Multiple sequence alignment - TraesCS6D01G245600

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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 TraesCS6D01G245600 chr6D 100.000 2126 0 0 1 2126 347689304 347687179 0.000000e+00 3927
1 TraesCS6D01G245600 chr6A 91.304 1380 71 17 1 1336 495683934 495685308 0.000000e+00 1838
2 TraesCS6D01G245600 chr6A 97.598 458 9 2 1670 2126 495685750 495686206 0.000000e+00 784
3 TraesCS6D01G245600 chr6A 95.297 404 13 3 1337 1739 495685388 495685786 8.270000e-179 636
4 TraesCS6D01G245600 chr6B 90.401 1396 70 11 1 1336 532336656 532338047 0.000000e+00 1777
5 TraesCS6D01G245600 chr6B 95.949 790 27 2 1337 2126 532338128 532338912 0.000000e+00 1277


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 TraesCS6D01G245600 chr6D 347687179 347689304 2125 True 3927 3927 100.000 1 2126 1 chr6D.!!$R1 2125
1 TraesCS6D01G245600 chr6A 495683934 495686206 2272 False 1086 1838 94.733 1 2126 3 chr6A.!!$F1 2125
2 TraesCS6D01G245600 chr6B 532336656 532338912 2256 False 1527 1777 93.175 1 2126 2 chr6B.!!$F1 2125

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
444 453 0.10852 TTGAGATGCCGGGTCGTTAC 60.109 55.0 2.18 0.0 0.0 2.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1753 0.31716 TCAGTCCGCACGAACAGATT 59.683 50.0 0.0 0.0 0.0 2.4 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
48 49 5.012239 AGCTTGTTTTCAGGATTATGCTGA 58.988 37.500 12.34 12.34 43.20 4.26
57 58 5.061853 TCAGGATTATGCTGAGATGCTTTC 58.938 41.667 12.34 0.00 39.98 2.62
71 72 5.787380 AGATGCTTTCCTGTTTGGATTTTC 58.213 37.500 0.00 0.00 45.68 2.29
97 99 6.084326 TCTTCCTTTTGTTGGCTGATTTAC 57.916 37.500 0.00 0.00 0.00 2.01
104 112 9.050601 CCTTTTGTTGGCTGATTTACATTTTTA 57.949 29.630 0.00 0.00 0.00 1.52
117 125 6.551385 TTACATTTTTACGCGGAAAGGTTA 57.449 33.333 17.28 9.86 32.74 2.85
140 149 1.525718 TTTCCCGTTAAAAGGCGCCC 61.526 55.000 26.15 5.24 0.00 6.13
235 244 4.001618 ACAGAAGTTTGAGAGAGAAGCC 57.998 45.455 0.00 0.00 0.00 4.35
249 258 4.019858 AGAGAAGCCCAGAAAAATAAGGC 58.980 43.478 0.00 0.00 44.20 4.35
255 264 3.588955 CCCAGAAAAATAAGGCAGCAAC 58.411 45.455 0.00 0.00 0.00 4.17
353 362 2.774687 ACGATAAAACCGTTTGAGCCT 58.225 42.857 0.00 0.00 36.83 4.58
359 368 4.929819 AAAACCGTTTGAGCCTGTAATT 57.070 36.364 0.00 0.00 0.00 1.40
444 453 0.108520 TTGAGATGCCGGGTCGTTAC 60.109 55.000 2.18 0.00 0.00 2.50
453 462 1.418342 CGGGTCGTTACTGCGATTGG 61.418 60.000 0.00 0.00 43.07 3.16
627 639 5.859521 TCATTTTGTGCATTAATGTTGGC 57.140 34.783 16.61 3.07 32.49 4.52
748 772 6.773976 TGGATGCTTTAAACTAGATTTGGG 57.226 37.500 0.00 0.00 0.00 4.12
831 855 3.006940 TCCAAATGGTTCTATGTCGCAC 58.993 45.455 0.00 0.00 36.34 5.34
892 942 5.550290 TGGCATACACTATACCATGTCATG 58.450 41.667 5.79 5.79 28.54 3.07
943 993 9.459640 CCACATCATTCTGATTCAAATACATTC 57.540 33.333 0.00 0.00 34.28 2.67
961 1011 6.762702 ACATTCATTGTATCAGATTGCACA 57.237 33.333 0.00 0.00 36.57 4.57
991 1041 6.035112 GTGATCTTAGGAGCTTAAAGTGTTCG 59.965 42.308 0.00 0.00 0.00 3.95
1266 1344 6.695429 TCTCTATTTATCAGCGCATCATCTT 58.305 36.000 11.47 0.00 0.00 2.40
1283 1361 8.977505 GCATCATCTTCAGAGTAACTTCTTATC 58.022 37.037 0.00 0.00 0.00 1.75
1302 1380 8.289939 TCTTATCGTAGTCAAATCCAGTAGTT 57.710 34.615 0.00 0.00 0.00 2.24
1325 1403 3.354948 TGCTGATCATGTAAACTGGCT 57.645 42.857 0.00 0.00 0.00 4.75
1375 1537 8.585189 ACATTCTGAATTTCTTTTCTCTTTGC 57.415 30.769 0.00 0.00 0.00 3.68
1376 1538 8.419442 ACATTCTGAATTTCTTTTCTCTTTGCT 58.581 29.630 0.00 0.00 0.00 3.91
1452 1614 5.417580 CCCTAGTTAGTTGCCATTTGCTTTA 59.582 40.000 0.00 0.00 42.00 1.85
1457 1619 3.981211 AGTTGCCATTTGCTTTACTGTG 58.019 40.909 0.00 0.00 42.00 3.66
1580 1742 1.177401 GGAGGCCCACTGTTCAATTC 58.823 55.000 0.00 0.00 0.00 2.17
1591 1753 5.353956 CCACTGTTCAATTCACGGATCATAA 59.646 40.000 0.00 0.00 0.00 1.90
1605 1767 3.059597 GGATCATAAATCTGTTCGTGCGG 60.060 47.826 0.00 0.00 0.00 5.69
1618 1780 1.749063 TCGTGCGGACTGATAGACAAT 59.251 47.619 5.27 0.00 0.00 2.71
1685 1881 8.698973 TGTTGATTTTTCTTGATACCTGGTTA 57.301 30.769 3.84 0.00 0.00 2.85
1707 1903 3.230976 TCCCAAAGGAAAAGGCTTCTTC 58.769 45.455 0.00 6.89 40.08 2.87
1757 1953 6.660949 AGCTTCTATCAGGCAACAAAATTACT 59.339 34.615 0.00 0.00 41.41 2.24
1833 2030 3.442273 TGTATTGAATTCCTGTTTCGGGC 59.558 43.478 2.27 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 2.892852 TCAGCCAACAAAAGGAAGATGG 59.107 45.455 0.00 0.00 0.00 3.51
97 99 5.038247 AGTAACCTTTCCGCGTAAAAATG 57.962 39.130 4.92 2.73 0.00 2.32
104 112 2.291465 GGAAAAAGTAACCTTTCCGCGT 59.709 45.455 4.92 0.00 40.80 6.01
117 125 2.544277 GCGCCTTTTAACGGGAAAAAGT 60.544 45.455 0.00 0.00 40.67 2.66
178 187 3.980134 TCACAATTTACATTGCAAGCACG 59.020 39.130 4.94 0.00 43.39 5.34
235 244 3.244976 CGTTGCTGCCTTATTTTTCTGG 58.755 45.455 0.00 0.00 0.00 3.86
255 264 2.436646 AATGGGAAGACGCCTGCG 60.437 61.111 10.40 10.40 46.03 5.18
283 292 1.664151 CGAACTCAAAATACCGCCTCC 59.336 52.381 0.00 0.00 0.00 4.30
290 299 7.365840 AGAAACATCTCCGAACTCAAAATAC 57.634 36.000 0.00 0.00 0.00 1.89
377 386 4.601019 CTGCTTGAAACATCGAAGTTTGT 58.399 39.130 22.18 3.34 41.48 2.83
379 388 3.632189 GCTGCTTGAAACATCGAAGTTT 58.368 40.909 17.87 17.87 43.90 2.66
444 453 2.874086 TGATGCTATTCACCAATCGCAG 59.126 45.455 1.18 0.00 42.28 5.18
453 462 9.556030 CATATTGACATCATTGATGCTATTCAC 57.444 33.333 23.43 9.17 43.15 3.18
466 475 6.880484 ACATTGCAAACCATATTGACATCAT 58.120 32.000 1.71 0.00 31.84 2.45
471 480 5.070770 TGGACATTGCAAACCATATTGAC 57.929 39.130 15.88 4.18 31.84 3.18
627 639 1.741770 GGCCCACGTGTTGCTAGAG 60.742 63.158 21.84 2.74 0.00 2.43
748 772 9.209297 GAAAACAACACAAATTTAGCAACATTC 57.791 29.630 0.00 0.00 0.00 2.67
831 855 2.291365 TCCATGAAGCATGAACATCGG 58.709 47.619 8.87 3.75 43.81 4.18
892 942 6.021704 GTCGATTATAAAACTTTTTGCGCTCC 60.022 38.462 9.73 0.00 0.00 4.70
961 1011 5.683876 TTAAGCTCCTAAGATCACTGCTT 57.316 39.130 0.00 0.00 41.32 3.91
974 1024 3.746045 TGACGAACACTTTAAGCTCCT 57.254 42.857 0.00 0.00 0.00 3.69
991 1041 3.636764 ACCACTTTTCCCATGTCTTTGAC 59.363 43.478 0.00 0.00 0.00 3.18
1266 1344 8.557592 TTGACTACGATAAGAAGTTACTCTGA 57.442 34.615 0.00 0.00 0.00 3.27
1283 1361 5.005779 GCATCAACTACTGGATTTGACTACG 59.994 44.000 0.00 0.00 32.21 3.51
1302 1380 3.628942 GCCAGTTTACATGATCAGCATCA 59.371 43.478 0.00 0.00 43.45 3.07
1325 1403 6.438186 TCAAGAGATATGGGCACATCATTA 57.562 37.500 3.67 0.00 38.53 1.90
1373 1535 4.103943 TGGTTGACCCTGCATATATTAGCA 59.896 41.667 0.00 2.36 39.25 3.49
1374 1536 4.651778 TGGTTGACCCTGCATATATTAGC 58.348 43.478 0.00 0.00 34.29 3.09
1375 1537 6.715280 AGATGGTTGACCCTGCATATATTAG 58.285 40.000 0.00 0.00 34.29 1.73
1376 1538 6.702449 AGATGGTTGACCCTGCATATATTA 57.298 37.500 0.00 0.00 34.29 0.98
1457 1619 1.834263 AGCCTTGACCTCAGATGGTAC 59.166 52.381 0.00 0.00 41.00 3.34
1540 1702 2.031682 CACTAGTTTGTGCTGTCTTGGC 60.032 50.000 0.00 0.00 0.00 4.52
1580 1742 4.550831 GCACGAACAGATTTATGATCCGTG 60.551 45.833 0.00 0.00 33.78 4.94
1591 1753 0.317160 TCAGTCCGCACGAACAGATT 59.683 50.000 0.00 0.00 0.00 2.40
1605 1767 7.316640 AGCGACCAATATATTGTCTATCAGTC 58.683 38.462 21.20 17.16 36.06 3.51
1618 1780 7.820386 TGTTTCAAAGTCTAAGCGACCAATATA 59.180 33.333 0.00 0.00 43.91 0.86
1685 1881 3.549898 AGAAGCCTTTTCCTTTGGGAT 57.450 42.857 0.00 0.00 41.87 3.85
1806 2003 6.072728 CCGAAACAGGAATTCAATACAACTGA 60.073 38.462 7.93 0.00 0.00 3.41
1833 2030 3.119708 AGGCGCTCTAAGAAAAATGCAAG 60.120 43.478 7.64 0.00 0.00 4.01
1984 2181 5.918011 TCAACTTTGTTGTTTCACAGTTCAC 59.082 36.000 9.78 0.00 36.57 3.18
2000 2197 8.506140 AATATGAAACATTGACGTCAACTTTG 57.494 30.769 31.87 26.56 38.86 2.77


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

AutoCloner maintained by Alex Coulton.