Multiple sequence alignment - TraesCS4A01G278300

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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 TraesCS4A01G278300 chr4A 100.000 5087 0 0 3513 8599 585689660 585694746 0.000000e+00 9395.0
1 TraesCS4A01G278300 chr4A 100.000 3238 0 0 1 3238 585686148 585689385 0.000000e+00 5980.0
2 TraesCS4A01G278300 chr4A 87.579 1739 160 23 766 2466 586678614 586676894 0.000000e+00 1964.0
3 TraesCS4A01G278300 chr4A 86.773 1754 159 28 766 2466 456415423 456413690 0.000000e+00 1886.0
4 TraesCS4A01G278300 chr4A 87.891 1536 123 25 768 2269 538493089 538491583 0.000000e+00 1748.0
5 TraesCS4A01G278300 chr4A 93.897 852 48 3 7752 8599 5352012 5351161 0.000000e+00 1282.0
6 TraesCS4A01G278300 chr4A 85.714 1211 122 26 4032 5208 456402327 456401134 0.000000e+00 1230.0
7 TraesCS4A01G278300 chr4A 85.467 1211 131 25 4032 5208 586676029 586674830 0.000000e+00 1219.0
8 TraesCS4A01G278300 chr4A 92.344 849 61 4 7752 8599 320723194 320722349 0.000000e+00 1205.0
9 TraesCS4A01G278300 chr4A 87.523 1082 85 17 4221 5267 538490076 538489010 0.000000e+00 1205.0
10 TraesCS4A01G278300 chr4A 88.758 765 81 5 2278 3040 538491545 538490784 0.000000e+00 931.0
11 TraesCS4A01G278300 chr4A 93.220 590 37 3 8011 8599 283599402 283598815 0.000000e+00 865.0
12 TraesCS4A01G278300 chr4A 92.662 586 41 2 2508 3093 586676896 586676313 0.000000e+00 843.0
13 TraesCS4A01G278300 chr4A 91.042 614 44 5 5411 6019 586089515 586090122 0.000000e+00 819.0
14 TraesCS4A01G278300 chr4A 89.628 646 50 8 5379 6019 456400803 456400170 0.000000e+00 806.0
15 TraesCS4A01G278300 chr4A 89.319 646 52 7 5379 6019 586674499 586673866 0.000000e+00 795.0
16 TraesCS4A01G278300 chr4A 87.387 555 47 6 4772 5308 586082062 586082611 4.410000e-172 616.0
17 TraesCS4A01G278300 chr4A 95.103 388 11 5 1 382 538494482 538494097 9.550000e-169 604.0
18 TraesCS4A01G278300 chr4A 94.972 358 15 3 403 757 538493523 538493166 7.540000e-155 558.0
19 TraesCS4A01G278300 chr4A 90.164 366 24 9 7112 7474 586091068 586091424 4.700000e-127 466.0
20 TraesCS4A01G278300 chr4A 92.473 279 20 1 6178 6455 586090121 586090399 1.740000e-106 398.0
21 TraesCS4A01G278300 chr4A 82.080 452 52 14 6181 6611 576593650 576593207 8.210000e-95 359.0
22 TraesCS4A01G278300 chr4A 92.237 219 11 4 3713 3927 538490664 538490448 1.080000e-78 305.0
23 TraesCS4A01G278300 chr4A 90.164 183 17 1 7479 7661 538487493 538487312 4.010000e-58 237.0
24 TraesCS4A01G278300 chr4A 85.141 249 14 8 519 760 456415729 456415497 5.190000e-57 233.0
25 TraesCS4A01G278300 chr4A 81.695 295 32 10 94 382 576611899 576611621 8.690000e-55 226.0
26 TraesCS4A01G278300 chr4A 81.293 294 38 10 94 382 576598691 576598410 1.120000e-53 222.0
27 TraesCS4A01G278300 chr4A 90.798 163 14 1 4030 4192 538490312 538490151 5.230000e-52 217.0
28 TraesCS4A01G278300 chr4A 87.368 190 19 3 7473 7661 586091489 586091674 6.760000e-51 213.0
29 TraesCS4A01G278300 chr4A 83.534 249 18 12 519 760 586678920 586678688 2.430000e-50 211.0
30 TraesCS4A01G278300 chr4A 86.339 183 25 0 7479 7661 456398841 456398659 5.260000e-47 200.0
31 TraesCS4A01G278300 chr4A 79.233 313 32 15 6 309 456416043 456415755 4.100000e-43 187.0
32 TraesCS4A01G278300 chr4A 80.282 213 32 8 7752 7957 377612328 377612537 1.500000e-32 152.0
33 TraesCS4A01G278300 chr4A 91.429 70 6 0 5305 5374 586088079 586088148 7.110000e-16 97.1
34 TraesCS4A01G278300 chr4A 82.500 120 5 5 5254 5373 538488846 538488743 3.310000e-14 91.6
35 TraesCS4A01G278300 chr4A 83.333 78 10 3 5300 5374 576606318 576606241 1.550000e-07 69.4
36 TraesCS4A01G278300 chr2A 99.077 5090 43 4 3513 8599 195820771 195825859 0.000000e+00 9136.0
37 TraesCS4A01G278300 chr2A 98.044 1585 19 5 555 2135 195818037 195819613 0.000000e+00 2745.0
38 TraesCS4A01G278300 chr2A 99.150 1059 9 0 2180 3238 195819622 195820680 0.000000e+00 1906.0
39 TraesCS4A01G278300 chr2A 87.883 1535 126 23 768 2269 196118688 196120195 0.000000e+00 1749.0
40 TraesCS4A01G278300 chr2A 87.523 1082 85 17 4221 5267 196121699 196122765 0.000000e+00 1205.0
41 TraesCS4A01G278300 chr2A 89.263 801 61 8 766 1545 196327879 196327083 0.000000e+00 979.0
42 TraesCS4A01G278300 chr2A 89.583 768 76 4 2275 3040 196120230 196120995 0.000000e+00 972.0
43 TraesCS4A01G278300 chr2A 89.000 800 64 10 766 1545 196317281 196316486 0.000000e+00 968.0
44 TraesCS4A01G278300 chr2A 89.014 801 63 8 766 1545 196346171 196345375 0.000000e+00 968.0
45 TraesCS4A01G278300 chr2A 88.155 802 69 8 766 1545 196356459 196355662 0.000000e+00 931.0
46 TraesCS4A01G278300 chr2A 88.030 802 70 8 766 1545 196324076 196323279 0.000000e+00 926.0
47 TraesCS4A01G278300 chr2A 98.698 384 3 2 1 382 196117088 196117471 0.000000e+00 680.0
48 TraesCS4A01G278300 chr2A 95.330 364 14 3 397 757 196118248 196118611 7.490000e-160 575.0
49 TraesCS4A01G278300 chr2A 88.985 463 34 9 6811 7269 196125250 196125699 2.710000e-154 556.0
50 TraesCS4A01G278300 chr2A 91.705 217 16 2 3713 3927 196121115 196121331 5.050000e-77 300.0
51 TraesCS4A01G278300 chr2A 88.845 251 14 6 6365 6611 196124257 196124497 6.530000e-76 296.0
52 TraesCS4A01G278300 chr2A 91.875 160 12 1 4030 4189 196121467 196121625 1.120000e-53 222.0
53 TraesCS4A01G278300 chr2A 83.936 249 17 13 519 760 196317587 196317355 5.230000e-52 217.0
54 TraesCS4A01G278300 chr2A 83.936 249 17 8 519 760 196320545 196320313 5.230000e-52 217.0
55 TraesCS4A01G278300 chr2A 83.673 245 16 9 522 759 196356761 196356534 8.750000e-50 209.0
56 TraesCS4A01G278300 chr2A 86.885 183 24 0 7479 7661 196315070 196314888 1.130000e-48 206.0
57 TraesCS4A01G278300 chr2A 82.500 120 5 5 5254 5373 196122969 196123072 3.310000e-14 91.6
58 TraesCS4A01G278300 chr2A 81.818 99 10 6 6 102 195817687 195817779 9.260000e-10 76.8
59 TraesCS4A01G278300 chr4B 94.208 2020 64 14 4030 6019 25388354 25386358 0.000000e+00 3033.0
60 TraesCS4A01G278300 chr4B 89.594 2364 178 31 766 3093 24764089 24766420 0.000000e+00 2940.0
61 TraesCS4A01G278300 chr4B 96.118 1623 47 5 1556 3178 25393535 25391929 0.000000e+00 2634.0
62 TraesCS4A01G278300 chr4B 85.722 1898 174 60 4185 6019 24766827 24768690 0.000000e+00 1914.0
63 TraesCS4A01G278300 chr4B 80.711 2390 300 78 816 3149 39241558 39243842 0.000000e+00 1711.0
64 TraesCS4A01G278300 chr4B 88.866 970 62 20 6811 7752 24769331 24770282 0.000000e+00 1151.0
65 TraesCS4A01G278300 chr4B 93.091 550 31 1 7208 7750 25385360 25384811 0.000000e+00 798.0
66 TraesCS4A01G278300 chr4B 88.410 673 53 15 6810 7473 24832665 24833321 0.000000e+00 787.0
67 TraesCS4A01G278300 chr4B 90.630 587 43 8 801 1382 25394276 25393697 0.000000e+00 769.0
68 TraesCS4A01G278300 chr4B 90.187 428 38 4 6181 6604 25386356 25385929 9.750000e-154 555.0
69 TraesCS4A01G278300 chr4B 85.385 520 45 12 6704 7206 25385933 25385428 2.140000e-140 510.0
70 TraesCS4A01G278300 chr4B 95.681 301 11 1 3626 3924 25388944 25388644 4.670000e-132 483.0
71 TraesCS4A01G278300 chr4B 87.745 408 37 7 7071 7474 25351967 25351569 1.690000e-126 464.0
72 TraesCS4A01G278300 chr4B 84.475 438 44 13 6178 6611 24768689 24769106 2.230000e-110 411.0
73 TraesCS4A01G278300 chr4B 85.106 282 38 4 1016 1294 24756058 24756338 1.410000e-72 285.0
74 TraesCS4A01G278300 chr4B 80.731 301 40 12 94 382 39240249 39240543 1.450000e-52 219.0
75 TraesCS4A01G278300 chr4B 80.464 302 41 14 7 304 39196391 39196678 1.880000e-51 215.0
76 TraesCS4A01G278300 chr4B 96.063 127 5 0 3513 3639 25390663 25390537 3.150000e-49 207.0
77 TraesCS4A01G278300 chr4B 92.523 107 8 0 1441 1547 25393685 25393579 4.160000e-33 154.0
78 TraesCS4A01G278300 chr4B 98.571 70 0 1 4030 4099 25388432 25388364 1.170000e-23 122.0
79 TraesCS4A01G278300 chr3B 88.248 2374 177 38 766 3093 452703323 452701006 0.000000e+00 2745.0
80 TraesCS4A01G278300 chr3B 85.150 1367 127 28 4032 5374 452699703 452698389 0.000000e+00 1330.0
81 TraesCS4A01G278300 chr3B 87.748 1110 73 22 6690 7752 452697322 452696229 0.000000e+00 1238.0
82 TraesCS4A01G278300 chr3B 88.910 532 41 13 6810 7336 452564204 452563686 2.620000e-179 640.0
83 TraesCS4A01G278300 chr3B 81.089 349 32 21 436 760 452703735 452703397 1.850000e-61 248.0
84 TraesCS4A01G278300 chr3B 80.363 331 36 14 1 311 452704054 452703733 3.120000e-54 224.0
85 TraesCS4A01G278300 chr3B 90.323 93 9 0 3938 4030 670397494 670397586 1.170000e-23 122.0
86 TraesCS4A01G278300 chr1D 85.642 2382 235 45 771 3077 320382064 320384413 0.000000e+00 2405.0
87 TraesCS4A01G278300 chr1D 82.948 1126 118 19 4031 5106 320387409 320388510 0.000000e+00 948.0
88 TraesCS4A01G278300 chr1D 86.795 674 69 12 6811 7478 320390444 320391103 0.000000e+00 734.0
89 TraesCS4A01G278300 chr1D 84.663 326 27 12 70 382 320381146 320381461 3.900000e-78 303.0
90 TraesCS4A01G278300 chr1D 93.750 112 7 0 3605 3716 320386989 320387100 1.480000e-37 169.0
91 TraesCS4A01G278300 chr1B 85.517 2389 237 52 766 3077 433420455 433422811 0.000000e+00 2394.0
92 TraesCS4A01G278300 chr1B 84.492 1122 112 17 4031 5106 433424445 433425550 0.000000e+00 1051.0
93 TraesCS4A01G278300 chr1B 84.000 325 30 11 70 382 433419940 433420254 8.440000e-75 292.0
94 TraesCS4A01G278300 chr1B 86.434 258 31 4 6188 6444 433426240 433426494 6.570000e-71 279.0
95 TraesCS4A01G278300 chr1B 92.778 180 10 2 6020 6199 62431332 62431508 3.080000e-64 257.0
96 TraesCS4A01G278300 chr1B 88.889 99 9 2 6598 6696 296488088 296487992 4.220000e-23 121.0
97 TraesCS4A01G278300 chr4D 90.220 1728 108 16 1441 3140 15157401 15155707 0.000000e+00 2198.0
98 TraesCS4A01G278300 chr4D 87.572 1561 124 17 959 2466 14924629 14926172 0.000000e+00 1744.0
99 TraesCS4A01G278300 chr4D 86.367 1401 124 15 4030 5374 15153820 15152431 0.000000e+00 1467.0
100 TraesCS4A01G278300 chr4D 86.398 1316 97 25 959 2211 14424392 14423096 0.000000e+00 1363.0
101 TraesCS4A01G278300 chr4D 92.356 955 65 6 2200 3149 14403828 14402877 0.000000e+00 1352.0
102 TraesCS4A01G278300 chr4D 81.901 1652 199 41 1474 3102 26896032 26897606 0.000000e+00 1303.0
103 TraesCS4A01G278300 chr4D 91.963 647 43 8 2505 3149 14926167 14926806 0.000000e+00 898.0
104 TraesCS4A01G278300 chr4D 86.935 796 76 18 6690 7474 14399697 14398919 0.000000e+00 869.0
105 TraesCS4A01G278300 chr4D 91.036 647 46 5 5379 6018 14400757 14400116 0.000000e+00 863.0
106 TraesCS4A01G278300 chr4D 91.063 649 43 6 5376 6019 14927054 14927692 0.000000e+00 863.0
107 TraesCS4A01G278300 chr4D 89.806 618 47 8 5412 6019 15151055 15150444 0.000000e+00 778.0
108 TraesCS4A01G278300 chr4D 88.026 618 67 5 766 1382 15158024 15157413 0.000000e+00 725.0
109 TraesCS4A01G278300 chr4D 86.991 638 48 13 4764 5374 14401427 14400798 0.000000e+00 686.0
110 TraesCS4A01G278300 chr4D 86.078 589 56 18 6690 7269 14928102 14928673 2.050000e-170 610.0
111 TraesCS4A01G278300 chr4D 87.558 434 40 11 6181 6611 14400113 14399691 2.790000e-134 490.0
112 TraesCS4A01G278300 chr4D 89.744 390 19 5 3539 3924 15154416 15154044 6.040000e-131 479.0
113 TraesCS4A01G278300 chr4D 90.244 369 28 8 7112 7477 15149566 15149203 7.810000e-130 475.0
114 TraesCS4A01G278300 chr4D 84.932 438 42 13 6178 6611 14927691 14928108 1.030000e-113 422.0
115 TraesCS4A01G278300 chr4D 92.029 276 21 1 6181 6455 15150442 15150167 3.760000e-103 387.0
116 TraesCS4A01G278300 chr4D 86.006 343 35 9 429 760 26894693 26895033 1.060000e-93 355.0
117 TraesCS4A01G278300 chr4D 86.943 314 28 2 4038 4338 14401971 14401658 2.970000e-89 340.0
118 TraesCS4A01G278300 chr4D 89.231 260 20 5 508 760 14424868 14424610 1.390000e-82 318.0
119 TraesCS4A01G278300 chr4D 89.837 246 12 10 526 760 14924168 14924411 3.900000e-78 303.0
120 TraesCS4A01G278300 chr4D 87.895 190 18 3 7473 7661 15149141 15148956 1.450000e-52 219.0
121 TraesCS4A01G278300 chr4D 80.428 327 20 21 6 311 14425219 14424916 8.750000e-50 209.0
122 TraesCS4A01G278300 chr4D 79.635 329 21 20 1 311 15158694 15158394 2.450000e-45 195.0
123 TraesCS4A01G278300 chr4D 78.154 325 33 20 6 311 14923810 14924115 1.150000e-38 172.0
124 TraesCS4A01G278300 chr4D 89.610 77 8 0 3160 3236 14926790 14926866 1.980000e-16 99.0
125 TraesCS4A01G278300 chr4D 90.141 71 6 1 3077 3147 14926793 14926862 3.310000e-14 91.6
126 TraesCS4A01G278300 chr4D 88.732 71 7 1 3077 3147 14402890 14402821 1.540000e-12 86.1
127 TraesCS4A01G278300 chr4D 91.228 57 5 0 3948 4004 9745500 9745444 2.570000e-10 78.7
128 TraesCS4A01G278300 chr5A 85.349 1406 114 31 4030 5374 40874652 40876026 0.000000e+00 1371.0
129 TraesCS4A01G278300 chr5A 92.874 856 56 4 7745 8599 349874970 349875821 0.000000e+00 1238.0
130 TraesCS4A01G278300 chr5A 88.743 533 42 11 6811 7336 40877374 40877895 3.390000e-178 636.0
131 TraesCS4A01G278300 chr5A 90.816 392 27 7 3539 3924 40874041 40874429 4.600000e-142 516.0
132 TraesCS4A01G278300 chr5A 86.239 436 50 8 6178 6609 40876698 40877127 1.690000e-126 464.0
133 TraesCS4A01G278300 chr5A 94.059 101 5 1 3933 4033 34326517 34326616 1.500000e-32 152.0
134 TraesCS4A01G278300 chr5A 89.691 97 10 0 3933 4029 350525103 350525199 3.260000e-24 124.0
135 TraesCS4A01G278300 chr5D 85.334 1391 125 33 4030 5374 51842513 51843870 0.000000e+00 1365.0
136 TraesCS4A01G278300 chr5D 89.541 392 34 5 3539 3924 51841902 51842292 2.790000e-134 490.0
137 TraesCS4A01G278300 chr5D 94.706 170 8 1 6020 6189 517855171 517855003 6.620000e-66 263.0
138 TraesCS4A01G278300 chr5D 92.754 138 10 0 5375 5512 51843907 51844044 5.260000e-47 200.0
139 TraesCS4A01G278300 chr5D 93.750 48 2 1 7746 7792 354870 354823 4.310000e-08 71.3
140 TraesCS4A01G278300 chr3A 92.857 854 54 6 7749 8599 324869054 324869903 0.000000e+00 1232.0
141 TraesCS4A01G278300 chr3A 95.238 168 8 0 6021 6188 568001200 568001367 5.120000e-67 267.0
142 TraesCS4A01G278300 chr3A 88.372 86 10 0 6609 6694 47074676 47074591 4.250000e-18 104.0
143 TraesCS4A01G278300 chr5B 86.236 712 66 11 4038 4721 54825699 54826406 0.000000e+00 743.0
144 TraesCS4A01G278300 chr5B 86.175 651 74 11 5375 6015 54827218 54827862 0.000000e+00 689.0
145 TraesCS4A01G278300 chr5B 89.269 438 43 3 6178 6611 54827865 54828302 5.870000e-151 545.0
146 TraesCS4A01G278300 chr5B 93.989 183 9 2 3592 3774 54825175 54825355 8.500000e-70 276.0
147 TraesCS4A01G278300 chr5B 90.526 95 7 2 3936 4029 600136411 600136318 3.260000e-24 124.0
148 TraesCS4A01G278300 chr5B 89.011 91 10 0 3936 4026 548312228 548312318 7.060000e-21 113.0
149 TraesCS4A01G278300 chr5B 85.859 99 12 2 6601 6698 211588018 211587921 4.250000e-18 104.0
150 TraesCS4A01G278300 chr2D 91.946 298 21 2 7751 8045 188883210 188882913 1.730000e-111 414.0
151 TraesCS4A01G278300 chr2D 95.679 162 7 0 6020 6181 56541156 56540995 2.380000e-65 261.0
152 TraesCS4A01G278300 chr2D 95.918 98 4 0 3936 4033 330456093 330456190 8.930000e-35 159.0
153 TraesCS4A01G278300 chr2D 89.773 88 7 2 6608 6694 500366523 500366609 2.540000e-20 111.0
154 TraesCS4A01G278300 chr2D 87.500 88 11 0 6609 6696 311551653 311551740 1.530000e-17 102.0
155 TraesCS4A01G278300 chr2B 96.364 165 6 0 6017 6181 454080652 454080488 1.100000e-68 272.0
156 TraesCS4A01G278300 chr3D 94.798 173 9 0 6016 6188 571465363 571465535 3.960000e-68 270.0
157 TraesCS4A01G278300 chr3D 94.798 173 9 0 6016 6188 579494957 579494785 3.960000e-68 270.0
158 TraesCS4A01G278300 chr7D 91.489 188 15 1 5996 6182 414094747 414094934 3.080000e-64 257.0
159 TraesCS4A01G278300 chrUn 80.402 199 32 2 7752 7943 98760386 98760584 2.500000e-30 145.0
160 TraesCS4A01G278300 chrUn 88.000 100 9 2 6598 6694 352394923 352394824 1.960000e-21 115.0
161 TraesCS4A01G278300 chr7A 94.624 93 5 0 3936 4028 3589558 3589650 2.500000e-30 145.0
162 TraesCS4A01G278300 chr7A 80.102 196 29 5 7751 7939 133421494 133421302 4.190000e-28 137.0
163 TraesCS4A01G278300 chr7B 91.489 94 8 0 3936 4029 61611957 61611864 7.010000e-26 130.0
164 TraesCS4A01G278300 chr7B 88.764 89 10 0 6608 6696 54323350 54323438 9.130000e-20 110.0
165 TraesCS4A01G278300 chr6D 90.110 91 7 2 6609 6698 438896968 438897057 5.450000e-22 117.0


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 TraesCS4A01G278300 chr4A 585686148 585694746 8598 False 7687.500000 9395 100.000000 1 8599 2 chr4A.!!$F3 8598
1 TraesCS4A01G278300 chr4A 5351161 5352012 851 True 1282.000000 1282 93.897000 7752 8599 1 chr4A.!!$R1 847
2 TraesCS4A01G278300 chr4A 320722349 320723194 845 True 1205.000000 1205 92.344000 7752 8599 1 chr4A.!!$R3 847
3 TraesCS4A01G278300 chr4A 586673866 586678920 5054 True 1006.400000 1964 87.712200 519 6019 5 chr4A.!!$R11 5500
4 TraesCS4A01G278300 chr4A 283598815 283599402 587 True 865.000000 865 93.220000 8011 8599 1 chr4A.!!$R2 588
5 TraesCS4A01G278300 chr4A 456413690 456416043 2353 True 768.666667 1886 83.715667 6 2466 3 chr4A.!!$R9 2460
6 TraesCS4A01G278300 chr4A 456398659 456402327 3668 True 745.333333 1230 87.227000 4032 7661 3 chr4A.!!$R8 3629
7 TraesCS4A01G278300 chr4A 538487312 538494482 7170 True 655.177778 1748 89.994000 1 7661 9 chr4A.!!$R10 7660
8 TraesCS4A01G278300 chr4A 586082062 586082611 549 False 616.000000 616 87.387000 4772 5308 1 chr4A.!!$F2 536
9 TraesCS4A01G278300 chr4A 586088079 586091674 3595 False 398.620000 819 90.495200 5305 7661 5 chr4A.!!$F4 2356
10 TraesCS4A01G278300 chr2A 195817687 195825859 8172 False 3465.950000 9136 94.522250 6 8599 4 chr2A.!!$F1 8593
11 TraesCS4A01G278300 chr2A 196345375 196346171 796 True 968.000000 968 89.014000 766 1545 1 chr2A.!!$R1 779
12 TraesCS4A01G278300 chr2A 196117088 196125699 8611 False 664.660000 1749 90.292700 1 7269 10 chr2A.!!$F2 7268
13 TraesCS4A01G278300 chr2A 196314888 196327879 12991 True 585.500000 979 86.841667 519 7661 6 chr2A.!!$R2 7142
14 TraesCS4A01G278300 chr2A 196355662 196356761 1099 True 570.000000 931 85.914000 522 1545 2 chr2A.!!$R3 1023
15 TraesCS4A01G278300 chr4B 24764089 24770282 6193 False 1604.000000 2940 87.164250 766 7752 4 chr4B.!!$F4 6986
16 TraesCS4A01G278300 chr4B 39240249 39243842 3593 False 965.000000 1711 80.721000 94 3149 2 chr4B.!!$F5 3055
17 TraesCS4A01G278300 chr4B 25384811 25394276 9465 True 926.500000 3033 93.245700 801 7750 10 chr4B.!!$R2 6949
18 TraesCS4A01G278300 chr4B 24832665 24833321 656 False 787.000000 787 88.410000 6810 7473 1 chr4B.!!$F2 663
19 TraesCS4A01G278300 chr3B 452696229 452704054 7825 True 1157.000000 2745 84.519600 1 7752 5 chr3B.!!$R2 7751
20 TraesCS4A01G278300 chr3B 452563686 452564204 518 True 640.000000 640 88.910000 6810 7336 1 chr3B.!!$R1 526
21 TraesCS4A01G278300 chr1D 320381146 320391103 9957 False 911.800000 2405 86.759600 70 7478 5 chr1D.!!$F1 7408
22 TraesCS4A01G278300 chr1B 433419940 433426494 6554 False 1004.000000 2394 85.110750 70 6444 4 chr1B.!!$F2 6374
23 TraesCS4A01G278300 chr4D 26894693 26897606 2913 False 829.000000 1303 83.953500 429 3102 2 chr4D.!!$F2 2673
24 TraesCS4A01G278300 chr4D 15148956 15158694 9738 True 769.222222 2198 88.218444 1 7661 9 chr4D.!!$R4 7660
25 TraesCS4A01G278300 chr4D 14398919 14403828 4909 True 669.442857 1352 88.650143 2200 7474 7 chr4D.!!$R2 5274
26 TraesCS4A01G278300 chr4D 14423096 14425219 2123 True 630.000000 1363 85.352333 6 2211 3 chr4D.!!$R3 2205
27 TraesCS4A01G278300 chr4D 14923810 14928673 4863 False 578.066667 1744 87.705556 6 7269 9 chr4D.!!$F1 7263
28 TraesCS4A01G278300 chr5A 349874970 349875821 851 False 1238.000000 1238 92.874000 7745 8599 1 chr5A.!!$F2 854
29 TraesCS4A01G278300 chr5A 40874041 40877895 3854 False 746.750000 1371 87.786750 3539 7336 4 chr5A.!!$F4 3797
30 TraesCS4A01G278300 chr5D 51841902 51844044 2142 False 685.000000 1365 89.209667 3539 5512 3 chr5D.!!$F1 1973
31 TraesCS4A01G278300 chr3A 324869054 324869903 849 False 1232.000000 1232 92.857000 7749 8599 1 chr3A.!!$F1 850
32 TraesCS4A01G278300 chr5B 54825175 54828302 3127 False 563.250000 743 88.917250 3592 6611 4 chr5B.!!$F2 3019

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
941 8376 0.407528 TTTCAGTGGCCCCTGCATAA 59.592 50.000 10.85 1.98 40.13 1.90 F
945 8380 2.243478 TCAGTGGCCCCTGCATAATAAA 59.757 45.455 10.85 0.00 40.13 1.40 F
2038 12896 0.166597 CGCACAGTTCGCAATGATGT 59.833 50.000 0.00 0.00 0.00 3.06 F
2344 13250 4.219288 GGCATCCTTTCATCTCAACTTGTT 59.781 41.667 0.00 0.00 0.00 2.83 F
3996 21748 4.522022 AGATTGCTATATTTGCCTTCTGCC 59.478 41.667 0.00 0.00 40.16 4.85 F
4344 22404 8.794335 TGCTATACGAGTTCATGATAGATACT 57.206 34.615 0.00 0.00 0.00 2.12 F
5972 27312 4.322057 AGAATATGTGCCCTTTCCTTGT 57.678 40.909 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 12627 2.967946 GCCCCGGCCTCTACAGTTT 61.968 63.158 0.00 0.0 34.56 2.66 R
2344 13250 9.834628 CAACAAACAAAAACTTTACACTCTCTA 57.165 29.630 0.00 0.0 0.00 2.43 R
3996 21748 3.743899 GCTAGAGAAGAAATGCTGGAGGG 60.744 52.174 0.00 0.0 0.00 4.30 R
4227 22281 3.738982 TGTTTGTCTGGTCAATGACGAT 58.261 40.909 7.35 0.0 36.10 3.73 R
5037 23330 6.266103 TGTCAATTTCTTCAGGCTTTCTTCAT 59.734 34.615 0.00 0.0 0.00 2.57 R
6122 27467 3.812156 TTCACTATGGACCACATACGG 57.188 47.619 0.00 0.0 41.03 4.02 R
7778 32186 2.822561 TGCACGCCAATTTATTTCTCCA 59.177 40.909 0.00 0.0 0.00 3.86 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
418 1284 5.072741 TGCTTTAAGATTCCAAGCTGTTCT 58.927 37.500 11.87 0.00 42.91 3.01
439 1305 6.182039 TCTTCATGTCAAAATGTCGAATCC 57.818 37.500 0.00 0.00 0.00 3.01
503 1369 1.121240 CGGCGCAGTATTTAGTCTCG 58.879 55.000 10.83 0.00 0.00 4.04
551 3564 8.501580 TGTATGTACTCTGCGAGTTGTATATAC 58.498 37.037 14.71 5.89 40.28 1.47
941 8376 0.407528 TTTCAGTGGCCCCTGCATAA 59.592 50.000 10.85 1.98 40.13 1.90
945 8380 2.243478 TCAGTGGCCCCTGCATAATAAA 59.757 45.455 10.85 0.00 40.13 1.40
1210 11721 7.065923 GTGTGATGTTTCTCTCCCCTTATTTAC 59.934 40.741 0.00 0.00 0.00 2.01
1769 12627 0.608640 GCTTCCTCCGACTCTTCCAA 59.391 55.000 0.00 0.00 0.00 3.53
2038 12896 0.166597 CGCACAGTTCGCAATGATGT 59.833 50.000 0.00 0.00 0.00 3.06
2143 13013 4.347876 TCTGGAGGACAATCTTTCTCACAA 59.652 41.667 0.00 0.00 0.00 3.33
2344 13250 4.219288 GGCATCCTTTCATCTCAACTTGTT 59.781 41.667 0.00 0.00 0.00 2.83
3996 21748 4.522022 AGATTGCTATATTTGCCTTCTGCC 59.478 41.667 0.00 0.00 40.16 4.85
4227 22281 9.733556 TGTCTGGCTACTTCTTTTATTTTATCA 57.266 29.630 0.00 0.00 0.00 2.15
4344 22404 8.794335 TGCTATACGAGTTCATGATAGATACT 57.206 34.615 0.00 0.00 0.00 2.12
4737 22934 8.948145 CATGGAAGATAAATTGGCAAAAATGAA 58.052 29.630 3.01 0.00 0.00 2.57
5037 23330 5.945191 TGAACTTCATTTGGATCATACAGCA 59.055 36.000 0.00 0.00 0.00 4.41
5971 27311 6.966534 ATAAGAATATGTGCCCTTTCCTTG 57.033 37.500 0.00 0.00 0.00 3.61
5972 27312 4.322057 AGAATATGTGCCCTTTCCTTGT 57.678 40.909 0.00 0.00 0.00 3.16
6360 27706 1.205893 ACGGCAACACACCAAACAAAT 59.794 42.857 0.00 0.00 0.00 2.32
6502 28896 4.605064 AGCTGGGAAGCTTTGCAA 57.395 50.000 0.00 0.00 43.52 4.08
6564 28962 6.014070 TGTGTTCTAATGGACTTTGGCTACTA 60.014 38.462 0.00 0.00 0.00 1.82
7053 30404 4.819769 TCTGAAATTTATTTGGTGCCTGC 58.180 39.130 0.00 0.00 0.00 4.85
7131 30551 7.856145 AAACCAATAACAAAGCATGTTTCAA 57.144 28.000 12.35 0.00 45.86 2.69
7778 32186 1.016627 ATATGCTCGTGCGTTGCAAT 58.983 45.000 9.76 0.00 41.47 3.56
7781 32189 2.965147 GCTCGTGCGTTGCAATGGA 61.965 57.895 19.93 14.92 41.47 3.41
8075 32488 1.247567 CCACACACACAATCCTTCCC 58.752 55.000 0.00 0.00 0.00 3.97
8187 32600 2.352814 CCTCTCGTCCGTTGTCATCTTT 60.353 50.000 0.00 0.00 0.00 2.52
8254 32667 4.457949 CCTATATAAACGGGTGGGAATTGC 59.542 45.833 0.00 0.00 0.00 3.56
8397 32811 1.185315 GCTCAAATAGGCCCAGCAAA 58.815 50.000 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
410 1276 5.561532 CGACATTTTGACATGAAGAACAGCT 60.562 40.000 0.00 0.00 0.00 4.24
418 1284 4.693095 TCGGATTCGACATTTTGACATGAA 59.307 37.500 0.00 0.00 40.88 2.57
439 1305 1.884235 AGCTTTCAGTCCAAGGTTCG 58.116 50.000 0.00 0.00 0.00 3.95
551 3564 1.070821 ACACGTCATGAATCAGTGCG 58.929 50.000 16.69 9.17 36.38 5.34
1210 11721 2.810852 GAGTCAGCAGTGGGAAAGAAAG 59.189 50.000 0.00 0.00 0.00 2.62
1769 12627 2.967946 GCCCCGGCCTCTACAGTTT 61.968 63.158 0.00 0.00 34.56 2.66
2344 13250 9.834628 CAACAAACAAAAACTTTACACTCTCTA 57.165 29.630 0.00 0.00 0.00 2.43
3703 20247 6.235664 AGGGCTCGAAAAAGTAGTAATTCAA 58.764 36.000 0.00 0.00 0.00 2.69
3996 21748 3.743899 GCTAGAGAAGAAATGCTGGAGGG 60.744 52.174 0.00 0.00 0.00 4.30
4227 22281 3.738982 TGTTTGTCTGGTCAATGACGAT 58.261 40.909 7.35 0.00 36.10 3.73
4344 22404 7.760794 GTGAATTCAATGCAGAAACCATCAATA 59.239 33.333 10.35 0.00 0.00 1.90
4482 22545 4.703897 TCGAGAGTTTCTGTCACCAATTT 58.296 39.130 0.00 0.00 0.00 1.82
5037 23330 6.266103 TGTCAATTTCTTCAGGCTTTCTTCAT 59.734 34.615 0.00 0.00 0.00 2.57
6024 27369 6.600882 AAGACTTACATTTAGGAACGGAGA 57.399 37.500 0.00 0.00 0.00 3.71
6122 27467 3.812156 TTCACTATGGACCACATACGG 57.188 47.619 0.00 0.00 41.03 4.02
6502 28896 9.823647 CTCTATAAATATGGCTGAATTCGGTAT 57.176 33.333 15.63 12.34 0.00 2.73
6564 28962 2.035066 GCAGCTTGAACATGTCCAGTTT 59.965 45.455 0.00 0.00 0.00 2.66
7778 32186 2.822561 TGCACGCCAATTTATTTCTCCA 59.177 40.909 0.00 0.00 0.00 3.86
7781 32189 4.175516 CACATGCACGCCAATTTATTTCT 58.824 39.130 0.00 0.00 0.00 2.52
8075 32488 4.761739 TGGGCTCAAAGAATGAACTTACTG 59.238 41.667 0.00 0.00 37.67 2.74
8187 32600 5.996644 TCAACAAGACACCTAGAAAAAGGA 58.003 37.500 0.00 0.00 39.15 3.36
8254 32667 3.519913 ACTCCTACCTTGCTCCTTTAAGG 59.480 47.826 4.29 4.29 46.99 2.69


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

AutoCloner maintained by Alex Coulton.