Multiple sequence alignment - TraesCS1D01G173900

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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 TraesCS1D01G173900 chr1D 100.000 2594 0 0 1 2594 247508648 247506055 0.000000e+00 4791.0
1 TraesCS1D01G173900 chr1D 95.161 62 3 0 2072 2133 59876028 59875967 5.910000e-17 99.0
2 TraesCS1D01G173900 chr1B 94.625 2307 81 11 58 2331 330230637 330232933 0.000000e+00 3533.0
3 TraesCS1D01G173900 chr1B 89.434 265 24 2 2330 2594 330233050 330233310 5.350000e-87 331.0
4 TraesCS1D01G173900 chr1B 95.714 70 3 0 1 70 330230549 330230618 2.110000e-21 113.0
5 TraesCS1D01G173900 chr1A 93.988 2129 68 17 1 2094 299718203 299720306 0.000000e+00 3168.0
6 TraesCS1D01G173900 chr1A 94.801 327 15 1 2268 2594 299720320 299720644 2.300000e-140 508.0
7 TraesCS1D01G173900 chr7B 82.536 481 80 4 1118 1596 584185897 584185419 1.110000e-113 420.0
8 TraesCS1D01G173900 chr7B 92.500 40 2 1 2075 2114 619589037 619589075 3.610000e-04 56.5
9 TraesCS1D01G173900 chr7A 81.980 505 82 7 1098 1596 622742096 622741595 1.110000e-113 420.0
10 TraesCS1D01G173900 chr7A 81.920 448 72 8 1153 1597 624772639 624773080 1.130000e-98 370.0
11 TraesCS1D01G173900 chr7A 94.737 38 2 0 2072 2109 653619550 653619513 2.790000e-05 60.2
12 TraesCS1D01G173900 chr7A 94.737 38 2 0 2072 2109 653636048 653636011 2.790000e-05 60.2
13 TraesCS1D01G173900 chr7A 94.737 38 2 0 2072 2109 653652085 653652048 2.790000e-05 60.2
14 TraesCS1D01G173900 chr5B 79.880 502 99 2 1101 1600 609484550 609485051 1.470000e-97 366.0
15 TraesCS1D01G173900 chr5B 79.518 498 101 1 1101 1597 609481805 609482302 1.140000e-93 353.0
16 TraesCS1D01G173900 chr5B 79.518 498 101 1 1101 1597 609494605 609495102 1.140000e-93 353.0
17 TraesCS1D01G173900 chr5D 79.835 486 98 0 1112 1597 493777645 493778130 3.170000e-94 355.0
18 TraesCS1D01G173900 chr5A 89.394 66 7 0 2068 2133 27727913 27727978 1.650000e-12 84.2
19 TraesCS1D01G173900 chr2A 100.000 31 0 0 2072 2102 194466493 194466463 1.000000e-04 58.4


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 TraesCS1D01G173900 chr1D 247506055 247508648 2593 True 4791.000000 4791 100.000000 1 2594 1 chr1D.!!$R2 2593
1 TraesCS1D01G173900 chr1B 330230549 330233310 2761 False 1325.666667 3533 93.257667 1 2594 3 chr1B.!!$F1 2593
2 TraesCS1D01G173900 chr1A 299718203 299720644 2441 False 1838.000000 3168 94.394500 1 2594 2 chr1A.!!$F1 2593
3 TraesCS1D01G173900 chr7A 622741595 622742096 501 True 420.000000 420 81.980000 1098 1596 1 chr7A.!!$R1 498
4 TraesCS1D01G173900 chr5B 609481805 609485051 3246 False 359.500000 366 79.699000 1101 1600 2 chr5B.!!$F2 499


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
872 923 2.089201 TGTGCAGCCAATCATCAAGAG 58.911 47.619 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1741 0.179227 CACACACACACACACACACG 60.179 55.0 0.0 0.0 0.0 4.49 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)



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AutoCloner maintained by Alex Coulton.