Multiple sequence alignment - TraesCS6B01G263700

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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 TraesCS6B01G263700 chr6B 100.000 5515 0 0 1 5515 474443039 474437525 0.000000e+00 10185.0
1 TraesCS6B01G263700 chr6B 94.660 206 11 0 1611 1816 474441322 474441117 2.480000e-83 320.0
2 TraesCS6B01G263700 chr6B 94.660 206 11 0 1718 1923 474441429 474441224 2.480000e-83 320.0
3 TraesCS6B01G263700 chr6B 94.949 99 5 0 1611 1709 474441215 474441117 7.400000e-34 156.0
4 TraesCS6B01G263700 chr6B 94.949 99 5 0 1825 1923 474441429 474441331 7.400000e-34 156.0
5 TraesCS6B01G263700 chr6D 92.792 1540 88 13 3681 5200 307120351 307118815 0.000000e+00 2207.0
6 TraesCS6B01G263700 chr6D 92.918 1285 53 18 557 1816 307123076 307121805 0.000000e+00 1834.0
7 TraesCS6B01G263700 chr6D 90.851 1246 55 24 1718 2952 307122011 307120814 0.000000e+00 1615.0
8 TraesCS6B01G263700 chr6D 89.888 445 39 4 50 489 307123520 307123077 8.020000e-158 568.0
9 TraesCS6B01G263700 chr6D 92.157 255 20 0 3096 3350 307120703 307120449 1.460000e-95 361.0
10 TraesCS6B01G263700 chr6D 83.918 342 28 10 5197 5515 307118735 307118398 8.980000e-78 302.0
11 TraesCS6B01G263700 chr6D 96.000 100 3 1 1611 1709 307121904 307121805 1.590000e-35 161.0
12 TraesCS6B01G263700 chr6D 94.118 102 6 0 1820 1921 307122016 307121915 7.400000e-34 156.0
13 TraesCS6B01G263700 chr6D 90.000 60 3 2 1912 1968 84938514 84938455 2.130000e-09 75.0
14 TraesCS6B01G263700 chr6D 92.593 54 1 2 1912 1962 84938487 84938540 2.130000e-09 75.0
15 TraesCS6B01G263700 chr6D 94.872 39 0 2 5158 5194 413075594 413075632 5.970000e-05 60.2
16 TraesCS6B01G263700 chr6A 89.340 1651 91 40 3936 5515 443424166 443422530 0.000000e+00 1995.0
17 TraesCS6B01G263700 chr6A 92.598 1270 63 14 557 1804 443427597 443426337 0.000000e+00 1796.0
18 TraesCS6B01G263700 chr6A 86.223 421 32 10 2234 2652 443425876 443425480 3.050000e-117 433.0
19 TraesCS6B01G263700 chr6A 87.227 321 24 7 2647 2952 443425168 443424850 3.160000e-92 350.0
20 TraesCS6B01G263700 chr6A 91.057 246 21 1 3105 3350 443424743 443424499 1.150000e-86 331.0
21 TraesCS6B01G263700 chr6A 87.226 274 33 2 218 489 443427871 443427598 1.490000e-80 311.0
22 TraesCS6B01G263700 chr6A 90.950 221 12 6 1718 1934 443426527 443426311 1.940000e-74 291.0
23 TraesCS6B01G263700 chr6A 94.068 118 5 2 1999 2115 443426299 443426183 1.580000e-40 178.0
24 TraesCS6B01G263700 chr6A 95.192 104 5 0 1820 1923 443426532 443426429 1.230000e-36 165.0
25 TraesCS6B01G263700 chr6A 93.103 87 6 0 1611 1697 443426423 443426337 1.610000e-25 128.0
26 TraesCS6B01G263700 chr5A 77.247 356 65 13 60 403 316663897 316663546 1.570000e-45 195.0
27 TraesCS6B01G263700 chr1D 98.780 82 1 0 2950 3031 23423941 23423860 4.450000e-31 147.0
28 TraesCS6B01G263700 chr1D 97.561 82 2 0 2950 3031 23423859 23423940 2.070000e-29 141.0
29 TraesCS6B01G263700 chr1D 91.919 99 4 3 2951 3047 476449451 476449355 9.640000e-28 135.0
30 TraesCS6B01G263700 chr1D 100.000 32 0 0 5160 5191 64895567 64895536 5.970000e-05 60.2
31 TraesCS6B01G263700 chr3D 95.556 90 1 2 2947 3034 112712673 112712761 2.070000e-29 141.0
32 TraesCS6B01G263700 chr4A 93.617 94 2 1 2951 3040 556767955 556768048 2.680000e-28 137.0
33 TraesCS6B01G263700 chr4A 92.453 53 4 0 1914 1966 606356727 606356779 5.920000e-10 76.8
34 TraesCS6B01G263700 chr4A 93.878 49 3 0 1 49 550914311 550914263 2.130000e-09 75.0
35 TraesCS6B01G263700 chr4A 100.000 29 0 0 821 849 559050000 559049972 3.000000e-03 54.7
36 TraesCS6B01G263700 chr2B 94.382 89 4 1 2949 3037 675337235 675337148 9.640000e-28 135.0
37 TraesCS6B01G263700 chr2B 94.318 88 5 0 2951 3038 726552211 726552124 9.640000e-28 135.0
38 TraesCS6B01G263700 chr2B 93.878 49 3 0 1 49 639176494 639176542 2.130000e-09 75.0
39 TraesCS6B01G263700 chr2B 88.333 60 3 3 1914 1969 749661618 749661559 9.910000e-08 69.4
40 TraesCS6B01G263700 chr2B 89.583 48 0 2 5147 5189 676588041 676588088 7.720000e-04 56.5
41 TraesCS6B01G263700 chr2D 91.000 100 4 2 2944 3039 381801150 381801248 4.480000e-26 130.0
42 TraesCS6B01G263700 chr2D 92.308 52 2 1 1912 1961 145889581 145889632 7.660000e-09 73.1
43 TraesCS6B01G263700 chr2D 89.583 48 0 2 5147 5189 564920711 564920758 7.720000e-04 56.5
44 TraesCS6B01G263700 chr7D 88.288 111 6 6 2950 3056 169823456 169823349 5.800000e-25 126.0
45 TraesCS6B01G263700 chr7D 98.039 51 1 0 1 51 271923214 271923264 7.610000e-14 89.8
46 TraesCS6B01G263700 chr7D 95.918 49 2 0 1 49 457052074 457052122 4.580000e-11 80.5
47 TraesCS6B01G263700 chr7D 94.000 50 3 0 1 50 616437690 616437739 5.920000e-10 76.8
48 TraesCS6B01G263700 chr7D 90.909 55 1 2 1908 1962 447070872 447070922 2.760000e-08 71.3
49 TraesCS6B01G263700 chr5B 80.000 180 28 7 227 400 267431453 267431276 5.800000e-25 126.0
50 TraesCS6B01G263700 chr5B 91.228 57 4 1 1912 1968 606015545 606015490 5.920000e-10 76.8
51 TraesCS6B01G263700 chr5B 92.000 50 4 0 1 50 71950615 71950664 2.760000e-08 71.3
52 TraesCS6B01G263700 chr5B 91.837 49 4 0 1 49 316462045 316461997 9.910000e-08 69.4
53 TraesCS6B01G263700 chr7A 93.103 58 3 1 1912 1968 98081868 98081925 3.540000e-12 84.2
54 TraesCS6B01G263700 chr7A 89.583 48 0 3 5147 5189 85209346 85209299 7.720000e-04 56.5
55 TraesCS6B01G263700 chr1B 81.731 104 15 4 1492 1593 327478913 327479014 3.540000e-12 84.2
56 TraesCS6B01G263700 chr4D 85.075 67 6 3 1912 1975 323099587 323099652 1.280000e-06 65.8
57 TraesCS6B01G263700 chr3A 97.222 36 1 0 814 849 628305838 628305803 1.660000e-05 62.1
58 TraesCS6B01G263700 chr3A 88.000 50 0 4 5144 5187 621664492 621664443 3.000000e-03 54.7
59 TraesCS6B01G263700 chr2A 100.000 29 0 0 5160 5188 475557182 475557154 3.000000e-03 54.7


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 TraesCS6B01G263700 chr6B 474437525 474443039 5514 True 2227.4 10185 95.84360 1 5515 5 chr6B.!!$R1 5514
1 TraesCS6B01G263700 chr6D 307118398 307123520 5122 True 900.5 2207 91.58025 50 5515 8 chr6D.!!$R2 5465
2 TraesCS6B01G263700 chr6A 443422530 443427871 5341 True 597.8 1995 90.69840 218 5515 10 chr6A.!!$R1 5297


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
130 131 0.183492 TATGTGAGGGGCCAATCAGC 59.817 55.0 4.39 4.95 0.00 4.26 F
542 548 0.236711 CAATCCTCATTGATCGCCGC 59.763 55.0 0.00 0.00 41.97 6.53 F
1740 1778 0.040067 CCTTGCTTTCCGTGTGCTTC 60.040 55.0 0.00 0.00 0.00 3.86 F
3356 3973 0.032403 TGTTGGCAAACTGATGCTGC 59.968 50.0 0.00 0.00 45.68 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1759 0.040067 GAAGCACACGGAAAGCAAGG 60.040 55.0 0.0 0.0 0.00 3.61 R
1794 1832 0.323957 AACTACAACCGAGGGGAAGC 59.676 55.0 0.0 0.0 36.97 3.86 R
3491 4108 0.111266 GCGACGACATGACACACAAC 60.111 55.0 0.0 0.0 0.00 3.32 R
4873 5504 0.863144 TCTACGCCGAAACAAACAGC 59.137 50.0 0.0 0.0 0.00 4.40 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.