Multiple sequence alignment - TraesCS2B01G397500

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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 TraesCS2B01G397500 chr2B 100.000 5104 0 0 1 5104 564236622 564231519 0 9426
1 TraesCS2B01G397500 chr2D 96.934 5121 123 16 1 5104 481055604 481050501 0 8556
2 TraesCS2B01G397500 chr2A 96.644 5125 130 22 1 5104 623945412 623940309 0 8473


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 TraesCS2B01G397500 chr2B 564231519 564236622 5103 True 9426 9426 100.000 1 5104 1 chr2B.!!$R1 5103
1 TraesCS2B01G397500 chr2D 481050501 481055604 5103 True 8556 8556 96.934 1 5104 1 chr2D.!!$R1 5103
2 TraesCS2B01G397500 chr2A 623940309 623945412 5103 True 8473 8473 96.644 1 5104 1 chr2A.!!$R1 5103

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
605 609 2.638480 TTCTTGTCTGTGACTTGGGG 57.362 50.0 0.0 0.0 33.15 4.96 F
2460 2466 1.899437 TTTTGTTTGCAACCGGCCCA 61.899 50.0 0.0 0.0 43.89 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 2502 1.546773 GGAGTGGTGTATTTGTGGGCA 60.547 52.381 0.00 0.00 0.0 5.36 R
4309 4330 0.179100 ATGTCACAGGAAGGCGATCG 60.179 55.000 11.69 11.69 0.0 3.69 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
25 26 7.483307 GTGAATTTATGGCATGTATTGTGACT 58.517 34.615 10.98 0.00 0.00 3.41
139 140 6.713762 TTTGGTCATTCAGTTGACATCTTT 57.286 33.333 6.88 0.00 46.32 2.52
432 433 7.826744 TGCTCCATTTGTAATCAGTAATGTGTA 59.173 33.333 0.00 0.00 0.00 2.90
512 516 5.363101 GAAGCTTGGATCTATGTGACATCA 58.637 41.667 2.10 0.00 0.00 3.07
593 597 7.708322 TGTCATCTGACTGCTATAATTCTTGTC 59.292 37.037 11.35 0.00 44.99 3.18
605 609 2.638480 TTCTTGTCTGTGACTTGGGG 57.362 50.000 0.00 0.00 33.15 4.96
668 673 6.940739 AGATGGTCATAATTATTCCTCTCCG 58.059 40.000 14.03 0.00 0.00 4.63
856 861 5.148651 ACTAAAGGACACTATCACACCAC 57.851 43.478 0.00 0.00 0.00 4.16
1113 1118 2.102925 CAGCACACTTGGTTTCCCATTT 59.897 45.455 0.00 0.00 41.49 2.32
1230 1235 3.947626 TGCTTAACTCTGTTGTTTTCGC 58.052 40.909 0.00 0.00 0.00 4.70
1234 1239 2.405892 ACTCTGTTGTTTTCGCATGC 57.594 45.000 7.91 7.91 0.00 4.06
1364 1369 2.572290 CTCTTTGGGTTTCTGAACGGT 58.428 47.619 0.00 0.00 36.61 4.83
1388 1393 7.666804 GGTACCTCAATTGGACTTTTAAACCTA 59.333 37.037 4.06 0.00 0.00 3.08
1452 1457 5.008118 GCTGCTCTATCTTGGTACCATTTTC 59.992 44.000 17.17 0.89 0.00 2.29
1668 1674 7.386299 GCGAAAAGATACAAGATAGATGATGGT 59.614 37.037 0.00 0.00 0.00 3.55
1777 1783 8.728596 TCAAAGGGGGAAATAACTTTAAATGA 57.271 30.769 0.00 0.00 32.38 2.57
1874 1880 2.241430 AGTTTTCCTGGGCCTATGGTAC 59.759 50.000 4.53 5.48 0.00 3.34
1950 1956 5.336150 TCAAGCTCTCTCTTATGGTCTTG 57.664 43.478 0.00 0.00 0.00 3.02
2207 2213 6.731467 TCTTAAAAGGCTGGAGAACCATATT 58.269 36.000 0.00 0.00 45.87 1.28
2241 2247 9.985730 TGTGAAGCATCAAAATTCTTATTTCTT 57.014 25.926 0.00 0.00 37.30 2.52
2460 2466 1.899437 TTTTGTTTGCAACCGGCCCA 61.899 50.000 0.00 0.00 43.89 5.36
2496 2502 2.616842 CCTTACAAACCGCAGTGTCTTT 59.383 45.455 0.00 0.00 0.00 2.52
2628 2634 2.141122 AAATGCCCGTCAAGCCAACG 62.141 55.000 0.00 0.00 39.78 4.10
2630 2636 3.723348 GCCCGTCAAGCCAACGAC 61.723 66.667 4.85 0.00 42.62 4.34
2795 2801 7.018826 CGACGAAAAATTGTTATAGCCTGAAA 58.981 34.615 0.00 0.00 0.00 2.69
2823 2829 6.077838 CGTATCACTTTTAGTGCTTTTCCAC 58.922 40.000 1.98 0.00 45.54 4.02
2835 2841 4.207019 GTGCTTTTCCACGAAAGAAATGTG 59.793 41.667 0.00 0.00 38.60 3.21
2837 2843 4.803613 GCTTTTCCACGAAAGAAATGTGTT 59.196 37.500 0.00 0.00 38.60 3.32
3079 3097 0.107800 CATGCTCCTGGGTGAGACAG 60.108 60.000 0.00 0.00 34.11 3.51
3091 3109 8.008332 TCCTGGGTGAGACAGTAAACATATATA 58.992 37.037 0.00 0.00 34.16 0.86
3400 3418 4.191544 TGGCATTGTATTCCTTCTTCTCG 58.808 43.478 0.00 0.00 0.00 4.04
3521 3540 4.365514 TCCTGTGGCACAAAATAGAAGA 57.634 40.909 22.31 5.62 44.16 2.87
3524 3543 6.480763 TCCTGTGGCACAAAATAGAAGATAA 58.519 36.000 22.31 0.00 44.16 1.75
3555 3574 7.012044 ACGAATGGCAGTTATACTAACAATTCC 59.988 37.037 0.00 0.00 0.00 3.01
3832 3853 1.334869 GCTTCTGCCAATCCATTACCG 59.665 52.381 0.00 0.00 0.00 4.02
3874 3895 7.784633 AGAGCTCATCAGTTTAGCTTAATTC 57.215 36.000 17.77 0.00 46.29 2.17
3911 3932 9.202273 CAATATGTCCTCTCTTAAGCATAGTTC 57.798 37.037 0.00 0.00 0.00 3.01
3940 3961 4.297510 TGAATGTGTTGAGAAAATTGGCG 58.702 39.130 0.00 0.00 0.00 5.69
3976 3997 5.649782 ATACAGTTCAATTTGCTCCCAAG 57.350 39.130 0.00 0.00 31.52 3.61
4110 4131 0.966179 TCACGGCTGCTAAGACTTCA 59.034 50.000 0.00 0.00 0.00 3.02
4111 4132 1.550524 TCACGGCTGCTAAGACTTCAT 59.449 47.619 0.00 0.00 0.00 2.57
4144 4165 7.022384 GTGTAGATATAGTATTCACGTCTGCC 58.978 42.308 0.00 0.00 0.00 4.85
4158 4179 2.427506 GTCTGCCCTTCGAGTTTCAAT 58.572 47.619 0.00 0.00 0.00 2.57
4291 4312 5.508200 TTTTCGCACTTAACAGTTCCATT 57.492 34.783 0.00 0.00 0.00 3.16
4301 4322 7.222611 CACTTAACAGTTCCATTTGAAGGTTTG 59.777 37.037 0.00 0.00 34.92 2.93
4309 4330 3.383761 CATTTGAAGGTTTGCTGGTGAC 58.616 45.455 0.00 0.00 0.00 3.67
4405 4426 9.023962 ACACATATTTGTTATGTCAACAGGATT 57.976 29.630 0.00 0.00 46.42 3.01
4437 4458 5.074115 AGAATTAGACTAGGGACGAGATGG 58.926 45.833 0.00 0.00 34.38 3.51
4443 4464 1.757118 CTAGGGACGAGATGGAAAGCA 59.243 52.381 0.00 0.00 30.78 3.91
4455 4476 3.228188 TGGAAAGCAATATAGCCCCAG 57.772 47.619 0.00 0.00 34.23 4.45
4468 4489 1.875963 CCCCAGCTGTTTAACTGCG 59.124 57.895 18.46 13.83 45.97 5.18
4644 4665 7.090808 CAGCTACTAACATCAGAAAGTACACA 58.909 38.462 0.00 0.00 0.00 3.72
4746 4767 2.808906 AGCCCCACAGTCCTTTATTC 57.191 50.000 0.00 0.00 0.00 1.75
4756 4777 7.441017 CCACAGTCCTTTATTCAAATCCAAAA 58.559 34.615 0.00 0.00 0.00 2.44
4849 4871 4.280929 TGAATACATGATCAGGGTAGACCG 59.719 45.833 12.66 0.00 46.96 4.79
5036 5059 5.667539 TTGAATTTTTGAACAGTCCACCA 57.332 34.783 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 6.765036 GGCTCTCAAATGATTGATACTTCAGA 59.235 38.462 0.00 0.00 44.29 3.27
432 433 6.154877 TGCACACCAAATCAGGATAATCATTT 59.845 34.615 0.00 0.00 0.00 2.32
568 572 7.925483 AGACAAGAATTATAGCAGTCAGATGAC 59.075 37.037 4.77 4.77 45.08 3.06
593 597 0.036732 TTAGCTGCCCCAAGTCACAG 59.963 55.000 0.00 0.00 0.00 3.66
605 609 4.440663 GGAATGGGTCAAATTCTTAGCTGC 60.441 45.833 0.00 0.00 34.95 5.25
694 699 7.504926 TGGGAGGTAGTTAGTGTTTGAATAT 57.495 36.000 0.00 0.00 0.00 1.28
856 861 6.036517 GTGAGACCATACAATTTCTGTAGCAG 59.963 42.308 0.00 0.00 43.78 4.24
910 915 4.330894 CACATGCTACACACTGAACATAGG 59.669 45.833 0.00 0.00 0.00 2.57
1113 1118 2.325484 TGAAGGCTTCTGTACTGACCA 58.675 47.619 26.26 1.39 0.00 4.02
1230 1235 4.560035 GCTTGTTAATGTTGTAGCTGCATG 59.440 41.667 4.98 0.00 0.00 4.06
1364 1369 9.292195 CTTAGGTTTAAAAGTCCAATTGAGGTA 57.708 33.333 7.12 0.00 0.00 3.08
1388 1393 6.552008 TCCAATGGAGTTGAATCCTAAACTT 58.448 36.000 0.00 0.00 40.37 2.66
1452 1457 5.596836 AATACTTGTGGCATGGTTTATGG 57.403 39.130 0.00 0.00 37.26 2.74
1600 1605 4.278419 GCAATTTACAGTGGTTGACTCCTT 59.722 41.667 0.00 0.00 29.75 3.36
1777 1783 7.922811 CCAAAAGTTGATGCTTCTAAAAGAACT 59.077 33.333 0.88 0.00 34.14 3.01
1787 1793 5.117592 CGTTTGATCCAAAAGTTGATGCTTC 59.882 40.000 0.00 0.00 35.03 3.86
1950 1956 1.576356 CGATGCCTACTCCAAGAAGC 58.424 55.000 0.00 0.00 0.00 3.86
2207 2213 9.545105 AGAATTTTGATGCTTCACAAATAACAA 57.455 25.926 15.96 0.00 36.21 2.83
2242 2248 9.950496 TTCAGAAAGAATCTAGCACTAAGAAAT 57.050 29.630 0.00 0.00 36.32 2.17
2243 2249 9.950496 ATTCAGAAAGAATCTAGCACTAAGAAA 57.050 29.630 0.00 0.00 43.42 2.52
2244 2250 9.950496 AATTCAGAAAGAATCTAGCACTAAGAA 57.050 29.630 0.00 0.00 46.09 2.52
2247 2253 9.823647 CCTAATTCAGAAAGAATCTAGCACTAA 57.176 33.333 0.00 0.00 46.09 2.24
2496 2502 1.546773 GGAGTGGTGTATTTGTGGGCA 60.547 52.381 0.00 0.00 0.00 5.36
2628 2634 7.010738 CCATGCATTATGAATTTCCACAAAGTC 59.989 37.037 0.00 0.00 39.21 3.01
2630 2636 6.238266 GCCATGCATTATGAATTTCCACAAAG 60.238 38.462 0.00 0.00 39.21 2.77
2795 2801 8.448615 GGAAAAGCACTAAAAGTGATACGTATT 58.551 33.333 9.92 0.00 45.10 1.89
2800 2806 6.073440 TCGTGGAAAAGCACTAAAAGTGATAC 60.073 38.462 11.14 0.00 45.10 2.24
2823 2829 7.860373 TGGTCTTCATTTAACACATTTCTTTCG 59.140 33.333 0.00 0.00 0.00 3.46
2835 2841 9.696917 AAATCACTGATTTGGTCTTCATTTAAC 57.303 29.630 14.98 0.00 40.24 2.01
2951 2969 9.710818 ACTTCTTTAGGACTGTAGGTATCAATA 57.289 33.333 0.00 0.00 0.00 1.90
3091 3109 3.664107 TCTGAGAGCGTTAACTTGCAAT 58.336 40.909 0.00 0.00 0.00 3.56
3400 3418 1.270907 TCTTCTTGCTCTCCCTGACC 58.729 55.000 0.00 0.00 0.00 4.02
3502 3520 7.641411 CGATTTATCTTCTATTTTGTGCCACAG 59.359 37.037 0.00 0.00 0.00 3.66
3521 3540 7.152645 AGTATAACTGCCATTCGTCGATTTAT 58.847 34.615 0.00 0.00 0.00 1.40
3524 3543 4.945246 AGTATAACTGCCATTCGTCGATT 58.055 39.130 0.00 0.00 0.00 3.34
3832 3853 5.423886 AGCTCTAGTTTGCTTCCAGTATTC 58.576 41.667 0.00 0.00 35.86 1.75
3885 3906 9.202273 GAACTATGCTTAAGAGAGGACATATTG 57.798 37.037 6.67 0.00 0.00 1.90
3893 3914 6.971602 TCATACGAACTATGCTTAAGAGAGG 58.028 40.000 6.67 0.00 33.32 3.69
3911 3932 8.791605 CAATTTTCTCAACACATTCATCATACG 58.208 33.333 0.00 0.00 0.00 3.06
3940 3961 7.672983 TTGAACTGTATTTCATGGAAGAGTC 57.327 36.000 0.00 0.00 35.42 3.36
4134 4155 1.461091 AACTCGAAGGGCAGACGTGA 61.461 55.000 0.00 0.00 0.00 4.35
4144 4165 4.507710 TCCAGATCATTGAAACTCGAAGG 58.492 43.478 0.00 0.00 0.00 3.46
4291 4312 1.021202 CGTCACCAGCAAACCTTCAA 58.979 50.000 0.00 0.00 0.00 2.69
4301 4322 2.125512 AAGGCGATCGTCACCAGC 60.126 61.111 23.45 0.00 0.00 4.85
4309 4330 0.179100 ATGTCACAGGAAGGCGATCG 60.179 55.000 11.69 11.69 0.00 3.69
4405 4426 4.101585 CCCTAGTCTAATTCTCACCATGCA 59.898 45.833 0.00 0.00 0.00 3.96
4784 4806 7.298374 AGTTAGATTCTTCCTTTCTTTTGGGT 58.702 34.615 0.00 0.00 0.00 4.51
5036 5059 4.090761 CATGTAGTAGCAACATGGGGAT 57.909 45.455 8.06 0.00 46.78 3.85


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

AutoCloner maintained by Alex Coulton.