Multiple sequence alignment - TraesCS5A01G126400

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 TraesCS5A01G126400 chr5A 100.000 2339 0 0 1 2339 279102487 279100149 0.000000e+00 4320.0
1 TraesCS5A01G126400 chr5D 95.040 1754 45 14 1 1746 213946601 213944882 0.000000e+00 2719.0
2 TraesCS5A01G126400 chr5D 89.871 543 20 17 1803 2339 213944865 213944352 0.000000e+00 665.0
3 TraesCS5A01G126400 chr5B 93.896 1671 59 22 114 1753 228498351 228496693 0.000000e+00 2481.0
4 TraesCS5A01G126400 chr5B 91.793 463 21 6 1884 2339 228496122 228495670 1.530000e-176 628.0
5 TraesCS5A01G126400 chr5B 99.180 122 1 0 1 122 228498598 228498477 1.090000e-53 220.0
6 TraesCS5A01G126400 chr5B 94.444 54 3 0 1821 1874 228496441 228496388 1.490000e-12 84.2


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 TraesCS5A01G126400 chr5A 279100149 279102487 2338 True 4320.0 4320 100.00000 1 2339 1 chr5A.!!$R1 2338
1 TraesCS5A01G126400 chr5D 213944352 213946601 2249 True 1692.0 2719 92.45550 1 2339 2 chr5D.!!$R1 2338
2 TraesCS5A01G126400 chr5B 228495670 228498598 2928 True 853.3 2481 94.82825 1 2339 4 chr5B.!!$R1 2338

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
820 968 0.179116 ACACATCGCAGCTAGCTCAG 60.179 55.0 16.15 11.97 42.61 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 2181 0.735978 CCGCCGCTTGCATCGATATA 60.736 55.0 10.01 0.0 41.33 0.86 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
77 82 6.939163 AGTAAACTCTCCTTCGTAAGTACTCA 59.061 38.462 0.00 0.00 39.48 3.41
78 83 5.625921 AACTCTCCTTCGTAAGTACTCAC 57.374 43.478 0.00 0.00 39.48 3.51
79 84 4.909001 ACTCTCCTTCGTAAGTACTCACT 58.091 43.478 0.00 0.00 36.19 3.41
80 85 4.937015 ACTCTCCTTCGTAAGTACTCACTC 59.063 45.833 0.00 0.00 32.29 3.51
130 269 3.939592 AGGGTTATAAAAGCTTGCTCGTC 59.060 43.478 0.00 0.00 33.51 4.20
273 412 4.042934 AGACACCATTTACCTAAAGTGGCT 59.957 41.667 0.00 0.00 35.87 4.75
668 814 2.225779 TGGAGGGATGTGGAAGGAAGTA 60.226 50.000 0.00 0.00 0.00 2.24
691 837 1.215679 AGAGGAAGAGGACGGAGGGA 61.216 60.000 0.00 0.00 0.00 4.20
813 959 2.113860 ACCAAATACACATCGCAGCT 57.886 45.000 0.00 0.00 0.00 4.24
814 960 3.260475 ACCAAATACACATCGCAGCTA 57.740 42.857 0.00 0.00 0.00 3.32
820 968 0.179116 ACACATCGCAGCTAGCTCAG 60.179 55.000 16.15 11.97 42.61 3.35
912 1060 2.170607 AGGAGTATGTTATGCCGCAGTT 59.829 45.455 0.00 0.00 0.00 3.16
942 1094 3.152341 CTGCACACCTGAAGAGGAAATT 58.848 45.455 0.00 0.00 42.93 1.82
1426 1603 2.052766 GCGATGCGCGAATCTTGG 60.053 61.111 24.26 10.56 44.55 3.61
1438 1615 1.284841 AATCTTGGGGCTGGAGGAGG 61.285 60.000 0.00 0.00 0.00 4.30
1565 1743 7.362315 GGGTTGGTCAGTTTAATTAGCGTTATT 60.362 37.037 0.00 0.00 0.00 1.40
1689 1867 2.935238 GCTAGCGATGGTTGTCTCCAAA 60.935 50.000 0.00 0.00 41.09 3.28
1690 1868 2.496899 AGCGATGGTTGTCTCCAAAT 57.503 45.000 0.00 0.00 41.09 2.32
1692 1870 3.950397 AGCGATGGTTGTCTCCAAATAA 58.050 40.909 0.00 0.00 41.09 1.40
1695 1873 5.418840 AGCGATGGTTGTCTCCAAATAATTT 59.581 36.000 0.00 0.00 41.09 1.82
1696 1874 5.516339 GCGATGGTTGTCTCCAAATAATTTG 59.484 40.000 0.00 0.00 41.09 2.32
1697 1875 6.620678 CGATGGTTGTCTCCAAATAATTTGT 58.379 36.000 0.00 0.00 41.09 2.83
1698 1876 7.627513 GCGATGGTTGTCTCCAAATAATTTGTA 60.628 37.037 0.00 0.00 41.09 2.41
1699 1877 7.696453 CGATGGTTGTCTCCAAATAATTTGTAC 59.304 37.037 0.00 0.00 41.09 2.90
1787 2172 4.377134 TCAAGGGCTTAATTAGGTAGGGT 58.623 43.478 0.00 0.00 0.00 4.34
1791 2176 2.103601 GGCTTAATTAGGTAGGGTGCGA 59.896 50.000 0.00 0.00 0.00 5.10
1792 2177 3.391049 GCTTAATTAGGTAGGGTGCGAG 58.609 50.000 0.00 0.00 0.00 5.03
1793 2178 3.181468 GCTTAATTAGGTAGGGTGCGAGT 60.181 47.826 0.00 0.00 0.00 4.18
1794 2179 4.038402 GCTTAATTAGGTAGGGTGCGAGTA 59.962 45.833 0.00 0.00 0.00 2.59
1795 2180 5.452356 GCTTAATTAGGTAGGGTGCGAGTAA 60.452 44.000 0.00 0.00 0.00 2.24
1796 2181 6.736110 TTAATTAGGTAGGGTGCGAGTAAT 57.264 37.500 0.00 0.00 0.00 1.89
1797 2182 7.524367 GCTTAATTAGGTAGGGTGCGAGTAATA 60.524 40.741 0.00 0.00 0.00 0.98
1798 2183 6.930068 AATTAGGTAGGGTGCGAGTAATAT 57.070 37.500 0.00 0.00 0.00 1.28
1799 2184 9.532494 TTAATTAGGTAGGGTGCGAGTAATATA 57.468 33.333 0.00 0.00 0.00 0.86
1800 2185 8.605325 AATTAGGTAGGGTGCGAGTAATATAT 57.395 34.615 0.00 0.00 0.00 0.86
1801 2186 7.636150 TTAGGTAGGGTGCGAGTAATATATC 57.364 40.000 0.00 0.00 0.00 1.63
1874 2263 7.593644 CCTGCCAAGTTAACACTAATTTTGTAC 59.406 37.037 8.61 0.00 30.68 2.90
1876 2265 8.132362 TGCCAAGTTAACACTAATTTTGTACTG 58.868 33.333 8.61 0.00 30.68 2.74
1878 2267 7.593644 CCAAGTTAACACTAATTTTGTACTGCC 59.406 37.037 8.61 0.00 30.68 4.85
1879 2268 6.894828 AGTTAACACTAATTTTGTACTGCCG 58.105 36.000 8.61 0.00 0.00 5.69
1880 2269 6.484308 AGTTAACACTAATTTTGTACTGCCGT 59.516 34.615 8.61 0.00 0.00 5.68
1881 2270 4.742438 ACACTAATTTTGTACTGCCGTG 57.258 40.909 0.00 0.00 0.00 4.94
1892 2537 0.535335 ACTGCCGTGATATTGTCCGT 59.465 50.000 0.00 0.00 0.00 4.69
1912 2557 4.653888 AACCCGTCCCCGCTTTGG 62.654 66.667 0.00 0.00 37.55 3.28
1959 2604 1.402968 AGTATTTGAGCCTTGCATGCG 59.597 47.619 14.09 0.00 0.00 4.73
2067 2713 2.273449 GGGTGAGGCATGGACTGG 59.727 66.667 0.00 0.00 0.00 4.00
2086 2732 1.510623 CGAAACACAGCAGCATCGC 60.511 57.895 0.00 0.00 0.00 4.58
2087 2733 1.154150 GAAACACAGCAGCATCGCC 60.154 57.895 0.00 0.00 0.00 5.54
2104 2750 1.308783 GCCCTCTGCAAAGTACAGGC 61.309 60.000 0.00 0.00 40.77 4.85
2105 2751 1.021390 CCCTCTGCAAAGTACAGGCG 61.021 60.000 0.00 0.00 35.78 5.52
2156 2802 3.882888 CACACTGGAAGGAAGTAAAAGCA 59.117 43.478 0.00 0.00 39.30 3.91
2199 2845 9.830294 CATTACACAATTATATAGTACGACGGA 57.170 33.333 0.00 0.00 0.00 4.69
2330 2983 2.192605 GGCACGGCCTGATCAAAAT 58.807 52.632 0.00 0.00 46.69 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 82 8.936864 CGTCTTTATTTCAATTCTTACAGGAGT 58.063 33.333 0.00 0.00 0.00 3.85
78 83 7.905493 GCGTCTTTATTTCAATTCTTACAGGAG 59.095 37.037 0.00 0.00 0.00 3.69
79 84 7.389330 TGCGTCTTTATTTCAATTCTTACAGGA 59.611 33.333 0.00 0.00 0.00 3.86
80 85 7.526608 TGCGTCTTTATTTCAATTCTTACAGG 58.473 34.615 0.00 0.00 0.00 4.00
130 269 4.520111 TGTGAAATGACATCTCACCCAAAG 59.480 41.667 17.28 0.00 38.97 2.77
236 375 4.156622 GTCTTTAACCGCGCGGCC 62.157 66.667 46.22 21.94 39.32 6.13
242 381 3.754850 AGGTAAATGGTGTCTTTAACCGC 59.245 43.478 0.00 0.00 40.86 5.68
370 509 3.007506 TCTTGAACGCCCTTTACTGATGA 59.992 43.478 0.00 0.00 0.00 2.92
633 779 1.834263 CCCTCCAACCCTACTCTCTTG 59.166 57.143 0.00 0.00 0.00 3.02
668 814 2.452505 CTCCGTCCTCTTCCTCTCTTT 58.547 52.381 0.00 0.00 0.00 2.52
691 837 3.763360 TGCTATTAATGCAACAGCAAGGT 59.237 39.130 7.28 0.00 42.37 3.50
720 866 3.034635 GGAGGAGAGGTCAATGCTTCTA 58.965 50.000 0.00 0.00 0.00 2.10
813 959 1.568597 AGGAGAGGAAGAGCTGAGCTA 59.431 52.381 7.08 0.00 39.88 3.32
814 960 0.336048 AGGAGAGGAAGAGCTGAGCT 59.664 55.000 6.69 6.69 43.88 4.09
820 968 1.215423 AGAGGAGAGGAGAGGAAGAGC 59.785 57.143 0.00 0.00 0.00 4.09
826 974 1.388547 CGTGAAGAGGAGAGGAGAGG 58.611 60.000 0.00 0.00 0.00 3.69
912 1060 1.762370 TCAGGTGTGCAGAACAGAAGA 59.238 47.619 0.10 0.00 40.26 2.87
925 1077 6.544928 AAACAAAATTTCCTCTTCAGGTGT 57.455 33.333 0.00 0.00 41.28 4.16
1224 1401 0.620556 AGTTGATGCAGGTGGGGTAG 59.379 55.000 0.00 0.00 0.00 3.18
1426 1603 3.086600 CACTCCCTCCTCCAGCCC 61.087 72.222 0.00 0.00 0.00 5.19
1537 1715 4.398044 CGCTAATTAAACTGACCAACCCAT 59.602 41.667 0.00 0.00 0.00 4.00
1565 1743 2.811431 CAACACCAATCGGAAACTAGCA 59.189 45.455 0.00 0.00 35.59 3.49
1692 1870 8.395633 GTGAAAACACAGTTGACTAGTACAAAT 58.604 33.333 0.00 0.00 0.00 2.32
1695 1873 5.813672 GGTGAAAACACAGTTGACTAGTACA 59.186 40.000 0.00 0.00 0.00 2.90
1696 1874 5.813672 TGGTGAAAACACAGTTGACTAGTAC 59.186 40.000 0.00 0.00 0.00 2.73
1697 1875 5.979993 TGGTGAAAACACAGTTGACTAGTA 58.020 37.500 0.00 0.00 0.00 1.82
1698 1876 4.839121 TGGTGAAAACACAGTTGACTAGT 58.161 39.130 0.00 0.00 0.00 2.57
1699 1877 5.296780 ACATGGTGAAAACACAGTTGACTAG 59.703 40.000 0.00 0.00 0.00 2.57
1754 1935 7.806680 AATTAAGCCCTTGAATCCCTAAAAA 57.193 32.000 0.00 0.00 0.00 1.94
1755 1936 7.563556 CCTAATTAAGCCCTTGAATCCCTAAAA 59.436 37.037 0.00 0.00 0.00 1.52
1787 2172 4.562789 GCTTGCATCGATATATTACTCGCA 59.437 41.667 0.00 0.00 34.94 5.10
1791 2176 3.865745 GCCGCTTGCATCGATATATTACT 59.134 43.478 10.01 0.00 40.77 2.24
1792 2177 3.301835 CGCCGCTTGCATCGATATATTAC 60.302 47.826 10.01 0.00 41.33 1.89
1793 2178 2.857748 CGCCGCTTGCATCGATATATTA 59.142 45.455 10.01 0.00 41.33 0.98
1794 2179 1.660607 CGCCGCTTGCATCGATATATT 59.339 47.619 10.01 0.00 41.33 1.28
1795 2180 1.280982 CGCCGCTTGCATCGATATAT 58.719 50.000 10.01 0.00 41.33 0.86
1796 2181 0.735978 CCGCCGCTTGCATCGATATA 60.736 55.000 10.01 0.00 41.33 0.86
1797 2182 2.029288 CCGCCGCTTGCATCGATAT 61.029 57.895 10.01 0.00 41.33 1.63
1798 2183 2.661537 CCGCCGCTTGCATCGATA 60.662 61.111 10.01 0.00 41.33 2.92
1819 2204 3.790177 GCGTTTCGCGGGATAAGT 58.210 55.556 6.13 0.00 44.55 2.24
1848 2237 6.512297 ACAAAATTAGTGTTAACTTGGCAGG 58.488 36.000 7.22 0.00 37.88 4.85
1874 2263 0.930310 CACGGACAATATCACGGCAG 59.070 55.000 0.00 0.00 0.00 4.85
1876 2265 1.647346 TTCACGGACAATATCACGGC 58.353 50.000 0.00 0.00 0.00 5.68
1878 2267 2.350498 GGGTTTCACGGACAATATCACG 59.650 50.000 0.00 0.00 0.00 4.35
1879 2268 2.350498 CGGGTTTCACGGACAATATCAC 59.650 50.000 0.00 0.00 0.00 3.06
1880 2269 2.027929 ACGGGTTTCACGGACAATATCA 60.028 45.455 0.00 0.00 35.23 2.15
1881 2270 2.606272 GACGGGTTTCACGGACAATATC 59.394 50.000 0.00 0.00 35.23 1.63
1912 2557 1.617947 AACCCTCGCACCTCAGGATC 61.618 60.000 0.00 0.00 30.32 3.36
1959 2604 4.317418 CGAACAGAGCTATGCAAATCGTAC 60.317 45.833 8.60 0.00 0.00 3.67
2067 2713 1.510623 CGATGCTGCTGTGTTTCGC 60.511 57.895 0.00 0.00 0.00 4.70
2086 2732 1.021390 CGCCTGTACTTTGCAGAGGG 61.021 60.000 9.34 1.17 36.12 4.30
2087 2733 1.639298 GCGCCTGTACTTTGCAGAGG 61.639 60.000 9.34 0.00 36.12 3.69
2105 2751 3.730761 CTGCAGTGAAGCACCGGC 61.731 66.667 5.25 0.00 40.11 6.13
2113 2759 2.431683 GTCAGCCCCTGCAGTGAA 59.568 61.111 13.81 0.00 41.13 3.18
2156 2802 5.594317 GTGTAATGATGCCCTTGTTTATCCT 59.406 40.000 0.00 0.00 0.00 3.24
2199 2845 2.436646 CCGCGCCCAGAGATTTGT 60.437 61.111 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.