Multiple sequence alignment - TraesCS7A01G113100

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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 TraesCS7A01G113100 chr7A 100.000 2258 0 0 1 2258 69525946 69528203 0.000000e+00 4170.0
1 TraesCS7A01G113100 chr7A 83.625 800 70 39 512 1272 69363571 69364348 0.000000e+00 695.0
2 TraesCS7A01G113100 chr7A 81.944 504 38 29 156 654 69363055 69363510 5.890000e-101 377.0
3 TraesCS7A01G113100 chr7A 77.601 567 67 35 712 1259 69224906 69225431 2.840000e-74 289.0
4 TraesCS7A01G113100 chr7A 80.224 268 34 13 512 778 69309970 69310219 1.380000e-42 183.0
5 TraesCS7A01G113100 chr7A 86.391 169 12 6 5 171 69362878 69363037 8.290000e-40 174.0
6 TraesCS7A01G113100 chr7A 89.109 101 10 1 2150 2249 33150631 33150731 8.470000e-25 124.0
7 TraesCS7A01G113100 chr7D 83.423 2051 184 91 75 2069 65389633 65391583 0.000000e+00 1760.0
8 TraesCS7A01G113100 chr7D 78.078 593 64 48 694 1259 64893569 64894122 4.680000e-82 315.0
9 TraesCS7A01G113100 chr7D 82.609 299 36 8 968 1258 64912481 64912771 1.340000e-62 250.0
10 TraesCS7A01G113100 chr7D 77.754 463 56 24 323 776 64911941 64912365 8.060000e-60 241.0
11 TraesCS7A01G113100 chr7D 79.909 219 29 11 1654 1866 468510075 468510284 1.810000e-31 147.0
12 TraesCS7A01G113100 chr7D 86.726 113 12 3 2139 2249 340264412 340264523 3.050000e-24 122.0
13 TraesCS7A01G113100 chr7D 97.222 36 1 0 42 77 65389105 65389140 6.730000e-06 62.1
14 TraesCS7A01G113100 chr7B 85.012 1728 135 59 512 2146 6796511 6798207 0.000000e+00 1642.0
15 TraesCS7A01G113100 chr7B 91.530 791 52 10 731 1513 6921539 6920756 0.000000e+00 1075.0
16 TraesCS7A01G113100 chr7B 90.922 683 22 15 32 703 6922189 6921536 0.000000e+00 881.0
17 TraesCS7A01G113100 chr7B 81.287 668 51 30 5 662 6795865 6796468 7.300000e-130 473.0
18 TraesCS7A01G113100 chr7B 75.223 783 114 52 681 1431 6755102 6755836 4.710000e-77 298.0
19 TraesCS7A01G113100 chr7B 78.599 514 56 27 276 778 6782633 6783103 7.890000e-75 291.0
20 TraesCS7A01G113100 chr7B 80.833 360 45 9 1498 1840 6920087 6919735 6.190000e-66 261.0
21 TraesCS7A01G113100 chr7B 80.365 219 28 12 1654 1866 491918830 491919039 3.880000e-33 152.0
22 TraesCS7A01G113100 chr7B 88.288 111 12 1 2149 2258 706131107 706130997 5.060000e-27 132.0
23 TraesCS7A01G113100 chr4A 80.321 249 37 7 1631 1871 54725309 54725065 6.410000e-41 178.0
24 TraesCS7A01G113100 chr4A 89.216 102 8 3 2150 2249 670153263 670153363 8.470000e-25 124.0
25 TraesCS7A01G113100 chr5D 77.737 274 39 11 1631 1885 181878565 181878295 5.020000e-32 148.0
26 TraesCS7A01G113100 chr2A 91.919 99 5 3 2162 2258 288987265 288987168 3.910000e-28 135.0
27 TraesCS7A01G113100 chr6A 89.796 98 9 1 2153 2249 501168877 501168780 8.470000e-25 124.0
28 TraesCS7A01G113100 chr3B 89.216 102 8 3 2150 2249 130625898 130625998 8.470000e-25 124.0
29 TraesCS7A01G113100 chr1B 87.963 108 10 3 2153 2258 547249314 547249208 8.470000e-25 124.0
30 TraesCS7A01G113100 chr1A 87.387 111 10 4 2151 2258 405146832 405146941 8.470000e-25 124.0
31 TraesCS7A01G113100 chr5B 77.901 181 35 1 1696 1871 153182971 153182791 8.530000e-20 108.0
32 TraesCS7A01G113100 chr5B 72.751 389 60 21 1589 1947 439971645 439972017 3.090000e-14 89.8
33 TraesCS7A01G113100 chr3A 76.555 209 38 10 1665 1867 646005737 646005534 1.100000e-18 104.0
34 TraesCS7A01G113100 chr3D 75.962 208 43 6 1665 1867 603747973 603747768 1.430000e-17 100.0
35 TraesCS7A01G113100 chr6B 100.000 31 0 0 1836 1866 693303324 693303354 8.710000e-05 58.4


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 TraesCS7A01G113100 chr7A 69525946 69528203 2257 False 4170.000000 4170 100.000000 1 2258 1 chr7A.!!$F4 2257
1 TraesCS7A01G113100 chr7A 69362878 69364348 1470 False 415.333333 695 83.986667 5 1272 3 chr7A.!!$F5 1267
2 TraesCS7A01G113100 chr7A 69224906 69225431 525 False 289.000000 289 77.601000 712 1259 1 chr7A.!!$F2 547
3 TraesCS7A01G113100 chr7D 65389105 65391583 2478 False 911.050000 1760 90.322500 42 2069 2 chr7D.!!$F5 2027
4 TraesCS7A01G113100 chr7D 64893569 64894122 553 False 315.000000 315 78.078000 694 1259 1 chr7D.!!$F1 565
5 TraesCS7A01G113100 chr7D 64911941 64912771 830 False 245.500000 250 80.181500 323 1258 2 chr7D.!!$F4 935
6 TraesCS7A01G113100 chr7B 6795865 6798207 2342 False 1057.500000 1642 83.149500 5 2146 2 chr7B.!!$F4 2141
7 TraesCS7A01G113100 chr7B 6919735 6922189 2454 True 739.000000 1075 87.761667 32 1840 3 chr7B.!!$R2 1808
8 TraesCS7A01G113100 chr7B 6755102 6755836 734 False 298.000000 298 75.223000 681 1431 1 chr7B.!!$F1 750

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
917 1773 0.035152 AGCATTCCATTCCACGAGCA 60.035 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 3805 1.009552 TGGGGATATCACTGTCCACCT 59.99 52.381 4.65 0.0 35.25 4.0 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
45 46 4.793353 GCCGTATGCATAGTATAGCTAGCC 60.793 50.000 12.13 0.00 40.77 3.93
117 618 1.671328 CTAGCTCAATGACTCGACCGA 59.329 52.381 0.00 0.00 0.00 4.69
118 619 1.107114 AGCTCAATGACTCGACCGAT 58.893 50.000 0.00 0.00 0.00 4.18
119 620 2.298610 AGCTCAATGACTCGACCGATA 58.701 47.619 0.00 0.00 0.00 2.92
120 621 2.292016 AGCTCAATGACTCGACCGATAG 59.708 50.000 0.00 0.00 0.00 2.08
167 701 2.097466 CGATGGAGTTACAAATGGGTGC 59.903 50.000 0.00 0.00 0.00 5.01
206 744 5.233957 TCTTTGACATATCAACAATGGCG 57.766 39.130 0.00 0.00 44.66 5.69
208 746 5.877564 TCTTTGACATATCAACAATGGCGTA 59.122 36.000 0.00 0.00 44.66 4.42
229 767 1.580893 TGCGCGCTTACGTACGTAG 60.581 57.895 33.29 20.09 42.83 3.51
296 834 1.797046 GCGGTGAGAGATATGCATGTG 59.203 52.381 10.16 0.00 0.00 3.21
297 835 1.797046 CGGTGAGAGATATGCATGTGC 59.203 52.381 10.16 0.00 42.50 4.57
321 863 1.978455 ATGAAGATTACGGCGGCCCA 61.978 55.000 14.55 2.88 0.00 5.36
507 1053 9.976511 AAAGAAAACATGCATGGATATCTATTG 57.023 29.630 29.41 2.68 0.00 1.90
598 1154 3.575805 TCTCCTCCAACTTGCCAATTTT 58.424 40.909 0.00 0.00 0.00 1.82
621 1177 8.870160 TTTGTATTTGCAACAAGGCATATATC 57.130 30.769 0.00 0.00 44.48 1.63
622 1178 7.579761 TGTATTTGCAACAAGGCATATATCA 57.420 32.000 0.00 0.00 44.48 2.15
663 1227 1.133253 CACGAGCATCAAGTTGCCG 59.867 57.895 0.00 10.35 43.83 5.69
666 1230 3.056313 GAGCATCAAGTTGCCGGCC 62.056 63.158 26.77 9.73 43.83 6.13
699 1489 1.092348 CGGTGAGTGACGGTATGAGA 58.908 55.000 0.00 0.00 0.00 3.27
705 1495 5.009710 GGTGAGTGACGGTATGAGATCATTA 59.990 44.000 0.00 0.00 37.76 1.90
862 1679 0.445436 AGCTACGTCGTACCGAACTG 59.555 55.000 0.00 0.00 37.72 3.16
885 1702 0.542232 ACCACCGGCAGTCTACTCTT 60.542 55.000 0.00 0.00 0.00 2.85
913 1769 2.213499 GAGGTAGCATTCCATTCCACG 58.787 52.381 0.00 0.00 0.00 4.94
914 1770 1.837439 AGGTAGCATTCCATTCCACGA 59.163 47.619 0.00 0.00 0.00 4.35
915 1771 2.158900 AGGTAGCATTCCATTCCACGAG 60.159 50.000 0.00 0.00 0.00 4.18
916 1772 1.599542 GTAGCATTCCATTCCACGAGC 59.400 52.381 0.00 0.00 0.00 5.03
917 1773 0.035152 AGCATTCCATTCCACGAGCA 60.035 50.000 0.00 0.00 0.00 4.26
918 1774 0.099436 GCATTCCATTCCACGAGCAC 59.901 55.000 0.00 0.00 0.00 4.40
965 1827 3.005472 GCGTTACCTCATAGGCTCATACA 59.995 47.826 0.00 0.00 39.63 2.29
1044 1906 2.358860 CTGCTGCTGCTGCTGTCT 60.359 61.111 27.67 0.00 39.81 3.41
1121 1989 4.740822 GGCCGGTGGGAGCAATGT 62.741 66.667 1.90 0.00 34.06 2.71
1280 2160 1.671880 GGTAAGCTCGCACGAACGTC 61.672 60.000 0.00 0.00 0.00 4.34
1304 2187 1.671850 GCGCTTGTCAAGTAGCCTGTA 60.672 52.381 18.38 0.00 33.86 2.74
1307 2190 3.676049 CGCTTGTCAAGTAGCCTGTATCA 60.676 47.826 14.03 0.00 33.86 2.15
1328 2211 3.242944 CAGTTAAGGACGATGTACGCATG 59.757 47.826 0.00 0.00 46.94 4.06
1363 2257 4.503741 GCATCTACTGTGCCAAGAAAAA 57.496 40.909 0.00 0.00 36.61 1.94
1364 2258 5.064441 GCATCTACTGTGCCAAGAAAAAT 57.936 39.130 0.00 0.00 36.61 1.82
1365 2259 4.860907 GCATCTACTGTGCCAAGAAAAATG 59.139 41.667 0.00 0.00 36.61 2.32
1366 2260 5.404946 CATCTACTGTGCCAAGAAAAATGG 58.595 41.667 0.00 0.00 41.08 3.16
1367 2261 3.826157 TCTACTGTGCCAAGAAAAATGGG 59.174 43.478 0.00 0.00 38.44 4.00
1406 2302 5.403897 ACATGAGTTTTGTACTTCGTGTG 57.596 39.130 0.00 0.00 37.17 3.82
1474 2373 0.458669 GTTTCCCGACTCGCCTATCA 59.541 55.000 0.00 0.00 0.00 2.15
1480 2383 1.068588 CCGACTCGCCTATCAATGGAA 59.931 52.381 0.00 0.00 0.00 3.53
1481 2384 2.398498 CGACTCGCCTATCAATGGAAG 58.602 52.381 0.00 0.00 0.00 3.46
1482 2385 2.139118 GACTCGCCTATCAATGGAAGC 58.861 52.381 0.00 0.00 0.00 3.86
1490 2393 2.198827 ATCAATGGAAGCACAACGGA 57.801 45.000 0.00 0.00 0.00 4.69
1549 3136 3.181501 CGTGCATTAATCCACCGTTGAAT 60.182 43.478 3.91 0.00 0.00 2.57
1550 3137 4.104776 GTGCATTAATCCACCGTTGAATG 58.895 43.478 0.00 0.00 0.00 2.67
1563 3151 4.024387 ACCGTTGAATGTGTGTTGTACATC 60.024 41.667 0.00 0.00 42.24 3.06
1622 3220 8.925161 TCACATAAAAACCAAGTTTCAAAGAG 57.075 30.769 0.00 0.00 34.43 2.85
1646 3259 9.211556 GAGAACTTCGTTTGAAAGTTTAAGAAG 57.788 33.333 9.59 9.59 39.54 2.85
1652 3265 9.902196 TTCGTTTGAAAGTTTAAGAAGAAAACT 57.098 25.926 0.00 0.00 46.45 2.66
1653 3266 9.337091 TCGTTTGAAAGTTTAAGAAGAAAACTG 57.663 29.630 2.26 0.00 44.35 3.16
1654 3267 9.337091 CGTTTGAAAGTTTAAGAAGAAAACTGA 57.663 29.630 2.26 0.00 44.35 3.41
1667 3283 9.889128 AAGAAGAAAACTGAAAAATGGAAATGA 57.111 25.926 0.00 0.00 0.00 2.57
1733 3349 7.859325 AAACACATTACCATTTACGAGCTAT 57.141 32.000 0.00 0.00 0.00 2.97
1787 3404 5.446143 TTGTTCGGCACTATTCAATGTTT 57.554 34.783 0.00 0.00 0.00 2.83
1867 3484 6.536224 CACATGCTAATAGAACATCACACTCA 59.464 38.462 0.00 0.00 0.00 3.41
1872 3489 7.928167 TGCTAATAGAACATCACACTCATAAGG 59.072 37.037 0.00 0.00 0.00 2.69
1873 3490 7.095439 GCTAATAGAACATCACACTCATAAGGC 60.095 40.741 0.00 0.00 0.00 4.35
1947 3578 5.880901 ACTTGGTTTCCATGTGATACTCTT 58.119 37.500 6.53 0.00 39.83 2.85
1949 3580 6.777580 ACTTGGTTTCCATGTGATACTCTTTT 59.222 34.615 6.53 0.00 39.83 2.27
1983 3614 9.182214 AGACATTACAAGACATTAAGATGCATT 57.818 29.630 0.00 0.00 36.72 3.56
2056 3687 5.826601 TCTTATTTTGCTGACACACAACA 57.173 34.783 0.00 0.00 0.00 3.33
2075 3708 9.713713 ACACAACACAACACTATATAATACACA 57.286 29.630 0.00 0.00 0.00 3.72
2146 3779 7.581213 AACAACATAAACTTGGTCAGAATCA 57.419 32.000 0.00 0.00 0.00 2.57
2147 3780 7.206981 ACAACATAAACTTGGTCAGAATCAG 57.793 36.000 0.00 0.00 0.00 2.90
2148 3781 6.998074 ACAACATAAACTTGGTCAGAATCAGA 59.002 34.615 0.00 0.00 0.00 3.27
2149 3782 7.502226 ACAACATAAACTTGGTCAGAATCAGAA 59.498 33.333 0.00 0.00 0.00 3.02
2150 3783 8.352201 CAACATAAACTTGGTCAGAATCAGAAA 58.648 33.333 0.00 0.00 0.00 2.52
2151 3784 8.463930 ACATAAACTTGGTCAGAATCAGAAAA 57.536 30.769 0.00 0.00 0.00 2.29
2152 3785 8.352942 ACATAAACTTGGTCAGAATCAGAAAAC 58.647 33.333 0.00 0.00 0.00 2.43
2153 3786 6.773976 AAACTTGGTCAGAATCAGAAAACA 57.226 33.333 0.00 0.00 0.00 2.83
2154 3787 6.773976 AACTTGGTCAGAATCAGAAAACAA 57.226 33.333 0.00 0.00 0.00 2.83
2155 3788 6.966534 ACTTGGTCAGAATCAGAAAACAAT 57.033 33.333 0.00 0.00 0.00 2.71
2156 3789 6.974965 ACTTGGTCAGAATCAGAAAACAATC 58.025 36.000 0.00 0.00 0.00 2.67
2157 3790 6.774656 ACTTGGTCAGAATCAGAAAACAATCT 59.225 34.615 0.00 0.00 0.00 2.40
2158 3791 6.564709 TGGTCAGAATCAGAAAACAATCTG 57.435 37.500 0.00 0.00 46.62 2.90
2159 3792 6.064060 TGGTCAGAATCAGAAAACAATCTGT 58.936 36.000 4.41 0.00 45.65 3.41
2160 3793 6.547141 TGGTCAGAATCAGAAAACAATCTGTT 59.453 34.615 4.41 0.00 45.65 3.16
2161 3794 6.860023 GGTCAGAATCAGAAAACAATCTGTTG 59.140 38.462 4.41 0.00 45.65 3.33
2173 3806 5.964958 ACAATCTGTTGTTGGATGGTTAG 57.035 39.130 0.00 0.00 46.07 2.34
2174 3807 4.766891 ACAATCTGTTGTTGGATGGTTAGG 59.233 41.667 0.00 0.00 46.07 2.69
2175 3808 4.657814 ATCTGTTGTTGGATGGTTAGGT 57.342 40.909 0.00 0.00 0.00 3.08
2176 3809 3.750371 TCTGTTGTTGGATGGTTAGGTG 58.250 45.455 0.00 0.00 0.00 4.00
2177 3810 2.819608 CTGTTGTTGGATGGTTAGGTGG 59.180 50.000 0.00 0.00 0.00 4.61
2178 3811 2.443632 TGTTGTTGGATGGTTAGGTGGA 59.556 45.455 0.00 0.00 0.00 4.02
2179 3812 2.817844 GTTGTTGGATGGTTAGGTGGAC 59.182 50.000 0.00 0.00 0.00 4.02
2180 3813 2.058705 TGTTGGATGGTTAGGTGGACA 58.941 47.619 0.00 0.00 0.00 4.02
2181 3814 2.039746 TGTTGGATGGTTAGGTGGACAG 59.960 50.000 0.00 0.00 0.00 3.51
2182 3815 2.038863 TGGATGGTTAGGTGGACAGT 57.961 50.000 0.00 0.00 0.00 3.55
2183 3816 1.628340 TGGATGGTTAGGTGGACAGTG 59.372 52.381 0.00 0.00 0.00 3.66
2184 3817 1.906574 GGATGGTTAGGTGGACAGTGA 59.093 52.381 0.00 0.00 0.00 3.41
2185 3818 2.505819 GGATGGTTAGGTGGACAGTGAT 59.494 50.000 0.00 0.00 0.00 3.06
2186 3819 3.709653 GGATGGTTAGGTGGACAGTGATA 59.290 47.826 0.00 0.00 0.00 2.15
2187 3820 4.348168 GGATGGTTAGGTGGACAGTGATAT 59.652 45.833 0.00 0.00 0.00 1.63
2188 3821 5.511545 GGATGGTTAGGTGGACAGTGATATC 60.512 48.000 0.00 0.00 0.00 1.63
2189 3822 3.709653 TGGTTAGGTGGACAGTGATATCC 59.290 47.826 0.00 0.00 0.00 2.59
2190 3823 3.071167 GGTTAGGTGGACAGTGATATCCC 59.929 52.174 0.00 0.00 0.00 3.85
2191 3824 1.807814 AGGTGGACAGTGATATCCCC 58.192 55.000 0.00 0.00 0.00 4.81
2192 3825 1.009552 AGGTGGACAGTGATATCCCCA 59.990 52.381 0.00 0.00 0.00 4.96
2193 3826 1.843851 GGTGGACAGTGATATCCCCAA 59.156 52.381 0.00 0.00 0.00 4.12
2194 3827 2.421529 GGTGGACAGTGATATCCCCAAC 60.422 54.545 0.00 0.00 0.00 3.77
2195 3828 1.843851 TGGACAGTGATATCCCCAACC 59.156 52.381 0.00 0.00 0.00 3.77
2196 3829 1.143073 GGACAGTGATATCCCCAACCC 59.857 57.143 0.00 0.00 0.00 4.11
2197 3830 1.843851 GACAGTGATATCCCCAACCCA 59.156 52.381 0.00 0.00 0.00 4.51
2198 3831 2.443255 GACAGTGATATCCCCAACCCAT 59.557 50.000 0.00 0.00 0.00 4.00
2199 3832 2.443255 ACAGTGATATCCCCAACCCATC 59.557 50.000 0.00 0.00 0.00 3.51
2200 3833 2.442878 CAGTGATATCCCCAACCCATCA 59.557 50.000 0.00 0.00 0.00 3.07
2201 3834 2.713167 AGTGATATCCCCAACCCATCAG 59.287 50.000 0.00 0.00 0.00 2.90
2202 3835 2.065007 TGATATCCCCAACCCATCAGG 58.935 52.381 0.00 0.00 43.78 3.86
2216 3849 4.408182 CCATCAGGGTTAAGTCCTAGTG 57.592 50.000 0.00 1.15 32.49 2.74
2217 3850 3.432326 CCATCAGGGTTAAGTCCTAGTGC 60.432 52.174 0.00 0.00 32.49 4.40
2218 3851 3.185880 TCAGGGTTAAGTCCTAGTGCT 57.814 47.619 0.00 0.00 32.49 4.40
2219 3852 3.097614 TCAGGGTTAAGTCCTAGTGCTC 58.902 50.000 0.00 0.00 32.49 4.26
2220 3853 2.100989 AGGGTTAAGTCCTAGTGCTCG 58.899 52.381 0.00 0.00 31.86 5.03
2221 3854 1.471153 GGGTTAAGTCCTAGTGCTCGC 60.471 57.143 0.00 0.00 0.00 5.03
2222 3855 1.203994 GGTTAAGTCCTAGTGCTCGCA 59.796 52.381 0.00 0.00 0.00 5.10
2223 3856 2.159085 GGTTAAGTCCTAGTGCTCGCAT 60.159 50.000 0.00 0.00 0.00 4.73
2224 3857 3.522553 GTTAAGTCCTAGTGCTCGCATT 58.477 45.455 0.00 0.00 0.00 3.56
2225 3858 2.770164 AAGTCCTAGTGCTCGCATTT 57.230 45.000 0.00 0.00 0.00 2.32
2226 3859 3.887621 AAGTCCTAGTGCTCGCATTTA 57.112 42.857 0.00 0.00 0.00 1.40
2227 3860 4.408182 AAGTCCTAGTGCTCGCATTTAT 57.592 40.909 0.00 0.00 0.00 1.40
2228 3861 4.408182 AGTCCTAGTGCTCGCATTTATT 57.592 40.909 0.00 0.00 0.00 1.40
2229 3862 4.372656 AGTCCTAGTGCTCGCATTTATTC 58.627 43.478 0.00 0.00 0.00 1.75
2230 3863 3.495001 GTCCTAGTGCTCGCATTTATTCC 59.505 47.826 0.00 0.00 0.00 3.01
2231 3864 3.388024 TCCTAGTGCTCGCATTTATTCCT 59.612 43.478 0.00 0.00 0.00 3.36
2232 3865 3.496130 CCTAGTGCTCGCATTTATTCCTG 59.504 47.826 0.00 0.00 0.00 3.86
2233 3866 3.266510 AGTGCTCGCATTTATTCCTGA 57.733 42.857 0.00 0.00 0.00 3.86
2234 3867 3.609853 AGTGCTCGCATTTATTCCTGAA 58.390 40.909 0.00 0.00 0.00 3.02
2235 3868 4.202441 AGTGCTCGCATTTATTCCTGAAT 58.798 39.130 0.00 0.00 34.93 2.57
2236 3869 4.641989 AGTGCTCGCATTTATTCCTGAATT 59.358 37.500 0.00 0.00 32.50 2.17
2237 3870 5.126061 AGTGCTCGCATTTATTCCTGAATTT 59.874 36.000 0.00 0.00 32.50 1.82
2238 3871 6.318648 AGTGCTCGCATTTATTCCTGAATTTA 59.681 34.615 0.00 0.00 32.50 1.40
2239 3872 7.013655 AGTGCTCGCATTTATTCCTGAATTTAT 59.986 33.333 0.00 0.00 32.50 1.40
2240 3873 7.649306 GTGCTCGCATTTATTCCTGAATTTATT 59.351 33.333 0.00 0.00 32.50 1.40
2241 3874 8.196771 TGCTCGCATTTATTCCTGAATTTATTT 58.803 29.630 0.00 0.00 32.50 1.40
2242 3875 8.694394 GCTCGCATTTATTCCTGAATTTATTTC 58.306 33.333 0.00 0.00 34.72 2.17
2243 3876 9.734620 CTCGCATTTATTCCTGAATTTATTTCA 57.265 29.630 0.00 0.00 42.09 2.69
2254 3887 9.753674 TCCTGAATTTATTTCAAGATTACAGGT 57.246 29.630 0.00 0.00 43.64 4.00
2255 3888 9.793252 CCTGAATTTATTTCAAGATTACAGGTG 57.207 33.333 0.00 0.00 43.64 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.500645 TGGCTAGCTATACTATGCATACG 57.499 43.478 15.72 2.13 30.85 3.06
25 26 5.285651 GCTGGCTAGCTATACTATGCATAC 58.714 45.833 15.78 0.00 46.57 2.39
26 27 5.521906 GCTGGCTAGCTATACTATGCATA 57.478 43.478 15.78 6.20 46.57 3.14
27 28 4.399004 GCTGGCTAGCTATACTATGCAT 57.601 45.455 15.78 3.79 46.57 3.96
45 46 0.179108 GCGAGTAACCACCCTAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
117 618 5.131642 TGCCAAATTGGAGTCTGAGATCTAT 59.868 40.000 17.47 0.00 40.96 1.98
118 619 4.471025 TGCCAAATTGGAGTCTGAGATCTA 59.529 41.667 17.47 0.00 40.96 1.98
119 620 3.265221 TGCCAAATTGGAGTCTGAGATCT 59.735 43.478 17.47 0.00 40.96 2.75
120 621 3.614092 TGCCAAATTGGAGTCTGAGATC 58.386 45.455 17.47 0.00 40.96 2.75
229 767 6.704493 TGATGAACTTTGTCCACACTACTTAC 59.296 38.462 0.00 0.00 0.00 2.34
274 812 1.001746 CATGCATATCTCTCACCGCCT 59.998 52.381 0.00 0.00 0.00 5.52
275 813 1.270518 ACATGCATATCTCTCACCGCC 60.271 52.381 0.00 0.00 0.00 6.13
276 814 1.797046 CACATGCATATCTCTCACCGC 59.203 52.381 0.00 0.00 0.00 5.68
277 815 1.797046 GCACATGCATATCTCTCACCG 59.203 52.381 0.00 0.00 41.59 4.94
296 834 1.228657 GCCGTAATCTTCATCCGGGC 61.229 60.000 0.00 0.00 39.05 6.13
297 835 0.944311 CGCCGTAATCTTCATCCGGG 60.944 60.000 0.00 0.00 39.05 5.73
321 863 3.460672 ATCACCGCGGGCGAATCAT 62.461 57.895 31.76 7.48 42.83 2.45
552 1102 4.546674 AGAGGCCTTTCTTTTTCTTTGGA 58.453 39.130 6.77 0.00 0.00 3.53
598 1154 7.579761 TGATATATGCCTTGTTGCAAATACA 57.420 32.000 0.00 0.00 45.84 2.29
680 1466 1.092348 TCTCATACCGTCACTCACCG 58.908 55.000 0.00 0.00 0.00 4.94
699 1489 1.609555 GAGCGACGAGAGGGTAATGAT 59.390 52.381 0.00 0.00 0.00 2.45
705 1495 2.672307 AACGAGCGACGAGAGGGT 60.672 61.111 12.62 0.00 45.77 4.34
815 1625 2.613977 CGCTGAGCTGATTTATAGGGGG 60.614 54.545 1.78 0.00 0.00 5.40
862 1679 2.280552 TAGACTGCCGGTGGTGGTC 61.281 63.158 1.90 4.89 0.00 4.02
885 1702 1.681793 GGAATGCTACCTCGCACTAGA 59.318 52.381 0.00 0.00 43.61 2.43
913 1769 1.195900 CTAGCTAGATCCGTCGTGCTC 59.804 57.143 16.15 0.00 38.25 4.26
914 1770 1.231221 CTAGCTAGATCCGTCGTGCT 58.769 55.000 16.15 0.00 39.65 4.40
915 1771 0.386226 GCTAGCTAGATCCGTCGTGC 60.386 60.000 25.15 1.53 0.00 5.34
916 1772 1.231221 AGCTAGCTAGATCCGTCGTG 58.769 55.000 25.15 0.00 0.00 4.35
917 1773 2.690786 CTAGCTAGCTAGATCCGTCGT 58.309 52.381 37.99 7.87 46.56 4.34
918 1774 1.395608 GCTAGCTAGCTAGATCCGTCG 59.604 57.143 42.59 22.79 46.56 5.12
965 1827 0.957395 CAAGCTGGACGCCATGAAGT 60.957 55.000 0.00 0.00 40.39 3.01
983 1845 2.343426 ATGCTCCTCGACGTGCTCA 61.343 57.895 0.00 0.00 0.00 4.26
1044 1906 4.600576 TCGCAACGTGAGGCAGCA 62.601 61.111 7.71 0.00 0.00 4.41
1175 2046 1.296068 GCTCTTCCAGCTGCTGACT 59.704 57.895 30.10 0.00 45.83 3.41
1209 2086 0.907230 GGCTGGACCTCTTGGACTCT 60.907 60.000 0.00 0.00 37.04 3.24
1280 2160 0.166814 GCTACTTGACAAGCGCTTGG 59.833 55.000 43.26 30.99 44.45 3.61
1304 2187 3.129813 TGCGTACATCGTCCTTAACTGAT 59.870 43.478 0.00 0.00 42.13 2.90
1307 2190 3.444916 CATGCGTACATCGTCCTTAACT 58.555 45.455 0.00 0.00 42.13 2.24
1328 2211 0.331616 AGATGCCAACTTACCACCCC 59.668 55.000 0.00 0.00 0.00 4.95
1406 2302 0.884704 TTCCCTTGCGTGCTTCAGAC 60.885 55.000 0.00 0.00 0.00 3.51
1448 2347 1.210870 CGAGTCGGGAAACGTGAAAA 58.789 50.000 4.10 0.00 44.69 2.29
1474 2373 1.608590 CACTTCCGTTGTGCTTCCATT 59.391 47.619 0.00 0.00 0.00 3.16
1480 2383 1.470051 AAAACCACTTCCGTTGTGCT 58.530 45.000 0.00 0.00 34.38 4.40
1481 2384 1.923864 CAAAAACCACTTCCGTTGTGC 59.076 47.619 0.00 0.00 34.38 4.57
1482 2385 3.224884 ACAAAAACCACTTCCGTTGTG 57.775 42.857 0.00 0.00 35.39 3.33
1549 3136 6.995686 ACTAAATTCCAGATGTACAACACACA 59.004 34.615 0.00 0.00 40.86 3.72
1550 3137 7.298122 CACTAAATTCCAGATGTACAACACAC 58.702 38.462 0.00 0.00 40.86 3.82
1563 3151 8.582437 TCGGTATCTTATACCACTAAATTCCAG 58.418 37.037 14.73 0.00 37.44 3.86
1603 3192 7.328493 CGAAGTTCTCTTTGAAACTTGGTTTTT 59.672 33.333 5.31 0.00 37.27 1.94
1604 3202 6.806739 CGAAGTTCTCTTTGAAACTTGGTTTT 59.193 34.615 5.31 0.00 37.27 2.43
1651 3264 9.784680 CACTCTCTTATCATTTCCATTTTTCAG 57.215 33.333 0.00 0.00 0.00 3.02
1652 3265 9.519191 TCACTCTCTTATCATTTCCATTTTTCA 57.481 29.630 0.00 0.00 0.00 2.69
1659 3272 7.855375 AGAACATCACTCTCTTATCATTTCCA 58.145 34.615 0.00 0.00 0.00 3.53
1660 3273 9.995003 ATAGAACATCACTCTCTTATCATTTCC 57.005 33.333 0.00 0.00 0.00 3.13
1667 3283 7.129457 TGCCAATAGAACATCACTCTCTTAT 57.871 36.000 0.00 0.00 0.00 1.73
1674 3290 5.363562 TCTCATGCCAATAGAACATCACT 57.636 39.130 0.00 0.00 0.00 3.41
1750 3366 8.250332 AGTGCCGAACAATAAACATCATTAATT 58.750 29.630 0.00 0.00 0.00 1.40
1755 3372 6.942532 ATAGTGCCGAACAATAAACATCAT 57.057 33.333 0.00 0.00 31.60 2.45
1787 3404 7.086230 ACGTGGTACAAAAGAAAACAACATA 57.914 32.000 0.00 0.00 44.16 2.29
1826 3443 6.585695 AGCATGTGAAATTCTCAAGTTCAT 57.414 33.333 1.72 0.00 45.65 2.57
1885 3506 8.920665 CATGTGAAAACAGTGTTTTGAAGTTAA 58.079 29.630 32.90 14.57 0.00 2.01
1886 3507 7.543868 CCATGTGAAAACAGTGTTTTGAAGTTA 59.456 33.333 32.90 15.37 0.00 2.24
1921 3552 7.633789 AGAGTATCACATGGAAACCAAGTTAT 58.366 34.615 0.00 0.00 32.85 1.89
1958 3589 9.443283 GAATGCATCTTAATGTCTTGTAATGTC 57.557 33.333 0.00 0.00 35.18 3.06
1969 3600 8.114331 TCTTGTTTCAGAATGCATCTTAATGT 57.886 30.769 0.00 0.00 35.73 2.71
2021 3652 8.726068 TCAGCAAAATAAGATCGTATTTGTTGA 58.274 29.630 22.12 22.11 34.61 3.18
2028 3659 6.593770 TGTGTGTCAGCAAAATAAGATCGTAT 59.406 34.615 0.00 0.00 0.00 3.06
2127 3760 8.352201 TGTTTTCTGATTCTGACCAAGTTTATG 58.648 33.333 0.00 0.00 0.00 1.90
2152 3785 4.766891 ACCTAACCATCCAACAACAGATTG 59.233 41.667 0.00 0.00 41.98 2.67
2153 3786 4.766891 CACCTAACCATCCAACAACAGATT 59.233 41.667 0.00 0.00 0.00 2.40
2154 3787 4.335416 CACCTAACCATCCAACAACAGAT 58.665 43.478 0.00 0.00 0.00 2.90
2155 3788 3.497763 CCACCTAACCATCCAACAACAGA 60.498 47.826 0.00 0.00 0.00 3.41
2156 3789 2.819608 CCACCTAACCATCCAACAACAG 59.180 50.000 0.00 0.00 0.00 3.16
2157 3790 2.443632 TCCACCTAACCATCCAACAACA 59.556 45.455 0.00 0.00 0.00 3.33
2158 3791 2.817844 GTCCACCTAACCATCCAACAAC 59.182 50.000 0.00 0.00 0.00 3.32
2159 3792 2.443632 TGTCCACCTAACCATCCAACAA 59.556 45.455 0.00 0.00 0.00 2.83
2160 3793 2.039746 CTGTCCACCTAACCATCCAACA 59.960 50.000 0.00 0.00 0.00 3.33
2161 3794 2.039879 ACTGTCCACCTAACCATCCAAC 59.960 50.000 0.00 0.00 0.00 3.77
2162 3795 2.039746 CACTGTCCACCTAACCATCCAA 59.960 50.000 0.00 0.00 0.00 3.53
2163 3796 1.628340 CACTGTCCACCTAACCATCCA 59.372 52.381 0.00 0.00 0.00 3.41
2164 3797 1.906574 TCACTGTCCACCTAACCATCC 59.093 52.381 0.00 0.00 0.00 3.51
2165 3798 3.914426 ATCACTGTCCACCTAACCATC 57.086 47.619 0.00 0.00 0.00 3.51
2166 3799 4.348168 GGATATCACTGTCCACCTAACCAT 59.652 45.833 4.83 0.00 33.05 3.55
2167 3800 3.709653 GGATATCACTGTCCACCTAACCA 59.290 47.826 4.83 0.00 33.05 3.67
2168 3801 3.071167 GGGATATCACTGTCCACCTAACC 59.929 52.174 4.83 0.00 34.44 2.85
2169 3802 3.071167 GGGGATATCACTGTCCACCTAAC 59.929 52.174 4.65 0.00 34.44 2.34
2170 3803 3.311028 TGGGGATATCACTGTCCACCTAA 60.311 47.826 4.65 0.00 35.25 2.69
2171 3804 2.248950 TGGGGATATCACTGTCCACCTA 59.751 50.000 4.65 0.00 35.25 3.08
2172 3805 1.009552 TGGGGATATCACTGTCCACCT 59.990 52.381 4.65 0.00 35.25 4.00
2173 3806 1.507140 TGGGGATATCACTGTCCACC 58.493 55.000 4.65 0.00 35.25 4.61
2174 3807 2.421529 GGTTGGGGATATCACTGTCCAC 60.422 54.545 4.65 0.00 36.63 4.02
2175 3808 1.843851 GGTTGGGGATATCACTGTCCA 59.156 52.381 4.65 1.40 34.44 4.02
2176 3809 1.143073 GGGTTGGGGATATCACTGTCC 59.857 57.143 4.65 4.82 32.06 4.02
2177 3810 1.843851 TGGGTTGGGGATATCACTGTC 59.156 52.381 4.65 0.00 0.00 3.51
2178 3811 1.979809 TGGGTTGGGGATATCACTGT 58.020 50.000 4.65 0.00 0.00 3.55
2179 3812 2.442878 TGATGGGTTGGGGATATCACTG 59.557 50.000 4.65 0.00 0.00 3.66
2180 3813 2.713167 CTGATGGGTTGGGGATATCACT 59.287 50.000 4.65 0.00 0.00 3.41
2181 3814 2.224867 CCTGATGGGTTGGGGATATCAC 60.225 54.545 4.83 0.00 0.00 3.06
2182 3815 2.065007 CCTGATGGGTTGGGGATATCA 58.935 52.381 4.83 0.00 0.00 2.15
2183 3816 2.887151 CCTGATGGGTTGGGGATATC 57.113 55.000 0.00 0.00 0.00 1.63
2195 3828 3.432326 GCACTAGGACTTAACCCTGATGG 60.432 52.174 0.00 0.00 41.37 3.51
2196 3829 3.452627 AGCACTAGGACTTAACCCTGATG 59.547 47.826 0.00 0.00 35.30 3.07
2197 3830 3.707102 GAGCACTAGGACTTAACCCTGAT 59.293 47.826 0.00 0.00 35.30 2.90
2198 3831 3.097614 GAGCACTAGGACTTAACCCTGA 58.902 50.000 0.00 0.00 35.30 3.86
2199 3832 2.159226 CGAGCACTAGGACTTAACCCTG 60.159 54.545 0.00 0.00 35.30 4.45
2200 3833 2.100989 CGAGCACTAGGACTTAACCCT 58.899 52.381 0.00 0.00 37.80 4.34
2201 3834 1.471153 GCGAGCACTAGGACTTAACCC 60.471 57.143 0.00 0.00 0.00 4.11
2202 3835 1.203994 TGCGAGCACTAGGACTTAACC 59.796 52.381 0.00 0.00 0.00 2.85
2203 3836 2.649331 TGCGAGCACTAGGACTTAAC 57.351 50.000 0.00 0.00 0.00 2.01
2204 3837 3.887621 AATGCGAGCACTAGGACTTAA 57.112 42.857 0.00 0.00 0.00 1.85
2205 3838 3.887621 AAATGCGAGCACTAGGACTTA 57.112 42.857 0.00 0.00 0.00 2.24
2206 3839 2.770164 AAATGCGAGCACTAGGACTT 57.230 45.000 0.00 0.00 0.00 3.01
2207 3840 4.372656 GAATAAATGCGAGCACTAGGACT 58.627 43.478 0.00 0.00 0.00 3.85
2208 3841 3.495001 GGAATAAATGCGAGCACTAGGAC 59.505 47.826 0.00 0.00 0.00 3.85
2209 3842 3.388024 AGGAATAAATGCGAGCACTAGGA 59.612 43.478 0.00 0.00 0.00 2.94
2210 3843 3.496130 CAGGAATAAATGCGAGCACTAGG 59.504 47.826 0.00 0.00 0.00 3.02
2211 3844 4.371786 TCAGGAATAAATGCGAGCACTAG 58.628 43.478 0.00 0.00 0.00 2.57
2212 3845 4.400529 TCAGGAATAAATGCGAGCACTA 57.599 40.909 0.00 0.00 0.00 2.74
2213 3846 3.266510 TCAGGAATAAATGCGAGCACT 57.733 42.857 0.00 0.00 0.00 4.40
2214 3847 4.558538 ATTCAGGAATAAATGCGAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
2215 3848 5.581126 AAATTCAGGAATAAATGCGAGCA 57.419 34.783 0.00 0.00 0.00 4.26
2216 3849 8.579682 AAATAAATTCAGGAATAAATGCGAGC 57.420 30.769 0.00 0.00 0.00 5.03
2217 3850 9.734620 TGAAATAAATTCAGGAATAAATGCGAG 57.265 29.630 0.00 0.00 43.08 5.03


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

AutoCloner maintained by Alex Coulton.