Multiple sequence alignment - TraesCS7A01G545400

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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 TraesCS7A01G545400 chr7A 100.000 3938 0 0 1 3938 721588648 721584711 0.000000e+00 7273.0
1 TraesCS7A01G545400 chr7A 99.644 3936 12 2 1 3936 721663302 721659369 0.000000e+00 7190.0
2 TraesCS7A01G545400 chr7D 93.348 1819 70 16 1235 3019 626052303 626050502 0.000000e+00 2641.0
3 TraesCS7A01G545400 chr7D 96.135 1242 39 7 1 1233 626053575 626052334 0.000000e+00 2019.0
4 TraesCS7A01G545400 chr7D 88.922 668 63 9 1812 2470 626031036 626030371 0.000000e+00 813.0
5 TraesCS7A01G545400 chr7D 83.099 142 14 3 1310 1451 626031474 626031343 1.920000e-23 121.0
6 TraesCS7A01G545400 chr7B 89.365 2031 135 30 1237 3232 725853375 725855359 0.000000e+00 2479.0
7 TraesCS7A01G545400 chr7B 94.378 498 21 2 735 1225 725852829 725853326 0.000000e+00 758.0
8 TraesCS7A01G545400 chr7B 89.189 222 13 3 999 1220 232271722 232271512 2.330000e-67 267.0
9 TraesCS7A01G545400 chr1D 87.210 1079 114 20 1930 3002 25956482 25955422 0.000000e+00 1206.0
10 TraesCS7A01G545400 chr1D 85.802 324 27 9 901 1216 25957760 25957448 3.790000e-85 326.0
11 TraesCS7A01G545400 chr1D 88.387 155 18 0 2783 2937 452348403 452348557 1.870000e-43 187.0
12 TraesCS7A01G545400 chr1B 86.784 1082 114 22 1929 3002 41642885 41641825 0.000000e+00 1179.0
13 TraesCS7A01G545400 chr1B 83.102 722 108 13 1967 2681 622180776 622180062 0.000000e+00 645.0
14 TraesCS7A01G545400 chr1B 96.020 201 8 0 999 1199 41644207 41644007 1.060000e-85 327.0
15 TraesCS7A01G545400 chr1A 86.368 1093 116 15 1923 3002 27259658 27260730 0.000000e+00 1162.0
16 TraesCS7A01G545400 chr1A 87.240 337 26 12 875 1200 27258285 27258615 6.220000e-98 368.0
17 TraesCS7A01G545400 chr3A 82.483 725 125 2 1958 2681 744195235 744194512 5.550000e-178 634.0
18 TraesCS7A01G545400 chr6D 93.627 204 12 1 995 1198 425870796 425870998 1.780000e-78 303.0
19 TraesCS7A01G545400 chr3B 89.744 156 16 0 2783 2938 817352002 817351847 2.400000e-47 200.0
20 TraesCS7A01G545400 chr3D 89.103 156 17 0 2783 2938 607665949 607665794 1.120000e-45 195.0
21 TraesCS7A01G545400 chr3D 86.335 161 17 3 3296 3454 505776272 505776429 1.880000e-38 171.0
22 TraesCS7A01G545400 chr5D 93.130 131 9 0 993 1123 165177916 165177786 4.020000e-45 193.0
23 TraesCS7A01G545400 chr5A 90.385 52 5 0 3714 3765 558688189 558688240 7.060000e-08 69.4


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 TraesCS7A01G545400 chr7A 721584711 721588648 3937 True 7273.0 7273 100.0000 1 3938 1 chr7A.!!$R1 3937
1 TraesCS7A01G545400 chr7A 721659369 721663302 3933 True 7190.0 7190 99.6440 1 3936 1 chr7A.!!$R2 3935
2 TraesCS7A01G545400 chr7D 626050502 626053575 3073 True 2330.0 2641 94.7415 1 3019 2 chr7D.!!$R2 3018
3 TraesCS7A01G545400 chr7D 626030371 626031474 1103 True 467.0 813 86.0105 1310 2470 2 chr7D.!!$R1 1160
4 TraesCS7A01G545400 chr7B 725852829 725855359 2530 False 1618.5 2479 91.8715 735 3232 2 chr7B.!!$F1 2497
5 TraesCS7A01G545400 chr1D 25955422 25957760 2338 True 766.0 1206 86.5060 901 3002 2 chr1D.!!$R1 2101
6 TraesCS7A01G545400 chr1B 41641825 41644207 2382 True 753.0 1179 91.4020 999 3002 2 chr1B.!!$R2 2003
7 TraesCS7A01G545400 chr1B 622180062 622180776 714 True 645.0 645 83.1020 1967 2681 1 chr1B.!!$R1 714
8 TraesCS7A01G545400 chr1A 27258285 27260730 2445 False 765.0 1162 86.8040 875 3002 2 chr1A.!!$F1 2127
9 TraesCS7A01G545400 chr3A 744194512 744195235 723 True 634.0 634 82.4830 1958 2681 1 chr3A.!!$R1 723

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
383 386 0.590195 CACTGGTGAAGCTTGCAGAC 59.41 55.0 2.1 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3133 3933 7.201099 CGAATTTAACGATCGATTGCATTCATC 60.201 37.037 24.34 6.3 38.82 2.92 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
274 277 3.595190 ACAAAAACTTCCCCTGCTAGT 57.405 42.857 0.00 0.00 0.00 2.57
383 386 0.590195 CACTGGTGAAGCTTGCAGAC 59.410 55.000 2.10 0.00 0.00 3.51
3133 3933 4.314121 GGCCTGAGCTATTATCAGAACTG 58.686 47.826 0.00 0.00 45.80 3.16
3671 4471 2.637382 TGATCACACAACTGCCTTCCTA 59.363 45.455 0.00 0.00 0.00 2.94
3920 4720 9.109393 GGCTAAGTCAGTCATTATCAATGTTAA 57.891 33.333 0.00 0.00 39.87 2.01
3928 4728 6.260714 AGTCATTATCAATGTTAATGCTGCGA 59.739 34.615 15.57 0.71 39.87 5.10
3936 4736 6.149142 TCAATGTTAATGCTGCGATATATGCA 59.851 34.615 8.79 8.79 40.70 3.96
3937 4737 6.688637 ATGTTAATGCTGCGATATATGCAT 57.311 33.333 3.79 3.79 46.46 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 277 4.314522 TGAACCCCTGCTTAATGATGAA 57.685 40.909 0.00 0.00 0.00 2.57
3133 3933 7.201099 CGAATTTAACGATCGATTGCATTCATC 60.201 37.037 24.34 6.30 38.82 2.92
3671 4471 4.322049 CCTTAGACTGAAACGATCACCTGT 60.322 45.833 0.00 0.00 33.47 4.00
3848 4648 0.249073 CGCTAGTGCTCACGCCTAAT 60.249 55.000 0.00 0.00 36.97 1.73
3889 4689 1.320344 ATGACTGACTTAGCCGGCGA 61.320 55.000 23.20 14.61 0.00 5.54


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

AutoCloner maintained by Alex Coulton.