Multiple sequence alignment - TraesCS7A01G323100

Loading Multiple Alignment...

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 TraesCS7A01G323100 chr7A 100.000 1741 0 0 865 2605 469984002 469985742 0.000000e+00 3216
1 TraesCS7A01G323100 chr7A 100.000 514 0 0 1 514 469983138 469983651 0.000000e+00 950
2 TraesCS7A01G323100 chr7D 96.796 1748 33 7 865 2605 409456772 409458503 0.000000e+00 2896
3 TraesCS7A01G323100 chr7D 97.665 514 12 0 1 514 409456211 409456724 0.000000e+00 883
4 TraesCS7A01G323100 chr7D 91.765 85 2 3 1824 1904 409457641 409457724 2.120000e-21 113
5 TraesCS7A01G323100 chr7B 94.362 940 26 3 912 1828 423766157 423767092 0.000000e+00 1417
6 TraesCS7A01G323100 chr7B 95.420 786 27 5 1828 2604 423767198 423767983 0.000000e+00 1243
7 TraesCS7A01G323100 chr7B 98.054 514 10 0 1 514 423765175 423765688 0.000000e+00 894
8 TraesCS7A01G323100 chr7B 92.000 75 1 3 1824 1894 423767005 423767078 1.650000e-17 100


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 TraesCS7A01G323100 chr7A 469983138 469985742 2604 False 2083.000000 3216 100.000000 1 2605 2 chr7A.!!$F1 2604
1 TraesCS7A01G323100 chr7D 409456211 409458503 2292 False 1297.333333 2896 95.408667 1 2605 3 chr7D.!!$F1 2604
2 TraesCS7A01G323100 chr7B 423765175 423767983 2808 False 913.500000 1417 94.959000 1 2604 4 chr7B.!!$F1 2603

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
311 312 0.320374 CACCTACGCTCCTCCAAACA 59.68 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1992 0.314935 GCATGAAACCAGTGTGGGTG 59.685 55.0 0.0 0.0 35.52 4.61 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
103 104 1.566703 TCTTTCCCTCCCACAACACAA 59.433 47.619 0.00 0.00 0.00 3.33
187 188 0.460987 CTACACCTACAGCAGCAGCC 60.461 60.000 0.00 0.00 43.56 4.85
311 312 0.320374 CACCTACGCTCCTCCAAACA 59.680 55.000 0.00 0.00 0.00 2.83
312 313 1.053424 ACCTACGCTCCTCCAAACAA 58.947 50.000 0.00 0.00 0.00 2.83
997 1372 2.285368 CCACTAGCCCCACCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
1146 1521 5.482163 AAGAAGAGGAAGACAGAAAGGAG 57.518 43.478 0.00 0.00 0.00 3.69
1204 1579 0.680921 ACAAATCGGCCATGTCAGGG 60.681 55.000 2.24 0.00 0.00 4.45
1287 1662 0.970937 AAGGAATCAGAGGCCGTCGA 60.971 55.000 0.00 0.00 0.00 4.20
1386 1761 1.936547 GGATTCAGAGGTCATCAACGC 59.063 52.381 0.00 0.00 0.00 4.84
1499 1877 4.269183 TGAAGAGGCAGACAACAAAGAAA 58.731 39.130 0.00 0.00 0.00 2.52
1500 1878 4.704540 TGAAGAGGCAGACAACAAAGAAAA 59.295 37.500 0.00 0.00 0.00 2.29
1501 1879 5.184864 TGAAGAGGCAGACAACAAAGAAAAA 59.815 36.000 0.00 0.00 0.00 1.94
1504 1882 5.360714 AGAGGCAGACAACAAAGAAAAATCA 59.639 36.000 0.00 0.00 0.00 2.57
1526 1904 0.938637 TGCAAAATCAAAGGCACGCG 60.939 50.000 3.53 3.53 0.00 6.01
1614 1992 2.945008 TCGAGGCAATGATCAAATCCAC 59.055 45.455 0.00 0.00 0.00 4.02
1625 2003 0.961019 CAAATCCACACCCACACTGG 59.039 55.000 0.00 0.00 37.25 4.00
1711 2112 5.016173 TCGGAGACCCAATTTGATTGAATT 58.984 37.500 0.00 0.00 42.83 2.17
1782 2183 8.956426 TGTCTTATGAATGGATTTCCTTAACAC 58.044 33.333 0.00 0.00 36.82 3.32
1818 2219 3.857157 ACAGTGAAAAGACCCTTAGCA 57.143 42.857 0.00 0.00 0.00 3.49
1883 2390 9.705290 ATTTCCTTAACAAAATATCACACAACC 57.295 29.630 0.00 0.00 0.00 3.77
1904 2415 3.246699 CCGTGAAAAGACACTTAGCGAAA 59.753 43.478 0.00 0.00 38.47 3.46
2262 2775 0.881118 ACCAACATCAACGTCCATGC 59.119 50.000 6.60 0.00 0.00 4.06
2347 2860 6.542821 ACAGAAGAATAACCATGAAAGGACA 58.457 36.000 0.00 0.00 0.00 4.02
2490 3005 2.423373 CCATACCCTTGGACCTTGATGG 60.423 54.545 0.00 0.00 39.25 3.51
2500 3015 7.257016 CCCTTGGACCTTGATGGATATACAATA 60.257 40.741 0.00 0.00 39.71 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 5.106038 GCATGCATGTGGTTATATATGTGCT 60.106 40.000 26.79 0.0 32.87 4.40
997 1372 1.920734 TTGGCGGGCTGATATGTGGT 61.921 55.000 0.00 0.0 0.00 4.16
1146 1521 1.623811 TGAAGTTCAGTACCTCTGCCC 59.376 52.381 0.08 0.0 43.32 5.36
1287 1662 1.598130 GCTGTGCCCGACTCTTTGT 60.598 57.895 0.00 0.0 0.00 2.83
1499 1877 5.410439 GTGCCTTTGATTTTGCAGATGATTT 59.590 36.000 0.00 0.0 33.80 2.17
1500 1878 4.933400 GTGCCTTTGATTTTGCAGATGATT 59.067 37.500 0.00 0.0 33.80 2.57
1501 1879 4.501071 GTGCCTTTGATTTTGCAGATGAT 58.499 39.130 0.00 0.0 33.80 2.45
1504 1882 2.927871 GCGTGCCTTTGATTTTGCAGAT 60.928 45.455 0.00 0.0 33.80 2.90
1526 1904 4.329256 GCCATCGTCTTAGAACTTGGTAAC 59.671 45.833 7.21 0.0 0.00 2.50
1614 1992 0.314935 GCATGAAACCAGTGTGGGTG 59.685 55.000 0.00 0.0 35.52 4.61
1664 2065 4.662145 GCCCTTATTTCAATCACACGAAG 58.338 43.478 0.00 0.0 0.00 3.79
1711 2112 6.150809 TGCTGACAACAATAGTTTGCATATCA 59.849 34.615 0.00 0.0 35.28 2.15
1782 2183 8.854979 TTTTCACTGTTTGTTCTGTGATATTG 57.145 30.769 7.10 0.0 42.56 1.90
1883 2390 4.446857 TTTCGCTAAGTGTCTTTTCACG 57.553 40.909 0.00 0.0 42.40 4.35
1904 2415 7.326063 GCGAGCACATTTTGTTAAGAAGTAATT 59.674 33.333 0.00 0.0 0.00 1.40
2201 2714 3.561143 AGCCAGTCCTATGTCTGTAGAG 58.439 50.000 0.00 0.0 0.00 2.43
2324 2837 6.656693 ACTGTCCTTTCATGGTTATTCTTCTG 59.343 38.462 0.00 0.0 0.00 3.02
2347 2860 1.071471 CACTTTCCCTGTGGCGACT 59.929 57.895 0.00 0.0 0.00 4.18


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

AutoCloner maintained by Alex Coulton.