Multiple sequence alignment - TraesCS3D01G482400

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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 TraesCS3D01G482400 chr3D 100.000 3352 0 0 1 3352 579696524 579699875 0.000000e+00 6191.0
1 TraesCS3D01G482400 chr3D 80.987 831 118 21 1055 1850 2991723 2990898 1.020000e-174 623.0
2 TraesCS3D01G482400 chr3D 84.760 479 73 0 1757 2235 2920451 2919973 6.500000e-132 481.0
3 TraesCS3D01G482400 chr3D 75.786 541 92 28 1754 2283 2932390 2932902 1.550000e-58 237.0
4 TraesCS3D01G482400 chr3D 100.000 30 0 0 1399 1428 565535853 565535882 4.670000e-04 56.5
5 TraesCS3D01G482400 chr3B 93.688 2028 85 14 779 2787 774456464 774458467 0.000000e+00 2996.0
6 TraesCS3D01G482400 chr3B 90.669 568 26 16 2787 3327 774458837 774459404 0.000000e+00 730.0
7 TraesCS3D01G482400 chr3B 90.476 273 25 1 252 523 734905662 734905390 3.180000e-95 359.0
8 TraesCS3D01G482400 chr3B 85.662 272 21 6 252 523 774411817 774412070 1.530000e-68 270.0
9 TraesCS3D01G482400 chr3B 90.058 171 12 4 41 207 734905904 734905735 2.030000e-52 217.0
10 TraesCS3D01G482400 chr3B 97.500 40 1 0 1 40 734905967 734905928 6.000000e-08 69.4
11 TraesCS3D01G482400 chr3A 93.952 1951 84 20 854 2787 714939068 714941001 0.000000e+00 2918.0
12 TraesCS3D01G482400 chr3A 92.353 1020 75 3 814 1832 679915853 679916870 0.000000e+00 1448.0
13 TraesCS3D01G482400 chr3A 93.585 530 33 1 1831 2360 679922820 679923348 0.000000e+00 789.0
14 TraesCS3D01G482400 chr3A 90.805 348 19 6 2451 2787 679923340 679923685 1.420000e-123 453.0
15 TraesCS3D01G482400 chr3A 93.248 311 15 4 2795 3103 714941372 714941678 1.420000e-123 453.0
16 TraesCS3D01G482400 chr3A 91.450 269 22 1 256 523 679877052 679877320 5.280000e-98 368.0
17 TraesCS3D01G482400 chr3A 90.110 273 26 1 252 523 607854736 607855008 1.480000e-93 353.0
18 TraesCS3D01G482400 chr3A 89.377 273 27 2 252 523 714797101 714797372 3.200000e-90 342.0
19 TraesCS3D01G482400 chr3A 85.022 227 20 5 3128 3352 679924812 679925026 5.630000e-53 219.0
20 TraesCS3D01G482400 chr3A 90.667 150 11 3 41 187 679876820 679876969 2.640000e-46 196.0
21 TraesCS3D01G482400 chr3A 85.795 176 15 6 41 207 607854489 607854663 9.560000e-41 178.0
22 TraesCS3D01G482400 chr3A 89.510 143 9 2 2962 3103 679924451 679924588 3.440000e-40 176.0
23 TraesCS3D01G482400 chr3A 86.842 152 11 7 64 207 714796878 714797028 9.620000e-36 161.0
24 TraesCS3D01G482400 chr3A 97.561 41 1 0 1 41 679876757 679876797 1.670000e-08 71.3
25 TraesCS3D01G482400 chr7B 91.651 1557 76 15 814 2360 7199518 7201030 0.000000e+00 2106.0
26 TraesCS3D01G482400 chr7B 93.040 273 16 3 252 523 7198641 7198911 2.420000e-106 396.0
27 TraesCS3D01G482400 chr7B 91.367 278 21 3 519 795 7199158 7199433 8.780000e-101 377.0
28 TraesCS3D01G482400 chr7B 89.224 232 8 8 2571 2787 7203392 7203621 1.180000e-69 274.0
29 TraesCS3D01G482400 chr7B 93.714 175 11 0 2451 2625 7201093 7201267 2.560000e-66 263.0
30 TraesCS3D01G482400 chr7B 93.125 160 8 3 50 207 7198415 7198573 7.230000e-57 231.0
31 TraesCS3D01G482400 chr7B 86.286 175 11 4 3131 3301 7185175 7185010 9.560000e-41 178.0
32 TraesCS3D01G482400 chr7B 85.955 178 12 4 3128 3301 7216597 7216765 9.560000e-41 178.0
33 TraesCS3D01G482400 chr7B 95.522 67 3 0 2451 2517 7201022 7201088 1.270000e-19 108.0
34 TraesCS3D01G482400 chr7B 89.583 48 5 0 2426 2473 3144723 3144676 1.000000e-05 62.1
35 TraesCS3D01G482400 chr4A 91.262 927 64 13 779 1692 9670628 9671550 0.000000e+00 1247.0
36 TraesCS3D01G482400 chr4A 93.759 673 42 0 1688 2360 9680672 9681344 0.000000e+00 1011.0
37 TraesCS3D01G482400 chr4A 83.984 512 49 18 41 523 9640762 9641269 8.470000e-126 460.0
38 TraesCS3D01G482400 chr4A 89.859 355 20 8 2444 2787 9681330 9681679 3.070000e-120 442.0
39 TraesCS3D01G482400 chr4A 90.615 309 25 2 2795 3103 9682043 9682347 1.120000e-109 407.0
40 TraesCS3D01G482400 chr4A 85.463 227 22 4 3128 3352 9682571 9682788 3.370000e-55 226.0
41 TraesCS3D01G482400 chr4A 97.436 39 1 0 2 40 9640700 9640738 2.160000e-07 67.6
42 TraesCS3D01G482400 chr4A 100.000 29 0 0 2447 2475 722924560 722924588 2.000000e-03 54.7
43 TraesCS3D01G482400 chr2B 90.621 885 71 7 779 1657 755344580 755345458 0.000000e+00 1164.0
44 TraesCS3D01G482400 chrUn 80.357 952 142 27 1049 1962 32127081 32126137 0.000000e+00 680.0
45 TraesCS3D01G482400 chrUn 85.955 178 12 4 3128 3301 341410623 341410791 9.560000e-41 178.0
46 TraesCS3D01G482400 chr1A 91.941 273 20 2 252 522 86035688 86035416 6.790000e-102 381.0
47 TraesCS3D01G482400 chr1A 92.547 161 10 2 41 199 86036479 86036319 2.600000e-56 230.0
48 TraesCS3D01G482400 chr7D 90.511 274 23 2 252 523 600071981 600072253 3.180000e-95 359.0
49 TraesCS3D01G482400 chr7D 89.412 170 14 4 41 207 600071744 600071912 9.420000e-51 211.0
50 TraesCS3D01G482400 chr5A 93.642 173 9 2 525 697 619371399 619371569 1.190000e-64 257.0
51 TraesCS3D01G482400 chr5A 91.026 78 6 1 703 779 619371607 619371684 1.650000e-18 104.0
52 TraesCS3D01G482400 chr1B 93.491 169 8 3 41 207 143109913 143110080 7.180000e-62 248.0
53 TraesCS3D01G482400 chr1B 100.000 41 0 0 1 41 143109850 143109890 3.590000e-10 76.8
54 TraesCS3D01G482400 chr1D 91.716 169 10 4 41 207 96027238 96027072 7.230000e-57 231.0
55 TraesCS3D01G482400 chr1D 92.073 164 11 2 40 201 64344695 64344858 2.600000e-56 230.0
56 TraesCS3D01G482400 chr1D 97.561 41 1 0 1 41 96027301 96027261 1.670000e-08 71.3
57 TraesCS3D01G482400 chr7A 100.000 29 0 0 2330 2358 32298368 32298396 2.000000e-03 54.7
58 TraesCS3D01G482400 chr6B 96.774 31 1 0 2447 2477 456071489 456071459 6.000000e-03 52.8


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 TraesCS3D01G482400 chr3D 579696524 579699875 3351 False 6191.000000 6191 100.000000 1 3352 1 chr3D.!!$F3 3351
1 TraesCS3D01G482400 chr3D 2990898 2991723 825 True 623.000000 623 80.987000 1055 1850 1 chr3D.!!$R2 795
2 TraesCS3D01G482400 chr3D 2932390 2932902 512 False 237.000000 237 75.786000 1754 2283 1 chr3D.!!$F1 529
3 TraesCS3D01G482400 chr3B 774456464 774459404 2940 False 1863.000000 2996 92.178500 779 3327 2 chr3B.!!$F2 2548
4 TraesCS3D01G482400 chr3B 734905390 734905967 577 True 215.133333 359 92.678000 1 523 3 chr3B.!!$R1 522
5 TraesCS3D01G482400 chr3A 714939068 714941678 2610 False 1685.500000 2918 93.600000 854 3103 2 chr3A.!!$F6 2249
6 TraesCS3D01G482400 chr3A 679915853 679916870 1017 False 1448.000000 1448 92.353000 814 1832 1 chr3A.!!$F1 1018
7 TraesCS3D01G482400 chr3A 679922820 679925026 2206 False 409.250000 789 89.730500 1831 3352 4 chr3A.!!$F4 1521
8 TraesCS3D01G482400 chr3A 607854489 607855008 519 False 265.500000 353 87.952500 41 523 2 chr3A.!!$F2 482
9 TraesCS3D01G482400 chr3A 679876757 679877320 563 False 211.766667 368 93.226000 1 523 3 chr3A.!!$F3 522
10 TraesCS3D01G482400 chr7B 7198415 7203621 5206 False 536.428571 2106 92.520429 50 2787 7 chr7B.!!$F2 2737
11 TraesCS3D01G482400 chr4A 9670628 9671550 922 False 1247.000000 1247 91.262000 779 1692 1 chr4A.!!$F1 913
12 TraesCS3D01G482400 chr4A 9680672 9682788 2116 False 521.500000 1011 89.924000 1688 3352 4 chr4A.!!$F4 1664
13 TraesCS3D01G482400 chr4A 9640700 9641269 569 False 263.800000 460 90.710000 2 523 2 chr4A.!!$F3 521
14 TraesCS3D01G482400 chr2B 755344580 755345458 878 False 1164.000000 1164 90.621000 779 1657 1 chr2B.!!$F1 878
15 TraesCS3D01G482400 chrUn 32126137 32127081 944 True 680.000000 680 80.357000 1049 1962 1 chrUn.!!$R1 913
16 TraesCS3D01G482400 chr1A 86035416 86036479 1063 True 305.500000 381 92.244000 41 522 2 chr1A.!!$R1 481
17 TraesCS3D01G482400 chr7D 600071744 600072253 509 False 285.000000 359 89.961500 41 523 2 chr7D.!!$F1 482

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
523 1168 0.098025 AAGTGTTTGGCGTGTGAACG 59.902 50.0 0.0 0.0 0.0 3.95 F
762 1659 0.239347 CCTTGCCTTCAGAACTTGCG 59.761 55.0 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
1679 2672 0.038744 CTTGAAGGTGCCACCAGGAT 59.961 55.0 17.8 0.0 41.95 3.24 R
2368 3386 0.252467 CTGAGTCCAACCTCCCTCCT 60.252 60.0 0.0 0.0 0.00 3.69 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
86 110 3.550275 TGATAGAAATACAACGCGAGCAC 59.450 43.478 15.93 0.00 0.00 4.40
189 223 6.404844 CCAATTTGTGGTACGTGCCAAATATA 60.405 38.462 27.66 10.76 43.20 0.86
225 867 5.629079 ACTAAAGTTGTGCCTAGCATTTC 57.371 39.130 0.00 0.00 41.91 2.17
226 868 5.316987 ACTAAAGTTGTGCCTAGCATTTCT 58.683 37.500 0.00 0.00 41.91 2.52
227 869 4.773323 AAAGTTGTGCCTAGCATTTCTC 57.227 40.909 0.00 0.00 41.91 2.87
228 870 3.710209 AGTTGTGCCTAGCATTTCTCT 57.290 42.857 0.00 0.00 41.91 3.10
229 871 4.826274 AGTTGTGCCTAGCATTTCTCTA 57.174 40.909 0.00 0.00 41.91 2.43
230 872 5.165961 AGTTGTGCCTAGCATTTCTCTAA 57.834 39.130 0.00 0.00 41.91 2.10
231 873 5.749462 AGTTGTGCCTAGCATTTCTCTAAT 58.251 37.500 0.00 0.00 41.91 1.73
232 874 6.889198 AGTTGTGCCTAGCATTTCTCTAATA 58.111 36.000 0.00 0.00 41.91 0.98
233 875 6.989169 AGTTGTGCCTAGCATTTCTCTAATAG 59.011 38.462 0.00 0.00 41.91 1.73
234 876 6.485830 TGTGCCTAGCATTTCTCTAATAGT 57.514 37.500 0.00 0.00 41.91 2.12
235 877 6.283694 TGTGCCTAGCATTTCTCTAATAGTG 58.716 40.000 0.00 0.00 41.91 2.74
236 878 6.098266 TGTGCCTAGCATTTCTCTAATAGTGA 59.902 38.462 0.00 0.00 41.91 3.41
237 879 6.422400 GTGCCTAGCATTTCTCTAATAGTGAC 59.578 42.308 0.00 0.00 41.91 3.67
238 880 5.929415 GCCTAGCATTTCTCTAATAGTGACC 59.071 44.000 0.00 0.00 0.00 4.02
239 881 6.459923 CCTAGCATTTCTCTAATAGTGACCC 58.540 44.000 0.00 0.00 0.00 4.46
240 882 5.297569 AGCATTTCTCTAATAGTGACCCC 57.702 43.478 0.00 0.00 0.00 4.95
241 883 4.971924 AGCATTTCTCTAATAGTGACCCCT 59.028 41.667 0.00 0.00 0.00 4.79
242 884 5.071115 AGCATTTCTCTAATAGTGACCCCTC 59.929 44.000 0.00 0.00 0.00 4.30
243 885 5.163301 GCATTTCTCTAATAGTGACCCCTCA 60.163 44.000 0.00 0.00 0.00 3.86
244 886 6.632672 GCATTTCTCTAATAGTGACCCCTCAA 60.633 42.308 0.00 0.00 0.00 3.02
245 887 6.945636 TTTCTCTAATAGTGACCCCTCAAA 57.054 37.500 0.00 0.00 0.00 2.69
246 888 6.945636 TTCTCTAATAGTGACCCCTCAAAA 57.054 37.500 0.00 0.00 0.00 2.44
247 889 6.945636 TCTCTAATAGTGACCCCTCAAAAA 57.054 37.500 0.00 0.00 0.00 1.94
392 1034 4.734398 TGCCAAATAAACCACATGATCC 57.266 40.909 0.00 0.00 0.00 3.36
403 1045 3.389329 ACCACATGATCCACACTATCTCC 59.611 47.826 0.00 0.00 0.00 3.71
451 1095 2.029288 CTGACAATGTCGCGTGCCT 61.029 57.895 5.77 0.00 34.95 4.75
523 1168 0.098025 AAGTGTTTGGCGTGTGAACG 59.902 50.000 0.00 0.00 0.00 3.95
540 1436 1.375523 CGTCCCAGCCACCTACAAC 60.376 63.158 0.00 0.00 0.00 3.32
547 1443 0.912486 AGCCACCTACAACTGGATCC 59.088 55.000 4.20 4.20 0.00 3.36
559 1455 4.263462 ACAACTGGATCCAATAGTTCAGCA 60.263 41.667 17.00 0.00 32.69 4.41
588 1484 4.944048 TCAATCAGTGTGTTTTCTCTCGA 58.056 39.130 0.00 0.00 0.00 4.04
590 1486 2.727777 TCAGTGTGTTTTCTCTCGACG 58.272 47.619 0.00 0.00 0.00 5.12
597 1493 4.025229 TGTGTTTTCTCTCGACGAAAATGG 60.025 41.667 16.43 0.00 40.98 3.16
602 1498 2.076863 CTCTCGACGAAAATGGCCTTT 58.923 47.619 3.32 0.00 0.00 3.11
603 1499 2.073816 TCTCGACGAAAATGGCCTTTC 58.926 47.619 3.32 5.80 32.88 2.62
610 1506 1.248101 AAAATGGCCTTTCGGTCCCG 61.248 55.000 3.32 0.00 41.35 5.14
632 1528 2.359975 CTCGGCAACCAAGGGTCC 60.360 66.667 0.00 0.00 33.12 4.46
651 1547 2.094675 CCTCCCACACCTTAATGCTTG 58.905 52.381 0.00 0.00 0.00 4.01
654 1550 1.067635 CCCACACCTTAATGCTTGTGC 60.068 52.381 0.00 0.00 38.42 4.57
669 1565 3.680196 TGCCGTCCCCTACCCTCT 61.680 66.667 0.00 0.00 0.00 3.69
670 1566 2.838693 GCCGTCCCCTACCCTCTC 60.839 72.222 0.00 0.00 0.00 3.20
679 1575 3.401683 TCCCCTACCCTCTCGATAATTCT 59.598 47.826 0.00 0.00 0.00 2.40
759 1656 4.439253 AAGTACCTTGCCTTCAGAACTT 57.561 40.909 0.00 0.00 0.00 2.66
761 1658 1.322442 ACCTTGCCTTCAGAACTTGC 58.678 50.000 0.00 0.00 0.00 4.01
762 1659 0.239347 CCTTGCCTTCAGAACTTGCG 59.761 55.000 0.00 0.00 0.00 4.85
796 1754 4.131596 TCCGGGTTAAAGTGTCAAAGAAG 58.868 43.478 0.00 0.00 0.00 2.85
797 1755 3.304458 CCGGGTTAAAGTGTCAAAGAAGC 60.304 47.826 0.00 0.00 0.00 3.86
798 1756 3.304458 CGGGTTAAAGTGTCAAAGAAGCC 60.304 47.826 0.00 0.00 0.00 4.35
799 1757 3.889538 GGGTTAAAGTGTCAAAGAAGCCT 59.110 43.478 0.00 0.00 32.88 4.58
801 1759 5.163447 GGGTTAAAGTGTCAAAGAAGCCTTT 60.163 40.000 0.00 0.00 42.98 3.11
808 1766 8.465273 AAGTGTCAAAGAAGCCTTTATAAACT 57.535 30.769 0.00 0.00 40.42 2.66
812 1770 9.174166 TGTCAAAGAAGCCTTTATAAACTATCC 57.826 33.333 0.00 0.00 40.42 2.59
827 1790 2.750166 ACTATCCGGCGATGAGACTATG 59.250 50.000 9.30 0.00 0.00 2.23
1679 2672 2.618816 GCCATCCATGAACAAGGACAGA 60.619 50.000 0.84 0.00 36.60 3.41
1832 2843 3.612247 ATCCACCAGCTCGGCACAC 62.612 63.158 2.50 0.00 39.03 3.82
1944 2956 4.179298 GGAAGTATGGTCGTCAAAGTACC 58.821 47.826 0.00 0.00 0.00 3.34
1945 2957 4.322198 GGAAGTATGGTCGTCAAAGTACCA 60.322 45.833 0.00 0.00 46.78 3.25
1948 2960 4.710375 AGTATGGTCGTCAAAGTACCAGAT 59.290 41.667 0.00 0.00 45.99 2.90
2090 3105 3.013921 GTTTCACTGTGACAACAAGGGA 58.986 45.455 10.56 0.00 35.37 4.20
2194 3209 3.055819 CCGTTCTTCCAGAGGAAAGATGA 60.056 47.826 6.95 0.00 41.54 2.92
2307 3324 8.409371 TCACTGTGAGTATCTAGCTAGAAAATG 58.591 37.037 26.62 13.98 35.69 2.32
2320 3337 4.142513 GCTAGAAAATGCTCCCTTTGTGAG 60.143 45.833 0.00 0.00 0.00 3.51
2367 3385 6.743788 ACAGAGGGAGTAATTCCTAAGTAGT 58.256 40.000 0.00 0.00 45.98 2.73
2368 3386 7.880623 ACAGAGGGAGTAATTCCTAAGTAGTA 58.119 38.462 0.00 0.00 45.98 1.82
2369 3387 8.000127 ACAGAGGGAGTAATTCCTAAGTAGTAG 59.000 40.741 0.00 0.00 45.98 2.57
2385 3403 1.007359 AGTAGGAGGGAGGTTGGACTC 59.993 57.143 0.00 0.00 36.76 3.36
2390 3408 2.627217 GGAGGGAGGTTGGACTCAGTAT 60.627 54.545 0.00 0.00 39.27 2.12
2391 3409 2.696187 GAGGGAGGTTGGACTCAGTATC 59.304 54.545 0.00 0.00 39.27 2.24
2392 3410 2.044492 AGGGAGGTTGGACTCAGTATCA 59.956 50.000 0.00 0.00 39.27 2.15
2393 3411 2.432510 GGGAGGTTGGACTCAGTATCAG 59.567 54.545 0.00 0.00 39.27 2.90
2394 3412 3.100671 GGAGGTTGGACTCAGTATCAGT 58.899 50.000 0.00 0.00 39.27 3.41
2395 3413 4.279145 GGAGGTTGGACTCAGTATCAGTA 58.721 47.826 0.00 0.00 39.27 2.74
2460 3478 2.093658 TGGGAGAGACAAGTAATTCCGC 60.094 50.000 0.00 0.00 0.00 5.54
2509 3529 0.678684 CATGCCTGCACTCACCATGA 60.679 55.000 0.00 0.00 36.32 3.07
2517 3537 2.815503 TGCACTCACCATGATTGTTCAG 59.184 45.455 0.00 0.00 34.73 3.02
2585 3605 4.819630 TGTGTATGAAACCTTGTGGAAGAC 59.180 41.667 0.00 0.00 37.04 3.01
2601 3621 0.681733 AGACGCAAGGATGACACTGT 59.318 50.000 0.00 0.00 46.39 3.55
2721 5920 8.709308 AGAGATTTGTGGTAGCTTACAGATAAT 58.291 33.333 0.00 0.00 0.00 1.28
2739 5939 9.201127 ACAGATAATGAAACTGATGATATGACG 57.799 33.333 0.00 0.00 0.00 4.35
2740 5940 9.201127 CAGATAATGAAACTGATGATATGACGT 57.799 33.333 0.00 0.00 0.00 4.34
2741 5941 9.770097 AGATAATGAAACTGATGATATGACGTT 57.230 29.630 0.00 0.00 0.00 3.99
2742 5942 9.803130 GATAATGAAACTGATGATATGACGTTG 57.197 33.333 0.00 0.00 0.00 4.10
2746 5946 6.818142 TGAAACTGATGATATGACGTTGTGAT 59.182 34.615 0.00 0.00 0.00 3.06
2747 5947 7.978975 TGAAACTGATGATATGACGTTGTGATA 59.021 33.333 0.00 0.00 0.00 2.15
2748 5948 7.936950 AACTGATGATATGACGTTGTGATAG 57.063 36.000 0.00 0.00 0.00 2.08
2749 5949 7.043961 ACTGATGATATGACGTTGTGATAGT 57.956 36.000 0.00 0.00 0.00 2.12
2750 5950 8.166422 ACTGATGATATGACGTTGTGATAGTA 57.834 34.615 0.00 0.00 0.00 1.82
2751 5951 8.797438 ACTGATGATATGACGTTGTGATAGTAT 58.203 33.333 0.00 0.00 0.00 2.12
2752 5952 9.283420 CTGATGATATGACGTTGTGATAGTATC 57.717 37.037 2.97 2.97 0.00 2.24
2951 6660 7.465245 CGCTTCTTCTAATCTTCAGAAACATCC 60.465 40.741 0.00 0.00 31.84 3.51
2978 6866 7.669722 TCATTTAGCTTCTGTTTATCCTGGTTT 59.330 33.333 0.00 0.00 0.00 3.27
3016 6905 2.875094 AGCAGGAGAACAGAGCAATT 57.125 45.000 0.00 0.00 0.00 2.32
3139 7227 1.975680 AGTTTACCCATCTGACGTGGT 59.024 47.619 0.00 0.00 34.87 4.16
3160 7248 5.636121 TGGTTGTCTACAAATATGTCACGAC 59.364 40.000 0.00 0.00 41.05 4.34
3209 7299 7.086376 GCATTATCTAAAATAGCACCACCATG 58.914 38.462 0.00 0.00 0.00 3.66
3225 7315 3.078097 ACCATGTACGCAGTTTGCAATA 58.922 40.909 0.00 0.00 45.36 1.90
3285 7389 1.982660 TCCACGAGAGTTGAGACAGT 58.017 50.000 0.00 0.00 46.40 3.55
3289 7393 1.341531 ACGAGAGTTGAGACAGTTGGG 59.658 52.381 0.00 0.00 46.40 4.12
3313 7417 4.467795 ACGCCTGGCATCAGTTATATAGAT 59.532 41.667 20.29 0.00 39.31 1.98
3345 7450 0.963962 TGGTGAACGTCTGAGTACCC 59.036 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 110 3.195610 TGTACTCACCAGGCACAATCTAG 59.804 47.826 0.00 0.00 0.00 2.43
138 166 5.009610 CCATTTAGTTAGTGTTGGTGTTGCT 59.990 40.000 0.00 0.00 0.00 3.91
189 223 5.351948 AACTTTAGTTGGTGGCATTTTGT 57.648 34.783 0.00 0.00 36.80 2.83
221 863 7.510675 TTTGAGGGGTCACTATTAGAGAAAT 57.489 36.000 0.00 0.00 0.00 2.17
222 864 6.945636 TTTGAGGGGTCACTATTAGAGAAA 57.054 37.500 0.00 0.00 0.00 2.52
246 888 8.798859 ACATGCACTCACTATTAGAGATTTTT 57.201 30.769 0.00 0.00 36.91 1.94
247 889 8.798859 AACATGCACTCACTATTAGAGATTTT 57.201 30.769 0.00 0.00 36.91 1.82
248 890 7.497249 GGAACATGCACTCACTATTAGAGATTT 59.503 37.037 0.00 0.00 36.91 2.17
249 891 6.989169 GGAACATGCACTCACTATTAGAGATT 59.011 38.462 0.00 0.00 36.91 2.40
250 892 6.326064 AGGAACATGCACTCACTATTAGAGAT 59.674 38.462 0.00 0.00 36.91 2.75
392 1034 3.057876 GGTGATAGAGCGGAGATAGTGTG 60.058 52.174 0.00 0.00 0.00 3.82
403 1045 1.239347 TCTCGGATGGTGATAGAGCG 58.761 55.000 0.00 0.00 0.00 5.03
451 1095 2.843401 TGACTTTGCCCGCTTACTTA 57.157 45.000 0.00 0.00 0.00 2.24
523 1168 0.321653 CAGTTGTAGGTGGCTGGGAC 60.322 60.000 0.00 0.00 0.00 4.46
540 1436 2.877168 GCTGCTGAACTATTGGATCCAG 59.123 50.000 15.53 6.22 0.00 3.86
547 1443 2.093288 TGAGAGGGCTGCTGAACTATTG 60.093 50.000 0.00 0.00 0.00 1.90
559 1455 1.356124 ACACACTGATTGAGAGGGCT 58.644 50.000 0.00 0.00 0.00 5.19
610 1506 3.668386 CTTGGTTGCCGAGGAACC 58.332 61.111 16.67 16.67 42.90 3.62
632 1528 2.489329 CACAAGCATTAAGGTGTGGGAG 59.511 50.000 3.63 0.00 0.00 4.30
651 1547 3.468140 GAGGGTAGGGGACGGCAC 61.468 72.222 0.00 0.00 0.00 5.01
654 1550 2.354755 ATCGAGAGGGTAGGGGACGG 62.355 65.000 0.00 0.00 0.00 4.79
669 1565 8.342634 GCAGGTTATAAAGCAAAGAATTATCGA 58.657 33.333 0.00 0.00 0.00 3.59
670 1566 8.128582 TGCAGGTTATAAAGCAAAGAATTATCG 58.871 33.333 6.15 0.00 33.48 2.92
759 1656 3.195002 GGATAGCTTGTGCGCGCA 61.195 61.111 33.09 33.09 45.42 6.09
761 1658 3.630148 CCGGATAGCTTGTGCGCG 61.630 66.667 0.00 0.00 45.42 6.86
762 1659 3.272334 CCCGGATAGCTTGTGCGC 61.272 66.667 0.73 0.00 45.42 6.09
770 1667 3.255969 TGACACTTTAACCCGGATAGC 57.744 47.619 0.73 0.00 0.00 2.97
796 1754 3.656559 TCGCCGGATAGTTTATAAAGGC 58.343 45.455 5.05 11.88 39.89 4.35
797 1755 5.475719 TCATCGCCGGATAGTTTATAAAGG 58.524 41.667 5.05 0.00 0.00 3.11
798 1756 6.308282 GTCTCATCGCCGGATAGTTTATAAAG 59.692 42.308 5.05 0.00 0.00 1.85
799 1757 6.015688 AGTCTCATCGCCGGATAGTTTATAAA 60.016 38.462 5.05 0.00 0.00 1.40
801 1759 5.008331 AGTCTCATCGCCGGATAGTTTATA 58.992 41.667 5.05 0.00 0.00 0.98
808 1766 2.092323 CCATAGTCTCATCGCCGGATA 58.908 52.381 5.05 0.00 0.00 2.59
812 1770 1.609072 TCTTCCATAGTCTCATCGCCG 59.391 52.381 0.00 0.00 0.00 6.46
1679 2672 0.038744 CTTGAAGGTGCCACCAGGAT 59.961 55.000 17.80 0.00 41.95 3.24
1815 2823 4.314440 GTGTGCCGAGCTGGTGGA 62.314 66.667 0.00 0.00 41.21 4.02
1832 2843 3.409570 CATACCATCCATCTGAAGCAGG 58.590 50.000 0.00 0.00 31.51 4.85
1944 2956 1.945394 CTCCTCCGGCAATTCAATCTG 59.055 52.381 0.00 0.00 0.00 2.90
1945 2957 1.133976 CCTCCTCCGGCAATTCAATCT 60.134 52.381 0.00 0.00 0.00 2.40
1948 2960 0.253044 CTCCTCCTCCGGCAATTCAA 59.747 55.000 0.00 0.00 0.00 2.69
2090 3105 6.410157 CCCATAGGAATTTCTGGATCAACTCT 60.410 42.308 0.00 0.00 33.47 3.24
2367 3385 1.007238 CTGAGTCCAACCTCCCTCCTA 59.993 57.143 0.00 0.00 0.00 2.94
2368 3386 0.252467 CTGAGTCCAACCTCCCTCCT 60.252 60.000 0.00 0.00 0.00 3.69
2369 3387 0.545548 ACTGAGTCCAACCTCCCTCC 60.546 60.000 0.00 0.00 0.00 4.30
2385 3403 9.457110 CAAGCAAAGTAGATACTACTGATACTG 57.543 37.037 11.39 6.56 34.99 2.74
2390 3408 7.704578 AGACAAGCAAAGTAGATACTACTGA 57.295 36.000 11.39 0.00 34.99 3.41
2430 3448 3.452627 ACTTGTCTCTCCCATGGATGTAC 59.547 47.826 15.22 5.32 0.00 2.90
2440 3458 2.093658 TGCGGAATTACTTGTCTCTCCC 60.094 50.000 0.00 0.00 0.00 4.30
2460 3478 1.704641 TGGATCATACTCCCTCCGTG 58.295 55.000 0.00 0.00 34.12 4.94
2569 3589 1.305201 TGCGTCTTCCACAAGGTTTC 58.695 50.000 0.00 0.00 35.89 2.78
2585 3605 1.462283 CAGAACAGTGTCATCCTTGCG 59.538 52.381 0.00 0.00 0.00 4.85
2601 3621 9.273016 CAGATTCTTACTGAGGTTAAAACAGAA 57.727 33.333 0.00 0.00 37.54 3.02
2721 5920 6.162777 TCACAACGTCATATCATCAGTTTCA 58.837 36.000 0.00 0.00 0.00 2.69
2747 5947 8.998277 TCTGCTATTTCAGTACTAAGGATACT 57.002 34.615 0.00 0.00 41.49 2.12
2751 5951 8.639761 GGTATTCTGCTATTTCAGTACTAAGGA 58.360 37.037 0.00 0.00 35.63 3.36
2752 5952 8.421784 TGGTATTCTGCTATTTCAGTACTAAGG 58.578 37.037 0.00 0.00 35.63 2.69
2787 5999 9.997172 TCCTTGCTGGATTCTATATATCTAAGA 57.003 33.333 0.00 0.00 40.56 2.10
2790 6002 9.775539 ACTTCCTTGCTGGATTCTATATATCTA 57.224 33.333 0.09 0.00 45.68 1.98
2791 6003 8.677870 ACTTCCTTGCTGGATTCTATATATCT 57.322 34.615 0.09 0.00 45.68 1.98
2793 6005 9.554053 ACTACTTCCTTGCTGGATTCTATATAT 57.446 33.333 0.09 0.00 45.68 0.86
2796 6487 8.005388 AGTACTACTTCCTTGCTGGATTCTATA 58.995 37.037 0.00 0.00 45.68 1.31
2815 6517 2.257034 GTTGCGGCACACTAGTACTAC 58.743 52.381 0.05 0.00 0.00 2.73
2951 6660 6.825721 ACCAGGATAAACAGAAGCTAAATGAG 59.174 38.462 0.00 0.00 0.00 2.90
3016 6905 6.999950 TCAGTTCCAAAATACTACTACAGCA 58.000 36.000 0.00 0.00 0.00 4.41
3024 6913 6.433093 GGCTTCCTTTCAGTTCCAAAATACTA 59.567 38.462 0.00 0.00 0.00 1.82
3026 6915 5.243954 AGGCTTCCTTTCAGTTCCAAAATAC 59.756 40.000 0.00 0.00 0.00 1.89
3139 7227 5.867174 CAGGTCGTGACATATTTGTAGACAA 59.133 40.000 15.38 0.00 36.95 3.18
3160 7248 5.043248 GTCATTCTGTTTTTGTGGTTCAGG 58.957 41.667 0.00 0.00 0.00 3.86
3225 7315 5.654603 TCATGAAAAATTCAGCTCAGCAT 57.345 34.783 0.00 0.00 43.98 3.79
3285 7389 3.626996 CTGATGCCAGGCGTCCCAA 62.627 63.158 27.97 11.13 43.20 4.12
3289 7393 2.526304 TATAACTGATGCCAGGCGTC 57.474 50.000 25.07 25.07 44.60 5.19
3313 7417 0.822944 TTCACCACCGTCGTAGGTCA 60.823 55.000 3.12 0.00 43.89 4.02


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

AutoCloner maintained by Alex Coulton.