Multiple sequence alignment - TraesCS2D01G512400

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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 TraesCS2D01G512400 chr2D 100.000 2252 0 0 1 2252 603649470 603647219 0.000000e+00 4159.0
1 TraesCS2D01G512400 chr2D 88.123 261 13 3 993 1250 603632589 603632344 6.080000e-76 294.0
2 TraesCS2D01G512400 chr2D 81.034 232 25 13 685 910 603632915 603632697 1.380000e-37 167.0
3 TraesCS2D01G512400 chr2B 89.225 1355 97 21 913 2250 734200334 734199012 0.000000e+00 1648.0
4 TraesCS2D01G512400 chr2B 91.590 868 31 10 57 912 734201209 734200372 0.000000e+00 1160.0
5 TraesCS2D01G512400 chr2B 86.590 261 14 4 993 1250 734185418 734185176 3.690000e-68 268.0
6 TraesCS2D01G512400 chr2A 96.092 870 23 3 53 912 735788771 735787903 0.000000e+00 1408.0
7 TraesCS2D01G512400 chr2A 92.491 586 33 4 913 1493 735787865 735787286 0.000000e+00 828.0
8 TraesCS2D01G512400 chr2A 98.361 61 1 0 1 61 735789012 735788952 8.500000e-20 108.0
9 TraesCS2D01G512400 chr5D 88.945 199 20 1 1440 1636 6163467 6163665 6.210000e-61 244.0
10 TraesCS2D01G512400 chr1D 85.106 188 26 1 1452 1637 289957578 289957765 8.210000e-45 191.0
11 TraesCS2D01G512400 chr5B 83.916 143 23 0 1072 1214 357132390 357132532 1.080000e-28 137.0
12 TraesCS2D01G512400 chr5B 91.045 67 6 0 1709 1775 689263978 689263912 8.570000e-15 91.6
13 TraesCS2D01G512400 chr4B 94.030 67 4 0 1708 1774 391565584 391565518 3.960000e-18 102.0
14 TraesCS2D01G512400 chr3B 92.537 67 4 1 1708 1774 204634740 204634675 6.620000e-16 95.3
15 TraesCS2D01G512400 chr3B 91.045 67 6 0 1709 1775 88422130 88422064 8.570000e-15 91.6
16 TraesCS2D01G512400 chr3B 90.909 66 6 0 1708 1773 543766760 543766695 3.080000e-14 89.8
17 TraesCS2D01G512400 chr3B 91.935 62 5 0 1709 1770 755868977 755869038 1.110000e-13 87.9
18 TraesCS2D01G512400 chr6B 91.045 67 6 0 1709 1775 306798834 306798768 8.570000e-15 91.6
19 TraesCS2D01G512400 chr6D 89.855 69 7 0 1705 1773 453284067 453283999 3.080000e-14 89.8


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 TraesCS2D01G512400 chr2D 603647219 603649470 2251 True 4159.000000 4159 100.0000 1 2252 1 chr2D.!!$R1 2251
1 TraesCS2D01G512400 chr2D 603632344 603632915 571 True 230.500000 294 84.5785 685 1250 2 chr2D.!!$R2 565
2 TraesCS2D01G512400 chr2B 734199012 734201209 2197 True 1404.000000 1648 90.4075 57 2250 2 chr2B.!!$R2 2193
3 TraesCS2D01G512400 chr2A 735787286 735789012 1726 True 781.333333 1408 95.6480 1 1493 3 chr2A.!!$R1 1492

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
477 669 0.387112 GCTCATCGGCTGATCTCTCG 60.387 60.0 4.63 0.0 32.1 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2175 0.039074 CCTCACCATCTCGTATCGGC 60.039 60.0 0.0 0.0 0.0 5.54 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
38 39 7.133483 ACATGTATTAGGGAAAGAGTAGAGGT 58.867 38.462 0.00 0.00 0.00 3.85
159 351 7.602265 TGTCGATTGTAATCAAACTTCAGATCA 59.398 33.333 5.55 0.00 37.11 2.92
171 363 6.777526 AACTTCAGATCAGAGAAAGAAACG 57.222 37.500 0.00 0.00 0.00 3.60
344 536 1.103398 GCTCCCATCCAATCAACCCG 61.103 60.000 0.00 0.00 0.00 5.28
477 669 0.387112 GCTCATCGGCTGATCTCTCG 60.387 60.000 4.63 0.00 32.10 4.04
503 698 2.860628 GAACGCTGCATACGCCTCG 61.861 63.158 9.00 0.00 37.32 4.63
812 1017 7.924358 TGGTTCTATATATGTAACCACCACT 57.076 36.000 21.18 0.00 44.84 4.00
975 1238 3.505386 TGCCTTTCTTGCAGGGAATTTA 58.495 40.909 0.00 0.00 34.05 1.40
990 1253 3.504520 GGAATTTAACCTGTGCGAAGGAA 59.495 43.478 11.27 0.00 40.02 3.36
991 1254 4.473199 GAATTTAACCTGTGCGAAGGAAC 58.527 43.478 11.27 0.00 40.02 3.62
1149 1415 1.617018 CGGAGAGCATGAGGGTGGAA 61.617 60.000 0.00 0.00 0.00 3.53
1258 1527 1.587613 CTCGCCTTCTAGCTGTCGC 60.588 63.158 0.00 0.00 0.00 5.19
1412 1686 5.175127 TGTAACCACACATGCAGTACTATG 58.825 41.667 0.00 0.00 0.00 2.23
1413 1687 4.551702 AACCACACATGCAGTACTATGA 57.448 40.909 11.75 0.00 0.00 2.15
1414 1688 4.760530 ACCACACATGCAGTACTATGAT 57.239 40.909 11.75 0.00 0.00 2.45
1421 1695 6.127225 ACACATGCAGTACTATGATCTGTCTT 60.127 38.462 11.75 0.00 0.00 3.01
1467 1741 3.585862 TCTTGACATTAGAAGTGACGCC 58.414 45.455 0.00 0.00 0.00 5.68
1471 1745 3.994392 TGACATTAGAAGTGACGCCTTTC 59.006 43.478 0.00 0.00 0.00 2.62
1506 1780 9.715121 ATCATGAATTACAAACAGCTGAAAAAT 57.285 25.926 23.35 9.41 0.00 1.82
1509 1783 8.578308 TGAATTACAAACAGCTGAAAAATCTG 57.422 30.769 23.35 8.54 0.00 2.90
1572 1846 2.293399 GTGAAGGACCCACAACAATGAC 59.707 50.000 0.00 0.00 34.81 3.06
1589 1865 0.179081 GACAGCACCCCGAGTAATCC 60.179 60.000 0.00 0.00 0.00 3.01
1614 1890 1.048601 TTTCCCAAGCAGAGTCTCGT 58.951 50.000 0.00 0.00 0.00 4.18
1616 1892 0.539669 TCCCAAGCAGAGTCTCGTGA 60.540 55.000 0.00 0.00 0.00 4.35
1630 1906 4.127907 GTCTCGTGAAACCTTTCCTCTTT 58.872 43.478 0.00 0.00 36.36 2.52
1650 1926 1.995376 ACCTTCCTTTTGGTTCGCAT 58.005 45.000 0.00 0.00 41.38 4.73
1653 1929 3.254903 ACCTTCCTTTTGGTTCGCATAAC 59.745 43.478 0.00 0.00 41.38 1.89
1654 1930 3.366985 CCTTCCTTTTGGTTCGCATAACC 60.367 47.826 10.38 10.38 41.38 2.85
1720 2002 7.599171 ACAAAAGTCCCAAAAATACTTATCGG 58.401 34.615 0.00 0.00 33.24 4.18
1722 2004 8.301002 CAAAAGTCCCAAAAATACTTATCGGAA 58.699 33.333 0.00 0.00 33.24 4.30
1728 2010 8.254508 TCCCAAAAATACTTATCGGAAAAATGG 58.745 33.333 0.00 0.00 0.00 3.16
1738 2020 9.712305 ACTTATCGGAAAAATGGATGTATCTAG 57.288 33.333 0.00 0.00 0.00 2.43
1741 2023 7.361457 TCGGAAAAATGGATGTATCTAGACT 57.639 36.000 0.00 0.00 0.00 3.24
1816 2098 8.746922 ATTATAAGTTGTTTCAGTCGTACGAA 57.253 30.769 21.39 0.89 0.00 3.85
1833 2115 6.034591 CGTACGAAATGACTTTATGGACTCT 58.965 40.000 10.44 0.00 0.00 3.24
1836 2118 6.334202 ACGAAATGACTTTATGGACTCTCTC 58.666 40.000 0.00 0.00 0.00 3.20
1854 2136 2.162681 CTCAAAACTGGATTTCGCCCT 58.837 47.619 0.00 0.00 0.00 5.19
1855 2137 3.008594 TCTCAAAACTGGATTTCGCCCTA 59.991 43.478 0.00 0.00 0.00 3.53
1868 2150 7.881232 TGGATTTCGCCCTACTTTATATAAAGG 59.119 37.037 29.82 18.28 45.23 3.11
1874 2156 7.712205 TCGCCCTACTTTATATAAAGGAACAAC 59.288 37.037 29.82 17.49 45.23 3.32
1892 2174 1.913778 ACCGAAAAATTACCCGGCTT 58.086 45.000 0.00 0.00 45.29 4.35
1893 2175 1.542472 ACCGAAAAATTACCCGGCTTG 59.458 47.619 0.00 0.00 45.29 4.01
1894 2176 1.624487 CGAAAAATTACCCGGCTTGC 58.376 50.000 0.00 0.00 0.00 4.01
1907 2189 0.946221 GGCTTGCCGATACGAGATGG 60.946 60.000 0.00 0.00 0.00 3.51
1929 2211 0.464452 AGGTAGCCCTCATACAACGC 59.536 55.000 0.00 0.00 35.62 4.84
1930 2212 0.532196 GGTAGCCCTCATACAACGCC 60.532 60.000 0.00 0.00 0.00 5.68
1931 2213 0.874607 GTAGCCCTCATACAACGCCG 60.875 60.000 0.00 0.00 0.00 6.46
1938 2220 0.104120 TCATACAACGCCGATCCCAG 59.896 55.000 0.00 0.00 0.00 4.45
1958 2240 2.093973 AGAATAACCGGAGCACACAGAG 60.094 50.000 9.46 0.00 0.00 3.35
1960 2242 1.468506 TAACCGGAGCACACAGAGCA 61.469 55.000 9.46 0.00 0.00 4.26
1998 2280 4.684703 ACCGAAAGAGTACAAATGAAGACG 59.315 41.667 0.00 0.00 0.00 4.18
1999 2281 4.091509 CCGAAAGAGTACAAATGAAGACGG 59.908 45.833 0.00 0.00 0.00 4.79
2029 2311 1.066605 ACACGCTACGCCCTATAACAG 59.933 52.381 0.00 0.00 0.00 3.16
2051 2333 0.773644 AAGCTCCATGACAACACCCT 59.226 50.000 0.00 0.00 0.00 4.34
2054 2336 1.947678 GCTCCATGACAACACCCTCAG 60.948 57.143 0.00 0.00 0.00 3.35
2064 2346 1.186267 ACACCCTCAGGACGGAGAAC 61.186 60.000 0.00 0.00 37.05 3.01
2065 2347 1.977544 ACCCTCAGGACGGAGAACG 60.978 63.158 0.00 0.00 42.55 3.95
2075 2357 3.204505 CGGAGAACGGTGTTAAGCA 57.795 52.632 0.00 0.00 39.42 3.91
2097 2379 3.842923 CGCTGCCGAGTCCAGGAT 61.843 66.667 0.00 0.00 36.29 3.24
2128 2410 3.402681 CACCCGGAGCCCTGACAT 61.403 66.667 0.73 0.00 0.00 3.06
2136 2418 1.004745 GGAGCCCTGACATGAAAAGGA 59.995 52.381 0.00 0.00 32.43 3.36
2182 2465 2.027024 GTGTCGTCACGAGTGGCA 59.973 61.111 0.00 0.00 36.23 4.92
2191 2474 0.943835 CACGAGTGGCATTGTCGTCA 60.944 55.000 16.50 0.00 44.82 4.35
2192 2475 0.249699 ACGAGTGGCATTGTCGTCAA 60.250 50.000 14.38 0.00 43.19 3.18
2193 2476 0.439985 CGAGTGGCATTGTCGTCAAG 59.560 55.000 0.97 0.00 36.97 3.02
2204 2487 0.784778 GTCGTCAAGGACAAAGCTCG 59.215 55.000 0.00 0.00 36.91 5.03
2205 2488 0.671796 TCGTCAAGGACAAAGCTCGA 59.328 50.000 0.00 0.00 32.09 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.124477 AAATTTTGCCTTCCGCCCCA 61.124 50.000 0.00 0.00 36.24 4.96
159 351 2.104963 ACTTCCTGCCGTTTCTTTCTCT 59.895 45.455 0.00 0.00 0.00 3.10
171 363 1.337167 GCCATTTGTCAACTTCCTGCC 60.337 52.381 0.00 0.00 0.00 4.85
344 536 3.818773 TCTCTTCGGTTTGAAATTGGGAC 59.181 43.478 0.00 0.00 35.79 4.46
459 651 0.387112 GCGAGAGATCAGCCGATGAG 60.387 60.000 0.00 0.00 42.53 2.90
477 669 1.078709 TATGCAGCGTTCAGACTTGC 58.921 50.000 0.00 0.00 35.71 4.01
622 817 1.065764 GGGAAATGAAATCGGCGCC 59.934 57.895 19.07 19.07 0.00 6.53
975 1238 1.523758 GATGTTCCTTCGCACAGGTT 58.476 50.000 0.00 0.00 35.15 3.50
1067 1330 4.468689 CCGTCCCCTTCTTCCCGC 62.469 72.222 0.00 0.00 0.00 6.13
1068 1331 3.782443 CCCGTCCCCTTCTTCCCG 61.782 72.222 0.00 0.00 0.00 5.14
1069 1332 3.408853 CCCCGTCCCCTTCTTCCC 61.409 72.222 0.00 0.00 0.00 3.97
1110 1376 0.461548 TCTTGCCCATCTGCTCGTAG 59.538 55.000 0.00 0.00 0.00 3.51
1203 1469 3.106986 GCTCCTGCGGCCTATGGAA 62.107 63.158 0.00 0.00 0.00 3.53
1280 1549 4.019860 AGCTCACATGTTAGAACAGGACAT 60.020 41.667 13.51 0.00 42.86 3.06
1412 1686 3.870633 AGTTCACGGGTAAGACAGATC 57.129 47.619 0.00 0.00 0.00 2.75
1413 1687 3.864921 GCAAGTTCACGGGTAAGACAGAT 60.865 47.826 0.00 0.00 0.00 2.90
1414 1688 2.547218 GCAAGTTCACGGGTAAGACAGA 60.547 50.000 0.00 0.00 0.00 3.41
1421 1695 0.470766 AAGTGGCAAGTTCACGGGTA 59.529 50.000 0.00 0.00 39.86 3.69
1448 1722 3.678056 AGGCGTCACTTCTAATGTCAA 57.322 42.857 0.00 0.00 0.00 3.18
1484 1758 8.196771 ACAGATTTTTCAGCTGTTTGTAATTCA 58.803 29.630 14.67 0.00 39.69 2.57
1495 1769 7.928103 AGATAGCAATACAGATTTTTCAGCTG 58.072 34.615 7.63 7.63 35.81 4.24
1535 1809 6.599244 GGTCCTTCACTTTCATCACATCAATA 59.401 38.462 0.00 0.00 0.00 1.90
1552 1826 2.092158 TGTCATTGTTGTGGGTCCTTCA 60.092 45.455 0.00 0.00 0.00 3.02
1572 1846 0.462047 GTGGATTACTCGGGGTGCTG 60.462 60.000 0.00 0.00 0.00 4.41
1589 1865 1.242076 CTCTGCTTGGGAAACAGGTG 58.758 55.000 0.00 0.00 32.19 4.00
1614 1890 5.133830 AGGAAGGTAAAGAGGAAAGGTTTCA 59.866 40.000 4.89 0.00 38.92 2.69
1616 1892 5.664815 AGGAAGGTAAAGAGGAAAGGTTT 57.335 39.130 0.00 0.00 0.00 3.27
1630 1906 2.642154 TGCGAACCAAAAGGAAGGTA 57.358 45.000 0.00 0.00 37.07 3.08
1704 1980 9.816354 ATCCATTTTTCCGATAAGTATTTTTGG 57.184 29.630 0.00 0.00 32.45 3.28
1712 1994 9.712305 CTAGATACATCCATTTTTCCGATAAGT 57.288 33.333 0.00 0.00 0.00 2.24
1716 1998 7.967908 AGTCTAGATACATCCATTTTTCCGAT 58.032 34.615 0.00 0.00 0.00 4.18
1789 2071 9.838975 TCGTACGACTGAAACAACTTATAATTA 57.161 29.630 15.28 0.00 0.00 1.40
1790 2072 8.746922 TCGTACGACTGAAACAACTTATAATT 57.253 30.769 15.28 0.00 0.00 1.40
1791 2073 8.746922 TTCGTACGACTGAAACAACTTATAAT 57.253 30.769 19.36 0.00 0.00 1.28
1792 2074 8.572828 TTTCGTACGACTGAAACAACTTATAA 57.427 30.769 19.36 0.32 0.00 0.98
1793 2075 8.641155 CATTTCGTACGACTGAAACAACTTATA 58.359 33.333 19.36 0.00 36.96 0.98
1794 2076 7.383029 TCATTTCGTACGACTGAAACAACTTAT 59.617 33.333 19.36 0.00 36.96 1.73
1806 2088 5.803967 GTCCATAAAGTCATTTCGTACGACT 59.196 40.000 19.36 9.22 41.70 4.18
1810 2092 7.259161 AGAGAGTCCATAAAGTCATTTCGTAC 58.741 38.462 0.00 0.00 0.00 3.67
1813 2095 6.333416 TGAGAGAGTCCATAAAGTCATTTCG 58.667 40.000 0.00 0.00 0.00 3.46
1814 2096 8.553459 TTTGAGAGAGTCCATAAAGTCATTTC 57.447 34.615 0.00 0.00 0.00 2.17
1816 2098 8.160106 AGTTTTGAGAGAGTCCATAAAGTCATT 58.840 33.333 0.00 0.00 0.00 2.57
1833 2115 2.159382 GGGCGAAATCCAGTTTTGAGA 58.841 47.619 0.00 0.00 33.71 3.27
1836 2118 3.081804 AGTAGGGCGAAATCCAGTTTTG 58.918 45.455 0.00 0.00 34.79 2.44
1868 2150 3.567530 CCGGGTAATTTTTCGGTTGTTC 58.432 45.455 0.00 0.00 37.92 3.18
1874 2156 1.734377 GCAAGCCGGGTAATTTTTCGG 60.734 52.381 6.57 8.17 44.70 4.30
1892 2174 0.668535 CTCACCATCTCGTATCGGCA 59.331 55.000 0.00 0.00 0.00 5.69
1893 2175 0.039074 CCTCACCATCTCGTATCGGC 60.039 60.000 0.00 0.00 0.00 5.54
1894 2176 1.319541 ACCTCACCATCTCGTATCGG 58.680 55.000 0.00 0.00 0.00 4.18
1928 2210 0.602905 CCGGTTATTCTGGGATCGGC 60.603 60.000 0.00 0.00 38.86 5.54
1929 2211 1.000955 CTCCGGTTATTCTGGGATCGG 59.999 57.143 0.00 0.00 42.62 4.18
1930 2212 1.605712 GCTCCGGTTATTCTGGGATCG 60.606 57.143 0.00 0.00 42.62 3.69
1931 2213 1.416401 TGCTCCGGTTATTCTGGGATC 59.584 52.381 0.00 0.00 42.62 3.36
1938 2220 2.271800 CTCTGTGTGCTCCGGTTATTC 58.728 52.381 0.00 0.00 0.00 1.75
1958 2240 2.356553 TACCGTGGTCGCTTGTGC 60.357 61.111 0.00 0.00 35.54 4.57
1960 2242 2.341176 GGTACCGTGGTCGCTTGT 59.659 61.111 0.00 0.00 35.54 3.16
1971 2253 4.487948 TCATTTGTACTCTTTCGGTACCG 58.512 43.478 28.66 28.66 38.84 4.02
1973 2255 6.183359 CGTCTTCATTTGTACTCTTTCGGTAC 60.183 42.308 0.00 0.00 39.70 3.34
1978 2260 5.927115 ACTCCGTCTTCATTTGTACTCTTTC 59.073 40.000 0.00 0.00 0.00 2.62
1998 2280 1.611043 GTAGCGTGTCGTTGTACTCC 58.389 55.000 0.00 0.00 0.00 3.85
1999 2281 1.245224 CGTAGCGTGTCGTTGTACTC 58.755 55.000 0.00 0.00 0.00 2.59
2029 2311 1.740025 GGTGTTGTCATGGAGCTTAGC 59.260 52.381 0.00 0.00 0.00 3.09
2051 2333 1.111116 AACACCGTTCTCCGTCCTGA 61.111 55.000 0.00 0.00 33.66 3.86
2054 2336 1.706443 CTTAACACCGTTCTCCGTCC 58.294 55.000 0.00 0.00 33.66 4.79
2065 2347 0.447801 CAGCGGTGATGCTTAACACC 59.552 55.000 9.50 0.00 44.46 4.16
2071 2353 4.393155 TCGGCAGCGGTGATGCTT 62.393 61.111 20.69 0.00 44.46 3.91
2075 2357 4.148825 GGACTCGGCAGCGGTGAT 62.149 66.667 20.69 0.00 0.00 3.06
2080 2362 3.842923 ATCCTGGACTCGGCAGCG 61.843 66.667 0.00 0.00 0.00 5.18
2082 2364 2.060383 TCCATCCTGGACTCGGCAG 61.060 63.158 0.00 0.00 42.67 4.85
2128 2410 0.179234 TGTCGTGGTGCTCCTTTTCA 59.821 50.000 6.34 0.00 34.23 2.69
2157 2439 0.873054 TCGTGACGACACTCTCTTCC 59.127 55.000 15.65 0.00 43.99 3.46
2189 2472 1.512926 GCTTCGAGCTTTGTCCTTGA 58.487 50.000 0.00 0.00 38.45 3.02
2204 2487 1.443363 GCTGCCGAGCAAAAGCTTC 60.443 57.895 0.00 0.00 45.46 3.86
2205 2488 2.647297 GCTGCCGAGCAAAAGCTT 59.353 55.556 0.00 0.00 45.46 3.74


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

AutoCloner maintained by Alex Coulton.