Multiple sequence alignment - TraesCS3A01G472700

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 TraesCS3A01G472700 chr3A 100.000 2398 0 0 1 2398 703853571 703851174 0.000000e+00 4429
1 TraesCS3A01G472700 chr7D 97.081 2398 69 1 1 2398 180439623 180442019 0.000000e+00 4039
2 TraesCS3A01G472700 chr3D 96.499 2399 79 5 1 2398 86081406 86079012 0.000000e+00 3960
3 TraesCS3A01G472700 chr6D 96.414 2398 82 1 1 2398 150886678 150884285 0.000000e+00 3949
4 TraesCS3A01G472700 chr4A 93.831 2399 129 4 1 2398 644923844 644921464 0.000000e+00 3592
5 TraesCS3A01G472700 chr2B 94.780 2299 116 4 102 2398 696855918 696858214 0.000000e+00 3578
6 TraesCS3A01G472700 chr3B 92.619 2398 140 19 1 2398 702151888 702149528 0.000000e+00 3413
7 TraesCS3A01G472700 chr7B 94.506 1893 103 1 1 1893 30075425 30073534 0.000000e+00 2918
8 TraesCS3A01G472700 chr5A 94.499 1618 58 5 146 1763 241459561 241457975 0.000000e+00 2466
9 TraesCS3A01G472700 chr5A 95.066 831 39 1 1 831 667547779 667548607 0.000000e+00 1306
10 TraesCS3A01G472700 chr5A 95.051 788 36 2 1613 2398 667565205 667565991 0.000000e+00 1236
11 TraesCS3A01G472700 chr2A 94.376 1618 56 3 146 1763 111272867 111271285 0.000000e+00 2451
12 TraesCS3A01G472700 chr2A 95.887 389 16 0 2010 2398 545065869 545066257 4.350000e-177 630
13 TraesCS3A01G472700 chr1A 96.406 1113 38 2 655 1767 67961590 67960480 0.000000e+00 1832
14 TraesCS3A01G472700 chr1A 92.172 511 33 5 1 508 548669993 548670499 0.000000e+00 715
15 TraesCS3A01G472700 chr4B 97.143 385 11 0 2014 2398 145028666 145029050 0.000000e+00 651
16 TraesCS3A01G472700 chr5D 84.826 402 16 11 1597 1974 483324110 483324490 1.750000e-96 363
17 TraesCS3A01G472700 chr7A 94.286 105 6 0 1881 1985 5194573 5194677 6.860000e-36 161


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 TraesCS3A01G472700 chr3A 703851174 703853571 2397 True 4429 4429 100.000 1 2398 1 chr3A.!!$R1 2397
1 TraesCS3A01G472700 chr7D 180439623 180442019 2396 False 4039 4039 97.081 1 2398 1 chr7D.!!$F1 2397
2 TraesCS3A01G472700 chr3D 86079012 86081406 2394 True 3960 3960 96.499 1 2398 1 chr3D.!!$R1 2397
3 TraesCS3A01G472700 chr6D 150884285 150886678 2393 True 3949 3949 96.414 1 2398 1 chr6D.!!$R1 2397
4 TraesCS3A01G472700 chr4A 644921464 644923844 2380 True 3592 3592 93.831 1 2398 1 chr4A.!!$R1 2397
5 TraesCS3A01G472700 chr2B 696855918 696858214 2296 False 3578 3578 94.780 102 2398 1 chr2B.!!$F1 2296
6 TraesCS3A01G472700 chr3B 702149528 702151888 2360 True 3413 3413 92.619 1 2398 1 chr3B.!!$R1 2397
7 TraesCS3A01G472700 chr7B 30073534 30075425 1891 True 2918 2918 94.506 1 1893 1 chr7B.!!$R1 1892
8 TraesCS3A01G472700 chr5A 241457975 241459561 1586 True 2466 2466 94.499 146 1763 1 chr5A.!!$R1 1617
9 TraesCS3A01G472700 chr5A 667547779 667548607 828 False 1306 1306 95.066 1 831 1 chr5A.!!$F1 830
10 TraesCS3A01G472700 chr5A 667565205 667565991 786 False 1236 1236 95.051 1613 2398 1 chr5A.!!$F2 785
11 TraesCS3A01G472700 chr2A 111271285 111272867 1582 True 2451 2451 94.376 146 1763 1 chr2A.!!$R1 1617
12 TraesCS3A01G472700 chr1A 67960480 67961590 1110 True 1832 1832 96.406 655 1767 1 chr1A.!!$R1 1112
13 TraesCS3A01G472700 chr1A 548669993 548670499 506 False 715 715 92.172 1 508 1 chr1A.!!$F1 507

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
129 130 1.486310 TGTAAGATTCTGGCGCTCCAT 59.514 47.619 7.64 0.0 42.51 3.41 F
908 914 4.816385 TGTGAGATGTCCACTCTTGTTTTC 59.184 41.667 0.00 0.0 35.66 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1096 1102 1.132495 ACCAGCTATAAGGGTAGGGGG 60.132 57.143 0.00 0.00 31.89 5.40 R
2166 2186 0.883370 AAAGAACAGGGAACGGCGAC 60.883 55.000 16.62 7.14 0.00 5.19 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
129 130 1.486310 TGTAAGATTCTGGCGCTCCAT 59.514 47.619 7.64 0.0 42.51 3.41
367 372 7.067251 CGCCAGGGTAAAGGTGTTATATTTTTA 59.933 37.037 0.00 0.0 0.00 1.52
768 774 7.268586 TGAATACTCCTCTGACTGCTATTTTC 58.731 38.462 0.00 0.0 0.00 2.29
834 840 5.044328 ACCACCTGTCTAGTATAGGACAAGA 60.044 44.000 13.91 0.0 38.77 3.02
908 914 4.816385 TGTGAGATGTCCACTCTTGTTTTC 59.184 41.667 0.00 0.0 35.66 2.29
936 942 5.635278 TCATCAGATAGCAGGAAATTCCA 57.365 39.130 15.21 0.0 39.61 3.53
1096 1102 2.200067 CCATGAAGCGATGTGAGAGAC 58.800 52.381 0.00 0.0 0.00 3.36
1359 1367 1.340889 TGCTGGATGTGTTTTGCCTTC 59.659 47.619 0.00 0.0 0.00 3.46
1500 1508 6.753409 CAACTCCAGTTTGCACACATGCTT 62.753 45.833 5.67 0.0 43.80 3.91
1626 1634 9.280174 AGATTTTCGTTGGTTTTAGAATGTCTA 57.720 29.630 0.00 0.0 0.00 2.59
1850 1869 1.911766 GTCGACCCTTGACCCTCCA 60.912 63.158 3.51 0.0 0.00 3.86
2051 2071 1.120530 AGTTCAAGGTGTCGGACTGT 58.879 50.000 9.88 0.0 0.00 3.55
2166 2186 4.985409 GGCTCAAGAAGATCAGGTATAACG 59.015 45.833 0.00 0.0 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.351938 CCCGACGAACAGCCACGA 62.352 66.667 0.00 0.00 0.00 4.35
109 110 0.901827 TGGAGCGCCAGAATCTTACA 59.098 50.000 4.49 0.00 39.92 2.41
129 130 1.806542 GCAAAGCGTGATCCAGAAAGA 59.193 47.619 0.00 0.00 0.00 2.52
367 372 6.428159 CCAAGAGTTTGTAGTATCAAGCAACT 59.572 38.462 0.00 0.00 32.42 3.16
664 670 3.273071 ATGGCCTGGGGAGTCCTGA 62.273 63.158 9.58 0.00 36.68 3.86
834 840 7.878127 AGTAAAACACATACTAGCATTCACTGT 59.122 33.333 0.00 0.00 31.96 3.55
936 942 0.180406 ACAGTTCGACAAAGCAGGGT 59.820 50.000 0.00 0.00 0.00 4.34
1036 1042 1.136984 CCGTGCTCCTCTCGTACAC 59.863 63.158 0.00 0.00 0.00 2.90
1040 1046 1.303398 TTCTCCGTGCTCCTCTCGT 60.303 57.895 0.00 0.00 0.00 4.18
1096 1102 1.132495 ACCAGCTATAAGGGTAGGGGG 60.132 57.143 0.00 0.00 31.89 5.40
1269 1277 2.092753 GGAGATGTTCCTCTTGCCATCA 60.093 50.000 0.00 0.00 43.16 3.07
1359 1367 4.201657 TGATTACCATCAGGCACAGAATG 58.798 43.478 0.00 0.00 40.11 2.67
1626 1634 8.827832 TCCATTATCAGAAAAGACCATGAAAT 57.172 30.769 0.00 0.00 0.00 2.17
1662 1681 5.600696 AGAAACCAACAACCAGCAAATTAG 58.399 37.500 0.00 0.00 0.00 1.73
1667 1686 3.957497 ACATAGAAACCAACAACCAGCAA 59.043 39.130 0.00 0.00 0.00 3.91
1850 1869 5.762711 GGCCAATTTTGTACCTGAAAAACAT 59.237 36.000 0.00 0.00 0.00 2.71
1969 1989 1.217942 AGAAGGTTGAGGGCAAGGTTT 59.782 47.619 0.00 0.00 34.01 3.27
2051 2071 3.716872 AGTCCTTCTTCCTGTTCAGGAAA 59.283 43.478 27.22 16.78 46.16 3.13
2166 2186 0.883370 AAAGAACAGGGAACGGCGAC 60.883 55.000 16.62 7.14 0.00 5.19


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

AutoCloner maintained by Alex Coulton.