Multiple sequence alignment - TraesCS5A01G036700

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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 TraesCS5A01G036700 chr5A 100.000 2222 0 0 1 2222 33881956 33879735 0.000000e+00 4104
1 TraesCS5A01G036700 chr5A 95.390 1540 70 1 1 1539 23905549 23904010 0.000000e+00 2449
2 TraesCS5A01G036700 chr5A 95.220 1548 70 4 1 1546 601068902 601070447 0.000000e+00 2446
3 TraesCS5A01G036700 chr3A 95.914 1542 60 3 1 1539 11599032 11597491 0.000000e+00 2495
4 TraesCS5A01G036700 chr3A 95.914 1542 60 3 1 1539 11605920 11604379 0.000000e+00 2495
5 TraesCS5A01G036700 chr3A 95.387 1539 68 2 1 1538 684743941 684745477 0.000000e+00 2446
6 TraesCS5A01G036700 chr3A 95.322 1539 71 1 1 1538 27580972 27582510 0.000000e+00 2442
7 TraesCS5A01G036700 chr7A 95.519 1540 65 4 1 1538 17368997 17370534 0.000000e+00 2459
8 TraesCS5A01G036700 chr4B 95.322 1539 69 2 1 1538 604142985 604144521 0.000000e+00 2440
9 TraesCS5A01G036700 chr2B 95.322 1539 69 2 1 1538 721723155 721724691 0.000000e+00 2440
10 TraesCS5A01G036700 chr5D 91.810 696 28 16 1543 2222 43914947 43914265 0.000000e+00 942
11 TraesCS5A01G036700 chr5B 92.694 219 6 5 1885 2098 41827829 41828042 7.710000e-80 307


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 TraesCS5A01G036700 chr5A 33879735 33881956 2221 True 4104 4104 100.000 1 2222 1 chr5A.!!$R2 2221
1 TraesCS5A01G036700 chr5A 23904010 23905549 1539 True 2449 2449 95.390 1 1539 1 chr5A.!!$R1 1538
2 TraesCS5A01G036700 chr5A 601068902 601070447 1545 False 2446 2446 95.220 1 1546 1 chr5A.!!$F1 1545
3 TraesCS5A01G036700 chr3A 11597491 11599032 1541 True 2495 2495 95.914 1 1539 1 chr3A.!!$R1 1538
4 TraesCS5A01G036700 chr3A 11604379 11605920 1541 True 2495 2495 95.914 1 1539 1 chr3A.!!$R2 1538
5 TraesCS5A01G036700 chr3A 684743941 684745477 1536 False 2446 2446 95.387 1 1538 1 chr3A.!!$F2 1537
6 TraesCS5A01G036700 chr3A 27580972 27582510 1538 False 2442 2442 95.322 1 1538 1 chr3A.!!$F1 1537
7 TraesCS5A01G036700 chr7A 17368997 17370534 1537 False 2459 2459 95.519 1 1538 1 chr7A.!!$F1 1537
8 TraesCS5A01G036700 chr4B 604142985 604144521 1536 False 2440 2440 95.322 1 1538 1 chr4B.!!$F1 1537
9 TraesCS5A01G036700 chr2B 721723155 721724691 1536 False 2440 2440 95.322 1 1538 1 chr2B.!!$F1 1537
10 TraesCS5A01G036700 chr5D 43914265 43914947 682 True 942 942 91.810 1543 2222 1 chr5D.!!$R1 679

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
714 718 2.716969 AGGAAGTAAAGCCCAAGGAAGT 59.283 45.455 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2126 0.533978 TGGCGAGCTGCTGTGTTTTA 60.534 50.0 7.01 0.0 45.43 1.52 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
156 159 8.572185 TCATGAAACAAAATAAATCCGACTGAA 58.428 29.630 0.00 0.00 0.00 3.02
327 330 7.168219 AGAGATTGCATACCTTTACAGAACAA 58.832 34.615 0.00 0.00 0.00 2.83
591 594 5.048294 CCTTAATTCCAGGTAAAGCAACGTT 60.048 40.000 0.00 0.00 0.00 3.99
654 658 2.910688 TCTAATCAAGGGGATGACGC 57.089 50.000 0.00 0.00 36.02 5.19
683 687 3.537580 TGATACGGTCCAGTTTAATGCC 58.462 45.455 0.00 0.00 0.00 4.40
694 698 4.821805 CCAGTTTAATGCCTATGGTGGTAG 59.178 45.833 0.00 0.00 0.00 3.18
714 718 2.716969 AGGAAGTAAAGCCCAAGGAAGT 59.283 45.455 0.00 0.00 0.00 3.01
789 793 6.868826 TCTTCAGTATCCCTCTTGATCCTAT 58.131 40.000 0.00 0.00 0.00 2.57
826 830 5.933187 TTGTTGCATTCTTATGTACGTGT 57.067 34.783 0.00 0.00 34.12 4.49
1115 1121 3.418675 CGATAGCACGTGTGTTCCT 57.581 52.632 18.38 7.64 0.00 3.36
1164 1170 1.645455 CATCATGGCTAGCGTGCAC 59.355 57.895 6.82 6.82 34.04 4.57
1171 1177 2.509111 CTAGCGTGCACGATGGCA 60.509 61.111 41.19 20.60 43.02 4.92
1176 1182 2.743538 GTGCACGATGGCAGCAGA 60.744 61.111 0.00 0.00 45.96 4.26
1217 1223 6.690948 CCTAATAGGATGGATGCGTCCGAC 62.691 54.167 20.05 15.18 42.25 4.79
1338 1345 5.509498 ATTAGTTTCCTAATTGCTCAGGCA 58.491 37.500 0.00 0.00 40.25 4.75
1353 1360 4.023365 GCTCAGGCATGGAGTTTCATATTC 60.023 45.833 0.00 0.00 38.54 1.75
1562 1569 9.512435 GAATAGATGAACCAAATGTTGAATGAG 57.488 33.333 0.00 0.00 37.29 2.90
1571 1578 7.363705 AACCAAATGTTGAATGAGTGAAAGTCA 60.364 33.333 0.00 0.00 42.92 3.41
1581 1589 1.463214 TGAAAGTCAGGCCAGGGGA 60.463 57.895 5.01 0.00 0.00 4.81
1597 1605 5.339118 GCCAGGGGATTTCAAAATTTACCAT 60.339 40.000 0.00 0.00 0.00 3.55
1599 1607 5.585844 CAGGGGATTTCAAAATTTACCATGC 59.414 40.000 0.00 0.00 29.31 4.06
1652 1660 3.272574 TCAAACTCCATCTCATCTGCC 57.727 47.619 0.00 0.00 0.00 4.85
1712 1720 3.772932 CGCGGTTGATTAACTACCTACA 58.227 45.455 0.00 0.00 41.08 2.74
1717 1725 4.866486 GGTTGATTAACTACCTACACCGTG 59.134 45.833 0.00 0.00 40.33 4.94
1770 1778 3.542648 GGATACAAAGGGAAGTAGTGCC 58.457 50.000 0.00 0.00 38.24 5.01
1843 1851 0.035881 CCTGCCTTCTGCTTCAGTGA 59.964 55.000 0.00 0.00 42.00 3.41
1852 1860 3.479489 TCTGCTTCAGTGAATGCTTTCA 58.521 40.909 20.56 10.76 39.54 2.69
1853 1861 3.501062 TCTGCTTCAGTGAATGCTTTCAG 59.499 43.478 14.79 14.20 42.41 3.02
1854 1862 3.216800 TGCTTCAGTGAATGCTTTCAGT 58.783 40.909 14.79 14.95 44.59 3.41
1855 1863 4.388485 TGCTTCAGTGAATGCTTTCAGTA 58.612 39.130 19.12 7.24 42.39 2.74
1863 1871 7.331934 TCAGTGAATGCTTTCAGTAAGTATGAC 59.668 37.037 19.12 3.93 42.39 3.06
1919 1928 9.528489 AAATGTAAACCCATAGACATGTAAAGT 57.472 29.630 0.00 0.00 32.92 2.66
1968 1977 7.985184 GGGAAGTACAAACTGTCATCATACATA 59.015 37.037 0.00 0.00 35.62 2.29
2005 2014 0.314935 CCAACAGTGGGCACATGAAC 59.685 55.000 0.00 0.00 41.77 3.18
2022 2031 7.603784 GCACATGAACCATCATAGACATGTATA 59.396 37.037 2.07 2.07 44.53 1.47
2050 2059 4.447724 TCAAGAAAGATCGAAGAACCAACG 59.552 41.667 0.00 0.00 43.58 4.10
2054 2063 2.338500 AGATCGAAGAACCAACGCTTC 58.662 47.619 0.00 0.00 43.58 3.86
2117 2126 6.154021 AGCAATCATTCAAGCAATTTAGAGGT 59.846 34.615 0.00 0.00 0.00 3.85
2118 2127 7.340232 AGCAATCATTCAAGCAATTTAGAGGTA 59.660 33.333 0.00 0.00 0.00 3.08
2123 2132 8.855110 TCATTCAAGCAATTTAGAGGTAAAACA 58.145 29.630 0.00 0.00 31.81 2.83
2125 2134 7.575414 TCAAGCAATTTAGAGGTAAAACACA 57.425 32.000 0.00 0.00 31.81 3.72
2130 2139 5.629079 ATTTAGAGGTAAAACACAGCAGC 57.371 39.130 0.00 0.00 31.81 5.25
2131 2140 2.938956 AGAGGTAAAACACAGCAGCT 57.061 45.000 0.00 0.00 0.00 4.24
2137 2146 2.063541 AAAACACAGCAGCTCGCCAC 62.064 55.000 0.00 0.00 44.04 5.01
2149 2158 2.493547 TCGCCACGAGTGATCATCT 58.506 52.632 0.00 0.00 0.00 2.90
2158 2167 0.248661 AGTGATCATCTTCGTCGCCG 60.249 55.000 0.00 0.00 0.00 6.46
2187 2196 2.815647 GGCAAAGGAGCCGACGAG 60.816 66.667 0.00 0.00 46.12 4.18
2188 2197 3.491652 GCAAAGGAGCCGACGAGC 61.492 66.667 0.00 0.00 0.00 5.03
2189 2198 2.048222 CAAAGGAGCCGACGAGCA 60.048 61.111 10.28 0.00 34.23 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 241 5.104693 TCCAATGAAGAAACTAATCCGGCTA 60.105 40.000 0.00 0.00 0.00 3.93
471 474 5.662211 AACTTTACACGCGTCACTTTAAT 57.338 34.783 9.86 0.00 0.00 1.40
591 594 8.590719 TTTGATCAGTGTGTGTTTTACGTATA 57.409 30.769 0.00 0.00 0.00 1.47
654 658 3.288964 ACTGGACCGTATCAAGAGGTAG 58.711 50.000 0.00 0.00 38.57 3.18
683 687 4.444449 GGGCTTTACTTCCTACCACCATAG 60.444 50.000 0.00 0.00 0.00 2.23
694 698 3.082548 GACTTCCTTGGGCTTTACTTCC 58.917 50.000 0.00 0.00 0.00 3.46
714 718 6.630071 TGATTACTTCTCATGTTCATGTCGA 58.370 36.000 11.73 7.70 0.00 4.20
754 758 5.723887 AGGGATACTGAAGAAGTCAAGATGT 59.276 40.000 0.00 0.00 40.56 3.06
789 793 8.196771 AGAATGCAACAATCTTGTCTTACAAAA 58.803 29.630 0.00 0.00 41.31 2.44
847 851 3.433306 AGGTTGCCAATTGCTGTACTA 57.567 42.857 0.00 0.00 42.00 1.82
859 864 7.577303 AGATTTGAGATTATCTTAGGTTGCCA 58.423 34.615 0.00 0.00 0.00 4.92
898 903 0.693049 AGAATCGTGGGGCTTCAAGT 59.307 50.000 0.00 0.00 0.00 3.16
977 983 1.217882 CGTTGACTTCAGCTCCGTTT 58.782 50.000 0.00 0.00 0.00 3.60
1115 1121 0.251832 AGGAGCTTCGTCTTCCTCCA 60.252 55.000 8.11 0.00 44.95 3.86
1176 1182 1.589196 GAAGCTAATCGCGAGCCGT 60.589 57.895 16.66 3.54 45.59 5.68
1361 1368 0.178984 TGACTGACCGTACTCCACCA 60.179 55.000 0.00 0.00 0.00 4.17
1539 1546 7.665145 TCACTCATTCAACATTTGGTTCATCTA 59.335 33.333 0.00 0.00 37.72 1.98
1540 1547 6.491062 TCACTCATTCAACATTTGGTTCATCT 59.509 34.615 0.00 0.00 37.72 2.90
1541 1548 6.680810 TCACTCATTCAACATTTGGTTCATC 58.319 36.000 0.00 0.00 37.72 2.92
1555 1562 2.106338 TGGCCTGACTTTCACTCATTCA 59.894 45.455 3.32 0.00 0.00 2.57
1562 1569 1.303643 CCCCTGGCCTGACTTTCAC 60.304 63.158 11.88 0.00 0.00 3.18
1571 1578 2.647846 ATTTTGAAATCCCCTGGCCT 57.352 45.000 3.32 0.00 0.00 5.19
1576 1584 5.250313 TGCATGGTAAATTTTGAAATCCCCT 59.750 36.000 0.00 0.00 0.00 4.79
1597 1605 8.860780 TTTGCACATATATAATATCCACTGCA 57.139 30.769 0.00 0.00 0.00 4.41
1612 1620 9.715121 AGTTTGATCTTGAAATTTTGCACATAT 57.285 25.926 0.00 0.00 0.00 1.78
1770 1778 8.404107 TCCTTCAAAGGGTTAACTGAAAATAG 57.596 34.615 8.89 0.00 46.47 1.73
1869 1877 5.483937 TCCTCTTGAGAACTGCCAGTTTATA 59.516 40.000 12.09 0.00 38.80 0.98
1870 1878 4.287067 TCCTCTTGAGAACTGCCAGTTTAT 59.713 41.667 12.09 3.70 38.80 1.40
1871 1879 3.646162 TCCTCTTGAGAACTGCCAGTTTA 59.354 43.478 12.09 0.00 38.80 2.01
1872 1880 2.439507 TCCTCTTGAGAACTGCCAGTTT 59.560 45.455 12.09 1.84 38.80 2.66
1875 1883 2.847327 TTCCTCTTGAGAACTGCCAG 57.153 50.000 0.00 0.00 0.00 4.85
1876 1884 3.181440 ACATTTCCTCTTGAGAACTGCCA 60.181 43.478 0.00 0.00 29.58 4.92
1877 1885 3.416156 ACATTTCCTCTTGAGAACTGCC 58.584 45.455 0.00 0.00 29.58 4.85
1918 1927 6.183360 CCCCTTTGTATGATTGATGGGTTTAC 60.183 42.308 0.00 0.00 0.00 2.01
1919 1928 5.896678 CCCCTTTGTATGATTGATGGGTTTA 59.103 40.000 0.00 0.00 0.00 2.01
1920 1929 4.716287 CCCCTTTGTATGATTGATGGGTTT 59.284 41.667 0.00 0.00 0.00 3.27
1921 1930 4.289245 CCCCTTTGTATGATTGATGGGTT 58.711 43.478 0.00 0.00 0.00 4.11
1922 1931 3.374098 CCCCCTTTGTATGATTGATGGGT 60.374 47.826 0.00 0.00 0.00 4.51
1978 1987 2.736531 CCACTGTTGGGGCAAAGC 59.263 61.111 0.00 0.00 39.57 3.51
2022 2031 7.940850 TGGTTCTTCGATCTTTCTTGATTTTT 58.059 30.769 0.00 0.00 0.00 1.94
2050 2059 4.134563 TGGTTGACAGTTAGGAAAGAAGC 58.865 43.478 0.00 0.00 0.00 3.86
2054 2063 2.814336 GCCTGGTTGACAGTTAGGAAAG 59.186 50.000 0.00 0.00 46.06 2.62
2117 2126 0.533978 TGGCGAGCTGCTGTGTTTTA 60.534 50.000 7.01 0.00 45.43 1.52
2118 2127 1.823470 TGGCGAGCTGCTGTGTTTT 60.823 52.632 7.01 0.00 45.43 2.43
2123 2132 4.731612 CTCGTGGCGAGCTGCTGT 62.732 66.667 7.01 0.00 46.75 4.40
2131 2140 0.817654 AAGATGATCACTCGTGGCGA 59.182 50.000 0.00 0.00 0.00 5.54
2137 2146 1.116436 GCGACGAAGATGATCACTCG 58.884 55.000 17.55 17.55 0.00 4.18
2184 2193 3.614176 TCTGAATTCGAATGAGTTGCTCG 59.386 43.478 12.25 1.23 32.35 5.03
2187 2196 4.935885 AGTCTGAATTCGAATGAGTTGC 57.064 40.909 12.25 6.42 0.00 4.17
2188 2197 7.475565 CGTTTAAGTCTGAATTCGAATGAGTTG 59.524 37.037 19.63 8.21 0.00 3.16
2189 2198 7.510630 CGTTTAAGTCTGAATTCGAATGAGTT 58.489 34.615 12.25 15.10 0.00 3.01


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

AutoCloner maintained by Alex Coulton.