Multiple sequence alignment - TraesCS1A01G235400

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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 TraesCS1A01G235400 chr1A 100.000 2255 0 0 1 2255 415654227 415656481 0 4165
1 TraesCS1A01G235400 chr1D 98.050 2256 42 2 1 2255 141314951 141312697 0 3921
2 TraesCS1A01G235400 chr3A 97.917 2256 46 1 1 2255 633109438 633111693 0 3904
3 TraesCS1A01G235400 chr7B 97.873 2257 46 2 1 2255 644465627 644467883 0 3901
4 TraesCS1A01G235400 chr7A 97.739 2256 50 1 1 2255 60150103 60147848 0 3882
5 TraesCS1A01G235400 chr1B 97.518 2256 55 1 1 2255 672477345 672479600 0 3855
6 TraesCS1A01G235400 chr1B 97.475 2257 54 3 1 2255 638702482 638700227 0 3849
7 TraesCS1A01G235400 chr4B 97.429 2256 56 2 1 2255 209079333 209077079 0 3843
8 TraesCS1A01G235400 chr2B 97.076 2257 59 4 1 2255 391114652 391112401 0 3795
9 TraesCS1A01G235400 chr2B 98.094 1784 32 2 473 2255 799246628 799248410 0 3105
10 TraesCS1A01G235400 chr2B 97.468 869 22 0 1 869 357197661 357196793 0 1483


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 TraesCS1A01G235400 chr1A 415654227 415656481 2254 False 4165 4165 100.000 1 2255 1 chr1A.!!$F1 2254
1 TraesCS1A01G235400 chr1D 141312697 141314951 2254 True 3921 3921 98.050 1 2255 1 chr1D.!!$R1 2254
2 TraesCS1A01G235400 chr3A 633109438 633111693 2255 False 3904 3904 97.917 1 2255 1 chr3A.!!$F1 2254
3 TraesCS1A01G235400 chr7B 644465627 644467883 2256 False 3901 3901 97.873 1 2255 1 chr7B.!!$F1 2254
4 TraesCS1A01G235400 chr7A 60147848 60150103 2255 True 3882 3882 97.739 1 2255 1 chr7A.!!$R1 2254
5 TraesCS1A01G235400 chr1B 672477345 672479600 2255 False 3855 3855 97.518 1 2255 1 chr1B.!!$F1 2254
6 TraesCS1A01G235400 chr1B 638700227 638702482 2255 True 3849 3849 97.475 1 2255 1 chr1B.!!$R1 2254
7 TraesCS1A01G235400 chr4B 209077079 209079333 2254 True 3843 3843 97.429 1 2255 1 chr4B.!!$R1 2254
8 TraesCS1A01G235400 chr2B 391112401 391114652 2251 True 3795 3795 97.076 1 2255 1 chr2B.!!$R2 2254
9 TraesCS1A01G235400 chr2B 799246628 799248410 1782 False 3105 3105 98.094 473 2255 1 chr2B.!!$F1 1782
10 TraesCS1A01G235400 chr2B 357196793 357197661 868 True 1483 1483 97.468 1 869 1 chr2B.!!$R1 868

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
923 925 0.187117 TTTCATTGCTGTGGGTCCCA 59.813 50.0 6.47 6.47 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 1774 1.226435 GATCGCTCAGTTCGCTCGT 60.226 57.895 0.0 0.0 0.0 4.18 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
235 236 4.913335 AAAGTAGTTGAGTCGTGTCTCA 57.087 40.909 4.30 4.30 41.85 3.27
253 254 0.593128 CACGGGAGCAAAAAGAGTGG 59.407 55.000 0.00 0.00 0.00 4.00
282 283 0.751452 GTAAGCCCCCTAGGTCTTCG 59.249 60.000 8.29 0.00 38.26 3.79
307 308 8.290325 CGTCTTCCTTCTAAACTAATTGCTTTT 58.710 33.333 0.00 0.00 0.00 2.27
322 323 3.715628 GCTTTTGCTTGACTCTTCCAA 57.284 42.857 0.00 0.00 43.35 3.53
394 395 0.324368 TGTACCAGATCCGGTGAGCT 60.324 55.000 11.10 0.00 40.39 4.09
787 788 6.983307 GTGACTGAGCAGATATGTCTATTGTT 59.017 38.462 4.21 0.00 32.09 2.83
887 889 0.755079 TCCATTCTCTGCTCGGATGG 59.245 55.000 2.45 2.45 0.00 3.51
890 892 2.636830 CATTCTCTGCTCGGATGGTTT 58.363 47.619 0.00 0.00 0.00 3.27
923 925 0.187117 TTTCATTGCTGTGGGTCCCA 59.813 50.000 6.47 6.47 0.00 4.37
980 982 7.745620 ATTTAGTTGAATTTCTTGACTCCGT 57.254 32.000 0.00 0.00 0.00 4.69
1040 1042 2.163818 AAAGTCAAAGATGGCGTCGA 57.836 45.000 0.00 0.00 35.88 4.20
1091 1093 3.264964 GTGGTCCCTTGGTATTCAGGTTA 59.735 47.826 0.00 0.00 0.00 2.85
1188 1190 7.433680 AGATAAGGATTTCGCAAAACTTTTGT 58.566 30.769 14.36 0.00 0.00 2.83
1232 1235 1.262417 CCTTACCATTTTTGGGCCGT 58.738 50.000 0.00 0.00 0.00 5.68
1233 1236 1.067213 CCTTACCATTTTTGGGCCGTG 60.067 52.381 0.00 0.00 0.00 4.94
1334 1337 2.025887 TCTTCTTCTGGCTCAAATCCCC 60.026 50.000 0.00 0.00 0.00 4.81
1347 1350 5.363580 GCTCAAATCCCCTTTTCATATCCAA 59.636 40.000 0.00 0.00 0.00 3.53
1425 1428 8.154203 TCGTTTATGTCCATGGTATCATTGTAT 58.846 33.333 12.58 0.00 0.00 2.29
1690 1698 1.282248 CGAGCTCCGCGTTGAAAAGA 61.282 55.000 8.47 0.00 0.00 2.52
1783 1791 1.515088 CACGAGCGAACTGAGCGAT 60.515 57.895 0.00 0.00 40.04 4.58
1871 1879 0.767446 TTCACCCGGGTCCAAACCTA 60.767 55.000 27.51 0.00 45.66 3.08
2064 2075 1.077445 AGGCTTTGCTCCCCCTTTC 59.923 57.895 0.00 0.00 0.00 2.62
2160 2171 0.759346 GGCGATCAGAATGGTACCCT 59.241 55.000 10.07 0.00 36.16 4.34
2201 2212 2.254546 TTCCAGACACATCGCACTTT 57.745 45.000 0.00 0.00 0.00 2.66
2202 2213 2.254546 TCCAGACACATCGCACTTTT 57.745 45.000 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.093771 GTCCACGAGTTGAGATAGAGAAGTTA 59.906 42.308 0.00 0.00 0.00 2.24
13 14 3.904717 AGATAGGTCCACGAGTTGAGAT 58.095 45.455 0.00 0.00 0.00 2.75
235 236 0.472471 TCCACTCTTTTTGCTCCCGT 59.528 50.000 0.00 0.00 0.00 5.28
237 238 3.157087 TCATTCCACTCTTTTTGCTCCC 58.843 45.455 0.00 0.00 0.00 4.30
253 254 0.179054 GGGGGCTTACGTCCTCATTC 60.179 60.000 0.00 0.00 34.66 2.67
282 283 9.399403 CAAAAGCAATTAGTTTAGAAGGAAGAC 57.601 33.333 0.00 0.00 0.00 3.01
394 395 6.839124 ATGTCCATTTTTGCTTGATGTCTA 57.161 33.333 0.00 0.00 0.00 2.59
787 788 2.810439 CAAATCTGTTTTTGCCGGGA 57.190 45.000 2.18 0.00 30.51 5.14
887 889 3.701241 TGAAATTCACACAAGCGGAAAC 58.299 40.909 0.00 0.00 0.00 2.78
890 892 3.856638 GCAATGAAATTCACACAAGCGGA 60.857 43.478 0.00 0.00 31.22 5.54
923 925 6.500684 AAACAATCTTATTCGAGCACACAT 57.499 33.333 0.00 0.00 0.00 3.21
980 982 2.851263 AAACTCGATAACCAGCACCA 57.149 45.000 0.00 0.00 0.00 4.17
1091 1093 7.928706 CAGTCGACTTTCCTATCAGGATTTTAT 59.071 37.037 17.26 0.00 45.34 1.40
1213 1215 1.067213 CACGGCCCAAAAATGGTAAGG 60.067 52.381 0.00 0.00 0.00 2.69
1232 1235 5.004361 TCAGGAAATGGAAATGGTAACCA 57.996 39.130 0.00 0.00 38.19 3.67
1233 1236 5.337250 GGTTCAGGAAATGGAAATGGTAACC 60.337 44.000 0.00 0.00 0.00 2.85
1334 1337 3.294214 AGCCTGCCTTGGATATGAAAAG 58.706 45.455 0.00 0.00 0.00 2.27
1347 1350 1.657804 AGTGTACCTAAAGCCTGCCT 58.342 50.000 0.00 0.00 0.00 4.75
1425 1428 7.123383 TCATCTGGTTGATAGTAGAAGGTACA 58.877 38.462 0.00 0.00 33.36 2.90
1644 1652 7.940850 TGCTGTCTTTTTAGCTTCAAAACTAT 58.059 30.769 0.00 0.00 40.52 2.12
1683 1691 2.827604 CGGCTCGCTTCTCTTTTCA 58.172 52.632 0.00 0.00 0.00 2.69
1766 1774 1.226435 GATCGCTCAGTTCGCTCGT 60.226 57.895 0.00 0.00 0.00 4.18
1783 1791 3.051210 CGATAGGCGCCTCATGGA 58.949 61.111 36.73 16.80 34.57 3.41
1871 1879 7.064728 CGTAAAGGAAAAATTAGCTAGCTCAGT 59.935 37.037 23.26 6.82 0.00 3.41
2064 2075 8.017946 CGACCCTTCTTTCTTTCTTCATTTAAG 58.982 37.037 0.00 0.00 36.45 1.85
2160 2171 5.540400 AACTCGGGATCGTAAATGGATTA 57.460 39.130 0.00 0.00 37.69 1.75
2232 2243 2.622436 CCACTCTTCTTTGATCCGTCC 58.378 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.