Multiple sequence alignment - TraesCS2D01G165800

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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 TraesCS2D01G165800 chr2D 100.000 2207 0 0 1 2207 109901090 109903296 0.000000e+00 4076.0
1 TraesCS2D01G165800 chr2D 85.075 670 44 22 1 667 109792604 109793220 1.110000e-177 632.0
2 TraesCS2D01G165800 chr2D 90.238 420 33 7 931 1347 109793374 109793788 1.930000e-150 542.0
3 TraesCS2D01G165800 chr2D 87.404 389 33 10 931 1310 109737600 109737981 1.210000e-117 433.0
4 TraesCS2D01G165800 chr2D 85.870 368 40 6 931 1294 109830840 109831199 4.450000e-102 381.0
5 TraesCS2D01G165800 chr2D 84.755 387 37 11 1361 1725 109796122 109796508 3.460000e-98 368.0
6 TraesCS2D01G165800 chr2D 89.941 169 14 2 326 492 109736928 109737095 4.770000e-52 215.0
7 TraesCS2D01G165800 chr2D 82.143 84 13 2 1873 1955 585659310 585659392 1.090000e-08 71.3
8 TraesCS2D01G165800 chr2B 95.062 1377 41 13 858 2207 159318981 159320357 0.000000e+00 2141.0
9 TraesCS2D01G165800 chr2B 91.551 864 55 7 15 861 159318061 159318923 0.000000e+00 1175.0
10 TraesCS2D01G165800 chr2B 85.273 421 47 12 270 679 159299411 159299827 9.420000e-114 420.0
11 TraesCS2D01G165800 chr2B 86.269 386 41 8 931 1310 159300170 159300549 2.040000e-110 409.0
12 TraesCS2D01G165800 chr2A 93.962 1209 40 12 718 1897 105541035 105542239 0.000000e+00 1797.0
13 TraesCS2D01G165800 chr2A 94.792 672 33 2 9 679 105540359 105541029 0.000000e+00 1046.0
14 TraesCS2D01G165800 chr2A 95.604 273 10 2 1937 2207 105542229 105542501 9.360000e-119 436.0
15 TraesCS2D01G165800 chr2A 88.251 366 30 7 931 1292 105531793 105532149 2.030000e-115 425.0
16 TraesCS2D01G165800 chr2A 84.257 451 49 12 237 667 105531049 105531497 9.420000e-114 420.0
17 TraesCS2D01G165800 chr2A 86.207 377 47 4 931 1307 105522787 105523158 9.490000e-109 403.0
18 TraesCS2D01G165800 chr3B 79.255 188 26 9 1774 1957 718347527 718347705 3.850000e-23 119.0
19 TraesCS2D01G165800 chr7D 79.487 156 25 6 1806 1957 152114743 152114895 1.080000e-18 104.0
20 TraesCS2D01G165800 chr3A 83.721 86 14 0 1854 1939 594521542 594521457 5.050000e-12 82.4
21 TraesCS2D01G165800 chr5A 75.000 196 37 11 1762 1950 633533509 633533699 1.820000e-11 80.5
22 TraesCS2D01G165800 chr5D 78.862 123 21 5 1838 1958 289348447 289348566 6.530000e-11 78.7
23 TraesCS2D01G165800 chr1A 85.897 78 6 5 1883 1959 84019521 84019448 6.530000e-11 78.7
24 TraesCS2D01G165800 chr6A 79.798 99 18 2 1861 1958 560193282 560193379 1.090000e-08 71.3


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 TraesCS2D01G165800 chr2D 109901090 109903296 2206 False 4076.0 4076 100.000000 1 2207 1 chr2D.!!$F2 2206
1 TraesCS2D01G165800 chr2D 109792604 109796508 3904 False 514.0 632 86.689333 1 1725 3 chr2D.!!$F5 1724
2 TraesCS2D01G165800 chr2D 109736928 109737981 1053 False 324.0 433 88.672500 326 1310 2 chr2D.!!$F4 984
3 TraesCS2D01G165800 chr2B 159318061 159320357 2296 False 1658.0 2141 93.306500 15 2207 2 chr2B.!!$F2 2192
4 TraesCS2D01G165800 chr2B 159299411 159300549 1138 False 414.5 420 85.771000 270 1310 2 chr2B.!!$F1 1040
5 TraesCS2D01G165800 chr2A 105540359 105542501 2142 False 1093.0 1797 94.786000 9 2207 3 chr2A.!!$F3 2198
6 TraesCS2D01G165800 chr2A 105531049 105532149 1100 False 422.5 425 86.254000 237 1292 2 chr2A.!!$F2 1055

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
919 1215 0.249868 TCGAGTTGTGACCAAGGCTG 60.25 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 4454 0.89832 CCTGGGTACACTCCACTGAG 59.102 60.0 0.0 0.0 44.62 3.35 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
55 56 2.399611 GCGCCGCATCACTTGTAC 59.600 61.111 3.15 0.00 0.00 2.90
74 75 0.526211 CGGAAGACGGTCTCATGTCA 59.474 55.000 11.71 0.00 37.58 3.58
136 137 6.233905 ACTTAACAGCCAAGAAACCAAAAT 57.766 33.333 0.00 0.00 0.00 1.82
177 200 3.529533 CTGCACTCCTCGATCAGATTTT 58.470 45.455 0.00 0.00 0.00 1.82
186 209 5.357878 TCCTCGATCAGATTTTGGATTTTGG 59.642 40.000 0.00 0.00 0.00 3.28
420 458 7.715657 TGAAAAGTTGACAATAGCAACATCTT 58.284 30.769 0.00 0.00 46.05 2.40
543 677 3.553511 CCGCTTCATCAAGACATCTACAC 59.446 47.826 0.00 0.00 0.00 2.90
547 688 5.728471 CTTCATCAAGACATCTACACCTGT 58.272 41.667 0.00 0.00 0.00 4.00
692 837 8.692710 TGACCTATCATTTAGTGATCTAAACGT 58.307 33.333 0.00 0.00 44.23 3.99
816 965 9.987272 CCATTTCCTTTCTTTCCATATTATTCC 57.013 33.333 0.00 0.00 0.00 3.01
839 1030 8.536340 TCCTTATCTTCTCCTTTTCTACTACC 57.464 38.462 0.00 0.00 0.00 3.18
919 1215 0.249868 TCGAGTTGTGACCAAGGCTG 60.250 55.000 0.00 0.00 0.00 4.85
961 1285 1.202639 TGATGTTGACCACGAAGCACT 60.203 47.619 0.00 0.00 0.00 4.40
962 1286 1.873591 GATGTTGACCACGAAGCACTT 59.126 47.619 0.00 0.00 0.00 3.16
1247 1587 2.762327 ACTGGAATAAAAGCCCATGCAG 59.238 45.455 0.00 0.00 41.13 4.41
1292 1632 1.802508 GCCGAACAAATAAGCATGGGC 60.803 52.381 0.00 0.00 41.61 5.36
1754 4454 8.283291 CCATGTCAACAAAAAGTACTACTTCTC 58.717 37.037 0.00 0.00 37.47 2.87
1823 4523 6.428159 CCTCCCGAACAATCCATAGATTTTAG 59.572 42.308 0.00 0.00 40.89 1.85
1910 4610 9.806203 TCATATATTCAAATTCCTTGCAACAAG 57.194 29.630 0.00 0.24 34.76 3.16
1911 4611 9.806203 CATATATTCAAATTCCTTGCAACAAGA 57.194 29.630 8.87 0.00 34.76 3.02
1913 4613 8.937634 ATATTCAAATTCCTTGCAACAAGATC 57.062 30.769 8.87 0.00 34.76 2.75
1914 4614 6.409524 TTCAAATTCCTTGCAACAAGATCT 57.590 33.333 8.87 0.00 34.76 2.75
1915 4615 6.409524 TCAAATTCCTTGCAACAAGATCTT 57.590 33.333 0.88 0.88 34.76 2.40
1916 4616 6.819284 TCAAATTCCTTGCAACAAGATCTTT 58.181 32.000 4.86 0.00 34.76 2.52
1917 4617 7.950512 TCAAATTCCTTGCAACAAGATCTTTA 58.049 30.769 4.86 0.00 34.76 1.85
1918 4618 8.084073 TCAAATTCCTTGCAACAAGATCTTTAG 58.916 33.333 4.86 0.00 34.76 1.85
1919 4619 7.765695 AATTCCTTGCAACAAGATCTTTAGA 57.234 32.000 4.86 0.00 0.00 2.10
1920 4620 7.765695 ATTCCTTGCAACAAGATCTTTAGAA 57.234 32.000 4.86 1.19 0.00 2.10
1921 4621 6.560253 TCCTTGCAACAAGATCTTTAGAAC 57.440 37.500 4.86 0.00 0.00 3.01
1922 4622 6.061441 TCCTTGCAACAAGATCTTTAGAACA 58.939 36.000 4.86 0.00 0.00 3.18
1923 4623 6.545666 TCCTTGCAACAAGATCTTTAGAACAA 59.454 34.615 4.86 6.40 0.00 2.83
1924 4624 6.860023 CCTTGCAACAAGATCTTTAGAACAAG 59.140 38.462 18.93 18.93 0.00 3.16
1925 4625 7.255242 CCTTGCAACAAGATCTTTAGAACAAGA 60.255 37.037 23.53 0.00 37.20 3.02
1926 4626 7.750229 TGCAACAAGATCTTTAGAACAAGAT 57.250 32.000 4.86 0.00 44.70 2.40
2095 4846 9.734620 TGTCTTGTTAATTCAAAATGAGTGAAG 57.265 29.630 0.00 0.00 38.34 3.02
2096 4847 8.694394 GTCTTGTTAATTCAAAATGAGTGAAGC 58.306 33.333 0.00 0.00 38.34 3.86
2137 4891 4.580167 TGAACCAGTTCTTGAAATGACTGG 59.420 41.667 17.28 17.28 41.06 4.00
2202 4956 6.698766 AGTGAAATGATTTTCTGTTGTTGAGC 59.301 34.615 0.00 0.00 41.54 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.741706 GACATGAGACCGTCTTCCGTA 59.258 52.381 1.71 0.00 33.66 4.02
55 56 0.526211 TGACATGAGACCGTCTTCCG 59.474 55.000 1.71 0.00 33.18 4.30
74 75 2.758979 AGTCGGTTTAGATCGTGATGGT 59.241 45.455 0.00 0.00 0.00 3.55
136 137 5.994054 TGCAGCTTTGTTTTGCCATTTTATA 59.006 32.000 0.00 0.00 37.03 0.98
177 200 3.066064 CGTGAATAATCCGCCAAAATCCA 59.934 43.478 0.00 0.00 0.00 3.41
186 209 3.308595 TGACATGTTCGTGAATAATCCGC 59.691 43.478 0.00 0.00 0.00 5.54
420 458 1.946081 ACACATTCACGTGCATGTTCA 59.054 42.857 27.60 0.00 40.73 3.18
543 677 1.875963 CACCGGCTTGCTTTACAGG 59.124 57.895 0.00 0.00 0.00 4.00
622 763 3.368531 CGGATCTTCTCGAAAAAGAGGGT 60.369 47.826 13.50 0.49 36.27 4.34
816 965 9.810545 CTTGGTAGTAGAAAAGGAGAAGATAAG 57.189 37.037 0.00 0.00 0.00 1.73
839 1030 8.709386 ATTTGTACAGTATTAGCAGTCTCTTG 57.291 34.615 0.00 0.00 0.00 3.02
919 1215 6.913170 TCAGGCAAATGAATACTCAACTTTC 58.087 36.000 0.00 0.00 34.49 2.62
1247 1587 2.457366 AACTGGACGATGTTGAGACC 57.543 50.000 0.00 0.00 0.00 3.85
1708 4408 1.994916 CCCCATTCAACGCACATTTC 58.005 50.000 0.00 0.00 0.00 2.17
1754 4454 0.898320 CCTGGGTACACTCCACTGAG 59.102 60.000 0.00 0.00 44.62 3.35
1888 4588 8.755977 AGATCTTGTTGCAAGGAATTTGAATAT 58.244 29.630 0.00 0.00 39.21 1.28
1889 4589 8.125978 AGATCTTGTTGCAAGGAATTTGAATA 57.874 30.769 0.00 0.00 39.21 1.75
1890 4590 7.001099 AGATCTTGTTGCAAGGAATTTGAAT 57.999 32.000 0.00 0.00 39.21 2.57
1891 4591 6.409524 AGATCTTGTTGCAAGGAATTTGAA 57.590 33.333 0.00 0.00 39.21 2.69
1892 4592 6.409524 AAGATCTTGTTGCAAGGAATTTGA 57.590 33.333 7.30 0.00 39.21 2.69
1893 4593 8.084073 TCTAAAGATCTTGTTGCAAGGAATTTG 58.916 33.333 9.17 0.00 39.88 2.32
1894 4594 8.181904 TCTAAAGATCTTGTTGCAAGGAATTT 57.818 30.769 9.17 7.39 0.00 1.82
1895 4595 7.765695 TCTAAAGATCTTGTTGCAAGGAATT 57.234 32.000 9.17 0.01 0.00 2.17
1896 4596 7.231317 TGTTCTAAAGATCTTGTTGCAAGGAAT 59.769 33.333 9.17 0.00 0.00 3.01
1897 4597 6.545666 TGTTCTAAAGATCTTGTTGCAAGGAA 59.454 34.615 9.17 0.00 0.00 3.36
1898 4598 6.061441 TGTTCTAAAGATCTTGTTGCAAGGA 58.939 36.000 9.17 0.00 0.00 3.36
1899 4599 6.317789 TGTTCTAAAGATCTTGTTGCAAGG 57.682 37.500 9.17 0.00 0.00 3.61
1900 4600 7.642669 TCTTGTTCTAAAGATCTTGTTGCAAG 58.357 34.615 21.35 21.35 31.19 4.01
1901 4601 7.566760 TCTTGTTCTAAAGATCTTGTTGCAA 57.433 32.000 9.17 9.91 31.19 4.08
1902 4602 7.750229 ATCTTGTTCTAAAGATCTTGTTGCA 57.250 32.000 9.17 2.59 42.01 4.08
2109 4862 5.296780 TCATTTCAAGAACTGGTTCACTCAC 59.703 40.000 14.67 0.00 41.84 3.51


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

AutoCloner maintained by Alex Coulton.