Multiple sequence alignment - TraesCS6B01G421400

Loading Multiple Alignment...

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 TraesCS6B01G421400 chr6B 100.000 3263 0 0 1 3263 692195802 692192540 0.000000e+00 6026.0
1 TraesCS6B01G421400 chr6B 97.863 3276 49 10 1 3263 691862850 691866117 0.000000e+00 5642.0
2 TraesCS6B01G421400 chr6B 89.954 1722 125 27 576 2280 692488851 692490541 0.000000e+00 2178.0
3 TraesCS6B01G421400 chr6D 90.987 2552 156 37 1 2505 455087244 455084720 0.000000e+00 3371.0
4 TraesCS6B01G421400 chr6D 90.850 1541 102 14 773 2280 455311592 455313126 0.000000e+00 2028.0
5 TraesCS6B01G421400 chr6D 88.922 334 28 6 2498 2829 372261969 372261643 1.410000e-108 403.0
6 TraesCS6B01G421400 chr6D 89.474 152 16 0 3101 3252 455084493 455084342 3.320000e-45 193.0
7 TraesCS6B01G421400 chr6A 90.334 2545 158 35 1 2505 601399365 601396869 0.000000e+00 3256.0
8 TraesCS6B01G421400 chr6A 89.498 1752 129 28 569 2282 601967712 601969446 0.000000e+00 2165.0
9 TraesCS6B01G421400 chr6A 87.281 228 25 4 3025 3252 601395662 601395439 1.160000e-64 257.0
10 TraesCS6B01G421400 chr6A 79.394 330 56 5 2500 2827 603373983 603374302 4.240000e-54 222.0
11 TraesCS6B01G421400 chr6A 89.189 148 15 1 2848 2995 601395807 601395661 2.000000e-42 183.0
12 TraesCS6B01G421400 chr6A 85.859 99 13 1 2990 3088 406264352 406264255 1.600000e-18 104.0
13 TraesCS6B01G421400 chr6A 80.392 102 10 7 3172 3263 280177729 280177628 5.840000e-08 69.4
14 TraesCS6B01G421400 chr6A 92.500 40 3 0 2390 2429 601397083 601397044 1.260000e-04 58.4
15 TraesCS6B01G421400 chrUn 100.000 388 0 0 1666 2053 480245409 480245796 0.000000e+00 717.0
16 TraesCS6B01G421400 chr7D 90.909 297 26 1 2546 2841 186509544 186509248 6.560000e-107 398.0
17 TraesCS6B01G421400 chr2D 88.690 336 25 9 2499 2831 256866356 256866031 6.560000e-107 398.0
18 TraesCS6B01G421400 chr2D 80.583 309 46 7 2498 2803 578007246 578007543 3.280000e-55 226.0
19 TraesCS6B01G421400 chr4A 91.873 283 19 3 2546 2826 584933028 584933308 3.050000e-105 392.0
20 TraesCS6B01G421400 chr4A 91.289 287 20 5 2546 2828 61740110 61740395 1.420000e-103 387.0
21 TraesCS6B01G421400 chr4A 82.555 321 44 5 2500 2818 429650056 429650366 4.150000e-69 272.0
22 TraesCS6B01G421400 chr2A 91.579 285 22 2 2546 2828 20010445 20010729 3.050000e-105 392.0
23 TraesCS6B01G421400 chr2A 86.350 337 30 8 2498 2831 96616156 96616479 1.440000e-93 353.0
24 TraesCS6B01G421400 chr3D 88.131 337 27 10 2498 2831 272003503 272003829 3.950000e-104 388.0
25 TraesCS6B01G421400 chr5D 91.228 285 23 2 2546 2828 127068916 127069200 1.420000e-103 387.0
26 TraesCS6B01G421400 chr5D 76.667 330 61 11 2896 3217 227733199 227732878 5.600000e-38 169.0
27 TraesCS6B01G421400 chr5D 75.000 208 46 5 2826 3031 246338390 246338187 1.250000e-14 91.6
28 TraesCS6B01G421400 chr1B 87.625 299 24 6 2495 2790 415684231 415683943 5.220000e-88 335.0
29 TraesCS6B01G421400 chr7A 78.571 434 79 10 2826 3250 20690865 20691293 1.150000e-69 274.0
30 TraesCS6B01G421400 chr7A 77.251 211 40 8 2824 3032 603289301 603289505 2.060000e-22 117.0
31 TraesCS6B01G421400 chr3A 79.880 333 52 9 2500 2829 490920593 490920273 2.530000e-56 230.0
32 TraesCS6B01G421400 chr5A 78.571 336 56 9 2497 2828 617124385 617124062 1.190000e-49 207.0
33 TraesCS6B01G421400 chr5A 73.519 287 67 6 2943 3223 493775416 493775699 2.070000e-17 100.0
34 TraesCS6B01G421400 chr7B 83.607 183 18 5 2497 2677 364700869 364700697 9.370000e-36 161.0
35 TraesCS6B01G421400 chr4B 80.132 151 24 3 2990 3135 538806069 538805920 1.240000e-19 108.0
36 TraesCS6B01G421400 chr2B 78.571 154 30 3 2825 2976 135694638 135694790 7.450000e-17 99.0
37 TraesCS6B01G421400 chr1D 79.452 146 24 3 2990 3130 422477325 422477469 7.450000e-17 99.0
38 TraesCS6B01G421400 chr4D 77.711 166 29 4 2991 3150 180501691 180501854 9.640000e-16 95.3
39 TraesCS6B01G421400 chr3B 83.951 81 11 2 2826 2905 685876420 685876499 3.490000e-10 76.8
40 TraesCS6B01G421400 chr3B 86.364 66 8 1 2857 2921 71407620 71407685 1.620000e-08 71.3


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 TraesCS6B01G421400 chr6B 692192540 692195802 3262 True 6026.0 6026 100.0000 1 3263 1 chr6B.!!$R1 3262
1 TraesCS6B01G421400 chr6B 691862850 691866117 3267 False 5642.0 5642 97.8630 1 3263 1 chr6B.!!$F1 3262
2 TraesCS6B01G421400 chr6B 692488851 692490541 1690 False 2178.0 2178 89.9540 576 2280 1 chr6B.!!$F2 1704
3 TraesCS6B01G421400 chr6D 455311592 455313126 1534 False 2028.0 2028 90.8500 773 2280 1 chr6D.!!$F1 1507
4 TraesCS6B01G421400 chr6D 455084342 455087244 2902 True 1782.0 3371 90.2305 1 3252 2 chr6D.!!$R2 3251
5 TraesCS6B01G421400 chr6A 601967712 601969446 1734 False 2165.0 2165 89.4980 569 2282 1 chr6A.!!$F1 1713
6 TraesCS6B01G421400 chr6A 601395439 601399365 3926 True 938.6 3256 89.8260 1 3252 4 chr6A.!!$R3 3251

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
641 664 0.947244 AGTGCAAGCGGTTGAAGAAG 59.053 50.0 30.14 3.53 35.46 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 2715 1.133915 TGTTTCTTCCTGGGTCACCAC 60.134 52.381 0.0 0.0 43.37 4.16 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
458 474 6.565234 CACCGTTGACATCTTCTCTATTACT 58.435 40.000 0.00 0.00 0.00 2.24
459 475 7.681304 GCACCGTTGACATCTTCTCTATTACTA 60.681 40.741 0.00 0.00 0.00 1.82
460 476 7.644551 CACCGTTGACATCTTCTCTATTACTAC 59.355 40.741 0.00 0.00 0.00 2.73
461 477 7.338703 ACCGTTGACATCTTCTCTATTACTACA 59.661 37.037 0.00 0.00 0.00 2.74
641 664 0.947244 AGTGCAAGCGGTTGAAGAAG 59.053 50.000 30.14 3.53 35.46 2.85
659 683 3.567585 AGAAGAGAAAAGACCAAGCAAGC 59.432 43.478 0.00 0.00 0.00 4.01
660 684 2.936202 AGAGAAAAGACCAAGCAAGCA 58.064 42.857 0.00 0.00 0.00 3.91
661 685 3.290710 AGAGAAAAGACCAAGCAAGCAA 58.709 40.909 0.00 0.00 0.00 3.91
662 686 3.317430 AGAGAAAAGACCAAGCAAGCAAG 59.683 43.478 0.00 0.00 0.00 4.01
733 771 2.501610 GCTCCCATCTCCGACCAC 59.498 66.667 0.00 0.00 0.00 4.16
939 1000 3.668447 TGGTCAGCTTCTTCTTAGCTTG 58.332 45.455 0.00 0.00 46.42 4.01
1429 1517 4.144703 GGGCCGTCGAGTTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
2522 2629 2.276740 CCCCTCCCAATGCTCCAC 59.723 66.667 0.00 0.00 0.00 4.02
2535 2642 6.431234 CCCAATGCTCCACCTTATACTAAATC 59.569 42.308 0.00 0.00 0.00 2.17
2607 2714 8.846423 AGGTAATTAAGAGGAGAGAGATGAAA 57.154 34.615 0.00 0.00 0.00 2.69
2608 2715 8.923270 AGGTAATTAAGAGGAGAGAGATGAAAG 58.077 37.037 0.00 0.00 0.00 2.62
2677 2784 3.826729 ACACTTAAATGGAAGAAGCCCAC 59.173 43.478 0.00 0.00 36.36 4.61
2977 4130 1.771854 TCAAGACAAACTAGGGTGGCA 59.228 47.619 3.82 0.00 0.00 4.92
3013 4166 4.451150 CTGCCACGCCCGCTTCTA 62.451 66.667 0.00 0.00 0.00 2.10
3113 4266 1.902918 AACGCTGCTTTCATGCCCA 60.903 52.632 0.00 0.00 0.00 5.36
3201 4354 1.295423 GCTTCCTGGTGTAGGCGAA 59.705 57.895 0.00 0.00 46.87 4.70
3252 4405 5.123820 CGGTCCATTGCCCTACATTAATATG 59.876 44.000 0.00 0.00 37.79 1.78
3253 4406 5.105756 GGTCCATTGCCCTACATTAATATGC 60.106 44.000 0.00 0.00 35.03 3.14
3254 4407 4.699735 TCCATTGCCCTACATTAATATGCG 59.300 41.667 0.00 0.00 35.03 4.73
3255 4408 4.458989 CCATTGCCCTACATTAATATGCGT 59.541 41.667 0.00 0.00 35.03 5.24
3256 4409 5.048083 CCATTGCCCTACATTAATATGCGTT 60.048 40.000 0.00 0.00 35.03 4.84
3257 4410 6.446318 CATTGCCCTACATTAATATGCGTTT 58.554 36.000 0.00 0.00 35.03 3.60
3258 4411 5.431420 TGCCCTACATTAATATGCGTTTG 57.569 39.130 0.00 0.00 35.03 2.93
3259 4412 4.226761 GCCCTACATTAATATGCGTTTGC 58.773 43.478 0.00 0.00 43.20 3.68
3260 4413 4.794169 CCCTACATTAATATGCGTTTGCC 58.206 43.478 0.00 0.00 41.78 4.52
3261 4414 4.463209 CCTACATTAATATGCGTTTGCCG 58.537 43.478 0.00 0.00 41.78 5.69
3262 4415 4.212425 CCTACATTAATATGCGTTTGCCGA 59.788 41.667 0.00 0.00 41.78 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
641 664 3.636381 CTTGCTTGCTTGGTCTTTTCTC 58.364 45.455 0.00 0.00 0.00 2.87
659 683 4.336889 TCTATTATCGACCCCTTGCTTG 57.663 45.455 0.00 0.00 0.00 4.01
660 684 4.202367 CCTTCTATTATCGACCCCTTGCTT 60.202 45.833 0.00 0.00 0.00 3.91
661 685 3.325135 CCTTCTATTATCGACCCCTTGCT 59.675 47.826 0.00 0.00 0.00 3.91
662 686 3.323979 TCCTTCTATTATCGACCCCTTGC 59.676 47.826 0.00 0.00 0.00 4.01
733 771 2.386064 TTTCGGGGTCGGTGTTGAGG 62.386 60.000 0.00 0.00 36.95 3.86
939 1000 2.869192 GGATCTTGGAGAGCGAATGAAC 59.131 50.000 0.00 0.00 29.85 3.18
1429 1517 1.241990 TGGTTCCTGACGACGGAGAG 61.242 60.000 0.00 0.00 0.00 3.20
2535 2642 5.068198 ACATGGCAGCCTTAGTAAATCATTG 59.932 40.000 14.15 0.00 0.00 2.82
2576 2683 8.290277 TCTCTCTCCTCTTAATTACCTTACCAT 58.710 37.037 0.00 0.00 0.00 3.55
2580 2687 9.937876 TTCATCTCTCTCCTCTTAATTACCTTA 57.062 33.333 0.00 0.00 0.00 2.69
2598 2705 2.304180 CTGGGTCACCACTTTCATCTCT 59.696 50.000 0.00 0.00 43.37 3.10
2599 2706 2.616510 CCTGGGTCACCACTTTCATCTC 60.617 54.545 0.00 0.00 43.37 2.75
2607 2714 1.143073 GTTTCTTCCTGGGTCACCACT 59.857 52.381 0.00 0.00 43.37 4.00
2608 2715 1.133915 TGTTTCTTCCTGGGTCACCAC 60.134 52.381 0.00 0.00 43.37 4.16
2677 2784 5.649782 AACTAAAGTTCTCCATGCATTGG 57.350 39.130 0.00 2.32 39.44 3.16
2841 2950 0.251165 CGGGTGGTTTGAGGATTGGT 60.251 55.000 0.00 0.00 0.00 3.67
2884 4037 2.095466 CGTTGGATGGCAAAACACGTAT 60.095 45.455 10.44 0.00 0.00 3.06
3004 4157 1.450312 CAGGGCAGTTAGAAGCGGG 60.450 63.158 0.00 0.00 0.00 6.13
3113 4266 1.901948 TGAGAGGTCACGTCCGCTT 60.902 57.895 1.13 0.00 37.72 4.68


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.