Multiple sequence alignment - TraesCS6D01G080700

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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 TraesCS6D01G080700 chr6D 100.000 2902 0 0 1 2902 46528042 46525141 0.000000e+00 5360.0
1 TraesCS6D01G080700 chr6D 94.905 2100 100 5 808 2902 452662260 452664357 0.000000e+00 3278.0
2 TraesCS6D01G080700 chr6D 100.000 34 0 0 628 661 202663209 202663242 2.410000e-06 63.9
3 TraesCS6D01G080700 chr6D 88.679 53 3 2 628 680 202663137 202663186 8.680000e-06 62.1
4 TraesCS6D01G080700 chr6D 100.000 28 0 0 631 658 386771384 386771357 5.000000e-03 52.8
5 TraesCS6D01G080700 chr4D 94.704 2908 114 8 1 2902 222630859 222627986 0.000000e+00 4481.0
6 TraesCS6D01G080700 chr4D 94.613 1318 60 5 1595 2902 261238234 261236918 0.000000e+00 2030.0
7 TraesCS6D01G080700 chr4D 95.392 217 9 1 82 298 125861612 125861397 7.700000e-91 344.0
8 TraesCS6D01G080700 chr4D 95.392 217 9 1 82 298 125872377 125872592 7.700000e-91 344.0
9 TraesCS6D01G080700 chr4D 95.392 217 9 1 82 298 125937205 125936990 7.700000e-91 344.0
10 TraesCS6D01G080700 chr4D 100.000 46 0 0 1 46 125872338 125872383 5.150000e-13 86.1
11 TraesCS6D01G080700 chr4D 100.000 46 0 0 1 46 125937244 125937199 5.150000e-13 86.1
12 TraesCS6D01G080700 chr4D 97.826 46 0 1 1 46 125861650 125861606 8.620000e-11 78.7
13 TraesCS6D01G080700 chr4D 84.416 77 4 7 609 680 196903930 196904003 5.190000e-08 69.4
14 TraesCS6D01G080700 chr4D 90.741 54 2 2 628 681 225341336 225341286 5.190000e-08 69.4
15 TraesCS6D01G080700 chr4D 90.566 53 2 2 628 680 410838944 410838993 1.870000e-07 67.6
16 TraesCS6D01G080700 chr3D 95.346 2428 103 4 473 2896 330477571 330475150 0.000000e+00 3849.0
17 TraesCS6D01G080700 chr3D 92.085 1933 79 16 82 1982 57606497 57608387 0.000000e+00 2654.0
18 TraesCS6D01G080700 chr3D 84.475 1314 132 31 656 1940 571760508 571759238 0.000000e+00 1230.0
19 TraesCS6D01G080700 chr3D 97.222 360 8 2 1 360 330477916 330477559 2.470000e-170 608.0
20 TraesCS6D01G080700 chr3D 91.542 402 20 8 61 451 6727697 6728095 2.540000e-150 542.0
21 TraesCS6D01G080700 chr3D 100.000 46 0 0 1 46 57606458 57606503 5.150000e-13 86.1
22 TraesCS6D01G080700 chr1D 95.299 2276 100 5 628 2902 417105799 417108068 0.000000e+00 3603.0
23 TraesCS6D01G080700 chr1D 94.476 2100 108 5 808 2902 336737274 336735178 0.000000e+00 3229.0
24 TraesCS6D01G080700 chr1D 94.118 102 2 1 531 632 417105665 417105762 5.010000e-33 152.0
25 TraesCS6D01G080700 chr1D 97.619 42 1 0 1 42 417105617 417105658 4.010000e-09 73.1
26 TraesCS6D01G080700 chr2D 93.765 2101 124 5 808 2902 239244439 239246538 0.000000e+00 3147.0
27 TraesCS6D01G080700 chr2D 93.812 2004 93 9 922 2902 397123831 397125826 0.000000e+00 2985.0
28 TraesCS6D01G080700 chr2D 96.835 632 18 1 1 632 397122924 397123553 0.000000e+00 1055.0
29 TraesCS6D01G080700 chr2D 98.214 224 3 1 628 850 397123590 397123813 9.750000e-105 390.0
30 TraesCS6D01G080700 chr2D 95.597 159 7 0 628 786 645241422 645241264 3.710000e-64 255.0
31 TraesCS6D01G080700 chr2D 87.586 145 4 1 850 994 648988754 648988884 3.870000e-34 156.0
32 TraesCS6D01G080700 chr2D 100.000 42 0 0 757 798 645241268 645241227 8.620000e-11 78.7
33 TraesCS6D01G080700 chr7D 92.356 2211 99 11 87 2268 103531819 103533988 0.000000e+00 3083.0
34 TraesCS6D01G080700 chr7D 94.969 159 8 0 628 786 17944456 17944298 1.730000e-62 250.0
35 TraesCS6D01G080700 chr7D 97.810 137 3 0 496 632 17944646 17944510 1.340000e-58 237.0
36 TraesCS6D01G080700 chr7D 100.000 42 0 0 757 798 17944302 17944261 8.620000e-11 78.7
37 TraesCS6D01G080700 chr4A 92.079 2222 87 19 82 2269 433610674 433608508 0.000000e+00 3046.0
38 TraesCS6D01G080700 chr4A 94.000 150 9 0 551 700 691942419 691942568 8.090000e-56 228.0
39 TraesCS6D01G080700 chr5D 93.189 2026 106 11 903 2902 384518892 384516873 0.000000e+00 2948.0
40 TraesCS6D01G080700 chr5D 91.489 2115 125 14 826 2902 401772744 401774841 0.000000e+00 2857.0
41 TraesCS6D01G080700 chr5D 97.152 632 18 0 1 632 16497016 16496385 0.000000e+00 1068.0
42 TraesCS6D01G080700 chr5D 92.105 190 15 0 628 817 20273109 20272920 4.770000e-68 268.0
43 TraesCS6D01G080700 chr5D 97.297 37 1 0 8 44 447391754 447391790 2.410000e-06 63.9
44 TraesCS6D01G080700 chr7A 92.616 1449 83 8 826 2269 734436642 734438071 0.000000e+00 2061.0
45 TraesCS6D01G080700 chr3B 92.340 1449 88 7 826 2269 787077789 787079219 0.000000e+00 2039.0
46 TraesCS6D01G080700 chr3B 86.035 1246 133 18 779 1996 318290771 318292003 0.000000e+00 1299.0
47 TraesCS6D01G080700 chr3B 87.822 854 59 18 749 1587 636097934 636097111 0.000000e+00 959.0
48 TraesCS6D01G080700 chr7B 91.707 1447 96 9 829 2269 719338877 719337449 0.000000e+00 1986.0
49 TraesCS6D01G080700 chr6B 91.960 1393 72 10 340 1728 518297552 518298908 0.000000e+00 1916.0
50 TraesCS6D01G080700 chr6B 95.333 150 7 0 551 700 208155310 208155459 3.740000e-59 239.0
51 TraesCS6D01G080700 chr2B 86.790 1355 134 21 628 1940 124027059 124025708 0.000000e+00 1469.0
52 TraesCS6D01G080700 chr2B 96.257 748 28 0 80 827 539864917 539865664 0.000000e+00 1227.0
53 TraesCS6D01G080700 chr5B 88.802 1027 91 10 762 1785 117418865 117419870 0.000000e+00 1238.0
54 TraesCS6D01G080700 chr5B 90.279 823 58 10 765 1587 565309232 565308432 0.000000e+00 1057.0
55 TraesCS6D01G080700 chr5B 85.415 1049 105 30 749 1782 345108491 345109506 0.000000e+00 1046.0
56 TraesCS6D01G080700 chr5B 93.385 257 15 1 447 703 345206528 345206274 2.110000e-101 379.0
57 TraesCS6D01G080700 chr5A 91.961 622 41 5 628 1240 384014159 384014780 0.000000e+00 863.0
58 TraesCS6D01G080700 chr3A 91.623 573 24 7 68 632 5993310 5992754 0.000000e+00 771.0
59 TraesCS6D01G080700 chr6A 94.278 367 8 4 199 552 136654996 136655362 1.520000e-152 549.0
60 TraesCS6D01G080700 chr6A 97.260 73 2 0 480 552 529359811 529359883 1.090000e-24 124.0
61 TraesCS6D01G080700 chr6A 100.000 29 0 0 410 438 136655263 136655291 1.000000e-03 54.7
62 TraesCS6D01G080700 chrUn 96.500 200 7 0 81 280 35192365 35192166 5.990000e-87 331.0
63 TraesCS6D01G080700 chrUn 96.059 203 8 0 78 280 236924954 236925156 5.990000e-87 331.0
64 TraesCS6D01G080700 chrUn 93.711 159 9 1 122 280 264980973 264981130 1.340000e-58 237.0
65 TraesCS6D01G080700 chrUn 92.453 159 11 1 122 280 290561517 290561360 2.910000e-55 226.0
66 TraesCS6D01G080700 chrUn 90.533 169 14 2 551 719 35191890 35191724 3.760000e-54 222.0
67 TraesCS6D01G080700 chrUn 93.333 150 10 0 551 700 236925432 236925581 3.760000e-54 222.0
68 TraesCS6D01G080700 chrUn 89.333 150 6 1 551 700 264981166 264981305 2.300000e-41 180.0
69 TraesCS6D01G080700 chrUn 88.889 153 7 1 551 703 356709726 356709584 2.300000e-41 180.0
70 TraesCS6D01G080700 chrUn 98.387 62 1 0 219 280 356709823 356709762 3.060000e-20 110.0
71 TraesCS6D01G080700 chrUn 94.118 68 4 0 659 726 38465246 38465313 1.420000e-18 104.0
72 TraesCS6D01G080700 chr4B 94.000 200 12 0 81 280 263067381 263067182 1.310000e-78 303.0
73 TraesCS6D01G080700 chr4B 96.429 140 5 0 493 632 368725484 368725623 6.250000e-57 231.0
74 TraesCS6D01G080700 chr4B 94.000 150 9 0 551 700 6822658 6822807 8.090000e-56 228.0
75 TraesCS6D01G080700 chr4B 96.350 137 5 0 493 629 644594278 644594414 2.910000e-55 226.0
76 TraesCS6D01G080700 chr4B 92.157 153 12 0 551 703 263066906 263066754 1.750000e-52 217.0
77 TraesCS6D01G080700 chr4B 94.949 99 5 0 628 726 200932641 200932739 3.870000e-34 156.0
78 TraesCS6D01G080700 chr1B 93.289 149 10 0 551 699 600347077 600346929 1.350000e-53 220.0


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 TraesCS6D01G080700 chr6D 46525141 46528042 2901 True 5360.000000 5360 100.000000 1 2902 1 chr6D.!!$R1 2901
1 TraesCS6D01G080700 chr6D 452662260 452664357 2097 False 3278.000000 3278 94.905000 808 2902 1 chr6D.!!$F1 2094
2 TraesCS6D01G080700 chr4D 222627986 222630859 2873 True 4481.000000 4481 94.704000 1 2902 1 chr4D.!!$R1 2901
3 TraesCS6D01G080700 chr4D 261236918 261238234 1316 True 2030.000000 2030 94.613000 1595 2902 1 chr4D.!!$R3 1307
4 TraesCS6D01G080700 chr3D 330475150 330477916 2766 True 2228.500000 3849 96.284000 1 2896 2 chr3D.!!$R2 2895
5 TraesCS6D01G080700 chr3D 57606458 57608387 1929 False 1370.050000 2654 96.042500 1 1982 2 chr3D.!!$F2 1981
6 TraesCS6D01G080700 chr3D 571759238 571760508 1270 True 1230.000000 1230 84.475000 656 1940 1 chr3D.!!$R1 1284
7 TraesCS6D01G080700 chr1D 336735178 336737274 2096 True 3229.000000 3229 94.476000 808 2902 1 chr1D.!!$R1 2094
8 TraesCS6D01G080700 chr1D 417105617 417108068 2451 False 1276.033333 3603 95.678667 1 2902 3 chr1D.!!$F1 2901
9 TraesCS6D01G080700 chr2D 239244439 239246538 2099 False 3147.000000 3147 93.765000 808 2902 1 chr2D.!!$F1 2094
10 TraesCS6D01G080700 chr2D 397122924 397125826 2902 False 1476.666667 2985 96.287000 1 2902 3 chr2D.!!$F3 2901
11 TraesCS6D01G080700 chr7D 103531819 103533988 2169 False 3083.000000 3083 92.356000 87 2268 1 chr7D.!!$F1 2181
12 TraesCS6D01G080700 chr4A 433608508 433610674 2166 True 3046.000000 3046 92.079000 82 2269 1 chr4A.!!$R1 2187
13 TraesCS6D01G080700 chr5D 384516873 384518892 2019 True 2948.000000 2948 93.189000 903 2902 1 chr5D.!!$R3 1999
14 TraesCS6D01G080700 chr5D 401772744 401774841 2097 False 2857.000000 2857 91.489000 826 2902 1 chr5D.!!$F1 2076
15 TraesCS6D01G080700 chr5D 16496385 16497016 631 True 1068.000000 1068 97.152000 1 632 1 chr5D.!!$R1 631
16 TraesCS6D01G080700 chr7A 734436642 734438071 1429 False 2061.000000 2061 92.616000 826 2269 1 chr7A.!!$F1 1443
17 TraesCS6D01G080700 chr3B 787077789 787079219 1430 False 2039.000000 2039 92.340000 826 2269 1 chr3B.!!$F2 1443
18 TraesCS6D01G080700 chr3B 318290771 318292003 1232 False 1299.000000 1299 86.035000 779 1996 1 chr3B.!!$F1 1217
19 TraesCS6D01G080700 chr3B 636097111 636097934 823 True 959.000000 959 87.822000 749 1587 1 chr3B.!!$R1 838
20 TraesCS6D01G080700 chr7B 719337449 719338877 1428 True 1986.000000 1986 91.707000 829 2269 1 chr7B.!!$R1 1440
21 TraesCS6D01G080700 chr6B 518297552 518298908 1356 False 1916.000000 1916 91.960000 340 1728 1 chr6B.!!$F2 1388
22 TraesCS6D01G080700 chr2B 124025708 124027059 1351 True 1469.000000 1469 86.790000 628 1940 1 chr2B.!!$R1 1312
23 TraesCS6D01G080700 chr2B 539864917 539865664 747 False 1227.000000 1227 96.257000 80 827 1 chr2B.!!$F1 747
24 TraesCS6D01G080700 chr5B 117418865 117419870 1005 False 1238.000000 1238 88.802000 762 1785 1 chr5B.!!$F1 1023
25 TraesCS6D01G080700 chr5B 565308432 565309232 800 True 1057.000000 1057 90.279000 765 1587 1 chr5B.!!$R2 822
26 TraesCS6D01G080700 chr5B 345108491 345109506 1015 False 1046.000000 1046 85.415000 749 1782 1 chr5B.!!$F2 1033
27 TraesCS6D01G080700 chr5A 384014159 384014780 621 False 863.000000 863 91.961000 628 1240 1 chr5A.!!$F1 612
28 TraesCS6D01G080700 chr3A 5992754 5993310 556 True 771.000000 771 91.623000 68 632 1 chr3A.!!$R1 564
29 TraesCS6D01G080700 chrUn 35191724 35192365 641 True 276.500000 331 93.516500 81 719 2 chrUn.!!$R2 638
30 TraesCS6D01G080700 chrUn 236924954 236925581 627 False 276.500000 331 94.696000 78 700 2 chrUn.!!$F2 622
31 TraesCS6D01G080700 chr4B 263066754 263067381 627 True 260.000000 303 93.078500 81 703 2 chr4B.!!$R1 622

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
672 847 0.30776 GCTGTGTTCTGGTCCGTTTG 59.692 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 3364 0.031449 CATGGTTTTTGGCGACCGTT 59.969 50.0 0.0 0.0 38.81 4.44 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
176 184 3.354467 ACTGTACTAGTGGAGTGTAGGC 58.646 50.000 5.39 0.00 39.39 3.93
178 186 3.618351 TGTACTAGTGGAGTGTAGGCTC 58.382 50.000 5.39 0.00 39.39 4.70
179 187 3.266254 TGTACTAGTGGAGTGTAGGCTCT 59.734 47.826 5.39 0.00 39.39 4.09
194 202 2.926778 GCTCTACTTGCCATGAGGAT 57.073 50.000 0.00 0.00 36.89 3.24
668 843 0.888619 TCTAGCTGTGTTCTGGTCCG 59.111 55.000 0.00 0.00 0.00 4.79
672 847 0.307760 GCTGTGTTCTGGTCCGTTTG 59.692 55.000 0.00 0.00 0.00 2.93
747 929 8.095169 TGTTGTTATTTTTGTTGTGGTTACCTT 58.905 29.630 2.07 0.00 0.00 3.50
895 1155 1.598701 GAGGCCCTGGCAAACACATC 61.599 60.000 10.86 0.00 44.11 3.06
964 1260 4.156008 CCAGTCCTGTTTATGGTAACTTGC 59.844 45.833 0.00 0.00 37.61 4.01
1020 1316 1.114722 TGGCTGGCTTGGAAGGTTTG 61.115 55.000 2.00 0.00 0.00 2.93
1085 1398 8.715998 GCAGGTATATTTATCAACACTCATCTG 58.284 37.037 0.00 0.00 0.00 2.90
1122 1435 4.464244 ACTCTGCTGTCTAGTGCTTGATTA 59.536 41.667 0.00 0.00 0.00 1.75
1222 1535 0.603707 CAAAGTGAAGCTGCGGGAGA 60.604 55.000 0.00 0.00 0.00 3.71
1317 1630 1.893808 CTGGGATCATTTCGCCCGG 60.894 63.158 0.00 0.00 45.08 5.73
1422 1735 0.321996 TGTGCCGCATGTACTACCAA 59.678 50.000 0.00 0.00 0.00 3.67
1447 1760 1.148157 CCACGATGCCAGTAAGCTCG 61.148 60.000 0.00 0.00 38.50 5.03
1611 2203 2.034532 TGGCTGACGACGACCCTA 59.965 61.111 0.00 0.00 0.00 3.53
1623 2215 0.104304 CGACCCTACTATGGTGGTGC 59.896 60.000 0.00 0.00 35.85 5.01
1636 2228 2.297129 TGGTGCCGGATGATGACCA 61.297 57.895 5.05 3.55 34.26 4.02
1677 2296 1.452108 GACCCTGCTATGGTGGTGC 60.452 63.158 0.00 0.00 35.85 5.01
1941 2629 5.009631 AGTGGCAATGTTAAGCATGTTAGA 58.990 37.500 0.00 0.00 37.96 2.10
2004 2692 6.687604 AGTATGTCAGGTTTAATTTTGTGCC 58.312 36.000 0.00 0.00 0.00 5.01
2022 2711 1.880271 CCTGCTCATGGATGCTGTAG 58.120 55.000 0.00 0.00 0.00 2.74
2510 3210 5.863397 CGTCTTATGATGGCAAACAATGTTT 59.137 36.000 5.41 5.41 0.00 2.83
2659 3364 7.707624 TCTCAAAGTAGACCCTATTTTACGA 57.292 36.000 0.00 0.00 0.00 3.43
2674 3379 4.199130 CGAACGGTCGCCAAAAAC 57.801 55.556 11.19 0.00 41.08 2.43
2724 3429 1.339610 CGGCCATTCAAACAACCTTCA 59.660 47.619 2.24 0.00 0.00 3.02
2801 3506 5.038683 CCCGTTATTTTCGCTAAAAATCCC 58.961 41.667 9.21 3.03 42.63 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 209 6.214412 TGCATCTAACCCCAACCAAAAATAAT 59.786 34.615 0.00 0.00 0.00 1.28
668 843 9.166126 GCAACAACACTAAAATCTACTACAAAC 57.834 33.333 0.00 0.00 0.00 2.93
672 847 8.084590 ACAGCAACAACACTAAAATCTACTAC 57.915 34.615 0.00 0.00 0.00 2.73
747 929 4.462132 CCATCAACATCAACAACACCCATA 59.538 41.667 0.00 0.00 0.00 2.74
1020 1316 5.579718 TCAATTACGATCTCGAAGAACTCC 58.420 41.667 6.60 0.00 43.02 3.85
1085 1398 8.430801 AGACAGCAGAGTGATGATAATTAAAC 57.569 34.615 0.00 0.00 35.45 2.01
1122 1435 3.004734 GTCAAGCAGTGGTTAATTGTGCT 59.995 43.478 7.35 0.00 46.35 4.40
1422 1735 1.529152 TACTGGCATCGTGGTCGTGT 61.529 55.000 0.00 0.00 38.33 4.49
1447 1760 0.612744 ACAGGAAGAAGAGAGGCAGC 59.387 55.000 0.00 0.00 0.00 5.25
1611 2203 0.980754 TCATCCGGCACCACCATAGT 60.981 55.000 0.00 0.00 39.03 2.12
1623 2215 2.353323 CATAGCATGGTCATCATCCGG 58.647 52.381 0.00 0.00 32.92 5.14
1636 2228 0.107017 GTCAGCCACCACCATAGCAT 60.107 55.000 0.00 0.00 0.00 3.79
1677 2296 2.001361 ATAGCAAGGTCGTCGTCCGG 62.001 60.000 0.00 0.00 37.11 5.14
2004 2692 1.415289 TCCTACAGCATCCATGAGCAG 59.585 52.381 0.00 0.00 0.00 4.24
2022 2711 5.237815 TGACATGTTTAGATGACACTGTCC 58.762 41.667 0.00 0.00 36.20 4.02
2224 2914 0.669619 AAAAACCGGCCGATTTCGTT 59.330 45.000 30.73 19.10 37.74 3.85
2510 3210 3.117663 ACAAGTTGGAACCTAGCTTTGGA 60.118 43.478 7.96 0.00 0.00 3.53
2559 3263 5.827568 AAACGCATGTTTTTAGCATTCAG 57.172 34.783 0.00 0.00 45.89 3.02
2613 3318 3.891400 CATGGAATGGCGCCGTGG 61.891 66.667 24.67 6.02 41.79 4.94
2614 3319 3.112126 GACATGGAATGGCGCCGTG 62.112 63.158 24.67 11.95 46.24 4.94
2659 3364 0.031449 CATGGTTTTTGGCGACCGTT 59.969 50.000 0.00 0.00 38.81 4.44
2674 3379 1.613437 ACAAGGGTCGAAAAAGCATGG 59.387 47.619 0.00 0.00 0.00 3.66
2801 3506 5.886960 ATGCCTACTTGTGAAGCTAAAAG 57.113 39.130 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.