Multiple sequence alignment - TraesCS3B01G274800

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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 TraesCS3B01G274800 chr3B 100.000 2537 0 0 1 2537 443391113 443388577 0.000000e+00 4686.0
1 TraesCS3B01G274800 chr3B 97.026 1681 48 2 1 1679 730664774 730666454 0.000000e+00 2826.0
2 TraesCS3B01G274800 chr3B 96.498 828 27 1 1710 2537 53258846 53259671 0.000000e+00 1367.0
3 TraesCS3B01G274800 chr3B 95.422 830 35 3 1710 2537 131404502 131403674 0.000000e+00 1319.0
4 TraesCS3B01G274800 chr6B 97.937 1406 28 1 275 1679 564999515 564998110 0.000000e+00 2435.0
5 TraesCS3B01G274800 chr6B 96.010 827 33 0 1710 2536 173353864 173353038 0.000000e+00 1345.0
6 TraesCS3B01G274800 chr6B 95.301 830 37 2 1709 2537 138481271 138480443 0.000000e+00 1315.0
7 TraesCS3B01G274800 chr6B 96.429 196 4 2 1 194 564999697 564999503 1.130000e-83 320.0
8 TraesCS3B01G274800 chr6A 97.010 1338 31 4 343 1679 260430716 260429387 0.000000e+00 2241.0
9 TraesCS3B01G274800 chr4A 90.530 1679 155 3 1 1679 583544889 583543215 0.000000e+00 2217.0
10 TraesCS3B01G274800 chr4A 95.296 829 38 1 1710 2537 728994058 728993230 0.000000e+00 1314.0
11 TraesCS3B01G274800 chr1D 92.818 1086 74 3 599 1681 199661408 199660324 0.000000e+00 1570.0
12 TraesCS3B01G274800 chr1D 95.652 69 3 0 551 619 199670117 199670049 7.420000e-21 111.0
13 TraesCS3B01G274800 chr1B 98.555 761 10 1 921 1680 328158965 328158205 0.000000e+00 1343.0
14 TraesCS3B01G274800 chr1B 95.422 830 35 3 1710 2537 300971472 300970644 0.000000e+00 1319.0
15 TraesCS3B01G274800 chr1B 78.400 250 49 5 1 248 624784491 624784245 9.400000e-35 158.0
16 TraesCS3B01G274800 chr1B 100.000 28 0 0 858 885 328158964 328158991 5.000000e-03 52.8
17 TraesCS3B01G274800 chr5B 95.438 833 32 4 1710 2537 66143475 66144306 0.000000e+00 1323.0
18 TraesCS3B01G274800 chr5B 95.169 828 40 0 1710 2537 213604960 213605787 0.000000e+00 1308.0
19 TraesCS3B01G274800 chr5B 86.591 619 80 3 3 619 216824438 216823821 0.000000e+00 680.0
20 TraesCS3B01G274800 chr5B 73.533 903 199 31 2 879 635900519 635901406 8.820000e-80 307.0
21 TraesCS3B01G274800 chr4B 95.175 829 38 2 1710 2537 130549048 130549875 0.000000e+00 1308.0
22 TraesCS3B01G274800 chr4B 97.623 547 12 1 1134 1679 310957636 310957090 0.000000e+00 937.0
23 TraesCS3B01G274800 chr2B 96.028 579 21 2 1101 1678 674043826 674044403 0.000000e+00 941.0
24 TraesCS3B01G274800 chr7A 94.671 319 15 2 1363 1679 516875290 516875608 6.310000e-136 494.0
25 TraesCS3B01G274800 chr7A 76.776 366 72 7 1 362 379299031 379298675 2.580000e-45 193.0
26 TraesCS3B01G274800 chr2D 77.440 461 98 4 1 459 196470757 196471213 1.160000e-68 270.0
27 TraesCS3B01G274800 chr1A 80.952 336 61 3 1 335 549071635 549071968 1.940000e-66 263.0


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 TraesCS3B01G274800 chr3B 443388577 443391113 2536 True 4686.0 4686 100.000 1 2537 1 chr3B.!!$R2 2536
1 TraesCS3B01G274800 chr3B 730664774 730666454 1680 False 2826.0 2826 97.026 1 1679 1 chr3B.!!$F2 1678
2 TraesCS3B01G274800 chr3B 53258846 53259671 825 False 1367.0 1367 96.498 1710 2537 1 chr3B.!!$F1 827
3 TraesCS3B01G274800 chr3B 131403674 131404502 828 True 1319.0 1319 95.422 1710 2537 1 chr3B.!!$R1 827
4 TraesCS3B01G274800 chr6B 564998110 564999697 1587 True 1377.5 2435 97.183 1 1679 2 chr6B.!!$R3 1678
5 TraesCS3B01G274800 chr6B 173353038 173353864 826 True 1345.0 1345 96.010 1710 2536 1 chr6B.!!$R2 826
6 TraesCS3B01G274800 chr6B 138480443 138481271 828 True 1315.0 1315 95.301 1709 2537 1 chr6B.!!$R1 828
7 TraesCS3B01G274800 chr6A 260429387 260430716 1329 True 2241.0 2241 97.010 343 1679 1 chr6A.!!$R1 1336
8 TraesCS3B01G274800 chr4A 583543215 583544889 1674 True 2217.0 2217 90.530 1 1679 1 chr4A.!!$R1 1678
9 TraesCS3B01G274800 chr4A 728993230 728994058 828 True 1314.0 1314 95.296 1710 2537 1 chr4A.!!$R2 827
10 TraesCS3B01G274800 chr1D 199660324 199661408 1084 True 1570.0 1570 92.818 599 1681 1 chr1D.!!$R1 1082
11 TraesCS3B01G274800 chr1B 328158205 328158965 760 True 1343.0 1343 98.555 921 1680 1 chr1B.!!$R2 759
12 TraesCS3B01G274800 chr1B 300970644 300971472 828 True 1319.0 1319 95.422 1710 2537 1 chr1B.!!$R1 827
13 TraesCS3B01G274800 chr5B 66143475 66144306 831 False 1323.0 1323 95.438 1710 2537 1 chr5B.!!$F1 827
14 TraesCS3B01G274800 chr5B 213604960 213605787 827 False 1308.0 1308 95.169 1710 2537 1 chr5B.!!$F2 827
15 TraesCS3B01G274800 chr5B 216823821 216824438 617 True 680.0 680 86.591 3 619 1 chr5B.!!$R1 616
16 TraesCS3B01G274800 chr5B 635900519 635901406 887 False 307.0 307 73.533 2 879 1 chr5B.!!$F3 877
17 TraesCS3B01G274800 chr4B 130549048 130549875 827 False 1308.0 1308 95.175 1710 2537 1 chr4B.!!$F1 827
18 TraesCS3B01G274800 chr4B 310957090 310957636 546 True 937.0 937 97.623 1134 1679 1 chr4B.!!$R1 545
19 TraesCS3B01G274800 chr2B 674043826 674044403 577 False 941.0 941 96.028 1101 1678 1 chr2B.!!$F1 577

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
115 116 1.139853 GAATGGGCTTCCGAGATGTCT 59.86 52.381 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1715 0.037882 AGTCCATCTGTCACACGCTG 60.038 55.0 0.0 0.0 0.0 5.18 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
115 116 1.139853 GAATGGGCTTCCGAGATGTCT 59.860 52.381 0.00 0.0 0.00 3.41
248 251 9.748708 CATTCTCAATTGTGAACTTAAAAAGGA 57.251 29.630 21.63 0.0 31.88 3.36
387 392 6.019075 CGAATAGTGCGTCAAGGAAAATCATA 60.019 38.462 0.00 0.0 0.00 2.15
419 424 2.750237 CCAAGTGCTAACCCGGGC 60.750 66.667 24.08 7.0 0.00 6.13
531 536 4.023707 CAGATCCCTTTATTTCATGCGGAC 60.024 45.833 0.00 0.0 0.00 4.79
653 665 2.314246 GGGCCTAGTACGTTACTCCAT 58.686 52.381 0.84 0.0 40.14 3.41
753 768 3.368248 ACACAATGCTATCCCATGCTTT 58.632 40.909 0.00 0.0 0.00 3.51
899 914 4.674101 CGGACTCAGTGAAGAGATTCAGTC 60.674 50.000 0.00 0.0 38.98 3.51
1082 1099 2.125106 GCAAACGCCGGAGAGGAT 60.125 61.111 13.83 0.0 45.00 3.24
1698 1716 6.403866 AAAAGTATTGTGGCATGAAAGTCA 57.596 33.333 0.00 0.0 0.00 3.41
1699 1717 5.633830 AAGTATTGTGGCATGAAAGTCAG 57.366 39.130 0.00 0.0 0.00 3.51
1700 1718 3.441572 AGTATTGTGGCATGAAAGTCAGC 59.558 43.478 0.00 0.0 0.00 4.26
1701 1719 0.592637 TTGTGGCATGAAAGTCAGCG 59.407 50.000 0.00 0.0 0.00 5.18
1702 1720 0.534877 TGTGGCATGAAAGTCAGCGT 60.535 50.000 0.00 0.0 0.00 5.07
1703 1721 0.110056 GTGGCATGAAAGTCAGCGTG 60.110 55.000 0.00 0.0 0.00 5.34
1704 1722 0.534877 TGGCATGAAAGTCAGCGTGT 60.535 50.000 0.00 0.0 0.00 4.49
1705 1723 0.110056 GGCATGAAAGTCAGCGTGTG 60.110 55.000 0.00 0.0 0.00 3.82
1706 1724 0.867746 GCATGAAAGTCAGCGTGTGA 59.132 50.000 0.00 0.0 0.00 3.58
1847 1865 0.388006 GACCCAACCAAAATTCGCCG 60.388 55.000 0.00 0.0 0.00 6.46
1883 1901 1.792757 AAAGGAGTGATGCCAGGCCA 61.793 55.000 9.64 0.0 0.00 5.36
2078 2096 1.202952 ACTTAAAATGCCCGGTCCACA 60.203 47.619 0.00 0.0 0.00 4.17
2373 2397 8.958175 AAAATACATTTTTCGCACGATCTTTA 57.042 26.923 0.00 0.0 36.65 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 4.513442 AGCATCGCCAAGTTGAAACTATA 58.487 39.130 3.87 0.00 38.57 1.31
248 251 5.099042 ACTTTGCCATACGTAAGAGGATT 57.901 39.130 14.15 0.00 43.62 3.01
387 392 1.569072 ACTTGGTTTCCCTGGACAGTT 59.431 47.619 0.00 0.00 0.00 3.16
419 424 8.400947 CAGAAATTGGGTCTATTAACTCACATG 58.599 37.037 0.00 0.00 26.58 3.21
531 536 4.082625 TGCCATGCTACAAAATCTTCTGTG 60.083 41.667 0.00 0.00 0.00 3.66
653 665 3.965258 AGATTGGGTGTGGCGCCA 61.965 61.111 29.03 29.03 35.42 5.69
899 914 2.860735 GCTCGGTCTATTACAACAGCAG 59.139 50.000 0.00 0.00 0.00 4.24
1082 1099 1.026182 CGCCAAGATTGCAGGTGCTA 61.026 55.000 3.18 0.00 42.66 3.49
1681 1699 1.200716 CGCTGACTTTCATGCCACAAT 59.799 47.619 0.00 0.00 0.00 2.71
1682 1700 0.592637 CGCTGACTTTCATGCCACAA 59.407 50.000 0.00 0.00 0.00 3.33
1683 1701 0.534877 ACGCTGACTTTCATGCCACA 60.535 50.000 0.00 0.00 0.00 4.17
1684 1702 0.110056 CACGCTGACTTTCATGCCAC 60.110 55.000 0.00 0.00 0.00 5.01
1685 1703 0.534877 ACACGCTGACTTTCATGCCA 60.535 50.000 0.00 0.00 0.00 4.92
1686 1704 0.110056 CACACGCTGACTTTCATGCC 60.110 55.000 0.00 0.00 0.00 4.40
1687 1705 0.867746 TCACACGCTGACTTTCATGC 59.132 50.000 0.00 0.00 0.00 4.06
1688 1706 2.584166 GTCACACGCTGACTTTCATG 57.416 50.000 6.58 0.00 45.38 3.07
1696 1714 0.038251 GTCCATCTGTCACACGCTGA 60.038 55.000 0.00 0.00 0.00 4.26
1697 1715 0.037882 AGTCCATCTGTCACACGCTG 60.038 55.000 0.00 0.00 0.00 5.18
1698 1716 0.037882 CAGTCCATCTGTCACACGCT 60.038 55.000 0.00 0.00 39.17 5.07
1699 1717 1.630244 GCAGTCCATCTGTCACACGC 61.630 60.000 0.00 0.00 45.23 5.34
1700 1718 0.037882 AGCAGTCCATCTGTCACACG 60.038 55.000 0.00 0.00 45.23 4.49
1701 1719 2.175878 AAGCAGTCCATCTGTCACAC 57.824 50.000 0.00 0.00 45.23 3.82
1702 1720 2.104622 TCAAAGCAGTCCATCTGTCACA 59.895 45.455 0.00 0.00 45.23 3.58
1703 1721 2.771089 TCAAAGCAGTCCATCTGTCAC 58.229 47.619 0.00 0.00 45.23 3.67
1704 1722 3.708403 ATCAAAGCAGTCCATCTGTCA 57.292 42.857 0.00 0.00 45.23 3.58
1705 1723 7.212976 TCTAATATCAAAGCAGTCCATCTGTC 58.787 38.462 0.00 0.00 45.23 3.51
1706 1724 7.129457 TCTAATATCAAAGCAGTCCATCTGT 57.871 36.000 0.00 0.00 45.23 3.41
1707 1725 7.333921 GGATCTAATATCAAAGCAGTCCATCTG 59.666 40.741 0.00 0.00 46.12 2.90
2078 2096 4.780815 TCCTTTTAATGAGATGATGCCGT 58.219 39.130 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.