Multiple sequence alignment - TraesCS3B01G023500

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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 TraesCS3B01G023500 chr3B 100.000 2831 0 0 1 2831 10052117 10049287 0.000000e+00 5228
1 TraesCS3B01G023500 chr3B 95.262 2617 98 13 1 2597 154423021 154420411 0.000000e+00 4122
2 TraesCS3B01G023500 chr3B 95.295 2614 96 11 1 2598 151117111 151114509 0.000000e+00 4120
3 TraesCS3B01G023500 chr3B 94.253 1218 52 8 1 1202 204205954 204207169 0.000000e+00 1845
4 TraesCS3B01G023500 chr3B 89.888 89 4 5 2512 2598 160700612 160700527 2.980000e-20 110
5 TraesCS3B01G023500 chr5B 95.481 2611 92 13 1 2595 75081125 75083725 0.000000e+00 4145
6 TraesCS3B01G023500 chr5B 94.990 2615 100 13 1 2595 67028359 67025756 0.000000e+00 4074
7 TraesCS3B01G023500 chr2B 94.759 2614 105 15 1 2597 480006172 480008770 0.000000e+00 4039
8 TraesCS3B01G023500 chr2B 94.927 1991 82 7 23 1997 72935137 72937124 0.000000e+00 3099
9 TraesCS3B01G023500 chr7B 94.423 2618 100 13 1 2598 671265637 671263046 0.000000e+00 3984
10 TraesCS3B01G023500 chr7B 93.637 1823 85 16 754 2553 554184071 554182257 0.000000e+00 2695
11 TraesCS3B01G023500 chr7B 98.707 232 2 1 2597 2827 612647037 612647268 7.300000e-111 411
12 TraesCS3B01G023500 chr1B 94.279 2622 109 15 1 2599 630554821 630552218 0.000000e+00 3973
13 TraesCS3B01G023500 chr4B 94.073 2615 108 18 1 2598 561750392 561747808 0.000000e+00 3927
14 TraesCS3B01G023500 chr4B 94.468 235 12 1 2597 2830 659968610 659968376 7.460000e-96 361
15 TraesCS3B01G023500 chr6B 94.991 2116 81 11 1 2095 678840773 678842884 0.000000e+00 3297
16 TraesCS3B01G023500 chr6B 95.463 2072 72 10 40 2095 678821581 678823646 0.000000e+00 3286
17 TraesCS3B01G023500 chr1D 94.609 1818 68 10 754 2553 492938487 492940292 0.000000e+00 2787
18 TraesCS3B01G023500 chr1D 96.070 229 8 1 2597 2824 42479349 42479577 3.440000e-99 372
19 TraesCS3B01G023500 chr6D 97.021 235 6 1 2597 2830 381402130 381401896 7.350000e-106 394
20 TraesCS3B01G023500 chr4D 96.596 235 7 1 2597 2830 106657451 106657217 3.420000e-104 388
21 TraesCS3B01G023500 chr5D 95.763 236 8 1 2597 2830 76938775 76938540 2.060000e-101 379
22 TraesCS3B01G023500 chr6A 95.708 233 8 1 2597 2827 615971013 615971245 9.580000e-100 374
23 TraesCS3B01G023500 chr4A 91.667 84 6 1 2517 2599 724550573 724550490 6.410000e-22 115


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 TraesCS3B01G023500 chr3B 10049287 10052117 2830 True 5228 5228 100.000 1 2831 1 chr3B.!!$R1 2830
1 TraesCS3B01G023500 chr3B 154420411 154423021 2610 True 4122 4122 95.262 1 2597 1 chr3B.!!$R3 2596
2 TraesCS3B01G023500 chr3B 151114509 151117111 2602 True 4120 4120 95.295 1 2598 1 chr3B.!!$R2 2597
3 TraesCS3B01G023500 chr3B 204205954 204207169 1215 False 1845 1845 94.253 1 1202 1 chr3B.!!$F1 1201
4 TraesCS3B01G023500 chr5B 75081125 75083725 2600 False 4145 4145 95.481 1 2595 1 chr5B.!!$F1 2594
5 TraesCS3B01G023500 chr5B 67025756 67028359 2603 True 4074 4074 94.990 1 2595 1 chr5B.!!$R1 2594
6 TraesCS3B01G023500 chr2B 480006172 480008770 2598 False 4039 4039 94.759 1 2597 1 chr2B.!!$F2 2596
7 TraesCS3B01G023500 chr2B 72935137 72937124 1987 False 3099 3099 94.927 23 1997 1 chr2B.!!$F1 1974
8 TraesCS3B01G023500 chr7B 671263046 671265637 2591 True 3984 3984 94.423 1 2598 1 chr7B.!!$R2 2597
9 TraesCS3B01G023500 chr7B 554182257 554184071 1814 True 2695 2695 93.637 754 2553 1 chr7B.!!$R1 1799
10 TraesCS3B01G023500 chr1B 630552218 630554821 2603 True 3973 3973 94.279 1 2599 1 chr1B.!!$R1 2598
11 TraesCS3B01G023500 chr4B 561747808 561750392 2584 True 3927 3927 94.073 1 2598 1 chr4B.!!$R1 2597
12 TraesCS3B01G023500 chr6B 678840773 678842884 2111 False 3297 3297 94.991 1 2095 1 chr6B.!!$F2 2094
13 TraesCS3B01G023500 chr6B 678821581 678823646 2065 False 3286 3286 95.463 40 2095 1 chr6B.!!$F1 2055
14 TraesCS3B01G023500 chr1D 492938487 492940292 1805 False 2787 2787 94.609 754 2553 1 chr1D.!!$F2 1799

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
199 201 0.762082 CTGCTCTGGGGATCCTAGCA 60.762 60.000 21.84 21.84 44.55 3.49 F
323 325 1.334243 GATCAGTAGTTCCGTCCCGAG 59.666 57.143 0.00 0.00 0.00 4.63 F
1055 1092 0.604578 GCCAACTACTACCACGACCA 59.395 55.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1092 0.886490 CTTCTCCTTGTTGCCGCTGT 60.886 55.000 0.00 0.00 0.00 4.40 R
1705 1750 1.302285 CAACCTGGCAGGAGCAGAT 59.698 57.895 38.99 13.75 44.61 2.90 R
2785 2841 0.251916 CGGGGTATGTCTTGAAGGCA 59.748 55.000 0.42 0.42 32.55 4.75 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
199 201 0.762082 CTGCTCTGGGGATCCTAGCA 60.762 60.000 21.84 21.84 44.55 3.49
279 281 1.977009 ACGTCTCATGTCCGGCTCA 60.977 57.895 0.00 0.00 0.00 4.26
323 325 1.334243 GATCAGTAGTTCCGTCCCGAG 59.666 57.143 0.00 0.00 0.00 4.63
948 972 5.347635 CGTCCAATCTATTCGAGTGTTTTCA 59.652 40.000 0.00 0.00 36.02 2.69
1026 1063 2.268076 GCAAAGAAGGCAGGGCGAA 61.268 57.895 0.00 0.00 0.00 4.70
1027 1064 1.581447 CAAAGAAGGCAGGGCGAAC 59.419 57.895 0.00 0.00 0.00 3.95
1055 1092 0.604578 GCCAACTACTACCACGACCA 59.395 55.000 0.00 0.00 0.00 4.02
1129 1166 2.013563 GCTTCACCATCCGCAAGATCA 61.014 52.381 0.00 0.00 43.02 2.92
1152 1189 1.972223 CGACAGTCCCGACCTCAGT 60.972 63.158 0.00 0.00 0.00 3.41
1283 1321 3.097728 CGACACTGACACCGTCGC 61.098 66.667 8.50 0.00 44.99 5.19
1494 1539 3.706373 ATGCCGACGCCCTTCACT 61.706 61.111 0.00 0.00 0.00 3.41
1705 1750 2.986979 TGCACGAGGACGGCTACA 60.987 61.111 0.00 0.00 44.46 2.74
1774 1819 1.596934 GAGTGGAAGATGGCCGACA 59.403 57.895 0.00 0.00 0.00 4.35
1909 1954 3.697542 GGAGTCCTCCTAGTCAAAGAGAC 59.302 52.174 0.41 0.00 46.16 3.36
1932 1977 2.363680 GGAGAGAAGAAGATGATGGCGA 59.636 50.000 0.00 0.00 0.00 5.54
2079 2124 6.949352 ACCATCGATGCTTAATTGATTCTT 57.051 33.333 20.25 0.00 37.30 2.52
2283 2334 1.824329 TGGGCGGTGAAGCGAAAAA 60.824 52.632 6.02 0.00 38.18 1.94
2290 2341 1.877443 GGTGAAGCGAAAAAGCAGGTA 59.123 47.619 0.00 0.00 40.15 3.08
2319 2370 4.240096 GAGACGAAAAATAACCGGTCAGA 58.760 43.478 8.04 0.00 0.00 3.27
2563 2619 0.444651 CAGCGAAAAATAACCGGCGA 59.555 50.000 9.30 0.00 0.00 5.54
2599 2655 6.815089 ACTGCTCCATTAGAAGTAGAGATTG 58.185 40.000 0.00 0.00 42.92 2.67
2600 2656 6.609212 ACTGCTCCATTAGAAGTAGAGATTGA 59.391 38.462 0.00 0.00 42.92 2.57
2601 2657 7.289782 ACTGCTCCATTAGAAGTAGAGATTGAT 59.710 37.037 0.00 0.00 42.92 2.57
2602 2658 7.440198 TGCTCCATTAGAAGTAGAGATTGATG 58.560 38.462 0.00 0.00 0.00 3.07
2603 2659 6.873076 GCTCCATTAGAAGTAGAGATTGATGG 59.127 42.308 0.00 0.00 34.31 3.51
2604 2660 7.308450 TCCATTAGAAGTAGAGATTGATGGG 57.692 40.000 0.00 0.00 33.92 4.00
2605 2661 7.075797 TCCATTAGAAGTAGAGATTGATGGGA 58.924 38.462 0.00 0.00 33.92 4.37
2606 2662 7.015682 TCCATTAGAAGTAGAGATTGATGGGAC 59.984 40.741 0.00 0.00 33.92 4.46
2607 2663 4.927978 AGAAGTAGAGATTGATGGGACG 57.072 45.455 0.00 0.00 0.00 4.79
2608 2664 3.068873 AGAAGTAGAGATTGATGGGACGC 59.931 47.826 0.00 0.00 0.00 5.19
2609 2665 2.388735 AGTAGAGATTGATGGGACGCA 58.611 47.619 0.00 0.00 0.00 5.24
2610 2666 2.101582 AGTAGAGATTGATGGGACGCAC 59.898 50.000 0.00 0.00 0.00 5.34
2611 2667 1.198713 AGAGATTGATGGGACGCACT 58.801 50.000 0.00 0.00 0.00 4.40
2612 2668 1.556911 AGAGATTGATGGGACGCACTT 59.443 47.619 0.00 0.00 0.00 3.16
2613 2669 2.026822 AGAGATTGATGGGACGCACTTT 60.027 45.455 0.00 0.00 0.00 2.66
2614 2670 2.749621 GAGATTGATGGGACGCACTTTT 59.250 45.455 0.00 0.00 0.00 2.27
2615 2671 3.157087 AGATTGATGGGACGCACTTTTT 58.843 40.909 0.00 0.00 0.00 1.94
2616 2672 2.791383 TTGATGGGACGCACTTTTTG 57.209 45.000 0.00 0.00 0.00 2.44
2617 2673 1.974265 TGATGGGACGCACTTTTTGA 58.026 45.000 0.00 0.00 0.00 2.69
2618 2674 2.302260 TGATGGGACGCACTTTTTGAA 58.698 42.857 0.00 0.00 0.00 2.69
2619 2675 2.293122 TGATGGGACGCACTTTTTGAAG 59.707 45.455 0.00 0.00 0.00 3.02
2620 2676 2.045561 TGGGACGCACTTTTTGAAGA 57.954 45.000 0.00 0.00 0.00 2.87
2621 2677 1.673920 TGGGACGCACTTTTTGAAGAC 59.326 47.619 0.00 0.00 0.00 3.01
2622 2678 1.947456 GGGACGCACTTTTTGAAGACT 59.053 47.619 0.00 0.00 0.00 3.24
2623 2679 3.135994 GGGACGCACTTTTTGAAGACTA 58.864 45.455 0.00 0.00 0.00 2.59
2624 2680 3.186613 GGGACGCACTTTTTGAAGACTAG 59.813 47.826 0.00 0.00 0.00 2.57
2625 2681 3.808174 GGACGCACTTTTTGAAGACTAGT 59.192 43.478 0.00 0.00 0.00 2.57
2626 2682 4.272748 GGACGCACTTTTTGAAGACTAGTT 59.727 41.667 0.00 0.00 0.00 2.24
2627 2683 5.220796 GGACGCACTTTTTGAAGACTAGTTT 60.221 40.000 0.00 0.00 0.00 2.66
2628 2684 6.190954 ACGCACTTTTTGAAGACTAGTTTT 57.809 33.333 0.00 0.00 0.00 2.43
2629 2685 6.255950 ACGCACTTTTTGAAGACTAGTTTTC 58.744 36.000 17.13 17.13 0.00 2.29
2630 2686 5.681543 CGCACTTTTTGAAGACTAGTTTTCC 59.318 40.000 20.17 6.27 0.00 3.13
2631 2687 6.458342 CGCACTTTTTGAAGACTAGTTTTCCT 60.458 38.462 20.17 0.07 0.00 3.36
2632 2688 7.254658 CGCACTTTTTGAAGACTAGTTTTCCTA 60.255 37.037 20.17 8.37 0.00 2.94
2633 2689 8.568794 GCACTTTTTGAAGACTAGTTTTCCTAT 58.431 33.333 20.17 1.54 0.00 2.57
2720 2776 5.537300 ACATACCATGTAGACATCCAGAC 57.463 43.478 0.00 0.00 42.78 3.51
2721 2777 4.345257 ACATACCATGTAGACATCCAGACC 59.655 45.833 0.00 0.00 42.78 3.85
2722 2778 2.119495 ACCATGTAGACATCCAGACCC 58.881 52.381 0.00 0.00 33.61 4.46
2723 2779 1.069204 CCATGTAGACATCCAGACCCG 59.931 57.143 0.00 0.00 33.61 5.28
2724 2780 2.031870 CATGTAGACATCCAGACCCGA 58.968 52.381 0.00 0.00 33.61 5.14
2725 2781 2.454336 TGTAGACATCCAGACCCGAT 57.546 50.000 0.00 0.00 0.00 4.18
2726 2782 3.588210 TGTAGACATCCAGACCCGATA 57.412 47.619 0.00 0.00 0.00 2.92
2727 2783 4.114015 TGTAGACATCCAGACCCGATAT 57.886 45.455 0.00 0.00 0.00 1.63
2728 2784 3.826729 TGTAGACATCCAGACCCGATATG 59.173 47.826 0.00 0.00 0.00 1.78
2729 2785 2.964209 AGACATCCAGACCCGATATGT 58.036 47.619 0.00 0.00 33.63 2.29
2730 2786 3.309296 AGACATCCAGACCCGATATGTT 58.691 45.455 0.00 0.00 31.19 2.71
2731 2787 3.711704 AGACATCCAGACCCGATATGTTT 59.288 43.478 0.00 0.00 31.19 2.83
2732 2788 4.899457 AGACATCCAGACCCGATATGTTTA 59.101 41.667 0.00 0.00 31.19 2.01
2733 2789 4.957296 ACATCCAGACCCGATATGTTTAC 58.043 43.478 0.00 0.00 0.00 2.01
2734 2790 4.407621 ACATCCAGACCCGATATGTTTACA 59.592 41.667 0.00 0.00 0.00 2.41
2735 2791 5.071788 ACATCCAGACCCGATATGTTTACAT 59.928 40.000 0.53 0.53 40.22 2.29
2736 2792 6.269077 ACATCCAGACCCGATATGTTTACATA 59.731 38.462 5.14 5.14 42.38 2.29
2737 2793 6.092955 TCCAGACCCGATATGTTTACATAC 57.907 41.667 4.79 0.18 41.15 2.39
2738 2794 5.599242 TCCAGACCCGATATGTTTACATACA 59.401 40.000 4.79 0.00 41.15 2.29
2739 2795 6.269077 TCCAGACCCGATATGTTTACATACAT 59.731 38.462 4.79 0.00 41.15 2.29
2740 2796 7.452189 TCCAGACCCGATATGTTTACATACATA 59.548 37.037 4.79 0.00 43.15 2.29
2744 2800 9.525409 GACCCGATATGTTTACATACATATACC 57.475 37.037 4.79 0.00 46.49 2.73
2745 2801 9.263446 ACCCGATATGTTTACATACATATACCT 57.737 33.333 4.79 0.00 46.49 3.08
2781 2837 6.090129 CCAACATCTGGGTTTTTAATACACG 58.910 40.000 0.00 0.00 42.17 4.49
2782 2838 6.294286 CCAACATCTGGGTTTTTAATACACGT 60.294 38.462 0.00 0.00 42.17 4.49
2783 2839 7.094720 CCAACATCTGGGTTTTTAATACACGTA 60.095 37.037 0.00 0.00 42.17 3.57
2784 2840 8.455682 CAACATCTGGGTTTTTAATACACGTAT 58.544 33.333 0.00 0.00 0.00 3.06
2785 2841 8.570068 ACATCTGGGTTTTTAATACACGTATT 57.430 30.769 7.54 7.54 39.02 1.89
2786 2842 8.455682 ACATCTGGGTTTTTAATACACGTATTG 58.544 33.333 11.79 0.00 36.52 1.90
2787 2843 6.844254 TCTGGGTTTTTAATACACGTATTGC 58.156 36.000 11.79 0.00 36.52 3.56
2788 2844 5.952033 TGGGTTTTTAATACACGTATTGCC 58.048 37.500 11.79 6.69 36.52 4.52
2789 2845 5.711036 TGGGTTTTTAATACACGTATTGCCT 59.289 36.000 11.79 0.00 36.52 4.75
2790 2846 6.208994 TGGGTTTTTAATACACGTATTGCCTT 59.791 34.615 11.79 0.00 36.52 4.35
2791 2847 6.748658 GGGTTTTTAATACACGTATTGCCTTC 59.251 38.462 11.79 1.87 36.52 3.46
2792 2848 7.306953 GGTTTTTAATACACGTATTGCCTTCA 58.693 34.615 11.79 0.00 36.52 3.02
2793 2849 7.808856 GGTTTTTAATACACGTATTGCCTTCAA 59.191 33.333 11.79 0.00 36.52 2.69
2794 2850 8.846607 GTTTTTAATACACGTATTGCCTTCAAG 58.153 33.333 11.79 0.00 36.52 3.02
2795 2851 7.908827 TTTAATACACGTATTGCCTTCAAGA 57.091 32.000 11.79 0.00 36.52 3.02
2796 2852 5.796350 AATACACGTATTGCCTTCAAGAC 57.204 39.130 1.66 0.00 40.11 3.01
2797 2853 3.120321 ACACGTATTGCCTTCAAGACA 57.880 42.857 0.00 0.00 42.77 3.41
2798 2854 3.674997 ACACGTATTGCCTTCAAGACAT 58.325 40.909 0.00 0.00 42.77 3.06
2799 2855 4.827692 ACACGTATTGCCTTCAAGACATA 58.172 39.130 0.00 0.00 42.77 2.29
2800 2856 4.630069 ACACGTATTGCCTTCAAGACATAC 59.370 41.667 0.00 0.00 42.77 2.39
2801 2857 4.034048 CACGTATTGCCTTCAAGACATACC 59.966 45.833 0.00 0.00 42.77 2.73
2802 2858 3.560068 CGTATTGCCTTCAAGACATACCC 59.440 47.826 4.12 0.00 42.77 3.69
2803 2859 2.507407 TTGCCTTCAAGACATACCCC 57.493 50.000 0.00 0.00 0.00 4.95
2804 2860 0.251916 TGCCTTCAAGACATACCCCG 59.748 55.000 0.00 0.00 0.00 5.73
2805 2861 0.539986 GCCTTCAAGACATACCCCGA 59.460 55.000 0.00 0.00 0.00 5.14
2806 2862 1.065709 GCCTTCAAGACATACCCCGAA 60.066 52.381 0.00 0.00 0.00 4.30
2807 2863 2.617021 GCCTTCAAGACATACCCCGAAA 60.617 50.000 0.00 0.00 0.00 3.46
2808 2864 3.681593 CCTTCAAGACATACCCCGAAAA 58.318 45.455 0.00 0.00 0.00 2.29
2809 2865 4.270008 CCTTCAAGACATACCCCGAAAAT 58.730 43.478 0.00 0.00 0.00 1.82
2810 2866 4.705023 CCTTCAAGACATACCCCGAAAATT 59.295 41.667 0.00 0.00 0.00 1.82
2811 2867 5.185056 CCTTCAAGACATACCCCGAAAATTT 59.815 40.000 0.00 0.00 0.00 1.82
2812 2868 6.295067 CCTTCAAGACATACCCCGAAAATTTT 60.295 38.462 2.28 2.28 0.00 1.82
2813 2869 6.019779 TCAAGACATACCCCGAAAATTTTG 57.980 37.500 8.47 1.04 0.00 2.44
2814 2870 5.536916 TCAAGACATACCCCGAAAATTTTGT 59.463 36.000 8.47 2.55 0.00 2.83
2815 2871 6.715718 TCAAGACATACCCCGAAAATTTTGTA 59.284 34.615 8.47 4.82 0.00 2.41
2816 2872 6.753107 AGACATACCCCGAAAATTTTGTAG 57.247 37.500 8.47 0.00 0.00 2.74
2817 2873 6.243148 AGACATACCCCGAAAATTTTGTAGT 58.757 36.000 8.47 3.27 0.00 2.73
2818 2874 6.717997 AGACATACCCCGAAAATTTTGTAGTT 59.282 34.615 8.47 0.00 0.00 2.24
2819 2875 7.231925 AGACATACCCCGAAAATTTTGTAGTTT 59.768 33.333 8.47 0.00 0.00 2.66
2820 2876 7.728148 ACATACCCCGAAAATTTTGTAGTTTT 58.272 30.769 8.47 0.00 0.00 2.43
2821 2877 8.858094 ACATACCCCGAAAATTTTGTAGTTTTA 58.142 29.630 8.47 0.00 0.00 1.52
2822 2878 9.349145 CATACCCCGAAAATTTTGTAGTTTTAG 57.651 33.333 8.47 0.00 0.00 1.85
2823 2879 7.350744 ACCCCGAAAATTTTGTAGTTTTAGT 57.649 32.000 8.47 0.00 0.00 2.24
2824 2880 7.204604 ACCCCGAAAATTTTGTAGTTTTAGTG 58.795 34.615 8.47 0.00 0.00 2.74
2825 2881 6.643360 CCCCGAAAATTTTGTAGTTTTAGTGG 59.357 38.462 8.47 0.00 0.00 4.00
2826 2882 7.204604 CCCGAAAATTTTGTAGTTTTAGTGGT 58.795 34.615 8.47 0.00 0.00 4.16
2827 2883 8.351461 CCCGAAAATTTTGTAGTTTTAGTGGTA 58.649 33.333 8.47 0.00 0.00 3.25
2828 2884 9.733219 CCGAAAATTTTGTAGTTTTAGTGGTAA 57.267 29.630 8.47 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 281 2.024655 ACTTGGTGATGGATTCCTGCAT 60.025 45.455 3.95 0.00 35.94 3.96
323 325 2.423577 AGGACTTGCAACATAACCGAC 58.576 47.619 0.00 0.00 0.00 4.79
451 458 8.807948 ATATACCAGTGCAAAAGTAAGTCAAT 57.192 30.769 0.00 0.00 0.00 2.57
627 645 0.181824 ACCTTTTGCTGTACCCGTGT 59.818 50.000 0.00 0.00 0.00 4.49
1026 1063 1.958288 AGTAGTTGGCCTCATCCTGT 58.042 50.000 3.32 0.00 0.00 4.00
1027 1064 2.103263 GGTAGTAGTTGGCCTCATCCTG 59.897 54.545 3.32 0.00 0.00 3.86
1055 1092 0.886490 CTTCTCCTTGTTGCCGCTGT 60.886 55.000 0.00 0.00 0.00 4.40
1129 1166 2.264794 GTCGGGACTGTCGGCATT 59.735 61.111 1.07 0.00 31.94 3.56
1152 1189 3.003173 CGGAGGACAAGGGAGGCA 61.003 66.667 0.00 0.00 0.00 4.75
1494 1539 6.238676 CGTAGGAGAAAATCATCTCGTCCTTA 60.239 42.308 3.10 0.00 45.54 2.69
1509 1554 1.736645 GTGCAGCGCGTAGGAGAAA 60.737 57.895 8.43 0.00 0.00 2.52
1668 1713 2.423898 CCCGACCCATGCGTCTAGT 61.424 63.158 8.78 0.00 0.00 2.57
1705 1750 1.302285 CAACCTGGCAGGAGCAGAT 59.698 57.895 38.99 13.75 44.61 2.90
1844 1889 2.627737 GCCGGCGACTCCTCGATAT 61.628 63.158 12.58 0.00 43.06 1.63
1873 1918 2.284921 CTCCTCTGTGCCCCAGGA 60.285 66.667 0.00 0.00 41.83 3.86
1904 1949 3.053991 TCATCTTCTTCTCTCCGGTCTCT 60.054 47.826 0.00 0.00 0.00 3.10
1909 1954 2.547642 GCCATCATCTTCTTCTCTCCGG 60.548 54.545 0.00 0.00 0.00 5.14
1932 1977 2.573869 CCTCATGTGTCCTCGCGT 59.426 61.111 5.77 0.00 0.00 6.01
2283 2334 1.311747 GTCTCCCCTCCTACCTGCT 59.688 63.158 0.00 0.00 0.00 4.24
2290 2341 3.054582 GGTTATTTTTCGTCTCCCCTCCT 60.055 47.826 0.00 0.00 0.00 3.69
2563 2619 3.788227 TGGAGCAGTTGGTGAATAGTT 57.212 42.857 0.00 0.00 0.00 2.24
2599 2655 2.552315 TCTTCAAAAAGTGCGTCCCATC 59.448 45.455 0.00 0.00 33.95 3.51
2600 2656 2.293399 GTCTTCAAAAAGTGCGTCCCAT 59.707 45.455 0.00 0.00 33.95 4.00
2601 2657 1.673920 GTCTTCAAAAAGTGCGTCCCA 59.326 47.619 0.00 0.00 33.95 4.37
2602 2658 1.947456 AGTCTTCAAAAAGTGCGTCCC 59.053 47.619 0.00 0.00 33.95 4.46
2603 2659 3.808174 ACTAGTCTTCAAAAAGTGCGTCC 59.192 43.478 0.00 0.00 33.95 4.79
2604 2660 5.405331 AACTAGTCTTCAAAAAGTGCGTC 57.595 39.130 0.00 0.00 33.95 5.19
2605 2661 5.813080 AAACTAGTCTTCAAAAAGTGCGT 57.187 34.783 0.00 0.00 33.95 5.24
2606 2662 5.681543 GGAAAACTAGTCTTCAAAAAGTGCG 59.318 40.000 10.99 0.00 33.95 5.34
2607 2663 6.796426 AGGAAAACTAGTCTTCAAAAAGTGC 58.204 36.000 10.99 0.00 33.95 4.40
2686 2742 9.772973 GTCTACATGGTATGTATATGTCCAAAA 57.227 33.333 0.00 0.00 44.11 2.44
2687 2743 8.929487 TGTCTACATGGTATGTATATGTCCAAA 58.071 33.333 0.00 0.00 44.11 3.28
2688 2744 8.485578 TGTCTACATGGTATGTATATGTCCAA 57.514 34.615 0.00 0.00 44.11 3.53
2689 2745 8.664669 ATGTCTACATGGTATGTATATGTCCA 57.335 34.615 0.00 2.00 44.11 4.02
2690 2746 8.198109 GGATGTCTACATGGTATGTATATGTCC 58.802 40.741 0.00 5.45 44.11 4.02
2691 2747 8.749354 TGGATGTCTACATGGTATGTATATGTC 58.251 37.037 0.00 1.07 44.11 3.06
2692 2748 8.664669 TGGATGTCTACATGGTATGTATATGT 57.335 34.615 0.00 0.00 44.11 2.29
2693 2749 8.971073 TCTGGATGTCTACATGGTATGTATATG 58.029 37.037 0.00 0.00 44.11 1.78
2694 2750 8.972127 GTCTGGATGTCTACATGGTATGTATAT 58.028 37.037 0.00 0.00 44.11 0.86
2695 2751 7.396339 GGTCTGGATGTCTACATGGTATGTATA 59.604 40.741 0.00 0.00 44.11 1.47
2696 2752 6.211584 GGTCTGGATGTCTACATGGTATGTAT 59.788 42.308 0.00 0.00 44.11 2.29
2697 2753 5.538813 GGTCTGGATGTCTACATGGTATGTA 59.461 44.000 0.00 2.11 44.38 2.29
2698 2754 4.345257 GGTCTGGATGTCTACATGGTATGT 59.655 45.833 0.00 0.00 46.92 2.29
2699 2755 4.262635 GGGTCTGGATGTCTACATGGTATG 60.263 50.000 0.00 0.00 36.57 2.39
2700 2756 3.904339 GGGTCTGGATGTCTACATGGTAT 59.096 47.826 0.00 0.00 36.57 2.73
2701 2757 3.305720 GGGTCTGGATGTCTACATGGTA 58.694 50.000 0.00 0.00 36.57 3.25
2702 2758 2.119495 GGGTCTGGATGTCTACATGGT 58.881 52.381 0.00 0.00 36.57 3.55
2703 2759 1.069204 CGGGTCTGGATGTCTACATGG 59.931 57.143 0.00 0.00 36.57 3.66
2704 2760 2.031870 TCGGGTCTGGATGTCTACATG 58.968 52.381 0.00 0.00 36.57 3.21
2705 2761 2.454336 TCGGGTCTGGATGTCTACAT 57.546 50.000 0.00 0.00 39.70 2.29
2706 2762 2.454336 ATCGGGTCTGGATGTCTACA 57.546 50.000 0.00 0.00 0.00 2.74
2707 2763 3.827302 ACATATCGGGTCTGGATGTCTAC 59.173 47.826 0.00 0.00 0.00 2.59
2708 2764 4.114015 ACATATCGGGTCTGGATGTCTA 57.886 45.455 0.00 0.00 0.00 2.59
2709 2765 2.964209 ACATATCGGGTCTGGATGTCT 58.036 47.619 0.00 0.00 0.00 3.41
2710 2766 3.753294 AACATATCGGGTCTGGATGTC 57.247 47.619 0.00 0.00 30.55 3.06
2711 2767 4.407621 TGTAAACATATCGGGTCTGGATGT 59.592 41.667 0.00 0.00 32.18 3.06
2712 2768 4.956085 TGTAAACATATCGGGTCTGGATG 58.044 43.478 0.00 0.00 0.00 3.51
2713 2769 5.825593 ATGTAAACATATCGGGTCTGGAT 57.174 39.130 0.00 0.00 34.26 3.41
2714 2770 5.599242 TGTATGTAAACATATCGGGTCTGGA 59.401 40.000 6.12 0.00 40.53 3.86
2715 2771 5.849510 TGTATGTAAACATATCGGGTCTGG 58.150 41.667 6.12 0.00 40.53 3.86
2718 2774 9.525409 GGTATATGTATGTAAACATATCGGGTC 57.475 37.037 11.63 0.00 45.61 4.46
2719 2775 9.263446 AGGTATATGTATGTAAACATATCGGGT 57.737 33.333 11.63 0.00 45.61 5.28
2742 2798 8.383175 CCCAGATGTTGGTACATTATATTAGGT 58.617 37.037 0.00 0.00 44.90 3.08
2743 2799 8.383175 ACCCAGATGTTGGTACATTATATTAGG 58.617 37.037 0.00 0.00 44.90 2.69
2744 2800 9.793259 AACCCAGATGTTGGTACATTATATTAG 57.207 33.333 0.00 0.00 44.90 1.73
2746 2802 9.487442 AAAACCCAGATGTTGGTACATTATATT 57.513 29.630 0.00 0.00 44.90 1.28
2747 2803 9.487442 AAAAACCCAGATGTTGGTACATTATAT 57.513 29.630 0.00 0.00 44.90 0.86
2748 2804 8.887264 AAAAACCCAGATGTTGGTACATTATA 57.113 30.769 0.00 0.00 44.90 0.98
2749 2805 7.790782 AAAAACCCAGATGTTGGTACATTAT 57.209 32.000 0.00 0.00 44.90 1.28
2750 2806 8.707796 TTAAAAACCCAGATGTTGGTACATTA 57.292 30.769 0.00 0.00 44.90 1.90
2751 2807 7.604657 TTAAAAACCCAGATGTTGGTACATT 57.395 32.000 0.00 0.00 44.90 2.71
2753 2809 7.724506 TGTATTAAAAACCCAGATGTTGGTACA 59.275 33.333 0.00 0.00 46.25 2.90
2754 2810 8.024865 GTGTATTAAAAACCCAGATGTTGGTAC 58.975 37.037 0.00 0.00 46.25 3.34
2755 2811 7.094720 CGTGTATTAAAAACCCAGATGTTGGTA 60.095 37.037 0.00 0.00 46.25 3.25
2756 2812 6.294286 CGTGTATTAAAAACCCAGATGTTGGT 60.294 38.462 0.00 0.00 46.25 3.67
2758 2814 6.674066 ACGTGTATTAAAAACCCAGATGTTG 58.326 36.000 0.00 0.00 0.00 3.33
2759 2815 6.887626 ACGTGTATTAAAAACCCAGATGTT 57.112 33.333 0.00 0.00 0.00 2.71
2760 2816 8.455682 CAATACGTGTATTAAAAACCCAGATGT 58.544 33.333 0.00 0.00 34.27 3.06
2761 2817 7.431084 GCAATACGTGTATTAAAAACCCAGATG 59.569 37.037 0.00 0.00 34.27 2.90
2762 2818 7.415877 GGCAATACGTGTATTAAAAACCCAGAT 60.416 37.037 0.00 0.00 34.27 2.90
2763 2819 6.127952 GGCAATACGTGTATTAAAAACCCAGA 60.128 38.462 0.00 0.00 34.27 3.86
2764 2820 6.031471 GGCAATACGTGTATTAAAAACCCAG 58.969 40.000 0.00 0.00 34.27 4.45
2765 2821 5.711036 AGGCAATACGTGTATTAAAAACCCA 59.289 36.000 0.00 0.00 34.27 4.51
2766 2822 6.198650 AGGCAATACGTGTATTAAAAACCC 57.801 37.500 0.00 1.14 34.27 4.11
2767 2823 7.306953 TGAAGGCAATACGTGTATTAAAAACC 58.693 34.615 0.00 3.40 34.27 3.27
2768 2824 8.730970 TTGAAGGCAATACGTGTATTAAAAAC 57.269 30.769 0.00 0.16 34.27 2.43
2769 2825 8.784994 TCTTGAAGGCAATACGTGTATTAAAAA 58.215 29.630 0.00 0.00 34.27 1.94
2770 2826 8.231837 GTCTTGAAGGCAATACGTGTATTAAAA 58.768 33.333 0.00 0.00 34.27 1.52
2771 2827 7.388224 TGTCTTGAAGGCAATACGTGTATTAAA 59.612 33.333 0.00 0.00 34.78 1.52
2772 2828 6.874664 TGTCTTGAAGGCAATACGTGTATTAA 59.125 34.615 0.00 0.00 34.78 1.40
2773 2829 6.399743 TGTCTTGAAGGCAATACGTGTATTA 58.600 36.000 0.00 0.00 34.78 0.98
2774 2830 5.242434 TGTCTTGAAGGCAATACGTGTATT 58.758 37.500 0.00 0.00 34.78 1.89
2775 2831 4.827692 TGTCTTGAAGGCAATACGTGTAT 58.172 39.130 0.00 0.00 34.78 2.29
2776 2832 4.260139 TGTCTTGAAGGCAATACGTGTA 57.740 40.909 0.00 0.00 34.78 2.90
2777 2833 3.120321 TGTCTTGAAGGCAATACGTGT 57.880 42.857 0.00 0.00 34.78 4.49
2778 2834 4.034048 GGTATGTCTTGAAGGCAATACGTG 59.966 45.833 2.63 0.00 31.33 4.49
2779 2835 4.189231 GGTATGTCTTGAAGGCAATACGT 58.811 43.478 2.63 0.00 31.33 3.57
2780 2836 3.560068 GGGTATGTCTTGAAGGCAATACG 59.440 47.826 2.63 0.00 31.33 3.06
2781 2837 3.883489 GGGGTATGTCTTGAAGGCAATAC 59.117 47.826 2.63 7.14 31.33 1.89
2782 2838 3.433031 CGGGGTATGTCTTGAAGGCAATA 60.433 47.826 2.63 0.00 31.33 1.90
2783 2839 2.683742 CGGGGTATGTCTTGAAGGCAAT 60.684 50.000 2.63 0.00 31.33 3.56
2784 2840 1.339631 CGGGGTATGTCTTGAAGGCAA 60.340 52.381 2.63 0.00 31.33 4.52
2785 2841 0.251916 CGGGGTATGTCTTGAAGGCA 59.748 55.000 0.42 0.42 32.55 4.75
2786 2842 0.539986 TCGGGGTATGTCTTGAAGGC 59.460 55.000 0.00 0.00 0.00 4.35
2787 2843 3.343941 TTTCGGGGTATGTCTTGAAGG 57.656 47.619 0.00 0.00 0.00 3.46
2788 2844 5.897377 AATTTTCGGGGTATGTCTTGAAG 57.103 39.130 0.00 0.00 0.00 3.02
2789 2845 6.041069 ACAAAATTTTCGGGGTATGTCTTGAA 59.959 34.615 0.00 0.00 0.00 2.69
2790 2846 5.536916 ACAAAATTTTCGGGGTATGTCTTGA 59.463 36.000 0.00 0.00 0.00 3.02
2791 2847 5.778862 ACAAAATTTTCGGGGTATGTCTTG 58.221 37.500 0.00 0.00 0.00 3.02
2792 2848 6.717997 ACTACAAAATTTTCGGGGTATGTCTT 59.282 34.615 0.00 0.00 0.00 3.01
2793 2849 6.243148 ACTACAAAATTTTCGGGGTATGTCT 58.757 36.000 0.00 0.00 0.00 3.41
2794 2850 6.505044 ACTACAAAATTTTCGGGGTATGTC 57.495 37.500 0.00 0.00 0.00 3.06
2795 2851 6.904463 AACTACAAAATTTTCGGGGTATGT 57.096 33.333 0.00 0.00 0.00 2.29
2796 2852 9.349145 CTAAAACTACAAAATTTTCGGGGTATG 57.651 33.333 0.00 0.00 30.80 2.39
2797 2853 9.081204 ACTAAAACTACAAAATTTTCGGGGTAT 57.919 29.630 0.00 0.00 30.80 2.73
2798 2854 8.351461 CACTAAAACTACAAAATTTTCGGGGTA 58.649 33.333 0.00 0.00 30.80 3.69
2799 2855 7.204604 CACTAAAACTACAAAATTTTCGGGGT 58.795 34.615 0.00 0.00 30.80 4.95
2800 2856 6.643360 CCACTAAAACTACAAAATTTTCGGGG 59.357 38.462 0.00 0.00 30.45 5.73
2801 2857 7.204604 ACCACTAAAACTACAAAATTTTCGGG 58.795 34.615 0.00 0.00 30.80 5.14
2802 2858 9.733219 TTACCACTAAAACTACAAAATTTTCGG 57.267 29.630 0.00 0.00 30.80 4.30


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

AutoCloner maintained by Alex Coulton.