Multiple sequence alignment - TraesCS3B01G205200

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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 TraesCS3B01G205200 chr3B 100.000 2345 0 0 1 2345 239901161 239898817 0.000000e+00 4331
1 TraesCS3B01G205200 chr3B 89.194 583 58 5 918 1499 34707165 34707743 0.000000e+00 723
2 TraesCS3B01G205200 chr3B 87.195 492 55 4 63 546 490890715 490891206 9.470000e-154 553
3 TraesCS3B01G205200 chr3B 87.500 144 15 2 2203 2345 201327162 201327303 1.860000e-36 163
4 TraesCS3B01G205200 chr3A 94.214 1711 71 8 1 1692 195455515 195453814 0.000000e+00 2586
5 TraesCS3B01G205200 chr3A 89.384 584 57 5 918 1499 743831623 743831043 0.000000e+00 730
6 TraesCS3B01G205200 chr3A 90.428 491 41 3 62 547 38273081 38273570 1.960000e-180 641
7 TraesCS3B01G205200 chr3A 87.375 499 47 8 63 546 500991444 500991941 2.040000e-155 558
8 TraesCS3B01G205200 chr3A 86.942 291 12 9 1712 1991 195453828 195453553 1.050000e-78 303
9 TraesCS3B01G205200 chr3A 88.889 144 15 1 2201 2344 71779958 71780100 2.400000e-40 176
10 TraesCS3B01G205200 chr3D 94.436 1366 47 8 344 1682 163118481 163117118 0.000000e+00 2074
11 TraesCS3B01G205200 chr3D 88.744 613 64 5 918 1529 465071238 465071846 0.000000e+00 745
12 TraesCS3B01G205200 chr3D 90.458 262 14 8 1731 1991 163117120 163116869 3.730000e-88 335
13 TraesCS3B01G205200 chr3D 89.231 195 12 3 2000 2187 163116896 163116704 3.900000e-58 235
14 TraesCS3B01G205200 chr2B 87.928 613 69 5 918 1529 276492578 276491970 0.000000e+00 717
15 TraesCS3B01G205200 chr2B 95.105 143 7 0 2203 2345 59645200 59645342 2.340000e-55 226
16 TraesCS3B01G205200 chr7B 87.765 613 70 5 918 1529 519228800 519228192 0.000000e+00 712
17 TraesCS3B01G205200 chr7B 89.357 451 47 1 62 512 709247261 709246812 1.220000e-157 566
18 TraesCS3B01G205200 chr7B 87.212 477 56 2 60 531 612313106 612313582 2.650000e-149 538
19 TraesCS3B01G205200 chr7B 85.315 143 20 1 2203 2345 97976287 97976146 1.880000e-31 147
20 TraesCS3B01G205200 chr2A 87.745 612 70 5 918 1527 479846970 479847578 0.000000e+00 710
21 TraesCS3B01G205200 chr2A 93.382 136 9 0 2210 2345 144018808 144018673 3.950000e-48 202
22 TraesCS3B01G205200 chr7A 89.135 451 45 3 62 512 498941094 498941540 2.040000e-155 558
23 TraesCS3B01G205200 chr7A 88.079 453 53 1 60 512 648144750 648145201 9.540000e-149 536
24 TraesCS3B01G205200 chr7A 84.464 457 65 5 60 513 648340389 648340842 1.650000e-121 446
25 TraesCS3B01G205200 chr7A 87.945 365 31 8 194 547 192661594 192661232 3.600000e-113 418
26 TraesCS3B01G205200 chr4D 87.319 276 32 3 1254 1529 20243014 20242742 1.750000e-81 313
27 TraesCS3B01G205200 chr6B 89.510 143 15 0 2203 2345 677778958 677779100 5.150000e-42 182
28 TraesCS3B01G205200 chr6B 89.510 143 15 0 2203 2345 677911233 677911375 5.150000e-42 182
29 TraesCS3B01G205200 chr7D 87.417 151 18 1 2196 2345 230975509 230975659 3.100000e-39 172
30 TraesCS3B01G205200 chr1D 86.207 145 15 5 2203 2345 411401767 411401626 4.040000e-33 152


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 TraesCS3B01G205200 chr3B 239898817 239901161 2344 True 4331.000000 4331 100.000 1 2345 1 chr3B.!!$R1 2344
1 TraesCS3B01G205200 chr3B 34707165 34707743 578 False 723.000000 723 89.194 918 1499 1 chr3B.!!$F1 581
2 TraesCS3B01G205200 chr3A 195453553 195455515 1962 True 1444.500000 2586 90.578 1 1991 2 chr3A.!!$R2 1990
3 TraesCS3B01G205200 chr3A 743831043 743831623 580 True 730.000000 730 89.384 918 1499 1 chr3A.!!$R1 581
4 TraesCS3B01G205200 chr3D 163116704 163118481 1777 True 881.333333 2074 91.375 344 2187 3 chr3D.!!$R1 1843
5 TraesCS3B01G205200 chr3D 465071238 465071846 608 False 745.000000 745 88.744 918 1529 1 chr3D.!!$F1 611
6 TraesCS3B01G205200 chr2B 276491970 276492578 608 True 717.000000 717 87.928 918 1529 1 chr2B.!!$R1 611
7 TraesCS3B01G205200 chr7B 519228192 519228800 608 True 712.000000 712 87.765 918 1529 1 chr7B.!!$R2 611
8 TraesCS3B01G205200 chr2A 479846970 479847578 608 False 710.000000 710 87.745 918 1527 1 chr2A.!!$F1 609

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
760 774 0.380378 TGCGCCCGCTATTGATTTTC 59.62 50.0 14.13 0.0 42.51 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2290 0.096281 TTAAAAATCAGGAGCGCGCG 59.904 50.0 28.44 28.44 0.0 6.86 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
295 298 3.633525 TGGCCTTGATGTTCTAATGATGC 59.366 43.478 3.32 0.00 0.00 3.91
315 318 2.008329 CTGCAGCTGATCTGGAAGTTC 58.992 52.381 20.43 0.00 42.76 3.01
349 352 6.697641 ACACTGAAAAGTAGGAAGGGAATA 57.302 37.500 0.00 0.00 0.00 1.75
440 443 3.837213 AATCGGCTTGTCAGACAAATG 57.163 42.857 16.85 7.70 37.69 2.32
496 499 1.150992 CTCGTATCGGGAGGGGTCT 59.849 63.158 0.00 0.00 0.00 3.85
637 651 6.892658 TGTGTATGAGCAAAAAGGTTATGT 57.107 33.333 0.00 0.00 0.00 2.29
681 695 3.761218 TGTCACAATGGTTCAAACACTGT 59.239 39.130 0.00 0.00 0.00 3.55
744 758 3.428534 GGCAACTTTACTTGGATTTTGCG 59.571 43.478 0.00 0.00 38.98 4.85
759 773 0.814457 TTGCGCCCGCTATTGATTTT 59.186 45.000 14.13 0.00 42.51 1.82
760 774 0.380378 TGCGCCCGCTATTGATTTTC 59.620 50.000 14.13 0.00 42.51 2.29
830 860 7.657761 CCCTGTCTATACCAGTATGAATTGTTC 59.342 40.741 0.45 0.00 39.69 3.18
832 862 9.599866 CTGTCTATACCAGTATGAATTGTTCAA 57.400 33.333 0.45 0.00 43.95 2.69
862 892 6.483307 TGCATTAATACTGTATTCCTCAGTGC 59.517 38.462 15.84 15.78 44.41 4.40
902 933 5.900339 TTAACATCGACCGCTGATAATTC 57.100 39.130 0.07 0.00 0.00 2.17
943 974 8.925161 ATTGGGTAAATTGAAATGTATTCACG 57.075 30.769 0.00 0.00 0.00 4.35
958 989 7.346208 TGTATTCACGTTGTCAATTGACTAG 57.654 36.000 32.57 25.31 44.99 2.57
998 1029 3.667497 TGCTACAGAGAAACCAGTGAG 57.333 47.619 0.00 0.00 0.00 3.51
1182 1213 1.664306 GAACTTGGAGTCGACCCGT 59.336 57.895 13.01 5.02 0.00 5.28
1302 1333 1.971695 CCACGGGAAAGTCAAGGCC 60.972 63.158 0.00 0.00 0.00 5.19
1308 1339 2.443416 GGGAAAGTCAAGGCCGTTATT 58.557 47.619 0.00 0.00 0.00 1.40
1314 1345 3.279434 AGTCAAGGCCGTTATTGATTCC 58.721 45.455 8.26 0.00 37.72 3.01
1355 1386 2.033299 AGCTGTTGTGATGGTGAAAACG 59.967 45.455 0.00 0.00 0.00 3.60
1365 1396 1.338973 TGGTGAAAACGTAGAGCTCGT 59.661 47.619 8.37 0.00 43.45 4.18
1506 1538 2.488545 GACTCTGTTGTAGGAGCTCGAA 59.511 50.000 7.83 0.00 33.29 3.71
1688 1723 9.927668 AATTTGGTATTCAAGACTGTTTAATGG 57.072 29.630 0.00 0.00 36.62 3.16
1689 1724 8.698973 TTTGGTATTCAAGACTGTTTAATGGA 57.301 30.769 0.00 0.00 36.62 3.41
1690 1725 7.921786 TGGTATTCAAGACTGTTTAATGGAG 57.078 36.000 0.00 0.00 0.00 3.86
1691 1726 6.374333 TGGTATTCAAGACTGTTTAATGGAGC 59.626 38.462 0.00 0.00 0.00 4.70
1692 1727 5.551760 ATTCAAGACTGTTTAATGGAGCG 57.448 39.130 0.00 0.00 0.00 5.03
1693 1728 3.334691 TCAAGACTGTTTAATGGAGCGG 58.665 45.455 0.00 0.00 0.00 5.52
1694 1729 3.007506 TCAAGACTGTTTAATGGAGCGGA 59.992 43.478 0.00 0.00 0.00 5.54
1695 1730 3.914426 AGACTGTTTAATGGAGCGGAT 57.086 42.857 0.00 0.00 0.00 4.18
1696 1731 3.535561 AGACTGTTTAATGGAGCGGATG 58.464 45.455 0.00 0.00 0.00 3.51
1697 1732 2.017049 ACTGTTTAATGGAGCGGATGC 58.983 47.619 0.00 0.00 43.24 3.91
1799 1834 4.392138 GTGTATCTTGCCGTTAAGCTTTCT 59.608 41.667 3.20 0.00 0.00 2.52
1800 1835 5.001232 TGTATCTTGCCGTTAAGCTTTCTT 58.999 37.500 3.20 0.00 36.35 2.52
1801 1836 4.686839 ATCTTGCCGTTAAGCTTTCTTC 57.313 40.909 3.20 0.00 33.85 2.87
1802 1837 3.472652 TCTTGCCGTTAAGCTTTCTTCA 58.527 40.909 3.20 0.00 33.85 3.02
1803 1838 3.498397 TCTTGCCGTTAAGCTTTCTTCAG 59.502 43.478 3.20 0.00 33.85 3.02
1804 1839 3.120321 TGCCGTTAAGCTTTCTTCAGA 57.880 42.857 3.20 0.00 33.85 3.27
1805 1840 3.674997 TGCCGTTAAGCTTTCTTCAGAT 58.325 40.909 3.20 0.00 33.85 2.90
1806 1841 3.436704 TGCCGTTAAGCTTTCTTCAGATG 59.563 43.478 3.20 0.00 33.85 2.90
1807 1842 3.729163 GCCGTTAAGCTTTCTTCAGATGC 60.729 47.826 3.20 0.00 33.85 3.91
1853 1897 5.469421 CCATGTGCCTATGAAGATTCTTCTC 59.531 44.000 23.29 10.47 0.00 2.87
1859 1903 6.703607 TGCCTATGAAGATTCTTCTCGATTTC 59.296 38.462 23.29 9.92 0.00 2.17
1862 1906 8.977505 CCTATGAAGATTCTTCTCGATTTCTTC 58.022 37.037 23.29 0.00 39.41 2.87
1863 1907 9.526713 CTATGAAGATTCTTCTCGATTTCTTCA 57.473 33.333 23.29 13.61 45.39 3.02
1864 1908 8.783833 ATGAAGATTCTTCTCGATTTCTTCAA 57.216 30.769 23.29 3.04 44.97 2.69
1865 1909 8.249327 TGAAGATTCTTCTCGATTTCTTCAAG 57.751 34.615 23.29 0.00 42.32 3.02
1866 1910 7.875041 TGAAGATTCTTCTCGATTTCTTCAAGT 59.125 33.333 23.29 0.00 42.32 3.16
1867 1911 9.360093 GAAGATTCTTCTCGATTTCTTCAAGTA 57.640 33.333 17.40 0.00 39.12 2.24
1873 1917 9.790389 TCTTCTCGATTTCTTCAAGTACTATTC 57.210 33.333 0.00 0.00 0.00 1.75
1909 1953 7.081349 CACGTTGATATTTTTCTGGCAAACTA 58.919 34.615 0.00 0.00 0.00 2.24
1929 1976 7.687941 AACTATTTGCTGTTAGTACATGCTT 57.312 32.000 0.00 0.00 32.86 3.91
1931 1978 8.425577 ACTATTTGCTGTTAGTACATGCTTAG 57.574 34.615 0.00 0.00 32.86 2.18
1937 1984 5.011090 TGTTAGTACATGCTTAGCCTCAG 57.989 43.478 0.29 0.00 0.00 3.35
1947 1994 3.388024 TGCTTAGCCTCAGGATCGTATTT 59.612 43.478 0.29 0.00 0.00 1.40
1948 1995 3.991121 GCTTAGCCTCAGGATCGTATTTC 59.009 47.826 0.00 0.00 0.00 2.17
2025 2080 7.504924 TTTTTGTGGGTGATTCTTAGTAGTG 57.495 36.000 0.00 0.00 0.00 2.74
2026 2081 6.428083 TTTGTGGGTGATTCTTAGTAGTGA 57.572 37.500 0.00 0.00 0.00 3.41
2027 2082 6.620877 TTGTGGGTGATTCTTAGTAGTGAT 57.379 37.500 0.00 0.00 0.00 3.06
2037 2092 8.466798 TGATTCTTAGTAGTGATGATCGTTTCA 58.533 33.333 0.00 0.00 39.12 2.69
2105 2167 0.895100 TTGTCATGTCCCTGGCAAGC 60.895 55.000 0.00 0.00 35.90 4.01
2123 2185 5.316770 GCAAGCAACAGTATTAAGAAGACG 58.683 41.667 0.00 0.00 0.00 4.18
2126 2188 5.178797 AGCAACAGTATTAAGAAGACGCAT 58.821 37.500 0.00 0.00 0.00 4.73
2130 2192 6.216801 ACAGTATTAAGAAGACGCATGGTA 57.783 37.500 0.00 0.00 0.00 3.25
2151 2213 1.675483 TGTGACTTTGTGTGCATGACC 59.325 47.619 0.00 0.00 0.00 4.02
2152 2214 1.949525 GTGACTTTGTGTGCATGACCT 59.050 47.619 0.00 0.00 0.00 3.85
2209 2271 9.988815 ACTATACATAGCTAAAATGGAGAGTTG 57.011 33.333 2.21 0.00 36.55 3.16
2210 2272 7.736447 ATACATAGCTAAAATGGAGAGTTGC 57.264 36.000 0.00 0.00 0.00 4.17
2211 2273 4.572389 ACATAGCTAAAATGGAGAGTTGCG 59.428 41.667 0.00 0.00 0.00 4.85
2212 2274 3.059352 AGCTAAAATGGAGAGTTGCGT 57.941 42.857 0.00 0.00 0.00 5.24
2213 2275 2.744202 AGCTAAAATGGAGAGTTGCGTG 59.256 45.455 0.00 0.00 0.00 5.34
2214 2276 2.484264 GCTAAAATGGAGAGTTGCGTGT 59.516 45.455 0.00 0.00 0.00 4.49
2215 2277 3.058224 GCTAAAATGGAGAGTTGCGTGTT 60.058 43.478 0.00 0.00 0.00 3.32
2216 2278 3.354089 AAAATGGAGAGTTGCGTGTTG 57.646 42.857 0.00 0.00 0.00 3.33
2217 2279 1.238439 AATGGAGAGTTGCGTGTTGG 58.762 50.000 0.00 0.00 0.00 3.77
2218 2280 1.237285 ATGGAGAGTTGCGTGTTGGC 61.237 55.000 0.00 0.00 0.00 4.52
2219 2281 1.891919 GGAGAGTTGCGTGTTGGCA 60.892 57.895 0.00 0.00 42.12 4.92
2220 2282 1.279840 GAGAGTTGCGTGTTGGCAC 59.720 57.895 0.00 0.00 43.82 5.01
2221 2283 1.436195 GAGAGTTGCGTGTTGGCACA 61.436 55.000 0.00 0.00 45.50 4.57
2222 2284 0.819259 AGAGTTGCGTGTTGGCACAT 60.819 50.000 0.00 0.00 45.50 3.21
2223 2285 0.661187 GAGTTGCGTGTTGGCACATG 60.661 55.000 0.00 0.00 45.50 3.21
2224 2286 1.661197 GTTGCGTGTTGGCACATGG 60.661 57.895 0.00 0.00 45.50 3.66
2225 2287 2.854401 TTGCGTGTTGGCACATGGG 61.854 57.895 0.00 0.00 45.50 4.00
2226 2288 2.983030 GCGTGTTGGCACATGGGA 60.983 61.111 0.00 0.00 45.50 4.37
2227 2289 2.981560 GCGTGTTGGCACATGGGAG 61.982 63.158 0.00 0.00 45.50 4.30
2228 2290 2.964978 GTGTTGGCACATGGGAGC 59.035 61.111 0.00 0.00 44.64 4.70
2229 2291 2.672651 TGTTGGCACATGGGAGCG 60.673 61.111 0.00 0.00 39.30 5.03
2230 2292 4.120331 GTTGGCACATGGGAGCGC 62.120 66.667 0.00 0.00 39.30 5.92
2244 2306 4.166011 GCGCGCGCTCCTGATTTT 62.166 61.111 44.38 0.00 38.26 1.82
2245 2307 2.480555 CGCGCGCTCCTGATTTTT 59.519 55.556 30.48 0.00 0.00 1.94
2246 2308 1.713246 CGCGCGCTCCTGATTTTTA 59.287 52.632 30.48 0.00 0.00 1.52
2247 2309 0.096281 CGCGCGCTCCTGATTTTTAA 59.904 50.000 30.48 0.00 0.00 1.52
2248 2310 1.465020 CGCGCGCTCCTGATTTTTAAA 60.465 47.619 30.48 0.00 0.00 1.52
2249 2311 2.591133 GCGCGCTCCTGATTTTTAAAA 58.409 42.857 26.67 0.00 0.00 1.52
2250 2312 3.179048 GCGCGCTCCTGATTTTTAAAAT 58.821 40.909 26.67 2.23 0.00 1.82
2251 2313 3.000773 GCGCGCTCCTGATTTTTAAAATG 60.001 43.478 26.67 0.00 0.00 2.32
2252 2314 4.165779 CGCGCTCCTGATTTTTAAAATGT 58.834 39.130 7.72 0.00 0.00 2.71
2253 2315 4.030529 CGCGCTCCTGATTTTTAAAATGTG 59.969 41.667 7.72 1.43 0.00 3.21
2254 2316 4.923281 GCGCTCCTGATTTTTAAAATGTGT 59.077 37.500 7.72 0.00 0.00 3.72
2255 2317 5.405269 GCGCTCCTGATTTTTAAAATGTGTT 59.595 36.000 7.72 0.00 0.00 3.32
2256 2318 6.073819 GCGCTCCTGATTTTTAAAATGTGTTT 60.074 34.615 7.72 0.00 0.00 2.83
2257 2319 7.282916 CGCTCCTGATTTTTAAAATGTGTTTG 58.717 34.615 7.72 0.00 0.00 2.93
2258 2320 7.168972 CGCTCCTGATTTTTAAAATGTGTTTGA 59.831 33.333 7.72 0.00 0.00 2.69
2259 2321 8.825745 GCTCCTGATTTTTAAAATGTGTTTGAA 58.174 29.630 7.72 0.00 0.00 2.69
2275 2337 8.954950 TGTGTTTGAAACATATTTGGAAATGT 57.045 26.923 14.40 0.00 44.35 2.71
2276 2338 9.039870 TGTGTTTGAAACATATTTGGAAATGTC 57.960 29.630 14.40 0.00 44.35 3.06
2277 2339 9.039870 GTGTTTGAAACATATTTGGAAATGTCA 57.960 29.630 14.40 0.00 44.35 3.58
2278 2340 9.605275 TGTTTGAAACATATTTGGAAATGTCAA 57.395 25.926 6.66 0.00 35.30 3.18
2303 2365 7.840342 AAAAATTCAAACAAAAATTTGGGGC 57.160 28.000 10.38 0.00 42.34 5.80
2304 2366 6.535963 AAATTCAAACAAAAATTTGGGGCA 57.464 29.167 10.38 0.00 42.34 5.36
2305 2367 6.728089 AATTCAAACAAAAATTTGGGGCAT 57.272 29.167 10.38 0.00 42.34 4.40
2306 2368 7.830099 AATTCAAACAAAAATTTGGGGCATA 57.170 28.000 10.38 0.00 42.34 3.14
2307 2369 6.625873 TTCAAACAAAAATTTGGGGCATAC 57.374 33.333 10.38 0.00 42.34 2.39
2308 2370 5.934781 TCAAACAAAAATTTGGGGCATACT 58.065 33.333 10.38 0.00 42.34 2.12
2309 2371 6.360618 TCAAACAAAAATTTGGGGCATACTT 58.639 32.000 10.38 0.00 42.34 2.24
2310 2372 6.484977 TCAAACAAAAATTTGGGGCATACTTC 59.515 34.615 10.38 0.00 42.34 3.01
2311 2373 5.823861 ACAAAAATTTGGGGCATACTTCT 57.176 34.783 10.38 0.00 42.34 2.85
2312 2374 5.793817 ACAAAAATTTGGGGCATACTTCTC 58.206 37.500 10.38 0.00 42.34 2.87
2313 2375 4.718940 AAAATTTGGGGCATACTTCTCG 57.281 40.909 0.00 0.00 0.00 4.04
2314 2376 3.644966 AATTTGGGGCATACTTCTCGA 57.355 42.857 0.00 0.00 0.00 4.04
2315 2377 3.864789 ATTTGGGGCATACTTCTCGAT 57.135 42.857 0.00 0.00 0.00 3.59
2316 2378 4.974645 ATTTGGGGCATACTTCTCGATA 57.025 40.909 0.00 0.00 0.00 2.92
2317 2379 4.974645 TTTGGGGCATACTTCTCGATAT 57.025 40.909 0.00 0.00 0.00 1.63
2318 2380 4.974645 TTGGGGCATACTTCTCGATATT 57.025 40.909 0.00 0.00 0.00 1.28
2319 2381 4.271696 TGGGGCATACTTCTCGATATTG 57.728 45.455 0.00 0.00 0.00 1.90
2320 2382 3.646162 TGGGGCATACTTCTCGATATTGT 59.354 43.478 0.00 0.00 0.00 2.71
2321 2383 4.836175 TGGGGCATACTTCTCGATATTGTA 59.164 41.667 0.00 0.00 0.00 2.41
2322 2384 5.169295 GGGGCATACTTCTCGATATTGTAC 58.831 45.833 0.00 0.00 0.00 2.90
2323 2385 5.279306 GGGGCATACTTCTCGATATTGTACA 60.279 44.000 0.00 0.00 0.00 2.90
2324 2386 6.398918 GGGCATACTTCTCGATATTGTACAT 58.601 40.000 0.00 0.00 0.00 2.29
2325 2387 6.311445 GGGCATACTTCTCGATATTGTACATG 59.689 42.308 0.00 0.00 0.00 3.21
2326 2388 6.183360 GGCATACTTCTCGATATTGTACATGC 60.183 42.308 0.00 0.00 0.00 4.06
2327 2389 6.587990 GCATACTTCTCGATATTGTACATGCT 59.412 38.462 0.00 0.00 0.00 3.79
2328 2390 7.201393 GCATACTTCTCGATATTGTACATGCTC 60.201 40.741 0.00 0.00 0.00 4.26
2329 2391 6.149129 ACTTCTCGATATTGTACATGCTCA 57.851 37.500 0.00 0.00 0.00 4.26
2330 2392 5.980116 ACTTCTCGATATTGTACATGCTCAC 59.020 40.000 0.00 0.00 0.00 3.51
2331 2393 5.514274 TCTCGATATTGTACATGCTCACA 57.486 39.130 0.00 0.00 0.00 3.58
2332 2394 5.901552 TCTCGATATTGTACATGCTCACAA 58.098 37.500 9.69 9.69 38.89 3.33
2333 2395 6.337356 TCTCGATATTGTACATGCTCACAAA 58.663 36.000 10.93 3.76 38.11 2.83
2334 2396 6.255670 TCTCGATATTGTACATGCTCACAAAC 59.744 38.462 10.93 6.46 38.11 2.93
2335 2397 6.106003 TCGATATTGTACATGCTCACAAACT 58.894 36.000 10.93 3.64 38.11 2.66
2336 2398 6.255670 TCGATATTGTACATGCTCACAAACTC 59.744 38.462 10.93 9.68 38.11 3.01
2337 2399 4.668576 ATTGTACATGCTCACAAACTCG 57.331 40.909 10.93 0.00 38.11 4.18
2338 2400 3.106242 TGTACATGCTCACAAACTCGT 57.894 42.857 0.00 0.00 0.00 4.18
2339 2401 3.462982 TGTACATGCTCACAAACTCGTT 58.537 40.909 0.00 0.00 0.00 3.85
2340 2402 3.874543 TGTACATGCTCACAAACTCGTTT 59.125 39.130 0.00 0.00 0.00 3.60
2341 2403 3.609103 ACATGCTCACAAACTCGTTTC 57.391 42.857 0.00 0.00 0.00 2.78
2342 2404 2.032894 ACATGCTCACAAACTCGTTTCG 60.033 45.455 0.00 0.00 0.00 3.46
2343 2405 0.303493 TGCTCACAAACTCGTTTCGC 59.697 50.000 0.00 0.00 0.00 4.70
2344 2406 0.718220 GCTCACAAACTCGTTTCGCG 60.718 55.000 0.00 0.00 43.01 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.870991 AGAGATACGAAAAAGTTGGCTAGC 59.129 41.667 6.04 6.04 0.00 3.42
37 38 4.454504 GTCCAAGCCAAGAGATACGAAAAA 59.545 41.667 0.00 0.00 0.00 1.94
42 43 1.207089 TGGTCCAAGCCAAGAGATACG 59.793 52.381 0.00 0.00 35.25 3.06
156 158 4.995487 CCTAGTTAACCTCCCGATAAATGC 59.005 45.833 0.88 0.00 0.00 3.56
210 213 4.645535 AGACACTCAGTACATTGCATGTT 58.354 39.130 7.02 0.00 41.63 2.71
213 216 7.222805 CGTATTTAGACACTCAGTACATTGCAT 59.777 37.037 0.00 0.00 0.00 3.96
261 264 4.837860 ACATCAAGGCCACAATTTTCCTTA 59.162 37.500 5.01 0.00 36.85 2.69
274 277 3.887716 AGCATCATTAGAACATCAAGGCC 59.112 43.478 0.00 0.00 0.00 5.19
295 298 2.008329 GAACTTCCAGATCAGCTGCAG 58.992 52.381 10.11 10.11 43.50 4.41
315 318 7.444183 TCCTACTTTTCAGTGTTCAGGTTTATG 59.556 37.037 0.00 0.00 34.06 1.90
329 332 5.126779 GGCTATTCCCTTCCTACTTTTCAG 58.873 45.833 0.00 0.00 0.00 3.02
387 390 1.654220 CCGAATTATTGGCTGGGCG 59.346 57.895 0.00 0.00 0.00 6.13
408 411 1.858091 AGCCGATTTATCAGCTGTCG 58.142 50.000 14.67 14.72 38.99 4.35
496 499 7.879070 ACTGTCGAGTAGTTAACTGTTATTCA 58.121 34.615 18.56 9.54 39.07 2.57
637 651 3.995636 AGGAGCTATACCAGGAAACTCA 58.004 45.455 0.00 0.00 40.21 3.41
681 695 9.727859 CCTGATACTGAATCTAGTACTTAGCTA 57.272 37.037 0.00 0.00 36.09 3.32
744 758 3.879892 AGAGAAGAAAATCAATAGCGGGC 59.120 43.478 0.00 0.00 0.00 6.13
759 773 9.712305 ATTGACGATCTTAAAAGAAAGAGAAGA 57.288 29.630 0.00 0.00 38.81 2.87
789 803 2.821366 GGGAGCGACAGTGCATGG 60.821 66.667 0.00 0.00 37.31 3.66
832 862 9.407380 TGAGGAATACAGTATTAATGCAATTGT 57.593 29.630 5.75 4.54 36.99 2.71
862 892 7.846107 CGATGTTAAAAATCAGGATACAGAACG 59.154 37.037 1.55 0.00 34.90 3.95
958 989 1.792006 AGGTAACAAGCAGCACGTAC 58.208 50.000 0.00 0.00 41.41 3.67
998 1029 1.221021 GGTGGAGGGACGACCATTC 59.779 63.158 6.20 0.00 44.92 2.67
1239 1270 2.064581 GGACACGGCAGGTATCCCT 61.065 63.158 0.00 0.00 44.02 4.20
1302 1333 5.980116 AGATTCTCTGACGGAATCAATAACG 59.020 40.000 17.02 0.00 46.60 3.18
1332 1363 3.988379 TTTCACCATCACAACAGCTTC 57.012 42.857 0.00 0.00 0.00 3.86
1355 1386 3.244111 GCAAATGCTAAGACGAGCTCTAC 59.756 47.826 12.85 5.54 43.27 2.59
1365 1396 2.099141 AGACTGCGCAAATGCTAAGA 57.901 45.000 13.05 0.00 39.32 2.10
1426 1457 2.163010 AGCGCCAAATTCATGAACAGAG 59.837 45.455 11.07 1.69 0.00 3.35
1428 1459 2.642139 AGCGCCAAATTCATGAACAG 57.358 45.000 11.07 3.51 0.00 3.16
1534 1569 6.336566 TGCTACTGCAGATTTGTTTCAAAAA 58.663 32.000 23.35 0.00 45.31 1.94
1535 1570 5.900425 TGCTACTGCAGATTTGTTTCAAAA 58.100 33.333 23.35 0.00 45.31 2.44
1705 1740 7.818930 CACCATGCTCCATTAAACAGTATTTTT 59.181 33.333 0.00 0.00 0.00 1.94
1706 1741 7.039082 ACACCATGCTCCATTAAACAGTATTTT 60.039 33.333 0.00 0.00 0.00 1.82
1707 1742 6.437162 ACACCATGCTCCATTAAACAGTATTT 59.563 34.615 0.00 0.00 0.00 1.40
1708 1743 5.951747 ACACCATGCTCCATTAAACAGTATT 59.048 36.000 0.00 0.00 0.00 1.89
1709 1744 5.357878 CACACCATGCTCCATTAAACAGTAT 59.642 40.000 0.00 0.00 0.00 2.12
1710 1745 4.699735 CACACCATGCTCCATTAAACAGTA 59.300 41.667 0.00 0.00 0.00 2.74
1711 1746 3.507233 CACACCATGCTCCATTAAACAGT 59.493 43.478 0.00 0.00 0.00 3.55
1712 1747 3.758023 TCACACCATGCTCCATTAAACAG 59.242 43.478 0.00 0.00 0.00 3.16
1713 1748 3.505680 GTCACACCATGCTCCATTAAACA 59.494 43.478 0.00 0.00 0.00 2.83
1714 1749 3.758554 AGTCACACCATGCTCCATTAAAC 59.241 43.478 0.00 0.00 0.00 2.01
1715 1750 4.032960 AGTCACACCATGCTCCATTAAA 57.967 40.909 0.00 0.00 0.00 1.52
1716 1751 3.719268 AGTCACACCATGCTCCATTAA 57.281 42.857 0.00 0.00 0.00 1.40
1717 1752 3.264193 AGAAGTCACACCATGCTCCATTA 59.736 43.478 0.00 0.00 0.00 1.90
1718 1753 2.040813 AGAAGTCACACCATGCTCCATT 59.959 45.455 0.00 0.00 0.00 3.16
1799 1834 5.402997 CTATGGATAGCTGAGCATCTGAA 57.597 43.478 7.39 0.00 35.94 3.02
1853 1897 8.812329 CCAAGAGAATAGTACTTGAAGAAATCG 58.188 37.037 0.00 0.00 42.12 3.34
1859 1903 6.978080 GCTCTCCAAGAGAATAGTACTTGAAG 59.022 42.308 0.00 0.00 45.07 3.02
1862 1906 6.039616 GTGCTCTCCAAGAGAATAGTACTTG 58.960 44.000 0.00 0.00 45.07 3.16
1863 1907 5.163602 CGTGCTCTCCAAGAGAATAGTACTT 60.164 44.000 0.00 0.00 45.07 2.24
1864 1908 4.336993 CGTGCTCTCCAAGAGAATAGTACT 59.663 45.833 8.14 0.00 45.07 2.73
1865 1909 4.096682 ACGTGCTCTCCAAGAGAATAGTAC 59.903 45.833 8.14 0.00 45.07 2.73
1866 1910 4.270834 ACGTGCTCTCCAAGAGAATAGTA 58.729 43.478 8.14 0.00 45.07 1.82
1867 1911 3.093057 ACGTGCTCTCCAAGAGAATAGT 58.907 45.455 8.14 0.08 45.07 2.12
1873 1917 2.376808 ATCAACGTGCTCTCCAAGAG 57.623 50.000 0.00 0.00 45.04 2.85
1909 1953 5.066505 GGCTAAGCATGTACTAACAGCAAAT 59.933 40.000 0.00 0.00 39.49 2.32
1929 1976 5.871396 AAAGAAATACGATCCTGAGGCTA 57.129 39.130 0.00 0.00 0.00 3.93
1931 1978 6.281405 TCTAAAAGAAATACGATCCTGAGGC 58.719 40.000 0.00 0.00 0.00 4.70
2001 2056 7.284074 TCACTACTAAGAATCACCCACAAAAA 58.716 34.615 0.00 0.00 0.00 1.94
2002 2057 6.833041 TCACTACTAAGAATCACCCACAAAA 58.167 36.000 0.00 0.00 0.00 2.44
2003 2058 6.428083 TCACTACTAAGAATCACCCACAAA 57.572 37.500 0.00 0.00 0.00 2.83
2004 2059 6.212589 TCATCACTACTAAGAATCACCCACAA 59.787 38.462 0.00 0.00 0.00 3.33
2005 2060 5.719563 TCATCACTACTAAGAATCACCCACA 59.280 40.000 0.00 0.00 0.00 4.17
2006 2061 6.222038 TCATCACTACTAAGAATCACCCAC 57.778 41.667 0.00 0.00 0.00 4.61
2007 2062 6.239036 CGATCATCACTACTAAGAATCACCCA 60.239 42.308 0.00 0.00 0.00 4.51
2008 2063 6.153067 CGATCATCACTACTAAGAATCACCC 58.847 44.000 0.00 0.00 0.00 4.61
2009 2064 6.740110 ACGATCATCACTACTAAGAATCACC 58.260 40.000 0.00 0.00 0.00 4.02
2010 2065 8.635877 AAACGATCATCACTACTAAGAATCAC 57.364 34.615 0.00 0.00 0.00 3.06
2011 2066 8.466798 TGAAACGATCATCACTACTAAGAATCA 58.533 33.333 0.00 0.00 31.50 2.57
2012 2067 8.858003 TGAAACGATCATCACTACTAAGAATC 57.142 34.615 0.00 0.00 31.50 2.52
2027 2082 3.873361 GCATCTCCTGAATGAAACGATCA 59.127 43.478 0.00 0.00 43.67 2.92
2037 2092 7.810260 ACCTTAAAGATTAGCATCTCCTGAAT 58.190 34.615 0.00 0.00 39.00 2.57
2077 2132 2.108075 AGGGACATGACAATGAACACCA 59.892 45.455 0.00 0.00 37.24 4.17
2105 2167 5.351465 ACCATGCGTCTTCTTAATACTGTTG 59.649 40.000 0.00 0.00 0.00 3.33
2123 2185 3.825308 CACACAAAGTCACATACCATGC 58.175 45.455 0.00 0.00 0.00 4.06
2126 2188 2.924421 TGCACACAAAGTCACATACCA 58.076 42.857 0.00 0.00 0.00 3.25
2130 2192 2.294233 GGTCATGCACACAAAGTCACAT 59.706 45.455 0.00 0.00 0.00 3.21
2187 2249 5.753438 CGCAACTCTCCATTTTAGCTATGTA 59.247 40.000 0.00 0.00 0.00 2.29
2188 2250 4.572389 CGCAACTCTCCATTTTAGCTATGT 59.428 41.667 0.00 0.00 0.00 2.29
2189 2251 4.572389 ACGCAACTCTCCATTTTAGCTATG 59.428 41.667 0.00 0.00 0.00 2.23
2190 2252 4.572389 CACGCAACTCTCCATTTTAGCTAT 59.428 41.667 0.00 0.00 0.00 2.97
2191 2253 3.932710 CACGCAACTCTCCATTTTAGCTA 59.067 43.478 0.00 0.00 0.00 3.32
2192 2254 2.744202 CACGCAACTCTCCATTTTAGCT 59.256 45.455 0.00 0.00 0.00 3.32
2193 2255 2.484264 ACACGCAACTCTCCATTTTAGC 59.516 45.455 0.00 0.00 0.00 3.09
2194 2256 4.466828 CAACACGCAACTCTCCATTTTAG 58.533 43.478 0.00 0.00 0.00 1.85
2195 2257 3.252215 CCAACACGCAACTCTCCATTTTA 59.748 43.478 0.00 0.00 0.00 1.52
2196 2258 2.034558 CCAACACGCAACTCTCCATTTT 59.965 45.455 0.00 0.00 0.00 1.82
2197 2259 1.608590 CCAACACGCAACTCTCCATTT 59.391 47.619 0.00 0.00 0.00 2.32
2198 2260 1.238439 CCAACACGCAACTCTCCATT 58.762 50.000 0.00 0.00 0.00 3.16
2199 2261 1.237285 GCCAACACGCAACTCTCCAT 61.237 55.000 0.00 0.00 0.00 3.41
2200 2262 1.891919 GCCAACACGCAACTCTCCA 60.892 57.895 0.00 0.00 0.00 3.86
2201 2263 1.891919 TGCCAACACGCAACTCTCC 60.892 57.895 0.00 0.00 35.32 3.71
2202 2264 1.279840 GTGCCAACACGCAACTCTC 59.720 57.895 0.00 0.00 41.30 3.20
2203 2265 3.420943 GTGCCAACACGCAACTCT 58.579 55.556 0.00 0.00 41.30 3.24
2212 2274 2.672651 CGCTCCCATGTGCCAACA 60.673 61.111 0.00 0.00 41.58 3.33
2213 2275 4.120331 GCGCTCCCATGTGCCAAC 62.120 66.667 0.00 0.00 37.48 3.77
2227 2289 2.304516 TAAAAATCAGGAGCGCGCGC 62.305 55.000 45.10 45.10 42.33 6.86
2228 2290 0.096281 TTAAAAATCAGGAGCGCGCG 59.904 50.000 28.44 28.44 0.00 6.86
2229 2291 2.256445 TTTAAAAATCAGGAGCGCGC 57.744 45.000 26.66 26.66 0.00 6.86
2230 2292 4.030529 CACATTTTAAAAATCAGGAGCGCG 59.969 41.667 0.00 0.00 0.00 6.86
2231 2293 4.923281 ACACATTTTAAAAATCAGGAGCGC 59.077 37.500 4.44 0.00 0.00 5.92
2232 2294 7.168972 TCAAACACATTTTAAAAATCAGGAGCG 59.831 33.333 4.44 0.00 0.00 5.03
2233 2295 8.364129 TCAAACACATTTTAAAAATCAGGAGC 57.636 30.769 4.44 0.00 0.00 4.70
2249 2311 9.558396 ACATTTCCAAATATGTTTCAAACACAT 57.442 25.926 4.73 0.00 45.50 3.21
2250 2312 8.954950 ACATTTCCAAATATGTTTCAAACACA 57.045 26.923 4.73 0.00 45.50 3.72
2251 2313 9.039870 TGACATTTCCAAATATGTTTCAAACAC 57.960 29.630 4.73 0.00 45.50 3.32
2252 2314 9.605275 TTGACATTTCCAAATATGTTTCAAACA 57.395 25.926 5.18 5.18 46.94 2.83
2279 2341 7.389232 TGCCCCAAATTTTTGTTTGAATTTTT 58.611 26.923 2.63 0.00 40.64 1.94
2280 2342 6.939622 TGCCCCAAATTTTTGTTTGAATTTT 58.060 28.000 2.63 0.00 40.64 1.82
2281 2343 6.535963 TGCCCCAAATTTTTGTTTGAATTT 57.464 29.167 2.63 0.00 40.64 1.82
2282 2344 6.728089 ATGCCCCAAATTTTTGTTTGAATT 57.272 29.167 2.63 0.00 40.64 2.17
2283 2345 7.003482 AGTATGCCCCAAATTTTTGTTTGAAT 58.997 30.769 2.63 0.00 40.64 2.57
2284 2346 6.360618 AGTATGCCCCAAATTTTTGTTTGAA 58.639 32.000 2.63 0.00 40.64 2.69
2285 2347 5.934781 AGTATGCCCCAAATTTTTGTTTGA 58.065 33.333 2.63 0.00 40.64 2.69
2286 2348 6.486320 AGAAGTATGCCCCAAATTTTTGTTTG 59.514 34.615 2.63 0.00 38.50 2.93
2287 2349 6.600388 AGAAGTATGCCCCAAATTTTTGTTT 58.400 32.000 2.63 0.00 36.45 2.83
2288 2350 6.186420 AGAAGTATGCCCCAAATTTTTGTT 57.814 33.333 2.63 0.00 36.45 2.83
2289 2351 5.566627 CGAGAAGTATGCCCCAAATTTTTGT 60.567 40.000 2.63 0.00 36.45 2.83
2290 2352 4.864247 CGAGAAGTATGCCCCAAATTTTTG 59.136 41.667 0.00 0.00 37.90 2.44
2291 2353 4.770010 TCGAGAAGTATGCCCCAAATTTTT 59.230 37.500 0.00 0.00 0.00 1.94
2292 2354 4.340617 TCGAGAAGTATGCCCCAAATTTT 58.659 39.130 0.00 0.00 0.00 1.82
2293 2355 3.963129 TCGAGAAGTATGCCCCAAATTT 58.037 40.909 0.00 0.00 0.00 1.82
2294 2356 3.644966 TCGAGAAGTATGCCCCAAATT 57.355 42.857 0.00 0.00 0.00 1.82
2295 2357 3.864789 ATCGAGAAGTATGCCCCAAAT 57.135 42.857 0.00 0.00 0.00 2.32
2296 2358 4.974645 ATATCGAGAAGTATGCCCCAAA 57.025 40.909 0.00 0.00 0.00 3.28
2297 2359 4.102524 ACAATATCGAGAAGTATGCCCCAA 59.897 41.667 0.00 0.00 0.00 4.12
2298 2360 3.646162 ACAATATCGAGAAGTATGCCCCA 59.354 43.478 0.00 0.00 0.00 4.96
2299 2361 4.273148 ACAATATCGAGAAGTATGCCCC 57.727 45.455 0.00 0.00 0.00 5.80
2300 2362 5.779922 TGTACAATATCGAGAAGTATGCCC 58.220 41.667 0.00 0.00 0.00 5.36
2301 2363 6.183360 GCATGTACAATATCGAGAAGTATGCC 60.183 42.308 0.00 0.00 0.00 4.40
2302 2364 6.587990 AGCATGTACAATATCGAGAAGTATGC 59.412 38.462 0.00 12.24 0.00 3.14
2303 2365 7.809806 TGAGCATGTACAATATCGAGAAGTATG 59.190 37.037 0.00 0.00 0.00 2.39
2304 2366 7.810282 GTGAGCATGTACAATATCGAGAAGTAT 59.190 37.037 0.00 0.00 0.00 2.12
2305 2367 7.139392 GTGAGCATGTACAATATCGAGAAGTA 58.861 38.462 0.00 0.00 0.00 2.24
2306 2368 5.980116 GTGAGCATGTACAATATCGAGAAGT 59.020 40.000 0.00 0.00 0.00 3.01
2307 2369 5.979517 TGTGAGCATGTACAATATCGAGAAG 59.020 40.000 0.00 0.00 0.00 2.85
2308 2370 5.901552 TGTGAGCATGTACAATATCGAGAA 58.098 37.500 0.00 0.00 0.00 2.87
2309 2371 5.514274 TGTGAGCATGTACAATATCGAGA 57.486 39.130 0.00 0.00 0.00 4.04
2310 2372 6.256539 AGTTTGTGAGCATGTACAATATCGAG 59.743 38.462 0.00 0.00 36.75 4.04
2311 2373 6.106003 AGTTTGTGAGCATGTACAATATCGA 58.894 36.000 0.00 0.00 36.75 3.59
2312 2374 6.349973 AGTTTGTGAGCATGTACAATATCG 57.650 37.500 0.00 0.00 36.75 2.92
2313 2375 6.036083 ACGAGTTTGTGAGCATGTACAATATC 59.964 38.462 0.00 0.00 36.75 1.63
2314 2376 5.874810 ACGAGTTTGTGAGCATGTACAATAT 59.125 36.000 0.00 5.50 36.75 1.28
2315 2377 5.234752 ACGAGTTTGTGAGCATGTACAATA 58.765 37.500 0.00 3.43 36.75 1.90
2316 2378 4.065088 ACGAGTTTGTGAGCATGTACAAT 58.935 39.130 0.00 0.00 36.75 2.71
2317 2379 3.462982 ACGAGTTTGTGAGCATGTACAA 58.537 40.909 0.00 7.82 35.20 2.41
2318 2380 3.106242 ACGAGTTTGTGAGCATGTACA 57.894 42.857 0.00 0.00 0.00 2.90
2319 2381 4.455124 GAAACGAGTTTGTGAGCATGTAC 58.545 43.478 5.89 0.00 32.11 2.90
2320 2382 3.183574 CGAAACGAGTTTGTGAGCATGTA 59.816 43.478 5.89 0.00 32.11 2.29
2321 2383 2.032894 CGAAACGAGTTTGTGAGCATGT 60.033 45.455 5.89 0.00 32.11 3.21
2322 2384 2.563976 CGAAACGAGTTTGTGAGCATG 58.436 47.619 5.89 0.00 32.11 4.06
2323 2385 1.069906 GCGAAACGAGTTTGTGAGCAT 60.070 47.619 5.89 0.00 32.11 3.79
2324 2386 0.303493 GCGAAACGAGTTTGTGAGCA 59.697 50.000 5.89 0.00 32.11 4.26
2325 2387 3.058457 GCGAAACGAGTTTGTGAGC 57.942 52.632 5.89 3.26 32.11 4.26


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

AutoCloner maintained by Alex Coulton.