Multiple sequence alignment - TraesCS4A01G420700

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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 TraesCS4A01G420700 chr4A 100.000 2537 0 0 1 2537 691124374 691126910 0.000000e+00 4686
1 TraesCS4A01G420700 chr4A 79.870 154 26 5 2191 2341 123878069 123877918 9.600000e-20 108
2 TraesCS4A01G420700 chr7A 89.118 1939 108 34 1 1875 34707990 34706091 0.000000e+00 2316
3 TraesCS4A01G420700 chr7A 95.516 223 9 1 2120 2341 34705913 34705691 3.100000e-94 355
4 TraesCS4A01G420700 chr7A 90.270 185 16 2 1900 2084 34706093 34705911 9.070000e-60 241
5 TraesCS4A01G420700 chr7A 81.818 132 23 1 2177 2307 37840031 37839900 2.670000e-20 110
6 TraesCS4A01G420700 chr7A 80.405 148 24 5 2180 2325 231046489 231046345 9.600000e-20 108
7 TraesCS4A01G420700 chr7D 88.411 1743 100 41 1 1693 34302843 34301153 0.000000e+00 2006
8 TraesCS4A01G420700 chr7D 87.448 239 30 0 1855 2093 34300796 34300558 2.490000e-70 276
9 TraesCS4A01G420700 chr7D 86.957 184 23 1 2158 2341 34300439 34300257 3.310000e-49 206
10 TraesCS4A01G420700 chr7D 87.647 170 16 5 2339 2505 469229034 469229201 2.580000e-45 193
11 TraesCS4A01G420700 chr4B 94.667 150 8 0 2340 2489 69146836 69146985 1.520000e-57 233
12 TraesCS4A01G420700 chr2B 91.566 166 14 0 2340 2505 5807818 5807983 1.960000e-56 230
13 TraesCS4A01G420700 chr3D 87.719 171 21 0 2335 2505 399411683 399411853 1.540000e-47 200
14 TraesCS4A01G420700 chr3B 88.095 168 20 0 2338 2505 809489972 809490139 1.540000e-47 200
15 TraesCS4A01G420700 chr5D 87.500 168 17 3 2340 2505 51894852 51894687 9.260000e-45 191
16 TraesCS4A01G420700 chr4D 86.826 167 22 0 2340 2506 500272035 500272201 1.200000e-43 187
17 TraesCS4A01G420700 chr4D 83.929 168 23 4 2175 2339 297843017 297843183 9.400000e-35 158
18 TraesCS4A01G420700 chr4D 80.892 157 25 5 2188 2341 342551319 342551473 4.430000e-23 119
19 TraesCS4A01G420700 chr4D 86.364 110 14 1 2211 2319 355791543 355791434 4.430000e-23 119
20 TraesCS4A01G420700 chr1B 95.098 102 5 0 2340 2441 534969554 534969453 7.260000e-36 161
21 TraesCS4A01G420700 chr5B 90.217 92 9 0 2340 2431 460223455 460223364 1.230000e-23 121
22 TraesCS4A01G420700 chr5A 82.836 134 15 7 2211 2341 539105720 539105592 2.060000e-21 113


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 TraesCS4A01G420700 chr4A 691124374 691126910 2536 False 4686.000000 4686 100.000000 1 2537 1 chr4A.!!$F1 2536
1 TraesCS4A01G420700 chr7A 34705691 34707990 2299 True 970.666667 2316 91.634667 1 2341 3 chr7A.!!$R3 2340
2 TraesCS4A01G420700 chr7D 34300257 34302843 2586 True 829.333333 2006 87.605333 1 2341 3 chr7D.!!$R1 2340

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
909 960 0.026803 GAGCGGCTGCAGATAAAACG 59.973 55.0 21.93 11.92 46.23 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2477 0.097325 CTTCCTCGAAGTCGTCTCCG 59.903 60.0 0.0 0.0 40.8 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
140 141 3.083997 GGGTCGCTGTCCATCCCT 61.084 66.667 0.00 0.00 35.63 4.20
147 148 3.083349 TGTCCATCCCTCTGGCCG 61.083 66.667 0.00 0.00 36.16 6.13
633 634 1.348594 GCCTCGTCGTAGCAAATGC 59.651 57.895 0.00 0.00 42.49 3.56
655 656 4.127171 CGTTCATCATAGACCGGGATTTT 58.873 43.478 6.32 0.00 0.00 1.82
688 695 9.569122 TGTAGAGTGTAGCTAATACATGTATCA 57.431 33.333 18.52 8.48 45.94 2.15
722 742 0.798776 CTCGGTGGTTCAAGCATGAC 59.201 55.000 0.00 0.00 34.61 3.06
728 748 2.096218 GTGGTTCAAGCATGACTCGTTC 60.096 50.000 0.00 0.00 34.61 3.95
729 749 2.224281 TGGTTCAAGCATGACTCGTTCT 60.224 45.455 0.00 0.00 34.61 3.01
730 750 2.808543 GGTTCAAGCATGACTCGTTCTT 59.191 45.455 0.00 0.00 34.61 2.52
756 776 1.630244 ATCGTGCTGCGTCAAAGCTC 61.630 55.000 0.00 0.00 41.42 4.09
764 784 1.868997 CGTCAAAGCTCGGCATTGT 59.131 52.632 11.65 0.00 38.23 2.71
788 808 6.096001 GTGCCATGAGTTTCTTCTTGGATAAT 59.904 38.462 10.94 0.00 42.19 1.28
802 822 4.038271 TGGATAATGGAGGAATGCCATC 57.962 45.455 0.00 0.00 45.11 3.51
803 823 3.398629 TGGATAATGGAGGAATGCCATCA 59.601 43.478 0.00 0.00 45.11 3.07
831 877 1.839354 TGGACATCCTAGCATTGCTCA 59.161 47.619 15.81 1.12 40.44 4.26
843 889 0.252479 ATTGCTCAGCTCTGGTCTGG 59.748 55.000 0.00 0.00 32.63 3.86
867 913 1.271934 CCAGTGGACTCAGAGTCAGTG 59.728 57.143 28.26 23.60 46.79 3.66
868 914 2.234143 CAGTGGACTCAGAGTCAGTGA 58.766 52.381 28.26 9.30 46.79 3.41
869 915 2.228582 CAGTGGACTCAGAGTCAGTGAG 59.771 54.545 28.26 12.39 46.79 3.51
870 916 2.107378 AGTGGACTCAGAGTCAGTGAGA 59.893 50.000 28.26 5.46 46.79 3.27
871 917 2.887783 GTGGACTCAGAGTCAGTGAGAA 59.112 50.000 28.26 5.42 46.79 2.87
872 918 2.887783 TGGACTCAGAGTCAGTGAGAAC 59.112 50.000 28.26 11.53 46.79 3.01
873 919 3.153919 GGACTCAGAGTCAGTGAGAACT 58.846 50.000 28.26 0.00 46.79 3.01
894 940 1.227205 GGAGATGTGGAGCAGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
909 960 0.026803 GAGCGGCTGCAGATAAAACG 59.973 55.000 21.93 11.92 46.23 3.60
1037 1094 3.760035 CAGTGTCCTCCCCGTCCG 61.760 72.222 0.00 0.00 0.00 4.79
1038 1095 4.296729 AGTGTCCTCCCCGTCCGT 62.297 66.667 0.00 0.00 0.00 4.69
1048 1105 4.675029 CCGTCCGTCCGCAACCTT 62.675 66.667 0.00 0.00 0.00 3.50
1358 1439 0.107752 GAGGCCAAGAAGAGGAGCAG 60.108 60.000 5.01 0.00 0.00 4.24
1360 1441 0.326264 GGCCAAGAAGAGGAGCAGAA 59.674 55.000 0.00 0.00 0.00 3.02
1537 1618 0.674895 CCTCCACAAGCACCAGTAGC 60.675 60.000 0.00 0.00 0.00 3.58
1542 1623 0.182537 ACAAGCACCAGTAGCAACCA 59.817 50.000 0.00 0.00 0.00 3.67
1546 1627 1.028905 GCACCAGTAGCAACCACAAA 58.971 50.000 0.00 0.00 0.00 2.83
1547 1628 1.407258 GCACCAGTAGCAACCACAAAA 59.593 47.619 0.00 0.00 0.00 2.44
1553 1634 4.487948 CAGTAGCAACCACAAAATCATGG 58.512 43.478 0.00 0.00 42.13 3.66
1622 1721 3.843240 CGGCGAAGAAGCGTGCTC 61.843 66.667 0.00 0.00 38.18 4.26
1676 1776 4.015084 AGACAGCTCTGCTTTTTATGCAT 58.985 39.130 3.79 3.79 39.86 3.96
1708 1808 3.303881 TCTGAGATTTGGTCACGAGTG 57.696 47.619 0.00 0.00 0.00 3.51
1709 1809 1.728971 CTGAGATTTGGTCACGAGTGC 59.271 52.381 0.00 0.00 0.00 4.40
1719 1828 1.131623 CACGAGTGCGCGCATTTTA 59.868 52.632 38.62 11.31 42.48 1.52
1735 1844 0.038166 TTTAGAGCCAGGGTGCAAGG 59.962 55.000 0.00 0.00 0.00 3.61
1779 1898 1.513158 CAAACACACGGCAAACCCA 59.487 52.632 0.00 0.00 0.00 4.51
1841 1961 1.833934 CCAAGGTGCTGCAAAGGGT 60.834 57.895 2.77 0.00 0.00 4.34
1847 1967 2.991540 GCTGCAAAGGGTGGGGAC 60.992 66.667 0.00 0.00 0.00 4.46
1848 1968 2.520458 CTGCAAAGGGTGGGGACA 59.480 61.111 0.00 0.00 38.70 4.02
1871 1991 0.108756 GGCCTCGCCGGAGTAATATC 60.109 60.000 5.05 0.00 39.62 1.63
1875 2221 0.601558 TCGCCGGAGTAATATCAGCC 59.398 55.000 5.05 0.00 0.00 4.85
1876 2222 0.317160 CGCCGGAGTAATATCAGCCA 59.683 55.000 5.05 0.00 0.00 4.75
1877 2223 1.797025 GCCGGAGTAATATCAGCCAC 58.203 55.000 5.05 0.00 0.00 5.01
1878 2224 1.608283 GCCGGAGTAATATCAGCCACC 60.608 57.143 5.05 0.00 0.00 4.61
1879 2225 1.002087 CCGGAGTAATATCAGCCACCC 59.998 57.143 0.00 0.00 0.00 4.61
1880 2226 1.971357 CGGAGTAATATCAGCCACCCT 59.029 52.381 0.00 0.00 0.00 4.34
1881 2227 3.162666 CGGAGTAATATCAGCCACCCTA 58.837 50.000 0.00 0.00 0.00 3.53
1882 2228 3.056749 CGGAGTAATATCAGCCACCCTAC 60.057 52.174 0.00 0.00 0.00 3.18
1883 2229 4.161102 GGAGTAATATCAGCCACCCTACT 58.839 47.826 0.00 0.00 0.00 2.57
1884 2230 4.593634 GGAGTAATATCAGCCACCCTACTT 59.406 45.833 0.00 0.00 0.00 2.24
1885 2231 5.279556 GGAGTAATATCAGCCACCCTACTTC 60.280 48.000 0.00 0.00 0.00 3.01
1886 2232 5.468658 AGTAATATCAGCCACCCTACTTCT 58.531 41.667 0.00 0.00 0.00 2.85
1887 2233 6.621394 AGTAATATCAGCCACCCTACTTCTA 58.379 40.000 0.00 0.00 0.00 2.10
1888 2234 5.810080 AATATCAGCCACCCTACTTCTAC 57.190 43.478 0.00 0.00 0.00 2.59
1889 2235 1.471119 TCAGCCACCCTACTTCTACG 58.529 55.000 0.00 0.00 0.00 3.51
1890 2236 0.179108 CAGCCACCCTACTTCTACGC 60.179 60.000 0.00 0.00 0.00 4.42
1891 2237 1.143401 GCCACCCTACTTCTACGCC 59.857 63.158 0.00 0.00 0.00 5.68
1892 2238 1.436336 CCACCCTACTTCTACGCCG 59.564 63.158 0.00 0.00 0.00 6.46
1893 2239 1.226888 CACCCTACTTCTACGCCGC 60.227 63.158 0.00 0.00 0.00 6.53
1894 2240 2.416260 CCCTACTTCTACGCCGCC 59.584 66.667 0.00 0.00 0.00 6.13
1895 2241 2.420568 CCCTACTTCTACGCCGCCA 61.421 63.158 0.00 0.00 0.00 5.69
1896 2242 1.514087 CCTACTTCTACGCCGCCAA 59.486 57.895 0.00 0.00 0.00 4.52
1897 2243 0.108520 CCTACTTCTACGCCGCCAAA 60.109 55.000 0.00 0.00 0.00 3.28
1898 2244 0.997196 CTACTTCTACGCCGCCAAAC 59.003 55.000 0.00 0.00 0.00 2.93
1899 2245 0.317799 TACTTCTACGCCGCCAAACA 59.682 50.000 0.00 0.00 0.00 2.83
1900 2246 0.949105 ACTTCTACGCCGCCAAACAG 60.949 55.000 0.00 0.00 0.00 3.16
1901 2247 2.240612 CTTCTACGCCGCCAAACAGC 62.241 60.000 0.00 0.00 0.00 4.40
1902 2248 3.799755 CTACGCCGCCAAACAGCC 61.800 66.667 0.00 0.00 0.00 4.85
1948 2294 1.735198 CGGGTGCGTGTCGTATTGT 60.735 57.895 0.00 0.00 0.00 2.71
2079 2425 1.821216 ATGTCTCAAACGGGCGAAAT 58.179 45.000 0.00 0.00 0.00 2.17
2093 2472 1.597195 GCGAAATGCCATATGACGACA 59.403 47.619 3.65 0.00 37.76 4.35
2098 2477 0.104855 TGCCATATGACGACAGAGGC 59.895 55.000 16.71 16.71 39.70 4.70
2100 2479 0.319040 CCATATGACGACAGAGGCGG 60.319 60.000 3.65 0.00 0.00 6.13
2175 2575 1.003866 GTAGCCGAAGCAAAATAGCGG 60.004 52.381 0.00 0.00 43.56 5.52
2184 2584 0.804544 CAAAATAGCGGCGAGACGGA 60.805 55.000 12.98 0.00 0.00 4.69
2306 2706 2.171209 TAGCATCGATCCGCCCATGG 62.171 60.000 4.14 4.14 0.00 3.66
2341 2742 3.429085 GCGCAATATTCTTGTCCAACAG 58.571 45.455 0.30 0.00 0.00 3.16
2342 2743 3.119849 GCGCAATATTCTTGTCCAACAGT 60.120 43.478 0.30 0.00 0.00 3.55
2343 2744 4.406069 CGCAATATTCTTGTCCAACAGTG 58.594 43.478 0.00 0.00 0.00 3.66
2345 2746 4.737054 CAATATTCTTGTCCAACAGTGGC 58.263 43.478 0.00 0.00 45.54 5.01
2346 2747 1.238439 ATTCTTGTCCAACAGTGGCG 58.762 50.000 0.00 0.00 45.54 5.69
2347 2748 0.179234 TTCTTGTCCAACAGTGGCGA 59.821 50.000 0.00 0.00 45.54 5.54
2348 2749 0.179234 TCTTGTCCAACAGTGGCGAA 59.821 50.000 0.00 0.00 45.54 4.70
2349 2750 0.588252 CTTGTCCAACAGTGGCGAAG 59.412 55.000 0.00 0.00 45.54 3.79
2365 2766 3.890527 AAGCCATACTTCAGCTGGG 57.109 52.632 15.13 6.99 36.84 4.45
2366 2767 0.995024 AAGCCATACTTCAGCTGGGT 59.005 50.000 15.13 15.24 42.32 4.51
2367 2768 1.879575 AGCCATACTTCAGCTGGGTA 58.120 50.000 15.13 16.87 38.92 3.69
2368 2769 1.765314 AGCCATACTTCAGCTGGGTAG 59.235 52.381 15.13 11.44 38.92 3.18
2369 2770 1.486726 GCCATACTTCAGCTGGGTAGT 59.513 52.381 15.13 16.42 0.00 2.73
2370 2771 2.483889 GCCATACTTCAGCTGGGTAGTC 60.484 54.545 15.13 7.23 0.00 2.59
2371 2772 2.766263 CCATACTTCAGCTGGGTAGTCA 59.234 50.000 15.13 5.36 0.00 3.41
2372 2773 3.197766 CCATACTTCAGCTGGGTAGTCAA 59.802 47.826 15.13 0.00 0.00 3.18
2373 2774 4.141620 CCATACTTCAGCTGGGTAGTCAAT 60.142 45.833 15.13 4.30 0.00 2.57
2374 2775 5.431765 CATACTTCAGCTGGGTAGTCAATT 58.568 41.667 15.13 0.00 0.00 2.32
2375 2776 3.679389 ACTTCAGCTGGGTAGTCAATTG 58.321 45.455 15.13 0.00 0.00 2.32
2376 2777 3.327757 ACTTCAGCTGGGTAGTCAATTGA 59.672 43.478 15.13 3.38 0.00 2.57
2377 2778 3.334583 TCAGCTGGGTAGTCAATTGAC 57.665 47.619 27.69 27.69 45.08 3.18
2391 2792 6.738352 GTCAATTGACTACACAGCTTTTTG 57.262 37.500 27.66 0.00 41.65 2.44
2392 2793 5.173854 GTCAATTGACTACACAGCTTTTTGC 59.826 40.000 27.66 0.00 41.65 3.68
2393 2794 4.916983 ATTGACTACACAGCTTTTTGCA 57.083 36.364 0.00 0.00 45.94 4.08
2394 2795 4.916983 TTGACTACACAGCTTTTTGCAT 57.083 36.364 0.00 0.00 45.94 3.96
2395 2796 6.573664 ATTGACTACACAGCTTTTTGCATA 57.426 33.333 0.00 0.00 45.94 3.14
2396 2797 6.384258 TTGACTACACAGCTTTTTGCATAA 57.616 33.333 0.00 0.00 45.94 1.90
2397 2798 6.384258 TGACTACACAGCTTTTTGCATAAA 57.616 33.333 2.28 2.28 45.94 1.40
2398 2799 6.205784 TGACTACACAGCTTTTTGCATAAAC 58.794 36.000 0.00 0.00 45.94 2.01
2399 2800 6.142818 ACTACACAGCTTTTTGCATAAACA 57.857 33.333 0.00 0.00 45.94 2.83
2400 2801 6.568869 ACTACACAGCTTTTTGCATAAACAA 58.431 32.000 0.00 0.00 45.94 2.83
2401 2802 7.038659 ACTACACAGCTTTTTGCATAAACAAA 58.961 30.769 0.00 0.00 45.94 2.83
2402 2803 6.734104 ACACAGCTTTTTGCATAAACAAAA 57.266 29.167 0.00 0.00 45.29 2.44
2403 2804 7.319142 ACACAGCTTTTTGCATAAACAAAAT 57.681 28.000 0.00 0.00 45.98 1.82
2404 2805 8.430801 ACACAGCTTTTTGCATAAACAAAATA 57.569 26.923 0.00 0.00 45.98 1.40
2405 2806 8.887717 ACACAGCTTTTTGCATAAACAAAATAA 58.112 25.926 0.00 0.00 45.98 1.40
2406 2807 9.713740 CACAGCTTTTTGCATAAACAAAATAAA 57.286 25.926 0.00 0.00 45.98 1.40
2459 2860 8.504812 AACAAATGCATACATATGACTACACA 57.495 30.769 10.38 0.30 34.62 3.72
2460 2861 8.504812 ACAAATGCATACATATGACTACACAA 57.495 30.769 10.38 0.00 34.62 3.33
2461 2862 8.397906 ACAAATGCATACATATGACTACACAAC 58.602 33.333 10.38 0.00 34.62 3.32
2462 2863 8.397148 CAAATGCATACATATGACTACACAACA 58.603 33.333 10.38 0.00 34.62 3.33
2463 2864 8.681486 AATGCATACATATGACTACACAACAT 57.319 30.769 10.38 0.00 34.62 2.71
2464 2865 8.681486 ATGCATACATATGACTACACAACATT 57.319 30.769 10.38 0.00 35.75 2.71
2465 2866 8.141835 TGCATACATATGACTACACAACATTC 57.858 34.615 10.38 0.00 35.75 2.67
2466 2867 7.768120 TGCATACATATGACTACACAACATTCA 59.232 33.333 10.38 0.00 35.75 2.57
2467 2868 8.278408 GCATACATATGACTACACAACATTCAG 58.722 37.037 10.38 0.00 35.75 3.02
2468 2869 9.317936 CATACATATGACTACACAACATTCAGT 57.682 33.333 10.38 0.00 35.75 3.41
2469 2870 9.890629 ATACATATGACTACACAACATTCAGTT 57.109 29.630 10.38 0.00 42.42 3.16
2480 2881 4.572985 AACATTCAGTTGACCACACATG 57.427 40.909 0.00 0.00 39.49 3.21
2481 2882 3.554934 ACATTCAGTTGACCACACATGT 58.445 40.909 0.00 0.00 0.00 3.21
2482 2883 3.953612 ACATTCAGTTGACCACACATGTT 59.046 39.130 0.00 0.00 0.00 2.71
2483 2884 4.402155 ACATTCAGTTGACCACACATGTTT 59.598 37.500 0.00 0.00 0.00 2.83
2484 2885 4.630894 TTCAGTTGACCACACATGTTTC 57.369 40.909 0.00 0.00 0.00 2.78
2485 2886 2.611751 TCAGTTGACCACACATGTTTCG 59.388 45.455 0.00 0.00 0.00 3.46
2486 2887 2.611751 CAGTTGACCACACATGTTTCGA 59.388 45.455 0.00 0.00 0.00 3.71
2487 2888 3.250762 CAGTTGACCACACATGTTTCGAT 59.749 43.478 0.00 0.00 0.00 3.59
2488 2889 3.882888 AGTTGACCACACATGTTTCGATT 59.117 39.130 0.00 0.00 0.00 3.34
2489 2890 3.894782 TGACCACACATGTTTCGATTG 57.105 42.857 0.00 0.00 0.00 2.67
2490 2891 2.031245 TGACCACACATGTTTCGATTGC 60.031 45.455 0.00 0.00 0.00 3.56
2491 2892 2.226437 GACCACACATGTTTCGATTGCT 59.774 45.455 0.00 0.00 0.00 3.91
2492 2893 2.030893 ACCACACATGTTTCGATTGCTG 60.031 45.455 0.00 0.00 0.00 4.41
2493 2894 2.587956 CACACATGTTTCGATTGCTGG 58.412 47.619 0.00 0.00 0.00 4.85
2494 2895 1.068333 ACACATGTTTCGATTGCTGGC 60.068 47.619 0.00 0.00 0.00 4.85
2495 2896 1.068402 CACATGTTTCGATTGCTGGCA 60.068 47.619 0.00 0.00 0.00 4.92
2496 2897 1.068333 ACATGTTTCGATTGCTGGCAC 60.068 47.619 0.00 0.00 0.00 5.01
2497 2898 0.527565 ATGTTTCGATTGCTGGCACC 59.472 50.000 0.00 0.00 0.00 5.01
2498 2899 1.154225 GTTTCGATTGCTGGCACCG 60.154 57.895 9.26 9.26 0.00 4.94
2499 2900 2.976840 TTTCGATTGCTGGCACCGC 61.977 57.895 10.28 0.00 0.00 5.68
2510 2911 3.660111 GCACCGCCACTGTTGTCC 61.660 66.667 0.00 0.00 0.00 4.02
2511 2912 2.203139 CACCGCCACTGTTGTCCA 60.203 61.111 0.00 0.00 0.00 4.02
2512 2913 1.821759 CACCGCCACTGTTGTCCAA 60.822 57.895 0.00 0.00 0.00 3.53
2513 2914 1.822186 ACCGCCACTGTTGTCCAAC 60.822 57.895 3.21 3.21 41.50 3.77
2524 2925 4.852134 TGTTGTCCAACATTCATCCTTG 57.148 40.909 8.71 0.00 45.42 3.61
2525 2926 3.573538 TGTTGTCCAACATTCATCCTTGG 59.426 43.478 8.71 0.00 45.42 3.61
2526 2927 3.524095 TGTCCAACATTCATCCTTGGT 57.476 42.857 0.00 0.00 36.57 3.67
2527 2928 3.843422 TGTCCAACATTCATCCTTGGTT 58.157 40.909 0.00 0.00 36.57 3.67
2528 2929 3.826157 TGTCCAACATTCATCCTTGGTTC 59.174 43.478 0.00 0.00 36.57 3.62
2529 2930 3.193479 GTCCAACATTCATCCTTGGTTCC 59.807 47.826 0.00 0.00 36.57 3.62
2530 2931 3.164268 CCAACATTCATCCTTGGTTCCA 58.836 45.455 0.00 0.00 31.39 3.53
2531 2932 3.770933 CCAACATTCATCCTTGGTTCCAT 59.229 43.478 0.00 0.00 31.39 3.41
2532 2933 4.382254 CCAACATTCATCCTTGGTTCCATG 60.382 45.833 0.00 0.00 31.39 3.66
2533 2934 3.368248 ACATTCATCCTTGGTTCCATGG 58.632 45.455 4.97 4.97 33.96 3.66
2534 2935 2.530460 TTCATCCTTGGTTCCATGGG 57.470 50.000 13.02 12.36 33.62 4.00
2535 2936 1.679981 TCATCCTTGGTTCCATGGGA 58.320 50.000 13.02 16.19 33.62 4.37
2536 2937 1.565759 TCATCCTTGGTTCCATGGGAG 59.434 52.381 13.02 13.56 33.62 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 4.176752 GGGATGGACAGCGACCCC 62.177 72.222 0.00 0.00 35.00 4.95
275 276 2.363018 TCCAGGCTCTCCAGGTCG 60.363 66.667 0.00 0.00 39.81 4.79
616 617 1.076533 ACGCATTTGCTACGACGAGG 61.077 55.000 0.00 0.00 39.32 4.63
633 634 3.386768 AATCCCGGTCTATGATGAACG 57.613 47.619 0.00 0.00 45.65 3.95
636 637 7.745717 AGAATAAAAATCCCGGTCTATGATGA 58.254 34.615 0.00 0.00 0.00 2.92
688 695 5.262804 ACCACCGAGAGATTAGAGTTTACT 58.737 41.667 0.00 0.00 0.00 2.24
722 742 2.410262 GCACGATGACAACAAGAACGAG 60.410 50.000 0.00 0.00 0.00 4.18
728 748 3.373020 GCAGCACGATGACAACAAG 57.627 52.632 0.00 0.00 0.00 3.16
764 784 3.507162 TCCAAGAAGAAACTCATGGCA 57.493 42.857 0.00 0.00 34.76 4.92
788 808 0.928505 ATGGTGATGGCATTCCTCCA 59.071 50.000 18.56 15.04 38.09 3.86
815 835 2.144730 GAGCTGAGCAATGCTAGGATG 58.855 52.381 8.12 0.00 39.88 3.51
816 836 2.048601 AGAGCTGAGCAATGCTAGGAT 58.951 47.619 8.12 2.09 39.88 3.24
817 837 1.138464 CAGAGCTGAGCAATGCTAGGA 59.862 52.381 8.12 0.00 39.88 2.94
818 838 1.584175 CAGAGCTGAGCAATGCTAGG 58.416 55.000 8.12 5.08 39.88 3.02
820 840 0.907486 ACCAGAGCTGAGCAATGCTA 59.093 50.000 8.12 0.00 39.88 3.49
826 872 0.616964 ATCCAGACCAGAGCTGAGCA 60.617 55.000 7.39 0.00 35.39 4.26
831 877 1.614525 TGGCATCCAGACCAGAGCT 60.615 57.895 0.00 0.00 0.00 4.09
843 889 0.901124 ACTCTGAGTCCACTGGCATC 59.099 55.000 4.06 0.00 0.00 3.91
867 913 2.159114 GCTCCACATCTCCTCAGTTCTC 60.159 54.545 0.00 0.00 0.00 2.87
868 914 1.830477 GCTCCACATCTCCTCAGTTCT 59.170 52.381 0.00 0.00 0.00 3.01
869 915 1.552337 TGCTCCACATCTCCTCAGTTC 59.448 52.381 0.00 0.00 0.00 3.01
870 916 1.554160 CTGCTCCACATCTCCTCAGTT 59.446 52.381 0.00 0.00 0.00 3.16
871 917 1.193323 CTGCTCCACATCTCCTCAGT 58.807 55.000 0.00 0.00 0.00 3.41
872 918 1.409790 CTCTGCTCCACATCTCCTCAG 59.590 57.143 0.00 0.00 0.00 3.35
873 919 1.482954 CTCTGCTCCACATCTCCTCA 58.517 55.000 0.00 0.00 0.00 3.86
894 940 1.398390 CACTCCGTTTTATCTGCAGCC 59.602 52.381 9.47 0.00 0.00 4.85
909 960 2.619177 TCGACTATAAGCAGAGCACTCC 59.381 50.000 0.00 0.00 0.00 3.85
950 1001 3.069289 TGCATTATCTTCAGCATAGCCG 58.931 45.455 0.00 0.00 31.05 5.52
1212 1269 2.400158 CGGCTCGTCTTCCTCGTCT 61.400 63.158 0.00 0.00 0.00 4.18
1542 1623 5.776173 TTAACCAACGACCATGATTTTGT 57.224 34.783 0.00 0.00 0.00 2.83
1546 1627 4.156008 GCTCTTTAACCAACGACCATGATT 59.844 41.667 0.00 0.00 0.00 2.57
1547 1628 3.689649 GCTCTTTAACCAACGACCATGAT 59.310 43.478 0.00 0.00 0.00 2.45
1553 1634 3.391049 ACAGAGCTCTTTAACCAACGAC 58.609 45.455 15.27 0.00 0.00 4.34
1556 1637 5.948992 ATCAACAGAGCTCTTTAACCAAC 57.051 39.130 15.27 0.00 0.00 3.77
1622 1721 8.922676 CCAAGAATCAAAATTCAACAGATTCAG 58.077 33.333 13.80 7.30 44.22 3.02
1668 1767 6.425735 TCAGAATGAGAAGGGAATGCATAAA 58.574 36.000 0.00 0.00 42.56 1.40
1703 1803 0.314578 CTCTAAAATGCGCGCACTCG 60.315 55.000 39.05 22.09 39.07 4.18
1708 1808 1.297893 CTGGCTCTAAAATGCGCGC 60.298 57.895 27.26 27.26 0.00 6.86
1709 1809 1.353103 CCTGGCTCTAAAATGCGCG 59.647 57.895 0.00 0.00 0.00 6.86
1719 1828 3.655211 CCCTTGCACCCTGGCTCT 61.655 66.667 0.00 0.00 34.04 4.09
1735 1844 1.796796 GCCGAGTTGATCTTGCACC 59.203 57.895 0.00 0.00 0.00 5.01
1757 1876 4.560856 TTGCCGTGTGTTTGCCGC 62.561 61.111 0.00 0.00 0.00 6.53
1758 1877 2.103143 TTTGCCGTGTGTTTGCCG 59.897 55.556 0.00 0.00 0.00 5.69
1759 1878 1.880796 GGTTTGCCGTGTGTTTGCC 60.881 57.895 0.00 0.00 0.00 4.52
1760 1879 1.880796 GGGTTTGCCGTGTGTTTGC 60.881 57.895 0.00 0.00 34.97 3.68
1761 1880 0.804156 GTGGGTTTGCCGTGTGTTTG 60.804 55.000 0.00 0.00 34.97 2.93
1762 1881 1.513622 GTGGGTTTGCCGTGTGTTT 59.486 52.632 0.00 0.00 34.97 2.83
1763 1882 2.419739 GGTGGGTTTGCCGTGTGTT 61.420 57.895 0.00 0.00 34.97 3.32
1764 1883 2.831284 GGTGGGTTTGCCGTGTGT 60.831 61.111 0.00 0.00 34.97 3.72
1765 1884 3.601685 GGGTGGGTTTGCCGTGTG 61.602 66.667 0.00 0.00 34.97 3.82
1766 1885 3.444818 ATGGGTGGGTTTGCCGTGT 62.445 57.895 0.00 0.00 34.97 4.49
1767 1886 2.600173 ATGGGTGGGTTTGCCGTG 60.600 61.111 0.00 0.00 34.97 4.94
1821 1941 2.049802 CTTTGCAGCACCTTGGCG 60.050 61.111 0.00 0.00 39.27 5.69
1832 1952 2.197324 GTGTCCCCACCCTTTGCA 59.803 61.111 0.00 0.00 35.44 4.08
1833 1953 1.903404 CAGTGTCCCCACCCTTTGC 60.903 63.158 0.00 0.00 42.88 3.68
1834 1954 1.228552 CCAGTGTCCCCACCCTTTG 60.229 63.158 0.00 0.00 42.88 2.77
1868 1988 3.220110 CGTAGAAGTAGGGTGGCTGATA 58.780 50.000 0.00 0.00 0.00 2.15
1871 1991 0.179108 GCGTAGAAGTAGGGTGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
1875 2221 1.226888 GCGGCGTAGAAGTAGGGTG 60.227 63.158 9.37 0.00 0.00 4.61
1876 2222 2.421399 GGCGGCGTAGAAGTAGGGT 61.421 63.158 9.37 0.00 0.00 4.34
1877 2223 1.952102 TTGGCGGCGTAGAAGTAGGG 61.952 60.000 9.37 0.00 0.00 3.53
1878 2224 0.108520 TTTGGCGGCGTAGAAGTAGG 60.109 55.000 9.37 0.00 0.00 3.18
1879 2225 0.997196 GTTTGGCGGCGTAGAAGTAG 59.003 55.000 9.37 0.00 0.00 2.57
1880 2226 0.317799 TGTTTGGCGGCGTAGAAGTA 59.682 50.000 9.37 0.00 0.00 2.24
1881 2227 0.949105 CTGTTTGGCGGCGTAGAAGT 60.949 55.000 9.37 0.00 0.00 3.01
1882 2228 1.787847 CTGTTTGGCGGCGTAGAAG 59.212 57.895 9.37 0.00 0.00 2.85
1883 2229 2.322081 GCTGTTTGGCGGCGTAGAA 61.322 57.895 9.37 0.00 39.99 2.10
1884 2230 2.740826 GCTGTTTGGCGGCGTAGA 60.741 61.111 9.37 0.00 39.99 2.59
1928 2274 0.804544 CAATACGACACGCACCCGAT 60.805 55.000 0.00 0.00 38.29 4.18
1948 2294 1.299089 CGCCGCATAGATGTCGACA 60.299 57.895 22.48 22.48 32.02 4.35
2038 2384 4.116328 TCGAACAGAGAGCGGGCG 62.116 66.667 0.00 0.00 0.00 6.13
2079 2425 0.104855 GCCTCTGTCGTCATATGGCA 59.895 55.000 8.28 0.00 38.79 4.92
2093 2472 2.400158 CGAAGTCGTCTCCGCCTCT 61.400 63.158 0.00 0.00 34.11 3.69
2098 2477 0.097325 CTTCCTCGAAGTCGTCTCCG 59.903 60.000 0.00 0.00 40.80 4.63
2107 2486 4.399618 TCATCTACTTGGACTTCCTCGAAG 59.600 45.833 0.00 0.00 44.37 3.79
2108 2487 4.158025 GTCATCTACTTGGACTTCCTCGAA 59.842 45.833 0.00 0.00 36.82 3.71
2115 2494 4.323104 GCTTGGAGTCATCTACTTGGACTT 60.323 45.833 0.00 0.00 41.68 3.01
2118 2497 2.501723 GGCTTGGAGTCATCTACTTGGA 59.498 50.000 0.00 0.00 39.07 3.53
2175 2575 3.269520 GGATTAAGGTCCGTCTCGC 57.730 57.895 0.00 0.00 0.00 5.03
2206 2606 0.543749 CCCTCTTCTTTGGATCGGCT 59.456 55.000 0.00 0.00 0.00 5.52
2313 2713 4.485163 GACAAGAATATTGCGCCTTTTGT 58.515 39.130 4.18 6.10 0.00 2.83
2347 2748 0.995024 ACCCAGCTGAAGTATGGCTT 59.005 50.000 17.39 0.00 40.76 4.35
2348 2749 1.765314 CTACCCAGCTGAAGTATGGCT 59.235 52.381 17.39 0.51 36.70 4.75
2349 2750 1.486726 ACTACCCAGCTGAAGTATGGC 59.513 52.381 17.39 0.00 32.46 4.40
2350 2751 2.766263 TGACTACCCAGCTGAAGTATGG 59.234 50.000 17.39 9.23 0.00 2.74
2351 2752 4.471904 TTGACTACCCAGCTGAAGTATG 57.528 45.455 17.39 12.02 0.00 2.39
2352 2753 5.189736 TCAATTGACTACCCAGCTGAAGTAT 59.810 40.000 17.39 4.52 0.00 2.12
2353 2754 4.530553 TCAATTGACTACCCAGCTGAAGTA 59.469 41.667 17.39 15.11 0.00 2.24
2354 2755 3.327757 TCAATTGACTACCCAGCTGAAGT 59.672 43.478 17.39 15.25 0.00 3.01
2355 2756 3.686726 GTCAATTGACTACCCAGCTGAAG 59.313 47.826 27.66 11.98 41.65 3.02
2356 2757 3.674997 GTCAATTGACTACCCAGCTGAA 58.325 45.455 27.66 0.00 41.65 3.02
2357 2758 3.334583 GTCAATTGACTACCCAGCTGA 57.665 47.619 27.66 0.00 41.65 4.26
2366 2767 7.731792 GCAAAAAGCTGTGTAGTCAATTGACTA 60.732 37.037 34.29 34.29 46.16 2.59
2368 2769 5.173854 GCAAAAAGCTGTGTAGTCAATTGAC 59.826 40.000 27.69 27.69 41.95 3.18
2369 2770 5.163571 TGCAAAAAGCTGTGTAGTCAATTGA 60.164 36.000 3.38 3.38 45.94 2.57
2370 2771 5.042593 TGCAAAAAGCTGTGTAGTCAATTG 58.957 37.500 0.00 0.00 45.94 2.32
2371 2772 5.261209 TGCAAAAAGCTGTGTAGTCAATT 57.739 34.783 0.00 0.00 45.94 2.32
2372 2773 4.916983 TGCAAAAAGCTGTGTAGTCAAT 57.083 36.364 0.00 0.00 45.94 2.57
2373 2774 4.916983 ATGCAAAAAGCTGTGTAGTCAA 57.083 36.364 0.00 0.00 45.94 3.18
2374 2775 6.183360 TGTTTATGCAAAAAGCTGTGTAGTCA 60.183 34.615 0.00 0.00 45.94 3.41
2375 2776 6.205784 TGTTTATGCAAAAAGCTGTGTAGTC 58.794 36.000 0.00 0.00 45.94 2.59
2376 2777 6.142818 TGTTTATGCAAAAAGCTGTGTAGT 57.857 33.333 0.00 0.00 45.94 2.73
2377 2778 7.462109 TTTGTTTATGCAAAAAGCTGTGTAG 57.538 32.000 0.00 0.00 45.94 2.74
2378 2779 7.834068 TTTTGTTTATGCAAAAAGCTGTGTA 57.166 28.000 0.00 0.00 42.95 2.90
2379 2780 6.734104 TTTTGTTTATGCAAAAAGCTGTGT 57.266 29.167 0.00 0.00 42.95 3.72
2380 2781 9.713740 TTTATTTTGTTTATGCAAAAAGCTGTG 57.286 25.926 7.84 0.00 46.91 3.66
2433 2834 9.606631 TGTGTAGTCATATGTATGCATTTGTTA 57.393 29.630 3.54 5.91 36.11 2.41
2434 2835 8.504812 TGTGTAGTCATATGTATGCATTTGTT 57.495 30.769 3.54 6.66 36.11 2.83
2435 2836 8.397906 GTTGTGTAGTCATATGTATGCATTTGT 58.602 33.333 3.54 0.00 36.11 2.83
2436 2837 8.397148 TGTTGTGTAGTCATATGTATGCATTTG 58.603 33.333 3.54 4.71 36.58 2.32
2437 2838 8.504812 TGTTGTGTAGTCATATGTATGCATTT 57.495 30.769 3.54 0.00 36.58 2.32
2438 2839 8.681486 ATGTTGTGTAGTCATATGTATGCATT 57.319 30.769 3.54 0.00 36.58 3.56
2439 2840 8.681486 AATGTTGTGTAGTCATATGTATGCAT 57.319 30.769 3.79 3.79 39.03 3.96
2440 2841 7.768120 TGAATGTTGTGTAGTCATATGTATGCA 59.232 33.333 1.90 0.00 33.76 3.96
2441 2842 8.141835 TGAATGTTGTGTAGTCATATGTATGC 57.858 34.615 1.90 0.00 33.76 3.14
2442 2843 9.317936 ACTGAATGTTGTGTAGTCATATGTATG 57.682 33.333 1.90 0.00 35.04 2.39
2443 2844 9.890629 AACTGAATGTTGTGTAGTCATATGTAT 57.109 29.630 1.90 0.00 37.52 2.29
2459 2860 3.953612 ACATGTGTGGTCAACTGAATGTT 59.046 39.130 0.00 0.00 39.92 2.71
2460 2861 3.554934 ACATGTGTGGTCAACTGAATGT 58.445 40.909 0.00 0.00 0.00 2.71
2461 2862 4.572985 AACATGTGTGGTCAACTGAATG 57.427 40.909 0.00 0.00 0.00 2.67
2462 2863 4.261155 CGAAACATGTGTGGTCAACTGAAT 60.261 41.667 0.00 0.00 0.00 2.57
2463 2864 3.064682 CGAAACATGTGTGGTCAACTGAA 59.935 43.478 0.00 0.00 0.00 3.02
2464 2865 2.611751 CGAAACATGTGTGGTCAACTGA 59.388 45.455 0.00 0.00 0.00 3.41
2465 2866 2.611751 TCGAAACATGTGTGGTCAACTG 59.388 45.455 0.00 0.00 0.00 3.16
2466 2867 2.912771 TCGAAACATGTGTGGTCAACT 58.087 42.857 0.00 0.00 0.00 3.16
2467 2868 3.896648 ATCGAAACATGTGTGGTCAAC 57.103 42.857 0.00 0.00 0.00 3.18
2468 2869 3.549827 GCAATCGAAACATGTGTGGTCAA 60.550 43.478 0.00 0.00 0.00 3.18
2469 2870 2.031245 GCAATCGAAACATGTGTGGTCA 60.031 45.455 0.00 0.00 0.00 4.02
2470 2871 2.226437 AGCAATCGAAACATGTGTGGTC 59.774 45.455 0.00 0.00 0.00 4.02
2471 2872 2.030893 CAGCAATCGAAACATGTGTGGT 60.031 45.455 0.00 0.00 0.00 4.16
2472 2873 2.587956 CAGCAATCGAAACATGTGTGG 58.412 47.619 0.00 0.00 0.00 4.17
2473 2874 2.587956 CCAGCAATCGAAACATGTGTG 58.412 47.619 0.00 0.00 0.00 3.82
2474 2875 1.068333 GCCAGCAATCGAAACATGTGT 60.068 47.619 0.00 0.00 0.00 3.72
2475 2876 1.068402 TGCCAGCAATCGAAACATGTG 60.068 47.619 0.00 0.00 0.00 3.21
2476 2877 1.068333 GTGCCAGCAATCGAAACATGT 60.068 47.619 0.00 0.00 0.00 3.21
2477 2878 1.621107 GTGCCAGCAATCGAAACATG 58.379 50.000 0.00 0.00 0.00 3.21
2478 2879 0.527565 GGTGCCAGCAATCGAAACAT 59.472 50.000 0.00 0.00 0.00 2.71
2479 2880 1.851021 CGGTGCCAGCAATCGAAACA 61.851 55.000 10.00 0.00 0.00 2.83
2480 2881 1.154225 CGGTGCCAGCAATCGAAAC 60.154 57.895 10.00 0.00 0.00 2.78
2481 2882 2.976840 GCGGTGCCAGCAATCGAAA 61.977 57.895 17.13 0.00 34.19 3.46
2482 2883 3.430862 GCGGTGCCAGCAATCGAA 61.431 61.111 17.13 0.00 34.19 3.71
2493 2894 3.660111 GGACAACAGTGGCGGTGC 61.660 66.667 0.00 0.00 31.03 5.01
2494 2895 1.821759 TTGGACAACAGTGGCGGTG 60.822 57.895 0.00 0.00 31.03 4.94
2495 2896 1.822186 GTTGGACAACAGTGGCGGT 60.822 57.895 10.13 0.00 40.84 5.68
2496 2897 1.821759 TGTTGGACAACAGTGGCGG 60.822 57.895 13.42 0.00 45.42 6.13
2497 2898 3.820590 TGTTGGACAACAGTGGCG 58.179 55.556 13.42 0.00 45.42 5.69
2504 2905 3.573967 ACCAAGGATGAATGTTGGACAAC 59.426 43.478 8.19 8.19 43.01 3.32
2505 2906 3.843422 ACCAAGGATGAATGTTGGACAA 58.157 40.909 7.32 0.00 43.01 3.18
2506 2907 3.524095 ACCAAGGATGAATGTTGGACA 57.476 42.857 7.32 0.00 43.01 4.02
2507 2908 3.193479 GGAACCAAGGATGAATGTTGGAC 59.807 47.826 7.32 1.63 43.01 4.02
2508 2909 3.181424 TGGAACCAAGGATGAATGTTGGA 60.181 43.478 7.32 0.00 43.01 3.53
2509 2910 3.164268 TGGAACCAAGGATGAATGTTGG 58.836 45.455 0.00 0.00 45.39 3.77
2510 2911 4.382254 CCATGGAACCAAGGATGAATGTTG 60.382 45.833 5.56 0.00 36.99 3.33
2511 2912 3.770933 CCATGGAACCAAGGATGAATGTT 59.229 43.478 5.56 0.00 36.99 2.71
2512 2913 3.368248 CCATGGAACCAAGGATGAATGT 58.632 45.455 5.56 0.00 36.99 2.71
2513 2914 2.696707 CCCATGGAACCAAGGATGAATG 59.303 50.000 15.22 0.00 36.99 2.67
2514 2915 2.586838 TCCCATGGAACCAAGGATGAAT 59.413 45.455 15.22 0.00 36.99 2.57
2515 2916 1.999295 TCCCATGGAACCAAGGATGAA 59.001 47.619 15.22 0.00 36.99 2.57
2516 2917 1.565759 CTCCCATGGAACCAAGGATGA 59.434 52.381 15.22 5.53 36.99 2.92
2517 2918 2.062971 CTCCCATGGAACCAAGGATG 57.937 55.000 15.22 5.16 36.99 3.51


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

AutoCloner maintained by Alex Coulton.