Multiple sequence alignment - TraesCS1A01G390600

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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 TraesCS1A01G390600 chr1A 100.000 2482 0 0 1 2482 558013636 558016117 0.000000e+00 4584.0
1 TraesCS1A01G390600 chr1A 90.382 759 55 12 12 766 360147173 360147917 0.000000e+00 981.0
2 TraesCS1A01G390600 chr4A 98.313 1719 28 1 764 2482 420019201 420017484 0.000000e+00 3013.0
3 TraesCS1A01G390600 chr2D 95.930 1720 61 8 765 2482 52284797 52286509 0.000000e+00 2780.0
4 TraesCS1A01G390600 chr2D 81.333 225 26 6 1927 2136 628160699 628160922 4.250000e-38 169.0
5 TraesCS1A01G390600 chr5B 95.116 1720 54 10 765 2482 634121069 634119378 0.000000e+00 2684.0
6 TraesCS1A01G390600 chr5B 82.727 110 12 6 2323 2431 184285349 184285246 9.450000e-15 91.6
7 TraesCS1A01G390600 chr5B 96.970 33 1 0 2101 2133 523136917 523136949 3.450000e-04 56.5
8 TraesCS1A01G390600 chr2A 95.022 1587 75 4 765 2350 315763019 315764602 0.000000e+00 2490.0
9 TraesCS1A01G390600 chr2A 95.244 757 22 12 12 763 122669786 122669039 0.000000e+00 1186.0
10 TraesCS1A01G390600 chr2A 89.290 775 64 11 1 764 130315885 130315119 0.000000e+00 953.0
11 TraesCS1A01G390600 chr3D 95.701 1512 61 3 765 2276 477613061 477611554 0.000000e+00 2429.0
12 TraesCS1A01G390600 chr3D 97.036 1147 33 1 765 1910 30970888 30972034 0.000000e+00 1929.0
13 TraesCS1A01G390600 chr3D 92.057 1196 91 2 765 1959 412103600 412104792 0.000000e+00 1679.0
14 TraesCS1A01G390600 chr3D 95.009 581 23 4 1906 2482 30972850 30973428 0.000000e+00 907.0
15 TraesCS1A01G390600 chr3D 91.753 485 32 7 2003 2482 412104790 412105271 0.000000e+00 667.0
16 TraesCS1A01G390600 chr3D 94.836 213 8 3 2271 2482 477571265 477571055 1.840000e-86 329.0
17 TraesCS1A01G390600 chr7A 97.482 1112 28 0 764 1875 299430600 299429489 0.000000e+00 1899.0
18 TraesCS1A01G390600 chr7A 94.525 621 28 6 1865 2482 299415275 299414658 0.000000e+00 953.0
19 TraesCS1A01G390600 chr7A 88.073 763 62 18 12 765 170372102 170372844 0.000000e+00 878.0
20 TraesCS1A01G390600 chr6D 91.912 952 64 8 1422 2363 169715444 169716392 0.000000e+00 1319.0
21 TraesCS1A01G390600 chr6D 91.051 257 23 0 1001 1257 169714691 169714947 5.080000e-92 348.0
22 TraesCS1A01G390600 chr6D 89.375 160 17 0 1008 1167 376850079 376849920 4.190000e-48 202.0
23 TraesCS1A01G390600 chr6D 84.536 97 11 3 2320 2416 462439494 462439586 2.630000e-15 93.5
24 TraesCS1A01G390600 chr5A 94.459 758 26 12 12 764 350137481 350136735 0.000000e+00 1153.0
25 TraesCS1A01G390600 chr5A 96.564 582 15 5 1 581 581226701 581227278 0.000000e+00 959.0
26 TraesCS1A01G390600 chr5A 86.423 766 76 20 12 763 122679229 122678478 0.000000e+00 813.0
27 TraesCS1A01G390600 chr5A 89.011 91 7 2 867 957 600890327 600890414 2.610000e-20 110.0
28 TraesCS1A01G390600 chr3A 93.750 768 35 8 1 764 183362592 183363350 0.000000e+00 1140.0
29 TraesCS1A01G390600 chr3B 88.305 838 61 14 1575 2409 726179274 726178471 0.000000e+00 970.0
30 TraesCS1A01G390600 chr3B 90.789 228 20 1 1004 1230 726180886 726180659 1.120000e-78 303.0
31 TraesCS1A01G390600 chr2B 88.773 766 61 19 12 763 313462632 313461878 0.000000e+00 915.0
32 TraesCS1A01G390600 chr2B 90.805 87 7 1 871 957 568669832 568669917 5.610000e-22 115.0
33 TraesCS1A01G390600 chr7B 86.894 763 72 21 12 763 98032266 98033011 0.000000e+00 830.0
34 TraesCS1A01G390600 chr7B 86.316 95 8 4 2320 2414 356684637 356684726 5.650000e-17 99.0
35 TraesCS1A01G390600 chrUn 92.025 163 13 0 1259 1421 394864046 394864208 1.920000e-56 230.0
36 TraesCS1A01G390600 chrUn 85.567 97 8 5 2317 2413 362465043 362464953 2.030000e-16 97.1
37 TraesCS1A01G390600 chrUn 83.168 101 11 4 2315 2415 27475948 27476042 1.220000e-13 87.9
38 TraesCS1A01G390600 chrUn 84.783 92 9 4 2323 2414 101630884 101630798 1.220000e-13 87.9
39 TraesCS1A01G390600 chrUn 83.168 101 10 6 2314 2413 158062320 158062226 4.400000e-13 86.1
40 TraesCS1A01G390600 chrUn 84.615 91 9 4 2323 2413 348315194 348315109 4.400000e-13 86.1
41 TraesCS1A01G390600 chrUn 84.615 91 9 4 2323 2413 427230613 427230698 4.400000e-13 86.1
42 TraesCS1A01G390600 chrUn 83.168 101 10 6 2314 2413 478545613 478545519 4.400000e-13 86.1
43 TraesCS1A01G390600 chrUn 84.444 90 9 4 2323 2412 361640201 361640285 1.580000e-12 84.2
44 TraesCS1A01G390600 chrUn 86.667 75 9 1 2322 2396 29722132 29722059 5.690000e-12 82.4
45 TraesCS1A01G390600 chr4D 85.567 97 8 5 2318 2414 64347449 64347359 2.030000e-16 97.1
46 TraesCS1A01G390600 chr4D 84.615 91 9 2 2323 2413 320593735 320593820 4.400000e-13 86.1
47 TraesCS1A01G390600 chr1D 85.417 96 8 5 2317 2412 468550702 468550791 7.310000e-16 95.3
48 TraesCS1A01G390600 chr5D 84.043 94 9 5 2319 2412 452219394 452219481 4.400000e-13 86.1
49 TraesCS1A01G390600 chr4B 92.982 57 4 0 891 947 456373027 456373083 1.580000e-12 84.2


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 TraesCS1A01G390600 chr1A 558013636 558016117 2481 False 4584.0 4584 100.0000 1 2482 1 chr1A.!!$F2 2481
1 TraesCS1A01G390600 chr1A 360147173 360147917 744 False 981.0 981 90.3820 12 766 1 chr1A.!!$F1 754
2 TraesCS1A01G390600 chr4A 420017484 420019201 1717 True 3013.0 3013 98.3130 764 2482 1 chr4A.!!$R1 1718
3 TraesCS1A01G390600 chr2D 52284797 52286509 1712 False 2780.0 2780 95.9300 765 2482 1 chr2D.!!$F1 1717
4 TraesCS1A01G390600 chr5B 634119378 634121069 1691 True 2684.0 2684 95.1160 765 2482 1 chr5B.!!$R2 1717
5 TraesCS1A01G390600 chr2A 315763019 315764602 1583 False 2490.0 2490 95.0220 765 2350 1 chr2A.!!$F1 1585
6 TraesCS1A01G390600 chr2A 122669039 122669786 747 True 1186.0 1186 95.2440 12 763 1 chr2A.!!$R1 751
7 TraesCS1A01G390600 chr2A 130315119 130315885 766 True 953.0 953 89.2900 1 764 1 chr2A.!!$R2 763
8 TraesCS1A01G390600 chr3D 477611554 477613061 1507 True 2429.0 2429 95.7010 765 2276 1 chr3D.!!$R2 1511
9 TraesCS1A01G390600 chr3D 30970888 30973428 2540 False 1418.0 1929 96.0225 765 2482 2 chr3D.!!$F1 1717
10 TraesCS1A01G390600 chr3D 412103600 412105271 1671 False 1173.0 1679 91.9050 765 2482 2 chr3D.!!$F2 1717
11 TraesCS1A01G390600 chr7A 299429489 299430600 1111 True 1899.0 1899 97.4820 764 1875 1 chr7A.!!$R2 1111
12 TraesCS1A01G390600 chr7A 299414658 299415275 617 True 953.0 953 94.5250 1865 2482 1 chr7A.!!$R1 617
13 TraesCS1A01G390600 chr7A 170372102 170372844 742 False 878.0 878 88.0730 12 765 1 chr7A.!!$F1 753
14 TraesCS1A01G390600 chr6D 169714691 169716392 1701 False 833.5 1319 91.4815 1001 2363 2 chr6D.!!$F2 1362
15 TraesCS1A01G390600 chr5A 350136735 350137481 746 True 1153.0 1153 94.4590 12 764 1 chr5A.!!$R2 752
16 TraesCS1A01G390600 chr5A 581226701 581227278 577 False 959.0 959 96.5640 1 581 1 chr5A.!!$F1 580
17 TraesCS1A01G390600 chr5A 122678478 122679229 751 True 813.0 813 86.4230 12 763 1 chr5A.!!$R1 751
18 TraesCS1A01G390600 chr3A 183362592 183363350 758 False 1140.0 1140 93.7500 1 764 1 chr3A.!!$F1 763
19 TraesCS1A01G390600 chr3B 726178471 726180886 2415 True 636.5 970 89.5470 1004 2409 2 chr3B.!!$R1 1405
20 TraesCS1A01G390600 chr2B 313461878 313462632 754 True 915.0 915 88.7730 12 763 1 chr2B.!!$R1 751
21 TraesCS1A01G390600 chr7B 98032266 98033011 745 False 830.0 830 86.8940 12 763 1 chr7B.!!$F1 751

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
716 759 2.358615 GGCGCACCACATGTCTGA 60.359 61.111 10.83 0.0 35.26 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2955 2.358737 GTTCACACCTCCGGCCAG 60.359 66.667 2.24 0.0 0.0 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
150 152 6.388619 TGAAGATAGCTTTCCCCTTACTTT 57.611 37.500 0.00 0.00 33.61 2.66
401 410 3.133691 CACAGACATGCGCCATTAGTAT 58.866 45.455 4.18 0.00 0.00 2.12
673 716 2.548057 ACACTAATGACGCACCAACAAG 59.452 45.455 0.00 0.00 0.00 3.16
716 759 2.358615 GGCGCACCACATGTCTGA 60.359 61.111 10.83 0.00 35.26 3.27
723 766 2.705220 CACATGTCTGATGCGCCG 59.295 61.111 4.18 0.00 0.00 6.46
745 788 6.704493 GCCGTTAGTGTCAATTCCATCTATAA 59.296 38.462 0.00 0.00 0.00 0.98
909 954 5.751680 ACAATTGTGTGTCTTGATCTTTCG 58.248 37.500 11.07 0.00 36.31 3.46
987 1033 8.286097 GGAGCATCTAATAGTAGTTGAAAATGC 58.714 37.037 11.47 10.62 36.83 3.56
1091 1137 3.632604 TGTAGAATCCCTCAGCTCTTACG 59.367 47.826 0.00 0.00 0.00 3.18
1141 1188 6.296026 TCTTTTAGTAGTTGGAGTGTTGCAT 58.704 36.000 0.00 0.00 0.00 3.96
1342 1593 4.425772 TCATTGGAGAAGGAGAGGTACAA 58.574 43.478 0.00 0.00 0.00 2.41
1414 1792 2.967201 AGAGGATCAGAAGCAGAGATGG 59.033 50.000 0.00 0.00 37.82 3.51
1432 1833 2.242926 TGGGTTCGATTCAATTGCCAA 58.757 42.857 0.00 0.00 0.00 4.52
1812 2955 4.215613 GGAGTGTATTTCAGTTGACCAACC 59.784 45.833 9.07 0.00 42.06 3.77
2013 3979 6.360370 AAAGATACATGTCACTGTGGTAGT 57.640 37.500 0.00 4.88 41.36 2.73
2182 4151 2.715046 TGAAGTAAGGCCAGCATCAAG 58.285 47.619 5.01 0.00 0.00 3.02
2384 4356 7.588854 CACTACTTTTAAAAACCTAAGCGTTCC 59.411 37.037 1.66 0.00 0.00 3.62
2428 4400 5.189736 AGGGAGTACTATGCACAAAGATCAA 59.810 40.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.703165 TGTTGCATATATGTTTGTGTTTGCAA 59.297 30.769 14.14 6.75 44.02 4.08
125 127 7.691993 AAGTAAGGGGAAAGCTATCTTCATA 57.308 36.000 0.00 0.00 0.00 2.15
267 272 2.872245 CCACACCTACACACTCACTTTG 59.128 50.000 0.00 0.00 0.00 2.77
373 382 2.253051 CGCATGTCTGTGTGGTGCA 61.253 57.895 0.00 0.00 35.63 4.57
716 759 1.396996 GAATTGACACTAACGGCGCAT 59.603 47.619 10.83 0.00 0.00 4.73
723 766 8.211629 AGGGTTATAGATGGAATTGACACTAAC 58.788 37.037 0.00 0.00 0.00 2.34
745 788 6.449830 AATGTTCACTACTAGGAAAAGGGT 57.550 37.500 0.00 0.00 0.00 4.34
909 954 2.536728 GCTGCAAAACCAAAGAAAACGC 60.537 45.455 0.00 0.00 0.00 4.84
1091 1137 2.480587 GGTTCGAAGCTAGAGCCTCTTC 60.481 54.545 19.71 0.00 43.38 2.87
1141 1188 3.558931 ACCTGCGATCAATTCCATGTA 57.441 42.857 0.00 0.00 0.00 2.29
1414 1792 4.108699 TCATTGGCAATTGAATCGAACC 57.891 40.909 10.65 0.00 0.00 3.62
1432 1833 8.404000 GCAAACTCAAGTCTGAATCATTATCAT 58.596 33.333 0.00 0.00 0.00 2.45
1812 2955 2.358737 GTTCACACCTCCGGCCAG 60.359 66.667 2.24 0.00 0.00 4.85
2013 3979 8.782144 GTTCTTGGCCATCAAATTATTTTTCAA 58.218 29.630 6.09 0.00 34.56 2.69
2182 4151 5.921962 AAATCATGGCCCTTAAGTTTCTC 57.078 39.130 0.00 0.00 0.00 2.87
2428 4400 8.650143 ATCCAACATTCAAGTAATTTAGGTGT 57.350 30.769 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.