Multiple sequence alignment - TraesCS3A01G285300

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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 TraesCS3A01G285300 chr3A 100.000 2234 0 0 1 2234 514109649 514107416 0.000000e+00 4126
1 TraesCS3A01G285300 chr3B 96.607 2240 64 4 1 2234 513994779 513992546 0.000000e+00 3705
2 TraesCS3A01G285300 chr3D 96.295 2240 75 3 1 2234 394753135 394750898 0.000000e+00 3670
3 TraesCS3A01G285300 chr7A 83.636 220 34 2 2012 2231 216340846 216341063 2.910000e-49 206


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 TraesCS3A01G285300 chr3A 514107416 514109649 2233 True 4126 4126 100.000 1 2234 1 chr3A.!!$R1 2233
1 TraesCS3A01G285300 chr3B 513992546 513994779 2233 True 3705 3705 96.607 1 2234 1 chr3B.!!$R1 2233
2 TraesCS3A01G285300 chr3D 394750898 394753135 2237 True 3670 3670 96.295 1 2234 1 chr3D.!!$R1 2233

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
900 907 1.477558 GCAATGGATACCAGGGACAGG 60.478 57.143 0.0 0.0 42.48 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2061 0.883833 CAATTGCTTTGGTCGGCTCT 59.116 50.0 0.0 0.0 0.0 4.09 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
24 25 7.827819 TGCAGTGTAGTCATGTTAGTATTTC 57.172 36.000 0.00 0.00 0.00 2.17
28 29 9.035607 CAGTGTAGTCATGTTAGTATTTCATCC 57.964 37.037 0.00 0.00 0.00 3.51
663 670 3.570125 TCACCGCAATTACAATTCCACAA 59.430 39.130 0.00 0.00 0.00 3.33
675 682 4.160252 ACAATTCCACAAGCTGTTTGAAGT 59.840 37.500 11.31 0.00 39.21 3.01
765 772 3.554934 TGAGCCACTTGAATTTGTGTCT 58.445 40.909 0.00 0.00 32.76 3.41
804 811 5.013079 TGCCTCAAAGGTTAAGATCTTCTCA 59.987 40.000 12.24 0.00 37.80 3.27
852 859 3.479203 TGCTCCCCCATGTAGGCG 61.479 66.667 0.00 0.00 35.39 5.52
869 876 2.226437 AGGCGAAATTGTAGTGTTGCAG 59.774 45.455 0.00 0.00 0.00 4.41
900 907 1.477558 GCAATGGATACCAGGGACAGG 60.478 57.143 0.00 0.00 42.48 4.00
1020 1027 0.630673 TGGGCTGCAAGGAACCATAT 59.369 50.000 0.50 0.00 0.00 1.78
1038 1045 5.008331 CCATATACCAATGCAGAGATGCTT 58.992 41.667 1.53 0.00 35.49 3.91
1120 1127 2.654863 CAGGTGGGGAAACATATGACC 58.345 52.381 10.38 9.42 0.00 4.02
1128 1135 3.617284 GGAAACATATGACCCGGTTTCT 58.383 45.455 10.38 0.00 45.12 2.52
1320 1327 3.698040 GCTCATCATGTGTCCCAATTTCT 59.302 43.478 0.00 0.00 0.00 2.52
1371 1378 0.931005 GATCGGCATTCTTCACGGTC 59.069 55.000 0.00 0.00 0.00 4.79
1400 1407 1.139947 GAGCTACGACCTGGTCAGC 59.860 63.158 24.27 24.27 33.57 4.26
1441 1448 2.558359 GTGCTACAGTGCCAAAGGATTT 59.442 45.455 0.00 0.00 40.26 2.17
1482 1489 5.948742 AGCATTCTAAAGTAGGAAGAGCT 57.051 39.130 0.00 0.00 34.38 4.09
1485 1492 6.070538 AGCATTCTAAAGTAGGAAGAGCTGAA 60.071 38.462 0.00 0.00 36.30 3.02
1661 1668 0.253044 TCTGGCCACCTGATAGCAAC 59.747 55.000 0.00 0.00 0.00 4.17
1667 1674 0.108186 CACCTGATAGCAACGCTCCA 60.108 55.000 0.00 0.00 40.44 3.86
1686 1693 0.957395 ACGCTCACCAATCTGCAAGG 60.957 55.000 0.00 0.00 0.00 3.61
1721 1728 1.216990 ATAAGGCAAGGGAGACAGGG 58.783 55.000 0.00 0.00 0.00 4.45
1722 1729 0.118346 TAAGGCAAGGGAGACAGGGA 59.882 55.000 0.00 0.00 0.00 4.20
1731 1738 1.133761 GGGAGACAGGGAATTAAGGCC 60.134 57.143 0.00 0.00 0.00 5.19
1741 1748 3.374764 GGAATTAAGGCCCTTGGATGTT 58.625 45.455 6.16 0.00 0.00 2.71
1742 1749 3.774766 GGAATTAAGGCCCTTGGATGTTT 59.225 43.478 6.16 0.00 0.00 2.83
1743 1750 4.225042 GGAATTAAGGCCCTTGGATGTTTT 59.775 41.667 6.16 0.00 0.00 2.43
1744 1751 4.824479 ATTAAGGCCCTTGGATGTTTTG 57.176 40.909 6.16 0.00 0.00 2.44
1761 1772 7.273381 GGATGTTTTGTTTCCTTATGATGAACG 59.727 37.037 0.00 0.00 0.00 3.95
1797 1808 0.183731 CCCTCAGGAAGCCCCATTAC 59.816 60.000 0.00 0.00 37.41 1.89
1813 1824 4.082787 CCCATTACGAAGTTGTGAGCATTT 60.083 41.667 0.00 0.00 37.78 2.32
1951 1962 5.344743 TGCTCCTAATCGACTTGAGATTT 57.655 39.130 7.13 0.00 38.96 2.17
1968 1979 8.601845 TTGAGATTTAGTTTCTTGATGTCGAA 57.398 30.769 0.00 0.00 0.00 3.71
1969 1980 8.244494 TGAGATTTAGTTTCTTGATGTCGAAG 57.756 34.615 0.00 0.00 0.00 3.79
2005 2016 4.177026 CAGTTCCTTCACTGGAATCGTAG 58.823 47.826 0.00 0.00 46.36 3.51
2050 2061 1.254975 TAGACTTGCCGCTGCCACTA 61.255 55.000 0.00 0.00 36.33 2.74
2135 2146 1.056660 ATTAGGCCTGGATGGGTACG 58.943 55.000 17.99 0.00 36.00 3.67
2149 2160 1.084289 GGTACGCAAAGTGGATGGAC 58.916 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.791029 TGCTGTAGGATGAAATACTAACATGA 58.209 34.615 0.00 0.00 42.59 3.07
24 25 4.020396 AGGATGCTAGATTGCTGTAGGATG 60.020 45.833 0.00 0.00 30.77 3.51
28 29 7.792374 TTTTTAGGATGCTAGATTGCTGTAG 57.208 36.000 0.00 0.00 0.00 2.74
219 226 1.736681 GTGAGCACAGGAAAGCTGATC 59.263 52.381 0.00 0.00 42.04 2.92
489 496 6.989169 AGTATGAAAGTACTCAGATTGCCATC 59.011 38.462 0.00 0.00 28.99 3.51
663 670 1.699634 TCCCTGCTACTTCAAACAGCT 59.300 47.619 0.00 0.00 36.26 4.24
744 751 3.988379 GACACAAATTCAAGTGGCTCA 57.012 42.857 9.53 0.00 40.62 4.26
765 772 1.820519 GAGGCAGCATGGTTTGATGAA 59.179 47.619 0.00 0.00 44.68 2.57
804 811 1.135083 CGTATCCGAGTCCAAGTGCTT 60.135 52.381 0.00 0.00 35.63 3.91
831 838 0.399949 CCTACATGGGGGAGCACCTA 60.400 60.000 0.00 0.00 40.03 3.08
834 841 2.193248 GCCTACATGGGGGAGCAC 59.807 66.667 9.91 0.00 36.00 4.40
852 859 9.543018 GTTAATCTACTGCAACACTACAATTTC 57.457 33.333 0.00 0.00 0.00 2.17
869 876 6.428159 CCTGGTATCCATTGCTGTTAATCTAC 59.572 42.308 0.00 0.00 30.82 2.59
900 907 4.296690 GCTATGCATTGATCTTTTGCTCC 58.703 43.478 12.54 0.00 37.28 4.70
1038 1045 1.908619 TGGAAGCAAGCACTCATAGGA 59.091 47.619 0.00 0.00 0.00 2.94
1086 1093 0.249868 CACCTGCACCGTCTTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
1120 1127 3.443976 CAGGTGTTTCAAAAGAAACCGG 58.556 45.455 15.91 0.00 42.58 5.28
1128 1135 3.192422 CACTCACACCAGGTGTTTCAAAA 59.808 43.478 23.68 3.79 45.08 2.44
1320 1327 0.471022 TCGATGGGGGTAGCATAGCA 60.471 55.000 0.00 0.00 41.82 3.49
1457 1464 8.580720 CAGCTCTTCCTACTTTAGAATGCTATA 58.419 37.037 0.00 0.00 0.00 1.31
1458 1465 7.288852 TCAGCTCTTCCTACTTTAGAATGCTAT 59.711 37.037 0.00 0.00 0.00 2.97
1482 1489 5.420725 ACACTGGTATATTGACTGCTTCA 57.579 39.130 0.00 0.00 0.00 3.02
1485 1492 5.165961 ACAACACTGGTATATTGACTGCT 57.834 39.130 0.00 0.00 0.00 4.24
1634 1641 3.365265 GGTGGCCAGAAACAGCGG 61.365 66.667 5.11 0.00 0.00 5.52
1667 1674 0.957395 CCTTGCAGATTGGTGAGCGT 60.957 55.000 0.00 0.00 0.00 5.07
1686 1693 4.458989 TGCCTTATTGGTGATTTCACTGTC 59.541 41.667 10.32 0.00 45.73 3.51
1721 1728 5.178061 CAAAACATCCAAGGGCCTTAATTC 58.822 41.667 20.44 0.00 0.00 2.17
1722 1729 4.597075 ACAAAACATCCAAGGGCCTTAATT 59.403 37.500 20.44 6.17 0.00 1.40
1731 1738 6.991938 TCATAAGGAAACAAAACATCCAAGG 58.008 36.000 0.00 0.00 35.62 3.61
1733 1740 8.187913 TCATCATAAGGAAACAAAACATCCAA 57.812 30.769 0.00 0.00 35.62 3.53
1736 1743 7.807907 ACGTTCATCATAAGGAAACAAAACATC 59.192 33.333 0.00 0.00 0.00 3.06
1741 1748 6.938030 AGGTACGTTCATCATAAGGAAACAAA 59.062 34.615 0.00 0.00 0.00 2.83
1742 1749 6.469410 AGGTACGTTCATCATAAGGAAACAA 58.531 36.000 0.00 0.00 0.00 2.83
1743 1750 6.045072 AGGTACGTTCATCATAAGGAAACA 57.955 37.500 0.00 0.00 0.00 2.83
1744 1751 6.980051 AAGGTACGTTCATCATAAGGAAAC 57.020 37.500 0.00 0.00 0.00 2.78
1761 1772 5.712917 CCTGAGGGATATGAGACTAAGGTAC 59.287 48.000 0.00 0.00 33.58 3.34
1813 1824 3.060000 GCAGCAGCCATGACAGCA 61.060 61.111 0.00 0.00 33.58 4.41
1951 1962 3.250744 CGGCTTCGACATCAAGAAACTA 58.749 45.455 0.00 0.00 35.61 2.24
1968 1979 1.745320 AACTGTCAAGGTCGACGGCT 61.745 55.000 9.92 0.00 44.68 5.52
1969 1980 1.282930 GAACTGTCAAGGTCGACGGC 61.283 60.000 9.92 0.00 44.68 5.68
1977 1988 2.104792 TCCAGTGAAGGAACTGTCAAGG 59.895 50.000 3.85 0.00 45.08 3.61
1998 2009 1.084370 GGTGCAGCGCTTCTACGATT 61.084 55.000 7.50 0.00 34.06 3.34
2050 2061 0.883833 CAATTGCTTTGGTCGGCTCT 59.116 50.000 0.00 0.00 0.00 4.09
2135 2146 2.887152 AGTTTGAGTCCATCCACTTTGC 59.113 45.455 0.00 0.00 0.00 3.68
2149 2160 2.478709 CCGTGGAGAGATCGAGTTTGAG 60.479 54.545 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.