Multiple sequence alignment - TraesCS6A01G332400

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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 TraesCS6A01G332400 chr6A 100.000 2488 0 0 1 2488 564190237 564192724 0.000000e+00 4595
1 TraesCS6A01G332400 chr6A 96.855 2385 66 6 1 2379 564237693 564240074 0.000000e+00 3980
2 TraesCS6A01G332400 chr6A 97.390 1724 40 3 615 2334 564132052 564133774 0.000000e+00 2929
3 TraesCS6A01G332400 chr6A 84.272 1208 124 37 698 1860 564117558 564118744 0.000000e+00 1118
4 TraesCS6A01G332400 chr6A 95.942 616 25 0 1 616 564224419 564225034 0.000000e+00 1000
5 TraesCS6A01G332400 chr6A 95.292 616 29 0 4 619 37858982 37858367 0.000000e+00 977
6 TraesCS6A01G332400 chr6A 95.292 616 29 0 1 616 564168441 564169056 0.000000e+00 977
7 TraesCS6A01G332400 chr6A 84.109 774 64 31 819 1580 564259894 564260620 0.000000e+00 693
8 TraesCS6A01G332400 chr6A 95.455 66 3 0 2423 2488 564134108 564134173 3.380000e-19 106
9 TraesCS6A01G332400 chr6B 90.503 1927 118 22 615 2481 634321516 634323437 0.000000e+00 2484
10 TraesCS6A01G332400 chr6B 84.080 1206 112 42 615 1766 634315287 634316466 0.000000e+00 1090
11 TraesCS6A01G332400 chr6B 89.535 602 37 15 982 1580 634329953 634330531 0.000000e+00 739
12 TraesCS6A01G332400 chr6D 91.412 1735 86 21 615 2303 420935323 420937040 0.000000e+00 2320
13 TraesCS6A01G332400 chr6D 83.956 1178 127 28 615 1750 420898769 420899926 0.000000e+00 1072
14 TraesCS6A01G332400 chr6D 86.047 774 62 17 819 1580 420956415 420957154 0.000000e+00 789
15 TraesCS6A01G332400 chr4A 95.617 616 27 0 1 616 257508102 257508717 0.000000e+00 989
16 TraesCS6A01G332400 chr2A 95.624 617 26 1 1 616 161413162 161413778 0.000000e+00 989
17 TraesCS6A01G332400 chr2A 95.130 616 30 0 1 616 676634223 676634838 0.000000e+00 972
18 TraesCS6A01G332400 chr5A 95.153 619 30 0 1 619 285804362 285803744 0.000000e+00 977
19 TraesCS6A01G332400 chr5A 94.992 619 31 0 1 619 316670289 316669671 0.000000e+00 972


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 TraesCS6A01G332400 chr6A 564190237 564192724 2487 False 4595.0 4595 100.0000 1 2488 1 chr6A.!!$F3 2487
1 TraesCS6A01G332400 chr6A 564237693 564240074 2381 False 3980.0 3980 96.8550 1 2379 1 chr6A.!!$F5 2378
2 TraesCS6A01G332400 chr6A 564132052 564134173 2121 False 1517.5 2929 96.4225 615 2488 2 chr6A.!!$F7 1873
3 TraesCS6A01G332400 chr6A 564117558 564118744 1186 False 1118.0 1118 84.2720 698 1860 1 chr6A.!!$F1 1162
4 TraesCS6A01G332400 chr6A 564224419 564225034 615 False 1000.0 1000 95.9420 1 616 1 chr6A.!!$F4 615
5 TraesCS6A01G332400 chr6A 37858367 37858982 615 True 977.0 977 95.2920 4 619 1 chr6A.!!$R1 615
6 TraesCS6A01G332400 chr6A 564168441 564169056 615 False 977.0 977 95.2920 1 616 1 chr6A.!!$F2 615
7 TraesCS6A01G332400 chr6A 564259894 564260620 726 False 693.0 693 84.1090 819 1580 1 chr6A.!!$F6 761
8 TraesCS6A01G332400 chr6B 634321516 634323437 1921 False 2484.0 2484 90.5030 615 2481 1 chr6B.!!$F2 1866
9 TraesCS6A01G332400 chr6B 634315287 634316466 1179 False 1090.0 1090 84.0800 615 1766 1 chr6B.!!$F1 1151
10 TraesCS6A01G332400 chr6B 634329953 634330531 578 False 739.0 739 89.5350 982 1580 1 chr6B.!!$F3 598
11 TraesCS6A01G332400 chr6D 420935323 420937040 1717 False 2320.0 2320 91.4120 615 2303 1 chr6D.!!$F2 1688
12 TraesCS6A01G332400 chr6D 420898769 420899926 1157 False 1072.0 1072 83.9560 615 1750 1 chr6D.!!$F1 1135
13 TraesCS6A01G332400 chr6D 420956415 420957154 739 False 789.0 789 86.0470 819 1580 1 chr6D.!!$F3 761
14 TraesCS6A01G332400 chr4A 257508102 257508717 615 False 989.0 989 95.6170 1 616 1 chr4A.!!$F1 615
15 TraesCS6A01G332400 chr2A 161413162 161413778 616 False 989.0 989 95.6240 1 616 1 chr2A.!!$F1 615
16 TraesCS6A01G332400 chr2A 676634223 676634838 615 False 972.0 972 95.1300 1 616 1 chr2A.!!$F2 615
17 TraesCS6A01G332400 chr5A 285803744 285804362 618 True 977.0 977 95.1530 1 619 1 chr5A.!!$R1 618
18 TraesCS6A01G332400 chr5A 316669671 316670289 618 True 972.0 972 94.9920 1 619 1 chr5A.!!$R2 618

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
380 381 1.405933 CCAGCGATCCACAATGACTCA 60.406 52.381 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2272 1.88034 CGACTTCGGCTCTGGCATC 60.88 63.158 0.0 0.0 40.87 3.91 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
26 27 6.778069 AGCACAATGACTAATAGTAGCTAGGA 59.222 38.462 0.00 0.00 0.00 2.94
29 30 8.851145 CACAATGACTAATAGTAGCTAGGAAGA 58.149 37.037 0.00 0.00 0.00 2.87
82 83 3.103447 TCAGAACAAGCAGTCACTCAG 57.897 47.619 0.00 0.00 0.00 3.35
362 363 2.680841 CCTTCACAAACTTCGTTCACCA 59.319 45.455 0.00 0.00 0.00 4.17
380 381 1.405933 CCAGCGATCCACAATGACTCA 60.406 52.381 0.00 0.00 0.00 3.41
489 490 4.999950 ACTTCAGTGATGCCTAACTCTTTG 59.000 41.667 5.95 0.00 0.00 2.77
539 540 4.641396 TCGCAAGGAATTCTCTCTCAAAA 58.359 39.130 5.23 0.00 38.47 2.44
546 547 5.180304 AGGAATTCTCTCTCAAAAACTTCGC 59.820 40.000 5.23 0.00 0.00 4.70
572 573 3.428316 GGGTTGCTCTCAAACGACAAAAA 60.428 43.478 0.00 0.00 40.76 1.94
622 623 5.183228 CGTTTATGGTTGTAGGGAGTTGAT 58.817 41.667 0.00 0.00 0.00 2.57
633 634 5.663106 TGTAGGGAGTTGATAAAGCTCTCAT 59.337 40.000 0.00 0.00 32.45 2.90
736 740 5.458041 AATGCTAAACAACAAGCTCACAT 57.542 34.783 0.00 0.00 39.53 3.21
843 868 7.542130 CCAGGTGCTTACTGTGATTAAAAATTC 59.458 37.037 0.00 0.00 34.16 2.17
905 931 1.625315 CTGGTGTCAGAATCAGGGTCA 59.375 52.381 0.00 0.00 43.49 4.02
1302 1370 3.390521 CCGCTGCCTCCAGGTACA 61.391 66.667 0.00 0.00 39.54 2.90
2012 2122 9.565213 CTCACAAATTCATCTCAAAATAGAACC 57.435 33.333 0.00 0.00 0.00 3.62
2053 2173 3.430374 GGTAGCACAATCCGATACACTGT 60.430 47.826 0.00 0.00 0.00 3.55
2142 2272 0.613260 TCTCCCAATCCACTTCACCG 59.387 55.000 0.00 0.00 0.00 4.94
2419 2564 2.494918 GGGGAGTCGACGGTGATG 59.505 66.667 10.46 0.00 0.00 3.07
2434 2813 1.483827 GTGATGAGCTCCAGGACATCA 59.516 52.381 12.15 14.55 44.05 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.661954 TCACTATATCTTCCTACCTCATCTTTT 57.338 33.333 0.00 0.00 0.00 2.27
36 37 5.775701 TGGCTTCACTATATCTTCCTACCTC 59.224 44.000 0.00 0.00 0.00 3.85
82 83 9.674824 CATGATTGCCTTATCTTTTATCTTCAC 57.325 33.333 0.00 0.00 0.00 3.18
292 293 1.003580 GAGTGATTGGGCAAGGACTGA 59.996 52.381 0.00 0.00 0.00 3.41
362 363 2.558378 CATGAGTCATTGTGGATCGCT 58.442 47.619 1.86 0.00 0.00 4.93
380 381 0.807667 GTCGCGTTCTGAGCATCCAT 60.808 55.000 5.77 0.00 34.19 3.41
489 490 0.831307 CCCTAACCACCTAGAGCCAC 59.169 60.000 0.00 0.00 0.00 5.01
539 540 3.284449 GCAACCCACCGCGAAGTT 61.284 61.111 8.23 2.03 0.00 2.66
546 547 1.841663 CGTTTGAGAGCAACCCACCG 61.842 60.000 0.00 0.00 32.79 4.94
572 573 2.488545 CTGCTCAGAGTTAGTGTACGGT 59.511 50.000 0.00 0.00 0.00 4.83
622 623 5.767665 TGCCTTGTTGTTTATGAGAGCTTTA 59.232 36.000 0.00 0.00 0.00 1.85
633 634 6.203723 GTGCCAAATATTTGCCTTGTTGTTTA 59.796 34.615 20.67 0.00 36.86 2.01
736 740 5.189928 TGCTTTGGTCACTTAAACTCTTGA 58.810 37.500 0.00 0.00 0.00 3.02
843 868 3.475566 TCATCGCCTTCCCTTAATCAG 57.524 47.619 0.00 0.00 0.00 2.90
1020 1088 3.118454 ACCGACATTCTTGCGCCG 61.118 61.111 4.18 0.00 0.00 6.46
1033 1101 3.509137 GAACCAGCACCGACACCGA 62.509 63.158 0.00 0.00 38.22 4.69
1302 1370 4.338682 GGAGATAGGGACGCGTATGATTAT 59.661 45.833 13.97 6.33 0.00 1.28
1773 1876 6.842163 ACATAAAATCTGTCATTTCGACCAC 58.158 36.000 0.00 0.00 44.71 4.16
2012 2122 2.034558 ACCTTTGTGTTTGAATCCAGCG 59.965 45.455 0.00 0.00 0.00 5.18
2142 2272 1.880340 CGACTTCGGCTCTGGCATC 60.880 63.158 0.00 0.00 40.87 3.91
2402 2547 2.005960 CTCATCACCGTCGACTCCCC 62.006 65.000 14.70 0.00 0.00 4.81
2403 2548 1.433879 CTCATCACCGTCGACTCCC 59.566 63.158 14.70 0.00 0.00 4.30
2404 2549 1.226717 GCTCATCACCGTCGACTCC 60.227 63.158 14.70 0.00 0.00 3.85
2405 2550 0.248296 GAGCTCATCACCGTCGACTC 60.248 60.000 14.70 0.00 0.00 3.36
2406 2551 1.658686 GGAGCTCATCACCGTCGACT 61.659 60.000 17.19 0.00 0.00 4.18
2407 2552 1.226717 GGAGCTCATCACCGTCGAC 60.227 63.158 17.19 5.18 0.00 4.20
2419 2564 1.126488 TCCATGATGTCCTGGAGCTC 58.874 55.000 4.71 4.71 36.63 4.09
2434 2813 5.755375 GTCGTGTGAAGATATTGACATCCAT 59.245 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.