Multiple sequence alignment - TraesCS6A01G141000

Loading Multiple Alignment...

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 TraesCS6A01G141000 chr6A 100.000 3112 0 0 1 3112 115506043 115502932 0.000000e+00 5747.0
1 TraesCS6A01G141000 chr6A 99.711 3112 9 0 1 3112 115538226 115535115 0.000000e+00 5698.0
2 TraesCS6A01G141000 chr6A 90.476 546 47 5 2010 2553 454803271 454803813 0.000000e+00 715.0
3 TraesCS6A01G141000 chr6A 95.732 328 14 0 2165 2492 110490857 110491184 2.130000e-146 529.0
4 TraesCS6A01G141000 chr6A 96.992 266 7 1 500 765 510214729 510214465 2.200000e-121 446.0
5 TraesCS6A01G141000 chr6A 96.283 269 8 2 496 763 169789414 169789147 1.020000e-119 440.0
6 TraesCS6A01G141000 chr6A 91.579 95 7 1 172 265 594338172 594338078 2.520000e-26 130.0
7 TraesCS6A01G141000 chr6A 90.625 96 8 1 171 265 181315181 181315086 3.260000e-25 126.0
8 TraesCS6A01G141000 chr6A 90.110 91 9 0 175 265 255053603 255053693 5.450000e-23 119.0
9 TraesCS6A01G141000 chr6A 91.765 85 7 0 913 997 399644160 399644076 5.450000e-23 119.0
10 TraesCS6A01G141000 chr6A 89.888 89 9 0 176 264 94273422 94273510 7.050000e-22 115.0
11 TraesCS6A01G141000 chr6A 88.506 87 10 0 911 997 555766411 555766325 4.240000e-19 106.0
12 TraesCS6A01G141000 chr7A 93.768 353 20 2 2163 2514 34843177 34843528 2.130000e-146 529.0
13 TraesCS6A01G141000 chr7A 95.732 328 14 0 2165 2492 142300215 142300542 2.130000e-146 529.0
14 TraesCS6A01G141000 chr7A 95.427 328 15 0 2165 2492 144534785 144534458 9.890000e-145 523.0
15 TraesCS6A01G141000 chr7A 92.542 295 17 4 472 762 731504815 731504522 4.800000e-113 418.0
16 TraesCS6A01G141000 chr7A 87.879 330 38 2 177 504 569118562 569118891 1.350000e-103 387.0
17 TraesCS6A01G141000 chr7A 84.937 239 32 4 761 997 490863704 490863940 4.010000e-59 239.0
18 TraesCS6A01G141000 chr7A 77.778 144 29 3 640 781 228265730 228265588 5.530000e-13 86.1
19 TraesCS6A01G141000 chr4A 82.696 601 98 6 259 857 638137728 638137132 2.130000e-146 529.0
20 TraesCS6A01G141000 chr4A 94.395 339 17 2 2165 2503 158289674 158290010 1.280000e-143 520.0
21 TraesCS6A01G141000 chr4A 91.209 91 8 0 175 265 614550830 614550740 1.170000e-24 124.0
22 TraesCS6A01G141000 chr4A 89.773 88 9 0 911 998 29461783 29461696 2.540000e-21 113.0
23 TraesCS6A01G141000 chr4A 89.655 87 9 0 911 997 503622147 503622233 9.120000e-21 111.0
24 TraesCS6A01G141000 chr1A 95.719 327 14 0 2165 2491 505806891 505806565 7.640000e-146 527.0
25 TraesCS6A01G141000 chr1A 96.255 267 9 1 497 763 13709542 13709807 1.330000e-118 436.0
26 TraesCS6A01G141000 chr1A 95.911 269 9 2 496 763 434540317 434540584 4.770000e-118 435.0
27 TraesCS6A01G141000 chr1A 93.818 275 13 1 264 538 579147298 579147028 8.030000e-111 411.0
28 TraesCS6A01G141000 chr1A 89.200 250 21 3 667 911 579137071 579136823 1.080000e-79 307.0
29 TraesCS6A01G141000 chr1A 93.258 89 6 0 177 265 576317307 576317219 7.000000e-27 132.0
30 TraesCS6A01G141000 chr1A 90.805 87 8 0 911 997 96147134 96147048 1.960000e-22 117.0
31 TraesCS6A01G141000 chr1A 89.655 87 9 0 911 997 506704649 506704735 9.120000e-21 111.0
32 TraesCS6A01G141000 chr1A 87.356 87 11 0 911 997 400542444 400542358 1.970000e-17 100.0
33 TraesCS6A01G141000 chr1A 87.356 87 11 0 911 997 535768949 535768863 1.970000e-17 100.0
34 TraesCS6A01G141000 chr1A 80.328 122 21 2 669 787 554878021 554877900 4.270000e-14 89.8
35 TraesCS6A01G141000 chr3A 95.427 328 15 0 2165 2492 659863415 659863742 9.890000e-145 523.0
36 TraesCS6A01G141000 chr3A 96.283 269 8 2 496 763 58274808 58275075 1.020000e-119 440.0
37 TraesCS6A01G141000 chr3A 92.135 89 7 0 177 265 587390063 587390151 3.260000e-25 126.0
38 TraesCS6A01G141000 chr3A 90.217 92 9 0 174 265 86612072 86611981 1.520000e-23 121.0
39 TraesCS6A01G141000 chr3A 73.067 401 84 13 1050 1441 698168748 698168363 1.520000e-23 121.0
40 TraesCS6A01G141000 chrUn 95.911 269 9 2 496 763 1525425 1525692 4.770000e-118 435.0
41 TraesCS6A01G141000 chrUn 92.262 168 12 1 2490 2656 297722172 297722005 1.440000e-58 237.0
42 TraesCS6A01G141000 chrUn 92.262 168 12 1 2000 2166 297722338 297722171 1.440000e-58 237.0
43 TraesCS6A01G141000 chrUn 86.207 87 12 0 911 997 359680840 359680926 9.190000e-16 95.3
44 TraesCS6A01G141000 chrUn 86.047 86 12 0 911 996 252262252 252262167 3.300000e-15 93.5
45 TraesCS6A01G141000 chrUn 85.057 87 13 0 911 997 69562912 69562998 4.270000e-14 89.8
46 TraesCS6A01G141000 chrUn 90.625 64 6 0 934 997 446000553 446000616 5.530000e-13 86.1
47 TraesCS6A01G141000 chrUn 82.955 88 15 0 911 998 286827394 286827481 2.570000e-11 80.5
48 TraesCS6A01G141000 chrUn 84.615 78 12 0 175 252 351320407 351320330 9.250000e-11 78.7
49 TraesCS6A01G141000 chrUn 84.615 78 12 0 175 252 351322638 351322715 9.250000e-11 78.7
50 TraesCS6A01G141000 chrUn 83.750 80 12 1 919 997 71721655 71721576 1.200000e-09 75.0
51 TraesCS6A01G141000 chr7B 96.694 242 7 1 263 504 540160797 540160557 4.830000e-108 401.0
52 TraesCS6A01G141000 chr7B 92.857 168 10 2 761 927 540160560 540160394 3.100000e-60 243.0
53 TraesCS6A01G141000 chr5D 95.918 245 10 0 260 504 480464101 480464345 6.250000e-107 398.0
54 TraesCS6A01G141000 chr5D 96.689 151 5 0 761 911 440319804 440319954 5.150000e-63 252.0
55 TraesCS6A01G141000 chr5D 91.411 163 14 0 2004 2166 137860367 137860529 1.120000e-54 224.0
56 TraesCS6A01G141000 chr4B 96.266 241 9 0 264 504 396387224 396386984 2.250000e-106 396.0
57 TraesCS6A01G141000 chr4B 94.904 157 8 0 761 917 396386987 396386831 2.400000e-61 246.0
58 TraesCS6A01G141000 chr4B 87.356 87 11 0 911 997 358253547 358253633 1.970000e-17 100.0
59 TraesCS6A01G141000 chr4B 94.915 59 3 0 177 235 20582643 20582585 3.300000e-15 93.5
60 TraesCS6A01G141000 chr4B 85.882 85 12 0 175 259 652780309 652780393 1.190000e-14 91.6
61 TraesCS6A01G141000 chr4B 84.444 90 12 1 175 264 642537542 642537455 1.540000e-13 87.9
62 TraesCS6A01G141000 chr4B 85.897 78 11 0 175 252 428180180 428180257 1.990000e-12 84.2
63 TraesCS6A01G141000 chr2A 95.181 249 12 0 256 504 96070403 96070651 8.090000e-106 394.0
64 TraesCS6A01G141000 chr2A 96.296 162 6 0 2490 2651 550050123 550049962 1.840000e-67 267.0
65 TraesCS6A01G141000 chr2A 95.570 158 7 0 2009 2166 550050279 550050122 1.430000e-63 254.0
66 TraesCS6A01G141000 chr2A 93.082 159 11 0 2008 2166 573943829 573943987 1.870000e-57 233.0
67 TraesCS6A01G141000 chr2A 92.500 160 12 0 2007 2166 240440853 240441012 2.410000e-56 230.0
68 TraesCS6A01G141000 chr2A 93.407 91 6 0 175 265 37237450 37237540 5.410000e-28 135.0
69 TraesCS6A01G141000 chr2A 92.222 90 7 0 175 264 46847078 46846989 9.060000e-26 128.0
70 TraesCS6A01G141000 chr2A 89.655 87 9 0 911 997 103238173 103238087 9.120000e-21 111.0
71 TraesCS6A01G141000 chr1B 95.200 250 11 1 256 504 453883556 453883307 8.090000e-106 394.0
72 TraesCS6A01G141000 chr7D 96.154 156 6 0 761 916 7470932 7470777 3.980000e-64 255.0
73 TraesCS6A01G141000 chr7D 93.210 162 11 0 2490 2651 53965362 53965201 4.010000e-59 239.0
74 TraesCS6A01G141000 chr7D 89.655 87 9 0 911 997 530031449 530031535 9.120000e-21 111.0
75 TraesCS6A01G141000 chr3D 93.827 162 10 0 2490 2651 339481921 339482082 8.620000e-61 244.0
76 TraesCS6A01G141000 chr3D 91.176 170 12 3 2490 2657 584345182 584345350 8.680000e-56 228.0
77 TraesCS6A01G141000 chr3D 73.383 402 81 14 1050 1441 563596160 563595775 3.260000e-25 126.0
78 TraesCS6A01G141000 chr1D 93.789 161 9 1 761 920 416482430 416482590 1.120000e-59 241.0
79 TraesCS6A01G141000 chr1D 92.121 165 13 0 2490 2654 361035362 361035198 1.870000e-57 233.0
80 TraesCS6A01G141000 chr1D 91.011 89 8 0 177 265 315380919 315380831 1.520000e-23 121.0
81 TraesCS6A01G141000 chr1D 88.506 87 10 0 911 997 331670325 331670239 4.240000e-19 106.0
82 TraesCS6A01G141000 chr1D 89.024 82 9 0 916 997 190474478 190474559 5.490000e-18 102.0
83 TraesCS6A01G141000 chr1D 84.615 91 14 0 175 265 411728030 411728120 1.190000e-14 91.6
84 TraesCS6A01G141000 chr4D 92.638 163 12 0 2490 2652 224081330 224081492 5.190000e-58 235.0
85 TraesCS6A01G141000 chr4D 92.391 92 7 0 174 265 289295320 289295229 7.000000e-27 132.0
86 TraesCS6A01G141000 chr4D 87.640 89 11 0 177 265 483409278 483409366 1.530000e-18 104.0
87 TraesCS6A01G141000 chr4D 86.207 87 12 0 911 997 403022994 403022908 9.190000e-16 95.3
88 TraesCS6A01G141000 chr4D 85.057 87 13 0 911 997 460165297 460165383 4.270000e-14 89.8
89 TraesCS6A01G141000 chr4D 83.908 87 14 0 911 997 155627402 155627488 1.990000e-12 84.2
90 TraesCS6A01G141000 chr4D 83.908 87 14 0 911 997 329303980 329304066 1.990000e-12 84.2
91 TraesCS6A01G141000 chr6D 92.357 157 12 0 2010 2166 199194466 199194622 1.120000e-54 224.0
92 TraesCS6A01G141000 chr6D 87.356 87 11 0 911 997 34649010 34649096 1.970000e-17 100.0
93 TraesCS6A01G141000 chr6D 87.209 86 11 0 912 997 460279597 460279682 7.100000e-17 99.0
94 TraesCS6A01G141000 chr6D 88.608 79 9 0 919 997 447759907 447759829 2.550000e-16 97.1
95 TraesCS6A01G141000 chr6D 86.207 87 12 0 911 997 183017073 183016987 9.190000e-16 95.3
96 TraesCS6A01G141000 chr6D 85.294 68 7 3 171 236 455885365 455885299 2.000000e-07 67.6
97 TraesCS6A01G141000 chr2D 89.831 177 15 2 2482 2655 347358977 347358801 1.120000e-54 224.0
98 TraesCS6A01G141000 chr6B 90.000 170 15 2 1998 2166 314444150 314443982 5.230000e-53 219.0
99 TraesCS6A01G141000 chr5A 93.182 88 6 0 177 264 370726642 370726729 2.520000e-26 130.0
100 TraesCS6A01G141000 chr3B 92.135 89 7 0 177 265 417053364 417053452 3.260000e-25 126.0
101 TraesCS6A01G141000 chr3B 72.938 388 79 14 1050 1427 751014989 751014618 9.120000e-21 111.0


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 TraesCS6A01G141000 chr6A 115502932 115506043 3111 True 5747 5747 100.000 1 3112 1 chr6A.!!$R1 3111
1 TraesCS6A01G141000 chr6A 115535115 115538226 3111 True 5698 5698 99.711 1 3112 1 chr6A.!!$R2 3111
2 TraesCS6A01G141000 chr6A 454803271 454803813 542 False 715 715 90.476 2010 2553 1 chr6A.!!$F4 543
3 TraesCS6A01G141000 chr4A 638137132 638137728 596 True 529 529 82.696 259 857 1 chr4A.!!$R3 598

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
133 134 3.194116 GGCATTGAATTCACACCATCTGT 59.806 43.478 7.89 0.0 0.00 3.41 F
1382 1387 1.469251 CGGACAGGAAGTACCATCACG 60.469 57.143 0.00 0.0 42.04 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 1351 2.815647 CGCCAGGACGAAGAAGCC 60.816 66.667 0.0 0.0 34.06 4.35 R
2475 2481 4.689062 ACTCATCTACTCCCTCCTTTTCA 58.311 43.478 0.0 0.0 0.00 2.69 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
133 134 3.194116 GGCATTGAATTCACACCATCTGT 59.806 43.478 7.89 0.0 0.00 3.41
1382 1387 1.469251 CGGACAGGAAGTACCATCACG 60.469 57.143 0.00 0.0 42.04 4.35
2017 2022 8.980832 ATTACTCCATTCATATCTACTCCCTT 57.019 34.615 0.00 0.0 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 3.465588 CAGGGGTTAAATAGGGGGATTGA 59.534 47.826 0.00 0.00 0.00 2.57
1346 1351 2.815647 CGCCAGGACGAAGAAGCC 60.816 66.667 0.00 0.00 34.06 4.35
1382 1387 3.144120 GATTGAGAAGACGCGCGGC 62.144 63.158 35.22 33.88 0.00 6.53
2017 2022 9.292195 AGATTTGAACCTTATAAACCGAAAAGA 57.708 29.630 0.00 0.00 0.00 2.52
2475 2481 4.689062 ACTCATCTACTCCCTCCTTTTCA 58.311 43.478 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.