Multiple sequence alignment - TraesCS3B01G245300

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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 TraesCS3B01G245300 chr3B 100.000 4283 0 0 1 4283 389259326 389263608 0.000000e+00 7910.0
1 TraesCS3B01G245300 chr3B 87.755 147 14 3 302 445 478986781 478986926 7.370000e-38 169.0
2 TraesCS3B01G245300 chr3B 85.227 88 6 2 159 246 714048548 714048628 2.740000e-12 84.2
3 TraesCS3B01G245300 chr3B 85.227 88 6 2 159 246 714106423 714106503 2.740000e-12 84.2
4 TraesCS3B01G245300 chr3D 98.160 2011 37 0 1357 3367 295141500 295143510 0.000000e+00 3509.0
5 TraesCS3B01G245300 chr3D 95.444 878 25 6 3415 4279 295143489 295144364 0.000000e+00 1386.0
6 TraesCS3B01G245300 chr3D 94.432 880 24 11 484 1356 295140461 295141322 0.000000e+00 1330.0
7 TraesCS3B01G245300 chr3D 89.189 148 10 5 302 445 595108431 595108576 3.400000e-41 180.0
8 TraesCS3B01G245300 chr3D 87.838 148 12 3 301 445 384654496 384654352 7.370000e-38 169.0
9 TraesCS3B01G245300 chr3D 80.745 161 20 8 6 155 295140157 295140317 9.730000e-22 115.0
10 TraesCS3B01G245300 chr3D 92.063 63 5 0 181 243 508385267 508385205 5.900000e-14 89.8
11 TraesCS3B01G245300 chr3D 85.882 85 6 3 159 243 228297098 228297176 7.630000e-13 86.1
12 TraesCS3B01G245300 chr3D 85.714 84 6 4 159 242 490039691 490039614 2.740000e-12 84.2
13 TraesCS3B01G245300 chr3A 97.315 2011 54 0 1357 3367 392800198 392802208 0.000000e+00 3415.0
14 TraesCS3B01G245300 chr3A 97.015 871 24 2 3415 4283 392802187 392803057 0.000000e+00 1463.0
15 TraesCS3B01G245300 chr3A 93.439 442 15 5 919 1356 392799589 392800020 1.000000e-180 643.0
16 TraesCS3B01G245300 chr3A 81.818 143 18 5 529 669 392781826 392781962 3.500000e-21 113.0
17 TraesCS3B01G245300 chrUn 92.424 132 9 1 314 445 57550167 57550037 2.030000e-43 187.0
18 TraesCS3B01G245300 chr7B 90.909 132 10 2 314 445 722225199 722225070 4.400000e-40 176.0
19 TraesCS3B01G245300 chr7B 86.486 74 10 0 181 254 618673663 618673590 9.870000e-12 82.4
20 TraesCS3B01G245300 chr2A 90.909 132 10 2 314 445 279427797 279427926 4.400000e-40 176.0
21 TraesCS3B01G245300 chr4B 88.514 148 11 5 302 445 152734084 152734229 1.580000e-39 174.0
22 TraesCS3B01G245300 chr2B 90.152 132 12 1 314 445 658489644 658489774 2.050000e-38 171.0
23 TraesCS3B01G245300 chr2B 86.486 74 10 0 181 254 215034855 215034782 9.870000e-12 82.4
24 TraesCS3B01G245300 chr7D 87.755 147 13 5 302 445 595719583 595719439 2.650000e-37 167.0
25 TraesCS3B01G245300 chr2D 86.047 86 6 4 159 244 206685573 206685652 2.120000e-13 87.9
26 TraesCS3B01G245300 chr6B 89.231 65 7 0 181 245 246296646 246296710 9.870000e-12 82.4


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 TraesCS3B01G245300 chr3B 389259326 389263608 4282 False 7910.000000 7910 100.00000 1 4283 1 chr3B.!!$F1 4282
1 TraesCS3B01G245300 chr3D 295140157 295144364 4207 False 1585.000000 3509 92.19525 6 4279 4 chr3D.!!$F3 4273
2 TraesCS3B01G245300 chr3A 392799589 392803057 3468 False 1840.333333 3415 95.92300 919 4283 3 chr3A.!!$F2 3364

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
312 331 0.033011 ATGCCGTCTACTCCCTCTGT 60.033 55.0 0.00 0.0 0.00 3.41 F
313 332 0.251653 TGCCGTCTACTCCCTCTGTT 60.252 55.0 0.00 0.0 0.00 3.16 F
542 561 0.251916 TACCCTTGGGTGAAGATGCG 59.748 55.0 20.78 0.0 32.82 4.73 F
1362 1573 0.462937 CACACAGGGACGTTGGTCAA 60.463 55.0 0.00 0.0 45.28 3.18 F
1509 1720 1.022735 CATGGAATGCTCTGCTCACC 58.977 55.0 0.00 0.0 37.62 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1987 1.135603 CAATGCACCACATCAGGTTCG 60.136 52.381 0.00 0.0 40.77 3.95 R
1967 2178 1.202405 CCAGCCCACTTTTCACAACAC 60.202 52.381 0.00 0.0 0.00 3.32 R
2536 2747 0.749454 CCACTGCCTAAGGATGCCAC 60.749 60.000 0.00 0.0 0.00 5.01 R
2607 2818 3.056250 ACATGTCAACTAGAGCACCAGAG 60.056 47.826 0.00 0.0 0.00 3.35 R
3419 3630 1.786937 CCAGCTCCTGGTCTCATAGT 58.213 55.000 3.09 0.0 45.82 2.12 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
26 27 5.097529 CGTTTATTTGTCGTACCAGAGCTA 58.902 41.667 0.00 0.00 0.00 3.32
32 33 2.496070 TGTCGTACCAGAGCTAGCAAAT 59.504 45.455 18.83 0.00 0.00 2.32
97 114 4.218200 TGGTTCAACAATCAACATAGGCAG 59.782 41.667 0.00 0.00 0.00 4.85
105 122 5.183904 ACAATCAACATAGGCAGTTTCCTTC 59.816 40.000 0.00 0.00 37.66 3.46
130 149 8.977505 TCTCTCTGAAAACAAAACAAAACTTTG 58.022 29.630 0.60 0.60 43.62 2.77
133 152 6.484977 TCTGAAAACAAAACAAAACTTTGCCT 59.515 30.769 2.07 0.00 41.79 4.75
148 167 2.943978 GCCTGTAGGTGGCTGTCGT 61.944 63.158 0.00 0.00 46.38 4.34
155 174 0.818296 AGGTGGCTGTCGTGATCTAC 59.182 55.000 0.00 0.00 0.00 2.59
157 176 1.202313 GGTGGCTGTCGTGATCTACTC 60.202 57.143 0.00 0.00 0.00 2.59
159 178 2.943690 GTGGCTGTCGTGATCTACTCTA 59.056 50.000 0.00 0.00 0.00 2.43
160 179 3.002862 GTGGCTGTCGTGATCTACTCTAG 59.997 52.174 0.00 0.00 0.00 2.43
161 180 3.118371 TGGCTGTCGTGATCTACTCTAGA 60.118 47.826 0.00 0.00 39.50 2.43
163 182 4.083537 GGCTGTCGTGATCTACTCTAGATG 60.084 50.000 0.00 0.00 45.16 2.90
164 183 4.752604 GCTGTCGTGATCTACTCTAGATGA 59.247 45.833 0.00 0.00 45.16 2.92
165 184 5.333798 GCTGTCGTGATCTACTCTAGATGAC 60.334 48.000 0.00 0.00 45.16 3.06
167 186 5.986741 TGTCGTGATCTACTCTAGATGACTC 59.013 44.000 0.00 2.58 44.11 3.36
169 188 6.480651 GTCGTGATCTACTCTAGATGACTCAA 59.519 42.308 0.00 0.00 44.11 3.02
170 189 6.480651 TCGTGATCTACTCTAGATGACTCAAC 59.519 42.308 0.00 0.00 44.11 3.18
172 191 7.011950 CGTGATCTACTCTAGATGACTCAACTT 59.988 40.741 0.00 0.00 44.11 2.66
174 193 8.681806 TGATCTACTCTAGATGACTCAACTTTG 58.318 37.037 0.00 0.00 45.16 2.77
175 194 8.588290 ATCTACTCTAGATGACTCAACTTTGT 57.412 34.615 0.00 0.00 43.59 2.83
176 195 9.688091 ATCTACTCTAGATGACTCAACTTTGTA 57.312 33.333 0.00 0.00 43.59 2.41
177 196 8.948145 TCTACTCTAGATGACTCAACTTTGTAC 58.052 37.037 0.00 0.00 0.00 2.90
179 198 8.865420 ACTCTAGATGACTCAACTTTGTACTA 57.135 34.615 0.00 0.00 0.00 1.82
180 199 8.952278 ACTCTAGATGACTCAACTTTGTACTAG 58.048 37.037 0.00 0.00 0.00 2.57
182 201 8.948145 TCTAGATGACTCAACTTTGTACTAGAC 58.052 37.037 0.00 0.00 31.38 2.59
183 202 7.768807 AGATGACTCAACTTTGTACTAGACT 57.231 36.000 0.00 0.00 0.00 3.24
184 203 7.822658 AGATGACTCAACTTTGTACTAGACTC 58.177 38.462 0.00 0.00 0.00 3.36
185 204 6.954487 TGACTCAACTTTGTACTAGACTCA 57.046 37.500 0.00 0.00 0.00 3.41
186 205 7.342769 TGACTCAACTTTGTACTAGACTCAA 57.657 36.000 0.00 0.00 0.00 3.02
187 206 7.201145 TGACTCAACTTTGTACTAGACTCAAC 58.799 38.462 0.00 0.00 0.00 3.18
189 208 7.783042 ACTCAACTTTGTACTAGACTCAACTT 58.217 34.615 0.00 0.00 0.00 2.66
191 210 8.420374 TCAACTTTGTACTAGACTCAACTTTG 57.580 34.615 0.00 5.16 0.00 2.77
192 211 8.038944 TCAACTTTGTACTAGACTCAACTTTGT 58.961 33.333 0.00 0.00 0.00 2.83
193 212 9.309516 CAACTTTGTACTAGACTCAACTTTGTA 57.690 33.333 0.00 0.00 0.00 2.41
194 213 8.868635 ACTTTGTACTAGACTCAACTTTGTAC 57.131 34.615 0.00 0.00 33.62 2.90
195 214 8.693625 ACTTTGTACTAGACTCAACTTTGTACT 58.306 33.333 0.00 0.00 33.87 2.73
204 223 8.747538 AGACTCAACTTTGTACTAAATTTGGT 57.252 30.769 12.16 12.16 0.00 3.67
205 224 9.841295 AGACTCAACTTTGTACTAAATTTGGTA 57.159 29.630 10.08 10.08 0.00 3.25
206 225 9.874215 GACTCAACTTTGTACTAAATTTGGTAC 57.126 33.333 28.40 28.40 43.06 3.34
227 246 8.783093 TGGTACAAAGTTGAGTCATCTATTTTG 58.217 33.333 4.14 8.00 40.82 2.44
229 248 7.823745 ACAAAGTTGAGTCATCTATTTTGGT 57.176 32.000 14.35 0.00 40.00 3.67
230 249 8.237811 ACAAAGTTGAGTCATCTATTTTGGTT 57.762 30.769 14.35 0.06 40.00 3.67
231 250 9.349713 ACAAAGTTGAGTCATCTATTTTGGTTA 57.650 29.630 14.35 0.00 40.00 2.85
233 252 8.567285 AAGTTGAGTCATCTATTTTGGTTAGG 57.433 34.615 4.14 0.00 0.00 2.69
234 253 7.112779 AGTTGAGTCATCTATTTTGGTTAGGG 58.887 38.462 1.70 0.00 0.00 3.53
235 254 6.001449 TGAGTCATCTATTTTGGTTAGGGG 57.999 41.667 0.00 0.00 0.00 4.79
236 255 5.104109 TGAGTCATCTATTTTGGTTAGGGGG 60.104 44.000 0.00 0.00 0.00 5.40
303 322 0.179073 ATGGTGCTGATGCCGTCTAC 60.179 55.000 0.00 0.00 38.71 2.59
304 323 1.257750 TGGTGCTGATGCCGTCTACT 61.258 55.000 0.00 0.00 38.71 2.57
305 324 0.528684 GGTGCTGATGCCGTCTACTC 60.529 60.000 0.00 0.00 38.71 2.59
306 325 0.528684 GTGCTGATGCCGTCTACTCC 60.529 60.000 0.00 0.00 38.71 3.85
307 326 1.068250 GCTGATGCCGTCTACTCCC 59.932 63.158 0.00 0.00 0.00 4.30
308 327 1.395826 GCTGATGCCGTCTACTCCCT 61.396 60.000 0.00 0.00 0.00 4.20
309 328 0.671251 CTGATGCCGTCTACTCCCTC 59.329 60.000 0.00 0.00 0.00 4.30
310 329 0.259065 TGATGCCGTCTACTCCCTCT 59.741 55.000 0.00 0.00 0.00 3.69
311 330 0.671251 GATGCCGTCTACTCCCTCTG 59.329 60.000 0.00 0.00 0.00 3.35
312 331 0.033011 ATGCCGTCTACTCCCTCTGT 60.033 55.000 0.00 0.00 0.00 3.41
313 332 0.251653 TGCCGTCTACTCCCTCTGTT 60.252 55.000 0.00 0.00 0.00 3.16
314 333 1.005097 TGCCGTCTACTCCCTCTGTTA 59.995 52.381 0.00 0.00 0.00 2.41
315 334 2.097825 GCCGTCTACTCCCTCTGTTAA 58.902 52.381 0.00 0.00 0.00 2.01
316 335 2.494870 GCCGTCTACTCCCTCTGTTAAA 59.505 50.000 0.00 0.00 0.00 1.52
317 336 3.132467 GCCGTCTACTCCCTCTGTTAAAT 59.868 47.826 0.00 0.00 0.00 1.40
318 337 4.340381 GCCGTCTACTCCCTCTGTTAAATA 59.660 45.833 0.00 0.00 0.00 1.40
319 338 5.010820 GCCGTCTACTCCCTCTGTTAAATAT 59.989 44.000 0.00 0.00 0.00 1.28
320 339 6.462628 GCCGTCTACTCCCTCTGTTAAATATT 60.463 42.308 0.00 0.00 0.00 1.28
321 340 7.498443 CCGTCTACTCCCTCTGTTAAATATTT 58.502 38.462 5.89 5.89 0.00 1.40
322 341 7.438459 CCGTCTACTCCCTCTGTTAAATATTTG 59.562 40.741 11.05 0.00 0.00 2.32
323 342 7.980099 CGTCTACTCCCTCTGTTAAATATTTGT 59.020 37.037 11.05 0.00 0.00 2.83
324 343 9.315525 GTCTACTCCCTCTGTTAAATATTTGTC 57.684 37.037 11.05 4.54 0.00 3.18
325 344 9.268282 TCTACTCCCTCTGTTAAATATTTGTCT 57.732 33.333 11.05 0.00 0.00 3.41
326 345 9.892130 CTACTCCCTCTGTTAAATATTTGTCTT 57.108 33.333 11.05 0.00 0.00 3.01
328 347 9.588096 ACTCCCTCTGTTAAATATTTGTCTTTT 57.412 29.630 11.05 0.00 0.00 2.27
346 365 9.965824 TTGTCTTTTTAGAGATTTTGAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
347 366 9.354673 TGTCTTTTTAGAGATTTTGAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
353 372 9.958180 TTTAGAGATTTTGAATGGACTATCACA 57.042 29.630 0.00 0.00 0.00 3.58
356 375 9.553064 AGAGATTTTGAATGGACTATCACATAC 57.447 33.333 0.00 0.00 0.00 2.39
357 376 8.370493 AGATTTTGAATGGACTATCACATACG 57.630 34.615 0.00 0.00 0.00 3.06
358 377 6.918892 TTTTGAATGGACTATCACATACGG 57.081 37.500 0.00 0.00 0.00 4.02
359 378 5.862678 TTGAATGGACTATCACATACGGA 57.137 39.130 0.00 0.00 0.00 4.69
360 379 6.419484 TTGAATGGACTATCACATACGGAT 57.581 37.500 0.00 0.00 0.00 4.18
361 380 6.419484 TGAATGGACTATCACATACGGATT 57.581 37.500 0.00 0.00 0.00 3.01
362 381 6.826668 TGAATGGACTATCACATACGGATTT 58.173 36.000 0.00 0.00 0.00 2.17
363 382 7.958088 TGAATGGACTATCACATACGGATTTA 58.042 34.615 0.00 0.00 0.00 1.40
364 383 8.593679 TGAATGGACTATCACATACGGATTTAT 58.406 33.333 0.00 0.00 0.00 1.40
402 421 9.638239 TTAAAGTGTAGATTCATCCATTTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
403 422 5.883661 AGTGTAGATTCATCCATTTTTGCG 58.116 37.500 0.00 0.00 0.00 4.85
404 423 4.500477 GTGTAGATTCATCCATTTTTGCGC 59.500 41.667 0.00 0.00 0.00 6.09
405 424 4.398988 TGTAGATTCATCCATTTTTGCGCT 59.601 37.500 9.73 0.00 0.00 5.92
406 425 3.777478 AGATTCATCCATTTTTGCGCTG 58.223 40.909 9.73 0.00 0.00 5.18
407 426 3.194116 AGATTCATCCATTTTTGCGCTGT 59.806 39.130 9.73 0.00 0.00 4.40
408 427 4.398988 AGATTCATCCATTTTTGCGCTGTA 59.601 37.500 9.73 0.00 0.00 2.74
409 428 4.717233 TTCATCCATTTTTGCGCTGTAT 57.283 36.364 9.73 0.00 0.00 2.29
410 429 4.031418 TCATCCATTTTTGCGCTGTATG 57.969 40.909 9.73 7.14 0.00 2.39
411 430 3.443329 TCATCCATTTTTGCGCTGTATGT 59.557 39.130 9.73 0.00 0.00 2.29
412 431 4.637977 TCATCCATTTTTGCGCTGTATGTA 59.362 37.500 9.73 0.00 0.00 2.29
413 432 4.614555 TCCATTTTTGCGCTGTATGTAG 57.385 40.909 9.73 0.00 0.00 2.74
414 433 4.006989 TCCATTTTTGCGCTGTATGTAGT 58.993 39.130 9.73 0.00 0.00 2.73
415 434 4.094294 TCCATTTTTGCGCTGTATGTAGTC 59.906 41.667 9.73 0.00 0.00 2.59
416 435 4.142708 CCATTTTTGCGCTGTATGTAGTCA 60.143 41.667 9.73 0.00 0.00 3.41
417 436 4.398549 TTTTTGCGCTGTATGTAGTCAC 57.601 40.909 9.73 0.00 0.00 3.67
418 437 3.313012 TTTGCGCTGTATGTAGTCACT 57.687 42.857 9.73 0.00 0.00 3.41
419 438 3.313012 TTGCGCTGTATGTAGTCACTT 57.687 42.857 9.73 0.00 0.00 3.16
420 439 2.606108 TGCGCTGTATGTAGTCACTTG 58.394 47.619 9.73 0.00 0.00 3.16
421 440 2.029380 TGCGCTGTATGTAGTCACTTGT 60.029 45.455 9.73 0.00 0.00 3.16
422 441 2.993899 GCGCTGTATGTAGTCACTTGTT 59.006 45.455 0.00 0.00 0.00 2.83
423 442 3.181530 GCGCTGTATGTAGTCACTTGTTG 60.182 47.826 0.00 0.00 0.00 3.33
424 443 4.234574 CGCTGTATGTAGTCACTTGTTGA 58.765 43.478 0.00 0.00 0.00 3.18
425 444 4.684242 CGCTGTATGTAGTCACTTGTTGAA 59.316 41.667 0.00 0.00 35.39 2.69
426 445 5.176774 CGCTGTATGTAGTCACTTGTTGAAA 59.823 40.000 0.00 0.00 35.39 2.69
427 446 6.128553 CGCTGTATGTAGTCACTTGTTGAAAT 60.129 38.462 0.00 0.00 35.39 2.17
428 447 7.571244 CGCTGTATGTAGTCACTTGTTGAAATT 60.571 37.037 0.00 0.00 35.39 1.82
429 448 8.076178 GCTGTATGTAGTCACTTGTTGAAATTT 58.924 33.333 0.00 0.00 35.39 1.82
430 449 9.599322 CTGTATGTAGTCACTTGTTGAAATTTC 57.401 33.333 11.41 11.41 35.39 2.17
431 450 9.337396 TGTATGTAGTCACTTGTTGAAATTTCT 57.663 29.630 18.64 0.00 35.39 2.52
478 497 6.555463 AGACATATTTTAGGAACGAAGGGA 57.445 37.500 0.00 0.00 0.00 4.20
479 498 6.583562 AGACATATTTTAGGAACGAAGGGAG 58.416 40.000 0.00 0.00 0.00 4.30
480 499 6.156429 AGACATATTTTAGGAACGAAGGGAGT 59.844 38.462 0.00 0.00 0.00 3.85
481 500 7.343833 AGACATATTTTAGGAACGAAGGGAGTA 59.656 37.037 0.00 0.00 0.00 2.59
482 501 8.030913 ACATATTTTAGGAACGAAGGGAGTAT 57.969 34.615 0.00 0.00 0.00 2.12
500 519 7.228706 AGGGAGTATTTTTGTTTGTAGTGAGTG 59.771 37.037 0.00 0.00 0.00 3.51
542 561 0.251916 TACCCTTGGGTGAAGATGCG 59.748 55.000 20.78 0.00 32.82 4.73
550 569 5.510690 CCTTGGGTGAAGATGCGTGTATATA 60.511 44.000 0.00 0.00 32.82 0.86
552 571 5.478407 TGGGTGAAGATGCGTGTATATATG 58.522 41.667 0.00 0.00 0.00 1.78
553 572 5.011635 TGGGTGAAGATGCGTGTATATATGT 59.988 40.000 0.00 0.00 0.00 2.29
554 573 5.577164 GGGTGAAGATGCGTGTATATATGTC 59.423 44.000 0.00 0.00 0.00 3.06
599 618 2.439156 GAAAGCCCATGAGCGCCT 60.439 61.111 2.29 0.00 38.01 5.52
757 776 9.942850 TCATGTTCTAGAGTGAAAATTGTCATA 57.057 29.630 0.61 0.00 0.00 2.15
812 831 1.600485 TGCTATGCGTACGATCGAGAA 59.400 47.619 24.34 7.64 0.00 2.87
864 883 6.921307 GCGAAATGTATATTGGGGTTAAAAGG 59.079 38.462 0.00 0.00 0.00 3.11
872 891 9.999660 GTATATTGGGGTTAAAAGGAAAAACAA 57.000 29.630 0.00 0.00 0.00 2.83
874 893 7.633193 ATTGGGGTTAAAAGGAAAAACAAAC 57.367 32.000 0.00 0.00 0.00 2.93
876 895 6.722328 TGGGGTTAAAAGGAAAAACAAACAT 58.278 32.000 0.00 0.00 0.00 2.71
877 896 7.858498 TGGGGTTAAAAGGAAAAACAAACATA 58.142 30.769 0.00 0.00 0.00 2.29
939 963 4.510038 CAATTTCTTTGCCTGTAGCTGT 57.490 40.909 0.00 0.00 44.23 4.40
940 964 5.627499 CAATTTCTTTGCCTGTAGCTGTA 57.373 39.130 0.00 0.00 44.23 2.74
941 965 5.634896 CAATTTCTTTGCCTGTAGCTGTAG 58.365 41.667 0.00 0.00 44.23 2.74
942 966 2.386661 TCTTTGCCTGTAGCTGTAGC 57.613 50.000 0.00 0.00 44.23 3.58
943 967 1.066143 TCTTTGCCTGTAGCTGTAGCC 60.066 52.381 0.00 0.00 44.23 3.93
975 999 4.639726 TGGTCACTGCCCACTACT 57.360 55.556 0.00 0.00 0.00 2.57
1044 1072 1.830145 CCCATTCTCCTACCACCGG 59.170 63.158 0.00 0.00 0.00 5.28
1362 1573 0.462937 CACACAGGGACGTTGGTCAA 60.463 55.000 0.00 0.00 45.28 3.18
1509 1720 1.022735 CATGGAATGCTCTGCTCACC 58.977 55.000 0.00 0.00 37.62 4.02
1560 1771 2.258755 GCCATGCGTGTTTTCCATAAC 58.741 47.619 4.96 0.00 0.00 1.89
1605 1816 7.217906 AGATAAGCAAGTATACTTTGCCTACC 58.782 38.462 24.22 14.36 33.11 3.18
1611 1822 5.873146 AGTATACTTTGCCTACCCTTCTC 57.127 43.478 0.00 0.00 0.00 2.87
1636 1847 1.865340 GTTGTGTGGAACTCGGTCTTC 59.135 52.381 0.00 0.00 38.04 2.87
1728 1939 3.334583 TGCCTTGTTGAGATGTACTCC 57.665 47.619 0.00 0.00 44.34 3.85
1776 1987 8.032451 GCCTATCAAGTCTTTATCAGGATAGAC 58.968 40.741 13.26 4.69 36.47 2.59
2097 2308 2.730090 GCATGAGCCTGACACATTTTCG 60.730 50.000 0.00 0.00 33.58 3.46
2260 2471 2.470990 ACCTGATGTATGGCACTCAGA 58.529 47.619 15.68 0.00 36.11 3.27
2294 2505 4.249661 GTTCTGAAAAGTGGGTTGCAAAA 58.750 39.130 0.00 0.00 0.00 2.44
2456 2667 1.280133 TGAAGCTGAGAAGGTGATGGG 59.720 52.381 0.00 0.00 0.00 4.00
2536 2747 6.206243 AGTTTCATTGAGTGTTTCCTCTGATG 59.794 38.462 0.00 0.00 32.50 3.07
2664 2875 4.130118 GGAACATAACGGATGCTGAGATT 58.870 43.478 0.00 0.00 39.39 2.40
2768 2979 0.529773 GCACTGGACACGTTCAGACA 60.530 55.000 12.50 0.00 35.20 3.41
3361 3572 6.363626 CGTGCTCATACATAAACTATGAGACC 59.636 42.308 16.25 6.99 45.78 3.85
3362 3573 7.210174 GTGCTCATACATAAACTATGAGACCA 58.790 38.462 16.25 5.90 45.78 4.02
3363 3574 7.383572 GTGCTCATACATAAACTATGAGACCAG 59.616 40.741 16.25 0.00 45.78 4.00
3364 3575 6.870965 GCTCATACATAAACTATGAGACCAGG 59.129 42.308 16.25 0.00 45.78 4.45
3365 3576 7.255977 GCTCATACATAAACTATGAGACCAGGA 60.256 40.741 16.25 0.00 45.78 3.86
3366 3577 8.183104 TCATACATAAACTATGAGACCAGGAG 57.817 38.462 0.00 0.00 39.45 3.69
3367 3578 5.878406 ACATAAACTATGAGACCAGGAGG 57.122 43.478 0.00 0.00 39.45 4.30
3368 3579 5.281314 ACATAAACTATGAGACCAGGAGGT 58.719 41.667 0.00 0.00 44.54 3.85
3369 3580 5.129485 ACATAAACTATGAGACCAGGAGGTG 59.871 44.000 0.00 0.00 43.11 4.00
3370 3581 5.363868 CATAAACTATGAGACCAGGAGGTGA 59.636 44.000 0.00 0.00 42.92 4.02
3371 3582 6.684111 CATAAACTATGAGACCAGGAGGTGAC 60.684 46.154 0.00 0.00 42.92 3.67
3372 3583 9.753591 CATAAACTATGAGACCAGGAGGTGACG 62.754 48.148 0.00 0.00 42.92 4.35
3380 3591 3.377346 CCAGGAGGTGACGATGAATAG 57.623 52.381 0.00 0.00 0.00 1.73
3381 3592 2.959030 CCAGGAGGTGACGATGAATAGA 59.041 50.000 0.00 0.00 0.00 1.98
3382 3593 3.576118 CCAGGAGGTGACGATGAATAGAT 59.424 47.826 0.00 0.00 0.00 1.98
3383 3594 4.039730 CCAGGAGGTGACGATGAATAGATT 59.960 45.833 0.00 0.00 0.00 2.40
3384 3595 4.987285 CAGGAGGTGACGATGAATAGATTG 59.013 45.833 0.00 0.00 0.00 2.67
3385 3596 4.895889 AGGAGGTGACGATGAATAGATTGA 59.104 41.667 0.00 0.00 0.00 2.57
3386 3597 5.363868 AGGAGGTGACGATGAATAGATTGAA 59.636 40.000 0.00 0.00 0.00 2.69
3387 3598 5.694006 GGAGGTGACGATGAATAGATTGAAG 59.306 44.000 0.00 0.00 0.00 3.02
3388 3599 5.605534 AGGTGACGATGAATAGATTGAAGG 58.394 41.667 0.00 0.00 0.00 3.46
3389 3600 5.129485 AGGTGACGATGAATAGATTGAAGGT 59.871 40.000 0.00 0.00 0.00 3.50
3390 3601 5.817816 GGTGACGATGAATAGATTGAAGGTT 59.182 40.000 0.00 0.00 0.00 3.50
3391 3602 6.316390 GGTGACGATGAATAGATTGAAGGTTT 59.684 38.462 0.00 0.00 0.00 3.27
3392 3603 7.148239 GGTGACGATGAATAGATTGAAGGTTTT 60.148 37.037 0.00 0.00 0.00 2.43
3393 3604 8.237267 GTGACGATGAATAGATTGAAGGTTTTT 58.763 33.333 0.00 0.00 0.00 1.94
3394 3605 8.450964 TGACGATGAATAGATTGAAGGTTTTTC 58.549 33.333 0.00 0.00 0.00 2.29
3395 3606 7.762382 ACGATGAATAGATTGAAGGTTTTTCC 58.238 34.615 0.00 0.00 0.00 3.13
3396 3607 7.148069 ACGATGAATAGATTGAAGGTTTTTCCC 60.148 37.037 0.00 0.00 36.75 3.97
3397 3608 6.509418 TGAATAGATTGAAGGTTTTTCCCG 57.491 37.500 0.00 0.00 36.75 5.14
3398 3609 4.983671 ATAGATTGAAGGTTTTTCCCGC 57.016 40.909 0.00 0.00 36.75 6.13
3399 3610 2.593026 AGATTGAAGGTTTTTCCCGCA 58.407 42.857 0.00 0.00 36.75 5.69
3400 3611 2.962421 AGATTGAAGGTTTTTCCCGCAA 59.038 40.909 0.00 0.00 36.75 4.85
3401 3612 3.386402 AGATTGAAGGTTTTTCCCGCAAA 59.614 39.130 0.00 0.00 34.83 3.68
3402 3613 3.611766 TTGAAGGTTTTTCCCGCAAAA 57.388 38.095 0.00 0.00 36.75 2.44
3403 3614 3.611766 TGAAGGTTTTTCCCGCAAAAA 57.388 38.095 0.46 0.46 40.93 1.94
3672 3883 3.251729 CGCATATGCTATCCTGCAGTTTT 59.748 43.478 24.56 0.00 46.71 2.43
3682 3893 6.986817 GCTATCCTGCAGTTTTATAAGAGACA 59.013 38.462 13.81 0.00 0.00 3.41
3708 3919 1.811965 TGCAGAAAATCCACCGACATG 59.188 47.619 0.00 0.00 0.00 3.21
3960 4172 2.880890 CAGCTTGTTCACCAGCTTAAGT 59.119 45.455 4.02 0.00 35.17 2.24
4119 4331 1.148498 GCAGTAATCCCCCTTCCCG 59.852 63.158 0.00 0.00 0.00 5.14
4162 4374 1.486310 TGTTCTTGGCACTGTCTGTCT 59.514 47.619 0.00 0.00 0.00 3.41
4222 4435 5.393866 AGTGAAATTTAGTTCATGGGTGGT 58.606 37.500 0.00 0.00 39.61 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.483085 GCTCTGGTACGACAAATAAACGC 60.483 47.826 0.00 0.00 0.00 4.84
3 4 3.924686 AGCTCTGGTACGACAAATAAACG 59.075 43.478 0.00 0.00 0.00 3.60
4 5 5.005490 GCTAGCTCTGGTACGACAAATAAAC 59.995 44.000 7.70 0.00 0.00 2.01
6 7 4.158949 TGCTAGCTCTGGTACGACAAATAA 59.841 41.667 17.23 0.00 0.00 1.40
8 9 2.496070 TGCTAGCTCTGGTACGACAAAT 59.504 45.455 17.23 0.00 0.00 2.32
15 16 5.215252 TGGATATTTGCTAGCTCTGGTAC 57.785 43.478 17.23 0.85 0.00 3.34
84 101 5.045286 AGAGAAGGAAACTGCCTATGTTGAT 60.045 40.000 0.00 0.00 42.68 2.57
85 102 4.287067 AGAGAAGGAAACTGCCTATGTTGA 59.713 41.667 0.00 0.00 42.68 3.18
86 103 4.583871 AGAGAAGGAAACTGCCTATGTTG 58.416 43.478 0.00 0.00 42.68 3.33
87 104 4.534103 AGAGAGAAGGAAACTGCCTATGTT 59.466 41.667 0.00 0.00 42.68 2.71
88 105 4.081198 CAGAGAGAAGGAAACTGCCTATGT 60.081 45.833 0.00 0.00 42.68 2.29
89 106 4.161189 TCAGAGAGAAGGAAACTGCCTATG 59.839 45.833 0.00 0.00 42.68 2.23
90 107 4.357325 TCAGAGAGAAGGAAACTGCCTAT 58.643 43.478 0.00 0.00 42.68 2.57
97 114 7.312899 TGTTTTGTTTTCAGAGAGAAGGAAAC 58.687 34.615 0.00 0.00 37.57 2.78
105 122 7.741652 GCAAAGTTTTGTTTTGTTTTCAGAGAG 59.258 33.333 6.48 0.00 40.24 3.20
133 152 0.530744 GATCACGACAGCCACCTACA 59.469 55.000 0.00 0.00 0.00 2.74
148 167 8.681806 CAAAGTTGAGTCATCTAGAGTAGATCA 58.318 37.037 4.14 0.00 43.41 2.92
155 174 9.168451 TCTAGTACAAAGTTGAGTCATCTAGAG 57.832 37.037 4.14 1.16 0.00 2.43
157 176 8.952278 AGTCTAGTACAAAGTTGAGTCATCTAG 58.048 37.037 4.14 3.67 0.00 2.43
159 178 7.448777 TGAGTCTAGTACAAAGTTGAGTCATCT 59.551 37.037 0.00 0.00 36.17 2.90
160 179 7.594714 TGAGTCTAGTACAAAGTTGAGTCATC 58.405 38.462 0.00 0.00 36.17 2.92
161 180 7.526142 TGAGTCTAGTACAAAGTTGAGTCAT 57.474 36.000 0.00 0.00 36.17 3.06
162 181 6.954487 TGAGTCTAGTACAAAGTTGAGTCA 57.046 37.500 0.00 0.00 37.68 3.41
163 182 7.427214 AGTTGAGTCTAGTACAAAGTTGAGTC 58.573 38.462 0.00 0.00 33.41 3.36
164 183 7.349412 AGTTGAGTCTAGTACAAAGTTGAGT 57.651 36.000 0.00 0.00 0.00 3.41
165 184 8.543774 CAAAGTTGAGTCTAGTACAAAGTTGAG 58.456 37.037 0.00 0.00 0.00 3.02
167 186 8.197988 ACAAAGTTGAGTCTAGTACAAAGTTG 57.802 34.615 0.00 0.00 0.00 3.16
169 188 8.693625 AGTACAAAGTTGAGTCTAGTACAAAGT 58.306 33.333 0.00 0.00 34.50 2.66
179 198 8.747538 ACCAAATTTAGTACAAAGTTGAGTCT 57.252 30.769 21.54 7.71 37.38 3.24
180 199 9.874215 GTACCAAATTTAGTACAAAGTTGAGTC 57.126 33.333 18.35 12.68 37.38 3.36
191 210 9.874215 GACTCAACTTTGTACCAAATTTAGTAC 57.126 33.333 16.96 16.96 39.44 2.73
192 211 9.616156 TGACTCAACTTTGTACCAAATTTAGTA 57.384 29.630 0.00 0.00 0.00 1.82
193 212 8.514330 TGACTCAACTTTGTACCAAATTTAGT 57.486 30.769 0.00 0.00 0.00 2.24
194 213 9.612620 GATGACTCAACTTTGTACCAAATTTAG 57.387 33.333 0.00 0.00 0.00 1.85
195 214 9.349713 AGATGACTCAACTTTGTACCAAATTTA 57.650 29.630 0.00 0.00 0.00 1.40
196 215 8.237811 AGATGACTCAACTTTGTACCAAATTT 57.762 30.769 0.00 0.00 0.00 1.82
197 216 7.823745 AGATGACTCAACTTTGTACCAAATT 57.176 32.000 0.00 0.00 0.00 1.82
199 218 8.918202 AATAGATGACTCAACTTTGTACCAAA 57.082 30.769 0.00 0.00 0.00 3.28
200 219 8.918202 AAATAGATGACTCAACTTTGTACCAA 57.082 30.769 0.00 0.00 0.00 3.67
201 220 8.783093 CAAAATAGATGACTCAACTTTGTACCA 58.217 33.333 0.00 0.00 0.00 3.25
202 221 8.237267 CCAAAATAGATGACTCAACTTTGTACC 58.763 37.037 0.00 0.00 0.00 3.34
203 222 8.784043 ACCAAAATAGATGACTCAACTTTGTAC 58.216 33.333 0.00 0.00 0.00 2.90
204 223 8.918202 ACCAAAATAGATGACTCAACTTTGTA 57.082 30.769 0.00 0.00 0.00 2.41
205 224 7.823745 ACCAAAATAGATGACTCAACTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
206 225 9.831737 CTAACCAAAATAGATGACTCAACTTTG 57.168 33.333 0.00 0.00 0.00 2.77
207 226 9.014297 CCTAACCAAAATAGATGACTCAACTTT 57.986 33.333 0.00 0.00 0.00 2.66
208 227 7.611855 CCCTAACCAAAATAGATGACTCAACTT 59.388 37.037 0.00 0.00 0.00 2.66
209 228 7.112779 CCCTAACCAAAATAGATGACTCAACT 58.887 38.462 0.00 0.00 0.00 3.16
211 230 6.423182 CCCCTAACCAAAATAGATGACTCAA 58.577 40.000 0.00 0.00 0.00 3.02
212 231 5.104109 CCCCCTAACCAAAATAGATGACTCA 60.104 44.000 0.00 0.00 0.00 3.41
213 232 5.377478 CCCCCTAACCAAAATAGATGACTC 58.623 45.833 0.00 0.00 0.00 3.36
214 233 5.388599 CCCCCTAACCAAAATAGATGACT 57.611 43.478 0.00 0.00 0.00 3.41
233 252 5.778750 TGCATTACTTAGATACTACTCCCCC 59.221 44.000 0.00 0.00 0.00 5.40
234 253 6.912951 TGCATTACTTAGATACTACTCCCC 57.087 41.667 0.00 0.00 0.00 4.81
235 254 9.780186 AAAATGCATTACTTAGATACTACTCCC 57.220 33.333 13.39 0.00 0.00 4.30
267 286 4.451774 GCACCATGCAAAGCTATTTTTGAA 59.548 37.500 0.00 0.00 44.26 2.69
320 339 9.965824 GTCCATTCAAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
321 340 9.354673 AGTCCATTCAAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
327 346 9.958180 TGTGATAGTCCATTCAAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
330 349 9.553064 GTATGTGATAGTCCATTCAAAATCTCT 57.447 33.333 0.00 0.00 0.00 3.10
331 350 8.491152 CGTATGTGATAGTCCATTCAAAATCTC 58.509 37.037 0.00 0.00 0.00 2.75
332 351 7.442364 CCGTATGTGATAGTCCATTCAAAATCT 59.558 37.037 0.00 0.00 0.00 2.40
333 352 7.441157 TCCGTATGTGATAGTCCATTCAAAATC 59.559 37.037 0.00 0.00 0.00 2.17
334 353 7.279615 TCCGTATGTGATAGTCCATTCAAAAT 58.720 34.615 0.00 0.00 0.00 1.82
335 354 6.645306 TCCGTATGTGATAGTCCATTCAAAA 58.355 36.000 0.00 0.00 0.00 2.44
336 355 6.228616 TCCGTATGTGATAGTCCATTCAAA 57.771 37.500 0.00 0.00 0.00 2.69
337 356 5.862678 TCCGTATGTGATAGTCCATTCAA 57.137 39.130 0.00 0.00 0.00 2.69
338 357 6.419484 AATCCGTATGTGATAGTCCATTCA 57.581 37.500 0.00 0.00 0.00 2.57
376 395 9.638239 GCAAAAATGGATGAATCTACACTTTAA 57.362 29.630 0.00 0.00 0.00 1.52
377 396 7.967854 CGCAAAAATGGATGAATCTACACTTTA 59.032 33.333 0.00 0.00 0.00 1.85
378 397 6.808212 CGCAAAAATGGATGAATCTACACTTT 59.192 34.615 0.00 0.00 0.00 2.66
379 398 6.324819 CGCAAAAATGGATGAATCTACACTT 58.675 36.000 0.00 0.00 0.00 3.16
380 399 5.677091 GCGCAAAAATGGATGAATCTACACT 60.677 40.000 0.30 0.00 0.00 3.55
381 400 4.500477 GCGCAAAAATGGATGAATCTACAC 59.500 41.667 0.30 0.00 0.00 2.90
382 401 4.398988 AGCGCAAAAATGGATGAATCTACA 59.601 37.500 11.47 0.00 0.00 2.74
383 402 4.736793 CAGCGCAAAAATGGATGAATCTAC 59.263 41.667 11.47 0.00 0.00 2.59
384 403 4.398988 ACAGCGCAAAAATGGATGAATCTA 59.601 37.500 11.47 0.00 0.00 1.98
385 404 3.194116 ACAGCGCAAAAATGGATGAATCT 59.806 39.130 11.47 0.00 0.00 2.40
386 405 3.514645 ACAGCGCAAAAATGGATGAATC 58.485 40.909 11.47 0.00 0.00 2.52
387 406 3.598019 ACAGCGCAAAAATGGATGAAT 57.402 38.095 11.47 0.00 0.00 2.57
388 407 4.082300 ACATACAGCGCAAAAATGGATGAA 60.082 37.500 21.72 0.00 37.44 2.57
389 408 3.443329 ACATACAGCGCAAAAATGGATGA 59.557 39.130 21.72 0.00 37.44 2.92
390 409 3.772932 ACATACAGCGCAAAAATGGATG 58.227 40.909 15.21 15.21 40.47 3.51
391 410 4.640201 ACTACATACAGCGCAAAAATGGAT 59.360 37.500 11.47 0.00 0.00 3.41
392 411 4.006989 ACTACATACAGCGCAAAAATGGA 58.993 39.130 11.47 3.36 0.00 3.41
393 412 4.142708 TGACTACATACAGCGCAAAAATGG 60.143 41.667 11.47 0.00 0.00 3.16
394 413 4.788100 GTGACTACATACAGCGCAAAAATG 59.212 41.667 11.47 10.25 0.00 2.32
395 414 4.695455 AGTGACTACATACAGCGCAAAAAT 59.305 37.500 11.47 0.00 0.00 1.82
396 415 4.062293 AGTGACTACATACAGCGCAAAAA 58.938 39.130 11.47 0.00 0.00 1.94
397 416 3.659786 AGTGACTACATACAGCGCAAAA 58.340 40.909 11.47 0.00 0.00 2.44
398 417 3.313012 AGTGACTACATACAGCGCAAA 57.687 42.857 11.47 0.00 0.00 3.68
399 418 2.993220 CAAGTGACTACATACAGCGCAA 59.007 45.455 11.47 0.00 0.00 4.85
400 419 2.029380 ACAAGTGACTACATACAGCGCA 60.029 45.455 11.47 0.00 0.00 6.09
401 420 2.607187 ACAAGTGACTACATACAGCGC 58.393 47.619 0.00 0.00 0.00 5.92
402 421 4.234574 TCAACAAGTGACTACATACAGCG 58.765 43.478 0.00 0.00 0.00 5.18
403 422 6.539649 TTTCAACAAGTGACTACATACAGC 57.460 37.500 0.00 0.00 35.39 4.40
404 423 9.599322 GAAATTTCAACAAGTGACTACATACAG 57.401 33.333 13.40 0.00 35.39 2.74
405 424 9.337396 AGAAATTTCAACAAGTGACTACATACA 57.663 29.630 19.99 0.00 35.39 2.29
452 471 9.370930 TCCCTTCGTTCCTAAAATATGTCTATA 57.629 33.333 0.00 0.00 0.00 1.31
453 472 8.258850 TCCCTTCGTTCCTAAAATATGTCTAT 57.741 34.615 0.00 0.00 0.00 1.98
454 473 7.343833 ACTCCCTTCGTTCCTAAAATATGTCTA 59.656 37.037 0.00 0.00 0.00 2.59
455 474 6.156429 ACTCCCTTCGTTCCTAAAATATGTCT 59.844 38.462 0.00 0.00 0.00 3.41
456 475 6.346896 ACTCCCTTCGTTCCTAAAATATGTC 58.653 40.000 0.00 0.00 0.00 3.06
457 476 6.309389 ACTCCCTTCGTTCCTAAAATATGT 57.691 37.500 0.00 0.00 0.00 2.29
458 477 8.904099 AATACTCCCTTCGTTCCTAAAATATG 57.096 34.615 0.00 0.00 0.00 1.78
459 478 9.916360 AAAATACTCCCTTCGTTCCTAAAATAT 57.084 29.630 0.00 0.00 0.00 1.28
460 479 9.743581 AAAAATACTCCCTTCGTTCCTAAAATA 57.256 29.630 0.00 0.00 0.00 1.40
461 480 8.520351 CAAAAATACTCCCTTCGTTCCTAAAAT 58.480 33.333 0.00 0.00 0.00 1.82
462 481 7.503230 ACAAAAATACTCCCTTCGTTCCTAAAA 59.497 33.333 0.00 0.00 0.00 1.52
463 482 6.999871 ACAAAAATACTCCCTTCGTTCCTAAA 59.000 34.615 0.00 0.00 0.00 1.85
464 483 6.536447 ACAAAAATACTCCCTTCGTTCCTAA 58.464 36.000 0.00 0.00 0.00 2.69
465 484 6.117975 ACAAAAATACTCCCTTCGTTCCTA 57.882 37.500 0.00 0.00 0.00 2.94
466 485 4.981812 ACAAAAATACTCCCTTCGTTCCT 58.018 39.130 0.00 0.00 0.00 3.36
467 486 5.700722 AACAAAAATACTCCCTTCGTTCC 57.299 39.130 0.00 0.00 0.00 3.62
468 487 6.500910 ACAAACAAAAATACTCCCTTCGTTC 58.499 36.000 0.00 0.00 0.00 3.95
469 488 6.459670 ACAAACAAAAATACTCCCTTCGTT 57.540 33.333 0.00 0.00 0.00 3.85
470 489 6.769341 ACTACAAACAAAAATACTCCCTTCGT 59.231 34.615 0.00 0.00 0.00 3.85
471 490 7.041644 TCACTACAAACAAAAATACTCCCTTCG 60.042 37.037 0.00 0.00 0.00 3.79
472 491 8.161699 TCACTACAAACAAAAATACTCCCTTC 57.838 34.615 0.00 0.00 0.00 3.46
473 492 7.778382 ACTCACTACAAACAAAAATACTCCCTT 59.222 33.333 0.00 0.00 0.00 3.95
474 493 7.228706 CACTCACTACAAACAAAAATACTCCCT 59.771 37.037 0.00 0.00 0.00 4.20
475 494 7.012989 ACACTCACTACAAACAAAAATACTCCC 59.987 37.037 0.00 0.00 0.00 4.30
476 495 7.927048 ACACTCACTACAAACAAAAATACTCC 58.073 34.615 0.00 0.00 0.00 3.85
477 496 9.434559 GAACACTCACTACAAACAAAAATACTC 57.565 33.333 0.00 0.00 0.00 2.59
478 497 8.120465 CGAACACTCACTACAAACAAAAATACT 58.880 33.333 0.00 0.00 0.00 2.12
479 498 7.906527 ACGAACACTCACTACAAACAAAAATAC 59.093 33.333 0.00 0.00 0.00 1.89
480 499 7.976826 ACGAACACTCACTACAAACAAAAATA 58.023 30.769 0.00 0.00 0.00 1.40
481 500 6.848451 ACGAACACTCACTACAAACAAAAAT 58.152 32.000 0.00 0.00 0.00 1.82
482 501 6.243811 ACGAACACTCACTACAAACAAAAA 57.756 33.333 0.00 0.00 0.00 1.94
500 519 7.218204 GGTAAACATAGCATCAAATCAACGAAC 59.782 37.037 0.00 0.00 0.00 3.95
542 561 5.470368 ACGGCACATGAGACATATATACAC 58.530 41.667 0.00 0.00 0.00 2.90
550 569 1.740380 GCACTACGGCACATGAGACAT 60.740 52.381 0.00 0.00 0.00 3.06
552 571 1.413767 CGCACTACGGCACATGAGAC 61.414 60.000 0.00 0.00 38.44 3.36
553 572 1.153842 CGCACTACGGCACATGAGA 60.154 57.895 0.00 0.00 38.44 3.27
554 573 3.388134 CGCACTACGGCACATGAG 58.612 61.111 0.00 0.00 38.44 2.90
757 776 4.923871 CAGCACGACAAGTTTCTACACTAT 59.076 41.667 0.00 0.00 0.00 2.12
765 784 0.658536 GCTGCAGCACGACAAGTTTC 60.659 55.000 33.36 0.00 41.59 2.78
812 831 0.611714 AAAATCTGAGGTACGCCGGT 59.388 50.000 1.90 0.00 40.50 5.28
840 859 8.228035 TCCTTTTAACCCCAATATACATTTCG 57.772 34.615 0.00 0.00 0.00 3.46
942 966 1.153823 CCACGAAGACGCCTACAGG 60.154 63.158 0.00 0.00 43.96 4.00
943 967 0.456312 GACCACGAAGACGCCTACAG 60.456 60.000 0.00 0.00 43.96 2.74
973 997 1.294780 CCTGCGAGAAGGCAAGAGT 59.705 57.895 0.00 0.00 43.39 3.24
974 998 4.198625 CCTGCGAGAAGGCAAGAG 57.801 61.111 0.00 0.00 43.39 2.85
1092 1120 3.577313 GGAGAAGAATGCGCCGGC 61.577 66.667 19.07 19.07 40.52 6.13
1093 1121 1.432270 GAAGGAGAAGAATGCGCCGG 61.432 60.000 4.18 0.00 0.00 6.13
1141 1169 3.934684 GAGCTCATCGGCTTGCGC 61.935 66.667 9.40 0.00 43.20 6.09
1142 1170 3.267860 GGAGCTCATCGGCTTGCG 61.268 66.667 17.19 0.00 43.20 4.85
1143 1171 3.267860 CGGAGCTCATCGGCTTGC 61.268 66.667 17.19 0.00 43.20 4.01
1144 1172 2.587194 CCGGAGCTCATCGGCTTG 60.587 66.667 17.19 0.00 43.20 4.01
1362 1573 3.214328 CAGACCTTGCAACTTAACCACT 58.786 45.455 0.00 0.00 0.00 4.00
1560 1771 4.002982 TCTCATCACCAAATTCCGACAAG 58.997 43.478 0.00 0.00 0.00 3.16
1605 1816 2.917933 TCCACACAACACTTGAGAAGG 58.082 47.619 0.00 0.00 0.00 3.46
1611 1822 1.330521 CCGAGTTCCACACAACACTTG 59.669 52.381 0.00 0.00 0.00 3.16
1776 1987 1.135603 CAATGCACCACATCAGGTTCG 60.136 52.381 0.00 0.00 40.77 3.95
1967 2178 1.202405 CCAGCCCACTTTTCACAACAC 60.202 52.381 0.00 0.00 0.00 3.32
2097 2308 2.076863 CCGGAGAGAAATGTGTTCCAC 58.923 52.381 0.00 0.00 34.56 4.02
2237 2448 2.092968 TGAGTGCCATACATCAGGTTCC 60.093 50.000 0.00 0.00 0.00 3.62
2260 2471 5.924254 CACTTTTCAGAACACATGCATGAAT 59.076 36.000 32.75 16.83 30.56 2.57
2294 2505 7.325660 AGCATTCTTGAAACATCATTATCGT 57.674 32.000 0.00 0.00 0.00 3.73
2456 2667 3.637432 TGCAACATTGAACGGAAACATC 58.363 40.909 0.00 0.00 0.00 3.06
2536 2747 0.749454 CCACTGCCTAAGGATGCCAC 60.749 60.000 0.00 0.00 0.00 5.01
2607 2818 3.056250 ACATGTCAACTAGAGCACCAGAG 60.056 47.826 0.00 0.00 0.00 3.35
2664 2875 8.971073 TCACATGTTTCTGACTCATAGAATAGA 58.029 33.333 0.00 0.00 34.42 1.98
2768 2979 4.446889 GCCTTTTCCCATCATCTACCATCT 60.447 45.833 0.00 0.00 0.00 2.90
3069 3280 7.094634 GGATCTAACTCAAACAATCTTTCTGCA 60.095 37.037 0.00 0.00 0.00 4.41
3341 3552 7.233553 CCTCCTGGTCTCATAGTTTATGTATGA 59.766 40.741 0.00 0.00 37.45 2.15
3361 3572 4.862902 ATCTATTCATCGTCACCTCCTG 57.137 45.455 0.00 0.00 0.00 3.86
3362 3573 4.895889 TCAATCTATTCATCGTCACCTCCT 59.104 41.667 0.00 0.00 0.00 3.69
3363 3574 5.201713 TCAATCTATTCATCGTCACCTCC 57.798 43.478 0.00 0.00 0.00 4.30
3364 3575 5.694006 CCTTCAATCTATTCATCGTCACCTC 59.306 44.000 0.00 0.00 0.00 3.85
3365 3576 5.129485 ACCTTCAATCTATTCATCGTCACCT 59.871 40.000 0.00 0.00 0.00 4.00
3366 3577 5.360591 ACCTTCAATCTATTCATCGTCACC 58.639 41.667 0.00 0.00 0.00 4.02
3367 3578 6.910536 AACCTTCAATCTATTCATCGTCAC 57.089 37.500 0.00 0.00 0.00 3.67
3368 3579 7.921786 AAAACCTTCAATCTATTCATCGTCA 57.078 32.000 0.00 0.00 0.00 4.35
3369 3580 7.910683 GGAAAAACCTTCAATCTATTCATCGTC 59.089 37.037 0.00 0.00 35.41 4.20
3370 3581 7.148069 GGGAAAAACCTTCAATCTATTCATCGT 60.148 37.037 0.00 0.00 38.98 3.73
3371 3582 7.196331 GGGAAAAACCTTCAATCTATTCATCG 58.804 38.462 0.00 0.00 38.98 3.84
3372 3583 7.196331 CGGGAAAAACCTTCAATCTATTCATC 58.804 38.462 0.00 0.00 38.98 2.92
3373 3584 6.405842 GCGGGAAAAACCTTCAATCTATTCAT 60.406 38.462 0.00 0.00 38.98 2.57
3374 3585 5.105917 GCGGGAAAAACCTTCAATCTATTCA 60.106 40.000 0.00 0.00 38.98 2.57
3375 3586 5.105917 TGCGGGAAAAACCTTCAATCTATTC 60.106 40.000 0.00 0.00 38.98 1.75
3376 3587 4.770010 TGCGGGAAAAACCTTCAATCTATT 59.230 37.500 0.00 0.00 38.98 1.73
3377 3588 4.340617 TGCGGGAAAAACCTTCAATCTAT 58.659 39.130 0.00 0.00 38.98 1.98
3378 3589 3.757270 TGCGGGAAAAACCTTCAATCTA 58.243 40.909 0.00 0.00 38.98 1.98
3379 3590 2.593026 TGCGGGAAAAACCTTCAATCT 58.407 42.857 0.00 0.00 38.98 2.40
3380 3591 3.378911 TTGCGGGAAAAACCTTCAATC 57.621 42.857 0.00 0.00 38.98 2.67
3381 3592 3.828875 TTTGCGGGAAAAACCTTCAAT 57.171 38.095 0.00 0.00 38.98 2.57
3382 3593 3.611766 TTTTGCGGGAAAAACCTTCAA 57.388 38.095 4.86 0.00 38.98 2.69
3383 3594 3.611766 TTTTTGCGGGAAAAACCTTCA 57.388 38.095 14.93 0.00 38.38 3.02
3405 3616 9.150348 CTGGTCTCATAGTTTTGTTTTGTTTTT 57.850 29.630 0.00 0.00 0.00 1.94
3406 3617 7.763985 CCTGGTCTCATAGTTTTGTTTTGTTTT 59.236 33.333 0.00 0.00 0.00 2.43
3407 3618 7.123547 TCCTGGTCTCATAGTTTTGTTTTGTTT 59.876 33.333 0.00 0.00 0.00 2.83
3408 3619 6.605594 TCCTGGTCTCATAGTTTTGTTTTGTT 59.394 34.615 0.00 0.00 0.00 2.83
3409 3620 6.126409 TCCTGGTCTCATAGTTTTGTTTTGT 58.874 36.000 0.00 0.00 0.00 2.83
3410 3621 6.633500 TCCTGGTCTCATAGTTTTGTTTTG 57.367 37.500 0.00 0.00 0.00 2.44
3411 3622 5.241728 GCTCCTGGTCTCATAGTTTTGTTTT 59.758 40.000 0.00 0.00 0.00 2.43
3412 3623 4.762251 GCTCCTGGTCTCATAGTTTTGTTT 59.238 41.667 0.00 0.00 0.00 2.83
3413 3624 4.042187 AGCTCCTGGTCTCATAGTTTTGTT 59.958 41.667 0.00 0.00 0.00 2.83
3414 3625 3.584848 AGCTCCTGGTCTCATAGTTTTGT 59.415 43.478 0.00 0.00 0.00 2.83
3415 3626 3.937706 CAGCTCCTGGTCTCATAGTTTTG 59.062 47.826 0.00 0.00 0.00 2.44
3416 3627 3.054802 CCAGCTCCTGGTCTCATAGTTTT 60.055 47.826 3.09 0.00 45.82 2.43
3417 3628 2.503356 CCAGCTCCTGGTCTCATAGTTT 59.497 50.000 3.09 0.00 45.82 2.66
3418 3629 2.114616 CCAGCTCCTGGTCTCATAGTT 58.885 52.381 3.09 0.00 45.82 2.24
3419 3630 1.786937 CCAGCTCCTGGTCTCATAGT 58.213 55.000 3.09 0.00 45.82 2.12
3594 3805 1.352622 ACAGGCAAGTTCAGGGACCA 61.353 55.000 0.00 0.00 0.00 4.02
3672 3883 7.977789 TTTTCTGCACATTGTGTCTCTTATA 57.022 32.000 17.64 0.00 35.75 0.98
3708 3919 5.049398 TGTAACAAATAATTGCACCGACC 57.951 39.130 0.00 0.00 40.34 4.79
3795 4007 2.699954 CTCACGGTACAGGCAAGATTT 58.300 47.619 0.00 0.00 0.00 2.17
4119 4331 4.621991 AGCACTTCATATACATCGGTGAC 58.378 43.478 0.65 0.00 0.00 3.67
4222 4435 3.564053 AAGTGGTGAAAACCGACCTTA 57.436 42.857 0.00 0.00 32.98 2.69


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

AutoCloner maintained by Alex Coulton.