Multiple sequence alignment - TraesCS6B01G304200

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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 TraesCS6B01G304200 chr6B 100.000 7662 0 0 1 7662 545215920 545223581 0.000000e+00 14150.0
1 TraesCS6B01G304200 chr6B 97.122 139 4 0 1767 1905 555720943 555721081 1.290000e-57 235.0
2 TraesCS6B01G304200 chr6B 96.479 142 5 0 1767 1908 680405579 680405720 1.290000e-57 235.0
3 TraesCS6B01G304200 chr6B 95.238 147 6 1 1767 1913 103700489 103700344 1.660000e-56 231.0
4 TraesCS6B01G304200 chr6B 95.041 121 5 1 3472 3591 379820008 379820128 1.010000e-43 189.0
5 TraesCS6B01G304200 chr6B 88.742 151 16 1 1767 1917 556794954 556795103 4.720000e-42 183.0
6 TraesCS6B01G304200 chr6A 95.669 4272 135 36 2713 6969 503763211 503767447 0.000000e+00 6818.0
7 TraesCS6B01G304200 chr6A 92.395 1591 69 26 189 1770 503760768 503762315 0.000000e+00 2220.0
8 TraesCS6B01G304200 chr6A 88.221 832 41 13 1905 2710 503762325 503763125 0.000000e+00 941.0
9 TraesCS6B01G304200 chr6A 85.511 352 23 10 6966 7291 503767527 503767876 7.360000e-90 342.0
10 TraesCS6B01G304200 chr6D 93.449 4152 153 50 1905 5982 363055512 363059618 0.000000e+00 6050.0
11 TraesCS6B01G304200 chr6D 95.466 1213 36 5 553 1764 363054302 363055496 0.000000e+00 1917.0
12 TraesCS6B01G304200 chr6D 90.467 1091 68 15 6079 7146 363059767 363060844 0.000000e+00 1406.0
13 TraesCS6B01G304200 chr6D 88.078 562 53 6 1 557 363041123 363041675 0.000000e+00 654.0
14 TraesCS6B01G304200 chr6D 94.815 135 6 1 1222 1356 42401438 42401305 7.790000e-50 209.0
15 TraesCS6B01G304200 chr6D 85.606 132 17 2 173 303 336208383 336208253 3.730000e-28 137.0
16 TraesCS6B01G304200 chr6D 83.221 149 21 4 2575 2721 346830428 346830574 4.820000e-27 134.0
17 TraesCS6B01G304200 chr3A 93.519 1543 83 11 2751 4282 136004998 136003462 0.000000e+00 2279.0
18 TraesCS6B01G304200 chr3A 84.211 684 47 23 1905 2578 136005622 136004990 6.570000e-170 608.0
19 TraesCS6B01G304200 chr3A 90.052 382 36 2 1230 1610 136006080 136005700 1.920000e-135 494.0
20 TraesCS6B01G304200 chr3A 94.977 219 10 1 7445 7662 468004995 468005213 7.360000e-90 342.0
21 TraesCS6B01G304200 chr3A 96.454 141 5 0 1767 1907 285775275 285775135 4.620000e-57 233.0
22 TraesCS6B01G304200 chr3A 95.172 145 6 1 1767 1911 688892726 688892583 2.150000e-55 228.0
23 TraesCS6B01G304200 chr3A 90.196 51 5 0 252 302 744267242 744267192 4.960000e-07 67.6
24 TraesCS6B01G304200 chr3A 100.000 31 0 0 252 282 744287525 744287495 2.990000e-04 58.4
25 TraesCS6B01G304200 chr1B 94.786 863 37 6 3076 3935 374013486 374012629 0.000000e+00 1338.0
26 TraesCS6B01G304200 chr1B 83.971 680 43 18 1905 2573 374014484 374013860 6.620000e-165 592.0
27 TraesCS6B01G304200 chr1B 92.749 331 17 4 2751 3076 374013863 374013535 9.000000e-129 472.0
28 TraesCS6B01G304200 chr5D 87.709 358 41 3 1222 1578 540196783 540196428 1.540000e-111 414.0
29 TraesCS6B01G304200 chr5D 91.053 190 16 1 1219 1408 44956890 44956702 9.870000e-64 255.0
30 TraesCS6B01G304200 chr5D 92.000 150 11 1 1767 1915 505463851 505463702 7.790000e-50 209.0
31 TraesCS6B01G304200 chr5D 85.075 134 18 2 2578 2710 44784362 44784494 1.340000e-27 135.0
32 TraesCS6B01G304200 chr5D 84.559 136 19 2 2579 2713 542696937 542696803 4.820000e-27 134.0
33 TraesCS6B01G304200 chr5D 96.667 60 2 0 2780 2839 403644270 403644211 4.890000e-17 100.0
34 TraesCS6B01G304200 chr7D 98.157 217 4 0 7446 7662 70150989 70150773 5.610000e-101 379.0
35 TraesCS6B01G304200 chr7D 85.385 130 17 2 175 303 30913288 30913416 4.820000e-27 134.0
36 TraesCS6B01G304200 chr4D 98.157 217 4 0 7446 7662 28848595 28848811 5.610000e-101 379.0
37 TraesCS6B01G304200 chr4D 97.706 218 4 1 7446 7662 401416711 401416494 2.610000e-99 374.0
38 TraesCS6B01G304200 chr4D 85.496 262 25 10 1222 1473 12041266 12041008 2.120000e-65 261.0
39 TraesCS6B01G304200 chr2B 96.330 218 8 0 7445 7662 379119042 379118825 7.310000e-95 359.0
40 TraesCS6B01G304200 chr2B 92.857 196 13 1 7468 7662 32631924 32632119 4.530000e-72 283.0
41 TraesCS6B01G304200 chr2B 82.734 139 21 3 173 309 131581007 131581144 3.760000e-23 121.0
42 TraesCS6B01G304200 chr7A 91.204 216 16 1 7447 7662 634478916 634478704 2.700000e-74 291.0
43 TraesCS6B01G304200 chr4B 88.745 231 25 1 1222 1451 580717672 580717442 1.630000e-71 281.0
44 TraesCS6B01G304200 chr4B 97.842 139 3 0 1767 1905 45773777 45773639 2.760000e-59 241.0
45 TraesCS6B01G304200 chr5B 93.923 181 10 1 1219 1399 648850992 648851171 9.800000e-69 272.0
46 TraesCS6B01G304200 chr5B 85.714 133 18 1 2578 2710 44657220 44657351 1.040000e-28 139.0
47 TraesCS6B01G304200 chr5B 84.397 141 17 5 2576 2715 509171383 509171519 4.820000e-27 134.0
48 TraesCS6B01G304200 chr5A 93.785 177 10 1 3415 3590 592001312 592001488 1.640000e-66 265.0
49 TraesCS6B01G304200 chr3D 95.238 168 7 1 7495 7662 395669524 395669690 1.640000e-66 265.0
50 TraesCS6B01G304200 chr7B 98.582 141 2 0 1767 1907 671719095 671719235 4.590000e-62 250.0
51 TraesCS6B01G304200 chr7B 97.842 139 3 0 1767 1905 227282569 227282707 2.760000e-59 241.0
52 TraesCS6B01G304200 chr7B 96.479 142 5 0 7444 7585 537841954 537842095 1.290000e-57 235.0
53 TraesCS6B01G304200 chr4A 96.403 139 5 0 1767 1905 696374879 696375017 5.980000e-56 230.0
54 TraesCS6B01G304200 chr3B 90.667 150 12 2 1770 1918 367582261 367582113 1.690000e-46 198.0
55 TraesCS6B01G304200 chr1A 85.714 140 18 2 2576 2713 202093227 202093088 6.200000e-31 147.0
56 TraesCS6B01G304200 chr1A 83.916 143 20 3 2568 2709 285535994 285535854 4.820000e-27 134.0
57 TraesCS6B01G304200 chr2D 81.609 174 24 7 2580 2747 22120398 22120227 3.730000e-28 137.0


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 TraesCS6B01G304200 chr6B 545215920 545223581 7661 False 14150.000000 14150 100.000000 1 7662 1 chr6B.!!$F2 7661
1 TraesCS6B01G304200 chr6A 503760768 503767876 7108 False 2580.250000 6818 90.449000 189 7291 4 chr6A.!!$F1 7102
2 TraesCS6B01G304200 chr6D 363054302 363060844 6542 False 3124.333333 6050 93.127333 553 7146 3 chr6D.!!$F3 6593
3 TraesCS6B01G304200 chr6D 363041123 363041675 552 False 654.000000 654 88.078000 1 557 1 chr6D.!!$F2 556
4 TraesCS6B01G304200 chr3A 136003462 136006080 2618 True 1127.000000 2279 89.260667 1230 4282 3 chr3A.!!$R5 3052
5 TraesCS6B01G304200 chr1B 374012629 374014484 1855 True 800.666667 1338 90.502000 1905 3935 3 chr1B.!!$R1 2030


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
223 224 0.167251 CCCGTCGTTTTTCATTCCGG 59.833 55.000 0.0 0.0 0.00 5.14 F
1779 1807 0.250295 TCTCCCGCCTTGTTCTGTTG 60.250 55.000 0.0 0.0 0.00 3.33 F
1866 1894 0.031817 CCAATCCTTGCCAATCCCCT 60.032 55.000 0.0 0.0 0.00 4.79 F
1871 1899 0.031817 CCTTGCCAATCCCCTCCAAT 60.032 55.000 0.0 0.0 0.00 3.16 F
1873 1901 0.032217 TTGCCAATCCCCTCCAATCC 60.032 55.000 0.0 0.0 0.00 3.01 F
1875 1903 0.178978 GCCAATCCCCTCCAATCCTC 60.179 60.000 0.0 0.0 0.00 3.71 F
2226 2279 0.392706 TGAAGAAGCAGGTCAAGCGA 59.607 50.000 0.0 0.0 37.01 4.93 F
4956 5164 1.517832 CGGAGGAGAACTGCCGAAT 59.482 57.895 0.0 0.0 40.22 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1880 0.031817 ATTGGAGGGGATTGGCAAGG 60.032 55.000 5.96 0.00 0.00 3.61 R
2677 2731 0.172578 TTACACGGAGAGACATGCGG 59.827 55.000 0.00 0.00 38.46 5.69 R
3297 3493 1.331756 GTCCTGCATTCCATTACAGCG 59.668 52.381 0.00 0.00 0.00 5.18 R
3455 3651 1.541379 AAACCCCGTGCCAAATACTC 58.459 50.000 0.00 0.00 0.00 2.59 R
4922 5130 0.107993 TCCGCTCAGCATCCTTCTTG 60.108 55.000 0.00 0.00 0.00 3.02 R
5008 5216 5.343249 ACAAGCTACAAACTTTGCAAAGAG 58.657 37.500 38.78 28.69 39.31 2.85 R
5138 5346 0.595095 CTGTGCTTTCCTCCAACTGC 59.405 55.000 0.00 0.00 0.00 4.40 R
7293 7723 0.032615 TCCCACCACAAGCAAAACCT 60.033 50.000 0.00 0.00 0.00 3.50 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.