Multiple sequence alignment - TraesCS4B01G238200

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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 TraesCS4B01G238200 chr4B 100.000 2234 0 0 1 2234 495567988 495565755 0.000000e+00 4126
1 TraesCS4B01G238200 chr6B 98.124 2239 35 5 1 2234 596601832 596604068 0.000000e+00 3895
2 TraesCS4B01G238200 chrUn 97.989 2238 40 3 1 2234 171008312 171006076 0.000000e+00 3879
3 TraesCS4B01G238200 chr7A 97.855 2238 42 3 1 2233 638507638 638509874 0.000000e+00 3862
4 TraesCS4B01G238200 chr7A 97.722 2239 44 4 1 2234 708245651 708243415 0.000000e+00 3845
5 TraesCS4B01G238200 chr1B 97.720 2237 46 4 1 2234 672541248 672539014 0.000000e+00 3843
6 TraesCS4B01G238200 chr5B 97.500 2240 49 4 1 2234 567280022 567277784 0.000000e+00 3819
7 TraesCS4B01G238200 chr7B 97.484 1908 40 6 330 2234 54050172 54052074 0.000000e+00 3251
8 TraesCS4B01G238200 chr7B 97.468 316 8 0 1 316 54049122 54049437 7.020000e-150 540


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 TraesCS4B01G238200 chr4B 495565755 495567988 2233 True 4126.0 4126 100.000 1 2234 1 chr4B.!!$R1 2233
1 TraesCS4B01G238200 chr6B 596601832 596604068 2236 False 3895.0 3895 98.124 1 2234 1 chr6B.!!$F1 2233
2 TraesCS4B01G238200 chrUn 171006076 171008312 2236 True 3879.0 3879 97.989 1 2234 1 chrUn.!!$R1 2233
3 TraesCS4B01G238200 chr7A 638507638 638509874 2236 False 3862.0 3862 97.855 1 2233 1 chr7A.!!$F1 2232
4 TraesCS4B01G238200 chr7A 708243415 708245651 2236 True 3845.0 3845 97.722 1 2234 1 chr7A.!!$R1 2233
5 TraesCS4B01G238200 chr1B 672539014 672541248 2234 True 3843.0 3843 97.720 1 2234 1 chr1B.!!$R1 2233
6 TraesCS4B01G238200 chr5B 567277784 567280022 2238 True 3819.0 3819 97.500 1 2234 1 chr5B.!!$R1 2233
7 TraesCS4B01G238200 chr7B 54049122 54052074 2952 False 1895.5 3251 97.476 1 2234 2 chr7B.!!$F1 2233

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
856 1578 0.612453 AGAAGGGTCGTCTGAGGGTC 60.612 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 2449 0.833949 GGTCCTTCCTTAGCTCCAGG 59.166 60.0 5.62 5.62 0.0 4.45 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
87 88 6.143278 GCGGTTGTTCGTATTTCATTTTCTTT 59.857 34.615 0.00 0.0 0.00 2.52
147 148 8.807118 ACTCACTGAATTACTTACTGAATCTCA 58.193 33.333 0.00 0.0 0.00 3.27
201 202 1.654954 CGGGTCGATCAGAGGTTCGT 61.655 60.000 0.00 0.0 37.47 3.85
444 581 7.969690 TGAAATTTGGATATTAAGGAAGCCA 57.030 32.000 0.00 0.0 0.00 4.75
451 588 9.653516 TTTGGATATTAAGGAAGCCATATTTCA 57.346 29.630 0.00 0.0 0.00 2.69
464 601 4.518211 GCCATATTTCACAATAGCAGCTCT 59.482 41.667 0.00 0.0 0.00 4.09
503 640 4.002797 GCCTCCTGCGGTCATTTT 57.997 55.556 0.00 0.0 0.00 1.82
516 653 5.935206 TGCGGTCATTTTAGTGACTCAATTA 59.065 36.000 6.94 0.0 46.02 1.40
529 666 2.295885 CTCAATTAGCTGGCTTCCCTG 58.704 52.381 0.00 0.0 0.00 4.45
602 739 2.634940 CCGATGGGTCTACATTCATCCT 59.365 50.000 0.00 0.0 34.24 3.24
616 753 1.548719 TCATCCTTGAATGTCGTCGGT 59.451 47.619 0.00 0.0 0.00 4.69
662 799 2.898612 TGTAACCGTCACCTGTAATCCA 59.101 45.455 0.00 0.0 0.00 3.41
856 1578 0.612453 AGAAGGGTCGTCTGAGGGTC 60.612 60.000 0.00 0.0 0.00 4.46
857 1579 0.612453 GAAGGGTCGTCTGAGGGTCT 60.612 60.000 0.00 0.0 0.00 3.85
862 1584 3.374402 CGTCTGAGGGTCTGCCGT 61.374 66.667 0.00 0.0 34.97 5.68
1590 2314 9.465199 CTACTCCTACTTTAAACTTAGAGTCCT 57.535 37.037 8.65 0.0 31.48 3.85
1688 2412 1.722034 GGCTACTCTGGGATGGATCA 58.278 55.000 0.00 0.0 0.00 2.92
1725 2449 1.379176 GGGGCTTGCTCCCTTTCTC 60.379 63.158 0.00 0.0 45.80 2.87
1769 2493 1.202794 GGTGGTGTTTCCGGTAAAGGA 60.203 52.381 0.00 0.0 39.52 3.36
1895 2619 2.434331 CCGGCCCTTTGTTCCTCA 59.566 61.111 0.00 0.0 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 2.105128 CGGCGCCGAGAGAAAGAT 59.895 61.111 44.86 0.00 42.83 2.40
201 202 2.231380 GGGTGGGGGAGAAGCAAGA 61.231 63.158 0.00 0.00 0.00 3.02
257 258 6.134535 TCAACAGAAGCCCTTAAAATCCTA 57.865 37.500 0.00 0.00 0.00 2.94
444 581 6.824553 TCTCAGAGCTGCTATTGTGAAATAT 58.175 36.000 0.15 0.00 0.00 1.28
451 588 2.903798 GCTTCTCAGAGCTGCTATTGT 58.096 47.619 0.15 0.00 39.57 2.71
464 601 0.547712 ACCCTAAGCCCAGCTTCTCA 60.548 55.000 4.87 0.00 46.77 3.27
499 636 6.183347 AGCCAGCTAATTGAGTCACTAAAAT 58.817 36.000 0.00 0.00 0.00 1.82
503 640 4.383118 GGAAGCCAGCTAATTGAGTCACTA 60.383 45.833 0.00 0.00 0.00 2.74
516 653 2.610233 AGCTCAGGGAAGCCAGCT 60.610 61.111 0.00 0.00 43.56 4.24
529 666 1.445238 GCGACACCAGTCTGAGCTC 60.445 63.158 6.82 6.82 42.73 4.09
602 739 3.928727 AGAGTAACCGACGACATTCAA 57.071 42.857 0.00 0.00 0.00 2.69
616 753 0.611714 GGCGGGGAAGTGAAGAGTAA 59.388 55.000 0.00 0.00 0.00 2.24
735 872 2.103153 AAGTGAACTCCTGGGTCTGA 57.897 50.000 0.00 0.00 31.77 3.27
856 1578 1.210931 CAGCAATGAACCACGGCAG 59.789 57.895 0.00 0.00 0.00 4.85
857 1579 1.528076 ACAGCAATGAACCACGGCA 60.528 52.632 0.00 0.00 0.00 5.69
862 1584 2.293122 GTGTAAGCACAGCAATGAACCA 59.707 45.455 0.00 0.00 44.64 3.67
1590 2314 8.704849 TTGTCTTTGGAAGAATTGGAAGAATA 57.295 30.769 0.00 0.00 39.67 1.75
1688 2412 1.075536 CCCTCTGTTGGCCTAAACCTT 59.924 52.381 3.32 0.00 0.00 3.50
1725 2449 0.833949 GGTCCTTCCTTAGCTCCAGG 59.166 60.000 5.62 5.62 0.00 4.45
1754 2478 5.221762 TGAGATTCTTCCTTTACCGGAAACA 60.222 40.000 9.46 0.00 42.20 2.83
1769 2493 3.111484 GGAGACCCTCCTTGAGATTCTT 58.889 50.000 5.78 0.00 46.41 2.52
1770 2494 2.758130 GGAGACCCTCCTTGAGATTCT 58.242 52.381 5.78 0.00 46.41 2.40
1895 2619 6.061441 TCCTTATTGTTATTGCGATGGTGAT 58.939 36.000 0.00 0.00 0.00 3.06
1992 2717 6.788684 TTGATAAACGAAACGAATCCAAGA 57.211 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.