Multiple sequence alignment - TraesCS6B01G299200

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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 TraesCS6B01G299200 chr6B 100.000 2966 0 0 1 2966 537297183 537300148 0.000000e+00 5478.0
1 TraesCS6B01G299200 chr6B 98.522 1556 23 0 1 1556 453247553 453249108 0.000000e+00 2747.0
2 TraesCS6B01G299200 chr6B 98.810 1008 11 1 1553 2559 453259142 453260149 0.000000e+00 1794.0
3 TraesCS6B01G299200 chr6B 96.671 841 26 2 2128 2966 413735775 413736615 0.000000e+00 1397.0
4 TraesCS6B01G299200 chr6B 85.936 839 76 17 53 877 453276269 453277079 0.000000e+00 857.0
5 TraesCS6B01G299200 chr6B 85.765 843 75 15 52 877 537315400 537316214 0.000000e+00 850.0
6 TraesCS6B01G299200 chr6B 95.172 145 7 0 560 704 453115286 453115430 2.300000e-56 230.0
7 TraesCS6B01G299200 chr6B 81.164 292 31 9 286 571 453114552 453114825 2.320000e-51 213.0
8 TraesCS6B01G299200 chr5B 97.738 840 18 1 2128 2966 277632888 277633727 0.000000e+00 1445.0
9 TraesCS6B01G299200 chr5B 87.864 1203 125 19 884 2074 535217250 535218443 0.000000e+00 1393.0
10 TraesCS6B01G299200 chr5B 86.964 1212 142 15 883 2086 592913439 592912236 0.000000e+00 1349.0
11 TraesCS6B01G299200 chr3B 97.294 850 20 3 2119 2966 245965683 245966531 0.000000e+00 1439.0
12 TraesCS6B01G299200 chr5D 97.262 840 22 1 2128 2966 371281098 371281937 0.000000e+00 1423.0
13 TraesCS6B01G299200 chr5D 96.790 841 25 2 2128 2966 363182225 363183065 0.000000e+00 1402.0
14 TraesCS6B01G299200 chr5D 86.732 1221 126 25 881 2086 448631118 448632317 0.000000e+00 1325.0
15 TraesCS6B01G299200 chr1D 97.143 840 23 1 2128 2966 107614134 107613295 0.000000e+00 1417.0
16 TraesCS6B01G299200 chr6D 97.470 830 20 1 2128 2956 72032924 72033753 0.000000e+00 1415.0
17 TraesCS6B01G299200 chr6D 87.827 879 75 17 3 876 291793531 291794382 0.000000e+00 1002.0
18 TraesCS6B01G299200 chr6D 83.125 320 36 7 277 596 291782940 291783241 2.910000e-70 276.0
19 TraesCS6B01G299200 chr6D 83.936 249 22 10 580 822 291783273 291783509 3.850000e-54 222.0
20 TraesCS6B01G299200 chr6A 97.139 839 23 1 2129 2966 610915753 610916591 0.000000e+00 1415.0
21 TraesCS6B01G299200 chr6A 88.260 1167 123 12 894 2051 52181399 52180238 0.000000e+00 1384.0
22 TraesCS6B01G299200 chr6A 86.759 506 39 7 4 508 431241196 431240718 3.360000e-149 538.0
23 TraesCS6B01G299200 chr6A 81.851 562 63 20 275 822 431491071 431490535 1.260000e-118 436.0
24 TraesCS6B01G299200 chr6A 82.872 397 29 20 511 876 431224461 431224073 1.330000e-83 320.0
25 TraesCS6B01G299200 chr3D 87.819 1174 130 13 894 2059 559267886 559269054 0.000000e+00 1363.0
26 TraesCS6B01G299200 chr7D 89.256 1089 105 7 893 1969 80371804 80372892 0.000000e+00 1352.0
27 TraesCS6B01G299200 chr7D 88.634 1003 103 9 883 1878 18591639 18592637 0.000000e+00 1210.0
28 TraesCS6B01G299200 chr4A 84.699 1196 162 18 901 2086 642633890 642632706 0.000000e+00 1175.0
29 TraesCS6B01G299200 chr4A 86.667 90 9 3 388 476 733879709 733879622 2.430000e-16 97.1
30 TraesCS6B01G299200 chrUn 100.000 399 0 0 530 928 478857134 478856736 0.000000e+00 737.0
31 TraesCS6B01G299200 chr2D 87.500 64 6 2 281 342 629971857 629971794 4.100000e-09 73.1


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 TraesCS6B01G299200 chr6B 537297183 537300148 2965 False 5478.0 5478 100.0000 1 2966 1 chr6B.!!$F5 2965
1 TraesCS6B01G299200 chr6B 453247553 453249108 1555 False 2747.0 2747 98.5220 1 1556 1 chr6B.!!$F2 1555
2 TraesCS6B01G299200 chr6B 453259142 453260149 1007 False 1794.0 1794 98.8100 1553 2559 1 chr6B.!!$F3 1006
3 TraesCS6B01G299200 chr6B 413735775 413736615 840 False 1397.0 1397 96.6710 2128 2966 1 chr6B.!!$F1 838
4 TraesCS6B01G299200 chr6B 453276269 453277079 810 False 857.0 857 85.9360 53 877 1 chr6B.!!$F4 824
5 TraesCS6B01G299200 chr6B 537315400 537316214 814 False 850.0 850 85.7650 52 877 1 chr6B.!!$F6 825
6 TraesCS6B01G299200 chr6B 453114552 453115430 878 False 221.5 230 88.1680 286 704 2 chr6B.!!$F7 418
7 TraesCS6B01G299200 chr5B 277632888 277633727 839 False 1445.0 1445 97.7380 2128 2966 1 chr5B.!!$F1 838
8 TraesCS6B01G299200 chr5B 535217250 535218443 1193 False 1393.0 1393 87.8640 884 2074 1 chr5B.!!$F2 1190
9 TraesCS6B01G299200 chr5B 592912236 592913439 1203 True 1349.0 1349 86.9640 883 2086 1 chr5B.!!$R1 1203
10 TraesCS6B01G299200 chr3B 245965683 245966531 848 False 1439.0 1439 97.2940 2119 2966 1 chr3B.!!$F1 847
11 TraesCS6B01G299200 chr5D 371281098 371281937 839 False 1423.0 1423 97.2620 2128 2966 1 chr5D.!!$F2 838
12 TraesCS6B01G299200 chr5D 363182225 363183065 840 False 1402.0 1402 96.7900 2128 2966 1 chr5D.!!$F1 838
13 TraesCS6B01G299200 chr5D 448631118 448632317 1199 False 1325.0 1325 86.7320 881 2086 1 chr5D.!!$F3 1205
14 TraesCS6B01G299200 chr1D 107613295 107614134 839 True 1417.0 1417 97.1430 2128 2966 1 chr1D.!!$R1 838
15 TraesCS6B01G299200 chr6D 72032924 72033753 829 False 1415.0 1415 97.4700 2128 2956 1 chr6D.!!$F1 828
16 TraesCS6B01G299200 chr6D 291793531 291794382 851 False 1002.0 1002 87.8270 3 876 1 chr6D.!!$F2 873
17 TraesCS6B01G299200 chr6D 291782940 291783509 569 False 249.0 276 83.5305 277 822 2 chr6D.!!$F3 545
18 TraesCS6B01G299200 chr6A 610915753 610916591 838 False 1415.0 1415 97.1390 2129 2966 1 chr6A.!!$F1 837
19 TraesCS6B01G299200 chr6A 52180238 52181399 1161 True 1384.0 1384 88.2600 894 2051 1 chr6A.!!$R1 1157
20 TraesCS6B01G299200 chr6A 431490535 431491071 536 True 436.0 436 81.8510 275 822 1 chr6A.!!$R4 547
21 TraesCS6B01G299200 chr3D 559267886 559269054 1168 False 1363.0 1363 87.8190 894 2059 1 chr3D.!!$F1 1165
22 TraesCS6B01G299200 chr7D 80371804 80372892 1088 False 1352.0 1352 89.2560 893 1969 1 chr7D.!!$F2 1076
23 TraesCS6B01G299200 chr7D 18591639 18592637 998 False 1210.0 1210 88.6340 883 1878 1 chr7D.!!$F1 995
24 TraesCS6B01G299200 chr4A 642632706 642633890 1184 True 1175.0 1175 84.6990 901 2086 1 chr4A.!!$R1 1185

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
389 408 0.105224 TCGAAAAGTGGTGCCTCGAA 59.895 50.0 0.0 0.0 35.74 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2888 1.06706 TCTCCGTGCTATCATCAACGG 59.933 52.381 6.75 6.75 41.53 4.44 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
72 74 3.853207 TGTCTACCCTCAGTGTAACCTT 58.147 45.455 0.00 0.0 37.80 3.50
379 398 3.721466 CGTTTCCGGTCGAAAAGTG 57.279 52.632 0.00 0.0 42.11 3.16
380 399 0.233848 CGTTTCCGGTCGAAAAGTGG 59.766 55.000 0.00 0.0 42.11 4.00
381 400 1.302366 GTTTCCGGTCGAAAAGTGGT 58.698 50.000 0.00 0.0 42.11 4.16
382 401 1.003223 GTTTCCGGTCGAAAAGTGGTG 60.003 52.381 0.00 0.0 42.11 4.17
383 402 1.161563 TTCCGGTCGAAAAGTGGTGC 61.162 55.000 0.00 0.0 0.00 5.01
384 403 2.613506 CCGGTCGAAAAGTGGTGCC 61.614 63.158 0.00 0.0 0.00 5.01
385 404 1.597027 CGGTCGAAAAGTGGTGCCT 60.597 57.895 0.00 0.0 0.00 4.75
386 405 1.566018 CGGTCGAAAAGTGGTGCCTC 61.566 60.000 0.00 0.0 0.00 4.70
387 406 1.566018 GGTCGAAAAGTGGTGCCTCG 61.566 60.000 0.00 0.0 0.00 4.63
388 407 0.599204 GTCGAAAAGTGGTGCCTCGA 60.599 55.000 0.00 0.0 36.27 4.04
389 408 0.105224 TCGAAAAGTGGTGCCTCGAA 59.895 50.000 0.00 0.0 35.74 3.71
390 409 0.941542 CGAAAAGTGGTGCCTCGAAA 59.058 50.000 0.00 0.0 0.00 3.46
391 410 1.332375 CGAAAAGTGGTGCCTCGAAAA 59.668 47.619 0.00 0.0 0.00 2.29
528 550 5.228665 AGCGGTTACTAGAAAGTTTGACTC 58.771 41.667 0.00 0.0 37.15 3.36
928 1492 6.655078 ATATTATCAAGCATCAACCAACCC 57.345 37.500 0.00 0.0 0.00 4.11
966 1530 0.175531 GGCCACAACACAAACAAGCT 59.824 50.000 0.00 0.0 0.00 3.74
1134 1709 0.527817 GGAAGGAATGCGACGACGAT 60.528 55.000 12.29 0.0 42.66 3.73
2285 2888 0.238553 GAGAACCCAAAGCTTGACGC 59.761 55.000 0.00 0.0 39.57 5.19
2447 3050 0.958382 TCGCTTTTCCCACCATTCCG 60.958 55.000 0.00 0.0 0.00 4.30
2629 3232 4.585526 CCGCGCCGCTCCAATCTA 62.586 66.667 7.78 0.0 0.00 1.98
2713 3317 4.280819 CCCAAGCCTTCCAGATCATAAAA 58.719 43.478 0.00 0.0 0.00 1.52
2716 3320 5.832060 CCAAGCCTTCCAGATCATAAAATCT 59.168 40.000 0.00 0.0 36.41 2.40
2734 3338 2.176045 TCTATGGGCGAAAGTGTCAGA 58.824 47.619 0.00 0.0 0.00 3.27
2747 3351 4.487714 AGTGTCAGACCAAGAAACTGAA 57.512 40.909 0.00 0.0 41.31 3.02
2758 3362 4.137543 CAAGAAACTGAACCTTGTAGGCT 58.862 43.478 0.00 0.0 39.63 4.58
2915 3519 4.113354 GTTGCGACCGATCTTAAGAATCT 58.887 43.478 9.71 0.0 0.00 2.40
2956 3561 2.038387 ACGCACTTTCCAGTTCTTGT 57.962 45.000 0.00 0.0 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 1.141019 GATGCCGTAGCTTCCACGA 59.859 57.895 9.06 0.00 41.91 4.35
377 396 4.448060 GCTATATACTTTTCGAGGCACCAC 59.552 45.833 0.00 0.00 0.00 4.16
378 397 4.344102 AGCTATATACTTTTCGAGGCACCA 59.656 41.667 0.00 0.00 0.00 4.17
379 398 4.686554 CAGCTATATACTTTTCGAGGCACC 59.313 45.833 0.00 0.00 0.00 5.01
380 399 4.686554 CCAGCTATATACTTTTCGAGGCAC 59.313 45.833 0.00 0.00 0.00 5.01
381 400 4.587262 TCCAGCTATATACTTTTCGAGGCA 59.413 41.667 0.00 0.00 0.00 4.75
382 401 4.924462 GTCCAGCTATATACTTTTCGAGGC 59.076 45.833 0.00 0.00 0.00 4.70
383 402 6.085555 TGTCCAGCTATATACTTTTCGAGG 57.914 41.667 0.00 0.00 0.00 4.63
384 403 7.116948 CCATTGTCCAGCTATATACTTTTCGAG 59.883 40.741 0.00 0.00 0.00 4.04
385 404 6.929049 CCATTGTCCAGCTATATACTTTTCGA 59.071 38.462 0.00 0.00 0.00 3.71
386 405 6.147821 CCCATTGTCCAGCTATATACTTTTCG 59.852 42.308 0.00 0.00 0.00 3.46
387 406 6.998673 ACCCATTGTCCAGCTATATACTTTTC 59.001 38.462 0.00 0.00 0.00 2.29
388 407 6.911308 ACCCATTGTCCAGCTATATACTTTT 58.089 36.000 0.00 0.00 0.00 2.27
389 408 6.515512 ACCCATTGTCCAGCTATATACTTT 57.484 37.500 0.00 0.00 0.00 2.66
390 409 7.016914 TCTACCCATTGTCCAGCTATATACTT 58.983 38.462 0.00 0.00 0.00 2.24
391 410 6.437793 GTCTACCCATTGTCCAGCTATATACT 59.562 42.308 0.00 0.00 0.00 2.12
487 507 4.202284 ACCGCTACTTTTCACCTCTTTGTA 60.202 41.667 0.00 0.00 0.00 2.41
528 550 2.544685 CTACAGCGAAGACCTGGAATG 58.455 52.381 0.00 0.00 34.65 2.67
1362 1940 3.509137 GACGGTGGAGTTGGTGCGA 62.509 63.158 0.00 0.00 0.00 5.10
2285 2888 1.067060 TCTCCGTGCTATCATCAACGG 59.933 52.381 6.75 6.75 41.53 4.44
2595 3198 0.673437 CGGTTGGCAAAACTGTGGAT 59.327 50.000 0.00 0.00 0.00 3.41
2629 3232 1.153168 CCGGATTTGGACAGCCGAT 60.153 57.895 0.00 0.00 46.29 4.18
2713 3317 2.766263 TCTGACACTTTCGCCCATAGAT 59.234 45.455 0.00 0.00 0.00 1.98
2716 3320 1.066430 GGTCTGACACTTTCGCCCATA 60.066 52.381 10.38 0.00 0.00 2.74
2734 3338 4.461198 CCTACAAGGTTCAGTTTCTTGGT 58.539 43.478 0.00 0.00 41.35 3.67
2915 3519 1.143684 GGCCCTCCATGAAGATGCTTA 59.856 52.381 0.00 0.00 0.00 3.09
2943 3548 1.021202 CCACGCACAAGAACTGGAAA 58.979 50.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.