Multiple sequence alignment - TraesCS5A01G534700

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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 TraesCS5A01G534700 chr5A 100.000 2552 0 0 1 2552 691814402 691811851 0.000000e+00 4713.0
1 TraesCS5A01G534700 chr5A 84.881 1217 149 16 136 1323 678082155 678083365 0.000000e+00 1195.0
2 TraesCS5A01G534700 chr5A 84.164 1124 136 23 1323 2429 678083440 678084538 0.000000e+00 1051.0
3 TraesCS5A01G534700 chr4B 92.835 2247 108 17 272 2494 654126344 654124127 0.000000e+00 3208.0
4 TraesCS5A01G534700 chr4B 91.094 1572 108 17 1 1564 654131858 654130311 0.000000e+00 2098.0
5 TraesCS5A01G534700 chr4B 85.879 1211 142 17 136 1323 638988593 638987389 0.000000e+00 1262.0
6 TraesCS5A01G534700 chr4B 81.842 1129 150 26 1323 2429 638987314 638986219 0.000000e+00 898.0
7 TraesCS5A01G534700 chr4B 77.647 850 146 27 328 1166 431795283 431796099 6.390000e-131 477.0
8 TraesCS5A01G534700 chr4B 82.600 477 72 5 2021 2496 654129302 654128836 6.570000e-111 411.0
9 TraesCS5A01G534700 chr4B 85.654 237 31 1 1788 2021 654129568 654129332 1.960000e-61 246.0
10 TraesCS5A01G534700 chr4B 82.659 173 24 4 1553 1725 654129765 654129599 5.690000e-32 148.0
11 TraesCS5A01G534700 chr4B 96.491 57 2 0 2494 2550 654124105 654124049 7.520000e-16 95.3
12 TraesCS5A01G534700 chr4B 90.164 61 4 2 2494 2552 654128818 654128758 7.570000e-11 78.7
13 TraesCS5A01G534700 chr2D 87.873 2243 228 25 271 2496 602009553 602007338 0.000000e+00 2595.0
14 TraesCS5A01G534700 chr2D 86.667 165 18 1 55 219 602009721 602009561 2.020000e-41 180.0
15 TraesCS5A01G534700 chr2B 87.299 2244 238 27 271 2496 732224562 732222348 0.000000e+00 2521.0
16 TraesCS5A01G534700 chr2B 85.455 165 20 1 55 219 732224730 732224570 4.370000e-38 169.0
17 TraesCS5A01G534700 chr2B 100.000 38 0 0 2511 2548 732222311 732222274 1.270000e-08 71.3
18 TraesCS5A01G534700 chr4D 85.538 1217 141 19 136 1323 497667736 497666526 0.000000e+00 1240.0
19 TraesCS5A01G534700 chr4D 83.260 1129 134 31 1323 2429 497666451 497665356 0.000000e+00 987.0
20 TraesCS5A01G534700 chr4D 75.669 859 146 45 328 1164 630997 630180 1.120000e-98 370.0
21 TraesCS5A01G534700 chr4A 85.225 934 120 13 312 1243 731002829 731003746 0.000000e+00 944.0
22 TraesCS5A01G534700 chr5B 81.624 936 140 20 322 1243 6918244 6919161 0.000000e+00 747.0


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 TraesCS5A01G534700 chr5A 691811851 691814402 2551 True 4713.000000 4713 100.000000 1 2552 1 chr5A.!!$R1 2551
1 TraesCS5A01G534700 chr5A 678082155 678084538 2383 False 1123.000000 1195 84.522500 136 2429 2 chr5A.!!$F1 2293
2 TraesCS5A01G534700 chr4B 638986219 638988593 2374 True 1080.000000 1262 83.860500 136 2429 2 chr4B.!!$R1 2293
3 TraesCS5A01G534700 chr4B 654124049 654131858 7809 True 897.857143 3208 88.785286 1 2552 7 chr4B.!!$R2 2551
4 TraesCS5A01G534700 chr4B 431795283 431796099 816 False 477.000000 477 77.647000 328 1166 1 chr4B.!!$F1 838
5 TraesCS5A01G534700 chr2D 602007338 602009721 2383 True 1387.500000 2595 87.270000 55 2496 2 chr2D.!!$R1 2441
6 TraesCS5A01G534700 chr2B 732222274 732224730 2456 True 920.433333 2521 90.918000 55 2548 3 chr2B.!!$R1 2493
7 TraesCS5A01G534700 chr4D 497665356 497667736 2380 True 1113.500000 1240 84.399000 136 2429 2 chr4D.!!$R2 2293
8 TraesCS5A01G534700 chr4D 630180 630997 817 True 370.000000 370 75.669000 328 1164 1 chr4D.!!$R1 836
9 TraesCS5A01G534700 chr4A 731002829 731003746 917 False 944.000000 944 85.225000 312 1243 1 chr4A.!!$F1 931
10 TraesCS5A01G534700 chr5B 6918244 6919161 917 False 747.000000 747 81.624000 322 1243 1 chr5B.!!$F1 921

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
186 189 0.235926 GGAGAACACTTTGCTGTCGC 59.764 55.0 0.0 0.0 0.0 5.19 F
956 6235 0.957395 AGCGTGCCTTTCTCCATGTG 60.957 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 6558 0.250467 GTCTGGGCTGAGCAGTTGAA 60.250 55.0 6.82 0.0 0.00 2.69 R
1798 7162 0.318360 CGTGGTGTACAAGACGCAGA 60.318 55.0 13.25 0.0 40.59 4.26 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
35 36 4.273318 ACAAATGAAATAGGAGAGGGTGC 58.727 43.478 0.00 0.00 0.00 5.01
58 59 5.572126 GCTCTATTTTTCTGAAGCTTTGCAG 59.428 40.000 0.00 4.45 0.00 4.41
84 85 3.873910 CATCTAAATGGGGTTCAGACGT 58.126 45.455 0.00 0.00 0.00 4.34
176 179 0.534412 CGCTCATCTGGGAGAACACT 59.466 55.000 0.00 0.00 37.05 3.55
186 189 0.235926 GGAGAACACTTTGCTGTCGC 59.764 55.000 0.00 0.00 0.00 5.19
219 222 1.882989 GCTCAAGCAGGTCTCGTCCT 61.883 60.000 0.00 0.00 41.59 3.85
244 250 2.551270 CGTCAACAAGCTCACGCC 59.449 61.111 0.00 0.00 36.60 5.68
307 325 2.594962 CGCTGTTGCCGAGTTCGTT 61.595 57.895 0.48 0.00 37.74 3.85
385 403 2.507854 CCATGGACGGCCGGTCTAT 61.508 63.158 31.76 22.74 46.57 1.98
490 508 2.107141 GATCTTGTCGAGCCCCCG 59.893 66.667 0.00 0.00 0.00 5.73
757 778 4.263572 CACCTTGGCCACGACCCA 62.264 66.667 11.54 0.00 0.00 4.51
760 789 4.308458 CTTGGCCACGACCCACGA 62.308 66.667 3.88 0.00 45.77 4.35
762 791 3.599285 TTGGCCACGACCCACGATC 62.599 63.158 3.88 0.00 45.77 3.69
763 792 4.077184 GGCCACGACCCACGATCA 62.077 66.667 0.00 0.00 45.77 2.92
956 6235 0.957395 AGCGTGCCTTTCTCCATGTG 60.957 55.000 0.00 0.00 0.00 3.21
1149 6428 1.540797 CCCTTGTACACGTTCCCGAAA 60.541 52.381 0.00 0.00 37.88 3.46
1279 6558 0.900647 CTCTCTGGACCACCGGTTCT 60.901 60.000 2.97 0.00 42.77 3.01
1297 6576 0.035881 CTTCAACTGCTCAGCCCAGA 59.964 55.000 0.00 0.00 34.47 3.86
1388 6745 2.312436 GCACCACCGACACCGTAAC 61.312 63.158 0.00 0.00 0.00 2.50
1727 7084 2.732619 GGTAGCGGGACCCTGGAAG 61.733 68.421 9.41 0.00 32.88 3.46
1729 7086 3.618855 TAGCGGGACCCTGGAAGCT 62.619 63.158 9.41 11.88 38.57 3.74
1766 7130 2.203422 TTGAAGCCCGGGGTTGTG 60.203 61.111 41.16 5.58 35.84 3.33
1786 7150 2.362369 CCTGCAGGAGGTCCGTCAT 61.362 63.158 29.88 0.00 42.08 3.06
1877 7241 1.118356 AGATGATCGGGCTGGAGGTC 61.118 60.000 0.00 0.00 0.00 3.85
1878 7242 2.427540 GATGATCGGGCTGGAGGTCG 62.428 65.000 0.00 0.00 0.00 4.79
1879 7243 2.833582 GATCGGGCTGGAGGTCGA 60.834 66.667 0.00 0.00 36.07 4.20
1880 7244 2.363795 ATCGGGCTGGAGGTCGAA 60.364 61.111 0.00 0.00 35.25 3.71
1883 7247 2.266055 GGGCTGGAGGTCGAACTG 59.734 66.667 8.28 0.00 0.00 3.16
1897 7261 2.377628 GAACTGACCACCGACTGCCA 62.378 60.000 0.00 0.00 0.00 4.92
1898 7262 2.357517 CTGACCACCGACTGCCAC 60.358 66.667 0.00 0.00 0.00 5.01
1939 7312 2.741092 GAGCCACGTCCTCCACAA 59.259 61.111 2.09 0.00 0.00 3.33
2102 7481 4.373116 GCCGGGAACAGCTCGACA 62.373 66.667 2.18 0.00 45.56 4.35
2164 7546 1.355210 CGGTGATATTGCCGCCAAC 59.645 57.895 6.07 0.00 41.53 3.77
2300 7685 5.268131 TGATGATATACTGAGAGGAGCCT 57.732 43.478 0.00 0.00 0.00 4.58
2550 7957 2.819595 GCCGCATGCGAGGAAGAA 60.820 61.111 39.90 0.00 42.83 2.52
2551 7958 2.182842 GCCGCATGCGAGGAAGAAT 61.183 57.895 39.90 0.00 42.83 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.012508 ACCCTCTCCTATTTCATTTGTCTGAA 60.013 38.462 0.00 0.00 33.42 3.02
24 25 4.080638 CAGAAAAATAGAGCACCCTCTCCT 60.081 45.833 0.00 0.00 45.21 3.69
35 36 5.572126 GCTGCAAAGCTTCAGAAAAATAGAG 59.428 40.000 17.04 0.00 32.26 2.43
67 68 4.069304 CTGAAACGTCTGAACCCCATTTA 58.931 43.478 0.00 0.00 0.00 1.40
84 85 0.183971 TCCTTTGGCGTTCCCTGAAA 59.816 50.000 0.00 0.00 0.00 2.69
124 125 3.132289 GGGACGATGATCTGAAGTTGGTA 59.868 47.826 0.00 0.00 0.00 3.25
163 166 1.490490 ACAGCAAAGTGTTCTCCCAGA 59.510 47.619 0.00 0.00 0.00 3.86
504 522 4.436998 CGAGTGGGCGGTGAGGAC 62.437 72.222 0.00 0.00 0.00 3.85
956 6235 1.683917 AGATGATCCTGGTGTACGAGC 59.316 52.381 0.00 0.00 0.00 5.03
1279 6558 0.250467 GTCTGGGCTGAGCAGTTGAA 60.250 55.000 6.82 0.00 0.00 2.69
1375 6729 0.314935 ATTGTCGTTACGGTGTCGGT 59.685 50.000 4.53 0.00 41.39 4.69
1388 6745 2.860735 GGGACGAAGAGAATCATTGTCG 59.139 50.000 0.00 0.00 45.67 4.35
1419 6776 0.683179 TCGATTTGAGCTCGAGGGGA 60.683 55.000 15.58 2.71 40.01 4.81
1545 6902 2.352388 GCCTTTTACATGGACTACGCA 58.648 47.619 0.00 0.00 0.00 5.24
1798 7162 0.318360 CGTGGTGTACAAGACGCAGA 60.318 55.000 13.25 0.00 40.59 4.26
1877 7241 2.022129 GCAGTCGGTGGTCAGTTCG 61.022 63.158 0.00 0.00 0.00 3.95
1878 7242 1.668151 GGCAGTCGGTGGTCAGTTC 60.668 63.158 0.00 0.00 0.00 3.01
1879 7243 2.426023 GGCAGTCGGTGGTCAGTT 59.574 61.111 0.00 0.00 0.00 3.16
1880 7244 2.842462 TGGCAGTCGGTGGTCAGT 60.842 61.111 0.00 0.00 0.00 3.41
1883 7247 4.699522 GGGTGGCAGTCGGTGGTC 62.700 72.222 0.00 0.00 0.00 4.02
1897 7261 2.281429 GCCCCTACCTCTACGGGT 59.719 66.667 0.00 0.00 42.86 5.28
1898 7262 2.523657 GGCCCCTACCTCTACGGG 60.524 72.222 0.00 0.00 38.70 5.28
2014 7387 1.078759 GAACGACGACATGGAGCTGG 61.079 60.000 0.00 0.00 0.00 4.85
2049 7422 1.885850 GGAACAACACGGCGACACT 60.886 57.895 16.62 0.00 0.00 3.55
2505 7912 0.687757 CTCCGTCTCCTTCCCATCCA 60.688 60.000 0.00 0.00 0.00 3.41
2509 7916 1.000486 CTCCTCCGTCTCCTTCCCA 60.000 63.158 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.