Multiple sequence alignment - TraesCS7A01G052300

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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 TraesCS7A01G052300 chr7A 100.000 2429 0 0 1 2429 25337468 25339896 0.000000e+00 4486.0
1 TraesCS7A01G052300 chr7A 86.007 293 33 8 313 600 216353392 216353681 8.440000e-80 307.0
2 TraesCS7A01G052300 chr7A 77.326 172 31 8 656 823 6780967 6781134 7.150000e-16 95.3
3 TraesCS7A01G052300 chr7A 95.833 48 2 0 1666 1713 25339090 25339137 7.200000e-11 78.7
4 TraesCS7A01G052300 chr7A 95.833 48 2 0 1623 1670 25339133 25339180 7.200000e-11 78.7
5 TraesCS7A01G052300 chr2B 92.435 423 27 4 1995 2415 707473038 707472619 1.240000e-167 599.0
6 TraesCS7A01G052300 chr2B 83.226 465 50 21 1226 1680 707473828 707473382 3.760000e-108 401.0
7 TraesCS7A01G052300 chr2B 84.653 202 26 5 417 616 786215713 786215515 1.910000e-46 196.0
8 TraesCS7A01G052300 chr2B 89.189 148 13 3 652 797 707471832 707471978 5.330000e-42 182.0
9 TraesCS7A01G052300 chr2B 82.036 167 21 7 451 611 25690972 25690809 1.520000e-27 134.0
10 TraesCS7A01G052300 chr4D 82.550 447 36 13 1995 2429 459226346 459225930 2.970000e-94 355.0
11 TraesCS7A01G052300 chr4D 86.301 219 30 0 654 872 459227640 459227422 3.120000e-59 239.0
12 TraesCS7A01G052300 chr4D 88.953 172 15 3 1364 1531 459227048 459226877 2.450000e-50 209.0
13 TraesCS7A01G052300 chr7B 83.120 391 42 10 1995 2361 602550772 602550382 3.870000e-88 335.0
14 TraesCS7A01G052300 chr7B 87.879 231 24 4 643 870 602552127 602551898 3.980000e-68 268.0
15 TraesCS7A01G052300 chr7B 90.909 121 11 0 652 772 602549297 602549417 1.930000e-36 163.0
16 TraesCS7A01G052300 chr2A 83.120 391 42 10 1995 2361 744291933 744291543 3.870000e-88 335.0
17 TraesCS7A01G052300 chr2A 88.584 219 24 1 652 870 744293221 744293004 5.150000e-67 265.0
18 TraesCS7A01G052300 chr2A 92.562 121 9 0 652 772 744290459 744290579 8.930000e-40 174.0
19 TraesCS7A01G052300 chr5B 82.913 357 41 13 244 598 539928877 539929215 1.090000e-78 303.0
20 TraesCS7A01G052300 chr5B 78.652 356 55 14 247 600 445968681 445968345 1.460000e-52 217.0
21 TraesCS7A01G052300 chr7D 86.282 277 28 9 313 585 204256033 204256303 2.360000e-75 292.0
22 TraesCS7A01G052300 chr7D 80.591 237 33 12 365 594 53481220 53480990 1.150000e-38 171.0
23 TraesCS7A01G052300 chr4B 82.123 358 45 12 244 599 663103673 663103333 3.060000e-74 289.0
24 TraesCS7A01G052300 chr4B 91.736 121 10 0 652 772 453776430 453776550 4.150000e-38 169.0
25 TraesCS7A01G052300 chr4B 78.947 247 43 8 328 568 671704230 671704473 2.500000e-35 159.0
26 TraesCS7A01G052300 chr4B 91.667 48 4 0 1995 2042 648942436 648942483 1.560000e-07 67.6
27 TraesCS7A01G052300 chr6B 84.083 289 32 11 319 598 192353802 192354085 1.430000e-67 267.0
28 TraesCS7A01G052300 chr6D 83.333 288 36 9 319 598 105823303 105823586 3.100000e-64 255.0
29 TraesCS7A01G052300 chr5D 78.947 323 46 15 243 563 374201498 374201196 1.470000e-47 200.0
30 TraesCS7A01G052300 chr6A 80.741 135 22 4 668 800 60037006 60036874 4.270000e-18 102.0
31 TraesCS7A01G052300 chr4A 90.196 51 5 0 1995 2045 695669164 695669114 1.560000e-07 67.6


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 TraesCS7A01G052300 chr7A 25337468 25339896 2428 False 1547.800000 4486 97.222000 1 2429 3 chr7A.!!$F3 2428
1 TraesCS7A01G052300 chr2B 707472619 707473828 1209 True 500.000000 599 87.830500 1226 2415 2 chr2B.!!$R3 1189
2 TraesCS7A01G052300 chr4D 459225930 459227640 1710 True 267.666667 355 85.934667 654 2429 3 chr4D.!!$R1 1775
3 TraesCS7A01G052300 chr7B 602550382 602552127 1745 True 301.500000 335 85.499500 643 2361 2 chr7B.!!$R1 1718
4 TraesCS7A01G052300 chr2A 744291543 744293221 1678 True 300.000000 335 85.852000 652 2361 2 chr2A.!!$R1 1709


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
924 935 0.031994 CGCAAGGTGGGGAACAAAAG 59.968 55.0 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2498 1.04816 GGAGCTGGAAGAGGGAGAGG 61.048 65.0 0.0 0.0 34.07 3.69 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)



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AutoCloner maintained by Alex Coulton.