Multiple sequence alignment - TraesCS3B01G278900

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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 TraesCS3B01G278900 chr3B 100.000 2687 0 0 1 2687 448772594 448775280 0.000000e+00 4963
1 TraesCS3B01G278900 chr3B 94.203 759 44 0 1929 2687 439336806 439336048 0.000000e+00 1158
2 TraesCS3B01G278900 chr3B 88.038 627 72 1 995 1618 449156866 449156240 0.000000e+00 739
3 TraesCS3B01G278900 chr3D 94.208 1174 36 9 645 1801 349860107 349861265 0.000000e+00 1762
4 TraesCS3B01G278900 chr3D 89.608 664 29 7 1 647 349855389 349856029 0.000000e+00 808
5 TraesCS3B01G278900 chr3D 88.379 654 76 0 1929 2582 433871353 433870700 0.000000e+00 787
6 TraesCS3B01G278900 chr3D 87.836 633 68 4 995 1618 350735956 350735324 0.000000e+00 734
7 TraesCS3B01G278900 chr3D 93.233 133 9 0 1797 1929 263400869 263401001 2.110000e-46 196
8 TraesCS3B01G278900 chr3A 91.524 1109 57 19 645 1728 468002944 468004040 0.000000e+00 1493
9 TraesCS3B01G278900 chr3A 88.296 675 26 15 1 647 468001917 468002566 0.000000e+00 760
10 TraesCS3B01G278900 chr3A 88.192 542 59 2 1080 1618 468317361 468316822 2.260000e-180 641
11 TraesCS3B01G278900 chr5A 94.730 759 38 2 1929 2687 328957971 328958727 0.000000e+00 1179
12 TraesCS3B01G278900 chr7D 94.350 761 42 1 1928 2687 206612153 206612913 0.000000e+00 1166
13 TraesCS3B01G278900 chr1A 94.211 760 44 0 1928 2687 179529701 179528942 0.000000e+00 1160
14 TraesCS3B01G278900 chr2B 91.974 760 61 0 1928 2687 313424536 313423777 0.000000e+00 1066
15 TraesCS3B01G278900 chr2B 90.436 596 57 0 2092 2687 215506290 215505695 0.000000e+00 785
16 TraesCS3B01G278900 chr2B 77.248 734 167 0 1944 2677 507823725 507822992 5.310000e-117 431
17 TraesCS3B01G278900 chr5D 93.883 703 43 0 1985 2687 271703515 271704217 0.000000e+00 1061
18 TraesCS3B01G278900 chr7B 77.381 756 171 0 1932 2687 234378284 234379039 1.470000e-122 449
19 TraesCS3B01G278900 chr6D 96.403 139 4 1 1791 1929 17368593 17368456 7.480000e-56 228
20 TraesCS3B01G278900 chr7A 93.233 133 7 2 1797 1929 267193798 267193668 7.590000e-46 195
21 TraesCS3B01G278900 chr5B 93.182 132 9 0 1795 1926 611822823 611822954 7.590000e-46 195
22 TraesCS3B01G278900 chr6A 92.481 133 10 0 1797 1929 13092840 13092972 9.820000e-45 191
23 TraesCS3B01G278900 chr6A 92.481 133 10 0 1797 1929 13150751 13150883 9.820000e-45 191
24 TraesCS3B01G278900 chr2A 91.971 137 8 2 1795 1929 121134114 121134249 3.530000e-44 189
25 TraesCS3B01G278900 chr2A 91.111 135 12 0 1795 1929 75644925 75644791 1.640000e-42 183
26 TraesCS3B01G278900 chr1D 90.511 137 13 0 1794 1930 409959405 409959541 5.910000e-42 182


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 TraesCS3B01G278900 chr3B 448772594 448775280 2686 False 4963.0 4963 100.000 1 2687 1 chr3B.!!$F1 2686
1 TraesCS3B01G278900 chr3B 439336048 439336806 758 True 1158.0 1158 94.203 1929 2687 1 chr3B.!!$R1 758
2 TraesCS3B01G278900 chr3B 449156240 449156866 626 True 739.0 739 88.038 995 1618 1 chr3B.!!$R2 623
3 TraesCS3B01G278900 chr3D 349860107 349861265 1158 False 1762.0 1762 94.208 645 1801 1 chr3D.!!$F3 1156
4 TraesCS3B01G278900 chr3D 349855389 349856029 640 False 808.0 808 89.608 1 647 1 chr3D.!!$F2 646
5 TraesCS3B01G278900 chr3D 433870700 433871353 653 True 787.0 787 88.379 1929 2582 1 chr3D.!!$R2 653
6 TraesCS3B01G278900 chr3D 350735324 350735956 632 True 734.0 734 87.836 995 1618 1 chr3D.!!$R1 623
7 TraesCS3B01G278900 chr3A 468001917 468004040 2123 False 1126.5 1493 89.910 1 1728 2 chr3A.!!$F1 1727
8 TraesCS3B01G278900 chr3A 468316822 468317361 539 True 641.0 641 88.192 1080 1618 1 chr3A.!!$R1 538
9 TraesCS3B01G278900 chr5A 328957971 328958727 756 False 1179.0 1179 94.730 1929 2687 1 chr5A.!!$F1 758
10 TraesCS3B01G278900 chr7D 206612153 206612913 760 False 1166.0 1166 94.350 1928 2687 1 chr7D.!!$F1 759
11 TraesCS3B01G278900 chr1A 179528942 179529701 759 True 1160.0 1160 94.211 1928 2687 1 chr1A.!!$R1 759
12 TraesCS3B01G278900 chr2B 313423777 313424536 759 True 1066.0 1066 91.974 1928 2687 1 chr2B.!!$R2 759
13 TraesCS3B01G278900 chr2B 215505695 215506290 595 True 785.0 785 90.436 2092 2687 1 chr2B.!!$R1 595
14 TraesCS3B01G278900 chr2B 507822992 507823725 733 True 431.0 431 77.248 1944 2677 1 chr2B.!!$R3 733
15 TraesCS3B01G278900 chr5D 271703515 271704217 702 False 1061.0 1061 93.883 1985 2687 1 chr5D.!!$F1 702
16 TraesCS3B01G278900 chr7B 234378284 234379039 755 False 449.0 449 77.381 1932 2687 1 chr7B.!!$F1 755

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
678 1089 0.46546 AGTGGTGTCGTTGCCATTGT 60.465 50.0 0.0 0.0 37.09 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2355 0.179 ATCCACCAGCTCCACGAATC 59.821 55.0 0.0 0.0 0.0 2.52 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
81 84 1.335810 ACAAACTGTGTGCATGCTCAG 59.664 47.619 22.00 23.71 39.72 3.35
107 129 4.638865 GTGGTGTCTTAAACAGGTGTCTTT 59.361 41.667 0.00 0.00 38.97 2.52
108 130 5.124936 GTGGTGTCTTAAACAGGTGTCTTTT 59.875 40.000 0.00 0.00 38.97 2.27
110 132 6.885376 TGGTGTCTTAAACAGGTGTCTTTTTA 59.115 34.615 0.00 0.00 38.97 1.52
111 133 7.393796 TGGTGTCTTAAACAGGTGTCTTTTTAA 59.606 33.333 0.00 0.00 38.97 1.52
112 134 7.699391 GGTGTCTTAAACAGGTGTCTTTTTAAC 59.301 37.037 0.00 0.00 38.97 2.01
126 148 8.615585 GTGTCTTTTTAACGTTCATGTAAATCG 58.384 33.333 2.82 0.00 0.00 3.34
155 177 7.655328 CAGGATACCATTCTCAATAGTGACTTC 59.345 40.741 0.00 0.00 37.17 3.01
156 178 7.566879 AGGATACCATTCTCAATAGTGACTTCT 59.433 37.037 0.00 0.00 37.17 2.85
157 179 7.655328 GGATACCATTCTCAATAGTGACTTCTG 59.345 40.741 0.00 0.00 0.00 3.02
158 180 6.611613 ACCATTCTCAATAGTGACTTCTGA 57.388 37.500 0.00 0.00 0.00 3.27
159 181 7.009179 ACCATTCTCAATAGTGACTTCTGAA 57.991 36.000 0.00 0.00 0.00 3.02
160 182 6.876257 ACCATTCTCAATAGTGACTTCTGAAC 59.124 38.462 0.00 0.00 0.00 3.18
161 183 6.875726 CCATTCTCAATAGTGACTTCTGAACA 59.124 38.462 0.00 0.00 0.00 3.18
162 184 7.388776 CCATTCTCAATAGTGACTTCTGAACAA 59.611 37.037 0.00 0.00 0.00 2.83
163 185 8.944029 CATTCTCAATAGTGACTTCTGAACAAT 58.056 33.333 0.00 0.00 0.00 2.71
164 186 8.539770 TTCTCAATAGTGACTTCTGAACAATC 57.460 34.615 0.00 0.00 0.00 2.67
165 187 7.901029 TCTCAATAGTGACTTCTGAACAATCT 58.099 34.615 0.00 0.00 0.00 2.40
166 188 9.025041 TCTCAATAGTGACTTCTGAACAATCTA 57.975 33.333 0.00 0.00 0.00 1.98
167 189 9.299963 CTCAATAGTGACTTCTGAACAATCTAG 57.700 37.037 0.00 0.00 0.00 2.43
168 190 8.807118 TCAATAGTGACTTCTGAACAATCTAGT 58.193 33.333 0.00 0.00 0.00 2.57
169 191 8.867935 CAATAGTGACTTCTGAACAATCTAGTG 58.132 37.037 0.00 0.00 0.00 2.74
170 192 6.656632 AGTGACTTCTGAACAATCTAGTGA 57.343 37.500 0.00 0.00 0.00 3.41
171 193 6.451393 AGTGACTTCTGAACAATCTAGTGAC 58.549 40.000 0.00 0.00 0.00 3.67
172 194 6.266558 AGTGACTTCTGAACAATCTAGTGACT 59.733 38.462 0.00 0.00 29.44 3.41
173 195 6.926272 GTGACTTCTGAACAATCTAGTGACTT 59.074 38.462 0.00 0.00 0.00 3.01
174 196 7.115663 GTGACTTCTGAACAATCTAGTGACTTC 59.884 40.741 0.00 0.00 0.00 3.01
195 217 6.429385 ACTTCTCAAGTTCCTGAACAATCATC 59.571 38.462 12.21 0.00 43.47 2.92
215 237 1.474077 CTTGTGCTGTATTTGGGGAGC 59.526 52.381 0.00 0.00 0.00 4.70
254 276 3.713858 TTGTGATGCTGAAACACAAGG 57.286 42.857 7.33 0.00 45.35 3.61
255 277 1.955778 TGTGATGCTGAAACACAAGGG 59.044 47.619 0.00 0.00 40.72 3.95
275 297 1.260544 GGGGCATGGATTCTTATGGC 58.739 55.000 14.87 14.87 45.83 4.40
321 345 1.263217 GGTGGTCACGTGTGTCATTTC 59.737 52.381 16.51 1.62 0.00 2.17
431 462 4.377021 CCGGCAAAGCTTATATAGTCACA 58.623 43.478 0.00 0.00 0.00 3.58
466 497 3.578716 GGATCCCAATCGATTGACCTCTA 59.421 47.826 34.21 15.44 40.14 2.43
562 593 1.209261 TCTTGTAATGATGCTCGGCCA 59.791 47.619 2.24 0.00 0.00 5.36
580 611 1.303309 CAGGATGATGAAAGCCGTCC 58.697 55.000 0.00 0.00 39.69 4.79
655 1066 0.610174 GTCCAGTGCATGAGAGACCA 59.390 55.000 0.00 0.00 0.00 4.02
658 1069 1.485480 CCAGTGCATGAGAGACCAGAT 59.515 52.381 0.00 0.00 0.00 2.90
678 1089 0.465460 AGTGGTGTCGTTGCCATTGT 60.465 50.000 0.00 0.00 37.09 2.71
801 1247 2.159226 CCTCACACACGGATTAGAGTCC 60.159 54.545 0.00 0.00 34.82 3.85
848 1294 4.635765 TGGCACAAATAGCACAAGAGATAC 59.364 41.667 0.00 0.00 31.92 2.24
855 1302 8.292448 ACAAATAGCACAAGAGATACTGTTTTG 58.708 33.333 0.00 0.00 0.00 2.44
950 1397 4.332543 CAGCCTACATATTCGCAAAACAGA 59.667 41.667 0.00 0.00 0.00 3.41
1227 1683 1.346395 AGTACCGCCTTCAACATCACA 59.654 47.619 0.00 0.00 0.00 3.58
1514 1970 2.261361 CAGACCGACGTGGATGCA 59.739 61.111 10.46 0.00 42.00 3.96
1602 2058 1.149101 ATTGGGCCTCGGATATTGGT 58.851 50.000 4.53 0.00 0.00 3.67
1695 2151 7.167535 TCAATCAGTTTGGTTGATGATCACTA 58.832 34.615 0.00 0.00 42.07 2.74
1737 2193 8.984112 ATATGTAATATTGGGTGTAGTAGGGT 57.016 34.615 0.00 0.00 35.58 4.34
1738 2194 7.701257 ATGTAATATTGGGTGTAGTAGGGTT 57.299 36.000 0.00 0.00 0.00 4.11
1739 2195 6.891388 TGTAATATTGGGTGTAGTAGGGTTG 58.109 40.000 0.00 0.00 0.00 3.77
1740 2196 6.444493 TGTAATATTGGGTGTAGTAGGGTTGT 59.556 38.462 0.00 0.00 0.00 3.32
1741 2197 3.713826 ATTGGGTGTAGTAGGGTTGTG 57.286 47.619 0.00 0.00 0.00 3.33
1742 2198 2.106187 TGGGTGTAGTAGGGTTGTGT 57.894 50.000 0.00 0.00 0.00 3.72
1746 2202 2.036346 GGTGTAGTAGGGTTGTGTTCGT 59.964 50.000 0.00 0.00 0.00 3.85
1758 2214 2.004017 TGTGTTCGTCTGTTTGTGACC 58.996 47.619 0.00 0.00 0.00 4.02
1766 2222 3.668491 CGTCTGTTTGTGACCGTGTTTTT 60.668 43.478 0.00 0.00 0.00 1.94
1804 2263 4.617808 TGAGTACTCGATGACTTAGTGC 57.382 45.455 17.85 0.00 0.00 4.40
1805 2264 3.377485 TGAGTACTCGATGACTTAGTGCC 59.623 47.826 17.85 0.00 0.00 5.01
1806 2265 2.688958 AGTACTCGATGACTTAGTGCCC 59.311 50.000 0.00 0.00 0.00 5.36
1807 2266 0.456221 ACTCGATGACTTAGTGCCCG 59.544 55.000 0.00 0.00 0.00 6.13
1808 2267 0.456221 CTCGATGACTTAGTGCCCGT 59.544 55.000 0.00 0.00 0.00 5.28
1809 2268 0.892755 TCGATGACTTAGTGCCCGTT 59.107 50.000 0.00 0.00 0.00 4.44
1810 2269 1.135199 TCGATGACTTAGTGCCCGTTC 60.135 52.381 0.00 0.00 0.00 3.95
1811 2270 1.403647 CGATGACTTAGTGCCCGTTCA 60.404 52.381 0.00 0.00 0.00 3.18
1812 2271 2.271800 GATGACTTAGTGCCCGTTCAG 58.728 52.381 0.00 0.00 0.00 3.02
1813 2272 1.334160 TGACTTAGTGCCCGTTCAGA 58.666 50.000 0.00 0.00 0.00 3.27
1814 2273 1.272490 TGACTTAGTGCCCGTTCAGAG 59.728 52.381 0.00 0.00 0.00 3.35
1815 2274 0.608640 ACTTAGTGCCCGTTCAGAGG 59.391 55.000 0.00 0.00 0.00 3.69
1820 2279 4.475135 GCCCGTTCAGAGGCCCTC 62.475 72.222 1.26 1.26 43.76 4.30
1821 2280 3.787001 CCCGTTCAGAGGCCCTCC 61.787 72.222 7.26 0.00 0.00 4.30
1822 2281 4.148825 CCGTTCAGAGGCCCTCCG 62.149 72.222 7.26 3.48 37.47 4.63
1823 2282 4.821589 CGTTCAGAGGCCCTCCGC 62.822 72.222 7.26 0.00 37.47 5.54
1824 2283 3.394836 GTTCAGAGGCCCTCCGCT 61.395 66.667 7.26 0.00 43.70 5.52
1825 2284 3.077556 TTCAGAGGCCCTCCGCTC 61.078 66.667 7.26 0.00 40.76 5.03
1832 2291 4.021925 GCCCTCCGCTCCACAACT 62.022 66.667 0.00 0.00 0.00 3.16
1833 2292 2.266055 CCCTCCGCTCCACAACTC 59.734 66.667 0.00 0.00 0.00 3.01
1834 2293 2.286523 CCCTCCGCTCCACAACTCT 61.287 63.158 0.00 0.00 0.00 3.24
1835 2294 1.079543 CCTCCGCTCCACAACTCTG 60.080 63.158 0.00 0.00 0.00 3.35
1836 2295 1.739562 CTCCGCTCCACAACTCTGC 60.740 63.158 0.00 0.00 0.00 4.26
1837 2296 2.743928 CCGCTCCACAACTCTGCC 60.744 66.667 0.00 0.00 0.00 4.85
1838 2297 2.031012 CGCTCCACAACTCTGCCA 59.969 61.111 0.00 0.00 0.00 4.92
1839 2298 2.320587 CGCTCCACAACTCTGCCAC 61.321 63.158 0.00 0.00 0.00 5.01
1840 2299 2.320587 GCTCCACAACTCTGCCACG 61.321 63.158 0.00 0.00 0.00 4.94
1841 2300 1.669115 CTCCACAACTCTGCCACGG 60.669 63.158 0.00 0.00 0.00 4.94
1842 2301 2.099652 CTCCACAACTCTGCCACGGA 62.100 60.000 0.00 0.00 0.00 4.69
1843 2302 1.669115 CCACAACTCTGCCACGGAG 60.669 63.158 1.86 1.86 42.15 4.63
1844 2303 2.031163 ACAACTCTGCCACGGAGC 59.969 61.111 3.33 0.00 40.26 4.70
1845 2304 3.114616 CAACTCTGCCACGGAGCG 61.115 66.667 3.33 0.00 40.26 5.03
1846 2305 4.379243 AACTCTGCCACGGAGCGG 62.379 66.667 3.33 1.55 40.26 5.52
1866 2325 3.900446 GCAGGCTGCAGTTCAAATT 57.100 47.368 33.33 0.00 44.26 1.82
1867 2326 2.159327 GCAGGCTGCAGTTCAAATTT 57.841 45.000 33.33 0.00 44.26 1.82
1868 2327 2.486918 GCAGGCTGCAGTTCAAATTTT 58.513 42.857 33.33 0.00 44.26 1.82
1869 2328 2.477754 GCAGGCTGCAGTTCAAATTTTC 59.522 45.455 33.33 0.00 44.26 2.29
1870 2329 3.719924 CAGGCTGCAGTTCAAATTTTCA 58.280 40.909 16.64 0.00 0.00 2.69
1871 2330 3.739300 CAGGCTGCAGTTCAAATTTTCAG 59.261 43.478 16.64 0.00 0.00 3.02
1872 2331 3.638160 AGGCTGCAGTTCAAATTTTCAGA 59.362 39.130 16.64 0.00 0.00 3.27
1873 2332 3.985925 GGCTGCAGTTCAAATTTTCAGAG 59.014 43.478 16.64 0.00 0.00 3.35
1874 2333 4.500375 GGCTGCAGTTCAAATTTTCAGAGT 60.500 41.667 16.64 0.00 0.00 3.24
1875 2334 4.443394 GCTGCAGTTCAAATTTTCAGAGTG 59.557 41.667 16.64 0.00 0.00 3.51
1876 2335 4.935702 TGCAGTTCAAATTTTCAGAGTGG 58.064 39.130 0.00 0.00 0.00 4.00
1877 2336 4.402155 TGCAGTTCAAATTTTCAGAGTGGT 59.598 37.500 0.00 0.00 0.00 4.16
1878 2337 4.741676 GCAGTTCAAATTTTCAGAGTGGTG 59.258 41.667 0.00 0.00 0.00 4.17
1879 2338 5.284079 CAGTTCAAATTTTCAGAGTGGTGG 58.716 41.667 0.00 0.00 0.00 4.61
1880 2339 5.067674 CAGTTCAAATTTTCAGAGTGGTGGA 59.932 40.000 0.00 0.00 0.00 4.02
1881 2340 5.656416 AGTTCAAATTTTCAGAGTGGTGGAA 59.344 36.000 0.00 0.00 0.00 3.53
1882 2341 6.324770 AGTTCAAATTTTCAGAGTGGTGGAAT 59.675 34.615 0.00 0.00 0.00 3.01
1883 2342 7.505585 AGTTCAAATTTTCAGAGTGGTGGAATA 59.494 33.333 0.00 0.00 0.00 1.75
1884 2343 7.452880 TCAAATTTTCAGAGTGGTGGAATAG 57.547 36.000 0.00 0.00 0.00 1.73
1885 2344 6.434028 TCAAATTTTCAGAGTGGTGGAATAGG 59.566 38.462 0.00 0.00 0.00 2.57
1886 2345 4.993705 TTTTCAGAGTGGTGGAATAGGT 57.006 40.909 0.00 0.00 0.00 3.08
1887 2346 3.981071 TTCAGAGTGGTGGAATAGGTG 57.019 47.619 0.00 0.00 0.00 4.00
1888 2347 1.555075 TCAGAGTGGTGGAATAGGTGC 59.445 52.381 0.00 0.00 0.00 5.01
1889 2348 1.556911 CAGAGTGGTGGAATAGGTGCT 59.443 52.381 0.00 0.00 0.00 4.40
1890 2349 1.834263 AGAGTGGTGGAATAGGTGCTC 59.166 52.381 0.00 0.00 0.00 4.26
1891 2350 0.912486 AGTGGTGGAATAGGTGCTCC 59.088 55.000 0.00 0.00 0.00 4.70
1892 2351 0.462047 GTGGTGGAATAGGTGCTCCG 60.462 60.000 0.00 0.00 39.05 4.63
1893 2352 1.523938 GGTGGAATAGGTGCTCCGC 60.524 63.158 0.00 0.00 40.81 5.54
1894 2353 1.523938 GTGGAATAGGTGCTCCGCC 60.524 63.158 0.00 1.09 36.41 6.13
1895 2354 1.992834 TGGAATAGGTGCTCCGCCA 60.993 57.895 0.00 3.68 36.32 5.69
1896 2355 1.227674 GGAATAGGTGCTCCGCCAG 60.228 63.158 0.00 0.00 36.32 4.85
1897 2356 1.686325 GGAATAGGTGCTCCGCCAGA 61.686 60.000 0.00 0.00 36.32 3.86
1898 2357 0.394565 GAATAGGTGCTCCGCCAGAT 59.605 55.000 0.00 0.00 36.32 2.90
1899 2358 0.839946 AATAGGTGCTCCGCCAGATT 59.160 50.000 0.00 0.00 36.32 2.40
1900 2359 0.394565 ATAGGTGCTCCGCCAGATTC 59.605 55.000 0.00 0.00 36.32 2.52
1901 2360 2.016393 TAGGTGCTCCGCCAGATTCG 62.016 60.000 0.00 0.00 36.32 3.34
1902 2361 2.125512 GTGCTCCGCCAGATTCGT 60.126 61.111 0.00 0.00 0.00 3.85
1903 2362 2.125552 TGCTCCGCCAGATTCGTG 60.126 61.111 0.00 0.00 0.00 4.35
1904 2363 2.892425 GCTCCGCCAGATTCGTGG 60.892 66.667 0.00 0.00 41.01 4.94
1905 2364 2.892640 CTCCGCCAGATTCGTGGA 59.107 61.111 6.40 1.24 40.44 4.02
1906 2365 2.892640 TCCGCCAGATTCGTGGAG 59.107 61.111 6.40 3.60 40.44 3.86
1907 2366 2.892425 CCGCCAGATTCGTGGAGC 60.892 66.667 6.40 0.00 40.44 4.70
1908 2367 2.185350 CGCCAGATTCGTGGAGCT 59.815 61.111 0.00 0.00 40.44 4.09
1909 2368 2.169789 CGCCAGATTCGTGGAGCTG 61.170 63.158 0.00 0.00 40.44 4.24
1910 2369 4.528674 CCAGATTCGTGGAGCTGG 57.471 61.111 0.00 0.00 40.44 4.85
1911 2370 1.599047 CCAGATTCGTGGAGCTGGT 59.401 57.895 4.21 0.00 42.26 4.00
1912 2371 0.742281 CCAGATTCGTGGAGCTGGTG 60.742 60.000 4.21 0.00 42.26 4.17
1913 2372 0.742281 CAGATTCGTGGAGCTGGTGG 60.742 60.000 0.00 0.00 0.00 4.61
1914 2373 0.904865 AGATTCGTGGAGCTGGTGGA 60.905 55.000 0.00 0.00 0.00 4.02
1915 2374 0.179000 GATTCGTGGAGCTGGTGGAT 59.821 55.000 0.00 0.00 0.00 3.41
1916 2375 0.620556 ATTCGTGGAGCTGGTGGATT 59.379 50.000 0.00 0.00 0.00 3.01
1917 2376 1.271856 TTCGTGGAGCTGGTGGATTA 58.728 50.000 0.00 0.00 0.00 1.75
1918 2377 0.535335 TCGTGGAGCTGGTGGATTAC 59.465 55.000 0.00 0.00 0.00 1.89
1938 2397 2.158475 ACCAAACAGGCCTCAAAGATGA 60.158 45.455 0.00 0.00 43.14 2.92
1952 2411 4.828939 TCAAAGATGAAGATGCCAACACTT 59.171 37.500 0.00 0.00 30.99 3.16
2098 2557 3.971702 GCCAAGAGGGGTGTGCCT 61.972 66.667 0.00 0.00 37.04 4.75
2118 2577 4.814234 GCCTCGTACCATTGACATCAATTA 59.186 41.667 4.32 0.00 43.48 1.40
2330 2790 0.819259 GAGCTTGCACACCTCCAACA 60.819 55.000 0.00 0.00 0.00 3.33
2388 2848 1.580059 AAGAAAGATGGGGCGGAGTA 58.420 50.000 0.00 0.00 0.00 2.59
2394 2854 0.759346 GATGGGGCGGAGTACATCTT 59.241 55.000 0.00 0.00 37.37 2.40
2425 2885 4.503123 CGTCCCATTAGTCTTATCCATGCA 60.503 45.833 0.00 0.00 0.00 3.96
2532 2993 5.627182 ATCAAGAAGAGGAGCATACATGT 57.373 39.130 2.69 2.69 0.00 3.21
2628 3089 6.100004 TCGATATCAAGAAAGCTTTCGACTT 58.900 36.000 28.67 17.56 41.92 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.618019 AATGGTATCAGAATAGCAAGGAGTA 57.382 36.000 1.89 0.00 46.01 2.59
68 71 1.209383 CACAGCTGAGCATGCACAC 59.791 57.895 23.35 13.96 0.00 3.82
81 84 2.290641 CACCTGTTTAAGACACCACAGC 59.709 50.000 0.00 0.00 36.16 4.40
107 129 4.454847 TGCCCGATTTACATGAACGTTAAA 59.545 37.500 0.00 0.00 0.00 1.52
108 130 4.001652 TGCCCGATTTACATGAACGTTAA 58.998 39.130 0.00 0.00 0.00 2.01
110 132 2.418628 CTGCCCGATTTACATGAACGTT 59.581 45.455 0.00 0.00 0.00 3.99
111 133 2.006888 CTGCCCGATTTACATGAACGT 58.993 47.619 0.00 0.00 0.00 3.99
112 134 1.330521 CCTGCCCGATTTACATGAACG 59.669 52.381 0.00 0.00 0.00 3.95
126 148 3.515602 ATTGAGAATGGTATCCTGCCC 57.484 47.619 0.00 0.00 0.00 5.36
155 177 7.151308 ACTTGAGAAGTCACTAGATTGTTCAG 58.849 38.462 0.00 0.00 37.02 3.02
156 178 7.055667 ACTTGAGAAGTCACTAGATTGTTCA 57.944 36.000 0.00 0.00 37.02 3.18
157 179 7.117092 GGAACTTGAGAAGTCACTAGATTGTTC 59.883 40.741 0.00 0.00 41.91 3.18
158 180 6.931840 GGAACTTGAGAAGTCACTAGATTGTT 59.068 38.462 0.00 0.00 41.91 2.83
159 181 6.268847 AGGAACTTGAGAAGTCACTAGATTGT 59.731 38.462 0.00 0.00 41.91 2.71
160 182 6.589523 CAGGAACTTGAGAAGTCACTAGATTG 59.410 42.308 0.00 0.00 41.91 2.67
161 183 6.495181 TCAGGAACTTGAGAAGTCACTAGATT 59.505 38.462 0.00 0.00 41.91 2.40
162 184 6.013379 TCAGGAACTTGAGAAGTCACTAGAT 58.987 40.000 0.00 0.00 41.91 1.98
163 185 5.386060 TCAGGAACTTGAGAAGTCACTAGA 58.614 41.667 0.00 0.00 41.91 2.43
164 186 5.713792 TCAGGAACTTGAGAAGTCACTAG 57.286 43.478 0.00 0.00 41.91 2.57
165 187 5.362717 TGTTCAGGAACTTGAGAAGTCACTA 59.637 40.000 12.86 0.00 41.91 2.74
166 188 4.162320 TGTTCAGGAACTTGAGAAGTCACT 59.838 41.667 12.86 0.00 41.91 3.41
167 189 4.442706 TGTTCAGGAACTTGAGAAGTCAC 58.557 43.478 12.86 0.00 41.91 3.67
168 190 4.753516 TGTTCAGGAACTTGAGAAGTCA 57.246 40.909 12.86 0.00 41.91 3.41
169 191 5.760253 TGATTGTTCAGGAACTTGAGAAGTC 59.240 40.000 12.86 0.08 41.91 3.01
170 192 5.684704 TGATTGTTCAGGAACTTGAGAAGT 58.315 37.500 12.86 0.00 45.46 3.01
171 193 6.654161 AGATGATTGTTCAGGAACTTGAGAAG 59.346 38.462 12.86 0.00 41.67 2.85
172 194 6.537355 AGATGATTGTTCAGGAACTTGAGAA 58.463 36.000 12.86 0.00 41.67 2.87
173 195 6.119240 AGATGATTGTTCAGGAACTTGAGA 57.881 37.500 12.86 0.00 41.67 3.27
174 196 6.206243 ACAAGATGATTGTTCAGGAACTTGAG 59.794 38.462 12.86 0.00 41.67 3.02
195 217 1.474077 GCTCCCCAAATACAGCACAAG 59.526 52.381 0.00 0.00 0.00 3.16
215 237 6.033341 TCACAAATCTCAACAAAAGTTTCCG 58.967 36.000 0.00 0.00 0.00 4.30
255 277 1.928868 CCATAAGAATCCATGCCCCC 58.071 55.000 0.00 0.00 0.00 5.40
321 345 3.806316 AGCGGAACAAATAAACGAGTG 57.194 42.857 0.00 0.00 0.00 3.51
368 392 2.202770 ACACCGTCGCGTGTTTCA 60.203 55.556 5.77 0.00 44.57 2.69
466 497 4.058817 GAGATGTGAAGTTCGGTCTGTTT 58.941 43.478 8.62 0.00 0.00 2.83
562 593 0.911769 TGGACGGCTTTCATCATCCT 59.088 50.000 0.00 0.00 0.00 3.24
580 611 0.107508 AACATGGAGCTCCGGTGATG 60.108 55.000 32.73 27.94 39.43 3.07
655 1066 0.973632 TGGCAACGACACCACTATCT 59.026 50.000 0.00 0.00 42.51 1.98
658 1069 1.202710 ACAATGGCAACGACACCACTA 60.203 47.619 0.00 0.00 39.19 2.74
678 1089 4.728102 CTCCGCCGCCGTGTTGTA 62.728 66.667 0.00 0.00 0.00 2.41
696 1120 0.811616 GGACCATCATCGCCTGACAC 60.812 60.000 0.00 0.00 36.48 3.67
801 1247 3.722780 GGTTGTTACTCGATCGATACGTG 59.277 47.826 19.78 9.07 0.00 4.49
950 1397 4.142093 GGTGATGCATGACCTATTTTGCTT 60.142 41.667 26.10 0.00 36.10 3.91
1514 1970 2.029073 CCGTCGTCACCTTGCACT 59.971 61.111 0.00 0.00 0.00 4.40
1728 2184 3.005155 ACAGACGAACACAACCCTACTAC 59.995 47.826 0.00 0.00 0.00 2.73
1729 2185 3.225104 ACAGACGAACACAACCCTACTA 58.775 45.455 0.00 0.00 0.00 1.82
1730 2186 2.037144 ACAGACGAACACAACCCTACT 58.963 47.619 0.00 0.00 0.00 2.57
1731 2187 2.521105 ACAGACGAACACAACCCTAC 57.479 50.000 0.00 0.00 0.00 3.18
1732 2188 3.199677 CAAACAGACGAACACAACCCTA 58.800 45.455 0.00 0.00 0.00 3.53
1733 2189 2.014128 CAAACAGACGAACACAACCCT 58.986 47.619 0.00 0.00 0.00 4.34
1734 2190 1.741145 ACAAACAGACGAACACAACCC 59.259 47.619 0.00 0.00 0.00 4.11
1735 2191 2.417239 TCACAAACAGACGAACACAACC 59.583 45.455 0.00 0.00 0.00 3.77
1736 2192 3.413558 GTCACAAACAGACGAACACAAC 58.586 45.455 0.00 0.00 0.00 3.32
1737 2193 2.417239 GGTCACAAACAGACGAACACAA 59.583 45.455 0.00 0.00 36.87 3.33
1738 2194 2.004017 GGTCACAAACAGACGAACACA 58.996 47.619 0.00 0.00 36.87 3.72
1739 2195 1.005347 CGGTCACAAACAGACGAACAC 60.005 52.381 0.00 0.00 36.87 3.32
1740 2196 1.282817 CGGTCACAAACAGACGAACA 58.717 50.000 0.00 0.00 36.87 3.18
1741 2197 1.005347 CACGGTCACAAACAGACGAAC 60.005 52.381 0.00 0.00 36.87 3.95
1742 2198 1.282817 CACGGTCACAAACAGACGAA 58.717 50.000 0.00 0.00 36.87 3.85
1746 2202 3.754323 AGAAAAACACGGTCACAAACAGA 59.246 39.130 0.00 0.00 0.00 3.41
1803 2262 4.475135 GAGGGCCTCTGAACGGGC 62.475 72.222 26.44 0.00 46.89 6.13
1804 2263 3.787001 GGAGGGCCTCTGAACGGG 61.787 72.222 31.39 0.00 0.00 5.28
1805 2264 4.148825 CGGAGGGCCTCTGAACGG 62.149 72.222 34.54 9.38 39.05 4.44
1806 2265 4.821589 GCGGAGGGCCTCTGAACG 62.822 72.222 40.18 30.14 39.05 3.95
1807 2266 3.378399 GAGCGGAGGGCCTCTGAAC 62.378 68.421 40.18 28.32 45.17 3.18
1808 2267 3.077556 GAGCGGAGGGCCTCTGAA 61.078 66.667 40.18 0.00 45.17 3.02
1815 2274 3.959991 GAGTTGTGGAGCGGAGGGC 62.960 68.421 0.00 0.00 44.05 5.19
1816 2275 2.266055 GAGTTGTGGAGCGGAGGG 59.734 66.667 0.00 0.00 0.00 4.30
1817 2276 1.079543 CAGAGTTGTGGAGCGGAGG 60.080 63.158 0.00 0.00 0.00 4.30
1818 2277 1.739562 GCAGAGTTGTGGAGCGGAG 60.740 63.158 0.00 0.00 0.00 4.63
1819 2278 2.343758 GCAGAGTTGTGGAGCGGA 59.656 61.111 0.00 0.00 0.00 5.54
1820 2279 2.743928 GGCAGAGTTGTGGAGCGG 60.744 66.667 0.00 0.00 0.00 5.52
1821 2280 2.031012 TGGCAGAGTTGTGGAGCG 59.969 61.111 0.00 0.00 0.00 5.03
1822 2281 2.320587 CGTGGCAGAGTTGTGGAGC 61.321 63.158 0.00 0.00 0.00 4.70
1823 2282 1.669115 CCGTGGCAGAGTTGTGGAG 60.669 63.158 0.00 0.00 0.00 3.86
1824 2283 2.099652 CTCCGTGGCAGAGTTGTGGA 62.100 60.000 0.00 0.00 0.00 4.02
1825 2284 1.669115 CTCCGTGGCAGAGTTGTGG 60.669 63.158 0.00 0.00 0.00 4.17
1826 2285 2.320587 GCTCCGTGGCAGAGTTGTG 61.321 63.158 5.74 0.00 33.69 3.33
1827 2286 2.031163 GCTCCGTGGCAGAGTTGT 59.969 61.111 5.74 0.00 33.69 3.32
1828 2287 3.114616 CGCTCCGTGGCAGAGTTG 61.115 66.667 5.74 0.00 33.69 3.16
1829 2288 4.379243 CCGCTCCGTGGCAGAGTT 62.379 66.667 5.74 0.00 33.69 3.01
1831 2290 4.504916 CTCCGCTCCGTGGCAGAG 62.505 72.222 0.00 0.00 32.51 3.35
1844 2303 3.123620 GAACTGCAGCCTGCTCCG 61.124 66.667 18.96 8.81 45.31 4.63
1845 2304 1.174712 TTTGAACTGCAGCCTGCTCC 61.175 55.000 18.96 4.89 45.31 4.70
1846 2305 0.886563 ATTTGAACTGCAGCCTGCTC 59.113 50.000 18.96 7.87 45.31 4.26
1847 2306 1.335145 AATTTGAACTGCAGCCTGCT 58.665 45.000 18.96 0.00 45.31 4.24
1848 2307 2.159327 AAATTTGAACTGCAGCCTGC 57.841 45.000 15.27 10.45 45.29 4.85
1849 2308 3.719924 TGAAAATTTGAACTGCAGCCTG 58.280 40.909 15.27 0.00 0.00 4.85
1850 2309 3.638160 TCTGAAAATTTGAACTGCAGCCT 59.362 39.130 15.27 0.00 0.00 4.58
1851 2310 3.981211 TCTGAAAATTTGAACTGCAGCC 58.019 40.909 15.27 6.70 0.00 4.85
1852 2311 4.443394 CACTCTGAAAATTTGAACTGCAGC 59.557 41.667 15.27 0.00 0.00 5.25
1853 2312 4.980434 CCACTCTGAAAATTTGAACTGCAG 59.020 41.667 13.48 13.48 0.00 4.41
1854 2313 4.402155 ACCACTCTGAAAATTTGAACTGCA 59.598 37.500 0.00 0.00 0.00 4.41
1855 2314 4.741676 CACCACTCTGAAAATTTGAACTGC 59.258 41.667 0.00 0.00 0.00 4.40
1856 2315 5.067674 TCCACCACTCTGAAAATTTGAACTG 59.932 40.000 0.00 0.00 0.00 3.16
1857 2316 5.200483 TCCACCACTCTGAAAATTTGAACT 58.800 37.500 0.00 0.00 0.00 3.01
1858 2317 5.514274 TCCACCACTCTGAAAATTTGAAC 57.486 39.130 0.00 0.00 0.00 3.18
1859 2318 6.729690 ATTCCACCACTCTGAAAATTTGAA 57.270 33.333 0.00 0.00 0.00 2.69
1860 2319 6.434028 CCTATTCCACCACTCTGAAAATTTGA 59.566 38.462 0.00 0.00 0.00 2.69
1861 2320 6.209391 ACCTATTCCACCACTCTGAAAATTTG 59.791 38.462 0.00 0.00 0.00 2.32
1862 2321 6.209391 CACCTATTCCACCACTCTGAAAATTT 59.791 38.462 0.00 0.00 0.00 1.82
1863 2322 5.711976 CACCTATTCCACCACTCTGAAAATT 59.288 40.000 0.00 0.00 0.00 1.82
1864 2323 5.256474 CACCTATTCCACCACTCTGAAAAT 58.744 41.667 0.00 0.00 0.00 1.82
1865 2324 4.651778 CACCTATTCCACCACTCTGAAAA 58.348 43.478 0.00 0.00 0.00 2.29
1866 2325 3.559171 GCACCTATTCCACCACTCTGAAA 60.559 47.826 0.00 0.00 0.00 2.69
1867 2326 2.027192 GCACCTATTCCACCACTCTGAA 60.027 50.000 0.00 0.00 0.00 3.02
1868 2327 1.555075 GCACCTATTCCACCACTCTGA 59.445 52.381 0.00 0.00 0.00 3.27
1869 2328 1.556911 AGCACCTATTCCACCACTCTG 59.443 52.381 0.00 0.00 0.00 3.35
1870 2329 1.834263 GAGCACCTATTCCACCACTCT 59.166 52.381 0.00 0.00 0.00 3.24
1871 2330 1.134371 GGAGCACCTATTCCACCACTC 60.134 57.143 0.00 0.00 33.55 3.51
1872 2331 0.912486 GGAGCACCTATTCCACCACT 59.088 55.000 0.00 0.00 33.55 4.00
1873 2332 0.462047 CGGAGCACCTATTCCACCAC 60.462 60.000 0.00 0.00 32.87 4.16
1874 2333 1.904771 CGGAGCACCTATTCCACCA 59.095 57.895 0.00 0.00 32.87 4.17
1875 2334 4.857251 CGGAGCACCTATTCCACC 57.143 61.111 0.00 0.00 32.87 4.61
1888 2347 1.227089 CTCCACGAATCTGGCGGAG 60.227 63.158 1.04 0.00 37.52 4.63
1889 2348 2.892640 CTCCACGAATCTGGCGGA 59.107 61.111 0.00 0.00 0.00 5.54
1890 2349 2.892425 GCTCCACGAATCTGGCGG 60.892 66.667 0.00 0.00 0.00 6.13
1891 2350 2.169789 CAGCTCCACGAATCTGGCG 61.170 63.158 0.00 0.00 0.00 5.69
1892 2351 1.817099 CCAGCTCCACGAATCTGGC 60.817 63.158 0.00 0.00 39.53 4.85
1893 2352 4.528674 CCAGCTCCACGAATCTGG 57.471 61.111 0.00 0.00 39.95 3.86
1894 2353 0.742281 CCACCAGCTCCACGAATCTG 60.742 60.000 0.00 0.00 0.00 2.90
1895 2354 0.904865 TCCACCAGCTCCACGAATCT 60.905 55.000 0.00 0.00 0.00 2.40
1896 2355 0.179000 ATCCACCAGCTCCACGAATC 59.821 55.000 0.00 0.00 0.00 2.52
1897 2356 0.620556 AATCCACCAGCTCCACGAAT 59.379 50.000 0.00 0.00 0.00 3.34
1898 2357 1.066430 GTAATCCACCAGCTCCACGAA 60.066 52.381 0.00 0.00 0.00 3.85
1899 2358 0.535335 GTAATCCACCAGCTCCACGA 59.465 55.000 0.00 0.00 0.00 4.35
1900 2359 3.065575 GTAATCCACCAGCTCCACG 57.934 57.895 0.00 0.00 0.00 4.94
1910 2369 2.092323 GAGGCCTGTTTGGTAATCCAC 58.908 52.381 12.00 0.00 44.22 4.02
1911 2370 1.707989 TGAGGCCTGTTTGGTAATCCA 59.292 47.619 12.00 0.00 42.66 3.41
1912 2371 2.507407 TGAGGCCTGTTTGGTAATCC 57.493 50.000 12.00 0.00 38.35 3.01
1913 2372 4.079253 TCTTTGAGGCCTGTTTGGTAATC 58.921 43.478 12.00 0.00 38.35 1.75
1914 2373 4.112634 TCTTTGAGGCCTGTTTGGTAAT 57.887 40.909 12.00 0.00 38.35 1.89
1915 2374 3.586470 TCTTTGAGGCCTGTTTGGTAA 57.414 42.857 12.00 0.00 38.35 2.85
1916 2375 3.073798 TCATCTTTGAGGCCTGTTTGGTA 59.926 43.478 12.00 0.00 38.35 3.25
1917 2376 2.158475 TCATCTTTGAGGCCTGTTTGGT 60.158 45.455 12.00 0.00 38.35 3.67
1918 2377 2.517959 TCATCTTTGAGGCCTGTTTGG 58.482 47.619 12.00 0.00 39.35 3.28
1919 2378 3.822735 TCTTCATCTTTGAGGCCTGTTTG 59.177 43.478 12.00 0.00 32.27 2.93
1920 2379 4.104383 TCTTCATCTTTGAGGCCTGTTT 57.896 40.909 12.00 0.00 32.27 2.83
1921 2380 3.795688 TCTTCATCTTTGAGGCCTGTT 57.204 42.857 12.00 0.00 32.27 3.16
1922 2381 3.618351 CATCTTCATCTTTGAGGCCTGT 58.382 45.455 12.00 0.00 32.27 4.00
1923 2382 2.358267 GCATCTTCATCTTTGAGGCCTG 59.642 50.000 12.00 0.00 32.27 4.85
1924 2383 2.652590 GCATCTTCATCTTTGAGGCCT 58.347 47.619 3.86 3.86 32.27 5.19
1925 2384 1.680207 GGCATCTTCATCTTTGAGGCC 59.320 52.381 0.00 0.00 32.97 5.19
1926 2385 2.372264 TGGCATCTTCATCTTTGAGGC 58.628 47.619 0.00 0.00 32.27 4.70
1938 2397 5.360714 TGAAAGAAGAAAGTGTTGGCATCTT 59.639 36.000 0.00 0.00 33.28 2.40
2081 2540 3.927481 GAGGCACACCCCTCTTGGC 62.927 68.421 1.07 0.00 46.39 4.52
2098 2557 6.228616 TCCTAATTGATGTCAATGGTACGA 57.771 37.500 8.86 0.00 45.06 3.43
2128 2587 2.244117 GATCGCAAGCAGGGACAGGA 62.244 60.000 0.00 0.00 42.47 3.86
2330 2790 1.760192 GCTGAGTTGAGCCAATGGAT 58.240 50.000 2.05 0.00 32.35 3.41
2388 2848 1.553248 TGGGACGGAAATCGAAGATGT 59.447 47.619 0.00 0.00 45.12 3.06
2394 2854 3.028850 AGACTAATGGGACGGAAATCGA 58.971 45.455 0.00 0.00 42.43 3.59
2425 2885 9.664332 ATCATCTTAGCTATAATCTTCGCAATT 57.336 29.630 0.00 0.00 0.00 2.32
2532 2993 7.067372 CCAAGCCTCTCACATACATGAAATTAA 59.933 37.037 0.00 0.00 0.00 1.40
2628 3089 4.527816 CCAAAAGGAAATCCCATCTCACAA 59.472 41.667 0.00 0.00 37.41 3.33


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

AutoCloner maintained by Alex Coulton.