Multiple sequence alignment - TraesCS5A01G040200

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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 TraesCS5A01G040200 chr5A 100.000 2549 0 0 1 2549 36350446 36352994 0 4708
1 TraesCS5A01G040200 chr5A 97.856 793 15 2 2 793 36334930 36335721 0 1369
2 TraesCS5A01G040200 chr5A 97.100 793 19 3 1 793 640044780 640043992 0 1334
3 TraesCS5A01G040200 chr5A 96.981 795 19 4 1 793 53376524 53375733 0 1330
4 TraesCS5A01G040200 chr7A 95.888 1751 59 9 787 2531 701582159 701583902 0 2822
5 TraesCS5A01G040200 chr7A 95.769 1749 63 9 787 2531 39015586 39017327 0 2809
6 TraesCS5A01G040200 chr7A 96.981 795 21 2 1 793 414068767 414069560 0 1332
7 TraesCS5A01G040200 chr7A 96.974 793 21 2 1 792 9068295 9067505 0 1328
8 TraesCS5A01G040200 chr2B 95.883 1749 61 8 787 2531 781094459 781096200 0 2820
9 TraesCS5A01G040200 chr2B 95.826 1749 62 9 787 2531 776223180 776224921 0 2815
10 TraesCS5A01G040200 chrUn 95.826 1749 61 8 787 2531 175762331 175764071 0 2815
11 TraesCS5A01G040200 chr3B 95.826 1749 62 9 787 2531 20305306 20307047 0 2815
12 TraesCS5A01G040200 chr4B 95.920 1740 61 8 797 2531 368430142 368428408 0 2811
13 TraesCS5A01G040200 chr2A 95.917 1739 62 7 797 2531 682508907 682507174 0 2809
14 TraesCS5A01G040200 chr2A 97.107 795 19 3 1 793 461647 462439 0 1338
15 TraesCS5A01G040200 chr6A 95.864 1741 60 9 797 2531 617222643 617220909 0 2806
16 TraesCS5A01G040200 chr1A 97.226 793 20 1 1 793 7137263 7138053 0 1341
17 TraesCS5A01G040200 chr4A 96.859 796 20 4 1 793 400662970 400663763 0 1327
18 TraesCS5A01G040200 chr3A 96.730 795 21 5 1 793 713909966 713909175 0 1319


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 TraesCS5A01G040200 chr5A 36350446 36352994 2548 False 4708 4708 100.000 1 2549 1 chr5A.!!$F2 2548
1 TraesCS5A01G040200 chr5A 36334930 36335721 791 False 1369 1369 97.856 2 793 1 chr5A.!!$F1 791
2 TraesCS5A01G040200 chr5A 640043992 640044780 788 True 1334 1334 97.100 1 793 1 chr5A.!!$R2 792
3 TraesCS5A01G040200 chr5A 53375733 53376524 791 True 1330 1330 96.981 1 793 1 chr5A.!!$R1 792
4 TraesCS5A01G040200 chr7A 701582159 701583902 1743 False 2822 2822 95.888 787 2531 1 chr7A.!!$F3 1744
5 TraesCS5A01G040200 chr7A 39015586 39017327 1741 False 2809 2809 95.769 787 2531 1 chr7A.!!$F1 1744
6 TraesCS5A01G040200 chr7A 414068767 414069560 793 False 1332 1332 96.981 1 793 1 chr7A.!!$F2 792
7 TraesCS5A01G040200 chr7A 9067505 9068295 790 True 1328 1328 96.974 1 792 1 chr7A.!!$R1 791
8 TraesCS5A01G040200 chr2B 781094459 781096200 1741 False 2820 2820 95.883 787 2531 1 chr2B.!!$F2 1744
9 TraesCS5A01G040200 chr2B 776223180 776224921 1741 False 2815 2815 95.826 787 2531 1 chr2B.!!$F1 1744
10 TraesCS5A01G040200 chrUn 175762331 175764071 1740 False 2815 2815 95.826 787 2531 1 chrUn.!!$F1 1744
11 TraesCS5A01G040200 chr3B 20305306 20307047 1741 False 2815 2815 95.826 787 2531 1 chr3B.!!$F1 1744
12 TraesCS5A01G040200 chr4B 368428408 368430142 1734 True 2811 2811 95.920 797 2531 1 chr4B.!!$R1 1734
13 TraesCS5A01G040200 chr2A 682507174 682508907 1733 True 2809 2809 95.917 797 2531 1 chr2A.!!$R1 1734
14 TraesCS5A01G040200 chr2A 461647 462439 792 False 1338 1338 97.107 1 793 1 chr2A.!!$F1 792
15 TraesCS5A01G040200 chr6A 617220909 617222643 1734 True 2806 2806 95.864 797 2531 1 chr6A.!!$R1 1734
16 TraesCS5A01G040200 chr1A 7137263 7138053 790 False 1341 1341 97.226 1 793 1 chr1A.!!$F1 792
17 TraesCS5A01G040200 chr4A 400662970 400663763 793 False 1327 1327 96.859 1 793 1 chr4A.!!$F1 792
18 TraesCS5A01G040200 chr3A 713909175 713909966 791 True 1319 1319 96.730 1 793 1 chr3A.!!$R1 792

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
795 807 0.250124 TGCTACGTTCCCCAACACAG 60.25 55.0 0.0 0.0 32.14 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2329 0.665835 TGTGCAAACATTCACGGTCC 59.334 50.0 0.0 0.0 36.06 4.46 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
42 43 4.319694 CGGAAAAGTTTCGGGTTTTATCGT 60.320 41.667 3.99 0.00 38.06 3.73
178 183 3.914713 CCCACCAAGGCCCAAGGT 61.915 66.667 0.00 1.39 35.39 3.50
682 694 0.672091 TTGAACGCTTCCGCATAGCA 60.672 50.000 0.00 0.00 38.55 3.49
795 807 0.250124 TGCTACGTTCCCCAACACAG 60.250 55.000 0.00 0.00 32.14 3.66
847 861 4.408921 TGTGCTATATAAGAGGGCAACAGT 59.591 41.667 0.00 0.00 34.65 3.55
876 890 4.103103 CCGCGACAGAGAGCACGA 62.103 66.667 8.23 0.00 0.00 4.35
891 905 2.204461 ACGACGGTGACCATGGTGA 61.204 57.895 25.52 12.35 0.00 4.02
892 906 1.446099 CGACGGTGACCATGGTGAG 60.446 63.158 25.52 12.74 0.00 3.51
893 907 1.873270 CGACGGTGACCATGGTGAGA 61.873 60.000 25.52 2.43 0.00 3.27
894 908 0.320374 GACGGTGACCATGGTGAGAA 59.680 55.000 25.52 1.61 0.00 2.87
909 925 2.486203 GTGAGAAAGAGAGAGAGCACGA 59.514 50.000 0.00 0.00 0.00 4.35
934 950 1.268283 GGAAGCTAGCTGTGGAGGGT 61.268 60.000 20.16 0.00 0.00 4.34
936 952 0.838122 AAGCTAGCTGTGGAGGGTGT 60.838 55.000 20.16 0.00 0.00 4.16
953 969 2.606519 TGGCGGTGGGAAGCTAGT 60.607 61.111 0.00 0.00 0.00 2.57
988 1004 1.515954 GCGTTGAGATCCCCTTCGA 59.484 57.895 0.00 0.00 0.00 3.71
1122 1138 0.966920 GGGTTTCTCAGACACCGAGA 59.033 55.000 3.82 0.00 33.60 4.04
1193 1209 1.460359 GGCAATTGCACCATTTTCGTG 59.540 47.619 30.32 0.00 44.36 4.35
1202 1218 1.014352 CCATTTTCGTGGTCGGGATC 58.986 55.000 0.00 0.00 37.69 3.36
1209 1225 0.530744 CGTGGTCGGGATCTTTGAGA 59.469 55.000 0.00 0.00 0.00 3.27
1227 1243 5.710513 TGAGAAATGGGTTGATCTGTTTG 57.289 39.130 0.00 0.00 0.00 2.93
1237 1253 4.037923 GGTTGATCTGTTTGGTGTTCATGT 59.962 41.667 0.00 0.00 0.00 3.21
1377 1393 2.430332 AGCTCCGAAAGAAGAGATGGAG 59.570 50.000 1.76 1.76 32.95 3.86
1408 1424 1.469595 GCACTGACAGAGAGCTAGCTG 60.470 57.143 24.99 11.34 35.53 4.24
1443 1459 6.887002 GGATGTTGAAGAAGAAGGTTAGGAAT 59.113 38.462 0.00 0.00 0.00 3.01
1456 1472 8.386264 AGAAGGTTAGGAATCTTGAAGATCAAA 58.614 33.333 8.32 0.00 35.73 2.69
1742 1759 1.696336 TCTCTGCTCTGCCTTTCTGTT 59.304 47.619 0.00 0.00 0.00 3.16
1833 1851 1.270550 GCATCCAATTAGGCCCATTCG 59.729 52.381 0.00 0.00 37.29 3.34
2065 2083 1.274447 GTAGAGGTTTACGCCAGGTGT 59.726 52.381 11.33 11.33 0.00 4.16
2114 2133 9.382275 GGGCATTACATTGAGAAAAACATAATT 57.618 29.630 0.00 0.00 0.00 1.40
2219 2240 0.324552 TAGGGCTACGCTGGTAACCA 60.325 55.000 0.00 0.00 36.73 3.67
2343 2367 3.972107 ACGCGTGAGAGTGGTTTTA 57.028 47.368 12.93 0.00 44.38 1.52
2429 2453 3.569194 TTTTGGTCAGAGTGGCACTTA 57.431 42.857 22.98 7.89 0.00 2.24
2468 2492 6.015772 GTGGCACTTGGTTTAGGATTTAAAGA 60.016 38.462 11.13 0.00 0.00 2.52
2496 2520 6.922247 AAATTTGCATGTTTGTTCATGACA 57.078 29.167 10.28 0.00 45.41 3.58
2534 2558 4.048470 GGGCTTCTCACCCCACCC 62.048 72.222 0.00 0.00 42.01 4.61
2535 2559 4.048470 GGCTTCTCACCCCACCCC 62.048 72.222 0.00 0.00 0.00 4.95
2536 2560 4.048470 GCTTCTCACCCCACCCCC 62.048 72.222 0.00 0.00 0.00 5.40
2537 2561 2.531685 CTTCTCACCCCACCCCCA 60.532 66.667 0.00 0.00 0.00 4.96
2538 2562 2.856988 TTCTCACCCCACCCCCAC 60.857 66.667 0.00 0.00 0.00 4.61
2539 2563 4.995058 TCTCACCCCACCCCCACC 62.995 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 183 2.284921 CCTCCCACTCTCCCTGCA 60.285 66.667 0.00 0.00 0.00 4.41
411 421 0.837272 AGAGACGAGGAGGAGAGAGG 59.163 60.000 0.00 0.00 0.00 3.69
412 422 2.288666 CAAGAGACGAGGAGGAGAGAG 58.711 57.143 0.00 0.00 0.00 3.20
795 807 1.809209 GCTCTGCTCAACGGCTCTC 60.809 63.158 0.00 0.00 0.00 3.20
816 830 4.562347 CCTCTTATATAGCACACCTGCCAG 60.562 50.000 0.00 0.00 45.53 4.85
821 835 3.587498 TGCCCTCTTATATAGCACACCT 58.413 45.455 0.00 0.00 0.00 4.00
837 851 4.954970 CACCGCCACTGTTGCCCT 62.955 66.667 0.00 0.00 0.00 5.19
860 874 2.872001 GTCGTGCTCTCTGTCGCG 60.872 66.667 0.00 0.00 37.53 5.87
876 890 0.762418 TTTCTCACCATGGTCACCGT 59.238 50.000 16.53 0.00 0.00 4.83
891 905 1.466950 CGTCGTGCTCTCTCTCTTTCT 59.533 52.381 0.00 0.00 0.00 2.52
892 906 1.466697 CCGTCGTGCTCTCTCTCTTTC 60.467 57.143 0.00 0.00 0.00 2.62
893 907 0.523966 CCGTCGTGCTCTCTCTCTTT 59.476 55.000 0.00 0.00 0.00 2.52
894 908 1.928706 GCCGTCGTGCTCTCTCTCTT 61.929 60.000 0.00 0.00 0.00 2.85
909 925 4.148825 CAGCTAGCTTCCCGCCGT 62.149 66.667 16.46 0.00 40.39 5.68
934 950 2.925706 TAGCTTCCCACCGCCACA 60.926 61.111 0.00 0.00 0.00 4.17
936 952 1.305465 TACTAGCTTCCCACCGCCA 60.305 57.895 0.00 0.00 0.00 5.69
988 1004 0.820871 GAAGACATGGAGCTCGGAGT 59.179 55.000 7.83 5.42 0.00 3.85
1061 1077 1.154016 CGCGGACAGACGAAGACAT 60.154 57.895 0.00 0.00 35.47 3.06
1101 1117 0.966920 TCGGTGTCTGAGAAACCCTC 59.033 55.000 16.02 0.00 36.63 4.30
1122 1138 2.833631 AGAACGGACGATTCTGGTTT 57.166 45.000 0.00 0.00 35.06 3.27
1193 1209 2.945668 CCATTTCTCAAAGATCCCGACC 59.054 50.000 0.00 0.00 0.00 4.79
1202 1218 5.972107 ACAGATCAACCCATTTCTCAAAG 57.028 39.130 0.00 0.00 0.00 2.77
1209 1225 3.966665 ACACCAAACAGATCAACCCATTT 59.033 39.130 0.00 0.00 0.00 2.32
1237 1253 4.761739 CCAAAGAAAGAAGCATGTCACCTA 59.238 41.667 0.00 0.00 0.00 3.08
1348 1364 2.357034 TTTCGGAGCTCGTGGTGC 60.357 61.111 7.83 0.00 40.32 5.01
1363 1379 1.573108 TCGCCCTCCATCTCTTCTTT 58.427 50.000 0.00 0.00 0.00 2.52
1408 1424 5.934625 TCTTCTTCAACATCCTAAGCTCAAC 59.065 40.000 0.00 0.00 0.00 3.18
1443 1459 7.606456 GGTATTGGTAGTGTTTGATCTTCAAGA 59.394 37.037 0.00 0.00 37.70 3.02
1456 1472 4.040936 TGCAAATGGGTATTGGTAGTGT 57.959 40.909 0.00 0.00 0.00 3.55
1582 1598 9.981114 CCAACATTTAAACTAGGTGAATTTCTT 57.019 29.630 0.00 0.00 0.00 2.52
1833 1851 3.671008 AAAATACGCAAAAGAACCCCC 57.329 42.857 0.00 0.00 0.00 5.40
1993 2011 9.190858 CATTTTGGTCTTTGATTTAAATCACGA 57.809 29.630 26.69 22.02 44.54 4.35
2219 2240 2.826488 AGTCTTGCCATCTGTCCTAGT 58.174 47.619 0.00 0.00 0.00 2.57
2306 2329 0.665835 TGTGCAAACATTCACGGTCC 59.334 50.000 0.00 0.00 36.06 4.46
2366 2390 3.680777 TTTTCAACCTTCCAACCCTCT 57.319 42.857 0.00 0.00 0.00 3.69
2429 2453 3.248888 AGTGCCACTCTAACCCTAAACT 58.751 45.455 0.00 0.00 0.00 2.66
2468 2492 9.491675 TCATGAACAAACATGCAAATTTATTCT 57.508 25.926 14.52 2.84 44.79 2.40
2486 2510 8.713737 TTCATTCAAACAAAATGTCATGAACA 57.286 26.923 0.00 0.00 38.24 3.18


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

AutoCloner maintained by Alex Coulton.