Multiple sequence alignment - TraesCS3A01G062900

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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 TraesCS3A01G062900 chr3A 100.000 3352 0 0 1 3352 37632289 37635640 0 6191
1 TraesCS3A01G062900 chr3A 94.860 2782 97 8 609 3352 715213480 715216253 0 4303
2 TraesCS3A01G062900 chr3A 94.720 2765 94 12 612 3352 27908720 27905984 0 4250
3 TraesCS3A01G062900 chr3A 96.732 612 20 0 1 612 37591594 37592205 0 1020
4 TraesCS3A01G062900 chr2A 96.222 2753 85 7 612 3352 461392281 461395026 0 4490
5 TraesCS3A01G062900 chr1A 95.547 2762 95 11 612 3352 302911829 302914583 0 4394
6 TraesCS3A01G062900 chr5A 93.505 2802 116 20 612 3352 701985671 701982875 0 4106
7 TraesCS3A01G062900 chr5A 96.111 1980 70 5 612 2587 680753169 680755145 0 3223
8 TraesCS3A01G062900 chr5A 94.688 1958 98 5 612 2567 647551125 647553078 0 3035
9 TraesCS3A01G062900 chr5A 94.987 778 24 5 2585 3352 680757884 680758656 0 1206
10 TraesCS3A01G062900 chr4A 94.753 2592 121 10 612 3194 521945178 521947763 0 4019
11 TraesCS3A01G062900 chr5D 92.981 2778 133 20 612 3352 408555343 408552591 0 3993
12 TraesCS3A01G062900 chr7A 94.825 2570 96 20 612 3153 147920462 147917902 0 3975
13 TraesCS3A01G062900 chr7D 92.759 2776 133 26 612 3352 631818588 631815846 0 3951
14 TraesCS3A01G062900 chr6A 95.996 2023 66 5 1340 3352 608061679 608063696 0 3273
15 TraesCS3A01G062900 chr6A 95.564 2029 74 11 596 2608 428285566 428287594 0 3234
16 TraesCS3A01G062900 chr6A 93.725 765 19 11 2602 3348 428296343 428297096 0 1120
17 TraesCS3A01G062900 chr3D 95.261 612 29 0 1 612 27529564 27530175 0 970
18 TraesCS3A01G062900 chr3B 93.182 616 38 1 1 612 45961848 45962463 0 902
19 TraesCS3A01G062900 chr3B 93.182 616 38 1 1 612 46011836 46012451 0 902
20 TraesCS3A01G062900 chr3B 92.857 616 40 1 1 612 45865556 45866171 0 891
21 TraesCS3A01G062900 chr3B 92.857 616 40 1 1 612 45879210 45879825 0 891
22 TraesCS3A01G062900 chr3B 92.857 616 40 1 1 612 45922870 45923485 0 891
23 TraesCS3A01G062900 chr3B 92.695 616 41 1 1 612 45781920 45782535 0 885
24 TraesCS3A01G062900 chr3B 92.695 616 41 1 1 612 45945403 45946018 0 885


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 TraesCS3A01G062900 chr3A 37632289 37635640 3351 False 6191.0 6191 100.000 1 3352 1 chr3A.!!$F2 3351
1 TraesCS3A01G062900 chr3A 715213480 715216253 2773 False 4303.0 4303 94.860 609 3352 1 chr3A.!!$F3 2743
2 TraesCS3A01G062900 chr3A 27905984 27908720 2736 True 4250.0 4250 94.720 612 3352 1 chr3A.!!$R1 2740
3 TraesCS3A01G062900 chr3A 37591594 37592205 611 False 1020.0 1020 96.732 1 612 1 chr3A.!!$F1 611
4 TraesCS3A01G062900 chr2A 461392281 461395026 2745 False 4490.0 4490 96.222 612 3352 1 chr2A.!!$F1 2740
5 TraesCS3A01G062900 chr1A 302911829 302914583 2754 False 4394.0 4394 95.547 612 3352 1 chr1A.!!$F1 2740
6 TraesCS3A01G062900 chr5A 701982875 701985671 2796 True 4106.0 4106 93.505 612 3352 1 chr5A.!!$R1 2740
7 TraesCS3A01G062900 chr5A 647551125 647553078 1953 False 3035.0 3035 94.688 612 2567 1 chr5A.!!$F1 1955
8 TraesCS3A01G062900 chr5A 680753169 680758656 5487 False 2214.5 3223 95.549 612 3352 2 chr5A.!!$F2 2740
9 TraesCS3A01G062900 chr4A 521945178 521947763 2585 False 4019.0 4019 94.753 612 3194 1 chr4A.!!$F1 2582
10 TraesCS3A01G062900 chr5D 408552591 408555343 2752 True 3993.0 3993 92.981 612 3352 1 chr5D.!!$R1 2740
11 TraesCS3A01G062900 chr7A 147917902 147920462 2560 True 3975.0 3975 94.825 612 3153 1 chr7A.!!$R1 2541
12 TraesCS3A01G062900 chr7D 631815846 631818588 2742 True 3951.0 3951 92.759 612 3352 1 chr7D.!!$R1 2740
13 TraesCS3A01G062900 chr6A 608061679 608063696 2017 False 3273.0 3273 95.996 1340 3352 1 chr6A.!!$F3 2012
14 TraesCS3A01G062900 chr6A 428285566 428287594 2028 False 3234.0 3234 95.564 596 2608 1 chr6A.!!$F1 2012
15 TraesCS3A01G062900 chr6A 428296343 428297096 753 False 1120.0 1120 93.725 2602 3348 1 chr6A.!!$F2 746
16 TraesCS3A01G062900 chr3D 27529564 27530175 611 False 970.0 970 95.261 1 612 1 chr3D.!!$F1 611
17 TraesCS3A01G062900 chr3B 45961848 45962463 615 False 902.0 902 93.182 1 612 1 chr3B.!!$F6 611
18 TraesCS3A01G062900 chr3B 46011836 46012451 615 False 902.0 902 93.182 1 612 1 chr3B.!!$F7 611
19 TraesCS3A01G062900 chr3B 45865556 45866171 615 False 891.0 891 92.857 1 612 1 chr3B.!!$F2 611
20 TraesCS3A01G062900 chr3B 45879210 45879825 615 False 891.0 891 92.857 1 612 1 chr3B.!!$F3 611
21 TraesCS3A01G062900 chr3B 45922870 45923485 615 False 891.0 891 92.857 1 612 1 chr3B.!!$F4 611
22 TraesCS3A01G062900 chr3B 45781920 45782535 615 False 885.0 885 92.695 1 612 1 chr3B.!!$F1 611
23 TraesCS3A01G062900 chr3B 45945403 45946018 615 False 885.0 885 92.695 1 612 1 chr3B.!!$F5 611

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
946 982 0.757188 CTCCCCTGCTCCAGTACGAT 60.757 60.0 0.0 0.0 0.0 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2786 5632 1.352352 CTGGTGGAGTGACTGGGAAAT 59.648 52.381 0.0 0.0 0.0 2.17 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
60 61 8.592809 TGTATTTCCTTCCAAATTTACTTGCAT 58.407 29.630 0.00 0.00 0.00 3.96
168 169 4.787551 TCTACACAACACCCTGATTTGTT 58.212 39.130 0.00 0.00 36.35 2.83
391 396 6.634837 CGCATGTGTGTTTTACAAGATTTGTA 59.365 34.615 0.00 0.00 43.27 2.41
482 487 2.376109 AGCATGAATTCCAAGAGGCAG 58.624 47.619 2.27 0.00 33.74 4.85
520 525 7.415877 CGAGTCTTTTGGGACTTTTAAAAGGAA 60.416 37.037 27.23 13.84 45.32 3.36
567 572 1.762957 ACATTCCCGGATTCTCGTCAT 59.237 47.619 0.73 0.00 0.00 3.06
703 708 4.183686 GCTACCAGTCGCGCGGTA 62.184 66.667 31.69 21.70 36.69 4.02
734 739 4.887190 AGCCCAAAACGCCCGTGT 62.887 61.111 0.00 0.00 0.00 4.49
777 782 4.715523 CGCCCGGACCCACATGTT 62.716 66.667 0.73 0.00 0.00 2.71
946 982 0.757188 CTCCCCTGCTCCAGTACGAT 60.757 60.000 0.00 0.00 0.00 3.73
1219 1268 8.662781 TTGATTGTAGGATTGATGTAAGCTAC 57.337 34.615 0.00 0.00 0.00 3.58
1229 1278 5.339008 TGATGTAAGCTACGGTTCATCTT 57.661 39.130 0.00 0.00 33.41 2.40
1256 1305 2.026822 AGTGTTAGGGTTCATGCTGAGG 60.027 50.000 0.00 0.00 0.00 3.86
1308 1359 2.838736 AGCGTGCAAGTATATTCTGGG 58.161 47.619 0.59 0.00 0.00 4.45
1357 1409 3.577848 TGCTGTTATTTTGGTTGCAGGAT 59.422 39.130 0.00 0.00 0.00 3.24
1475 1527 3.452627 TGCTTTTGAAGGGCCTTTAACAA 59.547 39.130 21.77 17.24 0.00 2.83
1727 1823 8.677300 GTTAATCATGGAACTGAAATAAGCTCA 58.323 33.333 0.00 0.00 0.00 4.26
1998 2097 4.014569 TGCATTGAGTACACCAAGCTTA 57.985 40.909 0.00 0.00 0.00 3.09
2162 2264 3.387397 GCTCAAACTTGCAAAAGAGCAT 58.613 40.909 24.92 0.00 45.67 3.79
2168 2270 3.754965 ACTTGCAAAAGAGCATAGGTGA 58.245 40.909 0.00 0.00 45.19 4.02
2230 2332 4.162040 AGGCTATGAAGGATGTTCAAGG 57.838 45.455 0.00 0.00 31.55 3.61
2231 2333 3.117738 AGGCTATGAAGGATGTTCAAGGG 60.118 47.826 0.00 0.00 31.55 3.95
2307 2409 1.017387 GCTGAAAGAAGGGTATGGCG 58.983 55.000 0.00 0.00 34.07 5.69
2367 2469 5.809001 AGTCTTGAAGTGGCTTTGATATGA 58.191 37.500 0.00 0.00 0.00 2.15
2905 5752 2.517638 ACAGCAGCAGCAGCACAA 60.518 55.556 12.92 0.00 45.49 3.33
3089 5951 2.318966 TGGGCAAGGATGAGGGCAT 61.319 57.895 0.00 0.00 37.47 4.40
3215 6094 9.642343 TCTATGTTGGTGTACTATGTAAGATCT 57.358 33.333 0.00 0.00 0.00 2.75
3276 6203 9.770097 ACTCTGAACCAATGTATCTATGTATTG 57.230 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 6.683715 TCTATACGAAAATGAGACACACACA 58.316 36.000 0.00 0.0 0.00 3.72
105 106 6.010219 TCCAGGCAAGAAATAAAAGCTTACT 58.990 36.000 0.00 0.0 0.00 2.24
168 169 8.752187 ACCTAGTAAAGATATTTTGTCCACGTA 58.248 33.333 0.00 0.0 0.00 3.57
482 487 4.392138 CCAAAAGACTCGTGTTTCTATCCC 59.608 45.833 0.00 0.0 0.00 3.85
520 525 1.555533 GGGAACTTACTGCCTAGCACT 59.444 52.381 0.00 0.0 33.79 4.40
567 572 1.618030 GAGCAGAGGAGAGGAGGGA 59.382 63.158 0.00 0.0 0.00 4.20
668 673 8.787852 ACTGGTAGCTTTCTGAGAAAAATTAAG 58.212 33.333 9.15 5.6 0.00 1.85
703 708 0.820871 TGGGCTTTTTGAAACAGCGT 59.179 45.000 9.64 0.0 34.09 5.07
718 723 4.337060 GACACGGGCGTTTTGGGC 62.337 66.667 0.00 0.0 0.00 5.36
734 739 4.151689 CAGAAAAACGGTTCAATCGCTAGA 59.848 41.667 0.00 0.0 0.00 2.43
878 890 3.580100 GAGTGAGCGAGCAGGTGCA 62.580 63.158 4.48 0.0 45.16 4.57
1219 1268 6.034591 CCTAACACTGTACTAAGATGAACCG 58.965 44.000 0.00 0.0 0.00 4.44
1229 1278 4.775780 AGCATGAACCCTAACACTGTACTA 59.224 41.667 0.00 0.0 0.00 1.82
1308 1359 4.757149 ACTAGTTTCAATCTGCACTCAACC 59.243 41.667 0.00 0.0 0.00 3.77
1357 1409 2.038426 CTCCACAGTGGTGTATGGTTCA 59.962 50.000 19.65 0.0 43.71 3.18
1364 1416 2.221299 GGGGCTCCACAGTGGTGTA 61.221 63.158 19.65 0.0 43.71 2.90
1475 1527 1.202348 GCAGCCATAAAAACGCCTTCT 59.798 47.619 0.00 0.0 0.00 2.85
1866 1965 3.720002 TCCTGTACCCTTCCAAAGTTCTT 59.280 43.478 0.00 0.0 0.00 2.52
2162 2264 3.153369 TGGCTCTGCAAAATTCACCTA 57.847 42.857 0.00 0.0 0.00 3.08
2168 2270 1.965643 TCAGCTTGGCTCTGCAAAATT 59.034 42.857 0.00 0.0 36.40 1.82
2197 2299 1.559682 TCATAGCCTTCCTGGTGTTCC 59.440 52.381 0.00 0.0 38.35 3.62
2230 2332 6.238648 TCCTTCTTAAGAACATCTTTGTCCC 58.761 40.000 13.99 0.0 37.89 4.46
2231 2333 7.162082 TCTCCTTCTTAAGAACATCTTTGTCC 58.838 38.462 13.99 0.0 37.89 4.02
2307 2409 2.770164 TGCTCTAACTTCTCCTTGCC 57.230 50.000 0.00 0.0 0.00 4.52
2367 2469 6.180472 CCTTTGGATGTACTTACTTCACCAT 58.820 40.000 0.00 0.0 33.47 3.55
2569 2672 7.561722 TCCACAACTTAGTAGCATAAGAGATCT 59.438 37.037 0.00 0.0 36.46 2.75
2786 5632 1.352352 CTGGTGGAGTGACTGGGAAAT 59.648 52.381 0.00 0.0 0.00 2.17
2905 5752 3.080121 CTGCGCCTCCTCCTCCTT 61.080 66.667 4.18 0.0 0.00 3.36
3089 5951 0.182061 GCTGGATGAGGAGCCATGAA 59.818 55.000 0.00 0.0 36.92 2.57
3215 6094 9.642343 ACACCAGTTATCACATAGAATAGAGTA 57.358 33.333 0.00 0.0 0.00 2.59
3216 6095 8.540507 ACACCAGTTATCACATAGAATAGAGT 57.459 34.615 0.00 0.0 0.00 3.24
3217 6096 9.823647 AAACACCAGTTATCACATAGAATAGAG 57.176 33.333 0.00 0.0 36.84 2.43
3230 6157 6.036517 CAGAGTAGCATCAAACACCAGTTATC 59.963 42.308 0.00 0.0 36.84 1.75
3276 6203 8.097078 AGCATAAATTCATTGAGAGTAGCATC 57.903 34.615 0.00 0.0 0.00 3.91


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

AutoCloner maintained by Alex Coulton.