Multiple sequence alignment - TraesCS3A01G169600

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 TraesCS3A01G169600 chr3A 100.000 3377 0 0 1 3377 177705082 177701706 0.000000e+00 6237
1 TraesCS3A01G169600 chr3D 98.815 2363 28 0 1 2363 152822151 152824513 0.000000e+00 4209
2 TraesCS3A01G169600 chr3B 98.019 2373 36 4 1 2363 223961833 223964204 0.000000e+00 4111
3 TraesCS3A01G169600 chr5A 99.112 1014 9 0 2364 3377 675471860 675470847 0.000000e+00 1823
4 TraesCS3A01G169600 chr5A 91.250 400 29 3 109 502 565536224 565536623 1.070000e-149 540
5 TraesCS3A01G169600 chr1A 99.112 1014 9 0 2364 3377 6930735 6929722 0.000000e+00 1823
6 TraesCS3A01G169600 chr2B 99.014 1014 10 0 2364 3377 161426333 161427346 0.000000e+00 1818
7 TraesCS3A01G169600 chr2B 99.014 1014 10 0 2364 3377 774204848 774205861 0.000000e+00 1818
8 TraesCS3A01G169600 chr2B 76.156 1254 244 31 1044 2259 675534128 675535364 2.880000e-170 608
9 TraesCS3A01G169600 chr2B 75.450 1332 257 40 990 2276 675524843 675526149 4.860000e-163 584
10 TraesCS3A01G169600 chr2B 78.553 387 74 4 1882 2259 675334071 675333685 2.600000e-61 246
11 TraesCS3A01G169600 chrUn 98.915 1014 11 0 2364 3377 83556210 83555197 0.000000e+00 1812
12 TraesCS3A01G169600 chr4A 98.821 1018 11 1 2361 3377 453307120 453306103 0.000000e+00 1812
13 TraesCS3A01G169600 chr4A 98.817 1014 12 0 2364 3377 210939890 210938877 0.000000e+00 1807
14 TraesCS3A01G169600 chr6A 98.819 1016 12 0 2362 3377 560546733 560547748 0.000000e+00 1810
15 TraesCS3A01G169600 chr6A 91.750 400 27 3 109 502 108078635 108079034 4.920000e-153 551
16 TraesCS3A01G169600 chr7B 98.718 1014 12 1 2364 3377 484612668 484611656 0.000000e+00 1799
17 TraesCS3A01G169600 chr2D 75.981 1249 249 27 1044 2259 564476327 564477557 6.240000e-167 597
18 TraesCS3A01G169600 chr2D 79.328 387 71 4 1882 2259 564072002 564071616 2.580000e-66 263
19 TraesCS3A01G169600 chr7D 91.250 400 29 3 109 502 239729549 239729948 1.070000e-149 540
20 TraesCS3A01G169600 chr2A 95.703 256 10 1 109 363 1217920 1217665 8.720000e-111 411
21 TraesCS3A01G169600 chr2A 79.381 388 69 6 1882 2259 704754687 704754301 2.580000e-66 263
22 TraesCS3A01G169600 chr4B 80.061 326 50 5 1949 2259 22438650 22438325 9.430000e-56 228
23 TraesCS3A01G169600 chr4B 85.315 143 21 0 2117 2259 22488446 22488304 7.550000e-32 148


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 TraesCS3A01G169600 chr3A 177701706 177705082 3376 True 6237 6237 100.000 1 3377 1 chr3A.!!$R1 3376
1 TraesCS3A01G169600 chr3D 152822151 152824513 2362 False 4209 4209 98.815 1 2363 1 chr3D.!!$F1 2362
2 TraesCS3A01G169600 chr3B 223961833 223964204 2371 False 4111 4111 98.019 1 2363 1 chr3B.!!$F1 2362
3 TraesCS3A01G169600 chr5A 675470847 675471860 1013 True 1823 1823 99.112 2364 3377 1 chr5A.!!$R1 1013
4 TraesCS3A01G169600 chr1A 6929722 6930735 1013 True 1823 1823 99.112 2364 3377 1 chr1A.!!$R1 1013
5 TraesCS3A01G169600 chr2B 161426333 161427346 1013 False 1818 1818 99.014 2364 3377 1 chr2B.!!$F1 1013
6 TraesCS3A01G169600 chr2B 774204848 774205861 1013 False 1818 1818 99.014 2364 3377 1 chr2B.!!$F4 1013
7 TraesCS3A01G169600 chr2B 675534128 675535364 1236 False 608 608 76.156 1044 2259 1 chr2B.!!$F3 1215
8 TraesCS3A01G169600 chr2B 675524843 675526149 1306 False 584 584 75.450 990 2276 1 chr2B.!!$F2 1286
9 TraesCS3A01G169600 chrUn 83555197 83556210 1013 True 1812 1812 98.915 2364 3377 1 chrUn.!!$R1 1013
10 TraesCS3A01G169600 chr4A 453306103 453307120 1017 True 1812 1812 98.821 2361 3377 1 chr4A.!!$R2 1016
11 TraesCS3A01G169600 chr4A 210938877 210939890 1013 True 1807 1807 98.817 2364 3377 1 chr4A.!!$R1 1013
12 TraesCS3A01G169600 chr6A 560546733 560547748 1015 False 1810 1810 98.819 2362 3377 1 chr6A.!!$F2 1015
13 TraesCS3A01G169600 chr7B 484611656 484612668 1012 True 1799 1799 98.718 2364 3377 1 chr7B.!!$R1 1013
14 TraesCS3A01G169600 chr2D 564476327 564477557 1230 False 597 597 75.981 1044 2259 1 chr2D.!!$F1 1215

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
609 619 0.881118 GATTTCTTCCACTTGCGCCA 59.119 50.0 4.18 0.00 0.00 5.69 F
1282 1296 2.159920 CGAACTGTGCTCACATCTTTCG 60.160 50.0 18.37 18.37 41.01 3.46 F
1542 1571 0.036732 ACCCGCTCAGCAATCTTTCA 59.963 50.0 0.00 0.00 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1571 0.254178 AGCCGCTTGACAGGATGATT 59.746 50.0 0.00 0.00 39.69 2.57 R
2199 2249 0.683504 GGAGTAGTTCGCCTCCCTCA 60.684 60.0 0.00 0.00 41.22 3.86 R
2907 2957 1.400737 CGGTGTCTCCTAACCCTAGG 58.599 60.0 0.06 0.06 45.65 3.02 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
229 239 7.167302 CGATGTTTGACATTTTTGTTGCTCTTA 59.833 33.333 0.00 0.00 39.27 2.10
394 404 4.446413 CGCCGCCCTTACCTCGTT 62.446 66.667 0.00 0.00 0.00 3.85
489 499 5.392380 GGTGACCTGTCATGCTTTATTTGAG 60.392 44.000 2.91 0.00 42.18 3.02
571 581 2.229792 ACACTGATGCATCACCGTTTT 58.770 42.857 25.42 9.27 32.50 2.43
572 582 2.622942 ACACTGATGCATCACCGTTTTT 59.377 40.909 25.42 6.97 32.50 1.94
609 619 0.881118 GATTTCTTCCACTTGCGCCA 59.119 50.000 4.18 0.00 0.00 5.69
892 902 4.852697 ACTATTCCAAGTCTTCCTCCCTTT 59.147 41.667 0.00 0.00 0.00 3.11
1282 1296 2.159920 CGAACTGTGCTCACATCTTTCG 60.160 50.000 18.37 18.37 41.01 3.46
1542 1571 0.036732 ACCCGCTCAGCAATCTTTCA 59.963 50.000 0.00 0.00 0.00 2.69
1854 1889 3.069443 TGGTTCTCATTGCCTTGGTTTTC 59.931 43.478 0.00 0.00 0.00 2.29
2187 2237 1.267806 CGCAACCTTGTCAAGCTGATT 59.732 47.619 7.09 0.00 0.00 2.57
2277 2327 1.472082 CTATTGTTCGCCAATGCCACA 59.528 47.619 9.55 0.00 43.63 4.17
2679 2729 1.009829 GGACATGGTGATGACGAAGC 58.990 55.000 0.00 0.00 33.36 3.86
2907 2957 1.361668 ATGTGATCTGTTCGTGGCGC 61.362 55.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 239 4.601857 TCCCTGTCTATTTGAGGAAAAGGT 59.398 41.667 0.00 0.00 0.00 3.50
394 404 5.801531 TTTGGCTGAGTGACTAGAACTAA 57.198 39.130 0.00 0.00 0.00 2.24
489 499 3.365969 CCGAAGTCCAAAGTGGTATTTGC 60.366 47.826 0.00 0.00 39.03 3.68
571 581 2.689073 CAGAGGCTCTTCCCTGGAA 58.311 57.895 15.90 0.00 34.69 3.53
572 582 4.468829 CAGAGGCTCTTCCCTGGA 57.531 61.111 15.90 0.00 34.69 3.86
609 619 1.880027 GTGAGGCGAATGTTTGACCTT 59.120 47.619 0.00 0.00 0.00 3.50
892 902 6.611642 AGATACCACTAAGCCTTTCAGTATCA 59.388 38.462 14.01 0.00 38.06 2.15
1282 1296 3.112709 GAGCGTGAACTGCGTCCC 61.113 66.667 0.00 0.00 37.44 4.46
1500 1529 6.038271 GGTACGGATAAACAGATTTGATGCTT 59.962 38.462 0.00 0.00 0.00 3.91
1542 1571 0.254178 AGCCGCTTGACAGGATGATT 59.746 50.000 0.00 0.00 39.69 2.57
1854 1889 6.241207 AGAAACGATGAACATGTAACAAGG 57.759 37.500 0.00 2.45 0.00 3.61
2199 2249 0.683504 GGAGTAGTTCGCCTCCCTCA 60.684 60.000 0.00 0.00 41.22 3.86
2692 2742 1.964552 TCCGATCGTCTACTTCCTCC 58.035 55.000 15.09 0.00 0.00 4.30
2725 2775 2.456577 AGGTTTTTGGGCAGCGATTAT 58.543 42.857 0.00 0.00 0.00 1.28
2907 2957 1.400737 CGGTGTCTCCTAACCCTAGG 58.599 60.000 0.06 0.06 45.65 3.02


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

AutoCloner maintained by Alex Coulton.