Multiple sequence alignment - TraesCS4B01G339800

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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 TraesCS4B01G339800 chr4B 100.000 5393 0 0 3514 8906 633285151 633290543 0.000000e+00 9960.0
1 TraesCS4B01G339800 chr4B 100.000 3285 0 0 1 3285 633281638 633284922 0.000000e+00 6067.0
2 TraesCS4B01G339800 chr4B 86.036 2399 231 53 5029 7357 632870689 632873053 0.000000e+00 2479.0
3 TraesCS4B01G339800 chr4B 88.348 1519 106 26 5535 7010 633147176 633148666 0.000000e+00 1759.0
4 TraesCS4B01G339800 chr4B 88.043 1313 108 24 5853 7129 633327465 633328764 0.000000e+00 1509.0
5 TraesCS4B01G339800 chr4B 88.275 1177 94 22 7009 8149 633148790 633149958 0.000000e+00 1369.0
6 TraesCS4B01G339800 chr4B 84.278 1164 113 42 7152 8266 633328915 633330057 0.000000e+00 1072.0
7 TraesCS4B01G339800 chr4B 86.483 799 82 16 5084 5868 633326663 633327449 0.000000e+00 854.0
8 TraesCS4B01G339800 chr4B 85.038 655 70 15 7352 7990 632874985 632875627 7.540000e-180 641.0
9 TraesCS4B01G339800 chr4B 88.350 412 42 5 5029 5438 633146723 633147130 2.890000e-134 490.0
10 TraesCS4B01G339800 chr4B 84.146 492 56 15 21 497 643669092 643668608 2.930000e-124 457.0
11 TraesCS4B01G339800 chr4B 86.635 419 33 14 864 1274 633142392 633142795 8.210000e-120 442.0
12 TraesCS4B01G339800 chr4B 86.717 399 26 10 919 1298 632863869 632864259 1.380000e-112 418.0
13 TraesCS4B01G339800 chr4B 88.201 339 18 13 1133 1452 633136394 633136729 1.400000e-102 385.0
14 TraesCS4B01G339800 chr4B 97.122 139 4 0 1135 1273 633325846 633325984 1.490000e-57 235.0
15 TraesCS4B01G339800 chr4B 95.868 121 5 0 3061 3181 633284554 633284674 7.050000e-46 196.0
16 TraesCS4B01G339800 chr4B 95.868 121 5 0 2917 3037 633284698 633284818 7.050000e-46 196.0
17 TraesCS4B01G339800 chr4B 82.096 229 27 9 1337 1558 632864339 632864560 5.490000e-42 183.0
18 TraesCS4B01G339800 chr4B 90.152 132 8 3 1324 1450 633326086 633326217 5.530000e-37 167.0
19 TraesCS4B01G339800 chr4B 96.774 62 2 0 1027 1088 633066645 633066706 4.400000e-18 104.0
20 TraesCS4B01G339800 chr5A 88.378 3330 278 57 5029 8273 673556699 673560004 0.000000e+00 3904.0
21 TraesCS4B01G339800 chr5A 86.879 1227 89 27 5940 7129 673691251 673692442 0.000000e+00 1308.0
22 TraesCS4B01G339800 chr5A 86.500 1163 93 39 7152 8266 673692602 673693748 0.000000e+00 1219.0
23 TraesCS4B01G339800 chr5A 84.885 827 91 18 5043 5847 673690405 673691219 0.000000e+00 804.0
24 TraesCS4B01G339800 chr5A 82.992 635 55 34 864 1454 673553151 673553776 7.920000e-145 525.0
25 TraesCS4B01G339800 chr5A 84.767 407 41 6 20 412 681172421 681172022 1.080000e-103 388.0
26 TraesCS4B01G339800 chr5A 84.275 407 43 6 20 412 681100100 681099701 2.350000e-100 377.0
27 TraesCS4B01G339800 chr5A 87.393 349 12 16 1136 1453 673678820 673679167 1.090000e-98 372.0
28 TraesCS4B01G339800 chr5A 82.477 428 29 23 1133 1517 673511612 673512036 5.150000e-87 333.0
29 TraesCS4B01G339800 chr5A 79.600 250 50 1 2540 2788 381708919 381709168 2.560000e-40 178.0
30 TraesCS4B01G339800 chr5A 93.636 110 7 0 8263 8372 673560329 673560438 1.990000e-36 165.0
31 TraesCS4B01G339800 chr5A 100.000 33 0 0 5852 5884 673691211 673691243 2.680000e-05 62.1
32 TraesCS4B01G339800 chr5A 97.059 34 1 0 4889 4922 673690209 673690242 3.470000e-04 58.4
33 TraesCS4B01G339800 chr4D 88.420 2703 217 44 5535 8159 494055155 494057839 0.000000e+00 3169.0
34 TraesCS4B01G339800 chr4D 86.115 2672 231 62 5411 7990 493976679 493979302 0.000000e+00 2750.0
35 TraesCS4B01G339800 chr4D 95.228 1362 39 6 5846 7205 494072643 494073980 0.000000e+00 2132.0
36 TraesCS4B01G339800 chr4D 93.363 1115 48 10 4777 5887 494071549 494072641 0.000000e+00 1626.0
37 TraesCS4B01G339800 chr4D 89.834 1082 80 15 6064 7127 494100469 494101538 0.000000e+00 1362.0
38 TraesCS4B01G339800 chr4D 84.638 1341 84 48 729 2000 494065596 494066883 0.000000e+00 1223.0
39 TraesCS4B01G339800 chr4D 84.231 1021 94 36 4922 5906 494099357 494100346 0.000000e+00 931.0
40 TraesCS4B01G339800 chr4D 93.309 553 28 4 7242 7787 494073974 494074524 0.000000e+00 808.0
41 TraesCS4B01G339800 chr4D 87.846 650 40 19 7110 7725 494101685 494102329 0.000000e+00 726.0
42 TraesCS4B01G339800 chr4D 88.738 515 38 9 7771 8273 494074542 494075048 5.910000e-171 612.0
43 TraesCS4B01G339800 chr4D 87.872 437 44 8 4055 4486 494069205 494069637 1.030000e-138 505.0
44 TraesCS4B01G339800 chr4D 82.401 608 77 19 21 609 363565473 363566069 3.710000e-138 503.0
45 TraesCS4B01G339800 chr4D 82.407 648 43 38 864 1450 494050526 494051163 4.800000e-137 499.0
46 TraesCS4B01G339800 chr4D 84.708 497 53 15 21 501 56734416 56734905 8.090000e-130 475.0
47 TraesCS4B01G339800 chr4D 87.321 418 47 5 5023 5438 494054696 494055109 2.910000e-129 473.0
48 TraesCS4B01G339800 chr4D 87.817 394 31 8 901 1281 493971967 493972356 6.340000e-121 446.0
49 TraesCS4B01G339800 chr4D 81.818 561 65 22 7724 8259 494102460 494103008 3.820000e-118 436.0
50 TraesCS4B01G339800 chr4D 88.060 335 17 15 1133 1450 494039396 494039724 8.440000e-100 375.0
51 TraesCS4B01G339800 chr4D 91.620 179 14 1 2237 2415 414346413 414346236 6.910000e-61 246.0
52 TraesCS4B01G339800 chr4D 90.164 183 18 0 2239 2421 76824557 76824375 1.160000e-58 239.0
53 TraesCS4B01G339800 chr4D 86.000 200 23 3 8396 8593 488937175 488937371 9.060000e-50 209.0
54 TraesCS4B01G339800 chr4D 86.592 179 16 5 3891 4061 494068997 494069175 3.280000e-44 191.0
55 TraesCS4B01G339800 chr4D 89.431 123 8 2 4573 4691 494069853 494069974 5.570000e-32 150.0
56 TraesCS4B01G339800 chr4D 78.400 250 36 6 2578 2812 460648587 460648833 7.210000e-31 147.0
57 TraesCS4B01G339800 chr4D 92.708 96 6 1 8281 8375 494090164 494090259 4.340000e-28 137.0
58 TraesCS4B01G339800 chr4D 94.872 78 4 0 2160 2237 292827808 292827731 1.210000e-23 122.0
59 TraesCS4B01G339800 chr4D 94.872 78 4 0 2160 2237 414346524 414346447 1.210000e-23 122.0
60 TraesCS4B01G339800 chr4D 98.387 62 1 0 1027 1088 494039326 494039387 9.450000e-20 110.0
61 TraesCS4B01G339800 chr4D 100.000 36 0 0 4889 4924 494054490 494054525 5.770000e-07 67.6
62 TraesCS4B01G339800 chr4D 94.595 37 0 2 3705 3740 208368670 208368635 1.000000e-03 56.5
63 TraesCS4B01G339800 chr1A 81.210 2166 296 48 5043 7125 568544596 568546733 0.000000e+00 1642.0
64 TraesCS4B01G339800 chr1A 91.866 209 15 2 8697 8904 577609226 577609433 3.150000e-74 291.0
65 TraesCS4B01G339800 chr1A 80.055 366 46 14 137 480 28978003 28978363 6.910000e-61 246.0
66 TraesCS4B01G339800 chr1A 89.785 186 16 3 2231 2415 518802421 518802604 1.490000e-57 235.0
67 TraesCS4B01G339800 chr1A 97.436 78 2 0 2160 2237 536940237 536940160 5.610000e-27 134.0
68 TraesCS4B01G339800 chr1A 94.937 79 4 0 2160 2238 461356295 461356217 3.380000e-24 124.0
69 TraesCS4B01G339800 chr1B 80.950 2147 302 62 5051 7125 659555642 659557753 0.000000e+00 1600.0
70 TraesCS4B01G339800 chr1B 96.296 108 4 0 8592 8699 359907240 359907347 2.560000e-40 178.0
71 TraesCS4B01G339800 chr1B 87.395 119 15 0 7790 7908 659532128 659532246 4.340000e-28 137.0
72 TraesCS4B01G339800 chr1B 76.140 285 50 13 2543 2812 632027786 632028067 5.610000e-27 134.0
73 TraesCS4B01G339800 chr1B 93.827 81 5 0 2157 2237 252324616 252324696 1.210000e-23 122.0
74 TraesCS4B01G339800 chr1D 78.872 1879 270 65 5043 6855 474053774 474055591 0.000000e+00 1153.0
75 TraesCS4B01G339800 chr1D 80.899 712 94 25 7232 7908 474055985 474056689 2.850000e-144 523.0
76 TraesCS4B01G339800 chr1D 82.863 496 60 10 21 501 43119174 43119659 1.070000e-113 422.0
77 TraesCS4B01G339800 chr1D 78.992 476 55 28 1016 1452 474052896 474053365 5.260000e-72 283.0
78 TraesCS4B01G339800 chr1D 89.175 194 18 2 8401 8592 450043458 450043266 1.160000e-58 239.0
79 TraesCS4B01G339800 chr1D 91.946 149 11 1 8401 8548 450043884 450043736 3.260000e-49 207.0
80 TraesCS4B01G339800 chr1D 86.885 61 7 1 5751 5810 474108452 474108512 5.770000e-07 67.6
81 TraesCS4B01G339800 chr4A 84.105 497 58 13 21 501 540420312 540419821 2.270000e-125 460.0
82 TraesCS4B01G339800 chr4A 79.641 167 25 8 8736 8899 176807289 176807129 2.630000e-20 111.0
83 TraesCS4B01G339800 chr3D 80.528 606 90 18 21 609 290818266 290817672 2.950000e-119 440.0
84 TraesCS4B01G339800 chr3D 95.122 205 9 1 8702 8906 70704076 70703873 1.120000e-83 322.0
85 TraesCS4B01G339800 chr3D 93.000 200 12 1 8396 8593 70704279 70704080 3.150000e-74 291.0
86 TraesCS4B01G339800 chr3D 78.201 289 42 12 2543 2815 598488179 598487896 1.990000e-36 165.0
87 TraesCS4B01G339800 chr3D 87.121 132 11 6 2538 2667 495275829 495275956 2.590000e-30 145.0
88 TraesCS4B01G339800 chr3D 96.774 31 1 0 3049 3079 540213178 540213208 1.600000e-02 52.8
89 TraesCS4B01G339800 chr3B 82.688 491 61 16 21 495 730341197 730341679 1.790000e-111 414.0
90 TraesCS4B01G339800 chr3B 82.883 222 36 2 2814 3034 821906699 821906919 1.960000e-46 198.0
91 TraesCS4B01G339800 chr3B 96.296 108 4 0 8591 8698 354378616 354378509 2.560000e-40 178.0
92 TraesCS4B01G339800 chr3B 94.017 117 6 1 8582 8698 40198611 40198726 9.190000e-40 176.0
93 TraesCS4B01G339800 chr3B 84.177 158 25 0 3062 3219 821906803 821906960 4.310000e-33 154.0
94 TraesCS4B01G339800 chr3B 76.389 288 49 13 2539 2812 144483686 144483404 4.340000e-28 137.0
95 TraesCS4B01G339800 chr5D 82.773 476 59 14 21 481 75271270 75271737 3.870000e-108 403.0
96 TraesCS4B01G339800 chr5D 76.214 618 111 23 21 610 168219959 168220568 2.430000e-75 294.0
97 TraesCS4B01G339800 chr5D 75.962 208 35 10 2532 2733 493123402 493123600 9.520000e-15 93.5
98 TraesCS4B01G339800 chr6D 80.962 499 68 15 21 501 399025738 399025249 3.930000e-98 370.0
99 TraesCS4B01G339800 chr6D 90.503 179 17 0 2237 2415 179949652 179949474 4.160000e-58 237.0
100 TraesCS4B01G339800 chr6D 78.276 290 46 8 2539 2815 144144179 144144464 4.280000e-38 171.0
101 TraesCS4B01G339800 chr2B 96.667 210 7 0 8697 8906 761696198 761695989 5.120000e-92 350.0
102 TraesCS4B01G339800 chr2B 96.190 210 8 0 8697 8906 761666305 761666096 2.380000e-90 344.0
103 TraesCS4B01G339800 chr2B 94.500 200 9 2 8396 8593 761666503 761666304 3.120000e-79 307.0
104 TraesCS4B01G339800 chr2B 93.500 200 11 2 8396 8593 761696396 761696197 6.760000e-76 296.0
105 TraesCS4B01G339800 chr2B 93.966 116 5 2 8597 8712 134367431 134367318 3.310000e-39 174.0
106 TraesCS4B01G339800 chr2B 84.127 63 4 5 3680 3736 453705715 453705777 1.000000e-03 56.5
107 TraesCS4B01G339800 chr6A 83.924 367 40 11 21 373 249293285 249293646 5.150000e-87 333.0
108 TraesCS4B01G339800 chr6A 89.947 189 17 2 2237 2424 265995520 265995333 8.930000e-60 243.0
109 TraesCS4B01G339800 chr6A 90.217 184 18 0 2237 2420 72362360 72362177 3.210000e-59 241.0
110 TraesCS4B01G339800 chr6A 94.872 78 4 0 2160 2237 265995631 265995554 1.210000e-23 122.0
111 TraesCS4B01G339800 chr6A 83.077 130 13 6 2539 2667 462214875 462214754 9.450000e-20 110.0
112 TraesCS4B01G339800 chr5B 80.222 450 60 16 68 501 530254647 530255083 2.410000e-80 311.0
113 TraesCS4B01G339800 chr5B 81.395 344 43 13 103 431 710759532 710759195 2.470000e-65 261.0
114 TraesCS4B01G339800 chr5B 96.364 110 4 0 8589 8698 512985212 512985321 1.980000e-41 182.0
115 TraesCS4B01G339800 chr5B 91.129 124 10 1 8575 8698 23351453 23351331 5.530000e-37 167.0
116 TraesCS4B01G339800 chr7A 91.257 183 15 1 2237 2418 148252241 148252423 1.920000e-61 248.0
117 TraesCS4B01G339800 chr7A 88.947 190 20 1 8396 8585 689256881 689257069 5.380000e-57 233.0
118 TraesCS4B01G339800 chr7A 79.061 277 42 11 2543 2805 642592456 642592182 9.190000e-40 176.0
119 TraesCS4B01G339800 chr7A 85.987 157 21 1 8697 8853 175869900 175870055 5.530000e-37 167.0
120 TraesCS4B01G339800 chr7A 78.924 223 43 3 2193 2415 36995831 36995613 2.000000e-31 148.0
121 TraesCS4B01G339800 chr7A 94.937 79 4 0 2160 2238 663527417 663527339 3.380000e-24 124.0
122 TraesCS4B01G339800 chr7A 89.831 59 3 3 3680 3735 74133027 74132969 1.240000e-08 73.1
123 TraesCS4B01G339800 chr7D 90.608 181 17 0 2237 2417 539381901 539382081 3.210000e-59 241.0
124 TraesCS4B01G339800 chr7D 78.292 281 50 8 2543 2812 631524456 631524736 4.280000e-38 171.0
125 TraesCS4B01G339800 chr2A 89.362 188 16 3 2237 2422 301843951 301843766 5.380000e-57 233.0
126 TraesCS4B01G339800 chr2A 88.083 193 17 3 8401 8593 644844677 644844863 3.240000e-54 224.0
127 TraesCS4B01G339800 chr2A 80.172 232 44 2 2814 3044 759322002 759321772 1.190000e-38 172.0
128 TraesCS4B01G339800 chr2A 77.419 279 49 9 2550 2815 692242473 692242196 4.310000e-33 154.0
129 TraesCS4B01G339800 chr2A 76.423 123 16 8 3626 3735 7508548 7508426 4.000000e-03 54.7
130 TraesCS4B01G339800 chr7B 87.047 193 19 3 8401 8593 652303463 652303649 7.000000e-51 213.0
131 TraesCS4B01G339800 chr7B 94.783 115 6 0 8592 8706 3887321 3887207 7.100000e-41 180.0
132 TraesCS4B01G339800 chr7B 77.823 248 42 7 2578 2812 43273187 43273434 3.350000e-29 141.0
133 TraesCS4B01G339800 chr7B 79.042 167 27 8 8736 8899 539995646 539995485 3.400000e-19 108.0
134 TraesCS4B01G339800 chr2D 96.296 108 4 0 8592 8699 352204267 352204160 2.560000e-40 178.0
135 TraesCS4B01G339800 chr2D 78.788 231 42 5 2563 2788 578707200 578706972 2.000000e-31 148.0
136 TraesCS4B01G339800 chr2D 94.872 78 4 0 2160 2237 613427443 613427366 1.210000e-23 122.0
137 TraesCS4B01G339800 chr2D 75.410 183 33 10 2848 3024 417540101 417540277 2.670000e-10 78.7
138 TraesCS4B01G339800 chr2D 90.476 42 4 0 3587 3628 647821706 647821747 1.000000e-03 56.5
139 TraesCS4B01G339800 chr3A 93.913 115 7 0 8584 8698 557229126 557229012 3.310000e-39 174.0
140 TraesCS4B01G339800 chr3A 86.364 132 14 3 2538 2667 681134005 681134134 3.350000e-29 141.0
141 TraesCS4B01G339800 chr3A 92.500 40 1 2 3084 3123 715668325 715668362 1.000000e-03 56.5
142 TraesCS4B01G339800 chr6B 80.500 200 27 10 8704 8899 158269501 158269310 9.320000e-30 143.0
143 TraesCS4B01G339800 chr6B 78.500 200 30 10 8704 8899 136515298 136515488 1.570000e-22 119.0
144 TraesCS4B01G339800 chrUn 77.689 251 43 7 2578 2815 342458924 342458674 3.350000e-29 141.0


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 TraesCS4B01G339800 chr4B 633281638 633290543 8905 False 4104.750000 9960 97.934000 1 8906 4 chr4B.!!$F6 8905
1 TraesCS4B01G339800 chr4B 632870689 632875627 4938 False 1560.000000 2479 85.537000 5029 7990 2 chr4B.!!$F4 2961
2 TraesCS4B01G339800 chr4B 633142392 633149958 7566 False 1015.000000 1759 87.902000 864 8149 4 chr4B.!!$F5 7285
3 TraesCS4B01G339800 chr4B 633325846 633330057 4211 False 767.400000 1509 89.215600 1135 8266 5 chr4B.!!$F7 7131
4 TraesCS4B01G339800 chr4B 632863869 632864560 691 False 300.500000 418 84.406500 919 1558 2 chr4B.!!$F3 639
5 TraesCS4B01G339800 chr5A 673553151 673560438 7287 False 1531.333333 3904 88.335333 864 8372 3 chr5A.!!$F4 7508
6 TraesCS4B01G339800 chr5A 673690209 673693748 3539 False 690.300000 1308 91.064600 4889 8266 5 chr5A.!!$F5 3377
7 TraesCS4B01G339800 chr4D 493976679 493979302 2623 False 2750.000000 2750 86.115000 5411 7990 1 chr4D.!!$F6 2579
8 TraesCS4B01G339800 chr4D 494050526 494057839 7313 False 1052.150000 3169 89.537000 864 8159 4 chr4D.!!$F9 7295
9 TraesCS4B01G339800 chr4D 494065596 494075048 9452 False 905.875000 2132 89.896375 729 8273 8 chr4D.!!$F10 7544
10 TraesCS4B01G339800 chr4D 494099357 494103008 3651 False 863.750000 1362 85.932250 4922 8259 4 chr4D.!!$F11 3337
11 TraesCS4B01G339800 chr4D 363565473 363566069 596 False 503.000000 503 82.401000 21 609 1 chr4D.!!$F2 588
12 TraesCS4B01G339800 chr1A 568544596 568546733 2137 False 1642.000000 1642 81.210000 5043 7125 1 chr1A.!!$F3 2082
13 TraesCS4B01G339800 chr1B 659555642 659557753 2111 False 1600.000000 1600 80.950000 5051 7125 1 chr1B.!!$F5 2074
14 TraesCS4B01G339800 chr1D 474052896 474056689 3793 False 653.000000 1153 79.587667 1016 7908 3 chr1D.!!$F3 6892
15 TraesCS4B01G339800 chr1D 450043266 450043884 618 True 223.000000 239 90.560500 8401 8592 2 chr1D.!!$R1 191
16 TraesCS4B01G339800 chr3D 290817672 290818266 594 True 440.000000 440 80.528000 21 609 1 chr3D.!!$R1 588
17 TraesCS4B01G339800 chr5D 168219959 168220568 609 False 294.000000 294 76.214000 21 610 1 chr5D.!!$F2 589

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
503 518 0.037590 ACCGCTGGCATGACCTAAAA 59.962 50.000 0.00 0.00 40.22 1.52 F
695 710 0.172352 CAACAGAGAGAGGAGGCGAC 59.828 60.000 0.00 0.00 0.00 5.19 F
1301 1447 0.240145 GCCCGCCTTTGTTTACAGTC 59.760 55.000 0.00 0.00 0.00 3.51 F
1856 2816 0.250513 GGTTACACTAGCTGCTGCCT 59.749 55.000 13.43 2.55 40.80 4.75 F
2826 4353 0.037326 TTCAATCTCCGCACGCTCTT 60.037 50.000 0.00 0.00 0.00 2.85 F
3119 4647 0.037447 AAAACAGAGCAGGAGCCCTC 59.963 55.000 0.00 0.00 43.56 4.30 F
3881 5417 0.106819 ATAGTCTACAGGGCCGTCGT 60.107 55.000 0.00 0.09 0.00 4.34 F
3937 5694 0.107654 GCGTCCACCATCTAAAGGCT 60.108 55.000 0.00 0.00 0.00 4.58 F
4235 6036 0.169672 CAAATCCAGCAACGCCTCTG 59.830 55.000 0.00 0.00 0.00 3.35 F
4477 6282 0.318441 TGAGGAAGAGCGAAGTGTGG 59.682 55.000 0.00 0.00 0.00 4.17 F
4704 7648 0.450983 GCTCAAGCTGATCAAGGTGC 59.549 55.000 0.00 0.00 36.51 5.01 F
4858 9805 0.526662 CTCAAAGTACGACGGGAGCT 59.473 55.000 0.00 0.00 0.00 4.09 F
5205 10315 2.268920 GGTTGGCTCGCCATCTCA 59.731 61.111 12.00 0.00 46.64 3.27 F
6583 12016 3.478857 TCGTGATTGTGGTACAACCTT 57.521 42.857 0.00 0.00 44.16 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2778 0.175760 CATGGTCTAGTCCACGGTGG 59.824 60.000 21.27 21.27 40.51 4.61 R
2105 3528 0.318445 GGCCTACCGTACGCATACTG 60.318 60.000 10.49 0.00 0.00 2.74 R
2807 4334 0.037326 AAGAGCGTGCGGAGATTGAA 60.037 50.000 0.00 0.00 0.00 2.69 R
3212 4740 0.042731 TCCTCCTAGGACCAGGGTTG 59.957 60.000 7.62 0.00 40.06 3.77 R
4217 6018 0.036732 TCAGAGGCGTTGCTGGATTT 59.963 50.000 0.00 0.00 33.05 2.17 R
4744 9598 0.038251 AGCGTCGTGTCATGTCATGT 60.038 50.000 12.54 0.00 0.00 3.21 R
5226 10336 0.110486 AAGCTCCGGAAAAGAAGGCA 59.890 50.000 5.23 0.00 0.00 4.75 R
5306 10429 0.865769 CGCCCCATATACAGAAACGC 59.134 55.000 0.00 0.00 0.00 4.84 R
5685 10881 3.011818 TGCACAATGAGTCCAGCATAAG 58.988 45.455 0.00 0.00 0.00 1.73 R
6013 11306 4.461081 ACACATTCGCTTAAGCCCATAAAA 59.539 37.500 21.53 7.10 37.91 1.52 R
6583 12016 0.394762 CAGGCCAATTCCTAGCTGCA 60.395 55.000 5.01 0.00 33.95 4.41 R
6700 12134 8.438676 AACACTATAATATTGCACTGAAGGAC 57.561 34.615 0.00 0.00 0.00 3.85 R
7016 12708 0.250901 TGGGAGTTGAAGCAAGAGCC 60.251 55.000 0.00 0.00 43.56 4.70 R
8482 16919 0.348370 AGATGGGATCCAAGGAGGGT 59.652 55.000 15.23 0.00 36.95 4.34 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.