Multiple sequence alignment - TraesCS3A01G366200

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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 TraesCS3A01G366200 chr3A 100.000 2324 0 0 1 2324 615136727 615134404 0.000000e+00 4292
1 TraesCS3A01G366200 chr3A 94.989 938 46 1 1 938 702240662 702241598 0.000000e+00 1471
2 TraesCS3A01G366200 chr2D 95.307 2344 79 12 1 2314 645236671 645234329 0.000000e+00 3690
3 TraesCS3A01G366200 chr2D 95.406 653 30 0 925 1577 239257809 239258461 0.000000e+00 1040
4 TraesCS3A01G366200 chr1D 94.423 2349 85 8 1 2315 463793651 463791315 0.000000e+00 3570
5 TraesCS3A01G366200 chr4D 93.784 2365 80 9 1 2314 236672665 236670317 0.000000e+00 3491
6 TraesCS3A01G366200 chr4D 85.795 1408 127 31 925 2314 239784666 239783314 0.000000e+00 1424
7 TraesCS3A01G366200 chr4D 92.219 951 31 7 925 1832 125802816 125801866 0.000000e+00 1306
8 TraesCS3A01G366200 chr4D 88.935 479 17 5 1390 1832 125903980 125903502 2.020000e-155 558
9 TraesCS3A01G366200 chr4A 93.627 2338 81 13 1 2314 129030516 129032809 0.000000e+00 3430
10 TraesCS3A01G366200 chr4A 87.121 132 8 7 2191 2314 714634853 714634983 8.660000e-30 141
11 TraesCS3A01G366200 chr2A 93.234 2350 90 12 1 2314 610789234 610791550 0.000000e+00 3395
12 TraesCS3A01G366200 chr7A 91.878 2364 110 24 1 2314 56073891 56076222 0.000000e+00 3227
13 TraesCS3A01G366200 chr7A 84.677 124 19 0 2192 2315 683478615 683478738 8.720000e-25 124
14 TraesCS3A01G366200 chr5A 91.301 2368 113 25 2 2314 235675088 235677417 0.000000e+00 3145
15 TraesCS3A01G366200 chr5A 92.045 1408 85 13 925 2316 178859713 178858317 0.000000e+00 1954
16 TraesCS3A01G366200 chr7D 94.792 1824 62 12 512 2316 17927137 17925328 0.000000e+00 2811
17 TraesCS3A01G366200 chr7D 91.437 1413 63 25 925 2314 79227557 79228934 0.000000e+00 1886
18 TraesCS3A01G366200 chr7D 96.162 938 34 2 1 938 79226582 79227517 0.000000e+00 1531
19 TraesCS3A01G366200 chr6D 93.469 1424 52 16 925 2314 297170540 297169124 0.000000e+00 2076
20 TraesCS3A01G366200 chr6D 92.959 1406 60 13 925 2314 446363447 446362065 0.000000e+00 2012
21 TraesCS3A01G366200 chr6D 96.375 938 32 2 1 938 446364422 446363487 0.000000e+00 1543
22 TraesCS3A01G366200 chr6D 95.416 938 32 3 1 938 297171506 297170580 0.000000e+00 1483
23 TraesCS3A01G366200 chr6D 87.400 627 33 8 925 1550 46519733 46519152 0.000000e+00 678
24 TraesCS3A01G366200 chr5D 92.153 1440 61 15 925 2314 140952298 140950861 0.000000e+00 1986
25 TraesCS3A01G366200 chr5D 91.483 1409 68 14 925 2315 363991484 363990110 0.000000e+00 1890
26 TraesCS3A01G366200 chr5D 95.949 938 37 1 1 938 29767695 29766759 0.000000e+00 1520
27 TraesCS3A01G366200 chr5D 95.522 938 31 4 1 938 384512126 384511200 0.000000e+00 1489
28 TraesCS3A01G366200 chr3D 94.613 1188 36 8 1133 2314 57608386 57609551 0.000000e+00 1814
29 TraesCS3A01G366200 chr4B 87.039 1057 76 28 531 1564 200943067 200944085 0.000000e+00 1136
30 TraesCS3A01G366200 chr4B 88.215 874 67 12 1471 2319 505002039 505001177 0.000000e+00 1011
31 TraesCS3A01G366200 chr1A 89.781 548 33 11 925 1470 575428223 575428749 0.000000e+00 680


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 TraesCS3A01G366200 chr3A 615134404 615136727 2323 True 4292.0 4292 100.0000 1 2324 1 chr3A.!!$R1 2323
1 TraesCS3A01G366200 chr3A 702240662 702241598 936 False 1471.0 1471 94.9890 1 938 1 chr3A.!!$F1 937
2 TraesCS3A01G366200 chr2D 645234329 645236671 2342 True 3690.0 3690 95.3070 1 2314 1 chr2D.!!$R1 2313
3 TraesCS3A01G366200 chr2D 239257809 239258461 652 False 1040.0 1040 95.4060 925 1577 1 chr2D.!!$F1 652
4 TraesCS3A01G366200 chr1D 463791315 463793651 2336 True 3570.0 3570 94.4230 1 2315 1 chr1D.!!$R1 2314
5 TraesCS3A01G366200 chr4D 236670317 236672665 2348 True 3491.0 3491 93.7840 1 2314 1 chr4D.!!$R3 2313
6 TraesCS3A01G366200 chr4D 239783314 239784666 1352 True 1424.0 1424 85.7950 925 2314 1 chr4D.!!$R4 1389
7 TraesCS3A01G366200 chr4D 125801866 125802816 950 True 1306.0 1306 92.2190 925 1832 1 chr4D.!!$R1 907
8 TraesCS3A01G366200 chr4A 129030516 129032809 2293 False 3430.0 3430 93.6270 1 2314 1 chr4A.!!$F1 2313
9 TraesCS3A01G366200 chr2A 610789234 610791550 2316 False 3395.0 3395 93.2340 1 2314 1 chr2A.!!$F1 2313
10 TraesCS3A01G366200 chr7A 56073891 56076222 2331 False 3227.0 3227 91.8780 1 2314 1 chr7A.!!$F1 2313
11 TraesCS3A01G366200 chr5A 235675088 235677417 2329 False 3145.0 3145 91.3010 2 2314 1 chr5A.!!$F1 2312
12 TraesCS3A01G366200 chr5A 178858317 178859713 1396 True 1954.0 1954 92.0450 925 2316 1 chr5A.!!$R1 1391
13 TraesCS3A01G366200 chr7D 17925328 17927137 1809 True 2811.0 2811 94.7920 512 2316 1 chr7D.!!$R1 1804
14 TraesCS3A01G366200 chr7D 79226582 79228934 2352 False 1708.5 1886 93.7995 1 2314 2 chr7D.!!$F1 2313
15 TraesCS3A01G366200 chr6D 297169124 297171506 2382 True 1779.5 2076 94.4425 1 2314 2 chr6D.!!$R2 2313
16 TraesCS3A01G366200 chr6D 446362065 446364422 2357 True 1777.5 2012 94.6670 1 2314 2 chr6D.!!$R3 2313
17 TraesCS3A01G366200 chr6D 46519152 46519733 581 True 678.0 678 87.4000 925 1550 1 chr6D.!!$R1 625
18 TraesCS3A01G366200 chr5D 140950861 140952298 1437 True 1986.0 1986 92.1530 925 2314 1 chr5D.!!$R2 1389
19 TraesCS3A01G366200 chr5D 363990110 363991484 1374 True 1890.0 1890 91.4830 925 2315 1 chr5D.!!$R3 1390
20 TraesCS3A01G366200 chr5D 29766759 29767695 936 True 1520.0 1520 95.9490 1 938 1 chr5D.!!$R1 937
21 TraesCS3A01G366200 chr5D 384511200 384512126 926 True 1489.0 1489 95.5220 1 938 1 chr5D.!!$R4 937
22 TraesCS3A01G366200 chr3D 57608386 57609551 1165 False 1814.0 1814 94.6130 1133 2314 1 chr3D.!!$F1 1181
23 TraesCS3A01G366200 chr4B 200943067 200944085 1018 False 1136.0 1136 87.0390 531 1564 1 chr4B.!!$F1 1033
24 TraesCS3A01G366200 chr4B 505001177 505002039 862 True 1011.0 1011 88.2150 1471 2319 1 chr4B.!!$R1 848
25 TraesCS3A01G366200 chr1A 575428223 575428749 526 False 680.0 680 89.7810 925 1470 1 chr1A.!!$F1 545

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
92 93 1.244019 GGACGGTGAATGGCAAGCTT 61.244 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1699 0.550914 AGTGCTCCCAGGTTCACAAA 59.449 50.0 11.53 0.0 32.25 2.83 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
59 60 1.550327 AGTCAGCATCAAGTCTCCGA 58.450 50.000 0.00 0.00 0.00 4.55
92 93 1.244019 GGACGGTGAATGGCAAGCTT 61.244 55.000 0.00 0.00 0.00 3.74
148 149 5.450412 GGTTTGTCTCTGCTTTGTTTGATGA 60.450 40.000 0.00 0.00 0.00 2.92
239 240 4.327357 GTGTGTCGAACAAGATGAATCGAT 59.673 41.667 13.03 0.00 41.57 3.59
302 303 4.081972 ACACAACACACATTTTTGCCACTA 60.082 37.500 0.00 0.00 0.00 2.74
560 591 2.275134 TTCACAGCCAGCTTTGATGA 57.725 45.000 9.16 0.00 33.46 2.92
585 616 5.293814 TGTTTGATGTTGTTTGATGCTTTGG 59.706 36.000 0.00 0.00 0.00 3.28
899 948 6.624352 TCATCTTCTTCTGTTTGAGTTTGG 57.376 37.500 0.00 0.00 0.00 3.28
1248 1349 2.264813 CAAGAAGAATTGGCGGCAATG 58.735 47.619 34.37 19.59 0.00 2.82
1304 1405 3.027419 AGGAACTTGAGCTGTTGCC 57.973 52.632 0.00 0.00 35.23 4.52
1527 1699 1.145738 AGCACTTGTGAACCTGGGATT 59.854 47.619 4.79 0.00 0.00 3.01
1551 1793 1.771854 TGAACCTGGGAGCACTTGTTA 59.228 47.619 0.00 0.00 0.00 2.41
1622 1939 5.474532 GTGATGGCTCATTTTGGATGCTATA 59.525 40.000 0.00 0.00 32.98 1.31
1682 1999 8.694540 TGTTTGGATCACAGAATATTATTTGGG 58.305 33.333 0.00 0.00 0.00 4.12
1807 2130 2.818921 TGGTAAAAGGCTGCATCCAAT 58.181 42.857 9.69 0.00 0.00 3.16
1935 2262 9.230122 CCAGAAAATAAAAGGCCAAATTATTGT 57.770 29.630 16.46 12.94 34.60 2.71
2067 2409 6.020971 ACCTTTTCATTTGGTCGTAATTCC 57.979 37.500 0.00 0.00 0.00 3.01
2081 2423 2.418368 AATTCCGCCACATCAGCTTA 57.582 45.000 0.00 0.00 0.00 3.09
2319 2687 3.194755 ACATATGTCTTGTAGTGTCCGCA 59.805 43.478 1.41 0.00 0.00 5.69
2320 2688 2.080286 ATGTCTTGTAGTGTCCGCAC 57.920 50.000 0.00 0.00 45.57 5.34
2321 2689 8.980333 GACATATGTCTTGTAGTGTCCGCACA 62.980 46.154 25.52 0.00 43.30 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.439228 CGTCCGTCAGATCTGGCAT 59.561 57.895 26.10 0.00 34.22 4.40
92 93 0.535335 GTAGACCACATCTCCGCCAA 59.465 55.000 0.00 0.00 39.04 4.52
96 97 0.686441 TGGGGTAGACCACATCTCCG 60.686 60.000 0.00 0.00 46.28 4.63
257 258 1.623811 GTGCCTGGAACCAGTTCTCTA 59.376 52.381 17.92 0.00 42.15 2.43
560 591 6.017770 CCAAAGCATCAAACAACATCAAACAT 60.018 34.615 0.00 0.00 0.00 2.71
585 616 7.148853 GCTCTGAATCAAACAACATCAAATCAC 60.149 37.037 0.00 0.00 0.00 3.06
1248 1349 1.668237 GCTTCTTCCGCCTTCATCTTC 59.332 52.381 0.00 0.00 0.00 2.87
1304 1405 6.987386 TCTTCTTACTCTTGAGACTTCTTGG 58.013 40.000 4.49 0.00 0.00 3.61
1527 1699 0.550914 AGTGCTCCCAGGTTCACAAA 59.449 50.000 11.53 0.00 32.25 2.83
1551 1793 4.279169 CCATCACAAGTTCACTGGTTCAAT 59.721 41.667 0.00 0.00 0.00 2.57
1682 1999 7.035612 CCAACTCAATTTAGAGCCCAATTAAC 58.964 38.462 0.00 0.00 39.26 2.01
1807 2130 4.561500 GGGCCTTGGCCTTTTTATTTTA 57.438 40.909 27.45 0.00 45.39 1.52
1935 2262 3.746436 ATCTGCATGGGCCTGGCA 61.746 61.111 22.05 19.05 40.13 4.92
1979 2320 1.067516 CCAAGCCCAATAATTCAGCCG 59.932 52.381 0.00 0.00 0.00 5.52
2067 2409 1.695893 CGTGGTAAGCTGATGTGGCG 61.696 60.000 0.00 0.00 34.52 5.69
2081 2423 1.906824 ACGTCAGATCCACCGTGGT 60.907 57.895 17.32 4.97 39.03 4.16
2137 2479 8.631480 ACCAAAAAGAAGGTCGTAGATTTAAT 57.369 30.769 0.00 0.00 40.67 1.40


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

AutoCloner maintained by Alex Coulton.