Multiple sequence alignment - TraesCS5D01G267800

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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 TraesCS5D01G267800 chr5D 100.000 3119 0 0 1 3119 371274308 371271190 0.000000e+00 5760.0
1 TraesCS5D01G267800 chr5D 98.525 1627 12 1 581 2195 371018469 371020095 0.000000e+00 2861.0
2 TraesCS5D01G267800 chr5D 99.863 728 1 0 1 728 507876582 507877309 0.000000e+00 1339.0
3 TraesCS5D01G267800 chr5D 77.000 500 95 14 1597 2077 52365626 52366124 5.130000e-68 268.0
4 TraesCS5D01G267800 chr5D 95.413 109 5 0 2998 3106 371020297 371020405 1.150000e-39 174.0
5 TraesCS5D01G267800 chr5A 93.355 1851 82 16 744 2569 474025344 474027178 0.000000e+00 2699.0
6 TraesCS5D01G267800 chr5A 93.355 1851 82 16 744 2569 474158671 474160505 0.000000e+00 2699.0
7 TraesCS5D01G267800 chr5A 93.251 1852 83 16 744 2569 474290979 474292814 0.000000e+00 2689.0
8 TraesCS5D01G267800 chr5A 92.593 378 24 4 2570 2943 474160532 474160909 9.840000e-150 540.0
9 TraesCS5D01G267800 chr5A 92.328 378 25 4 2570 2943 474027205 474027582 4.580000e-148 534.0
10 TraesCS5D01G267800 chr5A 92.328 378 25 4 2570 2943 474292841 474293218 4.580000e-148 534.0
11 TraesCS5D01G267800 chr5A 91.549 284 21 1 5 288 540059219 540058939 3.770000e-104 388.0
12 TraesCS5D01G267800 chr5A 87.316 339 21 7 222 558 540059052 540058734 4.910000e-98 368.0
13 TraesCS5D01G267800 chr5A 97.340 188 4 1 2930 3117 474050664 474050850 5.020000e-83 318.0
14 TraesCS5D01G267800 chr5A 97.802 182 4 0 2930 3111 474316087 474316268 6.490000e-82 315.0
15 TraesCS5D01G267800 chr5A 96.341 164 5 1 2954 3117 474184164 474184326 5.130000e-68 268.0
16 TraesCS5D01G267800 chrUn 93.984 1762 64 15 744 2486 272189556 272191294 0.000000e+00 2628.0
17 TraesCS5D01G267800 chrUn 93.984 1762 64 15 744 2486 281134716 281136454 0.000000e+00 2628.0
18 TraesCS5D01G267800 chrUn 96.721 549 14 4 2575 3119 272191361 272191909 0.000000e+00 911.0
19 TraesCS5D01G267800 chrUn 96.721 549 14 4 2575 3119 281136521 281137069 0.000000e+00 911.0
20 TraesCS5D01G267800 chrUn 100.000 42 0 0 2528 2569 272191293 272191334 9.270000e-11 78.7
21 TraesCS5D01G267800 chrUn 100.000 42 0 0 2528 2569 281136453 281136494 9.270000e-11 78.7
22 TraesCS5D01G267800 chr5B 93.984 1762 64 15 744 2486 440546615 440544877 0.000000e+00 2628.0
23 TraesCS5D01G267800 chr5B 93.132 1325 49 15 744 2049 440557424 440556123 0.000000e+00 1905.0
24 TraesCS5D01G267800 chr5B 97.076 513 14 1 2601 3112 440540506 440539994 0.000000e+00 863.0
25 TraesCS5D01G267800 chr5B 80.800 250 29 7 305 540 426622839 426622595 8.890000e-41 178.0
26 TraesCS5D01G267800 chr5B 100.000 42 0 0 2528 2569 440544878 440544837 9.270000e-11 78.7
27 TraesCS5D01G267800 chr7D 99.451 728 4 0 1 728 171753052 171753779 0.000000e+00 1323.0
28 TraesCS5D01G267800 chr2A 87.671 511 39 8 222 728 679000763 679001253 9.700000e-160 573.0
29 TraesCS5D01G267800 chr2A 87.033 509 44 8 222 728 773233529 773233041 3.510000e-154 555.0
30 TraesCS5D01G267800 chr2A 86.842 456 36 10 240 691 342645029 342645464 3.620000e-134 488.0
31 TraesCS5D01G267800 chr2A 92.361 288 19 1 5 292 679000596 679000880 1.040000e-109 407.0
32 TraesCS5D01G267800 chr2A 90.592 287 21 2 5 291 342644847 342645127 2.940000e-100 375.0
33 TraesCS5D01G267800 chr3A 87.931 464 32 8 269 728 747185400 747185843 2.760000e-145 525.0
34 TraesCS5D01G267800 chr3D 81.618 544 58 11 222 728 144760148 144759610 2.240000e-111 412.0
35 TraesCS5D01G267800 chr3D 81.356 531 52 10 222 711 565689354 565688830 3.770000e-104 388.0
36 TraesCS5D01G267800 chr3D 89.456 294 26 5 2 292 144760323 144760032 1.770000e-97 366.0
37 TraesCS5D01G267800 chr2B 89.275 345 16 6 398 721 96969793 96970137 2.240000e-111 412.0
38 TraesCS5D01G267800 chr6D 81.051 533 58 12 219 728 430313611 430314123 4.880000e-103 385.0
39 TraesCS5D01G267800 chr6D 88.814 295 26 7 2 292 430313439 430313730 3.830000e-94 355.0
40 TraesCS5D01G267800 chr1B 80.474 548 63 11 219 728 435188090 435188631 2.270000e-101 379.0
41 TraesCS5D01G267800 chr1B 89.456 294 26 5 2 292 435187918 435188209 1.770000e-97 366.0
42 TraesCS5D01G267800 chr4A 88.435 294 29 5 2 292 630901980 630901689 1.780000e-92 350.0


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 TraesCS5D01G267800 chr5D 371271190 371274308 3118 True 5760.00 5760 100.000000 1 3119 1 chr5D.!!$R1 3118
1 TraesCS5D01G267800 chr5D 371018469 371020405 1936 False 1517.50 2861 96.969000 581 3106 2 chr5D.!!$F3 2525
2 TraesCS5D01G267800 chr5D 507876582 507877309 727 False 1339.00 1339 99.863000 1 728 1 chr5D.!!$F2 727
3 TraesCS5D01G267800 chr5A 474158671 474160909 2238 False 1619.50 2699 92.974000 744 2943 2 chr5A.!!$F5 2199
4 TraesCS5D01G267800 chr5A 474025344 474027582 2238 False 1616.50 2699 92.841500 744 2943 2 chr5A.!!$F4 2199
5 TraesCS5D01G267800 chr5A 474290979 474293218 2239 False 1611.50 2689 92.789500 744 2943 2 chr5A.!!$F6 2199
6 TraesCS5D01G267800 chrUn 272189556 272191909 2353 False 1205.90 2628 96.901667 744 3119 3 chrUn.!!$F1 2375
7 TraesCS5D01G267800 chrUn 281134716 281137069 2353 False 1205.90 2628 96.901667 744 3119 3 chrUn.!!$F2 2375
8 TraesCS5D01G267800 chr5B 440556123 440557424 1301 True 1905.00 1905 93.132000 744 2049 1 chr5B.!!$R3 1305
9 TraesCS5D01G267800 chr5B 440544837 440546615 1778 True 1353.35 2628 96.992000 744 2569 2 chr5B.!!$R4 1825
10 TraesCS5D01G267800 chr5B 440539994 440540506 512 True 863.00 863 97.076000 2601 3112 1 chr5B.!!$R2 511
11 TraesCS5D01G267800 chr7D 171753052 171753779 727 False 1323.00 1323 99.451000 1 728 1 chr7D.!!$F1 727
12 TraesCS5D01G267800 chr2A 679000596 679001253 657 False 490.00 573 90.016000 5 728 2 chr2A.!!$F2 723
13 TraesCS5D01G267800 chr2A 342644847 342645464 617 False 431.50 488 88.717000 5 691 2 chr2A.!!$F1 686
14 TraesCS5D01G267800 chr3D 144759610 144760323 713 True 389.00 412 85.537000 2 728 2 chr3D.!!$R2 726
15 TraesCS5D01G267800 chr3D 565688830 565689354 524 True 388.00 388 81.356000 222 711 1 chr3D.!!$R1 489
16 TraesCS5D01G267800 chr6D 430313439 430314123 684 False 370.00 385 84.932500 2 728 2 chr6D.!!$F1 726
17 TraesCS5D01G267800 chr1B 435187918 435188631 713 False 372.50 379 84.965000 2 728 2 chr1B.!!$F1 726

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
2049 2146 2.591715 GAGGTTGTGCGCAGTGGT 60.592 61.111 12.22 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2980 3237 5.772393 ATTGGTATTTGGTAGAGGTGACA 57.228 39.13 0.0 0.0 0.0 3.58 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
2049 2146 2.591715 GAGGTTGTGCGCAGTGGT 60.592 61.111 12.22 0.00 0.00 4.16
2085 2182 4.699637 TGATCAACCACAAGTCTAAACGT 58.300 39.130 0.00 0.00 0.00 3.99
2173 2313 3.004734 GTGTGTGGGGTTCATTTCTTCTG 59.995 47.826 0.00 0.00 0.00 3.02
2501 2727 9.751542 ATTACTATCACTTATGCTTCAGTACAC 57.248 33.333 0.00 0.00 0.00 2.90
2502 2728 6.574350 ACTATCACTTATGCTTCAGTACACC 58.426 40.000 0.00 0.00 0.00 4.16
2503 2729 4.202245 TCACTTATGCTTCAGTACACCC 57.798 45.455 0.00 0.00 0.00 4.61
2504 2730 3.838317 TCACTTATGCTTCAGTACACCCT 59.162 43.478 0.00 0.00 0.00 4.34
2505 2731 4.081642 TCACTTATGCTTCAGTACACCCTC 60.082 45.833 0.00 0.00 0.00 4.30
2506 2732 3.197983 ACTTATGCTTCAGTACACCCTCC 59.802 47.826 0.00 0.00 0.00 4.30
2507 2733 1.958288 ATGCTTCAGTACACCCTCCT 58.042 50.000 0.00 0.00 0.00 3.69
2508 2734 1.729586 TGCTTCAGTACACCCTCCTT 58.270 50.000 0.00 0.00 0.00 3.36
2509 2735 2.054799 TGCTTCAGTACACCCTCCTTT 58.945 47.619 0.00 0.00 0.00 3.11
2510 2736 3.244582 TGCTTCAGTACACCCTCCTTTA 58.755 45.455 0.00 0.00 0.00 1.85
2511 2737 3.649023 TGCTTCAGTACACCCTCCTTTAA 59.351 43.478 0.00 0.00 0.00 1.52
2512 2738 4.254492 GCTTCAGTACACCCTCCTTTAAG 58.746 47.826 0.00 0.00 0.00 1.85
2513 2739 3.975168 TCAGTACACCCTCCTTTAAGC 57.025 47.619 0.00 0.00 0.00 3.09
2514 2740 2.232941 TCAGTACACCCTCCTTTAAGCG 59.767 50.000 0.00 0.00 0.00 4.68
2515 2741 1.553704 AGTACACCCTCCTTTAAGCGG 59.446 52.381 0.00 0.00 0.00 5.52
2516 2742 1.551883 GTACACCCTCCTTTAAGCGGA 59.448 52.381 1.02 0.00 0.00 5.54
2517 2743 1.061546 ACACCCTCCTTTAAGCGGAA 58.938 50.000 1.02 0.00 0.00 4.30
2518 2744 1.271217 ACACCCTCCTTTAAGCGGAAC 60.271 52.381 1.02 0.00 0.00 3.62
2519 2745 1.003233 CACCCTCCTTTAAGCGGAACT 59.997 52.381 1.02 0.00 0.00 3.01
2520 2746 1.278413 ACCCTCCTTTAAGCGGAACTC 59.722 52.381 1.02 0.00 0.00 3.01
2521 2747 1.278127 CCCTCCTTTAAGCGGAACTCA 59.722 52.381 1.02 0.00 0.00 3.41
2522 2748 2.290071 CCCTCCTTTAAGCGGAACTCAA 60.290 50.000 1.02 0.00 0.00 3.02
2523 2749 3.610911 CCTCCTTTAAGCGGAACTCAAT 58.389 45.455 0.00 0.00 0.00 2.57
2524 2750 4.010349 CCTCCTTTAAGCGGAACTCAATT 58.990 43.478 0.00 0.00 0.00 2.32
2525 2751 4.095036 CCTCCTTTAAGCGGAACTCAATTC 59.905 45.833 0.00 0.00 36.48 2.17
2526 2752 4.647611 TCCTTTAAGCGGAACTCAATTCA 58.352 39.130 0.00 0.00 39.30 2.57
2527 2753 5.067273 TCCTTTAAGCGGAACTCAATTCAA 58.933 37.500 0.00 0.00 39.30 2.69
2528 2754 5.048991 TCCTTTAAGCGGAACTCAATTCAAC 60.049 40.000 0.00 0.00 39.30 3.18
2576 2828 2.012937 TATTGCTTTGGCTGCATTGC 57.987 45.000 0.46 0.46 40.34 3.56
2980 3237 2.247358 CCAAGCCCCACAAATACAACT 58.753 47.619 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2044 2141 1.194781 ATCTTGAGCCCGTCACCACT 61.195 55.000 0.00 0.0 33.71 4.00
2049 2146 1.194218 TGATCATCTTGAGCCCGTCA 58.806 50.000 0.00 0.0 30.48 4.35
2085 2182 4.219070 CAGTGGATTTCAATGCCTTCAAGA 59.781 41.667 0.00 0.0 34.59 3.02
2173 2313 6.963049 AGCATATAATTTCGTTACGATCCC 57.037 37.500 8.67 0.0 35.23 3.85
2486 2712 3.450904 AGGAGGGTGTACTGAAGCATAA 58.549 45.455 0.00 0.0 0.00 1.90
2487 2713 3.116096 AGGAGGGTGTACTGAAGCATA 57.884 47.619 0.00 0.0 0.00 3.14
2488 2714 1.958288 AGGAGGGTGTACTGAAGCAT 58.042 50.000 0.00 0.0 0.00 3.79
2489 2715 1.729586 AAGGAGGGTGTACTGAAGCA 58.270 50.000 0.00 0.0 0.00 3.91
2490 2716 2.861147 AAAGGAGGGTGTACTGAAGC 57.139 50.000 0.00 0.0 0.00 3.86
2491 2717 4.254492 GCTTAAAGGAGGGTGTACTGAAG 58.746 47.826 0.00 0.0 0.00 3.02
2492 2718 3.306502 CGCTTAAAGGAGGGTGTACTGAA 60.307 47.826 0.00 0.0 0.00 3.02
2493 2719 2.232941 CGCTTAAAGGAGGGTGTACTGA 59.767 50.000 0.00 0.0 0.00 3.41
2494 2720 2.618053 CGCTTAAAGGAGGGTGTACTG 58.382 52.381 0.00 0.0 0.00 2.74
2495 2721 1.553704 CCGCTTAAAGGAGGGTGTACT 59.446 52.381 0.00 0.0 0.00 2.73
2496 2722 1.551883 TCCGCTTAAAGGAGGGTGTAC 59.448 52.381 0.00 0.0 33.19 2.90
2497 2723 1.941377 TCCGCTTAAAGGAGGGTGTA 58.059 50.000 0.00 0.0 33.19 2.90
2498 2724 1.061546 TTCCGCTTAAAGGAGGGTGT 58.938 50.000 0.40 0.0 39.22 4.16
2499 2725 1.003233 AGTTCCGCTTAAAGGAGGGTG 59.997 52.381 0.40 0.0 39.22 4.61
2500 2726 1.278413 GAGTTCCGCTTAAAGGAGGGT 59.722 52.381 0.40 0.0 39.22 4.34
2501 2727 1.278127 TGAGTTCCGCTTAAAGGAGGG 59.722 52.381 0.40 0.0 39.22 4.30
2502 2728 2.762535 TGAGTTCCGCTTAAAGGAGG 57.237 50.000 0.40 0.0 39.22 4.30
2503 2729 4.695455 TGAATTGAGTTCCGCTTAAAGGAG 59.305 41.667 0.40 0.0 39.22 3.69
2504 2730 4.647611 TGAATTGAGTTCCGCTTAAAGGA 58.352 39.130 0.00 0.0 35.91 3.36
2505 2731 5.154222 GTTGAATTGAGTTCCGCTTAAAGG 58.846 41.667 0.00 0.0 35.91 3.11
2506 2732 5.757886 TGTTGAATTGAGTTCCGCTTAAAG 58.242 37.500 0.00 0.0 35.91 1.85
2507 2733 5.759506 TGTTGAATTGAGTTCCGCTTAAA 57.240 34.783 0.00 0.0 35.91 1.52
2508 2734 5.759506 TTGTTGAATTGAGTTCCGCTTAA 57.240 34.783 0.00 0.0 35.91 1.85
2509 2735 5.759506 TTTGTTGAATTGAGTTCCGCTTA 57.240 34.783 0.00 0.0 35.91 3.09
2510 2736 4.647424 TTTGTTGAATTGAGTTCCGCTT 57.353 36.364 0.00 0.0 35.91 4.68
2511 2737 4.647424 TTTTGTTGAATTGAGTTCCGCT 57.353 36.364 0.00 0.0 35.91 5.52
2512 2738 5.905480 AATTTTGTTGAATTGAGTTCCGC 57.095 34.783 0.00 0.0 35.91 5.54
2513 2739 9.619316 TGTATAATTTTGTTGAATTGAGTTCCG 57.381 29.630 0.00 0.0 35.91 4.30
2595 2847 9.019656 GCATGTTCCATGGGTGTATATAAATAA 57.980 33.333 13.02 0.0 0.00 1.40
2717 2972 1.352017 TCACCATTGGCACTGATGAGT 59.648 47.619 6.39 0.0 0.00 3.41
2980 3237 5.772393 ATTGGTATTTGGTAGAGGTGACA 57.228 39.130 0.00 0.0 0.00 3.58


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

AutoCloner maintained by Alex Coulton.