Multiple sequence alignment - TraesCS6A01G332700

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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 TraesCS6A01G332700 chr6A 100.000 8193 0 0 1 8193 564268930 564260738 0.000000e+00 15130.0
1 TraesCS6A01G332700 chr6A 96.400 250 6 1 5240 5489 586578721 586578475 7.650000e-110 409.0
2 TraesCS6A01G332700 chr4A 98.955 4881 41 5 195 5066 668259975 668264854 0.000000e+00 8722.0
3 TraesCS6A01G332700 chr4A 98.832 4880 48 4 195 5066 668212913 668217791 0.000000e+00 8687.0
4 TraesCS6A01G332700 chr4A 98.832 4880 48 4 195 5066 668220699 668225577 0.000000e+00 8687.0
5 TraesCS6A01G332700 chr4A 98.811 4880 47 6 195 5066 668186127 668191003 0.000000e+00 8680.0
6 TraesCS6A01G332700 chr4A 98.709 4880 54 4 195 5066 668228581 668233459 0.000000e+00 8654.0
7 TraesCS6A01G332700 chr4A 98.668 4879 56 4 195 5066 668178246 668183122 0.000000e+00 8641.0
8 TraesCS6A01G332700 chr7B 98.423 4884 69 3 190 5066 537538710 537543592 0.000000e+00 8586.0
9 TraesCS6A01G332700 chr7B 91.525 413 28 6 7046 7454 692302595 692302186 5.550000e-156 562.0
10 TraesCS6A01G332700 chr7B 90.617 405 29 8 7045 7445 730403674 730403275 5.630000e-146 529.0
11 TraesCS6A01G332700 chr7B 96.691 272 7 2 6772 7041 692303197 692302926 1.250000e-122 451.0
12 TraesCS6A01G332700 chr7B 94.891 274 7 3 6775 7041 730404285 730404012 9.830000e-114 422.0
13 TraesCS6A01G332700 chr7B 86.316 285 29 6 7706 7980 181408295 181408011 1.340000e-77 302.0
14 TraesCS6A01G332700 chr7A 98.302 4887 74 4 189 5067 443976732 443971847 0.000000e+00 8556.0
15 TraesCS6A01G332700 chr7A 96.414 251 6 1 5240 5490 9210695 9210448 2.130000e-110 411.0
16 TraesCS6A01G332700 chr7A 96.414 251 6 2 5240 5490 463707622 463707869 2.130000e-110 411.0
17 TraesCS6A01G332700 chr3A 98.014 4884 88 4 191 5066 679657206 679652324 0.000000e+00 8473.0
18 TraesCS6A01G332700 chr3A 96.414 251 7 2 5240 5490 394385369 394385121 5.920000e-111 412.0
19 TraesCS6A01G332700 chr3A 96.063 254 7 1 5240 5493 58275059 58274809 2.130000e-110 411.0
20 TraesCS6A01G332700 chr3A 85.911 291 26 10 7703 7980 712651150 712650862 6.220000e-76 296.0
21 TraesCS6A01G332700 chr3A 83.432 169 21 6 7516 7680 41061824 41061989 5.120000e-32 150.0
22 TraesCS6A01G332700 chr5D 91.761 886 55 7 5487 6355 355431111 355431995 0.000000e+00 1216.0
23 TraesCS6A01G332700 chr5D 92.840 405 20 3 6638 7041 355432497 355432893 5.510000e-161 579.0
24 TraesCS6A01G332700 chr5D 90.032 311 20 5 7140 7450 355454762 355455061 7.710000e-105 392.0
25 TraesCS6A01G332700 chr5D 88.070 285 24 8 7706 7980 485395261 485394977 6.130000e-86 329.0
26 TraesCS6A01G332700 chr5D 93.780 209 12 1 6350 6558 355432091 355432298 6.170000e-81 313.0
27 TraesCS6A01G332700 chr5D 90.588 170 13 2 5067 5234 355430932 355431100 1.070000e-53 222.0
28 TraesCS6A01G332700 chr2B 95.058 688 20 6 6357 7041 34145354 34146030 0.000000e+00 1070.0
29 TraesCS6A01G332700 chr2B 88.204 763 54 11 5486 6216 34144431 34145189 0.000000e+00 878.0
30 TraesCS6A01G332700 chr2B 91.045 402 30 4 7047 7445 572755952 572756350 9.360000e-149 538.0
31 TraesCS6A01G332700 chr2B 97.004 267 4 1 6775 7041 572755350 572755612 5.830000e-121 446.0
32 TraesCS6A01G332700 chr2B 86.572 283 27 7 7706 7977 43228726 43229008 1.340000e-77 302.0
33 TraesCS6A01G332700 chr2B 93.878 147 6 1 6209 6355 34145152 34145295 1.380000e-52 219.0
34 TraesCS6A01G332700 chr2B 85.915 213 20 9 7462 7668 631168640 631168432 1.380000e-52 219.0
35 TraesCS6A01G332700 chr2B 86.935 199 19 7 7474 7669 157991885 157991691 4.980000e-52 217.0
36 TraesCS6A01G332700 chr2B 93.431 137 7 1 53 189 34144119 34144253 1.390000e-47 202.0
37 TraesCS6A01G332700 chr2B 79.667 300 39 14 5666 5945 550972093 550972390 6.490000e-46 196.0
38 TraesCS6A01G332700 chr2B 85.938 64 9 0 7065 7128 788531779 788531716 1.480000e-07 69.4
39 TraesCS6A01G332700 chr3B 89.049 694 49 15 5666 6355 119346112 119345442 0.000000e+00 835.0
40 TraesCS6A01G332700 chr3B 91.646 407 27 5 7042 7445 815965604 815966006 2.580000e-154 556.0
41 TraesCS6A01G332700 chr3B 93.143 350 21 3 6357 6703 119345343 119344994 2.040000e-140 510.0
42 TraesCS6A01G332700 chr3B 93.860 342 12 5 6701 7041 119334663 119334330 2.640000e-139 507.0
43 TraesCS6A01G332700 chr3B 89.894 376 30 8 7045 7417 119310236 119309866 2.070000e-130 477.0
44 TraesCS6A01G332700 chr3B 98.507 268 3 1 6775 7041 815965002 815965269 9.630000e-129 472.0
45 TraesCS6A01G332700 chr3B 86.316 285 25 8 7706 7977 544545846 544546129 1.730000e-76 298.0
46 TraesCS6A01G332700 chr3B 96.951 164 5 0 5487 5650 119354942 119354779 8.100000e-70 276.0
47 TraesCS6A01G332700 chr3B 81.159 276 32 13 5689 5945 496171026 496171300 3.880000e-48 204.0
48 TraesCS6A01G332700 chr3B 92.754 138 8 1 53 190 119355246 119355111 1.800000e-46 198.0
49 TraesCS6A01G332700 chr3B 80.797 276 32 15 5689 5945 496228251 496228524 6.490000e-46 196.0
50 TraesCS6A01G332700 chr3B 94.340 53 2 1 1 52 119355272 119355220 6.820000e-11 80.5
51 TraesCS6A01G332700 chr5B 90.594 404 32 4 7045 7445 584888110 584887710 1.570000e-146 531.0
52 TraesCS6A01G332700 chr5B 97.761 268 5 1 6775 7041 584888714 584888447 2.080000e-125 460.0
53 TraesCS6A01G332700 chr5B 87.189 281 23 10 7706 7975 340615701 340615423 2.870000e-79 307.0
54 TraesCS6A01G332700 chr5B 86.500 200 24 3 7470 7668 507982937 507983134 4.980000e-52 217.0
55 TraesCS6A01G332700 chr5B 85.354 198 24 5 7474 7669 80196079 80195885 5.010000e-47 200.0
56 TraesCS6A01G332700 chr5B 85.354 198 24 5 7474 7669 80600560 80600366 5.010000e-47 200.0
57 TraesCS6A01G332700 chr5A 96.400 250 6 1 5240 5489 137286203 137286449 7.650000e-110 409.0
58 TraesCS6A01G332700 chr5A 96.016 251 7 1 5240 5490 210736053 210736300 9.900000e-109 405.0
59 TraesCS6A01G332700 chr2A 96.032 252 7 1 5239 5490 81244437 81244189 2.750000e-109 407.0
60 TraesCS6A01G332700 chrUn 95.669 254 8 1 5240 5493 1525676 1525426 9.900000e-109 405.0
61 TraesCS6A01G332700 chrUn 84.360 211 23 10 7474 7680 92772778 92772574 1.800000e-46 198.0
62 TraesCS6A01G332700 chr1D 78.323 632 66 27 6394 6968 455631549 455630932 7.870000e-90 342.0
63 TraesCS6A01G332700 chr1D 86.473 207 21 7 7468 7671 41299268 41299470 3.850000e-53 220.0
64 TraesCS6A01G332700 chr1D 80.934 257 40 6 6005 6258 455632208 455631958 2.330000e-45 195.0
65 TraesCS6A01G332700 chr3D 88.070 285 21 7 7706 7977 418215942 418216226 7.930000e-85 326.0
66 TraesCS6A01G332700 chr3D 86.268 284 30 7 7706 7980 283311634 283311351 4.810000e-77 300.0
67 TraesCS6A01G332700 chr3D 88.119 202 17 7 7474 7672 166501407 166501210 4.940000e-57 233.0
68 TraesCS6A01G332700 chr3D 85.294 204 23 7 7468 7668 8906128 8906327 3.880000e-48 204.0
69 TraesCS6A01G332700 chr2D 87.589 282 27 5 7707 7980 56324321 56324040 3.690000e-83 320.0
70 TraesCS6A01G332700 chr2D 81.230 309 44 11 7680 7977 564703786 564704091 3.820000e-58 237.0
71 TraesCS6A01G332700 chr4B 79.000 300 40 13 5666 5945 504337726 504338022 5.050000e-42 183.0
72 TraesCS6A01G332700 chr4B 78.667 300 41 14 5666 5945 434104414 434104710 2.350000e-40 178.0
73 TraesCS6A01G332700 chr4B 79.422 277 36 13 5689 5945 266621335 266621610 8.450000e-40 176.0
74 TraesCS6A01G332700 chr6B 79.556 225 35 10 7462 7680 14387807 14387588 5.120000e-32 150.0
75 TraesCS6A01G332700 chr6B 87.903 124 5 4 8077 8192 634330761 634330640 3.990000e-28 137.0
76 TraesCS6A01G332700 chr6D 86.400 125 7 4 8077 8193 420957399 420957277 2.400000e-25 128.0
77 TraesCS6A01G332700 chr6D 88.525 61 3 3 8136 8193 420936565 420936506 4.100000e-08 71.3


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 TraesCS6A01G332700 chr6A 564260738 564268930 8192 True 15130.00 15130 100.00000 1 8193 1 chr6A.!!$R1 8192
1 TraesCS6A01G332700 chr4A 668259975 668264854 4879 False 8722.00 8722 98.95500 195 5066 1 chr4A.!!$F1 4871
2 TraesCS6A01G332700 chr4A 668212913 668233459 20546 False 8676.00 8687 98.79100 195 5066 3 chr4A.!!$F3 4871
3 TraesCS6A01G332700 chr4A 668178246 668191003 12757 False 8660.50 8680 98.73950 195 5066 2 chr4A.!!$F2 4871
4 TraesCS6A01G332700 chr7B 537538710 537543592 4882 False 8586.00 8586 98.42300 190 5066 1 chr7B.!!$F1 4876
5 TraesCS6A01G332700 chr7B 692302186 692303197 1011 True 506.50 562 94.10800 6772 7454 2 chr7B.!!$R2 682
6 TraesCS6A01G332700 chr7B 730403275 730404285 1010 True 475.50 529 92.75400 6775 7445 2 chr7B.!!$R3 670
7 TraesCS6A01G332700 chr7A 443971847 443976732 4885 True 8556.00 8556 98.30200 189 5067 1 chr7A.!!$R2 4878
8 TraesCS6A01G332700 chr3A 679652324 679657206 4882 True 8473.00 8473 98.01400 191 5066 1 chr3A.!!$R3 4875
9 TraesCS6A01G332700 chr5D 355430932 355432893 1961 False 582.50 1216 92.24225 5067 7041 4 chr5D.!!$F2 1974
10 TraesCS6A01G332700 chr2B 34144119 34146030 1911 False 592.25 1070 92.64275 53 7041 4 chr2B.!!$F3 6988
11 TraesCS6A01G332700 chr2B 572755350 572756350 1000 False 492.00 538 94.02450 6775 7445 2 chr2B.!!$F4 670
12 TraesCS6A01G332700 chr3B 119344994 119346112 1118 True 672.50 835 91.09600 5666 6703 2 chr3B.!!$R3 1037
13 TraesCS6A01G332700 chr3B 815965002 815966006 1004 False 514.00 556 95.07650 6775 7445 2 chr3B.!!$F4 670
14 TraesCS6A01G332700 chr5B 584887710 584888714 1004 True 495.50 531 94.17750 6775 7445 2 chr5B.!!$R4 670
15 TraesCS6A01G332700 chr1D 455630932 455632208 1276 True 268.50 342 79.62850 6005 6968 2 chr1D.!!$R1 963


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
162 163 0.033796 TGTACCCGTCCTACAGGAGG 60.034 60.000 10.41 10.41 46.49 4.30 F
235 237 0.101759 GCTACGGACCAAGCGATACA 59.898 55.000 0.31 0.00 0.00 2.29 F
524 527 0.251634 GAAGCTTGAGGACTGGAGGG 59.748 60.000 2.10 0.00 0.00 4.30 F
914 917 3.881688 GCATGCCTCTGAATCTACATGTT 59.118 43.478 6.36 0.00 37.73 2.71 F
2322 10118 4.103357 CAGGTATGTCTACTACACAACGC 58.897 47.826 0.00 0.00 42.09 4.84 F
2893 10692 5.047377 TGGAAAATACTCCTGTTGCAAATCC 60.047 40.000 0.00 0.00 36.35 3.01 F
4409 20094 0.657312 TGAGTCTGCACTTGTTTGCG 59.343 50.000 0.00 0.00 46.20 4.85 F
5112 20798 0.032952 TTGCGGATACATACGGAGCC 59.967 55.000 0.00 0.00 35.37 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 9282 0.674895 AGCCTTCGCTTCACATGGAC 60.675 55.000 0.00 0.00 45.55 4.02 R
1891 9687 5.927281 AATAGAGCACATCCAAGCAAAAT 57.073 34.783 0.00 0.00 0.00 1.82 R
2322 10118 5.021033 AGAAGGCATTCATACTCTCACTG 57.979 43.478 14.34 0.00 37.94 3.66 R
2554 10350 6.873997 ACTTCCGATCACAATACATCTTGTA 58.126 36.000 0.00 0.00 37.25 2.41 R
4409 20094 3.196469 TCTTGTCAGGACATGTCATCTCC 59.804 47.826 26.47 10.22 41.52 3.71 R
5074 20760 3.632145 GCAATGTTCGGATACCAAGGATT 59.368 43.478 0.00 0.00 0.00 3.01 R
5248 20943 0.109365 TTCGGCAAATCCAATGTGCG 60.109 50.000 0.00 0.00 39.22 5.34 R
7253 23800 0.320858 TGCGCACGTCTCCCAAATTA 60.321 50.000 5.66 0.00 0.00 1.40 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)



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AutoCloner maintained by Alex Coulton.