Multiple sequence alignment - TraesCS5B01G128500

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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 TraesCS5B01G128500 chr5B 100.000 2264 0 0 1 2264 234885605 234883342 0.000000e+00 4181
1 TraesCS5B01G128500 chr5B 94.923 2265 89 8 1 2264 506965557 506967796 0.000000e+00 3522
2 TraesCS5B01G128500 chr5B 97.381 1489 36 3 723 2210 584816207 584814721 0.000000e+00 2531
3 TraesCS5B01G128500 chr5B 95.250 779 24 5 1 779 584816880 584816115 0.000000e+00 1221
4 TraesCS5B01G128500 chr5B 87.395 119 13 2 2147 2264 535136340 535136457 3.920000e-28 135
5 TraesCS5B01G128500 chr5B 95.294 85 4 0 2180 2264 701831205 701831121 3.920000e-28 135
6 TraesCS5B01G128500 chr3B 96.118 2267 72 5 1 2264 604266029 604263776 0.000000e+00 3685
7 TraesCS5B01G128500 chr3B 93.588 2199 90 16 1 2196 558278359 558276209 0.000000e+00 3232
8 TraesCS5B01G128500 chr3B 95.664 1453 48 3 605 2057 776220016 776221453 0.000000e+00 2320
9 TraesCS5B01G128500 chr3B 91.000 100 9 0 2165 2264 420918900 420918801 3.920000e-28 135
10 TraesCS5B01G128500 chr2B 96.519 2212 59 6 1 2210 549352859 549355054 0.000000e+00 3642
11 TraesCS5B01G128500 chr2B 95.680 2060 69 9 1 2057 454473372 454475414 0.000000e+00 3293
12 TraesCS5B01G128500 chr2B 97.167 1765 36 6 1 1765 68145345 68147095 0.000000e+00 2970
13 TraesCS5B01G128500 chr2B 92.655 354 24 2 1911 2264 549354873 549355224 2.010000e-140 508
14 TraesCS5B01G128500 chr2B 91.304 184 12 3 2029 2210 549354756 549354937 4.830000e-62 248
15 TraesCS5B01G128500 chr2B 93.750 80 5 0 2182 2261 454451253 454451332 1.100000e-23 121
16 TraesCS5B01G128500 chr2B 93.750 80 5 0 2182 2261 454475386 454475465 1.100000e-23 121
17 TraesCS5B01G128500 chr4B 95.656 2141 70 10 1 2140 551060051 551062169 0.000000e+00 3417
18 TraesCS5B01G128500 chr4B 94.643 784 36 4 1 779 588824104 588824886 0.000000e+00 1210
19 TraesCS5B01G128500 chr6B 95.514 2140 81 4 1 2140 181111550 181109426 0.000000e+00 3406
20 TraesCS5B01G128500 chr6B 97.489 1991 35 4 188 2178 599876301 599878276 0.000000e+00 3386
21 TraesCS5B01G128500 chr6B 97.564 1765 30 5 1 1765 679251645 679253396 0.000000e+00 3009
22 TraesCS5B01G128500 chr6B 96.660 958 19 5 1 958 26497625 26496681 0.000000e+00 1580
23 TraesCS5B01G128500 chr1B 96.482 2018 57 6 1 2018 571422390 571420387 0.000000e+00 3321
24 TraesCS5B01G128500 chr4D 93.393 787 45 4 1 781 122177830 122178615 0.000000e+00 1158


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 TraesCS5B01G128500 chr5B 234883342 234885605 2263 True 4181 4181 100.000000 1 2264 1 chr5B.!!$R1 2263
1 TraesCS5B01G128500 chr5B 506965557 506967796 2239 False 3522 3522 94.923000 1 2264 1 chr5B.!!$F1 2263
2 TraesCS5B01G128500 chr5B 584814721 584816880 2159 True 1876 2531 96.315500 1 2210 2 chr5B.!!$R3 2209
3 TraesCS5B01G128500 chr3B 604263776 604266029 2253 True 3685 3685 96.118000 1 2264 1 chr3B.!!$R3 2263
4 TraesCS5B01G128500 chr3B 558276209 558278359 2150 True 3232 3232 93.588000 1 2196 1 chr3B.!!$R2 2195
5 TraesCS5B01G128500 chr3B 776220016 776221453 1437 False 2320 2320 95.664000 605 2057 1 chr3B.!!$F1 1452
6 TraesCS5B01G128500 chr2B 68145345 68147095 1750 False 2970 2970 97.167000 1 1765 1 chr2B.!!$F1 1764
7 TraesCS5B01G128500 chr2B 454473372 454475465 2093 False 1707 3293 94.715000 1 2261 2 chr2B.!!$F3 2260
8 TraesCS5B01G128500 chr2B 549352859 549355224 2365 False 1466 3642 93.492667 1 2264 3 chr2B.!!$F4 2263
9 TraesCS5B01G128500 chr4B 551060051 551062169 2118 False 3417 3417 95.656000 1 2140 1 chr4B.!!$F1 2139
10 TraesCS5B01G128500 chr4B 588824104 588824886 782 False 1210 1210 94.643000 1 779 1 chr4B.!!$F2 778
11 TraesCS5B01G128500 chr6B 181109426 181111550 2124 True 3406 3406 95.514000 1 2140 1 chr6B.!!$R2 2139
12 TraesCS5B01G128500 chr6B 599876301 599878276 1975 False 3386 3386 97.489000 188 2178 1 chr6B.!!$F1 1990
13 TraesCS5B01G128500 chr6B 679251645 679253396 1751 False 3009 3009 97.564000 1 1765 1 chr6B.!!$F2 1764
14 TraesCS5B01G128500 chr6B 26496681 26497625 944 True 1580 1580 96.660000 1 958 1 chr6B.!!$R1 957
15 TraesCS5B01G128500 chr1B 571420387 571422390 2003 True 3321 3321 96.482000 1 2018 1 chr1B.!!$R1 2017
16 TraesCS5B01G128500 chr4D 122177830 122178615 785 False 1158 1158 93.393000 1 781 1 chr4D.!!$F1 780

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
680 681 1.066303 CGGAGCAGTAGCCTTGTAGAG 59.934 57.143 0.0 0.0 43.56 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2315 0.117541 TAGGGTCCAGCAACCTACCA 59.882 55.0 3.36 0.0 39.42 3.25 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
224 225 1.731613 GGTGCGCCTTAAAAACCGC 60.732 57.895 9.68 0.0 45.99 5.68
472 473 1.564348 GGTGCCTATGAGGGGAAGAAA 59.436 52.381 0.00 0.0 35.37 2.52
676 677 1.592223 GACGGAGCAGTAGCCTTGT 59.408 57.895 0.00 0.0 43.56 3.16
679 680 1.103803 CGGAGCAGTAGCCTTGTAGA 58.896 55.000 0.00 0.0 43.56 2.59
680 681 1.066303 CGGAGCAGTAGCCTTGTAGAG 59.934 57.143 0.00 0.0 43.56 2.43
681 682 2.104170 GGAGCAGTAGCCTTGTAGAGT 58.896 52.381 0.00 0.0 43.56 3.24
682 683 3.288964 GGAGCAGTAGCCTTGTAGAGTA 58.711 50.000 0.00 0.0 43.56 2.59
683 684 3.316868 GGAGCAGTAGCCTTGTAGAGTAG 59.683 52.174 0.00 0.0 43.56 2.57
684 685 2.691011 AGCAGTAGCCTTGTAGAGTAGC 59.309 50.000 0.00 0.0 43.56 3.58
685 686 2.223852 GCAGTAGCCTTGTAGAGTAGCC 60.224 54.545 0.00 0.0 33.58 3.93
686 687 3.292460 CAGTAGCCTTGTAGAGTAGCCT 58.708 50.000 0.00 0.0 0.00 4.58
687 688 3.702045 CAGTAGCCTTGTAGAGTAGCCTT 59.298 47.826 0.00 0.0 0.00 4.35
688 689 3.702045 AGTAGCCTTGTAGAGTAGCCTTG 59.298 47.826 0.00 0.0 0.00 3.61
689 690 2.541466 AGCCTTGTAGAGTAGCCTTGT 58.459 47.619 0.00 0.0 0.00 3.16
690 691 3.709587 AGCCTTGTAGAGTAGCCTTGTA 58.290 45.455 0.00 0.0 0.00 2.41
691 692 3.702045 AGCCTTGTAGAGTAGCCTTGTAG 59.298 47.826 0.00 0.0 0.00 2.74
896 897 7.174253 GCTCAATCCGGATGGTTAAATAATGTA 59.826 37.037 19.95 0.0 36.30 2.29
1141 1142 2.229792 GGTGTGGAGATGTTTGCAAGA 58.770 47.619 0.00 0.0 0.00 3.02
1220 1221 3.146066 GCCCCAATTATGCTTACGATCA 58.854 45.455 0.00 0.0 0.00 2.92
1536 1537 1.347817 CGAAGCTTGCTCGTGAGGAC 61.348 60.000 2.10 0.0 0.00 3.85
1626 1627 0.916086 AATGGCCCCGTATGACTCAA 59.084 50.000 0.00 0.0 0.00 3.02
1879 1906 5.988561 GCTGTGAAGAGAAGTGGGATATAAG 59.011 44.000 0.00 0.0 0.00 1.73
1886 1913 8.560124 AAGAGAAGTGGGATATAAGAGAACAT 57.440 34.615 0.00 0.0 0.00 2.71
1893 1920 9.884814 AGTGGGATATAAGAGAACATAGTACTT 57.115 33.333 0.00 0.0 0.00 2.24
1925 1952 1.648116 TAGAACCCTACCGCCAAAGT 58.352 50.000 0.00 0.0 0.00 2.66
1932 1959 0.035439 CTACCGCCAAAGTCCATGGT 60.035 55.000 12.58 0.0 40.23 3.55
1996 2144 0.539438 GGGGCAATGGTTCTGTGACA 60.539 55.000 0.00 0.0 0.00 3.58
2008 2156 2.930950 TCTGTGACAAAGAACCCAAGG 58.069 47.619 0.00 0.0 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 0.251916 ACCCGGCTCATCGATTTGAA 59.748 50.000 0.00 0.0 0.00 2.69
472 473 5.012148 TCACTCCGGAATCTCTTCTTTCTTT 59.988 40.000 5.23 0.0 0.00 2.52
676 677 2.769602 CCCCCTACAAGGCTACTCTA 57.230 55.000 0.00 0.0 32.73 2.43
997 998 0.749454 GAACCGGATGAAGCCATGCT 60.749 55.000 9.46 0.0 42.56 3.79
1141 1142 1.605058 CGGTCGGTGGACTCCTTCAT 61.605 60.000 0.00 0.0 42.97 2.57
1220 1221 1.794222 GCGTTAGTTGGAAGCGCAT 59.206 52.632 11.47 0.0 46.23 4.73
1536 1537 0.801251 CAAGCTTTCTTGCCCTCTCG 59.199 55.000 0.00 0.0 42.66 4.04
1879 1906 7.384387 ACTCCGAAAACAAAGTACTATGTTCTC 59.616 37.037 0.00 0.0 38.75 2.87
1886 1913 7.653311 GGTTCTAACTCCGAAAACAAAGTACTA 59.347 37.037 0.00 0.0 0.00 1.82
1893 1920 4.426736 AGGGTTCTAACTCCGAAAACAA 57.573 40.909 0.00 0.0 0.00 2.83
1925 1952 0.327924 CAGCAACCTACCACCATGGA 59.672 55.000 21.47 0.0 40.96 3.41
1996 2144 0.537371 CCAGCGTCCTTGGGTTCTTT 60.537 55.000 0.00 0.0 31.87 2.52
2008 2156 4.509737 GGTCCTACCGCCAGCGTC 62.510 72.222 11.55 0.0 37.81 5.19
2167 2315 0.117541 TAGGGTCCAGCAACCTACCA 59.882 55.000 3.36 0.0 39.42 3.25


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

AutoCloner maintained by Alex Coulton.