Multiple sequence alignment - TraesCS5D01G183800

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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 TraesCS5D01G183800 chr5D 100.000 2123 0 0 1 2123 285464577 285466699 0.000000e+00 3921
1 TraesCS5D01G183800 chr5D 91.736 121 9 1 1 121 285300703 285300822 1.300000e-37 167
2 TraesCS5D01G183800 chr5A 94.111 1715 68 14 1 1692 377181744 377183448 0.000000e+00 2577
3 TraesCS5D01G183800 chr5A 97.895 285 6 0 1839 2123 377184148 377184432 5.260000e-136 494
4 TraesCS5D01G183800 chr5A 95.726 117 4 1 1681 1797 377183618 377183733 1.000000e-43 187
5 TraesCS5D01G183800 chr5B 89.695 2067 128 45 5 2016 322912959 322914995 0.000000e+00 2558


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 TraesCS5D01G183800 chr5D 285464577 285466699 2122 False 3921 3921 100.000000 1 2123 1 chr5D.!!$F2 2122
1 TraesCS5D01G183800 chr5A 377181744 377184432 2688 False 1086 2577 95.910667 1 2123 3 chr5A.!!$F1 2122
2 TraesCS5D01G183800 chr5B 322912959 322914995 2036 False 2558 2558 89.695000 5 2016 1 chr5B.!!$F1 2011


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
202 206 0.39034 AGCACGCATACACACAGAGG 60.39 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2722 0.110644 GCGACTTTGTCCTTTCTGCG 60.111 55.0 0.0 0.0 0.0 5.18 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
30 31 3.285484 CTCAGAAATCAACATGGGGAGG 58.715 50.000 0.00 0.00 0.00 4.30
115 116 5.344743 TGACTGGAAACTAGGCAAGATAG 57.655 43.478 0.00 0.00 28.13 2.08
156 157 1.729149 GCAGCATCAAACGGCTACAAC 60.729 52.381 0.00 0.00 38.56 3.32
191 195 0.823356 ACCTCAACCAAAGCACGCAT 60.823 50.000 0.00 0.00 0.00 4.73
199 203 1.400113 CCAAAGCACGCATACACACAG 60.400 52.381 0.00 0.00 0.00 3.66
201 205 1.432514 AAGCACGCATACACACAGAG 58.567 50.000 0.00 0.00 0.00 3.35
202 206 0.390340 AGCACGCATACACACAGAGG 60.390 55.000 0.00 0.00 0.00 3.69
203 207 1.361668 GCACGCATACACACAGAGGG 61.362 60.000 0.00 0.00 0.00 4.30
204 208 1.079127 ACGCATACACACAGAGGGC 60.079 57.895 0.00 0.00 0.00 5.19
457 478 9.028185 GTACTGCTACCACATAATACTGTTAAC 57.972 37.037 0.00 0.00 0.00 2.01
576 597 7.987458 TCCAAGTACCAAGATAGATAAGCAAAG 59.013 37.037 0.00 0.00 0.00 2.77
580 601 9.606631 AGTACCAAGATAGATAAGCAAAGAAAG 57.393 33.333 0.00 0.00 0.00 2.62
645 667 4.626287 GCCAGATACCAAGAACCTTCATCA 60.626 45.833 0.00 0.00 0.00 3.07
676 698 2.555199 GAACCGCTACTGAATCTGCAT 58.445 47.619 0.00 0.00 0.00 3.96
709 731 2.202987 CGGCAGGATGAGCTGTCC 60.203 66.667 6.63 6.63 39.69 4.02
721 743 2.167693 TGAGCTGTCCGTTATCCGAAAT 59.832 45.455 0.00 0.00 39.56 2.17
725 747 3.560068 GCTGTCCGTTATCCGAAATGATT 59.440 43.478 0.00 0.00 39.56 2.57
732 754 5.699001 CCGTTATCCGAAATGATTGTATCCA 59.301 40.000 0.00 0.00 39.56 3.41
839 861 7.765695 AAAGAGGAAATGAAGAATTAGCACA 57.234 32.000 0.00 0.00 0.00 4.57
885 907 3.454371 TGCTCGCCTCCTCTATAAAAC 57.546 47.619 0.00 0.00 0.00 2.43
944 966 2.406559 CTCCAACCAGGGATCAGATCT 58.593 52.381 10.36 0.00 36.09 2.75
975 997 4.499183 AGCAAACTCTCCTACTTTCATCG 58.501 43.478 0.00 0.00 0.00 3.84
997 1019 3.940221 GCATCTCTTCAGTTCATCAAGCT 59.060 43.478 0.00 0.00 0.00 3.74
1141 1163 3.025866 GCTCCAAGCTGCATTTTCG 57.974 52.632 1.02 0.00 38.45 3.46
1142 1164 0.242017 GCTCCAAGCTGCATTTTCGT 59.758 50.000 1.02 0.00 38.45 3.85
1176 1199 2.648059 CCATGAAGTCAAGGGTCCATC 58.352 52.381 0.00 0.00 31.48 3.51
1397 1431 3.935240 TCCCTTAGGCAGTGGGATATA 57.065 47.619 7.22 0.00 44.37 0.86
1398 1432 4.435977 TCCCTTAGGCAGTGGGATATAT 57.564 45.455 7.22 0.00 44.37 0.86
1406 1440 0.036010 AGTGGGATATATGCGGCTGC 60.036 55.000 11.65 11.65 43.20 5.25
1555 1598 3.417069 TTGGTTGTGGAGGTCATACAG 57.583 47.619 0.00 0.00 0.00 2.74
1585 1628 6.316390 AGCTGTCGATAAACTTTTAATCCTGG 59.684 38.462 0.00 0.00 0.00 4.45
1598 1641 5.628797 TTAATCCTGGTATGCATGTCTCA 57.371 39.130 10.16 1.39 0.00 3.27
1692 1935 7.795482 TCACCTCGATTTTTAAGAAAGAACA 57.205 32.000 0.00 0.00 0.00 3.18
1874 2490 6.094464 TCAATGATGAGTTGAAGTGCATAAGG 59.906 38.462 0.00 0.00 32.98 2.69
2061 2697 5.337250 GCACCCATCAGACGGTATAATATCA 60.337 44.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.071699 TGTGTGCCACTTTCTAGGGTC 59.928 52.381 0.00 0.00 35.11 4.46
115 116 2.223572 CGCCCTTTACTGCATTTCCATC 60.224 50.000 0.00 0.00 0.00 3.51
275 294 5.144832 TGGAATGAGTACTCGGATTATCCA 58.855 41.667 17.85 18.48 35.91 3.41
280 299 4.039730 CAGGATGGAATGAGTACTCGGATT 59.960 45.833 17.85 12.54 0.00 3.01
416 435 6.598850 GGTAGCAGTACTGTAGTATATCCTCC 59.401 46.154 23.44 8.68 32.54 4.30
676 698 2.347731 TGCCGCATACGTGTTGAAATA 58.652 42.857 0.00 0.00 37.70 1.40
732 754 7.253422 CCGACAAAAAGCTTGATCTTATTGAT 58.747 34.615 0.00 0.00 38.27 2.57
837 859 0.038744 CCTTCCTCCCATGCAACTGT 59.961 55.000 0.00 0.00 0.00 3.55
839 861 1.693640 CCCTTCCTCCCATGCAACT 59.306 57.895 0.00 0.00 0.00 3.16
898 920 2.360475 GGTGTGGAGCTGGGAAGC 60.360 66.667 0.00 0.00 0.00 3.86
907 929 1.228063 AGCTTGCTGTGGTGTGGAG 60.228 57.895 0.00 0.00 0.00 3.86
966 988 4.199432 ACTGAAGAGATGCGATGAAAGT 57.801 40.909 0.00 0.00 0.00 2.66
975 997 3.940221 AGCTTGATGAACTGAAGAGATGC 59.060 43.478 0.00 0.00 0.00 3.91
997 1019 1.559682 GCTCCTCACACTCCCCATTTA 59.440 52.381 0.00 0.00 0.00 1.40
1160 1182 2.648059 CATGGATGGACCCTTGACTTC 58.352 52.381 0.00 0.00 38.00 3.01
1176 1199 4.808414 TCTAAGTGTGACTTCTCCATGG 57.192 45.455 4.97 4.97 39.51 3.66
1397 1431 1.755179 AAAAGATACAGCAGCCGCAT 58.245 45.000 0.00 0.00 42.27 4.73
1398 1432 1.199789 CAAAAAGATACAGCAGCCGCA 59.800 47.619 0.00 0.00 42.27 5.69
1406 1440 6.738114 ACACAACATGTCCAAAAAGATACAG 58.262 36.000 0.00 0.00 36.54 2.74
1526 1560 2.821969 CCTCCACAACCAAAGAAGATGG 59.178 50.000 0.00 0.00 43.84 3.51
1527 1561 3.490348 ACCTCCACAACCAAAGAAGATG 58.510 45.455 0.00 0.00 0.00 2.90
1555 1598 4.670227 AAAGTTTATCGACAGCTCAAGC 57.330 40.909 0.00 0.00 42.49 4.01
1585 1628 7.606349 TCCAGAATATAGTGAGACATGCATAC 58.394 38.462 0.00 0.00 0.00 2.39
1598 1641 4.881019 ATTGCGAGCTCCAGAATATAGT 57.119 40.909 8.47 0.00 0.00 2.12
1817 2060 3.829886 TTTCTCGCAACCAATAAGCAG 57.170 42.857 0.00 0.00 0.00 4.24
1818 2061 4.782019 AATTTCTCGCAACCAATAAGCA 57.218 36.364 0.00 0.00 0.00 3.91
1819 2062 5.405269 ACAAAATTTCTCGCAACCAATAAGC 59.595 36.000 0.00 0.00 0.00 3.09
1831 2074 4.829064 TTGACCTGGACAAAATTTCTCG 57.171 40.909 9.12 0.00 0.00 4.04
1832 2075 6.331369 TCATTGACCTGGACAAAATTTCTC 57.669 37.500 15.11 0.00 0.00 2.87
1874 2490 8.425577 TGCTTAAGACACTATGAAGCTATTTC 57.574 34.615 6.67 0.00 42.38 2.17
2086 2722 0.110644 GCGACTTTGTCCTTTCTGCG 60.111 55.000 0.00 0.00 0.00 5.18



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

AutoCloner maintained by Alex Coulton.