Multiple sequence alignment - TraesCS6B01G005600

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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 TraesCS6B01G005600 chr6B 100.000 2295 0 0 1 2295 4162966 4160672 0.000000e+00 4239.0
1 TraesCS6B01G005600 chr6B 89.084 1649 127 16 3 1627 3871838 3873457 0.000000e+00 1999.0
2 TraesCS6B01G005600 chr6B 100.000 538 0 0 2705 3242 4160262 4159725 0.000000e+00 994.0
3 TraesCS6B01G005600 chr6B 83.585 1060 90 36 1282 2293 4154526 4153503 0.000000e+00 917.0
4 TraesCS6B01G005600 chr6B 84.668 587 51 19 986 1553 4172099 4171533 1.700000e-152 549.0
5 TraesCS6B01G005600 chr6B 85.000 360 40 6 2870 3229 4354488 4354143 1.430000e-93 353.0
6 TraesCS6B01G005600 chr6B 90.351 228 20 1 2068 2293 4170319 4170092 6.800000e-77 298.0
7 TraesCS6B01G005600 chr6B 82.403 233 21 4 1830 2062 3873858 3874070 5.520000e-43 185.0
8 TraesCS6B01G005600 chr6B 93.671 79 4 1 2705 2782 4170077 4169999 2.040000e-22 117.0
9 TraesCS6B01G005600 chr6A 86.450 738 85 10 1 727 687633 686900 0.000000e+00 795.0
10 TraesCS6B01G005600 chr6A 83.189 809 76 33 982 1749 684960 684171 0.000000e+00 686.0
11 TraesCS6B01G005600 chr6A 87.796 549 47 8 2707 3242 731169 730628 2.750000e-175 625.0
12 TraesCS6B01G005600 chr6A 85.329 593 67 8 1597 2183 731846 731268 2.150000e-166 595.0
13 TraesCS6B01G005600 chr6A 90.385 208 20 0 1346 1553 662672 662465 1.150000e-69 274.0
14 TraesCS6B01G005600 chr6A 85.496 131 17 2 148 277 733693 733564 5.640000e-28 135.0
15 TraesCS6B01G005600 chr6A 97.500 40 1 0 753 792 685341 685302 5.800000e-08 69.4
16 TraesCS6B01G005600 chr6D 85.050 602 51 21 971 1553 2169693 2170274 7.800000e-161 577.0
17 TraesCS6B01G005600 chr6D 83.594 512 53 16 1559 2070 2170915 2171395 4.930000e-123 451.0
18 TraesCS6B01G005600 chr6D 80.652 460 49 18 2707 3127 2190860 2191318 1.450000e-83 320.0
19 TraesCS6B01G005600 chr6D 77.925 530 82 16 1251 1766 2240367 2240875 6.800000e-77 298.0
20 TraesCS6B01G005600 chr6D 91.163 215 17 1 2057 2269 2188341 2188555 1.140000e-74 291.0
21 TraesCS6B01G005600 chr6D 77.333 525 92 18 1251 1766 2279322 2278816 5.290000e-73 285.0
22 TraesCS6B01G005600 chr6D 86.192 239 25 3 1828 2062 2188077 2188311 5.370000e-63 252.0
23 TraesCS6B01G005600 chr6D 94.048 84 4 1 2705 2787 2171666 2171749 3.400000e-25 126.0
24 TraesCS6B01G005600 chr6D 83.077 130 21 1 149 277 4204686 4204815 2.040000e-22 117.0
25 TraesCS6B01G005600 chr6D 82.308 130 22 1 149 277 2168430 2168559 9.510000e-21 111.0
26 TraesCS6B01G005600 chrUn 84.722 360 41 6 2870 3229 346747065 346746720 6.660000e-92 348.0
27 TraesCS6B01G005600 chrUn 85.028 354 39 6 2870 3223 350779135 350779474 6.660000e-92 348.0
28 TraesCS6B01G005600 chrUn 84.536 291 32 5 2933 3223 199056152 199056429 3.190000e-70 276.0
29 TraesCS6B01G005600 chr3B 77.401 531 95 15 1244 1766 772901217 772900704 3.160000e-75 292.0
30 TraesCS6B01G005600 chr1D 78.241 216 32 8 434 635 30226629 30226415 1.220000e-24 124.0
31 TraesCS6B01G005600 chr5A 87.342 79 7 3 434 511 600425469 600425393 1.600000e-13 87.9


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 TraesCS6B01G005600 chr6B 4159725 4162966 3241 True 2616.500000 4239 100.000000 1 3242 2 chr6B.!!$R3 3241
1 TraesCS6B01G005600 chr6B 3871838 3874070 2232 False 1092.000000 1999 85.743500 3 2062 2 chr6B.!!$F1 2059
2 TraesCS6B01G005600 chr6B 4153503 4154526 1023 True 917.000000 917 83.585000 1282 2293 1 chr6B.!!$R1 1011
3 TraesCS6B01G005600 chr6B 4169999 4172099 2100 True 321.333333 549 89.563333 986 2782 3 chr6B.!!$R4 1796
4 TraesCS6B01G005600 chr6A 684171 687633 3462 True 516.800000 795 89.046333 1 1749 3 chr6A.!!$R2 1748
5 TraesCS6B01G005600 chr6A 730628 733693 3065 True 451.666667 625 86.207000 148 3242 3 chr6A.!!$R3 3094
6 TraesCS6B01G005600 chr6D 2168430 2171749 3319 False 316.250000 577 86.250000 149 2787 4 chr6D.!!$F3 2638
7 TraesCS6B01G005600 chr6D 2240367 2240875 508 False 298.000000 298 77.925000 1251 1766 1 chr6D.!!$F1 515
8 TraesCS6B01G005600 chr6D 2188077 2191318 3241 False 287.666667 320 86.002333 1828 3127 3 chr6D.!!$F4 1299
9 TraesCS6B01G005600 chr6D 2278816 2279322 506 True 285.000000 285 77.333000 1251 1766 1 chr6D.!!$R1 515
10 TraesCS6B01G005600 chr3B 772900704 772901217 513 True 292.000000 292 77.401000 1244 1766 1 chr3B.!!$R1 522


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
417 429 0.179936 GTGCCTCTCATCCTCCCTTG 59.820 60.0 0.0 0.0 0.00 3.61 F
1021 3383 0.172803 GCCGATGTCCGTAGAACACT 59.827 55.0 0.0 0.0 36.31 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 3661 0.034960 GGAAGGAGGAGAAGTTGGCC 60.035 60.0 0.00 0.0 0.00 5.36 R
2856 8699 0.107703 TGCAGCTAATAGGCGCTTGT 60.108 50.0 7.64 0.0 33.45 3.16 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.