Multiple sequence alignment - TraesCS1D01G054700

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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 TraesCS1D01G054700 chr1D 100.000 2756 0 0 1 2756 36311646 36314401 0.000000e+00 5090.0
1 TraesCS1D01G054700 chr1D 100.000 29 0 0 2248 2276 36313842 36313870 1.000000e-03 54.7
2 TraesCS1D01G054700 chr1A 98.881 1788 17 3 1 1786 35531920 35533706 0.000000e+00 3188.0
3 TraesCS1D01G054700 chr1A 97.366 1215 28 4 1 1213 35499632 35500844 0.000000e+00 2063.0
4 TraesCS1D01G054700 chr1A 96.989 930 13 6 1830 2756 35533704 35534621 0.000000e+00 1548.0
5 TraesCS1D01G054700 chr1A 90.010 1051 44 13 1209 2236 35507257 35508269 0.000000e+00 1303.0
6 TraesCS1D01G054700 chr1A 96.277 188 5 1 2274 2461 35508278 35508463 9.590000e-80 307.0
7 TraesCS1D01G054700 chr1A 96.104 77 2 1 2489 2564 35513272 35513348 1.040000e-24 124.0
8 TraesCS1D01G054700 chr1A 96.296 54 1 1 2512 2564 35483745 35483798 1.360000e-13 87.9
9 TraesCS1D01G054700 chr1A 86.420 81 3 1 2619 2691 35483799 35483879 6.330000e-12 82.4
10 TraesCS1D01G054700 chr1A 85.366 82 3 4 2619 2691 35513349 35513430 2.940000e-10 76.8
11 TraesCS1D01G054700 chr1A 100.000 31 0 0 2246 2276 35534064 35534094 1.070000e-04 58.4
12 TraesCS1D01G054700 chr4D 93.986 1247 53 9 1004 2235 336661177 336662416 0.000000e+00 1868.0
13 TraesCS1D01G054700 chr4D 97.354 189 5 0 2273 2461 336662425 336662613 3.420000e-84 322.0
14 TraesCS1D01G054700 chr4D 96.104 77 2 1 2489 2564 336663339 336663415 1.040000e-24 124.0
15 TraesCS1D01G054700 chr4D 91.803 61 4 1 2693 2752 336663780 336663840 1.760000e-12 84.2
16 TraesCS1D01G054700 chr1B 94.842 1202 40 9 1 1187 56013083 56014277 0.000000e+00 1857.0
17 TraesCS1D01G054700 chr1B 93.896 1196 54 12 1 1187 55969921 55971106 0.000000e+00 1786.0
18 TraesCS1D01G054700 chr1B 93.896 1196 54 12 1 1187 55991919 55993104 0.000000e+00 1786.0
19 TraesCS1D01G054700 chr1B 90.746 1059 48 18 1192 2233 56014322 56015347 0.000000e+00 1367.0
20 TraesCS1D01G054700 chr1B 90.640 1047 48 18 1207 2236 55971373 55972386 0.000000e+00 1345.0
21 TraesCS1D01G054700 chr1B 91.372 904 53 12 1351 2236 55953601 55954497 0.000000e+00 1214.0
22 TraesCS1D01G054700 chr1B 91.150 904 55 11 1351 2236 55942347 55943243 0.000000e+00 1203.0
23 TraesCS1D01G054700 chr1B 90.707 721 31 12 1533 2236 55993410 55994111 0.000000e+00 928.0
24 TraesCS1D01G054700 chr1B 92.887 239 11 2 1192 1430 55971151 55971383 2.630000e-90 342.0
25 TraesCS1D01G054700 chr1B 95.238 189 9 0 2273 2461 55943251 55943439 1.600000e-77 300.0
26 TraesCS1D01G054700 chr1B 95.238 189 9 0 2273 2461 55954505 55954693 1.600000e-77 300.0
27 TraesCS1D01G054700 chr1B 94.652 187 6 2 2275 2461 55972396 55972578 1.250000e-73 287.0
28 TraesCS1D01G054700 chr1B 94.652 187 6 2 2275 2461 55994121 55994303 1.250000e-73 287.0
29 TraesCS1D01G054700 chr1B 94.656 131 5 1 2279 2409 56015362 56015490 4.650000e-48 202.0
30 TraesCS1D01G054700 chr1B 100.000 31 0 0 2246 2276 55943202 55943232 1.070000e-04 58.4
31 TraesCS1D01G054700 chr1B 100.000 31 0 0 2246 2276 55954456 55954486 1.070000e-04 58.4
32 TraesCS1D01G054700 chr1B 100.000 31 0 0 2246 2276 55972345 55972375 1.070000e-04 58.4
33 TraesCS1D01G054700 chr4B 93.750 1248 56 10 1004 2236 414862828 414864068 0.000000e+00 1853.0
34 TraesCS1D01G054700 chr4B 96.809 188 6 0 2273 2460 414864076 414864263 5.730000e-82 315.0
35 TraesCS1D01G054700 chr4B 96.104 77 2 1 2489 2564 414864992 414865068 1.040000e-24 124.0
36 TraesCS1D01G054700 chr4B 90.164 61 5 1 2693 2752 414865433 414865493 8.180000e-11 78.7
37 TraesCS1D01G054700 chr4A 93.371 1252 57 7 1004 2236 136756542 136755298 0.000000e+00 1829.0
38 TraesCS1D01G054700 chr4A 96.354 192 7 0 2273 2464 136755290 136755099 1.590000e-82 316.0
39 TraesCS1D01G054700 chr4A 96.250 80 2 1 2489 2567 136754361 136754282 2.230000e-26 130.0
40 TraesCS1D01G054700 chr4A 91.803 61 4 1 2693 2752 136753920 136753860 1.760000e-12 84.2
41 TraesCS1D01G054700 chrUn 90.707 721 31 12 1533 2236 319316023 319316724 0.000000e+00 928.0
42 TraesCS1D01G054700 chrUn 94.652 187 6 2 2275 2461 319316734 319316916 1.250000e-73 287.0
43 TraesCS1D01G054700 chrUn 100.000 31 0 0 2246 2276 319316683 319316713 1.070000e-04 58.4
44 TraesCS1D01G054700 chr2B 82.713 833 140 4 1010 1840 64994803 64993973 0.000000e+00 737.0
45 TraesCS1D01G054700 chr6A 74.390 492 92 26 476 963 575562391 575561930 2.180000e-41 180.0


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 TraesCS1D01G054700 chr1D 36311646 36314401 2755 False 2572.350000 5090 100.000000 1 2756 2 chr1D.!!$F1 2755
1 TraesCS1D01G054700 chr1A 35499632 35500844 1212 False 2063.000000 2063 97.366000 1 1213 1 chr1A.!!$F1 1212
2 TraesCS1D01G054700 chr1A 35531920 35534621 2701 False 1598.133333 3188 98.623333 1 2756 3 chr1A.!!$F5 2755
3 TraesCS1D01G054700 chr1A 35507257 35508463 1206 False 805.000000 1303 93.143500 1209 2461 2 chr1A.!!$F3 1252
4 TraesCS1D01G054700 chr4D 336661177 336663840 2663 False 599.550000 1868 94.811750 1004 2752 4 chr4D.!!$F1 1748
5 TraesCS1D01G054700 chr1B 56013083 56015490 2407 False 1142.000000 1857 93.414667 1 2409 3 chr1B.!!$F5 2408
6 TraesCS1D01G054700 chr1B 55991919 55994303 2384 False 1000.333333 1786 93.085000 1 2461 3 chr1B.!!$F4 2460
7 TraesCS1D01G054700 chr1B 55969921 55972578 2657 False 763.680000 1786 94.415000 1 2461 5 chr1B.!!$F3 2460
8 TraesCS1D01G054700 chr1B 55953601 55954693 1092 False 524.133333 1214 95.536667 1351 2461 3 chr1B.!!$F2 1110
9 TraesCS1D01G054700 chr1B 55942347 55943439 1092 False 520.466667 1203 95.462667 1351 2461 3 chr1B.!!$F1 1110
10 TraesCS1D01G054700 chr4B 414862828 414865493 2665 False 592.675000 1853 94.206750 1004 2752 4 chr4B.!!$F1 1748
11 TraesCS1D01G054700 chr4A 136753860 136756542 2682 True 589.800000 1829 94.444500 1004 2752 4 chr4A.!!$R1 1748
12 TraesCS1D01G054700 chrUn 319316023 319316916 893 False 424.466667 928 95.119667 1533 2461 3 chrUn.!!$F1 928
13 TraesCS1D01G054700 chr2B 64993973 64994803 830 True 737.000000 737 82.713000 1010 1840 1 chr2B.!!$R1 830

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
935 945 4.221041 GGTACTCAACTAGCAGAGAAAGGT 59.779 45.833 16.44 0.6 35.83 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2615 3642 2.08661 ACAAGGCCTGTGACCATTTT 57.913 45.0 5.69 0.0 36.69 1.82 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
655 665 7.765307 AGCAATGATAACATACCTGAAACAAG 58.235 34.615 0.00 0.0 35.50 3.16
935 945 4.221041 GGTACTCAACTAGCAGAGAAAGGT 59.779 45.833 16.44 0.6 35.83 3.50
1189 1207 0.250989 TTCTTGTGGCCGTAAAGGGG 60.251 55.000 10.88 0.0 41.48 4.79
1202 1260 5.279859 GCCGTAAAGGGGAGCTAACTATAAT 60.280 44.000 0.00 0.0 41.48 1.28
1895 2189 4.584743 TGGCTTTCTTCCTCTTTCTTTTCC 59.415 41.667 0.00 0.0 0.00 3.13
1976 2271 5.171339 ACAGTATCTTTTGTGCTCCAGAT 57.829 39.130 0.00 0.0 0.00 2.90
1977 2272 4.940046 ACAGTATCTTTTGTGCTCCAGATG 59.060 41.667 0.00 0.0 0.00 2.90
1978 2273 3.944015 AGTATCTTTTGTGCTCCAGATGC 59.056 43.478 0.00 0.0 0.00 3.91
1979 2274 1.538047 TCTTTTGTGCTCCAGATGCC 58.462 50.000 0.00 0.0 0.00 4.40
1980 2275 1.202915 TCTTTTGTGCTCCAGATGCCA 60.203 47.619 0.00 0.0 0.00 4.92
2195 2492 3.493350 GGCTTCTTCCATATTGAGAGCGA 60.493 47.826 0.00 0.0 0.00 4.93
2579 3606 4.331717 CGACGGCCTTGACTATTGTATTTT 59.668 41.667 0.00 0.0 0.00 1.82
2580 3607 5.163794 CGACGGCCTTGACTATTGTATTTTT 60.164 40.000 0.00 0.0 0.00 1.94
2698 4018 2.873472 ACCGCAATACGTTTCACAGAAA 59.127 40.909 0.00 0.0 41.42 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
655 665 3.845781 TTGTTCCTAGGCCATCATCTC 57.154 47.619 5.01 0.00 0.00 2.75
799 809 1.134848 TGCCTTTTGTTTCAGGTGTGC 60.135 47.619 0.00 0.00 32.06 4.57
935 945 9.941325 ATCCATTTGTAATTAGAATTTTGTGCA 57.059 25.926 0.00 0.00 0.00 4.57
987 1005 6.877855 CCAATGCATACATACTTCAGCTCTAT 59.122 38.462 0.00 0.00 34.62 1.98
1792 2067 5.123661 TGCAGTCTTCAAATTTATCGCATCA 59.876 36.000 0.00 0.00 0.00 3.07
1976 2271 4.278919 CAGATGTTATTACATGGCATGGCA 59.721 41.667 29.49 25.52 44.90 4.92
1977 2272 4.279169 ACAGATGTTATTACATGGCATGGC 59.721 41.667 29.49 13.29 44.90 4.40
1978 2273 6.395426 AACAGATGTTATTACATGGCATGG 57.605 37.500 29.49 13.03 44.90 3.66
1979 2274 8.192774 AGAAAACAGATGTTATTACATGGCATG 58.807 33.333 25.31 25.31 44.90 4.06
1980 2275 8.297470 AGAAAACAGATGTTATTACATGGCAT 57.703 30.769 1.31 0.00 44.90 4.40
2171 2468 4.202441 GCTCTCAATATGGAAGAAGCCAA 58.798 43.478 0.00 0.00 42.16 4.52
2612 3639 3.763897 ACAAGGCCTGTGACCATTTTATC 59.236 43.478 5.69 0.00 36.69 1.75
2613 3640 3.778265 ACAAGGCCTGTGACCATTTTAT 58.222 40.909 5.69 0.00 36.69 1.40
2614 3641 3.237268 ACAAGGCCTGTGACCATTTTA 57.763 42.857 5.69 0.00 36.69 1.52
2615 3642 2.086610 ACAAGGCCTGTGACCATTTT 57.913 45.000 5.69 0.00 36.69 1.82


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

AutoCloner maintained by Alex Coulton.