Multiple sequence alignment - TraesCS1D01G185400

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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 TraesCS1D01G185400 chr1D 100.000 3454 0 0 1 3454 256252314 256248861 0.000000e+00 6379
1 TraesCS1D01G185400 chr4D 98.938 2824 26 4 2 2825 490985545 490988364 0.000000e+00 5046
2 TraesCS1D01G185400 chr6D 98.865 1410 15 1 1418 2827 59097608 59099016 0.000000e+00 2514
3 TraesCS1D01G185400 chr3A 94.695 1508 68 9 1322 2825 148053146 148051647 0.000000e+00 2331
4 TraesCS1D01G185400 chr3A 93.254 1260 73 5 1579 2837 17714382 17715630 0.000000e+00 1845
5 TraesCS1D01G185400 chr6B 89.457 1252 69 27 1579 2825 131648920 131647727 0.000000e+00 1522
6 TraesCS1D01G185400 chr5A 93.864 766 41 5 2073 2838 169286200 169286959 0.000000e+00 1149
7 TraesCS1D01G185400 chr5A 93.603 766 44 4 2073 2838 169234977 169235737 0.000000e+00 1138
8 TraesCS1D01G185400 chr7B 94.297 754 36 4 2073 2826 513740971 513741717 0.000000e+00 1147
9 TraesCS1D01G185400 chr5B 94.164 754 37 4 2073 2826 79782151 79782897 0.000000e+00 1142
10 TraesCS1D01G185400 chr1A 93.620 768 41 6 2073 2840 278147504 278146745 0.000000e+00 1140
11 TraesCS1D01G185400 chr1A 93.641 629 32 7 2828 3454 329235373 329234751 0.000000e+00 933
12 TraesCS1D01G185400 chr7D 85.812 874 115 9 939 1808 87445035 87445903 0.000000e+00 918
13 TraesCS1D01G185400 chr7D 82.981 899 103 25 848 1736 87446776 87445918 0.000000e+00 767
14 TraesCS1D01G185400 chr1B 88.911 514 41 10 2945 3454 356892480 356892981 1.360000e-173 619


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 TraesCS1D01G185400 chr1D 256248861 256252314 3453 True 6379 6379 100.000 1 3454 1 chr1D.!!$R1 3453
1 TraesCS1D01G185400 chr4D 490985545 490988364 2819 False 5046 5046 98.938 2 2825 1 chr4D.!!$F1 2823
2 TraesCS1D01G185400 chr6D 59097608 59099016 1408 False 2514 2514 98.865 1418 2827 1 chr6D.!!$F1 1409
3 TraesCS1D01G185400 chr3A 148051647 148053146 1499 True 2331 2331 94.695 1322 2825 1 chr3A.!!$R1 1503
4 TraesCS1D01G185400 chr3A 17714382 17715630 1248 False 1845 1845 93.254 1579 2837 1 chr3A.!!$F1 1258
5 TraesCS1D01G185400 chr6B 131647727 131648920 1193 True 1522 1522 89.457 1579 2825 1 chr6B.!!$R1 1246
6 TraesCS1D01G185400 chr5A 169286200 169286959 759 False 1149 1149 93.864 2073 2838 1 chr5A.!!$F2 765
7 TraesCS1D01G185400 chr5A 169234977 169235737 760 False 1138 1138 93.603 2073 2838 1 chr5A.!!$F1 765
8 TraesCS1D01G185400 chr7B 513740971 513741717 746 False 1147 1147 94.297 2073 2826 1 chr7B.!!$F1 753
9 TraesCS1D01G185400 chr5B 79782151 79782897 746 False 1142 1142 94.164 2073 2826 1 chr5B.!!$F1 753
10 TraesCS1D01G185400 chr1A 278146745 278147504 759 True 1140 1140 93.620 2073 2840 1 chr1A.!!$R1 767
11 TraesCS1D01G185400 chr1A 329234751 329235373 622 True 933 933 93.641 2828 3454 1 chr1A.!!$R2 626
12 TraesCS1D01G185400 chr7D 87445035 87445903 868 False 918 918 85.812 939 1808 1 chr7D.!!$F1 869
13 TraesCS1D01G185400 chr7D 87445918 87446776 858 True 767 767 82.981 848 1736 1 chr7D.!!$R1 888
14 TraesCS1D01G185400 chr1B 356892480 356892981 501 False 619 619 88.911 2945 3454 1 chr1B.!!$F1 509

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
270 271 0.035820 TACCTGAATGCCCGTGGTTC 60.036 55.0 0.0 0.0 32.74 3.62 F
274 275 0.179004 TGAATGCCCGTGGTTCAGTT 60.179 50.0 0.0 0.0 0.00 3.16 F
684 685 0.976073 TAGGAGGAAGTTGGAGGCGG 60.976 60.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1525 2.290641 GACTCAACAAATGTCCTTGCGT 59.709 45.455 0.00 0.00 0.00 5.24 R
1765 1788 3.963374 TCCATGAAGGTGACCTCTCTATG 59.037 47.826 3.76 7.42 39.02 2.23 R
2485 2516 5.816258 ACAAATTGAAACACACAATCATGCA 59.184 32.000 0.00 0.00 37.04 3.96 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
29 30 0.657840 GCGACATTCCACATACAGGC 59.342 55.000 0.00 0.00 0.00 4.85
37 38 1.007842 TCCACATACAGGCCAGGTCTA 59.992 52.381 5.01 0.00 0.00 2.59
270 271 0.035820 TACCTGAATGCCCGTGGTTC 60.036 55.000 0.00 0.00 32.74 3.62
274 275 0.179004 TGAATGCCCGTGGTTCAGTT 60.179 50.000 0.00 0.00 0.00 3.16
668 669 8.443937 GTTCAAGCTCTACTGTTGTTTTATAGG 58.556 37.037 0.00 0.00 0.00 2.57
684 685 0.976073 TAGGAGGAAGTTGGAGGCGG 60.976 60.000 0.00 0.00 0.00 6.13
702 703 1.135431 CGGCATTCGAAAATCCAGCAA 60.135 47.619 0.00 0.00 42.43 3.91
954 962 8.721133 TTGTATCTATCCTTATTGCCACTCTA 57.279 34.615 0.00 0.00 0.00 2.43
1029 1037 5.041287 CCAATTAATCTTAGACGTCAGCGA 58.959 41.667 19.50 10.54 42.00 4.93
1741 1763 3.703286 ATGATGGACATGAACGCATTG 57.297 42.857 0.00 0.00 37.87 2.82
1765 1788 3.477530 GGATACCCAGGTGCTGAAATAC 58.522 50.000 0.00 0.00 32.44 1.89
2853 2890 7.331089 AGATAAAAGGGACAAAAGTACTCCT 57.669 36.000 0.00 0.00 0.00 3.69
2860 2897 3.006644 GGACAAAAGTACTCCTTCCGTCT 59.993 47.826 0.00 0.00 35.81 4.18
2863 2900 4.283722 ACAAAAGTACTCCTTCCGTCTCAT 59.716 41.667 0.00 0.00 31.27 2.90
2902 2939 6.384258 TTCAAGCTATGTAAAAAGCACACA 57.616 33.333 0.00 0.00 41.32 3.72
2903 2940 6.384258 TCAAGCTATGTAAAAAGCACACAA 57.616 33.333 0.00 0.00 41.32 3.33
2909 2946 7.222611 AGCTATGTAAAAAGCACACAAGTTTTG 59.777 33.333 0.00 0.00 41.32 2.44
2912 2949 7.804614 TGTAAAAAGCACACAAGTTTTGTAG 57.195 32.000 0.00 0.00 43.23 2.74
2913 2950 7.371936 TGTAAAAAGCACACAAGTTTTGTAGT 58.628 30.769 0.00 0.00 43.23 2.73
2918 2955 8.819643 AAAGCACACAAGTTTTGTAGTAAAAA 57.180 26.923 0.00 0.00 43.23 1.94
3026 3063 7.395190 AGCACACAATAACATACAACATGAT 57.605 32.000 0.00 0.00 0.00 2.45
3176 3213 7.148306 ACCTCGGATACAATACAAAACATGTTC 60.148 37.037 12.39 0.00 43.63 3.18
3214 3252 7.534085 TCCGCAAGTATAAATAAGTCAACAG 57.466 36.000 0.00 0.00 0.00 3.16
3274 3312 9.890629 TCACATGCTATATCAGAACTAAAGTTT 57.109 29.630 0.00 0.00 38.56 2.66
3336 3374 3.055458 TGTTCGGATGAGTAGCCAATCAA 60.055 43.478 0.00 0.00 30.94 2.57
3421 3462 9.451206 TTGAATCCTATATCTATATGATGCCCA 57.549 33.333 0.00 0.00 36.65 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.374252 GAATGTCGCAGGTGACCGT 60.374 57.895 10.20 0.00 38.11 4.83
29 30 5.480205 GGTAACTTCTCTGTTTAGACCTGG 58.520 45.833 0.00 0.00 0.00 4.45
173 174 5.825151 GCCTCTAAGATGCAAGGATTTACTT 59.175 40.000 3.98 0.00 0.00 2.24
247 248 1.416401 CCACGGGCATTCAGGTAGTAT 59.584 52.381 0.00 0.00 0.00 2.12
668 669 2.436824 GCCGCCTCCAACTTCCTC 60.437 66.667 0.00 0.00 0.00 3.71
684 685 3.221964 ACTTGCTGGATTTTCGAATGC 57.778 42.857 0.00 0.00 0.00 3.56
729 730 5.509840 GGCAGACCACGAAATCTATAGTCAT 60.510 44.000 0.00 0.00 35.26 3.06
954 962 8.851541 ATGTCACATTTAAATTTGGAAGCAAT 57.148 26.923 13.08 0.00 0.00 3.56
1053 1061 2.188817 ACTTACCTAGGCTCAACTGGG 58.811 52.381 9.30 0.00 44.03 4.45
1513 1525 2.290641 GACTCAACAAATGTCCTTGCGT 59.709 45.455 0.00 0.00 0.00 5.24
1693 1715 4.380531 ACGACTATGCCAATTATGTCTGG 58.619 43.478 0.00 0.00 35.67 3.86
1765 1788 3.963374 TCCATGAAGGTGACCTCTCTATG 59.037 47.826 3.76 7.42 39.02 2.23
2485 2516 5.816258 ACAAATTGAAACACACAATCATGCA 59.184 32.000 0.00 0.00 37.04 3.96
2892 2929 8.819643 TTTTACTACAAAACTTGTGTGCTTTT 57.180 26.923 2.30 0.00 45.03 2.27
2918 2955 7.936847 TCCATTTGTTCCATAATATAAGACGCT 59.063 33.333 0.00 0.00 0.00 5.07
3176 3213 2.042686 TGCGGAAATGAGAATCCAGG 57.957 50.000 0.00 0.00 35.34 4.45
3336 3374 7.855784 AAAGAGTAGATTTTGTTTTCCCCAT 57.144 32.000 0.00 0.00 0.00 4.00
3421 3462 3.620929 AATCGACTATATGACGCACGT 57.379 42.857 0.00 0.00 34.12 4.49


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

AutoCloner maintained by Alex Coulton.