Multiple sequence alignment - TraesCS7A01G018800

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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 TraesCS7A01G018800 chr7A 100.000 1469 0 0 1 1469 7844588 7843120 0.000000e+00 2713
1 TraesCS7A01G018800 chr7A 88.428 1469 166 2 1 1469 20254405 20252941 0.000000e+00 1768
2 TraesCS7A01G018800 chr7A 88.231 1470 168 3 1 1469 270771076 270772541 0.000000e+00 1751
3 TraesCS7A01G018800 chr7A 100.000 672 0 0 1722 2393 7842867 7842196 0.000000e+00 1242
4 TraesCS7A01G018800 chr7A 84.814 619 79 12 1782 2393 8200359 8200969 2.030000e-170 608
5 TraesCS7A01G018800 chr7A 83.612 598 83 14 1782 2372 8080093 8080682 4.500000e-152 547
6 TraesCS7A01G018800 chr7A 83.333 462 55 12 1950 2391 7967103 7967562 7.960000e-110 407
7 TraesCS7A01G018800 chr7A 82.468 462 59 12 1950 2391 8106321 8106780 3.730000e-103 385
8 TraesCS7A01G018800 chr3A 97.822 1469 29 1 1 1469 110312756 110311291 0.000000e+00 2532
9 TraesCS7A01G018800 chr2A 97.073 1469 40 2 1 1469 447899689 447898224 0.000000e+00 2471
10 TraesCS7A01G018800 chr2A 97.113 1455 39 1 1 1455 679988193 679986742 0.000000e+00 2451
11 TraesCS7A01G018800 chr4A 97.510 1446 33 1 1 1446 546006789 546005347 0.000000e+00 2468
12 TraesCS7A01G018800 chr4A 83.333 618 67 12 1782 2393 732965380 732964793 2.710000e-149 538
13 TraesCS7A01G018800 chr4A 86.538 416 48 7 1730 2140 732480914 732481326 3.630000e-123 451
14 TraesCS7A01G018800 chr4A 83.679 386 52 7 2018 2393 732968652 732968268 1.050000e-93 353
15 TraesCS7A01G018800 chr5A 91.695 1469 119 1 1 1469 707721229 707722694 0.000000e+00 2034
16 TraesCS7A01G018800 chr5A 89.721 1469 147 2 1 1469 622529039 622527575 0.000000e+00 1873
17 TraesCS7A01G018800 chr6B 86.249 1469 197 3 1 1468 68900869 68902333 0.000000e+00 1589
18 TraesCS7A01G018800 chrUn 87.097 682 69 13 1729 2393 51233879 51233200 0.000000e+00 754
19 TraesCS7A01G018800 chrUn 87.097 682 69 13 1729 2393 289094928 289095607 0.000000e+00 754
20 TraesCS7A01G018800 chrUn 80.064 311 45 9 1730 2026 51217009 51217316 5.180000e-52 215
21 TraesCS7A01G018800 chr7D 92.088 455 20 10 1730 2173 7068513 7068064 5.620000e-176 627
22 TraesCS7A01G018800 chr7D 81.493 643 79 24 1782 2393 7190605 7191238 2.140000e-135 492
23 TraesCS7A01G018800 chr7D 80.813 615 77 21 1782 2393 7187680 7188256 6.070000e-121 444
24 TraesCS7A01G018800 chr7D 89.503 181 16 2 1730 1907 6968317 6968137 2.390000e-55 226


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 TraesCS7A01G018800 chr7A 7842196 7844588 2392 True 1977.5 2713 100.000 1 2393 2 chr7A.!!$R2 2392
1 TraesCS7A01G018800 chr7A 20252941 20254405 1464 True 1768.0 1768 88.428 1 1469 1 chr7A.!!$R1 1468
2 TraesCS7A01G018800 chr7A 270771076 270772541 1465 False 1751.0 1751 88.231 1 1469 1 chr7A.!!$F5 1468
3 TraesCS7A01G018800 chr7A 8200359 8200969 610 False 608.0 608 84.814 1782 2393 1 chr7A.!!$F4 611
4 TraesCS7A01G018800 chr7A 8080093 8080682 589 False 547.0 547 83.612 1782 2372 1 chr7A.!!$F2 590
5 TraesCS7A01G018800 chr3A 110311291 110312756 1465 True 2532.0 2532 97.822 1 1469 1 chr3A.!!$R1 1468
6 TraesCS7A01G018800 chr2A 447898224 447899689 1465 True 2471.0 2471 97.073 1 1469 1 chr2A.!!$R1 1468
7 TraesCS7A01G018800 chr2A 679986742 679988193 1451 True 2451.0 2451 97.113 1 1455 1 chr2A.!!$R2 1454
8 TraesCS7A01G018800 chr4A 546005347 546006789 1442 True 2468.0 2468 97.510 1 1446 1 chr4A.!!$R1 1445
9 TraesCS7A01G018800 chr4A 732964793 732968652 3859 True 445.5 538 83.506 1782 2393 2 chr4A.!!$R2 611
10 TraesCS7A01G018800 chr5A 707721229 707722694 1465 False 2034.0 2034 91.695 1 1469 1 chr5A.!!$F1 1468
11 TraesCS7A01G018800 chr5A 622527575 622529039 1464 True 1873.0 1873 89.721 1 1469 1 chr5A.!!$R1 1468
12 TraesCS7A01G018800 chr6B 68900869 68902333 1464 False 1589.0 1589 86.249 1 1468 1 chr6B.!!$F1 1467
13 TraesCS7A01G018800 chrUn 51233200 51233879 679 True 754.0 754 87.097 1729 2393 1 chrUn.!!$R1 664
14 TraesCS7A01G018800 chrUn 289094928 289095607 679 False 754.0 754 87.097 1729 2393 1 chrUn.!!$F2 664
15 TraesCS7A01G018800 chr7D 7187680 7191238 3558 False 468.0 492 81.153 1782 2393 2 chr7D.!!$F1 611

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
796 797 0.458197 TGTGCTGTTGTTGTTGCTGC 60.458 50.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 6797 0.958822 TCACAGAGCAGCGACAACTA 59.041 50.0 0.0 0.0 0.0 2.24 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
148 149 3.753797 AGACAGCTTTCGAAAATTCCTCC 59.246 43.478 12.41 0.00 0.00 4.30
305 306 0.896226 AGGGCGTTCTTCTGGTCTAC 59.104 55.000 0.00 0.00 0.00 2.59
794 795 0.887247 TGTGTGCTGTTGTTGTTGCT 59.113 45.000 0.00 0.00 0.00 3.91
795 796 1.270971 GTGTGCTGTTGTTGTTGCTG 58.729 50.000 0.00 0.00 0.00 4.41
796 797 0.458197 TGTGCTGTTGTTGTTGCTGC 60.458 50.000 0.00 0.00 0.00 5.25
1260 1261 1.804372 GCGCTCGTCTTCAGGAATGAT 60.804 52.381 0.00 0.00 0.00 2.45
1357 1358 6.716934 AAGAAGACAATATCTCCGCTAGAA 57.283 37.500 0.00 0.00 36.27 2.10
1459 1462 9.799106 CCTCCTTTTGAGTGGTAATATATTCAT 57.201 33.333 0.00 0.00 39.65 2.57
1767 1770 5.934935 AACAACTAACCATACCAAACTCG 57.065 39.130 0.00 0.00 0.00 4.18
1894 3386 9.066892 AGAGTCAAAATAGCAAGTAAATGAACA 57.933 29.630 0.00 0.00 0.00 3.18
1945 6287 8.908678 CACAATTTATGTTCAAGAGTCACAATG 58.091 33.333 0.00 0.00 41.46 2.82
1948 6290 3.969117 TGTTCAAGAGTCACAATGTGC 57.031 42.857 8.78 4.15 32.98 4.57
1995 6425 6.891908 ACAAATAAACCTCCTATGTTCAGCAT 59.108 34.615 0.00 0.00 41.42 3.79
2050 6487 7.493971 CAGGAGTCACAATTTATACTGAAGAGG 59.506 40.741 0.00 0.00 0.00 3.69
2070 6507 9.591792 GAAGAGGCAAAATTCTAAGCAAATAAT 57.408 29.630 0.00 0.00 0.00 1.28
2155 6625 5.850128 GCAAATAAATCTCTTATCTGCAGCG 59.150 40.000 9.47 0.00 0.00 5.18
2210 6681 7.491682 TCAAGAGCAAAAGAGTAAGCAAAAAT 58.508 30.769 0.00 0.00 0.00 1.82
2211 6683 8.629158 TCAAGAGCAAAAGAGTAAGCAAAAATA 58.371 29.630 0.00 0.00 0.00 1.40
2212 6684 8.694394 CAAGAGCAAAAGAGTAAGCAAAAATAC 58.306 33.333 0.00 0.00 0.00 1.89
2213 6685 7.940850 AGAGCAAAAGAGTAAGCAAAAATACA 58.059 30.769 0.00 0.00 0.00 2.29
2345 6822 1.962822 CGCTGCTCTGTGAAGCCAA 60.963 57.895 4.20 0.00 41.77 4.52
2351 6828 1.612726 GCTCTGTGAAGCCAACCTCAT 60.613 52.381 0.00 0.00 36.22 2.90
2361 6838 1.310933 CCAACCTCATGCTGTGCCTC 61.311 60.000 0.00 0.00 0.00 4.70
2365 6842 1.226542 CTCATGCTGTGCCTCCCAT 59.773 57.895 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.103263 CGGGAAGGAGGATAAGGAACAG 59.897 54.545 0.00 0.00 0.00 3.16
305 306 3.052082 CAGTGCAGGTTGGCTCGG 61.052 66.667 0.00 0.00 32.81 4.63
341 342 2.737252 GGTTTGCAAACGTTTTTCCACA 59.263 40.909 30.40 2.25 39.77 4.17
1260 1261 2.093711 CGTGGTTCTGTGGGTATGATCA 60.094 50.000 0.00 0.00 0.00 2.92
1321 1322 9.965824 GATATTGTCTTCTTTCTTTTTGAACCA 57.034 29.630 0.00 0.00 33.88 3.67
1357 1358 4.202503 TGAAGAGAGGAAGTGAAGCCATTT 60.203 41.667 0.00 0.00 0.00 2.32
1735 1738 5.684550 ATGGTTAGTTGTTTTCTCGTTCC 57.315 39.130 0.00 0.00 0.00 3.62
1740 1743 7.937649 AGTTTGGTATGGTTAGTTGTTTTCTC 58.062 34.615 0.00 0.00 0.00 2.87
1747 1750 5.699458 AGTTCGAGTTTGGTATGGTTAGTTG 59.301 40.000 0.00 0.00 0.00 3.16
1767 1770 4.946784 AAATTGTGAGTATGGCGAGTTC 57.053 40.909 0.00 0.00 0.00 3.01
1806 3298 9.273016 GCATATAAGAGGTTCATTTACTTGCTA 57.727 33.333 0.00 0.00 0.00 3.49
1813 3305 7.053498 TGTGCTGCATATAAGAGGTTCATTTA 58.947 34.615 5.27 0.00 0.00 1.40
1929 3663 3.313526 AGTGCACATTGTGACTCTTGAAC 59.686 43.478 21.04 5.33 35.23 3.18
1945 6287 3.375299 ACACTTTTGACTCTTGAGTGCAC 59.625 43.478 9.40 9.40 40.95 4.57
1948 6290 7.072177 TGTTTACACTTTTGACTCTTGAGTG 57.928 36.000 8.11 0.00 42.48 3.51
2020 6457 8.722480 TCAGTATAAATTGTGACTCCTGAATG 57.278 34.615 0.00 0.00 0.00 2.67
2026 6463 6.258947 GCCTCTTCAGTATAAATTGTGACTCC 59.741 42.308 0.00 0.00 0.00 3.85
2110 6549 9.899226 ATTTGCTTACTTTTTGACTTGAGTATC 57.101 29.630 0.00 0.00 0.00 2.24
2184 6654 6.639632 TTTGCTTACTCTTTTGCTCTTGAT 57.360 33.333 0.00 0.00 0.00 2.57
2320 6797 0.958822 TCACAGAGCAGCGACAACTA 59.041 50.000 0.00 0.00 0.00 2.24
2345 6822 2.673523 GGAGGCACAGCATGAGGT 59.326 61.111 0.00 0.00 39.69 3.85
2351 6828 2.224843 CCATAATATGGGAGGCACAGCA 60.225 50.000 11.41 0.00 46.86 4.41


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

AutoCloner maintained by Alex Coulton.