Multiple sequence alignment - TraesCS5A01G117400

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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 TraesCS5A01G117400 chr5A 100.000 2960 0 0 1 2960 238899801 238902760 0.000000e+00 5467.0
1 TraesCS5A01G117400 chr6D 98.886 2961 31 2 1 2960 124514495 124511536 0.000000e+00 5284.0
2 TraesCS5A01G117400 chr7D 98.683 2961 38 1 1 2960 203496970 203494010 0.000000e+00 5251.0
3 TraesCS5A01G117400 chr7D 98.683 2961 38 1 1 2960 381976791 381979751 0.000000e+00 5251.0
4 TraesCS5A01G117400 chr7D 98.616 2962 39 2 1 2960 381916949 381913988 0.000000e+00 5241.0
5 TraesCS5A01G117400 chr4A 98.345 2961 45 3 1 2960 67593749 67590792 0.000000e+00 5193.0
6 TraesCS5A01G117400 chr4A 97.502 2962 67 5 1 2959 246660968 246663925 0.000000e+00 5053.0
7 TraesCS5A01G117400 chr4A 98.115 1061 19 1 1 1060 552145784 552146844 0.000000e+00 1847.0
8 TraesCS5A01G117400 chr4A 95.772 473 10 4 2306 2778 485004017 485004479 0.000000e+00 754.0
9 TraesCS5A01G117400 chr4A 99.367 158 1 0 819 976 3943796 3943953 1.340000e-73 287.0
10 TraesCS5A01G117400 chr4A 100.000 154 0 0 986 1139 331597512 331597665 4.830000e-73 285.0
11 TraesCS5A01G117400 chr4A 98.065 155 3 0 2791 2945 538332404 538332558 1.350000e-68 270.0
12 TraesCS5A01G117400 chr4A 92.105 190 12 2 1785 1974 572826731 572826917 6.290000e-67 265.0
13 TraesCS5A01G117400 chr4A 95.536 112 5 0 654 765 607881930 607882041 2.340000e-41 180.0
14 TraesCS5A01G117400 chr4A 100.000 73 0 0 1831 1903 48698406 48698478 5.150000e-28 135.0
15 TraesCS5A01G117400 chr4A 98.333 60 1 0 2787 2846 528085550 528085491 4.030000e-19 106.0
16 TraesCS5A01G117400 chr4A 100.000 28 0 0 381 408 591288892 591288919 5.000000e-03 52.8
17 TraesCS5A01G117400 chr4A 100.000 28 0 0 381 408 591289279 591289252 5.000000e-03 52.8
18 TraesCS5A01G117400 chr2A 89.910 555 36 11 2343 2895 202045057 202044521 0.000000e+00 697.0
19 TraesCS5A01G117400 chr2A 97.260 146 4 0 2317 2462 725215287 725215432 6.340000e-62 248.0
20 TraesCS5A01G117400 chr2A 96.396 111 4 0 2830 2940 740943942 740944052 1.810000e-42 183.0
21 TraesCS5A01G117400 chr2A 98.810 84 1 0 559 642 39736389 39736472 1.840000e-32 150.0
22 TraesCS5A01G117400 chr2A 98.000 50 1 0 2667 2716 632925488 632925439 1.460000e-13 87.9
23 TraesCS5A01G117400 chr2A 97.959 49 1 0 669 717 382045845 382045797 5.260000e-13 86.1


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 TraesCS5A01G117400 chr5A 238899801 238902760 2959 False 5467 5467 100.000 1 2960 1 chr5A.!!$F1 2959
1 TraesCS5A01G117400 chr6D 124511536 124514495 2959 True 5284 5284 98.886 1 2960 1 chr6D.!!$R1 2959
2 TraesCS5A01G117400 chr7D 203494010 203496970 2960 True 5251 5251 98.683 1 2960 1 chr7D.!!$R1 2959
3 TraesCS5A01G117400 chr7D 381976791 381979751 2960 False 5251 5251 98.683 1 2960 1 chr7D.!!$F1 2959
4 TraesCS5A01G117400 chr7D 381913988 381916949 2961 True 5241 5241 98.616 1 2960 1 chr7D.!!$R2 2959
5 TraesCS5A01G117400 chr4A 67590792 67593749 2957 True 5193 5193 98.345 1 2960 1 chr4A.!!$R1 2959
6 TraesCS5A01G117400 chr4A 246660968 246663925 2957 False 5053 5053 97.502 1 2959 1 chr4A.!!$F3 2958
7 TraesCS5A01G117400 chr4A 552145784 552146844 1060 False 1847 1847 98.115 1 1060 1 chr4A.!!$F7 1059
8 TraesCS5A01G117400 chr2A 202044521 202045057 536 True 697 697 89.910 2343 2895 1 chr2A.!!$R1 552

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
354 356 1.937223 TCTGCACTTGTTTGTACACGG 59.063 47.619 0.0 0.00 32.98 4.94 F
1782 1786 5.704515 GGTTCTTAAGAAAGGTCAAGGGTAC 59.295 44.000 19.3 3.27 35.58 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 1946 1.640917 TTCTAGATATCCCCCGTGGC 58.359 55.0 0.0 0.0 0.0 5.01 R
2912 2922 7.789273 TTGACGAACTTTCTGGTTAACATAA 57.211 32.0 8.1 0.0 0.0 1.90 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
187 189 7.171678 CACTCAGAGGAAAGTCTTTTCGTAATT 59.828 37.037 1.53 0.00 42.93 1.40
231 233 6.080648 TCTGTTGATATACGGCGTAAATCT 57.919 37.500 24.81 10.04 0.00 2.40
354 356 1.937223 TCTGCACTTGTTTGTACACGG 59.063 47.619 0.00 0.00 32.98 4.94
680 682 5.757850 AGCAGAAAGACTTGTCGAAAATT 57.242 34.783 0.00 0.00 0.00 1.82
971 973 8.437360 TTTCAGTCGTATTCGTATCCTTACTA 57.563 34.615 0.00 0.00 38.33 1.82
1440 1442 6.956435 AGGCTATCATGATTCATGTACTAGGA 59.044 38.462 22.64 5.64 41.98 2.94
1782 1786 5.704515 GGTTCTTAAGAAAGGTCAAGGGTAC 59.295 44.000 19.30 3.27 35.58 3.34
1792 1796 6.487299 AAGGTCAAGGGTACATAGAGAATC 57.513 41.667 0.00 0.00 0.00 2.52
1942 1946 7.500992 TCTGATAGGAGGTTACTTATGCAAAG 58.499 38.462 0.00 0.00 0.00 2.77
1983 1987 7.103641 AGAATCACTTTCGGCTATTAACTTCA 58.896 34.615 0.00 0.00 39.46 3.02
2103 2107 7.823745 AAACAAAAGGCTCTTGAGATTTCTA 57.176 32.000 7.72 0.00 0.00 2.10
2113 2117 9.606631 GGCTCTTGAGATTTCTAGAAAAGAATA 57.393 33.333 21.26 7.15 43.75 1.75
2540 2549 6.071896 GCAGCCTTTAAGTATCCAAAGTTCTT 60.072 38.462 0.00 0.00 31.20 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.170607 GCTAGTCCTTGGGAACAGCATA 59.829 50.000 12.76 0.00 44.54 3.14
51 52 1.065126 GCTAGTCCTTGGGAACAGCAT 60.065 52.381 12.76 0.00 44.54 3.79
52 53 0.324943 GCTAGTCCTTGGGAACAGCA 59.675 55.000 12.76 0.00 44.54 4.41
187 189 4.408921 AGATTATGGTTTCGAGGGTCATCA 59.591 41.667 0.00 0.00 0.00 3.07
231 233 4.706476 GGTGTTTCTTCCATCAATCATCCA 59.294 41.667 0.00 0.00 0.00 3.41
354 356 3.351020 ACTCGGTATAACTCACGCATC 57.649 47.619 0.00 0.00 0.00 3.91
568 570 9.983024 TTTCCAATATAGTTGGGAGATTTTACA 57.017 29.630 6.95 0.00 39.96 2.41
680 682 4.589675 GGACCAACCCAACCGGCA 62.590 66.667 0.00 0.00 33.26 5.69
971 973 8.916628 TTTATTTGTTACCCTTACTAAACCGT 57.083 30.769 0.00 0.00 0.00 4.83
1440 1442 6.126863 TCCTGAAGAGTGTTGAATACCAAT 57.873 37.500 0.00 0.00 37.08 3.16
1513 1515 4.642429 AGAAACCTTGCTTGTTCTCGTAT 58.358 39.130 0.00 0.00 0.00 3.06
1792 1796 8.434661 GTTCAAATTGCACATAACATAACAAGG 58.565 33.333 0.00 0.00 0.00 3.61
1942 1946 1.640917 TTCTAGATATCCCCCGTGGC 58.359 55.000 0.00 0.00 0.00 5.01
2113 2117 5.278957 GCCCACACTCAACTAAACATTGATT 60.279 40.000 0.00 0.00 35.57 2.57
2114 2118 4.218417 GCCCACACTCAACTAAACATTGAT 59.782 41.667 0.00 0.00 35.57 2.57
2325 2329 7.416664 GCTGGCAAATAGAATTGATAACCTTCA 60.417 37.037 0.00 0.00 31.84 3.02
2366 2370 4.099573 CACCTGAACGGTAGATTCTACCAT 59.900 45.833 32.26 23.73 46.94 3.55
2486 2495 5.474578 TGCTAAGTGTTGACTGAGATTCT 57.525 39.130 0.00 0.00 32.67 2.40
2540 2549 6.547141 CCATTTAAGGGCATCATCTAAGTTCA 59.453 38.462 0.00 0.00 0.00 3.18
2912 2922 7.789273 TTGACGAACTTTCTGGTTAACATAA 57.211 32.000 8.10 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.