Multiple sequence alignment - TraesCS1B01G246800

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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 TraesCS1B01G246800 chr1B 100.000 2357 0 0 1 2357 436931351 436928995 0.000000e+00 4353.0
1 TraesCS1B01G246800 chr1B 85.455 220 21 11 1795 2009 329484790 329485003 3.940000e-53 219.0
2 TraesCS1B01G246800 chr1B 100.000 81 0 0 2275 2355 63085076 63085156 1.460000e-32 150.0
3 TraesCS1B01G246800 chr1B 90.164 61 2 1 643 699 436930657 436930597 2.510000e-10 76.8
4 TraesCS1B01G246800 chr1B 90.164 61 2 1 695 755 436930709 436930653 2.510000e-10 76.8
5 TraesCS1B01G246800 chr1D 95.863 1813 53 11 1 1799 324623960 324622156 0.000000e+00 2913.0
6 TraesCS1B01G246800 chr1D 87.336 229 11 2 2007 2217 324622158 324621930 1.810000e-61 246.0
7 TraesCS1B01G246800 chr1D 87.692 195 15 8 1796 1989 135785175 135784989 3.940000e-53 219.0
8 TraesCS1B01G246800 chr1D 94.928 138 7 0 2218 2355 324621898 324621761 1.420000e-52 217.0
9 TraesCS1B01G246800 chr1D 96.000 50 1 1 651 699 324623261 324623212 1.940000e-11 80.5
10 TraesCS1B01G246800 chr1D 87.324 71 5 1 695 765 324623325 324623259 6.980000e-11 78.7
11 TraesCS1B01G246800 chr1A 95.131 1561 45 11 254 1799 420381401 420382945 0.000000e+00 2433.0
12 TraesCS1B01G246800 chr1A 94.510 255 12 1 1 255 420380842 420381094 2.200000e-105 392.0
13 TraesCS1B01G246800 chr1A 85.714 294 16 6 2007 2283 420382943 420383227 1.070000e-73 287.0
14 TraesCS1B01G246800 chr1A 96.471 85 2 1 2273 2356 508639816 508639732 3.160000e-29 139.0
15 TraesCS1B01G246800 chr1A 97.826 46 1 0 651 696 420381849 420381894 1.940000e-11 80.5
16 TraesCS1B01G246800 chr1A 91.379 58 1 1 695 752 420381785 420381838 2.510000e-10 76.8
17 TraesCS1B01G246800 chr5D 82.473 736 105 17 936 1656 233488887 233489613 7.150000e-175 623.0
18 TraesCS1B01G246800 chr5B 80.385 831 123 21 939 1754 271576685 271575880 1.560000e-166 595.0
19 TraesCS1B01G246800 chr5A 83.660 612 88 9 943 1547 321713135 321713741 1.220000e-157 566.0
20 TraesCS1B01G246800 chr5A 85.586 222 19 11 1795 2009 670399324 670399109 1.100000e-53 220.0
21 TraesCS1B01G246800 chr5A 90.909 66 4 2 1964 2028 456087028 456086964 1.160000e-13 87.9
22 TraesCS1B01G246800 chr2D 87.037 216 17 10 1796 2010 251324766 251324561 1.410000e-57 233.0
23 TraesCS1B01G246800 chr2D 87.692 195 15 8 1796 1989 68168580 68168766 3.940000e-53 219.0
24 TraesCS1B01G246800 chr2D 97.674 86 0 2 2273 2356 130424469 130424554 1.890000e-31 147.0
25 TraesCS1B01G246800 chr2D 96.364 55 1 1 1964 2018 196841701 196841754 3.230000e-14 89.8
26 TraesCS1B01G246800 chr7D 87.755 196 15 8 1795 1989 122768447 122768260 1.100000e-53 220.0
27 TraesCS1B01G246800 chr7D 87.692 195 15 8 1796 1989 144545806 144545992 3.940000e-53 219.0
28 TraesCS1B01G246800 chr7D 87.692 195 15 8 1796 1989 360914163 360913977 3.940000e-53 219.0
29 TraesCS1B01G246800 chr7D 98.113 53 0 1 1966 2018 264976413 264976362 8.970000e-15 91.6
30 TraesCS1B01G246800 chr2A 86.700 203 17 9 1796 1997 506856882 506857075 1.420000e-52 217.0
31 TraesCS1B01G246800 chr2A 98.780 82 1 0 2274 2355 756497037 756497118 1.890000e-31 147.0
32 TraesCS1B01G246800 chr3D 81.579 228 32 4 473 692 600167322 600167547 1.860000e-41 180.0
33 TraesCS1B01G246800 chr3D 77.570 107 22 1 1200 1306 323246319 323246423 1.960000e-06 63.9
34 TraesCS1B01G246800 chr2B 100.000 81 0 0 2273 2353 440215549 440215629 1.460000e-32 150.0
35 TraesCS1B01G246800 chr2B 97.647 85 0 2 2273 2355 183651617 183651701 6.790000e-31 145.0
36 TraesCS1B01G246800 chr2B 90.909 66 3 2 1959 2022 548626768 548626832 4.170000e-13 86.1
37 TraesCS1B01G246800 chr4D 97.647 85 1 1 2273 2356 506899319 506899235 6.790000e-31 145.0
38 TraesCS1B01G246800 chr4D 96.552 87 1 2 2273 2357 482238178 482238092 2.440000e-30 143.0
39 TraesCS1B01G246800 chr6B 93.548 62 3 1 1959 2020 160905255 160905315 8.970000e-15 91.6


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 TraesCS1B01G246800 chr1B 436928995 436931351 2356 True 1502.20 4353 93.442667 1 2357 3 chr1B.!!$R1 2356
1 TraesCS1B01G246800 chr1D 324621761 324623960 2199 True 707.04 2913 92.290200 1 2355 5 chr1D.!!$R2 2354
2 TraesCS1B01G246800 chr1A 420380842 420383227 2385 False 653.86 2433 92.912000 1 2283 5 chr1A.!!$F1 2282
3 TraesCS1B01G246800 chr5D 233488887 233489613 726 False 623.00 623 82.473000 936 1656 1 chr5D.!!$F1 720
4 TraesCS1B01G246800 chr5B 271575880 271576685 805 True 595.00 595 80.385000 939 1754 1 chr5B.!!$R1 815
5 TraesCS1B01G246800 chr5A 321713135 321713741 606 False 566.00 566 83.660000 943 1547 1 chr5A.!!$F1 604

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
450 761 1.347707 TGTTGGCTCCAGGAGTTGTAG 59.652 52.381 18.37 0.0 31.39 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2125 0.981183 AACGGAGGGAGTACATTGCA 59.019 50.0 0.0 0.0 0.0 4.08 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
87 88 8.579850 TCAAGATTAGTTGTATTTGAATGCCT 57.420 30.769 0.00 0.00 0.00 4.75
313 624 8.148999 CCTAGGTTTTTCTACTAGTTTGTGTCT 58.851 37.037 0.00 0.00 33.93 3.41
450 761 1.347707 TGTTGGCTCCAGGAGTTGTAG 59.652 52.381 18.37 0.00 31.39 2.74
462 773 6.497259 TCCAGGAGTTGTAGACTTGTAATCTT 59.503 38.462 0.00 0.00 39.19 2.40
467 778 7.760340 GGAGTTGTAGACTTGTAATCTTAGGTG 59.240 40.741 0.00 0.00 39.19 4.00
513 824 2.773993 TAAGGTTACTTTCTGCCCGG 57.226 50.000 0.00 0.00 38.14 5.73
712 1023 5.407407 TTTGTTCCCAGCTTGTTTGTTTA 57.593 34.783 0.00 0.00 0.00 2.01
864 1178 8.296713 AGCGCAATAATCTTTTTCTCTTTGTTA 58.703 29.630 11.47 0.00 0.00 2.41
865 1179 9.076596 GCGCAATAATCTTTTTCTCTTTGTTAT 57.923 29.630 0.30 0.00 0.00 1.89
903 1217 7.224522 AGTGGACATATAATTAGGGTACGAC 57.775 40.000 0.00 0.00 0.00 4.34
1079 1397 6.306356 CACATCTCACCTTTAAAATTTGAGCG 59.694 38.462 12.46 9.72 34.82 5.03
1080 1398 4.794169 TCTCACCTTTAAAATTTGAGCGC 58.206 39.130 0.00 0.00 34.82 5.92
1146 1465 8.681486 AAGGATTTCTGCTTTAATTTGCTTTT 57.319 26.923 0.00 0.00 26.80 2.27
1360 1679 4.431894 TTTCATAAATCGAAGTAGCGCG 57.568 40.909 0.00 0.00 0.00 6.86
1375 1695 0.864377 GCGCGCTACGTCATGACTTA 60.864 55.000 26.67 16.91 46.11 2.24
1493 1818 3.504375 TGATCATGATCCTCCTCGATGT 58.496 45.455 28.61 0.00 37.02 3.06
1607 1942 2.492881 TGCAGCACTGTGGATTAAATGG 59.507 45.455 10.21 0.00 0.00 3.16
1611 1946 4.218200 CAGCACTGTGGATTAAATGGTCAA 59.782 41.667 10.21 0.00 0.00 3.18
1670 2005 1.616374 CAAAGGGTTACCAATTGCCGT 59.384 47.619 2.98 0.00 40.13 5.68
1771 2106 5.412526 TTTAATCGAGTTTGCTGTTTCGT 57.587 34.783 0.00 0.00 34.83 3.85
1807 2142 2.332063 AATGCAATGTACTCCCTCCG 57.668 50.000 0.00 0.00 0.00 4.63
1808 2143 1.204146 ATGCAATGTACTCCCTCCGT 58.796 50.000 0.00 0.00 0.00 4.69
1809 2144 0.981183 TGCAATGTACTCCCTCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
1810 2145 1.066430 TGCAATGTACTCCCTCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
1811 2146 1.742750 GCAATGTACTCCCTCCGTTCC 60.743 57.143 0.00 0.00 0.00 3.62
1812 2147 1.831736 CAATGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
1813 2148 3.028850 CAATGTACTCCCTCCGTTCCTA 58.971 50.000 0.00 0.00 0.00 2.94
1814 2149 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
1815 2150 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
1816 2151 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
1817 2152 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
1818 2153 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
1819 2154 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
1820 2155 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1821 2156 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1822 2157 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1823 2158 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1824 2159 5.190132 TCCCTCCGTTCCTAAATATTTGTCA 59.810 40.000 11.05 0.00 0.00 3.58
1825 2160 6.062095 CCCTCCGTTCCTAAATATTTGTCAT 58.938 40.000 11.05 0.00 0.00 3.06
1826 2161 6.546034 CCCTCCGTTCCTAAATATTTGTCATT 59.454 38.462 11.05 0.00 0.00 2.57
1827 2162 7.255139 CCCTCCGTTCCTAAATATTTGTCATTC 60.255 40.741 11.05 0.00 0.00 2.67
1828 2163 7.499232 CCTCCGTTCCTAAATATTTGTCATTCT 59.501 37.037 11.05 0.00 0.00 2.40
1829 2164 9.542462 CTCCGTTCCTAAATATTTGTCATTCTA 57.458 33.333 11.05 0.00 0.00 2.10
1830 2165 9.542462 TCCGTTCCTAAATATTTGTCATTCTAG 57.458 33.333 11.05 0.00 0.00 2.43
1831 2166 9.542462 CCGTTCCTAAATATTTGTCATTCTAGA 57.458 33.333 11.05 0.00 0.00 2.43
1842 2177 8.853077 ATTTGTCATTCTAGACATCTCAACAA 57.147 30.769 0.00 0.00 46.90 2.83
1843 2178 7.895975 TTGTCATTCTAGACATCTCAACAAG 57.104 36.000 0.00 0.00 46.90 3.16
1844 2179 6.997655 TGTCATTCTAGACATCTCAACAAGT 58.002 36.000 0.00 0.00 43.18 3.16
1845 2180 6.870439 TGTCATTCTAGACATCTCAACAAGTG 59.130 38.462 0.00 0.00 43.18 3.16
1846 2181 7.093354 GTCATTCTAGACATCTCAACAAGTGA 58.907 38.462 0.00 0.00 38.40 3.41
1847 2182 7.062839 GTCATTCTAGACATCTCAACAAGTGAC 59.937 40.741 0.00 0.00 38.40 3.67
1848 2183 6.656632 TTCTAGACATCTCAACAAGTGACT 57.343 37.500 0.00 0.00 31.13 3.41
1849 2184 7.761038 TTCTAGACATCTCAACAAGTGACTA 57.239 36.000 0.00 0.00 31.13 2.59
1850 2185 7.147143 TCTAGACATCTCAACAAGTGACTAC 57.853 40.000 0.00 0.00 31.13 2.73
1851 2186 5.791336 AGACATCTCAACAAGTGACTACA 57.209 39.130 0.00 0.00 31.13 2.74
1852 2187 6.352016 AGACATCTCAACAAGTGACTACAT 57.648 37.500 0.00 0.00 31.13 2.29
1853 2188 7.468141 AGACATCTCAACAAGTGACTACATA 57.532 36.000 0.00 0.00 31.13 2.29
1854 2189 7.316640 AGACATCTCAACAAGTGACTACATAC 58.683 38.462 0.00 0.00 31.13 2.39
1855 2190 6.093404 ACATCTCAACAAGTGACTACATACG 58.907 40.000 0.00 0.00 31.13 3.06
1856 2191 5.055642 TCTCAACAAGTGACTACATACGG 57.944 43.478 0.00 0.00 31.13 4.02
1857 2192 4.763279 TCTCAACAAGTGACTACATACGGA 59.237 41.667 0.00 0.00 31.13 4.69
1858 2193 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
1859 2194 4.763279 TCAACAAGTGACTACATACGGAGA 59.237 41.667 0.00 0.00 0.00 3.71
1860 2195 5.242171 TCAACAAGTGACTACATACGGAGAA 59.758 40.000 0.00 0.00 0.00 2.87
1861 2196 5.717078 ACAAGTGACTACATACGGAGAAA 57.283 39.130 0.00 0.00 0.00 2.52
1862 2197 6.092955 ACAAGTGACTACATACGGAGAAAA 57.907 37.500 0.00 0.00 0.00 2.29
1863 2198 6.518493 ACAAGTGACTACATACGGAGAAAAA 58.482 36.000 0.00 0.00 0.00 1.94
1864 2199 7.159372 ACAAGTGACTACATACGGAGAAAAAT 58.841 34.615 0.00 0.00 0.00 1.82
1865 2200 7.117812 ACAAGTGACTACATACGGAGAAAAATG 59.882 37.037 0.00 0.00 0.00 2.32
1866 2201 6.931838 AGTGACTACATACGGAGAAAAATGA 58.068 36.000 0.00 0.00 0.00 2.57
1867 2202 7.383687 AGTGACTACATACGGAGAAAAATGAA 58.616 34.615 0.00 0.00 0.00 2.57
1868 2203 8.041323 AGTGACTACATACGGAGAAAAATGAAT 58.959 33.333 0.00 0.00 0.00 2.57
1869 2204 8.116753 GTGACTACATACGGAGAAAAATGAATG 58.883 37.037 0.00 0.00 0.00 2.67
1870 2205 8.038351 TGACTACATACGGAGAAAAATGAATGA 58.962 33.333 0.00 0.00 0.00 2.57
1871 2206 8.786826 ACTACATACGGAGAAAAATGAATGAA 57.213 30.769 0.00 0.00 0.00 2.57
1872 2207 9.396022 ACTACATACGGAGAAAAATGAATGAAT 57.604 29.630 0.00 0.00 0.00 2.57
1873 2208 9.869844 CTACATACGGAGAAAAATGAATGAATC 57.130 33.333 0.00 0.00 0.00 2.52
1874 2209 8.511604 ACATACGGAGAAAAATGAATGAATCT 57.488 30.769 0.00 0.00 0.00 2.40
1875 2210 9.613428 ACATACGGAGAAAAATGAATGAATCTA 57.387 29.630 0.00 0.00 0.00 1.98
1876 2211 9.869844 CATACGGAGAAAAATGAATGAATCTAC 57.130 33.333 0.00 0.00 0.00 2.59
1877 2212 7.921786 ACGGAGAAAAATGAATGAATCTACA 57.078 32.000 0.00 0.00 0.00 2.74
1878 2213 7.752695 ACGGAGAAAAATGAATGAATCTACAC 58.247 34.615 0.00 0.00 0.00 2.90
1879 2214 7.607991 ACGGAGAAAAATGAATGAATCTACACT 59.392 33.333 0.00 0.00 0.00 3.55
1880 2215 8.119226 CGGAGAAAAATGAATGAATCTACACTC 58.881 37.037 0.00 0.00 0.00 3.51
1881 2216 9.171877 GGAGAAAAATGAATGAATCTACACTCT 57.828 33.333 0.00 0.00 0.00 3.24
1913 2248 8.996651 TGTCTATATACATCTCCTCAACAAGA 57.003 34.615 0.00 0.00 0.00 3.02
1914 2249 9.072375 TGTCTATATACATCTCCTCAACAAGAG 57.928 37.037 0.00 0.00 44.31 2.85
1915 2250 9.073475 GTCTATATACATCTCCTCAACAAGAGT 57.927 37.037 0.00 0.00 43.12 3.24
1916 2251 9.290988 TCTATATACATCTCCTCAACAAGAGTC 57.709 37.037 0.00 0.00 43.12 3.36
1917 2252 3.971245 ACATCTCCTCAACAAGAGTCC 57.029 47.619 0.00 0.00 43.12 3.85
1918 2253 3.242867 ACATCTCCTCAACAAGAGTCCA 58.757 45.455 0.00 0.00 43.12 4.02
1919 2254 3.843027 ACATCTCCTCAACAAGAGTCCAT 59.157 43.478 0.00 0.00 43.12 3.41
1920 2255 4.288105 ACATCTCCTCAACAAGAGTCCATT 59.712 41.667 0.00 0.00 43.12 3.16
1921 2256 4.982241 TCTCCTCAACAAGAGTCCATTT 57.018 40.909 0.00 0.00 43.12 2.32
1922 2257 4.645535 TCTCCTCAACAAGAGTCCATTTG 58.354 43.478 0.00 0.00 43.12 2.32
1923 2258 4.347876 TCTCCTCAACAAGAGTCCATTTGA 59.652 41.667 0.00 0.00 43.12 2.69
1924 2259 5.047566 TCCTCAACAAGAGTCCATTTGAA 57.952 39.130 0.00 0.00 43.12 2.69
1925 2260 5.445069 TCCTCAACAAGAGTCCATTTGAAA 58.555 37.500 0.00 0.00 43.12 2.69
1926 2261 6.070656 TCCTCAACAAGAGTCCATTTGAAAT 58.929 36.000 0.00 0.00 43.12 2.17
1927 2262 6.207417 TCCTCAACAAGAGTCCATTTGAAATC 59.793 38.462 0.00 0.00 43.12 2.17
1928 2263 6.208204 CCTCAACAAGAGTCCATTTGAAATCT 59.792 38.462 0.00 0.00 43.12 2.40
1929 2264 7.206981 TCAACAAGAGTCCATTTGAAATCTC 57.793 36.000 0.00 0.00 0.00 2.75
1930 2265 7.000472 TCAACAAGAGTCCATTTGAAATCTCT 59.000 34.615 2.76 2.76 34.37 3.10
1931 2266 8.156820 TCAACAAGAGTCCATTTGAAATCTCTA 58.843 33.333 7.71 0.00 32.92 2.43
1932 2267 8.449397 CAACAAGAGTCCATTTGAAATCTCTAG 58.551 37.037 7.71 0.00 32.92 2.43
1933 2268 7.911651 ACAAGAGTCCATTTGAAATCTCTAGA 58.088 34.615 7.71 0.00 32.92 2.43
1934 2269 8.378565 ACAAGAGTCCATTTGAAATCTCTAGAA 58.621 33.333 7.71 0.00 32.92 2.10
1935 2270 9.224267 CAAGAGTCCATTTGAAATCTCTAGAAA 57.776 33.333 7.71 0.00 32.92 2.52
1936 2271 9.447157 AAGAGTCCATTTGAAATCTCTAGAAAG 57.553 33.333 7.71 0.00 32.92 2.62
1937 2272 8.820831 AGAGTCCATTTGAAATCTCTAGAAAGA 58.179 33.333 5.99 0.00 31.73 2.52
1938 2273 8.785329 AGTCCATTTGAAATCTCTAGAAAGAC 57.215 34.615 0.00 0.00 0.00 3.01
1939 2274 8.378565 AGTCCATTTGAAATCTCTAGAAAGACA 58.621 33.333 0.00 0.00 0.00 3.41
1940 2275 9.003658 GTCCATTTGAAATCTCTAGAAAGACAA 57.996 33.333 0.00 0.00 0.00 3.18
1941 2276 9.573166 TCCATTTGAAATCTCTAGAAAGACAAA 57.427 29.630 0.00 4.41 0.00 2.83
1960 2295 9.981460 AAGACAAATATTTTAGGAATGGAGAGT 57.019 29.630 0.00 0.00 0.00 3.24
1961 2296 9.620259 AGACAAATATTTTAGGAATGGAGAGTC 57.380 33.333 0.00 0.00 0.00 3.36
1962 2297 9.620259 GACAAATATTTTAGGAATGGAGAGTCT 57.380 33.333 0.00 0.00 0.00 3.24
1972 2307 9.838339 TTAGGAATGGAGAGTCTATTTGAAATC 57.162 33.333 0.00 0.00 27.21 2.17
1973 2308 8.100135 AGGAATGGAGAGTCTATTTGAAATCT 57.900 34.615 0.00 0.00 27.21 2.40
1974 2309 8.210265 AGGAATGGAGAGTCTATTTGAAATCTC 58.790 37.037 0.00 0.00 38.27 2.75
1975 2310 8.210265 GGAATGGAGAGTCTATTTGAAATCTCT 58.790 37.037 7.17 7.17 38.67 3.10
1978 2313 9.653516 ATGGAGAGTCTATTTGAAATCTCTAGA 57.346 33.333 7.38 0.00 38.67 2.43
1979 2314 9.480861 TGGAGAGTCTATTTGAAATCTCTAGAA 57.519 33.333 7.38 0.00 38.67 2.10
2001 2336 8.857694 AGAAAGACAAATATTTTAGGAACGGA 57.142 30.769 0.00 0.00 0.00 4.69
2002 2337 8.947115 AGAAAGACAAATATTTTAGGAACGGAG 58.053 33.333 0.00 0.00 0.00 4.63
2003 2338 7.625828 AAGACAAATATTTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2004 2339 6.120220 AGACAAATATTTTAGGAACGGAGGG 58.880 40.000 0.00 0.00 0.00 4.30
2005 2340 6.069705 ACAAATATTTTAGGAACGGAGGGA 57.930 37.500 0.00 0.00 0.00 4.20
2011 2346 3.967467 TTAGGAACGGAGGGAGTAGAT 57.033 47.619 0.00 0.00 0.00 1.98
2033 2368 8.662781 AGATAATAAAGCAATTTCACGAGCTA 57.337 30.769 0.00 0.00 36.07 3.32
2042 2377 1.860641 TTCACGAGCTATCCCCTCAA 58.139 50.000 0.00 0.00 0.00 3.02
2079 2414 5.359756 TGTATCTCTCATCAACCCATTTCG 58.640 41.667 0.00 0.00 0.00 3.46
2153 2506 1.938625 TTTGCCAGCTTGAAGTTTGC 58.061 45.000 0.00 0.00 0.00 3.68
2260 2644 6.724263 TGGTATTCATAATTTGCACGATGTC 58.276 36.000 0.00 0.00 0.00 3.06
2269 2653 1.655484 TGCACGATGTCTATTGCCAG 58.345 50.000 0.00 0.00 33.86 4.85
2348 2732 2.122167 CGAGCCCTCCTTCTAGCGT 61.122 63.158 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.134574 TGGCAGGACTACACGAAAATT 57.865 42.857 0.00 0.00 0.00 1.82
27 28 2.851263 TGGCAGGACTACACGAAAAT 57.149 45.000 0.00 0.00 0.00 1.82
30 31 2.851263 ATTTGGCAGGACTACACGAA 57.149 45.000 0.00 0.00 0.00 3.85
32 33 5.758296 ACATAATATTTGGCAGGACTACACG 59.242 40.000 0.00 0.00 0.00 4.49
33 34 8.671384 TTACATAATATTTGGCAGGACTACAC 57.329 34.615 0.00 0.00 0.00 2.90
87 88 6.428083 TCAACCTCTACCAATACAGTTGAA 57.572 37.500 0.00 0.00 39.17 2.69
172 173 7.322664 ACATGAAACCGCAAAGAATATGAATT 58.677 30.769 0.00 0.00 0.00 2.17
184 185 4.657436 AAAAAGGTACATGAAACCGCAA 57.343 36.364 13.81 0.00 42.15 4.85
212 215 3.788333 TCAAATTAGAGCTGCAATGGC 57.212 42.857 1.02 0.00 41.68 4.40
213 216 5.657474 ACAATCAAATTAGAGCTGCAATGG 58.343 37.500 1.02 0.00 0.00 3.16
313 624 7.446769 ACAGGACTACACATGTAACATGTTAA 58.553 34.615 19.63 10.66 32.53 2.01
450 761 5.808030 GTCTCTGCACCTAAGATTACAAGTC 59.192 44.000 0.00 0.00 0.00 3.01
513 824 6.438763 CAAGGTCACAAGTTATGAAACCTTC 58.561 40.000 4.67 0.00 46.29 3.46
712 1023 7.550906 GCTGAAAACTATACTCAGGATTCTTGT 59.449 37.037 0.00 0.00 37.62 3.16
887 1201 6.717997 TGATCTGCTGTCGTACCCTAATTATA 59.282 38.462 0.00 0.00 0.00 0.98
1146 1465 3.402110 CTGCCTGTGTGTCATAGTCAAA 58.598 45.455 0.00 0.00 0.00 2.69
1318 1637 2.154462 AGAACCAGTGCCAAGATTTCG 58.846 47.619 0.00 0.00 0.00 3.46
1360 1679 2.854777 CTGCACTAAGTCATGACGTAGC 59.145 50.000 34.57 26.88 43.87 3.58
1375 1695 2.566833 TTCAGTATTGGTGCTGCACT 57.433 45.000 29.54 14.68 37.90 4.40
1493 1818 7.491372 CAGAGTGTACTTTTGCCGATAATAGAA 59.509 37.037 0.00 0.00 0.00 2.10
1670 2005 5.084519 ACCACCTTCTGTTACAGAGATGTA 58.915 41.667 14.99 0.00 41.75 2.29
1790 2125 0.981183 AACGGAGGGAGTACATTGCA 59.019 50.000 0.00 0.00 0.00 4.08
1791 2126 1.653151 GAACGGAGGGAGTACATTGC 58.347 55.000 0.00 0.00 0.00 3.56
1792 2127 1.831736 AGGAACGGAGGGAGTACATTG 59.168 52.381 0.00 0.00 0.00 2.82
1793 2128 2.249309 AGGAACGGAGGGAGTACATT 57.751 50.000 0.00 0.00 0.00 2.71
1794 2129 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
1795 2130 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
1796 2131 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
1798 2133 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
1799 2134 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1800 2135 5.190132 TGACAAATATTTAGGAACGGAGGGA 59.810 40.000 0.00 0.00 0.00 4.20
1801 2136 5.433526 TGACAAATATTTAGGAACGGAGGG 58.566 41.667 0.00 0.00 0.00 4.30
1802 2137 7.499232 AGAATGACAAATATTTAGGAACGGAGG 59.501 37.037 0.00 0.00 0.00 4.30
1803 2138 8.438676 AGAATGACAAATATTTAGGAACGGAG 57.561 34.615 0.00 0.00 0.00 4.63
1804 2139 9.542462 CTAGAATGACAAATATTTAGGAACGGA 57.458 33.333 0.00 0.00 0.00 4.69
1805 2140 9.542462 TCTAGAATGACAAATATTTAGGAACGG 57.458 33.333 0.00 0.00 0.00 4.44
1821 2156 7.062839 GTCACTTGTTGAGATGTCTAGAATGAC 59.937 40.741 0.00 9.06 33.71 3.06
1822 2157 7.039434 AGTCACTTGTTGAGATGTCTAGAATGA 60.039 37.037 0.00 0.00 33.71 2.57
1823 2158 7.095910 AGTCACTTGTTGAGATGTCTAGAATG 58.904 38.462 0.00 0.00 33.71 2.67
1824 2159 7.238486 AGTCACTTGTTGAGATGTCTAGAAT 57.762 36.000 0.00 0.00 33.71 2.40
1825 2160 6.656632 AGTCACTTGTTGAGATGTCTAGAA 57.343 37.500 0.00 0.00 33.71 2.10
1826 2161 6.715264 TGTAGTCACTTGTTGAGATGTCTAGA 59.285 38.462 0.00 0.00 33.71 2.43
1827 2162 6.914259 TGTAGTCACTTGTTGAGATGTCTAG 58.086 40.000 0.00 0.00 33.71 2.43
1828 2163 6.894339 TGTAGTCACTTGTTGAGATGTCTA 57.106 37.500 0.00 0.00 33.71 2.59
1829 2164 5.791336 TGTAGTCACTTGTTGAGATGTCT 57.209 39.130 0.00 0.00 33.71 3.41
1830 2165 6.251589 CGTATGTAGTCACTTGTTGAGATGTC 59.748 42.308 0.00 0.00 33.71 3.06
1831 2166 6.093404 CGTATGTAGTCACTTGTTGAGATGT 58.907 40.000 0.00 0.00 33.71 3.06
1832 2167 5.516696 CCGTATGTAGTCACTTGTTGAGATG 59.483 44.000 0.00 0.00 33.71 2.90
1833 2168 5.417894 TCCGTATGTAGTCACTTGTTGAGAT 59.582 40.000 0.00 0.00 33.71 2.75
1834 2169 4.763279 TCCGTATGTAGTCACTTGTTGAGA 59.237 41.667 0.00 0.00 33.71 3.27
1835 2170 5.055642 TCCGTATGTAGTCACTTGTTGAG 57.944 43.478 0.00 0.00 33.71 3.02
1836 2171 4.763279 TCTCCGTATGTAGTCACTTGTTGA 59.237 41.667 0.00 0.00 0.00 3.18
1837 2172 5.055642 TCTCCGTATGTAGTCACTTGTTG 57.944 43.478 0.00 0.00 0.00 3.33
1838 2173 5.717078 TTCTCCGTATGTAGTCACTTGTT 57.283 39.130 0.00 0.00 0.00 2.83
1839 2174 5.717078 TTTCTCCGTATGTAGTCACTTGT 57.283 39.130 0.00 0.00 0.00 3.16
1840 2175 7.330946 TCATTTTTCTCCGTATGTAGTCACTTG 59.669 37.037 0.00 0.00 0.00 3.16
1841 2176 7.383687 TCATTTTTCTCCGTATGTAGTCACTT 58.616 34.615 0.00 0.00 0.00 3.16
1842 2177 6.931838 TCATTTTTCTCCGTATGTAGTCACT 58.068 36.000 0.00 0.00 0.00 3.41
1843 2178 7.591006 TTCATTTTTCTCCGTATGTAGTCAC 57.409 36.000 0.00 0.00 0.00 3.67
1844 2179 8.038351 TCATTCATTTTTCTCCGTATGTAGTCA 58.962 33.333 0.00 0.00 0.00 3.41
1845 2180 8.420374 TCATTCATTTTTCTCCGTATGTAGTC 57.580 34.615 0.00 0.00 0.00 2.59
1846 2181 8.786826 TTCATTCATTTTTCTCCGTATGTAGT 57.213 30.769 0.00 0.00 0.00 2.73
1847 2182 9.869844 GATTCATTCATTTTTCTCCGTATGTAG 57.130 33.333 0.00 0.00 0.00 2.74
1848 2183 9.613428 AGATTCATTCATTTTTCTCCGTATGTA 57.387 29.630 0.00 0.00 0.00 2.29
1849 2184 8.511604 AGATTCATTCATTTTTCTCCGTATGT 57.488 30.769 0.00 0.00 0.00 2.29
1850 2185 9.869844 GTAGATTCATTCATTTTTCTCCGTATG 57.130 33.333 0.00 0.00 0.00 2.39
1851 2186 9.613428 TGTAGATTCATTCATTTTTCTCCGTAT 57.387 29.630 0.00 0.00 0.00 3.06
1852 2187 8.879759 GTGTAGATTCATTCATTTTTCTCCGTA 58.120 33.333 0.00 0.00 0.00 4.02
1853 2188 7.607991 AGTGTAGATTCATTCATTTTTCTCCGT 59.392 33.333 0.00 0.00 0.00 4.69
1854 2189 7.978982 AGTGTAGATTCATTCATTTTTCTCCG 58.021 34.615 0.00 0.00 0.00 4.63
1855 2190 9.171877 AGAGTGTAGATTCATTCATTTTTCTCC 57.828 33.333 0.00 0.00 0.00 3.71
1887 2222 9.593565 TCTTGTTGAGGAGATGTATATAGACAT 57.406 33.333 12.70 12.70 42.82 3.06
1888 2223 8.996651 TCTTGTTGAGGAGATGTATATAGACA 57.003 34.615 2.07 2.07 0.00 3.41
1889 2224 9.073475 ACTCTTGTTGAGGAGATGTATATAGAC 57.927 37.037 0.00 0.00 46.72 2.59
1890 2225 9.290988 GACTCTTGTTGAGGAGATGTATATAGA 57.709 37.037 0.00 0.00 46.72 1.98
1891 2226 8.519526 GGACTCTTGTTGAGGAGATGTATATAG 58.480 40.741 0.00 0.00 46.72 1.31
1892 2227 8.004801 TGGACTCTTGTTGAGGAGATGTATATA 58.995 37.037 0.00 0.00 46.72 0.86
1893 2228 6.841229 TGGACTCTTGTTGAGGAGATGTATAT 59.159 38.462 0.00 0.00 46.72 0.86
1894 2229 6.194967 TGGACTCTTGTTGAGGAGATGTATA 58.805 40.000 0.00 0.00 46.72 1.47
1895 2230 5.026121 TGGACTCTTGTTGAGGAGATGTAT 58.974 41.667 0.00 0.00 46.72 2.29
1896 2231 4.416516 TGGACTCTTGTTGAGGAGATGTA 58.583 43.478 0.00 0.00 46.72 2.29
1897 2232 3.242867 TGGACTCTTGTTGAGGAGATGT 58.757 45.455 0.00 0.00 46.72 3.06
1898 2233 3.969287 TGGACTCTTGTTGAGGAGATG 57.031 47.619 0.00 0.00 46.72 2.90
1899 2234 5.013495 TCAAATGGACTCTTGTTGAGGAGAT 59.987 40.000 0.00 0.00 46.72 2.75
1900 2235 4.347876 TCAAATGGACTCTTGTTGAGGAGA 59.652 41.667 0.00 0.00 46.72 3.71
1901 2236 4.645535 TCAAATGGACTCTTGTTGAGGAG 58.354 43.478 0.00 0.00 46.72 3.69
1902 2237 4.705110 TCAAATGGACTCTTGTTGAGGA 57.295 40.909 0.00 0.00 46.72 3.71
1903 2238 5.772825 TTTCAAATGGACTCTTGTTGAGG 57.227 39.130 0.00 0.00 46.72 3.86
1905 2240 7.000472 AGAGATTTCAAATGGACTCTTGTTGA 59.000 34.615 0.00 0.00 31.93 3.18
1906 2241 7.211966 AGAGATTTCAAATGGACTCTTGTTG 57.788 36.000 0.00 0.00 31.93 3.33
1907 2242 8.378565 TCTAGAGATTTCAAATGGACTCTTGTT 58.621 33.333 5.41 0.00 36.39 2.83
1908 2243 7.911651 TCTAGAGATTTCAAATGGACTCTTGT 58.088 34.615 5.41 0.00 36.39 3.16
1909 2244 8.783833 TTCTAGAGATTTCAAATGGACTCTTG 57.216 34.615 5.41 4.49 36.39 3.02
1910 2245 9.447157 CTTTCTAGAGATTTCAAATGGACTCTT 57.553 33.333 5.41 0.00 36.39 2.85
1911 2246 8.820831 TCTTTCTAGAGATTTCAAATGGACTCT 58.179 33.333 5.43 5.43 38.15 3.24
1912 2247 8.878769 GTCTTTCTAGAGATTTCAAATGGACTC 58.121 37.037 0.00 0.00 0.00 3.36
1913 2248 8.378565 TGTCTTTCTAGAGATTTCAAATGGACT 58.621 33.333 0.00 0.00 0.00 3.85
1914 2249 8.553459 TGTCTTTCTAGAGATTTCAAATGGAC 57.447 34.615 0.00 0.00 0.00 4.02
1915 2250 9.573166 TTTGTCTTTCTAGAGATTTCAAATGGA 57.427 29.630 0.00 0.00 0.00 3.41
1934 2269 9.981460 ACTCTCCATTCCTAAAATATTTGTCTT 57.019 29.630 0.39 0.00 0.00 3.01
1935 2270 9.620259 GACTCTCCATTCCTAAAATATTTGTCT 57.380 33.333 0.39 0.00 0.00 3.41
1936 2271 9.620259 AGACTCTCCATTCCTAAAATATTTGTC 57.380 33.333 0.39 0.53 0.00 3.18
1946 2281 9.838339 GATTTCAAATAGACTCTCCATTCCTAA 57.162 33.333 0.00 0.00 0.00 2.69
1947 2282 9.218525 AGATTTCAAATAGACTCTCCATTCCTA 57.781 33.333 0.00 0.00 0.00 2.94
1948 2283 8.100135 AGATTTCAAATAGACTCTCCATTCCT 57.900 34.615 0.00 0.00 0.00 3.36
1949 2284 8.210265 AGAGATTTCAAATAGACTCTCCATTCC 58.790 37.037 0.00 0.00 36.57 3.01
1952 2287 9.653516 TCTAGAGATTTCAAATAGACTCTCCAT 57.346 33.333 3.65 0.00 36.57 3.41
1953 2288 9.480861 TTCTAGAGATTTCAAATAGACTCTCCA 57.519 33.333 3.65 0.00 36.57 3.86
1975 2310 9.947433 TCCGTTCCTAAAATATTTGTCTTTCTA 57.053 29.630 0.39 0.00 0.00 2.10
1976 2311 8.857694 TCCGTTCCTAAAATATTTGTCTTTCT 57.142 30.769 0.39 0.00 0.00 2.52
1977 2312 8.182227 CCTCCGTTCCTAAAATATTTGTCTTTC 58.818 37.037 0.39 0.00 0.00 2.62
1978 2313 7.122204 CCCTCCGTTCCTAAAATATTTGTCTTT 59.878 37.037 0.39 0.00 0.00 2.52
1979 2314 6.602009 CCCTCCGTTCCTAAAATATTTGTCTT 59.398 38.462 0.39 0.00 0.00 3.01
1980 2315 6.069847 TCCCTCCGTTCCTAAAATATTTGTCT 60.070 38.462 0.39 0.00 0.00 3.41
1981 2316 6.117488 TCCCTCCGTTCCTAAAATATTTGTC 58.883 40.000 0.39 0.00 0.00 3.18
1982 2317 6.069705 TCCCTCCGTTCCTAAAATATTTGT 57.930 37.500 0.39 0.00 0.00 2.83
1983 2318 6.120220 ACTCCCTCCGTTCCTAAAATATTTG 58.880 40.000 0.39 0.00 0.00 2.32
1984 2319 6.323210 ACTCCCTCCGTTCCTAAAATATTT 57.677 37.500 0.00 0.00 0.00 1.40
1985 2320 5.970501 ACTCCCTCCGTTCCTAAAATATT 57.029 39.130 0.00 0.00 0.00 1.28
1986 2321 6.379579 TCTACTCCCTCCGTTCCTAAAATAT 58.620 40.000 0.00 0.00 0.00 1.28
1987 2322 5.769835 TCTACTCCCTCCGTTCCTAAAATA 58.230 41.667 0.00 0.00 0.00 1.40
1988 2323 4.617593 TCTACTCCCTCCGTTCCTAAAAT 58.382 43.478 0.00 0.00 0.00 1.82
1989 2324 4.051661 TCTACTCCCTCCGTTCCTAAAA 57.948 45.455 0.00 0.00 0.00 1.52
1990 2325 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
1991 2326 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
1992 2327 5.595814 ATTATCTACTCCCTCCGTTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
1993 2328 3.967467 TTATCTACTCCCTCCGTTCCT 57.033 47.619 0.00 0.00 0.00 3.36
1994 2329 6.661304 TTTATTATCTACTCCCTCCGTTCC 57.339 41.667 0.00 0.00 0.00 3.62
1995 2330 6.157904 GCTTTATTATCTACTCCCTCCGTTC 58.842 44.000 0.00 0.00 0.00 3.95
1996 2331 5.601313 TGCTTTATTATCTACTCCCTCCGTT 59.399 40.000 0.00 0.00 0.00 4.44
1997 2332 5.145564 TGCTTTATTATCTACTCCCTCCGT 58.854 41.667 0.00 0.00 0.00 4.69
1998 2333 5.723672 TGCTTTATTATCTACTCCCTCCG 57.276 43.478 0.00 0.00 0.00 4.63
1999 2334 8.926092 AAATTGCTTTATTATCTACTCCCTCC 57.074 34.615 0.00 0.00 0.00 4.30
2000 2335 9.561069 TGAAATTGCTTTATTATCTACTCCCTC 57.439 33.333 0.00 0.00 0.00 4.30
2001 2336 9.343539 GTGAAATTGCTTTATTATCTACTCCCT 57.656 33.333 0.00 0.00 0.00 4.20
2002 2337 8.283291 CGTGAAATTGCTTTATTATCTACTCCC 58.717 37.037 0.00 0.00 0.00 4.30
2003 2338 9.042008 TCGTGAAATTGCTTTATTATCTACTCC 57.958 33.333 0.00 0.00 0.00 3.85
2005 2340 8.552034 GCTCGTGAAATTGCTTTATTATCTACT 58.448 33.333 0.00 0.00 0.00 2.57
2011 2346 7.041372 GGGATAGCTCGTGAAATTGCTTTATTA 60.041 37.037 0.00 0.00 37.02 0.98
2033 2368 6.889177 ACAAACAAAACAAAAATTGAGGGGAT 59.111 30.769 0.00 0.00 0.00 3.85
2120 2456 1.202114 TGGCAAAATTCAAGCTAGGCG 59.798 47.619 0.00 0.00 0.00 5.52
2177 2530 7.439955 ACAGTTCATGTTGATACAGAAACGTAA 59.560 33.333 0.00 0.00 39.96 3.18
2233 2617 8.196771 ACATCGTGCAAATTATGAATACCAAAT 58.803 29.630 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.