Multiple sequence alignment - TraesCS2A01G547900

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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 TraesCS2A01G547900 chr2A 100.000 5589 0 0 1 5589 755784726 755790314 0.000000e+00 10322
1 TraesCS2A01G547900 chr2D 93.110 5631 254 65 1 5583 624549986 624555530 0.000000e+00 8126
2 TraesCS2A01G547900 chr2B 91.948 5129 277 73 1 5082 767013661 767018700 0.000000e+00 7059
3 TraesCS2A01G547900 chr2B 92.958 213 9 4 5349 5560 767018995 767019202 7.030000e-79 305
4 TraesCS2A01G547900 chr2B 92.655 177 8 3 5165 5336 767018714 767018890 3.340000e-62 250


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 TraesCS2A01G547900 chr2A 755784726 755790314 5588 False 10322 10322 100.000000 1 5589 1 chr2A.!!$F1 5588
1 TraesCS2A01G547900 chr2D 624549986 624555530 5544 False 8126 8126 93.110000 1 5583 1 chr2D.!!$F1 5582
2 TraesCS2A01G547900 chr2B 767013661 767019202 5541 False 2538 7059 92.520333 1 5560 3 chr2B.!!$F1 5559

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
229 232 0.460311 AGTTACCTTCTCATCCGCCG 59.540 55.0 0.00 0.00 0.00 6.46 F
514 524 0.662085 TAAAAACCGCAACCCACGTC 59.338 50.0 0.00 0.00 0.00 4.34 F
1402 1436 0.107703 CGATGCTAGGGCTTGGTCAA 60.108 55.0 0.00 0.00 39.59 3.18 F
3153 3233 0.032952 CAAAACAGCATGCCAGCAGT 59.967 50.0 15.66 2.67 42.53 4.40 F
4187 4267 0.674895 GAGGAAACGACAGGCTGCAT 60.675 55.0 15.89 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1205 0.106967 GGCTAGCTTGGAAGGAAGGG 60.107 60.0 15.72 0.0 0.00 3.95 R
1570 1608 0.171007 CGTGATTCATGTTGCCACCC 59.829 55.0 0.00 0.0 0.00 4.61 R
3352 3432 0.323087 AAGCACCAGCATCTGCATCA 60.323 50.0 4.79 0.0 45.49 3.07 R
4465 4545 0.030908 CTTCGGTCGCCTCATACTCC 59.969 60.0 0.00 0.0 0.00 3.85 R
5435 5626 1.159285 CAATCTCGTGGCAAGCAAGA 58.841 50.0 0.00 0.0 0.00 3.02 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
38 39 4.323562 GGGGAGTGGAGTTATATGTATGCC 60.324 50.000 0.00 0.00 0.00 4.40
52 53 4.955925 TGTATGCCGGTTTAGAAATGTG 57.044 40.909 1.90 0.00 0.00 3.21
53 54 4.580868 TGTATGCCGGTTTAGAAATGTGA 58.419 39.130 1.90 0.00 0.00 3.58
68 69 1.348064 TGTGAACTCCCACCTACCTG 58.652 55.000 0.00 0.00 36.26 4.00
82 83 2.392662 CTACCTGCCTGAATGGAGAGA 58.607 52.381 0.00 0.00 38.35 3.10
96 97 8.203681 TGAATGGAGAGATGAAGATGATGTAT 57.796 34.615 0.00 0.00 0.00 2.29
162 163 2.742428 ATAGTACACTCCCGCCTACA 57.258 50.000 0.00 0.00 0.00 2.74
163 164 2.742428 TAGTACACTCCCGCCTACAT 57.258 50.000 0.00 0.00 0.00 2.29
165 166 0.822164 GTACACTCCCGCCTACATGT 59.178 55.000 2.69 2.69 0.00 3.21
166 167 0.821517 TACACTCCCGCCTACATGTG 59.178 55.000 9.11 0.00 0.00 3.21
167 168 1.192146 ACACTCCCGCCTACATGTGT 61.192 55.000 9.11 0.00 34.38 3.72
186 187 7.754027 ACATGTGTGTAAAGACGAAGATACTAC 59.246 37.037 0.00 0.00 36.63 2.73
189 190 7.040892 TGTGTGTAAAGACGAAGATACTACACT 60.041 37.037 0.00 0.00 36.99 3.55
191 192 7.173735 TGTGTAAAGACGAAGATACTACACTCA 59.826 37.037 9.95 0.00 36.99 3.41
192 193 8.019669 GTGTAAAGACGAAGATACTACACTCAA 58.980 37.037 0.00 0.00 34.30 3.02
193 194 8.737175 TGTAAAGACGAAGATACTACACTCAAT 58.263 33.333 0.00 0.00 0.00 2.57
194 195 9.011407 GTAAAGACGAAGATACTACACTCAATG 57.989 37.037 0.00 0.00 0.00 2.82
196 197 6.787225 AGACGAAGATACTACACTCAATGTC 58.213 40.000 0.00 0.00 42.09 3.06
197 198 6.374613 AGACGAAGATACTACACTCAATGTCA 59.625 38.462 0.00 0.00 42.09 3.58
207 210 4.191544 ACACTCAATGTCACGATATTGGG 58.808 43.478 13.12 13.12 43.40 4.12
229 232 0.460311 AGTTACCTTCTCATCCGCCG 59.540 55.000 0.00 0.00 0.00 6.46
236 239 1.963464 TTCTCATCCGCCGTTACCCC 61.963 60.000 0.00 0.00 0.00 4.95
237 240 2.684294 TCATCCGCCGTTACCCCA 60.684 61.111 0.00 0.00 0.00 4.96
238 241 2.512974 CATCCGCCGTTACCCCAC 60.513 66.667 0.00 0.00 0.00 4.61
239 242 4.151582 ATCCGCCGTTACCCCACG 62.152 66.667 0.00 0.00 40.02 4.94
241 244 4.685467 CCGCCGTTACCCCACGTT 62.685 66.667 0.00 0.00 38.57 3.99
242 245 3.416382 CGCCGTTACCCCACGTTG 61.416 66.667 0.00 0.00 38.57 4.10
243 246 3.729698 GCCGTTACCCCACGTTGC 61.730 66.667 0.00 0.00 38.57 4.17
244 247 3.416382 CCGTTACCCCACGTTGCG 61.416 66.667 0.00 0.00 38.57 4.85
245 248 2.356075 CGTTACCCCACGTTGCGA 60.356 61.111 0.00 0.00 35.34 5.10
246 249 2.377310 CGTTACCCCACGTTGCGAG 61.377 63.158 0.00 0.00 35.34 5.03
247 250 1.005867 GTTACCCCACGTTGCGAGA 60.006 57.895 0.00 0.00 0.00 4.04
315 319 4.766891 CCCACTAAAATTCAAGAGAAGCCA 59.233 41.667 0.00 0.00 37.14 4.75
372 376 5.951747 TCAAGCTGCAAAATACTAATCCCTT 59.048 36.000 1.02 0.00 0.00 3.95
373 377 6.437162 TCAAGCTGCAAAATACTAATCCCTTT 59.563 34.615 1.02 0.00 0.00 3.11
389 393 5.659440 TCCCTTTGATCCAAAATAAGTGC 57.341 39.130 0.00 0.00 32.75 4.40
392 396 4.157656 CCTTTGATCCAAAATAAGTGCCGA 59.842 41.667 0.00 0.00 32.75 5.54
393 397 4.695217 TTGATCCAAAATAAGTGCCGAC 57.305 40.909 0.00 0.00 0.00 4.79
397 401 2.028294 TCCAAAATAAGTGCCGACGGTA 60.028 45.455 16.73 8.50 0.00 4.02
398 402 2.940410 CCAAAATAAGTGCCGACGGTAT 59.060 45.455 16.73 2.15 0.00 2.73
399 403 4.121317 CCAAAATAAGTGCCGACGGTATA 58.879 43.478 16.73 1.39 0.00 1.47
404 408 3.323751 AAGTGCCGACGGTATAGTTTT 57.676 42.857 16.73 0.00 0.00 2.43
487 497 3.994729 CGTAACCACCACGTATCGA 57.005 52.632 0.00 0.00 34.74 3.59
511 521 1.866471 GCAGTAAAAACCGCAACCCAC 60.866 52.381 0.00 0.00 0.00 4.61
512 522 0.664224 AGTAAAAACCGCAACCCACG 59.336 50.000 0.00 0.00 0.00 4.94
514 524 0.662085 TAAAAACCGCAACCCACGTC 59.338 50.000 0.00 0.00 0.00 4.34
560 570 7.455641 TCAAGTCAAACTTTGTTAACCTTGA 57.544 32.000 2.48 8.32 36.03 3.02
602 612 6.845446 ACACTACTACTCTCTAGATGGTAGGA 59.155 42.308 23.92 18.96 36.81 2.94
651 667 4.881850 AGAGAAAGAGGAAAGAAACGCAAA 59.118 37.500 0.00 0.00 0.00 3.68
682 703 5.016173 TGGAGAGAAGAGAAGAGGAAAGAG 58.984 45.833 0.00 0.00 0.00 2.85
1170 1204 1.230314 CCTCCCCTTCCCTTCCCTT 60.230 63.158 0.00 0.00 0.00 3.95
1171 1205 1.282653 CCTCCCCTTCCCTTCCCTTC 61.283 65.000 0.00 0.00 0.00 3.46
1172 1206 1.230182 TCCCCTTCCCTTCCCTTCC 60.230 63.158 0.00 0.00 0.00 3.46
1173 1207 2.317378 CCCCTTCCCTTCCCTTCCC 61.317 68.421 0.00 0.00 0.00 3.97
1174 1208 1.230314 CCCTTCCCTTCCCTTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
1240 1274 0.778815 CGCGATTGGAGCTCGTAATC 59.221 55.000 22.66 22.66 38.37 1.75
1269 1303 3.711059 ATCGAGTCGCGGGTAGGGT 62.711 63.158 7.92 0.00 41.33 4.34
1307 1341 1.661112 CACCGGAGAGAAAGATTTCGC 59.339 52.381 9.46 1.32 41.92 4.70
1356 1390 2.037902 TGTTCTTTGCCGATGTGTAGGA 59.962 45.455 0.00 0.00 0.00 2.94
1402 1436 0.107703 CGATGCTAGGGCTTGGTCAA 60.108 55.000 0.00 0.00 39.59 3.18
1406 1440 1.982226 TGCTAGGGCTTGGTCAAGTTA 59.018 47.619 11.71 3.21 40.45 2.24
1414 1448 3.826729 GGCTTGGTCAAGTTATGTTCCTT 59.173 43.478 11.71 0.00 40.45 3.36
1420 1454 6.065374 TGGTCAAGTTATGTTCCTTTTGCTA 58.935 36.000 0.00 0.00 0.00 3.49
1438 1472 1.963464 TAGACGGGAATTGGGACGGC 61.963 60.000 0.00 0.00 33.82 5.68
1441 1475 2.355115 GGGAATTGGGACGGCAGT 59.645 61.111 0.00 0.00 0.00 4.40
1559 1597 6.335781 TGCCTTGATTATACCCCTTTTAGT 57.664 37.500 0.00 0.00 0.00 2.24
1562 1600 5.469084 CCTTGATTATACCCCTTTTAGTCGC 59.531 44.000 0.00 0.00 0.00 5.19
1611 1649 2.224426 ACGTCTGTTTGCCCAAGATGTA 60.224 45.455 0.00 0.00 0.00 2.29
1624 1662 4.580580 CCCAAGATGTAGATTTTACCTGGC 59.419 45.833 0.00 0.00 0.00 4.85
1641 1679 0.178978 GGCTCATGGGGAGGATTTCC 60.179 60.000 0.00 0.00 44.22 3.13
1664 1702 6.274436 TCCTGATAGGAATATGTTATTGCCCA 59.726 38.462 0.00 0.00 42.51 5.36
1692 1730 4.273318 GTTATGCTTCCCCTGTCTGAAAT 58.727 43.478 0.00 0.00 0.00 2.17
1702 1740 4.298332 CCCTGTCTGAAATTTTCGTTTGG 58.702 43.478 4.76 3.66 0.00 3.28
1823 1866 1.999648 AAAGGGTGAATGCTTGCTCA 58.000 45.000 0.00 0.00 0.00 4.26
1824 1867 1.999648 AAGGGTGAATGCTTGCTCAA 58.000 45.000 0.00 0.00 0.00 3.02
1825 1868 2.226962 AGGGTGAATGCTTGCTCAAT 57.773 45.000 0.00 0.00 0.00 2.57
1826 1869 1.822990 AGGGTGAATGCTTGCTCAATG 59.177 47.619 0.00 0.00 0.00 2.82
1827 1870 1.547372 GGGTGAATGCTTGCTCAATGT 59.453 47.619 0.00 0.00 0.00 2.71
1828 1871 2.416431 GGGTGAATGCTTGCTCAATGTC 60.416 50.000 0.00 0.00 0.00 3.06
1829 1872 2.229543 GGTGAATGCTTGCTCAATGTCA 59.770 45.455 0.00 0.00 0.00 3.58
1830 1873 3.305539 GGTGAATGCTTGCTCAATGTCAA 60.306 43.478 0.00 0.00 0.00 3.18
1831 1874 3.671928 GTGAATGCTTGCTCAATGTCAAC 59.328 43.478 0.00 0.00 0.00 3.18
1832 1875 3.248266 GAATGCTTGCTCAATGTCAACC 58.752 45.455 0.00 0.00 0.00 3.77
1833 1876 1.985473 TGCTTGCTCAATGTCAACCT 58.015 45.000 0.00 0.00 0.00 3.50
1834 1877 1.610038 TGCTTGCTCAATGTCAACCTG 59.390 47.619 0.00 0.00 0.00 4.00
1835 1878 1.610522 GCTTGCTCAATGTCAACCTGT 59.389 47.619 0.00 0.00 0.00 4.00
1836 1879 2.813754 GCTTGCTCAATGTCAACCTGTA 59.186 45.455 0.00 0.00 0.00 2.74
1837 1880 3.253188 GCTTGCTCAATGTCAACCTGTAA 59.747 43.478 0.00 0.00 0.00 2.41
1838 1881 4.787598 CTTGCTCAATGTCAACCTGTAAC 58.212 43.478 0.00 0.00 0.00 2.50
1839 1882 3.814625 TGCTCAATGTCAACCTGTAACA 58.185 40.909 0.00 0.00 0.00 2.41
1840 1883 4.203226 TGCTCAATGTCAACCTGTAACAA 58.797 39.130 0.00 0.00 0.00 2.83
1841 1884 4.036262 TGCTCAATGTCAACCTGTAACAAC 59.964 41.667 0.00 0.00 0.00 3.32
1842 1885 4.275936 GCTCAATGTCAACCTGTAACAACT 59.724 41.667 0.00 0.00 0.00 3.16
1963 2032 5.234466 ACACTTCTTCTTCTGTTATGCCT 57.766 39.130 0.00 0.00 0.00 4.75
1991 2064 7.692908 TTTTTGCTTCATTTAGTGCTTGTAC 57.307 32.000 0.00 0.00 0.00 2.90
2038 2113 7.556844 TGTCCACATAGGTCTTTTCTATCTTC 58.443 38.462 0.00 0.00 39.02 2.87
2040 2115 8.041323 GTCCACATAGGTCTTTTCTATCTTCAA 58.959 37.037 0.00 0.00 39.02 2.69
2085 2160 5.520376 AAATGCTGTAATGGGCTTATGTC 57.480 39.130 0.00 0.00 0.00 3.06
2087 2162 1.873591 GCTGTAATGGGCTTATGTCCG 59.126 52.381 0.00 0.00 41.88 4.79
2094 2169 2.472909 GGCTTATGTCCGCACCAGC 61.473 63.158 0.00 0.00 34.11 4.85
2285 2360 7.112122 TGCATTACAGACCATGATTTCTTACT 58.888 34.615 0.00 0.00 0.00 2.24
2320 2396 8.141298 TGGTTATTAGTTACCAGTGAGAATCA 57.859 34.615 0.00 0.00 40.51 2.57
2494 2572 5.010708 TCCTTTCCTTTATTTTCCCTGCT 57.989 39.130 0.00 0.00 0.00 4.24
2495 2573 4.772100 TCCTTTCCTTTATTTTCCCTGCTG 59.228 41.667 0.00 0.00 0.00 4.41
2496 2574 4.772100 CCTTTCCTTTATTTTCCCTGCTGA 59.228 41.667 0.00 0.00 0.00 4.26
2497 2575 5.423290 CCTTTCCTTTATTTTCCCTGCTGAT 59.577 40.000 0.00 0.00 0.00 2.90
2498 2576 6.070596 CCTTTCCTTTATTTTCCCTGCTGATT 60.071 38.462 0.00 0.00 0.00 2.57
2499 2577 7.124147 CCTTTCCTTTATTTTCCCTGCTGATTA 59.876 37.037 0.00 0.00 0.00 1.75
2513 2591 8.224025 TCCCTGCTGATTATTATTCACCATAAA 58.776 33.333 0.00 0.00 30.78 1.40
2531 2609 9.396022 CACCATAAAACCTCTTGTAATATCTGT 57.604 33.333 0.00 0.00 0.00 3.41
2599 2677 9.326413 ACAGTAACTAACAAGGCATGATTATAC 57.674 33.333 0.00 0.00 0.00 1.47
2616 2694 7.867921 TGATTATACAAACCCCTGTAGTGATT 58.132 34.615 0.00 0.00 35.32 2.57
2618 2696 5.772393 ATACAAACCCCTGTAGTGATTCA 57.228 39.130 0.00 0.00 35.32 2.57
2646 2726 7.807907 GTCATGGTCTTAATTCGTTTTGACATT 59.192 33.333 0.00 0.00 32.22 2.71
2647 2727 8.356657 TCATGGTCTTAATTCGTTTTGACATTT 58.643 29.630 0.00 0.00 0.00 2.32
2648 2728 8.977505 CATGGTCTTAATTCGTTTTGACATTTT 58.022 29.630 0.00 0.00 0.00 1.82
2735 2815 5.481105 CAATTGATGGTATGTTTGGTGCTT 58.519 37.500 0.00 0.00 0.00 3.91
2803 2883 2.356278 GGCAAGCAGATGGTCCCA 59.644 61.111 0.00 0.00 0.00 4.37
2806 2886 2.012902 GCAAGCAGATGGTCCCATGC 62.013 60.000 2.93 3.62 36.70 4.06
2839 2919 2.978156 AAGGGAACTGCATCAAAGGA 57.022 45.000 0.00 0.00 42.68 3.36
2851 2931 3.006217 GCATCAAAGGAGATAAATGCCCC 59.994 47.826 0.00 0.00 34.80 5.80
3048 3128 2.171448 AGTCAGTTAATAGGGCTGCAGG 59.829 50.000 17.12 0.00 0.00 4.85
3153 3233 0.032952 CAAAACAGCATGCCAGCAGT 59.967 50.000 15.66 2.67 42.53 4.40
3154 3234 0.032952 AAAACAGCATGCCAGCAGTG 59.967 50.000 15.66 7.49 42.53 3.66
3164 3244 4.813027 CATGCCAGCAGTGAATAAAAGTT 58.187 39.130 0.00 0.00 0.00 2.66
3167 3247 4.340666 TGCCAGCAGTGAATAAAAGTTTCA 59.659 37.500 0.00 0.00 0.00 2.69
3259 3339 5.127682 GCAAGATTGGAATCAACCTTACCAT 59.872 40.000 2.32 0.00 34.61 3.55
3352 3432 4.379652 GTTTTGATGTTCTTGTGGCCAAT 58.620 39.130 7.24 0.00 0.00 3.16
3613 3693 1.380689 TCGGCAGAGAGAGACTGGT 59.619 57.895 0.00 0.00 36.09 4.00
3619 3699 2.091541 CAGAGAGAGACTGGTCCTGTC 58.908 57.143 18.70 18.70 33.50 3.51
3910 3990 4.135153 CGGGACAGGCTGTCTCCG 62.135 72.222 38.41 38.41 44.86 4.63
3914 3994 1.374758 GACAGGCTGTCTCCGGTTG 60.375 63.158 34.49 0.75 43.73 3.77
3974 4054 2.371179 GGGCATCATCAAGAGAGGATCA 59.629 50.000 0.00 0.00 42.92 2.92
3991 4071 0.897621 TCAGGCAGAGATCAAGCGAA 59.102 50.000 0.00 0.00 0.00 4.70
4012 4092 1.251251 GTGCTTCAAGTGCCAGGATT 58.749 50.000 0.00 0.00 0.00 3.01
4035 4115 1.338960 TGATGGCAAGCATTCGAGACA 60.339 47.619 0.00 0.00 0.00 3.41
4091 4171 1.258676 AGACTTTGGTCCGGAGTCTC 58.741 55.000 15.56 0.00 45.06 3.36
4187 4267 0.674895 GAGGAAACGACAGGCTGCAT 60.675 55.000 15.89 0.00 0.00 3.96
4222 4302 0.737219 GCTCATCTGCCCACAATGTC 59.263 55.000 0.00 0.00 0.00 3.06
4294 4374 2.046292 GAAGCTGAGAAGGAGGGCTAT 58.954 52.381 0.00 0.00 32.64 2.97
4320 4400 7.386025 TGACAACACTATCAGTTCTGAAGAATG 59.614 37.037 6.60 6.05 36.33 2.67
4381 4461 1.519455 GGTCCCTGCATCTTCGTCG 60.519 63.158 0.00 0.00 0.00 5.12
4465 4545 3.465403 CAGAGGCAGGGGGAGTCG 61.465 72.222 0.00 0.00 0.00 4.18
4480 4560 1.102222 AGTCGGAGTATGAGGCGACC 61.102 60.000 0.00 0.00 0.00 4.79
4591 4671 0.892063 GGGTCGTCTTCTCTTGAGCT 59.108 55.000 0.00 0.00 0.00 4.09
4630 4710 2.354343 GCTTCTTCAGGCCAGGCT 59.646 61.111 12.43 0.00 0.00 4.58
4655 4735 3.634397 TGCTTGATTTCCCCTCTAGTG 57.366 47.619 0.00 0.00 0.00 2.74
4656 4736 3.181329 TGCTTGATTTCCCCTCTAGTGA 58.819 45.455 0.00 0.00 0.00 3.41
4657 4737 3.782523 TGCTTGATTTCCCCTCTAGTGAT 59.217 43.478 0.00 0.00 0.00 3.06
4658 4738 4.228210 TGCTTGATTTCCCCTCTAGTGATT 59.772 41.667 0.00 0.00 0.00 2.57
4699 4780 0.537143 TCTTGTGGCGCTCCATGTTT 60.537 50.000 7.64 0.00 45.62 2.83
4700 4781 0.387622 CTTGTGGCGCTCCATGTTTG 60.388 55.000 7.64 0.00 45.62 2.93
4803 4886 3.397482 GCATTGAGCGAGGTAGATGATT 58.603 45.455 0.00 0.00 0.00 2.57
4888 4975 7.382488 CGTATCCTGGAACTCTGTATTGTATTG 59.618 40.741 0.00 0.00 0.00 1.90
4893 4980 7.362056 CCTGGAACTCTGTATTGTATTGGTTTG 60.362 40.741 0.00 0.00 0.00 2.93
4976 5070 1.691219 TCCAACTTGGAGGGCATCC 59.309 57.895 12.10 12.10 42.67 3.51
4985 5079 1.769026 GGAGGGCATCCTTTCCTTTC 58.231 55.000 11.68 0.00 45.05 2.62
5082 5177 6.128742 GCGAAATCATTTTGCTTCATGAGTTT 60.129 34.615 14.35 4.46 44.79 2.66
5101 5196 4.821805 AGTTTATTTGTGACAGTGTGGGAG 59.178 41.667 0.00 0.00 0.00 4.30
5126 5221 3.126514 CCTGCTGATCATGTTTCTGTGAC 59.873 47.826 0.00 0.00 0.00 3.67
5158 5253 8.584157 CATCTATCTGAATAAGTACCTGCTCTT 58.416 37.037 0.00 0.00 0.00 2.85
5234 5332 8.033626 GCTGTTGGTTGTAGTACTAGTTTATCT 58.966 37.037 1.87 0.00 0.00 1.98
5259 5357 3.869832 CCATGACTATCTGTCTGCAGTTG 59.130 47.826 14.67 5.36 45.54 3.16
5261 5359 3.165071 TGACTATCTGTCTGCAGTTGGA 58.835 45.455 14.67 10.30 45.54 3.53
5468 5659 5.983720 CCACGAGATTGTTAGTGTATTAGGG 59.016 44.000 0.00 0.00 33.14 3.53
5540 5731 1.266891 GCTCGCACGTTAAGCATGTAC 60.267 52.381 8.33 0.00 36.06 2.90
5541 5732 2.259618 CTCGCACGTTAAGCATGTACT 58.740 47.619 0.00 0.00 0.00 2.73
5542 5733 3.431856 CTCGCACGTTAAGCATGTACTA 58.568 45.455 0.00 0.00 0.00 1.82
5578 5769 5.513233 ACTACCTCTGTCCCGAATTAGTTA 58.487 41.667 0.00 0.00 0.00 2.24
5583 5774 5.986135 CCTCTGTCCCGAATTAGTTATCTTG 59.014 44.000 0.00 0.00 0.00 3.02
5584 5775 5.914033 TCTGTCCCGAATTAGTTATCTTGG 58.086 41.667 0.00 0.00 0.00 3.61
5585 5776 5.659525 TCTGTCCCGAATTAGTTATCTTGGA 59.340 40.000 0.00 0.00 0.00 3.53
5586 5777 6.326583 TCTGTCCCGAATTAGTTATCTTGGAT 59.673 38.462 0.00 0.00 0.00 3.41
5587 5778 7.507956 TCTGTCCCGAATTAGTTATCTTGGATA 59.492 37.037 0.00 0.00 0.00 2.59
5588 5779 7.667557 TGTCCCGAATTAGTTATCTTGGATAG 58.332 38.462 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.042059 ACATATAACTCCACTCCCCGT 57.958 47.619 0.00 0.00 0.00 5.28
38 39 4.069304 TGGGAGTTCACATTTCTAAACCG 58.931 43.478 0.00 0.00 0.00 4.44
52 53 0.910088 AGGCAGGTAGGTGGGAGTTC 60.910 60.000 0.00 0.00 0.00 3.01
53 54 1.161113 AGGCAGGTAGGTGGGAGTT 59.839 57.895 0.00 0.00 0.00 3.01
68 69 3.834489 TCTTCATCTCTCCATTCAGGC 57.166 47.619 0.00 0.00 37.29 4.85
96 97 9.880157 GTTAGGTAGGAGTGTACATTTTGAATA 57.120 33.333 0.00 0.00 0.00 1.75
115 116 1.702957 ACCTTTGCAGGCAGTTAGGTA 59.297 47.619 17.61 0.00 45.56 3.08
156 157 3.581755 TCGTCTTTACACACATGTAGGC 58.418 45.455 0.00 0.00 42.29 3.93
162 163 7.754027 GTGTAGTATCTTCGTCTTTACACACAT 59.246 37.037 6.92 0.00 39.25 3.21
163 164 7.040892 AGTGTAGTATCTTCGTCTTTACACACA 60.041 37.037 12.61 0.00 40.91 3.72
165 166 7.173735 TGAGTGTAGTATCTTCGTCTTTACACA 59.826 37.037 12.61 0.00 40.91 3.72
166 167 7.524912 TGAGTGTAGTATCTTCGTCTTTACAC 58.475 38.462 4.24 4.24 39.56 2.90
167 168 7.677454 TGAGTGTAGTATCTTCGTCTTTACA 57.323 36.000 0.00 0.00 0.00 2.41
186 187 3.561310 CCCCAATATCGTGACATTGAGTG 59.439 47.826 2.53 0.00 34.69 3.51
189 190 4.080582 ACTTCCCCAATATCGTGACATTGA 60.081 41.667 2.53 0.00 34.69 2.57
191 192 4.503714 ACTTCCCCAATATCGTGACATT 57.496 40.909 0.00 0.00 0.00 2.71
192 193 4.503714 AACTTCCCCAATATCGTGACAT 57.496 40.909 0.00 0.00 0.00 3.06
193 194 3.992943 AACTTCCCCAATATCGTGACA 57.007 42.857 0.00 0.00 0.00 3.58
194 195 4.124970 GGTAACTTCCCCAATATCGTGAC 58.875 47.826 0.00 0.00 0.00 3.67
229 232 0.600782 TTCTCGCAACGTGGGGTAAC 60.601 55.000 6.91 0.00 0.00 2.50
236 239 2.679355 TGGATTTTTCTCGCAACGTG 57.321 45.000 0.00 0.00 0.00 4.49
237 240 3.915437 ATTGGATTTTTCTCGCAACGT 57.085 38.095 0.00 0.00 0.00 3.99
238 241 5.390613 AGTTATTGGATTTTTCTCGCAACG 58.609 37.500 0.00 0.00 0.00 4.10
239 242 8.398665 AGATAGTTATTGGATTTTTCTCGCAAC 58.601 33.333 0.00 0.00 0.00 4.17
240 243 8.506168 AGATAGTTATTGGATTTTTCTCGCAA 57.494 30.769 0.00 0.00 0.00 4.85
241 244 9.778741 ATAGATAGTTATTGGATTTTTCTCGCA 57.221 29.630 0.00 0.00 0.00 5.10
341 345 6.276832 AGTATTTTGCAGCTTGATTGTCAT 57.723 33.333 0.00 0.00 0.00 3.06
345 349 6.698766 GGGATTAGTATTTTGCAGCTTGATTG 59.301 38.462 0.00 0.00 0.00 2.67
372 376 3.126171 CGTCGGCACTTATTTTGGATCAA 59.874 43.478 0.00 0.00 0.00 2.57
373 377 2.675844 CGTCGGCACTTATTTTGGATCA 59.324 45.455 0.00 0.00 0.00 2.92
426 432 6.195600 ACCAATGAACCCGGTATATACATT 57.804 37.500 14.70 3.39 0.00 2.71
432 438 3.010361 ACCAAACCAATGAACCCGGTATA 59.990 43.478 0.00 0.00 31.12 1.47
462 472 2.029369 TGGTGGTTACGTCGGTGC 59.971 61.111 0.00 0.00 0.00 5.01
487 497 1.102222 TTGCGGTTTTTACTGCCCGT 61.102 50.000 6.64 0.00 42.36 5.28
512 522 1.209640 GAGAGACGTGACGGTGGAC 59.790 63.158 10.66 0.00 0.00 4.02
514 524 1.380524 ATAGAGAGACGTGACGGTGG 58.619 55.000 10.66 0.00 0.00 4.61
578 588 7.015877 ACTCCTACCATCTAGAGAGTAGTAGTG 59.984 44.444 20.39 13.71 32.68 2.74
595 605 9.822727 TGTGATGATTCTTATATACTCCTACCA 57.177 33.333 0.00 0.00 0.00 3.25
651 667 5.874093 TCTTCTCTTCTCTCCAATTTTGCT 58.126 37.500 0.00 0.00 0.00 3.91
682 703 1.275573 ACACCGTCCTAGCCTTTTCTC 59.724 52.381 0.00 0.00 0.00 2.87
734 755 1.796459 CGGGGTACAAACAAACTCGAG 59.204 52.381 11.84 11.84 0.00 4.04
1170 1204 0.912486 GCTAGCTTGGAAGGAAGGGA 59.088 55.000 7.70 0.00 0.00 4.20
1171 1205 0.106967 GGCTAGCTTGGAAGGAAGGG 60.107 60.000 15.72 0.00 0.00 3.95
1172 1206 0.106967 GGGCTAGCTTGGAAGGAAGG 60.107 60.000 15.72 0.00 0.00 3.46
1173 1207 0.462759 CGGGCTAGCTTGGAAGGAAG 60.463 60.000 15.72 0.00 0.00 3.46
1174 1208 1.602237 CGGGCTAGCTTGGAAGGAA 59.398 57.895 15.72 0.00 0.00 3.36
1307 1341 4.891727 CCGGGCGATCTTGGGTCG 62.892 72.222 0.00 0.00 41.77 4.79
1323 1357 2.354821 GCAAAGAACATCGTGGATACCC 59.645 50.000 0.00 0.00 0.00 3.69
1356 1390 3.057315 CCAAGAAAGATGGCAATTCACGT 60.057 43.478 11.84 0.00 0.00 4.49
1402 1436 4.935808 CCGTCTAGCAAAAGGAACATAACT 59.064 41.667 0.00 0.00 0.00 2.24
1406 1440 2.304761 TCCCGTCTAGCAAAAGGAACAT 59.695 45.455 0.00 0.00 0.00 2.71
1414 1448 1.631388 TCCCAATTCCCGTCTAGCAAA 59.369 47.619 0.00 0.00 0.00 3.68
1420 1454 2.987125 CCGTCCCAATTCCCGTCT 59.013 61.111 0.00 0.00 0.00 4.18
1475 1509 2.226330 TCAAATGGGTTGTCTTCACCG 58.774 47.619 0.00 0.00 38.47 4.94
1570 1608 0.171007 CGTGATTCATGTTGCCACCC 59.829 55.000 0.00 0.00 0.00 4.61
1611 1649 2.091665 CCCCATGAGCCAGGTAAAATCT 60.092 50.000 0.00 0.00 0.00 2.40
1624 1662 2.130193 TCAGGAAATCCTCCCCATGAG 58.870 52.381 0.00 0.00 46.65 2.90
1641 1679 7.448161 TGTTGGGCAATAACATATTCCTATCAG 59.552 37.037 0.00 0.00 33.43 2.90
1702 1740 3.513515 AGAGATGTTGAGGTCTTCAGGAC 59.486 47.826 0.00 0.00 43.79 3.85
1743 1785 7.275183 TGTAATCTGGACATCTGTTATTGGAG 58.725 38.462 0.00 0.00 0.00 3.86
1798 1841 5.016173 AGCAAGCATTCACCCTTTACATAA 58.984 37.500 0.00 0.00 0.00 1.90
1815 1858 1.610522 ACAGGTTGACATTGAGCAAGC 59.389 47.619 14.02 14.02 41.43 4.01
1823 1866 9.515226 AATACATAGTTGTTACAGGTTGACATT 57.485 29.630 0.00 0.00 37.28 2.71
1824 1867 9.515226 AAATACATAGTTGTTACAGGTTGACAT 57.485 29.630 0.00 0.00 37.28 3.06
1825 1868 8.911918 AAATACATAGTTGTTACAGGTTGACA 57.088 30.769 0.00 0.00 37.28 3.58
1829 1872 9.362539 CGTCTAAATACATAGTTGTTACAGGTT 57.637 33.333 0.00 0.00 37.28 3.50
1830 1873 8.526147 ACGTCTAAATACATAGTTGTTACAGGT 58.474 33.333 0.00 0.00 37.28 4.00
1831 1874 8.804743 CACGTCTAAATACATAGTTGTTACAGG 58.195 37.037 0.00 0.00 37.28 4.00
1832 1875 8.804743 CCACGTCTAAATACATAGTTGTTACAG 58.195 37.037 0.00 0.00 37.28 2.74
1833 1876 7.760794 CCCACGTCTAAATACATAGTTGTTACA 59.239 37.037 0.00 0.00 37.28 2.41
1834 1877 7.761249 ACCCACGTCTAAATACATAGTTGTTAC 59.239 37.037 0.00 0.00 37.28 2.50
1835 1878 7.839907 ACCCACGTCTAAATACATAGTTGTTA 58.160 34.615 0.00 0.00 37.28 2.41
1836 1879 6.704310 ACCCACGTCTAAATACATAGTTGTT 58.296 36.000 0.00 0.00 37.28 2.83
1837 1880 6.290294 ACCCACGTCTAAATACATAGTTGT 57.710 37.500 0.00 0.00 39.98 3.32
1838 1881 6.698766 GGTACCCACGTCTAAATACATAGTTG 59.301 42.308 0.00 0.00 0.00 3.16
1839 1882 6.608808 AGGTACCCACGTCTAAATACATAGTT 59.391 38.462 8.74 0.00 0.00 2.24
1840 1883 6.040166 CAGGTACCCACGTCTAAATACATAGT 59.960 42.308 8.74 0.00 0.00 2.12
1841 1884 6.444633 CAGGTACCCACGTCTAAATACATAG 58.555 44.000 8.74 0.00 0.00 2.23
1842 1885 5.221303 GCAGGTACCCACGTCTAAATACATA 60.221 44.000 8.74 0.00 0.00 2.29
1991 2064 7.220300 GGACATAATACATTAAGATCCTACGCG 59.780 40.741 3.53 3.53 0.00 6.01
2029 2104 6.552008 AGGGTGTTCCAAATTGAAGATAGAA 58.448 36.000 0.00 0.00 38.24 2.10
2038 2113 3.831911 ACCACATAGGGTGTTCCAAATTG 59.168 43.478 0.00 0.00 46.44 2.32
2040 2115 3.825908 ACCACATAGGGTGTTCCAAAT 57.174 42.857 0.00 0.00 46.44 2.32
2085 2160 2.549754 CAAGGATAATTAGCTGGTGCGG 59.450 50.000 0.00 0.00 45.42 5.69
2087 2162 2.887152 CCCAAGGATAATTAGCTGGTGC 59.113 50.000 0.00 0.00 40.05 5.01
2094 2169 2.568623 AGCGCCCCAAGGATAATTAG 57.431 50.000 2.29 0.00 33.47 1.73
2285 2360 6.466038 TGGTAACTAATAACCAAACTCTGGCA 60.466 38.462 0.00 0.00 42.74 4.92
2320 2396 2.362077 ACAAAGCAAGGTCAGCGAAAAT 59.638 40.909 0.00 0.00 37.01 1.82
2513 2591 6.299805 TGCTCACAGATATTACAAGAGGTT 57.700 37.500 0.00 0.00 0.00 3.50
2531 2609 6.546772 TGATAATTATTGATGCCAGTTGCTCA 59.453 34.615 0.00 0.00 42.00 4.26
2564 2642 7.717875 TGCCTTGTTAGTTACTGTTAACAGAAT 59.282 33.333 36.14 20.52 46.59 2.40
2565 2643 7.049133 TGCCTTGTTAGTTACTGTTAACAGAA 58.951 34.615 36.14 23.58 46.59 3.02
2572 2650 8.807948 ATAATCATGCCTTGTTAGTTACTGTT 57.192 30.769 0.00 0.00 0.00 3.16
2599 2677 4.398319 ACTTGAATCACTACAGGGGTTTG 58.602 43.478 0.00 0.00 0.00 2.93
2616 2694 7.227711 TCAAAACGAATTAAGACCATGACTTGA 59.772 33.333 12.91 7.24 0.00 3.02
2618 2696 7.012894 TGTCAAAACGAATTAAGACCATGACTT 59.987 33.333 0.00 2.24 35.64 3.01
2674 2754 9.915629 GTAGAGAAAACAGAATTAGACTTCAGA 57.084 33.333 0.00 0.00 0.00 3.27
2735 2815 2.237143 CTGCAGGTATTCCAGGAGTTGA 59.763 50.000 5.57 0.00 34.84 3.18
2803 2883 7.337942 CAGTTCCCTTTCTGAAAGTAATAGCAT 59.662 37.037 24.18 4.56 36.77 3.79
2806 2886 6.655003 TGCAGTTCCCTTTCTGAAAGTAATAG 59.345 38.462 24.18 15.70 36.77 1.73
2839 2919 3.774842 TGGGAAAAGGGGCATTTATCT 57.225 42.857 0.00 0.00 0.00 1.98
2851 2931 1.937546 GCTGCGGTCCATGGGAAAAG 61.938 60.000 13.02 5.03 31.38 2.27
3048 3128 1.067354 CAGCTGTCCTGGCAAAATTCC 60.067 52.381 5.25 0.00 37.93 3.01
3088 3168 1.342074 TCACTGCACTGGAAGCTAGT 58.658 50.000 0.00 0.00 37.60 2.57
3130 3210 1.967762 CTGGCATGCTGTTTTGTACG 58.032 50.000 18.92 0.00 0.00 3.67
3153 3233 8.746052 TGAAGAGGTTCTGAAACTTTTATTCA 57.254 30.769 9.69 13.73 35.61 2.57
3154 3234 8.293157 CCTGAAGAGGTTCTGAAACTTTTATTC 58.707 37.037 9.69 11.63 34.37 1.75
3164 3244 1.273606 CTCGCCTGAAGAGGTTCTGAA 59.726 52.381 0.00 0.00 42.15 3.02
3259 3339 2.919772 TGTCATCCTGAGGAGGTGTA 57.080 50.000 13.39 0.00 40.76 2.90
3352 3432 0.323087 AAGCACCAGCATCTGCATCA 60.323 50.000 4.79 0.00 45.49 3.07
3613 3693 4.042187 TCTGATCCATCTATCTCGACAGGA 59.958 45.833 0.00 0.00 0.00 3.86
3619 3699 6.847400 ACGTAAATCTGATCCATCTATCTCG 58.153 40.000 0.00 0.00 0.00 4.04
3691 3771 1.581954 CGACTCTCCACTGCGTTCT 59.418 57.895 0.00 0.00 0.00 3.01
3796 3876 0.460987 CTTGCAGACGGGAGCTTAGG 60.461 60.000 0.00 0.00 0.00 2.69
3910 3990 4.074970 CCTGAATATCCATAGGCACAACC 58.925 47.826 0.00 0.00 39.61 3.77
3914 3994 3.560025 CCACCCTGAATATCCATAGGCAC 60.560 52.174 0.00 0.00 0.00 5.01
3974 4054 0.459237 CGTTCGCTTGATCTCTGCCT 60.459 55.000 0.00 0.00 0.00 4.75
3991 4071 1.893808 CCTGGCACTTGAAGCACGT 60.894 57.895 0.00 0.00 0.00 4.49
4035 4115 7.116948 CGAAGTTGAGTGAATCTGTTACATTCT 59.883 37.037 1.25 0.00 32.32 2.40
4091 4171 0.673644 ACACTTCCATTCGCCTTCCG 60.674 55.000 0.00 0.00 38.61 4.30
4156 4236 3.852536 GTCGTTTCCTCTGTAAGATGACG 59.147 47.826 0.00 0.00 45.62 4.35
4187 4267 4.454319 GCCATTGCCATTGCCGCA 62.454 61.111 0.00 0.00 36.33 5.69
4222 4302 4.095483 ACCGCAGCAGATTTATCTTCTTTG 59.905 41.667 0.00 0.00 34.22 2.77
4294 4374 6.405278 TCTTCAGAACTGATAGTGTTGTCA 57.595 37.500 5.34 0.00 39.64 3.58
4320 4400 4.662468 TCATCACCTGATCTACTCTTGC 57.338 45.455 0.00 0.00 31.21 4.01
4381 4461 1.571460 CTCAGCTTTGTCACCGTGC 59.429 57.895 0.00 0.00 0.00 5.34
4465 4545 0.030908 CTTCGGTCGCCTCATACTCC 59.969 60.000 0.00 0.00 0.00 3.85
4480 4560 3.736252 CGGATTTGTACTCATAGCCTTCG 59.264 47.826 0.00 0.00 30.86 3.79
4489 4569 5.914898 TCTCATCTTCGGATTTGTACTCA 57.085 39.130 0.00 0.00 31.35 3.41
4591 4671 3.552684 CGCCAAGAAAATCAAAGCCAGAA 60.553 43.478 0.00 0.00 0.00 3.02
4599 4679 3.317711 TGAAGAAGCGCCAAGAAAATCAA 59.682 39.130 2.29 0.00 0.00 2.57
4602 4682 2.229784 CCTGAAGAAGCGCCAAGAAAAT 59.770 45.455 2.29 0.00 0.00 1.82
4699 4780 2.225491 GGCGCTATCAACTTGAAACACA 59.775 45.455 7.64 0.00 0.00 3.72
4700 4781 2.225491 TGGCGCTATCAACTTGAAACAC 59.775 45.455 7.64 0.00 0.00 3.32
4770 4851 3.324846 TCGCTCAATGCCTGACCTATATT 59.675 43.478 0.00 0.00 38.78 1.28
4888 4975 8.784043 GGGTATCATCATGTTAGTAATCAAACC 58.216 37.037 0.00 0.00 0.00 3.27
4893 4980 8.950210 CAATGGGGTATCATCATGTTAGTAATC 58.050 37.037 0.00 0.00 0.00 1.75
4976 5070 6.699575 TTTCTTCTGTGAAGGAAAGGAAAG 57.300 37.500 7.37 0.00 0.00 2.62
5014 5108 2.425143 TCCAGGCAAATGGAGCTTAG 57.575 50.000 0.70 0.00 44.56 2.18
5071 5166 7.588854 CACACTGTCACAAATAAACTCATGAAG 59.411 37.037 0.00 0.00 0.00 3.02
5077 5172 4.819630 TCCCACACTGTCACAAATAAACTC 59.180 41.667 0.00 0.00 0.00 3.01
5082 5177 4.262721 GGTACTCCCACACTGTCACAAATA 60.263 45.833 0.00 0.00 0.00 1.40
5101 5196 4.093998 CACAGAAACATGATCAGCAGGTAC 59.906 45.833 0.00 0.00 41.31 3.34
5126 5221 6.804295 GGTACTTATTCAGATAGATGTGCTCG 59.196 42.308 0.00 0.00 0.00 5.03
5158 5253 8.489489 AGATCCAGTTATAAGCTCAAAGAATGA 58.511 33.333 0.00 0.00 36.38 2.57
5259 5357 7.556844 TCAGGAATTATACTCAGTTGACTTCC 58.443 38.462 0.00 0.00 0.00 3.46
5261 5359 8.986991 AGATCAGGAATTATACTCAGTTGACTT 58.013 33.333 0.00 0.00 0.00 3.01
5276 5374 2.357009 GCATCGCACAAGATCAGGAATT 59.643 45.455 0.00 0.00 0.00 2.17
5424 5615 4.697352 GTGGCAAGCAAGATCGGATTATAT 59.303 41.667 0.00 0.00 0.00 0.86
5435 5626 1.159285 CAATCTCGTGGCAAGCAAGA 58.841 50.000 0.00 0.00 0.00 3.02
5438 5629 2.076100 CTAACAATCTCGTGGCAAGCA 58.924 47.619 0.00 0.00 0.00 3.91
5468 5659 2.223294 GCATGTGAGCTCTTGAGATTGC 60.223 50.000 16.19 10.30 0.00 3.56
5541 5732 9.902684 GGACAGAGGTAGTATATTATACTGCTA 57.097 37.037 22.97 6.37 32.04 3.49
5542 5733 7.835181 GGGACAGAGGTAGTATATTATACTGCT 59.165 40.741 22.97 13.75 32.04 4.24


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

AutoCloner maintained by Alex Coulton.