Multiple sequence alignment - TraesCS1B01G406400

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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 TraesCS1B01G406400 chr1B 100.000 2255 0 0 1 2255 633743345 633745599 0 4165
1 TraesCS1B01G406400 chr6D 98.098 2261 37 1 1 2255 389250442 389248182 0 3932
2 TraesCS1B01G406400 chr6D 98.098 2261 37 1 1 2255 389255237 389252977 0 3932
3 TraesCS1B01G406400 chr5D 97.966 2261 39 2 1 2255 503239094 503236835 0 3914
4 TraesCS1B01G406400 chr3D 97.877 2261 41 2 1 2255 589265455 589267714 0 3903
5 TraesCS1B01G406400 chrUn 97.521 2259 52 3 1 2255 216508050 216510308 0 3858
6 TraesCS1B01G406400 chrUn 98.069 1450 28 0 252 1701 398829610 398828161 0 2523


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 TraesCS1B01G406400 chr1B 633743345 633745599 2254 False 4165 4165 100.000 1 2255 1 chr1B.!!$F1 2254
1 TraesCS1B01G406400 chr6D 389248182 389255237 7055 True 3932 3932 98.098 1 2255 2 chr6D.!!$R1 2254
2 TraesCS1B01G406400 chr5D 503236835 503239094 2259 True 3914 3914 97.966 1 2255 1 chr5D.!!$R1 2254
3 TraesCS1B01G406400 chr3D 589265455 589267714 2259 False 3903 3903 97.877 1 2255 1 chr3D.!!$F1 2254
4 TraesCS1B01G406400 chrUn 216508050 216510308 2258 False 3858 3858 97.521 1 2255 1 chrUn.!!$F1 2254
5 TraesCS1B01G406400 chrUn 398828161 398829610 1449 True 2523 2523 98.069 252 1701 1 chrUn.!!$R1 1449

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
166 167 0.178958 AGGAGTCTGGGTCGTGTCTT 60.179 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 6246 1.754803 CATGGATTCTGGCAGTGCAAT 59.245 47.619 18.61 8.21 0.0 3.56 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
166 167 0.178958 AGGAGTCTGGGTCGTGTCTT 60.179 55.000 0.00 0.0 0.00 3.01
249 250 3.802948 ACCTCACCAACTAGCTAATCG 57.197 47.619 0.00 0.0 0.00 3.34
375 376 0.390735 GTTACTCACCCGTTCGCCAT 60.391 55.000 0.00 0.0 0.00 4.40
378 379 1.375396 CTCACCCGTTCGCCATTGA 60.375 57.895 0.00 0.0 0.00 2.57
417 418 4.249661 TCGACTTGCATGTGTTAAGCATA 58.750 39.130 10.37 0.0 38.19 3.14
510 511 7.778083 TCCTTATTCGTAGACAAAGCAGATTA 58.222 34.615 0.00 0.0 34.32 1.75
511 512 8.255206 TCCTTATTCGTAGACAAAGCAGATTAA 58.745 33.333 0.00 0.0 34.32 1.40
642 643 3.314693 AGCCTCTTATCCATTCCCGTTA 58.685 45.455 0.00 0.0 0.00 3.18
771 772 3.116862 TGAGTTATATCCCTTCCCCGTCT 60.117 47.826 0.00 0.0 0.00 4.18
850 851 1.003696 CTTCCTCCGGGCTTTCTTTCT 59.996 52.381 0.00 0.0 0.00 2.52
985 5781 5.828747 TCTGTACGATTTTCCCGATCTAAG 58.171 41.667 0.00 0.0 0.00 2.18
1226 6023 1.270839 CGCCCTTTTCTTGAGACCTCA 60.271 52.381 0.00 0.0 37.91 3.86
1448 6246 2.039418 CGATATGAGGACCCAACTCCA 58.961 52.381 0.00 0.0 34.06 3.86
1454 6252 0.251341 AGGACCCAACTCCATTGCAC 60.251 55.000 0.00 0.0 36.93 4.57
1496 6294 1.344065 TTGAAGCGGGTTGACCTCTA 58.656 50.000 0.00 0.0 36.97 2.43
1552 6350 0.983378 CCCCTTTCTCCTCGGTCCAT 60.983 60.000 0.00 0.0 0.00 3.41
1553 6351 0.466124 CCCTTTCTCCTCGGTCCATC 59.534 60.000 0.00 0.0 0.00 3.51
1591 6389 0.324614 TGGTGCCGACAGTTCATCAT 59.675 50.000 0.00 0.0 0.00 2.45
1613 6411 3.389329 TGGAAGAAAGAACTCACAGAGCT 59.611 43.478 0.00 0.0 32.04 4.09
1756 6554 1.202371 CCTCGTTCTATTGCTACCGCA 60.202 52.381 0.00 0.0 46.24 5.69
2120 6918 2.952978 TCGAAGATAGAAGAGCCCAGAC 59.047 50.000 0.00 0.0 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.202121 TGACGGTATCTGAGGAATAAGCAC 60.202 45.833 0.00 0.00 0.00 4.40
120 121 1.260544 GCAGCAGTGGGGAATTTTCT 58.739 50.000 0.00 0.00 0.00 2.52
158 159 1.611977 CACACTGGGACTAAGACACGA 59.388 52.381 0.00 0.00 0.00 4.35
375 376 2.131776 ACGGGAAGTGGTGTTTTCAA 57.868 45.000 0.00 0.00 0.00 2.69
378 379 1.018910 CGAACGGGAAGTGGTGTTTT 58.981 50.000 0.00 0.00 0.00 2.43
417 418 3.706373 AGGATGAACGCTGGCGGT 61.706 61.111 18.99 13.01 44.58 5.68
771 772 7.435488 GGATTCGTTAATTCTCTTTCTCGATGA 59.565 37.037 0.00 0.00 0.00 2.92
985 5781 1.734465 CTTCATGGAAACCTGCTCGAC 59.266 52.381 0.00 0.00 0.00 4.20
1226 6023 8.697507 AGAGAAGTAATTTGTCCTCATGTTTT 57.302 30.769 0.00 0.00 29.54 2.43
1448 6246 1.754803 CATGGATTCTGGCAGTGCAAT 59.245 47.619 18.61 8.21 0.00 3.56
1454 6252 2.133281 TGGAACATGGATTCTGGCAG 57.867 50.000 8.58 8.58 0.00 4.85
1496 6294 4.411540 AGGATTGTACCATGAGAGAAGCAT 59.588 41.667 0.00 0.00 0.00 3.79
1591 6389 3.389329 AGCTCTGTGAGTTCTTTCTTCCA 59.611 43.478 0.00 0.00 31.39 3.53
1613 6411 7.749666 AGTAGTACTATTAGTTACCGATCCCA 58.250 38.462 5.75 0.00 0.00 4.37
1756 6554 2.628178 TCCGATCGATTGCATAAGACCT 59.372 45.455 18.66 0.00 0.00 3.85
1982 6780 8.380742 AGAGAACCTTTTCCTCTGTATGAATA 57.619 34.615 0.00 0.00 31.28 1.75
2092 6890 6.153756 GGGCTCTTCTATCTTCGACTTATTC 58.846 44.000 0.00 0.00 0.00 1.75
2120 6918 6.072508 TCGAGTTTCCATTTCTTCATTTGGAG 60.073 38.462 0.00 0.00 39.33 3.86


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

AutoCloner maintained by Alex Coulton.