Multiple sequence alignment - TraesCS4B01G282700

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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 TraesCS4B01G282700 chr4B 100.000 4298 0 0 1 4298 565986200 565990497 0.000000e+00 7938.0
1 TraesCS4B01G282700 chr4B 100.000 4102 0 0 4614 8715 565990813 565994914 0.000000e+00 7576.0
2 TraesCS4B01G282700 chr4B 94.453 631 35 0 8085 8715 566007062 566007692 0.000000e+00 972.0
3 TraesCS4B01G282700 chr4B 90.205 633 59 3 8085 8715 452655906 452656537 0.000000e+00 822.0
4 TraesCS4B01G282700 chr4B 75.970 1082 174 45 2796 3829 377372662 377371619 6.120000e-131 479.0
5 TraesCS4B01G282700 chr4B 74.416 813 160 27 3198 3976 380691686 380690888 1.100000e-78 305.0
6 TraesCS4B01G282700 chr4B 76.560 593 83 33 3 557 611410373 611409799 3.100000e-69 274.0
7 TraesCS4B01G282700 chr4B 77.755 481 83 15 2713 3186 643760099 643760562 3.100000e-69 274.0
8 TraesCS4B01G282700 chr4B 78.174 449 66 19 129 557 629379750 629379314 3.120000e-64 257.0
9 TraesCS4B01G282700 chr4B 78.519 270 56 2 2879 3147 18141545 18141277 8.990000e-40 176.0
10 TraesCS4B01G282700 chr4B 94.681 94 5 0 5458 5551 565991565 565991658 7.050000e-31 147.0
11 TraesCS4B01G282700 chr4B 94.681 94 5 0 5366 5459 565991657 565991750 7.050000e-31 147.0
12 TraesCS4B01G282700 chr4B 78.788 99 15 5 2661 2754 489433566 489433469 2.630000e-05 62.1
13 TraesCS4B01G282700 chr4B 100.000 28 0 0 429 456 629379662 629379689 1.600000e-02 52.8
14 TraesCS4B01G282700 chr4D 90.556 2033 114 29 5567 7577 452808440 452810416 0.000000e+00 2619.0
15 TraesCS4B01G282700 chr4D 93.263 1232 55 7 712 1915 452803316 452804547 0.000000e+00 1790.0
16 TraesCS4B01G282700 chr4D 76.436 1549 287 49 2578 4058 499732129 499730591 0.000000e+00 767.0
17 TraesCS4B01G282700 chr4D 82.240 732 88 20 4747 5445 452807573 452808295 2.090000e-165 593.0
18 TraesCS4B01G282700 chr4D 93.137 306 20 1 2107 2411 27567424 27567119 1.730000e-121 448.0
19 TraesCS4B01G282700 chr4D 94.326 282 16 0 7579 7860 442392821 442392540 4.830000e-117 433.0
20 TraesCS4B01G282700 chr4D 77.372 685 122 23 3243 3901 9477368 9476691 8.260000e-100 375.0
21 TraesCS4B01G282700 chr4D 78.207 569 92 21 2876 3417 497254351 497254914 1.400000e-87 335.0
22 TraesCS4B01G282700 chr4D 87.681 138 9 7 1945 2075 452806821 452806957 4.210000e-33 154.0
23 TraesCS4B01G282700 chr4D 96.591 88 3 0 7957 8044 452850227 452850314 7.050000e-31 147.0
24 TraesCS4B01G282700 chr4D 95.122 41 2 0 2414 2454 454415150 454415110 2.030000e-06 65.8
25 TraesCS4B01G282700 chr4A 96.516 1550 47 6 6034 7577 14182517 14180969 0.000000e+00 2556.0
26 TraesCS4B01G282700 chr4A 94.141 990 44 7 986 1961 14185448 14184459 0.000000e+00 1495.0
27 TraesCS4B01G282700 chr4A 86.971 591 39 17 1 557 710818018 710818604 1.600000e-176 630.0
28 TraesCS4B01G282700 chr4A 76.812 897 151 27 2572 3431 34304987 34305863 1.330000e-122 451.0
29 TraesCS4B01G282700 chr4A 89.062 320 29 4 673 986 14185800 14185481 8.200000e-105 392.0
30 TraesCS4B01G282700 chr4A 84.211 95 6 5 558 651 14187471 14187385 5.610000e-12 84.2
31 TraesCS4B01G282700 chr7B 92.429 634 44 3 8085 8715 338196634 338196002 0.000000e+00 902.0
32 TraesCS4B01G282700 chr7B 92.089 632 49 1 8085 8715 338183896 338183265 0.000000e+00 889.0
33 TraesCS4B01G282700 chr7B 86.444 568 44 11 1 557 161241572 161241027 7.530000e-165 592.0
34 TraesCS4B01G282700 chr7B 94.667 300 15 1 2111 2409 395605299 395605000 1.710000e-126 464.0
35 TraesCS4B01G282700 chr7B 94.932 296 14 1 2111 2405 74202718 74203013 6.160000e-126 462.0
36 TraesCS4B01G282700 chr7B 94.000 300 15 3 2108 2406 605960583 605960880 1.330000e-122 451.0
37 TraesCS4B01G282700 chr7B 77.016 496 84 17 3246 3726 222703724 222703244 3.120000e-64 257.0
38 TraesCS4B01G282700 chr7B 92.683 41 3 0 2072 2112 649987168 649987128 9.450000e-05 60.2
39 TraesCS4B01G282700 chr2B 91.125 631 55 1 8085 8715 681284234 681284863 0.000000e+00 854.0
40 TraesCS4B01G282700 chr2B 75.659 1442 227 55 2551 3927 478186164 478187546 9.680000e-169 604.0
41 TraesCS4B01G282700 chr2B 85.473 592 45 20 1 557 444551439 444550854 5.870000e-161 579.0
42 TraesCS4B01G282700 chr2B 83.648 159 18 6 404 557 798654700 798654545 9.120000e-30 143.0
43 TraesCS4B01G282700 chr2B 82.222 90 12 3 2371 2457 2853852 2853764 3.370000e-09 75.0
44 TraesCS4B01G282700 chr2B 82.222 90 12 3 2371 2457 204508738 204508650 3.370000e-09 75.0
45 TraesCS4B01G282700 chr2B 88.679 53 6 0 2405 2457 644171870 644171922 2.030000e-06 65.8
46 TraesCS4B01G282700 chr2B 88.000 50 6 0 2402 2451 599908848 599908799 9.450000e-05 60.2
47 TraesCS4B01G282700 chr2B 96.970 33 0 1 2080 2112 148143881 148143850 4.000000e-03 54.7
48 TraesCS4B01G282700 chr6B 90.679 633 57 2 8085 8715 140842015 140841383 0.000000e+00 841.0
49 TraesCS4B01G282700 chr6B 90.236 635 56 6 8085 8715 140829129 140828497 0.000000e+00 824.0
50 TraesCS4B01G282700 chr6B 88.756 587 33 8 1 557 476551 475968 0.000000e+00 688.0
51 TraesCS4B01G282700 chr6B 80.055 361 54 8 212 557 207774057 207773700 1.450000e-62 252.0
52 TraesCS4B01G282700 chr6B 75.624 521 93 16 3264 3753 412111178 412110661 2.450000e-55 228.0
53 TraesCS4B01G282700 chr6B 83.544 158 21 3 404 557 170994470 170994314 9.120000e-30 143.0
54 TraesCS4B01G282700 chr1B 90.665 632 58 1 8085 8715 544974523 544973892 0.000000e+00 839.0
55 TraesCS4B01G282700 chr1B 90.032 632 61 2 8085 8715 544960007 544959377 0.000000e+00 817.0
56 TraesCS4B01G282700 chr1B 94.932 296 14 1 2111 2405 4647381 4647086 6.160000e-126 462.0
57 TraesCS4B01G282700 chr1B 90.411 73 6 1 3790 3862 290526127 290526198 2.590000e-15 95.3
58 TraesCS4B01G282700 chr1B 97.561 41 1 0 2072 2112 637475914 637475954 4.360000e-08 71.3
59 TraesCS4B01G282700 chr7A 75.720 1528 263 53 2572 4015 508569059 508567556 0.000000e+00 667.0
60 TraesCS4B01G282700 chr7A 92.905 296 20 1 7568 7862 458978873 458978578 6.250000e-116 429.0
61 TraesCS4B01G282700 chr7A 91.111 45 2 2 2661 2704 541877094 541877137 9.450000e-05 60.2
62 TraesCS4B01G282700 chr3B 87.500 592 37 19 1 558 617687508 617688096 0.000000e+00 649.0
63 TraesCS4B01G282700 chr3B 94.595 296 15 1 2111 2405 783126776 783126481 2.870000e-124 457.0
64 TraesCS4B01G282700 chr3B 84.393 173 26 1 2711 2882 684622103 684622275 1.500000e-37 169.0
65 TraesCS4B01G282700 chr5D 85.500 600 40 22 1 557 385126193 385126788 4.530000e-162 582.0
66 TraesCS4B01G282700 chr5D 85.429 501 51 11 72 557 460675647 460676140 1.310000e-137 501.0
67 TraesCS4B01G282700 chr5D 93.448 290 19 0 7573 7862 72764099 72764388 1.740000e-116 431.0
68 TraesCS4B01G282700 chr5D 81.373 306 53 4 2816 3119 227731876 227732179 6.760000e-61 246.0
69 TraesCS4B01G282700 chr5D 76.113 494 79 17 3220 3676 416589927 416590418 1.140000e-53 222.0
70 TraesCS4B01G282700 chr5D 75.735 408 76 13 3491 3879 388738083 388737680 5.370000e-42 183.0
71 TraesCS4B01G282700 chr5D 81.319 91 15 2 3968 4057 385692533 385692444 1.210000e-08 73.1
72 TraesCS4B01G282700 chr6D 85.333 600 42 20 1 558 78029655 78029060 5.870000e-161 579.0
73 TraesCS4B01G282700 chr6D 77.409 602 91 26 3187 3755 435010483 435011072 5.080000e-82 316.0
74 TraesCS4B01G282700 chr5B 96.119 335 12 1 1 335 613181260 613180927 5.950000e-151 545.0
75 TraesCS4B01G282700 chr5B 80.731 602 108 8 2600 3198 246591450 246590854 6.160000e-126 462.0
76 TraesCS4B01G282700 chr5B 92.880 309 20 2 2099 2405 382259068 382259376 1.730000e-121 448.0
77 TraesCS4B01G282700 chr5B 73.817 634 130 24 3451 4058 21366598 21367221 1.470000e-52 219.0
78 TraesCS4B01G282700 chr5B 72.337 676 138 26 3444 4082 636543089 636542426 5.410000e-37 167.0
79 TraesCS4B01G282700 chr5B 93.023 43 3 0 2408 2450 665899394 665899436 7.300000e-06 63.9
80 TraesCS4B01G282700 chr3A 86.561 506 45 17 69 557 27234865 27234366 3.580000e-148 536.0
81 TraesCS4B01G282700 chr3A 92.333 300 20 1 7563 7862 390010366 390010662 2.910000e-114 424.0
82 TraesCS4B01G282700 chr3A 80.126 317 52 10 2792 3101 681644878 681645190 8.800000e-55 226.0
83 TraesCS4B01G282700 chr3A 90.411 73 6 1 3790 3862 162667026 162666955 2.590000e-15 95.3
84 TraesCS4B01G282700 chr7D 83.986 562 76 13 2566 3122 4784183 4783631 2.150000e-145 527.0
85 TraesCS4B01G282700 chr7D 80.128 624 100 9 2578 3183 4736650 4736033 2.230000e-120 444.0
86 TraesCS4B01G282700 chr7D 75.292 599 110 18 3187 3753 384987559 384988151 1.450000e-62 252.0
87 TraesCS4B01G282700 chr7D 76.447 501 86 12 3246 3726 246527621 246527133 8.740000e-60 243.0
88 TraesCS4B01G282700 chr2D 93.645 299 18 1 2108 2405 518263573 518263871 6.210000e-121 446.0
89 TraesCS4B01G282700 chr2D 76.111 900 159 28 3221 4074 19591655 19590766 3.760000e-113 420.0
90 TraesCS4B01G282700 chr2D 82.271 361 34 14 1 332 144555095 144554736 1.430000e-72 285.0
91 TraesCS4B01G282700 chr2D 78.862 246 45 6 2878 3119 201822417 201822659 9.060000e-35 159.0
92 TraesCS4B01G282700 chr2D 84.314 153 16 6 411 557 622292230 622292380 9.120000e-30 143.0
93 TraesCS4B01G282700 chr3D 93.069 303 20 1 2104 2405 572420609 572420911 8.030000e-120 442.0
94 TraesCS4B01G282700 chr3D 83.544 158 25 1 2875 3031 537113550 537113707 7.050000e-31 147.0
95 TraesCS4B01G282700 chr3D 90.411 73 6 1 3790 3862 154160394 154160465 2.590000e-15 95.3
96 TraesCS4B01G282700 chr3D 89.286 56 4 2 2414 2468 75958836 75958890 1.570000e-07 69.4
97 TraesCS4B01G282700 chr3D 95.122 41 2 0 2414 2454 403817495 403817455 2.030000e-06 65.8
98 TraesCS4B01G282700 chr3D 88.889 45 4 1 3079 3122 172782766 172782722 4.000000e-03 54.7
99 TraesCS4B01G282700 chr2A 94.118 289 17 0 7579 7867 623148062 623147774 2.890000e-119 440.0
100 TraesCS4B01G282700 chr2A 94.386 285 15 1 7576 7860 387541365 387541648 3.740000e-118 436.0
101 TraesCS4B01G282700 chr2A 73.631 895 172 34 3187 4025 621441002 621440116 3.980000e-73 287.0
102 TraesCS4B01G282700 chr2A 76.894 528 93 17 3262 3778 54853649 54853140 1.110000e-68 272.0
103 TraesCS4B01G282700 chr2A 78.189 243 41 10 6176 6412 34119066 34118830 2.540000e-30 145.0
104 TraesCS4B01G282700 chr2A 95.238 42 2 0 2676 2717 429723403 429723444 5.650000e-07 67.6
105 TraesCS4B01G282700 chr2A 89.091 55 5 1 2404 2458 724498048 724498101 5.650000e-07 67.6
106 TraesCS4B01G282700 chr5A 93.836 292 16 2 7572 7862 141109095 141108805 1.040000e-118 438.0
107 TraesCS4B01G282700 chr5A 92.157 306 19 5 7562 7862 488597092 488596787 2.250000e-115 427.0
108 TraesCS4B01G282700 chr5A 72.123 1399 281 70 2710 4055 568684907 568683565 1.090000e-83 322.0
109 TraesCS4B01G282700 chr5A 78.800 500 76 12 2565 3040 68290615 68290122 8.500000e-80 309.0
110 TraesCS4B01G282700 chr5A 74.390 656 113 35 3258 3879 540287635 540287001 6.810000e-56 230.0
111 TraesCS4B01G282700 chr5A 73.428 636 130 24 3274 3879 22612250 22612876 1.480000e-47 202.0
112 TraesCS4B01G282700 chr5A 73.651 482 86 21 3484 3946 693304267 693304726 1.960000e-31 148.0
113 TraesCS4B01G282700 chr1A 93.793 290 18 0 7573 7862 27754265 27754554 3.740000e-118 436.0
114 TraesCS4B01G282700 chr1A 74.672 916 182 24 3187 4058 487460166 487461075 2.310000e-95 361.0
115 TraesCS4B01G282700 chr1A 100.000 29 0 0 2068 2096 516728827 516728855 4.000000e-03 54.7
116 TraesCS4B01G282700 chr1D 81.049 591 71 18 1 557 379575465 379574882 4.830000e-117 433.0
117 TraesCS4B01G282700 chr1D 80.000 300 54 6 2875 3171 387891402 387891698 5.300000e-52 217.0
118 TraesCS4B01G282700 chr1D 80.682 176 30 2 2711 2882 387891198 387891373 5.490000e-27 134.0
119 TraesCS4B01G282700 chr6A 77.886 511 93 14 3484 3980 591214375 591214879 5.110000e-77 300.0


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 TraesCS4B01G282700 chr4B 565986200 565994914 8714 False 3952.0 7938 97.3405 1 8715 4 chr4B.!!$F5 8714
1 TraesCS4B01G282700 chr4B 566007062 566007692 630 False 972.0 972 94.4530 8085 8715 1 chr4B.!!$F2 630
2 TraesCS4B01G282700 chr4B 452655906 452656537 631 False 822.0 822 90.2050 8085 8715 1 chr4B.!!$F1 630
3 TraesCS4B01G282700 chr4B 377371619 377372662 1043 True 479.0 479 75.9700 2796 3829 1 chr4B.!!$R2 1033
4 TraesCS4B01G282700 chr4B 380690888 380691686 798 True 305.0 305 74.4160 3198 3976 1 chr4B.!!$R3 778
5 TraesCS4B01G282700 chr4B 611409799 611410373 574 True 274.0 274 76.5600 3 557 1 chr4B.!!$R5 554
6 TraesCS4B01G282700 chr4D 452803316 452810416 7100 False 1289.0 2619 88.4350 712 7577 4 chr4D.!!$F3 6865
7 TraesCS4B01G282700 chr4D 499730591 499732129 1538 True 767.0 767 76.4360 2578 4058 1 chr4D.!!$R5 1480
8 TraesCS4B01G282700 chr4D 9476691 9477368 677 True 375.0 375 77.3720 3243 3901 1 chr4D.!!$R1 658
9 TraesCS4B01G282700 chr4D 497254351 497254914 563 False 335.0 335 78.2070 2876 3417 1 chr4D.!!$F2 541
10 TraesCS4B01G282700 chr4A 14180969 14187471 6502 True 1131.8 2556 90.9825 558 7577 4 chr4A.!!$R1 7019
11 TraesCS4B01G282700 chr4A 710818018 710818604 586 False 630.0 630 86.9710 1 557 1 chr4A.!!$F2 556
12 TraesCS4B01G282700 chr4A 34304987 34305863 876 False 451.0 451 76.8120 2572 3431 1 chr4A.!!$F1 859
13 TraesCS4B01G282700 chr7B 338196002 338196634 632 True 902.0 902 92.4290 8085 8715 1 chr7B.!!$R4 630
14 TraesCS4B01G282700 chr7B 338183265 338183896 631 True 889.0 889 92.0890 8085 8715 1 chr7B.!!$R3 630
15 TraesCS4B01G282700 chr7B 161241027 161241572 545 True 592.0 592 86.4440 1 557 1 chr7B.!!$R1 556
16 TraesCS4B01G282700 chr2B 681284234 681284863 629 False 854.0 854 91.1250 8085 8715 1 chr2B.!!$F3 630
17 TraesCS4B01G282700 chr2B 478186164 478187546 1382 False 604.0 604 75.6590 2551 3927 1 chr2B.!!$F1 1376
18 TraesCS4B01G282700 chr2B 444550854 444551439 585 True 579.0 579 85.4730 1 557 1 chr2B.!!$R4 556
19 TraesCS4B01G282700 chr6B 140841383 140842015 632 True 841.0 841 90.6790 8085 8715 1 chr6B.!!$R3 630
20 TraesCS4B01G282700 chr6B 140828497 140829129 632 True 824.0 824 90.2360 8085 8715 1 chr6B.!!$R2 630
21 TraesCS4B01G282700 chr6B 475968 476551 583 True 688.0 688 88.7560 1 557 1 chr6B.!!$R1 556
22 TraesCS4B01G282700 chr6B 412110661 412111178 517 True 228.0 228 75.6240 3264 3753 1 chr6B.!!$R6 489
23 TraesCS4B01G282700 chr1B 544973892 544974523 631 True 839.0 839 90.6650 8085 8715 1 chr1B.!!$R3 630
24 TraesCS4B01G282700 chr1B 544959377 544960007 630 True 817.0 817 90.0320 8085 8715 1 chr1B.!!$R2 630
25 TraesCS4B01G282700 chr7A 508567556 508569059 1503 True 667.0 667 75.7200 2572 4015 1 chr7A.!!$R2 1443
26 TraesCS4B01G282700 chr3B 617687508 617688096 588 False 649.0 649 87.5000 1 558 1 chr3B.!!$F1 557
27 TraesCS4B01G282700 chr5D 385126193 385126788 595 False 582.0 582 85.5000 1 557 1 chr5D.!!$F3 556
28 TraesCS4B01G282700 chr6D 78029060 78029655 595 True 579.0 579 85.3330 1 558 1 chr6D.!!$R1 557
29 TraesCS4B01G282700 chr6D 435010483 435011072 589 False 316.0 316 77.4090 3187 3755 1 chr6D.!!$F1 568
30 TraesCS4B01G282700 chr5B 246590854 246591450 596 True 462.0 462 80.7310 2600 3198 1 chr5B.!!$R1 598
31 TraesCS4B01G282700 chr5B 21366598 21367221 623 False 219.0 219 73.8170 3451 4058 1 chr5B.!!$F1 607
32 TraesCS4B01G282700 chr7D 4783631 4784183 552 True 527.0 527 83.9860 2566 3122 1 chr7D.!!$R2 556
33 TraesCS4B01G282700 chr7D 4736033 4736650 617 True 444.0 444 80.1280 2578 3183 1 chr7D.!!$R1 605
34 TraesCS4B01G282700 chr7D 384987559 384988151 592 False 252.0 252 75.2920 3187 3753 1 chr7D.!!$F1 566
35 TraesCS4B01G282700 chr2D 19590766 19591655 889 True 420.0 420 76.1110 3221 4074 1 chr2D.!!$R1 853
36 TraesCS4B01G282700 chr2A 621440116 621441002 886 True 287.0 287 73.6310 3187 4025 1 chr2A.!!$R3 838
37 TraesCS4B01G282700 chr2A 54853140 54853649 509 True 272.0 272 76.8940 3262 3778 1 chr2A.!!$R2 516
38 TraesCS4B01G282700 chr5A 568683565 568684907 1342 True 322.0 322 72.1230 2710 4055 1 chr5A.!!$R5 1345
39 TraesCS4B01G282700 chr5A 540287001 540287635 634 True 230.0 230 74.3900 3258 3879 1 chr5A.!!$R4 621
40 TraesCS4B01G282700 chr5A 22612250 22612876 626 False 202.0 202 73.4280 3274 3879 1 chr5A.!!$F1 605
41 TraesCS4B01G282700 chr1A 487460166 487461075 909 False 361.0 361 74.6720 3187 4058 1 chr1A.!!$F2 871
42 TraesCS4B01G282700 chr1D 379574882 379575465 583 True 433.0 433 81.0490 1 557 1 chr1D.!!$R1 556
43 TraesCS4B01G282700 chr6A 591214375 591214879 504 False 300.0 300 77.8860 3484 3980 1 chr6A.!!$F1 496

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
997 2667 0.036010 ACAGCGACCCTTCATCCAAG 60.036 55.000 0.00 0.00 0.00 3.61 F
1740 3413 1.078637 GGACTACCGGGCAGGAAAC 60.079 63.158 11.67 0.00 45.00 2.78 F
2380 6396 0.094730 GGTGCGCAACGTAAGATGAC 59.905 55.000 14.00 0.00 43.67 3.06 F
3547 8528 0.038892 GCGTCAGTCGTCCCAAAGTA 60.039 55.000 0.00 0.00 42.13 2.24 F
4086 9191 0.173481 CGGACATCGCGATCCCATAT 59.827 55.000 26.96 9.25 0.00 1.78 F
4639 9744 0.038343 CTTTGGGCATGAACGGTTGG 60.038 55.000 0.00 0.00 0.00 3.77 F
4682 9787 0.110486 GAACAGGGCTGAGGTTTGGA 59.890 55.000 0.00 0.00 0.00 3.53 F
4683 9788 0.111253 AACAGGGCTGAGGTTTGGAG 59.889 55.000 0.00 0.00 0.00 3.86 F
5210 10322 0.116342 TCTAGGCCCCTGTCTCAACA 59.884 55.000 0.00 0.00 0.00 3.33 F
5619 10872 0.179062 ATCGCTGGAGATGAAGCCAC 60.179 55.000 0.00 0.00 35.98 5.01 F
5629 10882 0.606401 ATGAAGCCACGGACAACCAG 60.606 55.000 0.00 0.00 35.59 4.00 F
7250 12582 0.105658 CGAGAGGGACAGGGGGATAA 60.106 60.000 0.00 0.00 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 6178 0.033781 TGTACCGCGCCTAAGTGTTT 59.966 50.000 0.00 0.00 0.00 2.83 R
3196 7551 0.037734 TGCTCGACTCCTACCACTCA 59.962 55.000 0.00 0.00 0.00 3.41 R
3718 8757 0.242825 GACCGTTCGTCTGTCCATCA 59.757 55.000 0.00 0.00 38.57 3.07 R
4620 9725 0.038343 CCAACCGTTCATGCCCAAAG 60.038 55.000 0.00 0.00 0.00 2.77 R
5446 10584 0.179032 TGGCCAGTGTTGTTGTCGAT 60.179 50.000 0.00 0.00 0.00 3.59 R
5667 10922 0.250513 GAACCGCAGATCTTGTCCCT 59.749 55.000 0.00 0.00 0.00 4.20 R
6310 11608 0.659957 CGTAGTAGCCGTCCAGGTAC 59.340 60.000 0.00 0.00 43.70 3.34 R
6492 11791 2.609984 CCGTGATCTGCATCAGAGGATC 60.610 54.545 6.07 5.46 44.08 3.36 R
6748 12080 0.031314 CGTCCTCCATGATCTGGTCG 59.969 60.000 9.98 0.00 46.08 4.79 R
6793 12125 1.750399 GTGGTAGACGGCGAGGGTA 60.750 63.158 16.62 0.00 0.00 3.69 R
7617 12953 2.492881 GGTGTTGATTGATGACATGGCA 59.507 45.455 2.18 2.18 0.00 4.92 R
8198 13534 0.251209 TAGTCGGCCTGTGAGACAGT 60.251 55.000 0.00 0.00 44.50 3.55 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.