Multiple sequence alignment - TraesCS5D01G544700

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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 TraesCS5D01G544700 chr5D 100.000 5339 0 0 2750 8088 554345109 554350447 0.000000e+00 9860
1 TraesCS5D01G544700 chr5D 86.767 4262 528 19 2935 7169 554142519 554146771 0.000000e+00 4713
2 TraesCS5D01G544700 chr5D 86.607 4271 526 11 2948 7199 553967839 553963596 0.000000e+00 4676
3 TraesCS5D01G544700 chr5D 100.000 2428 0 0 1 2428 554342360 554344787 0.000000e+00 4484
4 TraesCS5D01G544700 chr5D 80.508 354 42 13 1000 1335 554140920 554141264 6.270000e-61 246
5 TraesCS5D01G544700 chr4A 86.441 4425 516 25 2948 7310 614256666 614252264 0.000000e+00 4771
6 TraesCS5D01G544700 chr4A 87.500 168 17 4 7923 8088 604661766 604661931 2.980000e-44 191
7 TraesCS5D01G544700 chr5B 86.855 3507 421 16 3714 7193 696445507 696449000 0.000000e+00 3886
8 TraesCS5D01G544700 chr5B 85.911 1306 157 14 2955 4249 696437757 696439046 0.000000e+00 1367
9 TraesCS5D01G544700 chr5B 89.097 587 58 1 4252 4832 696444309 696444895 0.000000e+00 725
10 TraesCS5D01G544700 chr2D 73.856 1966 429 65 3140 5052 572067691 572069624 0.000000e+00 704
11 TraesCS5D01G544700 chrUn 72.744 1585 365 51 3083 4626 248487088 248488646 9.500000e-129 472
12 TraesCS5D01G544700 chr6D 72.989 1492 344 44 3295 4758 467787199 467785739 1.230000e-127 468
13 TraesCS5D01G544700 chr5A 73.031 1498 336 53 3295 4761 482355070 482356530 4.420000e-127 466
14 TraesCS5D01G544700 chr5A 72.721 1492 348 46 3295 4758 482369154 482370614 5.760000e-121 446
15 TraesCS5D01G544700 chr5A 89.820 167 14 3 7923 8088 546884312 546884148 2.290000e-50 211
16 TraesCS5D01G544700 chr5A 87.879 165 15 3 7925 8088 568049558 568049398 1.070000e-43 189
17 TraesCS5D01G544700 chr6B 74.476 1144 239 41 3298 4416 713067184 713066069 5.760000e-121 446
18 TraesCS5D01G544700 chr7D 71.761 1721 418 56 3083 4761 631231386 631233080 2.700000e-114 424
19 TraesCS5D01G544700 chr7D 89.222 167 16 2 7923 8088 117544236 117544071 2.960000e-49 207
20 TraesCS5D01G544700 chr2B 74.518 985 221 20 3296 4262 683752527 683753499 1.260000e-107 401
21 TraesCS5D01G544700 chr2B 73.114 1153 233 59 4265 5395 686812615 686813712 2.800000e-89 340
22 TraesCS5D01G544700 chr2A 74.595 988 215 24 3296 4262 710355616 710356588 1.260000e-107 401
23 TraesCS5D01G544700 chr7A 92.262 168 10 3 7923 8088 135898170 135898336 1.360000e-57 235
24 TraesCS5D01G544700 chr7A 88.757 169 16 2 7923 8088 56980244 56980076 3.830000e-48 204
25 TraesCS5D01G544700 chr7B 89.024 164 15 3 7923 8084 66884036 66883874 4.950000e-47 200
26 TraesCS5D01G544700 chr7B 87.879 165 18 2 7925 8088 711233387 711233550 8.280000e-45 193
27 TraesCS5D01G544700 chr1A 87.425 167 17 3 7923 8088 74276455 74276292 1.070000e-43 189


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 TraesCS5D01G544700 chr5D 554342360 554350447 8087 False 7172.0 9860 100.0000 1 8088 2 chr5D.!!$F2 8087
1 TraesCS5D01G544700 chr5D 553963596 553967839 4243 True 4676.0 4676 86.6070 2948 7199 1 chr5D.!!$R1 4251
2 TraesCS5D01G544700 chr5D 554140920 554146771 5851 False 2479.5 4713 83.6375 1000 7169 2 chr5D.!!$F1 6169
3 TraesCS5D01G544700 chr4A 614252264 614256666 4402 True 4771.0 4771 86.4410 2948 7310 1 chr4A.!!$R1 4362
4 TraesCS5D01G544700 chr5B 696444309 696449000 4691 False 2305.5 3886 87.9760 3714 7193 2 chr5B.!!$F2 3479
5 TraesCS5D01G544700 chr5B 696437757 696439046 1289 False 1367.0 1367 85.9110 2955 4249 1 chr5B.!!$F1 1294
6 TraesCS5D01G544700 chr2D 572067691 572069624 1933 False 704.0 704 73.8560 3140 5052 1 chr2D.!!$F1 1912
7 TraesCS5D01G544700 chrUn 248487088 248488646 1558 False 472.0 472 72.7440 3083 4626 1 chrUn.!!$F1 1543
8 TraesCS5D01G544700 chr6D 467785739 467787199 1460 True 468.0 468 72.9890 3295 4758 1 chr6D.!!$R1 1463
9 TraesCS5D01G544700 chr5A 482355070 482356530 1460 False 466.0 466 73.0310 3295 4761 1 chr5A.!!$F1 1466
10 TraesCS5D01G544700 chr5A 482369154 482370614 1460 False 446.0 446 72.7210 3295 4758 1 chr5A.!!$F2 1463
11 TraesCS5D01G544700 chr6B 713066069 713067184 1115 True 446.0 446 74.4760 3298 4416 1 chr6B.!!$R1 1118
12 TraesCS5D01G544700 chr7D 631231386 631233080 1694 False 424.0 424 71.7610 3083 4761 1 chr7D.!!$F1 1678
13 TraesCS5D01G544700 chr2B 683752527 683753499 972 False 401.0 401 74.5180 3296 4262 1 chr2B.!!$F1 966
14 TraesCS5D01G544700 chr2B 686812615 686813712 1097 False 340.0 340 73.1140 4265 5395 1 chr2B.!!$F2 1130
15 TraesCS5D01G544700 chr2A 710355616 710356588 972 False 401.0 401 74.5950 3296 4262 1 chr2A.!!$F1 966


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
188 189 0.035439 CGGCCACAAGGTATGTTCCT 60.035 55.000 2.24 0.00 41.46 3.36 F
1876 1929 0.029433 GATGAATTCGAAAGGCCCGC 59.971 55.000 0.00 0.00 0.00 6.13 F
2367 2420 0.030638 TTTCGCTGCTTTGCCTCAAC 59.969 50.000 0.00 0.00 0.00 3.18 F
2402 2455 0.039618 GGGGATTTGGTTGCTGAGGA 59.960 55.000 0.00 0.00 0.00 3.71 F
2897 3041 0.250858 TGGTGATGTCTTGGCCACAG 60.251 55.000 3.88 6.78 0.00 3.66 F
3117 3573 0.435008 GATGACGAGTCAACACACGC 59.565 55.000 10.15 0.00 43.58 5.34 F
3213 3669 1.637553 AGGCACATCAAGGGTTCTGAT 59.362 47.619 0.00 0.00 0.00 2.90 F
5148 5664 0.895559 CTTGAGGGCCTTCAACCACC 60.896 60.000 25.26 0.00 33.71 4.61 F
5224 5740 0.175760 GGCTTGCCGACAGTATCTCA 59.824 55.000 0.00 0.00 0.00 3.27 F
6540 7068 0.179100 CTACAGCTGCGTACCTGCAT 60.179 55.000 15.27 0.00 45.26 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 1949 0.034476 CAGTTGAGCTCTGAGCCACA 59.966 55.000 25.09 21.33 43.77 4.17 R
2880 2933 0.036732 TCCTGTGGCCAAGACATCAC 59.963 55.000 7.24 0.00 0.00 3.06 R
3882 4368 1.016627 TGCTATTCGCAGTCCAATGC 58.983 50.000 0.00 0.00 45.47 3.56 R
4195 4681 3.013219 GTCCATTCCTTTCTCCTCAAGC 58.987 50.000 0.00 0.00 0.00 4.01 R
4470 4980 1.391485 CGGCGAACATGTTCTTCTCAG 59.609 52.381 30.45 17.75 37.44 3.35 R
5061 5577 0.462581 TTCATCATCTGGCGAGGCAC 60.463 55.000 0.00 0.00 0.00 5.01 R
5191 5707 1.986882 CAAGCCAAGTTGGGAAGAGT 58.013 50.000 23.36 0.00 38.19 3.24 R
6803 7346 0.612229 TGAAGCCCTCTCTCTTGCTG 59.388 55.000 0.00 0.00 33.59 4.41 R
6896 7442 0.670546 TTCTTGAGCGAAGGAAGCCG 60.671 55.000 0.00 0.00 34.64 5.52 R
7595 8175 0.031043 CAACATGGCGGTGCATATGG 59.969 55.000 4.56 0.00 31.95 2.74 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)



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

AutoCloner maintained by Alex Coulton.