Multiple sequence alignment - TraesCS5A01G502900

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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 TraesCS5A01G502900 chr5A 100.000 2588 0 0 1 2588 667732680 667730093 0.000000e+00 4780.0
1 TraesCS5A01G502900 chr1A 97.263 2594 62 7 1 2588 94598960 94596370 0.000000e+00 4388.0
2 TraesCS5A01G502900 chr1A 96.951 2591 75 4 1 2588 94708072 94710661 0.000000e+00 4344.0
3 TraesCS5A01G502900 chr4A 95.306 2514 107 6 1 2504 295169725 295167213 0.000000e+00 3978.0
4 TraesCS5A01G502900 chr4A 91.176 306 27 0 2199 2504 79634684 79634989 1.430000e-112 416.0
5 TraesCS5A01G502900 chr4A 91.176 306 27 0 2199 2504 79644159 79643854 1.430000e-112 416.0
6 TraesCS5A01G502900 chr3A 97.835 2263 45 4 1 2260 51887216 51884955 0.000000e+00 3904.0
7 TraesCS5A01G502900 chr2A 98.540 2192 25 5 1 2185 755521016 755518825 0.000000e+00 3864.0
8 TraesCS5A01G502900 chr7D 98.537 2187 27 4 1 2182 381882009 381879823 0.000000e+00 3856.0
9 TraesCS5A01G502900 chr7D 94.444 90 4 1 2500 2588 382090476 382090565 1.250000e-28 137.0
10 TraesCS5A01G502900 chrUn 98.447 2189 27 5 1 2182 223715547 223717735 0.000000e+00 3847.0
11 TraesCS5A01G502900 chrUn 90.850 306 28 0 2199 2504 171008903 171009208 6.670000e-111 411.0
12 TraesCS5A01G502900 chrUn 94.444 90 4 1 2500 2588 369464835 369464746 1.250000e-28 137.0
13 TraesCS5A01G502900 chr5B 98.081 2189 37 5 1 2184 127798272 127796084 0.000000e+00 3805.0
14 TraesCS5A01G502900 chr4D 98.080 2187 36 5 1 2182 123731197 123729012 0.000000e+00 3801.0
15 TraesCS5A01G502900 chr4D 94.444 90 4 1 2500 2588 134963690 134963779 1.250000e-28 137.0
16 TraesCS5A01G502900 chr4D 93.333 90 4 2 2500 2588 123402195 123402283 5.810000e-27 132.0
17 TraesCS5A01G502900 chr6B 91.176 306 27 0 2199 2504 596601242 596600937 1.430000e-112 416.0
18 TraesCS5A01G502900 chr6B 91.176 306 27 0 2199 2504 715990455 715990150 1.430000e-112 416.0
19 TraesCS5A01G502900 chr7B 90.850 306 28 0 2199 2504 54048532 54048227 6.670000e-111 411.0
20 TraesCS5A01G502900 chr1D 94.444 90 4 1 2500 2588 212444040 212443951 1.250000e-28 137.0
21 TraesCS5A01G502900 chr1D 93.333 90 5 1 2500 2588 275785912 275785823 5.810000e-27 132.0
22 TraesCS5A01G502900 chr6D 93.333 90 5 1 2500 2588 57938372 57938283 5.810000e-27 132.0
23 TraesCS5A01G502900 chr2B 100.000 45 0 0 2170 2214 659856704 659856748 1.650000e-12 84.2


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 TraesCS5A01G502900 chr5A 667730093 667732680 2587 True 4780 4780 100.000 1 2588 1 chr5A.!!$R1 2587
1 TraesCS5A01G502900 chr1A 94596370 94598960 2590 True 4388 4388 97.263 1 2588 1 chr1A.!!$R1 2587
2 TraesCS5A01G502900 chr1A 94708072 94710661 2589 False 4344 4344 96.951 1 2588 1 chr1A.!!$F1 2587
3 TraesCS5A01G502900 chr4A 295167213 295169725 2512 True 3978 3978 95.306 1 2504 1 chr4A.!!$R2 2503
4 TraesCS5A01G502900 chr3A 51884955 51887216 2261 True 3904 3904 97.835 1 2260 1 chr3A.!!$R1 2259
5 TraesCS5A01G502900 chr2A 755518825 755521016 2191 True 3864 3864 98.540 1 2185 1 chr2A.!!$R1 2184
6 TraesCS5A01G502900 chr7D 381879823 381882009 2186 True 3856 3856 98.537 1 2182 1 chr7D.!!$R1 2181
7 TraesCS5A01G502900 chrUn 223715547 223717735 2188 False 3847 3847 98.447 1 2182 1 chrUn.!!$F2 2181
8 TraesCS5A01G502900 chr5B 127796084 127798272 2188 True 3805 3805 98.081 1 2184 1 chr5B.!!$R1 2183
9 TraesCS5A01G502900 chr4D 123729012 123731197 2185 True 3801 3801 98.080 1 2182 1 chr4D.!!$R1 2181

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
867 870 0.75085 GTAGCCCAGGTGATTCGCTA 59.249 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 2488 0.598419 CACTGCTTGTGCGAGTGAGA 60.598 55.0 11.98 0.0 43.88 3.27 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
218 219 9.372541 CGTTTGTTTTCTCGCTTAACTAATTTA 57.627 29.630 0.00 0.00 0.00 1.40
399 400 2.717639 ATCCTTGAATTCAGGGGTCG 57.282 50.000 30.18 10.28 42.72 4.79
497 498 7.235079 TGATTCATTTAGTTGGTAGAACCCAA 58.765 34.615 0.00 0.00 42.16 4.12
507 508 3.139077 GGTAGAACCCAAGCCAATATCG 58.861 50.000 0.00 0.00 30.04 2.92
578 579 6.542821 TCAAATTCTCTCCTTTCCAAAGCTA 58.457 36.000 0.00 0.00 34.69 3.32
695 696 2.162338 TAGGTAGTTTGCGCGCAGGT 62.162 55.000 34.25 23.47 0.00 4.00
707 708 1.461888 CGCGCAGGTAAAACTTCTTCG 60.462 52.381 8.75 0.00 0.00 3.79
867 870 0.750850 GTAGCCCAGGTGATTCGCTA 59.249 55.000 0.00 0.00 0.00 4.26
929 932 4.493547 CTTTTTGATTATTCAGGGCGCAA 58.506 39.130 10.83 0.00 32.27 4.85
1242 1245 2.044793 TGAGAGATGTTGAAGGGGGT 57.955 50.000 0.00 0.00 0.00 4.95
1550 1553 3.772387 TGGACAATGCCACCTTAAATCA 58.228 40.909 0.00 0.00 31.66 2.57
1614 1619 1.280133 CCAGTCTTCTTCATCTGGCCA 59.720 52.381 4.71 4.71 40.43 5.36
1880 1891 2.232696 TCGCAGTATACCTGACAAAGCA 59.767 45.455 0.00 0.00 44.49 3.91
2083 2096 9.444600 GTTACTATTGGACAAATTCCTTCTGTA 57.555 33.333 0.00 0.00 46.10 2.74
2216 2229 5.256474 GCCATAGCCATATAATGAACAGGT 58.744 41.667 0.00 0.00 0.00 4.00
2260 2273 3.387699 GCCATAGAAGAAGCTTCTCCTCT 59.612 47.826 28.58 27.18 36.28 3.69
2370 2387 6.529220 AGTGCAAGATAGACTCACTTCTTTT 58.471 36.000 0.00 0.00 32.23 2.27
2404 2421 4.429505 CTGGGGAGATCCTATTCATGGTA 58.570 47.826 0.00 0.00 35.95 3.25
2406 2423 3.195825 GGGGAGATCCTATTCATGGTACG 59.804 52.174 0.00 0.00 35.95 3.67
2446 2463 2.296792 TCTCTGCTCGAGATCTTGGAG 58.703 52.381 18.75 16.41 43.72 3.86
2449 2466 1.068921 GCTCGAGATCTTGGAGCCC 59.931 63.158 27.01 10.65 45.67 5.19
2451 2468 0.826715 CTCGAGATCTTGGAGCCCAA 59.173 55.000 6.58 6.50 41.69 4.12
2467 2484 5.104259 AGCCCAAGGATATCCGAAATATC 57.896 43.478 16.21 8.47 42.08 1.63
2471 2488 6.378280 GCCCAAGGATATCCGAAATATCATTT 59.622 38.462 16.21 0.00 42.08 2.32
2578 2596 4.353383 AAGAGCTCGTTTAGGGTTTTCT 57.647 40.909 8.37 0.00 0.00 2.52
2582 2600 2.611224 GCTCGTTTAGGGTTTTCTCGGA 60.611 50.000 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 181 5.497474 AGAAAACAAACGGCTACATAGGAT 58.503 37.500 0.00 0.00 0.00 3.24
218 219 3.425659 TCTCAGCTGTATCGCCTCATAT 58.574 45.455 14.67 0.00 0.00 1.78
399 400 0.960286 GAGACATACCTCCCGTAGCC 59.040 60.000 0.00 0.00 0.00 3.93
497 498 5.772672 AGAGAGAGTCAATACGATATTGGCT 59.227 40.000 18.45 18.45 45.50 4.75
507 508 4.966965 TTGGACGAGAGAGAGTCAATAC 57.033 45.455 0.00 0.00 39.01 1.89
695 696 6.988622 TTGACCTTTCACGAAGAAGTTTTA 57.011 33.333 0.00 0.00 37.57 1.52
707 708 7.272037 TCCAAGTCTATTTTTGACCTTTCAC 57.728 36.000 0.00 0.00 35.21 3.18
867 870 1.550869 CCATTTTGGCAAGAGGGAGGT 60.551 52.381 15.61 0.00 0.00 3.85
929 932 2.493278 CCTTGATGGAAATTGGCTTCGT 59.507 45.455 0.00 0.00 38.35 3.85
1242 1245 2.992593 TGCATATAACGGAGCAACCAA 58.007 42.857 0.00 0.00 38.90 3.67
1880 1891 0.753262 CTATTGCGGCTACACCTCCT 59.247 55.000 0.00 0.00 35.61 3.69
1952 1965 4.044336 TCGGTCGAAAACTTGAACTACA 57.956 40.909 0.00 0.00 0.00 2.74
2083 2096 9.045223 GTTATGGCAAAGAACAAGAAGAAAAAT 57.955 29.630 0.00 0.00 0.00 1.82
2216 2229 5.133221 GCTATGGCCAAAAGGAGAAATAGA 58.867 41.667 10.96 0.00 0.00 1.98
2370 2387 1.368203 TCTCCCCAGGTTCCAGGAATA 59.632 52.381 4.80 0.00 0.00 1.75
2446 2463 4.843728 TGATATTTCGGATATCCTTGGGC 58.156 43.478 19.61 4.00 31.69 5.36
2449 2466 9.440773 TGAGAAATGATATTTCGGATATCCTTG 57.559 33.333 19.61 5.28 33.86 3.61
2451 2468 8.820831 AGTGAGAAATGATATTTCGGATATCCT 58.179 33.333 19.61 3.34 33.86 3.24
2467 2484 1.532437 TGCTTGTGCGAGTGAGAAATG 59.468 47.619 0.00 0.00 43.34 2.32
2471 2488 0.598419 CACTGCTTGTGCGAGTGAGA 60.598 55.000 11.98 0.00 43.88 3.27
2564 2581 4.379082 CCAAATCCGAGAAAACCCTAAACG 60.379 45.833 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.