Multiple sequence alignment - TraesCS4A01G127300

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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 TraesCS4A01G127300 chr4A 100.000 2300 0 0 1 2300 164510785 164508486 0 4248
1 TraesCS4A01G127300 chr4D 95.637 2315 82 7 1 2300 310456528 310458838 0 3698
2 TraesCS4A01G127300 chr4B 94.372 2310 95 8 1 2300 387880950 387883234 0 3513


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 TraesCS4A01G127300 chr4A 164508486 164510785 2299 True 4248 4248 100.000 1 2300 1 chr4A.!!$R1 2299
1 TraesCS4A01G127300 chr4D 310456528 310458838 2310 False 3698 3698 95.637 1 2300 1 chr4D.!!$F1 2299
2 TraesCS4A01G127300 chr4B 387880950 387883234 2284 False 3513 3513 94.372 1 2300 1 chr4B.!!$F1 2299

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
40 41 1.002033 GCTGCCGCTAGAATTTGATGG 60.002 52.381 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1471 1472 0.250989 TTAACAGGAACTTGGCCCGG 60.251 55.0 0.0 0.0 34.6 5.73 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
40 41 1.002033 GCTGCCGCTAGAATTTGATGG 60.002 52.381 0.00 0.00 0.00 3.51
41 42 2.564771 CTGCCGCTAGAATTTGATGGA 58.435 47.619 0.00 0.00 0.00 3.41
55 56 3.378861 TGATGGAGAGAGAGAGCTGAA 57.621 47.619 0.00 0.00 0.00 3.02
57 58 3.700539 TGATGGAGAGAGAGAGCTGAAAG 59.299 47.826 0.00 0.00 0.00 2.62
264 265 3.603532 CCACTTCACTGTCAGCACATAT 58.396 45.455 0.00 0.00 0.00 1.78
315 316 3.838271 TGACAGCTCCGGCCGATC 61.838 66.667 30.73 15.07 39.73 3.69
345 346 4.804496 GCACGAGAGAGCTCTTCC 57.196 61.111 19.36 11.66 44.60 3.46
348 349 1.377987 ACGAGAGAGCTCTTCCGCT 60.378 57.895 27.53 17.51 44.33 5.52
435 436 1.661463 AGATGGAGTGATGGTGGTGT 58.339 50.000 0.00 0.00 0.00 4.16
474 475 7.024345 AGGTGATGATATCAATGAAGGCATA 57.976 36.000 9.99 0.00 41.69 3.14
501 502 3.637229 ACGCTGAGCTATCTTTAAGGCTA 59.363 43.478 1.78 0.00 35.01 3.93
564 565 2.751436 CCTTCCATGCCACCACGG 60.751 66.667 0.00 0.00 38.11 4.94
699 700 5.826643 ACAGAATTCTTATGTTGGCCCTTA 58.173 37.500 4.86 0.00 29.35 2.69
918 919 8.262933 GGATGGAAAGATGAATCAGGAAATTTT 58.737 33.333 0.00 0.00 0.00 1.82
1208 1209 5.367945 AGGTTTGAAGTCTGTACAGGAAA 57.632 39.130 22.48 10.82 0.00 3.13
1223 1224 4.704965 ACAGGAAAAACTGACAGGTCTAC 58.295 43.478 7.51 0.00 40.97 2.59
1329 1330 7.607991 AGCTTAGCTGCTGTAAAGAGATTTTTA 59.392 33.333 13.43 0.00 42.33 1.52
1344 1345 6.830838 AGAGATTTTTAGGTAAAGCTCCATGG 59.169 38.462 4.97 4.97 46.47 3.66
1346 1347 7.182060 AGATTTTTAGGTAAAGCTCCATGGAA 58.818 34.615 17.00 0.00 28.17 3.53
1356 1357 2.092538 AGCTCCATGGAACTGATTGAGG 60.093 50.000 17.00 1.41 0.00 3.86
1380 1381 5.994054 GCTAAGATCTATGGCAATCAACTCA 59.006 40.000 0.00 0.00 0.00 3.41
1387 1388 3.565764 TGGCAATCAACTCAGGATAGG 57.434 47.619 0.00 0.00 0.00 2.57
1401 1402 3.889520 GGATAGGTTCCGAGAACAGTT 57.110 47.619 15.57 0.00 33.93 3.16
1471 1472 4.082733 GCCTCAAAAATTGGGTAGTCTGAC 60.083 45.833 0.00 0.00 0.00 3.51
1479 1480 2.288025 GGTAGTCTGACCGGGCCAA 61.288 63.158 3.83 0.00 0.00 4.52
1632 1633 1.986882 AAGTTCCCTGAAGGCTGTTG 58.013 50.000 0.00 0.00 34.51 3.33
1729 1730 8.682936 AGATAAAATTAGAGGCAATCGACATT 57.317 30.769 0.00 0.00 0.00 2.71
1730 1731 8.562892 AGATAAAATTAGAGGCAATCGACATTG 58.437 33.333 0.00 0.00 42.26 2.82
1788 1789 2.851195 AGTATGGATTGATTCGGTGCC 58.149 47.619 0.00 0.00 0.00 5.01
1811 1812 5.512404 CCATAGAGGTTATTATGGCAACGGA 60.512 44.000 0.00 0.00 39.74 4.69
1856 1858 6.556212 TGTATTGTTTGCATGGGTTATTACG 58.444 36.000 0.00 0.00 0.00 3.18
1879 1881 6.865726 ACGCTGCAACATATTAATTGTTCAAA 59.134 30.769 0.00 3.21 35.18 2.69
1880 1882 7.062138 ACGCTGCAACATATTAATTGTTCAAAG 59.938 33.333 0.00 10.05 35.18 2.77
1881 1883 7.062138 CGCTGCAACATATTAATTGTTCAAAGT 59.938 33.333 0.00 0.00 35.18 2.66
1882 1884 8.164153 GCTGCAACATATTAATTGTTCAAAGTG 58.836 33.333 10.94 4.48 35.18 3.16
1885 1896 9.632807 GCAACATATTAATTGTTCAAAGTGGTA 57.367 29.630 10.94 0.00 35.18 3.25
1911 1928 9.118236 AGTAGTACGAACGACAAGTTTAATAAC 57.882 33.333 0.14 0.00 44.35 1.89
1916 1933 6.005289 CGAACGACAAGTTTAATAACGGAAG 58.995 40.000 0.00 0.00 44.35 3.46
1925 1942 9.465985 CAAGTTTAATAACGGAAGGCTTAAAAA 57.534 29.630 0.00 0.00 39.31 1.94
1929 1946 3.891056 AACGGAAGGCTTAAAAACGAG 57.109 42.857 0.00 0.00 0.00 4.18
1970 1987 5.335191 CCTGTGCAATGAGGAGTAGAAAAAC 60.335 44.000 2.08 0.00 0.00 2.43
2147 2164 3.188460 CCAGTAAGCGCATTGTAACTTGT 59.812 43.478 11.47 0.00 0.00 3.16
2181 2198 1.082756 GCTGTCGAACAAAGGCGTG 60.083 57.895 0.00 0.00 0.00 5.34
2196 2213 2.785258 GTGGGATCGCTCGCAAAC 59.215 61.111 7.64 0.00 44.87 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.824230 TGGCTTTCAGCTCTCTCTCTC 59.176 52.381 0.00 0.00 41.99 3.20
41 42 1.935799 TGGCTTTCAGCTCTCTCTCT 58.064 50.000 0.00 0.00 41.99 3.10
264 265 3.327757 ACAAGGCTACTCTTGACAATGGA 59.672 43.478 10.99 0.00 44.98 3.41
345 346 4.597079 ACAATTCTGTGTTGTTTACAGCG 58.403 39.130 0.00 0.00 43.97 5.18
348 349 6.424176 TTCGACAATTCTGTGTTGTTTACA 57.576 33.333 0.00 0.00 39.72 2.41
435 436 0.671472 CACCTTCTGATGTGCGCTCA 60.671 55.000 15.29 15.29 0.00 4.26
474 475 5.451242 CCTTAAAGATAGCTCAGCGTCTTCT 60.451 44.000 17.36 11.63 37.39 2.85
501 502 2.040278 TCAGCCAACTGGTAGCATTTCT 59.960 45.455 0.00 0.00 44.59 2.52
575 576 3.305181 TCTGCAGAGTATGGAGGCA 57.695 52.632 13.74 0.00 46.76 4.75
689 690 1.336517 GCGAAAAAGGTAAGGGCCAAC 60.337 52.381 6.18 2.91 0.00 3.77
699 700 1.239347 GGAAGAGCAGCGAAAAAGGT 58.761 50.000 0.00 0.00 0.00 3.50
1041 1042 6.832520 TCAATCACCAAGCTAAAGCATTTA 57.167 33.333 4.54 0.00 45.16 1.40
1152 1153 9.101655 CTTGATCTTTCAAACAATTCTTTTGGT 57.898 29.630 8.52 0.00 41.22 3.67
1208 1209 5.597182 TCAACTACTGTAGACCTGTCAGTTT 59.403 40.000 21.01 0.00 41.66 2.66
1223 1224 7.026631 TCTGAAACCAACAATTCAACTACTG 57.973 36.000 0.00 0.00 35.31 2.74
1329 1330 2.912956 TCAGTTCCATGGAGCTTTACCT 59.087 45.455 26.95 4.15 33.44 3.08
1344 1345 6.873076 CCATAGATCTTAGCCTCAATCAGTTC 59.127 42.308 0.00 0.00 0.00 3.01
1346 1347 5.279910 GCCATAGATCTTAGCCTCAATCAGT 60.280 44.000 0.00 0.00 0.00 3.41
1356 1357 5.994054 TGAGTTGATTGCCATAGATCTTAGC 59.006 40.000 0.00 2.21 0.00 3.09
1380 1381 3.103080 ACTGTTCTCGGAACCTATCCT 57.897 47.619 12.35 0.00 46.98 3.24
1387 1388 1.305201 TTGCCAACTGTTCTCGGAAC 58.695 50.000 9.13 9.13 0.00 3.62
1401 1402 0.620030 TGCTAGCAGGAGAATTGCCA 59.380 50.000 14.93 0.00 42.48 4.92
1471 1472 0.250989 TTAACAGGAACTTGGCCCGG 60.251 55.000 0.00 0.00 34.60 5.73
1479 1480 7.624549 TGAGCTCAAATAGATTAACAGGAACT 58.375 34.615 15.67 0.00 43.88 3.01
1632 1633 5.127845 TCTGAAGTACCTGAATCTGTCATCC 59.872 44.000 0.00 0.00 35.07 3.51
1729 1730 5.872070 TGATGTGTTGCGATTACTAATCACA 59.128 36.000 9.08 6.26 37.78 3.58
1730 1731 6.344572 TGATGTGTTGCGATTACTAATCAC 57.655 37.500 9.08 0.64 37.78 3.06
1788 1789 5.547465 TCCGTTGCCATAATAACCTCTATG 58.453 41.667 0.00 0.00 0.00 2.23
1834 1836 5.358442 AGCGTAATAACCCATGCAAACAATA 59.642 36.000 0.00 0.00 0.00 1.90
1856 1858 8.164153 CACTTTGAACAATTAATATGTTGCAGC 58.836 33.333 15.92 0.00 40.90 5.25
1879 1881 3.664107 TGTCGTTCGTACTACTACCACT 58.336 45.455 0.00 0.00 0.00 4.00
1880 1882 4.083802 ACTTGTCGTTCGTACTACTACCAC 60.084 45.833 0.00 0.00 0.00 4.16
1881 1883 4.065088 ACTTGTCGTTCGTACTACTACCA 58.935 43.478 0.00 0.00 0.00 3.25
1882 1884 4.670227 ACTTGTCGTTCGTACTACTACC 57.330 45.455 0.00 0.00 0.00 3.18
1885 1896 9.118236 GTTATTAAACTTGTCGTTCGTACTACT 57.882 33.333 0.00 0.00 33.90 2.57
1911 1928 3.497262 AGAACTCGTTTTTAAGCCTTCCG 59.503 43.478 0.00 0.00 0.00 4.30
1916 1933 8.316046 GTGTTAAAAAGAACTCGTTTTTAAGCC 58.684 33.333 11.76 4.91 44.25 4.35
1925 1942 6.317893 ACAGGATTGTGTTAAAAAGAACTCGT 59.682 34.615 0.00 0.00 35.83 4.18
1958 1975 7.660208 TCACAGGTAGATTTGTTTTTCTACTCC 59.340 37.037 9.28 0.00 42.50 3.85
1970 1987 3.340814 ACCAGCTCACAGGTAGATTTG 57.659 47.619 0.00 0.00 33.11 2.32
2181 2198 1.741770 AGTGTTTGCGAGCGATCCC 60.742 57.895 0.00 0.00 0.00 3.85
2196 2213 2.670934 GTGCTGTCAGGGCCAGTG 60.671 66.667 6.18 0.42 32.41 3.66
2245 2262 5.300539 TCTCTGATAACTCATCTGTGGCTAC 59.699 44.000 0.00 0.00 34.92 3.58


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

AutoCloner maintained by Alex Coulton.