Multiple sequence alignment - TraesCS1B01G085400

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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 TraesCS1B01G085400 chr1B 100.000 3926 0 0 1 3926 70184997 70188922 0 7251
1 TraesCS1B01G085400 chr1B 86.333 3139 357 37 806 3926 70170118 70173202 0 3354
2 TraesCS1B01G085400 chr1B 82.505 2172 366 13 806 2970 70334123 70336287 0 1893
3 TraesCS1B01G085400 chr1D 97.126 3132 72 7 806 3926 49617357 49620481 0 5269
4 TraesCS1B01G085400 chr1D 83.235 2368 374 21 806 3164 49973568 49975921 0 2152
5 TraesCS1B01G085400 chr1D 83.204 2191 345 20 806 2983 49956604 49958784 0 1986
6 TraesCS1B01G085400 chr1D 81.957 2300 380 28 807 3091 49426008 49423729 0 1916
7 TraesCS1B01G085400 chr1D 88.144 835 72 8 1 810 49615552 49616384 0 968
8 TraesCS1B01G085400 chr1A 89.168 3148 299 17 806 3926 49245513 49248645 0 3886
9 TraesCS1B01G085400 chr1A 82.846 2256 365 18 806 3049 49347097 49349342 0 2002
10 TraesCS1B01G085400 chr1A 82.373 2292 377 22 817 3092 49355136 49357416 0 1969


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 TraesCS1B01G085400 chr1B 70184997 70188922 3925 False 7251.0 7251 100.000 1 3926 1 chr1B.!!$F2 3925
1 TraesCS1B01G085400 chr1B 70170118 70173202 3084 False 3354.0 3354 86.333 806 3926 1 chr1B.!!$F1 3120
2 TraesCS1B01G085400 chr1B 70334123 70336287 2164 False 1893.0 1893 82.505 806 2970 1 chr1B.!!$F3 2164
3 TraesCS1B01G085400 chr1D 49615552 49620481 4929 False 3118.5 5269 92.635 1 3926 2 chr1D.!!$F3 3925
4 TraesCS1B01G085400 chr1D 49973568 49975921 2353 False 2152.0 2152 83.235 806 3164 1 chr1D.!!$F2 2358
5 TraesCS1B01G085400 chr1D 49956604 49958784 2180 False 1986.0 1986 83.204 806 2983 1 chr1D.!!$F1 2177
6 TraesCS1B01G085400 chr1D 49423729 49426008 2279 True 1916.0 1916 81.957 807 3091 1 chr1D.!!$R1 2284
7 TraesCS1B01G085400 chr1A 49245513 49248645 3132 False 3886.0 3886 89.168 806 3926 1 chr1A.!!$F1 3120
8 TraesCS1B01G085400 chr1A 49347097 49349342 2245 False 2002.0 2002 82.846 806 3049 1 chr1A.!!$F2 2243
9 TraesCS1B01G085400 chr1A 49355136 49357416 2280 False 1969.0 1969 82.373 817 3092 1 chr1A.!!$F3 2275

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
753 779 0.179134 GGGTGATCTCTTCCACGTCG 60.179 60.000 0.0 0.00 34.30 5.12 F
1400 2429 1.069049 CACTTTGGGCCAGTGGAAAAG 59.931 52.381 15.2 19.55 38.43 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 2583 3.062059 GCAGAACACGATACGTAACGATG 60.062 47.826 28.61 22.79 38.32 3.84 R
3208 4277 0.482887 TGAGACCAGAGTCCACCAGA 59.517 55.000 0.00 0.00 44.72 3.86 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 7.117667 ACAACCAAAAGAACAAGTTTTCATGTC 59.882 33.333 0.00 0.00 31.07 3.06
30 31 6.696411 ACCAAAAGAACAAGTTTTCATGTCA 58.304 32.000 0.00 0.00 31.07 3.58
32 33 7.035004 CCAAAAGAACAAGTTTTCATGTCAGA 58.965 34.615 0.00 0.00 31.07 3.27
135 143 1.215655 GGACGATGATGCGGCTGTAC 61.216 60.000 0.00 0.00 39.80 2.90
142 150 2.252072 GATGCGGCTGTACCCCTTCA 62.252 60.000 0.00 0.00 33.26 3.02
151 159 0.828677 GTACCCCTTCATGTAGGCGT 59.171 55.000 12.74 12.69 33.73 5.68
157 165 3.709880 TTCATGTAGGCGTCGGCGG 62.710 63.158 13.05 2.46 41.24 6.13
173 198 4.021925 GGCCGGAGTTGGAGCTGT 62.022 66.667 5.05 0.00 0.00 4.40
176 201 2.125912 CGGAGTTGGAGCTGTCGG 60.126 66.667 0.00 0.00 0.00 4.79
193 218 0.732880 CGGTGAGGTGCAAGTAGTCG 60.733 60.000 0.00 0.00 0.00 4.18
205 230 1.666054 AGTAGTCGTCGGAGGACATC 58.334 55.000 26.86 19.56 43.61 3.06
223 248 2.907458 TCTGTCTGGTCATCCTCTGA 57.093 50.000 0.00 0.00 34.23 3.27
270 295 2.597510 GGTTGCCTTCGCCTTGGT 60.598 61.111 0.00 0.00 0.00 3.67
301 326 3.173240 GTTGTCTCGCGCTCCGAC 61.173 66.667 5.56 9.66 41.89 4.79
306 331 4.785512 CTCGCGCTCCGACTGCTT 62.786 66.667 5.56 0.00 41.89 3.91
318 343 1.078848 ACTGCTTGATGGCGAGTCC 60.079 57.895 0.00 0.00 34.52 3.85
329 354 3.951332 CGAGTCCAAGCGCTTTGA 58.049 55.556 22.51 20.61 39.21 2.69
330 355 2.234613 CGAGTCCAAGCGCTTTGAA 58.765 52.632 23.85 8.53 39.21 2.69
428 454 1.303317 GTGCCTTTCCCCATGTCGT 60.303 57.895 0.00 0.00 0.00 4.34
441 467 1.202582 CATGTCGTCCTCTTCCTCGTT 59.797 52.381 0.00 0.00 0.00 3.85
448 474 1.301677 CCTCTTCCTCGTTTGCAGCC 61.302 60.000 0.00 0.00 0.00 4.85
531 557 1.692749 GAGTACCCAGGGATGGCCA 60.693 63.158 14.54 8.56 35.15 5.36
537 563 3.016971 CAGGGATGGCCAGGGACA 61.017 66.667 13.05 0.00 37.65 4.02
568 594 2.374184 CTAGTAGAGCAGGTGCAGAGT 58.626 52.381 4.48 0.00 45.16 3.24
592 618 3.797353 ATACCTGCAGGGGTGCGG 61.797 66.667 35.42 11.19 40.22 5.69
617 643 2.496817 GGAGCTGAGTACCTGCCG 59.503 66.667 0.00 0.00 40.16 5.69
618 644 2.352032 GGAGCTGAGTACCTGCCGT 61.352 63.158 0.00 0.00 40.16 5.68
622 648 1.878656 GCTGAGTACCTGCCGTGAGT 61.879 60.000 0.00 0.00 34.12 3.41
645 671 2.646719 GTGACGTCGCCCACACTA 59.353 61.111 18.36 0.00 33.72 2.74
711 737 3.314331 CCACCTCTGTCCAGGCGT 61.314 66.667 0.00 0.00 36.98 5.68
724 750 2.280797 GGCGTGACTGGCAGAACA 60.281 61.111 23.66 17.26 0.00 3.18
737 763 2.264794 GAACACGATGCGGAGGGT 59.735 61.111 0.00 0.00 0.00 4.34
753 779 0.179134 GGGTGATCTCTTCCACGTCG 60.179 60.000 0.00 0.00 34.30 5.12
755 781 1.467713 GGTGATCTCTTCCACGTCGTC 60.468 57.143 0.00 0.00 34.30 4.20
765 791 2.282251 ACGTCGTCTGGCTCCTCA 60.282 61.111 0.00 0.00 0.00 3.86
768 794 1.657751 CGTCGTCTGGCTCCTCATCA 61.658 60.000 0.00 0.00 0.00 3.07
770 796 1.226802 CGTCTGGCTCCTCATCACG 60.227 63.158 0.00 0.00 0.00 4.35
801 827 1.135527 TCCCTATTGTCGTTGTAGCCG 59.864 52.381 0.00 0.00 0.00 5.52
830 1833 1.153628 CAGCCTACACCTACGCCAC 60.154 63.158 0.00 0.00 0.00 5.01
921 1924 3.350833 GACAGGCCTCAAAACAGATGAT 58.649 45.455 0.00 0.00 0.00 2.45
928 1931 4.811024 GCCTCAAAACAGATGATATCGTCA 59.189 41.667 23.68 3.71 42.06 4.35
1231 2258 1.187567 AATGGTGCAGCAAGGGGTTC 61.188 55.000 24.18 0.00 0.00 3.62
1400 2429 1.069049 CACTTTGGGCCAGTGGAAAAG 59.931 52.381 15.20 19.55 38.43 2.27
1596 2625 2.572095 TTCACGGGTATGCCGCTGAG 62.572 60.000 0.00 0.00 34.97 3.35
1823 2853 3.846588 AGAATGGGTAGGTTGACTGATGT 59.153 43.478 0.00 0.00 0.00 3.06
1933 2966 3.390967 TGGTGATCTGGTGAAAGTGAAGA 59.609 43.478 0.00 0.00 0.00 2.87
2034 3067 3.007635 CAACGAAGGAAGGGTTATGGAC 58.992 50.000 0.00 0.00 0.00 4.02
2355 3391 2.495270 TGGAAGAACTGTTGCTGCAAAA 59.505 40.909 17.80 11.26 0.00 2.44
2507 3543 6.968904 GCAATGAATGTGAAGTTCGATATTGT 59.031 34.615 0.00 0.00 0.00 2.71
2735 3771 6.920758 AGCTCTCGTCTTGTAAATGATATCAC 59.079 38.462 7.78 0.00 0.00 3.06
3208 4277 3.096092 AGAGTTCATCGAGCTCTTCCTT 58.904 45.455 12.85 0.00 45.43 3.36
3232 4301 0.469892 TGGACTCTGGTCTCACTGCA 60.470 55.000 0.00 0.00 41.82 4.41
3319 4395 5.394005 GGCTAAATTGGTGTATGATGTGCAA 60.394 40.000 0.00 0.00 0.00 4.08
3325 4401 3.695556 TGGTGTATGATGTGCAATTCCAG 59.304 43.478 0.00 0.00 0.00 3.86
3494 4574 1.080995 GCTGTGAGATCTGGCGTGAC 61.081 60.000 0.00 0.00 0.00 3.67
3506 4586 0.173481 GGCGTGACTGTAGCATGAGA 59.827 55.000 0.00 0.00 0.00 3.27
3558 4638 8.597167 TCTACAGGTAGATGATGATAATTTGGG 58.403 37.037 5.08 0.00 37.28 4.12
3689 4769 3.937706 CCTTGTAGAGAACTTGCAGATGG 59.062 47.826 0.00 0.00 0.00 3.51
3771 4851 8.737168 ATATAAGCTCTGCAATGTTGAAAGTA 57.263 30.769 0.00 0.00 0.00 2.24
3888 4968 9.075519 TGAAAATGTGAAATAAAATCATCGCTC 57.924 29.630 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.117667 ACATGAAAACTTGTTCTTTTGGTTGTC 59.882 33.333 0.00 0.00 0.00 3.18
51 53 6.615316 TCTCCATCTCTCCATTGTATTTACCA 59.385 38.462 0.00 0.00 0.00 3.25
59 61 3.434739 GGCATTCTCCATCTCTCCATTGT 60.435 47.826 0.00 0.00 0.00 2.71
60 62 3.147629 GGCATTCTCCATCTCTCCATTG 58.852 50.000 0.00 0.00 0.00 2.82
71 73 0.331278 ATTTCCACCGGCATTCTCCA 59.669 50.000 0.00 0.00 0.00 3.86
72 74 1.025041 GATTTCCACCGGCATTCTCC 58.975 55.000 0.00 0.00 0.00 3.71
99 101 2.507944 CAGAAGGGGCCGATGAGG 59.492 66.667 0.00 0.00 44.97 3.86
103 105 3.470888 CGTCCAGAAGGGGCCGAT 61.471 66.667 0.00 0.00 38.37 4.18
157 165 2.435059 GACAGCTCCAACTCCGGC 60.435 66.667 0.00 0.00 0.00 6.13
173 198 0.601558 GACTACTTGCACCTCACCGA 59.398 55.000 0.00 0.00 0.00 4.69
176 201 1.699343 GACGACTACTTGCACCTCAC 58.301 55.000 0.00 0.00 0.00 3.51
193 218 0.457851 CCAGACAGATGTCCTCCGAC 59.542 60.000 9.31 0.00 45.85 4.79
205 230 2.093764 GGTTCAGAGGATGACCAGACAG 60.094 54.545 0.00 0.00 37.77 3.51
301 326 1.078918 TGGACTCGCCATCAAGCAG 60.079 57.895 0.00 0.00 43.33 4.24
318 343 2.160065 CGCAGAAAATTCAAAGCGCTTG 60.160 45.455 25.80 17.46 37.98 4.01
329 354 1.635663 CGACTCCGCCGCAGAAAATT 61.636 55.000 0.00 0.00 0.00 1.82
330 355 2.100631 CGACTCCGCCGCAGAAAAT 61.101 57.895 0.00 0.00 0.00 1.82
351 376 4.104417 ACGTGCTCCTCGAGACGC 62.104 66.667 20.38 18.18 37.01 5.19
353 378 2.486042 GGACGTGCTCCTCGAGAC 59.514 66.667 15.71 2.59 35.89 3.36
364 389 0.031314 CGATGGATCCAGAGGACGTG 59.969 60.000 21.33 0.00 32.98 4.49
365 390 1.109920 CCGATGGATCCAGAGGACGT 61.110 60.000 26.10 6.94 32.98 4.34
366 391 1.662608 CCGATGGATCCAGAGGACG 59.337 63.158 26.10 20.51 32.98 4.79
367 392 1.369321 GCCGATGGATCCAGAGGAC 59.631 63.158 31.44 21.72 32.98 3.85
410 436 1.303317 ACGACATGGGGAAAGGCAC 60.303 57.895 0.00 0.00 0.00 5.01
415 441 1.278127 GAAGAGGACGACATGGGGAAA 59.722 52.381 0.00 0.00 0.00 3.13
428 454 0.320771 GCTGCAAACGAGGAAGAGGA 60.321 55.000 0.00 0.00 0.00 3.71
512 538 1.692749 GGCCATCCCTGGGTACTCA 60.693 63.158 13.56 0.00 43.36 3.41
522 548 4.129148 GGTGTCCCTGGCCATCCC 62.129 72.222 5.51 0.00 0.00 3.85
523 549 4.129148 GGGTGTCCCTGGCCATCC 62.129 72.222 5.51 2.24 41.34 3.51
534 560 2.092321 TCTACTAGCTCCAGAGGGTGTC 60.092 54.545 0.00 0.00 34.93 3.67
561 587 2.125147 GTATGCCGCCACTCTGCA 60.125 61.111 0.00 0.00 39.23 4.41
596 622 2.760385 AGGTACTCAGCTCCGGCC 60.760 66.667 0.00 0.00 39.73 6.13
617 643 4.295119 ACGTCACCGGCCACTCAC 62.295 66.667 0.00 0.00 38.78 3.51
618 644 3.986006 GACGTCACCGGCCACTCA 61.986 66.667 11.55 0.00 35.50 3.41
629 655 1.529152 ATGTAGTGTGGGCGACGTCA 61.529 55.000 17.16 0.00 0.00 4.35
640 666 1.183549 GTCTCCCGGTGATGTAGTGT 58.816 55.000 0.00 0.00 0.00 3.55
641 667 0.100682 CGTCTCCCGGTGATGTAGTG 59.899 60.000 0.00 0.00 0.00 2.74
711 737 0.950555 GCATCGTGTTCTGCCAGTCA 60.951 55.000 0.00 0.00 32.15 3.41
724 750 1.739338 GAGATCACCCTCCGCATCGT 61.739 60.000 0.00 0.00 0.00 3.73
737 763 1.468914 CAGACGACGTGGAAGAGATCA 59.531 52.381 4.58 0.00 0.00 2.92
753 779 1.066303 CTACGTGATGAGGAGCCAGAC 59.934 57.143 0.00 0.00 0.00 3.51
755 781 0.249238 GCTACGTGATGAGGAGCCAG 60.249 60.000 0.00 0.00 0.00 4.85
765 791 1.395826 GGGAGAGCCTGCTACGTGAT 61.396 60.000 0.00 0.00 0.00 3.06
768 794 0.186386 ATAGGGAGAGCCTGCTACGT 59.814 55.000 0.00 0.00 0.00 3.57
770 796 2.036604 GACAATAGGGAGAGCCTGCTAC 59.963 54.545 0.00 0.00 0.00 3.58
801 827 3.161450 TAGGCTGTGGGCGGATCC 61.161 66.667 0.00 0.00 42.94 3.36
830 1833 1.654954 GCAGCAGCAGTTCATCAGGG 61.655 60.000 0.00 0.00 41.58 4.45
921 1924 0.899720 GGAGGGTGTTGGTGACGATA 59.100 55.000 0.00 0.00 0.00 2.92
928 1931 0.474184 CACTTGAGGAGGGTGTTGGT 59.526 55.000 0.00 0.00 0.00 3.67
1231 2258 6.812879 ATTATATGTCACCACATCATGCAG 57.187 37.500 0.00 0.00 42.66 4.41
1400 2429 3.596214 TCTCTAAACATTTGAGTCGCCC 58.404 45.455 2.42 0.00 0.00 6.13
1554 2583 3.062059 GCAGAACACGATACGTAACGATG 60.062 47.826 28.61 22.79 38.32 3.84
1596 2625 6.889301 TCAATCATATCTGCAAAGAATCCC 57.111 37.500 0.00 0.00 0.00 3.85
1823 2853 9.964303 CAATCATCCGATTAAAATTGTCCATAA 57.036 29.630 0.00 0.00 39.96 1.90
1933 2966 8.934507 TTGTCCGTTATTTCAAAAATCAACTT 57.065 26.923 0.00 0.00 0.00 2.66
2034 3067 3.181507 CCAAGTCAAAGATATGGTGTGCG 60.182 47.826 0.00 0.00 0.00 5.34
2735 3771 5.487131 TCCCCCTTTTCCAATAATTTTCTGG 59.513 40.000 0.00 0.00 0.00 3.86
3208 4277 0.482887 TGAGACCAGAGTCCACCAGA 59.517 55.000 0.00 0.00 44.72 3.86
3232 4301 0.606401 CCGTCAAGCACATCAGGGTT 60.606 55.000 0.00 0.00 0.00 4.11
3319 4395 1.541169 TGGCACAACACCCTGGAAT 59.459 52.632 0.00 0.00 31.92 3.01
3494 4574 6.094464 TCAATTCCAACATTCTCATGCTACAG 59.906 38.462 0.00 0.00 33.05 2.74
3506 4586 4.594491 AGGAGGCTTTTCAATTCCAACATT 59.406 37.500 0.00 0.00 0.00 2.71
3558 4638 0.402121 AGACTTGCCTCCTCCCAAAC 59.598 55.000 0.00 0.00 0.00 2.93
3689 4769 8.652290 AGAAGTTCCATATAAATCAGGAGGTAC 58.348 37.037 0.00 0.00 0.00 3.34
3744 4824 8.526147 ACTTTCAACATTGCAGAGCTTATATTT 58.474 29.630 0.00 0.00 0.00 1.40
3771 4851 6.774656 CCACTTCTCTCCCTATGCATATTTTT 59.225 38.462 6.92 0.00 0.00 1.94
3863 4943 8.255143 CGAGCGATGATTTTATTTCACATTTTC 58.745 33.333 0.00 0.00 0.00 2.29
3888 4968 3.004171 TCAACACCCCAAAATATCGTCG 58.996 45.455 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.