Multiple sequence alignment - TraesCS1D01G403900

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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 TraesCS1D01G403900 chr1D 100.000 2452 0 0 1 2452 468750199 468747748 0.000000e+00 4529
1 TraesCS1D01G403900 chr1B 94.740 1730 59 15 1 1718 648101433 648099724 0.000000e+00 2662
2 TraesCS1D01G403900 chr1B 89.815 648 28 11 1833 2443 648098730 648098084 0.000000e+00 797
3 TraesCS1D01G403900 chr1B 87.561 619 52 13 1109 1714 648063163 648062557 0.000000e+00 693
4 TraesCS1D01G403900 chr1A 93.959 1672 84 7 1 1665 561597381 561595720 0.000000e+00 2512
5 TraesCS1D01G403900 chr1A 88.841 699 32 15 1790 2443 561594836 561594139 0.000000e+00 817
6 TraesCS1D01G403900 chr1A 97.005 434 12 1 2020 2452 561588916 561588483 0.000000e+00 728
7 TraesCS1D01G403900 chr2A 89.809 157 15 1 2186 2341 698107709 698107553 1.490000e-47 200


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 TraesCS1D01G403900 chr1D 468747748 468750199 2451 True 4529.0 4529 100.0000 1 2452 1 chr1D.!!$R1 2451
1 TraesCS1D01G403900 chr1B 648098084 648101433 3349 True 1729.5 2662 92.2775 1 2443 2 chr1B.!!$R2 2442
2 TraesCS1D01G403900 chr1B 648062557 648063163 606 True 693.0 693 87.5610 1109 1714 1 chr1B.!!$R1 605
3 TraesCS1D01G403900 chr1A 561594139 561597381 3242 True 1664.5 2512 91.4000 1 2443 2 chr1A.!!$R2 2442

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
225 227 0.706729 GACACTAAACGGACTTCGCG 59.293 55.0 0.00 0.0 43.89 5.87 F
236 238 1.334054 GACTTCGCGCGAAAAGTCTA 58.666 50.0 38.24 22.9 45.08 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1190 0.310543 GTCAGTCCACAATGCGCAAA 59.689 50.0 17.11 0.0 0.00 3.68 R
1776 2399 0.816825 CATCAGCGTGCTGGGCTATT 60.817 55.0 20.78 0.0 43.75 1.73 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
76 78 3.579151 CCCTACCTTTATGAGTAGCTCCC 59.421 52.174 0.00 0.00 35.63 4.30
225 227 0.706729 GACACTAAACGGACTTCGCG 59.293 55.000 0.00 0.00 43.89 5.87
236 238 1.334054 GACTTCGCGCGAAAAGTCTA 58.666 50.000 38.24 22.90 45.08 2.59
268 270 3.430218 CAGAAAAGAACGAGCACTAGTGG 59.570 47.826 23.95 10.27 0.00 4.00
377 379 7.061673 CGTTTTTCACAACATGTCTCTGAAAAA 59.938 33.333 27.22 27.22 36.78 1.94
383 385 3.554934 ACATGTCTCTGAAAAAGCACCA 58.445 40.909 0.00 0.00 0.00 4.17
717 721 6.797439 AAAGTAACTTTGAGATCGGCAGATCA 60.797 38.462 25.60 7.76 42.40 2.92
806 810 7.526041 ACCAGAGTATATTTCCCATAATGCAA 58.474 34.615 0.00 0.00 0.00 4.08
844 852 1.453155 AACTCCGCGATCTGCAAATT 58.547 45.000 8.23 0.00 46.97 1.82
1011 1023 3.686227 AGATCAGACATGAGAGGGAGT 57.314 47.619 0.00 0.00 39.29 3.85
1220 1242 7.512992 ACATATTGCCTGTAGCTAGAAGAATT 58.487 34.615 0.00 0.00 44.23 2.17
1673 1706 0.818445 TTTGTCCGCCCGTTGCTTTA 60.818 50.000 0.00 0.00 38.05 1.85
1704 1737 1.125093 TGCCGTTCAGAAGGGGAGAA 61.125 55.000 21.04 0.00 36.93 2.87
1715 1748 1.760405 AGGGGAGAAGTGAAATGGGT 58.240 50.000 0.00 0.00 0.00 4.51
1810 2711 4.097437 ACGCTGATGGAGAAATCGTACTTA 59.903 41.667 0.00 0.00 0.00 2.24
1877 3069 7.752695 GGAGAAGTAATTTGTCCATACAACTG 58.247 38.462 0.00 0.00 46.07 3.16
1888 3080 2.536365 CATACAACTGCGATACCACGT 58.464 47.619 0.00 0.00 35.59 4.49
2048 3282 2.173382 CGCGAGGCCAAAAGTTCG 59.827 61.111 5.01 5.31 36.23 3.95
2103 3337 2.402564 TCCATTCAGTCCAGGATCTCC 58.597 52.381 0.00 0.00 0.00 3.71
2156 3390 3.889815 TCCCCTTCATGATGACAATGTC 58.110 45.455 6.41 6.41 0.00 3.06
2158 3392 2.615447 CCCTTCATGATGACAATGTCGG 59.385 50.000 9.00 1.09 34.95 4.79
2163 3397 2.399916 TGATGACAATGTCGGATGCA 57.600 45.000 9.00 0.00 34.95 3.96
2172 3409 6.751425 TGACAATGTCGGATGCAATTTTATTC 59.249 34.615 9.00 0.00 34.95 1.75
2173 3410 6.866480 ACAATGTCGGATGCAATTTTATTCT 58.134 32.000 0.00 0.00 0.00 2.40
2238 3477 4.266265 CAGTGACATTCATACTGCTGTACG 59.734 45.833 5.50 0.00 35.87 3.67
2259 3498 6.236017 ACGTTTTCACACATGTTTATCGAT 57.764 33.333 2.16 2.16 0.00 3.59
2314 3553 1.274167 TCACCTTGGTAAGCGTCGAAT 59.726 47.619 0.00 0.00 0.00 3.34
2377 3616 3.227276 CGCCGCTGTCCTCCCTAT 61.227 66.667 0.00 0.00 0.00 2.57
2443 3682 2.911102 GTCTCAATGCAAAACGCTAAGC 59.089 45.455 0.00 0.00 43.06 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 1.159713 TTCTGCCGGCTCAATATGCG 61.160 55.000 29.70 4.60 0.00 4.73
187 189 4.065321 GTCAGAAGACATTCCCATCGAT 57.935 45.455 0.00 0.00 44.34 3.59
236 238 8.968242 GTGCTCGTTCTTTTCTGAATTTATTTT 58.032 29.630 0.00 0.00 0.00 1.82
255 257 2.240279 AGACTTTCCACTAGTGCTCGT 58.760 47.619 17.86 10.65 0.00 4.18
383 385 0.107410 TCTCGGTGCAACACAAACCT 60.107 50.000 0.98 0.00 39.98 3.50
542 544 2.821366 CTGGTGCTGGTGATCCGC 60.821 66.667 0.00 0.00 36.30 5.54
649 651 2.776312 TCGTGCGAGATATTCCTGAC 57.224 50.000 0.00 0.00 0.00 3.51
717 721 2.831685 TGAATGCGTATAATCGGCCT 57.168 45.000 0.00 0.00 0.00 5.19
770 774 6.420913 AATATACTCTGGTAATCGCTGGTT 57.579 37.500 0.00 0.00 0.00 3.67
829 837 1.913403 GTTTCAATTTGCAGATCGCGG 59.087 47.619 6.13 0.00 46.97 6.46
830 838 1.574477 CGTTTCAATTTGCAGATCGCG 59.426 47.619 0.00 0.00 46.97 5.87
832 840 2.583739 TGCGTTTCAATTTGCAGATCG 58.416 42.857 0.00 0.00 32.73 3.69
844 852 0.870735 TACACGACGCTTGCGTTTCA 60.871 50.000 21.49 3.83 40.44 2.69
1163 1185 4.821260 TCAGTCCACAATGCGCAAATATAT 59.179 37.500 17.11 0.00 0.00 0.86
1164 1186 4.035091 GTCAGTCCACAATGCGCAAATATA 59.965 41.667 17.11 0.00 0.00 0.86
1165 1187 3.016031 TCAGTCCACAATGCGCAAATAT 58.984 40.909 17.11 0.00 0.00 1.28
1166 1188 2.161410 GTCAGTCCACAATGCGCAAATA 59.839 45.455 17.11 0.00 0.00 1.40
1167 1189 1.068333 GTCAGTCCACAATGCGCAAAT 60.068 47.619 17.11 2.99 0.00 2.32
1168 1190 0.310543 GTCAGTCCACAATGCGCAAA 59.689 50.000 17.11 0.00 0.00 3.68
1169 1191 0.817229 TGTCAGTCCACAATGCGCAA 60.817 50.000 17.11 0.00 0.00 4.85
1170 1192 0.817229 TTGTCAGTCCACAATGCGCA 60.817 50.000 14.96 14.96 31.08 6.09
1220 1242 8.892723 GTTATGTTGACATGATGGTCTTGATAA 58.107 33.333 0.00 0.00 38.61 1.75
1704 1737 4.431416 TCAGTGTGTTACCCATTTCACT 57.569 40.909 0.00 0.00 36.73 3.41
1715 1748 7.672240 TGTACAACTTCCATATCAGTGTGTTA 58.328 34.615 0.00 0.00 0.00 2.41
1763 2386 6.039717 GTGCTGGGCTATTTGAATCTGAATTA 59.960 38.462 0.00 0.00 0.00 1.40
1776 2399 0.816825 CATCAGCGTGCTGGGCTATT 60.817 55.000 20.78 0.00 43.75 1.73
1810 2711 9.502091 TGCTATTTATGTTGTCTCTTAGTTTGT 57.498 29.630 0.00 0.00 0.00 2.83
1877 3069 1.595489 CCACTACGTACGTGGTATCGC 60.595 57.143 32.61 0.00 45.36 4.58
1888 3080 4.940046 CAGACTAAAGAGGACCACTACGTA 59.060 45.833 0.00 0.00 0.00 3.57
1961 3181 1.739667 CCATCGGTCCGCACTATGA 59.260 57.895 6.34 0.00 0.00 2.15
2006 3226 2.175811 GCCGGTGCAACGTTGATC 59.824 61.111 31.62 20.79 38.12 2.92
2007 3227 2.593148 TGCCGGTGCAACGTTGAT 60.593 55.556 31.62 0.00 46.66 2.57
2103 3337 7.999545 TGAGATATCCGGGATTTCCTATACTAG 59.000 40.741 15.98 0.00 35.95 2.57
2119 3353 4.357918 AGGGGAACAAATGAGATATCCG 57.642 45.455 0.00 0.00 0.00 4.18
2156 3390 6.198966 GCACCTAAAGAATAAAATTGCATCCG 59.801 38.462 0.00 0.00 0.00 4.18
2158 3392 7.975616 TGAGCACCTAAAGAATAAAATTGCATC 59.024 33.333 0.00 0.00 0.00 3.91
2163 3397 6.974622 CGCATGAGCACCTAAAGAATAAAATT 59.025 34.615 0.00 0.00 42.27 1.82
2172 3409 1.737838 TTCCGCATGAGCACCTAAAG 58.262 50.000 0.00 0.00 42.27 1.85
2173 3410 2.192664 TTTCCGCATGAGCACCTAAA 57.807 45.000 0.00 0.00 42.27 1.85
2238 3477 8.116753 CCTAGATCGATAAACATGTGTGAAAAC 58.883 37.037 0.00 0.00 0.00 2.43
2259 3498 3.307059 GCCTCTCTGTTTGCTTTCCTAGA 60.307 47.826 0.00 0.00 0.00 2.43
2314 3553 1.345415 GTTCACCGGTCTTTACCTCCA 59.655 52.381 2.59 0.00 44.35 3.86
2377 3616 8.690203 ACATTAGTAAGCATTTACCATGCATA 57.310 30.769 0.00 0.00 46.77 3.14


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

AutoCloner maintained by Alex Coulton.