Multiple sequence alignment - TraesCS3A01G285400

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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 TraesCS3A01G285400 chr3A 100.000 2231 0 0 1 2231 514110447 514108217 0 4120
1 TraesCS3A01G285400 chr3B 97.406 2236 52 2 2 2231 513995576 513993341 0 3803
2 TraesCS3A01G285400 chr3D 97.004 2236 61 2 2 2231 394753932 394751697 0 3753


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 TraesCS3A01G285400 chr3A 514108217 514110447 2230 True 4120 4120 100.000 1 2231 1 chr3A.!!$R1 2230
1 TraesCS3A01G285400 chr3B 513993341 513995576 2235 True 3803 3803 97.406 2 2231 1 chr3B.!!$R1 2229
2 TraesCS3A01G285400 chr3D 394751697 394753932 2235 True 3753 3753 97.004 2 2231 1 chr3D.!!$R1 2229

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
343 344 0.969894 ATACGCTGGATAGTGGGAGC 59.03 55.0 0.0 0.0 38.76 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1891 0.249868 CACCTGCACCGTCTTTCTCA 60.25 55.0 0.0 0.0 0.0 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
197 198 8.116651 TCATCAAGAAGTAGTATAGCTGGATC 57.883 38.462 0.00 0.00 0.00 3.36
240 241 2.375173 CAATTCTTTGCTTCTGCCCC 57.625 50.000 0.00 0.00 38.71 5.80
258 259 1.774254 CCCCCTGATAGTTGTATGCCA 59.226 52.381 0.00 0.00 0.00 4.92
264 265 4.504514 CCTGATAGTTGTATGCCATGCTCT 60.505 45.833 0.00 0.00 0.00 4.09
276 277 2.420547 GCCATGCTCTCCACAATCAGTA 60.421 50.000 0.00 0.00 0.00 2.74
279 280 3.443099 TGCTCTCCACAATCAGTATCG 57.557 47.619 0.00 0.00 0.00 2.92
285 286 5.137551 TCTCCACAATCAGTATCGTATCCA 58.862 41.667 0.00 0.00 0.00 3.41
336 337 7.865707 AGCTTTAAATTTCATACGCTGGATAG 58.134 34.615 0.00 0.00 0.00 2.08
339 340 7.490962 TTAAATTTCATACGCTGGATAGTGG 57.509 36.000 0.00 0.00 38.76 4.00
343 344 0.969894 ATACGCTGGATAGTGGGAGC 59.030 55.000 0.00 0.00 38.76 4.70
500 501 1.269206 ACACTGCCAGAAAACATTGCG 60.269 47.619 0.00 0.00 0.00 4.85
560 561 3.533606 AGAACATTCATCTCCCTCACG 57.466 47.619 0.00 0.00 0.00 4.35
665 666 2.043652 CTCCCCACCAGGCCAATG 60.044 66.667 5.01 0.00 0.00 2.82
719 720 2.012902 GCAGGATCAGGCATTGTGGC 62.013 60.000 0.00 0.00 44.10 5.01
758 759 7.657354 GCAAAATCCACCTTTTTGAACTCTATT 59.343 33.333 11.82 0.00 43.50 1.73
808 809 2.487265 CCTTTTCCACCTGCAGTGTAGT 60.487 50.000 13.81 0.00 45.74 2.73
822 823 7.010552 CCTGCAGTGTAGTCATGTTAGTATTTC 59.989 40.741 13.81 0.00 0.00 2.17
826 827 9.035607 CAGTGTAGTCATGTTAGTATTTCATCC 57.964 37.037 0.00 0.00 0.00 3.51
1461 1468 3.570125 TCACCGCAATTACAATTCCACAA 59.430 39.130 0.00 0.00 0.00 3.33
1473 1480 4.160252 ACAATTCCACAAGCTGTTTGAAGT 59.840 37.500 11.31 0.00 39.21 3.01
1563 1570 3.554934 TGAGCCACTTGAATTTGTGTCT 58.445 40.909 0.00 0.00 32.76 3.41
1602 1609 5.013079 TGCCTCAAAGGTTAAGATCTTCTCA 59.987 40.000 12.24 0.00 37.80 3.27
1650 1657 3.479203 TGCTCCCCCATGTAGGCG 61.479 66.667 0.00 0.00 35.39 5.52
1667 1674 2.226437 AGGCGAAATTGTAGTGTTGCAG 59.774 45.455 0.00 0.00 0.00 4.41
1698 1705 1.477558 GCAATGGATACCAGGGACAGG 60.478 57.143 0.00 0.00 42.48 4.00
1818 1825 0.630673 TGGGCTGCAAGGAACCATAT 59.369 50.000 0.50 0.00 0.00 1.78
1836 1843 5.008331 CCATATACCAATGCAGAGATGCTT 58.992 41.667 1.53 0.00 35.49 3.91
1918 1925 2.654863 CAGGTGGGGAAACATATGACC 58.345 52.381 10.38 9.42 0.00 4.02
1926 1933 3.617284 GGAAACATATGACCCGGTTTCT 58.383 45.455 10.38 0.00 45.12 2.52
2118 2125 3.698040 GCTCATCATGTGTCCCAATTTCT 59.302 43.478 0.00 0.00 0.00 2.52
2169 2176 0.931005 GATCGGCATTCTTCACGGTC 59.069 55.000 0.00 0.00 0.00 4.79
2198 2205 1.139947 GAGCTACGACCTGGTCAGC 59.860 63.158 24.27 24.27 33.57 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.244450 TTGAGCGTGGTACTTACCCG 59.756 55.000 2.89 7.31 45.87 5.28
197 198 2.533318 GCGAGGGCAATAATCCGAG 58.467 57.895 0.00 0.00 39.62 4.63
240 241 2.816087 GCATGGCATACAACTATCAGGG 59.184 50.000 0.00 0.00 0.00 4.45
255 256 1.022735 CTGATTGTGGAGAGCATGGC 58.977 55.000 0.00 0.00 0.00 4.40
258 259 3.386078 ACGATACTGATTGTGGAGAGCAT 59.614 43.478 0.00 0.00 0.00 3.79
264 265 5.047306 GGATGGATACGATACTGATTGTGGA 60.047 44.000 0.00 0.00 42.51 4.02
276 277 5.418524 CAGATCTCTGAAGGATGGATACGAT 59.581 44.000 0.72 0.00 46.59 3.73
315 316 6.485313 CCCACTATCCAGCGTATGAAATTTAA 59.515 38.462 0.00 0.00 0.00 1.52
319 320 3.646162 TCCCACTATCCAGCGTATGAAAT 59.354 43.478 0.00 0.00 0.00 2.17
327 328 1.227380 GTGCTCCCACTATCCAGCG 60.227 63.158 0.00 0.00 38.93 5.18
329 330 2.289320 GCTATGTGCTCCCACTATCCAG 60.289 54.545 0.00 0.00 42.54 3.86
343 344 8.278408 CCGCTTGCATATATATTAAGCTATGTG 58.722 37.037 24.79 15.69 41.04 3.21
500 501 1.684450 GCTCTAGTTAGTCAGGAGCCC 59.316 57.143 0.00 0.00 42.20 5.19
521 522 5.046591 TGTTCTTTGGTATCGAGGATTCACT 60.047 40.000 0.00 0.00 0.00 3.41
560 561 4.810790 CTGTAAGGATCGATGGTATGGAC 58.189 47.826 0.54 0.00 0.00 4.02
665 666 0.663153 ACGTCAAAGCAGGAACAAGC 59.337 50.000 0.00 0.00 0.00 4.01
719 720 5.341872 TGGATTTTGCATATCCAACAAGG 57.658 39.130 22.21 0.00 46.46 3.61
746 747 8.842358 AAATACAAGGACGAATAGAGTTCAAA 57.158 30.769 0.00 0.00 0.00 2.69
758 759 3.678072 CGAAGAGCAAAATACAAGGACGA 59.322 43.478 0.00 0.00 0.00 4.20
808 809 7.791029 TGCTGTAGGATGAAATACTAACATGA 58.209 34.615 0.00 0.00 42.59 3.07
822 823 4.020396 AGGATGCTAGATTGCTGTAGGATG 60.020 45.833 0.00 0.00 30.77 3.51
826 827 7.792374 TTTTTAGGATGCTAGATTGCTGTAG 57.208 36.000 0.00 0.00 0.00 2.74
1017 1024 1.736681 GTGAGCACAGGAAAGCTGATC 59.263 52.381 0.00 0.00 42.04 2.92
1287 1294 6.989169 AGTATGAAAGTACTCAGATTGCCATC 59.011 38.462 0.00 0.00 28.99 3.51
1461 1468 1.699634 TCCCTGCTACTTCAAACAGCT 59.300 47.619 0.00 0.00 36.26 4.24
1542 1549 3.988379 GACACAAATTCAAGTGGCTCA 57.012 42.857 9.53 0.00 40.62 4.26
1563 1570 1.820519 GAGGCAGCATGGTTTGATGAA 59.179 47.619 0.00 0.00 44.68 2.57
1602 1609 1.135083 CGTATCCGAGTCCAAGTGCTT 60.135 52.381 0.00 0.00 35.63 3.91
1629 1636 0.399949 CCTACATGGGGGAGCACCTA 60.400 60.000 0.00 0.00 40.03 3.08
1632 1639 2.193248 GCCTACATGGGGGAGCAC 59.807 66.667 9.91 0.00 36.00 4.40
1650 1657 9.543018 GTTAATCTACTGCAACACTACAATTTC 57.457 33.333 0.00 0.00 0.00 2.17
1667 1674 6.428159 CCTGGTATCCATTGCTGTTAATCTAC 59.572 42.308 0.00 0.00 30.82 2.59
1698 1705 4.296690 GCTATGCATTGATCTTTTGCTCC 58.703 43.478 12.54 0.00 37.28 4.70
1836 1843 1.908619 TGGAAGCAAGCACTCATAGGA 59.091 47.619 0.00 0.00 0.00 2.94
1884 1891 0.249868 CACCTGCACCGTCTTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
1918 1925 3.443976 CAGGTGTTTCAAAAGAAACCGG 58.556 45.455 15.91 0.00 42.58 5.28
1926 1933 3.192422 CACTCACACCAGGTGTTTCAAAA 59.808 43.478 23.68 3.79 45.08 2.44
2118 2125 0.471022 TCGATGGGGGTAGCATAGCA 60.471 55.000 0.00 0.00 41.82 3.49


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

AutoCloner maintained by Alex Coulton.