Multiple sequence alignment - TraesCS2D01G264900

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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 TraesCS2D01G264900 chr2D 100.000 2999 0 0 1 2999 323748524 323745526 0.000000e+00 5539
1 TraesCS2D01G264900 chr2A 92.468 2496 107 28 529 2990 406662213 406664661 0.000000e+00 3493
2 TraesCS2D01G264900 chr2A 93.458 107 7 0 2480 2586 118669231 118669125 3.090000e-35 159
3 TraesCS2D01G264900 chr2B 92.870 2300 115 15 529 2798 391949837 391947557 0.000000e+00 3293
4 TraesCS2D01G264900 chr2B 88.670 203 15 3 2797 2999 391789531 391789337 1.070000e-59 241
5 TraesCS2D01G264900 chr2B 80.731 301 51 5 2288 2586 18971873 18972168 8.360000e-56 228
6 TraesCS2D01G264900 chr3B 92.410 527 40 0 1 527 156570417 156569891 0.000000e+00 752
7 TraesCS2D01G264900 chr3B 90.280 535 51 1 1 534 472742723 472743257 0.000000e+00 699
8 TraesCS2D01G264900 chr3B 79.286 280 51 6 2308 2584 298196962 298196687 3.950000e-44 189
9 TraesCS2D01G264900 chr5B 92.045 528 41 1 1 528 697984321 697984847 0.000000e+00 741
10 TraesCS2D01G264900 chr5B 90.672 536 50 0 1 536 35697741 35697206 0.000000e+00 713
11 TraesCS2D01G264900 chr4A 92.030 527 41 1 1 527 544873547 544873022 0.000000e+00 739
12 TraesCS2D01G264900 chr7B 91.871 529 42 1 1 528 336642425 336641897 0.000000e+00 737
13 TraesCS2D01G264900 chr6B 91.856 528 42 1 1 528 576213877 576214403 0.000000e+00 736
14 TraesCS2D01G264900 chr7D 92.308 520 34 2 9 528 187382271 187381758 0.000000e+00 734
15 TraesCS2D01G264900 chr3A 91.477 528 44 1 1 528 540949810 540949284 0.000000e+00 725
16 TraesCS2D01G264900 chr4D 81.518 303 53 3 2287 2587 467190277 467189976 2.310000e-61 246
17 TraesCS2D01G264900 chr1B 81.788 302 47 5 2288 2583 535013655 535013356 2.310000e-61 246
18 TraesCS2D01G264900 chr1B 82.117 274 48 1 2287 2560 302751643 302751915 1.800000e-57 233
19 TraesCS2D01G264900 chr7A 80.132 302 51 6 2287 2586 10196892 10197186 1.810000e-52 217


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 TraesCS2D01G264900 chr2D 323745526 323748524 2998 True 5539 5539 100.000 1 2999 1 chr2D.!!$R1 2998
1 TraesCS2D01G264900 chr2A 406662213 406664661 2448 False 3493 3493 92.468 529 2990 1 chr2A.!!$F1 2461
2 TraesCS2D01G264900 chr2B 391947557 391949837 2280 True 3293 3293 92.870 529 2798 1 chr2B.!!$R2 2269
3 TraesCS2D01G264900 chr3B 156569891 156570417 526 True 752 752 92.410 1 527 1 chr3B.!!$R1 526
4 TraesCS2D01G264900 chr3B 472742723 472743257 534 False 699 699 90.280 1 534 1 chr3B.!!$F1 533
5 TraesCS2D01G264900 chr5B 697984321 697984847 526 False 741 741 92.045 1 528 1 chr5B.!!$F1 527
6 TraesCS2D01G264900 chr5B 35697206 35697741 535 True 713 713 90.672 1 536 1 chr5B.!!$R1 535
7 TraesCS2D01G264900 chr4A 544873022 544873547 525 True 739 739 92.030 1 527 1 chr4A.!!$R1 526
8 TraesCS2D01G264900 chr7B 336641897 336642425 528 True 737 737 91.871 1 528 1 chr7B.!!$R1 527
9 TraesCS2D01G264900 chr6B 576213877 576214403 526 False 736 736 91.856 1 528 1 chr6B.!!$F1 527
10 TraesCS2D01G264900 chr7D 187381758 187382271 513 True 734 734 92.308 9 528 1 chr7D.!!$R1 519
11 TraesCS2D01G264900 chr3A 540949284 540949810 526 True 725 725 91.477 1 528 1 chr3A.!!$R1 527

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
598 601 1.197721 GGAAGCCATGAAACACGTCAG 59.802 52.381 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 2466 0.109689 GCACGTGTAGAGACTCGCTT 60.11 55.0 18.38 0.0 44.42 4.68 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
18 19 2.189833 ACGGAGCGAATACAGAGCA 58.810 52.632 0.00 0.00 0.00 4.26
65 66 2.715880 ACCGGAACTTAAAACCCCCTTA 59.284 45.455 9.46 0.00 0.00 2.69
83 84 8.218488 ACCCCCTTAAATCATAGAGAAATACAC 58.782 37.037 0.00 0.00 0.00 2.90
230 231 6.539826 GTGTGTGGTAGTAAAACTTGGTACTT 59.460 38.462 0.00 0.00 32.79 2.24
284 285 7.230510 ACTGTGTCATTGTGTATTGTTTGGTAT 59.769 33.333 0.00 0.00 0.00 2.73
367 368 2.600470 AAGTTCCGTTTCCACGTGTA 57.400 45.000 15.65 0.00 45.62 2.90
374 375 2.136728 CGTTTCCACGTGTATTCCACA 58.863 47.619 15.65 0.00 44.78 4.17
375 376 2.739913 CGTTTCCACGTGTATTCCACAT 59.260 45.455 15.65 0.00 44.78 3.21
403 404 3.244111 CACCATTCCGTTTTTGTTTTCGG 59.756 43.478 0.00 0.00 43.65 4.30
487 489 2.642807 TCCTCTCCGTTTCCATTTTCCT 59.357 45.455 0.00 0.00 0.00 3.36
598 601 1.197721 GGAAGCCATGAAACACGTCAG 59.802 52.381 0.00 0.00 0.00 3.51
680 683 2.224769 CCCCAACTAACAAAGAGCAGGA 60.225 50.000 0.00 0.00 0.00 3.86
681 684 3.486383 CCCAACTAACAAAGAGCAGGAA 58.514 45.455 0.00 0.00 0.00 3.36
699 702 5.807011 GCAGGAAACTAAAATAGGCAATGTG 59.193 40.000 0.00 0.00 40.21 3.21
1051 1057 0.445436 CACCTCGCATCTCAAACAGC 59.555 55.000 0.00 0.00 0.00 4.40
1106 1112 2.785269 AGGGTTCTATCCATGGCAATGA 59.215 45.455 6.96 0.00 35.67 2.57
1117 1123 0.251698 TGGCAATGATGGTGAAGGCA 60.252 50.000 0.00 0.00 0.00 4.75
1353 1361 1.670811 CGACCTGACAAACTTGTTGCT 59.329 47.619 0.00 0.00 42.43 3.91
1666 1674 1.373748 GGCAACCGACGAGCAGTTA 60.374 57.895 0.00 0.00 0.00 2.24
1708 1716 4.657824 ACACCGACGCCCAGTTCG 62.658 66.667 0.00 0.00 0.00 3.95
1837 1889 2.643551 ACCAAGGCTTAATCATGTCGG 58.356 47.619 0.00 0.00 0.00 4.79
1925 1983 1.902508 TCCTTCCTTCCTACAGTGCTG 59.097 52.381 0.00 0.00 0.00 4.41
1926 1984 1.902508 CCTTCCTTCCTACAGTGCTGA 59.097 52.381 6.17 0.00 0.00 4.26
1927 1985 2.503356 CCTTCCTTCCTACAGTGCTGAT 59.497 50.000 6.17 0.00 0.00 2.90
2015 2073 7.153217 TCACATTCTTTAGTATCGTCTGTCA 57.847 36.000 0.00 0.00 0.00 3.58
2232 2291 4.083003 CGTTAAGTGAGAAGCAGAGAGAGT 60.083 45.833 0.00 0.00 0.00 3.24
2302 2364 2.554893 CCCCGCTAAAAGCAAGTACAAA 59.445 45.455 0.00 0.00 42.58 2.83
2313 2389 4.843728 AGCAAGTACAAAAGCAGGCTATA 58.156 39.130 0.00 0.00 0.00 1.31
2314 2390 5.253330 AGCAAGTACAAAAGCAGGCTATAA 58.747 37.500 0.00 0.00 0.00 0.98
2315 2391 5.355350 AGCAAGTACAAAAGCAGGCTATAAG 59.645 40.000 0.00 0.00 0.00 1.73
2316 2392 5.573146 CAAGTACAAAAGCAGGCTATAAGC 58.427 41.667 0.00 0.00 41.46 3.09
2325 2401 4.141144 GCTATAAGCCCGCTTGCA 57.859 55.556 12.18 0.00 37.47 4.08
2326 2402 2.633860 GCTATAAGCCCGCTTGCAT 58.366 52.632 12.18 1.39 37.47 3.96
2336 2412 2.673610 GCCCGCTTGCATGACATTTTTA 60.674 45.455 3.33 0.00 0.00 1.52
2348 2424 8.791675 TGCATGACATTTTTAACTATGTGAAGA 58.208 29.630 0.00 0.00 35.24 2.87
2366 2442 8.970691 TGTGAAGAAGAAAGACAAAGAAAAAG 57.029 30.769 0.00 0.00 0.00 2.27
2368 2444 6.747280 TGAAGAAGAAAGACAAAGAAAAAGCG 59.253 34.615 0.00 0.00 0.00 4.68
2373 2449 6.852664 AGAAAGACAAAGAAAAAGCGAAAGA 58.147 32.000 0.00 0.00 0.00 2.52
2375 2451 5.819825 AGACAAAGAAAAAGCGAAAGAGT 57.180 34.783 0.00 0.00 0.00 3.24
2376 2452 6.920569 AGACAAAGAAAAAGCGAAAGAGTA 57.079 33.333 0.00 0.00 0.00 2.59
2377 2453 6.949449 AGACAAAGAAAAAGCGAAAGAGTAG 58.051 36.000 0.00 0.00 0.00 2.57
2411 2487 0.521659 GCGAGTCTCTACACGTGCTC 60.522 60.000 17.22 11.74 41.12 4.26
2412 2488 1.080298 CGAGTCTCTACACGTGCTCT 58.920 55.000 17.22 5.01 35.33 4.09
2424 2500 4.444536 ACACGTGCTCTTAGGTAAAAACA 58.555 39.130 17.22 0.00 0.00 2.83
2647 2723 2.708861 TCAGGGGCACTTTGAAAGTCTA 59.291 45.455 7.75 0.00 40.46 2.59
2663 2739 6.269077 TGAAAGTCTACTCCCACTGTTTGATA 59.731 38.462 0.00 0.00 0.00 2.15
2710 2786 8.900983 AGCACATAGAATTAGAGGAAAATCTC 57.099 34.615 0.00 0.00 0.00 2.75
2719 2795 1.286257 GAGGAAAATCTCCCCTTGCCT 59.714 52.381 0.00 0.00 46.81 4.75
2755 2831 3.118454 CTTCCGCAACCGACGCAT 61.118 61.111 0.00 0.00 36.29 4.73
2773 2849 2.479837 CATCTCTCTCTCTAGCGTCGT 58.520 52.381 0.00 0.00 0.00 4.34
2795 2871 4.621460 GTGTCCGTTCGGATCATACATATG 59.379 45.833 16.87 0.00 36.61 1.78
2845 2921 7.639113 AGTTTCCATTTACTTCAAACACTCA 57.361 32.000 0.00 0.00 30.74 3.41
2904 2980 3.000727 AGACGTGAACCGATGAAAATCC 58.999 45.455 0.00 0.00 40.70 3.01
2921 2997 1.187087 TCCTTCCGCTCCTCTCTTTC 58.813 55.000 0.00 0.00 0.00 2.62
2990 3066 2.087646 GAGTTGTTTGATGCCCCTCTC 58.912 52.381 0.00 0.00 0.00 3.20
2991 3067 1.425066 AGTTGTTTGATGCCCCTCTCA 59.575 47.619 0.00 0.00 0.00 3.27
2992 3068 1.815003 GTTGTTTGATGCCCCTCTCAG 59.185 52.381 0.00 0.00 0.00 3.35
2993 3069 0.322816 TGTTTGATGCCCCTCTCAGC 60.323 55.000 0.00 0.00 0.00 4.26
2994 3070 0.322816 GTTTGATGCCCCTCTCAGCA 60.323 55.000 0.00 0.00 44.45 4.41
2998 3074 3.824815 TGCCCCTCTCAGCATTGA 58.175 55.556 0.00 0.00 33.08 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 7.069852 TCCATCAATTTGTTTGTGTTTTGTG 57.930 32.000 0.00 0.00 36.65 3.33
90 91 9.649024 GTTAACAATTCCATCAATTTGTTTGTG 57.351 29.630 0.00 0.00 36.65 3.33
255 256 6.691754 AACAATACACAATGACACAGTGAA 57.308 33.333 7.81 0.00 37.05 3.18
314 315 7.119262 CCGCTAATATGGAATTTCCGTTTCTAT 59.881 37.037 15.20 2.59 40.17 1.98
367 368 4.321899 CGGAATGGTGTTTTCATGTGGAAT 60.322 41.667 0.00 0.00 34.91 3.01
374 375 5.423886 ACAAAAACGGAATGGTGTTTTCAT 58.576 33.333 3.84 0.00 44.92 2.57
375 376 4.822026 ACAAAAACGGAATGGTGTTTTCA 58.178 34.783 3.84 0.00 44.92 2.69
511 513 6.466904 CCTCTCACATAGGGATGAAAATGGAT 60.467 42.308 0.00 0.00 36.48 3.41
699 702 2.813754 TCAACAACTGCTACTCATTGGC 59.186 45.455 0.00 0.00 0.00 4.52
1051 1057 1.604604 TGCCAACCGAAAAGAGAAGG 58.395 50.000 0.00 0.00 0.00 3.46
1353 1361 3.124466 CGAAAATACTGCAACCATCGACA 59.876 43.478 0.00 0.00 0.00 4.35
1651 1659 1.080974 CGGTAACTGCTCGTCGGTT 60.081 57.895 9.01 9.01 45.69 4.44
1837 1889 5.219633 ACAAGAACAAATCCGCAAATGTAC 58.780 37.500 0.00 0.00 0.00 2.90
1950 2008 8.849490 CCGACAGACAAATACAACAAATAAATG 58.151 33.333 0.00 0.00 0.00 2.32
2232 2291 7.982919 ACGCACCAACTCTTTGTACATATATTA 59.017 33.333 0.00 0.00 0.00 0.98
2313 2389 1.252904 AATGTCATGCAAGCGGGCTT 61.253 50.000 0.00 0.00 36.60 4.35
2314 2390 1.252904 AAATGTCATGCAAGCGGGCT 61.253 50.000 0.00 0.00 34.04 5.19
2315 2391 0.390209 AAAATGTCATGCAAGCGGGC 60.390 50.000 0.00 0.00 0.00 6.13
2316 2392 2.083167 AAAAATGTCATGCAAGCGGG 57.917 45.000 0.00 0.00 0.00 6.13
2317 2393 4.236935 AGTTAAAAATGTCATGCAAGCGG 58.763 39.130 0.00 0.00 0.00 5.52
2318 2394 6.527722 ACATAGTTAAAAATGTCATGCAAGCG 59.472 34.615 0.00 0.00 30.54 4.68
2319 2395 7.541783 TCACATAGTTAAAAATGTCATGCAAGC 59.458 33.333 0.00 0.00 34.12 4.01
2320 2396 8.969121 TCACATAGTTAAAAATGTCATGCAAG 57.031 30.769 0.00 0.00 34.12 4.01
2321 2397 9.409312 CTTCACATAGTTAAAAATGTCATGCAA 57.591 29.630 0.00 0.00 34.12 4.08
2322 2398 8.791675 TCTTCACATAGTTAAAAATGTCATGCA 58.208 29.630 0.00 0.00 34.12 3.96
2323 2399 9.624697 TTCTTCACATAGTTAAAAATGTCATGC 57.375 29.630 1.84 0.00 34.12 4.06
2336 2412 8.964476 TCTTTGTCTTTCTTCTTCACATAGTT 57.036 30.769 0.00 0.00 0.00 2.24
2348 2424 7.312899 TCTTTCGCTTTTTCTTTGTCTTTCTT 58.687 30.769 0.00 0.00 0.00 2.52
2352 2428 6.196079 ACTCTTTCGCTTTTTCTTTGTCTT 57.804 33.333 0.00 0.00 0.00 3.01
2360 2436 4.329296 GAGCCTACTCTTTCGCTTTTTC 57.671 45.455 0.00 0.00 40.03 2.29
2373 2449 5.127356 ACTCGCTTTTACATTAGAGCCTACT 59.873 40.000 0.00 0.00 0.00 2.57
2375 2451 5.360144 AGACTCGCTTTTACATTAGAGCCTA 59.640 40.000 0.00 0.00 0.00 3.93
2376 2452 4.160626 AGACTCGCTTTTACATTAGAGCCT 59.839 41.667 0.00 0.00 0.00 4.58
2377 2453 4.434520 AGACTCGCTTTTACATTAGAGCC 58.565 43.478 0.00 0.00 0.00 4.70
2387 2463 3.818387 CACGTGTAGAGACTCGCTTTTA 58.182 45.455 7.58 0.00 44.42 1.52
2390 2466 0.109689 GCACGTGTAGAGACTCGCTT 60.110 55.000 18.38 0.00 44.42 4.68
2579 2655 8.921353 TCAGTAGTACTTCTGTTCTTTAGAGT 57.079 34.615 23.82 0.00 33.89 3.24
2598 2674 0.602638 TTGCGGCAACACCTCAGTAG 60.603 55.000 12.11 0.00 33.77 2.57
2624 2700 1.064017 ACTTTCAAAGTGCCCCTGACA 60.064 47.619 0.68 0.00 41.01 3.58
2628 2704 2.711547 AGTAGACTTTCAAAGTGCCCCT 59.288 45.455 7.75 0.78 43.03 4.79
2647 2723 4.104086 TGAGGATATCAAACAGTGGGAGT 58.896 43.478 4.83 0.00 34.02 3.85
2663 2739 8.408601 GTGCTAATTAATCACAACATTGAGGAT 58.591 33.333 10.84 0.00 0.00 3.24
2703 2779 3.077543 AGGTTTAGGCAAGGGGAGATTTT 59.922 43.478 0.00 0.00 0.00 1.82
2710 2786 2.102578 CATGAAGGTTTAGGCAAGGGG 58.897 52.381 0.00 0.00 0.00 4.79
2719 2795 3.237268 AGGCAACCACATGAAGGTTTA 57.763 42.857 19.82 0.00 46.85 2.01
2754 2830 2.159014 ACACGACGCTAGAGAGAGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
2755 2831 1.205179 ACACGACGCTAGAGAGAGAGA 59.795 52.381 0.00 0.00 0.00 3.10
2819 2895 8.527810 TGAGTGTTTGAAGTAAATGGAAACTTT 58.472 29.630 0.00 0.00 36.10 2.66
2836 2912 2.483538 CCCCTTGGCTTTTGAGTGTTTG 60.484 50.000 0.00 0.00 0.00 2.93
2861 2937 9.574458 CGTCTTACATATATTGAGGTAATGAGG 57.426 37.037 0.00 0.00 0.00 3.86
2863 2939 9.908152 CACGTCTTACATATATTGAGGTAATGA 57.092 33.333 0.00 0.00 0.00 2.57
2864 2940 9.908152 TCACGTCTTACATATATTGAGGTAATG 57.092 33.333 0.00 0.00 0.00 1.90
2866 2942 9.740239 GTTCACGTCTTACATATATTGAGGTAA 57.260 33.333 0.00 0.00 0.00 2.85
2867 2943 8.355169 GGTTCACGTCTTACATATATTGAGGTA 58.645 37.037 0.00 0.00 0.00 3.08
2891 2967 1.065418 AGCGGAAGGATTTTCATCGGT 60.065 47.619 0.00 0.00 0.00 4.69
2904 2980 0.811915 TCGAAAGAGAGGAGCGGAAG 59.188 55.000 0.00 0.00 34.84 3.46
2952 3028 1.216178 CCATTTGCCAAAGGAGCGG 59.784 57.895 2.94 0.00 0.00 5.52
2965 3041 2.302733 GGGGCATCAAACAACTCCATTT 59.697 45.455 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.