTGCAGTA
* * *
407651 GAACAGATTGAAGCTAAATTA-CAGATCTTAT
64 GAGCAGACTG-A---AAA-TAGCAAATCTTAT
* *
407682 CTCTCTGAAGTTGCAGTAGAGCAGGTCGAAG-TTACA-AGTCTTATCTC-CTTGAAGTTGCAGTA
1 CTCCCTGAAGTTGCAGTAGAGCAGATCGAAGATTACAGA-TCTTATCTCTC-TGAAGTTGCAGTA
407744 GAGCAGACTGAAAATAGCAAATCTTAT
64 GAGCAGACTGAAAATAGCAAATCTTAT
* * *
407771 TTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAG
1 CTCCCTGAAGTTGCAGTAGAGCAGATCGAAG----ATTACAGATCTTATCTCTCTGAAGTTGCAG
* * *
407836 TAGAGCAGA-T-CAAA-A-CAGATCTTGT
62 TAGAGCAGACTGAAAATAGCAAATCTTAT
* * *
407861 CTCCCTGAAGTTGTAGTGGAACAGATCGAA
1 CTCCCTGAAGTTGCAGTAGAGCAGATCGAA
407891 AACGGTAAAT
Statistics
Matches: 176, Mismatches: 21, Indels: 28
0.78 0.09 0.12
Matches are distributed among these distances:
88 2 0.01
89 38 0.22
90 34 0.19
91 1 0.01
92 6 0.03
93 31 0.18
94 61 0.35
95 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (90 bp):
CTCCCTGAAGTTGCAGTAGAGCAGATCGAAGATTACAGATCTTATCTCTCTGAAGTTGCAGTAGA
GCAGACTGAAAATAGCAAATCTTAT
Found at i:407869 original size:41 final size:41
Alignment explanation
Indices: 407809--407931 Score: 122
Period size: 41 Copynumber: 2.9 Consensus size: 41
407799 AAGCTAAATT
* *
407809 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC-AAA
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* *
407850 ACAGATCTTGTCTCCCTGAAGTTGTAGTGGAACAGATCGAAA
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* * *
407892 ACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGAT
1 AC---AGATCTTGTCTCCCTGAAGTTGCAGTG-AGCAGAT
407932 TCAAGCCATC
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 33 0.49
42 5 0.07
44 1 0.01
45 28 0.42
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
ACAGATCTTGTCTCCCTGAAGTTGCAGTGAGCAGATCGAAA
Found at i:407986 original size:224 final size:224
Alignment explanation
Indices: 407751--408249 Score: 820
Period size: 224 Copynumber: 2.2 Consensus size: 224
407741 GTAGAGCAGA
*
407751 CTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
1 CTGAAAATAGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
**
407816 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTGTAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
*
407881 ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCATCAAGC
131 ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGC
* *
407946 CTTAATCCCCAAAGCAGTAGGGTAATAGG
196 CTTAACCCCCAAAGCAATAGGGTAATAGG
* * *
407975 TTGAAAATAGCAAATTTTATATCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
1 CTGAAAATAGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
408040 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
* *
408105 ACAGATCGAAGACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGT
131 ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGC
*
408170 CTTAACCCCCTAAGCAATAGGGTAATAGG
196 CTTAACCCCCAAAGCAATAGGGTAATAGG
* * * * * *
408199 CCGAAAATCA-CTAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAG
1 CTGAAAAT-AGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAG
408250 ACAACGGATC
Statistics
Matches: 253, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
224 252 1.00
225 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (224 bp):
CTGAAAATAGCAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAATTACAGATC
TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAGATCTTGTCTCCCTGAAGTTACAGTGGA
ACAGATCGAAAACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGATTCAAGCCACCAAGC
CTTAACCCCCAAAGCAATAGGGTAATAGG
Found at i:408093 original size:41 final size:41
Alignment explanation
Indices: 408033--408155 Score: 113
Period size: 41 Copynumber: 2.9 Consensus size: 41
408023 AAGCTAAATT
* *
408033 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC-AAA
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* * *
408074 ACAGATCTTGTCTCCCTGAAGTTACAGTGGAACAGATCGAAG
1 ACAGATCTTGTCTCCCTGAAGTTGCAGT-GAGCAGATCGAAA
* * *
408116 ACGGTAAATCTTGCCTTCCTGAAGTTGCAGTGAAGCAGAT
1 AC---AGATCTTGTCTCCCTGAAGTTGCAGTG-AGCAGAT
408156 TCAAGCCACC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 33 0.50
42 4 0.06
44 1 0.02
45 28 0.42
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (41 bp):
ACAGATCTTGTCTCCCTGAAGTTGCAGTGAGCAGATCGAAA
Found at i:409799 original size:140 final size:139
Alignment explanation
Indices: 409386--409821 Score: 347
Period size: 140 Copynumber: 3.2 Consensus size: 139
409376 AATTAAATTA
409386 TTTTTTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTG
1 TTTTTTTATTTTTAATTT-GCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTG
* *
409451 TGCATTTTATAAAAGGGGTTATTGCACTTTAGGCCCTCTGTTGTTTCACGCGCATTTAAATAGGC
65 TGCATTTTATAAAGGGGGTTATTGCACTTTAGGCCCTCTATTGTTTCACGCGCATTTAAATAGGC
409516 CCTTTTCTTT
130 CCTTTTCTTT
* * * * * * * *
409526 TTTTTTTATTTTAAAATTTGCCCCAAAA-CT-TCG---TTTTTAATTCAAAT-TTAGTCT-CT-T
1 TTTTTTTATTTT-TAATTTGCACCAAAATTTGTCGCAATTTTCAATT-TAATCCTAG-CTGATGC
* ** * * ** * * * ** * * * *
409583 TTTTAATTTAACATTGGAGGAGCTATTTGCGCGTTTAGCCCCTCCGCTTTTTATTACTTCGCAAT
63 TGTGCATTTTATAAAGG-GG-GTTA-TTGCAC-TTTAGGCCCT-CTATTGTT-TCAC-GCGCATT
409648 T-AA-A-----------TT
121 TAAATAGGCCCTTTTCTTT
*
409654 ATTTTTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTG
1 TTTTTTTATTTTTAATTT-GCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTG
*
409719 TGCATTTTATAAAGGGGGTTATTGCACTTTAGGGCCTCTATTGTTTCACGCGCATTTAAATAGGC
65 TGCATTTTATAAAGGGGGTTATTGCACTTTAGGCCCTCTATTGTTTCACGCGCATTTAAATAGGC
409784 CCTTTTCTTT
130 CCTTTTCTTT
*
409794 TTTTTTTATTTTTAAATTTGCCCCAAAA
1 TTTTTTTATTTTT-AATTTGCACCAAAA
409822 CTTCGTTTTT
Statistics
Matches: 210, Mismatches: 53, Indels: 66
0.64 0.16 0.20
Matches are distributed among these distances:
127 11 0.05
128 26 0.12
129 7 0.03
130 11 0.05
131 5 0.02
132 8 0.04
133 14 0.07
134 19 0.09
135 14 0.07
136 8 0.04
137 5 0.02
138 12 0.06
139 7 0.03
140 47 0.22
141 16 0.08
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (139 bp):
TTTTTTTATTTTTAATTTGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTGT
GCATTTTATAAAGGGGGTTATTGCACTTTAGGCCCTCTATTGTTTCACGCGCATTTAAATAGGCC
CTTTTCTTT
Found at i:409803 original size:268 final size:269
Alignment explanation
Indices: 409325--409861 Score: 988
Period size: 268 Copynumber: 2.0 Consensus size: 269
409315 CGCGTGTTTT
* *
409325 CATTGGAGGGGCTATTTGCGCGTTTAGCCCCTCCGCTTTTATTTACTTTGCAATTAAATTATTTT
1 CATTGGAGGAGCTATTTGCGCGTTTAGCCCCTCCGCTTTTATTTACTTCGCAATTAAATTATTTT
409390 TTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTGTGCA
66 TTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTGTGCA
*
409455 TTTTATAAAAGGGGTTATTGCACTTTAGGCCCTCTGTTGTTTCACGCGCATTTAAATAGGCCCTT
131 TTTTATAAAAGGGGTTATTGCACTTTAGGCCCTCTATTGTTTCACGCGCATTTAAATAGGCCCTT
409520 TTCTTTTTTTTTTATTTTAAAATTTGCCCCAAAACTTCGTTTTTAATTCAAATTTAGTCTCTTTT
196 TTCTTTTTTTTTTATTTTAAAATTTGCCCCAAAACTTCGTTTTTAATTCAAATTTAGTCTCTTTT
409585 TTAATTTAA
261 TTAATTTAA
409594 CATTGGAGGAGCTATTTGCGCGTTTAGCCCCTCCGCTTTT-TATTACTTCGCAATTAAATTA-TT
1 CATTGGAGGAGCTATTTGCGCGTTTAGCCCCTCCGCTTTTAT-TTACTTCGCAATTAAATTATTT
409657 TTTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTGTGC
65 TTTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTGTGC
* *
409722 ATTTTATAAAGGGGGTTATTGCACTTTAGGGCCTCTATTGTTTCACGCGCATTTAAATAGGCCCT
130 ATTTTATAAAAGGGGTTATTGCACTTTAGGCCCTCTATTGTTTCACGCGCATTTAAATAGGCCCT
* *
409787 TTTCTTTTTTTTTTATTTTTAAATTTGCCCCAAAACTTCGTTTTTAATTCGAATTTAGTCTCTTT
195 TTTCTTTTTTTTTTATTTTAAAATTTGCCCCAAAACTTCGTTTTTAATTCAAATTTAGTCTCTTT
409852 TTTAATTTAA
260 TTTAATTTAA
409862 GTTGATTTTT
Statistics
Matches: 260, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
268 203 0.78
269 57 0.22
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (269 bp):
CATTGGAGGAGCTATTTGCGCGTTTAGCCCCTCCGCTTTTATTTACTTCGCAATTAAATTATTTT
TTTATTTTTAATTTGGCACCAAAATTTGTCGCAATTTTCAATTTAATCCTAGCTGATGCTGTGCA
TTTTATAAAAGGGGTTATTGCACTTTAGGCCCTCTATTGTTTCACGCGCATTTAAATAGGCCCTT
TTCTTTTTTTTTTATTTTAAAATTTGCCCCAAAACTTCGTTTTTAATTCAAATTTAGTCTCTTTT
TTAATTTAA
Found at i:410331 original size:2 final size:2
Alignment explanation
Indices: 410320--410406 Score: 51
Period size: 2 Copynumber: 46.0 Consensus size: 2
410310 TCTAATGTGC
* * *
410320 AT AT AT -T AT AT AT AT TT TT A- AT ACT AT AT -T AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
410360 -T AT AT -T AT AT AT AT AC AT AT AT AT TT AT -T AT AT TT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
410399 GT AT AT AT
1 AT AT AT AT
410407 TTTTAATATC
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
1 6 0.09
2 58 0.88
3 2 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (2 bp):
AT
Found at i:410347 original size:23 final size:22
Alignment explanation
Indices: 410320--410447 Score: 76
Period size: 23 Copynumber: 5.4 Consensus size: 22
410310 TCTAATGTGC
410320 ATATATTATATATATTTTTAAT
1 ATATATTATATATATTTTTAAT
* * *
410342 ACTATATTATGTATATATTATATT
1 A-TATATTATATATAT-TTTTAAT
* * *
410366 ATATATATACATATATATTTATT
1 ATATAT-TATATATATTTTTAAT
*
410389 ATATTTTTATGTATATATTTTTAAT
1 ATA-TATTA--TATATATTTTTAAT
* * **
410414 ATCACATTATTCATATGTTTTTTTT
1 AT-ATATTA-T-ATATATTTTTAAT
410439 ATATATTAT
1 ATATATTAT
410448 CCCATGTAAA
Statistics
Matches: 80, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
22 1 0.01
23 29 0.36
24 21 0.26
25 28 0.35
26 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATATTATATATATTTTTAAT
Found at i:410349 original size:14 final size:14
Alignment explanation
Indices: 410326--410415 Score: 62
Period size: 14 Copynumber: 6.4 Consensus size: 14
410316 GTGCATATAT
410326 TATATATATTTTTA
1 TATATATATTTTTA
*
410340 -ATACTATATTATGTA
1 TATA-TATATT-TTTA
*
410355 TATATTATATTATATA
1 TATA-TATATT-TTTA
* *
410371 TATACATATATATT-
1 TATATATAT-TTTTA
410385 TAT-TATATTTTTA
1 TATATATATTTTTA
*
410398 TGTATATATTTTTA
1 TATATATATTTTTA
410412 -ATAT
1 TATAT
410416 CACATTATTC
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
12 3 0.05
13 12 0.20
14 19 0.32
15 8 0.13
16 18 0.30
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
TATATATATTTTTA
Found at i:411650 original size:26 final size:26
Alignment explanation
Indices: 411606--411699 Score: 143
Period size: 26 Copynumber: 3.6 Consensus size: 26
411596 ACACGTCAAG
* * *
411606 AAATGGAAGCTTTTGTGGTGTGTCTG
1 AAATGGAAACCTTTGTGGTGTGTCTA
* *
411632 AAATGGAAACCTTTATGGTGTTTCTA
1 AAATGGAAACCTTTGTGGTGTGTCTA
411658 AAATGGAAACCTTTGTGGTGTGTCTA
1 AAATGGAAACCTTTGTGGTGTGTCTA
411684 AAATGGAAACCTTTGT
1 AAATGGAAACCTTTGT
411700 AGCATAGTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.36
Consensus pattern (26 bp):
AAATGGAAACCTTTGTGGTGTGTCTA
Found at i:415575 original size:36 final size:36
Alignment explanation
Indices: 415518--415597 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
415508 AATAGCTTGT
*
415518 TGATTTAATATCGCAGCTGATATCGTTAAGGTTCGC
1 TGATTTAATATCGCAGCTGATATCATTAAGGTTCGC
* * * *
415554 TGATTTAATATTGTAGTTGATATCATTAAGGTTCGT
1 TGATTTAATATCGCAGCTGATATCATTAAGGTTCGC
415590 TGATTTAA
1 TGATTTAA
415598 AACTATAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (36 bp):
TGATTTAATATCGCAGCTGATATCATTAAGGTTCGC
Found at i:415743 original size:131 final size:131
Alignment explanation
Indices: 415604--416425 Score: 791
Period size: 131 Copynumber: 6.3 Consensus size: 131
415594 TTAAAACTAT
* * * *
415604 AACCTAAGTTCATTCAATCTAATATCATGAACAATCTTATCTGAGTTAGTTTATTTAATATCGCT
1 AACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATCTGAGTTAGCTGATTTAATATCACT
* * * * *
415669 ACTCTAAATAGCTCGTTGATTTAATATCGTATCTAATATCGTTAAGGTTCGCTTATTTAAGATCA
66 ACTCTAAACAGCTCGTTGATTTAAGATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATCG
415734 C
131 C
*** * * * * * *
415735 AGTATAAGTTCATTCGATTTAATATCATGAACAACCTTATTTGA-TTCTGCTGATTTAATCTCGC
1 AACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATCTGAGTT-AGCTGATTTAATATCAC
* * * ** * * *
415799 TACTCTAAACAACTTGTTGATTTAAGATTGCAGATGATATTGTTAAGGTTCGCTAATTTAATATC
65 TACTCTAAACAGCTCGTTGATTTAAGATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATC
415864 GC
130 GC
* ** * * *
415866 AACCTAAGTTCATTCGATTTAATATCACAAACAATCTTATCTAAGTTAGTTGATTTAATATTACT
1 AACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATCTGAGTTAGCTGATTTAATATCACT
* ** * * *
415931 ACTTTAAACATTTCGCTGATTTAATATCGCAGT-TGATATCGTTAAGGTTTG-TTAATTTAAGAT
66 ACTCTAAACAGCTCGTTGATTTAAGATCGCA-TCTGATATCGTTAAGGTTCGCTT-ATTTAAGAT
415994 CGC
129 CGC
** * * **
415997 AACAGAAGTTCATTCGATTTAATATCATGAACAATCTTATTTGCA-TTAGCTGATTTAATATTGC
1 AACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATCTG-AGTTAGCTGATTTAATATCAC
* * * *
416061 TACTCTAAACAAG-TCATTGATTTAAGATTGCAACTGATATCG-TAAGG-TCTGCTAATTTAAGA
65 TACTCTAAAC-AGCTCGTTGATTTAAGATCGCATCTGATATCGTTAAGGTTC-GCTTATTTAAGA
*
416123 TTGC
128 TCGC
* * * * * *
416127 AATCTAAGTTCATTCAATTTAATATTATGAACAATCATATCTAAGTCAGCTGGTTTAATATCACT
1 AACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATCTGAGTTAGCTGATTTAATATCACT
* * *** * * * * *
416192 ACTCTAAACAACTTGCCAATTTAAGATCGCAACTGATATCGTTAAGGTTCACTGATTTAAAATTG
66 ACTCTAAACAGCTCGTTGATTTAAGATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATCG
416257 C
131 C
* * * * *
416258 AACCTAAGTTTATTAAATTTAATATTATGAA-AAGTTTTATCTGACTTAGCTGATTTAATATCAC
1 AACCTAAGTTCATTCAATTTAATATCATGAACAA-TCTTATCTGAGTTAGCTGATTTAATATCAC
* * * * *
416322 TACTATAAATAGCTCGTTGATTTAATATCCCAGT-TGATACCGTTAAGGTTCGC-TATTTTAAGA
65 TACTCTAAACAGCTCGTTGATTTAAGATCGCA-TCTGATATCGTTAAGGTTCGCTTA-TTTAAGA
*
416385 TTGC
128 TCGC
* *
416389 AACCTAATTTCATTCCATTTAATATCATGAACAATCT
1 AACCTAAGTTCATTCAATTTAATATCATGAACAATCT
416426 CATTTTTGCT
Statistics
Matches: 556, Mismatches: 118, Indels: 34
0.79 0.17 0.05
Matches are distributed among these distances:
129 3 0.01
130 106 0.19
131 439 0.79
132 8 0.01
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (131 bp):
AACCTAAGTTCATTCAATTTAATATCATGAACAATCTTATCTGAGTTAGCTGATTTAATATCACT
ACTCTAAACAGCTCGTTGATTTAAGATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATCG
C
Found at i:415953 original size:262 final size:261
Alignment explanation
Indices: 415554--416425 Score: 950
Period size: 262 Copynumber: 3.3 Consensus size: 261
415544 TAAGGTTCGC
* * * * * * * * **
415554 TGATTTAATATTGTAGTTGATATCATTAAGGTTCGTTGATTTAAAACTATAACCTAAGTTCATTC
1 TGATTTAAGATTGCAGATGATATCGTTAAGGTTCGCTAATTTAAGATTGCAACCTAAGTTCATTC
* * * * *
415619 AATCTAATATCATGAACAATCTTATCTGAGTTAGTTTATTTAATATCGCTACTCTAAATAGC-TC
66 AATTTAATATCATGAACAATCTTATCTAAGTTAGTTGATTTAATATCACTACTCTAAACA-CTTC
* * * * **
415683 GTTGATTTAATATCGTATCTAATATCGTTAAGGTTCGCTTATTTAAGATCACAGTATAAGTTCAT
130 GCTGATTTAATATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATCGCAACATAAGTTCAT
* * *
415748 TCGATTTAATATCATGAACAACCTTATTTGATTCTGCTGATTTAATCTCGCTACTCTAAACAACT
195 TCGATTTAATATCATGAACAATCTTATTTGATT-AGCTGATTTAATATCGCTACTCTAAACAACT
*
415813 TGT
259 CGT
* * *
415816 TGATTTAAGATTGCAGATGATATTGTTAAGGTTCGCTAATTTAATATCGCAACCTAAGTTCATTC
1 TGATTTAAGATTGCAGATGATATCGTTAAGGTTCGCTAATTTAAGATTGCAACCTAAGTTCATTC
* ** * * *
415881 GATTTAATATCACAAACAATCTTATCTAAGTTAGTTGATTTAATATTACTACTTTAAACATTTCG
66 AATTTAATATCATGAACAATCTTATCTAAGTTAGTTGATTTAATATCACTACTCTAAACACTTCG
* *
415946 CTGATTTAATATCGCAGT-TGATATCGTTAAGGTTTG-TTAATTTAAGATCGCAACAGAAGTTCA
131 CTGATTTAATATCGCA-TCTGATATCGTTAAGGTTCGCTT-ATTTAAGATCGCAACATAAGTTCA
* *
416009 TTCGATTTAATATCATGAACAATCTTATTTGCATTAGCTGATTTAATATTGCTACTCTAAACAAG
194 TTCGATTTAATATCATGAACAATCTTATTTG-ATTAGCTGATTTAATATCGCTACTCTAAACAAC
*
416074 TCAT
258 TCGT
*
416078 TGATTTAAGATTGCA-ACTGATATCG-TAAGG-TCTGCTAATTTAAGATTGCAATCTAAGTTCAT
1 TGATTTAAGATTGCAGA-TGATATCGTTAAGGTTC-GCTAATTTAAGATTGCAACCTAAGTTCAT
* * * * *
416140 TCAATTTAATATTATGAACAATCATATCTAAGTCAGCTGGTTTAATATCACTACTCTAAACAACT
64 TCAATTTAATATCATGAACAATCTTATCTAAGTTAGTTGATTTAATATCACTACTCTAAAC-ACT
** * * * * * * * *
416205 T-GCCAATTTAAGATCGCAACTGATATCGTTAAGGTTCACTGATTTAAAATTGCAACCTAAGTTT
128 TCGCTGATTTAATATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATCGCAACATAAGTTC
** * * * * * *
416269 ATTAAATTTAATATTATGAA-AAGTTTTATCTGACTTAGCTGATTTAATATCACTACTATAAATA
193 ATTCGATTTAATATCATGAACAA-TCTTATTTGA-TTAGCTGATTTAATATCGCTACTCTAAACA
*
416333 GCTCGT
256 ACTCGT
* ** * * * *
416339 TGATTTAATATCCCAGTTGATACCGTTAAGGTTCGCTATTTTAAGATTGCAACCTAATTTCATTC
1 TGATTTAAGATTGCAGATGATATCGTTAAGGTTCGCTAATTTAAGATTGCAACCTAAGTTCATTC
*
416404 CATTTAATATCATGAACAATCT
66 AATTTAATATCATGAACAATCT
416426 CATTTTTGCT
Statistics
Matches: 508, Mismatches: 88, Indels: 28
0.81 0.14 0.04
Matches are distributed among these distances:
260 5 0.01
261 205 0.40
262 292 0.57
263 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (261 bp):
TGATTTAAGATTGCAGATGATATCGTTAAGGTTCGCTAATTTAAGATTGCAACCTAAGTTCATTC
AATTTAATATCATGAACAATCTTATCTAAGTTAGTTGATTTAATATCACTACTCTAAACACTTCG
CTGATTTAATATCGCATCTGATATCGTTAAGGTTCGCTTATTTAAGATCGCAACATAAGTTCATT
CGATTTAATATCATGAACAATCTTATTTGATTAGCTGATTTAATATCGCTACTCTAAACAACTCG
T
Found at i:416314 original size:392 final size:393
Alignment explanation
Indices: 415548--416430 Score: 1015
Period size: 392 Copynumber: 2.2 Consensus size: 393
415538 TATCGTTAAG
* * * * * **
415548 GTTCGCTGATTTAATATTGTAGTTGATATCATTAAGGTTCGTTGATTTAA-AACTATAACCTAAG
1 GTTCGCTGATTTAATATCGCAGTTGATATCGTTAAGGTTCGTTAATTTAAGATC-GCAACCTAAG
* * * *
415612 TTCATTCAATCTAATATCATGAACAATCTTATCTGAGTTAGTTTATTTAATATCGCTACTCTAAA
65 TTCATTCAATTTAATATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCTAAA
* * * * * * *
415677 TAGCTCGTTGATTTAATATCGTATCTAATATCGTTAAGGTTCGCTTATTTAAGATCACAGTATAA
130 AAGCTCATTGATTTAAGATCGCAACTAATATCGTTAAGGTTCGCTAATTTAAGATCACAATATAA
* * * * * * * *
415742 GTTCATTCGATTTAATATCATGAACAACCTTATTTGATTCTGCTGATTTAATCTCGCTACTCTAA
195 GTTCATTCAATTTAATATCATGAACAACCATATCTAAGTCAGCTGATTTAATATCACTACTCTAA
*** * * * *
415807 ACAACTTGTTGATTTAAGATTGCAGATGATATTGTTAAGGTTCGCTAATTTAATATCGCAACCTA
260 ACAACTTGCCAATTTAAGATCGCAGATGATATCGTTAAGGTTCACTAATTTAAAATCGCAACCTA
** * * * *
415872 AGTTCATTCGATTTAATATCACAAACAATCTTATCTAAGTTAGTTGATTTAATATTACTACTTTA
325 AGTTCATTAAATTTAATATCACAAACAATCTTATCTAACTTAGCTGATTTAATATCACTACTATA
415937 AACA
390 AACA
* * **
415941 TTTCGCTGATTTAATATCGCAGTTGATATCGTTAAGGTTTGTTAATTTAAGATCGCAACAGAAGT
1 GTTCGCTGATTTAATATCGCAGTTGATATCGTTAAGGTTCGTTAATTTAAGATCGCAACCTAAGT
* *
416006 TCATTCGATTTAATATCATGAACAATCTTATTTGCA-TTAGCTGATTTAATATTGCTACTCTAAA
66 TCATTCAATTTAATATCATGAACAATCTTATTTG-AGTTAGCTGATTTAATATCGCTACTCTAAA
* * ** *
416070 CAAG-TCATTGATTTAAGATTGCAACTGATATCG-TAAGG-TCTGCTAATTTAAGATTGCAATCT
130 -AAGCTCATTGATTTAAGATCGCAACTAATATCGTTAAGGTTC-GCTAATTTAAGATCACAATAT
* * *
416132 AAGTTCATTCAATTTAATATTATGAACAATCATATCTAAGTCAGCTGGTTTAATATCACTACTCT
193 AAGTTCATTCAATTTAATATCATGAACAACCATATCTAAGTCAGCTGATTTAATATCACTACTCT
* *
416197 AAACAACTTGCCAATTTAAGATCGCA-ACTGATATCGTTAAGGTTCACTGATTTAAAATTGCAAC
258 AAACAACTTGCCAATTTAAGATCGCAGA-TGATATCGTTAAGGTTCACTAATTTAAAATCGCAAC
* * * * * *
416261 CTAAGTTTATTAAATTTAATATTATGAAA-AGTTTTATCTGACTTAGCTGATTTAATATCACTAC
322 CTAAGTTCATTAAATTTAATATCA-CAAACAATCTTATCTAACTTAGCTGATTTAATATCACTAC
*
416325 TATAAATA
386 TATAAACA
* * * * * * * *
416333 GCTCGTTGATTTAATATCCCAGTTGATACCGTTAAGGTTCGCTATTTTAAGATTGCAACCTAATT
1 GTTCGCTGATTTAATATCGCAGTTGATATCGTTAAGGTTCGTTAATTTAAGATCGCAACCTAAGT
* *
416398 TCATTCCATTTAATATCATGAACAATCTCATTT
66 TCATTCAATTTAATATCATGAACAATCTTATTT
416431 TTGCTAGCTT
Statistics
Matches: 408, Mismatches: 76, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
391 3 0.01
392 267 0.65
393 133 0.33
394 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (393 bp):
GTTCGCTGATTTAATATCGCAGTTGATATCGTTAAGGTTCGTTAATTTAAGATCGCAACCTAAGT
TCATTCAATTTAATATCATGAACAATCTTATTTGAGTTAGCTGATTTAATATCGCTACTCTAAAA
AGCTCATTGATTTAAGATCGCAACTAATATCGTTAAGGTTCGCTAATTTAAGATCACAATATAAG
TTCATTCAATTTAATATCATGAACAACCATATCTAAGTCAGCTGATTTAATATCACTACTCTAAA
CAACTTGCCAATTTAAGATCGCAGATGATATCGTTAAGGTTCACTAATTTAAAATCGCAACCTAA
GTTCATTAAATTTAATATCACAAACAATCTTATCTAACTTAGCTGATTTAATATCACTACTATAA
ACA
Found at i:422408 original size:6 final size:6
Alignment explanation
Indices: 422399--422428 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
422389 TTTTTTTATA
422399 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
422429 GTGATGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTAAT
Found at i:424410 original size:6 final size:6
Alignment explanation
Indices: 424401--424427 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
424391 GGCTAACGCT
424401 AAGGCA AAGGCA AAGGCA AAGGCA AAG
1 AAGGCA AAGGCA AAGGCA AAGGCA AAG
424428 TTTATTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGGCA
Found at i:424411 original size:18 final size:18
Alignment explanation
Indices: 424388--424427 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
424378 AGTTCCAACA
* *
424388 AAAGGCTAACGCTAAGGC
1 AAAGGCAAACGCAAAGGC
*
424406 AAAGGCAAAGGCAAAGGC
1 AAAGGCAAACGCAAAGGC
424424 AAAG
1 AAAG
424428 TTTATTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.30, T:0.05
Consensus pattern (18 bp):
AAAGGCAAACGCAAAGGC
Found at i:428991 original size:5 final size:5
Alignment explanation
Indices: 428981--429005 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
428971 TCAGCAATAG
428981 AAATC AAATC AAATC AAATC AAATC
1 AAATC AAATC AAATC AAATC AAATC
429006 GAACTGTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATC
Found at i:431064 original size:14 final size:14
Alignment explanation
Indices: 431045--431086 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
431035 ATTTTTTGTG
*
431045 ATTTTTAATAACTT
1 ATTTTTAATAAATT
*
431059 ATTTTTAAAAAATT
1 ATTTTTAATAAATT
*
431073 ATTTTTAATTAATT
1 ATTTTTAATAAATT
431087 TCTAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTTAATAAATT
Found at i:438921 original size:13 final size:13
Alignment explanation
Indices: 438903--438934 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
438893 AGGTTTAGCC
438903 CTGTTGGAGGATG
1 CTGTTGGAGGATG
438916 CTGTTGGAGGATG
1 CTGTTGGAGGATG
438929 CTGTTG
1 CTGTTG
438935 AAGTTCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.09, G:0.44, T:0.34
Consensus pattern (13 bp):
CTGTTGGAGGATG
Found at i:443603 original size:26 final size:27
Alignment explanation
Indices: 443574--443636 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
443564 TATAGAATTT
* * *
443574 ATTTATTATATTATTATAAAACCAA-A
1 ATTTATTATATTATAAAAAAAACAATA
*
443600 ATTTA-TATCTTATAAAAAAAACAATA
1 ATTTATTATATTATAAAAAAAACAATA
*
443626 AATTATTATAT
1 ATTTATTATAT
443637 CCTTTATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 15 0.52
26 10 0.34
27 4 0.14
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTATTATATTATAAAAAAAACAATA
Found at i:443893 original size:3 final size:3
Alignment explanation
Indices: 443849--443878 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
443839 TTTTTTTTTA
443849 ATT ACTT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT
443879 AGATATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:446078 original size:24 final size:22
Alignment explanation
Indices: 446030--446080 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
446020 AGAATTTAAT
* **
446030 TTTTATATTTTTATTTTTAGTA
1 TTTTAGATTTTTATTTTTAAAA
446052 TTTTAGATTCTTTATTTTTTAAAA
1 TTTTAGATT-TTTA-TTTTTAAAA
446076 TTTTA
1 TTTTA
446081 AAATTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.33
23 4 0.17
24 12 0.50
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTAGATTTTTATTTTTAAAA
Found at i:451410 original size:31 final size:31
Alignment explanation
Indices: 451351--451410 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
451341 TGATTTATAA
* **
451351 GTTATTATTATAAGGGTAAATATGTAAAATG
1 GTTATTATTATAAGGATAAATAAATAAAATG
451382 GTTATTATTATAA-GATAAATAAAATAAAA
1 GTTATTATTATAAGGATAAAT-AAATAAAA
451411 CAAATAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (31 bp):
GTTATTATTATAAGGATAAATAAATAAAATG
Found at i:452342 original size:22 final size:22
Alignment explanation
Indices: 452276--452401 Score: 101
Period size: 22 Copynumber: 5.4 Consensus size: 22
452266 ACAGCTCGTA
* *
452276 AGAGCTTACTGTTTCAGCTTATT
1 AGAGCTTACTG-TTCAGCTCAAT
* * *
452299 GGAGCTTAAC-GATTTAGCTCAAA
1 AGAGCTT-ACTG-TTCAGCTCAAT
452322 AGAGCTTACTGTTCAGCTCAAT
1 AGAGCTTACTGTTCAGCTCAAT
*
452344 AGAGCTTACCGTTTTCAGCTCAAT
1 AGAGCTTA-C-TGTTCAGCTCAAT
*
452368 AGAGCTTATTGTTCATTAGCTCAAT
1 AGAGCTTACTGTTC---AGCTCAAT
*
452393 AAAGCTTAC
1 AGAGCTTAC
452402 CGACCATGAC
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
22 23 0.28
23 22 0.27
24 22 0.27
25 15 0.18
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:452364 original size:46 final size:45
Alignment explanation
Indices: 452275--452404 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 45
452265 CACAGCTCGT
* * * *
452275 AAGAGCTTACTGTTTCAGCTTATTGGAGCTTAACGATTTAGCTCAA
1 AAGAGCTTACTG-TTCAGCTCAATAGAGCTTACCGATTTAGCTCAA
*
452321 AAGAGCTTACTGTTCAGCTCAATAGAGCTTACCGTTTTCAGCTCAA
1 AAGAGCTTACTGTTCAGCTCAATAGAGCTTACCGATTT-AGCTCAA
* * *
452367 TAGAGCTTATTGTTCATTAGCTCAATAAAGCTTACCGA
1 AAGAGCTTACTGTTC---AGCTCAATAGAGCTTACCGA
452405 CCATGACTCG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
45 21 0.30
46 32 0.45
49 18 0.25
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
AAGAGCTTACTGTTCAGCTCAATAGAGCTTACCGATTTAGCTCAA
Found at i:452365 original size:24 final size:24
Alignment explanation
Indices: 452276--452403 Score: 104
Period size: 24 Copynumber: 5.5 Consensus size: 24
452266 ACAGCTCGTA
* * *
452276 AGAGCTTACTG-TTTCAGCTTATT
1 AGAGCTTACCGTTTTCAGCTCAAT
* * * *
452299 GGAGCTTAACGATTT-AGCTCAAA
1 AGAGCTTACCGTTTTCAGCTCAAT
*
452322 AGAGCTTA-C-TGTTCAGCTCAAT
1 AGAGCTTACCGTTTTCAGCTCAAT
452344 AGAGCTTACCGTTTTCAGCTCAAT
1 AGAGCTTACCGTTTTCAGCTCAAT
**
452368 AGAGCTTATTGTTCATT-AGCTCAAT
1 AGAGCTTACCGTT--TTCAGCTCAAT
*
452393 AAAGCTTACCG
1 AGAGCTTACCG
452404 ACCATGACTC
Statistics
Matches: 83, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.02
22 16 0.19
23 21 0.25
24 26 0.31
25 16 0.19
26 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (24 bp):
AGAGCTTACCGTTTTCAGCTCAAT
Found at i:456638 original size:20 final size:20
Alignment explanation
Indices: 456605--456649 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
456595 ATAGAAACTG
* *
456605 ATAAAATTGTTATTTTGGAA
1 ATAAAATTGTTATTTAGAAA
456625 ATAAAATT-TATATTTAGAAA
1 ATAAAATTGT-TATTTAGAAA
456645 ATAAA
1 ATAAA
456650 TTCTCACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
ATAAAATTGTTATTTAGAAA
Found at i:460692 original size:23 final size:18
Alignment explanation
Indices: 460677--460719 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
460667 AATACTTAAG
460677 TATA-TAATATAATAATA
1 TATATTAATATAATAATA
460694 TATATTAATATAATAATA
1 TATATTAATATAATAATA
460712 TAATATTA
1 T-ATATTA
460720 GAAAACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 14 0.58
19 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATTAATATAATAATA
Found at i:460693 original size:8 final size:8
Alignment explanation
Indices: 460680--460716 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
460670 ACTTAAGTAT
460680 ATAATATA
1 ATAATATA
460688 ATAATATA
1 ATAATATA
460696 TATTAATATA
1 -A-TAATATA
460706 ATAATATA
1 ATAATATA
460714 ATA
1 ATA
460717 TTAGAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.67
9 2 0.07
10 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATA
Found at i:460771 original size:17 final size:18
Alignment explanation
Indices: 460749--460790 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
460739 AAATAAAACA
*
460749 AAAGAAT-AAGAACAGAG
1 AAAGAATGAAAAACAGAG
*
460766 AAAGAAATGAAAAAGAGAG
1 AAAG-AATGAAAAACAGAG
460785 AAAGAA
1 AAAGAA
460791 AGAAGGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 12 0.57
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (18 bp):
AAAGAATGAAAAACAGAG
Found at i:469604 original size:15 final size:15
Alignment explanation
Indices: 469560--469610 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
469550 ATACTTAAGT
*
469560 ATATAATATAATAAT
1 ATATAATATAATAAA
*
469575 ATATATTA-ATATAAA
1 ATATAATATA-ATAAA
469590 ATATAATATAATAAA
1 ATATAATATAATAAA
*
469605 ACATAA
1 ATATAA
469611 AAGAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAATATAATAAA
Found at i:469644 original size:22 final size:23
Alignment explanation
Indices: 469619--469684 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
469609 AAAAGAAATA
*
469619 AAAGAAAAAAAAGAATAAGA-AC
1 AAAGAAAAAAAAGAAAAAGAGAC
* * *
469641 AAAGAAAGAAACGAAAAAGAGAG
1 AAAGAAAAAAAAGAAAAAGAGAC
469664 AAAGAAAGAAGGAAAGAAAAA
1 AAAGAAA-AA--AAAGAAAAA
469685 AAGGGGAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 17 0.50
23 8 0.24
24 1 0.03
26 8 0.24
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (23 bp):
AAAGAAAAAAAAGAAAAAGAGAC
Found at i:469648 original size:17 final size:15
Alignment explanation
Indices: 469609--469683 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 15
469599 AATAAAACAT
*
469609 AAAAGAAATAAAAGA
1 AAAAGAAAGAAAAGA
469624 AAAA-AAAGAATAAGA
1 AAAAGAAAGAA-AAGA
*
469639 ACAAAGAAAGAAACGA
1 A-AAAGAAAGAAAAGA
*
469655 AAAAGAGAG-AAAGA
1 AAAAGAAAGAAAAGA
469669 AAGAAGGAAAGAAAA
1 AA-AA-GAAAGAAAA
469684 AAAGGGGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 11 0.22
15 18 0.37
16 11 0.22
17 9 0.18
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:469648 original size:26 final size:29
Alignment explanation
Indices: 469619--469686 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
469609 AAAAGAAATA
*
469619 AAAGAAAAAAAAGA-A-TAAGAACA-AA-G
1 AAAGAAAAAAAAGAGAGAAAGAA-AGAAGG
469645 AAAGAAACGAAAAAGAGAGAAAGAAAGAAGG
1 AAAGAAA--AAAAAGAGAGAAAGAAAGAAGG
469676 AAAGAAAAAAA
1 AAAGAAAAAAA
469687 GGGGAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 7 0.20
28 7 0.20
29 6 0.17
30 7 0.20
31 8 0.23
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (29 bp):
AAAGAAAAAAAAGAGAGAAAGAAAGAAGG
Found at i:470560 original size:43 final size:43
Alignment explanation
Indices: 470483--470567 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
470473 ACAGGGATAA
470483 TTCGACCTTGAGTCGATGAGGCACTAATATTGTCGTA-TGTTAC
1 TTCGACCTTGAGTCGATGAGGCACT-ATATTGTCGTACTGTTAC
* * *
470526 TTCGACTTTGTGTCGATGAGGCACT-TCGTGTGTCGTACTGTT
1 TTCGACCTTGAGTCGATGAGGCACTAT-AT-TGTCGTACTGTT
470568 TTCGATGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.03
42 1 0.03
43 30 0.83
44 4 0.11
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (43 bp):
TTCGACCTTGAGTCGATGAGGCACTATATTGTCGTACTGTTAC
Found at i:477220 original size:21 final size:22
Alignment explanation
Indices: 477194--477240 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
477184 AGGCTGAGAG
*
477194 ACGGCCGTGTGACCTATC-CAC
1 ACGGCCATGTGACCTATCTCAC
*
477215 ACGGCCATGTGGCCTATCTCAC
1 ACGGCCATGTGACCTATCTCAC
477237 ACGG
1 ACGG
477241 GCACGGCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.19, C:0.36, G:0.26, T:0.19
Consensus pattern (22 bp):
ACGGCCATGTGACCTATCTCAC
Found at i:495009 original size:22 final size:22
Alignment explanation
Indices: 494981--495022 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
494971 TATTATTCAC
494981 AAATTTGTAATTTAATTTTTCT
1 AAATTTGTAATTTAATTTTTCT
495003 AAATTTGTAATTTAATTTTT
1 AAATTTGTAATTTAATTTTT
495023 TTACTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
AAATTTGTAATTTAATTTTTCT
Found at i:495434 original size:14 final size:14
Alignment explanation
Indices: 495415--495453 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
495405 TTAGGAAAGT
495415 AAATCATTTTCCAA
1 AAATCATTTTCCAA
* *
495429 AAATCATTTTTCGA
1 AAATCATTTTCCAA
*
495443 AAGTCATTTTC
1 AAATCATTTTC
495454 AGTGAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:496481 original size:14 final size:14
Alignment explanation
Indices: 496450--496483 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
496440 TTGTCAAGTG
*
496450 TTTTTTTTTTAATA
1 TTTTATTTTTAATA
496464 -TTTATTTTTAATA
1 TTTTATTTTTAATA
496477 TTTTATT
1 TTTTATT
496484 GAGTTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTAATA
Found at i:496505 original size:102 final size:103
Alignment explanation
Indices: 496384--496569 Score: 248
Period size: 102 Copynumber: 1.8 Consensus size: 103
496374 AAAAAAAATG
* * * **
496384 GTTAATATTTGGTACACTGATATTATATTTTTTTATTTCACAAGCAGTCCTAAAAATTGTCAAGT
1 GTTAATATTTGATACACTGAGAATATATTTTTTTATCCCACAAGCAGTCCTAAAAATTGTCAAGT
**
496449 GT-TTTTTTTTTAATATTTATTTTTAATATTTTATTGA
66 GTGTCCTTTTTTAATATTTATTTTTAATATTTTATTGA
* * * * * *
496486 GTTAGTATTTGATATACTGAGAATGTATTTTTTTATCCCGCAAGTAGTCCTAAAAATTGTCATGT
1 GTTAATATTTGATACACTGAGAATATATTTTTTTATCCCACAAGCAGTCCTAAAAATTGTCAAGT
496551 GTGTCCTTTTTTAATATTT
66 GTGTCCTTTTTTAATATTT
496570 TACTGAATTA
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
102 56 0.80
103 14 0.20
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (103 bp):
GTTAATATTTGATACACTGAGAATATATTTTTTTATCCCACAAGCAGTCCTAAAAATTGTCAAGT
GTGTCCTTTTTTAATATTTATTTTTAATATTTTATTGA
Found at i:501560 original size:18 final size:18
Alignment explanation
Indices: 501523--501561 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
501513 TTGGAAATCA
*
501523 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
501541 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
501559 AAA
1 AAA
501562 AATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:506881 original size:218 final size:219
Alignment explanation
Indices: 506333--507012 Score: 970
Period size: 218 Copynumber: 3.0 Consensus size: 219
506323 CTTTTGCACA
* *
506333 AAATTTCCTAGAACCACCACCCCTATAGAA-TGGTCTAGAACCTCGATTAAACTGCCTAGTGCTT
1 AAATTTTCTAGAACCACCACCCCTATA-AAGTGGTCTAGAACCTCGATTGAACTGCCTAGTGCTT
* *
506397 TTATCATTATTACCACTGTGTTGAGCAACATTAGCCTGTAAAGGTACATTAGAAACAAAATCTTG
65 TTATCATTATTACAACTGTGTTGAGCAACATTAGCCTGTAAAGGTACATTAAAAACAAAATCTTG
* *
506462 TTGTCGAGCTTCACAATCAGTAAGCATCTCAGCAAGAAGATCAAGAGGGAGACACATTGCTGAAG
130 TTGTCGGGCTTAACAATCAGT----A----AGC------ATCAAGAGGGAGACACATTGCTGAAG
506527 CTACAACTCAAATTGACTCATACTCCGCTGACAGACACG
181 CTACAACTCAAATTGACTCATACTCCGCTGACAGACACG
**
506566 AAATTTTCTAGAACCACCACCCCTATAAAGTGGGGTAGAACCTCGATTGAACTGCCTAGTGCTTT
1 AAATTTTCTAGAACCACCACCCCTATAAAGTGGTCTAGAACCTCGATTGAACTGCCTAGTGCTTT
*
506631 TATCATTATTACAACTGTGTTGAGCAACATTAGCCTGTAAAGGCACATTAAAAACAAAATCTTGT
66 TATCATTATTACAACTGTGTTGAGCAACATTAGCCTGTAAAGGTACATTAAAAACAAAATCTTGT
*
506696 TGTCGGGCTTAACAATCAGTAAGCA-CAAGAGGGAGACACATTGCTGAAGCTACAACTCAAATTT
131 TGTCGGGCTTAACAATCAGTAAGCATCAAGAGGGAGACACATTGCTGAAGCTACAACTCAAATTG
506760 ACTCATACTCCGCTGACAGACACG
196 ACTCATACTCCGCTGACAGACACG
506784 AAATTTTCTAGAACCACCACCCCTATAAAGTGGTCTAGAACCTCGATTGAACTGCCTAGTGCTTT
1 AAATTTTCTAGAACCACCACCCCTATAAAGTGGTCTAGAACCTCGATTGAACTGCCTAGTGCTTT
506849 TATCATTATTACAACTGTGTTGAGCAACATTAGCCTGTAAAGGTACATTAAAAACAAAATCTTGT
66 TATCATTATTACAACTGTGTTGAGCAACATTAGCCTGTAAAGGTACATTAAAAACAAAATCTTGT
506914 TGTCGGGCTTAACAA-CAGTAAGCATCTCAGCAAGAAGATCAAGAGGGAGACACATTGCTGAAGC
131 TGTCGGGCTTAACAATCAGT----A----AGC------ATCAAGAGGGAGACACATTGCTGAAGC
* *
506978 TACAACTCGAATTGACTTATACTCCGCTGACAGAC
182 TACAACTCAAATTGACTCATACTCCGCTGACAGAC
507013 CAGCAAGAAT
Statistics
Matches: 415, Mismatches: 16, Indels: 33
0.89 0.03 0.07
Matches are distributed among these distances:
217 4 0.01
218 204 0.49
219 1 0.00
221 1 0.00
225 6 0.01
229 1 0.00
231 1 0.00
232 59 0.14
233 138 0.33
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (219 bp):
AAATTTTCTAGAACCACCACCCCTATAAAGTGGTCTAGAACCTCGATTGAACTGCCTAGTGCTTT
TATCATTATTACAACTGTGTTGAGCAACATTAGCCTGTAAAGGTACATTAAAAACAAAATCTTGT
TGTCGGGCTTAACAATCAGTAAGCATCAAGAGGGAGACACATTGCTGAAGCTACAACTCAAATTG
ACTCATACTCCGCTGACAGACACG
Found at i:507613 original size:40 final size:40
Alignment explanation
Indices: 507560--507665 Score: 142
Period size: 40 Copynumber: 2.6 Consensus size: 40
507550 ACTAACAGAA
* * * *
507560 AAACGCCGTAAAAGGTAAAGTATTAGCGGCATTTTT-GCAT
1 AAAC-CCGCAAAAGGTAAAGCAATAGCAGCATTTTTCGCAT
*
507600 AAACACCGCAAAAGGTAAAGCAATAGCAGCATTTTTCTCAT
1 AAAC-CCGCAAAAGGTAAAGCAATAGCAGCATTTTTCGCAT
507641 AAACCCGCAAAAGGTAAAGCAATAG
1 AAACCCGCAAAAGGTAAAGCAATAG
507666 TGGAAACGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 52 0.88
41 7 0.12
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (40 bp):
AAACCCGCAAAAGGTAAAGCAATAGCAGCATTTTTCGCAT
Found at i:511061 original size:13 final size:13
Alignment explanation
Indices: 511043--511068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
511033 TAACTAAAGG
511043 GTTAAAATTTAAA
1 GTTAAAATTTAAA
511056 GTTAAAATTTAAA
1 GTTAAAATTTAAA
511069 TATGATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:513318 original size:21 final size:21
Alignment explanation
Indices: 513265--513325 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
513255 AGGTAAATAC
*
513265 GGCTGGCACAAAGCCATAATCA
1 GGCTGGCACAGAGCCAT-ATCA
* * * *
513287 AGATAGCACAGAGCCATATTA
1 GGCTGGCACAGAGCCATATCA
513308 GGCTGGCACAGAGCCATA
1 GGCTGGCACAGAGCCATA
513326 AATAGATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (21 bp):
GGCTGGCACAGAGCCATATCA
Found at i:521047 original size:30 final size:30
Alignment explanation
Indices: 521011--521109 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
521001 CTAGCCTTTG
*
521011 CCACCACCAACTCCACTAGCCACACTTACT
1 CCACCACCAACTCCACTAGCCACACTTGCT
521041 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* ** *
521071 CCACCACCTACTCCGTTAGCCACAATTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
521101 CCACCACCA
1 CCACCACCA
521110 CTTGTACCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.27, C:0.49, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:521625 original size:23 final size:23
Alignment explanation
Indices: 521588--521717 Score: 86
Period size: 25 Copynumber: 5.5 Consensus size: 23
521578 TCTTTTTTAT
*
521588 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATACTA
* *
521611 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATACTA
** * *
521633 TATTAGGTATATTCTAAATTCTA
1 TATTATATATATTCTTAATACTA
*
521656 TATTACGTATATATATATT-ATACTA
1 TATTA--TATATAT-TCTTAATACTA
* *
521681 TTTTATGTATATATCTTTAATACTA
1 TATTATATATAT-TC-TTAATACTA
*
521706 TATTATTTATAT
1 TATTATATATAT
521718 ATATATTTTA
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
22 17 0.21
23 27 0.33
24 6 0.07
25 30 0.37
26 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (23 bp):
TATTATATATATTCTTAATACTA
Found at i:521796 original size:25 final size:25
Alignment explanation
Indices: 521653--521799 Score: 111
Period size: 25 Copynumber: 5.8 Consensus size: 25
521643 ATTCTAAATT
* * * *
521653 CTATATTACGTATATATATATTATA
1 CTATATTATGTATATATTTTTTACA
* * * *
521678 CTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATTTTTTACA
*
521703 CTATATTATTTATATATATATTTTACA
1 CTATATTATGTATATAT-T-TTTTACA
* *
521730 TGTTATCTTATGTATATA--TTTTA-A
1 --CTATATTATGTATATATTTTTTACA
* *
521754 TTATATTATGTATGTATTTTTTACA
1 CTATATTATGTATATATTTTTTACA
*
521779 CTATATTATGTACATATTTTT
1 CTATATTATGTATATATTTTT
521800 AATATTATCA
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
22 14 0.14
24 6 0.06
25 59 0.61
27 5 0.05
29 13 0.13
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (25 bp):
CTATATTATGTATATATTTTTTACA
Found at i:521806 original size:20 final size:20
Alignment explanation
Indices: 521781--521839 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
521771 TTTTTACACT
521781 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
521801 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
521824 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
521840 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:521978 original size:16 final size:15
Alignment explanation
Indices: 521954--521988 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
521944 TAATTATTAT
521954 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
521970 TATTTTAATATTTTA
1 TATTCTAATATTTTA
521985 TATT
1 TATT
521989 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:528893 original size:73 final size:73
Alignment explanation
Indices: 528773--528939 Score: 253
Period size: 73 Copynumber: 2.3 Consensus size: 73
528763 ATTTCCGTTT
*
528773 TTTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTATGCTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACG
528838 CTGAGGTAA
65 CTGAGGTAA
* * *
528847 TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGTCTCGGGGCACGC
1 TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACGC
*
528912 TGAGGTAT
66 TGAGGTAA
* * *
528920 TTTTAATTTCTGTTTTTCAA
1 TTTCAATTTATGCTTTTCAA
528940 TTTCTGCTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 67 0.79
74 18 0.21
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (73 bp):
TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACGC
TGAGGTAA
Found at i:528963 original size:13 final size:13
Alignment explanation
Indices: 528919--528963 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
528909 CGCTGAGGTA
528919 TTTTTAATTTCTG
1 TTTTTAATTTCTG
528932 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
528946 CTTTTAATTTCTG
1 TTTTTAATTTCTG
528959 TTTTT
1 TTTTT
528964 CAAAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:528986 original size:100 final size:100
Alignment explanation
Indices: 528851--529129 Score: 314
Period size: 100 Copynumber: 2.9 Consensus size: 100
528841 AGGTAATTTC
* * *
528851 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGTCTCGGGGCACGCTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACGCTGAG
*
528916 GTATTTTTAA-TTTCTGTTTTTCAATTTCTGCTTTT
66 GTATTTTCAATTTTC-GTTTTTCAATTTCTGCTTTT
* * *
528951 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACGCTGAG
* *
529016 GTATTTTCAATTTTCGTTTTTTTAATTTATG-TTTCT
66 GTATTTTCAATTTTCG-TTTTTCAATTTCTGCTTT-T
* *
529052 AA---A--------AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACGCTGAG
* * *
529106 GTAATTTCAATTTTTGTTTGTCAA
66 GTATTTTCAATTTTCGTTTTTCAA
529130 AACTCAACTC
Statistics
Matches: 161, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
89 6 0.04
90 64 0.40
100 72 0.45
101 19 0.12
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.38
Consensus pattern (100 bp):
AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGACACGCTGAG
GTATTTTCAATTTTCGTTTTTCAATTTCTGCTTTT
Found at i:529160 original size:73 final size:73
Alignment explanation
Indices: 529055--529461 Score: 580
Period size: 73 Copynumber: 5.5 Consensus size: 73
529045 TGTTTCTAAA
*
529055 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
529120 TGTTTGTC
66 TGTTTGTC
* * * ** * *
529128 AAAACTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
529193 TGTTTGTC
66 TGTTTGTC
* * *
529201 AAAAAAGTCAACTCATATTGTGATAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTCAATT
1 -AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
529266 TTTGTTTGTC
64 TTTGTTTGTC
* * * * *
529276 AAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
*
529341 TGTTTTTC
66 TGTTTGTC
* * * *
529349 AAAAAATCAACTTATATTGCGATAGGTAAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
529414 TTGTTTGTC
65 TTGTTTGTC
* *
529423 AAAAATCACCTCATATTGCGAGAGGTGAGTTGAACCTCA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
529462 AGACGCTAAG
Statistics
Matches: 288, Mismatches: 43, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
73 158 0.55
74 71 0.25
75 59 0.20
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
TGTTTGTC
Found at i:529181 original size:263 final size:264
Alignment explanation
Indices: 528681--529202 Score: 782
Period size: 263 Copynumber: 2.0 Consensus size: 264
528671 TATTTTGATG
* *
528681 TTTTTATTTCTGTCTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGGGCCTCAGGTCAC
1 TTTTAATTTCTGTCTTTC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG-CAC
*
528746 ACACTGAGGTATTTTCAATTTCCGTTTTTTCAATTTATGCTTTTCAAAAAATCAACTCATATTGC
64 ACACTGAGGTATTTTCAATTTCCGTTTTTTCAATTTATGCTTTTAAAAAAATCAACTCATATTGC
*
528811 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGCTTTTCAAAAATCAACT
129 GAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGCTTTTCAAAAATCAACT
* * ** * * * *
528876 CATATTGCGAGAGGTGAGATGAGTCTCGGGGCACGCTGAGGTATTTTTAATTTCTGTTTTTCAAT
194 CATATTGCGAGAGGTAAGATGAGCCTCAAGACACACTGAGGTATTTTCAATTTCTGTTTGTCAAT
528941 TTCTGC
259 TTCTGC
* *
528947 TTTTAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC
1 TTTTAATTTCTGTCTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCACAC
* * *
529010 GCTGAGGTATTTTCAATTTTCGTTTTTTTAATTTATG-TTTCTAAAAAAAATCAACTCATATTGC
66 ACTGAGGTATTTTCAATTTCCGTTTTTTCAATTTATGCTTT-T-AAAAAAATCAACTCATATTGC
* *
529074 GAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTG-TTTGTCAAAACTCAAC
129 GAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGCTTT-TCAAAAATCAAC
* *
529138 TCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGTTTGTCAA
193 TCATATTGCGAGAGGTAAGATGAGCCTCAAGACACACTGAGGTATTTTCAATTTCTGTTTGTCAA
529203 AAAAGTCAAC
Statistics
Matches: 232, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
261 3 0.01
262 42 0.18
263 132 0.57
264 39 0.17
266 16 0.07
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (264 bp):
TTTTAATTTCTGTCTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCACAC
ACTGAGGTATTTTCAATTTCCGTTTTTTCAATTTATGCTTTTAAAAAAATCAACTCATATTGCGA
GAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGCTTTTCAAAAATCAACTCA
TATTGCGAGAGGTAAGATGAGCCTCAAGACACACTGAGGTATTTTCAATTTCTGTTTGTCAATTT
CTGC
Found at i:529449 original size:147 final size:147
Alignment explanation
Indices: 529054--529495 Score: 699
Period size: 148 Copynumber: 3.0 Consensus size: 147
529044 ATGTTTCTAA
* *
529054 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* *
529119 TTGTTTGTCAAAACTCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAAGACACATTGAGGTATT
66 TTGTTTGTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATT
*
529184 TTCAATTTCTGTTTGTC
131 TTCAATTTCTGTTTTTC
* *
529201 AAAAAAGTCAACTCATATTGTGATAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTCAATT
1 AAAAAA-TCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
529266 TTTGTTTGTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAT
65 TTTGTTTGTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAT
529331 TTTCAATTTCTGTTTTTC
130 TTTCAATTTCTGTTTTTC
* * *
529349 AAAAAATCAACTTATATTGCGATAGGTAAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* * * * * *
529414 TTGTTTGTCAAAAATCACCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTAAGGTGTT
66 TTGTTTGTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATT
* *
529477 TTCCATTTCTGTTCTTC
131 TTCAATTTCTGTTTTTC
529494 AA
1 AA
529496 TTTCTATGTT
Statistics
Matches: 274, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
145 27 0.10
147 107 0.39
148 140 0.51
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (147 bp):
AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
TTGTTTGTCAAAACTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATT
TTCAATTTCTGTTTTTC
Found at i:529605 original size:92 final size:92
Alignment explanation
Indices: 529423--530124 Score: 401
Period size: 92 Copynumber: 7.8 Consensus size: 92
529413 TTTGTTTGTC
* * * * * * * * *
529423 AAAAATCACCTCATATTGCGAGAGGTGAGTTGAACCTC-A---AGACGCTAAGGTGTTTTCCATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAAT
* *
529484 TCTGTTCTTC-AAT-TTCTATGTTTCAAA
66 TCTGTTTTTCAAATATT-T-TTTTTCAAA
**
529511 AAAAAT-AAGCTCATATTGCGACTGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAA
1 AAAAATCAA-CTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAA
*
529575 TTCTGTTTTTCAAATATTTTTTTTCCAA
65 TTCTGTTTTTCAAATATTTTTTTTCAAA
* * * * * * * *
529603 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC-A---AGACGCTAAGGTGTTTTCCATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAAT
* *
529664 TCTGTTCTTC-AAT-TTCTATGTTTCAAA
66 TCTGTTTTTCAAATATT-T-TTTTTCAAA
* * *
529691 AAAAAT-AAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACTCATAAGCTGAGGTATTTTCAAA
1 AAAAATCAA-CTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAA
*
529755 TTCTGTTTTTCAAATATTTTTTTTCCAA
65 TTCTGTTTTTCAAATATTTTTTTTCAAA
** * * * *
529783 AAAAATCAACTCATATTGCGAGAGGTGAGTTC-AGCCTC-A-GGACACGCTGAGATATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAG-TCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAA
* *
529845 TTCTTTTTTTTTTC-AAT-TTATGTTTGTC-AA
65 TTC---TGTTTTTCAAATATT-T-TTTTTCAAA
* * ** * * *
529875 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGTTTC-AGGTCACACA-CCGAGGTATTTTC-A
1 AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGA-CTCATA-AGCTGAGGTATTTTCAA
* ** * *
529937 ATTGAT-TTTTTTTAAT-TTATGCTTTGC---
64 ATT-CTGTTTTTCAAATATT-T-TTTTTCAAA
* * ** * *
529964 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATA-CCGAGGTATTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATA-AGCTGAGGTATTTTCAAA
* * *
530028 ATCTGTTTTACAAAT-TTTGTTTT----
65 TTCTGTTTTTCAAATATTTTTTTTCAAA
* * * * *** * *
530051 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAAT
*
530116 TCTATTTTT
66 TCTGTTTTT
530125 AATGTCTAGT
Statistics
Matches: 490, Mismatches: 90, Indels: 69
0.76 0.14 0.11
Matches are distributed among these distances:
86 2 0.00
87 68 0.14
88 98 0.20
89 58 0.12
90 37 0.08
91 17 0.03
92 164 0.33
93 28 0.06
94 18 0.04
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (92 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAAT
TCTGTTTTTCAAATATTTTTTTTCAAA
Found at i:529704 original size:88 final size:88
Alignment explanation
Indices: 529423--529723 Score: 374
Period size: 88 Copynumber: 3.4 Consensus size: 88
529413 TTTGTTTGTC
* *
529423 AAAAATCACCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
1 AAAAATAAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
529488 TTCTTCAATTTCTATGTTTCAAA
66 TTCTTCAATTTCTATGTTTCAAA
** * * * * * * * *
529511 AAAAATAAGCTCATATTGCGACTGGTGAGTCGAGCCTCGACTCATAAGCTGAGGTATTTTCAAAT
1 AAAAATAAGCTCATATTGCGAGAGGTGAGTTGAACCTC-A---AGACGCTAAGGTGTTTTCCATT
* * *
529576 TCTGTTTTTCAAATATT-T-TTTTTCCAA
62 TCTGTTCTTC-AAT-TTCTATGTTTCAAA
529603 AAAAATCAA-CTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCT
1 AAAAAT-AAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCT
529667 GTTCTTCAATTTCTATGTTTCAAA
65 GTTCTTCAATTTCTATGTTTCAAA
*
529691 AAAAATAAGCTCATATTGCGAGTGGTGAGTTGA
1 AAAAATAAGCTCATATTGCGAGAGGTGAGTTGA
529724 GCCTTGACTC
Statistics
Matches: 174, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
86 2 0.01
87 6 0.03
88 93 0.53
89 1 0.01
91 1 0.01
92 63 0.36
93 6 0.03
94 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (88 bp):
AAAAATAAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
TTCTTCAATTTCTATGTTTCAAA
Found at i:529735 original size:180 final size:180
Alignment explanation
Indices: 529423--529813 Score: 746
Period size: 180 Copynumber: 2.2 Consensus size: 180
529413 TTTGTTTGTC
*
529423 AAAAATCACCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
529488 TTCTTCAATTTCTATGTTTCAAAAAAAATAAGCTCATATTGCGACTGGTGAGTCGAGCCTCGACT
66 TTCTTCAATTTCTATGTTTCAAAAAAAATAAGCTCATATTGCGACTGGTGAGTCGAGCCTCGACT
529553 CATAAGCTGAGGTATTTTCAAATTCTGTTTTTCAAATATTTTTTTTCCAA
131 CATAAGCTGAGGTATTTTCAAATTCTGTTTTTCAAATATTTTTTTTCCAA
529603 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
* * *
529668 TTCTTCAATTTCTATGTTTCAAAAAAAATAAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACT
66 TTCTTCAATTTCTATGTTTCAAAAAAAATAAGCTCATATTGCGACTGGTGAGTCGAGCCTCGACT
529733 CATAAGCTGAGGTATTTTCAAATTCTGTTTTTCAAATATTTTTTTTCCAA
131 CATAAGCTGAGGTATTTTCAAATTCTGTTTTTCAAATATTTTTTTTCCAA
529783 AAAAATCAACTCATATTGCGAGAGGTGAGTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTT
529814 CAGCCTCAGG
Statistics
Matches: 207, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 207 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (180 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTAAGGTGTTTTCCATTTCTG
TTCTTCAATTTCTATGTTTCAAAAAAAATAAGCTCATATTGCGACTGGTGAGTCGAGCCTCGACT
CATAAGCTGAGGTATTTTCAAATTCTGTTTTTCAAATATTTTTTTTCCAA
Found at i:529988 original size:89 final size:87
Alignment explanation
Indices: 529783--530087 Score: 323
Period size: 89 Copynumber: 3.4 Consensus size: 87
529773 TTTTTTCCAA
* * * *
529783 AAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGG--ACACGCTGAGATATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACCGAGGTATTTTCAA--
*
529846 TCTTTTTTTTTTCAATTTATGTTTGTC
64 T-TGTTTTTTTT-AATTTATGTTTG-C
* **
529873 AAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGTTTCAGGTCACACACCGAGGTATTTTCAA
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACCGAGGTATTTTCAA
529938 TTGATTTTTTTTAATTTATGCTTTGC
64 TTG-TTTTTTTTAATTTATG-TTTGC
* * *
529964 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACCGAGGTATTTTC--AA
*** *
530029 TCTG-TTTTACAAATTT-TGTTT-T
64 T-TGTTTTTTTTAATTTATGTTTGC
*
530051 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
530088 TGGCTCACGT
Statistics
Matches: 186, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
87 35 0.19
88 3 0.02
89 57 0.31
90 9 0.05
91 13 0.07
92 52 0.28
94 17 0.09
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACCGAGGTATTTTCAATT
GTTTTTTTTAATTTATGTTTGC
Found at i:530137 original size:87 final size:86
Alignment explanation
Indices: 529875--530169 Score: 229
Period size: 87 Copynumber: 3.4 Consensus size: 86
529865 TGTTTGTCAA
* * * ** * *
529875 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGTTTCAGG-TCACACACCGAGGTATTTTCAAT
1 AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTC-GGCTCACATACCGAGCTATTTTCAA-
* ** *
529939 TGAT-T-TTTTTTAATTTATGCTTTGC
64 -AATCTATTTTAAAATTTA-G-TTT-T
* * *
529964 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
* *
530029 TCTGTTTTACAAATTTTGTTTT
66 TCTATTTTA-AAATTTAGTTTT
* * * * * **
530051 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
*
530116 TCTATTTT-TAATGTCTAGTTTT
66 TCTATTTTAAAAT-T-TAGTTTT
* * *
530138 AAAGAGTCAATTCATATTACGAGAAATGAGTT
1 AAA-AATCAACTCATATTACGAGAAGTGAGTT
530170 AAGCTCATGA
Statistics
Matches: 172, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
85 3 0.02
86 1 0.01
87 73 0.42
88 30 0.17
89 60 0.35
90 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (86 bp):
AAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAA
TCTATTTTAAAATTTAGTTTT
Found at i:531369 original size:24 final size:23
Alignment explanation
Indices: 531321--531372 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
531311 TTTTTTTTTT
*
531321 TATTATTATATTTCTTAATATTA
1 TATTATTATATTTCTTAATAATA
*
531344 TATTATATATATATTCTT-TTAATA
1 TATTAT-TATAT-TTCTTAATAATA
531368 TATTA
1 TATTA
531373 GGTATATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTATATTTCTTAATAATA
Found at i:531426 original size:25 final size:25
Alignment explanation
Indices: 531388--531456 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
531378 ATTCTAAATT
*
531388 CTATATTACGTATATATA-TT-ATA
1 CTATATTATGTATATATATTTAATA
* *
531411 CTATTTTATGTATATATCTTTAATA
1 CTATATTATGTATATATATTTAATA
*
531436 CTATATTATTTATATATATTT
1 CTATATTATGTATATATATTT
531457 TTTTTTCTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.39
24 2 0.05
25 21 0.55
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (25 bp):
CTATATTATGTATATATATTTAATA
Found at i:531446 original size:30 final size:28
Alignment explanation
Indices: 531415--531525 Score: 81
Period size: 29 Copynumber: 4.0 Consensus size: 28
531405 ATTATACTAT
531415 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATACTATATTA
* ** * *
531444 TTTATATATAT-TTTTTTTTCTACATGTTA
1 TTTATGTATATATTTTAATACT--ATATTA
531473 TCTTATGTATATATTTTAAT--TATATTA
1 T-TTATGTATATATTTTAATACTATATTA
* *
531500 TGTATGTAT-T-TTTT-ACACTATATTA
1 TTTATGTATATATTTTAATACTATATTA
531525 T
1 T
531526 GTACATATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 9 0.14
26 7 0.11
27 12 0.18
28 1 0.02
29 17 0.26
30 9 0.14
31 5 0.08
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTATGTATATATTTTAATACTATATTA
Found at i:531495 original size:22 final size:22
Alignment explanation
Indices: 531470--531577 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
531460 TTTCTACATG
*
531470 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
531492 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTA-A
* *
531517 CTATATTATGTACATATTTTTAA
1 TTATATTATGTATATA-TTTTAA
* * *
531540 -TATTATCACGTATTTATTTT--
1 TTA-TATTATGTATATATTTTAA
*
531560 TTATA-TATGTACATATTT
1 TTATATTATGTATATATTT
531578 ATGTAGTATT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.13
20 2 0.03
21 2 0.03
22 17 0.25
23 12 0.18
24 13 0.19
25 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:531526 original size:25 final size:24
Alignment explanation
Indices: 531476--531562 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
531466 CATGTTATCT
*
531476 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
531502 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
** * *
531527 TACATA-TTTTTAA-TATTATCACG
1 TATGTATTTTTTAACTA-TATTATG
*
531550 TATTTATTTTTTA
1 TATGTATTTTTTA
531563 TATATGTACA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.04
23 10 0.20
24 17 0.33
25 15 0.29
26 7 0.14
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:531544 original size:20 final size:20
Alignment explanation
Indices: 531519--531577 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
531509 TTTTTACACT
531519 ATATTATGTACATATTTTTA
1 ATATTATGTACATATTTTTA
** *
531539 ATATTATCACGTATTTATTTTTT
1 ATATTAT---GTACATATTTTTA
531562 ATA-TATGTACATATTT
1 ATATTATGTACATATTT
531578 ATGTAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 3 0.10
23 13 0.42
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATTATGTACATATTTTTA
Found at i:531716 original size:16 final size:15
Alignment explanation
Indices: 531692--531739 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
531682 TAATTATTAT
*
531692 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
531708 TATTTTAATATTTTA
1 TATTTTAATATTTTA
*
531723 TATTTTATATACTTTA
1 TATTTTA-ATATTTTA
531739 T
1 T
531740 TATTCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:531727 original size:7 final size:8
Alignment explanation
Indices: 531692--531743 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
531682 TAATTATTAT
*
531692 TATTCTAA
1 TATTTTAA
*
531700 TATTTTGA
1 TATTTTAA
531708 TATTTTAA
1 TATTTTAA
531716 TATTTT-A
1 TATTTTAA
531723 TATTTTATA
1 TATTTTA-A
* *
531732 TACTTTAT
1 TATTTTAA
531740 TATT
1 TATT
531744 CACATCACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.61
9 7 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:532382 original size:21 final size:21
Alignment explanation
Indices: 532343--532382 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
532333 TCTTAGGATA
*
532343 TAGTTTTTCTAAATAAATGGT
1 TAGTTTTTCTAAAAAAATGGT
532364 TAGTTTTT-TAAAAACAATG
1 TAGTTTTTCTAAAAA-AATG
532383 TATGGGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
TAGTTTTTCTAAAAAAATGGT
Found at i:544839 original size:42 final size:42
Alignment explanation
Indices: 544777--544879 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
544767 CTTCTACCGG
* * *
544777 TCCTACTTCTTCCGGTTTACTTAGGAGTTCTCCTATGACTGC
1 TCCTACTTCTTCCGGGTTACTTAGGAGTTCTCCTATAACTAC
544819 TCCTACTTCTTCCGGGTTACTTAGGAGTTCTCCTATAACTAC
1 TCCTACTTCTTCCGGGTTACTTAGGAGTTCTCCTATAACTAC
* *
544861 TCTTACTTTTTCCGGGTTA
1 TCCTACTTCTTCCGGGTTA
544880 ATTGGGAATC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (42 bp):
TCCTACTTCTTCCGGGTTACTTAGGAGTTCTCCTATAACTAC
Found at i:544906 original size:42 final size:42
Alignment explanation
Indices: 544780--544906 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 42
544770 CTACCGGTCC
* * * *
544780 TACTTCTTCCGGTTTACTTAGGAGTTCTCCTATGACTGCTCC
1 TACTTCTTCCGGGTTAATTAGGAGATCTCCTATGACTGCTCT
* * * *
544822 TACTTCTTCCGGGTTACTTAGGAGTTCTCCTATAACTACTCT
1 TACTTCTTCCGGGTTAATTAGGAGATCTCCTATGACTGCTCT
* * *
544864 TACTTTTTCCGGGTTAATTGGGA-ATCATCCTATGCCTGCTCT
1 TACTTCTTCCGGGTTAATTAGGAGATC-TCCTATGACTGCTCT
544906 T
1 T
544907 CCTCAAAATA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 2 0.03
42 71 0.97
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.41
Consensus pattern (42 bp):
TACTTCTTCCGGGTTAATTAGGAGATCTCCTATGACTGCTCT
Found at i:555376 original size:2 final size:2
Alignment explanation
Indices: 555369--555431 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
555359 AAGTCTTCAT
555369 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
555411 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
555432 TTGCTTTCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:559196 original size:32 final size:32
Alignment explanation
Indices: 559160--559221 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
559150 TACTTTTAGG
*
559160 TTTAACTGTTAGCAT-TAATTGTTTTGTTAAGT
1 TTTAACTGTTAGCATGT-ATTGTTTGGTTAAGT
*
559192 TTTAACTGTTAGTATGTATTGTTTGGTTAA
1 TTTAACTGTTAGCATGTATTGTTTGGTTAA
559222 ATTTGTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (32 bp):
TTTAACTGTTAGCATGTATTGTTTGGTTAAGT
Found at i:559362 original size:30 final size:29
Alignment explanation
Indices: 559328--559413 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
559318 ATTGTTCAAC
559328 TTAAATTTTAAAATTTAAAATATAAGAAGA
1 TTAAATTTTAAAATTTAAAATATAA-AAGA
**
559358 TTAAATTTATTAAAAAATAAAA-ATAAAAGA
1 TTAAA-TT-TTAAAATTTAAAATATAAAAGA
*
559388 TTAAA-TTTAAAATTTAAAATTTAAAA
1 TTAAATTTTAAAATTTAAAATATAAAA
559414 TTTTAGAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 11 0.23
28 6 0.12
30 14 0.29
31 6 0.12
32 11 0.23
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAAATTTTAAAATTTAAAATATAAAAGA
Found at i:559398 original size:14 final size:14
Alignment explanation
Indices: 559328--559413 Score: 50
Period size: 14 Copynumber: 5.9 Consensus size: 14
559318 ATTGTTCAAC
* *
559328 TTAAATTTTAAAAT
1 TTAAAATTTAAAAA
*
559342 TTAAAATATAAGAAGA
1 TTAAAATTTAA-AA-A
*
559358 TTAAATTTATTAAAAA
1 TTAAA-AT-TTAAAAA
* *
559374 ATAAAA-ATAAAAGA
1 TTAAAATTTAAAA-A
*
559388 TT-AAATTTAAAAT
1 TTAAAATTTAAAAA
559401 TTAAAATTTAAAA
1 TTAAAATTTAAAA
559414 TTTTAGAAAG
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
13 10 0.19
14 26 0.48
15 2 0.04
16 10 0.19
17 3 0.06
18 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TTAAAATTTAAAAA
Found at i:559402 original size:7 final size:7
Alignment explanation
Indices: 559390--559416 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
559380 ATAAAAGATT
559390 AAATTTA
1 AAATTTA
559397 AAATTTA
1 AAATTTA
559404 AAATTTA
1 AAATTTA
559411 AAATTT
1 AAATTT
559417 TAGAAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:559459 original size:27 final size:28
Alignment explanation
Indices: 559403--559466 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
559393 TTTAAAATTT
*
559403 AAAATTTAAAATTTTAGAAAGATATAAA
1 AAAATTTAAAATTTTAGAAAAATATAAA
559431 AAAATTTAAAATTTTAGAAAAATAT-AA
1 AAAATTTAAAATTTTAGAAAAATATAAA
559458 AAAATTTAA
1 AAAATTTAA
559467 CCTGAAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATTTAAAATTTTAGAAAAATATAAA
Found at i:569700 original size:20 final size:20
Alignment explanation
Indices: 569664--569703 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
569654 TAAAAAAATT
*
569664 ATAATTTTTATACTTTTTAA
1 ATAATTTTAATACTTTTTAA
569684 ATAATTTTAATTA-TTTTTAA
1 ATAATTTTAA-TACTTTTTAA
569704 TTTATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATAATTTTAATACTTTTTAA
Found at i:569706 original size:16 final size:18
Alignment explanation
Indices: 569685--569720 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
569675 ACTTTTTAAA
569685 TAATTT-TAAT-TATTTT
1 TAATTTATAATATATTTT
569701 TAATTTATAATATATTTT
1 TAATTTATAATATATTTT
569719 TA
1 TA
569721 TTATTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTTATAATATATTTT
Found at i:570196 original size:17 final size:17
Alignment explanation
Indices: 570174--570207 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
570164 AAAATGCTTA
570174 TAAACAAATATTAATTT
1 TAAACAAATATTAATTT
570191 TAAACAAATATTAATTT
1 TAAACAAATATTAATTT
570208 ATTGATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAACAAATATTAATTT
Found at i:570739 original size:5 final size:5
Alignment explanation
Indices: 570729--570755 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
570719 AAAATTTGTG
570729 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
570756 TTTCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:581808 original size:2 final size:2
Alignment explanation
Indices: 581801--581825 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
581791 TGTGTTAAGT
581801 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
581826 TCGGATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:582179 original size:41 final size:41
Alignment explanation
Indices: 582013--582168 Score: 240
Period size: 41 Copynumber: 3.8 Consensus size: 41
582003 TTTATCGTTA
* * * *
582013 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* * *
582054 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
582095 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
582136 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
582169 AAGAGCCGGT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:582439 original size:33 final size:32
Alignment explanation
Indices: 582383--582446 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
582373 ATATATATAT
582383 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
582415 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
582447 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:582463 original size:33 final size:33
Alignment explanation
Indices: 582390--582463 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
582380 TATATATATA
* * **
582390 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
582422 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
582455 TGTATGTAT
1 TATATGTAT
582464 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:585836 original size:37 final size:37
Alignment explanation
Indices: 585786--585863 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
585776 TTTATATTTC
* **
585786 TTATTTTATAATTTTGTCTGATTGATGCCAAAACATT
1 TTATTTTATAATTTAGTCCAATTGATGCCAAAACATT
585823 TTATTTTATAATTTAGTCCAATTGATGCCAAAACATT
1 TTATTTTATAATTTAGTCCAATTGATGCCAAAACATT
585860 TTAT
1 TTAT
585864 ACTTATCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (37 bp):
TTATTTTATAATTTAGTCCAATTGATGCCAAAACATT
Found at i:587545 original size:98 final size:98
Alignment explanation
Indices: 587376--587562 Score: 329
Period size: 98 Copynumber: 1.9 Consensus size: 98
587366 AGAGGCTATA
587376 GAAATGAATTTGTAATGCACATAAGTGTTTTGCCATAACACATCAACCACGGGTTTTTATCACAT
1 GAAATGAATTTGTAATGCACATAAGTGTTTTGCCATAACACATCAACCACGGGTTTTTATCACAT
587441 CTTATATCACACATGCACATAAATCTCCTATTG
66 CTTATATCACACATGCACATAAATCTCCTATTG
* ** *
587474 GAAATGAATTTGTAATGCACATAAGTGTTTTGCCTTAAGGCATCAACCATGGGTTTTTATCACAT
1 GAAATGAATTTGTAATGCACATAAGTGTTTTGCCATAACACATCAACCACGGGTTTTTATCACAT
*
587539 CTTATATCACATATGCACATAAAT
66 CTTATATCACACATGCACATAAAT
587563 TAAGCTATTG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (98 bp):
GAAATGAATTTGTAATGCACATAAGTGTTTTGCCATAACACATCAACCACGGGTTTTTATCACAT
CTTATATCACACATGCACATAAATCTCCTATTG
Found at i:589395 original size:15 final size:17
Alignment explanation
Indices: 589377--589408 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
589367 TAGCATAATT
589377 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
589392 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
589409 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:595832 original size:15 final size:17
Alignment explanation
Indices: 595814--595845 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
595804 TAGCATAATT
595814 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
595829 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
595846 CAAGTATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:598095 original size:43 final size:43
Alignment explanation
Indices: 598006--598095 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
597996 ACCTACAGAG
* * * * **
598006 GACACACGGCCGTGTTAGATGGACGTGTGTCACACATGACTAA
1 GACACACAGCCGTGTCACATGGACATGTGTCACACACAACTAA
* *
598049 GACACACAGCCGTGTCACATGGCCATGTGTCACACACAACTGA
1 GACACACAGCCGTGTCACATGGACATGTGTCACACACAACTAA
598092 GACA
1 GACA
598096 TACGCTCGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (43 bp):
GACACACAGCCGTGTCACATGGACATGTGTCACACACAACTAA
Found at i:598106 original size:43 final size:42
Alignment explanation
Indices: 598031--598115 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
598021 TAGATGGACG
**
598031 TGTGTCACACATGACTAAGACACACAGCCGTGTCACATGGCCA
1 TGTGTCACACACAACTAAGACACACAGCCGTGTCACA-GGCCA
* * *
598074 TGTGTCACACACAACTGAGACATAC-GCTCGTGTCTCAGGCCA
1 TGTGTCACACACAACTAAGACACACAGC-CGTGTCACAGGCCA
598116 CGTGGACTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 7 0.19
43 29 0.81
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (42 bp):
TGTGTCACACACAACTAAGACACACAGCCGTGTCACAGGCCA
Found at i:600599 original size:21 final size:23
Alignment explanation
Indices: 600540--600605 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
600530 GCTTTACCGA
600540 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
600563 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
600585 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
600606 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 4 0.11
23 17 0.47
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:602230 original size:33 final size:33
Alignment explanation
Indices: 602193--602290 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
602183 TCACCTGAGT
* *
602193 TAATCCTTCCAACACACCAATGCTCATAAGAGC
1 TAATCCTACCATCACACCAATGCTCATAAGAGC
*
602226 TAAT-CTAACCATCACACCAATACTCATAAGAGC
1 TAATCCT-ACCATCACACCAATGCTCATAAGAGC
* * *
602259 TAAACCAACCATCACACCAATGCTTATAAGAG
1 TAATCCTACCATCACACCAATGCTCATAAGAG
602291 TTAAAGCAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.95
34 1 0.02
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.20
Consensus pattern (33 bp):
TAATCCTACCATCACACCAATGCTCATAAGAGC
Found at i:602305 original size:33 final size:33
Alignment explanation
Indices: 602205--602311 Score: 151
Period size: 33 Copynumber: 3.2 Consensus size: 33
602195 ATCCTTCCAA
* *
602205 CACACCAATGCTCATAAGAGCTAATCTAACCAT
1 CACACCAATGCTCATAAGAGCTAAACCAACCAT
*
602238 CACACCAATACTCATAAGAGCTAAACCAACCAT
1 CACACCAATGCTCATAAGAGCTAAACCAACCAT
* * * *
602271 CACACCAATGCTTATAAGAGTTAAAGCAATCAT
1 CACACCAATGCTCATAAGAGCTAAACCAACCAT
602304 CACACCAA
1 CACACCAA
602312 ACAGAGAGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.43, C:0.30, G:0.08, T:0.19
Consensus pattern (33 bp):
CACACCAATGCTCATAAGAGCTAAACCAACCAT
Found at i:605031 original size:50 final size:50
Alignment explanation
Indices: 604973--605072 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
604963 TCCTAAAGGT
*
604973 TGTAAACTAGTTTAAGGTGATAGAATAAAATGTTAATTGAGAAAAATCAG
1 TGTAAACTAGTTTAAGGCGATAGAATAAAATGTTAATTGAGAAAAATCAG
*
605023 TGTAAACTAGTTTAAGGCGATAGAATAAAATGTTAATTGCGAAAAATCAG
1 TGTAAACTAGTTTAAGGCGATAGAATAAAATGTTAATTGAGAAAAATCAG
605073 CTCAATTGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (50 bp):
TGTAAACTAGTTTAAGGCGATAGAATAAAATGTTAATTGAGAAAAATCAG
Found at i:609954 original size:212 final size:213
Alignment explanation
Indices: 609573--609957 Score: 693
Period size: 212 Copynumber: 1.8 Consensus size: 213
609563 ATTGGGCAAT
* * *
609573 TTACACTTTTGGGCTCTTATACTTTTCAAAATTTATAATTTGATTCTTTTTACCAAAATCTCATA
1 TTACACTTTTGGGATCTTATACTTTTCAAAATTTATAATTTGATCCTTTTTACCAAAATCTCAAA
609638 TTCACAACCATTCTCAAATAGTTCCTTTTCAAAAAATCAAATTAATTCATTAAGATTTCATTTAT
66 TTCACAACCATTCTCAAATAGTTCCTTTTCAAAAAATCAAATTAATTCATTAAGATTTCATTTAT
609703 TACACTTGTTTTCAAATGATTATTCATATTAAGATTATTATGTCTGGACTAACAATACATTGCAC
131 TACACTTGTTTTCAAATGATTATTCATATTAAGATTATTATGTCTGGACTAACAATACATTGCAC
609768 ATAAAATTCAATAACATA
196 ATAAAATTCAATAACATA
*
609786 TTACAC-TTTGGGATCTTATACTTTTCAAAATTTATAATTTGGTCCTTTTTACCAAAATCTCAAA
1 TTACACTTTTGGGATCTTATACTTTTCAAAATTTATAATTTGATCCTTTTTACCAAAATCTCAAA
*
609850 TTCACAACCATTCTCAAAT-GTTTCCTTTTCAAAAAATCAAATTAATTCTTTAAGATTTCATTTA
66 TTCACAACCATTCTCAAATAG-TTCCTTTTCAAAAAATCAAATTAATTCATTAAGATTTCATTTA
*
609914 TTACACTTGTTTTCAAATGATTATTCATATTAGGATTATTATGT
130 TTACACTTGTTTTCAAATGATTATTCATATTAAGATTATTATGT
609958 TGTCTATAAG
Statistics
Matches: 165, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
211 1 0.01
212 158 0.96
213 6 0.04
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (213 bp):
TTACACTTTTGGGATCTTATACTTTTCAAAATTTATAATTTGATCCTTTTTACCAAAATCTCAAA
TTCACAACCATTCTCAAATAGTTCCTTTTCAAAAAATCAAATTAATTCATTAAGATTTCATTTAT
TACACTTGTTTTCAAATGATTATTCATATTAAGATTATTATGTCTGGACTAACAATACATTGCAC
ATAAAATTCAATAACATA
Found at i:614012 original size:28 final size:27
Alignment explanation
Indices: 613972--614024 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
613962 ATTTTAAATT
613972 TTTTTTTTGAAATTTTAACTTTCTTTATA
1 TTTTTTTTGAAATTTTAA-TTT-TTTATA
614001 TTTTTTTT-AAATTTTAATTTTTTA
1 TTTTTTTTGAAATTTTAATTTTTTA
614025 AAATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 9 0.38
29 8 0.33
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTTTTTTGAAATTTTAATTTTTTATA
Found at i:614035 original size:24 final size:26
Alignment explanation
Indices: 614008--614056 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
613998 ATATTTTTTT
*
614008 TAAATTTTA-ATTTTTTA-AAATATA
1 TAAATTTTAGAATTTTTATAAATATA
614032 TAAATTTTAGAATTTTTATAAATAT
1 TAAATTTTAGAATTTTTATAAATAT
614057 TTTGAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 7 0.32
26 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TAAATTTTAGAATTTTTATAAATATA
Found at i:614067 original size:18 final size:19
Alignment explanation
Indices: 614030--614066 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
614020 TTTTAAAATA
*
614030 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
614048 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
614067 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:614072 original size:18 final size:21
Alignment explanation
Indices: 614035--614078 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
614025 AAATATATAA
*
614035 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTAAAAATT
614055 ATTTT-GAA-TTTTAAAAATT
1 ATTTTAGAATTTTTAAAAATT
614074 ATTTT
1 ATTTT
614079 TTAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTTAGAATTTTTAAAAATT
Found at i:614100 original size:11 final size:12
Alignment explanation
Indices: 614069--614100 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
614059 TGAATTTTAA
614069 AAATTATTTTTT
1 AAATTATTTTTT
614081 -AATTATTTTTT
1 AAATTATTTTTT
614092 AAATT-TTTT
1 AAATTATTTT
614101 GTTGAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
AAATTATTTTTT
Found at i:622174 original size:14 final size:14
Alignment explanation
Indices: 622136--622166 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
622126 TTGTTTCATT
622136 GAAAATAATTTTTG
1 GAAAATAATTTTTG
622150 GAAAATAATTTTTG
1 GAAAATAATTTTTG
622164 GAA
1 GAA
622167 TATGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (14 bp):
GAAAATAATTTTTG
Found at i:622754 original size:16 final size:16
Alignment explanation
Indices: 622723--622759 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
622713 ATGTGAATAA
622723 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
622739 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
622755 TATTA
1 TATTA
622760 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:625837 original size:24 final size:23
Alignment explanation
Indices: 625758--625838 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 23
625748 TTTTTGTCTC
* *
625758 ATTTTTTATTTGTTTTTTTTAAT
1 ATTTTTTATTTATTTTTTTAAAT
* *
625781 ATTTGTT-TTTATGTTTTTAAAT
1 ATTTTTTATTTATTTTTTTAAAT
* * *
625803 GTATTTGATTTATTATTTTTAAAT
1 ATTTTTTATTTATT-TTTTTAAAT
*
625827 TTTTTTTATTTA
1 ATTTTTTATTTA
625839 ATAAAAAAAG
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 15 0.34
23 11 0.25
24 18 0.41
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (23 bp):
ATTTTTTATTTATTTTTTTAAAT
Found at i:628236 original size:15 final size:15
Alignment explanation
Indices: 628216--628245 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
628206 TTGTTTGGTT
628216 TATATACAGGGAATA
1 TATATACAGGGAATA
628231 TATATACAGGGAATA
1 TATATACAGGGAATA
628246 GGAATTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (15 bp):
TATATACAGGGAATA
Found at i:639743 original size:16 final size:16
Alignment explanation
Indices: 639722--639752 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
639712 TATTTCTAGG
639722 TTACTATCGATTGTTT
1 TTACTATCGATTGTTT
639738 TTACTATCGATTGTT
1 TTACTATCGATTGTT
639753 CTTTGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (16 bp):
TTACTATCGATTGTTT
Found at i:642877 original size:18 final size:18
Alignment explanation
Indices: 642854--642905 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
642844 CCATGCTTTT
642854 ATTATAAATTAGAAAAAA
1 ATTATAAATTAGAAAAAA
* *
642872 ATTATAAAAATA-AAAATA
1 ATTAT-AAATTAGAAAAAA
*
642890 A-TATATATTAGAAAAA
1 ATTATAAATTAGAAAAA
642906 TTATTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 11 0.41
19 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
ATTATAAATTAGAAAAAA
Done.