Multiple sequence alignment - TraesCS5A01G543700

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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 TraesCS5A01G543700 chr5A 100.000 2804 0 0 1 2804 699536372 699533569 0.000000e+00 5179.0
1 TraesCS5A01G543700 chr5A 100.000 1647 0 0 1 1647 699551327 699549681 0.000000e+00 3042.0
2 TraesCS5A01G543700 chr5A 100.000 1647 0 0 1 1647 699875768 699877414 0.000000e+00 3042.0
3 TraesCS5A01G543700 chr5A 88.852 2422 179 34 436 2804 700381413 700383796 0.000000e+00 2892.0
4 TraesCS5A01G543700 chr5A 88.728 2422 182 34 436 2804 699565833 699568216 0.000000e+00 2876.0
5 TraesCS5A01G543700 chr5A 88.728 2422 182 34 436 2804 699633430 699635813 0.000000e+00 2876.0
6 TraesCS5A01G543700 chr5A 88.716 2375 177 34 436 2757 700375929 700378265 0.000000e+00 2817.0
7 TraesCS5A01G543700 chr5A 73.676 642 106 34 2193 2794 632530188 632530806 1.030000e-44 191.0
8 TraesCS5A01G543700 chr5A 80.315 127 18 4 307 426 699565661 699565787 3.850000e-14 89.8
9 TraesCS5A01G543700 chr5A 80.315 127 18 4 307 426 699711903 699712029 3.850000e-14 89.8
10 TraesCS5A01G543700 chr5A 80.315 127 18 4 307 426 700375757 700375883 3.850000e-14 89.8
11 TraesCS5A01G543700 chr5A 80.315 127 18 4 307 426 700381241 700381367 3.850000e-14 89.8
12 TraesCS5A01G543700 chrUn 91.476 2405 155 15 421 2800 156680514 156682893 0.000000e+00 3260.0
13 TraesCS5A01G543700 chrUn 92.797 2249 128 14 579 2804 156734350 156736587 0.000000e+00 3225.0
14 TraesCS5A01G543700 chrUn 89.946 2417 159 29 436 2804 110266208 110263828 0.000000e+00 3040.0
15 TraesCS5A01G543700 chrUn 89.450 2417 155 28 436 2804 156615914 156618278 0.000000e+00 2959.0
16 TraesCS5A01G543700 chrUn 91.671 1729 98 17 789 2492 371511182 371509475 0.000000e+00 2353.0
17 TraesCS5A01G543700 chrUn 90.431 1672 122 14 1161 2804 184202477 184204138 0.000000e+00 2167.0
18 TraesCS5A01G543700 chrUn 87.271 927 70 15 436 1341 110203545 110202646 0.000000e+00 1014.0
19 TraesCS5A01G543700 chrUn 85.538 325 28 10 129 436 156733878 156734200 3.480000e-84 322.0
20 TraesCS5A01G543700 chrUn 88.931 262 23 2 2543 2804 467308524 467308779 4.510000e-83 318.0
21 TraesCS5A01G543700 chrUn 83.168 303 36 10 146 438 156680195 156680492 2.140000e-66 263.0
22 TraesCS5A01G543700 chrUn 95.385 130 6 0 1 130 156733574 156733703 1.020000e-49 207.0
23 TraesCS5A01G543700 chrUn 80.315 127 18 4 307 426 436720385 436720511 3.850000e-14 89.8
24 TraesCS5A01G543700 chr4B 90.640 2329 169 25 436 2733 660337703 660335393 0.000000e+00 3048.0
25 TraesCS5A01G543700 chr4B 87.593 2297 209 30 535 2799 660358323 660360575 0.000000e+00 2593.0
26 TraesCS5A01G543700 chr4B 82.026 306 37 12 129 421 660338058 660337758 7.760000e-61 244.0
27 TraesCS5A01G543700 chr4B 81.311 305 40 11 146 438 660357853 660358152 6.040000e-57 231.0
28 TraesCS5A01G543700 chr4B 93.846 130 8 0 1 130 660357555 660357684 2.200000e-46 196.0
29 TraesCS5A01G543700 chr4B 88.060 134 12 2 1 130 660351996 660351863 3.740000e-34 156.0
30 TraesCS5A01G543700 chr4B 86.364 132 16 1 428 557 660358180 660358311 2.910000e-30 143.0
31 TraesCS5A01G543700 chr4B 86.087 115 11 5 160 270 660330950 660330837 4.910000e-23 119.0
32 TraesCS5A01G543700 chr7D 76.098 615 112 20 2211 2798 564077592 564078198 3.530000e-74 289.0
33 TraesCS5A01G543700 chr3D 73.569 594 94 28 2211 2776 540255027 540254469 4.800000e-38 169.0


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 TraesCS5A01G543700 chr5A 699533569 699536372 2803 True 5179.000000 5179 100.0000 1 2804 1 chr5A.!!$R1 2803
1 TraesCS5A01G543700 chr5A 699549681 699551327 1646 True 3042.000000 3042 100.0000 1 1647 1 chr5A.!!$R2 1646
2 TraesCS5A01G543700 chr5A 699875768 699877414 1646 False 3042.000000 3042 100.0000 1 1647 1 chr5A.!!$F4 1646
3 TraesCS5A01G543700 chr5A 699633430 699635813 2383 False 2876.000000 2876 88.7280 436 2804 1 chr5A.!!$F2 2368
4 TraesCS5A01G543700 chr5A 699565661 699568216 2555 False 1482.900000 2876 84.5215 307 2804 2 chr5A.!!$F5 2497
5 TraesCS5A01G543700 chr5A 700375757 700383796 8039 False 1472.150000 2892 84.5495 307 2804 4 chr5A.!!$F6 2497
6 TraesCS5A01G543700 chrUn 110263828 110266208 2380 True 3040.000000 3040 89.9460 436 2804 1 chrUn.!!$R2 2368
7 TraesCS5A01G543700 chrUn 156615914 156618278 2364 False 2959.000000 2959 89.4500 436 2804 1 chrUn.!!$F1 2368
8 TraesCS5A01G543700 chrUn 371509475 371511182 1707 True 2353.000000 2353 91.6710 789 2492 1 chrUn.!!$R3 1703
9 TraesCS5A01G543700 chrUn 184202477 184204138 1661 False 2167.000000 2167 90.4310 1161 2804 1 chrUn.!!$F2 1643
10 TraesCS5A01G543700 chrUn 156680195 156682893 2698 False 1761.500000 3260 87.3220 146 2800 2 chrUn.!!$F5 2654
11 TraesCS5A01G543700 chrUn 156733574 156736587 3013 False 1251.333333 3225 91.2400 1 2804 3 chrUn.!!$F6 2803
12 TraesCS5A01G543700 chrUn 110202646 110203545 899 True 1014.000000 1014 87.2710 436 1341 1 chrUn.!!$R1 905
13 TraesCS5A01G543700 chr4B 660335393 660338058 2665 True 1646.000000 3048 86.3330 129 2733 2 chr4B.!!$R3 2604
14 TraesCS5A01G543700 chr4B 660357555 660360575 3020 False 790.750000 2593 87.2785 1 2799 4 chr4B.!!$F1 2798
15 TraesCS5A01G543700 chr7D 564077592 564078198 606 False 289.000000 289 76.0980 2211 2798 1 chr7D.!!$F1 587

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
1701 2035 1.039068 CCAATGCAGTGTTTGGGTCA 58.961 50.0 13.82 0.0 38.98 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2620 8478 0.036671 AGGGGTGTGTAAACGCTAGC 60.037 55.0 4.06 4.06 33.72 3.42 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
1701 2035 1.039068 CCAATGCAGTGTTTGGGTCA 58.961 50.000 13.82 0.00 38.98 4.02
1809 2143 5.099042 AGAACAACCACAACTAAGTCAGT 57.901 39.130 0.00 0.00 40.05 3.41
1848 2182 7.230510 ACACAGAAGATTAGTGCATAAACCAAA 59.769 33.333 0.00 0.00 36.76 3.28
1849 2183 8.246180 CACAGAAGATTAGTGCATAAACCAAAT 58.754 33.333 0.00 0.00 0.00 2.32
1924 7744 0.179070 TGCCGCTGTGTGTCTGTAAA 60.179 50.000 0.00 0.00 0.00 2.01
1928 7748 1.260561 CGCTGTGTGTCTGTAAACCAC 59.739 52.381 0.00 0.00 0.00 4.16
1929 7749 1.602377 GCTGTGTGTCTGTAAACCACC 59.398 52.381 0.00 0.00 0.00 4.61
2051 7873 9.143631 CATAACAAATGAAAATTCAGGGTTCTC 57.856 33.333 10.94 0.00 41.08 2.87
2056 7879 5.324832 TGAAAATTCAGGGTTCTCTTCCT 57.675 39.130 0.00 0.00 32.50 3.36
2064 7887 2.112691 AGGGTTCTCTTCCTCTTCTCCA 59.887 50.000 0.00 0.00 0.00 3.86
2155 7978 7.290110 TCTACATATATAGTGCTTGTGTGCT 57.710 36.000 0.00 0.00 0.00 4.40
2174 7997 2.413112 GCTATACATGTGCGGCACTATG 59.587 50.000 30.81 29.15 35.11 2.23
2181 8004 1.754226 TGTGCGGCACTATGATGTCTA 59.246 47.619 30.81 6.52 35.11 2.59
2206 8031 3.512219 TGGTTATGACGAAAAAGGGGT 57.488 42.857 0.00 0.00 0.00 4.95
2207 8032 3.834938 TGGTTATGACGAAAAAGGGGTT 58.165 40.909 0.00 0.00 0.00 4.11
2243 8073 0.732571 ATAAAGCAACCATCACCGCG 59.267 50.000 0.00 0.00 0.00 6.46
2272 8102 3.255149 CCGAGTAGGCCGATATAAACACT 59.745 47.826 0.00 0.00 0.00 3.55
2275 8105 3.887716 AGTAGGCCGATATAAACACTCGT 59.112 43.478 0.00 0.00 0.00 4.18
2299 8129 2.745785 CCGCACACAACACACACGT 61.746 57.895 0.00 0.00 0.00 4.49
2370 8203 5.614324 ACCAAGCTAACTACAGATATGCA 57.386 39.130 0.00 0.00 0.00 3.96
2389 8222 1.946768 CAAAGAAGACCGTTTGGAGCA 59.053 47.619 0.00 0.00 39.21 4.26
2428 8264 2.104111 TGAACCACAACGAAGAGGTGAT 59.896 45.455 0.00 0.00 40.93 3.06
2534 8392 1.993370 GATGAAAGGAGTCGGAACACG 59.007 52.381 0.00 0.00 46.11 4.49
2556 8414 1.827969 CGATGGAGCCTATAGGAAGGG 59.172 57.143 23.61 0.00 37.11 3.95
2570 8428 2.370849 AGGAAGGGTACAACGTCAACAT 59.629 45.455 0.00 0.00 0.00 2.71
2571 8429 3.579586 AGGAAGGGTACAACGTCAACATA 59.420 43.478 0.00 0.00 0.00 2.29
2572 8430 4.224370 AGGAAGGGTACAACGTCAACATAT 59.776 41.667 0.00 0.00 0.00 1.78
2573 8431 4.569564 GGAAGGGTACAACGTCAACATATC 59.430 45.833 0.00 0.00 0.00 1.63
2574 8432 4.811969 AGGGTACAACGTCAACATATCA 57.188 40.909 0.00 0.00 0.00 2.15
2610 8468 1.746615 CAGGACACGGATTGGGCAG 60.747 63.158 0.00 0.00 0.00 4.85
2614 8472 2.751436 CACGGATTGGGCAGGTGG 60.751 66.667 0.00 0.00 0.00 4.61
2637 8497 2.075761 CGCTAGCGTTTACACACCC 58.924 57.895 28.66 0.00 34.35 4.61
2639 8499 0.036671 GCTAGCGTTTACACACCCCT 60.037 55.000 0.00 0.00 0.00 4.79
2656 8516 0.904865 CCTGTCACACCCTAGCTCCA 60.905 60.000 0.00 0.00 0.00 3.86
2800 8660 1.756538 CCAAGACCAGCCAAAGTGTTT 59.243 47.619 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1701 2035 4.264083 ACATCATCTGAAATTGGTGGGTCT 60.264 41.667 0.00 0.00 0.00 3.85
1713 2047 3.760151 CCTTGGCAAGAACATCATCTGAA 59.240 43.478 28.18 0.00 0.00 3.02
1848 2182 6.757897 TGCTCGAGAAATTCAACCAAATAT 57.242 33.333 18.75 0.00 0.00 1.28
1849 2183 6.183360 GGATGCTCGAGAAATTCAACCAAATA 60.183 38.462 18.75 0.00 0.00 1.40
1895 2231 1.480545 ACACAGCGGCATGACATACTA 59.519 47.619 10.76 0.00 0.00 1.82
1897 2233 0.374758 CACACAGCGGCATGACATAC 59.625 55.000 10.76 0.00 0.00 2.39
1924 7744 8.359875 TCATAACATTGAAATACATTGGTGGT 57.640 30.769 0.00 0.00 35.12 4.16
2051 7873 7.764443 TCGTTTATTGTATTGGAGAAGAGGAAG 59.236 37.037 0.00 0.00 0.00 3.46
2098 7921 2.276201 GTTCAACCAAACCAGCAAACC 58.724 47.619 0.00 0.00 0.00 3.27
2155 7978 4.244862 CATCATAGTGCCGCACATGTATA 58.755 43.478 24.97 8.91 36.74 1.47
2174 7997 5.597806 TCGTCATAACCAATGGTAGACATC 58.402 41.667 23.06 7.85 39.40 3.06
2181 8004 4.219725 CCCTTTTTCGTCATAACCAATGGT 59.780 41.667 0.00 0.00 37.65 3.55
2243 8073 0.527565 TCGGCCTACTCGGTTGTAAC 59.472 55.000 0.00 0.00 34.25 2.50
2258 8088 2.793232 GGTGACGAGTGTTTATATCGGC 59.207 50.000 0.00 0.00 44.75 5.54
2272 8102 3.372554 TTGTGTGCGGTGGTGACGA 62.373 57.895 0.00 0.00 0.00 4.20
2275 8105 2.109739 GTGTTGTGTGCGGTGGTGA 61.110 57.895 0.00 0.00 0.00 4.02
2299 8129 5.475719 CCGACACCTTTGTATCTTGTCTTA 58.524 41.667 0.00 0.00 35.47 2.10
2370 8203 2.158813 TCTGCTCCAAACGGTCTTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
2428 8264 0.604073 TGGCTTCATCGTTGTCCGTA 59.396 50.000 0.00 0.00 37.94 4.02
2539 8397 2.520980 TGTACCCTTCCTATAGGCTCCA 59.479 50.000 14.50 0.00 33.73 3.86
2595 8453 2.040544 CACCTGCCCAATCCGTGTC 61.041 63.158 0.00 0.00 0.00 3.67
2620 8478 0.036671 AGGGGTGTGTAAACGCTAGC 60.037 55.000 4.06 4.06 33.72 3.42
2622 8480 1.001181 GACAGGGGTGTGTAAACGCTA 59.999 52.381 0.00 0.00 33.72 4.26
2637 8497 0.904865 TGGAGCTAGGGTGTGACAGG 60.905 60.000 0.00 0.00 0.00 4.00
2639 8499 0.178932 AGTGGAGCTAGGGTGTGACA 60.179 55.000 0.00 0.00 0.00 3.58
2656 8516 1.064952 GCTTGGTTGCGTGTGTTTAGT 59.935 47.619 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.