Multiple sequence alignment - TraesCS7A01G274500

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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 TraesCS7A01G274500 chr7A 100.000 2708 0 0 1 2708 287549884 287552591 0.000000e+00 5001
1 TraesCS7A01G274500 chr7A 75.400 874 170 29 996 1851 287805237 287806083 5.470000e-102 381
2 TraesCS7A01G274500 chr7B 97.415 1934 45 3 1 1930 244423988 244425920 0.000000e+00 3290
3 TraesCS7A01G274500 chr7B 91.860 430 18 7 1927 2340 244426022 244426450 3.890000e-163 584
4 TraesCS7A01G274500 chr7B 78.097 904 157 27 972 1851 244631656 244632542 3.970000e-148 534
5 TraesCS7A01G274500 chr7B 78.059 752 143 16 974 1715 244635902 244636641 3.180000e-124 455
6 TraesCS7A01G274500 chr7B 81.201 383 50 16 2340 2706 244635798 244636174 3.410000e-74 289
7 TraesCS7A01G274500 chr7D 96.634 1931 60 2 1 1928 264072542 264074470 0.000000e+00 3201
8 TraesCS7A01G274500 chr7D 78.405 903 157 26 972 1851 264315369 264316256 1.100000e-153 553
9 TraesCS7A01G274500 chr7D 96.951 328 10 0 2340 2667 264076600 264076927 3.940000e-153 551
10 TraesCS7A01G274500 chr7D 80.488 656 104 14 1209 1850 264082504 264083149 5.240000e-132 481
11 TraesCS7A01G274500 chr7D 75.027 913 185 26 956 1851 264311927 264312813 1.520000e-102 383
12 TraesCS7A01G274500 chr7D 83.237 346 48 8 2362 2700 264315295 264315637 2.620000e-80 309
13 TraesCS7A01G274500 chr7D 84.326 319 47 2 2391 2706 264319948 264320266 2.620000e-80 309
14 TraesCS7A01G274500 chr7D 96.296 135 3 2 1927 2061 264074556 264074688 1.260000e-53 220
15 TraesCS7A01G274500 chr7D 89.535 172 8 3 2170 2340 264076316 264076478 2.730000e-50 209
16 TraesCS7A01G274500 chr6A 75.870 920 176 33 954 1854 34390516 34389624 6.930000e-116 427
17 TraesCS7A01G274500 chr6B 77.808 730 134 20 996 1715 62633904 62633193 2.490000e-115 425
18 TraesCS7A01G274500 chr6B 83.422 374 54 6 2339 2705 62676247 62675875 9.290000e-90 340
19 TraesCS7A01G274500 chr6B 83.422 374 54 6 2339 2705 62680794 62680422 9.290000e-90 340
20 TraesCS7A01G274500 chr6B 83.422 374 54 6 2339 2705 62685413 62685041 9.290000e-90 340
21 TraesCS7A01G274500 chrUn 75.599 877 168 30 974 1830 101984016 101983166 2.530000e-105 392
22 TraesCS7A01G274500 chrUn 83.200 375 50 10 2339 2705 41699122 41699491 5.590000e-87 331
23 TraesCS7A01G274500 chr3B 82.451 359 48 12 2358 2705 780295623 780295269 1.580000e-77 300


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 TraesCS7A01G274500 chr7A 287549884 287552591 2707 False 5001.00 5001 100.00000 1 2708 1 chr7A.!!$F1 2707
1 TraesCS7A01G274500 chr7A 287805237 287806083 846 False 381.00 381 75.40000 996 1851 1 chr7A.!!$F2 855
2 TraesCS7A01G274500 chr7B 244423988 244426450 2462 False 1937.00 3290 94.63750 1 2340 2 chr7B.!!$F1 2339
3 TraesCS7A01G274500 chr7B 244631656 244636641 4985 False 426.00 534 79.11900 972 2706 3 chr7B.!!$F2 1734
4 TraesCS7A01G274500 chr7D 264072542 264076927 4385 False 1045.25 3201 94.85400 1 2667 4 chr7D.!!$F2 2666
5 TraesCS7A01G274500 chr7D 264082504 264083149 645 False 481.00 481 80.48800 1209 1850 1 chr7D.!!$F1 641
6 TraesCS7A01G274500 chr7D 264311927 264320266 8339 False 388.50 553 80.24875 956 2706 4 chr7D.!!$F3 1750
7 TraesCS7A01G274500 chr6A 34389624 34390516 892 True 427.00 427 75.87000 954 1854 1 chr6A.!!$R1 900
8 TraesCS7A01G274500 chr6B 62633193 62633904 711 True 425.00 425 77.80800 996 1715 1 chr6B.!!$R1 719
9 TraesCS7A01G274500 chrUn 101983166 101984016 850 True 392.00 392 75.59900 974 1830 1 chrUn.!!$R1 856

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
221 222 3.257393 GGATAGCCTCATATGCTCAACG 58.743 50.0 0.0 0.0 40.23 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 8857 1.227205 GAGTGATGCAGAGGCCTCG 60.227 63.158 26.95 21.4 37.47 4.63 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
48 49 6.424207 CGCTGAAATAGGTTAGGTAGGAATTC 59.576 42.308 0.00 0.0 0.00 2.17
221 222 3.257393 GGATAGCCTCATATGCTCAACG 58.743 50.000 0.00 0.0 40.23 4.10
500 501 3.952535 GTTGAACGAACAACAAGCAGAT 58.047 40.909 18.54 0.0 46.19 2.90
528 529 4.350368 TGTACAGTGGATCTTGCTCAAA 57.650 40.909 0.00 0.0 0.00 2.69
859 861 6.078456 TCATGATTCCCTTTGTCTACCATT 57.922 37.500 0.00 0.0 0.00 3.16
949 951 3.391296 ACAACACTTGCTCTTTCCTCCTA 59.609 43.478 0.00 0.0 0.00 2.94
1238 3716 6.256819 AGATATTGGATGGAGAGACGGAATA 58.743 40.000 0.00 0.0 0.00 1.75
1444 3934 2.223735 GCGACTTCGGACAAGATGGATA 60.224 50.000 0.02 0.0 40.23 2.59
1464 3954 3.460857 AGCGGAATGGTCAGTCTATTC 57.539 47.619 0.00 0.0 41.35 1.75
1647 4146 1.138661 GATCTTGAGAGTGGAGCAGGG 59.861 57.143 0.00 0.0 0.00 4.45
1750 4249 6.431852 CACTCATATCATGTTATTGGCATCCA 59.568 38.462 0.00 0.0 0.00 3.41
1908 4427 4.314522 TGGTTGAGATCCTTATTTGCCA 57.685 40.909 0.00 0.0 0.00 4.92
1999 4781 7.636259 TGTGAAAATTACAAATTACTGCAGC 57.364 32.000 15.27 0.0 0.00 5.25
2125 8823 6.806739 GTGTAATTTGAAATGGAGCTGGTAAC 59.193 38.462 0.00 0.0 0.00 2.50
2166 9097 2.202987 GCCTCTGCATCACTCCCG 60.203 66.667 0.00 0.0 37.47 5.14
2172 9103 2.351276 GCATCACTCCCGTTGGGT 59.649 61.111 1.04 0.0 44.74 4.51
2179 9110 1.375013 CTCCCGTTGGGTTACACCG 60.375 63.158 1.04 0.0 44.74 4.94
2371 9438 7.071196 TGCTTCCACACATCTCTATAAATAGGT 59.929 37.037 0.00 0.0 0.00 3.08
2480 10830 0.991146 TGGCTTGCCACCTAAGATCA 59.009 50.000 10.65 0.0 0.00 2.92
2706 11056 3.072768 GGATGGAGAGATGGAATGCTCTT 59.927 47.826 0.00 0.0 41.33 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.009610 GCTAGATAGGAGGAGTTGACTTCAG 59.990 48.000 0.00 0.00 0.00 3.02
221 222 5.431765 TCCTTACTGCTGGAATGATCTTTC 58.568 41.667 11.89 11.89 0.00 2.62
404 405 0.984109 CCGACGAATTTGCAATGTGC 59.016 50.000 0.00 0.00 45.29 4.57
500 501 5.189736 AGCAAGATCCACTGTACAAGGATAA 59.810 40.000 22.75 3.68 42.03 1.75
528 529 0.967380 GCTGGCATGTTTAGGTGGCT 60.967 55.000 0.00 0.00 41.07 4.75
859 861 3.628942 GGATGTGATGCAGCATAGTTTCA 59.371 43.478 8.41 0.00 34.68 2.69
949 951 3.049344 AGTTGGAAGGAGTGAGGACTTT 58.951 45.455 0.00 0.00 30.16 2.66
1238 3716 3.565307 AGATCCAGAAGCTCGAGAGAAT 58.435 45.455 18.75 0.00 41.32 2.40
1444 3934 2.766263 TGAATAGACTGACCATTCCGCT 59.234 45.455 0.00 0.00 0.00 5.52
1464 3954 1.667724 GTCATCTCCCTTGCGTTGATG 59.332 52.381 0.00 0.00 36.73 3.07
1647 4146 3.181490 GGATTAATTTCCGGAACAGGTGC 60.181 47.826 18.64 5.55 0.00 5.01
1817 4325 9.844257 ATCAAAATTTGGGATTTGTTTCTGTAA 57.156 25.926 5.83 0.00 37.68 2.41
1908 4427 7.283127 ACACTTCATGTACACAAAACAAGATCT 59.717 33.333 0.00 0.00 40.88 2.75
2063 5377 9.454859 ACTAAGGATTGTTTTTATCAAGGAGAG 57.545 33.333 0.00 0.00 0.00 3.20
2137 8849 4.172512 AGAGGCCTCGCATGCAGG 62.173 66.667 26.95 23.86 34.09 4.85
2145 8857 1.227205 GAGTGATGCAGAGGCCTCG 60.227 63.158 26.95 21.40 37.47 4.63
2153 8865 3.895025 CCAACGGGAGTGATGCAG 58.105 61.111 0.00 0.00 46.69 4.41
2179 9110 2.909965 TGCAAGGGTTTCACCGCC 60.910 61.111 0.00 0.00 39.83 6.13
2200 9131 4.247380 CGAGGGAGGGGCTGATGC 62.247 72.222 0.00 0.00 38.76 3.91
2336 9270 2.270257 TGTGGAAGCAGTGGCATGC 61.270 57.895 9.90 9.90 46.88 4.06
2337 9271 1.174078 TGTGTGGAAGCAGTGGCATG 61.174 55.000 0.00 0.00 44.61 4.06
2338 9272 0.251474 ATGTGTGGAAGCAGTGGCAT 60.251 50.000 0.00 0.00 44.61 4.40
2371 9438 1.476891 GTGTCTACCATTCTGCCGAGA 59.523 52.381 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.