Multiple sequence alignment - TraesCS5A01G036500

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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 TraesCS5A01G036500 chr5A 100.000 2946 0 0 1 2946 33721712 33718767 0.000000e+00 5441.0
1 TraesCS5A01G036500 chr5A 92.500 720 37 5 1569 2284 263288716 263289422 0.000000e+00 1014.0
2 TraesCS5A01G036500 chr5A 87.946 589 59 10 35 618 144292744 144293325 0.000000e+00 684.0
3 TraesCS5A01G036500 chr5A 87.593 540 56 10 36 567 343026287 343025751 1.500000e-172 616.0
4 TraesCS5A01G036500 chr5A 87.356 522 57 9 35 552 304711731 304712247 9.090000e-165 590.0
5 TraesCS5A01G036500 chr5A 77.720 579 101 25 1594 2158 328239878 328240442 2.190000e-86 329.0
6 TraesCS5A01G036500 chr3D 86.185 1607 151 38 1 1559 230885253 230886836 0.000000e+00 1672.0
7 TraesCS5A01G036500 chr3D 85.599 1611 156 41 1 1559 230877789 230879375 0.000000e+00 1620.0
8 TraesCS5A01G036500 chr3D 81.317 653 86 28 1 632 246521219 246521856 5.670000e-137 497.0
9 TraesCS5A01G036500 chr6D 92.132 877 66 3 685 1559 169181566 169180691 0.000000e+00 1234.0
10 TraesCS5A01G036500 chr6D 84.576 979 94 34 251 1196 251441755 251442709 0.000000e+00 918.0
11 TraesCS5A01G036500 chr6D 91.870 369 29 1 1192 1559 251450309 251450677 5.630000e-142 514.0
12 TraesCS5A01G036500 chr6D 79.232 703 78 36 35 697 169182259 169181585 7.550000e-116 427.0
13 TraesCS5A01G036500 chr6D 80.756 582 80 28 35 601 126531899 126531335 2.710000e-115 425.0
14 TraesCS5A01G036500 chr6D 92.982 57 4 0 666 722 173274222 173274166 1.880000e-12 84.2
15 TraesCS5A01G036500 chr5D 95.331 664 30 1 2284 2946 45741647 45742310 0.000000e+00 1053.0
16 TraesCS5A01G036500 chr5D 93.675 664 39 3 2284 2946 266717657 266716996 0.000000e+00 990.0
17 TraesCS5A01G036500 chr5D 92.500 120 8 1 603 722 220784018 220784136 1.400000e-38 171.0
18 TraesCS5A01G036500 chr4D 94.880 664 33 1 2284 2946 41868007 41867344 0.000000e+00 1037.0
19 TraesCS5A01G036500 chr4D 84.877 529 63 15 35 553 191601320 191600799 4.350000e-143 518.0
20 TraesCS5A01G036500 chr4D 83.547 547 70 18 35 567 245041353 245041893 7.330000e-136 494.0
21 TraesCS5A01G036500 chr4D 80.597 670 86 31 1 638 205398638 205399295 7.390000e-131 477.0
22 TraesCS5A01G036500 chr4D 83.396 530 69 16 35 553 191609071 191608550 9.560000e-130 473.0
23 TraesCS5A01G036500 chr4D 80.781 640 79 31 1 621 228637310 228636696 7.440000e-126 460.0
24 TraesCS5A01G036500 chr4D 80.341 646 84 25 1 622 103655467 103654841 1.610000e-122 449.0
25 TraesCS5A01G036500 chr4D 79.559 680 99 27 1 652 128789736 128789069 1.610000e-122 449.0
26 TraesCS5A01G036500 chr4D 80.438 639 79 32 1 621 228644922 228644312 2.080000e-121 446.0
27 TraesCS5A01G036500 chr4D 84.188 468 49 16 1 451 134310441 134309982 5.830000e-117 431.0
28 TraesCS5A01G036500 chr4D 81.853 529 76 17 35 556 223363779 223364294 7.550000e-116 427.0
29 TraesCS5A01G036500 chr4D 79.608 613 101 21 36 638 103284331 103284929 4.540000e-113 418.0
30 TraesCS5A01G036500 chr4D 78.571 658 109 21 1 638 183794749 183795394 3.540000e-109 405.0
31 TraesCS5A01G036500 chr4D 78.485 660 84 37 1 630 439631931 439632562 2.140000e-101 379.0
32 TraesCS5A01G036500 chr4D 79.125 594 70 37 35 613 213335960 213336514 7.760000e-96 361.0
33 TraesCS5A01G036500 chr4D 76.957 677 107 38 1 642 163272080 163271418 1.010000e-89 340.0
34 TraesCS5A01G036500 chr4D 88.820 161 17 1 760 919 300358545 300358385 2.320000e-46 196.0
35 TraesCS5A01G036500 chr4D 88.820 161 17 1 760 919 439632780 439632940 2.320000e-46 196.0
36 TraesCS5A01G036500 chr4D 91.729 133 10 1 1419 1550 248741416 248741548 1.800000e-42 183.0
37 TraesCS5A01G036500 chr4D 86.875 160 20 1 760 918 313706298 313706139 8.390000e-41 178.0
38 TraesCS5A01G036500 chr4D 80.690 145 16 6 1 134 194933979 194933836 5.190000e-18 102.0
39 TraesCS5A01G036500 chr4D 90.000 60 6 0 663 722 162752442 162752501 8.750000e-11 78.7
40 TraesCS5A01G036500 chr4D 100.000 33 0 0 667 699 245042091 245042123 8.820000e-06 62.1
41 TraesCS5A01G036500 chr3A 94.880 664 33 1 2284 2946 593400207 593400870 0.000000e+00 1037.0
42 TraesCS5A01G036500 chr3A 93.976 664 38 2 2284 2946 644090827 644090165 0.000000e+00 1003.0
43 TraesCS5A01G036500 chr3A 85.448 591 67 15 36 615 242404578 242403996 5.430000e-167 597.0
44 TraesCS5A01G036500 chr3A 86.389 529 59 10 35 556 290278920 290279442 1.530000e-157 566.0
45 TraesCS5A01G036500 chr3A 90.584 308 26 2 609 915 347294957 347294652 3.540000e-109 405.0
46 TraesCS5A01G036500 chr3A 83.486 436 49 13 1 420 368235078 368234650 4.610000e-103 385.0
47 TraesCS5A01G036500 chr3A 88.961 308 31 2 609 915 347143930 347143625 7.710000e-101 377.0
48 TraesCS5A01G036500 chr3A 85.185 81 9 1 1352 1432 325471016 325470939 2.430000e-11 80.5
49 TraesCS5A01G036500 chr1D 94.729 664 34 1 2284 2946 129085587 129086250 0.000000e+00 1031.0
50 TraesCS5A01G036500 chr1D 81.719 640 85 24 1 621 350764899 350764273 3.390000e-139 505.0
51 TraesCS5A01G036500 chr1D 81.534 639 69 28 1 613 253028909 253029524 5.710000e-132 481.0
52 TraesCS5A01G036500 chr1D 80.841 642 87 27 1 622 408895777 408896402 3.440000e-129 472.0
53 TraesCS5A01G036500 chr1D 79.676 679 100 26 1 652 139490189 139489522 3.460000e-124 455.0
54 TraesCS5A01G036500 chr1D 80.220 637 90 24 1 613 321934820 321935444 2.080000e-121 446.0
55 TraesCS5A01G036500 chr1D 82.051 546 70 23 32 562 114999446 114998914 9.690000e-120 440.0
56 TraesCS5A01G036500 chr1D 87.719 171 18 3 752 919 30257031 30257201 2.320000e-46 196.0
57 TraesCS5A01G036500 chr1D 88.199 161 18 1 760 919 268078743 268078583 1.080000e-44 191.0
58 TraesCS5A01G036500 chr1D 93.333 120 7 1 603 722 230528500 230528618 3.020000e-40 176.0
59 TraesCS5A01G036500 chr1D 92.500 120 8 1 603 722 230551522 230551640 1.400000e-38 171.0
60 TraesCS5A01G036500 chr2D 94.428 664 36 1 2284 2946 522582801 522583464 0.000000e+00 1020.0
61 TraesCS5A01G036500 chr2D 80.734 654 78 27 1 629 249849518 249848888 1.600000e-127 466.0
62 TraesCS5A01G036500 chr2D 89.441 161 16 1 760 919 273376529 273376369 4.980000e-48 202.0
63 TraesCS5A01G036500 chr2B 94.419 663 36 1 2284 2945 459938848 459939510 0.000000e+00 1018.0
64 TraesCS5A01G036500 chr2B 80.741 135 14 6 1 124 213758072 213757939 8.690000e-16 95.3
65 TraesCS5A01G036500 chr7D 93.452 672 34 8 2284 2946 392594844 392594174 0.000000e+00 989.0
66 TraesCS5A01G036500 chr7D 80.670 657 90 27 1 632 329475019 329475663 2.660000e-130 475.0
67 TraesCS5A01G036500 chr7D 90.845 142 12 1 1419 1559 427967719 427967578 3.880000e-44 189.0
68 TraesCS5A01G036500 chr7D 89.437 142 14 1 1419 1559 427945773 427945632 8.390000e-41 178.0
69 TraesCS5A01G036500 chr7D 81.507 146 13 6 1 134 295694620 295694477 1.120000e-19 108.0
70 TraesCS5A01G036500 chr2A 82.333 1166 130 38 1 1120 445831731 445832866 0.000000e+00 942.0
71 TraesCS5A01G036500 chr2A 82.709 1122 128 40 35 1120 445839437 445840528 0.000000e+00 937.0
72 TraesCS5A01G036500 chr2A 94.146 615 25 8 1673 2284 533140297 533140903 0.000000e+00 926.0
73 TraesCS5A01G036500 chr2A 93.376 619 33 6 1673 2289 533133059 533133671 0.000000e+00 909.0
74 TraesCS5A01G036500 chr2A 94.671 563 26 4 1725 2284 223269464 223268903 0.000000e+00 870.0
75 TraesCS5A01G036500 chr2A 92.135 623 38 11 1673 2289 124748960 124748343 0.000000e+00 869.0
76 TraesCS5A01G036500 chr2A 94.190 568 31 2 1718 2284 124737159 124736593 0.000000e+00 865.0
77 TraesCS5A01G036500 chr2A 91.948 621 36 12 1678 2289 416728329 416727714 0.000000e+00 857.0
78 TraesCS5A01G036500 chr2A 90.560 625 47 11 1665 2284 416720260 416719643 0.000000e+00 817.0
79 TraesCS5A01G036500 chr2A 89.982 549 50 4 663 1208 372380659 372380113 0.000000e+00 704.0
80 TraesCS5A01G036500 chr2A 86.799 606 58 16 35 621 199949191 199949793 0.000000e+00 656.0
81 TraesCS5A01G036500 chr2A 79.814 753 107 34 1559 2289 285058581 285059310 9.420000e-140 507.0
82 TraesCS5A01G036500 chr6A 94.454 613 30 4 1673 2284 207244888 207245497 0.000000e+00 941.0
83 TraesCS5A01G036500 chr6A 89.583 528 54 1 760 1286 366576866 366577393 0.000000e+00 669.0
84 TraesCS5A01G036500 chr6A 86.168 535 58 14 37 567 496479581 496479059 5.510000e-157 564.0
85 TraesCS5A01G036500 chr6A 86.069 524 65 7 35 553 259798405 259797885 9.220000e-155 556.0
86 TraesCS5A01G036500 chr6A 85.661 537 62 13 36 568 496541040 496540515 4.290000e-153 551.0
87 TraesCS5A01G036500 chr6A 91.878 394 26 5 818 1208 449665270 449665660 2.000000e-151 545.0
88 TraesCS5A01G036500 chr6A 81.299 508 63 21 1 490 55919972 55919479 1.660000e-102 383.0
89 TraesCS5A01G036500 chr6A 84.242 165 18 8 1537 1698 413230497 413230338 1.410000e-33 154.0
90 TraesCS5A01G036500 chr6A 91.026 78 7 0 1355 1432 197826664 197826587 4.020000e-19 106.0
91 TraesCS5A01G036500 chr4A 90.209 623 52 8 1666 2284 348909942 348909325 0.000000e+00 804.0
92 TraesCS5A01G036500 chr4A 84.448 598 77 16 35 624 485339065 485338476 2.550000e-160 575.0
93 TraesCS5A01G036500 chr4A 84.242 165 18 8 1537 1698 261894722 261894881 1.410000e-33 154.0
94 TraesCS5A01G036500 chr7A 84.815 731 84 22 1569 2285 337604746 337605463 0.000000e+00 710.0
95 TraesCS5A01G036500 chr7A 83.673 735 93 22 1569 2289 337596095 337596816 0.000000e+00 667.0
96 TraesCS5A01G036500 chr7A 87.061 541 57 13 35 567 583003341 583003876 1.510000e-167 599.0
97 TraesCS5A01G036500 chr7A 77.157 591 99 32 1585 2157 273332168 273332740 7.930000e-81 311.0
98 TraesCS5A01G036500 chr7A 74.861 720 130 44 1585 2278 277289935 277290629 2.240000e-71 279.0
99 TraesCS5A01G036500 chr7A 88.750 80 7 2 1418 1496 609588010 609588088 2.420000e-16 97.1
100 TraesCS5A01G036500 chr7A 83.495 103 13 4 1444 1543 599414741 599414640 3.130000e-15 93.5
101 TraesCS5A01G036500 chr7A 91.111 45 3 1 1160 1203 242575503 242575547 3.170000e-05 60.2
102 TraesCS5A01G036500 chr1A 89.231 520 52 4 36 553 393824891 393824374 0.000000e+00 647.0
103 TraesCS5A01G036500 chr1A 84.178 651 71 23 1 621 156110875 156111523 1.170000e-168 603.0
104 TraesCS5A01G036500 chr1A 85.664 565 66 9 1 553 209588638 209589199 5.470000e-162 580.0
105 TraesCS5A01G036500 chr1A 86.085 539 63 12 36 566 177423870 177424404 1.180000e-158 569.0
106 TraesCS5A01G036500 chr1A 86.069 524 60 10 35 553 119652825 119652310 4.290000e-153 551.0
107 TraesCS5A01G036500 chr1A 82.722 654 77 26 1 621 156094352 156095002 1.540000e-152 549.0
108 TraesCS5A01G036500 chr1A 83.139 599 82 16 35 618 131925510 131926104 2.010000e-146 529.0
109 TraesCS5A01G036500 chr1A 85.086 523 66 9 35 553 119637482 119636968 9.360000e-145 523.0
110 TraesCS5A01G036500 chr1A 82.658 617 81 18 36 642 188567024 188566424 9.360000e-145 523.0
111 TraesCS5A01G036500 chr1A 83.590 585 69 22 1 564 188921783 188922361 9.360000e-145 523.0
112 TraesCS5A01G036500 chr1A 82.968 593 83 17 38 621 163219962 163219379 1.210000e-143 520.0
113 TraesCS5A01G036500 chr1A 86.829 205 24 3 603 806 315094461 315094663 2.950000e-55 226.0
114 TraesCS5A01G036500 chr1A 81.250 144 16 4 1 134 232351052 232350910 4.020000e-19 106.0
115 TraesCS5A01G036500 chr1A 80.822 146 15 5 1 134 243040700 243040556 5.190000e-18 102.0
116 TraesCS5A01G036500 chr1A 80.952 147 13 8 1 134 408256165 408256309 5.190000e-18 102.0
117 TraesCS5A01G036500 chr1A 79.592 147 15 8 1 134 443691257 443691113 1.120000e-14 91.6
118 TraesCS5A01G036500 chr1A 88.732 71 8 0 1238 1308 362586245 362586315 1.450000e-13 87.9
119 TraesCS5A01G036500 chr1A 89.091 55 4 2 1547 1601 446356493 446356545 1.890000e-07 67.6
120 TraesCS5A01G036500 chrUn 80.865 601 96 15 36 629 293953192 293952604 3.460000e-124 455.0
121 TraesCS5A01G036500 chrUn 80.865 601 96 15 36 629 336415560 336416148 3.460000e-124 455.0
122 TraesCS5A01G036500 chrUn 80.696 575 88 21 38 600 273883204 273882641 2.710000e-115 425.0
123 TraesCS5A01G036500 chrUn 80.100 603 95 23 35 623 387496108 387496699 2.710000e-115 425.0
124 TraesCS5A01G036500 chrUn 79.967 604 90 24 35 621 262755289 262754700 1.630000e-112 416.0
125 TraesCS5A01G036500 chrUn 80.348 575 90 21 38 600 356981858 356981295 5.870000e-112 414.0
126 TraesCS5A01G036500 chrUn 83.455 411 57 11 35 439 428334159 428333754 3.590000e-99 372.0
127 TraesCS5A01G036500 chrUn 83.715 393 54 10 35 423 427679315 427678929 2.160000e-96 363.0
128 TraesCS5A01G036500 chrUn 83.715 393 54 10 35 423 427681899 427681513 2.160000e-96 363.0
129 TraesCS5A01G036500 chrUn 83.376 391 54 11 38 423 447714861 447714477 4.670000e-93 351.0
130 TraesCS5A01G036500 chrUn 83.206 393 54 12 38 424 192795896 192795510 1.680000e-92 350.0
131 TraesCS5A01G036500 chrUn 95.833 48 1 1 654 701 47179466 47179420 3.150000e-10 76.8
132 TraesCS5A01G036500 chrUn 91.489 47 3 1 654 700 47187647 47187602 2.450000e-06 63.9
133 TraesCS5A01G036500 chr4B 79.350 615 89 28 35 630 286808951 286809546 5.920000e-107 398.0
134 TraesCS5A01G036500 chr4B 86.905 252 27 4 666 915 330045983 330046230 8.040000e-71 278.0
135 TraesCS5A01G036500 chr4B 87.907 215 24 2 706 919 344406929 344407142 4.870000e-63 252.0
136 TraesCS5A01G036500 chr4B 85.581 215 30 1 706 919 344414703 344414917 1.060000e-54 224.0
137 TraesCS5A01G036500 chr4B 91.304 115 10 0 609 723 21139581 21139695 1.090000e-34 158.0
138 TraesCS5A01G036500 chr4B 90.517 116 7 3 609 722 444563196 444563309 1.830000e-32 150.0
139 TraesCS5A01G036500 chr6B 79.421 622 78 25 35 622 579798083 579798688 7.650000e-106 394.0
140 TraesCS5A01G036500 chr6B 89.177 231 25 0 609 839 365592764 365592994 3.710000e-74 289.0
141 TraesCS5A01G036500 chr6B 87.045 247 30 2 669 913 627600034 627599788 8.040000e-71 278.0
142 TraesCS5A01G036500 chr6B 87.045 247 30 2 669 913 627827707 627827461 8.040000e-71 278.0
143 TraesCS5A01G036500 chr1B 82.759 145 11 8 1 133 299091772 299091630 1.860000e-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 TraesCS5A01G036500 chr5A 33718767 33721712 2945 True 5441.00 5441 100.0000 1 2946 1 chr5A.!!$R1 2945
1 TraesCS5A01G036500 chr5A 263288716 263289422 706 False 1014.00 1014 92.5000 1569 2284 1 chr5A.!!$F2 715
2 TraesCS5A01G036500 chr5A 144292744 144293325 581 False 684.00 684 87.9460 35 618 1 chr5A.!!$F1 583
3 TraesCS5A01G036500 chr5A 343025751 343026287 536 True 616.00 616 87.5930 36 567 1 chr5A.!!$R2 531
4 TraesCS5A01G036500 chr5A 304711731 304712247 516 False 590.00 590 87.3560 35 552 1 chr5A.!!$F3 517
5 TraesCS5A01G036500 chr5A 328239878 328240442 564 False 329.00 329 77.7200 1594 2158 1 chr5A.!!$F4 564
6 TraesCS5A01G036500 chr3D 230885253 230886836 1583 False 1672.00 1672 86.1850 1 1559 1 chr3D.!!$F2 1558
7 TraesCS5A01G036500 chr3D 230877789 230879375 1586 False 1620.00 1620 85.5990 1 1559 1 chr3D.!!$F1 1558
8 TraesCS5A01G036500 chr3D 246521219 246521856 637 False 497.00 497 81.3170 1 632 1 chr3D.!!$F3 631
9 TraesCS5A01G036500 chr6D 251441755 251442709 954 False 918.00 918 84.5760 251 1196 1 chr6D.!!$F1 945
10 TraesCS5A01G036500 chr6D 169180691 169182259 1568 True 830.50 1234 85.6820 35 1559 2 chr6D.!!$R3 1524
11 TraesCS5A01G036500 chr6D 126531335 126531899 564 True 425.00 425 80.7560 35 601 1 chr6D.!!$R1 566
12 TraesCS5A01G036500 chr5D 45741647 45742310 663 False 1053.00 1053 95.3310 2284 2946 1 chr5D.!!$F1 662
13 TraesCS5A01G036500 chr5D 266716996 266717657 661 True 990.00 990 93.6750 2284 2946 1 chr5D.!!$R1 662
14 TraesCS5A01G036500 chr4D 41867344 41868007 663 True 1037.00 1037 94.8800 2284 2946 1 chr4D.!!$R1 662
15 TraesCS5A01G036500 chr4D 191600799 191601320 521 True 518.00 518 84.8770 35 553 1 chr4D.!!$R6 518
16 TraesCS5A01G036500 chr4D 205398638 205399295 657 False 477.00 477 80.5970 1 638 1 chr4D.!!$F4 637
17 TraesCS5A01G036500 chr4D 191608550 191609071 521 True 473.00 473 83.3960 35 553 1 chr4D.!!$R7 518
18 TraesCS5A01G036500 chr4D 228636696 228637310 614 True 460.00 460 80.7810 1 621 1 chr4D.!!$R9 620
19 TraesCS5A01G036500 chr4D 103654841 103655467 626 True 449.00 449 80.3410 1 622 1 chr4D.!!$R2 621
20 TraesCS5A01G036500 chr4D 128789069 128789736 667 True 449.00 449 79.5590 1 652 1 chr4D.!!$R3 651
21 TraesCS5A01G036500 chr4D 228644312 228644922 610 True 446.00 446 80.4380 1 621 1 chr4D.!!$R10 620
22 TraesCS5A01G036500 chr4D 223363779 223364294 515 False 427.00 427 81.8530 35 556 1 chr4D.!!$F6 521
23 TraesCS5A01G036500 chr4D 103284331 103284929 598 False 418.00 418 79.6080 36 638 1 chr4D.!!$F1 602
24 TraesCS5A01G036500 chr4D 183794749 183795394 645 False 405.00 405 78.5710 1 638 1 chr4D.!!$F3 637
25 TraesCS5A01G036500 chr4D 213335960 213336514 554 False 361.00 361 79.1250 35 613 1 chr4D.!!$F5 578
26 TraesCS5A01G036500 chr4D 163271418 163272080 662 True 340.00 340 76.9570 1 642 1 chr4D.!!$R5 641
27 TraesCS5A01G036500 chr4D 439631931 439632940 1009 False 287.50 379 83.6525 1 919 2 chr4D.!!$F9 918
28 TraesCS5A01G036500 chr4D 245041353 245042123 770 False 278.05 494 91.7735 35 699 2 chr4D.!!$F8 664
29 TraesCS5A01G036500 chr3A 593400207 593400870 663 False 1037.00 1037 94.8800 2284 2946 1 chr3A.!!$F2 662
30 TraesCS5A01G036500 chr3A 644090165 644090827 662 True 1003.00 1003 93.9760 2284 2946 1 chr3A.!!$R6 662
31 TraesCS5A01G036500 chr3A 242403996 242404578 582 True 597.00 597 85.4480 36 615 1 chr3A.!!$R1 579
32 TraesCS5A01G036500 chr3A 290278920 290279442 522 False 566.00 566 86.3890 35 556 1 chr3A.!!$F1 521
33 TraesCS5A01G036500 chr1D 129085587 129086250 663 False 1031.00 1031 94.7290 2284 2946 1 chr1D.!!$F2 662
34 TraesCS5A01G036500 chr1D 350764273 350764899 626 True 505.00 505 81.7190 1 621 1 chr1D.!!$R4 620
35 TraesCS5A01G036500 chr1D 253028909 253029524 615 False 481.00 481 81.5340 1 613 1 chr1D.!!$F5 612
36 TraesCS5A01G036500 chr1D 408895777 408896402 625 False 472.00 472 80.8410 1 622 1 chr1D.!!$F7 621
37 TraesCS5A01G036500 chr1D 139489522 139490189 667 True 455.00 455 79.6760 1 652 1 chr1D.!!$R2 651
38 TraesCS5A01G036500 chr1D 321934820 321935444 624 False 446.00 446 80.2200 1 613 1 chr1D.!!$F6 612
39 TraesCS5A01G036500 chr1D 114998914 114999446 532 True 440.00 440 82.0510 32 562 1 chr1D.!!$R1 530
40 TraesCS5A01G036500 chr2D 522582801 522583464 663 False 1020.00 1020 94.4280 2284 2946 1 chr2D.!!$F1 662
41 TraesCS5A01G036500 chr2D 249848888 249849518 630 True 466.00 466 80.7340 1 629 1 chr2D.!!$R1 628
42 TraesCS5A01G036500 chr2B 459938848 459939510 662 False 1018.00 1018 94.4190 2284 2945 1 chr2B.!!$F1 661
43 TraesCS5A01G036500 chr7D 392594174 392594844 670 True 989.00 989 93.4520 2284 2946 1 chr7D.!!$R2 662
44 TraesCS5A01G036500 chr7D 329475019 329475663 644 False 475.00 475 80.6700 1 632 1 chr7D.!!$F1 631
45 TraesCS5A01G036500 chr2A 445831731 445832866 1135 False 942.00 942 82.3330 1 1120 1 chr2A.!!$F3 1119
46 TraesCS5A01G036500 chr2A 445839437 445840528 1091 False 937.00 937 82.7090 35 1120 1 chr2A.!!$F4 1085
47 TraesCS5A01G036500 chr2A 533140297 533140903 606 False 926.00 926 94.1460 1673 2284 1 chr2A.!!$F6 611
48 TraesCS5A01G036500 chr2A 533133059 533133671 612 False 909.00 909 93.3760 1673 2289 1 chr2A.!!$F5 616
49 TraesCS5A01G036500 chr2A 223268903 223269464 561 True 870.00 870 94.6710 1725 2284 1 chr2A.!!$R3 559
50 TraesCS5A01G036500 chr2A 124748343 124748960 617 True 869.00 869 92.1350 1673 2289 1 chr2A.!!$R2 616
51 TraesCS5A01G036500 chr2A 124736593 124737159 566 True 865.00 865 94.1900 1718 2284 1 chr2A.!!$R1 566
52 TraesCS5A01G036500 chr2A 416727714 416728329 615 True 857.00 857 91.9480 1678 2289 1 chr2A.!!$R6 611
53 TraesCS5A01G036500 chr2A 416719643 416720260 617 True 817.00 817 90.5600 1665 2284 1 chr2A.!!$R5 619
54 TraesCS5A01G036500 chr2A 372380113 372380659 546 True 704.00 704 89.9820 663 1208 1 chr2A.!!$R4 545
55 TraesCS5A01G036500 chr2A 199949191 199949793 602 False 656.00 656 86.7990 35 621 1 chr2A.!!$F1 586
56 TraesCS5A01G036500 chr2A 285058581 285059310 729 False 507.00 507 79.8140 1559 2289 1 chr2A.!!$F2 730
57 TraesCS5A01G036500 chr6A 207244888 207245497 609 False 941.00 941 94.4540 1673 2284 1 chr6A.!!$F1 611
58 TraesCS5A01G036500 chr6A 366576866 366577393 527 False 669.00 669 89.5830 760 1286 1 chr6A.!!$F2 526
59 TraesCS5A01G036500 chr6A 496479059 496479581 522 True 564.00 564 86.1680 37 567 1 chr6A.!!$R5 530
60 TraesCS5A01G036500 chr6A 259797885 259798405 520 True 556.00 556 86.0690 35 553 1 chr6A.!!$R3 518
61 TraesCS5A01G036500 chr6A 496540515 496541040 525 True 551.00 551 85.6610 36 568 1 chr6A.!!$R6 532
62 TraesCS5A01G036500 chr4A 348909325 348909942 617 True 804.00 804 90.2090 1666 2284 1 chr4A.!!$R1 618
63 TraesCS5A01G036500 chr4A 485338476 485339065 589 True 575.00 575 84.4480 35 624 1 chr4A.!!$R2 589
64 TraesCS5A01G036500 chr7A 337604746 337605463 717 False 710.00 710 84.8150 1569 2285 1 chr7A.!!$F5 716
65 TraesCS5A01G036500 chr7A 337596095 337596816 721 False 667.00 667 83.6730 1569 2289 1 chr7A.!!$F4 720
66 TraesCS5A01G036500 chr7A 583003341 583003876 535 False 599.00 599 87.0610 35 567 1 chr7A.!!$F6 532
67 TraesCS5A01G036500 chr7A 273332168 273332740 572 False 311.00 311 77.1570 1585 2157 1 chr7A.!!$F2 572
68 TraesCS5A01G036500 chr7A 277289935 277290629 694 False 279.00 279 74.8610 1585 2278 1 chr7A.!!$F3 693
69 TraesCS5A01G036500 chr1A 393824374 393824891 517 True 647.00 647 89.2310 36 553 1 chr1A.!!$R7 517
70 TraesCS5A01G036500 chr1A 156110875 156111523 648 False 603.00 603 84.1780 1 621 1 chr1A.!!$F3 620
71 TraesCS5A01G036500 chr1A 209588638 209589199 561 False 580.00 580 85.6640 1 553 1 chr1A.!!$F6 552
72 TraesCS5A01G036500 chr1A 177423870 177424404 534 False 569.00 569 86.0850 36 566 1 chr1A.!!$F4 530
73 TraesCS5A01G036500 chr1A 119652310 119652825 515 True 551.00 551 86.0690 35 553 1 chr1A.!!$R2 518
74 TraesCS5A01G036500 chr1A 156094352 156095002 650 False 549.00 549 82.7220 1 621 1 chr1A.!!$F2 620
75 TraesCS5A01G036500 chr1A 131925510 131926104 594 False 529.00 529 83.1390 35 618 1 chr1A.!!$F1 583
76 TraesCS5A01G036500 chr1A 119636968 119637482 514 True 523.00 523 85.0860 35 553 1 chr1A.!!$R1 518
77 TraesCS5A01G036500 chr1A 188566424 188567024 600 True 523.00 523 82.6580 36 642 1 chr1A.!!$R4 606
78 TraesCS5A01G036500 chr1A 188921783 188922361 578 False 523.00 523 83.5900 1 564 1 chr1A.!!$F5 563
79 TraesCS5A01G036500 chr1A 163219379 163219962 583 True 520.00 520 82.9680 38 621 1 chr1A.!!$R3 583
80 TraesCS5A01G036500 chrUn 293952604 293953192 588 True 455.00 455 80.8650 36 629 1 chrUn.!!$R6 593
81 TraesCS5A01G036500 chrUn 336415560 336416148 588 False 455.00 455 80.8650 36 629 1 chrUn.!!$F1 593
82 TraesCS5A01G036500 chrUn 273882641 273883204 563 True 425.00 425 80.6960 38 600 1 chrUn.!!$R5 562
83 TraesCS5A01G036500 chrUn 387496108 387496699 591 False 425.00 425 80.1000 35 623 1 chrUn.!!$F2 588
84 TraesCS5A01G036500 chrUn 262754700 262755289 589 True 416.00 416 79.9670 35 621 1 chrUn.!!$R4 586
85 TraesCS5A01G036500 chrUn 356981295 356981858 563 True 414.00 414 80.3480 38 600 1 chrUn.!!$R7 562
86 TraesCS5A01G036500 chrUn 427678929 427681899 2970 True 363.00 363 83.7150 35 423 2 chrUn.!!$R10 388
87 TraesCS5A01G036500 chr4B 286808951 286809546 595 False 398.00 398 79.3500 35 630 1 chr4B.!!$F2 595
88 TraesCS5A01G036500 chr6B 579798083 579798688 605 False 394.00 394 79.4210 35 622 1 chr6B.!!$F2 587

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
806 3727 1.189524 TGGGTGTCGAGGTACTTGGG 61.19 60.0 0.0 0.0 41.55 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 5586 1.81806 TCAATGGTGCAACAGGTATGC 59.182 47.619 11.62 0.0 44.08 3.14 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
125 148 4.519540 ACAACAATTCCGGAAAATCCTG 57.480 40.909 23.08 16.47 33.30 3.86
135 162 3.441163 CGGAAAATCCTGATGTGCATTG 58.559 45.455 0.00 0.00 33.30 2.82
393 3064 3.451793 GTGTCATGCACGGATGGTA 57.548 52.632 0.00 0.00 38.45 3.25
472 3166 3.852286 AGTAACATTCACGTGCGGATAA 58.148 40.909 11.67 0.00 0.00 1.75
735 3656 7.470147 CGGTAGTGATACATCTTGTAGTGGAAT 60.470 40.741 0.00 0.00 36.14 3.01
781 3702 5.993891 CGTAGTGGTACGCATTCTATAAGA 58.006 41.667 0.00 0.00 45.22 2.10
796 3717 1.608055 TAAGAGAACGTGGGTGTCGA 58.392 50.000 0.00 0.00 0.00 4.20
806 3727 1.189524 TGGGTGTCGAGGTACTTGGG 61.190 60.000 0.00 0.00 41.55 4.12
809 3730 1.192428 GTGTCGAGGTACTTGGGGAT 58.808 55.000 0.00 0.00 41.55 3.85
915 3843 1.973812 GGGGAGGTCAAAGCAGCAC 60.974 63.158 0.00 0.00 0.00 4.40
919 3847 2.281484 GGTCAAAGCAGCACCGGA 60.281 61.111 9.46 0.00 0.00 5.14
927 3855 2.749044 CAGCACCGGAGCAAGCAT 60.749 61.111 26.04 1.20 36.85 3.79
987 3915 2.586635 AACGGCAACAGCGAACGA 60.587 55.556 0.00 0.00 0.00 3.85
1018 3946 2.048444 CATGGATGGAGGTGGAAGTG 57.952 55.000 0.00 0.00 0.00 3.16
1022 3950 0.615331 GATGGAGGTGGAAGTGCAGA 59.385 55.000 0.00 0.00 0.00 4.26
1044 3972 1.754745 GGAGGTGGAAGTGCAGACA 59.245 57.895 0.00 0.00 0.00 3.41
1281 4212 3.717294 GTGGCCTCCATGGTCGGT 61.717 66.667 12.58 0.00 45.26 4.69
1376 4307 2.066999 GGAAGAGGATCCTGGGCGT 61.067 63.158 22.02 2.52 36.50 5.68
1492 4423 0.981277 GGGGAAGGGGAGATCGAACA 60.981 60.000 0.00 0.00 0.00 3.18
1506 4437 4.961511 AACAAGGCACGCGCTCGA 62.962 61.111 5.73 0.00 39.41 4.04
1515 4446 1.818363 ACGCGCTCGATGTCTCCTA 60.818 57.895 5.73 0.00 39.41 2.94
1555 4487 1.834822 GGAGAGACCAGGGGATCGG 60.835 68.421 0.00 0.00 38.79 4.18
1559 4491 2.282446 GACCAGGGGATCGGGAGA 59.718 66.667 0.00 0.00 46.90 3.71
1560 4492 1.834822 GACCAGGGGATCGGGAGAG 60.835 68.421 0.00 0.00 45.48 3.20
1561 4493 2.299727 GACCAGGGGATCGGGAGAGA 62.300 65.000 0.00 0.00 45.48 3.10
1562 4494 1.532794 CCAGGGGATCGGGAGAGAG 60.533 68.421 0.00 0.00 45.48 3.20
1563 4495 2.200092 AGGGGATCGGGAGAGAGC 59.800 66.667 0.00 0.00 45.48 4.09
1564 4496 3.299190 GGGGATCGGGAGAGAGCG 61.299 72.222 0.00 0.00 45.48 5.03
1565 4497 2.519780 GGGATCGGGAGAGAGCGT 60.520 66.667 0.00 0.00 45.48 5.07
1566 4498 2.725008 GGATCGGGAGAGAGCGTG 59.275 66.667 0.00 0.00 45.48 5.34
1567 4499 1.824329 GGATCGGGAGAGAGCGTGA 60.824 63.158 0.00 0.00 45.48 4.35
1576 4508 1.133407 GAGAGAGCGTGACTAGGGTTG 59.867 57.143 0.00 0.00 0.00 3.77
1577 4509 1.174783 GAGAGCGTGACTAGGGTTGA 58.825 55.000 0.00 0.00 0.00 3.18
1784 4732 3.451902 ACACGGATAAATTTCCCGGACTA 59.548 43.478 25.82 0.00 46.83 2.59
1918 4872 9.541143 GAAGGTCCAAAAATGTTCAGATTTTTA 57.459 29.630 6.99 0.00 41.47 1.52
1943 4897 4.042062 TGGAGCTCCGGAATATGATGAAAT 59.958 41.667 27.43 0.00 39.43 2.17
1961 4917 9.585369 TGATGAAATAATATATGGCAAGGTTGA 57.415 29.630 0.00 0.00 0.00 3.18
1984 4940 8.498054 TGAAGACCAAGAATTAAGATAGCAAG 57.502 34.615 0.00 0.00 0.00 4.01
2005 4969 3.717913 AGGGCATTGGGATATTTTGCAAT 59.282 39.130 0.00 0.00 35.04 3.56
2240 5229 4.055360 ACAAATCACACGACGAATCTCAA 58.945 39.130 0.00 0.00 0.00 3.02
2262 5251 6.155565 TCAAAAATCATGGAAGGCATCTGAAT 59.844 34.615 0.00 0.00 0.00 2.57
2272 5261 1.270041 GGCATCTGAATCTCCGGTCTC 60.270 57.143 0.00 0.00 0.00 3.36
2498 5498 3.636300 ACAACACTTGTAATGTGCATGGT 59.364 39.130 0.00 0.00 45.01 3.55
2549 5549 9.677567 TTGAAACTAAAATCAACATAGAGCAAC 57.322 29.630 0.00 0.00 30.94 4.17
2558 5558 7.928307 ATCAACATAGAGCAACTTACAACAT 57.072 32.000 0.00 0.00 0.00 2.71
2573 5573 7.754625 ACTTACAACATCAAACACGTTAAAGT 58.245 30.769 0.00 0.00 0.00 2.66
2576 5576 9.705471 TTACAACATCAAACACGTTAAAGTAAG 57.295 29.630 0.00 0.00 0.00 2.34
2586 5586 9.992910 AAACACGTTAAAGTAAGAGGTTTAAAG 57.007 29.630 5.54 0.00 35.21 1.85
2807 5807 2.614829 ACTAACTGCTCGTGTTTGGT 57.385 45.000 0.00 0.00 0.00 3.67
2811 5812 1.299541 ACTGCTCGTGTTTGGTTCTG 58.700 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.661222 TCACCTCTTGCCATGTTTTCATA 58.339 39.130 0.00 0.00 38.64 2.15
32 33 3.858503 GCTTCACCTCTTGCCATGTTTTC 60.859 47.826 0.00 0.00 0.00 2.29
33 34 2.036346 GCTTCACCTCTTGCCATGTTTT 59.964 45.455 0.00 0.00 0.00 2.43
78 98 5.317733 TGTTTCCGGCCATATTTAAACTG 57.682 39.130 2.24 0.00 0.00 3.16
89 109 0.173708 GTTGTTGTTGTTTCCGGCCA 59.826 50.000 2.24 0.00 0.00 5.36
135 162 7.927305 AAAATTGTTGTTGCATTAAATTGCC 57.073 28.000 0.00 0.00 42.06 4.52
472 3166 5.670792 ATGAGATGCATGTTTGGATGTTT 57.329 34.783 2.46 0.00 33.54 2.83
776 3697 2.163815 CTCGACACCCACGTTCTCTTAT 59.836 50.000 0.00 0.00 0.00 1.73
779 3700 1.524863 CCTCGACACCCACGTTCTCT 61.525 60.000 0.00 0.00 0.00 3.10
781 3702 0.538057 TACCTCGACACCCACGTTCT 60.538 55.000 0.00 0.00 0.00 3.01
796 3717 1.412649 CCCTCGTATCCCCAAGTACCT 60.413 57.143 0.00 0.00 0.00 3.08
806 3727 2.504519 GGTGCACCCCTCGTATCC 59.495 66.667 26.31 0.00 0.00 2.59
915 3843 2.409870 GGACCAATGCTTGCTCCGG 61.410 63.158 0.00 0.00 0.00 5.14
919 3847 2.338015 CGCTGGACCAATGCTTGCT 61.338 57.895 0.00 0.00 0.00 3.91
987 3915 2.683465 ATCCATGGTGCCTCCGCTT 61.683 57.895 12.58 0.00 39.52 4.68
1010 3938 0.946221 CTCCGTGTCTGCACTTCCAC 60.946 60.000 0.00 0.00 43.16 4.02
1012 3940 1.374758 CCTCCGTGTCTGCACTTCC 60.375 63.158 0.00 0.00 43.16 3.46
1014 3942 1.069765 CACCTCCGTGTCTGCACTT 59.930 57.895 0.00 0.00 43.16 3.16
1017 3945 2.099652 CTTCCACCTCCGTGTCTGCA 62.100 60.000 0.00 0.00 38.41 4.41
1018 3946 1.374758 CTTCCACCTCCGTGTCTGC 60.375 63.158 0.00 0.00 38.41 4.26
1022 3950 2.383245 CTGCACTTCCACCTCCGTGT 62.383 60.000 0.00 0.00 38.41 4.49
1025 3953 1.374758 GTCTGCACTTCCACCTCCG 60.375 63.158 0.00 0.00 0.00 4.63
1064 3992 2.097038 CCTTGCTCCGTCTCTTGCG 61.097 63.158 0.00 0.00 0.00 4.85
1217 4148 2.436646 CCATCGCTTTGCTCCCGT 60.437 61.111 0.00 0.00 0.00 5.28
1225 4156 2.040544 CCACCGCTTCCATCGCTTT 61.041 57.895 0.00 0.00 0.00 3.51
1345 4276 4.680237 CTTCCTCCACGCGTGCCA 62.680 66.667 33.17 20.07 0.00 4.92
1376 4307 1.984570 CCCTCCTTCGTCAGCTCCA 60.985 63.158 0.00 0.00 0.00 3.86
1434 4365 2.365370 CCTCCTCCCTCTGCTGCT 60.365 66.667 0.00 0.00 0.00 4.24
1492 4423 4.742201 ACATCGAGCGCGTGCCTT 62.742 61.111 19.02 0.00 44.31 4.35
1528 4460 1.099689 CTGGTCTCTCCCTCTCGTTC 58.900 60.000 0.00 0.00 34.77 3.95
1555 4487 0.394625 ACCCTAGTCACGCTCTCTCC 60.395 60.000 0.00 0.00 0.00 3.71
1559 4491 1.178276 CTCAACCCTAGTCACGCTCT 58.822 55.000 0.00 0.00 0.00 4.09
1560 4492 1.174783 TCTCAACCCTAGTCACGCTC 58.825 55.000 0.00 0.00 0.00 5.03
1561 4493 1.546476 CTTCTCAACCCTAGTCACGCT 59.454 52.381 0.00 0.00 0.00 5.07
1562 4494 1.404315 CCTTCTCAACCCTAGTCACGC 60.404 57.143 0.00 0.00 0.00 5.34
1563 4495 1.404315 GCCTTCTCAACCCTAGTCACG 60.404 57.143 0.00 0.00 0.00 4.35
1564 4496 1.623811 TGCCTTCTCAACCCTAGTCAC 59.376 52.381 0.00 0.00 0.00 3.67
1565 4497 1.902508 CTGCCTTCTCAACCCTAGTCA 59.097 52.381 0.00 0.00 0.00 3.41
1566 4498 1.208293 CCTGCCTTCTCAACCCTAGTC 59.792 57.143 0.00 0.00 0.00 2.59
1567 4499 1.280457 CCTGCCTTCTCAACCCTAGT 58.720 55.000 0.00 0.00 0.00 2.57
1711 4647 9.905171 CTCTTTCTTTTTCTCCTCTTTAATTGG 57.095 33.333 0.00 0.00 0.00 3.16
1784 4732 3.791973 TGGAACGAGCACATTTTTGTT 57.208 38.095 0.00 0.00 0.00 2.83
1918 4872 2.088104 TCATATTCCGGAGCTCCACT 57.912 50.000 31.67 14.96 35.14 4.00
1961 4917 6.830838 CCCTTGCTATCTTAATTCTTGGTCTT 59.169 38.462 0.00 0.00 0.00 3.01
1984 4940 3.557228 TTGCAAAATATCCCAATGCCC 57.443 42.857 0.00 0.00 36.20 5.36
2005 4969 6.678568 ATTTGGAATCACCCATAAACACAA 57.321 33.333 0.00 0.00 35.87 3.33
2240 5229 5.897824 AGATTCAGATGCCTTCCATGATTTT 59.102 36.000 0.00 0.00 33.29 1.82
2272 5261 3.866883 AAATGAGTTTGTAATGCCCCG 57.133 42.857 0.00 0.00 0.00 5.73
2311 5300 9.693739 TTTATGTTGTTATCATGTCCACCTTAT 57.306 29.630 0.00 0.00 0.00 1.73
2386 5386 8.007405 TCGAACTGTATCTATCTTGATTTGGA 57.993 34.615 0.00 0.00 0.00 3.53
2436 5436 7.914427 TCCCACACTTATATTCTGTCTATGT 57.086 36.000 0.00 0.00 0.00 2.29
2549 5549 9.705471 TTACTTTAACGTGTTTGATGTTGTAAG 57.295 29.630 0.00 0.00 35.33 2.34
2558 5558 7.614124 AAACCTCTTACTTTAACGTGTTTGA 57.386 32.000 0.00 0.00 0.00 2.69
2573 5573 6.150474 GCAACAGGTATGCTTTAAACCTCTTA 59.850 38.462 0.00 0.00 41.75 2.10
2576 5576 4.217550 TGCAACAGGTATGCTTTAAACCTC 59.782 41.667 0.00 0.00 41.75 3.85
2586 5586 1.818060 TCAATGGTGCAACAGGTATGC 59.182 47.619 11.62 0.00 44.08 3.14
2807 5807 1.046472 ACCGTCTCCACCACACAGAA 61.046 55.000 0.00 0.00 0.00 3.02
2811 5812 2.665185 GCACCGTCTCCACCACAC 60.665 66.667 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.