Multiple sequence alignment - TraesCS7A01G237500

Loading Multiple Alignment...

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 TraesCS7A01G237500 chr7A 100.000 3215 0 0 1 3215 211275127 211271913 0 5938
1 TraesCS7A01G237500 chr4D 98.041 3216 58 2 1 3215 123299974 123303185 0 5585
2 TraesCS7A01G237500 chr7D 97.855 3217 64 3 1 3215 203515560 203518773 0 5553
3 TraesCS7A01G237500 chr7B 97.823 3216 64 2 1 3215 644467528 644470738 0 5546
4 TraesCS7A01G237500 chr6B 97.543 3215 78 1 1 3215 306995906 306992693 0 5498
5 TraesCS7A01G237500 chr1B 97.542 3214 76 3 3 3215 638700580 638697369 0 5494
6 TraesCS7A01G237500 chr1B 97.014 3215 91 1 1 3215 672479245 672482454 0 5400
7 TraesCS7A01G237500 chr3A 97.449 3215 75 3 1 3215 633111338 633114545 0 5476
8 TraesCS7A01G237500 chr2B 96.922 3216 95 2 1 3215 391112757 391109545 0 5387
9 TraesCS7A01G237500 chr2A 96.891 3216 92 4 1 3215 332944213 332941005 0 5378


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 TraesCS7A01G237500 chr7A 211271913 211275127 3214 True 5938 5938 100.000 1 3215 1 chr7A.!!$R1 3214
1 TraesCS7A01G237500 chr4D 123299974 123303185 3211 False 5585 5585 98.041 1 3215 1 chr4D.!!$F1 3214
2 TraesCS7A01G237500 chr7D 203515560 203518773 3213 False 5553 5553 97.855 1 3215 1 chr7D.!!$F1 3214
3 TraesCS7A01G237500 chr7B 644467528 644470738 3210 False 5546 5546 97.823 1 3215 1 chr7B.!!$F1 3214
4 TraesCS7A01G237500 chr6B 306992693 306995906 3213 True 5498 5498 97.543 1 3215 1 chr6B.!!$R1 3214
5 TraesCS7A01G237500 chr1B 638697369 638700580 3211 True 5494 5494 97.542 3 3215 1 chr1B.!!$R1 3212
6 TraesCS7A01G237500 chr1B 672479245 672482454 3209 False 5400 5400 97.014 1 3215 1 chr1B.!!$F1 3214
7 TraesCS7A01G237500 chr3A 633111338 633114545 3207 False 5476 5476 97.449 1 3215 1 chr3A.!!$F1 3214
8 TraesCS7A01G237500 chr2B 391109545 391112757 3212 True 5387 5387 96.922 1 3215 1 chr2B.!!$R1 3214
9 TraesCS7A01G237500 chr2A 332941005 332944213 3208 True 5378 5378 96.891 1 3215 1 chr2A.!!$R1 3214

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
921 932 0.251077 CCTCAAGCCTCCTTTGCACT 60.251 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2486 0.247736 AAGCAACGATCTTCCGAGCT 59.752 50.0 0.0 0.0 42.45 4.09 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
107 108 4.692475 CCTTTCGTTCGGGCCGGT 62.692 66.667 27.98 0.00 0.00 5.28
868 879 2.009681 AATGCCTTTCGTTTTCCCCT 57.990 45.000 0.00 0.00 0.00 4.79
906 917 1.271926 GCCTTCCTTAACAAGCCCTCA 60.272 52.381 0.00 0.00 0.00 3.86
921 932 0.251077 CCTCAAGCCTCCTTTGCACT 60.251 55.000 0.00 0.00 0.00 4.40
1038 1049 2.621556 ATTGCAAAAGAAGGGGCCTA 57.378 45.000 1.71 0.00 0.00 3.93
1090 1101 3.027412 GTTATCAGGTCAGAGAGAGGCA 58.973 50.000 0.00 0.00 0.00 4.75
1283 1294 2.632377 CGCAGGATCAACAACCATAGT 58.368 47.619 0.00 0.00 0.00 2.12
1393 1404 0.388907 GCGTCTACGGGTAAAGCACA 60.389 55.000 4.49 0.00 40.23 4.57
1482 1493 5.211973 AGTATCCCTATCAAAGAGCTGACA 58.788 41.667 0.00 0.00 0.00 3.58
1644 1655 2.857186 TGTTGCATAGCTCAGGTCAA 57.143 45.000 0.00 0.00 0.00 3.18
1659 1670 0.109597 GTCAAAGCAAGGTGCCATCG 60.110 55.000 0.00 0.00 46.52 3.84
1675 1686 3.283684 CGGGCGTTCAACAGGCAA 61.284 61.111 7.90 0.00 38.09 4.52
1833 1845 9.669065 ATCAAAAAGATACTCCGAAGGCTTCGA 62.669 40.741 41.98 28.39 45.01 3.71
1853 1865 2.887783 GAGATCGAGGTCTCATTAGCCA 59.112 50.000 10.51 0.00 43.27 4.75
1906 1918 1.135489 TGACCAACGTCAGCGATAGAC 60.135 52.381 0.00 0.00 44.20 2.59
1922 1934 7.865889 CAGCGATAGACACATAGTAAATTGGTA 59.134 37.037 0.00 0.00 39.76 3.25
1923 1935 8.585881 AGCGATAGACACATAGTAAATTGGTAT 58.414 33.333 0.00 0.00 39.76 2.73
1991 2003 2.064014 CCTTTACCAAGTCCGAACGAC 58.936 52.381 0.00 0.00 42.32 4.34
2124 2136 1.073284 GAAGGTGGTAAGACCCTTGCA 59.927 52.381 0.00 0.00 38.68 4.08
2184 2196 2.618053 GGTCAAGATCCGAACAACGAT 58.382 47.619 0.00 0.00 45.77 3.73
2297 2309 7.038017 AGGCTTGCCTTATCTGCTATAAGATAA 60.038 37.037 8.56 10.87 43.59 1.75
2473 2486 5.048991 GCGTCAGAAAAATAGAACCTTTCCA 60.049 40.000 0.00 0.00 30.83 3.53
2476 2489 6.207614 GTCAGAAAAATAGAACCTTTCCAGCT 59.792 38.462 0.00 0.00 30.83 4.24
2487 2500 4.338815 TCCAGCTCGGAAGATCGT 57.661 55.556 2.78 0.00 42.52 3.73
2746 2760 0.177836 TCACCCGGTCTATGCACATG 59.822 55.000 0.00 0.00 0.00 3.21
3018 3032 3.632145 GTGCCAGGAAGTTTCTTCTGAAA 59.368 43.478 8.96 0.00 39.59 2.69
3079 3093 0.740737 CGTTGGGGATTCATTGCTCC 59.259 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.694150 CGGGGCTCTCTCCAATCATTA 59.306 52.381 0.00 0.00 0.00 1.90
107 108 1.362932 GATAGATCAGGGCCCCTCCTA 59.637 57.143 21.43 15.30 34.92 2.94
146 148 0.783850 AAAAGGGGGAGCAAAGCCTA 59.216 50.000 0.00 0.00 0.00 3.93
272 275 1.275291 GTGTCTGGAAACTCGGGATCA 59.725 52.381 0.00 0.00 0.00 2.92
566 569 4.036852 TGATCGAGCTTGTGTAGGTAGATG 59.963 45.833 0.90 0.00 43.74 2.90
837 847 2.978156 AAGGCATTTTCTGGTCTCCA 57.022 45.000 0.00 0.00 0.00 3.86
906 917 1.905354 GGCAGTGCAAAGGAGGCTT 60.905 57.895 18.61 0.00 0.00 4.35
1038 1049 2.136878 CCCGCCCAGCTCTATCAGT 61.137 63.158 0.00 0.00 0.00 3.41
1061 1072 8.035448 TCTCTCTGACCTGATAACTAGTATCA 57.965 38.462 0.00 5.45 45.24 2.15
1283 1294 1.246649 TTCTACCGTACTCCGTGCAA 58.753 50.000 0.00 0.00 33.66 4.08
1393 1404 3.909995 TGGCAGGCAGTTATATGGATACT 59.090 43.478 0.00 0.00 37.61 2.12
1482 1493 0.543749 CTCTTCCGCTCATCCCCTTT 59.456 55.000 0.00 0.00 0.00 3.11
1623 1634 3.354948 TGACCTGAGCTATGCAACAAT 57.645 42.857 0.00 0.00 0.00 2.71
1644 1655 2.361610 CCCGATGGCACCTTGCTT 60.362 61.111 0.00 0.00 44.28 3.91
1659 1670 1.212751 GATTGCCTGTTGAACGCCC 59.787 57.895 0.00 0.00 0.00 6.13
1701 1712 9.025041 CCAAAGGGAGTATACAATTTCTTCTTT 57.975 33.333 5.50 5.98 35.59 2.52
1833 1845 2.950781 TGGCTAATGAGACCTCGATCT 58.049 47.619 0.00 0.00 0.00 2.75
1853 1865 1.272704 GGATTGGCCTGGGTCTTCTTT 60.273 52.381 3.32 0.00 0.00 2.52
1902 1914 6.926826 CCGCATACCAATTTACTATGTGTCTA 59.073 38.462 0.00 0.00 29.85 2.59
1906 1918 4.320202 GCCCGCATACCAATTTACTATGTG 60.320 45.833 0.00 0.00 0.00 3.21
1991 2003 1.478510 AGCGGATCTGGTAGTTGACAG 59.521 52.381 3.92 0.00 36.07 3.51
2017 2029 3.936461 TGTGGGCTAGGGTGAATATAGT 58.064 45.455 0.00 0.00 0.00 2.12
2124 2136 3.620966 GCTCTATGCTGTTTGGGAACTCT 60.621 47.826 0.00 0.00 38.95 3.24
2184 2196 3.769739 AACATGTAGTTGAGTGCTCCA 57.230 42.857 0.00 0.00 39.49 3.86
2297 2309 1.053424 TCGAAAGCCCCACAACTAGT 58.947 50.000 0.00 0.00 0.00 2.57
2473 2486 0.247736 AAGCAACGATCTTCCGAGCT 59.752 50.000 0.00 0.00 42.45 4.09
2476 2489 3.030209 CGAAGCAACGATCTTCCGA 57.970 52.632 0.00 0.00 37.29 4.55
2639 2653 1.802960 GAACCGTACGTGAGACTCTCA 59.197 52.381 15.21 4.50 38.25 3.27
2746 2760 0.322906 CCAACCTCCTGGAAAGAGCC 60.323 60.000 0.00 0.00 38.96 4.70
2806 2820 6.574350 ACCTTGATACTAAACCAGATCGAAG 58.426 40.000 0.00 0.00 0.00 3.79
3079 3093 6.145696 GGCTACATTACTTATAACCGCAGAAG 59.854 42.308 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.