Multiple sequence alignment - TraesCS3A01G066400

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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 TraesCS3A01G066400 chr3A 100.000 2389 0 0 1 2389 39677462 39679850 0.000000e+00 4412
1 TraesCS3A01G066400 chr3A 94.673 2403 104 13 1 2389 39657802 39660194 0.000000e+00 3707
2 TraesCS3A01G066400 chr3A 94.588 2291 91 10 5 2277 39697697 39699972 0.000000e+00 3513
3 TraesCS3A01G066400 chr3A 94.350 1947 80 8 449 2386 39307172 39309097 0.000000e+00 2959
4 TraesCS3A01G066400 chr3A 94.350 1947 80 8 449 2386 39323904 39325829 0.000000e+00 2959
5 TraesCS3A01G066400 chr3A 93.907 1871 67 7 527 2389 39573909 39575740 0.000000e+00 2780
6 TraesCS3A01G066400 chr3A 92.509 1949 101 8 449 2389 39858271 39860182 0.000000e+00 2748
7 TraesCS3A01G066400 chr3A 92.308 1950 110 11 449 2386 39185054 39186975 0.000000e+00 2734
8 TraesCS3A01G066400 chr3A 94.022 1606 79 14 801 2389 38692377 38693982 0.000000e+00 2418
9 TraesCS3A01G066400 chr3A 94.543 733 39 1 1 732 39442588 39443320 0.000000e+00 1131
10 TraesCS3A01G066400 chr3A 93.187 455 28 2 1 453 39857672 39858125 0.000000e+00 665
11 TraesCS3A01G066400 chr3A 93.512 447 27 1 7 453 39573275 39573719 0.000000e+00 664
12 TraesCS3A01G066400 chr3A 91.611 453 35 1 1 453 39183984 39184433 7.250000e-175 623
13 TraesCS3A01G066400 chr3A 91.410 454 31 5 1 453 38691006 38691452 1.210000e-172 616
14 TraesCS3A01G066400 chr3A 92.361 432 32 1 1 431 39248345 39248776 4.360000e-172 614
15 TraesCS3A01G066400 chr3A 94.220 346 17 2 449 794 38692084 38692426 2.100000e-145 525
16 TraesCS3A01G066400 chr3D 86.702 940 85 19 1485 2386 29371740 29372677 0.000000e+00 1007
17 TraesCS3A01G066400 chr3D 87.970 532 52 8 830 1351 29361723 29362252 3.370000e-173 617
18 TraesCS3A01G066400 chr4A 88.612 281 32 0 155 435 466960250 466959970 2.270000e-90 342


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 TraesCS3A01G066400 chr3A 39677462 39679850 2388 False 4412.000000 4412 100.000000 1 2389 1 chr3A.!!$F6 2388
1 TraesCS3A01G066400 chr3A 39657802 39660194 2392 False 3707.000000 3707 94.673000 1 2389 1 chr3A.!!$F5 2388
2 TraesCS3A01G066400 chr3A 39697697 39699972 2275 False 3513.000000 3513 94.588000 5 2277 1 chr3A.!!$F7 2272
3 TraesCS3A01G066400 chr3A 39307172 39309097 1925 False 2959.000000 2959 94.350000 449 2386 1 chr3A.!!$F2 1937
4 TraesCS3A01G066400 chr3A 39323904 39325829 1925 False 2959.000000 2959 94.350000 449 2386 1 chr3A.!!$F3 1937
5 TraesCS3A01G066400 chr3A 39573275 39575740 2465 False 1722.000000 2780 93.709500 7 2389 2 chr3A.!!$F10 2382
6 TraesCS3A01G066400 chr3A 39857672 39860182 2510 False 1706.500000 2748 92.848000 1 2389 2 chr3A.!!$F11 2388
7 TraesCS3A01G066400 chr3A 39183984 39186975 2991 False 1678.500000 2734 91.959500 1 2386 2 chr3A.!!$F9 2385
8 TraesCS3A01G066400 chr3A 38691006 38693982 2976 False 1186.333333 2418 93.217333 1 2389 3 chr3A.!!$F8 2388
9 TraesCS3A01G066400 chr3A 39442588 39443320 732 False 1131.000000 1131 94.543000 1 732 1 chr3A.!!$F4 731
10 TraesCS3A01G066400 chr3D 29371740 29372677 937 False 1007.000000 1007 86.702000 1485 2386 1 chr3D.!!$F2 901
11 TraesCS3A01G066400 chr3D 29361723 29362252 529 False 617.000000 617 87.970000 830 1351 1 chr3D.!!$F1 521

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
179 181 1.339610 CTGAAATGGCAACGGTCCAAA 59.660 47.619 0.00 0.00 37.13 3.28 F
1007 2328 1.067425 TGTACTGTACACCATGGCGAC 60.067 52.381 16.26 8.02 32.89 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 2407 2.954753 CTCTTTGTGGGCGTCGCAC 61.955 63.158 20.50 17.41 45.53 5.34 R
1826 3179 3.009473 ACATGCACTGGACCTGTAGAAAT 59.991 43.478 3.37 0.00 0.00 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
137 139 9.424659 AAAGTACGTGAACTTTATTTTTACACG 57.575 29.630 13.48 0.00 45.53 4.49
179 181 1.339610 CTGAAATGGCAACGGTCCAAA 59.660 47.619 0.00 0.00 37.13 3.28
187 189 3.502979 TGGCAACGGTCCAAAGTAATTAC 59.497 43.478 7.57 7.57 42.51 1.89
313 317 9.836864 GATGCAGAAAAAGGGGAATAATTTATT 57.163 29.630 1.25 1.25 0.00 1.40
345 349 4.350346 TGTTTGCGAGAACATTCACTTTG 58.650 39.130 0.57 0.00 34.77 2.77
509 1774 2.062971 TCTACTACCCCTTACTGCCG 57.937 55.000 0.00 0.00 0.00 5.69
1007 2328 1.067425 TGTACTGTACACCATGGCGAC 60.067 52.381 16.26 8.02 32.89 5.19
1053 2374 1.228003 TTTCGTGGCCACCGTCATT 60.228 52.632 29.95 0.00 0.00 2.57
1086 2407 0.820871 CCACCCTTCTTCTCTCCTCG 59.179 60.000 0.00 0.00 0.00 4.63
1168 2489 7.586349 AGAAGATTAAGGGCATTTTCCAGATA 58.414 34.615 0.00 0.00 0.00 1.98
1179 2502 8.424133 GGGCATTTTCCAGATAATACTTGAAAT 58.576 33.333 0.00 0.00 33.67 2.17
1490 2813 1.668151 GACTGTTGCCCGGACTCAC 60.668 63.158 0.73 0.00 0.00 3.51
1560 2890 3.568007 TGTTCGGCAGCTTTTGTTTATCT 59.432 39.130 0.00 0.00 0.00 1.98
1826 3179 5.431420 AAAAATGACACACGATGCAAGTA 57.569 34.783 0.00 0.00 0.00 2.24
2103 3464 3.071479 GCATTACCGAAGTCCTTGTCAA 58.929 45.455 0.00 0.00 0.00 3.18
2122 3483 9.850628 CTTGTCAACATTATCATGATCTTGTTT 57.149 29.630 23.50 12.72 34.11 2.83
2193 3557 6.597832 AATTCCATCCCGTTTTCATTACAA 57.402 33.333 0.00 0.00 0.00 2.41
2225 3592 6.385649 TTTTGAAGTTTTCTCCTACGCAAT 57.614 33.333 0.00 0.00 0.00 3.56
2286 3655 7.660208 GGTTCTTCAACAAGGTTCTATTGAGTA 59.340 37.037 0.00 0.00 32.90 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 134 6.364945 TGTCAATTTGAAATCACACGTGTA 57.635 33.333 22.90 10.48 0.00 2.90
137 139 6.476380 TCAGCTTTGTCAATTTGAAATCACAC 59.524 34.615 0.00 0.00 0.00 3.82
179 181 9.213799 GGATGTAGCTACTACTACGTAATTACT 57.786 37.037 23.84 3.86 44.55 2.24
187 189 3.363772 GCACGGATGTAGCTACTACTACG 60.364 52.174 23.84 20.76 44.55 3.51
202 206 9.561069 AAACTAGAATTAAAGATATGCACGGAT 57.439 29.630 0.00 0.00 0.00 4.18
313 317 4.693095 TGTTCTCGCAAACATAGTATGCAA 59.307 37.500 10.16 0.00 40.04 4.08
345 349 3.065095 GCATCTCTGCTCCTTTTGATCAC 59.935 47.826 0.00 0.00 45.32 3.06
509 1774 4.874977 GCTCGGGCCGACTAGCAC 62.875 72.222 27.46 6.55 0.00 4.40
524 1789 0.685458 GCAGGGAATCACCAATGGCT 60.685 55.000 0.00 0.00 41.20 4.75
887 2198 9.830975 TTGTGTGTTTATATAGATGTGTATGCT 57.169 29.630 0.00 0.00 0.00 3.79
985 2302 1.067142 CGCCATGGTGTACAGTACAGT 60.067 52.381 17.59 0.80 39.77 3.55
1007 2328 3.121030 CCGTGCCCTTCTTCAGCG 61.121 66.667 0.00 0.00 0.00 5.18
1086 2407 2.954753 CTCTTTGTGGGCGTCGCAC 61.955 63.158 20.50 17.41 45.53 5.34
1560 2890 5.700722 ACACGAACTAGAGATACACACAA 57.299 39.130 0.00 0.00 0.00 3.33
1807 3160 5.412594 AGAAATACTTGCATCGTGTGTCATT 59.587 36.000 6.43 0.00 0.00 2.57
1808 3161 4.937620 AGAAATACTTGCATCGTGTGTCAT 59.062 37.500 6.43 0.00 0.00 3.06
1826 3179 3.009473 ACATGCACTGGACCTGTAGAAAT 59.991 43.478 3.37 0.00 0.00 2.17
2193 3557 6.097412 AGGAGAAAACTTCAAAAAGCTCATGT 59.903 34.615 0.00 0.00 35.81 3.21
2286 3655 5.525745 TCAGTGTGACAATTTATGACGTTGT 59.474 36.000 0.00 0.00 38.66 3.32


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

AutoCloner maintained by Alex Coulton.