Multiple sequence alignment - TraesCS6D01G330600

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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 TraesCS6D01G330600 chr6D 100.000 3466 0 0 1 3466 433769555 433766090 0.000000e+00 6401.0
1 TraesCS6D01G330600 chr6D 100.000 1423 0 0 3901 5323 433765655 433764233 0.000000e+00 2628.0
2 TraesCS6D01G330600 chr6D 93.031 287 18 2 4337 4622 433706746 433707031 8.250000e-113 418.0
3 TraesCS6D01G330600 chr6D 95.385 130 6 0 3307 3436 433766219 433766090 1.940000e-49 207.0
4 TraesCS6D01G330600 chr6D 95.385 130 6 0 3337 3466 433766249 433766120 1.940000e-49 207.0
5 TraesCS6D01G330600 chr6D 98.701 77 1 0 3901 3977 433765625 433765549 2.590000e-28 137.0
6 TraesCS6D01G330600 chr6D 98.701 77 1 0 3931 4007 433765655 433765579 2.590000e-28 137.0
7 TraesCS6D01G330600 chr6D 97.872 47 1 0 3901 3947 433765595 433765549 1.230000e-11 82.4
8 TraesCS6D01G330600 chr6D 97.872 47 1 0 3961 4007 433765655 433765609 1.230000e-11 82.4
9 TraesCS6D01G330600 chr6A 96.746 3473 89 17 1 3466 579956650 579953195 0.000000e+00 5766.0
10 TraesCS6D01G330600 chr6A 95.012 842 26 9 3903 4741 579952773 579951945 0.000000e+00 1308.0
11 TraesCS6D01G330600 chr6A 97.260 146 4 0 3307 3452 579953324 579953179 1.140000e-61 248.0
12 TraesCS6D01G330600 chr6A 95.763 118 5 0 3307 3424 579953294 579953177 1.960000e-44 191.0
13 TraesCS6D01G330600 chr6A 98.701 77 1 0 3901 3977 579952745 579952669 2.590000e-28 137.0
14 TraesCS6D01G330600 chr6A 96.386 83 3 0 3925 4007 579952781 579952699 2.590000e-28 137.0
15 TraesCS6D01G330600 chr6A 97.872 47 1 0 3901 3947 579952715 579952669 1.230000e-11 82.4
16 TraesCS6D01G330600 chr6A 94.340 53 3 0 3955 4007 579952781 579952729 1.230000e-11 82.4
17 TraesCS6D01G330600 chr6B 94.711 2666 99 17 830 3466 656033730 656031078 0.000000e+00 4104.0
18 TraesCS6D01G330600 chr6B 93.842 812 37 8 3904 4714 656030582 656029783 0.000000e+00 1210.0
19 TraesCS6D01G330600 chr6B 92.691 602 34 8 233 828 656034365 656033768 0.000000e+00 859.0
20 TraesCS6D01G330600 chr6B 93.852 244 15 0 3223 3466 656030756 656030513 8.420000e-98 368.0
21 TraesCS6D01G330600 chr6B 89.655 232 22 2 2641 2871 455134362 455134592 1.450000e-75 294.0
22 TraesCS6D01G330600 chr6B 93.478 138 9 0 3307 3444 656031207 656031070 6.990000e-49 206.0
23 TraesCS6D01G330600 chr6B 91.538 130 11 0 3337 3466 656031237 656031108 4.240000e-41 180.0
24 TraesCS6D01G330600 chr6B 91.429 105 9 0 3903 4007 656030613 656030509 1.550000e-30 145.0
25 TraesCS6D01G330600 chr6B 96.104 77 3 0 3901 3977 656030555 656030479 5.600000e-25 126.0
26 TraesCS6D01G330600 chr6B 93.617 47 3 0 3901 3947 656030525 656030479 2.660000e-08 71.3
27 TraesCS6D01G330600 chr1B 84.711 1210 124 32 7 1171 551720378 551721571 0.000000e+00 1153.0
28 TraesCS6D01G330600 chr1B 95.369 583 26 1 4741 5323 437868818 437868237 0.000000e+00 926.0
29 TraesCS6D01G330600 chr1B 84.895 907 103 17 30 907 622188490 622187589 0.000000e+00 885.0
30 TraesCS6D01G330600 chr1B 89.301 458 39 8 760 1212 167998580 167998128 2.780000e-157 566.0
31 TraesCS6D01G330600 chr4D 97.945 584 12 0 4740 5323 488129231 488129814 0.000000e+00 1013.0
32 TraesCS6D01G330600 chr3D 97.423 582 14 1 4742 5323 33191035 33191615 0.000000e+00 990.0
33 TraesCS6D01G330600 chr3D 87.449 247 30 1 2627 2872 225524814 225525060 3.140000e-72 283.0
34 TraesCS6D01G330600 chr5B 86.061 947 99 18 263 1186 692786556 692785620 0.000000e+00 987.0
35 TraesCS6D01G330600 chr5B 83.731 922 105 35 8 907 472746178 472745280 0.000000e+00 830.0
36 TraesCS6D01G330600 chr5B 90.428 397 30 6 8 400 644226435 644226043 2.840000e-142 516.0
37 TraesCS6D01G330600 chr5B 92.287 363 21 4 40 400 513827401 513827758 4.760000e-140 508.0
38 TraesCS6D01G330600 chr7B 95.712 583 24 1 4741 5322 710096528 710097110 0.000000e+00 937.0
39 TraesCS6D01G330600 chr3A 95.712 583 24 1 4742 5323 54983395 54983977 0.000000e+00 937.0
40 TraesCS6D01G330600 chr3A 95.400 587 25 2 4737 5322 114690595 114691180 0.000000e+00 933.0
41 TraesCS6D01G330600 chr7A 95.540 583 25 1 4741 5322 688481162 688480580 0.000000e+00 931.0
42 TraesCS6D01G330600 chr7A 95.385 585 25 2 4740 5322 162947910 162948494 0.000000e+00 929.0
43 TraesCS6D01G330600 chr2A 95.377 584 26 1 4740 5322 670240831 670241414 0.000000e+00 928.0
44 TraesCS6D01G330600 chr2A 89.286 252 18 4 2628 2874 73540767 73541014 1.860000e-79 307.0
45 TraesCS6D01G330600 chr1D 85.444 900 90 21 40 907 452340674 452341564 0.000000e+00 898.0
46 TraesCS6D01G330600 chr1D 88.519 540 40 9 678 1197 110519783 110519246 7.520000e-178 634.0
47 TraesCS6D01G330600 chr1D 87.755 245 27 3 2629 2871 291080819 291080576 3.140000e-72 283.0
48 TraesCS6D01G330600 chr1A 84.684 901 98 16 44 907 547253559 547254456 0.000000e+00 863.0
49 TraesCS6D01G330600 chr1A 84.603 643 80 12 44 672 547241453 547242090 5.860000e-174 621.0
50 TraesCS6D01G330600 chr1A 89.610 462 38 6 760 1212 115368207 115367747 3.570000e-161 579.0
51 TraesCS6D01G330600 chr7D 83.194 958 107 18 281 1213 79530038 79530966 0.000000e+00 828.0
52 TraesCS6D01G330600 chr7D 87.500 248 29 2 2625 2871 486463530 486463776 8.730000e-73 285.0
53 TraesCS6D01G330600 chr5D 87.246 690 64 11 544 1212 486900300 486899614 0.000000e+00 765.0
54 TraesCS6D01G330600 chr5D 85.479 303 26 9 924 1212 548629541 548629243 3.120000e-77 300.0
55 TraesCS6D01G330600 chrUn 100.000 388 0 0 1593 1980 480311289 480311676 0.000000e+00 717.0
56 TraesCS6D01G330600 chr4B 90.130 385 32 5 18 400 227918580 227918200 3.700000e-136 496.0
57 TraesCS6D01G330600 chr4B 89.367 395 27 11 8 399 126880595 126880213 2.880000e-132 483.0
58 TraesCS6D01G330600 chr3B 89.113 248 24 3 2629 2874 114096107 114096353 6.700000e-79 305.0
59 TraesCS6D01G330600 chr2D 89.451 237 24 1 2636 2871 27826574 27826810 1.120000e-76 298.0


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 TraesCS6D01G330600 chr6D 433764233 433769555 5322 True 1235.225 6401 97.989500 1 5323 8 chr6D.!!$R1 5322
1 TraesCS6D01G330600 chr6A 579951945 579956650 4705 True 993.975 5766 96.510000 1 4741 8 chr6A.!!$R1 4740
2 TraesCS6D01G330600 chr6B 656029783 656034365 4582 True 807.700 4104 93.473556 233 4714 9 chr6B.!!$R1 4481
3 TraesCS6D01G330600 chr1B 551720378 551721571 1193 False 1153.000 1153 84.711000 7 1171 1 chr1B.!!$F1 1164
4 TraesCS6D01G330600 chr1B 437868237 437868818 581 True 926.000 926 95.369000 4741 5323 1 chr1B.!!$R2 582
5 TraesCS6D01G330600 chr1B 622187589 622188490 901 True 885.000 885 84.895000 30 907 1 chr1B.!!$R3 877
6 TraesCS6D01G330600 chr4D 488129231 488129814 583 False 1013.000 1013 97.945000 4740 5323 1 chr4D.!!$F1 583
7 TraesCS6D01G330600 chr3D 33191035 33191615 580 False 990.000 990 97.423000 4742 5323 1 chr3D.!!$F1 581
8 TraesCS6D01G330600 chr5B 692785620 692786556 936 True 987.000 987 86.061000 263 1186 1 chr5B.!!$R3 923
9 TraesCS6D01G330600 chr5B 472745280 472746178 898 True 830.000 830 83.731000 8 907 1 chr5B.!!$R1 899
10 TraesCS6D01G330600 chr7B 710096528 710097110 582 False 937.000 937 95.712000 4741 5322 1 chr7B.!!$F1 581
11 TraesCS6D01G330600 chr3A 54983395 54983977 582 False 937.000 937 95.712000 4742 5323 1 chr3A.!!$F1 581
12 TraesCS6D01G330600 chr3A 114690595 114691180 585 False 933.000 933 95.400000 4737 5322 1 chr3A.!!$F2 585
13 TraesCS6D01G330600 chr7A 688480580 688481162 582 True 931.000 931 95.540000 4741 5322 1 chr7A.!!$R1 581
14 TraesCS6D01G330600 chr7A 162947910 162948494 584 False 929.000 929 95.385000 4740 5322 1 chr7A.!!$F1 582
15 TraesCS6D01G330600 chr2A 670240831 670241414 583 False 928.000 928 95.377000 4740 5322 1 chr2A.!!$F2 582
16 TraesCS6D01G330600 chr1D 452340674 452341564 890 False 898.000 898 85.444000 40 907 1 chr1D.!!$F1 867
17 TraesCS6D01G330600 chr1D 110519246 110519783 537 True 634.000 634 88.519000 678 1197 1 chr1D.!!$R1 519
18 TraesCS6D01G330600 chr1A 547253559 547254456 897 False 863.000 863 84.684000 44 907 1 chr1A.!!$F2 863
19 TraesCS6D01G330600 chr1A 547241453 547242090 637 False 621.000 621 84.603000 44 672 1 chr1A.!!$F1 628
20 TraesCS6D01G330600 chr7D 79530038 79530966 928 False 828.000 828 83.194000 281 1213 1 chr7D.!!$F1 932
21 TraesCS6D01G330600 chr5D 486899614 486900300 686 True 765.000 765 87.246000 544 1212 1 chr5D.!!$R1 668

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
579 646 1.265095 AGCAGTGAAACGTGCAATGAG 59.735 47.619 19.19 0.0 45.86 2.90 F
754 834 2.146342 GTTGGCATGATAGATGTCCCG 58.854 52.381 0.00 0.0 0.00 5.14 F
1591 1775 1.670087 CCTAGATGGACTAATGCGCCG 60.670 57.143 4.18 0.0 38.35 6.46 F
2981 3166 5.239306 TGCAAATTTCAGGACACTAGAACAG 59.761 40.000 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1775 1.028868 GGCTCCAGAGAATGCACCAC 61.029 60.000 0.00 0.0 0.00 4.16 R
2635 2819 3.617284 ACGCCTTACTTTTAGGAATGGG 58.383 45.455 0.00 0.0 34.56 4.00 R
3305 3492 3.282021 GGAAGTTCCTTGCTGATATGCA 58.718 45.455 15.09 0.0 41.65 3.96 R
4622 5255 0.881796 GCCAAGGGAAGTTAGTGCAC 59.118 55.000 9.40 9.4 0.00 4.57 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
372 426 7.229306 TGGGCACTTGATGTAGATTTGATATTC 59.771 37.037 0.00 0.00 0.00 1.75
376 430 9.212641 CACTTGATGTAGATTTGATATTCGGAT 57.787 33.333 0.00 0.00 0.00 4.18
377 431 9.212641 ACTTGATGTAGATTTGATATTCGGATG 57.787 33.333 0.00 0.00 0.00 3.51
419 473 3.941573 TGATGAGTACTTGCTGCATGAA 58.058 40.909 20.66 0.00 0.00 2.57
422 477 4.952262 TGAGTACTTGCTGCATGAATTC 57.048 40.909 20.66 13.88 0.00 2.17
485 549 6.449635 TTGATAGGTGTTTGTGATAATGCC 57.550 37.500 0.00 0.00 0.00 4.40
570 637 6.141685 GGTTTAAACATGTTAGCAGTGAAACG 59.858 38.462 19.57 0.00 45.86 3.60
579 646 1.265095 AGCAGTGAAACGTGCAATGAG 59.735 47.619 19.19 0.00 45.86 2.90
706 778 5.104859 TGTCTTGGTTATACTGGCCGAAATA 60.105 40.000 0.00 0.00 0.00 1.40
754 834 2.146342 GTTGGCATGATAGATGTCCCG 58.854 52.381 0.00 0.00 0.00 5.14
796 876 7.731235 TGGGAATATAGTGGTACTGTTATGCTA 59.269 37.037 0.00 0.00 0.00 3.49
1591 1775 1.670087 CCTAGATGGACTAATGCGCCG 60.670 57.143 4.18 0.00 38.35 6.46
2635 2819 5.379187 TGGTGAACTTACTTTTTACTCCCC 58.621 41.667 0.00 0.00 0.00 4.81
2855 3040 6.183360 ACGAAACGAAATACGCCTTATTCATT 60.183 34.615 0.00 0.00 46.94 2.57
2887 3072 7.456269 AGAGGGAGTAATAGCTTATGTGCTTAT 59.544 37.037 0.00 0.00 43.74 1.73
2981 3166 5.239306 TGCAAATTTCAGGACACTAGAACAG 59.761 40.000 0.00 0.00 0.00 3.16
3000 3185 8.870075 AGAACAGGAAGCTTATGAATAGTTTT 57.130 30.769 16.01 0.77 0.00 2.43
3022 3207 9.678941 GTTTTATTAAACAGCTCTAAACTTGCT 57.321 29.630 2.54 0.00 42.56 3.91
3305 3492 2.330216 GCATATACCAGTCACCCCTCT 58.670 52.381 0.00 0.00 0.00 3.69
4420 5052 6.710278 TCCTTCATGTACATTCATTCACTCA 58.290 36.000 5.37 0.00 0.00 3.41
4505 5138 9.768662 AATTGATTTGTATCTCTTGTTTTGCTT 57.231 25.926 0.00 0.00 0.00 3.91
4622 5255 4.679372 GCTGAGACTTCTTACCCTAGCTTG 60.679 50.000 0.00 0.00 0.00 4.01
4666 5304 7.414984 GCACCAGAAGAATAATTTCTCTCTTGG 60.415 40.741 12.73 12.73 41.42 3.61
4732 5370 2.556287 GCCGAGCAAAACAGTCCG 59.444 61.111 0.00 0.00 0.00 4.79
4807 5447 5.702065 ATTAGGAGAGGGAAAAGGTCTTC 57.298 43.478 0.00 0.00 0.00 2.87
5068 5708 1.990060 CGTGGATCCTCTGGGTGGT 60.990 63.158 14.23 0.00 0.00 4.16
5173 5813 1.214305 ACCAAGCCCCATAGCCTCAA 61.214 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 132 2.064581 GCTGGGATCCTGTACCGGT 61.065 63.158 13.98 13.98 39.70 5.28
348 400 7.293745 CGAATATCAAATCTACATCAAGTGCC 58.706 38.462 0.00 0.00 0.00 5.01
392 446 4.821260 TGCAGCAAGTACTCATCAAGAAAA 59.179 37.500 0.00 0.00 0.00 2.29
419 473 0.610174 TTGAGCGTGCTCTGGAGAAT 59.390 50.000 21.36 0.00 43.12 2.40
422 477 0.320247 AACTTGAGCGTGCTCTGGAG 60.320 55.000 21.36 17.36 43.12 3.86
485 549 7.872483 ACAATTTGTAAACATTTGCCCTTAGAG 59.128 33.333 0.00 0.00 0.00 2.43
570 637 3.865164 TCATACATCGTCACTCATTGCAC 59.135 43.478 0.00 0.00 0.00 4.57
579 646 6.100004 TCTTTTCCTTCTCATACATCGTCAC 58.900 40.000 0.00 0.00 0.00 3.67
681 750 2.167693 TCGGCCAGTATAACCAAGACAG 59.832 50.000 2.24 0.00 0.00 3.51
796 876 8.691661 AGGTCTGACTGTTAAAATAACAACAT 57.308 30.769 7.85 0.00 34.34 2.71
896 1040 6.008331 AGTTGTGCATCTATCATGGCATAAT 58.992 36.000 0.00 0.00 39.08 1.28
1199 1373 1.234821 CTCAAGGCTAAAACGCACCA 58.765 50.000 0.00 0.00 0.00 4.17
1591 1775 1.028868 GGCTCCAGAGAATGCACCAC 61.029 60.000 0.00 0.00 0.00 4.16
2446 2630 6.475076 CAGAAATGACAAATTTGGTGAAACGA 59.525 34.615 21.74 0.00 38.12 3.85
2635 2819 3.617284 ACGCCTTACTTTTAGGAATGGG 58.383 45.455 0.00 0.00 34.56 4.00
2855 3040 3.995636 AGCTATTACTCCCTCTGTTCCA 58.004 45.455 0.00 0.00 0.00 3.53
3000 3185 8.848474 AGAAGCAAGTTTAGAGCTGTTTAATA 57.152 30.769 0.00 0.00 38.86 0.98
3305 3492 3.282021 GGAAGTTCCTTGCTGATATGCA 58.718 45.455 15.09 0.00 41.65 3.96
3900 4532 1.521580 GCTCCTTGCTGATATGCTCC 58.478 55.000 0.00 0.00 38.95 4.70
3901 4533 1.521580 GGCTCCTTGCTGATATGCTC 58.478 55.000 0.00 0.00 42.39 4.26
4420 5052 3.417069 TGGTGTGCATAAAGCTACAGT 57.583 42.857 0.00 0.00 45.94 3.55
4461 5094 8.503458 AATCAATTCAAGACTCAGACCATAAG 57.497 34.615 0.00 0.00 0.00 1.73
4505 5138 2.618241 GCGCCTATCAATTCAACCATCA 59.382 45.455 0.00 0.00 0.00 3.07
4590 5223 1.287730 GAAGTCTCAGCACCACAGCG 61.288 60.000 0.00 0.00 40.15 5.18
4622 5255 0.881796 GCCAAGGGAAGTTAGTGCAC 59.118 55.000 9.40 9.40 0.00 4.57
4692 5330 4.260375 CCTCACAGAAAACTGAAACGAGTG 60.260 45.833 0.00 0.00 0.00 3.51
4807 5447 6.693315 TTTTCTTGTCCTCTGTAACTTTGG 57.307 37.500 0.00 0.00 0.00 3.28
5068 5708 0.034756 CTGGTGGTTCGACATGGTCA 59.965 55.000 0.00 0.00 32.09 4.02
5173 5813 3.818121 TTTGGCTGCCGCTACACGT 62.818 57.895 14.98 0.00 41.42 4.49


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

AutoCloner maintained by Alex Coulton.