Multiple sequence alignment - TraesCS1B01G353100

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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 TraesCS1B01G353100 chr1B 100.000 2243 0 0 1 2243 583561570 583559328 0.000000e+00 4143
1 TraesCS1B01G353100 chr5A 97.924 2264 25 7 1 2243 16544533 16546795 0.000000e+00 3901
2 TraesCS1B01G353100 chr5A 97.217 2264 29 7 1 2243 420185681 420187931 0.000000e+00 3801
3 TraesCS1B01G353100 chr7A 97.836 2264 27 6 1 2243 60168788 60166526 0.000000e+00 3890
4 TraesCS1B01G353100 chr7A 97.747 2264 29 6 1 2243 60084915 60087177 0.000000e+00 3879
5 TraesCS1B01G353100 chr7B 97.792 2264 28 6 1 2243 716784586 716786848 0.000000e+00 3884
6 TraesCS1B01G353100 chr7B 97.703 2264 30 6 1 2243 742948759 742946497 0.000000e+00 3873
7 TraesCS1B01G353100 chr1D 96.717 2254 50 8 1 2231 275778906 275781158 0.000000e+00 3731
8 TraesCS1B01G353100 chr2D 95.730 2248 74 12 7 2243 291773604 291775840 0.000000e+00 3600
9 TraesCS1B01G353100 chr2D 95.503 1312 29 12 1 1307 39656632 39657918 0.000000e+00 2069
10 TraesCS1B01G353100 chr2D 95.776 947 35 3 58 999 291453365 291452419 0.000000e+00 1522
11 TraesCS1B01G353100 chr6B 96.857 1718 48 4 530 2243 388227635 388225920 0.000000e+00 2868
12 TraesCS1B01G353100 chrUn 97.536 893 5 3 1 876 378556518 378557410 0.000000e+00 1511
13 TraesCS1B01G353100 chr2B 97.512 201 5 0 2043 2243 102608845 102609045 5.930000e-91 344


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 TraesCS1B01G353100 chr1B 583559328 583561570 2242 True 4143 4143 100.000 1 2243 1 chr1B.!!$R1 2242
1 TraesCS1B01G353100 chr5A 16544533 16546795 2262 False 3901 3901 97.924 1 2243 1 chr5A.!!$F1 2242
2 TraesCS1B01G353100 chr5A 420185681 420187931 2250 False 3801 3801 97.217 1 2243 1 chr5A.!!$F2 2242
3 TraesCS1B01G353100 chr7A 60166526 60168788 2262 True 3890 3890 97.836 1 2243 1 chr7A.!!$R1 2242
4 TraesCS1B01G353100 chr7A 60084915 60087177 2262 False 3879 3879 97.747 1 2243 1 chr7A.!!$F1 2242
5 TraesCS1B01G353100 chr7B 716784586 716786848 2262 False 3884 3884 97.792 1 2243 1 chr7B.!!$F1 2242
6 TraesCS1B01G353100 chr7B 742946497 742948759 2262 True 3873 3873 97.703 1 2243 1 chr7B.!!$R1 2242
7 TraesCS1B01G353100 chr1D 275778906 275781158 2252 False 3731 3731 96.717 1 2231 1 chr1D.!!$F1 2230
8 TraesCS1B01G353100 chr2D 291773604 291775840 2236 False 3600 3600 95.730 7 2243 1 chr2D.!!$F2 2236
9 TraesCS1B01G353100 chr2D 39656632 39657918 1286 False 2069 2069 95.503 1 1307 1 chr2D.!!$F1 1306
10 TraesCS1B01G353100 chr2D 291452419 291453365 946 True 1522 1522 95.776 58 999 1 chr2D.!!$R1 941
11 TraesCS1B01G353100 chr6B 388225920 388227635 1715 True 2868 2868 96.857 530 2243 1 chr6B.!!$R1 1713
12 TraesCS1B01G353100 chrUn 378556518 378557410 892 False 1511 1511 97.536 1 876 1 chrUn.!!$F1 875

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
925 955 0.539669 GGTGCAGGCCCAAGTACTTT 60.54 55.0 5.07 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1830 3.513515 ACAAGTTCATGTCTCTCCTCTCC 59.486 47.826 0.0 0.0 0.0 3.71 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
260 261 0.603065 GCCTTCGCTCAATTTGGGTT 59.397 50.000 0.00 0.00 0.00 4.11
262 263 2.230266 GCCTTCGCTCAATTTGGGTTAA 59.770 45.455 0.00 0.00 0.00 2.01
753 756 3.051341 TCCAGTAGTTCAGGATACCCCAT 60.051 47.826 0.00 0.00 37.41 4.00
786 789 1.914764 GTTGACGGACCCCCTACCA 60.915 63.158 0.00 0.00 0.00 3.25
925 955 0.539669 GGTGCAGGCCCAAGTACTTT 60.540 55.000 5.07 0.00 0.00 2.66
959 989 5.360714 ACAAGAAATCCAAGAAAGAACAGCA 59.639 36.000 0.00 0.00 0.00 4.41
1054 1084 2.164219 GCTGCTACAATTGCTTTAGCCA 59.836 45.455 18.65 9.66 37.95 4.75
1420 1451 6.825721 GTCCATTTATTTCTGTGTCCTCATCT 59.174 38.462 0.00 0.00 0.00 2.90
1531 1562 6.628919 ACCCGCATGTTTAGATTATTTACC 57.371 37.500 0.00 0.00 0.00 2.85
1708 1741 5.652452 AGGTCTTTAATTCGGCATTAGCTTT 59.348 36.000 0.00 0.00 41.70 3.51
1797 1830 4.689345 ACTTTTCAATAAGGTCCGACTTCG 59.311 41.667 0.00 0.00 39.44 3.79
1832 1866 5.408604 ACATGAACTTGTTTTAGGCGTAGAG 59.591 40.000 0.00 0.00 0.00 2.43
1988 2023 3.910627 AGCCTATACATCCGGGAATTTCT 59.089 43.478 0.00 0.00 0.00 2.52
2003 2038 5.481824 GGGAATTTCTCTCCAAACCAAAGAT 59.518 40.000 0.00 0.00 34.34 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 261 2.289382 TGAGTCGCAGCATCAAGGTTTA 60.289 45.455 0.00 0.0 0.00 2.01
262 263 0.035317 TGAGTCGCAGCATCAAGGTT 59.965 50.000 0.00 0.0 0.00 3.50
883 909 7.341769 CACCTCCATAGTTTTCAAATATTGGGA 59.658 37.037 0.00 0.0 0.00 4.37
925 955 7.764141 TCTTGGATTTCTTGTTGATGATTCA 57.236 32.000 0.00 0.0 0.00 2.57
959 989 6.364976 CACTTTTCTTGTCACGTTTTTCCTTT 59.635 34.615 0.00 0.0 0.00 3.11
1054 1084 2.034878 TCCAATATCGACAGCAGCTCT 58.965 47.619 0.00 0.0 0.00 4.09
1067 1097 5.422214 AGAACTGAGGACGTTTCCAATAT 57.578 39.130 0.00 0.0 45.72 1.28
1155 1185 2.080286 TAGCTTCGGTGAGAGCAAAC 57.920 50.000 0.00 0.0 0.00 2.93
1367 1398 4.771903 TCCGGTACTAAAATTGCATAGCA 58.228 39.130 0.00 0.0 36.47 3.49
1380 1411 0.177836 TGGACGTCGATCCGGTACTA 59.822 55.000 9.92 0.0 42.24 1.82
1420 1451 6.569801 GCCTATCTAACATAGACATACACGCA 60.570 42.308 0.00 0.0 37.69 5.24
1531 1562 3.550842 CCGAAGAAAAAGTGAAAGGGCAG 60.551 47.826 0.00 0.0 0.00 4.85
1605 1636 1.229082 TCTGAACCCGGTAGCCAGT 60.229 57.895 0.00 0.0 0.00 4.00
1708 1741 2.076100 CACGCATGGCTTTCTCTAACA 58.924 47.619 0.00 0.0 0.00 2.41
1797 1830 3.513515 ACAAGTTCATGTCTCTCCTCTCC 59.486 47.826 0.00 0.0 0.00 3.71
1832 1866 5.758296 TCAATCTTTCATACCGTATGCCTTC 59.242 40.000 12.94 0.0 36.14 3.46
1988 2023 3.569701 GCAAGTCATCTTTGGTTTGGAGA 59.430 43.478 0.00 0.0 0.00 3.71


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

AutoCloner maintained by Alex Coulton.