Multiple sequence alignment - TraesCS5D01G453400

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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 TraesCS5D01G453400 chr5D 100.000 3927 0 0 1 3927 500866210 500870136 0.000000e+00 7252
1 TraesCS5D01G453400 chr5D 88.416 587 52 7 3345 3920 399731616 399731035 0.000000e+00 693
2 TraesCS5D01G453400 chr5B 96.653 2958 79 10 1 2948 622396494 622399441 0.000000e+00 4896
3 TraesCS5D01G453400 chr5A 97.363 1820 41 3 1148 2960 624735469 624733650 0.000000e+00 3088
4 TraesCS5D01G453400 chr5A 94.516 1167 45 8 1 1163 624736640 624735489 0.000000e+00 1783
5 TraesCS5D01G453400 chr5A 95.351 968 41 3 2955 3921 626397368 626396404 0.000000e+00 1535
6 TraesCS5D01G453400 chr1D 90.138 578 47 4 3346 3921 10187294 10186725 0.000000e+00 743
7 TraesCS5D01G453400 chr2D 89.590 586 46 4 3347 3921 604048272 604048853 0.000000e+00 730
8 TraesCS5D01G453400 chr3D 88.927 587 50 4 3345 3920 4855777 4856359 0.000000e+00 710
9 TraesCS5D01G453400 chr6A 87.863 585 57 6 3345 3921 614100682 614101260 0.000000e+00 675
10 TraesCS5D01G453400 chr7D 87.585 588 59 3 3345 3921 299588875 299588291 0.000000e+00 669
11 TraesCS5D01G453400 chr3B 87.140 591 58 10 3345 3921 395946685 395947271 0.000000e+00 654
12 TraesCS5D01G453400 chr1B 86.815 584 54 11 3345 3912 29926911 29927487 7.160000e-177 630


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 TraesCS5D01G453400 chr5D 500866210 500870136 3926 False 7252.0 7252 100.0000 1 3927 1 chr5D.!!$F1 3926
1 TraesCS5D01G453400 chr5D 399731035 399731616 581 True 693.0 693 88.4160 3345 3920 1 chr5D.!!$R1 575
2 TraesCS5D01G453400 chr5B 622396494 622399441 2947 False 4896.0 4896 96.6530 1 2948 1 chr5B.!!$F1 2947
3 TraesCS5D01G453400 chr5A 624733650 624736640 2990 True 2435.5 3088 95.9395 1 2960 2 chr5A.!!$R2 2959
4 TraesCS5D01G453400 chr5A 626396404 626397368 964 True 1535.0 1535 95.3510 2955 3921 1 chr5A.!!$R1 966
5 TraesCS5D01G453400 chr1D 10186725 10187294 569 True 743.0 743 90.1380 3346 3921 1 chr1D.!!$R1 575
6 TraesCS5D01G453400 chr2D 604048272 604048853 581 False 730.0 730 89.5900 3347 3921 1 chr2D.!!$F1 574
7 TraesCS5D01G453400 chr3D 4855777 4856359 582 False 710.0 710 88.9270 3345 3920 1 chr3D.!!$F1 575
8 TraesCS5D01G453400 chr6A 614100682 614101260 578 False 675.0 675 87.8630 3345 3921 1 chr6A.!!$F1 576
9 TraesCS5D01G453400 chr7D 299588291 299588875 584 True 669.0 669 87.5850 3345 3921 1 chr7D.!!$R1 576
10 TraesCS5D01G453400 chr3B 395946685 395947271 586 False 654.0 654 87.1400 3345 3921 1 chr3B.!!$F1 576
11 TraesCS5D01G453400 chr1B 29926911 29927487 576 False 630.0 630 86.8150 3345 3912 1 chr1B.!!$F1 567

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
580 587 4.081406 CACATCTTCCATGGAACCAGAAA 58.919 43.478 23.63 1.03 0.0 2.52 F
1596 1640 2.285827 TTTTGTGCACGGAAGGTTTG 57.714 45.000 13.13 0.00 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 1940 1.112113 AGTAGCTACCGGGATGTGTG 58.888 55.000 20.31 0.0 0.00 3.82 R
3453 3515 1.451207 TGGTGTTGCTGCGTTCAGT 60.451 52.632 0.00 0.0 42.29 3.41 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
31 32 4.627284 TGAAAAACTAATGGGGACTCGA 57.373 40.909 0.00 0.00 0.00 4.04
188 190 6.183360 AGCTTTGGCCTTTACAAATAGTTTGT 60.183 34.615 3.32 12.13 46.69 2.83
580 587 4.081406 CACATCTTCCATGGAACCAGAAA 58.919 43.478 23.63 1.03 0.00 2.52
637 644 9.255304 GACATTTTCAAAATTGTACTAAGGCAA 57.745 29.630 0.00 0.00 33.94 4.52
643 650 6.038382 TCAAAATTGTACTAAGGCAACGACAA 59.962 34.615 0.00 0.00 46.39 3.18
665 672 6.488006 ACAATTAATTTGGATCGGAGAGGATG 59.512 38.462 0.00 0.00 39.05 3.51
769 776 5.393027 CCTTTGTTGTTATTTGATCTCCGGG 60.393 44.000 0.00 0.00 0.00 5.73
860 867 8.812147 TTCATTTACATCTCGTCCATATGTAC 57.188 34.615 1.24 0.00 36.19 2.90
861 868 8.178313 TCATTTACATCTCGTCCATATGTACT 57.822 34.615 1.24 0.00 36.19 2.73
862 869 9.292195 TCATTTACATCTCGTCCATATGTACTA 57.708 33.333 1.24 0.00 36.19 1.82
1107 1115 4.097589 CCAACCAACCAAAAGGTAAACGTA 59.902 41.667 0.00 0.00 37.07 3.57
1315 1359 4.881157 ATAGGAGTTGCTGGGGTTATTT 57.119 40.909 0.00 0.00 0.00 1.40
1596 1640 2.285827 TTTTGTGCACGGAAGGTTTG 57.714 45.000 13.13 0.00 0.00 2.93
1711 1761 3.266510 AGCCGAACAAGCAATATCTGA 57.733 42.857 0.00 0.00 0.00 3.27
1843 1893 4.079253 AGCCAATGTTTTCTTACCGTCAT 58.921 39.130 0.00 0.00 0.00 3.06
1890 1940 3.250744 TCTACAGTTTGCGACACATAGC 58.749 45.455 0.00 0.00 0.00 2.97
1922 1972 3.385111 GGTAGCTACTATGGACTTGCTGT 59.615 47.826 22.74 0.00 32.72 4.40
2140 2190 8.239314 CGATGCCATTTATAATGCTCTTAATGT 58.761 33.333 0.00 0.00 0.00 2.71
2938 2990 3.366577 GCTCCCGCTAGCTTAAGTAGATC 60.367 52.174 13.93 0.00 39.50 2.75
3082 3134 9.248291 CCTTTTCAAACCATATACATTATGCAC 57.752 33.333 0.00 0.00 0.00 4.57
3112 3164 6.458210 CAAAGCCAACAAAGATAATCCAACT 58.542 36.000 0.00 0.00 0.00 3.16
3121 3173 7.565680 ACAAAGATAATCCAACTTCTACCGAT 58.434 34.615 0.00 0.00 0.00 4.18
3171 3223 0.865111 CGCAATCTTCACAACCGACA 59.135 50.000 0.00 0.00 0.00 4.35
3183 3235 0.030101 AACCGACAAAACCACGCATG 59.970 50.000 0.00 0.00 0.00 4.06
3253 3305 2.867109 ATTTGGAGGTGACTGGTCAG 57.133 50.000 3.47 0.00 44.43 3.51
3348 3400 5.476254 TGTGTCAAAATGATCTTGCATACCA 59.524 36.000 0.00 0.00 0.00 3.25
3453 3515 1.421268 CCAAGGCAGGATACATAGGCA 59.579 52.381 0.00 0.00 41.41 4.75
3458 3520 2.104792 GGCAGGATACATAGGCACTGAA 59.895 50.000 0.00 0.00 38.50 3.02
3652 3715 1.971357 TCAAGAAGGGAACGAGCTTCT 59.029 47.619 0.00 0.00 36.34 2.85
3653 3716 2.368875 TCAAGAAGGGAACGAGCTTCTT 59.631 45.455 0.00 0.00 42.30 2.52
3660 3723 3.575351 AACGAGCTTCTTCGCCGCT 62.575 57.895 0.00 0.00 44.15 5.52
3661 3724 3.549150 CGAGCTTCTTCGCCGCTG 61.549 66.667 0.00 0.00 33.47 5.18
3662 3725 3.858989 GAGCTTCTTCGCCGCTGC 61.859 66.667 0.00 0.00 33.47 5.25
3884 3955 0.396811 CCCCAACCAAAGAGACGAGT 59.603 55.000 0.00 0.00 0.00 4.18
3896 3967 0.538977 AGACGAGTGGAAAGACCCGA 60.539 55.000 0.00 0.00 38.00 5.14
3906 3977 0.036306 AAAGACCCGACCTTTCGCAT 59.964 50.000 0.00 0.00 44.43 4.73
3926 3997 3.790437 CTGAGCGGCCCCTGACAT 61.790 66.667 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
580 587 6.627243 TGTATATCTGCAGAACACGTTTACT 58.373 36.000 22.50 2.10 0.00 2.24
637 644 5.424757 TCTCCGATCCAAATTAATTGTCGT 58.575 37.500 16.99 2.23 36.39 4.34
643 650 5.006386 GCATCCTCTCCGATCCAAATTAAT 58.994 41.667 0.00 0.00 0.00 1.40
665 672 7.688372 TCATTTCAGAAGATATGAAAGAACGC 58.312 34.615 6.36 0.00 46.59 4.84
693 700 2.948979 CGAGTCTGGTCTTCTGCTAGAT 59.051 50.000 0.00 0.00 0.00 1.98
694 701 2.290387 ACGAGTCTGGTCTTCTGCTAGA 60.290 50.000 0.00 0.00 0.00 2.43
769 776 9.058424 GGCGAAAACTTTGTCTTGTTATATTAC 57.942 33.333 0.00 0.00 0.00 1.89
1596 1640 4.850347 ATAGTTATAGCGGGTGACTGAC 57.150 45.455 0.00 0.00 39.98 3.51
1711 1761 3.944015 GGCTTCAGAGTGAGTATGCAATT 59.056 43.478 0.00 0.00 0.00 2.32
1772 1822 5.351465 ACTCACATAAACGATGTCATTGGAC 59.649 40.000 5.04 0.00 46.33 4.02
1863 1913 1.871039 GTCGCAAACTGTAGAAGGCAA 59.129 47.619 0.00 0.00 0.00 4.52
1890 1940 1.112113 AGTAGCTACCGGGATGTGTG 58.888 55.000 20.31 0.00 0.00 3.82
1922 1972 4.538746 TGTCCGTACACATCCATTGTAA 57.461 40.909 0.00 0.00 36.57 2.41
1989 2039 3.455910 CTGTCTTTGGATCACCCTCCATA 59.544 47.826 0.00 0.00 44.66 2.74
2140 2190 3.318313 ACCTGGGAAGAAACTGAAGAGA 58.682 45.455 0.00 0.00 0.00 3.10
2938 2990 9.645059 CCACATCCATGTACTTATATGAGTAAG 57.355 37.037 8.81 3.30 39.39 2.34
3082 3134 7.492344 GGATTATCTTTGTTGGCTTTGGTTATG 59.508 37.037 0.00 0.00 0.00 1.90
3112 3164 6.704310 AGCTTGGTTTTAAGTATCGGTAGAA 58.296 36.000 0.00 0.00 0.00 2.10
3171 3223 2.642700 GCGTCCATGCGTGGTTTT 59.357 55.556 24.24 0.00 46.16 2.43
3253 3305 6.467047 CACAATATTTCGTCTGATTGAAGTGC 59.533 38.462 8.94 0.00 34.18 4.40
3322 3374 3.887741 TGCAAGATCATTTTGACACACG 58.112 40.909 0.00 0.00 0.00 4.49
3323 3375 5.801947 GGTATGCAAGATCATTTTGACACAC 59.198 40.000 0.00 0.00 0.00 3.82
3453 3515 1.451207 TGGTGTTGCTGCGTTCAGT 60.451 52.632 0.00 0.00 42.29 3.41
3884 3955 0.034337 CGAAAGGTCGGGTCTTTCCA 59.966 55.000 15.19 0.00 44.15 3.53
3896 3967 1.078143 GCTCAGGGATGCGAAAGGT 60.078 57.895 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.