Multiple sequence alignment - TraesCS4B01G183700

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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 TraesCS4B01G183700 chr4B 100.000 3036 0 0 1 3036 403037223 403034188 0.000000e+00 5607
1 TraesCS4B01G183700 chr4B 81.879 596 94 12 1519 2105 403050407 403049817 9.780000e-135 490
2 TraesCS4B01G183700 chr4B 78.561 695 101 35 746 1409 403056239 403055562 6.060000e-112 414
3 TraesCS4B01G183700 chr7B 98.286 3033 45 3 5 3036 113133211 113130185 0.000000e+00 5306
4 TraesCS4B01G183700 chr7B 81.818 583 94 10 1519 2093 113138320 113137742 2.120000e-131 479
5 TraesCS4B01G183700 chr7B 78.398 699 101 37 746 1409 113143967 113143284 2.820000e-110 409
6 TraesCS4B01G183700 chr7D 90.542 793 63 10 1 790 151015061 151014278 0.000000e+00 1038
7 TraesCS4B01G183700 chr7D 81.465 669 83 23 805 1445 151014290 151013635 7.510000e-141 510
8 TraesCS4B01G183700 chr7D 83.022 536 84 7 101 632 475154871 475155403 2.120000e-131 479
9 TraesCS4B01G183700 chr7D 80.386 622 107 13 1504 2116 151019129 151018514 2.760000e-125 459
10 TraesCS4B01G183700 chr7D 78.112 699 105 32 746 1414 151024889 151024209 1.700000e-107 399
11 TraesCS4B01G183700 chr3D 84.023 532 79 6 101 629 24569184 24569712 9.710000e-140 507
12 TraesCS4B01G183700 chr3D 83.396 536 78 10 98 625 583321594 583322126 1.270000e-133 486
13 TraesCS4B01G183700 chr1D 83.427 531 80 8 101 627 466406600 466407126 1.270000e-133 486
14 TraesCS4B01G183700 chr2A 83.815 519 74 6 112 627 564613947 564613436 4.550000e-133 484
15 TraesCS4B01G183700 chr1A 83.051 531 84 6 101 628 556085993 556086520 7.620000e-131 477
16 TraesCS4B01G183700 chrUn 82.959 534 84 7 98 627 136394811 136395341 2.740000e-130 475
17 TraesCS4B01G183700 chr7A 80.676 621 107 11 1504 2116 150905402 150904787 1.270000e-128 470
18 TraesCS4B01G183700 chr7A 78.674 694 104 34 746 1413 150911027 150910352 3.620000e-114 422


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 TraesCS4B01G183700 chr4B 403034188 403037223 3035 True 5607 5607 100.000 1 3036 1 chr4B.!!$R1 3035
1 TraesCS4B01G183700 chr4B 403049817 403050407 590 True 490 490 81.879 1519 2105 1 chr4B.!!$R2 586
2 TraesCS4B01G183700 chr4B 403055562 403056239 677 True 414 414 78.561 746 1409 1 chr4B.!!$R3 663
3 TraesCS4B01G183700 chr7B 113130185 113133211 3026 True 5306 5306 98.286 5 3036 1 chr7B.!!$R1 3031
4 TraesCS4B01G183700 chr7B 113137742 113138320 578 True 479 479 81.818 1519 2093 1 chr7B.!!$R2 574
5 TraesCS4B01G183700 chr7B 113143284 113143967 683 True 409 409 78.398 746 1409 1 chr7B.!!$R3 663
6 TraesCS4B01G183700 chr7D 151013635 151019129 5494 True 669 1038 84.131 1 2116 3 chr7D.!!$R2 2115
7 TraesCS4B01G183700 chr7D 475154871 475155403 532 False 479 479 83.022 101 632 1 chr7D.!!$F1 531
8 TraesCS4B01G183700 chr7D 151024209 151024889 680 True 399 399 78.112 746 1414 1 chr7D.!!$R1 668
9 TraesCS4B01G183700 chr3D 24569184 24569712 528 False 507 507 84.023 101 629 1 chr3D.!!$F1 528
10 TraesCS4B01G183700 chr3D 583321594 583322126 532 False 486 486 83.396 98 625 1 chr3D.!!$F2 527
11 TraesCS4B01G183700 chr1D 466406600 466407126 526 False 486 486 83.427 101 627 1 chr1D.!!$F1 526
12 TraesCS4B01G183700 chr2A 564613436 564613947 511 True 484 484 83.815 112 627 1 chr2A.!!$R1 515
13 TraesCS4B01G183700 chr1A 556085993 556086520 527 False 477 477 83.051 101 628 1 chr1A.!!$F1 527
14 TraesCS4B01G183700 chrUn 136394811 136395341 530 False 475 475 82.959 98 627 1 chrUn.!!$F1 529
15 TraesCS4B01G183700 chr7A 150904787 150905402 615 True 470 470 80.676 1504 2116 1 chr7A.!!$R1 612
16 TraesCS4B01G183700 chr7A 150910352 150911027 675 True 422 422 78.674 746 1413 1 chr7A.!!$R2 667

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
781 4863 0.602638 CGTTGGTCAGCTGGCTACAA 60.603 55.0 19.48 12.06 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 6202 0.735287 GTAAGGACTCCGACAACCGC 60.735 60.0 0.0 0.0 36.84 5.68 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
99 4168 2.248950 TCCAGTCACCATATCCCCTGTA 59.751 50.000 0.00 0.00 0.00 2.74
230 4307 1.278238 GTGTTTCTAGCATCGTCGGG 58.722 55.000 0.00 0.00 0.00 5.14
302 4382 5.655090 TGTTTGTCTTCGATGGATCCTAGTA 59.345 40.000 14.23 0.00 0.00 1.82
309 4389 4.265893 TCGATGGATCCTAGTAGATCTGC 58.734 47.826 14.23 3.54 42.02 4.26
778 4860 1.292223 GACGTTGGTCAGCTGGCTA 59.708 57.895 19.48 9.90 42.91 3.93
779 4861 1.004918 ACGTTGGTCAGCTGGCTAC 60.005 57.895 19.48 15.20 0.00 3.58
780 4862 1.005037 CGTTGGTCAGCTGGCTACA 60.005 57.895 19.48 5.63 0.00 2.74
781 4863 0.602638 CGTTGGTCAGCTGGCTACAA 60.603 55.000 19.48 12.06 0.00 2.41
782 4864 1.160137 GTTGGTCAGCTGGCTACAAG 58.840 55.000 19.48 0.00 0.00 3.16
783 4865 1.055849 TTGGTCAGCTGGCTACAAGA 58.944 50.000 19.48 0.00 0.00 3.02
784 4866 1.055849 TGGTCAGCTGGCTACAAGAA 58.944 50.000 19.48 0.00 0.00 2.52
785 4867 1.630369 TGGTCAGCTGGCTACAAGAAT 59.370 47.619 19.48 0.00 0.00 2.40
786 4868 2.012673 GGTCAGCTGGCTACAAGAATG 58.987 52.381 19.48 0.00 0.00 2.67
787 4869 2.012673 GTCAGCTGGCTACAAGAATGG 58.987 52.381 12.09 0.00 0.00 3.16
788 4870 1.908619 TCAGCTGGCTACAAGAATGGA 59.091 47.619 15.13 0.00 0.00 3.41
789 4871 2.507058 TCAGCTGGCTACAAGAATGGAT 59.493 45.455 15.13 0.00 0.00 3.41
790 4872 3.054139 TCAGCTGGCTACAAGAATGGATT 60.054 43.478 15.13 0.00 0.00 3.01
791 4873 3.066342 CAGCTGGCTACAAGAATGGATTG 59.934 47.826 5.57 0.00 0.00 2.67
792 4874 2.223665 GCTGGCTACAAGAATGGATTGC 60.224 50.000 0.00 0.00 0.00 3.56
793 4875 3.285484 CTGGCTACAAGAATGGATTGCT 58.715 45.455 0.00 0.00 0.00 3.91
794 4876 3.698040 CTGGCTACAAGAATGGATTGCTT 59.302 43.478 0.00 0.00 0.00 3.91
795 4877 3.696051 TGGCTACAAGAATGGATTGCTTC 59.304 43.478 0.00 0.00 0.00 3.86
796 4878 3.950395 GGCTACAAGAATGGATTGCTTCT 59.050 43.478 0.00 0.00 33.19 2.85
797 4879 4.400567 GGCTACAAGAATGGATTGCTTCTT 59.599 41.667 0.00 0.00 41.24 2.52
798 4880 5.105595 GGCTACAAGAATGGATTGCTTCTTT 60.106 40.000 0.00 0.00 39.15 2.52
799 4881 6.095440 GGCTACAAGAATGGATTGCTTCTTTA 59.905 38.462 0.00 0.00 39.15 1.85
800 4882 7.192232 GCTACAAGAATGGATTGCTTCTTTAG 58.808 38.462 0.00 0.00 39.15 1.85
844 4952 6.085555 ACTAATGAACGTCACTTTCTGAGA 57.914 37.500 0.00 0.00 0.00 3.27
1976 6139 7.018769 TCCTGAAGACTCCATGGATGATTATA 58.981 38.462 16.63 0.00 0.00 0.98
2785 6953 7.613022 ACCACATCAATTCCATATATCATCACC 59.387 37.037 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 4198 2.157738 GCCTCTGAGCAGAACACAAAT 58.842 47.619 0.00 0.00 36.94 2.32
230 4307 1.802337 GAAAAACCTCCACACGCCCC 61.802 60.000 0.00 0.00 0.00 5.80
302 4382 2.088423 AGACGAACGAAGAGCAGATCT 58.912 47.619 0.14 0.00 41.27 2.75
309 4389 2.727777 TGAACACAGACGAACGAAGAG 58.272 47.619 0.14 0.00 0.00 2.85
564 4645 6.127423 GCTGTCAAGGTAGTAGGAAGAATACA 60.127 42.308 0.00 0.00 0.00 2.29
791 4873 5.120830 TCTCATTCTTGTTCGCTAAAGAAGC 59.879 40.000 10.55 0.00 43.59 3.86
792 4874 6.712241 TCTCATTCTTGTTCGCTAAAGAAG 57.288 37.500 10.55 3.71 43.59 2.85
793 4875 8.771920 TTATCTCATTCTTGTTCGCTAAAGAA 57.228 30.769 8.15 8.15 44.25 2.52
794 4876 8.948631 ATTATCTCATTCTTGTTCGCTAAAGA 57.051 30.769 0.00 0.00 0.00 2.52
797 4879 9.817809 AGTTATTATCTCATTCTTGTTCGCTAA 57.182 29.630 0.00 0.00 0.00 3.09
799 4881 9.817809 TTAGTTATTATCTCATTCTTGTTCGCT 57.182 29.630 0.00 0.00 0.00 4.93
844 4952 6.948886 TCTCTCCAGCTATTTCGTATATCCTT 59.051 38.462 0.00 0.00 0.00 3.36
2039 6202 0.735287 GTAAGGACTCCGACAACCGC 60.735 60.000 0.00 0.00 36.84 5.68


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

AutoCloner maintained by Alex Coulton.