Multiple sequence alignment - TraesCS4A01G393700

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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 TraesCS4A01G393700 chr4A 100.000 2462 0 0 1 2462 669381089 669383550 0.000 4547.0
1 TraesCS4A01G393700 chr7D 95.438 1973 71 11 505 2462 20459936 20461904 0.000 3127.0
2 TraesCS4A01G393700 chr7D 86.978 1605 192 11 866 2462 555196503 555194908 0.000 1790.0
3 TraesCS4A01G393700 chr7D 86.203 1580 207 8 890 2462 89533132 89531557 0.000 1700.0
4 TraesCS4A01G393700 chr7D 84.375 1696 239 18 778 2462 20442253 20443933 0.000 1640.0
5 TraesCS4A01G393700 chr7D 94.325 511 20 3 1 507 20459302 20459807 0.000 774.0
6 TraesCS4A01G393700 chr7A 95.522 1943 68 11 531 2461 20779079 20781014 0.000 3088.0
7 TraesCS4A01G393700 chr7A 85.422 1612 216 14 862 2462 20659531 20661134 0.000 1657.0
8 TraesCS4A01G393700 chr7A 92.308 507 31 2 1 507 20778362 20778860 0.000 713.0
9 TraesCS4A01G393700 chr7A 100.000 29 0 0 505 533 20779021 20779049 0.001 54.7
10 TraesCS4A01G393700 chr7B 84.798 1809 241 27 670 2462 601114160 601115950 0.000 1786.0
11 TraesCS4A01G393700 chr2A 84.496 1806 241 23 671 2462 733087482 733089262 0.000 1748.0
12 TraesCS4A01G393700 chr2D 86.300 1562 202 9 908 2462 598814004 598815560 0.000 1688.0


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 TraesCS4A01G393700 chr4A 669381089 669383550 2461 False 4547.000000 4547 100.000000 1 2462 1 chr4A.!!$F1 2461
1 TraesCS4A01G393700 chr7D 20459302 20461904 2602 False 1950.500000 3127 94.881500 1 2462 2 chr7D.!!$F2 2461
2 TraesCS4A01G393700 chr7D 555194908 555196503 1595 True 1790.000000 1790 86.978000 866 2462 1 chr7D.!!$R2 1596
3 TraesCS4A01G393700 chr7D 89531557 89533132 1575 True 1700.000000 1700 86.203000 890 2462 1 chr7D.!!$R1 1572
4 TraesCS4A01G393700 chr7D 20442253 20443933 1680 False 1640.000000 1640 84.375000 778 2462 1 chr7D.!!$F1 1684
5 TraesCS4A01G393700 chr7A 20659531 20661134 1603 False 1657.000000 1657 85.422000 862 2462 1 chr7A.!!$F1 1600
6 TraesCS4A01G393700 chr7A 20778362 20781014 2652 False 1285.233333 3088 95.943333 1 2461 3 chr7A.!!$F2 2460
7 TraesCS4A01G393700 chr7B 601114160 601115950 1790 False 1786.000000 1786 84.798000 670 2462 1 chr7B.!!$F1 1792
8 TraesCS4A01G393700 chr2A 733087482 733089262 1780 False 1748.000000 1748 84.496000 671 2462 1 chr2A.!!$F1 1791
9 TraesCS4A01G393700 chr2D 598814004 598815560 1556 False 1688.000000 1688 86.300000 908 2462 1 chr2D.!!$F1 1554

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
249 251 2.282701 TCTTAATGCGACGGTACCAC 57.717 50.0 13.54 4.32 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2296 1.278985 ACTCGGCTGGACATTCATGAA 59.721 47.619 11.26 11.26 0.0 2.57 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
202 204 5.555966 TGTTATCAACAACAGGATAGCACA 58.444 37.500 0.00 0.00 38.72 4.57
249 251 2.282701 TCTTAATGCGACGGTACCAC 57.717 50.000 13.54 4.32 0.00 4.16
253 255 2.824071 AATGCGACGGTACCACGGTC 62.824 60.000 23.38 16.32 42.70 4.79
301 303 6.599638 AGGTTTTAGTAGCCATTCATTGTCTC 59.400 38.462 0.00 0.00 0.00 3.36
370 372 5.350640 GCTTTTTACTGGCGACATACTTAGT 59.649 40.000 0.00 0.00 41.51 2.24
434 439 7.063898 CAGTATTCTTGTTGTGTGGATCTACTG 59.936 40.741 10.82 3.18 0.00 2.74
559 759 3.266772 AGTTGGCAGGTATTCAGATTGGA 59.733 43.478 0.00 0.00 0.00 3.53
567 767 3.244387 GGTATTCAGATTGGAGCCCTCTC 60.244 52.174 0.00 0.00 38.62 3.20
599 799 7.322664 ACTTGATTAAAATTGCAACATCCGAT 58.677 30.769 0.00 0.00 0.00 4.18
600 800 8.465999 ACTTGATTAAAATTGCAACATCCGATA 58.534 29.630 0.00 0.00 0.00 2.92
603 803 8.246871 TGATTAAAATTGCAACATCCGATACAA 58.753 29.630 0.00 0.00 0.00 2.41
604 804 9.248291 GATTAAAATTGCAACATCCGATACAAT 57.752 29.630 0.00 0.00 0.00 2.71
606 806 9.729023 TTAAAATTGCAACATCCGATACAATAG 57.271 29.630 0.00 0.00 0.00 1.73
811 1027 4.953579 AGGAGTACTTTGAAAGGTTTTGCA 59.046 37.500 10.02 0.00 0.00 4.08
812 1028 5.420739 AGGAGTACTTTGAAAGGTTTTGCAA 59.579 36.000 10.02 0.00 29.69 4.08
994 1219 5.877012 ACAGTGATACACTAGCAATTTCTGG 59.123 40.000 0.00 0.00 43.43 3.86
1477 1703 6.148480 GGGATACTAGCAGCTCAAAATACATG 59.852 42.308 0.00 0.00 0.00 3.21
1489 1715 6.317140 GCTCAAAATACATGGTCAAGAGATCA 59.683 38.462 0.00 0.00 39.67 2.92
1574 1800 3.999663 CAGAGAAAAACTAGAGCAGTGGG 59.000 47.826 0.00 0.00 37.63 4.61
1601 1827 5.009310 GCATGTGATGATTTGGAATGCTCTA 59.991 40.000 0.00 0.00 36.78 2.43
1916 2142 3.055385 TGACTTGTCTAGGGCGCTTATTT 60.055 43.478 9.23 0.00 0.00 1.40
1918 2147 5.093849 ACTTGTCTAGGGCGCTTATTTAA 57.906 39.130 9.23 0.00 0.00 1.52
2055 2284 7.934120 TCTCTTTTATAAGAAAGCCTATCCTGC 59.066 37.037 0.00 0.00 39.80 4.85
2067 2296 4.596643 AGCCTATCCTGCAAGAGATACAAT 59.403 41.667 0.00 0.00 34.07 2.71
2083 2312 5.533903 AGATACAATTCATGAATGTCCAGCC 59.466 40.000 21.39 8.18 0.00 4.85
2331 2560 5.484173 TTCCTGTATTGCAGCTTATTTCG 57.516 39.130 0.00 0.00 43.71 3.46
2425 2654 4.926832 GGTGAAAGCACTCTAGAAGAAGTC 59.073 45.833 0.00 0.00 44.52 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 204 8.401709 GCTCATCCTTCGAAGAATCTTTTTATT 58.598 33.333 26.61 0.00 45.90 1.40
249 251 2.898729 ATTGATAGCTCACCAGACCG 57.101 50.000 0.00 0.00 0.00 4.79
339 341 4.941263 TGTCGCCAGTAAAAAGCATTATCT 59.059 37.500 0.00 0.00 0.00 1.98
350 352 6.513806 TGTACTAAGTATGTCGCCAGTAAA 57.486 37.500 0.00 0.00 0.00 2.01
370 372 7.976414 AGAAATTCCAAATTCCCATCATGTA 57.024 32.000 0.00 0.00 0.00 2.29
434 439 3.305398 AGGAGACGTCATGTTCACTTC 57.695 47.619 19.50 2.60 0.00 3.01
533 701 0.323302 TGAATACCTGCCAACTCGCA 59.677 50.000 0.00 0.00 37.19 5.10
559 759 5.770685 AATCAAGTAAAAGAGAGAGGGCT 57.229 39.130 0.00 0.00 0.00 5.19
599 799 9.613428 CACTTTCTTATTGGGACATCTATTGTA 57.387 33.333 0.00 0.00 39.18 2.41
600 800 7.557719 CCACTTTCTTATTGGGACATCTATTGT 59.442 37.037 0.00 0.00 42.79 2.71
603 803 7.451731 TCCACTTTCTTATTGGGACATCTAT 57.548 36.000 0.00 0.00 39.30 1.98
604 804 6.884472 TCCACTTTCTTATTGGGACATCTA 57.116 37.500 0.00 0.00 39.30 1.98
605 805 5.779241 TCCACTTTCTTATTGGGACATCT 57.221 39.130 0.00 0.00 39.30 2.90
606 806 6.122277 TGATCCACTTTCTTATTGGGACATC 58.878 40.000 0.00 0.00 39.30 3.06
811 1027 3.456280 TCGCAGCAGAAAAGCAAAATTT 58.544 36.364 0.00 0.00 36.85 1.82
812 1028 3.054878 CTCGCAGCAGAAAAGCAAAATT 58.945 40.909 0.00 0.00 36.85 1.82
994 1219 4.046938 TCACGATCTCTGCCATTACTTC 57.953 45.455 0.00 0.00 0.00 3.01
1489 1715 7.849804 ACGTGAAATATTTGCTAGATCTTGT 57.150 32.000 5.17 0.00 0.00 3.16
1574 1800 3.872511 TTCCAAATCATCACATGCCAC 57.127 42.857 0.00 0.00 0.00 5.01
1601 1827 3.228453 CCATTCCAAGCAAGGCTATGAT 58.772 45.455 0.00 0.00 38.25 2.45
1918 2147 8.643324 GTGATTATCAATCTACTACCCTTGTCT 58.357 37.037 0.00 0.00 38.72 3.41
2053 2282 7.201758 GGACATTCATGAATTGTATCTCTTGCA 60.202 37.037 18.41 0.00 0.00 4.08
2054 2283 7.137426 GGACATTCATGAATTGTATCTCTTGC 58.863 38.462 18.41 6.05 0.00 4.01
2055 2284 8.217131 TGGACATTCATGAATTGTATCTCTTG 57.783 34.615 18.41 7.43 0.00 3.02
2067 2296 1.278985 ACTCGGCTGGACATTCATGAA 59.721 47.619 11.26 11.26 0.00 2.57
2083 2312 1.522668 TGGACAATGGCTTCAACTCG 58.477 50.000 0.00 0.00 0.00 4.18
2245 2474 5.324409 TGCAAAACATTCCTTATCTGACCT 58.676 37.500 0.00 0.00 0.00 3.85
2331 2560 7.653767 TTCCGTTTGAAAAGATAGTCTTCTC 57.346 36.000 0.00 0.00 35.27 2.87


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

AutoCloner maintained by Alex Coulton.