Multiple sequence alignment - TraesCS6D01G161300

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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 TraesCS6D01G161300 chr6D 100.000 2624 0 0 1 2624 139915253 139917876 0.000000e+00 4846
1 TraesCS6D01G161300 chr6A 93.428 2663 111 36 5 2624 183187103 183189744 0.000000e+00 3890
2 TraesCS6D01G161300 chr6B 95.038 2096 44 16 557 2624 239728741 239730804 0.000000e+00 3240
3 TraesCS6D01G161300 chr6B 94.139 563 31 2 4 566 239727129 239727689 0.000000e+00 856
4 TraesCS6D01G161300 chr2A 91.525 177 13 2 1071 1246 680357725 680357550 2.610000e-60 243
5 TraesCS6D01G161300 chr2B 90.270 185 15 3 1064 1246 640765321 640765138 3.380000e-59 239
6 TraesCS6D01G161300 chr2D 89.730 185 16 3 1064 1246 538055281 538055098 1.570000e-57 233
7 TraesCS6D01G161300 chr1B 84.862 218 26 6 1035 1249 552474296 552474083 2.050000e-51 213
8 TraesCS6D01G161300 chr1D 88.068 176 19 2 1075 1249 410072045 410071871 9.520000e-50 207
9 TraesCS6D01G161300 chr1D 84.804 204 22 7 1045 1243 409799230 409799031 2.060000e-46 196
10 TraesCS6D01G161300 chr1A 84.804 204 22 7 1045 1243 505681284 505681085 2.060000e-46 196


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 TraesCS6D01G161300 chr6D 139915253 139917876 2623 False 4846 4846 100.0000 1 2624 1 chr6D.!!$F1 2623
1 TraesCS6D01G161300 chr6A 183187103 183189744 2641 False 3890 3890 93.4280 5 2624 1 chr6A.!!$F1 2619
2 TraesCS6D01G161300 chr6B 239727129 239730804 3675 False 2048 3240 94.5885 4 2624 2 chr6B.!!$F1 2620

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
174 175 3.240861 GCACGTCAGAATACGAAGATCAC 59.759 47.826 3.1 0.0 45.68 3.06 F
1271 2383 0.695924 CCCCATCACCACCAACTACA 59.304 55.000 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 2558 1.153568 GCAGTCGCTATGGCAGTCA 60.154 57.895 0.74 0.00 38.60 3.41 R
2083 3196 4.884668 TTCAGGTAGAAGGTTGTACCAG 57.115 45.455 16.18 9.71 46.43 4.00 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
30 31 9.241317 GCTTCATAATTATTTGTGATGTCAAGG 57.759 33.333 0.00 0.00 33.62 3.61
83 84 8.865590 AACACCACAACAAACATTATAACTTC 57.134 30.769 0.00 0.00 0.00 3.01
99 100 6.716934 ATAACTTCTGCTATCCGAAAGAGA 57.283 37.500 0.00 0.00 0.00 3.10
174 175 3.240861 GCACGTCAGAATACGAAGATCAC 59.759 47.826 3.10 0.00 45.68 3.06
226 227 5.717078 TGCACGTAAGAATATAGTAGGGG 57.283 43.478 0.00 0.00 43.62 4.79
227 228 5.142639 TGCACGTAAGAATATAGTAGGGGT 58.857 41.667 0.00 0.00 43.62 4.95
229 230 5.336293 GCACGTAAGAATATAGTAGGGGTCC 60.336 48.000 0.00 0.00 43.62 4.46
232 233 7.833183 CACGTAAGAATATAGTAGGGGTCCTAT 59.167 40.741 0.00 0.00 38.63 2.57
265 266 4.487714 TGGTAAATGAGATGGTGGAGAC 57.512 45.455 0.00 0.00 0.00 3.36
329 330 6.979465 TGTTACAATGTTTGCAATGATGAGA 58.021 32.000 0.00 0.00 30.44 3.27
369 370 4.316645 GGATCATCCTGTCTCATCACATG 58.683 47.826 0.00 0.00 32.53 3.21
474 475 9.691362 GAGTCAAATTTAACTTTGGCATTTAGA 57.309 29.630 20.70 0.00 41.96 2.10
476 477 8.925700 GTCAAATTTAACTTTGGCATTTAGAGG 58.074 33.333 15.60 0.00 39.84 3.69
488 489 4.327680 GCATTTAGAGGGCTAATTCGGAT 58.672 43.478 0.00 0.00 36.54 4.18
491 492 5.825593 TTTAGAGGGCTAATTCGGATGAT 57.174 39.130 0.00 0.00 36.54 2.45
1269 2381 1.633432 CTTCCCCATCACCACCAACTA 59.367 52.381 0.00 0.00 0.00 2.24
1271 2383 0.695924 CCCCATCACCACCAACTACA 59.304 55.000 0.00 0.00 0.00 2.74
1273 2385 1.340017 CCCATCACCACCAACTACAGG 60.340 57.143 0.00 0.00 0.00 4.00
1639 2751 0.951040 CTGAAGTCAGAACCACCGGC 60.951 60.000 0.00 0.00 46.59 6.13
1743 2855 3.057245 TGTTGTTGCTGTTGCTGTTTACA 60.057 39.130 0.00 0.00 40.48 2.41
1777 2889 7.568349 TGATGATTAATATGGCCTGATCTACC 58.432 38.462 3.32 0.00 0.00 3.18
1862 2974 6.171932 TGTGGTTGTTGTAATATAGCAACG 57.828 37.500 9.69 0.00 45.54 4.10
2083 3196 6.834168 TGACCTTGATCTTAATTTCAACCC 57.166 37.500 0.00 0.00 0.00 4.11
2246 3359 5.100943 CACACTGATGTAGATGTCTGTCAG 58.899 45.833 14.72 14.72 36.72 3.51
2248 3361 5.478332 ACACTGATGTAGATGTCTGTCAGAA 59.522 40.000 19.51 0.00 37.26 3.02
2363 3479 4.823989 ACACCTTCAGCTATGATTAATGCC 59.176 41.667 0.00 0.00 34.73 4.40
2481 3597 9.107177 CAAGATGCTAACAAGATTAGTTCTGAT 57.893 33.333 0.00 0.00 33.93 2.90
2615 3733 9.884465 GCTAACGAGATTATATTTGATTGCTTT 57.116 29.630 0.00 0.00 0.00 3.51
2620 3738 9.817365 CGAGATTATATTTGATTGCTTTACTGG 57.183 33.333 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.195646 ACATCACAAATAATTATGAAGCACCG 58.804 34.615 0.00 0.00 0.00 4.94
1 2 8.190122 TGACATCACAAATAATTATGAAGCACC 58.810 33.333 0.00 0.00 0.00 5.01
2 3 9.571810 TTGACATCACAAATAATTATGAAGCAC 57.428 29.630 0.00 0.00 0.00 4.40
22 23 0.606401 CGGTTGAGTGCCCTTGACAT 60.606 55.000 0.00 0.00 0.00 3.06
30 31 1.999071 TTTGTGTGCGGTTGAGTGCC 61.999 55.000 0.00 0.00 0.00 5.01
83 84 3.247173 GTGCATTCTCTTTCGGATAGCAG 59.753 47.826 0.00 0.00 0.00 4.24
99 100 9.730420 GGATAATTTACGAGTTATTTGTGCATT 57.270 29.630 0.00 0.00 0.00 3.56
158 159 3.798878 ACATGCGTGATCTTCGTATTCTG 59.201 43.478 14.17 5.93 32.06 3.02
226 227 1.299541 CATGAACGGCCACATAGGAC 58.700 55.000 2.24 0.00 44.64 3.85
227 228 0.180171 CCATGAACGGCCACATAGGA 59.820 55.000 2.24 0.00 41.22 2.94
229 230 2.613026 TACCATGAACGGCCACATAG 57.387 50.000 2.24 0.95 0.00 2.23
232 233 1.815613 CATTTACCATGAACGGCCACA 59.184 47.619 2.24 0.00 0.00 4.17
265 266 0.174389 CACACATCAGGACTCTCCGG 59.826 60.000 0.00 0.00 42.75 5.14
329 330 6.753913 TGATCCTCTATGCCTTGTATCTTT 57.246 37.500 0.00 0.00 0.00 2.52
369 370 3.309954 GGGCTATTTGACATCTTGACGTC 59.690 47.826 9.11 9.11 0.00 4.34
474 475 3.815401 CGAAAATCATCCGAATTAGCCCT 59.185 43.478 0.00 0.00 0.00 5.19
476 477 4.527564 CACGAAAATCATCCGAATTAGCC 58.472 43.478 0.00 0.00 0.00 3.93
1446 2558 1.153568 GCAGTCGCTATGGCAGTCA 60.154 57.895 0.74 0.00 38.60 3.41
1637 2749 2.820197 CCTTTTTCTCTAACCACCAGCC 59.180 50.000 0.00 0.00 0.00 4.85
1639 2751 6.599638 CCTTATCCTTTTTCTCTAACCACCAG 59.400 42.308 0.00 0.00 0.00 4.00
1743 2855 8.503573 AGGCCATATTAATCATCATCAGATCAT 58.496 33.333 5.01 0.00 30.20 2.45
1777 2889 1.444895 GCAACAAGCAGGCCGATTG 60.445 57.895 19.29 19.29 46.67 2.67
1862 2974 5.751243 TCACAAGAGGAAGCAAGTAAAAC 57.249 39.130 0.00 0.00 0.00 2.43
2004 3117 4.766375 TCTAGCATTTAAGCACCCAGTAC 58.234 43.478 0.00 0.00 36.85 2.73
2041 3154 3.751698 GTCATCCCTCTAACACAACAACC 59.248 47.826 0.00 0.00 0.00 3.77
2083 3196 4.884668 TTCAGGTAGAAGGTTGTACCAG 57.115 45.455 16.18 9.71 46.43 4.00
2187 3300 6.867662 AGAACCAAAACTACATGTCAGAAG 57.132 37.500 0.00 0.00 0.00 2.85
2246 3359 6.199154 GCAGCCAAAGTAAACTTCTCTTTTTC 59.801 38.462 0.00 0.00 34.61 2.29
2248 3361 5.360999 AGCAGCCAAAGTAAACTTCTCTTTT 59.639 36.000 0.00 0.00 34.61 2.27
2378 3494 7.308529 CCAATTATACAAGCTAATGATTCGGCA 60.309 37.037 0.00 0.00 0.00 5.69
2393 3509 6.430925 GCTCATGAGTATGCCCAATTATACAA 59.569 38.462 23.38 0.00 33.30 2.41
2511 3629 8.960591 CCTTTTACTTTCATGTTACTCCATCAT 58.039 33.333 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.