Multiple sequence alignment - TraesCS7A01G512600

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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 TraesCS7A01G512600 chr7A 100.000 2273 0 0 1 2273 699870222 699867950 0.000000e+00 4198.0
1 TraesCS7A01G512600 chr7A 97.448 2273 54 2 1 2273 563511462 563513730 0.000000e+00 3873.0
2 TraesCS7A01G512600 chr7A 97.064 2282 54 3 1 2273 563578730 563581007 0.000000e+00 3832.0
3 TraesCS7A01G512600 chr7A 97.216 1868 48 2 157 2024 563582142 563584005 0.000000e+00 3158.0
4 TraesCS7A01G512600 chr1A 97.448 2273 55 2 1 2273 278534569 278532300 0.000000e+00 3873.0
5 TraesCS7A01G512600 chr3B 98.122 1544 24 2 730 2273 6000869 6002407 0.000000e+00 2686.0
6 TraesCS7A01G512600 chr2B 98.122 1544 24 2 730 2273 449209431 449210969 0.000000e+00 2686.0
7 TraesCS7A01G512600 chr2B 97.992 1544 25 2 730 2273 234531263 234532800 0.000000e+00 2675.0
8 TraesCS7A01G512600 chr3A 97.927 1544 26 2 730 2273 495092643 495094180 0.000000e+00 2669.0
9 TraesCS7A01G512600 chr7D 97.863 1544 30 2 730 2273 307049947 307048407 0.000000e+00 2665.0
10 TraesCS7A01G512600 chr5A 96.842 95 3 0 321 415 294916429 294916523 2.340000e-35 159.0
11 TraesCS7A01G512600 chr5A 97.619 84 2 0 106 189 206290793 206290876 6.540000e-31 145.0
12 TraesCS7A01G512600 chr2A 98.113 53 1 0 317 369 432016158 432016106 2.400000e-15 93.5
13 TraesCS7A01G512600 chrUn 100.000 48 0 0 682 729 36547806 36547853 3.110000e-14 89.8
14 TraesCS7A01G512600 chrUn 100.000 48 0 0 682 729 186205661 186205614 3.110000e-14 89.8
15 TraesCS7A01G512600 chrUn 100.000 48 0 0 682 729 464745638 464745591 3.110000e-14 89.8
16 TraesCS7A01G512600 chr6D 100.000 48 0 0 682 729 124520287 124520334 3.110000e-14 89.8
17 TraesCS7A01G512600 chr4D 100.000 48 0 0 682 729 123552685 123552732 3.110000e-14 89.8


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 TraesCS7A01G512600 chr7A 699867950 699870222 2272 True 4198 4198 100.000 1 2273 1 chr7A.!!$R1 2272
1 TraesCS7A01G512600 chr7A 563511462 563513730 2268 False 3873 3873 97.448 1 2273 1 chr7A.!!$F1 2272
2 TraesCS7A01G512600 chr7A 563578730 563584005 5275 False 3495 3832 97.140 1 2273 2 chr7A.!!$F2 2272
3 TraesCS7A01G512600 chr1A 278532300 278534569 2269 True 3873 3873 97.448 1 2273 1 chr1A.!!$R1 2272
4 TraesCS7A01G512600 chr3B 6000869 6002407 1538 False 2686 2686 98.122 730 2273 1 chr3B.!!$F1 1543
5 TraesCS7A01G512600 chr2B 449209431 449210969 1538 False 2686 2686 98.122 730 2273 1 chr2B.!!$F2 1543
6 TraesCS7A01G512600 chr2B 234531263 234532800 1537 False 2675 2675 97.992 730 2273 1 chr2B.!!$F1 1543
7 TraesCS7A01G512600 chr3A 495092643 495094180 1537 False 2669 2669 97.927 730 2273 1 chr3A.!!$F1 1543
8 TraesCS7A01G512600 chr7D 307048407 307049947 1540 True 2665 2665 97.863 730 2273 1 chr7D.!!$R1 1543

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
680 681 0.25363 TAGGAAGGAATGGCAGGGGT 60.254 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 2237 4.083324 TGAATCTAGGAACTTTTGCTTGCG 60.083 41.667 0.0 0.0 41.75 4.85 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
33 34 3.676172 GTCGTATCACGGATGTTGTTTCA 59.324 43.478 0.00 0.00 42.81 2.69
47 48 2.485903 TGTTTCACGCTTTATGTCCGT 58.514 42.857 0.00 0.00 35.29 4.69
78 79 1.007849 GGGTTGCGCACGTTTTCAT 60.008 52.632 11.12 0.00 0.00 2.57
95 96 6.279882 GTTTTCATGGGTTTGTCTTTCATCA 58.720 36.000 0.00 0.00 0.00 3.07
123 124 3.116096 TGAGTCTAGCATTACCCCAGT 57.884 47.619 0.00 0.00 0.00 4.00
170 171 1.463056 CGCAAAATGCAGGTACTTCGA 59.537 47.619 2.99 0.00 45.36 3.71
193 194 1.203237 TCAGAGAAGGAGCCTCCACTT 60.203 52.381 14.46 0.00 39.61 3.16
239 240 6.603599 GCTTATCCAGGAAAGTGAAAATAGGT 59.396 38.462 0.00 0.00 0.00 3.08
256 257 1.098712 GGTGTGGGAAACAAGTCGCA 61.099 55.000 0.00 0.00 41.57 5.10
649 650 4.643142 ACTTAAGAAAGTCCGGGGGTACC 61.643 52.174 10.09 2.17 46.29 3.34
680 681 0.253630 TAGGAAGGAATGGCAGGGGT 60.254 55.000 0.00 0.00 0.00 4.95
912 922 1.440938 CTCTCCCTGGACTCTACGCG 61.441 65.000 3.53 3.53 0.00 6.01
1176 1186 2.790433 TCATTAGTTCCAACAGTGGCC 58.210 47.619 0.00 0.00 45.54 5.36
1257 1267 7.329717 GGGACTATTGCTGTCGAATCTATAAAG 59.670 40.741 0.00 0.00 35.45 1.85
1610 1620 2.088104 TCCATAGGCTCGAATGACCT 57.912 50.000 0.00 0.00 37.61 3.85
1819 1829 4.651503 CAGCTAAAAGAGGGTATCCTGAGA 59.348 45.833 0.00 0.00 45.05 3.27
1833 1843 6.096001 GGTATCCTGAGAAATTGCAAGAATGT 59.904 38.462 4.94 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.515564 GCAACACGGACATAAAGCGT 59.484 50.000 0.00 0.00 0.00 5.07
63 64 1.007964 CCCATGAAAACGTGCGCAA 60.008 52.632 14.00 0.00 0.00 4.85
78 79 3.304911 TGGTGATGAAAGACAAACCCA 57.695 42.857 0.00 0.00 38.04 4.51
95 96 5.070580 GGGTAATGCTAGACTCAAGTATGGT 59.929 44.000 0.00 0.00 0.00 3.55
123 124 1.022451 GTTAACCGGCGAGCATTCCA 61.022 55.000 9.30 0.00 0.00 3.53
170 171 0.325203 GGAGGCTCCTTCTCTGACCT 60.325 60.000 26.44 0.00 32.53 3.85
193 194 3.303938 CTTATCCCAGAAGCTCTCCTCA 58.696 50.000 0.00 0.00 0.00 3.86
239 240 1.234821 GATGCGACTTGTTTCCCACA 58.765 50.000 0.00 0.00 0.00 4.17
256 257 0.038744 CAGGGGCTTGACTTGTGGAT 59.961 55.000 0.00 0.00 0.00 3.41
354 355 0.036010 CGGCTCAGTTGAAGGACCAT 60.036 55.000 0.00 0.00 0.00 3.55
439 440 1.438651 TCCTTTGGATTTCGTCTGCG 58.561 50.000 0.00 0.00 39.92 5.18
501 502 6.680810 TCAAGTATTTCCGAAAGACGTTCTA 58.319 36.000 11.88 0.00 37.65 2.10
554 555 4.202503 TGCTTTGAGACTCTGGAGGATTTT 60.203 41.667 3.68 0.00 0.00 1.82
649 650 5.334879 CCATTCCTTCCTAAGTTGTTGTTCG 60.335 44.000 0.00 0.00 0.00 3.95
680 681 1.481871 CTACGAAGGGGTTAGGAGCA 58.518 55.000 0.00 0.00 0.00 4.26
881 891 3.788142 TCCAGGGAGAGCCTATTTTGATT 59.212 43.478 0.00 0.00 0.00 2.57
912 922 3.008049 TGTGAGGCTTAGAAAGAAGTCCC 59.992 47.826 0.00 0.00 31.01 4.46
1010 1020 7.396906 AGGATTCCCCGAATACCTAAAATAA 57.603 36.000 0.00 0.00 40.87 1.40
1176 1186 0.234106 CAATAGCAGATTCCGCAGCG 59.766 55.000 8.18 8.18 0.00 5.18
1210 1220 5.185635 TCCCTCGGACTCGAAAAGTAATAAA 59.814 40.000 0.00 0.00 45.47 1.40
1257 1267 8.293867 TGTAGTTATGTTTAACCTTGAATGCAC 58.706 33.333 0.00 0.00 38.81 4.57
1427 1437 7.072177 TGAATCGAGAAATTGGATTGTACAC 57.928 36.000 0.00 0.00 34.78 2.90
1458 1468 1.640670 ACCATATGCACCTCTTTGGGT 59.359 47.619 0.00 0.00 41.11 4.51
1610 1620 6.479990 CCGTGCACATTCTTATTATGAGAAGA 59.520 38.462 18.64 0.00 36.64 2.87
1673 1683 8.421002 TGAACTTATAATCATGGAATCGACTCA 58.579 33.333 0.00 0.00 0.00 3.41
1819 1829 6.289834 TCAATGAACCACATTCTTGCAATTT 58.710 32.000 0.00 0.00 46.01 1.82
1833 1843 8.275187 ACTATACCAGGAATATCAATGAACCA 57.725 34.615 0.00 0.00 0.00 3.67
1891 1901 7.093377 CCCCTTTAAGATCAAACAATTCCATCA 60.093 37.037 0.00 0.00 0.00 3.07
2178 2188 7.382488 CGGAACTGATAACATTCGAGATTATGT 59.618 37.037 0.00 0.00 36.58 2.29
2227 2237 4.083324 TGAATCTAGGAACTTTTGCTTGCG 60.083 41.667 0.00 0.00 41.75 4.85


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

AutoCloner maintained by Alex Coulton.