Multiple sequence alignment - TraesCS4A01G190300

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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 TraesCS4A01G190300 chr4A 100.000 2365 0 0 1 2365 468848301 468850665 0 4368
1 TraesCS4A01G190300 chr4A 96.705 2367 71 7 1 2365 81354125 81351764 0 3932
2 TraesCS4A01G190300 chr4A 96.540 2370 77 4 1 2365 76561275 76563644 0 3917
3 TraesCS4A01G190300 chr4A 96.539 2369 75 7 1 2365 231356632 231354267 0 3914
4 TraesCS4A01G190300 chr7A 96.791 2368 71 5 1 2365 645171798 645174163 0 3947
5 TraesCS4A01G190300 chr7A 96.707 2369 70 7 1 2365 579878970 579876606 0 3936
6 TraesCS4A01G190300 chr7A 96.665 2369 71 7 1 2365 618748472 618746108 0 3930
7 TraesCS4A01G190300 chr3A 96.579 2368 76 4 1 2365 576841485 576839120 0 3919
8 TraesCS4A01G190300 chr3A 96.537 2368 75 7 1 2365 581335640 581338003 0 3912
9 TraesCS4A01G190300 chr6A 96.537 2368 77 5 1 2365 546318494 546320859 0 3914


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 TraesCS4A01G190300 chr4A 468848301 468850665 2364 False 4368 4368 100.000 1 2365 1 chr4A.!!$F2 2364
1 TraesCS4A01G190300 chr4A 81351764 81354125 2361 True 3932 3932 96.705 1 2365 1 chr4A.!!$R1 2364
2 TraesCS4A01G190300 chr4A 76561275 76563644 2369 False 3917 3917 96.540 1 2365 1 chr4A.!!$F1 2364
3 TraesCS4A01G190300 chr4A 231354267 231356632 2365 True 3914 3914 96.539 1 2365 1 chr4A.!!$R2 2364
4 TraesCS4A01G190300 chr7A 645171798 645174163 2365 False 3947 3947 96.791 1 2365 1 chr7A.!!$F1 2364
5 TraesCS4A01G190300 chr7A 579876606 579878970 2364 True 3936 3936 96.707 1 2365 1 chr7A.!!$R1 2364
6 TraesCS4A01G190300 chr7A 618746108 618748472 2364 True 3930 3930 96.665 1 2365 1 chr7A.!!$R2 2364
7 TraesCS4A01G190300 chr3A 576839120 576841485 2365 True 3919 3919 96.579 1 2365 1 chr3A.!!$R1 2364
8 TraesCS4A01G190300 chr3A 581335640 581338003 2363 False 3912 3912 96.537 1 2365 1 chr3A.!!$F1 2364
9 TraesCS4A01G190300 chr6A 546318494 546320859 2365 False 3914 3914 96.537 1 2365 1 chr6A.!!$F1 2364

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
832 836 1.252904 TACCTTTACTGCCGAGCCGT 61.253 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1808 0.25589 CATCTCCCCGGTTCCATTGT 59.744 55.0 0.0 0.0 0.0 2.71 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
222 223 2.875296 TGTTTGGCTAGCATTCCAGTT 58.125 42.857 18.24 0.00 33.32 3.16
472 473 6.887002 CCTGAAACCCTAGAAGCTTCTTATTT 59.113 38.462 32.70 24.33 38.70 1.40
523 524 3.680777 TTTTTGTCCCTTCCTCCAACT 57.319 42.857 0.00 0.00 0.00 3.16
587 589 4.751060 CATGCTGTGAAATTTGGCTACAT 58.249 39.130 0.00 0.00 0.00 2.29
652 656 3.068064 GGTTTGGCACATCCCCCG 61.068 66.667 0.00 0.00 39.30 5.73
683 687 5.351458 CCAATTTTGGCCTATTTACTCTGC 58.649 41.667 3.32 0.00 42.21 4.26
832 836 1.252904 TACCTTTACTGCCGAGCCGT 61.253 55.000 0.00 0.00 0.00 5.68
872 876 4.580580 GCTGGACAATAAGGGGAAGTATTG 59.419 45.833 0.00 0.00 41.48 1.90
930 934 1.814394 GTTCAACCCGTGTTTATCCCC 59.186 52.381 0.00 0.00 30.42 4.81
1153 1159 9.426534 TGAGGAATATTTCTCTAGTCAGATTGA 57.573 33.333 21.86 0.00 0.00 2.57
1225 1231 6.094881 TGCTCAGTTTTAAACACTGTTAGCTT 59.905 34.615 24.38 0.00 40.39 3.74
1355 1361 2.731374 GCGATTCTCTCCTCCGGG 59.269 66.667 0.00 0.00 0.00 5.73
1417 1424 2.500098 CAAGATCCCTCCAGAACCGTTA 59.500 50.000 0.00 0.00 0.00 3.18
1622 1629 2.165998 GCTGAAGACCATGAAGGCTTT 58.834 47.619 0.00 0.00 43.14 3.51
1683 1690 3.365265 CTTTGGCACCACTCGGGC 61.365 66.667 0.00 0.00 42.05 6.13
1712 1719 7.246674 TGTGTTATTCAGAGAACTTGTTCAC 57.753 36.000 14.80 9.12 0.00 3.18
1713 1720 6.821160 TGTGTTATTCAGAGAACTTGTTCACA 59.179 34.615 14.80 5.81 0.00 3.58
1717 1724 4.200838 TCAGAGAACTTGTTCACACACA 57.799 40.909 14.80 0.00 30.32 3.72
1737 1744 5.163174 ACACACCCCTAGTTTGTAGCTTTTA 60.163 40.000 0.00 0.00 37.62 1.52
1801 1808 8.298854 CAGAATATGTTGTGGTTTCATTCTCAA 58.701 33.333 0.00 0.00 30.84 3.02
1837 1845 5.789521 GGAGATGCTCCCTATTTCTCTAAC 58.210 45.833 1.97 0.00 44.36 2.34
1992 2002 3.806521 TGGATTGTTTTGGCACGAAAATG 59.193 39.130 0.00 0.00 0.00 2.32
2244 2254 4.399303 GCTACATTATTTGTTCACCCAGCT 59.601 41.667 0.00 0.00 39.87 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.829120 GAGGAAGTCAGCTAACTCCTGT 59.171 50.000 11.48 0.00 31.27 4.00
182 183 7.067372 CCAAACAAGCTTGTATGAGGATCAATA 59.933 37.037 31.31 0.00 45.62 1.90
222 223 6.155393 GGAACTTGAAGAAGGAGAGGAGATAA 59.845 42.308 0.00 0.00 32.95 1.75
472 473 9.244978 AGGTTTATTTCCTAGGTATTTATGGGA 57.755 33.333 9.08 0.00 33.04 4.37
523 524 6.836527 CCTTTCCAGAATCTAGAGGTCTTAGA 59.163 42.308 6.08 4.52 0.00 2.10
587 589 3.531059 CTCCCATCCCCTATGTTCCATA 58.469 50.000 0.00 0.00 33.34 2.74
683 687 7.729051 ACACTTTTGTTAAGCTCATTGCGGG 62.729 44.000 0.00 0.00 38.89 6.13
872 876 1.275856 CATGATAGAGGGAGCTGGAGC 59.724 57.143 0.00 0.00 42.49 4.70
930 934 2.693069 ACTCTCAATTTCCAGACAGCG 58.307 47.619 0.00 0.00 0.00 5.18
1153 1159 3.265791 GCGACAGATTCAAAGGATGAGT 58.734 45.455 0.00 0.00 39.77 3.41
1182 1188 2.562738 AGCACTTTTTGGTAGCAATCCC 59.437 45.455 8.40 0.00 32.76 3.85
1225 1231 0.324943 GAGGCACCAAAGGACAGCTA 59.675 55.000 0.00 0.00 0.00 3.32
1355 1361 3.192844 TCATCAACTTGTCCTAGTCCGAC 59.807 47.826 0.00 0.00 0.00 4.79
1362 1368 4.756642 CACAAAGCTCATCAACTTGTCCTA 59.243 41.667 0.00 0.00 0.00 2.94
1417 1424 0.035317 TTCAGCCACAAGTGATCGCT 59.965 50.000 2.02 2.02 0.00 4.93
1622 1629 1.768684 GACACAAGGAGGGTCCAGCA 61.769 60.000 0.00 0.00 45.24 4.41
1683 1690 7.576236 ACAAGTTCTCTGAATAACACAAATCG 58.424 34.615 5.63 0.00 0.00 3.34
1712 1719 2.038557 AGCTACAAACTAGGGGTGTGTG 59.961 50.000 2.27 0.00 45.21 3.82
1713 1720 2.335933 AGCTACAAACTAGGGGTGTGT 58.664 47.619 0.00 0.00 46.96 3.72
1717 1724 6.446110 AGGTATAAAAGCTACAAACTAGGGGT 59.554 38.462 0.00 0.00 32.98 4.95
1737 1744 6.038997 AGAGTAGTTCGAAAGCAAAGGTAT 57.961 37.500 0.00 0.00 0.00 2.73
1801 1808 0.255890 CATCTCCCCGGTTCCATTGT 59.744 55.000 0.00 0.00 0.00 2.71
1958 1968 7.723172 TGCCAAAACAATCCAGGATTTTATTTT 59.277 29.630 12.49 15.03 28.87 1.82
1992 2002 5.613358 AGCTTTTGTACACAATCACTAGC 57.387 39.130 0.00 0.00 35.55 3.42
2332 2347 4.928615 CCAAAAATGTGGCACGTATTCAAT 59.071 37.500 13.64 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.