Multiple sequence alignment - TraesCS2B01G165700

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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 TraesCS2B01G165700 chr2B 100.000 3243 0 0 1 3243 137857391 137854149 0.000000e+00 5989
1 TraesCS2B01G165700 chr2B 94.331 441 19 5 1 436 708795959 708796398 0.000000e+00 671
2 TraesCS2B01G165700 chr2B 89.545 220 16 5 2827 3040 597538265 597538483 4.120000e-69 272
3 TraesCS2B01G165700 chr2D 93.287 2011 86 17 745 2725 85759079 85757088 0.000000e+00 2920
4 TraesCS2B01G165700 chr2D 92.466 146 6 3 496 639 85766103 85765961 1.530000e-48 204
5 TraesCS2B01G165700 chr2D 92.523 107 8 0 3040 3146 85756737 85756631 1.560000e-33 154
6 TraesCS2B01G165700 chr2D 92.523 107 6 2 706 812 85759177 85759073 5.600000e-33 152
7 TraesCS2B01G165700 chr2A 93.326 1933 104 15 744 2665 86271885 86269967 0.000000e+00 2832
8 TraesCS2B01G165700 chr2A 92.347 196 15 0 3048 3243 86266942 86266747 2.460000e-71 279
9 TraesCS2B01G165700 chr2A 91.837 147 8 2 489 634 86273177 86273034 5.490000e-48 202
10 TraesCS2B01G165700 chr2A 90.260 154 9 4 489 639 86272201 86272051 2.550000e-46 196
11 TraesCS2B01G165700 chr2A 90.260 154 9 4 489 639 86274135 86273985 2.550000e-46 196
12 TraesCS2B01G165700 chr2A 92.920 113 6 2 700 812 86273992 86273882 2.590000e-36 163
13 TraesCS2B01G165700 chr2A 92.727 110 6 2 703 812 86273032 86272925 1.200000e-34 158
14 TraesCS2B01G165700 chr2A 91.228 114 8 2 700 813 86272058 86271947 1.560000e-33 154
15 TraesCS2B01G165700 chr2A 90.099 101 4 2 2678 2772 86267303 86267203 3.400000e-25 126
16 TraesCS2B01G165700 chr3B 87.343 2149 155 45 682 2769 167864067 167861975 0.000000e+00 2353
17 TraesCS2B01G165700 chr3B 94.554 202 10 1 3040 3240 167861941 167861740 8.740000e-81 311
18 TraesCS2B01G165700 chr3B 91.057 123 8 1 544 663 167864247 167864125 2.590000e-36 163
19 TraesCS2B01G165700 chr3D 86.252 2284 154 62 579 2768 112960444 112962661 0.000000e+00 2331
20 TraesCS2B01G165700 chr3D 91.038 212 9 2 3039 3240 112962686 112962897 8.860000e-71 278
21 TraesCS2B01G165700 chr3A 83.298 1910 165 67 752 2595 108729491 108731312 0.000000e+00 1618
22 TraesCS2B01G165700 chr3A 85.496 131 4 9 3039 3157 108731942 108732069 4.390000e-24 122
23 TraesCS2B01G165700 chr7B 93.651 441 22 5 1 436 13885440 13885001 0.000000e+00 654
24 TraesCS2B01G165700 chr7A 93.409 440 24 4 1 436 450370697 450370259 0.000000e+00 647
25 TraesCS2B01G165700 chr7A 89.921 506 32 12 1 488 696400440 696399936 4.560000e-178 634
26 TraesCS2B01G165700 chr6B 90.297 505 31 11 1 488 560646703 560647206 0.000000e+00 645
27 TraesCS2B01G165700 chr5B 93.228 443 22 5 1 436 608365316 608364875 0.000000e+00 645
28 TraesCS2B01G165700 chr5A 90.316 506 30 12 1 488 641403599 641403095 0.000000e+00 645
29 TraesCS2B01G165700 chr5A 89.921 506 32 12 1 488 59036066 59036570 4.560000e-178 634
30 TraesCS2B01G165700 chr5A 89.881 504 34 10 1 488 641404641 641404139 1.640000e-177 632
31 TraesCS2B01G165700 chr7D 93.467 199 10 3 2827 3023 38091642 38091445 3.160000e-75 292
32 TraesCS2B01G165700 chr7D 90.498 221 13 4 2827 3040 117216591 117216810 5.300000e-73 285
33 TraesCS2B01G165700 chr6D 90.498 221 12 5 2827 3040 72443751 72443533 1.900000e-72 283
34 TraesCS2B01G165700 chr1D 89.954 219 15 2 2827 3039 213551061 213551278 3.190000e-70 276
35 TraesCS2B01G165700 chrUn 91.919 198 13 3 2827 3023 340127383 340127578 1.150000e-69 274
36 TraesCS2B01G165700 chrUn 91.919 198 13 3 2827 3023 364704312 364704507 1.150000e-69 274
37 TraesCS2B01G165700 chrUn 89.189 222 14 5 2827 3040 362344084 362343865 5.330000e-68 268
38 TraesCS2B01G165700 chr1A 89.545 220 15 3 2827 3039 583603972 583603754 4.120000e-69 272


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 TraesCS2B01G165700 chr2B 137854149 137857391 3242 True 5989.000000 5989 100.000000 1 3243 1 chr2B.!!$R1 3242
1 TraesCS2B01G165700 chr2D 85756631 85759177 2546 True 1075.333333 2920 92.777667 706 3146 3 chr2D.!!$R2 2440
2 TraesCS2B01G165700 chr2A 86266747 86274135 7388 True 478.444444 2832 91.667111 489 3243 9 chr2A.!!$R1 2754
3 TraesCS2B01G165700 chr3B 167861740 167864247 2507 True 942.333333 2353 90.984667 544 3240 3 chr3B.!!$R1 2696
4 TraesCS2B01G165700 chr3D 112960444 112962897 2453 False 1304.500000 2331 88.645000 579 3240 2 chr3D.!!$F1 2661
5 TraesCS2B01G165700 chr3A 108729491 108732069 2578 False 870.000000 1618 84.397000 752 3157 2 chr3A.!!$F1 2405
6 TraesCS2B01G165700 chr7A 696399936 696400440 504 True 634.000000 634 89.921000 1 488 1 chr7A.!!$R2 487
7 TraesCS2B01G165700 chr6B 560646703 560647206 503 False 645.000000 645 90.297000 1 488 1 chr6B.!!$F1 487
8 TraesCS2B01G165700 chr5A 641403095 641404641 1546 True 638.500000 645 90.098500 1 488 2 chr5A.!!$R1 487
9 TraesCS2B01G165700 chr5A 59036066 59036570 504 False 634.000000 634 89.921000 1 488 1 chr5A.!!$F1 487

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
610 2629 0.396556 AGAACCCACGCCCAAACTTT 60.397 50.0 0.0 0.0 0.0 2.66 F
1743 4958 0.598680 CGCTCCAGGTCCATCGAATC 60.599 60.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 5295 0.439985 CAGATTCGTTCACGCACAGG 59.56 55.0 0.0 0.0 39.6 4.00 R
3020 9715 0.099613 CGGACAGAGATCAGGTGACG 59.90 60.0 0.0 0.0 0.0 4.35 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
213 1260 2.279935 TTTATGTCTTGGCGTTGGGT 57.720 45.000 0.00 0.00 0.00 4.51
220 1267 0.872388 CTTGGCGTTGGGTGTAGTTC 59.128 55.000 0.00 0.00 0.00 3.01
226 1273 1.223187 GTTGGGTGTAGTTCGTGGTG 58.777 55.000 0.00 0.00 0.00 4.17
264 1311 7.522901 TTTAAAGTTTTAAACGTTCCCTTGC 57.477 32.000 11.81 0.00 37.61 4.01
319 1366 5.127031 GCAAACTCATAGCCTTGGGATTTAA 59.873 40.000 0.00 0.00 0.00 1.52
342 1389 1.059692 CGTCGAGTGCATTGTGATCAC 59.940 52.381 19.27 19.27 0.00 3.06
364 1411 0.504384 GAACATCGCGACCATCATCG 59.496 55.000 12.93 0.00 45.09 3.84
376 1423 1.332195 CATCATCGCCTAGGGTGAGA 58.668 55.000 11.72 4.22 45.82 3.27
377 1424 1.271934 CATCATCGCCTAGGGTGAGAG 59.728 57.143 11.72 1.58 45.82 3.20
385 1434 3.369471 CGCCTAGGGTGAGAGAAAAATGA 60.369 47.826 11.72 0.00 34.74 2.57
420 1469 9.577110 TGAACCACTATGTTAAAATAGAGTACG 57.423 33.333 17.94 2.48 34.73 3.67
421 1470 7.998753 ACCACTATGTTAAAATAGAGTACGC 57.001 36.000 17.94 0.00 34.73 4.42
436 1485 4.082679 AGAGTACGCTCATATTTCGGGATC 60.083 45.833 0.00 0.00 44.00 3.36
437 1486 2.065993 ACGCTCATATTTCGGGATCG 57.934 50.000 0.00 0.00 37.82 3.69
438 1487 1.336887 ACGCTCATATTTCGGGATCGG 60.337 52.381 0.00 0.00 36.95 4.18
439 1488 1.067846 CGCTCATATTTCGGGATCGGA 60.068 52.381 0.00 0.00 36.95 4.55
440 1489 2.417379 CGCTCATATTTCGGGATCGGAT 60.417 50.000 0.00 0.00 36.95 4.18
441 1490 3.181490 CGCTCATATTTCGGGATCGGATA 60.181 47.826 0.00 0.00 36.95 2.59
443 1492 5.360591 GCTCATATTTCGGGATCGGATATT 58.639 41.667 0.00 0.00 36.95 1.28
444 1493 5.235186 GCTCATATTTCGGGATCGGATATTG 59.765 44.000 0.00 0.00 36.95 1.90
445 1494 6.538945 TCATATTTCGGGATCGGATATTGA 57.461 37.500 0.00 0.00 36.95 2.57
447 1496 7.564793 TCATATTTCGGGATCGGATATTGAAT 58.435 34.615 0.00 0.00 36.95 2.57
453 1514 5.423931 TCGGGATCGGATATTGAATCCATAA 59.576 40.000 4.98 0.00 38.08 1.90
479 1540 1.159713 TGTCTCCAGTTGCAACGCAG 61.160 55.000 23.21 18.77 40.61 5.18
482 1543 2.594303 CCAGTTGCAACGCAGGGA 60.594 61.111 23.21 0.00 40.61 4.20
488 1549 1.472480 GTTGCAACGCAGGGACATATT 59.528 47.619 14.90 0.00 40.61 1.28
489 1550 1.832883 TGCAACGCAGGGACATATTT 58.167 45.000 0.00 0.00 33.32 1.40
490 1551 1.472082 TGCAACGCAGGGACATATTTG 59.528 47.619 0.00 0.00 33.32 2.32
491 1552 1.798813 GCAACGCAGGGACATATTTGC 60.799 52.381 0.00 0.00 0.00 3.68
492 1553 1.745087 CAACGCAGGGACATATTTGCT 59.255 47.619 0.00 0.00 34.50 3.91
493 1554 2.942376 CAACGCAGGGACATATTTGCTA 59.058 45.455 0.00 0.00 34.50 3.49
494 1555 2.838736 ACGCAGGGACATATTTGCTAG 58.161 47.619 0.00 0.00 34.50 3.42
504 1565 8.945193 AGGGACATATTTGCTAGTTAAAGGATA 58.055 33.333 0.00 0.00 0.00 2.59
604 2623 2.203422 CCAAAGAACCCACGCCCA 60.203 61.111 0.00 0.00 0.00 5.36
610 2629 0.396556 AGAACCCACGCCCAAACTTT 60.397 50.000 0.00 0.00 0.00 2.66
626 2645 1.152860 TTTGCTCCCGCCACTTCAA 60.153 52.632 0.00 0.00 34.43 2.69
630 2649 1.172812 GCTCCCGCCACTTCAACTTT 61.173 55.000 0.00 0.00 0.00 2.66
638 2657 4.416620 CGCCACTTCAACTTTTAAACACA 58.583 39.130 0.00 0.00 0.00 3.72
663 2682 2.099405 GGTGCTAGCTGTCTCTCTCTT 58.901 52.381 17.23 0.00 0.00 2.85
668 2701 2.621556 AGCTGTCTCTCTCTTCCCTT 57.378 50.000 0.00 0.00 0.00 3.95
680 2713 1.351017 TCTTCCCTTGTCATGTGACCC 59.649 52.381 10.40 0.00 44.15 4.46
731 2789 2.823154 CAAGTCGTTCCTCTCTCCTCTT 59.177 50.000 0.00 0.00 0.00 2.85
772 2830 2.186076 CCGATTTAGCTCAGTGTCGAC 58.814 52.381 9.11 9.11 0.00 4.20
775 2833 2.724977 TTTAGCTCAGTGTCGACCTG 57.275 50.000 21.24 21.24 0.00 4.00
776 2834 1.905637 TTAGCTCAGTGTCGACCTGA 58.094 50.000 25.39 25.39 37.40 3.86
1268 4454 2.430921 CACGGTCAGCGACTCCAC 60.431 66.667 1.65 0.00 32.47 4.02
1271 4457 4.436998 GGTCAGCGACTCCACCGG 62.437 72.222 0.00 0.00 32.47 5.28
1607 4813 4.312052 CGAAAGGCCGAATTCCCA 57.688 55.556 11.72 0.00 0.00 4.37
1647 4853 1.442526 GCCACAATCGCAGGATCCTG 61.443 60.000 33.73 33.73 46.15 3.86
1743 4958 0.598680 CGCTCCAGGTCCATCGAATC 60.599 60.000 0.00 0.00 0.00 2.52
2012 5254 3.128589 CCACCGTCCGAATTCAATTCAAT 59.871 43.478 10.76 0.00 39.22 2.57
2013 5255 4.380444 CCACCGTCCGAATTCAATTCAATT 60.380 41.667 10.76 0.00 39.22 2.32
2014 5256 4.793216 CACCGTCCGAATTCAATTCAATTC 59.207 41.667 10.76 4.81 39.22 2.17
2015 5257 4.457603 ACCGTCCGAATTCAATTCAATTCA 59.542 37.500 14.18 0.00 41.19 2.57
2016 5258 5.048364 ACCGTCCGAATTCAATTCAATTCAA 60.048 36.000 14.18 0.12 41.19 2.69
2045 5295 3.344515 CACCCCTTTGCTAACTAACTCC 58.655 50.000 0.00 0.00 0.00 3.85
2072 5325 0.234625 TGAACGAATCTGTTGTGCGC 59.765 50.000 0.00 0.00 30.75 6.09
2149 5405 1.134159 CAGCAGCAGAGCCTTAGGAAT 60.134 52.381 0.69 0.00 34.23 3.01
2369 5680 4.058124 CGGGGTGTGATGATGTATGTAAG 58.942 47.826 0.00 0.00 0.00 2.34
2381 5692 9.155975 GATGATGTATGTAAGTCAGTTTGTTCT 57.844 33.333 0.00 0.00 0.00 3.01
2399 5710 4.589675 TTCCGGTGGGTGGTTGCC 62.590 66.667 0.00 0.00 33.83 4.52
2417 5728 4.686191 TGCCAATTTGTTCATTCTTGGT 57.314 36.364 0.00 0.00 38.85 3.67
2424 5735 7.039784 CCAATTTGTTCATTCTTGGTTCCTCTA 60.040 37.037 0.00 0.00 33.29 2.43
2531 5853 5.304686 TGTAACTCAGATTGGTTGAGGTT 57.695 39.130 7.13 2.58 39.51 3.50
2571 5899 3.254903 GGCGGGTTTTGTTCTATTTCTGT 59.745 43.478 0.00 0.00 0.00 3.41
2728 9079 2.558286 GCAGCTGCAACTGGAAGCA 61.558 57.895 33.36 0.00 41.59 3.91
2742 9100 0.671472 GAAGCAAACATGCAAGGGGC 60.671 55.000 3.41 0.00 45.13 5.80
2769 9127 5.591472 TCTCATTCCTTGCTGTTCCATAATG 59.409 40.000 0.00 0.00 0.00 1.90
2770 9128 5.508567 TCATTCCTTGCTGTTCCATAATGA 58.491 37.500 0.00 0.00 31.59 2.57
2771 9129 6.131264 TCATTCCTTGCTGTTCCATAATGAT 58.869 36.000 0.00 0.00 29.67 2.45
2772 9130 6.608405 TCATTCCTTGCTGTTCCATAATGATT 59.392 34.615 0.00 0.00 29.67 2.57
2773 9131 5.840243 TCCTTGCTGTTCCATAATGATTG 57.160 39.130 0.00 0.00 0.00 2.67
2774 9132 4.098349 TCCTTGCTGTTCCATAATGATTGC 59.902 41.667 0.00 0.00 0.00 3.56
2775 9133 3.696281 TGCTGTTCCATAATGATTGCG 57.304 42.857 0.00 0.00 0.00 4.85
2776 9134 3.016031 TGCTGTTCCATAATGATTGCGT 58.984 40.909 0.00 0.00 0.00 5.24
2777 9135 4.195416 TGCTGTTCCATAATGATTGCGTA 58.805 39.130 0.00 0.00 0.00 4.42
2778 9136 4.035091 TGCTGTTCCATAATGATTGCGTAC 59.965 41.667 0.00 0.00 0.00 3.67
2779 9137 4.273480 GCTGTTCCATAATGATTGCGTACT 59.727 41.667 0.00 0.00 0.00 2.73
2780 9138 5.559035 GCTGTTCCATAATGATTGCGTACTC 60.559 44.000 0.00 0.00 0.00 2.59
2781 9139 5.670485 TGTTCCATAATGATTGCGTACTCT 58.330 37.500 0.00 0.00 0.00 3.24
2782 9140 6.811954 TGTTCCATAATGATTGCGTACTCTA 58.188 36.000 0.00 0.00 0.00 2.43
2783 9141 7.269316 TGTTCCATAATGATTGCGTACTCTAA 58.731 34.615 0.00 0.00 0.00 2.10
2784 9142 7.766738 TGTTCCATAATGATTGCGTACTCTAAA 59.233 33.333 0.00 0.00 0.00 1.85
2785 9143 8.609176 GTTCCATAATGATTGCGTACTCTAAAA 58.391 33.333 0.00 0.00 0.00 1.52
2786 9144 8.725405 TCCATAATGATTGCGTACTCTAAAAA 57.275 30.769 0.00 0.00 0.00 1.94
2827 9522 1.609794 GACAACGAGAGGGGGAGGT 60.610 63.158 0.00 0.00 0.00 3.85
2828 9523 1.152096 ACAACGAGAGGGGGAGGTT 60.152 57.895 0.00 0.00 0.00 3.50
2829 9524 1.192803 ACAACGAGAGGGGGAGGTTC 61.193 60.000 0.00 0.00 0.00 3.62
2831 9526 3.839432 CGAGAGGGGGAGGTTCGC 61.839 72.222 0.00 0.00 0.00 4.70
2835 9530 2.687566 AGGGGGAGGTTCGCGAAT 60.688 61.111 26.23 10.17 0.00 3.34
2836 9531 2.513897 GGGGGAGGTTCGCGAATG 60.514 66.667 26.23 0.00 0.00 2.67
2837 9532 2.513897 GGGGAGGTTCGCGAATGG 60.514 66.667 26.23 0.00 0.00 3.16
2838 9533 2.267961 GGGAGGTTCGCGAATGGT 59.732 61.111 26.23 12.51 0.00 3.55
2839 9534 1.376812 GGGAGGTTCGCGAATGGTT 60.377 57.895 26.23 10.76 0.00 3.67
2840 9535 1.366854 GGGAGGTTCGCGAATGGTTC 61.367 60.000 26.23 18.16 0.00 3.62
2842 9537 1.000145 GAGGTTCGCGAATGGTTCTC 59.000 55.000 26.23 20.13 0.00 2.87
2844 9539 0.721718 GGTTCGCGAATGGTTCTCTG 59.278 55.000 26.23 0.00 0.00 3.35
2846 9541 2.602878 GTTCGCGAATGGTTCTCTGTA 58.397 47.619 26.23 0.00 0.00 2.74
2847 9542 2.561733 TCGCGAATGGTTCTCTGTAG 57.438 50.000 6.20 0.00 0.00 2.74
2848 9543 2.089201 TCGCGAATGGTTCTCTGTAGA 58.911 47.619 6.20 0.00 0.00 2.59
2849 9544 2.159421 TCGCGAATGGTTCTCTGTAGAC 60.159 50.000 6.20 0.00 0.00 2.59
2850 9545 2.159366 CGCGAATGGTTCTCTGTAGACT 60.159 50.000 0.00 0.00 0.00 3.24
2851 9546 3.064958 CGCGAATGGTTCTCTGTAGACTA 59.935 47.826 0.00 0.00 0.00 2.59
2852 9547 4.261238 CGCGAATGGTTCTCTGTAGACTAT 60.261 45.833 0.00 0.00 0.00 2.12
2853 9548 5.593010 GCGAATGGTTCTCTGTAGACTATT 58.407 41.667 0.00 0.00 0.00 1.73
2854 9549 5.688176 GCGAATGGTTCTCTGTAGACTATTC 59.312 44.000 0.00 0.00 33.08 1.75
2855 9550 6.680625 GCGAATGGTTCTCTGTAGACTATTCA 60.681 42.308 10.80 0.00 34.36 2.57
2856 9551 7.429633 CGAATGGTTCTCTGTAGACTATTCAT 58.570 38.462 10.80 0.00 34.36 2.57
2857 9552 8.568794 CGAATGGTTCTCTGTAGACTATTCATA 58.431 37.037 10.80 0.00 34.36 2.15
2860 9555 9.821240 ATGGTTCTCTGTAGACTATTCATATCT 57.179 33.333 0.00 0.00 0.00 1.98
2862 9557 9.290988 GGTTCTCTGTAGACTATTCATATCTGA 57.709 37.037 0.00 0.00 0.00 3.27
2937 9632 8.983702 TTTTTAGGGGTTATCTTAATATGCGT 57.016 30.769 0.00 0.00 0.00 5.24
2940 9635 5.937111 AGGGGTTATCTTAATATGCGTTGT 58.063 37.500 0.00 0.00 0.00 3.32
2941 9636 5.763204 AGGGGTTATCTTAATATGCGTTGTG 59.237 40.000 0.00 0.00 0.00 3.33
2942 9637 5.761234 GGGGTTATCTTAATATGCGTTGTGA 59.239 40.000 0.00 0.00 0.00 3.58
2943 9638 6.261381 GGGGTTATCTTAATATGCGTTGTGAA 59.739 38.462 0.00 0.00 0.00 3.18
2944 9639 7.130269 GGGTTATCTTAATATGCGTTGTGAAC 58.870 38.462 0.00 0.00 0.00 3.18
2946 9641 8.342634 GGTTATCTTAATATGCGTTGTGAACAT 58.657 33.333 0.00 0.00 0.00 2.71
2948 9643 5.568482 TCTTAATATGCGTTGTGAACATGC 58.432 37.500 0.00 2.25 0.00 4.06
2950 9645 4.374843 AATATGCGTTGTGAACATGCAT 57.625 36.364 20.51 20.51 44.74 3.96
2951 9646 2.728690 ATGCGTTGTGAACATGCATT 57.271 40.000 14.45 0.00 42.07 3.56
2952 9647 3.846423 ATGCGTTGTGAACATGCATTA 57.154 38.095 14.45 0.00 42.07 1.90
2953 9648 3.846423 TGCGTTGTGAACATGCATTAT 57.154 38.095 0.00 0.00 34.23 1.28
2954 9649 4.171663 TGCGTTGTGAACATGCATTATT 57.828 36.364 0.00 0.00 34.23 1.40
2956 9651 4.987285 TGCGTTGTGAACATGCATTATTTT 59.013 33.333 0.00 0.00 34.23 1.82
2957 9652 5.464722 TGCGTTGTGAACATGCATTATTTTT 59.535 32.000 0.00 0.00 34.23 1.94
2991 9686 9.657121 TTTTCGCAATGTTTAAATTTGAATTCC 57.343 25.926 14.55 0.00 0.00 3.01
2992 9687 7.043454 TCGCAATGTTTAAATTTGAATTCCG 57.957 32.000 14.55 9.56 0.00 4.30
2993 9688 6.090088 TCGCAATGTTTAAATTTGAATTCCGG 59.910 34.615 14.55 0.00 0.00 5.14
2995 9690 6.541969 CAATGTTTAAATTTGAATTCCGGCC 58.458 36.000 2.27 0.00 0.00 6.13
2996 9691 4.238514 TGTTTAAATTTGAATTCCGGCCG 58.761 39.130 21.04 21.04 0.00 6.13
2997 9692 2.570442 TAAATTTGAATTCCGGCCGC 57.430 45.000 22.85 6.12 0.00 6.53
2999 9694 0.823460 AATTTGAATTCCGGCCGCAT 59.177 45.000 22.85 11.37 0.00 4.73
3001 9696 1.943116 TTTGAATTCCGGCCGCATGG 61.943 55.000 22.85 6.13 38.77 3.66
3019 9714 2.726909 CACACGGTGCCATGCAAA 59.273 55.556 8.30 0.00 41.47 3.68
3020 9715 1.661197 CACACGGTGCCATGCAAAC 60.661 57.895 8.30 0.00 41.47 2.93
3022 9717 2.904866 ACGGTGCCATGCAAACGT 60.905 55.556 12.36 12.36 44.84 3.99
3023 9718 2.126888 CGGTGCCATGCAAACGTC 60.127 61.111 0.00 0.00 41.47 4.34
3024 9719 2.902419 CGGTGCCATGCAAACGTCA 61.902 57.895 0.00 0.00 41.47 4.35
3025 9720 1.371635 GGTGCCATGCAAACGTCAC 60.372 57.895 0.00 0.00 41.47 3.67
3026 9721 1.371635 GTGCCATGCAAACGTCACC 60.372 57.895 0.00 0.00 41.47 4.02
3027 9722 1.528076 TGCCATGCAAACGTCACCT 60.528 52.632 0.00 0.00 34.76 4.00
3028 9723 1.081242 GCCATGCAAACGTCACCTG 60.081 57.895 0.00 0.00 0.00 4.00
3030 9725 1.167851 CCATGCAAACGTCACCTGAT 58.832 50.000 0.00 0.00 0.00 2.90
3031 9726 1.131126 CCATGCAAACGTCACCTGATC 59.869 52.381 0.00 0.00 0.00 2.92
3032 9727 2.079158 CATGCAAACGTCACCTGATCT 58.921 47.619 0.00 0.00 0.00 2.75
3033 9728 1.795768 TGCAAACGTCACCTGATCTC 58.204 50.000 0.00 0.00 0.00 2.75
3035 9730 1.728971 GCAAACGTCACCTGATCTCTG 59.271 52.381 0.00 0.00 0.00 3.35
3037 9732 2.989840 CAAACGTCACCTGATCTCTGTC 59.010 50.000 0.00 0.00 0.00 3.51
3038 9733 1.178276 ACGTCACCTGATCTCTGTCC 58.822 55.000 0.00 0.00 0.00 4.02
3039 9734 0.099613 CGTCACCTGATCTCTGTCCG 59.900 60.000 0.00 0.00 0.00 4.79
3040 9735 1.464734 GTCACCTGATCTCTGTCCGA 58.535 55.000 0.00 0.00 0.00 4.55
3041 9736 1.403679 GTCACCTGATCTCTGTCCGAG 59.596 57.143 0.00 0.00 41.30 4.63
3043 9738 0.396417 ACCTGATCTCTGTCCGAGGG 60.396 60.000 0.00 0.00 40.30 4.30
3045 9740 0.396417 CTGATCTCTGTCCGAGGGGT 60.396 60.000 0.00 0.00 40.30 4.95
3046 9741 0.924090 TGATCTCTGTCCGAGGGGTA 59.076 55.000 0.00 0.00 40.30 3.69
3233 9947 3.187700 GTCGGTTCTTGCTTATCGTCAT 58.812 45.455 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 1171 8.633075 TGAATCAGTGAACAGTTTTTCAAATC 57.367 30.769 0.00 0.00 37.24 2.17
128 1175 8.087750 ACTTTTGAATCAGTGAACAGTTTTTCA 58.912 29.630 0.00 0.00 32.94 2.69
185 1232 6.144078 ACGCCAAGACATAAAAAGACTTTT 57.856 33.333 7.38 7.38 38.34 2.27
195 1242 1.202830 ACACCCAACGCCAAGACATAA 60.203 47.619 0.00 0.00 0.00 1.90
213 1260 4.801330 ATCTCATTCACCACGAACTACA 57.199 40.909 0.00 0.00 36.12 2.74
220 1267 7.922505 TTAAAAACAAATCTCATTCACCACG 57.077 32.000 0.00 0.00 0.00 4.94
264 1311 2.096268 CCACACTTGTCACTATGTTGCG 60.096 50.000 0.00 0.00 0.00 4.85
308 1355 3.122948 CACTCGACGTGTTAAATCCCAAG 59.877 47.826 0.00 0.00 38.84 3.61
319 1366 0.249280 TCACAATGCACTCGACGTGT 60.249 50.000 13.91 0.00 45.57 4.49
342 1389 1.075979 TGATGGTCGCGATGTTCACG 61.076 55.000 14.06 0.00 0.00 4.35
364 1411 3.942115 GTCATTTTTCTCTCACCCTAGGC 59.058 47.826 2.05 0.00 0.00 3.93
376 1423 6.925165 GTGGTTCATCATGTTGTCATTTTTCT 59.075 34.615 3.76 0.00 31.15 2.52
377 1424 6.925165 AGTGGTTCATCATGTTGTCATTTTTC 59.075 34.615 3.76 0.00 31.15 2.29
385 1434 7.994425 TTAACATAGTGGTTCATCATGTTGT 57.006 32.000 14.62 0.00 39.48 3.32
420 1469 2.743636 TCCGATCCCGAAATATGAGC 57.256 50.000 0.00 0.00 38.22 4.26
421 1470 6.573434 TCAATATCCGATCCCGAAATATGAG 58.427 40.000 0.00 0.00 38.22 2.90
428 1477 3.580895 TGGATTCAATATCCGATCCCGAA 59.419 43.478 8.08 0.00 41.03 4.30
467 1528 0.036164 TATGTCCCTGCGTTGCAACT 59.964 50.000 26.09 7.64 38.41 3.16
479 1540 9.569122 TTATCCTTTAACTAGCAAATATGTCCC 57.431 33.333 0.00 0.00 0.00 4.46
488 1549 9.791801 TCATGCATATTATCCTTTAACTAGCAA 57.208 29.630 0.00 0.00 0.00 3.91
489 1550 9.791801 TTCATGCATATTATCCTTTAACTAGCA 57.208 29.630 0.00 0.00 0.00 3.49
533 1594 6.626181 GCCCTCCGTAGATTCAACATATCTAG 60.626 46.154 0.00 0.00 35.78 2.43
626 2645 3.780902 GCACCAGCTTGTGTTTAAAAGT 58.219 40.909 18.30 0.00 38.52 2.66
663 2682 0.475632 AGGGGTCACATGACAAGGGA 60.476 55.000 13.77 0.00 46.47 4.20
668 2701 1.077828 AGAGAGAGGGGTCACATGACA 59.922 52.381 13.77 0.00 46.47 3.58
680 2713 1.006337 GCCTATGCGCAGAGAGAGG 60.006 63.158 32.36 23.19 0.00 3.69
731 2789 1.487300 CAATGGGCATGATTGGGACA 58.513 50.000 0.00 0.00 0.00 4.02
772 2830 2.438434 GATGGCGTGGGGTTCAGG 60.438 66.667 0.00 0.00 0.00 3.86
775 2833 1.379843 AATGGATGGCGTGGGGTTC 60.380 57.895 0.00 0.00 0.00 3.62
776 2834 1.379843 GAATGGATGGCGTGGGGTT 60.380 57.895 0.00 0.00 0.00 4.11
836 4002 3.272176 CGTTTTCGCTCACGTTGTCGT 62.272 52.381 0.00 0.00 43.33 4.34
839 4005 0.575390 CTCGTTTTCGCTCACGTTGT 59.425 50.000 0.00 0.00 43.73 3.32
914 4090 0.249826 CAACGCCCAAACCTTTGCAT 60.250 50.000 0.00 0.00 36.86 3.96
1268 4454 3.685214 CTGTCGTCGAGGAAGCCGG 62.685 68.421 9.78 0.00 0.00 6.13
1271 4457 0.737715 ATTGCTGTCGTCGAGGAAGC 60.738 55.000 23.37 23.37 0.00 3.86
1403 4601 4.152223 CGTTGATGCTGTTGTGATTAGACA 59.848 41.667 0.00 0.00 0.00 3.41
1408 4606 2.096268 CGTCGTTGATGCTGTTGTGATT 60.096 45.455 0.00 0.00 0.00 2.57
1556 4758 7.621991 CATTGCCGTAATTCTAAGAGTAACAG 58.378 38.462 0.00 0.00 0.00 3.16
1557 4759 6.036735 GCATTGCCGTAATTCTAAGAGTAACA 59.963 38.462 0.00 0.00 0.00 2.41
1558 4760 6.036735 TGCATTGCCGTAATTCTAAGAGTAAC 59.963 38.462 6.12 0.00 0.00 2.50
1598 4804 2.286294 CGCTGAGAAATCTGGGAATTCG 59.714 50.000 0.00 0.00 0.00 3.34
1607 4813 1.133407 GACGAGGACGCTGAGAAATCT 59.867 52.381 0.00 0.00 43.96 2.40
1717 4923 2.711922 GGACCTGGAGCGACGTGAT 61.712 63.158 0.00 0.00 0.00 3.06
1743 4958 1.012841 GCAGGGAAATCAAGCTCGAG 58.987 55.000 8.45 8.45 0.00 4.04
1815 5051 1.296715 GACAATGCCGACACCTCCT 59.703 57.895 0.00 0.00 0.00 3.69
2012 5254 3.432890 GCAAAGGGGTGGATTGTTTTGAA 60.433 43.478 0.00 0.00 0.00 2.69
2013 5255 2.103941 GCAAAGGGGTGGATTGTTTTGA 59.896 45.455 0.00 0.00 0.00 2.69
2014 5256 2.104622 AGCAAAGGGGTGGATTGTTTTG 59.895 45.455 0.00 0.00 0.00 2.44
2015 5257 2.407562 AGCAAAGGGGTGGATTGTTTT 58.592 42.857 0.00 0.00 0.00 2.43
2016 5258 2.101640 AGCAAAGGGGTGGATTGTTT 57.898 45.000 0.00 0.00 0.00 2.83
2045 5295 0.439985 CAGATTCGTTCACGCACAGG 59.560 55.000 0.00 0.00 39.60 4.00
2072 5325 1.067749 CCTCCTGATGAGCTGAGCG 59.932 63.158 0.00 0.00 39.98 5.03
2149 5405 2.527123 TGTGCCGGGGGTTCTACA 60.527 61.111 2.18 0.00 0.00 2.74
2369 5680 2.032924 CCACCGGAAAGAACAAACTGAC 59.967 50.000 9.46 0.00 0.00 3.51
2381 5692 2.519780 GCAACCACCCACCGGAAA 60.520 61.111 9.46 0.00 0.00 3.13
2399 5710 6.752168 AGAGGAACCAAGAATGAACAAATTG 58.248 36.000 0.00 0.00 0.00 2.32
2417 5728 7.015680 AGAATAATCAGGAGCAGATAGAGGAA 58.984 38.462 0.00 0.00 0.00 3.36
2424 5735 6.999705 AGAGAAGAATAATCAGGAGCAGAT 57.000 37.500 0.00 0.00 0.00 2.90
2531 5853 1.340889 GCCAAGCAATGAAACCACTCA 59.659 47.619 0.00 0.00 0.00 3.41
2571 5899 6.145858 CGGAGAAAACATTGCATTTGATTGAA 59.854 34.615 4.32 0.00 0.00 2.69
2728 9079 0.252375 AGATGGCCCCTTGCATGTTT 60.252 50.000 0.00 0.00 43.89 2.83
2742 9100 2.686915 GGAACAGCAAGGAATGAGATGG 59.313 50.000 0.00 0.00 0.00 3.51
2786 9144 9.378551 TGTCACTGCGTTTTTATATCTCTATTT 57.621 29.630 0.00 0.00 0.00 1.40
2792 9150 5.636121 TCGTTGTCACTGCGTTTTTATATCT 59.364 36.000 0.00 0.00 0.00 1.98
2798 9156 2.004017 TCTCGTTGTCACTGCGTTTTT 58.996 42.857 0.00 0.00 0.00 1.94
2827 9522 2.490509 TCTACAGAGAACCATTCGCGAA 59.509 45.455 25.66 25.66 34.46 4.70
2828 9523 2.089201 TCTACAGAGAACCATTCGCGA 58.911 47.619 3.71 3.71 34.46 5.87
2829 9524 2.159366 AGTCTACAGAGAACCATTCGCG 60.159 50.000 0.00 0.00 34.46 5.87
2831 9526 6.796426 TGAATAGTCTACAGAGAACCATTCG 58.204 40.000 0.00 0.00 32.81 3.34
2835 9530 9.072375 CAGATATGAATAGTCTACAGAGAACCA 57.928 37.037 0.00 0.00 31.96 3.67
2836 9531 9.290988 TCAGATATGAATAGTCTACAGAGAACC 57.709 37.037 0.00 0.00 31.96 3.62
2912 9607 8.983702 ACGCATATTAAGATAACCCCTAAAAA 57.016 30.769 0.00 0.00 0.00 1.94
2913 9608 8.842280 CAACGCATATTAAGATAACCCCTAAAA 58.158 33.333 0.00 0.00 0.00 1.52
2914 9609 7.994334 ACAACGCATATTAAGATAACCCCTAAA 59.006 33.333 0.00 0.00 0.00 1.85
2915 9610 7.442969 CACAACGCATATTAAGATAACCCCTAA 59.557 37.037 0.00 0.00 0.00 2.69
2916 9611 6.932400 CACAACGCATATTAAGATAACCCCTA 59.068 38.462 0.00 0.00 0.00 3.53
2917 9612 5.763204 CACAACGCATATTAAGATAACCCCT 59.237 40.000 0.00 0.00 0.00 4.79
2918 9613 5.761234 TCACAACGCATATTAAGATAACCCC 59.239 40.000 0.00 0.00 0.00 4.95
2919 9614 6.854496 TCACAACGCATATTAAGATAACCC 57.146 37.500 0.00 0.00 0.00 4.11
2920 9615 7.690228 TGTTCACAACGCATATTAAGATAACC 58.310 34.615 0.00 0.00 0.00 2.85
2921 9616 9.158364 CATGTTCACAACGCATATTAAGATAAC 57.842 33.333 0.00 0.00 0.00 1.89
2923 9618 7.011857 TGCATGTTCACAACGCATATTAAGATA 59.988 33.333 3.87 0.00 34.69 1.98
2929 9624 3.846423 TGCATGTTCACAACGCATATT 57.154 38.095 3.87 0.00 34.69 1.28
2930 9625 4.374843 AATGCATGTTCACAACGCATAT 57.625 36.364 16.39 7.88 43.64 1.78
2931 9626 3.846423 AATGCATGTTCACAACGCATA 57.154 38.095 16.39 0.00 43.64 3.14
2932 9627 2.728690 AATGCATGTTCACAACGCAT 57.271 40.000 0.00 12.24 45.19 4.73
2933 9628 3.846423 ATAATGCATGTTCACAACGCA 57.154 38.095 0.00 9.18 40.82 5.24
2934 9629 5.514059 AAAATAATGCATGTTCACAACGC 57.486 34.783 0.00 0.00 0.00 4.84
2968 9663 6.090088 CCGGAATTCAAATTTAAACATTGCGA 59.910 34.615 18.09 7.24 37.57 5.10
2969 9664 6.239945 CCGGAATTCAAATTTAAACATTGCG 58.760 36.000 7.93 13.23 35.85 4.85
2971 9666 6.541969 GGCCGGAATTCAAATTTAAACATTG 58.458 36.000 5.05 8.56 0.00 2.82
2972 9667 5.350091 CGGCCGGAATTCAAATTTAAACATT 59.650 36.000 20.10 0.00 0.00 2.71
2973 9668 4.867608 CGGCCGGAATTCAAATTTAAACAT 59.132 37.500 20.10 0.00 0.00 2.71
2977 9672 2.231478 TGCGGCCGGAATTCAAATTTAA 59.769 40.909 29.38 0.00 0.00 1.52
2978 9673 1.819288 TGCGGCCGGAATTCAAATTTA 59.181 42.857 29.38 0.00 0.00 1.40
2980 9675 0.823460 ATGCGGCCGGAATTCAAATT 59.177 45.000 27.18 0.00 0.00 1.82
2982 9677 1.510383 CATGCGGCCGGAATTCAAA 59.490 52.632 27.18 0.00 0.00 2.69
2983 9678 2.413963 CCATGCGGCCGGAATTCAA 61.414 57.895 27.18 0.00 0.00 2.69
2984 9679 2.828095 CCATGCGGCCGGAATTCA 60.828 61.111 27.18 14.93 0.00 2.57
3002 9697 1.661197 GTTTGCATGGCACCGTGTG 60.661 57.895 10.50 0.25 38.71 3.82
3003 9698 2.727544 GTTTGCATGGCACCGTGT 59.272 55.556 10.50 0.00 38.71 4.49
3004 9699 2.428902 CGTTTGCATGGCACCGTG 60.429 61.111 4.43 4.43 38.71 4.94
3005 9700 2.903547 GACGTTTGCATGGCACCGT 61.904 57.895 12.92 12.92 44.80 4.83
3006 9701 2.126888 GACGTTTGCATGGCACCG 60.127 61.111 0.00 7.62 38.71 4.94
3007 9702 1.371635 GTGACGTTTGCATGGCACC 60.372 57.895 8.50 0.00 41.68 5.01
3008 9703 1.371635 GGTGACGTTTGCATGGCAC 60.372 57.895 10.70 10.70 46.30 5.01
3009 9704 1.528076 AGGTGACGTTTGCATGGCA 60.528 52.632 0.00 0.00 36.47 4.92
3010 9705 1.081242 CAGGTGACGTTTGCATGGC 60.081 57.895 0.00 0.00 0.00 4.40
3012 9707 2.079158 AGATCAGGTGACGTTTGCATG 58.921 47.619 0.00 0.00 0.00 4.06
3013 9708 2.027745 AGAGATCAGGTGACGTTTGCAT 60.028 45.455 0.00 0.00 0.00 3.96
3014 9709 1.344438 AGAGATCAGGTGACGTTTGCA 59.656 47.619 0.00 0.00 0.00 4.08
3015 9710 1.728971 CAGAGATCAGGTGACGTTTGC 59.271 52.381 0.00 0.00 0.00 3.68
3016 9711 2.989840 GACAGAGATCAGGTGACGTTTG 59.010 50.000 0.00 0.00 0.00 2.93
3018 9713 1.546476 GGACAGAGATCAGGTGACGTT 59.454 52.381 0.00 0.00 0.00 3.99
3019 9714 1.178276 GGACAGAGATCAGGTGACGT 58.822 55.000 0.00 0.00 0.00 4.34
3020 9715 0.099613 CGGACAGAGATCAGGTGACG 59.900 60.000 0.00 0.00 0.00 4.35
3022 9717 3.978876 TCGGACAGAGATCAGGTGA 57.021 52.632 0.00 0.00 0.00 4.02
3031 9726 1.668101 GCACTACCCCTCGGACAGAG 61.668 65.000 0.00 0.00 46.44 3.35
3032 9727 1.681327 GCACTACCCCTCGGACAGA 60.681 63.158 0.00 0.00 0.00 3.41
3033 9728 2.722201 GGCACTACCCCTCGGACAG 61.722 68.421 0.00 0.00 0.00 3.51
3035 9730 1.957765 GAAGGCACTACCCCTCGGAC 61.958 65.000 0.00 0.00 38.49 4.79
3037 9732 2.732619 GGAAGGCACTACCCCTCGG 61.733 68.421 0.00 0.00 38.49 4.63
3038 9733 1.265454 AAGGAAGGCACTACCCCTCG 61.265 60.000 0.00 0.00 38.49 4.63
3039 9734 0.992695 AAAGGAAGGCACTACCCCTC 59.007 55.000 0.00 0.00 38.49 4.30
3040 9735 1.075536 CAAAAGGAAGGCACTACCCCT 59.924 52.381 0.00 0.00 38.49 4.79
3041 9736 1.545841 CAAAAGGAAGGCACTACCCC 58.454 55.000 0.00 0.00 38.49 4.95
3043 9738 1.886542 CACCAAAAGGAAGGCACTACC 59.113 52.381 0.00 0.00 38.49 3.18
3045 9740 1.133637 TGCACCAAAAGGAAGGCACTA 60.134 47.619 0.00 0.00 38.49 2.74
3110 9813 1.610522 GATACGTACGGGTACAGCCAT 59.389 52.381 21.06 0.00 39.65 4.40
3111 9814 1.024271 GATACGTACGGGTACAGCCA 58.976 55.000 21.06 0.00 39.65 4.75


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

AutoCloner maintained by Alex Coulton.