Multiple sequence alignment - TraesCS2A01G252500

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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 TraesCS2A01G252500 chr2A 100.000 3495 0 0 1 3495 384157664 384154170 0 6455
1 TraesCS2A01G252500 chr2A 97.502 2402 57 3 552 2950 685100063 685097662 0 4100
2 TraesCS2A01G252500 chr2A 97.004 2403 65 6 550 2948 284804167 284806566 0 4032
3 TraesCS2A01G252500 chr2A 96.721 549 18 0 1 549 384170219 384169671 0 915
4 TraesCS2A01G252500 chr2A 92.294 558 38 2 1 553 604841482 604842039 0 787
5 TraesCS2A01G252500 chr6A 97.586 2403 56 2 550 2950 158979213 158976811 0 4115
6 TraesCS2A01G252500 chr6A 97.692 520 12 0 2972 3491 67508159 67508678 0 894
7 TraesCS2A01G252500 chr6A 93.091 550 32 4 1 549 249049335 249049879 0 800
8 TraesCS2A01G252500 chr6A 93.091 550 32 4 1 549 249050829 249051373 0 800
9 TraesCS2A01G252500 chr1A 97.337 2403 59 4 550 2950 70941513 70939114 0 4078
10 TraesCS2A01G252500 chr1A 96.947 524 16 0 2972 3495 70930956 70930433 0 880
11 TraesCS2A01G252500 chr1A 93.455 550 31 3 1 549 273061222 273061767 0 811
12 TraesCS2A01G252500 chr7A 97.171 2404 61 6 550 2950 245431802 245429403 0 4056
13 TraesCS2A01G252500 chr7A 97.519 524 13 0 2972 3495 245421268 245420745 0 896
14 TraesCS2A01G252500 chr7A 94.161 548 27 3 3 549 43558058 43557515 0 830
15 TraesCS2A01G252500 chr7A 93.091 550 33 3 1 549 43568766 43568221 0 800
16 TraesCS2A01G252500 chr5A 97.163 2397 66 2 556 2950 541981155 541983551 0 4048
17 TraesCS2A01G252500 chr5A 97.006 2405 68 3 550 2950 34939112 34936708 0 4039
18 TraesCS2A01G252500 chr5A 96.966 2406 66 5 550 2950 465658369 465660772 0 4032
19 TraesCS2A01G252500 chr5A 97.519 524 13 0 2972 3495 465668973 465669496 0 896
20 TraesCS2A01G252500 chr5A 97.328 524 14 0 2972 3495 541991749 541992272 0 891
21 TraesCS2A01G252500 chr5A 97.137 524 15 0 2972 3495 141916890 141917413 0 885
22 TraesCS2A01G252500 chr5A 96.947 524 16 0 2972 3495 528086366 528086889 0 880
23 TraesCS2A01G252500 chr5A 93.273 550 32 3 1 549 683029386 683029931 0 806
24 TraesCS2A01G252500 chr5A 93.091 550 33 3 1 549 683020972 683020427 0 800
25 TraesCS2A01G252500 chr3A 96.801 2407 70 5 550 2950 662006153 662003748 0 4012
26 TraesCS2A01G252500 chr3A 97.328 524 14 0 2972 3495 417408264 417408787 0 891
27 TraesCS2A01G252500 chr3A 97.500 520 13 0 2972 3491 34460559 34460040 0 889


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 TraesCS2A01G252500 chr2A 384154170 384157664 3494 True 6455 6455 100.000 1 3495 1 chr2A.!!$R1 3494
1 TraesCS2A01G252500 chr2A 685097662 685100063 2401 True 4100 4100 97.502 552 2950 1 chr2A.!!$R3 2398
2 TraesCS2A01G252500 chr2A 284804167 284806566 2399 False 4032 4032 97.004 550 2948 1 chr2A.!!$F1 2398
3 TraesCS2A01G252500 chr2A 384169671 384170219 548 True 915 915 96.721 1 549 1 chr2A.!!$R2 548
4 TraesCS2A01G252500 chr2A 604841482 604842039 557 False 787 787 92.294 1 553 1 chr2A.!!$F2 552
5 TraesCS2A01G252500 chr6A 158976811 158979213 2402 True 4115 4115 97.586 550 2950 1 chr6A.!!$R1 2400
6 TraesCS2A01G252500 chr6A 67508159 67508678 519 False 894 894 97.692 2972 3491 1 chr6A.!!$F1 519
7 TraesCS2A01G252500 chr6A 249049335 249051373 2038 False 800 800 93.091 1 549 2 chr6A.!!$F2 548
8 TraesCS2A01G252500 chr1A 70939114 70941513 2399 True 4078 4078 97.337 550 2950 1 chr1A.!!$R2 2400
9 TraesCS2A01G252500 chr1A 70930433 70930956 523 True 880 880 96.947 2972 3495 1 chr1A.!!$R1 523
10 TraesCS2A01G252500 chr1A 273061222 273061767 545 False 811 811 93.455 1 549 1 chr1A.!!$F1 548
11 TraesCS2A01G252500 chr7A 245429403 245431802 2399 True 4056 4056 97.171 550 2950 1 chr7A.!!$R4 2400
12 TraesCS2A01G252500 chr7A 245420745 245421268 523 True 896 896 97.519 2972 3495 1 chr7A.!!$R3 523
13 TraesCS2A01G252500 chr7A 43557515 43558058 543 True 830 830 94.161 3 549 1 chr7A.!!$R1 546
14 TraesCS2A01G252500 chr7A 43568221 43568766 545 True 800 800 93.091 1 549 1 chr7A.!!$R2 548
15 TraesCS2A01G252500 chr5A 541981155 541983551 2396 False 4048 4048 97.163 556 2950 1 chr5A.!!$F5 2394
16 TraesCS2A01G252500 chr5A 34936708 34939112 2404 True 4039 4039 97.006 550 2950 1 chr5A.!!$R1 2400
17 TraesCS2A01G252500 chr5A 465658369 465660772 2403 False 4032 4032 96.966 550 2950 1 chr5A.!!$F2 2400
18 TraesCS2A01G252500 chr5A 465668973 465669496 523 False 896 896 97.519 2972 3495 1 chr5A.!!$F3 523
19 TraesCS2A01G252500 chr5A 541991749 541992272 523 False 891 891 97.328 2972 3495 1 chr5A.!!$F6 523
20 TraesCS2A01G252500 chr5A 141916890 141917413 523 False 885 885 97.137 2972 3495 1 chr5A.!!$F1 523
21 TraesCS2A01G252500 chr5A 528086366 528086889 523 False 880 880 96.947 2972 3495 1 chr5A.!!$F4 523
22 TraesCS2A01G252500 chr5A 683029386 683029931 545 False 806 806 93.273 1 549 1 chr5A.!!$F7 548
23 TraesCS2A01G252500 chr5A 683020427 683020972 545 True 800 800 93.091 1 549 1 chr5A.!!$R2 548
24 TraesCS2A01G252500 chr3A 662003748 662006153 2405 True 4012 4012 96.801 550 2950 1 chr3A.!!$R2 2400
25 TraesCS2A01G252500 chr3A 417408264 417408787 523 False 891 891 97.328 2972 3495 1 chr3A.!!$F1 523
26 TraesCS2A01G252500 chr3A 34460040 34460559 519 True 889 889 97.500 2972 3491 1 chr3A.!!$R1 519

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
345 1847 0.904649 TGCTAGCTGCTGGTGTGTAT 59.095 50.0 17.23 0.0 43.37 2.29 F
1282 2786 0.400213 AAAACCTCCACAGATGGCGA 59.600 50.0 0.00 0.0 46.80 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 2806 1.131638 ACACCAAGCAGAGTTCCTCA 58.868 50.0 0.0 0.0 32.06 3.86 R
3218 4735 0.532573 GTGGCTCCTCTGTTCATCGA 59.467 55.0 0.0 0.0 0.00 3.59 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
271 273 4.446889 CCTTGAGCATATAAAAGGAGGCCT 60.447 45.833 3.86 3.86 41.49 5.19
345 1847 0.904649 TGCTAGCTGCTGGTGTGTAT 59.095 50.000 17.23 0.00 43.37 2.29
404 1906 1.450312 CGCAAAGCAGGAGTAGGGG 60.450 63.158 0.00 0.00 0.00 4.79
596 2098 7.499321 AAACAATACTTAAACATCCACACGA 57.501 32.000 0.00 0.00 0.00 4.35
1025 2528 4.699522 GGAACCGTCCGCCAAGCT 62.700 66.667 0.00 0.00 33.05 3.74
1044 2547 0.530288 TTCATCATGCCGAGACGTCA 59.470 50.000 19.50 0.00 0.00 4.35
1045 2548 0.530288 TCATCATGCCGAGACGTCAA 59.470 50.000 19.50 0.00 0.00 3.18
1282 2786 0.400213 AAAACCTCCACAGATGGCGA 59.600 50.000 0.00 0.00 46.80 5.54
1385 2890 6.946340 TGTTCATTCATCTGTGTACCAGTAT 58.054 36.000 10.08 2.63 42.19 2.12
2092 3602 1.267121 AGCGCCTCAAAGACTTCCTA 58.733 50.000 2.29 0.00 0.00 2.94
2143 3653 2.655090 TCAGCATTGGAGGTGACAAA 57.345 45.000 0.00 0.00 40.73 2.83
2200 3710 3.304592 CCAACAACTTCATCGACATGCAA 60.305 43.478 0.00 0.00 0.00 4.08
2408 3918 5.245531 TGTACAAGTCATGGAAGACAATCC 58.754 41.667 0.00 0.00 40.98 3.01
2442 3952 5.480073 TGACAGGTTGGGATATTTCAAAAGG 59.520 40.000 0.00 0.00 0.00 3.11
2646 4156 6.371548 TGAACAAGTTTGCCTATGTCTATCAC 59.628 38.462 0.00 0.00 0.00 3.06
2891 4404 5.670149 AGACATGAACGGTAGTACTATCG 57.330 43.478 29.36 29.36 44.60 2.92
2950 4467 6.764560 ACTAAAAAGACTAAGTTTCAGCCGAA 59.235 34.615 0.00 0.00 0.00 4.30
2951 4468 6.445357 AAAAAGACTAAGTTTCAGCCGAAA 57.555 33.333 0.00 0.00 38.83 3.46
2959 4476 1.365699 TTTCAGCCGAAACTATCCGC 58.634 50.000 0.00 0.00 36.19 5.54
2960 4477 0.248012 TTCAGCCGAAACTATCCGCA 59.752 50.000 0.00 0.00 35.09 5.69
2961 4478 0.179111 TCAGCCGAAACTATCCGCAG 60.179 55.000 0.00 0.00 35.09 5.18
2962 4479 0.179111 CAGCCGAAACTATCCGCAGA 60.179 55.000 0.00 0.00 35.09 4.26
2963 4480 0.535335 AGCCGAAACTATCCGCAGAA 59.465 50.000 0.00 0.00 35.09 3.02
2964 4481 1.139058 AGCCGAAACTATCCGCAGAAT 59.861 47.619 0.00 0.00 35.09 2.40
2965 4482 1.527311 GCCGAAACTATCCGCAGAATC 59.473 52.381 0.00 0.00 33.17 2.52
2966 4483 2.803492 GCCGAAACTATCCGCAGAATCT 60.803 50.000 0.00 0.00 33.17 2.40
2967 4484 3.458189 CCGAAACTATCCGCAGAATCTT 58.542 45.455 0.00 0.00 0.00 2.40
2968 4485 3.491267 CCGAAACTATCCGCAGAATCTTC 59.509 47.826 0.00 0.00 0.00 2.87
2969 4486 4.363999 CGAAACTATCCGCAGAATCTTCT 58.636 43.478 0.00 0.00 38.25 2.85
3026 4543 3.496884 AGTACAAAACACATACCACTGCG 59.503 43.478 0.00 0.00 0.00 5.18
3218 4735 2.702592 TTGTCAAACCTCGTGGACTT 57.297 45.000 11.17 0.16 37.04 3.01
3319 4836 2.136298 TGGGAAACAGCTTTCACACA 57.864 45.000 0.00 0.00 43.59 3.72
3339 4856 2.139323 TGGACTACGCCTCTATGTGT 57.861 50.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 273 1.369692 CCCCTCTACGTTGCACACA 59.630 57.895 0.00 0.00 0.00 3.72
306 1808 0.464036 AGACCAAGCGTGAGTGTTCA 59.536 50.000 0.00 0.00 0.00 3.18
365 1867 3.441572 CGGTCTGGATTGATTTCTTGCTT 59.558 43.478 0.00 0.00 0.00 3.91
380 1882 2.032528 TCCTGCTTTGCGGTCTGG 59.967 61.111 0.00 0.00 32.22 3.86
424 1926 1.404986 CGAGCGATTTACCCAGGTTCA 60.405 52.381 0.00 0.00 0.00 3.18
509 2011 3.151710 CACCTATGGGACCGGCGA 61.152 66.667 9.30 0.00 36.25 5.54
791 2293 2.876879 CGCCGTTTGCACTTCGTCA 61.877 57.895 0.00 0.00 41.33 4.35
883 2386 3.054065 GGAGAGATGGAAGACAATGGGTT 60.054 47.826 0.00 0.00 0.00 4.11
1025 2528 0.530288 TGACGTCTCGGCATGATGAA 59.470 50.000 17.92 0.00 41.22 2.57
1282 2786 1.889105 CGCACAACTGCAGGACTGT 60.889 57.895 19.93 14.95 44.50 3.55
1302 2806 1.131638 ACACCAAGCAGAGTTCCTCA 58.868 50.000 0.00 0.00 32.06 3.86
1404 2909 9.959721 TTCATCTAGCTAGGAAACAGTTTTTAT 57.040 29.630 20.58 0.00 0.00 1.40
1411 2916 7.341445 AGTAGTTCATCTAGCTAGGAAACAG 57.659 40.000 20.58 5.06 0.00 3.16
2092 3602 2.635915 TGTGTACAATTTCTCCTCCCGT 59.364 45.455 0.00 0.00 0.00 5.28
2143 3653 1.986757 AGACTCCTGCAGCATCCGT 60.987 57.895 8.66 0.00 0.00 4.69
2408 3918 1.264020 CCAACCTGTCACGATGTTGTG 59.736 52.381 0.00 0.00 41.28 3.33
2963 4480 9.950496 AGTTGTACTTGTAATGATTCAGAAGAT 57.050 29.630 0.00 0.00 0.00 2.40
2966 4483 9.151471 GCTAGTTGTACTTGTAATGATTCAGAA 57.849 33.333 0.00 0.00 0.00 3.02
2967 4484 8.311109 TGCTAGTTGTACTTGTAATGATTCAGA 58.689 33.333 0.00 0.00 0.00 3.27
2968 4485 8.479313 TGCTAGTTGTACTTGTAATGATTCAG 57.521 34.615 0.00 0.00 0.00 3.02
2969 4486 8.840833 TTGCTAGTTGTACTTGTAATGATTCA 57.159 30.769 0.00 0.00 0.00 2.57
2970 4487 9.151471 TCTTGCTAGTTGTACTTGTAATGATTC 57.849 33.333 0.00 0.00 27.79 2.52
2978 4495 5.018539 TGTGTCTTGCTAGTTGTACTTGT 57.981 39.130 0.00 0.00 0.00 3.16
3218 4735 0.532573 GTGGCTCCTCTGTTCATCGA 59.467 55.000 0.00 0.00 0.00 3.59
3319 4836 2.623889 GACACATAGAGGCGTAGTCCAT 59.376 50.000 0.00 0.00 0.00 3.41
3339 4856 5.303845 AGATGTCAGATCGAAATCCTGATGA 59.696 40.000 11.67 4.90 38.97 2.92


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

AutoCloner maintained by Alex Coulton.