Multiple sequence alignment - TraesCS5A01G478400

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 TraesCS5A01G478400 chr5A 100.000 5214 0 0 1 5214 651787352 651792565 0.000000e+00 9629.0
1 TraesCS5A01G478400 chr5A 86.992 492 48 9 927 1405 651748934 651749422 1.650000e-149 540.0
2 TraesCS5A01G478400 chr5A 87.852 461 44 5 955 1405 651734257 651734715 9.940000e-147 531.0
3 TraesCS5A01G478400 chr5A 84.759 374 35 10 3849 4214 651635600 651635959 6.420000e-94 355.0
4 TraesCS5A01G478400 chr5A 83.554 377 37 12 3849 4214 651588650 651589012 3.890000e-86 329.0
5 TraesCS5A01G478400 chr5A 76.515 264 51 9 3921 4178 651540533 651540275 3.280000e-27 134.0
6 TraesCS5A01G478400 chr3A 96.346 903 32 1 1 903 9371277 9370376 0.000000e+00 1483.0
7 TraesCS5A01G478400 chr3A 95.050 202 9 1 702 903 194229847 194229647 3.030000e-82 316.0
8 TraesCS5A01G478400 chr5D 88.418 1226 82 27 3267 4467 23870491 23871681 0.000000e+00 1423.0
9 TraesCS5A01G478400 chr5D 85.806 1409 101 44 3267 4624 525387984 525389344 0.000000e+00 1402.0
10 TraesCS5A01G478400 chr5D 86.657 667 63 12 914 1564 525321790 525322446 0.000000e+00 715.0
11 TraesCS5A01G478400 chr5D 88.028 568 62 6 905 1469 525325619 525326183 0.000000e+00 667.0
12 TraesCS5A01G478400 chr5D 84.071 678 81 8 914 1573 23863494 23864162 3.430000e-176 628.0
13 TraesCS5A01G478400 chr5D 84.094 679 76 13 914 1573 525378522 525379187 1.230000e-175 627.0
14 TraesCS5A01G478400 chr5D 82.133 722 68 23 2448 3159 525381109 525381779 3.530000e-156 562.0
15 TraesCS5A01G478400 chr5D 84.127 567 74 9 4657 5209 525390242 525390806 7.690000e-148 534.0
16 TraesCS5A01G478400 chr5D 88.018 434 41 8 989 1421 525243283 525242860 2.170000e-138 503.0
17 TraesCS5A01G478400 chr5D 83.429 525 72 8 4657 5168 23872836 23873358 1.700000e-129 473.0
18 TraesCS5A01G478400 chr5D 84.375 384 41 10 3838 4214 525317393 525317764 4.960000e-95 359.0
19 TraesCS5A01G478400 chr5D 81.236 453 38 17 2554 2987 23869779 23870203 6.510000e-84 322.0
20 TraesCS5A01G478400 chr5D 87.018 285 29 7 1914 2197 525379619 525379896 1.090000e-81 315.0
21 TraesCS5A01G478400 chr5D 89.000 200 8 6 3037 3230 23870204 23870395 8.730000e-58 235.0
22 TraesCS5A01G478400 chr5D 86.628 172 18 5 4488 4656 23871764 23871933 8.920000e-43 185.0
23 TraesCS5A01G478400 chr5D 86.667 105 14 0 2093 2197 23867145 23867249 3.300000e-22 117.0
24 TraesCS5A01G478400 chr5D 88.608 79 6 1 2225 2303 23867397 23867472 5.560000e-15 93.5
25 TraesCS5A01G478400 chr5D 88.608 79 6 1 2225 2303 525380042 525380117 5.560000e-15 93.5
26 TraesCS5A01G478400 chr5B 87.125 1266 73 33 3267 4491 659747667 659748883 0.000000e+00 1352.0
27 TraesCS5A01G478400 chr5B 86.667 720 62 16 914 1605 659739456 659740169 0.000000e+00 767.0
28 TraesCS5A01G478400 chr5B 88.214 560 55 7 914 1472 659743542 659744091 0.000000e+00 658.0
29 TraesCS5A01G478400 chr5B 81.550 813 50 42 2448 3230 659746817 659747559 3.500000e-161 579.0
30 TraesCS5A01G478400 chr5B 87.676 284 27 5 1915 2197 659744556 659744832 1.810000e-84 324.0
31 TraesCS5A01G478400 chr5B 84.239 184 12 4 1626 1809 659744360 659744526 4.180000e-36 163.0
32 TraesCS5A01G478400 chr5B 97.727 44 1 0 3228 3271 659747578 659747621 5.600000e-10 76.8
33 TraesCS5A01G478400 chr3B 99.345 458 3 0 447 904 273749205 273749662 0.000000e+00 830.0
34 TraesCS5A01G478400 chr7A 89.389 622 63 3 288 908 37894940 37895559 0.000000e+00 780.0
35 TraesCS5A01G478400 chr7A 95.588 204 8 1 702 905 539437312 539437110 5.040000e-85 326.0
36 TraesCS5A01G478400 chr7A 94.634 205 9 2 699 903 23845017 23845219 3.030000e-82 316.0
37 TraesCS5A01G478400 chr6D 96.000 400 14 1 170 567 139364469 139364868 0.000000e+00 649.0
38 TraesCS5A01G478400 chr6D 94.805 308 14 2 597 904 139364866 139365171 3.650000e-131 479.0
39 TraesCS5A01G478400 chrUn 84.990 513 50 13 909 1405 67240667 67241168 3.630000e-136 496.0
40 TraesCS5A01G478400 chr4D 96.078 204 8 0 702 905 414345048 414344845 3.010000e-87 333.0
41 TraesCS5A01G478400 chr1D 95.588 204 9 0 702 905 38604892 38604689 1.400000e-85 327.0
42 TraesCS5A01G478400 chr2A 87.931 58 7 0 3938 3995 1365019 1364962 9.370000e-08 69.4
43 TraesCS5A01G478400 chr7D 100.000 31 0 0 2419 2449 543160678 543160648 2.030000e-04 58.4


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 TraesCS5A01G478400 chr5A 651787352 651792565 5213 False 9629.000000 9629 100.000000 1 5214 1 chr5A.!!$F5 5213
1 TraesCS5A01G478400 chr3A 9370376 9371277 901 True 1483.000000 1483 96.346000 1 903 1 chr3A.!!$R1 902
2 TraesCS5A01G478400 chr5D 525387984 525390806 2822 False 968.000000 1402 84.966500 3267 5209 2 chr5D.!!$F5 1942
3 TraesCS5A01G478400 chr5D 525321790 525326183 4393 False 691.000000 715 87.342500 905 1564 2 chr5D.!!$F3 659
4 TraesCS5A01G478400 chr5D 23863494 23873358 9864 False 434.562500 1423 86.007125 914 5168 8 chr5D.!!$F2 4254
5 TraesCS5A01G478400 chr5D 525378522 525381779 3257 False 399.375000 627 85.463250 914 3159 4 chr5D.!!$F4 2245
6 TraesCS5A01G478400 chr5B 659739456 659748883 9427 False 559.971429 1352 87.599714 914 4491 7 chr5B.!!$F1 3577
7 TraesCS5A01G478400 chr7A 37894940 37895559 619 False 780.000000 780 89.389000 288 908 1 chr7A.!!$F2 620
8 TraesCS5A01G478400 chr6D 139364469 139365171 702 False 564.000000 649 95.402500 170 904 2 chr6D.!!$F1 734
9 TraesCS5A01G478400 chrUn 67240667 67241168 501 False 496.000000 496 84.990000 909 1405 1 chrUn.!!$F1 496


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
588 591 1.684248 GCTGCATCCAAGGGAATCACT 60.684 52.381 0.00 0.0 34.34 3.41 F
2143 9739 0.389426 ACGTAAGGCATGACGGTGAC 60.389 55.000 13.66 0.0 43.32 3.67 F
3462 18452 0.107945 CAAGGAAGGAAGCGAGGGAG 60.108 60.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 10053 0.035820 GGGTAGCAAATCCACGACCA 60.036 55.0 0.0 0.0 0.0 4.02 R
3659 18652 0.040958 GCTGTTCCTGTTGTTGCGAG 60.041 55.0 0.0 0.0 0.0 5.03 R
5122 21135 0.103026 CATGATCCGCTGAGAACCGA 59.897 55.0 0.0 0.0 0.0 4.69 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)



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

AutoCloner maintained by Alex Coulton.