Multiple sequence alignment - TraesCS5A01G026500

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 TraesCS5A01G026500 chr5A 100.000 3059 0 0 1 3059 21448076 21451134 0.000000e+00 5650
1 TraesCS5A01G026500 chr5A 92.308 195 15 0 2416 2610 21450261 21450455 8.350000e-71 278
2 TraesCS5A01G026500 chr5A 92.308 195 15 0 2186 2380 21450491 21450685 8.350000e-71 278
3 TraesCS5A01G026500 chr5D 97.978 3066 44 9 1 3059 33070018 33073072 0.000000e+00 5302
4 TraesCS5A01G026500 chr5D 79.382 1780 305 37 361 2117 37025762 37024022 0.000000e+00 1197
5 TraesCS5A01G026500 chr5D 92.821 195 14 0 2186 2380 33072427 33072621 1.800000e-72 283
6 TraesCS5A01G026500 chr5D 88.205 195 15 1 2416 2610 33072205 33072391 3.070000e-55 226
7 TraesCS5A01G026500 chr5D 80.663 181 28 7 2879 3055 37021561 37021384 1.910000e-27 134
8 TraesCS5A01G026500 chr5B 92.989 2867 158 21 1 2857 24153648 24156481 0.000000e+00 4141
9 TraesCS5A01G026500 chr5B 92.308 195 15 0 2416 2610 24155819 24156013 8.350000e-71 278
10 TraesCS5A01G026500 chr5B 92.973 185 8 3 2880 3059 24157256 24157440 6.500000e-67 265
11 TraesCS5A01G026500 chr5B 90.811 185 16 1 2196 2380 24156051 24156234 2.360000e-61 246


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 TraesCS5A01G026500 chr5A 21448076 21451134 3058 False 2068.666667 5650 94.872000 1 3059 3 chr5A.!!$F1 3058
1 TraesCS5A01G026500 chr5D 33070018 33073072 3054 False 1937.000000 5302 93.001333 1 3059 3 chr5D.!!$F1 3058
2 TraesCS5A01G026500 chr5D 37021384 37025762 4378 True 665.500000 1197 80.022500 361 3055 2 chr5D.!!$R1 2694
3 TraesCS5A01G026500 chr5B 24153648 24157440 3792 False 1232.500000 4141 92.270250 1 3059 4 chr5B.!!$F1 3058

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
775 785 0.605589 AGGGTCGCTTACAGGTTTGC 60.606 55.000 0.0 0.0 0.0 3.68 F
981 993 2.551270 CTCGTGCGCAACTGGAAC 59.449 61.111 14.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1605 1.250154 GCCAAGGTGGTATGCAGCAA 61.250 55.0 0.0 0.0 40.46 3.91 R
2423 2717 2.408271 TGCCAGCATCTAAACAGAGG 57.592 50.0 0.0 0.0 0.00 3.69 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
84 86 7.920682 CCTTCATGCTATACAATTTAACCAACC 59.079 37.037 0.00 0.0 0.00 3.77
147 149 7.545362 AATGCATTCACTGATACTACAAGAC 57.455 36.000 5.99 0.0 0.00 3.01
164 169 4.516698 ACAAGACTTGGCACTCAAACATAG 59.483 41.667 19.16 0.0 34.56 2.23
239 247 5.342791 GCAAATTTATGCCACAACAAATTGC 59.657 36.000 0.00 0.0 40.49 3.56
408 418 3.470709 TGTGCTGCTCTTGGATATTAGC 58.529 45.455 0.00 0.0 35.51 3.09
462 472 2.898729 AGTATGTCCAATCAGCGAGG 57.101 50.000 0.00 0.0 0.00 4.63
666 676 1.130561 GTGCATGAGCTAAAACCGGAC 59.869 52.381 9.46 0.0 42.74 4.79
775 785 0.605589 AGGGTCGCTTACAGGTTTGC 60.606 55.000 0.00 0.0 0.00 3.68
864 874 6.133356 AGGTCTTTTTGTTGTTTATCTGGGA 58.867 36.000 0.00 0.0 0.00 4.37
981 993 2.551270 CTCGTGCGCAACTGGAAC 59.449 61.111 14.00 0.0 0.00 3.62
1129 1141 7.915923 TGAAGATTCTACAGTTAGATGCTTACG 59.084 37.037 0.00 0.0 34.15 3.18
1323 1335 2.814805 ATGTCAATGGGAAGGTGGAG 57.185 50.000 0.00 0.0 0.00 3.86
1478 1490 7.159322 ACAACAAGGTGTGTGTAAAATGTTA 57.841 32.000 0.00 0.0 40.60 2.41
1973 2000 1.883021 GGTGGCCAGGAATGTTTCG 59.117 57.895 5.11 0.0 0.00 3.46
2170 2201 6.179756 TGATTAATGGCTACACACTGATGTT 58.820 36.000 0.00 0.0 36.72 2.71
2367 2661 0.036952 TACTGCTCTGCCTTGCACTC 60.037 55.000 0.00 0.0 33.79 3.51
2423 2717 6.055588 TCATAAAGTCTAGTTGGCCATAAGC 58.944 40.000 6.09 0.0 42.60 3.09
2814 3110 2.972021 CCCCAAGGAAACTGTGGAAATT 59.028 45.455 0.00 0.0 42.68 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 3.326747 GTGCTTACAACAGTAGTCCCAG 58.673 50.000 0.00 0.00 0.00 4.45
147 149 2.927553 GGCTATGTTTGAGTGCCAAG 57.072 50.000 0.00 0.00 42.79 3.61
239 247 5.409520 TGCTGTTACTGTCAAAGAGCAATAG 59.590 40.000 11.38 0.00 46.48 1.73
462 472 4.585879 TGCCTTTCTTATAGTTCCACCAC 58.414 43.478 0.00 0.00 0.00 4.16
607 617 1.369625 GCTTTCACCCACCAGTATCG 58.630 55.000 0.00 0.00 0.00 2.92
666 676 3.594603 ATGTAGTTCTTCTGGTCACCG 57.405 47.619 0.00 0.00 0.00 4.94
775 785 4.094442 GGTGAATGCCTTTCTTAGGTAACG 59.906 45.833 0.00 0.00 46.61 3.18
864 874 4.846940 ACTATCTCAAACCTTGGACCTTCT 59.153 41.667 0.00 0.00 0.00 2.85
981 993 1.302366 TGGCATATTCGCTCAGCTTG 58.698 50.000 0.00 0.00 0.00 4.01
1323 1335 3.628032 GGGGCTGCTCTGTAAATAAACTC 59.372 47.826 0.00 0.00 0.00 3.01
1478 1490 6.232581 AGATATAGCTCTGAGTGCTGTTTT 57.767 37.500 18.33 4.07 41.32 2.43
1593 1605 1.250154 GCCAAGGTGGTATGCAGCAA 61.250 55.000 0.00 0.00 40.46 3.91
2084 2115 5.240623 CACCTTGGTGCTTATTTCAGTGTAA 59.759 40.000 6.88 0.00 0.00 2.41
2170 2201 7.982761 AATTTATGGCATTGCTTGAAGAAAA 57.017 28.000 4.78 0.00 0.00 2.29
2367 2661 5.714047 TGTAGCACTACAAATCTGAGTCAG 58.286 41.667 14.36 14.36 42.49 3.51
2423 2717 2.408271 TGCCAGCATCTAAACAGAGG 57.592 50.000 0.00 0.00 0.00 3.69
2814 3110 5.066634 CAGTAACTCGAGCATCTCTTTCCTA 59.933 44.000 13.61 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.