Multiple sequence alignment - TraesCS2A01G374700

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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 TraesCS2A01G374700 chr2A 100.000 4457 0 0 1 4457 617646555 617642099 0.000000e+00 8231.0
1 TraesCS2A01G374700 chr2A 94.000 100 4 1 1712 1809 617644755 617644656 2.780000e-32 150.0
2 TraesCS2A01G374700 chr2B 90.081 1845 125 29 2661 4457 556196454 556194620 0.000000e+00 2340.0
3 TraesCS2A01G374700 chr2B 92.043 1483 66 20 1 1445 556199184 556197716 0.000000e+00 2037.0
4 TraesCS2A01G374700 chr2B 88.065 863 52 20 1801 2655 556197478 556196659 0.000000e+00 976.0
5 TraesCS2A01G374700 chr2B 93.842 341 18 3 1470 1809 556197719 556197381 1.110000e-140 510.0
6 TraesCS2A01G374700 chr2B 96.875 32 0 1 2950 2980 500653185 500653216 8.000000e-03 52.8
7 TraesCS2A01G374700 chr2D 90.375 1787 97 44 1 1738 475090573 475088813 0.000000e+00 2278.0
8 TraesCS2A01G374700 chr2D 91.256 892 34 17 3001 3862 475085918 475085041 0.000000e+00 1175.0
9 TraesCS2A01G374700 chr2D 96.388 609 18 3 3853 4457 475084989 475084381 0.000000e+00 1000.0
10 TraesCS2A01G374700 chr2D 95.874 412 14 3 2124 2533 475088337 475087927 0.000000e+00 664.0
11 TraesCS2A01G374700 chr2D 91.495 388 12 4 2581 2951 475086300 475085917 8.550000e-142 514.0
12 TraesCS2A01G374700 chr2D 88.298 282 24 4 1854 2126 475088779 475088498 3.320000e-86 329.0
13 TraesCS2A01G374700 chr2D 94.444 36 2 0 2950 2985 605518598 605518563 6.230000e-04 56.5
14 TraesCS2A01G374700 chr4A 95.529 425 19 0 1 425 493269293 493269717 0.000000e+00 680.0
15 TraesCS2A01G374700 chr4A 94.836 426 22 0 1 426 738693612 738693187 0.000000e+00 665.0
16 TraesCS2A01G374700 chr4B 95.305 426 20 0 1 426 564751925 564752350 0.000000e+00 676.0
17 TraesCS2A01G374700 chr1B 95.305 426 20 0 1 426 124073789 124074214 0.000000e+00 676.0
18 TraesCS2A01G374700 chr1B 94.836 426 21 1 1 426 85712792 85713216 0.000000e+00 664.0
19 TraesCS2A01G374700 chr1B 100.000 29 0 0 2949 2977 226316680 226316708 2.000000e-03 54.7
20 TraesCS2A01G374700 chr5A 94.824 425 22 0 1 425 671855039 671854615 0.000000e+00 664.0
21 TraesCS2A01G374700 chr7A 94.118 425 25 0 1 425 289953578 289953154 0.000000e+00 647.0
22 TraesCS2A01G374700 chrUn 89.362 47 1 4 2935 2977 117380223 117380269 6.230000e-04 56.5
23 TraesCS2A01G374700 chr7D 100.000 30 0 0 2947 2976 590129236 590129265 6.230000e-04 56.5
24 TraesCS2A01G374700 chr5D 90.698 43 2 1 2944 2984 240087284 240087326 6.230000e-04 56.5
25 TraesCS2A01G374700 chr5D 94.286 35 2 0 2950 2984 240087379 240087345 2.000000e-03 54.7
26 TraesCS2A01G374700 chr6B 96.875 32 1 0 2945 2976 672156303 672156272 2.000000e-03 54.7
27 TraesCS2A01G374700 chr6B 96.875 32 0 1 2950 2980 599054940 599054971 8.000000e-03 52.8


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 TraesCS2A01G374700 chr2A 617642099 617646555 4456 True 4190.500000 8231 97.00000 1 4457 2 chr2A.!!$R1 4456
1 TraesCS2A01G374700 chr2B 556194620 556199184 4564 True 1465.750000 2340 91.00775 1 4457 4 chr2B.!!$R1 4456
2 TraesCS2A01G374700 chr2D 475084381 475090573 6192 True 993.333333 2278 92.28100 1 4457 6 chr2D.!!$R2 4456

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
756 781 2.189784 GAGGTTTAGGGGAGGCGC 59.810 66.667 0.0 0.0 0.00 6.53 F
1307 1338 0.824595 TCGCGGCAGCCTATAGGTTA 60.825 55.000 20.1 0.0 41.18 2.85 F
1994 2071 0.881118 CCGTGCCAGCATTAGTGTTT 59.119 50.000 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2037 1.261619 GCACGGATTAATGAGCCTTCG 59.738 52.381 0.00 0.00 0.00 3.79 R
2237 2477 2.596346 TCAACAAATCCACTGCCACAT 58.404 42.857 0.00 0.00 0.00 3.21 R
3737 5865 1.264020 CACTTTGGTGGACATGTCGTG 59.736 52.381 19.33 14.96 39.59 4.35 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
35 36 9.463443 AAAATTGTACAAGCTGAGTAATTTGAC 57.537 29.630 14.65 0.07 0.00 3.18
36 37 7.986085 ATTGTACAAGCTGAGTAATTTGACT 57.014 32.000 14.65 0.00 0.00 3.41
138 139 8.200792 GGACACAATCACAGTAAGATCTTATCT 58.799 37.037 17.95 13.41 42.61 1.98
168 169 9.547753 GTAGATTTATTATCTTTGTCAGGCTCA 57.452 33.333 0.00 0.00 0.00 4.26
249 250 2.826725 GACACTACCAGTTCTAGCCTGT 59.173 50.000 8.02 0.00 0.00 4.00
277 279 2.710377 ACAAGCAACATCGCAATCCTA 58.290 42.857 0.00 0.00 0.00 2.94
562 566 2.420547 CCGCAAATGGGAGAATCTGAGA 60.421 50.000 0.00 0.00 33.73 3.27
564 568 3.431346 CGCAAATGGGAGAATCTGAGAGA 60.431 47.826 0.00 0.00 33.73 3.10
753 778 2.908796 GCGGAGGTTTAGGGGAGG 59.091 66.667 0.00 0.00 0.00 4.30
754 779 2.908796 CGGAGGTTTAGGGGAGGC 59.091 66.667 0.00 0.00 0.00 4.70
755 780 2.908796 GGAGGTTTAGGGGAGGCG 59.091 66.667 0.00 0.00 0.00 5.52
756 781 2.189784 GAGGTTTAGGGGAGGCGC 59.810 66.667 0.00 0.00 0.00 6.53
757 782 3.402095 GAGGTTTAGGGGAGGCGCC 62.402 68.421 21.89 21.89 36.67 6.53
758 783 4.851179 GGTTTAGGGGAGGCGCCG 62.851 72.222 23.20 0.00 41.60 6.46
759 784 3.777910 GTTTAGGGGAGGCGCCGA 61.778 66.667 23.20 0.00 41.60 5.54
760 785 3.467226 TTTAGGGGAGGCGCCGAG 61.467 66.667 23.20 0.00 41.60 4.63
837 865 4.418328 CCGGCCCATGGAACGGAA 62.418 66.667 31.34 0.00 43.83 4.30
841 870 2.409870 GCCCATGGAACGGAAGCAG 61.410 63.158 15.22 0.00 0.00 4.24
1285 1316 4.556104 CGTTTCGAGTAGTGGTTCTCTTCA 60.556 45.833 0.00 0.00 0.00 3.02
1307 1338 0.824595 TCGCGGCAGCCTATAGGTTA 60.825 55.000 20.10 0.00 41.18 2.85
1371 1414 2.969262 AGCTCTAGGGAAGGATAGTTGC 59.031 50.000 0.00 0.00 0.00 4.17
1446 1498 6.791867 ATATGCAGTTCAGACCTTGTACTA 57.208 37.500 0.00 0.00 35.50 1.82
1448 1500 3.895656 TGCAGTTCAGACCTTGTACTAGT 59.104 43.478 0.00 0.00 35.50 2.57
1449 1501 5.074804 TGCAGTTCAGACCTTGTACTAGTA 58.925 41.667 0.00 0.00 35.50 1.82
1451 1503 5.415077 GCAGTTCAGACCTTGTACTAGTAGA 59.585 44.000 1.87 0.00 35.50 2.59
1453 1505 7.476667 CAGTTCAGACCTTGTACTAGTAGATG 58.523 42.308 1.87 4.43 35.50 2.90
1454 1506 6.603997 AGTTCAGACCTTGTACTAGTAGATGG 59.396 42.308 23.13 23.13 35.87 3.51
1455 1507 6.075949 TCAGACCTTGTACTAGTAGATGGT 57.924 41.667 27.83 27.83 38.83 3.55
1456 1508 5.886474 TCAGACCTTGTACTAGTAGATGGTG 59.114 44.000 30.80 21.29 37.12 4.17
1457 1509 5.886474 CAGACCTTGTACTAGTAGATGGTGA 59.114 44.000 30.80 5.50 37.12 4.02
1458 1510 6.377429 CAGACCTTGTACTAGTAGATGGTGAA 59.623 42.308 30.80 4.87 37.12 3.18
1459 1511 6.377712 AGACCTTGTACTAGTAGATGGTGAAC 59.622 42.308 30.80 20.64 37.12 3.18
1461 1513 6.724905 ACCTTGTACTAGTAGATGGTGAACTT 59.275 38.462 27.24 9.63 36.14 2.66
1463 1515 8.189460 CCTTGTACTAGTAGATGGTGAACTTAC 58.811 40.741 18.83 0.86 0.00 2.34
1464 1516 8.640063 TTGTACTAGTAGATGGTGAACTTACA 57.360 34.615 1.87 0.00 0.00 2.41
1465 1517 8.640063 TGTACTAGTAGATGGTGAACTTACAA 57.360 34.615 1.87 0.00 0.00 2.41
1472 1536 8.475639 AGTAGATGGTGAACTTACAAATCGTAT 58.524 33.333 0.00 0.00 0.00 3.06
1498 1562 1.062002 CTACGCGTTCATGCCGAAATT 59.938 47.619 20.78 0.00 34.69 1.82
1619 1687 4.884668 AAACGACTAGATTCCAGTTCCA 57.115 40.909 0.00 0.00 0.00 3.53
1620 1688 3.870633 ACGACTAGATTCCAGTTCCAC 57.129 47.619 0.00 0.00 0.00 4.02
1621 1689 3.162666 ACGACTAGATTCCAGTTCCACA 58.837 45.455 0.00 0.00 0.00 4.17
1622 1690 3.769844 ACGACTAGATTCCAGTTCCACAT 59.230 43.478 0.00 0.00 0.00 3.21
1623 1691 4.142138 ACGACTAGATTCCAGTTCCACATC 60.142 45.833 0.00 0.00 0.00 3.06
1624 1692 4.098654 CGACTAGATTCCAGTTCCACATCT 59.901 45.833 0.00 0.00 0.00 2.90
1625 1693 5.596845 GACTAGATTCCAGTTCCACATCTC 58.403 45.833 0.00 0.00 0.00 2.75
1659 1727 1.130955 CCAATGTGCACAAAGTTCGC 58.869 50.000 25.72 0.00 0.00 4.70
1794 1863 9.780186 AATAGTAGGATTACAACATTTCTAGGC 57.220 33.333 0.00 0.00 31.96 3.93
1795 1864 7.195374 AGTAGGATTACAACATTTCTAGGCA 57.805 36.000 0.00 0.00 31.96 4.75
1796 1865 7.630082 AGTAGGATTACAACATTTCTAGGCAA 58.370 34.615 0.00 0.00 31.96 4.52
1797 1866 6.759497 AGGATTACAACATTTCTAGGCAAC 57.241 37.500 0.00 0.00 0.00 4.17
1798 1867 6.245408 AGGATTACAACATTTCTAGGCAACA 58.755 36.000 0.00 0.00 41.41 3.33
1799 1868 6.375455 AGGATTACAACATTTCTAGGCAACAG 59.625 38.462 0.00 0.00 41.41 3.16
1800 1869 6.151144 GGATTACAACATTTCTAGGCAACAGT 59.849 38.462 0.00 0.00 41.41 3.55
1801 1870 6.554334 TTACAACATTTCTAGGCAACAGTC 57.446 37.500 0.00 0.00 41.41 3.51
1802 1871 4.718961 ACAACATTTCTAGGCAACAGTCT 58.281 39.130 0.00 0.00 41.41 3.24
1803 1872 5.865085 ACAACATTTCTAGGCAACAGTCTA 58.135 37.500 0.00 0.00 41.41 2.59
1804 1873 5.934625 ACAACATTTCTAGGCAACAGTCTAG 59.065 40.000 0.00 0.00 38.61 2.43
1805 1874 6.166279 CAACATTTCTAGGCAACAGTCTAGA 58.834 40.000 2.90 2.90 43.01 2.43
1806 1875 5.725362 ACATTTCTAGGCAACAGTCTAGAC 58.275 41.667 15.41 15.41 44.03 2.59
1807 1876 5.482175 ACATTTCTAGGCAACAGTCTAGACT 59.518 40.000 20.00 20.00 44.03 3.24
1818 1887 3.459710 AGTCTAGACTGCCCTTAGTGT 57.540 47.619 24.62 0.00 40.75 3.55
1819 1888 3.780626 AGTCTAGACTGCCCTTAGTGTT 58.219 45.455 24.62 0.00 40.75 3.32
1820 1889 3.764972 AGTCTAGACTGCCCTTAGTGTTC 59.235 47.826 24.62 0.00 40.75 3.18
1821 1890 3.097614 TCTAGACTGCCCTTAGTGTTCC 58.902 50.000 0.00 0.00 0.00 3.62
1822 1891 2.031495 AGACTGCCCTTAGTGTTCCT 57.969 50.000 0.00 0.00 0.00 3.36
1823 1892 2.339769 AGACTGCCCTTAGTGTTCCTT 58.660 47.619 0.00 0.00 0.00 3.36
1824 1893 2.711547 AGACTGCCCTTAGTGTTCCTTT 59.288 45.455 0.00 0.00 0.00 3.11
1825 1894 3.138468 AGACTGCCCTTAGTGTTCCTTTT 59.862 43.478 0.00 0.00 0.00 2.27
1826 1895 3.889538 GACTGCCCTTAGTGTTCCTTTTT 59.110 43.478 0.00 0.00 0.00 1.94
1850 1919 6.702716 TTTGGTATCAAAAGGAGTTTTCGT 57.297 33.333 0.00 0.00 39.64 3.85
1851 1920 6.702716 TTGGTATCAAAAGGAGTTTTCGTT 57.297 33.333 0.00 0.00 33.35 3.85
1852 1921 6.308371 TGGTATCAAAAGGAGTTTTCGTTC 57.692 37.500 0.00 0.00 33.35 3.95
1853 1922 5.823570 TGGTATCAAAAGGAGTTTTCGTTCA 59.176 36.000 0.00 0.00 33.35 3.18
1854 1923 6.488683 TGGTATCAAAAGGAGTTTTCGTTCAT 59.511 34.615 0.00 0.00 33.35 2.57
1855 1924 7.013846 TGGTATCAAAAGGAGTTTTCGTTCATT 59.986 33.333 0.00 0.00 33.35 2.57
1856 1925 8.508875 GGTATCAAAAGGAGTTTTCGTTCATTA 58.491 33.333 0.00 0.00 33.35 1.90
1857 1926 9.887406 GTATCAAAAGGAGTTTTCGTTCATTAA 57.113 29.630 0.00 0.00 33.35 1.40
1906 1978 9.632807 CTAGGCAACAATCTAGACTGATATTAC 57.367 37.037 8.44 0.00 36.08 1.89
1960 2037 3.491447 GCATGGGGTATGTTGCATCTTTC 60.491 47.826 0.00 0.00 39.08 2.62
1976 2053 5.561725 GCATCTTTCGAAGGCTCATTAATCC 60.562 44.000 1.73 0.00 0.00 3.01
1994 2071 0.881118 CCGTGCCAGCATTAGTGTTT 59.119 50.000 0.00 0.00 0.00 2.83
1998 2075 3.366273 CGTGCCAGCATTAGTGTTTTGAT 60.366 43.478 0.00 0.00 0.00 2.57
2091 2168 5.393866 AGACCTTTTATTTTGCTCCTGGAA 58.606 37.500 0.00 0.00 0.00 3.53
2237 2477 2.627699 GGCTGATTTGAAAACTGGACCA 59.372 45.455 0.00 0.00 0.00 4.02
2347 2587 7.313951 AGTTGCTTCAATTATAGCTGTCTTC 57.686 36.000 0.00 0.00 38.22 2.87
2350 2590 6.409704 TGCTTCAATTATAGCTGTCTTCTGT 58.590 36.000 0.00 0.00 38.22 3.41
2429 2670 7.556844 TCTAAACTTAACTCAATAGCTCAGGG 58.443 38.462 0.00 0.00 0.00 4.45
2541 2783 8.724229 GTGGTTAATTGATACCTTTTCTAACGT 58.276 33.333 7.47 0.00 35.41 3.99
2563 2807 9.784680 AACGTAGTCTTTATAATGAGTAGTGTG 57.215 33.333 13.51 8.52 45.00 3.82
2564 2808 8.404000 ACGTAGTCTTTATAATGAGTAGTGTGG 58.596 37.037 13.51 6.47 29.74 4.17
2571 2815 2.789409 ATGAGTAGTGTGGCCCTTTC 57.211 50.000 0.00 0.00 0.00 2.62
2572 2816 0.690762 TGAGTAGTGTGGCCCTTTCC 59.309 55.000 0.00 0.00 0.00 3.13
2719 4745 4.832248 TGACGGAGCACAATAAAGATCTT 58.168 39.130 0.88 0.88 0.00 2.40
2757 4783 7.275341 CGCATTTTCTTACAATCCAAATAGCAA 59.725 33.333 0.00 0.00 0.00 3.91
2806 4832 6.971527 TTGGTTACACTACGATGTTATTGG 57.028 37.500 0.00 0.00 33.85 3.16
2901 4930 2.716217 AGAATTTGCCCTCTTTCCTCG 58.284 47.619 0.00 0.00 0.00 4.63
2905 4934 0.984230 TTGCCCTCTTTCCTCGTCAT 59.016 50.000 0.00 0.00 0.00 3.06
2951 5032 9.982651 TGGAGATGCTATAACTCTTTGTAATAC 57.017 33.333 0.00 0.00 0.00 1.89
2955 5036 9.425577 GATGCTATAACTCTTTGTAATACTCCC 57.574 37.037 0.00 0.00 0.00 4.30
2956 5037 8.548880 TGCTATAACTCTTTGTAATACTCCCT 57.451 34.615 0.00 0.00 0.00 4.20
2957 5038 8.639761 TGCTATAACTCTTTGTAATACTCCCTC 58.360 37.037 0.00 0.00 0.00 4.30
2958 5039 8.862085 GCTATAACTCTTTGTAATACTCCCTCT 58.138 37.037 0.00 0.00 0.00 3.69
2960 5041 6.936968 AACTCTTTGTAATACTCCCTCTGT 57.063 37.500 0.00 0.00 0.00 3.41
2961 5042 9.710818 ATAACTCTTTGTAATACTCCCTCTGTA 57.289 33.333 0.00 0.00 0.00 2.74
2962 5043 8.431910 AACTCTTTGTAATACTCCCTCTGTAA 57.568 34.615 0.00 0.00 0.00 2.41
2963 5044 8.431910 ACTCTTTGTAATACTCCCTCTGTAAA 57.568 34.615 0.00 0.00 0.00 2.01
2964 5045 8.532819 ACTCTTTGTAATACTCCCTCTGTAAAG 58.467 37.037 0.00 0.00 0.00 1.85
2965 5046 8.660295 TCTTTGTAATACTCCCTCTGTAAAGA 57.340 34.615 0.00 0.00 0.00 2.52
2966 5047 9.096823 TCTTTGTAATACTCCCTCTGTAAAGAA 57.903 33.333 0.00 0.00 0.00 2.52
2967 5048 9.720769 CTTTGTAATACTCCCTCTGTAAAGAAA 57.279 33.333 0.00 0.00 0.00 2.52
2976 5057 8.371699 ACTCCCTCTGTAAAGAAATATATGAGC 58.628 37.037 0.00 0.00 0.00 4.26
2977 5058 8.497910 TCCCTCTGTAAAGAAATATATGAGCT 57.502 34.615 0.00 0.00 0.00 4.09
2978 5059 8.589338 TCCCTCTGTAAAGAAATATATGAGCTC 58.411 37.037 6.82 6.82 0.00 4.09
2979 5060 8.592809 CCCTCTGTAAAGAAATATATGAGCTCT 58.407 37.037 16.19 3.04 0.00 4.09
2980 5061 9.995003 CCTCTGTAAAGAAATATATGAGCTCTT 57.005 33.333 16.19 11.54 0.00 2.85
2997 5078 8.948631 TGAGCTCTTATATTTGTTTACAGAGG 57.051 34.615 16.19 0.00 0.00 3.69
2998 5079 7.987458 TGAGCTCTTATATTTGTTTACAGAGGG 59.013 37.037 16.19 0.00 0.00 4.30
2999 5080 6.768381 AGCTCTTATATTTGTTTACAGAGGGC 59.232 38.462 0.00 0.00 0.00 5.19
3006 5087 6.775594 ATTTGTTTACAGAGGGCTATTTCC 57.224 37.500 0.00 0.00 0.00 3.13
3363 5446 6.268617 CCTGATACAGAGATTACCCTGATTCA 59.731 42.308 0.00 0.00 32.44 2.57
3551 5645 5.308825 AGACATCAGTTTCTGAACGGATTT 58.691 37.500 3.58 0.00 44.68 2.17
3681 5809 5.885912 AGTGACAGTTATTTGACCTTGTTGT 59.114 36.000 0.00 0.00 0.00 3.32
3691 5819 3.023119 TGACCTTGTTGTGAATGTTGCT 58.977 40.909 0.00 0.00 0.00 3.91
3711 5839 6.691754 TGCTATCTGTCTCTTAACTCTGAG 57.308 41.667 2.45 2.45 0.00 3.35
3751 5879 2.671396 GTCATTACACGACATGTCCACC 59.329 50.000 20.03 0.00 42.09 4.61
3752 5880 2.300437 TCATTACACGACATGTCCACCA 59.700 45.455 20.03 1.27 42.09 4.17
3753 5881 2.912690 TTACACGACATGTCCACCAA 57.087 45.000 20.03 6.86 42.09 3.67
3754 5882 2.912690 TACACGACATGTCCACCAAA 57.087 45.000 20.03 0.00 42.09 3.28
3826 5954 1.332195 GCAAGAGCTTTTGGGGAAGT 58.668 50.000 17.82 0.00 37.91 3.01
3848 5976 2.414691 GCTCAACGATTTTCCTTCTGGC 60.415 50.000 0.00 0.00 0.00 4.85
4113 6308 1.599797 CGACCACCACCACCCTTTC 60.600 63.158 0.00 0.00 0.00 2.62
4117 6312 1.530655 CACCACCACCCTTTCCCAC 60.531 63.158 0.00 0.00 0.00 4.61
4282 6477 3.069318 GAGGCGGACGAGGAGGTT 61.069 66.667 0.00 0.00 0.00 3.50
4288 6483 1.592223 GGACGAGGAGGTTGAGGTG 59.408 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 9.547753 GTGAGCCTGACAAAGATAATAAATCTA 57.452 33.333 0.00 0.00 0.00 1.98
168 169 8.039538 CAGTCCATCATGATACATATAGCTTGT 58.960 37.037 8.15 0.00 0.00 3.16
180 181 9.314133 AGCTATTAGTAACAGTCCATCATGATA 57.686 33.333 8.15 0.00 0.00 2.15
249 250 2.286950 GCGATGTTGCTTGTTGAGTTGA 60.287 45.455 0.00 0.00 0.00 3.18
345 349 2.218603 GTTTGGTGGTTCTGTCGTGAT 58.781 47.619 0.00 0.00 0.00 3.06
456 460 0.692419 AGCAGAAGATGGGGATCCGT 60.692 55.000 5.45 0.00 35.24 4.69
776 801 1.924335 CGTTCCAGTGTGTGTGTCG 59.076 57.895 0.00 0.00 0.00 4.35
841 870 0.798776 CCAAGATTCGTGTGCAGGTC 59.201 55.000 0.00 0.00 0.00 3.85
1224 1255 6.001460 TGGAAAAACGAGAATAAGTGGACAT 58.999 36.000 0.00 0.00 0.00 3.06
1285 1316 1.364171 CTATAGGCTGCCGCGACTT 59.636 57.895 13.96 0.00 36.88 3.01
1307 1338 4.096003 CCCAGCAACCCGACGGAT 62.096 66.667 17.49 0.00 0.00 4.18
1371 1414 3.505464 ATCTCGTCCACCTAAAACTCG 57.495 47.619 0.00 0.00 0.00 4.18
1446 1498 6.698380 ACGATTTGTAAGTTCACCATCTACT 58.302 36.000 0.00 0.00 0.00 2.57
1449 1501 9.095065 GTTATACGATTTGTAAGTTCACCATCT 57.905 33.333 0.00 0.00 36.44 2.90
1451 1503 8.780846 TGTTATACGATTTGTAAGTTCACCAT 57.219 30.769 0.00 0.00 36.44 3.55
1453 1505 9.095065 AGATGTTATACGATTTGTAAGTTCACC 57.905 33.333 0.00 0.00 36.44 4.02
1457 1509 8.749499 GCGTAGATGTTATACGATTTGTAAGTT 58.251 33.333 9.48 0.00 46.89 2.66
1458 1510 7.112565 CGCGTAGATGTTATACGATTTGTAAGT 59.887 37.037 9.48 0.00 46.89 2.24
1459 1511 7.112565 ACGCGTAGATGTTATACGATTTGTAAG 59.887 37.037 11.67 0.00 46.89 2.34
1461 1513 6.429624 ACGCGTAGATGTTATACGATTTGTA 58.570 36.000 11.67 0.00 46.89 2.41
1463 1515 5.801176 ACGCGTAGATGTTATACGATTTG 57.199 39.130 11.67 0.00 46.89 2.32
1464 1516 5.972973 TGAACGCGTAGATGTTATACGATTT 59.027 36.000 14.46 0.00 46.89 2.17
1465 1517 5.513376 TGAACGCGTAGATGTTATACGATT 58.487 37.500 14.46 0.00 46.89 3.34
1472 1536 2.198406 GGCATGAACGCGTAGATGTTA 58.802 47.619 23.70 3.90 0.00 2.41
1498 1562 5.395324 GGCACTAGCATTAAAGACTACCTCA 60.395 44.000 0.00 0.00 44.61 3.86
1579 1644 4.363138 GTTTTGGCAAGATATTAGCAGGC 58.637 43.478 0.00 0.00 0.00 4.85
1659 1727 3.543494 CCATACAAATTTGAAAGAGCGCG 59.457 43.478 24.64 0.00 0.00 6.86
1768 1837 9.780186 GCCTAGAAATGTTGTAATCCTACTATT 57.220 33.333 0.00 0.00 0.00 1.73
1770 1839 8.313944 TGCCTAGAAATGTTGTAATCCTACTA 57.686 34.615 0.00 0.00 0.00 1.82
1771 1840 7.195374 TGCCTAGAAATGTTGTAATCCTACT 57.805 36.000 0.00 0.00 0.00 2.57
1772 1841 7.335924 TGTTGCCTAGAAATGTTGTAATCCTAC 59.664 37.037 0.00 0.00 0.00 3.18
1773 1842 7.398829 TGTTGCCTAGAAATGTTGTAATCCTA 58.601 34.615 0.00 0.00 0.00 2.94
1775 1844 6.151144 ACTGTTGCCTAGAAATGTTGTAATCC 59.849 38.462 0.00 0.00 0.00 3.01
1776 1845 7.119846 AGACTGTTGCCTAGAAATGTTGTAATC 59.880 37.037 0.00 0.00 0.00 1.75
1777 1846 6.942576 AGACTGTTGCCTAGAAATGTTGTAAT 59.057 34.615 0.00 0.00 0.00 1.89
1778 1847 6.296026 AGACTGTTGCCTAGAAATGTTGTAA 58.704 36.000 0.00 0.00 0.00 2.41
1779 1848 5.865085 AGACTGTTGCCTAGAAATGTTGTA 58.135 37.500 0.00 0.00 0.00 2.41
1780 1849 4.718961 AGACTGTTGCCTAGAAATGTTGT 58.281 39.130 0.00 0.00 0.00 3.32
1781 1850 6.091441 GTCTAGACTGTTGCCTAGAAATGTTG 59.909 42.308 15.91 0.00 41.88 3.33
1782 1851 6.014156 AGTCTAGACTGTTGCCTAGAAATGTT 60.014 38.462 24.62 0.00 41.88 2.71
1783 1852 5.482175 AGTCTAGACTGTTGCCTAGAAATGT 59.518 40.000 24.62 0.00 41.88 2.71
1784 1853 5.971763 AGTCTAGACTGTTGCCTAGAAATG 58.028 41.667 24.62 0.00 41.88 2.32
1798 1867 3.459710 ACACTAAGGGCAGTCTAGACT 57.540 47.619 20.00 20.00 43.61 3.24
1799 1868 3.119065 GGAACACTAAGGGCAGTCTAGAC 60.119 52.174 15.41 15.41 0.00 2.59
1800 1869 3.097614 GGAACACTAAGGGCAGTCTAGA 58.902 50.000 0.00 0.00 0.00 2.43
1801 1870 3.100671 AGGAACACTAAGGGCAGTCTAG 58.899 50.000 0.00 0.00 0.00 2.43
1802 1871 3.185880 AGGAACACTAAGGGCAGTCTA 57.814 47.619 0.00 0.00 0.00 2.59
1803 1872 2.031495 AGGAACACTAAGGGCAGTCT 57.969 50.000 0.00 0.00 0.00 3.24
1804 1873 2.861147 AAGGAACACTAAGGGCAGTC 57.139 50.000 0.00 0.00 0.00 3.51
1805 1874 3.595190 AAAAGGAACACTAAGGGCAGT 57.405 42.857 0.00 0.00 0.00 4.40
1826 1895 7.102847 ACGAAAACTCCTTTTGATACCAAAA 57.897 32.000 0.00 0.00 46.55 2.44
1827 1896 6.702716 ACGAAAACTCCTTTTGATACCAAA 57.297 33.333 0.00 0.00 40.24 3.28
1828 1897 6.319152 TGAACGAAAACTCCTTTTGATACCAA 59.681 34.615 0.00 0.00 33.20 3.67
1829 1898 5.823570 TGAACGAAAACTCCTTTTGATACCA 59.176 36.000 0.00 0.00 33.20 3.25
1830 1899 6.308371 TGAACGAAAACTCCTTTTGATACC 57.692 37.500 0.00 0.00 33.20 2.73
1831 1900 9.887406 TTAATGAACGAAAACTCCTTTTGATAC 57.113 29.630 0.00 0.00 33.20 2.24
1839 1908 9.391006 TGCTATTATTAATGAACGAAAACTCCT 57.609 29.630 0.00 0.00 0.00 3.69
1840 1909 9.651718 CTGCTATTATTAATGAACGAAAACTCC 57.348 33.333 0.00 0.00 0.00 3.85
1841 1910 9.651718 CCTGCTATTATTAATGAACGAAAACTC 57.348 33.333 0.00 0.00 0.00 3.01
1842 1911 9.391006 TCCTGCTATTATTAATGAACGAAAACT 57.609 29.630 0.00 0.00 0.00 2.66
1847 1916 9.990360 TGTAATCCTGCTATTATTAATGAACGA 57.010 29.630 0.00 0.00 0.00 3.85
1906 1978 7.021196 CACGGGTTAAAAGAACATCACATAAG 58.979 38.462 0.00 0.00 0.00 1.73
1960 2037 1.261619 GCACGGATTAATGAGCCTTCG 59.738 52.381 0.00 0.00 0.00 3.79
1976 2053 2.031245 TCAAAACACTAATGCTGGCACG 60.031 45.455 0.00 0.00 0.00 5.34
1994 2071 9.676861 ATTCAACATCAGTAATCAGAAGATCAA 57.323 29.630 0.00 0.00 31.90 2.57
2237 2477 2.596346 TCAACAAATCCACTGCCACAT 58.404 42.857 0.00 0.00 0.00 3.21
2388 2628 9.841295 TTAAGTTTAGAACAAAGAGGCTCTTTA 57.159 29.630 34.97 20.67 44.23 1.85
2541 2783 7.201974 GGGCCACACTACTCATTATAAAGACTA 60.202 40.741 4.39 0.00 0.00 2.59
2544 2788 5.665812 AGGGCCACACTACTCATTATAAAGA 59.334 40.000 6.18 0.00 0.00 2.52
2563 2807 4.039852 TGTTGACAATAAAAGGAAAGGGCC 59.960 41.667 0.00 0.00 0.00 5.80
2564 2808 5.208463 TGTTGACAATAAAAGGAAAGGGC 57.792 39.130 0.00 0.00 0.00 5.19
2607 4433 6.924060 AGAATTCGTCTGAAAATAGTATCGGG 59.076 38.462 0.00 0.00 37.71 5.14
2719 4745 4.630894 AGAAAATGCGACACAGAACAAA 57.369 36.364 0.00 0.00 0.00 2.83
2757 4783 4.080695 AGACAATGACTGCCATACATCTGT 60.081 41.667 0.00 0.00 34.45 3.41
2806 4832 9.066892 TGACCAGATTGAATTATAATTGGCTAC 57.933 33.333 15.39 1.60 0.00 3.58
2950 5031 8.371699 GCTCATATATTTCTTTACAGAGGGAGT 58.628 37.037 0.00 0.00 0.00 3.85
2951 5032 8.592809 AGCTCATATATTTCTTTACAGAGGGAG 58.407 37.037 0.00 0.00 0.00 4.30
2952 5033 8.497910 AGCTCATATATTTCTTTACAGAGGGA 57.502 34.615 0.00 0.00 0.00 4.20
2953 5034 8.592809 AGAGCTCATATATTTCTTTACAGAGGG 58.407 37.037 17.77 0.00 0.00 4.30
2954 5035 9.995003 AAGAGCTCATATATTTCTTTACAGAGG 57.005 33.333 17.77 0.00 0.00 3.69
2971 5052 9.553064 CCTCTGTAAACAAATATAAGAGCTCAT 57.447 33.333 17.77 6.59 0.00 2.90
2972 5053 7.987458 CCCTCTGTAAACAAATATAAGAGCTCA 59.013 37.037 17.77 0.00 0.00 4.26
2973 5054 7.041712 GCCCTCTGTAAACAAATATAAGAGCTC 60.042 40.741 5.27 5.27 0.00 4.09
2974 5055 6.768381 GCCCTCTGTAAACAAATATAAGAGCT 59.232 38.462 0.00 0.00 0.00 4.09
2975 5056 6.768381 AGCCCTCTGTAAACAAATATAAGAGC 59.232 38.462 0.00 0.00 0.00 4.09
2980 5061 9.569122 GGAAATAGCCCTCTGTAAACAAATATA 57.431 33.333 0.00 0.00 0.00 0.86
2981 5062 8.282256 AGGAAATAGCCCTCTGTAAACAAATAT 58.718 33.333 0.00 0.00 0.00 1.28
2982 5063 7.639378 AGGAAATAGCCCTCTGTAAACAAATA 58.361 34.615 0.00 0.00 0.00 1.40
2983 5064 6.494059 AGGAAATAGCCCTCTGTAAACAAAT 58.506 36.000 0.00 0.00 0.00 2.32
2984 5065 5.887754 AGGAAATAGCCCTCTGTAAACAAA 58.112 37.500 0.00 0.00 0.00 2.83
2985 5066 5.514500 AGGAAATAGCCCTCTGTAAACAA 57.486 39.130 0.00 0.00 0.00 2.83
2986 5067 6.630203 TTAGGAAATAGCCCTCTGTAAACA 57.370 37.500 0.00 0.00 35.30 2.83
2987 5068 7.054751 ACATTAGGAAATAGCCCTCTGTAAAC 58.945 38.462 0.00 0.00 35.30 2.01
2988 5069 7.127339 AGACATTAGGAAATAGCCCTCTGTAAA 59.873 37.037 0.00 0.00 32.96 2.01
2989 5070 6.615726 AGACATTAGGAAATAGCCCTCTGTAA 59.384 38.462 0.00 0.00 32.96 2.41
2990 5071 6.042093 CAGACATTAGGAAATAGCCCTCTGTA 59.958 42.308 0.00 0.00 32.96 2.74
2991 5072 4.971924 AGACATTAGGAAATAGCCCTCTGT 59.028 41.667 0.00 0.00 34.47 3.41
2992 5073 5.070981 TCAGACATTAGGAAATAGCCCTCTG 59.929 44.000 0.00 0.00 35.30 3.35
2993 5074 5.219739 TCAGACATTAGGAAATAGCCCTCT 58.780 41.667 0.00 0.00 35.30 3.69
2994 5075 5.552870 TCAGACATTAGGAAATAGCCCTC 57.447 43.478 0.00 0.00 35.30 4.30
2995 5076 5.975988 TTCAGACATTAGGAAATAGCCCT 57.024 39.130 0.00 0.00 37.80 5.19
2996 5077 5.409826 CGATTCAGACATTAGGAAATAGCCC 59.590 44.000 0.00 0.00 0.00 5.19
2997 5078 5.106908 GCGATTCAGACATTAGGAAATAGCC 60.107 44.000 0.00 0.00 0.00 3.93
2998 5079 5.698545 AGCGATTCAGACATTAGGAAATAGC 59.301 40.000 0.00 0.00 0.00 2.97
2999 5080 6.703607 ACAGCGATTCAGACATTAGGAAATAG 59.296 38.462 0.00 0.00 0.00 1.73
3006 5087 3.371898 TGCAACAGCGATTCAGACATTAG 59.628 43.478 0.00 0.00 0.00 1.73
3363 5446 3.456277 AGGAGAAACAAGGTGAAGAGTGT 59.544 43.478 0.00 0.00 0.00 3.55
3551 5645 1.295792 GACAACAAACCAGCTCGTCA 58.704 50.000 0.00 0.00 0.00 4.35
3681 5809 7.615403 AGTTAAGAGACAGATAGCAACATTCA 58.385 34.615 0.00 0.00 0.00 2.57
3691 5819 9.742144 AGTAAACTCAGAGTTAAGAGACAGATA 57.258 33.333 16.46 0.00 37.47 1.98
3737 5865 1.264020 CACTTTGGTGGACATGTCGTG 59.736 52.381 19.33 14.96 39.59 4.35
3753 5881 9.751542 CGAGAATAATTAAGACTATGTCCACTT 57.248 33.333 0.00 0.00 32.18 3.16
3754 5882 9.132923 TCGAGAATAATTAAGACTATGTCCACT 57.867 33.333 0.00 0.00 32.18 4.00
3826 5954 2.813754 CCAGAAGGAAAATCGTTGAGCA 59.186 45.455 0.00 0.00 36.89 4.26
3862 6051 6.478016 CCAGCTCTCAAAAGAAAAAGGAAAAG 59.522 38.462 0.00 0.00 0.00 2.27
3899 6088 2.802247 GACAACATGCTTTTTGGGCTTC 59.198 45.455 0.00 0.00 0.00 3.86
3900 6089 2.435437 AGACAACATGCTTTTTGGGCTT 59.565 40.909 0.00 0.00 0.00 4.35
3939 6129 4.163268 GGGAGAGAGGAAGAGCAGTAAAAT 59.837 45.833 0.00 0.00 0.00 1.82
4282 6477 1.305633 CAGCTCCTCCTCCACCTCA 60.306 63.158 0.00 0.00 0.00 3.86
4288 6483 4.154347 CACGGCAGCTCCTCCTCC 62.154 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.