Multiple sequence alignment - TraesCS6A01G130300

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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 TraesCS6A01G130300 chr6A 100.000 3534 0 0 1 3534 101897811 101894278 0.000000e+00 6527.0
1 TraesCS6A01G130300 chr6A 94.118 204 12 0 1602 1805 215047251 215047454 9.530000e-81 311.0
2 TraesCS6A01G130300 chr6A 93.137 102 7 0 1337 1438 215047142 215047243 2.200000e-32 150.0
3 TraesCS6A01G130300 chr6A 82.979 94 5 5 1819 1912 215047488 215047570 1.360000e-09 75.0
4 TraesCS6A01G130300 chr6B 90.802 2033 123 25 828 2837 161344225 161342234 0.000000e+00 2660.0
5 TraesCS6A01G130300 chr6B 87.671 365 32 11 3155 3509 161334695 161334334 2.540000e-111 412.0
6 TraesCS6A01G130300 chr6B 81.421 183 27 5 2829 3011 161335086 161334911 3.680000e-30 143.0
7 TraesCS6A01G130300 chr6B 92.000 100 8 0 3011 3110 161334801 161334702 1.320000e-29 141.0
8 TraesCS6A01G130300 chr6B 100.000 57 0 0 1 57 714418391 714418447 4.820000e-19 106.0
9 TraesCS6A01G130300 chr6D 92.742 1860 102 19 811 2649 84678546 84676699 0.000000e+00 2656.0
10 TraesCS6A01G130300 chr6D 94.242 990 49 5 826 1813 85553804 85554787 0.000000e+00 1506.0
11 TraesCS6A01G130300 chr6D 91.930 855 29 12 1883 2734 85554835 85555652 0.000000e+00 1160.0
12 TraesCS6A01G130300 chr6D 79.152 566 112 5 1923 2485 430243630 430243068 1.540000e-103 387.0
13 TraesCS6A01G130300 chr6D 89.453 256 25 2 3101 3354 85556198 85556453 4.400000e-84 322.0
14 TraesCS6A01G130300 chr6D 87.895 190 19 4 3322 3509 84674877 84674690 1.650000e-53 220.0
15 TraesCS6A01G130300 chr6D 84.524 168 25 1 2318 2485 430367452 430367618 7.850000e-37 165.0
16 TraesCS6A01G130300 chr6D 93.651 63 1 1 2759 2818 85555639 85555701 1.350000e-14 91.6
17 TraesCS6A01G130300 chr2D 95.889 754 27 3 57 810 647518273 647519022 0.000000e+00 1218.0
18 TraesCS6A01G130300 chr1A 95.623 754 28 3 57 810 492134636 492135384 0.000000e+00 1205.0
19 TraesCS6A01G130300 chr1A 95.093 754 33 3 57 810 577889642 577888893 0.000000e+00 1184.0
20 TraesCS6A01G130300 chr1A 94.841 756 33 4 57 812 291239190 291238441 0.000000e+00 1175.0
21 TraesCS6A01G130300 chrUn 95.232 755 30 4 57 811 380348814 380349562 0.000000e+00 1190.0
22 TraesCS6A01G130300 chrUn 95.232 755 30 4 57 811 380372485 380371737 0.000000e+00 1190.0
23 TraesCS6A01G130300 chrUn 94.967 755 31 5 57 811 263437630 263438377 0.000000e+00 1177.0
24 TraesCS6A01G130300 chrUn 92.208 77 6 0 2373 2449 32424672 32424596 3.730000e-20 110.0
25 TraesCS6A01G130300 chrUn 85.849 106 11 3 2348 2449 288681921 288682026 3.730000e-20 110.0
26 TraesCS6A01G130300 chrUn 100.000 57 0 0 1 57 211912642 211912586 4.820000e-19 106.0
27 TraesCS6A01G130300 chrUn 100.000 57 0 0 1 57 211936130 211936074 4.820000e-19 106.0
28 TraesCS6A01G130300 chr4B 94.980 757 30 6 57 812 647697235 647697984 0.000000e+00 1181.0
29 TraesCS6A01G130300 chr2A 94.967 755 34 4 57 810 775430109 775429358 0.000000e+00 1181.0
30 TraesCS6A01G130300 chr5B 79.469 565 106 9 1924 2486 609690575 609691131 3.310000e-105 392.0
31 TraesCS6A01G130300 chr5B 100.000 57 0 0 1 57 144585015 144585071 4.820000e-19 106.0
32 TraesCS6A01G130300 chr1B 86.574 216 13 10 1 216 171261233 171261034 1.280000e-54 224.0
33 TraesCS6A01G130300 chr7A 86.131 137 17 2 3010 3145 18090625 18090760 2.840000e-31 147.0
34 TraesCS6A01G130300 chr3D 85.088 114 15 2 2373 2485 11027225 11027337 8.020000e-22 115.0
35 TraesCS6A01G130300 chr7B 100.000 57 0 0 1 57 93962841 93962785 4.820000e-19 106.0
36 TraesCS6A01G130300 chr7B 84.906 106 12 3 2348 2449 353631149 353631254 1.740000e-18 104.0
37 TraesCS6A01G130300 chr4A 100.000 57 0 0 1 57 598576147 598576203 4.820000e-19 106.0
38 TraesCS6A01G130300 chr2B 100.000 57 0 0 1 57 569150112 569150168 4.820000e-19 106.0
39 TraesCS6A01G130300 chr2B 100.000 57 0 0 1 57 796434941 796434885 4.820000e-19 106.0
40 TraesCS6A01G130300 chr7D 90.909 77 7 0 2373 2449 351766750 351766674 1.740000e-18 104.0


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 TraesCS6A01G130300 chr6A 101894278 101897811 3533 True 6527.0 6527 100.000000 1 3534 1 chr6A.!!$R1 3533
1 TraesCS6A01G130300 chr6B 161342234 161344225 1991 True 2660.0 2660 90.802000 828 2837 1 chr6B.!!$R1 2009
2 TraesCS6A01G130300 chr6B 161334334 161335086 752 True 232.0 412 87.030667 2829 3509 3 chr6B.!!$R2 680
3 TraesCS6A01G130300 chr6D 84674690 84678546 3856 True 1438.0 2656 90.318500 811 3509 2 chr6D.!!$R2 2698
4 TraesCS6A01G130300 chr6D 85553804 85556453 2649 False 769.9 1506 92.319000 826 3354 4 chr6D.!!$F2 2528
5 TraesCS6A01G130300 chr6D 430243068 430243630 562 True 387.0 387 79.152000 1923 2485 1 chr6D.!!$R1 562
6 TraesCS6A01G130300 chr2D 647518273 647519022 749 False 1218.0 1218 95.889000 57 810 1 chr2D.!!$F1 753
7 TraesCS6A01G130300 chr1A 492134636 492135384 748 False 1205.0 1205 95.623000 57 810 1 chr1A.!!$F1 753
8 TraesCS6A01G130300 chr1A 577888893 577889642 749 True 1184.0 1184 95.093000 57 810 1 chr1A.!!$R2 753
9 TraesCS6A01G130300 chr1A 291238441 291239190 749 True 1175.0 1175 94.841000 57 812 1 chr1A.!!$R1 755
10 TraesCS6A01G130300 chrUn 380348814 380349562 748 False 1190.0 1190 95.232000 57 811 1 chrUn.!!$F3 754
11 TraesCS6A01G130300 chrUn 380371737 380372485 748 True 1190.0 1190 95.232000 57 811 1 chrUn.!!$R4 754
12 TraesCS6A01G130300 chrUn 263437630 263438377 747 False 1177.0 1177 94.967000 57 811 1 chrUn.!!$F1 754
13 TraesCS6A01G130300 chr4B 647697235 647697984 749 False 1181.0 1181 94.980000 57 812 1 chr4B.!!$F1 755
14 TraesCS6A01G130300 chr2A 775429358 775430109 751 True 1181.0 1181 94.967000 57 810 1 chr2A.!!$R1 753
15 TraesCS6A01G130300 chr5B 609690575 609691131 556 False 392.0 392 79.469000 1924 2486 1 chr5B.!!$F2 562

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
47 48 0.183971 TCGGTTGGCAGGAAAAGGAA 59.816 50.0 0.0 0.0 0.0 3.36 F
999 1007 0.322975 GCCAGAAGAGGAAGCTGTGA 59.677 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1826 0.171455 TTTGGCGAACAAACTGCGTT 59.829 45.0 2.13 0.0 43.81 4.84 R
2879 4297 0.098728 CCCGCGCCTTGTCAATTAAG 59.901 55.0 0.00 0.0 0.00 1.85 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
17 18 3.025107 AGGGCGGATGTAGGGAGA 58.975 61.111 0.00 0.00 0.00 3.71
18 19 1.457831 AGGGCGGATGTAGGGAGAC 60.458 63.158 0.00 0.00 0.00 3.36
19 20 2.728817 GGCGGATGTAGGGAGACG 59.271 66.667 0.00 0.00 0.00 4.18
20 21 2.728817 GCGGATGTAGGGAGACGG 59.271 66.667 0.00 0.00 0.00 4.79
21 22 2.857744 GCGGATGTAGGGAGACGGG 61.858 68.421 0.00 0.00 0.00 5.28
22 23 1.152819 CGGATGTAGGGAGACGGGA 60.153 63.158 0.00 0.00 0.00 5.14
23 24 1.453762 CGGATGTAGGGAGACGGGAC 61.454 65.000 0.00 0.00 0.00 4.46
42 43 2.281208 CGGTCGGTTGGCAGGAAA 60.281 61.111 0.00 0.00 0.00 3.13
43 44 1.894756 CGGTCGGTTGGCAGGAAAA 60.895 57.895 0.00 0.00 0.00 2.29
44 45 1.852067 CGGTCGGTTGGCAGGAAAAG 61.852 60.000 0.00 0.00 0.00 2.27
45 46 1.524008 GGTCGGTTGGCAGGAAAAGG 61.524 60.000 0.00 0.00 0.00 3.11
46 47 0.536460 GTCGGTTGGCAGGAAAAGGA 60.536 55.000 0.00 0.00 0.00 3.36
47 48 0.183971 TCGGTTGGCAGGAAAAGGAA 59.816 50.000 0.00 0.00 0.00 3.36
48 49 1.036707 CGGTTGGCAGGAAAAGGAAA 58.963 50.000 0.00 0.00 0.00 3.13
49 50 1.000274 CGGTTGGCAGGAAAAGGAAAG 60.000 52.381 0.00 0.00 0.00 2.62
50 51 1.270305 GGTTGGCAGGAAAAGGAAAGC 60.270 52.381 0.00 0.00 0.00 3.51
51 52 1.688735 GTTGGCAGGAAAAGGAAAGCT 59.311 47.619 0.00 0.00 0.00 3.74
52 53 2.890945 GTTGGCAGGAAAAGGAAAGCTA 59.109 45.455 0.00 0.00 0.00 3.32
53 54 2.514803 TGGCAGGAAAAGGAAAGCTAC 58.485 47.619 0.00 0.00 0.00 3.58
54 55 1.468914 GGCAGGAAAAGGAAAGCTACG 59.531 52.381 0.00 0.00 0.00 3.51
55 56 1.135660 GCAGGAAAAGGAAAGCTACGC 60.136 52.381 0.00 0.00 0.00 4.42
75 76 8.282592 GCTACGCAAAATCACATCAATATAAGA 58.717 33.333 0.00 0.00 0.00 2.10
266 268 8.272659 AGAGATGATTGATGATAAGAAAGGGA 57.727 34.615 0.00 0.00 0.00 4.20
438 442 1.229209 GACAGGTGGGAGGGAGACA 60.229 63.158 0.00 0.00 0.00 3.41
526 530 3.378339 CGGCGGACTATTCGTAGATTTT 58.622 45.455 0.00 0.00 35.04 1.82
568 572 1.111116 CGACGGGATGTTAGGGCCTA 61.111 60.000 9.81 9.81 0.00 3.93
652 658 2.273179 CGTGAGACGGGAGGTTGGA 61.273 63.158 0.00 0.00 38.08 3.53
718 724 1.132527 TGAGAGGGAGGTGGGAGAAAA 60.133 52.381 0.00 0.00 0.00 2.29
892 899 2.733517 GAGTCTTGTATACTGCCGCTC 58.266 52.381 4.17 2.56 0.00 5.03
977 985 2.412325 CCGGCGATTTATTTATGCGGTC 60.412 50.000 9.30 0.00 0.00 4.79
999 1007 0.322975 GCCAGAAGAGGAAGCTGTGA 59.677 55.000 0.00 0.00 0.00 3.58
1184 1193 1.686110 TCTTCCTCTTCCGCTCCCC 60.686 63.158 0.00 0.00 0.00 4.81
1425 1434 3.103911 GAACACGACCAGGACGCG 61.104 66.667 11.51 3.53 0.00 6.01
1528 1539 2.597305 CTCACACGTGTAAGTTATCCGC 59.403 50.000 22.90 0.00 0.00 5.54
1538 1549 2.005971 AGTTATCCGCGGTTGTCTTC 57.994 50.000 27.15 10.29 0.00 2.87
1699 1710 2.203280 CGGTGTTGAGGTTGGCCA 60.203 61.111 0.00 0.00 37.19 5.36
1805 1816 2.764637 AAATCGCCCCGAACTTGCCT 62.765 55.000 0.00 0.00 39.99 4.75
1807 1818 1.906105 ATCGCCCCGAACTTGCCTAA 61.906 55.000 0.00 0.00 39.99 2.69
1813 1824 1.271163 CCCGAACTTGCCTAAGGTGAA 60.271 52.381 0.00 0.00 38.26 3.18
1815 1826 2.489971 CGAACTTGCCTAAGGTGAACA 58.510 47.619 0.00 0.00 38.26 3.18
1816 1827 2.875933 CGAACTTGCCTAAGGTGAACAA 59.124 45.455 0.00 0.00 38.26 2.83
1817 1828 3.303791 CGAACTTGCCTAAGGTGAACAAC 60.304 47.826 0.00 0.00 38.26 3.32
1857 1888 3.678289 CTTCCAATCCATGTCACTGACA 58.322 45.455 14.26 14.26 46.90 3.58
1863 1894 2.319844 TCCATGTCACTGACAGTCACT 58.680 47.619 16.80 0.00 46.04 3.41
1871 1902 2.609459 CACTGACAGTCACTGAACCAAC 59.391 50.000 13.14 0.00 35.18 3.77
1885 1916 1.675310 CCAACCGCAGATTGCTCCA 60.675 57.895 0.00 0.00 42.25 3.86
2186 2223 4.478371 TCTGCATGGCCTCGCTGG 62.478 66.667 18.79 11.79 39.35 4.85
2575 2612 5.049818 GTGGTGATTATCAGTAAGCAGATGC 60.050 44.000 0.00 0.00 36.93 3.91
2596 2633 7.774157 AGATGCTGTTCTATGTTGAATGATCTT 59.226 33.333 0.00 0.00 0.00 2.40
2667 4045 2.623878 ATGCATGCTCCTCTCTGAAG 57.376 50.000 20.33 0.00 0.00 3.02
2668 4046 1.273759 TGCATGCTCCTCTCTGAAGT 58.726 50.000 20.33 0.00 0.00 3.01
2669 4047 1.206610 TGCATGCTCCTCTCTGAAGTC 59.793 52.381 20.33 0.00 0.00 3.01
2670 4048 1.481772 GCATGCTCCTCTCTGAAGTCT 59.518 52.381 11.37 0.00 0.00 3.24
2671 4049 2.739287 GCATGCTCCTCTCTGAAGTCTG 60.739 54.545 11.37 0.00 0.00 3.51
2672 4050 2.593925 TGCTCCTCTCTGAAGTCTGA 57.406 50.000 0.00 0.00 0.00 3.27
2673 4051 2.881734 TGCTCCTCTCTGAAGTCTGAA 58.118 47.619 0.00 0.00 0.00 3.02
2684 4062 6.998673 TCTCTGAAGTCTGAACATATCCGATA 59.001 38.462 0.00 0.00 0.00 2.92
2726 4105 1.617740 GCAAAGCGCAACAATAGTCC 58.382 50.000 11.47 0.00 41.79 3.85
2768 4147 5.933463 GGAGAGGAGAAATGATAATCTGCAG 59.067 44.000 7.63 7.63 36.58 4.41
2898 4316 0.098728 CTTAATTGACAAGGCGCGGG 59.901 55.000 8.83 0.00 0.00 6.13
2903 4321 2.102109 TTGACAAGGCGCGGGAGTTA 62.102 55.000 8.83 0.00 0.00 2.24
2905 4323 2.264794 CAAGGCGCGGGAGTTAGT 59.735 61.111 8.83 0.00 0.00 2.24
2907 4325 0.108520 CAAGGCGCGGGAGTTAGTAA 60.109 55.000 8.83 0.00 0.00 2.24
2912 4330 1.863219 GCGCGGGAGTTAGTAACTAGC 60.863 57.143 15.52 17.99 43.03 3.42
2920 4338 4.650131 GGAGTTAGTAACTAGCCCATCAGT 59.350 45.833 15.52 0.00 43.03 3.41
2934 4352 3.634448 CCCATCAGTGTTCGAGTCTAGAT 59.366 47.826 0.00 0.00 0.00 1.98
2937 4355 4.601621 TCAGTGTTCGAGTCTAGATTCG 57.398 45.455 26.56 26.56 41.13 3.34
2946 4364 3.064134 CGAGTCTAGATTCGAGTGCTTGA 59.936 47.826 27.98 0.00 42.14 3.02
2961 4379 3.746492 GTGCTTGATACTCGTGGAGTTTT 59.254 43.478 3.32 0.00 40.28 2.43
2963 4381 3.994392 GCTTGATACTCGTGGAGTTTTCA 59.006 43.478 3.32 5.50 40.28 2.69
2964 4382 4.631813 GCTTGATACTCGTGGAGTTTTCAT 59.368 41.667 3.32 0.00 40.28 2.57
2965 4383 5.220491 GCTTGATACTCGTGGAGTTTTCATC 60.220 44.000 3.32 2.07 40.28 2.92
2966 4384 5.661056 TGATACTCGTGGAGTTTTCATCT 57.339 39.130 3.32 0.00 40.28 2.90
2967 4385 6.769134 TGATACTCGTGGAGTTTTCATCTA 57.231 37.500 3.32 0.00 40.28 1.98
2970 4388 8.568794 TGATACTCGTGGAGTTTTCATCTATAG 58.431 37.037 3.32 0.00 40.28 1.31
2975 4393 9.319143 CTCGTGGAGTTTTCATCTATAGAAAAT 57.681 33.333 6.52 0.00 44.10 1.82
2976 4394 9.098355 TCGTGGAGTTTTCATCTATAGAAAATG 57.902 33.333 6.52 0.84 44.10 2.32
2983 4401 9.638239 GTTTTCATCTATAGAAAATGCCAACAA 57.362 29.630 6.52 0.00 44.10 2.83
3003 4421 0.746923 GCTAGTTTAGCCCGGGTTGG 60.747 60.000 24.63 5.23 45.95 3.77
3004 4422 0.616891 CTAGTTTAGCCCGGGTTGGT 59.383 55.000 24.63 7.21 35.15 3.67
3006 4424 1.131928 AGTTTAGCCCGGGTTGGTCT 61.132 55.000 24.63 12.87 35.15 3.85
3007 4425 0.675837 GTTTAGCCCGGGTTGGTCTC 60.676 60.000 24.63 2.54 35.15 3.36
3023 4960 3.498397 TGGTCTCGTTGAAAGAAATGCTC 59.502 43.478 0.00 0.00 0.00 4.26
3036 4973 0.322546 AATGCTCCCGAACTCCAACC 60.323 55.000 0.00 0.00 0.00 3.77
3037 4974 1.201429 ATGCTCCCGAACTCCAACCT 61.201 55.000 0.00 0.00 0.00 3.50
3074 5011 2.669781 CCATTATTGCCACATGAGGGT 58.330 47.619 11.42 0.00 0.00 4.34
3088 5025 6.306199 CACATGAGGGTCCAAATAATCCATA 58.694 40.000 0.00 0.00 0.00 2.74
3105 5042 4.104086 TCCATAGAGTTCAAGGTGTCCAT 58.896 43.478 0.00 0.00 0.00 3.41
3116 5053 7.724061 AGTTCAAGGTGTCCATAACAAATAAGT 59.276 33.333 0.00 0.00 40.31 2.24
3122 5059 9.396022 AGGTGTCCATAACAAATAAGTAATCTG 57.604 33.333 0.00 0.00 40.31 2.90
3146 5083 1.872952 CAACCTCGACTGAATTGCACA 59.127 47.619 0.00 0.00 0.00 4.57
3150 5087 2.743664 CCTCGACTGAATTGCACAATGA 59.256 45.455 0.00 0.00 0.00 2.57
3195 5132 9.617523 TGAGATGTATAAATGTGAACATGTCAT 57.382 29.630 0.00 0.00 43.52 3.06
3247 5191 5.122396 TGCCCAAAACAAACAACATACAAAC 59.878 36.000 0.00 0.00 0.00 2.93
3259 5203 4.098914 ACATACAAACAGGCCTCAAGAA 57.901 40.909 0.00 0.00 0.00 2.52
3262 5206 1.215423 ACAAACAGGCCTCAAGAACCT 59.785 47.619 0.00 0.00 0.00 3.50
3265 5209 1.763770 CAGGCCTCAAGAACCTGGT 59.236 57.895 0.00 0.00 45.97 4.00
3268 5212 0.402121 GGCCTCAAGAACCTGGTCTT 59.598 55.000 0.00 2.74 38.41 3.01
3289 5233 5.888724 TCTTGTTGATTTTGGTTGTGACCTA 59.111 36.000 0.00 0.00 46.66 3.08
3297 5241 3.815856 TGGTTGTGACCTAACACGTTA 57.184 42.857 0.00 0.00 46.66 3.18
3404 5349 7.411486 TTCCACAAAAACTTCATAAGAACCA 57.589 32.000 0.00 0.00 0.00 3.67
3420 5365 9.985730 CATAAGAACCAATAATATGTTTGGCAT 57.014 29.630 14.08 6.30 45.13 4.40
3462 5407 9.862371 AATATATCACTGCGAGAGTAATAAAGG 57.138 33.333 0.00 0.00 31.73 3.11
3464 5409 2.866762 CACTGCGAGAGTAATAAAGGCC 59.133 50.000 0.00 0.00 31.73 5.19
3487 5433 3.073798 TGTGTGAGTGTATGGGGTCATTT 59.926 43.478 0.00 0.00 34.96 2.32
3509 5455 4.394729 TGTCCCTACTTGCCTTGTTAAAG 58.605 43.478 0.00 0.00 0.00 1.85
3510 5456 4.103469 TGTCCCTACTTGCCTTGTTAAAGA 59.897 41.667 0.00 0.00 35.19 2.52
3511 5457 4.695928 GTCCCTACTTGCCTTGTTAAAGAG 59.304 45.833 0.00 0.00 35.19 2.85
3512 5458 4.595781 TCCCTACTTGCCTTGTTAAAGAGA 59.404 41.667 0.00 0.00 35.19 3.10
3513 5459 4.695928 CCCTACTTGCCTTGTTAAAGAGAC 59.304 45.833 0.00 0.00 35.19 3.36
3514 5460 4.695928 CCTACTTGCCTTGTTAAAGAGACC 59.304 45.833 0.00 0.00 35.19 3.85
3515 5461 4.439253 ACTTGCCTTGTTAAAGAGACCT 57.561 40.909 0.00 0.00 35.19 3.85
3516 5462 4.793201 ACTTGCCTTGTTAAAGAGACCTT 58.207 39.130 0.00 0.00 35.19 3.50
3517 5463 5.201243 ACTTGCCTTGTTAAAGAGACCTTT 58.799 37.500 0.00 0.00 44.26 3.11
3518 5464 5.656859 ACTTGCCTTGTTAAAGAGACCTTTT 59.343 36.000 0.00 0.00 42.26 2.27
3519 5465 6.831868 ACTTGCCTTGTTAAAGAGACCTTTTA 59.168 34.615 0.00 0.00 42.26 1.52
3520 5466 7.505923 ACTTGCCTTGTTAAAGAGACCTTTTAT 59.494 33.333 0.00 0.00 42.26 1.40
3521 5467 7.214467 TGCCTTGTTAAAGAGACCTTTTATG 57.786 36.000 0.00 0.00 42.26 1.90
3522 5468 6.208599 TGCCTTGTTAAAGAGACCTTTTATGG 59.791 38.462 0.00 0.00 42.26 2.74
3523 5469 6.208797 GCCTTGTTAAAGAGACCTTTTATGGT 59.791 38.462 0.00 0.00 42.26 3.55
3524 5470 7.255836 GCCTTGTTAAAGAGACCTTTTATGGTT 60.256 37.037 0.00 0.00 42.26 3.67
3525 5471 8.082242 CCTTGTTAAAGAGACCTTTTATGGTTG 58.918 37.037 0.00 0.00 42.26 3.77
3526 5472 8.528044 TTGTTAAAGAGACCTTTTATGGTTGT 57.472 30.769 0.00 0.00 42.26 3.32
3527 5473 9.629878 TTGTTAAAGAGACCTTTTATGGTTGTA 57.370 29.630 0.00 0.00 42.26 2.41
3528 5474 9.629878 TGTTAAAGAGACCTTTTATGGTTGTAA 57.370 29.630 0.00 0.00 42.26 2.41
3531 5477 7.703058 AAGAGACCTTTTATGGTTGTAATGG 57.297 36.000 0.00 0.00 41.00 3.16
3532 5478 6.187682 AGAGACCTTTTATGGTTGTAATGGG 58.812 40.000 0.00 0.00 41.00 4.00
3533 5479 6.011981 AGAGACCTTTTATGGTTGTAATGGGA 60.012 38.462 0.00 0.00 41.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.457831 GTCTCCCTACATCCGCCCT 60.458 63.158 0.00 0.00 0.00 5.19
1 2 2.857744 CGTCTCCCTACATCCGCCC 61.858 68.421 0.00 0.00 0.00 6.13
2 3 2.728817 CGTCTCCCTACATCCGCC 59.271 66.667 0.00 0.00 0.00 6.13
3 4 2.728817 CCGTCTCCCTACATCCGC 59.271 66.667 0.00 0.00 0.00 5.54
5 6 1.453762 CGTCCCGTCTCCCTACATCC 61.454 65.000 0.00 0.00 0.00 3.51
6 7 2.031360 CGTCCCGTCTCCCTACATC 58.969 63.158 0.00 0.00 0.00 3.06
7 8 2.125961 GCGTCCCGTCTCCCTACAT 61.126 63.158 0.00 0.00 0.00 2.29
8 9 2.753043 GCGTCCCGTCTCCCTACA 60.753 66.667 0.00 0.00 0.00 2.74
9 10 3.885521 CGCGTCCCGTCTCCCTAC 61.886 72.222 0.00 0.00 0.00 3.18
25 26 1.852067 CTTTTCCTGCCAACCGACCG 61.852 60.000 0.00 0.00 0.00 4.79
26 27 1.524008 CCTTTTCCTGCCAACCGACC 61.524 60.000 0.00 0.00 0.00 4.79
27 28 0.536460 TCCTTTTCCTGCCAACCGAC 60.536 55.000 0.00 0.00 0.00 4.79
28 29 0.183971 TTCCTTTTCCTGCCAACCGA 59.816 50.000 0.00 0.00 0.00 4.69
29 30 1.000274 CTTTCCTTTTCCTGCCAACCG 60.000 52.381 0.00 0.00 0.00 4.44
30 31 1.270305 GCTTTCCTTTTCCTGCCAACC 60.270 52.381 0.00 0.00 0.00 3.77
31 32 1.688735 AGCTTTCCTTTTCCTGCCAAC 59.311 47.619 0.00 0.00 0.00 3.77
32 33 2.086610 AGCTTTCCTTTTCCTGCCAA 57.913 45.000 0.00 0.00 0.00 4.52
33 34 2.514803 GTAGCTTTCCTTTTCCTGCCA 58.485 47.619 0.00 0.00 0.00 4.92
34 35 1.468914 CGTAGCTTTCCTTTTCCTGCC 59.531 52.381 0.00 0.00 0.00 4.85
35 36 2.902065 CGTAGCTTTCCTTTTCCTGC 57.098 50.000 0.00 0.00 0.00 4.85
52 53 9.853555 TTTTCTTATATTGATGTGATTTTGCGT 57.146 25.926 0.00 0.00 0.00 5.24
259 261 9.971922 CCTTATATTGATGTGATTTTCCCTTTC 57.028 33.333 0.00 0.00 0.00 2.62
405 409 2.154462 CCTGTCTTTTCGCTTCACCAT 58.846 47.619 0.00 0.00 0.00 3.55
438 442 8.664211 TGGTTTTATTTCGCTGGTTTTATTTT 57.336 26.923 0.00 0.00 0.00 1.82
526 530 3.127895 CACCAAGACAGACGAACCAAAAA 59.872 43.478 0.00 0.00 0.00 1.94
618 624 1.068588 TCACGCTAAGCCGCATAGAAT 59.931 47.619 6.82 0.00 0.00 2.40
652 658 3.338126 GATCGAGTCCCGCACACGT 62.338 63.158 0.00 0.00 39.80 4.49
675 681 3.183754 CCGCGAAAAACCAAGAAAAACT 58.816 40.909 8.23 0.00 0.00 2.66
740 746 0.615544 TCGTCCCACCTTATCCGGTT 60.616 55.000 0.00 0.00 34.29 4.44
746 752 5.419788 GGGTTTTATTTTCGTCCCACCTTAT 59.580 40.000 0.00 0.00 35.43 1.73
748 754 3.575256 GGGTTTTATTTTCGTCCCACCTT 59.425 43.478 0.00 0.00 35.43 3.50
777 783 4.466370 CCTAATGTCTCAGTTGGTAGGTCA 59.534 45.833 0.00 0.00 0.00 4.02
839 846 3.734231 TCAACGTGTCTTCGTCTGATTTC 59.266 43.478 0.00 0.00 43.38 2.17
848 855 2.055838 TCCGATTTCAACGTGTCTTCG 58.944 47.619 0.00 0.00 0.00 3.79
923 930 2.356913 TGTCTGCTTGCGCGCTTA 60.357 55.556 33.29 18.99 39.65 3.09
966 974 2.346766 TCTGGCATGACCGCATAAAT 57.653 45.000 0.00 0.00 43.94 1.40
967 975 2.016318 CTTCTGGCATGACCGCATAAA 58.984 47.619 0.00 0.00 43.94 1.40
977 985 1.339824 ACAGCTTCCTCTTCTGGCATG 60.340 52.381 0.00 0.00 32.42 4.06
999 1007 1.683011 CCCGATCTGTTCCTTGGCATT 60.683 52.381 0.00 0.00 0.00 3.56
1528 1539 1.006832 CGCATAAGGGAAGACAACCG 58.993 55.000 0.00 0.00 0.00 4.44
1538 1549 1.648720 CACGCATTCCGCATAAGGG 59.351 57.895 0.00 0.00 42.60 3.95
1607 1618 2.359354 GTATGGTGCACGGCCACA 60.359 61.111 11.45 2.65 39.03 4.17
1680 1691 2.112297 GCCAACCTCAACACCGGA 59.888 61.111 9.46 0.00 0.00 5.14
1764 1775 2.042831 GCAAGAACAGCCTGGCGAT 61.043 57.895 13.96 1.97 0.00 4.58
1805 1816 3.011119 ACAAACTGCGTTGTTCACCTTA 58.989 40.909 0.00 0.00 38.60 2.69
1807 1818 1.459450 ACAAACTGCGTTGTTCACCT 58.541 45.000 0.00 0.00 38.60 4.00
1813 1824 1.063488 GGCGAACAAACTGCGTTGT 59.937 52.632 0.00 0.00 43.58 3.32
1815 1826 0.171455 TTTGGCGAACAAACTGCGTT 59.829 45.000 2.13 0.00 43.81 4.84
1816 1827 0.248458 CTTTGGCGAACAAACTGCGT 60.248 50.000 2.13 0.00 43.81 5.24
1817 1828 1.539776 GCTTTGGCGAACAAACTGCG 61.540 55.000 2.13 0.00 43.81 5.18
1857 1888 0.532862 CTGCGGTTGGTTCAGTGACT 60.533 55.000 0.00 0.00 0.00 3.41
1863 1894 1.956043 GCAATCTGCGGTTGGTTCA 59.044 52.632 9.08 0.00 31.71 3.18
1885 1916 4.101448 AGCGCGGGATCTTGCCTT 62.101 61.111 8.83 0.00 0.00 4.35
2575 2612 7.080353 TGCAAGATCATTCAACATAGAACAG 57.920 36.000 0.00 0.00 0.00 3.16
2576 2613 7.451501 TTGCAAGATCATTCAACATAGAACA 57.548 32.000 0.00 0.00 0.00 3.18
2577 2614 8.922058 ATTTGCAAGATCATTCAACATAGAAC 57.078 30.769 0.00 0.00 0.00 3.01
2596 2633 8.219546 TCACCTGAAATTATCGATTATTTGCA 57.780 30.769 23.01 18.26 0.00 4.08
2611 2648 2.108952 AGGCCAAGTCTTCACCTGAAAT 59.891 45.455 5.01 0.00 33.07 2.17
2667 4045 6.455647 TGTTCCATATCGGATATGTTCAGAC 58.544 40.000 27.56 19.70 45.80 3.51
2668 4046 6.664428 TGTTCCATATCGGATATGTTCAGA 57.336 37.500 27.56 18.40 45.80 3.27
2669 4047 7.728847 TTTGTTCCATATCGGATATGTTCAG 57.271 36.000 27.56 16.87 45.80 3.02
2670 4048 7.936301 TCATTTGTTCCATATCGGATATGTTCA 59.064 33.333 27.56 21.21 45.80 3.18
2671 4049 8.322906 TCATTTGTTCCATATCGGATATGTTC 57.677 34.615 27.56 19.57 45.80 3.18
2672 4050 8.868522 ATCATTTGTTCCATATCGGATATGTT 57.131 30.769 27.56 1.18 45.80 2.71
2673 4051 9.958180 TTATCATTTGTTCCATATCGGATATGT 57.042 29.630 27.56 13.44 45.80 2.29
2684 4062 2.421775 TGCGCGTTATCATTTGTTCCAT 59.578 40.909 8.43 0.00 0.00 3.41
2695 4073 2.208427 GCTTTGCGTGCGCGTTATC 61.208 57.895 22.18 4.69 45.51 1.75
2740 4119 7.447853 GCAGATTATCATTTCTCCTCTCCAAAT 59.552 37.037 0.00 0.00 0.00 2.32
2744 4123 5.862845 TGCAGATTATCATTTCTCCTCTCC 58.137 41.667 0.00 0.00 0.00 3.71
2745 4124 6.523840 ACTGCAGATTATCATTTCTCCTCTC 58.476 40.000 23.35 0.00 0.00 3.20
2747 4126 6.017275 CCAACTGCAGATTATCATTTCTCCTC 60.017 42.308 23.35 0.00 0.00 3.71
2748 4127 5.826737 CCAACTGCAGATTATCATTTCTCCT 59.173 40.000 23.35 0.00 0.00 3.69
2757 4136 6.203723 GGTGATTCTACCAACTGCAGATTATC 59.796 42.308 23.35 11.05 40.54 1.75
2768 4147 2.271800 CGAGCAGGTGATTCTACCAAC 58.728 52.381 0.00 0.00 43.37 3.77
2879 4297 0.098728 CCCGCGCCTTGTCAATTAAG 59.901 55.000 0.00 0.00 0.00 1.85
2881 4299 0.742990 CTCCCGCGCCTTGTCAATTA 60.743 55.000 0.00 0.00 0.00 1.40
2887 4305 1.252904 TACTAACTCCCGCGCCTTGT 61.253 55.000 0.00 0.00 0.00 3.16
2889 4307 0.108472 GTTACTAACTCCCGCGCCTT 60.108 55.000 0.00 0.00 0.00 4.35
2891 4309 0.740737 TAGTTACTAACTCCCGCGCC 59.259 55.000 0.00 0.00 41.77 6.53
2892 4310 1.863219 GCTAGTTACTAACTCCCGCGC 60.863 57.143 0.00 0.00 41.77 6.86
2898 4316 5.127356 ACACTGATGGGCTAGTTACTAACTC 59.873 44.000 4.65 0.00 41.77 3.01
2903 4321 3.119101 CGAACACTGATGGGCTAGTTACT 60.119 47.826 0.00 0.00 0.00 2.24
2905 4323 3.093814 TCGAACACTGATGGGCTAGTTA 58.906 45.455 0.00 0.00 0.00 2.24
2907 4325 1.478510 CTCGAACACTGATGGGCTAGT 59.521 52.381 0.00 0.00 0.00 2.57
2912 4330 3.017442 TCTAGACTCGAACACTGATGGG 58.983 50.000 0.00 0.00 0.00 4.00
2920 4338 3.181509 GCACTCGAATCTAGACTCGAACA 60.182 47.826 24.60 5.62 43.03 3.18
2937 4355 2.164624 ACTCCACGAGTATCAAGCACTC 59.835 50.000 0.00 0.00 41.51 3.51
2939 4357 2.656560 ACTCCACGAGTATCAAGCAC 57.343 50.000 0.00 0.00 41.51 4.40
2940 4358 3.678056 AAACTCCACGAGTATCAAGCA 57.322 42.857 0.00 0.00 42.59 3.91
2941 4359 3.994392 TGAAAACTCCACGAGTATCAAGC 59.006 43.478 7.40 0.00 42.59 4.01
2946 4364 8.693120 TCTATAGATGAAAACTCCACGAGTAT 57.307 34.615 0.00 0.00 42.59 2.12
2952 4370 8.131731 GGCATTTTCTATAGATGAAAACTCCAC 58.868 37.037 2.58 0.00 43.34 4.02
2955 4373 9.508567 GTTGGCATTTTCTATAGATGAAAACTC 57.491 33.333 2.58 0.00 43.34 3.01
2961 4379 6.830324 AGCTTGTTGGCATTTTCTATAGATGA 59.170 34.615 2.58 0.00 34.17 2.92
2963 4381 7.995488 ACTAGCTTGTTGGCATTTTCTATAGAT 59.005 33.333 2.58 0.00 34.17 1.98
2964 4382 7.338710 ACTAGCTTGTTGGCATTTTCTATAGA 58.661 34.615 0.00 0.00 34.17 1.98
2965 4383 7.559590 ACTAGCTTGTTGGCATTTTCTATAG 57.440 36.000 0.00 0.00 34.17 1.31
2966 4384 7.938140 AACTAGCTTGTTGGCATTTTCTATA 57.062 32.000 12.87 0.00 34.17 1.31
2967 4385 6.840780 AACTAGCTTGTTGGCATTTTCTAT 57.159 33.333 12.87 0.00 34.17 1.98
2970 4388 6.934561 CTAAACTAGCTTGTTGGCATTTTC 57.065 37.500 14.32 0.00 34.17 2.29
2996 4414 0.865769 CTTTCAACGAGACCAACCCG 59.134 55.000 0.00 0.00 0.00 5.28
3003 4421 3.120165 GGGAGCATTTCTTTCAACGAGAC 60.120 47.826 0.00 0.00 0.00 3.36
3004 4422 3.074412 GGGAGCATTTCTTTCAACGAGA 58.926 45.455 0.00 0.00 0.00 4.04
3006 4424 1.804151 CGGGAGCATTTCTTTCAACGA 59.196 47.619 0.00 0.00 0.00 3.85
3007 4425 1.804151 TCGGGAGCATTTCTTTCAACG 59.196 47.619 0.00 0.00 0.00 4.10
3023 4960 1.346722 ACAACTAGGTTGGAGTTCGGG 59.653 52.381 13.75 0.00 46.50 5.14
3036 4973 8.810427 CAATAATGGCTAATTGCAAACAACTAG 58.190 33.333 1.71 1.18 45.15 2.57
3037 4974 8.700722 CAATAATGGCTAATTGCAAACAACTA 57.299 30.769 1.71 0.00 45.15 2.24
3074 5011 7.775093 CACCTTGAACTCTATGGATTATTTGGA 59.225 37.037 0.00 0.00 0.00 3.53
3088 5025 4.974645 TGTTATGGACACCTTGAACTCT 57.025 40.909 0.00 0.00 32.00 3.24
3116 5053 5.914898 TCAGTCGAGGTTGAATCAGATTA 57.085 39.130 0.00 0.00 0.00 1.75
3122 5059 3.436704 TGCAATTCAGTCGAGGTTGAATC 59.563 43.478 15.88 8.55 41.76 2.52
3168 5105 9.447157 TGACATGTTCACATTTATACATCTCAA 57.553 29.630 0.00 0.00 33.61 3.02
3183 5120 9.248291 ACACAAAGAAAATAATGACATGTTCAC 57.752 29.630 0.00 0.00 36.92 3.18
3202 5139 5.630680 GGCATGTTTTCATCTACACACAAAG 59.369 40.000 0.00 0.00 38.64 2.77
3215 5159 4.326826 TGTTTGTTTTGGGCATGTTTTCA 58.673 34.783 0.00 0.00 0.00 2.69
3247 5191 0.322008 GACCAGGTTCTTGAGGCCTG 60.322 60.000 12.00 0.00 46.83 4.85
3259 5203 3.642141 ACCAAAATCAACAAGACCAGGT 58.358 40.909 0.00 0.00 0.00 4.00
3262 5206 4.464244 TCACAACCAAAATCAACAAGACCA 59.536 37.500 0.00 0.00 0.00 4.02
3265 5209 5.004922 GGTCACAACCAAAATCAACAAGA 57.995 39.130 0.00 0.00 45.68 3.02
3297 5241 7.276218 TCGTCAGATAAAATCGATAAAACGGTT 59.724 33.333 0.00 0.00 38.26 4.44
3357 5302 1.531423 ACTGCAGCTCAACCATCAAG 58.469 50.000 15.27 0.00 0.00 3.02
3420 5365 8.040727 AGTGATATATTCAATGCGGCTATAACA 58.959 33.333 0.00 0.00 35.70 2.41
3460 5405 0.615331 CCATACACTCACACAGGCCT 59.385 55.000 0.00 0.00 0.00 5.19
3462 5407 0.392998 CCCCATACACTCACACAGGC 60.393 60.000 0.00 0.00 0.00 4.85
3464 5409 1.623311 TGACCCCATACACTCACACAG 59.377 52.381 0.00 0.00 0.00 3.66
3487 5433 4.103469 TCTTTAACAAGGCAAGTAGGGACA 59.897 41.667 0.00 0.00 0.00 4.02
3509 5455 6.184789 TCCCATTACAACCATAAAAGGTCTC 58.815 40.000 0.00 0.00 42.25 3.36
3510 5456 6.147437 TCCCATTACAACCATAAAAGGTCT 57.853 37.500 0.00 0.00 42.25 3.85


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

AutoCloner maintained by Alex Coulton.