Multiple sequence alignment - TraesCS4A01G024500

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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 TraesCS4A01G024500 chr4A 100.000 2359 0 0 1 2359 17096497 17094139 0 4357
1 TraesCS4A01G024500 chr4A 93.020 745 47 4 1615 2357 288631233 288630492 0 1083
2 TraesCS4A01G024500 chr4A 92.800 750 48 5 1610 2357 121180982 121180237 0 1081
3 TraesCS4A01G024500 chr5D 97.698 1607 34 3 1 1605 503225672 503224067 0 2760
4 TraesCS4A01G024500 chr5D 97.511 1607 37 3 1 1605 503270873 503272478 0 2743
5 TraesCS4A01G024500 chr5D 97.262 1607 40 4 1 1605 503235988 503234384 0 2721
6 TraesCS4A01G024500 chr3A 97.698 1607 33 4 1 1605 66010169 66011773 0 2760
7 TraesCS4A01G024500 chr3A 92.792 763 47 7 1598 2357 599392405 599391648 0 1098
8 TraesCS4A01G024500 chr2B 97.447 1606 38 2 1 1605 474915894 474914291 0 2736
9 TraesCS4A01G024500 chr2B 97.386 1607 39 3 1 1605 449213740 449212135 0 2732
10 TraesCS4A01G024500 chr4D 97.200 1607 40 4 1 1605 177441989 177443592 0 2713
11 TraesCS4A01G024500 chr6D 97.138 1607 43 3 1 1605 458922768 458921163 0 2710
12 TraesCS4A01G024500 chr1A 97.138 1607 43 3 1 1605 278526786 278528391 0 2710
13 TraesCS4A01G024500 chr1A 92.661 763 51 4 1598 2357 163031463 163030703 0 1094
14 TraesCS4A01G024500 chr2A 93.674 743 41 4 1615 2355 68798272 68797534 0 1107
15 TraesCS4A01G024500 chr6A 93.432 746 45 3 1614 2357 123368214 123367471 0 1103
16 TraesCS4A01G024500 chr6A 93.200 750 46 4 1610 2357 166881005 166880259 0 1098
17 TraesCS4A01G024500 chr7A 93.316 748 45 4 1613 2357 53008188 53007443 0 1099
18 TraesCS4A01G024500 chr5A 92.706 754 48 7 1607 2357 636360057 636360806 0 1081


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 TraesCS4A01G024500 chr4A 17094139 17096497 2358 True 4357 4357 100.000 1 2359 1 chr4A.!!$R1 2358
1 TraesCS4A01G024500 chr4A 288630492 288631233 741 True 1083 1083 93.020 1615 2357 1 chr4A.!!$R3 742
2 TraesCS4A01G024500 chr4A 121180237 121180982 745 True 1081 1081 92.800 1610 2357 1 chr4A.!!$R2 747
3 TraesCS4A01G024500 chr5D 503224067 503225672 1605 True 2760 2760 97.698 1 1605 1 chr5D.!!$R1 1604
4 TraesCS4A01G024500 chr5D 503270873 503272478 1605 False 2743 2743 97.511 1 1605 1 chr5D.!!$F1 1604
5 TraesCS4A01G024500 chr5D 503234384 503235988 1604 True 2721 2721 97.262 1 1605 1 chr5D.!!$R2 1604
6 TraesCS4A01G024500 chr3A 66010169 66011773 1604 False 2760 2760 97.698 1 1605 1 chr3A.!!$F1 1604
7 TraesCS4A01G024500 chr3A 599391648 599392405 757 True 1098 1098 92.792 1598 2357 1 chr3A.!!$R1 759
8 TraesCS4A01G024500 chr2B 474914291 474915894 1603 True 2736 2736 97.447 1 1605 1 chr2B.!!$R2 1604
9 TraesCS4A01G024500 chr2B 449212135 449213740 1605 True 2732 2732 97.386 1 1605 1 chr2B.!!$R1 1604
10 TraesCS4A01G024500 chr4D 177441989 177443592 1603 False 2713 2713 97.200 1 1605 1 chr4D.!!$F1 1604
11 TraesCS4A01G024500 chr6D 458921163 458922768 1605 True 2710 2710 97.138 1 1605 1 chr6D.!!$R1 1604
12 TraesCS4A01G024500 chr1A 278526786 278528391 1605 False 2710 2710 97.138 1 1605 1 chr1A.!!$F1 1604
13 TraesCS4A01G024500 chr1A 163030703 163031463 760 True 1094 1094 92.661 1598 2357 1 chr1A.!!$R1 759
14 TraesCS4A01G024500 chr2A 68797534 68798272 738 True 1107 1107 93.674 1615 2355 1 chr2A.!!$R1 740
15 TraesCS4A01G024500 chr6A 123367471 123368214 743 True 1103 1103 93.432 1614 2357 1 chr6A.!!$R1 743
16 TraesCS4A01G024500 chr6A 166880259 166881005 746 True 1098 1098 93.200 1610 2357 1 chr6A.!!$R2 747
17 TraesCS4A01G024500 chr7A 53007443 53008188 745 True 1099 1099 93.316 1613 2357 1 chr7A.!!$R1 744
18 TraesCS4A01G024500 chr5A 636360057 636360806 749 False 1081 1081 92.706 1607 2357 1 chr5A.!!$F1 750

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
858 863 1.482593 CAACTAAGCCCTCTCGATGGT 59.517 52.381 4.27 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1883 0.824109 CAATAGTGGAGCCCAGTCGA 59.176 55.0 4.98 0.0 38.3 4.2 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
62 63 5.299028 CCATACTCGATCTCATAGATCCCTG 59.701 48.000 10.52 4.77 46.42 4.45
98 99 3.520290 AGCCGTATTCGATGAAAGTCA 57.480 42.857 0.00 0.00 39.71 3.41
366 370 8.944029 CATTGGCTTATCAAATTCTCTATCGAT 58.056 33.333 2.16 2.16 0.00 3.59
564 568 6.252995 TGGTTATTAGAAGCATCCCAAAAGT 58.747 36.000 0.00 0.00 0.00 2.66
568 572 3.515602 AGAAGCATCCCAAAAGTGTCT 57.484 42.857 0.00 0.00 0.00 3.41
569 573 4.640771 AGAAGCATCCCAAAAGTGTCTA 57.359 40.909 0.00 0.00 0.00 2.59
709 714 6.629128 TGCACATTTTCGTTAATCCATGAAT 58.371 32.000 0.00 0.00 0.00 2.57
739 744 7.010160 TCTATGTATGTAGACACATGGATCCA 58.990 38.462 18.88 18.88 45.17 3.41
763 768 4.045104 ACATCTCGATCGGAAAAGAATCG 58.955 43.478 16.41 6.40 36.24 3.34
767 772 6.068473 TCTCGATCGGAAAAGAATCGATAA 57.932 37.500 16.41 0.00 42.65 1.75
782 787 4.994907 TCGATAAAAGGAGAATCGGACA 57.005 40.909 4.35 0.00 42.07 4.02
800 805 5.805486 TCGGACAATATCTTTCTCGAAACAG 59.195 40.000 0.00 0.00 0.00 3.16
855 860 3.300388 TGATCAACTAAGCCCTCTCGAT 58.700 45.455 0.00 0.00 0.00 3.59
858 863 1.482593 CAACTAAGCCCTCTCGATGGT 59.517 52.381 4.27 0.00 0.00 3.55
952 957 8.082242 GGATTCCGTAAATATCCCATTTCAAAG 58.918 37.037 0.00 0.00 33.26 2.77
958 963 8.223769 CGTAAATATCCCATTTCAAAGATCGAG 58.776 37.037 0.00 0.00 0.00 4.04
1102 1108 6.491714 TCAATGGAAGTTTCATTTTCCCAA 57.508 33.333 6.65 0.00 41.75 4.12
1261 1267 9.483916 GGAGAGAAGAACCTATAATTAGCTTTC 57.516 37.037 0.00 0.00 0.00 2.62
1423 1429 1.346068 CAGCTACTCTAGGGGGAATGC 59.654 57.143 0.00 0.00 0.00 3.56
1559 1565 9.944376 GGCTACTATGAAATATTTACTCATGGA 57.056 33.333 15.13 2.76 33.60 3.41
1605 1611 5.297029 GGTTCATGGTTTCTCTTGGCTATAC 59.703 44.000 0.00 0.00 0.00 1.47
1606 1612 5.957771 TCATGGTTTCTCTTGGCTATACT 57.042 39.130 0.00 0.00 0.00 2.12
1607 1613 7.272978 GTTCATGGTTTCTCTTGGCTATACTA 58.727 38.462 0.00 0.00 0.00 1.82
1608 1614 7.618019 TCATGGTTTCTCTTGGCTATACTAT 57.382 36.000 0.00 0.00 0.00 2.12
1648 1655 1.171308 GCGGCTATATCTCCCACGTA 58.829 55.000 0.00 0.00 0.00 3.57
1771 1779 1.424403 TACAATCGCCACTTCACACG 58.576 50.000 0.00 0.00 0.00 4.49
1854 1865 4.769345 AAAGAAGAAAACCCCAAATGCA 57.231 36.364 0.00 0.00 0.00 3.96
1872 1883 1.546476 GCAATAGATCCCCGATCGTCT 59.454 52.381 15.09 12.40 43.17 4.18
1977 1988 2.892374 CGTCATCTGCACTGGTATCAA 58.108 47.619 0.00 0.00 0.00 2.57
2013 2026 2.672961 TTGGAAGTATCTGTGAGCCG 57.327 50.000 0.00 0.00 0.00 5.52
2054 2067 2.552743 CACCCTCGCGATCAAGACTATA 59.447 50.000 10.36 0.00 0.00 1.31
2077 2092 6.841781 ATAAGCTTATGGGTAGGAAAAGGA 57.158 37.500 18.20 0.00 0.00 3.36
2122 2138 4.081420 AGCACTAGCATATATGGTGGCTAC 60.081 45.833 25.71 17.16 45.49 3.58
2242 2259 2.424302 CCGTGTTCACTTCCCGGT 59.576 61.111 0.00 0.00 34.10 5.28
2267 2284 0.530744 CCGGAAAGAGACCATCACGA 59.469 55.000 0.00 0.00 0.00 4.35
2357 2374 1.152984 CCATCTGCCCATAACCGCA 60.153 57.895 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.251750 TCGAGTATGGAATTTTGTTTACTCAG 57.748 34.615 8.20 2.69 36.80 3.35
62 63 3.335579 ACGGCTTTCCACAGAATTCTAC 58.664 45.455 7.86 0.00 0.00 2.59
98 99 1.971357 CTCCCTCCAAGCCGTACATAT 59.029 52.381 0.00 0.00 0.00 1.78
366 370 6.750039 GTCTTTTGTTGAATCTTTTTCACGGA 59.250 34.615 0.00 0.00 0.00 4.69
532 536 6.260050 GGATGCTTCTAATAACCAACGAATGA 59.740 38.462 0.00 0.00 0.00 2.57
564 568 6.480763 TGAAAGCCATATTTTGACCTAGACA 58.519 36.000 0.00 0.00 0.00 3.41
569 573 9.657419 CTTAATTTGAAAGCCATATTTTGACCT 57.343 29.630 0.00 0.00 30.75 3.85
709 714 9.807921 TCCATGTGTCTACATACATAGATTCTA 57.192 33.333 0.00 0.00 45.53 2.10
739 744 5.859114 CGATTCTTTTCCGATCGAGATGTAT 59.141 40.000 18.66 1.92 36.95 2.29
763 768 9.495572 AAGATATTGTCCGATTCTCCTTTTATC 57.504 33.333 0.00 0.00 0.00 1.75
767 772 7.569240 AGAAAGATATTGTCCGATTCTCCTTT 58.431 34.615 0.00 0.00 0.00 3.11
782 787 9.884465 CTTTTTGTCTGTTTCGAGAAAGATATT 57.116 29.630 0.00 0.00 29.48 1.28
800 805 9.203421 TGTTTTCTCTTTCTTTTCCTTTTTGTC 57.797 29.630 0.00 0.00 0.00 3.18
855 860 9.349713 TCTTCTTTCTTATTCTTAAGCAAACCA 57.650 29.630 0.00 0.00 35.72 3.67
958 963 0.675522 TCCGAAAAGCCCCGATTGTC 60.676 55.000 0.00 0.00 0.00 3.18
968 973 1.745087 TGCATCCAATCTCCGAAAAGC 59.255 47.619 0.00 0.00 0.00 3.51
1206 1212 4.072131 ACAATAGGGCCGTTATGCTTATG 58.928 43.478 1.81 0.00 0.00 1.90
1559 1565 2.782341 AGAATAGAAGAGCTTGCCCCAT 59.218 45.455 0.00 0.00 0.00 4.00
1605 1611 6.486248 CATCGTGGGTGTTACAAATTGATAG 58.514 40.000 0.00 0.00 0.00 2.08
1606 1612 5.163703 GCATCGTGGGTGTTACAAATTGATA 60.164 40.000 0.00 0.00 0.00 2.15
1607 1613 4.380444 GCATCGTGGGTGTTACAAATTGAT 60.380 41.667 0.00 0.00 0.00 2.57
1608 1614 3.057876 GCATCGTGGGTGTTACAAATTGA 60.058 43.478 0.00 0.00 0.00 2.57
1806 1816 1.553704 GGTTCCATAGTCGGACCTTGT 59.446 52.381 4.14 0.00 33.75 3.16
1872 1883 0.824109 CAATAGTGGAGCCCAGTCGA 59.176 55.000 4.98 0.00 38.30 4.20
1977 1988 1.752694 AAACAGTTGCAGGTGCCGT 60.753 52.632 0.00 0.00 41.18 5.68
2013 2026 2.615869 GTGAGATTGCTGAGTCCTCAC 58.384 52.381 8.57 8.57 44.31 3.51
2054 2067 6.841781 TCCTTTTCCTACCCATAAGCTTAT 57.158 37.500 13.37 13.37 0.00 1.73
2077 2092 0.829333 CTGCAGCTCCACCTCACTAT 59.171 55.000 0.00 0.00 0.00 2.12
2242 2259 2.348888 GGTCTCTTTCCGGCGGAGA 61.349 63.158 29.30 23.97 34.27 3.71
2267 2284 1.289109 GCATCAACCGCGTGTGTAGT 61.289 55.000 4.92 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.