Multiple sequence alignment - TraesCS5A01G535200

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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 TraesCS5A01G535200 chr5A 100.000 2848 0 0 1 2848 691996773 691993926 0.000000e+00 5260.0
1 TraesCS5A01G535200 chr5A 81.873 662 89 22 2192 2839 623489306 623489950 1.940000e-146 529.0
2 TraesCS5A01G535200 chr5A 97.647 85 2 0 1110 1194 691995748 691995664 2.290000e-31 147.0
3 TraesCS5A01G535200 chr5A 93.478 46 3 0 462 507 110284594 110284639 5.090000e-08 69.4
4 TraesCS5A01G535200 chr7B 99.228 2849 21 1 1 2848 381904376 381907224 0.000000e+00 5138.0
5 TraesCS5A01G535200 chr7B 83.791 765 103 12 2102 2848 711456775 711456014 0.000000e+00 706.0
6 TraesCS5A01G535200 chr7B 78.502 828 123 29 2057 2840 673590148 673590964 2.550000e-135 492.0
7 TraesCS5A01G535200 chr7B 97.647 85 2 0 1110 1194 381905402 381905486 2.290000e-31 147.0
8 TraesCS5A01G535200 chr7B 97.647 85 2 0 1026 1110 381905486 381905570 2.290000e-31 147.0
9 TraesCS5A01G535200 chr7B 90.476 105 7 3 523 625 191181607 191181710 4.950000e-28 135.0
10 TraesCS5A01G535200 chr7B 89.524 105 8 3 523 625 23644276 23644173 2.300000e-26 130.0
11 TraesCS5A01G535200 chr3A 99.193 2849 22 1 1 2848 442908336 442905488 0.000000e+00 5132.0
12 TraesCS5A01G535200 chr3A 97.647 85 2 0 1110 1194 442907310 442907226 2.290000e-31 147.0
13 TraesCS5A01G535200 chr2D 97.192 1959 42 8 1 1948 117195491 117193535 0.000000e+00 3301.0
14 TraesCS5A01G535200 chr2D 97.647 85 2 0 1026 1110 117194373 117194289 2.290000e-31 147.0
15 TraesCS5A01G535200 chr2D 97.647 85 2 0 1110 1194 117194457 117194373 2.290000e-31 147.0
16 TraesCS5A01G535200 chr2B 90.909 880 56 6 1961 2838 575832288 575831431 0.000000e+00 1160.0
17 TraesCS5A01G535200 chr2B 89.091 385 22 8 219 583 394246733 394247117 7.190000e-126 460.0
18 TraesCS5A01G535200 chr2B 90.647 139 4 3 485 614 394247112 394247250 2.920000e-40 176.0
19 TraesCS5A01G535200 chr2B 85.915 142 6 9 809 936 357881179 357881320 3.830000e-29 139.0
20 TraesCS5A01G535200 chr2A 90.036 823 74 6 1110 1924 240817721 240818543 0.000000e+00 1059.0
21 TraesCS5A01G535200 chr2A 87.714 350 35 5 762 1110 240817463 240817805 4.420000e-108 401.0
22 TraesCS5A01G535200 chr3B 88.571 840 70 20 1110 1924 612305487 612306325 0.000000e+00 996.0
23 TraesCS5A01G535200 chr3B 86.765 816 79 17 1110 1898 605454757 605453944 0.000000e+00 881.0
24 TraesCS5A01G535200 chr3B 83.665 753 97 13 1202 1945 324237686 324236951 0.000000e+00 686.0
25 TraesCS5A01G535200 chr3B 87.456 287 25 8 820 1096 324237966 324237681 1.270000e-83 320.0
26 TraesCS5A01G535200 chr3B 87.736 106 11 1 31 136 612305118 612305221 3.850000e-24 122.0
27 TraesCS5A01G535200 chr1B 87.843 839 76 18 1110 1923 199671029 199670192 0.000000e+00 961.0
28 TraesCS5A01G535200 chr1B 88.542 384 24 9 219 582 201921792 201922175 5.600000e-122 448.0
29 TraesCS5A01G535200 chr1B 89.884 346 14 8 258 583 199007718 199008062 2.620000e-115 425.0
30 TraesCS5A01G535200 chr1B 87.324 355 31 13 765 1110 199671294 199670945 7.400000e-106 394.0
31 TraesCS5A01G535200 chr1B 89.545 220 11 6 258 466 199007504 199007722 4.680000e-68 268.0
32 TraesCS5A01G535200 chr1B 89.209 139 6 3 485 614 201922171 201922309 6.310000e-37 165.0
33 TraesCS5A01G535200 chr1B 87.857 140 7 4 485 614 199008057 199008196 3.800000e-34 156.0
34 TraesCS5A01G535200 chr1B 87.156 109 9 4 34 142 199671396 199671293 4.980000e-23 119.0
35 TraesCS5A01G535200 chr7A 86.763 763 82 12 2102 2848 709968737 709967978 0.000000e+00 832.0
36 TraesCS5A01G535200 chr7D 83.963 767 96 16 2102 2848 617090920 617090161 0.000000e+00 710.0
37 TraesCS5A01G535200 chr7D 92.000 100 8 0 1964 2063 617091109 617091010 1.060000e-29 141.0
38 TraesCS5A01G535200 chr5B 83.400 753 100 11 1202 1945 208768252 208767516 0.000000e+00 675.0
39 TraesCS5A01G535200 chr5B 80.112 714 103 29 2146 2839 619851019 619851713 1.970000e-136 496.0
40 TraesCS5A01G535200 chr5B 89.812 373 18 8 231 583 321632873 321633245 7.190000e-126 460.0
41 TraesCS5A01G535200 chr5B 78.401 588 86 23 2146 2697 619549792 619550374 7.550000e-91 344.0
42 TraesCS5A01G535200 chr5B 86.713 286 27 8 820 1095 512584756 512584472 9.910000e-80 307.0
43 TraesCS5A01G535200 chr5B 83.217 286 26 10 820 1095 208768521 208768248 2.830000e-60 243.0
44 TraesCS5A01G535200 chr5B 90.647 139 4 3 485 614 321633342 321633480 2.920000e-40 176.0
45 TraesCS5A01G535200 chr5B 84.783 138 11 5 809 936 512584889 512584752 2.300000e-26 130.0
46 TraesCS5A01G535200 chr5D 77.949 907 150 38 1965 2839 499222236 499223124 3.250000e-144 521.0
47 TraesCS5A01G535200 chr5D 89.276 373 14 8 240 593 548081498 548081863 7.240000e-121 444.0


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 TraesCS5A01G535200 chr5A 691993926 691996773 2847 True 2703.500000 5260 98.823500 1 2848 2 chr5A.!!$R1 2847
1 TraesCS5A01G535200 chr5A 623489306 623489950 644 False 529.000000 529 81.873000 2192 2839 1 chr5A.!!$F2 647
2 TraesCS5A01G535200 chr7B 381904376 381907224 2848 False 1810.666667 5138 98.174000 1 2848 3 chr7B.!!$F3 2847
3 TraesCS5A01G535200 chr7B 711456014 711456775 761 True 706.000000 706 83.791000 2102 2848 1 chr7B.!!$R2 746
4 TraesCS5A01G535200 chr7B 673590148 673590964 816 False 492.000000 492 78.502000 2057 2840 1 chr7B.!!$F2 783
5 TraesCS5A01G535200 chr3A 442905488 442908336 2848 True 2639.500000 5132 98.420000 1 2848 2 chr3A.!!$R1 2847
6 TraesCS5A01G535200 chr2D 117193535 117195491 1956 True 1198.333333 3301 97.495333 1 1948 3 chr2D.!!$R1 1947
7 TraesCS5A01G535200 chr2B 575831431 575832288 857 True 1160.000000 1160 90.909000 1961 2838 1 chr2B.!!$R1 877
8 TraesCS5A01G535200 chr2B 394246733 394247250 517 False 318.000000 460 89.869000 219 614 2 chr2B.!!$F2 395
9 TraesCS5A01G535200 chr2A 240817463 240818543 1080 False 730.000000 1059 88.875000 762 1924 2 chr2A.!!$F1 1162
10 TraesCS5A01G535200 chr3B 605453944 605454757 813 True 881.000000 881 86.765000 1110 1898 1 chr3B.!!$R1 788
11 TraesCS5A01G535200 chr3B 612305118 612306325 1207 False 559.000000 996 88.153500 31 1924 2 chr3B.!!$F1 1893
12 TraesCS5A01G535200 chr3B 324236951 324237966 1015 True 503.000000 686 85.560500 820 1945 2 chr3B.!!$R2 1125
13 TraesCS5A01G535200 chr1B 199670192 199671396 1204 True 491.333333 961 87.441000 34 1923 3 chr1B.!!$R1 1889
14 TraesCS5A01G535200 chr1B 201921792 201922309 517 False 306.500000 448 88.875500 219 614 2 chr1B.!!$F2 395
15 TraesCS5A01G535200 chr1B 199007504 199008196 692 False 283.000000 425 89.095333 258 614 3 chr1B.!!$F1 356
16 TraesCS5A01G535200 chr7A 709967978 709968737 759 True 832.000000 832 86.763000 2102 2848 1 chr7A.!!$R1 746
17 TraesCS5A01G535200 chr7D 617090161 617091109 948 True 425.500000 710 87.981500 1964 2848 2 chr7D.!!$R1 884
18 TraesCS5A01G535200 chr5B 619851019 619851713 694 False 496.000000 496 80.112000 2146 2839 1 chr5B.!!$F2 693
19 TraesCS5A01G535200 chr5B 208767516 208768521 1005 True 459.000000 675 83.308500 820 1945 2 chr5B.!!$R1 1125
20 TraesCS5A01G535200 chr5B 619549792 619550374 582 False 344.000000 344 78.401000 2146 2697 1 chr5B.!!$F1 551
21 TraesCS5A01G535200 chr5B 321632873 321633480 607 False 318.000000 460 90.229500 231 614 2 chr5B.!!$F3 383
22 TraesCS5A01G535200 chr5D 499222236 499223124 888 False 521.000000 521 77.949000 1965 2839 1 chr5D.!!$F1 874

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
38 39 0.953727 GACAATGGCTGCAAGTGACA 59.046 50.000 11.96 0.0 35.30 3.58 F
1924 2295 5.717078 ATCAGTTGAATTGATGCACACTT 57.283 34.783 2.18 0.0 34.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1760 1.152419 TTGGTGTCACCCGAGGAGA 60.152 57.895 19.57 0.00 37.50 3.71 R
2748 3293 3.624861 GCCAGTACTGTCAAATGATCAGG 59.375 47.826 21.18 2.56 34.02 3.86 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
38 39 0.953727 GACAATGGCTGCAAGTGACA 59.046 50.000 11.96 0.0 35.30 3.58
1924 2295 5.717078 ATCAGTTGAATTGATGCACACTT 57.283 34.783 2.18 0.0 34.14 3.16
2600 3123 2.095853 CAGACAAACAGAACGCAACACT 59.904 45.455 0.00 0.0 0.00 3.55
2748 3293 5.063880 ACAAACTTGACCTCCACATACTTC 58.936 41.667 0.00 0.0 0.00 3.01
2840 3386 5.687166 AGCATTTGGTGAAAATCATCCAT 57.313 34.783 0.00 0.0 36.28 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.835941 CTAAGATGGGCTCCTGTGCT 59.164 55.000 0.00 0.00 0.00 4.40
1395 1760 1.152419 TTGGTGTCACCCGAGGAGA 60.152 57.895 19.57 0.00 37.50 3.71
1766 2137 1.797348 CGCACCAAGACAAACACCAAC 60.797 52.381 0.00 0.00 0.00 3.77
2600 3123 2.972713 AGGGTTGCAAGACAGTTCTCTA 59.027 45.455 0.00 0.00 0.00 2.43
2748 3293 3.624861 GCCAGTACTGTCAAATGATCAGG 59.375 47.826 21.18 2.56 34.02 3.86


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

AutoCloner maintained by Alex Coulton.