Multiple sequence alignment - TraesCS2D01G416100

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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 TraesCS2D01G416100 chr2D 100.000 2597 0 0 1 2597 529678039 529680635 0.000000e+00 4796
1 TraesCS2D01G416100 chr2D 79.227 621 108 15 2 616 403498293 403498898 1.860000e-111 412
2 TraesCS2D01G416100 chr2D 81.188 303 55 2 731 1032 88296666 88296365 2.580000e-60 243
3 TraesCS2D01G416100 chr3D 97.222 2448 51 8 1 2437 424620890 424618449 0.000000e+00 4128
4 TraesCS2D01G416100 chr3D 82.410 307 51 3 731 1036 561027705 561027401 5.510000e-67 265
5 TraesCS2D01G416100 chr6B 95.969 1836 53 8 614 2437 415032075 415033901 0.000000e+00 2961
6 TraesCS2D01G416100 chr6B 97.245 617 15 1 1 617 415031170 415031784 0.000000e+00 1044
7 TraesCS2D01G416100 chr4D 80.000 580 98 10 146 717 108902246 108901677 1.860000e-111 412
8 TraesCS2D01G416100 chr4D 80.311 386 63 9 1469 1842 108901141 108900757 1.970000e-71 279
9 TraesCS2D01G416100 chr7D 73.782 1026 221 36 755 1752 123875819 123876824 6.830000e-96 361
10 TraesCS2D01G416100 chr7D 73.352 1047 232 37 734 1752 123961211 123962238 6.880000e-91 344
11 TraesCS2D01G416100 chr7D 81.250 288 52 2 731 1017 558180554 558180840 5.590000e-57 231
12 TraesCS2D01G416100 chr5B 73.674 1037 205 49 755 1752 44054317 44055324 8.900000e-90 340
13 TraesCS2D01G416100 chr2B 75.802 686 132 26 731 1398 789860513 789861182 1.500000e-82 316
14 TraesCS2D01G416100 chr2B 93.210 162 8 3 2438 2597 629811374 629811534 4.320000e-58 235
15 TraesCS2D01G416100 chr3A 77.386 482 97 11 141 616 43137236 43136761 2.550000e-70 276
16 TraesCS2D01G416100 chr1D 81.944 288 50 2 731 1017 412176923 412177209 2.580000e-60 243
17 TraesCS2D01G416100 chr2A 95.556 135 5 1 2464 2597 674529120 674529254 5.630000e-52 215
18 TraesCS2D01G416100 chr1A 80.952 273 48 4 729 999 21633935 21633665 2.020000e-51 213
19 TraesCS2D01G416100 chr1A 81.111 270 47 4 729 996 573954991 573955258 2.020000e-51 213


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 TraesCS2D01G416100 chr2D 529678039 529680635 2596 False 4796.0 4796 100.0000 1 2597 1 chr2D.!!$F2 2596
1 TraesCS2D01G416100 chr2D 403498293 403498898 605 False 412.0 412 79.2270 2 616 1 chr2D.!!$F1 614
2 TraesCS2D01G416100 chr3D 424618449 424620890 2441 True 4128.0 4128 97.2220 1 2437 1 chr3D.!!$R1 2436
3 TraesCS2D01G416100 chr6B 415031170 415033901 2731 False 2002.5 2961 96.6070 1 2437 2 chr6B.!!$F1 2436
4 TraesCS2D01G416100 chr4D 108900757 108902246 1489 True 345.5 412 80.1555 146 1842 2 chr4D.!!$R1 1696
5 TraesCS2D01G416100 chr7D 123875819 123876824 1005 False 361.0 361 73.7820 755 1752 1 chr7D.!!$F1 997
6 TraesCS2D01G416100 chr7D 123961211 123962238 1027 False 344.0 344 73.3520 734 1752 1 chr7D.!!$F2 1018
7 TraesCS2D01G416100 chr5B 44054317 44055324 1007 False 340.0 340 73.6740 755 1752 1 chr5B.!!$F1 997
8 TraesCS2D01G416100 chr2B 789860513 789861182 669 False 316.0 316 75.8020 731 1398 1 chr2B.!!$F2 667

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
180 181 1.135257 GGGCTATGGAGATGTCGATCG 60.135 57.143 9.36 9.36 33.34 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2241 0.179034 GCCCCTGCAGATTGAGGTAG 60.179 60.0 17.39 0.0 37.47 3.18 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
63 64 3.504906 GCCGAAGTTTTAAAAGCCTACCT 59.495 43.478 0.00 0.00 0.00 3.08
180 181 1.135257 GGGCTATGGAGATGTCGATCG 60.135 57.143 9.36 9.36 33.34 3.69
516 517 4.223700 TGTTGAAGAGATGTACATGCCTCT 59.776 41.667 14.43 16.21 37.58 3.69
902 1205 4.852134 ATAACAGCTCACAACAATGCAA 57.148 36.364 0.00 0.00 0.00 4.08
1105 1468 1.871080 ACGCTTCTGTATGGCATAGC 58.129 50.000 7.61 8.28 33.77 2.97
1125 1488 8.637099 GCATAGCTCATGGATATACTTCATCTA 58.363 37.037 0.00 0.00 34.97 1.98
1382 1747 0.467804 GCAGAGAAGAGGGATGGGTC 59.532 60.000 0.00 0.00 0.00 4.46
1543 1912 2.715046 TGGAGCTCCAAACAAGCATAG 58.285 47.619 33.41 0.00 44.35 2.23
1666 2053 4.149019 TGCCAGGGGTTGTGCCAA 62.149 61.111 0.00 0.00 39.65 4.52
1667 2054 2.841988 GCCAGGGGTTGTGCCAAA 60.842 61.111 0.00 0.00 39.65 3.28
1668 2055 2.439104 GCCAGGGGTTGTGCCAAAA 61.439 57.895 0.00 0.00 39.65 2.44
1669 2056 1.977293 GCCAGGGGTTGTGCCAAAAA 61.977 55.000 0.00 0.00 39.65 1.94
1728 2115 2.548920 GGGATAGAAGGCCATCAACGAG 60.549 54.545 11.19 0.00 0.00 4.18
1767 2154 3.328931 ACTGGGTGTTGATGAGAACTGAT 59.671 43.478 0.00 0.00 0.00 2.90
1852 2241 2.358003 AGCACTGCTCCACGCTTC 60.358 61.111 0.00 0.00 40.11 3.86
1938 2327 7.428282 TGTTTGAACTATGTTCGATTAGCAA 57.572 32.000 6.05 0.00 0.00 3.91
1984 2373 2.923605 GCAGCGCTTGAACATGACAAAT 60.924 45.455 7.50 0.00 0.00 2.32
2218 2607 4.007940 CGTGGACGCCGTTTGTGG 62.008 66.667 0.00 0.00 0.00 4.17
2336 2725 4.831155 CCTCTGGCATGGACAAATTATCAT 59.169 41.667 0.00 0.00 0.00 2.45
2382 2771 3.576356 GCATGGATCCACACGCCG 61.576 66.667 18.99 2.69 0.00 6.46
2383 2772 2.125147 CATGGATCCACACGCCGT 60.125 61.111 18.99 0.00 0.00 5.68
2437 2827 2.552315 GGGCTCACAAACAGATTTTCGA 59.448 45.455 0.00 0.00 0.00 3.71
2438 2828 3.191371 GGGCTCACAAACAGATTTTCGAT 59.809 43.478 0.00 0.00 0.00 3.59
2439 2829 4.161333 GGCTCACAAACAGATTTTCGATG 58.839 43.478 0.00 0.00 0.00 3.84
2440 2830 4.083324 GGCTCACAAACAGATTTTCGATGA 60.083 41.667 0.00 0.00 0.00 2.92
2441 2831 5.451908 GCTCACAAACAGATTTTCGATGAA 58.548 37.500 0.00 0.00 0.00 2.57
2442 2832 5.914635 GCTCACAAACAGATTTTCGATGAAA 59.085 36.000 0.00 0.00 0.00 2.69
2443 2833 6.417635 GCTCACAAACAGATTTTCGATGAAAA 59.582 34.615 7.12 7.12 44.04 2.29
2444 2834 7.565789 GCTCACAAACAGATTTTCGATGAAAAC 60.566 37.037 6.84 2.73 42.98 2.43
2445 2835 6.695278 TCACAAACAGATTTTCGATGAAAACC 59.305 34.615 6.84 0.00 42.98 3.27
2446 2836 5.685511 ACAAACAGATTTTCGATGAAAACCG 59.314 36.000 6.84 2.32 42.98 4.44
2447 2837 5.432885 AACAGATTTTCGATGAAAACCGT 57.567 34.783 6.84 2.86 42.98 4.83
2448 2838 4.783242 ACAGATTTTCGATGAAAACCGTG 58.217 39.130 6.84 7.43 42.98 4.94
2449 2839 4.274950 ACAGATTTTCGATGAAAACCGTGT 59.725 37.500 6.84 7.94 42.98 4.49
2450 2840 5.212194 CAGATTTTCGATGAAAACCGTGTT 58.788 37.500 6.84 0.00 42.98 3.32
2451 2841 6.017770 ACAGATTTTCGATGAAAACCGTGTTA 60.018 34.615 6.84 0.00 42.98 2.41
2452 2842 7.021196 CAGATTTTCGATGAAAACCGTGTTAT 58.979 34.615 6.84 0.00 42.98 1.89
2453 2843 7.537306 CAGATTTTCGATGAAAACCGTGTTATT 59.463 33.333 6.84 0.00 42.98 1.40
2454 2844 8.079809 AGATTTTCGATGAAAACCGTGTTATTT 58.920 29.630 6.84 0.00 42.98 1.40
2455 2845 7.988904 TTTTCGATGAAAACCGTGTTATTTT 57.011 28.000 0.81 0.00 36.73 1.82
2456 2846 9.680315 ATTTTCGATGAAAACCGTGTTATTTTA 57.320 25.926 6.84 0.00 42.98 1.52
2457 2847 8.716619 TTTCGATGAAAACCGTGTTATTTTAG 57.283 30.769 0.00 0.00 0.00 1.85
2458 2848 7.655236 TCGATGAAAACCGTGTTATTTTAGA 57.345 32.000 0.00 0.00 0.00 2.10
2459 2849 7.735500 TCGATGAAAACCGTGTTATTTTAGAG 58.264 34.615 0.00 0.00 0.00 2.43
2460 2850 7.599621 TCGATGAAAACCGTGTTATTTTAGAGA 59.400 33.333 0.00 0.00 0.00 3.10
2461 2851 7.898309 CGATGAAAACCGTGTTATTTTAGAGAG 59.102 37.037 0.00 0.00 0.00 3.20
2462 2852 8.842358 ATGAAAACCGTGTTATTTTAGAGAGA 57.158 30.769 0.00 0.00 0.00 3.10
2463 2853 8.306680 TGAAAACCGTGTTATTTTAGAGAGAG 57.693 34.615 0.00 0.00 0.00 3.20
2464 2854 6.723131 AAACCGTGTTATTTTAGAGAGAGC 57.277 37.500 0.00 0.00 0.00 4.09
2465 2855 5.401531 ACCGTGTTATTTTAGAGAGAGCA 57.598 39.130 0.00 0.00 0.00 4.26
2466 2856 5.411781 ACCGTGTTATTTTAGAGAGAGCAG 58.588 41.667 0.00 0.00 0.00 4.24
2467 2857 4.268884 CCGTGTTATTTTAGAGAGAGCAGC 59.731 45.833 0.00 0.00 0.00 5.25
2468 2858 4.864806 CGTGTTATTTTAGAGAGAGCAGCA 59.135 41.667 0.00 0.00 0.00 4.41
2469 2859 5.521735 CGTGTTATTTTAGAGAGAGCAGCAT 59.478 40.000 0.00 0.00 0.00 3.79
2470 2860 6.509199 CGTGTTATTTTAGAGAGAGCAGCATG 60.509 42.308 0.00 0.00 40.87 4.06
2471 2861 5.819379 TGTTATTTTAGAGAGAGCAGCATGG 59.181 40.000 0.00 0.00 35.86 3.66
2472 2862 4.767578 ATTTTAGAGAGAGCAGCATGGA 57.232 40.909 0.00 0.00 35.86 3.41
2473 2863 4.558226 TTTTAGAGAGAGCAGCATGGAA 57.442 40.909 0.00 0.00 35.86 3.53
2474 2864 4.558226 TTTAGAGAGAGCAGCATGGAAA 57.442 40.909 0.00 0.00 35.86 3.13
2475 2865 4.558226 TTAGAGAGAGCAGCATGGAAAA 57.442 40.909 0.00 0.00 35.86 2.29
2476 2866 3.430042 AGAGAGAGCAGCATGGAAAAA 57.570 42.857 0.00 0.00 35.86 1.94
2477 2867 3.965694 AGAGAGAGCAGCATGGAAAAAT 58.034 40.909 0.00 0.00 35.86 1.82
2478 2868 3.695060 AGAGAGAGCAGCATGGAAAAATG 59.305 43.478 0.00 0.00 35.86 2.32
2479 2869 3.693085 GAGAGAGCAGCATGGAAAAATGA 59.307 43.478 0.00 0.00 35.86 2.57
2480 2870 3.695060 AGAGAGCAGCATGGAAAAATGAG 59.305 43.478 0.00 0.00 35.86 2.90
2481 2871 3.428532 AGAGCAGCATGGAAAAATGAGT 58.571 40.909 0.00 0.00 35.86 3.41
2482 2872 3.830755 AGAGCAGCATGGAAAAATGAGTT 59.169 39.130 0.00 0.00 35.86 3.01
2483 2873 3.921677 AGCAGCATGGAAAAATGAGTTG 58.078 40.909 0.00 0.00 35.86 3.16
2484 2874 2.997986 GCAGCATGGAAAAATGAGTTGG 59.002 45.455 0.00 0.00 35.86 3.77
2485 2875 3.306225 GCAGCATGGAAAAATGAGTTGGA 60.306 43.478 0.00 0.00 35.86 3.53
2486 2876 4.491676 CAGCATGGAAAAATGAGTTGGAG 58.508 43.478 0.00 0.00 0.00 3.86
2487 2877 3.056322 AGCATGGAAAAATGAGTTGGAGC 60.056 43.478 0.00 0.00 0.00 4.70
2488 2878 3.056322 GCATGGAAAAATGAGTTGGAGCT 60.056 43.478 0.00 0.00 0.00 4.09
2489 2879 4.741342 CATGGAAAAATGAGTTGGAGCTC 58.259 43.478 4.71 4.71 36.12 4.09
2490 2880 3.157087 TGGAAAAATGAGTTGGAGCTCC 58.843 45.455 26.78 26.78 34.74 4.70
2491 2881 3.157087 GGAAAAATGAGTTGGAGCTCCA 58.843 45.455 32.00 32.00 45.94 3.86
2503 2893 2.168521 TGGAGCTCCAACAGTATACAGC 59.831 50.000 33.41 4.14 44.35 4.40
2504 2894 2.432510 GGAGCTCCAACAGTATACAGCT 59.567 50.000 28.43 11.70 39.93 4.24
2505 2895 3.452474 GAGCTCCAACAGTATACAGCTG 58.548 50.000 13.48 13.48 37.34 4.24
2506 2896 1.936547 GCTCCAACAGTATACAGCTGC 59.063 52.381 15.27 0.00 37.47 5.25
2507 2897 2.555199 CTCCAACAGTATACAGCTGCC 58.445 52.381 15.27 0.00 37.47 4.85
2508 2898 1.905894 TCCAACAGTATACAGCTGCCA 59.094 47.619 15.27 1.58 37.47 4.92
2509 2899 2.304470 TCCAACAGTATACAGCTGCCAA 59.696 45.455 15.27 0.00 37.47 4.52
2510 2900 3.054434 TCCAACAGTATACAGCTGCCAAT 60.054 43.478 15.27 7.83 37.47 3.16
2511 2901 3.313526 CCAACAGTATACAGCTGCCAATC 59.686 47.826 15.27 0.87 37.47 2.67
2512 2902 3.199880 ACAGTATACAGCTGCCAATCC 57.800 47.619 15.27 0.00 37.47 3.01
2513 2903 2.505407 ACAGTATACAGCTGCCAATCCA 59.495 45.455 15.27 0.00 37.47 3.41
2514 2904 2.874701 CAGTATACAGCTGCCAATCCAC 59.125 50.000 15.27 2.43 0.00 4.02
2515 2905 2.505407 AGTATACAGCTGCCAATCCACA 59.495 45.455 15.27 0.00 0.00 4.17
2516 2906 2.742428 ATACAGCTGCCAATCCACAT 57.258 45.000 15.27 0.00 0.00 3.21
2517 2907 2.042686 TACAGCTGCCAATCCACATC 57.957 50.000 15.27 0.00 0.00 3.06
2518 2908 0.038599 ACAGCTGCCAATCCACATCA 59.961 50.000 15.27 0.00 0.00 3.07
2519 2909 0.454600 CAGCTGCCAATCCACATCAC 59.545 55.000 0.00 0.00 0.00 3.06
2520 2910 0.038599 AGCTGCCAATCCACATCACA 59.961 50.000 0.00 0.00 0.00 3.58
2521 2911 1.108776 GCTGCCAATCCACATCACAT 58.891 50.000 0.00 0.00 0.00 3.21
2522 2912 1.066605 GCTGCCAATCCACATCACATC 59.933 52.381 0.00 0.00 0.00 3.06
2523 2913 1.679680 CTGCCAATCCACATCACATCC 59.320 52.381 0.00 0.00 0.00 3.51
2524 2914 1.035139 GCCAATCCACATCACATCCC 58.965 55.000 0.00 0.00 0.00 3.85
2525 2915 1.685803 GCCAATCCACATCACATCCCA 60.686 52.381 0.00 0.00 0.00 4.37
2526 2916 2.737544 CCAATCCACATCACATCCCAA 58.262 47.619 0.00 0.00 0.00 4.12
2527 2917 3.098377 CCAATCCACATCACATCCCAAA 58.902 45.455 0.00 0.00 0.00 3.28
2528 2918 3.514706 CCAATCCACATCACATCCCAAAA 59.485 43.478 0.00 0.00 0.00 2.44
2529 2919 4.020396 CCAATCCACATCACATCCCAAAAA 60.020 41.667 0.00 0.00 0.00 1.94
2530 2920 4.806640 ATCCACATCACATCCCAAAAAC 57.193 40.909 0.00 0.00 0.00 2.43
2531 2921 3.570540 TCCACATCACATCCCAAAAACA 58.429 40.909 0.00 0.00 0.00 2.83
2532 2922 3.963374 TCCACATCACATCCCAAAAACAA 59.037 39.130 0.00 0.00 0.00 2.83
2533 2923 4.406972 TCCACATCACATCCCAAAAACAAA 59.593 37.500 0.00 0.00 0.00 2.83
2534 2924 5.071519 TCCACATCACATCCCAAAAACAAAT 59.928 36.000 0.00 0.00 0.00 2.32
2535 2925 6.268617 TCCACATCACATCCCAAAAACAAATA 59.731 34.615 0.00 0.00 0.00 1.40
2536 2926 7.038445 TCCACATCACATCCCAAAAACAAATAT 60.038 33.333 0.00 0.00 0.00 1.28
2537 2927 8.256605 CCACATCACATCCCAAAAACAAATATA 58.743 33.333 0.00 0.00 0.00 0.86
2538 2928 9.086336 CACATCACATCCCAAAAACAAATATAC 57.914 33.333 0.00 0.00 0.00 1.47
2539 2929 9.034800 ACATCACATCCCAAAAACAAATATACT 57.965 29.630 0.00 0.00 0.00 2.12
2540 2930 9.520204 CATCACATCCCAAAAACAAATATACTC 57.480 33.333 0.00 0.00 0.00 2.59
2541 2931 8.062065 TCACATCCCAAAAACAAATATACTCC 57.938 34.615 0.00 0.00 0.00 3.85
2542 2932 7.893302 TCACATCCCAAAAACAAATATACTCCT 59.107 33.333 0.00 0.00 0.00 3.69
2543 2933 9.184523 CACATCCCAAAAACAAATATACTCCTA 57.815 33.333 0.00 0.00 0.00 2.94
2544 2934 9.185680 ACATCCCAAAAACAAATATACTCCTAC 57.814 33.333 0.00 0.00 0.00 3.18
2545 2935 9.184523 CATCCCAAAAACAAATATACTCCTACA 57.815 33.333 0.00 0.00 0.00 2.74
2546 2936 9.762381 ATCCCAAAAACAAATATACTCCTACAA 57.238 29.630 0.00 0.00 0.00 2.41
2547 2937 9.589461 TCCCAAAAACAAATATACTCCTACAAA 57.411 29.630 0.00 0.00 0.00 2.83
2572 2962 8.693542 AAAAATTAGAAGGAAAGAATGCATCG 57.306 30.769 0.00 0.00 0.00 3.84
2573 2963 7.396540 AAATTAGAAGGAAAGAATGCATCGT 57.603 32.000 0.00 0.00 0.00 3.73
2574 2964 7.396540 AATTAGAAGGAAAGAATGCATCGTT 57.603 32.000 0.00 0.00 32.08 3.85
2575 2965 8.506168 AATTAGAAGGAAAGAATGCATCGTTA 57.494 30.769 0.00 0.00 29.37 3.18
2576 2966 7.539712 TTAGAAGGAAAGAATGCATCGTTAG 57.460 36.000 0.00 0.00 29.37 2.34
2577 2967 5.734720 AGAAGGAAAGAATGCATCGTTAGA 58.265 37.500 0.00 0.00 29.37 2.10
2578 2968 6.173339 AGAAGGAAAGAATGCATCGTTAGAA 58.827 36.000 0.00 0.00 29.37 2.10
2579 2969 6.655003 AGAAGGAAAGAATGCATCGTTAGAAA 59.345 34.615 0.00 0.00 29.37 2.52
2580 2970 6.817765 AGGAAAGAATGCATCGTTAGAAAA 57.182 33.333 0.00 0.00 29.37 2.29
2581 2971 7.396540 AGGAAAGAATGCATCGTTAGAAAAT 57.603 32.000 0.00 0.00 29.37 1.82
2582 2972 7.830739 AGGAAAGAATGCATCGTTAGAAAATT 58.169 30.769 0.00 0.00 29.37 1.82
2583 2973 8.306761 AGGAAAGAATGCATCGTTAGAAAATTT 58.693 29.630 0.00 0.00 29.37 1.82
2584 2974 8.587111 GGAAAGAATGCATCGTTAGAAAATTTC 58.413 33.333 0.00 0.00 29.37 2.17
2585 2975 8.466086 AAAGAATGCATCGTTAGAAAATTTCC 57.534 30.769 0.00 0.00 0.00 3.13
2586 2976 7.156876 AGAATGCATCGTTAGAAAATTTCCA 57.843 32.000 0.00 0.00 0.00 3.53
2587 2977 7.253422 AGAATGCATCGTTAGAAAATTTCCAG 58.747 34.615 0.00 0.00 0.00 3.86
2588 2978 5.957842 TGCATCGTTAGAAAATTTCCAGT 57.042 34.783 1.57 0.00 0.00 4.00
2589 2979 5.938322 TGCATCGTTAGAAAATTTCCAGTC 58.062 37.500 1.57 0.00 0.00 3.51
2590 2980 5.106317 TGCATCGTTAGAAAATTTCCAGTCC 60.106 40.000 1.57 0.00 0.00 3.85
2591 2981 5.123979 GCATCGTTAGAAAATTTCCAGTCCT 59.876 40.000 1.57 0.00 0.00 3.85
2592 2982 6.546395 CATCGTTAGAAAATTTCCAGTCCTG 58.454 40.000 1.57 0.00 0.00 3.86
2593 2983 5.617252 TCGTTAGAAAATTTCCAGTCCTGT 58.383 37.500 1.57 0.00 0.00 4.00
2594 2984 5.699458 TCGTTAGAAAATTTCCAGTCCTGTC 59.301 40.000 1.57 0.00 0.00 3.51
2595 2985 5.106673 CGTTAGAAAATTTCCAGTCCTGTCC 60.107 44.000 1.57 0.00 0.00 4.02
2596 2986 3.767711 AGAAAATTTCCAGTCCTGTCCC 58.232 45.455 1.57 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.806330 GGCAGGTAGGCTTTTAAAACTTC 58.194 43.478 0.00 0.00 40.24 3.01
63 64 6.155475 ACAAGTGCATTTAAAAGTTAGGCA 57.845 33.333 0.00 0.00 0.00 4.75
180 181 7.224949 GTGAACAGTAGCTGGATAAATCTTACC 59.775 40.741 0.00 0.00 35.51 2.85
516 517 1.559368 AACATGCATTGGGCTAGCAA 58.441 45.000 18.24 3.14 45.15 3.91
902 1205 5.453762 CCCTGCTCCATTTTTCTCTTTTTGT 60.454 40.000 0.00 0.00 0.00 2.83
1060 1394 6.460781 AGCATTTCAGATTTTTCAGATTGCA 58.539 32.000 0.00 0.00 0.00 4.08
1105 1468 9.473007 TTCCTCTAGATGAAGTATATCCATGAG 57.527 37.037 6.38 0.00 0.00 2.90
1202 1566 4.072131 TGCTGAATTGTCTTTCTGGTACC 58.928 43.478 4.43 4.43 0.00 3.34
1728 2115 1.945394 CAGTGGCCTCTTGCATGTATC 59.055 52.381 4.10 0.00 43.89 2.24
1767 2154 8.511321 ACGCATTACAAACTGAAAATTCATAGA 58.489 29.630 0.00 0.00 36.46 1.98
1852 2241 0.179034 GCCCCTGCAGATTGAGGTAG 60.179 60.000 17.39 0.00 37.47 3.18
1917 2306 9.340695 CAAATTTGCTAATCGAACATAGTTCAA 57.659 29.630 5.01 0.00 0.00 2.69
1938 2327 9.592720 GCAAACAAAACGATATTTAAGCAAATT 57.407 25.926 0.00 0.00 35.88 1.82
2172 2561 3.157087 CCATAAATGCCTACCCACCATC 58.843 50.000 0.00 0.00 0.00 3.51
2218 2607 1.838568 GCCGTGTTGTTCCTTCGTCC 61.839 60.000 0.00 0.00 0.00 4.79
2336 2725 4.219070 CCTGTATTTCCCGTCCGTATATCA 59.781 45.833 0.00 0.00 0.00 2.15
2382 2771 2.168521 TCCTGAAATCCAGACCGATGAC 59.831 50.000 0.00 0.00 45.78 3.06
2383 2772 2.466846 TCCTGAAATCCAGACCGATGA 58.533 47.619 0.00 0.00 45.78 2.92
2423 2813 5.685511 ACGGTTTTCATCGAAAATCTGTTTG 59.314 36.000 9.95 0.00 42.31 2.93
2437 2827 8.842358 TCTCTCTAAAATAACACGGTTTTCAT 57.158 30.769 0.00 0.00 0.00 2.57
2438 2828 7.095355 GCTCTCTCTAAAATAACACGGTTTTCA 60.095 37.037 0.00 0.00 0.00 2.69
2439 2829 7.095355 TGCTCTCTCTAAAATAACACGGTTTTC 60.095 37.037 0.00 0.00 0.00 2.29
2440 2830 6.708949 TGCTCTCTCTAAAATAACACGGTTTT 59.291 34.615 0.00 0.00 0.00 2.43
2441 2831 6.228258 TGCTCTCTCTAAAATAACACGGTTT 58.772 36.000 0.00 0.00 0.00 3.27
2442 2832 5.790593 TGCTCTCTCTAAAATAACACGGTT 58.209 37.500 0.00 0.00 0.00 4.44
2443 2833 5.401531 TGCTCTCTCTAAAATAACACGGT 57.598 39.130 0.00 0.00 0.00 4.83
2444 2834 4.268884 GCTGCTCTCTCTAAAATAACACGG 59.731 45.833 0.00 0.00 0.00 4.94
2445 2835 4.864806 TGCTGCTCTCTCTAAAATAACACG 59.135 41.667 0.00 0.00 0.00 4.49
2446 2836 6.238320 CCATGCTGCTCTCTCTAAAATAACAC 60.238 42.308 0.00 0.00 0.00 3.32
2447 2837 5.819379 CCATGCTGCTCTCTCTAAAATAACA 59.181 40.000 0.00 0.00 0.00 2.41
2448 2838 6.051717 TCCATGCTGCTCTCTCTAAAATAAC 58.948 40.000 0.00 0.00 0.00 1.89
2449 2839 6.239217 TCCATGCTGCTCTCTCTAAAATAA 57.761 37.500 0.00 0.00 0.00 1.40
2450 2840 5.876651 TCCATGCTGCTCTCTCTAAAATA 57.123 39.130 0.00 0.00 0.00 1.40
2451 2841 4.767578 TCCATGCTGCTCTCTCTAAAAT 57.232 40.909 0.00 0.00 0.00 1.82
2452 2842 4.558226 TTCCATGCTGCTCTCTCTAAAA 57.442 40.909 0.00 0.00 0.00 1.52
2453 2843 4.558226 TTTCCATGCTGCTCTCTCTAAA 57.442 40.909 0.00 0.00 0.00 1.85
2454 2844 4.558226 TTTTCCATGCTGCTCTCTCTAA 57.442 40.909 0.00 0.00 0.00 2.10
2455 2845 4.558226 TTTTTCCATGCTGCTCTCTCTA 57.442 40.909 0.00 0.00 0.00 2.43
2456 2846 3.430042 TTTTTCCATGCTGCTCTCTCT 57.570 42.857 0.00 0.00 0.00 3.10
2457 2847 3.693085 TCATTTTTCCATGCTGCTCTCTC 59.307 43.478 0.00 0.00 0.00 3.20
2458 2848 3.693807 TCATTTTTCCATGCTGCTCTCT 58.306 40.909 0.00 0.00 0.00 3.10
2459 2849 3.442977 ACTCATTTTTCCATGCTGCTCTC 59.557 43.478 0.00 0.00 0.00 3.20
2460 2850 3.428532 ACTCATTTTTCCATGCTGCTCT 58.571 40.909 0.00 0.00 0.00 4.09
2461 2851 3.863142 ACTCATTTTTCCATGCTGCTC 57.137 42.857 0.00 0.00 0.00 4.26
2462 2852 3.306502 CCAACTCATTTTTCCATGCTGCT 60.307 43.478 0.00 0.00 0.00 4.24
2463 2853 2.997986 CCAACTCATTTTTCCATGCTGC 59.002 45.455 0.00 0.00 0.00 5.25
2464 2854 4.491676 CTCCAACTCATTTTTCCATGCTG 58.508 43.478 0.00 0.00 0.00 4.41
2465 2855 3.056322 GCTCCAACTCATTTTTCCATGCT 60.056 43.478 0.00 0.00 0.00 3.79
2466 2856 3.056322 AGCTCCAACTCATTTTTCCATGC 60.056 43.478 0.00 0.00 0.00 4.06
2467 2857 4.381292 GGAGCTCCAACTCATTTTTCCATG 60.381 45.833 28.43 0.00 38.50 3.66
2468 2858 3.766051 GGAGCTCCAACTCATTTTTCCAT 59.234 43.478 28.43 0.00 38.50 3.41
2469 2859 3.157087 GGAGCTCCAACTCATTTTTCCA 58.843 45.455 28.43 0.00 38.50 3.53
2470 2860 3.157087 TGGAGCTCCAACTCATTTTTCC 58.843 45.455 33.41 2.05 44.35 3.13
2482 2872 2.168521 GCTGTATACTGTTGGAGCTCCA 59.831 50.000 32.00 32.00 45.94 3.86
2483 2873 2.432510 AGCTGTATACTGTTGGAGCTCC 59.567 50.000 26.78 26.78 31.05 4.70
2484 2874 3.452474 CAGCTGTATACTGTTGGAGCTC 58.548 50.000 15.80 4.71 34.57 4.09
2485 2875 2.419297 GCAGCTGTATACTGTTGGAGCT 60.419 50.000 22.02 15.23 37.26 4.09
2486 2876 1.936547 GCAGCTGTATACTGTTGGAGC 59.063 52.381 22.02 13.53 37.47 4.70
2487 2877 2.093500 TGGCAGCTGTATACTGTTGGAG 60.093 50.000 22.02 5.29 37.47 3.86
2488 2878 1.905894 TGGCAGCTGTATACTGTTGGA 59.094 47.619 22.02 0.00 37.47 3.53
2489 2879 2.401583 TGGCAGCTGTATACTGTTGG 57.598 50.000 22.02 9.66 37.47 3.77
2490 2880 3.313526 GGATTGGCAGCTGTATACTGTTG 59.686 47.826 16.64 18.27 37.47 3.33
2491 2881 3.054434 TGGATTGGCAGCTGTATACTGTT 60.054 43.478 16.64 2.68 37.47 3.16
2492 2882 2.505407 TGGATTGGCAGCTGTATACTGT 59.495 45.455 16.64 0.00 37.47 3.55
2493 2883 2.874701 GTGGATTGGCAGCTGTATACTG 59.125 50.000 16.64 4.85 38.22 2.74
2494 2884 2.505407 TGTGGATTGGCAGCTGTATACT 59.495 45.455 16.64 0.00 0.00 2.12
2495 2885 2.917933 TGTGGATTGGCAGCTGTATAC 58.082 47.619 16.64 8.11 0.00 1.47
2496 2886 3.136260 TGATGTGGATTGGCAGCTGTATA 59.864 43.478 16.64 0.63 0.00 1.47
2497 2887 2.092267 TGATGTGGATTGGCAGCTGTAT 60.092 45.455 16.64 6.70 0.00 2.29
2498 2888 1.281577 TGATGTGGATTGGCAGCTGTA 59.718 47.619 16.64 1.73 0.00 2.74
2499 2889 0.038599 TGATGTGGATTGGCAGCTGT 59.961 50.000 16.64 0.00 0.00 4.40
2500 2890 0.454600 GTGATGTGGATTGGCAGCTG 59.545 55.000 10.11 10.11 0.00 4.24
2501 2891 0.038599 TGTGATGTGGATTGGCAGCT 59.961 50.000 0.00 0.00 0.00 4.24
2502 2892 1.066605 GATGTGATGTGGATTGGCAGC 59.933 52.381 0.00 0.00 0.00 5.25
2503 2893 1.679680 GGATGTGATGTGGATTGGCAG 59.320 52.381 0.00 0.00 0.00 4.85
2504 2894 1.685803 GGGATGTGATGTGGATTGGCA 60.686 52.381 0.00 0.00 0.00 4.92
2505 2895 1.035139 GGGATGTGATGTGGATTGGC 58.965 55.000 0.00 0.00 0.00 4.52
2506 2896 2.440517 TGGGATGTGATGTGGATTGG 57.559 50.000 0.00 0.00 0.00 3.16
2507 2897 4.804868 TTTTGGGATGTGATGTGGATTG 57.195 40.909 0.00 0.00 0.00 2.67
2508 2898 4.592351 TGTTTTTGGGATGTGATGTGGATT 59.408 37.500 0.00 0.00 0.00 3.01
2509 2899 4.158786 TGTTTTTGGGATGTGATGTGGAT 58.841 39.130 0.00 0.00 0.00 3.41
2510 2900 3.570540 TGTTTTTGGGATGTGATGTGGA 58.429 40.909 0.00 0.00 0.00 4.02
2511 2901 4.333913 TTGTTTTTGGGATGTGATGTGG 57.666 40.909 0.00 0.00 0.00 4.17
2512 2902 9.086336 GTATATTTGTTTTTGGGATGTGATGTG 57.914 33.333 0.00 0.00 0.00 3.21
2513 2903 9.034800 AGTATATTTGTTTTTGGGATGTGATGT 57.965 29.630 0.00 0.00 0.00 3.06
2514 2904 9.520204 GAGTATATTTGTTTTTGGGATGTGATG 57.480 33.333 0.00 0.00 0.00 3.07
2515 2905 8.695456 GGAGTATATTTGTTTTTGGGATGTGAT 58.305 33.333 0.00 0.00 0.00 3.06
2516 2906 7.893302 AGGAGTATATTTGTTTTTGGGATGTGA 59.107 33.333 0.00 0.00 0.00 3.58
2517 2907 8.066612 AGGAGTATATTTGTTTTTGGGATGTG 57.933 34.615 0.00 0.00 0.00 3.21
2518 2908 9.185680 GTAGGAGTATATTTGTTTTTGGGATGT 57.814 33.333 0.00 0.00 0.00 3.06
2519 2909 9.184523 TGTAGGAGTATATTTGTTTTTGGGATG 57.815 33.333 0.00 0.00 0.00 3.51
2520 2910 9.762381 TTGTAGGAGTATATTTGTTTTTGGGAT 57.238 29.630 0.00 0.00 0.00 3.85
2521 2911 9.589461 TTTGTAGGAGTATATTTGTTTTTGGGA 57.411 29.630 0.00 0.00 0.00 4.37
2547 2937 8.306761 ACGATGCATTCTTTCCTTCTAATTTTT 58.693 29.630 0.00 0.00 0.00 1.94
2548 2938 7.830739 ACGATGCATTCTTTCCTTCTAATTTT 58.169 30.769 0.00 0.00 0.00 1.82
2549 2939 7.396540 ACGATGCATTCTTTCCTTCTAATTT 57.603 32.000 0.00 0.00 0.00 1.82
2550 2940 7.396540 AACGATGCATTCTTTCCTTCTAATT 57.603 32.000 0.00 0.00 0.00 1.40
2551 2941 7.987458 TCTAACGATGCATTCTTTCCTTCTAAT 59.013 33.333 0.00 0.00 0.00 1.73
2552 2942 7.327975 TCTAACGATGCATTCTTTCCTTCTAA 58.672 34.615 0.00 0.00 0.00 2.10
2553 2943 6.873997 TCTAACGATGCATTCTTTCCTTCTA 58.126 36.000 0.00 0.00 0.00 2.10
2554 2944 5.734720 TCTAACGATGCATTCTTTCCTTCT 58.265 37.500 0.00 0.00 0.00 2.85
2555 2945 6.422776 TTCTAACGATGCATTCTTTCCTTC 57.577 37.500 0.00 0.00 0.00 3.46
2556 2946 6.817765 TTTCTAACGATGCATTCTTTCCTT 57.182 33.333 0.00 0.00 0.00 3.36
2557 2947 6.817765 TTTTCTAACGATGCATTCTTTCCT 57.182 33.333 0.00 0.00 0.00 3.36
2558 2948 8.466086 AAATTTTCTAACGATGCATTCTTTCC 57.534 30.769 0.00 0.00 0.00 3.13
2559 2949 8.587111 GGAAATTTTCTAACGATGCATTCTTTC 58.413 33.333 0.00 0.00 0.00 2.62
2560 2950 8.087750 TGGAAATTTTCTAACGATGCATTCTTT 58.912 29.630 0.00 0.00 0.00 2.52
2561 2951 7.601856 TGGAAATTTTCTAACGATGCATTCTT 58.398 30.769 0.00 0.00 0.00 2.52
2562 2952 7.094205 ACTGGAAATTTTCTAACGATGCATTCT 60.094 33.333 0.00 0.00 0.00 2.40
2563 2953 7.029563 ACTGGAAATTTTCTAACGATGCATTC 58.970 34.615 0.00 0.00 0.00 2.67
2564 2954 6.924111 ACTGGAAATTTTCTAACGATGCATT 58.076 32.000 0.00 0.00 0.00 3.56
2565 2955 6.404734 GGACTGGAAATTTTCTAACGATGCAT 60.405 38.462 0.00 0.00 0.00 3.96
2566 2956 5.106317 GGACTGGAAATTTTCTAACGATGCA 60.106 40.000 8.93 0.00 0.00 3.96
2567 2957 5.123979 AGGACTGGAAATTTTCTAACGATGC 59.876 40.000 8.93 0.00 0.00 3.91
2568 2958 6.149474 ACAGGACTGGAAATTTTCTAACGATG 59.851 38.462 8.93 5.17 34.19 3.84
2569 2959 6.238648 ACAGGACTGGAAATTTTCTAACGAT 58.761 36.000 8.93 0.00 34.19 3.73
2570 2960 5.617252 ACAGGACTGGAAATTTTCTAACGA 58.383 37.500 8.93 0.00 34.19 3.85
2571 2961 5.106673 GGACAGGACTGGAAATTTTCTAACG 60.107 44.000 8.93 0.00 34.19 3.18
2572 2962 5.183331 GGGACAGGACTGGAAATTTTCTAAC 59.817 44.000 8.93 1.13 34.19 2.34
2573 2963 5.321927 GGGACAGGACTGGAAATTTTCTAA 58.678 41.667 8.93 0.00 34.19 2.10
2574 2964 4.918588 GGGACAGGACTGGAAATTTTCTA 58.081 43.478 8.93 2.20 34.19 2.10
2575 2965 3.767711 GGGACAGGACTGGAAATTTTCT 58.232 45.455 8.93 0.00 34.19 2.52


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

AutoCloner maintained by Alex Coulton.