Multiple sequence alignment - TraesCS3D01G156800

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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 TraesCS3D01G156800 chr3D 100.000 2404 0 0 1 2404 124495744 124493341 0.000000e+00 4440.0
1 TraesCS3D01G156800 chr2B 96.363 1677 59 1 728 2404 632565 634239 0.000000e+00 2758.0
2 TraesCS3D01G156800 chr2B 94.395 1677 75 5 728 2404 488702544 488704201 0.000000e+00 2558.0
3 TraesCS3D01G156800 chr2B 95.735 680 26 3 1 680 631890 632566 0.000000e+00 1092.0
4 TraesCS3D01G156800 chr2B 95.328 685 28 3 1 683 488701866 488702548 0.000000e+00 1085.0
5 TraesCS3D01G156800 chr4A 96.305 1678 61 1 728 2404 622162095 622163772 0.000000e+00 2754.0
6 TraesCS3D01G156800 chr4A 95.882 680 22 3 1 680 622161423 622162096 0.000000e+00 1096.0
7 TraesCS3D01G156800 chr4A 88.235 323 31 3 1980 2297 716535122 716534802 1.740000e-101 379.0
8 TraesCS3D01G156800 chr4A 96.970 33 1 0 2372 2404 726216881 726216913 3.340000e-04 56.5
9 TraesCS3D01G156800 chr1A 96.112 1672 62 3 734 2404 143378231 143376562 0.000000e+00 2724.0
10 TraesCS3D01G156800 chr1A 96.102 1103 41 2 731 1832 480975273 480974172 0.000000e+00 1797.0
11 TraesCS3D01G156800 chr1A 94.729 683 33 3 1 683 143378912 143378233 0.000000e+00 1059.0
12 TraesCS3D01G156800 chr1A 94.729 683 33 3 1 683 480975951 480975272 0.000000e+00 1059.0
13 TraesCS3D01G156800 chr1A 100.000 47 0 0 684 730 238128647 238128601 1.180000e-13 87.9
14 TraesCS3D01G156800 chr1A 98.000 50 1 0 681 730 416424446 416424495 1.180000e-13 87.9
15 TraesCS3D01G156800 chr7A 95.761 1675 69 2 731 2404 346768861 346767188 0.000000e+00 2699.0
16 TraesCS3D01G156800 chr7A 95.168 683 31 2 1 683 346769540 346768860 0.000000e+00 1077.0
17 TraesCS3D01G156800 chr7B 96.082 536 19 2 1 536 511463850 511463317 0.000000e+00 872.0
18 TraesCS3D01G156800 chrUn 88.964 444 32 8 3 444 53051295 53050867 1.270000e-147 532.0
19 TraesCS3D01G156800 chrUn 88.976 254 22 2 1912 2159 402215522 402215775 2.320000e-80 309.0
20 TraesCS3D01G156800 chrUn 89.189 74 4 1 1837 1910 333864591 333864660 3.290000e-14 89.8
21 TraesCS3D01G156800 chrUn 89.189 74 4 1 1837 1910 388630247 388630316 3.290000e-14 89.8
22 TraesCS3D01G156800 chrUn 100.000 47 0 0 684 730 86462355 86462309 1.180000e-13 87.9
23 TraesCS3D01G156800 chrUn 98.000 50 1 0 681 730 222672916 222672965 1.180000e-13 87.9
24 TraesCS3D01G156800 chrUn 98.000 50 1 0 681 730 229496244 229496293 1.180000e-13 87.9
25 TraesCS3D01G156800 chrUn 92.000 50 4 0 2355 2404 402215831 402215880 1.190000e-08 71.3
26 TraesCS3D01G156800 chr1B 90.617 373 30 5 1 373 200035716 200035349 7.720000e-135 490.0
27 TraesCS3D01G156800 chr1B 98.000 50 1 0 681 730 135111075 135111124 1.180000e-13 87.9
28 TraesCS3D01G156800 chr1B 98.000 50 1 0 681 730 638758338 638758387 1.180000e-13 87.9
29 TraesCS3D01G156800 chr5A 88.024 334 31 2 1837 2165 219128348 219128677 1.040000e-103 387.0
30 TraesCS3D01G156800 chr5A 92.000 50 4 0 2355 2404 208947633 208947682 1.190000e-08 71.3
31 TraesCS3D01G156800 chr5A 94.444 36 1 1 1482 1517 704455081 704455047 1.000000e-03 54.7
32 TraesCS3D01G156800 chr3B 88.699 292 20 2 1859 2137 462621384 462621093 6.360000e-91 344.0
33 TraesCS3D01G156800 chr5D 100.000 47 0 0 684 730 324464433 324464387 1.180000e-13 87.9
34 TraesCS3D01G156800 chr4D 100.000 47 0 0 684 730 123438155 123438109 1.180000e-13 87.9


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 TraesCS3D01G156800 chr3D 124493341 124495744 2403 True 4440.0 4440 100.0000 1 2404 1 chr3D.!!$R1 2403
1 TraesCS3D01G156800 chr2B 631890 634239 2349 False 1925.0 2758 96.0490 1 2404 2 chr2B.!!$F1 2403
2 TraesCS3D01G156800 chr2B 488701866 488704201 2335 False 1821.5 2558 94.8615 1 2404 2 chr2B.!!$F2 2403
3 TraesCS3D01G156800 chr4A 622161423 622163772 2349 False 1925.0 2754 96.0935 1 2404 2 chr4A.!!$F2 2403
4 TraesCS3D01G156800 chr1A 143376562 143378912 2350 True 1891.5 2724 95.4205 1 2404 2 chr1A.!!$R2 2403
5 TraesCS3D01G156800 chr1A 480974172 480975951 1779 True 1428.0 1797 95.4155 1 1832 2 chr1A.!!$R3 1831
6 TraesCS3D01G156800 chr7A 346767188 346769540 2352 True 1888.0 2699 95.4645 1 2404 2 chr7A.!!$R1 2403
7 TraesCS3D01G156800 chr7B 511463317 511463850 533 True 872.0 872 96.0820 1 536 1 chr7B.!!$R1 535

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
95 98 3.494626 ACTATGACATTCCTAAATGCGCG 59.505 43.478 0.0 0.0 45.16 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2101 0.674534 ACACAGAACTGTCCCGAGAC 59.325 55.0 4.38 0.0 42.83 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
95 98 3.494626 ACTATGACATTCCTAAATGCGCG 59.505 43.478 0.00 0.00 45.16 6.86
118 121 6.376978 CGAGTAAATACTACTGGGATTACGG 58.623 44.000 0.00 0.00 36.50 4.02
122 125 6.736110 AAATACTACTGGGATTACGGCTAA 57.264 37.500 0.00 0.00 0.00 3.09
168 172 5.880341 AGCAATTCTCGGTTTAAATACTGC 58.120 37.500 0.00 0.00 0.00 4.40
175 183 4.746729 TCGGTTTAAATACTGCGAGCTTA 58.253 39.130 0.00 0.00 0.00 3.09
176 184 5.170021 TCGGTTTAAATACTGCGAGCTTAA 58.830 37.500 0.00 0.00 0.00 1.85
177 185 5.638657 TCGGTTTAAATACTGCGAGCTTAAA 59.361 36.000 0.00 0.00 0.00 1.52
178 186 6.314400 TCGGTTTAAATACTGCGAGCTTAAAT 59.686 34.615 0.00 0.00 0.00 1.40
261 273 6.319658 ACTGCACATTCTGAAAGTATATTGGG 59.680 38.462 0.00 0.00 33.76 4.12
560 573 3.755378 AGCTCCATTTTGTCTTGCTACAG 59.245 43.478 0.00 0.00 0.00 2.74
690 703 8.801715 TCTTCATTTCTACAACTTCATTTTGC 57.198 30.769 0.00 0.00 0.00 3.68
691 704 8.412456 TCTTCATTTCTACAACTTCATTTTGCA 58.588 29.630 0.00 0.00 0.00 4.08
692 705 8.939201 TTCATTTCTACAACTTCATTTTGCAA 57.061 26.923 0.00 0.00 0.00 4.08
693 706 9.545105 TTCATTTCTACAACTTCATTTTGCAAT 57.455 25.926 0.00 0.00 0.00 3.56
696 709 9.979578 ATTTCTACAACTTCATTTTGCAATACA 57.020 25.926 0.00 0.00 0.00 2.29
697 710 9.809096 TTTCTACAACTTCATTTTGCAATACAA 57.191 25.926 0.00 0.00 36.13 2.41
698 711 9.809096 TTCTACAACTTCATTTTGCAATACAAA 57.191 25.926 0.00 0.00 46.51 2.83
727 740 7.818997 AGATCACTATTATTACGAGTGGTGA 57.181 36.000 0.00 0.00 40.81 4.02
728 741 8.234136 AGATCACTATTATTACGAGTGGTGAA 57.766 34.615 0.00 0.00 40.81 3.18
729 742 8.692710 AGATCACTATTATTACGAGTGGTGAAA 58.307 33.333 0.00 0.00 40.81 2.69
934 948 6.124088 AGTTTGATATTTTTCTAGGCGCAG 57.876 37.500 10.83 0.00 0.00 5.18
1250 1264 1.000955 ACCGACCTCATATTGGATCGC 59.999 52.381 0.00 0.00 31.65 4.58
1283 1297 2.098117 CAGGATTCTTGTGGCGAATTCC 59.902 50.000 0.00 0.00 31.62 3.01
1287 1301 2.559698 TCTTGTGGCGAATTCCTGAA 57.440 45.000 0.00 0.00 0.00 3.02
1288 1302 2.426522 TCTTGTGGCGAATTCCTGAAG 58.573 47.619 0.00 0.00 0.00 3.02
2030 2048 2.495155 TGCATACTGTGGAAGCACAT 57.505 45.000 0.00 0.00 34.25 3.21
2078 2096 1.077644 CTGCTCCATTCTGGCAGCT 60.078 57.895 10.34 0.00 45.04 4.24
2083 2101 0.035725 TCCATTCTGGCAGCTGTGAG 60.036 55.000 16.64 11.44 37.47 3.51
2118 2136 1.355381 TGTGTGGCCTTGGATCAATCT 59.645 47.619 3.32 0.00 0.00 2.40
2165 2183 6.263168 CCCATTCTCTTTACATGACCCAATAC 59.737 42.308 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 83 4.530094 TTTACTCGCGCATTTAGGAATG 57.470 40.909 8.75 0.00 44.42 2.67
95 98 6.015603 AGCCGTAATCCCAGTAGTATTTACTC 60.016 42.308 0.00 0.00 37.73 2.59
168 172 6.535508 AGTTTAGCTCCTGTTATTTAAGCTCG 59.464 38.462 0.00 0.00 42.10 5.03
261 273 0.681243 AATTTCCCGAGGGCAAGAGC 60.681 55.000 2.58 0.00 41.10 4.09
566 579 2.938354 CTGAACCACTCAGGCAAGG 58.062 57.895 0.00 0.00 46.89 3.61
574 587 0.836400 TCCTGACCCCTGAACCACTC 60.836 60.000 0.00 0.00 0.00 3.51
701 714 9.346005 TCACCACTCGTAATAATAGTGATCTTA 57.654 33.333 3.37 0.00 42.59 2.10
702 715 8.234136 TCACCACTCGTAATAATAGTGATCTT 57.766 34.615 3.37 0.00 42.59 2.40
703 716 7.818997 TCACCACTCGTAATAATAGTGATCT 57.181 36.000 3.37 0.00 42.59 2.75
704 717 8.867112 TTTCACCACTCGTAATAATAGTGATC 57.133 34.615 3.37 0.00 42.59 2.92
705 718 9.832445 AATTTCACCACTCGTAATAATAGTGAT 57.168 29.630 3.37 0.00 42.59 3.06
706 719 9.661563 AAATTTCACCACTCGTAATAATAGTGA 57.338 29.630 3.37 0.00 42.59 3.41
711 724 9.840427 CAAGAAAATTTCACCACTCGTAATAAT 57.160 29.630 8.55 0.00 0.00 1.28
712 725 8.842280 ACAAGAAAATTTCACCACTCGTAATAA 58.158 29.630 8.55 0.00 0.00 1.40
713 726 8.385898 ACAAGAAAATTTCACCACTCGTAATA 57.614 30.769 8.55 0.00 0.00 0.98
714 727 7.012894 TGACAAGAAAATTTCACCACTCGTAAT 59.987 33.333 8.55 0.00 0.00 1.89
715 728 6.316640 TGACAAGAAAATTTCACCACTCGTAA 59.683 34.615 8.55 0.00 0.00 3.18
716 729 5.818336 TGACAAGAAAATTTCACCACTCGTA 59.182 36.000 8.55 0.00 0.00 3.43
717 730 4.638421 TGACAAGAAAATTTCACCACTCGT 59.362 37.500 8.55 0.00 0.00 4.18
718 731 5.168526 TGACAAGAAAATTTCACCACTCG 57.831 39.130 8.55 0.00 0.00 4.18
719 732 7.202526 TCATTGACAAGAAAATTTCACCACTC 58.797 34.615 8.55 0.00 0.00 3.51
720 733 7.111247 TCATTGACAAGAAAATTTCACCACT 57.889 32.000 8.55 0.00 0.00 4.00
721 734 7.492344 AGTTCATTGACAAGAAAATTTCACCAC 59.508 33.333 8.55 0.00 0.00 4.16
722 735 7.555087 AGTTCATTGACAAGAAAATTTCACCA 58.445 30.769 8.55 0.00 0.00 4.17
723 736 8.424274 AAGTTCATTGACAAGAAAATTTCACC 57.576 30.769 8.55 0.00 0.00 4.02
727 740 9.030301 CCGTAAAGTTCATTGACAAGAAAATTT 57.970 29.630 12.45 12.45 0.00 1.82
728 741 7.169140 GCCGTAAAGTTCATTGACAAGAAAATT 59.831 33.333 0.00 0.00 0.00 1.82
729 742 6.640907 GCCGTAAAGTTCATTGACAAGAAAAT 59.359 34.615 0.00 0.00 0.00 1.82
1250 1264 6.201517 CACAAGAATCCTGTACAAAACACTG 58.798 40.000 0.00 0.00 33.45 3.66
1529 1546 0.901114 TAGGTGCAGCTACGACCCAA 60.901 55.000 21.35 0.00 0.00 4.12
1926 1944 8.581263 CAGTGCTATTCTTTTCGATTCAAATTG 58.419 33.333 0.00 0.00 0.00 2.32
2025 2043 4.062677 ACCATGAATATTTGCCATGTGC 57.937 40.909 12.24 0.00 36.77 4.57
2030 2048 9.814899 CATTTAGTTAACCATGAATATTTGCCA 57.185 29.630 0.88 0.00 0.00 4.92
2045 2063 5.818136 TGGAGCAGATGCATTTAGTTAAC 57.182 39.130 0.00 0.00 45.16 2.01
2078 2096 0.959553 GAACTGTCCCGAGACTCACA 59.040 55.000 2.82 0.00 43.91 3.58
2083 2101 0.674534 ACACAGAACTGTCCCGAGAC 59.325 55.000 4.38 0.00 42.83 3.36
2118 2136 4.458989 GGCAGATAACACCAATCAGTTCAA 59.541 41.667 0.00 0.00 0.00 2.69
2165 2183 4.802039 CAGCCAAAGCAGCTACAAATATTG 59.198 41.667 0.00 0.00 43.56 1.90
2184 2204 5.403466 GTGAAACAAACAATTCATCTCAGCC 59.597 40.000 0.00 0.00 37.82 4.85


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

AutoCloner maintained by Alex Coulton.