Multiple sequence alignment - TraesCS4B01G238300

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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 TraesCS4B01G238300 chr4B 100.000 2774 0 0 1 2774 495566951 495569724 0 5123
1 TraesCS4B01G238300 chr6B 98.381 2780 39 4 1 2774 596602873 596600094 0 4879
2 TraesCS4B01G238300 chr6B 98.226 2199 32 4 583 2774 715991505 715989307 0 3838
3 TraesCS4B01G238300 chrUn 98.345 2780 39 5 1 2774 171007271 171010049 0 4872
4 TraesCS4B01G238300 chr7A 98.130 2781 44 5 1 2774 638508680 638505901 0 4841
5 TraesCS4B01G238300 chr7A 98.129 2779 45 4 1 2774 708244612 708247388 0 4837
6 TraesCS4B01G238300 chr1B 97.806 2780 54 6 1 2774 672540209 672542987 0 4789
7 TraesCS4B01G238300 chr5B 97.664 2782 57 5 1 2774 567278980 567281761 0 4771
8 TraesCS4B01G238300 chr2B 97.446 2780 63 4 1 2773 391226258 391223480 0 4734
9 TraesCS4B01G238300 chr2B 97.372 2778 69 4 1 2774 391143790 391146567 0 4723
10 TraesCS4B01G238300 chr2B 96.900 1129 31 3 1 1126 357227773 357228900 0 1888


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 TraesCS4B01G238300 chr4B 495566951 495569724 2773 False 5123 5123 100.000 1 2774 1 chr4B.!!$F1 2773
1 TraesCS4B01G238300 chr6B 596600094 596602873 2779 True 4879 4879 98.381 1 2774 1 chr6B.!!$R1 2773
2 TraesCS4B01G238300 chr6B 715989307 715991505 2198 True 3838 3838 98.226 583 2774 1 chr6B.!!$R2 2191
3 TraesCS4B01G238300 chrUn 171007271 171010049 2778 False 4872 4872 98.345 1 2774 1 chrUn.!!$F1 2773
4 TraesCS4B01G238300 chr7A 638505901 638508680 2779 True 4841 4841 98.130 1 2774 1 chr7A.!!$R1 2773
5 TraesCS4B01G238300 chr7A 708244612 708247388 2776 False 4837 4837 98.129 1 2774 1 chr7A.!!$F1 2773
6 TraesCS4B01G238300 chr1B 672540209 672542987 2778 False 4789 4789 97.806 1 2774 1 chr1B.!!$F1 2773
7 TraesCS4B01G238300 chr5B 567278980 567281761 2781 False 4771 4771 97.664 1 2774 1 chr5B.!!$F1 2773
8 TraesCS4B01G238300 chr2B 391223480 391226258 2778 True 4734 4734 97.446 1 2773 1 chr2B.!!$R1 2772
9 TraesCS4B01G238300 chr2B 391143790 391146567 2777 False 4723 4723 97.372 1 2774 1 chr2B.!!$F2 2773
10 TraesCS4B01G238300 chr2B 357227773 357228900 1127 False 1888 1888 96.900 1 1126 1 chr2B.!!$F1 1125

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
421 422 0.611714 GGCGGGGAAGTGAAGAGTAA 59.388 55.000 0.00 0.00 0.00 2.24 F
508 509 1.445238 GCGACACCAGTCTGAGCTC 60.445 63.158 6.82 6.82 42.73 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1712 4.148174 GGTTTCTTTGTAATTGTCAAGCGC 59.852 41.667 0.0 0.0 0.0 5.92 R
2480 2497 4.569943 GAGTGCAACCAGATAAGAGTTCA 58.430 43.478 0.0 0.0 37.8 3.18 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
175 176 2.293122 GTGTAAGCACAGCAATGAACCA 59.707 45.455 0.00 0.00 44.64 3.67
180 181 1.528076 ACAGCAATGAACCACGGCA 60.528 52.632 0.00 0.00 0.00 5.69
181 182 1.210931 CAGCAATGAACCACGGCAG 59.789 57.895 0.00 0.00 0.00 4.85
302 303 2.103153 AAGTGAACTCCTGGGTCTGA 57.897 50.000 0.00 0.00 31.77 3.27
421 422 0.611714 GGCGGGGAAGTGAAGAGTAA 59.388 55.000 0.00 0.00 0.00 2.24
435 436 3.928727 AGAGTAACCGACGACATTCAA 57.071 42.857 0.00 0.00 0.00 2.69
508 509 1.445238 GCGACACCAGTCTGAGCTC 60.445 63.158 6.82 6.82 42.73 4.09
521 522 2.610233 AGCTCAGGGAAGCCAGCT 60.610 61.111 0.00 0.00 43.56 4.24
534 535 4.383118 GGAAGCCAGCTAATTGAGTCACTA 60.383 45.833 0.00 0.00 0.00 2.74
538 539 6.183347 AGCCAGCTAATTGAGTCACTAAAAT 58.817 36.000 0.00 0.00 0.00 1.82
586 587 2.903798 GCTTCTCAGAGCTGCTATTGT 58.096 47.619 0.15 0.00 39.57 2.71
593 594 6.824553 TCTCAGAGCTGCTATTGTGAAATAT 58.175 36.000 0.15 0.00 0.00 1.28
780 790 6.134535 TCAACAGAAGCCCTTAAAATCCTA 57.865 37.500 0.00 0.00 0.00 2.94
836 846 2.231380 GGGTGGGGGAGAAGCAAGA 61.231 63.158 0.00 0.00 0.00 3.02
890 900 2.105128 CGGCGCCGAGAGAAAGAT 59.895 61.111 44.86 0.00 42.83 2.40
1209 1220 3.747010 GTCTCGACTTCTCCGCTATGATA 59.253 47.826 0.00 0.00 0.00 2.15
1689 1700 3.387699 GCCATAGAAGAAGCTTCTCCTCT 59.612 47.826 28.58 27.18 36.28 3.69
2367 2384 1.680249 CCCTGCCTTTTGCTAGGAGAC 60.680 57.143 4.55 0.00 39.32 3.36
2421 2438 2.604914 CGTGATACGCAAAGCAATCTCT 59.395 45.455 0.00 0.00 33.65 3.10
2475 2492 2.548057 GACTTGCCATTGTCGTCTTTCA 59.452 45.455 0.00 0.00 0.00 2.69
2480 2497 3.380004 TGCCATTGTCGTCTTTCAAAAGT 59.620 39.130 2.63 0.00 37.31 2.66
2613 2630 2.821378 CCAAACTTGGCATGACTCATCA 59.179 45.455 7.45 0.00 42.21 3.07
2730 2747 9.958180 TCTTTGATGTTAGAAGTGATTCCAATA 57.042 29.630 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 176 3.374402 CGTCTGAGGGTCTGCCGT 61.374 66.667 0.00 0.0 34.97 5.68
180 181 0.612453 GAAGGGTCGTCTGAGGGTCT 60.612 60.000 0.00 0.0 0.00 3.85
181 182 0.612453 AGAAGGGTCGTCTGAGGGTC 60.612 60.000 0.00 0.0 0.00 4.46
375 376 2.898612 TGTAACCGTCACCTGTAATCCA 59.101 45.455 0.00 0.0 0.00 3.41
421 422 1.548719 TCATCCTTGAATGTCGTCGGT 59.451 47.619 0.00 0.0 0.00 4.69
435 436 2.634940 CCGATGGGTCTACATTCATCCT 59.365 50.000 0.00 0.0 34.24 3.24
508 509 2.295885 CTCAATTAGCTGGCTTCCCTG 58.704 52.381 0.00 0.0 0.00 4.45
521 522 5.935206 TGCGGTCATTTTAGTGACTCAATTA 59.065 36.000 6.94 0.0 46.02 1.40
534 535 4.002797 GCCTCCTGCGGTCATTTT 57.997 55.556 0.00 0.0 0.00 1.82
586 587 9.653516 TTTGGATATTAAGGAAGCCATATTTCA 57.346 29.630 0.00 0.0 0.00 2.69
593 594 7.969690 TGAAATTTGGATATTAAGGAAGCCA 57.030 32.000 0.00 0.0 0.00 4.75
836 846 1.654954 CGGGTCGATCAGAGGTTCGT 61.655 60.000 0.00 0.0 37.47 3.85
890 900 8.807118 ACTCACTGAATTACTTACTGAATCTCA 58.193 33.333 0.00 0.0 0.00 3.27
950 960 6.143278 GCGGTTGTTCGTATTTCATTTTCTTT 59.857 34.615 0.00 0.0 0.00 2.52
1209 1220 5.026790 GCTCCTATATGAACTACTGGGGAT 58.973 45.833 0.00 0.0 0.00 3.85
1390 1401 4.317488 GTCGTATTTCTGTGGGTTGGTAA 58.683 43.478 0.00 0.0 0.00 2.85
1701 1712 4.148174 GGTTTCTTTGTAATTGTCAAGCGC 59.852 41.667 0.00 0.0 0.00 5.92
2367 2384 5.807520 ACACAATAGAATGCTCGAACTACAG 59.192 40.000 0.00 0.0 0.00 2.74
2443 2460 5.316167 ACAATGGCAAGTCTCAATCAACTA 58.684 37.500 0.00 0.0 0.00 2.24
2475 2492 5.827797 TGCAACCAGATAAGAGTTCACTTTT 59.172 36.000 0.00 0.0 0.00 2.27
2480 2497 4.569943 GAGTGCAACCAGATAAGAGTTCA 58.430 43.478 0.00 0.0 37.80 3.18
2613 2630 8.038862 AGGTAAGATCATGAATACAAGATGGT 57.961 34.615 0.00 0.0 35.11 3.55


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

AutoCloner maintained by Alex Coulton.