Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold194
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: 2893263
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 119126 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:1916477 original size:98 final size:98
Alignment explanation
Indices: 1916308--1917152 Score: 1627
Period size: 98 Copynumber: 8.6 Consensus size: 98
1916298 NNNNNNNNNN
1916308 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1916373 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
1916406 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1916471 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
1916504 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1916569 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
1916602 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1916667 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
1916700 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1916765 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
1916798 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
1916863 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
* *
1916896 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
*
1916961 GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
* *
1916994 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAAAG
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
*
1917059 GAAATATTCCGAGTTTGGGATTCTAGAGGAATC
66 GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
*
1917092 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGT
1 GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGT
1917153 TTTATTGTAC
Statistics
Matches: 744, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 744 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (98 bp):
GTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGCGGATGTTCTTTTAAAGTGAAG
GAAATATTCCGAGTTTGGGATTCTAAAGGAATC
Found at i:1917659 original size:14 final size:14
Alignment explanation
Indices: 1917628--1917735 Score: 72
Period size: 14 Copynumber: 7.7 Consensus size: 14
1917618 ATAAATCTGC
* *
1917628 ATCTATGAGTACAT
1 ATCTATGAATCCAT
*
1917642 ATCTATGAATCCAC
1 ATCTATGAATCCAT
* ***
1917656 ATCTATGGATATGT
1 ATCTATGAATCCAT
**
1917670 ATCTATGAATCCGC
1 ATCTATGAATCCAT
* **
1917684 ATATATGAATCTGT
1 ATCTATGAATCCAT
* **
1917698 ATTTATGAATCTGT
1 ATCTATGAATCCAT
*
1917712 ATCTATGAATGCAT
1 ATCTATGAATCCAT
1917726 ATCTATGAAT
1 ATCTATGAAT
1917736 TCACATTTAC
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 74 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (14 bp):
ATCTATGAATCCAT
Found at i:1917661 original size:28 final size:28
Alignment explanation
Indices: 1917627--1917741 Score: 97
Period size: 28 Copynumber: 4.1 Consensus size: 28
1917617 TATAAATCTG
*
1917627 CATCTATGAGTACATATCTATGAATCCA
1 CATCTATGAATACATATCTATGAATCCA
* ** *
1917655 CATCTATGGATATGTATCTATGAATCCG
1 CATCTATGAATACATATCTATGAATCCA
* * * **
1917683 CATATATGAAT-CTGTATTTATGAATCTG
1 CATCTATGAATAC-ATATCTATGAATCCA
* * *
1917711 TATCTATGAATGCATATCTATGAATTCA
1 CATCTATGAATACATATCTATGAATCCA
1917739 CAT
1 CAT
1917742 TTACGAATCT
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
28 66 0.99
29 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (28 bp):
CATCTATGAATACATATCTATGAATCCA
Found at i:1917744 original size:42 final size:42
Alignment explanation
Indices: 1917621--1917752 Score: 126
Period size: 42 Copynumber: 3.1 Consensus size: 42
1917611 CATGTATATA
* * * * *
1917621 AATCTGCATCTATGAGTACATATCTATGAATCCACATCTATG
1 AATCTGTATCTATGAATGCATATCTATGAATTCACATTTATG
* * **
1917663 GATATGTATCTATGAATCCGCATA--TATGAA-TCTGTATTTATG
1 AATCTGTATCTATGAAT--GCATATCTATGAATTC-ACATTTATG
*
1917705 AATCTGTATCTATGAATGCATATCTATGAATTCACATTTACG
1 AATCTGTATCTATGAATGCATATCTATGAATTCACATTTATG
1917747 AATCTG
1 AATCTG
1917753 CATGTAAGAG
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
40 5 0.07
41 1 0.01
42 58 0.83
43 2 0.03
44 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (42 bp):
AATCTGTATCTATGAATGCATATCTATGAATTCACATTTATG
Found at i:1919436 original size:29 final size:30
Alignment explanation
Indices: 1919390--1919461 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
1919380 TAAAAAGTTC
* *
1919390 AAAAAATATATAAA-AATTAGTAAAAAAAT
1 AAAAATTATAAAAATAATTAGTAAAAAAAT
* * **
1919419 -AAAATTATTAAAATAATTTGTAAAAGTAT
1 AAAAATTATAAAAATAATTAGTAAAAAAAT
1919448 AAAAATTATAAAAA
1 AAAAATTATAAAAA
1919462 CATATATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 10 0.29
29 12 0.35
30 12 0.35
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (30 bp):
AAAAATTATAAAAATAATTAGTAAAAAAAT
Found at i:1923324 original size:34 final size:34
Alignment explanation
Indices: 1923281--1923347 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1923271 TTGAAGTATA
1923281 AATGGTATATATG-TATATACAATGTTCAAATATG
1 AATGGTATATA-GATATATACAATGTTCAAATATG
* * *
1923315 AATGGTATATAGATATATATATTGTTCGAATAT
1 AATGGTATATAGATATATACAATGTTCAAATAT
1923348 TTATATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (34 bp):
AATGGTATATAGATATATACAATGTTCAAATATG
Found at i:1923587 original size:149 final size:150
Alignment explanation
Indices: 1923410--1923712 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 150
1923400 GTTATATATG
1923410 TATACACAAGGTTCGAATACATATATGTATATACATGTATAAATTCTTGGTTTAATTAAAGGTAT
1 TATACACAAGGTTCGAATACATATATGTATATACATGTATAAATTCTTGGTTTAATTAAAGGTAT
*
1923475 GTATATTGTAATTGTATAGGTAATTTCGAATAAGTATGTATATATCGGTTGGAATGTATATGAAA
66 GTATATTGTAATTGTATAGGTAATTTCGAAAAAGTATGTATATATCGGTTGGAATGTATATGAAA
1923540 ATACTTGAATAAATCTTGAA
131 ATACTTGAATAAATCTTGAA
1923560 TATACACAAGGTT-GAATACATATATGTATATACATGTATAAATTCTTGGTTTAATTAAAGGTAT
1 TATACACAAGGTTCGAATACATATATGTATATACATGTATAAATTCTTGGTTTAATTAAAGGTAT
* *
1923624 GTATATTGTAATTGTATAGGTAATTTCGAAAAAGTATGTATATGTGGGTTGGAATGTATATGAAA
66 GTATATTGTAATTGTATAGGTAATTTCGAAAAAGTATGTATATATCGGTTGGAATGTATATGAAA
1923689 ATACTTGAATAAATCTTGAA
131 ATACTTGAATAAATCTTGAA
1923709 TATA
1 TATA
1923713 TTTTAAGGTA
Statistics
Matches: 150, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
149 137 0.91
150 13 0.09
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (150 bp):
TATACACAAGGTTCGAATACATATATGTATATACATGTATAAATTCTTGGTTTAATTAAAGGTAT
GTATATTGTAATTGTATAGGTAATTTCGAAAAAGTATGTATATATCGGTTGGAATGTATATGAAA
ATACTTGAATAAATCTTGAA
Found at i:1924025 original size:42 final size:42
Alignment explanation
Indices: 1923978--1924151 Score: 233
Period size: 42 Copynumber: 4.2 Consensus size: 42
1923968 TTAGTGCCTG
*
1923978 GCAGGCTTAGTGCCAGTGAAACAATATCAGACTTTACGTCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
* * * *
1924020 GCAGGCTTAATGTCGGTGAAATAATTTCAGACTTTACGTCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
*
1924062 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACATCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
** * * * *
1924104 GTTGGCTTAATGCCAGTGAAAC-ATTTTAGACTATATGTCTA
1 GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
1924145 GCAGGCT
1 GCAGGCT
1924152 AACTGTCGAT
Statistics
Matches: 113, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 19 0.17
42 94 0.83
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
GCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTA
Found at i:1935325 original size:24 final size:24
Alignment explanation
Indices: 1935293--1935354 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1935283 TTTATGTCCC
1935293 AAAATTACAGTGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
*
1935317 AAAATTACAATGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
*
1935341 AAGATTACAGTGGA
1 AAAATTACAGTGGA
1935355 GTGCAATCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAATTACAGTGGATTGAACCTTG
Found at i:1935800 original size:88 final size:87
Alignment explanation
Indices: 1935659--1936208 Score: 496
Period size: 88 Copynumber: 6.2 Consensus size: 87
1935649 ATAGATTGAA
* ** * *
1935659 GAAGATTGTAGATCTTGTCTTCCTGTGCTGTTAGTGAAGTAGATCAAAAACACCAGCCTTATCTC
1 GAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC-GAAACACCAGCCTTATCTC
*
1935724 CCTGAGTAGCAGTGGAGTAGGTT
65 CCTGAGCAGCAGTGGAGTAGGTT
* * * * * **
1935747 GAAGATTGCAGATCTTGTCTTCCTGTATTGGCAACAAAGTAGATCGAAGACACCAGTCTTGCCTC
1 GAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAA-ACACCAGCCTTATCTC
** * **
1935812 CCTGAGTTTGCAGTGGAGCAGACT
65 CCTGAG-CAGCAGTGGAGTAGGTT
** * * * **
1935836 GAAAGCA--ACAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATACCAGCCTTGCC
1 G-AAG-ATTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAA-ACACCAGCCTTATC
* * * * **
1935899 TCTCTGAGTTTA-CAGTAGAGCAGACT
63 TCCCTGAG--CAGCAGTGGAGTAGGTT
* * * *
1935925 GAA-AGTAGCAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAAGCACCAGCCTTATCT
1 GAAGA-TTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAA-CACCAGCCTTATCT
* *
1935989 CCCTAAGCAGCAGTGGAGTAAGTT
64 CCCTGAGCAGCAGTGGAGTAGGTT
* * *
1936013 GAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAGCACTAGCCTTCTCTC
1 GAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAA-CACCAGCCTTATCTC
* *
1936078 CCTGAGCAGCAATGGAATAGGTT
65 CCTGAGCAGCAGTGGAGTAGGTT
* * ** * ** *
1936101 AAAGATTATAGATCTTGTCTTCCAATACTGGCAGTGAAACAGATCGAAAACACCAACCTTATCTC
1 GAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCG-AAACACCAGCCTTATCTC
*
1936166 CCTGAGCAGTAGTGGAGTAGGTT
65 CCTGAGCAGCAGTGGAGTAGGTT
*
1936189 GAAGATTGTAGATCCTGTCT
1 GAAGATTGTAGATCTTGTCT
1936209 CCCTAAGCAG
Statistics
Matches: 387, Mismatches: 63, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
86 1 0.00
87 3 0.01
88 232 0.60
89 145 0.37
90 5 0.01
91 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (87 bp):
GAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATCGAAACACCAGCCTTATCTCC
CTGAGCAGCAGTGGAGTAGGTT
Found at i:1935863 original size:89 final size:89
Alignment explanation
Indices: 1935755--1935984 Score: 354
Period size: 89 Copynumber: 2.6 Consensus size: 89
1935745 TTGAAGATTG
* * * *
1935755 CAGATCTTGTCTTCCTGTATTGGCAACAAAGTAGATCGAAGACACCAGTCTTGCCTCCCTGAGTT
1 CAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
* *
1935820 TGCAGTGGAGCAGACTGAAAGCAA
66 TACAGTAGAGCAGACTGAAAGCAA
* *
1935844 CAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATACCAGCCTTGCCTCTCTGAGTT
1 CAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
* *
1935909 TACAGTAGAGCAGACTGAAAGTAG
66 TACAGTAGAGCAGACTGAAAGCAA
1935933 CAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAA-AGCACCAGCCTT
1 CAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGA-CACCAGCCTT
1935985 ATCTCCCTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
88 1 0.01
89 128 0.99
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (89 bp):
CAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
TACAGTAGAGCAGACTGAAAGCAA
Found at i:1936312 original size:132 final size:131
Alignment explanation
Indices: 1936133--1936736 Score: 447
Period size: 132 Copynumber: 4.6 Consensus size: 131
1936123 CAATACTGGC
* * * *
1936133 AGTGAAACAGATCGAAAACACCAACCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGT
1 AGTGGAACAGATTGAAGACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGT
* * *
1936198 AGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCCAAGGTA
66 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTGAATCTTATC-TCCCAAGGTA
1936263 GT
130 GT
* *
1936265 AG-GGAAACAGATTTAAGCCACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
1 AGTGG-AACAGATTGAAGACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
* * * * *** ** *
1936329 TAGATCTTGTCTTCCTGTA-CTGGTAGTGAAGCAGATCGAAAACACT-AGCCTTATCTCCC-TGA
65 TAGATCTTGTCTCCCT-AAGC-AGTAGTGGAGCAGATCGAAAATGGTGAATCTTATCTCCCAAG-
* *
1936391 GCAGC
127 GTAGT
** * **** * * * * * * * * *
1936396 AGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA-CTGGCAGTGAAGTAGATCGAAAAC
1 AGTGGAACAGATTGAAGACACCA-ACCTTATCTCCCTG-AGC-AGCAGTGGAGTAGGTTGAAGAT
*** * * ** * * * *
1936460 ACCAG-TCTTATCTCCTTTAAG-TTTCAGTGGAGCGGAT-TAAAATGATGGATCTTATCTCCCTG
63 TGTAGATCTTGTCTCC-CTAAGCAGT-AGTGGAGCAGATCGAAAATGGTGAATCTTATCTCCC--
*
1936522 AA-GTTGT
124 AAGGTAGT
* * *
1936529 AGTGGAGCAGATTGAAGAAACCAATCC-TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTG
1 AGTGGAACAGATTGAAGACACCAA-CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
* * *
1936593 TAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAAGGT
65 TAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTGAATCTTATC-TCCCAAGGT
1936658 AGT
129 AGT
* * * * * *
1936661 AG-GGAAGAATATTTAAGCCATCAACCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAAGATTG
1 AGTGGAA-CAGATTGAAGACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG
1936725 TAGATCTTGTCT
65 TAGATCTTGTCT
1936737 TCCTGTACTG
Statistics
Matches: 346, Mismatches: 102, Indels: 48
0.70 0.21 0.10
Matches are distributed among these distances:
130 1 0.00
131 66 0.19
132 217 0.63
133 62 0.18
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (131 bp):
AGTGGAACAGATTGAAGACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGT
AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGTGAATCTTATCTCCCAAGGTAG
T
Found at i:1936364 original size:88 final size:88
Alignment explanation
Indices: 1936283--1936604 Score: 357
Period size: 88 Copynumber: 3.7 Consensus size: 88
1936273 AGATTTAAGC
*
1936283 CACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
1 CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
1936348 CTGGTAGTGAAGCAGATCGAAAA
66 CTGGTAGTGAAGCAGATCGAAAA
* * *
1936371 CACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
1 CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
* *
1936436 CTGGCAGTGAAGTAGATCGAAAA
66 CTGGTAGTGAAGCAGATCGAAAA
** * *** * * * * *
1936459 CACCAGTCTTATCTCCTTTAAGTTTCAGTGGAG-CGGATT-AA-AATGATGGATCTTATCTCCCT
1 CACCAACCTTATCTCC-CTAAGCAGCAGTGGAGTAGG-TTGAAGATTG-TAGATCTTGTCTTCCT
* * * * *
1936521 GAAGTTGTAGTGGAGCAGATTGAAGAA
63 GTACTGGTAGTGAAGCAGATCGAA-AA
*
1936548 -ACCAATCC-TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCT
1 CACCAA-CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCT
1936605 CCCTAAGCAG
Statistics
Matches: 192, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
87 17 0.09
88 156 0.81
89 19 0.10
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (88 bp):
CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
CTGGTAGTGAAGCAGATCGAAAA
Found at i:1936471 original size:220 final size:220
Alignment explanation
Indices: 1936069--1936472 Score: 560
Period size: 220 Copynumber: 1.8 Consensus size: 220
1936059 AAAGCACTAG
*
1936069 CCTTCTCTCCCTGAGCAGCAATGGAATAGGTTAAAGATTATAGATCTTGTCTTCCAATACTGGCA
1 CCTTATCTCCCTGAGCAGCAATGGAATAGGTTAAAGATTATAGATCTTGTCTTCCAATACTGGCA
*
1936134 GTGAAACAGATCGAAAACACCAACCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTA
66 GTGAAACAGATCGAAAACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTA
* * *****
1936199 GATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCCAAGGTAG
131 GATCCTGTCTCCCTAAGCAGCAGTGAAGTAGATCGAAGAACACCAATCTTATCTTCCCAAGGTAG
1936264 TAGGGAAACAGATTTAAGCCACCAA
196 TAGGGAAACAGATTTAAGCCACCAA
* * * * ** *
1936289 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGTA
1 CCTTATCTCCCTGAGCAGCAATGGAATAGGTTAAAGATTATAGATCTTGTCTTCCAATACTGGCA
* * *
1936354 GTGAAGCAGATCGAAAACACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTA
66 GTGAAACAGATCGAAAACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTA
* * * * *
1936419 GATCTTGTCTTCCTGTA-CTGGCAGTGAAGTAGATCGAA-AACACCAGTCTTATCT
131 GATCCTGTCTCCCT-AAGC-AGCAGTGAAGTAGATCGAAGAACACCAATCTTATCT
1936473 CCTTTAAGTT
Statistics
Matches: 158, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
220 141 0.89
221 17 0.11
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (220 bp):
CCTTATCTCCCTGAGCAGCAATGGAATAGGTTAAAGATTATAGATCTTGTCTTCCAATACTGGCA
GTGAAACAGATCGAAAACACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTA
GATCCTGTCTCCCTAAGCAGCAGTGAAGTAGATCGAAGAACACCAATCTTATCTTCCCAAGGTAG
TAGGGAAACAGATTTAAGCCACCAA
Found at i:1936587 original size:43 final size:44
Alignment explanation
Indices: 1936529--1936633 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
1936519 CTGAAGTTGT
1936529 AGTGGAGCAGATTGAAGAAACCA-ATCCTATCTCCCTAAGCAGC
1 AGTGGAGCAGATTGAAGAAACCAGATCCTATCTCCCTAAGCAGC
* * **** * *
1936572 AGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGT
1 AGTGGAGCAGATTGAAGAAACCAGATCCTATCTCCCTAAGCAGC
*
1936616 AGTGGAGCAGATCGAAGA
1 AGTGGAGCAGATTGAAGA
1936634 TGGTGAATCT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
43 17 0.34
44 33 0.66
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (44 bp):
AGTGGAGCAGATTGAAGAAACCAGATCCTATCTCCCTAAGCAGC
Found at i:1936608 original size:308 final size:307
Alignment explanation
Indices: 1935975--1936818 Score: 848
Period size: 308 Copynumber: 2.7 Consensus size: 307
1935965 AGATCGAAAG
* *
1935975 CACCAGCCTTATCTCCCTAAGCAGCAGTGGAGTAAGTTGAAGATTGTAGATCTTGTCTTCCTGTA
1 CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
* * * * * * *
1936040 CTGGCAGTGAAGTAGATCGAAAGCACTAGCCTTCTCTCCCTGAGCAGCAATGGAATAGGTTAAAG
66 CTGGTAGTGAAGAAGATCGAAAACACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAG
* ** * *
1936105 ATTATAGATCTTGTCTTCCAATACTGGCAGTGAAACAGATCGAAAACACCAACCTTATCTCCCTG
131 ATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTG
* * *
1936170 AGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGA
196 A-CAGTAGTGGAGTAGGTTGAAGAATGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
**** * * * * *
1936235 AGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGC
260 AGATAACCAATCCTATCTTCCCAAGGCAGCAGGGAAACAGATTGAAGA
*
1936283 CACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
1 CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
*
1936348 CTGGTAGTGAAGCAGATCGAAAACACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAG
66 CTGGTAGTGAAGAAGATCGAAAACACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAG
* * * *
1936413 ATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAACACCAGTCTTATCTCCTTT
131 ATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTG
* * * **
1936478 A-AGTTTCAGTGGAG-CGGATT-AA-AATGATGGATCTTATCTCCCTGAAGTTGTAGTGGAGCAG
196 ACAG--T-AGTGGAGTAGG-TTGAAGAATG-TAGATCCTATCTCCCT-AAGCAGTAGTGGAGCAG
* ** *
1936539 ATTGAAGA-AACCAATCCTATC-TCCCTAA-GCAGCAGTGG-AGTAGGTTGAAGA
255 ATCGAAGATAACCAATCCTATCTTCCC-AAGGCAGCAG-GGAAACAGATTGAAGA
**** * * * * * * *
1936590 TTGTAGATCC-TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT-GAATCTTATCTT-CT
1 CACCA-A-CCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAG-ATCTTGTCTTCCT
** * * * * ** ** * *
1936652 CAAGGTAGTAGGGAAGAATATTTAAGCCA-TCAACCTTATCTCCATGAGCAGCAGTGGAGTAGGT
63 GTA-CTGGTAGTGAAGAAGATCGAAAACACT-AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGT
* *
1936716 TGAAGATTGTAGATCTTGTCTTCCTGTACTGGTAGTAAAGCAGATCGAAAACACCAGCCTTATCT
126 TGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAAACACCAGCCTTATCT
* * *
1936781 CCCTTAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATC
191 CCCTGA-CAGTAGTGGAGTAGGTTGAAGAATGTAGATC
1936819 TTGTCTTCCT
Statistics
Matches: 444, Mismatches: 74, Indels: 36
0.80 0.13 0.06
Matches are distributed among these distances:
306 2 0.00
307 35 0.08
308 370 0.83
309 35 0.08
310 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (307 bp):
CACCAACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTA
CTGGTAGTGAAGAAGATCGAAAACACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAG
ATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTG
ACAGTAGTGGAGTAGGTTGAAGAATGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
GATAACCAATCCTATCTTCCCAAGGCAGCAGGGAAACAGATTGAAGA
Found at i:1936666 original size:396 final size:396
Alignment explanation
Indices: 1935934--1936960 Score: 1553
Period size: 396 Copynumber: 2.6 Consensus size: 396
1935924 TGAAAGTAGC
* * * * * *
1935934 AGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAAGCACCAGCCTTATCTCCCTAAGCAG
1 AGATCTTGTCTTCCTGTACTGGTAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTAAGCAG
* *
1935999 CAGTGGAGTAAGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAGC
66 CAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAAC
* * * * * *** * ** * * * * *
1936064 ACTAGCCTTCTCTCC-CTGAGCAGCAATGGAATAGG-TTAAAGATTATAGATCTTGTCTTCC-AA
131 ACCAGTCTTATCTCCTTTAAGTTTCAGTGG-AGCGGATTAAA-ATGATGGATCTTATCTACCTGA
* * * * * * * *
1936126 TACTGGCAGTGAAACAGATCGAA-AACACCAA-CCTTATCTCCCTGAGCAGTAGTGGAGTAGGTT
194 -AGTCGTAGTGGAGCAGATTGAAGAA-ACCAATCC-TATCTCCCTAAGCAGCAGTGGAGTAGGTT
*
1936189 GAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTT
256 GAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTT
*
1936254 CCCAAGGTAGTAGGGAA-ACAGATTTAAGCCACCAACCTTATCTCCCTGAGCAGCAGTGGAGTAG
321 CCCAAGGTAGTAGGGAAGA-AGATTTAAGCCACCAACCTTATCTCCATGAGCAGCAGTGGAGTAG
1936318 GTTGAAGATTGT
385 GTTGAAGATTGT
* *
1936330 AGATCTTGTCTTCCTGTACTGGTAGTGAAGCAGATCGAAAACACTAGCCTTATCTCCCTGAGCAG
1 AGATCTTGTCTTCCTGTACTGGTAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTAAGCAG
1936395 CAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAAC
66 CAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAAC
*
1936460 ACCAGTCTTATCTCCTTTAAGTTTCAGTGGAGCGGATTAAAATGATGGATCTTATCTCCCTGAAG
131 ACCAGTCTTATCTCCTTTAAGTTTCAGTGGAGCGGATTAAAATGATGGATCTTATCTACCTGAAG
*
1936525 TTGTAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGA
196 TCGTAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGA
*
1936590 TTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAA
261 TTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
* *
1936655 GGTAGTAGGGAAGAATATTTAAGCCATCAACCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAA
326 GGTAGTAGGGAAGAAGATTTAAGCCACCAACCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAA
1936720 GATTGT
391 GATTGT
* *
1936726 AGATCTTGTCTTCCTGTACTGGTAGTAAAGCAGATCGAAAACACCAGCCTTATCTCCCTTAGCAG
1 AGATCTTGTCTTCCTGTACTGGTAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTAAGCAG
1936791 CAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAAC
66 CAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAAC
*
1936856 ACCAGTCCTATCTCCTTTAAGTTTCAGTGGAGCGGATTAAAATGATGGATCTTATCTACCTGAAG
131 ACCAGTCTTATCTCCTTTAAGTTTCAGTGGAGCGGATTAAAATGATGGATCTTATCTACCTGAAG
*
1936921 TCGTTGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCT
196 TCGTAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCT
1936961 GAAGTTGCAG
Statistics
Matches: 579, Mismatches: 46, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
396 560 0.97
397 19 0.03
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (396 bp):
AGATCTTGTCTTCCTGTACTGGTAGTGAAGCAGATCGAAAACACCAGCCTTATCTCCCTAAGCAG
CAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCGAAAAC
ACCAGTCTTATCTCCTTTAAGTTTCAGTGGAGCGGATTAAAATGATGGATCTTATCTACCTGAAG
TCGTAGTGGAGCAGATTGAAGAAACCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGA
TTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
GGTAGTAGGGAAGAAGATTTAAGCCACCAACCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAA
GATTGT
Found at i:1936860 original size:88 final size:89
Alignment explanation
Indices: 1936685--1936870 Score: 313
Period size: 88 Copynumber: 2.1 Consensus size: 89
1936675 AAGCCATCAA
*
1936685 CCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGTA
1 CCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCA
1936750 GTAAAGCAGATCGAAAACACCAG-
66 GTAAAGCAGATCGAAAACACCAGT
* *
1936773 CCTTATCTCCCTTAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCA
1 CCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCA
* *
1936838 GTGAAGTAGATCGAAAACACCAGT
66 GTAAAGCAGATCGAAAACACCAGT
1936862 CC-TATCTCC
1 CCTTATCTCC
1936871 TTTAAGTTTC
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 90 0.98
89 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (89 bp):
CCTTATCTCCATGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTGTCTTCCTGTACTGGCA
GTAAAGCAGATCGAAAACACCAGT
Found at i:1936995 original size:88 final size:88
Alignment explanation
Indices: 1936856--1937024 Score: 223
Period size: 88 Copynumber: 1.9 Consensus size: 88
1936846 GATCGAAAAC
* * * * * * *
1936856 ACCAGTCCTATCTCCTTTAAGTTTCAGTGGAGCGGATTAAAATGATGGATCTTATCTAC-CTGAA
1 ACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCGAATTAAAATGATAGATCTTATCT-CTCTGAA
* *
1936920 GTCGTTGTGGAGCAGATTGAAGAA
65 GTCGTAGTAGAGCAGATTGAAGAA
*
1936944 ACCAATCCTATCTCCCTGAAGTTGCAGTAGAGTGAATTAAAATGATAGATCTTATCTCTCTGAAG
1 ACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCGAATTAAAATGATAGATCTTATCTCTCTGAAG
*
1937009 TTGTAGTAGAGCAGAT
66 TCGTAGTAGAGCAGAT
1937025 CGCATCAGAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
87 1 0.01
88 68 0.99
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (88 bp):
ACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCGAATTAAAATGATAGATCTTATCTCTCTGAAG
TCGTAGTAGAGCAGATTGAAGAA
Found at i:1937196 original size:44 final size:44
Alignment explanation
Indices: 1937132--1937387 Score: 255
Period size: 44 Copynumber: 5.8 Consensus size: 44
1937122 ATGTTTCCTC
* *
1937132 GAAGATAACCAACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTT
1 GAAGAT-ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
**
1937177 GAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
1 GAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
* *
1937221 GAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCCGGTT
1 GAAGAT-ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
* * * *
1937266 GAAGATACCAGTCTTATCTCCCTGAAGTTGGAGTGGAGTAGATT
1 GAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
* * ** * * ** *
1937310 GATGCTATTAATCCTATCTCCTTGAAGTTATAGTGGAGCGGGTT
1 GAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
* ** *
1937354 -AAAATGATGAATCTTATAC-CTCTGAAGTTGCAGT
1 GAAGAT-ACCAATCTTAT-CTCCCTGAAGTTGCAGT
1937388 AGGTCGGATC
Statistics
Matches: 173, Mismatches: 35, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
43 2 0.01
44 124 0.72
45 47 0.27
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
GAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTT
Found at i:1937236 original size:89 final size:89
Alignment explanation
Indices: 1937132--1937303 Score: 308
Period size: 89 Copynumber: 1.9 Consensus size: 89
1937122 ATGTTTCCTC
*
1937132 GAAGATAACCAACCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGATACCAATCTTATCTC
1 GAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTC
1937197 CCTGAAGTTGCAGTGGAGCAGACT
66 CCTGAAGTTGCAGTGGAGCAGACT
* *
1937221 GAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCCGGTTGAAGATACCAGTCTTATCTC
1 GAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTC
*
1937286 CCTGAAGTTGGAGTGGAG
66 CCTGAAGTTGCAGTGGAG
1937304 TAGATTGATG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (89 bp):
GAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTC
CCTGAAGTTGCAGTGGAGCAGACT
Found at i:1937444 original size:94 final size:94
Alignment explanation
Indices: 1937321--1937536 Score: 319
Period size: 94 Copynumber: 2.3 Consensus size: 94
1937311 ATGCTATTAA
* * * *
1937321 TCCTATC-TCCTTGAAGTTATAGTGGAGCGGGTTAAAATGATGAATCTTATACCTCTGAAGTTGC
1 TCCTATCTTCC-TGAAGTTGTAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGC
1937385 AGTAGGTCGGATCAAATCTACCATAACAAG
65 AGTAGGTCGGATCAAATCTACCATAACAAG
* *
1937415 TCCTATCTTCCTGAAGTTGTAGTAGAGCGGATTAAAACGATGAATCCTATACCTTTGAAGTTGCA
1 TCCTATCTTCCTGAAGTTGTAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGCA
*
1937480 GTAGGTCGGATTAAATCTACCATAACAAG
66 GTAGGTCGGATCAAATCTACCATAACAAG
* *
1937509 TCTTATCTCCCT-AAGGTTGTAGTGGAGC
1 TCCTATCTTCCTGAA-GTTGTAGTGGAGC
1937537 AGACTGTAGA
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
93 2 0.02
94 105 0.95
95 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (94 bp):
TCCTATCTTCCTGAAGTTGTAGTGGAGCGGATTAAAACGATGAATCCTATACCTCTGAAGTTGCA
GTAGGTCGGATCAAATCTACCATAACAAG
Found at i:1937446 original size:50 final size:50
Alignment explanation
Indices: 1937375--1937516 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 50
1937365 TCTTATACCT
*
1937375 CTGAAGTTGCAGTAGGTCGGATCAAATCTACCATAACAAGTCCTATCTTC
1 CTGAAGTTGCAGTAGGTCGGATTAAATCTACCATAACAAGTCCTATCTTC
* * *
1937425 CTGAAGTTGTAGTAGAG-CGGATTAAA---ACGAT--GAA-TCCTATACCTT-
1 CTGAAGTTGCAGTAG-GTCGGATTAAATCTACCATAACAAGTCCTAT--CTTC
*
1937470 -TGAAGTTGCAGTAGGTCGGATTAAATCTACCATAACAAGTCTTATCT
1 CTGAAGTTGCAGTAGGTCGGATTAAATCTACCATAACAAGTCCTATCT
1937517 CCCTAAGGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
43 1 0.01
44 28 0.38
45 2 0.03
46 3 0.04
47 8 0.11
48 2 0.03
49 2 0.03
50 27 0.36
51 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
CTGAAGTTGCAGTAGGTCGGATTAAATCTACCATAACAAGTCCTATCTTC
Found at i:1941475 original size:42 final size:42
Alignment explanation
Indices: 1941427--1941704 Score: 290
Period size: 42 Copynumber: 6.9 Consensus size: 42
1941417 AATTGAGATT
* * *
1941427 TCAGACTTTACGCCTCGCAGGCTTATTGCCAGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
** * *
1941469 TCAGACTTTACGTCTAGCAGGCTTAATGCTGGTGAAATAATT
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
* * *
1941511 TTAGACTTTACGTCTAGTAGGCTTATTGCCAGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
* *
1941553 TCAGACTTTACG--T------C-TAATGCCAGTGAAATAATT
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
* *
1941586 TTAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATA
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
* * *
1941628 TCAGACTTTACATCTAGCAGGCTTAATGCCGGTGAAAC-ATT
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
* * *
1941669 TCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGAA
1 TCAGACTTTACGTCTAGCAGGCTTAA-TGCCAGTGAA
1941705 TTTGTTTAAA
Statistics
Matches: 196, Mismatches: 30, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
33 27 0.14
34 1 0.01
35 1 0.01
40 4 0.02
41 32 0.16
42 131 0.67
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
TCAGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAACAATA
Found at i:1941579 original size:33 final size:33
Alignment explanation
Indices: 1941537--1941601 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1941527 GTAGGCTTAT
1941537 TGCCAGTGAAACAATATCAGACTTTACGTCTAA
1 TGCCAGTGAAACAATATCAGACTTTACGTCTAA
* * *
1941570 TGCCAGTGAAATAATTTTAGACTTTACGTCTA
1 TGCCAGTGAAACAATATCAGACTTTACGTCTA
1941602 GCAGGCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TGCCAGTGAAACAATATCAGACTTTACGTCTAA
Found at i:1941616 original size:75 final size:75
Alignment explanation
Indices: 1941500--1941643 Score: 252
Period size: 75 Copynumber: 1.9 Consensus size: 75
1941490 CTTAATGCTG
* * * *
1941500 GTGAAATAATTTTAGACTTTACGTCTAGTAGGCTTATTGCCAGTGAAACAATATCAGACTTTACG
1 GTGAAATAATTTTAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACTTTACA
1941565 TCTAATGCCA
66 TCTAATGCCA
1941575 GTGAAATAATTTTAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACTTTACA
1 GTGAAATAATTTTAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACTTTACA
1941640 TCTA
66 TCTA
1941644 GCAGGCTTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (75 bp):
GTGAAATAATTTTAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACTTTACA
TCTAATGCCA
Found at i:1941663 original size:117 final size:116
Alignment explanation
Indices: 1941453--1941684 Score: 311
Period size: 117 Copynumber: 2.0 Consensus size: 116
1941443 GCAGGCTTAT
*** * * *
1941453 TGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCTGGTGAAATAATTTTAGACT
1 TGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACT
* * * *
1941518 TTACGTCTAGTAGGCTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAA
66 TTACATCTAGCAGGCTTAATGCCAGTGAAAC-ATATCAGACTATACGTCTAA
* * *
1941570 TGCCAGTGAAATAATTTTAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACT
1 TGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACT
* * *
1941635 TTACATCTAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTCTA
66 TTACATCTAGCAGGCTTAATGCCAGTGAAACATATCAGACTATACGTCTA
1941685 GCAGGCTAAG
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
116 16 0.16
117 83 0.84
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (116 bp):
TGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCAATGAAACAATATCAGACT
TTACATCTAGCAGGCTTAATGCCAGTGAAACATATCAGACTATACGTCTAA
Found at i:1945967 original size:40 final size:39
Alignment explanation
Indices: 1945907--1946044 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 39
1945897 AACACACCAG
*
1945907 TTTGGCACCCAGTGCCTCATCGGATAATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAA-TCAAAGTAATAA
* * *
1945947 TTTGACACCCAGTGTCTCATCGGCTAAACCAAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGAT-AATCAAAGTAATAA
* * * * *
1945985 -TTGGCACCCAGTGCCTCATTGAATTAATCTGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGGA-TAATC-AAAGTAATAA
* *
1946025 ATTGACACCCAGTGTCTCAT
1 TTTGACACCCAGTGCCTCAT
1946045 TGACTCAAAG
Statistics
Matches: 78, Mismatches: 14, Indels: 11
0.76 0.14 0.11
Matches are distributed among these distances:
37 21 0.27
38 7 0.09
39 1 0.01
40 30 0.38
41 19 0.24
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGGATAATCAAAGTAATAA
Found at i:1946003 original size:37 final size:40
Alignment explanation
Indices: 1945907--1946003 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
1945897 AACACACCAG
**
1945907 TTTGGCACCCAGTGCCTCATCGGATAATTCAAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCAAAGTAATAA
* * *
1945947 TTTGACACCCAGTGTCTCATCGGCTAAACCAAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCAAAGTAATAA
1945985 -TTGGCACCCAGTGCCTCAT
1 TTTGGCACCCAGTGCCTCAT
1946004 TGAATTAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 17 0.34
38 2 0.04
39 1 0.02
40 30 0.60
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCGGATAAACCAAAGTAATAA
Found at i:1949352 original size:28 final size:28
Alignment explanation
Indices: 1949320--1949375 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1949310 ACTGTAACTG
1949320 TCCCCCAAGAAGTACGAAAGCGGACGAC
1 TCCCCCAAGAAGTACGAAAGCGGACGAC
1949348 TCCCCCAAGAAGTACGAAAGCGGACGAC
1 TCCCCCAAGAAGTACGAAAGCGGACGAC
1949376 AGTTCTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.25, T:0.07
Consensus pattern (28 bp):
TCCCCCAAGAAGTACGAAAGCGGACGAC
Found at i:1966888 original size:21 final size:21
Alignment explanation
Indices: 1966862--1966914 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1966852 CGCTGTTTCT
*
1966862 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
1966883 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
1966904 AATCTCACCGC
1 AATCTCACCGC
1966915 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:1967168 original size:20 final size:20
Alignment explanation
Indices: 1967143--1967192 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1967133 TAATTGATGA
*
1967143 TTTAATG-TTTTTAATATATT
1 TTTAATGATTTAT-ATATATT
*
1967163 TTTAATGATTTATATTTATT
1 TTTAATGATTTATATATATT
1967183 TTTAA-GATTT
1 TTTAATGATTT
1967193 TTTTCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 18 0.67
21 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (20 bp):
TTTAATGATTTATATATATT
Found at i:1968841 original size:18 final size:18
Alignment explanation
Indices: 1968801--1968843 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1968791 TACTAACAGT
*
1968801 CGTCGGCCACCAAGACAC
1 CGTCGTCCACCAAGACAC
* *
1968819 TGTCGTCCACCAAGACGC
1 CGTCGTCCACCAAGACAC
1968837 CGTCGTC
1 CGTCGTC
1968844 ACAGCCACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.42, G:0.23, T:0.14
Consensus pattern (18 bp):
CGTCGTCCACCAAGACAC
Found at i:1973253 original size:21 final size:20
Alignment explanation
Indices: 1973237--1973327 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 20
1973227 GCCACATGTT
*
1973237 CGTGTGAGTGGTTCACATGGC
1 CGTGTGAGTGGGTCACAT-GC
* *
1973258 TGTCTGAGTGGGTCACATGGC
1 CGTGTGAGTGGGTCACAT-GC
*
1973279 CGTGTGAGTGGGTCAAATGAC
1 CGTGTGAGTGGGTCACATG-C
*
1973300 CGTGTGAGTGGGTCAAATGGC
1 CGTGTGAGTGGGTCACAT-GC
1973321 CGTGTGA
1 CGTGTGA
1973328 ACAAACTGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.26
Consensus pattern (20 bp):
CGTGTGAGTGGGTCACATGC
Found at i:1973288 original size:42 final size:42
Alignment explanation
Indices: 1973237--1973327 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
1973227 GCCACATGTT
* * * * *
1973237 CGTGTGAGTGGTTCACATGGCTGTCTGAGTGGGTCACATGGC
1 CGTGTGAGTGGGTCAAATGACCGTCTGAGTGGGTCAAATGGC
*
1973279 CGTGTGAGTGGGTCAAATGACCGTGTGAGTGGGTCAAATGGC
1 CGTGTGAGTGGGTCAAATGACCGTCTGAGTGGGTCAAATGGC
1973321 CGTGTGA
1 CGTGTGA
1973328 ACAAACTGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.26
Consensus pattern (42 bp):
CGTGTGAGTGGGTCAAATGACCGTCTGAGTGGGTCAAATGGC
Found at i:1975141 original size:40 final size:42
Alignment explanation
Indices: 1975097--1975185 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 42
1975087 CGGAATAGTG
1975097 TATTTTATTATAAAACTTAAA-GTTAA-AATATATAATATAA
1 TATTTTATTATAAAACTTAAATGTTAAGAATATATAATATAA
* * *
1975137 TATTTTA--ATAAAACTTAAATGTTAAGTATATATTATATTA
1 TATTTTATTATAAAACTTAAATGTTAAGAATATATAATATAA
*
1975177 TATTATATT
1 TATTTTATT
1975186 TAATAATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 12 0.29
39 5 0.12
40 24 0.59
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (42 bp):
TATTTTATTATAAAACTTAAATGTTAAGAATATATAATATAA
Found at i:1976266 original size:40 final size:40
Alignment explanation
Indices: 1976143--1976276 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 40
1976133 GACTTTGAGT
* * *
1976143 CGATAAGACACTGGGTGTCAATTTATTAC-TTCAGATTAATT
1 CGATGAGACACTGGGTGTCAATTTATTACTTTGA-ATT-ATC
* * * * * ** *
1976184 TGATGAGGCACTGGCTGCCAA--T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
*
1976221 AGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
**
1976261 CGATGAGGTACTGGGT
1 CGATGAGACACTGGGT
1976277 ACCAAACTGG
Statistics
Matches: 67, Mismatches: 22, Indels: 9
0.68 0.22 0.09
Matches are distributed among these distances:
37 18 0.27
38 6 0.09
39 3 0.04
40 24 0.36
41 16 0.24
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
Found at i:1977029 original size:20 final size:22
Alignment explanation
Indices: 1977004--1977043 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1976994 GGATTATAGT
1977004 TTTGA-TATGTTTT-AATTGTA
1 TTTGATTATGTTTTGAATTGTA
*
1977024 TTTGATTGTGTTTTGAATTG
1 TTTGATTATGTTTTGAATTG
1977044 GTTGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTGATTATGTTTTGAATTGTA
Found at i:1995751 original size:20 final size:20
Alignment explanation
Indices: 1995715--1995753 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1995705 ATTAAATTAA
*
1995715 GTTAAAATAATATAATAAAT
1 GTTAAAATAATAAAATAAAT
1995735 GTTAAAA-ACATAAAATAAA
1 GTTAAAATA-ATAAAATAAA
1995754 AGCAGCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
GTTAAAATAATAAAATAAAT
Found at i:1995914 original size:20 final size:20
Alignment explanation
Indices: 1995878--1995916 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1995868 TAATTAATAA
*
1995878 GTTAAAATAATATAATAAAT
1 GTTAAAATAATAAAATAAAT
1995898 GTTAAAA-ACATAAAATAAA
1 GTTAAAATA-ATAAAATAAA
1995917 AGCAGCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
GTTAAAATAATAAAATAAAT
Found at i:1995982 original size:163 final size:165
Alignment explanation
Indices: 1995701--1996028 Score: 642
Period size: 163 Copynumber: 2.0 Consensus size: 165
1995691 TAATTAAAAT
1995701 TTTAATTAAATTAAGTTAAAATAATATAATAAATGTTAAAAACATAAAATAAAAGCAGCTATTAT
1 TTTAATTAAATTAAGTTAAAATAATATAATAAATGTTAAAAACATAAAATAAAAGCAGCTATTAT
1995766 CATTTTTGCTCACCACCATTGAATATTAAAAACCAAAAATTACCATTGAAGGAGCTTCAAGGTCG
66 CATTTTTGCTCACCACCATTGAATATTAAAAACCAAAAATTACCATTGAAGGAGCTTCAAGGTCG
1995831 GCCAAAGTGTTTTGCTTGCATGGAGTTTTAATTGA
131 GCCAAAGTGTTTTGCTTGCATGGAGTTTTAATTGA
1995866 TTTAATT-AA-TAAGTTAAAATAATATAATAAATGTTAAAAACATAAAATAAAAGCAGCTATTAT
1 TTTAATTAAATTAAGTTAAAATAATATAATAAATGTTAAAAACATAAAATAAAAGCAGCTATTAT
1995929 CATTTTTGCTCACCACCATTGAATATTAAAAACCAAAAATTACCATTGAAGGAGCTTCAAGGTCG
66 CATTTTTGCTCACCACCATTGAATATTAAAAACCAAAAATTACCATTGAAGGAGCTTCAAGGTCG
1995994 GCCAAAGTGTTTTGCTTGCATGGAGTTTTAATTGA
131 GCCAAAGTGTTTTGCTTGCATGGAGTTTTAATTGA
1996029 GGTTCATTTT
Statistics
Matches: 163, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 154 0.94
164 2 0.01
165 7 0.04
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (165 bp):
TTTAATTAAATTAAGTTAAAATAATATAATAAATGTTAAAAACATAAAATAAAAGCAGCTATTAT
CATTTTTGCTCACCACCATTGAATATTAAAAACCAAAAATTACCATTGAAGGAGCTTCAAGGTCG
GCCAAAGTGTTTTGCTTGCATGGAGTTTTAATTGA
Found at i:1999537 original size:11 final size:11
Alignment explanation
Indices: 1999521--1999595 Score: 54
Period size: 10 Copynumber: 7.2 Consensus size: 11
1999511 AGGTTCTTTG
*
1999521 AATTATTATTT
1 AATTATTAATT
1999532 AATTA-TAATT
1 AATTATTAATT
1999542 AATTA-TAATT
1 AATTATTAATT
*
1999552 AAATT-TGAATT
1 -AATTATTAATT
*
1999563 -ATTATTTAAAT
1 AATTA-TTAATT
*
1999574 -ATAATTAATT
1 AATTATTAATT
1999584 AATTA-TAATT
1 AATTATTAATT
1999594 AA
1 AA
1999596 ATAACTGAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
9 3 0.06
10 26 0.50
11 23 0.44
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (11 bp):
AATTATTAATT
Found at i:1999542 original size:6 final size:6
Alignment explanation
Indices: 1999521--1999594 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
1999511 AGGTTCTTTG
*
1999521 AATTAT TATT-T AATTAT AA-T-T AATTAT AATTA- AATT-T GAATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT -AATTAT
* *
1999565 TATT-T AAATAT AATTAATT AATTAT AATTA
1 AATTAT AATTAT AATT-A-T AATTAT AATTA
1999595 AATAACTGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
4 3 0.06
5 13 0.25
6 29 0.55
7 3 0.06
8 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (6 bp):
AATTAT
Found at i:1999580 original size:14 final size:14
Alignment explanation
Indices: 1999525--1999594 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
1999515 TCTTTGAATT
*
1999525 ATTATTTAATTATA
1 ATTATTTAAATATA
*
1999539 ATTAATTATAAT-TA
1 ATTATTTA-AATATA
*
1999553 A--ATTTGAAT-T-
1 ATTATTTAAATATA
1999563 ATTATTTAAATATA
1 ATTATTTAAATATA
* *
1999577 ATTAATTAATTATA
1 ATTATTTAAATATA
1999591 ATTA
1 ATTA
1999595 AATAACTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
10 1 0.02
11 4 0.09
12 10 0.23
13 1 0.02
14 26 0.59
15 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTATTTAAATATA
Found at i:1999595 original size:10 final size:10
Alignment explanation
Indices: 1999530--1999584 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
1999520 GAATTATTAT
1999530 TTAATTATAA
1 TTAATTATAA
1999540 TTAATTATAA
1 TTAATTATAA
1999550 TTAAATT-TGAA
1 TT-AATTAT-AA
1999561 TT-ATTAT--
1 TTAATTATAA
*
1999568 TTAAATATAA
1 TTAATTATAA
1999578 TTAATTA
1 TTAATTA
1999585 ATTATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 4 0.11
9 3 0.08
10 20 0.54
11 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TTAATTATAA
Found at i:1999595 original size:14 final size:14
Alignment explanation
Indices: 1999537--1999595 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
1999527 TATTTAATTA
1999537 TAATTAATTATAAT
1 TAATTAATTATAAT
1999551 TAAATTTGAA-T-T-AT
1 T-AA-TT-AATTATAAT
* *
1999565 TATTTAAATATAAT
1 TAATTAATTATAAT
1999579 TAATTAATTATAAT
1 TAATTAATTATAAT
1999593 TAA
1 TAA
1999596 ATAACTGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
11 2 0.06
12 3 0.08
13 2 0.06
14 21 0.58
15 3 0.08
16 3 0.08
17 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TAATTAATTATAAT
Found at i:2002969 original size:2 final size:2
Alignment explanation
Indices: 2002962--2003003 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
2002952 CACAAAGGGA
* * *
2002962 TC TC TC TC TC TC TC TC TC TC TC TA AC TC AC TC TC TC TC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2003003 T
1 T
2003004 TTTCCTCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.07, C:0.48, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:2004053 original size:3 final size:3
Alignment explanation
Indices: 2004047--2004082 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2004037 AACCCCTCTA
2004047 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2004083 TGTTCTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:2013600 original size:12 final size:13
Alignment explanation
Indices: 2013580--2013609 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2013570 AATCAACTCG
*
2013580 AATTTTTTTTTCA
1 AATTTTTTGTTCA
2013593 AATTTTTTGTTCA
1 AATTTTTTGTTCA
2013606 AATT
1 AATT
2013610 GAGTTGAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (13 bp):
AATTTTTTGTTCA
Found at i:2014140 original size:26 final size:24
Alignment explanation
Indices: 2014109--2014159 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
2014099 CCCATTTTTT
* *
2014109 AATAAACATTAAAAAATTATTTTAAA
1 AATAAAAAATAAAAAA--ATTTTAAA
2014135 AATAAAAAATAAAAAAATTTTAAA
1 AATAAAAAATAAAAAAATTTTAAA
2014159 A
1 A
2014160 GCATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
26 14 0.61
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AATAAAAAATAAAAAAATTTTAAA
Found at i:2018823 original size:23 final size:23
Alignment explanation
Indices: 2018797--2018852 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2018787 TTCGTCTCCT
*
2018797 ATTTAGTTTTATTTTTATTTGTA
1 ATTTAGTTTTATTTTTAGTTGTA
* *
2018820 ATTTAGGTTTCTTTTTAGTTGTA
1 ATTTAGTTTTATTTTTAGTTGTA
2018843 ATTTTAGTTT
1 A-TTTAGTTT
2018853 AGTTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (23 bp):
ATTTAGTTTTATTTTTAGTTGTA
Found at i:2018858 original size:23 final size:22
Alignment explanation
Indices: 2018797--2018859 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
2018787 TTCGTCTCCT
*
2018797 ATTTAGTTTTATTTTTATTTGTA
1 ATTTAG-TTTATTTTTAGTTGTA
*
2018820 ATTTAGGTTTCTTTTTAGTTGTA
1 ATTTA-GTTTATTTTTAGTTGTA
2018843 ATTTTAGTTTAGTTTTT
1 A-TTTAGTTTA-TTTTT
2018860 TTTTTGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.19, C:0.02, G:0.13, T:0.67
Consensus pattern (22 bp):
ATTTAGTTTATTTTTAGTTGTA
Found at i:2035098 original size:30 final size:30
Alignment explanation
Indices: 2035062--2035126 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2035052 AATAGTTTAT
** *
2035062 ATTTTTATAATATTTAAATGATTAAATTA-A
1 ATTTTTATAAT-TTTAAAAAATTAAAATACA
*
2035092 ATTTTTATCATTTTAAAAAATTAAAATACA
1 ATTTTTATAATTTTAAAAAATTAAAATACA
2035122 ATTTT
1 ATTTT
2035127 ATCATTTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTTTTATAATTTTAAAAAATTAAAATACA
Found at i:2035747 original size:114 final size:113
Alignment explanation
Indices: 2035558--2035889 Score: 339
Period size: 114 Copynumber: 2.9 Consensus size: 113
2035548 CCTTTCTTAG
* * ** *
2035558 AAACACCGCAATATGCAAGAATTA-CTGGCGTTTGGTCATAAACGCCGCAACAACTGTTAAGAAA
1 AAACGCCGCAGTA-GCAAGAATTAGC-GGCGTTTTATCATAAGCGCCGCAA-AACTGTTAAGAAA
* * * * *
2035622 ACGCTACCGTTTTCAGTTTAGGTTTTGGGGACTTTAGTGGAG-TTTACTGGA
63 ACGATGCCGTTTTCAGTTTAGGTTTTAGAGACGTTAGTGGAGATTTAC-GGA
*
2035673 AAACGCTGCTA-TAGTCAAGAATTAGCGGCGTTTTATCATAAGCGCCGCAAAACTGTTAAGAAAA
1 AAACGCCGC-AGTAG-CAAGAATTAGCGGCGTTTTATCATAAGCGCCGCAAAACTGTTAAGAAAA
* ** * * *
2035737 CGTTGCCGTTTTTCA-TTTATCTTTTCGAGACGTTAGTGGCGATTTTCGGA
64 CGATGCCG-TTTTCAGTTTAGGTTTTAGAGACGTTAGTGGAGATTTACGGA
** * * * *
2035787 AAACGCCGCAGTAGCGAAGCTTTAGTGGCGCTTTATCAGAAGCGCTGCAAAACTGTTAAGAAAAC
1 AAACGCCGCAGTAGC-AAGAATTAGCGGCGTTTTATCATAAGCGCCGCAAAACTGTTAAGAAAAC
* *
2035852 GATGTCGTTTTTAGTTTAGGTTTTAGAGACGTTAGTGG
65 GATGCCGTTTTCAGTTTAGGTTTTAGAGACGTTAGTGG
2035890 CGCTTGTCTA
Statistics
Matches: 182, Mismatches: 27, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
113 7 0.04
114 124 0.68
115 49 0.27
116 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (113 bp):
AAACGCCGCAGTAGCAAGAATTAGCGGCGTTTTATCATAAGCGCCGCAAAACTGTTAAGAAAACG
ATGCCGTTTTCAGTTTAGGTTTTAGAGACGTTAGTGGAGATTTACGGA
Found at i:2036557 original size:7 final size:7
Alignment explanation
Indices: 2036492--2036596 Score: 61
Period size: 7 Copynumber: 15.0 Consensus size: 7
2036482 GTTCTACGAT
*
2036492 TTAAGGT
1 TTAAGGG
2036499 TTAAGGG
1 TTAAGGG
* *
2036506 ATATGGG
1 TTAAGGG
*
2036513 TTAGAGGC
1 TTA-AGGG
* *
2036521 TTATGGA
1 TTAAGGG
* *
2036528 TTATGGT
1 TTAAGGG
2036535 TTAAGGG
1 TTAAGGG
*
2036542 TT-GGGG
1 TTAAGGG
2036548 TTAAGGG
1 TTAAGGG
2036555 TTAAGGG
1 TTAAGGG
*
2036562 TTTAGGGG
1 -TTAAGGG
2036570 TTAAGGG
1 TTAAGGG
*
2036577 CT-AGGG
1 TTAAGGG
*
2036583 TTAGGGG
1 TTAAGGG
*
2036590 TTTAGGG
1 TTAAGGG
2036597 GTTTATAGTT
Statistics
Matches: 74, Mismatches: 20, Indels: 8
0.73 0.20 0.08
Matches are distributed among these distances:
6 10 0.14
7 53 0.72
8 11 0.15
ACGTcount: A:0.22, C:0.02, G:0.43, T:0.33
Consensus pattern (7 bp):
TTAAGGG
Found at i:2036560 original size:20 final size:21
Alignment explanation
Indices: 2036535--2036596 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 21
2036525 GGATTATGGT
2036535 TTAAGGGTT-GGGGTTAAGGG
1 TTAAGGGTTAGGGGTTAAGGG
2036555 TTAAGGGTTTAGGGGTTAAGGG
1 TTAAGGG-TTAGGGGTTAAGGG
* *
2036577 CT-AGGGTTAGGGGTTTAGGG
1 TTAAGGGTTAGGGGTTAAGGG
2036597 GTTTATAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 20 0.53
21 6 0.16
22 12 0.32
ACGTcount: A:0.19, C:0.02, G:0.48, T:0.31
Consensus pattern (21 bp):
TTAAGGGTTAGGGGTTAAGGG
Found at i:2036807 original size:14 final size:14
Alignment explanation
Indices: 2036760--2036815 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
2036750 GGCTTATGGA
*
2036760 TTATGGTTTAAGGG
1 TTATGGGTTAAGGG
*
2036774 TT-GGGGTTAAGGG
1 TTATGGGTTAAGGG
2036787 TTTATGGGTTAAGGG
1 -TTATGGGTTAAGGG
*
2036802 TTATGGGTTTAGGG
1 TTATGGGTTAAGGG
2036816 GTTTATAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 9 0.25
14 17 0.47
15 10 0.28
ACGTcount: A:0.18, C:0.00, G:0.43, T:0.39
Consensus pattern (14 bp):
TTATGGGTTAAGGG
Found at i:2036820 original size:8 final size:7
Alignment explanation
Indices: 2036724--2036815 Score: 51
Period size: 7 Copynumber: 13.0 Consensus size: 7
2036714 GTTCTACGAT
*
2036724 TTAAGGT
1 TTAAGGG
2036731 TTAAGGG
1 TTAAGGG
* *
2036738 ATATGGG
1 TTAAGGG
*
2036745 TTAGAGGC
1 TTA-AGGG
* *
2036753 TTATGGA
1 TTAAGGG
* *
2036760 TTATGGT
1 TTAAGGG
2036767 TTAAGGG
1 TTAAGGG
*
2036774 TT-GGGG
1 TTAAGGG
2036780 TTAAGGG
1 TTAAGGG
*
2036787 TTTATGGG
1 -TTAAGGG
2036795 TTAAGGG
1 TTAAGGG
*
2036802 TTATGGG
1 TTAAGGG
*
2036809 TTTAGGG
1 TTAAGGG
2036816 GTTTATAGTT
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
6 5 0.08
7 48 0.75
8 11 0.17
ACGTcount: A:0.22, C:0.01, G:0.40, T:0.37
Consensus pattern (7 bp):
TTAAGGG
Found at i:2037196 original size:14 final size:14
Alignment explanation
Indices: 2037177--2037203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2037167 ATTTAAAATC
2037177 GAACAATATTTCAT
1 GAACAATATTTCAT
2037191 GAACAATATTTCA
1 GAACAATATTTCA
2037204 ATTTGCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (14 bp):
GAACAATATTTCAT
Found at i:2049174 original size:44 final size:42
Alignment explanation
Indices: 2049094--2049441 Score: 198
Period size: 42 Copynumber: 8.2 Consensus size: 42
2049084 TTATGTTCTA
* *
2049094 TAGCGGCGTTTGTCA-AGAAAGTGCCGCTAAAGAACATTACTTT
1 TAGCGGCGTTTG-GATA-AAAGCGCCGCTAAAGAACATTACTTT
* * *
2049137 TCGCGGCGTTTGAGATAAAAAGCGCCGGTAAAGAACATGA-TCTT
1 TAGCGGCGTTTG-GAT-AAAAGCGCCGCTAAAGAACATTACT-TT
* ** **
2049181 TAGTGGCGTCTT-TTTTTAAGCGCCGCTAAAGAACATTACTTT
1 TAGCGGCGT-TTGGATAAAAGCGCCGCTAAAGAACATTACTTT
* *
2049223 TTGCGGCGTTTGTGATAAAAGCGCCGCTAAA-ATACATGA-TCTT
1 TAGCGGCGTTTG-GATAAAAGCGCCGCTAAAGA-ACATTACT-TT
* ** *
2049266 TAGCGGCATTT-TTTACAAAGCGCCGCTAAAAAACATTA-TCTT
1 TAGCGGCGTTTGGATA-AAAGCGCCGCTAAAGAACATTACT-TT
* * * *
2049308 TAGTGGCGTTTTTCG-T-TAAGCGCCGCTAAAGAACATGA-TCTT
1 TAGCGGCG--TTTGGATAAAAGCGCCGCTAAAGAACATTACT-TT
* ** **
2049350 TAGTGGCGTCTT-TTTTTAAGCGCCGCTAAAGAACATTACTTT
1 TAGCGGCGT-TTGGATAAAAGCGCCGCTAAAGAACATTACTTT
* * * *
2049392 TAGCAGCGTTTGTGATAATAGCACCGCTAAAGAACATGA-TCTT
1 TAGCGGCGTTTG-GATAAAAGCGCCGCTAAAGAACATTACT-TT
2049435 TAGCGGC
1 TAGCGGC
2049442 ATTTTTTTCT
Statistics
Matches: 240, Mismatches: 44, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
40 1 0.00
41 9 0.04
42 121 0.50
43 74 0.31
44 32 0.13
45 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (42 bp):
TAGCGGCGTTTGGATAAAAGCGCCGCTAAAGAACATTACTTT
Found at i:2049213 original size:42 final size:41
Alignment explanation
Indices: 2049156--2049491 Score: 309
Period size: 42 Copynumber: 8.0 Consensus size: 41
2049146 TTGAGATAAA
* *
2049156 AAGCGCCGGTAAAGAACATGATCTTTAGTGGCGTCTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTT
* * * **
2049198 AAGCGCCGCTAAAGAACATTA-CTTTTTGCGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-T-TTTT
* **
2049241 AAGCGCCGCTAAA-ATACATGATCTTTAGCGGCATTTTTTACA
1 AAGCGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTTTTT-TT
* * * *
2049283 AAGCGCCGCTAAAAAACATTATCTTTAGTGGCGTTTTTCGTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTT
*
2049325 AAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTCTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTT
* * ** *
2049367 AAGCGCCGCTAAAGAACATTA-CTTTTAGCAGCGTTTGTGATA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-TTTTT
* *
2049409 ATAGCACCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCT
1 A-AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-T
* ** *
2049452 AAACGCCGCTAAAGAACATGCCCTTTAGCGGCCTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
2049492 CTGTAAACGC
Statistics
Matches: 241, Mismatches: 39, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
41 7 0.03
42 167 0.69
43 65 0.27
44 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
Found at i:2049348 original size:169 final size:169
Alignment explanation
Indices: 2049156--2049470 Score: 535
Period size: 169 Copynumber: 1.9 Consensus size: 169
2049146 TTGAGATAAA
*
2049156 AAGCGCCGGTAAAGAACATGATCTTTAGTGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACT
1 AAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACT
* * *
2049221 TTTTGCGGCGTTTGTGATAAAAGCGCCGCTAAA-ATACATGATCTTTAGCGGCATTTTTTAC-AA
66 TTTAGCAGCGTTTGTGATAAAAGCACCGCTAAAGA-ACATGATCTTTAGCGGCATTTTTTACTAA
2049284 AGCGCCGCTAAAAAACATTATCTTTAGTGGCGTTTTTCGTT
130 A-CGCCGCTAAAAAACATTATCTTTAGTGGCGTTTTTCGTT
2049325 AAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACT
1 AAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACT
* *
2049390 TTTAGCAGCGTTTGTGATAATAGCACCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAA
66 TTTAGCAGCGTTTGTGATAAAAGCACCGCTAAAGAACATGATCTTTAGCGGCATTTTTTACTAAA
*
2049455 CGCCGCTAAAGAACAT
131 CGCCGCTAAAAAACAT
2049471 GCCCTTTAGC
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
169 133 0.97
170 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (169 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTCTTTTTTTAAGCGCCGCTAAAGAACATTACT
TTTAGCAGCGTTTGTGATAAAAGCACCGCTAAAGAACATGATCTTTAGCGGCATTTTTTACTAAA
CGCCGCTAAAAAACATTATCTTTAGTGGCGTTTTTCGTT
Found at i:2049480 original size:85 final size:85
Alignment explanation
Indices: 2049116--2049470 Score: 443
Period size: 85 Copynumber: 4.2 Consensus size: 85
2049106 TCAAGAAAGT
* * *
2049116 GCCGCTAAAGAACATTACTTTTCGCGGCGTTTGAGATAAAAAGCGCCGGTAAAGAACATGATCTT
1 GCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGAT-AAAAGCGCCGCTAAAGAACATGATCTT
* * *
2049181 TAGTGGCGTCTTTTTTTAAGC
65 TAGCGGCATCTTTTTTTAAAC
*
2049202 GCCGCTAAAGAACATTACTTTTTGCGGCGTTTGTGATAAAAGCGCCGCTAAA-ATACATGATCTT
1 GCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGA-ACATGATCTT
**
2049266 TAGCGGCAT-TTTTTACAAAGC
65 TAGCGGCATCTTTTTTTAAA-C
* * * *
2049287 GCCGCTAAAAAACATTA-TCTTTAGTGGCGTTTTTCG-T-TAAGCGCCGCTAAAGAACATGATCT
1 GCCGCTAAAGAACATTACT-TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGAACATGATCT
* * *
2049349 TTAGTGGCGTCTTTTTTTAAGC
64 TTAGCGGCATCTTTTTTTAAAC
* * *
2049371 GCCGCTAAAGAACATTACTTTTAGCAGCGTTTGTGATAATAGCACCGCTAAAGAACATGATCTTT
1 GCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTT
2049436 AGCGGCAT-TTTTTTCTAAAC
66 AGCGGCATCTTTTTT-TAAAC
2049456 GCCGCTAAAGAACAT
1 GCCGCTAAAGAACAT
2049471 GCCCTTTAGC
Statistics
Matches: 231, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
83 1 0.00
84 75 0.32
85 119 0.52
86 36 0.16
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (85 bp):
GCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTT
AGCGGCATCTTTTTTTAAAC
Found at i:2053143 original size:21 final size:22
Alignment explanation
Indices: 2053118--2053160 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2053108 TTAATATATA
2053118 TATGT-ATATTTATTGTTTTCT
1 TATGTAATATTTATTGTTTTCT
*
2053139 TATGTACATATTTATTTTTTTC
1 TATGTA-ATATTTATTGTTTTC
2053161 AACTAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (22 bp):
TATGTAATATTTATTGTTTTCT
Found at i:2060294 original size:7 final size:7
Alignment explanation
Indices: 2060282--2060323 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
2060272 ACATTATTTA
2060282 CATTTCC
1 CATTTCC
2060289 CATTTCC
1 CATTTCC
* *
2060296 C-CTCCC
1 CATTTCC
2060302 CATTTCC
1 CATTTCC
*
2060309 CATTTCT
1 CATTTCC
2060316 CATTTCC
1 CATTTCC
2060323 C
1 C
2060324 TGACCCTCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.12, C:0.48, G:0.00, T:0.40
Consensus pattern (7 bp):
CATTTCC
Found at i:2060506 original size:16 final size:16
Alignment explanation
Indices: 2060485--2060515 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2060475 GGTGAGTTTA
*
2060485 CTGTTAACCCTATTTC
1 CTGTTAACCCAATTTC
2060501 CTGTTAACCCAATTT
1 CTGTTAACCCAATTT
2060516 GAAGTAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (16 bp):
CTGTTAACCCAATTTC
Found at i:2061659 original size:18 final size:18
Alignment explanation
Indices: 2061624--2061657 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2061614 CTAGTATAGT
2061624 ATTCTTTGCAACATTTTA
1 ATTCTTTGCAACATTTTA
2061642 ATTC-TTGCAACATTTT
1 ATTCTTTGCAACATTTT
2061658 TATTTACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTCTTTGCAACATTTTA
Found at i:2062655 original size:13 final size:13
Alignment explanation
Indices: 2062637--2062752 Score: 105
Period size: 13 Copynumber: 9.1 Consensus size: 13
2062627 ATTTTTAATG
*
2062637 TAATATACTATTT
1 TAATATACTGTTT
*
2062650 TAATATACTGTTA
1 TAATATACTGTTT
*
2062663 TAA-A-A-T-TTG
1 TAATATACTGTTT
*
2062672 TAATATATTGTTT
1 TAATATACTGTTT
2062685 TAATATACTGTTAT
1 TAATATACTGTT-T
* *
2062699 AAATATATTGTTT
1 TAATATACTGTTT
2062712 TAATATACTGTTT
1 TAATATACTGTTT
*
2062725 TAGTATACTGTTAT
1 TAATATACTGTT-T
* *
2062739 AAATATACTATTT
1 TAATATACTGTTT
2062752 T
1 T
2062753 TATAATGTTA
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 2 0.02
12 2 0.02
13 51 0.61
14 21 0.25
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:2062732 original size:40 final size:37
Alignment explanation
Indices: 2062635--2062745 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 37
2062625 TAATTTTTAA
*
2062635 TGTAATATACTATTTTAATATACTGTTATAAA-AT-T
1 TGTAATATACTGTTTTAATATACTGTTATAAATATAT
*
2062670 TGTAATATATTGTTTTAATATACTGTTATAAATATAT
1 TGTAATATACTGTTTTAATATACTGTTATAAATATAT
*
2062707 TGTTTTAATATACTGTTTTAGTATACTGTTATAAATATA
1 TG---TAATATACTGTTTTAATATACTGTTATAAATATA
2062746 CTATTTTTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
35 30 0.45
36 2 0.03
37 3 0.04
40 32 0.48
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (37 bp):
TGTAATATACTGTTTTAATATACTGTTATAAATATAT
Found at i:2062752 original size:27 final size:26
Alignment explanation
Indices: 2062637--2062752 Score: 105
Period size: 27 Copynumber: 4.5 Consensus size: 26
2062627 ATTTTTAATG
*
2062637 TAATATACTATTTTAATATACTGTTA
1 TAATATACTATTTTAATATACTGTTT
* *
2062663 TAA-A-A-T-TTGTAATATATTGTTT
1 TAATATACTATTTTAATATACTGTTT
* * *
2062685 TAATATACTGTTATAAATATATTGTTT
1 TAATATACTATT-TTAATATACTGTTT
* *
2062712 TAATATACTGTTTTAGTATACTGTTAT
1 TAATATACTATTTTAATATACTGTT-T
*
2062739 AAATATACTATTTT
1 TAATATACTATTTT
2062753 TATAATGTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
22 16 0.22
23 2 0.03
24 2 0.03
25 2 0.03
26 15 0.20
27 37 0.50
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (26 bp):
TAATATACTATTTTAATATACTGTTT
Found at i:2063750 original size:123 final size:124
Alignment explanation
Indices: 2063393--2063802 Score: 669
Period size: 123 Copynumber: 3.3 Consensus size: 124
2063383 ATTTATTAAG
* * *
2063393 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCTTGAAAAAGTAATTTTGAGTTGGC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* *
2063458 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGAAGGATGCTTTACCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGAAGGATGTTTTATCAGAAGAATTTCT
* * *
2063518 GAAATCGCTCCCACATGGACGCGCTTTTGCTACAGTAGGTACTGAAAAAATAATTTTGAATTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* *
2063583 GTTTCTGAGCAAATAGTATAAAAACGCTTGAAGCAGGATGTTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGAAGGATGTTTTATCAGAAGAATTTCT
*
2063642 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-AAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
*
2063706 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGTAGGATGTTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGAAGGATGTTTTATCAGAAGAATTTCT
* * *
2063765 AAAATCGCTCCCACGTGGACGCGTTTTTGCTATAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
2063803 CATGTTTGGG
Statistics
Matches: 266, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
123 111 0.42
124 77 0.29
125 78 0.29
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGAAGGATGTTTTATCAGAAGAATTTCT
Found at i:2067041 original size:88 final size:88
Alignment explanation
Indices: 2066921--2067129 Score: 391
Period size: 88 Copynumber: 2.4 Consensus size: 88
2066911 CCTTATTCAA
*
2066921 AACTATTTTTTATTTTATTAAATGAAATAATATGCCAAGTGTTCAACATATTGCCTTATTTAAAA
1 AACTATTTTGTATTTTATTAAATGAAATAATATGCCAAGTGTTCAACATATTGCCTTATTTAAAA
2066986 GAATTTCTATTATTAAGAATATT
66 GAATTTCTATTATTAAGAATATT
* *
2067009 AACTATTTTGTATTTTATTAAATGAAATAATATGTCAAGTGTTCAACATATTTCCTTATTTAAAA
1 AACTATTTTGTATTTTATTAAATGAAATAATATGCCAAGTGTTCAACATATTGCCTTATTTAAAA
2067074 GAATTTCTATTATTAAGAATATT
66 GAATTTCTATTATTAAGAATATT
2067097 AACTATTTTGTATTTTATTAAATGAAATAATAT
1 AACTATTTTGTATTTTATTAAATGAAATAATAT
2067130 CAAAATATTA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 118 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (88 bp):
AACTATTTTGTATTTTATTAAATGAAATAATATGCCAAGTGTTCAACATATTGCCTTATTTAAAA
GAATTTCTATTATTAAGAATATT
Found at i:2067069 original size:46 final size:46
Alignment explanation
Indices: 2066930--2067069 Score: 116
Period size: 45 Copynumber: 3.1 Consensus size: 46
2066920 AAACTATTTT
* *
2066930 TTATTTTATTAAATGAAATAATATGCCAAGTGTTCAACATATTGCC
1 TTATTTTATTAAATGAAATAATATGTCAAGTGTTCAACATATTTCC
* ** * * *
2066976 TTA-TTTA--AAA-GAATTTCTATTATTAAGAATATT-AAC-TATTT--
1 TTATTTTATTAAATGAAATAATA-TGTCAAG--TGTTCAACATATTTCC
2067017 TGTATTTTATTAAATGAAATAATATGTCAAGTGTTCAACATATTTCC
1 T-TATTTTATTAAATGAAATAATATGTCAAGTGTTCAACATATTTCC
2067064 TTATTT
1 TTATTT
2067070 AAAAGAATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 24
0.64 0.13 0.23
Matches are distributed among these distances:
41 1 0.01
42 8 0.12
43 18 0.26
44 6 0.09
45 20 0.29
46 14 0.21
47 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (46 bp):
TTATTTTATTAAATGAAATAATATGTCAAGTGTTCAACATATTTCC
Found at i:2067151 original size:49 final size:49
Alignment explanation
Indices: 2067097--2067315 Score: 386
Period size: 49 Copynumber: 4.5 Consensus size: 49
2067087 TAAGAATATT
* * *
2067097 AACTATTTTGTATTTTATTAAAT-GAAATAATATCAAAATATTAAAAATA
1 AACTATTTTGTATTTTATTACATCG-AATAATATCAAATTATTCAAAATA
*
2067146 AACTATTTTGTATTTTATTACATCAAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTACATCGAATAATATCAAATTATTCAAAATA
2067195 AACTATTTTGTATTTTATTACATCGAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTACATCGAATAATATCAAATTATTCAAAATA
2067244 AACTATTTTGTATTTTATTACATCGAATAATATCAAATTATTCAAAATA
1 AACTATTTTGTATTTTATTACATCGAATAATATCAAATTATTCAAAATA
2067293 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
2067316 TAATATAAAC
Statistics
Matches: 164, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
49 164 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCGAATAATATCAAATTATTCAAAATA
Found at i:2069537 original size:14 final size:14
Alignment explanation
Indices: 2069508--2069537 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2069498 TTTACGATTT
2069508 AAAAAAAATTTAAA
1 AAAAAAAATTTAAA
2069522 AAAATAAAATTTAAA
1 AAAA-AAAATTTAAA
2069537 A
1 A
2069538 CTATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAAAATTTAAA
Found at i:2069573 original size:29 final size:26
Alignment explanation
Indices: 2069516--2069576 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
2069506 TTAAAAAAAA
2069516 TTTAAAAAAATAAAATTTAAAACTAT
1 TTTAAAAAAATAAAATTTAAAACTAT
* * *
2069542 TTTAAAAATAATTAAAAATTTGAAGCTCT
1 TTTAAAAA-AA-T-AAAATTTAAAACTAT
2069571 TTTAAA
1 TTTAAA
2069577 TAGAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 2 0.07
28 1 0.03
29 18 0.62
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (26 bp):
TTTAAAAAAATAAAATTTAAAACTAT
Found at i:2070725 original size:10 final size:10
Alignment explanation
Indices: 2070710--2070746 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
2070700 TTAGTTTTAA
2070710 TTAATTAAGT
1 TTAATTAAGT
2070720 TTAATTAA-T
1 TTAATTAAGT
*
2070729 TTAATTAAGA
1 TTAATTAAGT
2070739 TTAATTAA
1 TTAATTAA
2070747 TTACTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (10 bp):
TTAATTAAGT
Found at i:2070734 original size:19 final size:19
Alignment explanation
Indices: 2070706--2070748 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2070696 ATGTTTAGTT
*
2070706 TTAA-TTAATTAAGTTTAA
1 TTAATTTAATTAAGATTAA
2070724 TTAATTTAATTAAGATTAA
1 TTAATTTAATTAAGATTAA
2070743 TTAATT
1 TTAATT
2070749 ACTAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTAATTTAATTAAGATTAA
Found at i:2082280 original size:13 final size:13
Alignment explanation
Indices: 2082264--2082310 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2082254 TTTTTCCATG
2082264 TTTTTTTTCTT-T
1 TTTTTTTTCTTCT
2082276 TTTTTCTTTC-TCT
1 TTTTT-TTTCTTCT
*
2082289 TGTTTTTTCTTCT
1 TTTTTTTTCTTCT
*
2082302 TCTTTTTTC
1 TTTTTTTTC
2082311 GAAAAAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:2082305 original size:16 final size:14
Alignment explanation
Indices: 2082264--2082309 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
2082254 TTTTTCCATG
2082264 TTTT-TTTTCTTTT
1 TTTTCTTTTCTTTT
2082277 TTTTCTTTCTCTTGTT
1 TTTTCTTT-TCTT-TT
2082293 TTTTCTTCTTCTTTT
1 TTTTCTT-TTCTTTT
2082308 TT
1 TT
2082310 CGAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.14
14 3 0.10
15 8 0.28
16 13 0.45
17 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTCTTTT
Found at i:2090665 original size:16 final size:16
Alignment explanation
Indices: 2090644--2090699 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
2090634 CGTTTGGTTC
2090644 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
2090660 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
2090676 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
2090692 ACTGTAAT
1 GCTGTAAT
2090700 AGTAATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:2090732 original size:45 final size:44
Alignment explanation
Indices: 2090681--2090773 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
2090671 ATAGAGGTGT
2090681 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
2090726 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
2090770 AATG
1 AATG
2090774 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:2094699 original size:20 final size:21
Alignment explanation
Indices: 2094674--2094712 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2094664 TCGAAACCTA
*
2094674 ATAAA-GAAAACAAAACTAAT
1 ATAAAGGAAAAAAAAACTAAT
2094694 ATAAAGGAAAAAAAAACTA
1 ATAAAGGAAAAAAAAACTA
2094713 GGTTAATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.13
Consensus pattern (21 bp):
ATAAAGGAAAAAAAAACTAAT
Found at i:2095997 original size:13 final size:14
Alignment explanation
Indices: 2095979--2096007 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2095969 TCTACTCGTA
2095979 TGGA-TTTTCTTTT
1 TGGATTTTTCTTTT
2095992 TGGATTTTTCTTTT
1 TGGATTTTTCTTTT
2096006 TG
1 TG
2096008 TTTTGCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (14 bp):
TGGATTTTTCTTTT
Found at i:2105375 original size:57 final size:57
Alignment explanation
Indices: 2105316--2105442 Score: 177
Period size: 57 Copynumber: 2.2 Consensus size: 57
2105306 AGTAATGGTG
*
2105316 AAATGAAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCT-TCAAAATGAAAATGA
1 AAATGAAGAAAT-GGAAACATTTGGAAATGAATATGGTTTTCTCT-AAAATGAAAATGA
* * * *
2105374 AAAAGGAGAAATGGAATCATTTGGAAATGAATATGGTTTTCTCTAAGATGAAAATGA
1 AAATGAAGAAATGGAAACATTTGGAAATGAATATGGTTTTCTCTAAAATGAAAATGA
2105431 AAATGAA-AAATG
1 AAATGAAGAAATG
2105443 ACCTAAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
56 5 0.08
57 45 0.74
58 11 0.18
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (57 bp):
AAATGAAGAAATGGAAACATTTGGAAATGAATATGGTTTTCTCTAAAATGAAAATGA
Found at i:2107147 original size:21 final size:21
Alignment explanation
Indices: 2107121--2107184 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2107111 CATATGGAAT
2107121 TTATAATTTAGATTATATGCA
1 TTATAATTTAGATTATATGCA
**
2107142 TTATAA--T--ATGGTAT---
1 TTATAATTTAGATTATATGCA
2107156 TTATAATTTAGATTATATGCA
1 TTATAATTTAGATTATATGCA
2107177 TTATAATT
1 TTATAATT
2107185 ATATATATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
14 6 0.19
16 1 0.03
17 5 0.16
18 5 0.16
19 1 0.03
21 14 0.44
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (21 bp):
TTATAATTTAGATTATATGCA
Found at i:2107151 original size:35 final size:35
Alignment explanation
Indices: 2107112--2107183 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
2107102 AGGTTAGTTC
2107112 ATATGGAATTTATAATTTAGATTATATGCATTATA
1 ATATGGAATTTATAATTTAGATTATATGCATTATA
*
2107147 ATATGGTATTTATAATTTAGATTATATGCATTATA
1 ATATGGAATTTATAATTTAGATTATATGCATTATA
2107182 AT
1 AT
2107184 TATATATATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (35 bp):
ATATGGAATTTATAATTTAGATTATATGCATTATA
Found at i:2111543 original size:2 final size:2
Alignment explanation
Indices: 2111536--2111564 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2111526 ATAAAGTAAA
2111536 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2111565 GTCAAAAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2111555 original size:15 final size:15
Alignment explanation
Indices: 2111535--2111564 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2111525 AATAAAGTAA
2111535 AATATATATATATAT
1 AATATATATATATAT
2111550 AATATATATATATAT
1 AATATATATATATAT
2111565 GTCAAAAGTC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:2111556 original size:13 final size:13
Alignment explanation
Indices: 2111538--2111563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2111528 AAAGTAAAAT
2111538 ATATATATATATA
1 ATATATATATATA
2111551 ATATATATATATA
1 ATATATATATATA
2111564 TGTCAAAAGT
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:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:2111578 original size:148 final size:148
Alignment explanation
Indices: 2111419--2111698 Score: 474
Period size: 148 Copynumber: 1.9 Consensus size: 148
2111409 GATGTGTGTA
*
2111419 CAAAAGACATGAAAATAAAATATAAAATATAAATAAAAAATAAGCATAATATATTAATAAATTAT
1 CAAAAGACATGAAAATAAAATATAAAATATAAATAAAAAATAAGCATAATACATTAATAAATTAT
* * *
2111484 GGGTATATATATATATGTATATATAAAAGATATGAACATAGAATAAAGT-AAAATATAT-ATATA
66 AGGTATATATATATATGTATATA-AAAA-ATATGAAAATAGAATAAAGTAAAAAAATATAATATA
2111547 TATAATATATATATATATGT
129 TATAATATATATATATATGT
* *
2111567 CAAAAGTCATGAAAATAAAATATAAAATATAAATAAAAAATAAGTATAATACATTAATAAATTAT
1 CAAAAGACATGAAAATAAAATATAAAATATAAATAAAAAATAAGCATAATACATTAATAAATTAT
2111632 AGGTATATATATATATGTATATAAAAAATATGAAAATAGAATAAAGTAAAAAAATATAATATATA
66 AGGTATATATATATATGTATATAAAAAATATGAAAATAGAATAAAGTAAAAAAATATAATATATA
2111697 TA
131 TA
2111699 TGTATTTAAA
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
146 19 0.15
147 12 0.10
148 93 0.75
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (148 bp):
CAAAAGACATGAAAATAAAATATAAAATATAAATAAAAAATAAGCATAATACATTAATAAATTAT
AGGTATATATATATATGTATATAAAAAATATGAAAATAGAATAAAGTAAAAAAATATAATATATA
TAATATATATATATATGT
Found at i:2112435 original size:99 final size:99
Alignment explanation
Indices: 2112264--2112459 Score: 365
Period size: 99 Copynumber: 2.0 Consensus size: 99
2112254 CTCTGCCGCT
* * *
2112264 GCCAATCAAGGCCGACCCTACGGCCTCCGTCGATGCCCCTAATTTTCGATGGCGACGGAAAAGGG
1 GCCAATCAAGGCCGACCCTACGGCCTCCGTCGATGCCCCCAATTTCCGATGACGACGGAAAAGGG
2112329 AACACCGCAACAAGACCGGGTAAGTTTTCTTTCC
66 AACACCGCAACAAGACCGGGTAAGTTTTCTTTCC
2112363 GCCAATCAAGGCCGACCCTACGGCCTCCGTCGATGCCCCCAATTTCCGATGACGACGGAAAAGGG
1 GCCAATCAAGGCCGACCCTACGGCCTCCGTCGATGCCCCCAATTTCCGATGACGACGGAAAAGGG
2112428 AACACCGCAACAAGACCGGGTAAGTTTTCTTT
66 AACACCGCAACAAGACCGGGTAAGTTTTCTTT
2112460 TCTCCCTTTT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (99 bp):
GCCAATCAAGGCCGACCCTACGGCCTCCGTCGATGCCCCCAATTTCCGATGACGACGGAAAAGGG
AACACCGCAACAAGACCGGGTAAGTTTTCTTTCC
Found at i:2113501 original size:39 final size:39
Alignment explanation
Indices: 2113389--2113506 Score: 133
Period size: 39 Copynumber: 3.1 Consensus size: 39
2113379 TCAATACTTA
2113389 TACATTCTAAATAATTCAATAAATTTAACTCTCTACATT
1 TACATTCTAAATAATTCAATAAATTTAACTCTCTACATT
* *
2113428 TACGAATTCT--ATCAATT---T-GATTTAATTCTCTACATT
1 TAC--ATTCTAAAT-AATTCAATAAATTTAACTCTCTACATT
2113464 TACATTCTAAATAATTCAATAAATTTAAC-CTTCTACATT
1 TACATTCTAAATAATTCAATAAATTTAACTC-TCTACATT
2113503 TACA
1 TACA
2113507 CATTTAGTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
34 5 0.08
35 4 0.06
36 21 0.32
37 1 0.02
38 2 0.03
39 23 0.35
40 4 0.06
41 5 0.08
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (39 bp):
TACATTCTAAATAATTCAATAAATTTAACTCTCTACATT
Found at i:2121421 original size:13 final size:13
Alignment explanation
Indices: 2121403--2121478 Score: 125
Period size: 13 Copynumber: 5.8 Consensus size: 13
2121393 AGTTCTTTAT
2121403 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
2121416 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
2121429 TGATTTTCAGAAG
1 TGCTTTTGAGAAG
2121442 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
2121455 TGCTTTGGAGAAG
1 TGCTTTTGAGAAG
2121468 TGCTTTTGAGA
1 TGCTTTTGAGA
2121479 GTGTTTGGCA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.24, C:0.08, G:0.30, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:2121692 original size:20 final size:20
Alignment explanation
Indices: 2121669--2121720 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2121659 ATTAATTATT
*
2121669 TATAAAATTTAATTTAAATA
1 TATAAAATATAATTTAAATA
* *
2121689 TATAAACTATATTTTAAATA
1 TATAAAATATAATTTAAATA
2121709 T-TAAAATATAAT
1 TATAAAATATAAT
2121721 AAATAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAAATATAATTTAAATA
Found at i:2121914 original size:22 final size:21
Alignment explanation
Indices: 2121889--2121932 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2121879 AAGCATATGA
*
2121889 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
2121911 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
2121932 A
1 A
2121933 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:2121941 original size:22 final size:22
Alignment explanation
Indices: 2121916--2121986 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
2121906 TCAATAAATG
2121916 ATTTGGTTAATACAATACTTAT
1 ATTTGGTTAATACAATACTTAT
* * **
2121938 ATTT-GATAA-GCATATGA-AAAT
1 ATTTGGTTAATACA-AT-ACTTAT
2121959 GATTTGGTTAATACAATACTTAT
1 -ATTTGGTTAATACAATACTTAT
2121982 ATTTG
1 ATTTG
2121987 ATAAGCATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.23
22 15 0.43
23 8 0.23
24 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (22 bp):
ATTTGGTTAATACAATACTTAT
Found at i:2121959 original size:44 final size:44
Alignment explanation
Indices: 2121911--2122004 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
2121901 TATATTCAAT
2121911 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
2121955 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
2121999 AAATGA
1 AAATGA
2122005 AAGTCGAGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:2122023 original size:44 final size:43
Alignment explanation
Indices: 2121927--2122014 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
2121917 TTTGGTTAAT
** * *
2121927 ACAATACTTATATTTGATAAGCATATGAAAATGATTTGGTTAAT
1 ACAATACTTATATTTGATAAGCATATGAAAATGA-TAAGTCAAG
*
2121971 ACAATACTTATATTTGATAAGCATATGAAAATGA-AAGTCGAG
1 ACAATACTTATATTTGATAAGCATATGAAAATGATAAGTCAAG
2122013 AC
1 AC
2122015 TGTATACTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 5 0.13
44 34 0.87
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (43 bp):
ACAATACTTATATTTGATAAGCATATGAAAATGATAAGTCAAG
Found at i:2126147 original size:166 final size:166
Alignment explanation
Indices: 2125955--2126304 Score: 700
Period size: 166 Copynumber: 2.1 Consensus size: 166
2125945 ATAATAAACC
2125955 TGTAAATATTAAATAATATAATTTATGGGCTCTTTTGGGGGAAATGAGGTCCCGTACCTTCTTTT
1 TGTAAATATTAAATAATATAATTTATGGGCTCTTTTGGGGGAAATGAGGTCCCGTACCTTCTTTT
2126020 CCAAAACCACTGACTTTTAGTTCGAACCACTTGTACCTTGACTAACTGACCAATTAATAAAATCT
66 CCAAAACCACTGACTTTTAGTTCGAACCACTTGTACCTTGACTAACTGACCAATTAATAAAATCT
2126085 ATAAAATTGAAATTCATAATAATATCATATTTAACT
131 ATAAAATTGAAATTCATAATAATATCATATTTAACT
2126121 TGTAAATATTAAATAATATAATTTATGGGCTCTTTTGGGGGAAATGAGGTCCCGTACCTTCTTTT
1 TGTAAATATTAAATAATATAATTTATGGGCTCTTTTGGGGGAAATGAGGTCCCGTACCTTCTTTT
2126186 CCAAAACCACTGACTTTTAGTTCGAACCACTTGTACCTTGACTAACTGACCAATTAATAAAATCT
66 CCAAAACCACTGACTTTTAGTTCGAACCACTTGTACCTTGACTAACTGACCAATTAATAAAATCT
2126251 ATAAAATTGAAATTCATAATAATATCATATTTAACT
131 ATAAAATTGAAATTCATAATAATATCATATTTAACT
2126287 TGTAAATATTAAATAATA
1 TGTAAATATTAAATAATA
2126305 ATATTTAAGG
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 184 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (166 bp):
TGTAAATATTAAATAATATAATTTATGGGCTCTTTTGGGGGAAATGAGGTCCCGTACCTTCTTTT
CCAAAACCACTGACTTTTAGTTCGAACCACTTGTACCTTGACTAACTGACCAATTAATAAAATCT
ATAAAATTGAAATTCATAATAATATCATATTTAACT
Found at i:2135584 original size:18 final size:18
Alignment explanation
Indices: 2135561--2135595 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2135551 ATCATCACAT
2135561 CATGAACATGATCATGAC
1 CATGAACATGATCATGAC
*
2135579 CATGAACTTGATCATGA
1 CATGAACATGATCATGA
2135596 TGGTGTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (18 bp):
CATGAACATGATCATGAC
Found at i:2141390 original size:20 final size:20
Alignment explanation
Indices: 2141340--2141393 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2141330 GTACTGATCT
**
2141340 AGTATCGATACTTTTTGTCA
1 AGTATCGATAGATTTTGTCA
**
2141360 AGTATCGATAGATTTTGTTG
1 AGTATCGATAGATTTTGTCA
2141380 AGTATCGATAGATT
1 AGTATCGATAGATT
2141394 CAAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (20 bp):
AGTATCGATAGATTTTGTCA
Found at i:2141632 original size:134 final size:134
Alignment explanation
Indices: 2141399--2141645 Score: 309
Period size: 134 Copynumber: 1.8 Consensus size: 134
2141389 AGATTCAAAA
* *** * * *
2141399 TTTTATCGATATATTTTTCAATATCGATACGAAAATGACATTCTGTTTTTCAAAGTATTTATCCA
1 TTTTATCGATATATTTTTCAACATCGATACGAAAATGACATTCTAACTTCCAAAGGATTTATCAA
* ** * *
2141464 GTATCGATATGGTACTGATACCTTTTGTTGGGTATCGATAAATTTCTCCAAGTATCGATAGTGGT
66 GTATCGATACGGTACTGATACCTACTATTGGGTATCGATAAAATTCTCCAAGTATCGATAGTGGT
2141529 ATAC
131 ATAC
* * *
2141533 TTTTATCGATATGTTTTTCAGCATCGATACGAAATTGACATTCTAACTTCCAAAGGATTTATCAA
1 TTTTATCGATATATTTTTCAACATCGATACGAAAATGACATTCTAACTTCCAAAGGATTTATCAA
* *
2141598 GTA-CTGATACGGTA-TCGATACCTACTATTTGGTATTGATAAAATTCTC
66 GTATC-GATACGGTACT-GATACCTACTATTGGGTATCGATAAAATTCTC
2141646 TTGGTACCGA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
133 2 0.02
134 92 0.98
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (134 bp):
TTTTATCGATATATTTTTCAACATCGATACGAAAATGACATTCTAACTTCCAAAGGATTTATCAA
GTATCGATACGGTACTGATACCTACTATTGGGTATCGATAAAATTCTCCAAGTATCGATAGTGGT
ATAC
Found at i:2145844 original size:13 final size:14
Alignment explanation
Indices: 2145806--2145843 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
2145796 TATTTATTAA
2145806 TTTACATTTTTATCC
1 TTTA-ATTTTTATCC
2145821 TTTAATTTTTATCC
1 TTTAATTTTTATCC
2145835 TTTAATTTT
1 TTTAATTTT
2145844 AAATCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTAATTTTTATCC
Found at i:2147828 original size:578 final size:580
Alignment explanation
Indices: 2146695--2147869 Score: 1596
Period size: 578 Copynumber: 2.0 Consensus size: 580
2146685 CTTGTTCCTA
* *
2146695 TAAGGAGATTGGCAAGAGGAACCCAACGAATTCTTTCATTTCTAACATTAGCTCAATCATTCCTA
1 TAAGGAGATTGACAAGAGGAACCCAACGAATTCTTTCATTTCTAACATTAACTCAATCATTCCTA
* * * * *
2146760 CTCCTTTTGAAGGAGTCAGTCGAAAGAAGTGAAGACACTATTGAGGCGACGTTCCACTAAGTGAA
66 CTCCTTTTAAAGGAGTCAGTCGAAAAAAGTGAAGACACCATTGAGGCGACATTCCACTAAATGAA
*
2146825 AAAATATTTATTTCCCATTATATCTTTTCTTTATTGTAATTTTCCTCTCCTCAGTGAATCAGGTT
131 AAAATATTTATTTCCCATTATATCTTTTCTCTATTGTAATTTTCCTCTCCTCAGTGAATC-----
* *
2146890 AATGTACACACTTATTACACATTATTTTAAAATCAAACTATTTTCCCTATTTATAAAATAAACTT
191 -----ACACAC-TATT--A-ATTATTTTAAAATCAAAATATTTTCCCTATTTATAAAAGAAACTT
* * *
2146955 ACAATAGAGACTAAATTTCTAAATAAAGTTTGCTATCACTACTCTACCCTAAAGAAACTACATAA
247 ACAATAGAGACAAAATTTCTAAATAAAGTTTGCTACCACTACTCCACCCTAAAGAAACTACATAA
** *
2147020 TTACAATATATTCGCCCCCAAGGTGAAGTTCCTATGGTGCCCCCTTCCTATGTGCATGAATCTAT
312 TTACAATATATTCGCCCCCAAGGCAAAGTTCCTATGGTACCCCCTTCCTATGTGCATGAATCTAT
*
2147085 TAAAATAAATACTCGATTCCACCCAATTTGGCTTAGTCCCTCCATGAGTTCCTTATCCGCAATTC
377 TAAAATAAATACTCGATTCCACCCAATTTGGCTTAGTCCCTCCACGAGTTCCTTATCCGCAATTC
** *
2147150 CTGCAATCACAAATCAAACCCTTGTAAGTTCAAACGAACTTAGTGAGTTGCTTCGGTACACAAAA
442 CTGCAATCACAAATCAAACCCTTGTAAGTTCAAAAAAACTTAGTGAGTTGCTTCAGTACACAAAA
* * * *
2147215 CATACCCCATCTTTTTGGGGATTTAGATCAATAATAAATACAATAAACTCCCTGTTCGCTAGAAA
507 CATACCCCATCTTGTCGGGGATTTAGATAAATAATAAATACAATAAACTCCCTGTTCCCTAGAAA
2147280 CATTTCTCT
572 CATTTCTCT
* * * *
2147289 TAAGGATATTGACAGGAGGAACCCAA-TAACTTC-TTCTATTTCTAGCATTAACTCAATCATTCC
1 TAAGGAGATTGACAAGAGGAACCCAACGAA-TTCTTTC-ATTTCTAACATTAACTCAATCATTCC
*
2147352 TACT-CTTTTCAAAGGAGTTAGTCGAAAAAAGTGAAGACACCATTGAGGCGACATTCCACTAAAT
64 TACTCCTTTT-AAAGGAGTCAGTCGAAAAAAGTGAAGACACCATTGAGGCGACATTCCACTAAAT
*
2147416 GAATAAAAATATTTATTTCCCATTGTATCTTTTCTCTATTGTAATTTTCCTCTCCTCAGTGAA-C
128 G-A-AAAAATATTTATTTCCCATTATATCTTTTCTCTATTGTAATTTTCCTCTCCTCAGTGAATC
* *
2147480 -CAGAC-A-T-ATTATTTTAAAATCAAAATATTTTTCCTATTTATAAAAGAAACTTACAATAGAG
191 ACACACTATTAATTATTTTAAAATCAAAATATTTTCCCTATTTATAAAAGAAACTTACAATAGAG
* *
2147541 ACAAAATTTGTAAATAAAGTTTGCTACCACTACTCCACCCTAAAGGAACTACATAATTACAATAT
256 ACAAAATTTCTAAATAAAGTTTGCTACCACTACTCCACCCTAAAGAAACTACATAATTACAATAT
* * * ** * *
2147606 ATTCGCCTCCAAGGCAAAGTTCTTATGGGTACCCCCTTCTTATGTGCATGTCTTTATTCAAATAA
321 ATTCGCCCCCAAGGCAAAGTTCCTAT-GGTACCCCCTTCCTATGTGCATGAATCTATTAAAATAA
* * * * * *
2147671 ATACTCGATTCCACCCGATTTGGCTTGGTCCCTCCACGATTTCCTTTTCCGCAATTCTTGCAGTC
385 ATACTCGATTCCACCCAATTTGGCTTAGTCCCTCCACGAGTTCCTTATCCGCAATTCCTGCAATC
* * *
2147736 ACAAATCAAA-CCTCTGTAAGTTCAAAAAAACTTAGTGAGTTTCTTCAGTACAGAAAACATATCC
450 ACAAATCAAACCCT-TGTAAGTTCAAAAAAACTTAGTGAGTTGCTTCAGTACACAAAACATACCC
* * *
2147800 CA-CATTGTCGGGGATTTAGATAAATAATAAATACAATAAACTCTCTGTTCCCTGGGAACATTTC
514 CATC-TTGTCGGGGATTTAGATAAATAATAAATACAATAAACTCCCTGTTCCCTAGAAACATTTC
*
2147864 TTT
578 TCT
2147867 TAA
1 TAA
2147870 ACCGTTGTAG
Statistics
Matches: 519, Mismatches: 54, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
577 137 0.26
578 204 0.39
581 1 0.00
582 1 0.00
584 4 0.01
593 10 0.02
594 103 0.20
595 2 0.00
596 57 0.11
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (580 bp):
TAAGGAGATTGACAAGAGGAACCCAACGAATTCTTTCATTTCTAACATTAACTCAATCATTCCTA
CTCCTTTTAAAGGAGTCAGTCGAAAAAAGTGAAGACACCATTGAGGCGACATTCCACTAAATGAA
AAAATATTTATTTCCCATTATATCTTTTCTCTATTGTAATTTTCCTCTCCTCAGTGAATCACACA
CTATTAATTATTTTAAAATCAAAATATTTTCCCTATTTATAAAAGAAACTTACAATAGAGACAAA
ATTTCTAAATAAAGTTTGCTACCACTACTCCACCCTAAAGAAACTACATAATTACAATATATTCG
CCCCCAAGGCAAAGTTCCTATGGTACCCCCTTCCTATGTGCATGAATCTATTAAAATAAATACTC
GATTCCACCCAATTTGGCTTAGTCCCTCCACGAGTTCCTTATCCGCAATTCCTGCAATCACAAAT
CAAACCCTTGTAAGTTCAAAAAAACTTAGTGAGTTGCTTCAGTACACAAAACATACCCCATCTTG
TCGGGGATTTAGATAAATAATAAATACAATAAACTCCCTGTTCCCTAGAAACATTTCTCT
Found at i:2149165 original size:27 final size:27
Alignment explanation
Indices: 2149134--2149238 Score: 113
Period size: 27 Copynumber: 3.9 Consensus size: 27
2149124 ACATCTCGGT
* * * *
2149134 AGACTGTCCTGTGTTTAGTGTTTCATT
1 AGACTATCCTGTGTTTAATGTCTCATC
* * *
2149161 GGACTATCCCGTGTTTAATGTCTCGTC
1 AGACTATCCTGTGTTTAATGTCTCATC
*
2149188 AGACTATCCTGTGTTTAATGTCCCATC
1 AGACTATCCTGTGTTTAATGTCTCATC
*
2149215 AAACTAT-CTGATGTTTAATGTCTC
1 AGACTATCCTG-TGTTTAATGTCTC
2149239 GTCGAACTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.05
27 61 0.95
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (27 bp):
AGACTATCCTGTGTTTAATGTCTCATC
Found at i:2149246 original size:27 final size:25
Alignment explanation
Indices: 2149171--2149250 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 25
2149161 GGACTATCCC
2149171 GTGTTTAATGTCTCGTCAGACTATCCT
1 GTGTTTAATGTCTCGTCA-ACTAT-CT
* *
2149198 GTGTTTAATGTCCCATCAAACTATCT
1 GTGTTTAATGTCTCGTC-AACTATCT
2149224 GATGTTTAATGTCTCGTCGAACTATCT
1 G-TGTTTAATGTCTCGTC-AACTATCT
2149251 ATGATGCCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.07
27 42 0.91
28 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (25 bp):
GTGTTTAATGTCTCGTCAACTATCT
Found at i:2149350 original size:27 final size:27
Alignment explanation
Indices: 2149314--2149417 Score: 104
Period size: 27 Copynumber: 3.8 Consensus size: 27
2149304 ACCATCTCGA
*
2149314 TGGACCATCCTGTGTTTAATGTTCTGT
1 TGGACTATCCTGTGTTTAATGTTCTGT
* * *
2149341 TAGACTATCCTATGTTTAATGTTCCGT
1 TGGACTATCCTGTGTTTAATGTTCTGT
* * *
2149368 CGGACTAT-CTCGTGTTTAATATCCCAT-T
1 TGGACTATCCT-GTGTTTAATGT-TC-TGT
2149396 TGGACTATCCTGTGTTTAATGT
1 TGGACTATCCTGTGTTTAATGT
2149418 ATCAATTAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.03
27 38 0.62
28 19 0.31
29 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (27 bp):
TGGACTATCCTGTGTTTAATGTTCTGT
Found at i:2149718 original size:45 final size:45
Alignment explanation
Indices: 2149509--2149724 Score: 116
Period size: 45 Copynumber: 4.8 Consensus size: 45
2149499 CTACTAGGAT
* * * * * * *
2149509 GCCATAACGTCTTTCAGCTATGGTTTTAGTC-TTATTTACCATGAT
1 GCCATAGCATCTTTCAGCTATGGTCTTACTCATT-TTGATCATGAA
* * * * * * *
2149554 GCAATAGTATTTTTTAGCCATAGTCTTACTCATTTAT-ATCATGAT
1 GCCATAGCATCTTTCAGCTATGGTCTTACTCATTT-TGATCATGAA
* * * * * * * *
2149599 GCCATAACAT-TCTCCAACTATGATCTTATTTATCTTT-ACCATGAT
1 GCCATAGCATCT-TTCAGCTATGGTCTTACTCAT-TTTGATCATGAA
* * * *
2149644 GCCATATCATCTTTCAGTTATTGTTTTACTCATTTTGATCATGAA
1 GCCATAGCATCTTTCAGCTATGGTCTTACTCATTTTGATCATGAA
* *
2149689 GCCATAGCATCTTTCGGCTATGGTCTTACTTATTTT
1 GCCATAGCATCTTTCAGCTATGGTCTTACTCATTTT
2149725 AGGCATATAA
Statistics
Matches: 125, Mismatches: 40, Indels: 12
0.71 0.23 0.07
Matches are distributed among these distances:
44 4 0.03
45 115 0.92
46 6 0.05
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (45 bp):
GCCATAGCATCTTTCAGCTATGGTCTTACTCATTTTGATCATGAA
Found at i:2150289 original size:32 final size:32
Alignment explanation
Indices: 2150253--2150319 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
2150243 TTCATTCTCT
* *
2150253 TTATCCCTACGTTTATCGAAAGACTAAGAACC
1 TTATCCCTACATTTATAGAAAGACTAAGAACC
*
2150285 TTATCCCTACATTTATAGAAGGACTAAGAACC
1 TTATCCCTACATTTATAGAAAGACTAAGAACC
2150317 TTA
1 TTA
2150320 CCTGCTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (32 bp):
TTATCCCTACATTTATAGAAAGACTAAGAACC
Found at i:2158938 original size:52 final size:52
Alignment explanation
Indices: 2158875--2158978 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
2158865 AAGGAATTTA
*
2158875 ATAATTATTAGCTACTGA-TTTTCTAGTATATTATGGAATTAGGTGCTGACCC
1 ATAATTATTAGCTACTGATTTTTC-AGTATATTATGGAATTAGGTGCTAACCC
2158927 ATAATTATTAGCTACTGATTTTTCAGTATATTATGGAATTAGGTGCTAACCC
1 ATAATTATTAGCTACTGATTTTTCAGTATATTATGGAATTAGGTGCTAACCC
2158979 GAACACCTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 45 0.90
53 5 0.10
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (52 bp):
ATAATTATTAGCTACTGATTTTTCAGTATATTATGGAATTAGGTGCTAACCC
Found at i:2159779 original size:5 final size:5
Alignment explanation
Indices: 2159769--2159794 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2159759 GCATGTGCAT
2159769 TGGGA TGGGA TGGGA TGGGA TGGGA T
1 TGGGA TGGGA TGGGA TGGGA TGGGA T
2159795 TTTGTGGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.58, T:0.23
Consensus pattern (5 bp):
TGGGA
Found at i:2164425 original size:30 final size:30
Alignment explanation
Indices: 2164392--2164522 Score: 147
Period size: 30 Copynumber: 4.4 Consensus size: 30
2164382 GAAACTATAT
*
2164392 CTTTTCATAATTTGATGGTCGTCACCATCT
1 CTTTTCATAATTTGATGGTCGTCACCATCC
** * *
2164422 CTTTTCATTGTTCGATGATCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
* * * *
2164452 CTTTTCATAATTTGATAGCCG-AAGCTATCC
1 CTTTTCATAATTTGATGGTCGTCA-CCATCC
* *
2164482 CTTTTCATAGTTTGATGGTCGTCACCAGCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
2164512 CTTTTCATAAT
1 CTTTTCATAAT
2164523 CGATAGTCGA
Statistics
Matches: 79, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 77 0.97
31 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (30 bp):
CTTTTCATAATTTGATGGTCGTCACCATCC
Found at i:2164456 original size:60 final size:60
Alignment explanation
Indices: 2164392--2164548 Score: 174
Period size: 60 Copynumber: 2.6 Consensus size: 60
2164382 GAAACTATAT
* * * * * *
2164392 CTTTTCATAATTTGATGGTCGTCA-CCATCTCTTTTCATTGTTCGATGATCGTCACCATCC
1 CTTTTCATAATTTGATAGCCG-AAGCCATCCCTTTTCATAGTTCGATGATCGTCACCAGCC
* * *
2164452 CTTTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAGTTTGATGGTCGTCACCAGCC
1 CTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGATCGTCACCAGCC
* * * *
2164512 CTTTTCATAA-TCGATAGTCGAAGCTATCCATTTTCAT
1 CTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCAT
2164549 TCATCTATGA
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 25 0.30
60 59 0.70
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (60 bp):
CTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATGATCGTCACCAGCC
Found at i:2170618 original size:29 final size:29
Alignment explanation
Indices: 2170586--2170684 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
2170576 AGTTATCACC
*
2170586 ATCCCTTTTCGTAATTGATAGCCGAAACT
1 ATCCCTTTTCATAATTGATAGCCGAAACT
* * *
2170615 ATCCCTTTTCATATTTGATATCCGAAGCT
1 ATCCCTTTTCATAATTGATAGCCGAAACT
2170644 ATCCCTTTTCAT-ATTCGATAGCC-AAAGCT
1 ATCCCTTTTCATAATT-GATAGCCGAAA-CT
2170673 ATCCCTTTTCAT
1 ATCCCTTTTCAT
2170685 TCGCCGATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
28 4 0.07
29 57 0.93
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATAATTGATAGCCGAAACT
Found at i:2174427 original size:19 final size:20
Alignment explanation
Indices: 2174402--2174456 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2174392 GATACCAATA
2174402 GAAAAA-TATCGATACTT-T
1 GAAAAATTATCGATACTTAT
*
2174420 GTAAAAATTATCAATACTTAT
1 G-AAAAATTATCGATACTTAT
2174441 GAAAAATTATCGATAC
1 GAAAAATTATCGATAC
2174457 CTATCGGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 24 0.75
21 2 0.06
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (20 bp):
GAAAAATTATCGATACTTAT
Found at i:2176377 original size:19 final size:20
Alignment explanation
Indices: 2176353--2176404 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2176343 ATTTAACTAA
2176353 AAATGAATGAAAACTTT-AT
1 AAATGAATGAAAACTTTGAT
* *
2176372 AAATGAATGCCAAATTTTGAT
1 AAATGAATG-AAAACTTTGAT
2176393 -AATGAATGAAAA
1 AAATGAATGAAAA
2176405 AAAATCTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (20 bp):
AAATGAATGAAAACTTTGAT
Found at i:2182929 original size:10 final size:10
Alignment explanation
Indices: 2182914--2182939 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2182904 AAAAATTAAA
2182914 ATATATGTAT
1 ATATATGTAT
2182924 ATATATGTAT
1 ATATATGTAT
2182934 ATATAT
1 ATATAT
2182940 ATATGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:2182940 original size:14 final size:14
Alignment explanation
Indices: 2182921--2182947 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2182911 AAAATATATG
2182921 TATATATATGTATA
1 TATATATATGTATA
2182935 TATATATATGTAT
1 TATATATATGTAT
2182948 TTACAAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATATGTATA
Found at i:2183642 original size:20 final size:20
Alignment explanation
Indices: 2183617--2183666 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2183607 GCCCCTGTTG
2183617 CGCCGCCACTCGGCTCGCTA
1 CGCCGCCACTCGGCTCGCTA
2183637 CGCCGCCACTCGGCTCGCTA
1 CGCCGCCACTCGGCTCGCTA
*
2183657 CACCGCCACT
1 CGCCGCCACT
2183667 GCCTCTGACG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.52, G:0.22, T:0.14
Consensus pattern (20 bp):
CGCCGCCACTCGGCTCGCTA
Done.