Multiple sequence alignment - TraesCS6B01G437300

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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 TraesCS6B01G437300 chr6B 100.000 2862 0 0 1 2862 704394771 704397632 0.000000e+00 5286.0
1 TraesCS6B01G437300 chr6D 94.598 2647 127 6 1 2632 452940801 452943446 0.000000e+00 4082.0
2 TraesCS6B01G437300 chr6D 94.094 2252 116 6 3 2237 80591353 80589102 0.000000e+00 3406.0
3 TraesCS6B01G437300 chr7D 94.516 2644 132 4 1 2632 614686989 614689631 0.000000e+00 4067.0
4 TraesCS6B01G437300 chr7D 94.367 2645 113 11 1 2632 528809318 528806697 0.000000e+00 4026.0
5 TraesCS6B01G437300 chr7D 93.457 2644 129 10 1 2632 156196157 156198768 0.000000e+00 3884.0
6 TraesCS6B01G437300 chr7D 94.355 1860 100 3 775 2632 614905629 614903773 0.000000e+00 2848.0
7 TraesCS6B01G437300 chr7D 94.297 789 34 2 1 779 614916143 614915356 0.000000e+00 1197.0
8 TraesCS6B01G437300 chr4D 94.524 2648 110 10 1 2632 8877628 8875000 0.000000e+00 4054.0
9 TraesCS6B01G437300 chr7B 94.220 2647 138 5 1 2632 732133373 732130727 0.000000e+00 4026.0
10 TraesCS6B01G437300 chr7B 94.069 2647 132 7 1 2632 732182250 732179614 0.000000e+00 3995.0
11 TraesCS6B01G437300 chr7B 94.459 1895 100 4 743 2632 237928161 237926267 0.000000e+00 2913.0
12 TraesCS6B01G437300 chr7B 98.396 187 3 0 2676 2862 146948638 146948824 2.130000e-86 329.0
13 TraesCS6B01G437300 chr7A 94.113 2650 138 7 1 2632 712343566 712340917 0.000000e+00 4013.0
14 TraesCS6B01G437300 chr3B 93.955 2647 142 7 1 2632 23790615 23787972 0.000000e+00 3986.0
15 TraesCS6B01G437300 chr3B 94.627 1098 47 3 1 1087 20814304 20815400 0.000000e+00 1690.0
16 TraesCS6B01G437300 chr3B 97.396 192 5 0 2671 2862 550444247 550444056 7.650000e-86 327.0
17 TraesCS6B01G437300 chr3B 97.396 192 5 0 2671 2862 550451354 550451163 7.650000e-86 327.0
18 TraesCS6B01G437300 chr1B 93.144 2567 135 11 68 2632 611518582 611516055 0.000000e+00 3727.0
19 TraesCS6B01G437300 chr1B 94.541 403 20 2 2231 2632 58495851 58495450 3.130000e-174 621.0
20 TraesCS6B01G437300 chr1B 95.652 46 1 1 2634 2678 611495299 611495254 3.960000e-09 73.1
21 TraesCS6B01G437300 chr2D 93.976 2042 102 5 603 2632 622803637 622805669 0.000000e+00 3070.0
22 TraesCS6B01G437300 chrUn 98.396 187 3 0 2676 2862 162947734 162947920 2.130000e-86 329.0
23 TraesCS6B01G437300 chrUn 98.396 187 3 0 2676 2862 163015510 163015696 2.130000e-86 329.0
24 TraesCS6B01G437300 chr6A 98.396 187 3 0 2676 2862 465288668 465288482 2.130000e-86 329.0
25 TraesCS6B01G437300 chr5A 98.396 187 3 0 2676 2862 298975116 298974930 2.130000e-86 329.0
26 TraesCS6B01G437300 chr5A 96.000 200 5 3 2664 2862 326160356 326160159 3.560000e-84 322.0
27 TraesCS6B01G437300 chr4B 98.396 187 3 0 2676 2862 474105485 474105299 2.130000e-86 329.0


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 TraesCS6B01G437300 chr6B 704394771 704397632 2861 False 5286 5286 100.000 1 2862 1 chr6B.!!$F1 2861
1 TraesCS6B01G437300 chr6D 452940801 452943446 2645 False 4082 4082 94.598 1 2632 1 chr6D.!!$F1 2631
2 TraesCS6B01G437300 chr6D 80589102 80591353 2251 True 3406 3406 94.094 3 2237 1 chr6D.!!$R1 2234
3 TraesCS6B01G437300 chr7D 614686989 614689631 2642 False 4067 4067 94.516 1 2632 1 chr7D.!!$F2 2631
4 TraesCS6B01G437300 chr7D 528806697 528809318 2621 True 4026 4026 94.367 1 2632 1 chr7D.!!$R1 2631
5 TraesCS6B01G437300 chr7D 156196157 156198768 2611 False 3884 3884 93.457 1 2632 1 chr7D.!!$F1 2631
6 TraesCS6B01G437300 chr7D 614903773 614905629 1856 True 2848 2848 94.355 775 2632 1 chr7D.!!$R2 1857
7 TraesCS6B01G437300 chr7D 614915356 614916143 787 True 1197 1197 94.297 1 779 1 chr7D.!!$R3 778
8 TraesCS6B01G437300 chr4D 8875000 8877628 2628 True 4054 4054 94.524 1 2632 1 chr4D.!!$R1 2631
9 TraesCS6B01G437300 chr7B 732130727 732133373 2646 True 4026 4026 94.220 1 2632 1 chr7B.!!$R2 2631
10 TraesCS6B01G437300 chr7B 732179614 732182250 2636 True 3995 3995 94.069 1 2632 1 chr7B.!!$R3 2631
11 TraesCS6B01G437300 chr7B 237926267 237928161 1894 True 2913 2913 94.459 743 2632 1 chr7B.!!$R1 1889
12 TraesCS6B01G437300 chr7A 712340917 712343566 2649 True 4013 4013 94.113 1 2632 1 chr7A.!!$R1 2631
13 TraesCS6B01G437300 chr3B 23787972 23790615 2643 True 3986 3986 93.955 1 2632 1 chr3B.!!$R1 2631
14 TraesCS6B01G437300 chr3B 20814304 20815400 1096 False 1690 1690 94.627 1 1087 1 chr3B.!!$F1 1086
15 TraesCS6B01G437300 chr1B 611516055 611518582 2527 True 3727 3727 93.144 68 2632 1 chr1B.!!$R3 2564
16 TraesCS6B01G437300 chr2D 622803637 622805669 2032 False 3070 3070 93.976 603 2632 1 chr2D.!!$F1 2029

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
428 430 0.034896 GAAGAACTGGCCGGACAAGA 59.965 55.0 21.41 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2120 0.325933 CAGGAGGAGGAACATGCACA 59.674 55.0 0.0 0.0 0.0 4.57 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
37 38 0.966920 ACATCGAGAACGGAGTGGTT 59.033 50.000 0.00 0.00 45.00 3.67
54 55 3.936453 GTGGTTAATAGCACCGATCAACA 59.064 43.478 0.00 0.00 44.92 3.33
137 138 0.582005 GATGCTTCCGCCATTACGTC 59.418 55.000 0.00 0.00 34.43 4.34
141 142 1.806623 GCTTCCGCCATTACGTCTGAT 60.807 52.381 0.00 0.00 0.00 2.90
263 265 1.885388 CCAACGCTTGTCCACACGA 60.885 57.895 0.00 0.00 0.00 4.35
285 287 2.203139 CACAGCGTTGGTGGACCA 60.203 61.111 3.74 0.00 45.94 4.02
428 430 0.034896 GAAGAACTGGCCGGACAAGA 59.965 55.000 21.41 0.00 0.00 3.02
501 504 3.047807 TAGCACTGGCATGGCTCCC 62.048 63.158 21.08 6.28 44.61 4.30
531 534 1.660560 GCCGAATGCCTGCAAGATGT 61.661 55.000 0.00 0.00 34.07 3.06
536 539 3.216800 GAATGCCTGCAAGATGTGGATA 58.783 45.455 0.00 0.00 34.07 2.59
668 671 1.330655 CGACTGGGATGCAGGGTACT 61.331 60.000 0.00 0.00 0.00 2.73
839 852 0.396435 GATGTGTGGGTGTGTCTGGA 59.604 55.000 0.00 0.00 0.00 3.86
847 860 0.832135 GGTGTGTCTGGACCCTCTCA 60.832 60.000 0.00 0.00 0.00 3.27
856 869 1.004745 TGGACCCTCTCAATTTGGAGC 59.995 52.381 8.54 0.00 34.84 4.70
860 873 1.101331 CCTCTCAATTTGGAGCTGGC 58.899 55.000 0.00 0.00 34.84 4.85
864 877 0.540133 TCAATTTGGAGCTGGCAGCA 60.540 50.000 38.09 20.03 45.56 4.41
878 891 4.586235 AGCAGCTGCCGGTTGGTT 62.586 61.111 34.39 11.28 43.38 3.67
931 947 1.188219 AGTATGGCGAGGATGGCGAT 61.188 55.000 0.00 0.00 42.57 4.58
967 983 0.177141 CCGTCGCCTATTCTTGGGAA 59.823 55.000 0.00 0.00 35.78 3.97
1008 1025 3.009723 CAAGGGAAGTGCGATGTACAAT 58.990 45.455 0.00 0.00 0.00 2.71
1132 1149 5.664006 TGTATAGGTTAACTGGTGGCTGTAT 59.336 40.000 5.42 0.00 0.00 2.29
1205 1222 3.558746 CCTTCTCTTCTGGTGCATTGTCT 60.559 47.826 0.00 0.00 0.00 3.41
1428 1446 0.879400 CTATGCAGGAAGAGCAGGCG 60.879 60.000 0.00 0.00 46.36 5.52
1530 1548 4.476479 AGATGGAGAGAGGTTAGGCATTTT 59.524 41.667 0.00 0.00 0.00 1.82
1622 1640 0.821517 ATGGACGGAAGCGTACATGA 59.178 50.000 0.00 0.00 41.39 3.07
1711 1729 0.546122 ATTTCAGGGAGTATGCGCCA 59.454 50.000 4.18 0.00 36.19 5.69
1722 1740 1.737236 GTATGCGCCACTGATGAACAA 59.263 47.619 4.18 0.00 0.00 2.83
1892 1916 1.071699 GTGGAGGGTGACAACAAGCTA 59.928 52.381 0.00 0.00 0.00 3.32
1899 1923 3.219281 GGTGACAACAAGCTAAGGGAAA 58.781 45.455 0.00 0.00 0.00 3.13
1901 1925 3.630312 GTGACAACAAGCTAAGGGAAACA 59.370 43.478 0.00 0.00 0.00 2.83
1940 1964 4.596643 AGCCTCATAGCATTCTATTGGAGT 59.403 41.667 5.68 0.00 33.37 3.85
2044 2076 2.621338 TGCAGAAGATCATGAACCGTC 58.379 47.619 0.00 2.95 0.00 4.79
2045 2077 2.028203 TGCAGAAGATCATGAACCGTCA 60.028 45.455 0.00 0.00 38.41 4.35
2088 2120 1.672356 GTGTGCTGCCTCGGTTGAT 60.672 57.895 0.00 0.00 0.00 2.57
2171 2203 1.153086 GTTCCTCGAGCCATGCCAT 60.153 57.895 6.99 0.00 0.00 4.40
2177 2209 0.471191 TCGAGCCATGCCATCTCATT 59.529 50.000 0.00 0.00 0.00 2.57
2212 2244 1.003349 ACGAGACCGAGGAAGAAGAGA 59.997 52.381 0.00 0.00 39.50 3.10
2226 2282 4.817318 AGAAGAGAAAGTGGATGAGGAC 57.183 45.455 0.00 0.00 0.00 3.85
2250 2306 3.708451 AGAGGAAGAAGAGGGAGAAGAC 58.292 50.000 0.00 0.00 0.00 3.01
2304 2360 0.661552 AGTACGACGACGATGATGGG 59.338 55.000 15.32 0.00 42.66 4.00
2381 2437 1.089920 CTGAGCCCATCACCTTTTCG 58.910 55.000 0.00 0.00 33.22 3.46
2440 2496 1.452145 GGGCCGCTTGAAGACAAACA 61.452 55.000 0.00 0.00 35.49 2.83
2486 2545 2.576648 GGGGGAGGAACTAGTGATGTTT 59.423 50.000 0.00 0.00 41.55 2.83
2497 2556 8.228464 GGAACTAGTGATGTTTAACTTGCTAAC 58.772 37.037 0.00 0.00 0.00 2.34
2637 2697 8.902540 AAGTGCGAGGTTATTATAATGATCAA 57.097 30.769 8.28 0.00 0.00 2.57
2638 2698 8.539770 AGTGCGAGGTTATTATAATGATCAAG 57.460 34.615 8.28 0.43 0.00 3.02
2639 2699 8.150945 AGTGCGAGGTTATTATAATGATCAAGT 58.849 33.333 8.28 0.00 0.00 3.16
2640 2700 8.774586 GTGCGAGGTTATTATAATGATCAAGTT 58.225 33.333 8.28 0.00 0.00 2.66
2641 2701 9.990360 TGCGAGGTTATTATAATGATCAAGTTA 57.010 29.630 8.28 0.00 0.00 2.24
2665 2725 3.660343 AAAAAGCCAGAGAGGAGCC 57.340 52.632 0.00 0.00 41.22 4.70
2666 2726 1.071434 AAAAAGCCAGAGAGGAGCCT 58.929 50.000 0.00 0.00 41.22 4.58
2667 2727 1.958288 AAAAGCCAGAGAGGAGCCTA 58.042 50.000 0.00 0.00 41.22 3.93
2668 2728 1.199615 AAAGCCAGAGAGGAGCCTAC 58.800 55.000 0.00 0.00 41.22 3.18
2669 2729 0.689412 AAGCCAGAGAGGAGCCTACC 60.689 60.000 0.00 0.00 41.22 3.18
2670 2730 2.494530 GCCAGAGAGGAGCCTACCG 61.495 68.421 0.00 0.00 41.22 4.02
2671 2731 2.494530 CCAGAGAGGAGCCTACCGC 61.495 68.421 0.00 0.00 41.22 5.68
2672 2732 2.123640 AGAGAGGAGCCTACCGCC 60.124 66.667 0.00 0.00 38.78 6.13
2673 2733 2.442272 GAGAGGAGCCTACCGCCA 60.442 66.667 0.00 0.00 38.78 5.69
2674 2734 2.760385 AGAGGAGCCTACCGCCAC 60.760 66.667 0.00 0.00 38.78 5.01
2675 2735 4.208686 GAGGAGCCTACCGCCACG 62.209 72.222 0.00 0.00 38.78 4.94
2676 2736 4.753662 AGGAGCCTACCGCCACGA 62.754 66.667 0.00 0.00 38.78 4.35
2677 2737 4.208686 GGAGCCTACCGCCACGAG 62.209 72.222 0.00 0.00 38.78 4.18
2678 2738 4.208686 GAGCCTACCGCCACGAGG 62.209 72.222 0.00 0.00 38.78 4.63
2688 2748 4.473643 CCACGAGGCTGTTGGAAA 57.526 55.556 5.20 0.00 0.00 3.13
2689 2749 2.946947 CCACGAGGCTGTTGGAAAT 58.053 52.632 5.20 0.00 0.00 2.17
2690 2750 2.107950 CCACGAGGCTGTTGGAAATA 57.892 50.000 5.20 0.00 0.00 1.40
2691 2751 2.643551 CCACGAGGCTGTTGGAAATAT 58.356 47.619 5.20 0.00 0.00 1.28
2692 2752 2.355756 CCACGAGGCTGTTGGAAATATG 59.644 50.000 5.20 0.00 0.00 1.78
2693 2753 2.017049 ACGAGGCTGTTGGAAATATGC 58.983 47.619 0.00 0.00 0.00 3.14
2694 2754 1.334869 CGAGGCTGTTGGAAATATGCC 59.665 52.381 0.00 0.00 38.15 4.40
2695 2755 1.683385 GAGGCTGTTGGAAATATGCCC 59.317 52.381 0.00 0.00 38.46 5.36
2696 2756 1.288932 AGGCTGTTGGAAATATGCCCT 59.711 47.619 0.00 0.00 38.46 5.19
2697 2757 2.513738 AGGCTGTTGGAAATATGCCCTA 59.486 45.455 0.00 0.00 38.46 3.53
2698 2758 2.887152 GGCTGTTGGAAATATGCCCTAG 59.113 50.000 0.00 0.00 34.03 3.02
2699 2759 3.435026 GGCTGTTGGAAATATGCCCTAGA 60.435 47.826 0.00 0.00 34.03 2.43
2700 2760 3.817647 GCTGTTGGAAATATGCCCTAGAG 59.182 47.826 0.00 0.00 0.00 2.43
2701 2761 4.392940 CTGTTGGAAATATGCCCTAGAGG 58.607 47.826 0.00 0.00 39.47 3.69
2780 2840 9.910267 ATGCATGCTATAATTGTATTGATAGGA 57.090 29.630 20.33 0.00 0.00 2.94
2781 2841 9.737844 TGCATGCTATAATTGTATTGATAGGAA 57.262 29.630 20.33 0.00 0.00 3.36
2794 2854 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
2795 2855 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
2796 2856 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
2797 2857 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
2798 2858 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
2799 2859 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
2800 2860 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
2801 2861 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
2802 2862 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
2803 2863 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
2819 2879 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
2820 2880 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
2821 2881 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
2822 2882 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
2828 2888 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
2829 2889 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
2830 2890 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
2831 2891 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
2832 2892 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
2833 2893 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
2834 2894 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
2835 2895 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
2836 2896 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
2837 2897 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
2838 2898 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
2839 2899 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
2840 2900 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
2841 2901 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
2842 2902 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
2843 2903 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
2844 2904 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
2845 2905 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
2846 2906 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
2847 2907 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
2848 2908 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
2849 2909 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
2850 2910 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
2851 2911 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
2852 2912 3.690139 CCTCTAGTTGACTAGCTCGTTGA 59.310 47.826 12.30 0.00 44.24 3.18
2853 2913 4.336993 CCTCTAGTTGACTAGCTCGTTGAT 59.663 45.833 12.30 0.00 44.24 2.57
2854 2914 5.487153 TCTAGTTGACTAGCTCGTTGATC 57.513 43.478 12.30 0.00 44.24 2.92
2855 2915 4.941873 TCTAGTTGACTAGCTCGTTGATCA 59.058 41.667 12.30 0.00 44.24 2.92
2856 2916 4.521130 AGTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
2857 2917 4.238514 AGTTGACTAGCTCGTTGATCAAC 58.761 43.478 25.68 25.68 43.94 3.18
2858 2918 3.934457 TGACTAGCTCGTTGATCAACA 57.066 42.857 32.06 20.24 41.20 3.33
2859 2919 3.838120 TGACTAGCTCGTTGATCAACAG 58.162 45.455 32.06 26.93 41.20 3.16
2860 2920 3.506067 TGACTAGCTCGTTGATCAACAGA 59.494 43.478 32.06 26.81 41.20 3.41
2861 2921 4.158579 TGACTAGCTCGTTGATCAACAGAT 59.841 41.667 32.06 26.87 41.20 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.758979 ACCACTCCGTTCTCGATGTAAT 59.241 45.455 0.00 0.00 39.71 1.89
37 38 4.035091 GCAACATGTTGATCGGTGCTATTA 59.965 41.667 36.65 0.00 42.93 0.98
54 55 4.010667 AGGCAAAATTGTGATGCAACAT 57.989 36.364 0.00 0.00 41.80 2.71
137 138 1.679977 CCTTGGTGTGGCCCATCAG 60.680 63.158 0.00 0.00 35.07 2.90
141 142 2.230189 TTTGACCTTGGTGTGGCCCA 62.230 55.000 0.00 0.00 36.04 5.36
263 265 1.069765 CCACCAACGCTGTGAGAGT 59.930 57.895 0.00 0.00 35.74 3.24
327 329 0.596083 CTCGAGCGTCACCATCATCC 60.596 60.000 0.00 0.00 0.00 3.51
501 504 4.096003 ATTCGGCCCGGTGGTCTG 62.096 66.667 1.90 0.00 32.45 3.51
839 852 1.005215 CCAGCTCCAAATTGAGAGGGT 59.995 52.381 11.50 0.00 34.11 4.34
847 860 2.273908 CTGCTGCCAGCTCCAAATT 58.726 52.632 18.96 0.00 42.97 1.82
878 891 1.228245 GTGGCAGTTTCTCAGGGCA 60.228 57.895 0.00 0.00 0.00 5.36
931 947 3.733337 GACGGTAGGGTATCGAGAACTA 58.267 50.000 0.00 0.00 35.91 2.24
967 983 1.271762 GCCCGAAAGACCTTAACCCTT 60.272 52.381 0.00 0.00 0.00 3.95
1008 1025 1.597854 CAGCTCGTTGGTGAAGGCA 60.598 57.895 4.83 0.00 46.27 4.75
1132 1149 0.325296 ACCCCCAAGCTCTATCGTGA 60.325 55.000 0.00 0.00 0.00 4.35
1266 1283 1.678627 GTGGTGTGTGTTGCAATACCA 59.321 47.619 21.74 17.55 41.41 3.25
1428 1446 6.334102 AGTCCAATATCGACTGAGAATACC 57.666 41.667 4.94 0.00 39.14 2.73
1468 1486 3.253188 CGTCCCACATTGTCACAAAAGAT 59.747 43.478 0.00 0.00 0.00 2.40
1530 1548 3.106827 TGCCTCTCATACACATTCCAGA 58.893 45.455 0.00 0.00 0.00 3.86
1622 1640 2.465813 CTCCTCCTCCTGAAGTGATGT 58.534 52.381 0.00 0.00 0.00 3.06
1711 1729 6.377146 ACAAACTTACCACTTTGTTCATCAGT 59.623 34.615 0.00 0.00 37.31 3.41
1722 1740 5.971763 TGCATTTCAACAAACTTACCACTT 58.028 33.333 0.00 0.00 0.00 3.16
1846 1870 1.019805 GGGGTCAGAACTTAGCGCAC 61.020 60.000 11.47 0.00 0.00 5.34
1871 1895 0.465460 GCTTGTTGTCACCCTCCACA 60.465 55.000 0.00 0.00 0.00 4.17
1892 1916 8.541899 TTAAAGTTACCTTCATTGTTTCCCTT 57.458 30.769 0.00 0.00 0.00 3.95
1899 1923 6.303839 TGAGGCTTAAAGTTACCTTCATTGT 58.696 36.000 0.00 0.00 30.95 2.71
1901 1925 7.283354 GCTATGAGGCTTAAAGTTACCTTCATT 59.717 37.037 0.00 0.00 30.95 2.57
1940 1964 4.193090 GGCATGGATCAAATTTGCATTCA 58.807 39.130 13.54 12.34 35.04 2.57
2088 2120 0.325933 CAGGAGGAGGAACATGCACA 59.674 55.000 0.00 0.00 0.00 4.57
2171 2203 4.915667 CGTTAACAAGACGAGACAATGAGA 59.084 41.667 6.39 0.00 42.82 3.27
2212 2244 2.234908 CCTCTTCGTCCTCATCCACTTT 59.765 50.000 0.00 0.00 0.00 2.66
2226 2282 2.729194 TCTCCCTCTTCTTCCTCTTCG 58.271 52.381 0.00 0.00 0.00 3.79
2250 2306 0.454620 CTTCGTCGTCACCTCCTTCG 60.455 60.000 0.00 0.00 0.00 3.79
2304 2360 2.435059 GGCTGAGTCGGTTGAGGC 60.435 66.667 0.00 0.00 0.00 4.70
2429 2485 1.939934 CACGCTCCTTGTTTGTCTTCA 59.060 47.619 0.00 0.00 0.00 3.02
2486 2545 9.603921 ACACAACTACTTTAAGTTAGCAAGTTA 57.396 29.630 1.94 0.00 37.61 2.24
2647 2707 1.071434 AGGCTCCTCTCTGGCTTTTT 58.929 50.000 0.00 0.00 35.50 1.94
2648 2708 1.557371 GTAGGCTCCTCTCTGGCTTTT 59.443 52.381 0.00 0.00 39.76 2.27
2649 2709 1.199615 GTAGGCTCCTCTCTGGCTTT 58.800 55.000 0.00 0.00 39.76 3.51
2650 2710 0.689412 GGTAGGCTCCTCTCTGGCTT 60.689 60.000 0.00 0.00 39.76 4.35
2651 2711 1.075600 GGTAGGCTCCTCTCTGGCT 60.076 63.158 0.00 0.00 41.91 4.75
2652 2712 2.494530 CGGTAGGCTCCTCTCTGGC 61.495 68.421 0.00 0.00 35.26 4.85
2653 2713 2.494530 GCGGTAGGCTCCTCTCTGG 61.495 68.421 0.00 0.00 39.11 3.86
2654 2714 2.494530 GGCGGTAGGCTCCTCTCTG 61.495 68.421 0.00 0.00 42.94 3.35
2655 2715 2.123640 GGCGGTAGGCTCCTCTCT 60.124 66.667 0.00 0.00 42.94 3.10
2656 2716 2.442272 TGGCGGTAGGCTCCTCTC 60.442 66.667 0.00 0.00 44.18 3.20
2657 2717 2.760385 GTGGCGGTAGGCTCCTCT 60.760 66.667 0.00 0.00 44.18 3.69
2658 2718 4.208686 CGTGGCGGTAGGCTCCTC 62.209 72.222 0.00 0.00 44.18 3.71
2659 2719 4.753662 TCGTGGCGGTAGGCTCCT 62.754 66.667 0.00 0.00 44.18 3.69
2660 2720 4.208686 CTCGTGGCGGTAGGCTCC 62.209 72.222 0.00 0.00 44.18 4.70
2661 2721 4.208686 CCTCGTGGCGGTAGGCTC 62.209 72.222 0.00 0.00 44.18 4.70
2671 2731 2.107950 TATTTCCAACAGCCTCGTGG 57.892 50.000 0.00 0.00 0.00 4.94
2672 2732 2.223340 GCATATTTCCAACAGCCTCGTG 60.223 50.000 0.00 0.00 0.00 4.35
2673 2733 2.017049 GCATATTTCCAACAGCCTCGT 58.983 47.619 0.00 0.00 0.00 4.18
2674 2734 1.334869 GGCATATTTCCAACAGCCTCG 59.665 52.381 0.00 0.00 39.02 4.63
2675 2735 1.683385 GGGCATATTTCCAACAGCCTC 59.317 52.381 0.00 0.00 41.71 4.70
2676 2736 1.288932 AGGGCATATTTCCAACAGCCT 59.711 47.619 0.00 0.00 41.71 4.58
2677 2737 1.780503 AGGGCATATTTCCAACAGCC 58.219 50.000 0.00 0.00 41.29 4.85
2678 2738 3.817647 CTCTAGGGCATATTTCCAACAGC 59.182 47.826 0.00 0.00 0.00 4.40
2679 2739 4.392940 CCTCTAGGGCATATTTCCAACAG 58.607 47.826 0.00 0.00 0.00 3.16
2680 2740 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
2754 2814 9.910267 TCCTATCAATACAATTATAGCATGCAT 57.090 29.630 21.98 13.55 0.00 3.96
2755 2815 9.737844 TTCCTATCAATACAATTATAGCATGCA 57.262 29.630 21.98 6.36 0.00 3.96
2768 2828 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
2769 2829 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
2770 2830 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
2771 2831 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
2772 2832 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
2773 2833 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
2774 2834 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
2775 2835 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
2776 2836 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
2777 2837 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
2778 2838 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
2779 2839 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
2780 2840 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
2781 2841 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
2782 2842 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
2783 2843 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
2784 2844 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
2785 2845 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
2786 2846 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
2787 2847 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
2788 2848 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
2789 2849 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
2790 2850 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
2791 2851 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
2792 2852 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
2793 2853 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
2794 2854 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
2795 2855 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
2796 2856 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
2797 2857 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
2798 2858 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
2799 2859 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
2800 2860 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
2801 2861 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
2802 2862 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
2803 2863 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
2804 2864 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
2805 2865 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
2806 2866 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
2807 2867 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
2808 2868 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
2809 2869 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
2810 2870 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
2811 2871 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
2812 2872 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
2813 2873 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
2814 2874 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
2815 2875 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
2816 2876 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
2817 2877 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
2818 2878 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
2819 2879 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
2820 2880 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
2821 2881 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
2822 2882 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
2823 2883 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
2824 2884 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
2825 2885 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
2826 2886 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
2827 2887 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
2828 2888 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
2829 2889 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
2830 2890 3.690139 TCAACGAGCTAGTCAACTAGAGG 59.310 47.826 19.03 10.05 46.80 3.69
2831 2891 4.948608 TCAACGAGCTAGTCAACTAGAG 57.051 45.455 19.03 11.89 46.80 2.43
2832 2892 4.941873 TGATCAACGAGCTAGTCAACTAGA 59.058 41.667 19.03 0.00 46.80 2.43
2833 2893 5.236655 TGATCAACGAGCTAGTCAACTAG 57.763 43.478 11.99 11.99 46.63 2.57
2834 2894 5.048294 TGTTGATCAACGAGCTAGTCAACTA 60.048 40.000 28.55 7.59 43.38 2.24
2835 2895 4.238514 GTTGATCAACGAGCTAGTCAACT 58.761 43.478 22.09 0.00 41.13 3.16
2836 2896 3.987868 TGTTGATCAACGAGCTAGTCAAC 59.012 43.478 28.55 16.99 43.94 3.18
2837 2897 4.022329 TCTGTTGATCAACGAGCTAGTCAA 60.022 41.667 28.55 10.18 43.94 3.18
2838 2898 3.506067 TCTGTTGATCAACGAGCTAGTCA 59.494 43.478 28.55 10.88 43.94 3.41
2839 2899 4.098055 TCTGTTGATCAACGAGCTAGTC 57.902 45.455 28.55 6.98 43.94 2.59
2840 2900 4.727507 ATCTGTTGATCAACGAGCTAGT 57.272 40.909 28.55 13.33 43.94 2.57


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

AutoCloner maintained by Alex Coulton.