Multiple sequence alignment - TraesCS2B01G380300

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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 TraesCS2B01G380300 chr2B 100.000 3504 0 0 1 3504 544282971 544279468 0.000000e+00 6471.0
1 TraesCS2B01G380300 chr2B 98.123 2451 44 2 1 2450 543852846 543850397 0.000000e+00 4270.0
2 TraesCS2B01G380300 chr2B 94.605 1631 58 21 761 2363 544711501 544709873 0.000000e+00 2497.0
3 TraesCS2B01G380300 chr2B 99.075 973 9 0 2532 3504 544709866 544708894 0.000000e+00 1748.0
4 TraesCS2B01G380300 chr2B 91.304 69 6 0 59 127 550732352 550732284 1.040000e-15 95.3
5 TraesCS2B01G380300 chr2B 96.774 31 1 0 1660 1690 318883 318853 6.000000e-03 52.8
6 TraesCS2B01G380300 chr2D 90.705 1786 107 34 761 2512 461803262 461801502 0.000000e+00 2324.0
7 TraesCS2B01G380300 chr2D 93.878 882 38 3 570 1451 461674371 461673506 0.000000e+00 1315.0
8 TraesCS2B01G380300 chr2D 92.520 508 34 3 1553 2058 461673445 461672940 0.000000e+00 725.0
9 TraesCS2B01G380300 chr2D 93.913 460 28 0 2053 2512 461660005 461659546 0.000000e+00 695.0
10 TraesCS2B01G380300 chr2D 77.665 394 68 14 27 404 643189277 643188888 4.550000e-54 222.0
11 TraesCS2B01G380300 chr2D 83.193 238 33 4 465 701 608654583 608654814 9.850000e-51 211.0
12 TraesCS2B01G380300 chr2A 90.262 1715 110 34 764 2449 606814915 606813229 0.000000e+00 2189.0
13 TraesCS2B01G380300 chr2A 95.145 968 47 0 1545 2512 606712073 606711106 0.000000e+00 1528.0
14 TraesCS2B01G380300 chr2A 88.504 722 52 17 761 1455 606712930 606712213 0.000000e+00 845.0
15 TraesCS2B01G380300 chr2A 81.743 241 37 6 465 704 276305956 276306190 9.920000e-46 195.0
16 TraesCS2B01G380300 chr4B 88.247 485 54 2 974 1455 661122104 661121620 8.430000e-161 577.0
17 TraesCS2B01G380300 chr4B 79.211 558 79 23 2739 3293 622614468 622613945 1.550000e-93 353.0
18 TraesCS2B01G380300 chr4B 74.803 381 71 9 42 405 29275444 29275072 7.840000e-32 148.0
19 TraesCS2B01G380300 chr4B 96.875 32 1 0 3299 3330 622613852 622613821 2.000000e-03 54.7
20 TraesCS2B01G380300 chr3D 80.541 555 84 16 2743 3296 362019822 362019291 4.210000e-109 405.0
21 TraesCS2B01G380300 chr3D 77.436 390 67 11 27 402 303792239 303791857 2.740000e-51 213.0
22 TraesCS2B01G380300 chr3D 79.252 294 50 10 418 707 459141862 459142148 9.920000e-46 195.0
23 TraesCS2B01G380300 chr3D 96.875 32 1 0 3299 3330 418788310 418788341 2.000000e-03 54.7
24 TraesCS2B01G380300 chrUn 95.676 185 8 0 3320 3504 6622871 6622687 7.350000e-77 298.0
25 TraesCS2B01G380300 chrUn 95.238 189 6 3 3315 3501 13991202 13991389 2.640000e-76 296.0
26 TraesCS2B01G380300 chr3B 95.699 186 6 2 3321 3504 357749263 357749448 7.350000e-77 298.0
27 TraesCS2B01G380300 chr3B 74.747 396 73 19 26 402 659717568 659717955 6.060000e-33 152.0
28 TraesCS2B01G380300 chr1D 95.213 188 9 0 3317 3504 159660566 159660379 7.350000e-77 298.0
29 TraesCS2B01G380300 chr1D 79.156 379 65 10 27 402 484422593 484422960 2.090000e-62 250.0
30 TraesCS2B01G380300 chr1D 89.683 126 12 1 2516 2641 481307723 481307847 3.620000e-35 159.0
31 TraesCS2B01G380300 chr1D 89.091 110 11 1 2632 2740 169806130 169806239 6.100000e-28 135.0
32 TraesCS2B01G380300 chr1D 96.875 32 1 0 3299 3330 364126926 364126957 2.000000e-03 54.7
33 TraesCS2B01G380300 chr1B 96.175 183 5 2 3321 3501 213533520 213533702 7.350000e-77 298.0
34 TraesCS2B01G380300 chr1B 84.351 262 34 5 445 706 303684314 303684060 2.090000e-62 250.0
35 TraesCS2B01G380300 chr6D 93.878 196 10 2 3309 3504 307541889 307541696 9.510000e-76 294.0
36 TraesCS2B01G380300 chr6D 93.000 200 12 2 3303 3501 104385724 104385922 1.230000e-74 291.0
37 TraesCS2B01G380300 chr3A 92.233 206 12 2 3299 3504 717167822 717167621 4.430000e-74 289.0
38 TraesCS2B01G380300 chr4D 82.215 298 41 9 412 707 507884053 507884340 2.700000e-61 246.0
39 TraesCS2B01G380300 chr7D 78.261 391 65 10 27 402 474355317 474354932 2.100000e-57 233.0
40 TraesCS2B01G380300 chr7D 78.342 374 66 7 43 402 465570149 465570521 9.780000e-56 228.0
41 TraesCS2B01G380300 chr7D 77.749 391 66 11 28 402 602622108 602621723 1.640000e-53 220.0
42 TraesCS2B01G380300 chr7D 92.593 108 6 2 2634 2740 59727204 59727310 1.680000e-33 154.0
43 TraesCS2B01G380300 chr1A 79.202 351 59 6 65 402 113546705 113546356 7.560000e-57 231.0
44 TraesCS2B01G380300 chr5D 77.692 390 69 7 27 402 372101333 372100948 4.550000e-54 222.0
45 TraesCS2B01G380300 chr5D 80.916 262 34 10 412 669 487890083 487890332 3.570000e-45 193.0
46 TraesCS2B01G380300 chr5A 81.781 247 36 7 424 669 317229914 317230152 7.670000e-47 198.0
47 TraesCS2B01G380300 chr5A 89.908 109 9 2 2634 2740 170080994 170081102 4.720000e-29 139.0
48 TraesCS2B01G380300 chr5A 89.474 57 4 2 2628 2683 641054741 641054686 1.740000e-08 71.3
49 TraesCS2B01G380300 chr7B 82.008 239 36 4 466 703 525997668 525997436 2.760000e-46 196.0
50 TraesCS2B01G380300 chr7B 75.703 391 75 13 27 402 18104731 18105116 9.990000e-41 178.0
51 TraesCS2B01G380300 chr7B 75.521 384 76 13 29 402 313429506 313429131 4.650000e-39 172.0
52 TraesCS2B01G380300 chr7B 97.436 39 1 0 3258 3296 63372747 63372709 2.260000e-07 67.6
53 TraesCS2B01G380300 chr6B 78.873 284 45 9 73 342 5278984 5279266 9.990000e-41 178.0
54 TraesCS2B01G380300 chr6B 75.733 375 70 12 42 402 465876550 465876917 6.020000e-38 169.0
55 TraesCS2B01G380300 chr6B 90.991 111 6 4 2634 2740 63366857 63366747 2.820000e-31 147.0
56 TraesCS2B01G380300 chr6B 92.157 102 6 2 2640 2740 11285585 11285685 3.650000e-30 143.0
57 TraesCS2B01G380300 chr7A 75.591 381 69 13 38 402 686804336 686804708 2.160000e-37 167.0
58 TraesCS2B01G380300 chr7A 91.346 104 8 1 2638 2740 102037247 102037350 1.310000e-29 141.0
59 TraesCS2B01G380300 chr6A 92.157 102 7 1 2640 2740 135240907 135240806 3.650000e-30 143.0
60 TraesCS2B01G380300 chr6A 92.157 102 7 1 2640 2740 572408032 572408133 3.650000e-30 143.0


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 TraesCS2B01G380300 chr2B 544279468 544282971 3503 True 6471.00 6471 100.0000 1 3504 1 chr2B.!!$R3 3503
1 TraesCS2B01G380300 chr2B 543850397 543852846 2449 True 4270.00 4270 98.1230 1 2450 1 chr2B.!!$R2 2449
2 TraesCS2B01G380300 chr2B 544708894 544711501 2607 True 2122.50 2497 96.8400 761 3504 2 chr2B.!!$R5 2743
3 TraesCS2B01G380300 chr2D 461801502 461803262 1760 True 2324.00 2324 90.7050 761 2512 1 chr2D.!!$R2 1751
4 TraesCS2B01G380300 chr2D 461672940 461674371 1431 True 1020.00 1315 93.1990 570 2058 2 chr2D.!!$R4 1488
5 TraesCS2B01G380300 chr2A 606813229 606814915 1686 True 2189.00 2189 90.2620 764 2449 1 chr2A.!!$R1 1685
6 TraesCS2B01G380300 chr2A 606711106 606712930 1824 True 1186.50 1528 91.8245 761 2512 2 chr2A.!!$R2 1751
7 TraesCS2B01G380300 chr4B 622613821 622614468 647 True 203.85 353 88.0430 2739 3330 2 chr4B.!!$R3 591
8 TraesCS2B01G380300 chr3D 362019291 362019822 531 True 405.00 405 80.5410 2743 3296 1 chr3D.!!$R2 553

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
107 108 0.742635 CTTCCTTCTTCTCCTGCCGC 60.743 60.000 0.0 0.0 0.0 6.53 F
1314 1366 1.227853 GGTGTGGTTTGTCGAGGCT 60.228 57.895 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 2601 2.615493 CCTACATCTTGGAAAGCACGGT 60.615 50.0 0.0 0.0 45.7 4.83 R
2961 3090 0.242825 GGGCTTCTTAACGGGCAAAC 59.757 55.0 0.0 0.0 0.0 2.93 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
107 108 0.742635 CTTCCTTCTTCTCCTGCCGC 60.743 60.000 0.00 0.00 0.00 6.53
173 174 3.153919 TGTTGCCAATCCTTACCACTTC 58.846 45.455 0.00 0.00 0.00 3.01
1314 1366 1.227853 GGTGTGGTTTGTCGAGGCT 60.228 57.895 0.00 0.00 0.00 4.58
1350 1402 3.078560 GACGAATTCGGCGACACC 58.921 61.111 29.79 0.00 44.95 4.16
2472 2590 2.813908 CCGTGGGCGTTCTAGTGC 60.814 66.667 0.00 0.00 36.15 4.40
2483 2601 0.607217 TTCTAGTGCCGTGGAGTCGA 60.607 55.000 0.00 0.00 0.00 4.20
2491 2609 2.338984 GTGGAGTCGACCGTGCTT 59.661 61.111 13.01 0.00 0.00 3.91
2496 2614 0.599204 GAGTCGACCGTGCTTTCCAA 60.599 55.000 13.01 0.00 0.00 3.53
2512 2630 6.599244 TGCTTTCCAAGATGTAGGAATGTAAG 59.401 38.462 0.00 0.00 43.02 2.34
2513 2631 6.823689 GCTTTCCAAGATGTAGGAATGTAAGA 59.176 38.462 0.00 0.00 43.02 2.10
2514 2632 7.011857 GCTTTCCAAGATGTAGGAATGTAAGAG 59.988 40.741 0.00 0.00 43.02 2.85
2515 2633 5.918608 TCCAAGATGTAGGAATGTAAGAGC 58.081 41.667 0.00 0.00 0.00 4.09
2516 2634 5.059833 CCAAGATGTAGGAATGTAAGAGCC 58.940 45.833 0.00 0.00 0.00 4.70
2517 2635 5.396772 CCAAGATGTAGGAATGTAAGAGCCA 60.397 44.000 0.00 0.00 0.00 4.75
2518 2636 5.957771 AGATGTAGGAATGTAAGAGCCAA 57.042 39.130 0.00 0.00 0.00 4.52
2519 2637 5.675538 AGATGTAGGAATGTAAGAGCCAAC 58.324 41.667 0.00 0.00 0.00 3.77
2520 2638 4.901197 TGTAGGAATGTAAGAGCCAACA 57.099 40.909 0.00 0.00 0.00 3.33
2521 2639 4.832248 TGTAGGAATGTAAGAGCCAACAG 58.168 43.478 0.00 0.00 0.00 3.16
2522 2640 4.286032 TGTAGGAATGTAAGAGCCAACAGT 59.714 41.667 0.00 0.00 0.00 3.55
2523 2641 3.944087 AGGAATGTAAGAGCCAACAGTC 58.056 45.455 0.00 0.00 39.36 3.51
2524 2642 2.673368 GGAATGTAAGAGCCAACAGTCG 59.327 50.000 0.00 0.00 40.60 4.18
2525 2643 1.726853 ATGTAAGAGCCAACAGTCGC 58.273 50.000 0.00 0.00 0.00 5.19
2526 2644 0.679505 TGTAAGAGCCAACAGTCGCT 59.320 50.000 0.00 0.00 38.27 4.93
2530 2648 4.876701 AGCCAACAGTCGCTCAAA 57.123 50.000 0.00 0.00 0.00 2.69
2637 2755 2.025441 GGTGCGCGCTGAAAAACA 59.975 55.556 33.29 5.92 0.00 2.83
2645 2763 1.136336 GCGCTGAAAAACACTACTCCG 60.136 52.381 0.00 0.00 0.00 4.63
2684 2802 3.003378 GGGCCTAATGCGTATTTCAAGAC 59.997 47.826 3.47 0.00 42.61 3.01
3021 3150 3.822192 CCGTCGCCGATGTCCTCA 61.822 66.667 5.49 0.00 35.63 3.86
3398 3615 2.428530 CGATCAAGATCAGGGACTCACA 59.571 50.000 10.39 0.00 34.60 3.58
3399 3616 3.118992 CGATCAAGATCAGGGACTCACAA 60.119 47.826 10.39 0.00 34.60 3.33
3406 3623 6.627087 AGATCAGGGACTCACAAAAAGATA 57.373 37.500 0.00 0.00 34.60 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 1.303317 CGTGGGAAAGGTTGGAGGG 60.303 63.158 0.00 0.00 0.00 4.30
184 185 1.663445 CGATCTGGATAACGTCTCCGC 60.663 57.143 11.33 2.42 37.70 5.54
2483 2601 2.615493 CCTACATCTTGGAAAGCACGGT 60.615 50.000 0.00 0.00 45.70 4.83
2491 2609 6.349300 GCTCTTACATTCCTACATCTTGGAA 58.651 40.000 0.00 0.00 45.11 3.53
2496 2614 5.189736 TGTTGGCTCTTACATTCCTACATCT 59.810 40.000 0.00 0.00 31.38 2.90
2513 2631 1.388547 TTTTTGAGCGACTGTTGGCT 58.611 45.000 6.96 6.96 43.42 4.75
2514 2632 2.422276 ATTTTTGAGCGACTGTTGGC 57.578 45.000 0.00 0.00 0.00 4.52
2515 2633 3.052036 CCAATTTTTGAGCGACTGTTGG 58.948 45.455 0.00 0.00 0.00 3.77
2516 2634 3.052036 CCCAATTTTTGAGCGACTGTTG 58.948 45.455 0.00 0.00 0.00 3.33
2517 2635 2.545742 GCCCAATTTTTGAGCGACTGTT 60.546 45.455 0.00 0.00 0.00 3.16
2518 2636 1.000274 GCCCAATTTTTGAGCGACTGT 60.000 47.619 0.00 0.00 0.00 3.55
2519 2637 1.669795 GGCCCAATTTTTGAGCGACTG 60.670 52.381 0.00 0.00 34.93 3.51
2520 2638 0.603065 GGCCCAATTTTTGAGCGACT 59.397 50.000 0.00 0.00 34.93 4.18
2521 2639 0.732538 CGGCCCAATTTTTGAGCGAC 60.733 55.000 0.00 0.00 34.93 5.19
2522 2640 1.583986 CGGCCCAATTTTTGAGCGA 59.416 52.632 0.00 0.00 34.93 4.93
2523 2641 2.094066 GCGGCCCAATTTTTGAGCG 61.094 57.895 0.00 0.00 34.93 5.03
2524 2642 2.094066 CGCGGCCCAATTTTTGAGC 61.094 57.895 0.00 0.00 33.13 4.26
2525 2643 2.094066 GCGCGGCCCAATTTTTGAG 61.094 57.895 8.83 0.00 0.00 3.02
2526 2644 2.048690 GCGCGGCCCAATTTTTGA 60.049 55.556 8.83 0.00 0.00 2.69
2527 2645 3.477520 CGCGCGGCCCAATTTTTG 61.478 61.111 24.84 0.00 0.00 2.44
2616 2734 2.081425 TTTTTCAGCGCGCACCCAAT 62.081 50.000 35.10 8.46 0.00 3.16
2645 2763 7.735326 TTAGGCCCTATATAGATGAAAGGAC 57.265 40.000 11.53 4.87 0.00 3.85
2684 2802 9.840427 ATTAATTTTGTCAATAGTCAAAGACGG 57.160 29.630 0.00 0.00 37.67 4.79
2961 3090 0.242825 GGGCTTCTTAACGGGCAAAC 59.757 55.000 0.00 0.00 0.00 2.93
3021 3150 4.171841 ACAGAGGAGGGGAGAGAATAAGAT 59.828 45.833 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.