Multiple sequence alignment - TraesCS4A01G479900

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 TraesCS4A01G479900 chr4A 100.000 3215 0 0 1 3215 736569750 736572964 0.000000e+00 5938
1 TraesCS4A01G479900 chr4A 98.990 2575 18 4 643 3215 734730320 734732888 0.000000e+00 4604
2 TraesCS4A01G479900 chr4A 86.621 2205 266 21 1029 3215 735316354 735318547 0.000000e+00 2410
3 TraesCS4A01G479900 chr4A 86.317 2251 264 22 998 3215 736883975 736886214 0.000000e+00 2410
4 TraesCS4A01G479900 chr4A 86.133 2250 268 20 999 3215 735767122 735769360 0.000000e+00 2386
5 TraesCS4A01G479900 chr4A 85.295 2353 295 32 894 3215 734585034 734587366 0.000000e+00 2381
6 TraesCS4A01G479900 chr4A 84.792 2354 316 28 885 3215 736756218 736758552 0.000000e+00 2326
7 TraesCS4A01G479900 chr4A 85.871 2194 291 15 1032 3215 735747182 735749366 0.000000e+00 2316
8 TraesCS4A01G479900 chr4A 84.660 2223 275 27 1029 3215 736896812 736899004 0.000000e+00 2156
9 TraesCS4A01G479900 chr4A 96.462 650 11 3 1 645 734729588 734730230 0.000000e+00 1062
10 TraesCS4A01G479900 chr4A 78.009 432 70 14 237 645 736755414 736755843 6.890000e-62 248
11 TraesCS4A01G479900 chr7D 98.153 1895 34 1 1322 3215 5486535 5484641 0.000000e+00 3304
12 TraesCS4A01G479900 chr7D 85.708 2344 292 26 900 3215 5649479 5647151 0.000000e+00 2433
13 TraesCS4A01G479900 chr7D 85.869 2215 272 20 1029 3215 5449078 5446877 0.000000e+00 2318
14 TraesCS4A01G479900 chr7D 94.032 687 33 2 643 1329 5487372 5486694 0.000000e+00 1035
15 TraesCS4A01G479900 chr7D 98.148 594 10 1 52 645 5488054 5487462 0.000000e+00 1035
16 TraesCS4A01G479900 chr7A 85.830 2216 270 24 1030 3215 6928615 6926414 0.000000e+00 2313


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 TraesCS4A01G479900 chr4A 736569750 736572964 3214 False 5938.000000 5938 100.000000 1 3215 1 chr4A.!!$F5 3214
1 TraesCS4A01G479900 chr4A 734729588 734732888 3300 False 2833.000000 4604 97.726000 1 3215 2 chr4A.!!$F8 3214
2 TraesCS4A01G479900 chr4A 735316354 735318547 2193 False 2410.000000 2410 86.621000 1029 3215 1 chr4A.!!$F2 2186
3 TraesCS4A01G479900 chr4A 736883975 736886214 2239 False 2410.000000 2410 86.317000 998 3215 1 chr4A.!!$F6 2217
4 TraesCS4A01G479900 chr4A 735767122 735769360 2238 False 2386.000000 2386 86.133000 999 3215 1 chr4A.!!$F4 2216
5 TraesCS4A01G479900 chr4A 734585034 734587366 2332 False 2381.000000 2381 85.295000 894 3215 1 chr4A.!!$F1 2321
6 TraesCS4A01G479900 chr4A 735747182 735749366 2184 False 2316.000000 2316 85.871000 1032 3215 1 chr4A.!!$F3 2183
7 TraesCS4A01G479900 chr4A 736896812 736899004 2192 False 2156.000000 2156 84.660000 1029 3215 1 chr4A.!!$F7 2186
8 TraesCS4A01G479900 chr4A 736755414 736758552 3138 False 1287.000000 2326 81.400500 237 3215 2 chr4A.!!$F9 2978
9 TraesCS4A01G479900 chr7D 5647151 5649479 2328 True 2433.000000 2433 85.708000 900 3215 1 chr7D.!!$R2 2315
10 TraesCS4A01G479900 chr7D 5446877 5449078 2201 True 2318.000000 2318 85.869000 1029 3215 1 chr7D.!!$R1 2186
11 TraesCS4A01G479900 chr7D 5484641 5488054 3413 True 1791.333333 3304 96.777667 52 3215 3 chr7D.!!$R3 3163
12 TraesCS4A01G479900 chr7A 6926414 6928615 2201 True 2313.000000 2313 85.830000 1030 3215 1 chr7A.!!$R1 2185

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
956 1184 0.529555 CAAAGCAAACACAACCCCCG 60.53 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2380 2812 3.507622 CCAAAGAAGAACCAACTCATCCC 59.492 47.826 0.0 0.0 0.0 3.85 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
56 57 7.546250 TCTCTCCCAGGTGATAAATAAGATC 57.454 40.000 0.00 0.0 0.00 2.75
124 125 4.825422 TCTCGCAGAAACTCAGAATGATT 58.175 39.130 0.00 0.0 40.56 2.57
280 285 1.481363 TGTGTCCACGTTGGTTACTGA 59.519 47.619 0.00 0.0 39.03 3.41
304 309 9.914131 TGATTAGTTTATTATCGATCAGTGAGG 57.086 33.333 0.00 0.0 0.00 3.86
412 435 8.410673 TTCTATTAGTTCCTACTATCTGCCTG 57.589 38.462 0.00 0.0 36.76 4.85
740 862 1.550869 CCATCCCTTTGCCCAGAAACT 60.551 52.381 0.00 0.0 0.00 2.66
801 1007 8.926710 CGTTCTATGATTGGTATCTTTATGGAC 58.073 37.037 0.00 0.0 0.00 4.02
897 1119 5.357742 ACAGGAAAATTCTGCTTGGTTTT 57.642 34.783 0.00 0.0 35.78 2.43
956 1184 0.529555 CAAAGCAAACACAACCCCCG 60.530 55.000 0.00 0.0 0.00 5.73
1050 1290 2.169832 TAAGATTAGCTGCATCGCCC 57.830 50.000 1.02 0.0 0.00 6.13
1504 1910 0.983378 AGAGAGCCCCACCATACCAC 60.983 60.000 0.00 0.0 0.00 4.16
1965 2375 6.668283 ACCAACTATTAGCTCCTCTAGTTTCA 59.332 38.462 0.00 0.0 33.34 2.69
2380 2812 7.504924 TTCCAAAAGGTCACAAGTATGTTAG 57.495 36.000 0.00 0.0 37.82 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.842381 GACAAGGGAGGTGGGAGTGG 61.842 65.000 0.00 0.0 0.00 4.00
124 125 1.202758 AGTGTCCGTTTGCAGGAATCA 60.203 47.619 0.00 0.0 39.84 2.57
304 309 7.606839 ACAACTTGCCTATCTTTTAAGGTCTAC 59.393 37.037 0.00 0.0 35.16 2.59
433 456 1.553690 ATTGTAGGAGCCCGTGCAGT 61.554 55.000 0.00 0.0 41.13 4.40
740 862 1.540267 GATCCGTAGAGCGCTGGAATA 59.460 52.381 18.48 0.0 39.71 1.75
897 1119 3.253188 GGTGCAGAAAGACAAACTATGCA 59.747 43.478 0.00 0.0 39.01 3.96
956 1184 1.860676 TTGCGTATATGCCTTCGGAC 58.139 50.000 14.32 0.0 0.00 4.79
984 1212 4.154015 TCTGTCATCGGTATTGCAGTTTTG 59.846 41.667 0.00 0.0 0.00 2.44
1050 1290 2.654987 GCAAGGAGCTTCTTCAAAACG 58.345 47.619 3.55 0.0 41.15 3.60
1080 1320 0.963962 TGTCCACTCCAAGGTACGTC 59.036 55.000 0.00 0.0 0.00 4.34
1504 1910 1.815003 GGCCTCAAGAACATCAACTGG 59.185 52.381 0.00 0.0 0.00 4.00
1965 2375 4.961438 AATTTTGCTTCCCATCTGTTGT 57.039 36.364 0.00 0.0 0.00 3.32
2380 2812 3.507622 CCAAAGAAGAACCAACTCATCCC 59.492 47.826 0.00 0.0 0.00 3.85


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

AutoCloner maintained by Alex Coulton.