Multiple sequence alignment - TraesCS2A01G174800

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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 TraesCS2A01G174800 chr2A 100.000 2687 0 0 1 2687 133473054 133475740 0.000000e+00 4963
1 TraesCS2A01G174800 chr2A 76.024 659 124 26 1028 1671 133484893 133485532 7.220000e-81 311
2 TraesCS2A01G174800 chr2A 75.538 650 129 19 65 708 133484907 133485532 2.620000e-75 292
3 TraesCS2A01G174800 chr2D 95.072 2719 91 19 3 2687 126946589 126949298 0.000000e+00 4239
4 TraesCS2A01G174800 chr2D 75.889 900 140 51 955 1818 126958540 126959398 3.240000e-104 388
5 TraesCS2A01G174800 chr2D 76.471 680 130 20 65 738 126958614 126959269 2.560000e-90 342
6 TraesCS2A01G174800 chr2B 95.587 1994 69 11 1 1983 180539856 180541841 0.000000e+00 3177
7 TraesCS2A01G174800 chr2B 91.117 698 25 6 2010 2687 180541836 180542516 0.000000e+00 911
8 TraesCS2A01G174800 chr2B 75.806 682 129 23 65 738 180546256 180546909 2.010000e-81 313


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 TraesCS2A01G174800 chr2A 133473054 133475740 2686 False 4963.0 4963 100.000000 1 2687 1 chr2A.!!$F1 2686
1 TraesCS2A01G174800 chr2A 133484893 133485532 639 False 301.5 311 75.781000 65 1671 2 chr2A.!!$F2 1606
2 TraesCS2A01G174800 chr2D 126946589 126949298 2709 False 4239.0 4239 95.072000 3 2687 1 chr2D.!!$F1 2684
3 TraesCS2A01G174800 chr2D 126958540 126959398 858 False 365.0 388 76.180000 65 1818 2 chr2D.!!$F2 1753
4 TraesCS2A01G174800 chr2B 180539856 180546909 7053 False 1467.0 3177 87.503333 1 2687 3 chr2B.!!$F1 2686

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
724 735 3.17205 CCATCGTTCGACTACAAGTGAG 58.828 50.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1838 1.086696 AAATCATTGCCACCTCGTCG 58.913 50.0 0.0 0.0 0.0 5.12 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
363 374 3.790437 CTCTCCATGCGCCAGGGT 61.790 66.667 14.36 0.00 36.61 4.34
684 695 6.016610 AGTCGGAGATATTAGAGAGCTTTGAC 60.017 42.308 0.00 0.00 40.67 3.18
694 705 3.286751 GCTTTGACACGCCCAGCA 61.287 61.111 0.00 0.00 0.00 4.41
724 735 3.172050 CCATCGTTCGACTACAAGTGAG 58.828 50.000 0.00 0.00 0.00 3.51
835 859 5.914898 ATTTATTACTTGGTGTTGAGGCC 57.085 39.130 0.00 0.00 0.00 5.19
908 932 5.821470 TCCTTATATATCAGGGACGATCGAC 59.179 44.000 24.34 16.38 0.00 4.20
1133 1163 1.160137 CACTTTCTCAAGGGCCTTCG 58.840 55.000 17.86 12.36 33.82 3.79
1196 1226 3.664025 CTCGCATGAACGCCCCTCA 62.664 63.158 0.00 0.00 0.00 3.86
1203 1233 3.952628 GAACGCCCCTCAACTCGGG 62.953 68.421 0.00 0.00 42.82 5.14
1254 1284 1.669115 CACCTTCCACTGCACCTCG 60.669 63.158 0.00 0.00 0.00 4.63
1306 1336 2.043604 CTCCATCATAGGTGGCGCCA 62.044 60.000 29.03 29.03 40.61 5.69
1428 1458 3.053291 GCCAACCGATTCGCACCA 61.053 61.111 0.00 0.00 0.00 4.17
1540 1573 2.607750 TGTCCCCTGCAGAGGTCC 60.608 66.667 17.39 7.52 37.73 4.46
1581 1614 1.903404 CTGGTTTGGCGGCCTCTTT 60.903 57.895 21.46 0.00 0.00 2.52
1763 1808 8.751302 TCAGAAAGGTTGTTGTTTTTAAGTTC 57.249 30.769 0.00 0.00 0.00 3.01
1793 1838 6.371825 CACTCCTTGTTTCTGATACTTTACCC 59.628 42.308 0.17 0.00 0.00 3.69
1901 1952 8.911918 TTATTTACTTGTCCATGCCGTATAAT 57.088 30.769 0.00 0.00 0.00 1.28
1910 1961 4.067896 CCATGCCGTATAATCAAGAAGCT 58.932 43.478 0.00 0.00 0.00 3.74
1917 1968 8.988934 TGCCGTATAATCAAGAAGCTTTATTAG 58.011 33.333 0.00 0.00 0.00 1.73
1959 2010 9.844790 TTCAATTACAGAACATGATTGATTGTC 57.155 29.630 0.00 0.00 34.12 3.18
1989 2040 4.523943 AGCTGCTGTGGTTTTATTTCATCA 59.476 37.500 0.00 0.00 0.00 3.07
2000 2051 6.183360 GGTTTTATTTCATCACTCTGAGCTCC 60.183 42.308 12.15 0.00 0.00 4.70
2029 2080 9.529325 GGAAGCTTTTGTGGTTAATTATATTCC 57.471 33.333 0.00 0.00 0.00 3.01
2040 2091 8.644216 TGGTTAATTATATTCCGCTGAGTTCTA 58.356 33.333 0.00 0.00 0.00 2.10
2156 2207 6.062095 CCTGAAGATAATTAACGGACCCATT 58.938 40.000 0.00 0.00 0.00 3.16
2191 2242 2.910479 ATGATGCAGCGCCATGGG 60.910 61.111 15.13 4.77 0.00 4.00
2329 2397 6.627395 TGTTGGTTTATTAGTGGTGAGTTG 57.373 37.500 0.00 0.00 0.00 3.16
2373 2441 2.242043 CTGGTTGTTCTTCTGGCCAAT 58.758 47.619 7.01 0.00 0.00 3.16
2401 2471 8.556213 AACATCTCAAAATAAAGCATTTGCAT 57.444 26.923 5.20 0.00 45.16 3.96
2519 2589 7.180229 TGTCCTACTCCATTTGAGAACTCATAA 59.820 37.037 5.34 4.21 44.42 1.90
2531 2601 7.351414 TGAGAACTCATAAATCTGTGTTTCG 57.649 36.000 0.00 0.00 34.11 3.46
2635 2705 8.545229 ACTGAATTATTTCTTCTGACAGACAG 57.455 34.615 4.15 7.63 38.98 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.506061 CCCATCTCCTCCTCCTGCG 61.506 68.421 0.00 0.00 0.00 5.18
564 575 3.827898 GAGCTCCCGACCTCCACG 61.828 72.222 0.87 0.00 0.00 4.94
653 664 3.483421 TCTAATATCTCCGACTTGCCGA 58.517 45.455 0.00 0.00 0.00 5.54
684 695 3.076258 TATCGGAGTGCTGGGCGTG 62.076 63.158 0.00 0.00 0.00 5.34
835 859 2.101770 GACTCCTAACCGCGGACG 59.898 66.667 35.90 18.67 39.67 4.79
1133 1163 1.800681 GCACCATTGGGCGAGTTAC 59.199 57.895 7.78 0.00 37.90 2.50
1203 1233 2.270986 CCACACAGCAAAGCTCCCC 61.271 63.158 0.00 0.00 36.40 4.81
1230 1260 1.963515 GTGCAGTGGAAGGTGGAAAAT 59.036 47.619 0.00 0.00 0.00 1.82
1306 1336 0.545548 GAGAGAACCCCTCCAGTGGT 60.546 60.000 9.54 0.00 42.97 4.16
1318 1348 1.817099 CCTGCCGCATGGAGAGAAC 60.817 63.158 0.00 0.00 37.49 3.01
1339 1369 1.001641 AGCGGCCAGAAGCTTTGAT 60.002 52.632 2.24 0.00 41.52 2.57
1367 1397 3.799755 CGAGGAAAAAGCCGCCCG 61.800 66.667 0.00 0.00 0.00 6.13
1419 1449 0.745845 GGAGCATCTGTGGTGCGAAT 60.746 55.000 0.00 0.00 46.86 3.34
1476 1506 0.179026 CACCTCCTCCCGTCGAGATA 60.179 60.000 0.00 0.00 41.63 1.98
1484 1514 3.787001 GGAAGCCACCTCCTCCCG 61.787 72.222 0.00 0.00 0.00 5.14
1540 1573 2.435586 CCCACTGCTTGAGCTCGG 60.436 66.667 9.64 5.68 42.66 4.63
1581 1614 2.030027 TCTTCTCCTCCTTCTTGCCA 57.970 50.000 0.00 0.00 0.00 4.92
1615 1651 4.152647 TCTAATATCTCCGACATGCCAGT 58.847 43.478 0.00 0.00 0.00 4.00
1747 1788 7.090953 AGTGGATCGAACTTAAAAACAACAA 57.909 32.000 0.00 0.00 0.00 2.83
1763 1808 3.319137 TCAGAAACAAGGAGTGGATCG 57.681 47.619 0.00 0.00 0.00 3.69
1793 1838 1.086696 AAATCATTGCCACCTCGTCG 58.913 50.000 0.00 0.00 0.00 5.12
1828 1874 3.201290 ACTCAGCGGCAGAATCATTTAG 58.799 45.455 1.45 0.00 0.00 1.85
1917 1968 9.294030 CTGTAATTGAATTCTGTAATTGGAAGC 57.706 33.333 7.05 0.00 35.41 3.86
1927 1978 9.850628 CAATCATGTTCTGTAATTGAATTCTGT 57.149 29.630 7.05 0.00 30.64 3.41
1933 1984 9.844790 GACAATCAATCATGTTCTGTAATTGAA 57.155 29.630 7.55 0.00 39.15 2.69
1934 1985 8.177013 CGACAATCAATCATGTTCTGTAATTGA 58.823 33.333 6.28 6.28 39.78 2.57
1959 2010 7.421530 AATAAAACCACAGCAGCTATATACG 57.578 36.000 0.00 0.00 0.00 3.06
1989 2040 1.319614 GCTTCCTCGGAGCTCAGAGT 61.320 60.000 32.83 0.00 36.62 3.24
2000 2051 4.766404 ATTAACCACAAAAGCTTCCTCG 57.234 40.909 0.00 0.00 0.00 4.63
2029 2080 2.645802 AGTAGGAGGTAGAACTCAGCG 58.354 52.381 0.00 0.00 39.27 5.18
2040 2091 2.112279 TTGTGGTGGAAGTAGGAGGT 57.888 50.000 0.00 0.00 0.00 3.85
2156 2207 5.302568 GCATCATCAAAAATATGGTCTGGGA 59.697 40.000 0.00 0.00 0.00 4.37
2191 2242 4.081050 GGCAGAACCTCCCACAAC 57.919 61.111 0.00 0.00 34.51 3.32
2329 2397 5.050295 GCTTATAAACGGACAGCCATAGAAC 60.050 44.000 0.00 0.00 0.00 3.01
2373 2441 8.497554 GCAAATGCTTTATTTTGAGATGTTTCA 58.502 29.630 0.00 0.00 36.87 2.69
2519 2589 4.695455 CCCTATCACAACGAAACACAGATT 59.305 41.667 0.00 0.00 0.00 2.40
2531 2601 8.691661 ATATTTACCATGTTCCCTATCACAAC 57.308 34.615 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.