Multiple sequence alignment - TraesCS2B01G285200

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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 TraesCS2B01G285200 chr2B 100.000 3663 0 0 1 3663 392890921 392894583 0.000000e+00 6765.0
1 TraesCS2B01G285200 chr2B 100.000 1929 0 0 3972 5900 392894892 392896820 0.000000e+00 3563.0
2 TraesCS2B01G285200 chr2B 84.637 358 42 9 445 791 165105121 165105476 1.570000e-90 344.0
3 TraesCS2B01G285200 chr2B 100.000 78 0 0 5284 5361 392896281 392896204 1.710000e-30 145.0
4 TraesCS2B01G285200 chr2B 97.561 82 1 1 5283 5363 38398898 38398979 7.970000e-29 139.0
5 TraesCS2B01G285200 chr2B 97.468 79 1 1 5284 5361 38398977 38398899 3.710000e-27 134.0
6 TraesCS2B01G285200 chr2A 97.160 2113 42 8 810 2908 394625299 394623191 0.000000e+00 3554.0
7 TraesCS2B01G285200 chr2A 94.674 1333 35 15 3988 5285 394621738 394620407 0.000000e+00 2036.0
8 TraesCS2B01G285200 chr2A 96.960 329 8 1 2905 3231 394622788 394622460 8.640000e-153 551.0
9 TraesCS2B01G285200 chr2A 95.860 314 9 3 5360 5671 394620408 394620097 6.820000e-139 505.0
10 TraesCS2B01G285200 chr2A 96.947 262 5 2 3290 3548 394622460 394622199 2.520000e-118 436.0
11 TraesCS2B01G285200 chr2A 93.976 83 1 1 5284 5362 745051963 745051881 8.030000e-24 122.0
12 TraesCS2B01G285200 chr2A 93.902 82 1 1 5284 5361 745051882 745051963 2.890000e-23 121.0
13 TraesCS2B01G285200 chr2A 100.000 45 0 0 3596 3640 394622199 394622155 3.790000e-12 84.2
14 TraesCS2B01G285200 chr2D 93.992 1215 46 13 3973 5161 324218599 324219812 0.000000e+00 1814.0
15 TraesCS2B01G285200 chr2D 93.922 1201 60 6 1717 2908 324216095 324217291 0.000000e+00 1801.0
16 TraesCS2B01G285200 chr2D 96.752 739 18 4 2905 3640 324217686 324218421 0.000000e+00 1227.0
17 TraesCS2B01G285200 chr2D 95.155 516 22 3 1150 1664 324215581 324216094 0.000000e+00 811.0
18 TraesCS2B01G285200 chr2D 95.806 310 10 3 805 1111 324214932 324215241 1.140000e-136 497.0
19 TraesCS2B01G285200 chr2D 94.969 318 7 6 5360 5671 324219901 324220215 1.910000e-134 490.0
20 TraesCS2B01G285200 chr2D 91.416 233 19 1 32 263 645180996 645181228 9.540000e-83 318.0
21 TraesCS2B01G285200 chr2D 91.342 231 17 2 36 263 179332193 179332423 4.440000e-81 313.0
22 TraesCS2B01G285200 chr2D 83.429 350 33 9 446 787 512899368 512899700 9.610000e-78 302.0
23 TraesCS2B01G285200 chr2D 91.919 198 14 2 257 453 407055971 407055775 5.820000e-70 276.0
24 TraesCS2B01G285200 chr2D 88.764 178 13 5 5694 5866 200810105 200810280 1.670000e-50 211.0
25 TraesCS2B01G285200 chr2D 94.444 90 5 0 5196 5285 324219813 324219902 7.970000e-29 139.0
26 TraesCS2B01G285200 chr2D 88.525 61 6 1 5264 5323 649832170 649832230 8.200000e-09 73.1
27 TraesCS2B01G285200 chr2D 92.500 40 2 1 1 40 324212343 324212381 8.260000e-04 56.5
28 TraesCS2B01G285200 chr7B 89.744 351 30 4 445 790 52612447 52612098 1.510000e-120 444.0
29 TraesCS2B01G285200 chr7B 92.766 235 15 2 30 263 52612674 52612441 7.320000e-89 339.0
30 TraesCS2B01G285200 chr7B 92.174 230 15 3 35 262 31828191 31828419 7.380000e-84 322.0
31 TraesCS2B01G285200 chr7B 87.006 177 16 6 5695 5866 638739581 638739407 6.030000e-45 193.0
32 TraesCS2B01G285200 chr7B 97.917 48 1 0 5276 5323 133486962 133487009 3.790000e-12 84.2
33 TraesCS2B01G285200 chr7B 100.000 44 0 0 5280 5323 2327883 2327840 1.360000e-11 82.4
34 TraesCS2B01G285200 chr7B 97.872 47 1 0 5277 5323 369812160 369812114 1.360000e-11 82.4
35 TraesCS2B01G285200 chr7B 78.302 106 19 4 3539 3642 511320707 511320604 1.370000e-06 65.8
36 TraesCS2B01G285200 chr5A 84.840 343 41 6 456 787 584908428 584908770 9.470000e-88 335.0
37 TraesCS2B01G285200 chr5A 81.714 350 40 10 445 787 588558999 588559331 2.710000e-68 270.0
38 TraesCS2B01G285200 chr5A 95.062 81 3 1 5281 5361 676482246 676482167 6.210000e-25 126.0
39 TraesCS2B01G285200 chr5A 95.000 80 3 1 5282 5361 676482165 676482243 2.230000e-24 124.0
40 TraesCS2B01G285200 chr6B 91.845 233 17 2 32 263 474271442 474271211 2.050000e-84 324.0
41 TraesCS2B01G285200 chr6B 82.571 350 50 8 447 787 671882721 671882374 1.240000e-76 298.0
42 TraesCS2B01G285200 chr6B 85.311 177 19 6 5695 5866 81024223 81024397 6.080000e-40 176.0
43 TraesCS2B01G285200 chr6B 79.651 172 33 1 3470 3639 245994811 245994640 8.030000e-24 122.0
44 TraesCS2B01G285200 chr6B 100.000 45 0 0 5277 5321 52974438 52974394 3.790000e-12 84.2
45 TraesCS2B01G285200 chr6B 97.872 47 1 0 5277 5323 81012010 81012056 1.360000e-11 82.4
46 TraesCS2B01G285200 chr6B 83.146 89 10 3 5282 5366 46785203 46785116 6.340000e-10 76.8
47 TraesCS2B01G285200 chr1D 92.889 225 12 2 2927 3147 111058332 111058108 2.050000e-84 324.0
48 TraesCS2B01G285200 chr1D 82.857 350 33 12 448 787 476186581 476186913 7.480000e-74 289.0
49 TraesCS2B01G285200 chr1D 92.308 195 13 2 257 450 196243268 196243075 5.820000e-70 276.0
50 TraesCS2B01G285200 chr1D 92.308 195 13 2 257 450 329936827 329937020 5.820000e-70 276.0
51 TraesCS2B01G285200 chr1D 92.347 196 12 3 257 450 453019313 453019119 5.820000e-70 276.0
52 TraesCS2B01G285200 chr1D 93.421 152 7 2 3149 3299 111057951 111058100 7.700000e-54 222.0
53 TraesCS2B01G285200 chr1D 84.091 176 22 5 5695 5866 15877018 15877191 1.320000e-36 165.0
54 TraesCS2B01G285200 chr1D 83.333 108 11 6 5695 5799 222133263 222133366 6.300000e-15 93.5
55 TraesCS2B01G285200 chr1D 79.562 137 15 8 5741 5866 330535497 330535631 1.050000e-12 86.1
56 TraesCS2B01G285200 chr1D 95.918 49 1 1 5322 5370 178459599 178459646 1.760000e-10 78.7
57 TraesCS2B01G285200 chr1D 100.000 42 0 0 5280 5321 393087773 393087814 1.760000e-10 78.7
58 TraesCS2B01G285200 chr1D 94.231 52 2 1 5322 5373 443556635 443556685 1.760000e-10 78.7
59 TraesCS2B01G285200 chr1D 97.727 44 1 0 5280 5323 202557762 202557805 6.340000e-10 76.8
60 TraesCS2B01G285200 chr1D 97.727 44 1 0 5280 5323 435727302 435727259 6.340000e-10 76.8
61 TraesCS2B01G285200 chr1D 97.727 44 1 0 5280 5323 476873684 476873641 6.340000e-10 76.8
62 TraesCS2B01G285200 chr1D 94.000 50 1 2 5275 5323 488630180 488630228 2.280000e-09 75.0
63 TraesCS2B01G285200 chr1B 91.525 236 18 2 30 263 161207929 161207694 2.050000e-84 324.0
64 TraesCS2B01G285200 chr1B 91.139 237 17 4 32 266 58031151 58030917 9.540000e-83 318.0
65 TraesCS2B01G285200 chr1B 92.444 225 13 2 2927 3147 169678919 169678695 9.540000e-83 318.0
66 TraesCS2B01G285200 chr1B 93.919 148 6 2 3153 3299 169678542 169678687 2.770000e-53 220.0
67 TraesCS2B01G285200 chr1B 87.079 178 15 5 5695 5866 650478638 650478813 1.680000e-45 195.0
68 TraesCS2B01G285200 chr1B 81.356 177 26 4 5695 5866 609542358 609542184 2.870000e-28 137.0
69 TraesCS2B01G285200 chr1B 97.500 80 1 1 5284 5362 687182003 687182082 1.030000e-27 135.0
70 TraesCS2B01G285200 chr1B 95.294 85 3 1 5284 5367 687182081 687181997 3.710000e-27 134.0
71 TraesCS2B01G285200 chr1B 96.000 50 1 1 5322 5371 424541595 424541547 4.900000e-11 80.5
72 TraesCS2B01G285200 chr1B 95.918 49 1 1 5276 5323 616902651 616902603 1.760000e-10 78.7
73 TraesCS2B01G285200 chr1B 89.655 58 4 2 5322 5379 563743758 563743703 8.200000e-09 73.1
74 TraesCS2B01G285200 chr7A 91.416 233 19 1 33 264 621858771 621858539 9.540000e-83 318.0
75 TraesCS2B01G285200 chr7A 87.571 177 15 4 5695 5866 421717 421891 1.300000e-46 198.0
76 TraesCS2B01G285200 chr7A 96.078 51 0 2 5322 5371 463711447 463711496 1.360000e-11 82.4
77 TraesCS2B01G285200 chr1A 92.444 225 13 2 2927 3147 117238566 117238342 9.540000e-83 318.0
78 TraesCS2B01G285200 chr1A 83.239 352 34 11 445 787 292338223 292338558 3.460000e-77 300.0
79 TraesCS2B01G285200 chr1A 92.308 195 13 2 257 450 203453979 203454172 5.820000e-70 276.0
80 TraesCS2B01G285200 chr1A 92.308 195 13 2 257 450 382831022 382831215 5.820000e-70 276.0
81 TraesCS2B01G285200 chr1A 92.105 152 9 2 3149 3299 117238185 117238334 1.670000e-50 211.0
82 TraesCS2B01G285200 chr1A 84.483 174 23 3 5695 5866 557939505 557939334 1.020000e-37 169.0
83 TraesCS2B01G285200 chr1A 83.146 178 21 6 5695 5866 311035525 311035699 2.850000e-33 154.0
84 TraesCS2B01G285200 chr1A 85.185 81 10 2 5284 5362 566369574 566369494 1.360000e-11 82.4
85 TraesCS2B01G285200 chr1A 85.000 80 10 2 5284 5361 566369495 566369574 4.900000e-11 80.5
86 TraesCS2B01G285200 chr7D 91.304 230 20 0 34 263 82897574 82897803 1.230000e-81 315.0
87 TraesCS2B01G285200 chr7D 81.562 320 34 11 446 758 58892255 58892556 2.120000e-59 241.0
88 TraesCS2B01G285200 chr7D 86.441 177 17 4 5695 5866 432329209 432329383 2.810000e-43 187.0
89 TraesCS2B01G285200 chr7D 85.057 174 19 5 5695 5863 550842908 550843079 2.830000e-38 171.0
90 TraesCS2B01G285200 chr7D 84.181 177 21 5 5695 5866 535881145 535881319 1.320000e-36 165.0
91 TraesCS2B01G285200 chrUn 83.668 349 34 6 446 787 96376167 96376499 2.070000e-79 307.0
92 TraesCS2B01G285200 chrUn 82.963 135 17 4 5720 5850 88769616 88769484 3.740000e-22 117.0
93 TraesCS2B01G285200 chrUn 93.939 66 3 1 5284 5348 23532803 23532738 1.350000e-16 99.0
94 TraesCS2B01G285200 chrUn 93.939 66 3 1 5297 5361 23532738 23532803 1.350000e-16 99.0
95 TraesCS2B01G285200 chrUn 97.917 48 0 1 5322 5369 295724574 295724620 1.360000e-11 82.4
96 TraesCS2B01G285200 chrUn 97.917 48 0 1 5322 5369 295739998 295740044 1.360000e-11 82.4
97 TraesCS2B01G285200 chrUn 100.000 43 0 0 5322 5364 38663373 38663415 4.900000e-11 80.5
98 TraesCS2B01G285200 chrUn 94.231 52 1 2 5322 5372 16475875 16475825 1.760000e-10 78.7
99 TraesCS2B01G285200 chrUn 97.778 45 1 0 5324 5368 16890363 16890319 1.760000e-10 78.7
100 TraesCS2B01G285200 chrUn 100.000 41 0 0 5322 5362 1522157 1522117 6.340000e-10 76.8
101 TraesCS2B01G285200 chrUn 100.000 41 0 0 5283 5323 15779346 15779306 6.340000e-10 76.8
102 TraesCS2B01G285200 chrUn 100.000 41 0 0 5283 5323 21302363 21302403 6.340000e-10 76.8
103 TraesCS2B01G285200 chrUn 97.727 44 1 0 5280 5323 34537825 34537868 6.340000e-10 76.8
104 TraesCS2B01G285200 chrUn 100.000 41 0 0 5283 5323 40739404 40739444 6.340000e-10 76.8
105 TraesCS2B01G285200 chrUn 100.000 41 0 0 5283 5323 40748501 40748461 6.340000e-10 76.8
106 TraesCS2B01G285200 chrUn 100.000 41 0 0 5322 5362 57135407 57135447 6.340000e-10 76.8
107 TraesCS2B01G285200 chrUn 100.000 41 0 0 5283 5323 58368699 58368659 6.340000e-10 76.8
108 TraesCS2B01G285200 chrUn 97.727 44 1 0 5280 5323 85071885 85071842 6.340000e-10 76.8
109 TraesCS2B01G285200 chrUn 100.000 41 0 0 5322 5362 88207937 88207977 6.340000e-10 76.8
110 TraesCS2B01G285200 chrUn 100.000 41 0 0 5283 5323 303398958 303398998 6.340000e-10 76.8
111 TraesCS2B01G285200 chrUn 95.652 46 2 0 5278 5323 16475830 16475875 2.280000e-09 75.0
112 TraesCS2B01G285200 chrUn 93.878 49 2 1 5322 5370 63184969 63184922 8.200000e-09 73.1
113 TraesCS2B01G285200 chrUn 95.652 46 1 1 5322 5367 304504565 304504521 8.200000e-09 73.1
114 TraesCS2B01G285200 chrUn 93.750 48 2 1 5322 5369 79618460 79618506 2.950000e-08 71.3
115 TraesCS2B01G285200 chr6D 82.849 344 32 13 454 787 141270076 141269750 3.480000e-72 283.0
116 TraesCS2B01G285200 chr6D 92.347 196 12 3 257 450 330383434 330383628 5.820000e-70 276.0
117 TraesCS2B01G285200 chr6D 85.311 177 18 6 5695 5866 384304995 384305168 6.080000e-40 176.0
118 TraesCS2B01G285200 chr6D 83.523 176 22 4 5695 5865 96645519 96645346 2.200000e-34 158.0
119 TraesCS2B01G285200 chr6D 83.654 104 10 6 5695 5795 175464875 175464974 2.260000e-14 91.6
120 TraesCS2B01G285200 chr6D 96.000 50 1 1 5322 5371 2680681 2680729 4.900000e-11 80.5
121 TraesCS2B01G285200 chr6D 100.000 42 0 0 5321 5362 334619597 334619556 1.760000e-10 78.7
122 TraesCS2B01G285200 chr6D 97.727 44 1 0 5281 5324 334619554 334619597 6.340000e-10 76.8
123 TraesCS2B01G285200 chr5D 92.386 197 12 3 257 451 116080515 116080320 1.620000e-70 278.0
124 TraesCS2B01G285200 chr5D 86.441 177 17 4 5695 5866 69208904 69209078 2.810000e-43 187.0
125 TraesCS2B01G285200 chr5D 86.441 177 17 5 5695 5866 242568902 242569076 2.810000e-43 187.0
126 TraesCS2B01G285200 chr5D 85.955 178 15 7 5695 5866 51924098 51923925 1.310000e-41 182.0
127 TraesCS2B01G285200 chr4D 92.308 195 13 2 257 450 327196956 327197149 5.820000e-70 276.0
128 TraesCS2B01G285200 chr4D 80.737 353 42 12 445 787 419487875 419488211 9.820000e-63 252.0
129 TraesCS2B01G285200 chr4D 87.200 125 11 4 5695 5817 113186864 113186985 2.870000e-28 137.0
130 TraesCS2B01G285200 chr4D 80.503 159 19 8 5695 5847 141657909 141658061 1.740000e-20 111.0
131 TraesCS2B01G285200 chr4D 100.000 43 0 0 5280 5322 300788867 300788909 4.900000e-11 80.5
132 TraesCS2B01G285200 chr4D 100.000 43 0 0 5281 5323 441684691 441684649 4.900000e-11 80.5
133 TraesCS2B01G285200 chr4D 100.000 42 0 0 5282 5323 31651037 31650996 1.760000e-10 78.7
134 TraesCS2B01G285200 chr4D 95.918 49 1 1 5322 5370 127555029 127554982 1.760000e-10 78.7
135 TraesCS2B01G285200 chr4D 95.918 49 1 1 5322 5370 138278331 138278284 1.760000e-10 78.7
136 TraesCS2B01G285200 chr3B 81.250 352 40 12 446 787 5185894 5185559 1.630000e-65 261.0
137 TraesCS2B01G285200 chr3B 80.966 352 41 13 446 787 3650466 3650801 7.590000e-64 255.0
138 TraesCS2B01G285200 chr3B 87.571 177 15 4 5695 5866 112951803 112951629 1.300000e-46 198.0
139 TraesCS2B01G285200 chr3B 90.698 86 5 2 5283 5366 321594143 321594227 1.740000e-20 111.0
140 TraesCS2B01G285200 chr3B 91.250 80 5 1 5284 5361 321594223 321594144 2.250000e-19 108.0
141 TraesCS2B01G285200 chr6A 87.222 180 18 3 5695 5869 614841173 614840994 3.610000e-47 200.0
142 TraesCS2B01G285200 chr5B 86.441 177 17 4 5695 5866 477556970 477556796 2.810000e-43 187.0
143 TraesCS2B01G285200 chr4B 84.746 177 19 6 5695 5866 399752611 399752784 2.830000e-38 171.0
144 TraesCS2B01G285200 chr4B 81.215 181 26 5 5695 5869 657261284 657261462 7.970000e-29 139.0
145 TraesCS2B01G285200 chr4B 100.000 44 0 0 5280 5323 399269620 399269663 1.360000e-11 82.4
146 TraesCS2B01G285200 chr4B 100.000 43 0 0 5281 5323 85730853 85730895 4.900000e-11 80.5
147 TraesCS2B01G285200 chr4B 97.826 46 1 0 5276 5321 131706966 131706921 4.900000e-11 80.5
148 TraesCS2B01G285200 chr4B 95.918 49 2 0 5275 5323 300811313 300811361 4.900000e-11 80.5
149 TraesCS2B01G285200 chr4B 97.872 47 0 1 5322 5368 660670729 660670774 4.900000e-11 80.5
150 TraesCS2B01G285200 chr4B 97.778 45 1 0 5279 5323 413734313 413734269 1.760000e-10 78.7
151 TraesCS2B01G285200 chr4B 97.778 45 1 0 5277 5321 653214425 653214381 1.760000e-10 78.7
152 TraesCS2B01G285200 chr4B 85.294 68 9 1 3475 3541 498379994 498380061 1.060000e-07 69.4
153 TraesCS2B01G285200 chr3A 86.047 86 8 3 5280 5361 174623377 174623292 8.140000e-14 89.8
154 TraesCS2B01G285200 chr3A 86.585 82 7 3 5284 5361 174623292 174623373 2.930000e-13 87.9
155 TraesCS2B01G285200 chr3A 85.185 81 10 2 5282 5362 394454953 394454875 1.360000e-11 82.4
156 TraesCS2B01G285200 chr3A 77.778 108 18 6 3539 3643 550647866 550647762 1.780000e-05 62.1
157 TraesCS2B01G285200 chr4A 87.500 56 7 0 3475 3530 60022936 60022991 1.370000e-06 65.8
158 TraesCS2B01G285200 chr3D 77.778 108 17 7 3539 3643 104793217 104793320 6.390000e-05 60.2


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 TraesCS2B01G285200 chr2B 392890921 392896820 5899 False 5164.000000 6765 100.0000 1 5900 2 chr2B.!!$F3 5899
1 TraesCS2B01G285200 chr2A 394620097 394625299 5202 True 1194.366667 3554 96.9335 810 5671 6 chr2A.!!$R2 4861
2 TraesCS2B01G285200 chr2D 324212343 324220215 7872 False 854.437500 1814 94.6925 1 5671 8 chr2D.!!$F6 5670
3 TraesCS2B01G285200 chr7B 52612098 52612674 576 True 391.500000 444 91.2550 30 790 2 chr7B.!!$R5 760

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
787 2848 0.101939 GCATGAGCCCTTTTGCTAGC 59.898 55.000 8.10 8.10 42.95 3.42 F
792 2853 0.405585 AGCCCTTTTGCTAGCAAGGA 59.594 50.000 29.48 21.15 42.11 3.36 F
1608 3984 1.108776 ATGCCAGCAATTGCACCTAG 58.891 50.000 30.89 15.34 45.16 3.02 F
1627 4003 5.222048 ACCTAGGAACCTTAGATTTTGTGCA 60.222 40.000 17.98 0.00 0.00 4.57 F
3083 5892 4.225942 TGGTGGTTCTCAATATCTCTTGCT 59.774 41.667 0.00 0.00 0.00 3.91 F
4468 7447 2.135933 GTGTGGCTGTGTTCTGAGTAC 58.864 52.381 0.00 0.00 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 4389 2.430610 GGCCTCACGCTCCTCATCT 61.431 63.158 0.0 0.0 37.74 2.90 R
2574 4960 6.944862 ACTTCTGCTTCTGGAAAGTATGAAAT 59.055 34.615 0.0 0.0 0.00 2.17 R
2843 5231 1.394618 CGGCAGAGCTTAGTCTAGGT 58.605 55.000 0.0 0.0 0.00 3.08 R
3459 6270 3.936453 CCAAACGCTGCCTTACTGTATTA 59.064 43.478 0.0 0.0 0.00 0.98 R
4836 7828 0.673437 GGCTCTCCTCCTTCTCATCG 59.327 60.000 0.0 0.0 0.00 3.84 R
5347 8354 0.183252 ACTAGCTACTCCCTCCGTCC 59.817 60.000 0.0 0.0 0.00 4.79 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
133 935 7.768582 TCTGACATTAAACCCACAGTACATATG 59.231 37.037 0.00 0.00 0.00 1.78
139 941 8.871629 TTAAACCCACAGTACATATGAAATGT 57.128 30.769 10.38 7.59 36.13 2.71
318 1136 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
319 1137 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
320 1138 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
321 1139 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
322 1140 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
324 1142 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
325 1143 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
326 1144 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
327 1145 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
328 1146 6.058183 GTCACATCTAAGCTCCCACAAATAT 58.942 40.000 0.00 0.00 0.00 1.28
329 1147 7.147567 TGTCACATCTAAGCTCCCACAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
330 1148 7.880195 GTCACATCTAAGCTCCCACAAATATAT 59.120 37.037 0.00 0.00 0.00 0.86
331 1149 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
332 1150 9.725019 CACATCTAAGCTCCCACAAATATATAA 57.275 33.333 0.00 0.00 0.00 0.98
335 1153 8.792830 TCTAAGCTCCCACAAATATATAATGC 57.207 34.615 0.00 0.00 0.00 3.56
336 1154 8.382405 TCTAAGCTCCCACAAATATATAATGCA 58.618 33.333 0.00 0.00 0.00 3.96
337 1155 7.838079 AAGCTCCCACAAATATATAATGCAA 57.162 32.000 0.00 0.00 0.00 4.08
338 1156 7.458409 AGCTCCCACAAATATATAATGCAAG 57.542 36.000 0.00 0.00 0.00 4.01
339 1157 7.233632 AGCTCCCACAAATATATAATGCAAGA 58.766 34.615 0.00 0.00 0.00 3.02
340 1158 7.725397 AGCTCCCACAAATATATAATGCAAGAA 59.275 33.333 0.00 0.00 0.00 2.52
341 1159 7.809806 GCTCCCACAAATATATAATGCAAGAAC 59.190 37.037 0.00 0.00 0.00 3.01
342 1160 8.759481 TCCCACAAATATATAATGCAAGAACA 57.241 30.769 0.00 0.00 0.00 3.18
343 1161 9.194972 TCCCACAAATATATAATGCAAGAACAA 57.805 29.630 0.00 0.00 0.00 2.83
344 1162 9.467258 CCCACAAATATATAATGCAAGAACAAG 57.533 33.333 0.00 0.00 0.00 3.16
389 1207 9.787435 AAAAATAGACCATAAACAGAGTGTACA 57.213 29.630 0.00 0.00 0.00 2.90
390 1208 9.959721 AAAATAGACCATAAACAGAGTGTACAT 57.040 29.630 0.00 0.00 0.00 2.29
391 1209 9.601217 AAATAGACCATAAACAGAGTGTACATC 57.399 33.333 0.00 0.00 0.00 3.06
392 1210 6.605471 AGACCATAAACAGAGTGTACATCA 57.395 37.500 0.00 0.00 0.00 3.07
393 1211 6.634805 AGACCATAAACAGAGTGTACATCAG 58.365 40.000 0.00 0.00 0.00 2.90
394 1212 5.178797 ACCATAAACAGAGTGTACATCAGC 58.821 41.667 0.00 0.00 0.00 4.26
395 1213 5.046304 ACCATAAACAGAGTGTACATCAGCT 60.046 40.000 0.00 0.00 0.00 4.24
396 1214 5.877012 CCATAAACAGAGTGTACATCAGCTT 59.123 40.000 0.00 0.00 0.00 3.74
397 1215 7.041721 CCATAAACAGAGTGTACATCAGCTTA 58.958 38.462 0.00 0.00 0.00 3.09
398 1216 7.223582 CCATAAACAGAGTGTACATCAGCTTAG 59.776 40.741 0.00 0.00 0.00 2.18
399 1217 5.984695 AACAGAGTGTACATCAGCTTAGA 57.015 39.130 0.00 0.00 0.00 2.10
400 1218 6.537453 AACAGAGTGTACATCAGCTTAGAT 57.463 37.500 0.00 0.00 0.00 1.98
410 1228 5.627802 CATCAGCTTAGATGTGACGTAAC 57.372 43.478 5.99 0.00 40.35 2.50
411 1229 5.344066 CATCAGCTTAGATGTGACGTAACT 58.656 41.667 4.30 0.00 40.35 2.24
412 1230 6.495706 CATCAGCTTAGATGTGACGTAACTA 58.504 40.000 4.30 0.00 40.35 2.24
413 1231 5.877031 TCAGCTTAGATGTGACGTAACTAC 58.123 41.667 4.30 0.00 0.00 2.73
414 1232 8.658736 CATCAGCTTAGATGTGACGTAACTACG 61.659 44.444 4.30 7.70 45.33 3.51
428 1246 6.045698 CGTAACTACGTCACATCTAGATGT 57.954 41.667 28.95 28.95 46.62 3.06
441 1259 6.312399 CATCTAGATGTGTCCTAGACAGAC 57.688 45.833 22.42 0.00 43.57 3.51
442 1260 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
443 1261 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
444 1262 2.313342 AGATGTGTCCTAGACAGACCCT 59.687 50.000 0.00 0.00 43.57 4.34
450 1268 5.011738 TGTGTCCTAGACAGACCCTAAAAAG 59.988 44.000 0.00 0.00 43.57 2.27
473 1291 7.238486 AGATACTATCTAGGGTGCAATCTTG 57.762 40.000 0.00 0.00 38.00 3.02
479 1297 4.517285 TCTAGGGTGCAATCTTGATCAAC 58.483 43.478 3.38 0.00 0.00 3.18
507 1325 8.345565 GTGCATTATCCGTCTTTCTTTCATATT 58.654 33.333 0.00 0.00 0.00 1.28
518 2244 8.831550 GTCTTTCTTTCATATTGGTACTGATCC 58.168 37.037 0.00 0.00 0.00 3.36
540 2266 2.561569 GATTGGTACTGGTCCGGATTG 58.438 52.381 7.81 3.33 0.00 2.67
542 2268 0.611200 TGGTACTGGTCCGGATTGTG 59.389 55.000 7.81 0.88 0.00 3.33
559 2618 5.357878 GGATTGTGGATAAACATCTCAGCAA 59.642 40.000 0.00 0.00 0.00 3.91
581 2640 9.383519 AGCAAAATCAAGATTAGAGACGAAATA 57.616 29.630 0.00 0.00 0.00 1.40
596 2656 6.381801 AGACGAAATAAAAATCACTTGCCTG 58.618 36.000 0.00 0.00 0.00 4.85
603 2663 8.962884 AATAAAAATCACTTGCCTGTTTCTTT 57.037 26.923 0.00 0.00 0.00 2.52
646 2706 7.466746 TGCAAGCCTTGTTTAAATAGAAGAT 57.533 32.000 6.28 0.00 0.00 2.40
667 2727 7.692460 AGATATGTGAAATCTTGAACTTGCA 57.308 32.000 0.00 0.00 29.18 4.08
700 2760 1.632589 AGACCATCTTTGTTTGGGCC 58.367 50.000 0.00 0.00 42.45 5.80
704 2764 1.889829 CCATCTTTGTTTGGGCCGTAA 59.110 47.619 0.00 0.00 0.00 3.18
713 2773 5.362105 TGTTTGGGCCGTAATAATACTCT 57.638 39.130 0.00 0.00 0.00 3.24
753 2814 9.562583 TTTTTAAATTAAGAGCGTGCGATATTT 57.437 25.926 0.00 0.00 0.00 1.40
776 2837 3.552604 TTTTGTTCTAACGCATGAGCC 57.447 42.857 0.00 0.00 37.52 4.70
777 2838 1.448985 TTGTTCTAACGCATGAGCCC 58.551 50.000 0.00 0.00 37.52 5.19
778 2839 0.613260 TGTTCTAACGCATGAGCCCT 59.387 50.000 0.00 0.00 37.52 5.19
779 2840 1.003118 TGTTCTAACGCATGAGCCCTT 59.997 47.619 0.00 0.00 37.52 3.95
780 2841 2.084546 GTTCTAACGCATGAGCCCTTT 58.915 47.619 0.00 0.00 37.52 3.11
781 2842 2.488153 GTTCTAACGCATGAGCCCTTTT 59.512 45.455 0.00 0.00 37.52 2.27
782 2843 2.083774 TCTAACGCATGAGCCCTTTTG 58.916 47.619 0.00 0.00 37.52 2.44
783 2844 0.525761 TAACGCATGAGCCCTTTTGC 59.474 50.000 0.00 0.00 37.52 3.68
784 2845 1.181098 AACGCATGAGCCCTTTTGCT 61.181 50.000 0.00 0.00 46.37 3.91
785 2846 0.322456 ACGCATGAGCCCTTTTGCTA 60.322 50.000 0.00 0.00 42.95 3.49
786 2847 0.379669 CGCATGAGCCCTTTTGCTAG 59.620 55.000 0.00 0.00 42.95 3.42
787 2848 0.101939 GCATGAGCCCTTTTGCTAGC 59.898 55.000 8.10 8.10 42.95 3.42
788 2849 1.466856 CATGAGCCCTTTTGCTAGCA 58.533 50.000 14.93 14.93 42.95 3.49
789 2850 1.820519 CATGAGCCCTTTTGCTAGCAA 59.179 47.619 26.06 26.06 42.95 3.91
790 2851 1.538047 TGAGCCCTTTTGCTAGCAAG 58.462 50.000 27.82 18.44 42.95 4.01
791 2852 0.813821 GAGCCCTTTTGCTAGCAAGG 59.186 55.000 27.82 25.48 42.95 3.61
792 2853 0.405585 AGCCCTTTTGCTAGCAAGGA 59.594 50.000 29.48 21.15 42.11 3.36
793 2854 1.203050 AGCCCTTTTGCTAGCAAGGAA 60.203 47.619 29.48 21.30 42.11 3.36
794 2855 1.618343 GCCCTTTTGCTAGCAAGGAAA 59.382 47.619 29.48 20.68 42.11 3.13
795 2856 2.037121 GCCCTTTTGCTAGCAAGGAAAA 59.963 45.455 29.48 20.38 46.80 2.29
867 2928 1.572085 GCGTCTGAACTGCAGTGCAT 61.572 55.000 27.88 8.84 45.14 3.96
907 2970 1.929482 GCGTCCCCTATTCGATTCGAC 60.929 57.143 8.55 0.00 34.89 4.20
974 3048 2.225727 ACGAAGCAAAATCGAGGGTTTC 59.774 45.455 2.65 0.00 42.76 2.78
1230 3605 1.303309 AGCCAGTAATCTTGCATCGC 58.697 50.000 0.00 0.00 35.19 4.58
1236 3611 4.516698 CCAGTAATCTTGCATCGCCTAATT 59.483 41.667 0.00 0.00 0.00 1.40
1566 3942 4.407365 CCAGGTTGGTCAAAGAATTAGGT 58.593 43.478 0.00 0.00 31.35 3.08
1608 3984 1.108776 ATGCCAGCAATTGCACCTAG 58.891 50.000 30.89 15.34 45.16 3.02
1627 4003 5.222048 ACCTAGGAACCTTAGATTTTGTGCA 60.222 40.000 17.98 0.00 0.00 4.57
1791 4168 8.250143 TCCTTATACAAGATGACTGATTGCTA 57.750 34.615 0.00 0.00 33.20 3.49
1868 4253 5.967674 GCTTATTTGATTGTTCATCTCACGG 59.032 40.000 0.00 0.00 32.34 4.94
1982 4368 5.963594 AGGAGAACTAATCAAGACCGTTAC 58.036 41.667 0.00 0.00 0.00 2.50
2003 4389 5.228945 ACGAGGAAATGAGAAGGAAGAAA 57.771 39.130 0.00 0.00 0.00 2.52
2799 5187 5.560760 CGCGATGCATTGGTAGATAAAATGT 60.561 40.000 15.85 0.00 34.48 2.71
2966 5775 4.319177 AGCCTTACTTTACTGCACTTCTG 58.681 43.478 0.00 0.00 0.00 3.02
3083 5892 4.225942 TGGTGGTTCTCAATATCTCTTGCT 59.774 41.667 0.00 0.00 0.00 3.91
3169 5978 7.928873 ACCAGAGTCCCTTTTATTAAGATCAA 58.071 34.615 0.00 0.00 0.00 2.57
3288 6097 9.256477 CCTCAGTATTATTGCGATAAACTAACA 57.744 33.333 10.46 3.72 31.82 2.41
3543 6355 7.449086 TCCTATTTACCCTGTTTTAGTGTTTGG 59.551 37.037 0.00 0.00 0.00 3.28
3563 6375 3.079578 GGTTGACCTGCTTTTACCTACC 58.920 50.000 0.00 0.00 0.00 3.18
3646 6559 5.024118 ACCACAAACTGAGCCTAGTACTAT 58.976 41.667 2.33 0.00 0.00 2.12
4037 7008 9.916360 ATATATACCCGTAGACATCTTATCACA 57.084 33.333 0.00 0.00 0.00 3.58
4091 7063 9.709495 AGAAGCATCTAGAGCTAATAGATTTTG 57.291 33.333 15.19 9.46 42.53 2.44
4126 7098 7.130681 TGTTGTGGGTTAATTCCTTGAAAAT 57.869 32.000 0.00 0.00 0.00 1.82
4127 7099 8.251383 TGTTGTGGGTTAATTCCTTGAAAATA 57.749 30.769 0.00 0.00 0.00 1.40
4128 7100 8.875168 TGTTGTGGGTTAATTCCTTGAAAATAT 58.125 29.630 0.00 0.00 0.00 1.28
4296 7272 6.346838 GCAACTGAGTAAATTTTTGGATGTGC 60.347 38.462 0.00 0.00 0.00 4.57
4326 7305 5.947228 TTTGACCTAGAATGTCTTTGCAG 57.053 39.130 0.00 0.00 33.83 4.41
4355 7334 9.555727 GTAATGCCATAGTTATCTTTTCACCTA 57.444 33.333 0.00 0.00 0.00 3.08
4442 7421 5.048507 ACCTTCGTTTGAGTCTTTACAGTC 58.951 41.667 0.00 0.00 0.00 3.51
4468 7447 2.135933 GTGTGGCTGTGTTCTGAGTAC 58.864 52.381 0.00 0.00 0.00 2.73
4660 7652 3.254657 ACTGATACTGATAGGCTCGCTTC 59.745 47.826 0.00 0.00 0.00 3.86
4725 7717 9.476202 CGTGGAAAGTTCATCTACATATCAATA 57.524 33.333 0.00 0.00 0.00 1.90
4836 7828 1.378646 GGAGCCAAAGCCCCTGTAC 60.379 63.158 0.00 0.00 41.25 2.90
4987 7979 7.010923 GCAAGATCAGGTACATGTTTTCTAGAG 59.989 40.741 2.30 4.69 0.00 2.43
5084 8076 3.616956 TCATCGGAAATTCAGAGCTGT 57.383 42.857 0.00 0.00 0.00 4.40
5085 8077 3.264947 TCATCGGAAATTCAGAGCTGTG 58.735 45.455 4.05 4.05 0.00 3.66
5086 8078 1.442769 TCGGAAATTCAGAGCTGTGC 58.557 50.000 5.87 0.00 0.00 4.57
5087 8079 1.002430 TCGGAAATTCAGAGCTGTGCT 59.998 47.619 5.87 0.00 43.88 4.40
5088 8080 1.129998 CGGAAATTCAGAGCTGTGCTG 59.870 52.381 5.87 0.00 39.88 4.41
5094 8090 5.464030 AATTCAGAGCTGTGCTGATTTTT 57.536 34.783 5.87 0.00 41.60 1.94
5161 8157 3.181493 GCTGGTGCTGATACAATGAAAGG 60.181 47.826 0.00 0.00 36.03 3.11
5162 8158 4.012374 CTGGTGCTGATACAATGAAAGGT 58.988 43.478 0.00 0.00 0.00 3.50
5163 8159 4.406456 TGGTGCTGATACAATGAAAGGTT 58.594 39.130 0.00 0.00 0.00 3.50
5164 8160 4.832266 TGGTGCTGATACAATGAAAGGTTT 59.168 37.500 0.00 0.00 0.00 3.27
5165 8161 5.048083 TGGTGCTGATACAATGAAAGGTTTC 60.048 40.000 0.00 0.00 37.69 2.78
5255 8262 3.430374 GCCTGTAGGAACTAATGCGAAGA 60.430 47.826 1.17 0.00 45.48 2.87
5281 8288 1.558233 ACTAACGACTGGCCTAGCTT 58.442 50.000 3.32 0.00 0.00 3.74
5283 8290 3.297736 ACTAACGACTGGCCTAGCTTAT 58.702 45.455 3.32 0.00 0.00 1.73
5284 8291 4.467769 ACTAACGACTGGCCTAGCTTATA 58.532 43.478 3.32 0.00 0.00 0.98
5285 8292 3.729862 AACGACTGGCCTAGCTTATAC 57.270 47.619 3.32 0.00 0.00 1.47
5286 8293 2.946785 ACGACTGGCCTAGCTTATACT 58.053 47.619 3.32 0.00 0.00 2.12
5287 8294 2.885894 ACGACTGGCCTAGCTTATACTC 59.114 50.000 3.32 0.00 0.00 2.59
5288 8295 2.229302 CGACTGGCCTAGCTTATACTCC 59.771 54.545 3.32 0.00 0.00 3.85
5289 8296 2.563620 GACTGGCCTAGCTTATACTCCC 59.436 54.545 3.32 0.00 0.00 4.30
5290 8297 2.180308 ACTGGCCTAGCTTATACTCCCT 59.820 50.000 3.32 0.00 0.00 4.20
5291 8298 2.829120 CTGGCCTAGCTTATACTCCCTC 59.171 54.545 3.32 0.00 0.00 4.30
5292 8299 2.181125 GGCCTAGCTTATACTCCCTCC 58.819 57.143 0.00 0.00 0.00 4.30
5293 8300 1.819903 GCCTAGCTTATACTCCCTCCG 59.180 57.143 0.00 0.00 0.00 4.63
5294 8301 2.818593 GCCTAGCTTATACTCCCTCCGT 60.819 54.545 0.00 0.00 0.00 4.69
5295 8302 3.083293 CCTAGCTTATACTCCCTCCGTC 58.917 54.545 0.00 0.00 0.00 4.79
5296 8303 1.998222 AGCTTATACTCCCTCCGTCC 58.002 55.000 0.00 0.00 0.00 4.79
5297 8304 0.597072 GCTTATACTCCCTCCGTCCG 59.403 60.000 0.00 0.00 0.00 4.79
5298 8305 1.816961 GCTTATACTCCCTCCGTCCGA 60.817 57.143 0.00 0.00 0.00 4.55
5299 8306 2.579873 CTTATACTCCCTCCGTCCGAA 58.420 52.381 0.00 0.00 0.00 4.30
5300 8307 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
5301 8308 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
5302 8309 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
5303 8310 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
5304 8311 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
5305 8312 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
5306 8313 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
5307 8314 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5308 8315 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5309 8316 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5310 8317 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
5311 8318 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
5312 8319 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
5313 8320 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
5314 8321 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
5315 8322 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
5316 8323 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
5317 8324 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
5318 8325 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
5319 8326 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
5320 8327 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
5321 8328 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
5326 8333 9.645128 AATACTTGTCATCAAAATGGATATCCA 57.355 29.630 26.49 26.49 40.74 3.41
5343 8350 9.645128 TGGATATCCATTTTGATGACAAGTATT 57.355 29.630 20.98 0.00 42.01 1.89
5347 8354 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
5348 8355 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
5349 8356 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
5350 8357 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
5351 8358 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
5352 8359 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
5353 8360 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5354 8361 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
5355 8362 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5356 8363 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5357 8364 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
5358 8365 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
5434 8442 6.455646 GCCAATTATACGAAGTGTTGAGTCAG 60.456 42.308 0.00 0.00 45.73 3.51
5671 8684 2.103143 CTACTCACCTCGCAGGCG 59.897 66.667 7.46 7.46 39.63 5.52
5672 8685 2.360726 TACTCACCTCGCAGGCGA 60.361 61.111 16.15 16.15 46.87 5.54
5673 8686 2.600122 CTACTCACCTCGCAGGCGAC 62.600 65.000 12.94 0.00 44.01 5.19
5674 8687 4.056125 CTCACCTCGCAGGCGACA 62.056 66.667 12.94 0.00 44.01 4.35
5675 8688 3.573772 CTCACCTCGCAGGCGACAA 62.574 63.158 12.94 0.00 44.01 3.18
5676 8689 3.114616 CACCTCGCAGGCGACAAG 61.115 66.667 12.94 7.12 44.01 3.16
5677 8690 3.303135 ACCTCGCAGGCGACAAGA 61.303 61.111 12.94 0.00 44.01 3.02
5678 8691 2.048222 CCTCGCAGGCGACAAGAA 60.048 61.111 12.94 0.00 44.01 2.52
5679 8692 2.097038 CCTCGCAGGCGACAAGAAG 61.097 63.158 12.94 1.81 44.01 2.85
5680 8693 2.734673 CTCGCAGGCGACAAGAAGC 61.735 63.158 12.94 0.00 44.01 3.86
5681 8694 4.139420 CGCAGGCGACAAGAAGCG 62.139 66.667 8.15 0.00 42.83 4.68
5682 8695 2.738521 GCAGGCGACAAGAAGCGA 60.739 61.111 0.00 0.00 0.00 4.93
5683 8696 2.103042 GCAGGCGACAAGAAGCGAT 61.103 57.895 0.00 0.00 0.00 4.58
5684 8697 0.806102 GCAGGCGACAAGAAGCGATA 60.806 55.000 0.00 0.00 0.00 2.92
5685 8698 1.858091 CAGGCGACAAGAAGCGATAT 58.142 50.000 0.00 0.00 0.00 1.63
5686 8699 1.789464 CAGGCGACAAGAAGCGATATC 59.211 52.381 0.00 0.00 0.00 1.63
5687 8700 1.409064 AGGCGACAAGAAGCGATATCA 59.591 47.619 3.12 0.00 0.00 2.15
5688 8701 2.036475 AGGCGACAAGAAGCGATATCAT 59.964 45.455 3.12 0.00 0.00 2.45
5689 8702 2.410053 GGCGACAAGAAGCGATATCATC 59.590 50.000 3.12 0.00 0.00 2.92
5690 8703 3.312828 GCGACAAGAAGCGATATCATCT 58.687 45.455 3.12 0.44 0.00 2.90
5691 8704 3.738282 GCGACAAGAAGCGATATCATCTT 59.262 43.478 3.12 5.31 32.55 2.40
5692 8705 4.210120 GCGACAAGAAGCGATATCATCTTT 59.790 41.667 10.94 5.57 30.01 2.52
5693 8706 5.277058 GCGACAAGAAGCGATATCATCTTTT 60.277 40.000 10.94 6.87 30.01 2.27
5694 8707 6.709643 CGACAAGAAGCGATATCATCTTTTT 58.290 36.000 10.94 8.05 30.01 1.94
5695 8708 7.516785 GCGACAAGAAGCGATATCATCTTTTTA 60.517 37.037 10.94 0.00 30.01 1.52
5696 8709 7.789759 CGACAAGAAGCGATATCATCTTTTTAC 59.210 37.037 10.94 7.72 30.01 2.01
5697 8710 7.920738 ACAAGAAGCGATATCATCTTTTTACC 58.079 34.615 10.94 0.10 30.01 2.85
5698 8711 7.770897 ACAAGAAGCGATATCATCTTTTTACCT 59.229 33.333 10.94 1.87 30.01 3.08
5699 8712 7.954788 AGAAGCGATATCATCTTTTTACCTC 57.045 36.000 3.12 0.00 0.00 3.85
5700 8713 6.931840 AGAAGCGATATCATCTTTTTACCTCC 59.068 38.462 3.12 0.00 0.00 4.30
5701 8714 5.230942 AGCGATATCATCTTTTTACCTCCG 58.769 41.667 3.12 0.00 0.00 4.63
5702 8715 4.989168 GCGATATCATCTTTTTACCTCCGT 59.011 41.667 3.12 0.00 0.00 4.69
5703 8716 5.118817 GCGATATCATCTTTTTACCTCCGTC 59.881 44.000 3.12 0.00 0.00 4.79
5704 8717 5.634020 CGATATCATCTTTTTACCTCCGTCC 59.366 44.000 3.12 0.00 0.00 4.79
5705 8718 6.516860 CGATATCATCTTTTTACCTCCGTCCT 60.517 42.308 3.12 0.00 0.00 3.85
5706 8719 4.202245 TCATCTTTTTACCTCCGTCCTG 57.798 45.455 0.00 0.00 0.00 3.86
5707 8720 3.055385 TCATCTTTTTACCTCCGTCCTGG 60.055 47.826 0.00 0.00 40.09 4.45
5708 8721 2.332117 TCTTTTTACCTCCGTCCTGGT 58.668 47.619 0.00 0.00 39.52 4.00
5709 8722 2.707257 TCTTTTTACCTCCGTCCTGGTT 59.293 45.455 0.00 0.00 39.52 3.67
5710 8723 3.136992 TCTTTTTACCTCCGTCCTGGTTT 59.863 43.478 0.00 0.00 39.52 3.27
5711 8724 4.347583 TCTTTTTACCTCCGTCCTGGTTTA 59.652 41.667 0.00 0.00 39.52 2.01
5712 8725 4.914177 TTTTACCTCCGTCCTGGTTTAT 57.086 40.909 0.00 0.00 39.52 1.40
5713 8726 4.914177 TTTACCTCCGTCCTGGTTTATT 57.086 40.909 0.00 0.00 39.52 1.40
5714 8727 2.781681 ACCTCCGTCCTGGTTTATTG 57.218 50.000 0.00 0.00 39.52 1.90
5715 8728 1.280998 ACCTCCGTCCTGGTTTATTGG 59.719 52.381 0.00 0.00 39.52 3.16
5716 8729 1.280998 CCTCCGTCCTGGTTTATTGGT 59.719 52.381 0.00 0.00 39.52 3.67
5717 8730 2.629051 CTCCGTCCTGGTTTATTGGTC 58.371 52.381 0.00 0.00 39.52 4.02
5718 8731 1.279846 TCCGTCCTGGTTTATTGGTCC 59.720 52.381 0.00 0.00 39.52 4.46
5719 8732 1.280998 CCGTCCTGGTTTATTGGTCCT 59.719 52.381 0.00 0.00 0.00 3.85
5720 8733 2.290705 CCGTCCTGGTTTATTGGTCCTT 60.291 50.000 0.00 0.00 0.00 3.36
5721 8734 3.418047 CGTCCTGGTTTATTGGTCCTTT 58.582 45.455 0.00 0.00 0.00 3.11
5722 8735 3.190535 CGTCCTGGTTTATTGGTCCTTTG 59.809 47.826 0.00 0.00 0.00 2.77
5723 8736 4.149598 GTCCTGGTTTATTGGTCCTTTGT 58.850 43.478 0.00 0.00 0.00 2.83
5724 8737 5.318630 GTCCTGGTTTATTGGTCCTTTGTA 58.681 41.667 0.00 0.00 0.00 2.41
5725 8738 5.771165 GTCCTGGTTTATTGGTCCTTTGTAA 59.229 40.000 0.00 0.00 0.00 2.41
5726 8739 6.436218 GTCCTGGTTTATTGGTCCTTTGTAAT 59.564 38.462 0.00 0.00 0.00 1.89
5727 8740 7.013834 TCCTGGTTTATTGGTCCTTTGTAATT 58.986 34.615 0.00 0.00 0.00 1.40
5728 8741 7.511028 TCCTGGTTTATTGGTCCTTTGTAATTT 59.489 33.333 0.00 0.00 0.00 1.82
5729 8742 7.602265 CCTGGTTTATTGGTCCTTTGTAATTTG 59.398 37.037 0.00 0.00 0.00 2.32
5730 8743 8.024145 TGGTTTATTGGTCCTTTGTAATTTGT 57.976 30.769 0.00 0.00 0.00 2.83
5731 8744 7.928706 TGGTTTATTGGTCCTTTGTAATTTGTG 59.071 33.333 0.00 0.00 0.00 3.33
5732 8745 7.929245 GGTTTATTGGTCCTTTGTAATTTGTGT 59.071 33.333 0.00 0.00 0.00 3.72
5733 8746 8.974408 GTTTATTGGTCCTTTGTAATTTGTGTC 58.026 33.333 0.00 0.00 0.00 3.67
5734 8747 6.723298 ATTGGTCCTTTGTAATTTGTGTCA 57.277 33.333 0.00 0.00 0.00 3.58
5735 8748 6.531503 TTGGTCCTTTGTAATTTGTGTCAA 57.468 33.333 0.00 0.00 0.00 3.18
5736 8749 6.531503 TGGTCCTTTGTAATTTGTGTCAAA 57.468 33.333 0.00 0.00 0.00 2.69
5737 8750 7.118496 TGGTCCTTTGTAATTTGTGTCAAAT 57.882 32.000 2.42 2.42 31.08 2.32
5738 8751 7.560368 TGGTCCTTTGTAATTTGTGTCAAATT 58.440 30.769 19.42 19.42 34.55 1.82
5739 8752 8.043710 TGGTCCTTTGTAATTTGTGTCAAATTT 58.956 29.630 20.29 9.17 32.64 1.82
5740 8753 8.888716 GGTCCTTTGTAATTTGTGTCAAATTTT 58.111 29.630 20.29 6.18 32.64 1.82
5741 8754 9.701355 GTCCTTTGTAATTTGTGTCAAATTTTG 57.299 29.630 20.29 2.59 32.64 2.44
5742 8755 9.658799 TCCTTTGTAATTTGTGTCAAATTTTGA 57.341 25.926 20.29 7.74 37.33 2.69
5817 8830 7.962964 TCCTTGGATTCGTATTTAAGCATAG 57.037 36.000 0.00 0.00 0.00 2.23
5818 8831 7.506114 TCCTTGGATTCGTATTTAAGCATAGT 58.494 34.615 0.00 0.00 0.00 2.12
5819 8832 7.990886 TCCTTGGATTCGTATTTAAGCATAGTT 59.009 33.333 0.00 0.00 0.00 2.24
5820 8833 8.621286 CCTTGGATTCGTATTTAAGCATAGTTT 58.379 33.333 0.00 0.00 0.00 2.66
5821 8834 9.651718 CTTGGATTCGTATTTAAGCATAGTTTC 57.348 33.333 0.00 0.00 0.00 2.78
5822 8835 8.149973 TGGATTCGTATTTAAGCATAGTTTCC 57.850 34.615 0.00 0.00 0.00 3.13
5823 8836 7.771361 TGGATTCGTATTTAAGCATAGTTTCCA 59.229 33.333 0.00 0.00 0.00 3.53
5824 8837 8.068380 GGATTCGTATTTAAGCATAGTTTCCAC 58.932 37.037 0.00 0.00 0.00 4.02
5825 8838 8.732746 ATTCGTATTTAAGCATAGTTTCCACT 57.267 30.769 0.00 0.00 36.99 4.00
5826 8839 7.534085 TCGTATTTAAGCATAGTTTCCACTG 57.466 36.000 0.00 0.00 34.06 3.66
5827 8840 7.324935 TCGTATTTAAGCATAGTTTCCACTGA 58.675 34.615 0.00 0.00 34.06 3.41
5828 8841 7.985184 TCGTATTTAAGCATAGTTTCCACTGAT 59.015 33.333 0.00 0.00 34.06 2.90
5829 8842 9.256477 CGTATTTAAGCATAGTTTCCACTGATA 57.744 33.333 0.00 0.00 34.06 2.15
5882 8895 8.592105 TTAGTTAAACTAGTAAATGTGCACGT 57.408 30.769 13.13 9.52 31.47 4.49
5883 8896 6.884187 AGTTAAACTAGTAAATGTGCACGTG 58.116 36.000 13.39 12.28 0.00 4.49
5884 8897 3.806316 AACTAGTAAATGTGCACGTGC 57.194 42.857 33.11 33.11 42.50 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 1113 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
296 1114 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
297 1115 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
298 1116 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
299 1117 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
300 1118 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
301 1119 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
305 1123 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
306 1124 9.725019 TTATATATTTGTGGGAGCTTAGATGTG 57.275 33.333 0.00 0.00 0.00 3.21
310 1128 8.382405 TGCATTATATATTTGTGGGAGCTTAGA 58.618 33.333 0.00 0.00 0.00 2.10
311 1129 8.565896 TGCATTATATATTTGTGGGAGCTTAG 57.434 34.615 0.00 0.00 0.00 2.18
312 1130 8.932434 TTGCATTATATATTTGTGGGAGCTTA 57.068 30.769 0.00 0.00 0.00 3.09
316 1134 8.849168 TGTTCTTGCATTATATATTTGTGGGAG 58.151 33.333 0.00 0.00 0.00 4.30
317 1135 8.759481 TGTTCTTGCATTATATATTTGTGGGA 57.241 30.769 0.00 0.00 0.00 4.37
318 1136 9.467258 CTTGTTCTTGCATTATATATTTGTGGG 57.533 33.333 0.00 0.00 0.00 4.61
363 1181 9.787435 TGTACACTCTGTTTATGGTCTATTTTT 57.213 29.630 0.00 0.00 0.00 1.94
364 1182 9.959721 ATGTACACTCTGTTTATGGTCTATTTT 57.040 29.630 0.00 0.00 0.00 1.82
365 1183 9.601217 GATGTACACTCTGTTTATGGTCTATTT 57.399 33.333 0.00 0.00 0.00 1.40
366 1184 8.758829 TGATGTACACTCTGTTTATGGTCTATT 58.241 33.333 0.00 0.00 0.00 1.73
367 1185 8.306313 TGATGTACACTCTGTTTATGGTCTAT 57.694 34.615 0.00 0.00 0.00 1.98
368 1186 7.630728 GCTGATGTACACTCTGTTTATGGTCTA 60.631 40.741 0.00 0.00 0.00 2.59
369 1187 6.605471 TGATGTACACTCTGTTTATGGTCT 57.395 37.500 0.00 0.00 0.00 3.85
370 1188 5.292101 GCTGATGTACACTCTGTTTATGGTC 59.708 44.000 0.00 0.00 0.00 4.02
371 1189 5.046304 AGCTGATGTACACTCTGTTTATGGT 60.046 40.000 0.00 0.00 0.00 3.55
372 1190 5.423015 AGCTGATGTACACTCTGTTTATGG 58.577 41.667 0.00 0.00 0.00 2.74
373 1191 6.974932 AAGCTGATGTACACTCTGTTTATG 57.025 37.500 0.00 0.00 0.00 1.90
374 1192 8.067751 TCTAAGCTGATGTACACTCTGTTTAT 57.932 34.615 0.00 0.00 0.00 1.40
375 1193 7.462571 TCTAAGCTGATGTACACTCTGTTTA 57.537 36.000 0.00 8.85 0.00 2.01
376 1194 6.346477 TCTAAGCTGATGTACACTCTGTTT 57.654 37.500 0.00 8.23 0.00 2.83
377 1195 5.984695 TCTAAGCTGATGTACACTCTGTT 57.015 39.130 0.00 0.00 0.00 3.16
378 1196 5.900425 CATCTAAGCTGATGTACACTCTGT 58.100 41.667 0.00 0.00 39.05 3.41
388 1206 5.344066 AGTTACGTCACATCTAAGCTGATG 58.656 41.667 11.48 11.48 46.61 3.07
389 1207 5.584253 AGTTACGTCACATCTAAGCTGAT 57.416 39.130 2.23 0.00 0.00 2.90
390 1208 5.446875 CGTAGTTACGTCACATCTAAGCTGA 60.447 44.000 2.23 0.00 44.13 4.26
391 1209 4.729086 CGTAGTTACGTCACATCTAAGCTG 59.271 45.833 2.23 0.00 44.13 4.24
392 1210 4.906423 CGTAGTTACGTCACATCTAAGCT 58.094 43.478 2.23 0.00 44.13 3.74
418 1236 5.240623 GGTCTGTCTAGGACACATCTAGATG 59.759 48.000 27.63 27.63 43.25 2.90
419 1237 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
420 1238 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
421 1239 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
422 1240 3.528078 AGGGTCTGTCTAGGACACATCTA 59.472 47.826 3.18 0.00 39.36 1.98
423 1241 2.313342 AGGGTCTGTCTAGGACACATCT 59.687 50.000 3.18 0.00 39.36 2.90
424 1242 2.741145 AGGGTCTGTCTAGGACACATC 58.259 52.381 3.18 0.00 39.36 3.06
425 1243 2.930109 AGGGTCTGTCTAGGACACAT 57.070 50.000 3.18 0.00 39.36 3.21
426 1244 3.820195 TTAGGGTCTGTCTAGGACACA 57.180 47.619 3.18 0.00 39.36 3.72
427 1245 5.245526 TCTTTTTAGGGTCTGTCTAGGACAC 59.754 44.000 0.00 0.00 37.67 3.67
428 1246 5.399991 TCTTTTTAGGGTCTGTCTAGGACA 58.600 41.667 0.43 0.43 40.50 4.02
429 1247 5.997384 TCTTTTTAGGGTCTGTCTAGGAC 57.003 43.478 0.00 0.00 0.00 3.85
430 1248 7.420029 AGTATCTTTTTAGGGTCTGTCTAGGA 58.580 38.462 0.00 0.00 0.00 2.94
431 1249 7.663043 AGTATCTTTTTAGGGTCTGTCTAGG 57.337 40.000 0.00 0.00 0.00 3.02
436 1254 9.369672 CCTAGATAGTATCTTTTTAGGGTCTGT 57.630 37.037 17.70 0.00 40.76 3.41
437 1255 8.808092 CCCTAGATAGTATCTTTTTAGGGTCTG 58.192 40.741 25.70 10.10 42.69 3.51
438 1256 8.959676 CCCTAGATAGTATCTTTTTAGGGTCT 57.040 38.462 25.70 3.14 42.69 3.85
442 1260 7.963532 TGCACCCTAGATAGTATCTTTTTAGG 58.036 38.462 17.70 16.53 40.76 2.69
444 1262 9.998106 GATTGCACCCTAGATAGTATCTTTTTA 57.002 33.333 17.70 0.00 40.76 1.52
450 1268 7.233389 TCAAGATTGCACCCTAGATAGTATC 57.767 40.000 1.55 1.55 0.00 2.24
473 1291 4.122776 AGACGGATAATGCACTGTTGATC 58.877 43.478 0.00 0.00 0.00 2.92
479 1297 5.122239 TGAAAGAAAGACGGATAATGCACTG 59.878 40.000 0.00 0.00 0.00 3.66
507 1325 1.874129 ACCAATCCGGATCAGTACCA 58.126 50.000 19.43 0.00 38.63 3.25
540 2266 6.855836 TGATTTTGCTGAGATGTTTATCCAC 58.144 36.000 0.00 0.00 33.64 4.02
542 2268 7.765307 TCTTGATTTTGCTGAGATGTTTATCC 58.235 34.615 0.00 0.00 33.64 2.59
581 2640 6.172630 ACAAAGAAACAGGCAAGTGATTTTT 58.827 32.000 0.00 0.00 0.00 1.94
603 2663 7.042321 GGCTTGCATGTAGATTTAATACGTACA 60.042 37.037 0.00 0.00 0.00 2.90
646 2706 6.882610 AGTGCAAGTTCAAGATTTCACATA 57.117 33.333 0.00 0.00 0.00 2.29
664 2724 4.905429 TGGTCTTTGCTTATAGAAGTGCA 58.095 39.130 0.00 0.00 34.90 4.57
757 2818 1.810151 GGGCTCATGCGTTAGAACAAA 59.190 47.619 0.00 0.00 40.82 2.83
758 2819 1.003118 AGGGCTCATGCGTTAGAACAA 59.997 47.619 0.00 0.00 40.82 2.83
759 2820 0.613260 AGGGCTCATGCGTTAGAACA 59.387 50.000 0.00 0.00 40.82 3.18
760 2821 1.739067 AAGGGCTCATGCGTTAGAAC 58.261 50.000 0.00 0.00 40.82 3.01
761 2822 2.487762 CAAAAGGGCTCATGCGTTAGAA 59.512 45.455 0.00 0.00 40.82 2.10
762 2823 2.083774 CAAAAGGGCTCATGCGTTAGA 58.916 47.619 0.00 0.00 40.82 2.10
763 2824 1.468054 GCAAAAGGGCTCATGCGTTAG 60.468 52.381 0.00 0.00 40.82 2.34
764 2825 0.525761 GCAAAAGGGCTCATGCGTTA 59.474 50.000 0.00 0.00 40.82 3.18
765 2826 1.181098 AGCAAAAGGGCTCATGCGTT 61.181 50.000 3.75 0.00 41.05 4.84
766 2827 0.322456 TAGCAAAAGGGCTCATGCGT 60.322 50.000 3.75 0.00 44.54 5.24
767 2828 0.379669 CTAGCAAAAGGGCTCATGCG 59.620 55.000 3.75 0.00 44.54 4.73
768 2829 0.101939 GCTAGCAAAAGGGCTCATGC 59.898 55.000 10.63 1.14 44.54 4.06
769 2830 1.466856 TGCTAGCAAAAGGGCTCATG 58.533 50.000 16.84 0.00 44.54 3.07
770 2831 2.097825 CTTGCTAGCAAAAGGGCTCAT 58.902 47.619 28.95 0.00 44.54 2.90
771 2832 1.538047 CTTGCTAGCAAAAGGGCTCA 58.462 50.000 28.95 5.71 44.54 4.26
772 2833 0.813821 CCTTGCTAGCAAAAGGGCTC 59.186 55.000 28.95 0.00 44.54 4.70
774 2835 1.256812 TTCCTTGCTAGCAAAAGGGC 58.743 50.000 28.95 0.00 42.77 5.19
775 2836 4.335400 TTTTTCCTTGCTAGCAAAAGGG 57.665 40.909 28.95 25.30 42.77 3.95
793 2854 9.516314 GTTTGTTTGCTCTTCTATGTACTTTTT 57.484 29.630 0.00 0.00 0.00 1.94
794 2855 7.855904 CGTTTGTTTGCTCTTCTATGTACTTTT 59.144 33.333 0.00 0.00 0.00 2.27
795 2856 7.352739 CGTTTGTTTGCTCTTCTATGTACTTT 58.647 34.615 0.00 0.00 0.00 2.66
796 2857 6.073222 CCGTTTGTTTGCTCTTCTATGTACTT 60.073 38.462 0.00 0.00 0.00 2.24
797 2858 5.408604 CCGTTTGTTTGCTCTTCTATGTACT 59.591 40.000 0.00 0.00 0.00 2.73
798 2859 5.407387 TCCGTTTGTTTGCTCTTCTATGTAC 59.593 40.000 0.00 0.00 0.00 2.90
799 2860 5.543714 TCCGTTTGTTTGCTCTTCTATGTA 58.456 37.500 0.00 0.00 0.00 2.29
800 2861 4.385825 TCCGTTTGTTTGCTCTTCTATGT 58.614 39.130 0.00 0.00 0.00 2.29
801 2862 4.670221 GCTCCGTTTGTTTGCTCTTCTATG 60.670 45.833 0.00 0.00 0.00 2.23
802 2863 3.437049 GCTCCGTTTGTTTGCTCTTCTAT 59.563 43.478 0.00 0.00 0.00 1.98
803 2864 2.806244 GCTCCGTTTGTTTGCTCTTCTA 59.194 45.455 0.00 0.00 0.00 2.10
907 2970 4.035208 CCAATTTCTATTTTCCCGGACGAG 59.965 45.833 0.73 0.00 0.00 4.18
974 3048 1.064946 GCGTCTGATGTCCCTCTCG 59.935 63.158 0.00 0.00 0.00 4.04
1230 3605 1.933853 CCTGGAGCGAACGAAATTAGG 59.066 52.381 0.00 0.00 0.00 2.69
1236 3611 3.702048 CCCCCTGGAGCGAACGAA 61.702 66.667 0.00 0.00 0.00 3.85
1566 3942 8.777413 GCATAATAGAAGAATACATCAGTGCAA 58.223 33.333 0.00 0.00 0.00 4.08
1608 3984 7.728847 AATTTTGCACAAAATCTAAGGTTCC 57.271 32.000 18.79 0.00 46.76 3.62
1627 4003 9.793259 TGAAGGATTTGACTGAGTACTAATTTT 57.207 29.630 0.00 0.00 0.00 1.82
1868 4253 5.756195 TGCAATTATGTTCCATACTCTGC 57.244 39.130 0.00 0.00 0.00 4.26
1982 4368 5.482908 TCTTTCTTCCTTCTCATTTCCTCG 58.517 41.667 0.00 0.00 0.00 4.63
2003 4389 2.430610 GGCCTCACGCTCCTCATCT 61.431 63.158 0.00 0.00 37.74 2.90
2574 4960 6.944862 ACTTCTGCTTCTGGAAAGTATGAAAT 59.055 34.615 0.00 0.00 0.00 2.17
2691 5079 7.945707 GCAAATAAAACGTTAAACCATTTACCG 59.054 33.333 0.00 0.00 37.11 4.02
2799 5187 4.106909 CGTATGCCAGTCGTACATACAAA 58.893 43.478 11.60 0.00 44.05 2.83
2843 5231 1.394618 CGGCAGAGCTTAGTCTAGGT 58.605 55.000 0.00 0.00 0.00 3.08
2966 5775 5.535030 ACAAGTAACCTCTTTCCAATGGAAC 59.465 40.000 15.24 0.98 41.87 3.62
3083 5892 6.513230 CGACCATGATTTGACAGAACAAAAGA 60.513 38.462 0.00 0.00 41.88 2.52
3288 6097 8.102676 TCCATATCATTTCCGACACAATCATAT 58.897 33.333 0.00 0.00 0.00 1.78
3459 6270 3.936453 CCAAACGCTGCCTTACTGTATTA 59.064 43.478 0.00 0.00 0.00 0.98
3543 6355 4.017177 AGGTAGGTAAAAGCAGGTCAAC 57.983 45.455 0.00 0.00 0.00 3.18
3563 6375 8.455903 TCTCTCATGGAAAATTAGCCATAAAG 57.544 34.615 10.65 11.00 42.81 1.85
4037 7008 3.733337 CTGGAGACACTAAGCAAACACT 58.267 45.455 0.00 0.00 35.60 3.55
4091 7063 1.141053 ACCCACAACAGTTCTGGTCTC 59.859 52.381 6.82 0.00 0.00 3.36
4126 7098 8.348354 AGGGATGGGGTACTTGAAATTTTAATA 58.652 33.333 0.00 0.00 0.00 0.98
4127 7099 7.196187 AGGGATGGGGTACTTGAAATTTTAAT 58.804 34.615 0.00 0.00 0.00 1.40
4128 7100 6.566914 AGGGATGGGGTACTTGAAATTTTAA 58.433 36.000 0.00 0.00 0.00 1.52
4130 7102 5.023514 AGGGATGGGGTACTTGAAATTTT 57.976 39.130 0.00 0.00 0.00 1.82
4135 7107 3.265489 AGAAAGGGATGGGGTACTTGAA 58.735 45.455 0.00 0.00 0.00 2.69
4296 7272 6.648192 AGACATTCTAGGTCAAATTCAGGAG 58.352 40.000 0.00 0.00 37.74 3.69
4326 7305 9.937175 GTGAAAAGATAACTATGGCATTACTTC 57.063 33.333 4.78 0.00 0.00 3.01
4355 7334 5.763876 AGGAGTACATTTACAAAGAGCCT 57.236 39.130 0.00 0.00 0.00 4.58
4442 7421 1.498865 GAACACAGCCACACAGGACG 61.499 60.000 0.00 0.00 41.22 4.79
4563 7545 5.421277 CAGACAAGATGAGAATGAAGCTCT 58.579 41.667 0.00 0.00 33.57 4.09
4620 7612 3.663176 CCAAGTGGGTGCTGCACG 61.663 66.667 24.86 10.92 34.83 5.34
4660 7652 5.292765 AGATAATCTATCTGCACAACACCG 58.707 41.667 0.00 0.00 43.59 4.94
4725 7717 1.992277 AACGGCCTGCATCTCCTCT 60.992 57.895 0.00 0.00 0.00 3.69
4836 7828 0.673437 GGCTCTCCTCCTTCTCATCG 59.327 60.000 0.00 0.00 0.00 3.84
4987 7979 8.943909 AGGTTAGCACAAACTATAGTAACATC 57.056 34.615 5.65 0.00 0.00 3.06
5161 8157 8.299570 CCAAATCAGGGCAATACTATATGAAAC 58.700 37.037 0.00 0.00 0.00 2.78
5162 8158 8.408043 CCAAATCAGGGCAATACTATATGAAA 57.592 34.615 0.00 0.00 0.00 2.69
5255 8262 0.605589 GCCAGTCGTTAGTTTGGGCT 60.606 55.000 0.00 0.00 37.00 5.19
5281 8288 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
5283 8290 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
5284 8291 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
5285 8292 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
5286 8293 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
5287 8294 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5288 8295 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5289 8296 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
5290 8297 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5291 8298 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
5292 8299 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
5293 8300 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
5294 8301 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
5295 8302 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
5296 8303 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
5300 8307 9.645128 TGGATATCCATTTTGATGACAAGTATT 57.355 29.630 20.98 0.00 42.01 1.89
5317 8324 9.645128 AATACTTGTCATCAAAATGGATATCCA 57.355 29.630 26.49 26.49 40.74 3.41
5322 8329 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
5323 8330 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
5324 8331 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
5325 8332 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
5326 8333 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
5327 8334 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
5328 8335 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
5329 8336 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
5330 8337 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
5331 8338 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
5332 8339 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
5333 8340 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
5334 8341 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5335 8342 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5336 8343 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5337 8344 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
5338 8345 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
5339 8346 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
5340 8347 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
5341 8348 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
5342 8349 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
5343 8350 1.318158 GCTACTCCCTCCGTCCGAAA 61.318 60.000 0.00 0.00 0.00 3.46
5344 8351 1.751927 GCTACTCCCTCCGTCCGAA 60.752 63.158 0.00 0.00 0.00 4.30
5345 8352 1.340399 TAGCTACTCCCTCCGTCCGA 61.340 60.000 0.00 0.00 0.00 4.55
5346 8353 0.885596 CTAGCTACTCCCTCCGTCCG 60.886 65.000 0.00 0.00 0.00 4.79
5347 8354 0.183252 ACTAGCTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
5348 8355 2.055684 AACTAGCTACTCCCTCCGTC 57.944 55.000 0.00 0.00 0.00 4.79
5349 8356 2.100989 CAAACTAGCTACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
5350 8357 1.409427 CCAAACTAGCTACTCCCTCCG 59.591 57.143 0.00 0.00 0.00 4.63
5351 8358 1.763545 CCCAAACTAGCTACTCCCTCC 59.236 57.143 0.00 0.00 0.00 4.30
5352 8359 1.763545 CCCCAAACTAGCTACTCCCTC 59.236 57.143 0.00 0.00 0.00 4.30
5353 8360 1.365028 TCCCCAAACTAGCTACTCCCT 59.635 52.381 0.00 0.00 0.00 4.20
5354 8361 1.763545 CTCCCCAAACTAGCTACTCCC 59.236 57.143 0.00 0.00 0.00 4.30
5355 8362 2.431419 GACTCCCCAAACTAGCTACTCC 59.569 54.545 0.00 0.00 0.00 3.85
5356 8363 3.097614 TGACTCCCCAAACTAGCTACTC 58.902 50.000 0.00 0.00 0.00 2.59
5357 8364 3.185880 TGACTCCCCAAACTAGCTACT 57.814 47.619 0.00 0.00 0.00 2.57
5358 8365 5.304614 TCATATGACTCCCCAAACTAGCTAC 59.695 44.000 0.00 0.00 0.00 3.58
5419 8426 0.861837 GCCACTGACTCAACACTTCG 59.138 55.000 0.00 0.00 0.00 3.79
5434 8442 3.196648 CCAAAGGTATGGCGCCAC 58.803 61.111 35.50 20.94 32.78 5.01
5556 8566 6.359087 GCACGTACTACATTGCATACTACTAC 59.641 42.308 0.00 0.00 34.97 2.73
5557 8567 6.038492 TGCACGTACTACATTGCATACTACTA 59.962 38.462 7.96 0.00 40.01 1.82
5558 8568 5.163591 TGCACGTACTACATTGCATACTACT 60.164 40.000 7.96 0.00 40.01 2.57
5559 8569 5.038683 TGCACGTACTACATTGCATACTAC 58.961 41.667 7.96 0.00 40.01 2.73
5569 8579 4.137116 ACCAATCATGCACGTACTACAT 57.863 40.909 0.00 0.00 0.00 2.29
5671 8684 8.064814 GGTAAAAAGATGATATCGCTTCTTGTC 58.935 37.037 13.16 5.23 33.95 3.18
5672 8685 7.770897 AGGTAAAAAGATGATATCGCTTCTTGT 59.229 33.333 13.16 7.55 33.95 3.16
5673 8686 8.147642 AGGTAAAAAGATGATATCGCTTCTTG 57.852 34.615 13.16 0.00 33.95 3.02
5674 8687 7.442666 GGAGGTAAAAAGATGATATCGCTTCTT 59.557 37.037 10.09 9.37 34.79 2.52
5675 8688 6.931840 GGAGGTAAAAAGATGATATCGCTTCT 59.068 38.462 10.09 4.50 0.00 2.85
5676 8689 6.128795 CGGAGGTAAAAAGATGATATCGCTTC 60.129 42.308 10.09 2.52 0.00 3.86
5677 8690 5.696724 CGGAGGTAAAAAGATGATATCGCTT 59.303 40.000 5.16 5.16 0.00 4.68
5678 8691 5.221461 ACGGAGGTAAAAAGATGATATCGCT 60.221 40.000 0.00 0.00 0.00 4.93
5679 8692 4.989168 ACGGAGGTAAAAAGATGATATCGC 59.011 41.667 0.00 0.00 0.00 4.58
5680 8693 5.634020 GGACGGAGGTAAAAAGATGATATCG 59.366 44.000 0.00 0.00 0.00 2.92
5681 8694 6.647067 CAGGACGGAGGTAAAAAGATGATATC 59.353 42.308 0.00 0.00 0.00 1.63
5682 8695 6.464465 CCAGGACGGAGGTAAAAAGATGATAT 60.464 42.308 0.00 0.00 36.56 1.63
5683 8696 5.163343 CCAGGACGGAGGTAAAAAGATGATA 60.163 44.000 0.00 0.00 36.56 2.15
5684 8697 4.384208 CCAGGACGGAGGTAAAAAGATGAT 60.384 45.833 0.00 0.00 36.56 2.45
5685 8698 3.055385 CCAGGACGGAGGTAAAAAGATGA 60.055 47.826 0.00 0.00 36.56 2.92
5686 8699 3.270877 CCAGGACGGAGGTAAAAAGATG 58.729 50.000 0.00 0.00 36.56 2.90
5687 8700 2.910977 ACCAGGACGGAGGTAAAAAGAT 59.089 45.455 0.00 0.00 36.07 2.40
5688 8701 2.332117 ACCAGGACGGAGGTAAAAAGA 58.668 47.619 0.00 0.00 36.07 2.52
5689 8702 2.853235 ACCAGGACGGAGGTAAAAAG 57.147 50.000 0.00 0.00 36.07 2.27
5690 8703 3.581265 AAACCAGGACGGAGGTAAAAA 57.419 42.857 0.00 0.00 37.07 1.94
5691 8704 4.914177 ATAAACCAGGACGGAGGTAAAA 57.086 40.909 0.00 0.00 37.07 1.52
5692 8705 4.566070 CCAATAAACCAGGACGGAGGTAAA 60.566 45.833 0.00 0.00 37.07 2.01
5693 8706 3.054948 CCAATAAACCAGGACGGAGGTAA 60.055 47.826 0.00 0.00 37.07 2.85
5694 8707 2.502538 CCAATAAACCAGGACGGAGGTA 59.497 50.000 0.00 0.00 37.07 3.08
5695 8708 1.280998 CCAATAAACCAGGACGGAGGT 59.719 52.381 0.00 0.00 40.61 3.85
5696 8709 1.280998 ACCAATAAACCAGGACGGAGG 59.719 52.381 0.00 0.00 38.63 4.30
5697 8710 2.629051 GACCAATAAACCAGGACGGAG 58.371 52.381 0.00 0.00 38.63 4.63
5698 8711 1.279846 GGACCAATAAACCAGGACGGA 59.720 52.381 0.00 0.00 38.63 4.69
5699 8712 1.280998 AGGACCAATAAACCAGGACGG 59.719 52.381 0.00 0.00 42.50 4.79
5700 8713 2.781681 AGGACCAATAAACCAGGACG 57.218 50.000 0.00 0.00 0.00 4.79
5701 8714 4.149598 ACAAAGGACCAATAAACCAGGAC 58.850 43.478 0.00 0.00 0.00 3.85
5702 8715 4.463050 ACAAAGGACCAATAAACCAGGA 57.537 40.909 0.00 0.00 0.00 3.86
5703 8716 6.850752 ATTACAAAGGACCAATAAACCAGG 57.149 37.500 0.00 0.00 0.00 4.45
5704 8717 8.147704 ACAAATTACAAAGGACCAATAAACCAG 58.852 33.333 0.00 0.00 0.00 4.00
5705 8718 7.928706 CACAAATTACAAAGGACCAATAAACCA 59.071 33.333 0.00 0.00 0.00 3.67
5706 8719 7.929245 ACACAAATTACAAAGGACCAATAAACC 59.071 33.333 0.00 0.00 0.00 3.27
5707 8720 8.880878 ACACAAATTACAAAGGACCAATAAAC 57.119 30.769 0.00 0.00 0.00 2.01
5708 8721 8.696374 TGACACAAATTACAAAGGACCAATAAA 58.304 29.630 0.00 0.00 0.00 1.40
5709 8722 8.239038 TGACACAAATTACAAAGGACCAATAA 57.761 30.769 0.00 0.00 0.00 1.40
5710 8723 7.825331 TGACACAAATTACAAAGGACCAATA 57.175 32.000 0.00 0.00 0.00 1.90
5711 8724 6.723298 TGACACAAATTACAAAGGACCAAT 57.277 33.333 0.00 0.00 0.00 3.16
5712 8725 6.531503 TTGACACAAATTACAAAGGACCAA 57.468 33.333 0.00 0.00 0.00 3.67
5713 8726 6.531503 TTTGACACAAATTACAAAGGACCA 57.468 33.333 0.00 0.00 0.00 4.02
5714 8727 8.432110 AAATTTGACACAAATTACAAAGGACC 57.568 30.769 18.37 0.00 36.07 4.46
5715 8728 9.701355 CAAAATTTGACACAAATTACAAAGGAC 57.299 29.630 18.37 0.00 36.07 3.85
5716 8729 9.658799 TCAAAATTTGACACAAATTACAAAGGA 57.341 25.926 18.37 9.94 36.07 3.36
5791 8804 9.653287 CTATGCTTAAATACGAATCCAAGGATA 57.347 33.333 1.29 0.00 33.97 2.59
5792 8805 8.157476 ACTATGCTTAAATACGAATCCAAGGAT 58.843 33.333 0.00 0.00 36.23 3.24
5793 8806 7.506114 ACTATGCTTAAATACGAATCCAAGGA 58.494 34.615 0.00 0.00 0.00 3.36
5794 8807 7.730364 ACTATGCTTAAATACGAATCCAAGG 57.270 36.000 0.00 0.00 0.00 3.61
5795 8808 9.651718 GAAACTATGCTTAAATACGAATCCAAG 57.348 33.333 0.00 0.00 0.00 3.61
5796 8809 8.617809 GGAAACTATGCTTAAATACGAATCCAA 58.382 33.333 0.00 0.00 0.00 3.53
5797 8810 7.771361 TGGAAACTATGCTTAAATACGAATCCA 59.229 33.333 0.00 0.00 0.00 3.41
5798 8811 8.068380 GTGGAAACTATGCTTAAATACGAATCC 58.932 37.037 0.00 0.00 0.00 3.01
5799 8812 8.827677 AGTGGAAACTATGCTTAAATACGAATC 58.172 33.333 0.00 0.00 0.00 2.52
5800 8813 8.612619 CAGTGGAAACTATGCTTAAATACGAAT 58.387 33.333 0.00 0.00 0.00 3.34
5801 8814 7.820386 TCAGTGGAAACTATGCTTAAATACGAA 59.180 33.333 0.00 0.00 0.00 3.85
5802 8815 7.324935 TCAGTGGAAACTATGCTTAAATACGA 58.675 34.615 0.00 0.00 0.00 3.43
5803 8816 7.534085 TCAGTGGAAACTATGCTTAAATACG 57.466 36.000 0.00 0.00 0.00 3.06
5856 8869 9.211485 ACGTGCACATTTACTAGTTTAACTAAT 57.789 29.630 18.64 0.00 29.00 1.73
5857 8870 8.489559 CACGTGCACATTTACTAGTTTAACTAA 58.510 33.333 18.64 0.00 29.00 2.24
5858 8871 7.359431 GCACGTGCACATTTACTAGTTTAACTA 60.359 37.037 34.52 4.66 41.59 2.24
5859 8872 6.565247 GCACGTGCACATTTACTAGTTTAACT 60.565 38.462 34.52 2.32 41.59 2.24
5860 8873 5.562623 GCACGTGCACATTTACTAGTTTAAC 59.437 40.000 34.52 0.00 41.59 2.01
5861 8874 5.681880 GCACGTGCACATTTACTAGTTTAA 58.318 37.500 34.52 0.00 41.59 1.52
5862 8875 5.272167 GCACGTGCACATTTACTAGTTTA 57.728 39.130 34.52 0.00 41.59 2.01
5863 8876 4.141855 GCACGTGCACATTTACTAGTTT 57.858 40.909 34.52 0.00 41.59 2.66
5864 8877 3.806316 GCACGTGCACATTTACTAGTT 57.194 42.857 34.52 0.00 41.59 2.24


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

AutoCloner maintained by Alex Coulton.