Multiple sequence alignment - TraesCS6B01G008100

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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 TraesCS6B01G008100 chr6B 100.000 3081 0 0 1 3081 5100291 5103371 0.000000e+00 5690.0
1 TraesCS6B01G008100 chr6B 86.589 947 109 7 1323 2259 188696459 188697397 0.000000e+00 1029.0
2 TraesCS6B01G008100 chr6B 97.059 136 4 0 201 336 450089004 450088869 2.390000e-56 230.0
3 TraesCS6B01G008100 chr6B 91.071 56 4 1 3024 3079 42579949 42580003 1.180000e-09 75.0
4 TraesCS6B01G008100 chr6A 94.674 1746 78 5 647 2389 1061988 1063721 0.000000e+00 2695.0
5 TraesCS6B01G008100 chr6A 88.321 822 88 4 1323 2136 124311854 124312675 0.000000e+00 979.0
6 TraesCS6B01G008100 chr6A 80.408 490 80 10 821 1306 124311330 124311807 2.920000e-95 359.0
7 TraesCS6B01G008100 chr6A 94.170 223 8 2 2810 3032 1063750 1063967 4.920000e-88 335.0
8 TraesCS6B01G008100 chr6D 83.504 1370 167 29 821 2136 103035094 103036458 0.000000e+00 1223.0
9 TraesCS6B01G008100 chr6D 89.532 363 31 1 2393 2755 59707449 59707804 1.300000e-123 453.0
10 TraesCS6B01G008100 chr6D 96.324 136 5 0 201 336 135459485 135459620 1.110000e-54 224.0
11 TraesCS6B01G008100 chr4B 90.058 342 26 2 2414 2755 601786236 601786569 1.310000e-118 436.0
12 TraesCS6B01G008100 chr4B 85.205 365 44 6 2395 2755 601786999 601786641 1.750000e-97 366.0
13 TraesCS6B01G008100 chr4B 82.031 256 40 5 2772 3022 552748694 552748948 2.410000e-51 213.0
14 TraesCS6B01G008100 chr5B 92.424 264 16 3 2772 3032 508675162 508674900 1.040000e-99 374.0
15 TraesCS6B01G008100 chr1D 86.486 333 34 7 2386 2716 391070213 391069890 3.780000e-94 355.0
16 TraesCS6B01G008100 chr1D 98.500 200 2 1 1 200 254389779 254389977 4.890000e-93 351.0
17 TraesCS6B01G008100 chr1D 95.122 41 1 1 3038 3078 303305800 303305761 2.560000e-06 63.9
18 TraesCS6B01G008100 chrUn 98.500 200 2 1 1 200 216513296 216513494 4.890000e-93 351.0
19 TraesCS6B01G008100 chrUn 98.500 200 2 1 1 200 286270087 286269889 4.890000e-93 351.0
20 TraesCS6B01G008100 chrUn 95.122 41 1 1 3038 3078 293461550 293461589 2.560000e-06 63.9
21 TraesCS6B01G008100 chrUn 100.000 33 0 0 3038 3070 374857513 374857545 9.220000e-06 62.1
22 TraesCS6B01G008100 chr7D 98.500 200 2 1 1 200 231542724 231542922 4.890000e-93 351.0
23 TraesCS6B01G008100 chr7D 95.122 41 1 1 3038 3078 15026796 15026835 2.560000e-06 63.9
24 TraesCS6B01G008100 chr5D 98.500 200 2 1 1 200 503223528 503223330 4.890000e-93 351.0
25 TraesCS6B01G008100 chr5D 97.059 136 4 0 201 336 503223181 503223046 2.390000e-56 230.0
26 TraesCS6B01G008100 chr5D 97.059 136 4 0 201 336 541029056 541029191 2.390000e-56 230.0
27 TraesCS6B01G008100 chr5A 98.500 200 2 1 1 200 510134661 510134859 4.890000e-93 351.0
28 TraesCS6B01G008100 chr5A 97.059 136 4 0 201 336 330319710 330319575 2.390000e-56 230.0
29 TraesCS6B01G008100 chr5A 94.737 38 2 0 2259 2296 563509843 563509880 3.320000e-05 60.2
30 TraesCS6B01G008100 chr5A 94.737 38 2 0 2259 2296 563519103 563519140 3.320000e-05 60.2
31 TraesCS6B01G008100 chr3D 98.500 200 2 1 1 200 213376731 213376533 4.890000e-93 351.0
32 TraesCS6B01G008100 chr1A 98.500 200 2 1 1 200 278528930 278529128 4.890000e-93 351.0
33 TraesCS6B01G008100 chr1A 98.500 200 2 1 1 200 278531672 278531870 4.890000e-93 351.0
34 TraesCS6B01G008100 chr4A 86.280 328 38 4 2388 2709 150833054 150832728 1.760000e-92 350.0
35 TraesCS6B01G008100 chr3B 86.239 327 37 2 2386 2709 727471594 727471273 6.320000e-92 348.0
36 TraesCS6B01G008100 chr3B 97.794 136 3 0 201 336 201531989 201531854 5.140000e-58 235.0
37 TraesCS6B01G008100 chr3B 92.857 56 2 1 3024 3079 779380018 779380071 2.550000e-11 80.5
38 TraesCS6B01G008100 chr1B 85.417 336 39 4 2378 2709 6305974 6306303 1.060000e-89 340.0
39 TraesCS6B01G008100 chr1B 88.593 263 25 1 2385 2647 6309240 6308983 6.410000e-82 315.0
40 TraesCS6B01G008100 chr1B 100.000 33 0 0 3038 3070 540734230 540734262 9.220000e-06 62.1
41 TraesCS6B01G008100 chr2B 83.918 342 37 11 2386 2709 773465994 773466335 8.300000e-81 311.0
42 TraesCS6B01G008100 chr2B 97.059 136 4 0 201 336 449211248 449211113 2.390000e-56 230.0
43 TraesCS6B01G008100 chr2D 88.462 234 20 5 2805 3032 61274290 61274522 3.030000e-70 276.0
44 TraesCS6B01G008100 chr3A 97.059 136 4 0 201 336 66012660 66012795 2.390000e-56 230.0
45 TraesCS6B01G008100 chr3A 97.059 136 4 0 201 336 164859100 164859235 2.390000e-56 230.0
46 TraesCS6B01G008100 chr7A 83.571 140 17 4 2772 2910 720203983 720204117 3.230000e-25 126.0
47 TraesCS6B01G008100 chr7A 82.857 140 18 2 2772 2910 720274289 720274423 1.500000e-23 121.0
48 TraesCS6B01G008100 chr7A 82.707 133 17 2 2772 2903 720201952 720202079 2.510000e-21 113.0
49 TraesCS6B01G008100 chr7A 87.000 100 12 1 2805 2903 720332478 720332577 9.030000e-21 111.0
50 TraesCS6B01G008100 chr2A 97.297 37 0 1 2259 2295 731082282 731082317 9.220000e-06 62.1


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 TraesCS6B01G008100 chr6B 5100291 5103371 3080 False 5690 5690 100.0000 1 3081 1 chr6B.!!$F1 3080
1 TraesCS6B01G008100 chr6B 188696459 188697397 938 False 1029 1029 86.5890 1323 2259 1 chr6B.!!$F3 936
2 TraesCS6B01G008100 chr6A 1061988 1063967 1979 False 1515 2695 94.4220 647 3032 2 chr6A.!!$F1 2385
3 TraesCS6B01G008100 chr6A 124311330 124312675 1345 False 669 979 84.3645 821 2136 2 chr6A.!!$F2 1315
4 TraesCS6B01G008100 chr6D 103035094 103036458 1364 False 1223 1223 83.5040 821 2136 1 chr6D.!!$F2 1315
5 TraesCS6B01G008100 chr1A 278528930 278531870 2940 False 351 351 98.5000 1 200 2 chr1A.!!$F1 199


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
268 269 0.035317 TCAGCTTCAGCCACACGAAT 59.965 50.000 0.00 0.0 43.38 3.34 F
504 798 1.000274 ACGGCCAGAAAAACTCAATGC 60.000 47.619 2.24 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 2650 0.035152 CTGCATCCTTGGGTGCTACA 60.035 55.0 23.30 5.02 41.78 2.74 R
2263 3998 0.162082 GCAACGCATGTGCATTTGTG 59.838 50.0 6.08 9.94 42.21 3.33 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.