Multiple sequence alignment - TraesCS7D01G415100

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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 TraesCS7D01G415100 chr7D 100.000 2801 0 0 1 2801 533756855 533759655 0.000000e+00 5173.0
1 TraesCS7D01G415100 chr7B 92.060 2796 144 34 19 2801 573921972 573924702 0.000000e+00 3862.0
2 TraesCS7D01G415100 chr7A 91.867 2324 119 43 505 2801 613176241 613178521 0.000000e+00 3181.0
3 TraesCS7D01G415100 chr7A 95.612 433 18 1 19 450 613175808 613176240 0.000000e+00 693.0
4 TraesCS7D01G415100 chr5A 83.081 857 105 22 972 1813 18389855 18389024 0.000000e+00 743.0
5 TraesCS7D01G415100 chr5A 97.674 43 1 0 781 823 35742899 35742941 1.080000e-09 75.0
6 TraesCS7D01G415100 chr5A 92.157 51 4 0 781 831 606631208 606631158 3.870000e-09 73.1
7 TraesCS7D01G415100 chr5D 85.849 530 66 7 911 1435 26531865 26532390 3.150000e-154 555.0
8 TraesCS7D01G415100 chrUn 83.824 408 41 18 2401 2801 122475476 122475865 5.700000e-97 364.0
9 TraesCS7D01G415100 chrUn 97.674 43 1 0 781 823 31389490 31389448 1.080000e-09 75.0
10 TraesCS7D01G415100 chr2D 73.529 748 149 29 1047 1772 94328855 94328135 3.610000e-59 239.0
11 TraesCS7D01G415100 chr2B 73.243 740 157 24 1047 1769 146451971 146451256 6.030000e-57 231.0
12 TraesCS7D01G415100 chr6D 97.674 43 1 0 781 823 221839929 221839971 1.080000e-09 75.0
13 TraesCS7D01G415100 chr6D 97.674 43 1 0 781 823 434446217 434446259 1.080000e-09 75.0
14 TraesCS7D01G415100 chr3B 95.652 46 2 0 781 826 193137807 193137762 1.080000e-09 75.0
15 TraesCS7D01G415100 chr1A 97.674 43 1 0 781 823 556134643 556134601 1.080000e-09 75.0


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 TraesCS7D01G415100 chr7D 533756855 533759655 2800 False 5173 5173 100.0000 1 2801 1 chr7D.!!$F1 2800
1 TraesCS7D01G415100 chr7B 573921972 573924702 2730 False 3862 3862 92.0600 19 2801 1 chr7B.!!$F1 2782
2 TraesCS7D01G415100 chr7A 613175808 613178521 2713 False 1937 3181 93.7395 19 2801 2 chr7A.!!$F1 2782
3 TraesCS7D01G415100 chr5A 18389024 18389855 831 True 743 743 83.0810 972 1813 1 chr5A.!!$R1 841
4 TraesCS7D01G415100 chr5D 26531865 26532390 525 False 555 555 85.8490 911 1435 1 chr5D.!!$F1 524
5 TraesCS7D01G415100 chr2D 94328135 94328855 720 True 239 239 73.5290 1047 1772 1 chr2D.!!$R1 725
6 TraesCS7D01G415100 chr2B 146451256 146451971 715 True 231 231 73.2430 1047 1769 1 chr2B.!!$R1 722

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
917 924 1.012086 CATGGCCTCATCACTTCACG 58.988 55.0 3.32 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2451 0.445436 GACTCGCGGAAGACTCGTTA 59.555 55.0 6.13 0.0 0.0 3.18 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
40 41 9.755804 TGTATAAGAAGACAAATCTCTGCTATG 57.244 33.333 0.00 0.00 32.34 2.23
42 43 8.885494 ATAAGAAGACAAATCTCTGCTATGAC 57.115 34.615 0.00 0.00 32.34 3.06
56 57 6.333416 TCTGCTATGACTGTTCAGTTCATAC 58.667 40.000 6.91 10.18 34.35 2.39
123 125 7.014134 TGGTGTCTGATGTGTTGATTTGTTTAT 59.986 33.333 0.00 0.00 0.00 1.40
206 208 3.569194 TGAGTGTAGTTTTCTTGCCCA 57.431 42.857 0.00 0.00 0.00 5.36
317 319 5.711976 AGCTAGCCAGACAAATGTTTATGTT 59.288 36.000 12.13 0.00 0.00 2.71
359 361 2.539274 GACCTCGTCACGCTAGTAGTAG 59.461 54.545 0.00 0.00 32.09 2.57
399 401 4.464244 CCTTCCAGGATATTGAGATCGCTA 59.536 45.833 0.00 0.00 37.67 4.26
456 458 7.492669 GCTCTGAATGTGTTAGCTAGTGAATAA 59.507 37.037 0.00 0.00 0.00 1.40
474 476 7.230510 AGTGAATAATTTTGACTTGCCACTGTA 59.769 33.333 0.00 0.00 31.00 2.74
482 484 8.586570 TTTTGACTTGCCACTGTATTTATTTG 57.413 30.769 0.00 0.00 0.00 2.32
512 514 5.389520 TCCACATGACATTTTAAGGTTCCA 58.610 37.500 0.00 0.00 0.00 3.53
534 536 4.724074 ATGTCATGTAATTTGCACCCTG 57.276 40.909 0.00 0.00 0.00 4.45
698 705 5.808030 GGTTGCAGTTCTATAACAGAGTCTC 59.192 44.000 0.00 0.00 38.12 3.36
717 724 8.217799 AGAGTCTCTATGTAGATCTTGTTAGCT 58.782 37.037 0.00 0.00 0.00 3.32
718 725 8.760980 AGTCTCTATGTAGATCTTGTTAGCTT 57.239 34.615 0.00 0.00 0.00 3.74
767 774 4.154195 CCAAGTGACGAAATTCCTTAGGTG 59.846 45.833 0.00 0.00 0.00 4.00
809 816 3.219281 TGGGACTAAAGGCTTTGTTGTC 58.781 45.455 22.32 22.48 0.00 3.18
818 825 2.230266 AGGCTTTGTTGTCGTTGTTGTT 59.770 40.909 0.00 0.00 0.00 2.83
819 826 2.344142 GGCTTTGTTGTCGTTGTTGTTG 59.656 45.455 0.00 0.00 0.00 3.33
820 827 2.983803 GCTTTGTTGTCGTTGTTGTTGT 59.016 40.909 0.00 0.00 0.00 3.32
821 828 3.427193 GCTTTGTTGTCGTTGTTGTTGTT 59.573 39.130 0.00 0.00 0.00 2.83
822 829 4.662891 GCTTTGTTGTCGTTGTTGTTGTTG 60.663 41.667 0.00 0.00 0.00 3.33
823 830 2.320367 TGTTGTCGTTGTTGTTGTTGC 58.680 42.857 0.00 0.00 0.00 4.17
869 876 1.135859 GCCTGAATTTGTGTCTCTGCG 60.136 52.381 0.00 0.00 0.00 5.18
878 885 1.375908 TGTCTCTGCGTGATTGCCC 60.376 57.895 0.00 0.00 0.00 5.36
917 924 1.012086 CATGGCCTCATCACTTCACG 58.988 55.000 3.32 0.00 0.00 4.35
956 963 5.549742 TGTTTTCCTTGCAGGATTTTCAT 57.450 34.783 0.00 0.00 45.34 2.57
1416 1442 0.037232 CCTCTCAGTTCGTGAACCCC 60.037 60.000 9.03 0.00 42.06 4.95
1495 1521 4.904853 AGGAGAAGTCTGAGAAAAGGAAGT 59.095 41.667 0.00 0.00 0.00 3.01
1728 1782 3.570540 TGGATCTGAATCTGAGTCCGAT 58.429 45.455 10.99 10.99 32.12 4.18
1859 1916 4.586001 GCCCACATATCATGTCCTTTTCAT 59.414 41.667 0.00 0.00 42.70 2.57
1862 1919 6.097270 CCCACATATCATGTCCTTTTCATTGT 59.903 38.462 0.00 0.00 42.70 2.71
1908 1965 3.950395 GCCCTTTCAAGAGATGTATTGCT 59.050 43.478 0.00 0.00 0.00 3.91
1982 2039 4.024670 CCTGTGCTAAGTAGTACCCTCTT 58.975 47.826 4.41 0.00 38.01 2.85
2029 2086 4.142609 TGGAAGTGCTTGAAGCTATAGG 57.857 45.455 18.94 0.00 42.97 2.57
2092 2150 7.703058 TCCTGCGACTATATTCTTCATCATA 57.297 36.000 0.00 0.00 0.00 2.15
2138 2196 6.358030 GTGCTGTGCAATAATCGTTTGATATC 59.642 38.462 0.00 0.00 41.47 1.63
2183 2245 2.433239 GACCTTACTAATTCCCTCGCCA 59.567 50.000 0.00 0.00 0.00 5.69
2192 2254 6.838382 ACTAATTCCCTCGCCAAATTATAGT 58.162 36.000 0.00 0.00 0.00 2.12
2226 2290 8.888579 TTGAAAAGGTCAAACTTTGTAAACAA 57.111 26.923 1.44 0.00 43.43 2.83
2227 2291 8.300495 TGAAAAGGTCAAACTTTGTAAACAAC 57.700 30.769 1.44 0.00 40.36 3.32
2232 2296 9.930693 AAGGTCAAACTTTGTAAACAACATAAA 57.069 25.926 1.44 0.00 38.10 1.40
2275 2339 7.811653 TGTCAATGCTTACGATACAAAATCAA 58.188 30.769 0.00 0.00 0.00 2.57
2277 2341 8.947940 GTCAATGCTTACGATACAAAATCAATC 58.052 33.333 0.00 0.00 0.00 2.67
2282 2346 7.078228 GCTTACGATACAAAATCAATCCCATC 58.922 38.462 0.00 0.00 0.00 3.51
2284 2348 8.512966 TTACGATACAAAATCAATCCCATCAA 57.487 30.769 0.00 0.00 0.00 2.57
2297 2361 7.663827 TCAATCCCATCAAATTCATTATGAGC 58.336 34.615 0.00 0.00 0.00 4.26
2298 2362 7.507956 TCAATCCCATCAAATTCATTATGAGCT 59.492 33.333 0.00 0.00 0.00 4.09
2299 2363 7.850935 ATCCCATCAAATTCATTATGAGCTT 57.149 32.000 0.00 0.00 0.00 3.74
2300 2364 7.046292 TCCCATCAAATTCATTATGAGCTTG 57.954 36.000 10.31 10.31 0.00 4.01
2301 2365 6.608405 TCCCATCAAATTCATTATGAGCTTGT 59.392 34.615 14.02 4.29 0.00 3.16
2302 2366 7.779326 TCCCATCAAATTCATTATGAGCTTGTA 59.221 33.333 14.02 5.98 0.00 2.41
2303 2367 8.582437 CCCATCAAATTCATTATGAGCTTGTAT 58.418 33.333 14.02 7.35 0.00 2.29
2304 2368 9.406828 CCATCAAATTCATTATGAGCTTGTATG 57.593 33.333 14.02 14.35 0.00 2.39
2305 2369 9.961265 CATCAAATTCATTATGAGCTTGTATGT 57.039 29.630 14.02 0.00 0.00 2.29
2331 2395 6.811253 TTTCCCATGTTGTATATATTCGGC 57.189 37.500 0.00 0.00 0.00 5.54
2333 2397 5.242434 TCCCATGTTGTATATATTCGGCAC 58.758 41.667 0.00 0.00 0.00 5.01
2377 2441 3.018149 TGCTTAACCACTTGACGGTTTT 58.982 40.909 0.00 0.00 44.46 2.43
2378 2442 3.444388 TGCTTAACCACTTGACGGTTTTT 59.556 39.130 0.00 0.00 44.46 1.94
2387 2451 5.163591 CCACTTGACGGTTTTTCTTTTACCT 60.164 40.000 0.00 0.00 0.00 3.08
2624 2689 1.139853 GATCCTCCAGGTTGGTAGCTG 59.860 57.143 0.00 0.00 46.89 4.24
2628 2693 4.308526 CAGGTTGGTAGCTGGCTG 57.691 61.111 5.25 0.00 44.30 4.85
2629 2694 2.042831 CAGGTTGGTAGCTGGCTGC 61.043 63.158 8.47 8.47 44.30 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.755804 CATAGCAGAGATTTGTCTTCTTATACA 57.244 33.333 0.00 0.00 0.00 2.29
15 16 9.973450 TCATAGCAGAGATTTGTCTTCTTATAC 57.027 33.333 0.00 0.00 0.00 1.47
16 17 9.973450 GTCATAGCAGAGATTTGTCTTCTTATA 57.027 33.333 0.00 0.00 0.00 0.98
17 18 8.703743 AGTCATAGCAGAGATTTGTCTTCTTAT 58.296 33.333 0.00 0.00 0.00 1.73
40 41 2.325761 ACGCGTATGAACTGAACAGTC 58.674 47.619 11.67 3.36 41.58 3.51
42 43 2.324860 TGACGCGTATGAACTGAACAG 58.675 47.619 13.97 0.00 0.00 3.16
56 57 5.613964 AAACACAAATAAACTTTGACGCG 57.386 34.783 3.53 3.53 33.83 6.01
123 125 4.124238 AGCAACGAGTACTGCTTAAACAA 58.876 39.130 0.00 0.00 46.71 2.83
139 141 7.644490 AGAGACTCTGTTATAGAATAGCAACG 58.356 38.462 3.56 0.00 34.32 4.10
176 178 3.328382 AACTACACTCATGGCGCTAAA 57.672 42.857 7.64 0.00 0.00 1.85
317 319 9.601217 GAGGTCATCATCTTTTAGCTAAAGTAA 57.399 33.333 17.91 8.91 43.12 2.24
359 361 6.524101 TGGAAGGAAACAAACTATATTGGC 57.476 37.500 0.00 0.00 34.56 4.52
399 401 5.997384 AGAAGAAACGGTTATACAGGACT 57.003 39.130 0.00 0.00 0.00 3.85
456 458 9.206870 CAAATAAATACAGTGGCAAGTCAAAAT 57.793 29.630 0.00 0.00 0.00 1.82
482 484 9.705290 ACCTTAAAATGTCATGTGGAATTAAAC 57.295 29.630 0.00 0.00 0.00 2.01
512 514 4.081531 CCAGGGTGCAAATTACATGACATT 60.082 41.667 0.00 0.00 0.00 2.71
698 705 8.598924 CACACAAAGCTAACAAGATCTACATAG 58.401 37.037 0.00 0.00 0.00 2.23
717 724 4.564041 ACAAGAAAATGCACACACACAAA 58.436 34.783 0.00 0.00 0.00 2.83
718 725 4.172505 GACAAGAAAATGCACACACACAA 58.827 39.130 0.00 0.00 0.00 3.33
767 774 6.873076 TCCCAAACAAATTCATTTACTGCATC 59.127 34.615 0.00 0.00 0.00 3.91
809 816 1.255859 CTGCATGCAACAACAACAACG 59.744 47.619 22.88 0.96 0.00 4.10
818 825 5.342433 GCTATTCATTTACTGCATGCAACA 58.658 37.500 22.88 9.40 0.00 3.33
819 826 4.438797 CGCTATTCATTTACTGCATGCAAC 59.561 41.667 22.88 0.00 0.00 4.17
820 827 4.096231 ACGCTATTCATTTACTGCATGCAA 59.904 37.500 22.88 7.10 0.00 4.08
821 828 3.627123 ACGCTATTCATTTACTGCATGCA 59.373 39.130 21.29 21.29 0.00 3.96
822 829 3.970610 CACGCTATTCATTTACTGCATGC 59.029 43.478 11.82 11.82 0.00 4.06
823 830 5.408204 TCACGCTATTCATTTACTGCATG 57.592 39.130 0.00 0.00 0.00 4.06
869 876 2.723124 AAATTCACACGGGCAATCAC 57.277 45.000 0.00 0.00 0.00 3.06
878 885 6.907212 GCCATGACTTATCTAAAATTCACACG 59.093 38.462 0.00 0.00 0.00 4.49
917 924 6.872547 AGGAAAACAAACTCTATCGGTTAGTC 59.127 38.462 0.00 0.00 0.00 2.59
956 963 8.644374 AAAAGGTTATACAAGACCAGCAAATA 57.356 30.769 0.00 0.00 38.42 1.40
1416 1442 2.557924 CTCCATCTCCTTCTCCAGATCG 59.442 54.545 0.00 0.00 0.00 3.69
1495 1521 2.158769 TGCTCTTTGACTTGCTCCTTGA 60.159 45.455 0.00 0.00 0.00 3.02
1728 1782 3.055891 TGCCGTCAGAATCAGAATCAGAA 60.056 43.478 0.00 0.00 0.00 3.02
1908 1965 7.201609 GCGTTCAGGAAATCAACTGATACATTA 60.202 37.037 0.00 0.00 42.73 1.90
2029 2086 3.378427 GGCATCACAGGATAGGAAACAAC 59.622 47.826 0.00 0.00 30.87 3.32
2113 2171 3.820689 TCAAACGATTATTGCACAGCAC 58.179 40.909 0.00 0.00 38.71 4.40
2138 2196 9.618410 GTCAAAATGTTTATCTTCACAAAAACG 57.382 29.630 0.00 0.00 35.16 3.60
2171 2230 4.278419 GCACTATAATTTGGCGAGGGAATT 59.722 41.667 0.00 0.00 0.00 2.17
2173 2232 3.211045 GCACTATAATTTGGCGAGGGAA 58.789 45.455 0.00 0.00 0.00 3.97
2201 2263 8.766151 GTTGTTTACAAAGTTTGACCTTTTCAA 58.234 29.630 22.23 13.02 38.86 2.69
2203 2265 8.300495 TGTTGTTTACAAAGTTTGACCTTTTC 57.700 30.769 22.23 7.99 37.63 2.29
2243 2307 7.589395 TGTATCGTAAGCATTGACAAATTTGT 58.411 30.769 23.49 23.49 40.43 2.83
2244 2308 8.446489 TTGTATCGTAAGCATTGACAAATTTG 57.554 30.769 16.67 16.67 37.18 2.32
2245 2309 9.469807 TTTTGTATCGTAAGCATTGACAAATTT 57.530 25.926 0.00 0.00 35.80 1.82
2251 2315 8.841444 ATTGATTTTGTATCGTAAGCATTGAC 57.159 30.769 0.00 0.00 37.18 3.18
2256 2320 5.883115 TGGGATTGATTTTGTATCGTAAGCA 59.117 36.000 0.00 0.00 37.18 3.91
2257 2321 6.371809 TGGGATTGATTTTGTATCGTAAGC 57.628 37.500 0.00 0.00 37.18 3.09
2263 2327 9.820725 TGAATTTGATGGGATTGATTTTGTATC 57.179 29.630 0.00 0.00 0.00 2.24
2275 2339 7.289317 ACAAGCTCATAATGAATTTGATGGGAT 59.711 33.333 0.00 0.00 0.00 3.85
2277 2341 6.812998 ACAAGCTCATAATGAATTTGATGGG 58.187 36.000 0.00 0.00 0.00 4.00
2310 2374 5.012664 AGTGCCGAATATATACAACATGGGA 59.987 40.000 0.00 0.00 0.00 4.37
2311 2375 5.122239 CAGTGCCGAATATATACAACATGGG 59.878 44.000 0.00 0.00 0.00 4.00
2312 2376 5.700832 ACAGTGCCGAATATATACAACATGG 59.299 40.000 0.00 0.00 0.00 3.66
2313 2377 6.785488 ACAGTGCCGAATATATACAACATG 57.215 37.500 0.00 0.00 0.00 3.21
2314 2378 8.896320 TTTACAGTGCCGAATATATACAACAT 57.104 30.769 0.00 0.00 0.00 2.71
2315 2379 8.769891 CATTTACAGTGCCGAATATATACAACA 58.230 33.333 0.00 0.00 0.00 3.33
2316 2380 8.770828 ACATTTACAGTGCCGAATATATACAAC 58.229 33.333 0.00 0.00 0.00 3.32
2317 2381 8.896320 ACATTTACAGTGCCGAATATATACAA 57.104 30.769 0.00 0.00 0.00 2.41
2318 2382 8.896320 AACATTTACAGTGCCGAATATATACA 57.104 30.769 0.00 0.00 0.00 2.29
2319 2383 8.984764 TGAACATTTACAGTGCCGAATATATAC 58.015 33.333 0.00 0.00 0.00 1.47
2320 2384 9.719355 ATGAACATTTACAGTGCCGAATATATA 57.281 29.630 0.00 0.00 0.00 0.86
2331 2395 7.369803 AGAGCTGTAATGAACATTTACAGTG 57.630 36.000 19.21 0.00 37.50 3.66
2333 2397 6.744537 GCAAGAGCTGTAATGAACATTTACAG 59.255 38.462 15.72 15.72 37.50 2.74
2377 2441 5.464168 CGGAAGACTCGTTAGGTAAAAGAA 58.536 41.667 0.00 0.00 0.00 2.52
2378 2442 4.616835 GCGGAAGACTCGTTAGGTAAAAGA 60.617 45.833 0.00 0.00 0.00 2.52
2387 2451 0.445436 GACTCGCGGAAGACTCGTTA 59.555 55.000 6.13 0.00 0.00 3.18
2463 2528 2.815298 GACGAGGAGCGAGACGAGG 61.815 68.421 0.00 0.00 44.57 4.63
2467 2532 3.519930 GGGGACGAGGAGCGAGAC 61.520 72.222 0.00 0.00 44.57 3.36
2651 2716 1.153086 CCAGCGGAGGAAATCAGGG 60.153 63.158 0.00 0.00 0.00 4.45
2685 2761 3.403057 CGCCACCTGACAACGACG 61.403 66.667 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.