Multiple sequence alignment - TraesCS5A01G421100

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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 TraesCS5A01G421100 chr5A 100.000 2221 0 0 1 2221 607274526 607272306 0 4102
1 TraesCS5A01G421100 chr3D 97.571 2223 49 5 1 2221 589279416 589281635 0 3801
2 TraesCS5A01G421100 chr5D 97.526 2223 50 5 1 2221 503278100 503280319 0 3795
3 TraesCS5A01G421100 chr5D 97.392 2224 52 6 1 2221 6189066 6186846 0 3781
4 TraesCS5A01G421100 chr5D 96.403 2224 72 8 1 2221 432403371 432405589 0 3657
5 TraesCS5A01G421100 chr5D 98.161 1577 26 3 1 1576 503218344 503216770 0 2748
6 TraesCS5A01G421100 chr1D 97.480 2222 51 5 3 2221 254397985 254400204 0 3788
7 TraesCS5A01G421100 chr1A 97.212 2224 49 6 1 2221 554512374 554510161 0 3751
8 TraesCS5A01G421100 chr4A 95.650 2230 87 7 1 2221 309515257 309513029 0 3572
9 TraesCS5A01G421100 chr4A 94.784 2243 89 14 1 2221 310738723 310736487 0 3469
10 TraesCS5A01G421100 chr6D 98.035 1578 27 4 1 1576 168255052 168253477 0 2739


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 TraesCS5A01G421100 chr5A 607272306 607274526 2220 True 4102 4102 100.000 1 2221 1 chr5A.!!$R1 2220
1 TraesCS5A01G421100 chr3D 589279416 589281635 2219 False 3801 3801 97.571 1 2221 1 chr3D.!!$F1 2220
2 TraesCS5A01G421100 chr5D 503278100 503280319 2219 False 3795 3795 97.526 1 2221 1 chr5D.!!$F2 2220
3 TraesCS5A01G421100 chr5D 6186846 6189066 2220 True 3781 3781 97.392 1 2221 1 chr5D.!!$R1 2220
4 TraesCS5A01G421100 chr5D 432403371 432405589 2218 False 3657 3657 96.403 1 2221 1 chr5D.!!$F1 2220
5 TraesCS5A01G421100 chr5D 503216770 503218344 1574 True 2748 2748 98.161 1 1576 1 chr5D.!!$R2 1575
6 TraesCS5A01G421100 chr1D 254397985 254400204 2219 False 3788 3788 97.480 3 2221 1 chr1D.!!$F1 2218
7 TraesCS5A01G421100 chr1A 554510161 554512374 2213 True 3751 3751 97.212 1 2221 1 chr1A.!!$R1 2220
8 TraesCS5A01G421100 chr4A 309513029 309515257 2228 True 3572 3572 95.650 1 2221 1 chr4A.!!$R1 2220
9 TraesCS5A01G421100 chr4A 310736487 310738723 2236 True 3469 3469 94.784 1 2221 1 chr4A.!!$R2 2220
10 TraesCS5A01G421100 chr6D 168253477 168255052 1575 True 2739 2739 98.035 1 1576 1 chr6D.!!$R1 1575

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
752 772 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1917 1.092345 GCTGCTTGGCCTGTAGTAGC 61.092 60.0 20.48 20.48 41.62 3.58 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
154 155 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.0 0.00 4.02
155 156 4.982241 TGTTTCAAAGAGAGGAGGACAT 57.018 40.909 0.00 0.0 0.00 3.06
186 187 7.174413 TCACATTTAATTTGATGGTCAGAGGA 58.826 34.615 5.92 0.0 0.00 3.71
326 327 5.252547 TGCTACATGAAGAACATAAGCCAA 58.747 37.500 0.00 0.0 41.98 4.52
336 337 4.949856 AGAACATAAGCCAAATGACGGAAT 59.050 37.500 0.00 0.0 0.00 3.01
464 483 5.630121 AGATCCATCTGTCTAGAGATCGTT 58.370 41.667 10.21 0.0 38.60 3.85
752 772 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.00 0.0 0.00 5.36
871 891 2.282180 GGCGGTGAAGGGAAAGCA 60.282 61.111 0.00 0.0 0.00 3.91
904 925 1.959710 AAAAACCCACAACCCCTTGT 58.040 45.000 0.00 0.0 41.61 3.16
945 966 7.837187 TGGAAGAAGAACTAGGAAAAGGAAAAA 59.163 33.333 0.00 0.0 0.00 1.94
1191 1215 3.877559 TCTAACCTCCGTACTTCGATCA 58.122 45.455 0.00 0.0 42.86 2.92
1200 1224 6.387041 TCCGTACTTCGATCAAGATATTGT 57.613 37.500 10.61 0.0 42.86 2.71
1347 1373 5.479124 AGAAACAATAGTAACGTGGTCCT 57.521 39.130 0.00 0.0 0.00 3.85
1415 1441 7.752239 GCGATTCATAATGGAAAGGAACATATG 59.248 37.037 0.00 0.0 0.00 1.78
1922 1957 5.048434 GCAGCCAAGAAGAAGTGTAAAGAAT 60.048 40.000 0.00 0.0 0.00 2.40
1983 2018 3.133362 CCAAAATAACCATGAGCAGCCAT 59.867 43.478 0.00 0.0 0.00 4.40
2046 2081 6.207213 CCTCATTAGCAGATTCATTTTCAGC 58.793 40.000 0.00 0.0 0.00 4.26
2106 2141 3.455910 TGCATAGCACTGAATAGGGAACT 59.544 43.478 0.00 0.0 37.94 3.01
2115 2150 4.163458 ACTGAATAGGGAACTGCCGAATAA 59.837 41.667 0.00 0.0 43.88 1.40
2150 2186 5.771666 CCTAACATGTGGAAGGATGCATAAT 59.228 40.000 14.22 0.0 0.00 1.28
2159 2195 6.262944 GTGGAAGGATGCATAATGATGTTGTA 59.737 38.462 0.00 0.0 35.30 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 187 5.535753 ACCACTGCTTAGCTTTCAATTTT 57.464 34.783 5.60 0.00 0.00 1.82
326 327 1.556911 AGGTCTCTGCATTCCGTCATT 59.443 47.619 0.00 0.00 0.00 2.57
336 337 3.953542 TCTACATCCTAGGTCTCTGCA 57.046 47.619 9.08 0.00 0.00 4.41
629 649 5.491070 TGCAATGAGTTTCACTATAGCACT 58.509 37.500 0.00 0.00 0.00 4.40
639 659 3.960102 ACCCTCTTTTGCAATGAGTTTCA 59.040 39.130 21.02 0.00 32.43 2.69
904 925 0.326595 TTCCAAGCGCAGGATAACCA 59.673 50.000 20.31 4.53 38.94 3.67
1173 1197 3.087031 TCTTGATCGAAGTACGGAGGTT 58.913 45.455 0.00 0.00 42.82 3.50
1191 1215 8.256356 AGAGTGGCTTCTATGTACAATATCTT 57.744 34.615 0.00 0.00 0.00 2.40
1200 1224 8.380099 TCCTTTTTAAAGAGTGGCTTCTATGTA 58.620 33.333 5.15 0.00 38.28 2.29
1347 1373 1.699634 GGGTAGAATGCTAGATGCCCA 59.300 52.381 0.00 0.00 42.00 5.36
1415 1441 9.297037 ACCATAGGATTTGTTATGTAAATAGGC 57.703 33.333 0.00 0.00 0.00 3.93
1670 1698 7.828717 TGCTGTTGAAGTTCCATCTATTAATGA 59.171 33.333 0.00 0.00 0.00 2.57
1869 1903 5.127194 CCTGTAGTAGCAATCTGGTTCACTA 59.873 44.000 0.00 0.00 0.00 2.74
1883 1917 1.092345 GCTGCTTGGCCTGTAGTAGC 61.092 60.000 20.48 20.48 41.62 3.58
1922 1957 7.119699 CCAATATGCTAGTTTCAACAACTCTCA 59.880 37.037 0.00 0.00 0.00 3.27
2012 2047 7.283127 TGAATCTGCTAATGAGGGTTACAAATC 59.717 37.037 0.00 0.00 0.00 2.17
2046 2081 6.745474 AACCTCTAGTTTGATCAGGGAAACTG 60.745 42.308 17.11 9.54 41.43 3.16
2106 2141 2.352388 GTGTAGCTGGTTTATTCGGCA 58.648 47.619 0.00 0.00 38.87 5.69
2115 2150 3.559171 CCACATGTTAGGTGTAGCTGGTT 60.559 47.826 0.00 0.00 34.46 3.67
2150 2186 2.256306 TCCAGGCAGAGTACAACATCA 58.744 47.619 0.00 0.00 0.00 3.07
2159 2195 4.785346 ATGATTGTATTCCAGGCAGAGT 57.215 40.909 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.