Multiple sequence alignment - TraesCS7D01G098500

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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 TraesCS7D01G098500 chr7D 100.000 2860 0 0 1 2860 59086901 59084042 0.000000e+00 5282.0
1 TraesCS7D01G098500 chr7D 98.602 2862 34 5 1 2860 59045570 59042713 0.000000e+00 5059.0
2 TraesCS7D01G098500 chr7D 85.253 217 29 2 1919 2132 483694112 483693896 1.330000e-53 220.0
3 TraesCS7D01G098500 chr7D 76.014 296 39 13 1919 2199 5870839 5871117 1.080000e-24 124.0
4 TraesCS7D01G098500 chr2D 98.745 1913 22 2 1 1911 600584240 600586152 0.000000e+00 3398.0
5 TraesCS7D01G098500 chr2D 98.432 1913 28 2 1 1911 535237008 535238920 0.000000e+00 3365.0
6 TraesCS7D01G098500 chr2D 77.031 1071 235 11 11 1076 633507951 633506887 3.150000e-169 604.0
7 TraesCS7D01G098500 chr2D 82.700 237 39 2 2421 2656 469731106 469730871 2.890000e-50 209.0
8 TraesCS7D01G098500 chr2D 80.162 247 37 5 2391 2626 610169260 610169015 1.050000e-39 174.0
9 TraesCS7D01G098500 chr2D 80.000 230 25 11 1990 2199 12377284 12377512 1.780000e-32 150.0
10 TraesCS7D01G098500 chr1A 97.443 1916 47 2 1 1914 571570957 571569042 0.000000e+00 3265.0
11 TraesCS7D01G098500 chr1A 75.880 937 212 11 41 972 574818818 574817891 1.550000e-127 466.0
12 TraesCS7D01G098500 chr1A 79.386 228 28 10 1990 2199 1942207 1941981 2.970000e-30 143.0
13 TraesCS7D01G098500 chr1A 71.380 587 150 18 3 580 321286256 321285679 1.380000e-28 137.0
14 TraesCS7D01G098500 chr1A 100.000 29 0 0 2334 2362 388784256 388784284 1.000000e-03 54.7
15 TraesCS7D01G098500 chr6B 97.023 1915 52 4 1 1912 136340186 136338274 0.000000e+00 3216.0
16 TraesCS7D01G098500 chr6B 94.519 967 53 0 479 1445 642854276 642855242 0.000000e+00 1493.0
17 TraesCS7D01G098500 chr6B 96.096 871 30 4 1045 1913 198323015 198322147 0.000000e+00 1417.0
18 TraesCS7D01G098500 chr6B 75.464 1940 421 46 2 1915 18403402 18405312 0.000000e+00 894.0
19 TraesCS7D01G098500 chr6B 73.960 1947 431 63 2 1914 87654457 87652553 0.000000e+00 717.0
20 TraesCS7D01G098500 chr6B 93.049 446 26 5 1471 1914 642855501 642855943 0.000000e+00 647.0
21 TraesCS7D01G098500 chr5B 93.324 1468 92 6 447 1911 603893845 603895309 0.000000e+00 2163.0
22 TraesCS7D01G098500 chr5B 87.075 147 16 2 2192 2335 121249616 121249762 2.280000e-36 163.0
23 TraesCS7D01G098500 chr5B 76.549 226 33 6 2394 2616 639675435 639675227 3.900000e-19 106.0
24 TraesCS7D01G098500 chr6A 78.597 1668 316 23 5 1664 277517287 277518921 0.000000e+00 1064.0
25 TraesCS7D01G098500 chr6A 75.980 1020 216 20 2 1012 616906000 616905001 1.530000e-137 499.0
26 TraesCS7D01G098500 chr6A 84.333 300 26 8 1919 2199 423201057 423200760 1.010000e-69 274.0
27 TraesCS7D01G098500 chr6D 97.549 612 13 2 1305 1914 57896142 57895531 0.000000e+00 1046.0
28 TraesCS7D01G098500 chr6D 96.467 368 11 2 1398 1763 437170558 437170925 8.760000e-170 606.0
29 TraesCS7D01G098500 chr6D 79.310 203 22 6 2011 2199 367538581 367538385 1.080000e-24 124.0
30 TraesCS7D01G098500 chr7B 73.824 1765 400 50 176 1913 710481810 710480081 0.000000e+00 643.0
31 TraesCS7D01G098500 chr7B 77.966 236 49 2 2419 2653 57593750 57593517 8.260000e-31 145.0
32 TraesCS7D01G098500 chr4A 93.258 178 8 3 2686 2859 676496550 676496373 2.830000e-65 259.0
33 TraesCS7D01G098500 chr4A 77.656 273 41 14 2415 2675 146707765 146707501 6.380000e-32 148.0
34 TraesCS7D01G098500 chr4A 86.331 139 14 4 2200 2335 622124086 622123950 2.300000e-31 147.0
35 TraesCS7D01G098500 chr2A 82.895 304 31 5 1918 2200 26731059 26730756 1.320000e-63 254.0
36 TraesCS7D01G098500 chr3D 91.667 180 12 2 1919 2095 462544166 462544345 2.200000e-61 246.0
37 TraesCS7D01G098500 chr3D 81.757 296 34 11 1919 2199 470674125 470674415 2.220000e-56 230.0
38 TraesCS7D01G098500 chr3D 82.990 194 19 4 2020 2199 537518573 537518766 2.280000e-36 163.0
39 TraesCS7D01G098500 chr3D 85.612 139 17 2 2200 2335 31869857 31869719 2.970000e-30 143.0
40 TraesCS7D01G098500 chr7A 83.045 289 25 11 1919 2186 699065254 699065539 1.020000e-59 241.0
41 TraesCS7D01G098500 chr7A 94.175 103 3 1 2757 2859 63602359 63602260 1.370000e-33 154.0
42 TraesCS7D01G098500 chr7A 77.295 207 34 5 2459 2654 171551289 171551085 3.010000e-20 110.0
43 TraesCS7D01G098500 chr2B 91.160 181 11 3 1919 2095 107581470 107581291 1.020000e-59 241.0
44 TraesCS7D01G098500 chr2B 89.474 76 8 0 2124 2199 694579017 694579092 2.350000e-16 97.1
45 TraesCS7D01G098500 chr1D 81.789 313 27 13 1919 2204 288009502 288009811 4.760000e-58 235.0
46 TraesCS7D01G098500 chr1D 72.308 325 82 8 32 352 193462124 193462444 8.440000e-16 95.3
47 TraesCS7D01G098500 chr4D 81.481 297 33 11 1919 2201 147555116 147554828 1.030000e-54 224.0
48 TraesCS7D01G098500 chr4D 79.323 266 54 1 2392 2656 447992125 447991860 4.870000e-43 185.0
49 TraesCS7D01G098500 chr3B 80.844 308 29 10 1922 2203 370611390 370611087 6.210000e-52 215.0
50 TraesCS7D01G098500 chr5D 73.077 494 119 14 94 580 514413467 514413953 2.280000e-36 163.0
51 TraesCS7D01G098500 chr5A 78.077 260 46 3 2383 2632 650239315 650239573 1.370000e-33 154.0
52 TraesCS7D01G098500 chr5A 85.714 147 18 2 2192 2335 115095240 115095386 4.940000e-33 152.0
53 TraesCS7D01G098500 chr4B 86.131 137 17 2 2201 2336 654628441 654628306 2.300000e-31 147.0
54 TraesCS7D01G098500 chr4B 86.131 137 17 2 2201 2336 654645391 654645256 2.300000e-31 147.0
55 TraesCS7D01G098500 chr4B 86.131 137 17 2 2201 2336 654764800 654764665 2.300000e-31 147.0
56 TraesCS7D01G098500 chr4B 85.507 138 18 2 2200 2336 654706164 654706028 2.970000e-30 143.0
57 TraesCS7D01G098500 chr4B 100.000 29 0 0 2334 2362 422946962 422946934 1.000000e-03 54.7


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 TraesCS7D01G098500 chr7D 59084042 59086901 2859 True 5282 5282 100.000 1 2860 1 chr7D.!!$R2 2859
1 TraesCS7D01G098500 chr7D 59042713 59045570 2857 True 5059 5059 98.602 1 2860 1 chr7D.!!$R1 2859
2 TraesCS7D01G098500 chr2D 600584240 600586152 1912 False 3398 3398 98.745 1 1911 1 chr2D.!!$F3 1910
3 TraesCS7D01G098500 chr2D 535237008 535238920 1912 False 3365 3365 98.432 1 1911 1 chr2D.!!$F2 1910
4 TraesCS7D01G098500 chr2D 633506887 633507951 1064 True 604 604 77.031 11 1076 1 chr2D.!!$R3 1065
5 TraesCS7D01G098500 chr1A 571569042 571570957 1915 True 3265 3265 97.443 1 1914 1 chr1A.!!$R3 1913
6 TraesCS7D01G098500 chr1A 574817891 574818818 927 True 466 466 75.880 41 972 1 chr1A.!!$R4 931
7 TraesCS7D01G098500 chr6B 136338274 136340186 1912 True 3216 3216 97.023 1 1912 1 chr6B.!!$R2 1911
8 TraesCS7D01G098500 chr6B 198322147 198323015 868 True 1417 1417 96.096 1045 1913 1 chr6B.!!$R3 868
9 TraesCS7D01G098500 chr6B 642854276 642855943 1667 False 1070 1493 93.784 479 1914 2 chr6B.!!$F2 1435
10 TraesCS7D01G098500 chr6B 18403402 18405312 1910 False 894 894 75.464 2 1915 1 chr6B.!!$F1 1913
11 TraesCS7D01G098500 chr6B 87652553 87654457 1904 True 717 717 73.960 2 1914 1 chr6B.!!$R1 1912
12 TraesCS7D01G098500 chr5B 603893845 603895309 1464 False 2163 2163 93.324 447 1911 1 chr5B.!!$F2 1464
13 TraesCS7D01G098500 chr6A 277517287 277518921 1634 False 1064 1064 78.597 5 1664 1 chr6A.!!$F1 1659
14 TraesCS7D01G098500 chr6A 616905001 616906000 999 True 499 499 75.980 2 1012 1 chr6A.!!$R2 1010
15 TraesCS7D01G098500 chr6D 57895531 57896142 611 True 1046 1046 97.549 1305 1914 1 chr6D.!!$R1 609
16 TraesCS7D01G098500 chr7B 710480081 710481810 1729 True 643 643 73.824 176 1913 1 chr7B.!!$R2 1737

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
340 342 2.467880 TGGGGTTCAGAGATCTACACC 58.532 52.381 7.59 7.59 34.59 4.16 F
1174 1202 2.484264 GCAGTGTTGGCTAACCTACTTG 59.516 50.000 10.73 4.94 41.68 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1416 1.059584 TCCCTCACTTGGCTTGGTCA 61.060 55.0 0.00 0.0 0.0 4.02 R
2440 2708 1.263356 GGGTTTAGGCCTGGGTTTTC 58.737 55.0 17.99 0.0 0.0 2.29 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
340 342 2.467880 TGGGGTTCAGAGATCTACACC 58.532 52.381 7.59 7.59 34.59 4.16
1165 1193 2.668212 GTGCGGCAGTGTTGGCTA 60.668 61.111 1.18 0.00 46.99 3.93
1174 1202 2.484264 GCAGTGTTGGCTAACCTACTTG 59.516 50.000 10.73 4.94 41.68 3.16
1388 1416 3.434739 GGCCAGATTGAGAGACATGGATT 60.435 47.826 0.00 0.00 30.23 3.01
1821 2085 1.134401 CCATTGTATGGCAGTCCGAGT 60.134 52.381 0.00 0.00 44.70 4.18
2116 2383 2.101415 TGCCATGACGAATCAGGACTAG 59.899 50.000 0.00 0.00 39.01 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
340 342 3.628017 CCAAGAGTGCCAAGTTAAAACG 58.372 45.455 0.00 0.0 0.00 3.60
973 1001 1.136828 TTAGCCATAATGCCCCGACT 58.863 50.000 0.00 0.0 0.00 4.18
1165 1193 7.363268 CGGTACATTAGGAGTTACAAGTAGGTT 60.363 40.741 0.00 0.0 0.00 3.50
1174 1202 3.119029 TGTGCCGGTACATTAGGAGTTAC 60.119 47.826 22.40 0.0 0.00 2.50
1388 1416 1.059584 TCCCTCACTTGGCTTGGTCA 61.060 55.000 0.00 0.0 0.00 4.02
1571 1832 1.202758 TGTCGTTTGCCAGAATGAGGT 60.203 47.619 0.00 0.0 39.69 3.85
2378 2646 2.110420 GTATACCCGCACCCTGGC 59.890 66.667 0.00 0.0 0.00 4.85
2440 2708 1.263356 GGGTTTAGGCCTGGGTTTTC 58.737 55.000 17.99 0.0 0.00 2.29
2544 2812 5.250235 TGCGGAAAACAACATTTTAGTCA 57.750 34.783 0.00 0.0 0.00 3.41
2582 2850 1.586564 GAACTCGACGGGCAGATCG 60.587 63.158 0.00 0.0 39.72 3.69


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

AutoCloner maintained by Alex Coulton.