Multiple sequence alignment - TraesCS4A01G453800

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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 TraesCS4A01G453800 chr4A 100.000 2858 0 0 1 2858 718032180 718035037 0.000000e+00 5278
1 TraesCS4A01G453800 chr4A 74.121 711 149 25 659 1346 717047912 717047214 7.850000e-66 261
2 TraesCS4A01G453800 chr4A 78.926 242 24 4 621 858 717971275 717971493 3.840000e-29 139
3 TraesCS4A01G453800 chr7D 93.152 2687 147 17 5 2689 16692932 16690281 0.000000e+00 3908
4 TraesCS4A01G453800 chr7D 81.162 1497 218 24 605 2087 16705489 16704043 0.000000e+00 1144
5 TraesCS4A01G453800 chr7D 73.692 707 157 22 660 1346 17209446 17210143 6.110000e-62 248
6 TraesCS4A01G453800 chr7D 86.885 122 12 2 621 739 16705697 16705577 1.790000e-27 134
7 TraesCS4A01G453800 chr7A 91.185 2700 195 19 4 2689 15640839 15638169 0.000000e+00 3627
8 TraesCS4A01G453800 chr7A 80.665 331 55 6 1469 1799 15639743 15639422 6.110000e-62 248
9 TraesCS4A01G453800 chr7A 78.275 313 37 13 605 911 15690157 15689870 3.790000e-39 172


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 TraesCS4A01G453800 chr4A 718032180 718035037 2857 False 5278.0 5278 100.0000 1 2858 1 chr4A.!!$F2 2857
1 TraesCS4A01G453800 chr4A 717047214 717047912 698 True 261.0 261 74.1210 659 1346 1 chr4A.!!$R1 687
2 TraesCS4A01G453800 chr7D 16690281 16692932 2651 True 3908.0 3908 93.1520 5 2689 1 chr7D.!!$R1 2684
3 TraesCS4A01G453800 chr7D 16704043 16705697 1654 True 639.0 1144 84.0235 605 2087 2 chr7D.!!$R2 1482
4 TraesCS4A01G453800 chr7D 17209446 17210143 697 False 248.0 248 73.6920 660 1346 1 chr7D.!!$F1 686
5 TraesCS4A01G453800 chr7A 15638169 15640839 2670 True 1937.5 3627 85.9250 4 2689 2 chr7A.!!$R2 2685

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
911 936 1.241165 TGCAGCAAACAGACCATGAG 58.759 50.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 2754 0.035056 GACCATGCAGCAGTTACCCT 60.035 55.0 0.0 0.0 0.0 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.831741 CTTACTCAAGCTAGCTTCAACG 57.168 45.455 27.08 15.83 33.42 4.10
32 33 1.800586 CAAGCTAGCTTCAACGCTTCA 59.199 47.619 27.08 0.00 40.43 3.02
110 111 3.896648 ACACGTGACATCAAAATGACC 57.103 42.857 25.01 0.00 36.67 4.02
282 288 1.697394 TATGGATGGGCCTGGCAGT 60.697 57.895 22.05 5.11 37.63 4.40
356 362 7.497925 ACATCCTGTAGAAGAAAGAACAAAC 57.502 36.000 0.00 0.00 0.00 2.93
360 366 7.335627 TCCTGTAGAAGAAAGAACAAACTCAA 58.664 34.615 0.00 0.00 0.00 3.02
381 387 7.721399 ACTCAATTCAGTAAAGTTCAGTTCCAT 59.279 33.333 0.00 0.00 0.00 3.41
407 413 5.604231 ACATCAGAGTAGCTCCATGGAAATA 59.396 40.000 17.00 8.65 30.17 1.40
412 418 7.071698 TCAGAGTAGCTCCATGGAAATATCTTT 59.928 37.037 17.00 3.73 0.00 2.52
437 443 5.103940 ACATGTAAAGGGCATCCTATGAGTT 60.104 40.000 0.00 0.00 44.07 3.01
438 444 5.450818 TGTAAAGGGCATCCTATGAGTTT 57.549 39.130 0.00 0.00 44.07 2.66
549 556 4.074970 CCTCTTCACAGCTAATGGTTTGT 58.925 43.478 0.00 0.00 0.00 2.83
552 559 4.278170 TCTTCACAGCTAATGGTTTGTTGG 59.722 41.667 0.00 0.00 0.00 3.77
557 564 2.035832 AGCTAATGGTTTGTTGGTGTGC 59.964 45.455 0.00 0.00 0.00 4.57
601 608 8.417106 TGCAAGATTACAAACCATTAACTCAAA 58.583 29.630 0.00 0.00 0.00 2.69
602 609 9.255304 GCAAGATTACAAACCATTAACTCAAAA 57.745 29.630 0.00 0.00 0.00 2.44
642 649 8.464770 TCATGTGAATGCAAAAGCTAATTTAC 57.535 30.769 0.00 0.00 0.00 2.01
645 652 7.205992 TGTGAATGCAAAAGCTAATTTACACA 58.794 30.769 0.00 0.00 0.00 3.72
755 766 6.882678 TCATATGCATTATCAATCTCACCTGG 59.117 38.462 3.54 0.00 0.00 4.45
762 773 1.699083 TCAATCTCACCTGGCAGTCAA 59.301 47.619 14.43 0.00 0.00 3.18
911 936 1.241165 TGCAGCAAACAGACCATGAG 58.759 50.000 0.00 0.00 0.00 2.90
1091 1119 1.223487 GCCAGGGCTTCGGACAATA 59.777 57.895 2.30 0.00 38.26 1.90
1101 1132 3.364964 GCTTCGGACAATACCAACAACAG 60.365 47.826 0.00 0.00 0.00 3.16
1173 1204 2.254546 TCCTGCAACAACAGTGTAGG 57.745 50.000 0.00 0.00 46.85 3.18
1349 1380 0.387622 CAACAACAATGGCAGGAGCG 60.388 55.000 0.00 0.00 43.41 5.03
1450 1481 4.831698 GCCAGCAGCAACAACAAA 57.168 50.000 0.00 0.00 42.97 2.83
1457 1488 0.106335 CAGCAACAACAAATGGGGCA 59.894 50.000 0.00 0.00 35.41 5.36
1458 1489 0.835941 AGCAACAACAAATGGGGCAA 59.164 45.000 0.00 0.00 35.41 4.52
1459 1490 0.943673 GCAACAACAAATGGGGCAAC 59.056 50.000 0.00 0.00 33.79 4.17
1512 1543 1.374252 ACCGTGTGCGACATTCCTC 60.374 57.895 0.00 0.00 41.33 3.71
1632 1663 1.281867 TCACAGATCCCGGAGCAATTT 59.718 47.619 0.73 0.00 0.00 1.82
1741 1772 2.159421 CCAGCACAACATGAGAGCATTC 60.159 50.000 0.00 0.00 30.68 2.67
1874 1911 2.670414 GCTAGATGATCAATGTAGCGGC 59.330 50.000 14.88 0.00 45.20 6.53
1875 1912 2.175878 AGATGATCAATGTAGCGGCC 57.824 50.000 0.00 0.00 0.00 6.13
1877 1914 0.392706 ATGATCAATGTAGCGGCCGA 59.607 50.000 33.48 8.40 0.00 5.54
1890 1927 2.670905 AGCGGCCGAAAAATAAAAATGC 59.329 40.909 33.48 5.16 0.00 3.56
1913 1950 1.893801 TGCATCATCATGTGTGGCAAA 59.106 42.857 0.00 0.00 35.91 3.68
1966 2003 4.485163 ACGTTCCTGAATAAAGCATTTGC 58.515 39.130 0.00 0.00 39.63 3.68
2038 2075 4.141855 GTTGAACTTAACCATCACCGTG 57.858 45.455 0.00 0.00 0.00 4.94
2093 2131 7.592938 TCATAGCATGAAAACAAAGTTGGTAG 58.407 34.615 0.00 0.00 36.11 3.18
2117 2155 6.980978 AGACACGAGGAAAATACACATATGAG 59.019 38.462 10.38 3.79 0.00 2.90
2272 2310 5.406477 GCCCATCAAATCAAAAGAAGTTCAC 59.594 40.000 5.50 0.00 0.00 3.18
2279 2317 7.492020 TCAAATCAAAAGAAGTTCACAACATGG 59.508 33.333 5.50 0.00 0.00 3.66
2281 2319 6.135290 TCAAAAGAAGTTCACAACATGGAG 57.865 37.500 5.50 0.00 0.00 3.86
2381 2419 1.336755 ACCGGCTTTCAAACACATGTC 59.663 47.619 0.00 0.00 0.00 3.06
2440 2478 2.153645 CCAGTTGCTACATCACAAGCA 58.846 47.619 0.13 0.00 46.59 3.91
2452 2490 7.439356 GCTACATCACAAGCAGATTAATCACTA 59.561 37.037 17.56 0.64 38.63 2.74
2562 2601 2.109126 GTCAGCCGCAAGTCCATCC 61.109 63.158 0.00 0.00 0.00 3.51
2580 2619 4.150627 CCATCCGATAGTATCAAAACTGCG 59.849 45.833 10.71 0.00 0.00 5.18
2585 2624 4.207224 CGATAGTATCAAAACTGCGGTGAG 59.793 45.833 10.71 0.00 0.00 3.51
2587 2626 1.130561 GTATCAAAACTGCGGTGAGGC 59.869 52.381 0.00 0.00 0.00 4.70
2640 2679 1.745489 CTAGCCCCACGAGCAAACC 60.745 63.158 0.00 0.00 0.00 3.27
2662 2707 1.894466 TCAAACCATGATGGCACCAAG 59.106 47.619 12.25 0.00 42.67 3.61
2670 2715 1.364626 GATGGCACCAAGACTGCTCG 61.365 60.000 0.00 0.00 34.84 5.03
2678 2723 4.261656 GCACCAAGACTGCTCGTACTATAT 60.262 45.833 0.00 0.00 0.00 0.86
2689 2734 8.684520 ACTGCTCGTACTATATAGTTCAGTTTT 58.315 33.333 20.21 0.00 37.73 2.43
2690 2735 9.517609 CTGCTCGTACTATATAGTTCAGTTTTT 57.482 33.333 20.21 0.00 37.73 1.94
2710 2755 2.861462 TTTTTCCAGTTTGACGGCAG 57.139 45.000 0.00 0.00 0.00 4.85
2711 2756 1.028905 TTTTCCAGTTTGACGGCAGG 58.971 50.000 0.00 0.00 0.00 4.85
2712 2757 0.821711 TTTCCAGTTTGACGGCAGGG 60.822 55.000 0.00 0.00 0.00 4.45
2713 2758 1.990160 TTCCAGTTTGACGGCAGGGT 61.990 55.000 0.00 0.00 0.00 4.34
2714 2759 1.122632 TCCAGTTTGACGGCAGGGTA 61.123 55.000 0.00 0.00 0.00 3.69
2715 2760 0.250553 CCAGTTTGACGGCAGGGTAA 60.251 55.000 0.00 0.00 0.00 2.85
2716 2761 0.872388 CAGTTTGACGGCAGGGTAAC 59.128 55.000 0.00 0.00 0.00 2.50
2717 2762 0.763035 AGTTTGACGGCAGGGTAACT 59.237 50.000 0.05 0.05 0.00 2.24
2726 2771 2.485677 CAGGGTAACTGCTGCATGG 58.514 57.895 1.31 0.00 40.97 3.66
2727 2772 0.322816 CAGGGTAACTGCTGCATGGT 60.323 55.000 1.31 0.00 40.97 3.55
2728 2773 0.035056 AGGGTAACTGCTGCATGGTC 60.035 55.000 1.31 0.00 0.00 4.02
2729 2774 1.032114 GGGTAACTGCTGCATGGTCC 61.032 60.000 1.31 4.25 0.00 4.46
2730 2775 0.035056 GGTAACTGCTGCATGGTCCT 60.035 55.000 1.31 0.00 0.00 3.85
2731 2776 1.089920 GTAACTGCTGCATGGTCCTG 58.910 55.000 1.31 0.00 0.00 3.86
2732 2777 0.983467 TAACTGCTGCATGGTCCTGA 59.017 50.000 1.31 0.00 0.00 3.86
2733 2778 0.607489 AACTGCTGCATGGTCCTGAC 60.607 55.000 1.31 0.00 0.00 3.51
2734 2779 1.298993 CTGCTGCATGGTCCTGACT 59.701 57.895 1.31 0.00 0.00 3.41
2735 2780 0.538584 CTGCTGCATGGTCCTGACTA 59.461 55.000 1.31 0.00 0.00 2.59
2736 2781 0.538584 TGCTGCATGGTCCTGACTAG 59.461 55.000 0.00 0.00 0.00 2.57
2737 2782 0.813210 GCTGCATGGTCCTGACTAGC 60.813 60.000 0.00 0.61 0.00 3.42
2738 2783 0.829333 CTGCATGGTCCTGACTAGCT 59.171 55.000 0.00 0.00 0.00 3.32
2739 2784 1.209019 CTGCATGGTCCTGACTAGCTT 59.791 52.381 0.00 0.00 0.00 3.74
2740 2785 1.065926 TGCATGGTCCTGACTAGCTTG 60.066 52.381 0.00 0.00 0.00 4.01
2741 2786 1.745141 GCATGGTCCTGACTAGCTTGG 60.745 57.143 0.00 0.00 0.00 3.61
2742 2787 1.833630 CATGGTCCTGACTAGCTTGGA 59.166 52.381 0.00 0.00 0.00 3.53
2743 2788 2.254152 TGGTCCTGACTAGCTTGGAT 57.746 50.000 0.00 0.00 0.00 3.41
2744 2789 2.551270 TGGTCCTGACTAGCTTGGATT 58.449 47.619 0.00 0.00 0.00 3.01
2745 2790 3.719871 TGGTCCTGACTAGCTTGGATTA 58.280 45.455 0.00 0.00 0.00 1.75
2746 2791 4.298626 TGGTCCTGACTAGCTTGGATTAT 58.701 43.478 0.00 0.00 0.00 1.28
2747 2792 5.464069 TGGTCCTGACTAGCTTGGATTATA 58.536 41.667 0.00 0.00 0.00 0.98
2748 2793 5.903010 TGGTCCTGACTAGCTTGGATTATAA 59.097 40.000 0.00 0.00 0.00 0.98
2749 2794 6.042093 TGGTCCTGACTAGCTTGGATTATAAG 59.958 42.308 0.00 0.00 0.00 1.73
2750 2795 6.267928 GGTCCTGACTAGCTTGGATTATAAGA 59.732 42.308 0.00 0.00 0.00 2.10
2751 2796 7.149307 GTCCTGACTAGCTTGGATTATAAGAC 58.851 42.308 0.00 0.00 0.00 3.01
2752 2797 7.014808 GTCCTGACTAGCTTGGATTATAAGACT 59.985 40.741 0.00 0.00 0.00 3.24
2753 2798 7.565398 TCCTGACTAGCTTGGATTATAAGACTT 59.435 37.037 0.00 0.00 0.00 3.01
2754 2799 8.207545 CCTGACTAGCTTGGATTATAAGACTTT 58.792 37.037 0.00 0.00 0.00 2.66
2764 2809 8.732746 TGGATTATAAGACTTTAAGAGTTGCC 57.267 34.615 0.00 0.00 39.19 4.52
2765 2810 8.548877 TGGATTATAAGACTTTAAGAGTTGCCT 58.451 33.333 0.00 0.00 39.19 4.75
2766 2811 9.397280 GGATTATAAGACTTTAAGAGTTGCCTT 57.603 33.333 0.00 0.00 39.19 4.35
2768 2813 9.740710 ATTATAAGACTTTAAGAGTTGCCTTGT 57.259 29.630 0.00 0.00 39.19 3.16
2769 2814 9.569122 TTATAAGACTTTAAGAGTTGCCTTGTT 57.431 29.630 0.00 0.00 39.19 2.83
2770 2815 6.775594 AAGACTTTAAGAGTTGCCTTGTTT 57.224 33.333 0.00 0.00 39.19 2.83
2771 2816 6.378710 AGACTTTAAGAGTTGCCTTGTTTC 57.621 37.500 0.00 0.00 39.19 2.78
2772 2817 5.885912 AGACTTTAAGAGTTGCCTTGTTTCA 59.114 36.000 0.00 0.00 39.19 2.69
2773 2818 6.377146 AGACTTTAAGAGTTGCCTTGTTTCAA 59.623 34.615 0.00 0.00 39.19 2.69
2774 2819 6.930731 ACTTTAAGAGTTGCCTTGTTTCAAA 58.069 32.000 0.00 0.00 33.92 2.69
2775 2820 7.382898 ACTTTAAGAGTTGCCTTGTTTCAAAA 58.617 30.769 0.00 0.00 33.92 2.44
2776 2821 7.875554 ACTTTAAGAGTTGCCTTGTTTCAAAAA 59.124 29.630 0.00 0.00 33.92 1.94
2800 2845 8.502105 AAAAAGACTTTAAGAAACGGAAGAGA 57.498 30.769 0.00 0.00 0.00 3.10
2801 2846 7.479897 AAAGACTTTAAGAAACGGAAGAGAC 57.520 36.000 0.00 0.00 0.00 3.36
2802 2847 6.158023 AGACTTTAAGAAACGGAAGAGACA 57.842 37.500 0.00 0.00 0.00 3.41
2803 2848 6.217294 AGACTTTAAGAAACGGAAGAGACAG 58.783 40.000 0.00 0.00 0.00 3.51
2804 2849 5.298347 ACTTTAAGAAACGGAAGAGACAGG 58.702 41.667 0.00 0.00 0.00 4.00
2805 2850 2.171341 AAGAAACGGAAGAGACAGGC 57.829 50.000 0.00 0.00 0.00 4.85
2806 2851 1.048601 AGAAACGGAAGAGACAGGCA 58.951 50.000 0.00 0.00 0.00 4.75
2807 2852 1.416401 AGAAACGGAAGAGACAGGCAA 59.584 47.619 0.00 0.00 0.00 4.52
2808 2853 1.801178 GAAACGGAAGAGACAGGCAAG 59.199 52.381 0.00 0.00 0.00 4.01
2809 2854 0.035458 AACGGAAGAGACAGGCAAGG 59.965 55.000 0.00 0.00 0.00 3.61
2810 2855 1.122019 ACGGAAGAGACAGGCAAGGT 61.122 55.000 0.00 0.00 0.00 3.50
2811 2856 0.035458 CGGAAGAGACAGGCAAGGTT 59.965 55.000 0.00 0.00 0.00 3.50
2812 2857 1.275291 CGGAAGAGACAGGCAAGGTTA 59.725 52.381 0.00 0.00 0.00 2.85
2813 2858 2.675317 CGGAAGAGACAGGCAAGGTTAG 60.675 54.545 0.00 0.00 0.00 2.34
2814 2859 2.355209 GGAAGAGACAGGCAAGGTTAGG 60.355 54.545 0.00 0.00 0.00 2.69
2815 2860 1.280457 AGAGACAGGCAAGGTTAGGG 58.720 55.000 0.00 0.00 0.00 3.53
2816 2861 0.984995 GAGACAGGCAAGGTTAGGGT 59.015 55.000 0.00 0.00 0.00 4.34
2817 2862 0.693049 AGACAGGCAAGGTTAGGGTG 59.307 55.000 0.00 0.00 0.00 4.61
2818 2863 0.690762 GACAGGCAAGGTTAGGGTGA 59.309 55.000 0.00 0.00 0.00 4.02
2819 2864 0.693049 ACAGGCAAGGTTAGGGTGAG 59.307 55.000 0.00 0.00 0.00 3.51
2820 2865 0.678048 CAGGCAAGGTTAGGGTGAGC 60.678 60.000 0.00 0.00 0.00 4.26
2821 2866 1.745489 GGCAAGGTTAGGGTGAGCG 60.745 63.158 0.00 0.00 0.00 5.03
2822 2867 1.003718 GCAAGGTTAGGGTGAGCGT 60.004 57.895 0.00 0.00 0.00 5.07
2823 2868 1.019805 GCAAGGTTAGGGTGAGCGTC 61.020 60.000 0.00 0.00 0.00 5.19
2824 2869 0.736325 CAAGGTTAGGGTGAGCGTCG 60.736 60.000 0.00 0.00 0.00 5.12
2825 2870 1.183676 AAGGTTAGGGTGAGCGTCGT 61.184 55.000 0.00 0.00 0.00 4.34
2826 2871 1.445582 GGTTAGGGTGAGCGTCGTG 60.446 63.158 0.00 0.00 0.00 4.35
2827 2872 1.288127 GTTAGGGTGAGCGTCGTGT 59.712 57.895 0.00 0.00 0.00 4.49
2828 2873 0.523072 GTTAGGGTGAGCGTCGTGTA 59.477 55.000 0.00 0.00 0.00 2.90
2829 2874 1.133790 GTTAGGGTGAGCGTCGTGTAT 59.866 52.381 0.00 0.00 0.00 2.29
2830 2875 0.736636 TAGGGTGAGCGTCGTGTATG 59.263 55.000 0.00 0.00 0.00 2.39
2831 2876 1.518572 GGGTGAGCGTCGTGTATGG 60.519 63.158 0.00 0.00 0.00 2.74
2832 2877 1.509463 GGTGAGCGTCGTGTATGGA 59.491 57.895 0.00 0.00 0.00 3.41
2833 2878 0.801067 GGTGAGCGTCGTGTATGGAC 60.801 60.000 0.00 0.00 0.00 4.02
2834 2879 0.801067 GTGAGCGTCGTGTATGGACC 60.801 60.000 0.00 0.00 0.00 4.46
2835 2880 0.963856 TGAGCGTCGTGTATGGACCT 60.964 55.000 0.00 0.00 0.00 3.85
2836 2881 0.525668 GAGCGTCGTGTATGGACCTG 60.526 60.000 0.00 0.00 0.00 4.00
2837 2882 0.963856 AGCGTCGTGTATGGACCTGA 60.964 55.000 0.00 0.00 0.00 3.86
2838 2883 0.801067 GCGTCGTGTATGGACCTGAC 60.801 60.000 0.00 0.00 0.00 3.51
2839 2884 0.522705 CGTCGTGTATGGACCTGACG 60.523 60.000 0.00 0.00 42.37 4.35
2840 2885 0.801067 GTCGTGTATGGACCTGACGC 60.801 60.000 0.00 0.00 0.00 5.19
2841 2886 1.518572 CGTGTATGGACCTGACGCC 60.519 63.158 0.00 0.00 0.00 5.68
2842 2887 1.518572 GTGTATGGACCTGACGCCG 60.519 63.158 0.00 0.00 0.00 6.46
2843 2888 1.679641 TGTATGGACCTGACGCCGA 60.680 57.895 0.00 0.00 0.00 5.54
2844 2889 1.065928 GTATGGACCTGACGCCGAG 59.934 63.158 0.00 0.00 0.00 4.63
2845 2890 1.077285 TATGGACCTGACGCCGAGA 60.077 57.895 0.00 0.00 0.00 4.04
2846 2891 0.681887 TATGGACCTGACGCCGAGAA 60.682 55.000 0.00 0.00 0.00 2.87
2847 2892 1.330655 ATGGACCTGACGCCGAGAAT 61.331 55.000 0.00 0.00 0.00 2.40
2848 2893 1.519455 GGACCTGACGCCGAGAATG 60.519 63.158 0.00 0.00 0.00 2.67
2849 2894 1.215647 GACCTGACGCCGAGAATGT 59.784 57.895 0.00 0.00 0.00 2.71
2850 2895 0.454600 GACCTGACGCCGAGAATGTA 59.545 55.000 0.00 0.00 0.00 2.29
2851 2896 0.892755 ACCTGACGCCGAGAATGTAA 59.107 50.000 0.00 0.00 0.00 2.41
2852 2897 1.135083 ACCTGACGCCGAGAATGTAAG 60.135 52.381 0.00 0.00 0.00 2.34
2853 2898 0.924090 CTGACGCCGAGAATGTAAGC 59.076 55.000 0.00 0.00 0.00 3.09
2854 2899 0.459585 TGACGCCGAGAATGTAAGCC 60.460 55.000 0.00 0.00 0.00 4.35
2855 2900 1.152383 GACGCCGAGAATGTAAGCCC 61.152 60.000 0.00 0.00 0.00 5.19
2856 2901 1.153449 CGCCGAGAATGTAAGCCCA 60.153 57.895 0.00 0.00 0.00 5.36
2857 2902 0.742990 CGCCGAGAATGTAAGCCCAA 60.743 55.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.846248 AAACTTGAGTGAAATATGTAATGAAGC 57.154 29.630 0.00 0.00 0.00 3.86
82 83 8.296000 TCATTTTGATGTCACGTGTAATCAAAT 58.704 29.630 34.75 27.36 44.28 2.32
144 147 8.282801 TGGTACATATTCATTTAGGGGTACAT 57.717 34.615 0.00 0.00 33.39 2.29
210 213 7.310361 CCAAACCATATTTAGTGTTCATTGGGT 60.310 37.037 0.00 0.00 0.00 4.51
282 288 7.290014 TCTGTAATCTTCCATGGTTGCTATCTA 59.710 37.037 12.58 0.00 0.00 1.98
356 362 7.496529 TGGAACTGAACTTTACTGAATTGAG 57.503 36.000 0.00 0.00 0.00 3.02
360 366 6.998074 TGTGATGGAACTGAACTTTACTGAAT 59.002 34.615 0.00 0.00 0.00 2.57
381 387 2.697229 CCATGGAGCTACTCTGATGTGA 59.303 50.000 5.56 0.00 0.00 3.58
412 418 5.606749 ACTCATAGGATGCCCTTTACATGTA 59.393 40.000 0.08 0.08 40.78 2.29
437 443 3.920446 TGCATTAGTAGAGCACGACAAA 58.080 40.909 0.00 0.00 32.55 2.83
438 444 3.586100 TGCATTAGTAGAGCACGACAA 57.414 42.857 0.00 0.00 32.55 3.18
537 544 2.035832 AGCACACCAACAAACCATTAGC 59.964 45.455 0.00 0.00 0.00 3.09
549 556 2.948979 CTGTTTAGGTTGAGCACACCAA 59.051 45.455 2.20 0.00 0.00 3.67
552 559 2.222027 AGCTGTTTAGGTTGAGCACAC 58.778 47.619 0.00 0.00 33.67 3.82
557 564 5.412594 TCTTGCATTAGCTGTTTAGGTTGAG 59.587 40.000 0.00 0.00 42.74 3.02
603 610 5.804944 TTCACATGATCCATGGTGTTTTT 57.195 34.783 12.58 0.00 45.16 1.94
604 611 5.726397 CATTCACATGATCCATGGTGTTTT 58.274 37.500 12.58 0.00 45.16 2.43
608 615 2.691011 TGCATTCACATGATCCATGGTG 59.309 45.455 12.58 4.97 45.16 4.17
755 766 1.328680 CGGCACATATCACTTGACTGC 59.671 52.381 0.00 0.00 0.00 4.40
762 773 8.559536 CAAATATACTTTTCGGCACATATCACT 58.440 33.333 0.00 0.00 0.00 3.41
1091 1119 1.204467 CAGGTTGTTGCTGTTGTTGGT 59.796 47.619 0.00 0.00 0.00 3.67
1101 1132 2.027460 CGTTGCCCAGGTTGTTGC 59.973 61.111 0.00 0.00 0.00 4.17
1173 1204 0.743097 GGAATGGCATTCTCAGTGGC 59.257 55.000 32.48 15.31 41.99 5.01
1349 1380 0.249573 ATGTTGTGCTTGCTGTTGGC 60.250 50.000 0.00 0.00 42.22 4.52
1419 1450 1.298340 CTGGCATTGTACCGGGACA 59.702 57.895 17.93 17.93 0.00 4.02
1450 1481 1.198713 TGTTGTTGTTGTTGCCCCAT 58.801 45.000 0.00 0.00 0.00 4.00
1457 1488 5.649602 CAACTGTTGTTGTTGTTGTTGTT 57.350 34.783 12.30 0.00 46.08 2.83
1512 1543 1.003580 ACTGGGCTACACTGATGTTGG 59.996 52.381 0.00 0.00 40.48 3.77
1632 1663 0.254462 TATGGATGGCTTGGCAACGA 59.746 50.000 0.00 0.00 42.51 3.85
1713 1744 2.927580 ATGTTGTGCTGGCTGCTGC 61.928 57.895 17.45 7.10 43.37 5.25
1730 1761 1.871408 GCGACATCCGAATGCTCTCAT 60.871 52.381 0.00 0.00 41.76 2.90
1741 1772 2.892425 GGCCTGAAGCGACATCCG 60.892 66.667 0.00 0.00 45.17 4.18
1843 1880 2.436911 TGATCATCTAGCATGCACCACT 59.563 45.455 21.98 0.16 0.00 4.00
1851 1888 4.502016 CCGCTACATTGATCATCTAGCAT 58.498 43.478 19.24 0.00 31.84 3.79
1874 1911 5.542616 TGCATGGCATTTTTATTTTTCGG 57.457 34.783 0.00 0.00 31.71 4.30
1913 1950 9.797642 TCATCATTTCCATATTGCAACTAGTAT 57.202 29.630 0.00 0.00 0.00 2.12
1945 1982 3.859386 GGCAAATGCTTTATTCAGGAACG 59.141 43.478 5.25 0.00 41.70 3.95
2005 2042 5.412904 GGTTAAGTTCAACCAGAAGATCCAG 59.587 44.000 0.17 0.00 46.14 3.86
2038 2075 6.177610 TGGTTTAATGGGAGACATACAGAAC 58.822 40.000 0.00 0.00 39.40 3.01
2093 2131 6.757010 ACTCATATGTGTATTTTCCTCGTGTC 59.243 38.462 8.63 0.00 0.00 3.67
2141 2179 5.468746 CCCACGGTGGTATATTAAATCTGTG 59.531 44.000 24.70 0.79 35.17 3.66
2151 2189 2.039348 GGTTATGCCCACGGTGGTATAT 59.961 50.000 24.70 17.03 35.17 0.86
2152 2190 1.417145 GGTTATGCCCACGGTGGTATA 59.583 52.381 24.70 18.63 35.17 1.47
2294 2332 0.697854 AGGTCCCTGGTCCTTGTGTT 60.698 55.000 0.00 0.00 29.69 3.32
2308 2346 0.472471 TGTGTTCCTTCACCAGGTCC 59.528 55.000 0.00 0.00 44.37 4.46
2366 2404 2.772568 TGCCGACATGTGTTTGAAAG 57.227 45.000 1.15 0.00 0.00 2.62
2370 2408 2.682352 TGGATATGCCGACATGTGTTTG 59.318 45.455 1.15 0.00 40.66 2.93
2381 2419 3.441496 AGCACATTTTTGGATATGCCG 57.559 42.857 0.00 0.00 40.66 5.69
2452 2490 2.607635 CACGTCGCAATAACTATGGCTT 59.392 45.455 0.00 0.00 30.28 4.35
2562 2601 4.109766 TCACCGCAGTTTTGATACTATCG 58.890 43.478 0.00 0.00 0.00 2.92
2580 2619 2.079925 CTGCTCTTAAGTTGCCTCACC 58.920 52.381 16.28 0.00 0.00 4.02
2585 2624 5.277731 GCTGATTATCTGCTCTTAAGTTGCC 60.278 44.000 15.28 4.59 38.17 4.52
2587 2626 5.050499 CGGCTGATTATCTGCTCTTAAGTTG 60.050 44.000 20.33 0.00 40.57 3.16
2592 2631 2.365293 TGCGGCTGATTATCTGCTCTTA 59.635 45.455 20.33 5.70 40.57 2.10
2599 2638 3.070734 AGTGAGATTGCGGCTGATTATCT 59.929 43.478 0.00 0.02 0.00 1.98
2603 2642 1.209019 AGAGTGAGATTGCGGCTGATT 59.791 47.619 0.00 0.00 0.00 2.57
2662 2707 7.424227 ACTGAACTATATAGTACGAGCAGTC 57.576 40.000 15.74 7.73 34.99 3.51
2691 2736 1.407258 CCTGCCGTCAAACTGGAAAAA 59.593 47.619 0.00 0.00 0.00 1.94
2692 2737 1.028905 CCTGCCGTCAAACTGGAAAA 58.971 50.000 0.00 0.00 0.00 2.29
2693 2738 0.821711 CCCTGCCGTCAAACTGGAAA 60.822 55.000 0.00 0.00 0.00 3.13
2694 2739 1.228124 CCCTGCCGTCAAACTGGAA 60.228 57.895 0.00 0.00 0.00 3.53
2695 2740 1.122632 TACCCTGCCGTCAAACTGGA 61.123 55.000 0.00 0.00 0.00 3.86
2696 2741 0.250553 TTACCCTGCCGTCAAACTGG 60.251 55.000 0.00 0.00 0.00 4.00
2697 2742 0.872388 GTTACCCTGCCGTCAAACTG 59.128 55.000 0.00 0.00 0.00 3.16
2698 2743 0.763035 AGTTACCCTGCCGTCAAACT 59.237 50.000 0.00 0.00 0.00 2.66
2699 2744 0.872388 CAGTTACCCTGCCGTCAAAC 59.128 55.000 0.00 0.00 33.59 2.93
2700 2745 3.315765 CAGTTACCCTGCCGTCAAA 57.684 52.632 0.00 0.00 33.59 2.69
2708 2753 0.322816 ACCATGCAGCAGTTACCCTG 60.323 55.000 0.00 0.00 44.53 4.45
2709 2754 0.035056 GACCATGCAGCAGTTACCCT 60.035 55.000 0.00 0.00 0.00 4.34
2710 2755 1.032114 GGACCATGCAGCAGTTACCC 61.032 60.000 0.00 0.00 0.00 3.69
2711 2756 0.035056 AGGACCATGCAGCAGTTACC 60.035 55.000 0.00 2.31 0.00 2.85
2712 2757 1.089920 CAGGACCATGCAGCAGTTAC 58.910 55.000 0.00 0.00 0.00 2.50
2713 2758 0.983467 TCAGGACCATGCAGCAGTTA 59.017 50.000 0.00 0.00 0.00 2.24
2714 2759 0.607489 GTCAGGACCATGCAGCAGTT 60.607 55.000 0.00 0.00 0.00 3.16
2715 2760 1.002868 GTCAGGACCATGCAGCAGT 60.003 57.895 0.00 0.00 0.00 4.40
2716 2761 0.538584 TAGTCAGGACCATGCAGCAG 59.461 55.000 0.00 0.00 0.00 4.24
2717 2762 0.538584 CTAGTCAGGACCATGCAGCA 59.461 55.000 0.00 0.00 0.00 4.41
2718 2763 0.813210 GCTAGTCAGGACCATGCAGC 60.813 60.000 0.00 0.00 0.00 5.25
2719 2764 0.829333 AGCTAGTCAGGACCATGCAG 59.171 55.000 0.00 0.00 0.00 4.41
2720 2765 1.065926 CAAGCTAGTCAGGACCATGCA 60.066 52.381 0.00 0.00 0.00 3.96
2721 2766 1.661341 CAAGCTAGTCAGGACCATGC 58.339 55.000 0.00 0.00 0.00 4.06
2722 2767 1.833630 TCCAAGCTAGTCAGGACCATG 59.166 52.381 0.00 0.00 0.00 3.66
2723 2768 2.254152 TCCAAGCTAGTCAGGACCAT 57.746 50.000 0.00 0.00 0.00 3.55
2724 2769 2.254152 ATCCAAGCTAGTCAGGACCA 57.746 50.000 0.00 0.00 32.04 4.02
2725 2770 4.965200 ATAATCCAAGCTAGTCAGGACC 57.035 45.455 0.00 0.00 32.04 4.46
2726 2771 7.014808 AGTCTTATAATCCAAGCTAGTCAGGAC 59.985 40.741 0.00 0.00 32.04 3.85
2727 2772 7.069986 AGTCTTATAATCCAAGCTAGTCAGGA 58.930 38.462 0.00 2.40 34.12 3.86
2728 2773 7.296628 AGTCTTATAATCCAAGCTAGTCAGG 57.703 40.000 0.00 0.00 0.00 3.86
2738 2783 9.174166 GGCAACTCTTAAAGTCTTATAATCCAA 57.826 33.333 0.00 0.00 37.17 3.53
2739 2784 8.732746 GGCAACTCTTAAAGTCTTATAATCCA 57.267 34.615 0.00 0.00 37.17 3.41
2775 2820 8.396390 GTCTCTTCCGTTTCTTAAAGTCTTTTT 58.604 33.333 2.51 0.00 0.00 1.94
2776 2821 7.551617 TGTCTCTTCCGTTTCTTAAAGTCTTTT 59.448 33.333 2.51 0.00 0.00 2.27
2777 2822 7.046033 TGTCTCTTCCGTTTCTTAAAGTCTTT 58.954 34.615 2.81 2.81 0.00 2.52
2778 2823 6.579865 TGTCTCTTCCGTTTCTTAAAGTCTT 58.420 36.000 0.00 0.00 0.00 3.01
2779 2824 6.158023 TGTCTCTTCCGTTTCTTAAAGTCT 57.842 37.500 0.00 0.00 0.00 3.24
2780 2825 5.405873 CCTGTCTCTTCCGTTTCTTAAAGTC 59.594 44.000 0.00 0.00 0.00 3.01
2781 2826 5.298347 CCTGTCTCTTCCGTTTCTTAAAGT 58.702 41.667 0.00 0.00 0.00 2.66
2782 2827 4.152580 GCCTGTCTCTTCCGTTTCTTAAAG 59.847 45.833 0.00 0.00 0.00 1.85
2783 2828 4.062991 GCCTGTCTCTTCCGTTTCTTAAA 58.937 43.478 0.00 0.00 0.00 1.52
2784 2829 3.070446 TGCCTGTCTCTTCCGTTTCTTAA 59.930 43.478 0.00 0.00 0.00 1.85
2785 2830 2.631062 TGCCTGTCTCTTCCGTTTCTTA 59.369 45.455 0.00 0.00 0.00 2.10
2786 2831 1.416401 TGCCTGTCTCTTCCGTTTCTT 59.584 47.619 0.00 0.00 0.00 2.52
2787 2832 1.048601 TGCCTGTCTCTTCCGTTTCT 58.951 50.000 0.00 0.00 0.00 2.52
2788 2833 1.801178 CTTGCCTGTCTCTTCCGTTTC 59.199 52.381 0.00 0.00 0.00 2.78
2789 2834 1.543429 CCTTGCCTGTCTCTTCCGTTT 60.543 52.381 0.00 0.00 0.00 3.60
2790 2835 0.035458 CCTTGCCTGTCTCTTCCGTT 59.965 55.000 0.00 0.00 0.00 4.44
2791 2836 1.122019 ACCTTGCCTGTCTCTTCCGT 61.122 55.000 0.00 0.00 0.00 4.69
2792 2837 0.035458 AACCTTGCCTGTCTCTTCCG 59.965 55.000 0.00 0.00 0.00 4.30
2793 2838 2.355209 CCTAACCTTGCCTGTCTCTTCC 60.355 54.545 0.00 0.00 0.00 3.46
2794 2839 2.355209 CCCTAACCTTGCCTGTCTCTTC 60.355 54.545 0.00 0.00 0.00 2.87
2795 2840 1.630878 CCCTAACCTTGCCTGTCTCTT 59.369 52.381 0.00 0.00 0.00 2.85
2796 2841 1.280457 CCCTAACCTTGCCTGTCTCT 58.720 55.000 0.00 0.00 0.00 3.10
2797 2842 0.984995 ACCCTAACCTTGCCTGTCTC 59.015 55.000 0.00 0.00 0.00 3.36
2798 2843 0.693049 CACCCTAACCTTGCCTGTCT 59.307 55.000 0.00 0.00 0.00 3.41
2799 2844 0.690762 TCACCCTAACCTTGCCTGTC 59.309 55.000 0.00 0.00 0.00 3.51
2800 2845 0.693049 CTCACCCTAACCTTGCCTGT 59.307 55.000 0.00 0.00 0.00 4.00
2801 2846 0.678048 GCTCACCCTAACCTTGCCTG 60.678 60.000 0.00 0.00 0.00 4.85
2802 2847 1.685820 GCTCACCCTAACCTTGCCT 59.314 57.895 0.00 0.00 0.00 4.75
2803 2848 1.745489 CGCTCACCCTAACCTTGCC 60.745 63.158 0.00 0.00 0.00 4.52
2804 2849 1.003718 ACGCTCACCCTAACCTTGC 60.004 57.895 0.00 0.00 0.00 4.01
2805 2850 0.736325 CGACGCTCACCCTAACCTTG 60.736 60.000 0.00 0.00 0.00 3.61
2806 2851 1.183676 ACGACGCTCACCCTAACCTT 61.184 55.000 0.00 0.00 0.00 3.50
2807 2852 1.605738 ACGACGCTCACCCTAACCT 60.606 57.895 0.00 0.00 0.00 3.50
2808 2853 1.445582 CACGACGCTCACCCTAACC 60.446 63.158 0.00 0.00 0.00 2.85
2809 2854 0.523072 TACACGACGCTCACCCTAAC 59.477 55.000 0.00 0.00 0.00 2.34
2810 2855 1.133598 CATACACGACGCTCACCCTAA 59.866 52.381 0.00 0.00 0.00 2.69
2811 2856 0.736636 CATACACGACGCTCACCCTA 59.263 55.000 0.00 0.00 0.00 3.53
2812 2857 1.511305 CATACACGACGCTCACCCT 59.489 57.895 0.00 0.00 0.00 4.34
2813 2858 1.518572 CCATACACGACGCTCACCC 60.519 63.158 0.00 0.00 0.00 4.61
2814 2859 0.801067 GTCCATACACGACGCTCACC 60.801 60.000 0.00 0.00 0.00 4.02
2815 2860 0.801067 GGTCCATACACGACGCTCAC 60.801 60.000 0.00 0.00 0.00 3.51
2816 2861 0.963856 AGGTCCATACACGACGCTCA 60.964 55.000 0.00 0.00 0.00 4.26
2817 2862 0.525668 CAGGTCCATACACGACGCTC 60.526 60.000 0.00 0.00 0.00 5.03
2818 2863 0.963856 TCAGGTCCATACACGACGCT 60.964 55.000 0.00 0.00 0.00 5.07
2819 2864 0.801067 GTCAGGTCCATACACGACGC 60.801 60.000 0.00 0.00 0.00 5.19
2820 2865 0.522705 CGTCAGGTCCATACACGACG 60.523 60.000 0.00 0.00 41.95 5.12
2821 2866 0.801067 GCGTCAGGTCCATACACGAC 60.801 60.000 0.00 0.00 32.08 4.34
2822 2867 1.509463 GCGTCAGGTCCATACACGA 59.491 57.895 0.00 0.00 32.08 4.35
2823 2868 1.518572 GGCGTCAGGTCCATACACG 60.519 63.158 0.00 0.00 0.00 4.49
2824 2869 1.518572 CGGCGTCAGGTCCATACAC 60.519 63.158 0.00 0.00 0.00 2.90
2825 2870 1.663379 CTCGGCGTCAGGTCCATACA 61.663 60.000 6.85 0.00 0.00 2.29
2826 2871 1.065928 CTCGGCGTCAGGTCCATAC 59.934 63.158 6.85 0.00 0.00 2.39
2827 2872 0.681887 TTCTCGGCGTCAGGTCCATA 60.682 55.000 6.85 0.00 0.00 2.74
2828 2873 1.330655 ATTCTCGGCGTCAGGTCCAT 61.331 55.000 6.85 0.00 0.00 3.41
2829 2874 1.982395 ATTCTCGGCGTCAGGTCCA 60.982 57.895 6.85 0.00 0.00 4.02
2830 2875 1.519455 CATTCTCGGCGTCAGGTCC 60.519 63.158 6.85 0.00 0.00 4.46
2831 2876 0.454600 TACATTCTCGGCGTCAGGTC 59.545 55.000 6.85 0.00 0.00 3.85
2832 2877 0.892755 TTACATTCTCGGCGTCAGGT 59.107 50.000 6.85 2.46 0.00 4.00
2833 2878 1.560923 CTTACATTCTCGGCGTCAGG 58.439 55.000 6.85 0.00 0.00 3.86
2834 2879 0.924090 GCTTACATTCTCGGCGTCAG 59.076 55.000 6.85 0.00 0.00 3.51
2835 2880 0.459585 GGCTTACATTCTCGGCGTCA 60.460 55.000 6.85 0.00 0.00 4.35
2836 2881 1.152383 GGGCTTACATTCTCGGCGTC 61.152 60.000 6.85 0.00 0.00 5.19
2837 2882 1.153429 GGGCTTACATTCTCGGCGT 60.153 57.895 6.85 0.00 0.00 5.68
2838 2883 0.742990 TTGGGCTTACATTCTCGGCG 60.743 55.000 0.00 0.00 0.00 6.46
2839 2884 3.168773 TTGGGCTTACATTCTCGGC 57.831 52.632 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.