Multiple sequence alignment - TraesCS3A01G178200

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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 TraesCS3A01G178200 chr3A 100.000 3564 0 0 1 3564 202637266 202640829 0.000000e+00 6582
1 TraesCS3A01G178200 chr7A 95.874 3611 83 26 1 3564 84768683 84765092 0.000000e+00 5782
2 TraesCS3A01G178200 chr7A 93.668 2653 111 35 951 3564 107623463 107620829 0.000000e+00 3916
3 TraesCS3A01G178200 chr7A 92.746 965 54 9 1 953 107624458 107623498 0.000000e+00 1380
4 TraesCS3A01G178200 chr3D 94.439 2931 98 35 1 2896 591984244 591987144 0.000000e+00 4449
5 TraesCS3A01G178200 chr3D 94.136 648 14 14 2933 3563 591987139 591987779 0.000000e+00 965
6 TraesCS3A01G178200 chr6A 93.759 2660 103 37 951 3564 194724464 194721822 0.000000e+00 3934
7 TraesCS3A01G178200 chr6A 93.829 1815 77 21 951 2739 194775247 194773442 0.000000e+00 2699
8 TraesCS3A01G178200 chr6A 93.778 1816 78 21 951 2739 194747390 194745583 0.000000e+00 2695
9 TraesCS3A01G178200 chr6A 93.438 960 48 10 1 953 194776234 194775283 0.000000e+00 1410
10 TraesCS3A01G178200 chr6A 93.236 961 46 9 1 953 194725449 194724500 0.000000e+00 1397
11 TraesCS3A01G178200 chr6A 92.754 966 50 9 1 953 194748384 194747426 0.000000e+00 1378
12 TraesCS3A01G178200 chr3B 85.439 3379 311 100 1 3255 757876698 757873377 0.000000e+00 3347
13 TraesCS3A01G178200 chr3B 91.765 255 10 5 3314 3560 757873368 757873117 9.470000e-91 344
14 TraesCS3A01G178200 chr3B 91.700 253 11 4 3314 3559 757884778 757884529 3.410000e-90 342
15 TraesCS3A01G178200 chr3B 79.083 349 37 20 2934 3255 757885126 757884787 1.300000e-49 207


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 TraesCS3A01G178200 chr3A 202637266 202640829 3563 False 6582.0 6582 100.0000 1 3564 1 chr3A.!!$F1 3563
1 TraesCS3A01G178200 chr7A 84765092 84768683 3591 True 5782.0 5782 95.8740 1 3564 1 chr7A.!!$R1 3563
2 TraesCS3A01G178200 chr7A 107620829 107624458 3629 True 2648.0 3916 93.2070 1 3564 2 chr7A.!!$R2 3563
3 TraesCS3A01G178200 chr3D 591984244 591987779 3535 False 2707.0 4449 94.2875 1 3563 2 chr3D.!!$F1 3562
4 TraesCS3A01G178200 chr6A 194721822 194725449 3627 True 2665.5 3934 93.4975 1 3564 2 chr6A.!!$R1 3563
5 TraesCS3A01G178200 chr6A 194773442 194776234 2792 True 2054.5 2699 93.6335 1 2739 2 chr6A.!!$R3 2738
6 TraesCS3A01G178200 chr6A 194745583 194748384 2801 True 2036.5 2695 93.2660 1 2739 2 chr6A.!!$R2 2738
7 TraesCS3A01G178200 chr3B 757873117 757876698 3581 True 1845.5 3347 88.6020 1 3560 2 chr3B.!!$R1 3559
8 TraesCS3A01G178200 chr3B 757884529 757885126 597 True 274.5 342 85.3915 2934 3559 2 chr3B.!!$R2 625

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
289 304 2.560504 TGTGACGAGCAACACAGAAAT 58.439 42.857 0.00 0.00 41.19 2.17 F
1148 1230 0.323542 AGCAGGTACCGTAGCTCACT 60.324 55.000 19.58 5.77 33.57 3.41 F
1428 1519 2.040939 TGGACAGTTGGGTAACTCGAA 58.959 47.619 0.00 0.00 45.12 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1519 0.255033 GACCCGGCCACCTATTTTCT 59.745 55.00 2.24 0.0 0.0 2.52 R
2462 2608 2.423947 GGATCCTTGCATCTGGGACATT 60.424 50.00 3.84 0.0 38.2 2.71 R
2660 2809 3.380954 TCAGCACTTTTTCATGTCTGCAA 59.619 39.13 0.00 0.0 0.0 4.08 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
59 60 5.503662 TGCCATATTTTCAGTGCACATAG 57.496 39.130 21.04 8.65 0.00 2.23
214 227 6.435430 TCAAATCATTGCTATAAACGCTGT 57.565 33.333 0.00 0.00 36.45 4.40
289 304 2.560504 TGTGACGAGCAACACAGAAAT 58.439 42.857 0.00 0.00 41.19 2.17
1148 1230 0.323542 AGCAGGTACCGTAGCTCACT 60.324 55.000 19.58 5.77 33.57 3.41
1172 1254 3.324930 CTGCAGTGAGAGGGGCCA 61.325 66.667 4.39 0.00 0.00 5.36
1428 1519 2.040939 TGGACAGTTGGGTAACTCGAA 58.959 47.619 0.00 0.00 45.12 3.71
1730 1840 5.165961 TGGTGGAGGAAGAAACTGATTAG 57.834 43.478 0.00 0.00 0.00 1.73
1874 1988 7.739498 TTTCCTTCTTTCATACACACTAACC 57.261 36.000 0.00 0.00 0.00 2.85
1956 2071 4.202326 ACTTTCCAACACTACACGAGGAAT 60.202 41.667 0.00 0.00 35.32 3.01
2004 2119 5.848406 TCAAGGGTCGCACATTTTATTTTT 58.152 33.333 0.00 0.00 0.00 1.94
2131 2254 3.871485 TGCAAGTTTTCCTGCAAACATT 58.129 36.364 2.09 0.00 38.86 2.71
2229 2353 4.524802 ATGGATTTCAGTGCATTCCCTA 57.475 40.909 0.00 0.00 0.00 3.53
2284 2408 4.919168 CGAGTACGAAACCAAACATCTACA 59.081 41.667 0.00 0.00 42.66 2.74
2644 2793 7.946381 ACAGGATTTTATTAAGTTTCCCCCTA 58.054 34.615 0.00 0.00 0.00 3.53
2660 2809 3.727391 CCCCCTATGTTTTTATCCTCCCT 59.273 47.826 0.00 0.00 0.00 4.20
2763 2915 6.906157 AGCAAAATCAAAGGAAAGATGAGA 57.094 33.333 0.00 0.00 0.00 3.27
2860 3013 2.612212 ACACCTTTCTTGTTGCTGTACG 59.388 45.455 0.00 0.00 0.00 3.67
3009 3168 4.202090 TGCTCATGTGTTTATGTTTGCACA 60.202 37.500 0.00 0.00 44.43 4.57
3435 3641 3.261643 GGAGGAGAAACAATGCCCATTTT 59.738 43.478 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.537192 CACTGAAAATATGGCATTTATGTTGAT 57.463 29.630 4.78 0.00 0.00 2.57
189 201 7.483307 ACAGCGTTTATAGCAATGATTTGAAT 58.517 30.769 0.00 0.00 34.60 2.57
289 304 1.551883 GTTTGAACTACCGCTCCCCTA 59.448 52.381 0.00 0.00 0.00 3.53
471 488 2.310538 AGTCAACCCTGGAAAAGCTTG 58.689 47.619 0.00 0.00 0.00 4.01
476 493 4.358214 AGGAAAAAGTCAACCCTGGAAAA 58.642 39.130 0.00 0.00 0.00 2.29
1148 1230 1.032794 CCTCTCACTGCAGCCGTATA 58.967 55.000 15.27 0.00 0.00 1.47
1154 1236 4.792804 GGCCCCTCTCACTGCAGC 62.793 72.222 15.27 0.00 0.00 5.25
1172 1254 7.341256 ACATCTTTCTCTCATGTGGCATTATTT 59.659 33.333 0.00 0.00 29.36 1.40
1428 1519 0.255033 GACCCGGCCACCTATTTTCT 59.745 55.000 2.24 0.00 0.00 2.52
1730 1840 4.853924 TTTCCAGCTCCAATGAAACTTC 57.146 40.909 0.00 0.00 0.00 3.01
1852 1963 6.042781 ACAGGTTAGTGTGTATGAAAGAAGGA 59.957 38.462 0.00 0.00 0.00 3.36
1956 2071 5.281693 TCGACGACGAACAGAAAGTAATA 57.718 39.130 7.68 0.00 45.74 0.98
2004 2119 9.499479 GCTATTCTCATCATAGAAAGAATCCAA 57.501 33.333 9.75 0.00 38.90 3.53
2218 2342 3.014623 GGGTAAACAGTAGGGAATGCAC 58.985 50.000 0.00 0.00 0.00 4.57
2229 2353 4.237018 TGAGGGACTTTAGGGTAAACAGT 58.763 43.478 0.00 0.00 41.55 3.55
2284 2408 7.710907 GCAAAAGGAGTCAGGAAAAATAAAAGT 59.289 33.333 0.00 0.00 0.00 2.66
2330 2462 9.077674 GTACATGTGTTTGTGAACAAAAATGTA 57.922 29.630 21.69 21.69 46.62 2.29
2331 2463 7.064016 GGTACATGTGTTTGTGAACAAAAATGT 59.936 33.333 22.91 22.91 46.62 2.71
2332 2464 7.277539 AGGTACATGTGTTTGTGAACAAAAATG 59.722 33.333 9.11 14.72 46.62 2.32
2462 2608 2.423947 GGATCCTTGCATCTGGGACATT 60.424 50.000 3.84 0.00 38.20 2.71
2644 2793 4.706962 GTCTGCAAGGGAGGATAAAAACAT 59.293 41.667 0.00 0.00 0.00 2.71
2660 2809 3.380954 TCAGCACTTTTTCATGTCTGCAA 59.619 39.130 0.00 0.00 0.00 4.08
2968 3126 7.445402 ACATGAGCAAAACACTGTTATAGTTCT 59.555 33.333 0.00 0.00 37.60 3.01
3214 3407 9.264719 CAAAAGATGAGCAAAAAGATTTTAGGT 57.735 29.630 0.00 0.00 0.00 3.08
3435 3641 7.479352 TTCCTTGCATTATGAGAAAAATCCA 57.521 32.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.