Multiple sequence alignment - TraesCS7D01G530100

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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 TraesCS7D01G530100 chr7D 100.000 2591 0 0 1 2591 625182120 625179530 0.000000e+00 4785
1 TraesCS7D01G530100 chr7D 95.889 1873 54 11 1 1855 393113789 393111922 0.000000e+00 3011
2 TraesCS7D01G530100 chr7D 96.363 1732 42 12 875 2591 631817586 631815861 0.000000e+00 2830
3 TraesCS7D01G530100 chr7D 92.818 905 39 7 1 882 92234471 92233570 0.000000e+00 1288
4 TraesCS7D01G530100 chr7D 92.027 903 42 11 1 882 631818509 631817616 0.000000e+00 1242
5 TraesCS7D01G530100 chr7D 94.495 545 11 5 1 529 393111378 393111919 0.000000e+00 822
6 TraesCS7D01G530100 chr1D 98.687 2590 34 0 2 2591 444898445 444901034 0.000000e+00 4595
7 TraesCS7D01G530100 chr5D 97.929 2607 35 5 1 2591 545533223 545535826 0.000000e+00 4497
8 TraesCS7D01G530100 chr5D 96.356 1729 49 9 875 2591 408554332 408552606 0.000000e+00 2832
9 TraesCS7D01G530100 chr5D 93.046 906 37 7 1 882 408555265 408554362 0.000000e+00 1301
10 TraesCS7D01G530100 chr2D 97.314 2606 54 3 1 2591 547546018 547543414 0.000000e+00 4410
11 TraesCS7D01G530100 chr2D 97.277 2607 51 6 1 2591 489934814 489932212 0.000000e+00 4403
12 TraesCS7D01G530100 chr2D 97.319 2611 34 11 1 2591 624287247 624289841 0.000000e+00 4401
13 TraesCS7D01G530100 chrUn 95.614 2622 40 14 1 2591 70158514 70155937 0.000000e+00 4135
14 TraesCS7D01G530100 chr3D 96.904 1712 32 3 895 2591 19765755 19764050 0.000000e+00 2848
15 TraesCS7D01G530100 chr3D 96.363 1732 47 8 875 2591 45062228 45060498 0.000000e+00 2835
16 TraesCS7D01G530100 chr3D 91.160 905 39 11 1 882 45063144 45062258 0.000000e+00 1190
17 TraesCS7D01G530100 chr3A 94.997 1719 66 9 875 2591 37633925 37635625 0.000000e+00 2680
18 TraesCS7D01G530100 chr6D 98.326 239 4 0 2353 2591 137509349 137509111 1.110000e-113 420


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 TraesCS7D01G530100 chr7D 625179530 625182120 2590 True 4785.0 4785 100.0000 1 2591 1 chr7D.!!$R3 2590
1 TraesCS7D01G530100 chr7D 393111922 393113789 1867 True 3011.0 3011 95.8890 1 1855 1 chr7D.!!$R2 1854
2 TraesCS7D01G530100 chr7D 631815861 631818509 2648 True 2036.0 2830 94.1950 1 2591 2 chr7D.!!$R4 2590
3 TraesCS7D01G530100 chr7D 92233570 92234471 901 True 1288.0 1288 92.8180 1 882 1 chr7D.!!$R1 881
4 TraesCS7D01G530100 chr7D 393111378 393111919 541 False 822.0 822 94.4950 1 529 1 chr7D.!!$F1 528
5 TraesCS7D01G530100 chr1D 444898445 444901034 2589 False 4595.0 4595 98.6870 2 2591 1 chr1D.!!$F1 2589
6 TraesCS7D01G530100 chr5D 545533223 545535826 2603 False 4497.0 4497 97.9290 1 2591 1 chr5D.!!$F1 2590
7 TraesCS7D01G530100 chr5D 408552606 408555265 2659 True 2066.5 2832 94.7010 1 2591 2 chr5D.!!$R1 2590
8 TraesCS7D01G530100 chr2D 547543414 547546018 2604 True 4410.0 4410 97.3140 1 2591 1 chr2D.!!$R2 2590
9 TraesCS7D01G530100 chr2D 489932212 489934814 2602 True 4403.0 4403 97.2770 1 2591 1 chr2D.!!$R1 2590
10 TraesCS7D01G530100 chr2D 624287247 624289841 2594 False 4401.0 4401 97.3190 1 2591 1 chr2D.!!$F1 2590
11 TraesCS7D01G530100 chrUn 70155937 70158514 2577 True 4135.0 4135 95.6140 1 2591 1 chrUn.!!$R1 2590
12 TraesCS7D01G530100 chr3D 19764050 19765755 1705 True 2848.0 2848 96.9040 895 2591 1 chr3D.!!$R1 1696
13 TraesCS7D01G530100 chr3D 45060498 45063144 2646 True 2012.5 2835 93.7615 1 2591 2 chr3D.!!$R2 2590
14 TraesCS7D01G530100 chr3A 37633925 37635625 1700 False 2680.0 2680 94.9970 875 2591 1 chr3A.!!$F1 1716

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
218 236 0.039911 ACTGACTCCCCTACTCGCTT 59.96 55.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2258 2.672307 GCTGCTGCTGCTGTCCTT 60.672 61.111 22.1 0.0 39.81 3.36 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
202 220 2.433838 CCCACTCGCTGCTCACTG 60.434 66.667 0.00 0.0 0.00 3.66
211 229 0.972983 GCTGCTCACTGACTCCCCTA 60.973 60.000 0.00 0.0 0.00 3.53
218 236 0.039911 ACTGACTCCCCTACTCGCTT 59.960 55.000 0.00 0.0 0.00 4.68
321 359 1.454479 CGCCATGCCTTCCTGGAAT 60.454 57.895 10.03 0.0 38.35 3.01
606 671 3.144657 TGATTCTGGTGTTGAGTGCAT 57.855 42.857 0.00 0.0 0.00 3.96
779 845 3.418684 AACAGGAAGGCGTTTCTATGT 57.581 42.857 0.00 3.1 37.31 2.29
788 854 1.405526 GCGTTTCTATGTCTGCCCAGA 60.406 52.381 0.00 0.0 34.56 3.86
1092 1194 1.339055 TGTCTGTGCAAGCTATGGGAC 60.339 52.381 0.00 0.0 0.00 4.46
1574 1679 5.013599 AGGAGAAGTTAGAGCAAATCAAGGT 59.986 40.000 0.00 0.0 0.00 3.50
1597 1702 6.073003 GGTCATCCTTGAGTCTTAAACTTGTG 60.073 42.308 0.00 0.0 38.74 3.33
1756 1861 8.472007 TGTTTTTAAGTTGTAATGGATCACCT 57.528 30.769 0.00 0.0 37.04 4.00
1757 1862 9.575868 TGTTTTTAAGTTGTAATGGATCACCTA 57.424 29.630 0.00 0.0 37.04 3.08
1760 1865 7.801716 TTAAGTTGTAATGGATCACCTATGC 57.198 36.000 0.00 0.0 37.04 3.14
1761 1866 5.636903 AGTTGTAATGGATCACCTATGCT 57.363 39.130 0.00 0.0 37.04 3.79
1762 1867 6.747414 AGTTGTAATGGATCACCTATGCTA 57.253 37.500 0.00 0.0 37.04 3.49
1763 1868 7.321717 AGTTGTAATGGATCACCTATGCTAT 57.678 36.000 0.00 0.0 37.04 2.97
1764 1869 7.749666 AGTTGTAATGGATCACCTATGCTATT 58.250 34.615 0.00 0.0 37.04 1.73
1765 1870 8.880244 AGTTGTAATGGATCACCTATGCTATTA 58.120 33.333 0.00 0.0 37.04 0.98
1766 1871 9.502091 GTTGTAATGGATCACCTATGCTATTAA 57.498 33.333 0.00 0.0 37.04 1.40
1767 1872 9.725019 TTGTAATGGATCACCTATGCTATTAAG 57.275 33.333 0.00 0.0 37.04 1.85
1768 1873 8.880244 TGTAATGGATCACCTATGCTATTAAGT 58.120 33.333 0.00 0.0 37.04 2.24
2076 2211 5.716703 CCAAAAGAAACCCTACAGATGGATT 59.283 40.000 0.00 0.0 0.00 3.01
2123 2258 1.229723 GGGGGAGGTTGTGGAGGTA 60.230 63.158 0.00 0.0 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.279582 ACGGTTCAATCGCTAGTCAG 57.720 50.000 0.00 0.00 0.00 3.51
202 220 1.406180 GAGAAAGCGAGTAGGGGAGTC 59.594 57.143 0.00 0.00 0.00 3.36
211 229 1.893919 GAGCAGGGGAGAAAGCGAGT 61.894 60.000 0.00 0.00 0.00 4.18
218 236 1.613630 GAGTGGGAGCAGGGGAGAA 60.614 63.158 0.00 0.00 0.00 2.87
269 306 1.737008 GCGACCGACCTCAAAGACC 60.737 63.158 0.00 0.00 0.00 3.85
321 359 1.209383 CGAGCTCGTTTCCTCGTCA 59.791 57.895 27.79 0.00 44.25 4.35
606 671 6.952773 AACCAGCAAACACTAGTTTCAATA 57.047 33.333 0.00 0.00 45.80 1.90
779 845 3.300388 CATCTAACCTAGTCTGGGCAGA 58.700 50.000 1.33 5.93 34.56 4.26
788 854 8.879427 AAAAGTTTATTGGCATCTAACCTAGT 57.121 30.769 0.00 0.00 0.00 2.57
790 856 8.956426 CAGAAAAGTTTATTGGCATCTAACCTA 58.044 33.333 0.00 0.00 0.00 3.08
828 894 5.358725 TGCTGCATCATATCAAACATCAGTT 59.641 36.000 0.00 0.00 40.40 3.16
1424 1529 6.505048 TCCTGGTGTTCTTGATGATATCAT 57.495 37.500 18.21 18.21 39.39 2.45
1574 1679 5.997746 CCACAAGTTTAAGACTCAAGGATGA 59.002 40.000 0.00 0.00 37.72 2.92
1589 1694 5.136828 TCACCAACATATCACCACAAGTTT 58.863 37.500 0.00 0.00 0.00 2.66
1597 1702 7.101054 TGTACTTACTTCACCAACATATCACC 58.899 38.462 0.00 0.00 0.00 4.02
1656 1761 3.376234 CACCCATAATCACTTGCAGTCAG 59.624 47.826 0.00 0.00 0.00 3.51
1735 1840 8.052748 AGCATAGGTGATCCATTACAACTTAAA 58.947 33.333 0.00 0.00 35.58 1.52
1740 1845 7.986085 AATAGCATAGGTGATCCATTACAAC 57.014 36.000 0.00 0.00 35.89 3.32
1741 1846 9.725019 CTTAATAGCATAGGTGATCCATTACAA 57.275 33.333 0.00 0.00 35.89 2.41
1742 1847 8.880244 ACTTAATAGCATAGGTGATCCATTACA 58.120 33.333 0.00 0.00 35.89 2.41
1743 1848 9.155975 CACTTAATAGCATAGGTGATCCATTAC 57.844 37.037 0.00 0.00 35.53 1.89
1744 1849 8.880244 ACACTTAATAGCATAGGTGATCCATTA 58.120 33.333 11.56 0.00 36.63 1.90
1745 1850 7.749666 ACACTTAATAGCATAGGTGATCCATT 58.250 34.615 11.56 0.00 36.63 3.16
1746 1851 7.321717 ACACTTAATAGCATAGGTGATCCAT 57.678 36.000 11.56 0.00 36.63 3.41
1747 1852 6.747414 ACACTTAATAGCATAGGTGATCCA 57.253 37.500 11.56 0.00 36.63 3.41
1748 1853 6.992715 ACAACACTTAATAGCATAGGTGATCC 59.007 38.462 11.56 0.00 36.63 3.36
1749 1854 9.542462 TTACAACACTTAATAGCATAGGTGATC 57.458 33.333 11.56 0.00 36.63 2.92
1751 1856 9.325198 CATTACAACACTTAATAGCATAGGTGA 57.675 33.333 11.56 0.00 36.63 4.02
1752 1857 8.559536 CCATTACAACACTTAATAGCATAGGTG 58.440 37.037 5.35 5.35 38.45 4.00
1753 1858 8.491134 TCCATTACAACACTTAATAGCATAGGT 58.509 33.333 0.00 0.00 0.00 3.08
1754 1859 8.902540 TCCATTACAACACTTAATAGCATAGG 57.097 34.615 0.00 0.00 0.00 2.57
1757 1862 9.277783 GAGATCCATTACAACACTTAATAGCAT 57.722 33.333 0.00 0.00 0.00 3.79
1758 1863 7.715249 GGAGATCCATTACAACACTTAATAGCA 59.285 37.037 0.00 0.00 35.64 3.49
1759 1864 7.934120 AGGAGATCCATTACAACACTTAATAGC 59.066 37.037 0.92 0.00 38.89 2.97
1762 1867 9.784531 CATAGGAGATCCATTACAACACTTAAT 57.215 33.333 0.92 0.00 38.89 1.40
1763 1868 7.715249 GCATAGGAGATCCATTACAACACTTAA 59.285 37.037 0.92 0.00 38.89 1.85
1764 1869 7.071196 AGCATAGGAGATCCATTACAACACTTA 59.929 37.037 0.92 0.00 38.89 2.24
1765 1870 6.058183 GCATAGGAGATCCATTACAACACTT 58.942 40.000 0.92 0.00 38.89 3.16
1766 1871 5.367937 AGCATAGGAGATCCATTACAACACT 59.632 40.000 0.92 0.00 38.89 3.55
1767 1872 5.615289 AGCATAGGAGATCCATTACAACAC 58.385 41.667 0.92 0.00 38.89 3.32
1768 1873 5.894298 AGCATAGGAGATCCATTACAACA 57.106 39.130 0.92 0.00 38.89 3.33
2123 2258 2.672307 GCTGCTGCTGCTGTCCTT 60.672 61.111 22.10 0.00 39.81 3.36


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

AutoCloner maintained by Alex Coulton.