Multiple sequence alignment - TraesCS7B01G436000

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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 TraesCS7B01G436000 chr7B 100.000 2850 0 0 1 2850 702476402 702473553 0.000000e+00 5264
1 TraesCS7B01G436000 chr7B 98.862 791 9 0 1 791 34198722 34197932 0.000000e+00 1411
2 TraesCS7B01G436000 chr7B 71.209 1042 261 31 822 1843 643191846 643190824 2.860000e-55 226
3 TraesCS7B01G436000 chr7D 92.059 1977 133 13 788 2751 612965162 612963197 0.000000e+00 2760
4 TraesCS7B01G436000 chr7A 91.542 1667 121 12 794 2447 704337299 704335640 0.000000e+00 2279
5 TraesCS7B01G436000 chr7A 98.989 791 8 0 1 791 465649760 465648970 0.000000e+00 1417
6 TraesCS7B01G436000 chr7A 91.270 252 18 3 2500 2749 704335641 704335392 9.780000e-90 340
7 TraesCS7B01G436000 chr3A 99.241 791 6 0 1 791 193751182 193751972 0.000000e+00 1428
8 TraesCS7B01G436000 chr3A 99.115 791 7 0 1 791 189184081 189184871 0.000000e+00 1423
9 TraesCS7B01G436000 chr2A 99.115 791 6 1 1 791 743711872 743711083 0.000000e+00 1421
10 TraesCS7B01G436000 chr2A 98.989 791 8 0 1 791 137219469 137220259 0.000000e+00 1417
11 TraesCS7B01G436000 chr5B 98.989 791 8 0 1 791 37936440 37937230 0.000000e+00 1417
12 TraesCS7B01G436000 chr1A 98.987 790 8 0 1 790 7451141 7451930 0.000000e+00 1415
13 TraesCS7B01G436000 chr4B 98.862 791 9 0 1 791 456257832 456258622 0.000000e+00 1411


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 TraesCS7B01G436000 chr7B 702473553 702476402 2849 True 5264.0 5264 100.000 1 2850 1 chr7B.!!$R3 2849
1 TraesCS7B01G436000 chr7B 34197932 34198722 790 True 1411.0 1411 98.862 1 791 1 chr7B.!!$R1 790
2 TraesCS7B01G436000 chr7B 643190824 643191846 1022 True 226.0 226 71.209 822 1843 1 chr7B.!!$R2 1021
3 TraesCS7B01G436000 chr7D 612963197 612965162 1965 True 2760.0 2760 92.059 788 2751 1 chr7D.!!$R1 1963
4 TraesCS7B01G436000 chr7A 465648970 465649760 790 True 1417.0 1417 98.989 1 791 1 chr7A.!!$R1 790
5 TraesCS7B01G436000 chr7A 704335392 704337299 1907 True 1309.5 2279 91.406 794 2749 2 chr7A.!!$R2 1955
6 TraesCS7B01G436000 chr3A 193751182 193751972 790 False 1428.0 1428 99.241 1 791 1 chr3A.!!$F2 790
7 TraesCS7B01G436000 chr3A 189184081 189184871 790 False 1423.0 1423 99.115 1 791 1 chr3A.!!$F1 790
8 TraesCS7B01G436000 chr2A 743711083 743711872 789 True 1421.0 1421 99.115 1 791 1 chr2A.!!$R1 790
9 TraesCS7B01G436000 chr2A 137219469 137220259 790 False 1417.0 1417 98.989 1 791 1 chr2A.!!$F1 790
10 TraesCS7B01G436000 chr5B 37936440 37937230 790 False 1417.0 1417 98.989 1 791 1 chr5B.!!$F1 790
11 TraesCS7B01G436000 chr1A 7451141 7451930 789 False 1415.0 1415 98.987 1 790 1 chr1A.!!$F1 789
12 TraesCS7B01G436000 chr4B 456257832 456258622 790 False 1411.0 1411 98.862 1 791 1 chr4B.!!$F1 790

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
780 781 0.452987 GCTGATGATTGGCTTCGCAA 59.547 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2294 0.245266 GTTGCCAACCGGTAAATGGG 59.755 55.0 22.39 13.68 38.76 4.0 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
77 78 1.207791 CCCTATGGTCCACAAGCTCT 58.792 55.000 0.00 0.00 0.00 4.09
115 116 2.947652 CCGGATGATCATGTTGAGCTTT 59.052 45.455 14.30 0.00 33.24 3.51
780 781 0.452987 GCTGATGATTGGCTTCGCAA 59.547 50.000 0.00 0.00 0.00 4.85
792 793 3.636764 TGGCTTCGCAATATCTCTCACTA 59.363 43.478 0.00 0.00 0.00 2.74
892 893 1.000274 GCGGCTTCTTGTTTGACCAAT 60.000 47.619 0.00 0.00 0.00 3.16
1038 1045 0.820871 AGGTCAGCATCTCCGTCTTC 59.179 55.000 0.00 0.00 0.00 2.87
1308 1317 1.819632 GCGGGGCGATCAACTTCAT 60.820 57.895 0.00 0.00 0.00 2.57
1351 1360 1.257750 TTGCTGCCTTCTCCGCTCTA 61.258 55.000 0.00 0.00 0.00 2.43
1393 1402 2.349590 GGGCATGTTTTTGGAGCAATC 58.650 47.619 0.00 0.00 0.00 2.67
1399 1408 3.701241 TGTTTTTGGAGCAATCGTGTTC 58.299 40.909 0.00 0.00 34.41 3.18
1420 1429 3.774766 TCCTTCTCCTTGGAATGAATCGA 59.225 43.478 0.00 0.00 0.00 3.59
1451 1460 1.079127 GTGCGGAGGCTTAAGCTCA 60.079 57.895 25.88 13.38 41.70 4.26
1496 1505 6.701145 TTCTCAGCTCTGATTACGTATCTT 57.299 37.500 0.00 0.00 39.13 2.40
1523 1535 9.856488 AGTAATGTACAGTGTGTAGTAATTCAG 57.144 33.333 5.98 0.00 32.84 3.02
1550 1563 8.980143 TTTGTTTTTGTTTTAGGTGAGAGAAG 57.020 30.769 0.00 0.00 0.00 2.85
1582 1595 0.700564 ATTGTCCATGTCAGCCCACT 59.299 50.000 0.00 0.00 0.00 4.00
1693 1706 7.466805 TCTTAAAATTGATGCTCAGATGTTCG 58.533 34.615 0.00 0.00 0.00 3.95
1769 1782 8.196771 GGAAAGATGGATGCACAATAATAAACA 58.803 33.333 0.00 0.00 0.00 2.83
1780 1793 9.755804 TGCACAATAATAAACAACATCTTCAAA 57.244 25.926 0.00 0.00 0.00 2.69
1805 1818 3.769739 ATCCTTCCGTGCAATGCTATA 57.230 42.857 6.82 0.00 0.00 1.31
1835 1848 8.141298 TCTTTCCTATGGTAAGTGTATGTTCA 57.859 34.615 3.56 0.00 32.93 3.18
1867 1880 8.161699 TCTGTTAATCCTTGTAGGTTTTGTTC 57.838 34.615 0.00 0.00 36.53 3.18
1907 1921 7.978975 AGTTAAGTTGTGCTTATGCTTTTCAAA 59.021 29.630 1.96 0.00 39.23 2.69
1910 1924 7.181143 AGTTGTGCTTATGCTTTTCAAATTG 57.819 32.000 1.96 0.00 40.48 2.32
1916 1930 6.985645 TGCTTATGCTTTTCAAATTGTGAACT 59.014 30.769 1.96 0.00 42.05 3.01
1923 1937 8.031864 TGCTTTTCAAATTGTGAACTTAGACAA 58.968 29.630 0.00 0.00 46.09 3.18
1948 1962 1.225855 TTACAAAGTCTGGCTGCACG 58.774 50.000 0.50 0.00 0.00 5.34
1961 1975 0.740868 CTGCACGTGTGTATCCCAGG 60.741 60.000 18.38 0.00 0.00 4.45
1962 1976 1.295423 GCACGTGTGTATCCCAGGT 59.705 57.895 18.38 0.00 0.00 4.00
1974 1988 5.934625 GTGTATCCCAGGTATTAGCTCAATG 59.065 44.000 0.00 0.00 0.00 2.82
2063 2077 4.864704 TTTGTTTGATCCCTTTAGCACC 57.135 40.909 0.00 0.00 0.00 5.01
2096 2110 5.252547 ACCATGGTTGCTCTTTTTGTTTTT 58.747 33.333 13.00 0.00 0.00 1.94
2130 2144 3.565482 TGTTGCTCATGACCTTCTGTTTC 59.435 43.478 0.00 0.00 0.00 2.78
2134 2148 2.414481 CTCATGACCTTCTGTTTCGCTG 59.586 50.000 0.00 0.00 0.00 5.18
2175 2189 5.312895 GCCAAAATGGGTTTCTAAATTGGT 58.687 37.500 0.00 0.00 38.19 3.67
2177 2191 6.937465 GCCAAAATGGGTTTCTAAATTGGTTA 59.063 34.615 0.00 0.00 38.19 2.85
2242 2256 9.122779 CGGGTTTGGTATAAACTATAATTTCCA 57.877 33.333 0.00 0.00 0.00 3.53
2290 2304 5.576447 AGTTTGCTATTTCCCATTTACCG 57.424 39.130 0.00 0.00 0.00 4.02
2324 2344 7.275779 ACATTCTTTGCTGACGTAATACACTAG 59.724 37.037 0.00 0.00 0.00 2.57
2326 2346 7.096884 TCTTTGCTGACGTAATACACTAGAT 57.903 36.000 0.00 0.00 0.00 1.98
2333 2353 8.269424 GCTGACGTAATACACTAGATTGAATTG 58.731 37.037 0.00 0.00 0.00 2.32
2352 2372 3.281727 TGTTGACCAGAGCTTGTTTCT 57.718 42.857 0.00 0.00 0.00 2.52
2376 2396 0.693049 GCCTCTTCCTCAGGGTTCAA 59.307 55.000 0.00 0.00 0.00 2.69
2398 2418 6.324512 TCAAGCATGGCTACCAAAATTATCAT 59.675 34.615 0.00 0.00 38.25 2.45
2416 2436 9.809395 AATTATCATTGACATGATTCTCATCCT 57.191 29.630 0.00 0.00 46.45 3.24
2418 2438 9.636789 TTATCATTGACATGATTCTCATCCTTT 57.363 29.630 0.00 0.00 46.45 3.11
2420 2440 7.114095 TCATTGACATGATTCTCATCCTTTCA 58.886 34.615 0.00 0.00 34.28 2.69
2444 2465 3.726607 TGCAAATTCTTTGGTTCGCATT 58.273 36.364 2.15 0.00 40.94 3.56
2450 2471 1.410517 TCTTTGGTTCGCATTGGCAAA 59.589 42.857 3.01 0.00 41.24 3.68
2466 2487 4.618635 TGGCAAAATCATCCTTTCCCATA 58.381 39.130 0.00 0.00 0.00 2.74
2467 2488 5.218179 TGGCAAAATCATCCTTTCCCATAT 58.782 37.500 0.00 0.00 0.00 1.78
2470 2491 5.993441 GCAAAATCATCCTTTCCCATATTGG 59.007 40.000 0.00 0.00 37.25 3.16
2490 2511 3.126171 TGGGAAACTCGATACATTTTGCG 59.874 43.478 0.00 0.00 0.00 4.85
2589 2612 9.634163 CCAAAATCATGGATGTGATATATTGTG 57.366 33.333 0.00 0.00 43.54 3.33
2610 2633 0.321671 TCGGCCAACCTTTCTCTCTG 59.678 55.000 2.24 0.00 0.00 3.35
2643 2666 4.406972 TCCTACTGATTCTGCTAAGCACAT 59.593 41.667 0.00 0.00 33.79 3.21
2659 2682 4.517285 AGCACATGGTTCTAAATGTCGAT 58.483 39.130 0.00 0.00 34.81 3.59
2664 2687 5.815740 ACATGGTTCTAAATGTCGATACCAC 59.184 40.000 0.00 0.00 37.05 4.16
2700 2723 6.240894 ACAAAACTGGATAAATCTGCAGAGA 58.759 36.000 22.96 10.30 0.00 3.10
2751 2774 9.999009 CGACAGTTGAATATAACTAAGAGTACA 57.001 33.333 0.00 0.00 38.78 2.90
2760 2783 9.953565 AATATAACTAAGAGTACAAACAAGGCA 57.046 29.630 0.00 0.00 0.00 4.75
2761 2784 9.953565 ATATAACTAAGAGTACAAACAAGGCAA 57.046 29.630 0.00 0.00 0.00 4.52
2762 2785 8.685838 ATAACTAAGAGTACAAACAAGGCAAA 57.314 30.769 0.00 0.00 0.00 3.68
2763 2786 6.373186 ACTAAGAGTACAAACAAGGCAAAC 57.627 37.500 0.00 0.00 0.00 2.93
2764 2787 5.883673 ACTAAGAGTACAAACAAGGCAAACA 59.116 36.000 0.00 0.00 0.00 2.83
2765 2788 5.652994 AAGAGTACAAACAAGGCAAACAA 57.347 34.783 0.00 0.00 0.00 2.83
2766 2789 5.248870 AGAGTACAAACAAGGCAAACAAG 57.751 39.130 0.00 0.00 0.00 3.16
2767 2790 4.097892 AGAGTACAAACAAGGCAAACAAGG 59.902 41.667 0.00 0.00 0.00 3.61
2768 2791 2.022764 ACAAACAAGGCAAACAAGGC 57.977 45.000 0.00 0.00 0.00 4.35
2769 2792 1.277557 ACAAACAAGGCAAACAAGGCA 59.722 42.857 0.00 0.00 36.37 4.75
2770 2793 2.289945 ACAAACAAGGCAAACAAGGCAA 60.290 40.909 0.00 0.00 36.37 4.52
2771 2794 2.746362 CAAACAAGGCAAACAAGGCAAA 59.254 40.909 0.00 0.00 36.37 3.68
2772 2795 3.280197 AACAAGGCAAACAAGGCAAAT 57.720 38.095 0.00 0.00 36.37 2.32
2773 2796 3.280197 ACAAGGCAAACAAGGCAAATT 57.720 38.095 0.00 0.00 36.37 1.82
2774 2797 4.414337 ACAAGGCAAACAAGGCAAATTA 57.586 36.364 0.00 0.00 36.37 1.40
2775 2798 4.126437 ACAAGGCAAACAAGGCAAATTAC 58.874 39.130 0.00 0.00 36.37 1.89
2776 2799 4.141733 ACAAGGCAAACAAGGCAAATTACT 60.142 37.500 0.00 0.00 36.37 2.24
2777 2800 3.993920 AGGCAAACAAGGCAAATTACTG 58.006 40.909 0.00 0.00 36.37 2.74
2778 2801 3.640967 AGGCAAACAAGGCAAATTACTGA 59.359 39.130 0.00 0.00 36.37 3.41
2779 2802 4.100808 AGGCAAACAAGGCAAATTACTGAA 59.899 37.500 0.00 0.00 36.37 3.02
2780 2803 4.813697 GGCAAACAAGGCAAATTACTGAAA 59.186 37.500 0.00 0.00 0.00 2.69
2781 2804 5.469760 GGCAAACAAGGCAAATTACTGAAAT 59.530 36.000 0.00 0.00 0.00 2.17
2782 2805 6.347644 GGCAAACAAGGCAAATTACTGAAATC 60.348 38.462 0.00 0.00 0.00 2.17
2783 2806 6.347644 GCAAACAAGGCAAATTACTGAAATCC 60.348 38.462 0.00 0.00 0.00 3.01
2784 2807 5.405935 ACAAGGCAAATTACTGAAATCCC 57.594 39.130 0.00 0.00 0.00 3.85
2785 2808 4.082245 ACAAGGCAAATTACTGAAATCCCG 60.082 41.667 0.00 0.00 0.00 5.14
2786 2809 3.697166 AGGCAAATTACTGAAATCCCGT 58.303 40.909 0.00 0.00 0.00 5.28
2787 2810 4.086457 AGGCAAATTACTGAAATCCCGTT 58.914 39.130 0.00 0.00 0.00 4.44
2788 2811 4.082245 AGGCAAATTACTGAAATCCCGTTG 60.082 41.667 0.00 0.00 0.00 4.10
2789 2812 4.173256 GCAAATTACTGAAATCCCGTTGG 58.827 43.478 0.00 0.00 0.00 3.77
2790 2813 4.173256 CAAATTACTGAAATCCCGTTGGC 58.827 43.478 0.00 0.00 0.00 4.52
2791 2814 1.828979 TTACTGAAATCCCGTTGGCC 58.171 50.000 0.00 0.00 0.00 5.36
2792 2815 0.391927 TACTGAAATCCCGTTGGCCG 60.392 55.000 0.00 0.00 0.00 6.13
2801 2824 4.973055 CGTTGGCCGGACGTGGAA 62.973 66.667 19.85 0.00 35.88 3.53
2802 2825 2.592287 GTTGGCCGGACGTGGAAA 60.592 61.111 5.05 0.00 0.00 3.13
2803 2826 1.969589 GTTGGCCGGACGTGGAAAT 60.970 57.895 5.05 0.00 0.00 2.17
2804 2827 1.673009 TTGGCCGGACGTGGAAATC 60.673 57.895 5.05 0.00 0.00 2.17
2805 2828 2.822701 GGCCGGACGTGGAAATCC 60.823 66.667 5.05 0.00 0.00 3.01
2806 2829 2.822701 GCCGGACGTGGAAATCCC 60.823 66.667 5.05 0.00 34.29 3.85
2807 2830 2.124860 CCGGACGTGGAAATCCCC 60.125 66.667 0.00 0.00 34.29 4.81
2808 2831 2.666207 CGGACGTGGAAATCCCCA 59.334 61.111 0.00 0.00 34.29 4.96
2809 2832 1.003112 CGGACGTGGAAATCCCCAA 60.003 57.895 0.00 0.00 38.06 4.12
2810 2833 1.024579 CGGACGTGGAAATCCCCAAG 61.025 60.000 0.00 0.00 40.74 3.61
2811 2834 1.313091 GGACGTGGAAATCCCCAAGC 61.313 60.000 0.00 0.00 38.93 4.01
2812 2835 0.322546 GACGTGGAAATCCCCAAGCT 60.323 55.000 0.00 0.00 38.93 3.74
2813 2836 0.112412 ACGTGGAAATCCCCAAGCTT 59.888 50.000 0.00 0.00 38.93 3.74
2814 2837 1.353022 ACGTGGAAATCCCCAAGCTTA 59.647 47.619 0.00 0.00 38.93 3.09
2815 2838 2.224917 ACGTGGAAATCCCCAAGCTTAA 60.225 45.455 0.00 0.00 38.93 1.85
2816 2839 2.823154 CGTGGAAATCCCCAAGCTTAAA 59.177 45.455 0.00 0.00 38.06 1.52
2817 2840 3.119495 CGTGGAAATCCCCAAGCTTAAAG 60.119 47.826 0.00 0.00 38.06 1.85
2818 2841 3.195610 GTGGAAATCCCCAAGCTTAAAGG 59.804 47.826 0.00 0.00 38.06 3.11
2819 2842 3.181412 TGGAAATCCCCAAGCTTAAAGGT 60.181 43.478 0.00 0.00 32.31 3.50
2820 2843 3.195610 GGAAATCCCCAAGCTTAAAGGTG 59.804 47.826 0.00 0.00 0.00 4.00
2821 2844 1.852633 ATCCCCAAGCTTAAAGGTGC 58.147 50.000 0.00 0.00 0.00 5.01
2822 2845 0.480690 TCCCCAAGCTTAAAGGTGCA 59.519 50.000 0.00 0.00 0.00 4.57
2823 2846 0.890683 CCCCAAGCTTAAAGGTGCAG 59.109 55.000 0.00 0.00 0.00 4.41
2824 2847 0.244721 CCCAAGCTTAAAGGTGCAGC 59.755 55.000 8.11 8.11 0.00 5.25
2825 2848 0.109597 CCAAGCTTAAAGGTGCAGCG 60.110 55.000 10.78 0.00 38.66 5.18
2826 2849 0.730494 CAAGCTTAAAGGTGCAGCGC 60.730 55.000 10.78 0.00 38.66 5.92
2827 2850 1.172180 AAGCTTAAAGGTGCAGCGCA 61.172 50.000 11.47 0.00 38.66 6.09
2828 2851 1.172180 AGCTTAAAGGTGCAGCGCAA 61.172 50.000 11.47 5.07 41.47 4.85
2829 2852 0.318614 GCTTAAAGGTGCAGCGCAAA 60.319 50.000 11.47 5.07 41.47 3.68
2830 2853 1.408422 CTTAAAGGTGCAGCGCAAAC 58.592 50.000 11.47 4.12 41.47 2.93
2831 2854 0.741326 TTAAAGGTGCAGCGCAAACA 59.259 45.000 11.47 0.49 41.47 2.83
2832 2855 0.741326 TAAAGGTGCAGCGCAAACAA 59.259 45.000 11.47 0.00 41.47 2.83
2833 2856 0.528249 AAAGGTGCAGCGCAAACAAG 60.528 50.000 11.47 0.00 41.47 3.16
2834 2857 2.354074 AAGGTGCAGCGCAAACAAGG 62.354 55.000 11.47 0.00 41.47 3.61
2835 2858 3.032033 GTGCAGCGCAAACAAGGC 61.032 61.111 11.47 1.62 41.47 4.35
2836 2859 3.525545 TGCAGCGCAAACAAGGCA 61.526 55.556 11.47 4.52 34.76 4.75
2837 2860 2.279385 GCAGCGCAAACAAGGCAA 60.279 55.556 11.47 0.00 0.00 4.52
2838 2861 1.882167 GCAGCGCAAACAAGGCAAA 60.882 52.632 11.47 0.00 0.00 3.68
2839 2862 1.223417 GCAGCGCAAACAAGGCAAAT 61.223 50.000 11.47 0.00 0.00 2.32
2840 2863 1.219646 CAGCGCAAACAAGGCAAATT 58.780 45.000 11.47 0.00 0.00 1.82
2841 2864 2.402305 CAGCGCAAACAAGGCAAATTA 58.598 42.857 11.47 0.00 0.00 1.40
2842 2865 2.155539 CAGCGCAAACAAGGCAAATTAC 59.844 45.455 11.47 0.00 0.00 1.89
2843 2866 2.035832 AGCGCAAACAAGGCAAATTACT 59.964 40.909 11.47 0.00 0.00 2.24
2844 2867 2.155539 GCGCAAACAAGGCAAATTACTG 59.844 45.455 0.30 0.00 0.00 2.74
2845 2868 3.637432 CGCAAACAAGGCAAATTACTGA 58.363 40.909 0.00 0.00 0.00 3.41
2846 2869 4.047822 CGCAAACAAGGCAAATTACTGAA 58.952 39.130 0.00 0.00 0.00 3.02
2847 2870 4.505922 CGCAAACAAGGCAAATTACTGAAA 59.494 37.500 0.00 0.00 0.00 2.69
2848 2871 5.556194 CGCAAACAAGGCAAATTACTGAAAC 60.556 40.000 0.00 0.00 0.00 2.78
2849 2872 5.277297 GCAAACAAGGCAAATTACTGAAACC 60.277 40.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 0.456142 CGGAAACAGACGATCTCGCA 60.456 55.000 0.00 0.00 44.43 5.10
115 116 2.111384 GAAGTCACCTCCATAGCCTGA 58.889 52.381 0.00 0.00 0.00 3.86
780 781 5.007034 CACGACAGGGATAGTGAGAGATAT 58.993 45.833 0.00 0.00 36.79 1.63
792 793 3.740128 GATGCCGCACGACAGGGAT 62.740 63.158 0.00 0.00 41.39 3.85
978 982 2.359850 AATTGCTTGAGCGCGGGA 60.360 55.556 8.83 0.00 45.83 5.14
1308 1317 2.609427 ATGCTTCGCTATCTCTTGCA 57.391 45.000 0.00 0.00 0.00 4.08
1335 1344 0.667993 CTCTAGAGCGGAGAAGGCAG 59.332 60.000 6.86 0.00 33.03 4.85
1351 1360 3.993081 CGACTGTTTTGAGATGAAGCTCT 59.007 43.478 0.00 0.00 35.91 4.09
1393 1402 2.543777 TTCCAAGGAGAAGGAACACG 57.456 50.000 0.00 0.00 38.91 4.49
1399 1408 4.142609 TCGATTCATTCCAAGGAGAAGG 57.857 45.455 0.00 0.00 0.00 3.46
1420 1429 2.393768 CCGCACAGCTGCTCGAATT 61.394 57.895 24.17 0.00 41.77 2.17
1427 1436 3.958147 TAAGCCTCCGCACAGCTGC 62.958 63.158 15.27 0.00 40.38 5.25
1451 1460 8.107196 AGAATTACCTTTGTTCTCCATAGGAT 57.893 34.615 5.93 0.00 43.00 3.24
1523 1535 9.581099 TTCTCTCACCTAAAACAAAAACAAATC 57.419 29.630 0.00 0.00 0.00 2.17
1535 1547 3.846588 AGGCATCCTTCTCTCACCTAAAA 59.153 43.478 0.00 0.00 0.00 1.52
1550 1563 2.733956 TGGACAATTTGGTAGGCATCC 58.266 47.619 0.78 0.00 0.00 3.51
1835 1848 2.289694 ACAAGGATTAACAGAGCACGCT 60.290 45.455 0.00 0.00 0.00 5.07
1867 1880 5.221244 ACAACTTAACTTGGCTTTAGGCTTG 60.221 40.000 0.00 1.42 41.69 4.01
1907 1921 6.655078 AATTGGCTTGTCTAAGTTCACAAT 57.345 33.333 1.75 0.00 36.27 2.71
1910 1924 6.554334 TGTAATTGGCTTGTCTAAGTTCAC 57.446 37.500 0.00 0.00 36.27 3.18
1916 1930 6.206634 CCAGACTTTGTAATTGGCTTGTCTAA 59.793 38.462 0.00 0.00 33.04 2.10
1948 1962 4.344102 TGAGCTAATACCTGGGATACACAC 59.656 45.833 0.00 0.00 39.74 3.82
1962 1976 9.645059 GCAGTAAGATATCACATTGAGCTAATA 57.355 33.333 5.32 0.00 0.00 0.98
2003 2017 9.392259 CCGTACTAATATAGATGTGAGGATGTA 57.608 37.037 0.00 0.00 0.00 2.29
2034 2048 6.418057 AAAGGGATCAAACAAATTACTGCA 57.582 33.333 0.00 0.00 0.00 4.41
2063 2077 0.748005 CAACCATGGTAAGGGAGCCG 60.748 60.000 20.12 0.00 0.00 5.52
2117 2131 1.581934 CACAGCGAAACAGAAGGTCA 58.418 50.000 0.00 0.00 0.00 4.02
2119 2133 0.468226 TCCACAGCGAAACAGAAGGT 59.532 50.000 0.00 0.00 0.00 3.50
2130 2144 2.216046 ACTGAATGCATATCCACAGCG 58.784 47.619 0.00 0.00 0.00 5.18
2134 2148 3.743521 TGGCTACTGAATGCATATCCAC 58.256 45.455 0.00 0.00 0.00 4.02
2173 2187 7.873505 AGATGAGACAACTAGTTCACTTTAACC 59.126 37.037 4.77 0.00 0.00 2.85
2175 2189 8.638873 TCAGATGAGACAACTAGTTCACTTTAA 58.361 33.333 4.77 0.00 0.00 1.52
2177 2191 7.055667 TCAGATGAGACAACTAGTTCACTTT 57.944 36.000 4.77 0.84 0.00 2.66
2181 2195 8.908786 AAAATTCAGATGAGACAACTAGTTCA 57.091 30.769 4.77 0.77 0.00 3.18
2264 2278 8.842280 CGGTAAATGGGAAATAGCAAACTAATA 58.158 33.333 0.00 0.00 30.45 0.98
2280 2294 0.245266 GTTGCCAACCGGTAAATGGG 59.755 55.000 22.39 13.68 38.76 4.00
2283 2297 3.161866 AGAATGTTGCCAACCGGTAAAT 58.838 40.909 8.00 0.00 38.76 1.40
2287 2301 1.068434 CAAAGAATGTTGCCAACCGGT 59.932 47.619 0.00 0.00 33.28 5.28
2301 2315 6.916440 TCTAGTGTATTACGTCAGCAAAGAA 58.084 36.000 0.00 0.00 0.00 2.52
2324 2344 5.159209 CAAGCTCTGGTCAACAATTCAATC 58.841 41.667 0.00 0.00 0.00 2.67
2326 2346 3.953612 ACAAGCTCTGGTCAACAATTCAA 59.046 39.130 0.00 0.00 0.00 2.69
2333 2353 5.948992 AATAGAAACAAGCTCTGGTCAAC 57.051 39.130 0.00 0.00 0.00 3.18
2352 2372 2.562296 ACCCTGAGGAAGAGGCAAATA 58.438 47.619 0.00 0.00 36.73 1.40
2376 2396 6.324512 TCAATGATAATTTTGGTAGCCATGCT 59.675 34.615 0.00 0.00 43.41 3.79
2466 2487 5.650543 GCAAAATGTATCGAGTTTCCCAAT 58.349 37.500 0.00 0.00 0.00 3.16
2467 2488 4.378978 CGCAAAATGTATCGAGTTTCCCAA 60.379 41.667 0.00 0.00 0.00 4.12
2470 2491 4.336532 ACGCAAAATGTATCGAGTTTCC 57.663 40.909 0.00 0.00 0.00 3.13
2478 2499 6.092259 ACTCCTGAAACTACGCAAAATGTATC 59.908 38.462 0.00 0.00 0.00 2.24
2490 2511 7.084486 CCAAGCAAAATTACTCCTGAAACTAC 58.916 38.462 0.00 0.00 0.00 2.73
2535 2556 4.976116 GCAACCACTCAACAATTCACTTAC 59.024 41.667 0.00 0.00 0.00 2.34
2589 2612 1.157585 GAGAGAAAGGTTGGCCGAAC 58.842 55.000 0.00 0.00 40.50 3.95
2592 2615 0.674895 CCAGAGAGAAAGGTTGGCCG 60.675 60.000 0.00 0.00 40.50 6.13
2610 2633 3.133721 AGAATCAGTAGGAGCACATGACC 59.866 47.826 0.00 0.00 0.00 4.02
2643 2666 4.082081 ACGTGGTATCGACATTTAGAACCA 60.082 41.667 0.00 0.00 33.30 3.67
2684 2707 6.541641 ACTGAACATTCTCTGCAGATTTATCC 59.458 38.462 18.63 5.10 0.00 2.59
2700 2723 7.307989 CGAAGTGATGGAAGTAAACTGAACATT 60.308 37.037 0.00 0.00 0.00 2.71
2751 2774 2.777832 TTGCCTTGTTTGCCTTGTTT 57.222 40.000 0.00 0.00 0.00 2.83
2752 2775 2.777832 TTTGCCTTGTTTGCCTTGTT 57.222 40.000 0.00 0.00 0.00 2.83
2753 2776 3.280197 AATTTGCCTTGTTTGCCTTGT 57.720 38.095 0.00 0.00 0.00 3.16
2754 2777 4.211794 CAGTAATTTGCCTTGTTTGCCTTG 59.788 41.667 0.00 0.00 0.00 3.61
2755 2778 4.100808 TCAGTAATTTGCCTTGTTTGCCTT 59.899 37.500 0.00 0.00 0.00 4.35
2756 2779 3.640967 TCAGTAATTTGCCTTGTTTGCCT 59.359 39.130 0.00 0.00 0.00 4.75
2757 2780 3.988819 TCAGTAATTTGCCTTGTTTGCC 58.011 40.909 0.00 0.00 0.00 4.52
2758 2781 5.982465 TTTCAGTAATTTGCCTTGTTTGC 57.018 34.783 0.00 0.00 0.00 3.68
2759 2782 6.147656 GGGATTTCAGTAATTTGCCTTGTTTG 59.852 38.462 0.00 0.00 0.00 2.93
2760 2783 6.230472 GGGATTTCAGTAATTTGCCTTGTTT 58.770 36.000 0.00 0.00 0.00 2.83
2761 2784 5.566627 CGGGATTTCAGTAATTTGCCTTGTT 60.567 40.000 0.00 0.00 0.00 2.83
2762 2785 4.082245 CGGGATTTCAGTAATTTGCCTTGT 60.082 41.667 0.00 0.00 0.00 3.16
2763 2786 4.082245 ACGGGATTTCAGTAATTTGCCTTG 60.082 41.667 0.00 0.00 0.00 3.61
2764 2787 4.086457 ACGGGATTTCAGTAATTTGCCTT 58.914 39.130 0.00 0.00 0.00 4.35
2765 2788 3.697166 ACGGGATTTCAGTAATTTGCCT 58.303 40.909 0.00 0.00 0.00 4.75
2766 2789 4.173256 CAACGGGATTTCAGTAATTTGCC 58.827 43.478 0.00 0.00 0.00 4.52
2767 2790 4.173256 CCAACGGGATTTCAGTAATTTGC 58.827 43.478 0.00 0.00 35.59 3.68
2768 2791 4.173256 GCCAACGGGATTTCAGTAATTTG 58.827 43.478 0.00 0.00 35.59 2.32
2769 2792 3.194755 GGCCAACGGGATTTCAGTAATTT 59.805 43.478 0.00 0.00 35.59 1.82
2770 2793 2.758423 GGCCAACGGGATTTCAGTAATT 59.242 45.455 0.00 0.00 35.59 1.40
2771 2794 2.375146 GGCCAACGGGATTTCAGTAAT 58.625 47.619 0.00 0.00 35.59 1.89
2772 2795 1.828979 GGCCAACGGGATTTCAGTAA 58.171 50.000 0.00 0.00 35.59 2.24
2773 2796 0.391927 CGGCCAACGGGATTTCAGTA 60.392 55.000 2.24 0.00 39.42 2.74
2774 2797 1.674322 CGGCCAACGGGATTTCAGT 60.674 57.895 2.24 0.00 39.42 3.41
2775 2798 3.187058 CGGCCAACGGGATTTCAG 58.813 61.111 2.24 0.00 39.42 3.02
2784 2807 4.973055 TTCCACGTCCGGCCAACG 62.973 66.667 22.28 22.28 45.37 4.10
2785 2808 1.918868 GATTTCCACGTCCGGCCAAC 61.919 60.000 2.24 0.00 0.00 3.77
2786 2809 1.673009 GATTTCCACGTCCGGCCAA 60.673 57.895 2.24 0.00 0.00 4.52
2787 2810 2.046700 GATTTCCACGTCCGGCCA 60.047 61.111 2.24 0.00 0.00 5.36
2788 2811 2.822701 GGATTTCCACGTCCGGCC 60.823 66.667 0.00 0.00 35.64 6.13
2789 2812 2.822701 GGGATTTCCACGTCCGGC 60.823 66.667 0.00 0.00 37.91 6.13
2790 2813 2.124860 GGGGATTTCCACGTCCGG 60.125 66.667 0.00 0.00 37.91 5.14
2791 2814 1.003112 TTGGGGATTTCCACGTCCG 60.003 57.895 0.00 0.00 44.25 4.79
2792 2815 1.313091 GCTTGGGGATTTCCACGTCC 61.313 60.000 0.00 0.00 44.25 4.79
2793 2816 0.322546 AGCTTGGGGATTTCCACGTC 60.323 55.000 0.00 0.00 44.25 4.34
2794 2817 0.112412 AAGCTTGGGGATTTCCACGT 59.888 50.000 0.00 0.00 44.25 4.49
2795 2818 2.122783 TAAGCTTGGGGATTTCCACG 57.877 50.000 9.86 0.00 44.25 4.94
2796 2819 3.195610 CCTTTAAGCTTGGGGATTTCCAC 59.804 47.826 9.86 0.00 40.76 4.02
2797 2820 3.181412 ACCTTTAAGCTTGGGGATTTCCA 60.181 43.478 9.86 0.00 37.91 3.53
2798 2821 3.195610 CACCTTTAAGCTTGGGGATTTCC 59.804 47.826 9.86 0.00 0.00 3.13
2799 2822 3.368427 GCACCTTTAAGCTTGGGGATTTC 60.368 47.826 9.86 0.00 0.00 2.17
2800 2823 2.567169 GCACCTTTAAGCTTGGGGATTT 59.433 45.455 9.86 0.00 0.00 2.17
2801 2824 2.179427 GCACCTTTAAGCTTGGGGATT 58.821 47.619 9.86 0.00 0.00 3.01
2802 2825 1.077005 TGCACCTTTAAGCTTGGGGAT 59.923 47.619 9.86 0.00 0.00 3.85
2803 2826 0.480690 TGCACCTTTAAGCTTGGGGA 59.519 50.000 9.86 0.00 0.00 4.81
2804 2827 0.890683 CTGCACCTTTAAGCTTGGGG 59.109 55.000 9.86 10.62 0.00 4.96
2805 2828 0.244721 GCTGCACCTTTAAGCTTGGG 59.755 55.000 9.86 10.98 34.05 4.12
2806 2829 0.109597 CGCTGCACCTTTAAGCTTGG 60.110 55.000 9.86 4.28 34.72 3.61
2807 2830 0.730494 GCGCTGCACCTTTAAGCTTG 60.730 55.000 9.86 0.00 34.72 4.01
2808 2831 1.172180 TGCGCTGCACCTTTAAGCTT 61.172 50.000 9.73 3.48 34.72 3.74
2809 2832 1.172180 TTGCGCTGCACCTTTAAGCT 61.172 50.000 9.73 0.00 38.71 3.74
2810 2833 0.318614 TTTGCGCTGCACCTTTAAGC 60.319 50.000 9.73 0.00 38.71 3.09
2811 2834 1.268999 TGTTTGCGCTGCACCTTTAAG 60.269 47.619 9.73 0.00 38.71 1.85
2812 2835 0.741326 TGTTTGCGCTGCACCTTTAA 59.259 45.000 9.73 0.00 38.71 1.52
2813 2836 0.741326 TTGTTTGCGCTGCACCTTTA 59.259 45.000 9.73 0.00 38.71 1.85
2814 2837 0.528249 CTTGTTTGCGCTGCACCTTT 60.528 50.000 9.73 0.00 38.71 3.11
2815 2838 1.066257 CTTGTTTGCGCTGCACCTT 59.934 52.632 9.73 0.00 38.71 3.50
2816 2839 2.723746 CTTGTTTGCGCTGCACCT 59.276 55.556 9.73 0.00 38.71 4.00
2817 2840 2.355009 CCTTGTTTGCGCTGCACC 60.355 61.111 9.73 0.00 38.71 5.01
2818 2841 3.032033 GCCTTGTTTGCGCTGCAC 61.032 61.111 9.73 2.81 38.71 4.57
2819 2842 2.569072 TTTGCCTTGTTTGCGCTGCA 62.569 50.000 9.73 1.48 36.47 4.41
2820 2843 1.223417 ATTTGCCTTGTTTGCGCTGC 61.223 50.000 9.73 0.00 0.00 5.25
2821 2844 1.219646 AATTTGCCTTGTTTGCGCTG 58.780 45.000 9.73 0.00 0.00 5.18
2822 2845 2.035832 AGTAATTTGCCTTGTTTGCGCT 59.964 40.909 9.73 0.00 0.00 5.92
2823 2846 2.155539 CAGTAATTTGCCTTGTTTGCGC 59.844 45.455 0.00 0.00 0.00 6.09
2824 2847 3.637432 TCAGTAATTTGCCTTGTTTGCG 58.363 40.909 0.00 0.00 0.00 4.85
2825 2848 5.277297 GGTTTCAGTAATTTGCCTTGTTTGC 60.277 40.000 0.00 0.00 0.00 3.68
2826 2849 6.285790 GGTTTCAGTAATTTGCCTTGTTTG 57.714 37.500 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.