Multiple sequence alignment - TraesCS5A01G544400

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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 TraesCS5A01G544400 chr5A 100.000 3007 0 0 1 3007 699798367 699801373 0.000000e+00 5553
1 TraesCS5A01G544400 chr5A 99.036 3007 25 3 1 3007 699839716 699842718 0.000000e+00 5389
2 TraesCS5A01G544400 chr5A 90.466 2402 160 25 634 3003 699572812 699575176 0.000000e+00 3103
3 TraesCS5A01G544400 chr5A 91.271 2108 143 18 903 3003 699719396 699721469 0.000000e+00 2835
4 TraesCS5A01G544400 chr5A 90.969 2115 143 19 903 3003 699641414 699643494 0.000000e+00 2804
5 TraesCS5A01G544400 chr5A 76.443 433 84 12 2275 2695 699571264 699571690 5.050000e-53 219
6 TraesCS5A01G544400 chr4B 91.837 2928 176 38 114 3006 660297868 660294969 0.000000e+00 4024
7 TraesCS5A01G544400 chr4B 90.841 2948 206 35 114 3007 660252793 660249856 0.000000e+00 3890
8 TraesCS5A01G544400 chr4B 91.105 2361 146 34 114 2435 660322388 660320053 0.000000e+00 3138
9 TraesCS5A01G544400 chr4B 91.419 2121 148 20 114 2230 660289531 660287441 0.000000e+00 2878
10 TraesCS5A01G544400 chrUn 96.034 2446 85 8 114 2552 231251584 231254024 0.000000e+00 3969
11 TraesCS5A01G544400 chrUn 96.360 2253 73 6 114 2360 190742398 190744647 0.000000e+00 3698
12 TraesCS5A01G544400 chrUn 95.540 2242 88 7 772 3007 156743161 156745396 0.000000e+00 3576
13 TraesCS5A01G544400 chrUn 93.084 2328 148 13 114 2435 156635248 156637568 0.000000e+00 3395
14 TraesCS5A01G544400 chrUn 91.000 2111 145 19 903 3003 328173389 328175464 0.000000e+00 2804
15 TraesCS5A01G544400 chrUn 92.899 1718 108 10 1295 3007 190750547 190752255 0.000000e+00 2484
16 TraesCS5A01G544400 chrUn 95.101 939 41 5 114 1049 190749608 190750544 0.000000e+00 1474
17 TraesCS5A01G544400 chrUn 94.510 674 29 3 114 785 156740779 156741446 0.000000e+00 1033
18 TraesCS5A01G544400 chrUn 92.702 644 41 2 2368 3007 190746371 190747012 0.000000e+00 924
19 TraesCS5A01G544400 chrUn 91.919 495 36 4 114 605 354303502 354303995 0.000000e+00 689
20 TraesCS5A01G544400 chrUn 91.597 119 8 2 1 119 156694755 156694871 2.400000e-36 163


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 TraesCS5A01G544400 chr5A 699798367 699801373 3006 False 5553.0 5553 100.0000 1 3007 1 chr5A.!!$F3 3006
1 TraesCS5A01G544400 chr5A 699839716 699842718 3002 False 5389.0 5389 99.0360 1 3007 1 chr5A.!!$F4 3006
2 TraesCS5A01G544400 chr5A 699719396 699721469 2073 False 2835.0 2835 91.2710 903 3003 1 chr5A.!!$F2 2100
3 TraesCS5A01G544400 chr5A 699641414 699643494 2080 False 2804.0 2804 90.9690 903 3003 1 chr5A.!!$F1 2100
4 TraesCS5A01G544400 chr5A 699571264 699575176 3912 False 1661.0 3103 83.4545 634 3003 2 chr5A.!!$F5 2369
5 TraesCS5A01G544400 chr4B 660294969 660297868 2899 True 4024.0 4024 91.8370 114 3006 1 chr4B.!!$R3 2892
6 TraesCS5A01G544400 chr4B 660249856 660252793 2937 True 3890.0 3890 90.8410 114 3007 1 chr4B.!!$R1 2893
7 TraesCS5A01G544400 chr4B 660320053 660322388 2335 True 3138.0 3138 91.1050 114 2435 1 chr4B.!!$R4 2321
8 TraesCS5A01G544400 chr4B 660287441 660289531 2090 True 2878.0 2878 91.4190 114 2230 1 chr4B.!!$R2 2116
9 TraesCS5A01G544400 chrUn 231251584 231254024 2440 False 3969.0 3969 96.0340 114 2552 1 chrUn.!!$F3 2438
10 TraesCS5A01G544400 chrUn 156635248 156637568 2320 False 3395.0 3395 93.0840 114 2435 1 chrUn.!!$F1 2321
11 TraesCS5A01G544400 chrUn 328173389 328175464 2075 False 2804.0 2804 91.0000 903 3003 1 chrUn.!!$F4 2100
12 TraesCS5A01G544400 chrUn 156740779 156745396 4617 False 2304.5 3576 95.0250 114 3007 2 chrUn.!!$F6 2893
13 TraesCS5A01G544400 chrUn 190742398 190752255 9857 False 2145.0 3698 94.2655 114 3007 4 chrUn.!!$F7 2893

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
619 624 0.673644 ATTTGTCAAGGTCGGCCTCG 60.674 55.0 10.2 0.0 46.33 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 12153 5.75489 AGCTAAAACAAAACATGCTGGAAAG 59.245 36.0 0.0 0.0 0.0 2.62 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
82 83 8.469200 GGATTTCATGACATATCTGTTGGAAAA 58.531 33.333 0.00 0.00 35.04 2.29
119 120 8.019656 AGTTTATACTAGTGGTCATAGGTTGG 57.980 38.462 5.39 0.00 31.21 3.77
617 622 3.561313 ACATAATTTGTCAAGGTCGGCCT 60.561 43.478 0.35 0.35 40.01 5.19
618 623 1.534729 AATTTGTCAAGGTCGGCCTC 58.465 50.000 10.20 0.00 46.33 4.70
619 624 0.673644 ATTTGTCAAGGTCGGCCTCG 60.674 55.000 10.20 0.00 46.33 4.63
620 625 1.750341 TTTGTCAAGGTCGGCCTCGA 61.750 55.000 10.20 0.00 46.33 4.04
629 634 2.047274 CGGCCTCGAGCTGGAAAA 60.047 61.111 6.99 0.00 44.85 2.29
633 638 1.168714 GCCTCGAGCTGGAAAACAAT 58.831 50.000 6.99 0.00 38.99 2.71
634 639 1.541588 GCCTCGAGCTGGAAAACAATT 59.458 47.619 6.99 0.00 38.99 2.32
636 641 2.554032 CCTCGAGCTGGAAAACAATTGT 59.446 45.455 6.99 4.92 0.00 2.71
637 642 3.004734 CCTCGAGCTGGAAAACAATTGTT 59.995 43.478 18.13 18.13 40.50 2.83
1089 3808 1.543802 ACGAGAGAACAGAAGAGCCAG 59.456 52.381 0.00 0.00 0.00 4.85
1479 4203 2.298300 CAACGTCACTTTGATCAACGC 58.702 47.619 14.99 0.00 36.85 4.84
2437 12153 5.816919 TGCTTTAGTTGTTGTTAGCTTGAC 58.183 37.500 0.00 0.00 0.00 3.18
2552 12268 9.793252 GCTTGTTGTATCAAGAAACATATGAAT 57.207 29.630 10.38 0.00 45.11 2.57
2842 12574 7.921745 GGTGTAGAGTAAATCCTCATACAAGAC 59.078 40.741 0.00 0.00 32.27 3.01
2934 12667 2.398554 GCATGCCGCCGAGAAGAAA 61.399 57.895 6.36 0.00 32.94 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 7.622479 ACCAACCTATGACCACTAGTATAAACT 59.378 37.037 0.00 0.00 39.91 2.66
119 120 7.704271 AGTTAACTTCTTGCAAGGACTTTTAC 58.296 34.615 25.73 14.14 0.00 2.01
610 615 2.781595 TTTTCCAGCTCGAGGCCGAC 62.782 60.000 15.58 0.00 43.05 4.79
611 616 2.579657 TTTTCCAGCTCGAGGCCGA 61.580 57.895 15.58 2.76 43.05 5.54
612 617 2.047274 TTTTCCAGCTCGAGGCCG 60.047 61.111 15.58 0.00 43.05 6.13
614 619 1.168714 ATTGTTTTCCAGCTCGAGGC 58.831 50.000 15.58 6.66 42.19 4.70
615 620 2.554032 ACAATTGTTTTCCAGCTCGAGG 59.446 45.455 15.58 0.00 0.00 4.63
617 622 3.629855 TCAACAATTGTTTTCCAGCTCGA 59.370 39.130 21.10 9.28 35.83 4.04
618 623 3.730715 GTCAACAATTGTTTTCCAGCTCG 59.269 43.478 21.10 7.08 35.83 5.03
619 624 4.051237 GGTCAACAATTGTTTTCCAGCTC 58.949 43.478 21.10 6.58 35.83 4.09
620 625 3.706086 AGGTCAACAATTGTTTTCCAGCT 59.294 39.130 28.28 20.67 35.83 4.24
622 627 9.357652 CATATAAGGTCAACAATTGTTTTCCAG 57.642 33.333 28.28 17.01 35.83 3.86
623 628 9.083422 TCATATAAGGTCAACAATTGTTTTCCA 57.917 29.630 28.28 17.29 35.83 3.53
628 633 8.522830 CCAAGTCATATAAGGTCAACAATTGTT 58.477 33.333 18.13 18.13 39.12 2.83
629 634 7.362920 GCCAAGTCATATAAGGTCAACAATTGT 60.363 37.037 4.92 4.92 0.00 2.71
633 638 5.815581 AGCCAAGTCATATAAGGTCAACAA 58.184 37.500 0.00 0.00 0.00 2.83
634 639 5.435686 AGCCAAGTCATATAAGGTCAACA 57.564 39.130 0.00 0.00 0.00 3.33
636 641 5.885912 GGAAAGCCAAGTCATATAAGGTCAA 59.114 40.000 0.00 0.00 0.00 3.18
637 642 5.191722 AGGAAAGCCAAGTCATATAAGGTCA 59.808 40.000 0.00 0.00 36.29 4.02
1089 3808 4.742438 TGCCATTTCGTTTTAGTGTCTC 57.258 40.909 0.00 0.00 0.00 3.36
1393 4117 4.637534 GCCTTGAAGAAGTCATCTGCATTA 59.362 41.667 0.00 0.00 43.55 1.90
2365 12081 8.630054 ACTTACTTATTACATGCACCAGAAAA 57.370 30.769 0.00 0.00 0.00 2.29
2437 12153 5.754890 AGCTAAAACAAAACATGCTGGAAAG 59.245 36.000 0.00 0.00 0.00 2.62
2842 12574 6.363088 TGTTTTGCTATGCTTTTCTTTGATCG 59.637 34.615 0.00 0.00 0.00 3.69
2934 12667 2.997897 GTCCGGCCTCTCCTGTGT 60.998 66.667 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.