Multiple sequence alignment - TraesCS5B01G472300

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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 TraesCS5B01G472300 chr5B 100.000 2771 0 0 1 2771 645935635 645932865 0 5118
1 TraesCS5B01G472300 chr5B 94.638 2779 139 8 2 2771 508308655 508305878 0 4298
2 TraesCS5B01G472300 chr5B 93.876 2776 160 9 1 2771 381797199 381794429 0 4176
3 TraesCS5B01G472300 chr4B 94.382 2777 146 9 1 2771 654370442 654367670 0 4255
4 TraesCS5B01G472300 chr4B 94.306 2775 152 6 1 2771 609073147 609070375 0 4244
5 TraesCS5B01G472300 chr6B 94.088 2774 157 6 2 2771 161010555 161013325 0 4207
6 TraesCS5B01G472300 chr3B 94.086 2773 158 6 4 2771 627892265 627889494 0 4207
7 TraesCS5B01G472300 chr3B 94.056 2776 154 10 1 2771 810212905 810210136 0 4202
8 TraesCS5B01G472300 chr2B 93.910 2775 163 6 1 2771 661252578 661249806 0 4183
9 TraesCS5B01G472300 chr7B 93.880 2778 162 7 1 2771 155496468 155499244 0 4181


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 TraesCS5B01G472300 chr5B 645932865 645935635 2770 True 5118 5118 100.000 1 2771 1 chr5B.!!$R3 2770
1 TraesCS5B01G472300 chr5B 508305878 508308655 2777 True 4298 4298 94.638 2 2771 1 chr5B.!!$R2 2769
2 TraesCS5B01G472300 chr5B 381794429 381797199 2770 True 4176 4176 93.876 1 2771 1 chr5B.!!$R1 2770
3 TraesCS5B01G472300 chr4B 654367670 654370442 2772 True 4255 4255 94.382 1 2771 1 chr4B.!!$R2 2770
4 TraesCS5B01G472300 chr4B 609070375 609073147 2772 True 4244 4244 94.306 1 2771 1 chr4B.!!$R1 2770
5 TraesCS5B01G472300 chr6B 161010555 161013325 2770 False 4207 4207 94.088 2 2771 1 chr6B.!!$F1 2769
6 TraesCS5B01G472300 chr3B 627889494 627892265 2771 True 4207 4207 94.086 4 2771 1 chr3B.!!$R1 2767
7 TraesCS5B01G472300 chr3B 810210136 810212905 2769 True 4202 4202 94.056 1 2771 1 chr3B.!!$R2 2770
8 TraesCS5B01G472300 chr2B 661249806 661252578 2772 True 4183 4183 93.910 1 2771 1 chr2B.!!$R1 2770
9 TraesCS5B01G472300 chr7B 155496468 155499244 2776 False 4181 4181 93.880 1 2771 1 chr7B.!!$F1 2770

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
251 253 0.396811 CGAGGTGGAGTCCCAAAAGT 59.603 55.0 6.74 0.0 45.59 2.66 F
1208 1218 1.290203 GCGATGAAGAAGATTGCGGA 58.710 50.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1579 0.583438 CTTCAATGCATACGGAGCGG 59.417 55.0 0.0 0.0 33.85 5.52 R
2702 2724 0.175760 GGAGATAGCAAGCCACGTCA 59.824 55.0 0.0 0.0 0.00 4.35 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
17 18 3.211288 CGGCGGAGAGGAATGTCT 58.789 61.111 0.00 0.00 0.00 3.41
52 53 2.681344 CCCCTGGCAAAATCGTAAGTAC 59.319 50.000 0.00 0.00 39.48 2.73
251 253 0.396811 CGAGGTGGAGTCCCAAAAGT 59.603 55.000 6.74 0.00 45.59 2.66
437 439 2.202878 GCAAGCCTACGATGCCGA 60.203 61.111 0.00 0.00 39.50 5.54
516 519 4.717629 CGACGAGGAGCACCGCAA 62.718 66.667 4.63 0.00 41.83 4.85
708 712 8.577296 CGGACTGAGGATCTAAAAAGATATACA 58.423 37.037 0.00 0.00 34.92 2.29
722 726 9.877178 AAAAAGATATACACAGGAGTCTAACAG 57.123 33.333 0.00 0.00 0.00 3.16
771 776 3.677284 CTGCTGACCTCTGCCGCAT 62.677 63.158 0.00 0.00 39.65 4.73
871 876 3.442076 AGGACAAGGAAGGTAGGTAGTG 58.558 50.000 0.00 0.00 0.00 2.74
923 932 4.160252 GGTTGCAAATAATGACAGGACCAT 59.840 41.667 0.00 0.00 0.00 3.55
935 944 4.081142 TGACAGGACCATCGTGAATGTTAT 60.081 41.667 5.58 0.00 35.94 1.89
948 957 3.268334 TGAATGTTATAGGGGCCACAACT 59.732 43.478 8.31 0.00 0.00 3.16
1007 1016 3.142162 CAATGCGGCCATGGAGCA 61.142 61.111 29.18 29.18 45.46 4.26
1035 1044 1.731720 GAGAGAAACAAGAGGCGCAT 58.268 50.000 10.83 0.00 0.00 4.73
1183 1193 1.553184 CCCAAAAAGCCCTCCAGGAAT 60.553 52.381 0.00 0.00 38.24 3.01
1186 1196 3.306989 CCAAAAAGCCCTCCAGGAATTTC 60.307 47.826 0.00 0.00 38.24 2.17
1208 1218 1.290203 GCGATGAAGAAGATTGCGGA 58.710 50.000 0.00 0.00 0.00 5.54
1387 1397 2.500098 GTGTTCTGGTCCCAGTATGCTA 59.500 50.000 12.88 0.00 43.96 3.49
1547 1557 4.175337 GCGGCTGGTGGATGCCTA 62.175 66.667 0.00 0.00 46.42 3.93
1569 1579 3.084039 TCCATGGCTTGAAGTCATCAAC 58.916 45.455 9.69 0.00 38.74 3.18
1710 1720 2.877866 CCCGAGATGTACTATGAGGGT 58.122 52.381 0.00 0.00 33.22 4.34
1714 1724 4.138290 CGAGATGTACTATGAGGGTGTCT 58.862 47.826 0.00 0.00 0.00 3.41
1814 1825 4.023279 TGCGCTGAAAACTTGTTCATATGT 60.023 37.500 9.73 0.00 36.92 2.29
1891 1902 2.162681 TCTGAGAGATGCAAGTCGTCA 58.837 47.619 0.00 0.00 33.08 4.35
1977 1989 2.364448 GGTCCTTCGAGGGAGGCT 60.364 66.667 17.84 0.00 35.59 4.58
1988 2000 1.130054 AGGGAGGCTCTCAGCACAAA 61.130 55.000 18.31 0.00 44.75 2.83
2192 2209 1.579932 GAACAGCGACCGACTCTCA 59.420 57.895 0.00 0.00 0.00 3.27
2212 2229 2.956333 CACCCTATCATGACGGTCAGTA 59.044 50.000 16.84 7.28 0.00 2.74
2236 2253 4.529109 AGCTTTCTCTACTGAGGTGTTC 57.471 45.455 0.00 0.00 40.58 3.18
2240 2257 5.601662 CTTTCTCTACTGAGGTGTTCAACA 58.398 41.667 0.00 0.00 40.58 3.33
2267 2284 1.951510 CTGTGGCACAATCGCAGTT 59.048 52.632 22.31 0.00 44.16 3.16
2421 2443 1.579932 TCGTGAGAGTGTTCGCTCC 59.420 57.895 9.36 3.24 39.23 4.70
2464 2486 2.916934 ACTTAAGCCCCTGGTGTATTGA 59.083 45.455 1.29 0.00 0.00 2.57
2702 2724 5.337330 CGTTATAGAGACCACCTGGACTTTT 60.337 44.000 0.00 0.00 40.17 2.27
2726 2748 0.621571 TGGCTTGCTATCTCCCTGGT 60.622 55.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.012768 ACCATAAGTTATTCTGGTATCCGGG 59.987 44.000 0.00 0.00 42.42 5.73
76 77 6.952358 AGAAGGTACTGTACAATAGAGGAACA 59.048 38.462 18.79 0.00 40.86 3.18
251 253 0.178873 ACCTCCTCCTGGTTTAGCCA 60.179 55.000 0.00 0.00 46.95 4.75
402 404 3.721706 CCTTCTTGCGAGGGGGCT 61.722 66.667 0.00 0.00 32.98 5.19
464 467 3.843893 AAGCACCTCCAGCAAATTTTT 57.156 38.095 0.00 0.00 0.00 1.94
466 469 3.305335 CGTTAAGCACCTCCAGCAAATTT 60.305 43.478 0.00 0.00 0.00 1.82
516 519 2.170397 TGGATCACCGCACTCATAACAT 59.830 45.455 0.00 0.00 39.42 2.71
708 712 7.482169 TGACATATTTCTGTTAGACTCCTGT 57.518 36.000 0.00 0.00 0.00 4.00
722 726 7.318141 CCTGCATTCCCATATTGACATATTTC 58.682 38.462 0.00 0.00 0.00 2.17
771 776 1.215382 CATCGACCTCCGCAGTCAA 59.785 57.895 0.00 0.00 38.37 3.18
832 837 0.952497 CTCGAGCTGCTTCTTGGCAA 60.952 55.000 2.53 0.00 41.94 4.52
923 932 2.120312 TGGCCCCTATAACATTCACGA 58.880 47.619 0.00 0.00 0.00 4.35
935 944 1.151899 ACCTCAGTTGTGGCCCCTA 60.152 57.895 0.00 0.00 32.19 3.53
1007 1016 2.158957 TCTTGTTTCTCTCGCTTGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
1183 1193 3.127548 GCAATCTTCTTCATCGCCTGAAA 59.872 43.478 2.56 0.00 43.20 2.69
1186 1196 1.004185 CGCAATCTTCTTCATCGCCTG 60.004 52.381 0.00 0.00 0.00 4.85
1197 1207 1.954927 CCTTACCCTCCGCAATCTTC 58.045 55.000 0.00 0.00 0.00 2.87
1547 1557 3.657398 TGATGACTTCAAGCCATGGAT 57.343 42.857 18.40 6.18 0.00 3.41
1569 1579 0.583438 CTTCAATGCATACGGAGCGG 59.417 55.000 0.00 0.00 33.85 5.52
1648 1658 1.076549 GTGGCCCATCCTTCACCAA 59.923 57.895 0.00 0.00 35.26 3.67
1814 1825 8.709386 TTAAATTCAAAAAGTGTTGCTTAGCA 57.291 26.923 1.39 1.39 36.17 3.49
1891 1902 1.619363 TGGCATGGGGGTAGAAGCT 60.619 57.895 0.00 0.00 0.00 3.74
1977 1989 1.949525 GCCTTGTTCTTTGTGCTGAGA 59.050 47.619 0.00 0.00 0.00 3.27
1988 2000 3.914426 ATAGTCCGATTGCCTTGTTCT 57.086 42.857 0.00 0.00 0.00 3.01
2192 2209 2.160721 ACTGACCGTCATGATAGGGT 57.839 50.000 19.99 17.06 40.26 4.34
2212 2229 6.211584 TGAACACCTCAGTAGAGAAAGCTAAT 59.788 38.462 0.00 0.00 44.98 1.73
2252 2269 0.310543 GAACAACTGCGATTGTGCCA 59.689 50.000 6.19 0.00 42.01 4.92
2267 2284 1.729586 AAGGTAGCACTGGGAGAACA 58.270 50.000 0.00 0.00 0.00 3.18
2340 2357 4.881273 CCGAATCATGTCTTGGGTCAATAA 59.119 41.667 0.00 0.00 0.00 1.40
2418 2440 2.099921 CCAGAATACGGTGTGAGAGGAG 59.900 54.545 0.00 0.00 0.00 3.69
2421 2443 1.137086 CCCCAGAATACGGTGTGAGAG 59.863 57.143 0.00 0.00 0.00 3.20
2702 2724 0.175760 GGAGATAGCAAGCCACGTCA 59.824 55.000 0.00 0.00 0.00 4.35
2726 2748 0.306228 CCGAACACACGATGCAACAA 59.694 50.000 0.00 0.00 35.09 2.83


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

AutoCloner maintained by Alex Coulton.