Multiple sequence alignment - TraesCS6A01G258100

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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 TraesCS6A01G258100 chr6A 100.000 2549 0 0 1 2549 480458920 480461468 0.000000e+00 4708.0
1 TraesCS6A01G258100 chr6A 96.429 56 2 0 1938 1993 117401189 117401244 2.700000e-15 93.5
2 TraesCS6A01G258100 chr2D 93.586 1294 59 4 591 1860 177444317 177443024 0.000000e+00 1908.0
3 TraesCS6A01G258100 chr2D 96.828 536 17 0 2014 2549 177443026 177442491 0.000000e+00 896.0
4 TraesCS6A01G258100 chr2D 93.585 265 15 2 590 853 528445944 528446207 6.610000e-106 394.0
5 TraesCS6A01G258100 chr2D 93.077 130 7 2 1868 1996 177443096 177442968 3.350000e-44 189.0
6 TraesCS6A01G258100 chr4A 90.156 1412 101 25 591 1993 500090442 500091824 0.000000e+00 1803.0
7 TraesCS6A01G258100 chr4A 96.183 655 24 1 1857 2510 500091612 500092266 0.000000e+00 1070.0
8 TraesCS6A01G258100 chr7D 92.693 1177 61 5 591 1765 318857702 318858855 0.000000e+00 1674.0
9 TraesCS6A01G258100 chr7D 95.261 612 29 0 1938 2549 318859021 318859632 0.000000e+00 970.0
10 TraesCS6A01G258100 chr7D 91.638 586 44 5 1 585 408359603 408359022 0.000000e+00 806.0
11 TraesCS6A01G258100 chr7D 90.051 593 51 5 1 592 509938394 509937809 0.000000e+00 761.0
12 TraesCS6A01G258100 chr7D 94.495 109 4 2 1785 1893 318858905 318859011 1.570000e-37 167.0
13 TraesCS6A01G258100 chr7D 94.382 89 3 2 1850 1937 318858890 318858977 4.420000e-28 135.0
14 TraesCS6A01G258100 chr7D 91.765 85 6 1 1985 2069 318858993 318859076 1.600000e-22 117.0
15 TraesCS6A01G258100 chr7B 96.406 779 25 3 1772 2549 622461646 622462422 0.000000e+00 1280.0
16 TraesCS6A01G258100 chr7B 93.886 687 42 0 1057 1743 622460977 622461663 0.000000e+00 1037.0
17 TraesCS6A01G258100 chr7B 94.513 565 30 1 1985 2549 461210617 461210054 0.000000e+00 870.0
18 TraesCS6A01G258100 chr7B 90.576 573 53 1 591 1162 622460546 622461118 0.000000e+00 758.0
19 TraesCS6A01G258100 chr7B 82.584 712 83 26 1075 1776 461211303 461210623 7.850000e-165 590.0
20 TraesCS6A01G258100 chr7B 90.598 234 21 1 591 824 655058620 655058388 2.460000e-80 309.0
21 TraesCS6A01G258100 chr7B 77.880 217 27 18 1865 2069 622461659 622461866 5.760000e-22 115.0
22 TraesCS6A01G258100 chr6D 95.044 565 28 0 1985 2549 87581421 87580857 0.000000e+00 889.0
23 TraesCS6A01G258100 chr6D 81.976 749 93 28 1038 1776 87582143 87581427 4.690000e-167 597.0
24 TraesCS6A01G258100 chr6D 94.915 59 3 0 1938 1996 87581392 87581334 2.700000e-15 93.5
25 TraesCS6A01G258100 chr4D 95.292 531 25 0 2019 2549 498000079 498000609 0.000000e+00 843.0
26 TraesCS6A01G258100 chr4D 92.673 505 30 4 2047 2549 352496892 352497391 0.000000e+00 721.0
27 TraesCS6A01G258100 chr4D 82.865 712 81 26 1075 1776 497999369 498000049 3.630000e-168 601.0
28 TraesCS6A01G258100 chr4D 85.610 549 69 6 1019 1558 352487386 352487933 3.680000e-158 568.0
29 TraesCS6A01G258100 chr4D 86.081 273 37 1 973 1245 352487304 352487575 2.480000e-75 292.0
30 TraesCS6A01G258100 chr4D 94.915 59 3 0 1668 1726 352487965 352488023 2.700000e-15 93.5
31 TraesCS6A01G258100 chr1D 92.061 592 45 2 1 592 96575131 96574542 0.000000e+00 832.0
32 TraesCS6A01G258100 chr1D 88.934 497 40 7 2064 2549 194178169 194178661 1.310000e-167 599.0
33 TraesCS6A01G258100 chr3A 90.924 595 46 5 1 590 612354425 612355016 0.000000e+00 793.0
34 TraesCS6A01G258100 chr3A 90.863 591 51 3 3 592 103674533 103675121 0.000000e+00 789.0
35 TraesCS6A01G258100 chr3A 90.372 592 52 5 1 592 441424042 441424628 0.000000e+00 773.0
36 TraesCS6A01G258100 chr3A 91.556 225 16 2 591 813 441572206 441571983 8.860000e-80 307.0
37 TraesCS6A01G258100 chr5B 90.694 591 47 6 1 590 296050666 296050083 0.000000e+00 780.0
38 TraesCS6A01G258100 chr5B 90.203 592 55 3 1 592 261599140 261599728 0.000000e+00 769.0
39 TraesCS6A01G258100 chr5B 91.188 261 21 2 591 850 673670815 673671074 1.120000e-93 353.0
40 TraesCS6A01G258100 chr5D 90.508 590 50 4 1 590 386596263 386596846 0.000000e+00 774.0
41 TraesCS6A01G258100 chr7A 89.474 494 42 8 2064 2549 238118660 238119151 1.300000e-172 616.0
42 TraesCS6A01G258100 chr1A 89.474 494 42 8 2064 2549 369353036 369352545 1.300000e-172 616.0
43 TraesCS6A01G258100 chr1A 95.238 189 9 0 1938 2126 216481266 216481454 1.480000e-77 300.0
44 TraesCS6A01G258100 chr1A 94.059 101 5 1 1789 1889 216481153 216481252 4.390000e-33 152.0
45 TraesCS6A01G258100 chr1A 93.333 90 3 3 1850 1937 216481133 216481221 2.060000e-26 130.0
46 TraesCS6A01G258100 chr5A 89.212 241 24 2 591 830 546706909 546706670 1.480000e-77 300.0
47 TraesCS6A01G258100 chr6B 94.915 59 3 0 1938 1996 6473864 6473806 2.700000e-15 93.5
48 TraesCS6A01G258100 chr3B 96.429 56 2 0 1938 1993 662510937 662510992 2.700000e-15 93.5


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 TraesCS6A01G258100 chr6A 480458920 480461468 2548 False 4708.000000 4708 100.000000 1 2549 1 chr6A.!!$F2 2548
1 TraesCS6A01G258100 chr2D 177442491 177444317 1826 True 997.666667 1908 94.497000 591 2549 3 chr2D.!!$R1 1958
2 TraesCS6A01G258100 chr4A 500090442 500092266 1824 False 1436.500000 1803 93.169500 591 2510 2 chr4A.!!$F1 1919
3 TraesCS6A01G258100 chr7D 408359022 408359603 581 True 806.000000 806 91.638000 1 585 1 chr7D.!!$R1 584
4 TraesCS6A01G258100 chr7D 509937809 509938394 585 True 761.000000 761 90.051000 1 592 1 chr7D.!!$R2 591
5 TraesCS6A01G258100 chr7D 318857702 318859632 1930 False 612.600000 1674 93.719200 591 2549 5 chr7D.!!$F1 1958
6 TraesCS6A01G258100 chr7B 622460546 622462422 1876 False 797.500000 1280 89.687000 591 2549 4 chr7B.!!$F1 1958
7 TraesCS6A01G258100 chr7B 461210054 461211303 1249 True 730.000000 870 88.548500 1075 2549 2 chr7B.!!$R2 1474
8 TraesCS6A01G258100 chr6D 87580857 87582143 1286 True 526.500000 889 90.645000 1038 2549 3 chr6D.!!$R1 1511
9 TraesCS6A01G258100 chr4D 497999369 498000609 1240 False 722.000000 843 89.078500 1075 2549 2 chr4D.!!$F3 1474
10 TraesCS6A01G258100 chr4D 352487304 352488023 719 False 317.833333 568 88.868667 973 1726 3 chr4D.!!$F2 753
11 TraesCS6A01G258100 chr1D 96574542 96575131 589 True 832.000000 832 92.061000 1 592 1 chr1D.!!$R1 591
12 TraesCS6A01G258100 chr3A 612354425 612355016 591 False 793.000000 793 90.924000 1 590 1 chr3A.!!$F3 589
13 TraesCS6A01G258100 chr3A 103674533 103675121 588 False 789.000000 789 90.863000 3 592 1 chr3A.!!$F1 589
14 TraesCS6A01G258100 chr3A 441424042 441424628 586 False 773.000000 773 90.372000 1 592 1 chr3A.!!$F2 591
15 TraesCS6A01G258100 chr5B 296050083 296050666 583 True 780.000000 780 90.694000 1 590 1 chr5B.!!$R1 589
16 TraesCS6A01G258100 chr5B 261599140 261599728 588 False 769.000000 769 90.203000 1 592 1 chr5B.!!$F1 591
17 TraesCS6A01G258100 chr5D 386596263 386596846 583 False 774.000000 774 90.508000 1 590 1 chr5D.!!$F1 589

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
623 634 0.109597 CAGTTTGTTGGGCGCATCTC 60.11 55.0 10.83 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2136 0.179094 TTGAGTGGTGTGTGTCGGAC 60.179 55.0 0.0 0.0 0.0 4.79 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
28 29 3.290710 AGTGGCATGAGTTGTGAAACTT 58.709 40.909 0.00 0.00 38.04 2.66
40 41 7.068103 TGAGTTGTGAAACTTATTCCACATTGT 59.932 33.333 0.00 0.00 39.01 2.71
56 57 5.181056 CCACATTGTTTTTAAATGAAGGCCC 59.819 40.000 0.00 0.00 38.21 5.80
71 72 1.002087 AGGCCCAACTCGTAACTCAAG 59.998 52.381 0.00 0.00 0.00 3.02
142 144 8.037758 ACGATGATTCTTAACTTCACTCTGAAT 58.962 33.333 0.00 0.00 35.59 2.57
175 179 8.831715 AACTTTTCAAATGTTTCAGACTTGTT 57.168 26.923 0.00 0.00 0.00 2.83
225 229 7.911651 TCTTCTTAAATCATCTGTGAAGGTCT 58.088 34.615 0.00 0.00 38.01 3.85
307 311 9.920946 ATGTATTATTTCCAATAAGTCAGTGGT 57.079 29.630 0.00 0.00 43.17 4.16
326 330 0.756294 TTCGCTCCACTGTTCCAGAA 59.244 50.000 0.00 0.00 35.18 3.02
381 385 3.111098 GGTTCGCAAGCATCAAATGATC 58.889 45.455 0.00 0.00 31.21 2.92
447 458 4.162698 ACCAATATGACCTAAACGGCAGTA 59.837 41.667 0.00 0.00 35.61 2.74
623 634 0.109597 CAGTTTGTTGGGCGCATCTC 60.110 55.000 10.83 0.00 0.00 2.75
630 641 0.605319 TTGGGCGCATCTCGAAAACT 60.605 50.000 10.83 0.00 41.67 2.66
631 642 1.298157 TGGGCGCATCTCGAAAACTG 61.298 55.000 10.83 0.00 41.67 3.16
687 698 7.489757 CGCAGCTCCTTAACTATCCTATTAATC 59.510 40.741 0.00 0.00 0.00 1.75
701 712 0.759959 TTAATCGGGGCGCATTAGGA 59.240 50.000 10.83 0.00 0.00 2.94
796 808 0.396435 TGAGTGCAAGTGGGAATCGT 59.604 50.000 0.00 0.00 34.38 3.73
813 825 6.386654 GGAATCGTTTTCTTTATTTGCTCCA 58.613 36.000 0.00 0.00 0.00 3.86
830 842 3.410628 ACATGGCCTCCCGCATGA 61.411 61.111 3.32 0.00 40.31 3.07
898 932 0.478507 CCTCCTCTCCCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
928 966 7.014092 TCCTTTTTCATTTTGTGTTTGCATC 57.986 32.000 0.00 0.00 0.00 3.91
943 981 3.483808 TGCATCCACAAGTGTAGACAA 57.516 42.857 0.00 0.00 0.00 3.18
1003 1041 2.223479 GCACACAAACTCGAACCAATGT 60.223 45.455 0.00 0.00 0.00 2.71
1060 1098 0.183014 CATGGAGGAGATGCAAGGCT 59.817 55.000 0.00 0.00 30.55 4.58
1095 1169 2.128226 ATGGAGGAGGGGCAAGGT 59.872 61.111 0.00 0.00 0.00 3.50
1108 1182 0.598158 GCAAGGTGTGGTCGACGTTA 60.598 55.000 9.92 0.00 0.00 3.18
1218 1292 2.394563 GCAAGAGCAAGAGGTCGGC 61.395 63.158 0.00 0.00 46.62 5.54
1246 1364 2.409948 GCAAGAGCAAGAGGTGGTAT 57.590 50.000 0.00 0.00 38.34 2.73
1338 1456 3.197790 CGCGGTGAGGCTTCCATG 61.198 66.667 0.00 0.00 0.00 3.66
1367 1485 1.119574 TTAGGATGTAGGCTCCCGGC 61.120 60.000 0.00 0.00 40.90 6.13
1382 1500 0.033228 CCGGCACCAAAAGATTTGCA 59.967 50.000 0.00 0.00 36.66 4.08
1400 1518 2.135139 GCATTCTTGTGAGTCGTGTGA 58.865 47.619 0.00 0.00 0.00 3.58
1417 1535 3.057946 GTGTGAAAATCCTTGCCTCTGTC 60.058 47.826 0.00 0.00 0.00 3.51
1591 1709 9.047371 TGATGAAAATAAAGTGAGTTGTAACGA 57.953 29.630 0.00 0.00 0.00 3.85
1831 2082 1.355210 CACACCACTCAAACGCACC 59.645 57.895 0.00 0.00 0.00 5.01
1832 2083 1.822186 ACACCACTCAAACGCACCC 60.822 57.895 0.00 0.00 0.00 4.61
1833 2084 1.525995 CACCACTCAAACGCACCCT 60.526 57.895 0.00 0.00 0.00 4.34
1834 2085 1.227853 ACCACTCAAACGCACCCTC 60.228 57.895 0.00 0.00 0.00 4.30
1835 2086 1.227823 CCACTCAAACGCACCCTCA 60.228 57.895 0.00 0.00 0.00 3.86
1836 2087 0.817634 CCACTCAAACGCACCCTCAA 60.818 55.000 0.00 0.00 0.00 3.02
1837 2088 1.021202 CACTCAAACGCACCCTCAAA 58.979 50.000 0.00 0.00 0.00 2.69
1838 2089 1.403679 CACTCAAACGCACCCTCAAAA 59.596 47.619 0.00 0.00 0.00 2.44
1839 2090 2.096248 ACTCAAACGCACCCTCAAAAA 58.904 42.857 0.00 0.00 0.00 1.94
1840 2091 2.159296 ACTCAAACGCACCCTCAAAAAC 60.159 45.455 0.00 0.00 0.00 2.43
1841 2092 2.096248 TCAAACGCACCCTCAAAAACT 58.904 42.857 0.00 0.00 0.00 2.66
1842 2093 3.280295 TCAAACGCACCCTCAAAAACTA 58.720 40.909 0.00 0.00 0.00 2.24
1843 2094 3.695060 TCAAACGCACCCTCAAAAACTAA 59.305 39.130 0.00 0.00 0.00 2.24
1844 2095 4.158025 TCAAACGCACCCTCAAAAACTAAA 59.842 37.500 0.00 0.00 0.00 1.85
1845 2096 3.703286 ACGCACCCTCAAAAACTAAAC 57.297 42.857 0.00 0.00 0.00 2.01
1846 2097 3.018149 ACGCACCCTCAAAAACTAAACA 58.982 40.909 0.00 0.00 0.00 2.83
1847 2098 3.181494 ACGCACCCTCAAAAACTAAACAC 60.181 43.478 0.00 0.00 0.00 3.32
1848 2099 3.181495 CGCACCCTCAAAAACTAAACACA 60.181 43.478 0.00 0.00 0.00 3.72
1849 2100 4.109766 GCACCCTCAAAAACTAAACACAC 58.890 43.478 0.00 0.00 0.00 3.82
1850 2101 4.381079 GCACCCTCAAAAACTAAACACACA 60.381 41.667 0.00 0.00 0.00 3.72
1851 2102 5.715070 CACCCTCAAAAACTAAACACACAA 58.285 37.500 0.00 0.00 0.00 3.33
1852 2103 5.804979 CACCCTCAAAAACTAAACACACAAG 59.195 40.000 0.00 0.00 0.00 3.16
1853 2104 5.105513 ACCCTCAAAAACTAAACACACAAGG 60.106 40.000 0.00 0.00 0.00 3.61
1854 2105 5.348164 CCTCAAAAACTAAACACACAAGGG 58.652 41.667 0.00 0.00 0.00 3.95
1855 2106 5.126384 CCTCAAAAACTAAACACACAAGGGA 59.874 40.000 0.00 0.00 0.00 4.20
1856 2107 6.202516 TCAAAAACTAAACACACAAGGGAG 57.797 37.500 0.00 0.00 0.00 4.30
1857 2108 5.946972 TCAAAAACTAAACACACAAGGGAGA 59.053 36.000 0.00 0.00 0.00 3.71
1858 2109 6.434652 TCAAAAACTAAACACACAAGGGAGAA 59.565 34.615 0.00 0.00 0.00 2.87
1859 2110 6.844097 AAAACTAAACACACAAGGGAGAAA 57.156 33.333 0.00 0.00 0.00 2.52
1860 2111 6.844097 AAACTAAACACACAAGGGAGAAAA 57.156 33.333 0.00 0.00 0.00 2.29
1861 2112 6.451064 AACTAAACACACAAGGGAGAAAAG 57.549 37.500 0.00 0.00 0.00 2.27
1862 2113 3.801114 AAACACACAAGGGAGAAAAGC 57.199 42.857 0.00 0.00 0.00 3.51
1863 2114 2.435372 ACACACAAGGGAGAAAAGCA 57.565 45.000 0.00 0.00 0.00 3.91
1864 2115 2.949447 ACACACAAGGGAGAAAAGCAT 58.051 42.857 0.00 0.00 0.00 3.79
1865 2116 4.098914 ACACACAAGGGAGAAAAGCATA 57.901 40.909 0.00 0.00 0.00 3.14
1866 2117 4.469657 ACACACAAGGGAGAAAAGCATAA 58.530 39.130 0.00 0.00 0.00 1.90
1867 2118 4.892934 ACACACAAGGGAGAAAAGCATAAA 59.107 37.500 0.00 0.00 0.00 1.40
1868 2119 5.539955 ACACACAAGGGAGAAAAGCATAAAT 59.460 36.000 0.00 0.00 0.00 1.40
1869 2120 6.041979 ACACACAAGGGAGAAAAGCATAAATT 59.958 34.615 0.00 0.00 0.00 1.82
1870 2121 6.930722 CACACAAGGGAGAAAAGCATAAATTT 59.069 34.615 0.00 0.00 0.00 1.82
1871 2122 7.442062 CACACAAGGGAGAAAAGCATAAATTTT 59.558 33.333 0.00 0.00 32.68 1.82
1872 2123 7.992608 ACACAAGGGAGAAAAGCATAAATTTTT 59.007 29.630 0.00 0.00 30.22 1.94
1873 2124 8.498358 CACAAGGGAGAAAAGCATAAATTTTTC 58.502 33.333 0.00 2.39 41.38 2.29
1874 2125 8.210265 ACAAGGGAGAAAAGCATAAATTTTTCA 58.790 29.630 11.01 0.00 42.75 2.69
1875 2126 8.715088 CAAGGGAGAAAAGCATAAATTTTTCAG 58.285 33.333 11.01 0.00 42.75 3.02
1876 2127 7.966812 AGGGAGAAAAGCATAAATTTTTCAGT 58.033 30.769 11.01 0.00 42.75 3.41
1877 2128 8.432013 AGGGAGAAAAGCATAAATTTTTCAGTT 58.568 29.630 11.01 0.00 42.75 3.16
1878 2129 8.712363 GGGAGAAAAGCATAAATTTTTCAGTTC 58.288 33.333 11.01 0.00 42.75 3.01
1879 2130 9.260002 GGAGAAAAGCATAAATTTTTCAGTTCA 57.740 29.630 11.01 0.00 42.75 3.18
1886 2137 9.382275 AGCATAAATTTTTCAGTTCAAAACAGT 57.618 25.926 0.00 0.00 0.00 3.55
1887 2138 9.636965 GCATAAATTTTTCAGTTCAAAACAGTC 57.363 29.630 0.00 0.00 0.00 3.51
1889 2140 6.885735 AATTTTTCAGTTCAAAACAGTCCG 57.114 33.333 0.00 0.00 0.00 4.79
1890 2141 5.630661 TTTTTCAGTTCAAAACAGTCCGA 57.369 34.783 0.00 0.00 0.00 4.55
1891 2142 4.609691 TTTCAGTTCAAAACAGTCCGAC 57.390 40.909 0.00 0.00 0.00 4.79
1892 2143 3.254470 TCAGTTCAAAACAGTCCGACA 57.746 42.857 0.40 0.00 0.00 4.35
1893 2144 2.933906 TCAGTTCAAAACAGTCCGACAC 59.066 45.455 0.40 0.00 0.00 3.67
1894 2145 2.675844 CAGTTCAAAACAGTCCGACACA 59.324 45.455 0.40 0.00 0.00 3.72
1895 2146 2.676342 AGTTCAAAACAGTCCGACACAC 59.324 45.455 0.40 0.00 0.00 3.82
1896 2147 2.388310 TCAAAACAGTCCGACACACA 57.612 45.000 0.40 0.00 0.00 3.72
1897 2148 2.004017 TCAAAACAGTCCGACACACAC 58.996 47.619 0.40 0.00 0.00 3.82
1898 2149 1.063469 CAAAACAGTCCGACACACACC 59.937 52.381 0.40 0.00 0.00 4.16
1899 2150 0.250793 AAACAGTCCGACACACACCA 59.749 50.000 0.40 0.00 0.00 4.17
1900 2151 0.461339 AACAGTCCGACACACACCAC 60.461 55.000 0.40 0.00 0.00 4.16
1901 2152 1.327690 ACAGTCCGACACACACCACT 61.328 55.000 0.40 0.00 0.00 4.00
1902 2153 0.597637 CAGTCCGACACACACCACTC 60.598 60.000 0.40 0.00 0.00 3.51
1903 2154 1.040893 AGTCCGACACACACCACTCA 61.041 55.000 0.40 0.00 0.00 3.41
1904 2155 0.179094 GTCCGACACACACCACTCAA 60.179 55.000 0.00 0.00 0.00 3.02
1905 2156 0.537653 TCCGACACACACCACTCAAA 59.462 50.000 0.00 0.00 0.00 2.69
1906 2157 1.140052 TCCGACACACACCACTCAAAT 59.860 47.619 0.00 0.00 0.00 2.32
1907 2158 1.264020 CCGACACACACCACTCAAATG 59.736 52.381 0.00 0.00 0.00 2.32
1908 2159 1.334059 CGACACACACCACTCAAATGC 60.334 52.381 0.00 0.00 0.00 3.56
1909 2160 1.675483 GACACACACCACTCAAATGCA 59.325 47.619 0.00 0.00 0.00 3.96
1910 2161 1.405105 ACACACACCACTCAAATGCAC 59.595 47.619 0.00 0.00 0.00 4.57
2078 2329 5.069318 TGAGGCAGTACAAATCATGTTGAA 58.931 37.500 3.26 0.00 43.63 2.69
2143 2394 1.046204 AAACGAACCGGGAGAAGTCT 58.954 50.000 6.32 0.00 0.00 3.24
2183 2434 0.756294 TCTTCAAGTGAGGAACCGCA 59.244 50.000 0.00 0.00 0.00 5.69
2223 2474 4.404715 TGTGCTTGATGATCTCTCTCATGA 59.595 41.667 0.00 0.00 36.01 3.07
2241 2492 2.832563 TGAACGCTTGATGACTCAACA 58.167 42.857 0.00 0.00 36.46 3.33
2284 2535 2.409570 GGGGTACTCAGCTAGGGATTT 58.590 52.381 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.213799 GCCTTCATTTAAAAACAATGTGGAATA 57.786 29.630 0.00 0.00 33.91 1.75
40 41 4.342665 ACGAGTTGGGCCTTCATTTAAAAA 59.657 37.500 4.53 0.00 0.00 1.94
56 57 5.408604 AGGCAAATACTTGAGTTACGAGTTG 59.591 40.000 0.00 0.00 42.58 3.16
71 72 0.861837 CTGATCGCGGAGGCAAATAC 59.138 55.000 6.13 0.00 39.92 1.89
225 229 2.937799 GTGGCGGGTATCGTTATTTTCA 59.062 45.455 0.00 0.00 41.72 2.69
326 330 5.185828 GGGCAAGATGACTAAAACTCCATTT 59.814 40.000 0.00 0.00 0.00 2.32
381 385 7.093814 TGGACTTTTGGAATCACTTGATTATGG 60.094 37.037 4.42 0.00 44.14 2.74
447 458 5.932619 TGATAGTGCAACATACTAGTGGT 57.067 39.130 5.39 0.45 41.43 4.16
651 662 1.153168 GGAGCTGCGCCCTATTTCA 60.153 57.895 11.72 0.00 0.00 2.69
701 712 4.487714 TGAGGAAGATAAACGGAAGCAT 57.512 40.909 0.00 0.00 0.00 3.79
713 725 0.035152 TGCATGCGGTTGAGGAAGAT 60.035 50.000 14.09 0.00 0.00 2.40
796 808 5.237048 GCCATGTGGAGCAAATAAAGAAAA 58.763 37.500 2.55 0.00 37.39 2.29
813 825 2.497792 TTTCATGCGGGAGGCCATGT 62.498 55.000 5.01 0.00 42.61 3.21
830 842 4.233123 CATGCACTCATGTTCACACTTT 57.767 40.909 0.00 0.00 43.85 2.66
854 866 2.624316 CATGCACTCATGTTCACACC 57.376 50.000 0.00 0.00 43.85 4.16
898 932 3.983344 CACAAAATGAAAAAGGAGCCGAG 59.017 43.478 0.00 0.00 0.00 4.63
928 966 2.158813 ACCCTGTTGTCTACACTTGTGG 60.159 50.000 5.72 0.00 32.10 4.17
992 1030 2.901192 TCCTTGGAGTACATTGGTTCGA 59.099 45.455 0.00 0.00 0.00 3.71
1060 1098 0.409092 ATGGCATGAACCTCCACCAA 59.591 50.000 0.00 0.00 31.94 3.67
1095 1169 1.007038 GGCAGTAACGTCGACCACA 60.007 57.895 10.58 0.00 0.00 4.17
1108 1182 2.976490 GCACCTCCTCCATGGCAGT 61.976 63.158 6.96 0.00 35.26 4.40
1246 1364 1.816183 CGGGTTGGAGTAGGTTTTGCA 60.816 52.381 0.00 0.00 0.00 4.08
1367 1485 5.754406 TCACAAGAATGCAAATCTTTTGGTG 59.246 36.000 21.77 20.12 36.00 4.17
1382 1500 5.049405 GGATTTTCACACGACTCACAAGAAT 60.049 40.000 0.00 0.00 0.00 2.40
1400 1518 3.228188 TGTGACAGAGGCAAGGATTTT 57.772 42.857 0.00 0.00 0.00 1.82
1417 1535 6.121613 ACAATCTTTGCACCAAAAATTGTG 57.878 33.333 16.94 0.00 46.45 3.33
1457 1575 6.461509 CCTTATGCATACCCCATCTTTGTTTC 60.462 42.308 5.74 0.00 0.00 2.78
1546 1664 7.119709 TCATCATCCGGTGAATCTAAACTTA 57.880 36.000 0.00 0.00 40.97 2.24
1831 2082 5.126384 TCCCTTGTGTGTTTAGTTTTTGAGG 59.874 40.000 0.00 0.00 0.00 3.86
1832 2083 6.094881 TCTCCCTTGTGTGTTTAGTTTTTGAG 59.905 38.462 0.00 0.00 0.00 3.02
1833 2084 5.946972 TCTCCCTTGTGTGTTTAGTTTTTGA 59.053 36.000 0.00 0.00 0.00 2.69
1834 2085 6.202516 TCTCCCTTGTGTGTTTAGTTTTTG 57.797 37.500 0.00 0.00 0.00 2.44
1835 2086 6.844097 TTCTCCCTTGTGTGTTTAGTTTTT 57.156 33.333 0.00 0.00 0.00 1.94
1836 2087 6.844097 TTTCTCCCTTGTGTGTTTAGTTTT 57.156 33.333 0.00 0.00 0.00 2.43
1837 2088 6.627287 GCTTTTCTCCCTTGTGTGTTTAGTTT 60.627 38.462 0.00 0.00 0.00 2.66
1838 2089 5.163550 GCTTTTCTCCCTTGTGTGTTTAGTT 60.164 40.000 0.00 0.00 0.00 2.24
1839 2090 4.338400 GCTTTTCTCCCTTGTGTGTTTAGT 59.662 41.667 0.00 0.00 0.00 2.24
1840 2091 4.338118 TGCTTTTCTCCCTTGTGTGTTTAG 59.662 41.667 0.00 0.00 0.00 1.85
1841 2092 4.274147 TGCTTTTCTCCCTTGTGTGTTTA 58.726 39.130 0.00 0.00 0.00 2.01
1842 2093 3.096092 TGCTTTTCTCCCTTGTGTGTTT 58.904 40.909 0.00 0.00 0.00 2.83
1843 2094 2.733956 TGCTTTTCTCCCTTGTGTGTT 58.266 42.857 0.00 0.00 0.00 3.32
1844 2095 2.435372 TGCTTTTCTCCCTTGTGTGT 57.565 45.000 0.00 0.00 0.00 3.72
1845 2096 5.452078 TTTATGCTTTTCTCCCTTGTGTG 57.548 39.130 0.00 0.00 0.00 3.82
1846 2097 6.670695 AATTTATGCTTTTCTCCCTTGTGT 57.329 33.333 0.00 0.00 0.00 3.72
1847 2098 7.967890 AAAATTTATGCTTTTCTCCCTTGTG 57.032 32.000 0.00 0.00 0.00 3.33
1848 2099 8.210265 TGAAAAATTTATGCTTTTCTCCCTTGT 58.790 29.630 8.31 0.00 40.58 3.16
1849 2100 8.606040 TGAAAAATTTATGCTTTTCTCCCTTG 57.394 30.769 8.31 0.00 40.58 3.61
1850 2101 8.432013 ACTGAAAAATTTATGCTTTTCTCCCTT 58.568 29.630 8.31 0.00 40.58 3.95
1851 2102 7.966812 ACTGAAAAATTTATGCTTTTCTCCCT 58.033 30.769 8.31 0.00 40.58 4.20
1852 2103 8.607441 AACTGAAAAATTTATGCTTTTCTCCC 57.393 30.769 8.31 0.00 40.58 4.30
1853 2104 9.260002 TGAACTGAAAAATTTATGCTTTTCTCC 57.740 29.630 8.31 0.00 40.58 3.71
1860 2111 9.382275 ACTGTTTTGAACTGAAAAATTTATGCT 57.618 25.926 0.00 0.00 34.78 3.79
1861 2112 9.636965 GACTGTTTTGAACTGAAAAATTTATGC 57.363 29.630 0.00 0.00 34.78 3.14
1863 2114 9.030301 CGGACTGTTTTGAACTGAAAAATTTAT 57.970 29.630 0.00 0.00 34.78 1.40
1864 2115 8.244802 TCGGACTGTTTTGAACTGAAAAATTTA 58.755 29.630 0.00 0.00 34.78 1.40
1865 2116 7.062956 GTCGGACTGTTTTGAACTGAAAAATTT 59.937 33.333 0.00 0.00 34.78 1.82
1866 2117 6.530181 GTCGGACTGTTTTGAACTGAAAAATT 59.470 34.615 0.00 0.00 34.78 1.82
1867 2118 6.033966 GTCGGACTGTTTTGAACTGAAAAAT 58.966 36.000 0.00 0.00 34.78 1.82
1868 2119 5.048643 TGTCGGACTGTTTTGAACTGAAAAA 60.049 36.000 9.88 0.00 34.78 1.94
1869 2120 4.456222 TGTCGGACTGTTTTGAACTGAAAA 59.544 37.500 9.88 0.00 34.78 2.29
1870 2121 4.004314 TGTCGGACTGTTTTGAACTGAAA 58.996 39.130 9.88 0.00 34.78 2.69
1871 2122 3.372822 GTGTCGGACTGTTTTGAACTGAA 59.627 43.478 9.88 0.00 34.78 3.02
1872 2123 2.933906 GTGTCGGACTGTTTTGAACTGA 59.066 45.455 9.88 0.00 34.78 3.41
1873 2124 2.675844 TGTGTCGGACTGTTTTGAACTG 59.324 45.455 9.88 0.00 36.53 3.16
1874 2125 2.676342 GTGTGTCGGACTGTTTTGAACT 59.324 45.455 9.88 0.00 0.00 3.01
1875 2126 2.417239 TGTGTGTCGGACTGTTTTGAAC 59.583 45.455 9.88 0.00 0.00 3.18
1876 2127 2.417239 GTGTGTGTCGGACTGTTTTGAA 59.583 45.455 9.88 0.00 0.00 2.69
1877 2128 2.004017 GTGTGTGTCGGACTGTTTTGA 58.996 47.619 9.88 0.00 0.00 2.69
1878 2129 1.063469 GGTGTGTGTCGGACTGTTTTG 59.937 52.381 9.88 0.00 0.00 2.44
1879 2130 1.339247 TGGTGTGTGTCGGACTGTTTT 60.339 47.619 9.88 0.00 0.00 2.43
1880 2131 0.250793 TGGTGTGTGTCGGACTGTTT 59.749 50.000 9.88 0.00 0.00 2.83
1881 2132 0.461339 GTGGTGTGTGTCGGACTGTT 60.461 55.000 9.88 0.00 0.00 3.16
1882 2133 1.143183 GTGGTGTGTGTCGGACTGT 59.857 57.895 9.88 0.00 0.00 3.55
1883 2134 0.597637 GAGTGGTGTGTGTCGGACTG 60.598 60.000 9.88 0.00 0.00 3.51
1884 2135 1.040893 TGAGTGGTGTGTGTCGGACT 61.041 55.000 9.88 0.00 0.00 3.85
1885 2136 0.179094 TTGAGTGGTGTGTGTCGGAC 60.179 55.000 0.00 0.00 0.00 4.79
1886 2137 0.537653 TTTGAGTGGTGTGTGTCGGA 59.462 50.000 0.00 0.00 0.00 4.55
1887 2138 1.264020 CATTTGAGTGGTGTGTGTCGG 59.736 52.381 0.00 0.00 0.00 4.79
1888 2139 1.334059 GCATTTGAGTGGTGTGTGTCG 60.334 52.381 0.00 0.00 0.00 4.35
1889 2140 1.675483 TGCATTTGAGTGGTGTGTGTC 59.325 47.619 0.00 0.00 0.00 3.67
1890 2141 1.405105 GTGCATTTGAGTGGTGTGTGT 59.595 47.619 0.00 0.00 0.00 3.72
1891 2142 1.269206 GGTGCATTTGAGTGGTGTGTG 60.269 52.381 0.00 0.00 0.00 3.82
1892 2143 1.032014 GGTGCATTTGAGTGGTGTGT 58.968 50.000 0.00 0.00 0.00 3.72
1893 2144 0.314935 GGGTGCATTTGAGTGGTGTG 59.685 55.000 0.00 0.00 0.00 3.82
1894 2145 0.185901 AGGGTGCATTTGAGTGGTGT 59.814 50.000 0.00 0.00 0.00 4.16
1895 2146 0.883833 GAGGGTGCATTTGAGTGGTG 59.116 55.000 0.00 0.00 0.00 4.17
1896 2147 0.478072 TGAGGGTGCATTTGAGTGGT 59.522 50.000 0.00 0.00 0.00 4.16
1897 2148 1.619654 TTGAGGGTGCATTTGAGTGG 58.380 50.000 0.00 0.00 0.00 4.00
1898 2149 3.731652 TTTTGAGGGTGCATTTGAGTG 57.268 42.857 0.00 0.00 0.00 3.51
1899 2150 3.181466 GGTTTTTGAGGGTGCATTTGAGT 60.181 43.478 0.00 0.00 0.00 3.41
1900 2151 3.181467 TGGTTTTTGAGGGTGCATTTGAG 60.181 43.478 0.00 0.00 0.00 3.02
1901 2152 2.768527 TGGTTTTTGAGGGTGCATTTGA 59.231 40.909 0.00 0.00 0.00 2.69
1902 2153 3.191078 TGGTTTTTGAGGGTGCATTTG 57.809 42.857 0.00 0.00 0.00 2.32
1903 2154 3.922171 TTGGTTTTTGAGGGTGCATTT 57.078 38.095 0.00 0.00 0.00 2.32
1904 2155 3.054802 TGTTTGGTTTTTGAGGGTGCATT 60.055 39.130 0.00 0.00 0.00 3.56
1905 2156 2.503356 TGTTTGGTTTTTGAGGGTGCAT 59.497 40.909 0.00 0.00 0.00 3.96
1906 2157 1.902508 TGTTTGGTTTTTGAGGGTGCA 59.097 42.857 0.00 0.00 0.00 4.57
1907 2158 2.276201 GTGTTTGGTTTTTGAGGGTGC 58.724 47.619 0.00 0.00 0.00 5.01
1908 2159 3.258228 GTGTGTTTGGTTTTTGAGGGTG 58.742 45.455 0.00 0.00 0.00 4.61
1909 2160 2.900546 TGTGTGTTTGGTTTTTGAGGGT 59.099 40.909 0.00 0.00 0.00 4.34
1910 2161 3.601443 TGTGTGTTTGGTTTTTGAGGG 57.399 42.857 0.00 0.00 0.00 4.30
1959 2210 5.453762 CCTCATGTGATGGTGCTACTATTCA 60.454 44.000 0.00 0.00 0.00 2.57
2078 2329 3.830755 AGCAGGCAATTGAGTTCTTGAAT 59.169 39.130 10.34 0.00 0.00 2.57
2223 2474 3.466836 TCTTGTTGAGTCATCAAGCGTT 58.533 40.909 28.10 0.00 45.96 4.84
2241 2492 5.832060 CCCATCAAAAGCTCAATAGGATCTT 59.168 40.000 0.00 0.00 33.53 2.40
2284 2535 9.325198 CTTGCTGTTATGTGTCATAGGTTAATA 57.675 33.333 0.00 0.00 0.00 0.98
2357 2608 9.813080 GCAATCTTCCGTTTGAGTATTTATATC 57.187 33.333 0.00 0.00 0.00 1.63
2373 2624 3.568538 CAAAAGGTCTTGCAATCTTCCG 58.431 45.455 0.00 0.00 0.00 4.30
2378 2629 4.320608 TTGTCCAAAAGGTCTTGCAATC 57.679 40.909 0.00 0.00 0.00 2.67
2455 2706 8.862325 ACACAAACATATTAGATCTTGGTTGA 57.138 30.769 23.43 0.00 38.71 3.18


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

AutoCloner maintained by Alex Coulton.