Multiple sequence alignment - TraesCS3B01G122300

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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 TraesCS3B01G122300 chr3B 100.000 2816 0 0 1 2816 92326383 92329198 0.000000e+00 5201.0
1 TraesCS3B01G122300 chr3B 93.636 220 11 3 2360 2577 707418736 707418518 2.710000e-85 326.0
2 TraesCS3B01G122300 chr3B 96.552 116 4 0 1933 2048 222388583 222388468 2.860000e-45 193.0
3 TraesCS3B01G122300 chr3B 97.468 79 2 0 2728 2806 450530506 450530428 4.890000e-28 135.0
4 TraesCS3B01G122300 chr3B 96.341 82 2 1 2518 2599 359976256 359976176 1.760000e-27 134.0
5 TraesCS3B01G122300 chr3B 98.214 56 1 0 2735 2790 819645718 819645773 6.420000e-17 99.0
6 TraesCS3B01G122300 chr3B 95.833 48 2 0 2442 2489 693725821 693725774 8.360000e-11 78.7
7 TraesCS3B01G122300 chr3B 100.000 33 0 0 487 519 119052207 119052175 8.420000e-06 62.1
8 TraesCS3B01G122300 chr3B 90.909 44 2 2 768 810 515569322 515569364 1.090000e-04 58.4
9 TraesCS3B01G122300 chr3B 90.909 44 2 2 768 810 516052885 516052927 1.090000e-04 58.4
10 TraesCS3B01G122300 chrUn 99.112 2816 24 1 1 2816 222680159 222677345 0.000000e+00 5060.0
11 TraesCS3B01G122300 chrUn 99.077 2816 24 2 1 2816 86449118 86451931 0.000000e+00 5055.0
12 TraesCS3B01G122300 chrUn 99.006 2816 25 2 1 2816 86455118 86457930 0.000000e+00 5042.0
13 TraesCS3B01G122300 chr5B 99.112 2816 24 1 1 2816 533066665 533069479 0.000000e+00 5060.0
14 TraesCS3B01G122300 chr1A 99.042 2817 25 2 1 2816 238117486 238120301 0.000000e+00 5051.0
15 TraesCS3B01G122300 chr1A 98.935 2816 28 2 1 2816 238121409 238124222 0.000000e+00 5033.0
16 TraesCS3B01G122300 chr6B 98.864 2816 29 2 1 2816 596628845 596631657 0.000000e+00 5020.0


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 TraesCS3B01G122300 chr3B 92326383 92329198 2815 False 5201.0 5201 100.0000 1 2816 1 chr3B.!!$F1 2815
1 TraesCS3B01G122300 chrUn 222677345 222680159 2814 True 5060.0 5060 99.1120 1 2816 1 chrUn.!!$R1 2815
2 TraesCS3B01G122300 chrUn 86449118 86457930 8812 False 5048.5 5055 99.0415 1 2816 2 chrUn.!!$F1 2815
3 TraesCS3B01G122300 chr5B 533066665 533069479 2814 False 5060.0 5060 99.1120 1 2816 1 chr5B.!!$F1 2815
4 TraesCS3B01G122300 chr1A 238117486 238124222 6736 False 5042.0 5051 98.9885 1 2816 2 chr1A.!!$F1 2815
5 TraesCS3B01G122300 chr6B 596628845 596631657 2812 False 5020.0 5020 98.8640 1 2816 1 chr6B.!!$F1 2815

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
213 214 0.678048 GGTCATGTCCACAGGCCTTC 60.678 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 12018 0.681733 TGCAACCACCTGTCTCTCTC 59.318 55.0 0.0 0.0 0.0 3.2 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
213 214 0.678048 GGTCATGTCCACAGGCCTTC 60.678 60.000 0.00 0.00 0.00 3.46
341 342 1.681229 ACTAAGGATGGGCCCAAAGA 58.319 50.000 32.58 11.84 37.37 2.52
460 461 6.417191 TGAACGAGGCATATTAAAGTGAAC 57.583 37.500 0.00 0.00 0.00 3.18
585 586 1.900351 CTGCTCAGGACGATCCCAA 59.100 57.895 0.00 0.00 37.19 4.12
968 969 2.223923 CGCAAACAAAGAAATGGTCCCA 60.224 45.455 0.00 0.00 0.00 4.37
1444 1446 2.037902 TGGCACTTTCCATACTTCGTGA 59.962 45.455 0.00 0.00 0.00 4.35
1611 1613 2.036387 TCTGTGGAAACCTTCACGAGA 58.964 47.619 0.00 0.00 36.74 4.04
1764 11687 2.696707 TGTACAAGTTCGTGAAGAGGGT 59.303 45.455 0.00 0.00 0.00 4.34
1990 11913 1.001706 CAGTTCGAACCTGACGAGTCA 60.002 52.381 24.22 5.76 40.72 3.41
2000 11923 5.446143 ACCTGACGAGTCATTATCATCTC 57.554 43.478 6.37 0.00 39.13 2.75
2357 12280 6.353404 GGAAAAGAATGGTTCCCAATACAA 57.647 37.500 0.00 0.00 37.87 2.41
2664 12587 6.115446 CACTAGTGAGAAGGCCAATAAATCA 58.885 40.000 18.45 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 214 5.581085 AGAAAGACGAATAAAGACGAATGGG 59.419 40.000 0.00 0.00 0.00 4.00
341 342 2.693074 ACCGATGCCTTTCAAAAGTGTT 59.307 40.909 2.09 0.00 34.20 3.32
460 461 0.109226 GGACTCGACCTGGAACTTCG 60.109 60.000 0.00 0.00 0.00 3.79
585 586 1.774856 CCCCCTCCAGAAAATCCGTAT 59.225 52.381 0.00 0.00 0.00 3.06
656 657 3.476552 TCGTTCTGCTTTTGGTCTTCAT 58.523 40.909 0.00 0.00 0.00 2.57
927 928 0.032515 TCAGAGAATCCCGCACCCTA 60.033 55.000 0.00 0.00 33.66 3.53
968 969 5.779771 ACTGAAGAGACTGATTCCTTTCTCT 59.220 40.000 0.00 0.00 45.46 3.10
1241 1243 3.868077 AGAGCATGCTATTGAAGACGTTC 59.132 43.478 22.74 3.18 0.00 3.95
1420 1422 3.502211 ACGAAGTATGGAAAGTGCCAAAG 59.498 43.478 0.00 0.00 41.94 2.77
1444 1446 3.052036 GCGAATTTGTTGATGTTGCACT 58.948 40.909 0.00 0.00 0.00 4.40
1524 1526 3.476552 GGAGCATACCGATGGAATGAAA 58.523 45.455 0.00 0.00 33.26 2.69
1764 11687 3.095912 TCCCTCATTCTACTCGTCCAA 57.904 47.619 0.00 0.00 0.00 3.53
1990 11913 6.328672 ACTCAGTTAGGGCAAGAGATGATAAT 59.671 38.462 0.00 0.00 0.00 1.28
2000 11923 3.356529 AATGGACTCAGTTAGGGCAAG 57.643 47.619 0.00 0.00 0.00 4.01
2095 12018 0.681733 TGCAACCACCTGTCTCTCTC 59.318 55.000 0.00 0.00 0.00 3.20
2357 12280 1.316706 CGTCTCTCTTCTTCGGGCCT 61.317 60.000 0.84 0.00 0.00 5.19
2677 12600 2.578480 GGATGGTCCTTCTTTCCCTTCT 59.422 50.000 4.85 0.00 32.53 2.85


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

AutoCloner maintained by Alex Coulton.