Multiple sequence alignment - TraesCS7A01G206600

Loading Multiple Alignment...

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 TraesCS7A01G206600 chr7A 100.000 2393 0 0 1 2393 169039493 169037101 0.000000e+00 4420
1 TraesCS7A01G206600 chr7A 94.694 735 35 4 4 735 669491698 669490965 0.000000e+00 1138
2 TraesCS7A01G206600 chr7A 94.142 734 34 6 4 734 64206449 64205722 0.000000e+00 1109
3 TraesCS7A01G206600 chr7B 90.009 1071 86 14 734 1796 131957263 131956206 0.000000e+00 1365
4 TraesCS7A01G206600 chr7B 93.289 298 15 3 2097 2393 131956209 131955916 3.650000e-118 435
5 TraesCS7A01G206600 chr7B 85.859 297 35 6 1793 2087 528751272 528751563 2.310000e-80 309
6 TraesCS7A01G206600 chr3A 96.317 733 24 3 4 734 53892785 53892054 0.000000e+00 1201
7 TraesCS7A01G206600 chr3A 94.158 736 37 4 4 734 290364781 290364047 0.000000e+00 1116
8 TraesCS7A01G206600 chr3A 83.706 313 41 6 1793 2099 490622582 490622890 1.080000e-73 287
9 TraesCS7A01G206600 chr5A 95.424 743 31 3 1 741 510438417 510439158 0.000000e+00 1181
10 TraesCS7A01G206600 chr5A 89.098 266 24 4 1808 2071 476664742 476665004 2.290000e-85 326
11 TraesCS7A01G206600 chr1A 94.851 738 34 3 1 736 590564070 590564805 0.000000e+00 1149
12 TraesCS7A01G206600 chr7D 95.125 718 35 0 782 1499 167551474 167550757 0.000000e+00 1133
13 TraesCS7A01G206600 chr7D 91.919 297 20 2 2097 2393 167549557 167549265 1.710000e-111 412
14 TraesCS7A01G206600 chr7D 86.218 312 34 8 1793 2100 500618666 500618972 1.770000e-86 329
15 TraesCS7A01G206600 chr7D 94.536 183 10 0 1614 1796 167549736 167549554 1.400000e-72 283
16 TraesCS7A01G206600 chr7D 96.226 106 3 1 1497 1601 167550685 167550580 3.160000e-39 172
17 TraesCS7A01G206600 chr2A 94.437 737 36 5 1 734 154810384 154811118 0.000000e+00 1129
18 TraesCS7A01G206600 chr2A 93.775 739 37 5 4 736 586356089 586356824 0.000000e+00 1101
19 TraesCS7A01G206600 chr6A 94.166 737 38 5 1 734 98302743 98303477 0.000000e+00 1118
20 TraesCS7A01G206600 chr3D 86.364 308 39 3 1793 2099 29470565 29470260 1.370000e-87 333
21 TraesCS7A01G206600 chr3D 85.161 310 40 5 1793 2099 369413402 369413708 1.790000e-81 313
22 TraesCS7A01G206600 chr5D 86.395 294 35 4 1794 2086 317387086 317386797 1.380000e-82 316
23 TraesCS7A01G206600 chr5D 83.333 312 41 8 1792 2099 5155416 5155112 6.510000e-71 278
24 TraesCS7A01G206600 chr2B 85.209 311 32 13 1794 2099 1978443 1978744 8.310000e-80 307


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 TraesCS7A01G206600 chr7A 169037101 169039493 2392 True 4420 4420 100.0000 1 2393 1 chr7A.!!$R2 2392
1 TraesCS7A01G206600 chr7A 669490965 669491698 733 True 1138 1138 94.6940 4 735 1 chr7A.!!$R3 731
2 TraesCS7A01G206600 chr7A 64205722 64206449 727 True 1109 1109 94.1420 4 734 1 chr7A.!!$R1 730
3 TraesCS7A01G206600 chr7B 131955916 131957263 1347 True 900 1365 91.6490 734 2393 2 chr7B.!!$R1 1659
4 TraesCS7A01G206600 chr3A 53892054 53892785 731 True 1201 1201 96.3170 4 734 1 chr3A.!!$R1 730
5 TraesCS7A01G206600 chr3A 290364047 290364781 734 True 1116 1116 94.1580 4 734 1 chr3A.!!$R2 730
6 TraesCS7A01G206600 chr5A 510438417 510439158 741 False 1181 1181 95.4240 1 741 1 chr5A.!!$F2 740
7 TraesCS7A01G206600 chr1A 590564070 590564805 735 False 1149 1149 94.8510 1 736 1 chr1A.!!$F1 735
8 TraesCS7A01G206600 chr7D 167549265 167551474 2209 True 500 1133 94.4515 782 2393 4 chr7D.!!$R1 1611
9 TraesCS7A01G206600 chr2A 154810384 154811118 734 False 1129 1129 94.4370 1 734 1 chr2A.!!$F1 733
10 TraesCS7A01G206600 chr2A 586356089 586356824 735 False 1101 1101 93.7750 4 736 1 chr2A.!!$F2 732
11 TraesCS7A01G206600 chr6A 98302743 98303477 734 False 1118 1118 94.1660 1 734 1 chr6A.!!$F1 733

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
807 817 1.133482 TCCAGCGATCCTGATCCTACA 60.133 52.381 11.48 0.0 44.64 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 3011 0.105039 GAAGCCATGTACTCCCTCCG 59.895 60.0 0.0 0.0 0.0 4.63 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
315 320 6.837312 TCCTCTTTTCAACAAACCATAGAGA 58.163 36.000 0.00 0.00 29.44 3.10
322 327 8.924511 TTTCAACAAACCATAGAGATCTCTTT 57.075 30.769 29.54 19.46 40.93 2.52
332 337 7.786943 ACCATAGAGATCTCTTTCCACTATTGA 59.213 37.037 29.54 8.16 40.93 2.57
550 555 7.555554 CAGGAGACATGTTGATTAAGGAGAAAT 59.444 37.037 0.00 0.00 0.00 2.17
708 717 9.926751 CATGCACACTTATTAGTTCAAATAGAG 57.073 33.333 0.00 0.00 30.26 2.43
712 721 9.653287 CACACTTATTAGTTCAAATAGAGGTGA 57.347 33.333 0.00 0.00 30.26 4.02
741 751 6.356977 CACGTGCACACTTATAGTTTTTGAAG 59.643 38.462 18.64 0.00 0.00 3.02
743 753 6.573725 CGTGCACACTTATAGTTTTTGAAGAC 59.426 38.462 18.64 0.00 0.00 3.01
745 755 6.480651 TGCACACTTATAGTTTTTGAAGACGA 59.519 34.615 0.00 0.00 0.00 4.20
746 756 7.011576 TGCACACTTATAGTTTTTGAAGACGAA 59.988 33.333 0.00 0.00 0.00 3.85
772 782 2.892425 CGTCCGCCAGAAGCATCC 60.892 66.667 0.00 0.00 44.04 3.51
807 817 1.133482 TCCAGCGATCCTGATCCTACA 60.133 52.381 11.48 0.00 44.64 2.74
814 824 3.070159 CGATCCTGATCCTACATGGTGTT 59.930 47.826 0.00 0.00 37.07 3.32
821 831 1.555075 TCCTACATGGTGTTGGCTCTC 59.445 52.381 0.00 0.00 41.89 3.20
842 852 2.099638 CGAGATTCGTGCGACGGA 59.900 61.111 8.46 0.00 42.81 4.69
987 997 4.728772 ACCATCTCTGAAATCCAAACACA 58.271 39.130 0.00 0.00 0.00 3.72
1412 1423 0.670546 CGACGGCTGGTTCTTGTCAT 60.671 55.000 0.00 0.00 0.00 3.06
1426 1437 7.120579 TGGTTCTTGTCATTGACATGGTAATAC 59.879 37.037 24.39 16.52 42.40 1.89
1427 1438 7.336931 GGTTCTTGTCATTGACATGGTAATACT 59.663 37.037 24.39 0.00 42.40 2.12
1445 1456 8.305317 GGTAATACTACCTCTGAATATTTCGCT 58.695 37.037 0.00 0.00 43.92 4.93
1509 1594 2.165167 TGAATCGAACGGTAGGACTGT 58.835 47.619 0.00 0.00 39.91 3.55
1551 1636 7.770801 TCCATTCAGTTAGATTCAATACACG 57.229 36.000 0.00 0.00 0.00 4.49
1552 1637 6.761242 TCCATTCAGTTAGATTCAATACACGG 59.239 38.462 0.00 0.00 0.00 4.94
1744 2667 7.816995 AGATTATCAAGCGAATCTCTTATCACC 59.183 37.037 0.00 0.00 37.80 4.02
1747 2670 3.742433 AGCGAATCTCTTATCACCCAG 57.258 47.619 0.00 0.00 0.00 4.45
1766 2689 5.598830 ACCCAGTCTGTCGAATAGTTCATAT 59.401 40.000 0.00 0.00 0.00 1.78
1775 2698 9.144747 CTGTCGAATAGTTCATATAATTCAGGG 57.855 37.037 0.00 0.00 0.00 4.45
1796 2719 6.016555 AGGGCAAGGAAAATAAATGTGTACT 58.983 36.000 0.00 0.00 0.00 2.73
1797 2720 6.152831 AGGGCAAGGAAAATAAATGTGTACTC 59.847 38.462 0.00 0.00 0.00 2.59
1798 2721 6.330278 GGCAAGGAAAATAAATGTGTACTCC 58.670 40.000 0.00 0.00 0.00 3.85
1799 2722 6.330278 GCAAGGAAAATAAATGTGTACTCCC 58.670 40.000 0.00 0.00 0.00 4.30
1800 2723 6.152831 GCAAGGAAAATAAATGTGTACTCCCT 59.847 38.462 0.00 0.00 0.00 4.20
1801 2724 7.628580 GCAAGGAAAATAAATGTGTACTCCCTC 60.629 40.741 0.00 0.00 0.00 4.30
1802 2725 7.272144 AGGAAAATAAATGTGTACTCCCTCT 57.728 36.000 0.00 0.00 0.00 3.69
1803 2726 7.112779 AGGAAAATAAATGTGTACTCCCTCTG 58.887 38.462 0.00 0.00 0.00 3.35
1804 2727 6.884836 GGAAAATAAATGTGTACTCCCTCTGT 59.115 38.462 0.00 0.00 0.00 3.41
1805 2728 7.065923 GGAAAATAAATGTGTACTCCCTCTGTC 59.934 40.741 0.00 0.00 0.00 3.51
1806 2729 3.983044 AAATGTGTACTCCCTCTGTCC 57.017 47.619 0.00 0.00 0.00 4.02
1807 2730 2.623418 ATGTGTACTCCCTCTGTCCA 57.377 50.000 0.00 0.00 0.00 4.02
1808 2731 1.629043 TGTGTACTCCCTCTGTCCAC 58.371 55.000 0.00 0.00 0.00 4.02
1809 2732 0.526662 GTGTACTCCCTCTGTCCACG 59.473 60.000 0.00 0.00 0.00 4.94
1810 2733 0.402887 TGTACTCCCTCTGTCCACGA 59.597 55.000 0.00 0.00 0.00 4.35
1811 2734 1.202964 TGTACTCCCTCTGTCCACGAA 60.203 52.381 0.00 0.00 0.00 3.85
1812 2735 2.100989 GTACTCCCTCTGTCCACGAAT 58.899 52.381 0.00 0.00 0.00 3.34
1813 2736 2.526888 ACTCCCTCTGTCCACGAATA 57.473 50.000 0.00 0.00 0.00 1.75
1814 2737 2.816411 ACTCCCTCTGTCCACGAATAA 58.184 47.619 0.00 0.00 0.00 1.40
1815 2738 2.761208 ACTCCCTCTGTCCACGAATAAG 59.239 50.000 0.00 0.00 0.00 1.73
1816 2739 2.761208 CTCCCTCTGTCCACGAATAAGT 59.239 50.000 0.00 0.00 0.00 2.24
1817 2740 2.496070 TCCCTCTGTCCACGAATAAGTG 59.504 50.000 0.00 0.00 41.53 3.16
1818 2741 2.233922 CCCTCTGTCCACGAATAAGTGT 59.766 50.000 0.00 0.00 40.33 3.55
1819 2742 3.446161 CCCTCTGTCCACGAATAAGTGTA 59.554 47.826 0.00 0.00 40.33 2.90
1820 2743 4.421948 CCTCTGTCCACGAATAAGTGTAC 58.578 47.826 0.00 0.00 40.33 2.90
1821 2744 4.082408 CCTCTGTCCACGAATAAGTGTACA 60.082 45.833 0.00 0.00 38.37 2.90
1822 2745 5.394224 CCTCTGTCCACGAATAAGTGTACAT 60.394 44.000 0.00 0.00 39.59 2.29
1823 2746 6.183360 CCTCTGTCCACGAATAAGTGTACATA 60.183 42.308 0.00 0.00 39.59 2.29
1824 2747 7.342769 TCTGTCCACGAATAAGTGTACATAT 57.657 36.000 0.00 0.00 39.59 1.78
1825 2748 8.454570 TCTGTCCACGAATAAGTGTACATATA 57.545 34.615 0.00 0.00 39.59 0.86
1826 2749 8.565416 TCTGTCCACGAATAAGTGTACATATAG 58.435 37.037 0.00 0.00 39.59 1.31
1827 2750 8.454570 TGTCCACGAATAAGTGTACATATAGA 57.545 34.615 0.00 0.00 36.32 1.98
1828 2751 8.905850 TGTCCACGAATAAGTGTACATATAGAA 58.094 33.333 0.00 0.00 36.32 2.10
1829 2752 9.740239 GTCCACGAATAAGTGTACATATAGAAA 57.260 33.333 0.00 0.00 40.33 2.52
1864 2787 9.683069 CATATTATGGAGTGGAGTAAAAATTGC 57.317 33.333 0.00 0.00 0.00 3.56
1865 2788 7.716799 ATTATGGAGTGGAGTAAAAATTGCA 57.283 32.000 0.00 0.00 0.00 4.08
1866 2789 7.716799 TTATGGAGTGGAGTAAAAATTGCAT 57.283 32.000 0.00 0.00 0.00 3.96
1867 2790 6.610075 ATGGAGTGGAGTAAAAATTGCATT 57.390 33.333 0.00 0.00 0.00 3.56
1868 2791 5.782047 TGGAGTGGAGTAAAAATTGCATTG 58.218 37.500 0.00 0.00 0.00 2.82
1869 2792 5.170748 GGAGTGGAGTAAAAATTGCATTGG 58.829 41.667 0.00 0.00 0.00 3.16
1870 2793 5.151297 AGTGGAGTAAAAATTGCATTGGG 57.849 39.130 0.00 0.00 0.00 4.12
1871 2794 4.837860 AGTGGAGTAAAAATTGCATTGGGA 59.162 37.500 0.00 0.00 0.00 4.37
1872 2795 5.306678 AGTGGAGTAAAAATTGCATTGGGAA 59.693 36.000 0.00 0.00 0.00 3.97
1873 2796 5.639082 GTGGAGTAAAAATTGCATTGGGAAG 59.361 40.000 0.00 0.00 0.00 3.46
1874 2797 5.178061 GGAGTAAAAATTGCATTGGGAAGG 58.822 41.667 0.00 0.00 0.00 3.46
1875 2798 5.279960 GGAGTAAAAATTGCATTGGGAAGGT 60.280 40.000 0.00 0.00 0.00 3.50
1876 2799 5.550290 AGTAAAAATTGCATTGGGAAGGTG 58.450 37.500 0.00 0.00 0.00 4.00
1877 2800 2.477845 AAATTGCATTGGGAAGGTGC 57.522 45.000 0.00 0.00 39.26 5.01
1878 2801 1.350071 AATTGCATTGGGAAGGTGCA 58.650 45.000 0.00 0.00 46.15 4.57
1879 2802 4.615170 TGCATTGGGAAGGTGCAA 57.385 50.000 0.00 0.00 44.99 4.08
1880 2803 2.831859 TGCATTGGGAAGGTGCAAA 58.168 47.368 0.00 0.00 44.99 3.68
1881 2804 0.392336 TGCATTGGGAAGGTGCAAAC 59.608 50.000 0.00 0.00 44.99 2.93
1882 2805 0.320683 GCATTGGGAAGGTGCAAACC 60.321 55.000 0.00 0.00 38.68 3.27
1883 2806 1.047002 CATTGGGAAGGTGCAAACCA 58.953 50.000 0.00 0.00 0.00 3.67
1884 2807 1.624813 CATTGGGAAGGTGCAAACCAT 59.375 47.619 0.00 0.00 0.00 3.55
1885 2808 1.337118 TTGGGAAGGTGCAAACCATC 58.663 50.000 0.00 0.00 0.00 3.51
1886 2809 0.187117 TGGGAAGGTGCAAACCATCA 59.813 50.000 0.00 0.00 0.00 3.07
1887 2810 1.203162 TGGGAAGGTGCAAACCATCAT 60.203 47.619 0.00 0.00 0.00 2.45
1888 2811 1.478105 GGGAAGGTGCAAACCATCATC 59.522 52.381 0.00 0.00 0.00 2.92
1889 2812 2.450476 GGAAGGTGCAAACCATCATCT 58.550 47.619 0.00 0.00 0.00 2.90
1890 2813 2.424956 GGAAGGTGCAAACCATCATCTC 59.575 50.000 0.00 0.00 0.00 2.75
1891 2814 3.350833 GAAGGTGCAAACCATCATCTCT 58.649 45.455 0.00 0.00 0.00 3.10
1892 2815 2.996631 AGGTGCAAACCATCATCTCTC 58.003 47.619 0.00 0.00 0.00 3.20
1893 2816 2.575279 AGGTGCAAACCATCATCTCTCT 59.425 45.455 0.00 0.00 0.00 3.10
1894 2817 3.776969 AGGTGCAAACCATCATCTCTCTA 59.223 43.478 0.00 0.00 0.00 2.43
1895 2818 4.411540 AGGTGCAAACCATCATCTCTCTAT 59.588 41.667 0.00 0.00 0.00 1.98
1896 2819 5.104193 AGGTGCAAACCATCATCTCTCTATT 60.104 40.000 0.00 0.00 0.00 1.73
1897 2820 5.238214 GGTGCAAACCATCATCTCTCTATTC 59.762 44.000 0.00 0.00 0.00 1.75
1898 2821 6.054295 GTGCAAACCATCATCTCTCTATTCT 58.946 40.000 0.00 0.00 0.00 2.40
1899 2822 6.541641 GTGCAAACCATCATCTCTCTATTCTT 59.458 38.462 0.00 0.00 0.00 2.52
1900 2823 7.066766 GTGCAAACCATCATCTCTCTATTCTTT 59.933 37.037 0.00 0.00 0.00 2.52
1901 2824 8.267183 TGCAAACCATCATCTCTCTATTCTTTA 58.733 33.333 0.00 0.00 0.00 1.85
1902 2825 9.113838 GCAAACCATCATCTCTCTATTCTTTAA 57.886 33.333 0.00 0.00 0.00 1.52
1910 2833 9.447279 TCATCTCTCTATTCTTTAATTACCCCA 57.553 33.333 0.00 0.00 0.00 4.96
1911 2834 9.495572 CATCTCTCTATTCTTTAATTACCCCAC 57.504 37.037 0.00 0.00 0.00 4.61
1912 2835 8.030913 TCTCTCTATTCTTTAATTACCCCACC 57.969 38.462 0.00 0.00 0.00 4.61
1913 2836 7.849904 TCTCTCTATTCTTTAATTACCCCACCT 59.150 37.037 0.00 0.00 0.00 4.00
1914 2837 8.030913 TCTCTATTCTTTAATTACCCCACCTC 57.969 38.462 0.00 0.00 0.00 3.85
1915 2838 7.072076 TCTCTATTCTTTAATTACCCCACCTCC 59.928 40.741 0.00 0.00 0.00 4.30
1916 2839 5.806955 ATTCTTTAATTACCCCACCTCCA 57.193 39.130 0.00 0.00 0.00 3.86
1917 2840 5.602291 TTCTTTAATTACCCCACCTCCAA 57.398 39.130 0.00 0.00 0.00 3.53
1918 2841 5.806955 TCTTTAATTACCCCACCTCCAAT 57.193 39.130 0.00 0.00 0.00 3.16
1919 2842 5.515106 TCTTTAATTACCCCACCTCCAATG 58.485 41.667 0.00 0.00 0.00 2.82
1920 2843 5.254267 TCTTTAATTACCCCACCTCCAATGA 59.746 40.000 0.00 0.00 0.00 2.57
1921 2844 3.669939 AATTACCCCACCTCCAATGAG 57.330 47.619 0.00 0.00 38.42 2.90
1922 2845 0.623723 TTACCCCACCTCCAATGAGC 59.376 55.000 0.00 0.00 37.29 4.26
1923 2846 0.253160 TACCCCACCTCCAATGAGCT 60.253 55.000 0.00 0.00 37.29 4.09
1924 2847 0.253160 ACCCCACCTCCAATGAGCTA 60.253 55.000 0.00 0.00 37.29 3.32
1925 2848 0.918983 CCCCACCTCCAATGAGCTAA 59.081 55.000 0.00 0.00 37.29 3.09
1926 2849 1.133976 CCCCACCTCCAATGAGCTAAG 60.134 57.143 0.00 0.00 37.29 2.18
1927 2850 1.561542 CCCACCTCCAATGAGCTAAGT 59.438 52.381 0.00 0.00 37.29 2.24
1928 2851 2.420687 CCCACCTCCAATGAGCTAAGTC 60.421 54.545 0.00 0.00 37.29 3.01
1929 2852 2.420687 CCACCTCCAATGAGCTAAGTCC 60.421 54.545 0.00 0.00 37.29 3.85
1930 2853 2.237143 CACCTCCAATGAGCTAAGTCCA 59.763 50.000 0.00 0.00 37.29 4.02
1931 2854 3.118112 CACCTCCAATGAGCTAAGTCCAT 60.118 47.826 0.00 0.00 37.29 3.41
1932 2855 3.118112 ACCTCCAATGAGCTAAGTCCATG 60.118 47.826 0.00 0.00 37.29 3.66
1933 2856 3.118112 CCTCCAATGAGCTAAGTCCATGT 60.118 47.826 0.00 0.00 37.29 3.21
1934 2857 4.101585 CCTCCAATGAGCTAAGTCCATGTA 59.898 45.833 0.00 0.00 37.29 2.29
1935 2858 5.282055 TCCAATGAGCTAAGTCCATGTAG 57.718 43.478 0.00 0.00 0.00 2.74
1936 2859 4.962362 TCCAATGAGCTAAGTCCATGTAGA 59.038 41.667 0.00 0.00 0.00 2.59
1937 2860 5.425217 TCCAATGAGCTAAGTCCATGTAGAA 59.575 40.000 0.00 0.00 0.00 2.10
1938 2861 6.070251 TCCAATGAGCTAAGTCCATGTAGAAA 60.070 38.462 0.00 0.00 0.00 2.52
1939 2862 6.259608 CCAATGAGCTAAGTCCATGTAGAAAG 59.740 42.308 0.00 0.00 0.00 2.62
1940 2863 6.552445 ATGAGCTAAGTCCATGTAGAAAGT 57.448 37.500 0.00 0.00 0.00 2.66
1941 2864 5.724328 TGAGCTAAGTCCATGTAGAAAGTG 58.276 41.667 0.00 0.00 0.00 3.16
1942 2865 5.480422 TGAGCTAAGTCCATGTAGAAAGTGA 59.520 40.000 0.00 0.00 0.00 3.41
1943 2866 5.971763 AGCTAAGTCCATGTAGAAAGTGAG 58.028 41.667 0.00 0.00 0.00 3.51
1944 2867 5.105146 AGCTAAGTCCATGTAGAAAGTGAGG 60.105 44.000 0.00 0.00 0.00 3.86
1945 2868 5.105310 GCTAAGTCCATGTAGAAAGTGAGGA 60.105 44.000 0.00 0.00 0.00 3.71
1946 2869 5.413309 AAGTCCATGTAGAAAGTGAGGAG 57.587 43.478 0.00 0.00 0.00 3.69
1947 2870 4.678256 AGTCCATGTAGAAAGTGAGGAGA 58.322 43.478 0.00 0.00 0.00 3.71
1948 2871 4.464597 AGTCCATGTAGAAAGTGAGGAGAC 59.535 45.833 0.00 0.00 0.00 3.36
1949 2872 3.769844 TCCATGTAGAAAGTGAGGAGACC 59.230 47.826 0.00 0.00 0.00 3.85
1950 2873 3.515502 CCATGTAGAAAGTGAGGAGACCA 59.484 47.826 0.00 0.00 0.00 4.02
1951 2874 4.499183 CATGTAGAAAGTGAGGAGACCAC 58.501 47.826 0.00 0.00 34.89 4.16
1952 2875 3.572642 TGTAGAAAGTGAGGAGACCACA 58.427 45.455 0.00 0.00 37.01 4.17
1953 2876 4.160329 TGTAGAAAGTGAGGAGACCACAT 58.840 43.478 0.00 0.00 37.01 3.21
1954 2877 3.692257 AGAAAGTGAGGAGACCACATG 57.308 47.619 0.00 0.00 37.01 3.21
1955 2878 2.975489 AGAAAGTGAGGAGACCACATGT 59.025 45.455 0.00 0.00 37.01 3.21
1956 2879 3.392616 AGAAAGTGAGGAGACCACATGTT 59.607 43.478 0.00 0.00 37.01 2.71
1957 2880 2.847327 AGTGAGGAGACCACATGTTG 57.153 50.000 0.00 0.00 37.01 3.33
1974 2897 8.224389 CACATGTTGGATATTATTGGTCTTGA 57.776 34.615 0.00 0.00 0.00 3.02
1975 2898 8.853126 CACATGTTGGATATTATTGGTCTTGAT 58.147 33.333 0.00 0.00 0.00 2.57
1976 2899 9.425248 ACATGTTGGATATTATTGGTCTTGATT 57.575 29.630 0.00 0.00 0.00 2.57
1989 2912 8.768957 ATTGGTCTTGATTATCGTATGATGAG 57.231 34.615 7.74 0.00 35.99 2.90
1990 2913 7.524717 TGGTCTTGATTATCGTATGATGAGA 57.475 36.000 7.74 1.32 35.99 3.27
1991 2914 7.597386 TGGTCTTGATTATCGTATGATGAGAG 58.403 38.462 7.74 0.56 35.99 3.20
1992 2915 7.448469 TGGTCTTGATTATCGTATGATGAGAGA 59.552 37.037 7.74 2.72 35.99 3.10
1993 2916 7.967854 GGTCTTGATTATCGTATGATGAGAGAG 59.032 40.741 7.74 1.36 35.99 3.20
1994 2917 8.726068 GTCTTGATTATCGTATGATGAGAGAGA 58.274 37.037 7.74 3.50 35.99 3.10
1995 2918 9.289782 TCTTGATTATCGTATGATGAGAGAGAA 57.710 33.333 7.74 0.00 35.99 2.87
1998 2921 9.236006 TGATTATCGTATGATGAGAGAGAATCA 57.764 33.333 7.74 9.61 43.05 2.57
2003 2926 9.775854 ATCGTATGATGAGAGAGAATCATTTTT 57.224 29.630 0.00 0.00 39.89 1.94
2035 2958 9.696917 ACTTTAAAATGCATTAGAAAGTCTTGG 57.303 29.630 28.89 15.97 33.28 3.61
2036 2959 9.696917 CTTTAAAATGCATTAGAAAGTCTTGGT 57.303 29.630 24.62 2.75 0.00 3.67
2039 2962 7.759489 AAATGCATTAGAAAGTCTTGGTACA 57.241 32.000 13.39 0.00 0.00 2.90
2040 2963 6.743575 ATGCATTAGAAAGTCTTGGTACAC 57.256 37.500 0.00 0.00 39.29 2.90
2041 2964 5.865085 TGCATTAGAAAGTCTTGGTACACT 58.135 37.500 0.00 0.00 39.29 3.55
2042 2965 5.932303 TGCATTAGAAAGTCTTGGTACACTC 59.068 40.000 0.00 0.00 39.29 3.51
2043 2966 6.166982 GCATTAGAAAGTCTTGGTACACTCT 58.833 40.000 0.00 0.00 39.29 3.24
2044 2967 6.651225 GCATTAGAAAGTCTTGGTACACTCTT 59.349 38.462 0.00 0.00 39.29 2.85
2045 2968 7.173390 GCATTAGAAAGTCTTGGTACACTCTTT 59.827 37.037 0.00 0.00 39.29 2.52
2046 2969 9.057089 CATTAGAAAGTCTTGGTACACTCTTTT 57.943 33.333 0.00 0.00 39.29 2.27
2047 2970 9.628500 ATTAGAAAGTCTTGGTACACTCTTTTT 57.372 29.630 0.00 0.00 39.29 1.94
2070 2993 9.741647 TTTTTGGATAAATTTTGAATGCCAAAC 57.258 25.926 0.00 0.00 43.82 2.93
2071 2994 8.455903 TTTGGATAAATTTTGAATGCCAAACA 57.544 26.923 0.00 0.00 43.82 2.83
2072 2995 8.632906 TTGGATAAATTTTGAATGCCAAACAT 57.367 26.923 0.00 0.00 43.82 2.71
2073 2996 9.730705 TTGGATAAATTTTGAATGCCAAACATA 57.269 25.926 0.00 0.00 43.82 2.29
2074 2997 9.160496 TGGATAAATTTTGAATGCCAAACATAC 57.840 29.630 0.00 0.00 43.82 2.39
2075 2998 9.160496 GGATAAATTTTGAATGCCAAACATACA 57.840 29.630 0.00 0.00 43.82 2.29
2076 2999 9.971744 GATAAATTTTGAATGCCAAACATACAC 57.028 29.630 0.00 0.00 43.82 2.90
2077 3000 9.723601 ATAAATTTTGAATGCCAAACATACACT 57.276 25.926 0.00 0.00 43.82 3.55
2078 3001 8.449251 AAATTTTGAATGCCAAACATACACTT 57.551 26.923 0.00 0.00 43.82 3.16
2079 3002 9.553064 AAATTTTGAATGCCAAACATACACTTA 57.447 25.926 0.00 0.00 43.82 2.24
2080 3003 9.723601 AATTTTGAATGCCAAACATACACTTAT 57.276 25.926 0.00 0.00 43.82 1.73
2081 3004 9.723601 ATTTTGAATGCCAAACATACACTTATT 57.276 25.926 0.00 0.00 43.82 1.40
2082 3005 8.755696 TTTGAATGCCAAACATACACTTATTC 57.244 30.769 0.00 0.00 39.65 1.75
2083 3006 6.550843 TGAATGCCAAACATACACTTATTCG 58.449 36.000 0.00 0.00 38.34 3.34
2084 3007 6.150307 TGAATGCCAAACATACACTTATTCGT 59.850 34.615 0.00 0.00 38.34 3.85
2085 3008 5.289917 TGCCAAACATACACTTATTCGTG 57.710 39.130 0.00 0.00 40.67 4.35
2086 3009 4.998033 TGCCAAACATACACTTATTCGTGA 59.002 37.500 0.00 0.00 38.27 4.35
2087 3010 5.470437 TGCCAAACATACACTTATTCGTGAA 59.530 36.000 0.00 0.00 38.27 3.18
2088 3011 5.793457 GCCAAACATACACTTATTCGTGAAC 59.207 40.000 0.00 0.00 38.27 3.18
2089 3012 6.013085 CCAAACATACACTTATTCGTGAACG 58.987 40.000 0.00 0.00 38.27 3.95
2090 3013 5.773239 AACATACACTTATTCGTGAACGG 57.227 39.130 2.59 0.00 40.29 4.44
2091 3014 5.063180 ACATACACTTATTCGTGAACGGA 57.937 39.130 2.59 0.00 40.29 4.69
2092 3015 5.100259 ACATACACTTATTCGTGAACGGAG 58.900 41.667 2.59 0.00 40.29 4.63
2093 3016 2.955614 ACACTTATTCGTGAACGGAGG 58.044 47.619 2.59 0.00 40.29 4.30
2094 3017 2.268298 CACTTATTCGTGAACGGAGGG 58.732 52.381 2.59 0.00 40.29 4.30
2095 3018 2.094390 CACTTATTCGTGAACGGAGGGA 60.094 50.000 2.59 0.00 40.29 4.20
2096 3019 2.165845 ACTTATTCGTGAACGGAGGGAG 59.834 50.000 2.59 0.00 40.29 4.30
2097 3020 1.843368 TATTCGTGAACGGAGGGAGT 58.157 50.000 2.59 0.00 40.29 3.85
2098 3021 1.843368 ATTCGTGAACGGAGGGAGTA 58.157 50.000 2.59 0.00 40.29 2.59
2099 3022 0.883833 TTCGTGAACGGAGGGAGTAC 59.116 55.000 2.59 0.00 40.29 2.73
2100 3023 0.250858 TCGTGAACGGAGGGAGTACA 60.251 55.000 2.59 0.00 40.29 2.90
2101 3024 0.815734 CGTGAACGGAGGGAGTACAT 59.184 55.000 0.00 0.00 35.37 2.29
2153 3076 5.408299 CAGATTTCATCAACGTTACCACTCA 59.592 40.000 0.00 0.00 0.00 3.41
2159 3082 1.199097 CAACGTTACCACTCATTGCCC 59.801 52.381 0.00 0.00 0.00 5.36
2177 3100 1.269988 CCCGTCTATCCTGCAGATGTG 60.270 57.143 17.39 0.00 36.33 3.21
2189 3112 1.800655 GCAGATGTGCCAGTCGACTAG 60.801 57.143 19.57 12.85 44.72 2.57
2190 3113 1.474478 CAGATGTGCCAGTCGACTAGT 59.526 52.381 19.57 0.00 0.00 2.57
2191 3114 2.683362 CAGATGTGCCAGTCGACTAGTA 59.317 50.000 19.57 7.89 0.00 1.82
2201 3124 5.757320 GCCAGTCGACTAGTACTACTCAATA 59.243 44.000 19.57 0.00 0.00 1.90
2257 3180 2.350522 CTCCATTCAACGACCTCCAAG 58.649 52.381 0.00 0.00 0.00 3.61
2272 3195 1.032014 CCAAGTGTCACCAACAAGGG 58.968 55.000 0.00 0.00 43.89 3.95
2340 3263 6.831868 TCAATGGTTGATGATCATTGATGTCT 59.168 34.615 10.14 0.00 46.49 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.935808 ACTACACATTTCTTTAAGGGCTCG 59.064 41.667 0.00 0.00 0.00 5.03
231 235 5.191426 ACTGCATAGAATCAGCTGTGAAAT 58.809 37.500 14.67 0.00 38.69 2.17
315 320 6.013379 TGTCAACCTCAATAGTGGAAAGAGAT 60.013 38.462 0.00 0.00 32.71 2.75
322 327 3.901222 TGAGTGTCAACCTCAATAGTGGA 59.099 43.478 0.00 0.00 36.07 4.02
367 372 2.097466 CGTTTCACTGCCAACAAACTCT 59.903 45.455 0.00 0.00 0.00 3.24
731 741 4.854839 CGTGGTTTTTCGTCTTCAAAAACT 59.145 37.500 16.78 0.00 46.30 2.66
732 742 4.489682 GCGTGGTTTTTCGTCTTCAAAAAC 60.490 41.667 11.61 11.61 46.33 2.43
741 751 4.484297 GACGCGTGGTTTTTCGTC 57.516 55.556 20.70 0.00 43.23 4.20
743 753 2.127906 CGGACGCGTGGTTTTTCG 60.128 61.111 20.70 0.00 0.00 3.46
745 755 3.956317 GGCGGACGCGTGGTTTTT 61.956 61.111 20.70 0.00 43.06 1.94
769 779 0.389948 GAGTGGTTCGCTGTTCGGAT 60.390 55.000 0.00 0.00 39.05 4.18
772 782 1.284982 CTGGAGTGGTTCGCTGTTCG 61.285 60.000 0.00 0.00 40.15 3.95
807 817 2.045926 GCGGAGAGCCAACACCAT 60.046 61.111 0.00 0.00 40.81 3.55
842 852 1.004918 CCAGCGAACGTTCTCCCTT 60.005 57.895 24.80 0.00 0.00 3.95
981 991 5.505181 ACATTCTGGAGGAGTATGTGTTT 57.495 39.130 0.00 0.00 40.24 2.83
987 997 4.014273 AGGGAACATTCTGGAGGAGTAT 57.986 45.455 0.00 0.00 0.00 2.12
1359 1370 3.702048 CGGTGGAAGCCCTCGGAA 61.702 66.667 0.00 0.00 0.00 4.30
1393 1404 0.670546 ATGACAAGAACCAGCCGTCG 60.671 55.000 0.00 0.00 0.00 5.12
1397 1408 2.229792 TGTCAATGACAAGAACCAGCC 58.770 47.619 14.37 0.00 39.78 4.85
1398 1409 3.366679 CCATGTCAATGACAAGAACCAGC 60.367 47.826 20.64 0.00 45.96 4.85
1426 1437 7.539712 TTGAAAGCGAAATATTCAGAGGTAG 57.460 36.000 0.00 0.00 34.80 3.18
1427 1438 7.768582 TCATTGAAAGCGAAATATTCAGAGGTA 59.231 33.333 0.00 0.00 34.80 3.08
1445 1456 9.872721 TCAATAGCATGCTAAAAATCATTGAAA 57.127 25.926 30.06 11.79 31.73 2.69
1509 1594 3.601435 TGGAAACAAACTCGACAACTCA 58.399 40.909 0.00 0.00 37.44 3.41
1551 1636 2.166664 TGGGCTTACACACAAACAAACC 59.833 45.455 0.00 0.00 0.00 3.27
1552 1637 3.512033 TGGGCTTACACACAAACAAAC 57.488 42.857 0.00 0.00 0.00 2.93
1724 2645 3.450817 TGGGTGATAAGAGATTCGCTTGA 59.549 43.478 12.29 0.00 0.00 3.02
1744 2667 9.698309 AATTATATGAACTATTCGACAGACTGG 57.302 33.333 7.51 0.00 0.00 4.00
1766 2689 8.040132 CACATTTATTTTCCTTGCCCTGAATTA 58.960 33.333 0.00 0.00 0.00 1.40
1775 2698 6.152831 AGGGAGTACACATTTATTTTCCTTGC 59.847 38.462 0.00 0.00 0.00 4.01
1796 2719 2.496070 CACTTATTCGTGGACAGAGGGA 59.504 50.000 0.00 0.00 0.00 4.20
1797 2720 2.233922 ACACTTATTCGTGGACAGAGGG 59.766 50.000 0.00 0.00 39.19 4.30
1798 2721 3.594603 ACACTTATTCGTGGACAGAGG 57.405 47.619 0.00 0.00 39.19 3.69
1803 2726 9.740239 TTTCTATATGTACACTTATTCGTGGAC 57.260 33.333 0.00 0.00 46.62 4.02
1838 2761 9.683069 GCAATTTTTACTCCACTCCATAATATG 57.317 33.333 0.00 0.00 0.00 1.78
1839 2762 9.420118 TGCAATTTTTACTCCACTCCATAATAT 57.580 29.630 0.00 0.00 0.00 1.28
1840 2763 8.815565 TGCAATTTTTACTCCACTCCATAATA 57.184 30.769 0.00 0.00 0.00 0.98
1841 2764 7.716799 TGCAATTTTTACTCCACTCCATAAT 57.283 32.000 0.00 0.00 0.00 1.28
1842 2765 7.716799 ATGCAATTTTTACTCCACTCCATAA 57.283 32.000 0.00 0.00 0.00 1.90
1843 2766 7.363705 CCAATGCAATTTTTACTCCACTCCATA 60.364 37.037 0.00 0.00 31.22 2.74
1844 2767 6.400568 CAATGCAATTTTTACTCCACTCCAT 58.599 36.000 0.00 0.00 31.22 3.41
1845 2768 5.279406 CCAATGCAATTTTTACTCCACTCCA 60.279 40.000 0.00 0.00 31.22 3.86
1846 2769 5.170748 CCAATGCAATTTTTACTCCACTCC 58.829 41.667 0.00 0.00 31.22 3.85
1847 2770 5.047377 TCCCAATGCAATTTTTACTCCACTC 60.047 40.000 0.00 0.00 31.22 3.51
1848 2771 4.837860 TCCCAATGCAATTTTTACTCCACT 59.162 37.500 0.00 0.00 31.22 4.00
1849 2772 5.146010 TCCCAATGCAATTTTTACTCCAC 57.854 39.130 0.00 0.00 31.22 4.02
1850 2773 5.279910 CCTTCCCAATGCAATTTTTACTCCA 60.280 40.000 0.00 0.00 31.22 3.86
1851 2774 5.178061 CCTTCCCAATGCAATTTTTACTCC 58.822 41.667 0.00 0.00 31.22 3.85
1852 2775 5.639082 CACCTTCCCAATGCAATTTTTACTC 59.361 40.000 0.00 0.00 31.22 2.59
1853 2776 5.550290 CACCTTCCCAATGCAATTTTTACT 58.450 37.500 0.00 0.00 31.22 2.24
1854 2777 4.154015 GCACCTTCCCAATGCAATTTTTAC 59.846 41.667 0.00 0.00 39.23 2.01
1855 2778 4.202398 TGCACCTTCCCAATGCAATTTTTA 60.202 37.500 0.00 0.00 45.96 1.52
1856 2779 3.148412 GCACCTTCCCAATGCAATTTTT 58.852 40.909 0.00 0.00 39.23 1.94
1857 2780 2.106166 TGCACCTTCCCAATGCAATTTT 59.894 40.909 0.00 0.00 45.96 1.82
1858 2781 1.698532 TGCACCTTCCCAATGCAATTT 59.301 42.857 0.00 0.00 45.96 1.82
1859 2782 1.350071 TGCACCTTCCCAATGCAATT 58.650 45.000 0.00 0.00 45.96 2.32
1860 2783 3.070115 TGCACCTTCCCAATGCAAT 57.930 47.368 0.00 0.00 45.96 3.56
1861 2784 4.615170 TGCACCTTCCCAATGCAA 57.385 50.000 0.00 0.00 45.96 4.08
1863 2786 0.320683 GGTTTGCACCTTCCCAATGC 60.321 55.000 0.00 0.00 40.44 3.56
1864 2787 1.047002 TGGTTTGCACCTTCCCAATG 58.953 50.000 0.00 0.00 44.61 2.82
1865 2788 1.901833 GATGGTTTGCACCTTCCCAAT 59.098 47.619 0.00 0.00 44.61 3.16
1866 2789 1.337118 GATGGTTTGCACCTTCCCAA 58.663 50.000 0.00 0.00 44.61 4.12
1867 2790 0.187117 TGATGGTTTGCACCTTCCCA 59.813 50.000 6.75 0.32 43.72 4.37
1868 2791 1.478105 GATGATGGTTTGCACCTTCCC 59.522 52.381 6.75 0.00 43.72 3.97
1869 2792 2.424956 GAGATGATGGTTTGCACCTTCC 59.575 50.000 6.75 0.00 43.72 3.46
1870 2793 3.350833 AGAGATGATGGTTTGCACCTTC 58.649 45.455 0.00 0.00 44.61 3.46
1871 2794 3.009916 AGAGAGATGATGGTTTGCACCTT 59.990 43.478 0.00 0.00 44.61 3.50
1872 2795 2.575279 AGAGAGATGATGGTTTGCACCT 59.425 45.455 0.00 0.00 44.61 4.00
1873 2796 2.996631 AGAGAGATGATGGTTTGCACC 58.003 47.619 0.00 0.00 44.56 5.01
1874 2797 6.054295 AGAATAGAGAGATGATGGTTTGCAC 58.946 40.000 0.00 0.00 0.00 4.57
1875 2798 6.244552 AGAATAGAGAGATGATGGTTTGCA 57.755 37.500 0.00 0.00 0.00 4.08
1876 2799 7.565323 AAAGAATAGAGAGATGATGGTTTGC 57.435 36.000 0.00 0.00 0.00 3.68
1884 2807 9.447279 TGGGGTAATTAAAGAATAGAGAGATGA 57.553 33.333 0.00 0.00 0.00 2.92
1885 2808 9.495572 GTGGGGTAATTAAAGAATAGAGAGATG 57.504 37.037 0.00 0.00 0.00 2.90
1886 2809 8.661345 GGTGGGGTAATTAAAGAATAGAGAGAT 58.339 37.037 0.00 0.00 0.00 2.75
1887 2810 7.849904 AGGTGGGGTAATTAAAGAATAGAGAGA 59.150 37.037 0.00 0.00 0.00 3.10
1888 2811 8.035448 AGGTGGGGTAATTAAAGAATAGAGAG 57.965 38.462 0.00 0.00 0.00 3.20
1889 2812 7.072076 GGAGGTGGGGTAATTAAAGAATAGAGA 59.928 40.741 0.00 0.00 0.00 3.10
1890 2813 7.147373 TGGAGGTGGGGTAATTAAAGAATAGAG 60.147 40.741 0.00 0.00 0.00 2.43
1891 2814 6.679303 TGGAGGTGGGGTAATTAAAGAATAGA 59.321 38.462 0.00 0.00 0.00 1.98
1892 2815 6.906848 TGGAGGTGGGGTAATTAAAGAATAG 58.093 40.000 0.00 0.00 0.00 1.73
1893 2816 6.911993 TGGAGGTGGGGTAATTAAAGAATA 57.088 37.500 0.00 0.00 0.00 1.75
1894 2817 5.806955 TGGAGGTGGGGTAATTAAAGAAT 57.193 39.130 0.00 0.00 0.00 2.40
1895 2818 5.602291 TTGGAGGTGGGGTAATTAAAGAA 57.398 39.130 0.00 0.00 0.00 2.52
1896 2819 5.254267 TCATTGGAGGTGGGGTAATTAAAGA 59.746 40.000 0.00 0.00 0.00 2.52
1897 2820 5.515106 TCATTGGAGGTGGGGTAATTAAAG 58.485 41.667 0.00 0.00 0.00 1.85
1898 2821 5.515106 CTCATTGGAGGTGGGGTAATTAAA 58.485 41.667 0.00 0.00 37.51 1.52
1899 2822 4.630184 GCTCATTGGAGGTGGGGTAATTAA 60.630 45.833 0.00 0.00 41.67 1.40
1900 2823 3.117663 GCTCATTGGAGGTGGGGTAATTA 60.118 47.826 0.00 0.00 41.67 1.40
1901 2824 2.358195 GCTCATTGGAGGTGGGGTAATT 60.358 50.000 0.00 0.00 41.67 1.40
1902 2825 1.215423 GCTCATTGGAGGTGGGGTAAT 59.785 52.381 0.00 0.00 41.67 1.89
1903 2826 0.623723 GCTCATTGGAGGTGGGGTAA 59.376 55.000 0.00 0.00 41.67 2.85
1904 2827 2.307153 GCTCATTGGAGGTGGGGTA 58.693 57.895 0.00 0.00 41.67 3.69
1905 2828 3.090765 GCTCATTGGAGGTGGGGT 58.909 61.111 0.00 0.00 41.67 4.95
1911 2834 3.118112 ACATGGACTTAGCTCATTGGAGG 60.118 47.826 0.00 0.00 41.67 4.30
1912 2835 4.148128 ACATGGACTTAGCTCATTGGAG 57.852 45.455 0.00 0.00 44.33 3.86
1913 2836 4.962362 TCTACATGGACTTAGCTCATTGGA 59.038 41.667 0.00 0.00 0.00 3.53
1914 2837 5.282055 TCTACATGGACTTAGCTCATTGG 57.718 43.478 0.00 0.00 0.00 3.16
1915 2838 6.820656 ACTTTCTACATGGACTTAGCTCATTG 59.179 38.462 0.00 0.00 0.00 2.82
1916 2839 6.820656 CACTTTCTACATGGACTTAGCTCATT 59.179 38.462 0.00 0.00 0.00 2.57
1917 2840 6.155221 TCACTTTCTACATGGACTTAGCTCAT 59.845 38.462 0.00 0.00 0.00 2.90
1918 2841 5.480422 TCACTTTCTACATGGACTTAGCTCA 59.520 40.000 0.00 0.00 0.00 4.26
1919 2842 5.967088 TCACTTTCTACATGGACTTAGCTC 58.033 41.667 0.00 0.00 0.00 4.09
1920 2843 5.105146 CCTCACTTTCTACATGGACTTAGCT 60.105 44.000 0.00 0.00 0.00 3.32
1921 2844 5.105310 TCCTCACTTTCTACATGGACTTAGC 60.105 44.000 0.00 0.00 0.00 3.09
1922 2845 6.378564 TCTCCTCACTTTCTACATGGACTTAG 59.621 42.308 0.00 0.00 0.00 2.18
1923 2846 6.153000 GTCTCCTCACTTTCTACATGGACTTA 59.847 42.308 0.00 0.00 0.00 2.24
1924 2847 5.046950 GTCTCCTCACTTTCTACATGGACTT 60.047 44.000 0.00 0.00 0.00 3.01
1925 2848 4.464597 GTCTCCTCACTTTCTACATGGACT 59.535 45.833 0.00 0.00 0.00 3.85
1926 2849 4.382147 GGTCTCCTCACTTTCTACATGGAC 60.382 50.000 0.00 0.00 0.00 4.02
1927 2850 3.769844 GGTCTCCTCACTTTCTACATGGA 59.230 47.826 0.00 0.00 0.00 3.41
1928 2851 3.515502 TGGTCTCCTCACTTTCTACATGG 59.484 47.826 0.00 0.00 0.00 3.66
1929 2852 4.021104 TGTGGTCTCCTCACTTTCTACATG 60.021 45.833 0.00 0.00 36.21 3.21
1930 2853 4.160329 TGTGGTCTCCTCACTTTCTACAT 58.840 43.478 0.00 0.00 36.21 2.29
1931 2854 3.572642 TGTGGTCTCCTCACTTTCTACA 58.427 45.455 0.00 0.00 36.21 2.74
1932 2855 4.021016 ACATGTGGTCTCCTCACTTTCTAC 60.021 45.833 0.00 0.00 36.21 2.59
1933 2856 4.160329 ACATGTGGTCTCCTCACTTTCTA 58.840 43.478 0.00 0.00 36.21 2.10
1934 2857 2.975489 ACATGTGGTCTCCTCACTTTCT 59.025 45.455 0.00 0.00 36.21 2.52
1935 2858 3.409026 ACATGTGGTCTCCTCACTTTC 57.591 47.619 0.00 0.00 36.21 2.62
1936 2859 3.480470 CAACATGTGGTCTCCTCACTTT 58.520 45.455 0.00 0.00 36.21 2.66
1937 2860 2.224621 CCAACATGTGGTCTCCTCACTT 60.225 50.000 0.00 0.00 43.20 3.16
1938 2861 1.349026 CCAACATGTGGTCTCCTCACT 59.651 52.381 0.00 0.00 43.20 3.41
1939 2862 1.813513 CCAACATGTGGTCTCCTCAC 58.186 55.000 0.00 0.00 43.20 3.51
1949 2872 8.224389 TCAAGACCAATAATATCCAACATGTG 57.776 34.615 0.00 0.00 0.00 3.21
1950 2873 9.425248 AATCAAGACCAATAATATCCAACATGT 57.575 29.630 0.00 0.00 0.00 3.21
1963 2886 9.860898 CTCATCATACGATAATCAAGACCAATA 57.139 33.333 0.00 0.00 0.00 1.90
1964 2887 8.588472 TCTCATCATACGATAATCAAGACCAAT 58.412 33.333 0.00 0.00 0.00 3.16
1965 2888 7.951591 TCTCATCATACGATAATCAAGACCAA 58.048 34.615 0.00 0.00 0.00 3.67
1966 2889 7.448469 TCTCTCATCATACGATAATCAAGACCA 59.552 37.037 0.00 0.00 0.00 4.02
1967 2890 7.821652 TCTCTCATCATACGATAATCAAGACC 58.178 38.462 0.00 0.00 0.00 3.85
1968 2891 8.726068 TCTCTCTCATCATACGATAATCAAGAC 58.274 37.037 0.00 0.00 0.00 3.01
1969 2892 8.854614 TCTCTCTCATCATACGATAATCAAGA 57.145 34.615 0.00 0.00 0.00 3.02
1972 2895 9.236006 TGATTCTCTCTCATCATACGATAATCA 57.764 33.333 0.00 0.00 30.02 2.57
1977 2900 9.775854 AAAAATGATTCTCTCTCATCATACGAT 57.224 29.630 0.00 0.00 38.88 3.73
2009 2932 9.696917 CCAAGACTTTCTAATGCATTTTAAAGT 57.303 29.630 31.46 31.46 36.79 2.66
2010 2933 9.696917 ACCAAGACTTTCTAATGCATTTTAAAG 57.303 29.630 27.71 27.71 0.00 1.85
2013 2936 9.290988 TGTACCAAGACTTTCTAATGCATTTTA 57.709 29.630 18.75 3.11 0.00 1.52
2014 2937 8.082242 GTGTACCAAGACTTTCTAATGCATTTT 58.918 33.333 18.75 0.00 0.00 1.82
2015 2938 7.448469 AGTGTACCAAGACTTTCTAATGCATTT 59.552 33.333 18.75 0.00 0.00 2.32
2016 2939 6.942576 AGTGTACCAAGACTTTCTAATGCATT 59.057 34.615 17.56 17.56 0.00 3.56
2017 2940 6.476378 AGTGTACCAAGACTTTCTAATGCAT 58.524 36.000 0.00 0.00 0.00 3.96
2018 2941 5.865085 AGTGTACCAAGACTTTCTAATGCA 58.135 37.500 0.00 0.00 0.00 3.96
2019 2942 6.166982 AGAGTGTACCAAGACTTTCTAATGC 58.833 40.000 0.00 0.00 27.27 3.56
2020 2943 8.608844 AAAGAGTGTACCAAGACTTTCTAATG 57.391 34.615 0.00 0.00 27.27 1.90
2021 2944 9.628500 AAAAAGAGTGTACCAAGACTTTCTAAT 57.372 29.630 0.00 0.00 27.27 1.73
2044 2967 9.741647 GTTTGGCATTCAAAATTTATCCAAAAA 57.258 25.926 14.37 0.76 45.74 1.94
2045 2968 8.906867 TGTTTGGCATTCAAAATTTATCCAAAA 58.093 25.926 14.37 7.51 45.74 2.44
2046 2969 8.455903 TGTTTGGCATTCAAAATTTATCCAAA 57.544 26.923 0.00 0.00 45.74 3.28
2047 2970 8.632906 ATGTTTGGCATTCAAAATTTATCCAA 57.367 26.923 0.00 0.00 45.74 3.53
2048 2971 9.160496 GTATGTTTGGCATTCAAAATTTATCCA 57.840 29.630 0.00 0.00 45.74 3.41
2049 2972 9.160496 TGTATGTTTGGCATTCAAAATTTATCC 57.840 29.630 0.00 0.00 45.74 2.59
2050 2973 9.971744 GTGTATGTTTGGCATTCAAAATTTATC 57.028 29.630 0.00 0.00 45.74 1.75
2051 2974 9.723601 AGTGTATGTTTGGCATTCAAAATTTAT 57.276 25.926 0.00 0.00 45.74 1.40
2052 2975 9.553064 AAGTGTATGTTTGGCATTCAAAATTTA 57.447 25.926 0.00 0.00 45.74 1.40
2053 2976 8.449251 AAGTGTATGTTTGGCATTCAAAATTT 57.551 26.923 0.00 0.00 45.74 1.82
2054 2977 9.723601 ATAAGTGTATGTTTGGCATTCAAAATT 57.276 25.926 0.00 0.00 45.74 1.82
2055 2978 9.723601 AATAAGTGTATGTTTGGCATTCAAAAT 57.276 25.926 0.00 0.00 45.74 1.82
2056 2979 9.202273 GAATAAGTGTATGTTTGGCATTCAAAA 57.798 29.630 0.00 0.00 45.74 2.44
2057 2980 7.540400 CGAATAAGTGTATGTTTGGCATTCAAA 59.460 33.333 0.00 0.00 42.50 2.69
2058 2981 7.026562 CGAATAAGTGTATGTTTGGCATTCAA 58.973 34.615 0.00 0.00 36.78 2.69
2059 2982 6.150307 ACGAATAAGTGTATGTTTGGCATTCA 59.850 34.615 0.00 0.00 38.94 2.57
2060 2983 6.468956 CACGAATAAGTGTATGTTTGGCATTC 59.531 38.462 0.00 0.00 37.35 2.67
2061 2984 6.150307 TCACGAATAAGTGTATGTTTGGCATT 59.850 34.615 0.00 0.00 42.40 3.56
2062 2985 5.645929 TCACGAATAAGTGTATGTTTGGCAT 59.354 36.000 0.00 0.00 42.40 4.40
2063 2986 4.998033 TCACGAATAAGTGTATGTTTGGCA 59.002 37.500 0.00 0.00 42.40 4.92
2064 2987 5.539582 TCACGAATAAGTGTATGTTTGGC 57.460 39.130 0.00 0.00 42.40 4.52
2065 2988 6.013085 CGTTCACGAATAAGTGTATGTTTGG 58.987 40.000 0.00 0.00 42.40 3.28
2066 2989 6.013085 CCGTTCACGAATAAGTGTATGTTTG 58.987 40.000 0.00 0.00 42.40 2.93
2067 2990 5.927689 TCCGTTCACGAATAAGTGTATGTTT 59.072 36.000 0.00 0.00 42.40 2.83
2068 2991 5.472148 TCCGTTCACGAATAAGTGTATGTT 58.528 37.500 0.00 0.00 42.40 2.71
2069 2992 5.063180 TCCGTTCACGAATAAGTGTATGT 57.937 39.130 0.00 0.00 42.40 2.29
2070 2993 4.503007 CCTCCGTTCACGAATAAGTGTATG 59.497 45.833 0.00 0.00 42.40 2.39
2071 2994 4.441079 CCCTCCGTTCACGAATAAGTGTAT 60.441 45.833 0.00 0.00 42.40 2.29
2072 2995 3.119388 CCCTCCGTTCACGAATAAGTGTA 60.119 47.826 0.00 0.00 42.40 2.90
2073 2996 2.353406 CCCTCCGTTCACGAATAAGTGT 60.353 50.000 0.00 0.00 42.40 3.55
2074 2997 2.094390 TCCCTCCGTTCACGAATAAGTG 60.094 50.000 0.00 0.00 43.02 3.16
2075 2998 2.165845 CTCCCTCCGTTCACGAATAAGT 59.834 50.000 0.00 0.00 43.02 2.24
2076 2999 2.165845 ACTCCCTCCGTTCACGAATAAG 59.834 50.000 0.00 0.00 43.02 1.73
2077 3000 2.173519 ACTCCCTCCGTTCACGAATAA 58.826 47.619 0.00 0.00 43.02 1.40
2078 3001 1.843368 ACTCCCTCCGTTCACGAATA 58.157 50.000 0.00 0.00 43.02 1.75
2079 3002 1.475682 GTACTCCCTCCGTTCACGAAT 59.524 52.381 0.00 0.00 43.02 3.34
2080 3003 0.883833 GTACTCCCTCCGTTCACGAA 59.116 55.000 0.00 0.00 43.02 3.85
2081 3004 0.250858 TGTACTCCCTCCGTTCACGA 60.251 55.000 0.00 0.00 43.02 4.35
2082 3005 0.815734 ATGTACTCCCTCCGTTCACG 59.184 55.000 0.00 0.00 39.44 4.35
2083 3006 1.134788 CCATGTACTCCCTCCGTTCAC 60.135 57.143 0.00 0.00 0.00 3.18
2084 3007 1.191535 CCATGTACTCCCTCCGTTCA 58.808 55.000 0.00 0.00 0.00 3.18
2085 3008 0.179081 GCCATGTACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
2086 3009 0.617820 AGCCATGTACTCCCTCCGTT 60.618 55.000 0.00 0.00 0.00 4.44
2087 3010 0.617820 AAGCCATGTACTCCCTCCGT 60.618 55.000 0.00 0.00 0.00 4.69
2088 3011 0.105039 GAAGCCATGTACTCCCTCCG 59.895 60.000 0.00 0.00 0.00 4.63
2089 3012 1.414550 GAGAAGCCATGTACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
2090 3013 2.393646 AGAGAAGCCATGTACTCCCTC 58.606 52.381 0.00 0.51 0.00 4.30
2091 3014 2.503356 CAAGAGAAGCCATGTACTCCCT 59.497 50.000 0.00 0.00 0.00 4.20
2092 3015 2.420687 CCAAGAGAAGCCATGTACTCCC 60.421 54.545 0.00 0.00 0.00 4.30
2093 3016 2.237392 ACCAAGAGAAGCCATGTACTCC 59.763 50.000 0.00 0.00 0.00 3.85
2094 3017 3.618690 ACCAAGAGAAGCCATGTACTC 57.381 47.619 0.00 0.00 0.00 2.59
2095 3018 4.777896 TCTTACCAAGAGAAGCCATGTACT 59.222 41.667 0.00 0.00 32.71 2.73
2096 3019 5.086104 TCTTACCAAGAGAAGCCATGTAC 57.914 43.478 0.00 0.00 32.71 2.90
2097 3020 5.755409 TTCTTACCAAGAGAAGCCATGTA 57.245 39.130 0.00 0.00 39.03 2.29
2098 3021 4.640771 TTCTTACCAAGAGAAGCCATGT 57.359 40.909 0.00 0.00 39.03 3.21
2099 3022 4.761739 TGTTTCTTACCAAGAGAAGCCATG 59.238 41.667 0.00 0.00 39.03 3.66
2100 3023 4.985538 TGTTTCTTACCAAGAGAAGCCAT 58.014 39.130 0.00 0.00 39.03 4.40
2101 3024 4.431416 TGTTTCTTACCAAGAGAAGCCA 57.569 40.909 0.00 0.00 39.03 4.75
2153 3076 0.107456 CTGCAGGATAGACGGGCAAT 59.893 55.000 5.57 0.00 33.58 3.56
2159 3082 1.495878 GCACATCTGCAGGATAGACG 58.504 55.000 15.13 0.00 43.62 4.18
2177 3100 3.529533 TGAGTAGTACTAGTCGACTGGC 58.470 50.000 28.12 12.96 38.12 4.85
2189 3112 5.472137 CAGAGGAGAGGCTATTGAGTAGTAC 59.528 48.000 0.00 0.00 32.72 2.73
2190 3113 5.626142 CAGAGGAGAGGCTATTGAGTAGTA 58.374 45.833 0.00 0.00 32.72 1.82
2191 3114 4.469657 CAGAGGAGAGGCTATTGAGTAGT 58.530 47.826 0.00 0.00 32.72 2.73
2232 3155 1.079405 GTCGTTGAATGGAGGCCGA 60.079 57.895 0.00 0.00 0.00 5.54
2234 3157 0.744771 GAGGTCGTTGAATGGAGGCC 60.745 60.000 0.00 0.00 0.00 5.19
2241 3164 2.104111 TGACACTTGGAGGTCGTTGAAT 59.896 45.455 0.00 0.00 36.83 2.57
2257 3180 0.465460 TGCTCCCTTGTTGGTGACAC 60.465 55.000 0.00 0.00 42.67 3.67
2340 3263 0.175760 GAGGCGATGTTGGAGCAGTA 59.824 55.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.