Multiple sequence alignment - TraesCS2A01G240900

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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 TraesCS2A01G240900 chr2A 100.000 2251 0 0 1 2251 335826562 335824312 0.000000e+00 4157.0
1 TraesCS2A01G240900 chr2A 96.992 399 10 1 1568 1966 42772663 42773059 0.000000e+00 669.0
2 TraesCS2A01G240900 chr2A 95.385 65 3 0 2059 2123 113954619 113954555 1.100000e-18 104.0
3 TraesCS2A01G240900 chr2A 98.182 55 1 0 2197 2251 102678341 102678395 1.840000e-16 97.1
4 TraesCS2A01G240900 chr2D 97.475 2257 47 7 1 2251 628285951 628283699 0.000000e+00 3843.0
5 TraesCS2A01G240900 chr6D 97.038 2262 52 7 1 2251 431400309 431398052 0.000000e+00 3792.0
6 TraesCS2A01G240900 chr1D 96.947 2260 60 4 1 2251 254489984 254487725 0.000000e+00 3783.0
7 TraesCS2A01G240900 chr1D 94.914 1750 79 7 506 2251 244408395 244406652 0.000000e+00 2730.0
8 TraesCS2A01G240900 chr1D 97.043 1623 37 5 1 1612 394179195 394177573 0.000000e+00 2721.0
9 TraesCS2A01G240900 chr1D 94.800 1750 80 7 506 2251 244401944 244400202 0.000000e+00 2717.0
10 TraesCS2A01G240900 chr1D 93.832 1751 97 6 506 2251 244423932 244422188 0.000000e+00 2625.0
11 TraesCS2A01G240900 chr3D 96.636 2259 62 6 1 2251 21897838 21895586 0.000000e+00 3738.0
12 TraesCS2A01G240900 chr1A 97.533 2148 47 6 1 2145 256025884 256028028 0.000000e+00 3668.0
13 TraesCS2A01G240900 chrUn 97.698 782 16 1 1 780 404958519 404957738 0.000000e+00 1343.0
14 TraesCS2A01G240900 chr7D 93.103 174 12 0 1 174 231589523 231589350 2.870000e-64 255.0


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 TraesCS2A01G240900 chr2A 335824312 335826562 2250 True 4157 4157 100.000 1 2251 1 chr2A.!!$R2 2250
1 TraesCS2A01G240900 chr2D 628283699 628285951 2252 True 3843 3843 97.475 1 2251 1 chr2D.!!$R1 2250
2 TraesCS2A01G240900 chr6D 431398052 431400309 2257 True 3792 3792 97.038 1 2251 1 chr6D.!!$R1 2250
3 TraesCS2A01G240900 chr1D 254487725 254489984 2259 True 3783 3783 96.947 1 2251 1 chr1D.!!$R4 2250
4 TraesCS2A01G240900 chr1D 244406652 244408395 1743 True 2730 2730 94.914 506 2251 1 chr1D.!!$R2 1745
5 TraesCS2A01G240900 chr1D 394177573 394179195 1622 True 2721 2721 97.043 1 1612 1 chr1D.!!$R5 1611
6 TraesCS2A01G240900 chr1D 244400202 244401944 1742 True 2717 2717 94.800 506 2251 1 chr1D.!!$R1 1745
7 TraesCS2A01G240900 chr1D 244422188 244423932 1744 True 2625 2625 93.832 506 2251 1 chr1D.!!$R3 1745
8 TraesCS2A01G240900 chr3D 21895586 21897838 2252 True 3738 3738 96.636 1 2251 1 chr3D.!!$R1 2250
9 TraesCS2A01G240900 chr1A 256025884 256028028 2144 False 3668 3668 97.533 1 2145 1 chr1A.!!$F1 2144
10 TraesCS2A01G240900 chrUn 404957738 404958519 781 True 1343 1343 97.698 1 780 1 chrUn.!!$R1 779

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
945 964 4.579454 TTCTATTTACTGGTCGATCCCG 57.421 45.455 0.0 0.0 34.77 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2206 1.276622 AGCCGAGGTAGTGGACAAAT 58.723 50.0 0.0 0.0 0.0 2.32 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 6.487299 AAGAACTAGATCATCTAACCCCAC 57.513 41.667 0.00 0.0 0.00 4.61
488 497 7.419711 TCCCTATTTCATCTCGTAAAGTTCT 57.580 36.000 0.00 0.0 0.00 3.01
490 499 7.042335 CCCTATTTCATCTCGTAAAGTTCTGT 58.958 38.462 0.00 0.0 0.00 3.41
698 709 8.812329 GCTGCTATTCCGAATTACTCTATTATG 58.188 37.037 0.00 0.0 0.00 1.90
706 717 6.870965 CCGAATTACTCTATTATGCTGAAGCT 59.129 38.462 3.61 0.0 42.66 3.74
708 719 8.855279 CGAATTACTCTATTATGCTGAAGCTAC 58.145 37.037 3.61 0.0 42.66 3.58
945 964 4.579454 TTCTATTTACTGGTCGATCCCG 57.421 45.455 0.00 0.0 34.77 5.14
1100 1119 1.564348 ACCTTCCCTATTCATTGCGGT 59.436 47.619 0.00 0.0 0.00 5.68
1110 1130 6.816140 CCCTATTCATTGCGGTTTGTTATTTT 59.184 34.615 0.00 0.0 0.00 1.82
1118 1138 6.132791 TGCGGTTTGTTATTTTTCAGTACA 57.867 33.333 0.00 0.0 0.00 2.90
1119 1139 6.740110 TGCGGTTTGTTATTTTTCAGTACAT 58.260 32.000 0.00 0.0 0.00 2.29
1190 1210 2.159382 GAAAGCCGACAAGGAATTCCA 58.841 47.619 26.22 0.0 45.00 3.53
1389 1409 8.427012 CAGTTCATCCAACGATAAAACAAATTG 58.573 33.333 0.00 0.0 40.32 2.32
1659 1680 2.901839 GGGGAAATGGCCGATACTACTA 59.098 50.000 0.00 0.0 0.00 1.82
1729 1750 7.227910 TGTGATTGGTTTAGTAGGTGTTTTCTC 59.772 37.037 0.00 0.0 0.00 2.87
1741 1762 6.824305 AGGTGTTTTCTCTTATGGTTCATG 57.176 37.500 0.00 0.0 0.00 3.07
1876 1897 6.769341 ACCCGCGGAATTTTTACTCTTATAAT 59.231 34.615 30.73 0.0 0.00 1.28
2123 2149 9.476202 GAAGTTGAACTTAATTAAACAAGCCAT 57.524 29.630 11.01 0.0 38.80 4.40
2179 2206 3.072476 CCGCCATATTTTCTTCCCCTCTA 59.928 47.826 0.00 0.0 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.327214 GGAATTAGGGACTCATGTATCATCTC 58.673 42.308 0.00 0.00 41.75 2.75
347 351 8.470657 AAAGTAAATTCAAGGAAGAGCTTTCT 57.529 30.769 0.00 0.00 0.00 2.52
488 497 0.746204 TTGACCAAACTGCGAGCACA 60.746 50.000 0.00 0.00 0.00 4.57
490 499 0.179059 TCTTGACCAAACTGCGAGCA 60.179 50.000 0.00 0.00 0.00 4.26
698 709 7.091443 TCTACTTACTTTTCAGTAGCTTCAGC 58.909 38.462 0.00 0.00 41.59 4.26
789 800 6.349860 GCCTGGTTCCGAAACATAATTACTTT 60.350 38.462 0.00 0.00 37.10 2.66
790 801 5.124936 GCCTGGTTCCGAAACATAATTACTT 59.875 40.000 0.00 0.00 37.10 2.24
875 894 6.223120 AGATTGTCAATTTTGTACCAAAGGC 58.777 36.000 0.00 0.00 0.00 4.35
969 988 9.625747 AACTCCCAAAATTTTTGTACATTCAAT 57.374 25.926 18.05 0.00 0.00 2.57
1110 1130 7.062956 CACGTCATAAGCTAAACATGTACTGAA 59.937 37.037 0.00 0.00 0.00 3.02
1118 1138 5.703592 TCCAAACACGTCATAAGCTAAACAT 59.296 36.000 0.00 0.00 0.00 2.71
1119 1139 5.057819 TCCAAACACGTCATAAGCTAAACA 58.942 37.500 0.00 0.00 0.00 2.83
1190 1210 7.619964 AGAATCAAAACGGTCGGTTATTAAT 57.380 32.000 0.00 0.00 38.08 1.40
1355 1375 2.419673 CGTTGGATGAACTGCATTGCTA 59.580 45.455 10.49 0.00 37.34 3.49
1389 1409 8.648557 TGATTGTGTCATAGTTCTATAGTTGC 57.351 34.615 0.00 0.00 0.00 4.17
1459 1479 9.541884 AAGTACAAAATGAGTAATAAACCCCAT 57.458 29.630 0.00 0.00 0.00 4.00
1625 1646 3.205282 CCATTTCCCCTACTTTCCTCCAT 59.795 47.826 0.00 0.00 0.00 3.41
1659 1680 4.647564 TCAGCCAAAGAGGAATTCTTCT 57.352 40.909 13.98 13.98 45.41 2.85
1694 1715 3.848272 AAACCAATCACAGCAATACCG 57.152 42.857 0.00 0.00 0.00 4.02
1729 1750 5.068198 CCCAATCCAGAACATGAACCATAAG 59.932 44.000 0.00 0.00 0.00 1.73
1741 1762 4.227864 AGAGATGAACCCAATCCAGAAC 57.772 45.455 0.00 0.00 0.00 3.01
2010 2031 9.959721 AGGCTAGTTGAATAGTTTTGATTAAGA 57.040 29.630 0.00 0.00 0.00 2.10
2179 2206 1.276622 AGCCGAGGTAGTGGACAAAT 58.723 50.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.