Multiple sequence alignment - TraesCS3A01G159100

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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 TraesCS3A01G159100 chr3A 100.000 2600 0 0 1 2600 158169626 158172225 0.000000e+00 4802
1 TraesCS3A01G159100 chr3B 97.917 1104 20 3 812 1913 202385914 202387016 0.000000e+00 1908
2 TraesCS3A01G159100 chr3B 91.695 590 25 14 2033 2599 202387292 202387880 0.000000e+00 797
3 TraesCS3A01G159100 chr3B 88.798 491 47 4 1 485 202384804 202385292 1.720000e-166 595
4 TraesCS3A01G159100 chr3B 93.651 126 8 0 1910 2035 202387128 202387253 3.420000e-44 189
5 TraesCS3A01G159100 chr3D 97.574 1113 22 4 812 1920 140417649 140418760 0.000000e+00 1901
6 TraesCS3A01G159100 chr3D 92.007 588 24 13 2033 2599 140420133 140420718 0.000000e+00 804
7 TraesCS3A01G159100 chr3D 86.521 549 39 13 1 535 140416760 140417287 2.900000e-159 571
8 TraesCS3A01G159100 chr3D 84.912 285 29 9 523 801 140417321 140417597 2.550000e-70 276
9 TraesCS3A01G159100 chr3D 95.276 127 6 0 1909 2035 140419968 140420094 4.390000e-48 202


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 TraesCS3A01G159100 chr3A 158169626 158172225 2599 False 4802.00 4802 100.00000 1 2600 1 chr3A.!!$F1 2599
1 TraesCS3A01G159100 chr3B 202384804 202387880 3076 False 872.25 1908 93.01525 1 2599 4 chr3B.!!$F1 2598
2 TraesCS3A01G159100 chr3D 140416760 140420718 3958 False 750.80 1901 91.25800 1 2599 5 chr3D.!!$F1 2598

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
213 216 0.035152 ACATGAGGCGCCAAGATCAA 60.035 50.0 31.54 8.49 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2061 0.099436 GCCATAGTTTTGCTCAGCCG 59.901 55.0 0.0 0.0 0.0 5.52 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
44 47 6.767902 AGAACTGACAGACACATACAAAACAT 59.232 34.615 10.08 0.00 0.00 2.71
45 48 7.931407 AGAACTGACAGACACATACAAAACATA 59.069 33.333 10.08 0.00 0.00 2.29
109 112 1.525923 AGCAGGCGAATCAGCTCAT 59.474 52.632 0.00 0.00 37.29 2.90
173 176 4.261155 GCGTGCACATGTTGTATATCCAAT 60.261 41.667 18.64 0.00 0.00 3.16
174 177 5.443261 CGTGCACATGTTGTATATCCAATC 58.557 41.667 18.64 0.00 0.00 2.67
175 178 5.007528 CGTGCACATGTTGTATATCCAATCA 59.992 40.000 18.64 0.00 0.00 2.57
213 216 0.035152 ACATGAGGCGCCAAGATCAA 60.035 50.000 31.54 8.49 0.00 2.57
290 293 4.288531 GCGACTTACGTGTAGAGCATTAT 58.711 43.478 0.00 0.00 44.60 1.28
300 303 5.450550 CGTGTAGAGCATTATGAGTCCTCAA 60.451 44.000 0.37 0.00 43.58 3.02
302 305 6.989169 GTGTAGAGCATTATGAGTCCTCAAAT 59.011 38.462 0.37 1.03 43.58 2.32
314 317 2.293399 GTCCTCAAATTTCAAGTGCGGT 59.707 45.455 0.00 0.00 0.00 5.68
331 334 1.405821 CGGTTCTAGCTTGTCCTCGAT 59.594 52.381 0.00 0.00 0.00 3.59
332 335 2.617308 CGGTTCTAGCTTGTCCTCGATA 59.383 50.000 0.00 0.00 0.00 2.92
337 340 5.440234 TCTAGCTTGTCCTCGATAATGTC 57.560 43.478 0.00 0.00 0.00 3.06
354 357 3.044235 TGTCGATGAGCTTGTTGATGT 57.956 42.857 0.00 0.00 0.00 3.06
372 375 3.708403 TGTCCATCTGCATGAAGTTCT 57.292 42.857 0.00 0.00 30.57 3.01
377 380 4.020307 TCCATCTGCATGAAGTTCTACACA 60.020 41.667 0.00 0.00 30.57 3.72
379 382 5.356190 CCATCTGCATGAAGTTCTACACATT 59.644 40.000 0.00 0.00 30.57 2.71
388 391 7.718334 TGAAGTTCTACACATTCTCCAGATA 57.282 36.000 4.17 0.00 0.00 1.98
406 409 6.064060 CCAGATAAATGGTCTTGCAATCCTA 58.936 40.000 17.64 3.78 35.47 2.94
426 433 1.675310 CCTTGCCAAGTCGCCATCA 60.675 57.895 3.37 0.00 0.00 3.07
427 434 1.503542 CTTGCCAAGTCGCCATCAC 59.496 57.895 0.00 0.00 0.00 3.06
430 437 2.438434 CCAAGTCGCCATCACCCC 60.438 66.667 0.00 0.00 0.00 4.95
453 460 1.664321 TAGCCGCCGGTTCTCTTCTC 61.664 60.000 4.45 0.00 0.00 2.87
454 461 3.007973 GCCGCCGGTTCTCTTCTCT 62.008 63.158 4.45 0.00 0.00 3.10
462 469 1.270893 GGTTCTCTTCTCTTTGGCGGT 60.271 52.381 0.00 0.00 0.00 5.68
474 481 0.183014 TTGGCGGTCACAAACCCTAA 59.817 50.000 0.00 0.00 46.27 2.69
486 493 0.408309 AACCCTAAAGGAGGTTGGGC 59.592 55.000 0.00 0.00 44.70 5.36
494 501 1.062488 AGGAGGTTGGGCTCAGTTGT 61.062 55.000 0.00 0.00 0.00 3.32
508 523 1.136828 AGTTGTCTGTGTGGGGCTTA 58.863 50.000 0.00 0.00 0.00 3.09
518 533 1.087771 GTGGGGCTTACGTCGATTGG 61.088 60.000 0.00 0.00 0.00 3.16
544 605 1.127343 GAGAGAGAGATGGTTGGGGG 58.873 60.000 0.00 0.00 0.00 5.40
545 606 0.419459 AGAGAGAGATGGTTGGGGGT 59.581 55.000 0.00 0.00 0.00 4.95
548 609 1.926426 GAGAGATGGTTGGGGGTGGG 61.926 65.000 0.00 0.00 0.00 4.61
549 610 1.928567 GAGATGGTTGGGGGTGGGA 60.929 63.158 0.00 0.00 0.00 4.37
550 611 1.926426 GAGATGGTTGGGGGTGGGAG 61.926 65.000 0.00 0.00 0.00 4.30
570 829 4.518970 GGAGCGGGCAAAGATTATGATTAA 59.481 41.667 0.00 0.00 0.00 1.40
594 853 4.812626 GGGTTTTGTCTCTAACGTTTCAGA 59.187 41.667 5.91 5.39 0.00 3.27
614 874 0.677288 TGGAGAAAGTTCGCTTCCGA 59.323 50.000 0.00 0.00 42.66 4.55
645 905 1.544825 CCAGGAAGGAGGAGCGAACA 61.545 60.000 0.00 0.00 41.22 3.18
694 954 1.827969 ACTCTTGCCGCAGATCTTAGT 59.172 47.619 0.00 0.00 0.00 2.24
827 1136 7.178451 AGGATTTCCGAAACACCATTTTAGATT 59.822 33.333 16.37 0.00 42.08 2.40
832 1141 6.435904 TCCGAAACACCATTTTAGATTTCCAT 59.564 34.615 0.00 0.00 0.00 3.41
871 1183 7.703058 AAGAATTTTAGTACCCATTCCACAG 57.297 36.000 0.00 0.00 0.00 3.66
934 1246 2.121963 TCCTTGTGCAGTCCCCCT 60.122 61.111 0.00 0.00 0.00 4.79
1389 1701 4.427661 GAGGCTGCTGACGTCGCT 62.428 66.667 25.00 11.13 0.00 4.93
1778 2090 3.067320 GCAAAACTATGGCCTGAATCTCC 59.933 47.826 3.32 0.00 0.00 3.71
1933 3465 8.833493 CAAGTATGATCATGAAATGCTAAGACA 58.167 33.333 18.72 0.00 46.21 3.41
1938 3470 3.943381 TCATGAAATGCTAAGACAGGCAG 59.057 43.478 0.00 0.00 46.21 4.85
1959 3491 0.822811 ACAATGTGTGCAAGTTGGCA 59.177 45.000 4.75 0.38 42.53 4.92
2073 3646 1.960689 GCTCAAAGTTGCCAGGGTTAA 59.039 47.619 0.00 0.00 0.00 2.01
2076 3649 3.219281 TCAAAGTTGCCAGGGTTAAGTC 58.781 45.455 0.00 0.00 0.00 3.01
2303 3885 9.976511 TTTCCTAACTTATAACATATGACGAGG 57.023 33.333 10.38 3.13 0.00 4.63
2474 4070 1.741706 CAGTGATCCTGGTGAATGTGC 59.258 52.381 0.00 0.00 37.54 4.57
2527 4123 0.887933 CTAAAATGCGGGGCTGTTGT 59.112 50.000 0.00 0.00 0.00 3.32
2599 4195 4.305769 CTGGCTTGTGTAGATATGCTCTC 58.694 47.826 0.00 0.00 35.28 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.318332 TCAGTTCTCTGATGCAACGAATT 58.682 39.130 0.00 0.00 44.58 2.17
122 125 0.522180 CCTCACGACTACTCGCAGTT 59.478 55.000 0.00 0.00 44.33 3.16
191 194 2.288666 GATCTTGGCGCCTCATGTTTA 58.711 47.619 29.70 0.07 0.00 2.01
197 200 0.955428 GTGTTGATCTTGGCGCCTCA 60.955 55.000 29.70 20.16 0.00 3.86
213 216 5.304101 GGTCTGATTCTATCTGATCTGGTGT 59.696 44.000 0.00 0.00 39.06 4.16
254 257 4.129737 TCGCCTCCGCCTCTTTCG 62.130 66.667 0.00 0.00 0.00 3.46
255 258 2.508586 AAGTCGCCTCCGCCTCTTTC 62.509 60.000 0.00 0.00 0.00 2.62
257 260 1.681327 TAAGTCGCCTCCGCCTCTT 60.681 57.895 0.00 0.00 0.00 2.85
290 293 3.250762 CGCACTTGAAATTTGAGGACTCA 59.749 43.478 0.00 0.00 37.91 3.41
300 303 3.412386 AGCTAGAACCGCACTTGAAATT 58.588 40.909 0.00 0.00 0.00 1.82
302 305 2.543777 AGCTAGAACCGCACTTGAAA 57.456 45.000 0.00 0.00 0.00 2.69
314 317 5.833082 GACATTATCGAGGACAAGCTAGAA 58.167 41.667 0.00 0.00 0.00 2.10
331 334 5.178061 ACATCAACAAGCTCATCGACATTA 58.822 37.500 0.00 0.00 0.00 1.90
332 335 4.005650 ACATCAACAAGCTCATCGACATT 58.994 39.130 0.00 0.00 0.00 2.71
337 340 2.349590 TGGACATCAACAAGCTCATCG 58.650 47.619 0.00 0.00 0.00 3.84
354 357 4.020307 TGTGTAGAACTTCATGCAGATGGA 60.020 41.667 0.00 0.00 0.00 3.41
372 375 7.437713 AGACCATTTATCTGGAGAATGTGTA 57.562 36.000 0.00 0.00 39.73 2.90
377 380 5.759059 TGCAAGACCATTTATCTGGAGAAT 58.241 37.500 0.00 0.00 39.73 2.40
379 382 4.842531 TGCAAGACCATTTATCTGGAGA 57.157 40.909 0.00 0.00 39.73 3.71
388 391 3.011708 AGGGTAGGATTGCAAGACCATTT 59.988 43.478 21.88 8.77 31.41 2.32
462 469 3.435890 CCAACCTCCTTTAGGGTTTGTGA 60.436 47.826 0.00 0.00 46.28 3.58
474 481 0.111253 CAACTGAGCCCAACCTCCTT 59.889 55.000 0.00 0.00 0.00 3.36
486 493 0.886490 GCCCCACACAGACAACTGAG 60.886 60.000 0.00 0.00 46.03 3.35
494 501 1.669440 GACGTAAGCCCCACACAGA 59.331 57.895 0.00 0.00 45.62 3.41
508 523 0.818296 CTCTCTTCCCCAATCGACGT 59.182 55.000 0.00 0.00 0.00 4.34
518 533 3.312736 ACCATCTCTCTCTCTCTTCCC 57.687 52.381 0.00 0.00 0.00 3.97
544 605 0.393808 TAATCTTTGCCCGCTCCCAC 60.394 55.000 0.00 0.00 0.00 4.61
545 606 0.550914 ATAATCTTTGCCCGCTCCCA 59.449 50.000 0.00 0.00 0.00 4.37
548 609 5.335191 CCTTAATCATAATCTTTGCCCGCTC 60.335 44.000 0.00 0.00 0.00 5.03
549 610 4.520492 CCTTAATCATAATCTTTGCCCGCT 59.480 41.667 0.00 0.00 0.00 5.52
550 611 4.321230 CCCTTAATCATAATCTTTGCCCGC 60.321 45.833 0.00 0.00 0.00 6.13
570 829 4.773013 TGAAACGTTAGAGACAAAACCCT 58.227 39.130 0.00 0.00 0.00 4.34
594 853 1.275291 TCGGAAGCGAACTTTCTCCAT 59.725 47.619 0.00 0.00 35.82 3.41
614 874 1.915078 CTTCCTGGACCCCGCAGAAT 61.915 60.000 0.00 0.00 0.00 2.40
645 905 3.710722 CTGCTTGACGCCCCTCCT 61.711 66.667 0.00 0.00 38.05 3.69
661 921 0.393077 CAAGAGTGAACCCCGTGTCT 59.607 55.000 0.00 0.00 0.00 3.41
728 990 6.964908 TCTCGTGCTTTCACATCATTTTAAA 58.035 32.000 0.00 0.00 43.28 1.52
733 995 3.005554 CCTCTCGTGCTTTCACATCATT 58.994 45.455 0.00 0.00 43.28 2.57
738 1000 2.626266 TCTAACCTCTCGTGCTTTCACA 59.374 45.455 0.00 0.00 43.28 3.58
801 1069 6.007703 TCTAAAATGGTGTTTCGGAAATCCT 58.992 36.000 20.15 9.19 0.00 3.24
802 1070 6.262193 TCTAAAATGGTGTTTCGGAAATCC 57.738 37.500 6.43 12.29 0.00 3.01
805 1073 7.149307 GGAAATCTAAAATGGTGTTTCGGAAA 58.851 34.615 0.00 0.00 0.00 3.13
806 1074 6.265649 TGGAAATCTAAAATGGTGTTTCGGAA 59.734 34.615 0.00 0.00 0.00 4.30
807 1075 5.770663 TGGAAATCTAAAATGGTGTTTCGGA 59.229 36.000 0.00 0.00 0.00 4.55
808 1076 6.019779 TGGAAATCTAAAATGGTGTTTCGG 57.980 37.500 0.00 0.00 0.00 4.30
809 1077 7.312154 TCATGGAAATCTAAAATGGTGTTTCG 58.688 34.615 0.00 0.00 0.00 3.46
827 1136 6.653526 TCTTTTGAATGCTTCTTCATGGAA 57.346 33.333 0.00 0.00 35.20 3.53
871 1183 3.975035 GGAGCGTTGTTTGATTTGAGTTC 59.025 43.478 0.00 0.00 0.00 3.01
1665 1977 4.218852 GCTCTGGTTCTACAGTCTACACTT 59.781 45.833 0.00 0.00 39.48 3.16
1749 2061 0.099436 GCCATAGTTTTGCTCAGCCG 59.901 55.000 0.00 0.00 0.00 5.52
1778 2090 5.654650 ACACATGACCTCTCCTTTAGTAGAG 59.345 44.000 0.00 0.00 39.19 2.43
1795 2108 0.179059 ACGGCTGAACACACACATGA 60.179 50.000 0.00 0.00 0.00 3.07
1798 2111 0.391793 TCAACGGCTGAACACACACA 60.392 50.000 0.00 0.00 0.00 3.72
1959 3491 4.222124 ACACAAGATAAAAGCCGGATCT 57.778 40.909 5.05 0.00 0.00 2.75
2073 3646 5.960811 TGAAGAATGGTCCAATCTAGAGACT 59.039 40.000 9.97 0.00 0.00 3.24
2076 3649 7.772292 TCAAATGAAGAATGGTCCAATCTAGAG 59.228 37.037 9.97 0.00 0.00 2.43
2196 3777 7.115378 CACAAGCTTGTATGAAAAGGTTTCATC 59.885 37.037 30.67 10.95 41.96 2.92
2295 3877 7.441836 TGCTTACATTATTATGTCCTCGTCAT 58.558 34.615 0.00 0.00 43.81 3.06
2314 3896 6.645415 TGTTAGCTCTAAGTTTCACTGCTTAC 59.355 38.462 0.00 0.00 29.46 2.34
2331 3913 6.462073 TTGAACTGATAACGTTGTTAGCTC 57.538 37.500 15.27 13.32 0.00 4.09
2387 3971 8.772250 TCTGGTAATCAGGATTTTACAGAATCT 58.228 33.333 14.80 0.00 43.53 2.40
2388 3972 8.964476 TCTGGTAATCAGGATTTTACAGAATC 57.036 34.615 14.80 0.00 43.53 2.52
2474 4070 3.249320 CACTTGGCATGATATCGAACAGG 59.751 47.826 7.45 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.