Multiple sequence alignment - TraesCS3A01G504600

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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 TraesCS3A01G504600 chr3A 100.000 8637 0 0 1 8637 726534971 726543607 0.000000e+00 15950.0
1 TraesCS3A01G504600 chr3A 95.719 841 30 3 1 841 636491268 636492102 0.000000e+00 1349.0
2 TraesCS3A01G504600 chr3A 95.244 841 34 3 1 841 457218485 457219319 0.000000e+00 1327.0
3 TraesCS3A01G504600 chr3A 85.969 898 90 22 2550 3430 726440155 726441033 0.000000e+00 928.0
4 TraesCS3A01G504600 chr3A 86.529 824 100 8 3641 4462 726688625 726689439 0.000000e+00 896.0
5 TraesCS3A01G504600 chr3A 87.445 677 62 8 1952 2618 726686868 726687531 0.000000e+00 758.0
6 TraesCS3A01G504600 chr3A 83.632 837 88 23 2201 3012 726389293 726388481 0.000000e+00 741.0
7 TraesCS3A01G504600 chr3A 85.133 565 59 17 2880 3429 726687683 726688237 9.800000e-154 555.0
8 TraesCS3A01G504600 chr3A 90.998 411 22 5 4680 5088 681554972 681554575 2.740000e-149 540.0
9 TraesCS3A01G504600 chr3A 88.318 428 31 10 6829 7244 681527911 681527491 6.020000e-136 496.0
10 TraesCS3A01G504600 chr3A 97.368 190 4 1 5880 6069 681528572 681528384 1.080000e-83 322.0
11 TraesCS3A01G504600 chr3A 88.281 256 23 5 3641 3890 726441395 726441649 5.070000e-77 300.0
12 TraesCS3A01G504600 chr3A 79.335 421 57 25 7733 8143 726862928 726862528 1.430000e-67 268.0
13 TraesCS3A01G504600 chr3A 78.973 409 51 18 1187 1567 726513738 726514139 6.700000e-61 246.0
14 TraesCS3A01G504600 chr3A 90.503 179 13 1 1773 1951 726390002 726389828 5.210000e-57 233.0
15 TraesCS3A01G504600 chr3A 81.702 235 30 7 7486 7720 726444626 726444847 5.330000e-42 183.0
16 TraesCS3A01G504600 chr3A 81.095 201 8 9 1540 1732 726390612 726390434 5.440000e-27 134.0
17 TraesCS3A01G504600 chr3A 94.737 76 4 0 3499 3574 726441364 726441439 1.520000e-22 119.0
18 TraesCS3A01G504600 chr3A 92.593 81 4 1 3496 3574 726688589 726688669 1.970000e-21 115.0
19 TraesCS3A01G504600 chr3A 100.000 28 0 0 1746 1773 217822263 217822236 1.600000e-02 52.8
20 TraesCS3A01G504600 chr7B 99.781 2742 5 1 4675 7416 630128863 630131603 0.000000e+00 5029.0
21 TraesCS3A01G504600 chr7B 98.605 2151 27 2 4680 6828 607324666 607326815 0.000000e+00 3803.0
22 TraesCS3A01G504600 chr7B 96.271 590 13 4 6829 7409 607327540 607328129 0.000000e+00 959.0
23 TraesCS3A01G504600 chr7B 85.530 774 77 17 4671 5438 288170144 288169400 0.000000e+00 776.0
24 TraesCS3A01G504600 chr7B 79.202 351 36 21 8322 8637 44238129 44238477 8.790000e-50 209.0
25 TraesCS3A01G504600 chr7B 77.647 340 46 22 8322 8637 705531735 705532068 6.890000e-41 180.0
26 TraesCS3A01G504600 chr2B 99.122 2734 19 4 4680 7410 549705169 549707900 0.000000e+00 4911.0
27 TraesCS3A01G504600 chr6A 99.158 2732 13 3 4680 7410 426957314 426960036 0.000000e+00 4909.0
28 TraesCS3A01G504600 chr5B 98.377 2157 26 3 4680 6828 6685585 6683430 0.000000e+00 3781.0
29 TraesCS3A01G504600 chr5B 96.748 492 12 3 6923 7410 6682071 6681580 0.000000e+00 817.0
30 TraesCS3A01G504600 chr2A 97.908 2151 41 3 4680 6828 731338712 731336564 0.000000e+00 3720.0
31 TraesCS3A01G504600 chr2A 95.363 841 33 3 1 841 560769738 560770572 0.000000e+00 1332.0
32 TraesCS3A01G504600 chr2A 95.244 841 36 1 1 841 264895084 264894248 0.000000e+00 1328.0
33 TraesCS3A01G504600 chr2A 95.000 840 38 2 2 841 319899919 319899084 0.000000e+00 1315.0
34 TraesCS3A01G504600 chr2A 94.887 841 38 3 1 841 390815978 390815143 0.000000e+00 1310.0
35 TraesCS3A01G504600 chr2A 92.386 591 22 14 6829 7410 731335792 731335216 0.000000e+00 821.0
36 TraesCS3A01G504600 chr2A 76.812 276 45 14 8336 8609 751499485 751499227 4.200000e-28 137.0
37 TraesCS3A01G504600 chr3D 93.504 1832 72 23 1770 3574 595760665 595762476 0.000000e+00 2680.0
38 TraesCS3A01G504600 chr3D 92.062 1285 36 15 7405 8637 595763474 595764744 0.000000e+00 1748.0
39 TraesCS3A01G504600 chr3D 95.415 1047 41 1 3641 4680 595762432 595763478 0.000000e+00 1661.0
40 TraesCS3A01G504600 chr3D 84.766 1733 158 46 1770 3430 595678879 595680577 0.000000e+00 1640.0
41 TraesCS3A01G504600 chr3D 88.698 991 100 9 3641 4627 595680941 595681923 0.000000e+00 1199.0
42 TraesCS3A01G504600 chr3D 86.282 1006 115 21 3641 4638 595858816 595859806 0.000000e+00 1072.0
43 TraesCS3A01G504600 chr3D 86.660 982 107 18 3643 4614 595711913 595712880 0.000000e+00 1066.0
44 TraesCS3A01G504600 chr3D 83.363 1142 105 35 1770 2852 595276996 595275881 0.000000e+00 977.0
45 TraesCS3A01G504600 chr3D 93.217 575 26 5 935 1500 595759767 595760337 0.000000e+00 833.0
46 TraesCS3A01G504600 chr3D 84.994 833 106 12 3861 4680 595286611 595285785 0.000000e+00 828.0
47 TraesCS3A01G504600 chr3D 84.383 794 81 26 2663 3429 595857643 595858420 0.000000e+00 739.0
48 TraesCS3A01G504600 chr3D 82.753 632 73 20 1770 2387 595855611 595856220 1.650000e-146 531.0
49 TraesCS3A01G504600 chr3D 96.281 242 9 0 1532 1773 595760338 595760579 1.750000e-106 398.0
50 TraesCS3A01G504600 chr3D 75.485 567 87 35 7573 8134 596096126 596095607 6.740000e-56 230.0
51 TraesCS3A01G504600 chr3D 78.607 402 44 17 1771 2134 596113143 596112746 2.430000e-55 228.0
52 TraesCS3A01G504600 chr3D 78.977 352 36 19 8322 8637 506005816 506006165 1.140000e-48 206.0
53 TraesCS3A01G504600 chr3D 76.096 502 47 35 1187 1666 595278155 595277705 2.460000e-45 195.0
54 TraesCS3A01G504600 chr3D 78.438 320 35 15 8322 8613 515670251 515669938 2.480000e-40 178.0
55 TraesCS3A01G504600 chr3D 79.916 239 34 7 7625 7862 595675419 595675644 6.940000e-36 163.0
56 TraesCS3A01G504600 chr3D 88.073 109 6 1 2379 2480 595857224 595857332 1.180000e-23 122.0
57 TraesCS3A01G504600 chr3D 94.737 76 4 0 3499 3574 595680910 595680985 1.520000e-22 119.0
58 TraesCS3A01G504600 chr3D 94.667 75 4 0 3500 3574 595858786 595858860 5.480000e-22 117.0
59 TraesCS3A01G504600 chr3D 83.471 121 16 2 8024 8140 595304758 595304878 9.170000e-20 110.0
60 TraesCS3A01G504600 chr3D 90.789 76 7 0 3499 3574 595711880 595711955 1.530000e-17 102.0
61 TraesCS3A01G504600 chr3D 90.566 53 5 0 1187 1239 595737388 595737440 4.330000e-08 71.3
62 TraesCS3A01G504600 chr3D 100.000 28 0 0 1748 1775 32951519 32951546 1.600000e-02 52.8
63 TraesCS3A01G504600 chr3D 100.000 28 0 0 1746 1773 170677736 170677763 1.600000e-02 52.8
64 TraesCS3A01G504600 chr3B 93.052 1540 68 24 2840 4362 798952730 798954247 0.000000e+00 2215.0
65 TraesCS3A01G504600 chr3B 92.713 1043 39 8 1772 2814 798951616 798952621 0.000000e+00 1471.0
66 TraesCS3A01G504600 chr3B 86.895 1053 106 21 3644 4680 798639536 798640572 0.000000e+00 1151.0
67 TraesCS3A01G504600 chr3B 85.785 1013 115 19 3641 4638 798992484 798993482 0.000000e+00 1046.0
68 TraesCS3A01G504600 chr3B 100.000 531 0 0 6880 7410 762382412 762382942 0.000000e+00 981.0
69 TraesCS3A01G504600 chr3B 86.989 930 49 25 7742 8633 798967002 798967897 0.000000e+00 981.0
70 TraesCS3A01G504600 chr3B 84.244 787 88 20 2663 3429 798991147 798991917 0.000000e+00 734.0
71 TraesCS3A01G504600 chr3B 94.189 413 23 1 1361 1773 798951117 798951528 5.690000e-176 628.0
72 TraesCS3A01G504600 chr3B 100.000 337 0 0 4680 5016 762380188 762380524 2.650000e-174 623.0
73 TraesCS3A01G504600 chr3B 83.604 677 68 20 1952 2618 798990501 798991144 5.770000e-166 595.0
74 TraesCS3A01G504600 chr3B 84.690 516 53 10 2927 3430 798638603 798639104 7.790000e-135 492.0
75 TraesCS3A01G504600 chr3B 85.270 482 25 16 916 1362 798950431 798950901 1.020000e-123 455.0
76 TraesCS3A01G504600 chr3B 90.741 324 23 1 4364 4680 798966452 798966775 8.010000e-115 425.0
77 TraesCS3A01G504600 chr3B 96.552 232 8 0 7405 7636 798966771 798967002 1.360000e-102 385.0
78 TraesCS3A01G504600 chr3B 78.466 339 41 17 8322 8631 785200427 785200762 8.850000e-45 193.0
79 TraesCS3A01G504600 chr3B 90.826 109 10 0 1770 1878 798660359 798660467 6.990000e-31 147.0
80 TraesCS3A01G504600 chr3B 82.993 147 17 6 7565 7710 799515577 799515438 9.100000e-25 126.0
81 TraesCS3A01G504600 chr3B 94.667 75 4 0 3500 3574 798992454 798992528 5.480000e-22 117.0
82 TraesCS3A01G504600 chr3B 95.455 44 1 1 3501 3543 798953470 798953513 1.560000e-07 69.4
83 TraesCS3A01G504600 chr3B 100.000 28 0 0 1746 1773 447029588 447029615 1.600000e-02 52.8
84 TraesCS3A01G504600 chr7A 95.600 841 33 1 1 841 567566631 567567467 0.000000e+00 1345.0
85 TraesCS3A01G504600 chr7A 96.188 446 17 0 5439 5884 4492789 4493234 0.000000e+00 730.0
86 TraesCS3A01G504600 chr7A 90.157 508 22 11 5880 6362 4493288 4493792 3.400000e-178 636.0
87 TraesCS3A01G504600 chr7A 91.484 411 20 5 4680 5088 4492053 4492450 1.270000e-152 551.0
88 TraesCS3A01G504600 chr7A 90.698 172 13 2 7241 7410 4494380 4494550 8.720000e-55 226.0
89 TraesCS3A01G504600 chr7A 75.465 269 31 22 8382 8632 291813327 291813578 1.980000e-16 99.0
90 TraesCS3A01G504600 chr7A 86.047 86 10 2 8380 8463 688627597 688627512 3.320000e-14 91.6
91 TraesCS3A01G504600 chr5A 95.249 842 36 1 1 842 462964296 462965133 0.000000e+00 1330.0
92 TraesCS3A01G504600 chr1A 94.887 841 39 1 1 841 565947880 565947044 0.000000e+00 1312.0
93 TraesCS3A01G504600 chr1A 85.452 763 79 15 4680 5438 207688128 207687394 0.000000e+00 765.0
94 TraesCS3A01G504600 chr1A 91.566 166 13 1 6659 6824 207680936 207680772 2.430000e-55 228.0
95 TraesCS3A01G504600 chr1A 87.273 110 7 4 1518 1625 37142557 37142661 1.520000e-22 119.0
96 TraesCS3A01G504600 chr1A 87.273 110 7 4 1518 1625 289628573 289628677 1.520000e-22 119.0
97 TraesCS3A01G504600 chr1B 86.065 775 60 14 4675 5438 558778044 558778781 0.000000e+00 789.0
98 TraesCS3A01G504600 chr1B 91.716 169 13 1 6656 6824 558783637 558783804 5.210000e-57 233.0
99 TraesCS3A01G504600 chr6D 90.945 508 17 4 5880 6362 148005913 148005410 0.000000e+00 656.0
100 TraesCS3A01G504600 chr6D 95.696 395 15 2 5439 5832 148006393 148006000 1.220000e-177 634.0
101 TraesCS3A01G504600 chr6D 85.227 616 49 20 6830 7410 148005261 148004653 5.770000e-166 595.0
102 TraesCS3A01G504600 chr2D 90.551 508 17 8 5880 6362 294865311 294865812 2.030000e-180 643.0
103 TraesCS3A01G504600 chr2D 95.949 395 14 2 5439 5832 294864829 294865222 2.630000e-179 640.0
104 TraesCS3A01G504600 chr2D 84.976 619 51 18 6829 7412 294865959 294866570 2.690000e-164 590.0
105 TraesCS3A01G504600 chr2D 81.098 328 30 15 8322 8628 595407051 595407367 5.210000e-57 233.0
106 TraesCS3A01G504600 chr2D 89.216 102 3 5 1521 1620 395318583 395318678 4.230000e-23 121.0
107 TraesCS3A01G504600 chr7D 91.124 169 14 1 6656 6824 498115575 498115742 2.430000e-55 228.0
108 TraesCS3A01G504600 chr4A 79.941 339 44 15 8322 8637 739967283 739967620 2.430000e-55 228.0
109 TraesCS3A01G504600 chr4A 97.059 34 1 0 1742 1775 700445051 700445018 3.370000e-04 58.4
110 TraesCS3A01G504600 chr4D 82.007 289 23 14 8376 8637 490401091 490401377 1.460000e-52 219.0
111 TraesCS3A01G504600 chr4D 81.333 150 16 7 8322 8462 279298572 279298718 2.550000e-20 111.0
112 TraesCS3A01G504600 chrUn 77.011 348 46 21 8322 8636 150140901 150141247 1.490000e-37 169.0
113 TraesCS3A01G504600 chrUn 77.011 348 46 21 8322 8636 321413599 321413945 1.490000e-37 169.0
114 TraesCS3A01G504600 chrUn 76.724 348 47 21 8322 8636 172387216 172386870 6.940000e-36 163.0
115 TraesCS3A01G504600 chrUn 81.982 111 11 4 8322 8424 172394323 172394214 1.540000e-12 86.1
116 TraesCS3A01G504600 chr1D 76.608 342 46 20 8322 8631 474234152 474233813 3.230000e-34 158.0
117 TraesCS3A01G504600 chr5D 86.822 129 8 5 1541 1666 529794473 529794595 1.510000e-27 135.0
118 TraesCS3A01G504600 chr5D 90.000 50 5 0 8323 8372 545696814 545696863 2.010000e-06 65.8
119 TraesCS3A01G504600 chr6B 97.222 36 0 1 1504 1539 359604225 359604191 9.360000e-05 60.2
120 TraesCS3A01G504600 chr6B 100.000 28 0 0 1746 1773 18739920 18739947 1.600000e-02 52.8


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 TraesCS3A01G504600 chr3A 726534971 726543607 8636 False 15950.000000 15950 100.000000 1 8637 1 chr3A.!!$F4 8636
1 TraesCS3A01G504600 chr3A 636491268 636492102 834 False 1349.000000 1349 95.719000 1 841 1 chr3A.!!$F2 840
2 TraesCS3A01G504600 chr3A 457218485 457219319 834 False 1327.000000 1327 95.244000 1 841 1 chr3A.!!$F1 840
3 TraesCS3A01G504600 chr3A 726686868 726689439 2571 False 581.000000 896 87.925000 1952 4462 4 chr3A.!!$F6 2510
4 TraesCS3A01G504600 chr3A 681527491 681528572 1081 True 409.000000 496 92.843000 5880 7244 2 chr3A.!!$R4 1364
5 TraesCS3A01G504600 chr3A 726440155 726444847 4692 False 382.500000 928 87.672250 2550 7720 4 chr3A.!!$F5 5170
6 TraesCS3A01G504600 chr3A 726388481 726390612 2131 True 369.333333 741 85.076667 1540 3012 3 chr3A.!!$R5 1472
7 TraesCS3A01G504600 chr7B 630128863 630131603 2740 False 5029.000000 5029 99.781000 4675 7416 1 chr7B.!!$F2 2741
8 TraesCS3A01G504600 chr7B 607324666 607328129 3463 False 2381.000000 3803 97.438000 4680 7409 2 chr7B.!!$F4 2729
9 TraesCS3A01G504600 chr7B 288169400 288170144 744 True 776.000000 776 85.530000 4671 5438 1 chr7B.!!$R1 767
10 TraesCS3A01G504600 chr2B 549705169 549707900 2731 False 4911.000000 4911 99.122000 4680 7410 1 chr2B.!!$F1 2730
11 TraesCS3A01G504600 chr6A 426957314 426960036 2722 False 4909.000000 4909 99.158000 4680 7410 1 chr6A.!!$F1 2730
12 TraesCS3A01G504600 chr5B 6681580 6685585 4005 True 2299.000000 3781 97.562500 4680 7410 2 chr5B.!!$R1 2730
13 TraesCS3A01G504600 chr2A 731335216 731338712 3496 True 2270.500000 3720 95.147000 4680 7410 2 chr2A.!!$R5 2730
14 TraesCS3A01G504600 chr2A 560769738 560770572 834 False 1332.000000 1332 95.363000 1 841 1 chr2A.!!$F1 840
15 TraesCS3A01G504600 chr2A 264894248 264895084 836 True 1328.000000 1328 95.244000 1 841 1 chr2A.!!$R1 840
16 TraesCS3A01G504600 chr2A 319899084 319899919 835 True 1315.000000 1315 95.000000 2 841 1 chr2A.!!$R2 839
17 TraesCS3A01G504600 chr2A 390815143 390815978 835 True 1310.000000 1310 94.887000 1 841 1 chr2A.!!$R3 840
18 TraesCS3A01G504600 chr3D 595759767 595764744 4977 False 1464.000000 2680 94.095800 935 8637 5 chr3D.!!$F8 7702
19 TraesCS3A01G504600 chr3D 595285785 595286611 826 True 828.000000 828 84.994000 3861 4680 1 chr3D.!!$R2 819
20 TraesCS3A01G504600 chr3D 595675419 595681923 6504 False 780.250000 1640 87.029250 1770 7862 4 chr3D.!!$F6 6092
21 TraesCS3A01G504600 chr3D 595275881 595278155 2274 True 586.000000 977 79.729500 1187 2852 2 chr3D.!!$R5 1665
22 TraesCS3A01G504600 chr3D 595711880 595712880 1000 False 584.000000 1066 88.724500 3499 4614 2 chr3D.!!$F7 1115
23 TraesCS3A01G504600 chr3D 595855611 595859806 4195 False 516.200000 1072 87.231600 1770 4638 5 chr3D.!!$F9 2868
24 TraesCS3A01G504600 chr3D 596095607 596096126 519 True 230.000000 230 75.485000 7573 8134 1 chr3D.!!$R3 561
25 TraesCS3A01G504600 chr3B 798950431 798954247 3816 False 967.680000 2215 92.135800 916 4362 5 chr3B.!!$F6 3446
26 TraesCS3A01G504600 chr3B 798638603 798640572 1969 False 821.500000 1151 85.792500 2927 4680 2 chr3B.!!$F5 1753
27 TraesCS3A01G504600 chr3B 762380188 762382942 2754 False 802.000000 981 100.000000 4680 7410 2 chr3B.!!$F4 2730
28 TraesCS3A01G504600 chr3B 798990501 798993482 2981 False 623.000000 1046 87.075000 1952 4638 4 chr3B.!!$F8 2686
29 TraesCS3A01G504600 chr3B 798966452 798967897 1445 False 597.000000 981 91.427333 4364 8633 3 chr3B.!!$F7 4269
30 TraesCS3A01G504600 chr7A 567566631 567567467 836 False 1345.000000 1345 95.600000 1 841 1 chr7A.!!$F2 840
31 TraesCS3A01G504600 chr7A 4492053 4494550 2497 False 535.750000 730 92.131750 4680 7410 4 chr7A.!!$F3 2730
32 TraesCS3A01G504600 chr5A 462964296 462965133 837 False 1330.000000 1330 95.249000 1 842 1 chr5A.!!$F1 841
33 TraesCS3A01G504600 chr1A 565947044 565947880 836 True 1312.000000 1312 94.887000 1 841 1 chr1A.!!$R3 840
34 TraesCS3A01G504600 chr1A 207687394 207688128 734 True 765.000000 765 85.452000 4680 5438 1 chr1A.!!$R2 758
35 TraesCS3A01G504600 chr1B 558778044 558778781 737 False 789.000000 789 86.065000 4675 5438 1 chr1B.!!$F1 763
36 TraesCS3A01G504600 chr6D 148004653 148006393 1740 True 628.333333 656 90.622667 5439 7410 3 chr6D.!!$R1 1971
37 TraesCS3A01G504600 chr2D 294864829 294866570 1741 False 624.333333 643 90.492000 5439 7412 3 chr2D.!!$F3 1973

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
890 893 0.401738 ACTCATGTCTTGGTGTGGGG 59.598 55.0 0.00 0.00 0.00 4.96 F
894 897 0.620556 ATGTCTTGGTGTGGGGCTAG 59.379 55.0 0.00 0.00 0.00 3.42 F
1235 1254 0.760567 AGGCTACCGAGATGCATCCA 60.761 55.0 23.06 3.02 0.00 3.41 F
1390 1645 0.839946 ACTGATTTCCATCCCTCGGG 59.160 55.0 0.00 0.00 0.00 5.14 F
2978 6436 0.801251 CTGCACACAAAGCTAGCCTC 59.199 55.0 12.13 0.00 0.00 4.70 F
3575 7722 0.249489 ACAGAACTGAGTGACACCGC 60.249 55.0 8.87 0.00 0.00 5.68 F
3604 7751 0.394352 GGGGAGATGCCGACATTTGT 60.394 55.0 0.00 0.00 36.35 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 3634 0.977627 TGCATCGTCCTCACCATCCT 60.978 55.000 0.00 0.00 0.00 3.24 R
2098 3847 1.228094 TTGGCACCGTCAATCTGCA 60.228 52.632 0.00 0.00 32.20 4.41 R
2819 6193 2.232239 GCAGAAAGCACACATGTACG 57.768 50.000 0.00 0.00 44.79 3.67 R
3305 6788 2.169769 TGGAAACAAGACTCTTGTCCGT 59.830 45.455 22.07 12.17 38.72 4.69 R
4643 10889 1.203994 ACTGATAACGCGCCACTACTT 59.796 47.619 5.73 0.00 0.00 2.24 R
5016 11369 1.227943 GGAGCTGCTGGTGTGTGAA 60.228 57.895 7.01 0.00 0.00 3.18 R
7672 15517 9.545105 GAAATTAATTGCAATGGGTATGAATGA 57.455 29.630 13.82 0.00 0.00 2.57 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)


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

AutoCloner maintained by Alex Coulton.