Multiple sequence alignment - TraesCS5B01G395600

Loading Multiple Alignment...

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 TraesCS5B01G395600 chr5B 100.000 3605 0 0 1 3605 572947178 572943574 0.000000e+00 6658
1 TraesCS5B01G395600 chr5D 96.013 3637 78 29 1 3605 465714825 465711224 0.000000e+00 5851
2 TraesCS5B01G395600 chr5A 94.896 3605 112 35 1 3576 586145219 586141658 0.000000e+00 5572
3 TraesCS5B01G395600 chr7D 76.778 478 57 31 1243 1700 58140942 58141385 6.060000e-53 219
4 TraesCS5B01G395600 chr1A 74.170 542 80 37 1147 1677 465248713 465248221 1.720000e-38 171
5 TraesCS5B01G395600 chr2D 83.893 149 19 3 1811 1956 565858161 565858015 1.750000e-28 137
6 TraesCS5B01G395600 chr4A 82.877 146 23 1 1811 1956 37899831 37899688 2.920000e-26 130
7 TraesCS5B01G395600 chr2A 82.993 147 22 2 1811 1956 364404220 364404364 2.920000e-26 130


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 TraesCS5B01G395600 chr5B 572943574 572947178 3604 True 6658 6658 100.000 1 3605 1 chr5B.!!$R1 3604
1 TraesCS5B01G395600 chr5D 465711224 465714825 3601 True 5851 5851 96.013 1 3605 1 chr5D.!!$R1 3604
2 TraesCS5B01G395600 chr5A 586141658 586145219 3561 True 5572 5572 94.896 1 3576 1 chr5A.!!$R1 3575

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
134 135 0.618458 TCACCCATACTTGGAGGTGC 59.382 55.000 3.13 0.0 46.92 5.01 F
1131 1148 1.667724 CGGCTCAGCAAGGTATGAAAG 59.332 52.381 0.00 0.0 0.00 2.62 F
2164 2187 1.062365 CCACAAGCACACACACACG 59.938 57.895 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1139 1156 1.202336 GCATTTTGGAATCAGGAGCCG 60.202 52.381 0.00 0.0 0.00 5.52 R
2180 2203 0.163146 GAACTTCCTTACGTGCGTGC 59.837 55.000 7.55 0.0 0.00 5.34 R
3138 3184 0.181350 AATCACGGGATCTTGGCTCC 59.819 55.000 0.00 0.0 31.88 4.70 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
90 91 7.668052 ACATCTCTGATATACTCCTGGTTAGAC 59.332 40.741 0.00 0.00 0.00 2.59
134 135 0.618458 TCACCCATACTTGGAGGTGC 59.382 55.000 3.13 0.00 46.92 5.01
249 250 4.402155 ACAAAACAGATTTCACAGGCAGAA 59.598 37.500 0.00 0.00 0.00 3.02
558 560 9.782900 TCCACTATATGTATGATCCATCCTAAA 57.217 33.333 0.00 0.00 0.00 1.85
573 575 2.158871 TCCTAAATACGTGCACCCATCC 60.159 50.000 12.15 0.00 0.00 3.51
574 576 2.420827 CCTAAATACGTGCACCCATCCA 60.421 50.000 12.15 0.00 0.00 3.41
575 577 2.208132 AAATACGTGCACCCATCCAA 57.792 45.000 12.15 0.00 0.00 3.53
576 578 2.208132 AATACGTGCACCCATCCAAA 57.792 45.000 12.15 0.00 0.00 3.28
577 579 2.208132 ATACGTGCACCCATCCAAAA 57.792 45.000 12.15 0.00 0.00 2.44
578 580 2.208132 TACGTGCACCCATCCAAAAT 57.792 45.000 12.15 0.00 0.00 1.82
579 581 2.208132 ACGTGCACCCATCCAAAATA 57.792 45.000 12.15 0.00 0.00 1.40
580 582 2.733956 ACGTGCACCCATCCAAAATAT 58.266 42.857 12.15 0.00 0.00 1.28
690 700 8.579006 TGTTCACTTATTTCATTGCAGAATTCT 58.421 29.630 0.88 0.88 0.00 2.40
740 750 7.201644 CCATTGTCTTACATCACTGGTAATCAC 60.202 40.741 0.00 0.00 32.28 3.06
743 755 6.210584 TGTCTTACATCACTGGTAATCACTGA 59.789 38.462 0.00 0.00 30.93 3.41
812 825 7.174599 CAGAAAAAGATTCTCAGAAGTGTCCAT 59.825 37.037 0.00 0.00 0.00 3.41
1131 1148 1.667724 CGGCTCAGCAAGGTATGAAAG 59.332 52.381 0.00 0.00 0.00 2.62
1139 1156 5.938125 TCAGCAAGGTATGAAAGTAACTTCC 59.062 40.000 0.00 0.00 29.33 3.46
1425 1443 4.119363 GTAAACCGGGGGAGGGGC 62.119 72.222 6.32 0.00 35.02 5.80
1486 1504 6.680874 AAGCAGATTTCTGTCAGATTCATC 57.319 37.500 2.68 6.28 45.45 2.92
1492 1510 5.488262 TTTCTGTCAGATTCATCAGTGGA 57.512 39.130 2.68 0.00 0.00 4.02
1615 1635 7.506114 AGATAAAGTCAACTGTAACCTTGACA 58.494 34.615 11.89 0.00 45.90 3.58
1677 1697 7.496346 AGAACCATCCAGTAACTGAAATAGA 57.504 36.000 0.00 0.00 32.44 1.98
1718 1741 7.121168 GTCTCCCAGATAAATCAATGAAACACA 59.879 37.037 0.00 0.00 0.00 3.72
1901 1924 4.271049 ACGATGATTGAGCCTAACAAATCG 59.729 41.667 0.00 0.00 40.55 3.34
1973 1996 5.858581 CAGCTACTGGCAAAAATACAAGAAC 59.141 40.000 0.00 0.00 44.79 3.01
1978 2001 4.314121 TGGCAAAAATACAAGAACCATGC 58.686 39.130 0.00 0.00 0.00 4.06
2110 2133 2.753452 AGCAAGATCAAACATGCAGAGG 59.247 45.455 0.00 0.00 41.18 3.69
2122 2145 2.607892 GCAGAGGACAACCACGCAC 61.608 63.158 0.00 0.00 38.94 5.34
2164 2187 1.062365 CCACAAGCACACACACACG 59.938 57.895 0.00 0.00 0.00 4.49
2522 2547 7.630242 ATGACAGGGAGTATACAAAAACATG 57.370 36.000 5.50 0.00 0.00 3.21
2721 2746 0.324943 CGTCTTTGTGGAGGGGATGT 59.675 55.000 0.00 0.00 0.00 3.06
2747 2772 0.464373 TCGAATCAGGAGGGCAATGC 60.464 55.000 0.00 0.00 0.00 3.56
2783 2808 7.657336 TCCATACTTCAAAATGTTTCAACTCC 58.343 34.615 0.00 0.00 0.00 3.85
3138 3184 0.248866 GTTTGCAAGGACAACCACGG 60.249 55.000 0.00 0.00 38.94 4.94
3158 3204 1.587547 GAGCCAAGATCCCGTGATTC 58.412 55.000 0.00 0.00 0.00 2.52
3223 3269 1.103803 AGCTTCATTGGCATGAGCAG 58.896 50.000 0.00 5.12 40.66 4.24
3290 3336 8.141268 TGAAACATCAAGGGAACTGTTTTATTC 58.859 33.333 0.00 0.00 42.68 1.75
3558 3608 4.866508 ATCATTGTGCAATCCCATCATC 57.133 40.909 0.00 0.00 0.00 2.92
3559 3609 3.633418 TCATTGTGCAATCCCATCATCA 58.367 40.909 0.00 0.00 0.00 3.07
3560 3610 4.219919 TCATTGTGCAATCCCATCATCAT 58.780 39.130 0.00 0.00 0.00 2.45
3561 3611 4.651962 TCATTGTGCAATCCCATCATCATT 59.348 37.500 0.00 0.00 0.00 2.57
3562 3612 4.659111 TTGTGCAATCCCATCATCATTC 57.341 40.909 0.00 0.00 0.00 2.67
3563 3613 2.960384 TGTGCAATCCCATCATCATTCC 59.040 45.455 0.00 0.00 0.00 3.01
3564 3614 2.960384 GTGCAATCCCATCATCATTCCA 59.040 45.455 0.00 0.00 0.00 3.53
3565 3615 3.385433 GTGCAATCCCATCATCATTCCAA 59.615 43.478 0.00 0.00 0.00 3.53
3566 3616 4.031611 TGCAATCCCATCATCATTCCAAA 58.968 39.130 0.00 0.00 0.00 3.28
3567 3617 4.141892 TGCAATCCCATCATCATTCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
3568 3618 4.141892 GCAATCCCATCATCATTCCAAACA 60.142 41.667 0.00 0.00 0.00 2.83
3569 3619 5.627272 GCAATCCCATCATCATTCCAAACAA 60.627 40.000 0.00 0.00 0.00 2.83
3570 3620 6.588204 CAATCCCATCATCATTCCAAACAAT 58.412 36.000 0.00 0.00 0.00 2.71
3571 3621 5.601583 TCCCATCATCATTCCAAACAATG 57.398 39.130 0.00 0.00 35.39 2.82
3585 3635 4.143030 CCAAACAATGAAACAACGCAAACA 60.143 37.500 0.00 0.00 0.00 2.83
3596 3646 4.111916 ACAACGCAAACAAAATCCAAGAG 58.888 39.130 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.743664 CAAGGACATTGAGAACATCGCA 59.256 45.455 0.00 0.00 41.83 5.10
90 91 0.464193 TCATCATGGCACCATCACCG 60.464 55.000 0.00 0.00 33.90 4.94
134 135 3.264947 TGATTCAACTGCTCTTCATCGG 58.735 45.455 0.00 0.00 0.00 4.18
249 250 6.252599 TCTTTCCAGTTGCCATATATGACT 57.747 37.500 14.54 6.98 0.00 3.41
558 560 2.208132 TTTTGGATGGGTGCACGTAT 57.792 45.000 11.45 7.49 0.00 3.06
673 683 9.947433 TTTATTTCCAGAATTCTGCAATGAAAT 57.053 25.926 31.13 31.13 42.47 2.17
785 798 6.311055 ACACTTCTGAGAATCTTTTTCTGC 57.689 37.500 0.00 0.00 34.92 4.26
812 825 6.094048 GCATCCTGCACTTATTCTTTACTTCA 59.906 38.462 0.00 0.00 44.26 3.02
1131 1148 2.552031 GAATCAGGAGCCGGAAGTTAC 58.448 52.381 5.05 0.00 0.00 2.50
1139 1156 1.202336 GCATTTTGGAATCAGGAGCCG 60.202 52.381 0.00 0.00 0.00 5.52
1201 1219 7.961351 AGAAACACTGGGATGATTAGAGATAG 58.039 38.462 0.00 0.00 0.00 2.08
1425 1443 1.287730 GATCTGGCAATAGCGGCTCG 61.288 60.000 5.39 0.00 43.41 5.03
1486 1504 9.716531 TCTCAAGAGCAATAAATATATCCACTG 57.283 33.333 0.00 0.00 0.00 3.66
1518 1538 7.309377 CCATGATTTCTCAGGCTCAAAAGTTTA 60.309 37.037 0.00 0.00 34.12 2.01
1677 1697 3.584406 TGGGAGACATGAATTCAGACACT 59.416 43.478 14.54 10.03 0.00 3.55
1901 1924 4.901868 TGACTGTATTGGGAAGGTAACAC 58.098 43.478 0.00 0.00 41.41 3.32
1978 2001 3.503363 TGCATTGAAGTAGCAAGAACCAG 59.497 43.478 0.00 0.00 34.97 4.00
2110 2133 2.109739 TGTGTGGTGCGTGGTTGTC 61.110 57.895 0.00 0.00 0.00 3.18
2122 2145 1.438651 CGGGTATCTTGTGTGTGTGG 58.561 55.000 0.00 0.00 0.00 4.17
2178 2201 0.249741 ACTTCCTTACGTGCGTGCTT 60.250 50.000 7.55 0.00 0.00 3.91
2180 2203 0.163146 GAACTTCCTTACGTGCGTGC 59.837 55.000 7.55 0.00 0.00 5.34
2181 2204 1.779569 AGAACTTCCTTACGTGCGTG 58.220 50.000 7.55 0.00 0.00 5.34
2183 2206 3.493503 AGAAAAGAACTTCCTTACGTGCG 59.506 43.478 0.00 0.00 0.00 5.34
2184 2207 5.419760 AAGAAAAGAACTTCCTTACGTGC 57.580 39.130 0.00 0.00 0.00 5.34
2522 2547 2.299993 TGACATGGCTGAGAACGATC 57.700 50.000 0.00 0.00 0.00 3.69
2721 2746 2.365617 GCCCTCCTGATTCGAGTAATGA 59.634 50.000 0.00 0.00 0.00 2.57
2747 2772 9.740239 CATTTTGAAGTATGGATCAATGTTAGG 57.260 33.333 0.00 0.00 35.63 2.69
2752 2777 9.642327 TGAAACATTTTGAAGTATGGATCAATG 57.358 29.630 0.00 0.00 35.63 2.82
2757 2782 8.306761 GGAGTTGAAACATTTTGAAGTATGGAT 58.693 33.333 0.00 0.00 0.00 3.41
2775 2800 2.628178 ACAGATGAGACACGGAGTTGAA 59.372 45.455 0.00 0.00 41.61 2.69
2783 2808 8.955061 AAAATTGAAATTACAGATGAGACACG 57.045 30.769 0.00 0.00 0.00 4.49
3138 3184 0.181350 AATCACGGGATCTTGGCTCC 59.819 55.000 0.00 0.00 31.88 4.70
3158 3204 9.603921 ATTTAATGCCAATACTTTTTCCATGAG 57.396 29.630 0.00 0.00 0.00 2.90
3223 3269 2.673368 CCTGCTTAACAGTCCGATCAAC 59.327 50.000 0.00 0.00 45.68 3.18
3299 3345 7.468084 GCACACAACTTTCTCATACCTTTACAA 60.468 37.037 0.00 0.00 0.00 2.41
3301 3347 6.371389 GCACACAACTTTCTCATACCTTTAC 58.629 40.000 0.00 0.00 0.00 2.01
3558 3608 4.269603 TGCGTTGTTTCATTGTTTGGAATG 59.730 37.500 0.00 0.00 35.05 2.67
3559 3609 4.437239 TGCGTTGTTTCATTGTTTGGAAT 58.563 34.783 0.00 0.00 0.00 3.01
3560 3610 3.849911 TGCGTTGTTTCATTGTTTGGAA 58.150 36.364 0.00 0.00 0.00 3.53
3561 3611 3.510388 TGCGTTGTTTCATTGTTTGGA 57.490 38.095 0.00 0.00 0.00 3.53
3562 3612 4.143030 TGTTTGCGTTGTTTCATTGTTTGG 60.143 37.500 0.00 0.00 0.00 3.28
3563 3613 4.950926 TGTTTGCGTTGTTTCATTGTTTG 58.049 34.783 0.00 0.00 0.00 2.93
3564 3614 5.597813 TTGTTTGCGTTGTTTCATTGTTT 57.402 30.435 0.00 0.00 0.00 2.83
3565 3615 5.597813 TTTGTTTGCGTTGTTTCATTGTT 57.402 30.435 0.00 0.00 0.00 2.83
3566 3616 5.597813 TTTTGTTTGCGTTGTTTCATTGT 57.402 30.435 0.00 0.00 0.00 2.71
3567 3617 5.676310 GGATTTTGTTTGCGTTGTTTCATTG 59.324 36.000 0.00 0.00 0.00 2.82
3568 3618 5.352569 TGGATTTTGTTTGCGTTGTTTCATT 59.647 32.000 0.00 0.00 0.00 2.57
3569 3619 4.872691 TGGATTTTGTTTGCGTTGTTTCAT 59.127 33.333 0.00 0.00 0.00 2.57
3570 3620 4.245660 TGGATTTTGTTTGCGTTGTTTCA 58.754 34.783 0.00 0.00 0.00 2.69
3571 3621 4.849111 TGGATTTTGTTTGCGTTGTTTC 57.151 36.364 0.00 0.00 0.00 2.78
3585 3635 1.168714 GACCGCTGCTCTTGGATTTT 58.831 50.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.