Multiple sequence alignment - TraesCS3B01G053300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G053300 chr3B 100.000 2615 0 0 1 2615 27053139 27055753 0.000000e+00 4830.0
1 TraesCS3B01G053300 chr3B 89.982 1667 103 14 19 1649 27203216 27201578 0.000000e+00 2095.0
2 TraesCS3B01G053300 chr3B 91.840 1446 104 7 184 1624 14250627 14252063 0.000000e+00 2004.0
3 TraesCS3B01G053300 chr3B 85.122 699 93 4 927 1625 27103769 27104456 0.000000e+00 704.0
4 TraesCS3B01G053300 chr3B 77.638 1033 177 43 622 1617 50039355 50038340 1.740000e-161 579.0
5 TraesCS3B01G053300 chr3B 77.435 1037 161 37 621 1617 50034582 50033579 3.800000e-153 551.0
6 TraesCS3B01G053300 chr3B 93.548 310 15 4 2169 2474 27199641 27199333 8.530000e-125 457.0
7 TraesCS3B01G053300 chr3B 80.123 649 95 20 988 1617 49863317 49863950 1.100000e-123 453.0
8 TraesCS3B01G053300 chr3B 96.981 265 8 0 2207 2471 14252403 14252667 1.850000e-121 446.0
9 TraesCS3B01G053300 chr3B 94.650 243 11 2 1929 2170 244234083 244233842 2.460000e-100 375.0
10 TraesCS3B01G053300 chr3B 93.625 251 14 2 1929 2178 798008211 798008460 8.840000e-100 374.0
11 TraesCS3B01G053300 chr3B 95.082 183 8 1 1648 1830 14252168 14252349 1.180000e-73 287.0
12 TraesCS3B01G053300 chr3B 93.878 147 7 2 2326 2471 27086097 27086242 1.220000e-53 220.0
13 TraesCS3B01G053300 chr3B 100.000 84 0 0 1718 1801 27201538 27201455 3.480000e-34 156.0
14 TraesCS3B01G053300 chr3B 89.565 115 11 1 1820 1934 27199753 27199640 7.540000e-31 145.0
15 TraesCS3B01G053300 chr3B 97.778 45 1 0 109 153 14248126 14248170 7.760000e-11 78.7
16 TraesCS3B01G053300 chr3B 94.118 51 3 0 2421 2471 27106173 27106223 7.760000e-11 78.7
17 TraesCS3B01G053300 chr7D 92.431 1123 63 10 513 1625 64667297 64668407 0.000000e+00 1583.0
18 TraesCS3B01G053300 chr7D 89.394 660 29 8 1 634 64666654 64667298 0.000000e+00 793.0
19 TraesCS3B01G053300 chr7D 90.722 97 8 1 1812 1908 606791137 606791232 7.600000e-26 128.0
20 TraesCS3B01G053300 chr7D 80.117 171 21 11 1648 1811 64668495 64668659 5.910000e-22 115.0
21 TraesCS3B01G053300 chr4D 80.683 761 126 15 855 1609 81393570 81394315 2.920000e-159 571.0
22 TraesCS3B01G053300 chr4A 80.289 761 129 13 855 1609 490920052 490920797 2.940000e-154 555.0
23 TraesCS3B01G053300 chr4A 95.070 142 4 3 2472 2610 709787666 709787807 1.220000e-53 220.0
24 TraesCS3B01G053300 chr3A 81.790 648 91 19 937 1566 38658159 38657521 3.860000e-143 518.0
25 TraesCS3B01G053300 chr3A 88.073 109 7 4 1813 1918 28126657 28126762 9.830000e-25 124.0
26 TraesCS3B01G053300 chr1B 94.094 254 13 2 1929 2181 641330574 641330322 4.080000e-103 385.0
27 TraesCS3B01G053300 chr1B 93.574 249 14 2 1933 2180 56209352 56209105 1.140000e-98 370.0
28 TraesCS3B01G053300 chr1B 93.281 253 14 3 1933 2183 157363006 157362755 1.140000e-98 370.0
29 TraesCS3B01G053300 chr1B 87.097 124 13 3 1812 1934 304186400 304186521 1.260000e-28 137.0
30 TraesCS3B01G053300 chr5B 94.650 243 12 1 1929 2170 393770044 393769802 2.460000e-100 375.0
31 TraesCS3B01G053300 chr5B 93.919 148 5 4 2467 2610 648258646 648258499 1.220000e-53 220.0
32 TraesCS3B01G053300 chr5B 89.516 124 9 3 1814 1934 213632145 213632267 1.250000e-33 154.0
33 TraesCS3B01G053300 chr2B 95.000 240 11 1 1933 2171 35246305 35246066 2.460000e-100 375.0
34 TraesCS3B01G053300 chr2B 87.200 125 14 2 1812 1934 37108376 37108500 9.760000e-30 141.0
35 TraesCS3B01G053300 chr4B 93.281 253 15 2 1933 2184 638780030 638780281 3.180000e-99 372.0
36 TraesCS3B01G053300 chr4B 92.885 253 16 2 1933 2184 286644356 286644607 1.480000e-97 366.0
37 TraesCS3B01G053300 chr7B 96.429 140 1 4 2475 2610 13257883 13257744 7.280000e-56 228.0
38 TraesCS3B01G053300 chr7B 85.870 92 12 1 1838 1928 726813882 726813791 2.140000e-16 97.1
39 TraesCS3B01G053300 chr7B 94.595 37 2 0 87 123 713845381 713845345 1.010000e-04 58.4
40 TraesCS3B01G053300 chr7B 94.595 37 2 0 87 123 713895582 713895546 1.010000e-04 58.4
41 TraesCS3B01G053300 chr7B 94.595 37 2 0 87 123 713950356 713950320 1.010000e-04 58.4
42 TraesCS3B01G053300 chr7B 94.595 37 2 0 87 123 713999519 713999483 1.010000e-04 58.4
43 TraesCS3B01G053300 chr6A 95.172 145 3 4 2475 2615 574237296 574237152 2.620000e-55 226.0
44 TraesCS3B01G053300 chr1A 95.172 145 3 4 2475 2615 27328797 27328653 2.620000e-55 226.0
45 TraesCS3B01G053300 chr1A 94.483 145 4 4 2475 2615 579107258 579107402 1.220000e-53 220.0
46 TraesCS3B01G053300 chr1A 87.903 124 13 2 1812 1934 492020022 492020144 7.540000e-31 145.0
47 TraesCS3B01G053300 chr7A 95.714 140 3 3 2474 2610 640496592 640496731 3.390000e-54 222.0
48 TraesCS3B01G053300 chr6D 94.483 145 4 4 2475 2615 4658260 4658116 1.220000e-53 220.0
49 TraesCS3B01G053300 chr6B 94.406 143 5 3 2471 2610 25980261 25980119 1.580000e-52 217.0
50 TraesCS3B01G053300 chr2D 88.095 126 11 4 1812 1934 435338996 435339120 2.100000e-31 147.0
51 TraesCS3B01G053300 chr5A 87.805 123 13 2 1813 1934 564391754 564391633 2.710000e-30 143.0
52 TraesCS3B01G053300 chr1D 88.785 107 8 4 1825 1930 247242658 247242555 7.600000e-26 128.0
53 TraesCS3B01G053300 chr2A 85.859 99 12 2 1838 1934 739869422 739869520 1.280000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G053300 chr3B 27053139 27055753 2614 False 4830.000000 4830 100.00000 1 2615 1 chr3B.!!$F1 2614
1 TraesCS3B01G053300 chr3B 27199333 27203216 3883 True 713.250000 2095 93.27375 19 2474 4 chr3B.!!$R2 2455
2 TraesCS3B01G053300 chr3B 14248126 14252667 4541 False 703.925000 2004 95.42025 109 2471 4 chr3B.!!$F5 2362
3 TraesCS3B01G053300 chr3B 50033579 50039355 5776 True 565.000000 579 77.53650 621 1617 2 chr3B.!!$R3 996
4 TraesCS3B01G053300 chr3B 49863317 49863950 633 False 453.000000 453 80.12300 988 1617 1 chr3B.!!$F3 629
5 TraesCS3B01G053300 chr3B 27103769 27106223 2454 False 391.350000 704 89.62000 927 2471 2 chr3B.!!$F6 1544
6 TraesCS3B01G053300 chr7D 64666654 64668659 2005 False 830.333333 1583 87.31400 1 1811 3 chr7D.!!$F2 1810
7 TraesCS3B01G053300 chr4D 81393570 81394315 745 False 571.000000 571 80.68300 855 1609 1 chr4D.!!$F1 754
8 TraesCS3B01G053300 chr4A 490920052 490920797 745 False 555.000000 555 80.28900 855 1609 1 chr4A.!!$F1 754
9 TraesCS3B01G053300 chr3A 38657521 38658159 638 True 518.000000 518 81.79000 937 1566 1 chr3A.!!$R1 629

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
895 3512 0.454452 GTGCGAAACGGAGCATTTCC 60.454 55.0 0.0 0.0 45.69 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 12444 0.039618 AACCCGGACGGAGGTAGTAA 59.96 55.0 13.13 0.0 34.45 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.534203 TTGGAGCTTGGGACGTCAAC 60.534 55.000 18.91 10.22 0.00 3.18
67 79 4.101119 ACTTGTACTGAACCAAGCAGTAGT 59.899 41.667 0.00 0.00 46.22 2.73
190 2628 0.744414 GCTTCTTCGGCACTATGGCA 60.744 55.000 3.13 0.00 43.94 4.92
206 2644 1.557269 GGCAGAGCAGGGGAAGAAGA 61.557 60.000 0.00 0.00 0.00 2.87
277 2715 2.032681 GGCGCCAAGAAGTCCAGT 59.967 61.111 24.80 0.00 0.00 4.00
283 2721 1.784525 CCAAGAAGTCCAGTGTCGTC 58.215 55.000 0.00 0.00 0.00 4.20
378 2831 2.912025 CAGCCCCGTTGCAAAGGT 60.912 61.111 26.58 8.75 0.00 3.50
490 2948 2.587194 CTGGCCGAGCTCAATCCG 60.587 66.667 15.40 0.00 0.00 4.18
637 3215 2.282462 CCCAGTCAAGTGGCCACC 60.282 66.667 32.29 16.87 36.11 4.61
724 3302 3.905678 CTCGCGGCGGAAGAGGAT 61.906 66.667 23.46 0.00 0.00 3.24
807 3385 2.359975 GCCTCCGGTGTTCAAGGG 60.360 66.667 0.00 0.00 0.00 3.95
835 3436 5.477291 CCTCCTACATTCGAATTAGCTCCTA 59.523 44.000 8.21 0.00 0.00 2.94
884 3501 1.797537 GCGGATTGCAGTGCGAAAC 60.798 57.895 26.38 5.41 45.45 2.78
895 3512 0.454452 GTGCGAAACGGAGCATTTCC 60.454 55.000 0.00 0.00 45.69 3.13
1006 3626 1.296392 CACTCCGGCTTCATGGACA 59.704 57.895 0.00 0.00 0.00 4.02
1128 3751 3.503363 GCGCCCTGCTACTGCTTG 61.503 66.667 0.00 0.00 41.73 4.01
1301 3927 4.148825 GGTCGCAGAGGACGGCAT 62.149 66.667 0.00 0.00 36.95 4.40
1667 10481 3.194542 ACTTTGCACTGTTTTGGCTGTAA 59.805 39.130 0.00 0.00 0.00 2.41
1670 10484 4.399004 TGCACTGTTTTGGCTGTAAATT 57.601 36.364 0.00 0.00 0.00 1.82
1715 10529 4.280929 GCAAGGAAAAACCCAGTATGAACT 59.719 41.667 0.00 0.00 40.05 3.01
1830 12343 3.127376 CAGCAGCAATGCTACACATACAA 59.873 43.478 7.70 0.00 44.30 2.41
1833 12346 3.376234 CAGCAATGCTACACATACAAGCT 59.624 43.478 7.70 0.00 38.34 3.74
1839 12352 7.201350 GCAATGCTACACATACAAGCTTTTTAC 60.201 37.037 0.00 0.00 38.34 2.01
1851 12364 7.582667 ACAAGCTTTTTACAGGAGTTTACAT 57.417 32.000 0.00 0.00 0.00 2.29
1863 12376 8.585471 ACAGGAGTTTACATGATTGATTTGAT 57.415 30.769 0.00 0.00 0.00 2.57
1899 12412 3.344535 TGGGTATAAGAGGAGGATGCA 57.655 47.619 0.00 0.00 0.00 3.96
1900 12413 3.874316 TGGGTATAAGAGGAGGATGCAT 58.126 45.455 0.00 0.00 0.00 3.96
1906 12419 1.527844 GAGGAGGATGCATGCCCAC 60.528 63.158 21.69 14.70 0.00 4.61
1911 12424 3.149648 GATGCATGCCCACCCCAC 61.150 66.667 16.68 0.00 0.00 4.61
1922 12435 0.037590 CCACCCCACGAAAATCAGGA 59.962 55.000 0.00 0.00 0.00 3.86
1923 12436 1.453155 CACCCCACGAAAATCAGGAG 58.547 55.000 0.00 0.00 0.00 3.69
1924 12437 0.328258 ACCCCACGAAAATCAGGAGG 59.672 55.000 0.00 0.00 0.00 4.30
1925 12438 0.328258 CCCCACGAAAATCAGGAGGT 59.672 55.000 0.00 0.00 0.00 3.85
1927 12440 1.453155 CCACGAAAATCAGGAGGTGG 58.547 55.000 0.00 0.00 38.97 4.61
1928 12441 1.271379 CCACGAAAATCAGGAGGTGGT 60.271 52.381 0.00 0.00 39.95 4.16
1929 12442 2.504367 CACGAAAATCAGGAGGTGGTT 58.496 47.619 0.00 0.00 0.00 3.67
1930 12443 3.558321 CCACGAAAATCAGGAGGTGGTTA 60.558 47.826 0.00 0.00 39.95 2.85
1931 12444 4.261801 CACGAAAATCAGGAGGTGGTTAT 58.738 43.478 0.00 0.00 0.00 1.89
1932 12445 4.700213 CACGAAAATCAGGAGGTGGTTATT 59.300 41.667 0.00 0.00 0.00 1.40
1933 12446 5.878116 CACGAAAATCAGGAGGTGGTTATTA 59.122 40.000 0.00 0.00 0.00 0.98
1934 12447 5.878669 ACGAAAATCAGGAGGTGGTTATTAC 59.121 40.000 0.00 0.00 0.00 1.89
1935 12448 6.113411 CGAAAATCAGGAGGTGGTTATTACT 58.887 40.000 0.00 0.00 0.00 2.24
1936 12449 7.093201 ACGAAAATCAGGAGGTGGTTATTACTA 60.093 37.037 0.00 0.00 0.00 1.82
1937 12450 7.224167 CGAAAATCAGGAGGTGGTTATTACTAC 59.776 40.741 0.00 0.00 35.21 2.73
1945 12458 4.313277 GTGGTTATTACTACCTCCGTCC 57.687 50.000 0.00 0.00 36.60 4.79
1946 12459 2.951642 TGGTTATTACTACCTCCGTCCG 59.048 50.000 0.00 0.00 36.60 4.79
1947 12460 2.294512 GGTTATTACTACCTCCGTCCGG 59.705 54.545 0.00 0.00 32.75 5.14
1948 12461 2.276732 TATTACTACCTCCGTCCGGG 57.723 55.000 0.00 0.00 35.59 5.73
1949 12462 0.259938 ATTACTACCTCCGTCCGGGT 59.740 55.000 0.00 0.00 39.40 5.28
1950 12463 0.039618 TTACTACCTCCGTCCGGGTT 59.960 55.000 0.00 0.00 37.07 4.11
1951 12464 0.039618 TACTACCTCCGTCCGGGTTT 59.960 55.000 0.00 0.00 37.07 3.27
1952 12465 0.039618 ACTACCTCCGTCCGGGTTTA 59.960 55.000 0.00 0.00 37.07 2.01
1953 12466 1.342374 ACTACCTCCGTCCGGGTTTAT 60.342 52.381 0.00 0.00 37.07 1.40
1954 12467 1.758862 CTACCTCCGTCCGGGTTTATT 59.241 52.381 0.00 0.00 37.07 1.40
1955 12468 0.251073 ACCTCCGTCCGGGTTTATTG 59.749 55.000 0.00 0.00 37.00 1.90
1956 12469 0.463116 CCTCCGTCCGGGTTTATTGG 60.463 60.000 0.00 0.00 37.00 3.16
1957 12470 0.251073 CTCCGTCCGGGTTTATTGGT 59.749 55.000 0.00 0.00 37.00 3.67
1958 12471 0.249955 TCCGTCCGGGTTTATTGGTC 59.750 55.000 0.00 0.00 37.00 4.02
1959 12472 0.745486 CCGTCCGGGTTTATTGGTCC 60.745 60.000 0.00 0.00 0.00 4.46
1960 12473 0.745486 CGTCCGGGTTTATTGGTCCC 60.745 60.000 0.00 0.00 37.98 4.46
1961 12474 0.394762 GTCCGGGTTTATTGGTCCCC 60.395 60.000 0.00 0.00 38.09 4.81
1962 12475 0.845543 TCCGGGTTTATTGGTCCCCA 60.846 55.000 0.00 0.00 38.09 4.96
1963 12476 0.260523 CCGGGTTTATTGGTCCCCAT 59.739 55.000 0.00 0.00 38.09 4.00
1964 12477 1.342574 CCGGGTTTATTGGTCCCCATT 60.343 52.381 0.00 0.00 38.09 3.16
1965 12478 1.754226 CGGGTTTATTGGTCCCCATTG 59.246 52.381 0.00 0.00 38.09 2.82
1966 12479 2.827755 GGGTTTATTGGTCCCCATTGT 58.172 47.619 0.00 0.00 37.09 2.71
1967 12480 3.625211 CGGGTTTATTGGTCCCCATTGTA 60.625 47.826 0.00 0.00 38.09 2.41
1968 12481 4.552674 GGGTTTATTGGTCCCCATTGTAT 58.447 43.478 0.00 0.00 37.09 2.29
1969 12482 4.966168 GGGTTTATTGGTCCCCATTGTATT 59.034 41.667 0.00 0.00 37.09 1.89
1970 12483 5.427157 GGGTTTATTGGTCCCCATTGTATTT 59.573 40.000 0.00 0.00 37.09 1.40
1971 12484 6.407639 GGGTTTATTGGTCCCCATTGTATTTC 60.408 42.308 0.00 0.00 37.09 2.17
1972 12485 6.155393 GGTTTATTGGTCCCCATTGTATTTCA 59.845 38.462 0.00 0.00 31.53 2.69
1973 12486 7.147567 GGTTTATTGGTCCCCATTGTATTTCAT 60.148 37.037 0.00 0.00 31.53 2.57
1974 12487 5.874897 ATTGGTCCCCATTGTATTTCATG 57.125 39.130 0.00 0.00 31.53 3.07
1975 12488 3.030291 TGGTCCCCATTGTATTTCATGC 58.970 45.455 0.00 0.00 0.00 4.06
1976 12489 3.030291 GGTCCCCATTGTATTTCATGCA 58.970 45.455 0.00 0.00 0.00 3.96
1977 12490 3.450457 GGTCCCCATTGTATTTCATGCAA 59.550 43.478 0.00 0.00 39.16 4.08
1978 12491 4.081198 GGTCCCCATTGTATTTCATGCAAA 60.081 41.667 0.00 0.00 38.34 3.68
1979 12492 5.486526 GTCCCCATTGTATTTCATGCAAAA 58.513 37.500 0.00 0.00 38.34 2.44
1980 12493 6.114767 GTCCCCATTGTATTTCATGCAAAAT 58.885 36.000 0.00 0.00 38.34 1.82
1981 12494 6.598850 GTCCCCATTGTATTTCATGCAAAATT 59.401 34.615 1.86 0.00 38.34 1.82
1982 12495 7.121020 GTCCCCATTGTATTTCATGCAAAATTT 59.879 33.333 1.86 0.00 38.34 1.82
1983 12496 7.668886 TCCCCATTGTATTTCATGCAAAATTTT 59.331 29.630 1.86 0.00 38.34 1.82
1984 12497 7.755822 CCCCATTGTATTTCATGCAAAATTTTG 59.244 33.333 23.74 23.74 38.34 2.44
1985 12498 8.512956 CCCATTGTATTTCATGCAAAATTTTGA 58.487 29.630 30.40 17.35 40.55 2.69
1986 12499 9.332301 CCATTGTATTTCATGCAAAATTTTGAC 57.668 29.630 30.40 21.63 40.55 3.18
1987 12500 9.880064 CATTGTATTTCATGCAAAATTTTGACA 57.120 25.926 30.40 25.53 40.55 3.58
2016 12529 8.941977 AGATTAAACTAACAACATATTCACGCA 58.058 29.630 0.00 0.00 0.00 5.24
2017 12530 9.716507 GATTAAACTAACAACATATTCACGCAT 57.283 29.630 0.00 0.00 0.00 4.73
2018 12531 8.888332 TTAAACTAACAACATATTCACGCATG 57.112 30.769 0.00 0.00 0.00 4.06
2019 12532 6.494893 AACTAACAACATATTCACGCATGT 57.505 33.333 0.00 0.00 36.96 3.21
2020 12533 6.106877 ACTAACAACATATTCACGCATGTC 57.893 37.500 0.00 0.00 34.32 3.06
2021 12534 5.641636 ACTAACAACATATTCACGCATGTCA 59.358 36.000 0.00 0.00 34.32 3.58
2022 12535 4.340894 ACAACATATTCACGCATGTCAC 57.659 40.909 0.00 0.00 34.32 3.67
2023 12536 3.126858 ACAACATATTCACGCATGTCACC 59.873 43.478 0.00 0.00 34.32 4.02
2024 12537 2.984562 ACATATTCACGCATGTCACCA 58.015 42.857 0.00 0.00 29.34 4.17
2025 12538 3.342719 ACATATTCACGCATGTCACCAA 58.657 40.909 0.00 0.00 29.34 3.67
2026 12539 3.755905 ACATATTCACGCATGTCACCAAA 59.244 39.130 0.00 0.00 29.34 3.28
2027 12540 2.704725 ATTCACGCATGTCACCAAAC 57.295 45.000 0.00 0.00 0.00 2.93
2028 12541 1.383523 TTCACGCATGTCACCAAACA 58.616 45.000 0.00 0.00 0.00 2.83
2029 12542 1.603456 TCACGCATGTCACCAAACAT 58.397 45.000 0.00 0.00 40.49 2.71
2030 12543 1.952990 TCACGCATGTCACCAAACATT 59.047 42.857 0.00 0.00 37.78 2.71
2031 12544 3.142174 TCACGCATGTCACCAAACATTA 58.858 40.909 0.00 0.00 37.78 1.90
2032 12545 3.058570 TCACGCATGTCACCAAACATTAC 60.059 43.478 0.00 0.00 37.78 1.89
2033 12546 2.881513 ACGCATGTCACCAAACATTACA 59.118 40.909 0.00 0.00 37.78 2.41
2034 12547 3.505680 ACGCATGTCACCAAACATTACAT 59.494 39.130 0.00 0.00 37.78 2.29
2035 12548 4.022416 ACGCATGTCACCAAACATTACATT 60.022 37.500 0.00 0.00 37.78 2.71
2036 12549 4.922692 CGCATGTCACCAAACATTACATTT 59.077 37.500 0.00 0.00 37.78 2.32
2037 12550 5.404968 CGCATGTCACCAAACATTACATTTT 59.595 36.000 0.00 0.00 37.78 1.82
2038 12551 6.073873 CGCATGTCACCAAACATTACATTTTT 60.074 34.615 0.00 0.00 37.78 1.94
2039 12552 7.070798 GCATGTCACCAAACATTACATTTTTG 58.929 34.615 0.00 0.00 37.78 2.44
2040 12553 7.042187 GCATGTCACCAAACATTACATTTTTGA 60.042 33.333 0.00 0.00 37.78 2.69
2041 12554 8.824781 CATGTCACCAAACATTACATTTTTGAA 58.175 29.630 0.00 0.00 37.78 2.69
2042 12555 8.777865 TGTCACCAAACATTACATTTTTGAAA 57.222 26.923 0.00 0.00 32.91 2.69
2043 12556 9.219603 TGTCACCAAACATTACATTTTTGAAAA 57.780 25.926 0.00 0.00 32.91 2.29
2063 12576 8.183830 TGAAAATTATGTTCAAATGCGAATCC 57.816 30.769 0.00 0.00 32.13 3.01
2064 12577 7.816513 TGAAAATTATGTTCAAATGCGAATCCA 59.183 29.630 0.00 0.00 32.13 3.41
2065 12578 8.545229 AAAATTATGTTCAAATGCGAATCCAA 57.455 26.923 0.00 0.00 0.00 3.53
2066 12579 8.721019 AAATTATGTTCAAATGCGAATCCAAT 57.279 26.923 0.00 0.00 0.00 3.16
2067 12580 7.703298 ATTATGTTCAAATGCGAATCCAATG 57.297 32.000 0.00 0.00 0.00 2.82
2068 12581 4.780275 TGTTCAAATGCGAATCCAATGA 57.220 36.364 0.00 0.00 0.00 2.57
2069 12582 4.735985 TGTTCAAATGCGAATCCAATGAG 58.264 39.130 0.00 0.00 0.00 2.90
2070 12583 4.458642 TGTTCAAATGCGAATCCAATGAGA 59.541 37.500 0.00 0.00 0.00 3.27
2071 12584 5.125900 TGTTCAAATGCGAATCCAATGAGAT 59.874 36.000 0.00 0.00 0.00 2.75
2072 12585 6.318396 TGTTCAAATGCGAATCCAATGAGATA 59.682 34.615 0.00 0.00 0.00 1.98
2073 12586 6.940831 TCAAATGCGAATCCAATGAGATAA 57.059 33.333 0.00 0.00 0.00 1.75
2074 12587 7.514784 TCAAATGCGAATCCAATGAGATAAT 57.485 32.000 0.00 0.00 0.00 1.28
2075 12588 7.944061 TCAAATGCGAATCCAATGAGATAATT 58.056 30.769 0.00 0.00 0.00 1.40
2076 12589 8.415553 TCAAATGCGAATCCAATGAGATAATTT 58.584 29.630 0.00 0.00 0.00 1.82
2077 12590 9.037737 CAAATGCGAATCCAATGAGATAATTTT 57.962 29.630 0.00 0.00 0.00 1.82
2078 12591 9.603921 AAATGCGAATCCAATGAGATAATTTTT 57.396 25.926 0.00 0.00 0.00 1.94
2079 12592 8.807667 ATGCGAATCCAATGAGATAATTTTTC 57.192 30.769 0.00 0.00 0.00 2.29
2080 12593 7.999679 TGCGAATCCAATGAGATAATTTTTCT 58.000 30.769 0.00 0.00 0.00 2.52
2081 12594 8.469200 TGCGAATCCAATGAGATAATTTTTCTT 58.531 29.630 0.00 0.00 0.00 2.52
2082 12595 8.749499 GCGAATCCAATGAGATAATTTTTCTTG 58.251 33.333 0.00 0.00 0.00 3.02
2088 12601 8.814235 CCAATGAGATAATTTTTCTTGACATGC 58.186 33.333 0.00 0.00 0.00 4.06
2089 12602 9.361315 CAATGAGATAATTTTTCTTGACATGCA 57.639 29.630 0.00 0.00 0.00 3.96
2100 12613 9.932699 TTTTTCTTGACATGCATTAACATTTTG 57.067 25.926 0.00 0.00 0.00 2.44
2101 12614 8.659925 TTTCTTGACATGCATTAACATTTTGT 57.340 26.923 0.00 0.00 0.00 2.83
2102 12615 8.659925 TTCTTGACATGCATTAACATTTTGTT 57.340 26.923 0.00 0.00 43.88 2.83
2103 12616 9.755804 TTCTTGACATGCATTAACATTTTGTTA 57.244 25.926 0.00 0.00 41.45 2.41
2104 12617 9.409312 TCTTGACATGCATTAACATTTTGTTAG 57.591 29.630 0.00 0.00 42.93 2.34
2105 12618 9.195411 CTTGACATGCATTAACATTTTGTTAGT 57.805 29.630 0.00 0.00 42.93 2.24
2106 12619 9.539825 TTGACATGCATTAACATTTTGTTAGTT 57.460 25.926 0.00 0.00 42.93 2.24
2142 12655 8.472683 TCAAAATTTGACACAAACTACAAAGG 57.527 30.769 4.03 0.00 36.07 3.11
2143 12656 7.547370 TCAAAATTTGACACAAACTACAAAGGG 59.453 33.333 4.03 0.00 36.07 3.95
2144 12657 4.993029 TTTGACACAAACTACAAAGGGG 57.007 40.909 0.00 0.00 0.00 4.79
2145 12658 2.938838 TGACACAAACTACAAAGGGGG 58.061 47.619 0.00 0.00 0.00 5.40
2146 12659 1.611977 GACACAAACTACAAAGGGGGC 59.388 52.381 0.00 0.00 0.00 5.80
2147 12660 1.216930 ACACAAACTACAAAGGGGGCT 59.783 47.619 0.00 0.00 0.00 5.19
2148 12661 2.444010 ACACAAACTACAAAGGGGGCTA 59.556 45.455 0.00 0.00 0.00 3.93
2149 12662 3.075432 ACACAAACTACAAAGGGGGCTAT 59.925 43.478 0.00 0.00 0.00 2.97
2150 12663 4.290196 ACACAAACTACAAAGGGGGCTATA 59.710 41.667 0.00 0.00 0.00 1.31
2151 12664 5.222171 ACACAAACTACAAAGGGGGCTATAA 60.222 40.000 0.00 0.00 0.00 0.98
2152 12665 5.712917 CACAAACTACAAAGGGGGCTATAAA 59.287 40.000 0.00 0.00 0.00 1.40
2153 12666 5.713389 ACAAACTACAAAGGGGGCTATAAAC 59.287 40.000 0.00 0.00 0.00 2.01
2154 12667 4.515028 ACTACAAAGGGGGCTATAAACC 57.485 45.455 0.00 0.00 0.00 3.27
2155 12668 3.853784 ACTACAAAGGGGGCTATAAACCA 59.146 43.478 0.00 0.00 0.00 3.67
2156 12669 3.382083 ACAAAGGGGGCTATAAACCAG 57.618 47.619 0.00 0.00 0.00 4.00
2157 12670 2.024369 ACAAAGGGGGCTATAAACCAGG 60.024 50.000 0.00 0.00 0.00 4.45
2158 12671 2.243736 CAAAGGGGGCTATAAACCAGGA 59.756 50.000 0.00 0.00 0.00 3.86
2159 12672 1.519498 AGGGGGCTATAAACCAGGAC 58.481 55.000 0.00 0.00 0.00 3.85
2160 12673 0.108019 GGGGGCTATAAACCAGGACG 59.892 60.000 0.00 0.00 0.00 4.79
2161 12674 0.108019 GGGGCTATAAACCAGGACGG 59.892 60.000 0.00 0.00 42.50 4.79
2162 12675 1.125633 GGGCTATAAACCAGGACGGA 58.874 55.000 0.00 0.00 38.63 4.69
2163 12676 1.070289 GGGCTATAAACCAGGACGGAG 59.930 57.143 0.00 0.00 38.63 4.63
2164 12677 1.070289 GGCTATAAACCAGGACGGAGG 59.930 57.143 0.00 0.00 38.63 4.30
2167 12680 3.005578 GCTATAAACCAGGACGGAGGTAG 59.994 52.174 0.00 0.00 37.07 3.18
2180 12693 3.197116 ACGGAGGTAGTATGTTTGGAAGG 59.803 47.826 0.00 0.00 0.00 3.46
2193 12709 2.194460 GGAAGGAGTCCGTGAGAGG 58.806 63.158 0.93 0.00 36.40 3.69
2205 12721 0.035343 GTGAGAGGCTGTAAACCCCC 60.035 60.000 0.00 0.00 0.00 5.40
2209 12725 1.203389 AGAGGCTGTAAACCCCCTACA 60.203 52.381 0.00 0.00 0.00 2.74
2226 12742 4.097892 CCCTACATGTAGCATTTTTGGGTC 59.902 45.833 24.85 0.00 31.95 4.46
2251 12767 7.971722 TCATCAGTGTTCAGAATGCATAAATTG 59.028 33.333 0.00 0.00 34.76 2.32
2471 13024 6.999272 TGACCTGCATAGTTTAACCAAGTTTA 59.001 34.615 0.00 0.00 0.00 2.01
2474 13027 9.174166 ACCTGCATAGTTTAACCAAGTTTATAG 57.826 33.333 0.00 0.00 0.00 1.31
2475 13028 8.621286 CCTGCATAGTTTAACCAAGTTTATAGG 58.379 37.037 0.00 0.00 0.00 2.57
2476 13029 9.391006 CTGCATAGTTTAACCAAGTTTATAGGA 57.609 33.333 0.00 0.00 0.00 2.94
2477 13030 9.391006 TGCATAGTTTAACCAAGTTTATAGGAG 57.609 33.333 0.00 0.00 0.00 3.69
2478 13031 8.837389 GCATAGTTTAACCAAGTTTATAGGAGG 58.163 37.037 0.00 0.00 0.00 4.30
2479 13032 9.338622 CATAGTTTAACCAAGTTTATAGGAGGG 57.661 37.037 0.00 0.00 0.00 4.30
2480 13033 6.728411 AGTTTAACCAAGTTTATAGGAGGGG 58.272 40.000 0.00 0.00 0.00 4.79
2481 13034 6.506413 AGTTTAACCAAGTTTATAGGAGGGGA 59.494 38.462 0.00 0.00 0.00 4.81
2482 13035 6.973700 TTAACCAAGTTTATAGGAGGGGAA 57.026 37.500 0.00 0.00 0.00 3.97
2483 13036 4.857130 ACCAAGTTTATAGGAGGGGAAC 57.143 45.455 0.00 0.00 0.00 3.62
2484 13037 4.445564 ACCAAGTTTATAGGAGGGGAACT 58.554 43.478 0.00 0.00 32.33 3.01
2485 13038 4.856182 ACCAAGTTTATAGGAGGGGAACTT 59.144 41.667 0.00 0.00 40.17 2.66
2486 13039 5.315109 ACCAAGTTTATAGGAGGGGAACTTT 59.685 40.000 0.00 0.00 38.19 2.66
2487 13040 6.183361 ACCAAGTTTATAGGAGGGGAACTTTT 60.183 38.462 0.00 0.00 38.19 2.27
2488 13041 6.152831 CCAAGTTTATAGGAGGGGAACTTTTG 59.847 42.308 0.00 0.00 38.19 2.44
2489 13042 5.827756 AGTTTATAGGAGGGGAACTTTTGG 58.172 41.667 0.00 0.00 0.00 3.28
2490 13043 5.315109 AGTTTATAGGAGGGGAACTTTTGGT 59.685 40.000 0.00 0.00 0.00 3.67
2491 13044 5.446260 TTATAGGAGGGGAACTTTTGGTC 57.554 43.478 0.00 0.00 34.82 4.02
2492 13045 1.834540 AGGAGGGGAACTTTTGGTCT 58.165 50.000 0.00 0.00 36.15 3.85
2493 13046 2.999928 AGGAGGGGAACTTTTGGTCTA 58.000 47.619 0.00 0.00 36.15 2.59
2494 13047 3.542604 AGGAGGGGAACTTTTGGTCTAT 58.457 45.455 0.00 0.00 36.15 1.98
2495 13048 3.267031 AGGAGGGGAACTTTTGGTCTATG 59.733 47.826 0.00 0.00 36.15 2.23
2496 13049 3.621558 GAGGGGAACTTTTGGTCTATGG 58.378 50.000 0.00 0.00 36.15 2.74
2497 13050 2.311841 AGGGGAACTTTTGGTCTATGGG 59.688 50.000 0.00 0.00 36.15 4.00
2498 13051 2.623239 GGGGAACTTTTGGTCTATGGGG 60.623 54.545 0.00 0.00 36.15 4.96
2499 13052 2.310647 GGGAACTTTTGGTCTATGGGGA 59.689 50.000 0.00 0.00 36.15 4.81
2500 13053 3.353557 GGAACTTTTGGTCTATGGGGAC 58.646 50.000 0.00 0.00 36.15 4.46
2501 13054 3.245122 GGAACTTTTGGTCTATGGGGACA 60.245 47.826 0.00 0.00 39.95 4.02
2502 13055 4.569865 GGAACTTTTGGTCTATGGGGACAT 60.570 45.833 0.00 0.00 43.22 3.06
2511 13064 4.518056 TGGGGACATATGCACCCT 57.482 55.556 26.78 0.12 43.72 4.34
2512 13065 3.664869 TGGGGACATATGCACCCTA 57.335 52.632 26.78 21.97 43.72 3.53
2513 13066 2.132303 TGGGGACATATGCACCCTAT 57.868 50.000 26.78 0.00 43.72 2.57
2514 13067 3.283712 TGGGGACATATGCACCCTATA 57.716 47.619 26.78 16.20 43.72 1.31
2515 13068 3.814284 TGGGGACATATGCACCCTATAT 58.186 45.455 26.78 0.00 43.72 0.86
2516 13069 3.523157 TGGGGACATATGCACCCTATATG 59.477 47.826 26.78 6.07 43.72 1.78
2517 13070 3.117888 GGGGACATATGCACCCTATATGG 60.118 52.174 26.98 0.00 40.92 2.74
2518 13071 3.780294 GGGACATATGCACCCTATATGGA 59.220 47.826 23.37 0.00 40.92 3.41
2519 13072 4.227300 GGGACATATGCACCCTATATGGAA 59.773 45.833 23.37 0.00 40.92 3.53
2520 13073 5.280985 GGGACATATGCACCCTATATGGAAA 60.281 44.000 23.37 0.00 40.92 3.13
2521 13074 6.245408 GGACATATGCACCCTATATGGAAAA 58.755 40.000 1.58 0.00 40.92 2.29
2522 13075 6.719370 GGACATATGCACCCTATATGGAAAAA 59.281 38.462 1.58 0.00 40.92 1.94
2553 13106 9.843874 GTAATTCAACAAAAAGTCGAAAATTCC 57.156 29.630 0.00 0.00 0.00 3.01
2554 13107 8.716646 AATTCAACAAAAAGTCGAAAATTCCT 57.283 26.923 0.00 0.00 0.00 3.36
2555 13108 7.518731 TTCAACAAAAAGTCGAAAATTCCTG 57.481 32.000 0.00 0.00 0.00 3.86
2556 13109 6.857956 TCAACAAAAAGTCGAAAATTCCTGA 58.142 32.000 0.00 0.00 0.00 3.86
2557 13110 7.316640 TCAACAAAAAGTCGAAAATTCCTGAA 58.683 30.769 0.00 0.00 0.00 3.02
2558 13111 7.815068 TCAACAAAAAGTCGAAAATTCCTGAAA 59.185 29.630 0.00 0.00 0.00 2.69
2559 13112 8.603181 CAACAAAAAGTCGAAAATTCCTGAAAT 58.397 29.630 0.00 0.00 0.00 2.17
2560 13113 9.810545 AACAAAAAGTCGAAAATTCCTGAAATA 57.189 25.926 0.00 0.00 0.00 1.40
2561 13114 9.981114 ACAAAAAGTCGAAAATTCCTGAAATAT 57.019 25.926 0.00 0.00 0.00 1.28
2594 13147 8.928270 ATAAACTTGACCTTCTATTGTACTCG 57.072 34.615 0.00 0.00 0.00 4.18
2595 13148 4.745649 ACTTGACCTTCTATTGTACTCGC 58.254 43.478 0.00 0.00 0.00 5.03
2596 13149 3.416119 TGACCTTCTATTGTACTCGCG 57.584 47.619 0.00 0.00 0.00 5.87
2597 13150 3.011818 TGACCTTCTATTGTACTCGCGA 58.988 45.455 9.26 9.26 0.00 5.87
2598 13151 3.064958 TGACCTTCTATTGTACTCGCGAG 59.935 47.826 33.45 33.45 0.00 5.03
2599 13152 3.276857 ACCTTCTATTGTACTCGCGAGA 58.723 45.455 40.58 21.98 39.12 4.04
2600 13153 3.693085 ACCTTCTATTGTACTCGCGAGAA 59.307 43.478 40.58 25.26 41.32 2.87
2601 13154 4.157289 ACCTTCTATTGTACTCGCGAGAAA 59.843 41.667 40.58 28.74 41.32 2.52
2602 13155 5.100259 CCTTCTATTGTACTCGCGAGAAAA 58.900 41.667 40.58 28.41 41.32 2.29
2603 13156 5.575606 CCTTCTATTGTACTCGCGAGAAAAA 59.424 40.000 40.58 28.09 41.32 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 4.632153 ACTACTGCTTGGTTCAGTACAAG 58.368 43.478 0.00 0.00 43.75 3.16
67 79 0.105504 TGCTATGCTAGGCCCTCTGA 60.106 55.000 0.00 0.00 0.00 3.27
169 204 1.293924 CCATAGTGCCGAAGAAGCTG 58.706 55.000 0.00 0.00 0.00 4.24
190 2628 1.261238 CCGTCTTCTTCCCCTGCTCT 61.261 60.000 0.00 0.00 0.00 4.09
206 2644 3.322466 CTTGTCCTGCTCCCCCGT 61.322 66.667 0.00 0.00 0.00 5.28
378 2831 4.308458 CCGTGGTGACCGGCTTCA 62.308 66.667 0.00 0.00 37.36 3.02
566 3024 4.373116 GAGCACCCTCGTTGCCGA 62.373 66.667 0.00 0.00 41.73 5.54
588 3166 3.311110 TGGCCACCGGACTCTGTC 61.311 66.667 9.46 0.00 0.00 3.51
724 3302 1.228245 GTCCAAGTTGGCAGGCTCA 60.228 57.895 17.68 0.00 37.47 4.26
807 3385 2.510768 ATTCGAATGTAGGAGGCGTC 57.489 50.000 10.50 0.00 0.00 5.19
835 3436 6.095432 TCCATCATTTTTCACGGTGATTTT 57.905 33.333 12.26 0.00 0.00 1.82
1301 3927 3.691342 CGGCCAGGAGGAACACGA 61.691 66.667 2.24 0.00 36.89 4.35
1464 8886 1.764571 CGTCCCCTTTCACCTGGACA 61.765 60.000 0.00 0.00 46.09 4.02
1667 10481 7.937394 GCACTAGTTCATATACTGGGGTTAATT 59.063 37.037 0.00 0.00 33.04 1.40
1670 10484 5.900699 TGCACTAGTTCATATACTGGGGTTA 59.099 40.000 0.00 0.00 33.04 2.85
1715 10529 6.037610 GCCAAACACATTCCAACATTAACAAA 59.962 34.615 0.00 0.00 0.00 2.83
1830 12343 8.299570 CAATCATGTAAACTCCTGTAAAAAGCT 58.700 33.333 0.00 0.00 0.00 3.74
1839 12352 8.464404 ACATCAAATCAATCATGTAAACTCCTG 58.536 33.333 0.00 0.00 0.00 3.86
1851 12364 5.471556 AAACTGCCACATCAAATCAATCA 57.528 34.783 0.00 0.00 0.00 2.57
1863 12376 2.114616 ACCCAATCAAAAACTGCCACA 58.885 42.857 0.00 0.00 0.00 4.17
1899 12412 0.970427 GATTTTCGTGGGGTGGGCAT 60.970 55.000 0.00 0.00 0.00 4.40
1900 12413 1.605165 GATTTTCGTGGGGTGGGCA 60.605 57.895 0.00 0.00 0.00 5.36
1906 12419 0.328258 ACCTCCTGATTTTCGTGGGG 59.672 55.000 0.00 0.00 0.00 4.96
1911 12424 6.113411 AGTAATAACCACCTCCTGATTTTCG 58.887 40.000 0.00 0.00 0.00 3.46
1923 12436 3.068732 GGACGGAGGTAGTAATAACCACC 59.931 52.174 0.00 0.00 42.49 4.61
1924 12437 3.243201 CGGACGGAGGTAGTAATAACCAC 60.243 52.174 0.00 0.00 39.64 4.16
1925 12438 2.951642 CGGACGGAGGTAGTAATAACCA 59.048 50.000 0.00 0.00 39.64 3.67
1927 12440 2.294512 CCCGGACGGAGGTAGTAATAAC 59.705 54.545 13.13 0.00 37.50 1.89
1928 12441 2.091885 ACCCGGACGGAGGTAGTAATAA 60.092 50.000 13.13 0.00 37.50 1.40
1929 12442 1.494721 ACCCGGACGGAGGTAGTAATA 59.505 52.381 13.13 0.00 37.50 0.98
1930 12443 0.259938 ACCCGGACGGAGGTAGTAAT 59.740 55.000 13.13 0.00 37.50 1.89
1931 12444 0.039618 AACCCGGACGGAGGTAGTAA 59.960 55.000 13.13 0.00 34.45 2.24
1932 12445 0.039618 AAACCCGGACGGAGGTAGTA 59.960 55.000 13.13 0.00 34.45 1.82
1933 12446 0.039618 TAAACCCGGACGGAGGTAGT 59.960 55.000 13.13 0.00 34.45 2.73
1934 12447 1.406903 ATAAACCCGGACGGAGGTAG 58.593 55.000 13.13 0.00 34.45 3.18
1935 12448 1.481772 CAATAAACCCGGACGGAGGTA 59.518 52.381 13.13 1.24 34.45 3.08
1936 12449 0.251073 CAATAAACCCGGACGGAGGT 59.749 55.000 13.13 0.00 38.27 3.85
1937 12450 0.463116 CCAATAAACCCGGACGGAGG 60.463 60.000 13.13 0.00 37.50 4.30
1938 12451 0.251073 ACCAATAAACCCGGACGGAG 59.749 55.000 13.13 5.04 37.50 4.63
1939 12452 0.249955 GACCAATAAACCCGGACGGA 59.750 55.000 13.13 0.00 37.50 4.69
1940 12453 0.745486 GGACCAATAAACCCGGACGG 60.745 60.000 0.73 3.25 37.81 4.79
1941 12454 0.745486 GGGACCAATAAACCCGGACG 60.745 60.000 0.73 0.00 34.03 4.79
1942 12455 3.179925 GGGACCAATAAACCCGGAC 57.820 57.895 0.73 0.00 34.03 4.79
1956 12469 4.734398 TTGCATGAAATACAATGGGGAC 57.266 40.909 0.00 0.00 0.00 4.46
1957 12470 5.752036 TTTTGCATGAAATACAATGGGGA 57.248 34.783 0.00 0.00 27.99 4.81
1958 12471 7.393841 AAATTTTGCATGAAATACAATGGGG 57.606 32.000 0.00 0.00 27.99 4.96
1959 12472 8.512956 TCAAAATTTTGCATGAAATACAATGGG 58.487 29.630 23.36 0.00 38.05 4.00
1960 12473 9.332301 GTCAAAATTTTGCATGAAATACAATGG 57.668 29.630 23.36 0.00 38.05 3.16
1961 12474 9.880064 TGTCAAAATTTTGCATGAAATACAATG 57.120 25.926 23.36 0.00 38.05 2.82
1990 12503 8.941977 TGCGTGAATATGTTGTTAGTTTAATCT 58.058 29.630 0.00 0.00 0.00 2.40
1991 12504 9.716507 ATGCGTGAATATGTTGTTAGTTTAATC 57.283 29.630 0.00 0.00 0.00 1.75
1992 12505 9.502145 CATGCGTGAATATGTTGTTAGTTTAAT 57.498 29.630 0.00 0.00 0.00 1.40
1993 12506 8.508062 ACATGCGTGAATATGTTGTTAGTTTAA 58.492 29.630 14.17 0.00 34.00 1.52
1994 12507 8.035165 ACATGCGTGAATATGTTGTTAGTTTA 57.965 30.769 14.17 0.00 34.00 2.01
1995 12508 6.908825 ACATGCGTGAATATGTTGTTAGTTT 58.091 32.000 14.17 0.00 34.00 2.66
1996 12509 6.148645 TGACATGCGTGAATATGTTGTTAGTT 59.851 34.615 14.17 0.00 37.63 2.24
1997 12510 5.641636 TGACATGCGTGAATATGTTGTTAGT 59.358 36.000 14.17 0.00 37.63 2.24
1998 12511 5.959527 GTGACATGCGTGAATATGTTGTTAG 59.040 40.000 14.17 0.00 37.63 2.34
1999 12512 5.163804 GGTGACATGCGTGAATATGTTGTTA 60.164 40.000 14.17 0.00 37.63 2.41
2000 12513 4.379394 GGTGACATGCGTGAATATGTTGTT 60.379 41.667 14.17 0.00 37.63 2.83
2001 12514 3.126858 GGTGACATGCGTGAATATGTTGT 59.873 43.478 14.17 0.00 37.63 3.32
2002 12515 3.126686 TGGTGACATGCGTGAATATGTTG 59.873 43.478 14.17 0.00 37.63 3.33
2003 12516 3.342719 TGGTGACATGCGTGAATATGTT 58.657 40.909 14.17 0.00 37.63 2.71
2004 12517 2.984562 TGGTGACATGCGTGAATATGT 58.015 42.857 14.17 0.00 40.04 2.29
2005 12518 4.097714 GTTTGGTGACATGCGTGAATATG 58.902 43.478 14.17 0.00 42.32 1.78
2006 12519 3.755905 TGTTTGGTGACATGCGTGAATAT 59.244 39.130 14.17 0.00 42.32 1.28
2007 12520 3.142174 TGTTTGGTGACATGCGTGAATA 58.858 40.909 14.17 0.00 42.32 1.75
2008 12521 1.952990 TGTTTGGTGACATGCGTGAAT 59.047 42.857 14.17 0.00 42.32 2.57
2009 12522 1.383523 TGTTTGGTGACATGCGTGAA 58.616 45.000 14.17 0.00 42.32 3.18
2010 12523 1.603456 ATGTTTGGTGACATGCGTGA 58.397 45.000 14.17 0.00 42.32 4.35
2011 12524 2.420628 AATGTTTGGTGACATGCGTG 57.579 45.000 3.82 3.82 40.03 5.34
2012 12525 2.881513 TGTAATGTTTGGTGACATGCGT 59.118 40.909 0.00 0.00 40.03 5.24
2013 12526 3.550950 TGTAATGTTTGGTGACATGCG 57.449 42.857 0.00 0.00 40.03 4.73
2014 12527 6.783892 AAAATGTAATGTTTGGTGACATGC 57.216 33.333 0.00 0.00 40.03 4.06
2037 12550 8.655092 GGATTCGCATTTGAACATAATTTTCAA 58.345 29.630 0.62 0.62 40.42 2.69
2038 12551 7.816513 TGGATTCGCATTTGAACATAATTTTCA 59.183 29.630 0.00 0.00 0.00 2.69
2039 12552 8.183830 TGGATTCGCATTTGAACATAATTTTC 57.816 30.769 0.00 0.00 0.00 2.29
2040 12553 8.545229 TTGGATTCGCATTTGAACATAATTTT 57.455 26.923 0.00 0.00 0.00 1.82
2041 12554 8.605746 CATTGGATTCGCATTTGAACATAATTT 58.394 29.630 0.00 0.00 0.00 1.82
2042 12555 7.980662 TCATTGGATTCGCATTTGAACATAATT 59.019 29.630 0.00 0.00 0.00 1.40
2043 12556 7.490840 TCATTGGATTCGCATTTGAACATAAT 58.509 30.769 0.00 0.00 0.00 1.28
2044 12557 6.861144 TCATTGGATTCGCATTTGAACATAA 58.139 32.000 0.00 0.00 0.00 1.90
2045 12558 6.318396 TCTCATTGGATTCGCATTTGAACATA 59.682 34.615 0.00 0.00 0.00 2.29
2046 12559 5.125900 TCTCATTGGATTCGCATTTGAACAT 59.874 36.000 0.00 0.00 0.00 2.71
2047 12560 4.458642 TCTCATTGGATTCGCATTTGAACA 59.541 37.500 0.00 0.00 0.00 3.18
2048 12561 4.985413 TCTCATTGGATTCGCATTTGAAC 58.015 39.130 0.00 0.00 0.00 3.18
2049 12562 5.840243 ATCTCATTGGATTCGCATTTGAA 57.160 34.783 0.00 0.00 0.00 2.69
2050 12563 6.940831 TTATCTCATTGGATTCGCATTTGA 57.059 33.333 0.00 0.00 0.00 2.69
2051 12564 8.583810 AAATTATCTCATTGGATTCGCATTTG 57.416 30.769 0.00 0.00 0.00 2.32
2052 12565 9.603921 AAAAATTATCTCATTGGATTCGCATTT 57.396 25.926 0.00 0.00 0.00 2.32
2053 12566 9.252962 GAAAAATTATCTCATTGGATTCGCATT 57.747 29.630 0.00 0.00 0.00 3.56
2054 12567 8.636213 AGAAAAATTATCTCATTGGATTCGCAT 58.364 29.630 0.00 0.00 0.00 4.73
2055 12568 7.999679 AGAAAAATTATCTCATTGGATTCGCA 58.000 30.769 0.00 0.00 0.00 5.10
2056 12569 8.749499 CAAGAAAAATTATCTCATTGGATTCGC 58.251 33.333 0.00 0.00 0.00 4.70
2062 12575 8.814235 GCATGTCAAGAAAAATTATCTCATTGG 58.186 33.333 0.00 0.00 0.00 3.16
2063 12576 9.361315 TGCATGTCAAGAAAAATTATCTCATTG 57.639 29.630 0.00 0.00 0.00 2.82
2074 12587 9.932699 CAAAATGTTAATGCATGTCAAGAAAAA 57.067 25.926 0.00 0.00 0.00 1.94
2075 12588 9.107177 ACAAAATGTTAATGCATGTCAAGAAAA 57.893 25.926 0.00 0.00 0.00 2.29
2076 12589 8.659925 ACAAAATGTTAATGCATGTCAAGAAA 57.340 26.923 0.00 0.00 0.00 2.52
2077 12590 8.659925 AACAAAATGTTAATGCATGTCAAGAA 57.340 26.923 0.00 0.00 39.09 2.52
2078 12591 9.409312 CTAACAAAATGTTAATGCATGTCAAGA 57.591 29.630 0.00 0.00 41.70 3.02
2079 12592 9.195411 ACTAACAAAATGTTAATGCATGTCAAG 57.805 29.630 0.00 0.00 41.70 3.02
2080 12593 9.539825 AACTAACAAAATGTTAATGCATGTCAA 57.460 25.926 0.00 0.00 41.70 3.18
2117 12630 7.547370 CCCTTTGTAGTTTGTGTCAAATTTTGA 59.453 33.333 7.74 7.74 37.33 2.69
2118 12631 7.201600 CCCCTTTGTAGTTTGTGTCAAATTTTG 60.202 37.037 2.59 2.59 31.08 2.44
2119 12632 6.821160 CCCCTTTGTAGTTTGTGTCAAATTTT 59.179 34.615 0.00 0.00 31.08 1.82
2120 12633 6.345298 CCCCTTTGTAGTTTGTGTCAAATTT 58.655 36.000 0.00 0.00 31.08 1.82
2121 12634 5.163353 CCCCCTTTGTAGTTTGTGTCAAATT 60.163 40.000 0.00 0.00 31.08 1.82
2122 12635 4.343814 CCCCCTTTGTAGTTTGTGTCAAAT 59.656 41.667 0.00 0.00 31.08 2.32
2123 12636 3.702045 CCCCCTTTGTAGTTTGTGTCAAA 59.298 43.478 0.00 0.00 0.00 2.69
2124 12637 3.292460 CCCCCTTTGTAGTTTGTGTCAA 58.708 45.455 0.00 0.00 0.00 3.18
2125 12638 2.938838 CCCCCTTTGTAGTTTGTGTCA 58.061 47.619 0.00 0.00 0.00 3.58
2126 12639 1.611977 GCCCCCTTTGTAGTTTGTGTC 59.388 52.381 0.00 0.00 0.00 3.67
2127 12640 1.216930 AGCCCCCTTTGTAGTTTGTGT 59.783 47.619 0.00 0.00 0.00 3.72
2128 12641 1.995376 AGCCCCCTTTGTAGTTTGTG 58.005 50.000 0.00 0.00 0.00 3.33
2129 12642 5.523883 TTATAGCCCCCTTTGTAGTTTGT 57.476 39.130 0.00 0.00 0.00 2.83
2130 12643 5.126545 GGTTTATAGCCCCCTTTGTAGTTTG 59.873 44.000 0.00 0.00 0.00 2.93
2131 12644 5.222379 TGGTTTATAGCCCCCTTTGTAGTTT 60.222 40.000 0.00 0.00 0.00 2.66
2132 12645 4.292836 TGGTTTATAGCCCCCTTTGTAGTT 59.707 41.667 0.00 0.00 0.00 2.24
2133 12646 3.853784 TGGTTTATAGCCCCCTTTGTAGT 59.146 43.478 0.00 0.00 0.00 2.73
2134 12647 4.461198 CTGGTTTATAGCCCCCTTTGTAG 58.539 47.826 0.00 0.00 0.00 2.74
2135 12648 3.203487 CCTGGTTTATAGCCCCCTTTGTA 59.797 47.826 0.00 0.00 0.00 2.41
2136 12649 2.024369 CCTGGTTTATAGCCCCCTTTGT 60.024 50.000 0.00 0.00 0.00 2.83
2137 12650 2.243736 TCCTGGTTTATAGCCCCCTTTG 59.756 50.000 0.00 0.00 0.00 2.77
2138 12651 2.243994 GTCCTGGTTTATAGCCCCCTTT 59.756 50.000 0.00 0.00 0.00 3.11
2139 12652 1.850998 GTCCTGGTTTATAGCCCCCTT 59.149 52.381 0.00 0.00 0.00 3.95
2140 12653 1.519498 GTCCTGGTTTATAGCCCCCT 58.481 55.000 0.00 0.00 0.00 4.79
2141 12654 0.108019 CGTCCTGGTTTATAGCCCCC 59.892 60.000 0.00 0.00 0.00 5.40
2142 12655 0.108019 CCGTCCTGGTTTATAGCCCC 59.892 60.000 0.00 0.00 0.00 5.80
2143 12656 1.070289 CTCCGTCCTGGTTTATAGCCC 59.930 57.143 0.00 0.00 39.52 5.19
2144 12657 1.070289 CCTCCGTCCTGGTTTATAGCC 59.930 57.143 0.00 0.00 39.52 3.93
2145 12658 1.761198 ACCTCCGTCCTGGTTTATAGC 59.239 52.381 0.00 0.00 39.52 2.97
2146 12659 4.213513 ACTACCTCCGTCCTGGTTTATAG 58.786 47.826 0.00 0.00 39.52 1.31
2147 12660 4.255510 ACTACCTCCGTCCTGGTTTATA 57.744 45.455 0.00 0.00 39.52 0.98
2148 12661 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
2149 12662 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
2150 12663 2.610438 TACTACCTCCGTCCTGGTTT 57.390 50.000 0.00 0.00 39.52 3.27
2151 12664 2.292061 ACATACTACCTCCGTCCTGGTT 60.292 50.000 0.00 0.00 39.52 3.67
2152 12665 1.287146 ACATACTACCTCCGTCCTGGT 59.713 52.381 0.00 0.00 39.52 4.00
2153 12666 2.068834 ACATACTACCTCCGTCCTGG 57.931 55.000 0.00 0.00 40.09 4.45
2154 12667 3.430374 CCAAACATACTACCTCCGTCCTG 60.430 52.174 0.00 0.00 0.00 3.86
2155 12668 2.764572 CCAAACATACTACCTCCGTCCT 59.235 50.000 0.00 0.00 0.00 3.85
2156 12669 2.762327 TCCAAACATACTACCTCCGTCC 59.238 50.000 0.00 0.00 0.00 4.79
2157 12670 4.430908 CTTCCAAACATACTACCTCCGTC 58.569 47.826 0.00 0.00 0.00 4.79
2158 12671 3.197116 CCTTCCAAACATACTACCTCCGT 59.803 47.826 0.00 0.00 0.00 4.69
2159 12672 3.449737 TCCTTCCAAACATACTACCTCCG 59.550 47.826 0.00 0.00 0.00 4.63
2160 12673 4.470304 ACTCCTTCCAAACATACTACCTCC 59.530 45.833 0.00 0.00 0.00 4.30
2161 12674 5.395435 GGACTCCTTCCAAACATACTACCTC 60.395 48.000 0.00 0.00 45.10 3.85
2162 12675 4.470304 GGACTCCTTCCAAACATACTACCT 59.530 45.833 0.00 0.00 45.10 3.08
2163 12676 4.679905 CGGACTCCTTCCAAACATACTACC 60.680 50.000 0.00 0.00 46.29 3.18
2164 12677 4.081807 ACGGACTCCTTCCAAACATACTAC 60.082 45.833 0.00 0.00 46.29 2.73
2167 12680 3.000727 CACGGACTCCTTCCAAACATAC 58.999 50.000 0.00 0.00 46.29 2.39
2180 12693 1.174783 TTACAGCCTCTCACGGACTC 58.825 55.000 0.00 0.00 0.00 3.36
2193 12709 2.801077 ACATGTAGGGGGTTTACAGC 57.199 50.000 0.00 0.00 34.76 4.40
2205 12721 5.895636 TGACCCAAAAATGCTACATGTAG 57.104 39.130 25.68 25.68 36.29 2.74
2209 12725 5.018809 ACTGATGACCCAAAAATGCTACAT 58.981 37.500 0.00 0.00 0.00 2.29
2226 12742 8.115491 CAATTTATGCATTCTGAACACTGATG 57.885 34.615 3.54 0.00 0.00 3.07
2471 13024 3.542604 AGACCAAAAGTTCCCCTCCTAT 58.457 45.455 0.00 0.00 0.00 2.57
2474 13027 3.621558 CATAGACCAAAAGTTCCCCTCC 58.378 50.000 0.00 0.00 0.00 4.30
2475 13028 3.621558 CCATAGACCAAAAGTTCCCCTC 58.378 50.000 0.00 0.00 0.00 4.30
2476 13029 2.311841 CCCATAGACCAAAAGTTCCCCT 59.688 50.000 0.00 0.00 0.00 4.79
2477 13030 2.623239 CCCCATAGACCAAAAGTTCCCC 60.623 54.545 0.00 0.00 0.00 4.81
2478 13031 2.310647 TCCCCATAGACCAAAAGTTCCC 59.689 50.000 0.00 0.00 0.00 3.97
2479 13032 3.245122 TGTCCCCATAGACCAAAAGTTCC 60.245 47.826 0.00 0.00 35.83 3.62
2480 13033 4.028993 TGTCCCCATAGACCAAAAGTTC 57.971 45.455 0.00 0.00 35.83 3.01
2481 13034 4.675063 ATGTCCCCATAGACCAAAAGTT 57.325 40.909 0.00 0.00 35.83 2.66
2482 13035 5.694995 CATATGTCCCCATAGACCAAAAGT 58.305 41.667 0.00 0.00 36.99 2.66
2483 13036 4.520492 GCATATGTCCCCATAGACCAAAAG 59.480 45.833 4.29 0.00 36.99 2.27
2484 13037 4.079500 TGCATATGTCCCCATAGACCAAAA 60.080 41.667 4.29 0.00 36.99 2.44
2485 13038 3.461458 TGCATATGTCCCCATAGACCAAA 59.539 43.478 4.29 0.00 36.99 3.28
2486 13039 3.052329 TGCATATGTCCCCATAGACCAA 58.948 45.455 4.29 0.00 36.99 3.67
2487 13040 2.371841 GTGCATATGTCCCCATAGACCA 59.628 50.000 4.29 0.00 36.99 4.02
2488 13041 2.290323 GGTGCATATGTCCCCATAGACC 60.290 54.545 4.29 0.00 36.99 3.85
2489 13042 2.290323 GGGTGCATATGTCCCCATAGAC 60.290 54.545 20.72 0.00 36.99 2.59
2490 13043 1.985159 GGGTGCATATGTCCCCATAGA 59.015 52.381 20.72 0.00 36.99 1.98
2491 13044 1.988107 AGGGTGCATATGTCCCCATAG 59.012 52.381 24.95 0.00 41.95 2.23
2492 13045 2.132303 AGGGTGCATATGTCCCCATA 57.868 50.000 24.95 0.00 41.95 2.74
2493 13046 2.132303 TAGGGTGCATATGTCCCCAT 57.868 50.000 24.95 14.11 41.95 4.00
2494 13047 2.132303 ATAGGGTGCATATGTCCCCA 57.868 50.000 24.95 17.03 41.95 4.96
2495 13048 3.117888 CCATATAGGGTGCATATGTCCCC 60.118 52.174 24.48 21.88 41.95 4.81
2496 13049 3.780294 TCCATATAGGGTGCATATGTCCC 59.220 47.826 22.23 22.23 41.36 4.46
2497 13050 5.435686 TTCCATATAGGGTGCATATGTCC 57.564 43.478 2.85 7.47 35.47 4.02
2498 13051 7.759489 TTTTTCCATATAGGGTGCATATGTC 57.241 36.000 2.85 0.00 35.47 3.06
2527 13080 9.843874 GGAATTTTCGACTTTTTGTTGAATTAC 57.156 29.630 0.00 0.00 45.50 1.89
2528 13081 9.810545 AGGAATTTTCGACTTTTTGTTGAATTA 57.189 25.926 0.00 0.00 45.50 1.40
2529 13082 8.603181 CAGGAATTTTCGACTTTTTGTTGAATT 58.397 29.630 0.00 0.00 45.50 2.17
2530 13083 7.978975 TCAGGAATTTTCGACTTTTTGTTGAAT 59.021 29.630 0.00 0.00 45.50 2.57
2531 13084 7.316640 TCAGGAATTTTCGACTTTTTGTTGAA 58.683 30.769 0.00 0.00 44.79 2.69
2532 13085 6.857956 TCAGGAATTTTCGACTTTTTGTTGA 58.142 32.000 0.00 0.00 37.30 3.18
2533 13086 7.518731 TTCAGGAATTTTCGACTTTTTGTTG 57.481 32.000 0.00 0.00 0.00 3.33
2534 13087 8.716646 ATTTCAGGAATTTTCGACTTTTTGTT 57.283 26.923 0.00 0.00 0.00 2.83
2535 13088 9.981114 ATATTTCAGGAATTTTCGACTTTTTGT 57.019 25.926 0.00 0.00 0.00 2.83
2568 13121 9.367444 CGAGTACAATAGAAGGTCAAGTTTATT 57.633 33.333 0.00 0.00 0.00 1.40
2569 13122 7.491696 GCGAGTACAATAGAAGGTCAAGTTTAT 59.508 37.037 0.00 0.00 0.00 1.40
2570 13123 6.810182 GCGAGTACAATAGAAGGTCAAGTTTA 59.190 38.462 0.00 0.00 0.00 2.01
2571 13124 5.638234 GCGAGTACAATAGAAGGTCAAGTTT 59.362 40.000 0.00 0.00 0.00 2.66
2572 13125 5.169295 GCGAGTACAATAGAAGGTCAAGTT 58.831 41.667 0.00 0.00 0.00 2.66
2573 13126 4.674623 CGCGAGTACAATAGAAGGTCAAGT 60.675 45.833 0.00 0.00 0.00 3.16
2574 13127 3.791887 CGCGAGTACAATAGAAGGTCAAG 59.208 47.826 0.00 0.00 0.00 3.02
2575 13128 3.441222 TCGCGAGTACAATAGAAGGTCAA 59.559 43.478 3.71 0.00 0.00 3.18
2576 13129 3.011818 TCGCGAGTACAATAGAAGGTCA 58.988 45.455 3.71 0.00 0.00 4.02
2577 13130 3.311871 TCTCGCGAGTACAATAGAAGGTC 59.688 47.826 33.33 0.00 0.00 3.85
2578 13131 3.276857 TCTCGCGAGTACAATAGAAGGT 58.723 45.455 33.33 0.00 0.00 3.50
2579 13132 3.965292 TCTCGCGAGTACAATAGAAGG 57.035 47.619 33.33 6.41 0.00 3.46
2580 13133 6.627690 TTTTTCTCGCGAGTACAATAGAAG 57.372 37.500 33.33 6.63 0.00 2.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.