Multiple sequence alignment - TraesCS5A01G536000

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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 TraesCS5A01G536000 chr5A 100.000 2522 0 0 1 2522 692540486 692543007 0.000000e+00 4658.0
1 TraesCS5A01G536000 chr5A 99.002 1604 16 0 919 2522 692547973 692549576 0.000000e+00 2874.0
2 TraesCS5A01G536000 chr5A 98.223 394 7 0 471 864 692547230 692547623 0.000000e+00 689.0
3 TraesCS5A01G536000 chr5A 100.000 52 0 0 753 804 692547176 692547227 2.070000e-16 97.1
4 TraesCS5A01G536000 chr5A 96.296 54 2 0 864 917 426932601 426932548 3.460000e-14 89.8
5 TraesCS5A01G536000 chr5A 100.000 42 0 0 594 635 692547144 692547185 7.480000e-11 78.7
6 TraesCS5A01G536000 chr2A 94.059 1616 69 9 919 2522 737426292 737424692 0.000000e+00 2427.0
7 TraesCS5A01G536000 chr2A 93.333 165 8 2 471 635 21627715 21627554 9.010000e-60 241.0
8 TraesCS5A01G536000 chr2A 99.038 104 1 0 753 856 21627563 21627460 1.190000e-43 187.0
9 TraesCS5A01G536000 chr2A 98.925 93 1 0 1848 1940 74111936 74112028 1.550000e-37 167.0
10 TraesCS5A01G536000 chr2A 96.296 54 2 0 864 917 27532586 27532639 3.460000e-14 89.8
11 TraesCS5A01G536000 chr2A 96.296 54 2 0 864 917 166773372 166773319 3.460000e-14 89.8
12 TraesCS5A01G536000 chr2A 96.296 54 2 0 864 917 747147676 747147729 3.460000e-14 89.8
13 TraesCS5A01G536000 chr2D 94.982 817 26 6 1713 2522 331548382 331547574 0.000000e+00 1267.0
14 TraesCS5A01G536000 chr2D 92.692 780 46 7 921 1691 331549151 331548374 0.000000e+00 1114.0
15 TraesCS5A01G536000 chr2D 93.269 104 4 1 753 853 25037041 25037144 1.560000e-32 150.0
16 TraesCS5A01G536000 chr4D 92.327 782 50 4 919 1691 508474489 508475269 0.000000e+00 1103.0
17 TraesCS5A01G536000 chr4D 93.980 598 17 7 1932 2522 508476607 508477192 0.000000e+00 887.0
18 TraesCS5A01G536000 chr4D 97.357 227 6 0 1713 1939 508475261 508475487 1.090000e-103 387.0
19 TraesCS5A01G536000 chr4D 87.050 139 12 2 1009 1141 346454091 346453953 4.350000e-33 152.0
20 TraesCS5A01G536000 chr4D 74.519 416 67 11 1490 1877 114277457 114277861 7.270000e-31 145.0
21 TraesCS5A01G536000 chr4A 90.191 418 20 8 1 411 678885625 678886028 2.220000e-145 525.0
22 TraesCS5A01G536000 chr4A 89.759 332 31 2 1160 1491 538908476 538908148 3.000000e-114 422.0
23 TraesCS5A01G536000 chr4A 93.082 159 10 1 1009 1166 119080851 119081009 5.430000e-57 231.0
24 TraesCS5A01G536000 chr4A 77.285 361 62 11 1526 1877 34570578 34570229 7.120000e-46 195.0
25 TraesCS5A01G536000 chr4A 90.323 124 10 2 622 743 657496335 657496212 7.220000e-36 161.0
26 TraesCS5A01G536000 chr4A 96.154 52 2 0 421 472 678886078 678886129 4.470000e-13 86.1
27 TraesCS5A01G536000 chr1D 92.157 357 19 4 2175 2522 303804696 303805052 1.740000e-136 496.0
28 TraesCS5A01G536000 chr1D 99.138 116 1 0 636 751 109471409 109471294 2.540000e-50 209.0
29 TraesCS5A01G536000 chr1D 98.305 118 2 0 634 751 269992289 269992406 9.140000e-50 207.0
30 TraesCS5A01G536000 chr2B 89.458 332 31 3 1160 1491 17219742 17219415 1.400000e-112 416.0
31 TraesCS5A01G536000 chr2B 86.446 332 42 2 1160 1491 414953424 414953752 6.630000e-96 361.0
32 TraesCS5A01G536000 chr2B 97.849 93 2 0 1848 1940 118095413 118095321 7.220000e-36 161.0
33 TraesCS5A01G536000 chr2B 94.545 55 3 0 863 917 197578174 197578228 4.470000e-13 86.1
34 TraesCS5A01G536000 chr4B 89.157 332 33 2 1160 1491 385957702 385958030 6.490000e-111 411.0
35 TraesCS5A01G536000 chr1B 87.107 318 39 1 1160 1477 686995221 686994906 2.390000e-95 359.0
36 TraesCS5A01G536000 chr1B 93.269 104 4 1 753 853 34234155 34234258 1.560000e-32 150.0
37 TraesCS5A01G536000 chr1B 91.549 71 2 2 849 917 55440181 55440249 7.430000e-16 95.3
38 TraesCS5A01G536000 chr7B 100.000 118 0 0 634 751 210510007 210509890 4.220000e-53 219.0
39 TraesCS5A01G536000 chr7B 77.008 361 63 11 1526 1877 168308742 168309091 3.310000e-44 189.0
40 TraesCS5A01G536000 chr7B 77.008 361 63 11 1526 1877 263737247 263737596 3.310000e-44 189.0
41 TraesCS5A01G536000 chr7B 97.849 93 2 0 1848 1940 394823834 394823742 7.220000e-36 161.0
42 TraesCS5A01G536000 chr5D 92.715 151 11 0 1790 1940 28995402 28995552 4.220000e-53 219.0
43 TraesCS5A01G536000 chr1A 97.656 128 2 1 624 751 518022619 518022493 4.220000e-53 219.0
44 TraesCS5A01G536000 chr1A 99.153 118 1 0 634 751 582229056 582229173 1.970000e-51 213.0
45 TraesCS5A01G536000 chr1A 90.196 153 10 3 2175 2322 573386939 573386787 7.120000e-46 195.0
46 TraesCS5A01G536000 chr1A 81.865 193 29 4 1684 1876 510301071 510300885 9.340000e-35 158.0
47 TraesCS5A01G536000 chr7D 99.160 119 1 0 633 751 587250889 587250771 5.460000e-52 215.0
48 TraesCS5A01G536000 chr3B 99.160 119 1 0 633 751 817034945 817034827 5.460000e-52 215.0
49 TraesCS5A01G536000 chr3B 97.849 93 2 0 1848 1940 71883629 71883721 7.220000e-36 161.0
50 TraesCS5A01G536000 chr3A 98.361 122 2 0 630 751 689110871 689110750 5.460000e-52 215.0
51 TraesCS5A01G536000 chr3A 77.285 361 62 11 1526 1877 20219617 20219966 7.120000e-46 195.0
52 TraesCS5A01G536000 chr6D 83.688 141 18 2 1684 1824 436501358 436501223 7.320000e-26 128.0
53 TraesCS5A01G536000 chr6A 95.312 64 2 1 854 917 97078386 97078448 1.600000e-17 100.0
54 TraesCS5A01G536000 chr6A 96.296 54 2 0 864 917 128643479 128643426 3.460000e-14 89.8
55 TraesCS5A01G536000 chr6A 96.154 52 2 0 421 472 384451372 384451423 4.470000e-13 86.1
56 TraesCS5A01G536000 chr7A 90.769 65 4 1 851 915 321638916 321638854 4.470000e-13 86.1


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 TraesCS5A01G536000 chr5A 692540486 692543007 2521 False 4658.000000 4658 100.000000 1 2522 1 chr5A.!!$F1 2521
1 TraesCS5A01G536000 chr5A 692547144 692549576 2432 False 934.700000 2874 99.306250 471 2522 4 chr5A.!!$F2 2051
2 TraesCS5A01G536000 chr2A 737424692 737426292 1600 True 2427.000000 2427 94.059000 919 2522 1 chr2A.!!$R2 1603
3 TraesCS5A01G536000 chr2D 331547574 331549151 1577 True 1190.500000 1267 93.837000 921 2522 2 chr2D.!!$R1 1601
4 TraesCS5A01G536000 chr4D 508474489 508477192 2703 False 792.333333 1103 94.554667 919 2522 3 chr4D.!!$F2 1603
5 TraesCS5A01G536000 chr4A 678885625 678886129 504 False 305.550000 525 93.172500 1 472 2 chr4A.!!$F2 471

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
474 522 0.696501 GTCCAAGTACCACCACCCAT 59.303 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 3583 6.264292 AGACCTGATACATGCTACTTCTACTG 59.736 42.308 0.0 0.0 0.0 2.74 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
24 25 4.390603 TCGACCACTGATATTGTTTTTCCG 59.609 41.667 0.00 0.00 0.00 4.30
30 31 8.147704 ACCACTGATATTGTTTTTCCGAAAAAT 58.852 29.630 19.36 8.69 41.85 1.82
40 41 8.256611 TGTTTTTCCGAAAAATTTCATGAACA 57.743 26.923 19.36 9.31 41.85 3.18
92 93 9.352191 TCAAATTCATGAATTGTTTCCCAAATT 57.648 25.926 29.52 10.37 40.57 1.82
362 370 2.572191 TGTCCTGTATTTAGTCGCCG 57.428 50.000 0.00 0.00 0.00 6.46
367 375 2.544486 CCTGTATTTAGTCGCCGGTACC 60.544 54.545 1.90 0.16 0.00 3.34
376 384 2.202837 GCCGGTACCTAGTTGGCG 60.203 66.667 10.90 0.00 40.22 5.69
378 386 1.153706 CCGGTACCTAGTTGGCGTG 60.154 63.158 10.90 0.00 40.22 5.34
411 419 0.723790 CTCGAACGTTGTAGTCGCGT 60.724 55.000 5.00 0.00 40.81 6.01
412 420 0.993251 TCGAACGTTGTAGTCGCGTG 60.993 55.000 5.00 0.00 38.92 5.34
414 422 0.936297 GAACGTTGTAGTCGCGTGGT 60.936 55.000 5.00 0.00 38.92 4.16
416 424 2.369629 CGTTGTAGTCGCGTGGTGG 61.370 63.158 5.77 0.00 0.00 4.61
417 425 1.300388 GTTGTAGTCGCGTGGTGGT 60.300 57.895 5.77 0.00 0.00 4.16
419 427 0.876777 TTGTAGTCGCGTGGTGGTTG 60.877 55.000 5.77 0.00 0.00 3.77
456 504 4.204028 AAGTGTTGCTGGGCCGGT 62.204 61.111 15.16 0.00 0.00 5.28
464 512 2.267961 CTGGGCCGGTCCAAGTAC 59.732 66.667 31.08 0.00 36.21 2.73
472 520 1.377612 GGTCCAAGTACCACCACCC 59.622 63.158 0.00 0.00 39.50 4.61
473 521 1.420532 GGTCCAAGTACCACCACCCA 61.421 60.000 0.00 0.00 39.50 4.51
474 522 0.696501 GTCCAAGTACCACCACCCAT 59.303 55.000 0.00 0.00 0.00 4.00
481 529 2.465010 TACCACCACCCATCGTCCCT 62.465 60.000 0.00 0.00 0.00 4.20
520 568 1.837439 TGCAAGTACGAGGGATGGAAT 59.163 47.619 0.00 0.00 0.00 3.01
533 581 1.682849 TGGAATTCCCACCGTCCTG 59.317 57.895 21.90 0.00 40.82 3.86
548 596 3.491104 CCGTCCTGTTCAGTCTATAAGGC 60.491 52.174 0.00 0.00 0.00 4.35
855 903 6.494952 AGGAGGTGAGATAACGGATGTATAT 58.505 40.000 0.00 0.00 0.00 0.86
856 904 6.603997 AGGAGGTGAGATAACGGATGTATATC 59.396 42.308 0.00 0.00 0.00 1.63
857 905 6.603997 GGAGGTGAGATAACGGATGTATATCT 59.396 42.308 0.00 0.00 38.70 1.98
858 906 7.122948 GGAGGTGAGATAACGGATGTATATCTT 59.877 40.741 0.00 0.00 36.71 2.40
859 907 8.423906 AGGTGAGATAACGGATGTATATCTTT 57.576 34.615 0.00 0.00 36.71 2.52
860 908 9.529823 AGGTGAGATAACGGATGTATATCTTTA 57.470 33.333 0.00 0.00 36.71 1.85
861 909 9.570488 GGTGAGATAACGGATGTATATCTTTAC 57.430 37.037 0.00 0.00 36.71 2.01
862 910 9.275231 GTGAGATAACGGATGTATATCTTTACG 57.725 37.037 0.00 0.00 36.71 3.18
886 934 6.749118 CGTCTTTACGTACTAATAAACCAGCT 59.251 38.462 0.00 0.00 44.21 4.24
887 935 7.910162 CGTCTTTACGTACTAATAAACCAGCTA 59.090 37.037 0.00 0.00 44.21 3.32
888 936 9.741647 GTCTTTACGTACTAATAAACCAGCTAT 57.258 33.333 0.00 0.00 0.00 2.97
891 939 6.839820 ACGTACTAATAAACCAGCTATTGC 57.160 37.500 0.00 0.00 40.05 3.56
917 965 2.654912 CGTCCGTCGTGGCTGTTTC 61.655 63.158 0.00 0.00 37.80 2.78
1995 3505 1.339610 ACACTCTGACTGTGAGCTCAC 59.660 52.381 35.04 35.04 46.59 3.51
2073 3583 6.377327 TGGAATTTTAGCTGCTTAGTATGC 57.623 37.500 7.79 1.12 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.715123 AATGTTCATGAAATTTTTCGGAAAAAC 57.285 25.926 25.92 16.19 42.57 2.43
51 52 8.423349 TCATGAATTTGAAAAGGAGTTCATTGT 58.577 29.630 0.00 0.00 37.36 2.71
52 53 8.821147 TCATGAATTTGAAAAGGAGTTCATTG 57.179 30.769 0.00 0.44 37.36 2.82
254 258 6.873076 AGCGCCTTGATTTTTGAATTATTTCA 59.127 30.769 2.29 0.00 40.09 2.69
325 333 7.820648 ACAGGACAAACATTTTAATAGCAGAG 58.179 34.615 0.00 0.00 0.00 3.35
362 370 0.390735 CACCACGCCAACTAGGTACC 60.391 60.000 2.73 2.73 40.61 3.34
367 375 1.722011 CTAACCACCACGCCAACTAG 58.278 55.000 0.00 0.00 0.00 2.57
376 384 2.032071 AGCACGGCTAACCACCAC 59.968 61.111 0.00 0.00 36.99 4.16
378 386 2.775032 TTCGAGCACGGCTAACCACC 62.775 60.000 3.11 0.00 39.88 4.61
411 419 3.579302 CTCCCAGGCCAACCACCA 61.579 66.667 5.01 0.00 39.06 4.17
456 504 0.988832 GATGGGTGGTGGTACTTGGA 59.011 55.000 0.00 0.00 0.00 3.53
464 512 3.009115 AGGGACGATGGGTGGTGG 61.009 66.667 0.00 0.00 0.00 4.61
472 520 2.819595 CGTTGGGCAGGGACGATG 60.820 66.667 0.00 0.00 38.99 3.84
473 521 4.778143 GCGTTGGGCAGGGACGAT 62.778 66.667 0.00 0.00 42.87 3.73
520 568 1.052124 ACTGAACAGGACGGTGGGAA 61.052 55.000 6.76 0.00 0.00 3.97
526 574 3.491104 GCCTTATAGACTGAACAGGACGG 60.491 52.174 6.76 0.00 0.00 4.79
533 581 2.869192 GCTGCAGCCTTATAGACTGAAC 59.131 50.000 28.76 0.00 33.10 3.18
548 596 1.456296 TGTAGCTCAATTGGCTGCAG 58.544 50.000 24.71 10.11 44.74 4.41
552 600 3.490348 ACTTGTTGTAGCTCAATTGGCT 58.510 40.909 20.45 20.45 43.02 4.75
862 910 9.741647 ATAGCTGGTTTATTAGTACGTAAAGAC 57.258 33.333 0.00 0.00 0.00 3.01
886 934 0.892755 ACGGACGACCAGAAGCAATA 59.107 50.000 4.48 0.00 35.59 1.90
887 935 0.389948 GACGGACGACCAGAAGCAAT 60.390 55.000 4.48 0.00 35.59 3.56
888 936 1.006571 GACGGACGACCAGAAGCAA 60.007 57.895 4.48 0.00 35.59 3.91
889 937 2.649034 GACGGACGACCAGAAGCA 59.351 61.111 4.48 0.00 35.59 3.91
890 938 2.504244 CGACGGACGACCAGAAGC 60.504 66.667 4.48 0.00 45.77 3.86
891 939 1.442184 CACGACGGACGACCAGAAG 60.442 63.158 6.90 0.00 45.77 2.85
892 940 2.640989 CACGACGGACGACCAGAA 59.359 61.111 6.90 0.00 45.77 3.02
893 941 3.359523 CCACGACGGACGACCAGA 61.360 66.667 6.90 0.00 45.77 3.86
2073 3583 6.264292 AGACCTGATACATGCTACTTCTACTG 59.736 42.308 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.