Multiple sequence alignment - TraesCS7A01G497500

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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 TraesCS7A01G497500 chr7A 100.000 2321 0 0 1 2321 688205834 688203514 0.000000e+00 4287
1 TraesCS7A01G497500 chr7A 97.590 83 1 1 1762 1844 688204148 688204067 8.650000e-30 141
2 TraesCS7A01G497500 chr3A 98.701 2155 17 2 1 2147 494806628 494804477 0.000000e+00 3814
3 TraesCS7A01G497500 chr3A 97.661 171 3 1 2151 2321 649162618 649162449 2.260000e-75 292
4 TraesCS7A01G497500 chr3A 92.473 186 9 4 682 867 169875365 169875185 6.360000e-66 261
5 TraesCS7A01G497500 chr1A 99.548 1768 8 0 1 1768 350417718 350415951 0.000000e+00 3221
6 TraesCS7A01G497500 chr1A 98.446 386 5 1 1762 2147 350416032 350415648 0.000000e+00 678
7 TraesCS7A01G497500 chr1A 98.246 171 3 0 2151 2321 321527669 321527499 1.350000e-77 300
8 TraesCS7A01G497500 chr3B 99.212 1776 6 1 1 1768 739939871 739938096 0.000000e+00 3195
9 TraesCS7A01G497500 chr3B 95.096 1203 20 10 596 1768 398845735 398846928 0.000000e+00 1858
10 TraesCS7A01G497500 chr3B 95.070 568 22 5 2 567 398845245 398845808 0.000000e+00 889
11 TraesCS7A01G497500 chr3B 98.708 387 3 2 1762 2147 739938177 739937792 0.000000e+00 686
12 TraesCS7A01G497500 chr3B 95.939 394 6 3 1762 2147 398846839 398847230 4.210000e-177 630
13 TraesCS7A01G497500 chr3B 98.235 170 3 0 2152 2321 17350547 17350378 4.850000e-77 298
14 TraesCS7A01G497500 chr2B 96.663 1768 37 9 2 1768 629345908 629347654 0.000000e+00 2918
15 TraesCS7A01G497500 chr2B 98.741 1271 7 2 888 2150 188257494 188256225 0.000000e+00 2250
16 TraesCS7A01G497500 chr2B 99.213 635 5 0 1 635 188258138 188257504 0.000000e+00 1146
17 TraesCS7A01G497500 chr2B 96.667 390 11 2 1762 2151 629347573 629347960 0.000000e+00 647
18 TraesCS7A01G497500 chr2B 98.235 170 3 0 2152 2321 583409738 583409907 4.850000e-77 298
19 TraesCS7A01G497500 chr2B 97.126 174 5 0 2148 2321 470470828 470471001 6.270000e-76 294
20 TraesCS7A01G497500 chr5B 95.644 1676 25 14 1 1644 257533946 257532287 0.000000e+00 2647
21 TraesCS7A01G497500 chr5B 97.143 175 4 1 2148 2321 572909134 572909308 6.270000e-76 294
22 TraesCS7A01G497500 chr5A 98.748 1278 14 2 491 1768 414313196 414311921 0.000000e+00 2270
23 TraesCS7A01G497500 chr5A 98.705 386 4 1 1762 2147 414312002 414311618 0.000000e+00 684
24 TraesCS7A01G497500 chr5A 95.431 394 8 3 1762 2147 426297078 426297469 9.110000e-174 619
25 TraesCS7A01G497500 chr5A 98.235 170 3 0 2152 2321 383894800 383894631 4.850000e-77 298
26 TraesCS7A01G497500 chr1B 95.732 1195 25 8 596 1768 647919147 647917957 0.000000e+00 1901
27 TraesCS7A01G497500 chr1B 94.903 569 22 5 2 567 647919638 647919074 0.000000e+00 883
28 TraesCS7A01G497500 chr1B 95.939 394 6 3 1762 2147 647918046 647917655 4.210000e-177 630
29 TraesCS7A01G497500 chr1B 97.126 174 5 0 2148 2321 666981187 666981360 6.270000e-76 294
30 TraesCS7A01G497500 chr7B 95.649 1195 22 10 596 1768 122293968 122292782 0.000000e+00 1892
31 TraesCS7A01G497500 chr7B 95.070 568 22 4 2 567 122294458 122293895 0.000000e+00 889
32 TraesCS7A01G497500 chr6A 97.647 170 4 0 2152 2321 922374 922205 2.260000e-75 292


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 TraesCS7A01G497500 chr7A 688203514 688205834 2320 True 2214.000000 4287 98.795000 1 2321 2 chr7A.!!$R1 2320
1 TraesCS7A01G497500 chr3A 494804477 494806628 2151 True 3814.000000 3814 98.701000 1 2147 1 chr3A.!!$R2 2146
2 TraesCS7A01G497500 chr1A 350415648 350417718 2070 True 1949.500000 3221 98.997000 1 2147 2 chr1A.!!$R2 2146
3 TraesCS7A01G497500 chr3B 739937792 739939871 2079 True 1940.500000 3195 98.960000 1 2147 2 chr3B.!!$R2 2146
4 TraesCS7A01G497500 chr3B 398845245 398847230 1985 False 1125.666667 1858 95.368333 2 2147 3 chr3B.!!$F1 2145
5 TraesCS7A01G497500 chr2B 629345908 629347960 2052 False 1782.500000 2918 96.665000 2 2151 2 chr2B.!!$F3 2149
6 TraesCS7A01G497500 chr2B 188256225 188258138 1913 True 1698.000000 2250 98.977000 1 2150 2 chr2B.!!$R1 2149
7 TraesCS7A01G497500 chr5B 257532287 257533946 1659 True 2647.000000 2647 95.644000 1 1644 1 chr5B.!!$R1 1643
8 TraesCS7A01G497500 chr5A 414311618 414313196 1578 True 1477.000000 2270 98.726500 491 2147 2 chr5A.!!$R2 1656
9 TraesCS7A01G497500 chr1B 647917655 647919638 1983 True 1138.000000 1901 95.524667 2 2147 3 chr1B.!!$R1 2145
10 TraesCS7A01G497500 chr7B 122292782 122294458 1676 True 1390.500000 1892 95.359500 2 1768 2 chr7B.!!$R1 1766

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
235 237 2.034532 CTCCACTGCACATGGCCA 59.965 61.111 8.56 8.56 43.89 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 2242 0.037605 GCAAGGAGCAAGCAAAGCAT 60.038 50.0 0.0 0.0 44.79 3.79 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
235 237 2.034532 CTCCACTGCACATGGCCA 59.965 61.111 8.56 8.56 43.89 5.36
366 368 2.172679 TGCATGCTGGTTGTCAATGAT 58.827 42.857 20.33 0.00 0.00 2.45
835 1091 5.075493 AGAAACTGGAGTGCATTTGAATCT 58.925 37.500 0.00 0.00 0.00 2.40
1087 1362 3.863041 ACCGAAGCTCAAGGATTTCTAC 58.137 45.455 8.79 0.00 0.00 2.59
1305 1581 7.669427 AGATAGTGGATGAAGATGAGATTGAC 58.331 38.462 0.00 0.00 0.00 3.18
1756 2200 0.103572 CTTGCTTGTTGGTTGCTGCT 59.896 50.000 0.00 0.00 0.00 4.24
1757 2201 0.179105 TTGCTTGTTGGTTGCTGCTG 60.179 50.000 0.00 0.00 0.00 4.41
1758 2202 1.952635 GCTTGTTGGTTGCTGCTGC 60.953 57.895 8.89 8.89 40.20 5.25
1759 2203 1.737816 CTTGTTGGTTGCTGCTGCT 59.262 52.632 17.00 0.00 40.48 4.24
1760 2204 0.953727 CTTGTTGGTTGCTGCTGCTA 59.046 50.000 17.00 6.36 40.48 3.49
1761 2205 1.337703 CTTGTTGGTTGCTGCTGCTAA 59.662 47.619 17.00 6.73 40.48 3.09
1762 2206 0.667993 TGTTGGTTGCTGCTGCTAAC 59.332 50.000 17.00 16.82 40.48 2.34
1763 2207 0.667993 GTTGGTTGCTGCTGCTAACA 59.332 50.000 22.29 18.82 39.65 2.41
1764 2208 1.270550 GTTGGTTGCTGCTGCTAACAT 59.729 47.619 17.36 0.00 40.87 2.71
1765 2209 1.167851 TGGTTGCTGCTGCTAACATC 58.832 50.000 22.29 12.61 36.77 3.06
1766 2210 1.271543 TGGTTGCTGCTGCTAACATCT 60.272 47.619 22.29 0.00 36.77 2.90
1767 2211 1.815003 GGTTGCTGCTGCTAACATCTT 59.185 47.619 22.29 0.00 40.48 2.40
1768 2212 2.229784 GGTTGCTGCTGCTAACATCTTT 59.770 45.455 22.29 0.00 40.48 2.52
1769 2213 3.440173 GGTTGCTGCTGCTAACATCTTTA 59.560 43.478 22.29 0.00 40.48 1.85
1770 2214 4.406943 GTTGCTGCTGCTAACATCTTTAC 58.593 43.478 17.00 0.00 40.48 2.01
1771 2215 3.673902 TGCTGCTGCTAACATCTTTACA 58.326 40.909 17.00 0.00 40.48 2.41
1772 2216 4.264253 TGCTGCTGCTAACATCTTTACAT 58.736 39.130 17.00 0.00 40.48 2.29
1773 2217 5.427378 TGCTGCTGCTAACATCTTTACATA 58.573 37.500 17.00 0.00 40.48 2.29
1774 2218 6.057533 TGCTGCTGCTAACATCTTTACATAT 58.942 36.000 17.00 0.00 40.48 1.78
1775 2219 7.216494 TGCTGCTGCTAACATCTTTACATATA 58.784 34.615 17.00 0.00 40.48 0.86
1776 2220 7.879677 TGCTGCTGCTAACATCTTTACATATAT 59.120 33.333 17.00 0.00 40.48 0.86
1777 2221 8.173775 GCTGCTGCTAACATCTTTACATATATG 58.826 37.037 11.29 11.29 36.03 1.78
1778 2222 9.428097 CTGCTGCTAACATCTTTACATATATGA 57.572 33.333 19.63 0.49 0.00 2.15
1779 2223 9.777297 TGCTGCTAACATCTTTACATATATGAA 57.223 29.630 19.63 6.61 0.00 2.57
1810 2254 9.286946 GAATCTCATATATAATGCTTTGCTTGC 57.713 33.333 0.00 0.00 0.00 4.01
1811 2255 7.991084 TCTCATATATAATGCTTTGCTTGCT 57.009 32.000 0.00 0.00 0.00 3.91
1812 2256 8.037382 TCTCATATATAATGCTTTGCTTGCTC 57.963 34.615 0.00 0.00 0.00 4.26
1813 2257 7.120285 TCTCATATATAATGCTTTGCTTGCTCC 59.880 37.037 0.00 0.00 0.00 4.70
1814 2258 6.944290 TCATATATAATGCTTTGCTTGCTCCT 59.056 34.615 0.00 0.00 0.00 3.69
1815 2259 7.449395 TCATATATAATGCTTTGCTTGCTCCTT 59.551 33.333 0.00 0.00 0.00 3.36
1816 2260 2.450609 AATGCTTTGCTTGCTCCTTG 57.549 45.000 0.00 0.00 0.00 3.61
1817 2261 0.037605 ATGCTTTGCTTGCTCCTTGC 60.038 50.000 0.00 0.00 43.25 4.01
1818 2262 1.111116 TGCTTTGCTTGCTCCTTGCT 61.111 50.000 0.00 0.00 43.37 3.91
1819 2263 0.033090 GCTTTGCTTGCTCCTTGCTT 59.967 50.000 0.00 0.00 43.37 3.91
1820 2264 1.779569 CTTTGCTTGCTCCTTGCTTG 58.220 50.000 0.00 0.00 43.37 4.01
1821 2265 1.068127 CTTTGCTTGCTCCTTGCTTGT 59.932 47.619 0.00 0.00 43.37 3.16
1822 2266 1.113788 TTGCTTGCTCCTTGCTTGTT 58.886 45.000 0.00 0.00 43.37 2.83
1823 2267 0.386476 TGCTTGCTCCTTGCTTGTTG 59.614 50.000 0.00 0.00 43.37 3.33
1824 2268 0.319297 GCTTGCTCCTTGCTTGTTGG 60.319 55.000 0.00 0.00 43.37 3.77
1825 2269 1.035139 CTTGCTCCTTGCTTGTTGGT 58.965 50.000 0.00 0.00 43.37 3.67
1826 2270 1.410153 CTTGCTCCTTGCTTGTTGGTT 59.590 47.619 0.00 0.00 43.37 3.67
1827 2271 0.746063 TGCTCCTTGCTTGTTGGTTG 59.254 50.000 0.00 0.00 43.37 3.77
1828 2272 0.598419 GCTCCTTGCTTGTTGGTTGC 60.598 55.000 0.00 0.00 38.95 4.17
1829 2273 1.035139 CTCCTTGCTTGTTGGTTGCT 58.965 50.000 0.00 0.00 0.00 3.91
1830 2274 0.746063 TCCTTGCTTGTTGGTTGCTG 59.254 50.000 0.00 0.00 0.00 4.41
1831 2275 0.877213 CCTTGCTTGTTGGTTGCTGC 60.877 55.000 0.00 0.00 0.00 5.25
1850 2294 2.931969 TGCTGCTAACATCTTGTCATCG 59.068 45.455 0.00 0.00 0.00 3.84
1930 2374 0.704076 TACAAAGAGGCAGGGGCAAT 59.296 50.000 0.00 0.00 43.71 3.56
2147 2592 2.781945 AGCGCTTTCTCAAACTTTGG 57.218 45.000 2.64 0.00 0.00 3.28
2151 2596 3.616821 GCGCTTTCTCAAACTTTGGTTTT 59.383 39.130 0.00 0.00 42.96 2.43
2152 2597 4.801516 GCGCTTTCTCAAACTTTGGTTTTA 59.198 37.500 0.00 0.00 42.96 1.52
2153 2598 5.051708 GCGCTTTCTCAAACTTTGGTTTTAG 60.052 40.000 0.00 0.00 42.96 1.85
2154 2599 5.458779 CGCTTTCTCAAACTTTGGTTTTAGG 59.541 40.000 1.62 0.00 42.96 2.69
2155 2600 6.569780 GCTTTCTCAAACTTTGGTTTTAGGA 58.430 36.000 1.62 0.00 42.96 2.94
2156 2601 6.475727 GCTTTCTCAAACTTTGGTTTTAGGAC 59.524 38.462 1.62 0.00 42.96 3.85
2157 2602 7.630728 GCTTTCTCAAACTTTGGTTTTAGGACT 60.631 37.037 1.62 0.00 42.96 3.85
2158 2603 7.712204 TTCTCAAACTTTGGTTTTAGGACTT 57.288 32.000 1.62 0.00 42.96 3.01
2159 2604 7.712204 TCTCAAACTTTGGTTTTAGGACTTT 57.288 32.000 1.62 0.00 42.96 2.66
2160 2605 8.129496 TCTCAAACTTTGGTTTTAGGACTTTT 57.871 30.769 1.62 0.00 42.96 2.27
2161 2606 8.590204 TCTCAAACTTTGGTTTTAGGACTTTTT 58.410 29.630 1.62 0.00 42.96 1.94
2186 2631 9.720769 TTTTAGTCCCAACTTATAAGTCTCAAG 57.279 33.333 18.28 6.66 38.57 3.02
2187 2632 6.936968 AGTCCCAACTTATAAGTCTCAAGT 57.063 37.500 18.28 5.74 38.57 3.16
2188 2633 6.937392 AGTCCCAACTTATAAGTCTCAAGTC 58.063 40.000 18.28 6.78 38.57 3.01
2189 2634 6.070710 AGTCCCAACTTATAAGTCTCAAGTCC 60.071 42.308 18.28 3.21 38.57 3.85
2190 2635 5.189145 TCCCAACTTATAAGTCTCAAGTCCC 59.811 44.000 18.28 0.00 38.57 4.46
2191 2636 5.189934 CCCAACTTATAAGTCTCAAGTCCCT 59.810 44.000 18.28 0.00 38.57 4.20
2192 2637 6.383147 CCCAACTTATAAGTCTCAAGTCCCTA 59.617 42.308 18.28 0.00 38.57 3.53
2193 2638 7.093024 CCCAACTTATAAGTCTCAAGTCCCTAA 60.093 40.741 18.28 0.00 38.57 2.69
2194 2639 8.319146 CCAACTTATAAGTCTCAAGTCCCTAAA 58.681 37.037 18.28 0.00 38.57 1.85
2195 2640 9.720769 CAACTTATAAGTCTCAAGTCCCTAAAA 57.279 33.333 18.28 0.00 38.57 1.52
2197 2642 9.945904 ACTTATAAGTCTCAAGTCCCTAAAAAG 57.054 33.333 12.50 0.00 32.86 2.27
2198 2643 9.945904 CTTATAAGTCTCAAGTCCCTAAAAAGT 57.054 33.333 4.18 0.00 0.00 2.66
2199 2644 9.939802 TTATAAGTCTCAAGTCCCTAAAAAGTC 57.060 33.333 0.00 0.00 0.00 3.01
2200 2645 5.230323 AGTCTCAAGTCCCTAAAAAGTCC 57.770 43.478 0.00 0.00 0.00 3.85
2201 2646 4.041815 AGTCTCAAGTCCCTAAAAAGTCCC 59.958 45.833 0.00 0.00 0.00 4.46
2202 2647 4.041815 GTCTCAAGTCCCTAAAAAGTCCCT 59.958 45.833 0.00 0.00 0.00 4.20
2203 2648 5.247792 GTCTCAAGTCCCTAAAAAGTCCCTA 59.752 44.000 0.00 0.00 0.00 3.53
2204 2649 5.247792 TCTCAAGTCCCTAAAAAGTCCCTAC 59.752 44.000 0.00 0.00 0.00 3.18
2205 2650 4.287845 TCAAGTCCCTAAAAAGTCCCTACC 59.712 45.833 0.00 0.00 0.00 3.18
2206 2651 4.157668 AGTCCCTAAAAAGTCCCTACCT 57.842 45.455 0.00 0.00 0.00 3.08
2207 2652 3.844804 AGTCCCTAAAAAGTCCCTACCTG 59.155 47.826 0.00 0.00 0.00 4.00
2208 2653 3.586174 GTCCCTAAAAAGTCCCTACCTGT 59.414 47.826 0.00 0.00 0.00 4.00
2209 2654 4.042560 GTCCCTAAAAAGTCCCTACCTGTT 59.957 45.833 0.00 0.00 0.00 3.16
2210 2655 4.666431 TCCCTAAAAAGTCCCTACCTGTTT 59.334 41.667 0.00 0.00 0.00 2.83
2211 2656 4.765339 CCCTAAAAAGTCCCTACCTGTTTG 59.235 45.833 0.00 0.00 0.00 2.93
2212 2657 4.765339 CCTAAAAAGTCCCTACCTGTTTGG 59.235 45.833 0.00 0.00 42.93 3.28
2222 2667 3.036431 CCTGTTTGGTTCCTGGGAC 57.964 57.895 0.00 0.00 0.00 4.46
2223 2668 0.478507 CCTGTTTGGTTCCTGGGACT 59.521 55.000 4.84 0.00 0.00 3.85
2224 2669 1.133482 CCTGTTTGGTTCCTGGGACTT 60.133 52.381 4.84 0.00 0.00 3.01
2225 2670 2.107552 CCTGTTTGGTTCCTGGGACTTA 59.892 50.000 4.84 0.00 0.00 2.24
2226 2671 3.245264 CCTGTTTGGTTCCTGGGACTTAT 60.245 47.826 4.84 0.00 0.00 1.73
2227 2672 4.018779 CCTGTTTGGTTCCTGGGACTTATA 60.019 45.833 4.84 0.00 0.00 0.98
2228 2673 5.515886 CCTGTTTGGTTCCTGGGACTTATAA 60.516 44.000 4.84 0.00 0.00 0.98
2229 2674 5.566469 TGTTTGGTTCCTGGGACTTATAAG 58.434 41.667 11.05 11.05 0.00 1.73
2230 2675 5.073965 TGTTTGGTTCCTGGGACTTATAAGT 59.926 40.000 18.05 18.05 43.16 2.24
2263 2708 9.448587 AAGACCATATTACAACTATAAGTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
2272 2717 7.852550 ACAACTATAAGTCCCTATAAGTCCC 57.147 40.000 0.00 0.00 0.00 4.46
2273 2718 7.602868 ACAACTATAAGTCCCTATAAGTCCCT 58.397 38.462 0.00 0.00 0.00 4.20
2274 2719 7.729431 ACAACTATAAGTCCCTATAAGTCCCTC 59.271 40.741 0.00 0.00 0.00 4.30
2275 2720 6.803017 ACTATAAGTCCCTATAAGTCCCTCC 58.197 44.000 0.00 0.00 0.00 4.30
2276 2721 5.970692 ATAAGTCCCTATAAGTCCCTCCT 57.029 43.478 0.00 0.00 0.00 3.69
2277 2722 4.645968 AAGTCCCTATAAGTCCCTCCTT 57.354 45.455 0.00 0.00 0.00 3.36
2278 2723 3.930035 AGTCCCTATAAGTCCCTCCTTG 58.070 50.000 0.00 0.00 0.00 3.61
2279 2724 3.536434 AGTCCCTATAAGTCCCTCCTTGA 59.464 47.826 0.00 0.00 0.00 3.02
2280 2725 3.898741 GTCCCTATAAGTCCCTCCTTGAG 59.101 52.174 0.00 0.00 0.00 3.02
2281 2726 3.797845 TCCCTATAAGTCCCTCCTTGAGA 59.202 47.826 0.00 0.00 0.00 3.27
2282 2727 4.140900 TCCCTATAAGTCCCTCCTTGAGAG 60.141 50.000 0.00 0.00 42.83 3.20
2283 2728 4.388118 CCCTATAAGTCCCTCCTTGAGAGT 60.388 50.000 0.00 0.00 41.47 3.24
2284 2729 4.830600 CCTATAAGTCCCTCCTTGAGAGTC 59.169 50.000 0.00 0.00 41.47 3.36
2285 2730 4.618378 ATAAGTCCCTCCTTGAGAGTCT 57.382 45.455 0.00 0.00 41.47 3.24
2286 2731 3.268034 AAGTCCCTCCTTGAGAGTCTT 57.732 47.619 0.00 0.00 41.47 3.01
2287 2732 4.405756 AAGTCCCTCCTTGAGAGTCTTA 57.594 45.455 0.00 0.00 41.47 2.10
2288 2733 4.618378 AGTCCCTCCTTGAGAGTCTTAT 57.382 45.455 0.00 0.00 41.47 1.73
2289 2734 4.954089 AGTCCCTCCTTGAGAGTCTTATT 58.046 43.478 0.00 0.00 41.47 1.40
2290 2735 5.346270 AGTCCCTCCTTGAGAGTCTTATTT 58.654 41.667 0.00 0.00 41.47 1.40
2291 2736 5.423931 AGTCCCTCCTTGAGAGTCTTATTTC 59.576 44.000 0.00 0.00 41.47 2.17
2292 2737 5.187967 GTCCCTCCTTGAGAGTCTTATTTCA 59.812 44.000 0.00 0.00 41.47 2.69
2293 2738 5.966935 TCCCTCCTTGAGAGTCTTATTTCAT 59.033 40.000 0.00 0.00 41.47 2.57
2294 2739 7.070074 GTCCCTCCTTGAGAGTCTTATTTCATA 59.930 40.741 0.00 0.00 41.47 2.15
2295 2740 7.623677 TCCCTCCTTGAGAGTCTTATTTCATAA 59.376 37.037 0.00 0.00 41.47 1.90
2296 2741 7.930865 CCCTCCTTGAGAGTCTTATTTCATAAG 59.069 40.741 0.00 0.00 41.47 1.73
2297 2742 8.482128 CCTCCTTGAGAGTCTTATTTCATAAGT 58.518 37.037 0.00 0.00 41.47 2.24
2298 2743 9.528018 CTCCTTGAGAGTCTTATTTCATAAGTC 57.472 37.037 0.00 0.00 37.60 3.01
2299 2744 9.261035 TCCTTGAGAGTCTTATTTCATAAGTCT 57.739 33.333 0.00 3.77 41.61 3.24
2307 2752 8.897752 AGTCTTATTTCATAAGTCTCAAATGCC 58.102 33.333 3.93 0.00 42.21 4.40
2308 2753 8.897752 GTCTTATTTCATAAGTCTCAAATGCCT 58.102 33.333 3.93 0.00 42.21 4.75
2311 2756 9.905713 TTATTTCATAAGTCTCAAATGCCTACT 57.094 29.630 0.00 0.00 0.00 2.57
2312 2757 8.814038 ATTTCATAAGTCTCAAATGCCTACTT 57.186 30.769 0.00 0.00 34.86 2.24
2313 2758 8.635765 TTTCATAAGTCTCAAATGCCTACTTT 57.364 30.769 0.00 0.00 32.85 2.66
2314 2759 9.733556 TTTCATAAGTCTCAAATGCCTACTTTA 57.266 29.630 0.00 0.00 32.85 1.85
2315 2760 9.733556 TTCATAAGTCTCAAATGCCTACTTTAA 57.266 29.630 0.00 0.00 32.85 1.52
2316 2761 9.383519 TCATAAGTCTCAAATGCCTACTTTAAG 57.616 33.333 0.00 0.00 32.85 1.85
2317 2762 9.167311 CATAAGTCTCAAATGCCTACTTTAAGT 57.833 33.333 2.32 2.32 32.85 2.24
2318 2763 7.674471 AAGTCTCAAATGCCTACTTTAAGTC 57.326 36.000 0.00 0.00 0.00 3.01
2319 2764 6.174049 AGTCTCAAATGCCTACTTTAAGTCC 58.826 40.000 0.00 0.00 0.00 3.85
2320 2765 5.354513 GTCTCAAATGCCTACTTTAAGTCCC 59.645 44.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1087 1362 4.077822 GCATAATCATCCCCTCCTTCAAG 58.922 47.826 0.00 0.00 0.00 3.02
1305 1581 4.886496 TGCCTCTCAATCATCCTCATAG 57.114 45.455 0.00 0.00 0.00 2.23
1784 2228 9.286946 GCAAGCAAAGCATTATATATGAGATTC 57.713 33.333 0.00 0.00 0.00 2.52
1785 2229 9.021807 AGCAAGCAAAGCATTATATATGAGATT 57.978 29.630 0.00 0.00 0.00 2.40
1786 2230 8.577048 AGCAAGCAAAGCATTATATATGAGAT 57.423 30.769 0.00 0.00 0.00 2.75
1787 2231 7.120285 GGAGCAAGCAAAGCATTATATATGAGA 59.880 37.037 0.00 0.00 0.00 3.27
1788 2232 7.120873 AGGAGCAAGCAAAGCATTATATATGAG 59.879 37.037 0.00 0.00 0.00 2.90
1789 2233 6.944290 AGGAGCAAGCAAAGCATTATATATGA 59.056 34.615 0.00 0.00 0.00 2.15
1790 2234 7.154435 AGGAGCAAGCAAAGCATTATATATG 57.846 36.000 0.00 0.00 0.00 1.78
1791 2235 7.600065 CAAGGAGCAAGCAAAGCATTATATAT 58.400 34.615 0.00 0.00 0.00 0.86
1792 2236 6.515531 GCAAGGAGCAAGCAAAGCATTATATA 60.516 38.462 0.00 0.00 44.79 0.86
1793 2237 5.738208 GCAAGGAGCAAGCAAAGCATTATAT 60.738 40.000 0.00 0.00 44.79 0.86
1794 2238 4.440525 GCAAGGAGCAAGCAAAGCATTATA 60.441 41.667 0.00 0.00 44.79 0.98
1795 2239 3.677976 GCAAGGAGCAAGCAAAGCATTAT 60.678 43.478 0.00 0.00 44.79 1.28
1796 2240 2.353011 GCAAGGAGCAAGCAAAGCATTA 60.353 45.455 0.00 0.00 44.79 1.90
1797 2241 1.607251 GCAAGGAGCAAGCAAAGCATT 60.607 47.619 0.00 0.00 44.79 3.56
1798 2242 0.037605 GCAAGGAGCAAGCAAAGCAT 60.038 50.000 0.00 0.00 44.79 3.79
1799 2243 1.364901 GCAAGGAGCAAGCAAAGCA 59.635 52.632 0.00 0.00 44.79 3.91
1800 2244 4.256813 GCAAGGAGCAAGCAAAGC 57.743 55.556 0.00 0.00 44.79 3.51
1809 2253 0.598419 GCAACCAACAAGCAAGGAGC 60.598 55.000 0.00 0.00 46.19 4.70
1810 2254 1.035139 AGCAACCAACAAGCAAGGAG 58.965 50.000 0.00 0.00 0.00 3.69
1811 2255 0.746063 CAGCAACCAACAAGCAAGGA 59.254 50.000 0.00 0.00 0.00 3.36
1812 2256 0.877213 GCAGCAACCAACAAGCAAGG 60.877 55.000 0.00 0.00 0.00 3.61
1813 2257 0.103572 AGCAGCAACCAACAAGCAAG 59.896 50.000 0.00 0.00 0.00 4.01
1814 2258 0.179105 CAGCAGCAACCAACAAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
1815 2259 1.438399 CAGCAGCAACCAACAAGCA 59.562 52.632 0.00 0.00 0.00 3.91
1816 2260 1.952635 GCAGCAGCAACCAACAAGC 60.953 57.895 0.00 0.00 41.58 4.01
1817 2261 0.953727 TAGCAGCAGCAACCAACAAG 59.046 50.000 3.17 0.00 45.49 3.16
1818 2262 1.066908 GTTAGCAGCAGCAACCAACAA 59.933 47.619 3.17 0.00 45.49 2.83
1819 2263 0.667993 GTTAGCAGCAGCAACCAACA 59.332 50.000 3.17 0.00 45.49 3.33
1820 2264 0.667993 TGTTAGCAGCAGCAACCAAC 59.332 50.000 3.17 2.71 45.49 3.77
1821 2265 1.541147 GATGTTAGCAGCAGCAACCAA 59.459 47.619 3.17 0.00 45.49 3.67
1822 2266 1.167851 GATGTTAGCAGCAGCAACCA 58.832 50.000 3.17 0.00 45.49 3.67
1823 2267 1.457346 AGATGTTAGCAGCAGCAACC 58.543 50.000 3.17 0.00 45.49 3.77
1824 2268 2.227388 ACAAGATGTTAGCAGCAGCAAC 59.773 45.455 3.17 6.66 45.49 4.17
1825 2269 2.485426 GACAAGATGTTAGCAGCAGCAA 59.515 45.455 3.17 0.00 45.49 3.91
1826 2270 2.079158 GACAAGATGTTAGCAGCAGCA 58.921 47.619 3.17 0.00 45.49 4.41
1827 2271 2.079158 TGACAAGATGTTAGCAGCAGC 58.921 47.619 0.00 0.00 42.56 5.25
1828 2272 3.001026 CGATGACAAGATGTTAGCAGCAG 59.999 47.826 0.00 0.00 32.61 4.24
1829 2273 2.931969 CGATGACAAGATGTTAGCAGCA 59.068 45.455 0.00 0.00 32.61 4.41
1830 2274 2.932614 ACGATGACAAGATGTTAGCAGC 59.067 45.455 0.00 0.00 0.00 5.25
1831 2275 4.428209 AGACGATGACAAGATGTTAGCAG 58.572 43.478 0.00 0.00 0.00 4.24
1850 2294 7.439356 TGCAACAGCTAAATACATCATAGAGAC 59.561 37.037 0.00 0.00 0.00 3.36
2160 2605 9.720769 CTTGAGACTTATAAGTTGGGACTAAAA 57.279 33.333 18.96 8.46 39.88 1.52
2161 2606 8.877195 ACTTGAGACTTATAAGTTGGGACTAAA 58.123 33.333 18.96 9.53 39.88 1.85
2162 2607 8.431910 ACTTGAGACTTATAAGTTGGGACTAA 57.568 34.615 18.96 2.28 39.88 2.24
2163 2608 7.123847 GGACTTGAGACTTATAAGTTGGGACTA 59.876 40.741 18.96 6.16 39.88 2.59
2164 2609 6.070710 GGACTTGAGACTTATAAGTTGGGACT 60.071 42.308 18.96 10.98 39.88 3.85
2165 2610 6.107343 GGACTTGAGACTTATAAGTTGGGAC 58.893 44.000 18.96 6.39 39.88 4.46
2166 2611 5.189145 GGGACTTGAGACTTATAAGTTGGGA 59.811 44.000 18.96 6.15 39.88 4.37
2167 2612 5.189934 AGGGACTTGAGACTTATAAGTTGGG 59.810 44.000 18.96 10.37 34.84 4.12
2168 2613 6.301169 AGGGACTTGAGACTTATAAGTTGG 57.699 41.667 18.96 10.07 34.84 3.77
2169 2614 9.720769 TTTTAGGGACTTGAGACTTATAAGTTG 57.279 33.333 18.96 9.81 38.78 3.16
2171 2616 9.945904 CTTTTTAGGGACTTGAGACTTATAAGT 57.054 33.333 18.05 18.05 40.66 2.24
2172 2617 9.945904 ACTTTTTAGGGACTTGAGACTTATAAG 57.054 33.333 11.05 11.05 41.75 1.73
2173 2618 9.939802 GACTTTTTAGGGACTTGAGACTTATAA 57.060 33.333 0.00 0.00 41.75 0.98
2174 2619 8.537858 GGACTTTTTAGGGACTTGAGACTTATA 58.462 37.037 0.00 0.00 41.75 0.98
2175 2620 7.395617 GGACTTTTTAGGGACTTGAGACTTAT 58.604 38.462 0.00 0.00 41.75 1.73
2176 2621 6.239800 GGGACTTTTTAGGGACTTGAGACTTA 60.240 42.308 0.00 0.00 41.75 2.24
2177 2622 5.456330 GGGACTTTTTAGGGACTTGAGACTT 60.456 44.000 0.00 0.00 41.75 3.01
2178 2623 4.041815 GGGACTTTTTAGGGACTTGAGACT 59.958 45.833 0.00 0.00 41.75 3.24
2179 2624 4.041815 AGGGACTTTTTAGGGACTTGAGAC 59.958 45.833 0.00 0.00 34.75 3.36
2180 2625 4.240323 AGGGACTTTTTAGGGACTTGAGA 58.760 43.478 0.00 0.00 34.75 3.27
2181 2626 4.642466 AGGGACTTTTTAGGGACTTGAG 57.358 45.455 0.00 0.00 34.75 3.02
2182 2627 4.287845 GGTAGGGACTTTTTAGGGACTTGA 59.712 45.833 0.00 0.00 39.49 3.02
2183 2628 4.288887 AGGTAGGGACTTTTTAGGGACTTG 59.711 45.833 0.00 0.00 39.49 3.16
2184 2629 4.288887 CAGGTAGGGACTTTTTAGGGACTT 59.711 45.833 0.00 0.00 39.49 3.01
2185 2630 3.844804 CAGGTAGGGACTTTTTAGGGACT 59.155 47.826 0.00 0.00 41.75 3.85
2186 2631 3.586174 ACAGGTAGGGACTTTTTAGGGAC 59.414 47.826 0.00 0.00 41.75 4.46
2187 2632 3.878086 ACAGGTAGGGACTTTTTAGGGA 58.122 45.455 0.00 0.00 41.75 4.20
2188 2633 4.652679 AACAGGTAGGGACTTTTTAGGG 57.347 45.455 0.00 0.00 41.75 3.53
2189 2634 4.765339 CCAAACAGGTAGGGACTTTTTAGG 59.235 45.833 0.00 0.00 41.75 2.69
2190 2635 5.959618 CCAAACAGGTAGGGACTTTTTAG 57.040 43.478 0.00 0.00 41.75 1.85
2204 2649 0.478507 AGTCCCAGGAACCAAACAGG 59.521 55.000 0.00 0.00 45.67 4.00
2205 2650 2.364972 AAGTCCCAGGAACCAAACAG 57.635 50.000 0.00 0.00 0.00 3.16
2206 2651 5.073965 ACTTATAAGTCCCAGGAACCAAACA 59.926 40.000 12.50 0.00 32.86 2.83
2207 2652 5.567430 ACTTATAAGTCCCAGGAACCAAAC 58.433 41.667 12.50 0.00 32.86 2.93
2208 2653 5.853572 ACTTATAAGTCCCAGGAACCAAA 57.146 39.130 12.50 0.00 32.86 3.28
2237 2682 9.448587 AGGGACTTATAGTTGTAATATGGTCTT 57.551 33.333 0.00 0.00 27.25 3.01
2246 2691 9.372189 GGGACTTATAGGGACTTATAGTTGTAA 57.628 37.037 0.00 0.00 41.75 2.41
2247 2692 8.740512 AGGGACTTATAGGGACTTATAGTTGTA 58.259 37.037 0.00 0.00 34.75 2.41
2248 2693 7.602868 AGGGACTTATAGGGACTTATAGTTGT 58.397 38.462 0.00 0.00 34.75 3.32
2249 2694 7.178805 GGAGGGACTTATAGGGACTTATAGTTG 59.821 44.444 0.00 0.00 41.55 3.16
2250 2695 7.076566 AGGAGGGACTTATAGGGACTTATAGTT 59.923 40.741 0.00 0.00 41.55 2.24
2251 2696 6.571180 AGGAGGGACTTATAGGGACTTATAGT 59.429 42.308 0.00 0.00 41.55 2.12
2252 2697 7.046891 AGGAGGGACTTATAGGGACTTATAG 57.953 44.000 0.00 0.00 41.55 1.31
2253 2698 7.075915 TCAAGGAGGGACTTATAGGGACTTATA 59.924 40.741 0.00 0.00 41.55 0.98
2254 2699 5.970692 AGGAGGGACTTATAGGGACTTAT 57.029 43.478 0.00 0.00 41.55 1.73
2255 2700 5.197189 TCAAGGAGGGACTTATAGGGACTTA 59.803 44.000 0.00 0.00 41.55 2.24
2256 2701 4.015541 TCAAGGAGGGACTTATAGGGACTT 60.016 45.833 0.00 0.00 41.55 3.01
2257 2702 3.536434 TCAAGGAGGGACTTATAGGGACT 59.464 47.826 0.00 0.00 41.55 3.85
2258 2703 3.898741 CTCAAGGAGGGACTTATAGGGAC 59.101 52.174 0.00 0.00 41.55 4.46
2259 2704 3.797845 TCTCAAGGAGGGACTTATAGGGA 59.202 47.826 0.00 0.00 41.55 4.20
2260 2705 4.156477 CTCTCAAGGAGGGACTTATAGGG 58.844 52.174 0.00 0.00 41.55 3.53
2261 2706 4.810345 ACTCTCAAGGAGGGACTTATAGG 58.190 47.826 0.00 0.00 45.83 2.57
2262 2707 5.701224 AGACTCTCAAGGAGGGACTTATAG 58.299 45.833 0.00 0.00 45.83 1.31
2263 2708 5.735733 AGACTCTCAAGGAGGGACTTATA 57.264 43.478 0.00 0.00 45.83 0.98
2264 2709 4.618378 AGACTCTCAAGGAGGGACTTAT 57.382 45.455 0.00 0.00 45.83 1.73
2265 2710 4.405756 AAGACTCTCAAGGAGGGACTTA 57.594 45.455 8.68 0.00 41.64 2.24
2266 2711 3.268034 AAGACTCTCAAGGAGGGACTT 57.732 47.619 5.25 5.25 45.83 3.01
2267 2712 4.618378 ATAAGACTCTCAAGGAGGGACT 57.382 45.455 0.00 0.00 45.83 3.85
2268 2713 5.187967 TGAAATAAGACTCTCAAGGAGGGAC 59.812 44.000 0.00 0.00 45.83 4.46
2269 2714 5.342017 TGAAATAAGACTCTCAAGGAGGGA 58.658 41.667 0.00 0.00 45.83 4.20
2270 2715 5.683876 TGAAATAAGACTCTCAAGGAGGG 57.316 43.478 0.00 0.00 45.83 4.30
2285 2730 9.905713 AGTAGGCATTTGAGACTTATGAAATAA 57.094 29.630 0.00 0.00 36.20 1.40
2286 2731 9.905713 AAGTAGGCATTTGAGACTTATGAAATA 57.094 29.630 0.00 0.00 0.00 1.40
2287 2732 8.814038 AAGTAGGCATTTGAGACTTATGAAAT 57.186 30.769 0.00 0.00 0.00 2.17
2288 2733 8.635765 AAAGTAGGCATTTGAGACTTATGAAA 57.364 30.769 0.00 0.00 30.34 2.69
2289 2734 9.733556 TTAAAGTAGGCATTTGAGACTTATGAA 57.266 29.630 0.00 0.00 30.34 2.57
2290 2735 9.383519 CTTAAAGTAGGCATTTGAGACTTATGA 57.616 33.333 0.00 0.00 30.34 2.15
2291 2736 9.167311 ACTTAAAGTAGGCATTTGAGACTTATG 57.833 33.333 8.07 0.00 30.34 1.90
2292 2737 9.384764 GACTTAAAGTAGGCATTTGAGACTTAT 57.615 33.333 8.07 0.00 30.34 1.73
2293 2738 7.822822 GGACTTAAAGTAGGCATTTGAGACTTA 59.177 37.037 8.07 0.00 30.34 2.24
2294 2739 6.655425 GGACTTAAAGTAGGCATTTGAGACTT 59.345 38.462 8.07 0.00 30.26 3.01
2295 2740 6.174049 GGACTTAAAGTAGGCATTTGAGACT 58.826 40.000 8.07 0.00 30.26 3.24
2296 2741 5.354513 GGGACTTAAAGTAGGCATTTGAGAC 59.645 44.000 8.07 3.46 30.26 3.36
2297 2742 5.497474 GGGACTTAAAGTAGGCATTTGAGA 58.503 41.667 8.07 0.00 30.26 3.27
2298 2743 5.819825 GGGACTTAAAGTAGGCATTTGAG 57.180 43.478 0.00 0.00 31.53 3.02


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

AutoCloner maintained by Alex Coulton.