Multiple sequence alignment - TraesCS5B01G282500

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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 TraesCS5B01G282500 chr5B 100.000 2786 0 0 1 2786 467228827 467226042 0.000000e+00 5145.0
1 TraesCS5B01G282500 chr5B 84.298 121 14 1 2334 2449 700370255 700370375 2.270000e-21 113.0
2 TraesCS5B01G282500 chr5B 97.674 43 1 0 2744 2786 467178347 467178305 1.070000e-09 75.0
3 TraesCS5B01G282500 chr5D 92.295 1207 49 19 781 1970 388831393 388830214 0.000000e+00 1674.0
4 TraesCS5B01G282500 chr5D 90.173 692 35 12 1 686 388832118 388831454 0.000000e+00 870.0
5 TraesCS5B01G282500 chr5D 88.950 181 12 2 1981 2157 388830128 388829952 1.680000e-52 217.0
6 TraesCS5B01G282500 chr5D 82.946 129 20 2 2454 2582 443502005 443501879 6.310000e-22 115.0
7 TraesCS5B01G282500 chr5D 94.000 50 1 2 2739 2786 388829611 388829562 1.070000e-09 75.0
8 TraesCS5B01G282500 chr5A 89.713 1254 69 28 747 1969 491949822 491948598 0.000000e+00 1546.0
9 TraesCS5B01G282500 chr5A 83.924 734 70 20 2077 2784 491948451 491947740 0.000000e+00 658.0
10 TraesCS5B01G282500 chr6A 92.466 146 10 1 129 273 609034187 609034332 1.010000e-49 207.0
11 TraesCS5B01G282500 chr6A 89.423 104 10 1 2454 2556 452304460 452304357 2.250000e-26 130.0
12 TraesCS5B01G282500 chr7D 87.742 155 17 2 113 265 575360437 575360591 2.200000e-41 180.0
13 TraesCS5B01G282500 chr3A 90.909 110 10 0 153 262 586084416 586084307 6.220000e-32 148.0
14 TraesCS5B01G282500 chr1A 83.893 149 19 5 133 277 20921936 20921789 1.350000e-28 137.0
15 TraesCS5B01G282500 chr6D 89.423 104 10 1 2454 2556 315366014 315365911 2.250000e-26 130.0
16 TraesCS5B01G282500 chr6D 81.818 121 15 3 2331 2445 315652575 315652694 8.210000e-16 95.3
17 TraesCS5B01G282500 chr4D 83.088 136 20 3 2454 2589 374625225 374625093 1.360000e-23 121.0
18 TraesCS5B01G282500 chr7B 83.333 132 19 1 130 261 453629764 453629636 4.870000e-23 119.0
19 TraesCS5B01G282500 chr7B 82.203 118 15 2 2334 2445 535500158 535500041 2.280000e-16 97.1
20 TraesCS5B01G282500 chr3D 87.379 103 13 0 2454 2556 13175169 13175067 4.870000e-23 119.0
21 TraesCS5B01G282500 chr1D 88.660 97 11 0 129 225 339966611 339966707 4.870000e-23 119.0
22 TraesCS5B01G282500 chr1D 81.818 121 15 3 2331 2445 440714937 440714818 8.210000e-16 95.3
23 TraesCS5B01G282500 chr2A 84.746 118 17 1 2465 2582 720375395 720375511 1.750000e-22 117.0
24 TraesCS5B01G282500 chr6B 83.898 118 13 2 2334 2445 127601078 127601195 1.060000e-19 108.0
25 TraesCS5B01G282500 chr3B 81.679 131 21 3 2454 2582 673299839 673299710 3.800000e-19 106.0
26 TraesCS5B01G282500 chr3B 83.051 118 14 2 2334 2445 809037054 809036937 4.910000e-18 102.0
27 TraesCS5B01G282500 chr2B 81.538 130 21 3 2454 2582 458340034 458340161 1.360000e-18 104.0
28 TraesCS5B01G282500 chr2B 83.051 118 14 2 2334 2445 40324332 40324215 4.910000e-18 102.0
29 TraesCS5B01G282500 chr1B 83.051 118 14 2 2334 2445 622939143 622939260 4.910000e-18 102.0


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 TraesCS5B01G282500 chr5B 467226042 467228827 2785 True 5145 5145 100.0000 1 2786 1 chr5B.!!$R2 2785
1 TraesCS5B01G282500 chr5D 388829562 388832118 2556 True 709 1674 91.3545 1 2786 4 chr5D.!!$R2 2785
2 TraesCS5B01G282500 chr5A 491947740 491949822 2082 True 1102 1546 86.8185 747 2784 2 chr5A.!!$R1 2037

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
253 254 0.038892 GGCACACAACCATGCTCTTG 60.039 55.0 0.00 0.00 41.74 3.02 F
481 483 0.109342 AGTGGGTGGAGCAAGTCTTG 59.891 55.0 8.31 8.31 0.00 3.02 F
778 790 0.316841 TGCGCGGATATCTATGCACA 59.683 50.0 8.83 2.65 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1657 0.390492 CTACCGATCCTGCTGCATCA 59.610 55.0 1.31 0.0 0.0 3.07 R
1612 1658 0.676184 TCTACCGATCCTGCTGCATC 59.324 55.0 1.31 0.0 0.0 3.91 R
2534 2769 0.310854 GTGGAGGTTTGTCTTTGGCG 59.689 55.0 0.00 0.0 0.0 5.69 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
163 164 6.488683 CCCGTGGCATTATAATTAAGAAGGAA 59.511 38.462 0.00 0.00 0.00 3.36
190 191 5.888724 TGTGAGACACCAAGTTTTAAATCCA 59.111 36.000 0.00 0.00 32.73 3.41
253 254 0.038892 GGCACACAACCATGCTCTTG 60.039 55.000 0.00 0.00 41.74 3.02
256 257 0.467844 ACACAACCATGCTCTTGCCA 60.468 50.000 0.00 0.00 38.71 4.92
283 285 5.246307 GCTAGGTTCCCATCCACAATATAC 58.754 45.833 0.00 0.00 0.00 1.47
293 295 6.000219 CCATCCACAATATACTTTCTGGAGG 59.000 44.000 0.00 0.00 31.40 4.30
295 297 6.485830 TCCACAATATACTTTCTGGAGGAG 57.514 41.667 0.00 0.00 0.00 3.69
296 298 5.366768 TCCACAATATACTTTCTGGAGGAGG 59.633 44.000 0.00 0.00 0.00 4.30
297 299 5.366768 CCACAATATACTTTCTGGAGGAGGA 59.633 44.000 0.00 0.00 0.00 3.71
298 300 6.463614 CCACAATATACTTTCTGGAGGAGGAG 60.464 46.154 0.00 0.00 0.00 3.69
299 301 6.325028 CACAATATACTTTCTGGAGGAGGAGA 59.675 42.308 0.00 0.00 0.00 3.71
301 303 2.246091 ACTTTCTGGAGGAGGAGAGG 57.754 55.000 0.00 0.00 0.00 3.69
302 304 1.273552 ACTTTCTGGAGGAGGAGAGGG 60.274 57.143 0.00 0.00 0.00 4.30
303 305 0.618968 TTTCTGGAGGAGGAGAGGGC 60.619 60.000 0.00 0.00 0.00 5.19
304 306 2.837291 CTGGAGGAGGAGAGGGCG 60.837 72.222 0.00 0.00 0.00 6.13
309 311 2.185310 GAGGAGGAGAGGGCGCAAAA 62.185 60.000 10.83 0.00 0.00 2.44
310 312 1.077429 GGAGGAGAGGGCGCAAAAT 60.077 57.895 10.83 0.00 0.00 1.82
311 313 0.180406 GGAGGAGAGGGCGCAAAATA 59.820 55.000 10.83 0.00 0.00 1.40
312 314 1.408266 GGAGGAGAGGGCGCAAAATAA 60.408 52.381 10.83 0.00 0.00 1.40
313 315 2.365582 GAGGAGAGGGCGCAAAATAAA 58.634 47.619 10.83 0.00 0.00 1.40
314 316 2.952310 GAGGAGAGGGCGCAAAATAAAT 59.048 45.455 10.83 0.00 0.00 1.40
315 317 3.365472 AGGAGAGGGCGCAAAATAAATT 58.635 40.909 10.83 0.00 0.00 1.82
316 318 3.381590 AGGAGAGGGCGCAAAATAAATTC 59.618 43.478 10.83 0.00 0.00 2.17
317 319 3.130340 GGAGAGGGCGCAAAATAAATTCA 59.870 43.478 10.83 0.00 0.00 2.57
318 320 4.381505 GGAGAGGGCGCAAAATAAATTCAA 60.382 41.667 10.83 0.00 0.00 2.69
319 321 4.747810 AGAGGGCGCAAAATAAATTCAAG 58.252 39.130 10.83 0.00 0.00 3.02
320 322 4.462483 AGAGGGCGCAAAATAAATTCAAGA 59.538 37.500 10.83 0.00 0.00 3.02
321 323 4.747810 AGGGCGCAAAATAAATTCAAGAG 58.252 39.130 10.83 0.00 0.00 2.85
322 324 4.220602 AGGGCGCAAAATAAATTCAAGAGT 59.779 37.500 10.83 0.00 0.00 3.24
323 325 4.327087 GGGCGCAAAATAAATTCAAGAGTG 59.673 41.667 10.83 0.00 0.00 3.51
324 326 4.923281 GGCGCAAAATAAATTCAAGAGTGT 59.077 37.500 10.83 0.00 0.00 3.55
325 327 5.405269 GGCGCAAAATAAATTCAAGAGTGTT 59.595 36.000 10.83 0.00 0.00 3.32
326 328 6.399986 GGCGCAAAATAAATTCAAGAGTGTTC 60.400 38.462 10.83 0.00 0.00 3.18
327 329 6.363357 GCGCAAAATAAATTCAAGAGTGTTCT 59.637 34.615 0.30 0.00 34.29 3.01
328 330 7.096065 GCGCAAAATAAATTCAAGAGTGTTCTT 60.096 33.333 0.30 0.00 44.45 2.52
366 368 5.982516 GTCACCAACAACATAAAGATGCAAA 59.017 36.000 0.00 0.00 36.43 3.68
393 395 9.450807 CAGATCTTAAATTTCACTTTGTTTCGT 57.549 29.630 0.00 0.00 0.00 3.85
435 437 8.819974 CAAACATGAAACTAATGTGAAAAAGCT 58.180 29.630 0.00 0.00 38.27 3.74
446 448 1.133915 TGAAAAAGCTTCGGAGGGTGT 60.134 47.619 0.00 0.00 0.00 4.16
457 459 4.801330 TCGGAGGGTGTAGCATATTATG 57.199 45.455 0.00 0.00 0.00 1.90
481 483 0.109342 AGTGGGTGGAGCAAGTCTTG 59.891 55.000 8.31 8.31 0.00 3.02
497 499 2.746362 GTCTTGGTGAAATCTCTGCCAG 59.254 50.000 0.00 0.00 31.93 4.85
521 523 1.633774 ACACTGTGTGGAGTCCCTAG 58.366 55.000 13.50 2.26 37.94 3.02
532 534 5.221581 TGTGGAGTCCCTAGAAAAAGTACAC 60.222 44.000 6.74 0.00 0.00 2.90
547 549 7.730364 AAAAGTACACTGTGTGGAGAATAAG 57.270 36.000 22.97 0.00 37.94 1.73
558 560 3.135530 GTGGAGAATAAGGACTGGCTGAT 59.864 47.826 0.00 0.00 0.00 2.90
559 561 3.135348 TGGAGAATAAGGACTGGCTGATG 59.865 47.826 0.00 0.00 0.00 3.07
560 562 3.495806 GGAGAATAAGGACTGGCTGATGG 60.496 52.174 0.00 0.00 0.00 3.51
663 672 3.557908 GCAATGCACGTGAAATATTGC 57.442 42.857 27.73 27.73 44.33 3.56
680 690 2.513204 CGAGCCCAGGACTGCATG 60.513 66.667 0.00 0.00 0.00 4.06
690 700 4.796038 CAGGACTGCATGGATTCTTTTT 57.204 40.909 4.61 0.00 0.00 1.94
691 701 4.741342 CAGGACTGCATGGATTCTTTTTC 58.259 43.478 4.61 0.00 0.00 2.29
692 702 4.461781 CAGGACTGCATGGATTCTTTTTCT 59.538 41.667 4.61 0.00 0.00 2.52
693 703 5.047519 CAGGACTGCATGGATTCTTTTTCTT 60.048 40.000 4.61 0.00 0.00 2.52
694 704 5.541484 AGGACTGCATGGATTCTTTTTCTTT 59.459 36.000 4.61 0.00 0.00 2.52
695 705 6.042437 AGGACTGCATGGATTCTTTTTCTTTT 59.958 34.615 4.61 0.00 0.00 2.27
696 706 6.367149 GGACTGCATGGATTCTTTTTCTTTTC 59.633 38.462 4.61 0.00 0.00 2.29
697 707 7.059202 ACTGCATGGATTCTTTTTCTTTTCT 57.941 32.000 0.00 0.00 0.00 2.52
698 708 7.503549 ACTGCATGGATTCTTTTTCTTTTCTT 58.496 30.769 0.00 0.00 0.00 2.52
699 709 7.989170 ACTGCATGGATTCTTTTTCTTTTCTTT 59.011 29.630 0.00 0.00 0.00 2.52
701 711 9.176460 TGCATGGATTCTTTTTCTTTTCTTTTT 57.824 25.926 0.00 0.00 0.00 1.94
731 743 2.029838 AGGACTGCATGGATTCGAAC 57.970 50.000 0.00 0.00 0.00 3.95
738 750 2.091541 GCATGGATTCGAACCTCCAAA 58.908 47.619 21.19 2.95 44.41 3.28
740 752 3.131046 GCATGGATTCGAACCTCCAAAAT 59.869 43.478 21.19 5.73 44.41 1.82
741 753 4.381932 GCATGGATTCGAACCTCCAAAATT 60.382 41.667 21.19 5.41 44.41 1.82
742 754 4.782019 TGGATTCGAACCTCCAAAATTG 57.218 40.909 16.38 0.00 38.59 2.32
743 755 4.402829 TGGATTCGAACCTCCAAAATTGA 58.597 39.130 16.38 0.00 38.59 2.57
744 756 5.016173 TGGATTCGAACCTCCAAAATTGAT 58.984 37.500 16.38 0.00 38.59 2.57
745 757 5.125417 TGGATTCGAACCTCCAAAATTGATC 59.875 40.000 16.38 0.00 38.59 2.92
756 768 3.448301 CCAAAATTGATCAAGGGCTGCTA 59.552 43.478 14.54 0.00 0.00 3.49
758 770 3.659183 AATTGATCAAGGGCTGCTACT 57.341 42.857 14.54 0.00 0.00 2.57
762 774 0.745845 ATCAAGGGCTGCTACTTGCG 60.746 55.000 23.23 9.37 46.63 4.85
767 779 2.892425 GCTGCTACTTGCGCGGAT 60.892 61.111 8.83 0.00 46.63 4.18
771 783 0.673985 TGCTACTTGCGCGGATATCT 59.326 50.000 8.83 0.00 46.63 1.98
772 784 1.883926 TGCTACTTGCGCGGATATCTA 59.116 47.619 8.83 0.00 46.63 1.98
777 789 1.391485 CTTGCGCGGATATCTATGCAC 59.609 52.381 8.83 6.16 31.16 4.57
778 790 0.316841 TGCGCGGATATCTATGCACA 59.683 50.000 8.83 2.65 0.00 4.57
779 791 0.716108 GCGCGGATATCTATGCACAC 59.284 55.000 8.83 0.00 0.00 3.82
888 905 8.545420 TCGTTCAAAATATAAATCCTCTTACGC 58.455 33.333 0.00 0.00 0.00 4.42
911 928 0.342313 CCCCTCTACCAACCCCTACT 59.658 60.000 0.00 0.00 0.00 2.57
953 973 2.837883 GCCCCTGCATGCATACGTG 61.838 63.158 22.97 9.00 37.47 4.49
1308 1338 2.362369 CGAGATCCCCACCAGCTGT 61.362 63.158 13.81 0.00 0.00 4.40
1386 1422 3.501828 CCTCTCATGATCGATCGAACTCT 59.498 47.826 23.50 5.07 0.00 3.24
1463 1503 1.102809 TTGCAGTGCAAGGAGTGGTG 61.103 55.000 26.36 0.00 43.99 4.17
1544 1590 2.199291 CCGGTATGTACTGGTCGTTC 57.801 55.000 9.45 0.00 45.63 3.95
1586 1632 2.349297 ACTTTCGGTCGATGTCTGAC 57.651 50.000 0.00 0.00 35.60 3.51
1611 1657 8.682936 CCAGAGCTTTGGTTTGACTATATTAT 57.317 34.615 15.18 0.00 33.38 1.28
1612 1658 8.562892 CCAGAGCTTTGGTTTGACTATATTATG 58.437 37.037 15.18 0.00 33.38 1.90
1755 1801 1.444553 CCTCGTGCTCTTCACCGTC 60.445 63.158 0.00 0.00 42.69 4.79
1792 1838 2.989639 CCGTGGCCTGAAGATGGA 59.010 61.111 3.32 0.00 0.00 3.41
1803 1849 2.494471 CTGAAGATGGAAATTGCAGCCA 59.506 45.455 0.00 2.78 35.91 4.75
1811 1857 4.279982 TGGAAATTGCAGCCATGATAAGA 58.720 39.130 0.00 0.00 0.00 2.10
1818 1864 6.997239 TTGCAGCCATGATAAGATATGATC 57.003 37.500 0.00 0.00 0.00 2.92
1839 1885 3.703556 TCTCAGGACTTGCAGATTAGGAG 59.296 47.826 0.00 0.00 0.00 3.69
1856 1902 4.348863 AGGAGTATTAGCTGCAGATTGG 57.651 45.455 20.43 0.00 0.00 3.16
1955 2010 9.140286 GGGTTTTCTCTTTGTTAATCAAATAGC 57.860 33.333 9.21 0.00 43.78 2.97
1956 2011 9.914131 GGTTTTCTCTTTGTTAATCAAATAGCT 57.086 29.630 0.00 0.00 43.78 3.32
2007 2143 9.110382 AGGAATAGATGAGTATTAGCAAATCCT 57.890 33.333 0.00 0.00 0.00 3.24
2014 2150 9.508567 GATGAGTATTAGCAAATCCTTTGTTTC 57.491 33.333 1.97 0.00 42.56 2.78
2015 2151 8.635765 TGAGTATTAGCAAATCCTTTGTTTCT 57.364 30.769 1.97 0.00 42.56 2.52
2016 2152 9.077885 TGAGTATTAGCAAATCCTTTGTTTCTT 57.922 29.630 1.97 0.00 42.56 2.52
2017 2153 9.914131 GAGTATTAGCAAATCCTTTGTTTCTTT 57.086 29.630 1.97 0.00 42.56 2.52
2074 2210 2.095919 GGTGTTTCTTGCGTGTATGACC 60.096 50.000 0.00 0.00 0.00 4.02
2116 2252 6.624423 GCCTATATCCAAGTGCATGCATTAAG 60.624 42.308 25.64 15.29 0.00 1.85
2183 2397 7.907214 AAGGTGTCAATAGAACATAGTCAAC 57.093 36.000 0.00 0.00 0.00 3.18
2202 2416 7.267857 AGTCAACGTACTTTACCCATATTACC 58.732 38.462 0.00 0.00 0.00 2.85
2214 2428 4.658901 ACCCATATTACCGAGTTTCTCCAT 59.341 41.667 0.00 0.00 0.00 3.41
2220 2434 3.601443 ACCGAGTTTCTCCATTCTCAG 57.399 47.619 0.00 0.00 0.00 3.35
2221 2435 3.165875 ACCGAGTTTCTCCATTCTCAGA 58.834 45.455 0.00 0.00 0.00 3.27
2280 2494 2.674220 GCCACTCTCCCAGGGAAGG 61.674 68.421 10.32 10.36 0.00 3.46
2297 2511 4.263018 GAAGGCAATGCTTCTTCCTTTT 57.737 40.909 4.82 0.00 37.28 2.27
2361 2596 9.626045 CCAGAAGTAAAATTTACATTCAGGTTC 57.374 33.333 17.00 10.09 0.00 3.62
2376 2611 2.932614 CAGGTTCTTTCATCACCTAGCG 59.067 50.000 0.00 0.00 39.01 4.26
2395 2630 1.406970 GACGACTACAAGCAGCGAGC 61.407 60.000 0.00 0.00 46.19 5.03
2421 2656 4.321966 TGCCGCCGTCATCAACCA 62.322 61.111 0.00 0.00 0.00 3.67
2443 2678 1.532794 ATCACCAAAGCCGGGCAAA 60.533 52.632 23.09 0.00 0.00 3.68
2444 2679 1.815817 ATCACCAAAGCCGGGCAAAC 61.816 55.000 23.09 0.00 0.00 2.93
2445 2680 3.230990 ACCAAAGCCGGGCAAACC 61.231 61.111 23.09 0.00 0.00 3.27
2446 2681 2.917227 CCAAAGCCGGGCAAACCT 60.917 61.111 23.09 0.00 36.97 3.50
2447 2682 2.506957 CCAAAGCCGGGCAAACCTT 61.507 57.895 23.09 2.81 36.97 3.50
2469 2704 4.592485 AAGTCTAGACACAGGAACACAG 57.408 45.455 24.44 0.00 0.00 3.66
2481 2716 1.257155 GGAACACAGACGAACGAACAC 59.743 52.381 0.14 0.00 0.00 3.32
2514 2749 0.953960 ATCCACCGAAGACAAACGCC 60.954 55.000 0.00 0.00 0.00 5.68
2515 2750 1.890041 CCACCGAAGACAAACGCCA 60.890 57.895 0.00 0.00 0.00 5.69
2534 2769 2.408050 CAATCGAATCCCACGAGATCC 58.592 52.381 0.00 0.00 42.81 3.36
2539 2774 1.622607 AATCCCACGAGATCCGCCAA 61.623 55.000 0.00 0.00 43.32 4.52
2553 2788 0.310854 CGCCAAAGACAAACCTCCAC 59.689 55.000 0.00 0.00 0.00 4.02
2556 2791 2.374184 CCAAAGACAAACCTCCACACA 58.626 47.619 0.00 0.00 0.00 3.72
2557 2792 2.358898 CCAAAGACAAACCTCCACACAG 59.641 50.000 0.00 0.00 0.00 3.66
2558 2793 3.016736 CAAAGACAAACCTCCACACAGT 58.983 45.455 0.00 0.00 0.00 3.55
2559 2794 2.332063 AGACAAACCTCCACACAGTG 57.668 50.000 0.00 0.00 0.00 3.66
2562 2797 1.308998 CAAACCTCCACACAGTGTCC 58.691 55.000 2.14 0.00 0.00 4.02
2563 2798 1.134098 CAAACCTCCACACAGTGTCCT 60.134 52.381 2.14 0.00 0.00 3.85
2587 2822 0.713883 CGCTAGCAAACACCTACACG 59.286 55.000 16.45 0.00 0.00 4.49
2617 2852 1.889170 AGATGACTCAACGCTCAGTGA 59.111 47.619 0.00 0.00 0.00 3.41
2628 2863 2.037251 ACGCTCAGTGAGTAATGGTTGT 59.963 45.455 21.06 5.13 31.39 3.32
2643 2878 1.754226 GGTTGTGCCACCTTCTTTTGA 59.246 47.619 0.00 0.00 37.17 2.69
2647 2882 3.499338 TGTGCCACCTTCTTTTGATCAT 58.501 40.909 0.00 0.00 0.00 2.45
2704 2971 2.579201 CGGCACTACTCCCACCAG 59.421 66.667 0.00 0.00 0.00 4.00
2731 2998 5.914898 ACCATAATGCCCTTGTCTAAAAC 57.085 39.130 0.00 0.00 0.00 2.43
2733 3000 5.777732 ACCATAATGCCCTTGTCTAAAACAA 59.222 36.000 0.00 0.00 45.60 2.83
2751 3018 3.367321 ACAATTGTGCATGATGGGATCA 58.633 40.909 11.07 0.00 44.55 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.922676 ACTGTTAAACTCGTATCATGTTTACTG 58.077 33.333 0.00 0.00 36.35 2.74
45 46 8.121086 GTGGAACTCTACAAAACTGTTAAACTC 58.879 37.037 0.00 0.00 0.00 3.01
114 115 3.641906 CTCCTCCCCGAAGCTCTAATTTA 59.358 47.826 0.00 0.00 0.00 1.40
190 191 2.495669 CTGTGGGCCGAATTTATTTGGT 59.504 45.455 9.86 0.00 42.30 3.67
283 285 1.494960 CCCTCTCCTCCTCCAGAAAG 58.505 60.000 0.00 0.00 0.00 2.62
293 295 2.038387 TTATTTTGCGCCCTCTCCTC 57.962 50.000 4.18 0.00 0.00 3.71
295 297 3.130340 TGAATTTATTTTGCGCCCTCTCC 59.870 43.478 4.18 0.00 0.00 3.71
296 298 4.370364 TGAATTTATTTTGCGCCCTCTC 57.630 40.909 4.18 0.00 0.00 3.20
297 299 4.462483 TCTTGAATTTATTTTGCGCCCTCT 59.538 37.500 4.18 0.00 0.00 3.69
298 300 4.743493 TCTTGAATTTATTTTGCGCCCTC 58.257 39.130 4.18 0.00 0.00 4.30
299 301 4.220602 ACTCTTGAATTTATTTTGCGCCCT 59.779 37.500 4.18 0.00 0.00 5.19
301 303 4.923281 ACACTCTTGAATTTATTTTGCGCC 59.077 37.500 4.18 0.00 0.00 6.53
302 304 6.363357 AGAACACTCTTGAATTTATTTTGCGC 59.637 34.615 0.00 0.00 0.00 6.09
303 305 7.858052 AGAACACTCTTGAATTTATTTTGCG 57.142 32.000 0.00 0.00 0.00 4.85
317 319 3.699538 GGGTTTTGACCAAGAACACTCTT 59.300 43.478 0.00 0.00 42.96 2.85
318 320 3.053619 AGGGTTTTGACCAAGAACACTCT 60.054 43.478 0.00 0.00 31.73 3.24
319 321 3.288092 AGGGTTTTGACCAAGAACACTC 58.712 45.455 0.00 0.00 31.73 3.51
320 322 3.288092 GAGGGTTTTGACCAAGAACACT 58.712 45.455 10.23 10.23 39.58 3.55
321 323 2.032924 CGAGGGTTTTGACCAAGAACAC 59.967 50.000 0.00 0.00 0.00 3.32
322 324 2.294074 CGAGGGTTTTGACCAAGAACA 58.706 47.619 0.00 0.00 0.00 3.18
323 325 2.289820 GACGAGGGTTTTGACCAAGAAC 59.710 50.000 0.00 0.00 0.00 3.01
324 326 2.092861 TGACGAGGGTTTTGACCAAGAA 60.093 45.455 0.00 0.00 0.00 2.52
325 327 1.487142 TGACGAGGGTTTTGACCAAGA 59.513 47.619 0.00 0.00 0.00 3.02
326 328 1.602377 GTGACGAGGGTTTTGACCAAG 59.398 52.381 0.00 0.00 0.00 3.61
327 329 1.670791 GTGACGAGGGTTTTGACCAA 58.329 50.000 0.00 0.00 0.00 3.67
328 330 0.179040 GGTGACGAGGGTTTTGACCA 60.179 55.000 0.00 0.00 0.00 4.02
329 331 0.179040 TGGTGACGAGGGTTTTGACC 60.179 55.000 0.00 0.00 0.00 4.02
366 368 9.450807 CGAAACAAAGTGAAATTTAAGATCTGT 57.549 29.630 0.00 0.00 0.00 3.41
432 434 0.978146 ATGCTACACCCTCCGAAGCT 60.978 55.000 0.00 0.00 34.28 3.74
435 437 4.020573 CCATAATATGCTACACCCTCCGAA 60.021 45.833 0.00 0.00 0.00 4.30
446 448 5.012664 CCACCCACTGTACCATAATATGCTA 59.987 44.000 0.00 0.00 0.00 3.49
457 459 0.321653 CTTGCTCCACCCACTGTACC 60.322 60.000 0.00 0.00 0.00 3.34
481 483 3.064900 ACTTCTGGCAGAGATTTCACC 57.935 47.619 17.91 0.00 0.00 4.02
497 499 2.288886 GGGACTCCACACAGTGTACTTC 60.289 54.545 5.69 0.81 0.00 3.01
521 523 6.619801 ATTCTCCACACAGTGTACTTTTTC 57.380 37.500 5.69 0.00 0.00 2.29
532 534 3.866651 CCAGTCCTTATTCTCCACACAG 58.133 50.000 0.00 0.00 0.00 3.66
547 549 1.486310 TGTCATACCATCAGCCAGTCC 59.514 52.381 0.00 0.00 0.00 3.85
630 632 9.579768 TTCACGTGCATTGCTTATTTTATTATT 57.420 25.926 11.67 0.00 0.00 1.40
631 633 9.579768 TTTCACGTGCATTGCTTATTTTATTAT 57.420 25.926 11.67 0.00 0.00 1.28
632 634 8.972262 TTTCACGTGCATTGCTTATTTTATTA 57.028 26.923 11.67 0.00 0.00 0.98
633 635 7.881643 TTTCACGTGCATTGCTTATTTTATT 57.118 28.000 11.67 0.00 0.00 1.40
647 649 1.202020 GCTCGCAATATTTCACGTGCA 60.202 47.619 11.67 0.00 42.61 4.57
648 650 1.456732 GCTCGCAATATTTCACGTGC 58.543 50.000 11.67 11.28 37.77 5.34
663 672 2.513204 CATGCAGTCCTGGGCTCG 60.513 66.667 0.00 0.00 0.00 5.03
701 711 5.136828 TCCATGCAGTCCTAGTTTCAAAAA 58.863 37.500 0.00 0.00 0.00 1.94
702 712 4.724399 TCCATGCAGTCCTAGTTTCAAAA 58.276 39.130 0.00 0.00 0.00 2.44
703 713 4.365514 TCCATGCAGTCCTAGTTTCAAA 57.634 40.909 0.00 0.00 0.00 2.69
704 714 4.574674 ATCCATGCAGTCCTAGTTTCAA 57.425 40.909 0.00 0.00 0.00 2.69
705 715 4.517285 GAATCCATGCAGTCCTAGTTTCA 58.483 43.478 0.00 0.00 0.00 2.69
707 717 3.197766 TCGAATCCATGCAGTCCTAGTTT 59.802 43.478 0.00 0.00 0.00 2.66
708 718 2.766263 TCGAATCCATGCAGTCCTAGTT 59.234 45.455 0.00 0.00 0.00 2.24
710 720 3.126831 GTTCGAATCCATGCAGTCCTAG 58.873 50.000 0.00 0.00 0.00 3.02
711 721 2.158957 GGTTCGAATCCATGCAGTCCTA 60.159 50.000 0.00 0.00 0.00 2.94
731 743 3.102204 AGCCCTTGATCAATTTTGGAGG 58.898 45.455 8.96 4.44 0.00 4.30
738 750 3.659183 AGTAGCAGCCCTTGATCAATT 57.341 42.857 8.96 0.00 0.00 2.32
740 752 2.715046 CAAGTAGCAGCCCTTGATCAA 58.285 47.619 14.55 8.12 40.36 2.57
741 753 1.679944 GCAAGTAGCAGCCCTTGATCA 60.680 52.381 21.17 0.00 44.79 2.92
742 754 1.020437 GCAAGTAGCAGCCCTTGATC 58.980 55.000 21.17 5.74 44.79 2.92
743 755 0.745845 CGCAAGTAGCAGCCCTTGAT 60.746 55.000 21.17 0.00 46.13 2.57
744 756 1.375908 CGCAAGTAGCAGCCCTTGA 60.376 57.895 21.17 0.00 46.13 3.02
745 757 3.044059 GCGCAAGTAGCAGCCCTTG 62.044 63.158 15.15 15.15 46.13 3.61
756 768 1.000843 TGCATAGATATCCGCGCAAGT 59.999 47.619 8.75 0.00 41.68 3.16
758 770 1.270041 TGTGCATAGATATCCGCGCAA 60.270 47.619 18.15 0.00 41.53 4.85
762 774 1.336887 ACCGTGTGCATAGATATCCGC 60.337 52.381 0.00 0.72 0.00 5.54
766 778 8.123639 AGTAATTCTACCGTGTGCATAGATAT 57.876 34.615 0.00 0.00 0.00 1.63
767 779 7.520451 AGTAATTCTACCGTGTGCATAGATA 57.480 36.000 0.00 0.00 0.00 1.98
771 783 7.101054 AGAAAAGTAATTCTACCGTGTGCATA 58.899 34.615 0.00 0.00 37.88 3.14
772 784 5.938125 AGAAAAGTAATTCTACCGTGTGCAT 59.062 36.000 0.00 0.00 37.88 3.96
777 789 5.404946 TCCGAGAAAAGTAATTCTACCGTG 58.595 41.667 0.00 0.00 39.70 4.94
778 790 5.393896 CCTCCGAGAAAAGTAATTCTACCGT 60.394 44.000 0.00 0.00 39.70 4.83
779 791 5.041940 CCTCCGAGAAAAGTAATTCTACCG 58.958 45.833 0.00 0.00 39.70 4.02
888 905 1.272554 GGGGTTGGTAGAGGGGTCAG 61.273 65.000 0.00 0.00 0.00 3.51
911 928 3.820467 CGCAGCTTATTTATTGATGGGGA 59.180 43.478 0.00 0.00 0.00 4.81
953 973 3.717400 TCTAGATCGTGATTGAGGTGC 57.283 47.619 0.00 0.00 0.00 5.01
964 984 3.760537 GAGTTGCTCGTTTCTAGATCGT 58.239 45.455 14.43 0.00 0.00 3.73
1092 1122 1.215647 GTCCTGGCAGTACTCCGTG 59.784 63.158 14.43 0.00 0.00 4.94
1386 1422 2.126071 GCGCACGTAGGCAGAGAA 60.126 61.111 0.30 0.00 0.00 2.87
1463 1503 2.816012 GGCTCGTAGGGAGGAAGC 59.184 66.667 0.00 0.00 43.36 3.86
1526 1569 1.398041 TCGAACGACCAGTACATACCG 59.602 52.381 0.00 0.00 0.00 4.02
1540 1583 1.422662 TCGATCTCGGTGTCGAACG 59.577 57.895 0.00 0.00 45.47 3.95
1544 1590 1.461512 CTCCTATCGATCTCGGTGTCG 59.538 57.143 0.00 0.00 40.29 4.35
1586 1632 8.562892 CATAATATAGTCAAACCAAAGCTCTGG 58.437 37.037 3.94 3.94 42.68 3.86
1607 1653 2.039480 ACCGATCCTGCTGCATCATAAT 59.961 45.455 1.31 0.00 0.00 1.28
1608 1654 1.417517 ACCGATCCTGCTGCATCATAA 59.582 47.619 1.31 0.00 0.00 1.90
1609 1655 1.051008 ACCGATCCTGCTGCATCATA 58.949 50.000 1.31 0.00 0.00 2.15
1610 1656 1.001746 CTACCGATCCTGCTGCATCAT 59.998 52.381 1.31 0.00 0.00 2.45
1611 1657 0.390492 CTACCGATCCTGCTGCATCA 59.610 55.000 1.31 0.00 0.00 3.07
1612 1658 0.676184 TCTACCGATCCTGCTGCATC 59.324 55.000 1.31 0.00 0.00 3.91
1792 1838 7.770366 TCATATCTTATCATGGCTGCAATTT 57.230 32.000 0.50 0.00 0.00 1.82
1803 1849 8.259411 GCAAGTCCTGAGATCATATCTTATCAT 58.741 37.037 0.00 0.00 40.38 2.45
1811 1857 6.436738 AATCTGCAAGTCCTGAGATCATAT 57.563 37.500 0.00 0.00 33.76 1.78
1818 1864 3.450457 ACTCCTAATCTGCAAGTCCTGAG 59.550 47.826 0.00 0.00 33.76 3.35
1839 1885 9.971922 ATTTAAATTCCAATCTGCAGCTAATAC 57.028 29.630 9.47 0.00 0.00 1.89
2037 2173 9.418045 CAAGAAACACCGAAATAACCAATTTAT 57.582 29.630 0.00 0.00 37.93 1.40
2052 2188 1.795872 TCATACACGCAAGAAACACCG 59.204 47.619 0.00 0.00 43.62 4.94
2074 2210 9.486497 GGATATAGGCAGATTATGTATGTCATG 57.514 37.037 0.00 0.00 37.91 3.07
2183 2397 6.076981 ACTCGGTAATATGGGTAAAGTACG 57.923 41.667 0.00 0.00 0.00 3.67
2202 2416 6.148480 ACAAATTCTGAGAATGGAGAAACTCG 59.852 38.462 8.68 0.00 32.07 4.18
2214 2428 5.940617 TCCTTCCAAGACAAATTCTGAGAA 58.059 37.500 0.00 0.00 33.46 2.87
2220 2434 5.728637 ACCAATCCTTCCAAGACAAATTC 57.271 39.130 0.00 0.00 0.00 2.17
2221 2435 5.012046 GGAACCAATCCTTCCAAGACAAATT 59.988 40.000 0.00 0.00 45.56 1.82
2316 2531 8.543774 ACTTCTGGTAGTTGATGAATAGATTGT 58.456 33.333 0.00 0.00 0.00 2.71
2317 2532 8.954950 ACTTCTGGTAGTTGATGAATAGATTG 57.045 34.615 0.00 0.00 0.00 2.67
2334 2549 8.706322 ACCTGAATGTAAATTTTACTTCTGGT 57.294 30.769 28.57 28.57 38.98 4.00
2335 2550 9.626045 GAACCTGAATGTAAATTTTACTTCTGG 57.374 33.333 27.90 27.90 37.58 3.86
2351 2586 5.065731 GCTAGGTGATGAAAGAACCTGAATG 59.934 44.000 3.85 0.00 44.13 2.67
2356 2591 2.832129 TCGCTAGGTGATGAAAGAACCT 59.168 45.455 0.00 0.00 46.14 3.50
2361 2596 2.159366 AGTCGTCGCTAGGTGATGAAAG 60.159 50.000 4.84 0.00 39.34 2.62
2362 2597 1.816835 AGTCGTCGCTAGGTGATGAAA 59.183 47.619 4.84 0.00 39.34 2.69
2364 2599 1.938577 GTAGTCGTCGCTAGGTGATGA 59.061 52.381 0.00 0.00 36.00 2.92
2365 2600 1.669265 TGTAGTCGTCGCTAGGTGATG 59.331 52.381 0.00 0.00 0.00 3.07
2367 2602 1.736126 CTTGTAGTCGTCGCTAGGTGA 59.264 52.381 0.00 0.00 0.00 4.02
2376 2611 1.406970 GCTCGCTGCTTGTAGTCGTC 61.407 60.000 0.00 0.00 38.95 4.20
2409 2644 1.942657 GTGATGGATGGTTGATGACGG 59.057 52.381 0.00 0.00 0.00 4.79
2421 2656 1.076777 CCCGGCTTTGGTGATGGAT 60.077 57.895 0.00 0.00 0.00 3.41
2443 2678 5.010820 GTGTTCCTGTGTCTAGACTTAAGGT 59.989 44.000 25.42 0.00 31.95 3.50
2444 2679 5.010719 TGTGTTCCTGTGTCTAGACTTAAGG 59.989 44.000 23.01 22.91 0.00 2.69
2445 2680 6.016192 TCTGTGTTCCTGTGTCTAGACTTAAG 60.016 42.308 23.01 16.18 0.00 1.85
2446 2681 5.831525 TCTGTGTTCCTGTGTCTAGACTTAA 59.168 40.000 23.01 8.25 0.00 1.85
2447 2682 5.241064 GTCTGTGTTCCTGTGTCTAGACTTA 59.759 44.000 23.01 11.22 32.68 2.24
2469 2704 1.074872 GGATCCGGTGTTCGTTCGTC 61.075 60.000 0.00 0.00 37.11 4.20
2501 2736 0.787787 TCGATTGGCGTTTGTCTTCG 59.212 50.000 0.00 0.00 41.80 3.79
2514 2749 2.408050 GGATCTCGTGGGATTCGATTG 58.592 52.381 0.00 0.00 36.73 2.67
2515 2750 1.000163 CGGATCTCGTGGGATTCGATT 60.000 52.381 4.33 0.00 44.78 3.34
2534 2769 0.310854 GTGGAGGTTTGTCTTTGGCG 59.689 55.000 0.00 0.00 0.00 5.69
2539 2774 2.026262 ACACTGTGTGGAGGTTTGTCTT 60.026 45.455 13.50 0.00 37.94 3.01
2553 2788 2.796383 GCTAGCGTCATAGGACACTGTG 60.796 54.545 8.26 6.19 44.54 3.66
2556 2791 1.763968 TGCTAGCGTCATAGGACACT 58.236 50.000 10.77 5.79 44.54 3.55
2557 2792 2.579207 TTGCTAGCGTCATAGGACAC 57.421 50.000 10.77 0.00 44.54 3.67
2558 2793 2.232696 TGTTTGCTAGCGTCATAGGACA 59.767 45.455 10.77 3.10 44.54 4.02
2559 2794 2.603560 GTGTTTGCTAGCGTCATAGGAC 59.396 50.000 10.77 0.00 40.77 3.85
2562 2797 2.893637 AGGTGTTTGCTAGCGTCATAG 58.106 47.619 10.77 0.00 0.00 2.23
2563 2798 3.193903 TGTAGGTGTTTGCTAGCGTCATA 59.806 43.478 10.77 0.00 0.00 2.15
2573 2808 1.145803 GAGGTCGTGTAGGTGTTTGC 58.854 55.000 0.00 0.00 0.00 3.68
2608 2843 2.413112 CACAACCATTACTCACTGAGCG 59.587 50.000 5.92 0.00 32.04 5.03
2611 2846 2.105649 TGGCACAACCATTACTCACTGA 59.894 45.455 0.00 0.00 46.36 3.41
2612 2847 2.503331 TGGCACAACCATTACTCACTG 58.497 47.619 0.00 0.00 46.36 3.66
2628 2863 3.507233 GTCATGATCAAAAGAAGGTGGCA 59.493 43.478 0.00 0.00 0.00 4.92
2643 2878 6.458630 TTTGGGAGGATCATATGTCATGAT 57.541 37.500 0.00 0.00 41.08 2.45
2647 2882 4.386312 GGGTTTTGGGAGGATCATATGTCA 60.386 45.833 1.90 0.00 36.25 3.58
2704 2971 5.914898 AGACAAGGGCATTATGGTTTTAC 57.085 39.130 0.00 0.00 0.00 2.01
2731 2998 4.368315 CTTGATCCCATCATGCACAATTG 58.632 43.478 3.24 3.24 39.39 2.32
2751 3018 6.258068 GGTTAGTCTATTACGCAATGAAGCTT 59.742 38.462 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.