Multiple sequence alignment - TraesCS2A01G304500

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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 TraesCS2A01G304500 chr2A 100.000 2294 0 0 1 2294 523472504 523474797 0 4237
1 TraesCS2A01G304500 chr7A 95.588 2312 71 8 1 2294 149843374 149845672 0 3675
2 TraesCS2A01G304500 chr7A 95.125 2318 74 5 1 2294 681099711 681102013 0 3618
3 TraesCS2A01G304500 chr1A 95.384 2318 81 7 1 2294 555987104 555989419 0 3664
4 TraesCS2A01G304500 chr1A 95.298 2318 85 5 1 2294 95285976 95283659 0 3655
5 TraesCS2A01G304500 chr1A 95.376 2314 79 8 1 2294 471502815 471500510 0 3655
6 TraesCS2A01G304500 chr1A 95.069 2312 82 9 1 2294 530880303 530878006 0 3609
7 TraesCS2A01G304500 chr1A 94.857 2314 69 5 1 2294 497039802 497037519 0 3568
8 TraesCS2A01G304500 chr1A 94.941 2194 76 18 135 2294 59874166 59871974 0 3404
9 TraesCS2A01G304500 chr1A 95.464 1918 67 4 397 2294 49515212 49513295 0 3042
10 TraesCS2A01G304500 chr3A 95.160 2314 90 7 1 2294 713943556 713941245 0 3633
11 TraesCS2A01G304500 chr3A 94.518 2335 66 17 1 2294 540686388 540688701 0 3546
12 TraesCS2A01G304500 chr5A 95.242 2312 79 7 1 2294 299084970 299087268 0 3631
13 TraesCS2A01G304500 chr5A 95.246 2314 70 15 1 2294 657074536 657072243 0 3627
14 TraesCS2A01G304500 chr5A 96.320 1875 48 9 2 1859 644329250 644327380 0 3061
15 TraesCS2A01G304500 chr4A 94.778 2317 86 14 1 2294 518032770 518035074 0 3576
16 TraesCS2A01G304500 chrUn 96.437 1740 60 2 557 2294 365891906 365893645 0 2868


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 TraesCS2A01G304500 chr2A 523472504 523474797 2293 False 4237 4237 100.000 1 2294 1 chr2A.!!$F1 2293
1 TraesCS2A01G304500 chr7A 149843374 149845672 2298 False 3675 3675 95.588 1 2294 1 chr7A.!!$F1 2293
2 TraesCS2A01G304500 chr7A 681099711 681102013 2302 False 3618 3618 95.125 1 2294 1 chr7A.!!$F2 2293
3 TraesCS2A01G304500 chr1A 555987104 555989419 2315 False 3664 3664 95.384 1 2294 1 chr1A.!!$F1 2293
4 TraesCS2A01G304500 chr1A 95283659 95285976 2317 True 3655 3655 95.298 1 2294 1 chr1A.!!$R3 2293
5 TraesCS2A01G304500 chr1A 471500510 471502815 2305 True 3655 3655 95.376 1 2294 1 chr1A.!!$R4 2293
6 TraesCS2A01G304500 chr1A 530878006 530880303 2297 True 3609 3609 95.069 1 2294 1 chr1A.!!$R6 2293
7 TraesCS2A01G304500 chr1A 497037519 497039802 2283 True 3568 3568 94.857 1 2294 1 chr1A.!!$R5 2293
8 TraesCS2A01G304500 chr1A 59871974 59874166 2192 True 3404 3404 94.941 135 2294 1 chr1A.!!$R2 2159
9 TraesCS2A01G304500 chr1A 49513295 49515212 1917 True 3042 3042 95.464 397 2294 1 chr1A.!!$R1 1897
10 TraesCS2A01G304500 chr3A 713941245 713943556 2311 True 3633 3633 95.160 1 2294 1 chr3A.!!$R1 2293
11 TraesCS2A01G304500 chr3A 540686388 540688701 2313 False 3546 3546 94.518 1 2294 1 chr3A.!!$F1 2293
12 TraesCS2A01G304500 chr5A 299084970 299087268 2298 False 3631 3631 95.242 1 2294 1 chr5A.!!$F1 2293
13 TraesCS2A01G304500 chr5A 657072243 657074536 2293 True 3627 3627 95.246 1 2294 1 chr5A.!!$R2 2293
14 TraesCS2A01G304500 chr5A 644327380 644329250 1870 True 3061 3061 96.320 2 1859 1 chr5A.!!$R1 1857
15 TraesCS2A01G304500 chr4A 518032770 518035074 2304 False 3576 3576 94.778 1 2294 1 chr4A.!!$F1 2293
16 TraesCS2A01G304500 chrUn 365891906 365893645 1739 False 2868 2868 96.437 557 2294 1 chrUn.!!$F1 1737

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
55 56 3.408634 AGAATTTGTCCGTGGATTTCGT 58.591 40.909 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2057 0.03582 GGTGCCCTTGTATTGTCCGA 60.036 55.0 0.0 0.0 0.0 4.55 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
55 56 3.408634 AGAATTTGTCCGTGGATTTCGT 58.591 40.909 0.00 0.00 0.00 3.85
307 366 6.126097 GGGTTATGGTTAGGGTTAGGGTTATT 60.126 42.308 0.00 0.00 0.00 1.40
603 738 5.507650 GGACCCTAGTGATATCGTTGAGTTC 60.508 48.000 0.00 0.00 0.00 3.01
730 865 4.212214 CACTTGACAAGGCTCTTGAGTTAC 59.788 45.833 19.16 7.44 0.00 2.50
775 910 5.343307 AAGTTTGCATTTGGACTTGAACT 57.657 34.783 0.00 0.00 31.59 3.01
838 973 6.258230 TGAAGCGAGATGAAATTGTTGAAT 57.742 33.333 0.00 0.00 0.00 2.57
1047 1182 3.207474 GCATATGCATTGGATTCGGAC 57.793 47.619 22.84 0.00 41.59 4.79
1101 1236 1.371558 GTTCACGGTGAAGGAGGCT 59.628 57.895 22.99 0.00 37.00 4.58
1106 1241 1.078848 CGGTGAAGGAGGCTGAAGG 60.079 63.158 0.00 0.00 0.00 3.46
1219 1355 0.696501 TCTCTTGGGGTTAGGCCAAC 59.303 55.000 5.01 7.55 39.65 3.77
1275 1411 5.497474 GGATTGCTAAAGGGTCTAAGTTCA 58.503 41.667 0.00 0.00 0.00 3.18
1290 1426 7.147966 GGTCTAAGTTCAAAACCTTCTTGGAAA 60.148 37.037 0.00 0.00 39.71 3.13
1298 1434 8.021898 TCAAAACCTTCTTGGAAATGAAGATT 57.978 30.769 0.00 0.00 41.38 2.40
1501 1639 0.609131 CGAGGCAAAAGGGTGGATGT 60.609 55.000 0.00 0.00 0.00 3.06
1539 1681 0.389391 CCACAGACAACTCACGTCCT 59.611 55.000 0.00 0.00 33.70 3.85
1717 1859 1.668826 TGGGAGGAAGCATACAACCT 58.331 50.000 0.00 0.00 35.29 3.50
1822 1964 4.398319 GTTCATGAAGGAAGGAAAGTCCA 58.602 43.478 8.80 0.00 39.61 4.02
1976 2119 0.111639 AGCCAATAACCGGGTGTTGT 59.888 50.000 25.13 7.22 37.83 3.32
2058 2201 4.100498 TCTTTTGAGGACGAAGGTGTTACT 59.900 41.667 0.00 0.00 0.00 2.24
2074 2217 4.000988 TGTTACTCGCTCAAAGGGAAATC 58.999 43.478 0.00 0.00 36.71 2.17
2104 2247 1.967779 TCGGATCGGCATCAAGGAATA 59.032 47.619 0.00 0.00 0.00 1.75
2240 2384 6.312180 CGATGATCTTCAAGATTGTTGTCTCA 59.688 38.462 0.16 0.00 34.53 3.27
2287 2431 4.562394 ACTTTGTTGAACAAATTGCTCACG 59.438 37.500 22.10 11.35 45.79 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.266279 CCTTGAGGGAGGGTTTGACTA 58.734 52.381 0.00 0.00 37.23 2.59
307 366 6.126420 CCCTAACCATAACCATAACCCTAACA 60.126 42.308 0.00 0.00 0.00 2.41
603 738 2.368875 ACCTACATTATGCCTTCCCTCG 59.631 50.000 0.00 0.00 0.00 4.63
665 800 3.834726 CAACCCAACGTTGCTCCA 58.165 55.556 22.93 0.00 45.16 3.86
730 865 3.904136 ATCAACCTTCTTCGTTGCAAG 57.096 42.857 0.00 0.00 40.35 4.01
838 973 4.444876 CCTCACTTCTTGGGTCAAAAGAGA 60.445 45.833 0.00 0.00 35.20 3.10
1037 1172 1.136305 GACCTTCATCGTCCGAATCCA 59.864 52.381 0.00 0.00 0.00 3.41
1047 1182 1.134818 TGTTCATCGGGACCTTCATCG 60.135 52.381 0.00 0.00 0.00 3.84
1101 1236 4.491676 CGAATACCTTCTCGAAACCTTCA 58.508 43.478 0.00 0.00 37.23 3.02
1106 1241 3.370061 CCAACCGAATACCTTCTCGAAAC 59.630 47.826 0.00 0.00 37.23 2.78
1219 1355 2.568956 TCTCCCAAATCACAGTGAGAGG 59.431 50.000 9.64 10.10 0.00 3.69
1227 1363 2.367241 TCTTGTCGTCTCCCAAATCACA 59.633 45.455 0.00 0.00 0.00 3.58
1290 1426 3.679389 AGTTGTCGAGCCAAATCTTCAT 58.321 40.909 0.00 0.00 0.00 2.57
1298 1434 0.242825 CCGAGTAGTTGTCGAGCCAA 59.757 55.000 0.00 0.00 39.92 4.52
1501 1639 2.441375 TGGTCTTGGGACACAATCTTGA 59.559 45.455 0.00 0.00 43.77 3.02
1539 1681 3.024547 AGAGCCTGTAAGCGATGAACTA 58.975 45.455 0.00 0.00 38.01 2.24
1717 1859 4.536888 TGGCTAACAACAACCTAGGGATTA 59.463 41.667 14.81 1.66 0.00 1.75
1822 1964 3.324993 CAAAATGCACGGCCAAATACTT 58.675 40.909 2.24 0.00 0.00 2.24
1847 1989 1.315690 CCCTCATGCATTGCTCGAAT 58.684 50.000 10.49 0.00 0.00 3.34
1915 2057 0.035820 GGTGCCCTTGTATTGTCCGA 60.036 55.000 0.00 0.00 0.00 4.55
1976 2119 3.139850 CAACCAAAGCAAATGCCAATGA 58.860 40.909 0.94 0.00 43.38 2.57
2058 2201 2.224523 ACACAGATTTCCCTTTGAGCGA 60.225 45.455 0.00 0.00 0.00 4.93
2074 2217 1.000274 TGCCGATCCGATATGACACAG 60.000 52.381 0.00 0.00 0.00 3.66
2104 2247 1.274167 TCAATCTCCACCGCGTTAAGT 59.726 47.619 4.92 0.00 0.00 2.24
2240 2384 2.405172 GAACCGCTTCTCGAAGAAAGT 58.595 47.619 10.68 1.68 40.79 2.66


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

AutoCloner maintained by Alex Coulton.