Multiple sequence alignment - TraesCS6D01G347900

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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 TraesCS6D01G347900 chr6D 100.000 2853 0 0 1 2853 446392581 446389729 0.000000e+00 5269.0
1 TraesCS6D01G347900 chr6D 96.714 1278 37 4 1578 2853 452663082 452664356 0.000000e+00 2122.0
2 TraesCS6D01G347900 chr6D 92.991 856 34 5 903 1733 452662356 452663210 0.000000e+00 1225.0
3 TraesCS6D01G347900 chr6D 89.796 98 10 0 69 166 46527227 46527130 2.980000e-25 126.0
4 TraesCS6D01G347900 chr6D 91.209 91 8 0 69 159 452662268 452662358 1.070000e-24 124.0
5 TraesCS6D01G347900 chr6D 89.873 79 8 0 70 148 75486495 75486573 5.030000e-18 102.0
6 TraesCS6D01G347900 chr6D 100.000 49 0 0 607 655 446391916 446391868 1.090000e-14 91.6
7 TraesCS6D01G347900 chr6D 100.000 49 0 0 666 714 446391975 446391927 1.090000e-14 91.6
8 TraesCS6D01G347900 chr6D 97.959 49 1 0 27 75 452662117 452662165 5.060000e-13 86.1
9 TraesCS6D01G347900 chr6D 93.182 44 3 0 235 278 446392227 446392184 6.600000e-07 65.8
10 TraesCS6D01G347900 chr6D 100.000 34 0 0 861 894 452662070 452662103 2.370000e-06 63.9
11 TraesCS6D01G347900 chr6D 94.595 37 2 0 858 894 452661951 452661987 1.100000e-04 58.4
12 TraesCS6D01G347900 chr7D 95.506 1958 72 12 903 2853 51245752 51243804 0.000000e+00 3114.0
13 TraesCS6D01G347900 chr7D 94.257 1985 77 20 903 2853 79219491 79221472 0.000000e+00 3000.0
14 TraesCS6D01G347900 chr7D 92.308 91 7 0 69 159 103532529 103532619 2.310000e-26 130.0
15 TraesCS6D01G347900 chr7D 92.188 64 5 0 7 70 228427503 228427440 1.090000e-14 91.6
16 TraesCS6D01G347900 chr7D 97.917 48 1 0 28 75 51245990 51245943 1.820000e-12 84.2
17 TraesCS6D01G347900 chr7D 85.897 78 10 1 527 603 418723869 418723792 6.550000e-12 82.4
18 TraesCS6D01G347900 chr7D 95.918 49 2 0 27 75 79219252 79219300 2.360000e-11 80.5
19 TraesCS6D01G347900 chr4D 93.273 1977 92 13 902 2848 222629957 222627992 0.000000e+00 2876.0
20 TraesCS6D01G347900 chr4D 90.816 98 9 0 69 166 222630044 222629947 6.410000e-27 132.0
21 TraesCS6D01G347900 chr4D 89.691 97 10 0 69 165 236680816 236680720 1.070000e-24 124.0
22 TraesCS6D01G347900 chr5D 93.938 1897 80 21 982 2846 364022595 364020702 0.000000e+00 2833.0
23 TraesCS6D01G347900 chr5D 94.692 1752 71 8 1 1733 384519794 384518046 0.000000e+00 2700.0
24 TraesCS6D01G347900 chr5D 96.319 1277 43 3 1578 2853 384518147 384516874 0.000000e+00 2095.0
25 TraesCS6D01G347900 chr5D 95.856 1279 47 6 1578 2853 401773565 401774840 0.000000e+00 2063.0
26 TraesCS6D01G347900 chr5D 92.280 1399 59 16 354 1733 313520738 313519370 0.000000e+00 1940.0
27 TraesCS6D01G347900 chr5D 95.245 736 32 3 902 1636 16496073 16495340 0.000000e+00 1162.0
28 TraesCS6D01G347900 chr5D 98.091 419 8 0 1 419 313521139 313520721 0.000000e+00 730.0
29 TraesCS6D01G347900 chr5D 93.333 255 16 1 602 856 20273473 20273220 2.680000e-100 375.0
30 TraesCS6D01G347900 chr5D 80.108 186 22 11 392 566 20273656 20273475 1.070000e-24 124.0
31 TraesCS6D01G347900 chr5D 100.000 49 0 0 607 655 313520425 313520377 1.090000e-14 91.6
32 TraesCS6D01G347900 chr5D 100.000 49 0 0 666 714 313520485 313520437 1.090000e-14 91.6
33 TraesCS6D01G347900 chr5D 100.000 49 0 0 607 655 384519128 384519080 1.090000e-14 91.6
34 TraesCS6D01G347900 chr5D 81.319 91 13 4 517 607 29560961 29560875 1.420000e-08 71.3
35 TraesCS6D01G347900 chr5D 93.023 43 3 0 236 278 313520784 313520742 2.370000e-06 63.9
36 TraesCS6D01G347900 chr5D 93.023 43 3 0 236 278 384519439 384519397 2.370000e-06 63.9
37 TraesCS6D01G347900 chr5D 92.857 42 3 0 235 276 313520737 313520696 8.530000e-06 62.1
38 TraesCS6D01G347900 chr1D 92.800 1736 79 8 1 1735 463801914 463800224 0.000000e+00 2471.0
39 TraesCS6D01G347900 chr1D 96.633 1277 40 3 1578 2853 336736453 336735179 0.000000e+00 2117.0
40 TraesCS6D01G347900 chr1D 89.691 97 10 0 69 165 336737266 336737170 1.070000e-24 124.0
41 TraesCS6D01G347900 chr1D 88.776 98 11 0 69 166 417105987 417106084 1.390000e-23 121.0
42 TraesCS6D01G347900 chr1D 100.000 49 0 0 607 655 463801276 463801228 1.090000e-14 91.6
43 TraesCS6D01G347900 chr1D 97.959 49 1 0 27 75 336737417 336737369 5.060000e-13 86.1
44 TraesCS6D01G347900 chr1D 100.000 34 0 0 861 894 336737464 336737431 2.370000e-06 63.9
45 TraesCS6D01G347900 chr1D 92.857 42 1 1 247 286 463801548 463801507 3.070000e-05 60.2
46 TraesCS6D01G347900 chr2D 95.387 1279 54 5 1578 2853 239245261 239246537 0.000000e+00 2030.0
47 TraesCS6D01G347900 chr2D 96.774 62 2 0 418 479 648988700 648988761 1.400000e-18 104.0
48 TraesCS6D01G347900 chr2A 93.219 1283 67 4 293 1562 259675756 259677031 0.000000e+00 1869.0
49 TraesCS6D01G347900 chr2A 93.423 897 58 1 666 1562 259577462 259578357 0.000000e+00 1328.0
50 TraesCS6D01G347900 chr2A 94.198 655 16 4 1 655 259576878 259577510 0.000000e+00 979.0
51 TraesCS6D01G347900 chr7B 95.317 1025 47 1 539 1562 122461222 122462246 0.000000e+00 1626.0
52 TraesCS6D01G347900 chr7B 93.023 258 16 2 370 626 725302046 725302302 2.680000e-100 375.0
53 TraesCS6D01G347900 chr7B 93.151 73 4 1 1 72 692733116 692733188 3.890000e-19 106.0
54 TraesCS6D01G347900 chr7B 91.111 45 3 1 858 901 681245817 681245861 3.070000e-05 60.2
55 TraesCS6D01G347900 chr7B 97.059 34 1 0 1 34 692733032 692733065 1.100000e-04 58.4
56 TraesCS6D01G347900 chr3B 90.000 950 70 6 805 1733 320731865 320730920 0.000000e+00 1205.0
57 TraesCS6D01G347900 chr3B 94.366 213 9 2 539 748 320732069 320731857 9.860000e-85 324.0
58 TraesCS6D01G347900 chr3B 94.737 76 3 1 1 75 632392782 632392707 1.800000e-22 117.0
59 TraesCS6D01G347900 chr7A 95.893 487 19 1 370 856 220992640 220993125 0.000000e+00 787.0
60 TraesCS6D01G347900 chr7A 96.244 213 4 4 212 420 579483350 579483138 2.100000e-91 346.0
61 TraesCS6D01G347900 chr7A 96.094 128 5 0 1 128 579483456 579483329 2.880000e-50 209.0
62 TraesCS6D01G347900 chr7A 96.154 52 2 0 852 903 220993316 220993367 5.060000e-13 86.1
63 TraesCS6D01G347900 chr5A 96.894 322 10 0 158 479 544898369 544898690 8.990000e-150 540.0
64 TraesCS6D01G347900 chr5A 90.816 98 9 0 69 166 384014347 384014444 6.410000e-27 132.0
65 TraesCS6D01G347900 chr5A 97.143 70 2 0 1 70 544898111 544898180 4.990000e-23 119.0
66 TraesCS6D01G347900 chr5A 97.101 69 2 0 1 69 384013793 384013861 1.800000e-22 117.0
67 TraesCS6D01G347900 chr4B 96.026 302 9 2 370 671 644593701 644593999 3.300000e-134 488.0
68 TraesCS6D01G347900 chr4B 84.858 317 15 16 370 655 368724968 368725282 3.600000e-74 289.0
69 TraesCS6D01G347900 chr4B 97.059 136 4 0 663 798 644594025 644594160 2.210000e-56 230.0
70 TraesCS6D01G347900 chr4B 95.745 141 4 2 666 806 368725234 368725372 2.860000e-55 226.0
71 TraesCS6D01G347900 chr4B 90.722 97 9 0 69 165 288476855 288476759 2.310000e-26 130.0
72 TraesCS6D01G347900 chr4B 96.875 64 2 0 792 855 160257625 160257688 1.080000e-19 108.0
73 TraesCS6D01G347900 chr4B 100.000 29 0 0 250 278 644593701 644593729 1.000000e-03 54.7
74 TraesCS6D01G347900 chr4B 96.875 32 0 1 31 61 15097855 15097824 5.000000e-03 52.8
75 TraesCS6D01G347900 chr3D 94.510 255 13 1 602 856 571760837 571760584 2.660000e-105 392.0
76 TraesCS6D01G347900 chr3D 94.969 159 8 0 1 159 416545014 416545172 1.700000e-62 250.0
77 TraesCS6D01G347900 chr3D 91.919 99 3 4 160 258 416545207 416545300 1.780000e-27 134.0
78 TraesCS6D01G347900 chr3D 90.816 98 9 0 69 166 330477228 330477131 6.410000e-27 132.0
79 TraesCS6D01G347900 chr3D 89.796 98 10 0 69 166 57607214 57607311 2.980000e-25 126.0
80 TraesCS6D01G347900 chr3D 100.000 34 0 0 861 894 330477328 330477295 2.370000e-06 63.9
81 TraesCS6D01G347900 chr3D 100.000 34 0 0 861 894 571760448 571760415 2.370000e-06 63.9
82 TraesCS6D01G347900 chr6B 87.296 307 17 13 370 655 238445511 238445206 5.890000e-87 331.0
83 TraesCS6D01G347900 chr6B 93.780 209 13 0 370 578 425112513 425112721 5.930000e-82 315.0
84 TraesCS6D01G347900 chr6B 94.737 76 3 1 1 75 152492535 152492610 1.800000e-22 117.0
85 TraesCS6D01G347900 chr5B 82.682 179 11 1 1 159 399756579 399756757 1.070000e-29 141.0
86 TraesCS6D01G347900 chr5B 97.143 70 2 0 1 70 189704496 189704565 4.990000e-23 119.0
87 TraesCS6D01G347900 chr4A 90.816 98 9 0 69 166 433609969 433609872 6.410000e-27 132.0
88 TraesCS6D01G347900 chr4A 95.714 70 3 0 1 70 24458168 24458237 2.320000e-21 113.0
89 TraesCS6D01G347900 chr4A 88.889 90 9 1 510 598 723201821 723201732 3.010000e-20 110.0
90 TraesCS6D01G347900 chr1A 89.691 97 10 0 69 165 50647834 50647738 1.070000e-24 124.0
91 TraesCS6D01G347900 chr6A 91.463 82 7 0 70 151 202729607 202729526 2.320000e-21 113.0
92 TraesCS6D01G347900 chrUn 92.105 76 5 1 1 75 35789960 35790035 3.890000e-19 106.0
93 TraesCS6D01G347900 chr2B 97.674 43 1 0 852 894 124026974 124026932 1.100000e-09 75.0
94 TraesCS6D01G347900 chr1B 96.875 32 0 1 31 61 516774548 516774579 5.000000e-03 52.8
95 TraesCS6D01G347900 chr1B 96.875 32 0 1 31 61 681885408 681885439 5.000000e-03 52.8


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 TraesCS6D01G347900 chr6D 446389729 446392581 2852 True 1379.500000 5269 98.295500 1 2853 4 chr6D.!!$R2 2852
1 TraesCS6D01G347900 chr6D 452661951 452664356 2405 False 613.233333 2122 95.578000 27 2853 6 chr6D.!!$F2 2826
2 TraesCS6D01G347900 chr7D 51243804 51245990 2186 True 1599.100000 3114 96.711500 28 2853 2 chr7D.!!$R3 2825
3 TraesCS6D01G347900 chr7D 79219252 79221472 2220 False 1540.250000 3000 95.087500 27 2853 2 chr7D.!!$F2 2826
4 TraesCS6D01G347900 chr4D 222627992 222630044 2052 True 1504.000000 2876 92.044500 69 2848 2 chr4D.!!$R2 2779
5 TraesCS6D01G347900 chr5D 364020702 364022595 1893 True 2833.000000 2833 93.938000 982 2846 1 chr5D.!!$R3 1864
6 TraesCS6D01G347900 chr5D 401773565 401774840 1275 False 2063.000000 2063 95.856000 1578 2853 1 chr5D.!!$F1 1275
7 TraesCS6D01G347900 chr5D 384516874 384519794 2920 True 1237.625000 2700 96.008500 1 2853 4 chr5D.!!$R6 2852
8 TraesCS6D01G347900 chr5D 16495340 16496073 733 True 1162.000000 1162 95.245000 902 1636 1 chr5D.!!$R1 734
9 TraesCS6D01G347900 chr5D 313519370 313521139 1769 True 496.533333 1940 96.041833 1 1733 6 chr5D.!!$R5 1732
10 TraesCS6D01G347900 chr1D 463800224 463801914 1690 True 874.266667 2471 95.219000 1 1735 3 chr1D.!!$R2 1734
11 TraesCS6D01G347900 chr1D 336735179 336737464 2285 True 597.750000 2117 96.070750 27 2853 4 chr1D.!!$R1 2826
12 TraesCS6D01G347900 chr2D 239245261 239246537 1276 False 2030.000000 2030 95.387000 1578 2853 1 chr2D.!!$F1 1275
13 TraesCS6D01G347900 chr2A 259675756 259677031 1275 False 1869.000000 1869 93.219000 293 1562 1 chr2A.!!$F1 1269
14 TraesCS6D01G347900 chr2A 259576878 259578357 1479 False 1153.500000 1328 93.810500 1 1562 2 chr2A.!!$F2 1561
15 TraesCS6D01G347900 chr7B 122461222 122462246 1024 False 1626.000000 1626 95.317000 539 1562 1 chr7B.!!$F1 1023
16 TraesCS6D01G347900 chr3B 320730920 320732069 1149 True 764.500000 1205 92.183000 539 1733 2 chr3B.!!$R2 1194
17 TraesCS6D01G347900 chr7A 220992640 220993367 727 False 436.550000 787 96.023500 370 903 2 chr7A.!!$F1 533
18 TraesCS6D01G347900 chr5A 544898111 544898690 579 False 329.500000 540 97.018500 1 479 2 chr5A.!!$F2 478

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
138 388 5.450818 AGTATTCCAAATACAGGCCTTGA 57.549 39.13 0.0 0.0 0.0 3.02 F
1723 2516 0.037326 TGCCTGACAATGACCTCGTC 60.037 55.00 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2584 1.593209 GCGAATCCCAACGCGGATA 60.593 57.895 12.47 0.0 42.05 2.59 R
2767 3577 5.879777 TCGATTCTTTGATGAAATGCCTACA 59.120 36.000 0.00 0.0 0.00 2.74 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
33 174 5.986135 TGAGTAGAAGAAGAAAACAGAGTGC 59.014 40.000 0.00 0.00 0.00 4.40
80 330 5.860941 TGTCCTTGTTTTTGCCAAGATAA 57.139 34.783 1.89 0.00 41.44 1.75
93 343 7.753309 TTGCCAAGATAAAGTAGTAGCAAAA 57.247 32.000 0.00 0.00 35.01 2.44
138 388 5.450818 AGTATTCCAAATACAGGCCTTGA 57.549 39.130 0.00 0.00 0.00 3.02
506 841 9.399797 AGATTGAGATTGAATATTTGTGCAGTA 57.600 29.630 0.00 0.00 0.00 2.74
600 935 7.669304 TGGAGATGTTAGAAATTTGATGGTTGA 59.331 33.333 0.00 0.00 0.00 3.18
1140 1690 3.568538 GCACAATTAACCACTGCTTGAG 58.431 45.455 0.00 0.00 0.00 3.02
1182 1732 2.221169 ACAAGTTTGCGAAGATGCTCA 58.779 42.857 0.00 0.00 35.36 4.26
1723 2516 0.037326 TGCCTGACAATGACCTCGTC 60.037 55.000 0.00 0.00 0.00 4.20
1976 2772 3.782656 TGCTCATGGATGCTGTATGAT 57.217 42.857 0.00 0.00 31.11 2.45
2040 2836 7.169158 TCAGTTTGGTAATTGATGGGAATTC 57.831 36.000 0.00 0.00 0.00 2.17
2389 3191 3.890756 CCAAACTAGCAATGATATGGCCA 59.109 43.478 8.56 8.56 0.00 5.36
2547 3354 1.010462 GCGTTTTTCGTGAAGCGGT 60.010 52.632 10.37 0.00 42.13 5.68
2767 3577 7.444792 TGCCAAAAATCATTTTTAGCTTCACAT 59.555 29.630 21.64 0.00 44.12 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 330 4.301072 TGGCCTCATTTTGCTACTACTT 57.699 40.909 3.32 0.00 0.00 2.24
128 378 1.682854 CATGTGTTTGTCAAGGCCTGT 59.317 47.619 5.69 0.00 0.00 4.00
129 379 1.682854 ACATGTGTTTGTCAAGGCCTG 59.317 47.619 5.69 0.00 0.00 4.85
138 388 9.515226 AGTTGGATATTTACTACATGTGTTTGT 57.485 29.630 9.11 4.85 0.00 2.83
506 841 8.080417 CAGAAAACAATCTCAATGTTCAGTCAT 58.920 33.333 0.00 0.00 39.98 3.06
600 935 9.104713 TGTTCATAAGTGGAGATATATGGACAT 57.895 33.333 2.43 0.00 38.64 3.06
826 1176 7.656707 AAATATTGTTTCTGAACATTGGCAC 57.343 32.000 0.00 0.00 44.71 5.01
1789 2584 1.593209 GCGAATCCCAACGCGGATA 60.593 57.895 12.47 0.00 42.05 2.59
1976 2772 7.611467 AGAAATTGACATGTTTAGATGGCACTA 59.389 33.333 0.00 0.00 41.26 2.74
2010 2806 9.265862 TCCCATCAATTACCAAACTGAATATTT 57.734 29.630 0.00 0.00 0.00 1.40
2245 3047 3.128589 GGCCACATTTGATGATGTTACGT 59.871 43.478 0.00 0.00 38.15 3.57
2512 3319 3.747099 ACGCATGTCTTTAGCATTCAC 57.253 42.857 0.00 0.00 0.00 3.18
2767 3577 5.879777 TCGATTCTTTGATGAAATGCCTACA 59.120 36.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.