Multiple sequence alignment - TraesCS4B01G267100

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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 TraesCS4B01G267100 chr4B 100.000 2756 0 0 1 2756 539964046 539961291 0.000000e+00 5090
1 TraesCS4B01G267100 chr1D 96.738 2759 77 10 1 2756 58485512 58482764 0.000000e+00 4584
2 TraesCS4B01G267100 chr1D 96.308 2763 86 11 1 2756 108798529 108795776 0.000000e+00 4523
3 TraesCS4B01G267100 chr1D 96.397 2720 78 12 48 2756 10804203 10801493 0.000000e+00 4462
4 TraesCS4B01G267100 chr1D 94.515 2771 119 23 1 2756 466346197 466343445 0.000000e+00 4244
5 TraesCS4B01G267100 chr7D 96.667 2760 79 10 1 2756 30312809 30315559 0.000000e+00 4575
6 TraesCS4B01G267100 chrUn 95.692 2762 100 12 1 2755 52473336 52476085 0.000000e+00 4423
7 TraesCS4B01G267100 chr3D 95.924 2674 91 16 89 2756 175422130 175419469 0.000000e+00 4318
8 TraesCS4B01G267100 chr3D 93.398 2772 152 24 1 2755 64822361 64819604 0.000000e+00 4076
9 TraesCS4B01G267100 chr3D 92.963 2771 162 26 1 2755 613553147 613555900 0.000000e+00 4006
10 TraesCS4B01G267100 chr5D 95.254 2676 105 16 88 2756 526633342 526636002 0.000000e+00 4218
11 TraesCS4B01G267100 chr2B 93.840 2776 131 28 1 2756 95264406 95261651 0.000000e+00 4143
12 TraesCS4B01G267100 chr2A 83.735 166 21 4 192 352 614204273 614204437 4.750000e-33 152
13 TraesCS4B01G267100 chr5A 82.353 170 22 6 192 354 33905285 33905453 1.030000e-29 141
14 TraesCS4B01G267100 chr3A 81.481 162 24 4 196 352 32205420 32205580 8.010000e-26 128


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 TraesCS4B01G267100 chr4B 539961291 539964046 2755 True 5090 5090 100.000 1 2756 1 chr4B.!!$R1 2755
1 TraesCS4B01G267100 chr1D 58482764 58485512 2748 True 4584 4584 96.738 1 2756 1 chr1D.!!$R2 2755
2 TraesCS4B01G267100 chr1D 108795776 108798529 2753 True 4523 4523 96.308 1 2756 1 chr1D.!!$R3 2755
3 TraesCS4B01G267100 chr1D 10801493 10804203 2710 True 4462 4462 96.397 48 2756 1 chr1D.!!$R1 2708
4 TraesCS4B01G267100 chr1D 466343445 466346197 2752 True 4244 4244 94.515 1 2756 1 chr1D.!!$R4 2755
5 TraesCS4B01G267100 chr7D 30312809 30315559 2750 False 4575 4575 96.667 1 2756 1 chr7D.!!$F1 2755
6 TraesCS4B01G267100 chrUn 52473336 52476085 2749 False 4423 4423 95.692 1 2755 1 chrUn.!!$F1 2754
7 TraesCS4B01G267100 chr3D 175419469 175422130 2661 True 4318 4318 95.924 89 2756 1 chr3D.!!$R2 2667
8 TraesCS4B01G267100 chr3D 64819604 64822361 2757 True 4076 4076 93.398 1 2755 1 chr3D.!!$R1 2754
9 TraesCS4B01G267100 chr3D 613553147 613555900 2753 False 4006 4006 92.963 1 2755 1 chr3D.!!$F1 2754
10 TraesCS4B01G267100 chr5D 526633342 526636002 2660 False 4218 4218 95.254 88 2756 1 chr5D.!!$F1 2668
11 TraesCS4B01G267100 chr2B 95261651 95264406 2755 True 4143 4143 93.840 1 2756 1 chr2B.!!$R1 2755

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
489 506 1.408266 GGTCCCACACCTATCGCAAAT 60.408 52.381 0.0 0.0 42.84 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 2313 0.17902 TCCGAATGGCACCATCATCC 60.179 55.0 1.88 0.0 35.31 3.51 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
35 37 7.160726 AGCCAAAACTAAAACATGCATTGTAT 58.839 30.769 0.00 0.00 37.68 2.29
46 48 3.552132 TGCATTGTATCCCACGTGTAT 57.448 42.857 15.65 10.15 0.00 2.29
104 115 8.484641 TGTGCAAATAAAAACATGTTTTCTGA 57.515 26.923 31.10 21.20 41.45 3.27
107 118 7.062848 GCAAATAAAAACATGTTTTCTGACCG 58.937 34.615 31.10 20.15 41.45 4.79
111 122 6.687081 AAAAACATGTTTTCTGACCGACTA 57.313 33.333 31.10 0.00 41.45 2.59
244 257 3.834231 ACTGAAATAAATGCAACCTGGCT 59.166 39.130 0.00 0.00 34.04 4.75
311 325 4.535781 ACTGAATATGTATGCTGGCCAAA 58.464 39.130 7.01 0.00 0.00 3.28
483 500 6.213600 ACATATATTCTGGTCCCACACCTATC 59.786 42.308 0.00 0.00 46.98 2.08
489 506 1.408266 GGTCCCACACCTATCGCAAAT 60.408 52.381 0.00 0.00 42.84 2.32
1070 1101 1.675310 CGGATCAGCAGCAACCCAA 60.675 57.895 0.00 0.00 0.00 4.12
1122 1153 3.916172 GTCGATCTGTTTACTACACGCAA 59.084 43.478 0.00 0.00 32.10 4.85
1167 1198 3.269578 CCATGACAATGTGGCAGGA 57.730 52.632 0.00 0.00 40.08 3.86
1386 1417 4.724399 TGAGGTTTGACAGCCTTCAAATA 58.276 39.130 12.19 0.44 45.04 1.40
1584 1616 7.504911 CCTATTCCAGATCCAAAATCTGTTGAT 59.495 37.037 12.62 7.07 42.88 2.57
1636 1669 5.371526 CAATATTTGCTGAAGAGGAGGCTA 58.628 41.667 0.00 0.00 0.00 3.93
1747 1781 2.810400 CGATGGGAGGTGACACACTTTT 60.810 50.000 8.08 0.00 34.40 2.27
1752 1786 3.013921 GGAGGTGACACACTTTTGTTCA 58.986 45.455 8.08 0.00 31.66 3.18
1793 1827 3.066064 CGTGAACAAACCTTCATTGTCCA 59.934 43.478 0.00 0.00 39.98 4.02
1823 1857 0.533755 GATCCCACCAAGGCATCTCG 60.534 60.000 0.00 0.00 35.39 4.04
2005 2041 2.306847 GTGTCCAACTTCCCATGTTGT 58.693 47.619 0.00 0.00 42.09 3.32
2108 2144 7.139896 AGTGCAAAAGTGTTTTTAAAAAGGG 57.860 32.000 13.58 0.95 34.81 3.95
2112 2148 6.405286 GCAAAAGTGTTTTTAAAAAGGGGCAT 60.405 34.615 13.58 0.00 34.81 4.40
2272 2313 2.702478 TGGCAGAGTTCTATGGATCTGG 59.298 50.000 10.60 0.00 39.63 3.86
2639 2683 3.921677 AGTTGGCATTGAGCTTTGATTG 58.078 40.909 0.00 0.00 44.79 2.67
2673 2717 3.517100 GCATTCCTAGAGGCTATGGATGA 59.483 47.826 0.00 0.00 34.44 2.92
2698 2742 2.975489 ACCTCCTGACAACTTCATCACT 59.025 45.455 0.00 0.00 32.17 3.41
2699 2743 4.160329 ACCTCCTGACAACTTCATCACTA 58.840 43.478 0.00 0.00 32.17 2.74
2750 2794 2.629617 CAAAGCATCTTTCCAACCACCT 59.370 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 0.461163 CATGCCGAATACACGTGGGA 60.461 55.000 21.57 7.77 0.00 4.37
244 257 7.561722 AGTTGGCTAGAATAGATGTCTCAGTTA 59.438 37.037 0.00 0.00 42.77 2.24
326 340 5.028549 AGAATAGACGTCTCAATTGCCAT 57.971 39.130 23.89 4.16 0.00 4.40
568 587 7.201857 CCAGGTGAAAGAAGAAAGAAGAATTGT 60.202 37.037 0.00 0.00 0.00 2.71
638 657 2.828520 TGTTGGCAAGGAGTTGTTTCAA 59.171 40.909 0.00 0.00 35.92 2.69
727 746 2.953284 ATAGCTGGCAAGAGCATGAT 57.047 45.000 0.00 0.00 44.61 2.45
1070 1101 6.068010 TCTGTCCATTTTCCTTGTTGTATGT 58.932 36.000 0.00 0.00 0.00 2.29
1122 1153 2.578021 AGGGTTACCATCATGACTTGCT 59.422 45.455 2.98 0.00 40.13 3.91
1386 1417 3.772025 AGCTGTTGTAGTGATCCTTAGCT 59.228 43.478 0.00 0.00 34.45 3.32
1584 1616 5.770919 TCTTCTTCCATCTCCTCATCACTA 58.229 41.667 0.00 0.00 0.00 2.74
1636 1669 7.626876 GCGCTTCTTCTTCTTCTTACTAGTACT 60.627 40.741 0.91 0.00 0.00 2.73
1673 1707 5.300286 ACTTTGCACTGAGTCTGCTTTATTT 59.700 36.000 6.00 0.00 35.53 1.40
1747 1781 3.009026 CGGATGATTGTGGTCATGAACA 58.991 45.455 10.05 10.05 38.88 3.18
1752 1786 1.807755 CGAGCGGATGATTGTGGTCAT 60.808 52.381 0.00 0.00 41.36 3.06
1793 1827 5.264395 CCTTGGTGGGATCTCAAGTATTTT 58.736 41.667 0.00 0.00 36.94 1.82
1823 1857 3.742882 GCAAAAACTCCTTTTCATCAGGC 59.257 43.478 0.00 0.00 34.91 4.85
2005 2041 7.721402 ACAAGCACCAAAAGTGATATACAAAA 58.279 30.769 0.00 0.00 46.71 2.44
2108 2144 2.173569 AGGAAATGGACACCTAGATGCC 59.826 50.000 0.00 0.00 31.78 4.40
2112 2148 2.265367 TGCAGGAAATGGACACCTAGA 58.735 47.619 0.00 0.00 32.35 2.43
2210 2247 9.347934 CGTCCTGCATAATACAAAAACAAATAA 57.652 29.630 0.00 0.00 0.00 1.40
2272 2313 0.179020 TCCGAATGGCACCATCATCC 60.179 55.000 1.88 0.00 35.31 3.51
2627 2671 2.892852 CAAAGACCCCAATCAAAGCTCA 59.107 45.455 0.00 0.00 0.00 4.26
2639 2683 0.332972 AGGAATGCTCCAAAGACCCC 59.667 55.000 0.00 0.00 45.24 4.95
2673 2717 3.644966 TGAAGTTGTCAGGAGGTTTGT 57.355 42.857 0.00 0.00 0.00 2.83
2698 2742 3.824133 CCTCATTGCACCATCCTGATTA 58.176 45.455 0.00 0.00 0.00 1.75
2699 2743 2.662866 CCTCATTGCACCATCCTGATT 58.337 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.