Multiple sequence alignment - TraesCS7A01G080800

Loading Multiple Alignment...

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 TraesCS7A01G080800 chr7A 100.000 2246 0 0 1 2246 46421127 46423372 0 4148
1 TraesCS7A01G080800 chr6D 98.179 2252 32 8 1 2246 124501730 124503978 0 3923
2 TraesCS7A01G080800 chr4D 98.046 2252 31 4 1 2246 123319685 123321929 0 3903
3 TraesCS7A01G080800 chrUn 98.002 2252 32 5 1 2246 206782860 206785104 0 3897
4 TraesCS7A01G080800 chr1B 97.643 2249 38 5 1 2246 672569887 672567651 0 3845
5 TraesCS7A01G080800 chr3B 97.467 2250 50 4 1 2246 483384915 483387161 0 3832
6 TraesCS7A01G080800 chr3B 96.978 2250 62 5 1 2246 669796317 669794070 0 3773
7 TraesCS7A01G080800 chr2B 97.291 2252 47 7 1 2246 391092650 391090407 0 3808
8 TraesCS7A01G080800 chr4A 97.243 2249 58 3 1 2246 246673733 246671486 0 3807
9 TraesCS7A01G080800 chr3D 97.112 2251 56 8 1 2246 523767545 523769791 0 3788


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 TraesCS7A01G080800 chr7A 46421127 46423372 2245 False 4148 4148 100.000 1 2246 1 chr7A.!!$F1 2245
1 TraesCS7A01G080800 chr6D 124501730 124503978 2248 False 3923 3923 98.179 1 2246 1 chr6D.!!$F1 2245
2 TraesCS7A01G080800 chr4D 123319685 123321929 2244 False 3903 3903 98.046 1 2246 1 chr4D.!!$F1 2245
3 TraesCS7A01G080800 chrUn 206782860 206785104 2244 False 3897 3897 98.002 1 2246 1 chrUn.!!$F1 2245
4 TraesCS7A01G080800 chr1B 672567651 672569887 2236 True 3845 3845 97.643 1 2246 1 chr1B.!!$R1 2245
5 TraesCS7A01G080800 chr3B 483384915 483387161 2246 False 3832 3832 97.467 1 2246 1 chr3B.!!$F1 2245
6 TraesCS7A01G080800 chr3B 669794070 669796317 2247 True 3773 3773 96.978 1 2246 1 chr3B.!!$R1 2245
7 TraesCS7A01G080800 chr2B 391090407 391092650 2243 True 3808 3808 97.291 1 2246 1 chr2B.!!$R1 2245
8 TraesCS7A01G080800 chr4A 246671486 246673733 2247 True 3807 3807 97.243 1 2246 1 chr4A.!!$R1 2245
9 TraesCS7A01G080800 chr3D 523767545 523769791 2246 False 3788 3788 97.112 1 2246 1 chr3D.!!$F1 2245

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
95 96 0.320421 CTTCTTCGCTTCGGGGACAA 60.32 55.0 0.0 0.0 36.63 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1318 1.151668 GCTTTTTGAGAGAGCGAGCA 58.848 50.0 0.0 0.0 0.0 4.26 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
94 95 1.292223 CTTCTTCGCTTCGGGGACA 59.708 57.895 0.00 0.0 36.63 4.02
95 96 0.320421 CTTCTTCGCTTCGGGGACAA 60.320 55.000 0.00 0.0 36.63 3.18
118 119 1.601430 GTCCTACGGTAGGTAAGAGCG 59.399 57.143 28.55 5.9 46.32 5.03
158 159 3.842869 GGGACCAGTGCTTCTACTG 57.157 57.895 0.00 0.0 45.93 2.74
206 207 0.949105 GCAAGGGATGTCGTGAACGT 60.949 55.000 2.37 0.0 40.80 3.99
317 322 1.004436 GAAATTGGGGGTGGGACCTA 58.996 55.000 0.00 0.0 38.64 3.08
431 438 1.684983 CCTTTTAGATCTACGGGCCGA 59.315 52.381 35.78 15.5 0.00 5.54
472 479 3.119779 GGAATCTATACTCGAGCCTTCGG 60.120 52.174 13.61 0.0 46.67 4.30
567 574 1.134788 CGACTAGCATCCCTTTCCGTT 60.135 52.381 0.00 0.0 0.00 4.44
569 576 1.906574 ACTAGCATCCCTTTCCGTTGA 59.093 47.619 0.00 0.0 0.00 3.18
570 577 2.505819 ACTAGCATCCCTTTCCGTTGAT 59.494 45.455 0.00 0.0 0.00 2.57
886 893 5.301045 TCGGACTATAACAGTTCCGATGAAT 59.699 40.000 8.93 0.0 44.65 2.57
1141 1148 1.552337 ACTATGGTCAGTGCAGTGAGG 59.448 52.381 24.49 13.8 0.00 3.86
1311 1318 0.038890 GGAAGCTCCAGGAAGGCTTT 59.961 55.000 15.42 2.3 44.81 3.51
1320 1327 1.376553 GGAAGGCTTTGCTCGCTCT 60.377 57.895 0.00 0.0 0.00 4.09
1581 1589 1.226746 CGTCAAAAGGAAAGGCGAGT 58.773 50.000 0.00 0.0 0.00 4.18
1790 1798 1.098050 GCTTGATGTACCAGCCAAGG 58.902 55.000 0.00 0.0 37.18 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 0.898326 TCGGTGGAGCAGTAGAAGCA 60.898 55.000 0.00 0.0 0.00 3.91
206 207 4.788925 TTCTCTTTCTTTGACCTCCCAA 57.211 40.909 0.00 0.0 0.00 4.12
290 295 2.171003 CACCCCCAATTTCTTGAGTCC 58.829 52.381 0.00 0.0 34.04 3.85
317 322 0.754217 CCAGCCTGCATTATGCCAGT 60.754 55.000 15.06 0.0 44.23 4.00
431 438 1.134401 CCCTATGCTCATGTGAACGGT 60.134 52.381 0.00 0.0 0.00 4.83
567 574 1.414919 GTATGGGACGGCCAGTTATCA 59.585 52.381 11.00 0.0 35.15 2.15
569 576 0.763035 GGTATGGGACGGCCAGTTAT 59.237 55.000 11.00 0.0 35.15 1.89
570 577 0.325860 AGGTATGGGACGGCCAGTTA 60.326 55.000 11.00 0.0 35.15 2.24
812 819 3.131850 CCCCCAAACTTGACTTGCT 57.868 52.632 0.00 0.0 0.00 3.91
850 857 9.352191 ACTGTTATAGTCCGAATACTCATAAGT 57.648 33.333 0.00 0.0 33.17 2.24
886 893 7.806487 CGTATAACTGTCAAAAGTGAGTGACTA 59.194 37.037 5.49 0.0 43.73 2.59
1141 1148 3.270877 AGGCATGATTAGTTCCACGAAC 58.729 45.455 0.00 0.0 42.25 3.95
1311 1318 1.151668 GCTTTTTGAGAGAGCGAGCA 58.848 50.000 0.00 0.0 0.00 4.26


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

AutoCloner maintained by Alex Coulton.