Multiple sequence alignment - TraesCS7B01G070500

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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 TraesCS7B01G070500 chr7B 100.000 2528 0 0 1 2528 77444354 77441827 0 4669
1 TraesCS7B01G070500 chr7B 96.164 2529 91 4 1 2528 709309598 709312121 0 4128
2 TraesCS7B01G070500 chr5D 96.718 2529 78 3 1 2528 21194645 21197169 0 4205
3 TraesCS7B01G070500 chr1D 96.504 2517 83 3 13 2528 482446592 482444080 0 4156
4 TraesCS7B01G070500 chr6D 96.361 2528 87 3 1 2528 365464929 365462407 0 4154
5 TraesCS7B01G070500 chrUn 96.204 2529 91 3 1 2528 70522588 70525112 0 4133
6 TraesCS7B01G070500 chr7D 96.204 2529 88 5 1 2528 110005543 110003022 0 4132
7 TraesCS7B01G070500 chr1B 96.204 2529 89 5 1 2528 549682455 549679933 0 4132
8 TraesCS7B01G070500 chr4A 95.930 2531 96 3 1 2528 712103781 712106307 0 4096
9 TraesCS7B01G070500 chr3B 95.652 2530 103 5 1 2528 758586061 758583537 0 4056


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 TraesCS7B01G070500 chr7B 77441827 77444354 2527 True 4669 4669 100.000 1 2528 1 chr7B.!!$R1 2527
1 TraesCS7B01G070500 chr7B 709309598 709312121 2523 False 4128 4128 96.164 1 2528 1 chr7B.!!$F1 2527
2 TraesCS7B01G070500 chr5D 21194645 21197169 2524 False 4205 4205 96.718 1 2528 1 chr5D.!!$F1 2527
3 TraesCS7B01G070500 chr1D 482444080 482446592 2512 True 4156 4156 96.504 13 2528 1 chr1D.!!$R1 2515
4 TraesCS7B01G070500 chr6D 365462407 365464929 2522 True 4154 4154 96.361 1 2528 1 chr6D.!!$R1 2527
5 TraesCS7B01G070500 chrUn 70522588 70525112 2524 False 4133 4133 96.204 1 2528 1 chrUn.!!$F1 2527
6 TraesCS7B01G070500 chr7D 110003022 110005543 2521 True 4132 4132 96.204 1 2528 1 chr7D.!!$R1 2527
7 TraesCS7B01G070500 chr1B 549679933 549682455 2522 True 4132 4132 96.204 1 2528 1 chr1B.!!$R1 2527
8 TraesCS7B01G070500 chr4A 712103781 712106307 2526 False 4096 4096 95.930 1 2528 1 chr4A.!!$F1 2527
9 TraesCS7B01G070500 chr3B 758583537 758586061 2524 True 4056 4056 95.652 1 2528 1 chr3B.!!$R1 2527

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
337 346 0.036952 CCACGATCTCCTGTTGCAGT 60.037 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 1908 1.597027 CGCCAGTCTTCGGTTTGGT 60.597 57.895 0.0 0.0 33.21 3.67 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
81 86 3.141767 ACCTTTGCTAAACTCTCCACC 57.858 47.619 0.00 0.00 0.00 4.61
185 194 7.524367 CGGGTTGTTACGATCCCTATAAATAGT 60.524 40.741 0.00 0.00 37.92 2.12
215 224 9.401058 CCTTTGAAACCTCATAGATCATAGTTT 57.599 33.333 0.00 0.00 33.72 2.66
246 255 2.263741 CGCCCAAAGCAGCAAGACT 61.264 57.895 0.00 0.00 44.04 3.24
331 340 0.252284 AACTCCCCACGATCTCCTGT 60.252 55.000 0.00 0.00 0.00 4.00
337 346 0.036952 CCACGATCTCCTGTTGCAGT 60.037 55.000 0.00 0.00 0.00 4.40
403 412 1.310904 GCAACCCCACTCGTTGTTTA 58.689 50.000 2.97 0.00 42.12 2.01
408 417 3.667360 ACCCCACTCGTTGTTTACATAC 58.333 45.455 0.00 0.00 0.00 2.39
477 488 1.300481 GAGGGCGCTAGGATTTGTTC 58.700 55.000 7.64 0.00 0.00 3.18
509 520 8.195436 CAGATTGGCAGTTCATTGATTAATTCT 58.805 33.333 0.00 0.00 0.00 2.40
542 553 5.419155 TCTTAGATTCTGGTCTTGTCGATGT 59.581 40.000 0.00 0.00 0.00 3.06
603 615 2.905075 CACGAGTTATGGAAGGCATCA 58.095 47.619 0.00 0.00 0.00 3.07
662 674 0.818296 GCGCCTAGAGTTGAGGAGAA 59.182 55.000 0.00 0.00 36.05 2.87
666 678 2.563179 GCCTAGAGTTGAGGAGAACACA 59.437 50.000 0.00 0.00 35.99 3.72
776 788 6.257849 CGTAACCAAGCTGAATCTAATGCTAA 59.742 38.462 0.00 0.00 35.09 3.09
800 812 5.670792 ATTTGCACATTCATGGAACTCAT 57.329 34.783 0.00 0.00 36.31 2.90
837 849 7.101054 ACAAATTACCTCATGAAGTAGCGTAA 58.899 34.615 4.42 2.18 0.00 3.18
930 942 6.037500 GCTGAATCTAATCACACTTGCACATA 59.962 38.462 0.00 0.00 0.00 2.29
941 953 2.487762 ACTTGCACATACATTGAACCCG 59.512 45.455 0.00 0.00 0.00 5.28
1046 1058 3.515901 GGTGGACTTCTCAAGACACCTAT 59.484 47.826 18.89 0.00 46.47 2.57
1175 1188 0.109597 GCGCATATAACAGGCATGCC 60.110 55.000 30.12 30.12 41.60 4.40
1176 1189 0.166597 CGCATATAACAGGCATGCCG 59.833 55.000 30.50 25.58 41.60 5.69
1177 1190 0.109597 GCATATAACAGGCATGCCGC 60.110 55.000 30.50 20.74 39.30 6.53
1332 1348 4.023878 CCAAATTTTGTCAGGCCATTTGTG 60.024 41.667 16.75 2.68 34.40 3.33
1650 1666 5.168569 CGAGAAGTTTAGAGTGCACCAATA 58.831 41.667 14.63 0.77 0.00 1.90
1802 1818 7.369607 GCACATTGCATGGATTATGTAACATA 58.630 34.615 4.44 0.00 42.84 2.29
1877 1893 1.101331 GAGGCCTTTCATTCCAGCAG 58.899 55.000 6.77 0.00 0.00 4.24
1892 1908 0.684479 AGCAGGAGATGGTACGCTGA 60.684 55.000 0.00 0.00 38.04 4.26
2059 2075 1.528129 CAAGAAGTTGCCTCCCTCAC 58.472 55.000 0.00 0.00 0.00 3.51
2376 2393 1.077265 CACACCCAATGGAGGCCTT 59.923 57.895 6.77 0.00 34.81 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 194 7.199167 TGATCTATGAGGTTTCAAAGGATCA 57.801 36.000 0.00 0.00 40.29 2.92
246 255 2.111999 CTGGGTTGCTCCGTCCTTCA 62.112 60.000 0.00 0.00 37.00 3.02
337 346 0.446222 GGCACGAAAAATAGCAGCGA 59.554 50.000 0.00 0.00 0.00 4.93
408 417 8.905702 GTTTAAAAACATGCTGAGTTACATGAG 58.094 33.333 9.77 0.00 45.23 2.90
509 520 8.424918 CAAGACCAGAATCTAAGATTTAGCCTA 58.575 37.037 0.00 0.00 0.00 3.93
542 553 1.305219 GCACCCGCTGCACTAATTGA 61.305 55.000 0.00 0.00 46.29 2.57
580 592 0.459585 GCCTTCCATAACTCGTGCGA 60.460 55.000 0.00 0.00 0.00 5.10
603 615 5.713760 ATGGAATTAAAACATGGGCCATT 57.286 34.783 18.46 5.71 31.22 3.16
776 788 6.778834 TGAGTTCCATGAATGTGCAAATAT 57.221 33.333 0.00 0.00 0.00 1.28
800 812 7.575414 TGAGGTAATTTGTTTACAAGCAAGA 57.425 32.000 0.00 0.00 41.74 3.02
867 879 9.607988 TTTAAACACTCATACGGATGAATACAT 57.392 29.630 12.36 1.19 41.62 2.29
930 942 0.039618 AAGCATCCCGGGTTCAATGT 59.960 50.000 22.86 4.90 0.00 2.71
941 953 2.491621 GCGGCAAAGAAGCATCCC 59.508 61.111 0.00 0.00 35.83 3.85
1046 1058 5.405269 CACAGTACACGTCTGATTTTGATGA 59.595 40.000 9.51 0.00 36.81 2.92
1332 1348 6.693315 ACATATTTGCCTATGGTGTACAAC 57.307 37.500 3.20 3.20 34.11 3.32
1596 1612 2.791004 GTCTGCATGACAACAAAAGCAC 59.209 45.455 0.00 0.00 44.73 4.40
1624 1640 4.038282 TGGTGCACTCTAAACTTCTCGTAA 59.962 41.667 17.98 0.00 0.00 3.18
1650 1666 4.359434 TCATACGAGATGCTAGAGTCCT 57.641 45.455 0.00 0.00 0.00 3.85
1877 1893 2.199117 TGGTCAGCGTACCATCTCC 58.801 57.895 8.92 0.00 44.68 3.71
1892 1908 1.597027 CGCCAGTCTTCGGTTTGGT 60.597 57.895 0.00 0.00 33.21 3.67
2261 2277 7.907214 AATACATGTTAGTCTGAGGTGTTTC 57.093 36.000 2.30 0.00 0.00 2.78
2376 2393 2.156917 CCTGCTCAGCATTCTCAACAA 58.843 47.619 0.00 0.00 38.13 2.83


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

AutoCloner maintained by Alex Coulton.