Multiple sequence alignment - TraesCS1A01G140600

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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 TraesCS1A01G140600 chr1A 100.000 2916 0 0 1 2916 238650170 238647255 0.000000e+00 5385.0
1 TraesCS1A01G140600 chr7A 98.841 2589 23 2 1 2588 577480906 577483488 0.000000e+00 4608.0
2 TraesCS1A01G140600 chr7A 93.077 2600 141 18 1 2587 496901242 496898669 0.000000e+00 3768.0
3 TraesCS1A01G140600 chr7A 96.089 2148 66 9 1 2137 450364430 450362290 0.000000e+00 3485.0
4 TraesCS1A01G140600 chr7A 95.395 456 19 2 2133 2587 450327688 450327234 0.000000e+00 725.0
5 TraesCS1A01G140600 chr5A 92.269 2600 146 17 1 2587 228645334 228642777 0.000000e+00 3637.0
6 TraesCS1A01G140600 chr2A 93.807 1421 72 6 1170 2587 427174422 427175829 0.000000e+00 2122.0
7 TraesCS1A01G140600 chr2A 95.796 999 33 4 1 991 427173423 427174420 0.000000e+00 1604.0
8 TraesCS1A01G140600 chr3B 94.611 1002 36 7 1587 2587 1266270 1267254 0.000000e+00 1535.0
9 TraesCS1A01G140600 chr3B 96.563 611 15 6 1 608 1265674 1266281 0.000000e+00 1007.0
10 TraesCS1A01G140600 chr3B 84.877 324 39 8 2598 2914 437507756 437507436 4.690000e-83 318.0
11 TraesCS1A01G140600 chr6A 94.428 1005 43 7 1587 2587 447423138 447422143 0.000000e+00 1533.0
12 TraesCS1A01G140600 chr6A 95.417 611 20 7 1 608 447423732 447423127 0.000000e+00 966.0
13 TraesCS1A01G140600 chr6A 81.510 384 52 14 1856 2225 181911819 181912197 6.110000e-77 298.0
14 TraesCS1A01G140600 chrUn 94.606 723 33 4 909 1628 96518701 96517982 0.000000e+00 1114.0
15 TraesCS1A01G140600 chrUn 91.268 355 15 3 2094 2445 96517971 96517630 1.220000e-128 470.0
16 TraesCS1A01G140600 chrUn 92.308 104 4 4 2487 2587 96517634 96517532 8.420000e-31 145.0
17 TraesCS1A01G140600 chr3D 79.700 867 119 36 1607 2449 47134730 47135563 9.060000e-160 573.0
18 TraesCS1A01G140600 chr3D 84.848 330 38 10 2590 2916 2578214 2578534 3.630000e-84 322.0
19 TraesCS1A01G140600 chr4B 79.720 572 66 36 1874 2414 446513806 446514358 4.590000e-98 368.0
20 TraesCS1A01G140600 chr4B 84.337 332 40 9 2590 2913 607637189 607637516 6.070000e-82 315.0
21 TraesCS1A01G140600 chr4B 92.593 54 2 2 2536 2587 309422675 309422622 3.120000e-10 76.8
22 TraesCS1A01G140600 chr4B 79.825 114 16 6 1129 1236 592707746 592707858 3.120000e-10 76.8
23 TraesCS1A01G140600 chr2D 86.103 331 38 6 2590 2916 467889040 467889366 1.660000e-92 350.0
24 TraesCS1A01G140600 chr2D 84.084 333 44 8 2590 2916 372514907 372514578 2.180000e-81 313.0
25 TraesCS1A01G140600 chr5D 85.970 335 36 9 2590 2916 59940686 59940355 5.980000e-92 348.0
26 TraesCS1A01G140600 chr5D 85.329 334 38 9 2590 2916 541528027 541527698 4.660000e-88 335.0
27 TraesCS1A01G140600 chr7B 85.503 338 38 9 2586 2916 44764353 44764020 2.780000e-90 342.0
28 TraesCS1A01G140600 chr7B 81.771 384 51 14 1856 2225 558893165 558893543 1.310000e-78 303.0
29 TraesCS1A01G140600 chr7D 84.412 340 38 11 2586 2916 74401093 74401426 1.300000e-83 320.0
30 TraesCS1A01G140600 chr4A 80.870 115 13 7 1129 1236 665692628 665692516 6.700000e-12 82.4
31 TraesCS1A01G140600 chr1B 88.710 62 7 0 1722 1783 159189380 159189319 3.120000e-10 76.8
32 TraesCS1A01G140600 chr6B 87.097 62 8 0 1722 1783 59407893 59407954 1.450000e-08 71.3
33 TraesCS1A01G140600 chr5B 87.097 62 8 0 1722 1783 439680960 439680899 1.450000e-08 71.3
34 TraesCS1A01G140600 chr4D 87.097 62 8 0 1722 1783 98864830 98864769 1.450000e-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 TraesCS1A01G140600 chr1A 238647255 238650170 2915 True 5385.000000 5385 100.000000 1 2916 1 chr1A.!!$R1 2915
1 TraesCS1A01G140600 chr7A 577480906 577483488 2582 False 4608.000000 4608 98.841000 1 2588 1 chr7A.!!$F1 2587
2 TraesCS1A01G140600 chr7A 496898669 496901242 2573 True 3768.000000 3768 93.077000 1 2587 1 chr7A.!!$R3 2586
3 TraesCS1A01G140600 chr7A 450362290 450364430 2140 True 3485.000000 3485 96.089000 1 2137 1 chr7A.!!$R2 2136
4 TraesCS1A01G140600 chr5A 228642777 228645334 2557 True 3637.000000 3637 92.269000 1 2587 1 chr5A.!!$R1 2586
5 TraesCS1A01G140600 chr2A 427173423 427175829 2406 False 1863.000000 2122 94.801500 1 2587 2 chr2A.!!$F1 2586
6 TraesCS1A01G140600 chr3B 1265674 1267254 1580 False 1271.000000 1535 95.587000 1 2587 2 chr3B.!!$F1 2586
7 TraesCS1A01G140600 chr6A 447422143 447423732 1589 True 1249.500000 1533 94.922500 1 2587 2 chr6A.!!$R1 2586
8 TraesCS1A01G140600 chrUn 96517532 96518701 1169 True 576.333333 1114 92.727333 909 2587 3 chrUn.!!$R1 1678
9 TraesCS1A01G140600 chr3D 47134730 47135563 833 False 573.000000 573 79.700000 1607 2449 1 chr3D.!!$F2 842
10 TraesCS1A01G140600 chr4B 446513806 446514358 552 False 368.000000 368 79.720000 1874 2414 1 chr4B.!!$F1 540

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
991 1002 2.228822 GCCGCCCGATATTGATGATTTT 59.771 45.455 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1973 0.397535 AATGCTAATGCCCCACCTGG 60.398 55.0 0.0 0.0 38.71 4.45 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
589 593 5.735892 CACATGTGAATCTTGTTATTCTGCG 59.264 40.000 21.64 0.00 36.90 5.18
991 1002 2.228822 GCCGCCCGATATTGATGATTTT 59.771 45.455 0.00 0.00 0.00 1.82
1412 1423 1.494628 CATGTCACTGTCACAGCGC 59.505 57.895 4.13 0.00 34.37 5.92
1617 1628 5.122239 CAGCTTCTTCACGGACATTATTCAA 59.878 40.000 0.00 0.00 0.00 2.69
1930 1973 3.004734 AGTGTTAGCCAAAGCATGTTGAC 59.995 43.478 0.00 0.00 43.56 3.18
2588 2679 1.002624 CGGGCCCTTTTGCTAGTGA 60.003 57.895 22.43 0.00 0.00 3.41
2589 2680 1.026718 CGGGCCCTTTTGCTAGTGAG 61.027 60.000 22.43 0.00 0.00 3.51
2605 2696 4.815533 AGTGAGCACTCATGTGAATAGT 57.184 40.909 3.24 0.00 46.55 2.12
2606 2697 5.921962 AGTGAGCACTCATGTGAATAGTA 57.078 39.130 3.24 0.00 46.55 1.82
2607 2698 6.286240 AGTGAGCACTCATGTGAATAGTAA 57.714 37.500 3.24 0.00 46.55 2.24
2608 2699 6.701340 AGTGAGCACTCATGTGAATAGTAAA 58.299 36.000 3.24 0.00 46.55 2.01
2609 2700 7.334090 AGTGAGCACTCATGTGAATAGTAAAT 58.666 34.615 3.24 0.00 46.55 1.40
2610 2701 7.826252 AGTGAGCACTCATGTGAATAGTAAATT 59.174 33.333 3.24 0.00 46.55 1.82
2611 2702 8.454106 GTGAGCACTCATGTGAATAGTAAATTT 58.546 33.333 3.24 0.00 46.55 1.82
2612 2703 9.665719 TGAGCACTCATGTGAATAGTAAATTTA 57.334 29.630 0.94 0.00 46.55 1.40
2613 2704 9.922305 GAGCACTCATGTGAATAGTAAATTTAC 57.078 33.333 18.77 18.77 46.55 2.01
2614 2705 9.448438 AGCACTCATGTGAATAGTAAATTTACA 57.552 29.630 26.06 14.60 46.55 2.41
2659 2750 7.475137 AAATTTCTGAAATTTCGGGGTATGA 57.525 32.000 27.05 3.76 45.32 2.15
2660 2751 7.475137 AATTTCTGAAATTTCGGGGTATGAA 57.525 32.000 23.64 9.28 37.84 2.57
2661 2752 6.902771 TTTCTGAAATTTCGGGGTATGAAA 57.097 33.333 23.64 13.98 39.45 2.69
2662 2753 5.890424 TCTGAAATTTCGGGGTATGAAAC 57.110 39.130 23.64 0.00 38.08 2.78
2663 2754 5.566469 TCTGAAATTTCGGGGTATGAAACT 58.434 37.500 23.64 0.00 38.08 2.66
2664 2755 6.007703 TCTGAAATTTCGGGGTATGAAACTT 58.992 36.000 23.64 0.00 38.08 2.66
2665 2756 7.169591 TCTGAAATTTCGGGGTATGAAACTTA 58.830 34.615 23.64 0.38 38.08 2.24
2666 2757 7.335924 TCTGAAATTTCGGGGTATGAAACTTAG 59.664 37.037 23.64 6.05 38.08 2.18
2667 2758 6.943718 TGAAATTTCGGGGTATGAAACTTAGT 59.056 34.615 13.34 0.00 38.08 2.24
2668 2759 6.997239 AATTTCGGGGTATGAAACTTAGTC 57.003 37.500 0.00 0.00 38.08 2.59
2669 2760 3.788333 TCGGGGTATGAAACTTAGTCG 57.212 47.619 0.00 0.00 0.00 4.18
2670 2761 3.355378 TCGGGGTATGAAACTTAGTCGA 58.645 45.455 0.00 0.00 0.00 4.20
2671 2762 3.129287 TCGGGGTATGAAACTTAGTCGAC 59.871 47.826 7.70 7.70 0.00 4.20
2672 2763 3.736126 CGGGGTATGAAACTTAGTCGACC 60.736 52.174 13.01 0.00 0.00 4.79
2673 2764 3.196254 GGGGTATGAAACTTAGTCGACCA 59.804 47.826 13.01 0.92 0.00 4.02
2674 2765 4.141779 GGGGTATGAAACTTAGTCGACCAT 60.142 45.833 13.01 9.06 0.00 3.55
2675 2766 5.425630 GGGTATGAAACTTAGTCGACCATT 58.574 41.667 13.01 0.07 0.00 3.16
2676 2767 5.522824 GGGTATGAAACTTAGTCGACCATTC 59.477 44.000 13.01 10.17 0.00 2.67
2677 2768 6.338937 GGTATGAAACTTAGTCGACCATTCT 58.661 40.000 13.01 0.00 0.00 2.40
2678 2769 7.417116 GGGTATGAAACTTAGTCGACCATTCTA 60.417 40.741 13.01 0.00 0.00 2.10
2679 2770 7.434602 GGTATGAAACTTAGTCGACCATTCTAC 59.565 40.741 13.01 12.11 0.00 2.59
2680 2771 6.585695 TGAAACTTAGTCGACCATTCTACT 57.414 37.500 13.01 0.00 32.67 2.57
2681 2772 6.618811 TGAAACTTAGTCGACCATTCTACTC 58.381 40.000 13.01 0.80 30.63 2.59
2682 2773 6.208007 TGAAACTTAGTCGACCATTCTACTCA 59.792 38.462 13.01 3.50 30.63 3.41
2683 2774 5.564048 ACTTAGTCGACCATTCTACTCAC 57.436 43.478 13.01 0.00 30.63 3.51
2684 2775 5.008331 ACTTAGTCGACCATTCTACTCACA 58.992 41.667 13.01 0.00 30.63 3.58
2685 2776 5.652891 ACTTAGTCGACCATTCTACTCACAT 59.347 40.000 13.01 0.00 30.63 3.21
2686 2777 4.377839 AGTCGACCATTCTACTCACATG 57.622 45.455 13.01 0.00 0.00 3.21
2687 2778 3.764434 AGTCGACCATTCTACTCACATGT 59.236 43.478 13.01 0.00 0.00 3.21
2688 2779 3.859961 GTCGACCATTCTACTCACATGTG 59.140 47.826 20.18 20.18 0.00 3.21
2689 2780 3.761752 TCGACCATTCTACTCACATGTGA 59.238 43.478 26.33 26.33 38.06 3.58
2690 2781 4.219725 TCGACCATTCTACTCACATGTGAA 59.780 41.667 27.63 14.24 39.39 3.18
2691 2782 4.564372 CGACCATTCTACTCACATGTGAAG 59.436 45.833 27.63 22.38 39.39 3.02
2692 2783 5.482908 GACCATTCTACTCACATGTGAAGT 58.517 41.667 27.63 25.77 39.39 3.01
2693 2784 5.869579 ACCATTCTACTCACATGTGAAGTT 58.130 37.500 27.63 17.36 39.39 2.66
2694 2785 6.299141 ACCATTCTACTCACATGTGAAGTTT 58.701 36.000 27.63 15.11 39.39 2.66
2695 2786 6.772716 ACCATTCTACTCACATGTGAAGTTTT 59.227 34.615 27.63 12.89 39.39 2.43
2696 2787 7.080099 CCATTCTACTCACATGTGAAGTTTTG 58.920 38.462 27.63 17.56 39.39 2.44
2697 2788 7.255242 CCATTCTACTCACATGTGAAGTTTTGT 60.255 37.037 27.63 21.80 39.39 2.83
2698 2789 7.624360 TTCTACTCACATGTGAAGTTTTGTT 57.376 32.000 27.63 9.51 39.39 2.83
2699 2790 8.725405 TTCTACTCACATGTGAAGTTTTGTTA 57.275 30.769 27.63 10.91 39.39 2.41
2700 2791 8.902540 TCTACTCACATGTGAAGTTTTGTTAT 57.097 30.769 27.63 7.68 39.39 1.89
2701 2792 8.773645 TCTACTCACATGTGAAGTTTTGTTATG 58.226 33.333 27.63 14.41 39.39 1.90
2702 2793 7.333528 ACTCACATGTGAAGTTTTGTTATGT 57.666 32.000 27.63 15.01 39.39 2.29
2703 2794 8.445275 ACTCACATGTGAAGTTTTGTTATGTA 57.555 30.769 27.63 1.53 39.39 2.29
2704 2795 9.066892 ACTCACATGTGAAGTTTTGTTATGTAT 57.933 29.630 27.63 1.41 39.39 2.29
2705 2796 9.897744 CTCACATGTGAAGTTTTGTTATGTATT 57.102 29.630 27.63 0.00 39.39 1.89
2706 2797 9.676195 TCACATGTGAAGTTTTGTTATGTATTG 57.324 29.630 26.02 0.00 36.53 1.90
2707 2798 9.676195 CACATGTGAAGTTTTGTTATGTATTGA 57.324 29.630 21.64 0.00 0.00 2.57
2708 2799 9.677567 ACATGTGAAGTTTTGTTATGTATTGAC 57.322 29.630 0.00 0.00 0.00 3.18
2709 2800 9.676195 CATGTGAAGTTTTGTTATGTATTGACA 57.324 29.630 0.00 0.00 40.72 3.58
2710 2801 9.677567 ATGTGAAGTTTTGTTATGTATTGACAC 57.322 29.630 0.00 0.00 38.76 3.67
2711 2802 8.132362 TGTGAAGTTTTGTTATGTATTGACACC 58.868 33.333 0.00 0.00 38.76 4.16
2712 2803 7.593644 GTGAAGTTTTGTTATGTATTGACACCC 59.406 37.037 0.00 0.00 38.76 4.61
2713 2804 6.584185 AGTTTTGTTATGTATTGACACCCC 57.416 37.500 0.00 0.00 38.76 4.95
2714 2805 6.311735 AGTTTTGTTATGTATTGACACCCCT 58.688 36.000 0.00 0.00 38.76 4.79
2715 2806 6.208599 AGTTTTGTTATGTATTGACACCCCTG 59.791 38.462 0.00 0.00 38.76 4.45
2716 2807 4.229304 TGTTATGTATTGACACCCCTGG 57.771 45.455 0.00 0.00 38.76 4.45
2717 2808 3.589735 TGTTATGTATTGACACCCCTGGT 59.410 43.478 0.00 0.00 38.76 4.00
2718 2809 4.783763 TGTTATGTATTGACACCCCTGGTA 59.216 41.667 0.00 0.00 38.76 3.25
2719 2810 5.430417 TGTTATGTATTGACACCCCTGGTAT 59.570 40.000 0.00 0.00 38.76 2.73
2720 2811 6.069323 TGTTATGTATTGACACCCCTGGTATT 60.069 38.462 0.00 0.00 38.76 1.89
2721 2812 4.497291 TGTATTGACACCCCTGGTATTC 57.503 45.455 0.00 0.00 32.11 1.75
2722 2813 4.108570 TGTATTGACACCCCTGGTATTCT 58.891 43.478 0.00 0.00 32.11 2.40
2723 2814 4.538490 TGTATTGACACCCCTGGTATTCTT 59.462 41.667 0.00 0.00 32.11 2.52
2724 2815 5.727279 TGTATTGACACCCCTGGTATTCTTA 59.273 40.000 0.00 0.00 32.11 2.10
2725 2816 4.837093 TTGACACCCCTGGTATTCTTAG 57.163 45.455 0.00 0.00 32.11 2.18
2726 2817 3.798515 TGACACCCCTGGTATTCTTAGT 58.201 45.455 0.00 0.00 32.11 2.24
2727 2818 3.517901 TGACACCCCTGGTATTCTTAGTG 59.482 47.826 0.00 0.00 32.11 2.74
2728 2819 3.773119 GACACCCCTGGTATTCTTAGTGA 59.227 47.826 0.00 0.00 32.11 3.41
2729 2820 4.172807 ACACCCCTGGTATTCTTAGTGAA 58.827 43.478 0.00 0.00 34.39 3.18
2730 2821 4.225267 ACACCCCTGGTATTCTTAGTGAAG 59.775 45.833 0.00 0.00 33.70 3.02
2731 2822 4.469945 CACCCCTGGTATTCTTAGTGAAGA 59.530 45.833 0.00 0.00 35.30 2.87
2732 2823 5.045869 CACCCCTGGTATTCTTAGTGAAGAA 60.046 44.000 2.80 2.80 44.02 2.52
2733 2824 6.521770 CACCCCTGGTATTCTTAGTGAAGAAA 60.522 42.308 4.36 0.00 43.53 2.52
2734 2825 7.962217 CACCCCTGGTATTCTTAGTGAAGAAAA 60.962 40.741 4.36 0.00 43.53 2.29
2753 2844 4.492791 AAAAATACAACTGGCACCGTAC 57.507 40.909 0.00 0.00 0.00 3.67
2754 2845 3.412237 AAATACAACTGGCACCGTACT 57.588 42.857 0.00 0.00 0.00 2.73
2755 2846 4.540359 AAATACAACTGGCACCGTACTA 57.460 40.909 0.00 0.00 0.00 1.82
2756 2847 4.748277 AATACAACTGGCACCGTACTAT 57.252 40.909 0.00 0.00 0.00 2.12
2757 2848 4.748277 ATACAACTGGCACCGTACTATT 57.252 40.909 0.00 0.00 0.00 1.73
2758 2849 2.968675 ACAACTGGCACCGTACTATTC 58.031 47.619 0.00 0.00 0.00 1.75
2759 2850 2.300723 ACAACTGGCACCGTACTATTCA 59.699 45.455 0.00 0.00 0.00 2.57
2760 2851 3.055385 ACAACTGGCACCGTACTATTCAT 60.055 43.478 0.00 0.00 0.00 2.57
2761 2852 3.454371 ACTGGCACCGTACTATTCATC 57.546 47.619 0.00 0.00 0.00 2.92
2762 2853 2.764010 ACTGGCACCGTACTATTCATCA 59.236 45.455 0.00 0.00 0.00 3.07
2763 2854 3.196901 ACTGGCACCGTACTATTCATCAA 59.803 43.478 0.00 0.00 0.00 2.57
2764 2855 4.188462 CTGGCACCGTACTATTCATCAAA 58.812 43.478 0.00 0.00 0.00 2.69
2765 2856 3.936453 TGGCACCGTACTATTCATCAAAC 59.064 43.478 0.00 0.00 0.00 2.93
2766 2857 3.936453 GGCACCGTACTATTCATCAAACA 59.064 43.478 0.00 0.00 0.00 2.83
2767 2858 4.034048 GGCACCGTACTATTCATCAAACAG 59.966 45.833 0.00 0.00 0.00 3.16
2768 2859 4.630069 GCACCGTACTATTCATCAAACAGT 59.370 41.667 0.00 0.00 0.00 3.55
2769 2860 5.445939 GCACCGTACTATTCATCAAACAGTG 60.446 44.000 0.00 0.00 0.00 3.66
2770 2861 5.637810 CACCGTACTATTCATCAAACAGTGT 59.362 40.000 0.00 0.00 0.00 3.55
2771 2862 6.147164 CACCGTACTATTCATCAAACAGTGTT 59.853 38.462 1.64 1.64 0.00 3.32
2772 2863 6.708949 ACCGTACTATTCATCAAACAGTGTTT 59.291 34.615 15.58 15.58 0.00 2.83
2773 2864 7.227910 ACCGTACTATTCATCAAACAGTGTTTT 59.772 33.333 18.59 6.09 0.00 2.43
2774 2865 7.744715 CCGTACTATTCATCAAACAGTGTTTTC 59.255 37.037 18.59 0.00 0.00 2.29
2775 2866 8.495949 CGTACTATTCATCAAACAGTGTTTTCT 58.504 33.333 18.59 6.28 0.00 2.52
2816 2907 6.773976 TTCATTTTGCCCAGATTACTAAGG 57.226 37.500 0.00 0.00 0.00 2.69
2817 2908 6.073447 TCATTTTGCCCAGATTACTAAGGA 57.927 37.500 0.00 0.00 0.00 3.36
2818 2909 6.672593 TCATTTTGCCCAGATTACTAAGGAT 58.327 36.000 0.00 0.00 0.00 3.24
2819 2910 7.811282 TCATTTTGCCCAGATTACTAAGGATA 58.189 34.615 0.00 0.00 0.00 2.59
2820 2911 8.448008 TCATTTTGCCCAGATTACTAAGGATAT 58.552 33.333 0.00 0.00 0.00 1.63
2821 2912 8.517878 CATTTTGCCCAGATTACTAAGGATATG 58.482 37.037 0.00 0.00 0.00 1.78
2822 2913 7.387265 TTTGCCCAGATTACTAAGGATATGA 57.613 36.000 0.00 0.00 0.00 2.15
2823 2914 7.574021 TTGCCCAGATTACTAAGGATATGAT 57.426 36.000 0.00 0.00 0.00 2.45
2824 2915 7.574021 TGCCCAGATTACTAAGGATATGATT 57.426 36.000 0.00 0.00 0.00 2.57
2825 2916 7.988937 TGCCCAGATTACTAAGGATATGATTT 58.011 34.615 0.00 0.00 0.00 2.17
2826 2917 8.103305 TGCCCAGATTACTAAGGATATGATTTC 58.897 37.037 0.00 0.00 0.00 2.17
2827 2918 8.325046 GCCCAGATTACTAAGGATATGATTTCT 58.675 37.037 0.00 0.00 0.00 2.52
2836 2927 9.099454 ACTAAGGATATGATTTCTTCGTGAAAC 57.901 33.333 8.09 4.80 46.08 2.78
2837 2928 9.319143 CTAAGGATATGATTTCTTCGTGAAACT 57.681 33.333 8.09 0.00 46.08 2.66
2838 2929 8.567285 AAGGATATGATTTCTTCGTGAAACTT 57.433 30.769 8.09 4.19 46.08 2.66
2839 2930 8.202745 AGGATATGATTTCTTCGTGAAACTTC 57.797 34.615 8.09 5.07 46.08 3.01
2840 2931 7.824289 AGGATATGATTTCTTCGTGAAACTTCA 59.176 33.333 8.09 9.23 46.08 3.02
2841 2932 8.616076 GGATATGATTTCTTCGTGAAACTTCAT 58.384 33.333 17.57 17.57 46.08 2.57
2845 2936 7.243487 TGATTTCTTCGTGAAACTTCATATGC 58.757 34.615 0.00 0.00 46.08 3.14
2846 2937 4.840401 TCTTCGTGAAACTTCATATGCG 57.160 40.909 0.00 0.00 39.73 4.73
2847 2938 4.490743 TCTTCGTGAAACTTCATATGCGA 58.509 39.130 0.00 0.00 39.73 5.10
2848 2939 4.562789 TCTTCGTGAAACTTCATATGCGAG 59.437 41.667 0.00 1.21 39.73 5.03
2849 2940 3.845178 TCGTGAAACTTCATATGCGAGT 58.155 40.909 0.00 1.86 39.73 4.18
2850 2941 4.989044 TCGTGAAACTTCATATGCGAGTA 58.011 39.130 10.69 0.00 39.73 2.59
2851 2942 5.588240 TCGTGAAACTTCATATGCGAGTAT 58.412 37.500 10.69 2.01 39.73 2.12
2852 2943 6.731164 TCGTGAAACTTCATATGCGAGTATA 58.269 36.000 10.69 1.18 39.73 1.47
2853 2944 6.635641 TCGTGAAACTTCATATGCGAGTATAC 59.364 38.462 10.69 0.00 39.73 1.47
2854 2945 6.129168 CGTGAAACTTCATATGCGAGTATACC 60.129 42.308 10.69 0.00 39.73 2.73
2855 2946 5.918576 TGAAACTTCATATGCGAGTATACCG 59.081 40.000 10.69 4.41 31.01 4.02
2856 2947 5.700722 AACTTCATATGCGAGTATACCGA 57.299 39.130 15.19 4.13 0.00 4.69
2857 2948 5.899120 ACTTCATATGCGAGTATACCGAT 57.101 39.130 15.19 9.42 0.00 4.18
2858 2949 6.268825 ACTTCATATGCGAGTATACCGATT 57.731 37.500 15.19 6.20 0.00 3.34
2859 2950 6.093404 ACTTCATATGCGAGTATACCGATTG 58.907 40.000 15.19 7.93 0.00 2.67
2860 2951 5.890424 TCATATGCGAGTATACCGATTGA 57.110 39.130 15.19 9.50 0.00 2.57
2861 2952 5.637809 TCATATGCGAGTATACCGATTGAC 58.362 41.667 15.19 1.46 0.00 3.18
2862 2953 5.414765 TCATATGCGAGTATACCGATTGACT 59.585 40.000 15.19 0.00 0.00 3.41
2863 2954 6.596497 TCATATGCGAGTATACCGATTGACTA 59.404 38.462 15.19 1.45 0.00 2.59
2864 2955 5.899120 ATGCGAGTATACCGATTGACTAT 57.101 39.130 15.19 0.00 0.00 2.12
2865 2956 5.043189 TGCGAGTATACCGATTGACTATG 57.957 43.478 15.19 0.00 0.00 2.23
2866 2957 4.517832 TGCGAGTATACCGATTGACTATGT 59.482 41.667 15.19 0.00 0.00 2.29
2867 2958 5.702209 TGCGAGTATACCGATTGACTATGTA 59.298 40.000 15.19 0.00 0.00 2.29
2868 2959 6.373495 TGCGAGTATACCGATTGACTATGTAT 59.627 38.462 15.19 0.00 0.00 2.29
2869 2960 7.550196 TGCGAGTATACCGATTGACTATGTATA 59.450 37.037 15.19 0.00 0.00 1.47
2870 2961 8.557864 GCGAGTATACCGATTGACTATGTATAT 58.442 37.037 15.19 0.00 29.87 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
589 593 8.931385 AACCATGAGCATGTAACATAAATTTC 57.069 30.769 9.39 0.00 37.11 2.17
853 857 5.048573 ACAGTTTTTGGTAAACACACTCGTT 60.049 36.000 0.00 0.00 32.81 3.85
1412 1423 1.227263 CCTACCATCCGCGAACAGG 60.227 63.158 8.23 6.48 0.00 4.00
1617 1628 9.553064 CTGAATTTGGTAAGAAGATACAGCTAT 57.447 33.333 0.00 0.00 0.00 2.97
1830 1870 6.051717 GCTTAGAATCACAGGTACATCACAT 58.948 40.000 0.00 0.00 0.00 3.21
1930 1973 0.397535 AATGCTAATGCCCCACCTGG 60.398 55.000 0.00 0.00 38.71 4.45
2138 2189 8.822805 AGGAAACATACCTCTTCTATGTAACAA 58.177 33.333 0.00 0.00 34.37 2.83
2139 2190 8.375493 AGGAAACATACCTCTTCTATGTAACA 57.625 34.615 0.00 0.00 34.37 2.41
2588 2679 9.448438 TGTAAATTTACTATTCACATGAGTGCT 57.552 29.630 24.81 0.00 38.74 4.40
2636 2727 7.475137 TTCATACCCCGAAATTTCAGAAATT 57.525 32.000 17.99 14.43 42.62 1.82
2637 2728 7.178451 AGTTTCATACCCCGAAATTTCAGAAAT 59.822 33.333 17.99 2.20 35.01 2.17
2638 2729 6.492087 AGTTTCATACCCCGAAATTTCAGAAA 59.508 34.615 17.99 11.56 35.01 2.52
2639 2730 6.007703 AGTTTCATACCCCGAAATTTCAGAA 58.992 36.000 17.99 7.01 35.01 3.02
2640 2731 5.566469 AGTTTCATACCCCGAAATTTCAGA 58.434 37.500 17.99 1.74 35.01 3.27
2641 2732 5.897377 AGTTTCATACCCCGAAATTTCAG 57.103 39.130 17.99 6.71 35.01 3.02
2642 2733 6.943718 ACTAAGTTTCATACCCCGAAATTTCA 59.056 34.615 17.99 0.00 35.02 2.69
2643 2734 7.387119 ACTAAGTTTCATACCCCGAAATTTC 57.613 36.000 8.20 8.20 35.02 2.17
2644 2735 6.093082 CGACTAAGTTTCATACCCCGAAATTT 59.907 38.462 0.00 0.00 36.59 1.82
2645 2736 5.583457 CGACTAAGTTTCATACCCCGAAATT 59.417 40.000 0.00 0.00 35.01 1.82
2646 2737 5.105228 TCGACTAAGTTTCATACCCCGAAAT 60.105 40.000 0.00 0.00 35.01 2.17
2647 2738 4.220382 TCGACTAAGTTTCATACCCCGAAA 59.780 41.667 0.00 0.00 0.00 3.46
2648 2739 3.763360 TCGACTAAGTTTCATACCCCGAA 59.237 43.478 0.00 0.00 0.00 4.30
2649 2740 3.129287 GTCGACTAAGTTTCATACCCCGA 59.871 47.826 8.70 0.00 0.00 5.14
2650 2741 3.442100 GTCGACTAAGTTTCATACCCCG 58.558 50.000 8.70 0.00 0.00 5.73
2651 2742 3.196254 TGGTCGACTAAGTTTCATACCCC 59.804 47.826 16.46 0.00 0.00 4.95
2652 2743 4.460948 TGGTCGACTAAGTTTCATACCC 57.539 45.455 16.46 0.00 0.00 3.69
2653 2744 6.338937 AGAATGGTCGACTAAGTTTCATACC 58.661 40.000 16.46 4.64 0.00 2.73
2654 2745 8.189460 AGTAGAATGGTCGACTAAGTTTCATAC 58.811 37.037 16.46 12.88 37.89 2.39
2655 2746 8.289939 AGTAGAATGGTCGACTAAGTTTCATA 57.710 34.615 16.46 3.00 37.89 2.15
2656 2747 7.093902 TGAGTAGAATGGTCGACTAAGTTTCAT 60.094 37.037 16.46 5.46 39.55 2.57
2657 2748 6.208007 TGAGTAGAATGGTCGACTAAGTTTCA 59.792 38.462 16.46 7.65 39.55 2.69
2658 2749 6.527372 GTGAGTAGAATGGTCGACTAAGTTTC 59.473 42.308 16.46 10.35 39.55 2.78
2659 2750 6.015688 TGTGAGTAGAATGGTCGACTAAGTTT 60.016 38.462 16.46 0.08 39.55 2.66
2660 2751 5.475909 TGTGAGTAGAATGGTCGACTAAGTT 59.524 40.000 16.46 0.90 39.55 2.66
2661 2752 5.008331 TGTGAGTAGAATGGTCGACTAAGT 58.992 41.667 16.46 3.31 39.55 2.24
2662 2753 5.562506 TGTGAGTAGAATGGTCGACTAAG 57.437 43.478 16.46 0.00 39.55 2.18
2663 2754 5.417894 ACATGTGAGTAGAATGGTCGACTAA 59.582 40.000 16.46 4.64 39.55 2.24
2664 2755 4.948004 ACATGTGAGTAGAATGGTCGACTA 59.052 41.667 16.46 10.40 39.55 2.59
2665 2756 3.764434 ACATGTGAGTAGAATGGTCGACT 59.236 43.478 16.46 0.00 41.85 4.18
2666 2757 3.859961 CACATGTGAGTAGAATGGTCGAC 59.140 47.826 21.64 7.13 0.00 4.20
2667 2758 3.761752 TCACATGTGAGTAGAATGGTCGA 59.238 43.478 24.56 0.00 34.14 4.20
2668 2759 4.110036 TCACATGTGAGTAGAATGGTCG 57.890 45.455 24.56 0.00 34.14 4.79
2669 2760 5.482908 ACTTCACATGTGAGTAGAATGGTC 58.517 41.667 26.84 0.00 41.13 4.02
2670 2761 5.489792 ACTTCACATGTGAGTAGAATGGT 57.510 39.130 26.84 15.05 41.13 3.55
2671 2762 6.808008 AAACTTCACATGTGAGTAGAATGG 57.192 37.500 26.84 14.57 41.13 3.16
2672 2763 7.642669 ACAAAACTTCACATGTGAGTAGAATG 58.357 34.615 26.84 22.71 41.13 2.67
2673 2764 7.807977 ACAAAACTTCACATGTGAGTAGAAT 57.192 32.000 26.84 15.66 41.13 2.40
2674 2765 7.624360 AACAAAACTTCACATGTGAGTAGAA 57.376 32.000 26.84 14.05 41.13 2.10
2675 2766 8.773645 CATAACAAAACTTCACATGTGAGTAGA 58.226 33.333 26.84 14.37 41.13 2.59
2676 2767 8.559536 ACATAACAAAACTTCACATGTGAGTAG 58.440 33.333 26.48 23.47 41.13 2.57
2677 2768 8.445275 ACATAACAAAACTTCACATGTGAGTA 57.555 30.769 26.48 13.71 41.13 2.59
2678 2769 7.333528 ACATAACAAAACTTCACATGTGAGT 57.666 32.000 26.48 22.26 41.13 3.41
2679 2770 9.897744 AATACATAACAAAACTTCACATGTGAG 57.102 29.630 26.48 21.69 41.13 3.51
2680 2771 9.676195 CAATACATAACAAAACTTCACATGTGA 57.324 29.630 24.56 24.56 37.91 3.58
2681 2772 9.676195 TCAATACATAACAAAACTTCACATGTG 57.324 29.630 20.18 20.18 0.00 3.21
2682 2773 9.677567 GTCAATACATAACAAAACTTCACATGT 57.322 29.630 0.00 0.00 0.00 3.21
2683 2774 9.676195 TGTCAATACATAACAAAACTTCACATG 57.324 29.630 0.00 0.00 0.00 3.21
2684 2775 9.677567 GTGTCAATACATAACAAAACTTCACAT 57.322 29.630 0.00 0.00 38.08 3.21
2685 2776 8.132362 GGTGTCAATACATAACAAAACTTCACA 58.868 33.333 0.00 0.00 38.08 3.58
2686 2777 7.593644 GGGTGTCAATACATAACAAAACTTCAC 59.406 37.037 0.00 0.00 38.08 3.18
2687 2778 7.255660 GGGGTGTCAATACATAACAAAACTTCA 60.256 37.037 0.00 0.00 38.08 3.02
2688 2779 7.039993 AGGGGTGTCAATACATAACAAAACTTC 60.040 37.037 0.00 0.00 38.08 3.01
2689 2780 6.780522 AGGGGTGTCAATACATAACAAAACTT 59.219 34.615 0.00 0.00 38.08 2.66
2690 2781 6.208599 CAGGGGTGTCAATACATAACAAAACT 59.791 38.462 0.00 0.00 38.08 2.66
2691 2782 6.386654 CAGGGGTGTCAATACATAACAAAAC 58.613 40.000 0.00 0.00 38.08 2.43
2692 2783 5.478679 CCAGGGGTGTCAATACATAACAAAA 59.521 40.000 0.00 0.00 38.08 2.44
2693 2784 5.013547 CCAGGGGTGTCAATACATAACAAA 58.986 41.667 0.00 0.00 38.08 2.83
2694 2785 4.043561 ACCAGGGGTGTCAATACATAACAA 59.956 41.667 0.00 0.00 38.08 2.83
2695 2786 3.589735 ACCAGGGGTGTCAATACATAACA 59.410 43.478 0.00 0.00 38.08 2.41
2696 2787 4.230745 ACCAGGGGTGTCAATACATAAC 57.769 45.455 0.00 0.00 38.08 1.89
2697 2788 6.388689 AGAATACCAGGGGTGTCAATACATAA 59.611 38.462 0.00 0.00 38.08 1.90
2698 2789 5.908831 AGAATACCAGGGGTGTCAATACATA 59.091 40.000 0.00 0.00 38.08 2.29
2699 2790 4.726825 AGAATACCAGGGGTGTCAATACAT 59.273 41.667 0.00 0.00 38.08 2.29
2700 2791 4.108570 AGAATACCAGGGGTGTCAATACA 58.891 43.478 0.00 0.00 36.19 2.29
2701 2792 4.772886 AGAATACCAGGGGTGTCAATAC 57.227 45.455 0.00 0.00 36.19 1.89
2702 2793 5.968167 ACTAAGAATACCAGGGGTGTCAATA 59.032 40.000 0.00 0.00 36.19 1.90
2703 2794 4.788617 ACTAAGAATACCAGGGGTGTCAAT 59.211 41.667 0.00 0.00 36.19 2.57
2704 2795 4.019681 CACTAAGAATACCAGGGGTGTCAA 60.020 45.833 0.00 0.00 36.19 3.18
2705 2796 3.517901 CACTAAGAATACCAGGGGTGTCA 59.482 47.826 0.00 0.00 36.19 3.58
2706 2797 3.773119 TCACTAAGAATACCAGGGGTGTC 59.227 47.826 0.00 0.00 36.19 3.67
2707 2798 3.798515 TCACTAAGAATACCAGGGGTGT 58.201 45.455 0.00 0.00 36.19 4.16
2708 2799 4.469945 TCTTCACTAAGAATACCAGGGGTG 59.530 45.833 0.00 0.00 38.81 4.61
2709 2800 4.695606 TCTTCACTAAGAATACCAGGGGT 58.304 43.478 0.00 0.00 38.81 4.95
2710 2801 5.693769 TTCTTCACTAAGAATACCAGGGG 57.306 43.478 0.00 0.00 44.85 4.79
2732 2823 4.139038 AGTACGGTGCCAGTTGTATTTTT 58.861 39.130 0.00 0.00 0.00 1.94
2733 2824 3.746940 AGTACGGTGCCAGTTGTATTTT 58.253 40.909 0.00 0.00 0.00 1.82
2734 2825 3.412237 AGTACGGTGCCAGTTGTATTT 57.588 42.857 0.00 0.00 0.00 1.40
2735 2826 4.748277 ATAGTACGGTGCCAGTTGTATT 57.252 40.909 0.00 0.00 0.00 1.89
2736 2827 4.160814 TGAATAGTACGGTGCCAGTTGTAT 59.839 41.667 0.00 0.00 0.00 2.29
2737 2828 3.510753 TGAATAGTACGGTGCCAGTTGTA 59.489 43.478 0.00 0.00 0.00 2.41
2738 2829 2.300723 TGAATAGTACGGTGCCAGTTGT 59.699 45.455 0.00 0.00 0.00 3.32
2739 2830 2.967362 TGAATAGTACGGTGCCAGTTG 58.033 47.619 0.00 0.00 0.00 3.16
2740 2831 3.196901 TGATGAATAGTACGGTGCCAGTT 59.803 43.478 0.00 0.00 0.00 3.16
2741 2832 2.764010 TGATGAATAGTACGGTGCCAGT 59.236 45.455 0.00 0.00 0.00 4.00
2742 2833 3.452755 TGATGAATAGTACGGTGCCAG 57.547 47.619 0.00 0.00 0.00 4.85
2743 2834 3.897141 TTGATGAATAGTACGGTGCCA 57.103 42.857 0.00 0.00 0.00 4.92
2744 2835 3.936453 TGTTTGATGAATAGTACGGTGCC 59.064 43.478 0.00 0.00 0.00 5.01
2745 2836 4.630069 ACTGTTTGATGAATAGTACGGTGC 59.370 41.667 0.00 0.00 37.86 5.01
2746 2837 5.637810 ACACTGTTTGATGAATAGTACGGTG 59.362 40.000 0.00 0.00 44.40 4.94
2747 2838 5.790593 ACACTGTTTGATGAATAGTACGGT 58.209 37.500 0.00 0.00 37.58 4.83
2748 2839 6.721571 AACACTGTTTGATGAATAGTACGG 57.278 37.500 0.00 0.00 37.58 4.02
2749 2840 8.495949 AGAAAACACTGTTTGATGAATAGTACG 58.504 33.333 7.93 0.00 37.58 3.67
2790 2881 8.093927 CCTTAGTAATCTGGGCAAAATGAAAAA 58.906 33.333 0.00 0.00 0.00 1.94
2791 2882 7.453126 TCCTTAGTAATCTGGGCAAAATGAAAA 59.547 33.333 0.00 0.00 0.00 2.29
2792 2883 6.951198 TCCTTAGTAATCTGGGCAAAATGAAA 59.049 34.615 0.00 0.00 0.00 2.69
2793 2884 6.489603 TCCTTAGTAATCTGGGCAAAATGAA 58.510 36.000 0.00 0.00 0.00 2.57
2794 2885 6.073447 TCCTTAGTAATCTGGGCAAAATGA 57.927 37.500 0.00 0.00 0.00 2.57
2795 2886 6.966534 ATCCTTAGTAATCTGGGCAAAATG 57.033 37.500 0.00 0.00 0.00 2.32
2796 2887 8.448008 TCATATCCTTAGTAATCTGGGCAAAAT 58.552 33.333 0.00 0.00 0.00 1.82
2797 2888 7.811282 TCATATCCTTAGTAATCTGGGCAAAA 58.189 34.615 0.00 0.00 0.00 2.44
2798 2889 7.387265 TCATATCCTTAGTAATCTGGGCAAA 57.613 36.000 0.00 0.00 0.00 3.68
2799 2890 7.574021 ATCATATCCTTAGTAATCTGGGCAA 57.426 36.000 0.00 0.00 0.00 4.52
2800 2891 7.574021 AATCATATCCTTAGTAATCTGGGCA 57.426 36.000 0.00 0.00 0.00 5.36
2801 2892 8.325046 AGAAATCATATCCTTAGTAATCTGGGC 58.675 37.037 0.00 0.00 0.00 5.36
2823 2914 5.407084 TCGCATATGAAGTTTCACGAAGAAA 59.593 36.000 6.97 0.00 43.71 2.52
2824 2915 4.926832 TCGCATATGAAGTTTCACGAAGAA 59.073 37.500 6.97 0.00 40.49 2.52
2825 2916 4.490743 TCGCATATGAAGTTTCACGAAGA 58.509 39.130 6.97 0.00 40.49 2.87
2826 2917 4.327357 ACTCGCATATGAAGTTTCACGAAG 59.673 41.667 6.97 1.12 40.49 3.79
2827 2918 4.242475 ACTCGCATATGAAGTTTCACGAA 58.758 39.130 6.97 0.00 40.49 3.85
2828 2919 3.845178 ACTCGCATATGAAGTTTCACGA 58.155 40.909 6.97 2.35 40.49 4.35
2829 2920 5.890110 ATACTCGCATATGAAGTTTCACG 57.110 39.130 6.97 0.00 40.49 4.35
2830 2921 6.129168 CGGTATACTCGCATATGAAGTTTCAC 60.129 42.308 6.97 7.42 40.49 3.18
2831 2922 5.918576 CGGTATACTCGCATATGAAGTTTCA 59.081 40.000 6.97 0.00 42.14 2.69
2832 2923 6.147581 TCGGTATACTCGCATATGAAGTTTC 58.852 40.000 6.97 3.70 0.00 2.78
2833 2924 6.080648 TCGGTATACTCGCATATGAAGTTT 57.919 37.500 6.97 6.85 0.00 2.66
2834 2925 5.700722 TCGGTATACTCGCATATGAAGTT 57.299 39.130 6.97 3.51 0.00 2.66
2835 2926 5.899120 ATCGGTATACTCGCATATGAAGT 57.101 39.130 6.97 11.22 0.00 3.01
2836 2927 6.251589 GTCAATCGGTATACTCGCATATGAAG 59.748 42.308 6.97 5.46 0.00 3.02
2837 2928 6.072119 AGTCAATCGGTATACTCGCATATGAA 60.072 38.462 6.97 0.00 0.00 2.57
2838 2929 5.414765 AGTCAATCGGTATACTCGCATATGA 59.585 40.000 6.97 5.17 0.00 2.15
2839 2930 5.641709 AGTCAATCGGTATACTCGCATATG 58.358 41.667 2.25 0.00 0.00 1.78
2840 2931 5.899120 AGTCAATCGGTATACTCGCATAT 57.101 39.130 2.25 0.00 0.00 1.78
2841 2932 6.373495 ACATAGTCAATCGGTATACTCGCATA 59.627 38.462 2.25 0.00 0.00 3.14
2842 2933 5.183331 ACATAGTCAATCGGTATACTCGCAT 59.817 40.000 2.25 0.00 0.00 4.73
2843 2934 4.517832 ACATAGTCAATCGGTATACTCGCA 59.482 41.667 2.25 0.00 0.00 5.10
2844 2935 5.044428 ACATAGTCAATCGGTATACTCGC 57.956 43.478 2.25 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.