Multiple sequence alignment - TraesCS1B01G194000

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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 TraesCS1B01G194000 chr1B 100.000 2804 0 0 1 2804 349350492 349347689 0.000000e+00 5179.0
1 TraesCS1B01G194000 chr1B 94.355 248 14 0 2557 2804 568717865 568718112 5.670000e-102 381.0
2 TraesCS1B01G194000 chr1B 93.927 247 15 0 2558 2804 354562414 354562168 9.480000e-100 374.0
3 TraesCS1B01G194000 chr1B 92.578 256 19 0 2549 2804 154882890 154883145 4.410000e-98 368.0
4 TraesCS1B01G194000 chr1B 80.000 315 55 7 1024 1334 348905759 348905449 2.810000e-55 226.0
5 TraesCS1B01G194000 chr1B 79.394 330 55 9 1011 1334 349564108 349563786 1.310000e-53 220.0
6 TraesCS1B01G194000 chr1B 88.136 118 13 1 2441 2557 647047641 647047758 3.770000e-29 139.0
7 TraesCS1B01G194000 chr1B 97.727 44 1 0 776 819 349349678 349349635 3.000000e-10 76.8
8 TraesCS1B01G194000 chr1B 97.727 44 1 0 815 858 349349717 349349674 3.000000e-10 76.8
9 TraesCS1B01G194000 chr1A 90.999 1311 71 20 503 1786 337630331 337629041 0.000000e+00 1724.0
10 TraesCS1B01G194000 chr1A 87.137 241 25 3 2106 2342 337629044 337628806 4.600000e-68 268.0
11 TraesCS1B01G194000 chr1A 79.299 314 59 6 1024 1334 337301739 337301429 6.080000e-52 215.0
12 TraesCS1B01G194000 chr1D 91.406 1152 61 16 642 1786 262341132 262342252 0.000000e+00 1544.0
13 TraesCS1B01G194000 chr1D 91.281 367 30 2 2 368 262336897 262337261 1.500000e-137 499.0
14 TraesCS1B01G194000 chr1D 88.546 227 20 6 2103 2327 262342246 262342468 1.280000e-68 270.0
15 TraesCS1B01G194000 chr1D 96.429 140 5 0 473 612 262340992 262341131 6.040000e-57 231.0
16 TraesCS1B01G194000 chr1D 80.317 315 54 8 1024 1334 263198930 263198620 6.040000e-57 231.0
17 TraesCS1B01G194000 chr1D 79.205 327 61 6 1011 1334 262252734 262253056 1.310000e-53 220.0
18 TraesCS1B01G194000 chr5B 94.190 327 18 1 1780 2106 322151875 322151550 5.390000e-137 497.0
19 TraesCS1B01G194000 chr5B 92.899 338 23 1 1769 2106 44770988 44771324 9.030000e-135 490.0
20 TraesCS1B01G194000 chr5B 93.750 320 20 0 1787 2106 478698825 478699144 5.430000e-132 481.0
21 TraesCS1B01G194000 chr5B 93.769 321 19 1 1787 2106 603888797 603888477 5.430000e-132 481.0
22 TraesCS1B01G194000 chr5B 83.929 112 18 0 2430 2541 711276928 711277039 1.060000e-19 108.0
23 TraesCS1B01G194000 chr5B 80.620 129 24 1 2430 2557 15003373 15003501 6.390000e-17 99.0
24 TraesCS1B01G194000 chr3B 94.118 323 19 0 1787 2109 369098415 369098093 2.510000e-135 492.0
25 TraesCS1B01G194000 chr3B 94.099 322 19 0 1787 2108 596965147 596964826 9.030000e-135 490.0
26 TraesCS1B01G194000 chr3B 93.353 331 21 1 1779 2109 344956726 344956397 3.250000e-134 488.0
27 TraesCS1B01G194000 chr3B 94.378 249 12 1 2558 2804 261927323 261927571 5.670000e-102 381.0
28 TraesCS1B01G194000 chr2B 94.118 323 18 1 1787 2109 789530259 789529938 9.030000e-135 490.0
29 TraesCS1B01G194000 chr2B 93.927 247 15 0 2558 2804 568061257 568061011 9.480000e-100 374.0
30 TraesCS1B01G194000 chr4B 93.293 328 22 0 1782 2109 481800329 481800002 4.200000e-133 484.0
31 TraesCS1B01G194000 chr4B 94.332 247 14 0 2558 2804 403396522 403396276 2.040000e-101 379.0
32 TraesCS1B01G194000 chr4B 92.913 254 17 1 2552 2804 607173581 607173328 4.410000e-98 368.0
33 TraesCS1B01G194000 chr4B 78.387 310 67 0 1031 1340 471776062 471775753 4.740000e-48 202.0
34 TraesCS1B01G194000 chr7B 95.181 249 10 2 2558 2804 43607145 43606897 2.620000e-105 392.0
35 TraesCS1B01G194000 chr7B 93.254 252 17 0 2553 2804 400562624 400562373 3.410000e-99 372.0
36 TraesCS1B01G194000 chr7D 80.195 308 57 3 1029 1334 579536264 579535959 7.810000e-56 228.0
37 TraesCS1B01G194000 chr7D 82.946 129 20 2 2423 2549 11657449 11657577 6.350000e-22 115.0
38 TraesCS1B01G194000 chr7A 80.065 306 61 0 1029 1334 671219687 671219382 7.810000e-56 228.0
39 TraesCS1B01G194000 chr7A 79.180 317 64 2 1019 1334 29165568 29165253 4.700000e-53 219.0
40 TraesCS1B01G194000 chr4D 78.916 332 68 2 1012 1342 384951441 384951111 1.010000e-54 224.0
41 TraesCS1B01G194000 chr4A 78.593 327 65 4 1009 1334 66559387 66559065 7.870000e-51 211.0
42 TraesCS1B01G194000 chr3D 77.399 323 64 7 1009 1330 8860948 8860634 1.720000e-42 183.0
43 TraesCS1B01G194000 chr3D 80.426 235 41 4 1100 1333 544277867 544277637 1.030000e-39 174.0
44 TraesCS1B01G194000 chr3D 78.481 237 46 3 1100 1335 544353522 544353754 1.740000e-32 150.0
45 TraesCS1B01G194000 chr6D 86.822 129 17 0 2430 2558 288075747 288075619 8.090000e-31 145.0


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 TraesCS1B01G194000 chr1B 349347689 349350492 2803 True 1777.533333 5179 98.484667 1 2804 3 chr1B.!!$R4 2803
1 TraesCS1B01G194000 chr1A 337628806 337630331 1525 True 996.000000 1724 89.068000 503 2342 2 chr1A.!!$R2 1839
2 TraesCS1B01G194000 chr1D 262336897 262342468 5571 False 636.000000 1544 91.915500 2 2327 4 chr1D.!!$F2 2325


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
669 4322 0.174162 TACCGGCGCTTTTCTCCTAC 59.826 55.0 7.64 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 5482 0.035317 TCCGATCCTACATGGCATGC 59.965 55.0 26.7 9.9 35.26 4.06 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.