Multiple sequence alignment - TraesCS3A01G202900

Loading Multiple Alignment...

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 TraesCS3A01G202900 chr3A 100.000 2339 0 0 1 2339 346952422 346954760 0 4320
1 TraesCS3A01G202900 chr3D 96.525 2302 50 12 34 2334 269285639 269283367 0 3781


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 TraesCS3A01G202900 chr3A 346952422 346954760 2338 False 4320 4320 100.000 1 2339 1 chr3A.!!$F1 2338
1 TraesCS3A01G202900 chr3D 269283367 269285639 2272 True 3781 3781 96.525 34 2334 1 chr3D.!!$R1 2300

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
505 506 1.069022 GTACGTGCTGGTTGTCTCGTA 60.069 52.381 0.0 0.0 33.7 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 1939 1.202336 CCCCACTAGTAAGTAACGCGG 60.202 57.143 12.47 0.0 33.48 6.46 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
20 21 3.107661 GCACGCATGCCAGTTTGC 61.108 61.111 13.15 9.42 46.97 3.68
21 22 2.646719 CACGCATGCCAGTTTGCT 59.353 55.556 13.15 0.00 36.71 3.91
22 23 1.731613 CACGCATGCCAGTTTGCTG 60.732 57.895 13.15 0.00 42.22 4.41
23 24 1.898094 ACGCATGCCAGTTTGCTGA 60.898 52.632 13.15 0.00 45.28 4.26
24 25 1.154093 CGCATGCCAGTTTGCTGAG 60.154 57.895 13.15 0.00 45.28 3.35
25 26 1.214589 GCATGCCAGTTTGCTGAGG 59.785 57.895 6.36 0.00 45.28 3.86
26 27 1.214589 CATGCCAGTTTGCTGAGGC 59.785 57.895 0.00 0.00 45.28 4.70
27 28 1.228644 ATGCCAGTTTGCTGAGGCA 60.229 52.632 7.50 7.50 45.28 4.75
128 129 7.228906 TGCTATCCTAGACAACATAGTGTAGTC 59.771 40.741 0.00 0.00 34.53 2.59
134 135 7.909121 CCTAGACAACATAGTGTAGTCTTAACG 59.091 40.741 0.00 0.00 39.92 3.18
378 379 3.773630 CGTTGCCGTTCGCGTGAT 61.774 61.111 5.77 0.00 42.08 3.06
437 438 2.418368 ACAAGAAGTGGACTGCACAA 57.582 45.000 3.27 0.00 0.00 3.33
441 442 2.936202 AGAAGTGGACTGCACAACAAT 58.064 42.857 3.27 0.00 0.00 2.71
452 453 4.444056 ACTGCACAACAATCGCAAATAAAC 59.556 37.500 0.00 0.00 34.75 2.01
505 506 1.069022 GTACGTGCTGGTTGTCTCGTA 60.069 52.381 0.00 0.00 33.70 3.43
517 518 4.034742 GGTTGTCTCGTAACAAAGAAGCAA 59.965 41.667 6.88 0.00 40.62 3.91
584 585 2.010145 ATGTGACGTTCCATCCTTCG 57.990 50.000 0.00 0.00 0.00 3.79
613 614 7.282224 TCAAAATCACTGGATTAATTAGGACCG 59.718 37.037 0.00 0.00 42.87 4.79
614 615 5.888982 ATCACTGGATTAATTAGGACCGT 57.111 39.130 0.00 0.00 0.00 4.83
617 618 6.478129 TCACTGGATTAATTAGGACCGTTTT 58.522 36.000 0.00 0.00 0.00 2.43
618 619 6.943718 TCACTGGATTAATTAGGACCGTTTTT 59.056 34.615 0.00 0.00 0.00 1.94
717 718 6.149474 TCTCAATTGGAAATCGACTTCCTTTC 59.851 38.462 24.71 12.70 44.57 2.62
729 731 9.503399 AATCGACTTCCTTTCTTTAGTTTATGT 57.497 29.630 0.00 0.00 0.00 2.29
753 755 2.554370 AAAATTCCCTCACCGACGAA 57.446 45.000 0.00 0.00 0.00 3.85
761 763 1.459592 CCTCACCGACGAATGTTTGTC 59.540 52.381 0.00 3.50 38.06 3.18
762 764 2.404215 CTCACCGACGAATGTTTGTCT 58.596 47.619 10.51 0.00 39.04 3.41
763 765 2.131972 TCACCGACGAATGTTTGTCTG 58.868 47.619 10.51 7.14 39.04 3.51
764 766 2.131972 CACCGACGAATGTTTGTCTGA 58.868 47.619 10.37 0.00 39.04 3.27
765 767 2.542178 CACCGACGAATGTTTGTCTGAA 59.458 45.455 10.37 0.00 39.04 3.02
766 768 3.186409 CACCGACGAATGTTTGTCTGAAT 59.814 43.478 10.37 0.00 39.04 2.57
767 769 3.186409 ACCGACGAATGTTTGTCTGAATG 59.814 43.478 10.37 0.00 39.04 2.67
768 770 3.431912 CCGACGAATGTTTGTCTGAATGA 59.568 43.478 10.51 0.00 39.04 2.57
769 771 4.093408 CCGACGAATGTTTGTCTGAATGAT 59.907 41.667 10.51 0.00 39.04 2.45
770 772 5.017612 CGACGAATGTTTGTCTGAATGATG 58.982 41.667 10.51 0.00 39.04 3.07
771 773 5.163963 CGACGAATGTTTGTCTGAATGATGA 60.164 40.000 10.51 0.00 39.04 2.92
1203 1205 3.449227 TCGGAGAGCACGGCGATT 61.449 61.111 16.62 0.00 0.00 3.34
1266 1268 2.445614 AGGACCGCCTCTTCCTCA 59.554 61.111 0.00 0.00 42.19 3.86
1269 1271 1.330655 GGACCGCCTCTTCCTCATCA 61.331 60.000 0.00 0.00 0.00 3.07
1272 1274 0.755079 CCGCCTCTTCCTCATCATCA 59.245 55.000 0.00 0.00 0.00 3.07
1275 1277 2.686235 GCCTCTTCCTCATCATCATCG 58.314 52.381 0.00 0.00 0.00 3.84
1284 1286 2.510551 ATCATCATCGCCGCCCTCA 61.511 57.895 0.00 0.00 0.00 3.86
1377 1379 0.112995 TGATGAAACTGCAGGCCCTT 59.887 50.000 19.93 5.49 0.00 3.95
1545 1547 0.601558 GTCGTGGGTGAAGCTAGTCA 59.398 55.000 0.00 0.00 0.00 3.41
1559 1561 7.010645 GTGAAGCTAGTCAGTCTAAAATTAGGC 59.989 40.741 0.00 0.00 35.65 3.93
1849 1851 0.175531 GCCAACTGCAAACCACAAGT 59.824 50.000 0.00 0.00 40.77 3.16
1870 1872 8.922676 ACAAGTCGAGTAATTAACAACACATAG 58.077 33.333 0.00 0.00 0.00 2.23
1898 1900 0.249911 GGCCGGCGAGACAGAAATAT 60.250 55.000 22.54 0.00 0.00 1.28
1899 1901 1.000506 GGCCGGCGAGACAGAAATATA 59.999 52.381 22.54 0.00 0.00 0.86
1900 1902 2.059541 GCCGGCGAGACAGAAATATAC 58.940 52.381 12.58 0.00 0.00 1.47
1901 1903 2.288273 GCCGGCGAGACAGAAATATACT 60.288 50.000 12.58 0.00 0.00 2.12
1902 1904 3.309388 CCGGCGAGACAGAAATATACTG 58.691 50.000 9.30 7.88 40.68 2.74
1903 1905 2.726760 CGGCGAGACAGAAATATACTGC 59.273 50.000 0.00 4.09 38.74 4.40
1904 1906 2.726760 GGCGAGACAGAAATATACTGCG 59.273 50.000 8.98 6.78 38.74 5.18
1905 1907 3.372954 GCGAGACAGAAATATACTGCGT 58.627 45.455 8.98 0.00 38.74 5.24
1906 1908 4.534168 GCGAGACAGAAATATACTGCGTA 58.466 43.478 8.98 0.00 38.74 4.42
1937 1939 3.832615 ATACGTAGTTTGGGGTGGATC 57.167 47.619 0.08 0.00 37.78 3.36
2044 2046 3.144506 AGCATTTCCAGAACTGACACAG 58.855 45.455 3.19 0.00 37.52 3.66
2122 2124 0.972883 ACTCTGTGAGGAAGCTGACC 59.027 55.000 2.38 2.38 33.35 4.02
2202 2204 7.189512 CGATTCAGATCCACTTTAAATTCCAC 58.810 38.462 0.00 0.00 0.00 4.02
2223 2225 8.415950 TCCACTTTGCCAGAAATAGAAATAAA 57.584 30.769 0.00 0.00 0.00 1.40
2255 2257 3.762407 TCAACACTTGCTGGCTACTTA 57.238 42.857 0.00 0.00 0.00 2.24
2263 2265 4.081862 ACTTGCTGGCTACTTACGACAATA 60.082 41.667 0.00 0.00 0.00 1.90
2273 2275 6.183360 GCTACTTACGACAATATGCACAAGTT 60.183 38.462 0.00 0.00 0.00 2.66
2278 2280 6.795098 ACGACAATATGCACAAGTTTTAGA 57.205 33.333 0.00 0.00 0.00 2.10
2279 2281 7.377766 ACGACAATATGCACAAGTTTTAGAT 57.622 32.000 0.00 0.00 0.00 1.98
2280 2282 7.816640 ACGACAATATGCACAAGTTTTAGATT 58.183 30.769 0.00 0.00 0.00 2.40
2281 2283 8.296713 ACGACAATATGCACAAGTTTTAGATTT 58.703 29.630 0.00 0.00 0.00 2.17
2282 2284 9.128107 CGACAATATGCACAAGTTTTAGATTTT 57.872 29.630 0.00 0.00 0.00 1.82
2284 2286 9.762933 ACAATATGCACAAGTTTTAGATTTTGT 57.237 25.926 0.00 0.00 34.31 2.83
2299 2301 9.606631 TTTAGATTTTGTGTTAGCACCAAAATT 57.393 25.926 21.52 16.68 41.48 1.82
2306 2308 6.058833 TGTGTTAGCACCAAAATTGAGACTA 58.941 36.000 7.29 0.00 44.65 2.59
2334 2336 4.414852 CGGGAGCATTTCACAAATTAGTG 58.585 43.478 0.00 0.00 40.85 2.74
2335 2337 4.082787 CGGGAGCATTTCACAAATTAGTGT 60.083 41.667 0.00 0.00 40.37 3.55
2337 2339 4.622740 GGAGCATTTCACAAATTAGTGTGC 59.377 41.667 5.54 0.00 46.97 4.57
2338 2340 4.559153 AGCATTTCACAAATTAGTGTGCC 58.441 39.130 5.54 0.00 46.97 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.731613 CAGCAAACTGGCATGCGTG 60.732 57.895 12.44 9.30 46.98 5.34
5 6 1.859427 CTCAGCAAACTGGCATGCGT 61.859 55.000 12.44 1.37 46.98 5.24
6 7 1.154093 CTCAGCAAACTGGCATGCG 60.154 57.895 12.44 0.62 46.98 4.73
7 8 1.214589 CCTCAGCAAACTGGCATGC 59.785 57.895 9.90 9.90 44.59 4.06
8 9 1.214589 GCCTCAGCAAACTGGCATG 59.785 57.895 0.00 0.00 44.59 4.06
9 10 3.690745 GCCTCAGCAAACTGGCAT 58.309 55.556 0.00 0.00 44.59 4.40
20 21 2.296365 TTCTCCAGGGCTGCCTCAG 61.296 63.158 19.68 9.24 34.12 3.35
21 22 2.203983 TTCTCCAGGGCTGCCTCA 60.204 61.111 19.68 0.00 0.00 3.86
22 23 2.129555 TTGTTCTCCAGGGCTGCCTC 62.130 60.000 19.68 8.86 0.00 4.70
23 24 1.504275 ATTGTTCTCCAGGGCTGCCT 61.504 55.000 19.68 1.35 0.00 4.75
24 25 0.613012 AATTGTTCTCCAGGGCTGCC 60.613 55.000 11.05 11.05 0.00 4.85
25 26 0.529378 CAATTGTTCTCCAGGGCTGC 59.471 55.000 0.00 0.00 0.00 5.25
26 27 1.180029 CCAATTGTTCTCCAGGGCTG 58.820 55.000 4.43 0.00 0.00 4.85
27 28 1.075601 TCCAATTGTTCTCCAGGGCT 58.924 50.000 4.43 0.00 0.00 5.19
28 29 1.753073 CATCCAATTGTTCTCCAGGGC 59.247 52.381 4.43 0.00 0.00 5.19
29 30 3.370840 TCATCCAATTGTTCTCCAGGG 57.629 47.619 4.43 0.00 0.00 4.45
30 31 5.010922 TGTTTTCATCCAATTGTTCTCCAGG 59.989 40.000 4.43 0.00 0.00 4.45
31 32 6.088016 TGTTTTCATCCAATTGTTCTCCAG 57.912 37.500 4.43 0.00 0.00 3.86
32 33 6.477053 TTGTTTTCATCCAATTGTTCTCCA 57.523 33.333 4.43 0.00 0.00 3.86
366 367 1.006825 TTGACAGATCACGCGAACGG 61.007 55.000 15.93 4.18 46.04 4.44
413 414 1.264288 GCAGTCCACTTCTTGTTTCGG 59.736 52.381 0.00 0.00 0.00 4.30
415 416 2.682856 TGTGCAGTCCACTTCTTGTTTC 59.317 45.455 0.00 0.00 44.92 2.78
437 438 7.144722 TCAAGATCTGTTTATTTGCGATTGT 57.855 32.000 0.00 0.00 0.00 2.71
441 442 7.592938 ACAAATCAAGATCTGTTTATTTGCGA 58.407 30.769 20.86 1.25 37.67 5.10
452 453 6.366061 TGACGACAGTAACAAATCAAGATCTG 59.634 38.462 0.00 0.00 0.00 2.90
505 506 1.008538 CGGCGCTTGCTTCTTTGTT 60.009 52.632 7.64 0.00 39.13 2.83
517 518 1.217882 GCTACATTGTTATCGGCGCT 58.782 50.000 7.64 0.00 0.00 5.92
729 731 3.414269 GTCGGTGAGGGAATTTTAACCA 58.586 45.455 0.00 0.00 0.00 3.67
753 755 7.392393 TCATTCAGTCATCATTCAGACAAACAT 59.608 33.333 0.00 0.00 37.23 2.71
761 763 9.803315 AAAAATCATCATTCAGTCATCATTCAG 57.197 29.630 0.00 0.00 0.00 3.02
765 767 9.417561 AGGTAAAAATCATCATTCAGTCATCAT 57.582 29.630 0.00 0.00 0.00 2.45
766 768 8.680001 CAGGTAAAAATCATCATTCAGTCATCA 58.320 33.333 0.00 0.00 0.00 3.07
767 769 8.133627 CCAGGTAAAAATCATCATTCAGTCATC 58.866 37.037 0.00 0.00 0.00 2.92
768 770 7.835682 TCCAGGTAAAAATCATCATTCAGTCAT 59.164 33.333 0.00 0.00 0.00 3.06
769 771 7.174413 TCCAGGTAAAAATCATCATTCAGTCA 58.826 34.615 0.00 0.00 0.00 3.41
770 772 7.201767 CCTCCAGGTAAAAATCATCATTCAGTC 60.202 40.741 0.00 0.00 0.00 3.51
771 773 6.604795 CCTCCAGGTAAAAATCATCATTCAGT 59.395 38.462 0.00 0.00 0.00 3.41
1203 1205 3.262660 GGCTCATCCTCATGACCATCATA 59.737 47.826 0.00 0.00 34.28 2.15
1260 1262 0.601046 GCGGCGATGATGATGAGGAA 60.601 55.000 12.98 0.00 0.00 3.36
1266 1268 2.043604 TTGAGGGCGGCGATGATGAT 62.044 55.000 12.98 0.00 0.00 2.45
1269 1271 1.302033 GATTGAGGGCGGCGATGAT 60.302 57.895 12.98 0.00 0.00 2.45
1272 1274 2.423446 GAGATTGAGGGCGGCGAT 59.577 61.111 12.98 0.00 0.00 4.58
1275 1277 2.203126 CAGGAGATTGAGGGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
1377 1379 2.601666 ACGGTGCTGGAGCTCTCA 60.602 61.111 14.64 9.11 42.66 3.27
1545 1547 4.760204 AGTTGCAACGCCTAATTTTAGACT 59.240 37.500 23.21 0.00 32.47 3.24
1576 1578 2.751259 GCATTTCTCAATCTCAGCACCA 59.249 45.455 0.00 0.00 0.00 4.17
1849 1851 9.647797 AACATCTATGTGTTGTTAATTACTCGA 57.352 29.630 0.00 0.00 40.60 4.04
1889 1891 8.899427 TCTACTACTACGCAGTATATTTCTGT 57.101 34.615 0.00 0.00 44.56 3.41
1898 1900 9.561270 CTACGTATATTCTACTACTACGCAGTA 57.439 37.037 0.00 0.00 45.11 2.74
1900 1902 8.459521 ACTACGTATATTCTACTACTACGCAG 57.540 38.462 0.00 0.00 38.90 5.18
1901 1903 8.818141 AACTACGTATATTCTACTACTACGCA 57.182 34.615 0.00 0.00 38.90 5.24
1902 1904 9.522454 CAAACTACGTATATTCTACTACTACGC 57.478 37.037 0.00 0.00 38.90 4.42
1905 1907 9.507329 CCCCAAACTACGTATATTCTACTACTA 57.493 37.037 0.00 0.00 0.00 1.82
1906 1908 8.001292 ACCCCAAACTACGTATATTCTACTACT 58.999 37.037 0.00 0.00 0.00 2.57
1915 1917 4.285260 GGATCCACCCCAAACTACGTATAT 59.715 45.833 6.95 0.00 0.00 0.86
1937 1939 1.202336 CCCCACTAGTAAGTAACGCGG 60.202 57.143 12.47 0.00 33.48 6.46
1940 1942 1.826720 TGGCCCCACTAGTAAGTAACG 59.173 52.381 0.00 0.00 33.48 3.18
2044 2046 2.866762 CGGGATGCTTTAACTGTAGCTC 59.133 50.000 0.00 0.00 38.22 4.09
2079 2081 2.019984 CATTTGCTCCTCTTGCTACCC 58.980 52.381 0.00 0.00 0.00 3.69
2081 2083 2.840296 GCATTTGCTCCTCTTGCTAC 57.160 50.000 0.00 0.00 38.21 3.58
2122 2124 1.523258 CATTCCTCTGGCTGAGCGG 60.523 63.158 15.25 4.74 41.35 5.52
2223 2225 7.315142 CCAGCAAGTGTTGATGTGTTATAATT 58.685 34.615 4.38 0.00 45.11 1.40
2255 2257 6.795098 TCTAAAACTTGTGCATATTGTCGT 57.205 33.333 0.00 0.00 0.00 4.34
2273 2275 9.606631 AATTTTGGTGCTAACACAAAATCTAAA 57.393 25.926 13.04 2.72 46.60 1.85
2278 2280 7.224557 GTCTCAATTTTGGTGCTAACACAAAAT 59.775 33.333 0.00 8.34 46.60 1.82
2283 2285 5.438761 AGTCTCAATTTTGGTGCTAACAC 57.561 39.130 0.00 0.00 46.66 3.32
2284 2286 7.575414 TTTAGTCTCAATTTTGGTGCTAACA 57.425 32.000 0.00 0.00 0.00 2.41
2285 2287 8.915654 CAATTTAGTCTCAATTTTGGTGCTAAC 58.084 33.333 0.00 0.00 0.00 2.34
2286 2288 7.598493 GCAATTTAGTCTCAATTTTGGTGCTAA 59.402 33.333 0.00 0.00 0.00 3.09
2287 2289 7.090173 GCAATTTAGTCTCAATTTTGGTGCTA 58.910 34.615 0.00 0.00 0.00 3.49
2288 2290 5.928264 GCAATTTAGTCTCAATTTTGGTGCT 59.072 36.000 0.00 0.00 0.00 4.40
2289 2291 5.164061 CGCAATTTAGTCTCAATTTTGGTGC 60.164 40.000 0.00 0.00 0.00 5.01
2299 2301 1.277842 TGCTCCCGCAATTTAGTCTCA 59.722 47.619 0.00 0.00 44.62 3.27


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

AutoCloner maintained by Alex Coulton.