Multiple sequence alignment - TraesCS6D01G218300

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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 TraesCS6D01G218300 chr6D 100.000 3308 0 0 1 3308 308589672 308592979 0.000000e+00 6109.0
1 TraesCS6D01G218300 chr6D 97.561 41 1 0 320 360 266416876 266416916 1.650000e-08 71.3
2 TraesCS6D01G218300 chr6B 92.133 2504 119 22 814 3308 475730687 475733121 0.000000e+00 3461.0
3 TraesCS6D01G218300 chr6B 93.093 333 13 4 376 702 475730312 475730640 2.310000e-131 479.0
4 TraesCS6D01G218300 chr6B 96.682 211 7 0 1 211 475730101 475730311 5.250000e-93 351.0
5 TraesCS6D01G218300 chr6A 93.319 1856 77 19 825 2657 445304235 445306066 0.000000e+00 2697.0
6 TraesCS6D01G218300 chr6A 83.738 412 31 16 361 745 445303807 445304209 1.130000e-94 357.0
7 TraesCS6D01G218300 chr6A 94.144 222 12 1 1 221 445303594 445303815 1.470000e-88 337.0
8 TraesCS6D01G218300 chr5D 96.479 142 5 0 219 360 473441468 473441609 5.520000e-58 235.0
9 TraesCS6D01G218300 chr5D 96.454 141 5 0 222 362 530601753 530601613 1.980000e-57 233.0
10 TraesCS6D01G218300 chr5D 94.074 135 8 0 226 360 391806163 391806297 4.330000e-49 206.0
11 TraesCS6D01G218300 chr1D 95.714 140 6 0 221 360 464932534 464932395 3.320000e-55 226.0
12 TraesCS6D01G218300 chr7D 84.507 142 19 3 222 361 518779040 518779180 1.600000e-28 137.0


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 TraesCS6D01G218300 chr6D 308589672 308592979 3307 False 6109.000000 6109 100.000000 1 3308 1 chr6D.!!$F2 3307
1 TraesCS6D01G218300 chr6B 475730101 475733121 3020 False 1430.333333 3461 93.969333 1 3308 3 chr6B.!!$F1 3307
2 TraesCS6D01G218300 chr6A 445303594 445306066 2472 False 1130.333333 2697 90.400333 1 2657 3 chr6A.!!$F1 2656

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
322 324 0.037734 TGCTGAGGACTGTCGTAGGA 59.962 55.0 2.59 0.0 0.00 2.94 F
543 579 0.543277 CCCAGCCTGTATGAAGCAGA 59.457 55.0 0.00 0.0 36.12 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1221 0.249155 GACCTTGACGACGGACAACA 60.249 55.0 0.00 0.0 0.0 3.33 R
2360 2426 0.104304 GGGAAATCGCCGAGCTCTAA 59.896 55.0 12.85 0.0 0.0 2.10 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
128 129 4.622364 GACGTGTTCGAAGACCGT 57.378 55.556 18.68 18.19 40.62 4.83
178 179 2.359975 CCGTTCCAGGGCTTGTCC 60.360 66.667 0.00 0.00 0.00 4.02
218 220 4.147133 GCTGTTGCTCGTCTCAAAATTTTC 59.853 41.667 0.00 0.00 36.03 2.29
219 221 5.499139 TGTTGCTCGTCTCAAAATTTTCT 57.501 34.783 0.00 0.00 0.00 2.52
220 222 6.612247 TGTTGCTCGTCTCAAAATTTTCTA 57.388 33.333 0.00 0.00 0.00 2.10
221 223 6.427150 TGTTGCTCGTCTCAAAATTTTCTAC 58.573 36.000 0.00 0.00 0.00 2.59
222 224 5.264060 TGCTCGTCTCAAAATTTTCTACG 57.736 39.130 17.04 17.04 0.00 3.51
223 225 4.986034 TGCTCGTCTCAAAATTTTCTACGA 59.014 37.500 21.29 21.29 36.56 3.43
224 226 5.464057 TGCTCGTCTCAAAATTTTCTACGAA 59.536 36.000 22.15 12.58 37.43 3.85
225 227 6.018588 TGCTCGTCTCAAAATTTTCTACGAAA 60.019 34.615 22.15 15.25 37.43 3.46
226 228 7.015877 GCTCGTCTCAAAATTTTCTACGAAAT 58.984 34.615 22.15 0.00 37.43 2.17
227 229 7.534239 GCTCGTCTCAAAATTTTCTACGAAATT 59.466 33.333 22.15 0.00 40.06 1.82
228 230 8.708075 TCGTCTCAAAATTTTCTACGAAATTG 57.292 30.769 20.78 2.34 38.75 2.32
229 231 7.322699 TCGTCTCAAAATTTTCTACGAAATTGC 59.677 33.333 20.78 0.00 38.75 3.56
230 232 7.323656 CGTCTCAAAATTTTCTACGAAATTGCT 59.676 33.333 17.79 0.00 38.75 3.91
231 233 9.607285 GTCTCAAAATTTTCTACGAAATTGCTA 57.393 29.630 0.00 0.00 38.75 3.49
234 236 8.859156 TCAAAATTTTCTACGAAATTGCTATGC 58.141 29.630 0.00 0.00 38.75 3.14
235 237 7.436536 AAATTTTCTACGAAATTGCTATGCG 57.563 32.000 0.00 2.99 38.75 4.73
236 238 5.539582 TTTTCTACGAAATTGCTATGCGT 57.460 34.783 12.27 12.27 38.81 5.24
237 239 6.650239 TTTTCTACGAAATTGCTATGCGTA 57.350 33.333 12.98 12.98 36.51 4.42
238 240 6.838198 TTTCTACGAAATTGCTATGCGTAT 57.162 33.333 13.66 0.00 36.92 3.06
239 241 5.822584 TCTACGAAATTGCTATGCGTATG 57.177 39.130 13.66 9.82 36.92 2.39
240 242 5.525199 TCTACGAAATTGCTATGCGTATGA 58.475 37.500 13.66 11.24 36.92 2.15
241 243 6.156519 TCTACGAAATTGCTATGCGTATGAT 58.843 36.000 13.66 0.00 36.92 2.45
242 244 5.022335 ACGAAATTGCTATGCGTATGATG 57.978 39.130 7.35 0.00 32.94 3.07
243 245 4.749598 ACGAAATTGCTATGCGTATGATGA 59.250 37.500 7.35 0.00 32.94 2.92
244 246 5.236263 ACGAAATTGCTATGCGTATGATGAA 59.764 36.000 7.35 0.00 32.94 2.57
245 247 6.073058 ACGAAATTGCTATGCGTATGATGAAT 60.073 34.615 7.35 0.00 32.94 2.57
246 248 6.798476 CGAAATTGCTATGCGTATGATGAATT 59.202 34.615 0.00 0.00 0.00 2.17
247 249 7.201207 CGAAATTGCTATGCGTATGATGAATTG 60.201 37.037 0.00 0.00 0.00 2.32
248 250 6.564709 ATTGCTATGCGTATGATGAATTGT 57.435 33.333 0.00 0.00 0.00 2.71
249 251 5.347012 TGCTATGCGTATGATGAATTGTG 57.653 39.130 0.00 0.00 0.00 3.33
250 252 4.153986 GCTATGCGTATGATGAATTGTGC 58.846 43.478 0.00 0.00 0.00 4.57
251 253 2.735643 TGCGTATGATGAATTGTGCG 57.264 45.000 0.00 0.00 0.00 5.34
252 254 2.006169 TGCGTATGATGAATTGTGCGT 58.994 42.857 0.00 0.00 0.00 5.24
253 255 3.190874 TGCGTATGATGAATTGTGCGTA 58.809 40.909 0.00 0.00 0.00 4.42
254 256 3.000825 TGCGTATGATGAATTGTGCGTAC 59.999 43.478 0.00 0.00 0.00 3.67
255 257 3.772344 CGTATGATGAATTGTGCGTACG 58.228 45.455 11.84 11.84 39.07 3.67
256 258 3.484285 CGTATGATGAATTGTGCGTACGA 59.516 43.478 21.65 0.80 44.54 3.43
257 259 3.925688 ATGATGAATTGTGCGTACGAC 57.074 42.857 21.65 14.50 0.00 4.34
258 260 2.954316 TGATGAATTGTGCGTACGACT 58.046 42.857 21.65 0.00 0.00 4.18
259 261 3.322369 TGATGAATTGTGCGTACGACTT 58.678 40.909 21.65 5.84 0.00 3.01
260 262 3.743911 TGATGAATTGTGCGTACGACTTT 59.256 39.130 21.65 11.63 0.00 2.66
261 263 3.513462 TGAATTGTGCGTACGACTTTG 57.487 42.857 21.65 0.00 0.00 2.77
262 264 2.867368 TGAATTGTGCGTACGACTTTGT 59.133 40.909 21.65 0.00 0.00 2.83
263 265 4.049869 TGAATTGTGCGTACGACTTTGTA 58.950 39.130 21.65 0.00 0.00 2.41
264 266 4.084952 TGAATTGTGCGTACGACTTTGTAC 60.085 41.667 21.65 6.02 41.01 2.90
273 275 5.661768 GTACGACTTTGTACGACTTGATC 57.338 43.478 0.00 0.00 35.78 2.92
274 276 4.500603 ACGACTTTGTACGACTTGATCT 57.499 40.909 0.00 0.00 0.00 2.75
275 277 4.474113 ACGACTTTGTACGACTTGATCTC 58.526 43.478 0.00 0.00 0.00 2.75
276 278 4.023450 ACGACTTTGTACGACTTGATCTCA 60.023 41.667 0.00 0.00 0.00 3.27
277 279 4.321217 CGACTTTGTACGACTTGATCTCAC 59.679 45.833 0.00 0.00 0.00 3.51
278 280 5.455056 ACTTTGTACGACTTGATCTCACT 57.545 39.130 0.00 0.00 0.00 3.41
279 281 5.462405 ACTTTGTACGACTTGATCTCACTC 58.538 41.667 0.00 0.00 0.00 3.51
280 282 3.741805 TGTACGACTTGATCTCACTCG 57.258 47.619 0.00 5.37 34.30 4.18
281 283 3.072211 TGTACGACTTGATCTCACTCGT 58.928 45.455 13.62 13.62 40.51 4.18
282 284 2.904011 ACGACTTGATCTCACTCGTC 57.096 50.000 6.37 1.68 35.70 4.20
283 285 1.469308 ACGACTTGATCTCACTCGTCC 59.531 52.381 6.37 0.00 35.70 4.79
284 286 1.530031 CGACTTGATCTCACTCGTCCG 60.530 57.143 0.00 0.00 0.00 4.79
285 287 0.171455 ACTTGATCTCACTCGTCCGC 59.829 55.000 0.00 0.00 0.00 5.54
286 288 0.526524 CTTGATCTCACTCGTCCGCC 60.527 60.000 0.00 0.00 0.00 6.13
287 289 1.945354 TTGATCTCACTCGTCCGCCC 61.945 60.000 0.00 0.00 0.00 6.13
288 290 2.362503 ATCTCACTCGTCCGCCCA 60.363 61.111 0.00 0.00 0.00 5.36
289 291 2.343163 GATCTCACTCGTCCGCCCAG 62.343 65.000 0.00 0.00 0.00 4.45
290 292 3.374402 CTCACTCGTCCGCCCAGT 61.374 66.667 0.00 0.00 0.00 4.00
291 293 2.915659 TCACTCGTCCGCCCAGTT 60.916 61.111 0.00 0.00 0.00 3.16
292 294 2.738521 CACTCGTCCGCCCAGTTG 60.739 66.667 0.00 0.00 0.00 3.16
293 295 2.915659 ACTCGTCCGCCCAGTTGA 60.916 61.111 0.00 0.00 0.00 3.18
294 296 2.283529 ACTCGTCCGCCCAGTTGAT 61.284 57.895 0.00 0.00 0.00 2.57
295 297 1.519455 CTCGTCCGCCCAGTTGATC 60.519 63.158 0.00 0.00 0.00 2.92
296 298 2.225791 CTCGTCCGCCCAGTTGATCA 62.226 60.000 0.00 0.00 0.00 2.92
297 299 1.375396 CGTCCGCCCAGTTGATCAA 60.375 57.895 3.38 3.38 0.00 2.57
298 300 0.744414 CGTCCGCCCAGTTGATCAAT 60.744 55.000 12.12 0.00 0.00 2.57
299 301 1.017387 GTCCGCCCAGTTGATCAATC 58.983 55.000 12.12 5.72 0.00 2.67
300 302 0.461870 TCCGCCCAGTTGATCAATCG 60.462 55.000 12.12 10.01 0.00 3.34
301 303 1.439353 CCGCCCAGTTGATCAATCGG 61.439 60.000 12.12 14.34 0.00 4.18
302 304 1.729881 GCCCAGTTGATCAATCGGC 59.270 57.895 20.77 20.77 0.00 5.54
303 305 0.749454 GCCCAGTTGATCAATCGGCT 60.749 55.000 24.93 11.72 0.00 5.52
304 306 1.019673 CCCAGTTGATCAATCGGCTG 58.980 55.000 12.12 13.29 33.73 4.85
305 307 0.379669 CCAGTTGATCAATCGGCTGC 59.620 55.000 12.12 0.00 33.08 5.25
306 308 1.376543 CAGTTGATCAATCGGCTGCT 58.623 50.000 12.12 0.00 0.00 4.24
307 309 1.063616 CAGTTGATCAATCGGCTGCTG 59.936 52.381 12.12 8.36 0.00 4.41
308 310 1.065926 AGTTGATCAATCGGCTGCTGA 60.066 47.619 14.42 14.42 0.00 4.26
309 311 1.329906 GTTGATCAATCGGCTGCTGAG 59.670 52.381 17.21 4.37 0.00 3.35
310 312 0.179065 TGATCAATCGGCTGCTGAGG 60.179 55.000 17.21 11.41 0.00 3.86
311 313 0.105593 GATCAATCGGCTGCTGAGGA 59.894 55.000 17.21 16.11 0.00 3.71
312 314 0.179062 ATCAATCGGCTGCTGAGGAC 60.179 55.000 17.21 0.00 0.00 3.85
313 315 1.220206 CAATCGGCTGCTGAGGACT 59.780 57.895 17.21 0.00 0.00 3.85
314 316 1.088340 CAATCGGCTGCTGAGGACTG 61.088 60.000 17.21 7.62 0.00 3.51
315 317 1.548357 AATCGGCTGCTGAGGACTGT 61.548 55.000 17.21 0.00 0.00 3.55
316 318 1.954362 ATCGGCTGCTGAGGACTGTC 61.954 60.000 17.21 0.00 0.00 3.51
317 319 2.125753 GGCTGCTGAGGACTGTCG 60.126 66.667 0.00 0.00 0.00 4.35
318 320 2.653702 GCTGCTGAGGACTGTCGT 59.346 61.111 2.15 2.15 0.00 4.34
319 321 1.595993 GGCTGCTGAGGACTGTCGTA 61.596 60.000 2.59 0.00 0.00 3.43
320 322 0.179150 GCTGCTGAGGACTGTCGTAG 60.179 60.000 2.59 2.05 0.00 3.51
321 323 0.453793 CTGCTGAGGACTGTCGTAGG 59.546 60.000 2.59 1.07 0.00 3.18
322 324 0.037734 TGCTGAGGACTGTCGTAGGA 59.962 55.000 2.59 0.00 0.00 2.94
323 325 1.174783 GCTGAGGACTGTCGTAGGAA 58.825 55.000 2.59 0.00 0.00 3.36
324 326 1.544691 GCTGAGGACTGTCGTAGGAAA 59.455 52.381 2.59 0.00 0.00 3.13
325 327 2.029290 GCTGAGGACTGTCGTAGGAAAA 60.029 50.000 2.59 0.00 0.00 2.29
326 328 3.554337 GCTGAGGACTGTCGTAGGAAAAA 60.554 47.826 2.59 0.00 0.00 1.94
327 329 4.822026 CTGAGGACTGTCGTAGGAAAAAT 58.178 43.478 2.59 0.00 0.00 1.82
328 330 4.817517 TGAGGACTGTCGTAGGAAAAATC 58.182 43.478 2.59 0.00 0.00 2.17
329 331 3.846360 AGGACTGTCGTAGGAAAAATCG 58.154 45.455 0.39 0.00 0.00 3.34
330 332 3.257624 AGGACTGTCGTAGGAAAAATCGT 59.742 43.478 0.39 0.00 0.00 3.73
331 333 4.460382 AGGACTGTCGTAGGAAAAATCGTA 59.540 41.667 0.39 0.00 0.00 3.43
332 334 5.126707 AGGACTGTCGTAGGAAAAATCGTAT 59.873 40.000 0.39 0.00 0.00 3.06
333 335 6.319658 AGGACTGTCGTAGGAAAAATCGTATA 59.680 38.462 0.39 0.00 0.00 1.47
334 336 6.974622 GGACTGTCGTAGGAAAAATCGTATAA 59.025 38.462 1.07 0.00 0.00 0.98
335 337 7.489113 GGACTGTCGTAGGAAAAATCGTATAAA 59.511 37.037 1.07 0.00 0.00 1.40
336 338 8.937634 ACTGTCGTAGGAAAAATCGTATAAAT 57.062 30.769 0.00 0.00 0.00 1.40
337 339 9.374838 ACTGTCGTAGGAAAAATCGTATAAATT 57.625 29.630 0.00 0.00 0.00 1.82
338 340 9.845305 CTGTCGTAGGAAAAATCGTATAAATTC 57.155 33.333 0.00 0.00 0.00 2.17
339 341 8.533965 TGTCGTAGGAAAAATCGTATAAATTCG 58.466 33.333 0.00 0.00 0.00 3.34
340 342 8.534778 GTCGTAGGAAAAATCGTATAAATTCGT 58.465 33.333 0.00 0.00 0.00 3.85
341 343 8.745837 TCGTAGGAAAAATCGTATAAATTCGTC 58.254 33.333 0.00 0.00 0.00 4.20
342 344 7.728751 CGTAGGAAAAATCGTATAAATTCGTCG 59.271 37.037 0.00 0.00 0.00 5.12
343 345 7.529880 AGGAAAAATCGTATAAATTCGTCGT 57.470 32.000 0.00 0.00 0.00 4.34
344 346 8.633075 AGGAAAAATCGTATAAATTCGTCGTA 57.367 30.769 0.00 0.00 0.00 3.43
345 347 8.534778 AGGAAAAATCGTATAAATTCGTCGTAC 58.465 33.333 0.00 0.00 0.00 3.67
346 348 7.520590 GGAAAAATCGTATAAATTCGTCGTACG 59.479 37.037 9.53 9.53 44.19 3.67
347 349 7.436536 AAAATCGTATAAATTCGTCGTACGT 57.563 32.000 16.05 0.00 43.14 3.57
348 350 6.410931 AATCGTATAAATTCGTCGTACGTG 57.589 37.500 16.05 9.46 43.14 4.49
349 351 4.892655 TCGTATAAATTCGTCGTACGTGT 58.107 39.130 16.05 0.00 43.14 4.49
350 352 6.026873 TCGTATAAATTCGTCGTACGTGTA 57.973 37.500 16.05 3.69 43.14 2.90
351 353 6.120157 TCGTATAAATTCGTCGTACGTGTAG 58.880 40.000 16.05 5.51 43.14 2.74
352 354 5.164471 CGTATAAATTCGTCGTACGTGTAGC 60.164 44.000 16.05 1.30 43.14 3.58
353 355 2.617250 AATTCGTCGTACGTGTAGCA 57.383 45.000 16.05 0.00 43.14 3.49
354 356 2.169663 ATTCGTCGTACGTGTAGCAG 57.830 50.000 16.05 0.65 43.14 4.24
355 357 0.867746 TTCGTCGTACGTGTAGCAGT 59.132 50.000 16.05 0.00 43.14 4.40
356 358 0.867746 TCGTCGTACGTGTAGCAGTT 59.132 50.000 16.05 0.00 43.14 3.16
357 359 1.136252 TCGTCGTACGTGTAGCAGTTC 60.136 52.381 16.05 0.00 43.14 3.01
358 360 1.136141 CGTCGTACGTGTAGCAGTTCT 60.136 52.381 16.05 0.00 36.74 3.01
359 361 2.503871 GTCGTACGTGTAGCAGTTCTC 58.496 52.381 16.05 0.00 0.00 2.87
360 362 2.096069 GTCGTACGTGTAGCAGTTCTCA 60.096 50.000 16.05 0.00 0.00 3.27
361 363 2.549329 TCGTACGTGTAGCAGTTCTCAA 59.451 45.455 16.05 0.00 0.00 3.02
362 364 3.189910 TCGTACGTGTAGCAGTTCTCAAT 59.810 43.478 16.05 0.00 0.00 2.57
363 365 3.918591 CGTACGTGTAGCAGTTCTCAATT 59.081 43.478 7.22 0.00 0.00 2.32
364 366 4.384846 CGTACGTGTAGCAGTTCTCAATTT 59.615 41.667 7.22 0.00 0.00 1.82
365 367 5.107607 CGTACGTGTAGCAGTTCTCAATTTT 60.108 40.000 7.22 0.00 0.00 1.82
438 440 1.153349 GACAGGACGCATCTTCCCC 60.153 63.158 0.00 0.00 33.01 4.81
447 449 1.153628 CATCTTCCCCGTCGTGTCC 60.154 63.158 0.00 0.00 0.00 4.02
475 477 8.227791 CCGTGGCAAATGTTAATATACTGTATC 58.772 37.037 3.09 0.00 0.00 2.24
476 478 8.769891 CGTGGCAAATGTTAATATACTGTATCA 58.230 33.333 3.09 0.00 0.00 2.15
482 484 8.758633 AATGTTAATATACTGTATCAGCGACC 57.241 34.615 3.09 0.00 34.37 4.79
484 486 4.436242 AATATACTGTATCAGCGACCGG 57.564 45.455 0.00 0.00 34.37 5.28
543 579 0.543277 CCCAGCCTGTATGAAGCAGA 59.457 55.000 0.00 0.00 36.12 4.26
559 595 4.311816 AGCAGAACAAATTGAAGTGGTG 57.688 40.909 0.00 0.00 0.00 4.17
627 663 2.673368 GAGGTTGTTTGGTGCTCGATAG 59.327 50.000 0.00 0.00 0.00 2.08
628 664 2.038557 AGGTTGTTTGGTGCTCGATAGT 59.961 45.455 0.00 0.00 37.40 2.12
629 665 3.259876 AGGTTGTTTGGTGCTCGATAGTA 59.740 43.478 0.00 0.00 37.40 1.82
734 783 2.715763 TAACCTCTGGTGGTCTTCCT 57.284 50.000 0.00 0.00 39.83 3.36
781 830 5.924475 AATGTTACTCCGCATACAATAGC 57.076 39.130 0.00 0.00 0.00 2.97
796 845 7.521585 GCATACAATAGCGTAATTTAGGCCTTT 60.522 37.037 12.58 0.78 40.23 3.11
803 852 5.594317 AGCGTAATTTAGGCCTTTCATCAAT 59.406 36.000 12.58 0.00 40.23 2.57
804 853 5.915196 GCGTAATTTAGGCCTTTCATCAATC 59.085 40.000 12.58 0.00 33.72 2.67
805 854 6.459573 GCGTAATTTAGGCCTTTCATCAATCA 60.460 38.462 12.58 0.00 33.72 2.57
806 855 7.651808 CGTAATTTAGGCCTTTCATCAATCAT 58.348 34.615 12.58 0.00 0.00 2.45
807 856 7.805071 CGTAATTTAGGCCTTTCATCAATCATC 59.195 37.037 12.58 0.00 0.00 2.92
808 857 7.664552 AATTTAGGCCTTTCATCAATCATCA 57.335 32.000 12.58 0.00 0.00 3.07
809 858 7.664552 ATTTAGGCCTTTCATCAATCATCAA 57.335 32.000 12.58 0.00 0.00 2.57
810 859 7.479352 TTTAGGCCTTTCATCAATCATCAAA 57.521 32.000 12.58 0.00 0.00 2.69
811 860 7.664552 TTAGGCCTTTCATCAATCATCAAAT 57.335 32.000 12.58 0.00 0.00 2.32
812 861 6.555463 AGGCCTTTCATCAATCATCAAATT 57.445 33.333 0.00 0.00 0.00 1.82
813 862 7.664552 AGGCCTTTCATCAATCATCAAATTA 57.335 32.000 0.00 0.00 0.00 1.40
814 863 7.723324 AGGCCTTTCATCAATCATCAAATTAG 58.277 34.615 0.00 0.00 0.00 1.73
815 864 7.343833 AGGCCTTTCATCAATCATCAAATTAGT 59.656 33.333 0.00 0.00 0.00 2.24
816 865 8.632679 GGCCTTTCATCAATCATCAAATTAGTA 58.367 33.333 0.00 0.00 0.00 1.82
822 871 9.955208 TCATCAATCATCAAATTAGTAATGTGC 57.045 29.630 8.04 0.00 0.00 4.57
823 872 8.898792 CATCAATCATCAAATTAGTAATGTGCG 58.101 33.333 8.04 2.88 0.00 5.34
863 912 6.647334 TTCTGTTGCAGAACATTCCAAATA 57.353 33.333 7.41 0.00 44.27 1.40
864 913 6.258230 TCTGTTGCAGAACATTCCAAATAG 57.742 37.500 0.00 0.00 41.33 1.73
865 914 5.183713 TCTGTTGCAGAACATTCCAAATAGG 59.816 40.000 0.00 0.00 41.33 2.57
866 915 5.076182 TGTTGCAGAACATTCCAAATAGGA 58.924 37.500 0.00 0.00 40.03 2.94
867 916 5.716228 TGTTGCAGAACATTCCAAATAGGAT 59.284 36.000 0.00 0.00 40.82 3.24
868 917 6.889177 TGTTGCAGAACATTCCAAATAGGATA 59.111 34.615 0.00 0.00 40.82 2.59
927 976 3.368531 GCTCCACCTATAAATAGCCCTCG 60.369 52.174 0.00 0.00 0.00 4.63
964 1013 4.292178 GCCTCATCCCGCTCTCCG 62.292 72.222 0.00 0.00 0.00 4.63
1008 1057 3.120385 CGTGCGAGAATGGCTGCA 61.120 61.111 0.50 0.00 41.95 4.41
1212 1261 2.885861 GTCGCGGAGATCCTGTGT 59.114 61.111 6.13 0.00 0.00 3.72
1223 1281 0.108804 ATCCTGTGTTACGTCTGCGG 60.109 55.000 0.00 0.00 43.45 5.69
1224 1282 2.380410 CCTGTGTTACGTCTGCGGC 61.380 63.158 0.00 0.00 43.45 6.53
1225 1283 2.716828 CTGTGTTACGTCTGCGGCG 61.717 63.158 0.51 0.51 43.45 6.46
1226 1284 2.429571 GTGTTACGTCTGCGGCGA 60.430 61.111 12.98 0.00 43.45 5.54
1227 1285 2.429571 TGTTACGTCTGCGGCGAC 60.430 61.111 12.98 12.71 43.45 5.19
1240 1298 4.980805 GCGACGGTGGCAACCTCA 62.981 66.667 9.09 0.00 45.17 3.86
1432 1490 0.172352 GGAACTGTCTCTCTCAGCCG 59.828 60.000 0.00 0.00 36.50 5.52
1433 1491 0.457681 GAACTGTCTCTCTCAGCCGC 60.458 60.000 0.00 0.00 36.50 6.53
1577 1642 1.157870 CGAAAGAAGCACCACCACGT 61.158 55.000 0.00 0.00 0.00 4.49
2193 2258 3.064324 GTCATGGCCCAAGCGCTT 61.064 61.111 18.98 18.98 41.24 4.68
2298 2363 3.917760 CTCCGGGACCATCTCCGC 61.918 72.222 0.00 0.00 44.45 5.54
2307 2372 2.060383 CCATCTCCGCCCAGAGTGA 61.060 63.158 0.00 0.00 35.28 3.41
2343 2409 1.745653 TGATCGATCCTATAGCCTGCG 59.254 52.381 22.31 0.00 0.00 5.18
2348 2414 1.827969 GATCCTATAGCCTGCGGATGT 59.172 52.381 0.00 0.00 36.44 3.06
2360 2426 1.138859 TGCGGATGTGTAAGCATAGCT 59.861 47.619 0.00 0.00 42.56 3.32
2478 2555 8.800370 ACATGTTGGTTCCAGTTTTTATTTTT 57.200 26.923 0.00 0.00 0.00 1.94
2479 2556 8.672815 ACATGTTGGTTCCAGTTTTTATTTTTG 58.327 29.630 0.00 0.00 0.00 2.44
2480 2557 8.672815 CATGTTGGTTCCAGTTTTTATTTTTGT 58.327 29.630 0.00 0.00 0.00 2.83
2481 2558 8.622948 TGTTGGTTCCAGTTTTTATTTTTGTT 57.377 26.923 0.00 0.00 0.00 2.83
2482 2559 9.067986 TGTTGGTTCCAGTTTTTATTTTTGTTT 57.932 25.926 0.00 0.00 0.00 2.83
2483 2560 9.900710 GTTGGTTCCAGTTTTTATTTTTGTTTT 57.099 25.926 0.00 0.00 0.00 2.43
2485 2562 9.899226 TGGTTCCAGTTTTTATTTTTGTTTTTG 57.101 25.926 0.00 0.00 0.00 2.44
2547 2624 4.221482 CCAGGAATACATCTCGGATCATGA 59.779 45.833 0.00 0.00 0.00 3.07
2566 2643 0.751643 AGGTTGACCAAGCCACACAC 60.752 55.000 8.16 0.00 39.46 3.82
2572 2649 2.967076 CAAGCCACACACGACGCT 60.967 61.111 0.00 0.00 0.00 5.07
2579 2656 0.869880 CACACACGACGCTCTTGACA 60.870 55.000 0.00 0.00 0.00 3.58
2590 2667 4.495422 ACGCTCTTGACATAAAGAACGAT 58.505 39.130 14.50 0.00 44.56 3.73
2599 2676 6.898041 TGACATAAAGAACGATCAAACTTGG 58.102 36.000 0.00 0.00 0.00 3.61
2670 2752 6.258230 TGACAAGTAAAACTAGTAGCGCTA 57.742 37.500 14.45 14.45 0.00 4.26
2708 2790 4.212716 ACAATAGTACTGTATCTCCCGCA 58.787 43.478 5.39 0.00 0.00 5.69
2717 2799 0.179020 TATCTCCCGCAATTGCCCTG 60.179 55.000 24.24 12.79 37.91 4.45
2718 2800 2.215451 ATCTCCCGCAATTGCCCTGT 62.215 55.000 24.24 3.55 37.91 4.00
2719 2801 2.676121 TCCCGCAATTGCCCTGTG 60.676 61.111 24.24 9.89 37.91 3.66
2720 2802 3.762247 CCCGCAATTGCCCTGTGG 61.762 66.667 24.24 17.98 42.95 4.17
2725 2808 0.609662 GCAATTGCCCTGTGGATGTT 59.390 50.000 20.06 0.00 34.31 2.71
2747 2830 1.202927 CCCACCACATGTTTGGAGTCT 60.203 52.381 20.64 0.00 39.24 3.24
2749 2832 2.487086 CCACCACATGTTTGGAGTCTGA 60.487 50.000 15.68 0.00 39.24 3.27
2750 2833 3.415212 CACCACATGTTTGGAGTCTGAT 58.585 45.455 9.25 0.00 39.24 2.90
2760 2843 1.344393 TGGAGTCTGATAGGCCACCAT 60.344 52.381 5.01 0.00 0.00 3.55
2772 2855 3.673902 AGGCCACCATAAAATTTTGCAC 58.326 40.909 13.76 2.34 0.00 4.57
2790 2873 1.536766 CACGAGCAAATCTTCTGCCAA 59.463 47.619 0.00 0.00 40.86 4.52
2798 2881 2.770164 ATCTTCTGCCAACGCTAACT 57.230 45.000 0.00 0.00 35.36 2.24
2800 2883 1.079503 CTTCTGCCAACGCTAACTCC 58.920 55.000 0.00 0.00 35.36 3.85
2807 2890 0.608640 CAACGCTAACTCCTCCCTGT 59.391 55.000 0.00 0.00 0.00 4.00
2809 2892 1.765230 ACGCTAACTCCTCCCTGTAG 58.235 55.000 0.00 0.00 0.00 2.74
2816 2899 2.399580 ACTCCTCCCTGTAGGCAATAC 58.600 52.381 0.00 0.00 36.51 1.89
2829 2912 3.301274 AGGCAATACCCTCTAGAGTCAC 58.699 50.000 18.42 1.06 40.58 3.67
2856 2939 1.302832 GGAGTCCAGGCACAACCAG 60.303 63.158 3.60 0.00 43.14 4.00
2937 3020 3.124921 CGATGGCGTTGACACCCC 61.125 66.667 0.00 0.00 0.00 4.95
3004 3087 2.972713 TCTTCTAACACCTCTTGGCACT 59.027 45.455 0.00 0.00 36.63 4.40
3005 3088 4.021368 GTCTTCTAACACCTCTTGGCACTA 60.021 45.833 0.00 0.00 36.63 2.74
3016 3099 2.141312 TGGCACTACTGCAGTTCCA 58.859 52.632 27.06 22.19 46.80 3.53
3036 3119 0.451783 GTGTTTTGCATCGGCCTAGG 59.548 55.000 3.67 3.67 40.13 3.02
3055 3138 2.504996 AGGCTCCTTCAGAATCTCCAAG 59.495 50.000 0.00 0.00 0.00 3.61
3111 3194 2.290367 GCTTGCGGCCTTTGAAAAATTT 59.710 40.909 0.00 0.00 34.27 1.82
3113 3196 3.185246 TGCGGCCTTTGAAAAATTTCA 57.815 38.095 0.00 4.52 44.78 2.69
3114 3197 3.737850 TGCGGCCTTTGAAAAATTTCAT 58.262 36.364 9.23 0.00 45.65 2.57
3115 3198 3.745458 TGCGGCCTTTGAAAAATTTCATC 59.255 39.130 9.23 0.00 45.65 2.92
3116 3199 3.181531 GCGGCCTTTGAAAAATTTCATCG 60.182 43.478 9.23 9.39 45.65 3.84
3166 3249 0.676782 GCCCAAACAGTGACCGCTAT 60.677 55.000 0.00 0.00 0.00 2.97
3170 3253 0.892755 AAACAGTGACCGCTATCCGA 59.107 50.000 0.00 0.00 40.02 4.55
3171 3254 0.892755 AACAGTGACCGCTATCCGAA 59.107 50.000 0.00 0.00 40.02 4.30
3179 3262 3.131396 GACCGCTATCCGAATGAATTGT 58.869 45.455 0.00 0.00 40.02 2.71
3198 3281 0.673985 TGTGTGTGGAAGAGACTCCG 59.326 55.000 0.00 0.00 38.44 4.63
3206 3289 1.473278 GGAAGAGACTCCGTCAACGAT 59.527 52.381 3.71 0.00 43.02 3.73
3213 3296 3.255149 AGACTCCGTCAACGATAACAACT 59.745 43.478 3.71 0.00 43.02 3.16
3220 3303 4.028757 CGTCAACGATAACAACTAGTGTCG 59.971 45.833 0.00 4.87 40.01 4.35
3232 3315 1.394917 CTAGTGTCGTGCATTTGGCTC 59.605 52.381 0.00 0.00 45.15 4.70
3234 3317 0.110056 GTGTCGTGCATTTGGCTCTG 60.110 55.000 0.00 0.00 45.15 3.35
3270 3353 3.189287 GTGTTGAGCAATTTCGTCATCCT 59.811 43.478 0.00 0.00 0.00 3.24
3291 3374 1.490490 CCAGTGCCCACATACACCTAT 59.510 52.381 0.82 0.00 37.51 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.059190 TTGGGGCCGTATCGCTACA 61.059 57.895 0.00 0.00 0.00 2.74
55 56 1.334419 CCTCGCCGTACGTATCGAAAT 60.334 52.381 15.21 0.00 44.19 2.17
128 129 2.727392 CCGGTAGACGCCAATCCCA 61.727 63.158 0.00 0.00 42.52 4.37
178 179 0.033504 AGCTATTACACCCGGATGCG 59.966 55.000 0.73 0.00 0.00 4.73
218 220 5.822584 TCATACGCATAGCAATTTCGTAG 57.177 39.130 0.00 0.00 38.71 3.51
219 221 5.923684 TCATCATACGCATAGCAATTTCGTA 59.076 36.000 0.00 0.00 39.47 3.43
220 222 4.749598 TCATCATACGCATAGCAATTTCGT 59.250 37.500 0.00 0.00 37.19 3.85
221 223 5.268107 TCATCATACGCATAGCAATTTCG 57.732 39.130 0.00 0.00 0.00 3.46
222 224 7.592533 ACAATTCATCATACGCATAGCAATTTC 59.407 33.333 0.00 0.00 0.00 2.17
223 225 7.380333 CACAATTCATCATACGCATAGCAATTT 59.620 33.333 0.00 0.00 0.00 1.82
224 226 6.859508 CACAATTCATCATACGCATAGCAATT 59.140 34.615 0.00 0.00 0.00 2.32
225 227 6.376177 CACAATTCATCATACGCATAGCAAT 58.624 36.000 0.00 0.00 0.00 3.56
226 228 5.750650 CACAATTCATCATACGCATAGCAA 58.249 37.500 0.00 0.00 0.00 3.91
227 229 4.319694 GCACAATTCATCATACGCATAGCA 60.320 41.667 0.00 0.00 0.00 3.49
228 230 4.153986 GCACAATTCATCATACGCATAGC 58.846 43.478 0.00 0.00 0.00 2.97
229 231 4.084380 ACGCACAATTCATCATACGCATAG 60.084 41.667 0.00 0.00 0.00 2.23
230 232 3.807071 ACGCACAATTCATCATACGCATA 59.193 39.130 0.00 0.00 0.00 3.14
231 233 2.613595 ACGCACAATTCATCATACGCAT 59.386 40.909 0.00 0.00 0.00 4.73
232 234 2.006169 ACGCACAATTCATCATACGCA 58.994 42.857 0.00 0.00 0.00 5.24
233 235 2.737467 ACGCACAATTCATCATACGC 57.263 45.000 0.00 0.00 0.00 4.42
234 236 3.484285 TCGTACGCACAATTCATCATACG 59.516 43.478 11.24 0.00 36.41 3.06
235 237 4.503007 AGTCGTACGCACAATTCATCATAC 59.497 41.667 11.24 0.00 0.00 2.39
236 238 4.678622 AGTCGTACGCACAATTCATCATA 58.321 39.130 11.24 0.00 0.00 2.15
237 239 3.521560 AGTCGTACGCACAATTCATCAT 58.478 40.909 11.24 0.00 0.00 2.45
238 240 2.954316 AGTCGTACGCACAATTCATCA 58.046 42.857 11.24 0.00 0.00 3.07
239 241 3.991605 AAGTCGTACGCACAATTCATC 57.008 42.857 11.24 0.00 0.00 2.92
240 242 3.496884 ACAAAGTCGTACGCACAATTCAT 59.503 39.130 11.24 0.00 0.00 2.57
241 243 2.867368 ACAAAGTCGTACGCACAATTCA 59.133 40.909 11.24 0.00 0.00 2.57
242 244 3.515071 ACAAAGTCGTACGCACAATTC 57.485 42.857 11.24 0.00 0.00 2.17
243 245 4.379374 GTACAAAGTCGTACGCACAATT 57.621 40.909 11.24 6.72 32.99 2.32
251 253 5.388944 AGATCAAGTCGTACAAAGTCGTAC 58.611 41.667 0.00 0.00 38.71 3.67
252 254 5.179929 TGAGATCAAGTCGTACAAAGTCGTA 59.820 40.000 0.00 0.00 0.00 3.43
253 255 4.023450 TGAGATCAAGTCGTACAAAGTCGT 60.023 41.667 0.00 0.00 0.00 4.34
254 256 4.321217 GTGAGATCAAGTCGTACAAAGTCG 59.679 45.833 0.00 0.00 0.00 4.18
255 257 5.462405 AGTGAGATCAAGTCGTACAAAGTC 58.538 41.667 0.00 0.00 0.00 3.01
256 258 5.455056 AGTGAGATCAAGTCGTACAAAGT 57.545 39.130 0.00 0.00 0.00 2.66
257 259 4.555360 CGAGTGAGATCAAGTCGTACAAAG 59.445 45.833 14.34 0.00 32.82 2.77
258 260 4.023450 ACGAGTGAGATCAAGTCGTACAAA 60.023 41.667 22.50 0.00 42.44 2.83
259 261 3.501062 ACGAGTGAGATCAAGTCGTACAA 59.499 43.478 22.50 0.00 42.44 2.41
260 262 3.072211 ACGAGTGAGATCAAGTCGTACA 58.928 45.455 22.50 0.00 42.44 2.90
261 263 3.485546 GGACGAGTGAGATCAAGTCGTAC 60.486 52.174 23.34 21.34 43.51 3.67
262 264 2.676839 GGACGAGTGAGATCAAGTCGTA 59.323 50.000 23.34 0.00 43.51 3.43
263 265 1.469308 GGACGAGTGAGATCAAGTCGT 59.531 52.381 23.45 23.45 45.05 4.34
264 266 1.530031 CGGACGAGTGAGATCAAGTCG 60.530 57.143 18.74 18.74 39.27 4.18
265 267 1.795889 GCGGACGAGTGAGATCAAGTC 60.796 57.143 0.00 6.05 0.00 3.01
266 268 0.171455 GCGGACGAGTGAGATCAAGT 59.829 55.000 0.00 0.00 0.00 3.16
267 269 0.526524 GGCGGACGAGTGAGATCAAG 60.527 60.000 0.00 0.00 0.00 3.02
268 270 1.511305 GGCGGACGAGTGAGATCAA 59.489 57.895 0.00 0.00 0.00 2.57
269 271 2.415608 GGGCGGACGAGTGAGATCA 61.416 63.158 0.00 0.00 0.00 2.92
270 272 2.343163 CTGGGCGGACGAGTGAGATC 62.343 65.000 0.00 0.00 0.00 2.75
271 273 2.362503 TGGGCGGACGAGTGAGAT 60.363 61.111 0.00 0.00 0.00 2.75
272 274 3.062466 CTGGGCGGACGAGTGAGA 61.062 66.667 0.00 0.00 0.00 3.27
273 275 2.932234 AACTGGGCGGACGAGTGAG 61.932 63.158 0.00 0.00 38.24 3.51
274 276 2.915659 AACTGGGCGGACGAGTGA 60.916 61.111 0.00 0.00 38.24 3.41
275 277 2.507110 ATCAACTGGGCGGACGAGTG 62.507 60.000 0.00 0.00 38.24 3.51
276 278 2.227089 GATCAACTGGGCGGACGAGT 62.227 60.000 0.00 0.00 40.11 4.18
277 279 1.519455 GATCAACTGGGCGGACGAG 60.519 63.158 0.00 0.00 0.00 4.18
278 280 1.822114 TTGATCAACTGGGCGGACGA 61.822 55.000 3.38 0.00 0.00 4.20
279 281 0.744414 ATTGATCAACTGGGCGGACG 60.744 55.000 11.07 0.00 0.00 4.79
280 282 1.017387 GATTGATCAACTGGGCGGAC 58.983 55.000 11.07 0.00 0.00 4.79
281 283 0.461870 CGATTGATCAACTGGGCGGA 60.462 55.000 11.07 0.00 0.00 5.54
282 284 1.439353 CCGATTGATCAACTGGGCGG 61.439 60.000 11.07 14.28 0.00 6.13
283 285 2.016961 CCGATTGATCAACTGGGCG 58.983 57.895 11.07 9.46 0.00 6.13
284 286 0.749454 AGCCGATTGATCAACTGGGC 60.749 55.000 26.83 26.83 0.00 5.36
285 287 1.019673 CAGCCGATTGATCAACTGGG 58.980 55.000 22.66 18.47 0.00 4.45
286 288 0.379669 GCAGCCGATTGATCAACTGG 59.620 55.000 19.64 19.33 32.81 4.00
287 289 1.063616 CAGCAGCCGATTGATCAACTG 59.936 52.381 11.07 14.06 34.36 3.16
288 290 1.065926 TCAGCAGCCGATTGATCAACT 60.066 47.619 11.07 0.00 0.00 3.16
289 291 1.329906 CTCAGCAGCCGATTGATCAAC 59.670 52.381 11.07 4.22 0.00 3.18
290 292 1.660167 CTCAGCAGCCGATTGATCAA 58.340 50.000 11.26 11.26 0.00 2.57
291 293 0.179065 CCTCAGCAGCCGATTGATCA 60.179 55.000 0.00 0.00 0.00 2.92
292 294 0.105593 TCCTCAGCAGCCGATTGATC 59.894 55.000 0.00 0.00 0.00 2.92
293 295 0.179062 GTCCTCAGCAGCCGATTGAT 60.179 55.000 0.00 0.00 0.00 2.57
294 296 1.219124 GTCCTCAGCAGCCGATTGA 59.781 57.895 0.00 0.00 0.00 2.57
295 297 1.088340 CAGTCCTCAGCAGCCGATTG 61.088 60.000 0.00 0.00 0.00 2.67
296 298 1.220206 CAGTCCTCAGCAGCCGATT 59.780 57.895 0.00 0.00 0.00 3.34
297 299 1.954362 GACAGTCCTCAGCAGCCGAT 61.954 60.000 0.00 0.00 0.00 4.18
298 300 2.601666 ACAGTCCTCAGCAGCCGA 60.602 61.111 0.00 0.00 0.00 5.54
299 301 2.125753 GACAGTCCTCAGCAGCCG 60.126 66.667 0.00 0.00 0.00 5.52
300 302 1.595993 TACGACAGTCCTCAGCAGCC 61.596 60.000 0.00 0.00 0.00 4.85
301 303 0.179150 CTACGACAGTCCTCAGCAGC 60.179 60.000 0.00 0.00 0.00 5.25
302 304 0.453793 CCTACGACAGTCCTCAGCAG 59.546 60.000 0.00 0.00 0.00 4.24
303 305 0.037734 TCCTACGACAGTCCTCAGCA 59.962 55.000 0.00 0.00 0.00 4.41
304 306 1.174783 TTCCTACGACAGTCCTCAGC 58.825 55.000 0.00 0.00 0.00 4.26
305 307 3.936372 TTTTCCTACGACAGTCCTCAG 57.064 47.619 0.00 0.00 0.00 3.35
306 308 4.617530 CGATTTTTCCTACGACAGTCCTCA 60.618 45.833 0.00 0.00 0.00 3.86
307 309 3.858238 CGATTTTTCCTACGACAGTCCTC 59.142 47.826 0.00 0.00 0.00 3.71
308 310 3.257624 ACGATTTTTCCTACGACAGTCCT 59.742 43.478 0.00 0.00 0.00 3.85
309 311 3.582780 ACGATTTTTCCTACGACAGTCC 58.417 45.455 0.00 0.00 0.00 3.85
310 312 7.975866 TTATACGATTTTTCCTACGACAGTC 57.024 36.000 0.00 0.00 0.00 3.51
311 313 8.937634 ATTTATACGATTTTTCCTACGACAGT 57.062 30.769 0.00 0.00 0.00 3.55
312 314 9.845305 GAATTTATACGATTTTTCCTACGACAG 57.155 33.333 0.00 0.00 0.00 3.51
313 315 8.533965 CGAATTTATACGATTTTTCCTACGACA 58.466 33.333 0.00 0.00 0.00 4.35
314 316 8.534778 ACGAATTTATACGATTTTTCCTACGAC 58.465 33.333 0.00 0.00 0.00 4.34
315 317 8.633075 ACGAATTTATACGATTTTTCCTACGA 57.367 30.769 0.00 0.00 0.00 3.43
316 318 7.728751 CGACGAATTTATACGATTTTTCCTACG 59.271 37.037 0.00 0.00 0.00 3.51
317 319 8.534778 ACGACGAATTTATACGATTTTTCCTAC 58.465 33.333 0.00 0.00 0.00 3.18
318 320 8.633075 ACGACGAATTTATACGATTTTTCCTA 57.367 30.769 0.00 0.00 0.00 2.94
319 321 7.529880 ACGACGAATTTATACGATTTTTCCT 57.470 32.000 0.00 0.00 0.00 3.36
320 322 7.520590 CGTACGACGAATTTATACGATTTTTCC 59.479 37.037 10.44 0.00 46.05 3.13
321 323 8.044409 ACGTACGACGAATTTATACGATTTTTC 58.956 33.333 24.41 0.00 46.05 2.29
322 324 7.836017 CACGTACGACGAATTTATACGATTTTT 59.164 33.333 24.41 0.00 46.05 1.94
323 325 7.008266 ACACGTACGACGAATTTATACGATTTT 59.992 33.333 24.41 0.00 46.05 1.82
324 326 6.468956 ACACGTACGACGAATTTATACGATTT 59.531 34.615 24.41 0.00 46.05 2.17
325 327 5.965334 ACACGTACGACGAATTTATACGATT 59.035 36.000 24.41 4.05 46.05 3.34
326 328 5.501715 ACACGTACGACGAATTTATACGAT 58.498 37.500 24.41 5.30 46.05 3.73
327 329 4.892655 ACACGTACGACGAATTTATACGA 58.107 39.130 24.41 0.00 46.05 3.43
328 330 5.164471 GCTACACGTACGACGAATTTATACG 60.164 44.000 24.41 6.88 46.05 3.06
329 331 5.676744 TGCTACACGTACGACGAATTTATAC 59.323 40.000 24.41 0.00 46.05 1.47
330 332 5.805229 TGCTACACGTACGACGAATTTATA 58.195 37.500 24.41 0.00 46.05 0.98
331 333 4.661125 TGCTACACGTACGACGAATTTAT 58.339 39.130 24.41 0.00 46.05 1.40
332 334 4.077063 TGCTACACGTACGACGAATTTA 57.923 40.909 24.41 0.00 46.05 1.40
333 335 2.912967 CTGCTACACGTACGACGAATTT 59.087 45.455 24.41 0.00 46.05 1.82
334 336 2.095567 ACTGCTACACGTACGACGAATT 60.096 45.455 24.41 0.00 46.05 2.17
335 337 1.466167 ACTGCTACACGTACGACGAAT 59.534 47.619 24.41 4.57 46.05 3.34
336 338 0.867746 ACTGCTACACGTACGACGAA 59.132 50.000 24.41 3.26 46.05 3.85
337 339 0.867746 AACTGCTACACGTACGACGA 59.132 50.000 24.41 4.92 46.05 4.20
339 341 2.096069 TGAGAACTGCTACACGTACGAC 60.096 50.000 24.41 6.19 0.00 4.34
340 342 2.145536 TGAGAACTGCTACACGTACGA 58.854 47.619 24.41 0.00 0.00 3.43
341 343 2.606717 TGAGAACTGCTACACGTACG 57.393 50.000 15.01 15.01 0.00 3.67
342 344 5.840940 AAATTGAGAACTGCTACACGTAC 57.159 39.130 0.00 0.00 0.00 3.67
343 345 6.220930 AGAAAATTGAGAACTGCTACACGTA 58.779 36.000 0.00 0.00 0.00 3.57
344 346 5.057149 AGAAAATTGAGAACTGCTACACGT 58.943 37.500 0.00 0.00 0.00 4.49
345 347 5.597813 AGAAAATTGAGAACTGCTACACG 57.402 39.130 0.00 0.00 0.00 4.49
350 352 9.118300 CCATCTAATAGAAAATTGAGAACTGCT 57.882 33.333 0.00 0.00 0.00 4.24
351 353 8.348507 CCCATCTAATAGAAAATTGAGAACTGC 58.651 37.037 0.00 0.00 0.00 4.40
352 354 9.401058 ACCCATCTAATAGAAAATTGAGAACTG 57.599 33.333 0.00 0.00 0.00 3.16
353 355 9.401058 CACCCATCTAATAGAAAATTGAGAACT 57.599 33.333 0.00 0.00 0.00 3.01
354 356 9.178758 ACACCCATCTAATAGAAAATTGAGAAC 57.821 33.333 0.00 0.00 0.00 3.01
360 362 9.847224 ACGAATACACCCATCTAATAGAAAATT 57.153 29.630 0.00 0.00 0.00 1.82
362 364 9.754382 GTACGAATACACCCATCTAATAGAAAA 57.246 33.333 0.00 0.00 0.00 2.29
363 365 9.139734 AGTACGAATACACCCATCTAATAGAAA 57.860 33.333 0.00 0.00 33.30 2.52
364 366 8.701908 AGTACGAATACACCCATCTAATAGAA 57.298 34.615 0.00 0.00 33.30 2.10
365 367 8.701908 AAGTACGAATACACCCATCTAATAGA 57.298 34.615 0.00 0.00 33.30 1.98
447 449 2.834574 TATTAACATTTGCCACGGCG 57.165 45.000 4.80 4.80 45.51 6.46
475 477 3.792047 CACACATGCCGGTCGCTG 61.792 66.667 1.90 0.00 38.78 5.18
476 478 3.825160 AACACACATGCCGGTCGCT 62.825 57.895 1.90 0.00 38.78 4.93
477 479 2.400896 AAAACACACATGCCGGTCGC 62.401 55.000 1.90 0.00 38.31 5.19
482 484 1.664333 GCCCAAAACACACATGCCG 60.664 57.895 0.00 0.00 0.00 5.69
484 486 1.219646 CTTGCCCAAAACACACATGC 58.780 50.000 0.00 0.00 0.00 4.06
543 579 5.048713 GCTACTAGCACCACTTCAATTTGTT 60.049 40.000 2.96 0.00 41.89 2.83
559 595 1.590238 CAATCAGTGCGTGCTACTAGC 59.410 52.381 0.61 0.61 42.82 3.42
607 643 2.038557 ACTATCGAGCACCAAACAACCT 59.961 45.455 0.00 0.00 0.00 3.50
608 644 2.423577 ACTATCGAGCACCAAACAACC 58.576 47.619 0.00 0.00 0.00 3.77
627 663 4.555708 CGAGATAGCTCAGGTGTCATGTAC 60.556 50.000 8.99 0.00 41.36 2.90
628 664 3.565902 CGAGATAGCTCAGGTGTCATGTA 59.434 47.826 8.99 0.00 41.36 2.29
629 665 2.360483 CGAGATAGCTCAGGTGTCATGT 59.640 50.000 8.99 0.00 41.36 3.21
679 720 7.556635 AGTGGTAATACTTTTCCTTTGATAGGC 59.443 37.037 0.00 0.00 44.37 3.93
702 743 5.643777 CACCAGAGGTTATTTCCAGTTAGTG 59.356 44.000 0.00 0.00 31.02 2.74
704 745 5.186198 CCACCAGAGGTTATTTCCAGTTAG 58.814 45.833 0.00 0.00 31.02 2.34
707 748 2.986728 ACCACCAGAGGTTATTTCCAGT 59.013 45.455 0.00 0.00 39.34 4.00
708 749 3.264450 AGACCACCAGAGGTTATTTCCAG 59.736 47.826 0.00 0.00 43.38 3.86
709 750 3.256704 AGACCACCAGAGGTTATTTCCA 58.743 45.455 0.00 0.00 43.38 3.53
757 806 7.596749 GCTATTGTATGCGGAGTAACATTAT 57.403 36.000 0.00 0.00 0.00 1.28
774 823 5.883673 TGAAAGGCCTAAATTACGCTATTGT 59.116 36.000 5.16 0.00 0.00 2.71
781 830 7.026631 TGATTGATGAAAGGCCTAAATTACG 57.973 36.000 5.16 0.00 0.00 3.18
796 845 9.955208 GCACATTACTAATTTGATGATTGATGA 57.045 29.630 0.00 0.00 0.00 2.92
803 852 5.877564 TCACCGCACATTACTAATTTGATGA 59.122 36.000 0.00 0.00 0.00 2.92
804 853 6.117911 TCACCGCACATTACTAATTTGATG 57.882 37.500 0.00 0.00 0.00 3.07
805 854 6.751514 TTCACCGCACATTACTAATTTGAT 57.248 33.333 0.00 0.00 0.00 2.57
806 855 6.017026 TGTTTCACCGCACATTACTAATTTGA 60.017 34.615 0.00 0.00 0.00 2.69
807 856 6.087555 GTGTTTCACCGCACATTACTAATTTG 59.912 38.462 0.00 0.00 35.81 2.32
808 857 6.146898 GTGTTTCACCGCACATTACTAATTT 58.853 36.000 0.00 0.00 35.81 1.82
809 858 5.615984 CGTGTTTCACCGCACATTACTAATT 60.616 40.000 0.00 0.00 35.51 1.40
810 859 4.142988 CGTGTTTCACCGCACATTACTAAT 60.143 41.667 0.00 0.00 35.51 1.73
811 860 3.184783 CGTGTTTCACCGCACATTACTAA 59.815 43.478 0.00 0.00 35.51 2.24
812 861 2.732500 CGTGTTTCACCGCACATTACTA 59.267 45.455 0.00 0.00 35.51 1.82
813 862 1.529438 CGTGTTTCACCGCACATTACT 59.471 47.619 0.00 0.00 35.51 2.24
814 863 1.399215 CCGTGTTTCACCGCACATTAC 60.399 52.381 0.00 0.00 35.51 1.89
815 864 0.869068 CCGTGTTTCACCGCACATTA 59.131 50.000 0.00 0.00 35.51 1.90
816 865 0.816018 TCCGTGTTTCACCGCACATT 60.816 50.000 0.00 0.00 35.51 2.71
817 866 0.605319 ATCCGTGTTTCACCGCACAT 60.605 50.000 0.00 0.00 35.51 3.21
818 867 0.816018 AATCCGTGTTTCACCGCACA 60.816 50.000 0.00 0.00 35.51 4.57
819 868 0.385473 CAATCCGTGTTTCACCGCAC 60.385 55.000 0.00 0.00 0.00 5.34
820 869 0.533085 TCAATCCGTGTTTCACCGCA 60.533 50.000 0.00 0.00 0.00 5.69
821 870 0.802494 ATCAATCCGTGTTTCACCGC 59.198 50.000 0.00 0.00 0.00 5.68
822 871 2.742053 AGAATCAATCCGTGTTTCACCG 59.258 45.455 0.00 0.00 38.09 4.94
823 872 3.502211 ACAGAATCAATCCGTGTTTCACC 59.498 43.478 0.00 0.00 38.09 4.02
864 913 3.929610 GCTGTAATCTTGCGAGGATATCC 59.070 47.826 14.41 14.41 0.00 2.59
865 914 4.387256 GTGCTGTAATCTTGCGAGGATATC 59.613 45.833 0.00 0.00 0.00 1.63
866 915 4.202253 TGTGCTGTAATCTTGCGAGGATAT 60.202 41.667 0.00 0.00 0.00 1.63
867 916 3.132111 TGTGCTGTAATCTTGCGAGGATA 59.868 43.478 0.00 0.00 0.00 2.59
868 917 2.093500 TGTGCTGTAATCTTGCGAGGAT 60.093 45.455 0.00 0.00 0.00 3.24
927 976 1.401670 CGATACTAGTCATGGAGCGGC 60.402 57.143 0.00 0.00 0.00 6.53
964 1013 3.846360 AGTGCAGAGAACGTGTATTACC 58.154 45.455 0.00 0.00 0.00 2.85
996 1045 1.749634 AGAATGCTTGCAGCCATTCTC 59.250 47.619 25.83 12.30 41.08 2.87
1008 1057 1.238439 CAACGTGGGACAGAATGCTT 58.762 50.000 0.00 0.00 41.80 3.91
1172 1221 0.249155 GACCTTGACGACGGACAACA 60.249 55.000 0.00 0.00 0.00 3.33
1228 1286 3.050275 GTCGCTGAGGTTGCCACC 61.050 66.667 0.00 0.00 44.67 4.61
1229 1287 3.050275 GGTCGCTGAGGTTGCCAC 61.050 66.667 0.00 0.00 0.00 5.01
1230 1288 4.329545 GGGTCGCTGAGGTTGCCA 62.330 66.667 0.00 0.00 0.00 4.92
1316 1374 0.898320 CCTCGTCTGTGGATCCACTT 59.102 55.000 37.92 0.00 46.30 3.16
1368 1426 1.310216 ATTCAAAAGGTACGGCGGCC 61.310 55.000 13.24 9.54 0.00 6.13
1418 1476 3.071206 GGGCGGCTGAGAGAGACA 61.071 66.667 9.56 0.00 0.00 3.41
1432 1490 1.209261 CCAAAATGGGTTGGTATGGGC 59.791 52.381 0.00 0.00 42.74 5.36
1433 1491 2.826488 TCCAAAATGGGTTGGTATGGG 58.174 47.619 4.00 0.00 46.93 4.00
2027 2092 0.448197 TGATGACGACGACAGAGCTC 59.552 55.000 5.27 5.27 0.00 4.09
2058 2123 1.619654 CCAATGGCAAACACTCCTCA 58.380 50.000 0.00 0.00 0.00 3.86
2298 2363 4.554960 ATCATCTGCATATCACTCTGGG 57.445 45.455 0.00 0.00 0.00 4.45
2307 2372 6.315642 GGATCGATCACAAATCATCTGCATAT 59.684 38.462 25.93 0.00 0.00 1.78
2360 2426 0.104304 GGGAAATCGCCGAGCTCTAA 59.896 55.000 12.85 0.00 0.00 2.10
2478 2555 6.070767 TGGTTACACCCTCAAAATCAAAAACA 60.071 34.615 0.00 0.00 37.50 2.83
2479 2556 6.342111 TGGTTACACCCTCAAAATCAAAAAC 58.658 36.000 0.00 0.00 37.50 2.43
2480 2557 6.546428 TGGTTACACCCTCAAAATCAAAAA 57.454 33.333 0.00 0.00 37.50 1.94
2481 2558 6.155393 ACTTGGTTACACCCTCAAAATCAAAA 59.845 34.615 0.00 0.00 37.50 2.44
2482 2559 5.659079 ACTTGGTTACACCCTCAAAATCAAA 59.341 36.000 0.00 0.00 37.50 2.69
2483 2560 5.205056 ACTTGGTTACACCCTCAAAATCAA 58.795 37.500 0.00 0.00 37.50 2.57
2484 2561 4.798882 ACTTGGTTACACCCTCAAAATCA 58.201 39.130 0.00 0.00 37.50 2.57
2485 2562 5.784578 AACTTGGTTACACCCTCAAAATC 57.215 39.130 0.00 0.00 37.50 2.17
2486 2563 6.553953 AAAACTTGGTTACACCCTCAAAAT 57.446 33.333 0.00 0.00 37.50 1.82
2491 2568 8.570068 TGAATATAAAACTTGGTTACACCCTC 57.430 34.615 0.00 0.00 37.50 4.30
2492 2569 9.185680 GATGAATATAAAACTTGGTTACACCCT 57.814 33.333 0.00 0.00 37.50 4.34
2547 2624 0.751643 GTGTGTGGCTTGGTCAACCT 60.752 55.000 0.10 0.00 36.82 3.50
2566 2643 3.241364 CGTTCTTTATGTCAAGAGCGTCG 60.241 47.826 10.44 0.00 46.51 5.12
2572 2649 7.962964 AGTTTGATCGTTCTTTATGTCAAGA 57.037 32.000 0.00 0.00 0.00 3.02
2579 2656 7.064728 GTCTAGCCAAGTTTGATCGTTCTTTAT 59.935 37.037 0.00 0.00 0.00 1.40
2590 2667 4.467795 AGCTCATAGTCTAGCCAAGTTTGA 59.532 41.667 0.00 0.00 39.64 2.69
2662 2744 4.865776 AGTGAGATTCTTCATAGCGCTAC 58.134 43.478 21.49 4.46 0.00 3.58
2667 2749 9.757227 ACTATTGTTAGTGAGATTCTTCATAGC 57.243 33.333 0.00 0.00 37.28 2.97
2696 2778 0.465460 GGGCAATTGCGGGAGATACA 60.465 55.000 23.48 0.00 43.26 2.29
2708 2790 1.901833 GGAAACATCCACAGGGCAATT 59.098 47.619 0.00 0.00 0.00 2.32
2718 2800 1.146774 ACATGTGGTGGGAAACATCCA 59.853 47.619 0.00 0.00 34.81 3.41
2719 2801 1.923356 ACATGTGGTGGGAAACATCC 58.077 50.000 0.00 0.00 34.81 3.51
2720 2802 3.554752 CCAAACATGTGGTGGGAAACATC 60.555 47.826 17.50 0.00 34.81 3.06
2725 2808 1.216678 ACTCCAAACATGTGGTGGGAA 59.783 47.619 22.51 8.76 39.88 3.97
2735 2818 2.846206 TGGCCTATCAGACTCCAAACAT 59.154 45.455 3.32 0.00 0.00 2.71
2747 2830 5.188555 TGCAAAATTTTATGGTGGCCTATCA 59.811 36.000 3.32 0.00 0.00 2.15
2749 2832 5.427378 GTGCAAAATTTTATGGTGGCCTAT 58.573 37.500 3.32 0.00 0.00 2.57
2750 2833 4.619394 CGTGCAAAATTTTATGGTGGCCTA 60.619 41.667 3.32 0.00 0.00 3.93
2772 2855 1.464687 CGTTGGCAGAAGATTTGCTCG 60.465 52.381 0.00 0.00 41.27 5.03
2783 2866 0.246635 GAGGAGTTAGCGTTGGCAGA 59.753 55.000 0.00 0.00 43.41 4.26
2790 2873 1.685491 CCTACAGGGAGGAGTTAGCGT 60.685 57.143 0.00 0.00 39.15 5.07
2798 2881 1.694693 GGGTATTGCCTACAGGGAGGA 60.695 57.143 0.47 0.00 39.15 3.71
2800 2883 1.694696 GAGGGTATTGCCTACAGGGAG 59.305 57.143 0.00 0.00 36.70 4.30
2807 2890 4.471548 GTGACTCTAGAGGGTATTGCCTA 58.528 47.826 23.50 0.00 37.43 3.93
2809 2892 2.365941 GGTGACTCTAGAGGGTATTGCC 59.634 54.545 23.50 11.24 0.00 4.52
2816 2899 0.752376 GACCCGGTGACTCTAGAGGG 60.752 65.000 23.50 16.55 44.17 4.30
2829 2912 2.660064 CCTGGACTCCAAGACCCGG 61.660 68.421 0.00 0.00 30.80 5.73
2856 2939 5.176592 GGAATTATATGGGAAGCTCGGTAC 58.823 45.833 0.00 0.00 0.00 3.34
2906 2989 2.692368 ATCGAGGGGTGGCATGGT 60.692 61.111 0.00 0.00 0.00 3.55
2975 3058 3.196685 AGAGGTGTTAGAAGACAGATGGC 59.803 47.826 0.00 0.00 0.00 4.40
2983 3066 2.972713 AGTGCCAAGAGGTGTTAGAAGA 59.027 45.455 0.00 0.00 37.19 2.87
3004 3087 2.357637 GCAAAACACTGGAACTGCAGTA 59.642 45.455 22.01 3.28 0.00 2.74
3005 3088 1.134946 GCAAAACACTGGAACTGCAGT 59.865 47.619 15.25 15.25 0.00 4.40
3016 3099 1.453155 CTAGGCCGATGCAAAACACT 58.547 50.000 0.00 0.00 40.13 3.55
3036 3119 3.197549 AGACTTGGAGATTCTGAAGGAGC 59.802 47.826 0.00 0.00 0.00 4.70
3067 3150 6.204688 AGCGACTCATATTTTCACTGACAAAA 59.795 34.615 0.00 0.00 0.00 2.44
3075 3158 3.345714 CGCAAGCGACTCATATTTTCAC 58.654 45.455 9.11 0.00 42.83 3.18
3089 3172 0.873743 TTTTTCAAAGGCCGCAAGCG 60.874 50.000 7.60 7.60 45.17 4.68
3111 3194 2.158813 GGGGGAAAGCTATTCACGATGA 60.159 50.000 9.75 0.00 0.00 2.92
3113 3196 2.104963 GAGGGGGAAAGCTATTCACGAT 59.895 50.000 9.75 0.73 0.00 3.73
3114 3197 1.485066 GAGGGGGAAAGCTATTCACGA 59.515 52.381 9.75 0.00 0.00 4.35
3115 3198 1.806623 CGAGGGGGAAAGCTATTCACG 60.807 57.143 9.75 0.00 0.00 4.35
3116 3199 1.485066 TCGAGGGGGAAAGCTATTCAC 59.515 52.381 9.75 6.65 0.00 3.18
3166 3249 2.551887 CCACACACACAATTCATTCGGA 59.448 45.455 0.00 0.00 0.00 4.55
3170 3253 5.009010 GTCTCTTCCACACACACAATTCATT 59.991 40.000 0.00 0.00 0.00 2.57
3171 3254 4.516698 GTCTCTTCCACACACACAATTCAT 59.483 41.667 0.00 0.00 0.00 2.57
3179 3262 0.673985 CGGAGTCTCTTCCACACACA 59.326 55.000 0.00 0.00 37.05 3.72
3198 3281 4.913924 ACGACACTAGTTGTTATCGTTGAC 59.086 41.667 7.63 0.00 39.36 3.18
3206 3289 4.212425 CCAAATGCACGACACTAGTTGTTA 59.788 41.667 0.00 0.00 40.44 2.41
3213 3296 1.001974 AGAGCCAAATGCACGACACTA 59.998 47.619 0.00 0.00 44.83 2.74
3220 3303 2.129607 CAACAACAGAGCCAAATGCAC 58.870 47.619 0.00 0.00 44.83 4.57
3232 3315 4.930963 TCAACACCTTATTGCAACAACAG 58.069 39.130 0.00 0.00 0.00 3.16
3234 3317 3.735746 GCTCAACACCTTATTGCAACAAC 59.264 43.478 0.00 0.00 0.00 3.32
3270 3353 0.840288 AGGTGTATGTGGGCACTGGA 60.840 55.000 0.00 0.00 36.03 3.86


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

AutoCloner maintained by Alex Coulton.