Multiple sequence alignment - TraesCS4A01G154000

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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 TraesCS4A01G154000 chr4A 100.000 3476 0 0 1 3476 310238660 310242135 0.000000e+00 6420.0
1 TraesCS4A01G154000 chr4A 88.657 670 75 1 14 682 337463893 337463224 0.000000e+00 815.0
2 TraesCS4A01G154000 chr4A 87.630 671 77 6 12 679 651206309 651205642 0.000000e+00 774.0
3 TraesCS4A01G154000 chr4A 85.587 673 87 10 12 679 651463642 651462975 0.000000e+00 697.0
4 TraesCS4A01G154000 chr4A 85.420 679 89 10 5 679 651468652 651467980 0.000000e+00 697.0
5 TraesCS4A01G154000 chr3D 96.448 1689 46 8 904 2588 424002688 424001010 0.000000e+00 2774.0
6 TraesCS4A01G154000 chr3D 96.855 159 4 1 2430 2588 424001001 424000844 7.400000e-67 265.0
7 TraesCS4A01G154000 chr3D 87.692 65 6 2 2106 2170 335667467 335667405 1.340000e-09 75.0
8 TraesCS4A01G154000 chr4B 95.003 1621 64 8 1018 2636 200657993 200656388 0.000000e+00 2529.0
9 TraesCS4A01G154000 chr4B 97.208 394 11 0 3083 3476 200655958 200655565 0.000000e+00 667.0
10 TraesCS4A01G154000 chr4B 100.000 51 0 0 2637 2687 200656431 200656381 1.030000e-15 95.3
11 TraesCS4A01G154000 chr4D 95.212 1462 51 9 679 2138 183382654 183384098 0.000000e+00 2294.0
12 TraesCS4A01G154000 chr4D 91.981 636 29 8 2842 3476 183385094 183385708 0.000000e+00 872.0
13 TraesCS4A01G154000 chr4D 95.592 363 14 2 2276 2636 183384086 183384448 6.470000e-162 580.0
14 TraesCS4A01G154000 chr4D 94.215 121 7 0 2625 2745 183384393 183384513 5.920000e-43 185.0
15 TraesCS4A01G154000 chr3B 95.063 1357 41 16 764 2118 552475484 552476816 0.000000e+00 2111.0
16 TraesCS4A01G154000 chr3B 95.238 441 20 1 2148 2588 552476814 552477253 0.000000e+00 697.0
17 TraesCS4A01G154000 chr3A 93.977 880 23 12 904 1756 565041983 565042859 0.000000e+00 1304.0
18 TraesCS4A01G154000 chr3A 96.345 383 12 2 1761 2142 565042824 565043205 2.280000e-176 628.0
19 TraesCS4A01G154000 chr3A 97.568 329 7 1 2260 2588 565043247 565043574 2.340000e-156 562.0
20 TraesCS4A01G154000 chr3A 87.692 65 6 2 2106 2170 453656368 453656306 1.340000e-09 75.0
21 TraesCS4A01G154000 chr6A 93.630 675 40 2 5 677 608785838 608786511 0.000000e+00 1005.0
22 TraesCS4A01G154000 chr5D 91.098 674 54 6 8 679 487591569 487590900 0.000000e+00 907.0
23 TraesCS4A01G154000 chr5D 92.593 54 3 1 2108 2161 315936004 315936056 3.720000e-10 76.8
24 TraesCS4A01G154000 chr7B 87.481 671 77 7 12 679 633246718 633246052 0.000000e+00 767.0
25 TraesCS4A01G154000 chr6B 86.607 672 84 6 12 681 185118468 185117801 0.000000e+00 737.0
26 TraesCS4A01G154000 chr5B 85.395 671 88 9 12 679 706426955 706426292 0.000000e+00 688.0
27 TraesCS4A01G154000 chr1D 91.071 56 4 1 2106 2161 404253191 404253137 1.340000e-09 75.0
28 TraesCS4A01G154000 chr1D 90.741 54 4 1 2106 2159 39956493 39956545 1.730000e-08 71.3


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 TraesCS4A01G154000 chr4A 310238660 310242135 3475 False 6420.000000 6420 100.000000 1 3476 1 chr4A.!!$F1 3475
1 TraesCS4A01G154000 chr4A 337463224 337463893 669 True 815.000000 815 88.657000 14 682 1 chr4A.!!$R1 668
2 TraesCS4A01G154000 chr4A 651205642 651206309 667 True 774.000000 774 87.630000 12 679 1 chr4A.!!$R2 667
3 TraesCS4A01G154000 chr4A 651462975 651463642 667 True 697.000000 697 85.587000 12 679 1 chr4A.!!$R3 667
4 TraesCS4A01G154000 chr4A 651467980 651468652 672 True 697.000000 697 85.420000 5 679 1 chr4A.!!$R4 674
5 TraesCS4A01G154000 chr3D 424000844 424002688 1844 True 1519.500000 2774 96.651500 904 2588 2 chr3D.!!$R2 1684
6 TraesCS4A01G154000 chr4B 200655565 200657993 2428 True 1097.100000 2529 97.403667 1018 3476 3 chr4B.!!$R1 2458
7 TraesCS4A01G154000 chr4D 183382654 183385708 3054 False 982.750000 2294 94.250000 679 3476 4 chr4D.!!$F1 2797
8 TraesCS4A01G154000 chr3B 552475484 552477253 1769 False 1404.000000 2111 95.150500 764 2588 2 chr3B.!!$F1 1824
9 TraesCS4A01G154000 chr3A 565041983 565043574 1591 False 831.333333 1304 95.963333 904 2588 3 chr3A.!!$F1 1684
10 TraesCS4A01G154000 chr6A 608785838 608786511 673 False 1005.000000 1005 93.630000 5 677 1 chr6A.!!$F1 672
11 TraesCS4A01G154000 chr5D 487590900 487591569 669 True 907.000000 907 91.098000 8 679 1 chr5D.!!$R1 671
12 TraesCS4A01G154000 chr7B 633246052 633246718 666 True 767.000000 767 87.481000 12 679 1 chr7B.!!$R1 667
13 TraesCS4A01G154000 chr6B 185117801 185118468 667 True 737.000000 737 86.607000 12 681 1 chr6B.!!$R1 669
14 TraesCS4A01G154000 chr5B 706426292 706426955 663 True 688.000000 688 85.395000 12 679 1 chr5B.!!$R1 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
937 953 0.475828 ACCCTAACAAGCCCCTCACT 60.476 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2836 2911 0.102481 CTGGATGCAGGCTTCAATGC 59.898 55.0 6.28 0.0 42.86 3.56 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
141 143 1.747355 CTCCTTGAGCATTTTGCCGAT 59.253 47.619 0.00 0.00 46.52 4.18
287 289 1.498865 CTGGAGCTTGAAACGCGTGT 61.499 55.000 14.98 7.31 0.00 4.49
302 304 3.220658 TGTCGTGGACGTGGCTCA 61.221 61.111 0.00 0.00 40.80 4.26
513 521 4.256110 CGACGGGAAGTATTTAAACCCTT 58.744 43.478 8.70 5.37 38.51 3.95
515 523 5.181811 CGACGGGAAGTATTTAAACCCTTTT 59.818 40.000 8.70 0.00 38.51 2.27
549 557 1.406887 GCTTAGCGGGTTCAATCTGGA 60.407 52.381 0.00 0.00 0.00 3.86
589 597 0.541863 CCTCTTGTTACGGATGGGCT 59.458 55.000 0.00 0.00 0.00 5.19
628 637 4.314440 AGTTGCTCGCTTCCCGCA 62.314 61.111 0.00 0.00 39.08 5.69
739 748 4.168283 TCCCGGTAAAATATGGGATTGGAA 59.832 41.667 0.00 0.00 45.66 3.53
740 749 4.896482 CCCGGTAAAATATGGGATTGGAAA 59.104 41.667 0.00 0.00 44.88 3.13
794 803 2.027837 CGCATGGATAGATCACCCATCA 60.028 50.000 9.67 0.00 38.53 3.07
795 804 3.370209 CGCATGGATAGATCACCCATCAT 60.370 47.826 9.67 0.00 38.53 2.45
796 805 4.197750 GCATGGATAGATCACCCATCATC 58.802 47.826 9.67 1.77 38.53 2.92
805 814 2.393646 TCACCCATCATCGTCCATACA 58.606 47.619 0.00 0.00 0.00 2.29
832 841 2.356135 CCCATCTGAAAAACGATCCGT 58.644 47.619 0.00 0.00 43.97 4.69
928 937 5.237236 TCCTCCACTAAAACCCTAACAAG 57.763 43.478 0.00 0.00 0.00 3.16
937 953 0.475828 ACCCTAACAAGCCCCTCACT 60.476 55.000 0.00 0.00 0.00 3.41
957 973 1.213537 CTCGTCGCCGAAACCCTTA 59.786 57.895 0.00 0.00 43.69 2.69
1411 1446 3.064207 TCAACGAATCAGTAAGCGCTTT 58.936 40.909 30.13 9.05 0.00 3.51
1511 1546 5.220970 GCTTTGTTGGAGTTAGCAGTTTACA 60.221 40.000 0.00 0.00 0.00 2.41
1812 1851 7.383687 TGTAGTATTTCTCGGTCAAGATGTTT 58.616 34.615 0.00 0.00 0.00 2.83
2015 2054 6.327934 TGGCTAACTCTTATTCAGTTCGTAC 58.672 40.000 0.00 0.00 35.63 3.67
2042 2081 9.990360 TGTATTGATAAGTTTGAACTGACTACA 57.010 29.630 0.00 0.00 39.66 2.74
2049 2088 6.771188 AGTTTGAACTGACTACATTCTTCG 57.229 37.500 0.00 0.00 37.98 3.79
2075 2114 2.822561 TGAAACCAGCAGTGTCAAAACA 59.177 40.909 0.00 0.00 39.92 2.83
2181 2251 8.577048 AATATCAGCAGCATTCTTAGCATTAT 57.423 30.769 0.00 0.00 0.00 1.28
2226 2296 4.503741 AGTGTACATGTGGAAAATGCAC 57.496 40.909 9.11 0.00 33.78 4.57
2327 2399 1.549203 CTTGTTGTATGCAGGGGCTT 58.451 50.000 0.00 0.00 41.91 4.35
2349 2421 3.466881 CCAAGAGGTGGTGGTCGA 58.533 61.111 0.00 0.00 43.20 4.20
2525 2597 9.612066 TGTTGAAACATGATGCTCTACATTATA 57.388 29.630 0.00 0.00 33.44 0.98
2589 2661 6.332630 CACTTTGTGTGGAAGTTGAATTCTT 58.667 36.000 7.05 0.00 42.68 2.52
2590 2662 6.813152 CACTTTGTGTGGAAGTTGAATTCTTT 59.187 34.615 7.05 0.00 42.68 2.52
2591 2663 6.813152 ACTTTGTGTGGAAGTTGAATTCTTTG 59.187 34.615 7.05 0.00 33.76 2.77
2592 2664 5.913137 TGTGTGGAAGTTGAATTCTTTGT 57.087 34.783 7.05 0.00 0.00 2.83
2593 2665 5.649557 TGTGTGGAAGTTGAATTCTTTGTG 58.350 37.500 7.05 0.00 0.00 3.33
2595 2667 6.071672 TGTGTGGAAGTTGAATTCTTTGTGAA 60.072 34.615 7.05 0.00 39.24 3.18
2596 2668 6.811170 GTGTGGAAGTTGAATTCTTTGTGAAA 59.189 34.615 7.05 0.00 38.29 2.69
2616 2688 8.995419 GTGAAACAAAGTCTTGTATCTCTTTC 57.005 34.615 0.00 0.00 45.25 2.62
2622 2694 9.699703 ACAAAGTCTTGTATCTCTTTCTTAGTC 57.300 33.333 0.00 0.00 44.14 2.59
2626 2698 7.978975 AGTCTTGTATCTCTTTCTTAGTCATGC 59.021 37.037 0.00 0.00 0.00 4.06
2627 2699 7.761704 GTCTTGTATCTCTTTCTTAGTCATGCA 59.238 37.037 0.00 0.00 0.00 3.96
2628 2700 8.481314 TCTTGTATCTCTTTCTTAGTCATGCAT 58.519 33.333 0.00 0.00 0.00 3.96
2629 2701 9.107177 CTTGTATCTCTTTCTTAGTCATGCATT 57.893 33.333 0.00 0.00 0.00 3.56
2630 2702 8.654230 TGTATCTCTTTCTTAGTCATGCATTC 57.346 34.615 0.00 0.00 0.00 2.67
2631 2703 8.260114 TGTATCTCTTTCTTAGTCATGCATTCA 58.740 33.333 0.00 0.00 0.00 2.57
2632 2704 9.270640 GTATCTCTTTCTTAGTCATGCATTCAT 57.729 33.333 0.00 0.00 0.00 2.57
2716 2791 4.561735 TGTTCCTTGTTTCTTAAAGCCG 57.438 40.909 0.00 0.00 0.00 5.52
2733 2808 1.130955 CCGTTGCAGAAATGTGTTGC 58.869 50.000 0.00 0.00 38.30 4.17
2745 2820 1.174078 TGTGTTGCCCAGCATGTCAG 61.174 55.000 0.00 0.00 38.76 3.51
2746 2821 1.151221 TGTTGCCCAGCATGTCAGT 59.849 52.632 0.00 0.00 38.76 3.41
2747 2822 1.174078 TGTTGCCCAGCATGTCAGTG 61.174 55.000 0.00 0.00 38.76 3.66
2749 2824 0.399833 TTGCCCAGCATGTCAGTGTA 59.600 50.000 0.00 0.00 38.76 2.90
2750 2825 0.399833 TGCCCAGCATGTCAGTGTAA 59.600 50.000 0.00 0.00 31.71 2.41
2751 2826 1.202867 TGCCCAGCATGTCAGTGTAAA 60.203 47.619 0.00 0.00 31.71 2.01
2752 2827 2.094675 GCCCAGCATGTCAGTGTAAAT 58.905 47.619 0.00 0.00 0.00 1.40
2754 2829 3.056607 GCCCAGCATGTCAGTGTAAATTT 60.057 43.478 0.00 0.00 0.00 1.82
2755 2830 4.561326 GCCCAGCATGTCAGTGTAAATTTT 60.561 41.667 0.00 0.00 0.00 1.82
2758 2833 6.215121 CCAGCATGTCAGTGTAAATTTTTGA 58.785 36.000 0.00 0.00 0.00 2.69
2760 2835 7.224362 CCAGCATGTCAGTGTAAATTTTTGAAA 59.776 33.333 0.00 0.00 0.00 2.69
2761 2836 8.057742 CAGCATGTCAGTGTAAATTTTTGAAAC 58.942 33.333 0.00 0.00 0.00 2.78
2762 2837 7.763528 AGCATGTCAGTGTAAATTTTTGAAACA 59.236 29.630 0.00 0.00 0.00 2.83
2763 2838 8.386606 GCATGTCAGTGTAAATTTTTGAAACAA 58.613 29.630 0.00 0.00 0.00 2.83
2764 2839 9.904647 CATGTCAGTGTAAATTTTTGAAACAAG 57.095 29.630 0.00 0.00 0.00 3.16
2765 2840 9.651913 ATGTCAGTGTAAATTTTTGAAACAAGT 57.348 25.926 0.00 0.00 0.00 3.16
2766 2841 9.134734 TGTCAGTGTAAATTTTTGAAACAAGTC 57.865 29.630 0.00 0.00 0.00 3.01
2767 2842 9.134734 GTCAGTGTAAATTTTTGAAACAAGTCA 57.865 29.630 0.00 0.00 0.00 3.41
2769 2844 9.139174 CAGTGTAAATTTTTGAAACAAGTCAGT 57.861 29.630 0.00 0.00 0.00 3.41
2770 2845 9.139174 AGTGTAAATTTTTGAAACAAGTCAGTG 57.861 29.630 0.00 0.00 0.00 3.66
2771 2846 8.921670 GTGTAAATTTTTGAAACAAGTCAGTGT 58.078 29.630 0.00 0.00 0.00 3.55
2772 2847 9.482627 TGTAAATTTTTGAAACAAGTCAGTGTT 57.517 25.926 0.00 0.00 43.58 3.32
2783 2858 7.923414 AACAAGTCAGTGTTTTAGTTTCTCT 57.077 32.000 0.00 0.00 38.60 3.10
2784 2859 7.923414 ACAAGTCAGTGTTTTAGTTTCTCTT 57.077 32.000 0.00 0.00 0.00 2.85
2785 2860 7.752695 ACAAGTCAGTGTTTTAGTTTCTCTTG 58.247 34.615 0.00 0.00 35.20 3.02
2786 2861 7.390718 ACAAGTCAGTGTTTTAGTTTCTCTTGT 59.609 33.333 0.00 0.00 36.74 3.16
2787 2862 8.879759 CAAGTCAGTGTTTTAGTTTCTCTTGTA 58.120 33.333 0.00 0.00 0.00 2.41
2788 2863 8.649973 AGTCAGTGTTTTAGTTTCTCTTGTAG 57.350 34.615 0.00 0.00 0.00 2.74
2789 2864 8.475639 AGTCAGTGTTTTAGTTTCTCTTGTAGA 58.524 33.333 0.00 0.00 0.00 2.59
2790 2865 9.262358 GTCAGTGTTTTAGTTTCTCTTGTAGAT 57.738 33.333 0.00 0.00 33.05 1.98
2801 2876 9.442047 AGTTTCTCTTGTAGATATTCAAACCTG 57.558 33.333 0.00 0.00 33.05 4.00
2802 2877 9.220767 GTTTCTCTTGTAGATATTCAAACCTGT 57.779 33.333 0.00 0.00 33.05 4.00
2803 2878 8.777865 TTCTCTTGTAGATATTCAAACCTGTG 57.222 34.615 0.00 0.00 33.05 3.66
2804 2879 6.818644 TCTCTTGTAGATATTCAAACCTGTGC 59.181 38.462 0.00 0.00 0.00 4.57
2805 2880 6.472016 TCTTGTAGATATTCAAACCTGTGCA 58.528 36.000 0.00 0.00 0.00 4.57
2806 2881 6.595326 TCTTGTAGATATTCAAACCTGTGCAG 59.405 38.462 0.00 0.00 0.00 4.41
2807 2882 5.804639 TGTAGATATTCAAACCTGTGCAGT 58.195 37.500 0.00 0.00 0.00 4.40
2808 2883 6.941857 TGTAGATATTCAAACCTGTGCAGTA 58.058 36.000 0.00 0.00 0.00 2.74
2809 2884 6.816640 TGTAGATATTCAAACCTGTGCAGTAC 59.183 38.462 0.00 0.00 0.00 2.73
2810 2885 5.804639 AGATATTCAAACCTGTGCAGTACA 58.195 37.500 0.00 0.00 37.78 2.90
2811 2886 6.418101 AGATATTCAAACCTGTGCAGTACAT 58.582 36.000 0.00 0.00 38.92 2.29
2812 2887 7.564793 AGATATTCAAACCTGTGCAGTACATA 58.435 34.615 0.00 0.00 38.92 2.29
2813 2888 8.046708 AGATATTCAAACCTGTGCAGTACATAA 58.953 33.333 0.00 0.00 38.92 1.90
2814 2889 6.892658 ATTCAAACCTGTGCAGTACATAAA 57.107 33.333 0.00 0.00 38.92 1.40
2815 2890 5.682943 TCAAACCTGTGCAGTACATAAAC 57.317 39.130 0.00 0.00 38.92 2.01
2816 2891 5.373222 TCAAACCTGTGCAGTACATAAACT 58.627 37.500 0.00 0.00 38.92 2.66
2819 2894 4.504858 ACCTGTGCAGTACATAAACTAGC 58.495 43.478 0.00 0.00 38.92 3.42
2825 2900 6.103997 GTGCAGTACATAAACTAGCCTGTTA 58.896 40.000 0.00 0.00 0.00 2.41
2836 2911 7.617041 AAACTAGCCTGTTAAATTCAGCTAG 57.383 36.000 13.70 13.70 40.70 3.42
2839 2914 4.530875 AGCCTGTTAAATTCAGCTAGCAT 58.469 39.130 18.83 0.00 0.00 3.79
2840 2915 4.952335 AGCCTGTTAAATTCAGCTAGCATT 59.048 37.500 18.83 5.15 0.00 3.56
2843 2918 6.625740 GCCTGTTAAATTCAGCTAGCATTGAA 60.626 38.462 18.83 18.63 37.68 2.69
2846 2921 4.382345 AAATTCAGCTAGCATTGAAGCC 57.618 40.909 18.83 0.00 39.64 4.35
2912 3510 5.738118 ACAGACAACCAAATGCAATTTTG 57.262 34.783 5.90 5.90 46.10 2.44
2929 3527 6.513066 GCAATTTTGTTTTGGCAGATTTAGCA 60.513 34.615 0.00 0.00 0.00 3.49
2986 3584 7.355778 GCATACAGCTGACAAATTATTACTCC 58.644 38.462 23.35 0.00 41.15 3.85
2987 3585 7.520614 GCATACAGCTGACAAATTATTACTCCC 60.521 40.741 23.35 0.00 41.15 4.30
2988 3586 6.067217 ACAGCTGACAAATTATTACTCCCT 57.933 37.500 23.35 0.00 0.00 4.20
2990 3588 5.529060 CAGCTGACAAATTATTACTCCCTCC 59.471 44.000 8.42 0.00 0.00 4.30
2991 3589 4.511826 GCTGACAAATTATTACTCCCTCCG 59.488 45.833 0.00 0.00 0.00 4.63
2992 3590 5.671493 CTGACAAATTATTACTCCCTCCGT 58.329 41.667 0.00 0.00 0.00 4.69
2993 3591 6.684613 GCTGACAAATTATTACTCCCTCCGTA 60.685 42.308 0.00 0.00 0.00 4.02
2995 3593 7.622713 TGACAAATTATTACTCCCTCCGTAAA 58.377 34.615 0.00 0.00 31.36 2.01
2996 3594 7.767198 TGACAAATTATTACTCCCTCCGTAAAG 59.233 37.037 0.00 0.00 31.36 1.85
2997 3595 7.052248 ACAAATTATTACTCCCTCCGTAAAGG 58.948 38.462 0.00 0.00 42.97 3.11
2998 3596 6.819947 AATTATTACTCCCTCCGTAAAGGT 57.180 37.500 0.00 0.00 41.99 3.50
2999 3597 5.603170 TTATTACTCCCTCCGTAAAGGTG 57.397 43.478 0.00 0.00 41.99 4.00
3007 3605 4.317671 CCTCCGTAAAGGTGGTATGTAG 57.682 50.000 0.00 0.00 46.13 2.74
3008 3606 3.492137 CCTCCGTAAAGGTGGTATGTAGC 60.492 52.174 0.00 0.00 46.13 3.58
3009 3607 3.368248 TCCGTAAAGGTGGTATGTAGCT 58.632 45.455 0.00 0.00 41.99 3.32
3010 3608 4.535781 TCCGTAAAGGTGGTATGTAGCTA 58.464 43.478 0.00 0.00 41.99 3.32
3011 3609 4.955450 TCCGTAAAGGTGGTATGTAGCTAA 59.045 41.667 0.00 0.00 41.99 3.09
3014 3612 6.764560 CCGTAAAGGTGGTATGTAGCTAAAAT 59.235 38.462 0.00 0.00 34.51 1.82
3109 3882 4.036518 ACATTCAGAGCTCTTCCTGGTAT 58.963 43.478 15.27 0.00 0.00 2.73
3113 3886 4.873010 TCAGAGCTCTTCCTGGTATAAGT 58.127 43.478 15.27 0.00 0.00 2.24
3224 3997 1.746615 AGCAGCGTGTGGCCTAATG 60.747 57.895 3.32 0.00 45.17 1.90
3249 4022 2.563620 TCGACAAAGGTGGTATGTAGCA 59.436 45.455 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.329386 CTGCGACAAGGAAGAGATTTCA 58.671 45.455 0.00 0.00 0.00 2.69
2 3 2.095053 GCTGCGACAAGGAAGAGATTTC 59.905 50.000 0.00 0.00 0.00 2.17
3 4 2.079925 GCTGCGACAAGGAAGAGATTT 58.920 47.619 0.00 0.00 0.00 2.17
10 11 2.738521 GAGCGCTGCGACAAGGAA 60.739 61.111 28.07 0.00 0.00 3.36
141 143 1.410517 GCGAGGAGATCATCAAGTCCA 59.589 52.381 0.00 0.00 0.00 4.02
287 289 3.680786 CCTGAGCCACGTCCACGA 61.681 66.667 6.03 0.00 43.02 4.35
335 337 5.026121 TGGAGGTAGCAGGATCCTTATATG 58.974 45.833 13.00 1.99 32.79 1.78
338 340 3.637821 TGGAGGTAGCAGGATCCTTAT 57.362 47.619 13.00 6.08 32.79 1.73
513 521 2.252976 AAGCGGGTGTAACGGTAAAA 57.747 45.000 0.00 0.00 41.63 1.52
515 523 1.404047 GCTAAGCGGGTGTAACGGTAA 60.404 52.381 0.00 0.00 41.63 2.85
539 547 1.888512 GGCTTGCAAGTCCAGATTGAA 59.111 47.619 26.55 0.00 0.00 2.69
540 548 1.202915 TGGCTTGCAAGTCCAGATTGA 60.203 47.619 27.96 9.23 31.61 2.57
543 551 0.403271 AGTGGCTTGCAAGTCCAGAT 59.597 50.000 30.58 22.79 34.46 2.90
549 557 0.396974 TTTCCCAGTGGCTTGCAAGT 60.397 50.000 26.55 4.83 0.00 3.16
607 616 1.227999 CGGGAAGCGAGCAACTCAAA 61.228 55.000 0.00 0.00 0.00 2.69
628 637 4.768448 AGATGATGCTGATCGAGAAGAGAT 59.232 41.667 1.46 0.00 0.00 2.75
739 748 1.534163 GGCTTTTCGTAACGAGCCTTT 59.466 47.619 9.53 0.00 40.15 3.11
740 749 1.154197 GGCTTTTCGTAACGAGCCTT 58.846 50.000 9.53 0.00 40.15 4.35
794 803 1.122019 GGGAGGGCTGTATGGACGAT 61.122 60.000 0.00 0.00 0.00 3.73
795 804 1.760875 GGGAGGGCTGTATGGACGA 60.761 63.158 0.00 0.00 0.00 4.20
796 805 2.808206 GGGGAGGGCTGTATGGACG 61.808 68.421 0.00 0.00 0.00 4.79
805 814 1.084018 TTTTTCAGATGGGGAGGGCT 58.916 50.000 0.00 0.00 0.00 5.19
867 876 0.467290 GGTTGTTTGGGAGACTGGCA 60.467 55.000 0.00 0.00 0.00 4.92
928 937 3.827898 CGACGAGGAGTGAGGGGC 61.828 72.222 0.00 0.00 0.00 5.80
1411 1446 6.296087 GCACTATATTGATGATGAGGGGAAGA 60.296 42.308 0.00 0.00 0.00 2.87
1486 1521 2.930950 ACTGCTAACTCCAACAAAGCA 58.069 42.857 0.00 0.00 40.68 3.91
1490 1525 6.126568 GTTGTAAACTGCTAACTCCAACAA 57.873 37.500 0.00 0.00 45.32 2.83
1491 1526 5.744666 GTTGTAAACTGCTAACTCCAACA 57.255 39.130 0.00 0.00 45.32 3.33
1784 1823 6.829229 TCTTGACCGAGAAATACTACAGAA 57.171 37.500 0.00 0.00 0.00 3.02
1812 1851 2.306805 AGATGTTGCAATGACTCCCTCA 59.693 45.455 0.59 0.00 0.00 3.86
1968 2007 6.925165 CCATGAAAAGACATGTTGCTAAGTTT 59.075 34.615 0.00 0.00 44.00 2.66
2042 2081 3.882888 TGCTGGTTTCAAGTTCGAAGAAT 59.117 39.130 0.00 0.00 45.90 2.40
2049 2088 2.682856 TGACACTGCTGGTTTCAAGTTC 59.317 45.455 0.00 0.00 32.46 3.01
2075 2114 4.607293 TTCACAGAGACAGTATGCAAGT 57.393 40.909 0.00 0.00 42.53 3.16
2204 2274 4.340666 TGTGCATTTTCCACATGTACACTT 59.659 37.500 0.00 0.00 40.87 3.16
2226 2296 7.115378 GCTGAACACTTTATTTGGTTTCTCATG 59.885 37.037 0.00 0.00 0.00 3.07
2349 2421 1.073706 ACCACCACCTCTTCCACCT 60.074 57.895 0.00 0.00 0.00 4.00
2525 2597 4.708421 AGCATAATGTTTCCAGCTGAACAT 59.292 37.500 21.87 21.87 31.05 2.71
2589 2661 8.506168 AAGAGATACAAGACTTTGTTTCACAA 57.494 30.769 11.51 0.00 45.01 3.33
2590 2662 8.506168 AAAGAGATACAAGACTTTGTTTCACA 57.494 30.769 11.51 0.00 45.01 3.58
2591 2663 8.831550 AGAAAGAGATACAAGACTTTGTTTCAC 58.168 33.333 11.51 6.82 45.01 3.18
2592 2664 8.964476 AGAAAGAGATACAAGACTTTGTTTCA 57.036 30.769 11.51 0.00 45.01 2.69
2599 2671 9.868277 CATGACTAAGAAAGAGATACAAGACTT 57.132 33.333 0.00 0.00 0.00 3.01
2602 2674 7.840931 TGCATGACTAAGAAAGAGATACAAGA 58.159 34.615 0.00 0.00 0.00 3.02
2603 2675 8.659925 ATGCATGACTAAGAAAGAGATACAAG 57.340 34.615 0.00 0.00 0.00 3.16
2604 2676 9.102757 GAATGCATGACTAAGAAAGAGATACAA 57.897 33.333 0.00 0.00 0.00 2.41
2607 2679 9.842775 AATGAATGCATGACTAAGAAAGAGATA 57.157 29.630 0.00 0.00 34.26 1.98
2609 2681 7.609146 ACAATGAATGCATGACTAAGAAAGAGA 59.391 33.333 0.00 0.00 34.26 3.10
2610 2682 7.696872 CACAATGAATGCATGACTAAGAAAGAG 59.303 37.037 0.00 0.00 34.26 2.85
2611 2683 7.362315 CCACAATGAATGCATGACTAAGAAAGA 60.362 37.037 0.00 0.00 34.26 2.52
2613 2685 6.433716 TCCACAATGAATGCATGACTAAGAAA 59.566 34.615 0.00 0.00 34.26 2.52
2615 2687 5.499313 TCCACAATGAATGCATGACTAAGA 58.501 37.500 0.00 0.00 34.26 2.10
2616 2688 5.823209 TCCACAATGAATGCATGACTAAG 57.177 39.130 0.00 0.00 34.26 2.18
2619 2691 3.827876 TGTTCCACAATGAATGCATGACT 59.172 39.130 0.00 0.00 34.26 3.41
2620 2692 4.177165 TGTTCCACAATGAATGCATGAC 57.823 40.909 0.00 0.00 34.26 3.06
2621 2693 4.868314 TTGTTCCACAATGAATGCATGA 57.132 36.364 0.00 0.00 32.34 3.07
2622 2694 4.992319 ACTTTGTTCCACAATGAATGCATG 59.008 37.500 0.00 0.00 38.00 4.06
2624 2696 4.341806 AGACTTTGTTCCACAATGAATGCA 59.658 37.500 8.94 0.00 38.00 3.96
2626 2698 7.169035 CAAAGACTTTGTTCCACAATGAATG 57.831 36.000 18.12 0.00 38.00 2.67
2696 2771 4.563337 ACGGCTTTAAGAAACAAGGAAC 57.437 40.909 0.00 0.00 0.00 3.62
2716 2791 1.202510 TGGGCAACACATTTCTGCAAC 60.203 47.619 0.00 0.00 37.83 4.17
2733 2808 4.789012 AAATTTACACTGACATGCTGGG 57.211 40.909 0.00 0.00 0.00 4.45
2745 2820 8.921670 ACACTGACTTGTTTCAAAAATTTACAC 58.078 29.630 0.00 0.00 0.00 2.90
2746 2821 9.482627 AACACTGACTTGTTTCAAAAATTTACA 57.517 25.926 0.00 0.00 36.22 2.41
2751 2826 9.705290 ACTAAAACACTGACTTGTTTCAAAAAT 57.295 25.926 1.92 0.00 46.68 1.82
2752 2827 9.535878 AACTAAAACACTGACTTGTTTCAAAAA 57.464 25.926 1.92 0.00 46.68 1.94
2754 2829 9.187455 GAAACTAAAACACTGACTTGTTTCAAA 57.813 29.630 0.00 0.00 46.68 2.69
2755 2830 8.573035 AGAAACTAAAACACTGACTTGTTTCAA 58.427 29.630 14.69 0.00 46.68 2.69
2760 2835 7.390718 ACAAGAGAAACTAAAACACTGACTTGT 59.609 33.333 0.00 0.00 38.34 3.16
2761 2836 7.752695 ACAAGAGAAACTAAAACACTGACTTG 58.247 34.615 0.00 0.00 36.81 3.16
2762 2837 7.923414 ACAAGAGAAACTAAAACACTGACTT 57.077 32.000 0.00 0.00 0.00 3.01
2763 2838 8.475639 TCTACAAGAGAAACTAAAACACTGACT 58.524 33.333 0.00 0.00 0.00 3.41
2764 2839 8.644318 TCTACAAGAGAAACTAAAACACTGAC 57.356 34.615 0.00 0.00 0.00 3.51
2775 2850 9.442047 CAGGTTTGAATATCTACAAGAGAAACT 57.558 33.333 0.00 0.00 37.85 2.66
2776 2851 9.220767 ACAGGTTTGAATATCTACAAGAGAAAC 57.779 33.333 0.00 0.00 37.85 2.78
2777 2852 9.219603 CACAGGTTTGAATATCTACAAGAGAAA 57.780 33.333 0.00 0.00 37.85 2.52
2778 2853 7.334421 GCACAGGTTTGAATATCTACAAGAGAA 59.666 37.037 0.00 0.00 37.85 2.87
2779 2854 6.818644 GCACAGGTTTGAATATCTACAAGAGA 59.181 38.462 0.00 0.00 39.01 3.10
2780 2855 6.595326 TGCACAGGTTTGAATATCTACAAGAG 59.405 38.462 0.00 0.00 0.00 2.85
2781 2856 6.472016 TGCACAGGTTTGAATATCTACAAGA 58.528 36.000 0.00 0.00 0.00 3.02
2782 2857 6.372659 ACTGCACAGGTTTGAATATCTACAAG 59.627 38.462 2.21 0.00 0.00 3.16
2783 2858 6.237901 ACTGCACAGGTTTGAATATCTACAA 58.762 36.000 2.21 0.00 0.00 2.41
2784 2859 5.804639 ACTGCACAGGTTTGAATATCTACA 58.195 37.500 2.21 0.00 0.00 2.74
2785 2860 6.816640 TGTACTGCACAGGTTTGAATATCTAC 59.183 38.462 2.21 0.00 31.89 2.59
2786 2861 6.941857 TGTACTGCACAGGTTTGAATATCTA 58.058 36.000 2.21 0.00 31.89 1.98
2787 2862 5.804639 TGTACTGCACAGGTTTGAATATCT 58.195 37.500 2.21 0.00 31.89 1.98
2788 2863 6.683974 ATGTACTGCACAGGTTTGAATATC 57.316 37.500 2.21 0.00 41.51 1.63
2789 2864 8.458843 GTTTATGTACTGCACAGGTTTGAATAT 58.541 33.333 2.21 0.00 41.51 1.28
2790 2865 7.663905 AGTTTATGTACTGCACAGGTTTGAATA 59.336 33.333 2.21 0.00 41.51 1.75
2791 2866 6.490040 AGTTTATGTACTGCACAGGTTTGAAT 59.510 34.615 2.21 0.00 41.51 2.57
2792 2867 5.825679 AGTTTATGTACTGCACAGGTTTGAA 59.174 36.000 2.21 0.00 41.51 2.69
2793 2868 5.373222 AGTTTATGTACTGCACAGGTTTGA 58.627 37.500 2.21 0.00 41.51 2.69
2794 2869 5.689383 AGTTTATGTACTGCACAGGTTTG 57.311 39.130 2.21 0.00 41.51 2.93
2795 2870 5.411669 GCTAGTTTATGTACTGCACAGGTTT 59.588 40.000 2.21 0.00 41.51 3.27
2796 2871 4.935808 GCTAGTTTATGTACTGCACAGGTT 59.064 41.667 2.21 0.00 41.51 3.50
2797 2872 4.504858 GCTAGTTTATGTACTGCACAGGT 58.495 43.478 2.21 0.00 41.51 4.00
2798 2873 3.871594 GGCTAGTTTATGTACTGCACAGG 59.128 47.826 2.21 0.00 41.51 4.00
2799 2874 4.568359 CAGGCTAGTTTATGTACTGCACAG 59.432 45.833 0.00 0.00 41.51 3.66
2800 2875 4.020573 ACAGGCTAGTTTATGTACTGCACA 60.021 41.667 0.00 0.00 42.69 4.57
2801 2876 4.504858 ACAGGCTAGTTTATGTACTGCAC 58.495 43.478 0.00 0.00 0.00 4.57
2802 2877 4.819105 ACAGGCTAGTTTATGTACTGCA 57.181 40.909 0.00 0.00 0.00 4.41
2803 2878 7.605410 TTTAACAGGCTAGTTTATGTACTGC 57.395 36.000 7.46 0.00 33.07 4.40
2805 2880 9.953565 TGAATTTAACAGGCTAGTTTATGTACT 57.046 29.630 7.46 0.00 33.07 2.73
2807 2882 8.889717 GCTGAATTTAACAGGCTAGTTTATGTA 58.110 33.333 7.46 0.00 36.09 2.29
2808 2883 7.611855 AGCTGAATTTAACAGGCTAGTTTATGT 59.388 33.333 7.46 0.00 36.09 2.29
2809 2884 7.989826 AGCTGAATTTAACAGGCTAGTTTATG 58.010 34.615 7.46 0.00 36.09 1.90
2810 2885 9.331282 CTAGCTGAATTTAACAGGCTAGTTTAT 57.669 33.333 0.00 1.48 37.35 1.40
2811 2886 7.280205 GCTAGCTGAATTTAACAGGCTAGTTTA 59.720 37.037 7.70 0.00 40.19 2.01
2812 2887 6.094186 GCTAGCTGAATTTAACAGGCTAGTTT 59.906 38.462 7.70 0.00 40.19 2.66
2813 2888 5.586643 GCTAGCTGAATTTAACAGGCTAGTT 59.413 40.000 7.70 7.34 40.19 2.24
2814 2889 5.119694 GCTAGCTGAATTTAACAGGCTAGT 58.880 41.667 7.70 0.00 40.19 2.57
2815 2890 5.118990 TGCTAGCTGAATTTAACAGGCTAG 58.881 41.667 17.23 13.35 40.52 3.42
2816 2891 5.097742 TGCTAGCTGAATTTAACAGGCTA 57.902 39.130 17.23 0.00 36.09 3.93
2819 2894 6.441093 TCAATGCTAGCTGAATTTAACAGG 57.559 37.500 17.23 0.00 36.09 4.00
2825 2900 4.021916 AGGCTTCAATGCTAGCTGAATTT 58.978 39.130 17.23 4.50 37.54 1.82
2836 2911 0.102481 CTGGATGCAGGCTTCAATGC 59.898 55.000 6.28 0.00 42.86 3.56
2839 2914 0.627451 ATCCTGGATGCAGGCTTCAA 59.373 50.000 27.43 11.18 42.00 2.69
2840 2915 0.627451 AATCCTGGATGCAGGCTTCA 59.373 50.000 27.43 11.57 42.00 3.02
2843 2918 1.142465 CTACAATCCTGGATGCAGGCT 59.858 52.381 27.43 16.43 42.00 4.58
2846 2921 3.834489 ACTCTACAATCCTGGATGCAG 57.166 47.619 10.54 7.35 0.00 4.41
2862 3460 7.334090 AGTTGTATCATCTGCACAATTACTCT 58.666 34.615 0.00 0.00 34.89 3.24
2912 3510 6.212955 TGTAGTTTGCTAAATCTGCCAAAAC 58.787 36.000 0.00 0.00 31.05 2.43
2974 3572 7.052248 CACCTTTACGGAGGGAGTAATAATTT 58.948 38.462 6.69 0.00 41.31 1.82
2976 3574 5.071384 CCACCTTTACGGAGGGAGTAATAAT 59.929 44.000 6.69 0.00 41.31 1.28
2983 3581 1.856629 TACCACCTTTACGGAGGGAG 58.143 55.000 6.69 0.80 46.85 4.30
2984 3582 2.112998 CATACCACCTTTACGGAGGGA 58.887 52.381 6.69 0.00 46.85 4.20
2985 3583 1.835531 ACATACCACCTTTACGGAGGG 59.164 52.381 6.69 0.00 46.85 4.30
2987 3585 3.383825 AGCTACATACCACCTTTACGGAG 59.616 47.826 0.00 0.00 36.31 4.63
2988 3586 3.368248 AGCTACATACCACCTTTACGGA 58.632 45.455 0.00 0.00 36.31 4.69
2990 3588 7.781548 ATTTTAGCTACATACCACCTTTACG 57.218 36.000 0.00 0.00 0.00 3.18
3021 3619 8.332464 TGTATTTTGCGCATGTATAGAAACTAC 58.668 33.333 12.75 9.15 0.00 2.73
3025 3623 7.315247 AGTGTATTTTGCGCATGTATAGAAA 57.685 32.000 12.75 7.35 0.00 2.52
3109 3882 2.745281 GTTTTGTAGCCATCCGCACTTA 59.255 45.455 0.00 0.00 41.38 2.24
3113 3886 1.448985 GAGTTTTGTAGCCATCCGCA 58.551 50.000 0.00 0.00 41.38 5.69
3224 3997 0.252197 ATACCACCTTTGTCGAGGCC 59.748 55.000 0.00 0.00 40.65 5.19
3249 4022 2.530460 TGTTTAATCATGCAGGGGCT 57.470 45.000 0.00 0.00 41.91 5.19
3251 4024 5.593909 TCAAGTATGTTTAATCATGCAGGGG 59.406 40.000 14.54 4.07 33.91 4.79
3294 4067 2.042639 ATTGATGCACCCCCAGCC 60.043 61.111 0.00 0.00 0.00 4.85
3336 4109 4.923281 GGCAATTTCGTTATTCAAACAGCT 59.077 37.500 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.