Multiple sequence alignment - TraesCS3A01G487000

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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 TraesCS3A01G487000 chr3A 100.000 2612 0 0 1 2612 714787753 714790364 0.000000e+00 4824
1 TraesCS3A01G487000 chr3A 98.325 1731 29 0 882 2612 607845896 607847626 0.000000e+00 3037
2 TraesCS3A01G487000 chr3A 88.931 1834 135 23 490 2287 638855097 638853296 0.000000e+00 2200
3 TraesCS3A01G487000 chr3A 98.262 863 15 0 1 863 607844836 607845698 0.000000e+00 1511
4 TraesCS3A01G487000 chr3D 96.269 2198 47 11 16 2211 579687387 579689551 0.000000e+00 3572
5 TraesCS3A01G487000 chr3D 91.349 393 9 2 2245 2612 579689548 579689940 4.980000e-142 514
6 TraesCS3A01G487000 chr1D 91.821 2164 119 22 488 2612 96035628 96033484 0.000000e+00 2963
7 TraesCS3A01G487000 chr1D 90.774 2157 134 25 488 2601 64336405 64338539 0.000000e+00 2820
8 TraesCS3A01G487000 chr1D 92.948 1886 87 17 529 2391 439404021 439405883 0.000000e+00 2704
9 TraesCS3A01G487000 chr1D 92.880 632 34 6 16 646 64335600 64336221 0.000000e+00 907
10 TraesCS3A01G487000 chr1D 92.744 634 33 7 16 646 96036435 96035812 0.000000e+00 904
11 TraesCS3A01G487000 chr1D 84.894 331 24 19 2285 2612 439405824 439406131 7.020000e-81 311
12 TraesCS3A01G487000 chr6A 89.296 2158 162 27 490 2612 121725070 121722947 0.000000e+00 2641
13 TraesCS3A01G487000 chr6A 92.147 573 35 6 75 646 121725818 121725255 0.000000e+00 800
14 TraesCS3A01G487000 chr7D 89.337 2157 150 34 490 2612 600063428 600065538 0.000000e+00 2636
15 TraesCS3A01G487000 chr7D 93.987 632 30 6 16 646 600062618 600063242 0.000000e+00 950
16 TraesCS3A01G487000 chr1B 91.521 1887 95 24 529 2392 596176024 596177868 0.000000e+00 2538
17 TraesCS3A01G487000 chr4A 88.607 2168 136 24 490 2610 554698659 554700762 0.000000e+00 2532
18 TraesCS3A01G487000 chr4A 88.509 2167 139 26 490 2610 557663660 557661558 0.000000e+00 2521
19 TraesCS3A01G487000 chr4A 92.537 603 28 9 16 618 554697863 554698448 0.000000e+00 848
20 TraesCS3A01G487000 chr2B 87.713 1758 118 30 530 2261 755329850 755331535 0.000000e+00 1960
21 TraesCS3A01G487000 chr2B 86.508 378 25 6 2261 2612 755331619 755331996 2.440000e-105 392
22 TraesCS3A01G487000 chr3B 91.874 1329 78 9 1309 2612 734913177 734911854 0.000000e+00 1829
23 TraesCS3A01G487000 chr3B 92.247 632 41 6 16 646 774217399 774218023 0.000000e+00 889
24 TraesCS3A01G487000 chr4D 90.909 1188 71 10 472 1636 42334341 42335514 0.000000e+00 1561
25 TraesCS3A01G487000 chr7B 91.101 1135 73 4 1504 2612 7000041 7001173 0.000000e+00 1511
26 TraesCS3A01G487000 chr7B 88.845 1004 71 8 490 1473 6999058 7000040 0.000000e+00 1195
27 TraesCS3A01G487000 chr7B 93.829 632 30 7 16 646 6998249 6998872 0.000000e+00 942
28 TraesCS3A01G487000 chr2A 85.510 1470 110 29 1185 2612 749651367 749652775 0.000000e+00 1439


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 TraesCS3A01G487000 chr3A 714787753 714790364 2611 False 4824.0 4824 100.000000 1 2612 1 chr3A.!!$F1 2611
1 TraesCS3A01G487000 chr3A 607844836 607847626 2790 False 2274.0 3037 98.293500 1 2612 2 chr3A.!!$F2 2611
2 TraesCS3A01G487000 chr3A 638853296 638855097 1801 True 2200.0 2200 88.931000 490 2287 1 chr3A.!!$R1 1797
3 TraesCS3A01G487000 chr3D 579687387 579689940 2553 False 2043.0 3572 93.809000 16 2612 2 chr3D.!!$F1 2596
4 TraesCS3A01G487000 chr1D 96033484 96036435 2951 True 1933.5 2963 92.282500 16 2612 2 chr1D.!!$R1 2596
5 TraesCS3A01G487000 chr1D 64335600 64338539 2939 False 1863.5 2820 91.827000 16 2601 2 chr1D.!!$F1 2585
6 TraesCS3A01G487000 chr1D 439404021 439406131 2110 False 1507.5 2704 88.921000 529 2612 2 chr1D.!!$F2 2083
7 TraesCS3A01G487000 chr6A 121722947 121725818 2871 True 1720.5 2641 90.721500 75 2612 2 chr6A.!!$R1 2537
8 TraesCS3A01G487000 chr7D 600062618 600065538 2920 False 1793.0 2636 91.662000 16 2612 2 chr7D.!!$F1 2596
9 TraesCS3A01G487000 chr1B 596176024 596177868 1844 False 2538.0 2538 91.521000 529 2392 1 chr1B.!!$F1 1863
10 TraesCS3A01G487000 chr4A 557661558 557663660 2102 True 2521.0 2521 88.509000 490 2610 1 chr4A.!!$R1 2120
11 TraesCS3A01G487000 chr4A 554697863 554700762 2899 False 1690.0 2532 90.572000 16 2610 2 chr4A.!!$F1 2594
12 TraesCS3A01G487000 chr2B 755329850 755331996 2146 False 1176.0 1960 87.110500 530 2612 2 chr2B.!!$F1 2082
13 TraesCS3A01G487000 chr3B 734911854 734913177 1323 True 1829.0 1829 91.874000 1309 2612 1 chr3B.!!$R1 1303
14 TraesCS3A01G487000 chr3B 774217399 774218023 624 False 889.0 889 92.247000 16 646 1 chr3B.!!$F1 630
15 TraesCS3A01G487000 chr4D 42334341 42335514 1173 False 1561.0 1561 90.909000 472 1636 1 chr4D.!!$F1 1164
16 TraesCS3A01G487000 chr7B 6998249 7001173 2924 False 1216.0 1511 91.258333 16 2612 3 chr7B.!!$F1 2596
17 TraesCS3A01G487000 chr2A 749651367 749652775 1408 False 1439.0 1439 85.510000 1185 2612 1 chr2A.!!$F1 1427

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
929 1478 4.682787 TCATACTTGACTGGCTTCATACG 58.317 43.478 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 3014 1.76523 GCGAGAGGAGGAGAGGTAAA 58.235 55.0 0.0 0.0 0.0 2.01 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
362 366 7.961326 ATCTTAACTGCCATAACCAAAAGAT 57.039 32.000 0.00 0.00 0.00 2.40
477 481 8.934697 TGTTAGGCATGGACTAGACTATTTAAT 58.065 33.333 0.00 0.00 0.00 1.40
929 1478 4.682787 TCATACTTGACTGGCTTCATACG 58.317 43.478 0.00 0.00 0.00 3.06
1107 1657 1.499007 GATTATCCCTTCAAGCCCCCA 59.501 52.381 0.00 0.00 0.00 4.96
1299 1918 3.023832 CAAGGTGTTCCACTTCCACTTT 58.976 45.455 0.00 0.00 34.40 2.66
1523 2150 0.320697 ACCCGTCTCTGTTAACAGGC 59.679 55.000 30.35 20.45 43.91 4.85
1610 2237 6.036577 TGCTCACATGTACAAGACTGATTA 57.963 37.500 4.87 0.00 0.00 1.75
1684 2312 3.884693 TGGATGTATAGGCAAGCAATGTG 59.115 43.478 0.00 0.00 0.00 3.21
1801 2445 7.730364 AGTTACTTCCATTTGTGTACTTCTG 57.270 36.000 0.00 0.00 0.00 3.02
2512 3277 6.043411 GCTCGTCCTAGATTCACTTGTTTAT 58.957 40.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.415765 CCATGACCAGTAACAACAGTTAACAAA 60.416 37.037 8.61 0.00 30.13 2.83
226 230 3.751479 AACAGAACAAAATCCAAGGGC 57.249 42.857 0.00 0.00 0.00 5.19
281 285 4.021229 CCATGTGGTACTGGTACTGACTA 58.979 47.826 10.19 1.79 36.36 2.59
362 366 6.753180 TGTGAAGTGCTTGGCAATTTTAATA 58.247 32.000 0.00 0.00 46.68 0.98
477 481 7.502895 TGATTTGGTTGGTACTGCTTAAGTTTA 59.497 33.333 4.02 0.00 40.56 2.01
606 955 7.596248 ACATTATGAATGCTGAAGTTGTTTCAC 59.404 33.333 0.00 0.00 40.39 3.18
729 1081 8.437575 TCTTAATTTCAAGAGGTTAGTGGAACT 58.562 33.333 0.00 0.00 39.27 3.01
929 1478 3.313526 ACACAACAGTCAGACAAGCATTC 59.686 43.478 2.66 0.00 0.00 2.67
1188 1766 2.940514 TGAGGACCCCAAGACATCTA 57.059 50.000 0.00 0.00 0.00 1.98
1190 1768 2.224769 TGTTTGAGGACCCCAAGACATC 60.225 50.000 0.00 0.00 0.00 3.06
1299 1918 3.243234 CGTTGCTGTTAATGTTTGGGTGA 60.243 43.478 0.00 0.00 0.00 4.02
1523 2150 4.096984 GCAACAAATAGATTGACAGGAGGG 59.903 45.833 0.00 0.00 41.85 4.30
1610 2237 0.537188 CGTGGACTCATACTTGGCCT 59.463 55.000 3.32 0.00 0.00 5.19
1684 2312 7.826744 AGAACAATCAAAAGAATACCTCTCTCC 59.173 37.037 0.00 0.00 31.02 3.71
1801 2445 6.852858 AGCTGAGAAGAACTAAGAACAAAC 57.147 37.500 0.00 0.00 0.00 2.93
2083 2731 8.192774 CACCAGCAGTCATATTTACAAATGAAT 58.807 33.333 0.00 0.00 34.06 2.57
2165 2813 7.443879 TGAGCAACTTAAAATGTGAGTGTGATA 59.556 33.333 0.00 0.00 0.00 2.15
2280 3014 1.765230 GCGAGAGGAGGAGAGGTAAA 58.235 55.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.