Multiple sequence alignment - TraesCS1B01G168000

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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 TraesCS1B01G168000 chr1B 100.000 4447 0 0 4056 8502 297297424 297301870 0.000000e+00 8213.0
1 TraesCS1B01G168000 chr1B 100.000 3531 0 0 1 3531 297293369 297296899 0.000000e+00 6521.0
2 TraesCS1B01G168000 chr1B 95.362 884 38 3 4067 4947 59836644 59837527 0.000000e+00 1402.0
3 TraesCS1B01G168000 chr1B 91.572 878 46 5 7650 8502 38271135 38270261 0.000000e+00 1186.0
4 TraesCS1B01G168000 chr1B 96.416 279 10 0 129 407 37568564 37568286 2.160000e-125 460.0
5 TraesCS1B01G168000 chr1B 95.789 285 12 0 123 407 660398561 660398845 2.160000e-125 460.0
6 TraesCS1B01G168000 chr1B 89.767 215 20 1 3319 3531 59836394 59836608 3.020000e-69 274.0
7 TraesCS1B01G168000 chr1B 92.754 138 10 0 5217 5354 138773797 138773660 5.200000e-47 200.0
8 TraesCS1B01G168000 chr1B 91.803 122 9 1 5591 5712 292206389 292206269 1.470000e-37 169.0
9 TraesCS1B01G168000 chr1A 96.785 1804 47 6 5800 7600 257967420 257969215 0.000000e+00 3000.0
10 TraesCS1B01G168000 chr1A 90.870 931 27 20 852 1731 257959788 257960711 0.000000e+00 1195.0
11 TraesCS1B01G168000 chr1A 90.730 356 32 1 2443 2798 257965750 257966104 2.780000e-129 473.0
12 TraesCS1B01G168000 chr1A 88.427 337 18 6 405 724 257959325 257959657 3.720000e-103 387.0
13 TraesCS1B01G168000 chr1A 92.029 276 18 3 4942 5216 257966782 257967054 1.340000e-102 385.0
14 TraesCS1B01G168000 chr1A 87.795 254 29 2 5339 5592 257967052 257967303 6.450000e-76 296.0
15 TraesCS1B01G168000 chr1A 86.250 240 16 9 3003 3241 257966572 257966795 2.370000e-60 244.0
16 TraesCS1B01G168000 chr1A 86.425 221 19 3 1727 1937 257964515 257964734 1.850000e-56 231.0
17 TraesCS1B01G168000 chr1A 95.327 107 5 0 1731 1837 257965213 257965319 4.080000e-38 171.0
18 TraesCS1B01G168000 chr1A 88.889 126 8 3 2321 2443 257965591 257965713 5.320000e-32 150.0
19 TraesCS1B01G168000 chr1A 91.489 94 7 1 2875 2967 257966140 257966233 2.490000e-25 128.0
20 TraesCS1B01G168000 chr1A 91.837 49 3 1 2071 2118 579321967 579321919 5.510000e-07 67.6
21 TraesCS1B01G168000 chr1D 96.280 1801 61 2 5800 7600 203430719 203432513 0.000000e+00 2950.0
22 TraesCS1B01G168000 chr1D 89.574 1621 74 33 405 1948 203427288 203428890 0.000000e+00 1969.0
23 TraesCS1B01G168000 chr1D 91.656 815 52 7 2443 3241 203429269 203430083 0.000000e+00 1114.0
24 TraesCS1B01G168000 chr1D 93.116 276 16 2 4942 5216 203430070 203430343 1.330000e-107 401.0
25 TraesCS1B01G168000 chr1D 89.370 254 26 1 5339 5592 203430341 203430593 1.380000e-82 318.0
26 TraesCS1B01G168000 chr1D 91.538 130 5 3 2318 2443 203429104 203429231 3.150000e-39 174.0
27 TraesCS1B01G168000 chr1D 87.879 66 6 2 2071 2134 490133015 490132950 9.150000e-10 76.8
28 TraesCS1B01G168000 chr5B 97.377 877 20 3 4067 4942 618139126 618140000 0.000000e+00 1489.0
29 TraesCS1B01G168000 chr5B 95.632 847 34 3 7656 8502 375421236 375420393 0.000000e+00 1356.0
30 TraesCS1B01G168000 chr5B 93.310 852 54 3 7651 8502 639760689 639759841 0.000000e+00 1254.0
31 TraesCS1B01G168000 chr5B 95.088 285 14 0 123 407 487639393 487639109 4.680000e-122 449.0
32 TraesCS1B01G168000 chr5B 89.677 155 14 2 5201 5354 408718875 408718722 6.730000e-46 196.0
33 TraesCS1B01G168000 chr5B 91.608 143 10 2 5201 5342 440648877 440649018 6.730000e-46 196.0
34 TraesCS1B01G168000 chr5B 89.706 136 11 3 5584 5718 469125865 469125998 4.080000e-38 171.0
35 TraesCS1B01G168000 chr5B 91.129 124 11 0 5591 5714 562793820 562793697 1.470000e-37 169.0
36 TraesCS1B01G168000 chr5B 84.211 114 15 2 5380 5491 528369868 528369980 3.250000e-19 108.0
37 TraesCS1B01G168000 chr2B 96.818 880 26 2 4064 4942 29532113 29531235 0.000000e+00 1469.0
38 TraesCS1B01G168000 chr2B 96.057 279 11 0 129 407 198448733 198449011 1.010000e-123 455.0
39 TraesCS1B01G168000 chr2B 91.608 143 10 2 5201 5342 244099195 244099336 6.730000e-46 196.0
40 TraesCS1B01G168000 chr4A 95.682 880 38 0 4065 4944 733779039 733779918 0.000000e+00 1415.0
41 TraesCS1B01G168000 chr4A 95.439 285 12 1 129 413 738612156 738612439 3.620000e-123 453.0
42 TraesCS1B01G168000 chr4A 92.562 121 9 0 5587 5707 286746917 286746797 3.150000e-39 174.0
43 TraesCS1B01G168000 chr4A 81.203 133 18 5 5380 5512 497020492 497020367 5.430000e-17 100.0
44 TraesCS1B01G168000 chr4A 93.023 43 2 1 2085 2126 34673996 34674038 2.560000e-05 62.1
45 TraesCS1B01G168000 chr3B 96.083 868 30 2 4076 4943 586726924 586727787 0.000000e+00 1411.0
46 TraesCS1B01G168000 chr3B 97.105 829 21 2 4119 4944 725179387 725180215 0.000000e+00 1395.0
47 TraesCS1B01G168000 chr3B 93.220 118 8 0 5590 5707 457968799 457968682 3.150000e-39 174.0
48 TraesCS1B01G168000 chr3B 93.220 118 8 0 5590 5707 805003333 805003450 3.150000e-39 174.0
49 TraesCS1B01G168000 chr3B 80.769 104 19 1 3066 3168 713878661 713878764 7.070000e-11 80.5
50 TraesCS1B01G168000 chr4B 94.965 854 37 6 7650 8502 609321802 609320954 0.000000e+00 1334.0
51 TraesCS1B01G168000 chr4B 79.262 1355 223 44 6044 7372 631572221 631570899 0.000000e+00 893.0
52 TraesCS1B01G168000 chr4B 95.439 285 13 0 123 407 453049522 453049238 1.010000e-123 455.0
53 TraesCS1B01G168000 chr4B 96.057 279 11 0 129 407 595706116 595705838 1.010000e-123 455.0
54 TraesCS1B01G168000 chr4B 94.276 297 14 2 124 418 483526494 483526199 1.300000e-122 451.0
55 TraesCS1B01G168000 chr4B 95.088 285 14 0 127 411 590862207 590861923 4.680000e-122 449.0
56 TraesCS1B01G168000 chr4B 88.341 223 26 0 1340 1562 631575125 631574903 1.410000e-67 268.0
57 TraesCS1B01G168000 chr4B 92.000 125 9 1 5591 5714 612251209 612251085 3.150000e-39 174.0
58 TraesCS1B01G168000 chr4B 93.162 117 8 0 5591 5707 144758157 144758041 1.130000e-38 172.0
59 TraesCS1B01G168000 chr7A 93.378 891 56 3 4056 4944 701034625 701035514 0.000000e+00 1315.0
60 TraesCS1B01G168000 chr6B 93.213 884 55 5 4065 4945 707905464 707906345 0.000000e+00 1295.0
61 TraesCS1B01G168000 chr6B 89.659 880 55 16 7650 8502 715208810 715207940 0.000000e+00 1088.0
62 TraesCS1B01G168000 chr6B 73.713 1438 312 46 6044 7454 36809461 36808063 1.270000e-137 501.0
63 TraesCS1B01G168000 chr6B 78.935 413 67 16 1156 1562 36811310 36810912 6.540000e-66 263.0
64 TraesCS1B01G168000 chr6B 94.815 135 7 0 5209 5343 160666149 160666283 2.400000e-50 211.0
65 TraesCS1B01G168000 chr6B 92.361 144 8 3 5201 5342 112462503 112462645 1.450000e-47 202.0
66 TraesCS1B01G168000 chr6B 92.199 141 11 0 5214 5354 244146379 244146239 5.200000e-47 200.0
67 TraesCS1B01G168000 chr6B 90.604 149 12 2 5201 5348 128506236 128506089 6.730000e-46 196.0
68 TraesCS1B01G168000 chr6B 100.000 29 0 0 3008 3036 686510713 686510741 4.000000e-03 54.7
69 TraesCS1B01G168000 chr7B 92.937 892 54 8 4056 4941 617551632 617550744 0.000000e+00 1290.0
70 TraesCS1B01G168000 chr7B 90.604 149 12 2 5201 5348 157542362 157542215 6.730000e-46 196.0
71 TraesCS1B01G168000 chr7B 93.478 46 3 0 2071 2116 503503472 503503517 1.530000e-07 69.4
72 TraesCS1B01G168000 chr7B 95.000 40 1 1 3006 3044 155471319 155471280 2.560000e-05 62.1
73 TraesCS1B01G168000 chr3D 90.899 879 49 7 7650 8502 377906923 377907796 0.000000e+00 1151.0
74 TraesCS1B01G168000 chr3D 82.109 313 48 7 6135 6443 177348175 177347867 2.350000e-65 261.0
75 TraesCS1B01G168000 chr3D 83.007 153 24 2 3006 3158 425983546 425983696 4.140000e-28 137.0
76 TraesCS1B01G168000 chr3D 76.623 154 23 10 3009 3155 615121354 615121501 1.180000e-08 73.1
77 TraesCS1B01G168000 chr3D 90.566 53 5 0 1486 1538 40754369 40754317 4.260000e-08 71.3
78 TraesCS1B01G168000 chr6D 90.330 879 54 7 7650 8502 1554112 1554985 0.000000e+00 1123.0
79 TraesCS1B01G168000 chr6D 78.374 578 117 8 6046 6619 22174124 22173551 1.350000e-97 368.0
80 TraesCS1B01G168000 chr6D 78.537 410 69 11 1156 1562 22175293 22174900 1.420000e-62 252.0
81 TraesCS1B01G168000 chr6D 91.406 128 11 0 1946 2073 126108389 126108262 8.770000e-40 176.0
82 TraesCS1B01G168000 chr6D 91.406 128 11 0 1946 2073 408047489 408047616 8.770000e-40 176.0
83 TraesCS1B01G168000 chr6D 82.099 162 29 0 5373 5534 304768867 304769028 1.150000e-28 139.0
84 TraesCS1B01G168000 chr6D 91.304 46 3 1 2084 2128 93604 93559 2.560000e-05 62.1
85 TraesCS1B01G168000 chr5D 89.989 879 59 7 7650 8502 37155583 37156458 0.000000e+00 1109.0
86 TraesCS1B01G168000 chr5D 88.610 878 58 27 7650 8502 344463911 344463051 0.000000e+00 1029.0
87 TraesCS1B01G168000 chr5D 91.111 135 12 0 1942 2076 354741254 354741120 5.240000e-42 183.0
88 TraesCS1B01G168000 chr5D 92.188 128 10 0 1946 2073 14868763 14868636 1.890000e-41 182.0
89 TraesCS1B01G168000 chr5D 92.188 128 10 0 1946 2073 364050414 364050541 1.890000e-41 182.0
90 TraesCS1B01G168000 chr5D 91.935 124 9 1 5591 5713 486173644 486173521 1.130000e-38 172.0
91 TraesCS1B01G168000 chr5D 88.679 53 5 1 2272 2324 551739889 551739940 7.120000e-06 63.9
92 TraesCS1B01G168000 chr2A 90.046 874 61 10 7650 8502 669843830 669842962 0.000000e+00 1109.0
93 TraesCS1B01G168000 chr2A 95.455 44 2 0 2071 2114 75305879 75305836 4.260000e-08 71.3
94 TraesCS1B01G168000 chr2A 92.000 50 2 2 2998 3045 537461155 537461106 1.530000e-07 69.4
95 TraesCS1B01G168000 chr2A 100.000 29 0 0 5773 5801 688549990 688549962 4.000000e-03 54.7
96 TraesCS1B01G168000 chr5A 79.377 1348 231 32 6044 7372 672837461 672836142 0.000000e+00 905.0
97 TraesCS1B01G168000 chr5A 89.686 223 23 0 1340 1562 672841298 672841076 1.400000e-72 285.0
98 TraesCS1B01G168000 chr5A 78.289 152 24 5 3007 3158 183434864 183435006 1.180000e-13 89.8
99 TraesCS1B01G168000 chr5A 85.526 76 10 1 3084 3158 7720001 7719926 2.540000e-10 78.7
100 TraesCS1B01G168000 chr5A 91.667 48 3 1 2079 2125 605797979 605798026 1.980000e-06 65.8
101 TraesCS1B01G168000 chr5A 90.000 50 3 1 2079 2128 83288561 83288514 7.120000e-06 63.9
102 TraesCS1B01G168000 chr4D 78.830 1351 236 36 6044 7372 493329843 493328521 0.000000e+00 865.0
103 TraesCS1B01G168000 chr4D 89.238 223 24 0 1340 1562 493336872 493336650 6.500000e-71 279.0
104 TraesCS1B01G168000 chr4D 93.182 44 3 0 2071 2114 40952182 40952139 1.980000e-06 65.8
105 TraesCS1B01G168000 chr4D 100.000 29 0 0 5773 5801 491948624 491948596 4.000000e-03 54.7
106 TraesCS1B01G168000 chr6A 75.148 1348 279 38 6044 7369 21636461 21635148 4.420000e-162 582.0
107 TraesCS1B01G168000 chr6A 79.512 410 65 11 1156 1562 21637459 21637066 3.020000e-69 274.0
108 TraesCS1B01G168000 chr6A 91.667 60 5 0 5376 5435 410576092 410576033 5.470000e-12 84.2
109 TraesCS1B01G168000 chrUn 92.188 128 10 0 1946 2073 98153915 98153788 1.890000e-41 182.0
110 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 144878633 144878564 3.290000e-09 75.0
111 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 144917222 144917153 3.290000e-09 75.0
112 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 179841888 179841819 3.290000e-09 75.0
113 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 179880059 179879990 3.290000e-09 75.0
114 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 246179657 246179588 3.290000e-09 75.0
115 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 272673732 272673663 3.290000e-09 75.0
116 TraesCS1B01G168000 chrUn 85.714 70 10 0 3084 3153 400259851 400259782 3.290000e-09 75.0
117 TraesCS1B01G168000 chrUn 92.157 51 4 0 3103 3153 446035574 446035624 1.180000e-08 73.1
118 TraesCS1B01G168000 chr7D 92.188 128 10 0 1946 2073 205474850 205474723 1.890000e-41 182.0
119 TraesCS1B01G168000 chr7D 83.007 153 26 0 3006 3158 575593984 575594136 1.150000e-28 139.0
120 TraesCS1B01G168000 chr7D 78.378 148 29 2 3012 3158 10723600 10723455 9.090000e-15 93.5
121 TraesCS1B01G168000 chr7D 89.796 49 5 0 2079 2127 495823381 495823429 7.120000e-06 63.9
122 TraesCS1B01G168000 chr2D 91.538 130 11 0 1946 2075 242564004 242564133 6.780000e-41 180.0
123 TraesCS1B01G168000 chr2D 92.126 127 10 0 1947 2073 605712386 605712260 6.780000e-41 180.0
124 TraesCS1B01G168000 chr2D 78.261 161 29 5 3006 3164 444766117 444766273 1.950000e-16 99.0
125 TraesCS1B01G168000 chr2D 86.957 69 7 2 2273 2341 642240155 642240221 9.150000e-10 76.8
126 TraesCS1B01G168000 chr2D 93.182 44 3 0 2071 2114 97871072 97871029 1.980000e-06 65.8
127 TraesCS1B01G168000 chr2D 100.000 31 0 0 5505 5535 459105984 459106014 3.310000e-04 58.4
128 TraesCS1B01G168000 chr3A 80.132 151 28 2 5382 5532 637465284 637465432 2.510000e-20 111.0
129 TraesCS1B01G168000 chr3A 78.947 95 20 0 7095 7189 640679416 640679322 1.980000e-06 65.8
130 TraesCS1B01G168000 chr3A 78.947 95 20 0 7095 7189 640699298 640699204 1.980000e-06 65.8
131 TraesCS1B01G168000 chr3A 78.947 95 20 0 7095 7189 640749353 640749259 1.980000e-06 65.8
132 TraesCS1B01G168000 chr3A 100.000 28 0 0 3004 3031 111556189 111556162 1.500000e-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 TraesCS1B01G168000 chr1B 297293369 297301870 8501 False 7367.000000 8213 100.000000 1 8502 2 chr1B.!!$F3 8501
1 TraesCS1B01G168000 chr1B 38270261 38271135 874 True 1186.000000 1186 91.572000 7650 8502 1 chr1B.!!$R2 852
2 TraesCS1B01G168000 chr1B 59836394 59837527 1133 False 838.000000 1402 92.564500 3319 4947 2 chr1B.!!$F2 1628
3 TraesCS1B01G168000 chr1A 257959325 257969215 9890 False 605.454545 3000 90.456000 405 7600 11 chr1A.!!$F1 7195
4 TraesCS1B01G168000 chr1D 203427288 203432513 5225 False 1154.333333 2950 91.922333 405 7600 6 chr1D.!!$F1 7195
5 TraesCS1B01G168000 chr5B 618139126 618140000 874 False 1489.000000 1489 97.377000 4067 4942 1 chr5B.!!$F4 875
6 TraesCS1B01G168000 chr5B 375420393 375421236 843 True 1356.000000 1356 95.632000 7656 8502 1 chr5B.!!$R1 846
7 TraesCS1B01G168000 chr5B 639759841 639760689 848 True 1254.000000 1254 93.310000 7651 8502 1 chr5B.!!$R5 851
8 TraesCS1B01G168000 chr2B 29531235 29532113 878 True 1469.000000 1469 96.818000 4064 4942 1 chr2B.!!$R1 878
9 TraesCS1B01G168000 chr4A 733779039 733779918 879 False 1415.000000 1415 95.682000 4065 4944 1 chr4A.!!$F2 879
10 TraesCS1B01G168000 chr3B 586726924 586727787 863 False 1411.000000 1411 96.083000 4076 4943 1 chr3B.!!$F1 867
11 TraesCS1B01G168000 chr3B 725179387 725180215 828 False 1395.000000 1395 97.105000 4119 4944 1 chr3B.!!$F3 825
12 TraesCS1B01G168000 chr4B 609320954 609321802 848 True 1334.000000 1334 94.965000 7650 8502 1 chr4B.!!$R6 852
13 TraesCS1B01G168000 chr4B 631570899 631575125 4226 True 580.500000 893 83.801500 1340 7372 2 chr4B.!!$R8 6032
14 TraesCS1B01G168000 chr7A 701034625 701035514 889 False 1315.000000 1315 93.378000 4056 4944 1 chr7A.!!$F1 888
15 TraesCS1B01G168000 chr6B 707905464 707906345 881 False 1295.000000 1295 93.213000 4065 4945 1 chr6B.!!$F4 880
16 TraesCS1B01G168000 chr6B 715207940 715208810 870 True 1088.000000 1088 89.659000 7650 8502 1 chr6B.!!$R3 852
17 TraesCS1B01G168000 chr6B 36808063 36811310 3247 True 382.000000 501 76.324000 1156 7454 2 chr6B.!!$R4 6298
18 TraesCS1B01G168000 chr7B 617550744 617551632 888 True 1290.000000 1290 92.937000 4056 4941 1 chr7B.!!$R3 885
19 TraesCS1B01G168000 chr3D 377906923 377907796 873 False 1151.000000 1151 90.899000 7650 8502 1 chr3D.!!$F1 852
20 TraesCS1B01G168000 chr6D 1554112 1554985 873 False 1123.000000 1123 90.330000 7650 8502 1 chr6D.!!$F1 852
21 TraesCS1B01G168000 chr6D 22173551 22175293 1742 True 310.000000 368 78.455500 1156 6619 2 chr6D.!!$R3 5463
22 TraesCS1B01G168000 chr5D 37155583 37156458 875 False 1109.000000 1109 89.989000 7650 8502 1 chr5D.!!$F1 852
23 TraesCS1B01G168000 chr5D 344463051 344463911 860 True 1029.000000 1029 88.610000 7650 8502 1 chr5D.!!$R2 852
24 TraesCS1B01G168000 chr2A 669842962 669843830 868 True 1109.000000 1109 90.046000 7650 8502 1 chr2A.!!$R3 852
25 TraesCS1B01G168000 chr5A 672836142 672841298 5156 True 595.000000 905 84.531500 1340 7372 2 chr5A.!!$R3 6032
26 TraesCS1B01G168000 chr4D 493328521 493329843 1322 True 865.000000 865 78.830000 6044 7372 1 chr4D.!!$R3 1328
27 TraesCS1B01G168000 chr6A 21635148 21637459 2311 True 428.000000 582 77.330000 1156 7369 2 chr6A.!!$R2 6213

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
865 932 0.323178 CACTCTTCAGCCAGGGCATT 60.323 55.000 13.63 0.0 44.88 3.56 F
1351 1473 0.104120 TGTGTGCAGTGTACGAGCTT 59.896 50.000 6.88 0.0 0.00 3.74 F
2349 7962 0.328258 CATTTTGGGACCGGGAGAGT 59.672 55.000 6.32 0.0 0.00 3.24 F
2350 7963 1.557832 CATTTTGGGACCGGGAGAGTA 59.442 52.381 6.32 0.0 0.00 2.59 F
3246 9345 2.981805 TGAAACTATTCGACGTGGTTCG 59.018 45.455 0.00 0.0 40.89 3.95 F
3261 9360 0.041576 GTTCGTTCTTCAACACCGGC 60.042 55.000 0.00 0.0 32.14 6.13 F
5076 11187 0.107831 GGCCGTATCCACATTAGGCA 59.892 55.000 6.61 0.0 45.79 4.75 F
5230 11341 0.043637 AATACTCCCTCCGTCCCCAA 59.956 55.000 0.00 0.0 0.00 4.12 F
5234 11345 0.107165 CTCCCTCCGTCCCCAAATTC 60.107 60.000 0.00 0.0 0.00 2.17 F
5236 11347 0.331616 CCCTCCGTCCCCAAATTCTT 59.668 55.000 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 8256 0.035458 GACAGTCAGTCACCCCCAAG 59.965 60.000 0.00 0.00 46.77 3.61 R
3242 9341 0.041576 GCCGGTGTTGAAGAACGAAC 60.042 55.000 0.00 0.00 34.49 3.95 R
3249 9348 0.108329 AGATACCGCCGGTGTTGAAG 60.108 55.000 21.20 0.00 36.19 3.02 R
3250 9349 0.108520 GAGATACCGCCGGTGTTGAA 60.109 55.000 21.20 0.00 36.19 2.69 R
5211 11322 0.043637 TTGGGGACGGAGGGAGTATT 59.956 55.000 0.00 0.00 0.00 1.89 R
5215 11326 0.107165 GAATTTGGGGACGGAGGGAG 60.107 60.000 0.00 0.00 0.00 4.30 R
6631 15619 3.653078 TTGGCGTCCCCGGGATTT 61.653 61.111 26.32 0.00 32.73 2.17 R
7240 16237 4.017877 GCGCTGCTGAGCACGTTT 62.018 61.111 22.91 0.00 46.62 3.60 R
7468 16468 1.134280 GCTGGCTCTGAATGAAGCCTA 60.134 52.381 13.99 1.17 46.77 3.93 R
7600 16600 5.657470 TTCAGTAATGAGTATTGCATCGC 57.343 39.130 0.00 0.00 32.09 4.58 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.