Multiple sequence alignment - TraesCS6B01G169400

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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 TraesCS6B01G169400 chr6B 100.000 2264 0 0 1 2264 181111563 181109300 0.000000e+00 4181
1 TraesCS6B01G169400 chr6B 96.169 1305 37 2 973 2264 84604350 84605654 0.000000e+00 2121
2 TraesCS6B01G169400 chr4B 96.869 2140 61 4 1 2140 551060038 551062171 0.000000e+00 3576
3 TraesCS6B01G169400 chr4B 95.035 141 6 1 2125 2264 588826062 588826202 1.050000e-53 220
4 TraesCS6B01G169400 chr4B 93.243 148 9 1 2118 2264 551062285 551062432 1.360000e-52 217
5 TraesCS6B01G169400 chr5B 96.777 2141 66 2 1 2140 506965544 506967682 0.000000e+00 3568
6 TraesCS6B01G169400 chr5B 96.324 136 5 0 2129 2264 535136394 535136529 8.140000e-55 224
7 TraesCS6B01G169400 chr5B 95.588 136 6 0 2129 2264 709184589 709184454 3.790000e-53 219
8 TraesCS6B01G169400 chr5B 92.568 148 10 1 2118 2264 506967721 506967868 6.340000e-51 211
9 TraesCS6B01G169400 chr2B 96.355 2140 75 3 1 2138 549352846 549354984 0.000000e+00 3517
10 TraesCS6B01G169400 chr2B 96.522 2070 67 5 1 2068 454449226 454451292 0.000000e+00 3419
11 TraesCS6B01G169400 chr2B 96.377 2070 70 5 1 2068 454473359 454475425 0.000000e+00 3402
12 TraesCS6B01G169400 chr3B 96.148 2155 75 6 1 2149 604266042 604263890 0.000000e+00 3513
13 TraesCS6B01G169400 chr3B 93.243 148 9 1 2118 2264 420918876 420918729 1.360000e-52 217
14 TraesCS6B01G169400 chr1B 97.918 2017 42 0 1 2017 571422403 571420387 0.000000e+00 3493
15 TraesCS6B01G169400 chr1B 93.919 148 8 1 2118 2264 571420294 571420147 2.930000e-54 222
16 TraesCS6B01G169400 chr4D 93.113 2149 134 14 1 2140 470196637 470194494 0.000000e+00 3136
17 TraesCS6B01G169400 chr7D 92.670 2142 152 5 1 2140 131689395 131691533 0.000000e+00 3081
18 TraesCS6B01G169400 chr6A 92.568 148 10 1 2118 2264 23006915 23007062 6.340000e-51 211


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 TraesCS6B01G169400 chr6B 181109300 181111563 2263 True 4181.0 4181 100.0000 1 2264 1 chr6B.!!$R1 2263
1 TraesCS6B01G169400 chr6B 84604350 84605654 1304 False 2121.0 2121 96.1690 973 2264 1 chr6B.!!$F1 1291
2 TraesCS6B01G169400 chr4B 551060038 551062432 2394 False 1896.5 3576 95.0560 1 2264 2 chr4B.!!$F2 2263
3 TraesCS6B01G169400 chr5B 506965544 506967868 2324 False 1889.5 3568 94.6725 1 2264 2 chr5B.!!$F2 2263
4 TraesCS6B01G169400 chr2B 549352846 549354984 2138 False 3517.0 3517 96.3550 1 2138 1 chr2B.!!$F3 2137
5 TraesCS6B01G169400 chr2B 454449226 454451292 2066 False 3419.0 3419 96.5220 1 2068 1 chr2B.!!$F1 2067
6 TraesCS6B01G169400 chr2B 454473359 454475425 2066 False 3402.0 3402 96.3770 1 2068 1 chr2B.!!$F2 2067
7 TraesCS6B01G169400 chr3B 604263890 604266042 2152 True 3513.0 3513 96.1480 1 2149 1 chr3B.!!$R2 2148
8 TraesCS6B01G169400 chr1B 571420147 571422403 2256 True 1857.5 3493 95.9185 1 2264 2 chr1B.!!$R1 2263
9 TraesCS6B01G169400 chr4D 470194494 470196637 2143 True 3136.0 3136 93.1130 1 2140 1 chr4D.!!$R1 2139
10 TraesCS6B01G169400 chr7D 131689395 131691533 2138 False 3081.0 3081 92.6700 1 2140 1 chr7D.!!$F1 2139

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
336 337 0.248012 ACGTATCCGATGGCACAACA 59.752 50.0 0.0 0.0 39.05 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1648 1.136305 CCGGTTACATGACGAGTCCAT 59.864 52.381 0.0 0.0 0.0 3.41 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
89 90 6.773976 TCCATTAAAGGTTCATGATTGGTC 57.226 37.500 0.00 0.00 0.00 4.02
182 183 2.270874 GATGAGCCGGGTGGGACAAT 62.271 60.000 12.94 0.00 44.16 2.71
295 296 1.469703 CTTGCTCGCATTTGATGACCA 59.530 47.619 0.00 0.00 0.00 4.02
301 302 1.133598 CGCATTTGATGACCACAGCAT 59.866 47.619 0.00 0.00 42.04 3.79
336 337 0.248012 ACGTATCCGATGGCACAACA 59.752 50.000 0.00 0.00 39.05 3.33
488 491 3.137360 GTGCCTATGAGGGGAAGAAGAAT 59.863 47.826 0.00 0.00 35.37 2.40
1010 1014 2.102578 GTTGTAGGGCATGGCTTCATT 58.897 47.619 19.78 2.97 0.00 2.57
1107 1111 3.652869 AGGTGAAGGAGAAGGATGTGAAA 59.347 43.478 0.00 0.00 0.00 2.69
1254 1258 0.907704 ACGCCTATGACCTTCCACCA 60.908 55.000 0.00 0.00 0.00 4.17
1352 1356 5.201243 TCCTCTATGCAAGTACTTCAGCTA 58.799 41.667 16.32 6.17 0.00 3.32
1402 1406 7.651027 ATCCAAAAGGACCAATTAGAAGATG 57.349 36.000 0.00 0.00 0.00 2.90
1644 1648 0.606604 AGTAAAGCCTTCGCCTTCGA 59.393 50.000 0.00 0.00 43.89 3.71
1715 1719 8.788325 AACTATGTAGTACTAAGGCAAAAAGG 57.212 34.615 3.61 0.00 34.99 3.11
1744 1748 3.866327 TCGTCAACTTGTCGTGAATGAAA 59.134 39.130 8.03 0.00 31.27 2.69
1759 1763 8.504815 TCGTGAATGAAATTTCCGTTTGTATTA 58.495 29.630 15.48 0.00 36.07 0.98
1956 1963 2.606519 TTGCTGGACCCTACCGCT 60.607 61.111 0.00 0.00 33.32 5.52
2123 2210 0.670546 ATGTGACGAGAAACGCCAGG 60.671 55.000 0.00 0.00 46.94 4.45
2177 2401 2.566724 CCTGTTTTGCCCCATATGTGTT 59.433 45.455 1.24 0.00 0.00 3.32
2178 2402 3.766591 CCTGTTTTGCCCCATATGTGTTA 59.233 43.478 1.24 0.00 0.00 2.41
2248 2472 2.857748 TCGCAAGCACATACATAACTCG 59.142 45.455 0.00 0.00 37.18 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 4.740062 TGCGCGCTTGATGCAACG 62.740 61.111 33.29 0.00 43.06 4.10
182 183 2.643551 CGTAAGACCTACCGTCCCTTA 58.356 52.381 0.00 0.00 43.08 2.69
295 296 2.165167 CATGTTTCTCACCCATGCTGT 58.835 47.619 0.00 0.00 30.63 4.40
301 302 2.631160 ACGTTCATGTTTCTCACCCA 57.369 45.000 0.00 0.00 0.00 4.51
348 349 6.605594 ACCTTGTTCTTTCCAATGTAAACTCA 59.394 34.615 0.00 0.00 0.00 3.41
388 389 3.511146 GCATCAAGGAAAGGATTGAACCA 59.489 43.478 0.00 0.00 38.80 3.67
488 491 4.770531 TGTCACTCCGGAATCTCTTCTTTA 59.229 41.667 5.23 0.00 0.00 1.85
536 539 5.304101 TGACCACTACCAAATTGCTTCATTT 59.696 36.000 0.00 0.00 0.00 2.32
1010 1014 1.002624 GGCCTTGTCATGGAACCGA 60.003 57.895 8.93 0.00 0.00 4.69
1107 1111 0.602562 CACACCAACATGGCGGAATT 59.397 50.000 9.48 0.00 42.67 2.17
1352 1356 6.656902 TCTTTTGGCACTTCATGATCTATCT 58.343 36.000 0.00 0.00 0.00 1.98
1402 1406 2.564458 CCGTTGGCGCCTAAAACC 59.436 61.111 29.70 7.10 36.67 3.27
1644 1648 1.136305 CCGGTTACATGACGAGTCCAT 59.864 52.381 0.00 0.00 0.00 3.41
1715 1719 1.397190 CGACAAGTTGACGACACATGC 60.397 52.381 20.59 0.00 37.72 4.06
1744 1748 8.983724 CACACCAAATTTAATACAAACGGAAAT 58.016 29.630 0.00 0.00 0.00 2.17
1759 1763 5.426504 TGCAAACATCTTCACACCAAATTT 58.573 33.333 0.00 0.00 0.00 1.82
1956 1963 1.600107 CCTACCGCCAAGCAACCTA 59.400 57.895 0.00 0.00 0.00 3.08
2214 2438 2.870411 TGCTTGCGAGATGATCATTCTG 59.130 45.455 10.14 3.79 0.00 3.02


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

AutoCloner maintained by Alex Coulton.