Multiple sequence alignment - TraesCS1A01G222500

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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 TraesCS1A01G222500 chr1A 100.000 2855 0 0 1 2855 392086142 392083288 0.000000e+00 5273
1 TraesCS1A01G222500 chr1A 86.728 437 51 6 1175 1606 492046028 492046462 1.990000e-131 479
2 TraesCS1A01G222500 chr1B 95.510 2851 74 30 2 2831 422564398 422561581 0.000000e+00 4506
3 TraesCS1A01G222500 chr1B 86.005 443 52 9 1169 1606 529288172 529288609 1.550000e-127 466
4 TraesCS1A01G222500 chr1D 96.060 2716 68 14 147 2838 311989781 311987081 0.000000e+00 4386
5 TraesCS1A01G222500 chr1D 88.806 402 41 4 1207 1606 393750476 393750077 9.190000e-135 490
6 TraesCS1A01G222500 chr1D 92.500 160 7 3 2 161 311989961 311989807 1.030000e-54 224
7 TraesCS1A01G222500 chr3B 88.942 416 42 4 1207 1620 598468515 598468102 7.060000e-141 510
8 TraesCS1A01G222500 chr3D 88.221 416 45 4 1207 1620 455106860 455106447 7.110000e-136 494
9 TraesCS1A01G222500 chr3A 87.981 416 46 4 1207 1620 597547647 597547234 3.310000e-134 488
10 TraesCS1A01G222500 chr6B 85.287 435 54 9 1207 1633 687525401 687524969 9.390000e-120 440


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 TraesCS1A01G222500 chr1A 392083288 392086142 2854 True 5273 5273 100.00 1 2855 1 chr1A.!!$R1 2854
1 TraesCS1A01G222500 chr1B 422561581 422564398 2817 True 4506 4506 95.51 2 2831 1 chr1B.!!$R1 2829
2 TraesCS1A01G222500 chr1D 311987081 311989961 2880 True 2305 4386 94.28 2 2838 2 chr1D.!!$R2 2836

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
939 1005 0.109723 CGTAGGAGGGGAGAGAGAGG 59.89 65.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2746 2822 0.74299 ATCGTACCGGCAACCACATG 60.743 55.0 0.0 0.0 0.0 3.21 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
25 26 6.723298 TCTCCTCTCTAATCTCCAATCAAC 57.277 41.667 0.00 0.00 0.00 3.18
58 59 5.506815 CGTAGCTACAAACCATAGAATCCGA 60.507 44.000 23.21 0.00 0.00 4.55
141 142 5.067674 GGATGCACACCTATGCTATTTTGAA 59.932 40.000 0.00 0.00 46.28 2.69
142 143 6.239120 GGATGCACACCTATGCTATTTTGAAT 60.239 38.462 0.00 0.00 46.28 2.57
321 365 6.646240 ACAAAAGCATACATAGGCAACAAAAG 59.354 34.615 0.00 0.00 41.41 2.27
414 458 3.753294 AGAACAACAAGGACACGATCT 57.247 42.857 0.00 0.00 0.00 2.75
478 522 3.708631 TGATTTCAACCCCAAGAAAAGCA 59.291 39.130 0.00 0.00 37.30 3.91
484 528 3.173953 ACCCCAAGAAAAGCATCATCA 57.826 42.857 0.00 0.00 0.00 3.07
487 531 4.263905 ACCCCAAGAAAAGCATCATCAGTA 60.264 41.667 0.00 0.00 0.00 2.74
489 533 5.009410 CCCCAAGAAAAGCATCATCAGTATC 59.991 44.000 0.00 0.00 0.00 2.24
588 637 4.318546 CCGAAGATACGAATAAAAAGCCGG 60.319 45.833 0.00 0.00 35.09 6.13
819 872 3.181405 ACAAGTCTTCTTCTACCTCCCCT 60.181 47.826 0.00 0.00 0.00 4.79
883 940 1.494721 CCAGGTAGCCTCTCTCTCTCT 59.505 57.143 0.00 0.00 0.00 3.10
884 941 2.487265 CCAGGTAGCCTCTCTCTCTCTC 60.487 59.091 0.00 0.00 0.00 3.20
925 982 4.900664 ACAAAAACAAGAAACGACGTAGG 58.099 39.130 0.00 0.00 0.00 3.18
939 1005 0.109723 CGTAGGAGGGGAGAGAGAGG 59.890 65.000 0.00 0.00 0.00 3.69
982 1048 4.087892 TGGGAGAGAAGCAGGCGC 62.088 66.667 0.00 0.00 38.99 6.53
1113 1179 0.322277 CTGAAGAGCCACAGCCACAT 60.322 55.000 0.00 0.00 41.25 3.21
1698 1764 3.437795 GAGGACGACGAGGGCGAA 61.438 66.667 0.00 0.00 41.64 4.70
1722 1788 1.146041 ACAGTCCGCTGAGCAACAA 59.854 52.632 4.88 0.00 45.28 2.83
1724 1790 1.956170 AGTCCGCTGAGCAACAACG 60.956 57.895 4.88 0.00 37.75 4.10
1726 1792 4.724697 CCGCTGAGCAACAACGCG 62.725 66.667 3.53 3.53 40.94 6.01
1922 1991 4.202182 CCAAATTCTAATCCCTGCACCATG 60.202 45.833 0.00 0.00 0.00 3.66
2007 2082 4.193865 AGAGAGAGGTCTAAGTAGTTCGC 58.806 47.826 0.00 0.00 30.97 4.70
2335 2411 2.034685 CAGTCTCAACGGACACTCTTCA 59.965 50.000 0.00 0.00 38.57 3.02
2351 2427 4.177026 CTCTTCAGAAAGGGACGTACATG 58.823 47.826 0.00 0.00 34.65 3.21
2476 2552 1.998315 CTTCGGAGACAATGAGCAGTG 59.002 52.381 0.00 0.00 34.32 3.66
2536 2612 5.469760 TGTGGTCTGTGAAATGTATGAACAG 59.530 40.000 0.00 0.00 39.49 3.16
2746 2822 3.997021 TCTCATCGCCTTTCTTTTCTCAC 59.003 43.478 0.00 0.00 0.00 3.51
2747 2823 3.738982 TCATCGCCTTTCTTTTCTCACA 58.261 40.909 0.00 0.00 0.00 3.58
2834 2912 8.921353 TCTATTATACTTACTCACAGAGGGTC 57.079 38.462 0.00 0.00 33.35 4.46
2838 2916 3.521727 ACTTACTCACAGAGGGTCCATT 58.478 45.455 0.00 0.00 33.35 3.16
2839 2917 3.261897 ACTTACTCACAGAGGGTCCATTG 59.738 47.826 0.00 0.00 33.35 2.82
2840 2918 1.734655 ACTCACAGAGGGTCCATTGT 58.265 50.000 0.00 0.00 33.35 2.71
2841 2919 2.057922 ACTCACAGAGGGTCCATTGTT 58.942 47.619 0.00 0.00 33.35 2.83
2842 2920 2.039084 ACTCACAGAGGGTCCATTGTTC 59.961 50.000 0.00 0.00 33.35 3.18
2843 2921 2.038952 CTCACAGAGGGTCCATTGTTCA 59.961 50.000 0.00 0.00 0.00 3.18
2844 2922 2.038952 TCACAGAGGGTCCATTGTTCAG 59.961 50.000 0.00 0.00 0.00 3.02
2845 2923 2.057922 ACAGAGGGTCCATTGTTCAGT 58.942 47.619 0.00 0.00 0.00 3.41
2846 2924 3.007940 CACAGAGGGTCCATTGTTCAGTA 59.992 47.826 0.00 0.00 0.00 2.74
2847 2925 3.261897 ACAGAGGGTCCATTGTTCAGTAG 59.738 47.826 0.00 0.00 0.00 2.57
2848 2926 3.261897 CAGAGGGTCCATTGTTCAGTAGT 59.738 47.826 0.00 0.00 0.00 2.73
2849 2927 3.261897 AGAGGGTCCATTGTTCAGTAGTG 59.738 47.826 0.00 0.00 0.00 2.74
2850 2928 2.305927 AGGGTCCATTGTTCAGTAGTGG 59.694 50.000 0.00 0.00 0.00 4.00
2851 2929 2.039879 GGGTCCATTGTTCAGTAGTGGT 59.960 50.000 0.00 0.00 0.00 4.16
2852 2930 3.262405 GGGTCCATTGTTCAGTAGTGGTA 59.738 47.826 0.00 0.00 0.00 3.25
2853 2931 4.080526 GGGTCCATTGTTCAGTAGTGGTAT 60.081 45.833 0.00 0.00 0.00 2.73
2854 2932 5.497474 GGTCCATTGTTCAGTAGTGGTATT 58.503 41.667 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.180946 TGTTGATTGGAGATTAGAGAGGAGAAA 59.819 37.037 0.00 0.00 0.00 2.52
25 26 1.790755 TTGTAGCTACGTGGCAGTTG 58.209 50.000 26.36 0.00 34.17 3.16
58 59 2.833631 AGACTCACGGACGGATTTTT 57.166 45.000 0.00 0.00 0.00 1.94
141 142 6.865726 GGCGCGATATTTGATATATCAGAGAT 59.134 38.462 12.10 13.30 38.19 2.75
142 143 6.209361 GGCGCGATATTTGATATATCAGAGA 58.791 40.000 12.10 9.07 38.19 3.10
478 522 4.560739 TGAACCCTCTGGATACTGATGAT 58.439 43.478 0.00 0.00 44.16 2.45
484 528 1.344496 CCCCTGAACCCTCTGGATACT 60.344 57.143 0.02 0.00 41.99 2.12
487 531 0.722676 TACCCCTGAACCCTCTGGAT 59.277 55.000 0.02 0.00 41.99 3.41
489 533 0.839946 CATACCCCTGAACCCTCTGG 59.160 60.000 0.00 0.00 39.74 3.86
588 637 0.907704 ATTTCTTTTTCCCCGGCCCC 60.908 55.000 0.00 0.00 0.00 5.80
819 872 2.287584 AGGGAATGGAATGGGTTCAGA 58.712 47.619 0.00 0.00 36.01 3.27
872 929 2.483714 CGTGGAGGAGAGAGAGAGAGAG 60.484 59.091 0.00 0.00 0.00 3.20
883 940 3.071206 GCAGGAGCGTGGAGGAGA 61.071 66.667 0.00 0.00 0.00 3.71
884 941 4.154347 GGCAGGAGCGTGGAGGAG 62.154 72.222 0.00 0.00 43.41 3.69
925 982 0.478507 CTCTCCCTCTCTCTCCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
939 1005 1.107945 GCTACCAGTGGTCTCTCTCC 58.892 60.000 20.72 0.00 37.09 3.71
1581 1647 2.717580 TGCGCTTCTTCTTCTCGTAA 57.282 45.000 9.73 0.00 0.00 3.18
1694 1760 3.103911 CGGACTGTGACGGTTCGC 61.104 66.667 12.85 0.00 34.87 4.70
1698 1764 2.910479 TCAGCGGACTGTGACGGT 60.910 61.111 0.00 0.00 44.77 4.83
2007 2082 4.406972 ACCCCGTCATATCATGATCCTATG 59.593 45.833 12.53 10.83 42.04 2.23
2335 2411 4.039973 TCAGAAACATGTACGTCCCTTTCT 59.960 41.667 0.00 0.00 0.00 2.52
2351 2427 3.141398 TCATCAGCCACTGTTCAGAAAC 58.859 45.455 6.83 0.00 35.85 2.78
2503 2579 7.274447 ACATTTCACAGACCACATGAATTTTT 58.726 30.769 0.00 0.00 32.61 1.94
2506 2582 7.394077 TCATACATTTCACAGACCACATGAATT 59.606 33.333 0.00 0.00 32.61 2.17
2507 2583 6.885918 TCATACATTTCACAGACCACATGAAT 59.114 34.615 0.00 0.00 32.61 2.57
2536 2612 2.545952 CGTGTATGTGCATACCTCCCTC 60.546 54.545 16.79 3.67 42.19 4.30
2746 2822 0.742990 ATCGTACCGGCAACCACATG 60.743 55.000 0.00 0.00 0.00 3.21
2747 2823 0.825410 TATCGTACCGGCAACCACAT 59.175 50.000 0.00 0.00 0.00 3.21
2826 2904 2.867109 ACTGAACAATGGACCCTCTG 57.133 50.000 0.00 0.00 0.00 3.35
2831 2909 3.418684 ACCACTACTGAACAATGGACC 57.581 47.619 0.00 0.00 34.38 4.46


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

AutoCloner maintained by Alex Coulton.