Multiple sequence alignment - TraesCS6A01G204600

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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 TraesCS6A01G204600 chr6A 100.000 4406 0 0 1 4406 356969068 356973473 0.000000e+00 8137.0
1 TraesCS6A01G204600 chr6D 95.234 3945 133 16 441 4356 262749695 262753613 0.000000e+00 6192.0
2 TraesCS6A01G204600 chr6D 91.200 125 5 1 51 169 262749575 262749699 9.800000e-37 165.0
3 TraesCS6A01G204600 chr6D 100.000 28 0 0 1236 1263 21723587 21723560 8.000000e-03 52.8
4 TraesCS6A01G204600 chr6B 91.354 3065 134 40 686 3710 347232187 347229214 0.000000e+00 4071.0
5 TraesCS6A01G204600 chr6B 91.074 605 31 9 3807 4406 347229187 347228601 0.000000e+00 797.0
6 TraesCS6A01G204600 chr6B 100.000 28 0 0 471 498 347232238 347232211 8.000000e-03 52.8
7 TraesCS6A01G204600 chr7A 94.326 282 16 0 165 446 22164696 22164415 2.430000e-117 433.0
8 TraesCS6A01G204600 chr5B 94.014 284 16 1 168 451 439840237 439839955 3.150000e-116 429.0
9 TraesCS6A01G204600 chr4B 93.640 283 18 0 163 445 514215934 514215652 1.460000e-114 424.0
10 TraesCS6A01G204600 chr5D 93.617 282 18 0 166 447 526871678 526871397 5.270000e-114 422.0
11 TraesCS6A01G204600 chr2B 93.907 279 17 0 166 444 139650363 139650085 5.270000e-114 422.0
12 TraesCS6A01G204600 chr2B 100.000 28 0 0 1236 1263 318542899 318542872 8.000000e-03 52.8
13 TraesCS6A01G204600 chr2B 100.000 28 0 0 1236 1263 417640431 417640404 8.000000e-03 52.8
14 TraesCS6A01G204600 chr3B 93.310 284 19 0 166 449 811824877 811825160 1.900000e-113 420.0
15 TraesCS6A01G204600 chr3B 93.310 284 19 0 166 449 811898851 811899134 1.900000e-113 420.0
16 TraesCS6A01G204600 chr3B 93.310 284 19 0 166 449 811980360 811980643 1.900000e-113 420.0
17 TraesCS6A01G204600 chr1D 93.907 279 15 1 166 444 127157104 127156828 1.900000e-113 420.0
18 TraesCS6A01G204600 chr3D 79.762 84 17 0 2891 2974 4972422 4972505 1.320000e-05 62.1
19 TraesCS6A01G204600 chr5A 100.000 32 0 0 1232 1263 546554360 546554391 4.760000e-05 60.2
20 TraesCS6A01G204600 chr7B 100.000 28 0 0 1236 1263 535289720 535289693 8.000000e-03 52.8


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 TraesCS6A01G204600 chr6A 356969068 356973473 4405 False 8137.000000 8137 100.000000 1 4406 1 chr6A.!!$F1 4405
1 TraesCS6A01G204600 chr6D 262749575 262753613 4038 False 3178.500000 6192 93.217000 51 4356 2 chr6D.!!$F1 4305
2 TraesCS6A01G204600 chr6B 347228601 347232238 3637 True 1640.266667 4071 94.142667 471 4406 3 chr6B.!!$R1 3935

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
360 367 0.104409 ACCACAAACCCCTCTCTCCT 60.104 55.0 0.0 0.0 0.0 3.69 F
1196 1209 0.458025 GTCTACCTCCTCGCCGTTTG 60.458 60.0 0.0 0.0 0.0 2.93 F
1880 1911 0.034059 CGGAACTTCTGTGAGGCTGT 59.966 55.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1259 0.039035 AGTGTGGTGTTGGTGTTGGT 59.961 50.0 0.0 0.0 0.0 3.67 R
2197 2234 0.387565 TTTTTCCAGCAAGAACCGCC 59.612 50.0 0.0 0.0 0.0 6.13 R
3722 3773 0.036875 GTTCCTAACCAGCCTGCACT 59.963 55.0 0.0 0.0 0.0 4.40 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
88 89 8.121305 TCATAACCTGAAAACATAGCACAAAT 57.879 30.769 0.00 0.00 0.00 2.32
98 99 8.630054 AAAACATAGCACAAATAGAGTACCAA 57.370 30.769 0.00 0.00 0.00 3.67
104 105 6.476378 AGCACAAATAGAGTACCAAAGACAT 58.524 36.000 0.00 0.00 0.00 3.06
125 126 3.146066 TCATGTACCACAAGGAAACAGC 58.854 45.455 0.00 0.00 37.60 4.40
169 176 2.165845 GAGCTAGAAACACCGGCTAAGA 59.834 50.000 0.00 0.00 33.13 2.10
170 177 2.094130 AGCTAGAAACACCGGCTAAGAC 60.094 50.000 0.00 0.00 0.00 3.01
171 178 2.094130 GCTAGAAACACCGGCTAAGACT 60.094 50.000 0.00 0.00 0.00 3.24
172 179 2.457366 AGAAACACCGGCTAAGACTG 57.543 50.000 0.00 0.00 0.00 3.51
173 180 0.796927 GAAACACCGGCTAAGACTGC 59.203 55.000 0.00 0.00 0.00 4.40
174 181 0.396811 AAACACCGGCTAAGACTGCT 59.603 50.000 0.00 0.00 0.00 4.24
175 182 0.396811 AACACCGGCTAAGACTGCTT 59.603 50.000 0.00 0.00 38.15 3.91
176 183 1.263356 ACACCGGCTAAGACTGCTTA 58.737 50.000 0.00 0.00 35.56 3.09
177 184 1.067071 ACACCGGCTAAGACTGCTTAC 60.067 52.381 0.00 0.00 35.56 2.34
178 185 1.067142 CACCGGCTAAGACTGCTTACA 60.067 52.381 0.00 0.00 35.56 2.41
191 198 4.521130 CTGCTTACAGTGAGGAGTAACA 57.479 45.455 5.75 0.00 39.22 2.41
192 199 5.078411 CTGCTTACAGTGAGGAGTAACAT 57.922 43.478 5.75 0.00 39.22 2.71
193 200 6.208988 CTGCTTACAGTGAGGAGTAACATA 57.791 41.667 5.75 0.00 39.22 2.29
194 201 6.208988 TGCTTACAGTGAGGAGTAACATAG 57.791 41.667 0.00 0.00 0.00 2.23
195 202 5.949952 TGCTTACAGTGAGGAGTAACATAGA 59.050 40.000 0.00 0.00 0.00 1.98
196 203 6.095580 TGCTTACAGTGAGGAGTAACATAGAG 59.904 42.308 0.00 0.00 0.00 2.43
197 204 4.993029 ACAGTGAGGAGTAACATAGAGC 57.007 45.455 0.00 0.00 0.00 4.09
198 205 4.344978 ACAGTGAGGAGTAACATAGAGCA 58.655 43.478 0.00 0.00 0.00 4.26
199 206 4.400884 ACAGTGAGGAGTAACATAGAGCAG 59.599 45.833 0.00 0.00 0.00 4.24
200 207 4.400884 CAGTGAGGAGTAACATAGAGCAGT 59.599 45.833 0.00 0.00 0.00 4.40
201 208 5.590663 CAGTGAGGAGTAACATAGAGCAGTA 59.409 44.000 0.00 0.00 0.00 2.74
202 209 6.095580 CAGTGAGGAGTAACATAGAGCAGTAA 59.904 42.308 0.00 0.00 0.00 2.24
203 210 6.095720 AGTGAGGAGTAACATAGAGCAGTAAC 59.904 42.308 0.00 0.00 0.00 2.50
204 211 6.095720 GTGAGGAGTAACATAGAGCAGTAACT 59.904 42.308 0.00 0.00 0.00 2.24
205 212 6.663953 TGAGGAGTAACATAGAGCAGTAACTT 59.336 38.462 0.00 0.00 0.00 2.66
206 213 6.868622 AGGAGTAACATAGAGCAGTAACTTG 58.131 40.000 0.00 0.00 0.00 3.16
207 214 5.520649 GGAGTAACATAGAGCAGTAACTTGC 59.479 44.000 0.00 0.00 44.41 4.01
208 215 5.420409 AGTAACATAGAGCAGTAACTTGCC 58.580 41.667 0.00 0.00 45.18 4.52
209 216 3.981071 ACATAGAGCAGTAACTTGCCA 57.019 42.857 0.00 0.00 45.18 4.92
210 217 4.286297 ACATAGAGCAGTAACTTGCCAA 57.714 40.909 0.00 0.00 45.18 4.52
211 218 4.848357 ACATAGAGCAGTAACTTGCCAAT 58.152 39.130 0.00 0.00 45.18 3.16
212 219 4.637534 ACATAGAGCAGTAACTTGCCAATG 59.362 41.667 0.00 0.03 45.18 2.82
213 220 3.146104 AGAGCAGTAACTTGCCAATGT 57.854 42.857 0.00 0.00 45.18 2.71
214 221 3.490348 AGAGCAGTAACTTGCCAATGTT 58.510 40.909 0.00 0.00 45.18 2.71
215 222 4.651778 AGAGCAGTAACTTGCCAATGTTA 58.348 39.130 0.00 0.00 45.18 2.41
216 223 4.455877 AGAGCAGTAACTTGCCAATGTTAC 59.544 41.667 15.86 15.86 45.18 2.50
224 231 8.943909 GTAACTTGCCAATGTTACTAGTCTAT 57.056 34.615 16.13 0.00 42.82 1.98
241 248 8.947305 ACTAGTCTATATTACTACCTCCACAGT 58.053 37.037 0.00 0.00 0.00 3.55
242 249 9.221933 CTAGTCTATATTACTACCTCCACAGTG 57.778 40.741 0.00 0.00 0.00 3.66
243 250 7.005296 AGTCTATATTACTACCTCCACAGTGG 58.995 42.308 14.19 14.19 39.43 4.00
244 251 7.002879 GTCTATATTACTACCTCCACAGTGGA 58.997 42.308 21.68 21.68 45.98 4.02
251 258 7.287235 ATTACTACCTCCACAGTGGATAGTAAC 59.713 40.741 34.16 0.00 46.49 2.50
258 265 7.290110 TCCACAGTGGATAGTAACATATGAG 57.710 40.000 19.21 0.00 42.67 2.90
259 266 6.839134 TCCACAGTGGATAGTAACATATGAGT 59.161 38.462 19.21 0.00 42.67 3.41
260 267 6.925718 CCACAGTGGATAGTAACATATGAGTG 59.074 42.308 15.35 0.00 40.96 3.51
261 268 7.417911 CCACAGTGGATAGTAACATATGAGTGT 60.418 40.741 15.35 0.00 40.96 3.55
262 269 7.981789 CACAGTGGATAGTAACATATGAGTGTT 59.018 37.037 10.38 0.00 44.09 3.32
263 270 9.197306 ACAGTGGATAGTAACATATGAGTGTTA 57.803 33.333 10.38 0.00 42.08 2.41
275 282 9.896645 AACATATGAGTGTTATCATGAAAGAGT 57.103 29.630 10.38 0.00 40.35 3.24
276 283 9.896645 ACATATGAGTGTTATCATGAAAGAGTT 57.103 29.630 10.38 0.00 40.16 3.01
308 315 9.610705 ATTAGGCTATAGACTCATTATGCATTG 57.389 33.333 12.64 0.00 33.72 2.82
309 316 7.250032 AGGCTATAGACTCATTATGCATTGA 57.750 36.000 3.54 2.16 0.00 2.57
310 317 7.683578 AGGCTATAGACTCATTATGCATTGAA 58.316 34.615 3.54 0.00 0.00 2.69
311 318 8.159447 AGGCTATAGACTCATTATGCATTGAAA 58.841 33.333 3.54 0.00 0.00 2.69
312 319 8.954350 GGCTATAGACTCATTATGCATTGAAAT 58.046 33.333 3.54 0.00 0.00 2.17
313 320 9.770503 GCTATAGACTCATTATGCATTGAAATG 57.229 33.333 3.54 9.45 39.40 2.32
316 323 7.400599 AGACTCATTATGCATTGAAATGTGT 57.599 32.000 20.33 20.33 39.01 3.72
317 324 7.255569 AGACTCATTATGCATTGAAATGTGTG 58.744 34.615 23.22 15.30 37.42 3.82
318 325 7.121611 AGACTCATTATGCATTGAAATGTGTGA 59.878 33.333 23.22 7.37 37.42 3.58
319 326 7.778083 ACTCATTATGCATTGAAATGTGTGAT 58.222 30.769 19.87 4.21 36.51 3.06
320 327 7.704899 ACTCATTATGCATTGAAATGTGTGATG 59.295 33.333 19.87 2.54 36.51 3.07
321 328 7.548967 TCATTATGCATTGAAATGTGTGATGT 58.451 30.769 16.53 0.00 38.65 3.06
322 329 8.035984 TCATTATGCATTGAAATGTGTGATGTT 58.964 29.630 16.53 0.00 38.65 2.71
323 330 9.303537 CATTATGCATTGAAATGTGTGATGTTA 57.696 29.630 3.54 0.00 38.65 2.41
324 331 8.686397 TTATGCATTGAAATGTGTGATGTTAC 57.314 30.769 3.54 0.00 38.65 2.50
325 332 6.081872 TGCATTGAAATGTGTGATGTTACA 57.918 33.333 5.02 0.00 38.65 2.41
326 333 6.151004 TGCATTGAAATGTGTGATGTTACAG 58.849 36.000 5.02 0.00 38.65 2.74
327 334 6.151691 GCATTGAAATGTGTGATGTTACAGT 58.848 36.000 5.02 0.00 38.65 3.55
328 335 7.040823 TGCATTGAAATGTGTGATGTTACAGTA 60.041 33.333 5.02 0.00 38.65 2.74
329 336 7.807433 GCATTGAAATGTGTGATGTTACAGTAA 59.193 33.333 5.02 0.00 38.65 2.24
330 337 9.117145 CATTGAAATGTGTGATGTTACAGTAAC 57.883 33.333 15.58 15.58 39.11 2.50
331 338 8.445275 TTGAAATGTGTGATGTTACAGTAACT 57.555 30.769 21.56 9.41 39.38 2.24
332 339 9.549078 TTGAAATGTGTGATGTTACAGTAACTA 57.451 29.630 21.56 10.50 39.38 2.24
333 340 8.984764 TGAAATGTGTGATGTTACAGTAACTAC 58.015 33.333 21.56 17.34 39.38 2.73
334 341 7.900782 AATGTGTGATGTTACAGTAACTACC 57.099 36.000 21.56 12.18 39.38 3.18
335 342 6.659745 TGTGTGATGTTACAGTAACTACCT 57.340 37.500 21.56 6.57 39.38 3.08
336 343 7.764141 TGTGTGATGTTACAGTAACTACCTA 57.236 36.000 21.56 4.25 39.38 3.08
337 344 8.180706 TGTGTGATGTTACAGTAACTACCTAA 57.819 34.615 21.56 3.59 39.38 2.69
338 345 8.301720 TGTGTGATGTTACAGTAACTACCTAAG 58.698 37.037 21.56 0.00 39.38 2.18
339 346 8.302438 GTGTGATGTTACAGTAACTACCTAAGT 58.698 37.037 21.56 1.47 41.49 2.24
351 358 5.233083 ACTACCTAAGTTACCACAAACCC 57.767 43.478 0.00 0.00 33.35 4.11
352 359 3.513909 ACCTAAGTTACCACAAACCCC 57.486 47.619 0.00 0.00 0.00 4.95
353 360 3.058341 ACCTAAGTTACCACAAACCCCT 58.942 45.455 0.00 0.00 0.00 4.79
354 361 3.073503 ACCTAAGTTACCACAAACCCCTC 59.926 47.826 0.00 0.00 0.00 4.30
355 362 3.329814 CCTAAGTTACCACAAACCCCTCT 59.670 47.826 0.00 0.00 0.00 3.69
356 363 3.503800 AAGTTACCACAAACCCCTCTC 57.496 47.619 0.00 0.00 0.00 3.20
357 364 2.702748 AGTTACCACAAACCCCTCTCT 58.297 47.619 0.00 0.00 0.00 3.10
358 365 2.638363 AGTTACCACAAACCCCTCTCTC 59.362 50.000 0.00 0.00 0.00 3.20
359 366 1.652947 TACCACAAACCCCTCTCTCC 58.347 55.000 0.00 0.00 0.00 3.71
360 367 0.104409 ACCACAAACCCCTCTCTCCT 60.104 55.000 0.00 0.00 0.00 3.69
361 368 1.068121 CCACAAACCCCTCTCTCCTT 58.932 55.000 0.00 0.00 0.00 3.36
362 369 2.266279 CCACAAACCCCTCTCTCCTTA 58.734 52.381 0.00 0.00 0.00 2.69
363 370 2.846827 CCACAAACCCCTCTCTCCTTAT 59.153 50.000 0.00 0.00 0.00 1.73
364 371 3.267031 CCACAAACCCCTCTCTCCTTATT 59.733 47.826 0.00 0.00 0.00 1.40
365 372 4.473559 CCACAAACCCCTCTCTCCTTATTA 59.526 45.833 0.00 0.00 0.00 0.98
366 373 5.045140 CCACAAACCCCTCTCTCCTTATTAA 60.045 44.000 0.00 0.00 0.00 1.40
367 374 6.353951 CCACAAACCCCTCTCTCCTTATTAAT 60.354 42.308 0.00 0.00 0.00 1.40
368 375 7.119387 CACAAACCCCTCTCTCCTTATTAATT 58.881 38.462 0.00 0.00 0.00 1.40
369 376 8.272173 CACAAACCCCTCTCTCCTTATTAATTA 58.728 37.037 0.00 0.00 0.00 1.40
370 377 8.495260 ACAAACCCCTCTCTCCTTATTAATTAG 58.505 37.037 0.00 0.00 0.00 1.73
371 378 6.689663 ACCCCTCTCTCCTTATTAATTAGC 57.310 41.667 0.00 0.00 0.00 3.09
372 379 6.394747 ACCCCTCTCTCCTTATTAATTAGCT 58.605 40.000 0.00 0.00 0.00 3.32
373 380 6.271159 ACCCCTCTCTCCTTATTAATTAGCTG 59.729 42.308 0.00 0.00 0.00 4.24
374 381 6.169800 CCCTCTCTCCTTATTAATTAGCTGC 58.830 44.000 0.00 0.00 0.00 5.25
375 382 6.169800 CCTCTCTCCTTATTAATTAGCTGCC 58.830 44.000 0.00 0.00 0.00 4.85
376 383 6.239714 CCTCTCTCCTTATTAATTAGCTGCCA 60.240 42.308 0.00 0.00 0.00 4.92
377 384 6.525629 TCTCTCCTTATTAATTAGCTGCCAC 58.474 40.000 0.00 0.00 0.00 5.01
378 385 6.099701 TCTCTCCTTATTAATTAGCTGCCACA 59.900 38.462 0.00 0.00 0.00 4.17
379 386 6.841601 TCTCCTTATTAATTAGCTGCCACAT 58.158 36.000 0.00 0.00 0.00 3.21
380 387 7.973402 TCTCCTTATTAATTAGCTGCCACATA 58.027 34.615 0.00 0.00 0.00 2.29
381 388 8.436778 TCTCCTTATTAATTAGCTGCCACATAA 58.563 33.333 0.00 0.00 0.00 1.90
382 389 8.621532 TCCTTATTAATTAGCTGCCACATAAG 57.378 34.615 0.00 3.41 0.00 1.73
383 390 8.217799 TCCTTATTAATTAGCTGCCACATAAGT 58.782 33.333 0.00 0.00 0.00 2.24
384 391 9.502091 CCTTATTAATTAGCTGCCACATAAGTA 57.498 33.333 0.00 0.00 0.00 2.24
390 397 8.931385 AATTAGCTGCCACATAAGTAATTTTG 57.069 30.769 0.00 0.00 0.00 2.44
391 398 5.982890 AGCTGCCACATAAGTAATTTTGT 57.017 34.783 0.00 0.00 0.00 2.83
392 399 8.568676 TTAGCTGCCACATAAGTAATTTTGTA 57.431 30.769 0.00 0.00 0.00 2.41
393 400 7.645058 AGCTGCCACATAAGTAATTTTGTAT 57.355 32.000 0.00 0.00 0.00 2.29
394 401 8.066612 AGCTGCCACATAAGTAATTTTGTATT 57.933 30.769 0.00 0.00 0.00 1.89
395 402 7.975616 AGCTGCCACATAAGTAATTTTGTATTG 59.024 33.333 0.00 0.00 0.00 1.90
396 403 7.973388 GCTGCCACATAAGTAATTTTGTATTGA 59.027 33.333 0.00 0.00 0.00 2.57
397 404 9.853555 CTGCCACATAAGTAATTTTGTATTGAA 57.146 29.630 0.00 0.00 0.00 2.69
415 422 9.719355 TGTATTGAAATGTGTGATGTTACTAGT 57.281 29.630 0.00 0.00 0.00 2.57
420 427 9.772973 TGAAATGTGTGATGTTACTAGTTAAGT 57.227 29.630 0.00 0.00 42.62 2.24
444 451 9.915629 AGTTACTTTCATTGTGACTAGTCTAAG 57.084 33.333 23.01 15.11 33.46 2.18
456 463 1.736645 GTCTAAGCACGGCGCAGAA 60.737 57.895 16.26 0.00 46.13 3.02
466 473 0.804544 CGGCGCAGAACTCGGAAATA 60.805 55.000 10.83 0.00 0.00 1.40
521 534 6.566079 AGAGTCCACCAATTCATAATCTGA 57.434 37.500 0.00 0.00 0.00 3.27
555 568 6.364945 TCAGATAGAGACAACATGTACGAG 57.635 41.667 0.00 0.00 0.00 4.18
556 569 5.297029 TCAGATAGAGACAACATGTACGAGG 59.703 44.000 0.00 0.00 0.00 4.63
557 570 5.297029 CAGATAGAGACAACATGTACGAGGA 59.703 44.000 0.00 0.00 0.00 3.71
570 583 2.943653 GAGGAAACAACACGCCCG 59.056 61.111 0.00 0.00 0.00 6.13
681 694 1.302832 CCAGGCAAGTGGACTCACC 60.303 63.158 0.00 0.00 44.64 4.02
692 705 1.131638 GGACTCACCTGCCCATCATA 58.868 55.000 0.00 0.00 35.41 2.15
703 716 1.972872 CCCATCATACTGGTCAAGGC 58.027 55.000 0.00 0.00 34.23 4.35
745 758 4.663334 AGAAAATAACCTTGGTCTCCACC 58.337 43.478 0.00 0.00 44.10 4.61
793 806 2.356135 GGCATCCTTACGAGCAGAAAA 58.644 47.619 0.00 0.00 0.00 2.29
794 807 2.747446 GGCATCCTTACGAGCAGAAAAA 59.253 45.455 0.00 0.00 0.00 1.94
835 848 2.504026 TGATGTGCGAGCGACGTC 60.504 61.111 5.18 5.18 44.60 4.34
1049 1062 1.678425 CCTCTTGCTTCAAGCTCCCTC 60.678 57.143 11.57 0.00 42.97 4.30
1104 1117 1.418908 CCACCCTGACCACTCAAGGT 61.419 60.000 0.00 0.00 41.34 3.50
1194 1207 1.303888 TGTCTACCTCCTCGCCGTT 60.304 57.895 0.00 0.00 0.00 4.44
1196 1209 0.458025 GTCTACCTCCTCGCCGTTTG 60.458 60.000 0.00 0.00 0.00 2.93
1223 1236 1.200020 CAAGATCACCTCCAAAACCGC 59.800 52.381 0.00 0.00 0.00 5.68
1237 1250 4.063967 CCGCTGTCTGGTACGCCA 62.064 66.667 0.00 0.00 43.73 5.69
1238 1251 2.048597 CGCTGTCTGGTACGCCAA 60.049 61.111 0.00 0.00 45.51 4.52
1239 1252 2.380410 CGCTGTCTGGTACGCCAAC 61.380 63.158 0.00 0.00 45.51 3.77
1240 1253 1.301401 GCTGTCTGGTACGCCAACA 60.301 57.895 0.00 0.00 45.51 3.33
1241 1254 1.566018 GCTGTCTGGTACGCCAACAC 61.566 60.000 0.00 0.00 45.51 3.32
1242 1255 0.949105 CTGTCTGGTACGCCAACACC 60.949 60.000 0.00 0.00 45.51 4.16
1243 1256 1.070105 GTCTGGTACGCCAACACCA 59.930 57.895 0.00 0.00 45.51 4.17
1244 1257 0.533308 GTCTGGTACGCCAACACCAA 60.533 55.000 0.00 0.00 45.51 3.67
1245 1258 0.533308 TCTGGTACGCCAACACCAAC 60.533 55.000 0.00 0.00 45.51 3.77
1246 1259 0.816018 CTGGTACGCCAACACCAACA 60.816 55.000 0.00 0.00 45.51 3.33
1247 1260 1.096386 TGGTACGCCAACACCAACAC 61.096 55.000 0.00 0.00 41.83 3.32
1248 1261 1.650363 GTACGCCAACACCAACACC 59.350 57.895 0.00 0.00 0.00 4.16
1260 1273 0.174617 CCAACACCAACACCAACACC 59.825 55.000 0.00 0.00 0.00 4.16
1271 1284 2.723746 CAACACCACACTGCCAGC 59.276 61.111 0.00 0.00 0.00 4.85
1296 1309 4.081030 CAACTGCAGCTCACGCCG 62.081 66.667 15.27 0.00 36.60 6.46
1326 1339 4.704103 TCGCTCCAGGACCCTGCT 62.704 66.667 10.50 0.00 42.35 4.24
1371 1384 1.374252 GACCAACGTCGACCATGCT 60.374 57.895 10.58 0.00 0.00 3.79
1512 1525 2.123428 GCAAAGCCGGCTCATGGAT 61.123 57.895 32.93 10.49 0.00 3.41
1533 1546 2.201921 ACGACTACTCAGCTGGAAGA 57.798 50.000 15.13 0.00 34.07 2.87
1549 1562 4.537936 GGAAGATTCCAAATCAGCGTAC 57.462 45.455 6.74 0.00 46.76 3.67
1553 1566 3.197766 AGATTCCAAATCAGCGTACAGGA 59.802 43.478 2.79 0.00 0.00 3.86
1564 1577 1.299541 CGTACAGGATGATGGCAACC 58.700 55.000 0.00 0.00 39.69 3.77
1590 1603 4.564319 GGTTTTACACCATGGCTGTTCCA 61.564 47.826 20.34 5.22 46.42 3.53
1611 1642 1.420138 TCCCTTTTCCGCTATGATCCC 59.580 52.381 0.00 0.00 0.00 3.85
1691 1722 4.363999 GGCAGCATCTACTACACTACAAG 58.636 47.826 0.00 0.00 0.00 3.16
1699 1730 3.299340 ACTACACTACAAGTTCTGGCG 57.701 47.619 0.00 0.00 0.00 5.69
1705 1736 2.038557 ACTACAAGTTCTGGCGGACAAT 59.961 45.455 0.00 0.00 0.00 2.71
1746 1777 1.371558 GGACTCACCGGCAGACTTT 59.628 57.895 0.00 0.00 0.00 2.66
1826 1857 0.743701 GCAGCTCAGACCAGTGGATG 60.744 60.000 18.40 14.20 0.00 3.51
1853 1884 4.381612 CGCTGAGTGGAAAGTTATGGACTA 60.382 45.833 0.00 0.00 37.72 2.59
1854 1885 4.870991 GCTGAGTGGAAAGTTATGGACTAC 59.129 45.833 0.00 0.00 37.72 2.73
1863 1894 1.411612 GTTATGGACTACCTCCCACGG 59.588 57.143 0.00 0.00 38.49 4.94
1880 1911 0.034059 CGGAACTTCTGTGAGGCTGT 59.966 55.000 0.00 0.00 0.00 4.40
1882 1913 1.070758 GGAACTTCTGTGAGGCTGTCA 59.929 52.381 0.00 0.00 0.00 3.58
1883 1914 2.411904 GAACTTCTGTGAGGCTGTCAG 58.588 52.381 0.00 0.00 35.13 3.51
1927 1958 1.202348 GTGGGTTCAACAGCTATTGCC 59.798 52.381 0.00 0.00 40.80 4.52
1931 1962 1.086696 TTCAACAGCTATTGCCGCTC 58.913 50.000 0.00 0.00 40.80 5.03
1943 1980 1.008538 GCCGCTCCAACACAAACAG 60.009 57.895 0.00 0.00 0.00 3.16
1957 1994 4.133820 CACAAACAGGAGTGTGGAATGTA 58.866 43.478 0.00 0.00 41.19 2.29
1966 2003 2.158534 AGTGTGGAATGTAAGTGCCCAA 60.159 45.455 0.00 0.00 0.00 4.12
1967 2004 2.825532 GTGTGGAATGTAAGTGCCCAAT 59.174 45.455 0.00 0.00 0.00 3.16
2022 2059 3.055891 ACAAAGGTTGCAAGCAAGACTTT 60.056 39.130 28.75 21.72 41.11 2.66
2109 2146 6.013898 TGAACAATATCAATTGGCCTTTTGGA 60.014 34.615 3.32 0.66 45.72 3.53
2122 2159 3.190874 CCTTTTGGAGACTATGAGCGTC 58.809 50.000 0.00 0.00 44.07 5.19
2196 2233 1.001520 TGTGTTGCTGCGGTGTACTAT 59.998 47.619 0.00 0.00 0.00 2.12
2197 2234 1.393539 GTGTTGCTGCGGTGTACTATG 59.606 52.381 0.00 0.00 0.00 2.23
2198 2235 1.006832 GTTGCTGCGGTGTACTATGG 58.993 55.000 0.00 0.00 0.00 2.74
2200 2237 2.237751 GCTGCGGTGTACTATGGCG 61.238 63.158 0.00 0.00 0.00 5.69
2974 3011 2.371841 TCAGACTTTGGCCTAGCAAAGA 59.628 45.455 22.25 0.71 39.91 2.52
3710 3761 3.569701 TCAAACTGGAAGATGCAAGGAAC 59.430 43.478 0.00 0.00 37.43 3.62
3799 3850 4.159693 GGGACATCCACTAAAATTGGAACC 59.840 45.833 0.00 0.61 46.37 3.62
3850 3901 4.158579 ACGACTGAAATGCTAGAGATGTCA 59.841 41.667 0.00 0.00 0.00 3.58
3896 3947 3.426159 CCCATTTGTTACAACTAGCAGCG 60.426 47.826 0.00 0.00 0.00 5.18
4018 4071 6.765036 ACTGGAAATTAGACACTGCATCTATG 59.235 38.462 0.00 0.00 0.00 2.23
4048 4101 8.606040 TTAGTGTAACAGTGGGTATTAACAAC 57.394 34.615 0.00 0.00 41.43 3.32
4146 4202 7.328404 TCATGAGATCTAGTATGGAGAGTCT 57.672 40.000 0.00 0.00 0.00 3.24
4160 4216 3.449018 GGAGAGTCTGGAGCTTTATGTGA 59.551 47.826 0.00 0.00 0.00 3.58
4215 4271 4.644234 TGAACTGCAAAATCAAAGTCAGGA 59.356 37.500 0.00 0.00 0.00 3.86
4372 4428 7.660208 CCATATTTAGAATTAGTAGGCCGTTGT 59.340 37.037 0.00 0.00 0.00 3.32
4392 4448 9.999883 CCGTTGTTTATCTTAGCGTAATAATAC 57.000 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.596338 AAAAACTCCCCCGTGCCG 60.596 61.111 0.00 0.00 0.00 5.69
37 38 3.005367 GGTGGAAGATGAAAGCGGAAAAA 59.995 43.478 0.00 0.00 0.00 1.94
38 39 2.556622 GGTGGAAGATGAAAGCGGAAAA 59.443 45.455 0.00 0.00 0.00 2.29
39 40 2.159382 GGTGGAAGATGAAAGCGGAAA 58.841 47.619 0.00 0.00 0.00 3.13
40 41 1.073125 TGGTGGAAGATGAAAGCGGAA 59.927 47.619 0.00 0.00 0.00 4.30
41 42 0.690192 TGGTGGAAGATGAAAGCGGA 59.310 50.000 0.00 0.00 0.00 5.54
42 43 1.533625 TTGGTGGAAGATGAAAGCGG 58.466 50.000 0.00 0.00 0.00 5.52
43 44 3.191162 TGAATTGGTGGAAGATGAAAGCG 59.809 43.478 0.00 0.00 0.00 4.68
44 45 4.789012 TGAATTGGTGGAAGATGAAAGC 57.211 40.909 0.00 0.00 0.00 3.51
45 46 7.123247 AGGTTATGAATTGGTGGAAGATGAAAG 59.877 37.037 0.00 0.00 0.00 2.62
46 47 6.953520 AGGTTATGAATTGGTGGAAGATGAAA 59.046 34.615 0.00 0.00 0.00 2.69
47 48 6.377996 CAGGTTATGAATTGGTGGAAGATGAA 59.622 38.462 0.00 0.00 0.00 2.57
48 49 5.887598 CAGGTTATGAATTGGTGGAAGATGA 59.112 40.000 0.00 0.00 0.00 2.92
49 50 5.887598 TCAGGTTATGAATTGGTGGAAGATG 59.112 40.000 0.00 0.00 34.02 2.90
88 89 6.666113 TGGTACATGATGTCTTTGGTACTCTA 59.334 38.462 0.00 0.00 33.47 2.43
98 99 4.908601 TCCTTGTGGTACATGATGTCTT 57.091 40.909 0.00 0.00 44.52 3.01
104 105 3.146066 GCTGTTTCCTTGTGGTACATGA 58.854 45.455 0.00 0.00 44.52 3.07
141 142 2.029828 CGGTGTTTCTAGCTCAGTCTGT 60.030 50.000 0.00 0.00 0.00 3.41
171 178 5.949952 TCTATGTTACTCCTCACTGTAAGCA 59.050 40.000 0.00 0.00 37.60 3.91
172 179 6.452494 TCTATGTTACTCCTCACTGTAAGC 57.548 41.667 0.00 0.00 37.60 3.09
173 180 6.095580 TGCTCTATGTTACTCCTCACTGTAAG 59.904 42.308 0.00 0.00 42.29 2.34
174 181 5.949952 TGCTCTATGTTACTCCTCACTGTAA 59.050 40.000 0.00 0.00 0.00 2.41
175 182 5.506708 TGCTCTATGTTACTCCTCACTGTA 58.493 41.667 0.00 0.00 0.00 2.74
176 183 4.344978 TGCTCTATGTTACTCCTCACTGT 58.655 43.478 0.00 0.00 0.00 3.55
177 184 4.400884 ACTGCTCTATGTTACTCCTCACTG 59.599 45.833 0.00 0.00 0.00 3.66
178 185 4.605183 ACTGCTCTATGTTACTCCTCACT 58.395 43.478 0.00 0.00 0.00 3.41
179 186 4.993029 ACTGCTCTATGTTACTCCTCAC 57.007 45.455 0.00 0.00 0.00 3.51
180 187 6.188407 AGTTACTGCTCTATGTTACTCCTCA 58.812 40.000 0.00 0.00 0.00 3.86
181 188 6.702716 AGTTACTGCTCTATGTTACTCCTC 57.297 41.667 0.00 0.00 0.00 3.71
182 189 6.628398 GCAAGTTACTGCTCTATGTTACTCCT 60.628 42.308 0.00 0.00 39.34 3.69
183 190 5.520649 GCAAGTTACTGCTCTATGTTACTCC 59.479 44.000 0.00 0.00 39.34 3.85
184 191 5.520649 GGCAAGTTACTGCTCTATGTTACTC 59.479 44.000 6.72 0.00 42.25 2.59
185 192 5.046591 TGGCAAGTTACTGCTCTATGTTACT 60.047 40.000 6.72 0.00 42.25 2.24
186 193 5.175859 TGGCAAGTTACTGCTCTATGTTAC 58.824 41.667 6.72 0.00 42.25 2.50
187 194 5.414789 TGGCAAGTTACTGCTCTATGTTA 57.585 39.130 6.72 0.00 42.25 2.41
188 195 4.286297 TGGCAAGTTACTGCTCTATGTT 57.714 40.909 6.72 0.00 42.25 2.71
189 196 3.981071 TGGCAAGTTACTGCTCTATGT 57.019 42.857 6.72 0.00 42.25 2.29
190 197 4.637534 ACATTGGCAAGTTACTGCTCTATG 59.362 41.667 5.96 0.00 42.25 2.23
191 198 4.848357 ACATTGGCAAGTTACTGCTCTAT 58.152 39.130 5.96 0.00 42.25 1.98
192 199 4.286297 ACATTGGCAAGTTACTGCTCTA 57.714 40.909 5.96 0.00 42.25 2.43
193 200 3.146104 ACATTGGCAAGTTACTGCTCT 57.854 42.857 5.96 0.00 42.25 4.09
194 201 3.923017 AACATTGGCAAGTTACTGCTC 57.077 42.857 5.96 0.14 42.25 4.26
195 202 4.766404 GTAACATTGGCAAGTTACTGCT 57.234 40.909 27.10 10.47 44.04 4.24
199 206 8.943909 ATAGACTAGTAACATTGGCAAGTTAC 57.056 34.615 27.11 27.11 46.42 2.50
215 222 8.947305 ACTGTGGAGGTAGTAATATAGACTAGT 58.053 37.037 0.00 0.00 30.08 2.57
216 223 9.221933 CACTGTGGAGGTAGTAATATAGACTAG 57.778 40.741 0.00 0.00 30.08 2.57
217 224 8.162085 CCACTGTGGAGGTAGTAATATAGACTA 58.838 40.741 22.33 0.00 40.96 2.59
218 225 7.005296 CCACTGTGGAGGTAGTAATATAGACT 58.995 42.308 22.33 0.00 40.96 3.24
219 226 7.002879 TCCACTGTGGAGGTAGTAATATAGAC 58.997 42.308 25.12 0.00 42.67 2.59
220 227 7.157947 TCCACTGTGGAGGTAGTAATATAGA 57.842 40.000 25.12 0.00 42.67 1.98
235 242 6.925718 CACTCATATGTTACTATCCACTGTGG 59.074 42.308 20.86 20.86 39.43 4.17
236 243 7.492524 ACACTCATATGTTACTATCCACTGTG 58.507 38.462 1.90 0.00 0.00 3.66
237 244 7.661536 ACACTCATATGTTACTATCCACTGT 57.338 36.000 1.90 0.00 0.00 3.55
249 256 9.896645 ACTCTTTCATGATAACACTCATATGTT 57.103 29.630 1.90 0.00 44.87 2.71
250 257 9.896645 AACTCTTTCATGATAACACTCATATGT 57.103 29.630 1.90 0.00 34.11 2.29
282 289 9.610705 CAATGCATAATGAGTCTATAGCCTAAT 57.389 33.333 0.00 0.00 0.00 1.73
283 290 8.815912 TCAATGCATAATGAGTCTATAGCCTAA 58.184 33.333 0.00 0.00 0.00 2.69
284 291 8.366359 TCAATGCATAATGAGTCTATAGCCTA 57.634 34.615 0.00 0.00 0.00 3.93
285 292 7.250032 TCAATGCATAATGAGTCTATAGCCT 57.750 36.000 0.00 0.00 0.00 4.58
286 293 7.912056 TTCAATGCATAATGAGTCTATAGCC 57.088 36.000 0.00 0.00 0.00 3.93
287 294 9.770503 CATTTCAATGCATAATGAGTCTATAGC 57.229 33.333 13.25 0.00 32.36 2.97
290 297 9.128404 ACACATTTCAATGCATAATGAGTCTAT 57.872 29.630 21.86 5.19 40.04 1.98
291 298 8.400186 CACACATTTCAATGCATAATGAGTCTA 58.600 33.333 21.86 0.00 40.04 2.59
292 299 7.121611 TCACACATTTCAATGCATAATGAGTCT 59.878 33.333 21.86 2.76 40.04 3.24
293 300 7.252708 TCACACATTTCAATGCATAATGAGTC 58.747 34.615 21.86 0.00 40.04 3.36
294 301 7.160547 TCACACATTTCAATGCATAATGAGT 57.839 32.000 21.86 17.98 40.04 3.41
295 302 7.704899 ACATCACACATTTCAATGCATAATGAG 59.295 33.333 21.86 17.47 40.04 2.90
296 303 7.548967 ACATCACACATTTCAATGCATAATGA 58.451 30.769 21.86 11.49 40.04 2.57
297 304 7.764695 ACATCACACATTTCAATGCATAATG 57.235 32.000 15.89 15.89 40.04 1.90
298 305 9.304731 GTAACATCACACATTTCAATGCATAAT 57.695 29.630 0.00 0.00 40.04 1.28
299 306 8.302438 TGTAACATCACACATTTCAATGCATAA 58.698 29.630 0.00 0.00 40.04 1.90
300 307 7.824672 TGTAACATCACACATTTCAATGCATA 58.175 30.769 0.00 0.00 40.04 3.14
301 308 6.689554 TGTAACATCACACATTTCAATGCAT 58.310 32.000 0.00 0.00 40.04 3.96
302 309 6.081872 TGTAACATCACACATTTCAATGCA 57.918 33.333 0.00 0.00 40.04 3.96
303 310 6.151691 ACTGTAACATCACACATTTCAATGC 58.848 36.000 0.00 0.00 40.04 3.56
304 311 9.117145 GTTACTGTAACATCACACATTTCAATG 57.883 33.333 22.30 0.00 39.09 2.82
305 312 9.066892 AGTTACTGTAACATCACACATTTCAAT 57.933 29.630 27.12 3.45 41.07 2.57
306 313 8.445275 AGTTACTGTAACATCACACATTTCAA 57.555 30.769 27.12 0.00 41.07 2.69
307 314 8.984764 GTAGTTACTGTAACATCACACATTTCA 58.015 33.333 27.12 0.00 41.07 2.69
308 315 8.440833 GGTAGTTACTGTAACATCACACATTTC 58.559 37.037 27.12 6.28 41.07 2.17
309 316 8.154856 AGGTAGTTACTGTAACATCACACATTT 58.845 33.333 27.12 9.43 41.07 2.32
310 317 7.676947 AGGTAGTTACTGTAACATCACACATT 58.323 34.615 27.12 10.04 41.07 2.71
311 318 7.241042 AGGTAGTTACTGTAACATCACACAT 57.759 36.000 27.12 13.91 41.07 3.21
312 319 6.659745 AGGTAGTTACTGTAACATCACACA 57.340 37.500 27.12 5.66 41.07 3.72
313 320 8.302438 ACTTAGGTAGTTACTGTAACATCACAC 58.698 37.037 27.12 17.04 41.07 3.82
314 321 8.413309 ACTTAGGTAGTTACTGTAACATCACA 57.587 34.615 27.12 10.61 41.07 3.58
327 334 6.239858 GGGGTTTGTGGTAACTTAGGTAGTTA 60.240 42.308 0.00 0.00 45.22 2.24
329 336 4.042062 GGGGTTTGTGGTAACTTAGGTAGT 59.958 45.833 0.00 0.00 39.32 2.73
330 337 4.287845 AGGGGTTTGTGGTAACTTAGGTAG 59.712 45.833 0.00 0.00 37.61 3.18
331 338 4.241981 AGGGGTTTGTGGTAACTTAGGTA 58.758 43.478 0.00 0.00 37.61 3.08
332 339 3.058341 AGGGGTTTGTGGTAACTTAGGT 58.942 45.455 0.00 0.00 37.61 3.08
333 340 3.329814 AGAGGGGTTTGTGGTAACTTAGG 59.670 47.826 0.00 0.00 37.61 2.69
334 341 4.286291 AGAGAGGGGTTTGTGGTAACTTAG 59.714 45.833 0.00 0.00 37.61 2.18
335 342 4.237018 AGAGAGGGGTTTGTGGTAACTTA 58.763 43.478 0.00 0.00 37.61 2.24
336 343 3.053826 AGAGAGGGGTTTGTGGTAACTT 58.946 45.455 0.00 0.00 37.61 2.66
337 344 2.638363 GAGAGAGGGGTTTGTGGTAACT 59.362 50.000 0.00 0.00 37.61 2.24
338 345 2.290134 GGAGAGAGGGGTTTGTGGTAAC 60.290 54.545 0.00 0.00 0.00 2.50
339 346 1.982958 GGAGAGAGGGGTTTGTGGTAA 59.017 52.381 0.00 0.00 0.00 2.85
340 347 1.151413 AGGAGAGAGGGGTTTGTGGTA 59.849 52.381 0.00 0.00 0.00 3.25
341 348 0.104409 AGGAGAGAGGGGTTTGTGGT 60.104 55.000 0.00 0.00 0.00 4.16
342 349 1.068121 AAGGAGAGAGGGGTTTGTGG 58.932 55.000 0.00 0.00 0.00 4.17
343 350 4.576330 AATAAGGAGAGAGGGGTTTGTG 57.424 45.455 0.00 0.00 0.00 3.33
344 351 6.910259 ATTAATAAGGAGAGAGGGGTTTGT 57.090 37.500 0.00 0.00 0.00 2.83
345 352 7.445707 GCTAATTAATAAGGAGAGAGGGGTTTG 59.554 40.741 0.00 0.00 0.00 2.93
346 353 7.351187 AGCTAATTAATAAGGAGAGAGGGGTTT 59.649 37.037 0.00 0.00 0.00 3.27
347 354 6.852372 AGCTAATTAATAAGGAGAGAGGGGTT 59.148 38.462 0.00 0.00 0.00 4.11
348 355 6.271159 CAGCTAATTAATAAGGAGAGAGGGGT 59.729 42.308 0.00 0.00 0.00 4.95
349 356 6.706295 CAGCTAATTAATAAGGAGAGAGGGG 58.294 44.000 0.00 0.00 0.00 4.79
350 357 6.169800 GCAGCTAATTAATAAGGAGAGAGGG 58.830 44.000 0.00 0.00 0.00 4.30
351 358 6.169800 GGCAGCTAATTAATAAGGAGAGAGG 58.830 44.000 0.00 0.00 0.00 3.69
352 359 6.648725 GTGGCAGCTAATTAATAAGGAGAGAG 59.351 42.308 0.00 0.00 0.00 3.20
353 360 6.099701 TGTGGCAGCTAATTAATAAGGAGAGA 59.900 38.462 0.00 0.00 0.00 3.10
354 361 6.291377 TGTGGCAGCTAATTAATAAGGAGAG 58.709 40.000 0.00 0.00 0.00 3.20
355 362 6.247229 TGTGGCAGCTAATTAATAAGGAGA 57.753 37.500 0.00 0.00 0.00 3.71
356 363 8.621532 TTATGTGGCAGCTAATTAATAAGGAG 57.378 34.615 0.00 0.00 0.00 3.69
357 364 8.217799 ACTTATGTGGCAGCTAATTAATAAGGA 58.782 33.333 16.08 0.00 32.95 3.36
358 365 8.396272 ACTTATGTGGCAGCTAATTAATAAGG 57.604 34.615 16.08 5.11 32.95 2.69
365 372 8.531146 ACAAAATTACTTATGTGGCAGCTAATT 58.469 29.630 0.00 0.00 0.00 1.40
366 373 8.066612 ACAAAATTACTTATGTGGCAGCTAAT 57.933 30.769 0.00 0.00 0.00 1.73
367 374 7.461182 ACAAAATTACTTATGTGGCAGCTAA 57.539 32.000 0.00 0.00 0.00 3.09
368 375 8.746052 ATACAAAATTACTTATGTGGCAGCTA 57.254 30.769 0.00 0.00 0.00 3.32
369 376 5.982890 ACAAAATTACTTATGTGGCAGCT 57.017 34.783 0.00 0.00 0.00 4.24
370 377 7.973388 TCAATACAAAATTACTTATGTGGCAGC 59.027 33.333 0.00 0.00 0.00 5.25
371 378 9.853555 TTCAATACAAAATTACTTATGTGGCAG 57.146 29.630 0.00 0.00 0.00 4.85
389 396 9.719355 ACTAGTAACATCACACATTTCAATACA 57.281 29.630 0.00 0.00 0.00 2.29
394 401 9.772973 ACTTAACTAGTAACATCACACATTTCA 57.227 29.630 0.00 0.00 34.56 2.69
418 425 9.915629 CTTAGACTAGTCACAATGAAAGTAACT 57.084 33.333 24.44 0.80 28.57 2.24
419 426 8.648968 GCTTAGACTAGTCACAATGAAAGTAAC 58.351 37.037 24.44 3.02 28.57 2.50
420 427 8.364894 TGCTTAGACTAGTCACAATGAAAGTAA 58.635 33.333 24.44 9.17 28.57 2.24
421 428 7.813148 GTGCTTAGACTAGTCACAATGAAAGTA 59.187 37.037 24.44 11.61 28.57 2.24
422 429 6.647067 GTGCTTAGACTAGTCACAATGAAAGT 59.353 38.462 24.44 2.59 30.37 2.66
423 430 6.183360 CGTGCTTAGACTAGTCACAATGAAAG 60.183 42.308 24.44 14.78 0.00 2.62
424 431 5.633601 CGTGCTTAGACTAGTCACAATGAAA 59.366 40.000 24.44 6.31 0.00 2.69
425 432 5.161358 CGTGCTTAGACTAGTCACAATGAA 58.839 41.667 24.44 7.67 0.00 2.57
426 433 4.380550 CCGTGCTTAGACTAGTCACAATGA 60.381 45.833 24.44 0.10 0.00 2.57
427 434 3.859961 CCGTGCTTAGACTAGTCACAATG 59.140 47.826 24.44 12.10 0.00 2.82
428 435 3.676324 GCCGTGCTTAGACTAGTCACAAT 60.676 47.826 24.44 6.62 0.00 2.71
429 436 2.352421 GCCGTGCTTAGACTAGTCACAA 60.352 50.000 24.44 15.86 0.00 3.33
430 437 1.201647 GCCGTGCTTAGACTAGTCACA 59.798 52.381 24.44 13.55 0.00 3.58
431 438 1.794437 CGCCGTGCTTAGACTAGTCAC 60.794 57.143 24.44 12.84 0.00 3.67
432 439 0.450583 CGCCGTGCTTAGACTAGTCA 59.549 55.000 24.44 8.16 0.00 3.41
433 440 0.866483 GCGCCGTGCTTAGACTAGTC 60.866 60.000 15.41 15.41 41.73 2.59
434 441 1.139095 GCGCCGTGCTTAGACTAGT 59.861 57.895 0.00 0.00 41.73 2.57
435 442 0.867753 CTGCGCCGTGCTTAGACTAG 60.868 60.000 4.18 0.00 46.63 2.57
436 443 1.138883 CTGCGCCGTGCTTAGACTA 59.861 57.895 4.18 0.00 46.63 2.59
437 444 2.125912 CTGCGCCGTGCTTAGACT 60.126 61.111 4.18 0.00 46.63 3.24
438 445 1.736645 TTCTGCGCCGTGCTTAGAC 60.737 57.895 4.18 0.00 46.63 2.59
439 446 1.736645 GTTCTGCGCCGTGCTTAGA 60.737 57.895 4.18 0.00 46.63 2.10
440 447 1.687494 GAGTTCTGCGCCGTGCTTAG 61.687 60.000 4.18 0.00 46.63 2.18
441 448 1.736645 GAGTTCTGCGCCGTGCTTA 60.737 57.895 4.18 0.00 46.63 3.09
442 449 3.044305 GAGTTCTGCGCCGTGCTT 61.044 61.111 4.18 0.00 46.63 3.91
456 463 3.947910 TCGGTCAAGTTATTTCCGAGT 57.052 42.857 0.00 0.00 44.04 4.18
460 467 4.392138 CCAAGACTCGGTCAAGTTATTTCC 59.608 45.833 6.78 0.00 34.60 3.13
466 473 1.810412 GCACCAAGACTCGGTCAAGTT 60.810 52.381 6.78 0.00 33.25 2.66
521 534 8.097038 TGTTGTCTCTATCTGAGCTATGTTTTT 58.903 33.333 0.00 0.00 42.38 1.94
529 542 5.220951 CGTACATGTTGTCTCTATCTGAGCT 60.221 44.000 2.30 0.00 42.38 4.09
555 568 4.337060 GGCGGGCGTGTTGTTTCC 62.337 66.667 0.00 0.00 0.00 3.13
556 569 4.337060 GGGCGGGCGTGTTGTTTC 62.337 66.667 0.00 0.00 0.00 2.78
583 596 0.796927 GCCGGTGTTTCTAGTTCAGC 59.203 55.000 1.90 0.00 0.00 4.26
692 705 0.251922 AATGCATGGCCTTGACCAGT 60.252 50.000 22.21 7.97 44.71 4.00
703 716 3.191791 TCTTGTGTGATGTGAATGCATGG 59.808 43.478 0.00 0.00 0.00 3.66
745 758 0.038343 CAGGTTTTGATTGGCACCCG 60.038 55.000 0.00 0.00 0.00 5.28
793 806 2.484889 GGAGAGTTGACGAGCAAGTTT 58.515 47.619 0.00 0.00 40.20 2.66
794 807 1.603172 CGGAGAGTTGACGAGCAAGTT 60.603 52.381 0.00 0.00 40.20 2.66
795 808 0.039074 CGGAGAGTTGACGAGCAAGT 60.039 55.000 0.00 0.00 42.75 3.16
799 812 0.171455 ACATCGGAGAGTTGACGAGC 59.829 55.000 0.00 0.00 43.63 5.03
835 848 8.119226 GCAGTTTTATCTATGTTGAGCAGTTAG 58.881 37.037 0.00 0.00 0.00 2.34
964 977 3.005791 GCTGTTGCTTCTGGTAATGGTTT 59.994 43.478 0.00 0.00 36.03 3.27
1167 1180 1.385756 GGAGGTAGACAGAGGCGTCC 61.386 65.000 2.06 0.00 36.52 4.79
1194 1207 2.289444 GGAGGTGATCTTGTCGAACCAA 60.289 50.000 3.21 0.00 0.00 3.67
1196 1209 1.275291 TGGAGGTGATCTTGTCGAACC 59.725 52.381 0.00 0.00 0.00 3.62
1237 1250 1.273886 GTTGGTGTTGGTGTTGGTGTT 59.726 47.619 0.00 0.00 0.00 3.32
1238 1251 0.892063 GTTGGTGTTGGTGTTGGTGT 59.108 50.000 0.00 0.00 0.00 4.16
1239 1252 0.891373 TGTTGGTGTTGGTGTTGGTG 59.109 50.000 0.00 0.00 0.00 4.17
1240 1253 0.892063 GTGTTGGTGTTGGTGTTGGT 59.108 50.000 0.00 0.00 0.00 3.67
1241 1254 0.174617 GGTGTTGGTGTTGGTGTTGG 59.825 55.000 0.00 0.00 0.00 3.77
1242 1255 0.891373 TGGTGTTGGTGTTGGTGTTG 59.109 50.000 0.00 0.00 0.00 3.33
1243 1256 0.892063 GTGGTGTTGGTGTTGGTGTT 59.108 50.000 0.00 0.00 0.00 3.32
1244 1257 0.251386 TGTGGTGTTGGTGTTGGTGT 60.251 50.000 0.00 0.00 0.00 4.16
1245 1258 0.172352 GTGTGGTGTTGGTGTTGGTG 59.828 55.000 0.00 0.00 0.00 4.17
1246 1259 0.039035 AGTGTGGTGTTGGTGTTGGT 59.961 50.000 0.00 0.00 0.00 3.67
1247 1260 0.455410 CAGTGTGGTGTTGGTGTTGG 59.545 55.000 0.00 0.00 0.00 3.77
1248 1261 0.179140 GCAGTGTGGTGTTGGTGTTG 60.179 55.000 0.00 0.00 0.00 3.33
1326 1339 1.490490 GGGTTCCATATCTCTGTGCCA 59.510 52.381 0.00 0.00 0.00 4.92
1371 1384 2.046988 CCTGTGTCGAGCATGGCA 60.047 61.111 0.00 0.00 0.00 4.92
1512 1525 3.682696 TCTTCCAGCTGAGTAGTCGTTA 58.317 45.455 17.39 0.00 0.00 3.18
1533 1546 3.627395 TCCTGTACGCTGATTTGGAAT 57.373 42.857 0.00 0.00 0.00 3.01
1540 1553 1.270518 GCCATCATCCTGTACGCTGAT 60.271 52.381 0.00 0.00 0.00 2.90
1549 1562 2.092212 ACCTTAGGTTGCCATCATCCTG 60.092 50.000 0.00 0.00 41.32 3.86
1553 1566 5.185056 GTGTAAAACCTTAGGTTGCCATCAT 59.815 40.000 18.22 0.00 46.20 2.45
1564 1577 8.232087 GGAACAGCCATGGTGTAAAACCTTAG 62.232 46.154 14.67 0.00 43.73 2.18
1590 1603 2.040412 GGGATCATAGCGGAAAAGGGAT 59.960 50.000 0.00 0.00 0.00 3.85
1627 1658 3.593442 TGAACCATTTCCACCAGTCTT 57.407 42.857 0.00 0.00 0.00 3.01
1629 1660 2.029918 GCTTGAACCATTTCCACCAGTC 60.030 50.000 0.00 0.00 0.00 3.51
1668 1699 2.357952 TGTAGTGTAGTAGATGCTGCCG 59.642 50.000 0.00 0.00 0.00 5.69
1691 1722 4.900635 ATATTGAATTGTCCGCCAGAAC 57.099 40.909 0.00 0.00 0.00 3.01
1705 1736 8.946085 GTCCAGTGTTTCTGATGTAATATTGAA 58.054 33.333 0.00 0.00 46.27 2.69
1728 1759 0.250338 AAAAGTCTGCCGGTGAGTCC 60.250 55.000 1.90 0.00 0.00 3.85
1767 1798 1.746615 CCTGAACACCCCATCTGCG 60.747 63.158 0.00 0.00 0.00 5.18
1826 1857 1.594331 AACTTTCCACTCAGCGTTCC 58.406 50.000 0.00 0.00 0.00 3.62
1831 1862 3.944087 AGTCCATAACTTTCCACTCAGC 58.056 45.455 0.00 0.00 33.03 4.26
1833 1864 5.091552 AGGTAGTCCATAACTTTCCACTCA 58.908 41.667 0.00 0.00 39.55 3.41
1853 1884 0.763223 ACAGAAGTTCCGTGGGAGGT 60.763 55.000 0.00 0.00 31.21 3.85
1854 1885 0.320771 CACAGAAGTTCCGTGGGAGG 60.321 60.000 10.85 0.00 31.21 4.30
1863 1894 2.411904 CTGACAGCCTCACAGAAGTTC 58.588 52.381 0.00 0.00 34.07 3.01
1873 1904 1.107945 GTCTCTACCCTGACAGCCTC 58.892 60.000 0.00 0.00 33.75 4.70
1874 1905 0.707616 AGTCTCTACCCTGACAGCCT 59.292 55.000 0.00 0.00 35.81 4.58
1880 1911 2.557676 CCACTTCCAGTCTCTACCCTGA 60.558 54.545 0.00 0.00 0.00 3.86
1882 1913 1.433592 ACCACTTCCAGTCTCTACCCT 59.566 52.381 0.00 0.00 0.00 4.34
1883 1914 1.550976 CACCACTTCCAGTCTCTACCC 59.449 57.143 0.00 0.00 0.00 3.69
1927 1958 0.588252 CTCCTGTTTGTGTTGGAGCG 59.412 55.000 0.00 0.00 39.46 5.03
1931 1962 1.405105 CCACACTCCTGTTTGTGTTGG 59.595 52.381 0.00 0.00 43.88 3.77
1943 1980 2.084546 GGCACTTACATTCCACACTCC 58.915 52.381 0.00 0.00 0.00 3.85
1957 1994 6.245408 TGAATGAGTAGTTTATTGGGCACTT 58.755 36.000 0.00 0.00 0.00 3.16
1966 2003 7.255569 TCGTTGTCGATGAATGAGTAGTTTAT 58.744 34.615 0.00 0.00 41.35 1.40
1967 2004 6.614160 TCGTTGTCGATGAATGAGTAGTTTA 58.386 36.000 0.00 0.00 41.35 2.01
1995 2032 1.746220 TGCTTGCAACCTTTGTACGTT 59.254 42.857 0.00 0.00 0.00 3.99
1997 2034 2.032799 TCTTGCTTGCAACCTTTGTACG 59.967 45.455 3.70 0.00 0.00 3.67
2109 2146 0.457851 GGCTGTGACGCTCATAGTCT 59.542 55.000 11.30 0.00 37.27 3.24
2122 2159 1.679977 CCTCACCAATGGGGCTGTG 60.680 63.158 3.55 0.00 40.56 3.66
2196 2233 0.753479 TTTTCCAGCAAGAACCGCCA 60.753 50.000 0.00 0.00 0.00 5.69
2197 2234 0.387565 TTTTTCCAGCAAGAACCGCC 59.612 50.000 0.00 0.00 0.00 6.13
2198 2235 1.336755 TCTTTTTCCAGCAAGAACCGC 59.663 47.619 0.00 0.00 0.00 5.68
2200 2237 3.222603 TCCTCTTTTTCCAGCAAGAACC 58.777 45.455 0.00 0.00 0.00 3.62
2248 2285 8.877864 TTGATAAAAACTGATCCCACTATGTT 57.122 30.769 0.00 0.00 0.00 2.71
2974 3011 3.244665 TGTGTCTGATTTGTCCTGAGCAT 60.245 43.478 0.00 0.00 0.00 3.79
3075 3112 6.542370 AGATCACCCCAAAACTATAAATGTCG 59.458 38.462 0.00 0.00 0.00 4.35
3256 3293 2.746277 GGCCACGAAGCGTTCCAT 60.746 61.111 0.00 0.00 38.32 3.41
3500 3550 6.245408 ACTTACATTCCTGCTTCCATTTACA 58.755 36.000 0.00 0.00 0.00 2.41
3710 3761 1.964891 CTGCACTGCACCTCACTGG 60.965 63.158 0.00 0.00 42.93 4.00
3722 3773 0.036875 GTTCCTAACCAGCCTGCACT 59.963 55.000 0.00 0.00 0.00 4.40
3896 3947 2.092323 GTAAAGCAACATGGGAGTCCC 58.908 52.381 22.54 22.54 45.71 4.46
3965 4017 8.137437 ACATAAAACACTGGATAATGCTAATGC 58.863 33.333 0.00 0.00 40.20 3.56
4018 4071 6.812879 ATACCCACTGTTACACTAAAAAGC 57.187 37.500 0.00 0.00 0.00 3.51
4048 4101 9.138062 CATTCAATATCTAGAGTCCAATTCTCG 57.862 37.037 0.00 0.00 37.07 4.04
4146 4202 9.507329 GAATAAGGAATATCACATAAAGCTCCA 57.493 33.333 0.00 0.00 0.00 3.86
4215 4271 5.653769 AGGACATATTTGTAAGCATGTTGCT 59.346 36.000 0.00 0.00 46.53 3.91
4372 4428 9.918630 GGAGGTGTATTATTACGCTAAGATAAA 57.081 33.333 7.94 0.00 38.59 1.40


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

AutoCloner maintained by Alex Coulton.