Multiple sequence alignment - TraesCS7A01G525300

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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 TraesCS7A01G525300 chr7A 100.000 1500 0 0 795 2294 707844389 707845888 0.000000e+00 2771
1 TraesCS7A01G525300 chr7A 96.800 1500 48 0 795 2294 650324561 650323062 0.000000e+00 2505
2 TraesCS7A01G525300 chr7A 96.667 1500 48 2 795 2294 650260745 650259248 0.000000e+00 2492
3 TraesCS7A01G525300 chr7A 100.000 414 0 0 1 414 707843595 707844008 0.000000e+00 765
4 TraesCS7A01G525300 chr7A 94.699 415 20 2 1 413 650261511 650261097 0.000000e+00 643
5 TraesCS7A01G525300 chr2A 97.010 1505 39 2 795 2294 600113435 600111932 0.000000e+00 2525
6 TraesCS7A01G525300 chr2A 97.290 1476 39 1 819 2294 23796207 23797681 0.000000e+00 2503
7 TraesCS7A01G525300 chr2A 97.141 1434 39 2 861 2294 571019198 571020629 0.000000e+00 2420
8 TraesCS7A01G525300 chr2A 95.250 400 17 2 1 399 571018510 571018908 1.160000e-177 632
9 TraesCS7A01G525300 chr2A 93.269 416 24 4 1 413 23795505 23795919 5.420000e-171 610
10 TraesCS7A01G525300 chr2A 92.092 392 15 5 1 389 600114240 600113862 2.590000e-149 538
11 TraesCS7A01G525300 chr2A 97.753 89 0 2 1 87 734856626 734856714 3.950000e-33 152
12 TraesCS7A01G525300 chr1A 96.929 1498 46 0 796 2293 380400812 380402309 0.000000e+00 2512
13 TraesCS7A01G525300 chr1A 96.000 1500 57 3 796 2294 531840051 531838554 0.000000e+00 2435
14 TraesCS7A01G525300 chr1A 95.904 415 15 1 1 413 11026946 11026532 0.000000e+00 671
15 TraesCS7A01G525300 chr1B 96.040 1490 56 3 806 2294 658504122 658502635 0.000000e+00 2422
16 TraesCS7A01G525300 chr1B 95.860 314 12 1 83 396 658504799 658504487 7.310000e-140 507
17 TraesCS7A01G525300 chr5A 95.667 1500 48 4 795 2294 507565707 507564225 0.000000e+00 2394
18 TraesCS7A01G525300 chr5A 95.663 415 15 3 1 413 507566346 507565933 0.000000e+00 664
19 TraesCS7A01G525300 chr5A 94.940 415 17 3 1 413 603018574 603018986 0.000000e+00 647
20 TraesCS7A01G525300 chr5A 98.305 118 2 0 795 912 603019042 603019159 8.310000e-50 207
21 TraesCS7A01G525300 chr4A 94.818 1486 73 4 810 2294 382145490 382146972 0.000000e+00 2314
22 TraesCS7A01G525300 chrUn 94.505 364 18 2 1 362 248381235 248380872 5.530000e-156 560


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 TraesCS7A01G525300 chr7A 707843595 707845888 2293 False 1768.0 2771 100.0000 1 2294 2 chr7A.!!$F1 2293
1 TraesCS7A01G525300 chr7A 650323062 650324561 1499 True 2505.0 2505 96.8000 795 2294 1 chr7A.!!$R1 1499
2 TraesCS7A01G525300 chr7A 650259248 650261511 2263 True 1567.5 2492 95.6830 1 2294 2 chr7A.!!$R2 2293
3 TraesCS7A01G525300 chr2A 23795505 23797681 2176 False 1556.5 2503 95.2795 1 2294 2 chr2A.!!$F2 2293
4 TraesCS7A01G525300 chr2A 600111932 600114240 2308 True 1531.5 2525 94.5510 1 2294 2 chr2A.!!$R1 2293
5 TraesCS7A01G525300 chr2A 571018510 571020629 2119 False 1526.0 2420 96.1955 1 2294 2 chr2A.!!$F3 2293
6 TraesCS7A01G525300 chr1A 380400812 380402309 1497 False 2512.0 2512 96.9290 796 2293 1 chr1A.!!$F1 1497
7 TraesCS7A01G525300 chr1A 531838554 531840051 1497 True 2435.0 2435 96.0000 796 2294 1 chr1A.!!$R2 1498
8 TraesCS7A01G525300 chr1B 658502635 658504799 2164 True 1464.5 2422 95.9500 83 2294 2 chr1B.!!$R1 2211
9 TraesCS7A01G525300 chr5A 507564225 507566346 2121 True 1529.0 2394 95.6650 1 2294 2 chr5A.!!$R1 2293
10 TraesCS7A01G525300 chr5A 603018574 603019159 585 False 427.0 647 96.6225 1 912 2 chr5A.!!$F1 911
11 TraesCS7A01G525300 chr4A 382145490 382146972 1482 False 2314.0 2314 94.8180 810 2294 1 chr4A.!!$F1 1484

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
173 179 0.036765 GAGCCGTCCACACCATACAA 60.037 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2414 1.068588 ACATATCGGACGACCACATGG 59.931 52.381 4.48 0.0 42.17 3.66 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
173 179 0.036765 GAGCCGTCCACACCATACAA 60.037 55.000 0.00 0.00 0.00 2.41
186 192 4.253685 CACCATACAAATCCAACGTCTCT 58.746 43.478 0.00 0.00 0.00 3.10
189 195 6.036083 CACCATACAAATCCAACGTCTCTTAG 59.964 42.308 0.00 0.00 0.00 2.18
220 226 1.890573 GCCAACCAAACCCTAGCATCA 60.891 52.381 0.00 0.00 0.00 3.07
312 318 2.284699 CTCCCCGACCCAGACCTT 60.285 66.667 0.00 0.00 0.00 3.50
321 327 0.419459 ACCCAGACCTTCCTCTCCAT 59.581 55.000 0.00 0.00 0.00 3.41
1074 1308 4.093952 CGCCTTGTCAAGCGCTGG 62.094 66.667 12.58 8.66 46.50 4.85
1150 1384 1.862827 CGGTTCGTTTTCCTCTTTCGT 59.137 47.619 0.00 0.00 0.00 3.85
1434 1668 6.929049 TGCGATCTGACCAATATTTAGTAAGG 59.071 38.462 0.00 0.00 0.00 2.69
1602 1837 1.615262 GGGCATAGGCTGGTTCCTT 59.385 57.895 0.00 0.00 40.87 3.36
1757 1992 1.803334 TTGTCCATGGTTCGTGCTAC 58.197 50.000 12.58 0.00 0.00 3.58
1799 2034 4.203226 TCTTTAATGCACCTGTGTTCACA 58.797 39.130 5.52 5.52 0.00 3.58
1967 2204 2.301346 GCATGGCCAGCTTTATGTAGT 58.699 47.619 13.05 0.00 0.00 2.73
2170 2414 4.416620 CGACCAGTCTGTTCTATCTGTTC 58.583 47.826 0.00 0.00 0.00 3.18
2210 2454 0.965439 GTGGTGCCAACTGCCATTTA 59.035 50.000 0.00 0.00 40.16 1.40
2271 2515 7.101700 CAGCTTAGTGCCTCATATATGAATGA 58.898 38.462 16.08 0.68 44.23 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 156 2.048127 GGTGTGGACGGCTCAGAC 60.048 66.667 0.00 0.00 0.00 3.51
186 192 3.523087 TTGGCCAGCGTGCGTCTAA 62.523 57.895 5.11 0.00 0.00 2.10
220 226 2.673523 GAGGGGAGTGTGCTGCAT 59.326 61.111 5.27 0.00 34.49 3.96
312 318 0.041238 AGTTGGGACGATGGAGAGGA 59.959 55.000 0.00 0.00 0.00 3.71
321 327 0.613853 CAGGGTAGGAGTTGGGACGA 60.614 60.000 0.00 0.00 0.00 4.20
1036 1270 4.065110 GCTGTCCTTGGCGAACTT 57.935 55.556 0.00 0.00 0.00 2.66
1062 1296 2.515757 TTGTGCCAGCGCTTGACA 60.516 55.556 13.50 10.62 35.36 3.58
1150 1384 1.137675 CCCAATCAGCGTCAGATCTGA 59.862 52.381 21.67 21.67 42.72 3.27
1403 1637 1.847328 TTGGTCAGATCGCAGGACTA 58.153 50.000 8.87 2.25 0.00 2.59
1602 1837 4.586841 CCTCTTTTCCCAAATTGTGTGGTA 59.413 41.667 0.00 0.00 34.01 3.25
1644 1879 2.884012 CTGGTGGTATGTGCAGAAACAA 59.116 45.455 0.00 0.00 32.81 2.83
1757 1992 6.575083 AAGAATGAAGAATACATCGACACG 57.425 37.500 0.00 0.00 0.00 4.49
1799 2034 4.339247 GTGAATACATAAAGCTGGCCATGT 59.661 41.667 5.51 9.57 35.81 3.21
1967 2204 1.167781 TGAGGTCACACGCGACACTA 61.168 55.000 15.93 0.00 37.66 2.74
2170 2414 1.068588 ACATATCGGACGACCACATGG 59.931 52.381 4.48 0.00 42.17 3.66
2210 2454 6.590068 AGACTATTGACATCAGCTAGCAAAT 58.410 36.000 18.83 6.77 0.00 2.32


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

AutoCloner maintained by Alex Coulton.