Multiple sequence alignment - TraesCS3B01G164500

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 TraesCS3B01G164500 chr3B 100.000 3353 0 0 1 3353 162221924 162225276 0.000000e+00 6192
1 TraesCS3B01G164500 chr3B 85.143 175 26 0 1248 1422 529404978 529405152 2.660000e-41 180
2 TraesCS3B01G164500 chr3D 93.878 3430 89 49 7 3353 111205614 111209005 0.000000e+00 5059
3 TraesCS3B01G164500 chr3D 84.571 175 27 0 1248 1422 403111198 403111372 1.240000e-39 174
4 TraesCS3B01G164500 chr3A 87.953 3005 130 88 42 2892 119140517 119137591 0.000000e+00 3330
5 TraesCS3B01G164500 chr3A 92.553 470 27 6 2890 3353 119137540 119137073 0.000000e+00 667
6 TraesCS3B01G164500 chr3A 84.571 175 27 0 1248 1422 524756998 524757172 1.240000e-39 174


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 TraesCS3B01G164500 chr3B 162221924 162225276 3352 False 6192.0 6192 100.000 1 3353 1 chr3B.!!$F1 3352
1 TraesCS3B01G164500 chr3D 111205614 111209005 3391 False 5059.0 5059 93.878 7 3353 1 chr3D.!!$F1 3346
2 TraesCS3B01G164500 chr3A 119137073 119140517 3444 True 1998.5 3330 90.253 42 3353 2 chr3A.!!$R1 3311

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
276 278 0.100503 GCAAGCGGTCTCTCTCTCTC 59.899 60.000 0.0 0.0 0.00 3.20 F
314 316 1.002888 CTCTCTCTTTTCTGCCCTGCA 59.997 52.381 0.0 0.0 36.92 4.41 F
1761 1865 1.600023 TGGGTTTTCAAGGCTACACG 58.400 50.000 0.0 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1889 0.037447 GGAGTTCTTGGCTCTGGCTT 59.963 55.000 0.00 0.00 38.73 4.35 R
1806 1910 3.220999 TAACGGCTGCAGCGACAGT 62.221 57.895 31.19 23.66 43.26 3.55 R
2788 2949 0.250640 ACAAAGAGGCTGGCTGACTG 60.251 55.000 9.06 5.02 31.30 3.51 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
38 39 3.108144 GTCATTTCAGCAACACACACAC 58.892 45.455 0.00 0.00 0.00 3.82
39 40 2.751806 TCATTTCAGCAACACACACACA 59.248 40.909 0.00 0.00 0.00 3.72
92 94 7.123355 TGAACACATCATCATGTCTATACCA 57.877 36.000 0.00 0.00 41.69 3.25
182 184 3.998341 CCCAAATTGGCTTTCAATCACTG 59.002 43.478 6.48 0.00 44.68 3.66
239 241 0.250234 CTCAGCTCGGATGTTCCCAA 59.750 55.000 0.00 0.00 31.13 4.12
240 242 0.250234 TCAGCTCGGATGTTCCCAAG 59.750 55.000 0.00 0.00 31.13 3.61
242 244 1.078143 GCTCGGATGTTCCCAAGCT 60.078 57.895 7.85 0.00 38.26 3.74
244 246 0.250234 CTCGGATGTTCCCAAGCTGA 59.750 55.000 0.00 0.00 31.13 4.26
245 247 0.250234 TCGGATGTTCCCAAGCTGAG 59.750 55.000 0.00 0.00 31.13 3.35
246 248 1.372087 CGGATGTTCCCAAGCTGAGC 61.372 60.000 0.00 0.00 31.13 4.26
247 249 0.322816 GGATGTTCCCAAGCTGAGCA 60.323 55.000 7.39 0.00 0.00 4.26
263 265 2.654912 GCAAGCAAGCAAGCAAGCG 61.655 57.895 3.19 0.00 40.15 4.68
273 275 0.246086 CAAGCAAGCGGTCTCTCTCT 59.754 55.000 0.00 0.00 0.00 3.10
274 276 0.530288 AAGCAAGCGGTCTCTCTCTC 59.470 55.000 0.00 0.00 0.00 3.20
275 277 0.323360 AGCAAGCGGTCTCTCTCTCT 60.323 55.000 0.00 0.00 0.00 3.10
276 278 0.100503 GCAAGCGGTCTCTCTCTCTC 59.899 60.000 0.00 0.00 0.00 3.20
277 279 1.750193 CAAGCGGTCTCTCTCTCTCT 58.250 55.000 0.00 0.00 0.00 3.10
314 316 1.002888 CTCTCTCTTTTCTGCCCTGCA 59.997 52.381 0.00 0.00 36.92 4.41
807 884 2.693017 GCAGGAGGAGGAGGAGGA 59.307 66.667 0.00 0.00 0.00 3.71
810 887 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1359 1463 2.260434 GACGTGCAAGACCGGCTA 59.740 61.111 6.65 0.00 0.00 3.93
1761 1865 1.600023 TGGGTTTTCAAGGCTACACG 58.400 50.000 0.00 0.00 0.00 4.49
1806 1910 1.975327 CCAGAGCCAAGAACTCCGA 59.025 57.895 0.00 0.00 34.56 4.55
2530 2673 1.448893 GCATTGCCGTCGACCCTTA 60.449 57.895 10.58 0.00 0.00 2.69
2542 2685 1.734707 CGACCCTTACTTGAACGCGAT 60.735 52.381 15.93 0.00 0.00 4.58
2543 2686 2.344025 GACCCTTACTTGAACGCGATT 58.656 47.619 15.93 2.74 0.00 3.34
2544 2687 2.344025 ACCCTTACTTGAACGCGATTC 58.656 47.619 15.93 13.70 37.88 2.52
2545 2688 1.664151 CCCTTACTTGAACGCGATTCC 59.336 52.381 15.93 0.00 36.36 3.01
2546 2689 2.618053 CCTTACTTGAACGCGATTCCT 58.382 47.619 15.93 1.41 36.36 3.36
2547 2690 2.348666 CCTTACTTGAACGCGATTCCTG 59.651 50.000 15.93 10.46 36.36 3.86
2548 2691 3.250744 CTTACTTGAACGCGATTCCTGA 58.749 45.455 15.93 1.67 36.36 3.86
2549 2692 2.386661 ACTTGAACGCGATTCCTGAT 57.613 45.000 15.93 0.00 36.36 2.90
2550 2693 2.699954 ACTTGAACGCGATTCCTGATT 58.300 42.857 15.93 0.00 36.36 2.57
2551 2694 2.416547 ACTTGAACGCGATTCCTGATTG 59.583 45.455 15.93 2.82 36.36 2.67
2580 2726 1.988107 TCTTCATCCTCTTGCAGGGTT 59.012 47.619 0.00 0.00 43.67 4.11
2593 2739 6.248433 TCTTGCAGGGTTCTAATTTGATTCT 58.752 36.000 0.00 0.00 0.00 2.40
2648 2795 3.244875 TGCAACTAGGAGGAGCAAAATCA 60.245 43.478 0.00 0.00 31.42 2.57
2652 2799 3.846588 ACTAGGAGGAGCAAAATCAGGAA 59.153 43.478 0.00 0.00 0.00 3.36
2735 2896 2.297033 TGGCTTTTGCTTCAAGATCACC 59.703 45.455 0.00 0.00 46.54 4.02
2773 2934 2.675056 GCTTGTGAGAGTGCAGCGG 61.675 63.158 0.00 0.00 0.00 5.52
2788 2949 1.666234 GCGGCATAGCTAGCTGGTC 60.666 63.158 27.68 18.70 38.78 4.02
2789 2950 1.742146 CGGCATAGCTAGCTGGTCA 59.258 57.895 27.68 7.52 34.75 4.02
2790 2951 0.319383 CGGCATAGCTAGCTGGTCAG 60.319 60.000 27.68 11.71 34.75 3.51
2791 2952 0.755686 GGCATAGCTAGCTGGTCAGT 59.244 55.000 27.68 1.05 0.00 3.41
2792 2953 1.270041 GGCATAGCTAGCTGGTCAGTC 60.270 57.143 27.68 9.72 0.00 3.51
2926 3153 9.573133 GATGTTGTTCTCAAACTTATAAATGGG 57.427 33.333 0.00 0.00 36.30 4.00
3065 3300 1.899814 TGCCTGTCGTGGAGTATCTTT 59.100 47.619 0.00 0.00 33.73 2.52
3258 3502 3.063704 CGCAAGCTCCCATGGCAA 61.064 61.111 6.09 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.612725 AATGACACTGTTGGTTCCAAAAT 57.387 34.783 5.81 0.00 0.00 1.82
1 2 5.047021 TGAAATGACACTGTTGGTTCCAAAA 60.047 36.000 5.81 0.00 0.00 2.44
2 3 4.464244 TGAAATGACACTGTTGGTTCCAAA 59.536 37.500 5.81 0.00 0.00 3.28
3 4 4.019858 TGAAATGACACTGTTGGTTCCAA 58.980 39.130 0.00 0.00 0.00 3.53
4 5 3.625853 TGAAATGACACTGTTGGTTCCA 58.374 40.909 0.00 0.00 0.00 3.53
5 6 3.550842 GCTGAAATGACACTGTTGGTTCC 60.551 47.826 0.00 0.00 0.00 3.62
16 17 2.751806 TGTGTGTGTTGCTGAAATGACA 59.248 40.909 0.00 0.00 0.00 3.58
38 39 5.751028 TGAAAAATTTACGGCCTGTTCTTTG 59.249 36.000 0.00 0.00 0.00 2.77
39 40 5.751509 GTGAAAAATTTACGGCCTGTTCTTT 59.248 36.000 0.00 0.00 0.00 2.52
92 94 9.996554 CTGGTTACTTTTCTAATTTGGGAAAAT 57.003 29.630 11.35 0.00 39.60 1.82
142 144 2.674380 GGGTGCTGCTCCAGTTGG 60.674 66.667 21.01 0.00 33.43 3.77
242 244 0.031585 CTTGCTTGCTTGCTTGCTCA 59.968 50.000 10.35 0.00 0.00 4.26
244 246 1.300697 GCTTGCTTGCTTGCTTGCT 60.301 52.632 10.35 0.00 0.00 3.91
245 247 2.654912 CGCTTGCTTGCTTGCTTGC 61.655 57.895 3.47 6.27 0.00 4.01
246 248 2.019951 CCGCTTGCTTGCTTGCTTG 61.020 57.895 3.47 0.00 0.00 4.01
247 249 2.337532 CCGCTTGCTTGCTTGCTT 59.662 55.556 3.47 0.00 0.00 3.91
263 265 5.871396 TTAGAGAGAGAGAGAGAGAGACC 57.129 47.826 0.00 0.00 0.00 3.85
292 294 1.278699 CAGGGCAGAAAAGAGAGAGCT 59.721 52.381 0.00 0.00 0.00 4.09
314 316 3.391382 GCCGCTCCCTGTGTAGGT 61.391 66.667 0.00 0.00 42.96 3.08
827 913 2.042404 CTCCTCATCTGCAGCCTCCC 62.042 65.000 9.47 0.00 0.00 4.30
879 980 1.521450 CCTGCTGCACTTCTTGGTGG 61.521 60.000 0.00 0.00 37.65 4.61
1305 1409 4.228567 TGTGCCGACAGCCGAACA 62.229 61.111 0.00 0.00 42.71 3.18
1308 1412 4.961511 GTGTGTGCCGACAGCCGA 62.962 66.667 0.00 0.00 42.71 5.54
1785 1889 0.037447 GGAGTTCTTGGCTCTGGCTT 59.963 55.000 0.00 0.00 38.73 4.35
1806 1910 3.220999 TAACGGCTGCAGCGACAGT 62.221 57.895 31.19 23.66 43.26 3.55
1821 1925 4.259356 GGTGAAACATAGGGTCTGGTAAC 58.741 47.826 0.00 0.00 39.98 2.50
2530 2673 2.386661 ATCAGGAATCGCGTTCAAGT 57.613 45.000 18.49 0.00 38.64 3.16
2542 2685 5.384336 TGAAGAACCAATCACAATCAGGAA 58.616 37.500 0.00 0.00 0.00 3.36
2543 2686 4.984295 TGAAGAACCAATCACAATCAGGA 58.016 39.130 0.00 0.00 0.00 3.86
2544 2687 5.163581 GGATGAAGAACCAATCACAATCAGG 60.164 44.000 0.00 0.00 0.00 3.86
2545 2688 5.651139 AGGATGAAGAACCAATCACAATCAG 59.349 40.000 0.00 0.00 0.00 2.90
2546 2689 5.573219 AGGATGAAGAACCAATCACAATCA 58.427 37.500 0.00 0.00 0.00 2.57
2547 2690 5.884792 AGAGGATGAAGAACCAATCACAATC 59.115 40.000 0.00 0.00 0.00 2.67
2548 2691 5.824421 AGAGGATGAAGAACCAATCACAAT 58.176 37.500 0.00 0.00 0.00 2.71
2549 2692 5.246981 AGAGGATGAAGAACCAATCACAA 57.753 39.130 0.00 0.00 0.00 3.33
2550 2693 4.916041 AGAGGATGAAGAACCAATCACA 57.084 40.909 0.00 0.00 0.00 3.58
2551 2694 4.142513 GCAAGAGGATGAAGAACCAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
2580 2726 9.181061 TGAATGATGAAGCAGAATCAAATTAGA 57.819 29.630 0.17 0.00 36.44 2.10
2593 2739 4.386711 CAGCTCCTATGAATGATGAAGCA 58.613 43.478 0.00 0.00 0.00 3.91
2648 2795 3.521727 ACCAGACATAGAACCAGTTCCT 58.478 45.455 6.91 0.00 40.33 3.36
2652 2799 2.979678 ACCAACCAGACATAGAACCAGT 59.020 45.455 0.00 0.00 0.00 4.00
2662 2823 0.333312 ACCAACCAACCAACCAGACA 59.667 50.000 0.00 0.00 0.00 3.41
2735 2896 3.070302 AGCCTAATTCTAAGAAGCTCCGG 59.930 47.826 0.00 0.00 0.00 5.14
2773 2934 1.410517 TGACTGACCAGCTAGCTATGC 59.589 52.381 18.86 9.81 0.00 3.14
2788 2949 0.250640 ACAAAGAGGCTGGCTGACTG 60.251 55.000 9.06 5.02 31.30 3.51
2789 2950 0.250640 CACAAAGAGGCTGGCTGACT 60.251 55.000 9.06 0.00 36.16 3.41
2790 2951 1.239968 CCACAAAGAGGCTGGCTGAC 61.240 60.000 9.06 0.00 0.00 3.51
2791 2952 1.073722 CCACAAAGAGGCTGGCTGA 59.926 57.895 9.06 0.00 0.00 4.26
2792 2953 3.677527 CCACAAAGAGGCTGGCTG 58.322 61.111 9.06 0.00 0.00 4.85
2926 3153 1.055040 CTCCTCTCCCCATCCATCAC 58.945 60.000 0.00 0.00 0.00 3.06
3032 3267 2.161855 GACAGGCACCAATCAACATCA 58.838 47.619 0.00 0.00 0.00 3.07
3088 3323 9.206690 TGGATTTGGTTCCAAAGCATAATAATA 57.793 29.630 26.33 1.80 42.82 0.98
3103 3342 7.441836 AGAAATAACAAGGTTGGATTTGGTTC 58.558 34.615 8.69 0.00 31.89 3.62
3160 3399 2.371510 AGCAAGTTCTTTCTCAGCTCCT 59.628 45.455 0.00 0.00 0.00 3.69
3199 3438 8.900983 AGCTTAAAAGTTTGCATTAAATCCAA 57.099 26.923 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.