Multiple sequence alignment - TraesCS1A01G226600

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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 TraesCS1A01G226600 chr1A 100.000 2462 0 0 1 2462 397052250 397054711 0.000000e+00 4547.0
1 TraesCS1A01G226600 chr1D 95.552 2428 91 9 1 2420 316204442 316206860 0.000000e+00 3869.0
2 TraesCS1A01G226600 chr1B 93.278 2410 119 22 61 2462 428535119 428537493 0.000000e+00 3513.0
3 TraesCS1A01G226600 chr6D 96.774 62 2 0 1 62 91548636 91548697 1.200000e-18 104.0
4 TraesCS1A01G226600 chr6D 91.549 71 1 4 1 67 272098049 272098118 2.610000e-15 93.5
5 TraesCS1A01G226600 chr6D 90.278 72 6 1 1 72 277551621 277551691 2.610000e-15 93.5
6 TraesCS1A01G226600 chr5B 96.667 60 2 0 1 60 334362917 334362976 1.560000e-17 100.0
7 TraesCS1A01G226600 chr2A 91.892 74 2 2 1 70 543319360 543319287 1.560000e-17 100.0
8 TraesCS1A01G226600 chr5A 96.610 59 2 0 1 59 296387582 296387640 5.600000e-17 99.0
9 TraesCS1A01G226600 chr3B 92.537 67 3 2 1 65 435802019 435801953 7.250000e-16 95.3
10 TraesCS1A01G226600 chr6B 94.915 59 3 0 1 59 55667263 55667321 2.610000e-15 93.5


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 TraesCS1A01G226600 chr1A 397052250 397054711 2461 False 4547 4547 100.000 1 2462 1 chr1A.!!$F1 2461
1 TraesCS1A01G226600 chr1D 316204442 316206860 2418 False 3869 3869 95.552 1 2420 1 chr1D.!!$F1 2419
2 TraesCS1A01G226600 chr1B 428535119 428537493 2374 False 3513 3513 93.278 61 2462 1 chr1B.!!$F1 2401

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
217 222 0.036732 ATGCGTGTTGTCCCATGTCT 59.963 50.000 0.00 0.0 0.00 3.41 F
1190 1200 1.263484 GCGGATCGAGATCTACACGAA 59.737 52.381 8.82 0.0 43.63 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1438 1.418334 AGATATCGGAGCACTTGCCT 58.582 50.0 0.0 0.0 43.38 4.75 R
2308 2319 0.318614 GAACCAAACCATGCCACACG 60.319 55.0 0.0 0.0 0.00 4.49 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
48 53 7.036220 GGACTACGATTGATCCCATATACTTG 58.964 42.308 0.00 0.00 0.00 3.16
50 55 7.378966 ACTACGATTGATCCCATATACTTGTG 58.621 38.462 0.00 0.00 0.00 3.33
184 189 5.471116 GTCGGTAACCTTTAAGTGAAATGGT 59.529 40.000 0.00 0.00 32.90 3.55
185 190 5.702209 TCGGTAACCTTTAAGTGAAATGGTC 59.298 40.000 0.00 0.00 31.33 4.02
195 200 2.439507 AGTGAAATGGTCTGGTGACTGT 59.560 45.455 0.00 0.00 42.54 3.55
206 211 2.548057 CTGGTGACTGTTAATGCGTGTT 59.452 45.455 0.00 0.00 0.00 3.32
210 215 2.546368 TGACTGTTAATGCGTGTTGTCC 59.454 45.455 0.00 0.00 0.00 4.02
217 222 0.036732 ATGCGTGTTGTCCCATGTCT 59.963 50.000 0.00 0.00 0.00 3.41
449 455 3.827008 TGCATACTCTCATGTCCCTTC 57.173 47.619 0.00 0.00 0.00 3.46
453 459 4.445448 GCATACTCTCATGTCCCTTCCAAT 60.445 45.833 0.00 0.00 0.00 3.16
463 470 5.993748 TGTCCCTTCCAATAAACCATTTC 57.006 39.130 0.00 0.00 0.00 2.17
467 474 6.210584 GTCCCTTCCAATAAACCATTTCTTGA 59.789 38.462 2.09 0.00 30.81 3.02
475 482 6.950860 ATAAACCATTTCTTGAAACCCCAT 57.049 33.333 0.00 0.00 0.00 4.00
557 564 2.292569 GTCCTCGATTGCATGCATGAAT 59.707 45.455 30.64 23.31 0.00 2.57
570 577 4.200838 TGCATGAATTAGACCTTCGTGA 57.799 40.909 0.00 0.00 40.50 4.35
582 589 5.556915 AGACCTTCGTGATTAAATTGACCA 58.443 37.500 0.00 0.00 0.00 4.02
600 607 3.686016 ACCATGCCGTAAACTTCAAGAT 58.314 40.909 0.00 0.00 0.00 2.40
606 613 6.662414 TGCCGTAAACTTCAAGATATTGAG 57.338 37.500 2.58 1.08 31.87 3.02
637 644 5.006844 ACTGATTATCACTCGTGTCGTCTAG 59.993 44.000 0.00 0.00 0.00 2.43
639 646 6.044682 TGATTATCACTCGTGTCGTCTAGTA 58.955 40.000 0.00 0.00 0.00 1.82
660 667 9.698309 CTAGTATCCAATGTAAGATGTAGTTGG 57.302 37.037 0.00 0.00 37.91 3.77
661 668 8.319057 AGTATCCAATGTAAGATGTAGTTGGA 57.681 34.615 7.05 7.05 46.25 3.53
677 684 5.263968 AGTTGGATCGTCAAAGTCGATAT 57.736 39.130 0.93 0.00 45.90 1.63
689 696 6.984474 GTCAAAGTCGATATCCATCCAACTTA 59.016 38.462 0.00 0.00 34.75 2.24
720 727 4.498177 GCTTCTTGTTGAAAGGTCAGAACC 60.498 45.833 0.00 0.00 46.87 3.62
787 795 9.762381 AGTAATATGGATTAGAGGAAGTAGGAG 57.238 37.037 0.00 0.00 0.00 3.69
788 796 9.536510 GTAATATGGATTAGAGGAAGTAGGAGT 57.463 37.037 0.00 0.00 0.00 3.85
837 847 9.353999 CGAGGGGTTGAAATAAGAAAAATAAAG 57.646 33.333 0.00 0.00 0.00 1.85
921 931 5.067805 ACTGTCCTTCCAAACAAAAAGCTAG 59.932 40.000 0.00 0.00 0.00 3.42
943 953 2.132762 CGACTATTCCGAATTTCCCCG 58.867 52.381 0.00 0.00 0.00 5.73
1098 1108 2.093447 CGGCAATGGTTACTTCTCCTCT 60.093 50.000 0.00 0.00 0.00 3.69
1190 1200 1.263484 GCGGATCGAGATCTACACGAA 59.737 52.381 8.82 0.00 43.63 3.85
1371 1381 2.820037 GTGGCGAGCTACAAGGCC 60.820 66.667 6.71 0.00 45.76 5.19
1428 1438 2.282180 GGCCTCCGCTGGTTCAAA 60.282 61.111 0.00 0.00 34.44 2.69
1453 1463 2.388735 AGTGCTCCGATATCTTCCACA 58.611 47.619 0.34 0.00 0.00 4.17
1499 1509 0.107831 TGACAGGGTCCCAAGAAACG 59.892 55.000 11.55 0.00 0.00 3.60
1500 1510 1.228154 ACAGGGTCCCAAGAAACGC 60.228 57.895 11.55 0.00 0.00 4.84
1644 1654 2.221906 TAGAGGAACTTGCGACGGGC 62.222 60.000 0.00 0.00 41.55 6.13
1682 1692 1.264672 TGTGATGTGTCGTATTCGCG 58.735 50.000 0.00 0.00 36.96 5.87
1965 1975 1.444933 TCCATTGGAGTGGGTGTTCT 58.555 50.000 0.00 0.00 39.80 3.01
2003 2013 7.077605 TGAAGTGCAATAAATTCTTTCAGACG 58.922 34.615 0.00 0.00 0.00 4.18
2014 2024 4.092771 TCTTTCAGACGAGTACGGATTG 57.907 45.455 0.00 0.00 44.46 2.67
2155 2166 5.035443 CACTGGTAGTCTGATAACTAACGC 58.965 45.833 0.00 0.00 41.47 4.84
2190 2201 8.356657 TGAACATAGTTTGGTCCAGTATTTTTG 58.643 33.333 0.00 0.00 41.74 2.44
2308 2319 5.473796 TGTTTGTTTCAACTCTACGTTCC 57.526 39.130 0.00 0.00 32.27 3.62
2447 2458 1.284785 TCAGCCCCTTTGGTCCTTATG 59.715 52.381 0.00 0.00 36.04 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.512082 CGTAGTCCTTTCAATAAGAGTGTCG 59.488 44.000 0.00 0.00 0.00 4.35
48 53 5.028549 ACTGTGAAGATATGATGACCCAC 57.971 43.478 0.00 0.00 0.00 4.61
50 55 5.923204 AGAACTGTGAAGATATGATGACCC 58.077 41.667 0.00 0.00 0.00 4.46
184 189 2.224185 ACACGCATTAACAGTCACCAGA 60.224 45.455 0.00 0.00 0.00 3.86
185 190 2.143122 ACACGCATTAACAGTCACCAG 58.857 47.619 0.00 0.00 0.00 4.00
210 215 2.561733 ACATCGTACGTCAGACATGG 57.438 50.000 16.05 0.00 0.00 3.66
368 374 6.953520 TGGTTTCTTTCCCATGTATGAAATCT 59.046 34.615 0.00 0.00 30.67 2.40
386 392 6.323739 TGGAAGCTACAAGAATTTTGGTTTCT 59.676 34.615 0.00 0.00 34.95 2.52
449 455 5.937540 GGGGTTTCAAGAAATGGTTTATTGG 59.062 40.000 9.17 0.00 41.03 3.16
453 459 6.081356 AGATGGGGTTTCAAGAAATGGTTTA 58.919 36.000 0.00 0.00 32.36 2.01
463 470 4.301072 TGGTAGAAGATGGGGTTTCAAG 57.699 45.455 0.00 0.00 0.00 3.02
467 474 4.675063 ACATTGGTAGAAGATGGGGTTT 57.325 40.909 0.00 0.00 0.00 3.27
557 564 7.162761 TGGTCAATTTAATCACGAAGGTCTAA 58.837 34.615 0.00 0.00 0.00 2.10
570 577 6.524101 AGTTTACGGCATGGTCAATTTAAT 57.476 33.333 0.00 0.00 0.00 1.40
578 585 3.071479 TCTTGAAGTTTACGGCATGGTC 58.929 45.455 0.00 0.00 0.00 4.02
582 589 6.823689 ACTCAATATCTTGAAGTTTACGGCAT 59.176 34.615 0.00 0.00 40.78 4.40
624 631 4.035324 ACATTGGATACTAGACGACACGAG 59.965 45.833 0.00 0.00 37.61 4.18
626 633 4.288670 ACATTGGATACTAGACGACACG 57.711 45.455 0.00 0.00 37.61 4.49
631 638 8.784994 ACTACATCTTACATTGGATACTAGACG 58.215 37.037 0.00 0.00 37.61 4.18
660 667 4.859798 GGATGGATATCGACTTTGACGATC 59.140 45.833 8.00 0.00 45.32 3.69
677 684 3.330701 AGCACTCCTTTAAGTTGGATGGA 59.669 43.478 0.00 0.00 0.00 3.41
689 696 4.098501 CCTTTCAACAAGAAGCACTCCTTT 59.901 41.667 0.00 0.00 37.57 3.11
720 727 6.064060 TGGCTTGATGATATAAACCTTGGAG 58.936 40.000 0.00 0.00 0.00 3.86
737 744 7.230510 ACTTGTCACAGTTTTAATATGGCTTGA 59.769 33.333 0.00 0.00 0.00 3.02
756 764 9.213777 ACTTCCTCTAATCCATATTACTTGTCA 57.786 33.333 0.00 0.00 0.00 3.58
837 847 0.035439 TTTCCTTCGGGATGTGGAGC 60.035 55.000 0.00 0.00 44.61 4.70
861 871 6.688073 AAGAAGAGGACAGACCAAAGAATA 57.312 37.500 0.00 0.00 42.04 1.75
868 878 1.978580 GGGAAAGAAGAGGACAGACCA 59.021 52.381 0.00 0.00 42.04 4.02
872 882 4.564613 GGAGAAAGGGAAAGAAGAGGACAG 60.565 50.000 0.00 0.00 0.00 3.51
921 931 3.129109 GGGGAAATTCGGAATAGTCGTC 58.871 50.000 3.22 1.97 0.00 4.20
943 953 1.076705 GGGGAGGAAATGGAGTGCC 60.077 63.158 0.00 0.00 0.00 5.01
1314 1324 2.045926 GGGTCGCTGAAGCACCAT 60.046 61.111 19.01 0.00 41.08 3.55
1371 1381 3.578716 TCACTTTCCCTTCCACTGAGTAG 59.421 47.826 0.00 0.00 0.00 2.57
1428 1438 1.418334 AGATATCGGAGCACTTGCCT 58.582 50.000 0.00 0.00 43.38 4.75
1453 1463 1.552792 GAGCAGAAGAGGTTACCAGCT 59.447 52.381 3.51 2.78 0.00 4.24
1499 1509 3.572584 CAGACATTTTTCAGGAGCTTGC 58.427 45.455 0.00 0.00 0.00 4.01
1500 1510 3.005050 TGCAGACATTTTTCAGGAGCTTG 59.995 43.478 0.00 0.00 0.00 4.01
1644 1654 6.989796 TCACAAACATTTCATGAATTCACG 57.010 33.333 11.07 1.83 0.00 4.35
1682 1692 4.213059 GCTTGCAGATAAATCTACAGAGGC 59.787 45.833 0.00 0.00 34.85 4.70
1867 1877 7.080353 CTGACAATTCAGCATTCATAGTGAA 57.920 36.000 0.00 0.00 42.99 3.18
1965 1975 1.559682 GCACTTCAATCCCTCCTACCA 59.440 52.381 0.00 0.00 0.00 3.25
2003 2013 4.395959 TCAATGTACCCAATCCGTACTC 57.604 45.455 0.00 0.00 37.55 2.59
2014 2024 5.297776 CAGATGGAAGTTCATCAATGTACCC 59.702 44.000 5.01 0.00 44.30 3.69
2155 2166 6.127730 GGACCAAACTATGTTCAAATAGGTGG 60.128 42.308 11.63 11.63 41.14 4.61
2190 2201 8.738645 ACCACAGGATAACTTCATATTTTCTC 57.261 34.615 0.00 0.00 0.00 2.87
2308 2319 0.318614 GAACCAAACCATGCCACACG 60.319 55.000 0.00 0.00 0.00 4.49
2431 2442 6.126594 TGTTACTATCATAAGGACCAAAGGGG 60.127 42.308 0.00 0.00 44.81 4.79


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

AutoCloner maintained by Alex Coulton.