Multiple sequence alignment - TraesCS1A01G220400

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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 TraesCS1A01G220400 chr1A 100.000 4425 0 0 721 5145 389767396 389771820 0.000000e+00 8172.0
1 TraesCS1A01G220400 chr1A 86.049 853 84 19 1494 2329 389798990 389799824 0.000000e+00 883.0
2 TraesCS1A01G220400 chr1A 100.000 476 0 0 1 476 389766676 389767151 0.000000e+00 880.0
3 TraesCS1A01G220400 chr1A 91.297 563 48 1 3113 3674 389801374 389801936 0.000000e+00 767.0
4 TraesCS1A01G220400 chr1A 88.000 500 29 13 869 1337 389798167 389798666 3.480000e-156 562.0
5 TraesCS1A01G220400 chr1A 90.756 357 31 1 3791 4145 389802141 389802497 4.660000e-130 475.0
6 TraesCS1A01G220400 chr1A 80.781 640 71 21 4271 4880 389802712 389803329 2.180000e-123 453.0
7 TraesCS1A01G220400 chr1A 84.356 326 37 4 2737 3059 389800789 389801103 1.800000e-79 307.0
8 TraesCS1A01G220400 chr1A 88.446 251 20 6 4133 4382 389802524 389802766 1.400000e-75 294.0
9 TraesCS1A01G220400 chr1A 90.374 187 13 5 2432 2614 389799899 389800084 1.850000e-59 241.0
10 TraesCS1A01G220400 chr1A 93.827 81 5 0 3703 3783 389802024 389802104 7.000000e-24 122.0
11 TraesCS1A01G220400 chr1A 100.000 33 0 0 4680 4712 521899667 521899635 1.550000e-05 62.1
12 TraesCS1A01G220400 chr1A 97.143 35 1 0 4680 4714 535439267 535439301 5.560000e-05 60.2
13 TraesCS1A01G220400 chr3A 98.804 4430 47 5 721 5145 128720439 128716011 0.000000e+00 7882.0
14 TraesCS1A01G220400 chr3A 84.486 954 88 31 1394 2329 128585664 128584753 0.000000e+00 887.0
15 TraesCS1A01G220400 chr3A 96.646 477 14 2 1 476 128720987 128720512 0.000000e+00 791.0
16 TraesCS1A01G220400 chr3A 91.119 563 49 1 3113 3674 128583204 128582642 0.000000e+00 761.0
17 TraesCS1A01G220400 chr3A 88.713 505 26 13 868 1341 128586711 128586207 5.740000e-164 588.0
18 TraesCS1A01G220400 chr3A 90.000 360 31 2 3791 4145 128582437 128582078 1.310000e-125 460.0
19 TraesCS1A01G220400 chr3A 80.645 651 73 21 4271 4891 128581864 128581237 6.070000e-124 455.0
20 TraesCS1A01G220400 chr3A 84.356 326 37 4 2737 3059 128583788 128583474 1.800000e-79 307.0
21 TraesCS1A01G220400 chr3A 89.024 246 17 6 4139 4382 128582045 128581808 3.900000e-76 296.0
22 TraesCS1A01G220400 chr3A 90.374 187 13 5 2432 2614 128584678 128584493 1.850000e-59 241.0
23 TraesCS1A01G220400 chr3A 93.827 81 5 0 3703 3783 128582554 128582474 7.000000e-24 122.0
24 TraesCS1A01G220400 chr3A 97.222 36 1 0 4679 4714 655588445 655588410 1.550000e-05 62.1
25 TraesCS1A01G220400 chr3A 94.444 36 2 0 4680 4715 181697722 181697687 7.200000e-04 56.5
26 TraesCS1A01G220400 chr3A 94.444 36 2 0 4679 4714 197848162 197848197 7.200000e-04 56.5
27 TraesCS1A01G220400 chr1D 96.484 1792 62 1 835 2625 309852144 309853935 0.000000e+00 2959.0
28 TraesCS1A01G220400 chr1D 96.841 1393 31 6 2624 4010 309853968 309855353 0.000000e+00 2316.0
29 TraesCS1A01G220400 chr1D 86.804 1508 121 44 869 2329 309916800 309918276 0.000000e+00 1611.0
30 TraesCS1A01G220400 chr1D 96.484 711 22 2 4006 4716 309901242 309901949 0.000000e+00 1171.0
31 TraesCS1A01G220400 chr1D 91.935 558 44 1 3113 3669 309919839 309920396 0.000000e+00 780.0
32 TraesCS1A01G220400 chr1D 90.476 357 32 1 3791 4145 309920605 309920961 2.170000e-128 470.0
33 TraesCS1A01G220400 chr1D 79.882 507 61 19 4271 4748 309921175 309921669 2.970000e-87 333.0
34 TraesCS1A01G220400 chr1D 84.098 327 36 4 2737 3059 309919243 309919557 8.370000e-78 302.0
35 TraesCS1A01G220400 chr1D 92.718 206 15 0 4722 4927 309911933 309912138 1.080000e-76 298.0
36 TraesCS1A01G220400 chr1D 88.710 248 13 9 4139 4382 309920995 309921231 6.520000e-74 289.0
37 TraesCS1A01G220400 chr1D 89.167 120 10 3 4770 4887 309921741 309921859 4.150000e-31 147.0
38 TraesCS1A01G220400 chr1D 92.593 81 6 0 3703 3783 309920488 309920568 3.250000e-22 117.0
39 TraesCS1A01G220400 chr1D 92.500 80 6 0 5066 5145 309912136 309912215 1.170000e-21 115.0
40 TraesCS1A01G220400 chr1D 93.478 46 1 2 2622 2667 305586148 305586105 3.320000e-07 67.6
41 TraesCS1A01G220400 chr1D 94.872 39 2 0 2624 2662 393970777 393970739 1.550000e-05 62.1
42 TraesCS1A01G220400 chr1B 95.387 1756 68 10 870 2620 419768964 419770711 0.000000e+00 2782.0
43 TraesCS1A01G220400 chr1B 85.139 1514 113 55 869 2329 419940766 419942220 0.000000e+00 1447.0
44 TraesCS1A01G220400 chr1B 96.291 728 17 2 3703 4420 419772060 419772787 0.000000e+00 1186.0
45 TraesCS1A01G220400 chr1B 94.286 595 31 3 3113 3704 419771400 419771994 0.000000e+00 907.0
46 TraesCS1A01G220400 chr1B 94.208 518 22 5 4410 4927 419780423 419780932 0.000000e+00 784.0
47 TraesCS1A01G220400 chr1B 91.474 563 44 3 3113 3674 419949043 419949602 0.000000e+00 771.0
48 TraesCS1A01G220400 chr1B 89.955 448 35 8 1 441 307134594 307135038 2.080000e-158 569.0
49 TraesCS1A01G220400 chr1B 92.689 383 17 3 2718 3096 419770749 419771124 4.530000e-150 542.0
50 TraesCS1A01G220400 chr1B 91.667 348 29 0 3791 4138 419949808 419950155 2.790000e-132 483.0
51 TraesCS1A01G220400 chr1B 83.742 326 39 4 2737 3059 419948449 419948763 3.900000e-76 296.0
52 TraesCS1A01G220400 chr1B 90.374 187 13 5 2432 2614 419942301 419942486 1.850000e-59 241.0
53 TraesCS1A01G220400 chr1B 87.129 202 9 10 4133 4326 419950191 419950383 4.040000e-51 213.0
54 TraesCS1A01G220400 chr1B 90.385 156 13 2 4913 5068 634163060 634162907 2.430000e-48 204.0
55 TraesCS1A01G220400 chr1B 93.827 81 5 0 3703 3783 419949691 419949771 7.000000e-24 122.0
56 TraesCS1A01G220400 chr5B 91.925 483 32 4 1 476 48875360 48874878 0.000000e+00 669.0
57 TraesCS1A01G220400 chr5B 89.116 147 16 0 4926 5072 531737477 531737331 3.160000e-42 183.0
58 TraesCS1A01G220400 chr5B 100.000 35 0 0 2623 2657 474771483 474771517 1.200000e-06 65.8
59 TraesCS1A01G220400 chr5B 100.000 28 0 0 4687 4714 102078850 102078823 9.000000e-03 52.8
60 TraesCS1A01G220400 chr6B 91.909 482 31 5 1 476 637853038 637853517 0.000000e+00 667.0
61 TraesCS1A01G220400 chr6D 89.669 484 36 11 1 476 53760482 53760959 5.700000e-169 604.0
62 TraesCS1A01G220400 chr6D 81.742 356 47 14 1 346 462179821 462180168 1.090000e-71 281.0
63 TraesCS1A01G220400 chr2A 88.866 485 44 8 1 476 767802519 767803002 5.740000e-164 588.0
64 TraesCS1A01G220400 chr2A 75.000 152 24 9 4471 4608 368129130 368128979 2.000000e-04 58.4
65 TraesCS1A01G220400 chr3D 87.967 482 47 8 1 476 104828178 104827702 4.500000e-155 558.0
66 TraesCS1A01G220400 chr3D 84.127 63 7 3 2624 2684 126973450 126973511 2.000000e-04 58.4
67 TraesCS1A01G220400 chr2D 82.687 335 45 11 22 346 37832961 37832630 8.430000e-73 285.0
68 TraesCS1A01G220400 chr7A 88.435 147 17 0 4924 5070 75200230 75200084 1.470000e-40 178.0
69 TraesCS1A01G220400 chr7A 87.770 139 17 0 4927 5065 492846079 492846217 4.120000e-36 163.0
70 TraesCS1A01G220400 chr5D 100.000 32 0 0 416 447 390419427 390419458 5.560000e-05 60.2
71 TraesCS1A01G220400 chr3B 92.857 42 1 2 2621 2660 796016743 796016702 5.560000e-05 60.2
72 TraesCS1A01G220400 chr6A 90.909 44 2 1 2624 2667 480647995 480648036 2.000000e-04 58.4
73 TraesCS1A01G220400 chr4D 87.500 48 4 2 2624 2670 504343789 504343743 3.000000e-03 54.7


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 TraesCS1A01G220400 chr1A 389766676 389771820 5144 False 4526.000000 8172 100.000000 1 5145 2 chr1A.!!$F2 5144
1 TraesCS1A01G220400 chr1A 389798167 389803329 5162 False 456.000000 883 88.209556 869 4880 9 chr1A.!!$F3 4011
2 TraesCS1A01G220400 chr3A 128716011 128720987 4976 True 4336.500000 7882 97.725000 1 5145 2 chr3A.!!$R4 5144
3 TraesCS1A01G220400 chr3A 128581237 128586711 5474 True 457.444444 887 88.060444 868 4891 9 chr3A.!!$R3 4023
4 TraesCS1A01G220400 chr1D 309852144 309855353 3209 False 2637.500000 2959 96.662500 835 4010 2 chr1D.!!$F2 3175
5 TraesCS1A01G220400 chr1D 309901242 309901949 707 False 1171.000000 1171 96.484000 4006 4716 1 chr1D.!!$F1 710
6 TraesCS1A01G220400 chr1D 309916800 309921859 5059 False 506.125000 1611 87.958125 869 4887 8 chr1D.!!$F4 4018
7 TraesCS1A01G220400 chr1B 419768964 419772787 3823 False 1354.250000 2782 94.663250 870 4420 4 chr1B.!!$F3 3550
8 TraesCS1A01G220400 chr1B 419940766 419942486 1720 False 844.000000 1447 87.756500 869 2614 2 chr1B.!!$F4 1745
9 TraesCS1A01G220400 chr1B 419780423 419780932 509 False 784.000000 784 94.208000 4410 4927 1 chr1B.!!$F2 517
10 TraesCS1A01G220400 chr1B 419948449 419950383 1934 False 377.000000 771 89.567800 2737 4326 5 chr1B.!!$F5 1589

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
337 339 0.254395 AGGGGAGGAGTAGAGAGGGT 60.254 60.000 0.0 0.00 0.00 4.34 F
1658 2240 2.165641 CTGACGTGTTACCATAGAGGCA 59.834 50.000 0.0 0.00 43.14 4.75 F
3184 4750 4.630069 AGTCCGCACAGTTTTCATATGTAC 59.370 41.667 1.9 0.41 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2573 1.422531 AAATTTCTGGCTGGCAACCA 58.577 45.0 9.65 9.65 35.4 3.67 R
3349 4915 0.244450 ATGCAATGCCACCTTCAACG 59.756 50.0 1.53 0.00 0.0 4.10 R
4856 6717 1.062364 ATCACCCATCTCCGCATCAT 58.938 50.0 0.00 0.00 0.0 2.45 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
104 105 7.004555 ACTAGTGAGTGGTTCATATTCAACA 57.995 36.000 0.00 0.00 38.29 3.33
217 219 4.583426 CAAATAATGCGTCGAATCGGAAA 58.417 39.130 1.76 0.00 34.56 3.13
248 250 7.625828 AACTAAAAGTAATTGAAGGGATCGG 57.374 36.000 0.00 0.00 0.00 4.18
258 260 2.252714 GAAGGGATCGGAGGAGCTTAT 58.747 52.381 0.00 0.00 0.00 1.73
273 275 5.416013 AGGAGCTTATTTTTCTTTCTTCGGG 59.584 40.000 0.00 0.00 0.00 5.14
281 283 0.991920 TCTTTCTTCGGGGCCATCTT 59.008 50.000 4.39 0.00 0.00 2.40
307 309 1.262151 GCAAAAGCGGTGTAGAAACGA 59.738 47.619 0.00 0.00 0.00 3.85
322 324 2.717639 AACGATGAAGATCCAAGGGG 57.282 50.000 0.00 0.00 0.00 4.79
337 339 0.254395 AGGGGAGGAGTAGAGAGGGT 60.254 60.000 0.00 0.00 0.00 4.34
366 368 3.181454 GGAACTTCCTCTGTTCTTGGTGA 60.181 47.826 0.00 0.00 42.27 4.02
468 470 2.686119 TCCCCAGCTGTAGGGTTATAC 58.314 52.381 22.99 0.00 45.28 1.47
806 811 5.770162 AGGGTCAAATCTCAATTTTCTTCGT 59.230 36.000 0.00 0.00 32.69 3.85
807 812 6.940298 AGGGTCAAATCTCAATTTTCTTCGTA 59.060 34.615 0.00 0.00 32.69 3.43
1453 2016 5.122239 CCTAGACTGATCGCACATTCAAAAA 59.878 40.000 0.00 0.00 0.00 1.94
1561 2142 2.297033 GGATTGTGTTGCTGTGGTTCAT 59.703 45.455 0.00 0.00 0.00 2.57
1658 2240 2.165641 CTGACGTGTTACCATAGAGGCA 59.834 50.000 0.00 0.00 43.14 4.75
1925 2516 9.579610 CTTTGGAAATTTTAATTGCAAACTACG 57.420 29.630 1.71 0.00 41.27 3.51
2021 2614 6.756299 TTTGTGTTACCTCCTTTTTACGTT 57.244 33.333 0.00 0.00 0.00 3.99
2492 3125 7.652524 TTTCATATTGCAAGCCTTTATGGTA 57.347 32.000 14.12 4.02 38.35 3.25
3062 4355 6.418819 CCCGAAAGCTTAAATGAATAGCATTG 59.581 38.462 0.00 0.00 46.25 2.82
3184 4750 4.630069 AGTCCGCACAGTTTTCATATGTAC 59.370 41.667 1.90 0.41 0.00 2.90
3349 4915 1.211969 CACTTGCCATGCTGTCTGC 59.788 57.895 0.00 0.00 43.25 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 8.824756 TTAGATGTTCTCTAATCACTAGTGGT 57.175 34.615 22.48 13.58 40.72 4.16
162 163 8.348285 TCACCCCTATTTTTGAACTAAGATTG 57.652 34.615 0.00 0.00 0.00 2.67
163 164 9.547279 AATCACCCCTATTTTTGAACTAAGATT 57.453 29.630 0.00 0.00 0.00 2.40
248 250 6.403746 CCCGAAGAAAGAAAAATAAGCTCCTC 60.404 42.308 0.00 0.00 0.00 3.71
258 260 2.074729 TGGCCCCGAAGAAAGAAAAA 57.925 45.000 0.00 0.00 0.00 1.94
273 275 0.817013 TTTTGCGGATCAAGATGGCC 59.183 50.000 0.00 0.00 35.84 5.36
307 309 2.294127 ACTCCTCCCCTTGGATCTTCAT 60.294 50.000 0.00 0.00 40.80 2.57
322 324 2.775384 TCTCTCACCCTCTCTACTCCTC 59.225 54.545 0.00 0.00 0.00 3.71
366 368 1.221781 CCATTCCCCTCTCCTCCTAGT 59.778 57.143 0.00 0.00 0.00 2.57
777 782 8.712228 AGAAAATTGAGATTTGACCCTAGTTT 57.288 30.769 0.00 0.00 35.69 2.66
783 788 6.013842 ACGAAGAAAATTGAGATTTGACCC 57.986 37.500 0.00 0.00 35.69 4.46
807 812 9.949174 GGCAAAATTTCATGTTTTGACTATTTT 57.051 25.926 18.93 7.26 46.24 1.82
1453 2016 9.363763 CTATCAGCATATCAAAACTATCACGAT 57.636 33.333 0.00 0.00 0.00 3.73
1561 2142 2.027192 GTGATAGCCACAAACCCTGAGA 60.027 50.000 0.00 0.00 45.03 3.27
1980 2573 1.422531 AAATTTCTGGCTGGCAACCA 58.577 45.000 9.65 9.65 35.40 3.67
2021 2614 7.040340 TGTTTGAAAACTGTCTCAACTGGTAAA 60.040 33.333 7.39 0.00 39.59 2.01
2365 2996 2.510613 GAAAATGACGACCCAGGGAAA 58.489 47.619 14.54 0.00 0.00 3.13
2903 4196 7.122138 AGACATCTCTAGATTGAAAGCATCA 57.878 36.000 9.22 0.00 35.85 3.07
3034 4327 5.971792 GCTATTCATTTAAGCTTTCGGGTTC 59.028 40.000 3.20 0.00 36.91 3.62
3062 4355 3.553922 CCATTAGCTACAGCCTACAGAGC 60.554 52.174 0.00 0.00 43.38 4.09
3184 4750 8.394877 CAGAAGTATCTCGGAATATAGCAGTAG 58.605 40.741 0.00 0.00 32.03 2.57
3349 4915 0.244450 ATGCAATGCCACCTTCAACG 59.756 50.000 1.53 0.00 0.00 4.10
4856 6717 1.062364 ATCACCCATCTCCGCATCAT 58.938 50.000 0.00 0.00 0.00 2.45
5002 6864 1.701031 TTGTGGAGCCAGGAAACCGA 61.701 55.000 0.00 0.00 0.00 4.69
5098 6960 1.448540 CAAGCCGCCACCTCTACTG 60.449 63.158 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.