Multiple sequence alignment - TraesCS6A01G317300

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 TraesCS6A01G317300 chr6A 100.000 2636 0 0 1 2636 553572807 553570172 0.000000e+00 4868
1 TraesCS6A01G317300 chr6A 96.288 2182 64 6 337 2506 577152224 577154400 0.000000e+00 3565
2 TraesCS6A01G317300 chr5A 97.626 2317 40 6 331 2636 562122936 562120624 0.000000e+00 3960
3 TraesCS6A01G317300 chr5A 97.288 2323 40 3 337 2636 687969726 687972048 0.000000e+00 3919
4 TraesCS6A01G317300 chr5A 97.809 1871 40 1 767 2636 511207011 511208881 0.000000e+00 3227
5 TraesCS6A01G317300 chr5A 91.087 2345 127 30 335 2633 310018227 310020535 0.000000e+00 3097
6 TraesCS6A01G317300 chr5A 98.780 328 3 1 1 328 687968645 687968971 1.360000e-162 582
7 TraesCS6A01G317300 chr7A 97.276 2313 55 3 331 2636 49821427 49823738 0.000000e+00 3916
8 TraesCS6A01G317300 chr7A 97.256 328 7 2 1 328 626867988 626868313 2.960000e-154 555
9 TraesCS6A01G317300 chr7A 86.186 333 34 10 1 328 704621367 704621042 1.500000e-92 350
10 TraesCS6A01G317300 chr1A 96.556 2323 59 6 331 2636 16225046 16227364 0.000000e+00 3827
11 TraesCS6A01G317300 chr1A 97.340 1917 50 1 719 2634 16218850 16220766 0.000000e+00 3256
12 TraesCS6A01G317300 chr1A 96.933 326 10 0 1 326 16224118 16224443 4.960000e-152 547
13 TraesCS6A01G317300 chr1A 98.513 269 3 1 1 269 16217406 16217673 8.540000e-130 473
14 TraesCS6A01G317300 chr5D 95.955 2200 54 6 340 2506 437728263 437726066 0.000000e+00 3537
15 TraesCS6A01G317300 chr1D 95.247 2209 66 7 337 2506 152626279 152628487 0.000000e+00 3461
16 TraesCS6A01G317300 chr1D 95.750 400 10 2 335 728 152476832 152477230 2.860000e-179 638
17 TraesCS6A01G317300 chr3B 95.043 2199 63 15 331 2506 823895692 823893517 0.000000e+00 3415
18 TraesCS6A01G317300 chr2A 97.916 1871 38 1 767 2636 5148332 5150202 0.000000e+00 3238
19 TraesCS6A01G317300 chr4A 97.755 1871 41 1 767 2636 238128279 238126409 0.000000e+00 3221
20 TraesCS6A01G317300 chr2D 94.396 1374 49 12 340 1692 104541671 104540305 0.000000e+00 2085
21 TraesCS6A01G317300 chr2D 95.716 1167 35 3 331 1482 165664151 165665317 0.000000e+00 1864
22 TraesCS6A01G317300 chr7D 97.194 392 5 1 343 728 509205626 509205235 0.000000e+00 658
23 TraesCS6A01G317300 chr7D 93.958 331 16 2 1 328 613124706 613124377 5.070000e-137 497
24 TraesCS6A01G317300 chr7B 92.308 312 18 4 22 328 702626416 702626726 3.110000e-119 438


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 TraesCS6A01G317300 chr6A 553570172 553572807 2635 True 4868.00 4868 100.0000 1 2636 1 chr6A.!!$R1 2635
1 TraesCS6A01G317300 chr6A 577152224 577154400 2176 False 3565.00 3565 96.2880 337 2506 1 chr6A.!!$F1 2169
2 TraesCS6A01G317300 chr5A 562120624 562122936 2312 True 3960.00 3960 97.6260 331 2636 1 chr5A.!!$R1 2305
3 TraesCS6A01G317300 chr5A 511207011 511208881 1870 False 3227.00 3227 97.8090 767 2636 1 chr5A.!!$F2 1869
4 TraesCS6A01G317300 chr5A 310018227 310020535 2308 False 3097.00 3097 91.0870 335 2633 1 chr5A.!!$F1 2298
5 TraesCS6A01G317300 chr5A 687968645 687972048 3403 False 2250.50 3919 98.0340 1 2636 2 chr5A.!!$F3 2635
6 TraesCS6A01G317300 chr7A 49821427 49823738 2311 False 3916.00 3916 97.2760 331 2636 1 chr7A.!!$F1 2305
7 TraesCS6A01G317300 chr1A 16217406 16227364 9958 False 2025.75 3827 97.3355 1 2636 4 chr1A.!!$F1 2635
8 TraesCS6A01G317300 chr5D 437726066 437728263 2197 True 3537.00 3537 95.9550 340 2506 1 chr5D.!!$R1 2166
9 TraesCS6A01G317300 chr1D 152626279 152628487 2208 False 3461.00 3461 95.2470 337 2506 1 chr1D.!!$F2 2169
10 TraesCS6A01G317300 chr3B 823893517 823895692 2175 True 3415.00 3415 95.0430 331 2506 1 chr3B.!!$R1 2175
11 TraesCS6A01G317300 chr2A 5148332 5150202 1870 False 3238.00 3238 97.9160 767 2636 1 chr2A.!!$F1 1869
12 TraesCS6A01G317300 chr4A 238126409 238128279 1870 True 3221.00 3221 97.7550 767 2636 1 chr4A.!!$R1 1869
13 TraesCS6A01G317300 chr2D 104540305 104541671 1366 True 2085.00 2085 94.3960 340 1692 1 chr2D.!!$R1 1352
14 TraesCS6A01G317300 chr2D 165664151 165665317 1166 False 1864.00 1864 95.7160 331 1482 1 chr2D.!!$F1 1151

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
291 292 0.036010 ATAAGCTGAGGCACGCTTGT 60.036 50.000 18.27 12.08 45.31 3.16 F
633 1388 1.067354 CCCAAACCATCTTGCTGCTTC 60.067 52.381 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1199 8641 1.019673 GCATCAGCACCATGGTAGTG 58.980 55.0 19.28 17.52 41.58 2.74 R
1824 9271 4.447054 CACATTGCGCCTGAAACAAAATAA 59.553 37.5 4.18 0.00 0.00 1.40 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 4.706035 TCCTTTTGTTGCTGCATTTGAAT 58.294 34.783 1.84 0.00 0.00 2.57
291 292 0.036010 ATAAGCTGAGGCACGCTTGT 60.036 50.000 18.27 12.08 45.31 3.16
301 302 2.434336 AGGCACGCTTGTTGGATATCTA 59.566 45.455 2.05 0.00 0.00 1.98
633 1388 1.067354 CCCAAACCATCTTGCTGCTTC 60.067 52.381 0.00 0.00 0.00 3.86
905 8335 8.213679 AGCCTTCTATCATGCTTACAAGATTTA 58.786 33.333 0.00 0.00 35.85 1.40
1112 8543 1.205655 CCTCGACTTCAAGGATGCTCA 59.794 52.381 0.00 0.00 34.35 4.26
1199 8641 8.997621 TTGATGTCCTACTACTGTTAATTGTC 57.002 34.615 0.00 0.00 0.00 3.18
1824 9271 6.954487 TGTATGGTCGTGATAGTAGAATGT 57.046 37.500 0.00 0.00 0.00 2.71
1848 9295 0.597118 TTGTTTCAGGCGCAATGTGC 60.597 50.000 10.83 10.74 40.69 4.57
2039 9486 7.397192 GGTCTGTTCATAATATATTTGCCCCAT 59.603 37.037 2.68 0.00 0.00 4.00
2236 9700 0.251386 AGAGAGTCCAGCGAGTCCAA 60.251 55.000 0.00 0.00 39.00 3.53
2442 9932 1.880941 AGATGGGACCCACTTACCTC 58.119 55.000 17.78 8.54 35.80 3.85
2483 9973 4.202673 ACCAGAACCTAACAATTGGGACAT 60.203 41.667 10.83 0.00 39.30 3.06
2498 9988 4.878968 TGGGACATATCTGACTAGTGGAA 58.121 43.478 0.00 0.00 0.00 3.53
2574 10064 4.339814 TCGTTTAGACAAAAAGGCCACAAT 59.660 37.500 5.01 0.00 0.00 2.71
2623 10114 1.751733 GCTTGGCCCATGAAGCTGATA 60.752 52.381 16.26 0.00 41.21 2.15
2628 10119 4.032310 TGGCCCATGAAGCTGATAAAAAT 58.968 39.130 0.00 0.00 0.00 1.82
2630 10121 4.812626 GGCCCATGAAGCTGATAAAAATTG 59.187 41.667 0.00 0.00 0.00 2.32
2631 10122 5.395546 GGCCCATGAAGCTGATAAAAATTGA 60.396 40.000 0.00 0.00 0.00 2.57
2632 10123 6.285990 GCCCATGAAGCTGATAAAAATTGAT 58.714 36.000 0.00 0.00 0.00 2.57
2633 10124 7.436118 GCCCATGAAGCTGATAAAAATTGATA 58.564 34.615 0.00 0.00 0.00 2.15
2634 10125 7.597743 GCCCATGAAGCTGATAAAAATTGATAG 59.402 37.037 0.00 0.00 0.00 2.08
2635 10126 8.853126 CCCATGAAGCTGATAAAAATTGATAGA 58.147 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
329 330 9.312904 AGTAGTAGTAGTAGTAGTAGCATAGCT 57.687 37.037 0.00 0.00 43.41 3.32
359 1107 8.381636 AGCTACTAATCAGGATTAAATGCAGAT 58.618 33.333 15.47 0.00 33.34 2.90
633 1388 2.114616 ACAGAGAGTATTCCCTGCCAG 58.885 52.381 0.00 0.00 0.00 4.85
905 8335 2.624838 GGTGCTACTGCCATGCAAATAT 59.375 45.455 0.00 0.00 38.41 1.28
907 8337 0.819582 GGTGCTACTGCCATGCAAAT 59.180 50.000 0.00 0.00 38.41 2.32
1112 8543 2.685380 CCTTCTCGAGGCAGGGGT 60.685 66.667 19.06 0.00 39.09 4.95
1199 8641 1.019673 GCATCAGCACCATGGTAGTG 58.980 55.000 19.28 17.52 41.58 2.74
1824 9271 4.447054 CACATTGCGCCTGAAACAAAATAA 59.553 37.500 4.18 0.00 0.00 1.40
2442 9932 4.927978 TGGTAACAGGTTTCCATTTGTG 57.072 40.909 6.44 0.00 46.17 3.33
2483 9973 7.285629 CAGATAAGTGGTTCCACTAGTCAGATA 59.714 40.741 22.46 11.20 45.37 1.98


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

AutoCloner maintained by Alex Coulton.