Multiple sequence alignment - TraesCS7A01G539600

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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 TraesCS7A01G539600 chr7A 100.000 3544 0 0 1 3544 716504095 716507638 0.000000e+00 6545.0
1 TraesCS7A01G539600 chr7A 97.663 3552 53 8 1 3544 716607653 716604124 0.000000e+00 6072.0
2 TraesCS7A01G539600 chr7A 75.208 960 159 56 292 1217 697825528 697826442 7.180000e-102 381.0
3 TraesCS7A01G539600 chr7B 94.491 3576 153 17 1 3544 718574106 718577669 0.000000e+00 5472.0
4 TraesCS7A01G539600 chr7B 95.620 2397 85 9 1158 3544 718508683 718511069 0.000000e+00 3827.0
5 TraesCS7A01G539600 chr7B 93.843 1543 70 9 1 1520 718597596 718599136 0.000000e+00 2300.0
6 TraesCS7A01G539600 chr7B 91.011 356 26 5 2919 3272 718572856 718573207 3.200000e-130 475.0
7 TraesCS7A01G539600 chr7B 91.011 356 26 5 2919 3272 718596346 718596697 3.200000e-130 475.0
8 TraesCS7A01G539600 chr7B 74.857 1050 183 63 247 1257 690032349 690033356 5.510000e-108 401.0
9 TraesCS7A01G539600 chr7B 77.123 424 90 6 2112 2533 690919082 690919500 4.570000e-59 239.0
10 TraesCS7A01G539600 chr7D 95.042 3469 134 17 1 3439 621313659 621310199 0.000000e+00 5419.0
11 TraesCS7A01G539600 chr7D 74.802 1008 164 67 292 1257 606108884 606109843 4.320000e-99 372.0
12 TraesCS7A01G539600 chr7D 95.000 80 4 0 3464 3543 28072050 28071971 3.710000e-25 126.0
13 TraesCS7A01G539600 chrUn 95.620 2397 85 9 1158 3544 293895833 293898219 0.000000e+00 3827.0
14 TraesCS7A01G539600 chrUn 96.178 1413 50 4 1158 2568 270666414 270667824 0.000000e+00 2307.0
15 TraesCS7A01G539600 chrUn 96.254 614 23 0 1 614 329800618 329800005 0.000000e+00 1007.0
16 TraesCS7A01G539600 chrUn 96.254 614 23 0 1 614 429197970 429198583 0.000000e+00 1007.0
17 TraesCS7A01G539600 chrUn 74.714 1400 283 43 450 1820 33121126 33122483 3.090000e-155 558.0
18 TraesCS7A01G539600 chrUn 91.292 356 25 5 2919 3272 329801867 329801516 6.880000e-132 481.0
19 TraesCS7A01G539600 chrUn 91.292 356 25 5 2919 3272 384893442 384893091 6.880000e-132 481.0
20 TraesCS7A01G539600 chr3A 74.713 1396 291 38 450 1820 704579253 704580611 1.850000e-157 566.0
21 TraesCS7A01G539600 chr3A 76.970 495 98 11 1337 1820 704777947 704777458 5.830000e-68 268.0
22 TraesCS7A01G539600 chr3A 76.037 434 91 8 2104 2532 704777276 704776851 2.770000e-51 213.0
23 TraesCS7A01G539600 chr3B 75.870 431 95 8 2104 2531 760051909 760051485 9.970000e-51 211.0
24 TraesCS7A01G539600 chr4A 95.062 81 4 0 3464 3544 484342033 484341953 1.030000e-25 128.0
25 TraesCS7A01G539600 chr1D 91.358 81 7 0 3464 3544 382774771 382774691 1.040000e-20 111.0
26 TraesCS7A01G539600 chr6B 87.640 89 11 0 3456 3544 500643948 500643860 1.740000e-18 104.0
27 TraesCS7A01G539600 chr6D 87.654 81 10 0 3464 3544 51262388 51262308 1.050000e-15 95.3


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 TraesCS7A01G539600 chr7A 716504095 716507638 3543 False 6545.0 6545 100.0000 1 3544 1 chr7A.!!$F2 3543
1 TraesCS7A01G539600 chr7A 716604124 716607653 3529 True 6072.0 6072 97.6630 1 3544 1 chr7A.!!$R1 3543
2 TraesCS7A01G539600 chr7A 697825528 697826442 914 False 381.0 381 75.2080 292 1217 1 chr7A.!!$F1 925
3 TraesCS7A01G539600 chr7B 718508683 718511069 2386 False 3827.0 3827 95.6200 1158 3544 1 chr7B.!!$F3 2386
4 TraesCS7A01G539600 chr7B 718572856 718577669 4813 False 2973.5 5472 92.7510 1 3544 2 chr7B.!!$F4 3543
5 TraesCS7A01G539600 chr7B 718596346 718599136 2790 False 1387.5 2300 92.4270 1 3272 2 chr7B.!!$F5 3271
6 TraesCS7A01G539600 chr7B 690032349 690033356 1007 False 401.0 401 74.8570 247 1257 1 chr7B.!!$F1 1010
7 TraesCS7A01G539600 chr7D 621310199 621313659 3460 True 5419.0 5419 95.0420 1 3439 1 chr7D.!!$R2 3438
8 TraesCS7A01G539600 chr7D 606108884 606109843 959 False 372.0 372 74.8020 292 1257 1 chr7D.!!$F1 965
9 TraesCS7A01G539600 chrUn 293895833 293898219 2386 False 3827.0 3827 95.6200 1158 3544 1 chrUn.!!$F3 2386
10 TraesCS7A01G539600 chrUn 270666414 270667824 1410 False 2307.0 2307 96.1780 1158 2568 1 chrUn.!!$F2 1410
11 TraesCS7A01G539600 chrUn 429197970 429198583 613 False 1007.0 1007 96.2540 1 614 1 chrUn.!!$F4 613
12 TraesCS7A01G539600 chrUn 329800005 329801867 1862 True 744.0 1007 93.7730 1 3272 2 chrUn.!!$R2 3271
13 TraesCS7A01G539600 chrUn 33121126 33122483 1357 False 558.0 558 74.7140 450 1820 1 chrUn.!!$F1 1370
14 TraesCS7A01G539600 chr3A 704579253 704580611 1358 False 566.0 566 74.7130 450 1820 1 chr3A.!!$F1 1370
15 TraesCS7A01G539600 chr3A 704776851 704777947 1096 True 240.5 268 76.5035 1337 2532 2 chr3A.!!$R1 1195

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
767 2045 6.719301 AGGGCAATGAAGGATATGATTCTAG 58.281 40.0 0.0 0.0 0.0 2.43 F
1319 2649 0.323629 TCCCTACACCTTTTGCTCCG 59.676 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 3798 2.268920 GCATCCAGCGGGTTGAGA 59.731 61.111 16.97 0.0 36.19 3.27 R
2887 4284 2.501723 GTCTGAAGCATGGGTCCTAAGA 59.498 50.000 0.00 0.0 0.00 2.10 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
767 2045 6.719301 AGGGCAATGAAGGATATGATTCTAG 58.281 40.000 0.00 0.0 0.00 2.43
1083 2370 6.407202 ACCATTATCCTTATATTCACTCGCC 58.593 40.000 0.00 0.0 0.00 5.54
1309 2601 7.074653 TCTTATACAATGGATTCCCTACACC 57.925 40.000 0.00 0.0 0.00 4.16
1319 2649 0.323629 TCCCTACACCTTTTGCTCCG 59.676 55.000 0.00 0.0 0.00 4.63
1371 2702 4.508124 CGTGCTTCTCATACCTGGTTTATC 59.492 45.833 3.84 0.0 0.00 1.75
1742 3082 8.472007 ACATACCCAATGAAACAACTTTAGAA 57.528 30.769 0.00 0.0 39.07 2.10
2261 3650 5.557866 ACTATTTCTACACTTCCCAACCAC 58.442 41.667 0.00 0.0 0.00 4.16
2319 3708 2.190578 GCGGGGATGCAGTTAGCT 59.809 61.111 0.00 0.0 45.94 3.32
2500 3889 8.132362 TGTTGAGTTGGACATGTGTATTTAAAC 58.868 33.333 1.15 1.4 0.00 2.01
2838 4234 5.028549 ACCATACGATGCATCTCTTTTCT 57.971 39.130 23.73 0.0 0.00 2.52
2854 4251 6.989169 TCTCTTTTCTGAGAGAACCTTCAAAG 59.011 38.462 2.30 0.0 46.80 2.77
3424 4822 3.330701 TGCCTGGTCAAAGGAAGTAAGAT 59.669 43.478 0.00 0.0 40.02 2.40
3519 4917 8.578151 GTCTAGGATTTGTATTTCGTCTCCTAT 58.422 37.037 0.00 0.0 34.37 2.57
3539 4937 3.426787 TCTTATCTCTAGGAGAGGCGG 57.573 52.381 3.73 0.0 42.26 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
506 1766 1.859427 CTGCATGACATATGGCCCGC 61.859 60.000 5.99 9.23 0.00 6.13
767 2045 3.058639 GTGTGTGATCTCTTGGTTCTTGC 60.059 47.826 0.00 0.00 0.00 4.01
1273 2565 9.965902 ATCCATTGTATAAGAAGACCCATTATC 57.034 33.333 0.00 0.00 0.00 1.75
1309 2601 3.557595 GGATAGACATGTCGGAGCAAAAG 59.442 47.826 19.85 0.00 34.09 2.27
1319 2649 6.650120 TGGGAAAAGTAAGGATAGACATGTC 58.350 40.000 18.47 18.47 0.00 3.06
1742 3082 9.753674 TCACCAAAACTATATGAAGGAAATTCT 57.246 29.630 0.00 0.00 38.83 2.40
2409 3798 2.268920 GCATCCAGCGGGTTGAGA 59.731 61.111 16.97 0.00 36.19 3.27
2500 3889 6.542370 TCCTACAGTGAGAAAGAAAACTTTGG 59.458 38.462 0.00 0.00 0.00 3.28
2838 4234 6.601613 TGCTTTTTACTTTGAAGGTTCTCTCA 59.398 34.615 0.00 0.00 0.00 3.27
2854 4251 7.707893 TCATAGATAGGGTAACGTGCTTTTTAC 59.292 37.037 0.00 0.00 35.44 2.01
2887 4284 2.501723 GTCTGAAGCATGGGTCCTAAGA 59.498 50.000 0.00 0.00 0.00 2.10
3243 4640 7.078228 AGAAAGAAAGATATGTCGTTTGCAAC 58.922 34.615 0.00 0.00 0.00 4.17
3424 4822 1.004560 CAACGGAGAGGCTCTTGCA 60.005 57.895 19.80 0.00 41.91 4.08
3519 4917 2.553466 GCCGCCTCTCCTAGAGATAAGA 60.553 54.545 5.50 0.00 45.07 2.10


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

AutoCloner maintained by Alex Coulton.