Multiple sequence alignment - TraesCS3B01G246300

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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 TraesCS3B01G246300 chr3B 100.000 3319 0 0 1 3319 391870439 391873757 0.000000e+00 6130.0
1 TraesCS3B01G246300 chr3A 96.927 2864 73 9 469 3319 391492741 391489880 0.000000e+00 4787.0
2 TraesCS3B01G246300 chr3A 96.797 281 9 0 158 438 488725308 488725028 1.390000e-128 470.0
3 TraesCS3B01G246300 chr3A 93.421 152 10 0 3 154 391492889 391492738 3.330000e-55 226.0
4 TraesCS3B01G246300 chr3D 96.643 2860 77 12 469 3319 297463542 297466391 0.000000e+00 4732.0
5 TraesCS3B01G246300 chr3D 92.857 154 9 2 3 154 297463392 297463545 4.310000e-54 222.0
6 TraesCS3B01G246300 chr1D 89.045 995 70 16 2338 3318 44640966 44641935 0.000000e+00 1197.0
7 TraesCS3B01G246300 chr1D 86.611 239 26 2 2541 2778 44640700 44640933 3.280000e-65 259.0
8 TraesCS3B01G246300 chr1D 91.228 57 2 3 425 479 320585099 320585154 1.280000e-09 75.0
9 TraesCS3B01G246300 chr1B 89.075 897 64 17 2400 3283 63958594 63959469 0.000000e+00 1083.0
10 TraesCS3B01G246300 chr1B 97.849 279 6 0 161 439 642731963 642732241 1.790000e-132 483.0
11 TraesCS3B01G246300 chr1B 97.509 281 7 0 159 439 593922514 593922794 6.440000e-132 481.0
12 TraesCS3B01G246300 chr1B 92.157 51 3 1 425 475 333623738 333623787 1.650000e-08 71.3
13 TraesCS3B01G246300 chr1A 89.588 826 64 12 2501 3319 44406250 44407060 0.000000e+00 1029.0
14 TraesCS3B01G246300 chr1A 87.500 160 15 2 2338 2492 44406027 44406186 2.630000e-41 180.0
15 TraesCS3B01G246300 chr1A 94.231 52 1 2 425 476 463291812 463291763 9.870000e-11 78.7
16 TraesCS3B01G246300 chr1A 97.436 39 1 0 2501 2539 44406179 44406217 2.140000e-07 67.6
17 TraesCS3B01G246300 chr7A 97.491 279 7 0 160 438 696538845 696538567 8.330000e-131 477.0
18 TraesCS3B01G246300 chr7A 97.143 280 8 0 160 439 126117996 126117717 1.080000e-129 473.0
19 TraesCS3B01G246300 chr6B 97.482 278 7 0 161 438 707744118 707744395 3.000000e-130 475.0
20 TraesCS3B01G246300 chr6B 97.143 280 8 0 159 438 347118524 347118245 1.080000e-129 473.0
21 TraesCS3B01G246300 chr5B 96.154 286 11 0 153 438 501963933 501964218 5.010000e-128 468.0
22 TraesCS3B01G246300 chr5B 92.593 54 3 1 425 478 344328982 344328930 3.550000e-10 76.8
23 TraesCS3B01G246300 chr5A 95.517 290 11 2 158 446 534990733 534990445 2.330000e-126 462.0
24 TraesCS3B01G246300 chr4D 94.444 54 1 2 425 477 484726784 484726732 7.630000e-12 82.4
25 TraesCS3B01G246300 chr6D 94.231 52 2 1 425 476 10733328 10733378 9.870000e-11 78.7
26 TraesCS3B01G246300 chr2D 94.118 51 2 1 425 475 442014774 442014725 3.550000e-10 76.8
27 TraesCS3B01G246300 chr2A 92.593 54 2 2 425 478 184499459 184499510 3.550000e-10 76.8
28 TraesCS3B01G246300 chr7D 95.652 46 1 1 425 470 65605253 65605209 4.590000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G246300 chr3B 391870439 391873757 3318 False 6130.000000 6130 100.000 1 3319 1 chr3B.!!$F1 3318
1 TraesCS3B01G246300 chr3A 391489880 391492889 3009 True 2506.500000 4787 95.174 3 3319 2 chr3A.!!$R2 3316
2 TraesCS3B01G246300 chr3D 297463392 297466391 2999 False 2477.000000 4732 94.750 3 3319 2 chr3D.!!$F1 3316
3 TraesCS3B01G246300 chr1D 44640700 44641935 1235 False 728.000000 1197 87.828 2338 3318 2 chr1D.!!$F2 980
4 TraesCS3B01G246300 chr1B 63958594 63959469 875 False 1083.000000 1083 89.075 2400 3283 1 chr1B.!!$F1 883
5 TraesCS3B01G246300 chr1A 44406027 44407060 1033 False 425.533333 1029 91.508 2338 3319 3 chr1A.!!$F1 981

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
296 299 0.034756 CCGGAACATCACACACTCCA 59.965 55.0 0.0 0.0 0.00 3.86 F
437 440 0.323360 GCCCATTGTGACCAGCCTTA 60.323 55.0 0.0 0.0 0.00 2.69 F
2126 2136 0.608035 TCGTTGATGGGCTTTGGTCC 60.608 55.0 0.0 0.0 37.81 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2136 0.545309 TCCTCTCCTCCCCACTTGTG 60.545 60.000 0.0 0.0 0.00 3.33 R
2292 2303 1.954382 CTTCGATCTCCGGGTATGTGA 59.046 52.381 0.0 0.0 39.14 3.58 R
2993 3087 6.392354 ACCATGTCTGTGCTCATTTATTTTG 58.608 36.000 0.0 0.0 0.00 2.44 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
94 96 7.160049 TCACCCGTTTGTGTATACATTCTTTA 58.840 34.615 9.18 0.00 36.53 1.85
118 121 1.363807 GCCTGACAGCACCAAAACC 59.636 57.895 0.00 0.00 0.00 3.27
125 128 1.289276 CAGCACCAAAACCAAAGCAC 58.711 50.000 0.00 0.00 0.00 4.40
155 158 2.429235 TACCGGGGGCCTTGGAAAAC 62.429 60.000 19.32 0.00 0.00 2.43
156 159 2.203567 CGGGGGCCTTGGAAAACA 60.204 61.111 0.84 0.00 0.00 2.83
158 161 1.604147 CGGGGGCCTTGGAAAACATC 61.604 60.000 0.84 0.00 0.00 3.06
169 172 3.087370 GGAAAACATCCTTAGGCTGGT 57.913 47.619 7.06 0.00 45.56 4.00
170 173 3.017442 GGAAAACATCCTTAGGCTGGTC 58.983 50.000 7.06 1.40 45.56 4.02
171 174 3.561313 GGAAAACATCCTTAGGCTGGTCA 60.561 47.826 7.06 0.00 45.56 4.02
173 176 1.656587 ACATCCTTAGGCTGGTCACA 58.343 50.000 7.06 0.00 0.00 3.58
176 179 2.787473 TCCTTAGGCTGGTCACAATG 57.213 50.000 0.00 0.00 0.00 2.82
177 180 1.281867 TCCTTAGGCTGGTCACAATGG 59.718 52.381 0.00 0.00 0.00 3.16
179 182 0.331278 TTAGGCTGGTCACAATGGGG 59.669 55.000 0.00 0.00 0.00 4.96
181 184 1.379044 GGCTGGTCACAATGGGGAG 60.379 63.158 0.00 0.00 0.00 4.30
183 186 1.852157 GCTGGTCACAATGGGGAGGA 61.852 60.000 0.00 0.00 0.00 3.71
187 190 1.075536 GGTCACAATGGGGAGGAACTT 59.924 52.381 0.00 0.00 41.55 2.66
189 192 3.610911 GTCACAATGGGGAGGAACTTAG 58.389 50.000 0.00 0.00 41.55 2.18
192 195 4.019321 TCACAATGGGGAGGAACTTAGAAG 60.019 45.833 0.00 0.00 41.55 2.85
193 196 3.916989 ACAATGGGGAGGAACTTAGAAGT 59.083 43.478 0.00 0.00 41.55 3.01
194 197 5.045869 CACAATGGGGAGGAACTTAGAAGTA 60.046 44.000 0.00 0.00 41.55 2.24
195 198 5.550403 ACAATGGGGAGGAACTTAGAAGTAA 59.450 40.000 0.00 0.00 41.55 2.24
198 201 5.098663 TGGGGAGGAACTTAGAAGTAACAT 58.901 41.667 0.00 0.00 41.55 2.71
199 202 5.189145 TGGGGAGGAACTTAGAAGTAACATC 59.811 44.000 0.00 1.41 41.55 3.06
201 204 6.107343 GGGAGGAACTTAGAAGTAACATCAC 58.893 44.000 12.59 7.90 41.55 3.06
203 206 6.590677 GGAGGAACTTAGAAGTAACATCACAC 59.409 42.308 12.59 0.00 41.55 3.82
204 207 7.062749 AGGAACTTAGAAGTAACATCACACA 57.937 36.000 0.00 0.00 38.57 3.72
206 209 6.929606 GGAACTTAGAAGTAACATCACACACT 59.070 38.462 0.00 0.00 38.57 3.55
207 210 7.116519 GGAACTTAGAAGTAACATCACACACTC 59.883 40.741 0.00 0.00 38.57 3.51
208 211 6.456501 ACTTAGAAGTAACATCACACACTCC 58.543 40.000 0.00 0.00 37.52 3.85
209 212 4.955811 AGAAGTAACATCACACACTCCA 57.044 40.909 0.00 0.00 0.00 3.86
210 213 5.290493 AGAAGTAACATCACACACTCCAA 57.710 39.130 0.00 0.00 0.00 3.53
211 214 5.869579 AGAAGTAACATCACACACTCCAAT 58.130 37.500 0.00 0.00 0.00 3.16
212 215 7.004555 AGAAGTAACATCACACACTCCAATA 57.995 36.000 0.00 0.00 0.00 1.90
213 216 6.874134 AGAAGTAACATCACACACTCCAATAC 59.126 38.462 0.00 0.00 0.00 1.89
215 218 6.530120 AGTAACATCACACACTCCAATACAA 58.470 36.000 0.00 0.00 0.00 2.41
216 219 5.689383 AACATCACACACTCCAATACAAC 57.311 39.130 0.00 0.00 0.00 3.32
219 222 5.827797 ACATCACACACTCCAATACAACTTT 59.172 36.000 0.00 0.00 0.00 2.66
220 223 5.749596 TCACACACTCCAATACAACTTTG 57.250 39.130 0.00 0.00 0.00 2.77
221 224 4.036262 TCACACACTCCAATACAACTTTGC 59.964 41.667 0.00 0.00 0.00 3.68
222 225 4.036734 CACACACTCCAATACAACTTTGCT 59.963 41.667 0.00 0.00 0.00 3.91
225 228 6.490040 ACACACTCCAATACAACTTTGCTTAT 59.510 34.615 0.00 0.00 0.00 1.73
226 229 6.803320 CACACTCCAATACAACTTTGCTTATG 59.197 38.462 0.00 0.00 0.00 1.90
227 230 6.490040 ACACTCCAATACAACTTTGCTTATGT 59.510 34.615 0.00 0.00 0.00 2.29
228 231 6.803320 CACTCCAATACAACTTTGCTTATGTG 59.197 38.462 0.00 0.00 0.00 3.21
230 233 4.864247 CCAATACAACTTTGCTTATGTGGC 59.136 41.667 0.00 0.00 0.00 5.01
231 234 5.468592 CAATACAACTTTGCTTATGTGGCA 58.531 37.500 0.00 0.00 37.97 4.92
232 235 3.369546 ACAACTTTGCTTATGTGGCAC 57.630 42.857 11.55 11.55 39.55 5.01
233 236 2.287547 ACAACTTTGCTTATGTGGCACG 60.288 45.455 13.77 0.00 39.55 5.34
234 237 1.604604 ACTTTGCTTATGTGGCACGT 58.395 45.000 17.65 17.65 39.55 4.49
236 239 3.343617 ACTTTGCTTATGTGGCACGTAT 58.656 40.909 19.55 7.98 39.55 3.06
237 240 3.756434 ACTTTGCTTATGTGGCACGTATT 59.244 39.130 19.55 4.10 39.55 1.89
240 243 5.881777 TTGCTTATGTGGCACGTATTTAA 57.118 34.783 19.55 11.84 39.55 1.52
242 245 5.815850 TGCTTATGTGGCACGTATTTAATG 58.184 37.500 19.55 4.53 34.56 1.90
243 246 5.586643 TGCTTATGTGGCACGTATTTAATGA 59.413 36.000 19.55 3.01 34.56 2.57
244 247 6.094186 TGCTTATGTGGCACGTATTTAATGAA 59.906 34.615 19.55 4.06 34.56 2.57
246 249 7.466725 GCTTATGTGGCACGTATTTAATGAAGA 60.467 37.037 19.55 0.94 0.00 2.87
247 250 5.794687 TGTGGCACGTATTTAATGAAGAG 57.205 39.130 13.77 0.00 0.00 2.85
248 251 5.483811 TGTGGCACGTATTTAATGAAGAGA 58.516 37.500 13.77 0.00 0.00 3.10
249 252 5.580691 TGTGGCACGTATTTAATGAAGAGAG 59.419 40.000 13.77 0.00 0.00 3.20
250 253 5.810587 GTGGCACGTATTTAATGAAGAGAGA 59.189 40.000 0.00 0.00 0.00 3.10
251 254 6.019479 GTGGCACGTATTTAATGAAGAGAGAG 60.019 42.308 0.00 0.00 0.00 3.20
252 255 5.463724 GGCACGTATTTAATGAAGAGAGAGG 59.536 44.000 0.00 0.00 0.00 3.69
253 256 6.043411 GCACGTATTTAATGAAGAGAGAGGT 58.957 40.000 0.00 0.00 0.00 3.85
254 257 7.201145 GCACGTATTTAATGAAGAGAGAGGTA 58.799 38.462 0.00 0.00 0.00 3.08
255 258 7.167801 GCACGTATTTAATGAAGAGAGAGGTAC 59.832 40.741 0.00 0.00 0.00 3.34
257 260 8.968969 ACGTATTTAATGAAGAGAGAGGTACTT 58.031 33.333 0.00 0.00 41.55 2.24
258 261 9.239002 CGTATTTAATGAAGAGAGAGGTACTTG 57.761 37.037 0.00 0.00 41.55 3.16
261 264 5.413309 AATGAAGAGAGAGGTACTTGTGG 57.587 43.478 0.00 0.00 41.55 4.17
262 265 3.845860 TGAAGAGAGAGGTACTTGTGGT 58.154 45.455 0.00 0.00 41.55 4.16
263 266 4.994282 TGAAGAGAGAGGTACTTGTGGTA 58.006 43.478 0.00 0.00 41.55 3.25
264 267 5.391256 TGAAGAGAGAGGTACTTGTGGTAA 58.609 41.667 0.00 0.00 41.55 2.85
265 268 5.243283 TGAAGAGAGAGGTACTTGTGGTAAC 59.757 44.000 0.00 0.00 41.55 2.50
274 277 7.846101 AGGTACTTGTGGTAACTAGTTAAGT 57.154 36.000 16.82 18.40 45.68 2.24
275 278 8.255111 AGGTACTTGTGGTAACTAGTTAAGTT 57.745 34.615 20.31 5.83 45.68 2.66
276 279 9.367160 AGGTACTTGTGGTAACTAGTTAAGTTA 57.633 33.333 20.31 6.47 45.68 2.24
287 290 6.594788 ACTAGTTAAGTTACCGGAACATCA 57.405 37.500 9.46 0.00 40.86 3.07
288 291 6.393171 ACTAGTTAAGTTACCGGAACATCAC 58.607 40.000 9.46 3.51 40.86 3.06
289 292 5.217978 AGTTAAGTTACCGGAACATCACA 57.782 39.130 9.46 0.00 40.86 3.58
290 293 4.992951 AGTTAAGTTACCGGAACATCACAC 59.007 41.667 9.46 3.08 40.86 3.82
291 294 3.478857 AAGTTACCGGAACATCACACA 57.521 42.857 9.46 0.00 40.86 3.72
292 295 2.762745 AGTTACCGGAACATCACACAC 58.237 47.619 9.46 0.00 40.86 3.82
293 296 2.367567 AGTTACCGGAACATCACACACT 59.632 45.455 9.46 0.00 40.86 3.55
294 297 2.735134 GTTACCGGAACATCACACACTC 59.265 50.000 9.46 0.00 38.02 3.51
295 298 0.034896 ACCGGAACATCACACACTCC 59.965 55.000 9.46 0.00 0.00 3.85
296 299 0.034756 CCGGAACATCACACACTCCA 59.965 55.000 0.00 0.00 0.00 3.86
297 300 1.542328 CCGGAACATCACACACTCCAA 60.542 52.381 0.00 0.00 0.00 3.53
298 301 1.800586 CGGAACATCACACACTCCAAG 59.199 52.381 0.00 0.00 0.00 3.61
299 302 2.547855 CGGAACATCACACACTCCAAGA 60.548 50.000 0.00 0.00 0.00 3.02
300 303 3.476552 GGAACATCACACACTCCAAGAA 58.523 45.455 0.00 0.00 0.00 2.52
301 304 3.882888 GGAACATCACACACTCCAAGAAA 59.117 43.478 0.00 0.00 0.00 2.52
302 305 4.261197 GGAACATCACACACTCCAAGAAAC 60.261 45.833 0.00 0.00 0.00 2.78
303 306 3.884895 ACATCACACACTCCAAGAAACA 58.115 40.909 0.00 0.00 0.00 2.83
304 307 4.269183 ACATCACACACTCCAAGAAACAA 58.731 39.130 0.00 0.00 0.00 2.83
305 308 4.889409 ACATCACACACTCCAAGAAACAAT 59.111 37.500 0.00 0.00 0.00 2.71
306 309 4.898829 TCACACACTCCAAGAAACAATG 57.101 40.909 0.00 0.00 0.00 2.82
307 310 4.522114 TCACACACTCCAAGAAACAATGA 58.478 39.130 0.00 0.00 0.00 2.57
308 311 4.576053 TCACACACTCCAAGAAACAATGAG 59.424 41.667 0.00 0.00 0.00 2.90
309 312 4.336433 CACACACTCCAAGAAACAATGAGT 59.664 41.667 0.00 0.00 36.77 3.41
310 313 4.576463 ACACACTCCAAGAAACAATGAGTC 59.424 41.667 0.00 0.00 34.21 3.36
311 314 4.818546 CACACTCCAAGAAACAATGAGTCT 59.181 41.667 0.00 0.00 34.21 3.24
312 315 5.991606 CACACTCCAAGAAACAATGAGTCTA 59.008 40.000 0.00 0.00 34.21 2.59
313 316 6.652481 CACACTCCAAGAAACAATGAGTCTAT 59.348 38.462 0.00 0.00 34.21 1.98
314 317 7.819415 CACACTCCAAGAAACAATGAGTCTATA 59.181 37.037 0.00 0.00 34.21 1.31
315 318 8.375506 ACACTCCAAGAAACAATGAGTCTATAA 58.624 33.333 0.00 0.00 34.21 0.98
316 319 8.660373 CACTCCAAGAAACAATGAGTCTATAAC 58.340 37.037 0.00 0.00 34.21 1.89
317 320 7.824779 ACTCCAAGAAACAATGAGTCTATAACC 59.175 37.037 0.00 0.00 30.81 2.85
318 321 7.918076 TCCAAGAAACAATGAGTCTATAACCT 58.082 34.615 0.00 0.00 0.00 3.50
319 322 9.042450 TCCAAGAAACAATGAGTCTATAACCTA 57.958 33.333 0.00 0.00 0.00 3.08
320 323 9.667107 CCAAGAAACAATGAGTCTATAACCTAA 57.333 33.333 0.00 0.00 0.00 2.69
339 342 8.995027 AACCTAATAAATACATCCTTGCATGA 57.005 30.769 0.00 0.00 0.00 3.07
340 343 8.396272 ACCTAATAAATACATCCTTGCATGAC 57.604 34.615 0.00 0.00 0.00 3.06
341 344 7.998383 ACCTAATAAATACATCCTTGCATGACA 59.002 33.333 0.00 0.00 0.00 3.58
342 345 8.292448 CCTAATAAATACATCCTTGCATGACAC 58.708 37.037 0.00 0.00 0.00 3.67
343 346 7.886629 AATAAATACATCCTTGCATGACACT 57.113 32.000 0.00 0.00 0.00 3.55
344 347 8.978874 AATAAATACATCCTTGCATGACACTA 57.021 30.769 0.00 0.00 0.00 2.74
345 348 6.683974 AAATACATCCTTGCATGACACTAC 57.316 37.500 0.00 0.00 0.00 2.73
346 349 3.701205 ACATCCTTGCATGACACTACA 57.299 42.857 0.00 0.00 0.00 2.74
347 350 4.226427 ACATCCTTGCATGACACTACAT 57.774 40.909 0.00 0.00 0.00 2.29
348 351 5.357742 ACATCCTTGCATGACACTACATA 57.642 39.130 0.00 0.00 0.00 2.29
349 352 5.744171 ACATCCTTGCATGACACTACATAA 58.256 37.500 0.00 0.00 0.00 1.90
350 353 6.179756 ACATCCTTGCATGACACTACATAAA 58.820 36.000 0.00 0.00 0.00 1.40
351 354 6.830324 ACATCCTTGCATGACACTACATAAAT 59.170 34.615 0.00 0.00 0.00 1.40
352 355 6.682423 TCCTTGCATGACACTACATAAATG 57.318 37.500 0.00 0.00 0.00 2.32
353 356 6.179756 TCCTTGCATGACACTACATAAATGT 58.820 36.000 0.00 0.63 44.48 2.71
354 357 6.658816 TCCTTGCATGACACTACATAAATGTT 59.341 34.615 0.00 0.00 41.97 2.71
355 358 6.968904 CCTTGCATGACACTACATAAATGTTC 59.031 38.462 0.00 0.00 41.97 3.18
356 359 6.435430 TGCATGACACTACATAAATGTTCC 57.565 37.500 0.00 0.00 41.97 3.62
357 360 6.179756 TGCATGACACTACATAAATGTTCCT 58.820 36.000 0.00 0.00 41.97 3.36
358 361 7.334858 TGCATGACACTACATAAATGTTCCTA 58.665 34.615 0.00 0.00 41.97 2.94
359 362 7.279981 TGCATGACACTACATAAATGTTCCTAC 59.720 37.037 0.00 0.00 41.97 3.18
360 363 7.254795 GCATGACACTACATAAATGTTCCTACC 60.255 40.741 0.00 0.00 41.97 3.18
361 364 6.646267 TGACACTACATAAATGTTCCTACCC 58.354 40.000 0.12 0.00 41.97 3.69
362 365 6.213802 TGACACTACATAAATGTTCCTACCCA 59.786 38.462 0.12 0.00 41.97 4.51
363 366 6.412214 ACACTACATAAATGTTCCTACCCAC 58.588 40.000 0.12 0.00 41.97 4.61
364 367 6.214819 ACACTACATAAATGTTCCTACCCACT 59.785 38.462 0.12 0.00 41.97 4.00
365 368 7.400915 ACACTACATAAATGTTCCTACCCACTA 59.599 37.037 0.12 0.00 41.97 2.74
366 369 8.429641 CACTACATAAATGTTCCTACCCACTAT 58.570 37.037 0.12 0.00 41.97 2.12
367 370 8.429641 ACTACATAAATGTTCCTACCCACTATG 58.570 37.037 0.12 0.00 41.97 2.23
368 371 6.601332 ACATAAATGTTCCTACCCACTATGG 58.399 40.000 0.00 0.00 37.90 2.74
369 372 6.388689 ACATAAATGTTCCTACCCACTATGGA 59.611 38.462 0.00 0.00 37.45 3.41
370 373 5.373812 AAATGTTCCTACCCACTATGGAG 57.626 43.478 0.00 0.00 40.96 3.86
371 374 2.759355 TGTTCCTACCCACTATGGAGG 58.241 52.381 0.00 0.00 40.96 4.30
372 375 2.045326 TGTTCCTACCCACTATGGAGGT 59.955 50.000 0.00 1.66 40.96 3.85
373 376 3.272818 TGTTCCTACCCACTATGGAGGTA 59.727 47.826 0.00 3.53 40.96 3.08
379 382 4.341863 ACCCACTATGGAGGTAGTAACA 57.658 45.455 0.00 0.00 40.96 2.41
380 383 4.892198 ACCCACTATGGAGGTAGTAACAT 58.108 43.478 0.00 0.00 40.96 2.71
381 384 6.034442 ACCCACTATGGAGGTAGTAACATA 57.966 41.667 0.00 0.00 40.96 2.29
382 385 6.075984 ACCCACTATGGAGGTAGTAACATAG 58.924 44.000 8.52 8.52 45.07 2.23
388 391 8.795842 CTATGGAGGTAGTAACATAGTCTAGG 57.204 42.308 0.00 0.00 38.48 3.02
389 392 5.950023 TGGAGGTAGTAACATAGTCTAGGG 58.050 45.833 0.00 0.00 0.00 3.53
390 393 5.673574 TGGAGGTAGTAACATAGTCTAGGGA 59.326 44.000 0.00 0.00 0.00 4.20
391 394 6.160992 TGGAGGTAGTAACATAGTCTAGGGAA 59.839 42.308 0.00 0.00 0.00 3.97
392 395 6.716173 GGAGGTAGTAACATAGTCTAGGGAAG 59.284 46.154 0.00 0.00 0.00 3.46
393 396 7.223472 AGGTAGTAACATAGTCTAGGGAAGT 57.777 40.000 0.00 0.00 0.00 3.01
394 397 7.061688 AGGTAGTAACATAGTCTAGGGAAGTG 58.938 42.308 0.00 0.00 0.00 3.16
395 398 6.832900 GGTAGTAACATAGTCTAGGGAAGTGT 59.167 42.308 0.00 0.00 0.00 3.55
396 399 6.777213 AGTAACATAGTCTAGGGAAGTGTG 57.223 41.667 0.00 0.00 0.00 3.82
397 400 6.491383 AGTAACATAGTCTAGGGAAGTGTGA 58.509 40.000 0.00 0.00 0.00 3.58
398 401 6.952358 AGTAACATAGTCTAGGGAAGTGTGAA 59.048 38.462 0.00 0.00 0.00 3.18
399 402 5.923733 ACATAGTCTAGGGAAGTGTGAAG 57.076 43.478 0.00 0.00 0.00 3.02
400 403 5.334421 ACATAGTCTAGGGAAGTGTGAAGT 58.666 41.667 0.00 0.00 0.00 3.01
401 404 5.780793 ACATAGTCTAGGGAAGTGTGAAGTT 59.219 40.000 0.00 0.00 0.00 2.66
402 405 6.952358 ACATAGTCTAGGGAAGTGTGAAGTTA 59.048 38.462 0.00 0.00 0.00 2.24
403 406 7.620094 ACATAGTCTAGGGAAGTGTGAAGTTAT 59.380 37.037 0.00 0.00 0.00 1.89
404 407 6.936968 AGTCTAGGGAAGTGTGAAGTTATT 57.063 37.500 0.00 0.00 0.00 1.40
405 408 9.710818 ATAGTCTAGGGAAGTGTGAAGTTATTA 57.289 33.333 0.00 0.00 0.00 0.98
406 409 8.068892 AGTCTAGGGAAGTGTGAAGTTATTAG 57.931 38.462 0.00 0.00 0.00 1.73
407 410 6.757478 GTCTAGGGAAGTGTGAAGTTATTAGC 59.243 42.308 0.00 0.00 0.00 3.09
408 411 5.763876 AGGGAAGTGTGAAGTTATTAGCT 57.236 39.130 0.00 0.00 0.00 3.32
409 412 6.128138 AGGGAAGTGTGAAGTTATTAGCTT 57.872 37.500 0.00 0.00 0.00 3.74
410 413 7.253905 AGGGAAGTGTGAAGTTATTAGCTTA 57.746 36.000 0.00 0.00 0.00 3.09
411 414 7.862675 AGGGAAGTGTGAAGTTATTAGCTTAT 58.137 34.615 0.00 0.00 0.00 1.73
412 415 7.770897 AGGGAAGTGTGAAGTTATTAGCTTATG 59.229 37.037 0.00 0.00 0.00 1.90
413 416 7.553044 GGGAAGTGTGAAGTTATTAGCTTATGT 59.447 37.037 0.00 0.00 0.00 2.29
414 417 8.947115 GGAAGTGTGAAGTTATTAGCTTATGTT 58.053 33.333 0.00 0.00 0.00 2.71
415 418 9.974750 GAAGTGTGAAGTTATTAGCTTATGTTC 57.025 33.333 0.00 0.00 0.00 3.18
416 419 9.726438 AAGTGTGAAGTTATTAGCTTATGTTCT 57.274 29.630 0.00 0.00 0.00 3.01
417 420 9.726438 AGTGTGAAGTTATTAGCTTATGTTCTT 57.274 29.630 0.00 0.00 0.00 2.52
418 421 9.760660 GTGTGAAGTTATTAGCTTATGTTCTTG 57.239 33.333 0.00 0.00 0.00 3.02
419 422 8.450964 TGTGAAGTTATTAGCTTATGTTCTTGC 58.549 33.333 0.00 0.00 0.00 4.01
420 423 7.910683 GTGAAGTTATTAGCTTATGTTCTTGCC 59.089 37.037 0.00 0.00 0.00 4.52
421 424 6.944234 AGTTATTAGCTTATGTTCTTGCCC 57.056 37.500 0.00 0.00 0.00 5.36
422 425 6.423182 AGTTATTAGCTTATGTTCTTGCCCA 58.577 36.000 0.00 0.00 0.00 5.36
423 426 7.062957 AGTTATTAGCTTATGTTCTTGCCCAT 58.937 34.615 0.00 0.00 0.00 4.00
424 427 7.561356 AGTTATTAGCTTATGTTCTTGCCCATT 59.439 33.333 0.00 0.00 0.00 3.16
425 428 5.581126 TTAGCTTATGTTCTTGCCCATTG 57.419 39.130 0.00 0.00 0.00 2.82
426 429 3.434309 AGCTTATGTTCTTGCCCATTGT 58.566 40.909 0.00 0.00 0.00 2.71
427 430 3.194116 AGCTTATGTTCTTGCCCATTGTG 59.806 43.478 0.00 0.00 0.00 3.33
428 431 3.193267 GCTTATGTTCTTGCCCATTGTGA 59.807 43.478 0.00 0.00 0.00 3.58
429 432 4.737054 CTTATGTTCTTGCCCATTGTGAC 58.263 43.478 0.00 0.00 0.00 3.67
430 433 1.327303 TGTTCTTGCCCATTGTGACC 58.673 50.000 0.00 0.00 0.00 4.02
431 434 1.327303 GTTCTTGCCCATTGTGACCA 58.673 50.000 0.00 0.00 0.00 4.02
432 435 1.270550 GTTCTTGCCCATTGTGACCAG 59.729 52.381 0.00 0.00 0.00 4.00
433 436 0.895100 TCTTGCCCATTGTGACCAGC 60.895 55.000 0.00 0.00 0.00 4.85
434 437 1.880819 CTTGCCCATTGTGACCAGCC 61.881 60.000 0.00 0.00 0.00 4.85
435 438 2.036256 GCCCATTGTGACCAGCCT 59.964 61.111 0.00 0.00 0.00 4.58
436 439 1.607467 GCCCATTGTGACCAGCCTT 60.607 57.895 0.00 0.00 0.00 4.35
437 440 0.323360 GCCCATTGTGACCAGCCTTA 60.323 55.000 0.00 0.00 0.00 2.69
438 441 1.890573 GCCCATTGTGACCAGCCTTAA 60.891 52.381 0.00 0.00 0.00 1.85
439 442 2.524306 CCCATTGTGACCAGCCTTAAA 58.476 47.619 0.00 0.00 0.00 1.52
440 443 2.896685 CCCATTGTGACCAGCCTTAAAA 59.103 45.455 0.00 0.00 0.00 1.52
441 444 3.323403 CCCATTGTGACCAGCCTTAAAAA 59.677 43.478 0.00 0.00 0.00 1.94
521 524 8.703336 CACATACTACATCATTGGTTTATCGAG 58.297 37.037 0.00 0.00 0.00 4.04
522 525 8.421784 ACATACTACATCATTGGTTTATCGAGT 58.578 33.333 0.00 0.00 0.00 4.18
578 581 2.016905 ACTCCTACTCAACAGCAGGT 57.983 50.000 0.00 0.00 34.89 4.00
581 584 4.868268 ACTCCTACTCAACAGCAGGTATA 58.132 43.478 0.00 0.00 34.89 1.47
624 628 2.450502 AAGTGGGGGTCCAGCAGT 60.451 61.111 0.00 0.00 45.05 4.40
791 799 5.352284 CACCACTCAGACCAATACAGTATC 58.648 45.833 0.00 0.00 0.00 2.24
829 837 1.152839 CCCGTCACCCAACCACTTT 60.153 57.895 0.00 0.00 0.00 2.66
842 850 1.546476 ACCACTTTGACGCAAACCAAA 59.454 42.857 1.63 0.00 0.00 3.28
857 865 5.510690 GCAAACCAAACCAGCTATAAAACCT 60.511 40.000 0.00 0.00 0.00 3.50
897 905 1.227999 ATTCAACACCGACCAGCACG 61.228 55.000 0.00 0.00 0.00 5.34
927 935 3.893753 TGGAAGGTTCAAATCTCCCAA 57.106 42.857 0.00 0.00 0.00 4.12
1190 1198 1.878088 CCAGCACACCATCATCATAGC 59.122 52.381 0.00 0.00 0.00 2.97
1422 1430 2.987547 AGCAGCAGCAACGGCAAT 60.988 55.556 3.17 0.00 45.49 3.56
1596 1604 2.065993 ACATGAACGAAGGTGAGTCG 57.934 50.000 0.00 0.00 44.10 4.18
1953 1961 2.747855 CAACAGCGGGAGGAAGGC 60.748 66.667 0.00 0.00 0.00 4.35
2032 2040 6.788598 TGATATTTCCCTTGCATTGCTTAA 57.211 33.333 10.49 0.00 0.00 1.85
2039 2049 4.081531 TCCCTTGCATTGCTTAATTCCTTG 60.082 41.667 10.49 0.00 0.00 3.61
2126 2136 0.608035 TCGTTGATGGGCTTTGGTCC 60.608 55.000 0.00 0.00 37.81 4.46
2292 2303 5.273208 ACTACCACTCTAAGATCACCATGT 58.727 41.667 0.00 0.00 0.00 3.21
2315 2326 3.028850 ACATACCCGGAGATCGAAGAAA 58.971 45.455 0.73 0.00 43.58 2.52
2495 2510 6.315891 GGAAGAACAAGAGAAAGAGATGATGG 59.684 42.308 0.00 0.00 0.00 3.51
2498 2513 4.260170 ACAAGAGAAAGAGATGATGGCAC 58.740 43.478 0.00 0.00 0.00 5.01
2556 2641 5.263599 TGGGAGCAAAGAATGATGTGTATT 58.736 37.500 0.00 0.00 0.00 1.89
2586 2671 6.368791 GCGAATATCATACAATTAGTGCCAGA 59.631 38.462 0.00 0.00 0.00 3.86
2978 3072 7.967854 GTGTGCAGTGCATGTTAGAAAATAATA 59.032 33.333 22.87 0.00 41.91 0.98
2984 3078 8.960591 AGTGCATGTTAGAAAATAATAAGCAGT 58.039 29.630 0.00 0.00 0.00 4.40
3266 3368 6.441093 TCAAAACTAGCTTCCTGCAATATG 57.559 37.500 0.00 0.00 45.94 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.814457 GTTGAAGTTGCACCACACCA 59.186 50.000 0.00 0.00 0.00 4.17
1 2 0.814457 TGTTGAAGTTGCACCACACC 59.186 50.000 0.00 0.00 0.00 4.16
94 96 2.974698 GTGCTGTCAGGCGCTGTT 60.975 61.111 7.64 0.00 39.35 3.16
155 158 2.787473 TTGTGACCAGCCTAAGGATG 57.213 50.000 0.00 0.00 39.04 3.51
156 159 2.092212 CCATTGTGACCAGCCTAAGGAT 60.092 50.000 0.00 0.00 0.00 3.24
158 161 1.683011 CCCATTGTGACCAGCCTAAGG 60.683 57.143 0.00 0.00 0.00 2.69
159 162 1.683011 CCCCATTGTGACCAGCCTAAG 60.683 57.143 0.00 0.00 0.00 2.18
160 163 0.331278 CCCCATTGTGACCAGCCTAA 59.669 55.000 0.00 0.00 0.00 2.69
161 164 0.548926 TCCCCATTGTGACCAGCCTA 60.549 55.000 0.00 0.00 0.00 3.93
163 166 1.379044 CTCCCCATTGTGACCAGCC 60.379 63.158 0.00 0.00 0.00 4.85
164 167 1.379044 CCTCCCCATTGTGACCAGC 60.379 63.158 0.00 0.00 0.00 4.85
165 168 0.698238 TTCCTCCCCATTGTGACCAG 59.302 55.000 0.00 0.00 0.00 4.00
166 169 0.404040 GTTCCTCCCCATTGTGACCA 59.596 55.000 0.00 0.00 0.00 4.02
168 171 2.586648 AAGTTCCTCCCCATTGTGAC 57.413 50.000 0.00 0.00 0.00 3.67
169 172 3.526899 TCTAAGTTCCTCCCCATTGTGA 58.473 45.455 0.00 0.00 0.00 3.58
170 173 4.263506 ACTTCTAAGTTCCTCCCCATTGTG 60.264 45.833 0.00 0.00 35.21 3.33
171 174 3.916989 ACTTCTAAGTTCCTCCCCATTGT 59.083 43.478 0.00 0.00 35.21 2.71
173 176 5.550403 TGTTACTTCTAAGTTCCTCCCCATT 59.450 40.000 0.00 0.00 40.37 3.16
176 179 5.189145 TGATGTTACTTCTAAGTTCCTCCCC 59.811 44.000 0.00 0.00 40.37 4.81
177 180 6.107343 GTGATGTTACTTCTAAGTTCCTCCC 58.893 44.000 0.00 0.00 40.37 4.30
179 182 7.116519 GTGTGTGATGTTACTTCTAAGTTCCTC 59.883 40.741 0.00 0.01 40.37 3.71
181 184 6.929606 AGTGTGTGATGTTACTTCTAAGTTCC 59.070 38.462 0.00 0.00 40.37 3.62
183 186 6.929606 GGAGTGTGTGATGTTACTTCTAAGTT 59.070 38.462 0.00 0.00 40.37 2.66
186 189 6.413783 TGGAGTGTGTGATGTTACTTCTAA 57.586 37.500 0.17 0.00 0.00 2.10
187 190 6.413783 TTGGAGTGTGTGATGTTACTTCTA 57.586 37.500 0.17 0.00 0.00 2.10
189 192 6.649141 TGTATTGGAGTGTGTGATGTTACTTC 59.351 38.462 0.00 0.00 0.00 3.01
192 195 6.426937 AGTTGTATTGGAGTGTGTGATGTTAC 59.573 38.462 0.00 0.00 0.00 2.50
193 196 6.530120 AGTTGTATTGGAGTGTGTGATGTTA 58.470 36.000 0.00 0.00 0.00 2.41
194 197 5.376625 AGTTGTATTGGAGTGTGTGATGTT 58.623 37.500 0.00 0.00 0.00 2.71
195 198 4.973168 AGTTGTATTGGAGTGTGTGATGT 58.027 39.130 0.00 0.00 0.00 3.06
198 201 4.036262 GCAAAGTTGTATTGGAGTGTGTGA 59.964 41.667 0.00 0.00 0.00 3.58
199 202 4.036734 AGCAAAGTTGTATTGGAGTGTGTG 59.963 41.667 0.00 0.00 0.00 3.82
201 204 4.836125 AGCAAAGTTGTATTGGAGTGTG 57.164 40.909 0.00 0.00 0.00 3.82
203 206 6.803320 CACATAAGCAAAGTTGTATTGGAGTG 59.197 38.462 0.00 0.00 0.00 3.51
204 207 6.071952 CCACATAAGCAAAGTTGTATTGGAGT 60.072 38.462 0.00 0.00 0.00 3.85
206 209 5.336372 GCCACATAAGCAAAGTTGTATTGGA 60.336 40.000 0.00 0.00 0.00 3.53
207 210 4.864247 GCCACATAAGCAAAGTTGTATTGG 59.136 41.667 0.00 0.00 0.00 3.16
208 211 5.345741 GTGCCACATAAGCAAAGTTGTATTG 59.654 40.000 0.00 0.00 43.02 1.90
209 212 5.469479 GTGCCACATAAGCAAAGTTGTATT 58.531 37.500 0.00 0.00 43.02 1.89
210 213 4.379394 CGTGCCACATAAGCAAAGTTGTAT 60.379 41.667 0.00 0.00 43.02 2.29
211 214 3.058570 CGTGCCACATAAGCAAAGTTGTA 60.059 43.478 0.00 0.00 43.02 2.41
212 215 2.287547 CGTGCCACATAAGCAAAGTTGT 60.288 45.455 0.00 0.00 43.02 3.32
213 216 2.287547 ACGTGCCACATAAGCAAAGTTG 60.288 45.455 0.00 0.00 43.02 3.16
215 218 1.604604 ACGTGCCACATAAGCAAAGT 58.395 45.000 0.00 0.00 43.02 2.66
216 219 4.355543 AATACGTGCCACATAAGCAAAG 57.644 40.909 0.00 0.00 43.02 2.77
219 222 5.586643 TCATTAAATACGTGCCACATAAGCA 59.413 36.000 0.00 0.00 38.08 3.91
220 223 6.055231 TCATTAAATACGTGCCACATAAGC 57.945 37.500 0.00 0.00 0.00 3.09
221 224 7.915508 TCTTCATTAAATACGTGCCACATAAG 58.084 34.615 0.00 0.00 0.00 1.73
222 225 7.766738 TCTCTTCATTAAATACGTGCCACATAA 59.233 33.333 0.00 0.00 0.00 1.90
225 228 5.483811 TCTCTTCATTAAATACGTGCCACA 58.516 37.500 0.00 0.00 0.00 4.17
226 229 5.810587 TCTCTCTTCATTAAATACGTGCCAC 59.189 40.000 0.00 0.00 0.00 5.01
227 230 5.972935 TCTCTCTTCATTAAATACGTGCCA 58.027 37.500 0.00 0.00 0.00 4.92
228 231 5.463724 CCTCTCTCTTCATTAAATACGTGCC 59.536 44.000 0.00 0.00 0.00 5.01
230 233 8.407064 AGTACCTCTCTCTTCATTAAATACGTG 58.593 37.037 0.00 0.00 0.00 4.49
231 234 8.522542 AGTACCTCTCTCTTCATTAAATACGT 57.477 34.615 0.00 0.00 0.00 3.57
232 235 9.239002 CAAGTACCTCTCTCTTCATTAAATACG 57.761 37.037 0.00 0.00 0.00 3.06
236 239 7.016268 ACCACAAGTACCTCTCTCTTCATTAAA 59.984 37.037 0.00 0.00 0.00 1.52
237 240 6.497259 ACCACAAGTACCTCTCTCTTCATTAA 59.503 38.462 0.00 0.00 0.00 1.40
240 243 4.421131 ACCACAAGTACCTCTCTCTTCAT 58.579 43.478 0.00 0.00 0.00 2.57
242 245 5.477637 AGTTACCACAAGTACCTCTCTCTTC 59.522 44.000 0.00 0.00 0.00 2.87
243 246 5.395611 AGTTACCACAAGTACCTCTCTCTT 58.604 41.667 0.00 0.00 0.00 2.85
244 247 5.000570 AGTTACCACAAGTACCTCTCTCT 57.999 43.478 0.00 0.00 0.00 3.10
246 249 5.890049 ACTAGTTACCACAAGTACCTCTCT 58.110 41.667 0.00 0.00 0.00 3.10
247 250 6.587206 AACTAGTTACCACAAGTACCTCTC 57.413 41.667 6.26 0.00 0.00 3.20
248 251 7.727634 ACTTAACTAGTTACCACAAGTACCTCT 59.272 37.037 14.96 0.00 31.29 3.69
249 252 7.890515 ACTTAACTAGTTACCACAAGTACCTC 58.109 38.462 14.96 0.00 31.29 3.85
250 253 7.846101 ACTTAACTAGTTACCACAAGTACCT 57.154 36.000 14.96 0.00 31.29 3.08
262 265 8.028938 GTGATGTTCCGGTAACTTAACTAGTTA 58.971 37.037 11.38 11.38 45.22 2.24
264 267 6.015180 TGTGATGTTCCGGTAACTTAACTAGT 60.015 38.462 0.00 0.00 38.99 2.57
265 268 6.309737 GTGTGATGTTCCGGTAACTTAACTAG 59.690 42.308 0.00 0.00 38.99 2.57
266 269 6.158598 GTGTGATGTTCCGGTAACTTAACTA 58.841 40.000 0.00 0.00 38.99 2.24
267 270 4.992951 GTGTGATGTTCCGGTAACTTAACT 59.007 41.667 0.00 0.00 38.99 2.24
268 271 4.751098 TGTGTGATGTTCCGGTAACTTAAC 59.249 41.667 0.00 7.19 38.99 2.01
269 272 4.751098 GTGTGTGATGTTCCGGTAACTTAA 59.249 41.667 0.00 0.00 38.99 1.85
270 273 4.039488 AGTGTGTGATGTTCCGGTAACTTA 59.961 41.667 0.00 0.00 38.99 2.24
271 274 3.135994 GTGTGTGATGTTCCGGTAACTT 58.864 45.455 0.00 3.15 38.99 2.66
272 275 2.367567 AGTGTGTGATGTTCCGGTAACT 59.632 45.455 0.00 0.00 38.99 2.24
273 276 2.735134 GAGTGTGTGATGTTCCGGTAAC 59.265 50.000 0.00 5.56 38.67 2.50
274 277 2.289195 GGAGTGTGTGATGTTCCGGTAA 60.289 50.000 0.00 0.00 0.00 2.85
275 278 1.274167 GGAGTGTGTGATGTTCCGGTA 59.726 52.381 0.00 0.00 0.00 4.02
276 279 0.034896 GGAGTGTGTGATGTTCCGGT 59.965 55.000 0.00 0.00 0.00 5.28
277 280 0.034756 TGGAGTGTGTGATGTTCCGG 59.965 55.000 0.00 0.00 0.00 5.14
278 281 1.800586 CTTGGAGTGTGTGATGTTCCG 59.199 52.381 0.00 0.00 0.00 4.30
279 282 3.126001 TCTTGGAGTGTGTGATGTTCC 57.874 47.619 0.00 0.00 0.00 3.62
280 283 4.335315 TGTTTCTTGGAGTGTGTGATGTTC 59.665 41.667 0.00 0.00 0.00 3.18
281 284 4.269183 TGTTTCTTGGAGTGTGTGATGTT 58.731 39.130 0.00 0.00 0.00 2.71
282 285 3.884895 TGTTTCTTGGAGTGTGTGATGT 58.115 40.909 0.00 0.00 0.00 3.06
283 286 4.898829 TTGTTTCTTGGAGTGTGTGATG 57.101 40.909 0.00 0.00 0.00 3.07
284 287 5.132502 TCATTGTTTCTTGGAGTGTGTGAT 58.867 37.500 0.00 0.00 0.00 3.06
285 288 4.522114 TCATTGTTTCTTGGAGTGTGTGA 58.478 39.130 0.00 0.00 0.00 3.58
286 289 4.336433 ACTCATTGTTTCTTGGAGTGTGTG 59.664 41.667 0.00 0.00 37.43 3.82
287 290 4.526970 ACTCATTGTTTCTTGGAGTGTGT 58.473 39.130 0.00 0.00 37.43 3.72
288 291 4.818546 AGACTCATTGTTTCTTGGAGTGTG 59.181 41.667 0.00 0.00 38.82 3.82
289 292 5.041191 AGACTCATTGTTTCTTGGAGTGT 57.959 39.130 0.00 0.00 38.82 3.55
290 293 8.660373 GTTATAGACTCATTGTTTCTTGGAGTG 58.340 37.037 0.00 0.00 38.82 3.51
291 294 7.824779 GGTTATAGACTCATTGTTTCTTGGAGT 59.175 37.037 0.00 0.00 41.22 3.85
292 295 8.043710 AGGTTATAGACTCATTGTTTCTTGGAG 58.956 37.037 0.00 0.00 0.00 3.86
293 296 7.918076 AGGTTATAGACTCATTGTTTCTTGGA 58.082 34.615 0.00 0.00 0.00 3.53
294 297 9.667107 TTAGGTTATAGACTCATTGTTTCTTGG 57.333 33.333 0.00 0.00 0.00 3.61
314 317 8.850156 GTCATGCAAGGATGTATTTATTAGGTT 58.150 33.333 0.00 0.00 28.42 3.50
315 318 7.998383 TGTCATGCAAGGATGTATTTATTAGGT 59.002 33.333 0.00 0.00 28.42 3.08
316 319 8.292448 GTGTCATGCAAGGATGTATTTATTAGG 58.708 37.037 0.00 0.00 28.42 2.69
317 320 9.060347 AGTGTCATGCAAGGATGTATTTATTAG 57.940 33.333 0.00 0.00 28.42 1.73
318 321 8.978874 AGTGTCATGCAAGGATGTATTTATTA 57.021 30.769 0.00 0.00 28.42 0.98
319 322 7.886629 AGTGTCATGCAAGGATGTATTTATT 57.113 32.000 0.00 0.00 28.42 1.40
320 323 7.992608 TGTAGTGTCATGCAAGGATGTATTTAT 59.007 33.333 0.00 0.00 28.42 1.40
321 324 7.334858 TGTAGTGTCATGCAAGGATGTATTTA 58.665 34.615 0.00 0.00 28.42 1.40
322 325 6.179756 TGTAGTGTCATGCAAGGATGTATTT 58.820 36.000 0.00 0.00 28.42 1.40
323 326 5.744171 TGTAGTGTCATGCAAGGATGTATT 58.256 37.500 0.00 0.00 28.42 1.89
324 327 5.357742 TGTAGTGTCATGCAAGGATGTAT 57.642 39.130 0.00 0.00 31.41 2.29
325 328 4.817318 TGTAGTGTCATGCAAGGATGTA 57.183 40.909 0.00 0.00 0.00 2.29
326 329 3.701205 TGTAGTGTCATGCAAGGATGT 57.299 42.857 0.00 0.00 0.00 3.06
327 330 6.682423 TTTATGTAGTGTCATGCAAGGATG 57.318 37.500 0.00 0.00 0.00 3.51
328 331 6.830324 ACATTTATGTAGTGTCATGCAAGGAT 59.170 34.615 0.00 0.00 39.68 3.24
329 332 6.179756 ACATTTATGTAGTGTCATGCAAGGA 58.820 36.000 0.00 0.00 39.68 3.36
330 333 6.441093 ACATTTATGTAGTGTCATGCAAGG 57.559 37.500 0.00 0.00 39.68 3.61
331 334 6.968904 GGAACATTTATGTAGTGTCATGCAAG 59.031 38.462 0.00 0.00 40.80 4.01
332 335 6.658816 AGGAACATTTATGTAGTGTCATGCAA 59.341 34.615 0.00 0.00 40.80 4.08
333 336 6.179756 AGGAACATTTATGTAGTGTCATGCA 58.820 36.000 0.00 0.00 40.80 3.96
334 337 6.683974 AGGAACATTTATGTAGTGTCATGC 57.316 37.500 0.00 0.00 40.80 4.06
335 338 7.226720 GGGTAGGAACATTTATGTAGTGTCATG 59.773 40.741 0.00 0.00 40.80 3.07
336 339 7.092623 TGGGTAGGAACATTTATGTAGTGTCAT 60.093 37.037 0.00 0.00 40.80 3.06
337 340 6.213802 TGGGTAGGAACATTTATGTAGTGTCA 59.786 38.462 0.00 0.00 40.80 3.58
338 341 6.537660 GTGGGTAGGAACATTTATGTAGTGTC 59.462 42.308 0.00 0.00 40.80 3.67
339 342 6.214819 AGTGGGTAGGAACATTTATGTAGTGT 59.785 38.462 0.00 0.00 40.80 3.55
340 343 6.650120 AGTGGGTAGGAACATTTATGTAGTG 58.350 40.000 0.00 0.00 40.80 2.74
341 344 6.886178 AGTGGGTAGGAACATTTATGTAGT 57.114 37.500 0.00 0.00 40.80 2.73
342 345 7.878127 CCATAGTGGGTAGGAACATTTATGTAG 59.122 40.741 0.00 0.00 35.14 2.74
343 346 7.569485 TCCATAGTGGGTAGGAACATTTATGTA 59.431 37.037 0.00 0.00 37.90 2.29
344 347 6.388689 TCCATAGTGGGTAGGAACATTTATGT 59.611 38.462 0.00 0.00 39.54 2.29
345 348 6.837312 TCCATAGTGGGTAGGAACATTTATG 58.163 40.000 0.00 0.00 38.32 1.90
346 349 6.044404 CCTCCATAGTGGGTAGGAACATTTAT 59.956 42.308 0.00 0.00 38.32 1.40
347 350 5.368523 CCTCCATAGTGGGTAGGAACATTTA 59.631 44.000 0.00 0.00 38.32 1.40
348 351 4.166144 CCTCCATAGTGGGTAGGAACATTT 59.834 45.833 0.00 0.00 38.32 2.32
349 352 3.716872 CCTCCATAGTGGGTAGGAACATT 59.283 47.826 0.00 0.00 38.32 2.71
350 353 3.311402 ACCTCCATAGTGGGTAGGAACAT 60.311 47.826 9.90 0.00 38.32 2.71
351 354 2.045326 ACCTCCATAGTGGGTAGGAACA 59.955 50.000 9.90 0.00 38.32 3.18
352 355 2.760581 ACCTCCATAGTGGGTAGGAAC 58.239 52.381 9.90 0.00 38.32 3.62
353 356 4.194678 CTACCTCCATAGTGGGTAGGAA 57.805 50.000 9.90 0.00 45.09 3.36
354 357 3.897657 CTACCTCCATAGTGGGTAGGA 57.102 52.381 9.90 0.00 45.09 2.94
357 360 5.470755 TGTTACTACCTCCATAGTGGGTA 57.529 43.478 0.00 0.00 38.32 3.69
358 361 4.341863 TGTTACTACCTCCATAGTGGGT 57.658 45.455 0.00 0.00 38.32 4.51
359 362 6.075984 ACTATGTTACTACCTCCATAGTGGG 58.924 44.000 9.63 0.00 44.96 4.61
360 363 7.005296 AGACTATGTTACTACCTCCATAGTGG 58.995 42.308 14.01 0.00 46.02 4.00
361 364 9.221933 CTAGACTATGTTACTACCTCCATAGTG 57.778 40.741 14.01 0.00 46.02 2.74
363 366 7.830201 CCCTAGACTATGTTACTACCTCCATAG 59.170 44.444 0.00 0.00 41.50 2.23
364 367 7.518653 TCCCTAGACTATGTTACTACCTCCATA 59.481 40.741 0.00 0.00 0.00 2.74
365 368 6.334774 TCCCTAGACTATGTTACTACCTCCAT 59.665 42.308 0.00 0.00 0.00 3.41
366 369 5.673574 TCCCTAGACTATGTTACTACCTCCA 59.326 44.000 0.00 0.00 0.00 3.86
367 370 6.198237 TCCCTAGACTATGTTACTACCTCC 57.802 45.833 0.00 0.00 0.00 4.30
368 371 7.229106 CACTTCCCTAGACTATGTTACTACCTC 59.771 44.444 0.00 0.00 0.00 3.85
369 372 7.061688 CACTTCCCTAGACTATGTTACTACCT 58.938 42.308 0.00 0.00 0.00 3.08
370 373 6.832900 ACACTTCCCTAGACTATGTTACTACC 59.167 42.308 0.00 0.00 0.00 3.18
371 374 7.555554 TCACACTTCCCTAGACTATGTTACTAC 59.444 40.741 0.00 0.00 0.00 2.73
372 375 7.636579 TCACACTTCCCTAGACTATGTTACTA 58.363 38.462 0.00 0.00 0.00 1.82
373 376 6.491383 TCACACTTCCCTAGACTATGTTACT 58.509 40.000 0.00 0.00 0.00 2.24
374 377 6.770746 TCACACTTCCCTAGACTATGTTAC 57.229 41.667 0.00 0.00 0.00 2.50
375 378 6.952358 ACTTCACACTTCCCTAGACTATGTTA 59.048 38.462 0.00 0.00 0.00 2.41
376 379 5.780793 ACTTCACACTTCCCTAGACTATGTT 59.219 40.000 0.00 0.00 0.00 2.71
377 380 5.334421 ACTTCACACTTCCCTAGACTATGT 58.666 41.667 0.00 0.00 0.00 2.29
378 381 5.923733 ACTTCACACTTCCCTAGACTATG 57.076 43.478 0.00 0.00 0.00 2.23
379 382 8.611051 AATAACTTCACACTTCCCTAGACTAT 57.389 34.615 0.00 0.00 0.00 2.12
380 383 9.186837 CTAATAACTTCACACTTCCCTAGACTA 57.813 37.037 0.00 0.00 0.00 2.59
381 384 6.936968 AATAACTTCACACTTCCCTAGACT 57.063 37.500 0.00 0.00 0.00 3.24
382 385 6.757478 GCTAATAACTTCACACTTCCCTAGAC 59.243 42.308 0.00 0.00 0.00 2.59
383 386 6.668283 AGCTAATAACTTCACACTTCCCTAGA 59.332 38.462 0.00 0.00 0.00 2.43
384 387 6.879400 AGCTAATAACTTCACACTTCCCTAG 58.121 40.000 0.00 0.00 0.00 3.02
385 388 6.869206 AGCTAATAACTTCACACTTCCCTA 57.131 37.500 0.00 0.00 0.00 3.53
386 389 5.763876 AGCTAATAACTTCACACTTCCCT 57.236 39.130 0.00 0.00 0.00 4.20
387 390 7.553044 ACATAAGCTAATAACTTCACACTTCCC 59.447 37.037 0.00 0.00 0.00 3.97
388 391 8.494016 ACATAAGCTAATAACTTCACACTTCC 57.506 34.615 0.00 0.00 0.00 3.46
389 392 9.974750 GAACATAAGCTAATAACTTCACACTTC 57.025 33.333 0.00 0.00 0.00 3.01
390 393 9.726438 AGAACATAAGCTAATAACTTCACACTT 57.274 29.630 0.00 0.00 0.00 3.16
391 394 9.726438 AAGAACATAAGCTAATAACTTCACACT 57.274 29.630 0.00 0.00 0.00 3.55
392 395 9.760660 CAAGAACATAAGCTAATAACTTCACAC 57.239 33.333 0.00 0.00 0.00 3.82
393 396 8.450964 GCAAGAACATAAGCTAATAACTTCACA 58.549 33.333 0.00 0.00 0.00 3.58
394 397 7.910683 GGCAAGAACATAAGCTAATAACTTCAC 59.089 37.037 0.00 0.00 0.00 3.18
395 398 7.067008 GGGCAAGAACATAAGCTAATAACTTCA 59.933 37.037 0.00 0.00 0.00 3.02
396 399 7.067008 TGGGCAAGAACATAAGCTAATAACTTC 59.933 37.037 0.00 0.00 0.00 3.01
397 400 6.889722 TGGGCAAGAACATAAGCTAATAACTT 59.110 34.615 0.00 0.00 0.00 2.66
398 401 6.423182 TGGGCAAGAACATAAGCTAATAACT 58.577 36.000 0.00 0.00 0.00 2.24
399 402 6.693315 TGGGCAAGAACATAAGCTAATAAC 57.307 37.500 0.00 0.00 0.00 1.89
400 403 7.341769 ACAATGGGCAAGAACATAAGCTAATAA 59.658 33.333 0.00 0.00 0.00 1.40
401 404 6.833416 ACAATGGGCAAGAACATAAGCTAATA 59.167 34.615 0.00 0.00 0.00 0.98
402 405 5.658190 ACAATGGGCAAGAACATAAGCTAAT 59.342 36.000 0.00 0.00 0.00 1.73
403 406 5.016173 ACAATGGGCAAGAACATAAGCTAA 58.984 37.500 0.00 0.00 0.00 3.09
404 407 4.398988 CACAATGGGCAAGAACATAAGCTA 59.601 41.667 0.00 0.00 0.00 3.32
405 408 3.194116 CACAATGGGCAAGAACATAAGCT 59.806 43.478 0.00 0.00 0.00 3.74
406 409 3.193267 TCACAATGGGCAAGAACATAAGC 59.807 43.478 0.00 0.00 0.00 3.09
407 410 4.380867 GGTCACAATGGGCAAGAACATAAG 60.381 45.833 0.00 0.00 0.00 1.73
408 411 3.509575 GGTCACAATGGGCAAGAACATAA 59.490 43.478 0.00 0.00 0.00 1.90
409 412 3.088532 GGTCACAATGGGCAAGAACATA 58.911 45.455 0.00 0.00 0.00 2.29
410 413 1.895131 GGTCACAATGGGCAAGAACAT 59.105 47.619 0.00 0.00 0.00 2.71
411 414 1.327303 GGTCACAATGGGCAAGAACA 58.673 50.000 0.00 0.00 0.00 3.18
412 415 1.270550 CTGGTCACAATGGGCAAGAAC 59.729 52.381 0.00 0.00 0.00 3.01
413 416 1.619654 CTGGTCACAATGGGCAAGAA 58.380 50.000 0.00 0.00 0.00 2.52
414 417 0.895100 GCTGGTCACAATGGGCAAGA 60.895 55.000 0.00 0.00 0.00 3.02
415 418 1.588082 GCTGGTCACAATGGGCAAG 59.412 57.895 0.00 0.00 0.00 4.01
416 419 1.907807 GGCTGGTCACAATGGGCAA 60.908 57.895 0.00 0.00 0.00 4.52
417 420 2.283101 GGCTGGTCACAATGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
418 421 0.323360 TAAGGCTGGTCACAATGGGC 60.323 55.000 0.00 0.00 0.00 5.36
419 422 2.214376 TTAAGGCTGGTCACAATGGG 57.786 50.000 0.00 0.00 0.00 4.00
420 423 4.599047 TTTTTAAGGCTGGTCACAATGG 57.401 40.909 0.00 0.00 0.00 3.16
447 450 9.554395 TGTTTCAGTTTGTCTAATTCACATCTA 57.446 29.630 0.00 0.00 0.00 1.98
448 451 8.450578 TGTTTCAGTTTGTCTAATTCACATCT 57.549 30.769 0.00 0.00 0.00 2.90
449 452 9.515020 TTTGTTTCAGTTTGTCTAATTCACATC 57.485 29.630 0.00 0.00 0.00 3.06
456 459 9.846248 GAGCATATTTGTTTCAGTTTGTCTAAT 57.154 29.630 0.00 0.00 0.00 1.73
457 460 8.845227 TGAGCATATTTGTTTCAGTTTGTCTAA 58.155 29.630 0.00 0.00 0.00 2.10
458 461 8.389779 TGAGCATATTTGTTTCAGTTTGTCTA 57.610 30.769 0.00 0.00 0.00 2.59
459 462 7.275888 TGAGCATATTTGTTTCAGTTTGTCT 57.724 32.000 0.00 0.00 0.00 3.41
460 463 7.809331 TCATGAGCATATTTGTTTCAGTTTGTC 59.191 33.333 0.00 0.00 0.00 3.18
461 464 7.660112 TCATGAGCATATTTGTTTCAGTTTGT 58.340 30.769 0.00 0.00 0.00 2.83
462 465 8.697846 ATCATGAGCATATTTGTTTCAGTTTG 57.302 30.769 0.09 0.00 0.00 2.93
463 466 9.362539 GAATCATGAGCATATTTGTTTCAGTTT 57.637 29.630 0.09 0.00 0.00 2.66
464 467 8.746530 AGAATCATGAGCATATTTGTTTCAGTT 58.253 29.630 0.09 0.00 0.00 3.16
465 468 8.289939 AGAATCATGAGCATATTTGTTTCAGT 57.710 30.769 0.09 0.00 0.00 3.41
466 469 8.403236 TGAGAATCATGAGCATATTTGTTTCAG 58.597 33.333 0.09 0.00 42.56 3.02
467 470 8.283699 TGAGAATCATGAGCATATTTGTTTCA 57.716 30.769 0.09 0.00 42.56 2.69
521 524 3.486108 CCTGTTGATACTCGAATGCGTAC 59.514 47.826 0.00 0.00 38.98 3.67
522 525 3.379057 TCCTGTTGATACTCGAATGCGTA 59.621 43.478 0.00 0.00 38.98 4.42
578 581 7.733773 TTGAGGAGATGGTTGTCTCTTTATA 57.266 36.000 4.16 0.00 43.31 0.98
581 584 4.982241 TTGAGGAGATGGTTGTCTCTTT 57.018 40.909 4.16 0.00 43.31 2.52
624 628 1.337447 CCTCAAAGCCGAACCGACTAA 60.337 52.381 0.00 0.00 0.00 2.24
651 655 1.515221 CCGTGCAAAACAAACGCTAAC 59.485 47.619 0.00 0.00 36.02 2.34
652 656 1.828832 CCGTGCAAAACAAACGCTAA 58.171 45.000 0.00 0.00 36.02 3.09
708 712 2.884639 GGCATCACACTACTTGGTGTTT 59.115 45.455 0.00 0.00 46.71 2.83
709 713 2.158682 TGGCATCACACTACTTGGTGTT 60.159 45.455 0.00 0.00 46.71 3.32
791 799 2.349886 GGCGAGTCAGTCAAGCTAAATG 59.650 50.000 0.00 0.00 0.00 2.32
829 837 1.034838 AGCTGGTTTGGTTTGCGTCA 61.035 50.000 0.00 0.00 0.00 4.35
842 850 1.935933 CGCGAGGTTTTATAGCTGGT 58.064 50.000 0.00 0.00 33.94 4.00
897 905 2.783135 TGAACCTTCCAAGCAGTGATC 58.217 47.619 0.00 0.00 0.00 2.92
927 935 5.104485 ACTTTCCTTCAAGACCAAGTAGTGT 60.104 40.000 0.00 0.00 0.00 3.55
969 977 0.248289 GGCTACGGGCAAAGTCACTA 59.752 55.000 5.12 0.00 44.01 2.74
1953 1961 1.380380 GGATTTGGTGCCCTCCTGG 60.380 63.158 0.00 0.00 37.09 4.45
2032 2040 6.554605 TCAGAATGGAAAGAAAACCAAGGAAT 59.445 34.615 0.00 0.00 39.69 3.01
2039 2049 5.478332 AGGACATCAGAATGGAAAGAAAACC 59.522 40.000 0.00 0.00 37.19 3.27
2126 2136 0.545309 TCCTCTCCTCCCCACTTGTG 60.545 60.000 0.00 0.00 0.00 3.33
2174 2184 3.438017 AAGCGCAGGATCGAGCCTC 62.438 63.158 21.79 13.75 35.66 4.70
2292 2303 1.954382 CTTCGATCTCCGGGTATGTGA 59.046 52.381 0.00 0.00 39.14 3.58
2315 2326 3.117745 TCACCATGACCTCCTTGATCAT 58.882 45.455 0.00 0.00 33.28 2.45
2495 2510 2.618241 TGTCTGGAACATCACTTTGTGC 59.382 45.455 0.00 0.00 38.20 4.57
2498 2513 5.694231 TGATTGTCTGGAACATCACTTTG 57.306 39.130 0.00 0.00 37.82 2.77
2556 2641 8.708742 GCACTAATTGTATGATATTCGCACTAA 58.291 33.333 0.00 0.00 0.00 2.24
2586 2671 5.940192 TGATACATTGTTGCTCGAAGTTT 57.060 34.783 0.00 0.00 0.00 2.66
2993 3087 6.392354 ACCATGTCTGTGCTCATTTATTTTG 58.608 36.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.