Multiple sequence alignment - TraesCS3A01G072800

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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 TraesCS3A01G072800 chr3A 100.000 2264 0 0 1 2264 44774223 44771960 0.000000e+00 4181.0
1 TraesCS3A01G072800 chr3B 96.461 1780 53 6 1 1771 112909781 112911559 0.000000e+00 2929.0
2 TraesCS3A01G072800 chr3B 96.533 1702 47 6 1 1702 179362658 179360969 0.000000e+00 2806.0
3 TraesCS3A01G072800 chr2B 96.857 1750 49 1 1 1750 798600952 798602695 0.000000e+00 2922.0
4 TraesCS3A01G072800 chr7B 96.629 1750 53 1 1 1750 707572950 707571207 0.000000e+00 2900.0
5 TraesCS3A01G072800 chr7B 93.709 1812 112 2 1 1812 34282305 34280496 0.000000e+00 2713.0
6 TraesCS3A01G072800 chr7B 93.579 732 23 4 1206 1916 720234752 720234024 0.000000e+00 1070.0
7 TraesCS3A01G072800 chr7B 92.000 225 11 3 2022 2246 720232912 720232695 2.180000e-80 309.0
8 TraesCS3A01G072800 chr2A 94.515 1805 93 3 1 1803 372742765 372744565 0.000000e+00 2780.0
9 TraesCS3A01G072800 chr2A 97.531 243 6 0 2022 2264 601812818 601812576 1.250000e-112 416.0
10 TraesCS3A01G072800 chr2A 85.787 197 7 1 1692 1867 372744517 372744713 2.970000e-44 189.0
11 TraesCS3A01G072800 chr2A 98.611 72 1 0 1942 2013 601812983 601813054 6.560000e-26 128.0
12 TraesCS3A01G072800 chr5D 93.612 1769 96 8 1 1761 387840680 387838921 0.000000e+00 2625.0
13 TraesCS3A01G072800 chr5B 93.307 1763 111 7 1 1761 578837549 578835792 0.000000e+00 2595.0
14 TraesCS3A01G072800 chr5B 92.300 1052 60 1 837 1867 35438901 35439952 0.000000e+00 1474.0
15 TraesCS3A01G072800 chr5B 93.827 81 5 0 1941 2021 215734608 215734688 3.050000e-24 122.0
16 TraesCS3A01G072800 chr5B 90.123 81 8 0 1941 2021 215734679 215734759 3.080000e-19 106.0
17 TraesCS3A01G072800 chr5B 90.566 53 4 1 1872 1924 215734669 215734618 4.040000e-08 69.4
18 TraesCS3A01G072800 chr4A 92.713 1784 116 8 1 1771 737660732 737662514 0.000000e+00 2562.0
19 TraesCS3A01G072800 chr4A 91.615 1288 76 7 602 1867 514407014 514405737 0.000000e+00 1751.0
20 TraesCS3A01G072800 chr4A 93.878 49 3 0 1755 1803 698021844 698021796 8.670000e-10 75.0
21 TraesCS3A01G072800 chr7D 91.770 1288 68 9 602 1867 16799081 16797810 0.000000e+00 1757.0
22 TraesCS3A01G072800 chr1D 89.837 551 34 2 1338 1867 490889982 490890531 0.000000e+00 688.0
23 TraesCS3A01G072800 chr6A 99.177 243 2 0 2022 2264 74989638 74989396 2.670000e-119 438.0
24 TraesCS3A01G072800 chr6A 98.354 243 4 0 2022 2264 387218282 387218524 5.780000e-116 427.0
25 TraesCS3A01G072800 chr6A 90.667 225 10 2 2022 2246 79830018 79829805 2.850000e-74 289.0
26 TraesCS3A01G072800 chr6A 98.611 72 1 0 1942 2013 387218117 387218046 6.560000e-26 128.0
27 TraesCS3A01G072800 chr6A 92.593 81 6 0 1941 2021 74990265 74990345 1.420000e-22 117.0
28 TraesCS3A01G072800 chr6A 100.000 29 0 0 1917 1945 74990338 74990310 1.000000e-03 54.7
29 TraesCS3A01G072800 chr6B 93.333 225 8 3 2022 2246 275798511 275798294 2.170000e-85 326.0
30 TraesCS3A01G072800 chr7A 91.111 225 9 2 2022 2246 699320468 699320255 6.120000e-76 294.0
31 TraesCS3A01G072800 chr7A 90.749 227 7 5 2022 2246 134598642 134598856 7.910000e-75 291.0
32 TraesCS3A01G072800 chr7A 87.336 229 7 2 1715 1922 7463045 7462818 2.250000e-60 243.0
33 TraesCS3A01G072800 chr7A 91.358 81 7 0 1941 2021 595030858 595030938 6.610000e-21 111.0
34 TraesCS3A01G072800 chr7A 90.123 81 8 0 1941 2021 595029793 595029873 3.080000e-19 106.0
35 TraesCS3A01G072800 chr7A 87.654 81 10 0 1941 2021 7462446 7462526 6.660000e-16 95.3
36 TraesCS3A01G072800 chr7A 90.741 54 2 2 1872 1924 7462507 7462456 4.040000e-08 69.4
37 TraesCS3A01G072800 chr7A 90.566 53 4 1 1872 1924 595030067 595030016 4.040000e-08 69.4
38 TraesCS3A01G072800 chr7A 90.566 53 4 1 1872 1924 595030138 595030087 4.040000e-08 69.4
39 TraesCS3A01G072800 chr7A 90.566 53 4 1 1872 1924 595030280 595030229 4.040000e-08 69.4
40 TraesCS3A01G072800 chr7A 90.566 53 4 1 1872 1924 595030351 595030300 4.040000e-08 69.4
41 TraesCS3A01G072800 chr1A 90.667 225 10 2 2022 2246 559591983 559592196 2.850000e-74 289.0
42 TraesCS3A01G072800 chr1B 91.358 81 7 0 1941 2021 14540941 14541021 6.610000e-21 111.0


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 TraesCS3A01G072800 chr3A 44771960 44774223 2263 True 4181.00 4181 100.0000 1 2264 1 chr3A.!!$R1 2263
1 TraesCS3A01G072800 chr3B 112909781 112911559 1778 False 2929.00 2929 96.4610 1 1771 1 chr3B.!!$F1 1770
2 TraesCS3A01G072800 chr3B 179360969 179362658 1689 True 2806.00 2806 96.5330 1 1702 1 chr3B.!!$R1 1701
3 TraesCS3A01G072800 chr2B 798600952 798602695 1743 False 2922.00 2922 96.8570 1 1750 1 chr2B.!!$F1 1749
4 TraesCS3A01G072800 chr7B 707571207 707572950 1743 True 2900.00 2900 96.6290 1 1750 1 chr7B.!!$R2 1749
5 TraesCS3A01G072800 chr7B 34280496 34282305 1809 True 2713.00 2713 93.7090 1 1812 1 chr7B.!!$R1 1811
6 TraesCS3A01G072800 chr7B 720232695 720234752 2057 True 689.50 1070 92.7895 1206 2246 2 chr7B.!!$R3 1040
7 TraesCS3A01G072800 chr2A 372742765 372744713 1948 False 1484.50 2780 90.1510 1 1867 2 chr2A.!!$F2 1866
8 TraesCS3A01G072800 chr5D 387838921 387840680 1759 True 2625.00 2625 93.6120 1 1761 1 chr5D.!!$R1 1760
9 TraesCS3A01G072800 chr5B 578835792 578837549 1757 True 2595.00 2595 93.3070 1 1761 1 chr5B.!!$R2 1760
10 TraesCS3A01G072800 chr5B 35438901 35439952 1051 False 1474.00 1474 92.3000 837 1867 1 chr5B.!!$F1 1030
11 TraesCS3A01G072800 chr4A 737660732 737662514 1782 False 2562.00 2562 92.7130 1 1771 1 chr4A.!!$F1 1770
12 TraesCS3A01G072800 chr4A 514405737 514407014 1277 True 1751.00 1751 91.6150 602 1867 1 chr4A.!!$R1 1265
13 TraesCS3A01G072800 chr7D 16797810 16799081 1271 True 1757.00 1757 91.7700 602 1867 1 chr7D.!!$R1 1265
14 TraesCS3A01G072800 chr1D 490889982 490890531 549 False 688.00 688 89.8370 1338 1867 1 chr1D.!!$F1 529
15 TraesCS3A01G072800 chr6A 74989396 74990338 942 True 246.35 438 99.5885 1917 2264 2 chr6A.!!$R3 347

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
762 833 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.0 16.64 0.0 33.17 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2862 0.189822 GGGTCCCTATCCAGAGAGCT 59.81 60.0 0.0 0.0 0.0 4.09 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
478 479 1.019673 CGGTCATTTCATGGAGGCTG 58.980 55.000 0.00 0.00 0.00 4.85
578 579 2.270352 AAAACAAGTCATGGAGGCGA 57.730 45.000 0.00 0.00 0.00 5.54
762 833 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.00 33.17 4.09
1233 1304 0.462047 ATGATCGTCGAAGGCCAACC 60.462 55.000 5.01 0.00 0.00 3.77
1507 1578 0.937304 GTGAGCACAAGAAGCGTGAA 59.063 50.000 0.00 0.00 36.43 3.18
1511 1582 1.949525 AGCACAAGAAGCGTGAACAAT 59.050 42.857 0.00 0.00 36.43 2.71
1566 1637 3.584733 AGAGAGGGCAAGAAAACTTGT 57.415 42.857 10.82 0.00 36.74 3.16
1771 1843 6.926826 AGACATCGTGTGTGAACTTGTTATTA 59.073 34.615 1.13 0.00 42.36 0.98
1773 1845 6.147164 ACATCGTGTGTGAACTTGTTATTAGG 59.853 38.462 0.00 0.00 40.28 2.69
1883 2201 7.463251 GCAACAAGTTTAAAAGAGAGCACTTTG 60.463 37.037 0.00 0.00 39.57 2.77
1884 2202 6.036470 ACAAGTTTAAAAGAGAGCACTTTGC 58.964 36.000 0.00 0.00 45.46 3.68
1885 2203 5.188327 AGTTTAAAAGAGAGCACTTTGCC 57.812 39.130 0.00 0.00 46.52 4.52
1886 2204 4.889995 AGTTTAAAAGAGAGCACTTTGCCT 59.110 37.500 0.00 0.00 46.52 4.75
1972 2768 4.704833 CCCTGGCGTCTGGGTGTG 62.705 72.222 22.99 0.00 44.42 3.82
1975 2771 4.927782 TGGCGTCTGGGTGTGCAC 62.928 66.667 10.75 10.75 0.00 4.57
1976 2772 4.626081 GGCGTCTGGGTGTGCACT 62.626 66.667 19.41 0.00 0.00 4.40
1977 2773 2.591715 GCGTCTGGGTGTGCACTT 60.592 61.111 19.41 0.00 0.00 3.16
1979 2775 0.673644 GCGTCTGGGTGTGCACTTAT 60.674 55.000 19.41 0.00 0.00 1.73
2047 3437 3.401385 ACCCCTCTCATCCATTCATCTT 58.599 45.455 0.00 0.00 0.00 2.40
2048 3438 3.393941 ACCCCTCTCATCCATTCATCTTC 59.606 47.826 0.00 0.00 0.00 2.87
2049 3439 3.393609 CCCCTCTCATCCATTCATCTTCA 59.606 47.826 0.00 0.00 0.00 3.02
2050 3440 4.387598 CCCTCTCATCCATTCATCTTCAC 58.612 47.826 0.00 0.00 0.00 3.18
2051 3441 4.387598 CCTCTCATCCATTCATCTTCACC 58.612 47.826 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 233 5.163854 ACTCTTGCATCCTTACGATTTTTCG 60.164 40.000 0.00 0.00 39.31 3.46
243 244 3.087031 CACATGGAACTCTTGCATCCTT 58.913 45.455 4.96 0.00 39.89 3.36
478 479 2.684881 CCCCACAGTTGATAATGTCAGC 59.315 50.000 0.00 0.00 38.29 4.26
762 833 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
1233 1304 2.220824 CGGTGGTATGTCATATGCGTTG 59.779 50.000 0.00 0.00 0.00 4.10
1436 1507 1.338136 CCCCGTGCATAGGACTCCTT 61.338 60.000 12.15 0.00 34.61 3.36
1507 1578 1.003118 TCTTTGCGTGCCCTCTATTGT 59.997 47.619 0.00 0.00 0.00 2.71
1511 1582 0.973632 TTCTCTTTGCGTGCCCTCTA 59.026 50.000 0.00 0.00 0.00 2.43
1566 1637 2.202878 GTGCATCGCGAGCCCTTA 60.203 61.111 16.66 0.00 0.00 2.69
1994 2862 0.189822 GGGTCCCTATCCAGAGAGCT 59.810 60.000 0.00 0.00 0.00 4.09
2008 2876 3.674050 TAGAGGGGCGTCTGGGTCC 62.674 68.421 0.00 0.00 0.00 4.46
2047 3437 2.181773 AGGGGTAGAGGTGGGGTGA 61.182 63.158 0.00 0.00 0.00 4.02
2048 3438 1.995626 CAGGGGTAGAGGTGGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
2049 3439 2.454941 CAGGGGTAGAGGTGGGGT 59.545 66.667 0.00 0.00 0.00 4.95
2050 3440 1.689582 GACAGGGGTAGAGGTGGGG 60.690 68.421 0.00 0.00 0.00 4.96
2051 3441 0.326618 ATGACAGGGGTAGAGGTGGG 60.327 60.000 0.00 0.00 0.00 4.61
2159 3554 0.388907 TGAAACCGGACCGATTCGTC 60.389 55.000 17.49 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.