Multiple sequence alignment - TraesCS6B01G303000

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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 TraesCS6B01G303000 chr6B 100.000 2935 0 0 1 2935 542498978 542501912 0.000000e+00 5421.0
1 TraesCS6B01G303000 chr6B 88.050 159 15 4 210 367 64201340 64201185 5.000000e-43 185.0
2 TraesCS6B01G303000 chr6D 90.722 2436 99 49 402 2771 361178524 361180898 0.000000e+00 3129.0
3 TraesCS6B01G303000 chr6A 92.899 2056 70 22 361 2373 502147434 502149456 0.000000e+00 2918.0
4 TraesCS6B01G303000 chr6A 88.400 500 39 7 2441 2921 502149559 502150058 4.220000e-163 584.0
5 TraesCS6B01G303000 chr6A 86.364 308 31 7 59 360 601202893 601203195 2.820000e-85 326.0
6 TraesCS6B01G303000 chr6A 97.143 35 1 0 2328 2362 502149505 502149539 3.160000e-05 60.2
7 TraesCS6B01G303000 chr6A 100.000 30 0 0 1 30 502147316 502147345 4.090000e-04 56.5
8 TraesCS6B01G303000 chr2A 87.500 320 22 6 59 360 755767979 755768298 1.290000e-93 353.0
9 TraesCS6B01G303000 chr2A 81.988 322 38 10 54 369 469199983 469199676 3.750000e-64 255.0
10 TraesCS6B01G303000 chr1B 87.097 310 32 5 59 361 550935774 550936082 7.790000e-91 344.0
11 TraesCS6B01G303000 chr1B 84.026 313 36 8 55 360 330990413 330990718 3.700000e-74 289.0
12 TraesCS6B01G303000 chr2B 86.728 324 21 8 59 360 198358345 198358022 1.010000e-89 340.0
13 TraesCS6B01G303000 chr2B 80.588 340 51 9 54 380 409803829 409803492 6.280000e-62 248.0
14 TraesCS6B01G303000 chr3A 87.338 308 24 7 59 360 660194886 660195184 3.620000e-89 339.0
15 TraesCS6B01G303000 chr3A 80.220 273 34 10 63 327 20172813 20173073 1.390000e-43 187.0
16 TraesCS6B01G303000 chr3B 86.520 319 28 7 59 364 160351051 160350735 1.300000e-88 337.0
17 TraesCS6B01G303000 chr3B 87.097 310 25 7 57 360 672772064 672772364 1.300000e-88 337.0
18 TraesCS6B01G303000 chr3B 87.459 303 21 6 78 363 407251566 407251264 1.690000e-87 333.0
19 TraesCS6B01G303000 chr3B 87.000 300 22 8 78 360 582990297 582990596 3.650000e-84 322.0
20 TraesCS6B01G303000 chr7A 86.885 305 22 6 77 363 43514247 43513943 2.820000e-85 326.0
21 TraesCS6B01G303000 chr7A 81.250 288 40 12 1270 1544 200510087 200509801 1.370000e-53 220.0
22 TraesCS6B01G303000 chr7D 82.972 323 47 7 52 372 571867940 571867624 4.790000e-73 285.0
23 TraesCS6B01G303000 chr4A 83.828 303 35 7 77 367 713899344 713899644 2.880000e-70 276.0
24 TraesCS6B01G303000 chr4A 85.650 223 25 4 152 367 91287212 91287434 8.180000e-56 228.0
25 TraesCS6B01G303000 chr2D 82.353 306 35 11 78 366 177985982 177986285 6.280000e-62 248.0
26 TraesCS6B01G303000 chr2D 81.481 297 35 7 77 366 473137359 473137642 2.940000e-55 226.0
27 TraesCS6B01G303000 chr7B 83.026 271 35 8 1270 1530 337024326 337024057 4.890000e-58 235.0
28 TraesCS6B01G303000 chr5B 79.635 329 40 11 59 360 452638013 452638341 8.240000e-51 211.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G303000 chr6B 542498978 542501912 2934 False 5421.000 5421 100.0000 1 2935 1 chr6B.!!$F1 2934
1 TraesCS6B01G303000 chr6D 361178524 361180898 2374 False 3129.000 3129 90.7220 402 2771 1 chr6D.!!$F1 2369
2 TraesCS6B01G303000 chr6A 502147316 502150058 2742 False 904.675 2918 94.6105 1 2921 4 chr6A.!!$F2 2920

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
176 245 0.038744 CAGGCCTGGACCAGTCATTT 59.961 55.0 26.14 0.0 0.00 2.32 F
234 303 0.107848 CCCGACGGGCTTTTAGATGT 60.108 55.0 22.37 0.0 35.35 3.06 F
272 341 0.249280 CAAAAACAGGCCCGTTGGTC 60.249 55.0 4.78 0.0 36.05 4.02 F
310 379 0.307760 GGATTATTGCGTCGGGCTTG 59.692 55.0 0.00 0.0 44.05 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1690 1.135689 GCTTGCGGGTTAATCTGTGTG 60.136 52.381 0.00 0.00 0.0 3.82 R
1584 1691 1.165270 GCTTGCGGGTTAATCTGTGT 58.835 50.000 0.00 0.00 0.0 3.72 R
1901 2009 1.395826 GGTAGATGCTGAGCTCGGGT 61.396 60.000 23.87 2.47 0.0 5.28 R
2286 2399 1.801771 CACAATTTACGTGCGGAAGGA 59.198 47.619 0.00 0.00 0.0 3.36 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
30 31 1.672881 GTCCGCAGTAGGTACGTACAT 59.327 52.381 26.02 22.06 0.00 2.29
31 32 1.942657 TCCGCAGTAGGTACGTACATC 59.057 52.381 26.02 15.09 0.00 3.06
33 34 3.133691 CCGCAGTAGGTACGTACATCTA 58.866 50.000 26.02 16.06 0.00 1.98
63 132 0.472898 GGTGAGCCCTGGGTTATACC 59.527 60.000 15.56 15.96 37.60 2.73
64 133 1.508256 GTGAGCCCTGGGTTATACCT 58.492 55.000 15.56 0.69 38.64 3.08
65 134 1.141053 GTGAGCCCTGGGTTATACCTG 59.859 57.143 15.56 0.00 38.64 4.00
66 135 0.765510 GAGCCCTGGGTTATACCTGG 59.234 60.000 15.56 0.00 46.13 4.45
67 136 1.150764 GCCCTGGGTTATACCTGGC 59.849 63.158 15.56 8.18 45.45 4.85
68 137 1.844130 CCCTGGGTTATACCTGGCC 59.156 63.158 3.97 0.00 45.45 5.36
69 138 0.991355 CCCTGGGTTATACCTGGCCA 60.991 60.000 4.71 4.71 45.45 5.36
70 139 1.149101 CCTGGGTTATACCTGGCCAT 58.851 55.000 5.51 0.00 41.82 4.40
71 140 1.202927 CCTGGGTTATACCTGGCCATG 60.203 57.143 5.51 6.06 41.82 3.66
72 141 0.850100 TGGGTTATACCTGGCCATGG 59.150 55.000 5.51 13.05 38.64 3.66
73 142 0.112412 GGGTTATACCTGGCCATGGG 59.888 60.000 20.97 16.10 38.64 4.00
74 143 1.145571 GGTTATACCTGGCCATGGGA 58.854 55.000 17.65 12.89 34.73 4.37
75 144 1.497286 GGTTATACCTGGCCATGGGAA 59.503 52.381 17.65 9.02 34.73 3.97
76 145 2.489073 GGTTATACCTGGCCATGGGAAG 60.489 54.545 17.65 0.00 34.73 3.46
77 146 0.771127 TATACCTGGCCATGGGAAGC 59.229 55.000 17.65 0.00 0.00 3.86
90 159 3.440415 GAAGCCCGGCCCGAAAAG 61.440 66.667 3.71 0.00 0.00 2.27
122 191 4.436998 GACCCGACGCTGTCCCTG 62.437 72.222 4.85 0.00 0.00 4.45
128 197 4.715130 ACGCTGTCCCTGGGCCTA 62.715 66.667 8.22 0.00 0.00 3.93
129 198 3.854669 CGCTGTCCCTGGGCCTAG 61.855 72.222 9.64 9.64 0.00 3.02
130 199 2.365635 GCTGTCCCTGGGCCTAGA 60.366 66.667 19.36 0.00 0.00 2.43
131 200 1.768077 GCTGTCCCTGGGCCTAGAT 60.768 63.158 19.36 0.00 0.00 1.98
132 201 1.348775 GCTGTCCCTGGGCCTAGATT 61.349 60.000 19.36 0.00 0.00 2.40
133 202 1.216990 CTGTCCCTGGGCCTAGATTT 58.783 55.000 19.36 0.00 0.00 2.17
134 203 1.566231 CTGTCCCTGGGCCTAGATTTT 59.434 52.381 19.36 0.00 0.00 1.82
135 204 1.284785 TGTCCCTGGGCCTAGATTTTG 59.715 52.381 19.36 0.00 0.00 2.44
136 205 1.564348 GTCCCTGGGCCTAGATTTTGA 59.436 52.381 19.36 3.06 0.00 2.69
137 206 1.846439 TCCCTGGGCCTAGATTTTGAG 59.154 52.381 19.36 0.00 0.00 3.02
138 207 1.685148 CCTGGGCCTAGATTTTGAGC 58.315 55.000 19.36 0.00 0.00 4.26
139 208 1.685148 CTGGGCCTAGATTTTGAGCC 58.315 55.000 11.42 0.00 43.09 4.70
140 209 1.213926 CTGGGCCTAGATTTTGAGCCT 59.786 52.381 11.42 0.00 43.36 4.58
141 210 1.064463 TGGGCCTAGATTTTGAGCCTG 60.064 52.381 4.53 0.00 43.36 4.85
142 211 1.212935 GGGCCTAGATTTTGAGCCTGA 59.787 52.381 0.84 0.00 43.36 3.86
143 212 2.357154 GGGCCTAGATTTTGAGCCTGAA 60.357 50.000 0.84 0.00 43.36 3.02
144 213 2.948315 GGCCTAGATTTTGAGCCTGAAG 59.052 50.000 0.00 0.00 40.57 3.02
145 214 2.948315 GCCTAGATTTTGAGCCTGAAGG 59.052 50.000 0.00 0.00 38.53 3.46
174 243 3.408229 CAGGCCTGGACCAGTCAT 58.592 61.111 26.14 1.51 0.00 3.06
175 244 1.687612 CAGGCCTGGACCAGTCATT 59.312 57.895 26.14 0.00 0.00 2.57
176 245 0.038744 CAGGCCTGGACCAGTCATTT 59.961 55.000 26.14 0.00 0.00 2.32
177 246 0.779997 AGGCCTGGACCAGTCATTTT 59.220 50.000 20.24 0.00 0.00 1.82
178 247 1.147817 AGGCCTGGACCAGTCATTTTT 59.852 47.619 20.24 0.00 0.00 1.94
179 248 1.273327 GGCCTGGACCAGTCATTTTTG 59.727 52.381 20.24 3.39 0.00 2.44
180 249 1.337167 GCCTGGACCAGTCATTTTTGC 60.337 52.381 20.24 9.76 0.00 3.68
181 250 1.068333 CCTGGACCAGTCATTTTTGCG 60.068 52.381 20.24 0.00 0.00 4.85
182 251 0.313672 TGGACCAGTCATTTTTGCGC 59.686 50.000 0.00 0.00 0.00 6.09
183 252 0.598065 GGACCAGTCATTTTTGCGCT 59.402 50.000 9.73 0.00 0.00 5.92
184 253 1.000274 GGACCAGTCATTTTTGCGCTT 60.000 47.619 9.73 0.00 0.00 4.68
185 254 2.545742 GGACCAGTCATTTTTGCGCTTT 60.546 45.455 9.73 0.00 0.00 3.51
186 255 2.726241 GACCAGTCATTTTTGCGCTTTC 59.274 45.455 9.73 0.00 0.00 2.62
187 256 2.061028 CCAGTCATTTTTGCGCTTTCC 58.939 47.619 9.73 0.00 0.00 3.13
188 257 2.288395 CCAGTCATTTTTGCGCTTTCCT 60.288 45.455 9.73 0.00 0.00 3.36
189 258 2.727798 CAGTCATTTTTGCGCTTTCCTG 59.272 45.455 9.73 0.91 0.00 3.86
190 259 2.622942 AGTCATTTTTGCGCTTTCCTGA 59.377 40.909 9.73 3.60 0.00 3.86
191 260 3.068024 AGTCATTTTTGCGCTTTCCTGAA 59.932 39.130 9.73 0.00 0.00 3.02
192 261 3.426525 GTCATTTTTGCGCTTTCCTGAAG 59.573 43.478 9.73 0.00 38.45 3.02
193 262 2.507339 TTTTTGCGCTTTCCTGAAGG 57.493 45.000 9.73 0.00 35.82 3.46
194 263 1.398692 TTTTGCGCTTTCCTGAAGGT 58.601 45.000 9.73 0.00 35.82 3.50
195 264 0.951558 TTTGCGCTTTCCTGAAGGTC 59.048 50.000 9.73 0.00 35.82 3.85
196 265 1.227999 TTGCGCTTTCCTGAAGGTCG 61.228 55.000 9.73 0.00 35.82 4.79
197 266 2.391389 GCGCTTTCCTGAAGGTCGG 61.391 63.158 0.00 0.00 35.82 4.79
198 267 1.741770 CGCTTTCCTGAAGGTCGGG 60.742 63.158 0.00 0.00 44.41 5.14
199 268 2.041115 GCTTTCCTGAAGGTCGGGC 61.041 63.158 0.00 0.00 42.73 6.13
200 269 1.377333 CTTTCCTGAAGGTCGGGCC 60.377 63.158 0.00 0.00 42.73 5.80
201 270 3.248446 TTTCCTGAAGGTCGGGCCG 62.248 63.158 22.51 22.51 42.73 6.13
202 271 4.689549 TCCTGAAGGTCGGGCCGA 62.690 66.667 27.46 27.46 42.73 5.54
233 302 2.690326 CCCGACGGGCTTTTAGATG 58.310 57.895 22.37 0.00 35.35 2.90
234 303 0.107848 CCCGACGGGCTTTTAGATGT 60.108 55.000 22.37 0.00 35.35 3.06
235 304 1.677820 CCCGACGGGCTTTTAGATGTT 60.678 52.381 22.37 0.00 35.35 2.71
236 305 1.664151 CCGACGGGCTTTTAGATGTTC 59.336 52.381 5.81 0.00 0.00 3.18
237 306 2.343101 CGACGGGCTTTTAGATGTTCA 58.657 47.619 0.00 0.00 0.00 3.18
238 307 2.348666 CGACGGGCTTTTAGATGTTCAG 59.651 50.000 0.00 0.00 0.00 3.02
239 308 2.678336 GACGGGCTTTTAGATGTTCAGG 59.322 50.000 0.00 0.00 0.00 3.86
240 309 1.401905 CGGGCTTTTAGATGTTCAGGC 59.598 52.381 0.00 0.00 0.00 4.85
241 310 1.751351 GGGCTTTTAGATGTTCAGGCC 59.249 52.381 0.00 0.00 42.39 5.19
242 311 1.401905 GGCTTTTAGATGTTCAGGCCG 59.598 52.381 0.00 0.00 0.00 6.13
243 312 1.401905 GCTTTTAGATGTTCAGGCCGG 59.598 52.381 0.00 0.00 0.00 6.13
244 313 2.017049 CTTTTAGATGTTCAGGCCGGG 58.983 52.381 2.18 0.00 0.00 5.73
245 314 0.393808 TTTAGATGTTCAGGCCGGGC 60.394 55.000 22.67 22.67 0.00 6.13
246 315 1.271840 TTAGATGTTCAGGCCGGGCT 61.272 55.000 27.45 27.45 0.00 5.19
247 316 1.686325 TAGATGTTCAGGCCGGGCTC 61.686 60.000 30.43 18.17 0.00 4.70
248 317 3.329542 GATGTTCAGGCCGGGCTCA 62.330 63.158 30.43 23.60 0.00 4.26
249 318 3.335356 ATGTTCAGGCCGGGCTCAG 62.335 63.158 30.43 18.74 0.00 3.35
250 319 4.785453 GTTCAGGCCGGGCTCAGG 62.785 72.222 30.43 17.92 0.00 3.86
262 331 1.667722 GCTCAGGCCCAAAAACAGG 59.332 57.895 0.00 0.00 0.00 4.00
267 336 3.230990 GCCCAAAAACAGGCCCGT 61.231 61.111 0.00 0.00 43.76 5.28
268 337 2.802724 GCCCAAAAACAGGCCCGTT 61.803 57.895 0.00 0.00 43.76 4.44
269 338 1.068921 CCCAAAAACAGGCCCGTTG 59.931 57.895 4.78 0.00 0.00 4.10
270 339 1.068921 CCAAAAACAGGCCCGTTGG 59.931 57.895 4.78 5.65 33.30 3.77
271 340 1.681486 CCAAAAACAGGCCCGTTGGT 61.681 55.000 4.78 0.00 35.12 3.67
272 341 0.249280 CAAAAACAGGCCCGTTGGTC 60.249 55.000 4.78 0.00 36.05 4.02
273 342 1.730451 AAAAACAGGCCCGTTGGTCG 61.730 55.000 4.78 0.00 42.85 4.79
299 368 4.500265 CCGGGCCTGGGATTATTG 57.500 61.111 24.51 0.00 0.00 1.90
300 369 1.903404 CCGGGCCTGGGATTATTGC 60.903 63.158 24.51 0.00 0.00 3.56
301 370 2.260869 CGGGCCTGGGATTATTGCG 61.261 63.158 2.57 0.00 0.00 4.85
302 371 1.152756 GGGCCTGGGATTATTGCGT 60.153 57.895 0.84 0.00 0.00 5.24
303 372 1.172812 GGGCCTGGGATTATTGCGTC 61.173 60.000 0.84 0.00 0.00 5.19
304 373 1.507141 GGCCTGGGATTATTGCGTCG 61.507 60.000 0.00 0.00 0.00 5.12
305 374 1.507141 GCCTGGGATTATTGCGTCGG 61.507 60.000 0.00 0.00 0.00 4.79
306 375 0.884704 CCTGGGATTATTGCGTCGGG 60.885 60.000 0.00 0.00 0.00 5.14
307 376 1.507141 CTGGGATTATTGCGTCGGGC 61.507 60.000 0.00 0.00 43.96 6.13
308 377 1.227853 GGGATTATTGCGTCGGGCT 60.228 57.895 0.00 0.00 44.05 5.19
309 378 0.818040 GGGATTATTGCGTCGGGCTT 60.818 55.000 0.00 0.00 44.05 4.35
310 379 0.307760 GGATTATTGCGTCGGGCTTG 59.692 55.000 0.00 0.00 44.05 4.01
311 380 0.307760 GATTATTGCGTCGGGCTTGG 59.692 55.000 0.00 0.00 44.05 3.61
312 381 1.724582 ATTATTGCGTCGGGCTTGGC 61.725 55.000 0.00 0.00 44.05 4.52
313 382 2.813226 TTATTGCGTCGGGCTTGGCT 62.813 55.000 0.00 0.00 44.05 4.75
314 383 1.962321 TATTGCGTCGGGCTTGGCTA 61.962 55.000 0.00 0.00 44.05 3.93
315 384 3.824028 TATTGCGTCGGGCTTGGCTAG 62.824 57.143 0.00 0.00 44.05 3.42
349 418 3.925090 GGCCCGACCCGAGGTATG 61.925 72.222 0.00 0.00 35.25 2.39
350 419 3.925090 GCCCGACCCGAGGTATGG 61.925 72.222 0.00 2.06 35.25 2.74
351 420 3.925090 CCCGACCCGAGGTATGGC 61.925 72.222 7.78 0.00 35.25 4.40
352 421 3.925090 CCGACCCGAGGTATGGCC 61.925 72.222 0.00 0.00 35.25 5.36
353 422 3.151710 CGACCCGAGGTATGGCCA 61.152 66.667 8.56 8.56 40.61 5.36
354 423 2.822399 GACCCGAGGTATGGCCAG 59.178 66.667 13.05 0.00 40.61 4.85
355 424 2.768344 ACCCGAGGTATGGCCAGG 60.768 66.667 13.05 7.59 40.61 4.45
356 425 2.768344 CCCGAGGTATGGCCAGGT 60.768 66.667 13.05 0.00 40.61 4.00
357 426 1.458777 CCCGAGGTATGGCCAGGTA 60.459 63.158 13.05 0.00 40.61 3.08
358 427 0.836400 CCCGAGGTATGGCCAGGTAT 60.836 60.000 13.05 0.00 40.61 2.73
359 428 1.551560 CCCGAGGTATGGCCAGGTATA 60.552 57.143 13.05 0.00 40.61 1.47
360 429 1.549170 CCGAGGTATGGCCAGGTATAC 59.451 57.143 13.05 8.77 40.61 1.47
361 430 1.549170 CGAGGTATGGCCAGGTATACC 59.451 57.143 21.19 21.19 45.90 2.73
362 431 1.907255 GAGGTATGGCCAGGTATACCC 59.093 57.143 23.86 14.60 46.45 3.69
363 432 1.512643 AGGTATGGCCAGGTATACCCT 59.487 52.381 23.86 12.48 46.45 4.34
375 444 1.411612 GTATACCCTGGGTGTCCGAAG 59.588 57.143 28.64 0.00 36.19 3.79
387 456 3.126343 GGTGTCCGAAGCGATAAACAAAT 59.874 43.478 0.00 0.00 0.00 2.32
392 461 6.143118 TGTCCGAAGCGATAAACAAATTTTTG 59.857 34.615 1.56 1.56 43.62 2.44
514 585 2.470057 AAGGAAAAAGGTGCCAAGGA 57.530 45.000 0.00 0.00 0.00 3.36
515 586 2.001076 AGGAAAAAGGTGCCAAGGAG 57.999 50.000 0.00 0.00 0.00 3.69
578 649 0.601576 TGTCAACCATGGAACGTCGG 60.602 55.000 21.47 0.00 0.00 4.79
590 661 3.897502 CGTCGGCACATGTACGCG 61.898 66.667 3.53 3.53 0.00 6.01
1197 1283 2.364842 GAGGAGGAGGCTGGAGCA 60.365 66.667 0.00 0.00 44.36 4.26
1248 1343 2.757917 GGCGAGCAGTCCTCCTCT 60.758 66.667 0.00 0.00 37.27 3.69
1251 1346 1.813192 CGAGCAGTCCTCCTCTTCC 59.187 63.158 0.00 0.00 37.27 3.46
1555 1653 3.379445 CAGGTACGTCCGCCACCT 61.379 66.667 0.94 0.94 43.56 4.00
1562 1660 1.079405 CGTCCGCCACCTGTACAAT 60.079 57.895 0.00 0.00 0.00 2.71
1601 1709 1.529226 CCACACAGATTAACCCGCAA 58.471 50.000 0.00 0.00 0.00 4.85
1941 2049 2.033602 TCAGAGTCTGACGGCCGA 59.966 61.111 35.90 9.83 35.39 5.54
1951 2060 2.799540 GACGGCCGATCGAGCAAAC 61.800 63.158 35.90 9.01 0.00 2.93
2036 2149 4.536090 TCTCTTGGGTTCCATGTATTCTGT 59.464 41.667 0.00 0.00 31.53 3.41
2181 2294 9.921637 CATTAGAGCAAAGGTTAACCAAATTTA 57.078 29.630 26.26 7.21 38.89 1.40
2286 2399 4.139786 CAATCCCATCCATTCGATCAACT 58.860 43.478 0.00 0.00 0.00 3.16
2320 2455 5.344665 CGTAAATTGTGTGCCCATAGTTTTG 59.655 40.000 0.00 0.00 0.00 2.44
2321 2456 2.810439 TTGTGTGCCCATAGTTTTGC 57.190 45.000 0.00 0.00 0.00 3.68
2326 2461 2.584835 TGCCCATAGTTTTGCACTCT 57.415 45.000 0.00 0.00 36.88 3.24
2327 2462 2.875296 TGCCCATAGTTTTGCACTCTT 58.125 42.857 0.00 0.00 36.88 2.85
2328 2463 4.027674 TGCCCATAGTTTTGCACTCTTA 57.972 40.909 0.00 0.00 36.88 2.10
2329 2464 4.402829 TGCCCATAGTTTTGCACTCTTAA 58.597 39.130 0.00 0.00 36.88 1.85
2330 2465 4.830046 TGCCCATAGTTTTGCACTCTTAAA 59.170 37.500 0.00 0.00 36.88 1.52
2331 2466 5.303078 TGCCCATAGTTTTGCACTCTTAAAA 59.697 36.000 0.00 0.00 36.88 1.52
2332 2467 6.014669 TGCCCATAGTTTTGCACTCTTAAAAT 60.015 34.615 0.00 0.00 36.88 1.82
2376 2511 0.954449 CAGGCAAGCTCTCACCACAG 60.954 60.000 0.00 0.00 0.00 3.66
2377 2512 1.123861 AGGCAAGCTCTCACCACAGA 61.124 55.000 0.00 0.00 0.00 3.41
2378 2513 0.250467 GGCAAGCTCTCACCACAGAA 60.250 55.000 0.00 0.00 0.00 3.02
2379 2514 1.597742 GCAAGCTCTCACCACAGAAA 58.402 50.000 0.00 0.00 0.00 2.52
2380 2515 1.949525 GCAAGCTCTCACCACAGAAAA 59.050 47.619 0.00 0.00 0.00 2.29
2381 2516 2.555757 GCAAGCTCTCACCACAGAAAAT 59.444 45.455 0.00 0.00 0.00 1.82
2382 2517 3.005155 GCAAGCTCTCACCACAGAAAATT 59.995 43.478 0.00 0.00 0.00 1.82
2383 2518 4.791974 CAAGCTCTCACCACAGAAAATTC 58.208 43.478 0.00 0.00 0.00 2.17
2384 2519 4.090761 AGCTCTCACCACAGAAAATTCA 57.909 40.909 0.00 0.00 0.00 2.57
2385 2520 4.070716 AGCTCTCACCACAGAAAATTCAG 58.929 43.478 0.00 0.00 0.00 3.02
2386 2521 3.190118 GCTCTCACCACAGAAAATTCAGG 59.810 47.826 0.00 0.00 0.00 3.86
2387 2522 3.149196 TCTCACCACAGAAAATTCAGGC 58.851 45.455 0.00 0.00 0.00 4.85
2388 2523 2.886523 CTCACCACAGAAAATTCAGGCA 59.113 45.455 0.00 0.00 0.00 4.75
2389 2524 3.295093 TCACCACAGAAAATTCAGGCAA 58.705 40.909 0.00 0.00 0.00 4.52
2390 2525 3.318839 TCACCACAGAAAATTCAGGCAAG 59.681 43.478 0.00 0.00 0.00 4.01
2391 2526 2.036346 ACCACAGAAAATTCAGGCAAGC 59.964 45.455 0.00 0.00 0.00 4.01
2392 2527 2.298163 CCACAGAAAATTCAGGCAAGCT 59.702 45.455 0.00 0.00 0.00 3.74
2393 2528 3.572584 CACAGAAAATTCAGGCAAGCTC 58.427 45.455 0.00 0.00 0.00 4.09
2394 2529 3.255149 CACAGAAAATTCAGGCAAGCTCT 59.745 43.478 0.00 0.00 0.00 4.09
2395 2530 3.505293 ACAGAAAATTCAGGCAAGCTCTC 59.495 43.478 0.00 0.00 0.00 3.20
2396 2531 3.504906 CAGAAAATTCAGGCAAGCTCTCA 59.495 43.478 0.00 0.00 0.00 3.27
2397 2532 3.505293 AGAAAATTCAGGCAAGCTCTCAC 59.495 43.478 0.00 0.00 0.00 3.51
2398 2533 1.831580 AATTCAGGCAAGCTCTCACC 58.168 50.000 0.00 0.00 0.00 4.02
2399 2534 0.694771 ATTCAGGCAAGCTCTCACCA 59.305 50.000 0.00 0.00 0.00 4.17
2400 2535 0.250467 TTCAGGCAAGCTCTCACCAC 60.250 55.000 0.00 0.00 0.00 4.16
2401 2536 1.071987 CAGGCAAGCTCTCACCACA 59.928 57.895 0.00 0.00 0.00 4.17
2402 2537 0.535780 CAGGCAAGCTCTCACCACAA 60.536 55.000 0.00 0.00 0.00 3.33
2403 2538 0.536006 AGGCAAGCTCTCACCACAAC 60.536 55.000 0.00 0.00 0.00 3.32
2404 2539 1.518903 GGCAAGCTCTCACCACAACC 61.519 60.000 0.00 0.00 0.00 3.77
2405 2540 0.819259 GCAAGCTCTCACCACAACCA 60.819 55.000 0.00 0.00 0.00 3.67
2427 2562 3.375922 AGGGTGAAAAGTAAACACACACG 59.624 43.478 0.00 0.00 39.96 4.49
2429 2564 2.774074 GTGAAAAGTAAACACACACGCG 59.226 45.455 3.53 3.53 35.06 6.01
2471 2668 1.603455 CAACCCCAACGCATGAGGT 60.603 57.895 0.00 0.00 0.00 3.85
2507 2704 0.238289 CAACAAAGCCGCGTCTTGAT 59.762 50.000 1.91 0.00 0.00 2.57
2516 2713 0.179240 CGCGTCTTGATCAACACTGC 60.179 55.000 11.42 13.66 0.00 4.40
2563 2760 1.149148 GTCCTGGTCAACTCGAAAGC 58.851 55.000 0.00 0.00 0.00 3.51
2568 2765 1.352156 GGTCAACTCGAAAGCGCGAT 61.352 55.000 12.10 0.00 39.85 4.58
2570 2767 1.007319 GTCAACTCGAAAGCGCGATAC 60.007 52.381 12.10 0.00 39.85 2.24
2583 2780 1.717194 GCGATACCTCCAAACGAACA 58.283 50.000 0.00 0.00 0.00 3.18
2606 2803 2.356553 TGCCGACGCACCAACTAC 60.357 61.111 0.00 0.00 41.12 2.73
2630 2847 2.739943 TGAGTGGGTGATAGGACTCAG 58.260 52.381 0.00 0.00 39.86 3.35
2685 2902 2.032924 CCATGACGACGTACATAGCTCA 59.967 50.000 0.00 0.00 0.00 4.26
2707 2924 4.580167 CACCTGAAGAACAATCCAGAACAA 59.420 41.667 0.00 0.00 0.00 2.83
2712 2929 4.345859 AGAACAATCCAGAACAACGGTA 57.654 40.909 0.00 0.00 0.00 4.02
2723 2940 1.752683 ACAACGGTAAGCACCAACAA 58.247 45.000 0.00 0.00 46.14 2.83
2739 2956 3.315191 CCAACAAAGGAACAATGTCGAGT 59.685 43.478 0.00 0.00 0.00 4.18
2757 2974 1.153529 TGCGTCGCCATTACCGATT 60.154 52.632 15.88 0.00 37.04 3.34
2773 2990 2.093869 CCGATTTGGAACCGAACCTAGA 60.094 50.000 0.00 0.00 42.00 2.43
2783 3000 0.459759 CGAACCTAGACTTTCGCCCC 60.460 60.000 7.78 0.00 38.31 5.80
2795 3012 2.999739 TTCGCCCCGAGACAACCAAC 63.000 60.000 0.00 0.00 37.14 3.77
2806 3023 1.604278 GACAACCAACCAAGTGAGAGC 59.396 52.381 0.00 0.00 0.00 4.09
2843 3060 0.606401 ACCACAATGACGCCTCCAAG 60.606 55.000 0.00 0.00 0.00 3.61
2844 3061 0.321564 CCACAATGACGCCTCCAAGA 60.322 55.000 0.00 0.00 0.00 3.02
2848 3065 0.035056 AATGACGCCTCCAAGAAGGG 60.035 55.000 0.00 0.00 36.88 3.95
2921 3138 4.191544 TGACTTTCATCCGAATCATCACC 58.808 43.478 0.00 0.00 0.00 4.02
2922 3139 4.191544 GACTTTCATCCGAATCATCACCA 58.808 43.478 0.00 0.00 0.00 4.17
2923 3140 4.785301 ACTTTCATCCGAATCATCACCAT 58.215 39.130 0.00 0.00 0.00 3.55
2924 3141 5.195940 ACTTTCATCCGAATCATCACCATT 58.804 37.500 0.00 0.00 0.00 3.16
2925 3142 5.297776 ACTTTCATCCGAATCATCACCATTC 59.702 40.000 0.00 0.00 0.00 2.67
2926 3143 3.743521 TCATCCGAATCATCACCATTCC 58.256 45.455 0.00 0.00 0.00 3.01
2927 3144 3.392285 TCATCCGAATCATCACCATTCCT 59.608 43.478 0.00 0.00 0.00 3.36
2928 3145 3.198409 TCCGAATCATCACCATTCCTG 57.802 47.619 0.00 0.00 0.00 3.86
2929 3146 1.605710 CCGAATCATCACCATTCCTGC 59.394 52.381 0.00 0.00 0.00 4.85
2930 3147 1.605710 CGAATCATCACCATTCCTGCC 59.394 52.381 0.00 0.00 0.00 4.85
2931 3148 1.959282 GAATCATCACCATTCCTGCCC 59.041 52.381 0.00 0.00 0.00 5.36
2932 3149 0.928505 ATCATCACCATTCCTGCCCA 59.071 50.000 0.00 0.00 0.00 5.36
2933 3150 0.928505 TCATCACCATTCCTGCCCAT 59.071 50.000 0.00 0.00 0.00 4.00
2934 3151 1.133699 TCATCACCATTCCTGCCCATC 60.134 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.179009 CTCACCCCGTATCCCGTAGA 60.179 60.000 0.00 0.00 33.66 2.59
31 32 1.803366 GCTCACCCCGTATCCCGTAG 61.803 65.000 0.00 0.00 33.66 3.51
33 34 3.152400 GCTCACCCCGTATCCCGT 61.152 66.667 0.00 0.00 33.66 5.28
58 127 0.771127 GCTTCCCATGGCCAGGTATA 59.229 55.000 17.55 0.00 0.00 1.47
59 128 1.538666 GCTTCCCATGGCCAGGTAT 59.461 57.895 17.55 0.00 0.00 2.73
60 129 2.689691 GGCTTCCCATGGCCAGGTA 61.690 63.158 17.55 3.27 46.84 3.08
61 130 4.066139 GGCTTCCCATGGCCAGGT 62.066 66.667 17.55 0.00 46.84 4.00
73 142 3.440415 CTTTTCGGGCCGGGCTTC 61.440 66.667 28.80 11.34 0.00 3.86
105 174 4.436998 CAGGGACAGCGTCGGGTC 62.437 72.222 0.00 0.00 32.65 4.46
111 180 4.715130 TAGGCCCAGGGACAGCGT 62.715 66.667 16.27 0.00 29.21 5.07
112 181 3.854669 CTAGGCCCAGGGACAGCG 61.855 72.222 16.27 0.00 29.21 5.18
113 182 1.348775 AATCTAGGCCCAGGGACAGC 61.349 60.000 16.27 0.00 29.21 4.40
114 183 1.216990 AAATCTAGGCCCAGGGACAG 58.783 55.000 16.27 9.40 29.21 3.51
115 184 1.284785 CAAAATCTAGGCCCAGGGACA 59.715 52.381 16.27 0.00 29.21 4.02
116 185 1.564348 TCAAAATCTAGGCCCAGGGAC 59.436 52.381 10.89 6.38 0.00 4.46
117 186 1.846439 CTCAAAATCTAGGCCCAGGGA 59.154 52.381 10.89 0.00 0.00 4.20
118 187 1.752084 GCTCAAAATCTAGGCCCAGGG 60.752 57.143 0.00 0.00 0.00 4.45
119 188 1.685148 GCTCAAAATCTAGGCCCAGG 58.315 55.000 0.00 0.00 0.00 4.45
120 189 1.213926 AGGCTCAAAATCTAGGCCCAG 59.786 52.381 0.00 0.00 43.36 4.45
121 190 1.064463 CAGGCTCAAAATCTAGGCCCA 60.064 52.381 0.00 0.00 43.36 5.36
122 191 1.212935 TCAGGCTCAAAATCTAGGCCC 59.787 52.381 0.00 0.00 43.36 5.80
123 192 2.717639 TCAGGCTCAAAATCTAGGCC 57.282 50.000 0.00 0.00 42.74 5.19
124 193 2.948315 CCTTCAGGCTCAAAATCTAGGC 59.052 50.000 0.00 0.00 38.50 3.93
157 226 0.038744 AAATGACTGGTCCAGGCCTG 59.961 55.000 26.87 26.87 39.07 4.85
158 227 0.779997 AAAATGACTGGTCCAGGCCT 59.220 50.000 22.69 9.79 39.07 5.19
159 228 1.273327 CAAAAATGACTGGTCCAGGCC 59.727 52.381 22.69 13.68 39.07 5.19
160 229 1.337167 GCAAAAATGACTGGTCCAGGC 60.337 52.381 23.06 21.11 40.49 4.85
161 230 1.068333 CGCAAAAATGACTGGTCCAGG 60.068 52.381 23.06 5.37 35.51 4.45
162 231 1.666888 GCGCAAAAATGACTGGTCCAG 60.667 52.381 17.88 17.88 37.52 3.86
163 232 0.313672 GCGCAAAAATGACTGGTCCA 59.686 50.000 0.30 0.00 0.00 4.02
164 233 0.598065 AGCGCAAAAATGACTGGTCC 59.402 50.000 11.47 0.00 0.00 4.46
165 234 2.422276 AAGCGCAAAAATGACTGGTC 57.578 45.000 11.47 0.00 0.00 4.02
166 235 2.545742 GGAAAGCGCAAAAATGACTGGT 60.546 45.455 11.47 0.00 0.00 4.00
167 236 2.061028 GGAAAGCGCAAAAATGACTGG 58.939 47.619 11.47 0.00 0.00 4.00
168 237 2.727798 CAGGAAAGCGCAAAAATGACTG 59.272 45.455 11.47 2.85 0.00 3.51
169 238 2.622942 TCAGGAAAGCGCAAAAATGACT 59.377 40.909 11.47 0.00 0.00 3.41
170 239 3.011949 TCAGGAAAGCGCAAAAATGAC 57.988 42.857 11.47 0.00 0.00 3.06
171 240 3.552684 CCTTCAGGAAAGCGCAAAAATGA 60.553 43.478 11.47 5.25 37.39 2.57
172 241 2.733026 CCTTCAGGAAAGCGCAAAAATG 59.267 45.455 11.47 2.50 37.39 2.32
173 242 2.365293 ACCTTCAGGAAAGCGCAAAAAT 59.635 40.909 11.47 0.00 38.94 1.82
174 243 1.754226 ACCTTCAGGAAAGCGCAAAAA 59.246 42.857 11.47 0.00 38.94 1.94
175 244 1.336755 GACCTTCAGGAAAGCGCAAAA 59.663 47.619 11.47 0.00 38.94 2.44
176 245 0.951558 GACCTTCAGGAAAGCGCAAA 59.048 50.000 11.47 0.00 38.94 3.68
177 246 1.227999 CGACCTTCAGGAAAGCGCAA 61.228 55.000 11.47 0.00 38.94 4.85
178 247 1.667830 CGACCTTCAGGAAAGCGCA 60.668 57.895 11.47 0.00 38.94 6.09
179 248 2.391389 CCGACCTTCAGGAAAGCGC 61.391 63.158 0.00 0.00 38.94 5.92
180 249 1.741770 CCCGACCTTCAGGAAAGCG 60.742 63.158 0.00 0.00 38.94 4.68
181 250 2.041115 GCCCGACCTTCAGGAAAGC 61.041 63.158 0.00 0.00 38.94 3.51
182 251 1.377333 GGCCCGACCTTCAGGAAAG 60.377 63.158 0.00 0.00 38.94 2.62
183 252 2.754375 GGCCCGACCTTCAGGAAA 59.246 61.111 0.00 0.00 38.94 3.13
184 253 3.702048 CGGCCCGACCTTCAGGAA 61.702 66.667 0.00 0.00 38.94 3.36
185 254 4.689549 TCGGCCCGACCTTCAGGA 62.690 66.667 0.00 0.00 38.94 3.86
216 285 1.664151 GAACATCTAAAAGCCCGTCGG 59.336 52.381 3.60 3.60 0.00 4.79
217 286 2.343101 TGAACATCTAAAAGCCCGTCG 58.657 47.619 0.00 0.00 0.00 5.12
218 287 2.678336 CCTGAACATCTAAAAGCCCGTC 59.322 50.000 0.00 0.00 0.00 4.79
219 288 2.711542 CCTGAACATCTAAAAGCCCGT 58.288 47.619 0.00 0.00 0.00 5.28
220 289 1.401905 GCCTGAACATCTAAAAGCCCG 59.598 52.381 0.00 0.00 0.00 6.13
221 290 1.751351 GGCCTGAACATCTAAAAGCCC 59.249 52.381 0.00 0.00 32.93 5.19
222 291 1.401905 CGGCCTGAACATCTAAAAGCC 59.598 52.381 0.00 0.00 35.78 4.35
223 292 1.401905 CCGGCCTGAACATCTAAAAGC 59.598 52.381 0.00 0.00 0.00 3.51
224 293 2.017049 CCCGGCCTGAACATCTAAAAG 58.983 52.381 0.00 0.00 0.00 2.27
225 294 1.953311 GCCCGGCCTGAACATCTAAAA 60.953 52.381 0.00 0.00 0.00 1.52
226 295 0.393808 GCCCGGCCTGAACATCTAAA 60.394 55.000 0.00 0.00 0.00 1.85
227 296 1.223487 GCCCGGCCTGAACATCTAA 59.777 57.895 0.00 0.00 0.00 2.10
228 297 1.686325 GAGCCCGGCCTGAACATCTA 61.686 60.000 5.55 0.00 0.00 1.98
229 298 3.011517 AGCCCGGCCTGAACATCT 61.012 61.111 5.55 0.00 0.00 2.90
230 299 2.514824 GAGCCCGGCCTGAACATC 60.515 66.667 5.55 0.00 0.00 3.06
231 300 3.329889 TGAGCCCGGCCTGAACAT 61.330 61.111 5.55 0.00 0.00 2.71
232 301 4.020617 CTGAGCCCGGCCTGAACA 62.021 66.667 5.55 0.00 0.00 3.18
233 302 4.785453 CCTGAGCCCGGCCTGAAC 62.785 72.222 5.55 0.00 0.00 3.18
244 313 1.667722 CCTGTTTTTGGGCCTGAGC 59.332 57.895 4.53 0.00 38.76 4.26
245 314 1.667722 GCCTGTTTTTGGGCCTGAG 59.332 57.895 4.53 0.00 42.30 3.35
246 315 3.869481 GCCTGTTTTTGGGCCTGA 58.131 55.556 4.53 0.00 42.30 3.86
251 320 1.068921 CAACGGGCCTGTTTTTGGG 59.931 57.895 27.83 12.20 0.00 4.12
252 321 1.068921 CCAACGGGCCTGTTTTTGG 59.931 57.895 27.83 22.25 0.00 3.28
253 322 0.249280 GACCAACGGGCCTGTTTTTG 60.249 55.000 27.83 19.82 37.90 2.44
254 323 1.730451 CGACCAACGGGCCTGTTTTT 61.730 55.000 27.83 16.86 37.90 1.94
255 324 2.190841 CGACCAACGGGCCTGTTTT 61.191 57.895 27.83 17.24 37.90 2.43
256 325 2.593436 CGACCAACGGGCCTGTTT 60.593 61.111 27.83 14.63 37.90 2.83
280 349 3.146828 AATAATCCCAGGCCCGGGC 62.147 63.158 38.57 38.57 46.92 6.13
282 351 1.903404 GCAATAATCCCAGGCCCGG 60.903 63.158 0.00 0.00 0.00 5.73
283 352 2.260869 CGCAATAATCCCAGGCCCG 61.261 63.158 0.00 0.00 0.00 6.13
284 353 1.152756 ACGCAATAATCCCAGGCCC 60.153 57.895 0.00 0.00 0.00 5.80
285 354 1.507141 CGACGCAATAATCCCAGGCC 61.507 60.000 0.00 0.00 0.00 5.19
286 355 1.507141 CCGACGCAATAATCCCAGGC 61.507 60.000 0.00 0.00 0.00 4.85
287 356 0.884704 CCCGACGCAATAATCCCAGG 60.885 60.000 0.00 0.00 0.00 4.45
288 357 1.507141 GCCCGACGCAATAATCCCAG 61.507 60.000 0.00 0.00 37.47 4.45
289 358 1.525077 GCCCGACGCAATAATCCCA 60.525 57.895 0.00 0.00 37.47 4.37
290 359 0.818040 AAGCCCGACGCAATAATCCC 60.818 55.000 0.00 0.00 41.38 3.85
291 360 0.307760 CAAGCCCGACGCAATAATCC 59.692 55.000 0.00 0.00 41.38 3.01
292 361 0.307760 CCAAGCCCGACGCAATAATC 59.692 55.000 0.00 0.00 41.38 1.75
293 362 1.724582 GCCAAGCCCGACGCAATAAT 61.725 55.000 0.00 0.00 41.38 1.28
294 363 2.403378 GCCAAGCCCGACGCAATAA 61.403 57.895 0.00 0.00 41.38 1.40
295 364 1.962321 TAGCCAAGCCCGACGCAATA 61.962 55.000 0.00 0.00 41.38 1.90
296 365 3.323758 TAGCCAAGCCCGACGCAAT 62.324 57.895 0.00 0.00 41.38 3.56
297 366 3.950794 CTAGCCAAGCCCGACGCAA 62.951 63.158 0.00 0.00 41.38 4.85
298 367 4.451150 CTAGCCAAGCCCGACGCA 62.451 66.667 0.00 0.00 41.38 5.24
332 401 3.925090 CATACCTCGGGTCGGGCC 61.925 72.222 0.00 0.00 37.09 5.80
333 402 3.925090 CCATACCTCGGGTCGGGC 61.925 72.222 0.00 0.00 37.09 6.13
334 403 3.925090 GCCATACCTCGGGTCGGG 61.925 72.222 0.00 4.21 37.09 5.14
335 404 3.925090 GGCCATACCTCGGGTCGG 61.925 72.222 0.00 3.55 37.09 4.79
336 405 3.151710 TGGCCATACCTCGGGTCG 61.152 66.667 0.00 0.00 40.22 4.79
337 406 2.808206 CCTGGCCATACCTCGGGTC 61.808 68.421 5.51 0.00 40.22 4.46
338 407 2.246513 TACCTGGCCATACCTCGGGT 62.247 60.000 5.51 11.24 40.22 5.28
339 408 0.836400 ATACCTGGCCATACCTCGGG 60.836 60.000 5.51 4.26 40.22 5.14
340 409 1.549170 GTATACCTGGCCATACCTCGG 59.451 57.143 5.51 5.16 40.22 4.63
341 410 1.549170 GGTATACCTGGCCATACCTCG 59.451 57.143 21.37 3.42 42.28 4.63
342 411 1.907255 GGGTATACCTGGCCATACCTC 59.093 57.143 25.52 15.64 44.14 3.85
343 412 2.040342 GGGTATACCTGGCCATACCT 57.960 55.000 25.52 7.96 44.14 3.08
354 423 0.397535 TCGGACACCCAGGGTATACC 60.398 60.000 12.21 13.99 40.67 2.73
355 424 1.411612 CTTCGGACACCCAGGGTATAC 59.588 57.143 12.21 0.00 32.11 1.47
356 425 1.784358 CTTCGGACACCCAGGGTATA 58.216 55.000 12.21 0.00 32.11 1.47
357 426 1.623542 GCTTCGGACACCCAGGGTAT 61.624 60.000 12.21 0.00 32.11 2.73
358 427 2.288025 GCTTCGGACACCCAGGGTA 61.288 63.158 12.21 0.00 32.11 3.69
359 428 3.637273 GCTTCGGACACCCAGGGT 61.637 66.667 4.76 4.76 35.62 4.34
360 429 4.760047 CGCTTCGGACACCCAGGG 62.760 72.222 2.85 2.85 0.00 4.45
361 430 1.672854 TATCGCTTCGGACACCCAGG 61.673 60.000 0.00 0.00 0.00 4.45
362 431 0.174845 TTATCGCTTCGGACACCCAG 59.825 55.000 0.00 0.00 0.00 4.45
363 432 0.609151 TTTATCGCTTCGGACACCCA 59.391 50.000 0.00 0.00 0.00 4.51
364 433 1.004595 GTTTATCGCTTCGGACACCC 58.995 55.000 0.00 0.00 0.00 4.61
365 434 1.717194 TGTTTATCGCTTCGGACACC 58.283 50.000 0.00 0.00 0.00 4.16
366 435 3.799137 TTTGTTTATCGCTTCGGACAC 57.201 42.857 0.00 0.00 0.00 3.67
367 436 5.365403 AAATTTGTTTATCGCTTCGGACA 57.635 34.783 0.00 0.00 0.00 4.02
368 437 6.513317 CAAAAATTTGTTTATCGCTTCGGAC 58.487 36.000 0.00 0.00 33.59 4.79
392 461 9.712359 GGAAATGTTTATCGGTTCTATTTGTAC 57.288 33.333 0.00 0.00 0.00 2.90
396 465 9.801873 CAATGGAAATGTTTATCGGTTCTATTT 57.198 29.630 0.00 0.00 30.00 1.40
442 513 0.099436 CGTGCAGCTTATTGAAGGGC 59.901 55.000 0.00 0.00 32.84 5.19
514 585 2.673833 CTCGGCGTCAGTAAAAGTTCT 58.326 47.619 6.85 0.00 0.00 3.01
515 586 1.126296 GCTCGGCGTCAGTAAAAGTTC 59.874 52.381 6.85 0.00 0.00 3.01
1158 1244 4.824515 CCCTCGTCCTCCGCCTCT 62.825 72.222 0.00 0.00 36.19 3.69
1218 1304 3.685214 CTCGCCGGTGGAAGACGAG 62.685 68.421 16.49 12.91 43.46 4.18
1555 1653 2.068519 CGCTTGAGCTGTGATTGTACA 58.931 47.619 0.00 0.00 39.32 2.90
1562 1660 1.962822 CTTGGCGCTTGAGCTGTGA 60.963 57.895 7.64 0.00 39.32 3.58
1580 1687 1.654023 GCGGGTTAATCTGTGTGGCC 61.654 60.000 0.00 0.00 0.00 5.36
1583 1690 1.135689 GCTTGCGGGTTAATCTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
1584 1691 1.165270 GCTTGCGGGTTAATCTGTGT 58.835 50.000 0.00 0.00 0.00 3.72
1601 1709 3.241530 TTCTCCCCTGCACGTGCT 61.242 61.111 37.59 0.00 42.66 4.40
1901 2009 1.395826 GGTAGATGCTGAGCTCGGGT 61.396 60.000 23.87 2.47 0.00 5.28
1941 2049 4.074970 ACAGGAAGAATTGTTTGCTCGAT 58.925 39.130 0.00 0.00 0.00 3.59
2005 2118 3.832527 TGGAACCCAAGAGAAAGAAAGG 58.167 45.455 0.00 0.00 0.00 3.11
2036 2149 2.170166 CCAGCCAATTAAGTCCTGCAA 58.830 47.619 0.00 0.00 0.00 4.08
2125 2238 8.761689 ACTGCATGTTAAAATGGAGGAAATATT 58.238 29.630 25.69 5.46 46.88 1.28
2286 2399 1.801771 CACAATTTACGTGCGGAAGGA 59.198 47.619 0.00 0.00 0.00 3.36
2314 2444 7.719633 TCCTCTGTATTTTAAGAGTGCAAAACT 59.280 33.333 0.00 0.00 43.85 2.66
2376 2511 3.366781 GGTGAGAGCTTGCCTGAATTTTC 60.367 47.826 0.00 0.00 0.00 2.29
2377 2512 2.560105 GGTGAGAGCTTGCCTGAATTTT 59.440 45.455 0.00 0.00 0.00 1.82
2378 2513 2.165998 GGTGAGAGCTTGCCTGAATTT 58.834 47.619 0.00 0.00 0.00 1.82
2379 2514 1.074405 TGGTGAGAGCTTGCCTGAATT 59.926 47.619 0.00 0.00 0.00 2.17
2380 2515 0.694771 TGGTGAGAGCTTGCCTGAAT 59.305 50.000 0.00 0.00 0.00 2.57
2381 2516 0.250467 GTGGTGAGAGCTTGCCTGAA 60.250 55.000 0.00 0.00 0.00 3.02
2382 2517 1.372683 GTGGTGAGAGCTTGCCTGA 59.627 57.895 0.00 0.00 0.00 3.86
2383 2518 0.535780 TTGTGGTGAGAGCTTGCCTG 60.536 55.000 0.00 0.00 0.00 4.85
2384 2519 0.536006 GTTGTGGTGAGAGCTTGCCT 60.536 55.000 0.00 0.00 0.00 4.75
2385 2520 1.518903 GGTTGTGGTGAGAGCTTGCC 61.519 60.000 0.00 0.00 0.00 4.52
2386 2521 0.819259 TGGTTGTGGTGAGAGCTTGC 60.819 55.000 0.00 0.00 0.00 4.01
2387 2522 1.233019 CTGGTTGTGGTGAGAGCTTG 58.767 55.000 0.00 0.00 0.00 4.01
2388 2523 0.109342 CCTGGTTGTGGTGAGAGCTT 59.891 55.000 0.00 0.00 0.00 3.74
2389 2524 1.757306 CCTGGTTGTGGTGAGAGCT 59.243 57.895 0.00 0.00 0.00 4.09
2390 2525 1.302832 CCCTGGTTGTGGTGAGAGC 60.303 63.158 0.00 0.00 0.00 4.09
2391 2526 2.145865 ACCCTGGTTGTGGTGAGAG 58.854 57.895 0.00 0.00 32.36 3.20
2392 2527 4.411164 ACCCTGGTTGTGGTGAGA 57.589 55.556 0.00 0.00 32.36 3.27
2396 2531 1.006639 ACTTTTCACCCTGGTTGTGGT 59.993 47.619 3.70 0.00 34.46 4.16
2397 2532 1.775385 ACTTTTCACCCTGGTTGTGG 58.225 50.000 3.70 0.00 34.46 4.17
2398 2533 4.158764 TGTTTACTTTTCACCCTGGTTGTG 59.841 41.667 0.00 0.00 35.01 3.33
2399 2534 4.158949 GTGTTTACTTTTCACCCTGGTTGT 59.841 41.667 0.00 0.00 0.00 3.32
2400 2535 4.158764 TGTGTTTACTTTTCACCCTGGTTG 59.841 41.667 0.00 0.00 0.00 3.77
2401 2536 4.158949 GTGTGTTTACTTTTCACCCTGGTT 59.841 41.667 0.00 0.00 0.00 3.67
2402 2537 3.697542 GTGTGTTTACTTTTCACCCTGGT 59.302 43.478 0.00 0.00 0.00 4.00
2403 2538 3.697045 TGTGTGTTTACTTTTCACCCTGG 59.303 43.478 0.00 0.00 0.00 4.45
2404 2539 4.668289 GTGTGTGTTTACTTTTCACCCTG 58.332 43.478 0.00 0.00 0.00 4.45
2405 2540 3.375922 CGTGTGTGTTTACTTTTCACCCT 59.624 43.478 0.00 0.00 0.00 4.34
2412 2547 0.315544 CGCGCGTGTGTGTTTACTTT 60.316 50.000 24.19 0.00 0.00 2.66
2439 2636 1.000717 GGGGTTGTATTGTGTGTGTGC 60.001 52.381 0.00 0.00 0.00 4.57
2471 2668 6.460953 GCTTTGTTGGTCAATTTAGGACAGAA 60.461 38.462 0.00 0.00 37.00 3.02
2507 2704 2.653726 ACAAAGTCCATGCAGTGTTGA 58.346 42.857 0.00 0.00 0.00 3.18
2563 2760 0.643820 GTTCGTTTGGAGGTATCGCG 59.356 55.000 0.00 0.00 0.00 5.87
2568 2765 4.069304 CAAGGATTGTTCGTTTGGAGGTA 58.931 43.478 0.00 0.00 42.34 3.08
2570 2767 3.559238 CAAGGATTGTTCGTTTGGAGG 57.441 47.619 0.00 0.00 42.34 4.30
2606 2803 0.824109 TCCTATCACCCACTCAAGCG 59.176 55.000 0.00 0.00 0.00 4.68
2630 2847 4.536765 ACCATGACATTTCCAGGGTTATC 58.463 43.478 0.00 0.00 45.19 1.75
2672 2889 3.353557 TCTTCAGGTGAGCTATGTACGT 58.646 45.455 0.00 0.00 0.00 3.57
2685 2902 4.437682 TGTTCTGGATTGTTCTTCAGGT 57.562 40.909 0.00 0.00 0.00 4.00
2707 2924 1.134037 TCCTTTGTTGGTGCTTACCGT 60.134 47.619 0.00 0.00 0.00 4.83
2712 2929 3.197549 ACATTGTTCCTTTGTTGGTGCTT 59.802 39.130 0.00 0.00 0.00 3.91
2723 2940 1.148310 CGCACTCGACATTGTTCCTT 58.852 50.000 0.00 0.00 38.10 3.36
2739 2956 0.741574 AAATCGGTAATGGCGACGCA 60.742 50.000 23.09 8.33 0.00 5.24
2757 2974 3.553508 CGAAAGTCTAGGTTCGGTTCCAA 60.554 47.826 13.18 0.00 42.21 3.53
2773 2990 1.301479 GTTGTCTCGGGGCGAAAGT 60.301 57.895 0.00 0.00 34.74 2.66
2783 3000 1.867233 CTCACTTGGTTGGTTGTCTCG 59.133 52.381 0.00 0.00 0.00 4.04
2795 3012 1.515952 CTCGCTCGCTCTCACTTGG 60.516 63.158 0.00 0.00 0.00 3.61
2806 3023 1.153647 TATGTTGGCACCTCGCTCG 60.154 57.895 0.00 0.00 41.91 5.03
2843 3060 0.541764 TGTGGGCATTGTTCCCCTTC 60.542 55.000 0.00 0.00 43.24 3.46
2844 3061 0.116940 ATGTGGGCATTGTTCCCCTT 59.883 50.000 0.00 0.00 43.24 3.95
2848 3065 1.153784 CGCATGTGGGCATTGTTCC 60.154 57.895 0.00 0.00 31.99 3.62


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

AutoCloner maintained by Alex Coulton.