Multiple sequence alignment - TraesCS2B01G202400

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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 TraesCS2B01G202400 chr2B 100.000 4432 0 0 1 4432 182134646 182130215 0.000000e+00 8185.0
1 TraesCS2B01G202400 chr2B 96.066 2491 66 15 1711 4175 135464705 135467189 0.000000e+00 4028.0
2 TraesCS2B01G202400 chr2B 92.083 1301 49 9 1663 2933 135513547 135514823 0.000000e+00 1783.0
3 TraesCS2B01G202400 chr2B 91.796 963 68 9 1712 2668 136813863 136812906 0.000000e+00 1330.0
4 TraesCS2B01G202400 chr2B 90.985 954 71 9 1719 2668 137013547 137012605 0.000000e+00 1271.0
5 TraesCS2B01G202400 chr2B 90.843 961 59 12 1712 2668 136637695 136636760 0.000000e+00 1260.0
6 TraesCS2B01G202400 chr2B 88.126 918 32 29 755 1666 135512545 135513391 0.000000e+00 1020.0
7 TraesCS2B01G202400 chr2B 95.825 527 22 0 1 527 127790981 127790455 0.000000e+00 852.0
8 TraesCS2B01G202400 chr2B 91.218 353 22 4 2665 3010 135128429 135128779 5.190000e-129 472.0
9 TraesCS2B01G202400 chr2B 97.133 279 6 1 790 1066 127790207 127789929 1.870000e-128 470.0
10 TraesCS2B01G202400 chr2B 95.593 295 10 2 3010 3303 135128817 135129109 1.870000e-128 470.0
11 TraesCS2B01G202400 chr2B 90.598 351 27 3 1 349 135511788 135512134 1.120000e-125 460.0
12 TraesCS2B01G202400 chr2B 96.310 271 9 1 510 780 127790439 127790170 1.130000e-120 444.0
13 TraesCS2B01G202400 chr2B 98.305 236 4 0 4197 4432 135467174 135467409 8.870000e-112 414.0
14 TraesCS2B01G202400 chr2B 91.732 254 11 3 2767 3010 135516444 135516697 1.180000e-90 344.0
15 TraesCS2B01G202400 chr2B 96.825 126 4 0 3010 3135 135515417 135515542 1.250000e-50 211.0
16 TraesCS2B01G202400 chr2B 94.737 76 4 0 3059 3134 136812898 136812823 7.790000e-23 119.0
17 TraesCS2B01G202400 chr2B 92.405 79 6 0 3056 3134 136636755 136636677 3.620000e-21 113.0
18 TraesCS2B01G202400 chr2B 93.421 76 5 0 3059 3134 137012597 137012522 3.620000e-21 113.0
19 TraesCS2B01G202400 chr2B 86.598 97 11 1 2916 3010 135128328 135128424 6.060000e-19 106.0
20 TraesCS2B01G202400 chr2B 86.598 97 11 1 2916 3010 182132326 182132230 6.060000e-19 106.0
21 TraesCS2B01G202400 chr2A 95.199 1354 52 10 1664 3010 84144575 84145922 0.000000e+00 2128.0
22 TraesCS2B01G202400 chr2A 93.605 860 47 7 1663 2517 84229253 84230109 0.000000e+00 1277.0
23 TraesCS2B01G202400 chr2A 91.389 929 73 6 1711 2636 134866476 134865552 0.000000e+00 1266.0
24 TraesCS2B01G202400 chr2A 90.671 954 74 14 1711 2655 83991118 83992065 0.000000e+00 1254.0
25 TraesCS2B01G202400 chr2A 94.286 350 16 2 2665 3010 83991834 83992183 2.350000e-147 532.0
26 TraesCS2B01G202400 chr2A 93.291 313 2 1 3010 3303 84145960 84146272 1.130000e-120 444.0
27 TraesCS2B01G202400 chr2A 87.324 213 21 5 2668 2876 134865762 134865552 5.730000e-59 239.0
28 TraesCS2B01G202400 chr2A 89.683 126 3 2 3010 3135 83992221 83992336 7.680000e-33 152.0
29 TraesCS2B01G202400 chr2A 78.125 288 21 17 3056 3303 134865530 134865245 1.280000e-30 145.0
30 TraesCS2B01G202400 chr2A 96.053 76 3 0 3059 3134 85611558 85611483 1.670000e-24 124.0
31 TraesCS2B01G202400 chr2D 90.707 990 60 18 1663 2630 127820435 127819456 0.000000e+00 1290.0
32 TraesCS2B01G202400 chr2D 86.321 212 22 6 2664 2870 127819665 127819456 1.600000e-54 224.0
33 TraesCS2B01G202400 chr2D 91.209 91 8 0 3213 3303 127819239 127819149 1.670000e-24 124.0
34 TraesCS2B01G202400 chr2D 93.671 79 5 0 3056 3134 85250001 85249923 7.790000e-23 119.0
35 TraesCS2B01G202400 chr7D 89.636 907 67 13 767 1666 518768806 518769692 0.000000e+00 1129.0
36 TraesCS2B01G202400 chr7D 87.253 1012 80 27 666 1659 545267174 545266194 0.000000e+00 1109.0
37 TraesCS2B01G202400 chr7D 91.597 357 10 8 3550 3895 545648026 545648373 4.010000e-130 475.0
38 TraesCS2B01G202400 chr7D 93.077 260 12 2 3596 3855 545651413 545651666 4.190000e-100 375.0
39 TraesCS2B01G202400 chr7D 87.172 343 27 12 3513 3854 545621682 545621356 1.510000e-99 374.0
40 TraesCS2B01G202400 chr7D 86.517 267 20 9 3921 4178 545621457 545621198 3.380000e-71 279.0
41 TraesCS2B01G202400 chr7D 91.603 131 11 0 4302 4432 509571818 509571688 9.790000e-42 182.0
42 TraesCS2B01G202400 chr7D 89.764 127 5 4 661 780 545650345 545650470 5.940000e-34 156.0
43 TraesCS2B01G202400 chr7B 88.071 964 80 22 705 1666 589735204 589736134 0.000000e+00 1110.0
44 TraesCS2B01G202400 chr7B 87.714 936 58 18 737 1666 588823563 588822679 0.000000e+00 1038.0
45 TraesCS2B01G202400 chr7B 86.308 891 79 23 764 1651 589934904 589935754 0.000000e+00 929.0
46 TraesCS2B01G202400 chr7B 86.994 346 35 9 3513 3853 589699782 589699442 9.000000e-102 381.0
47 TraesCS2B01G202400 chr7B 85.279 394 27 8 143 505 589734528 589734921 1.160000e-100 377.0
48 TraesCS2B01G202400 chr7B 92.308 260 14 2 3596 3855 589935898 589936151 9.060000e-97 364.0
49 TraesCS2B01G202400 chr7B 81.308 428 33 14 201 604 588824117 588823713 2.000000e-78 303.0
50 TraesCS2B01G202400 chr7B 91.954 174 13 1 3723 3895 589692329 589692156 4.430000e-60 243.0
51 TraesCS2B01G202400 chr7B 94.340 159 8 1 3955 4113 589694115 589693958 4.430000e-60 243.0
52 TraesCS2B01G202400 chr7B 85.106 235 26 7 3946 4175 589737773 589738003 9.590000e-57 231.0
53 TraesCS2B01G202400 chr7B 90.751 173 12 3 3723 3895 589737728 589737896 1.240000e-55 228.0
54 TraesCS2B01G202400 chr7B 92.000 150 12 0 4283 4432 588820548 588820399 1.250000e-50 211.0
55 TraesCS2B01G202400 chr7B 92.466 146 9 2 3895 4040 588821625 588821482 1.620000e-49 207.0
56 TraesCS2B01G202400 chr7B 90.667 150 14 0 4283 4432 588875232 588875083 2.700000e-47 200.0
57 TraesCS2B01G202400 chr7B 88.435 147 17 0 4286 4432 537732803 537732657 1.270000e-40 178.0
58 TraesCS2B01G202400 chr7B 96.154 52 2 0 4197 4248 588821485 588821434 7.900000e-13 86.1
59 TraesCS2B01G202400 chr7B 86.747 83 4 3 661 737 589696383 589696302 7.900000e-13 86.1
60 TraesCS2B01G202400 chr7B 92.308 52 4 0 4197 4248 589699323 589699272 1.710000e-09 75.0
61 TraesCS2B01G202400 chr7A 88.474 911 76 12 767 1665 594434392 594435285 0.000000e+00 1074.0
62 TraesCS2B01G202400 chr7A 89.245 874 69 16 804 1666 626992695 626991836 0.000000e+00 1070.0
63 TraesCS2B01G202400 chr7A 87.978 915 86 15 752 1666 627008775 627007885 0.000000e+00 1059.0
64 TraesCS2B01G202400 chr7A 86.934 773 34 17 3319 4031 626991934 626991169 0.000000e+00 806.0
65 TraesCS2B01G202400 chr7A 93.973 448 15 3 3742 4178 627230421 627229975 0.000000e+00 667.0
66 TraesCS2B01G202400 chr7A 86.679 533 43 7 1 505 627046239 627045707 2.310000e-157 566.0
67 TraesCS2B01G202400 chr7A 86.492 533 43 8 1 505 627120426 627119895 3.870000e-155 558.0
68 TraesCS2B01G202400 chr7A 89.736 341 31 4 1 338 627234847 627234508 2.450000e-117 433.0
69 TraesCS2B01G202400 chr7A 85.049 408 36 11 3319 3710 628521116 628521514 4.160000e-105 392.0
70 TraesCS2B01G202400 chr7A 87.906 339 22 13 3516 3853 628491377 628491057 9.000000e-102 381.0
71 TraesCS2B01G202400 chr7A 86.337 344 22 11 3512 3853 628487183 628486863 7.050000e-93 351.0
72 TraesCS2B01G202400 chr7A 84.022 363 42 14 3541 3895 629771927 629771573 7.100000e-88 335.0
73 TraesCS2B01G202400 chr7A 91.388 209 15 3 3319 3526 628646219 628646425 2.610000e-72 283.0
74 TraesCS2B01G202400 chr7A 90.865 208 17 2 3319 3525 627231847 627231641 1.210000e-70 278.0
75 TraesCS2B01G202400 chr7A 86.667 240 18 11 3921 4156 628388921 628388692 2.050000e-63 254.0
76 TraesCS2B01G202400 chr7A 88.182 220 16 5 3946 4156 628522604 628522822 2.050000e-63 254.0
77 TraesCS2B01G202400 chr7A 92.045 176 9 4 3720 3895 628388949 628388779 4.430000e-60 243.0
78 TraesCS2B01G202400 chr7A 84.942 259 17 14 3921 4178 628491157 628490920 4.430000e-60 243.0
79 TraesCS2B01G202400 chr7A 92.727 165 11 1 4014 4178 626990606 626990443 2.060000e-58 237.0
80 TraesCS2B01G202400 chr7A 88.136 177 7 8 3508 3681 169957623 169957458 9.720000e-47 198.0
81 TraesCS2B01G202400 chr7A 88.608 158 3 3 3541 3690 627230572 627230422 1.270000e-40 178.0
82 TraesCS2B01G202400 chr7A 86.111 108 12 2 510 617 627008969 627008865 3.620000e-21 113.0
83 TraesCS2B01G202400 chr7A 84.259 108 14 2 510 617 626992943 626992839 7.840000e-18 102.0
84 TraesCS2B01G202400 chr7A 96.154 52 2 0 4197 4248 626990461 626990410 7.900000e-13 86.1
85 TraesCS2B01G202400 chr7A 96.154 52 2 0 4197 4248 627229993 627229942 7.900000e-13 86.1
86 TraesCS2B01G202400 chr6A 88.790 901 62 16 766 1666 107264329 107265190 0.000000e+00 1068.0
87 TraesCS2B01G202400 chr6A 90.286 350 28 3 1 349 107263420 107263764 1.880000e-123 453.0
88 TraesCS2B01G202400 chr6A 91.388 209 16 2 3319 3526 107265092 107265299 7.260000e-73 285.0
89 TraesCS2B01G202400 chr6A 92.308 143 8 3 3898 4040 107262275 107262136 2.700000e-47 200.0
90 TraesCS2B01G202400 chr6A 92.857 140 7 3 3895 4034 107266309 107266445 2.700000e-47 200.0
91 TraesCS2B01G202400 chr6A 89.286 140 15 0 368 507 107263837 107263976 4.560000e-40 176.0
92 TraesCS2B01G202400 chr6A 92.308 52 2 2 4197 4248 107262139 107262090 6.150000e-09 73.1
93 TraesCS2B01G202400 chr1B 86.567 1005 77 29 679 1666 426497144 426496181 0.000000e+00 1055.0
94 TraesCS2B01G202400 chr1B 87.903 868 80 19 814 1666 398961889 398962746 0.000000e+00 998.0
95 TraesCS2B01G202400 chr1B 89.398 698 59 4 969 1666 398840324 398839642 0.000000e+00 865.0
96 TraesCS2B01G202400 chr1B 84.758 538 65 8 1 527 133112383 133111852 1.410000e-144 523.0
97 TraesCS2B01G202400 chr1B 85.259 502 44 12 143 617 426482874 426482376 1.430000e-134 490.0
98 TraesCS2B01G202400 chr1B 91.496 341 24 3 1 340 133125371 133125035 8.680000e-127 464.0
99 TraesCS2B01G202400 chr1B 80.500 600 68 27 708 1289 426482208 426481640 8.870000e-112 414.0
100 TraesCS2B01G202400 chr1B 78.869 601 71 31 708 1289 133111613 133111050 5.450000e-94 355.0
101 TraesCS2B01G202400 chr1B 92.344 209 14 2 3319 3526 426496279 426496072 3.350000e-76 296.0
102 TraesCS2B01G202400 chr1B 93.820 178 11 0 348 525 426497611 426497434 7.310000e-68 268.0
103 TraesCS2B01G202400 chr1B 91.713 181 15 0 4252 4432 426493519 426493339 7.360000e-63 252.0
104 TraesCS2B01G202400 chr1B 85.714 196 22 5 2664 2856 426495375 426495183 7.520000e-48 202.0
105 TraesCS2B01G202400 chr1B 94.118 102 5 1 3993 4094 398839227 398839127 2.130000e-33 154.0
106 TraesCS2B01G202400 chr1B 85.185 108 13 2 510 617 133111837 133111733 1.690000e-19 108.0
107 TraesCS2B01G202400 chr1B 89.157 83 2 4 661 737 398961790 398961871 3.650000e-16 97.1
108 TraesCS2B01G202400 chr5D 88.048 912 74 17 755 1666 289355374 289354498 0.000000e+00 1048.0
109 TraesCS2B01G202400 chr5D 86.325 585 30 16 3319 3895 331838432 331838974 3.820000e-165 592.0
110 TraesCS2B01G202400 chr5D 91.545 343 27 1 1 341 289421871 289421529 5.190000e-129 472.0
111 TraesCS2B01G202400 chr5D 97.872 188 4 0 4245 4432 289725227 289725040 4.270000e-85 326.0
112 TraesCS2B01G202400 chr5D 92.344 209 14 2 3319 3526 289354596 289354389 3.350000e-76 296.0
113 TraesCS2B01G202400 chr5D 92.021 188 15 0 4245 4432 289418227 289418040 9.450000e-67 265.0
114 TraesCS2B01G202400 chr5D 90.000 150 15 0 4283 4432 289352145 289351996 1.260000e-45 195.0
115 TraesCS2B01G202400 chr5D 91.608 143 9 3 3898 4040 289419182 289419043 1.260000e-45 195.0
116 TraesCS2B01G202400 chr5D 85.465 172 19 6 790 959 42081802 42081635 1.640000e-39 174.0
117 TraesCS2B01G202400 chr5D 95.098 102 5 0 425 526 289727576 289727475 1.280000e-35 161.0
118 TraesCS2B01G202400 chr5D 86.111 108 12 2 510 617 289727449 289727345 3.620000e-21 113.0
119 TraesCS2B01G202400 chr5D 91.463 82 5 2 787 867 29906523 29906603 1.300000e-20 111.0
120 TraesCS2B01G202400 chr5D 86.139 101 11 2 2916 3014 283108760 283108661 6.060000e-19 106.0
121 TraesCS2B01G202400 chr5D 96.154 52 2 0 4197 4248 289419046 289418995 7.900000e-13 86.1
122 TraesCS2B01G202400 chr5D 96.154 52 2 0 4197 4248 331839066 331839117 7.900000e-13 86.1
123 TraesCS2B01G202400 chr6D 89.557 699 64 4 968 1666 124609299 124608610 0.000000e+00 878.0
124 TraesCS2B01G202400 chr6D 84.644 547 61 17 3319 3853 124608708 124608173 1.410000e-144 523.0
125 TraesCS2B01G202400 chr6D 87.774 319 24 11 3541 3853 122980462 122980771 4.210000e-95 359.0
126 TraesCS2B01G202400 chr6D 89.669 242 15 6 3946 4178 124608254 124608014 2.590000e-77 300.0
127 TraesCS2B01G202400 chr5B 85.149 101 12 3 2916 3014 321476677 321476578 2.820000e-17 100.0
128 TraesCS2B01G202400 chrUn 96.154 52 2 0 4197 4248 479833301 479833250 7.900000e-13 86.1


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 TraesCS2B01G202400 chr2B 182130215 182134646 4431 True 4145.500000 8185 93.299000 1 4432 2 chr2B.!!$R5 4431
1 TraesCS2B01G202400 chr2B 135464705 135467409 2704 False 2221.000000 4028 97.185500 1711 4432 2 chr2B.!!$F2 2721
2 TraesCS2B01G202400 chr2B 135511788 135516697 4909 False 763.600000 1783 91.872800 1 3135 5 chr2B.!!$F3 3134
3 TraesCS2B01G202400 chr2B 136812823 136813863 1040 True 724.500000 1330 93.266500 1712 3134 2 chr2B.!!$R3 1422
4 TraesCS2B01G202400 chr2B 137012522 137013547 1025 True 692.000000 1271 92.203000 1719 3134 2 chr2B.!!$R4 1415
5 TraesCS2B01G202400 chr2B 136636677 136637695 1018 True 686.500000 1260 91.624000 1712 3134 2 chr2B.!!$R2 1422
6 TraesCS2B01G202400 chr2B 127789929 127790981 1052 True 588.666667 852 96.422667 1 1066 3 chr2B.!!$R1 1065
7 TraesCS2B01G202400 chr2B 135128328 135129109 781 False 349.333333 472 91.136333 2665 3303 3 chr2B.!!$F1 638
8 TraesCS2B01G202400 chr2A 84144575 84146272 1697 False 1286.000000 2128 94.245000 1664 3303 2 chr2A.!!$F3 1639
9 TraesCS2B01G202400 chr2A 84229253 84230109 856 False 1277.000000 1277 93.605000 1663 2517 1 chr2A.!!$F1 854
10 TraesCS2B01G202400 chr2A 83991118 83992336 1218 False 646.000000 1254 91.546667 1711 3135 3 chr2A.!!$F2 1424
11 TraesCS2B01G202400 chr2A 134865245 134866476 1231 True 550.000000 1266 85.612667 1711 3303 3 chr2A.!!$R2 1592
12 TraesCS2B01G202400 chr2D 127819149 127820435 1286 True 546.000000 1290 89.412333 1663 3303 3 chr2D.!!$R2 1640
13 TraesCS2B01G202400 chr7D 518768806 518769692 886 False 1129.000000 1129 89.636000 767 1666 1 chr7D.!!$F1 899
14 TraesCS2B01G202400 chr7D 545266194 545267174 980 True 1109.000000 1109 87.253000 666 1659 1 chr7D.!!$R2 993
15 TraesCS2B01G202400 chr7D 545648026 545651666 3640 False 335.333333 475 91.479333 661 3895 3 chr7D.!!$F2 3234
16 TraesCS2B01G202400 chr7B 589934904 589936151 1247 False 646.500000 929 89.308000 764 3855 2 chr7B.!!$F2 3091
17 TraesCS2B01G202400 chr7B 589734528 589738003 3475 False 486.500000 1110 87.301750 143 4175 4 chr7B.!!$F1 4032
18 TraesCS2B01G202400 chr7B 588820399 588824117 3718 True 369.020000 1038 89.928400 201 4432 5 chr7B.!!$R3 4231
19 TraesCS2B01G202400 chr7B 589692156 589699782 7626 True 205.620000 381 90.468600 661 4248 5 chr7B.!!$R4 3587
20 TraesCS2B01G202400 chr7A 594434392 594435285 893 False 1074.000000 1074 88.474000 767 1665 1 chr7A.!!$F1 898
21 TraesCS2B01G202400 chr7A 627007885 627008969 1084 True 586.000000 1059 87.044500 510 1666 2 chr7A.!!$R6 1156
22 TraesCS2B01G202400 chr7A 627045707 627046239 532 True 566.000000 566 86.679000 1 505 1 chr7A.!!$R2 504
23 TraesCS2B01G202400 chr7A 627119895 627120426 531 True 558.000000 558 86.492000 1 505 1 chr7A.!!$R3 504
24 TraesCS2B01G202400 chr7A 626990410 626992943 2533 True 460.220000 1070 89.863800 510 4248 5 chr7A.!!$R5 3738
25 TraesCS2B01G202400 chr7A 627229942 627234847 4905 True 328.420000 667 91.867200 1 4248 5 chr7A.!!$R7 4247
26 TraesCS2B01G202400 chr7A 628486863 628491377 4514 True 325.000000 381 86.395000 3512 4178 3 chr7A.!!$R9 666
27 TraesCS2B01G202400 chr7A 628521116 628522822 1706 False 323.000000 392 86.615500 3319 4156 2 chr7A.!!$F3 837
28 TraesCS2B01G202400 chr6A 107263420 107266445 3025 False 436.400000 1068 90.521400 1 4034 5 chr6A.!!$F1 4033
29 TraesCS2B01G202400 chr1B 398961790 398962746 956 False 547.550000 998 88.530000 661 1666 2 chr1B.!!$F1 1005
30 TraesCS2B01G202400 chr1B 398839127 398840324 1197 True 509.500000 865 91.758000 969 4094 2 chr1B.!!$R3 3125
31 TraesCS2B01G202400 chr1B 426481640 426482874 1234 True 452.000000 490 82.879500 143 1289 2 chr1B.!!$R4 1146
32 TraesCS2B01G202400 chr1B 426493339 426497611 4272 True 414.600000 1055 90.031600 348 4432 5 chr1B.!!$R5 4084
33 TraesCS2B01G202400 chr1B 133111050 133112383 1333 True 328.666667 523 82.937333 1 1289 3 chr1B.!!$R2 1288
34 TraesCS2B01G202400 chr5D 289351996 289355374 3378 True 513.000000 1048 90.130667 755 4432 3 chr5D.!!$R3 3677
35 TraesCS2B01G202400 chr5D 331838432 331839117 685 False 339.050000 592 91.239500 3319 4248 2 chr5D.!!$F2 929
36 TraesCS2B01G202400 chr5D 289418040 289421871 3831 True 254.525000 472 92.832000 1 4432 4 chr5D.!!$R4 4431
37 TraesCS2B01G202400 chr6D 124608014 124609299 1285 True 567.000000 878 87.956667 968 4178 3 chr6D.!!$R1 3210

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
158 159 1.659098 CATAACGAGTTCCGCTCCAAC 59.341 52.381 0.00 0.00 43.32 3.77 F
812 5146 1.747206 CGTTTTAGCTATGCCTGGGCT 60.747 52.381 13.05 3.88 42.51 5.19 F
2448 7123 0.108945 GGCCTGAATTTGTGCAGAGC 60.109 55.000 0.00 0.00 34.06 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1092 5548 0.331278 CCATCAGGGCTGGGTTTACA 59.669 55.0 0.0 0.0 0.0 2.41 R
2516 7191 0.037605 ACACGCCCTTTTCCGACTAG 60.038 55.0 0.0 0.0 0.0 2.57 R
3437 9202 0.614697 TCCTCTGCTTCGATCACCCA 60.615 55.0 0.0 0.0 0.0 4.51 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
91 92 2.430921 GGTGTGCCGACAGAGACG 60.431 66.667 0.00 0.00 30.74 4.18
150 151 7.763071 ACAATAGAAGTAACCATAACGAGTTCC 59.237 37.037 0.00 0.00 0.00 3.62
158 159 1.659098 CATAACGAGTTCCGCTCCAAC 59.341 52.381 0.00 0.00 43.32 3.77
556 787 3.935203 AGCAATGACATAACTCCGAGTTG 59.065 43.478 21.78 10.79 39.11 3.16
812 5146 1.747206 CGTTTTAGCTATGCCTGGGCT 60.747 52.381 13.05 3.88 42.51 5.19
1120 5576 2.190578 CCCTGATGGCGAACCCTC 59.809 66.667 0.00 0.00 33.59 4.30
1285 5745 1.225426 CCCAGCAGCAGCAAGGATA 59.775 57.895 13.07 0.00 45.49 2.59
1308 5768 3.343788 GAGTCCGACGTGCCTCCAG 62.344 68.421 0.00 0.00 0.00 3.86
1778 6440 3.629142 ACGCCCTTGCTAGTCTTTTAT 57.371 42.857 0.00 0.00 34.43 1.40
1879 6547 7.461749 TCTAGTGTTCTTTGAATCCCTTTCAT 58.538 34.615 0.00 0.00 43.73 2.57
1919 6587 1.549620 AGTGTCAGCAGAGTCTCCATG 59.450 52.381 0.00 0.00 0.00 3.66
1920 6588 0.248565 TGTCAGCAGAGTCTCCATGC 59.751 55.000 6.06 6.06 40.29 4.06
1922 6590 1.134461 GTCAGCAGAGTCTCCATGCAT 60.134 52.381 14.55 0.00 42.45 3.96
2098 6770 0.798771 GGCACGAGACAGAGCGTAAG 60.799 60.000 0.00 0.00 38.92 2.34
2120 6792 1.259316 GCACTCGCCGCAAAATAAAG 58.741 50.000 0.00 0.00 0.00 1.85
2372 7047 3.769739 TTGAGCTAAGCAAGTCCTCAA 57.230 42.857 0.00 0.00 0.00 3.02
2431 7106 7.709947 TCAGATATGAATGAGAAATTGTTGGC 58.290 34.615 0.00 0.00 0.00 4.52
2432 7107 6.921857 CAGATATGAATGAGAAATTGTTGGCC 59.078 38.462 0.00 0.00 0.00 5.36
2433 7108 6.837568 AGATATGAATGAGAAATTGTTGGCCT 59.162 34.615 3.32 0.00 0.00 5.19
2434 7109 4.524316 TGAATGAGAAATTGTTGGCCTG 57.476 40.909 3.32 0.00 0.00 4.85
2436 7111 4.588106 TGAATGAGAAATTGTTGGCCTGAA 59.412 37.500 3.32 0.00 0.00 3.02
2438 7113 5.750352 ATGAGAAATTGTTGGCCTGAATT 57.250 34.783 3.32 2.75 0.00 2.17
2439 7114 5.549742 TGAGAAATTGTTGGCCTGAATTT 57.450 34.783 15.52 15.52 33.10 1.82
2440 7115 5.299148 TGAGAAATTGTTGGCCTGAATTTG 58.701 37.500 18.70 0.00 31.10 2.32
2441 7116 5.163322 TGAGAAATTGTTGGCCTGAATTTGT 60.163 36.000 18.70 15.99 31.10 2.83
2442 7117 5.058490 AGAAATTGTTGGCCTGAATTTGTG 58.942 37.500 18.70 0.00 31.10 3.33
2443 7118 2.237393 TTGTTGGCCTGAATTTGTGC 57.763 45.000 3.32 0.00 0.00 4.57
2448 7123 0.108945 GGCCTGAATTTGTGCAGAGC 60.109 55.000 0.00 0.00 34.06 4.09
2449 7124 0.599558 GCCTGAATTTGTGCAGAGCA 59.400 50.000 0.00 0.00 34.06 4.26
2450 7125 1.203994 GCCTGAATTTGTGCAGAGCAT 59.796 47.619 0.00 0.00 41.91 3.79
2451 7126 2.353406 GCCTGAATTTGTGCAGAGCATT 60.353 45.455 0.00 0.00 41.91 3.56
2452 7127 3.863400 GCCTGAATTTGTGCAGAGCATTT 60.863 43.478 0.00 0.00 41.91 2.32
2453 7128 3.678072 CCTGAATTTGTGCAGAGCATTTG 59.322 43.478 0.00 0.00 41.91 2.32
2454 7129 4.552355 CTGAATTTGTGCAGAGCATTTGA 58.448 39.130 0.00 0.00 41.91 2.69
2455 7130 4.552355 TGAATTTGTGCAGAGCATTTGAG 58.448 39.130 0.00 0.00 41.91 3.02
2456 7131 4.038282 TGAATTTGTGCAGAGCATTTGAGT 59.962 37.500 0.00 0.00 41.91 3.41
2457 7132 5.241285 TGAATTTGTGCAGAGCATTTGAGTA 59.759 36.000 0.00 0.00 41.91 2.59
2458 7133 5.710513 ATTTGTGCAGAGCATTTGAGTAA 57.289 34.783 0.00 0.00 41.91 2.24
2459 7134 4.488126 TTGTGCAGAGCATTTGAGTAAC 57.512 40.909 0.00 0.00 41.91 2.50
2460 7135 3.743521 TGTGCAGAGCATTTGAGTAACT 58.256 40.909 0.00 0.00 41.91 2.24
2461 7136 4.136796 TGTGCAGAGCATTTGAGTAACTT 58.863 39.130 0.00 0.00 41.91 2.66
2462 7137 4.580167 TGTGCAGAGCATTTGAGTAACTTT 59.420 37.500 0.00 0.00 41.91 2.66
2463 7138 5.149977 GTGCAGAGCATTTGAGTAACTTTC 58.850 41.667 0.00 0.00 41.91 2.62
2464 7139 5.049129 GTGCAGAGCATTTGAGTAACTTTCT 60.049 40.000 0.00 0.00 41.91 2.52
2465 7140 5.049198 TGCAGAGCATTTGAGTAACTTTCTG 60.049 40.000 0.00 0.00 31.71 3.02
2466 7141 5.049129 GCAGAGCATTTGAGTAACTTTCTGT 60.049 40.000 0.00 0.00 33.79 3.41
2467 7142 6.147821 GCAGAGCATTTGAGTAACTTTCTGTA 59.852 38.462 0.00 0.00 33.79 2.74
2468 7143 7.148340 GCAGAGCATTTGAGTAACTTTCTGTAT 60.148 37.037 0.00 0.00 33.79 2.29
2469 7144 9.371136 CAGAGCATTTGAGTAACTTTCTGTATA 57.629 33.333 0.00 0.00 0.00 1.47
2495 7170 7.870509 ATGTTTGTTGTATGCATCTATGACT 57.129 32.000 0.19 0.00 0.00 3.41
2496 7171 7.686438 TGTTTGTTGTATGCATCTATGACTT 57.314 32.000 0.19 0.00 0.00 3.01
2497 7172 8.785329 TGTTTGTTGTATGCATCTATGACTTA 57.215 30.769 0.19 0.00 0.00 2.24
2498 7173 9.394767 TGTTTGTTGTATGCATCTATGACTTAT 57.605 29.630 0.19 0.00 0.00 1.73
2514 7189 9.443283 CTATGACTTATTAAAACATTCTGCTGC 57.557 33.333 0.00 0.00 0.00 5.25
2515 7190 7.452880 TGACTTATTAAAACATTCTGCTGCT 57.547 32.000 0.00 0.00 0.00 4.24
2516 7191 7.530010 TGACTTATTAAAACATTCTGCTGCTC 58.470 34.615 0.00 0.00 0.00 4.26
2517 7192 7.391554 TGACTTATTAAAACATTCTGCTGCTCT 59.608 33.333 0.00 0.00 0.00 4.09
2518 7193 8.792830 ACTTATTAAAACATTCTGCTGCTCTA 57.207 30.769 0.00 0.00 0.00 2.43
2519 7194 8.887717 ACTTATTAAAACATTCTGCTGCTCTAG 58.112 33.333 0.00 0.00 0.00 2.43
2520 7195 8.792830 TTATTAAAACATTCTGCTGCTCTAGT 57.207 30.769 0.00 0.00 0.00 2.57
2521 7196 6.727824 TTAAAACATTCTGCTGCTCTAGTC 57.272 37.500 0.00 0.00 0.00 2.59
2522 7197 2.575694 ACATTCTGCTGCTCTAGTCG 57.424 50.000 0.00 0.00 0.00 4.18
2523 7198 1.135915 ACATTCTGCTGCTCTAGTCGG 59.864 52.381 0.00 0.00 0.00 4.79
2524 7199 1.406898 CATTCTGCTGCTCTAGTCGGA 59.593 52.381 0.00 0.00 0.00 4.55
2525 7200 1.545841 TTCTGCTGCTCTAGTCGGAA 58.454 50.000 0.00 0.00 0.00 4.30
2526 7201 1.545841 TCTGCTGCTCTAGTCGGAAA 58.454 50.000 0.00 0.00 0.00 3.13
2527 7202 1.893137 TCTGCTGCTCTAGTCGGAAAA 59.107 47.619 0.00 0.00 0.00 2.29
2528 7203 2.094494 TCTGCTGCTCTAGTCGGAAAAG 60.094 50.000 0.00 0.00 0.00 2.27
2529 7204 1.066858 TGCTGCTCTAGTCGGAAAAGG 60.067 52.381 0.00 0.00 0.00 3.11
2530 7205 1.740718 GCTGCTCTAGTCGGAAAAGGG 60.741 57.143 0.00 0.00 0.00 3.95
2531 7206 0.249398 TGCTCTAGTCGGAAAAGGGC 59.751 55.000 5.90 5.90 37.25 5.19
2532 7207 0.806492 GCTCTAGTCGGAAAAGGGCG 60.806 60.000 0.00 0.00 0.00 6.13
2533 7208 0.531200 CTCTAGTCGGAAAAGGGCGT 59.469 55.000 0.00 0.00 0.00 5.68
2534 7209 0.245539 TCTAGTCGGAAAAGGGCGTG 59.754 55.000 0.00 0.00 0.00 5.34
2535 7210 0.037605 CTAGTCGGAAAAGGGCGTGT 60.038 55.000 0.00 0.00 0.00 4.49
2536 7211 1.203052 CTAGTCGGAAAAGGGCGTGTA 59.797 52.381 0.00 0.00 0.00 2.90
2537 7212 0.320160 AGTCGGAAAAGGGCGTGTAC 60.320 55.000 0.00 0.00 0.00 2.90
2538 7213 0.320160 GTCGGAAAAGGGCGTGTACT 60.320 55.000 0.00 0.00 0.00 2.73
2539 7214 0.320073 TCGGAAAAGGGCGTGTACTG 60.320 55.000 0.00 0.00 0.00 2.74
2540 7215 0.320073 CGGAAAAGGGCGTGTACTGA 60.320 55.000 0.00 0.00 0.00 3.41
2541 7216 1.439679 GGAAAAGGGCGTGTACTGAG 58.560 55.000 0.00 0.00 0.00 3.35
2542 7217 1.439679 GAAAAGGGCGTGTACTGAGG 58.560 55.000 0.00 0.00 0.00 3.86
2543 7218 0.605589 AAAAGGGCGTGTACTGAGGC 60.606 55.000 0.00 0.00 0.00 4.70
2544 7219 1.764571 AAAGGGCGTGTACTGAGGCA 61.765 55.000 10.32 0.00 0.00 4.75
2545 7220 2.434359 GGGCGTGTACTGAGGCAC 60.434 66.667 10.32 0.37 0.00 5.01
2546 7221 2.434359 GGCGTGTACTGAGGCACC 60.434 66.667 0.00 0.00 32.40 5.01
2547 7222 2.809601 GCGTGTACTGAGGCACCG 60.810 66.667 0.00 2.07 32.40 4.94
2548 7223 2.959372 CGTGTACTGAGGCACCGA 59.041 61.111 0.00 0.00 32.40 4.69
2549 7224 1.511305 CGTGTACTGAGGCACCGAT 59.489 57.895 0.00 0.00 32.40 4.18
2550 7225 0.525668 CGTGTACTGAGGCACCGATC 60.526 60.000 0.00 0.00 32.40 3.69
2551 7226 0.179108 GTGTACTGAGGCACCGATCC 60.179 60.000 0.00 0.00 0.00 3.36
2552 7227 0.613572 TGTACTGAGGCACCGATCCA 60.614 55.000 0.00 0.00 0.00 3.41
2553 7228 0.535335 GTACTGAGGCACCGATCCAA 59.465 55.000 0.00 0.00 0.00 3.53
2554 7229 1.139058 GTACTGAGGCACCGATCCAAT 59.861 52.381 0.00 0.00 0.00 3.16
2555 7230 1.496060 ACTGAGGCACCGATCCAATA 58.504 50.000 0.00 0.00 0.00 1.90
2556 7231 1.414181 ACTGAGGCACCGATCCAATAG 59.586 52.381 0.00 0.00 0.00 1.73
2557 7232 1.688735 CTGAGGCACCGATCCAATAGA 59.311 52.381 0.00 0.00 0.00 1.98
2558 7233 2.103094 CTGAGGCACCGATCCAATAGAA 59.897 50.000 0.00 0.00 0.00 2.10
2559 7234 2.158957 TGAGGCACCGATCCAATAGAAC 60.159 50.000 0.00 0.00 0.00 3.01
2560 7235 2.103263 GAGGCACCGATCCAATAGAACT 59.897 50.000 0.00 0.00 0.00 3.01
2561 7236 2.103263 AGGCACCGATCCAATAGAACTC 59.897 50.000 0.00 0.00 0.00 3.01
2562 7237 2.158957 GGCACCGATCCAATAGAACTCA 60.159 50.000 0.00 0.00 0.00 3.41
2563 7238 3.126831 GCACCGATCCAATAGAACTCAG 58.873 50.000 0.00 0.00 0.00 3.35
2564 7239 3.126831 CACCGATCCAATAGAACTCAGC 58.873 50.000 0.00 0.00 0.00 4.26
2565 7240 3.034635 ACCGATCCAATAGAACTCAGCT 58.965 45.455 0.00 0.00 0.00 4.24
2566 7241 3.068873 ACCGATCCAATAGAACTCAGCTC 59.931 47.826 0.00 0.00 0.00 4.09
2567 7242 3.320541 CCGATCCAATAGAACTCAGCTCT 59.679 47.826 0.00 0.00 0.00 4.09
2568 7243 4.297510 CGATCCAATAGAACTCAGCTCTG 58.702 47.826 0.00 0.00 0.00 3.35
2569 7244 4.037327 CGATCCAATAGAACTCAGCTCTGA 59.963 45.833 0.00 0.00 38.06 3.27
2570 7245 5.278907 CGATCCAATAGAACTCAGCTCTGAT 60.279 44.000 0.00 0.00 39.13 2.90
2571 7246 5.946942 TCCAATAGAACTCAGCTCTGATT 57.053 39.130 0.00 0.00 39.13 2.57
2572 7247 6.305272 TCCAATAGAACTCAGCTCTGATTT 57.695 37.500 0.00 1.22 39.13 2.17
2573 7248 6.344500 TCCAATAGAACTCAGCTCTGATTTC 58.656 40.000 17.15 17.15 44.56 2.17
2580 7255 7.232945 GAACTCAGCTCTGATTTCTCAATAC 57.767 40.000 17.43 0.00 42.43 1.89
2581 7256 6.543430 ACTCAGCTCTGATTTCTCAATACT 57.457 37.500 0.00 0.00 39.13 2.12
2582 7257 6.945218 ACTCAGCTCTGATTTCTCAATACTT 58.055 36.000 0.00 0.00 39.13 2.24
2583 7258 7.041107 ACTCAGCTCTGATTTCTCAATACTTC 58.959 38.462 0.00 0.00 39.13 3.01
2584 7259 6.939622 TCAGCTCTGATTTCTCAATACTTCA 58.060 36.000 0.00 0.00 34.14 3.02
2585 7260 7.563020 TCAGCTCTGATTTCTCAATACTTCAT 58.437 34.615 0.00 0.00 34.14 2.57
2586 7261 8.045507 TCAGCTCTGATTTCTCAATACTTCATT 58.954 33.333 0.00 0.00 34.14 2.57
2587 7262 8.675504 CAGCTCTGATTTCTCAATACTTCATTT 58.324 33.333 0.00 0.00 0.00 2.32
2588 7263 8.675504 AGCTCTGATTTCTCAATACTTCATTTG 58.324 33.333 0.00 0.00 0.00 2.32
2589 7264 8.671921 GCTCTGATTTCTCAATACTTCATTTGA 58.328 33.333 0.00 0.00 0.00 2.69
2591 7266 9.730705 TCTGATTTCTCAATACTTCATTTGAGT 57.269 29.630 11.24 0.00 45.77 3.41
2592 7267 9.770503 CTGATTTCTCAATACTTCATTTGAGTG 57.229 33.333 11.24 0.00 45.77 3.51
2593 7268 8.733458 TGATTTCTCAATACTTCATTTGAGTGG 58.267 33.333 11.24 0.00 45.77 4.00
2594 7269 8.641498 ATTTCTCAATACTTCATTTGAGTGGT 57.359 30.769 11.24 0.00 45.77 4.16
2595 7270 7.439157 TTCTCAATACTTCATTTGAGTGGTG 57.561 36.000 11.24 0.00 45.77 4.17
2596 7271 6.768483 TCTCAATACTTCATTTGAGTGGTGA 58.232 36.000 11.24 0.00 45.77 4.02
2597 7272 7.223584 TCTCAATACTTCATTTGAGTGGTGAA 58.776 34.615 11.24 0.00 45.77 3.18
2601 7276 3.893720 CTTCATTTGAGTGGTGAAGCAC 58.106 45.455 4.48 4.48 41.41 4.40
2602 7277 2.929641 TCATTTGAGTGGTGAAGCACA 58.070 42.857 14.49 0.00 35.86 4.57
2603 7278 2.880268 TCATTTGAGTGGTGAAGCACAG 59.120 45.455 14.49 0.00 35.86 3.66
2604 7279 2.708216 TTTGAGTGGTGAAGCACAGA 57.292 45.000 14.49 0.00 35.86 3.41
2605 7280 2.708216 TTGAGTGGTGAAGCACAGAA 57.292 45.000 14.49 4.26 35.86 3.02
2606 7281 1.953559 TGAGTGGTGAAGCACAGAAC 58.046 50.000 14.49 4.41 35.86 3.01
2607 7282 1.230324 GAGTGGTGAAGCACAGAACC 58.770 55.000 14.49 0.00 35.86 3.62
2608 7283 0.546122 AGTGGTGAAGCACAGAACCA 59.454 50.000 14.49 0.00 40.36 3.67
2609 7284 1.143684 AGTGGTGAAGCACAGAACCAT 59.856 47.619 14.49 0.00 44.18 3.55
2610 7285 1.267806 GTGGTGAAGCACAGAACCATG 59.732 52.381 7.73 0.00 44.18 3.66
2611 7286 1.133823 TGGTGAAGCACAGAACCATGT 60.134 47.619 0.00 0.00 37.77 3.21
2612 7287 1.956477 GGTGAAGCACAGAACCATGTT 59.044 47.619 0.00 0.00 35.86 2.71
2613 7288 2.362077 GGTGAAGCACAGAACCATGTTT 59.638 45.455 0.00 0.00 35.86 2.83
2614 7289 3.181476 GGTGAAGCACAGAACCATGTTTT 60.181 43.478 0.00 0.00 35.86 2.43
2615 7290 4.432712 GTGAAGCACAGAACCATGTTTTT 58.567 39.130 0.00 0.00 34.08 1.94
2616 7291 4.268405 GTGAAGCACAGAACCATGTTTTTG 59.732 41.667 0.00 0.00 34.08 2.44
2617 7292 4.159321 TGAAGCACAGAACCATGTTTTTGA 59.841 37.500 0.31 0.00 0.00 2.69
2618 7293 4.045636 AGCACAGAACCATGTTTTTGAC 57.954 40.909 0.31 0.00 0.00 3.18
2619 7294 3.446873 AGCACAGAACCATGTTTTTGACA 59.553 39.130 0.31 0.00 43.71 3.58
2620 7295 3.798337 GCACAGAACCATGTTTTTGACAG 59.202 43.478 0.31 0.00 42.62 3.51
2621 7296 4.677779 GCACAGAACCATGTTTTTGACAGT 60.678 41.667 0.31 0.00 42.62 3.55
2622 7297 5.410067 CACAGAACCATGTTTTTGACAGTT 58.590 37.500 0.31 0.00 42.62 3.16
2623 7298 6.559810 CACAGAACCATGTTTTTGACAGTTA 58.440 36.000 0.31 0.00 42.62 2.24
2624 7299 7.032580 CACAGAACCATGTTTTTGACAGTTAA 58.967 34.615 0.31 0.00 42.62 2.01
2625 7300 7.706179 CACAGAACCATGTTTTTGACAGTTAAT 59.294 33.333 0.31 0.00 42.62 1.40
2626 7301 7.706179 ACAGAACCATGTTTTTGACAGTTAATG 59.294 33.333 0.31 0.00 42.62 1.90
2627 7302 7.169645 CAGAACCATGTTTTTGACAGTTAATGG 59.830 37.037 0.00 0.00 42.62 3.16
2628 7303 6.478512 ACCATGTTTTTGACAGTTAATGGT 57.521 33.333 0.00 0.00 42.62 3.55
2629 7304 6.883744 ACCATGTTTTTGACAGTTAATGGTT 58.116 32.000 0.00 0.00 41.56 3.67
2630 7305 8.012957 ACCATGTTTTTGACAGTTAATGGTTA 57.987 30.769 0.00 0.00 41.56 2.85
2631 7306 8.141268 ACCATGTTTTTGACAGTTAATGGTTAG 58.859 33.333 0.00 0.00 41.56 2.34
2632 7307 8.356657 CCATGTTTTTGACAGTTAATGGTTAGA 58.643 33.333 0.00 0.00 42.62 2.10
2633 7308 9.743057 CATGTTTTTGACAGTTAATGGTTAGAA 57.257 29.630 0.00 0.00 42.62 2.10
2634 7309 9.965824 ATGTTTTTGACAGTTAATGGTTAGAAG 57.034 29.630 0.00 0.00 42.62 2.85
2635 7310 9.179909 TGTTTTTGACAGTTAATGGTTAGAAGA 57.820 29.630 0.00 0.00 33.40 2.87
2663 7338 7.439157 TTTTGGTTTGAGATACTGTGATCTG 57.561 36.000 0.00 0.00 36.27 2.90
2664 7339 6.358974 TTGGTTTGAGATACTGTGATCTGA 57.641 37.500 0.00 0.00 36.27 3.27
2665 7340 6.358974 TGGTTTGAGATACTGTGATCTGAA 57.641 37.500 0.00 0.00 36.27 3.02
2666 7341 6.950842 TGGTTTGAGATACTGTGATCTGAAT 58.049 36.000 0.00 0.00 36.27 2.57
2667 7342 7.397221 TGGTTTGAGATACTGTGATCTGAATT 58.603 34.615 0.00 0.00 36.27 2.17
2668 7343 7.884877 TGGTTTGAGATACTGTGATCTGAATTT 59.115 33.333 0.00 0.00 36.27 1.82
2924 7859 8.082852 GTCTACTTGTCAAGAATGTGAACTCTA 58.917 37.037 19.53 0.00 0.00 2.43
2977 8393 5.648092 AGCAAGTCCTCAATGTACCAAATAC 59.352 40.000 0.00 0.00 0.00 1.89
3293 9058 1.676916 CCACATCAACTCATCCAGCGT 60.677 52.381 0.00 0.00 0.00 5.07
3381 9146 3.785486 CGTTATCAAGCTCACCTCATCA 58.215 45.455 0.00 0.00 0.00 3.07
3437 9202 2.086869 CAAATCCACGGATGAGTGCTT 58.913 47.619 0.00 0.00 40.59 3.91
3817 10474 6.989169 GTGCTTGAACTACTATTCCAGATGAT 59.011 38.462 0.00 0.00 0.00 2.45
3946 10746 1.478105 TGGATCTGATGGATGCAAGCC 60.478 52.381 0.00 0.00 47.00 4.35
3996 10796 5.782893 ACTACTATTCCAGATGACTGCTC 57.217 43.478 0.00 0.00 42.25 4.26
4041 11422 6.575162 ATGTTGTCTGAATTTTACACCTCC 57.425 37.500 0.00 0.00 0.00 4.30
4161 11780 9.793252 ACAGATATGTTATCTGAATTTTGCAAC 57.207 29.630 24.24 0.00 46.25 4.17
4166 11785 8.752766 ATGTTATCTGAATTTTGCAACTTCTG 57.247 30.769 17.37 16.62 0.00 3.02
4274 16894 5.295292 CGCTTCATCATAAGTGGTTTGATCT 59.705 40.000 0.00 0.00 34.12 2.75
4337 17307 4.608269 AGTGATCTCAGAATCTCACCTGA 58.392 43.478 3.65 0.00 39.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.568612 CCCATGTATGTCGATGCCGC 61.569 60.000 0.00 0.00 35.37 6.53
150 151 2.805353 CTGGTCGACGTTGGAGCG 60.805 66.667 9.92 0.00 34.75 5.03
158 159 1.135774 TGATTCGAACTCTGGTCGACG 60.136 52.381 9.92 0.00 35.53 5.12
240 245 1.475034 GCCCATAATCCTCGCTCACAA 60.475 52.381 0.00 0.00 0.00 3.33
556 787 2.094286 AGTGTGTACAGCTGCAGATCTC 60.094 50.000 20.43 4.19 0.00 2.75
723 5052 5.699001 ACGCGCACTAATGAATCCAAATATA 59.301 36.000 5.73 0.00 0.00 0.86
729 5058 1.732941 AACGCGCACTAATGAATCCA 58.267 45.000 5.73 0.00 0.00 3.41
783 5114 0.513820 TAGCTAAAACGCGCGCTTTT 59.486 45.000 32.53 31.35 34.14 2.27
812 5146 4.797471 CAAAGCAATTTGAATCCGAGTCA 58.203 39.130 0.00 0.00 33.95 3.41
1092 5548 0.331278 CCATCAGGGCTGGGTTTACA 59.669 55.000 0.00 0.00 0.00 2.41
1285 5745 1.300697 GGCACGTCGGACTCTTTGT 60.301 57.895 6.57 0.00 0.00 2.83
1308 5768 1.275291 TGGTTCTTGATCACGGAGGAC 59.725 52.381 0.00 0.00 0.00 3.85
1593 6053 1.859427 AACGCCATGCTTGCTGTCTG 61.859 55.000 0.00 0.00 0.00 3.51
1778 6440 3.244735 TGTGTGCATGGTTTAGGAAGCTA 60.245 43.478 0.00 0.00 34.41 3.32
1919 6587 1.467920 AGGTTTTGCTGCCTAGATGC 58.532 50.000 0.00 0.00 32.49 3.91
1920 6588 2.821969 ACAAGGTTTTGCTGCCTAGATG 59.178 45.455 0.00 0.00 37.85 2.90
1922 6590 2.656947 ACAAGGTTTTGCTGCCTAGA 57.343 45.000 0.00 0.00 37.85 2.43
2098 6770 1.962092 TATTTTGCGGCGAGTGCGTC 61.962 55.000 12.98 0.00 44.10 5.19
2120 6792 2.683859 GGGTAGCAAACGGGCGTTC 61.684 63.158 0.00 0.00 37.35 3.95
2405 7080 8.358148 GCCAACAATTTCTCATTCATATCTGAT 58.642 33.333 0.00 0.00 0.00 2.90
2406 7081 7.201848 GGCCAACAATTTCTCATTCATATCTGA 60.202 37.037 0.00 0.00 0.00 3.27
2407 7082 6.921857 GGCCAACAATTTCTCATTCATATCTG 59.078 38.462 0.00 0.00 0.00 2.90
2408 7083 6.837568 AGGCCAACAATTTCTCATTCATATCT 59.162 34.615 5.01 0.00 0.00 1.98
2409 7084 6.921857 CAGGCCAACAATTTCTCATTCATATC 59.078 38.462 5.01 0.00 0.00 1.63
2411 7086 5.951148 TCAGGCCAACAATTTCTCATTCATA 59.049 36.000 5.01 0.00 0.00 2.15
2412 7087 4.773674 TCAGGCCAACAATTTCTCATTCAT 59.226 37.500 5.01 0.00 0.00 2.57
2413 7088 4.151121 TCAGGCCAACAATTTCTCATTCA 58.849 39.130 5.01 0.00 0.00 2.57
2415 7090 5.750352 ATTCAGGCCAACAATTTCTCATT 57.250 34.783 5.01 0.00 0.00 2.57
2418 7093 5.178067 CACAAATTCAGGCCAACAATTTCTC 59.822 40.000 5.01 0.00 29.17 2.87
2419 7094 5.058490 CACAAATTCAGGCCAACAATTTCT 58.942 37.500 5.01 0.00 29.17 2.52
2420 7095 4.319694 GCACAAATTCAGGCCAACAATTTC 60.320 41.667 5.01 0.00 29.17 2.17
2423 7098 2.104451 TGCACAAATTCAGGCCAACAAT 59.896 40.909 5.01 0.00 0.00 2.71
2425 7100 1.068895 CTGCACAAATTCAGGCCAACA 59.931 47.619 5.01 0.00 0.00 3.33
2429 7104 0.108945 GCTCTGCACAAATTCAGGCC 60.109 55.000 0.00 0.00 0.00 5.19
2430 7105 0.599558 TGCTCTGCACAAATTCAGGC 59.400 50.000 0.00 0.00 31.71 4.85
2431 7106 3.587797 AATGCTCTGCACAAATTCAGG 57.412 42.857 0.00 0.00 43.04 3.86
2432 7107 4.552355 TCAAATGCTCTGCACAAATTCAG 58.448 39.130 0.00 0.00 43.04 3.02
2433 7108 4.038282 ACTCAAATGCTCTGCACAAATTCA 59.962 37.500 0.00 0.00 43.04 2.57
2434 7109 4.553323 ACTCAAATGCTCTGCACAAATTC 58.447 39.130 0.00 0.00 43.04 2.17
2436 7111 5.242393 AGTTACTCAAATGCTCTGCACAAAT 59.758 36.000 0.00 0.00 43.04 2.32
2438 7113 4.136796 AGTTACTCAAATGCTCTGCACAA 58.863 39.130 0.00 0.00 43.04 3.33
2439 7114 3.743521 AGTTACTCAAATGCTCTGCACA 58.256 40.909 0.00 0.00 43.04 4.57
2440 7115 4.756084 AAGTTACTCAAATGCTCTGCAC 57.244 40.909 0.00 0.00 43.04 4.57
2441 7116 5.049198 CAGAAAGTTACTCAAATGCTCTGCA 60.049 40.000 0.00 0.00 44.86 4.41
2442 7117 5.049129 ACAGAAAGTTACTCAAATGCTCTGC 60.049 40.000 0.00 0.00 30.97 4.26
2443 7118 6.551385 ACAGAAAGTTACTCAAATGCTCTG 57.449 37.500 0.00 0.00 32.69 3.35
2469 7144 9.565090 AGTCATAGATGCATACAACAAACATAT 57.435 29.630 0.00 0.00 0.00 1.78
2470 7145 8.962884 AGTCATAGATGCATACAACAAACATA 57.037 30.769 0.00 0.00 0.00 2.29
2471 7146 7.870509 AGTCATAGATGCATACAACAAACAT 57.129 32.000 0.00 0.00 0.00 2.71
2472 7147 7.686438 AAGTCATAGATGCATACAACAAACA 57.314 32.000 0.00 0.00 0.00 2.83
2488 7163 9.443283 GCAGCAGAATGTTTTAATAAGTCATAG 57.557 33.333 0.00 0.00 39.31 2.23
2489 7164 9.177608 AGCAGCAGAATGTTTTAATAAGTCATA 57.822 29.630 0.00 0.00 39.31 2.15
2490 7165 8.059798 AGCAGCAGAATGTTTTAATAAGTCAT 57.940 30.769 0.00 0.00 39.31 3.06
2491 7166 7.391554 AGAGCAGCAGAATGTTTTAATAAGTCA 59.608 33.333 0.00 0.00 39.31 3.41
2492 7167 7.756558 AGAGCAGCAGAATGTTTTAATAAGTC 58.243 34.615 0.00 0.00 39.31 3.01
2493 7168 7.693969 AGAGCAGCAGAATGTTTTAATAAGT 57.306 32.000 0.00 0.00 39.31 2.24
2494 7169 8.887717 ACTAGAGCAGCAGAATGTTTTAATAAG 58.112 33.333 0.00 0.00 39.31 1.73
2495 7170 8.792830 ACTAGAGCAGCAGAATGTTTTAATAA 57.207 30.769 0.00 0.00 39.31 1.40
2496 7171 7.222805 CGACTAGAGCAGCAGAATGTTTTAATA 59.777 37.037 0.00 0.00 39.31 0.98
2497 7172 6.036517 CGACTAGAGCAGCAGAATGTTTTAAT 59.963 38.462 0.00 0.00 39.31 1.40
2498 7173 5.348724 CGACTAGAGCAGCAGAATGTTTTAA 59.651 40.000 0.00 0.00 39.31 1.52
2499 7174 4.864806 CGACTAGAGCAGCAGAATGTTTTA 59.135 41.667 0.00 0.00 39.31 1.52
2500 7175 3.681897 CGACTAGAGCAGCAGAATGTTTT 59.318 43.478 0.00 0.00 39.31 2.43
2501 7176 3.257393 CGACTAGAGCAGCAGAATGTTT 58.743 45.455 0.00 0.00 39.31 2.83
2502 7177 2.417924 CCGACTAGAGCAGCAGAATGTT 60.418 50.000 0.00 0.00 39.31 2.71
2503 7178 1.135915 CCGACTAGAGCAGCAGAATGT 59.864 52.381 0.00 0.00 39.31 2.71
2504 7179 1.406898 TCCGACTAGAGCAGCAGAATG 59.593 52.381 0.00 0.00 40.87 2.67
2505 7180 1.769026 TCCGACTAGAGCAGCAGAAT 58.231 50.000 0.00 0.00 0.00 2.40
2506 7181 1.545841 TTCCGACTAGAGCAGCAGAA 58.454 50.000 0.00 0.00 0.00 3.02
2507 7182 1.545841 TTTCCGACTAGAGCAGCAGA 58.454 50.000 0.00 0.00 0.00 4.26
2508 7183 2.266554 CTTTTCCGACTAGAGCAGCAG 58.733 52.381 0.00 0.00 0.00 4.24
2509 7184 1.066858 CCTTTTCCGACTAGAGCAGCA 60.067 52.381 0.00 0.00 0.00 4.41
2510 7185 1.646189 CCTTTTCCGACTAGAGCAGC 58.354 55.000 0.00 0.00 0.00 5.25
2511 7186 1.740718 GCCCTTTTCCGACTAGAGCAG 60.741 57.143 0.00 0.00 0.00 4.24
2512 7187 0.249398 GCCCTTTTCCGACTAGAGCA 59.751 55.000 0.00 0.00 0.00 4.26
2513 7188 0.806492 CGCCCTTTTCCGACTAGAGC 60.806 60.000 0.00 0.00 0.00 4.09
2514 7189 0.531200 ACGCCCTTTTCCGACTAGAG 59.469 55.000 0.00 0.00 0.00 2.43
2515 7190 0.245539 CACGCCCTTTTCCGACTAGA 59.754 55.000 0.00 0.00 0.00 2.43
2516 7191 0.037605 ACACGCCCTTTTCCGACTAG 60.038 55.000 0.00 0.00 0.00 2.57
2517 7192 1.067635 GTACACGCCCTTTTCCGACTA 60.068 52.381 0.00 0.00 0.00 2.59
2518 7193 0.320160 GTACACGCCCTTTTCCGACT 60.320 55.000 0.00 0.00 0.00 4.18
2519 7194 0.320160 AGTACACGCCCTTTTCCGAC 60.320 55.000 0.00 0.00 0.00 4.79
2520 7195 0.320073 CAGTACACGCCCTTTTCCGA 60.320 55.000 0.00 0.00 0.00 4.55
2521 7196 0.320073 TCAGTACACGCCCTTTTCCG 60.320 55.000 0.00 0.00 0.00 4.30
2522 7197 1.439679 CTCAGTACACGCCCTTTTCC 58.560 55.000 0.00 0.00 0.00 3.13
2523 7198 1.439679 CCTCAGTACACGCCCTTTTC 58.560 55.000 0.00 0.00 0.00 2.29
2524 7199 0.605589 GCCTCAGTACACGCCCTTTT 60.606 55.000 0.00 0.00 0.00 2.27
2525 7200 1.003718 GCCTCAGTACACGCCCTTT 60.004 57.895 0.00 0.00 0.00 3.11
2526 7201 2.214216 TGCCTCAGTACACGCCCTT 61.214 57.895 0.00 0.00 0.00 3.95
2527 7202 2.603473 TGCCTCAGTACACGCCCT 60.603 61.111 0.00 0.00 0.00 5.19
2528 7203 2.434359 GTGCCTCAGTACACGCCC 60.434 66.667 0.00 0.00 0.00 6.13
2529 7204 2.434359 GGTGCCTCAGTACACGCC 60.434 66.667 0.00 0.00 37.68 5.68
2530 7205 2.558554 ATCGGTGCCTCAGTACACGC 62.559 60.000 0.00 0.00 37.68 5.34
2531 7206 0.525668 GATCGGTGCCTCAGTACACG 60.526 60.000 0.00 0.00 37.68 4.49
2532 7207 0.179108 GGATCGGTGCCTCAGTACAC 60.179 60.000 0.00 0.00 36.03 2.90
2533 7208 0.613572 TGGATCGGTGCCTCAGTACA 60.614 55.000 0.00 0.00 0.00 2.90
2534 7209 0.535335 TTGGATCGGTGCCTCAGTAC 59.465 55.000 0.00 0.00 0.00 2.73
2535 7210 1.496060 ATTGGATCGGTGCCTCAGTA 58.504 50.000 0.00 0.00 0.00 2.74
2536 7211 1.414181 CTATTGGATCGGTGCCTCAGT 59.586 52.381 0.00 0.00 0.00 3.41
2537 7212 1.688735 TCTATTGGATCGGTGCCTCAG 59.311 52.381 0.00 0.00 0.00 3.35
2538 7213 1.788229 TCTATTGGATCGGTGCCTCA 58.212 50.000 0.00 0.00 0.00 3.86
2539 7214 2.103263 AGTTCTATTGGATCGGTGCCTC 59.897 50.000 0.00 0.00 0.00 4.70
2540 7215 2.103263 GAGTTCTATTGGATCGGTGCCT 59.897 50.000 0.00 0.00 0.00 4.75
2541 7216 2.158957 TGAGTTCTATTGGATCGGTGCC 60.159 50.000 0.00 0.00 0.00 5.01
2542 7217 3.126831 CTGAGTTCTATTGGATCGGTGC 58.873 50.000 0.00 0.00 0.00 5.01
2543 7218 3.126831 GCTGAGTTCTATTGGATCGGTG 58.873 50.000 0.00 0.00 0.00 4.94
2544 7219 3.034635 AGCTGAGTTCTATTGGATCGGT 58.965 45.455 0.00 0.00 0.00 4.69
2545 7220 3.320541 AGAGCTGAGTTCTATTGGATCGG 59.679 47.826 0.00 0.00 0.00 4.18
2546 7221 4.037327 TCAGAGCTGAGTTCTATTGGATCG 59.963 45.833 0.00 0.00 34.14 3.69
2547 7222 5.528043 TCAGAGCTGAGTTCTATTGGATC 57.472 43.478 0.00 0.00 34.14 3.36
2548 7223 6.497624 AATCAGAGCTGAGTTCTATTGGAT 57.502 37.500 0.00 0.00 43.61 3.41
2549 7224 5.946942 AATCAGAGCTGAGTTCTATTGGA 57.053 39.130 0.00 0.00 43.61 3.53
2558 7233 6.543430 AGTATTGAGAAATCAGAGCTGAGT 57.457 37.500 6.34 0.16 43.61 3.41
2559 7234 7.040494 TGAAGTATTGAGAAATCAGAGCTGAG 58.960 38.462 6.34 0.00 43.61 3.35
2560 7235 6.939622 TGAAGTATTGAGAAATCAGAGCTGA 58.060 36.000 2.23 2.23 44.59 4.26
2561 7236 7.789273 ATGAAGTATTGAGAAATCAGAGCTG 57.211 36.000 0.00 0.00 0.00 4.24
2562 7237 8.675504 CAAATGAAGTATTGAGAAATCAGAGCT 58.324 33.333 0.00 0.00 0.00 4.09
2563 7238 8.671921 TCAAATGAAGTATTGAGAAATCAGAGC 58.328 33.333 0.00 0.00 32.14 4.09
2574 7249 7.439157 CTTCACCACTCAAATGAAGTATTGA 57.561 36.000 5.28 0.00 42.82 2.57
2581 7256 3.286353 TGTGCTTCACCACTCAAATGAA 58.714 40.909 0.00 0.00 36.68 2.57
2582 7257 2.880268 CTGTGCTTCACCACTCAAATGA 59.120 45.455 0.00 0.00 36.68 2.57
2583 7258 2.880268 TCTGTGCTTCACCACTCAAATG 59.120 45.455 0.00 0.00 36.68 2.32
2584 7259 3.213206 TCTGTGCTTCACCACTCAAAT 57.787 42.857 0.00 0.00 36.68 2.32
2585 7260 2.682856 GTTCTGTGCTTCACCACTCAAA 59.317 45.455 0.00 0.00 36.68 2.69
2586 7261 2.288666 GTTCTGTGCTTCACCACTCAA 58.711 47.619 0.00 0.00 36.68 3.02
2587 7262 1.475034 GGTTCTGTGCTTCACCACTCA 60.475 52.381 0.00 0.00 36.68 3.41
2588 7263 1.230324 GGTTCTGTGCTTCACCACTC 58.770 55.000 0.00 0.00 36.68 3.51
2589 7264 0.546122 TGGTTCTGTGCTTCACCACT 59.454 50.000 0.00 0.00 36.68 4.00
2590 7265 1.267806 CATGGTTCTGTGCTTCACCAC 59.732 52.381 0.00 0.00 32.73 4.16
2591 7266 1.133823 ACATGGTTCTGTGCTTCACCA 60.134 47.619 0.00 0.00 32.73 4.17
2592 7267 1.609208 ACATGGTTCTGTGCTTCACC 58.391 50.000 0.00 0.00 32.73 4.02
2593 7268 3.715628 AAACATGGTTCTGTGCTTCAC 57.284 42.857 0.00 0.00 34.56 3.18
2594 7269 4.159321 TCAAAAACATGGTTCTGTGCTTCA 59.841 37.500 0.00 0.00 0.00 3.02
2595 7270 4.504097 GTCAAAAACATGGTTCTGTGCTTC 59.496 41.667 0.00 0.00 0.00 3.86
2596 7271 4.081752 TGTCAAAAACATGGTTCTGTGCTT 60.082 37.500 0.00 0.00 31.20 3.91
2597 7272 3.446873 TGTCAAAAACATGGTTCTGTGCT 59.553 39.130 0.00 0.00 31.20 4.40
2598 7273 3.779759 TGTCAAAAACATGGTTCTGTGC 58.220 40.909 0.00 0.00 31.20 4.57
2599 7274 4.997565 ACTGTCAAAAACATGGTTCTGTG 58.002 39.130 0.00 0.00 37.23 3.66
2600 7275 5.659440 AACTGTCAAAAACATGGTTCTGT 57.341 34.783 0.00 0.00 37.23 3.41
2601 7276 7.169645 CCATTAACTGTCAAAAACATGGTTCTG 59.830 37.037 0.00 0.00 37.23 3.02
2602 7277 7.147742 ACCATTAACTGTCAAAAACATGGTTCT 60.148 33.333 0.00 0.00 41.39 3.01
2603 7278 6.983890 ACCATTAACTGTCAAAAACATGGTTC 59.016 34.615 0.00 0.00 41.39 3.62
2604 7279 6.883744 ACCATTAACTGTCAAAAACATGGTT 58.116 32.000 0.00 0.00 41.39 3.67
2605 7280 6.478512 ACCATTAACTGTCAAAAACATGGT 57.521 33.333 0.00 0.00 40.05 3.55
2606 7281 8.356657 TCTAACCATTAACTGTCAAAAACATGG 58.643 33.333 0.00 0.00 38.47 3.66
2607 7282 9.743057 TTCTAACCATTAACTGTCAAAAACATG 57.257 29.630 0.00 0.00 37.23 3.21
2608 7283 9.965824 CTTCTAACCATTAACTGTCAAAAACAT 57.034 29.630 0.00 0.00 37.23 2.71
2609 7284 9.179909 TCTTCTAACCATTAACTGTCAAAAACA 57.820 29.630 0.00 0.00 36.18 2.83
2638 7313 7.719193 TCAGATCACAGTATCTCAAACCAAAAA 59.281 33.333 0.00 0.00 33.87 1.94
2639 7314 7.223584 TCAGATCACAGTATCTCAAACCAAAA 58.776 34.615 0.00 0.00 33.87 2.44
2640 7315 6.768483 TCAGATCACAGTATCTCAAACCAAA 58.232 36.000 0.00 0.00 33.87 3.28
2641 7316 6.358974 TCAGATCACAGTATCTCAAACCAA 57.641 37.500 0.00 0.00 33.87 3.67
2642 7317 6.358974 TTCAGATCACAGTATCTCAAACCA 57.641 37.500 0.00 0.00 33.87 3.67
2643 7318 7.856145 AATTCAGATCACAGTATCTCAAACC 57.144 36.000 0.00 0.00 33.87 3.27
2644 7319 8.725148 ACAAATTCAGATCACAGTATCTCAAAC 58.275 33.333 0.00 0.00 33.87 2.93
2645 7320 8.853077 ACAAATTCAGATCACAGTATCTCAAA 57.147 30.769 0.00 0.00 33.87 2.69
2646 7321 8.724229 CAACAAATTCAGATCACAGTATCTCAA 58.276 33.333 0.00 0.00 33.87 3.02
2647 7322 7.335171 CCAACAAATTCAGATCACAGTATCTCA 59.665 37.037 0.00 0.00 33.87 3.27
2648 7323 7.678218 GCCAACAAATTCAGATCACAGTATCTC 60.678 40.741 0.00 0.00 33.87 2.75
2649 7324 6.094603 GCCAACAAATTCAGATCACAGTATCT 59.905 38.462 0.00 0.00 36.64 1.98
2650 7325 6.261118 GCCAACAAATTCAGATCACAGTATC 58.739 40.000 0.00 0.00 0.00 2.24
2651 7326 5.126061 GGCCAACAAATTCAGATCACAGTAT 59.874 40.000 0.00 0.00 0.00 2.12
2652 7327 4.458989 GGCCAACAAATTCAGATCACAGTA 59.541 41.667 0.00 0.00 0.00 2.74
2653 7328 3.256631 GGCCAACAAATTCAGATCACAGT 59.743 43.478 0.00 0.00 0.00 3.55
2654 7329 3.508793 AGGCCAACAAATTCAGATCACAG 59.491 43.478 5.01 0.00 0.00 3.66
2655 7330 3.256383 CAGGCCAACAAATTCAGATCACA 59.744 43.478 5.01 0.00 0.00 3.58
2656 7331 3.507233 TCAGGCCAACAAATTCAGATCAC 59.493 43.478 5.01 0.00 0.00 3.06
2657 7332 3.765381 TCAGGCCAACAAATTCAGATCA 58.235 40.909 5.01 0.00 0.00 2.92
2658 7333 4.789012 TTCAGGCCAACAAATTCAGATC 57.211 40.909 5.01 0.00 0.00 2.75
2659 7334 5.021458 AGATTCAGGCCAACAAATTCAGAT 58.979 37.500 5.01 0.00 0.00 2.90
2660 7335 4.219070 CAGATTCAGGCCAACAAATTCAGA 59.781 41.667 5.01 0.00 0.00 3.27
2661 7336 4.021719 ACAGATTCAGGCCAACAAATTCAG 60.022 41.667 5.01 0.00 0.00 3.02
2662 7337 3.896888 ACAGATTCAGGCCAACAAATTCA 59.103 39.130 5.01 0.00 0.00 2.57
2663 7338 4.240096 CACAGATTCAGGCCAACAAATTC 58.760 43.478 5.01 0.00 0.00 2.17
2664 7339 3.555586 GCACAGATTCAGGCCAACAAATT 60.556 43.478 5.01 0.00 0.00 1.82
2665 7340 2.028748 GCACAGATTCAGGCCAACAAAT 60.029 45.455 5.01 0.00 0.00 2.32
2666 7341 1.340889 GCACAGATTCAGGCCAACAAA 59.659 47.619 5.01 0.00 0.00 2.83
2667 7342 0.961019 GCACAGATTCAGGCCAACAA 59.039 50.000 5.01 0.00 0.00 2.83
2668 7343 0.178995 TGCACAGATTCAGGCCAACA 60.179 50.000 5.01 0.00 0.00 3.33
2924 7859 1.094785 GCTTCACCAACACACACACT 58.905 50.000 0.00 0.00 0.00 3.55
2977 8393 6.969366 TGAAATTGATCACACTACAACTTGG 58.031 36.000 0.00 0.00 0.00 3.61
3293 9058 5.045359 ACATCAGAGAACATTCCAGATCCAA 60.045 40.000 0.00 0.00 0.00 3.53
3381 9146 2.490217 CCGTCGACGAGCCATCTT 59.510 61.111 37.65 0.00 43.02 2.40
3437 9202 0.614697 TCCTCTGCTTCGATCACCCA 60.615 55.000 0.00 0.00 0.00 4.51
3817 10474 7.745717 TCTGTTCTTCTCCAGGAAAATAGAAA 58.254 34.615 0.00 0.00 33.07 2.52
3996 10796 7.108847 ACATATCTGTTCTTCTCCAGGAAAAG 58.891 38.462 0.00 0.00 29.66 2.27
4041 11422 7.640616 TGTGACAAATAAATTCTGCATTGTG 57.359 32.000 2.96 0.00 31.68 3.33
4193 11812 8.496707 ACTGAATGAAATTTGCAGAAGTTTTT 57.503 26.923 0.00 0.00 36.07 1.94
4194 11813 9.034544 GTACTGAATGAAATTTGCAGAAGTTTT 57.965 29.630 0.00 0.00 36.07 2.43
4195 11814 8.196771 TGTACTGAATGAAATTTGCAGAAGTTT 58.803 29.630 0.00 0.00 36.07 2.66


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

AutoCloner maintained by Alex Coulton.