Multiple sequence alignment - TraesCS2D01G195300

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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 TraesCS2D01G195300 chr2D 100.000 7448 0 0 1 7448 141483301 141475854 0.000000e+00 13754.0
1 TraesCS2D01G195300 chr2D 91.503 459 27 3 6981 7429 553365735 553366191 8.210000e-174 621.0
2 TraesCS2D01G195300 chr2A 94.336 3178 100 40 3 3145 159869419 159872551 0.000000e+00 4798.0
3 TraesCS2D01G195300 chr2A 95.879 1990 63 13 4848 6829 159875437 159877415 0.000000e+00 3203.0
4 TraesCS2D01G195300 chr2A 96.069 1094 26 6 3723 4816 159874359 159875435 0.000000e+00 1766.0
5 TraesCS2D01G195300 chr2A 95.032 624 14 5 3125 3732 159873359 159873981 0.000000e+00 965.0
6 TraesCS2D01G195300 chr2A 90.407 688 50 7 1 686 159867885 159868558 0.000000e+00 891.0
7 TraesCS2D01G195300 chr2A 88.166 338 14 9 7112 7448 159877837 159878149 5.450000e-101 379.0
8 TraesCS2D01G195300 chr2A 91.089 101 8 1 3724 3824 116449089 116448990 1.300000e-27 135.0
9 TraesCS2D01G195300 chr2B 90.135 2960 174 42 558 3445 199010814 199013727 0.000000e+00 3740.0
10 TraesCS2D01G195300 chr2B 92.877 1460 54 12 3444 4891 199013851 199015272 0.000000e+00 2074.0
11 TraesCS2D01G195300 chr2B 92.269 983 44 10 5832 6803 199018695 199019656 0.000000e+00 1365.0
12 TraesCS2D01G195300 chr2B 92.916 847 36 9 4889 5723 199015352 199016186 0.000000e+00 1210.0
13 TraesCS2D01G195300 chr2B 89.439 303 31 1 1 303 199009485 199009786 1.520000e-101 381.0
14 TraesCS2D01G195300 chr2B 88.104 269 22 5 303 571 199010539 199010797 2.020000e-80 311.0
15 TraesCS2D01G195300 chr2B 89.423 104 11 0 3727 3830 519666436 519666333 1.690000e-26 132.0
16 TraesCS2D01G195300 chr1B 85.289 1074 89 31 1466 2491 564711133 564710081 0.000000e+00 1044.0
17 TraesCS2D01G195300 chr1B 85.343 846 75 31 4843 5682 274862561 274863363 0.000000e+00 830.0
18 TraesCS2D01G195300 chr1B 87.255 612 39 13 1949 2559 564710607 564710034 0.000000e+00 662.0
19 TraesCS2D01G195300 chr1B 80.733 737 85 34 5681 6379 274863394 274864111 8.560000e-144 521.0
20 TraesCS2D01G195300 chr1B 85.098 510 54 12 979 1472 564716144 564715641 1.120000e-137 501.0
21 TraesCS2D01G195300 chr1B 90.654 107 10 0 3724 3830 507850360 507850466 7.790000e-30 143.0
22 TraesCS2D01G195300 chr1B 88.073 109 13 0 3722 3830 656252847 656252739 6.060000e-26 130.0
23 TraesCS2D01G195300 chr1B 89.744 78 4 2 2554 2627 564697708 564697631 6.150000e-16 97.1
24 TraesCS2D01G195300 chr7B 84.623 1021 105 26 979 1959 424554668 424553660 0.000000e+00 968.0
25 TraesCS2D01G195300 chr7B 88.567 691 47 16 1942 2627 424553648 424552985 0.000000e+00 809.0
26 TraesCS2D01G195300 chr7B 88.197 466 36 13 4862 5320 16921783 16921330 8.500000e-149 538.0
27 TraesCS2D01G195300 chr4A 86.777 847 83 15 4843 5682 423377456 423376632 0.000000e+00 917.0
28 TraesCS2D01G195300 chr4A 80.711 731 87 32 5681 6379 423376178 423375470 3.080000e-143 520.0
29 TraesCS2D01G195300 chr4A 86.047 387 36 8 5296 5682 423376578 423376210 4.190000e-107 399.0
30 TraesCS2D01G195300 chr6B 88.741 675 56 15 4843 5509 557774459 557773797 0.000000e+00 808.0
31 TraesCS2D01G195300 chr6B 85.178 533 65 9 5852 6379 557773166 557772643 1.100000e-147 534.0
32 TraesCS2D01G195300 chr6B 83.558 371 49 6 5838 6202 275770013 275769649 3.330000e-88 337.0
33 TraesCS2D01G195300 chr6B 83.851 322 31 15 4843 5157 275771188 275770881 3.400000e-73 287.0
34 TraesCS2D01G195300 chr5B 86.479 710 73 14 4857 5559 247686610 247685917 0.000000e+00 758.0
35 TraesCS2D01G195300 chr5B 87.027 370 32 10 4872 5236 346440375 346440733 3.240000e-108 403.0
36 TraesCS2D01G195300 chr1A 89.114 542 24 13 6921 7429 451522055 451521516 6.300000e-180 641.0
37 TraesCS2D01G195300 chr1A 90.088 454 31 6 6986 7429 552086825 552087274 1.800000e-160 577.0
38 TraesCS2D01G195300 chr1A 96.721 61 1 1 6921 6980 552086735 552086795 4.760000e-17 100.0
39 TraesCS2D01G195300 chrUn 91.921 458 23 6 6984 7429 22375968 22375513 4.900000e-176 628.0
40 TraesCS2D01G195300 chr6D 91.410 454 26 4 6986 7429 19564985 19564535 1.780000e-170 610.0
41 TraesCS2D01G195300 chr6D 96.364 55 1 1 6921 6974 19565074 19565020 1.030000e-13 89.8
42 TraesCS2D01G195300 chr5A 90.529 454 31 4 6986 7429 19264402 19264853 2.310000e-164 590.0
43 TraesCS2D01G195300 chr5A 86.777 121 15 1 3711 3831 119997825 119997706 4.690000e-27 134.0
44 TraesCS2D01G195300 chr5A 93.333 60 3 1 6921 6979 19264311 19264370 3.700000e-13 87.9
45 TraesCS2D01G195300 chr3B 86.852 540 47 14 4996 5530 217400104 217400624 3.870000e-162 582.0
46 TraesCS2D01G195300 chr7A 90.088 454 33 4 6986 7429 606317847 606317396 5.010000e-161 579.0
47 TraesCS2D01G195300 chr7A 89.427 454 31 7 6986 7429 110398630 110399076 2.350000e-154 556.0
48 TraesCS2D01G195300 chr7A 95.082 61 2 1 6921 6980 606317938 606317878 2.210000e-15 95.3
49 TraesCS2D01G195300 chr7A 93.333 60 3 1 6921 6979 110398540 110398599 3.700000e-13 87.9
50 TraesCS2D01G195300 chr4B 90.066 453 33 4 6987 7429 279320883 279320433 1.800000e-160 577.0
51 TraesCS2D01G195300 chr7D 88.140 430 40 10 4846 5270 632829695 632830118 1.120000e-137 501.0
52 TraesCS2D01G195300 chr7D 91.480 223 13 6 5309 5530 632830115 632830332 1.210000e-77 302.0
53 TraesCS2D01G195300 chr6A 91.228 114 9 1 3723 3836 465229028 465228916 3.600000e-33 154.0
54 TraesCS2D01G195300 chr6A 85.366 123 13 5 3724 3843 50253385 50253265 1.010000e-23 122.0
55 TraesCS2D01G195300 chr3D 90.654 107 10 0 3724 3830 450875292 450875186 7.790000e-30 143.0
56 TraesCS2D01G195300 chr1D 89.720 107 11 0 3724 3830 128528616 128528722 3.620000e-28 137.0
57 TraesCS2D01G195300 chr1D 90.196 102 10 0 3724 3825 379139897 379139998 4.690000e-27 134.0


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 TraesCS2D01G195300 chr2D 141475854 141483301 7447 True 13754.000000 13754 100.000000 1 7448 1 chr2D.!!$R1 7447
1 TraesCS2D01G195300 chr2A 159867885 159878149 10264 False 2000.333333 4798 93.314833 1 7448 6 chr2A.!!$F1 7447
2 TraesCS2D01G195300 chr2B 199009485 199019656 10171 False 1513.500000 3740 90.956667 1 6803 6 chr2B.!!$F1 6802
3 TraesCS2D01G195300 chr1B 564710034 564711133 1099 True 853.000000 1044 86.272000 1466 2559 2 chr1B.!!$R4 1093
4 TraesCS2D01G195300 chr1B 274862561 274864111 1550 False 675.500000 830 83.038000 4843 6379 2 chr1B.!!$F2 1536
5 TraesCS2D01G195300 chr1B 564715641 564716144 503 True 501.000000 501 85.098000 979 1472 1 chr1B.!!$R2 493
6 TraesCS2D01G195300 chr7B 424552985 424554668 1683 True 888.500000 968 86.595000 979 2627 2 chr7B.!!$R2 1648
7 TraesCS2D01G195300 chr4A 423375470 423377456 1986 True 612.000000 917 84.511667 4843 6379 3 chr4A.!!$R1 1536
8 TraesCS2D01G195300 chr6B 557772643 557774459 1816 True 671.000000 808 86.959500 4843 6379 2 chr6B.!!$R2 1536
9 TraesCS2D01G195300 chr6B 275769649 275771188 1539 True 312.000000 337 83.704500 4843 6202 2 chr6B.!!$R1 1359
10 TraesCS2D01G195300 chr5B 247685917 247686610 693 True 758.000000 758 86.479000 4857 5559 1 chr5B.!!$R1 702
11 TraesCS2D01G195300 chr1A 451521516 451522055 539 True 641.000000 641 89.114000 6921 7429 1 chr1A.!!$R1 508
12 TraesCS2D01G195300 chr1A 552086735 552087274 539 False 338.500000 577 93.404500 6921 7429 2 chr1A.!!$F1 508
13 TraesCS2D01G195300 chr6D 19564535 19565074 539 True 349.900000 610 93.887000 6921 7429 2 chr6D.!!$R1 508
14 TraesCS2D01G195300 chr5A 19264311 19264853 542 False 338.950000 590 91.931000 6921 7429 2 chr5A.!!$F1 508
15 TraesCS2D01G195300 chr3B 217400104 217400624 520 False 582.000000 582 86.852000 4996 5530 1 chr3B.!!$F1 534
16 TraesCS2D01G195300 chr7A 606317396 606317938 542 True 337.150000 579 92.585000 6921 7429 2 chr7A.!!$R1 508
17 TraesCS2D01G195300 chr7A 110398540 110399076 536 False 321.950000 556 91.380000 6921 7429 2 chr7A.!!$F1 508
18 TraesCS2D01G195300 chr7D 632829695 632830332 637 False 401.500000 501 89.810000 4846 5530 2 chr7D.!!$F1 684


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
149 150 0.673644 CCATCGGCGAAGAACCAACT 60.674 55.000 15.93 0.00 0.00 3.16 F
900 3231 1.118356 CCTCCCTTCCTCCATCTCCG 61.118 65.000 0.00 0.00 0.00 4.63 F
2608 5037 0.622665 CCTTCCACTTGAGATGGCCT 59.377 55.000 3.32 0.00 37.13 5.19 F
3822 7631 1.135315 CGACAACTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69 F
3824 7633 1.206371 ACAACTAATTCCGGACGGAGG 59.794 52.381 13.64 8.21 46.06 4.30 F
4350 8167 2.643551 CAAAATGGTAGCTCGTGGGAT 58.356 47.619 0.00 0.00 0.00 3.85 F
5904 13534 2.582172 TGATGATTTCCCACTGTCCCAT 59.418 45.455 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 3677 0.111253 AGCAAGGGGCCATGTATAGC 59.889 55.000 4.39 0.00 46.50 2.97 R
2864 5299 1.655484 TGTCAACCATATGCAGAGCG 58.345 50.000 0.00 0.00 0.00 5.03 R
4050 7867 1.893544 TTGCCCAAACAATGCAATGG 58.106 45.000 6.73 3.05 39.86 3.16 R
5477 10294 0.954452 GAAACACAAGGGCCACAGAG 59.046 55.000 6.18 0.00 0.00 3.35 R
5787 13384 5.915758 GCACAAGAGTCGTCATACCTAATAG 59.084 44.000 0.00 0.00 0.00 1.73 R
6249 13898 1.446792 ACGCGCACTGGATGAAGAG 60.447 57.895 5.73 0.00 0.00 2.85 R
7389 15239 0.234884 CCGGAAATTAGCGCGGATTC 59.765 55.000 8.83 5.74 0.00 2.52 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.