Multiple sequence alignment - TraesCS5D01G397500

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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 TraesCS5D01G397500 chr5D 100.000 1865 0 0 499 2363 464225944 464227808 0.000000e+00 3445
1 TraesCS5D01G397500 chr5D 100.000 119 0 0 1 119 464225446 464225564 1.100000e-53 220
2 TraesCS5D01G397500 chr5B 91.186 1838 79 31 514 2344 571321259 571323020 0.000000e+00 2420
3 TraesCS5D01G397500 chr5A 92.258 1550 65 22 514 2058 584662906 584664405 0.000000e+00 2146
4 TraesCS5D01G397500 chr5A 93.688 301 9 3 2064 2363 584664485 584664776 2.160000e-120 442
5 TraesCS5D01G397500 chr5A 91.525 118 10 0 1 118 584662797 584662914 1.880000e-36 163


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 TraesCS5D01G397500 chr5D 464225446 464227808 2362 False 1832.5 3445 100.000000 1 2363 2 chr5D.!!$F1 2362
1 TraesCS5D01G397500 chr5B 571321259 571323020 1761 False 2420.0 2420 91.186000 514 2344 1 chr5B.!!$F1 1830
2 TraesCS5D01G397500 chr5A 584662797 584664776 1979 False 917.0 2146 92.490333 1 2363 3 chr5A.!!$F1 2362

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
91 92 0.604073 TGCCCGAGTAACGAATCACA 59.396 50.0 0.0 0.0 45.77 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1671 0.098376 CACAGGCTCTACGTACGGAC 59.902 60.0 21.06 3.28 0.0 4.79 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
70 71 8.447924 AAACTAAGGAAAAAGTACCAACTCTC 57.552 34.615 0.00 0.00 33.75 3.20
71 72 6.531923 ACTAAGGAAAAAGTACCAACTCTCC 58.468 40.000 0.00 0.00 33.75 3.71
83 84 0.896226 AACTCTCCTGCCCGAGTAAC 59.104 55.000 0.00 0.00 39.44 2.50
91 92 0.604073 TGCCCGAGTAACGAATCACA 59.396 50.000 0.00 0.00 45.77 3.58
92 93 1.206132 TGCCCGAGTAACGAATCACAT 59.794 47.619 0.00 0.00 45.77 3.21
101 102 3.940209 AACGAATCACATGGTGCAAAT 57.060 38.095 0.00 0.00 32.98 2.32
117 118 4.864916 GCAAATTGCGATCTACTCTTCA 57.135 40.909 0.90 0.00 31.71 3.02
118 119 4.830912 GCAAATTGCGATCTACTCTTCAG 58.169 43.478 0.90 0.00 31.71 3.02
572 573 7.093771 ACGTATCACTTGCATGAGATCCATATA 60.094 37.037 14.30 0.00 33.31 0.86
634 635 2.434359 CTTTCGGTGCGAGACCCC 60.434 66.667 0.00 0.00 42.62 4.95
635 636 3.952628 CTTTCGGTGCGAGACCCCC 62.953 68.421 0.00 0.00 42.62 5.40
676 679 6.968131 ATCTATAATAATGAACGCGTGCAT 57.032 33.333 27.21 27.21 0.00 3.96
678 681 2.473530 AATAATGAACGCGTGCATGG 57.526 45.000 32.61 0.31 0.00 3.66
706 709 6.664816 TGAGGCAAGAATTAATTTCTCCACAT 59.335 34.615 1.43 0.00 44.09 3.21
1050 1055 1.448540 CTACAAGGCGCTGGTGGAG 60.449 63.158 7.64 5.30 0.00 3.86
1392 1397 1.474478 TCGATCTGCAGGTCTCTTGTC 59.526 52.381 24.11 0.00 0.00 3.18
1495 1501 5.696270 TGCAGATAAATTCGTCGCATTATCT 59.304 36.000 15.35 15.35 42.74 1.98
1567 1573 1.227999 ATTGCTGCGTACGTGTTGCT 61.228 50.000 17.90 0.00 0.00 3.91
1572 1578 1.728426 GCGTACGTGTTGCTCTCGT 60.728 57.895 17.90 12.23 45.83 4.18
1600 1606 1.202031 GCGACCTTTTAACATGGCGAG 60.202 52.381 0.00 0.00 0.00 5.03
1654 1662 1.006922 GGGAGTTGCAAGTTGCTGC 60.007 57.895 27.17 19.02 45.31 5.25
1660 1668 0.536260 TTGCAAGTTGCTGCCAAAGT 59.464 45.000 27.17 0.00 45.31 2.66
1663 1671 1.480205 CAAGTTGCTGCCAAAGTTCG 58.520 50.000 0.00 0.00 31.68 3.95
1667 1675 1.781025 TTGCTGCCAAAGTTCGTCCG 61.781 55.000 0.00 0.00 0.00 4.79
1732 1740 6.018425 CACATACAAGAATAAGAAGCAGCGAT 60.018 38.462 0.00 0.00 0.00 4.58
1740 1748 2.278466 AAGCAGCGATCGAGCGAG 60.278 61.111 29.29 18.97 43.00 5.03
1741 1749 2.928313 GAAGCAGCGATCGAGCGAGT 62.928 60.000 29.29 10.22 43.00 4.18
1742 1750 3.318555 GCAGCGATCGAGCGAGTG 61.319 66.667 29.29 22.77 43.00 3.51
1743 1751 2.405191 CAGCGATCGAGCGAGTGA 59.595 61.111 29.29 0.00 43.00 3.41
1804 1812 5.109903 CAAATCCAAAGTAGGAGTAGGACG 58.890 45.833 0.00 0.00 41.90 4.79
1805 1813 3.726557 TCCAAAGTAGGAGTAGGACGA 57.273 47.619 0.00 0.00 32.77 4.20
1806 1814 3.618351 TCCAAAGTAGGAGTAGGACGAG 58.382 50.000 0.00 0.00 32.77 4.18
1807 1815 2.099427 CCAAAGTAGGAGTAGGACGAGC 59.901 54.545 0.00 0.00 0.00 5.03
1808 1816 2.055684 AAGTAGGAGTAGGACGAGCC 57.944 55.000 0.00 0.00 0.00 4.70
1809 1817 0.183252 AGTAGGAGTAGGACGAGCCC 59.817 60.000 0.00 0.00 37.37 5.19
1810 1818 0.822944 GTAGGAGTAGGACGAGCCCC 60.823 65.000 0.00 0.00 37.37 5.80
1811 1819 2.335092 TAGGAGTAGGACGAGCCCCG 62.335 65.000 0.00 0.00 45.44 5.73
1812 1820 3.217743 GAGTAGGACGAGCCCCGG 61.218 72.222 0.00 0.00 43.93 5.73
1951 1961 6.920569 TTCAGTTTAGGAAGTTTGTCTGAC 57.079 37.500 0.00 0.00 31.82 3.51
1997 2007 1.216977 CACAGCCCAATCGTACGGA 59.783 57.895 16.52 2.44 0.00 4.69
2058 2069 0.250901 GTGTCATGTCAGCTTGGGGT 60.251 55.000 0.00 0.00 0.00 4.95
2059 2070 0.478072 TGTCATGTCAGCTTGGGGTT 59.522 50.000 0.00 0.00 0.00 4.11
2103 2188 0.249238 CCTAGTCGGCAGAGATGTGC 60.249 60.000 0.00 0.00 43.19 4.57
2164 2249 0.598562 AGGTGACAGTGACGCTACAG 59.401 55.000 0.00 0.00 0.00 2.74
2175 2260 1.065928 CGCTACAGGATGGTCCGAC 59.934 63.158 0.00 0.00 42.75 4.79
2194 2279 1.208259 CGCAAAGCCTTTTTGTGTCC 58.792 50.000 5.32 0.00 35.76 4.02
2273 2358 5.652014 TCCAAACTGACAAAACAGAGAATGT 59.348 36.000 0.00 0.00 46.97 2.71
2274 2359 5.973565 CCAAACTGACAAAACAGAGAATGTC 59.026 40.000 0.00 0.00 43.00 3.06
2275 2360 6.183360 CCAAACTGACAAAACAGAGAATGTCT 60.183 38.462 0.00 0.00 43.00 3.41
2276 2361 7.253422 CAAACTGACAAAACAGAGAATGTCTT 58.747 34.615 0.00 0.00 43.00 3.01
2277 2362 8.397906 CAAACTGACAAAACAGAGAATGTCTTA 58.602 33.333 0.00 0.00 43.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.659830 ACGTAGAATTGTGTGTTTAGAAATTTC 57.340 29.630 10.33 10.33 0.00 2.17
17 18 7.792925 TCATTCACGTAGAATTGTGTGTTTAG 58.207 34.615 9.56 0.00 44.48 1.85
19 20 6.612247 TCATTCACGTAGAATTGTGTGTTT 57.388 33.333 9.56 0.00 44.48 2.83
68 69 0.460311 ATTCGTTACTCGGGCAGGAG 59.540 55.000 3.56 3.56 40.32 3.69
70 71 0.174845 TGATTCGTTACTCGGGCAGG 59.825 55.000 0.00 0.00 40.32 4.85
71 72 1.278238 GTGATTCGTTACTCGGGCAG 58.722 55.000 0.00 0.00 40.32 4.85
83 84 2.346244 GCAATTTGCACCATGTGATTCG 59.654 45.455 16.35 0.00 44.26 3.34
91 92 3.282021 AGTAGATCGCAATTTGCACCAT 58.718 40.909 20.56 9.27 45.36 3.55
92 93 2.677836 GAGTAGATCGCAATTTGCACCA 59.322 45.455 20.56 4.82 45.36 4.17
501 502 0.173708 GAAGAGTACCAGTGGCGGAG 59.826 60.000 9.78 0.00 0.00 4.63
502 503 0.541063 TGAAGAGTACCAGTGGCGGA 60.541 55.000 9.78 0.00 0.00 5.54
503 504 0.320374 TTGAAGAGTACCAGTGGCGG 59.680 55.000 9.78 0.00 0.00 6.13
504 505 1.673033 CCTTGAAGAGTACCAGTGGCG 60.673 57.143 9.78 0.00 0.00 5.69
505 506 1.946283 GCCTTGAAGAGTACCAGTGGC 60.946 57.143 9.78 0.00 0.00 5.01
506 507 1.673033 CGCCTTGAAGAGTACCAGTGG 60.673 57.143 7.91 7.91 0.00 4.00
507 508 1.714794 CGCCTTGAAGAGTACCAGTG 58.285 55.000 0.00 0.00 0.00 3.66
508 509 0.037232 GCGCCTTGAAGAGTACCAGT 60.037 55.000 0.00 0.00 0.00 4.00
509 510 1.078759 CGCGCCTTGAAGAGTACCAG 61.079 60.000 0.00 0.00 0.00 4.00
510 511 1.080093 CGCGCCTTGAAGAGTACCA 60.080 57.895 0.00 0.00 0.00 3.25
511 512 0.179108 ATCGCGCCTTGAAGAGTACC 60.179 55.000 0.00 0.00 0.00 3.34
512 513 1.201343 GATCGCGCCTTGAAGAGTAC 58.799 55.000 0.00 0.00 0.00 2.73
572 573 1.409064 TCTCAGAAAGTGACACGTGCT 59.591 47.619 17.22 1.20 0.00 4.40
676 679 7.722949 AGAAATTAATTCTTGCCTCATTCCA 57.277 32.000 0.10 0.00 46.39 3.53
1266 1271 3.403249 CTCGTCTCCGTCGTCGTCG 62.403 68.421 4.87 4.87 38.55 5.12
1267 1272 2.394912 CTCGTCTCCGTCGTCGTC 59.605 66.667 0.71 0.00 35.01 4.20
1268 1273 3.117171 CCTCGTCTCCGTCGTCGT 61.117 66.667 0.71 0.00 35.01 4.34
1289 1294 2.276740 CCTTCCCATCCTGCACCC 59.723 66.667 0.00 0.00 0.00 4.61
1353 1358 3.717400 GATGGATCGAGCTAGTTGTCA 57.283 47.619 0.00 0.00 0.00 3.58
1380 1385 1.734477 CACGGCGACAAGAGACCTG 60.734 63.158 16.62 0.00 0.00 4.00
1381 1386 1.251527 ATCACGGCGACAAGAGACCT 61.252 55.000 16.62 0.00 0.00 3.85
1382 1387 1.078759 CATCACGGCGACAAGAGACC 61.079 60.000 16.62 0.00 0.00 3.85
1392 1397 0.792640 GATGGATTAGCATCACGGCG 59.207 55.000 4.80 4.80 39.27 6.46
1427 1432 6.180472 TCCATATGACTCACTATATCAGCGA 58.820 40.000 3.65 0.00 0.00 4.93
1428 1433 6.442513 TCCATATGACTCACTATATCAGCG 57.557 41.667 3.65 0.00 0.00 5.18
1502 1508 9.429359 GATCAGTTCTTGTTTTCTCTCAATCTA 57.571 33.333 0.00 0.00 0.00 1.98
1539 1545 2.471370 CGTACGCAGCAATATCACGATT 59.529 45.455 0.52 0.00 0.00 3.34
1600 1606 4.450080 CGTACCCCTGTTTTTCTACTGTTC 59.550 45.833 0.00 0.00 0.00 3.18
1663 1671 0.098376 CACAGGCTCTACGTACGGAC 59.902 60.000 21.06 3.28 0.00 4.79
1667 1675 2.541178 CGAATCCACAGGCTCTACGTAC 60.541 54.545 0.00 0.00 0.00 3.67
1699 1707 9.838339 CTTCTTATTCTTGTATGTGGAGGTTAT 57.162 33.333 0.00 0.00 0.00 1.89
1732 1740 1.134670 TCAGATCTCTCACTCGCTCGA 60.135 52.381 0.00 0.00 0.00 4.04
1740 1748 4.639755 TCACTGTCAGATCAGATCTCTCAC 59.360 45.833 10.25 8.09 37.58 3.51
1741 1749 4.853007 TCACTGTCAGATCAGATCTCTCA 58.147 43.478 10.25 10.98 37.58 3.27
1742 1750 5.833406 TTCACTGTCAGATCAGATCTCTC 57.167 43.478 10.25 7.11 37.58 3.20
1743 1751 6.397272 GTTTTCACTGTCAGATCAGATCTCT 58.603 40.000 10.25 0.00 37.58 3.10
1809 1817 4.394712 GTGACAGGACAGGGCCGG 62.395 72.222 0.79 0.79 0.00 6.13
1810 1818 3.302347 GAGTGACAGGACAGGGCCG 62.302 68.421 0.00 0.00 0.00 6.13
1811 1819 1.484444 AAGAGTGACAGGACAGGGCC 61.484 60.000 0.00 0.00 0.00 5.80
1812 1820 0.321122 CAAGAGTGACAGGACAGGGC 60.321 60.000 0.00 0.00 0.00 5.19
1813 1821 1.051812 ACAAGAGTGACAGGACAGGG 58.948 55.000 0.00 0.00 0.00 4.45
1817 1825 3.973657 TCGTTTACAAGAGTGACAGGAC 58.026 45.455 0.00 0.00 0.00 3.85
1951 1961 2.348872 GCAACAACAGATATCGCCATCG 60.349 50.000 0.00 0.00 0.00 3.84
1997 2007 3.402681 CCCTCCATCCACCTGCGT 61.403 66.667 0.00 0.00 0.00 5.24
2058 2069 2.432444 CGGTCTCCTTGCAAACCATAA 58.568 47.619 16.30 0.00 0.00 1.90
2059 2070 1.339631 CCGGTCTCCTTGCAAACCATA 60.340 52.381 16.30 0.00 0.00 2.74
2164 2249 2.750888 GCTTTGCGTCGGACCATCC 61.751 63.158 1.91 0.00 0.00 3.51
2175 2260 1.202405 AGGACACAAAAAGGCTTTGCG 60.202 47.619 14.19 10.11 32.93 4.85
2194 2279 1.364626 GCGATGGAACTGGAGTGCAG 61.365 60.000 10.51 10.51 0.00 4.41
2273 2358 7.786030 AGCTAGCAGTGTCAAATAAGATAAGA 58.214 34.615 18.83 0.00 0.00 2.10
2274 2359 8.430801 AAGCTAGCAGTGTCAAATAAGATAAG 57.569 34.615 18.83 0.00 0.00 1.73
2275 2360 8.260818 AGAAGCTAGCAGTGTCAAATAAGATAA 58.739 33.333 18.83 0.00 0.00 1.75
2276 2361 7.786030 AGAAGCTAGCAGTGTCAAATAAGATA 58.214 34.615 18.83 0.00 0.00 1.98
2277 2362 6.648192 AGAAGCTAGCAGTGTCAAATAAGAT 58.352 36.000 18.83 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.