Multiple sequence alignment - TraesCS1A01G317500

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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 TraesCS1A01G317500 chr1A 100.000 2690 0 0 1 2690 508931124 508928435 0.000000e+00 4968.0
1 TraesCS1A01G317500 chr1A 88.601 193 12 7 680 866 508733575 508733387 2.690000e-55 226.0
2 TraesCS1A01G317500 chr1A 89.423 104 11 0 915 1018 508733382 508733279 6.040000e-27 132.0
3 TraesCS1A01G317500 chr1A 92.857 42 3 0 2113 2154 474704541 474704500 8.040000e-06 62.1
4 TraesCS1A01G317500 chr1A 85.714 56 7 1 2087 2141 551637028 551637083 1.040000e-04 58.4
5 TraesCS1A01G317500 chr1D 94.617 1802 70 15 21 1819 412225080 412223303 0.000000e+00 2765.0
6 TraesCS1A01G317500 chr1D 93.241 577 34 3 2116 2690 412223003 412222430 0.000000e+00 845.0
7 TraesCS1A01G317500 chr1D 89.011 182 19 1 1918 2099 412223233 412223053 9.690000e-55 224.0
8 TraesCS1A01G317500 chr1D 87.435 191 16 5 680 866 412173273 412173087 2.100000e-51 213.0
9 TraesCS1A01G317500 chr1D 91.346 104 9 0 915 1018 412173082 412172979 2.790000e-30 143.0
10 TraesCS1A01G317500 chr1B 92.082 1667 89 17 207 1862 555940236 555938602 0.000000e+00 2307.0
11 TraesCS1A01G317500 chr1B 89.018 601 38 17 915 1511 555846330 555845754 0.000000e+00 719.0
12 TraesCS1A01G317500 chr1B 90.594 202 14 3 2 201 555940400 555940202 2.050000e-66 263.0
13 TraesCS1A01G317500 chr1B 82.051 312 33 8 1650 1945 555794138 555793834 7.440000e-61 244.0
14 TraesCS1A01G317500 chr1B 90.728 151 9 4 715 864 555848032 555847886 2.110000e-46 196.0
15 TraesCS1A01G317500 chr1B 95.833 48 2 0 2463 2510 555938471 555938424 7.980000e-11 78.7
16 TraesCS1A01G317500 chr7A 84.762 105 12 4 480 583 201067764 201067865 4.740000e-18 102.0
17 TraesCS1A01G317500 chr7A 89.552 67 4 3 614 678 439754209 439754274 6.170000e-12 82.4
18 TraesCS1A01G317500 chr7A 94.737 38 0 2 2111 2146 101469024 101468987 1.040000e-04 58.4
19 TraesCS1A01G317500 chr7A 91.111 45 0 2 2103 2143 220098154 220098110 1.040000e-04 58.4
20 TraesCS1A01G317500 chr2D 96.491 57 0 2 623 678 490126813 490126868 2.850000e-15 93.5
21 TraesCS1A01G317500 chr2D 94.828 58 0 2 623 678 537450883 537450827 1.330000e-13 87.9
22 TraesCS1A01G317500 chr3D 96.296 54 2 0 621 674 573284986 573284933 3.690000e-14 89.8
23 TraesCS1A01G317500 chr3D 90.909 66 3 3 615 678 609936088 609936024 4.770000e-13 86.1
24 TraesCS1A01G317500 chr3B 94.545 55 0 2 621 675 152960368 152960317 6.170000e-12 82.4
25 TraesCS1A01G317500 chr3B 88.333 60 7 0 2095 2154 452681677 452681618 3.710000e-09 73.1
26 TraesCS1A01G317500 chr2A 79.412 102 19 1 2373 2472 42318310 42318209 1.340000e-08 71.3
27 TraesCS1A01G317500 chr7D 93.333 45 3 0 2107 2151 124517291 124517335 1.730000e-07 67.6
28 TraesCS1A01G317500 chr4A 80.412 97 12 7 601 695 716117840 716117931 1.730000e-07 67.6
29 TraesCS1A01G317500 chr7B 87.500 56 6 1 2107 2162 651339197 651339251 2.240000e-06 63.9
30 TraesCS1A01G317500 chr2B 92.857 42 3 0 2113 2154 80629009 80628968 8.040000e-06 62.1


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 TraesCS1A01G317500 chr1A 508928435 508931124 2689 True 4968.0 4968 100.000000 1 2690 1 chr1A.!!$R2 2689
1 TraesCS1A01G317500 chr1D 412222430 412225080 2650 True 1278.0 2765 92.289667 21 2690 3 chr1D.!!$R2 2669
2 TraesCS1A01G317500 chr1B 555938424 555940400 1976 True 882.9 2307 92.836333 2 2510 3 chr1B.!!$R3 2508
3 TraesCS1A01G317500 chr1B 555845754 555848032 2278 True 457.5 719 89.873000 715 1511 2 chr1B.!!$R2 796

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
200 203 0.109153 ACAGTCAAGCATGCAGACCA 59.891 50.0 28.71 5.43 32.82 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 3560 0.24912 AAATCGTGATGTGCCCTCGA 59.751 50.0 0.0 0.0 34.7 4.04 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
27 30 2.012673 GGTGGAACAATAGCTGCAGAG 58.987 52.381 20.43 3.40 44.16 3.35
36 39 3.588336 GCTGCAGAGCCAAAGGAG 58.412 61.111 20.43 0.00 39.57 3.69
148 151 1.969256 GCATTGTACTTTTCGCACACG 59.031 47.619 0.00 0.00 42.01 4.49
150 153 0.938713 TTGTACTTTTCGCACACGGG 59.061 50.000 0.00 0.00 40.63 5.28
165 168 1.064825 ACGGGAGTTTCCACTGGAAT 58.935 50.000 11.47 0.00 41.71 3.01
166 169 1.423921 ACGGGAGTTTCCACTGGAATT 59.576 47.619 11.47 3.41 41.71 2.17
167 170 2.158519 ACGGGAGTTTCCACTGGAATTT 60.159 45.455 11.47 3.06 41.71 1.82
168 171 3.073356 ACGGGAGTTTCCACTGGAATTTA 59.927 43.478 11.47 0.00 41.71 1.40
169 172 3.689649 CGGGAGTTTCCACTGGAATTTAG 59.310 47.826 11.47 0.00 41.71 1.85
170 173 3.444034 GGGAGTTTCCACTGGAATTTAGC 59.556 47.826 11.47 0.74 41.71 3.09
171 174 4.079253 GGAGTTTCCACTGGAATTTAGCA 58.921 43.478 11.47 0.00 41.71 3.49
172 175 4.706962 GGAGTTTCCACTGGAATTTAGCAT 59.293 41.667 11.47 0.00 41.71 3.79
173 176 5.393461 GGAGTTTCCACTGGAATTTAGCATG 60.393 44.000 11.47 0.00 41.71 4.06
174 177 5.324409 AGTTTCCACTGGAATTTAGCATGA 58.676 37.500 11.47 0.00 41.71 3.07
175 178 5.954150 AGTTTCCACTGGAATTTAGCATGAT 59.046 36.000 11.47 0.00 41.71 2.45
176 179 6.438425 AGTTTCCACTGGAATTTAGCATGATT 59.562 34.615 11.47 0.00 41.71 2.57
177 180 6.855763 TTCCACTGGAATTTAGCATGATTT 57.144 33.333 6.39 0.00 36.71 2.17
178 181 6.455360 TCCACTGGAATTTAGCATGATTTC 57.545 37.500 0.00 0.00 0.00 2.17
179 182 5.951148 TCCACTGGAATTTAGCATGATTTCA 59.049 36.000 0.00 0.00 0.00 2.69
180 183 6.095860 TCCACTGGAATTTAGCATGATTTCAG 59.904 38.462 10.28 10.28 42.20 3.02
181 184 6.095860 CCACTGGAATTTAGCATGATTTCAGA 59.904 38.462 16.33 0.00 40.00 3.27
182 185 6.971184 CACTGGAATTTAGCATGATTTCAGAC 59.029 38.462 16.33 0.00 40.00 3.51
183 186 6.660521 ACTGGAATTTAGCATGATTTCAGACA 59.339 34.615 16.33 0.00 40.00 3.41
184 187 7.092137 TGGAATTTAGCATGATTTCAGACAG 57.908 36.000 0.00 0.00 0.00 3.51
185 188 6.660521 TGGAATTTAGCATGATTTCAGACAGT 59.339 34.615 0.00 0.00 0.00 3.55
186 189 7.148188 TGGAATTTAGCATGATTTCAGACAGTC 60.148 37.037 0.00 0.00 0.00 3.51
187 190 7.148188 GGAATTTAGCATGATTTCAGACAGTCA 60.148 37.037 2.66 0.00 0.00 3.41
188 191 7.692460 ATTTAGCATGATTTCAGACAGTCAA 57.308 32.000 2.66 0.00 0.00 3.18
189 192 6.732531 TTAGCATGATTTCAGACAGTCAAG 57.267 37.500 2.66 0.00 0.00 3.02
190 193 3.439476 AGCATGATTTCAGACAGTCAAGC 59.561 43.478 2.66 0.00 36.03 4.01
191 194 3.189910 GCATGATTTCAGACAGTCAAGCA 59.810 43.478 2.66 0.00 35.90 3.91
192 195 4.142447 GCATGATTTCAGACAGTCAAGCAT 60.142 41.667 2.66 0.22 35.90 3.79
193 196 5.332707 CATGATTTCAGACAGTCAAGCATG 58.667 41.667 13.10 13.10 36.87 4.06
194 197 3.189910 TGATTTCAGACAGTCAAGCATGC 59.810 43.478 10.51 10.51 0.00 4.06
195 198 2.259266 TTCAGACAGTCAAGCATGCA 57.741 45.000 21.98 0.00 0.00 3.96
196 199 1.804601 TCAGACAGTCAAGCATGCAG 58.195 50.000 21.98 12.28 0.00 4.41
197 200 1.345415 TCAGACAGTCAAGCATGCAGA 59.655 47.619 21.98 14.63 0.00 4.26
198 201 1.463831 CAGACAGTCAAGCATGCAGAC 59.536 52.381 26.55 26.55 0.00 3.51
199 202 0.801251 GACAGTCAAGCATGCAGACC 59.199 55.000 28.71 16.40 32.82 3.85
200 203 0.109153 ACAGTCAAGCATGCAGACCA 59.891 50.000 28.71 5.43 32.82 4.02
201 204 1.271762 ACAGTCAAGCATGCAGACCAT 60.272 47.619 28.71 19.24 32.82 3.55
227 230 9.166173 TGAATTTTATGATGATTTCGACAGTCT 57.834 29.630 0.00 0.00 0.00 3.24
322 365 0.907704 AATAGGGCAGTGGTCGGACA 60.908 55.000 10.76 0.00 0.00 4.02
323 366 1.330655 ATAGGGCAGTGGTCGGACAG 61.331 60.000 10.76 0.00 0.00 3.51
363 406 5.269313 CGAAGTGACCGGAGTAGTATTAAC 58.731 45.833 9.46 0.00 0.00 2.01
364 407 5.163723 CGAAGTGACCGGAGTAGTATTAACA 60.164 44.000 9.46 0.00 0.00 2.41
390 433 7.893124 ATCTTCCCGTCTTATCAGTTAAGTA 57.107 36.000 0.00 0.00 38.76 2.24
423 466 4.442753 GGAAGAGAGAATCCAGATGGTCAC 60.443 50.000 0.00 0.00 35.71 3.67
432 475 1.338484 CCAGATGGTCACAGTGGTCTG 60.338 57.143 0.00 9.35 46.18 3.51
433 476 1.620323 CAGATGGTCACAGTGGTCTGA 59.380 52.381 15.34 0.00 43.76 3.27
434 477 2.037641 CAGATGGTCACAGTGGTCTGAA 59.962 50.000 15.34 0.00 43.76 3.02
436 479 3.328931 AGATGGTCACAGTGGTCTGAATT 59.671 43.478 0.00 0.00 43.76 2.17
437 480 3.576078 TGGTCACAGTGGTCTGAATTT 57.424 42.857 0.00 0.00 43.76 1.82
438 481 3.213506 TGGTCACAGTGGTCTGAATTTG 58.786 45.455 0.00 0.00 43.76 2.32
439 482 3.214328 GGTCACAGTGGTCTGAATTTGT 58.786 45.455 0.00 0.00 43.76 2.83
440 483 3.251004 GGTCACAGTGGTCTGAATTTGTC 59.749 47.826 0.00 0.00 43.76 3.18
441 484 3.876914 GTCACAGTGGTCTGAATTTGTCA 59.123 43.478 0.00 0.00 43.76 3.58
442 485 3.876914 TCACAGTGGTCTGAATTTGTCAC 59.123 43.478 0.00 0.00 43.76 3.67
443 486 3.879295 CACAGTGGTCTGAATTTGTCACT 59.121 43.478 2.17 0.00 43.76 3.41
444 487 4.478843 CAGTGGTCTGAATTTGTCACTG 57.521 45.455 0.00 0.00 43.76 3.66
445 488 2.880890 AGTGGTCTGAATTTGTCACTGC 59.119 45.455 0.00 0.00 34.65 4.40
470 513 1.819632 GATACCCAGCGTTGGCCAG 60.820 63.158 13.64 1.86 43.58 4.85
551 594 5.893255 AGCTGATTGATTAACCCTTTGCATA 59.107 36.000 0.00 0.00 0.00 3.14
577 620 8.661345 AGTTCCTATATCAGATTTAGGAAACCC 58.339 37.037 29.82 21.92 46.97 4.11
588 631 8.534496 CAGATTTAGGAAACCCTCAAAATTCAT 58.466 33.333 0.00 0.00 35.26 2.57
601 644 6.700960 CCTCAAAATTCATTGCAAAGTGTACA 59.299 34.615 1.71 0.00 0.00 2.90
654 700 2.746359 GATCATCCCCGGCCTCTG 59.254 66.667 0.00 0.00 0.00 3.35
658 704 3.564218 ATCCCCGGCCTCTGCATC 61.564 66.667 0.00 0.00 40.13 3.91
696 749 6.654161 GCAGCCAGAACAAGATTATCATAGAT 59.346 38.462 0.00 0.00 0.00 1.98
791 844 4.457810 CAAAAGACGTTACATGCTGAGTG 58.542 43.478 0.00 0.00 0.00 3.51
806 859 4.649218 TGCTGAGTGCTACATCCATACTTA 59.351 41.667 0.00 0.00 43.37 2.24
856 909 2.026822 ACTTTCCAGCTCATCCGACATT 60.027 45.455 0.00 0.00 0.00 2.71
878 931 7.117812 ACATTATCCGGAAATCGTTTATAGCAG 59.882 37.037 9.01 0.00 37.11 4.24
994 2553 2.095919 GCAACCACATTTCGTACTGGAC 60.096 50.000 3.75 0.00 0.00 4.02
997 2556 2.259618 CCACATTTCGTACTGGACTCG 58.740 52.381 0.00 0.00 0.00 4.18
1005 2564 1.068472 CGTACTGGACTCGATATGGGC 60.068 57.143 0.00 0.00 0.00 5.36
1007 2566 1.496060 ACTGGACTCGATATGGGCAA 58.504 50.000 0.00 0.00 0.00 4.52
1686 3251 0.659957 CCGCCGACCAGTACTACTAC 59.340 60.000 0.00 0.00 0.00 2.73
1687 3252 1.661341 CGCCGACCAGTACTACTACT 58.339 55.000 0.00 0.00 33.01 2.57
1688 3253 2.483714 CCGCCGACCAGTACTACTACTA 60.484 54.545 0.00 0.00 31.46 1.82
1784 3349 6.470235 GCGGAAATGACAGTGATAATGAAAAG 59.530 38.462 0.00 0.00 0.00 2.27
1838 3426 3.801114 ACCGGTTAAGTATCCCGTAAC 57.199 47.619 0.00 0.00 40.10 2.50
1866 3454 9.678247 CTTTTACTTTCAAAATTTAAAACGCGT 57.322 25.926 5.58 5.58 0.00 6.01
1868 3456 6.872670 ACTTTCAAAATTTAAAACGCGTGA 57.127 29.167 14.98 0.00 0.00 4.35
1869 3457 7.458038 ACTTTCAAAATTTAAAACGCGTGAT 57.542 28.000 14.98 7.51 0.00 3.06
1872 3460 7.451281 TTCAAAATTTAAAACGCGTGATTCA 57.549 28.000 14.98 0.00 0.00 2.57
1873 3461 6.858057 TCAAAATTTAAAACGCGTGATTCAC 58.142 32.000 14.98 6.73 0.00 3.18
1875 3463 6.814076 AAATTTAAAACGCGTGATTCACAA 57.186 29.167 14.98 6.15 33.40 3.33
1876 3464 6.814076 AATTTAAAACGCGTGATTCACAAA 57.186 29.167 14.98 9.44 33.40 2.83
1877 3465 6.814076 ATTTAAAACGCGTGATTCACAAAA 57.186 29.167 14.98 9.09 33.40 2.44
1878 3466 5.607858 TTAAAACGCGTGATTCACAAAAC 57.392 34.783 14.98 2.47 33.40 2.43
1880 3468 2.663279 ACGCGTGATTCACAAAACTC 57.337 45.000 12.93 0.00 33.40 3.01
1881 3469 1.263217 ACGCGTGATTCACAAAACTCC 59.737 47.619 12.93 0.00 33.40 3.85
1882 3470 1.399727 CGCGTGATTCACAAAACTCCC 60.400 52.381 16.61 0.00 33.40 4.30
1883 3471 1.606668 GCGTGATTCACAAAACTCCCA 59.393 47.619 16.61 0.00 33.40 4.37
1884 3472 2.034053 GCGTGATTCACAAAACTCCCAA 59.966 45.455 16.61 0.00 33.40 4.12
1886 3474 4.677584 CGTGATTCACAAAACTCCCAAAA 58.322 39.130 16.61 0.00 33.40 2.44
1887 3475 5.105752 CGTGATTCACAAAACTCCCAAAAA 58.894 37.500 16.61 0.00 33.40 1.94
1910 3498 8.560355 AAAAGTCACTAATGTATGCATGTACA 57.440 30.769 10.16 7.15 38.79 2.90
1911 3499 7.539712 AAGTCACTAATGTATGCATGTACAC 57.460 36.000 10.16 0.00 37.40 2.90
1912 3500 5.748630 AGTCACTAATGTATGCATGTACACG 59.251 40.000 10.16 0.00 37.40 4.49
1913 3501 5.047188 TCACTAATGTATGCATGTACACGG 58.953 41.667 10.16 3.53 37.40 4.94
1914 3502 3.807622 ACTAATGTATGCATGTACACGGC 59.192 43.478 10.16 13.06 37.40 5.68
1915 3503 2.323968 ATGTATGCATGTACACGGCA 57.676 45.000 21.97 21.97 42.43 5.69
1916 3504 1.364721 TGTATGCATGTACACGGCAC 58.635 50.000 22.11 13.28 40.83 5.01
1971 3559 5.002516 TGGGAAAATGCTTTTATTTGCAGG 58.997 37.500 0.00 0.00 42.74 4.85
1972 3560 5.003160 GGGAAAATGCTTTTATTTGCAGGT 58.997 37.500 0.00 0.00 42.74 4.00
1977 3565 2.487762 TGCTTTTATTTGCAGGTCGAGG 59.512 45.455 0.00 0.00 34.84 4.63
1985 3573 2.981302 CAGGTCGAGGGCACATCA 59.019 61.111 0.00 0.00 0.00 3.07
1987 3575 2.509336 GGTCGAGGGCACATCACG 60.509 66.667 0.00 0.00 0.00 4.35
1993 3581 1.737838 GAGGGCACATCACGATTTGA 58.262 50.000 0.00 0.00 39.11 2.69
2008 3596 7.285172 ATCACGATTTGAAATTATGGATCACCA 59.715 33.333 0.00 0.00 43.79 4.17
2033 3621 8.286800 CACATTTCATTTTCATTTTCAGTGCAT 58.713 29.630 0.00 0.00 0.00 3.96
2035 3623 8.499967 CATTTCATTTTCATTTTCAGTGCATCA 58.500 29.630 0.00 0.00 0.00 3.07
2075 3663 9.650371 GAATCTTTTTGGAACTTAAAAATGCAC 57.350 29.630 0.00 0.00 36.68 4.57
2081 3669 5.112686 TGGAACTTAAAAATGCACGCTTTT 58.887 33.333 0.00 0.00 0.00 2.27
2093 3681 4.486090 TGCACGCTTTTAACTTTTCAACA 58.514 34.783 0.00 0.00 0.00 3.33
2102 3719 7.739911 GCTTTTAACTTTTCAACATAAATGCCG 59.260 33.333 0.00 0.00 33.79 5.69
2104 3721 7.630470 TTAACTTTTCAACATAAATGCCGTG 57.370 32.000 0.00 0.00 0.00 4.94
2114 3731 6.091718 ACATAAATGCCGTGGTTTTAGTTT 57.908 33.333 0.00 0.00 0.00 2.66
2151 3772 3.711190 ACATTTATTTTGGATGGGAGGGC 59.289 43.478 0.00 0.00 0.00 5.19
2162 3784 2.457813 TGGGAGGGCGTGTAGTTATA 57.542 50.000 0.00 0.00 0.00 0.98
2168 3790 4.038883 GGAGGGCGTGTAGTTATAAGTGAT 59.961 45.833 2.90 0.00 0.00 3.06
2169 3791 5.242393 GGAGGGCGTGTAGTTATAAGTGATA 59.758 44.000 2.90 0.00 0.00 2.15
2170 3792 6.328641 AGGGCGTGTAGTTATAAGTGATAG 57.671 41.667 2.90 0.00 0.00 2.08
2228 3850 9.636965 GACAATTTTGAAGTGAATAAGTTTTGC 57.363 29.630 0.00 0.00 0.00 3.68
2233 3855 6.125327 TGAAGTGAATAAGTTTTGCGTTGA 57.875 33.333 0.00 0.00 0.00 3.18
2304 3927 5.144359 GTGTAAAAGTTACATCGGTTGCTG 58.856 41.667 4.28 0.00 0.00 4.41
2309 3932 4.946784 AGTTACATCGGTTGCTGATTTC 57.053 40.909 0.00 0.00 0.00 2.17
2311 3934 4.943705 AGTTACATCGGTTGCTGATTTCAT 59.056 37.500 0.00 0.00 0.00 2.57
2346 3969 0.179062 AAGATTCCTGCTAGCTGCCG 60.179 55.000 17.23 3.94 42.00 5.69
2358 3981 0.108138 AGCTGCCGCCTGTTAGTAAG 60.108 55.000 0.00 0.00 36.60 2.34
2394 4021 8.137437 AGAATTACAAGCTAAAATATGCGCAAT 58.863 29.630 17.11 6.72 0.00 3.56
2442 4069 6.640499 TGATCGAATTTGACATTCACAAAACC 59.360 34.615 0.00 0.00 39.95 3.27
2478 4105 4.094887 GGAGCATTCTTCGTAAATTGCAGA 59.905 41.667 0.00 0.00 0.00 4.26
2530 4157 2.491152 GTGCCGGCAACATCATGG 59.509 61.111 34.66 0.00 0.00 3.66
2534 4161 0.461135 GCCGGCAACATCATGGAATT 59.539 50.000 24.80 0.00 0.00 2.17
2543 4170 6.372103 GGCAACATCATGGAATTTGAATTCAA 59.628 34.615 16.91 16.91 45.10 2.69
2565 4192 2.871453 AGAATTGTGTTACACCCCACC 58.129 47.619 13.29 0.00 32.73 4.61
2574 4201 2.974435 TACACCCCACCTGTCCAGCA 62.974 60.000 0.00 0.00 0.00 4.41
2591 4218 1.635487 AGCAAGGACCAGGCTATTTCA 59.365 47.619 8.04 0.00 35.82 2.69
2621 4248 1.113517 GCCTCTACCATGGTAGCCGA 61.114 60.000 37.28 24.19 45.51 5.54
2627 4254 1.204146 ACCATGGTAGCCGAGTTGAT 58.796 50.000 18.10 0.00 0.00 2.57
2629 4256 1.134401 CCATGGTAGCCGAGTTGATGT 60.134 52.381 2.57 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.027192 AGCTATTGTTCCACCGTGATGT 60.027 45.455 0.00 0.00 0.00 3.06
12 15 2.205022 TTGGCTCTGCAGCTATTGTT 57.795 45.000 9.47 0.00 46.03 2.83
19 22 0.036010 TACTCCTTTGGCTCTGCAGC 60.036 55.000 9.47 0.00 46.06 5.25
27 30 4.332828 AGTGGTATGTTTACTCCTTTGGC 58.667 43.478 0.00 0.00 0.00 4.52
32 35 4.956582 AGGGTAGTGGTATGTTTACTCCT 58.043 43.478 0.00 0.00 0.00 3.69
33 36 5.688814 AAGGGTAGTGGTATGTTTACTCC 57.311 43.478 0.00 0.00 0.00 3.85
36 39 7.496920 GGATACAAAGGGTAGTGGTATGTTTAC 59.503 40.741 0.00 0.00 34.92 2.01
133 136 0.788391 CTCCCGTGTGCGAAAAGTAC 59.212 55.000 0.00 0.00 41.33 2.73
148 151 3.444034 GCTAAATTCCAGTGGAAACTCCC 59.556 47.826 27.93 12.97 45.41 4.30
150 153 5.415701 TCATGCTAAATTCCAGTGGAAACTC 59.584 40.000 27.93 15.20 45.41 3.01
165 168 6.348786 GCTTGACTGTCTGAAATCATGCTAAA 60.349 38.462 9.51 0.00 38.52 1.85
166 169 5.122869 GCTTGACTGTCTGAAATCATGCTAA 59.877 40.000 9.51 0.00 38.52 3.09
167 170 4.633126 GCTTGACTGTCTGAAATCATGCTA 59.367 41.667 9.51 0.00 38.52 3.49
168 171 3.439476 GCTTGACTGTCTGAAATCATGCT 59.561 43.478 9.51 0.00 38.52 3.79
169 172 3.189910 TGCTTGACTGTCTGAAATCATGC 59.810 43.478 9.51 13.49 40.68 4.06
170 173 5.332707 CATGCTTGACTGTCTGAAATCATG 58.667 41.667 9.51 8.61 0.00 3.07
171 174 4.142447 GCATGCTTGACTGTCTGAAATCAT 60.142 41.667 11.37 0.27 0.00 2.45
172 175 3.189910 GCATGCTTGACTGTCTGAAATCA 59.810 43.478 11.37 0.00 0.00 2.57
173 176 3.189910 TGCATGCTTGACTGTCTGAAATC 59.810 43.478 20.33 0.00 0.00 2.17
174 177 3.151554 TGCATGCTTGACTGTCTGAAAT 58.848 40.909 20.33 0.00 0.00 2.17
175 178 2.551032 CTGCATGCTTGACTGTCTGAAA 59.449 45.455 20.33 0.00 0.00 2.69
176 179 2.148768 CTGCATGCTTGACTGTCTGAA 58.851 47.619 20.33 0.00 0.00 3.02
177 180 1.345415 TCTGCATGCTTGACTGTCTGA 59.655 47.619 20.33 0.00 0.00 3.27
178 181 1.463831 GTCTGCATGCTTGACTGTCTG 59.536 52.381 25.93 3.43 0.00 3.51
179 182 1.610102 GGTCTGCATGCTTGACTGTCT 60.610 52.381 29.18 0.00 0.00 3.41
180 183 0.801251 GGTCTGCATGCTTGACTGTC 59.199 55.000 29.18 17.35 0.00 3.51
181 184 0.109153 TGGTCTGCATGCTTGACTGT 59.891 50.000 29.18 0.00 0.00 3.55
182 185 1.132453 CATGGTCTGCATGCTTGACTG 59.868 52.381 29.18 21.65 0.00 3.51
183 186 1.003928 TCATGGTCTGCATGCTTGACT 59.996 47.619 29.18 16.78 0.00 3.41
184 187 1.456296 TCATGGTCTGCATGCTTGAC 58.544 50.000 25.53 25.53 0.00 3.18
185 188 2.203470 TTCATGGTCTGCATGCTTGA 57.797 45.000 20.33 14.11 0.00 3.02
186 189 3.520290 AATTCATGGTCTGCATGCTTG 57.480 42.857 20.33 11.88 0.00 4.01
187 190 4.546829 AAAATTCATGGTCTGCATGCTT 57.453 36.364 20.33 0.00 0.00 3.91
188 191 5.361571 TCATAAAATTCATGGTCTGCATGCT 59.638 36.000 20.33 0.00 0.00 3.79
189 192 5.593968 TCATAAAATTCATGGTCTGCATGC 58.406 37.500 11.82 11.82 0.00 4.06
190 193 7.430441 TCATCATAAAATTCATGGTCTGCATG 58.570 34.615 0.00 0.00 0.00 4.06
191 194 7.591421 TCATCATAAAATTCATGGTCTGCAT 57.409 32.000 0.00 0.00 0.00 3.96
192 195 7.591421 ATCATCATAAAATTCATGGTCTGCA 57.409 32.000 0.00 0.00 0.00 4.41
193 196 8.882415 AAATCATCATAAAATTCATGGTCTGC 57.118 30.769 0.00 0.00 0.00 4.26
194 197 9.177304 CGAAATCATCATAAAATTCATGGTCTG 57.823 33.333 0.00 0.00 0.00 3.51
195 198 9.123902 TCGAAATCATCATAAAATTCATGGTCT 57.876 29.630 0.00 0.00 0.00 3.85
196 199 9.173939 GTCGAAATCATCATAAAATTCATGGTC 57.826 33.333 0.00 0.00 0.00 4.02
197 200 8.685427 TGTCGAAATCATCATAAAATTCATGGT 58.315 29.630 0.00 0.00 0.00 3.55
198 201 9.177304 CTGTCGAAATCATCATAAAATTCATGG 57.823 33.333 0.00 0.00 0.00 3.66
199 202 9.726232 ACTGTCGAAATCATCATAAAATTCATG 57.274 29.630 0.00 0.00 0.00 3.07
200 203 9.941664 GACTGTCGAAATCATCATAAAATTCAT 57.058 29.630 0.00 0.00 0.00 2.57
201 204 9.166173 AGACTGTCGAAATCATCATAAAATTCA 57.834 29.630 1.52 0.00 0.00 2.57
204 207 8.768955 GCTAGACTGTCGAAATCATCATAAAAT 58.231 33.333 1.52 0.00 0.00 1.82
205 208 7.763985 TGCTAGACTGTCGAAATCATCATAAAA 59.236 33.333 1.52 0.00 0.00 1.52
211 214 4.084641 GCATGCTAGACTGTCGAAATCATC 60.085 45.833 11.37 0.00 0.00 2.92
227 230 2.125147 GCCGTGGTCTGCATGCTA 60.125 61.111 20.33 4.02 0.00 3.49
263 306 4.423732 CAATAAGAAACTTCCATTGCCGG 58.576 43.478 0.00 0.00 0.00 6.13
322 365 2.974698 GTGAGGTGCTGCAACGCT 60.975 61.111 21.59 0.43 0.00 5.07
323 366 4.030452 GGTGAGGTGCTGCAACGC 62.030 66.667 14.75 14.75 0.00 4.84
360 403 7.834881 ACTGATAAGACGGGAAGATATGTTA 57.165 36.000 0.00 0.00 0.00 2.41
363 406 8.361139 ACTTAACTGATAAGACGGGAAGATATG 58.639 37.037 11.11 0.00 43.16 1.78
364 407 8.480133 ACTTAACTGATAAGACGGGAAGATAT 57.520 34.615 11.11 0.00 43.16 1.63
390 433 6.077322 TGGATTCTCTCTTCCAAACCAAAAT 58.923 36.000 0.00 0.00 39.05 1.82
423 466 4.478843 CAGTGACAAATTCAGACCACTG 57.521 45.455 0.00 0.00 43.29 3.66
432 475 4.209452 TCGAAGTTGCAGTGACAAATTC 57.791 40.909 20.57 20.57 46.03 2.17
433 476 4.836125 ATCGAAGTTGCAGTGACAAATT 57.164 36.364 11.06 11.06 40.24 1.82
434 477 4.154195 GGTATCGAAGTTGCAGTGACAAAT 59.846 41.667 0.00 0.00 0.00 2.32
436 479 3.064207 GGTATCGAAGTTGCAGTGACAA 58.936 45.455 0.00 0.00 0.00 3.18
437 480 2.611971 GGGTATCGAAGTTGCAGTGACA 60.612 50.000 0.00 0.00 0.00 3.58
438 481 2.000447 GGGTATCGAAGTTGCAGTGAC 59.000 52.381 0.00 0.00 0.00 3.67
439 482 1.621317 TGGGTATCGAAGTTGCAGTGA 59.379 47.619 0.00 0.00 0.00 3.41
440 483 2.002586 CTGGGTATCGAAGTTGCAGTG 58.997 52.381 0.00 0.00 0.00 3.66
441 484 1.676014 GCTGGGTATCGAAGTTGCAGT 60.676 52.381 0.00 0.00 0.00 4.40
442 485 1.009829 GCTGGGTATCGAAGTTGCAG 58.990 55.000 0.00 0.00 0.00 4.41
443 486 0.739462 CGCTGGGTATCGAAGTTGCA 60.739 55.000 0.00 0.00 0.00 4.08
444 487 0.739813 ACGCTGGGTATCGAAGTTGC 60.740 55.000 0.00 0.00 0.00 4.17
445 488 1.393539 CAACGCTGGGTATCGAAGTTG 59.606 52.381 0.00 0.00 32.92 3.16
470 513 4.553330 TGAGTGGTATTTCAGGAGGAAC 57.447 45.455 0.00 0.00 34.56 3.62
577 620 7.697352 TGTACACTTTGCAATGAATTTTGAG 57.303 32.000 18.35 3.53 0.00 3.02
588 631 6.678878 TGTTTGTACTTTGTACACTTTGCAA 58.321 32.000 9.70 0.00 0.00 4.08
629 672 0.846693 CCGGGGATGATCCTCCTTTT 59.153 55.000 15.68 0.00 31.67 2.27
658 704 0.744281 TGGCTGCATGCATCATTCTG 59.256 50.000 22.97 8.76 45.15 3.02
791 844 7.591165 TCTTATCGTGTAAGTATGGATGTAGC 58.409 38.462 9.15 0.00 0.00 3.58
806 859 3.674997 ACTGCCAACAATCTTATCGTGT 58.325 40.909 0.00 0.00 0.00 4.49
856 909 6.015688 AGTCTGCTATAAACGATTTCCGGATA 60.016 38.462 4.15 0.00 43.93 2.59
878 931 4.305989 TGCAGTGACAAATTTTGGAGTC 57.694 40.909 13.42 3.19 34.12 3.36
994 2553 2.128035 GACGAACTTGCCCATATCGAG 58.872 52.381 0.07 0.00 37.27 4.04
997 2556 3.798202 AGAAGACGAACTTGCCCATATC 58.202 45.455 0.00 0.00 39.13 1.63
1005 2564 0.435008 CCGCGAAGAAGACGAACTTG 59.565 55.000 8.23 0.00 39.13 3.16
1007 2566 0.663568 CACCGCGAAGAAGACGAACT 60.664 55.000 8.23 0.00 0.00 3.01
1686 3251 1.957177 TCGACCAATCAGCTAGCCTAG 59.043 52.381 12.13 1.69 0.00 3.02
1687 3252 2.067365 TCGACCAATCAGCTAGCCTA 57.933 50.000 12.13 0.00 0.00 3.93
1688 3253 1.069823 CATCGACCAATCAGCTAGCCT 59.930 52.381 12.13 0.00 0.00 4.58
1827 3400 8.538409 TTGAAAGTAAAAGAGTTACGGGATAC 57.462 34.615 0.00 0.00 0.00 2.24
1862 3450 1.399727 GGGAGTTTTGTGAATCACGCG 60.400 52.381 3.53 3.53 37.14 6.01
1863 3451 1.606668 TGGGAGTTTTGTGAATCACGC 59.393 47.619 9.00 0.00 37.14 5.34
1864 3452 3.980646 TTGGGAGTTTTGTGAATCACG 57.019 42.857 9.00 0.00 37.14 4.35
1884 3472 9.008965 TGTACATGCATACATTAGTGACTTTTT 57.991 29.630 0.00 0.00 32.87 1.94
1886 3474 7.201522 CGTGTACATGCATACATTAGTGACTTT 60.202 37.037 5.62 0.00 37.40 2.66
1887 3475 6.255670 CGTGTACATGCATACATTAGTGACTT 59.744 38.462 5.62 0.00 37.40 3.01
1888 3476 5.748630 CGTGTACATGCATACATTAGTGACT 59.251 40.000 5.62 0.00 37.40 3.41
1891 3479 4.318760 GCCGTGTACATGCATACATTAGTG 60.319 45.833 9.72 0.00 37.40 2.74
1893 3481 3.807071 TGCCGTGTACATGCATACATTAG 59.193 43.478 16.36 1.84 37.40 1.73
1895 3483 2.354510 GTGCCGTGTACATGCATACATT 59.645 45.455 21.27 0.00 37.40 2.71
1896 3484 1.939934 GTGCCGTGTACATGCATACAT 59.060 47.619 21.27 0.00 37.40 2.29
1897 3485 1.338200 TGTGCCGTGTACATGCATACA 60.338 47.619 21.27 15.93 37.34 2.29
1898 3486 1.327460 CTGTGCCGTGTACATGCATAC 59.673 52.381 21.27 14.02 37.34 2.39
1899 3487 1.650825 CTGTGCCGTGTACATGCATA 58.349 50.000 21.27 18.25 37.34 3.14
1900 3488 1.026182 CCTGTGCCGTGTACATGCAT 61.026 55.000 21.27 0.00 37.34 3.96
1901 3489 1.670730 CCTGTGCCGTGTACATGCA 60.671 57.895 16.36 16.36 0.00 3.96
1902 3490 0.953471 TTCCTGTGCCGTGTACATGC 60.953 55.000 9.72 11.05 0.00 4.06
1903 3491 1.737838 ATTCCTGTGCCGTGTACATG 58.262 50.000 8.18 8.18 0.00 3.21
1904 3492 2.235155 TGTATTCCTGTGCCGTGTACAT 59.765 45.455 0.00 0.00 0.00 2.29
1905 3493 1.619332 TGTATTCCTGTGCCGTGTACA 59.381 47.619 0.00 0.00 0.00 2.90
1906 3494 2.373540 TGTATTCCTGTGCCGTGTAC 57.626 50.000 0.00 0.00 0.00 2.90
1907 3495 3.404224 TTTGTATTCCTGTGCCGTGTA 57.596 42.857 0.00 0.00 0.00 2.90
1908 3496 2.264005 TTTGTATTCCTGTGCCGTGT 57.736 45.000 0.00 0.00 0.00 4.49
1909 3497 3.848272 ATTTTGTATTCCTGTGCCGTG 57.152 42.857 0.00 0.00 0.00 4.94
1910 3498 5.968528 TTTATTTTGTATTCCTGTGCCGT 57.031 34.783 0.00 0.00 0.00 5.68
1911 3499 6.795399 AGATTTATTTTGTATTCCTGTGCCG 58.205 36.000 0.00 0.00 0.00 5.69
1912 3500 8.250332 TCAAGATTTATTTTGTATTCCTGTGCC 58.750 33.333 0.00 0.00 0.00 5.01
1913 3501 9.638239 TTCAAGATTTATTTTGTATTCCTGTGC 57.362 29.630 0.00 0.00 0.00 4.57
1971 3559 0.460284 AATCGTGATGTGCCCTCGAC 60.460 55.000 0.00 0.00 33.35 4.20
1972 3560 0.249120 AAATCGTGATGTGCCCTCGA 59.751 50.000 0.00 0.00 34.70 4.04
1977 3565 5.459762 CCATAATTTCAAATCGTGATGTGCC 59.540 40.000 0.00 0.00 35.70 5.01
1985 3573 6.376864 TGTGGTGATCCATAATTTCAAATCGT 59.623 34.615 0.00 0.00 46.20 3.73
1987 3575 9.603921 AAATGTGGTGATCCATAATTTCAAATC 57.396 29.630 0.00 0.00 46.20 2.17
1993 3581 9.962809 AAAATGAAATGTGGTGATCCATAATTT 57.037 25.926 9.17 9.17 46.20 1.82
2008 3596 7.789273 TGCACTGAAAATGAAAATGAAATGT 57.211 28.000 0.00 0.00 0.00 2.71
2014 3602 6.772770 TGTGATGCACTGAAAATGAAAATG 57.227 33.333 0.00 0.00 35.11 2.32
2015 3603 7.972832 AATGTGATGCACTGAAAATGAAAAT 57.027 28.000 0.00 0.00 35.11 1.82
2066 3654 7.066374 TGAAAAGTTAAAAGCGTGCATTTTT 57.934 28.000 2.09 6.76 32.38 1.94
2067 3655 6.654793 TGAAAAGTTAAAAGCGTGCATTTT 57.345 29.167 0.08 0.00 34.40 1.82
2075 3663 7.739911 GGCATTTATGTTGAAAAGTTAAAAGCG 59.260 33.333 0.00 0.00 32.96 4.68
2081 3669 6.153067 CCACGGCATTTATGTTGAAAAGTTA 58.847 36.000 0.00 0.00 0.00 2.24
2093 3681 6.334102 TCAAACTAAAACCACGGCATTTAT 57.666 33.333 0.00 0.00 0.00 1.40
2128 3749 4.164030 GCCCTCCCATCCAAAATAAATGTT 59.836 41.667 0.00 0.00 0.00 2.71
2140 3761 1.623542 AACTACACGCCCTCCCATCC 61.624 60.000 0.00 0.00 0.00 3.51
2144 3765 2.697229 ACTTATAACTACACGCCCTCCC 59.303 50.000 0.00 0.00 0.00 4.30
2188 3810 5.539574 TCAAAATTGTCACCATCCAGTCATT 59.460 36.000 0.00 0.00 0.00 2.57
2193 3815 5.009911 TCACTTCAAAATTGTCACCATCCAG 59.990 40.000 0.00 0.00 0.00 3.86
2207 3829 7.542477 TCAACGCAAAACTTATTCACTTCAAAA 59.458 29.630 0.00 0.00 0.00 2.44
2212 3834 5.741982 GTGTCAACGCAAAACTTATTCACTT 59.258 36.000 0.00 0.00 0.00 3.16
2228 3850 6.126568 TCCCTTAAAAAGAAAGTGTCAACG 57.873 37.500 0.00 0.00 0.00 4.10
2233 3855 6.070481 TGGCTTTTCCCTTAAAAAGAAAGTGT 60.070 34.615 12.06 0.00 45.12 3.55
2346 3969 8.773404 TTCTAATGTTTCTCTTACTAACAGGC 57.227 34.615 0.00 0.00 35.48 4.85
2385 4012 3.446799 GAAGCCAATCAAATTGCGCATA 58.553 40.909 12.75 2.21 38.25 3.14
2394 4021 2.647299 TGTCCTAGGGAAGCCAATCAAA 59.353 45.455 9.46 0.00 31.38 2.69
2442 4069 6.238049 CGAAGAATGCTCCTTTCTATGTCAAG 60.238 42.308 0.00 0.00 33.17 3.02
2478 4105 2.134346 GCAATTCAATTGGTGTTGCGT 58.866 42.857 19.73 0.00 40.57 5.24
2534 4161 9.906660 GGTGTAACACAATTCTATTGAATTCAA 57.093 29.630 22.52 22.52 44.01 2.69
2574 4201 2.507471 CCTCTGAAATAGCCTGGTCCTT 59.493 50.000 0.00 0.00 0.00 3.36
2581 4208 1.428869 ATCGCCCTCTGAAATAGCCT 58.571 50.000 0.00 0.00 0.00 4.58
2583 4210 2.342179 GCTATCGCCCTCTGAAATAGC 58.658 52.381 0.00 0.00 38.38 2.97
2608 4235 1.134401 CATCAACTCGGCTACCATGGT 60.134 52.381 23.55 23.55 0.00 3.55
2615 4242 4.018490 TGTAACCTACATCAACTCGGCTA 58.982 43.478 0.00 0.00 32.89 3.93
2621 4248 3.994392 CTGCGTTGTAACCTACATCAACT 59.006 43.478 0.00 0.00 38.68 3.16
2627 4254 1.868498 GCAACTGCGTTGTAACCTACA 59.132 47.619 18.15 0.00 44.40 2.74
2629 4256 2.536761 AGCAACTGCGTTGTAACCTA 57.463 45.000 18.15 0.00 44.40 3.08


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

AutoCloner maintained by Alex Coulton.