Multiple sequence alignment - TraesCS4D01G146600

Loading Multiple Alignment...

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 TraesCS4D01G146600 chr4D 100.000 2558 0 0 1 2558 135042736 135045293 0 4724
1 TraesCS4D01G146600 chrUn 97.816 2564 50 3 1 2558 246703766 246701203 0 4420
2 TraesCS4D01G146600 chr7B 97.815 2563 51 2 1 2558 698133381 698130819 0 4418
3 TraesCS4D01G146600 chr7B 97.581 2563 57 2 1 2558 742930715 742933277 0 4385
4 TraesCS4D01G146600 chr7B 97.308 2563 64 2 1 2558 716802615 716800053 0 4346
5 TraesCS4D01G146600 chr6B 97.815 2563 51 2 1 2558 128896753 128894191 0 4418
6 TraesCS4D01G146600 chr3D 97.581 2563 56 3 1 2558 202630990 202628429 0 4385
7 TraesCS4D01G146600 chr3D 97.113 2563 67 4 1 2558 498438303 498440863 0 4316
8 TraesCS4D01G146600 chr5B 97.346 2562 63 2 1 2558 127825768 127823208 0 4349
9 TraesCS4D01G146600 chr5B 97.191 2563 66 3 1 2558 713088991 713091552 0 4329


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 TraesCS4D01G146600 chr4D 135042736 135045293 2557 False 4724 4724 100.000 1 2558 1 chr4D.!!$F1 2557
1 TraesCS4D01G146600 chrUn 246701203 246703766 2563 True 4420 4420 97.816 1 2558 1 chrUn.!!$R1 2557
2 TraesCS4D01G146600 chr7B 698130819 698133381 2562 True 4418 4418 97.815 1 2558 1 chr7B.!!$R1 2557
3 TraesCS4D01G146600 chr7B 742930715 742933277 2562 False 4385 4385 97.581 1 2558 1 chr7B.!!$F1 2557
4 TraesCS4D01G146600 chr7B 716800053 716802615 2562 True 4346 4346 97.308 1 2558 1 chr7B.!!$R2 2557
5 TraesCS4D01G146600 chr6B 128894191 128896753 2562 True 4418 4418 97.815 1 2558 1 chr6B.!!$R1 2557
6 TraesCS4D01G146600 chr3D 202628429 202630990 2561 True 4385 4385 97.581 1 2558 1 chr3D.!!$R1 2557
7 TraesCS4D01G146600 chr3D 498438303 498440863 2560 False 4316 4316 97.113 1 2558 1 chr3D.!!$F1 2557
8 TraesCS4D01G146600 chr5B 127823208 127825768 2560 True 4349 4349 97.346 1 2558 1 chr5B.!!$R1 2557
9 TraesCS4D01G146600 chr5B 713088991 713091552 2561 False 4329 4329 97.191 1 2558 1 chr5B.!!$F1 2557

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
308 311 2.660064 GGAGCGAAGGGAGGAAGCA 61.66 63.158 0.00 0.00 0.00 3.91 F
1280 1288 2.679934 CCATTGAAGCAGCGCGTCA 61.68 57.895 8.43 13.06 44.27 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1427 0.390603 CACGAGCAATCCAACCCGTA 60.391 55.000 0.0 0.0 0.00 4.02 R
2153 2161 1.416401 AGAAGAAGCAAGGAACGACCA 59.584 47.619 0.0 0.0 42.04 4.02 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
185 186 2.930950 CGCCCCTCCTTGAATTATTCA 58.069 47.619 3.20 3.20 38.04 2.57
261 262 4.012374 AGTTCTCAATCATTTCGTGGCAT 58.988 39.130 0.00 0.00 0.00 4.40
308 311 2.660064 GGAGCGAAGGGAGGAAGCA 61.660 63.158 0.00 0.00 0.00 3.91
323 326 8.128346 AGGGAGGAAGCATAGATAAGAGAATAT 58.872 37.037 0.00 0.00 0.00 1.28
402 406 3.766051 GAGCCAAAAAGAGGTTGATCCAT 59.234 43.478 0.00 0.00 39.02 3.41
415 419 3.781079 TGATCCATTTCATTCGCCAAC 57.219 42.857 0.00 0.00 0.00 3.77
637 641 9.083422 TGATAGAGAAATTCATAGACCTAGGTG 57.917 37.037 22.10 4.74 0.00 4.00
730 734 5.613329 ACGGGTACAACTCTTATTTGAACA 58.387 37.500 0.00 0.00 0.00 3.18
966 974 5.733620 TTGTTGTTCTAGTCGATTAGGGT 57.266 39.130 14.24 0.00 0.00 4.34
970 978 4.084287 TGTTCTAGTCGATTAGGGTGTGT 58.916 43.478 14.24 0.00 0.00 3.72
1257 1265 3.512033 AGAGCTGGTCGTCTTTCATAC 57.488 47.619 0.00 0.00 0.00 2.39
1280 1288 2.679934 CCATTGAAGCAGCGCGTCA 61.680 57.895 8.43 13.06 44.27 4.35
1446 1454 1.298859 GGATTGCTCGTGTGTCCACC 61.299 60.000 0.00 0.00 38.41 4.61
1447 1455 1.298859 GATTGCTCGTGTGTCCACCC 61.299 60.000 0.00 0.00 38.41 4.61
1494 1502 2.942376 TGTGAGTTTGTCAAATGCTCGT 59.058 40.909 0.40 0.00 36.74 4.18
1888 1896 5.638596 TTCTGTTCGTACTCTGATTGCTA 57.361 39.130 0.00 0.00 0.00 3.49
1894 1902 4.142038 TCGTACTCTGATTGCTATGGCTA 58.858 43.478 1.68 0.00 39.59 3.93
2153 2161 4.801330 TTTCACTCATACATCTGACCGT 57.199 40.909 0.00 0.00 0.00 4.83
2237 2245 8.947055 AGTACATTGCTTTTGTGAAGAAAAAT 57.053 26.923 0.00 0.00 0.00 1.82
2295 2303 8.567285 TTCTCTCAGTTATTTTCTGGGAATTC 57.433 34.615 0.00 0.00 41.13 2.17
2332 2340 8.330466 ACTAATGATGGTTACTATCTCTCTCG 57.670 38.462 9.96 0.00 0.00 4.04
2366 2374 1.857217 CAGGATTTGATCTCACGCTCG 59.143 52.381 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 7.364762 GGGTCCTTTTTAGTAGATGACTCATCA 60.365 40.741 19.21 4.82 42.72 3.07
130 131 6.023603 AGGGTCCTTTTTAGTAGATGACTCA 58.976 40.000 0.00 0.00 39.81 3.41
261 262 3.164977 TGGTTCAGCCACACCCGA 61.165 61.111 0.00 0.00 43.61 5.14
637 641 8.727100 ATTCCCTTTATCAATTTTCCTATCCC 57.273 34.615 0.00 0.00 0.00 3.85
767 771 9.590451 CCGACTCAATTAAGGTATTAGTGTTTA 57.410 33.333 0.00 0.00 0.00 2.01
966 974 5.738619 TCAGTTCTAGCTATTTCCACACA 57.261 39.130 0.00 0.00 0.00 3.72
970 978 4.811024 CGCATTCAGTTCTAGCTATTTCCA 59.189 41.667 0.00 0.00 0.00 3.53
999 1007 9.590451 AAATACATTACAAGATGCTTTTCCATG 57.410 29.630 0.00 0.00 0.00 3.66
1029 1037 3.873952 GCAGGAGCATACTCGATTTTCTT 59.126 43.478 0.00 0.00 44.48 2.52
1199 1207 6.389906 CCATATCTTCCAAAACCAAGTTGTC 58.610 40.000 1.45 0.00 0.00 3.18
1257 1265 2.796651 GCTGCTTCAATGGCTCGG 59.203 61.111 0.00 0.00 0.00 4.63
1280 1288 2.919228 GGAATTGTCCGATTGTAGCCT 58.081 47.619 0.00 0.00 33.05 4.58
1419 1427 0.390603 CACGAGCAATCCAACCCGTA 60.391 55.000 0.00 0.00 0.00 4.02
1888 1896 1.069823 CCAAGATCGAGCTGTAGCCAT 59.930 52.381 2.80 0.00 43.38 4.40
1894 1902 2.012673 GATTTGCCAAGATCGAGCTGT 58.987 47.619 2.80 0.00 0.00 4.40
2153 2161 1.416401 AGAAGAAGCAAGGAACGACCA 59.584 47.619 0.00 0.00 42.04 4.02
2160 2168 5.745312 TCAACATAGAGAAGAAGCAAGGA 57.255 39.130 0.00 0.00 0.00 3.36
2237 2245 5.532032 TGACATCTTGAATTGCTCACTCAAA 59.468 36.000 0.00 0.00 32.21 2.69
2295 2303 6.764308 ACCATCATTAGTTTGATCAACCTG 57.236 37.500 15.19 5.83 35.77 4.00
2332 2340 3.601443 AATCCTGAGTATAGCGATGCC 57.399 47.619 0.00 0.00 0.00 4.40
2366 2374 4.495422 CAGTGTGTGTATCAGTAAGACCC 58.505 47.826 0.00 0.00 0.00 4.46
2524 2532 4.464008 ACAAACTGACTGACAATGTGGAT 58.536 39.130 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.