Multiple sequence alignment - TraesCS1A01G434400

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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 TraesCS1A01G434400 chr1A 100.000 3067 0 0 1 3067 584970255 584973321 0.000000e+00 5664
1 TraesCS1A01G434400 chr1A 93.240 1997 99 10 23 1986 532735357 532733364 0.000000e+00 2907
2 TraesCS1A01G434400 chr1A 93.519 1296 54 9 23 1292 12307824 12309115 0.000000e+00 1901
3 TraesCS1A01G434400 chr3B 98.596 2350 21 3 21 2367 772227340 772229680 0.000000e+00 4146
4 TraesCS1A01G434400 chr5B 97.580 2355 45 8 23 2367 26737128 26734776 0.000000e+00 4023
5 TraesCS1A01G434400 chr7B 95.707 2236 82 7 23 2256 706976399 706974176 0.000000e+00 3585
6 TraesCS1A01G434400 chr1B 94.220 2353 99 14 23 2371 182058483 182060802 0.000000e+00 3557
7 TraesCS1A01G434400 chr5A 93.477 1993 97 11 23 1986 673237857 673239845 0.000000e+00 2929
8 TraesCS1A01G434400 chr2A 93.266 1990 102 9 23 1986 776173510 776175493 0.000000e+00 2904
9 TraesCS1A01G434400 chr2A 93.015 1990 103 11 23 1986 9951340 9953319 0.000000e+00 2872
10 TraesCS1A01G434400 chr2A 93.675 332 18 3 2038 2367 9953313 9953643 7.640000e-136 494
11 TraesCS1A01G434400 chr2A 91.071 336 17 3 2038 2371 776175487 776175811 2.810000e-120 442
12 TraesCS1A01G434400 chr2A 83.436 163 24 3 2206 2367 759809205 759809045 6.850000e-32 148
13 TraesCS1A01G434400 chr2A 83.439 157 18 8 2216 2368 347830007 347830159 4.120000e-29 139
14 TraesCS1A01G434400 chr3A 92.643 1971 102 16 20 1957 698295902 698297862 0.000000e+00 2796
15 TraesCS1A01G434400 chrUn 90.759 1331 95 10 1048 2367 117079696 117081009 0.000000e+00 1751
16 TraesCS1A01G434400 chr7A 82.594 586 74 17 1541 2111 684294958 684295530 2.750000e-135 492
17 TraesCS1A01G434400 chr7A 83.735 166 20 7 2205 2367 50167802 50167963 1.910000e-32 150
18 TraesCS1A01G434400 chr7A 84.615 156 16 8 2216 2367 733264385 733264234 6.850000e-32 148
19 TraesCS1A01G434400 chr1D 87.138 311 14 6 2762 3054 427860082 427859780 2.280000e-86 329
20 TraesCS1A01G434400 chr1D 81.200 250 17 11 2359 2592 427860422 427860187 1.130000e-39 174


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 TraesCS1A01G434400 chr1A 584970255 584973321 3066 False 5664.0 5664 100.0000 1 3067 1 chr1A.!!$F2 3066
1 TraesCS1A01G434400 chr1A 532733364 532735357 1993 True 2907.0 2907 93.2400 23 1986 1 chr1A.!!$R1 1963
2 TraesCS1A01G434400 chr1A 12307824 12309115 1291 False 1901.0 1901 93.5190 23 1292 1 chr1A.!!$F1 1269
3 TraesCS1A01G434400 chr3B 772227340 772229680 2340 False 4146.0 4146 98.5960 21 2367 1 chr3B.!!$F1 2346
4 TraesCS1A01G434400 chr5B 26734776 26737128 2352 True 4023.0 4023 97.5800 23 2367 1 chr5B.!!$R1 2344
5 TraesCS1A01G434400 chr7B 706974176 706976399 2223 True 3585.0 3585 95.7070 23 2256 1 chr7B.!!$R1 2233
6 TraesCS1A01G434400 chr1B 182058483 182060802 2319 False 3557.0 3557 94.2200 23 2371 1 chr1B.!!$F1 2348
7 TraesCS1A01G434400 chr5A 673237857 673239845 1988 False 2929.0 2929 93.4770 23 1986 1 chr5A.!!$F1 1963
8 TraesCS1A01G434400 chr2A 9951340 9953643 2303 False 1683.0 2872 93.3450 23 2367 2 chr2A.!!$F2 2344
9 TraesCS1A01G434400 chr2A 776173510 776175811 2301 False 1673.0 2904 92.1685 23 2371 2 chr2A.!!$F3 2348
10 TraesCS1A01G434400 chr3A 698295902 698297862 1960 False 2796.0 2796 92.6430 20 1957 1 chr3A.!!$F1 1937
11 TraesCS1A01G434400 chrUn 117079696 117081009 1313 False 1751.0 1751 90.7590 1048 2367 1 chrUn.!!$F1 1319
12 TraesCS1A01G434400 chr7A 684294958 684295530 572 False 492.0 492 82.5940 1541 2111 1 chr7A.!!$F2 570
13 TraesCS1A01G434400 chr1D 427859780 427860422 642 True 251.5 329 84.1690 2359 3054 2 chr1D.!!$R1 695

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
809 841 1.291335 GGGGAAGTAGAGGAGGAGGAA 59.709 57.143 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 2733 0.036199 ACGAGCTCGAGGTACTGAGT 60.036 55.0 40.58 13.0 41.55 3.41 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
19 20 2.440539 GACACTAGGCCATATCCGTG 57.559 55.000 5.01 5.05 0.00 4.94
657 684 4.158209 TGCACGAATTTGATTGATGGATGT 59.842 37.500 0.00 0.00 0.00 3.06
809 841 1.291335 GGGGAAGTAGAGGAGGAGGAA 59.709 57.143 0.00 0.00 0.00 3.36
1564 1628 3.936564 TGTGTGTGCAAGCTCATGTATA 58.063 40.909 0.00 0.00 0.00 1.47
1580 1644 9.801873 GCTCATGTATATGTTGTTTTTGGTATT 57.198 29.630 0.00 0.00 35.73 1.89
2399 2499 1.141881 GGCATCGAGGACGTCATGT 59.858 57.895 18.91 0.24 40.69 3.21
2440 2540 2.424246 GCGACTAGCTACTGGAAGAACT 59.576 50.000 0.00 0.00 44.04 3.01
2441 2541 3.732471 GCGACTAGCTACTGGAAGAACTG 60.732 52.174 0.00 0.00 44.04 3.16
2442 2542 3.732471 CGACTAGCTACTGGAAGAACTGC 60.732 52.174 0.00 0.00 37.43 4.40
2443 2543 3.165875 ACTAGCTACTGGAAGAACTGCA 58.834 45.455 0.00 0.00 37.43 4.41
2444 2544 2.464157 AGCTACTGGAAGAACTGCAC 57.536 50.000 0.00 0.00 37.43 4.57
2445 2545 1.694150 AGCTACTGGAAGAACTGCACA 59.306 47.619 0.00 0.00 37.43 4.57
2446 2546 2.072298 GCTACTGGAAGAACTGCACAG 58.928 52.381 0.00 0.00 37.43 3.66
2447 2547 2.072298 CTACTGGAAGAACTGCACAGC 58.928 52.381 0.00 0.00 37.43 4.40
2448 2548 0.882042 ACTGGAAGAACTGCACAGCG 60.882 55.000 0.00 0.00 37.43 5.18
2456 2559 2.063541 AACTGCACAGCGAAGTTGCC 62.064 55.000 0.00 0.00 44.63 4.52
2479 2582 2.663852 CGGAAGTTTGGCGTCGGT 60.664 61.111 0.00 0.00 0.00 4.69
2481 2584 2.613506 GGAAGTTTGGCGTCGGTGG 61.614 63.158 0.00 0.00 0.00 4.61
2482 2585 1.890510 GAAGTTTGGCGTCGGTGGT 60.891 57.895 0.00 0.00 0.00 4.16
2483 2586 0.600782 GAAGTTTGGCGTCGGTGGTA 60.601 55.000 0.00 0.00 0.00 3.25
2485 2588 1.594836 GTTTGGCGTCGGTGGTACA 60.595 57.895 0.00 0.00 0.00 2.90
2486 2589 0.952010 GTTTGGCGTCGGTGGTACAT 60.952 55.000 0.00 0.00 44.52 2.29
2487 2590 0.951525 TTTGGCGTCGGTGGTACATG 60.952 55.000 0.00 0.00 44.52 3.21
2488 2591 3.192922 GGCGTCGGTGGTACATGC 61.193 66.667 0.00 0.00 44.52 4.06
2489 2592 3.192922 GCGTCGGTGGTACATGCC 61.193 66.667 0.00 0.00 44.52 4.40
2491 2594 2.263540 GTCGGTGGTACATGCCGT 59.736 61.111 17.36 0.00 46.24 5.68
2492 2595 1.375013 GTCGGTGGTACATGCCGTT 60.375 57.895 17.36 0.00 46.24 4.44
2494 2597 0.607112 TCGGTGGTACATGCCGTTAA 59.393 50.000 17.36 1.42 46.24 2.01
2551 2663 0.175760 GACGATGCAGTTAGGCCTCA 59.824 55.000 9.68 0.00 0.00 3.86
2552 2664 0.613260 ACGATGCAGTTAGGCCTCAA 59.387 50.000 9.68 0.00 0.00 3.02
2553 2665 1.293924 CGATGCAGTTAGGCCTCAAG 58.706 55.000 9.68 0.00 0.00 3.02
2554 2666 1.020437 GATGCAGTTAGGCCTCAAGC 58.980 55.000 9.68 10.74 42.60 4.01
2555 2667 0.745845 ATGCAGTTAGGCCTCAAGCG 60.746 55.000 9.68 0.00 45.17 4.68
2556 2668 2.109126 GCAGTTAGGCCTCAAGCGG 61.109 63.158 9.68 0.00 45.17 5.52
2577 2689 2.169789 CAGCGAGCAAGGACATCCG 61.170 63.158 0.00 0.00 42.08 4.18
2598 2710 3.583383 GCAGAACAGCCTCGCATT 58.417 55.556 0.00 0.00 0.00 3.56
2599 2711 1.427020 GCAGAACAGCCTCGCATTC 59.573 57.895 0.00 0.00 0.00 2.67
2600 2712 1.986575 GCAGAACAGCCTCGCATTCC 61.987 60.000 0.00 0.00 29.85 3.01
2601 2713 0.392193 CAGAACAGCCTCGCATTCCT 60.392 55.000 0.00 0.00 29.85 3.36
2602 2714 0.107945 AGAACAGCCTCGCATTCCTC 60.108 55.000 0.00 0.00 29.85 3.71
2603 2715 1.424493 GAACAGCCTCGCATTCCTCG 61.424 60.000 0.00 0.00 0.00 4.63
2606 2718 4.162690 GCCTCGCATTCCTCGGGT 62.163 66.667 0.00 0.00 0.00 5.28
2607 2719 2.792947 GCCTCGCATTCCTCGGGTA 61.793 63.158 0.00 0.00 0.00 3.69
2609 2721 1.672854 CCTCGCATTCCTCGGGTACA 61.673 60.000 0.00 0.00 0.00 2.90
2610 2722 0.527817 CTCGCATTCCTCGGGTACAC 60.528 60.000 0.00 0.00 0.00 2.90
2611 2723 1.520787 CGCATTCCTCGGGTACACC 60.521 63.158 0.00 0.00 0.00 4.16
2622 2734 2.868253 GGTACACCCAGCCATGAAC 58.132 57.895 0.00 0.00 0.00 3.18
2624 2736 1.679032 GGTACACCCAGCCATGAACTC 60.679 57.143 0.00 0.00 0.00 3.01
2625 2737 1.003118 GTACACCCAGCCATGAACTCA 59.997 52.381 0.00 0.00 0.00 3.41
2626 2738 0.037303 ACACCCAGCCATGAACTCAG 59.963 55.000 0.00 0.00 0.00 3.35
2628 2740 1.278985 CACCCAGCCATGAACTCAGTA 59.721 52.381 0.00 0.00 0.00 2.74
2629 2741 1.279271 ACCCAGCCATGAACTCAGTAC 59.721 52.381 0.00 0.00 0.00 2.73
2630 2742 1.407437 CCCAGCCATGAACTCAGTACC 60.407 57.143 0.00 0.00 0.00 3.34
2633 2745 1.478510 AGCCATGAACTCAGTACCTCG 59.521 52.381 0.00 0.00 0.00 4.63
2634 2746 1.476891 GCCATGAACTCAGTACCTCGA 59.523 52.381 0.00 0.00 0.00 4.04
2635 2747 2.480416 GCCATGAACTCAGTACCTCGAG 60.480 54.545 5.13 5.13 35.30 4.04
2636 2748 2.480416 CCATGAACTCAGTACCTCGAGC 60.480 54.545 6.99 0.00 32.21 5.03
2638 2750 2.085320 TGAACTCAGTACCTCGAGCTC 58.915 52.381 6.99 2.73 32.21 4.09
2640 2752 0.036199 ACTCAGTACCTCGAGCTCGT 60.036 55.000 33.33 18.64 40.80 4.18
2641 2753 0.653636 CTCAGTACCTCGAGCTCGTC 59.346 60.000 33.33 19.19 40.80 4.20
2657 2769 2.360794 GTCGAAGTAGACGGCAAGC 58.639 57.895 0.00 0.00 35.39 4.01
2658 2770 1.077089 GTCGAAGTAGACGGCAAGCC 61.077 60.000 0.00 0.00 35.39 4.35
2659 2771 1.810030 CGAAGTAGACGGCAAGCCC 60.810 63.158 5.34 0.00 0.00 5.19
2660 2772 1.295423 GAAGTAGACGGCAAGCCCA 59.705 57.895 5.34 0.00 0.00 5.36
2661 2773 0.741221 GAAGTAGACGGCAAGCCCAG 60.741 60.000 5.34 0.00 0.00 4.45
2662 2774 2.804828 AAGTAGACGGCAAGCCCAGC 62.805 60.000 5.34 0.00 0.00 4.85
2663 2775 4.451150 TAGACGGCAAGCCCAGCG 62.451 66.667 5.34 0.00 0.00 5.18
2685 2797 3.348647 GGCCATGCCCTTTTAATTTGT 57.651 42.857 0.00 0.00 44.06 2.83
2686 2798 3.009026 GGCCATGCCCTTTTAATTTGTG 58.991 45.455 0.00 0.00 44.06 3.33
2687 2799 2.419673 GCCATGCCCTTTTAATTTGTGC 59.580 45.455 0.00 0.00 0.00 4.57
2689 2801 2.447244 TGCCCTTTTAATTTGTGCGG 57.553 45.000 0.00 0.00 0.00 5.69
2690 2802 1.001406 TGCCCTTTTAATTTGTGCGGG 59.999 47.619 0.00 0.00 0.00 6.13
2691 2803 1.273886 GCCCTTTTAATTTGTGCGGGA 59.726 47.619 0.00 0.00 31.85 5.14
2692 2804 2.673893 GCCCTTTTAATTTGTGCGGGAG 60.674 50.000 0.00 0.00 31.85 4.30
2693 2805 2.094234 CCCTTTTAATTTGTGCGGGAGG 60.094 50.000 0.00 0.00 31.85 4.30
2694 2806 2.823154 CCTTTTAATTTGTGCGGGAGGA 59.177 45.455 0.00 0.00 0.00 3.71
2695 2807 3.119495 CCTTTTAATTTGTGCGGGAGGAG 60.119 47.826 0.00 0.00 0.00 3.69
2696 2808 1.459450 TTAATTTGTGCGGGAGGAGC 58.541 50.000 0.00 0.00 0.00 4.70
2697 2809 0.618458 TAATTTGTGCGGGAGGAGCT 59.382 50.000 0.00 0.00 35.28 4.09
2698 2810 0.618458 AATTTGTGCGGGAGGAGCTA 59.382 50.000 0.00 0.00 35.28 3.32
2699 2811 0.179000 ATTTGTGCGGGAGGAGCTAG 59.821 55.000 0.00 0.00 35.28 3.42
2700 2812 2.521958 TTTGTGCGGGAGGAGCTAGC 62.522 60.000 6.62 6.62 35.28 3.42
2701 2813 3.461773 GTGCGGGAGGAGCTAGCA 61.462 66.667 18.83 0.00 35.28 3.49
2702 2814 2.444706 TGCGGGAGGAGCTAGCAT 60.445 61.111 18.83 1.59 35.28 3.79
2703 2815 2.341911 GCGGGAGGAGCTAGCATC 59.658 66.667 18.83 11.52 0.00 3.91
2704 2816 2.502492 GCGGGAGGAGCTAGCATCA 61.502 63.158 18.83 0.00 0.00 3.07
2705 2817 1.365633 CGGGAGGAGCTAGCATCAC 59.634 63.158 18.83 11.85 0.00 3.06
2706 2818 1.751563 GGGAGGAGCTAGCATCACC 59.248 63.158 18.83 15.18 0.00 4.02
2707 2819 1.050988 GGGAGGAGCTAGCATCACCA 61.051 60.000 18.83 0.00 0.00 4.17
2708 2820 0.392336 GGAGGAGCTAGCATCACCAG 59.608 60.000 18.83 0.00 0.00 4.00
2709 2821 0.249826 GAGGAGCTAGCATCACCAGC 60.250 60.000 18.83 7.30 35.49 4.85
2710 2822 1.593750 GGAGCTAGCATCACCAGCG 60.594 63.158 18.83 0.00 40.29 5.18
2711 2823 1.439228 GAGCTAGCATCACCAGCGA 59.561 57.895 18.83 0.00 40.29 4.93
2712 2824 0.597118 GAGCTAGCATCACCAGCGAG 60.597 60.000 18.83 0.00 40.29 5.03
2713 2825 1.593750 GCTAGCATCACCAGCGAGG 60.594 63.158 10.63 0.00 45.67 4.63
2723 2835 3.322514 CCAGCGAGGTTTCCTTTGA 57.677 52.632 0.00 0.00 31.76 2.69
2724 2836 1.160137 CCAGCGAGGTTTCCTTTGAG 58.840 55.000 0.00 0.00 31.76 3.02
2725 2837 1.160137 CAGCGAGGTTTCCTTTGAGG 58.840 55.000 0.00 0.00 31.76 3.86
2726 2838 0.606673 AGCGAGGTTTCCTTTGAGGC 60.607 55.000 0.00 0.00 34.61 4.70
2727 2839 0.889186 GCGAGGTTTCCTTTGAGGCA 60.889 55.000 0.00 0.00 34.61 4.75
2728 2840 1.604604 CGAGGTTTCCTTTGAGGCAA 58.395 50.000 0.00 0.00 34.61 4.52
2729 2841 1.953686 CGAGGTTTCCTTTGAGGCAAA 59.046 47.619 0.00 0.00 34.61 3.68
2731 2843 1.688735 AGGTTTCCTTTGAGGCAAAGC 59.311 47.619 13.03 7.12 46.44 3.51
2732 2844 5.418607 GAGGTTTCCTTTGAGGCAAAGCC 62.419 52.174 13.03 0.00 46.44 4.35
2744 2856 3.236632 GGCAAAGCCTTGAATAGGTTG 57.763 47.619 0.00 0.00 46.69 3.77
2745 2857 2.610433 GCAAAGCCTTGAATAGGTTGC 58.390 47.619 0.00 0.00 46.61 4.17
2746 2858 2.232208 GCAAAGCCTTGAATAGGTTGCT 59.768 45.455 0.00 0.00 45.67 3.91
2747 2859 3.841643 CAAAGCCTTGAATAGGTTGCTG 58.158 45.455 0.00 0.00 46.61 4.41
2748 2860 2.134789 AGCCTTGAATAGGTTGCTGG 57.865 50.000 0.00 0.00 46.61 4.85
2749 2861 0.457443 GCCTTGAATAGGTTGCTGGC 59.543 55.000 0.00 0.00 46.61 4.85
2750 2862 1.838112 CCTTGAATAGGTTGCTGGCA 58.162 50.000 0.00 0.00 39.39 4.92
2751 2863 2.170166 CCTTGAATAGGTTGCTGGCAA 58.830 47.619 3.72 3.72 39.39 4.52
2752 2864 2.562298 CCTTGAATAGGTTGCTGGCAAA 59.438 45.455 9.67 0.00 39.39 3.68
2753 2865 3.196254 CCTTGAATAGGTTGCTGGCAAAT 59.804 43.478 9.67 4.79 39.39 2.32
2754 2866 4.322953 CCTTGAATAGGTTGCTGGCAAATT 60.323 41.667 9.67 6.51 39.39 1.82
2755 2867 5.105392 CCTTGAATAGGTTGCTGGCAAATTA 60.105 40.000 9.67 6.12 39.39 1.40
2756 2868 5.991933 TGAATAGGTTGCTGGCAAATTAA 57.008 34.783 9.67 0.00 37.70 1.40
2757 2869 5.964758 TGAATAGGTTGCTGGCAAATTAAG 58.035 37.500 9.67 0.00 37.70 1.85
2758 2870 5.714333 TGAATAGGTTGCTGGCAAATTAAGA 59.286 36.000 9.67 0.00 37.70 2.10
2759 2871 5.841957 ATAGGTTGCTGGCAAATTAAGAG 57.158 39.130 9.67 0.00 37.70 2.85
2760 2872 2.232208 AGGTTGCTGGCAAATTAAGAGC 59.768 45.455 9.67 0.00 37.70 4.09
2769 2881 5.804639 TGGCAAATTAAGAGCTCTTCAGTA 58.195 37.500 31.67 12.47 37.40 2.74
2788 2900 2.198827 ATCATGCGTGTTTCCCTGAA 57.801 45.000 5.68 0.00 0.00 3.02
2798 2910 3.028130 TGTTTCCCTGAAAACCAGTTCC 58.972 45.455 0.00 0.00 41.33 3.62
2809 2925 4.722361 AAACCAGTTCCGCTGTTTAAAA 57.278 36.364 0.00 0.00 43.55 1.52
2817 2933 3.391965 TCCGCTGTTTAAAAACGAGCTA 58.608 40.909 18.77 10.29 41.74 3.32
2818 2934 3.808726 TCCGCTGTTTAAAAACGAGCTAA 59.191 39.130 18.77 10.07 41.74 3.09
2819 2935 4.453136 TCCGCTGTTTAAAAACGAGCTAAT 59.547 37.500 18.77 0.00 41.74 1.73
2820 2936 5.638657 TCCGCTGTTTAAAAACGAGCTAATA 59.361 36.000 18.77 7.05 41.74 0.98
2821 2937 6.147492 TCCGCTGTTTAAAAACGAGCTAATAA 59.853 34.615 18.77 6.00 41.74 1.40
2822 2938 6.964934 CCGCTGTTTAAAAACGAGCTAATAAT 59.035 34.615 18.77 0.00 41.74 1.28
2823 2939 7.483691 CCGCTGTTTAAAAACGAGCTAATAATT 59.516 33.333 18.77 0.00 41.74 1.40
2824 2940 8.304138 CGCTGTTTAAAAACGAGCTAATAATTG 58.696 33.333 18.77 6.07 41.74 2.32
2825 2941 9.124807 GCTGTTTAAAAACGAGCTAATAATTGT 57.875 29.630 16.14 0.00 41.74 2.71
2852 2968 5.296151 TCAATGCTTTCTATCCTACCCAG 57.704 43.478 0.00 0.00 0.00 4.45
2872 2988 5.397899 CCCAGTGATGGTGGTTAGATGTAAT 60.398 44.000 0.00 0.00 32.62 1.89
2873 2989 6.122277 CCAGTGATGGTGGTTAGATGTAATT 58.878 40.000 0.00 0.00 0.00 1.40
2874 2990 6.603201 CCAGTGATGGTGGTTAGATGTAATTT 59.397 38.462 0.00 0.00 0.00 1.82
2875 2991 7.773224 CCAGTGATGGTGGTTAGATGTAATTTA 59.227 37.037 0.00 0.00 0.00 1.40
2876 2992 8.612619 CAGTGATGGTGGTTAGATGTAATTTAC 58.387 37.037 0.00 0.00 0.00 2.01
2939 3069 6.897259 TTACTCAGTGTTACAAGTTGTCAC 57.103 37.500 12.82 14.98 0.00 3.67
2979 3109 7.578310 AATTGTTCATCTACCATTCATCCAG 57.422 36.000 0.00 0.00 0.00 3.86
2996 3126 3.275143 TCCAGCCACGGTAACAATAATG 58.725 45.455 0.00 0.00 0.00 1.90
3049 3179 6.761242 ACTTTGTAAAGAGAATTGCAAAACCC 59.239 34.615 1.71 0.00 41.92 4.11
3054 3184 7.940137 TGTAAAGAGAATTGCAAAACCCTACTA 59.060 33.333 1.71 0.00 0.00 1.82
3055 3185 7.454260 AAAGAGAATTGCAAAACCCTACTAG 57.546 36.000 1.71 0.00 0.00 2.57
3056 3186 4.944317 AGAGAATTGCAAAACCCTACTAGC 59.056 41.667 1.71 0.00 0.00 3.42
3057 3187 4.923415 AGAATTGCAAAACCCTACTAGCT 58.077 39.130 1.71 0.00 0.00 3.32
3058 3188 6.062258 AGAATTGCAAAACCCTACTAGCTA 57.938 37.500 1.71 0.00 0.00 3.32
3059 3189 6.116126 AGAATTGCAAAACCCTACTAGCTAG 58.884 40.000 19.44 19.44 0.00 3.42
3060 3190 4.903045 TTGCAAAACCCTACTAGCTAGT 57.097 40.909 28.50 28.50 40.24 2.57
3061 3191 6.555463 ATTGCAAAACCCTACTAGCTAGTA 57.445 37.500 27.73 27.73 37.73 1.82
3062 3192 5.334724 TGCAAAACCCTACTAGCTAGTAC 57.665 43.478 26.36 15.73 37.73 2.73
3063 3193 4.142315 TGCAAAACCCTACTAGCTAGTACG 60.142 45.833 26.36 21.76 37.73 3.67
3064 3194 4.735873 GCAAAACCCTACTAGCTAGTACGG 60.736 50.000 31.46 31.46 39.41 4.02
3065 3195 4.510167 AAACCCTACTAGCTAGTACGGA 57.490 45.455 36.07 20.01 37.23 4.69
3066 3196 3.767902 ACCCTACTAGCTAGTACGGAG 57.232 52.381 36.07 27.48 37.23 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.048601 CCACGGATATGGCCTAGTGT 58.951 55.000 3.32 0.00 31.52 3.55
3 4 1.802553 AACCACGGATATGGCCTAGT 58.197 50.000 3.32 0.00 44.33 2.57
4 5 2.233922 CCTAACCACGGATATGGCCTAG 59.766 54.545 3.32 0.00 44.33 3.02
7 8 0.036306 CCCTAACCACGGATATGGCC 59.964 60.000 0.00 0.00 44.33 5.36
9 10 1.056660 AGCCCTAACCACGGATATGG 58.943 55.000 0.00 0.00 46.10 2.74
11 12 1.056660 CCAGCCCTAACCACGGATAT 58.943 55.000 0.00 0.00 0.00 1.63
12 13 0.031917 TCCAGCCCTAACCACGGATA 60.032 55.000 0.00 0.00 0.00 2.59
13 14 1.306654 TCCAGCCCTAACCACGGAT 60.307 57.895 0.00 0.00 0.00 4.18
14 15 2.120940 TCCAGCCCTAACCACGGA 59.879 61.111 0.00 0.00 0.00 4.69
15 16 2.267961 GTCCAGCCCTAACCACGG 59.732 66.667 0.00 0.00 0.00 4.94
16 17 2.125673 CGTCCAGCCCTAACCACG 60.126 66.667 0.00 0.00 0.00 4.94
17 18 1.079336 GACGTCCAGCCCTAACCAC 60.079 63.158 3.51 0.00 0.00 4.16
18 19 2.288025 GGACGTCCAGCCCTAACCA 61.288 63.158 29.75 0.00 35.64 3.67
19 20 2.582978 GGACGTCCAGCCCTAACC 59.417 66.667 29.75 0.00 35.64 2.85
657 684 7.710044 ACACAATCAAGCACAAACAAATTCATA 59.290 29.630 0.00 0.00 0.00 2.15
809 841 3.008923 CCAAGCTTCTCTCCTTCTCCTTT 59.991 47.826 0.00 0.00 0.00 3.11
1205 1259 6.777580 GCCTTCAATTTCCATAGATTAAGGGA 59.222 38.462 0.00 0.00 33.21 4.20
1904 1981 8.641499 ACAACAAAAATATTGAACGTTGACAT 57.359 26.923 5.00 0.00 36.60 3.06
2042 2125 9.959749 GTTTAAAAGTTGGTCATAGTGATGAAA 57.040 29.630 0.00 0.00 43.77 2.69
2384 2484 1.030488 ACCGACATGACGTCCTCGAT 61.030 55.000 22.06 8.31 42.07 3.59
2390 2490 2.430244 ACGCACCGACATGACGTC 60.430 61.111 15.98 9.11 41.62 4.34
2392 2492 2.126463 AGACGCACCGACATGACG 60.126 61.111 10.68 10.68 0.00 4.35
2399 2499 3.138798 GGGCTAGAGACGCACCGA 61.139 66.667 0.00 0.00 0.00 4.69
2406 2506 0.465824 TAGTCGCTGGGGCTAGAGAC 60.466 60.000 14.54 14.54 44.59 3.36
2428 2528 1.605457 CGCTGTGCAGTTCTTCCAGTA 60.605 52.381 0.00 0.00 0.00 2.74
2440 2540 3.286751 GGGCAACTTCGCTGTGCA 61.287 61.111 0.00 0.00 0.00 4.57
2441 2541 4.389576 CGGGCAACTTCGCTGTGC 62.390 66.667 0.00 0.00 0.00 4.57
2442 2542 1.970917 GATCGGGCAACTTCGCTGTG 61.971 60.000 0.00 0.00 0.00 3.66
2443 2543 1.741770 GATCGGGCAACTTCGCTGT 60.742 57.895 0.00 0.00 0.00 4.40
2444 2544 2.464459 GGATCGGGCAACTTCGCTG 61.464 63.158 0.00 0.00 0.00 5.18
2445 2545 2.125106 GGATCGGGCAACTTCGCT 60.125 61.111 0.00 0.00 0.00 4.93
2446 2546 3.564027 CGGATCGGGCAACTTCGC 61.564 66.667 0.00 0.00 0.00 4.70
2447 2547 2.890474 CCGGATCGGGCAACTTCG 60.890 66.667 6.35 0.00 44.15 3.79
2469 2572 1.374885 CATGTACCACCGACGCCAA 60.375 57.895 0.00 0.00 0.00 4.52
2479 2582 3.692101 CCAAGAATTAACGGCATGTACCA 59.308 43.478 0.00 0.00 0.00 3.25
2481 2584 4.393680 TGACCAAGAATTAACGGCATGTAC 59.606 41.667 0.00 0.00 0.00 2.90
2482 2585 4.580868 TGACCAAGAATTAACGGCATGTA 58.419 39.130 0.00 0.00 0.00 2.29
2483 2586 3.417101 TGACCAAGAATTAACGGCATGT 58.583 40.909 0.00 0.00 0.00 3.21
2485 2588 3.016736 CCTGACCAAGAATTAACGGCAT 58.983 45.455 0.00 0.00 0.00 4.40
2486 2589 2.224670 ACCTGACCAAGAATTAACGGCA 60.225 45.455 0.00 0.00 0.00 5.69
2487 2590 2.433436 ACCTGACCAAGAATTAACGGC 58.567 47.619 0.00 0.00 0.00 5.68
2488 2591 5.448632 GCATAACCTGACCAAGAATTAACGG 60.449 44.000 0.00 0.00 0.00 4.44
2489 2592 5.123186 TGCATAACCTGACCAAGAATTAACG 59.877 40.000 0.00 0.00 0.00 3.18
2490 2593 6.072175 TGTGCATAACCTGACCAAGAATTAAC 60.072 38.462 0.00 0.00 0.00 2.01
2491 2594 6.007076 TGTGCATAACCTGACCAAGAATTAA 58.993 36.000 0.00 0.00 0.00 1.40
2492 2595 5.414454 GTGTGCATAACCTGACCAAGAATTA 59.586 40.000 0.00 0.00 0.00 1.40
2494 2597 3.758554 GTGTGCATAACCTGACCAAGAAT 59.241 43.478 0.00 0.00 0.00 2.40
2523 2630 1.869574 CTGCATCGTCGACCTCACG 60.870 63.158 10.58 0.00 38.67 4.35
2525 2632 1.132453 CTAACTGCATCGTCGACCTCA 59.868 52.381 10.58 1.94 0.00 3.86
2557 2669 0.809241 GGATGTCCTTGCTCGCTGAG 60.809 60.000 1.80 1.80 0.00 3.35
2558 2670 1.219124 GGATGTCCTTGCTCGCTGA 59.781 57.895 0.00 0.00 0.00 4.26
2559 2671 2.169789 CGGATGTCCTTGCTCGCTG 61.170 63.158 0.00 0.00 0.00 5.18
2560 2672 2.185350 CGGATGTCCTTGCTCGCT 59.815 61.111 0.00 0.00 0.00 4.93
2571 2683 1.003355 CTGTTCTGCCACCGGATGT 60.003 57.895 9.46 0.00 0.00 3.06
2592 2704 1.514087 GTGTACCCGAGGAATGCGA 59.486 57.895 0.00 0.00 0.00 5.10
2593 2705 1.520787 GGTGTACCCGAGGAATGCG 60.521 63.158 0.00 0.00 0.00 4.73
2594 2706 4.534401 GGTGTACCCGAGGAATGC 57.466 61.111 0.00 0.00 0.00 3.56
2606 2718 1.278985 CTGAGTTCATGGCTGGGTGTA 59.721 52.381 0.00 0.00 0.00 2.90
2607 2719 0.037303 CTGAGTTCATGGCTGGGTGT 59.963 55.000 0.00 0.00 0.00 4.16
2609 2721 1.279271 GTACTGAGTTCATGGCTGGGT 59.721 52.381 0.00 0.00 0.00 4.51
2610 2722 1.407437 GGTACTGAGTTCATGGCTGGG 60.407 57.143 0.00 0.00 0.00 4.45
2611 2723 1.556911 AGGTACTGAGTTCATGGCTGG 59.443 52.381 0.00 0.00 37.18 4.85
2612 2724 2.736719 CGAGGTACTGAGTTCATGGCTG 60.737 54.545 0.00 0.00 41.55 4.85
2613 2725 1.478510 CGAGGTACTGAGTTCATGGCT 59.521 52.381 0.00 0.00 41.55 4.75
2614 2726 1.476891 TCGAGGTACTGAGTTCATGGC 59.523 52.381 0.00 0.00 41.55 4.40
2615 2727 2.480416 GCTCGAGGTACTGAGTTCATGG 60.480 54.545 15.58 0.00 41.55 3.66
2616 2728 2.425312 AGCTCGAGGTACTGAGTTCATG 59.575 50.000 16.99 0.00 41.55 3.07
2617 2729 2.685897 GAGCTCGAGGTACTGAGTTCAT 59.314 50.000 18.63 0.00 41.55 2.57
2618 2730 2.085320 GAGCTCGAGGTACTGAGTTCA 58.915 52.381 18.63 0.00 41.55 3.18
2619 2731 1.062880 CGAGCTCGAGGTACTGAGTTC 59.937 57.143 32.06 13.18 41.55 3.01
2620 2732 1.088306 CGAGCTCGAGGTACTGAGTT 58.912 55.000 32.06 5.99 41.55 3.01
2621 2733 0.036199 ACGAGCTCGAGGTACTGAGT 60.036 55.000 40.58 13.00 41.55 3.41
2622 2734 0.653636 GACGAGCTCGAGGTACTGAG 59.346 60.000 40.58 9.75 41.55 3.35
2624 2736 1.082679 TCGACGAGCTCGAGGTACTG 61.083 60.000 40.58 20.36 46.75 2.74
2625 2737 1.217511 TCGACGAGCTCGAGGTACT 59.782 57.895 40.58 18.93 46.75 2.73
2626 2738 3.791539 TCGACGAGCTCGAGGTAC 58.208 61.111 40.58 22.63 46.75 3.34
2640 2752 1.214589 GGCTTGCCGTCTACTTCGA 59.785 57.895 0.00 0.00 0.00 3.71
2641 2753 1.810030 GGGCTTGCCGTCTACTTCG 60.810 63.158 5.49 0.00 0.00 3.79
2643 2755 1.296715 CTGGGCTTGCCGTCTACTT 59.703 57.895 5.49 0.00 0.00 2.24
2644 2756 2.982130 CTGGGCTTGCCGTCTACT 59.018 61.111 5.49 0.00 0.00 2.57
2645 2757 2.820037 GCTGGGCTTGCCGTCTAC 60.820 66.667 5.49 0.00 0.00 2.59
2646 2758 4.451150 CGCTGGGCTTGCCGTCTA 62.451 66.667 5.49 0.00 0.00 2.59
2666 2778 2.419673 GCACAAATTAAAAGGGCATGGC 59.580 45.455 11.56 11.56 0.00 4.40
2667 2779 2.672381 CGCACAAATTAAAAGGGCATGG 59.328 45.455 0.00 0.00 0.00 3.66
2673 2785 2.823154 TCCTCCCGCACAAATTAAAAGG 59.177 45.455 0.00 0.00 0.00 3.11
2674 2786 3.673323 GCTCCTCCCGCACAAATTAAAAG 60.673 47.826 0.00 0.00 0.00 2.27
2675 2787 2.230266 GCTCCTCCCGCACAAATTAAAA 59.770 45.455 0.00 0.00 0.00 1.52
2679 2791 0.618458 TAGCTCCTCCCGCACAAATT 59.382 50.000 0.00 0.00 0.00 1.82
2680 2792 0.179000 CTAGCTCCTCCCGCACAAAT 59.821 55.000 0.00 0.00 0.00 2.32
2683 2795 3.461773 GCTAGCTCCTCCCGCACA 61.462 66.667 7.70 0.00 0.00 4.57
2684 2796 2.707529 GATGCTAGCTCCTCCCGCAC 62.708 65.000 17.23 0.00 32.94 5.34
2685 2797 2.444706 ATGCTAGCTCCTCCCGCA 60.445 61.111 17.23 0.00 34.83 5.69
2686 2798 2.341911 GATGCTAGCTCCTCCCGC 59.658 66.667 17.23 0.00 0.00 6.13
2687 2799 1.365633 GTGATGCTAGCTCCTCCCG 59.634 63.158 17.23 0.00 0.00 5.14
2689 2801 0.392336 CTGGTGATGCTAGCTCCTCC 59.608 60.000 17.23 16.49 0.00 4.30
2690 2802 0.249826 GCTGGTGATGCTAGCTCCTC 60.250 60.000 17.23 10.53 46.57 3.71
2691 2803 1.828768 GCTGGTGATGCTAGCTCCT 59.171 57.895 17.23 0.01 46.57 3.69
2692 2804 4.453093 GCTGGTGATGCTAGCTCC 57.547 61.111 17.23 13.02 46.57 4.70
2695 2807 1.593750 CCTCGCTGGTGATGCTAGC 60.594 63.158 8.10 8.10 46.61 3.42
2696 2808 4.746361 CCTCGCTGGTGATGCTAG 57.254 61.111 0.00 0.00 0.00 3.42
2704 2816 4.775163 CCTCAAAGGAAACCTCGCTGGT 62.775 54.545 0.00 0.00 45.12 4.00
2705 2817 1.160137 CTCAAAGGAAACCTCGCTGG 58.840 55.000 0.00 0.00 42.93 4.85
2706 2818 1.160137 CCTCAAAGGAAACCTCGCTG 58.840 55.000 0.00 0.00 37.67 5.18
2707 2819 0.606673 GCCTCAAAGGAAACCTCGCT 60.607 55.000 0.00 0.00 37.67 4.93
2708 2820 0.889186 TGCCTCAAAGGAAACCTCGC 60.889 55.000 0.00 0.00 37.67 5.03
2709 2821 1.604604 TTGCCTCAAAGGAAACCTCG 58.395 50.000 0.00 0.00 37.67 4.63
2710 2822 3.650070 CTTTGCCTCAAAGGAAACCTC 57.350 47.619 10.54 0.00 44.75 3.85
2732 2844 3.940209 TTTGCCAGCAACCTATTCAAG 57.060 42.857 4.18 0.00 35.46 3.02
2733 2845 4.888326 AATTTGCCAGCAACCTATTCAA 57.112 36.364 4.18 0.00 35.46 2.69
2734 2846 5.714333 TCTTAATTTGCCAGCAACCTATTCA 59.286 36.000 4.18 0.00 35.46 2.57
2735 2847 6.207691 TCTTAATTTGCCAGCAACCTATTC 57.792 37.500 4.18 0.00 35.46 1.75
2736 2848 5.394553 GCTCTTAATTTGCCAGCAACCTATT 60.395 40.000 4.18 5.40 35.46 1.73
2737 2849 4.098501 GCTCTTAATTTGCCAGCAACCTAT 59.901 41.667 4.18 0.00 35.46 2.57
2738 2850 3.443681 GCTCTTAATTTGCCAGCAACCTA 59.556 43.478 4.18 0.00 35.46 3.08
2739 2851 2.232208 GCTCTTAATTTGCCAGCAACCT 59.768 45.455 4.18 0.00 35.46 3.50
2740 2852 2.232208 AGCTCTTAATTTGCCAGCAACC 59.768 45.455 4.18 0.00 35.46 3.77
2741 2853 3.192212 AGAGCTCTTAATTTGCCAGCAAC 59.808 43.478 11.45 0.00 35.46 4.17
2742 2854 3.424703 AGAGCTCTTAATTTGCCAGCAA 58.575 40.909 11.45 0.00 32.17 3.91
2743 2855 3.077484 AGAGCTCTTAATTTGCCAGCA 57.923 42.857 11.45 0.00 32.17 4.41
2744 2856 3.441572 TGAAGAGCTCTTAATTTGCCAGC 59.558 43.478 28.53 12.53 36.11 4.85
2745 2857 4.699257 ACTGAAGAGCTCTTAATTTGCCAG 59.301 41.667 28.53 26.85 36.11 4.85
2746 2858 4.655963 ACTGAAGAGCTCTTAATTTGCCA 58.344 39.130 28.53 18.21 36.11 4.92
2747 2859 6.540189 TGATACTGAAGAGCTCTTAATTTGCC 59.460 38.462 28.53 14.65 36.11 4.52
2748 2860 7.545362 TGATACTGAAGAGCTCTTAATTTGC 57.455 36.000 28.53 15.35 36.11 3.68
2749 2861 8.068977 GCATGATACTGAAGAGCTCTTAATTTG 58.931 37.037 28.53 17.56 36.11 2.32
2750 2862 7.042187 CGCATGATACTGAAGAGCTCTTAATTT 60.042 37.037 28.53 13.67 36.11 1.82
2751 2863 6.423302 CGCATGATACTGAAGAGCTCTTAATT 59.577 38.462 28.53 18.01 36.11 1.40
2752 2864 5.925397 CGCATGATACTGAAGAGCTCTTAAT 59.075 40.000 28.53 18.38 36.11 1.40
2753 2865 5.163509 ACGCATGATACTGAAGAGCTCTTAA 60.164 40.000 28.53 20.82 36.11 1.85
2754 2866 4.339530 ACGCATGATACTGAAGAGCTCTTA 59.660 41.667 28.53 13.90 36.11 2.10
2755 2867 3.131933 ACGCATGATACTGAAGAGCTCTT 59.868 43.478 28.83 28.83 39.23 2.85
2756 2868 2.692557 ACGCATGATACTGAAGAGCTCT 59.307 45.455 11.45 11.45 0.00 4.09
2757 2869 2.793790 CACGCATGATACTGAAGAGCTC 59.206 50.000 5.27 5.27 0.00 4.09
2758 2870 2.167281 ACACGCATGATACTGAAGAGCT 59.833 45.455 0.00 0.00 0.00 4.09
2759 2871 2.544685 ACACGCATGATACTGAAGAGC 58.455 47.619 0.00 0.00 0.00 4.09
2760 2872 4.033358 GGAAACACGCATGATACTGAAGAG 59.967 45.833 0.00 0.00 0.00 2.85
2769 2881 2.198827 TTCAGGGAAACACGCATGAT 57.801 45.000 0.00 0.00 0.00 2.45
2798 2910 7.948513 ATTATTAGCTCGTTTTTAAACAGCG 57.051 32.000 16.55 0.00 42.46 5.18
2809 2925 5.597806 TGATCCGACAATTATTAGCTCGTT 58.402 37.500 0.00 0.00 0.00 3.85
2817 2933 7.338800 AGAAAGCATTGATCCGACAATTATT 57.661 32.000 0.00 0.00 38.25 1.40
2818 2934 6.949352 AGAAAGCATTGATCCGACAATTAT 57.051 33.333 0.00 0.00 38.25 1.28
2819 2935 7.173218 GGATAGAAAGCATTGATCCGACAATTA 59.827 37.037 0.00 0.00 38.25 1.40
2820 2936 6.016777 GGATAGAAAGCATTGATCCGACAATT 60.017 38.462 0.00 0.00 38.25 2.32
2821 2937 5.471456 GGATAGAAAGCATTGATCCGACAAT 59.529 40.000 0.00 0.00 40.50 2.71
2822 2938 4.816385 GGATAGAAAGCATTGATCCGACAA 59.184 41.667 0.00 0.00 0.00 3.18
2823 2939 4.101585 AGGATAGAAAGCATTGATCCGACA 59.898 41.667 6.57 0.00 40.89 4.35
2824 2940 4.636249 AGGATAGAAAGCATTGATCCGAC 58.364 43.478 6.57 0.00 40.89 4.79
2825 2941 4.963318 AGGATAGAAAGCATTGATCCGA 57.037 40.909 6.57 0.00 40.89 4.55
2852 2968 8.732746 AGTAAATTACATCTAACCACCATCAC 57.267 34.615 5.89 0.00 0.00 3.06
2872 2988 8.812972 TCTTTAAGGCTAAGTCATCAGAGTAAA 58.187 33.333 0.00 0.00 0.00 2.01
2873 2989 8.362464 TCTTTAAGGCTAAGTCATCAGAGTAA 57.638 34.615 0.00 0.00 0.00 2.24
2874 2990 7.956328 TCTTTAAGGCTAAGTCATCAGAGTA 57.044 36.000 0.00 0.00 0.00 2.59
2875 2991 6.859112 TCTTTAAGGCTAAGTCATCAGAGT 57.141 37.500 0.00 0.00 0.00 3.24
2876 2992 9.995003 ATTATCTTTAAGGCTAAGTCATCAGAG 57.005 33.333 0.00 0.00 0.00 3.35
2889 3019 6.364945 ACGAAGAAGCATTATCTTTAAGGC 57.635 37.500 0.00 0.00 43.64 4.35
2939 3069 3.448686 ACAATTTCTCGAGGATGCTACG 58.551 45.455 13.56 0.00 0.00 3.51
3016 3146 8.507249 GCAATTCTCTTTACAAAGTGACAGTAT 58.493 33.333 6.08 0.00 38.00 2.12


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

AutoCloner maintained by Alex Coulton.