Multiple sequence alignment - TraesCS1D01G096800

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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 TraesCS1D01G096800 chr1D 100.000 3393 0 0 1 3393 83721966 83718574 0.000000e+00 6266
1 TraesCS1D01G096800 chr1B 93.703 1858 92 11 542 2389 136646918 136645076 0.000000e+00 2760
2 TraesCS1D01G096800 chr1B 83.436 163 14 6 15 165 136647285 136647124 4.570000e-29 139
3 TraesCS1D01G096800 chr1B 93.407 91 6 0 286 376 342365993 342365903 5.910000e-28 135
4 TraesCS1D01G096800 chr1A 91.409 2037 135 24 377 2394 100291745 100289730 0.000000e+00 2756
5 TraesCS1D01G096800 chr1A 94.890 998 47 3 2399 3393 375330549 375329553 0.000000e+00 1557
6 TraesCS1D01G096800 chr1A 84.255 235 28 4 16 241 100291900 100291666 1.580000e-53 220
7 TraesCS1D01G096800 chr1A 90.110 91 9 0 286 376 308777428 308777518 5.950000e-23 119
8 TraesCS1D01G096800 chr3D 96.822 1007 29 3 2390 3393 526981819 526982825 0.000000e+00 1679
9 TraesCS1D01G096800 chr3D 95.090 998 42 6 2399 3393 614989440 614988447 0.000000e+00 1565
10 TraesCS1D01G096800 chr4B 84.261 1760 200 38 638 2387 514506247 514504555 0.000000e+00 1644
11 TraesCS1D01G096800 chr6D 96.104 1001 35 3 2397 3393 28757842 28756842 0.000000e+00 1629
12 TraesCS1D01G096800 chrUn 95.040 1008 46 3 2390 3393 1602761 1603768 0.000000e+00 1581
13 TraesCS1D01G096800 chr7A 94.716 1003 47 4 2394 3393 91857300 91858299 0.000000e+00 1554
14 TraesCS1D01G096800 chr7B 93.781 997 54 7 2405 3393 470855272 470854276 0.000000e+00 1491
15 TraesCS1D01G096800 chr2B 92.786 998 64 5 2400 3393 790324702 790325695 0.000000e+00 1437
16 TraesCS1D01G096800 chr2B 91.876 997 69 11 2405 3393 533539952 533540944 0.000000e+00 1382
17 TraesCS1D01G096800 chr4A 84.743 1206 132 26 1186 2387 46617223 46618380 0.000000e+00 1160
18 TraesCS1D01G096800 chr4A 81.455 550 76 17 620 1162 46616702 46617232 8.700000e-116 427
19 TraesCS1D01G096800 chr4D 83.319 1139 146 17 638 1770 418246233 418245133 0.000000e+00 1011
20 TraesCS1D01G096800 chr4D 85.400 637 60 16 1761 2391 418244194 418243585 6.180000e-177 630


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 TraesCS1D01G096800 chr1D 83718574 83721966 3392 True 6266.0 6266 100.0000 1 3393 1 chr1D.!!$R1 3392
1 TraesCS1D01G096800 chr1B 136645076 136647285 2209 True 1449.5 2760 88.5695 15 2389 2 chr1B.!!$R2 2374
2 TraesCS1D01G096800 chr1A 375329553 375330549 996 True 1557.0 1557 94.8900 2399 3393 1 chr1A.!!$R1 994
3 TraesCS1D01G096800 chr1A 100289730 100291900 2170 True 1488.0 2756 87.8320 16 2394 2 chr1A.!!$R2 2378
4 TraesCS1D01G096800 chr3D 526981819 526982825 1006 False 1679.0 1679 96.8220 2390 3393 1 chr3D.!!$F1 1003
5 TraesCS1D01G096800 chr3D 614988447 614989440 993 True 1565.0 1565 95.0900 2399 3393 1 chr3D.!!$R1 994
6 TraesCS1D01G096800 chr4B 514504555 514506247 1692 True 1644.0 1644 84.2610 638 2387 1 chr4B.!!$R1 1749
7 TraesCS1D01G096800 chr6D 28756842 28757842 1000 True 1629.0 1629 96.1040 2397 3393 1 chr6D.!!$R1 996
8 TraesCS1D01G096800 chrUn 1602761 1603768 1007 False 1581.0 1581 95.0400 2390 3393 1 chrUn.!!$F1 1003
9 TraesCS1D01G096800 chr7A 91857300 91858299 999 False 1554.0 1554 94.7160 2394 3393 1 chr7A.!!$F1 999
10 TraesCS1D01G096800 chr7B 470854276 470855272 996 True 1491.0 1491 93.7810 2405 3393 1 chr7B.!!$R1 988
11 TraesCS1D01G096800 chr2B 790324702 790325695 993 False 1437.0 1437 92.7860 2400 3393 1 chr2B.!!$F2 993
12 TraesCS1D01G096800 chr2B 533539952 533540944 992 False 1382.0 1382 91.8760 2405 3393 1 chr2B.!!$F1 988
13 TraesCS1D01G096800 chr4A 46616702 46618380 1678 False 793.5 1160 83.0990 620 2387 2 chr4A.!!$F1 1767
14 TraesCS1D01G096800 chr4D 418243585 418246233 2648 True 820.5 1011 84.3595 638 2391 2 chr4D.!!$R1 1753

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
308 352 0.036388 AATGCTACACACACGGGGAG 60.036 55.0 0.00 0.0 0.00 4.30 F
516 596 0.040204 AAGCAAGCAAGCCCCATAGT 59.960 50.0 0.00 0.0 34.23 2.12 F
517 597 0.394899 AGCAAGCAAGCCCCATAGTC 60.395 55.0 0.00 0.0 34.23 2.59 F
1395 1497 0.474184 ACCAGAAGTTCCAGGGTGTG 59.526 55.0 14.51 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1806 1.148310 CAATGGCGTCGAACTCTTGT 58.852 50.000 0.0 0.0 0.0 3.16 R
2032 3095 2.475339 AGATCAGCTCCTCCATGTCT 57.525 50.000 0.0 0.0 0.0 3.41 R
2373 3440 4.019411 TGAATTATGACTCACTGCCCTTGA 60.019 41.667 0.0 0.0 0.0 3.02 R
3002 4075 1.072489 TGGTTGTGGCAGTATCCGAAA 59.928 47.619 0.0 0.0 0.0 3.46 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
23 24 1.278238 CGGTTGCGGAAGTACTGATC 58.722 55.000 0.00 0.00 0.00 2.92
91 104 7.531857 TCCATGCTTTATTGTTCAAAGGTAA 57.468 32.000 0.00 0.00 34.28 2.85
129 142 7.667557 TCACACTACATAATAGGCCATCTAAC 58.332 38.462 5.01 0.00 0.00 2.34
131 144 7.931407 CACACTACATAATAGGCCATCTAACAA 59.069 37.037 5.01 0.00 0.00 2.83
153 166 4.837896 AAAAGAGTAGCTTTGCTTCACC 57.162 40.909 0.00 0.00 45.85 4.02
155 168 3.492102 AGAGTAGCTTTGCTTCACCAA 57.508 42.857 0.00 0.00 40.44 3.67
170 214 6.425721 TGCTTCACCAATACTTTACTGTACAC 59.574 38.462 0.00 0.00 0.00 2.90
172 216 7.119262 GCTTCACCAATACTTTACTGTACACAT 59.881 37.037 0.00 0.00 0.00 3.21
173 217 8.542497 TTCACCAATACTTTACTGTACACATC 57.458 34.615 0.00 0.00 0.00 3.06
174 218 7.903145 TCACCAATACTTTACTGTACACATCT 58.097 34.615 0.00 0.00 0.00 2.90
175 219 8.372459 TCACCAATACTTTACTGTACACATCTT 58.628 33.333 0.00 0.00 0.00 2.40
176 220 8.999431 CACCAATACTTTACTGTACACATCTTT 58.001 33.333 0.00 0.00 0.00 2.52
177 221 8.999431 ACCAATACTTTACTGTACACATCTTTG 58.001 33.333 0.00 0.00 0.00 2.77
178 222 7.962918 CCAATACTTTACTGTACACATCTTTGC 59.037 37.037 0.00 0.00 0.00 3.68
179 223 8.503196 CAATACTTTACTGTACACATCTTTGCA 58.497 33.333 0.00 0.00 0.00 4.08
180 224 8.792830 ATACTTTACTGTACACATCTTTGCAT 57.207 30.769 0.00 0.00 0.00 3.96
181 225 9.884636 ATACTTTACTGTACACATCTTTGCATA 57.115 29.630 0.00 0.00 0.00 3.14
182 226 8.256611 ACTTTACTGTACACATCTTTGCATAG 57.743 34.615 0.00 0.00 0.00 2.23
183 227 7.878127 ACTTTACTGTACACATCTTTGCATAGT 59.122 33.333 4.00 0.00 0.00 2.12
184 228 8.615878 TTTACTGTACACATCTTTGCATAGTT 57.384 30.769 4.00 0.00 0.00 2.24
185 229 8.615878 TTACTGTACACATCTTTGCATAGTTT 57.384 30.769 4.00 0.00 0.00 2.66
186 230 6.902341 ACTGTACACATCTTTGCATAGTTTG 58.098 36.000 4.00 6.26 0.00 2.93
187 231 6.710295 ACTGTACACATCTTTGCATAGTTTGA 59.290 34.615 13.51 0.00 0.00 2.69
188 232 7.391554 ACTGTACACATCTTTGCATAGTTTGAT 59.608 33.333 13.51 6.70 0.00 2.57
189 233 7.529158 TGTACACATCTTTGCATAGTTTGATG 58.471 34.615 13.51 8.81 37.77 3.07
190 234 5.957798 ACACATCTTTGCATAGTTTGATGG 58.042 37.500 13.51 4.91 36.56 3.51
191 235 4.802039 CACATCTTTGCATAGTTTGATGGC 59.198 41.667 13.51 0.00 36.56 4.40
192 236 4.463539 ACATCTTTGCATAGTTTGATGGCA 59.536 37.500 13.51 0.00 36.56 4.92
193 237 4.439305 TCTTTGCATAGTTTGATGGCAC 57.561 40.909 4.00 0.00 0.00 5.01
210 254 5.794687 TGGCACAATAAGTTTCGACATAG 57.205 39.130 0.00 0.00 31.92 2.23
211 255 5.483811 TGGCACAATAAGTTTCGACATAGA 58.516 37.500 0.00 0.00 31.92 1.98
212 256 5.935206 TGGCACAATAAGTTTCGACATAGAA 59.065 36.000 0.00 0.00 31.92 2.10
213 257 6.128391 TGGCACAATAAGTTTCGACATAGAAC 60.128 38.462 0.00 0.00 31.92 3.01
214 258 6.128391 GGCACAATAAGTTTCGACATAGAACA 60.128 38.462 0.22 0.00 0.00 3.18
215 259 6.736853 GCACAATAAGTTTCGACATAGAACAC 59.263 38.462 0.22 0.00 0.00 3.32
216 260 7.570507 GCACAATAAGTTTCGACATAGAACACA 60.571 37.037 0.22 0.00 0.00 3.72
217 261 7.952101 CACAATAAGTTTCGACATAGAACACAG 59.048 37.037 0.22 0.00 0.00 3.66
218 262 7.870954 ACAATAAGTTTCGACATAGAACACAGA 59.129 33.333 0.22 0.00 0.00 3.41
219 263 8.708742 CAATAAGTTTCGACATAGAACACAGAA 58.291 33.333 0.22 0.00 0.00 3.02
220 264 8.827177 ATAAGTTTCGACATAGAACACAGAAA 57.173 30.769 0.22 0.00 0.00 2.52
221 265 6.771188 AGTTTCGACATAGAACACAGAAAG 57.229 37.500 0.22 0.00 0.00 2.62
222 266 6.513180 AGTTTCGACATAGAACACAGAAAGA 58.487 36.000 0.22 0.00 0.00 2.52
223 267 6.984474 AGTTTCGACATAGAACACAGAAAGAA 59.016 34.615 0.22 0.00 0.00 2.52
224 268 7.657761 AGTTTCGACATAGAACACAGAAAGAAT 59.342 33.333 0.22 0.00 0.00 2.40
225 269 6.951256 TCGACATAGAACACAGAAAGAATG 57.049 37.500 0.00 0.00 0.00 2.67
226 270 5.348724 TCGACATAGAACACAGAAAGAATGC 59.651 40.000 0.00 0.00 0.00 3.56
227 271 5.349817 CGACATAGAACACAGAAAGAATGCT 59.650 40.000 0.00 0.00 0.00 3.79
228 272 6.128445 CGACATAGAACACAGAAAGAATGCTT 60.128 38.462 0.00 0.00 35.37 3.91
229 273 6.906659 ACATAGAACACAGAAAGAATGCTTG 58.093 36.000 0.00 0.00 33.79 4.01
230 274 6.488006 ACATAGAACACAGAAAGAATGCTTGT 59.512 34.615 0.00 0.00 33.79 3.16
231 275 7.661437 ACATAGAACACAGAAAGAATGCTTGTA 59.339 33.333 0.00 0.00 33.79 2.41
232 276 6.942532 AGAACACAGAAAGAATGCTTGTAA 57.057 33.333 0.00 0.00 33.79 2.41
233 277 7.333528 AGAACACAGAAAGAATGCTTGTAAA 57.666 32.000 0.00 0.00 33.79 2.01
234 278 7.771183 AGAACACAGAAAGAATGCTTGTAAAA 58.229 30.769 0.00 0.00 33.79 1.52
235 279 7.917505 AGAACACAGAAAGAATGCTTGTAAAAG 59.082 33.333 0.00 0.00 33.79 2.27
236 280 7.333528 ACACAGAAAGAATGCTTGTAAAAGA 57.666 32.000 0.00 0.00 33.79 2.52
237 281 7.420800 ACACAGAAAGAATGCTTGTAAAAGAG 58.579 34.615 0.00 0.00 33.79 2.85
238 282 6.860023 CACAGAAAGAATGCTTGTAAAAGAGG 59.140 38.462 0.00 0.00 33.79 3.69
239 283 6.015940 ACAGAAAGAATGCTTGTAAAAGAGGG 60.016 38.462 0.00 0.00 33.79 4.30
240 284 4.790765 AAGAATGCTTGTAAAAGAGGGC 57.209 40.909 0.00 0.00 31.83 5.19
241 285 4.039603 AGAATGCTTGTAAAAGAGGGCT 57.960 40.909 0.00 0.00 0.00 5.19
242 286 4.411013 AGAATGCTTGTAAAAGAGGGCTT 58.589 39.130 0.00 0.00 35.37 4.35
243 287 4.219288 AGAATGCTTGTAAAAGAGGGCTTG 59.781 41.667 0.00 0.00 33.79 4.01
244 288 1.613437 TGCTTGTAAAAGAGGGCTTGC 59.387 47.619 0.00 0.00 33.79 4.01
245 289 1.613437 GCTTGTAAAAGAGGGCTTGCA 59.387 47.619 0.00 0.00 33.79 4.08
246 290 2.035832 GCTTGTAAAAGAGGGCTTGCAA 59.964 45.455 0.00 0.00 33.79 4.08
247 291 3.492482 GCTTGTAAAAGAGGGCTTGCAAA 60.492 43.478 0.00 0.00 33.79 3.68
263 307 6.738352 CTTGCAAAGTTTGACTTGACATAC 57.262 37.500 19.82 0.00 38.66 2.39
264 308 5.826601 TGCAAAGTTTGACTTGACATACA 57.173 34.783 19.82 0.77 38.66 2.29
265 309 6.389830 TGCAAAGTTTGACTTGACATACAT 57.610 33.333 19.82 0.00 38.66 2.29
266 310 6.437928 TGCAAAGTTTGACTTGACATACATC 58.562 36.000 19.82 0.00 38.66 3.06
267 311 6.262944 TGCAAAGTTTGACTTGACATACATCT 59.737 34.615 19.82 0.00 38.66 2.90
268 312 7.443879 TGCAAAGTTTGACTTGACATACATCTA 59.556 33.333 19.82 0.00 38.66 1.98
269 313 8.289618 GCAAAGTTTGACTTGACATACATCTAA 58.710 33.333 19.82 0.00 38.66 2.10
275 319 8.628882 TTGACTTGACATACATCTAATACACG 57.371 34.615 0.00 0.00 0.00 4.49
276 320 7.200455 TGACTTGACATACATCTAATACACGG 58.800 38.462 0.00 0.00 0.00 4.94
277 321 7.067737 TGACTTGACATACATCTAATACACGGA 59.932 37.037 0.00 0.00 0.00 4.69
278 322 7.426410 ACTTGACATACATCTAATACACGGAG 58.574 38.462 0.00 0.00 0.00 4.63
280 324 8.454570 TTGACATACATCTAATACACGGAGTA 57.545 34.615 0.00 0.00 41.61 2.59
281 325 8.454570 TGACATACATCTAATACACGGAGTAA 57.545 34.615 0.00 0.00 41.61 2.24
282 326 8.905850 TGACATACATCTAATACACGGAGTAAA 58.094 33.333 0.00 0.00 41.61 2.01
283 327 9.740239 GACATACATCTAATACACGGAGTAAAA 57.260 33.333 0.00 0.00 41.61 1.52
287 331 8.928270 ACATCTAATACACGGAGTAAAAAGAG 57.072 34.615 0.00 0.00 41.61 2.85
288 332 7.491696 ACATCTAATACACGGAGTAAAAAGAGC 59.508 37.037 0.00 0.00 41.61 4.09
289 333 6.927416 TCTAATACACGGAGTAAAAAGAGCA 58.073 36.000 0.00 0.00 41.61 4.26
290 334 7.380536 TCTAATACACGGAGTAAAAAGAGCAA 58.619 34.615 0.00 0.00 41.61 3.91
291 335 8.038944 TCTAATACACGGAGTAAAAAGAGCAAT 58.961 33.333 0.00 0.00 41.61 3.56
292 336 4.749245 ACACGGAGTAAAAAGAGCAATG 57.251 40.909 0.00 0.00 41.61 2.82
293 337 3.058224 ACACGGAGTAAAAAGAGCAATGC 60.058 43.478 0.00 0.00 41.61 3.56
294 338 3.189287 CACGGAGTAAAAAGAGCAATGCT 59.811 43.478 7.79 7.79 41.61 3.79
295 339 4.391830 CACGGAGTAAAAAGAGCAATGCTA 59.608 41.667 8.12 0.00 41.61 3.49
296 340 4.392138 ACGGAGTAAAAAGAGCAATGCTAC 59.608 41.667 8.12 0.93 41.94 3.58
297 341 4.391830 CGGAGTAAAAAGAGCAATGCTACA 59.608 41.667 8.12 0.00 39.88 2.74
298 342 5.631992 GGAGTAAAAAGAGCAATGCTACAC 58.368 41.667 8.12 0.00 39.88 2.90
299 343 5.181245 GGAGTAAAAAGAGCAATGCTACACA 59.819 40.000 8.12 0.00 39.88 3.72
300 344 6.002062 AGTAAAAAGAGCAATGCTACACAC 57.998 37.500 8.12 1.96 39.88 3.82
301 345 4.916983 AAAAAGAGCAATGCTACACACA 57.083 36.364 8.12 0.00 39.88 3.72
302 346 3.904136 AAAGAGCAATGCTACACACAC 57.096 42.857 8.12 0.00 39.88 3.82
303 347 1.432514 AGAGCAATGCTACACACACG 58.567 50.000 8.12 0.00 39.88 4.49
304 348 0.443869 GAGCAATGCTACACACACGG 59.556 55.000 8.12 0.00 39.88 4.94
305 349 0.955428 AGCAATGCTACACACACGGG 60.955 55.000 5.69 0.00 36.99 5.28
306 350 1.922135 GCAATGCTACACACACGGGG 61.922 60.000 0.00 0.00 0.00 5.73
307 351 0.321210 CAATGCTACACACACGGGGA 60.321 55.000 0.00 0.00 0.00 4.81
308 352 0.036388 AATGCTACACACACGGGGAG 60.036 55.000 0.00 0.00 0.00 4.30
309 353 0.902984 ATGCTACACACACGGGGAGA 60.903 55.000 0.00 0.00 0.00 3.71
310 354 1.215647 GCTACACACACGGGGAGAG 59.784 63.158 0.00 0.00 0.00 3.20
311 355 1.533469 GCTACACACACGGGGAGAGT 61.533 60.000 0.00 0.00 0.00 3.24
312 356 0.966920 CTACACACACGGGGAGAGTT 59.033 55.000 0.00 0.00 0.00 3.01
313 357 1.343465 CTACACACACGGGGAGAGTTT 59.657 52.381 0.00 0.00 0.00 2.66
314 358 0.544697 ACACACACGGGGAGAGTTTT 59.455 50.000 0.00 0.00 0.00 2.43
315 359 1.764134 ACACACACGGGGAGAGTTTTA 59.236 47.619 0.00 0.00 0.00 1.52
316 360 2.224209 ACACACACGGGGAGAGTTTTAG 60.224 50.000 0.00 0.00 0.00 1.85
317 361 1.346722 ACACACGGGGAGAGTTTTAGG 59.653 52.381 0.00 0.00 0.00 2.69
318 362 0.981943 ACACGGGGAGAGTTTTAGGG 59.018 55.000 0.00 0.00 0.00 3.53
319 363 0.252197 CACGGGGAGAGTTTTAGGGG 59.748 60.000 0.00 0.00 0.00 4.79
320 364 0.117742 ACGGGGAGAGTTTTAGGGGA 59.882 55.000 0.00 0.00 0.00 4.81
321 365 1.274242 ACGGGGAGAGTTTTAGGGGAT 60.274 52.381 0.00 0.00 0.00 3.85
322 366 1.844497 CGGGGAGAGTTTTAGGGGATT 59.156 52.381 0.00 0.00 0.00 3.01
323 367 2.158798 CGGGGAGAGTTTTAGGGGATTC 60.159 54.545 0.00 0.00 0.00 2.52
324 368 2.850568 GGGGAGAGTTTTAGGGGATTCA 59.149 50.000 0.00 0.00 0.00 2.57
325 369 3.371702 GGGGAGAGTTTTAGGGGATTCAC 60.372 52.174 0.00 0.00 0.00 3.18
326 370 3.532542 GGAGAGTTTTAGGGGATTCACG 58.467 50.000 0.00 0.00 0.00 4.35
327 371 3.532542 GAGAGTTTTAGGGGATTCACGG 58.467 50.000 0.00 0.00 0.00 4.94
328 372 2.238898 AGAGTTTTAGGGGATTCACGGG 59.761 50.000 0.00 0.00 0.00 5.28
329 373 2.237893 GAGTTTTAGGGGATTCACGGGA 59.762 50.000 0.00 0.00 0.00 5.14
330 374 2.850568 AGTTTTAGGGGATTCACGGGAT 59.149 45.455 0.00 0.00 0.00 3.85
331 375 4.042174 AGTTTTAGGGGATTCACGGGATA 58.958 43.478 0.00 0.00 0.00 2.59
332 376 4.102681 AGTTTTAGGGGATTCACGGGATAG 59.897 45.833 0.00 0.00 0.00 2.08
333 377 1.640917 TAGGGGATTCACGGGATAGC 58.359 55.000 0.00 0.00 0.00 2.97
334 378 0.104934 AGGGGATTCACGGGATAGCT 60.105 55.000 0.00 0.00 0.00 3.32
335 379 0.765510 GGGGATTCACGGGATAGCTT 59.234 55.000 0.00 0.00 0.00 3.74
336 380 1.975680 GGGGATTCACGGGATAGCTTA 59.024 52.381 0.00 0.00 0.00 3.09
337 381 2.028020 GGGGATTCACGGGATAGCTTAG 60.028 54.545 0.00 0.00 0.00 2.18
338 382 2.633481 GGGATTCACGGGATAGCTTAGT 59.367 50.000 0.00 0.00 0.00 2.24
339 383 3.071167 GGGATTCACGGGATAGCTTAGTT 59.929 47.826 0.00 0.00 0.00 2.24
340 384 4.058817 GGATTCACGGGATAGCTTAGTTG 58.941 47.826 0.00 0.00 0.00 3.16
341 385 3.536956 TTCACGGGATAGCTTAGTTGG 57.463 47.619 0.00 0.00 0.00 3.77
342 386 1.760613 TCACGGGATAGCTTAGTTGGG 59.239 52.381 0.00 0.00 0.00 4.12
343 387 1.760613 CACGGGATAGCTTAGTTGGGA 59.239 52.381 0.00 0.00 0.00 4.37
344 388 2.368875 CACGGGATAGCTTAGTTGGGAT 59.631 50.000 0.00 0.00 0.00 3.85
345 389 2.633481 ACGGGATAGCTTAGTTGGGATC 59.367 50.000 0.00 0.00 0.00 3.36
346 390 2.900546 CGGGATAGCTTAGTTGGGATCT 59.099 50.000 0.00 0.00 0.00 2.75
347 391 3.056465 CGGGATAGCTTAGTTGGGATCTC 60.056 52.174 0.00 0.00 0.00 2.75
348 392 4.164204 GGGATAGCTTAGTTGGGATCTCT 58.836 47.826 0.00 0.00 0.00 3.10
349 393 4.595350 GGGATAGCTTAGTTGGGATCTCTT 59.405 45.833 0.00 0.00 0.00 2.85
350 394 5.512232 GGGATAGCTTAGTTGGGATCTCTTG 60.512 48.000 0.00 0.00 0.00 3.02
351 395 5.305644 GGATAGCTTAGTTGGGATCTCTTGA 59.694 44.000 0.00 0.00 0.00 3.02
352 396 6.013812 GGATAGCTTAGTTGGGATCTCTTGAT 60.014 42.308 0.00 0.00 35.26 2.57
353 397 5.707066 AGCTTAGTTGGGATCTCTTGATT 57.293 39.130 0.00 0.00 32.19 2.57
354 398 5.435291 AGCTTAGTTGGGATCTCTTGATTG 58.565 41.667 0.00 0.00 32.19 2.67
355 399 4.578105 GCTTAGTTGGGATCTCTTGATTGG 59.422 45.833 0.00 0.00 32.19 3.16
356 400 5.630069 GCTTAGTTGGGATCTCTTGATTGGA 60.630 44.000 0.00 0.00 32.19 3.53
357 401 6.581388 TTAGTTGGGATCTCTTGATTGGAT 57.419 37.500 0.00 0.00 32.19 3.41
358 402 7.690301 GCTTAGTTGGGATCTCTTGATTGGATA 60.690 40.741 0.00 0.00 32.19 2.59
359 403 6.581388 AGTTGGGATCTCTTGATTGGATAA 57.419 37.500 0.00 0.00 32.19 1.75
360 404 6.973642 AGTTGGGATCTCTTGATTGGATAAA 58.026 36.000 0.00 0.00 32.19 1.40
361 405 7.413446 AGTTGGGATCTCTTGATTGGATAAAA 58.587 34.615 0.00 0.00 32.19 1.52
362 406 7.895429 AGTTGGGATCTCTTGATTGGATAAAAA 59.105 33.333 0.00 0.00 32.19 1.94
379 423 3.965470 AAAAACAGGGTGAAGGGTACT 57.035 42.857 0.00 0.00 0.00 2.73
380 424 2.951229 AAACAGGGTGAAGGGTACTG 57.049 50.000 0.00 0.00 35.40 2.74
381 425 1.815757 AACAGGGTGAAGGGTACTGT 58.184 50.000 0.00 0.00 43.61 3.55
382 426 2.708037 ACAGGGTGAAGGGTACTGTA 57.292 50.000 0.00 0.00 40.31 2.74
383 427 2.254508 ACAGGGTGAAGGGTACTGTAC 58.745 52.381 9.46 9.46 40.31 2.90
384 428 1.203994 CAGGGTGAAGGGTACTGTACG 59.796 57.143 11.52 0.00 0.00 3.67
385 429 0.108472 GGGTGAAGGGTACTGTACGC 60.108 60.000 22.92 22.92 41.44 4.42
386 430 0.604578 GGTGAAGGGTACTGTACGCA 59.395 55.000 29.13 14.64 43.32 5.24
387 431 1.206371 GGTGAAGGGTACTGTACGCAT 59.794 52.381 29.13 21.26 43.32 4.73
403 447 7.010183 ACTGTACGCATCATTACATAGTTTGAC 59.990 37.037 0.00 0.00 0.00 3.18
411 455 7.686438 TCATTACATAGTTTGACTGCACAAT 57.314 32.000 0.00 0.00 0.00 2.71
415 459 5.942872 ACATAGTTTGACTGCACAATAAGC 58.057 37.500 0.00 0.00 0.00 3.09
434 511 9.462174 CAATAAGCTTCAACATAAAACACAGAA 57.538 29.630 0.00 0.00 0.00 3.02
471 551 2.339556 GGCATACGCAAACAGCCCA 61.340 57.895 0.00 0.00 41.38 5.36
477 557 1.943693 CGCAAACAGCCCAAACACG 60.944 57.895 0.00 0.00 41.38 4.49
481 561 0.738389 AAACAGCCCAAACACGACAG 59.262 50.000 0.00 0.00 0.00 3.51
502 582 1.896220 GTGGACATCACAGGAAGCAA 58.104 50.000 0.00 0.00 45.39 3.91
503 583 1.808945 GTGGACATCACAGGAAGCAAG 59.191 52.381 0.00 0.00 45.39 4.01
506 586 1.881973 GACATCACAGGAAGCAAGCAA 59.118 47.619 0.00 0.00 0.00 3.91
508 588 0.886563 ATCACAGGAAGCAAGCAAGC 59.113 50.000 0.00 0.00 0.00 4.01
510 590 1.905354 ACAGGAAGCAAGCAAGCCC 60.905 57.895 0.00 0.00 34.23 5.19
513 593 1.986210 GGAAGCAAGCAAGCCCCAT 60.986 57.895 0.00 0.00 34.23 4.00
514 594 0.684153 GGAAGCAAGCAAGCCCCATA 60.684 55.000 0.00 0.00 34.23 2.74
515 595 0.743097 GAAGCAAGCAAGCCCCATAG 59.257 55.000 0.00 0.00 34.23 2.23
516 596 0.040204 AAGCAAGCAAGCCCCATAGT 59.960 50.000 0.00 0.00 34.23 2.12
517 597 0.394899 AGCAAGCAAGCCCCATAGTC 60.395 55.000 0.00 0.00 34.23 2.59
518 598 0.680921 GCAAGCAAGCCCCATAGTCA 60.681 55.000 0.00 0.00 0.00 3.41
519 599 1.838112 CAAGCAAGCCCCATAGTCAA 58.162 50.000 0.00 0.00 0.00 3.18
520 600 1.747355 CAAGCAAGCCCCATAGTCAAG 59.253 52.381 0.00 0.00 0.00 3.02
526 606 2.834113 AGCCCCATAGTCAAGTAGTGT 58.166 47.619 0.00 0.00 0.00 3.55
535 615 2.232452 AGTCAAGTAGTGTAGGCTGCTG 59.768 50.000 3.77 0.00 31.90 4.41
540 620 1.532604 TAGTGTAGGCTGCTGCACGT 61.533 55.000 17.89 3.88 43.18 4.49
571 651 7.234782 TGGTAGCTAGCAACCAACATATACTAT 59.765 37.037 22.80 0.00 42.74 2.12
572 652 8.746530 GGTAGCTAGCAACCAACATATACTATA 58.253 37.037 18.83 0.00 35.73 1.31
628 708 5.560183 CGATCTTGTACACTCCAAACAAACC 60.560 44.000 0.00 0.00 33.05 3.27
636 716 1.880027 CTCCAAACAAACCGGGAAGAG 59.120 52.381 6.32 0.00 0.00 2.85
746 833 3.951037 TGATGAATCCCAATTGGTTACCG 59.049 43.478 22.91 7.51 34.77 4.02
769 856 7.227910 ACCGACTTCAACAGTTAATGTGTTTAT 59.772 33.333 3.96 0.00 43.00 1.40
812 899 3.268013 AGAAGCGAAAATTTCCGTGTG 57.732 42.857 0.00 0.00 0.00 3.82
817 904 3.109619 GCGAAAATTTCCGTGTGTTGAA 58.890 40.909 0.00 0.00 0.00 2.69
818 905 3.548268 GCGAAAATTTCCGTGTGTTGAAA 59.452 39.130 0.00 0.00 35.17 2.69
1139 1241 1.740585 CAGTGACCTAGACTCGTCTGG 59.259 57.143 9.73 6.64 40.71 3.86
1323 1425 0.741221 GGCGGGCTTCTGTTACTGAG 60.741 60.000 0.00 0.00 0.00 3.35
1382 1484 4.398044 GGAAGTTTCAGTCAACAACCAGAA 59.602 41.667 0.00 0.00 0.00 3.02
1391 1493 1.956477 CAACAACCAGAAGTTCCAGGG 59.044 52.381 14.51 9.77 36.18 4.45
1395 1497 0.474184 ACCAGAAGTTCCAGGGTGTG 59.526 55.000 14.51 0.00 0.00 3.82
1578 1683 2.183811 CTGGAGCTGCTGGAGTCG 59.816 66.667 7.01 0.00 0.00 4.18
1701 1806 1.130054 AGGTTGCCAGGAAGAGCAGA 61.130 55.000 0.00 0.00 40.73 4.26
1764 2817 3.473647 CGGGAGGCAGAGATGGCA 61.474 66.667 4.56 0.00 36.76 4.92
1861 2914 4.436242 ACAGACAGTGAGGTACGTATTG 57.564 45.455 0.00 0.00 0.00 1.90
1891 2946 3.274288 GCTTCATCGACATTTCCTTCCT 58.726 45.455 0.00 0.00 0.00 3.36
1892 2947 3.311048 GCTTCATCGACATTTCCTTCCTC 59.689 47.826 0.00 0.00 0.00 3.71
1893 2948 3.543680 TCATCGACATTTCCTTCCTCC 57.456 47.619 0.00 0.00 0.00 4.30
1913 2969 6.098266 TCCTCCATTTTCGTCTGATCAAGATA 59.902 38.462 0.00 0.00 37.23 1.98
2002 3065 2.526873 AAGGACCTGCTGGACGGT 60.527 61.111 17.64 0.00 37.04 4.83
2150 3214 2.569657 CGATTGGGGACGACGACA 59.430 61.111 0.00 0.00 0.00 4.35
2159 3226 2.774951 GACGACGACAATGACGCCG 61.775 63.158 11.90 11.90 41.66 6.46
2252 3319 4.394078 TCCGCAAGACGTCGTCCG 62.394 66.667 21.40 16.93 41.42 4.79
2459 3526 2.624169 GCGGCCGGCTATTAAATGA 58.376 52.632 29.38 0.00 39.11 2.57
2482 3549 6.831353 TGAAAAGTGTTTGTCTCTTTATCCCA 59.169 34.615 0.00 0.00 38.42 4.37
2487 3554 8.934023 AGTGTTTGTCTCTTTATCCCAATTAA 57.066 30.769 0.00 0.00 0.00 1.40
2702 3770 6.459024 CGACGAGATCTTTGAAACTAGATCCT 60.459 42.308 0.00 0.00 45.05 3.24
2724 3792 3.531538 ACATGGCTATGTTTCGACGAAT 58.468 40.909 10.30 0.00 45.01 3.34
2872 3945 1.368374 CCCCTCAAACTACCCCTTCA 58.632 55.000 0.00 0.00 0.00 3.02
3002 4075 6.006275 ACTTCCTAGTAATGGATGTGCAAT 57.994 37.500 0.00 0.00 39.50 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.278238 GATCAGTACTTCCGCAACCG 58.722 55.000 0.00 0.00 0.00 4.44
5 6 2.380084 TGATCAGTACTTCCGCAACC 57.620 50.000 0.00 0.00 0.00 3.77
6 7 4.391830 TGAAATGATCAGTACTTCCGCAAC 59.608 41.667 0.09 0.00 33.04 4.17
7 8 4.574892 TGAAATGATCAGTACTTCCGCAA 58.425 39.130 0.09 0.00 33.04 4.85
8 9 4.200838 TGAAATGATCAGTACTTCCGCA 57.799 40.909 0.09 0.00 33.04 5.69
9 10 4.391830 TGTTGAAATGATCAGTACTTCCGC 59.608 41.667 0.09 0.00 39.77 5.54
10 11 6.668541 ATGTTGAAATGATCAGTACTTCCG 57.331 37.500 0.09 0.00 39.77 4.30
11 12 7.965107 GTCAATGTTGAAATGATCAGTACTTCC 59.035 37.037 0.09 0.00 39.77 3.46
12 13 8.506437 TGTCAATGTTGAAATGATCAGTACTTC 58.494 33.333 0.09 2.45 39.77 3.01
13 14 8.394971 TGTCAATGTTGAAATGATCAGTACTT 57.605 30.769 0.09 0.00 39.77 2.24
23 24 4.508461 TGCTCCTGTCAATGTTGAAATG 57.492 40.909 0.00 0.00 39.21 2.32
97 110 9.283768 TGGCCTATTATGTAGTGTGATTTTATG 57.716 33.333 3.32 0.00 0.00 1.90
99 112 9.502091 GATGGCCTATTATGTAGTGTGATTTTA 57.498 33.333 3.32 0.00 0.00 1.52
101 114 7.749666 AGATGGCCTATTATGTAGTGTGATTT 58.250 34.615 3.32 0.00 0.00 2.17
102 115 7.321717 AGATGGCCTATTATGTAGTGTGATT 57.678 36.000 3.32 0.00 0.00 2.57
131 144 4.644685 TGGTGAAGCAAAGCTACTCTTTTT 59.355 37.500 0.00 0.00 42.82 1.94
136 149 4.938226 AGTATTGGTGAAGCAAAGCTACTC 59.062 41.667 0.00 0.00 38.25 2.59
153 166 8.503196 TGCAAAGATGTGTACAGTAAAGTATTG 58.497 33.333 0.00 0.00 0.00 1.90
155 168 8.792830 ATGCAAAGATGTGTACAGTAAAGTAT 57.207 30.769 0.00 0.00 0.00 2.12
170 214 4.802039 GTGCCATCAAACTATGCAAAGATG 59.198 41.667 0.00 0.00 34.25 2.90
172 216 3.825585 TGTGCCATCAAACTATGCAAAGA 59.174 39.130 0.00 0.00 0.00 2.52
173 217 4.177165 TGTGCCATCAAACTATGCAAAG 57.823 40.909 0.00 0.00 0.00 2.77
174 218 4.597404 TTGTGCCATCAAACTATGCAAA 57.403 36.364 0.00 0.00 0.00 3.68
175 219 4.804868 ATTGTGCCATCAAACTATGCAA 57.195 36.364 0.00 0.00 0.00 4.08
176 220 5.418524 ACTTATTGTGCCATCAAACTATGCA 59.581 36.000 0.00 0.00 0.00 3.96
177 221 5.894807 ACTTATTGTGCCATCAAACTATGC 58.105 37.500 0.00 0.00 0.00 3.14
178 222 7.218773 CGAAACTTATTGTGCCATCAAACTATG 59.781 37.037 0.00 0.00 0.00 2.23
179 223 7.120579 TCGAAACTTATTGTGCCATCAAACTAT 59.879 33.333 0.00 0.00 0.00 2.12
180 224 6.428465 TCGAAACTTATTGTGCCATCAAACTA 59.572 34.615 0.00 0.00 0.00 2.24
181 225 5.240623 TCGAAACTTATTGTGCCATCAAACT 59.759 36.000 0.00 0.00 0.00 2.66
182 226 5.342259 GTCGAAACTTATTGTGCCATCAAAC 59.658 40.000 0.00 0.00 0.00 2.93
183 227 5.009110 TGTCGAAACTTATTGTGCCATCAAA 59.991 36.000 0.00 0.00 0.00 2.69
184 228 4.517075 TGTCGAAACTTATTGTGCCATCAA 59.483 37.500 0.00 0.00 0.00 2.57
185 229 4.068599 TGTCGAAACTTATTGTGCCATCA 58.931 39.130 0.00 0.00 0.00 3.07
186 230 4.678509 TGTCGAAACTTATTGTGCCATC 57.321 40.909 0.00 0.00 0.00 3.51
187 231 6.112734 TCTATGTCGAAACTTATTGTGCCAT 58.887 36.000 0.00 0.00 0.00 4.40
188 232 5.483811 TCTATGTCGAAACTTATTGTGCCA 58.516 37.500 0.00 0.00 0.00 4.92
189 233 6.128391 TGTTCTATGTCGAAACTTATTGTGCC 60.128 38.462 0.00 0.00 0.00 5.01
190 234 6.736853 GTGTTCTATGTCGAAACTTATTGTGC 59.263 38.462 0.00 0.00 0.00 4.57
191 235 7.792925 TGTGTTCTATGTCGAAACTTATTGTG 58.207 34.615 0.00 0.00 0.00 3.33
192 236 7.870954 TCTGTGTTCTATGTCGAAACTTATTGT 59.129 33.333 0.00 0.00 0.00 2.71
193 237 8.239681 TCTGTGTTCTATGTCGAAACTTATTG 57.760 34.615 0.00 0.00 0.00 1.90
194 238 8.827177 TTCTGTGTTCTATGTCGAAACTTATT 57.173 30.769 0.00 0.00 0.00 1.40
195 239 8.827177 TTTCTGTGTTCTATGTCGAAACTTAT 57.173 30.769 0.00 0.00 0.00 1.73
196 240 8.139350 TCTTTCTGTGTTCTATGTCGAAACTTA 58.861 33.333 0.00 0.00 0.00 2.24
197 241 6.984474 TCTTTCTGTGTTCTATGTCGAAACTT 59.016 34.615 0.00 0.00 0.00 2.66
198 242 6.513180 TCTTTCTGTGTTCTATGTCGAAACT 58.487 36.000 0.00 0.00 0.00 2.66
199 243 6.764877 TCTTTCTGTGTTCTATGTCGAAAC 57.235 37.500 0.00 0.00 0.00 2.78
200 244 7.571244 GCATTCTTTCTGTGTTCTATGTCGAAA 60.571 37.037 0.00 0.00 0.00 3.46
201 245 6.128553 GCATTCTTTCTGTGTTCTATGTCGAA 60.129 38.462 0.00 0.00 0.00 3.71
202 246 5.348724 GCATTCTTTCTGTGTTCTATGTCGA 59.651 40.000 0.00 0.00 0.00 4.20
203 247 5.349817 AGCATTCTTTCTGTGTTCTATGTCG 59.650 40.000 0.00 0.00 0.00 4.35
204 248 6.734104 AGCATTCTTTCTGTGTTCTATGTC 57.266 37.500 0.00 0.00 0.00 3.06
205 249 6.488006 ACAAGCATTCTTTCTGTGTTCTATGT 59.512 34.615 0.00 0.00 0.00 2.29
206 250 6.906659 ACAAGCATTCTTTCTGTGTTCTATG 58.093 36.000 0.00 0.00 0.00 2.23
207 251 8.621532 TTACAAGCATTCTTTCTGTGTTCTAT 57.378 30.769 0.00 0.00 0.00 1.98
208 252 8.445275 TTTACAAGCATTCTTTCTGTGTTCTA 57.555 30.769 0.00 0.00 0.00 2.10
209 253 6.942532 TTACAAGCATTCTTTCTGTGTTCT 57.057 33.333 0.00 0.00 0.00 3.01
210 254 7.915397 TCTTTTACAAGCATTCTTTCTGTGTTC 59.085 33.333 0.00 0.00 0.00 3.18
211 255 7.771183 TCTTTTACAAGCATTCTTTCTGTGTT 58.229 30.769 0.00 0.00 0.00 3.32
212 256 7.333528 TCTTTTACAAGCATTCTTTCTGTGT 57.666 32.000 0.00 0.00 0.00 3.72
213 257 6.860023 CCTCTTTTACAAGCATTCTTTCTGTG 59.140 38.462 0.00 0.00 0.00 3.66
214 258 6.015940 CCCTCTTTTACAAGCATTCTTTCTGT 60.016 38.462 0.00 0.00 0.00 3.41
215 259 6.385033 CCCTCTTTTACAAGCATTCTTTCTG 58.615 40.000 0.00 0.00 0.00 3.02
216 260 5.047731 GCCCTCTTTTACAAGCATTCTTTCT 60.048 40.000 0.00 0.00 0.00 2.52
217 261 5.047731 AGCCCTCTTTTACAAGCATTCTTTC 60.048 40.000 0.00 0.00 0.00 2.62
218 262 4.835056 AGCCCTCTTTTACAAGCATTCTTT 59.165 37.500 0.00 0.00 0.00 2.52
219 263 4.411013 AGCCCTCTTTTACAAGCATTCTT 58.589 39.130 0.00 0.00 0.00 2.52
220 264 4.039603 AGCCCTCTTTTACAAGCATTCT 57.960 40.909 0.00 0.00 0.00 2.40
221 265 4.488879 CAAGCCCTCTTTTACAAGCATTC 58.511 43.478 0.00 0.00 0.00 2.67
222 266 3.306294 GCAAGCCCTCTTTTACAAGCATT 60.306 43.478 0.00 0.00 0.00 3.56
223 267 2.232208 GCAAGCCCTCTTTTACAAGCAT 59.768 45.455 0.00 0.00 0.00 3.79
224 268 1.613437 GCAAGCCCTCTTTTACAAGCA 59.387 47.619 0.00 0.00 0.00 3.91
225 269 1.613437 TGCAAGCCCTCTTTTACAAGC 59.387 47.619 0.00 0.00 0.00 4.01
226 270 4.202151 ACTTTGCAAGCCCTCTTTTACAAG 60.202 41.667 0.00 0.00 0.00 3.16
227 271 3.704061 ACTTTGCAAGCCCTCTTTTACAA 59.296 39.130 0.00 0.00 0.00 2.41
228 272 3.295973 ACTTTGCAAGCCCTCTTTTACA 58.704 40.909 0.00 0.00 0.00 2.41
229 273 4.322080 AACTTTGCAAGCCCTCTTTTAC 57.678 40.909 0.00 0.00 0.00 2.01
230 274 4.404073 TCAAACTTTGCAAGCCCTCTTTTA 59.596 37.500 0.00 0.00 0.00 1.52
231 275 3.197549 TCAAACTTTGCAAGCCCTCTTTT 59.802 39.130 0.00 0.00 0.00 2.27
232 276 2.765699 TCAAACTTTGCAAGCCCTCTTT 59.234 40.909 0.00 0.00 0.00 2.52
233 277 2.101415 GTCAAACTTTGCAAGCCCTCTT 59.899 45.455 0.00 0.00 0.00 2.85
234 278 1.683385 GTCAAACTTTGCAAGCCCTCT 59.317 47.619 0.00 0.00 0.00 3.69
235 279 1.683385 AGTCAAACTTTGCAAGCCCTC 59.317 47.619 0.00 0.00 0.00 4.30
236 280 1.780503 AGTCAAACTTTGCAAGCCCT 58.219 45.000 0.00 0.00 0.00 5.19
237 281 2.159114 TCAAGTCAAACTTTGCAAGCCC 60.159 45.455 0.00 0.00 36.03 5.19
238 282 2.860136 GTCAAGTCAAACTTTGCAAGCC 59.140 45.455 0.00 0.00 36.03 4.35
239 283 3.510719 TGTCAAGTCAAACTTTGCAAGC 58.489 40.909 0.00 0.00 36.03 4.01
240 284 6.264832 TGTATGTCAAGTCAAACTTTGCAAG 58.735 36.000 0.00 0.00 36.03 4.01
241 285 6.201226 TGTATGTCAAGTCAAACTTTGCAA 57.799 33.333 0.00 0.00 36.03 4.08
242 286 5.826601 TGTATGTCAAGTCAAACTTTGCA 57.173 34.783 0.00 0.00 36.03 4.08
243 287 6.672147 AGATGTATGTCAAGTCAAACTTTGC 58.328 36.000 0.00 0.00 36.03 3.68
249 293 9.083080 CGTGTATTAGATGTATGTCAAGTCAAA 57.917 33.333 0.00 0.00 0.00 2.69
250 294 7.704899 CCGTGTATTAGATGTATGTCAAGTCAA 59.295 37.037 0.00 0.00 0.00 3.18
251 295 7.067737 TCCGTGTATTAGATGTATGTCAAGTCA 59.932 37.037 0.00 0.00 0.00 3.41
252 296 7.423199 TCCGTGTATTAGATGTATGTCAAGTC 58.577 38.462 0.00 0.00 0.00 3.01
253 297 7.068348 ACTCCGTGTATTAGATGTATGTCAAGT 59.932 37.037 0.00 0.00 0.00 3.16
254 298 7.426410 ACTCCGTGTATTAGATGTATGTCAAG 58.574 38.462 0.00 0.00 0.00 3.02
255 299 7.342769 ACTCCGTGTATTAGATGTATGTCAA 57.657 36.000 0.00 0.00 0.00 3.18
256 300 6.954487 ACTCCGTGTATTAGATGTATGTCA 57.046 37.500 0.00 0.00 0.00 3.58
257 301 9.740239 TTTTACTCCGTGTATTAGATGTATGTC 57.260 33.333 0.00 0.00 0.00 3.06
262 306 7.491696 GCTCTTTTTACTCCGTGTATTAGATGT 59.508 37.037 0.00 0.00 0.00 3.06
263 307 7.491372 TGCTCTTTTTACTCCGTGTATTAGATG 59.509 37.037 0.00 0.00 0.00 2.90
264 308 7.553334 TGCTCTTTTTACTCCGTGTATTAGAT 58.447 34.615 0.00 0.00 0.00 1.98
265 309 6.927416 TGCTCTTTTTACTCCGTGTATTAGA 58.073 36.000 0.00 0.00 0.00 2.10
266 310 7.591006 TTGCTCTTTTTACTCCGTGTATTAG 57.409 36.000 0.00 0.00 0.00 1.73
267 311 7.413657 GCATTGCTCTTTTTACTCCGTGTATTA 60.414 37.037 0.16 0.00 0.00 0.98
268 312 6.622896 GCATTGCTCTTTTTACTCCGTGTATT 60.623 38.462 0.16 0.00 0.00 1.89
269 313 5.163754 GCATTGCTCTTTTTACTCCGTGTAT 60.164 40.000 0.16 0.00 0.00 2.29
270 314 4.153475 GCATTGCTCTTTTTACTCCGTGTA 59.847 41.667 0.16 0.00 0.00 2.90
271 315 3.058224 GCATTGCTCTTTTTACTCCGTGT 60.058 43.478 0.16 0.00 0.00 4.49
272 316 3.189287 AGCATTGCTCTTTTTACTCCGTG 59.811 43.478 5.03 0.00 30.62 4.94
273 317 3.412386 AGCATTGCTCTTTTTACTCCGT 58.588 40.909 5.03 0.00 30.62 4.69
274 318 4.391830 TGTAGCATTGCTCTTTTTACTCCG 59.608 41.667 15.81 0.00 40.44 4.63
275 319 5.181245 TGTGTAGCATTGCTCTTTTTACTCC 59.819 40.000 15.81 2.95 40.44 3.85
276 320 6.080406 GTGTGTAGCATTGCTCTTTTTACTC 58.920 40.000 15.81 8.10 40.44 2.59
277 321 5.530915 TGTGTGTAGCATTGCTCTTTTTACT 59.469 36.000 15.81 0.00 40.44 2.24
278 322 5.625311 GTGTGTGTAGCATTGCTCTTTTTAC 59.375 40.000 15.81 7.23 40.44 2.01
279 323 5.559991 CGTGTGTGTAGCATTGCTCTTTTTA 60.560 40.000 15.81 0.00 40.44 1.52
280 324 4.610945 GTGTGTGTAGCATTGCTCTTTTT 58.389 39.130 15.81 0.00 40.44 1.94
281 325 3.303990 CGTGTGTGTAGCATTGCTCTTTT 60.304 43.478 15.81 0.00 40.44 2.27
282 326 2.224079 CGTGTGTGTAGCATTGCTCTTT 59.776 45.455 15.81 0.00 40.44 2.52
283 327 1.800586 CGTGTGTGTAGCATTGCTCTT 59.199 47.619 15.81 0.00 40.44 2.85
284 328 1.432514 CGTGTGTGTAGCATTGCTCT 58.567 50.000 15.81 0.00 40.44 4.09
285 329 0.443869 CCGTGTGTGTAGCATTGCTC 59.556 55.000 15.81 7.72 40.44 4.26
286 330 0.955428 CCCGTGTGTGTAGCATTGCT 60.955 55.000 16.63 16.63 43.41 3.91
287 331 1.501741 CCCGTGTGTGTAGCATTGC 59.498 57.895 0.00 0.00 0.00 3.56
288 332 0.321210 TCCCCGTGTGTGTAGCATTG 60.321 55.000 0.00 0.00 0.00 2.82
289 333 0.036388 CTCCCCGTGTGTGTAGCATT 60.036 55.000 0.00 0.00 0.00 3.56
290 334 0.902984 TCTCCCCGTGTGTGTAGCAT 60.903 55.000 0.00 0.00 0.00 3.79
291 335 1.532078 TCTCCCCGTGTGTGTAGCA 60.532 57.895 0.00 0.00 0.00 3.49
292 336 1.215647 CTCTCCCCGTGTGTGTAGC 59.784 63.158 0.00 0.00 0.00 3.58
293 337 0.966920 AACTCTCCCCGTGTGTGTAG 59.033 55.000 0.00 0.00 0.00 2.74
294 338 1.416243 AAACTCTCCCCGTGTGTGTA 58.584 50.000 0.00 0.00 0.00 2.90
295 339 0.544697 AAAACTCTCCCCGTGTGTGT 59.455 50.000 0.00 0.00 0.00 3.72
296 340 2.413837 CTAAAACTCTCCCCGTGTGTG 58.586 52.381 0.00 0.00 0.00 3.82
297 341 1.346722 CCTAAAACTCTCCCCGTGTGT 59.653 52.381 0.00 0.00 0.00 3.72
298 342 1.338769 CCCTAAAACTCTCCCCGTGTG 60.339 57.143 0.00 0.00 0.00 3.82
299 343 0.981943 CCCTAAAACTCTCCCCGTGT 59.018 55.000 0.00 0.00 0.00 4.49
300 344 0.252197 CCCCTAAAACTCTCCCCGTG 59.748 60.000 0.00 0.00 0.00 4.94
301 345 0.117742 TCCCCTAAAACTCTCCCCGT 59.882 55.000 0.00 0.00 0.00 5.28
302 346 1.508256 ATCCCCTAAAACTCTCCCCG 58.492 55.000 0.00 0.00 0.00 5.73
303 347 2.850568 TGAATCCCCTAAAACTCTCCCC 59.149 50.000 0.00 0.00 0.00 4.81
304 348 3.681874 CGTGAATCCCCTAAAACTCTCCC 60.682 52.174 0.00 0.00 0.00 4.30
305 349 3.532542 CGTGAATCCCCTAAAACTCTCC 58.467 50.000 0.00 0.00 0.00 3.71
306 350 3.532542 CCGTGAATCCCCTAAAACTCTC 58.467 50.000 0.00 0.00 0.00 3.20
307 351 2.238898 CCCGTGAATCCCCTAAAACTCT 59.761 50.000 0.00 0.00 0.00 3.24
308 352 2.237893 TCCCGTGAATCCCCTAAAACTC 59.762 50.000 0.00 0.00 0.00 3.01
309 353 2.271777 TCCCGTGAATCCCCTAAAACT 58.728 47.619 0.00 0.00 0.00 2.66
310 354 2.793288 TCCCGTGAATCCCCTAAAAC 57.207 50.000 0.00 0.00 0.00 2.43
311 355 3.181448 GCTATCCCGTGAATCCCCTAAAA 60.181 47.826 0.00 0.00 0.00 1.52
312 356 2.370849 GCTATCCCGTGAATCCCCTAAA 59.629 50.000 0.00 0.00 0.00 1.85
313 357 1.975680 GCTATCCCGTGAATCCCCTAA 59.024 52.381 0.00 0.00 0.00 2.69
314 358 1.149288 AGCTATCCCGTGAATCCCCTA 59.851 52.381 0.00 0.00 0.00 3.53
315 359 0.104934 AGCTATCCCGTGAATCCCCT 60.105 55.000 0.00 0.00 0.00 4.79
316 360 0.765510 AAGCTATCCCGTGAATCCCC 59.234 55.000 0.00 0.00 0.00 4.81
317 361 2.633481 ACTAAGCTATCCCGTGAATCCC 59.367 50.000 0.00 0.00 0.00 3.85
318 362 4.058817 CAACTAAGCTATCCCGTGAATCC 58.941 47.826 0.00 0.00 0.00 3.01
319 363 4.058817 CCAACTAAGCTATCCCGTGAATC 58.941 47.826 0.00 0.00 0.00 2.52
320 364 3.181454 CCCAACTAAGCTATCCCGTGAAT 60.181 47.826 0.00 0.00 0.00 2.57
321 365 2.169769 CCCAACTAAGCTATCCCGTGAA 59.830 50.000 0.00 0.00 0.00 3.18
322 366 1.760613 CCCAACTAAGCTATCCCGTGA 59.239 52.381 0.00 0.00 0.00 4.35
323 367 1.760613 TCCCAACTAAGCTATCCCGTG 59.239 52.381 0.00 0.00 0.00 4.94
324 368 2.170012 TCCCAACTAAGCTATCCCGT 57.830 50.000 0.00 0.00 0.00 5.28
325 369 2.900546 AGATCCCAACTAAGCTATCCCG 59.099 50.000 0.00 0.00 0.00 5.14
326 370 4.164204 AGAGATCCCAACTAAGCTATCCC 58.836 47.826 0.00 0.00 0.00 3.85
327 371 5.305644 TCAAGAGATCCCAACTAAGCTATCC 59.694 44.000 0.00 0.00 0.00 2.59
328 372 6.412362 TCAAGAGATCCCAACTAAGCTATC 57.588 41.667 0.00 0.00 0.00 2.08
329 373 7.222872 CAATCAAGAGATCCCAACTAAGCTAT 58.777 38.462 0.00 0.00 31.90 2.97
330 374 6.408548 CCAATCAAGAGATCCCAACTAAGCTA 60.409 42.308 0.00 0.00 31.90 3.32
331 375 5.435291 CAATCAAGAGATCCCAACTAAGCT 58.565 41.667 0.00 0.00 31.90 3.74
332 376 4.578105 CCAATCAAGAGATCCCAACTAAGC 59.422 45.833 0.00 0.00 31.90 3.09
333 377 5.994250 TCCAATCAAGAGATCCCAACTAAG 58.006 41.667 0.00 0.00 31.90 2.18
334 378 6.581388 ATCCAATCAAGAGATCCCAACTAA 57.419 37.500 0.00 0.00 31.90 2.24
335 379 7.690454 TTATCCAATCAAGAGATCCCAACTA 57.310 36.000 0.00 0.00 31.90 2.24
336 380 6.581388 TTATCCAATCAAGAGATCCCAACT 57.419 37.500 0.00 0.00 31.90 3.16
337 381 7.645058 TTTTATCCAATCAAGAGATCCCAAC 57.355 36.000 0.00 0.00 31.90 3.77
359 403 3.053170 ACAGTACCCTTCACCCTGTTTTT 60.053 43.478 0.00 0.00 32.72 1.94
360 404 2.512476 ACAGTACCCTTCACCCTGTTTT 59.488 45.455 0.00 0.00 32.72 2.43
361 405 2.132686 ACAGTACCCTTCACCCTGTTT 58.867 47.619 0.00 0.00 32.72 2.83
362 406 1.815757 ACAGTACCCTTCACCCTGTT 58.184 50.000 0.00 0.00 32.72 3.16
363 407 2.254508 GTACAGTACCCTTCACCCTGT 58.745 52.381 0.00 0.00 39.53 4.00
364 408 1.203994 CGTACAGTACCCTTCACCCTG 59.796 57.143 5.07 0.00 0.00 4.45
365 409 1.553706 CGTACAGTACCCTTCACCCT 58.446 55.000 5.07 0.00 0.00 4.34
366 410 0.108472 GCGTACAGTACCCTTCACCC 60.108 60.000 5.07 0.00 0.00 4.61
367 411 0.604578 TGCGTACAGTACCCTTCACC 59.395 55.000 5.07 0.00 0.00 4.02
368 412 2.094390 TGATGCGTACAGTACCCTTCAC 60.094 50.000 5.07 0.00 0.00 3.18
369 413 2.172679 TGATGCGTACAGTACCCTTCA 58.827 47.619 5.07 7.38 0.00 3.02
370 414 2.953466 TGATGCGTACAGTACCCTTC 57.047 50.000 5.07 4.96 0.00 3.46
371 415 3.906720 AATGATGCGTACAGTACCCTT 57.093 42.857 5.07 0.00 0.00 3.95
372 416 3.702548 TGTAATGATGCGTACAGTACCCT 59.297 43.478 5.07 0.00 37.80 4.34
373 417 4.049546 TGTAATGATGCGTACAGTACCC 57.950 45.455 5.07 0.00 37.80 3.69
374 418 6.444633 ACTATGTAATGATGCGTACAGTACC 58.555 40.000 5.07 0.00 37.80 3.34
375 419 7.925703 AACTATGTAATGATGCGTACAGTAC 57.074 36.000 0.00 0.00 38.65 2.73
376 420 8.192110 TCAAACTATGTAATGATGCGTACAGTA 58.808 33.333 0.00 0.00 33.89 2.74
377 421 7.010183 GTCAAACTATGTAATGATGCGTACAGT 59.990 37.037 0.00 0.00 33.89 3.55
378 422 7.222805 AGTCAAACTATGTAATGATGCGTACAG 59.777 37.037 0.00 0.00 33.89 2.74
379 423 7.010091 CAGTCAAACTATGTAATGATGCGTACA 59.990 37.037 0.00 0.00 34.84 2.90
380 424 7.337718 CAGTCAAACTATGTAATGATGCGTAC 58.662 38.462 0.00 0.00 0.00 3.67
381 425 6.019075 GCAGTCAAACTATGTAATGATGCGTA 60.019 38.462 0.00 0.00 0.00 4.42
382 426 5.220662 GCAGTCAAACTATGTAATGATGCGT 60.221 40.000 0.00 0.00 0.00 5.24
383 427 5.200454 GCAGTCAAACTATGTAATGATGCG 58.800 41.667 0.00 0.00 0.00 4.73
384 428 5.967674 GTGCAGTCAAACTATGTAATGATGC 59.032 40.000 0.00 0.00 32.24 3.91
385 429 7.075674 TGTGCAGTCAAACTATGTAATGATG 57.924 36.000 0.00 0.00 0.00 3.07
386 430 7.686438 TTGTGCAGTCAAACTATGTAATGAT 57.314 32.000 0.00 0.00 0.00 2.45
387 431 7.686438 ATTGTGCAGTCAAACTATGTAATGA 57.314 32.000 0.00 0.00 0.00 2.57
403 447 7.381948 TGTTTTATGTTGAAGCTTATTGTGCAG 59.618 33.333 0.00 0.00 0.00 4.41
411 455 8.898761 TCTTTCTGTGTTTTATGTTGAAGCTTA 58.101 29.630 0.00 0.00 0.00 3.09
434 511 7.280205 CGTATGCCCTCTTTTACAAGTATTCTT 59.720 37.037 0.00 0.00 0.00 2.52
483 563 1.808945 CTTGCTTCCTGTGATGTCCAC 59.191 52.381 0.00 0.00 45.88 4.02
496 576 0.743097 CTATGGGGCTTGCTTGCTTC 59.257 55.000 1.96 0.00 0.00 3.86
497 577 0.040204 ACTATGGGGCTTGCTTGCTT 59.960 50.000 1.96 0.00 0.00 3.91
498 578 0.394899 GACTATGGGGCTTGCTTGCT 60.395 55.000 1.96 0.00 0.00 3.91
499 579 0.680921 TGACTATGGGGCTTGCTTGC 60.681 55.000 0.00 0.00 0.00 4.01
502 582 0.995024 ACTTGACTATGGGGCTTGCT 59.005 50.000 0.00 0.00 0.00 3.91
503 583 2.092914 ACTACTTGACTATGGGGCTTGC 60.093 50.000 0.00 0.00 0.00 4.01
506 586 2.834113 ACACTACTTGACTATGGGGCT 58.166 47.619 0.00 0.00 0.00 5.19
508 588 3.069729 GCCTACACTACTTGACTATGGGG 59.930 52.174 0.00 0.00 0.00 4.96
510 590 4.737946 GCAGCCTACACTACTTGACTATGG 60.738 50.000 0.00 0.00 0.00 2.74
513 593 3.444034 CAGCAGCCTACACTACTTGACTA 59.556 47.826 0.00 0.00 0.00 2.59
514 594 2.232452 CAGCAGCCTACACTACTTGACT 59.768 50.000 0.00 0.00 0.00 3.41
515 595 2.611518 CAGCAGCCTACACTACTTGAC 58.388 52.381 0.00 0.00 0.00 3.18
516 596 1.066858 GCAGCAGCCTACACTACTTGA 60.067 52.381 0.00 0.00 33.58 3.02
517 597 1.338105 TGCAGCAGCCTACACTACTTG 60.338 52.381 0.00 0.00 41.13 3.16
518 598 0.976641 TGCAGCAGCCTACACTACTT 59.023 50.000 0.00 0.00 41.13 2.24
519 599 0.247736 GTGCAGCAGCCTACACTACT 59.752 55.000 0.00 0.00 41.13 2.57
520 600 1.078759 CGTGCAGCAGCCTACACTAC 61.079 60.000 0.00 0.00 41.13 2.73
526 606 4.833811 CATACGTGCAGCAGCCTA 57.166 55.556 0.00 0.00 41.13 3.93
594 674 4.948004 AGTGTACAAGATCGTCACCTATGA 59.052 41.667 0.00 0.00 0.00 2.15
628 708 1.369091 CCGGATGCAAACTCTTCCCG 61.369 60.000 0.00 0.00 0.00 5.14
657 737 1.768275 TGAGAGAGGAAAGCACAACCA 59.232 47.619 0.00 0.00 0.00 3.67
769 856 7.156000 TCTTCGGTGTGATTTGACAGTATTAA 58.844 34.615 0.00 0.00 0.00 1.40
772 859 5.147330 TCTTCGGTGTGATTTGACAGTAT 57.853 39.130 0.00 0.00 0.00 2.12
773 860 4.594123 TCTTCGGTGTGATTTGACAGTA 57.406 40.909 0.00 0.00 0.00 2.74
774 861 3.469008 TCTTCGGTGTGATTTGACAGT 57.531 42.857 0.00 0.00 0.00 3.55
789 876 2.902484 CACGGAAATTTTCGCTTCTTCG 59.098 45.455 18.80 0.00 0.00 3.79
812 899 6.638468 GGTGACATCTTTGATCAAGTTTCAAC 59.362 38.462 8.41 7.41 33.03 3.18
817 904 4.728772 TGGGTGACATCTTTGATCAAGTT 58.271 39.130 8.41 0.00 33.66 2.66
818 905 4.371624 TGGGTGACATCTTTGATCAAGT 57.628 40.909 8.41 2.91 33.66 3.16
1161 1263 3.119137 TCAAACCGTCTGACGATGATGAT 60.119 43.478 29.93 6.09 46.05 2.45
1162 1264 2.230266 TCAAACCGTCTGACGATGATGA 59.770 45.455 29.93 22.46 46.05 2.92
1163 1265 2.600420 CTCAAACCGTCTGACGATGATG 59.400 50.000 29.93 20.84 46.05 3.07
1240 1342 2.979676 CGCTTGCACCAGCTTCCA 60.980 61.111 8.67 0.00 42.74 3.53
1307 1409 3.418684 TTTCCTCAGTAACAGAAGCCC 57.581 47.619 0.00 0.00 0.00 5.19
1315 1417 3.000727 CCACCGTGATTTCCTCAGTAAC 58.999 50.000 0.00 0.00 33.51 2.50
1323 1425 3.039202 CTGCGCCACCGTGATTTCC 62.039 63.158 4.18 0.00 36.67 3.13
1391 1493 4.065281 CGGACGTCCCCTCCACAC 62.065 72.222 28.52 0.58 0.00 3.82
1419 1524 1.813192 CTTCAGGCTCTCGACCTCC 59.187 63.158 0.00 0.00 34.42 4.30
1578 1683 4.742201 TCGAGCCGCTGGTTCTGC 62.742 66.667 0.00 0.00 30.56 4.26
1701 1806 1.148310 CAATGGCGTCGAACTCTTGT 58.852 50.000 0.00 0.00 0.00 3.16
1764 2817 3.178540 AAAGCCTCGGCACCTCGTT 62.179 57.895 11.02 0.00 44.88 3.85
1861 2914 2.596452 TGTCGATGAAGCGAAGAAGAC 58.404 47.619 0.00 0.00 42.55 3.01
1891 2946 7.442364 GGAATATCTTGATCAGACGAAAATGGA 59.558 37.037 0.00 0.00 32.83 3.41
1892 2947 7.443575 AGGAATATCTTGATCAGACGAAAATGG 59.556 37.037 0.00 0.00 32.83 3.16
1893 2948 8.375608 AGGAATATCTTGATCAGACGAAAATG 57.624 34.615 0.00 0.00 32.83 2.32
1913 2969 2.616330 CCGTGCACGCACAAGGAAT 61.616 57.895 33.17 0.00 46.47 3.01
2032 3095 2.475339 AGATCAGCTCCTCCATGTCT 57.525 50.000 0.00 0.00 0.00 3.41
2373 3440 4.019411 TGAATTATGACTCACTGCCCTTGA 60.019 41.667 0.00 0.00 0.00 3.02
2378 3445 4.274459 GTCCATGAATTATGACTCACTGCC 59.726 45.833 0.00 0.00 39.21 4.85
2459 3526 7.654022 TTGGGATAAAGAGACAAACACTTTT 57.346 32.000 0.00 0.00 39.39 2.27
2702 3770 3.786516 TCGTCGAAACATAGCCATGTA 57.213 42.857 0.00 0.00 44.83 2.29
2872 3945 2.143122 ACGAAATTGCACATCTCACGT 58.857 42.857 0.00 0.00 0.00 4.49
3002 4075 1.072489 TGGTTGTGGCAGTATCCGAAA 59.928 47.619 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.