Multiple sequence alignment - TraesCS1A01G102800

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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 TraesCS1A01G102800 chr1A 100.000 2768 0 0 1 2768 99070111 99072878 0.000000e+00 5112.0
1 TraesCS1A01G102800 chr1A 82.902 772 106 19 1006 1768 99234405 99235159 0.000000e+00 671.0
2 TraesCS1A01G102800 chr1A 81.795 791 125 12 980 1766 99048754 99049529 0.000000e+00 645.0
3 TraesCS1A01G102800 chr1A 85.124 484 66 4 1292 1772 99018898 99019378 8.910000e-135 490.0
4 TraesCS1A01G102800 chr1A 93.885 278 10 2 53 330 522241941 522241671 1.980000e-111 412.0
5 TraesCS1A01G102800 chr1A 88.050 318 26 8 923 1234 99018548 99018859 1.570000e-97 366.0
6 TraesCS1A01G102800 chr1A 93.836 146 6 2 577 719 522240192 522240047 1.670000e-52 217.0
7 TraesCS1A01G102800 chr1A 87.578 161 15 5 404 560 522240429 522240270 6.090000e-42 182.0
8 TraesCS1A01G102800 chr1A 100.000 81 0 0 2688 2768 438595234 438595314 1.720000e-32 150.0
9 TraesCS1A01G102800 chr1A 96.667 90 1 1 2681 2768 129523478 129523389 6.180000e-32 148.0
10 TraesCS1A01G102800 chr1A 98.750 80 1 0 2689 2768 458423241 458423162 2.870000e-30 143.0
11 TraesCS1A01G102800 chr1A 92.647 68 3 1 334 399 522241619 522241552 2.270000e-16 97.1
12 TraesCS1A01G102800 chr1A 100.000 30 0 0 718 747 522240008 522239979 3.850000e-04 56.5
13 TraesCS1A01G102800 chr1D 93.770 1573 57 20 745 2312 80540749 80542285 0.000000e+00 2324.0
14 TraesCS1A01G102800 chr1D 82.536 773 108 19 1006 1768 80817021 80817776 0.000000e+00 654.0
15 TraesCS1A01G102800 chr1D 94.444 342 19 0 2348 2689 80542286 80542627 6.790000e-146 527.0
16 TraesCS1A01G102800 chr1D 85.331 484 71 0 1292 1775 80537403 80537886 4.120000e-138 501.0
17 TraesCS1A01G102800 chr1D 84.440 482 73 2 1292 1772 80448594 80449074 8.970000e-130 473.0
18 TraesCS1A01G102800 chr1D 88.660 291 27 5 949 1234 80448266 80448555 1.580000e-92 350.0
19 TraesCS1A01G102800 chr1D 90.476 252 20 2 980 1230 80537068 80537316 2.060000e-86 329.0
20 TraesCS1A01G102800 chr1D 92.500 40 2 1 2556 2595 267337927 267337889 3.850000e-04 56.5
21 TraesCS1A01G102800 chr1B 96.067 890 32 1 967 1856 133075644 133076530 0.000000e+00 1447.0
22 TraesCS1A01G102800 chr1B 88.576 639 71 2 2053 2689 133099679 133100317 0.000000e+00 774.0
23 TraesCS1A01G102800 chr1B 83.141 866 118 18 923 1772 132938166 132939019 0.000000e+00 765.0
24 TraesCS1A01G102800 chr1B 82.875 800 114 14 980 1775 133032471 133033251 0.000000e+00 697.0
25 TraesCS1A01G102800 chr1B 91.089 202 9 3 745 938 133075446 133075646 5.880000e-67 265.0
26 TraesCS1A01G102800 chr1B 88.785 214 14 6 1856 2068 133079017 133079221 1.270000e-63 254.0
27 TraesCS1A01G102800 chr7B 82.428 865 109 32 923 1768 95337200 95338040 0.000000e+00 715.0
28 TraesCS1A01G102800 chr7B 86.093 151 12 5 577 719 84454449 84454300 1.330000e-33 154.0
29 TraesCS1A01G102800 chr7D 95.114 307 14 1 21 327 47215577 47215882 1.490000e-132 483.0
30 TraesCS1A01G102800 chr7D 82.812 256 30 8 334 578 47215936 47216188 1.670000e-52 217.0
31 TraesCS1A01G102800 chr7D 92.517 147 6 4 577 719 47216229 47216374 3.610000e-49 206.0
32 TraesCS1A01G102800 chr7D 84.286 70 10 1 2307 2376 4870612 4870680 1.780000e-07 67.6
33 TraesCS1A01G102800 chr5B 92.565 269 17 2 61 328 488851022 488850756 1.560000e-102 383.0
34 TraesCS1A01G102800 chr5B 90.672 268 24 1 61 328 656724584 656724850 3.390000e-94 355.0
35 TraesCS1A01G102800 chr5B 92.121 165 13 0 166 330 17797755 17797591 1.660000e-57 233.0
36 TraesCS1A01G102800 chr5B 94.483 145 6 1 577 719 488850420 488850276 3.590000e-54 222.0
37 TraesCS1A01G102800 chr5B 93.333 150 9 1 21 170 17810079 17809931 1.290000e-53 220.0
38 TraesCS1A01G102800 chr5B 89.041 146 12 3 577 719 17797246 17797102 7.880000e-41 178.0
39 TraesCS1A01G102800 chr5B 88.079 151 9 5 577 718 656725191 656725341 1.320000e-38 171.0
40 TraesCS1A01G102800 chr5B 91.667 96 7 1 2212 2307 622382718 622382624 6.220000e-27 132.0
41 TraesCS1A01G102800 chr5B 90.722 97 7 2 2213 2308 314297469 314297374 8.050000e-26 128.0
42 TraesCS1A01G102800 chr5B 100.000 28 0 0 718 745 488850237 488850210 5.000000e-03 52.8
43 TraesCS1A01G102800 chr3A 88.387 310 8 5 21 330 655651238 655651519 5.670000e-92 348.0
44 TraesCS1A01G102800 chr3A 88.800 250 19 7 334 578 655651569 655651814 5.800000e-77 298.0
45 TraesCS1A01G102800 chr3A 93.878 147 4 4 577 719 655661603 655661748 1.670000e-52 217.0
46 TraesCS1A01G102800 chr3A 93.197 147 5 4 577 719 655651855 655652000 7.770000e-51 211.0
47 TraesCS1A01G102800 chr3A 88.571 175 14 5 406 578 655661392 655661562 1.000000e-49 207.0
48 TraesCS1A01G102800 chr3A 84.286 70 10 1 2312 2381 12523679 12523611 1.780000e-07 67.6
49 TraesCS1A01G102800 chr3A 100.000 28 0 0 718 745 655661787 655661814 5.000000e-03 52.8
50 TraesCS1A01G102800 chr4A 94.000 100 6 0 577 676 708429835 708429934 4.770000e-33 152.0
51 TraesCS1A01G102800 chr4A 95.604 91 2 1 2680 2768 4396284 4396194 7.990000e-31 145.0
52 TraesCS1A01G102800 chr4A 95.556 90 2 2 2681 2768 165929997 165930086 2.870000e-30 143.0
53 TraesCS1A01G102800 chr4A 90.654 107 6 4 2665 2768 154560899 154561004 3.720000e-29 139.0
54 TraesCS1A01G102800 chr4A 87.324 71 7 2 2312 2381 32466884 32466953 2.290000e-11 80.5
55 TraesCS1A01G102800 chr6A 97.701 87 0 1 2684 2768 457458684 457458770 6.180000e-32 148.0
56 TraesCS1A01G102800 chr6A 94.565 92 4 1 2678 2768 364159946 364160037 1.030000e-29 141.0
57 TraesCS1A01G102800 chr7A 95.556 90 2 1 2681 2768 616586133 616586222 2.870000e-30 143.0
58 TraesCS1A01G102800 chr7A 90.625 96 7 2 2214 2308 628392850 628392944 2.890000e-25 126.0
59 TraesCS1A01G102800 chr6B 96.341 82 3 0 131 212 72380799 72380718 4.810000e-28 135.0
60 TraesCS1A01G102800 chr6B 89.655 58 6 0 2324 2381 114081229 114081172 1.060000e-09 75.0
61 TraesCS1A01G102800 chr6B 84.722 72 11 0 2310 2381 671226064 671225993 3.820000e-09 73.1
62 TraesCS1A01G102800 chr4D 91.667 96 6 2 2214 2308 9306374 9306280 6.220000e-27 132.0
63 TraesCS1A01G102800 chr4D 100.000 29 0 0 2567 2595 482161638 482161610 1.000000e-03 54.7
64 TraesCS1A01G102800 chr4B 94.253 87 4 1 2222 2308 86649500 86649585 6.220000e-27 132.0
65 TraesCS1A01G102800 chr4B 100.000 29 0 0 2567 2595 112038199 112038227 1.000000e-03 54.7
66 TraesCS1A01G102800 chr4B 100.000 29 0 0 2567 2595 611856058 611856030 1.000000e-03 54.7
67 TraesCS1A01G102800 chr6D 91.209 91 7 1 2218 2308 348087605 348087694 3.740000e-24 122.0
68 TraesCS1A01G102800 chr6D 95.161 62 3 0 151 212 35001063 35001002 6.310000e-17 99.0
69 TraesCS1A01G102800 chr5A 89.583 96 8 2 2214 2308 83023085 83022991 1.350000e-23 121.0
70 TraesCS1A01G102800 chr5A 100.000 31 0 0 2565 2595 660440733 660440763 1.070000e-04 58.4
71 TraesCS1A01G102800 chr3B 90.278 72 7 0 2310 2381 679271502 679271431 8.160000e-16 95.3
72 TraesCS1A01G102800 chr2A 87.671 73 8 1 2379 2450 29649416 29649488 1.770000e-12 84.2
73 TraesCS1A01G102800 chr2D 90.476 42 4 0 2340 2381 398784053 398784094 3.850000e-04 56.5
74 TraesCS1A01G102800 chr5D 100.000 29 0 0 2567 2595 42084188 42084216 1.000000e-03 54.7
75 TraesCS1A01G102800 chr3D 100.000 29 0 0 2567 2595 84483849 84483877 1.000000e-03 54.7


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 TraesCS1A01G102800 chr1A 99070111 99072878 2767 False 5112.000000 5112 100.000000 1 2768 1 chr1A.!!$F2 2767
1 TraesCS1A01G102800 chr1A 99234405 99235159 754 False 671.000000 671 82.902000 1006 1768 1 chr1A.!!$F3 762
2 TraesCS1A01G102800 chr1A 99048754 99049529 775 False 645.000000 645 81.795000 980 1766 1 chr1A.!!$F1 786
3 TraesCS1A01G102800 chr1A 99018548 99019378 830 False 428.000000 490 86.587000 923 1772 2 chr1A.!!$F5 849
4 TraesCS1A01G102800 chr1D 80537068 80542627 5559 False 920.250000 2324 91.005250 745 2689 4 chr1D.!!$F3 1944
5 TraesCS1A01G102800 chr1D 80817021 80817776 755 False 654.000000 654 82.536000 1006 1768 1 chr1D.!!$F1 762
6 TraesCS1A01G102800 chr1D 80448266 80449074 808 False 411.500000 473 86.550000 949 1772 2 chr1D.!!$F2 823
7 TraesCS1A01G102800 chr1B 133099679 133100317 638 False 774.000000 774 88.576000 2053 2689 1 chr1B.!!$F3 636
8 TraesCS1A01G102800 chr1B 132938166 132939019 853 False 765.000000 765 83.141000 923 1772 1 chr1B.!!$F1 849
9 TraesCS1A01G102800 chr1B 133032471 133033251 780 False 697.000000 697 82.875000 980 1775 1 chr1B.!!$F2 795
10 TraesCS1A01G102800 chr1B 133075446 133079221 3775 False 655.333333 1447 91.980333 745 2068 3 chr1B.!!$F4 1323
11 TraesCS1A01G102800 chr7B 95337200 95338040 840 False 715.000000 715 82.428000 923 1768 1 chr7B.!!$F1 845
12 TraesCS1A01G102800 chr7D 47215577 47216374 797 False 302.000000 483 90.147667 21 719 3 chr7D.!!$F2 698
13 TraesCS1A01G102800 chr5B 656724584 656725341 757 False 263.000000 355 89.375500 61 718 2 chr5B.!!$F1 657
14 TraesCS1A01G102800 chr5B 488850210 488851022 812 True 219.266667 383 95.682667 61 745 3 chr5B.!!$R5 684
15 TraesCS1A01G102800 chr5B 17797102 17797755 653 True 205.500000 233 90.581000 166 719 2 chr5B.!!$R4 553
16 TraesCS1A01G102800 chr3A 655651238 655652000 762 False 285.666667 348 90.128000 21 719 3 chr3A.!!$F1 698

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
823 3769 0.1078 CAGTGGGATCTGGACTGCAG 60.108 60.0 13.48 13.48 31.31 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 8079 0.036483 TCGTGTGTGCCTACATGCAT 60.036 50.0 0.0 0.0 44.3 3.96 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
29 30 6.319658 ACATGCATTTGTATCCGAGAAAAGAT 59.680 34.615 0.00 0.00 0.00 2.40
274 276 7.147567 ACCCTTGAATACATTTGGACAGTTTTT 60.148 33.333 0.00 0.00 0.00 1.94
331 333 9.701098 TTAAATATATAGCGAAAATGGTCGAGT 57.299 29.630 2.63 0.00 43.86 4.18
336 387 4.859629 AGCGAAAATGGTCGAGTATTTC 57.140 40.909 7.13 5.44 43.86 2.17
342 395 7.747357 GCGAAAATGGTCGAGTATTTCTTTTTA 59.253 33.333 7.13 0.00 43.86 1.52
366 421 5.237779 ACGAAGAAAAGCCTTTCGTTATTGA 59.762 36.000 5.75 0.00 44.83 2.57
503 567 2.552743 GCCAGTAGGTCAAGTTTGTTCC 59.447 50.000 0.00 0.00 37.19 3.62
570 643 6.273071 AGCATGTTCTTTTTACCAGTTTCAC 58.727 36.000 0.00 0.00 0.00 3.18
721 849 1.204704 CACTGTCTAGCACGAATCCCA 59.795 52.381 0.00 0.00 0.00 4.37
724 852 1.221414 GTCTAGCACGAATCCCATGC 58.779 55.000 0.00 0.00 39.74 4.06
725 853 0.829990 TCTAGCACGAATCCCATGCA 59.170 50.000 0.00 0.00 41.97 3.96
728 856 3.101209 CACGAATCCCATGCACGG 58.899 61.111 0.00 0.00 0.00 4.94
730 858 0.461163 CACGAATCCCATGCACGGTA 60.461 55.000 0.00 0.00 0.00 4.02
732 860 0.179084 CGAATCCCATGCACGGTAGT 60.179 55.000 0.00 0.00 0.00 2.73
733 861 1.742411 CGAATCCCATGCACGGTAGTT 60.742 52.381 0.00 0.00 0.00 2.24
734 862 2.482316 CGAATCCCATGCACGGTAGTTA 60.482 50.000 0.00 0.00 0.00 2.24
736 864 3.857157 ATCCCATGCACGGTAGTTAAT 57.143 42.857 0.00 0.00 0.00 1.40
737 865 3.188159 TCCCATGCACGGTAGTTAATC 57.812 47.619 0.00 0.00 0.00 1.75
738 866 2.158871 TCCCATGCACGGTAGTTAATCC 60.159 50.000 0.00 0.00 0.00 3.01
739 867 2.420827 CCCATGCACGGTAGTTAATCCA 60.421 50.000 0.00 0.00 0.00 3.41
741 869 3.882888 CCATGCACGGTAGTTAATCCAAT 59.117 43.478 0.00 0.00 0.00 3.16
742 870 4.024048 CCATGCACGGTAGTTAATCCAATC 60.024 45.833 0.00 0.00 0.00 2.67
743 871 4.481368 TGCACGGTAGTTAATCCAATCT 57.519 40.909 0.00 0.00 0.00 2.40
754 3692 7.047460 AGTTAATCCAATCTCATTTGCATCC 57.953 36.000 0.00 0.00 0.00 3.51
823 3769 0.107800 CAGTGGGATCTGGACTGCAG 60.108 60.000 13.48 13.48 31.31 4.41
835 3781 1.281899 GACTGCAGCGATAGTCAACC 58.718 55.000 15.27 0.00 42.18 3.77
885 3831 1.197721 CCTCCAAACGATGAGCAACAC 59.802 52.381 0.00 0.00 0.00 3.32
914 3860 6.428159 GCCTATTTAATGGTGATGAACTCGAT 59.572 38.462 0.00 0.00 0.00 3.59
1652 4643 4.712425 GTACGCGTCGCTGGTGGT 62.712 66.667 18.63 7.78 0.00 4.16
1759 4750 1.574702 CGGGTTCGGAAAGAAGGCAC 61.575 60.000 0.00 0.00 39.95 5.01
1856 4847 5.175090 TGTTTGTGTTTCACGCATGAATA 57.825 34.783 0.00 0.00 44.36 1.75
1859 4850 6.198029 TGTTTGTGTTTCACGCATGAATAAAG 59.802 34.615 0.00 0.00 44.36 1.85
1914 7392 9.924650 TTCTTCCAAATTCTAACTAGTACAGTC 57.075 33.333 0.00 0.00 36.04 3.51
1915 7393 9.310449 TCTTCCAAATTCTAACTAGTACAGTCT 57.690 33.333 0.00 0.00 36.04 3.24
1980 7458 9.724839 CAAATTTTCTGCAACAATTTTCTGAAT 57.275 25.926 7.20 0.00 29.49 2.57
2105 7584 3.593096 TGAACTGTAGATTGCTGCTCTG 58.407 45.455 0.00 0.00 0.00 3.35
2107 7586 0.928922 CTGTAGATTGCTGCTCTGCG 59.071 55.000 0.00 0.00 35.36 5.18
2220 7701 6.607004 TCTTAGCTAAAAGCAGTACTCCTT 57.393 37.500 7.74 0.00 45.56 3.36
2237 7718 8.370182 AGTACTCCTTCGTTTTTATTTACTCCA 58.630 33.333 0.00 0.00 0.00 3.86
2321 7802 1.563924 AGCATACGGGTGTGGTTAGA 58.436 50.000 0.00 0.00 0.00 2.10
2329 7810 2.159226 CGGGTGTGGTTAGATCTCAGTC 60.159 54.545 0.00 0.00 0.00 3.51
2333 7814 3.190744 GTGTGGTTAGATCTCAGTCGACA 59.809 47.826 19.50 0.00 0.00 4.35
2334 7815 3.440522 TGTGGTTAGATCTCAGTCGACAG 59.559 47.826 19.50 10.43 0.00 3.51
2336 7817 3.942115 TGGTTAGATCTCAGTCGACAGAG 59.058 47.826 26.93 26.93 0.00 3.35
2344 7825 5.959618 TCTCAGTCGACAGAGATTTAACA 57.040 39.130 30.13 11.82 34.25 2.41
2347 7828 6.641314 TCTCAGTCGACAGAGATTTAACAAAC 59.359 38.462 30.13 0.00 34.25 2.93
2352 7833 5.856986 TCGACAGAGATTTAACAAACTCTCG 59.143 40.000 0.00 0.00 39.27 4.04
2466 7947 5.350091 CCAACGGTCAACAACAAAGAAAAAT 59.650 36.000 0.00 0.00 0.00 1.82
2598 8079 2.290641 ACCACCAAATCAATACCAGCGA 60.291 45.455 0.00 0.00 0.00 4.93
2691 8172 9.658799 TCTCATATTTAAGACAAAGACAAGAGG 57.341 33.333 0.00 0.00 0.00 3.69
2692 8173 8.792830 TCATATTTAAGACAAAGACAAGAGGG 57.207 34.615 0.00 0.00 0.00 4.30
2693 8174 8.602424 TCATATTTAAGACAAAGACAAGAGGGA 58.398 33.333 0.00 0.00 0.00 4.20
2694 8175 8.887717 CATATTTAAGACAAAGACAAGAGGGAG 58.112 37.037 0.00 0.00 0.00 4.30
2695 8176 5.888982 TTAAGACAAAGACAAGAGGGAGT 57.111 39.130 0.00 0.00 0.00 3.85
2696 8177 4.344359 AAGACAAAGACAAGAGGGAGTC 57.656 45.455 0.00 0.00 35.02 3.36
2697 8178 2.635427 AGACAAAGACAAGAGGGAGTCC 59.365 50.000 0.00 0.00 35.38 3.85
2699 8180 2.370189 ACAAAGACAAGAGGGAGTCCTG 59.630 50.000 9.58 1.49 45.05 3.86
2700 8181 1.650528 AAGACAAGAGGGAGTCCTGG 58.349 55.000 9.58 0.00 45.05 4.45
2701 8182 0.787084 AGACAAGAGGGAGTCCTGGA 59.213 55.000 9.58 0.00 45.05 3.86
2702 8183 1.364328 AGACAAGAGGGAGTCCTGGAT 59.636 52.381 9.58 0.00 45.05 3.41
2703 8184 2.192263 GACAAGAGGGAGTCCTGGATT 58.808 52.381 9.58 0.00 45.05 3.01
2704 8185 3.012959 AGACAAGAGGGAGTCCTGGATTA 59.987 47.826 9.58 0.00 45.05 1.75
2705 8186 3.379452 ACAAGAGGGAGTCCTGGATTAG 58.621 50.000 9.58 0.00 45.05 1.73
2706 8187 2.703007 CAAGAGGGAGTCCTGGATTAGG 59.297 54.545 9.58 0.00 45.05 2.69
2714 8195 2.855669 CCTGGATTAGGGGGTCTCC 58.144 63.158 0.00 0.00 43.33 3.71
2715 8196 1.122019 CCTGGATTAGGGGGTCTCCG 61.122 65.000 0.00 0.00 43.33 4.63
2716 8197 1.074775 TGGATTAGGGGGTCTCCGG 60.075 63.158 0.00 0.00 36.01 5.14
2717 8198 1.235112 GGATTAGGGGGTCTCCGGA 59.765 63.158 2.93 2.93 36.01 5.14
2718 8199 0.178900 GGATTAGGGGGTCTCCGGAT 60.179 60.000 3.57 0.00 36.01 4.18
2719 8200 1.078324 GGATTAGGGGGTCTCCGGATA 59.922 57.143 3.57 0.00 36.01 2.59
2720 8201 2.458620 GATTAGGGGGTCTCCGGATAG 58.541 57.143 3.57 0.00 36.01 2.08
2721 8202 0.178941 TTAGGGGGTCTCCGGATAGC 60.179 60.000 3.57 7.72 36.01 2.97
2722 8203 2.090377 TAGGGGGTCTCCGGATAGCC 62.090 65.000 25.67 25.67 36.01 3.93
2738 8219 1.051812 AGCCGGACTATCTCCATTGG 58.948 55.000 5.05 0.00 39.39 3.16
2739 8220 0.603975 GCCGGACTATCTCCATTGGC 60.604 60.000 5.05 0.00 39.39 4.52
2740 8221 0.035458 CCGGACTATCTCCATTGGCC 59.965 60.000 0.00 0.00 39.39 5.36
2741 8222 3.614399 GGACTATCTCCATTGGCCG 57.386 57.895 0.00 0.00 39.21 6.13
2742 8223 0.035458 GGACTATCTCCATTGGCCGG 59.965 60.000 0.00 0.00 39.21 6.13
2743 8224 1.048601 GACTATCTCCATTGGCCGGA 58.951 55.000 5.05 0.00 0.00 5.14
2744 8225 0.759346 ACTATCTCCATTGGCCGGAC 59.241 55.000 5.05 0.56 0.00 4.79
2745 8226 1.051812 CTATCTCCATTGGCCGGACT 58.948 55.000 9.82 0.00 0.00 3.85
2746 8227 0.758734 TATCTCCATTGGCCGGACTG 59.241 55.000 9.82 0.00 0.00 3.51
2747 8228 1.274703 ATCTCCATTGGCCGGACTGT 61.275 55.000 9.82 0.00 0.00 3.55
2748 8229 1.002134 CTCCATTGGCCGGACTGTT 60.002 57.895 9.82 0.00 0.00 3.16
2749 8230 0.251916 CTCCATTGGCCGGACTGTTA 59.748 55.000 9.82 0.00 0.00 2.41
2750 8231 0.251916 TCCATTGGCCGGACTGTTAG 59.748 55.000 9.82 0.00 0.00 2.34
2751 8232 0.251916 CCATTGGCCGGACTGTTAGA 59.748 55.000 9.82 0.00 0.00 2.10
2752 8233 1.369625 CATTGGCCGGACTGTTAGAC 58.630 55.000 9.82 0.00 0.00 2.59
2753 8234 1.066143 CATTGGCCGGACTGTTAGACT 60.066 52.381 9.82 0.00 0.00 3.24
2754 8235 1.927487 TTGGCCGGACTGTTAGACTA 58.073 50.000 9.82 0.00 0.00 2.59
2755 8236 2.154567 TGGCCGGACTGTTAGACTAT 57.845 50.000 9.82 0.00 0.00 2.12
2756 8237 1.754803 TGGCCGGACTGTTAGACTATG 59.245 52.381 9.82 0.00 0.00 2.23
2757 8238 2.029623 GGCCGGACTGTTAGACTATGA 58.970 52.381 5.05 0.00 0.00 2.15
2758 8239 2.429610 GGCCGGACTGTTAGACTATGAA 59.570 50.000 5.05 0.00 0.00 2.57
2759 8240 3.491104 GGCCGGACTGTTAGACTATGAAG 60.491 52.174 5.05 0.00 0.00 3.02
2760 8241 3.380637 GCCGGACTGTTAGACTATGAAGA 59.619 47.826 5.05 0.00 0.00 2.87
2761 8242 4.038162 GCCGGACTGTTAGACTATGAAGAT 59.962 45.833 5.05 0.00 0.00 2.40
2762 8243 5.241064 GCCGGACTGTTAGACTATGAAGATA 59.759 44.000 5.05 0.00 0.00 1.98
2763 8244 6.670233 CCGGACTGTTAGACTATGAAGATAC 58.330 44.000 0.00 0.00 0.00 2.24
2764 8245 6.262496 CCGGACTGTTAGACTATGAAGATACA 59.738 42.308 0.00 0.00 0.00 2.29
2765 8246 7.201794 CCGGACTGTTAGACTATGAAGATACAA 60.202 40.741 0.00 0.00 0.00 2.41
2766 8247 7.858382 CGGACTGTTAGACTATGAAGATACAAG 59.142 40.741 0.00 0.00 0.00 3.16
2767 8248 8.904834 GGACTGTTAGACTATGAAGATACAAGA 58.095 37.037 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.031560 TCGGATACAAATGCATGTTCGC 59.968 45.455 0.00 0.00 34.75 4.70
1 2 3.555547 TCTCGGATACAAATGCATGTTCG 59.444 43.478 0.00 2.40 34.75 3.95
2 3 5.484173 TTCTCGGATACAAATGCATGTTC 57.516 39.130 0.00 0.00 34.75 3.18
4 5 5.647658 TCTTTTCTCGGATACAAATGCATGT 59.352 36.000 0.00 0.00 37.32 3.21
5 6 6.122850 TCTTTTCTCGGATACAAATGCATG 57.877 37.500 0.00 0.00 0.00 4.06
6 7 6.949352 ATCTTTTCTCGGATACAAATGCAT 57.051 33.333 0.00 0.00 0.00 3.96
7 8 8.450578 AATATCTTTTCTCGGATACAAATGCA 57.549 30.769 0.00 0.00 0.00 3.96
8 9 8.778358 AGAATATCTTTTCTCGGATACAAATGC 58.222 33.333 0.00 0.00 29.99 3.56
11 12 9.760077 GGTAGAATATCTTTTCTCGGATACAAA 57.240 33.333 0.00 0.00 37.20 2.83
12 13 8.920174 TGGTAGAATATCTTTTCTCGGATACAA 58.080 33.333 0.00 0.00 37.20 2.41
13 14 8.473358 TGGTAGAATATCTTTTCTCGGATACA 57.527 34.615 0.00 0.00 37.20 2.29
15 16 8.035394 GCATGGTAGAATATCTTTTCTCGGATA 58.965 37.037 0.00 0.00 37.20 2.59
16 17 6.876257 GCATGGTAGAATATCTTTTCTCGGAT 59.124 38.462 0.00 0.00 37.20 4.18
17 18 6.183360 TGCATGGTAGAATATCTTTTCTCGGA 60.183 38.462 0.00 0.00 37.20 4.55
18 19 5.991606 TGCATGGTAGAATATCTTTTCTCGG 59.008 40.000 0.00 0.00 37.20 4.63
19 20 6.346120 CGTGCATGGTAGAATATCTTTTCTCG 60.346 42.308 0.00 0.00 37.20 4.04
29 30 1.691976 CCTCCCGTGCATGGTAGAATA 59.308 52.381 23.39 1.29 0.00 1.75
336 387 5.969435 ACGAAAGGCTTTTCTTCGTAAAAAG 59.031 36.000 19.75 12.25 43.44 2.27
342 395 5.237779 TCAATAACGAAAGGCTTTTCTTCGT 59.762 36.000 16.55 16.55 40.43 3.85
366 421 3.989817 GCTGATTTTGTTTTCTTCGCCAT 59.010 39.130 0.00 0.00 0.00 4.40
553 626 6.783708 AACATGGTGAAACTGGTAAAAAGA 57.216 33.333 0.00 0.00 36.74 2.52
554 627 7.038659 TCAAACATGGTGAAACTGGTAAAAAG 58.961 34.615 0.00 0.00 36.74 2.27
570 643 5.277925 GCCTTCCAAACAAAATCAAACATGG 60.278 40.000 0.00 0.00 0.00 3.66
697 819 1.783284 TTCGTGCTAGACAGTGCAAG 58.217 50.000 0.00 0.00 41.10 4.01
721 849 5.036117 AGATTGGATTAACTACCGTGCAT 57.964 39.130 0.00 0.00 0.00 3.96
724 852 7.409697 CAAATGAGATTGGATTAACTACCGTG 58.590 38.462 0.00 0.00 0.00 4.94
725 853 6.038271 GCAAATGAGATTGGATTAACTACCGT 59.962 38.462 0.00 0.00 0.00 4.83
728 856 8.078596 GGATGCAAATGAGATTGGATTAACTAC 58.921 37.037 0.00 0.00 40.81 2.73
730 858 6.608405 TGGATGCAAATGAGATTGGATTAACT 59.392 34.615 0.00 0.00 40.81 2.24
732 860 6.183360 GGTGGATGCAAATGAGATTGGATTAA 60.183 38.462 0.00 0.00 40.81 1.40
733 861 5.302568 GGTGGATGCAAATGAGATTGGATTA 59.697 40.000 0.00 0.00 40.81 1.75
734 862 4.100498 GGTGGATGCAAATGAGATTGGATT 59.900 41.667 0.00 0.00 40.81 3.01
736 864 3.025978 GGTGGATGCAAATGAGATTGGA 58.974 45.455 0.00 0.00 35.04 3.53
737 865 2.761767 TGGTGGATGCAAATGAGATTGG 59.238 45.455 0.00 0.00 0.00 3.16
738 866 4.665833 ATGGTGGATGCAAATGAGATTG 57.334 40.909 0.00 0.00 0.00 2.67
739 867 5.687166 AAATGGTGGATGCAAATGAGATT 57.313 34.783 0.00 0.00 0.00 2.40
741 869 5.105392 GGTTAAATGGTGGATGCAAATGAGA 60.105 40.000 0.00 0.00 0.00 3.27
742 870 5.105228 AGGTTAAATGGTGGATGCAAATGAG 60.105 40.000 0.00 0.00 0.00 2.90
743 871 4.776837 AGGTTAAATGGTGGATGCAAATGA 59.223 37.500 0.00 0.00 0.00 2.57
754 3692 2.416547 CGAGCTGTCAGGTTAAATGGTG 59.583 50.000 5.91 0.00 0.00 4.17
823 3769 1.227176 GTCCGGGGTTGACTATCGC 60.227 63.158 0.00 0.00 0.00 4.58
835 3781 4.680237 TCACTGCTTGCGTCCGGG 62.680 66.667 0.00 0.00 0.00 5.73
885 3831 1.588674 TCACCATTAAATAGGCGCGG 58.411 50.000 8.83 0.00 0.00 6.46
1379 4370 3.941188 CCAGCCACACGTCCACCT 61.941 66.667 0.00 0.00 0.00 4.00
1486 4477 2.181021 GTTCTCGTCGATGGCGGT 59.819 61.111 4.48 0.00 38.28 5.68
1673 4664 1.461268 TTGAGCTCCTCCCACCACA 60.461 57.895 12.15 0.00 0.00 4.17
1759 4750 3.312828 CTCGTTCTTGTCTTCACTCCTG 58.687 50.000 0.00 0.00 0.00 3.86
1859 4850 3.732212 AGAGAAACCCAAAGCATTTTGC 58.268 40.909 0.00 0.00 45.46 3.68
1909 7387 6.891388 AGCTCAGTGTATACTACTAGACTGT 58.109 40.000 14.81 0.00 41.41 3.55
1910 7388 7.635423 CAAGCTCAGTGTATACTACTAGACTG 58.365 42.308 10.90 10.90 41.80 3.51
1911 7389 6.261381 GCAAGCTCAGTGTATACTACTAGACT 59.739 42.308 4.17 0.00 34.74 3.24
1912 7390 6.432107 GCAAGCTCAGTGTATACTACTAGAC 58.568 44.000 4.17 0.00 34.74 2.59
1913 7391 5.531659 GGCAAGCTCAGTGTATACTACTAGA 59.468 44.000 4.17 6.12 34.74 2.43
1914 7392 5.299531 TGGCAAGCTCAGTGTATACTACTAG 59.700 44.000 4.17 0.00 34.74 2.57
1915 7393 5.067413 GTGGCAAGCTCAGTGTATACTACTA 59.933 44.000 4.17 0.00 34.74 1.82
1916 7394 4.023980 TGGCAAGCTCAGTGTATACTACT 58.976 43.478 4.17 3.55 34.74 2.57
1917 7395 4.113354 GTGGCAAGCTCAGTGTATACTAC 58.887 47.826 4.17 1.23 34.74 2.73
1925 7403 0.954449 CAGGAGTGGCAAGCTCAGTG 60.954 60.000 7.34 1.15 34.83 3.66
1927 7405 0.954449 CACAGGAGTGGCAAGCTCAG 60.954 60.000 7.34 2.37 42.13 3.35
2030 7509 6.001449 TCCACTCTCCTCTTTTTGAAAGAA 57.999 37.500 4.84 0.00 0.00 2.52
2032 7511 6.890979 AATCCACTCTCCTCTTTTTGAAAG 57.109 37.500 0.00 0.00 0.00 2.62
2034 7513 6.833416 TCAAAATCCACTCTCCTCTTTTTGAA 59.167 34.615 5.68 0.00 38.15 2.69
2035 7514 6.364701 TCAAAATCCACTCTCCTCTTTTTGA 58.635 36.000 0.00 0.00 38.53 2.69
2036 7515 6.639632 TCAAAATCCACTCTCCTCTTTTTG 57.360 37.500 0.00 0.00 35.16 2.44
2105 7584 3.274067 AAAAATCTCCACCGGCGC 58.726 55.556 0.00 0.00 0.00 6.53
2173 7654 1.746787 CTGAACATGCTTGCATGGCTA 59.253 47.619 30.86 18.61 36.91 3.93
2303 7784 2.102588 AGATCTAACCACACCCGTATGC 59.897 50.000 0.00 0.00 0.00 3.14
2308 7789 1.825474 ACTGAGATCTAACCACACCCG 59.175 52.381 0.00 0.00 0.00 5.28
2314 7795 3.942115 CTCTGTCGACTGAGATCTAACCA 59.058 47.826 35.84 9.22 42.37 3.67
2329 7810 7.278950 ACCGAGAGTTTGTTAAATCTCTGTCG 61.279 42.308 11.89 0.00 44.22 4.35
2334 7815 6.424207 ACTTGACCGAGAGTTTGTTAAATCTC 59.576 38.462 5.53 5.53 46.68 2.75
2336 7817 6.202188 TCACTTGACCGAGAGTTTGTTAAATC 59.798 38.462 0.00 0.00 0.00 2.17
2344 7825 6.931838 TGTTATATCACTTGACCGAGAGTTT 58.068 36.000 0.00 0.00 0.00 2.66
2347 7828 6.507900 ACATGTTATATCACTTGACCGAGAG 58.492 40.000 9.27 0.00 0.00 3.20
2378 7859 1.272490 TCATCAGCCGACTTCGAGTTT 59.728 47.619 0.00 0.00 43.02 2.66
2466 7947 5.255710 TCCGTGCAGATTTTCTTTTCAAA 57.744 34.783 0.00 0.00 0.00 2.69
2479 7960 5.982890 TCATATATTGAGATCCGTGCAGA 57.017 39.130 0.00 0.00 0.00 4.26
2480 7961 6.020041 CGAATCATATATTGAGATCCGTGCAG 60.020 42.308 0.00 0.00 37.89 4.41
2598 8079 0.036483 TCGTGTGTGCCTACATGCAT 60.036 50.000 0.00 0.00 44.30 3.96
2611 8092 5.972382 TCCGTTTCCTTTAATTTTTCGTGTG 59.028 36.000 0.00 0.00 0.00 3.82
2615 8096 5.216648 TGCTCCGTTTCCTTTAATTTTTCG 58.783 37.500 0.00 0.00 0.00 3.46
2696 8177 1.122019 CGGAGACCCCCTAATCCAGG 61.122 65.000 0.00 0.00 45.07 4.45
2697 8178 1.122019 CCGGAGACCCCCTAATCCAG 61.122 65.000 0.00 0.00 0.00 3.86
2698 8179 1.074775 CCGGAGACCCCCTAATCCA 60.075 63.158 0.00 0.00 0.00 3.41
2699 8180 0.178900 ATCCGGAGACCCCCTAATCC 60.179 60.000 11.34 0.00 0.00 3.01
2700 8181 2.458620 CTATCCGGAGACCCCCTAATC 58.541 57.143 11.34 0.00 0.00 1.75
2701 8182 1.552719 GCTATCCGGAGACCCCCTAAT 60.553 57.143 11.34 0.00 0.00 1.73
2702 8183 0.178941 GCTATCCGGAGACCCCCTAA 60.179 60.000 11.34 0.00 0.00 2.69
2703 8184 1.463824 GCTATCCGGAGACCCCCTA 59.536 63.158 11.34 0.00 0.00 3.53
2704 8185 2.201771 GCTATCCGGAGACCCCCT 59.798 66.667 11.34 0.00 0.00 4.79
2705 8186 2.923568 GGCTATCCGGAGACCCCC 60.924 72.222 11.34 1.76 0.00 5.40
2724 8205 1.048601 TCCGGCCAATGGAGATAGTC 58.951 55.000 2.05 0.00 0.00 2.59
2725 8206 0.759346 GTCCGGCCAATGGAGATAGT 59.241 55.000 2.05 0.00 35.82 2.12
2726 8207 1.051812 AGTCCGGCCAATGGAGATAG 58.948 55.000 2.05 0.00 35.82 2.08
2727 8208 0.758734 CAGTCCGGCCAATGGAGATA 59.241 55.000 2.05 0.00 35.82 1.98
2728 8209 1.274703 ACAGTCCGGCCAATGGAGAT 61.275 55.000 2.05 0.00 35.82 2.75
2729 8210 1.488705 AACAGTCCGGCCAATGGAGA 61.489 55.000 2.05 0.00 35.82 3.71
2730 8211 0.251916 TAACAGTCCGGCCAATGGAG 59.748 55.000 2.05 0.00 35.82 3.86
2731 8212 0.251916 CTAACAGTCCGGCCAATGGA 59.748 55.000 2.05 0.00 0.00 3.41
2732 8213 0.251916 TCTAACAGTCCGGCCAATGG 59.748 55.000 2.24 0.00 0.00 3.16
2733 8214 1.066143 AGTCTAACAGTCCGGCCAATG 60.066 52.381 2.24 0.00 0.00 2.82
2734 8215 1.276622 AGTCTAACAGTCCGGCCAAT 58.723 50.000 2.24 0.00 0.00 3.16
2735 8216 1.927487 TAGTCTAACAGTCCGGCCAA 58.073 50.000 2.24 0.00 0.00 4.52
2736 8217 1.754803 CATAGTCTAACAGTCCGGCCA 59.245 52.381 2.24 0.00 0.00 5.36
2737 8218 2.029623 TCATAGTCTAACAGTCCGGCC 58.970 52.381 0.00 0.00 0.00 6.13
2738 8219 3.380637 TCTTCATAGTCTAACAGTCCGGC 59.619 47.826 0.00 0.00 0.00 6.13
2739 8220 5.776173 ATCTTCATAGTCTAACAGTCCGG 57.224 43.478 0.00 0.00 0.00 5.14
2740 8221 7.260558 TGTATCTTCATAGTCTAACAGTCCG 57.739 40.000 0.00 0.00 0.00 4.79
2741 8222 8.904834 TCTTGTATCTTCATAGTCTAACAGTCC 58.095 37.037 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.