Multiple sequence alignment - TraesCS1D01G068400

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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 TraesCS1D01G068400 chr1D 100.000 3808 0 0 1 3808 49955256 49959063 0.000000e+00 7033.0
1 TraesCS1D01G068400 chr1D 86.559 2485 328 5 1045 3526 50059258 50061739 0.000000e+00 2734.0
2 TraesCS1D01G068400 chr1D 83.025 2598 386 44 970 3529 49616960 49619540 0.000000e+00 2303.0
3 TraesCS1D01G068400 chr1D 83.535 2478 383 20 1003 3465 50022574 50025041 0.000000e+00 2292.0
4 TraesCS1D01G068400 chr1D 81.034 696 103 17 895 1582 50007350 50008024 1.100000e-145 527.0
5 TraesCS1D01G068400 chr1D 100.000 146 0 0 4327 4472 49959582 49959727 2.050000e-68 270.0
6 TraesCS1D01G068400 chr1A 91.683 3475 209 36 385 3808 49292749 49296194 0.000000e+00 4743.0
7 TraesCS1D01G068400 chr1A 86.499 2711 327 17 1019 3702 49346758 49349456 0.000000e+00 2942.0
8 TraesCS1D01G068400 chr1A 85.533 2758 361 19 970 3701 49354739 49357484 0.000000e+00 2848.0
9 TraesCS1D01G068400 chr1A 87.565 957 105 4 2755 3699 49304903 49305857 0.000000e+00 1096.0
10 TraesCS1D01G068400 chr1A 87.868 272 24 8 1 266 523367580 523367848 1.210000e-80 311.0
11 TraesCS1D01G068400 chr1A 97.436 117 3 0 4356 4472 49296940 49297056 2.730000e-47 200.0
12 TraesCS1D01G068400 chr1A 92.593 108 8 0 3701 3808 49305893 49306000 5.990000e-34 156.0
13 TraesCS1D01G068400 chr1B 93.390 2965 147 20 863 3808 70333655 70336589 0.000000e+00 4344.0
14 TraesCS1D01G068400 chr1B 82.330 2592 416 34 960 3518 70169708 70172290 0.000000e+00 2211.0
15 TraesCS1D01G068400 chr1B 96.396 111 4 0 4356 4466 70337055 70337165 2.750000e-42 183.0
16 TraesCS1D01G068400 chr1B 85.938 64 5 3 3576 3636 69355373 69355311 1.040000e-06 65.8
17 TraesCS1D01G068400 chr6A 83.162 2726 415 30 946 3640 547815065 547817777 0.000000e+00 2451.0
18 TraesCS1D01G068400 chr6B 82.919 2693 397 35 982 3640 601865816 601868479 0.000000e+00 2366.0
19 TraesCS1D01G068400 chr6B 85.352 355 33 11 1 339 182141781 182141430 2.560000e-92 350.0
20 TraesCS1D01G068400 chr6B 89.630 270 22 5 2 265 138299730 138299999 5.540000e-89 339.0
21 TraesCS1D01G068400 chr5A 89.773 352 20 7 2 340 670139603 670139951 1.910000e-118 436.0
22 TraesCS1D01G068400 chr5A 88.060 268 28 4 1 265 298550346 298550080 9.340000e-82 315.0
23 TraesCS1D01G068400 chr5A 86.380 279 21 6 1 265 298550625 298550900 5.660000e-74 289.0
24 TraesCS1D01G068400 chr3A 87.705 366 28 6 1 352 152658676 152659038 1.160000e-110 411.0
25 TraesCS1D01G068400 chr3A 85.399 363 35 10 1 347 706280184 706280544 1.180000e-95 361.0
26 TraesCS1D01G068400 chr7A 89.695 262 19 3 80 340 690434971 690434717 1.200000e-85 327.0
27 TraesCS1D01G068400 chrUn 87.868 272 24 8 1 266 410922988 410923256 1.210000e-80 311.0
28 TraesCS1D01G068400 chr3D 86.973 261 19 8 2 248 494651363 494651104 3.410000e-71 279.0
29 TraesCS1D01G068400 chr4A 80.795 302 22 8 1 266 641479453 641479754 2.110000e-48 204.0
30 TraesCS1D01G068400 chr7D 88.690 168 9 4 1 168 101744072 101744229 3.530000e-46 196.0
31 TraesCS1D01G068400 chr7D 90.345 145 10 2 125 266 101743454 101743311 2.120000e-43 187.0
32 TraesCS1D01G068400 chr4B 90.476 147 13 1 202 348 179845392 179845537 4.570000e-45 193.0
33 TraesCS1D01G068400 chr7B 87.952 166 15 5 184 347 466711365 466711203 1.640000e-44 191.0
34 TraesCS1D01G068400 chr4D 90.476 147 11 2 201 347 318469993 318469850 1.640000e-44 191.0
35 TraesCS1D01G068400 chr3B 87.273 165 18 3 184 347 42046156 42046318 7.640000e-43 185.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G068400 chr1D 49955256 49959727 4471 False 3651.5 7033 100.0000 1 4472 2 chr1D.!!$F5 4471
1 TraesCS1D01G068400 chr1D 50059258 50061739 2481 False 2734.0 2734 86.5590 1045 3526 1 chr1D.!!$F4 2481
2 TraesCS1D01G068400 chr1D 49616960 49619540 2580 False 2303.0 2303 83.0250 970 3529 1 chr1D.!!$F1 2559
3 TraesCS1D01G068400 chr1D 50022574 50025041 2467 False 2292.0 2292 83.5350 1003 3465 1 chr1D.!!$F3 2462
4 TraesCS1D01G068400 chr1D 50007350 50008024 674 False 527.0 527 81.0340 895 1582 1 chr1D.!!$F2 687
5 TraesCS1D01G068400 chr1A 49346758 49349456 2698 False 2942.0 2942 86.4990 1019 3702 1 chr1A.!!$F1 2683
6 TraesCS1D01G068400 chr1A 49354739 49357484 2745 False 2848.0 2848 85.5330 970 3701 1 chr1A.!!$F2 2731
7 TraesCS1D01G068400 chr1A 49292749 49297056 4307 False 2471.5 4743 94.5595 385 4472 2 chr1A.!!$F4 4087
8 TraesCS1D01G068400 chr1A 49304903 49306000 1097 False 626.0 1096 90.0790 2755 3808 2 chr1A.!!$F5 1053
9 TraesCS1D01G068400 chr1B 70333655 70337165 3510 False 2263.5 4344 94.8930 863 4466 2 chr1B.!!$F2 3603
10 TraesCS1D01G068400 chr1B 70169708 70172290 2582 False 2211.0 2211 82.3300 960 3518 1 chr1B.!!$F1 2558
11 TraesCS1D01G068400 chr6A 547815065 547817777 2712 False 2451.0 2451 83.1620 946 3640 1 chr6A.!!$F1 2694
12 TraesCS1D01G068400 chr6B 601865816 601868479 2663 False 2366.0 2366 82.9190 982 3640 1 chr6B.!!$F2 2658

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
254 255 0.106708 GATCCAATCGGCCAGCAGTA 59.893 55.0 2.24 0.0 0.0 2.74 F
423 424 0.107017 GCTGTGTGTGGAGGGCATAT 60.107 55.0 0.00 0.0 0.0 1.78 F
563 576 0.179161 CGAACGCGTCTCTCCAATCT 60.179 55.0 14.44 0.0 0.0 2.40 F
739 789 0.180642 TGTAACGCCCAAACCTGACA 59.819 50.0 0.00 0.0 0.0 3.58 F
775 825 0.323725 AACGCTGCCAAGATCCCATT 60.324 50.0 0.00 0.0 0.0 3.16 F
778 828 0.396139 GCTGCCAAGATCCCATTCCA 60.396 55.0 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1972 1.197721 GGAACAACTCTGCATTGTCCG 59.802 52.381 4.71 0.0 39.36 4.79 R
2138 2275 1.772836 ATCAGCAAAGCATCCTTCCC 58.227 50.000 0.00 0.0 0.00 3.97 R
2351 2488 2.906458 CATCAGCGAGCTTCCCCT 59.094 61.111 0.00 0.0 0.00 4.79 R
2382 2519 3.104512 TCCCGTACCAATCATCTCACTT 58.895 45.455 0.00 0.0 0.00 3.16 R
2415 2555 8.598916 TGAATTAGGGAGTGATAAACAACTGTA 58.401 33.333 0.00 0.0 0.00 2.74 R
3487 3630 3.243234 CCAAACCACGCAAACACTTATCA 60.243 43.478 0.00 0.0 0.00 2.15 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
57 58 9.829507 ATTCAACAGTTTCAAATATGTTTTCCA 57.170 25.926 1.89 0.00 33.76 3.53
58 59 8.870160 TCAACAGTTTCAAATATGTTTTCCAG 57.130 30.769 1.89 0.00 33.76 3.86
59 60 8.690884 TCAACAGTTTCAAATATGTTTTCCAGA 58.309 29.630 1.89 0.00 33.76 3.86
60 61 9.480053 CAACAGTTTCAAATATGTTTTCCAGAT 57.520 29.630 1.89 0.00 33.76 2.90
178 179 7.527568 TTCAATAGATAAATGGATGCATGCA 57.472 32.000 25.04 25.04 0.00 3.96
179 180 6.916440 TCAATAGATAAATGGATGCATGCAC 58.084 36.000 25.37 16.53 0.00 4.57
180 181 5.909621 ATAGATAAATGGATGCATGCACC 57.090 39.130 25.37 24.57 0.00 5.01
181 182 3.840991 AGATAAATGGATGCATGCACCT 58.159 40.909 25.37 15.25 0.00 4.00
182 183 3.572682 AGATAAATGGATGCATGCACCTG 59.427 43.478 25.37 0.00 0.00 4.00
183 184 1.563924 AAATGGATGCATGCACCTGT 58.436 45.000 25.37 6.94 0.00 4.00
184 185 1.108776 AATGGATGCATGCACCTGTC 58.891 50.000 25.37 16.57 0.00 3.51
185 186 1.099295 ATGGATGCATGCACCTGTCG 61.099 55.000 25.37 0.00 0.00 4.35
186 187 2.475466 GGATGCATGCACCTGTCGG 61.475 63.158 25.37 0.00 0.00 4.79
187 188 3.117175 GATGCATGCACCTGTCGGC 62.117 63.158 25.37 1.33 0.00 5.54
190 191 2.584064 CATGCACCTGTCGGCCTA 59.416 61.111 0.00 0.00 0.00 3.93
191 192 1.522355 CATGCACCTGTCGGCCTAG 60.522 63.158 0.00 0.00 0.00 3.02
192 193 1.685765 ATGCACCTGTCGGCCTAGA 60.686 57.895 0.00 0.00 0.00 2.43
193 194 1.680522 ATGCACCTGTCGGCCTAGAG 61.681 60.000 0.00 0.00 0.00 2.43
194 195 3.082579 GCACCTGTCGGCCTAGAGG 62.083 68.421 18.14 18.14 36.01 3.69
195 196 1.379977 CACCTGTCGGCCTAGAGGA 60.380 63.158 25.56 0.00 37.39 3.71
196 197 0.970937 CACCTGTCGGCCTAGAGGAA 60.971 60.000 25.56 0.00 37.39 3.36
197 198 0.684805 ACCTGTCGGCCTAGAGGAAG 60.685 60.000 25.56 1.27 37.39 3.46
198 199 1.439644 CTGTCGGCCTAGAGGAAGC 59.560 63.158 0.00 0.00 37.39 3.86
199 200 1.304962 TGTCGGCCTAGAGGAAGCA 60.305 57.895 0.00 0.00 37.39 3.91
200 201 1.323271 TGTCGGCCTAGAGGAAGCAG 61.323 60.000 0.00 0.00 37.39 4.24
201 202 1.038130 GTCGGCCTAGAGGAAGCAGA 61.038 60.000 0.00 0.00 37.39 4.26
202 203 1.038130 TCGGCCTAGAGGAAGCAGAC 61.038 60.000 0.00 0.00 37.39 3.51
203 204 1.040339 CGGCCTAGAGGAAGCAGACT 61.040 60.000 0.00 0.00 37.39 3.24
204 205 0.463620 GGCCTAGAGGAAGCAGACTG 59.536 60.000 0.00 0.00 37.39 3.51
205 206 0.463620 GCCTAGAGGAAGCAGACTGG 59.536 60.000 4.26 0.00 37.39 4.00
206 207 1.118838 CCTAGAGGAAGCAGACTGGG 58.881 60.000 4.26 0.00 37.39 4.45
207 208 0.463620 CTAGAGGAAGCAGACTGGGC 59.536 60.000 4.26 0.00 0.00 5.36
208 209 1.323271 TAGAGGAAGCAGACTGGGCG 61.323 60.000 4.26 0.00 36.08 6.13
209 210 4.400961 AGGAAGCAGACTGGGCGC 62.401 66.667 0.00 0.00 36.08 6.53
211 212 4.704833 GAAGCAGACTGGGCGCCA 62.705 66.667 30.85 13.75 36.08 5.69
215 216 3.052082 CAGACTGGGCGCCACTTG 61.052 66.667 30.85 16.68 0.00 3.16
216 217 4.335647 AGACTGGGCGCCACTTGG 62.336 66.667 30.85 14.73 38.53 3.61
227 228 2.987547 CACTTGGCCAGCAGTGGG 60.988 66.667 24.41 5.31 45.17 4.61
228 229 3.501911 ACTTGGCCAGCAGTGGGT 61.502 61.111 9.36 0.00 45.17 4.51
229 230 2.674380 CTTGGCCAGCAGTGGGTC 60.674 66.667 5.11 0.00 45.17 4.46
230 231 4.641645 TTGGCCAGCAGTGGGTCG 62.642 66.667 5.11 0.00 45.17 4.79
233 234 4.008933 GCCAGCAGTGGGTCGACT 62.009 66.667 16.46 0.00 45.17 4.18
234 235 2.047844 CCAGCAGTGGGTCGACTG 60.048 66.667 16.46 6.85 45.34 3.51
235 236 2.047844 CAGCAGTGGGTCGACTGG 60.048 66.667 16.46 2.04 43.17 4.00
236 237 2.203640 AGCAGTGGGTCGACTGGA 60.204 61.111 16.46 0.00 43.17 3.86
237 238 1.610673 AGCAGTGGGTCGACTGGAT 60.611 57.895 16.46 0.00 43.17 3.41
238 239 1.153549 GCAGTGGGTCGACTGGATC 60.154 63.158 16.46 0.00 43.17 3.36
243 244 3.688553 GGGTCGACTGGATCCAATC 57.311 57.895 17.00 15.09 46.04 2.67
244 245 0.249489 GGGTCGACTGGATCCAATCG 60.249 60.000 33.87 33.87 46.04 3.34
245 246 0.249489 GGTCGACTGGATCCAATCGG 60.249 60.000 36.90 22.48 44.36 4.18
246 247 0.876342 GTCGACTGGATCCAATCGGC 60.876 60.000 36.90 34.29 44.36 5.54
247 248 1.595382 CGACTGGATCCAATCGGCC 60.595 63.158 32.52 6.34 41.20 6.13
248 249 1.526887 GACTGGATCCAATCGGCCA 59.473 57.895 17.00 0.00 0.00 5.36
249 250 4.469883 CTGGATCCAATCGGCCAG 57.530 61.111 17.00 0.00 41.62 4.85
250 251 1.895707 CTGGATCCAATCGGCCAGC 60.896 63.158 17.00 0.00 41.17 4.85
251 252 2.192979 GGATCCAATCGGCCAGCA 59.807 61.111 6.95 0.00 0.00 4.41
252 253 1.895707 GGATCCAATCGGCCAGCAG 60.896 63.158 6.95 0.00 0.00 4.24
253 254 1.153086 GATCCAATCGGCCAGCAGT 60.153 57.895 2.24 0.00 0.00 4.40
254 255 0.106708 GATCCAATCGGCCAGCAGTA 59.893 55.000 2.24 0.00 0.00 2.74
255 256 0.107456 ATCCAATCGGCCAGCAGTAG 59.893 55.000 2.24 0.00 0.00 2.57
256 257 1.524621 CCAATCGGCCAGCAGTAGG 60.525 63.158 2.24 0.00 0.00 3.18
266 267 3.393360 GCAGTAGGCTGACTGGGT 58.607 61.111 19.01 0.00 45.85 4.51
267 268 2.591915 GCAGTAGGCTGACTGGGTA 58.408 57.895 19.01 0.00 45.85 3.69
268 269 1.123928 GCAGTAGGCTGACTGGGTAT 58.876 55.000 19.01 0.00 45.85 2.73
269 270 1.486726 GCAGTAGGCTGACTGGGTATT 59.513 52.381 19.01 0.00 45.85 1.89
270 271 2.698797 GCAGTAGGCTGACTGGGTATTA 59.301 50.000 19.01 0.00 45.85 0.98
271 272 3.325135 GCAGTAGGCTGACTGGGTATTAT 59.675 47.826 19.01 0.00 45.85 1.28
272 273 4.202367 GCAGTAGGCTGACTGGGTATTATT 60.202 45.833 19.01 0.00 45.85 1.40
273 274 5.687706 GCAGTAGGCTGACTGGGTATTATTT 60.688 44.000 19.01 0.00 45.85 1.40
274 275 6.357367 CAGTAGGCTGACTGGGTATTATTTT 58.643 40.000 13.17 0.00 45.28 1.82
275 276 6.828785 CAGTAGGCTGACTGGGTATTATTTTT 59.171 38.462 13.17 0.00 45.28 1.94
276 277 6.828785 AGTAGGCTGACTGGGTATTATTTTTG 59.171 38.462 0.00 0.00 0.00 2.44
277 278 5.826643 AGGCTGACTGGGTATTATTTTTGA 58.173 37.500 0.00 0.00 0.00 2.69
278 279 6.252995 AGGCTGACTGGGTATTATTTTTGAA 58.747 36.000 0.00 0.00 0.00 2.69
279 280 6.723977 AGGCTGACTGGGTATTATTTTTGAAA 59.276 34.615 0.00 0.00 0.00 2.69
280 281 7.234577 AGGCTGACTGGGTATTATTTTTGAAAA 59.765 33.333 0.00 0.00 0.00 2.29
281 282 7.875554 GGCTGACTGGGTATTATTTTTGAAAAA 59.124 33.333 5.47 5.47 0.00 1.94
282 283 9.435688 GCTGACTGGGTATTATTTTTGAAAAAT 57.564 29.630 18.56 18.56 0.00 1.82
365 366 2.919666 CTGAAAACCAGCCGTTATGG 57.080 50.000 0.00 0.00 43.87 2.74
374 375 4.813346 CCGTTATGGCCATACCCC 57.187 61.111 25.39 14.40 37.83 4.95
375 376 1.840598 CCGTTATGGCCATACCCCA 59.159 57.895 25.39 7.91 37.83 4.96
376 377 0.404040 CCGTTATGGCCATACCCCAT 59.596 55.000 25.39 0.68 44.85 4.00
377 378 1.613255 CCGTTATGGCCATACCCCATC 60.613 57.143 25.39 10.22 41.97 3.51
378 379 1.821216 GTTATGGCCATACCCCATCG 58.179 55.000 25.39 0.00 41.97 3.84
379 380 1.073284 GTTATGGCCATACCCCATCGT 59.927 52.381 25.39 0.00 41.97 3.73
380 381 0.690192 TATGGCCATACCCCATCGTG 59.310 55.000 21.94 0.00 41.97 4.35
381 382 2.067932 ATGGCCATACCCCATCGTGG 62.068 60.000 19.18 0.00 38.71 4.94
382 383 2.448582 GGCCATACCCCATCGTGGA 61.449 63.158 0.00 0.00 40.96 4.02
383 384 1.071471 GCCATACCCCATCGTGGAG 59.929 63.158 5.71 0.00 40.96 3.86
409 410 3.073735 AGGAGCTCCTCGGCTGTG 61.074 66.667 30.40 0.00 44.77 3.66
410 411 3.386237 GGAGCTCCTCGGCTGTGT 61.386 66.667 26.25 0.00 43.20 3.72
411 412 2.125753 GAGCTCCTCGGCTGTGTG 60.126 66.667 0.87 0.00 43.20 3.82
412 413 2.919856 AGCTCCTCGGCTGTGTGT 60.920 61.111 0.00 0.00 41.43 3.72
413 414 2.740055 GCTCCTCGGCTGTGTGTG 60.740 66.667 0.00 0.00 0.00 3.82
414 415 2.047844 CTCCTCGGCTGTGTGTGG 60.048 66.667 0.00 0.00 0.00 4.17
415 416 2.523168 TCCTCGGCTGTGTGTGGA 60.523 61.111 0.00 0.00 0.00 4.02
416 417 2.047844 CCTCGGCTGTGTGTGGAG 60.048 66.667 0.00 0.00 0.00 3.86
420 421 4.269523 GGCTGTGTGTGGAGGGCA 62.270 66.667 0.00 0.00 0.00 5.36
421 422 2.034687 GCTGTGTGTGGAGGGCAT 59.965 61.111 0.00 0.00 0.00 4.40
422 423 1.299648 GCTGTGTGTGGAGGGCATA 59.700 57.895 0.00 0.00 0.00 3.14
423 424 0.107017 GCTGTGTGTGGAGGGCATAT 60.107 55.000 0.00 0.00 0.00 1.78
424 425 1.671979 CTGTGTGTGGAGGGCATATG 58.328 55.000 0.00 0.00 0.00 1.78
426 427 1.210234 TGTGTGTGGAGGGCATATGAG 59.790 52.381 6.97 0.00 0.00 2.90
443 444 1.970917 GAGATGTGCTTTGGCCGACG 61.971 60.000 0.00 0.00 37.74 5.12
468 469 2.430332 TGCTTAAATAGTTGGGGCATGC 59.570 45.455 9.90 9.90 0.00 4.06
469 470 2.543653 GCTTAAATAGTTGGGGCATGCG 60.544 50.000 12.44 0.00 0.00 4.73
472 473 1.392589 AATAGTTGGGGCATGCGAAG 58.607 50.000 12.44 0.00 0.00 3.79
491 492 0.725784 GCGACACCGTTTCATTGCAG 60.726 55.000 0.00 0.00 38.24 4.41
497 498 3.193267 ACACCGTTTCATTGCAGCATAAT 59.807 39.130 0.00 0.00 0.00 1.28
499 500 3.193267 ACCGTTTCATTGCAGCATAATGT 59.807 39.130 0.00 0.00 36.97 2.71
500 501 3.792956 CCGTTTCATTGCAGCATAATGTC 59.207 43.478 0.00 0.00 36.97 3.06
505 506 1.667236 TTGCAGCATAATGTCCGGAG 58.333 50.000 3.06 0.00 0.00 4.63
516 517 0.331954 TGTCCGGAGTAGGCTTCTCT 59.668 55.000 18.85 3.94 33.06 3.10
531 544 1.297893 CTCTGCATTAAAGCGGCGC 60.298 57.895 26.86 26.86 40.71 6.53
533 546 3.050166 CTGCATTAAAGCGGCGCCA 62.050 57.895 30.40 16.27 37.31 5.69
534 547 2.579518 GCATTAAAGCGGCGCCAC 60.580 61.111 30.40 18.62 0.00 5.01
563 576 0.179161 CGAACGCGTCTCTCCAATCT 60.179 55.000 14.44 0.00 0.00 2.40
569 582 1.067565 GCGTCTCTCCAATCTGTGTCA 60.068 52.381 0.00 0.00 0.00 3.58
641 683 1.453155 GCATGACGATGAGTTTGGGT 58.547 50.000 0.00 0.00 0.00 4.51
642 684 1.131126 GCATGACGATGAGTTTGGGTG 59.869 52.381 0.00 0.00 0.00 4.61
643 685 2.698803 CATGACGATGAGTTTGGGTGA 58.301 47.619 0.00 0.00 0.00 4.02
644 686 2.455674 TGACGATGAGTTTGGGTGAG 57.544 50.000 0.00 0.00 0.00 3.51
645 687 1.079503 GACGATGAGTTTGGGTGAGC 58.920 55.000 0.00 0.00 0.00 4.26
646 688 0.396435 ACGATGAGTTTGGGTGAGCA 59.604 50.000 0.00 0.00 0.00 4.26
647 689 1.202758 ACGATGAGTTTGGGTGAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
648 690 1.197721 CGATGAGTTTGGGTGAGCAAC 59.802 52.381 0.00 0.00 0.00 4.17
674 716 1.342174 AGGTTTGATGCTGGTTTGCAG 59.658 47.619 0.00 0.00 46.71 4.41
715 765 0.729690 GCGTTGGATGCCTTCTTCTC 59.270 55.000 0.00 0.00 0.00 2.87
716 766 1.677217 GCGTTGGATGCCTTCTTCTCT 60.677 52.381 0.00 0.00 0.00 3.10
717 767 2.005451 CGTTGGATGCCTTCTTCTCTG 58.995 52.381 0.00 0.00 0.00 3.35
718 768 2.354103 CGTTGGATGCCTTCTTCTCTGA 60.354 50.000 0.00 0.00 0.00 3.27
719 769 3.679389 GTTGGATGCCTTCTTCTCTGAA 58.321 45.455 0.00 0.00 0.00 3.02
721 771 3.882444 TGGATGCCTTCTTCTCTGAATG 58.118 45.455 0.00 0.00 0.00 2.67
722 772 3.265221 TGGATGCCTTCTTCTCTGAATGT 59.735 43.478 0.00 0.00 0.00 2.71
723 773 4.471025 TGGATGCCTTCTTCTCTGAATGTA 59.529 41.667 0.00 0.00 0.00 2.29
724 774 5.045651 TGGATGCCTTCTTCTCTGAATGTAA 60.046 40.000 0.00 0.00 0.00 2.41
725 775 5.295540 GGATGCCTTCTTCTCTGAATGTAAC 59.704 44.000 0.00 0.00 0.00 2.50
727 777 3.062774 GCCTTCTTCTCTGAATGTAACGC 59.937 47.826 0.00 0.00 0.00 4.84
729 779 3.247006 TCTTCTCTGAATGTAACGCCC 57.753 47.619 0.00 0.00 0.00 6.13
730 780 2.565391 TCTTCTCTGAATGTAACGCCCA 59.435 45.455 0.00 0.00 0.00 5.36
732 782 3.410631 TCTCTGAATGTAACGCCCAAA 57.589 42.857 0.00 0.00 0.00 3.28
733 783 3.071479 TCTCTGAATGTAACGCCCAAAC 58.929 45.455 0.00 0.00 0.00 2.93
734 784 2.156098 TCTGAATGTAACGCCCAAACC 58.844 47.619 0.00 0.00 0.00 3.27
735 785 2.159382 CTGAATGTAACGCCCAAACCT 58.841 47.619 0.00 0.00 0.00 3.50
736 786 1.883275 TGAATGTAACGCCCAAACCTG 59.117 47.619 0.00 0.00 0.00 4.00
737 787 2.156098 GAATGTAACGCCCAAACCTGA 58.844 47.619 0.00 0.00 0.00 3.86
738 788 1.530323 ATGTAACGCCCAAACCTGAC 58.470 50.000 0.00 0.00 0.00 3.51
739 789 0.180642 TGTAACGCCCAAACCTGACA 59.819 50.000 0.00 0.00 0.00 3.58
740 790 1.202830 TGTAACGCCCAAACCTGACAT 60.203 47.619 0.00 0.00 0.00 3.06
741 791 2.038689 TGTAACGCCCAAACCTGACATA 59.961 45.455 0.00 0.00 0.00 2.29
742 792 2.507407 AACGCCCAAACCTGACATAT 57.493 45.000 0.00 0.00 0.00 1.78
743 793 3.637911 AACGCCCAAACCTGACATATA 57.362 42.857 0.00 0.00 0.00 0.86
744 794 2.914059 ACGCCCAAACCTGACATATAC 58.086 47.619 0.00 0.00 0.00 1.47
745 795 2.504175 ACGCCCAAACCTGACATATACT 59.496 45.455 0.00 0.00 0.00 2.12
746 796 3.131396 CGCCCAAACCTGACATATACTC 58.869 50.000 0.00 0.00 0.00 2.59
747 797 3.131396 GCCCAAACCTGACATATACTCG 58.869 50.000 0.00 0.00 0.00 4.18
748 798 3.431766 GCCCAAACCTGACATATACTCGT 60.432 47.826 0.00 0.00 0.00 4.18
749 799 4.202182 GCCCAAACCTGACATATACTCGTA 60.202 45.833 0.00 0.00 0.00 3.43
753 803 5.415415 AACCTGACATATACTCGTACGTC 57.585 43.478 16.05 3.18 0.00 4.34
755 805 3.467766 CTGACATATACTCGTACGTCGC 58.532 50.000 16.05 0.00 39.67 5.19
775 825 0.323725 AACGCTGCCAAGATCCCATT 60.324 50.000 0.00 0.00 0.00 3.16
776 826 0.749454 ACGCTGCCAAGATCCCATTC 60.749 55.000 0.00 0.00 0.00 2.67
777 827 1.450531 CGCTGCCAAGATCCCATTCC 61.451 60.000 0.00 0.00 0.00 3.01
778 828 0.396139 GCTGCCAAGATCCCATTCCA 60.396 55.000 0.00 0.00 0.00 3.53
779 829 1.756690 GCTGCCAAGATCCCATTCCAT 60.757 52.381 0.00 0.00 0.00 3.41
780 830 2.489619 GCTGCCAAGATCCCATTCCATA 60.490 50.000 0.00 0.00 0.00 2.74
782 832 2.165998 GCCAAGATCCCATTCCATAGC 58.834 52.381 0.00 0.00 0.00 2.97
783 833 2.800250 CCAAGATCCCATTCCATAGCC 58.200 52.381 0.00 0.00 0.00 3.93
785 835 3.181425 CCAAGATCCCATTCCATAGCCTT 60.181 47.826 0.00 0.00 0.00 4.35
787 837 4.379302 AGATCCCATTCCATAGCCTTTC 57.621 45.455 0.00 0.00 0.00 2.62
790 840 4.329638 TCCCATTCCATAGCCTTTCAAA 57.670 40.909 0.00 0.00 0.00 2.69
792 842 5.090139 TCCCATTCCATAGCCTTTCAAAAA 58.910 37.500 0.00 0.00 0.00 1.94
829 879 1.154205 CCCATTCCTTAGCGCAGACG 61.154 60.000 11.47 0.00 44.07 4.18
831 881 0.647410 CATTCCTTAGCGCAGACGTG 59.353 55.000 11.47 0.00 42.83 4.49
853 903 0.746204 TTGAACACGCTCCAGCAACA 60.746 50.000 0.00 0.00 42.21 3.33
865 919 1.408822 CCAGCAACAGTAATCCCCTCC 60.409 57.143 0.00 0.00 0.00 4.30
869 923 1.632965 AACAGTAATCCCCTCCCGCC 61.633 60.000 0.00 0.00 0.00 6.13
1394 1519 0.958876 CTCATGAACTGCTGCTGCCA 60.959 55.000 13.47 3.94 38.71 4.92
1835 1972 4.043200 GTGCAAGGCCCGAGCAAC 62.043 66.667 15.00 7.08 42.56 4.17
2138 2275 1.078497 TGCTCCACGGGTATGCAAG 60.078 57.895 0.00 0.00 0.00 4.01
2139 2276 1.819632 GCTCCACGGGTATGCAAGG 60.820 63.158 0.00 0.00 0.00 3.61
2210 2347 1.406887 CGGTATTGTAGCCAACTGCCT 60.407 52.381 0.00 0.00 42.71 4.75
2219 2356 1.136891 AGCCAACTGCCTTGTTTTCAC 59.863 47.619 0.00 0.00 42.71 3.18
2361 2498 1.543358 CTTTGCAGAAAGGGGAAGCTC 59.457 52.381 0.00 0.00 35.78 4.09
2382 2519 5.714047 CTCGCTGATGCTATGGATAAGTTA 58.286 41.667 0.00 0.00 36.97 2.24
2501 2641 7.396540 AGGAGTTGGTTTATGAAATGATGAC 57.603 36.000 0.00 0.00 0.00 3.06
2824 2967 6.875726 TCTGTTCAGAGAAATGTCACATAAGG 59.124 38.462 0.00 0.00 0.00 2.69
2957 3100 2.738846 CAGTGAGCTTGTCCACATACAC 59.261 50.000 6.11 0.00 35.84 2.90
3487 3630 2.089980 GTTGATGCACTGGAATCAGCT 58.910 47.619 0.00 0.00 40.23 4.24
3498 3649 5.413833 CACTGGAATCAGCTGATAAGTGTTT 59.586 40.000 33.47 20.84 44.59 2.83
3716 3939 7.833682 TGGTGAAAGATATCAAGCTATTTGGAA 59.166 33.333 5.32 0.00 37.39 3.53
3733 3956 2.275318 GGAATTCTCTGAACCTCAGCG 58.725 52.381 5.23 0.00 43.95 5.18
4408 5318 3.581755 TGCTCCAACATGTACGTTCTAC 58.418 45.455 0.00 0.00 0.00 2.59
4415 5325 8.192068 TCCAACATGTACGTTCTACAAATATG 57.808 34.615 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.829507 TGGAAAACATATTTGAAACTGTTGAAT 57.170 25.926 8.04 0.00 32.47 2.57
32 33 9.311916 CTGGAAAACATATTTGAAACTGTTGAA 57.688 29.630 8.04 0.00 32.47 2.69
33 34 8.690884 TCTGGAAAACATATTTGAAACTGTTGA 58.309 29.630 8.04 0.62 32.47 3.18
34 35 8.870160 TCTGGAAAACATATTTGAAACTGTTG 57.130 30.769 8.04 0.00 32.47 3.33
152 153 9.245481 TGCATGCATCCATTTATCTATTGAATA 57.755 29.630 18.46 0.00 0.00 1.75
153 154 8.033038 GTGCATGCATCCATTTATCTATTGAAT 58.967 33.333 25.64 0.00 0.00 2.57
154 155 7.372714 GTGCATGCATCCATTTATCTATTGAA 58.627 34.615 25.64 0.00 0.00 2.69
155 156 6.071784 GGTGCATGCATCCATTTATCTATTGA 60.072 38.462 25.64 0.00 0.00 2.57
156 157 6.071560 AGGTGCATGCATCCATTTATCTATTG 60.072 38.462 27.12 0.00 0.00 1.90
157 158 6.014647 AGGTGCATGCATCCATTTATCTATT 58.985 36.000 27.12 0.88 0.00 1.73
158 159 5.417894 CAGGTGCATGCATCCATTTATCTAT 59.582 40.000 27.12 1.45 0.00 1.98
159 160 4.763279 CAGGTGCATGCATCCATTTATCTA 59.237 41.667 27.12 0.00 0.00 1.98
160 161 3.572682 CAGGTGCATGCATCCATTTATCT 59.427 43.478 27.12 3.05 0.00 1.98
161 162 3.319972 ACAGGTGCATGCATCCATTTATC 59.680 43.478 27.12 8.92 0.00 1.75
162 163 3.302161 ACAGGTGCATGCATCCATTTAT 58.698 40.909 27.12 4.68 0.00 1.40
163 164 2.689471 GACAGGTGCATGCATCCATTTA 59.311 45.455 27.12 0.00 0.00 1.40
164 165 1.479323 GACAGGTGCATGCATCCATTT 59.521 47.619 27.12 14.91 0.00 2.32
165 166 1.108776 GACAGGTGCATGCATCCATT 58.891 50.000 27.12 17.09 0.00 3.16
166 167 1.099295 CGACAGGTGCATGCATCCAT 61.099 55.000 27.12 15.73 0.00 3.41
167 168 1.746239 CGACAGGTGCATGCATCCA 60.746 57.895 27.12 0.00 0.00 3.41
168 169 2.475466 CCGACAGGTGCATGCATCC 61.475 63.158 27.12 25.11 0.00 3.51
169 170 3.104766 CCGACAGGTGCATGCATC 58.895 61.111 25.64 24.66 0.00 3.91
170 171 3.136123 GCCGACAGGTGCATGCAT 61.136 61.111 25.64 7.59 40.50 3.96
172 173 3.680620 TAGGCCGACAGGTGCATGC 62.681 63.158 11.82 11.82 40.50 4.06
173 174 1.522355 CTAGGCCGACAGGTGCATG 60.522 63.158 0.00 0.00 40.50 4.06
174 175 1.680522 CTCTAGGCCGACAGGTGCAT 61.681 60.000 0.00 0.00 40.50 3.96
175 176 2.283604 TCTAGGCCGACAGGTGCA 60.284 61.111 0.00 0.00 40.50 4.57
176 177 2.496817 CTCTAGGCCGACAGGTGC 59.503 66.667 0.00 0.00 40.50 5.01
177 178 0.970937 TTCCTCTAGGCCGACAGGTG 60.971 60.000 14.53 3.88 40.50 4.00
178 179 0.684805 CTTCCTCTAGGCCGACAGGT 60.685 60.000 14.53 0.00 40.50 4.00
179 180 2.022240 GCTTCCTCTAGGCCGACAGG 62.022 65.000 9.98 9.98 41.62 4.00
180 181 1.323271 TGCTTCCTCTAGGCCGACAG 61.323 60.000 0.00 0.00 34.44 3.51
181 182 1.304962 TGCTTCCTCTAGGCCGACA 60.305 57.895 0.00 0.00 34.44 4.35
182 183 1.038130 TCTGCTTCCTCTAGGCCGAC 61.038 60.000 0.00 0.00 34.44 4.79
183 184 1.038130 GTCTGCTTCCTCTAGGCCGA 61.038 60.000 0.00 0.00 34.44 5.54
184 185 1.040339 AGTCTGCTTCCTCTAGGCCG 61.040 60.000 0.00 0.00 34.44 6.13
185 186 0.463620 CAGTCTGCTTCCTCTAGGCC 59.536 60.000 0.00 0.00 34.44 5.19
186 187 0.463620 CCAGTCTGCTTCCTCTAGGC 59.536 60.000 0.00 0.00 34.44 3.93
187 188 1.118838 CCCAGTCTGCTTCCTCTAGG 58.881 60.000 0.00 0.00 0.00 3.02
188 189 0.463620 GCCCAGTCTGCTTCCTCTAG 59.536 60.000 0.00 0.00 0.00 2.43
189 190 1.323271 CGCCCAGTCTGCTTCCTCTA 61.323 60.000 0.00 0.00 0.00 2.43
190 191 2.654079 CGCCCAGTCTGCTTCCTCT 61.654 63.158 0.00 0.00 0.00 3.69
191 192 2.125350 CGCCCAGTCTGCTTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
192 193 4.400961 GCGCCCAGTCTGCTTCCT 62.401 66.667 0.00 0.00 0.00 3.36
194 195 4.704833 TGGCGCCCAGTCTGCTTC 62.705 66.667 26.77 0.00 0.00 3.86
198 199 3.052082 CAAGTGGCGCCCAGTCTG 61.052 66.667 26.77 10.35 35.94 3.51
199 200 4.335647 CCAAGTGGCGCCCAGTCT 62.336 66.667 26.77 14.14 35.94 3.24
209 210 2.987547 CCACTGCTGGCCAAGTGG 60.988 66.667 32.51 32.51 44.55 4.00
210 211 2.987547 CCCACTGCTGGCCAAGTG 60.988 66.667 24.96 24.96 36.00 3.16
211 212 3.497884 GACCCACTGCTGGCCAAGT 62.498 63.158 7.01 5.37 36.00 3.16
212 213 2.674380 GACCCACTGCTGGCCAAG 60.674 66.667 7.01 4.55 36.00 3.61
213 214 4.641645 CGACCCACTGCTGGCCAA 62.642 66.667 7.01 0.00 36.00 4.52
216 217 4.008933 AGTCGACCCACTGCTGGC 62.009 66.667 13.01 0.00 36.00 4.85
217 218 2.047844 CAGTCGACCCACTGCTGG 60.048 66.667 13.01 0.00 37.58 4.85
218 219 1.892819 ATCCAGTCGACCCACTGCTG 61.893 60.000 13.01 1.50 42.29 4.41
219 220 1.608717 GATCCAGTCGACCCACTGCT 61.609 60.000 13.01 0.00 42.29 4.24
220 221 1.153549 GATCCAGTCGACCCACTGC 60.154 63.158 13.01 0.00 42.29 4.40
221 222 1.257750 TGGATCCAGTCGACCCACTG 61.258 60.000 11.44 3.52 43.13 3.66
222 223 0.544357 TTGGATCCAGTCGACCCACT 60.544 55.000 15.53 0.00 0.00 4.00
223 224 0.541863 ATTGGATCCAGTCGACCCAC 59.458 55.000 15.53 0.00 0.00 4.61
224 225 0.830648 GATTGGATCCAGTCGACCCA 59.169 55.000 20.21 9.26 0.00 4.51
225 226 3.688553 GATTGGATCCAGTCGACCC 57.311 57.895 20.21 6.38 0.00 4.46
230 231 0.533755 CTGGCCGATTGGATCCAGTC 60.534 60.000 23.82 23.82 39.45 3.51
231 232 1.528824 CTGGCCGATTGGATCCAGT 59.471 57.895 15.53 12.79 39.45 4.00
232 233 1.895707 GCTGGCCGATTGGATCCAG 60.896 63.158 15.53 17.48 44.28 3.86
233 234 2.192979 GCTGGCCGATTGGATCCA 59.807 61.111 11.44 11.44 37.49 3.41
234 235 1.895707 CTGCTGGCCGATTGGATCC 60.896 63.158 4.20 4.20 37.49 3.36
235 236 0.106708 TACTGCTGGCCGATTGGATC 59.893 55.000 1.98 0.00 37.49 3.36
236 237 0.107456 CTACTGCTGGCCGATTGGAT 59.893 55.000 1.98 0.00 37.49 3.41
237 238 1.522092 CTACTGCTGGCCGATTGGA 59.478 57.895 1.98 0.00 37.49 3.53
238 239 1.524621 CCTACTGCTGGCCGATTGG 60.525 63.158 0.00 0.00 38.77 3.16
239 240 2.182842 GCCTACTGCTGGCCGATTG 61.183 63.158 0.00 0.00 44.32 2.67
240 241 2.190578 GCCTACTGCTGGCCGATT 59.809 61.111 0.00 0.00 44.32 3.34
249 250 1.123928 ATACCCAGTCAGCCTACTGC 58.876 55.000 9.94 0.00 44.56 4.40
250 251 5.552870 AATAATACCCAGTCAGCCTACTG 57.447 43.478 8.70 8.70 45.33 2.74
251 252 6.576778 AAAATAATACCCAGTCAGCCTACT 57.423 37.500 0.00 0.00 0.00 2.57
252 253 6.826741 TCAAAAATAATACCCAGTCAGCCTAC 59.173 38.462 0.00 0.00 0.00 3.18
253 254 6.964464 TCAAAAATAATACCCAGTCAGCCTA 58.036 36.000 0.00 0.00 0.00 3.93
254 255 5.826643 TCAAAAATAATACCCAGTCAGCCT 58.173 37.500 0.00 0.00 0.00 4.58
255 256 6.524101 TTCAAAAATAATACCCAGTCAGCC 57.476 37.500 0.00 0.00 0.00 4.85
256 257 8.825667 TTTTTCAAAAATAATACCCAGTCAGC 57.174 30.769 0.00 0.00 0.00 4.26
346 347 2.919666 CCATAACGGCTGGTTTTCAG 57.080 50.000 0.00 0.00 46.03 3.02
357 358 0.404040 ATGGGGTATGGCCATAACGG 59.596 55.000 30.05 0.00 39.65 4.44
358 359 1.821216 GATGGGGTATGGCCATAACG 58.179 55.000 30.05 0.00 39.65 3.18
359 360 1.073284 ACGATGGGGTATGGCCATAAC 59.927 52.381 29.69 29.69 39.65 1.89
360 361 1.073125 CACGATGGGGTATGGCCATAA 59.927 52.381 27.04 12.17 39.65 1.90
361 362 0.690192 CACGATGGGGTATGGCCATA 59.310 55.000 21.94 21.94 39.65 2.74
362 363 1.455849 CACGATGGGGTATGGCCAT 59.544 57.895 24.45 24.45 39.65 4.40
363 364 2.751731 CCACGATGGGGTATGGCCA 61.752 63.158 8.56 8.56 39.65 5.36
364 365 2.113139 CCACGATGGGGTATGGCC 59.887 66.667 0.00 0.00 32.67 5.36
365 366 1.071471 CTCCACGATGGGGTATGGC 59.929 63.158 0.00 0.00 38.32 4.40
366 367 0.762842 TCCTCCACGATGGGGTATGG 60.763 60.000 0.00 0.00 35.80 2.74
367 368 0.681733 CTCCTCCACGATGGGGTATG 59.318 60.000 0.00 0.00 35.80 2.39
368 369 0.561184 TCTCCTCCACGATGGGGTAT 59.439 55.000 0.00 0.00 35.80 2.73
369 370 0.106167 CTCTCCTCCACGATGGGGTA 60.106 60.000 0.00 0.00 35.80 3.69
370 371 1.381872 CTCTCCTCCACGATGGGGT 60.382 63.158 0.00 0.00 35.80 4.95
371 372 2.136878 CCTCTCCTCCACGATGGGG 61.137 68.421 0.00 0.00 37.90 4.96
372 373 1.075970 TCCTCTCCTCCACGATGGG 60.076 63.158 0.00 0.00 38.32 4.00
373 374 0.106469 TCTCCTCTCCTCCACGATGG 60.106 60.000 0.00 0.00 39.43 3.51
374 375 1.317613 CTCTCCTCTCCTCCACGATG 58.682 60.000 0.00 0.00 0.00 3.84
375 376 0.184933 CCTCTCCTCTCCTCCACGAT 59.815 60.000 0.00 0.00 0.00 3.73
376 377 0.914902 TCCTCTCCTCTCCTCCACGA 60.915 60.000 0.00 0.00 0.00 4.35
377 378 0.465460 CTCCTCTCCTCTCCTCCACG 60.465 65.000 0.00 0.00 0.00 4.94
378 379 0.755327 GCTCCTCTCCTCTCCTCCAC 60.755 65.000 0.00 0.00 0.00 4.02
379 380 0.923729 AGCTCCTCTCCTCTCCTCCA 60.924 60.000 0.00 0.00 0.00 3.86
380 381 0.178990 GAGCTCCTCTCCTCTCCTCC 60.179 65.000 0.87 0.00 35.77 4.30
381 382 3.421567 GAGCTCCTCTCCTCTCCTC 57.578 63.158 0.87 0.00 35.77 3.71
406 407 1.210234 CTCATATGCCCTCCACACACA 59.790 52.381 0.00 0.00 0.00 3.72
408 409 1.878211 TCTCATATGCCCTCCACACA 58.122 50.000 0.00 0.00 0.00 3.72
409 410 2.105477 ACATCTCATATGCCCTCCACAC 59.895 50.000 0.00 0.00 0.00 3.82
410 411 2.105306 CACATCTCATATGCCCTCCACA 59.895 50.000 0.00 0.00 0.00 4.17
411 412 2.775890 CACATCTCATATGCCCTCCAC 58.224 52.381 0.00 0.00 0.00 4.02
412 413 1.072806 GCACATCTCATATGCCCTCCA 59.927 52.381 0.00 0.00 33.06 3.86
413 414 1.350351 AGCACATCTCATATGCCCTCC 59.650 52.381 0.00 0.00 40.33 4.30
414 415 2.855209 AGCACATCTCATATGCCCTC 57.145 50.000 0.00 0.00 40.33 4.30
415 416 3.220110 CAAAGCACATCTCATATGCCCT 58.780 45.455 0.00 0.00 40.33 5.19
416 417 2.295349 CCAAAGCACATCTCATATGCCC 59.705 50.000 0.00 0.00 40.33 5.36
419 420 2.031420 CGGCCAAAGCACATCTCATATG 60.031 50.000 2.24 0.00 42.56 1.78
420 421 2.158769 TCGGCCAAAGCACATCTCATAT 60.159 45.455 2.24 0.00 42.56 1.78
421 422 1.209261 TCGGCCAAAGCACATCTCATA 59.791 47.619 2.24 0.00 42.56 2.15
422 423 0.035152 TCGGCCAAAGCACATCTCAT 60.035 50.000 2.24 0.00 42.56 2.90
423 424 0.955428 GTCGGCCAAAGCACATCTCA 60.955 55.000 2.24 0.00 42.56 3.27
424 425 1.796796 GTCGGCCAAAGCACATCTC 59.203 57.895 2.24 0.00 42.56 2.75
426 427 2.480555 CGTCGGCCAAAGCACATC 59.519 61.111 2.24 0.00 42.56 3.06
443 444 2.031870 CCCCAACTATTTAAGCAGGGC 58.968 52.381 0.00 0.00 39.97 5.19
445 446 2.733956 TGCCCCAACTATTTAAGCAGG 58.266 47.619 0.00 0.00 0.00 4.85
449 450 2.948979 TCGCATGCCCCAACTATTTAAG 59.051 45.455 13.15 0.00 0.00 1.85
452 453 1.750778 CTTCGCATGCCCCAACTATTT 59.249 47.619 13.15 0.00 0.00 1.40
468 469 0.511221 AATGAAACGGTGTCGCTTCG 59.489 50.000 0.00 0.00 42.42 3.79
469 470 1.950472 CAATGAAACGGTGTCGCTTC 58.050 50.000 0.00 0.00 40.62 3.86
472 473 0.725784 CTGCAATGAAACGGTGTCGC 60.726 55.000 0.00 0.00 40.63 5.19
473 474 0.725784 GCTGCAATGAAACGGTGTCG 60.726 55.000 0.00 0.00 43.02 4.35
477 478 3.193267 ACATTATGCTGCAATGAAACGGT 59.807 39.130 18.40 6.57 36.95 4.83
481 482 3.181488 CCGGACATTATGCTGCAATGAAA 60.181 43.478 18.40 6.87 36.95 2.69
486 487 1.065491 ACTCCGGACATTATGCTGCAA 60.065 47.619 6.36 0.00 0.00 4.08
491 492 1.344763 AGCCTACTCCGGACATTATGC 59.655 52.381 0.00 1.06 0.00 3.14
497 498 0.331954 AGAGAAGCCTACTCCGGACA 59.668 55.000 0.00 0.00 35.27 4.02
499 500 1.038130 GCAGAGAAGCCTACTCCGGA 61.038 60.000 2.93 2.93 35.27 5.14
500 501 1.323271 TGCAGAGAAGCCTACTCCGG 61.323 60.000 0.00 0.00 35.27 5.14
505 506 3.001736 CGCTTTAATGCAGAGAAGCCTAC 59.998 47.826 19.01 0.52 40.96 3.18
516 517 3.058773 TGGCGCCGCTTTAATGCA 61.059 55.556 23.90 0.00 0.00 3.96
547 560 0.109086 CACAGATTGGAGAGACGCGT 60.109 55.000 13.85 13.85 0.00 6.01
557 570 0.606401 ACGGCCTTGACACAGATTGG 60.606 55.000 0.00 0.00 0.00 3.16
558 571 0.798776 GACGGCCTTGACACAGATTG 59.201 55.000 0.00 0.00 0.00 2.67
559 572 0.670546 CGACGGCCTTGACACAGATT 60.671 55.000 0.00 0.00 0.00 2.40
563 576 2.338620 CTCGACGGCCTTGACACA 59.661 61.111 0.00 0.00 0.00 3.72
618 660 1.726248 CAAACTCATCGTCATGCGTCA 59.274 47.619 8.91 0.00 42.13 4.35
627 669 0.396435 TGCTCACCCAAACTCATCGT 59.604 50.000 0.00 0.00 0.00 3.73
630 672 1.620822 GGTTGCTCACCCAAACTCAT 58.379 50.000 0.00 0.00 40.19 2.90
648 690 1.004044 ACCAGCATCAAACCTGAGAGG 59.996 52.381 0.00 0.00 42.49 3.69
649 691 2.486472 ACCAGCATCAAACCTGAGAG 57.514 50.000 0.00 0.00 34.23 3.20
650 692 2.886523 CAAACCAGCATCAAACCTGAGA 59.113 45.455 0.00 0.00 34.23 3.27
651 693 2.608752 GCAAACCAGCATCAAACCTGAG 60.609 50.000 0.00 0.00 34.23 3.35
652 694 1.340889 GCAAACCAGCATCAAACCTGA 59.659 47.619 0.00 0.00 35.56 3.86
653 695 1.068895 TGCAAACCAGCATCAAACCTG 59.931 47.619 0.00 0.00 40.11 4.00
654 696 1.342174 CTGCAAACCAGCATCAAACCT 59.658 47.619 0.00 0.00 44.68 3.50
655 697 1.606224 CCTGCAAACCAGCATCAAACC 60.606 52.381 0.00 0.00 44.68 3.27
656 698 1.340889 TCCTGCAAACCAGCATCAAAC 59.659 47.619 0.00 0.00 44.68 2.93
657 699 1.702182 TCCTGCAAACCAGCATCAAA 58.298 45.000 0.00 0.00 44.68 2.69
658 700 1.702182 TTCCTGCAAACCAGCATCAA 58.298 45.000 0.00 0.00 44.68 2.57
659 701 1.927487 ATTCCTGCAAACCAGCATCA 58.073 45.000 0.00 0.00 44.68 3.07
660 702 2.613691 CAATTCCTGCAAACCAGCATC 58.386 47.619 0.00 0.00 44.68 3.91
674 716 2.030946 CCGTCTCTCAAATCGCAATTCC 59.969 50.000 0.00 0.00 0.00 3.01
685 735 1.541310 ATCCAACGCCCGTCTCTCAA 61.541 55.000 0.00 0.00 0.00 3.02
690 740 4.778143 GGCATCCAACGCCCGTCT 62.778 66.667 0.00 0.00 44.22 4.18
715 765 2.095263 CAGGTTTGGGCGTTACATTCAG 60.095 50.000 0.00 0.00 0.00 3.02
716 766 1.883275 CAGGTTTGGGCGTTACATTCA 59.117 47.619 0.00 0.00 0.00 2.57
717 767 2.095415 GTCAGGTTTGGGCGTTACATTC 60.095 50.000 0.00 0.00 0.00 2.67
718 768 1.883926 GTCAGGTTTGGGCGTTACATT 59.116 47.619 0.00 0.00 0.00 2.71
719 769 1.202830 TGTCAGGTTTGGGCGTTACAT 60.203 47.619 0.00 0.00 0.00 2.29
721 771 1.530323 ATGTCAGGTTTGGGCGTTAC 58.470 50.000 0.00 0.00 0.00 2.50
722 772 3.637911 ATATGTCAGGTTTGGGCGTTA 57.362 42.857 0.00 0.00 0.00 3.18
723 773 2.507407 ATATGTCAGGTTTGGGCGTT 57.493 45.000 0.00 0.00 0.00 4.84
724 774 2.504175 AGTATATGTCAGGTTTGGGCGT 59.496 45.455 0.00 0.00 0.00 5.68
725 775 3.131396 GAGTATATGTCAGGTTTGGGCG 58.869 50.000 0.00 0.00 0.00 6.13
727 777 4.402056 ACGAGTATATGTCAGGTTTGGG 57.598 45.455 0.00 0.00 0.00 4.12
729 779 5.575957 ACGTACGAGTATATGTCAGGTTTG 58.424 41.667 24.41 0.00 0.00 2.93
730 780 5.503031 CGACGTACGAGTATATGTCAGGTTT 60.503 44.000 24.41 0.00 45.77 3.27
732 782 3.492383 CGACGTACGAGTATATGTCAGGT 59.508 47.826 24.41 0.00 45.77 4.00
733 783 3.663754 GCGACGTACGAGTATATGTCAGG 60.664 52.174 24.41 0.00 45.77 3.86
734 784 3.060070 TGCGACGTACGAGTATATGTCAG 60.060 47.826 24.41 4.33 45.77 3.51
735 785 2.865551 TGCGACGTACGAGTATATGTCA 59.134 45.455 24.41 4.25 45.77 3.58
736 786 3.510251 TGCGACGTACGAGTATATGTC 57.490 47.619 24.41 5.17 45.77 3.06
737 787 3.611517 GTTGCGACGTACGAGTATATGT 58.388 45.455 24.41 0.00 45.77 2.29
738 788 2.644262 CGTTGCGACGTACGAGTATATG 59.356 50.000 24.41 5.83 44.08 1.78
739 789 2.896289 CGTTGCGACGTACGAGTATAT 58.104 47.619 24.41 0.00 44.08 0.86
740 790 2.351696 CGTTGCGACGTACGAGTATA 57.648 50.000 24.41 0.96 44.08 1.47
741 791 3.209429 CGTTGCGACGTACGAGTAT 57.791 52.632 24.41 0.00 44.08 2.12
742 792 4.723794 CGTTGCGACGTACGAGTA 57.276 55.556 24.41 12.04 44.08 2.59
755 805 1.033746 ATGGGATCTTGGCAGCGTTG 61.034 55.000 0.00 0.00 0.00 4.10
804 854 3.096092 TGCGCTAAGGAATGGGATTTTT 58.904 40.909 9.73 0.00 0.00 1.94
805 855 2.689983 CTGCGCTAAGGAATGGGATTTT 59.310 45.455 9.73 0.00 0.00 1.82
806 856 2.092429 TCTGCGCTAAGGAATGGGATTT 60.092 45.455 9.73 0.00 0.00 2.17
807 857 1.490490 TCTGCGCTAAGGAATGGGATT 59.510 47.619 9.73 0.00 0.00 3.01
808 858 1.131638 TCTGCGCTAAGGAATGGGAT 58.868 50.000 9.73 0.00 0.00 3.85
809 859 0.178068 GTCTGCGCTAAGGAATGGGA 59.822 55.000 9.73 0.00 0.00 4.37
810 860 1.154205 CGTCTGCGCTAAGGAATGGG 61.154 60.000 9.73 0.00 0.00 4.00
811 861 0.460284 ACGTCTGCGCTAAGGAATGG 60.460 55.000 9.73 0.00 42.83 3.16
812 862 0.647410 CACGTCTGCGCTAAGGAATG 59.353 55.000 9.73 0.91 42.83 2.67
818 868 2.073117 TCAATTCACGTCTGCGCTAA 57.927 45.000 9.73 0.00 42.83 3.09
829 879 1.400242 GCTGGAGCGTGTTCAATTCAC 60.400 52.381 0.00 0.00 0.00 3.18
831 881 0.874390 TGCTGGAGCGTGTTCAATTC 59.126 50.000 0.00 0.00 45.83 2.17
847 897 0.919710 GGGAGGGGATTACTGTTGCT 59.080 55.000 0.00 0.00 0.00 3.91
853 903 2.447959 GGGCGGGAGGGGATTACT 60.448 66.667 0.00 0.00 0.00 2.24
900 957 2.423088 CGGCTAGGTAGAGGAGGAAGAA 60.423 54.545 0.00 0.00 0.00 2.52
903 960 1.133853 GTCGGCTAGGTAGAGGAGGAA 60.134 57.143 0.00 0.00 0.00 3.36
1156 1270 3.050275 GTGTGCGTCTTGAGGGCC 61.050 66.667 0.00 0.00 0.00 5.80
1394 1519 4.988486 GTTCCGGACGACGCGTGT 62.988 66.667 20.70 15.84 41.37 4.49
1835 1972 1.197721 GGAACAACTCTGCATTGTCCG 59.802 52.381 4.71 0.00 39.36 4.79
2058 2195 4.696402 GCAGCCATGGAATCAAAAATTTCA 59.304 37.500 18.40 0.00 0.00 2.69
2093 2230 7.900782 ATGCCATACGTAACAATATTAGGTC 57.099 36.000 0.00 0.00 0.00 3.85
2094 2231 8.154856 AGAATGCCATACGTAACAATATTAGGT 58.845 33.333 0.00 0.00 0.00 3.08
2138 2275 1.772836 ATCAGCAAAGCATCCTTCCC 58.227 50.000 0.00 0.00 0.00 3.97
2139 2276 4.139786 TCATATCAGCAAAGCATCCTTCC 58.860 43.478 0.00 0.00 0.00 3.46
2210 2347 8.442632 TGCATCAATTAAAATGGTGAAAACAA 57.557 26.923 8.60 0.00 30.24 2.83
2351 2488 2.906458 CATCAGCGAGCTTCCCCT 59.094 61.111 0.00 0.00 0.00 4.79
2382 2519 3.104512 TCCCGTACCAATCATCTCACTT 58.895 45.455 0.00 0.00 0.00 3.16
2415 2555 8.598916 TGAATTAGGGAGTGATAAACAACTGTA 58.401 33.333 0.00 0.00 0.00 2.74
3487 3630 3.243234 CCAAACCACGCAAACACTTATCA 60.243 43.478 0.00 0.00 0.00 2.15
3498 3649 2.281484 GGAGCTCCAAACCACGCA 60.281 61.111 28.43 0.00 35.64 5.24
3733 3956 1.539827 GGCCCAACACACACTTGATAC 59.460 52.381 0.00 0.00 0.00 2.24
4345 4568 6.438425 AGTGCCAATTTCAATACCTCAAGATT 59.562 34.615 0.00 0.00 0.00 2.40
4350 4573 5.183713 CAGAAGTGCCAATTTCAATACCTCA 59.816 40.000 0.00 0.00 0.00 3.86
4408 5318 8.327941 TGAGGAAGTCTGAAAAGACATATTTG 57.672 34.615 8.47 0.00 41.02 2.32
4415 5325 7.155328 TGTTCTATGAGGAAGTCTGAAAAGAC 58.845 38.462 0.00 0.00 39.00 3.01


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

AutoCloner maintained by Alex Coulton.