Multiple sequence alignment - TraesCS3A01G246200

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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 TraesCS3A01G246200 chr3A 100.000 4178 0 0 1 4178 461862463 461858286 0.000000e+00 7716
1 TraesCS3A01G246200 chr3B 95.091 4217 144 12 1 4178 440127292 440131484 0.000000e+00 6582
2 TraesCS3A01G246200 chr3D 97.192 2101 36 4 2095 4178 341465254 341467348 0.000000e+00 3531
3 TraesCS3A01G246200 chr3D 95.539 1457 47 7 1 1455 341463655 341465095 0.000000e+00 2314
4 TraesCS3A01G246200 chr3D 100.000 78 0 0 2021 2098 341465096 341465173 1.210000e-30 145
5 TraesCS3A01G246200 chrUn 100.000 399 0 0 2221 2619 478834780 478835178 0.000000e+00 737


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 TraesCS3A01G246200 chr3A 461858286 461862463 4177 True 7716.000000 7716 100.000 1 4178 1 chr3A.!!$R1 4177
1 TraesCS3A01G246200 chr3B 440127292 440131484 4192 False 6582.000000 6582 95.091 1 4178 1 chr3B.!!$F1 4177
2 TraesCS3A01G246200 chr3D 341463655 341467348 3693 False 1996.666667 3531 97.577 1 4178 3 chr3D.!!$F1 4177

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
972 998 1.276622 ATGGAAGCAGTACCTTCGGT 58.723 50.0 5.98 0.00 41.63 4.69 F
1840 1866 0.394216 TGTGCATGGGCTATGTGGAC 60.394 55.0 12.66 7.59 41.91 4.02 F
1951 1977 1.065358 CAAGCCGCAATTCAGCAAAG 58.935 50.0 0.00 0.00 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2650 2760 0.467290 TCAGAGCAAAACCCCCACAC 60.467 55.000 0.00 0.0 0.00 3.82 R
3000 3110 0.315382 CGTCGATCGGCAAATTCAGC 60.315 55.000 21.12 0.0 35.71 4.26 R
3471 3612 4.083110 AGACAACATTCAATACAGTGCAGC 60.083 41.667 0.00 0.0 0.00 5.25 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
78 79 2.289694 ACCTAGTGTGAGGAACATGCAC 60.290 50.000 0.00 0.00 41.97 4.57
79 80 2.350522 CTAGTGTGAGGAACATGCACC 58.649 52.381 0.00 0.00 41.97 5.01
235 237 2.590092 GCCAAGCTACCCGGTCAT 59.410 61.111 0.00 0.00 0.00 3.06
270 272 2.671070 CCAAGGATCGGTGGCAGT 59.329 61.111 0.69 0.00 0.00 4.40
271 273 1.746615 CCAAGGATCGGTGGCAGTG 60.747 63.158 0.69 0.00 0.00 3.66
272 274 1.296392 CAAGGATCGGTGGCAGTGA 59.704 57.895 0.00 0.00 0.00 3.41
377 379 3.420893 CACCTCTTCAAGTGGGCAATAA 58.579 45.455 10.30 0.00 33.33 1.40
405 407 2.009774 AGCATGTCAAAGACGGCATAC 58.990 47.619 13.52 0.00 37.73 2.39
460 462 8.454570 TCAAGCTTGCTAAATGATTATCATCA 57.545 30.769 21.99 0.00 43.85 3.07
532 556 4.460382 ACTTCTGACGCCAATTCAATCAAT 59.540 37.500 0.00 0.00 0.00 2.57
558 582 4.870123 AGCATCTCATAACTAGCTCAGG 57.130 45.455 0.00 0.00 0.00 3.86
602 626 9.956720 CCATAATAAACTAATGCTCAGAAAAGG 57.043 33.333 0.00 0.00 0.00 3.11
613 637 4.165950 TGCTCAGAAAAGGAGGCCAATATA 59.834 41.667 5.01 0.00 32.96 0.86
614 638 5.163055 TGCTCAGAAAAGGAGGCCAATATAT 60.163 40.000 5.01 0.00 32.96 0.86
627 651 7.015584 GGAGGCCAATATATGAAACAAAAGGAT 59.984 37.037 5.01 0.00 0.00 3.24
683 707 3.300388 TGGGACAAACTATTTTGCACCA 58.700 40.909 14.07 14.07 45.32 4.17
707 731 3.188460 GCAGCTTTCGTCAATTTGGACTA 59.812 43.478 0.00 0.00 35.63 2.59
708 732 4.320202 GCAGCTTTCGTCAATTTGGACTAA 60.320 41.667 0.00 0.00 35.63 2.24
726 750 8.404107 TGGACTAAAAACTTCCTAAAATGGAG 57.596 34.615 0.00 0.00 37.43 3.86
972 998 1.276622 ATGGAAGCAGTACCTTCGGT 58.723 50.000 5.98 0.00 41.63 4.69
1021 1047 3.423539 TGGACACATTCCTCTTCCTTG 57.576 47.619 0.00 0.00 46.10 3.61
1041 1067 2.097825 GCCATTCTTCCATTGCTCACT 58.902 47.619 0.00 0.00 0.00 3.41
1323 1349 1.277842 ACTGATGTCAATGGCACCGTA 59.722 47.619 0.00 0.00 0.00 4.02
1495 1521 0.608640 AGGTACAAAGCTGGTCTCCG 59.391 55.000 0.00 0.00 30.51 4.63
1515 1541 7.066645 GTCTCCGGTTATTACAGCCTTTATTTT 59.933 37.037 0.00 0.00 0.00 1.82
1521 1547 9.869757 GGTTATTACAGCCTTTATTTTGACAAT 57.130 29.630 0.00 0.00 0.00 2.71
1597 1623 2.483714 CCAAGTGCAGACTACACAGTGT 60.484 50.000 11.87 11.87 40.59 3.55
1598 1624 3.198068 CAAGTGCAGACTACACAGTGTT 58.802 45.455 12.53 0.00 40.59 3.32
1604 1630 4.697828 TGCAGACTACACAGTGTTTCAAAA 59.302 37.500 12.53 0.00 34.21 2.44
1686 1712 3.087031 CTCAAGTGATGGGCTGAATGTT 58.913 45.455 0.00 0.00 0.00 2.71
1710 1736 2.091885 GGCTTCTGATTGGGGTAATGGA 60.092 50.000 0.00 0.00 0.00 3.41
1717 1743 2.507407 TTGGGGTAATGGAGTCAAGC 57.493 50.000 0.00 0.00 0.00 4.01
1789 1815 4.588899 TGTGTCAAATGGGAGTTGGATAG 58.411 43.478 0.00 0.00 0.00 2.08
1813 1839 3.836146 TCATGGCAGGCTATAGCAAAAT 58.164 40.909 25.53 9.03 44.36 1.82
1840 1866 0.394216 TGTGCATGGGCTATGTGGAC 60.394 55.000 12.66 7.59 41.91 4.02
1938 1964 1.576421 GAACAGAGGTTGCAAGCCG 59.424 57.895 24.26 15.54 37.36 5.52
1951 1977 1.065358 CAAGCCGCAATTCAGCAAAG 58.935 50.000 0.00 0.00 0.00 2.77
1999 2025 1.704628 TCATCAAGCTCCCTCAAACCA 59.295 47.619 0.00 0.00 0.00 3.67
2217 2327 1.189752 TGAGCATCTCCAGACAGTCC 58.810 55.000 0.00 0.00 34.92 3.85
2650 2760 9.014297 GGATCAACCATATGAATTTAGTAAGGG 57.986 37.037 3.65 0.00 38.79 3.95
2703 2813 3.349927 ACTGCTGGTGTACGAGTATGTA 58.650 45.455 0.00 0.00 0.00 2.29
2708 2818 4.024725 GCTGGTGTACGAGTATGTAGAGAG 60.025 50.000 0.00 0.00 0.00 3.20
2835 2945 2.356432 CCTCCATCATGAGTGCCTTGAA 60.356 50.000 0.09 0.00 33.42 2.69
3333 3444 1.026718 CGAAGACAATCACCCAGCCC 61.027 60.000 0.00 0.00 0.00 5.19
3631 3772 5.450453 TGTAACAACTTCCAAAGATTCCCA 58.550 37.500 0.00 0.00 0.00 4.37
3687 3828 1.004044 CCCTTCAGTGCAACCAGAGAT 59.996 52.381 0.00 0.00 37.80 2.75
3688 3829 2.553904 CCCTTCAGTGCAACCAGAGATT 60.554 50.000 0.00 0.00 37.80 2.40
3690 3831 2.936919 TCAGTGCAACCAGAGATTGT 57.063 45.000 0.00 0.00 37.80 2.71
3740 3881 7.283127 AGTTAACAACTGACAACATTCACTCAT 59.717 33.333 8.61 0.00 41.01 2.90
4043 4185 3.055167 AGCACCAGGGCCAAATTATTTTC 60.055 43.478 6.18 0.00 0.00 2.29
4044 4186 3.872696 CACCAGGGCCAAATTATTTTCC 58.127 45.455 6.18 0.00 0.00 3.13
4057 4199 2.470057 ATTTTCCCCGGCAATATGGT 57.530 45.000 0.00 0.00 0.00 3.55
4081 4223 9.821662 GGTAAAACTTTAGCACTTATAACTGTG 57.178 33.333 6.54 1.45 40.03 3.66
4118 4260 4.333649 TCTTTCAGAACACTGCTCAAGTTG 59.666 41.667 0.00 0.00 36.83 3.16
4134 4276 6.205658 GCTCAAGTTGGGAATATCTACAATCC 59.794 42.308 7.01 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 256 1.021390 GTCACTGCCACCGATCCTTG 61.021 60.000 0.00 0.00 0.00 3.61
267 269 2.558378 CTGATAGCCATGGTGTCACTG 58.442 52.381 14.67 1.49 29.12 3.66
268 270 1.487976 CCTGATAGCCATGGTGTCACT 59.512 52.381 14.67 3.68 29.12 3.41
269 271 1.475751 CCCTGATAGCCATGGTGTCAC 60.476 57.143 14.67 0.00 29.12 3.67
270 272 0.839277 CCCTGATAGCCATGGTGTCA 59.161 55.000 14.67 13.63 31.14 3.58
271 273 0.536006 GCCCTGATAGCCATGGTGTC 60.536 60.000 14.67 9.67 33.62 3.67
272 274 1.281199 TGCCCTGATAGCCATGGTGT 61.281 55.000 14.67 3.61 33.62 4.16
377 379 4.433615 CGTCTTTGACATGCTATGGTAGT 58.566 43.478 0.00 0.00 32.09 2.73
405 407 9.474920 ACATTTTATTTGTGAGTGTGTTTATGG 57.525 29.630 0.00 0.00 0.00 2.74
460 462 3.532641 ACCTTTCTTCTTCTGGGCAAT 57.467 42.857 0.00 0.00 0.00 3.56
532 556 7.309683 CCTGAGCTAGTTATGAGATGCTAATCA 60.310 40.741 0.00 0.00 35.03 2.57
558 582 3.071874 TGGACCTTGATGATGTTGGTC 57.928 47.619 0.00 0.00 44.51 4.02
602 626 7.346751 TCCTTTTGTTTCATATATTGGCCTC 57.653 36.000 3.32 0.00 0.00 4.70
638 662 9.705290 CCATGGTTTTATTACTTACTTTTTGCT 57.295 29.630 2.57 0.00 0.00 3.91
646 670 8.799367 AGTTTGTCCCATGGTTTTATTACTTAC 58.201 33.333 11.73 1.04 0.00 2.34
648 672 7.849322 AGTTTGTCCCATGGTTTTATTACTT 57.151 32.000 11.73 0.00 0.00 2.24
683 707 2.557924 TCCAAATTGACGAAAGCTGCAT 59.442 40.909 1.02 0.00 0.00 3.96
691 715 7.067737 AGGAAGTTTTTAGTCCAAATTGACGAA 59.932 33.333 0.00 0.00 40.26 3.85
692 716 6.544564 AGGAAGTTTTTAGTCCAAATTGACGA 59.455 34.615 0.00 0.00 40.26 4.20
759 783 2.028876 GGCTTCTAGACAGAGAGGACC 58.971 57.143 0.00 0.00 30.73 4.46
826 852 4.944962 TTCTTGGTCTAACATGCGAATG 57.055 40.909 0.40 0.40 0.00 2.67
972 998 2.036604 TGGTGTTCAGCGAGTTGTATGA 59.963 45.455 0.00 0.00 0.00 2.15
1021 1047 2.097825 AGTGAGCAATGGAAGAATGGC 58.902 47.619 0.00 0.00 0.00 4.40
1041 1067 1.892209 CATATGAGCATGGCAGAGCA 58.108 50.000 15.74 1.52 0.00 4.26
1323 1349 2.856222 CTTGTCTTGCTCTCCCAAGTT 58.144 47.619 2.31 0.00 42.16 2.66
1350 1376 2.112297 GAAACCACCGTGCCCTCA 59.888 61.111 0.00 0.00 0.00 3.86
1484 1510 2.431057 CTGTAATAACCGGAGACCAGCT 59.569 50.000 9.46 0.00 0.00 4.24
1495 1521 9.869757 ATTGTCAAAATAAAGGCTGTAATAACC 57.130 29.630 0.00 0.00 0.00 2.85
1597 1623 1.816224 GCTAGTCCGCCCATTTTGAAA 59.184 47.619 0.00 0.00 0.00 2.69
1598 1624 1.004277 AGCTAGTCCGCCCATTTTGAA 59.996 47.619 0.00 0.00 0.00 2.69
1604 1630 0.464452 GTTGTAGCTAGTCCGCCCAT 59.536 55.000 0.00 0.00 0.00 4.00
1686 1712 4.386312 CCATTACCCCAATCAGAAGCCTTA 60.386 45.833 0.00 0.00 0.00 2.69
1717 1743 2.420022 CAGACCCAATTGTAAGCCTTCG 59.580 50.000 4.43 0.00 0.00 3.79
1725 1751 4.044065 AGGTTTCCATCAGACCCAATTGTA 59.956 41.667 4.43 0.00 33.89 2.41
1772 1798 6.432162 CCATGATACTATCCAACTCCCATTTG 59.568 42.308 0.00 0.00 0.00 2.32
1789 1815 3.616956 TGCTATAGCCTGCCATGATAC 57.383 47.619 21.84 0.00 41.18 2.24
1840 1866 6.038356 GCAAGAACTCACATATCCCATTTTG 58.962 40.000 0.00 0.00 0.00 2.44
1912 1938 2.687935 TGCAACCTCTGTTCCAGTTTTC 59.312 45.455 0.00 0.00 32.61 2.29
1947 1973 1.068417 TGCTTTGCTGCAGCCTTTG 59.932 52.632 34.64 21.90 41.18 2.77
1999 2025 5.774690 TGGTCAGATCAAAGCCATAAAAGTT 59.225 36.000 0.00 0.00 0.00 2.66
2217 2327 0.867746 CCGGATTGCATGTGATACGG 59.132 55.000 16.32 16.32 42.79 4.02
2650 2760 0.467290 TCAGAGCAAAACCCCCACAC 60.467 55.000 0.00 0.00 0.00 3.82
2703 2813 5.543507 ACTTGTCAAGTGATTCACTCTCT 57.456 39.130 19.23 1.72 44.62 3.10
3000 3110 0.315382 CGTCGATCGGCAAATTCAGC 60.315 55.000 21.12 0.00 35.71 4.26
3468 3609 5.106555 ACAACATTCAATACAGTGCAGCTAC 60.107 40.000 0.00 0.00 0.00 3.58
3471 3612 4.083110 AGACAACATTCAATACAGTGCAGC 60.083 41.667 0.00 0.00 0.00 5.25
3631 3772 6.451064 AGAACGGATTTTTGAAGAAACAGT 57.549 33.333 0.00 0.00 0.00 3.55
3687 3828 6.293407 GCTATTTGCTAACAAGAGTCACACAA 60.293 38.462 0.00 0.00 37.04 3.33
3688 3829 5.179368 GCTATTTGCTAACAAGAGTCACACA 59.821 40.000 0.00 0.00 37.04 3.72
3690 3831 4.695455 GGCTATTTGCTAACAAGAGTCACA 59.305 41.667 0.00 0.00 42.39 3.58
4043 4185 2.661718 AGTTTTACCATATTGCCGGGG 58.338 47.619 2.18 0.00 0.00 5.73
4044 4186 4.729227 AAAGTTTTACCATATTGCCGGG 57.271 40.909 2.18 0.00 0.00 5.73
4118 4260 6.441088 ACTCCAAGGATTGTAGATATTCCC 57.559 41.667 0.00 0.00 46.99 3.97


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

AutoCloner maintained by Alex Coulton.