Multiple sequence alignment - TraesCS4B01G117400

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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 TraesCS4B01G117400 chr4B 100.000 3339 0 0 2002 5340 136060145 136056807 0.000000e+00 6167
1 TraesCS4B01G117400 chr4B 100.000 1803 0 0 1 1803 136062146 136060344 0.000000e+00 3330
2 TraesCS4B01G117400 chr4A 94.976 2886 100 21 2004 4871 483175055 483177913 0.000000e+00 4484
3 TraesCS4B01G117400 chr4A 93.837 1574 63 10 243 1803 483173498 483175050 0.000000e+00 2338
4 TraesCS4B01G117400 chr4A 89.384 292 26 3 5014 5303 483178152 483178440 3.930000e-96 363
5 TraesCS4B01G117400 chr4A 91.124 169 14 1 1 168 483173324 483173492 1.500000e-55 228
6 TraesCS4B01G117400 chr4D 95.182 2864 79 19 2051 4900 96046238 96043420 0.000000e+00 4470
7 TraesCS4B01G117400 chr4D 95.090 1772 55 14 1 1751 96047996 96046236 0.000000e+00 2761
8 TraesCS4B01G117400 chr5D 88.889 90 9 1 2050 2139 214174865 214174953 5.650000e-20 110
9 TraesCS4B01G117400 chr5B 88.889 90 9 1 2050 2139 228818831 228818919 5.650000e-20 110
10 TraesCS4B01G117400 chr5A 88.889 90 9 1 2050 2139 279745219 279745307 5.650000e-20 110


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 TraesCS4B01G117400 chr4B 136056807 136062146 5339 True 4748.50 6167 100.00000 1 5340 2 chr4B.!!$R1 5339
1 TraesCS4B01G117400 chr4A 483173324 483178440 5116 False 1853.25 4484 92.33025 1 5303 4 chr4A.!!$F1 5302
2 TraesCS4B01G117400 chr4D 96043420 96047996 4576 True 3615.50 4470 95.13600 1 4900 2 chr4D.!!$R1 4899

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
607 686 0.101399 CAGATTGGGGACGACGAGAG 59.899 60.0 0.00 0.00 0.00 3.20 F
1783 1872 0.095245 CACTTGCTACGTTGCATCGG 59.905 55.0 24.61 18.56 42.96 4.18 F
2645 2739 0.323542 CCCACGAGAGGACTACCAGT 60.324 60.0 0.00 0.00 38.94 4.00 F
3087 3181 0.179073 CGGTCTGGGAGGCTATTGTG 60.179 60.0 0.00 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2298 0.043822 GCGCGAATCGTGTCAGAATC 60.044 55.0 17.69 0.0 39.70 2.52 R
3042 3136 0.249238 ATCTGAAGTCGCGATGCTCC 60.249 55.0 14.06 0.0 0.00 4.70 R
4163 4262 0.879090 CTTTGGTAAGCGTTGGGACC 59.121 55.0 0.00 0.0 0.00 4.46 R
5069 5316 0.184933 CCCTAAATTGGCCGGGATCA 59.815 55.0 2.18 0.0 39.08 2.92 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
40 41 8.871686 AAACATCACTACACCATTTTTCTTTC 57.128 30.769 0.00 0.00 0.00 2.62
79 81 2.351350 GCCCCACACAAAAGTAACATCG 60.351 50.000 0.00 0.00 0.00 3.84
128 130 3.963383 AAAGTTGTTTGTACAGGAGCG 57.037 42.857 0.00 0.00 35.28 5.03
171 245 7.778185 ACAGTAGTTCTATTGTTCACTACCT 57.222 36.000 4.99 0.00 41.72 3.08
172 246 8.191534 ACAGTAGTTCTATTGTTCACTACCTT 57.808 34.615 4.99 0.00 41.72 3.50
173 247 9.305555 ACAGTAGTTCTATTGTTCACTACCTTA 57.694 33.333 4.99 0.00 41.72 2.69
178 252 9.654663 AGTTCTATTGTTCACTACCTTATCAAC 57.345 33.333 0.00 0.00 0.00 3.18
179 253 8.880750 GTTCTATTGTTCACTACCTTATCAACC 58.119 37.037 0.00 0.00 0.00 3.77
180 254 8.141298 TCTATTGTTCACTACCTTATCAACCA 57.859 34.615 0.00 0.00 0.00 3.67
181 255 8.598916 TCTATTGTTCACTACCTTATCAACCAA 58.401 33.333 0.00 0.00 0.00 3.67
182 256 6.870971 TTGTTCACTACCTTATCAACCAAC 57.129 37.500 0.00 0.00 0.00 3.77
183 257 6.182507 TGTTCACTACCTTATCAACCAACT 57.817 37.500 0.00 0.00 0.00 3.16
184 258 6.597562 TGTTCACTACCTTATCAACCAACTT 58.402 36.000 0.00 0.00 0.00 2.66
185 259 6.485313 TGTTCACTACCTTATCAACCAACTTG 59.515 38.462 0.00 0.00 0.00 3.16
186 260 6.428083 TCACTACCTTATCAACCAACTTGA 57.572 37.500 0.00 0.00 43.28 3.02
187 261 6.833041 TCACTACCTTATCAACCAACTTGAA 58.167 36.000 0.00 0.00 42.37 2.69
188 262 7.284074 TCACTACCTTATCAACCAACTTGAAA 58.716 34.615 0.00 0.00 42.37 2.69
189 263 7.227910 TCACTACCTTATCAACCAACTTGAAAC 59.772 37.037 0.00 0.00 42.37 2.78
190 264 7.228706 CACTACCTTATCAACCAACTTGAAACT 59.771 37.037 0.00 0.00 42.37 2.66
191 265 8.434392 ACTACCTTATCAACCAACTTGAAACTA 58.566 33.333 0.00 0.00 42.37 2.24
192 266 7.506328 ACCTTATCAACCAACTTGAAACTAC 57.494 36.000 0.00 0.00 42.37 2.73
193 267 7.057894 ACCTTATCAACCAACTTGAAACTACA 58.942 34.615 0.00 0.00 42.37 2.74
194 268 7.724061 ACCTTATCAACCAACTTGAAACTACAT 59.276 33.333 0.00 0.00 42.37 2.29
195 269 8.576442 CCTTATCAACCAACTTGAAACTACATT 58.424 33.333 0.00 0.00 42.37 2.71
196 270 9.398170 CTTATCAACCAACTTGAAACTACATTG 57.602 33.333 0.00 0.00 42.37 2.82
197 271 6.767524 TCAACCAACTTGAAACTACATTGT 57.232 33.333 0.00 0.00 35.84 2.71
198 272 7.164230 TCAACCAACTTGAAACTACATTGTT 57.836 32.000 0.00 0.00 35.84 2.83
199 273 7.607250 TCAACCAACTTGAAACTACATTGTTT 58.393 30.769 0.00 0.00 42.11 2.83
200 274 8.740906 TCAACCAACTTGAAACTACATTGTTTA 58.259 29.630 0.00 0.00 39.86 2.01
201 275 9.528018 CAACCAACTTGAAACTACATTGTTTAT 57.472 29.630 0.00 0.00 39.86 1.40
202 276 9.528018 AACCAACTTGAAACTACATTGTTTATG 57.472 29.630 0.00 0.00 39.86 1.90
203 277 7.651704 ACCAACTTGAAACTACATTGTTTATGC 59.348 33.333 0.00 0.00 39.86 3.14
204 278 7.651304 CCAACTTGAAACTACATTGTTTATGCA 59.349 33.333 0.00 0.00 39.86 3.96
205 279 9.029243 CAACTTGAAACTACATTGTTTATGCAA 57.971 29.630 0.00 0.00 39.86 4.08
206 280 9.593134 AACTTGAAACTACATTGTTTATGCAAA 57.407 25.926 0.00 0.00 39.86 3.68
207 281 9.762933 ACTTGAAACTACATTGTTTATGCAAAT 57.237 25.926 0.00 0.00 39.86 2.32
210 284 9.853555 TGAAACTACATTGTTTATGCAAATAGG 57.146 29.630 0.00 0.00 39.86 2.57
211 285 8.702163 AAACTACATTGTTTATGCAAATAGGC 57.298 30.769 0.00 0.00 38.25 3.93
212 286 6.494842 ACTACATTGTTTATGCAAATAGGCG 58.505 36.000 0.00 0.00 37.81 5.52
213 287 4.111916 ACATTGTTTATGCAAATAGGCGC 58.888 39.130 0.00 0.00 37.81 6.53
214 288 3.857549 TTGTTTATGCAAATAGGCGCA 57.142 38.095 10.83 0.00 43.45 6.09
216 290 5.506686 TTGTTTATGCAAATAGGCGCATA 57.493 34.783 10.83 7.12 46.73 3.14
221 295 3.186702 TGCAAATAGGCGCATACTACA 57.813 42.857 10.83 0.30 36.28 2.74
222 296 3.738982 TGCAAATAGGCGCATACTACAT 58.261 40.909 10.83 0.00 36.28 2.29
223 297 3.745975 TGCAAATAGGCGCATACTACATC 59.254 43.478 10.83 0.00 36.28 3.06
224 298 3.997021 GCAAATAGGCGCATACTACATCT 59.003 43.478 10.83 0.00 0.00 2.90
225 299 4.452455 GCAAATAGGCGCATACTACATCTT 59.548 41.667 10.83 0.00 0.00 2.40
226 300 5.637810 GCAAATAGGCGCATACTACATCTTA 59.362 40.000 10.83 0.00 0.00 2.10
227 301 6.147164 GCAAATAGGCGCATACTACATCTTAA 59.853 38.462 10.83 0.00 0.00 1.85
228 302 7.622256 GCAAATAGGCGCATACTACATCTTAAG 60.622 40.741 10.83 0.00 0.00 1.85
229 303 3.654414 AGGCGCATACTACATCTTAAGC 58.346 45.455 10.83 0.00 0.00 3.09
230 304 3.069586 AGGCGCATACTACATCTTAAGCA 59.930 43.478 10.83 0.00 0.00 3.91
231 305 3.997021 GGCGCATACTACATCTTAAGCAT 59.003 43.478 10.83 0.00 0.00 3.79
232 306 4.452455 GGCGCATACTACATCTTAAGCATT 59.548 41.667 10.83 0.00 0.00 3.56
233 307 5.049405 GGCGCATACTACATCTTAAGCATTT 60.049 40.000 10.83 0.00 0.00 2.32
234 308 6.430451 GCGCATACTACATCTTAAGCATTTT 58.570 36.000 0.30 0.00 0.00 1.82
235 309 7.307751 GGCGCATACTACATCTTAAGCATTTTA 60.308 37.037 10.83 0.00 0.00 1.52
236 310 7.742089 GCGCATACTACATCTTAAGCATTTTAG 59.258 37.037 0.30 0.00 0.00 1.85
237 311 7.742089 CGCATACTACATCTTAAGCATTTTAGC 59.258 37.037 0.00 0.00 0.00 3.09
238 312 8.559536 GCATACTACATCTTAAGCATTTTAGCA 58.440 33.333 0.00 0.00 36.85 3.49
241 315 8.970859 ACTACATCTTAAGCATTTTAGCATCT 57.029 30.769 0.00 0.00 36.85 2.90
259 333 4.860907 GCATCTTGACATTTAGGCAACAAG 59.139 41.667 0.00 0.00 41.37 3.16
264 338 6.547880 TCTTGACATTTAGGCAACAAGGTTAA 59.452 34.615 0.00 0.00 41.37 2.01
272 346 4.082125 AGGCAACAAGGTTAAGATTCCAG 58.918 43.478 0.00 0.00 41.41 3.86
279 353 6.234177 ACAAGGTTAAGATTCCAGAGTTCAG 58.766 40.000 0.00 0.00 0.00 3.02
280 354 6.183361 ACAAGGTTAAGATTCCAGAGTTCAGT 60.183 38.462 0.00 0.00 0.00 3.41
281 355 7.016268 ACAAGGTTAAGATTCCAGAGTTCAGTA 59.984 37.037 0.00 0.00 0.00 2.74
292 366 5.585445 TCCAGAGTTCAGTAATCTAGACGAC 59.415 44.000 0.00 0.00 0.00 4.34
299 373 7.971168 AGTTCAGTAATCTAGACGACTCAATTG 59.029 37.037 0.00 0.00 0.00 2.32
303 377 8.399425 CAGTAATCTAGACGACTCAATTGTACT 58.601 37.037 5.13 0.00 0.00 2.73
445 519 3.993920 AGGATGCAAAAACGAAAGCAAT 58.006 36.364 0.00 0.00 40.76 3.56
450 524 4.118410 TGCAAAAACGAAAGCAATCACAT 58.882 34.783 0.00 0.00 33.48 3.21
451 525 5.284864 TGCAAAAACGAAAGCAATCACATA 58.715 33.333 0.00 0.00 33.48 2.29
452 526 5.401972 TGCAAAAACGAAAGCAATCACATAG 59.598 36.000 0.00 0.00 33.48 2.23
461 535 7.148407 ACGAAAGCAATCACATAGACCTAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
523 597 5.287274 CACACTTGAACACGATCTAGCTTAG 59.713 44.000 0.00 0.00 0.00 2.18
583 662 0.810031 ATACTTCGCATCGGCACACC 60.810 55.000 0.00 0.00 41.24 4.16
607 686 0.101399 CAGATTGGGGACGACGAGAG 59.899 60.000 0.00 0.00 0.00 3.20
672 751 4.428615 TTACTATTTTGTTTCGGCTGCC 57.571 40.909 9.11 9.11 0.00 4.85
1163 1247 1.676635 CGGTACCACCTGTCCGAGA 60.677 63.158 13.54 0.00 44.86 4.04
1296 1385 0.179037 CACCCATGCCGACTGATCAT 60.179 55.000 0.00 0.00 0.00 2.45
1534 1623 4.055360 GGTTTTCGGTTTGGAAGGATTTG 58.945 43.478 0.00 0.00 0.00 2.32
1650 1739 2.692368 GGCATCCAGTCCTCCCCA 60.692 66.667 0.00 0.00 0.00 4.96
1653 1742 1.639635 GCATCCAGTCCTCCCCATGT 61.640 60.000 0.00 0.00 0.00 3.21
1759 1848 4.081087 ACATGCTCACCGAGGTAATTAACT 60.081 41.667 1.66 1.66 0.00 2.24
1769 1858 5.704217 GAGGTAATTAACTCGCTCACTTG 57.296 43.478 14.60 0.00 0.00 3.16
1770 1859 3.933332 AGGTAATTAACTCGCTCACTTGC 59.067 43.478 0.00 0.00 0.00 4.01
1783 1872 0.095245 CACTTGCTACGTTGCATCGG 59.905 55.000 24.61 18.56 42.96 4.18
1784 1873 1.060937 CTTGCTACGTTGCATCGGC 59.939 57.895 24.61 15.01 42.96 5.54
1785 1874 1.361668 CTTGCTACGTTGCATCGGCT 61.362 55.000 24.61 4.02 42.96 5.52
2120 2209 2.679996 GCCCGGCAAACCATCCTT 60.680 61.111 3.91 0.00 34.57 3.36
2164 2254 1.590932 CTAGCTCCATCCATGTGCAC 58.409 55.000 10.75 10.75 0.00 4.57
2316 2406 4.810790 ACGAGAACATGAAGAAGGTACTG 58.189 43.478 0.00 0.00 40.86 2.74
2336 2426 5.416083 ACTGTAATTAAGCAGCGTCATGTA 58.584 37.500 3.60 0.00 36.26 2.29
2342 2432 7.728847 AATTAAGCAGCGTCATGTATATTCA 57.271 32.000 0.00 0.00 0.00 2.57
2391 2481 7.615365 TCACCATCAAGTTGCTTAATTAATCCT 59.385 33.333 0.00 0.00 0.00 3.24
2489 2579 2.481952 GGCACATCATCTATCGCTTTCC 59.518 50.000 0.00 0.00 0.00 3.13
2540 2634 3.009143 CCATTATTAGTACTCCCCCTGCC 59.991 52.174 0.00 0.00 0.00 4.85
2642 2736 1.757340 CCCCCACGAGAGGACTACC 60.757 68.421 0.00 0.00 0.00 3.18
2643 2737 1.000019 CCCCACGAGAGGACTACCA 60.000 63.158 0.00 0.00 38.94 3.25
2644 2738 1.038130 CCCCACGAGAGGACTACCAG 61.038 65.000 0.00 0.00 38.94 4.00
2645 2739 0.323542 CCCACGAGAGGACTACCAGT 60.324 60.000 0.00 0.00 38.94 4.00
2646 2740 1.096416 CCACGAGAGGACTACCAGTC 58.904 60.000 0.00 0.00 44.32 3.51
2647 2741 1.613520 CCACGAGAGGACTACCAGTCA 60.614 57.143 8.47 0.00 46.79 3.41
2648 2742 1.469308 CACGAGAGGACTACCAGTCAC 59.531 57.143 8.47 2.50 46.79 3.67
2673 2767 4.557695 GCTGCAGTACACCTATGCTAGTAG 60.558 50.000 16.64 0.00 40.62 2.57
2675 2769 3.305471 GCAGTACACCTATGCTAGTAGGC 60.305 52.174 6.37 0.00 44.20 3.93
3071 3165 1.600013 CGACTTCAGATCGATCTCGGT 59.400 52.381 25.00 21.05 42.25 4.69
3087 3181 0.179073 CGGTCTGGGAGGCTATTGTG 60.179 60.000 0.00 0.00 0.00 3.33
3107 3201 4.039973 TGTGTTCGGTCTGGATAAACTCTT 59.960 41.667 0.00 0.00 0.00 2.85
3109 3203 4.282449 TGTTCGGTCTGGATAAACTCTTGA 59.718 41.667 0.00 0.00 0.00 3.02
3121 3215 0.967887 ACTCTTGAGGCGAGCTAGCA 60.968 55.000 20.82 0.00 39.27 3.49
3156 3250 1.856802 GCGAAATTTCCATGGATGCC 58.143 50.000 17.06 2.83 0.00 4.40
3216 3310 2.767505 AGAATCTCGGCAAACTTCGTT 58.232 42.857 0.00 0.00 0.00 3.85
3229 3323 2.783135 ACTTCGTTACGGGTGTCTCTA 58.217 47.619 4.53 0.00 0.00 2.43
3230 3324 3.149196 ACTTCGTTACGGGTGTCTCTAA 58.851 45.455 4.53 0.00 0.00 2.10
3239 3337 5.326200 ACGGGTGTCTCTAATAAAGTCTG 57.674 43.478 0.00 0.00 0.00 3.51
3408 3506 3.197715 ATGGCAATGGCATGCAGCAAT 62.198 47.619 21.71 13.23 46.89 3.56
3451 3549 5.523013 GTTCCTCTGAACGAATCTTCTTG 57.477 43.478 0.00 0.00 41.35 3.02
3459 3557 6.542370 TCTGAACGAATCTTCTTGTTTTTCCT 59.458 34.615 0.00 0.00 0.00 3.36
3592 3690 3.989698 ATGCGTTCGCCAGACGGAG 62.990 63.158 14.44 0.00 43.89 4.63
3598 3696 2.202623 CGCCAGACGGAGCACTAC 60.203 66.667 0.00 0.00 38.44 2.73
3606 3704 3.057174 CAGACGGAGCACTACTTTTCTCT 60.057 47.826 0.00 0.00 0.00 3.10
3674 3773 1.329292 TGTCACACGCAAAGTAAGTGC 59.671 47.619 0.00 0.00 39.31 4.40
3691 3790 1.185618 TGCTAAGTGCTGAGTCGGGT 61.186 55.000 0.05 0.00 43.37 5.28
3692 3791 0.815734 GCTAAGTGCTGAGTCGGGTA 59.184 55.000 0.05 0.00 38.95 3.69
3693 3792 1.203994 GCTAAGTGCTGAGTCGGGTAA 59.796 52.381 0.05 0.00 38.95 2.85
3694 3793 2.159085 GCTAAGTGCTGAGTCGGGTAAT 60.159 50.000 0.05 0.00 38.95 1.89
3925 4024 2.666098 GGGGGTGTACGAGCATGGT 61.666 63.158 0.00 0.00 0.00 3.55
4135 4234 2.105128 CTGACCCTCGCCATCGAC 59.895 66.667 0.00 0.00 40.21 4.20
4184 4283 2.550639 GGTCCCAACGCTTACCAAAGTA 60.551 50.000 0.00 0.00 34.99 2.24
4305 4404 0.038892 AAGCTGAAGCAAATGCACGG 60.039 50.000 8.28 7.48 45.16 4.94
4471 4570 0.598065 GTTCCTTGGACGCAAGCAAT 59.402 50.000 0.00 0.00 45.62 3.56
4670 4769 2.229062 CGATCATGTATAGCACCGGAGT 59.771 50.000 9.46 0.00 0.00 3.85
4703 4802 3.947910 AACGATTCTTTACGTCCCAGA 57.052 42.857 0.00 0.00 41.87 3.86
4819 4930 7.606135 TGAATCTGAAATATACCGGGACTTA 57.394 36.000 6.32 0.00 0.00 2.24
4839 4950 8.471609 GGACTTAAGAGTAACTCTAGCAGATTT 58.528 37.037 10.09 0.00 40.28 2.17
4857 4968 9.646427 AGCAGATTTTCTACTAAACAGTCTTAG 57.354 33.333 0.00 0.00 35.40 2.18
4869 5015 9.790344 ACTAAACAGTCTTAGTACTAAGTCTCA 57.210 33.333 31.98 16.97 39.75 3.27
4871 5017 8.694581 AAACAGTCTTAGTACTAAGTCTCAGT 57.305 34.615 31.98 24.66 42.29 3.41
4897 5043 9.784680 TTATATACGCGAGATCTTTAAGATTCC 57.215 33.333 15.93 3.65 34.53 3.01
4907 5126 9.308318 GAGATCTTTAAGATTCCTGTGTTAGTC 57.692 37.037 8.99 0.00 34.53 2.59
4910 5129 7.837863 TCTTTAAGATTCCTGTGTTAGTCGAT 58.162 34.615 0.00 0.00 0.00 3.59
4916 5135 4.436242 TCCTGTGTTAGTCGATTGAGAC 57.564 45.455 0.00 0.00 41.23 3.36
4921 5140 5.008331 TGTGTTAGTCGATTGAGACCTAGT 58.992 41.667 0.00 0.00 41.83 2.57
4927 5146 3.440872 GTCGATTGAGACCTAGTCACACT 59.559 47.826 0.00 0.00 33.37 3.55
4928 5147 3.690139 TCGATTGAGACCTAGTCACACTC 59.310 47.826 0.00 0.74 33.37 3.51
4929 5148 3.440522 CGATTGAGACCTAGTCACACTCA 59.559 47.826 11.11 0.00 34.49 3.41
4930 5149 4.097135 CGATTGAGACCTAGTCACACTCAT 59.903 45.833 11.11 0.00 34.49 2.90
4931 5150 5.587289 GATTGAGACCTAGTCACACTCATC 58.413 45.833 0.00 0.77 34.76 2.92
4932 5151 4.308526 TGAGACCTAGTCACACTCATCT 57.691 45.455 0.00 0.00 34.60 2.90
4933 5152 5.437191 TGAGACCTAGTCACACTCATCTA 57.563 43.478 0.00 0.00 34.60 1.98
4934 5153 6.007485 TGAGACCTAGTCACACTCATCTAT 57.993 41.667 0.00 0.00 34.60 1.98
4935 5154 7.138054 TGAGACCTAGTCACACTCATCTATA 57.862 40.000 0.00 0.00 34.60 1.31
4936 5155 7.220740 TGAGACCTAGTCACACTCATCTATAG 58.779 42.308 0.00 0.00 34.60 1.31
4937 5156 7.071321 TGAGACCTAGTCACACTCATCTATAGA 59.929 40.741 4.57 4.57 34.60 1.98
4938 5157 7.807198 AGACCTAGTCACACTCATCTATAGAA 58.193 38.462 6.52 0.00 34.60 2.10
4939 5158 7.717875 AGACCTAGTCACACTCATCTATAGAAC 59.282 40.741 6.52 0.00 34.60 3.01
4940 5159 6.773685 ACCTAGTCACACTCATCTATAGAACC 59.226 42.308 6.52 0.00 0.00 3.62
4941 5160 7.001674 CCTAGTCACACTCATCTATAGAACCT 58.998 42.308 6.52 0.00 0.00 3.50
4942 5161 6.952773 AGTCACACTCATCTATAGAACCTC 57.047 41.667 6.52 0.00 0.00 3.85
4943 5162 6.427441 AGTCACACTCATCTATAGAACCTCA 58.573 40.000 6.52 0.00 0.00 3.86
4944 5163 6.320164 AGTCACACTCATCTATAGAACCTCAC 59.680 42.308 6.52 0.00 0.00 3.51
4945 5164 6.095580 GTCACACTCATCTATAGAACCTCACA 59.904 42.308 6.52 0.00 0.00 3.58
4946 5165 6.663523 TCACACTCATCTATAGAACCTCACAA 59.336 38.462 6.52 0.00 0.00 3.33
4947 5166 7.343057 TCACACTCATCTATAGAACCTCACAAT 59.657 37.037 6.52 0.00 0.00 2.71
4948 5167 7.651304 CACACTCATCTATAGAACCTCACAATC 59.349 40.741 6.52 0.00 0.00 2.67
4949 5168 7.151308 CACTCATCTATAGAACCTCACAATCC 58.849 42.308 6.52 0.00 0.00 3.01
4950 5169 6.268847 ACTCATCTATAGAACCTCACAATCCC 59.731 42.308 6.52 0.00 0.00 3.85
4951 5170 5.243954 TCATCTATAGAACCTCACAATCCCG 59.756 44.000 6.52 0.00 0.00 5.14
4952 5171 4.800023 TCTATAGAACCTCACAATCCCGA 58.200 43.478 0.00 0.00 0.00 5.14
4953 5172 5.394738 TCTATAGAACCTCACAATCCCGAT 58.605 41.667 0.00 0.00 0.00 4.18
4954 5173 5.839063 TCTATAGAACCTCACAATCCCGATT 59.161 40.000 0.00 0.00 0.00 3.34
4966 5185 2.820728 TCCCGATTGAGACCTAGTCA 57.179 50.000 0.00 0.00 34.60 3.41
4967 5186 2.376109 TCCCGATTGAGACCTAGTCAC 58.624 52.381 0.00 0.00 34.60 3.67
4968 5187 2.100197 CCCGATTGAGACCTAGTCACA 58.900 52.381 0.00 0.00 34.60 3.58
4969 5188 2.159226 CCCGATTGAGACCTAGTCACAC 60.159 54.545 0.00 0.00 33.37 3.82
4970 5189 2.159226 CCGATTGAGACCTAGTCACACC 60.159 54.545 0.00 0.00 33.37 4.16
4971 5190 2.159226 CGATTGAGACCTAGTCACACCC 60.159 54.545 0.00 0.00 33.37 4.61
4987 5206 4.649674 TCACACCCATCTATAGAACCTCAC 59.350 45.833 6.52 0.00 0.00 3.51
4991 5210 6.183361 ACACCCATCTATAGAACCTCACAATC 60.183 42.308 6.52 0.00 0.00 2.67
5005 5224 9.178758 GAACCTCACAATCCTTATAATTTCTGT 57.821 33.333 0.00 0.00 0.00 3.41
5007 5226 9.614792 ACCTCACAATCCTTATAATTTCTGTAC 57.385 33.333 0.00 0.00 0.00 2.90
5011 5230 9.916397 CACAATCCTTATAATTTCTGTACGTTC 57.084 33.333 0.00 0.00 0.00 3.95
5012 5231 8.814235 ACAATCCTTATAATTTCTGTACGTTCG 58.186 33.333 0.00 0.00 0.00 3.95
5032 5279 4.370917 TCGGCCCGTAAGAATATACAAAC 58.629 43.478 1.63 0.00 43.02 2.93
5047 5294 9.106070 GAATATACAAACGGACCATATATTCCC 57.894 37.037 9.61 0.00 38.32 3.97
5068 5315 3.985925 CCGACTTCGCCACTATATTTACC 59.014 47.826 0.00 0.00 38.18 2.85
5069 5316 4.261909 CCGACTTCGCCACTATATTTACCT 60.262 45.833 0.00 0.00 38.18 3.08
5075 5322 4.222145 TCGCCACTATATTTACCTGATCCC 59.778 45.833 0.00 0.00 0.00 3.85
5116 5363 1.409521 CCGGCATTTCTCCAACCCATA 60.410 52.381 0.00 0.00 0.00 2.74
5120 5367 3.823304 GGCATTTCTCCAACCCATATCTC 59.177 47.826 0.00 0.00 0.00 2.75
5129 5376 3.244353 CCAACCCATATCTCTCGCAATCT 60.244 47.826 0.00 0.00 0.00 2.40
5130 5377 4.384056 CAACCCATATCTCTCGCAATCTT 58.616 43.478 0.00 0.00 0.00 2.40
5140 5387 2.034685 TCTCGCAATCTTCATACTCCGG 59.965 50.000 0.00 0.00 0.00 5.14
5141 5388 0.861837 CGCAATCTTCATACTCCGGC 59.138 55.000 0.00 0.00 0.00 6.13
5144 5391 2.128035 CAATCTTCATACTCCGGCGAC 58.872 52.381 9.30 0.00 0.00 5.19
5151 5398 0.674534 ATACTCCGGCGACTGATTCC 59.325 55.000 9.30 0.00 0.00 3.01
5161 5410 0.792640 GACTGATTCCTGCACACACG 59.207 55.000 0.00 0.00 0.00 4.49
5177 5426 3.165498 CGCACCCGTTTAGAGCAC 58.835 61.111 0.00 0.00 0.00 4.40
5186 5435 2.223340 CCGTTTAGAGCACATCAATGGC 60.223 50.000 0.00 0.00 0.00 4.40
5191 5440 4.557605 GCACATCAATGGCCGGCG 62.558 66.667 22.54 6.52 0.00 6.46
5229 5478 4.020617 TGCCCTCTCCTGCAACCG 62.021 66.667 0.00 0.00 33.87 4.44
5253 5502 0.531974 TCGAAAGCGTGCCAAAGAGT 60.532 50.000 0.00 0.00 38.98 3.24
5255 5504 0.661483 GAAAGCGTGCCAAAGAGTGC 60.661 55.000 0.00 0.00 0.00 4.40
5256 5505 2.392613 AAAGCGTGCCAAAGAGTGCG 62.393 55.000 0.00 0.00 0.00 5.34
5257 5506 4.389576 GCGTGCCAAAGAGTGCGG 62.390 66.667 0.00 0.00 0.00 5.69
5258 5507 4.389576 CGTGCCAAAGAGTGCGGC 62.390 66.667 0.00 0.00 46.43 6.53
5278 5527 1.993653 CCCTCTCCTGCAACCATGA 59.006 57.895 0.00 0.00 0.00 3.07
5279 5528 0.393537 CCCTCTCCTGCAACCATGAC 60.394 60.000 0.00 0.00 0.00 3.06
5306 5555 2.659016 TGGAGCAGCTTCCACGAG 59.341 61.111 2.82 0.00 42.24 4.18
5307 5556 2.125350 GGAGCAGCTTCCACGAGG 60.125 66.667 0.00 0.00 37.20 4.63
5308 5557 2.659610 GAGCAGCTTCCACGAGGT 59.340 61.111 0.00 0.00 35.89 3.85
5309 5558 1.446966 GAGCAGCTTCCACGAGGTC 60.447 63.158 0.00 0.00 35.89 3.85
5310 5559 2.811317 GCAGCTTCCACGAGGTCG 60.811 66.667 0.00 0.00 46.33 4.79
5311 5560 2.125912 CAGCTTCCACGAGGTCGG 60.126 66.667 4.13 0.00 44.95 4.79
5312 5561 3.382832 AGCTTCCACGAGGTCGGG 61.383 66.667 4.13 0.00 44.95 5.14
5318 5567 4.873129 CACGAGGTCGGGGATGCG 62.873 72.222 4.13 0.00 44.95 4.73
5321 5570 4.162690 GAGGTCGGGGATGCGCTT 62.163 66.667 9.73 0.55 0.00 4.68
5322 5571 3.682292 GAGGTCGGGGATGCGCTTT 62.682 63.158 9.73 0.00 0.00 3.51
5323 5572 3.508840 GGTCGGGGATGCGCTTTG 61.509 66.667 9.73 0.00 0.00 2.77
5324 5573 3.508840 GTCGGGGATGCGCTTTGG 61.509 66.667 9.73 0.00 0.00 3.28
5329 5578 4.133796 GGATGCGCTTTGGCCCAC 62.134 66.667 9.73 0.00 34.44 4.61
5330 5579 4.133796 GATGCGCTTTGGCCCACC 62.134 66.667 9.73 0.00 34.44 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 1.484240 CTTTTGTGTGGGGCCTTGAAA 59.516 47.619 0.84 0.00 0.00 2.69
79 81 8.700439 TTAAAGGTAGGTATATGCCAAAATCC 57.300 34.615 12.79 6.64 0.00 3.01
128 130 8.852135 ACTACTGTTATAGCTCCTAAGATTGTC 58.148 37.037 0.00 0.00 0.00 3.18
168 242 7.057894 TGTAGTTTCAAGTTGGTTGATAAGGT 58.942 34.615 2.34 0.00 44.89 3.50
169 243 7.504924 TGTAGTTTCAAGTTGGTTGATAAGG 57.495 36.000 2.34 0.00 44.89 2.69
170 244 9.398170 CAATGTAGTTTCAAGTTGGTTGATAAG 57.602 33.333 2.34 0.00 44.89 1.73
171 245 8.908903 ACAATGTAGTTTCAAGTTGGTTGATAA 58.091 29.630 2.34 0.00 44.89 1.75
172 246 8.458573 ACAATGTAGTTTCAAGTTGGTTGATA 57.541 30.769 2.34 0.00 44.89 2.15
173 247 7.346751 ACAATGTAGTTTCAAGTTGGTTGAT 57.653 32.000 2.34 0.00 44.89 2.57
174 248 6.767524 ACAATGTAGTTTCAAGTTGGTTGA 57.232 33.333 2.34 0.00 43.82 3.18
175 249 7.826260 AAACAATGTAGTTTCAAGTTGGTTG 57.174 32.000 2.34 0.00 37.11 3.77
176 250 9.528018 CATAAACAATGTAGTTTCAAGTTGGTT 57.472 29.630 2.34 0.00 41.58 3.67
177 251 7.651704 GCATAAACAATGTAGTTTCAAGTTGGT 59.348 33.333 2.34 0.00 41.58 3.67
178 252 7.651304 TGCATAAACAATGTAGTTTCAAGTTGG 59.349 33.333 2.34 0.00 41.58 3.77
179 253 8.572828 TGCATAAACAATGTAGTTTCAAGTTG 57.427 30.769 0.00 0.00 41.58 3.16
180 254 9.593134 TTTGCATAAACAATGTAGTTTCAAGTT 57.407 25.926 0.00 0.00 41.58 2.66
181 255 9.762933 ATTTGCATAAACAATGTAGTTTCAAGT 57.237 25.926 0.00 0.00 41.58 3.16
184 258 9.853555 CCTATTTGCATAAACAATGTAGTTTCA 57.146 29.630 0.00 0.00 41.58 2.69
185 259 8.807581 GCCTATTTGCATAAACAATGTAGTTTC 58.192 33.333 0.00 0.00 41.58 2.78
186 260 7.487829 CGCCTATTTGCATAAACAATGTAGTTT 59.512 33.333 0.00 0.00 43.58 2.66
187 261 6.972328 CGCCTATTTGCATAAACAATGTAGTT 59.028 34.615 0.00 0.00 37.93 2.24
188 262 6.494842 CGCCTATTTGCATAAACAATGTAGT 58.505 36.000 0.00 0.00 37.93 2.73
189 263 5.399301 GCGCCTATTTGCATAAACAATGTAG 59.601 40.000 0.00 0.00 37.93 2.74
190 264 5.163612 TGCGCCTATTTGCATAAACAATGTA 60.164 36.000 4.18 0.00 37.93 2.29
191 265 4.111916 GCGCCTATTTGCATAAACAATGT 58.888 39.130 0.00 0.00 37.93 2.71
192 266 4.111198 TGCGCCTATTTGCATAAACAATG 58.889 39.130 4.18 0.00 35.90 2.82
193 267 4.383850 TGCGCCTATTTGCATAAACAAT 57.616 36.364 4.18 0.00 35.90 2.71
194 268 3.857549 TGCGCCTATTTGCATAAACAA 57.142 38.095 4.18 0.00 35.90 2.83
201 275 3.186702 TGTAGTATGCGCCTATTTGCA 57.813 42.857 4.18 0.00 46.51 4.08
202 276 3.997021 AGATGTAGTATGCGCCTATTTGC 59.003 43.478 4.18 0.00 0.00 3.68
203 277 7.622256 GCTTAAGATGTAGTATGCGCCTATTTG 60.622 40.741 6.67 0.00 0.00 2.32
204 278 6.369065 GCTTAAGATGTAGTATGCGCCTATTT 59.631 38.462 6.67 0.00 0.00 1.40
205 279 5.869888 GCTTAAGATGTAGTATGCGCCTATT 59.130 40.000 6.67 0.00 0.00 1.73
206 280 5.047306 TGCTTAAGATGTAGTATGCGCCTAT 60.047 40.000 6.67 0.00 0.00 2.57
207 281 4.279922 TGCTTAAGATGTAGTATGCGCCTA 59.720 41.667 6.67 0.00 0.00 3.93
208 282 3.069586 TGCTTAAGATGTAGTATGCGCCT 59.930 43.478 6.67 0.00 0.00 5.52
209 283 3.390135 TGCTTAAGATGTAGTATGCGCC 58.610 45.455 6.67 0.00 0.00 6.53
210 284 5.597813 AATGCTTAAGATGTAGTATGCGC 57.402 39.130 6.67 0.00 0.00 6.09
211 285 7.742089 GCTAAAATGCTTAAGATGTAGTATGCG 59.258 37.037 6.67 0.00 0.00 4.73
212 286 8.559536 TGCTAAAATGCTTAAGATGTAGTATGC 58.440 33.333 6.67 0.56 0.00 3.14
216 290 8.970859 AGATGCTAAAATGCTTAAGATGTAGT 57.029 30.769 6.67 0.00 0.00 2.73
217 291 9.661187 CAAGATGCTAAAATGCTTAAGATGTAG 57.339 33.333 6.67 1.85 0.00 2.74
218 292 9.394767 TCAAGATGCTAAAATGCTTAAGATGTA 57.605 29.630 6.67 0.00 0.00 2.29
219 293 8.186821 GTCAAGATGCTAAAATGCTTAAGATGT 58.813 33.333 6.67 0.00 0.00 3.06
220 294 8.186163 TGTCAAGATGCTAAAATGCTTAAGATG 58.814 33.333 6.67 0.00 0.00 2.90
221 295 8.284945 TGTCAAGATGCTAAAATGCTTAAGAT 57.715 30.769 6.67 0.00 0.00 2.40
222 296 7.686438 TGTCAAGATGCTAAAATGCTTAAGA 57.314 32.000 6.67 0.00 0.00 2.10
223 297 8.922058 AATGTCAAGATGCTAAAATGCTTAAG 57.078 30.769 0.00 0.00 0.00 1.85
226 300 7.977853 CCTAAATGTCAAGATGCTAAAATGCTT 59.022 33.333 0.00 0.00 0.00 3.91
227 301 7.486647 CCTAAATGTCAAGATGCTAAAATGCT 58.513 34.615 0.00 0.00 0.00 3.79
228 302 6.199719 GCCTAAATGTCAAGATGCTAAAATGC 59.800 38.462 0.00 0.00 0.00 3.56
229 303 7.259882 TGCCTAAATGTCAAGATGCTAAAATG 58.740 34.615 0.00 0.00 0.00 2.32
230 304 7.408756 TGCCTAAATGTCAAGATGCTAAAAT 57.591 32.000 0.00 0.00 0.00 1.82
231 305 6.832520 TGCCTAAATGTCAAGATGCTAAAA 57.167 33.333 0.00 0.00 0.00 1.52
232 306 6.208402 TGTTGCCTAAATGTCAAGATGCTAAA 59.792 34.615 0.00 0.00 0.00 1.85
233 307 5.709631 TGTTGCCTAAATGTCAAGATGCTAA 59.290 36.000 0.00 0.00 0.00 3.09
234 308 5.252547 TGTTGCCTAAATGTCAAGATGCTA 58.747 37.500 0.00 0.00 0.00 3.49
235 309 4.081406 TGTTGCCTAAATGTCAAGATGCT 58.919 39.130 0.00 0.00 0.00 3.79
236 310 4.439305 TGTTGCCTAAATGTCAAGATGC 57.561 40.909 0.00 0.00 0.00 3.91
237 311 5.047802 ACCTTGTTGCCTAAATGTCAAGATG 60.048 40.000 0.00 0.00 35.69 2.90
238 312 5.079643 ACCTTGTTGCCTAAATGTCAAGAT 58.920 37.500 0.00 0.00 35.69 2.40
239 313 4.469657 ACCTTGTTGCCTAAATGTCAAGA 58.530 39.130 0.00 0.00 35.69 3.02
240 314 4.853924 ACCTTGTTGCCTAAATGTCAAG 57.146 40.909 0.00 0.00 34.14 3.02
241 315 6.547880 TCTTAACCTTGTTGCCTAAATGTCAA 59.452 34.615 0.00 0.00 0.00 3.18
259 333 8.261522 AGATTACTGAACTCTGGAATCTTAACC 58.738 37.037 14.95 0.00 46.66 2.85
272 346 6.665474 TGAGTCGTCTAGATTACTGAACTC 57.335 41.667 13.06 10.25 0.00 3.01
281 355 8.353684 CCATAGTACAATTGAGTCGTCTAGATT 58.646 37.037 13.59 0.00 0.00 2.40
445 519 5.046591 CCTGTGTCCTTTTAGGTCTATGTGA 60.047 44.000 0.00 0.00 36.53 3.58
450 524 2.570302 GGCCTGTGTCCTTTTAGGTCTA 59.430 50.000 0.00 0.00 36.53 2.59
451 525 1.351350 GGCCTGTGTCCTTTTAGGTCT 59.649 52.381 0.00 0.00 36.53 3.85
452 526 1.073284 TGGCCTGTGTCCTTTTAGGTC 59.927 52.381 3.32 0.00 36.53 3.85
461 535 0.037975 CAAGCAATTGGCCTGTGTCC 60.038 55.000 3.32 0.00 46.50 4.02
523 597 2.380084 TGATGTTCCCGTTGTCTAGC 57.620 50.000 0.00 0.00 0.00 3.42
583 662 1.196808 CGTCGTCCCCAATCTGTTTTG 59.803 52.381 0.00 0.00 0.00 2.44
607 686 5.739161 GTCTATGCATGATTCCGTTTTTGTC 59.261 40.000 10.16 0.00 0.00 3.18
672 751 2.324477 GCCGATGCGTTTCATCCG 59.676 61.111 0.00 0.00 46.93 4.18
678 757 1.136565 CGAAATGGCCGATGCGTTT 59.863 52.632 0.00 0.00 38.85 3.60
829 913 4.341783 AGCCCACAGGTCAGCAGC 62.342 66.667 0.00 0.00 34.57 5.25
1180 1264 3.326747 CCGCTTTAAATATCCTCTCCCG 58.673 50.000 0.00 0.00 0.00 5.14
1467 1556 2.474816 GCGAAATCGATTACCTGAGCT 58.525 47.619 11.83 0.00 43.02 4.09
1495 1584 2.736670 ACCAAAATAGGGCCAGCTAG 57.263 50.000 6.18 0.00 0.00 3.42
1534 1623 2.814604 GGCCGGCCAAATCAATCC 59.185 61.111 40.73 8.62 35.81 3.01
1581 1670 4.200283 GCCAGCTCCTCGTCCTCG 62.200 72.222 0.00 0.00 38.55 4.63
1650 1739 1.378250 GCTGGAGCTGCTGGAACAT 60.378 57.895 7.01 0.00 36.18 2.71
1653 1742 4.399395 CCGCTGGAGCTGCTGGAA 62.399 66.667 7.01 0.00 39.32 3.53
1759 1848 1.282248 GCAACGTAGCAAGTGAGCGA 61.282 55.000 0.00 0.00 40.15 4.93
1769 1858 0.300789 GTTAGCCGATGCAACGTAGC 59.699 55.000 15.54 12.06 41.13 3.58
1770 1859 0.928229 GGTTAGCCGATGCAACGTAG 59.072 55.000 15.54 1.95 41.13 3.51
2027 2116 1.977594 ATGTTTCGTCGATTGGCGGC 61.978 55.000 7.19 0.00 42.28 6.53
2120 2209 0.107410 AATTAATCACCTGGCGGCGA 60.107 50.000 12.98 0.00 0.00 5.54
2164 2254 3.181487 GGCAGCTGTGGTGGTAATTAATG 60.181 47.826 16.64 0.00 0.00 1.90
2208 2298 0.043822 GCGCGAATCGTGTCAGAATC 60.044 55.000 17.69 0.00 39.70 2.52
2316 2406 8.708742 TGAATATACATGACGCTGCTTAATTAC 58.291 33.333 0.00 0.00 0.00 1.89
2336 2426 8.222637 TGACATTTCAAGATCCTCCATGAATAT 58.777 33.333 0.00 0.00 32.35 1.28
2342 2432 5.705397 TCTGACATTTCAAGATCCTCCAT 57.295 39.130 0.00 0.00 0.00 3.41
2391 2481 1.118965 TCCTTCTCCTGCACCGTTCA 61.119 55.000 0.00 0.00 0.00 3.18
2509 2603 5.479375 GGAGTACTAATAATGGATGACGGGA 59.521 44.000 0.00 0.00 0.00 5.14
2540 2634 1.068610 CGTTGCCTAACAATGGTGGTG 60.069 52.381 0.00 0.00 41.27 4.17
2642 2736 1.006220 TGTACTGCAGCGGTGACTG 60.006 57.895 20.69 15.21 40.80 3.51
2643 2737 1.006102 GTGTACTGCAGCGGTGACT 60.006 57.895 20.69 1.33 0.00 3.41
2644 2738 2.027625 GGTGTACTGCAGCGGTGAC 61.028 63.158 20.69 12.75 35.77 3.67
2645 2739 2.342279 GGTGTACTGCAGCGGTGA 59.658 61.111 20.69 0.11 35.77 4.02
2673 2767 4.025480 CGGTTTGACCATAATTAGTACGCC 60.025 45.833 0.00 0.00 38.47 5.68
2675 2769 4.508861 CCCGGTTTGACCATAATTAGTACG 59.491 45.833 0.00 0.00 38.47 3.67
2743 2837 1.778334 TTGTCCGAACATCACTGTCG 58.222 50.000 0.00 0.00 34.73 4.35
2898 2992 1.769098 CGATCGCGGAACCGACTAGA 61.769 60.000 17.63 9.90 40.40 2.43
3042 3136 0.249238 ATCTGAAGTCGCGATGCTCC 60.249 55.000 14.06 0.00 0.00 4.70
3043 3137 1.127701 GATCTGAAGTCGCGATGCTC 58.872 55.000 14.06 10.10 0.00 4.26
3071 3165 1.207089 CGAACACAATAGCCTCCCAGA 59.793 52.381 0.00 0.00 0.00 3.86
3087 3181 4.817517 TCAAGAGTTTATCCAGACCGAAC 58.182 43.478 0.00 0.00 0.00 3.95
3107 3201 3.150335 CCCTGCTAGCTCGCCTCA 61.150 66.667 17.23 0.00 0.00 3.86
3216 3310 6.182627 TCAGACTTTATTAGAGACACCCGTA 58.817 40.000 0.00 0.00 0.00 4.02
3229 3323 6.059484 TCCGTTTCTTGGTTCAGACTTTATT 58.941 36.000 0.00 0.00 0.00 1.40
3230 3324 5.617252 TCCGTTTCTTGGTTCAGACTTTAT 58.383 37.500 0.00 0.00 0.00 1.40
3239 3337 1.947456 ACTGCTTCCGTTTCTTGGTTC 59.053 47.619 0.00 0.00 0.00 3.62
3443 3541 7.445402 TCGAAAGATGAGGAAAAACAAGAAGAT 59.555 33.333 0.00 0.00 33.31 2.40
3449 3547 5.820423 TCTGTCGAAAGATGAGGAAAAACAA 59.180 36.000 0.00 0.00 45.19 2.83
3451 3549 5.924475 TCTGTCGAAAGATGAGGAAAAAC 57.076 39.130 0.00 0.00 45.19 2.43
3459 3557 5.171476 GTTTCCAGATCTGTCGAAAGATGA 58.829 41.667 22.94 11.05 45.19 2.92
3592 3690 6.022821 CAGTACGTAGAGAGAAAAGTAGTGC 58.977 44.000 0.00 0.00 31.57 4.40
3598 3696 5.624344 TCCACAGTACGTAGAGAGAAAAG 57.376 43.478 0.00 0.00 0.00 2.27
3606 3704 4.617530 GCATGTTCTTCCACAGTACGTAGA 60.618 45.833 0.00 0.00 0.00 2.59
3674 3773 3.802948 ATTACCCGACTCAGCACTTAG 57.197 47.619 0.00 0.00 0.00 2.18
3904 4003 3.968837 ATGCTCGTACACCCCCGGA 62.969 63.158 0.73 0.00 0.00 5.14
4135 4234 2.734673 GCTCTTCTTGTCGGCAGCG 61.735 63.158 0.00 0.00 0.00 5.18
4163 4262 0.879090 CTTTGGTAAGCGTTGGGACC 59.121 55.000 0.00 0.00 0.00 4.46
4255 4354 2.485795 CCTCCTCTTCCTCGCCTCG 61.486 68.421 0.00 0.00 0.00 4.63
4471 4570 6.307776 AGGAGCTGTACTAATATCAGTGCTA 58.692 40.000 0.00 0.00 32.89 3.49
4670 4769 5.849357 AAGAATCGTTACATTACGCACAA 57.151 34.783 0.00 0.00 41.16 3.33
4819 4930 9.250246 AGTAGAAAATCTGCTAGAGTTACTCTT 57.750 33.333 20.59 5.00 41.50 2.85
4857 4968 8.012151 TCGCGTATATAACTGAGACTTAGTAC 57.988 38.462 5.77 0.00 0.00 2.73
4862 4976 6.651643 AGATCTCGCGTATATAACTGAGACTT 59.348 38.462 5.77 0.00 38.97 3.01
4867 5013 8.996271 TCTTAAAGATCTCGCGTATATAACTGA 58.004 33.333 5.77 0.00 0.00 3.41
4868 5014 9.776158 ATCTTAAAGATCTCGCGTATATAACTG 57.224 33.333 5.77 0.00 25.75 3.16
4871 5017 9.784680 GGAATCTTAAAGATCTCGCGTATATAA 57.215 33.333 5.77 2.13 32.89 0.98
4897 5043 4.442375 AGGTCTCAATCGACTAACACAG 57.558 45.455 0.00 0.00 34.38 3.66
4907 5126 3.440522 TGAGTGTGACTAGGTCTCAATCG 59.559 47.826 18.25 0.00 46.68 3.34
4910 5129 4.667573 AGATGAGTGTGACTAGGTCTCAA 58.332 43.478 0.00 0.00 37.70 3.02
4916 5135 7.001674 AGGTTCTATAGATGAGTGTGACTAGG 58.998 42.308 2.58 0.00 0.00 3.02
4921 5140 6.187682 TGTGAGGTTCTATAGATGAGTGTGA 58.812 40.000 2.58 0.00 0.00 3.58
4927 5146 5.243954 CGGGATTGTGAGGTTCTATAGATGA 59.756 44.000 2.58 0.00 0.00 2.92
4928 5147 5.243954 TCGGGATTGTGAGGTTCTATAGATG 59.756 44.000 2.58 0.00 0.00 2.90
4929 5148 5.394738 TCGGGATTGTGAGGTTCTATAGAT 58.605 41.667 2.58 0.00 0.00 1.98
4930 5149 4.800023 TCGGGATTGTGAGGTTCTATAGA 58.200 43.478 0.00 0.00 0.00 1.98
4931 5150 5.730296 ATCGGGATTGTGAGGTTCTATAG 57.270 43.478 0.00 0.00 0.00 1.31
4932 5151 5.600898 TCAATCGGGATTGTGAGGTTCTATA 59.399 40.000 18.11 0.00 46.15 1.31
4933 5152 4.408921 TCAATCGGGATTGTGAGGTTCTAT 59.591 41.667 18.11 0.00 46.15 1.98
4934 5153 3.772572 TCAATCGGGATTGTGAGGTTCTA 59.227 43.478 18.11 0.00 46.15 2.10
4935 5154 2.571653 TCAATCGGGATTGTGAGGTTCT 59.428 45.455 18.11 0.00 46.15 3.01
4936 5155 2.939103 CTCAATCGGGATTGTGAGGTTC 59.061 50.000 18.11 0.00 46.15 3.62
4937 5156 2.571653 TCTCAATCGGGATTGTGAGGTT 59.428 45.455 18.11 0.00 46.15 3.50
4938 5157 2.093447 GTCTCAATCGGGATTGTGAGGT 60.093 50.000 20.38 0.00 45.87 3.85
4939 5158 2.555199 GTCTCAATCGGGATTGTGAGG 58.445 52.381 20.38 10.92 45.87 3.86
4940 5159 2.169352 AGGTCTCAATCGGGATTGTGAG 59.831 50.000 20.38 12.86 45.87 3.51
4941 5160 2.187958 AGGTCTCAATCGGGATTGTGA 58.812 47.619 18.11 17.78 46.15 3.58
4942 5161 2.698855 AGGTCTCAATCGGGATTGTG 57.301 50.000 18.11 16.10 46.15 3.33
4943 5162 3.375699 ACTAGGTCTCAATCGGGATTGT 58.624 45.455 18.11 4.52 46.15 2.71
4945 5164 3.385111 GTGACTAGGTCTCAATCGGGATT 59.615 47.826 0.00 0.00 33.15 3.01
4946 5165 2.959707 GTGACTAGGTCTCAATCGGGAT 59.040 50.000 0.00 0.00 33.15 3.85
4947 5166 2.291346 TGTGACTAGGTCTCAATCGGGA 60.291 50.000 0.00 0.00 33.95 5.14
4948 5167 2.100197 TGTGACTAGGTCTCAATCGGG 58.900 52.381 0.00 0.00 33.95 5.14
4949 5168 2.159226 GGTGTGACTAGGTCTCAATCGG 60.159 54.545 0.00 0.00 37.70 4.18
4950 5169 2.159226 GGGTGTGACTAGGTCTCAATCG 60.159 54.545 0.00 0.00 37.70 3.34
4951 5170 2.832129 TGGGTGTGACTAGGTCTCAATC 59.168 50.000 0.00 2.06 37.70 2.67
4952 5171 2.902608 TGGGTGTGACTAGGTCTCAAT 58.097 47.619 0.00 0.00 37.70 2.57
4953 5172 2.391926 TGGGTGTGACTAGGTCTCAA 57.608 50.000 0.00 0.00 37.70 3.02
4954 5173 2.043115 AGATGGGTGTGACTAGGTCTCA 59.957 50.000 0.00 0.00 34.38 3.27
4955 5174 2.741145 AGATGGGTGTGACTAGGTCTC 58.259 52.381 0.00 0.00 33.15 3.36
4956 5175 2.930109 AGATGGGTGTGACTAGGTCT 57.070 50.000 0.00 0.00 33.15 3.85
4957 5176 5.632118 TCTATAGATGGGTGTGACTAGGTC 58.368 45.833 0.00 0.00 0.00 3.85
4958 5177 5.664815 TCTATAGATGGGTGTGACTAGGT 57.335 43.478 0.00 0.00 0.00 3.08
4959 5178 5.244178 GGTTCTATAGATGGGTGTGACTAGG 59.756 48.000 2.58 0.00 0.00 3.02
4960 5179 6.071984 AGGTTCTATAGATGGGTGTGACTAG 58.928 44.000 2.58 0.00 0.00 2.57
4961 5180 6.027025 AGGTTCTATAGATGGGTGTGACTA 57.973 41.667 2.58 0.00 0.00 2.59
4962 5181 4.884961 AGGTTCTATAGATGGGTGTGACT 58.115 43.478 2.58 0.00 0.00 3.41
4963 5182 4.649674 TGAGGTTCTATAGATGGGTGTGAC 59.350 45.833 2.58 0.00 0.00 3.67
4964 5183 4.649674 GTGAGGTTCTATAGATGGGTGTGA 59.350 45.833 2.58 0.00 0.00 3.58
4965 5184 4.405680 TGTGAGGTTCTATAGATGGGTGTG 59.594 45.833 2.58 0.00 0.00 3.82
4966 5185 4.620723 TGTGAGGTTCTATAGATGGGTGT 58.379 43.478 2.58 0.00 0.00 4.16
4967 5186 5.614324 TTGTGAGGTTCTATAGATGGGTG 57.386 43.478 2.58 0.00 0.00 4.61
4968 5187 5.308237 GGATTGTGAGGTTCTATAGATGGGT 59.692 44.000 2.58 0.00 0.00 4.51
4969 5188 5.545723 AGGATTGTGAGGTTCTATAGATGGG 59.454 44.000 2.58 0.00 0.00 4.00
4970 5189 6.678568 AGGATTGTGAGGTTCTATAGATGG 57.321 41.667 2.58 0.00 0.00 3.51
4987 5206 8.273557 CCGAACGTACAGAAATTATAAGGATTG 58.726 37.037 0.00 0.00 0.00 2.67
4991 5210 5.050567 GGCCGAACGTACAGAAATTATAAGG 60.051 44.000 0.00 0.00 0.00 2.69
5002 5221 0.799534 CTTACGGGCCGAACGTACAG 60.800 60.000 35.78 12.57 45.30 2.74
5005 5224 0.817013 ATTCTTACGGGCCGAACGTA 59.183 50.000 35.78 11.98 44.93 3.57
5007 5226 2.144482 ATATTCTTACGGGCCGAACG 57.856 50.000 35.78 19.07 37.36 3.95
5011 5230 3.182972 CGTTTGTATATTCTTACGGGCCG 59.817 47.826 27.06 27.06 0.00 6.13
5012 5231 3.495753 CCGTTTGTATATTCTTACGGGCC 59.504 47.826 13.87 0.00 43.42 5.80
5032 5279 3.672511 CGAAGTCGGGAATATATGGTCCG 60.673 52.174 12.65 12.65 41.80 4.79
5038 5285 2.897969 AGTGGCGAAGTCGGGAATATAT 59.102 45.455 2.47 0.00 40.23 0.86
5045 5292 2.814280 AATATAGTGGCGAAGTCGGG 57.186 50.000 2.47 0.00 40.23 5.14
5047 5294 4.680110 CAGGTAAATATAGTGGCGAAGTCG 59.320 45.833 0.00 0.00 43.27 4.18
5068 5315 1.609208 CCTAAATTGGCCGGGATCAG 58.391 55.000 2.18 0.00 0.00 2.90
5069 5316 0.184933 CCCTAAATTGGCCGGGATCA 59.815 55.000 2.18 0.00 39.08 2.92
5116 5363 4.320861 CGGAGTATGAAGATTGCGAGAGAT 60.321 45.833 0.00 0.00 0.00 2.75
5120 5367 2.398498 CCGGAGTATGAAGATTGCGAG 58.602 52.381 0.00 0.00 0.00 5.03
5129 5376 1.399714 ATCAGTCGCCGGAGTATGAA 58.600 50.000 5.05 0.00 0.00 2.57
5130 5377 1.337071 GAATCAGTCGCCGGAGTATGA 59.663 52.381 5.05 11.73 0.00 2.15
5140 5387 0.950555 TGTGTGCAGGAATCAGTCGC 60.951 55.000 0.00 0.00 0.00 5.19
5141 5388 0.792640 GTGTGTGCAGGAATCAGTCG 59.207 55.000 0.00 0.00 0.00 4.18
5144 5391 1.229975 TGCGTGTGTGCAGGAATCAG 61.230 55.000 0.00 0.00 40.62 2.90
5161 5410 0.727398 GATGTGCTCTAAACGGGTGC 59.273 55.000 0.00 0.00 0.00 5.01
5177 5426 3.282157 CTCCGCCGGCCATTGATG 61.282 66.667 23.46 4.25 0.00 3.07
5212 5461 4.020617 CGGTTGCAGGAGAGGGCA 62.021 66.667 0.00 0.00 38.46 5.36
5235 5484 0.384725 CACTCTTTGGCACGCTTTCG 60.385 55.000 0.00 0.00 42.43 3.46
5258 5507 3.335356 ATGGTTGCAGGAGAGGGCG 62.335 63.158 0.00 0.00 0.00 6.13
5278 5527 1.302033 CTGCTCCACGCTTTCCAGT 60.302 57.895 0.00 0.00 40.11 4.00
5279 5528 2.684843 GCTGCTCCACGCTTTCCAG 61.685 63.158 0.00 0.00 40.11 3.86
5304 5553 3.682292 AAAGCGCATCCCCGACCTC 62.682 63.158 11.47 0.00 0.00 3.85
5305 5554 3.717294 AAAGCGCATCCCCGACCT 61.717 61.111 11.47 0.00 0.00 3.85
5306 5555 3.508840 CAAAGCGCATCCCCGACC 61.509 66.667 11.47 0.00 0.00 4.79
5307 5556 3.508840 CCAAAGCGCATCCCCGAC 61.509 66.667 11.47 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.