Multiple sequence alignment - TraesCS2A01G549100

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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 TraesCS2A01G549100 chr2A 100.000 2989 0 0 1 2989 756523374 756526362 0.000000e+00 5520.0
1 TraesCS2A01G549100 chr7A 98.561 2989 43 0 1 2989 617597407 617600395 0.000000e+00 5282.0
2 TraesCS2A01G549100 chr7A 97.730 2995 42 2 1 2989 41465877 41462903 0.000000e+00 5131.0
3 TraesCS2A01G549100 chr7D 92.799 1097 52 10 1455 2549 621797432 621798503 0.000000e+00 1563.0
4 TraesCS2A01G549100 chr7D 92.616 1097 55 9 1455 2549 449503417 449502345 0.000000e+00 1554.0
5 TraesCS2A01G549100 chr7D 90.862 383 16 1 2626 2989 340192899 340193281 2.070000e-136 496.0
6 TraesCS2A01G549100 chr3D 92.792 1096 54 8 1455 2549 583596393 583597464 0.000000e+00 1563.0
7 TraesCS2A01G549100 chr3D 96.335 191 7 0 514 704 553215157 553214967 6.220000e-82 315.0
8 TraesCS2A01G549100 chr3D 94.231 156 7 1 860 1013 553214395 553214240 1.380000e-58 237.0
9 TraesCS2A01G549100 chr3D 93.396 106 7 0 705 810 553214933 553214828 1.110000e-34 158.0
10 TraesCS2A01G549100 chr3A 92.343 1097 59 8 1455 2549 703814313 703815386 0.000000e+00 1537.0
11 TraesCS2A01G549100 chr3A 90.130 385 17 2 2626 2989 703816547 703816931 5.790000e-132 481.0
12 TraesCS2A01G549100 chr3A 84.683 457 26 3 2552 2989 662572023 662571592 1.660000e-112 416.0
13 TraesCS2A01G549100 chr3A 91.639 299 20 4 1010 1303 662597936 662597638 2.770000e-110 409.0
14 TraesCS2A01G549100 chr3A 89.032 310 16 4 705 1013 689496439 689496147 4.710000e-98 368.0
15 TraesCS2A01G549100 chr3A 97.382 191 5 0 514 704 689496663 689496473 2.870000e-85 326.0
16 TraesCS2A01G549100 chr3A 89.706 204 19 2 311 513 662598134 662597932 2.960000e-65 259.0
17 TraesCS2A01G549100 chrUn 92.157 1071 59 8 1455 2523 344422306 344423353 0.000000e+00 1489.0
18 TraesCS2A01G549100 chrUn 91.847 1018 59 7 1533 2549 314367743 314368737 0.000000e+00 1399.0
19 TraesCS2A01G549100 chrUn 92.036 992 55 7 1533 2523 455429912 455430880 0.000000e+00 1373.0
20 TraesCS2A01G549100 chrUn 90.390 385 16 2 2626 2989 314369268 314369652 1.250000e-133 486.0
21 TraesCS2A01G549100 chrUn 86.722 241 31 1 1 240 94308419 94308179 1.770000e-67 267.0
22 TraesCS2A01G549100 chr2B 89.684 824 59 13 1083 1891 134341437 134342249 0.000000e+00 1027.0
23 TraesCS2A01G549100 chr2B 91.639 299 20 4 1010 1303 100101772 100101474 2.770000e-110 409.0
24 TraesCS2A01G549100 chr2B 84.245 457 30 12 2552 2989 100091188 100090755 9.980000e-110 407.0
25 TraesCS2A01G549100 chr2B 92.893 197 12 2 311 506 759994054 759994249 4.880000e-73 285.0
26 TraesCS2A01G549100 chr1B 93.195 676 37 6 1010 1683 675900497 675901165 0.000000e+00 985.0
27 TraesCS2A01G549100 chr1B 92.118 203 8 6 311 513 675900307 675900501 2.270000e-71 279.0
28 TraesCS2A01G549100 chr1B 85.057 261 18 8 1 240 289692540 289692800 2.300000e-61 246.0
29 TraesCS2A01G549100 chr6D 88.485 825 68 15 1083 1891 440673450 440674263 0.000000e+00 972.0
30 TraesCS2A01G549100 chr6D 90.862 383 16 1 2626 2989 450178314 450177932 2.070000e-136 496.0
31 TraesCS2A01G549100 chr6D 88.512 383 25 1 2626 2989 13480419 13480801 2.110000e-121 446.0
32 TraesCS2A01G549100 chr6D 83.090 343 23 10 1 308 13475314 13475656 2.270000e-71 279.0
33 TraesCS2A01G549100 chr6D 91.083 157 14 0 2393 2549 440675727 440675883 2.330000e-51 213.0
34 TraesCS2A01G549100 chr6D 93.103 58 4 0 2573 2630 450178344 450178287 5.310000e-13 86.1
35 TraesCS2A01G549100 chr6A 91.384 383 14 1 2626 2989 163162549 163162167 9.560000e-140 507.0
36 TraesCS2A01G549100 chr6A 82.789 337 23 12 1 302 589344247 589344583 4.910000e-68 268.0
37 TraesCS2A01G549100 chr6A 83.796 216 35 0 3 218 557415724 557415939 3.910000e-49 206.0
38 TraesCS2A01G549100 chr6A 94.828 58 3 0 2573 2630 163162579 163162522 1.140000e-14 91.6
39 TraesCS2A01G549100 chr6A 95.745 47 2 0 1010 1056 163168135 163168089 3.190000e-10 76.8
40 TraesCS2A01G549100 chr5D 90.862 383 16 1 2626 2989 127929097 127928715 2.070000e-136 496.0
41 TraesCS2A01G549100 chr5D 91.391 151 13 0 2399 2549 27284964 27285114 1.090000e-49 207.0
42 TraesCS2A01G549100 chr5A 90.339 383 18 1 2626 2989 3897906 3897524 4.480000e-133 484.0
43 TraesCS2A01G549100 chr5A 89.333 375 21 1 2634 2989 470943296 470943670 1.260000e-123 453.0
44 TraesCS2A01G549100 chr5A 92.230 296 18 4 1010 1300 470930907 470931202 5.960000e-112 414.0
45 TraesCS2A01G549100 chr5A 89.216 204 20 2 311 513 470930709 470930911 1.380000e-63 254.0
46 TraesCS2A01G549100 chr5A 81.050 343 31 10 3 311 3949589 3949247 2.980000e-60 243.0
47 TraesCS2A01G549100 chr5A 81.679 262 18 8 2076 2337 470931858 470932089 1.090000e-44 191.0
48 TraesCS2A01G549100 chr1D 90.078 383 19 6 2626 2989 415606542 415606924 2.080000e-131 479.0
49 TraesCS2A01G549100 chr1D 83.382 343 22 10 1 308 62893263 62893605 4.880000e-73 285.0
50 TraesCS2A01G549100 chr1D 93.103 58 4 0 2573 2630 415606512 415606569 5.310000e-13 86.1
51 TraesCS2A01G549100 chr7B 85.120 457 26 10 2552 2989 593328483 593328050 2.130000e-116 429.0
52 TraesCS2A01G549100 chr7B 91.582 297 21 4 1010 1303 593348547 593348252 9.980000e-110 407.0
53 TraesCS2A01G549100 chr7B 76.721 494 46 22 2076 2549 593347599 593347155 8.390000e-51 211.0
54 TraesCS2A01G549100 chr4A 91.275 298 22 4 1010 1303 742008686 742008389 1.290000e-108 403.0
55 TraesCS2A01G549100 chr4A 93.103 203 14 0 311 513 658381287 658381489 6.260000e-77 298.0
56 TraesCS2A01G549100 chr4A 89.216 204 20 2 311 513 742008884 742008682 1.380000e-63 254.0
57 TraesCS2A01G549100 chr4A 82.772 267 25 7 2263 2510 31395895 31395631 5.020000e-53 219.0
58 TraesCS2A01G549100 chr3B 89.320 309 16 4 705 1013 734429039 734428748 3.640000e-99 372.0
59 TraesCS2A01G549100 chr3B 96.859 191 6 0 514 704 734429263 734429073 1.340000e-83 320.0
60 TraesCS2A01G549100 chr3B 79.688 320 27 16 1 304 775660221 775659924 2.350000e-46 196.0
61 TraesCS2A01G549100 chr2D 83.768 345 22 7 1 311 23117260 23116916 2.250000e-76 296.0
62 TraesCS2A01G549100 chr2D 83.041 342 24 9 1 308 517750 518091 2.270000e-71 279.0
63 TraesCS2A01G549100 chr2D 89.573 211 14 5 311 513 29096891 29096681 8.220000e-66 261.0
64 TraesCS2A01G549100 chr2D 89.172 157 17 0 2393 2549 519871 520027 2.350000e-46 196.0
65 TraesCS2A01G549100 chr4D 90.789 152 12 1 2400 2549 85850332 85850181 5.050000e-48 202.0


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 TraesCS2A01G549100 chr2A 756523374 756526362 2988 False 5520.000000 5520 100.000000 1 2989 1 chr2A.!!$F1 2988
1 TraesCS2A01G549100 chr7A 617597407 617600395 2988 False 5282.000000 5282 98.561000 1 2989 1 chr7A.!!$F1 2988
2 TraesCS2A01G549100 chr7A 41462903 41465877 2974 True 5131.000000 5131 97.730000 1 2989 1 chr7A.!!$R1 2988
3 TraesCS2A01G549100 chr7D 621797432 621798503 1071 False 1563.000000 1563 92.799000 1455 2549 1 chr7D.!!$F2 1094
4 TraesCS2A01G549100 chr7D 449502345 449503417 1072 True 1554.000000 1554 92.616000 1455 2549 1 chr7D.!!$R1 1094
5 TraesCS2A01G549100 chr3D 583596393 583597464 1071 False 1563.000000 1563 92.792000 1455 2549 1 chr3D.!!$F1 1094
6 TraesCS2A01G549100 chr3D 553214240 553215157 917 True 236.666667 315 94.654000 514 1013 3 chr3D.!!$R1 499
7 TraesCS2A01G549100 chr3A 703814313 703816931 2618 False 1009.000000 1537 91.236500 1455 2989 2 chr3A.!!$F1 1534
8 TraesCS2A01G549100 chr3A 689496147 689496663 516 True 347.000000 368 93.207000 514 1013 2 chr3A.!!$R3 499
9 TraesCS2A01G549100 chrUn 344422306 344423353 1047 False 1489.000000 1489 92.157000 1455 2523 1 chrUn.!!$F1 1068
10 TraesCS2A01G549100 chrUn 455429912 455430880 968 False 1373.000000 1373 92.036000 1533 2523 1 chrUn.!!$F2 990
11 TraesCS2A01G549100 chrUn 314367743 314369652 1909 False 942.500000 1399 91.118500 1533 2989 2 chrUn.!!$F3 1456
12 TraesCS2A01G549100 chr2B 134341437 134342249 812 False 1027.000000 1027 89.684000 1083 1891 1 chr2B.!!$F1 808
13 TraesCS2A01G549100 chr1B 675900307 675901165 858 False 632.000000 985 92.656500 311 1683 2 chr1B.!!$F2 1372
14 TraesCS2A01G549100 chr6D 440673450 440675883 2433 False 592.500000 972 89.784000 1083 2549 2 chr6D.!!$F3 1466
15 TraesCS2A01G549100 chr5A 470930709 470932089 1380 False 286.333333 414 87.708333 311 2337 3 chr5A.!!$F2 2026
16 TraesCS2A01G549100 chr7B 593347155 593348547 1392 True 309.000000 407 84.151500 1010 2549 2 chr7B.!!$R2 1539
17 TraesCS2A01G549100 chr3B 734428748 734429263 515 True 346.000000 372 93.089500 514 1013 2 chr3B.!!$R2 499
18 TraesCS2A01G549100 chr2D 517750 520027 2277 False 237.500000 279 86.106500 1 2549 2 chr2D.!!$F1 2548

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
580 828 1.754803 CAATGCCAGCAAGTCCATCAT 59.245 47.619 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 4061 2.507484 CTGCTGTTTCCTGGATGTCAA 58.493 47.619 0.0 0.0 0.0 3.18 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
132 153 2.042537 TCCAGCGCAGGAGGATCT 60.043 61.111 18.72 0.00 32.77 2.75
254 289 2.270850 GGCATGTAGTCCGCCCAA 59.729 61.111 0.00 0.00 40.07 4.12
580 828 1.754803 CAATGCCAGCAAGTCCATCAT 59.245 47.619 0.00 0.00 0.00 2.45
795 1076 4.036027 AGGAGCATCTGCATTAACAAATCG 59.964 41.667 4.79 0.00 45.16 3.34
806 1087 5.405269 GCATTAACAAATCGGCAAAGTTTCT 59.595 36.000 0.00 0.00 0.00 2.52
1003 1687 9.956720 GAGAACACCTTTCAAATATATTCATGG 57.043 33.333 0.00 1.52 0.00 3.66
1147 1832 2.417586 TGATTCTGCAGTTGCTGATTCG 59.582 45.455 14.67 0.00 45.95 3.34
1548 3393 3.054875 ACCTGCTATGCAAGATTCTGTCA 60.055 43.478 0.00 0.00 38.41 3.58
1802 3649 7.342799 AGCTATGTCCACAAATACCATGATTTT 59.657 33.333 0.00 0.00 0.00 1.82
2090 4061 1.968540 GCAAGGAGCGGCAAGTTCT 60.969 57.895 1.45 0.00 0.00 3.01
2499 5509 4.989279 TTGGAAGAATGGCTGCTTTATC 57.011 40.909 0.00 0.00 0.00 1.75
2523 5533 4.646945 TGAATTTGTTACCCTCTTTGCACA 59.353 37.500 0.00 0.00 0.00 4.57
2584 6709 8.750515 TTGCATGATGATCTAAATACCTTTCA 57.249 30.769 0.00 0.00 0.00 2.69
2670 6795 2.684943 TGTGGGTACATGGATATCGGT 58.315 47.619 0.00 0.00 0.00 4.69
2716 6841 3.193479 GTCATCGCCCAAAAGGAAGAAAT 59.807 43.478 0.00 0.00 38.24 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 153 2.747022 CACCACCACGACCATCCA 59.253 61.111 0.00 0.0 0.00 3.41
348 383 6.912426 AGTAAGAGATATGGACCTGTAGACA 58.088 40.000 0.00 0.0 0.00 3.41
580 828 3.365666 CGTGTTAACGTAAGAGGAGCAGA 60.366 47.826 0.26 0.0 44.93 4.26
724 1005 6.109156 TCCTGATACTTGCAGAAACTGTTA 57.891 37.500 0.00 0.0 35.39 2.41
795 1076 3.416156 AGACCATCTCAGAAACTTTGCC 58.584 45.455 0.00 0.0 0.00 4.52
806 1087 5.576563 TTTTTCCCTGTAAGACCATCTCA 57.423 39.130 0.00 0.0 34.07 3.27
1115 1799 5.363562 ACTGCAGAATCAATCATGACCTA 57.636 39.130 23.35 0.0 38.69 3.08
1802 3649 6.500751 AGTTCTACTTCACTTTCCCCTCAATA 59.499 38.462 0.00 0.0 0.00 1.90
2090 4061 2.507484 CTGCTGTTTCCTGGATGTCAA 58.493 47.619 0.00 0.0 0.00 3.18
2416 5426 6.420913 AATTACTGTCCATTCTATACGGCT 57.579 37.500 0.00 0.0 0.00 5.52
2499 5509 5.221224 TGTGCAAAGAGGGTAACAAATTCAG 60.221 40.000 0.00 0.0 39.74 3.02
2523 5533 4.078537 TGGTAATGCACTTGTAGCAACAT 58.921 39.130 0.00 0.0 46.27 2.71
2584 6709 1.216064 TGTCCTGCCCAGAAGCATAT 58.784 50.000 0.00 0.0 43.09 1.78
2670 6795 2.649742 ATTCTCCCAAGTCCCTCTCA 57.350 50.000 0.00 0.0 0.00 3.27
2716 6841 3.673052 GCTGCCGAATTGTTATCTGCAAA 60.673 43.478 0.00 0.0 36.74 3.68


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

AutoCloner maintained by Alex Coulton.