Multiple sequence alignment - TraesCS1A01G112000

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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 TraesCS1A01G112000 chr1A 100.000 6874 0 0 1 6874 113849685 113856558 0.000000e+00 12694.0
1 TraesCS1A01G112000 chr1A 92.827 3276 163 45 3631 6860 382566346 382563097 0.000000e+00 4682.0
2 TraesCS1A01G112000 chr1A 95.666 2584 87 15 4312 6874 543984064 543981485 0.000000e+00 4128.0
3 TraesCS1A01G112000 chr1A 100.000 1713 0 0 7381 9093 113857065 113858777 0.000000e+00 3164.0
4 TraesCS1A01G112000 chr1A 97.843 510 5 2 7381 7890 543981198 543980695 0.000000e+00 876.0
5 TraesCS1A01G112000 chr2A 93.112 2976 156 26 3631 6594 463604369 463607307 0.000000e+00 4314.0
6 TraesCS1A01G112000 chr2A 93.857 2230 111 23 3631 5846 751934024 751931807 0.000000e+00 3336.0
7 TraesCS1A01G112000 chr2A 93.777 1366 64 8 5463 6822 463597951 463599301 0.000000e+00 2032.0
8 TraesCS1A01G112000 chr1D 97.018 2549 62 9 764 3307 109969237 109971776 0.000000e+00 4274.0
9 TraesCS1A01G112000 chr1D 94.694 867 14 5 8259 9093 109972676 109973542 0.000000e+00 1317.0
10 TraesCS1A01G112000 chr1D 88.289 760 67 9 3 757 192417944 192417202 0.000000e+00 891.0
11 TraesCS1A01G112000 chr1D 87.386 769 71 10 1 755 456128212 456128968 0.000000e+00 859.0
12 TraesCS1A01G112000 chr1D 87.186 757 70 11 1 753 448218909 448219642 0.000000e+00 835.0
13 TraesCS1A01G112000 chr1D 85.733 764 81 16 1 758 454401177 454401918 0.000000e+00 782.0
14 TraesCS1A01G112000 chr1D 85.547 768 82 21 1 755 473271201 473270450 0.000000e+00 776.0
15 TraesCS1A01G112000 chr1D 84.585 759 81 12 1 752 32764175 32764904 0.000000e+00 721.0
16 TraesCS1A01G112000 chr1D 83.808 772 96 18 1 755 474070947 474070188 0.000000e+00 706.0
17 TraesCS1A01G112000 chr1D 83.791 765 91 19 1 755 103691179 103691920 0.000000e+00 695.0
18 TraesCS1A01G112000 chr1D 82.898 766 84 29 1 756 296686685 296687413 0.000000e+00 645.0
19 TraesCS1A01G112000 chr1D 81.806 775 112 26 1 757 65560694 65561457 2.790000e-174 623.0
20 TraesCS1A01G112000 chr1D 82.309 667 94 21 1 652 448538227 448538884 2.870000e-154 556.0
21 TraesCS1A01G112000 chr1D 86.667 480 58 5 288 763 296161657 296162134 2.250000e-145 527.0
22 TraesCS1A01G112000 chr1D 95.098 306 13 2 3328 3631 109972017 109972322 1.780000e-131 481.0
23 TraesCS1A01G112000 chr1D 96.923 260 8 0 7962 8221 109972419 109972678 3.900000e-118 436.0
24 TraesCS1A01G112000 chr1D 96.341 82 3 0 7888 7969 109972317 109972398 1.590000e-27 135.0
25 TraesCS1A01G112000 chr7A 95.289 2547 93 13 4312 6836 465668954 465666413 0.000000e+00 4013.0
26 TraesCS1A01G112000 chr7A 94.319 2218 107 18 3631 5837 122317256 122315047 0.000000e+00 3380.0
27 TraesCS1A01G112000 chr7A 98.004 501 3 3 7386 7886 221843126 221842633 0.000000e+00 863.0
28 TraesCS1A01G112000 chr7A 93.469 245 16 0 8487 8731 149286593 149286837 1.870000e-96 364.0
29 TraesCS1A01G112000 chr7A 95.152 165 5 1 6711 6872 221843483 221843319 3.260000e-64 257.0
30 TraesCS1A01G112000 chr7A 96.203 79 3 0 8421 8499 149284923 149285001 7.410000e-26 130.0
31 TraesCS1A01G112000 chr7A 97.561 41 1 0 6829 6869 692971135 692971175 4.550000e-08 71.3
32 TraesCS1A01G112000 chr7A 90.000 50 2 2 6642 6688 406863537 406863586 2.740000e-05 62.1
33 TraesCS1A01G112000 chr4B 92.893 2617 149 26 4273 6874 279732580 279729986 0.000000e+00 3768.0
34 TraesCS1A01G112000 chr6B 94.362 2217 106 19 3632 5837 40766505 40768713 0.000000e+00 3384.0
35 TraesCS1A01G112000 chr6B 91.636 1913 116 29 4980 6874 687904872 687906758 0.000000e+00 2606.0
36 TraesCS1A01G112000 chr6B 97.826 506 7 2 7381 7886 687906783 687907284 0.000000e+00 870.0
37 TraesCS1A01G112000 chr6B 83.290 772 102 18 1 755 413958943 413959704 0.000000e+00 686.0
38 TraesCS1A01G112000 chr3A 94.237 2221 104 22 3631 5837 743611895 743609685 0.000000e+00 3371.0
39 TraesCS1A01G112000 chr3A 94.107 2223 105 21 3631 5837 743603887 743601675 0.000000e+00 3356.0
40 TraesCS1A01G112000 chr3A 97.633 507 5 3 7381 7886 486163157 486162657 0.000000e+00 863.0
41 TraesCS1A01G112000 chr6A 94.181 2217 111 18 3631 5837 384244265 384242057 0.000000e+00 3363.0
42 TraesCS1A01G112000 chr6A 92.282 2384 135 36 3631 5997 362822830 362820479 0.000000e+00 3338.0
43 TraesCS1A01G112000 chr6A 86.509 719 76 9 1 715 47441930 47441229 0.000000e+00 771.0
44 TraesCS1A01G112000 chr5B 94.049 2218 112 19 3632 5837 501949171 501946962 0.000000e+00 3347.0
45 TraesCS1A01G112000 chr5B 91.642 2405 144 44 3631 6008 247088872 247086498 0.000000e+00 3275.0
46 TraesCS1A01G112000 chr5B 85.733 764 90 11 1 755 678830475 678831228 0.000000e+00 789.0
47 TraesCS1A01G112000 chr5B 85.602 764 91 11 1 755 678841737 678842490 0.000000e+00 784.0
48 TraesCS1A01G112000 chr2B 90.999 1911 128 32 4980 6874 141552843 141550961 0.000000e+00 2536.0
49 TraesCS1A01G112000 chr2B 90.904 1847 125 31 4980 6810 141544870 141543051 0.000000e+00 2440.0
50 TraesCS1A01G112000 chr2B 98.246 513 3 4 7381 7893 141550937 141550431 0.000000e+00 893.0
51 TraesCS1A01G112000 chr1B 93.864 1043 56 2 875 1909 166579254 166580296 0.000000e+00 1565.0
52 TraesCS1A01G112000 chr1B 95.034 725 26 4 2588 3312 166589507 166590221 0.000000e+00 1131.0
53 TraesCS1A01G112000 chr1B 87.270 762 83 7 1 757 264369279 264368527 0.000000e+00 857.0
54 TraesCS1A01G112000 chr1B 91.141 587 25 10 7962 8529 166590801 166591379 0.000000e+00 771.0
55 TraesCS1A01G112000 chr1B 94.501 491 20 5 1908 2394 166580534 166581021 0.000000e+00 750.0
56 TraesCS1A01G112000 chr1B 93.824 340 16 4 8512 8849 166591557 166591893 2.930000e-139 507.0
57 TraesCS1A01G112000 chr1B 95.139 288 12 2 3328 3614 166590419 166590705 3.870000e-123 453.0
58 TraesCS1A01G112000 chr1B 96.735 245 8 0 8849 9093 166591926 166592170 8.500000e-110 409.0
59 TraesCS1A01G112000 chr2D 88.699 761 71 7 1 755 346011287 346010536 0.000000e+00 915.0
60 TraesCS1A01G112000 chr2D 86.826 668 79 7 95 756 579125401 579126065 0.000000e+00 737.0
61 TraesCS1A01G112000 chr2D 84.005 769 96 15 1 755 118408986 118408231 0.000000e+00 713.0
62 TraesCS1A01G112000 chr2D 90.000 540 47 6 36 573 498870496 498869962 0.000000e+00 691.0
63 TraesCS1A01G112000 chr7D 88.442 770 70 8 1 762 426182834 426183592 0.000000e+00 911.0
64 TraesCS1A01G112000 chr7D 88.568 761 72 9 1 757 153418356 153417607 0.000000e+00 909.0
65 TraesCS1A01G112000 chr7D 86.089 762 78 15 1 757 264982405 264981667 0.000000e+00 795.0
66 TraesCS1A01G112000 chr7D 84.655 769 94 15 1 756 78762513 78761756 0.000000e+00 745.0
67 TraesCS1A01G112000 chr7D 91.403 442 34 3 1 440 199898674 199898235 3.630000e-168 603.0
68 TraesCS1A01G112000 chr5A 98.397 499 2 3 7388 7886 688029314 688028822 0.000000e+00 872.0
69 TraesCS1A01G112000 chr5A 97.250 509 5 3 7381 7886 688037545 688037043 0.000000e+00 854.0
70 TraesCS1A01G112000 chr5A 94.595 148 4 2 6731 6874 311627346 311627493 9.190000e-55 226.0
71 TraesCS1A01G112000 chrUn 87.565 764 71 11 1 758 89763629 89764374 0.000000e+00 863.0
72 TraesCS1A01G112000 chrUn 97.628 506 5 3 7381 7886 228290495 228289997 0.000000e+00 861.0
73 TraesCS1A01G112000 chrUn 86.465 628 61 16 1 617 29978339 29977725 0.000000e+00 667.0
74 TraesCS1A01G112000 chrUn 86.465 628 61 16 1 617 29980460 29979846 0.000000e+00 667.0
75 TraesCS1A01G112000 chrUn 86.465 628 61 16 1 617 29982912 29982298 0.000000e+00 667.0
76 TraesCS1A01G112000 chrUn 83.607 671 88 13 97 757 20828114 20828772 2.170000e-170 610.0
77 TraesCS1A01G112000 chrUn 78.175 504 69 25 292 755 20488724 20488222 5.370000e-72 283.0
78 TraesCS1A01G112000 chrUn 92.199 141 11 0 1 141 20488922 20488782 5.570000e-47 200.0
79 TraesCS1A01G112000 chrUn 94.792 96 5 0 1 96 20785966 20786061 5.690000e-32 150.0
80 TraesCS1A01G112000 chr7B 87.156 763 84 7 1 758 594710749 594709996 0.000000e+00 854.0
81 TraesCS1A01G112000 chr7B 97.239 507 9 3 7381 7886 662817232 662817734 0.000000e+00 854.0
82 TraesCS1A01G112000 chr4D 87.516 761 68 14 1 754 506341970 506341230 0.000000e+00 854.0
83 TraesCS1A01G112000 chr4D 86.269 772 78 16 1 756 44417738 44418497 0.000000e+00 813.0
84 TraesCS1A01G112000 chr4D 86.202 761 78 16 1 756 380342081 380341343 0.000000e+00 798.0
85 TraesCS1A01G112000 chr6D 86.974 760 87 6 1 757 211679274 211678524 0.000000e+00 845.0
86 TraesCS1A01G112000 chr6D 85.992 771 66 16 1 756 372162008 372162751 0.000000e+00 787.0
87 TraesCS1A01G112000 chr6D 85.658 760 82 12 1 754 465948146 465948884 0.000000e+00 774.0
88 TraesCS1A01G112000 chr6D 84.726 766 82 13 1 758 392574817 392575555 0.000000e+00 734.0
89 TraesCS1A01G112000 chr6D 83.574 761 92 20 7 757 398168168 398167431 0.000000e+00 682.0
90 TraesCS1A01G112000 chr5D 87.240 721 83 7 1 715 367758463 367757746 0.000000e+00 813.0
91 TraesCS1A01G112000 chr5D 86.334 761 71 9 1 755 535149949 535150682 0.000000e+00 798.0
92 TraesCS1A01G112000 chr5D 84.169 758 88 24 1 750 376185282 376184549 0.000000e+00 706.0
93 TraesCS1A01G112000 chr5D 84.231 761 80 20 1 756 51511277 51512002 0.000000e+00 704.0
94 TraesCS1A01G112000 chr3D 86.107 763 80 15 1 759 363516352 363517092 0.000000e+00 798.0


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 TraesCS1A01G112000 chr1A 113849685 113858777 9092 False 7929.0 12694 100.0000 1 9093 2 chr1A.!!$F1 9092
1 TraesCS1A01G112000 chr1A 382563097 382566346 3249 True 4682.0 4682 92.8270 3631 6860 1 chr1A.!!$R1 3229
2 TraesCS1A01G112000 chr1A 543980695 543984064 3369 True 2502.0 4128 96.7545 4312 7890 2 chr1A.!!$R2 3578
3 TraesCS1A01G112000 chr2A 463604369 463607307 2938 False 4314.0 4314 93.1120 3631 6594 1 chr2A.!!$F2 2963
4 TraesCS1A01G112000 chr2A 751931807 751934024 2217 True 3336.0 3336 93.8570 3631 5846 1 chr2A.!!$R1 2215
5 TraesCS1A01G112000 chr2A 463597951 463599301 1350 False 2032.0 2032 93.7770 5463 6822 1 chr2A.!!$F1 1359
6 TraesCS1A01G112000 chr1D 109969237 109973542 4305 False 1328.6 4274 96.0148 764 9093 5 chr1D.!!$F10 8329
7 TraesCS1A01G112000 chr1D 192417202 192417944 742 True 891.0 891 88.2890 3 757 1 chr1D.!!$R1 754
8 TraesCS1A01G112000 chr1D 456128212 456128968 756 False 859.0 859 87.3860 1 755 1 chr1D.!!$F9 754
9 TraesCS1A01G112000 chr1D 448218909 448219642 733 False 835.0 835 87.1860 1 753 1 chr1D.!!$F6 752
10 TraesCS1A01G112000 chr1D 454401177 454401918 741 False 782.0 782 85.7330 1 758 1 chr1D.!!$F8 757
11 TraesCS1A01G112000 chr1D 473270450 473271201 751 True 776.0 776 85.5470 1 755 1 chr1D.!!$R2 754
12 TraesCS1A01G112000 chr1D 32764175 32764904 729 False 721.0 721 84.5850 1 752 1 chr1D.!!$F1 751
13 TraesCS1A01G112000 chr1D 474070188 474070947 759 True 706.0 706 83.8080 1 755 1 chr1D.!!$R3 754
14 TraesCS1A01G112000 chr1D 103691179 103691920 741 False 695.0 695 83.7910 1 755 1 chr1D.!!$F3 754
15 TraesCS1A01G112000 chr1D 296686685 296687413 728 False 645.0 645 82.8980 1 756 1 chr1D.!!$F5 755
16 TraesCS1A01G112000 chr1D 65560694 65561457 763 False 623.0 623 81.8060 1 757 1 chr1D.!!$F2 756
17 TraesCS1A01G112000 chr1D 448538227 448538884 657 False 556.0 556 82.3090 1 652 1 chr1D.!!$F7 651
18 TraesCS1A01G112000 chr7A 465666413 465668954 2541 True 4013.0 4013 95.2890 4312 6836 1 chr7A.!!$R2 2524
19 TraesCS1A01G112000 chr7A 122315047 122317256 2209 True 3380.0 3380 94.3190 3631 5837 1 chr7A.!!$R1 2206
20 TraesCS1A01G112000 chr7A 221842633 221843483 850 True 560.0 863 96.5780 6711 7886 2 chr7A.!!$R3 1175
21 TraesCS1A01G112000 chr7A 149284923 149286837 1914 False 247.0 364 94.8360 8421 8731 2 chr7A.!!$F3 310
22 TraesCS1A01G112000 chr4B 279729986 279732580 2594 True 3768.0 3768 92.8930 4273 6874 1 chr4B.!!$R1 2601
23 TraesCS1A01G112000 chr6B 40766505 40768713 2208 False 3384.0 3384 94.3620 3632 5837 1 chr6B.!!$F1 2205
24 TraesCS1A01G112000 chr6B 687904872 687907284 2412 False 1738.0 2606 94.7310 4980 7886 2 chr6B.!!$F3 2906
25 TraesCS1A01G112000 chr6B 413958943 413959704 761 False 686.0 686 83.2900 1 755 1 chr6B.!!$F2 754
26 TraesCS1A01G112000 chr3A 743609685 743611895 2210 True 3371.0 3371 94.2370 3631 5837 1 chr3A.!!$R3 2206
27 TraesCS1A01G112000 chr3A 743601675 743603887 2212 True 3356.0 3356 94.1070 3631 5837 1 chr3A.!!$R2 2206
28 TraesCS1A01G112000 chr3A 486162657 486163157 500 True 863.0 863 97.6330 7381 7886 1 chr3A.!!$R1 505
29 TraesCS1A01G112000 chr6A 384242057 384244265 2208 True 3363.0 3363 94.1810 3631 5837 1 chr6A.!!$R3 2206
30 TraesCS1A01G112000 chr6A 362820479 362822830 2351 True 3338.0 3338 92.2820 3631 5997 1 chr6A.!!$R2 2366
31 TraesCS1A01G112000 chr6A 47441229 47441930 701 True 771.0 771 86.5090 1 715 1 chr6A.!!$R1 714
32 TraesCS1A01G112000 chr5B 501946962 501949171 2209 True 3347.0 3347 94.0490 3632 5837 1 chr5B.!!$R2 2205
33 TraesCS1A01G112000 chr5B 247086498 247088872 2374 True 3275.0 3275 91.6420 3631 6008 1 chr5B.!!$R1 2377
34 TraesCS1A01G112000 chr5B 678830475 678831228 753 False 789.0 789 85.7330 1 755 1 chr5B.!!$F1 754
35 TraesCS1A01G112000 chr5B 678841737 678842490 753 False 784.0 784 85.6020 1 755 1 chr5B.!!$F2 754
36 TraesCS1A01G112000 chr2B 141543051 141544870 1819 True 2440.0 2440 90.9040 4980 6810 1 chr2B.!!$R1 1830
37 TraesCS1A01G112000 chr2B 141550431 141552843 2412 True 1714.5 2536 94.6225 4980 7893 2 chr2B.!!$R2 2913
38 TraesCS1A01G112000 chr1B 166579254 166581021 1767 False 1157.5 1565 94.1825 875 2394 2 chr1B.!!$F1 1519
39 TraesCS1A01G112000 chr1B 264368527 264369279 752 True 857.0 857 87.2700 1 757 1 chr1B.!!$R1 756
40 TraesCS1A01G112000 chr1B 166589507 166592170 2663 False 654.2 1131 94.3746 2588 9093 5 chr1B.!!$F2 6505
41 TraesCS1A01G112000 chr2D 346010536 346011287 751 True 915.0 915 88.6990 1 755 1 chr2D.!!$R2 754
42 TraesCS1A01G112000 chr2D 579125401 579126065 664 False 737.0 737 86.8260 95 756 1 chr2D.!!$F1 661
43 TraesCS1A01G112000 chr2D 118408231 118408986 755 True 713.0 713 84.0050 1 755 1 chr2D.!!$R1 754
44 TraesCS1A01G112000 chr2D 498869962 498870496 534 True 691.0 691 90.0000 36 573 1 chr2D.!!$R3 537
45 TraesCS1A01G112000 chr7D 426182834 426183592 758 False 911.0 911 88.4420 1 762 1 chr7D.!!$F1 761
46 TraesCS1A01G112000 chr7D 153417607 153418356 749 True 909.0 909 88.5680 1 757 1 chr7D.!!$R2 756
47 TraesCS1A01G112000 chr7D 264981667 264982405 738 True 795.0 795 86.0890 1 757 1 chr7D.!!$R4 756
48 TraesCS1A01G112000 chr7D 78761756 78762513 757 True 745.0 745 84.6550 1 756 1 chr7D.!!$R1 755
49 TraesCS1A01G112000 chr5A 688037043 688037545 502 True 854.0 854 97.2500 7381 7886 1 chr5A.!!$R2 505
50 TraesCS1A01G112000 chrUn 89763629 89764374 745 False 863.0 863 87.5650 1 758 1 chrUn.!!$F3 757
51 TraesCS1A01G112000 chrUn 29977725 29982912 5187 True 667.0 667 86.4650 1 617 3 chrUn.!!$R3 616
52 TraesCS1A01G112000 chrUn 20828114 20828772 658 False 610.0 610 83.6070 97 757 1 chrUn.!!$F2 660
53 TraesCS1A01G112000 chrUn 20488222 20488922 700 True 241.5 283 85.1870 1 755 2 chrUn.!!$R2 754
54 TraesCS1A01G112000 chr7B 594709996 594710749 753 True 854.0 854 87.1560 1 758 1 chr7B.!!$R1 757
55 TraesCS1A01G112000 chr7B 662817232 662817734 502 False 854.0 854 97.2390 7381 7886 1 chr7B.!!$F1 505
56 TraesCS1A01G112000 chr4D 506341230 506341970 740 True 854.0 854 87.5160 1 754 1 chr4D.!!$R2 753
57 TraesCS1A01G112000 chr4D 44417738 44418497 759 False 813.0 813 86.2690 1 756 1 chr4D.!!$F1 755
58 TraesCS1A01G112000 chr4D 380341343 380342081 738 True 798.0 798 86.2020 1 756 1 chr4D.!!$R1 755
59 TraesCS1A01G112000 chr6D 211678524 211679274 750 True 845.0 845 86.9740 1 757 1 chr6D.!!$R1 756
60 TraesCS1A01G112000 chr6D 372162008 372162751 743 False 787.0 787 85.9920 1 756 1 chr6D.!!$F1 755
61 TraesCS1A01G112000 chr6D 465948146 465948884 738 False 774.0 774 85.6580 1 754 1 chr6D.!!$F3 753
62 TraesCS1A01G112000 chr6D 392574817 392575555 738 False 734.0 734 84.7260 1 758 1 chr6D.!!$F2 757
63 TraesCS1A01G112000 chr6D 398167431 398168168 737 True 682.0 682 83.5740 7 757 1 chr6D.!!$R2 750
64 TraesCS1A01G112000 chr5D 367757746 367758463 717 True 813.0 813 87.2400 1 715 1 chr5D.!!$R1 714
65 TraesCS1A01G112000 chr5D 535149949 535150682 733 False 798.0 798 86.3340 1 755 1 chr5D.!!$F2 754
66 TraesCS1A01G112000 chr5D 376184549 376185282 733 True 706.0 706 84.1690 1 750 1 chr5D.!!$R2 749
67 TraesCS1A01G112000 chr5D 51511277 51512002 725 False 704.0 704 84.2310 1 756 1 chr5D.!!$F1 755
68 TraesCS1A01G112000 chr3D 363516352 363517092 740 False 798.0 798 86.1070 1 759 1 chr3D.!!$F1 758

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
50 51 0.114560 AGGTCCAGAACTTCGAGGGA 59.885 55.000 0.00 1.10 0.00 4.20 F
85 88 0.175989 CGGGGCTGGAACTACTTCTC 59.824 60.000 0.00 0.00 0.00 2.87 F
1334 6102 0.321996 GGGTTTCTCGGAACTGCTCT 59.678 55.000 0.00 0.00 0.00 4.09 F
2880 7901 1.001181 CCCTGTTGGAAGGCACATTTG 59.999 52.381 0.00 0.00 35.85 2.32 F
3603 8854 1.246056 GCTGTCCTTGCAATCCAGCA 61.246 55.000 26.98 12.15 45.94 4.41 F
3686 8937 2.223021 GCACGCAAATGTGTACGATCAT 60.223 45.455 0.00 0.00 41.94 2.45 F
4529 9807 2.354729 GCAGGGGTGCACCACATA 59.645 61.111 38.54 0.00 43.57 2.29 F
4542 9820 0.802494 CCACATAACCCAACACGCTC 59.198 55.000 0.00 0.00 0.00 5.03 F
4568 9846 1.068434 CATTTGGCCGGACACACTTTT 59.932 47.619 11.33 0.00 0.00 2.27 F
6510 11877 0.832135 ACGACCATGGTGAGGTGAGT 60.832 55.000 25.52 7.54 40.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 6293 1.001487 TCACACAAGCAATTTGCCTCG 60.001 47.619 17.51 8.94 46.52 4.63 R
1939 6954 2.159572 CCAGCAACCTTACGAATTTCCG 60.160 50.000 0.00 0.00 0.00 4.30 R
3048 8079 0.467290 TGAAGTTCCACAACTGCCCC 60.467 55.000 0.00 0.00 42.45 5.80 R
3686 8937 0.252057 TTCCCGTGAGTCCCTGATCA 60.252 55.000 0.00 0.00 0.00 2.92 R
4529 9807 1.375523 GGATCGAGCGTGTTGGGTT 60.376 57.895 0.00 0.00 0.00 4.11 R
4542 9820 2.186826 GTCCGGCCAAATGGGATCG 61.187 63.158 2.24 0.00 40.01 3.69 R
6034 11379 1.152881 CCAGGGGCCTATGACAAGC 60.153 63.158 0.84 0.00 0.00 4.01 R
6510 11877 1.276622 GGGCTCCTTTCTGTACCTCA 58.723 55.000 0.00 0.00 0.00 3.86 R
6622 11989 2.658593 CGGCGCCGTTCCATCTAG 60.659 66.667 39.71 8.63 34.35 2.43 R
8223 13641 2.217750 TCCGTACAATGCATGCATACC 58.782 47.619 32.36 18.43 35.31 2.73 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
50 51 0.114560 AGGTCCAGAACTTCGAGGGA 59.885 55.000 0.00 1.10 0.00 4.20
85 88 0.175989 CGGGGCTGGAACTACTTCTC 59.824 60.000 0.00 0.00 0.00 2.87
188 193 0.900182 ACTCCTCGGTCATGTGCAGA 60.900 55.000 0.00 0.00 0.00 4.26
231 237 3.719268 ACCTTGGTGACATTGAGCATA 57.281 42.857 0.00 0.00 42.32 3.14
272 284 8.828688 AAGTATAAGGTGTTAGTGTTGAACTC 57.171 34.615 0.00 0.00 40.56 3.01
296 317 1.616374 TGGTGTGTGCGAGACTTATGA 59.384 47.619 0.00 0.00 0.00 2.15
383 414 1.288932 AGGATGCCCCTGCTGTTAATT 59.711 47.619 0.00 0.00 45.61 1.40
431 481 8.034804 AGTAGTTTGCTGTCATTTTCTTGTTTT 58.965 29.630 0.00 0.00 0.00 2.43
475 572 6.292488 GGTTGCTTGTTTTGTTTGATCTCATG 60.292 38.462 0.00 0.00 0.00 3.07
553 722 4.505191 GTGAGTAGAACACAAACGCTGTTA 59.495 41.667 0.00 0.00 35.47 2.41
588 5331 7.865706 ACTAAAGTTTTCATCTGTTCACACT 57.134 32.000 0.00 0.00 0.00 3.55
619 5371 7.009357 GCACAAAAACGATAACCAAACAGTAAA 59.991 33.333 0.00 0.00 0.00 2.01
634 5395 5.571791 ACAGTAAAAGTAAGTGCCCCTTA 57.428 39.130 0.00 0.00 34.46 2.69
715 5479 3.753272 ACCAAACTGATTGAAGATGGACG 59.247 43.478 0.00 0.00 41.85 4.79
717 5481 4.935205 CCAAACTGATTGAAGATGGACGTA 59.065 41.667 0.00 0.00 41.85 3.57
759 5525 2.289756 TGCAACTAAACACGCCCTATCA 60.290 45.455 0.00 0.00 0.00 2.15
760 5526 2.943033 GCAACTAAACACGCCCTATCAT 59.057 45.455 0.00 0.00 0.00 2.45
761 5527 3.242739 GCAACTAAACACGCCCTATCATG 60.243 47.826 0.00 0.00 0.00 3.07
762 5528 4.188462 CAACTAAACACGCCCTATCATGA 58.812 43.478 0.00 0.00 0.00 3.07
778 5544 1.667724 CATGAATGAGGAGTTGCGTCC 59.332 52.381 0.00 0.00 36.79 4.79
912 5679 1.305465 AAGCAATGGGCCAGCATCA 60.305 52.632 18.72 0.00 46.50 3.07
1056 5823 1.143277 CGCCTTCTCCTACTCCTCCTA 59.857 57.143 0.00 0.00 0.00 2.94
1334 6102 0.321996 GGGTTTCTCGGAACTGCTCT 59.678 55.000 0.00 0.00 0.00 4.09
1420 6188 1.453745 GCTGATGCCGATCCCCAAA 60.454 57.895 0.00 0.00 0.00 3.28
1423 6191 1.828224 GATGCCGATCCCCAAACCC 60.828 63.158 0.00 0.00 0.00 4.11
1521 6290 1.204704 TGACACTGCTATCCTCCAACG 59.795 52.381 0.00 0.00 0.00 4.10
1524 6293 2.271800 CACTGCTATCCTCCAACGTTC 58.728 52.381 0.00 0.00 0.00 3.95
1569 6338 6.418057 TCAGTCAAATTGGCTAATTGGTTT 57.582 33.333 8.97 0.00 36.65 3.27
1605 6374 1.761711 TGGATTTTCCAGGGTGGGTA 58.238 50.000 0.00 0.00 42.67 3.69
1668 6444 7.899178 TGATGACTGTTGTAATTCGTAATGT 57.101 32.000 0.00 0.00 0.00 2.71
1710 6486 3.308035 ACATCCATGCCATGAGACATT 57.692 42.857 6.18 0.00 0.00 2.71
1716 6492 4.340097 TCCATGCCATGAGACATTTGATTC 59.660 41.667 6.18 0.00 0.00 2.52
1771 6547 7.621102 TCAATACGATCATTTCACGAAAGATG 58.379 34.615 0.00 0.00 33.32 2.90
1804 6580 9.276590 TGCAAATCTGAATTGGTGATATACTAG 57.723 33.333 7.51 0.00 0.00 2.57
1885 6661 8.911965 TGGTATGCAAAATTTATGCTATCTCAA 58.088 29.630 19.20 5.10 44.14 3.02
1939 6954 8.247562 ACTTAGACTCAGTAATGATGAAGTCAC 58.752 37.037 11.37 0.00 40.28 3.67
1974 6989 1.487300 TGCTGGCATGCATGGTAAAT 58.513 45.000 27.34 0.00 38.12 1.40
2171 7190 4.855340 TGATTTCCATTTAGTGAGTCCCC 58.145 43.478 0.00 0.00 0.00 4.81
2290 7310 4.178545 TGGTGTTACGGCTAAAGTAGTC 57.821 45.455 0.00 0.00 0.00 2.59
2338 7358 3.194542 GCTATCGCCTCTCCTCACAATAT 59.805 47.826 0.00 0.00 0.00 1.28
2339 7359 4.399618 GCTATCGCCTCTCCTCACAATATA 59.600 45.833 0.00 0.00 0.00 0.86
2340 7360 5.068460 GCTATCGCCTCTCCTCACAATATAT 59.932 44.000 0.00 0.00 0.00 0.86
2349 7370 7.877097 CCTCTCCTCACAATATATCCTTTTCTG 59.123 40.741 0.00 0.00 0.00 3.02
2354 7375 9.784531 CCTCACAATATATCCTTTTCTGTGTAT 57.215 33.333 9.95 0.00 35.38 2.29
2385 7406 7.176589 AGTTTATATCCCTAGCATCTGTAGC 57.823 40.000 0.00 0.00 0.00 3.58
2408 7429 8.087982 AGCGATGTATTTATTGTCATGTAAGG 57.912 34.615 0.00 0.00 0.00 2.69
2422 7443 6.126911 TGTCATGTAAGGAAGTACCATGCATA 60.127 38.462 0.00 0.00 39.80 3.14
2519 7540 6.873997 AGTTTCTGTTTCCAAAAACCTAAGG 58.126 36.000 0.00 0.00 43.44 2.69
2567 7588 7.434897 TGTTTGACAAGATTAATCTGTTGTTGC 59.565 33.333 18.61 9.59 37.19 4.17
2827 7848 8.733092 TCATGACTTCCTCTAAATCCATCTAT 57.267 34.615 0.00 0.00 0.00 1.98
2862 7883 1.409790 TGCTGCAATGACATTATGCCC 59.590 47.619 0.00 2.50 39.31 5.36
2878 7899 1.187567 GCCCTGTTGGAAGGCACATT 61.188 55.000 0.00 0.00 46.34 2.71
2879 7900 1.341080 CCCTGTTGGAAGGCACATTT 58.659 50.000 0.00 0.00 35.85 2.32
2880 7901 1.001181 CCCTGTTGGAAGGCACATTTG 59.999 52.381 0.00 0.00 35.85 2.32
2881 7902 1.606224 CCTGTTGGAAGGCACATTTGC 60.606 52.381 0.00 0.00 41.36 3.68
2882 7903 3.923519 CCTGTTGGAAGGCACATTTGCT 61.924 50.000 3.47 0.00 41.64 3.91
2883 7904 4.622562 CCTGTTGGAAGGCACATTTGCTA 61.623 47.826 3.47 0.00 41.64 3.49
3047 8078 4.218200 TGCTAACCCATCTGTGTTTCATTG 59.782 41.667 0.00 0.00 0.00 2.82
3048 8079 4.380867 GCTAACCCATCTGTGTTTCATTGG 60.381 45.833 0.00 0.00 0.00 3.16
3084 8115 6.317391 GGAACTTCATCCTGACATAAAGAAGG 59.683 42.308 0.00 0.00 36.29 3.46
3097 8128 6.973642 ACATAAAGAAGGATTTCTGGGATCA 58.026 36.000 0.00 0.00 42.80 2.92
3224 8255 1.705256 TGAAGCGTGACATTACGACC 58.295 50.000 0.00 0.00 46.46 4.79
3263 8294 5.032846 ACAGGGAGGAACAATCAGAGATAA 58.967 41.667 0.00 0.00 0.00 1.75
3312 8343 4.503714 TTGGATCTGGTGAGTTAATCCC 57.496 45.455 0.00 0.00 35.96 3.85
3313 8344 2.777692 TGGATCTGGTGAGTTAATCCCC 59.222 50.000 0.00 0.00 35.96 4.81
3314 8345 2.106684 GGATCTGGTGAGTTAATCCCCC 59.893 54.545 0.00 0.00 31.56 5.40
3315 8346 2.352561 TCTGGTGAGTTAATCCCCCA 57.647 50.000 0.00 0.00 0.00 4.96
3316 8347 2.638325 TCTGGTGAGTTAATCCCCCAA 58.362 47.619 0.00 0.00 30.05 4.12
3317 8348 2.990284 TCTGGTGAGTTAATCCCCCAAA 59.010 45.455 0.00 0.00 30.05 3.28
3318 8349 3.089284 CTGGTGAGTTAATCCCCCAAAC 58.911 50.000 0.00 0.00 30.05 2.93
3319 8350 2.225167 TGGTGAGTTAATCCCCCAAACC 60.225 50.000 0.00 0.00 0.00 3.27
3320 8351 2.225167 GGTGAGTTAATCCCCCAAACCA 60.225 50.000 0.00 0.00 0.00 3.67
3321 8352 3.502356 GTGAGTTAATCCCCCAAACCAA 58.498 45.455 0.00 0.00 0.00 3.67
3322 8353 3.898741 GTGAGTTAATCCCCCAAACCAAA 59.101 43.478 0.00 0.00 0.00 3.28
3323 8354 4.345547 GTGAGTTAATCCCCCAAACCAAAA 59.654 41.667 0.00 0.00 0.00 2.44
3324 8355 4.969359 TGAGTTAATCCCCCAAACCAAAAA 59.031 37.500 0.00 0.00 0.00 1.94
3603 8854 1.246056 GCTGTCCTTGCAATCCAGCA 61.246 55.000 26.98 12.15 45.94 4.41
3686 8937 2.223021 GCACGCAAATGTGTACGATCAT 60.223 45.455 0.00 0.00 41.94 2.45
3726 8977 6.758886 GGGAAGATATCACAACACAACTCTAG 59.241 42.308 5.32 0.00 0.00 2.43
4287 9550 3.840666 TGAAGTCCTCCAAGTAGCATCTT 59.159 43.478 0.00 0.00 0.00 2.40
4309 9572 3.133003 TCAAGTAGCATCTCCAAGTAGCC 59.867 47.826 0.00 0.00 0.00 3.93
4527 9805 4.584518 CTGCAGGGGTGCACCACA 62.585 66.667 38.54 26.01 43.57 4.17
4529 9807 2.354729 GCAGGGGTGCACCACATA 59.645 61.111 38.54 0.00 43.57 2.29
4542 9820 0.802494 CCACATAACCCAACACGCTC 59.198 55.000 0.00 0.00 0.00 5.03
4568 9846 1.068434 CATTTGGCCGGACACACTTTT 59.932 47.619 11.33 0.00 0.00 2.27
6311 11678 4.124351 GATGGTGACGACGGCCGA 62.124 66.667 35.90 5.52 41.76 5.54
6510 11877 0.832135 ACGACCATGGTGAGGTGAGT 60.832 55.000 25.52 7.54 40.09 3.41
7521 12895 1.417506 GGGAATGGATAAGGGGAGGGA 60.418 57.143 0.00 0.00 0.00 4.20
7886 13264 1.878102 GCTTGATTATCCGGGCGTCAT 60.878 52.381 0.00 0.00 0.00 3.06
7941 13320 8.870879 GTCATAGTTAGCTAGGTTGTTTAGTTG 58.129 37.037 0.00 0.00 31.54 3.16
7946 13325 4.777463 AGCTAGGTTGTTTAGTTGTGTGT 58.223 39.130 0.00 0.00 0.00 3.72
8100 13511 3.068024 GCAAAGGTTGAGTGATGTTTCCA 59.932 43.478 0.00 0.00 0.00 3.53
8102 13513 3.576078 AGGTTGAGTGATGTTTCCACA 57.424 42.857 0.00 0.00 37.01 4.17
8114 13525 0.260230 TTTCCACAAGGGGCTGTTGA 59.740 50.000 6.41 0.00 37.22 3.18
8223 13641 2.621055 TGAAGAACCGGTGAACCATTTG 59.379 45.455 8.52 0.00 35.14 2.32
8239 13657 4.946445 CCATTTGGTATGCATGCATTGTA 58.054 39.130 36.23 17.76 37.82 2.41
8251 13669 2.412870 TGCATTGTACGGAACTGACAG 58.587 47.619 0.00 0.00 0.00 3.51
8281 13699 3.797039 TGGCGAGTTAAATGAGAGATGG 58.203 45.455 0.00 0.00 0.00 3.51
8359 13777 5.182001 AGTTGCTAGCTCATTACAGTTTTGG 59.818 40.000 17.23 0.00 0.00 3.28
8726 15953 1.961277 GCAGACCAGTGTCCCAACG 60.961 63.158 0.00 0.00 42.81 4.10
8799 16026 9.149225 CAATATCTGCTATCTAGTTTCATGGTC 57.851 37.037 0.00 0.00 0.00 4.02
8962 16222 0.738975 CATCCGCCGTCTAAGAGACA 59.261 55.000 7.36 0.00 45.30 3.41
8968 16228 3.062234 CCGCCGTCTAAGAGACAAAATTC 59.938 47.826 7.36 0.00 45.30 2.17
9046 16306 3.960102 TCACCTCCATTTTCAACTTTGCT 59.040 39.130 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.985282 CGGCCAAGCACCATGTGT 60.985 61.111 2.24 0.00 35.75 3.72
188 193 2.562912 CGCCTGCTGCAACGAAAT 59.437 55.556 16.93 0.00 41.33 2.17
272 284 2.370281 AGTCTCGCACACACCATAAG 57.630 50.000 0.00 0.00 0.00 1.73
296 317 4.230745 ACAAGTTCCCAACACAAGTACT 57.769 40.909 0.00 0.00 0.00 2.73
431 481 6.822676 AGCAACCAAATGAAATCAAACAAAGA 59.177 30.769 0.00 0.00 0.00 2.52
475 572 3.624326 TCAGCACAACAACAAGCATAC 57.376 42.857 0.00 0.00 0.00 2.39
553 722 8.311109 AGATGAAAACTTTAGTTGTTTGGTTGT 58.689 29.630 0.00 0.00 38.44 3.32
588 5331 6.621316 TTGGTTATCGTTTTTGTGCTTAGA 57.379 33.333 0.00 0.00 0.00 2.10
619 5371 2.026636 TCGCATTAAGGGGCACTTACTT 60.027 45.455 9.14 0.00 41.24 2.24
744 5510 5.029807 TCATTCATGATAGGGCGTGTTTA 57.970 39.130 0.00 0.00 0.00 2.01
759 5525 1.556911 AGGACGCAACTCCTCATTCAT 59.443 47.619 0.00 0.00 35.56 2.57
760 5526 0.976641 AGGACGCAACTCCTCATTCA 59.023 50.000 0.00 0.00 35.56 2.57
761 5527 3.842869 AGGACGCAACTCCTCATTC 57.157 52.632 0.00 0.00 35.56 2.67
882 5649 2.665165 CCATTGCTTGGCCCAGTAATA 58.335 47.619 17.94 0.00 39.09 0.98
912 5679 1.208293 GCTTACTGGACTTGGCTAGCT 59.792 52.381 15.72 0.00 0.00 3.32
1041 5808 2.514582 CAAGGGTAGGAGGAGTAGGAGA 59.485 54.545 0.00 0.00 0.00 3.71
1056 5823 1.452108 GCCGATTAGCAGCAAGGGT 60.452 57.895 0.00 0.00 0.00 4.34
1334 6102 1.559368 TCCCCAAAGATCGAACCGTA 58.441 50.000 0.00 0.00 0.00 4.02
1521 6290 2.053627 CACAAGCAATTTGCCTCGAAC 58.946 47.619 17.51 0.00 46.52 3.95
1524 6293 1.001487 TCACACAAGCAATTTGCCTCG 60.001 47.619 17.51 8.94 46.52 4.63
1569 6338 5.426689 AATCCAGCATCTTGTAGTCTTGA 57.573 39.130 0.00 0.00 0.00 3.02
1605 6374 6.270231 CACCTATAACATTAGGCTAACCCTCT 59.730 42.308 9.55 0.00 44.96 3.69
1678 6454 8.550585 TCATGGCATGGATGTATGAATATTCTA 58.449 33.333 26.15 3.85 33.69 2.10
1710 6486 3.058450 CAATTTGCACTTGCGGAATCAA 58.942 40.909 0.00 0.00 45.83 2.57
1716 6492 2.652941 ATACCAATTTGCACTTGCGG 57.347 45.000 3.19 0.00 45.83 5.69
1763 6539 7.077605 TCAGATTTGCAAACTTACATCTTTCG 58.922 34.615 15.41 1.38 0.00 3.46
1771 6547 6.922957 TCACCAATTCAGATTTGCAAACTTAC 59.077 34.615 15.41 6.70 0.00 2.34
1804 6580 3.760580 AATCAGGAGCCATAGTAGTGC 57.239 47.619 0.00 0.00 0.00 4.40
1813 6589 8.995027 AATGTATAAACATAAATCAGGAGCCA 57.005 30.769 0.00 0.00 45.79 4.75
1922 6937 6.668541 ATTTCCGTGACTTCATCATTACTG 57.331 37.500 0.00 0.00 40.28 2.74
1939 6954 2.159572 CCAGCAACCTTACGAATTTCCG 60.160 50.000 0.00 0.00 0.00 4.30
2001 7018 7.810658 ACAGATCATTCACAAAACACAGATAC 58.189 34.615 0.00 0.00 0.00 2.24
2195 7214 4.289672 AGCAGAAAGAAAGTATTCCCCTGA 59.710 41.667 0.00 0.00 36.12 3.86
2290 7310 2.022764 TACAATGGTGAGGCATGTCG 57.977 50.000 0.00 0.00 0.00 4.35
2422 7443 5.697633 GTCAAACAATCCAACTTGAATGCAT 59.302 36.000 0.00 0.00 30.03 3.96
2484 7505 4.515567 GGAAACAGAAACTCCGAGAAACAT 59.484 41.667 1.33 0.00 0.00 2.71
2519 7540 5.126061 ACAATTCATGCTATCACAGGAAACC 59.874 40.000 0.00 0.00 42.85 3.27
2567 7588 4.095932 ACAAGATGCATGATACAACAGCAG 59.904 41.667 2.46 0.00 38.75 4.24
2827 7848 1.753847 GCAGCAGGCCAATAATACCCA 60.754 52.381 5.01 0.00 36.11 4.51
2830 7851 3.318839 TCATTGCAGCAGGCCAATAATAC 59.681 43.478 5.01 0.00 43.89 1.89
2862 7883 1.787012 GCAAATGTGCCTTCCAACAG 58.213 50.000 0.00 0.00 45.68 3.16
2998 8029 5.514500 AGGCTACCCAATTCAGAAACTTA 57.486 39.130 0.00 0.00 0.00 2.24
3047 8078 1.152546 AAGTTCCACAACTGCCCCC 60.153 57.895 0.00 0.00 42.45 5.40
3048 8079 0.467290 TGAAGTTCCACAACTGCCCC 60.467 55.000 0.00 0.00 42.45 5.80
3097 8128 7.480760 AGTACATATTTTGGCCAATTCTGTT 57.519 32.000 21.26 5.69 0.00 3.16
3193 8224 4.155099 TGTCACGCTTCAAAGTTTTCTCAA 59.845 37.500 0.00 0.00 0.00 3.02
3224 8255 7.338710 TCCTCCCTGTACAGAAGAATTATTTG 58.661 38.462 24.68 6.72 0.00 2.32
3263 8294 6.418101 ACACATAGAATCCTGCAGTAACATT 58.582 36.000 13.81 5.12 0.00 2.71
3332 8583 4.098960 GTGGAAGATGGCATGATGAAACAT 59.901 41.667 3.81 0.00 0.00 2.71
3342 8593 5.954150 GGGATTATTATGTGGAAGATGGCAT 59.046 40.000 0.00 0.00 0.00 4.40
3398 8649 2.396590 ACAAGGCCTGTAATACCACG 57.603 50.000 5.69 0.00 36.10 4.94
3584 8835 1.509923 GCTGGATTGCAAGGACAGC 59.490 57.895 26.38 26.38 46.24 4.40
3618 8869 1.405526 GCGTCACAAAGCATCTCCCTA 60.406 52.381 0.00 0.00 0.00 3.53
3619 8870 0.674895 GCGTCACAAAGCATCTCCCT 60.675 55.000 0.00 0.00 0.00 4.20
3620 8871 1.648467 GGCGTCACAAAGCATCTCCC 61.648 60.000 0.00 0.00 34.54 4.30
3623 8874 1.675641 GGGGCGTCACAAAGCATCT 60.676 57.895 0.00 0.00 34.54 2.90
3624 8875 2.700773 GGGGGCGTCACAAAGCATC 61.701 63.158 0.00 0.00 34.54 3.91
3628 8879 1.241315 AAATCGGGGGCGTCACAAAG 61.241 55.000 0.00 0.00 0.00 2.77
3629 8880 1.228306 AAATCGGGGGCGTCACAAA 60.228 52.632 0.00 0.00 0.00 2.83
3686 8937 0.252057 TTCCCGTGAGTCCCTGATCA 60.252 55.000 0.00 0.00 0.00 2.92
3952 9205 1.203052 GGTGCCTACTACTACGTGCAA 59.797 52.381 0.00 0.00 0.00 4.08
4034 9290 5.137551 CCCTTTCCTTTCTTTCTGGTTGTA 58.862 41.667 0.00 0.00 0.00 2.41
4065 9324 2.154074 ACGGTTGCTTTCTCCCCCT 61.154 57.895 0.00 0.00 0.00 4.79
4287 9550 3.133003 GGCTACTTGGAGATGCTACTTGA 59.867 47.826 0.00 0.00 0.00 3.02
4309 9572 2.670789 GCTATGCGATGCTACTGGAGAG 60.671 54.545 0.00 0.00 0.00 3.20
4526 9804 1.593006 GATCGAGCGTGTTGGGTTATG 59.407 52.381 0.00 0.00 0.00 1.90
4527 9805 1.472728 GGATCGAGCGTGTTGGGTTAT 60.473 52.381 0.00 0.00 0.00 1.89
4529 9807 1.375523 GGATCGAGCGTGTTGGGTT 60.376 57.895 0.00 0.00 0.00 4.11
4542 9820 2.186826 GTCCGGCCAAATGGGATCG 61.187 63.158 2.24 0.00 40.01 3.69
4758 10048 3.310253 GACGTCAGCGACTGAGCGA 62.310 63.158 23.47 2.28 41.46 4.93
5161 10457 7.664758 ACTACTGTTGTTACCTTTACCTGTAG 58.335 38.462 0.00 0.00 0.00 2.74
6034 11379 1.152881 CCAGGGGCCTATGACAAGC 60.153 63.158 0.84 0.00 0.00 4.01
6109 11476 2.611172 TGACCGGTGGCCCCAATA 60.611 61.111 14.63 0.00 0.00 1.90
6510 11877 1.276622 GGGCTCCTTTCTGTACCTCA 58.723 55.000 0.00 0.00 0.00 3.86
6622 11989 2.658593 CGGCGCCGTTCCATCTAG 60.659 66.667 39.71 8.63 34.35 2.43
7886 13264 5.597806 CGGTGTCCAGATAAGTTAAGCATA 58.402 41.667 0.00 0.00 0.00 3.14
7941 13320 2.358898 GGATATCAATGGGCACACACAC 59.641 50.000 4.83 0.00 0.00 3.82
7946 13325 4.248174 TGAAAGGATATCAATGGGCACA 57.752 40.909 4.83 0.00 0.00 4.57
8100 13511 3.016736 CGATAATTCAACAGCCCCTTGT 58.983 45.455 0.00 0.00 0.00 3.16
8102 13513 3.279434 GTCGATAATTCAACAGCCCCTT 58.721 45.455 0.00 0.00 0.00 3.95
8223 13641 2.217750 TCCGTACAATGCATGCATACC 58.782 47.619 32.36 18.43 35.31 2.73
8230 13648 3.002791 CTGTCAGTTCCGTACAATGCAT 58.997 45.455 0.00 0.00 0.00 3.96
8239 13657 3.530265 TGTTGTAACTGTCAGTTCCGT 57.470 42.857 21.40 0.58 39.51 4.69
8251 13669 5.933790 TCATTTAACTCGCCATGTTGTAAC 58.066 37.500 0.00 0.00 0.00 2.50
8307 13725 8.292448 CACATACTTCAGTTTGCTAAATGTTCT 58.708 33.333 8.12 0.00 31.55 3.01
8359 13777 8.213518 ACATTGAAATCACACAGGTCATATAC 57.786 34.615 0.00 0.00 0.00 1.47
8418 13836 4.451774 GTGTACACGGTGCCTGTTTTTATA 59.548 41.667 10.84 0.00 0.00 0.98
8419 13837 3.251487 GTGTACACGGTGCCTGTTTTTAT 59.749 43.478 10.84 0.00 0.00 1.40
8726 15953 6.706270 TCCAAATCTTCTCACTGTAACTTCAC 59.294 38.462 0.00 0.00 0.00 3.18
8799 16026 3.855689 ACCTTCCAAAATTGCAGATCG 57.144 42.857 0.00 0.00 0.00 3.69
8962 16222 2.863809 ACTCAAGGGCGTGAGAATTTT 58.136 42.857 19.99 0.00 46.76 1.82
9046 16306 5.413833 GCACCTTTGATCTCTGATTCTTTGA 59.586 40.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.