Multiple sequence alignment - TraesCS3A01G462300

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 TraesCS3A01G462300 chr3A 100.000 2627 0 0 1 2627 697520128 697522754 0.000000e+00 4852
1 TraesCS3A01G462300 chr5A 97.726 2638 48 4 1 2627 609823853 609821217 0.000000e+00 4529
2 TraesCS3A01G462300 chr5A 91.618 859 42 13 426 1271 688243208 688244049 0.000000e+00 1160
3 TraesCS3A01G462300 chr5A 89.877 405 33 4 1356 1753 688244181 688244584 5.010000e-142 514
4 TraesCS3A01G462300 chr5A 85.371 458 36 14 1356 1812 680364945 680365372 1.860000e-121 446
5 TraesCS3A01G462300 chr5A 89.558 249 19 4 1117 1359 680364641 680364888 2.540000e-80 309
6 TraesCS3A01G462300 chr5A 100.000 73 0 0 2114 2186 605038938 605038866 4.560000e-28 135
7 TraesCS3A01G462300 chr4A 97.247 2325 47 4 1 2308 17244806 17247130 0.000000e+00 3923
8 TraesCS3A01G462300 chr4A 96.907 388 10 2 2235 2622 17247111 17247496 0.000000e+00 649
9 TraesCS3A01G462300 chr7A 97.154 2319 54 4 1 2308 672599465 672597148 0.000000e+00 3906
10 TraesCS3A01G462300 chr7A 96.723 2319 64 4 1 2308 113794937 113797254 0.000000e+00 3851
11 TraesCS3A01G462300 chr7A 97.260 1788 26 3 524 2308 674116095 674114328 0.000000e+00 3009
12 TraesCS3A01G462300 chr7A 96.111 540 13 2 1 532 674121714 674121175 0.000000e+00 874
13 TraesCS3A01G462300 chr7A 98.728 393 4 1 2235 2627 674114347 674113956 0.000000e+00 697
14 TraesCS3A01G462300 chr7A 98.718 390 4 1 2235 2624 672597167 672596779 0.000000e+00 691
15 TraesCS3A01G462300 chr7A 97.938 388 7 1 2235 2622 113797235 113797621 0.000000e+00 671
16 TraesCS3A01G462300 chr7A 93.805 113 7 0 1984 2096 613712209 613712321 1.250000e-38 171
17 TraesCS3A01G462300 chr7A 98.630 73 1 0 2114 2186 613713189 613713117 2.120000e-26 130
18 TraesCS3A01G462300 chr4B 89.396 943 66 15 426 1350 649491307 649492233 0.000000e+00 1157
19 TraesCS3A01G462300 chr4B 91.447 456 24 2 1356 1811 649492303 649492743 1.730000e-171 612
20 TraesCS3A01G462300 chr4D 86.710 933 59 25 426 1344 503669221 503670102 0.000000e+00 976
21 TraesCS3A01G462300 chr4D 88.715 638 41 13 724 1359 503639662 503640270 0.000000e+00 750
22 TraesCS3A01G462300 chr4D 88.631 431 36 5 1356 1778 503670177 503670602 1.800000e-141 512
23 TraesCS3A01G462300 chr4D 86.750 400 23 13 1412 1811 503641746 503642115 4.040000e-113 418
24 TraesCS3A01G462300 chr4D 93.805 113 7 0 1984 2096 198583169 198583281 1.250000e-38 171
25 TraesCS3A01G462300 chr4D 84.000 200 9 6 431 622 503639481 503639665 1.250000e-38 171
26 TraesCS3A01G462300 chr4D 100.000 73 0 0 2114 2186 198584148 198584076 4.560000e-28 135
27 TraesCS3A01G462300 chr1B 92.140 598 20 6 426 1005 117290240 117289652 0.000000e+00 819
28 TraesCS3A01G462300 chr1B 96.594 411 10 3 2220 2627 117289653 117289244 0.000000e+00 678
29 TraesCS3A01G462300 chr1B 94.059 404 23 1 1 403 117290929 117290526 1.730000e-171 612
30 TraesCS3A01G462300 chr2A 92.255 439 21 7 2195 2622 207108732 207109168 6.220000e-171 610
31 TraesCS3A01G462300 chr3B 91.991 437 30 4 2195 2627 742768198 742767763 2.240000e-170 608
32 TraesCS3A01G462300 chr3B 91.533 437 31 5 2195 2627 742625192 742624758 4.840000e-167 597
33 TraesCS3A01G462300 chr5D 95.330 364 12 4 2220 2580 358667910 358667549 8.160000e-160 573
34 TraesCS3A01G462300 chr5D 92.308 130 10 0 1830 1959 548028003 548027874 4.460000e-43 185
35 TraesCS3A01G462300 chr5D 96.040 101 4 0 1827 1927 358668096 358667996 5.820000e-37 165
36 TraesCS3A01G462300 chr7D 94.769 325 16 1 23 346 32582889 32582565 3.020000e-139 505
37 TraesCS3A01G462300 chr5B 91.667 132 11 0 1828 1959 692215151 692215020 1.610000e-42 183
38 TraesCS3A01G462300 chr5B 92.920 113 8 0 1984 2096 386154126 386154238 5.820000e-37 165
39 TraesCS3A01G462300 chr5B 100.000 73 0 0 2114 2186 386155100 386155028 4.560000e-28 135
40 TraesCS3A01G462300 chr6A 93.805 113 7 0 1984 2096 36692100 36692212 1.250000e-38 171


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 TraesCS3A01G462300 chr3A 697520128 697522754 2626 False 4852.000000 4852 100.000000 1 2627 1 chr3A.!!$F1 2626
1 TraesCS3A01G462300 chr5A 609821217 609823853 2636 True 4529.000000 4529 97.726000 1 2627 1 chr5A.!!$R2 2626
2 TraesCS3A01G462300 chr5A 688243208 688244584 1376 False 837.000000 1160 90.747500 426 1753 2 chr5A.!!$F2 1327
3 TraesCS3A01G462300 chr5A 680364641 680365372 731 False 377.500000 446 87.464500 1117 1812 2 chr5A.!!$F1 695
4 TraesCS3A01G462300 chr4A 17244806 17247496 2690 False 2286.000000 3923 97.077000 1 2622 2 chr4A.!!$F1 2621
5 TraesCS3A01G462300 chr7A 672596779 672599465 2686 True 2298.500000 3906 97.936000 1 2624 2 chr7A.!!$R3 2623
6 TraesCS3A01G462300 chr7A 113794937 113797621 2684 False 2261.000000 3851 97.330500 1 2622 2 chr7A.!!$F2 2621
7 TraesCS3A01G462300 chr7A 674113956 674116095 2139 True 1853.000000 3009 97.994000 524 2627 2 chr7A.!!$R4 2103
8 TraesCS3A01G462300 chr7A 674121175 674121714 539 True 874.000000 874 96.111000 1 532 1 chr7A.!!$R2 531
9 TraesCS3A01G462300 chr4B 649491307 649492743 1436 False 884.500000 1157 90.421500 426 1811 2 chr4B.!!$F1 1385
10 TraesCS3A01G462300 chr4D 503669221 503670602 1381 False 744.000000 976 87.670500 426 1778 2 chr4D.!!$F3 1352
11 TraesCS3A01G462300 chr4D 503639481 503642115 2634 False 446.333333 750 86.488333 431 1811 3 chr4D.!!$F2 1380
12 TraesCS3A01G462300 chr1B 117289244 117290929 1685 True 703.000000 819 94.264333 1 2627 3 chr1B.!!$R1 2626
13 TraesCS3A01G462300 chr5D 358667549 358668096 547 True 369.000000 573 95.685000 1827 2580 2 chr5D.!!$R2 753

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
351 352 2.952310 GGCCAGGTGAGTTTGGATATTC 59.048 50.000 0.0 0.0 36.55 1.75 F
400 401 7.276438 GGGCAAATCATTAAGTTTCTAGCAAAG 59.724 37.037 0.0 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1601 2.103094 AGGGAGGCAAAACAAAAGCTTC 59.897 45.455 0.00 0.0 34.10 3.86 R
2499 4457 9.061435 CCTTGGGCAAAGATTAACAAAATAAAA 57.939 29.630 2.31 0.0 38.24 1.52 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
351 352 2.952310 GGCCAGGTGAGTTTGGATATTC 59.048 50.000 0.00 0.00 36.55 1.75
400 401 7.276438 GGGCAAATCATTAAGTTTCTAGCAAAG 59.724 37.037 0.00 0.00 0.00 2.77
962 1269 7.305418 GCTTAAGTTTGTTTTGTCGACATCAAG 60.305 37.037 20.80 12.19 0.00 3.02
1291 1601 2.831333 AGTCATGCTTCTCTATTGGCG 58.169 47.619 0.00 0.00 0.00 5.69
1452 3256 5.884792 GGTGATTCTCATGTTCTCTGGATTT 59.115 40.000 0.00 0.00 0.00 2.17
1453 3257 6.038050 GGTGATTCTCATGTTCTCTGGATTTC 59.962 42.308 0.00 0.00 0.00 2.17
2378 4335 6.086785 TCATGACTGAATTTTGCATTGTGA 57.913 33.333 0.00 0.00 0.00 3.58
2480 4438 6.016192 TGACTTAGAGACACTACAAGTCCTTG 60.016 42.308 10.98 5.51 40.60 3.61
2499 4457 5.608437 TCCTTGGAGTCATCTAAGCCAATAT 59.392 40.000 0.00 0.00 41.41 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
351 352 0.830023 ACAAAATTCCCCCACGGTGG 60.830 55.000 20.41 20.41 37.25 4.61
400 401 5.631512 TGCGAAACTAAATATTTGCCACAAC 59.368 36.000 11.05 0.00 35.49 3.32
539 823 3.366396 CCTAGAAGTTGGGCTCTGTCTA 58.634 50.000 0.00 0.00 0.00 2.59
757 1053 3.073062 AGAACCTAACTTGCACACCTCAT 59.927 43.478 0.00 0.00 0.00 2.90
758 1054 2.438021 AGAACCTAACTTGCACACCTCA 59.562 45.455 0.00 0.00 0.00 3.86
759 1055 2.808543 CAGAACCTAACTTGCACACCTC 59.191 50.000 0.00 0.00 0.00 3.85
760 1056 2.172717 ACAGAACCTAACTTGCACACCT 59.827 45.455 0.00 0.00 0.00 4.00
761 1057 2.290641 CACAGAACCTAACTTGCACACC 59.709 50.000 0.00 0.00 0.00 4.16
1291 1601 2.103094 AGGGAGGCAAAACAAAAGCTTC 59.897 45.455 0.00 0.00 34.10 3.86
2499 4457 9.061435 CCTTGGGCAAAGATTAACAAAATAAAA 57.939 29.630 2.31 0.00 38.24 1.52


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

AutoCloner maintained by Alex Coulton.