Multiple sequence alignment - TraesCS2A01G201700

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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 TraesCS2A01G201700 chr2A 100.000 2823 0 0 1 2823 175436488 175439310 0.000000e+00 5214
1 TraesCS2A01G201700 chr2B 92.782 2757 102 43 32 2736 223090341 223093052 0.000000e+00 3899
2 TraesCS2A01G201700 chr2D 91.926 2663 102 49 1 2613 175299466 175302065 0.000000e+00 3622
3 TraesCS2A01G201700 chr2D 93.333 90 6 0 2733 2822 175302223 175302312 1.760000e-27 134


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 TraesCS2A01G201700 chr2A 175436488 175439310 2822 False 5214 5214 100.0000 1 2823 1 chr2A.!!$F1 2822
1 TraesCS2A01G201700 chr2B 223090341 223093052 2711 False 3899 3899 92.7820 32 2736 1 chr2B.!!$F1 2704
2 TraesCS2A01G201700 chr2D 175299466 175302312 2846 False 1878 3622 92.6295 1 2822 2 chr2D.!!$F1 2821


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
741 772 0.042013 CGTACGTGGAGAGCTCGATC 60.042 60.0 8.37 0.68 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2300 0.100682 GCAGGCTGCATGATCAACAG 59.899 55.0 33.33 19.69 44.26 3.16 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
29 30 2.238898 AGGGTTAATTTGGACGAGGAGG 59.761 50.000 0.00 0.00 0.00 4.30
30 31 2.026542 GGGTTAATTTGGACGAGGAGGT 60.027 50.000 0.00 0.00 0.00 3.85
79 85 2.964438 AAAGCGAACGCAGACACGGA 62.964 55.000 20.66 0.00 44.88 4.69
80 86 3.764049 GCGAACGCAGACACGGAC 61.764 66.667 14.26 0.00 41.49 4.79
81 87 3.458579 CGAACGCAGACACGGACG 61.459 66.667 0.00 0.00 37.37 4.79
82 88 2.354305 GAACGCAGACACGGACGT 60.354 61.111 0.00 0.00 41.16 4.34
183 193 0.247460 AAACGGTAGTTCTACCCGCC 59.753 55.000 19.44 0.09 45.49 6.13
185 195 2.810403 GGTAGTTCTACCCGCCCG 59.190 66.667 15.81 0.00 34.06 6.13
187 197 3.520862 TAGTTCTACCCGCCCGCG 61.521 66.667 0.00 0.00 39.44 6.46
239 261 1.888638 CGTCCCGTCGGTTGGTTTT 60.889 57.895 11.06 0.00 0.00 2.43
269 291 6.619437 TCTCCCAATCCATCTAAAATACTCCA 59.381 38.462 0.00 0.00 0.00 3.86
270 292 6.601332 TCCCAATCCATCTAAAATACTCCAC 58.399 40.000 0.00 0.00 0.00 4.02
354 376 1.894282 GCTGCCTAGAATTCGCCCC 60.894 63.158 0.00 0.00 0.00 5.80
356 378 0.250081 CTGCCTAGAATTCGCCCCTC 60.250 60.000 0.00 0.00 0.00 4.30
358 380 0.180406 GCCTAGAATTCGCCCCTCAA 59.820 55.000 0.00 0.00 0.00 3.02
360 382 2.749800 GCCTAGAATTCGCCCCTCAATT 60.750 50.000 0.00 0.00 0.00 2.32
361 383 3.142174 CCTAGAATTCGCCCCTCAATTC 58.858 50.000 0.00 0.00 38.70 2.17
362 384 1.668419 AGAATTCGCCCCTCAATTCG 58.332 50.000 0.00 0.00 41.84 3.34
364 386 1.743394 GAATTCGCCCCTCAATTCGTT 59.257 47.619 0.00 0.00 31.17 3.85
365 387 1.379527 ATTCGCCCCTCAATTCGTTC 58.620 50.000 0.00 0.00 0.00 3.95
366 388 0.675522 TTCGCCCCTCAATTCGTTCC 60.676 55.000 0.00 0.00 0.00 3.62
380 402 1.773496 GTTCCTTCGTTCGTCGCAG 59.227 57.895 0.00 0.00 39.67 5.18
440 462 1.070175 ACGCAAACCGATGAACGAAAG 60.070 47.619 0.00 0.00 45.77 2.62
442 464 2.571206 GCAAACCGATGAACGAAAGAC 58.429 47.619 0.00 0.00 45.77 3.01
452 476 5.960683 CGATGAACGAAAGACACTAGTAGAG 59.039 44.000 3.59 0.00 45.77 2.43
453 477 6.183360 CGATGAACGAAAGACACTAGTAGAGA 60.183 42.308 3.59 0.00 45.77 3.10
528 559 1.940613 GGTCTGTCTGTGTGTTGGTTC 59.059 52.381 0.00 0.00 0.00 3.62
540 571 0.733223 GTTGGTTCCTCTCGCGTCTC 60.733 60.000 5.77 0.00 0.00 3.36
619 650 0.460109 TGCTCCGTACGCGTCTACTA 60.460 55.000 18.63 0.00 36.15 1.82
730 761 2.278596 CTCCATCGCCGTACGTGG 60.279 66.667 15.21 14.91 44.19 4.94
738 769 2.403987 CCGTACGTGGAGAGCTCG 59.596 66.667 15.21 0.00 0.00 5.03
739 770 2.104859 CCGTACGTGGAGAGCTCGA 61.105 63.158 15.21 0.00 0.00 4.04
740 771 1.437772 CCGTACGTGGAGAGCTCGAT 61.438 60.000 15.21 0.00 0.00 3.59
741 772 0.042013 CGTACGTGGAGAGCTCGATC 60.042 60.000 8.37 0.68 0.00 3.69
759 790 0.532417 TCGTAGCTCCCGCTCTCTAC 60.532 60.000 0.00 0.00 45.15 2.59
859 890 1.807573 GGCTGCTGTCGTGAGCTAC 60.808 63.158 0.00 2.62 39.90 3.58
863 894 1.292223 GCTGTCGTGAGCTACCCAA 59.708 57.895 0.00 0.00 35.95 4.12
865 896 0.603569 CTGTCGTGAGCTACCCAACT 59.396 55.000 0.00 0.00 0.00 3.16
866 897 0.317160 TGTCGTGAGCTACCCAACTG 59.683 55.000 0.00 0.00 0.00 3.16
867 898 0.317479 GTCGTGAGCTACCCAACTGT 59.683 55.000 0.00 0.00 0.00 3.55
868 899 1.542915 GTCGTGAGCTACCCAACTGTA 59.457 52.381 0.00 0.00 0.00 2.74
912 943 2.028130 CTAGCTAGCTACCTGCACACT 58.972 52.381 20.67 0.00 45.94 3.55
919 950 0.179171 CTACCTGCACACTCGTACGG 60.179 60.000 16.52 8.79 0.00 4.02
948 979 4.148838 GGTAGCAGTACAGATCTCCATCT 58.851 47.826 0.00 0.00 40.32 2.90
995 1026 1.227118 GCTTGCTCGACCTAGCTCC 60.227 63.158 6.88 0.00 43.19 4.70
1020 1051 1.674651 GGCCTCAACCGGAGTTTCC 60.675 63.158 9.46 0.00 42.40 3.13
1149 1180 3.844090 GAGGAGTCTCTGGCCGGC 61.844 72.222 21.18 21.18 37.07 6.13
1503 1534 1.153823 CTACCTCCCGCAAGACGTG 60.154 63.158 0.00 0.00 41.42 4.49
1623 1670 8.439286 GCATCATTTTCTTCCTCTTCGATATAC 58.561 37.037 0.00 0.00 0.00 1.47
1624 1671 9.703892 CATCATTTTCTTCCTCTTCGATATACT 57.296 33.333 0.00 0.00 0.00 2.12
1989 2043 7.038659 ACATTCGTTTTTCTTTGGTTGATTCA 58.961 30.769 0.00 0.00 0.00 2.57
1997 2051 4.555262 TCTTTGGTTGATTCATTTTCGGC 58.445 39.130 0.00 0.00 0.00 5.54
2020 2076 2.491152 GTTCATGGGTGCATGCCG 59.509 61.111 16.68 0.00 32.87 5.69
2036 2092 2.749865 CCGTAGCCGCCAATGTGTG 61.750 63.158 0.00 0.00 0.00 3.82
2162 2221 6.599244 AGTTCGATCACATATTCCACAATTGT 59.401 34.615 4.92 4.92 0.00 2.71
2234 2300 0.681175 AACCATGCCCAAACAGCTTC 59.319 50.000 0.00 0.00 0.00 3.86
2252 2318 1.746470 TCTGTTGATCATGCAGCCTG 58.254 50.000 17.89 0.00 0.00 4.85
2339 2405 7.154656 GCCCACTAAAAAGAAACAATTGATCT 58.845 34.615 13.59 12.10 0.00 2.75
2366 2432 4.640201 GCCATTTCTAGAGTGCCACAATTA 59.360 41.667 0.00 0.00 0.00 1.40
2373 2439 6.245408 TCTAGAGTGCCACAATTATTTTGGT 58.755 36.000 11.23 0.00 32.50 3.67
2399 2465 3.282885 AGCAGATCAGTGTCGTCATCTA 58.717 45.455 0.00 0.00 0.00 1.98
2404 2470 6.268566 CAGATCAGTGTCGTCATCTATGAAA 58.731 40.000 0.00 0.00 38.75 2.69
2406 2472 5.644977 TCAGTGTCGTCATCTATGAAAGT 57.355 39.130 0.00 0.00 38.75 2.66
2440 2506 1.760192 TACCAACTCCTCGAGCTACC 58.240 55.000 6.99 0.00 32.04 3.18
2462 2528 1.716826 GCCTCGCGTAGTACTGCTCT 61.717 60.000 5.77 0.00 0.00 4.09
2463 2529 0.305313 CCTCGCGTAGTACTGCTCTC 59.695 60.000 5.77 0.00 0.00 3.20
2618 2699 2.866762 ACGATGCTCGAAATAGGCTTTC 59.133 45.455 11.64 0.00 43.74 2.62
2638 2719 8.870375 GGCTTTCGTGCCGCTTTATAAATAAAG 61.870 40.741 15.20 15.20 45.02 1.85
2680 2761 5.356470 AGCATCCAAGTTCTGAAATAGCTTC 59.644 40.000 0.00 0.00 34.31 3.86
2775 2933 2.865079 TGTCCTTCGGTTGGCATTTTA 58.135 42.857 0.00 0.00 0.00 1.52
2822 2980 3.338249 ACATGAACCTTGAAGACGATGG 58.662 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.830104 ACTTTCAACACCTCGTACCAC 58.170 47.619 0.00 0.00 0.00 4.16
30 31 3.118702 TCAACTTTCAACACCTCGTACCA 60.119 43.478 0.00 0.00 0.00 3.25
79 85 1.337260 ACTCTCCGACTGTACGTACGT 60.337 52.381 25.98 25.98 0.00 3.57
80 86 1.322936 GACTCTCCGACTGTACGTACG 59.677 57.143 20.18 15.01 0.00 3.67
81 87 1.663135 GGACTCTCCGACTGTACGTAC 59.337 57.143 18.90 18.90 0.00 3.67
82 88 1.276138 TGGACTCTCCGACTGTACGTA 59.724 52.381 0.00 0.00 40.17 3.57
188 198 2.124487 AGAGACTCCGGCGAGAGG 60.124 66.667 22.97 8.15 38.52 3.69
190 200 1.303398 AACAGAGACTCCGGCGAGA 60.303 57.895 9.30 2.74 38.52 4.04
192 202 2.341101 GGAACAGAGACTCCGGCGA 61.341 63.158 9.30 0.00 0.00 5.54
195 205 0.900647 AGGTGGAACAGAGACTCCGG 60.901 60.000 0.00 0.00 41.80 5.14
196 206 0.528470 GAGGTGGAACAGAGACTCCG 59.472 60.000 0.00 0.00 41.80 4.63
239 261 6.387192 TTTTAGATGGATTGGGAGACAAGA 57.613 37.500 0.00 0.00 43.48 3.02
354 376 2.729882 ACGAACGAAGGAACGAATTGAG 59.270 45.455 0.14 0.00 37.03 3.02
356 378 2.470140 CGACGAACGAAGGAACGAATTG 60.470 50.000 0.14 0.00 45.77 2.32
358 380 1.334054 CGACGAACGAAGGAACGAAT 58.666 50.000 0.14 0.00 45.77 3.34
360 382 1.727022 GCGACGAACGAAGGAACGA 60.727 57.895 0.00 0.00 45.77 3.85
361 383 1.930816 CTGCGACGAACGAAGGAACG 61.931 60.000 0.00 0.00 43.40 3.95
362 384 0.662374 TCTGCGACGAACGAAGGAAC 60.662 55.000 12.83 0.00 46.77 3.62
364 386 0.031043 TTTCTGCGACGAACGAAGGA 59.969 50.000 12.83 3.83 46.77 3.36
365 387 0.435008 CTTTCTGCGACGAACGAAGG 59.565 55.000 12.83 0.00 46.77 3.46
380 402 1.224722 GCAGATCGATCCGGCCTTTC 61.225 60.000 21.66 0.00 0.00 2.62
408 430 4.637276 TCGGTTTGCGTGGATAATATCAT 58.363 39.130 2.41 0.00 0.00 2.45
409 431 4.061357 TCGGTTTGCGTGGATAATATCA 57.939 40.909 2.41 0.00 0.00 2.15
410 432 4.688879 TCATCGGTTTGCGTGGATAATATC 59.311 41.667 0.00 0.00 0.00 1.63
452 476 9.690434 GATCTTACGTTGATCACTTTACAATTC 57.310 33.333 19.64 0.00 39.85 2.17
453 477 9.214957 TGATCTTACGTTGATCACTTTACAATT 57.785 29.630 21.93 0.00 43.47 2.32
540 571 2.745884 TTCAATGGTGCCCTCGCG 60.746 61.111 0.00 0.00 38.08 5.87
619 650 7.067859 GGTTTGAAAAGGTGGAAAACTAGTAGT 59.932 37.037 0.00 0.00 32.60 2.73
759 790 3.055312 GGGAGCTCGGGTTTATATAAGGG 60.055 52.174 7.83 0.00 0.00 3.95
859 890 1.531264 CGATCGAGACGTACAGTTGGG 60.531 57.143 10.26 0.00 0.00 4.12
863 894 1.396301 GGAACGATCGAGACGTACAGT 59.604 52.381 24.34 5.47 43.16 3.55
902 933 1.900016 TCCGTACGAGTGTGCAGGT 60.900 57.895 18.76 0.00 0.00 4.00
919 950 2.103736 GTACTGCTACCGGCCGTC 59.896 66.667 26.12 10.61 39.11 4.79
948 979 2.807470 CGTGTGCGTGCGTGGATA 60.807 61.111 0.00 0.00 0.00 2.59
971 1002 2.271607 TAGGTCGAGCAAGCTCAGCG 62.272 60.000 20.75 8.84 42.86 5.18
995 1026 0.394216 TCCGGTTGAGGCCATTGATG 60.394 55.000 5.01 0.00 0.00 3.07
1020 1051 0.681733 CCATGATGGAGGACCTACGG 59.318 60.000 5.27 0.00 40.96 4.02
1149 1180 1.443194 CACGTCGTACTGGGGTTCG 60.443 63.158 0.00 0.00 37.53 3.95
1158 1189 2.154389 GTGGTTGATGAACACGTCGTAC 59.846 50.000 0.00 0.00 33.27 3.67
1503 1534 3.689411 GCGTACTTGTAGCGCTCC 58.311 61.111 16.34 1.51 46.55 4.70
1623 1670 6.146184 CACGGCACAGATGGAATTATACTTAG 59.854 42.308 0.00 0.00 0.00 2.18
1624 1671 5.989168 CACGGCACAGATGGAATTATACTTA 59.011 40.000 0.00 0.00 0.00 2.24
1625 1672 4.816385 CACGGCACAGATGGAATTATACTT 59.184 41.667 0.00 0.00 0.00 2.24
1714 1761 1.227380 CTCGGCTATGTCCCTGCAC 60.227 63.158 0.00 0.00 0.00 4.57
1927 1975 5.532025 AAAACGAACGAATGAATCCTCTC 57.468 39.130 0.14 0.00 0.00 3.20
1953 2007 5.128008 AGAAAAACGAATGTCCCCTCAAAAA 59.872 36.000 0.00 0.00 0.00 1.94
1989 2043 3.384467 CCCATGAACCTAATGCCGAAAAT 59.616 43.478 0.00 0.00 0.00 1.82
2020 2076 3.187058 CCACACATTGGCGGCTAC 58.813 61.111 11.43 0.00 39.07 3.58
2036 2092 4.153655 GCCAGCCGTATAGCTTATTTTACC 59.846 45.833 0.00 0.00 42.61 2.85
2162 2221 6.536941 GGCCTCACAAATTTTGTAAACAGAAA 59.463 34.615 14.13 0.00 43.23 2.52
2234 2300 0.100682 GCAGGCTGCATGATCAACAG 59.899 55.000 33.33 19.69 44.26 3.16
2252 2318 1.644786 ATTGTTTGCTCGTAGGGCGC 61.645 55.000 0.00 0.00 41.07 6.53
2339 2405 1.406887 GGCACTCTAGAAATGGCGGAA 60.407 52.381 12.72 0.00 0.00 4.30
2366 2432 4.946157 CACTGATCTGCTCCTTACCAAAAT 59.054 41.667 0.00 0.00 0.00 1.82
2373 2439 2.423892 GACGACACTGATCTGCTCCTTA 59.576 50.000 0.00 0.00 0.00 2.69
2420 2486 2.097825 GGTAGCTCGAGGAGTTGGTAA 58.902 52.381 15.58 0.00 31.39 2.85
2421 2487 1.760192 GGTAGCTCGAGGAGTTGGTA 58.240 55.000 15.58 0.00 31.39 3.25
2563 2641 5.014755 ACCATTGGTTAAGATCCAACACCTA 59.985 40.000 1.37 0.33 45.84 3.08
2639 2720 1.468127 TGCTGGTTGTATGCATCGTTG 59.532 47.619 0.19 0.00 0.00 4.10
2657 2738 5.449725 GGAAGCTATTTCAGAACTTGGATGC 60.450 44.000 0.00 0.00 37.54 3.91
2736 2818 7.630242 AGGACATCTACATTGTTTATGGTTG 57.370 36.000 12.82 0.00 38.64 3.77
2739 2821 6.948353 CGAAGGACATCTACATTGTTTATGG 58.052 40.000 12.82 0.00 38.64 2.74
2796 2954 7.362056 CCATCGTCTTCAAGGTTCATGTAAAAT 60.362 37.037 0.00 0.00 0.00 1.82



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

AutoCloner maintained by Alex Coulton.