Multiple sequence alignment - TraesCS5D01G049600

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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 TraesCS5D01G049600 chr5D 100.000 2688 0 0 1 2688 47081560 47084247 0.000000e+00 4964.0
1 TraesCS5D01G049600 chr5D 97.852 931 14 6 1760 2688 560418074 560417148 0.000000e+00 1604.0
2 TraesCS5D01G049600 chr5D 97.642 933 15 7 1760 2688 499745685 499746614 0.000000e+00 1594.0
3 TraesCS5D01G049600 chr5D 88.508 905 36 18 870 1759 47286615 47285764 0.000000e+00 1033.0
4 TraesCS5D01G049600 chr5D 89.881 504 23 11 999 1477 47517094 47516594 8.170000e-175 623.0
5 TraesCS5D01G049600 chr5B 94.866 1383 58 10 385 1759 49882190 49883567 0.000000e+00 2148.0
6 TraesCS5D01G049600 chr5B 83.436 652 59 27 1053 1688 688589489 688588871 6.500000e-156 560.0
7 TraesCS5D01G049600 chr5B 77.477 222 31 15 1473 1688 664243822 664244030 6.080000e-22 115.0
8 TraesCS5D01G049600 chr4D 99.462 929 3 2 1760 2688 111582348 111583274 0.000000e+00 1687.0
9 TraesCS5D01G049600 chr6D 98.174 931 13 4 1760 2688 453650226 453649298 0.000000e+00 1622.0
10 TraesCS5D01G049600 chr6D 97.744 931 16 3 1760 2688 373374340 373375267 0.000000e+00 1598.0
11 TraesCS5D01G049600 chr6D 87.054 448 47 5 45 490 101897243 101896805 1.860000e-136 496.0
12 TraesCS5D01G049600 chr7D 97.744 931 14 7 1760 2688 615765408 615764483 0.000000e+00 1596.0
13 TraesCS5D01G049600 chr7D 97.210 932 21 5 1760 2688 266019646 266018717 0.000000e+00 1572.0
14 TraesCS5D01G049600 chr7D 83.282 652 62 34 1053 1688 484694369 484693749 8.410000e-155 556.0
15 TraesCS5D01G049600 chr7D 86.344 454 53 4 42 493 242706988 242706542 1.120000e-133 486.0
16 TraesCS5D01G049600 chr2D 97.530 931 19 4 1760 2688 3029586 3028658 0.000000e+00 1589.0
17 TraesCS5D01G049600 chr1D 97.131 941 20 5 1751 2688 62937245 62938181 0.000000e+00 1581.0
18 TraesCS5D01G049600 chr5A 92.905 902 24 12 870 1759 37922644 37923517 0.000000e+00 1275.0
19 TraesCS5D01G049600 chr4B 88.989 445 42 2 45 489 66704875 66704438 6.540000e-151 544.0
20 TraesCS5D01G049600 chr4B 87.333 450 47 6 45 493 177893404 177892964 8.590000e-140 507.0
21 TraesCS5D01G049600 chr4B 77.734 256 34 8 618 850 86365000 86365255 4.670000e-28 135.0
22 TraesCS5D01G049600 chr1B 88.692 451 42 8 45 493 264321412 264320969 2.350000e-150 542.0
23 TraesCS5D01G049600 chr3D 87.444 446 48 5 48 492 140573038 140572600 8.590000e-140 507.0
24 TraesCS5D01G049600 chr6B 85.865 474 60 6 21 493 522849717 522850184 5.170000e-137 497.0
25 TraesCS5D01G049600 chr4A 86.996 446 52 1 48 493 225957965 225957526 5.170000e-137 497.0
26 TraesCS5D01G049600 chr2B 86.996 446 49 6 45 489 200523604 200523167 6.690000e-136 494.0
27 TraesCS5D01G049600 chr2B 78.210 257 30 15 618 850 30242752 30243006 1.000000e-29 141.0
28 TraesCS5D01G049600 chr3B 83.051 236 32 7 618 850 547346037 547345807 9.750000e-50 207.0
29 TraesCS5D01G049600 chr3B 95.122 41 2 0 776 816 642060176 642060216 6.210000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G049600 chr5D 47081560 47084247 2687 False 4964 4964 100.000 1 2688 1 chr5D.!!$F1 2687
1 TraesCS5D01G049600 chr5D 560417148 560418074 926 True 1604 1604 97.852 1760 2688 1 chr5D.!!$R3 928
2 TraesCS5D01G049600 chr5D 499745685 499746614 929 False 1594 1594 97.642 1760 2688 1 chr5D.!!$F2 928
3 TraesCS5D01G049600 chr5D 47285764 47286615 851 True 1033 1033 88.508 870 1759 1 chr5D.!!$R1 889
4 TraesCS5D01G049600 chr5D 47516594 47517094 500 True 623 623 89.881 999 1477 1 chr5D.!!$R2 478
5 TraesCS5D01G049600 chr5B 49882190 49883567 1377 False 2148 2148 94.866 385 1759 1 chr5B.!!$F1 1374
6 TraesCS5D01G049600 chr5B 688588871 688589489 618 True 560 560 83.436 1053 1688 1 chr5B.!!$R1 635
7 TraesCS5D01G049600 chr4D 111582348 111583274 926 False 1687 1687 99.462 1760 2688 1 chr4D.!!$F1 928
8 TraesCS5D01G049600 chr6D 453649298 453650226 928 True 1622 1622 98.174 1760 2688 1 chr6D.!!$R2 928
9 TraesCS5D01G049600 chr6D 373374340 373375267 927 False 1598 1598 97.744 1760 2688 1 chr6D.!!$F1 928
10 TraesCS5D01G049600 chr7D 615764483 615765408 925 True 1596 1596 97.744 1760 2688 1 chr7D.!!$R4 928
11 TraesCS5D01G049600 chr7D 266018717 266019646 929 True 1572 1572 97.210 1760 2688 1 chr7D.!!$R2 928
12 TraesCS5D01G049600 chr7D 484693749 484694369 620 True 556 556 83.282 1053 1688 1 chr7D.!!$R3 635
13 TraesCS5D01G049600 chr2D 3028658 3029586 928 True 1589 1589 97.530 1760 2688 1 chr2D.!!$R1 928
14 TraesCS5D01G049600 chr1D 62937245 62938181 936 False 1581 1581 97.131 1751 2688 1 chr1D.!!$F1 937
15 TraesCS5D01G049600 chr5A 37922644 37923517 873 False 1275 1275 92.905 870 1759 1 chr5A.!!$F1 889

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
807 810 0.402121 AAAAAGAGAAGCCCGAGCCT 59.598 50.0 0.0 0.0 41.25 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2020 1.278127 CTGGTTCTTTCCTAGGGCGAA 59.722 52.381 9.46 6.58 0.0 4.7 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
33 34 9.902196 CATGATTGCAAAGTATAAATGCTATGA 57.098 29.630 1.71 1.49 40.66 2.15
52 53 9.287373 TGCTATGAATATCAATTGTGCTAATGA 57.713 29.630 5.13 0.00 0.00 2.57
62 63 7.430441 TCAATTGTGCTAATGATCATGATTGG 58.570 34.615 9.46 0.00 0.00 3.16
63 64 5.777850 TTGTGCTAATGATCATGATTGGG 57.222 39.130 9.46 0.80 0.00 4.12
64 65 4.146564 TGTGCTAATGATCATGATTGGGG 58.853 43.478 9.46 1.49 0.00 4.96
65 66 4.147321 GTGCTAATGATCATGATTGGGGT 58.853 43.478 9.46 0.00 0.00 4.95
66 67 4.022589 GTGCTAATGATCATGATTGGGGTG 60.023 45.833 9.46 0.97 0.00 4.61
67 68 4.141205 TGCTAATGATCATGATTGGGGTGA 60.141 41.667 9.46 0.00 0.00 4.02
68 69 5.014858 GCTAATGATCATGATTGGGGTGAT 58.985 41.667 9.46 0.00 35.42 3.06
69 70 6.182627 GCTAATGATCATGATTGGGGTGATA 58.817 40.000 9.46 0.00 33.03 2.15
70 71 6.660521 GCTAATGATCATGATTGGGGTGATAA 59.339 38.462 9.46 0.00 33.03 1.75
71 72 7.341256 GCTAATGATCATGATTGGGGTGATAAT 59.659 37.037 9.46 0.00 33.03 1.28
72 73 9.251440 CTAATGATCATGATTGGGGTGATAATT 57.749 33.333 9.46 0.00 37.28 1.40
74 75 9.778479 AATGATCATGATTGGGGTGATAATTAT 57.222 29.630 9.46 0.00 33.61 1.28
75 76 8.584063 TGATCATGATTGGGGTGATAATTATG 57.416 34.615 10.14 0.00 33.03 1.90
76 77 8.392479 TGATCATGATTGGGGTGATAATTATGA 58.608 33.333 10.14 0.00 40.90 2.15
77 78 9.417561 GATCATGATTGGGGTGATAATTATGAT 57.582 33.333 10.14 13.54 45.12 2.45
78 79 8.584063 TCATGATTGGGGTGATAATTATGATG 57.416 34.615 1.78 0.00 35.61 3.07
79 80 6.839124 TGATTGGGGTGATAATTATGATGC 57.161 37.500 1.78 0.00 0.00 3.91
80 81 6.554784 TGATTGGGGTGATAATTATGATGCT 58.445 36.000 1.78 0.00 0.00 3.79
81 82 7.011994 TGATTGGGGTGATAATTATGATGCTT 58.988 34.615 1.78 0.00 0.00 3.91
82 83 6.899393 TTGGGGTGATAATTATGATGCTTC 57.101 37.500 1.78 0.00 0.00 3.86
83 84 6.204852 TGGGGTGATAATTATGATGCTTCT 57.795 37.500 1.78 0.00 0.00 2.85
84 85 6.613699 TGGGGTGATAATTATGATGCTTCTT 58.386 36.000 1.78 0.00 0.00 2.52
85 86 7.754624 TGGGGTGATAATTATGATGCTTCTTA 58.245 34.615 1.78 0.00 0.00 2.10
86 87 8.393259 TGGGGTGATAATTATGATGCTTCTTAT 58.607 33.333 1.78 0.00 0.00 1.73
87 88 8.680903 GGGGTGATAATTATGATGCTTCTTATG 58.319 37.037 1.78 0.00 0.00 1.90
88 89 9.453572 GGGTGATAATTATGATGCTTCTTATGA 57.546 33.333 1.78 0.00 0.00 2.15
95 96 8.631480 ATTATGATGCTTCTTATGATCTTGCA 57.369 30.769 0.88 0.00 0.00 4.08
96 97 6.954487 ATGATGCTTCTTATGATCTTGCAA 57.046 33.333 0.00 0.00 32.66 4.08
97 98 6.762702 TGATGCTTCTTATGATCTTGCAAA 57.237 33.333 0.00 0.00 32.66 3.68
98 99 7.342769 TGATGCTTCTTATGATCTTGCAAAT 57.657 32.000 0.00 0.00 32.66 2.32
99 100 7.778083 TGATGCTTCTTATGATCTTGCAAATT 58.222 30.769 0.00 0.00 32.66 1.82
100 101 8.255206 TGATGCTTCTTATGATCTTGCAAATTT 58.745 29.630 0.00 0.00 32.66 1.82
101 102 9.740239 GATGCTTCTTATGATCTTGCAAATTTA 57.260 29.630 0.00 0.00 32.66 1.40
161 162 9.590451 AATGGTTGCAATTATATTGAAAGTGAG 57.410 29.630 0.59 0.00 0.00 3.51
162 163 8.121305 TGGTTGCAATTATATTGAAAGTGAGT 57.879 30.769 0.59 0.00 0.00 3.41
163 164 8.584157 TGGTTGCAATTATATTGAAAGTGAGTT 58.416 29.630 0.59 0.00 0.00 3.01
164 165 9.423061 GGTTGCAATTATATTGAAAGTGAGTTT 57.577 29.630 0.59 0.00 0.00 2.66
166 167 8.984891 TGCAATTATATTGAAAGTGAGTTTGG 57.015 30.769 3.70 0.00 0.00 3.28
167 168 8.801299 TGCAATTATATTGAAAGTGAGTTTGGA 58.199 29.630 3.70 0.00 0.00 3.53
168 169 9.638239 GCAATTATATTGAAAGTGAGTTTGGAA 57.362 29.630 3.70 0.00 0.00 3.53
172 173 4.900635 TTGAAAGTGAGTTTGGAAGAGC 57.099 40.909 0.00 0.00 0.00 4.09
173 174 3.884895 TGAAAGTGAGTTTGGAAGAGCA 58.115 40.909 0.00 0.00 0.00 4.26
174 175 4.464008 TGAAAGTGAGTTTGGAAGAGCAT 58.536 39.130 0.00 0.00 0.00 3.79
175 176 4.516698 TGAAAGTGAGTTTGGAAGAGCATC 59.483 41.667 0.00 0.00 0.00 3.91
176 177 3.777106 AGTGAGTTTGGAAGAGCATCA 57.223 42.857 0.00 0.00 37.82 3.07
177 178 4.090761 AGTGAGTTTGGAAGAGCATCAA 57.909 40.909 0.00 0.00 37.82 2.57
178 179 3.817647 AGTGAGTTTGGAAGAGCATCAAC 59.182 43.478 0.00 0.00 37.82 3.18
179 180 3.817647 GTGAGTTTGGAAGAGCATCAACT 59.182 43.478 0.00 0.00 37.82 3.16
180 181 4.276926 GTGAGTTTGGAAGAGCATCAACTT 59.723 41.667 0.00 0.00 37.82 2.66
181 182 4.889409 TGAGTTTGGAAGAGCATCAACTTT 59.111 37.500 0.00 0.00 37.82 2.66
182 183 6.017109 GTGAGTTTGGAAGAGCATCAACTTTA 60.017 38.462 0.00 0.00 37.82 1.85
183 184 6.205464 TGAGTTTGGAAGAGCATCAACTTTAG 59.795 38.462 0.00 0.00 37.82 1.85
184 185 5.474876 AGTTTGGAAGAGCATCAACTTTAGG 59.525 40.000 0.00 0.00 37.82 2.69
185 186 4.640771 TGGAAGAGCATCAACTTTAGGT 57.359 40.909 0.00 0.00 37.82 3.08
186 187 5.755409 TGGAAGAGCATCAACTTTAGGTA 57.245 39.130 0.00 0.00 37.82 3.08
187 188 6.121776 TGGAAGAGCATCAACTTTAGGTAA 57.878 37.500 0.00 0.00 37.82 2.85
188 189 6.721318 TGGAAGAGCATCAACTTTAGGTAAT 58.279 36.000 0.00 0.00 37.82 1.89
189 190 7.857456 TGGAAGAGCATCAACTTTAGGTAATA 58.143 34.615 0.00 0.00 37.82 0.98
190 191 8.325787 TGGAAGAGCATCAACTTTAGGTAATAA 58.674 33.333 0.00 0.00 37.82 1.40
191 192 9.343539 GGAAGAGCATCAACTTTAGGTAATAAT 57.656 33.333 0.00 0.00 37.82 1.28
193 194 9.905713 AAGAGCATCAACTTTAGGTAATAATGA 57.094 29.630 0.00 0.00 37.82 2.57
196 197 9.289782 AGCATCAACTTTAGGTAATAATGATCC 57.710 33.333 0.00 0.00 0.00 3.36
197 198 8.515414 GCATCAACTTTAGGTAATAATGATCCC 58.485 37.037 0.00 0.00 0.00 3.85
198 199 9.573166 CATCAACTTTAGGTAATAATGATCCCA 57.427 33.333 0.00 0.00 0.00 4.37
199 200 8.974060 TCAACTTTAGGTAATAATGATCCCAC 57.026 34.615 0.00 0.00 0.00 4.61
200 201 8.778059 TCAACTTTAGGTAATAATGATCCCACT 58.222 33.333 0.00 0.00 0.00 4.00
203 204 9.448587 ACTTTAGGTAATAATGATCCCACTACT 57.551 33.333 0.00 0.00 0.00 2.57
207 208 7.518188 AGGTAATAATGATCCCACTACTTTGG 58.482 38.462 0.00 0.00 36.26 3.28
208 209 7.349859 AGGTAATAATGATCCCACTACTTTGGA 59.650 37.037 0.00 0.00 39.24 3.53
209 210 7.661847 GGTAATAATGATCCCACTACTTTGGAG 59.338 40.741 0.00 0.00 39.24 3.86
210 211 7.451731 AATAATGATCCCACTACTTTGGAGA 57.548 36.000 0.00 0.00 39.24 3.71
211 212 5.779241 AATGATCCCACTACTTTGGAGAA 57.221 39.130 0.00 0.00 39.24 2.87
212 213 5.983333 ATGATCCCACTACTTTGGAGAAT 57.017 39.130 0.00 0.00 39.24 2.40
213 214 5.102953 TGATCCCACTACTTTGGAGAATG 57.897 43.478 0.00 0.00 39.24 2.67
214 215 4.080356 TGATCCCACTACTTTGGAGAATGG 60.080 45.833 0.00 0.00 39.24 3.16
215 216 3.256704 TCCCACTACTTTGGAGAATGGT 58.743 45.455 0.00 0.00 39.24 3.55
216 217 3.263425 TCCCACTACTTTGGAGAATGGTC 59.737 47.826 0.00 0.00 39.24 4.02
217 218 3.009033 CCCACTACTTTGGAGAATGGTCA 59.991 47.826 0.00 0.00 39.24 4.02
218 219 4.506625 CCCACTACTTTGGAGAATGGTCAA 60.507 45.833 0.00 0.00 39.24 3.18
219 220 5.256474 CCACTACTTTGGAGAATGGTCAAT 58.744 41.667 0.00 0.00 39.24 2.57
220 221 5.355350 CCACTACTTTGGAGAATGGTCAATC 59.645 44.000 0.00 0.00 39.24 2.67
221 222 6.176183 CACTACTTTGGAGAATGGTCAATCT 58.824 40.000 0.00 0.00 0.00 2.40
222 223 6.656693 CACTACTTTGGAGAATGGTCAATCTT 59.343 38.462 0.00 0.00 0.00 2.40
223 224 7.824289 CACTACTTTGGAGAATGGTCAATCTTA 59.176 37.037 0.00 0.00 0.00 2.10
224 225 8.552296 ACTACTTTGGAGAATGGTCAATCTTAT 58.448 33.333 0.00 0.00 0.00 1.73
225 226 7.636150 ACTTTGGAGAATGGTCAATCTTATG 57.364 36.000 0.00 0.00 0.00 1.90
226 227 7.405292 ACTTTGGAGAATGGTCAATCTTATGA 58.595 34.615 0.00 0.00 0.00 2.15
227 228 7.890127 ACTTTGGAGAATGGTCAATCTTATGAA 59.110 33.333 0.00 0.00 0.00 2.57
228 229 8.648698 TTTGGAGAATGGTCAATCTTATGAAA 57.351 30.769 0.00 0.00 0.00 2.69
229 230 8.827832 TTGGAGAATGGTCAATCTTATGAAAT 57.172 30.769 0.00 0.00 0.00 2.17
230 231 8.827832 TGGAGAATGGTCAATCTTATGAAATT 57.172 30.769 0.00 0.00 0.00 1.82
231 232 9.258629 TGGAGAATGGTCAATCTTATGAAATTT 57.741 29.630 0.00 0.00 0.00 1.82
250 251 8.897752 TGAAATTTTTGATAAAAGTGGGTTTGG 58.102 29.630 0.00 0.00 36.73 3.28
251 252 9.114952 GAAATTTTTGATAAAAGTGGGTTTGGA 57.885 29.630 0.00 0.00 36.73 3.53
252 253 8.675705 AATTTTTGATAAAAGTGGGTTTGGAG 57.324 30.769 0.00 0.00 36.73 3.86
253 254 7.425224 TTTTTGATAAAAGTGGGTTTGGAGA 57.575 32.000 0.00 0.00 0.00 3.71
254 255 6.648879 TTTGATAAAAGTGGGTTTGGAGAG 57.351 37.500 0.00 0.00 0.00 3.20
255 256 4.662278 TGATAAAAGTGGGTTTGGAGAGG 58.338 43.478 0.00 0.00 0.00 3.69
256 257 4.105697 TGATAAAAGTGGGTTTGGAGAGGT 59.894 41.667 0.00 0.00 0.00 3.85
257 258 2.658807 AAAGTGGGTTTGGAGAGGTC 57.341 50.000 0.00 0.00 0.00 3.85
258 259 1.518367 AAGTGGGTTTGGAGAGGTCA 58.482 50.000 0.00 0.00 0.00 4.02
259 260 1.747444 AGTGGGTTTGGAGAGGTCAT 58.253 50.000 0.00 0.00 0.00 3.06
260 261 1.352352 AGTGGGTTTGGAGAGGTCATG 59.648 52.381 0.00 0.00 0.00 3.07
261 262 1.351017 GTGGGTTTGGAGAGGTCATGA 59.649 52.381 0.00 0.00 0.00 3.07
262 263 1.351017 TGGGTTTGGAGAGGTCATGAC 59.649 52.381 17.91 17.91 0.00 3.06
263 264 1.630878 GGGTTTGGAGAGGTCATGACT 59.369 52.381 24.50 11.25 0.00 3.41
264 265 2.040412 GGGTTTGGAGAGGTCATGACTT 59.960 50.000 24.50 18.30 0.00 3.01
265 266 3.339141 GGTTTGGAGAGGTCATGACTTC 58.661 50.000 26.02 26.02 37.65 3.01
266 267 3.244561 GGTTTGGAGAGGTCATGACTTCA 60.245 47.826 32.12 15.37 39.56 3.02
267 268 4.566488 GGTTTGGAGAGGTCATGACTTCAT 60.566 45.833 32.12 20.38 39.56 2.57
268 269 4.916041 TTGGAGAGGTCATGACTTCATT 57.084 40.909 32.12 17.69 39.56 2.57
269 270 4.916041 TGGAGAGGTCATGACTTCATTT 57.084 40.909 32.12 17.04 39.56 2.32
270 271 4.582869 TGGAGAGGTCATGACTTCATTTG 58.417 43.478 32.12 0.00 39.56 2.32
271 272 4.286808 TGGAGAGGTCATGACTTCATTTGA 59.713 41.667 32.12 13.61 39.56 2.69
272 273 5.045359 TGGAGAGGTCATGACTTCATTTGAT 60.045 40.000 32.12 15.75 39.56 2.57
273 274 5.296283 GGAGAGGTCATGACTTCATTTGATG 59.704 44.000 32.12 0.00 39.56 3.07
274 275 6.058553 AGAGGTCATGACTTCATTTGATGA 57.941 37.500 32.12 0.00 39.56 2.92
275 276 6.660800 AGAGGTCATGACTTCATTTGATGAT 58.339 36.000 32.12 11.62 39.56 2.45
276 277 7.799081 AGAGGTCATGACTTCATTTGATGATA 58.201 34.615 32.12 0.00 39.56 2.15
277 278 8.270030 AGAGGTCATGACTTCATTTGATGATAA 58.730 33.333 32.12 0.00 39.56 1.75
278 279 8.991783 AGGTCATGACTTCATTTGATGATAAT 57.008 30.769 24.50 0.00 39.39 1.28
279 280 9.064706 AGGTCATGACTTCATTTGATGATAATC 57.935 33.333 24.50 2.22 39.39 1.75
280 281 8.295288 GGTCATGACTTCATTTGATGATAATCC 58.705 37.037 24.50 0.00 39.39 3.01
281 282 8.295288 GTCATGACTTCATTTGATGATAATCCC 58.705 37.037 18.83 0.00 39.39 3.85
282 283 8.000127 TCATGACTTCATTTGATGATAATCCCA 59.000 33.333 0.00 0.00 39.39 4.37
283 284 7.572523 TGACTTCATTTGATGATAATCCCAC 57.427 36.000 0.94 0.00 39.39 4.61
284 285 7.348815 TGACTTCATTTGATGATAATCCCACT 58.651 34.615 0.94 0.00 39.39 4.00
285 286 8.493607 TGACTTCATTTGATGATAATCCCACTA 58.506 33.333 0.94 0.00 39.39 2.74
286 287 9.512588 GACTTCATTTGATGATAATCCCACTAT 57.487 33.333 0.94 0.00 39.39 2.12
287 288 9.872684 ACTTCATTTGATGATAATCCCACTATT 57.127 29.630 0.94 0.00 39.39 1.73
295 296 9.919416 TGATGATAATCCCACTATTTTGAAAGA 57.081 29.630 0.00 0.00 0.00 2.52
328 329 6.587206 TTTTGTGCATGTGGATCATAAAGA 57.413 33.333 0.00 0.00 34.67 2.52
329 330 5.823209 TTGTGCATGTGGATCATAAAGAG 57.177 39.130 0.00 0.00 34.67 2.85
330 331 5.101648 TGTGCATGTGGATCATAAAGAGA 57.898 39.130 0.00 0.00 34.67 3.10
331 332 5.499313 TGTGCATGTGGATCATAAAGAGAA 58.501 37.500 0.00 0.00 34.67 2.87
332 333 6.124340 TGTGCATGTGGATCATAAAGAGAAT 58.876 36.000 0.00 0.00 34.67 2.40
333 334 7.281841 TGTGCATGTGGATCATAAAGAGAATA 58.718 34.615 0.00 0.00 34.67 1.75
334 335 7.940688 TGTGCATGTGGATCATAAAGAGAATAT 59.059 33.333 0.00 0.00 34.67 1.28
335 336 8.790718 GTGCATGTGGATCATAAAGAGAATATT 58.209 33.333 0.00 0.00 34.67 1.28
336 337 8.789762 TGCATGTGGATCATAAAGAGAATATTG 58.210 33.333 0.00 0.00 34.67 1.90
337 338 8.790718 GCATGTGGATCATAAAGAGAATATTGT 58.209 33.333 0.00 0.00 34.67 2.71
377 378 9.685276 ATTGTTGAACTTGAATATGATCCTACA 57.315 29.630 0.00 0.00 0.00 2.74
378 379 9.685276 TTGTTGAACTTGAATATGATCCTACAT 57.315 29.630 0.00 0.00 0.00 2.29
379 380 9.112725 TGTTGAACTTGAATATGATCCTACATG 57.887 33.333 0.00 0.00 0.00 3.21
380 381 9.113838 GTTGAACTTGAATATGATCCTACATGT 57.886 33.333 2.69 2.69 0.00 3.21
456 457 5.972107 ACCTCTCTTGATGTTCAAATTGG 57.028 39.130 0.00 0.00 35.73 3.16
462 463 7.315142 TCTCTTGATGTTCAAATTGGTAATGC 58.685 34.615 0.00 0.00 35.73 3.56
548 550 2.481185 GAGGTATCGACTGATCTCCGTC 59.519 54.545 0.00 0.00 35.99 4.79
551 553 3.120130 GGTATCGACTGATCTCCGTCATC 60.120 52.174 0.00 0.00 35.99 2.92
563 565 6.430000 TGATCTCCGTCATCGATGTATCTAAA 59.570 38.462 24.09 7.28 39.71 1.85
564 566 6.242508 TCTCCGTCATCGATGTATCTAAAG 57.757 41.667 24.09 13.34 39.71 1.85
574 576 5.768662 TCGATGTATCTAAAGGGGTCTACTG 59.231 44.000 0.00 0.00 0.00 2.74
603 606 3.184541 AGTGTTATTACTAACCTGCGCG 58.815 45.455 0.00 0.00 37.09 6.86
634 637 0.803117 GAGCCGGACTTGTAAAAGCC 59.197 55.000 5.05 0.00 0.00 4.35
639 642 2.489971 CGGACTTGTAAAAGCCTGACA 58.510 47.619 0.00 0.00 0.00 3.58
697 700 5.606348 AATACACTTTGTTTTCAAGCCCA 57.394 34.783 0.00 0.00 41.09 5.36
702 705 1.494960 TTGTTTTCAAGCCCAAGCCT 58.505 45.000 0.00 0.00 41.25 4.58
716 719 2.028748 CCAAGCCTGTCCCAAAATCAAG 60.029 50.000 0.00 0.00 0.00 3.02
743 746 2.337170 CGAAAACCCGGCCCAAAC 59.663 61.111 0.00 0.00 0.00 2.93
807 810 0.402121 AAAAAGAGAAGCCCGAGCCT 59.598 50.000 0.00 0.00 41.25 4.58
850 853 4.589675 AAACAAAGCCCGGCCCGA 62.590 61.111 3.71 0.00 0.00 5.14
904 915 5.024555 GCTAGAAATGTCAAATTGTCTCGC 58.975 41.667 0.00 0.00 0.00 5.03
911 922 0.449388 CAAATTGTCTCGCTGCTCCC 59.551 55.000 0.00 0.00 0.00 4.30
992 1003 2.849007 CAGAGCGCAACACAGACG 59.151 61.111 11.47 0.00 0.00 4.18
1291 1340 2.741726 CGAGCAAGAGCAGCAGCAG 61.742 63.158 3.17 0.00 45.49 4.24
1305 1354 2.184322 GCAGATGAACTCCGGCGA 59.816 61.111 9.30 0.00 0.00 5.54
1392 1450 2.953821 GTGCATGGTGGACAACGG 59.046 61.111 0.00 0.00 38.66 4.44
1622 1695 1.823169 TTTTAGCTGCCCGTCGACCT 61.823 55.000 10.58 2.33 0.00 3.85
1942 2020 1.808945 GCTTAGCATGCACAGACAACT 59.191 47.619 21.98 0.00 0.00 3.16
1985 2063 2.756829 TGCCATACGTTTTCTCGTTCA 58.243 42.857 0.00 0.00 43.80 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.902196 TCATAGCATTTATACTTTGCAATCATG 57.098 29.630 0.00 0.00 38.84 3.07
26 27 9.287373 TCATTAGCACAATTGATATTCATAGCA 57.713 29.630 13.59 0.00 0.00 3.49
36 37 8.088365 CCAATCATGATCATTAGCACAATTGAT 58.912 33.333 13.59 0.27 32.22 2.57
37 38 7.430441 CCAATCATGATCATTAGCACAATTGA 58.570 34.615 13.59 0.00 32.22 2.57
38 39 6.645003 CCCAATCATGATCATTAGCACAATTG 59.355 38.462 9.06 3.24 31.18 2.32
39 40 6.239487 CCCCAATCATGATCATTAGCACAATT 60.239 38.462 9.06 0.00 0.00 2.32
40 41 5.245301 CCCCAATCATGATCATTAGCACAAT 59.755 40.000 9.06 0.00 0.00 2.71
41 42 4.585581 CCCCAATCATGATCATTAGCACAA 59.414 41.667 9.06 0.00 0.00 3.33
42 43 4.146564 CCCCAATCATGATCATTAGCACA 58.853 43.478 9.06 0.00 0.00 4.57
43 44 4.022589 CACCCCAATCATGATCATTAGCAC 60.023 45.833 9.06 0.00 0.00 4.40
44 45 4.141205 TCACCCCAATCATGATCATTAGCA 60.141 41.667 9.06 0.00 0.00 3.49
45 46 4.401022 TCACCCCAATCATGATCATTAGC 58.599 43.478 9.06 0.00 0.00 3.09
46 47 8.818622 ATTATCACCCCAATCATGATCATTAG 57.181 34.615 9.06 0.00 34.86 1.73
48 49 9.778479 ATAATTATCACCCCAATCATGATCATT 57.222 29.630 9.06 0.00 34.86 2.57
49 50 9.197306 CATAATTATCACCCCAATCATGATCAT 57.803 33.333 9.06 1.18 34.86 2.45
50 51 8.392479 TCATAATTATCACCCCAATCATGATCA 58.608 33.333 9.06 0.00 34.86 2.92
51 52 8.812513 TCATAATTATCACCCCAATCATGATC 57.187 34.615 9.06 0.00 34.86 2.92
52 53 9.197306 CATCATAATTATCACCCCAATCATGAT 57.803 33.333 1.18 1.18 36.95 2.45
53 54 7.123098 GCATCATAATTATCACCCCAATCATGA 59.877 37.037 0.00 0.00 0.00 3.07
54 55 7.123697 AGCATCATAATTATCACCCCAATCATG 59.876 37.037 0.00 0.00 0.00 3.07
55 56 7.186972 AGCATCATAATTATCACCCCAATCAT 58.813 34.615 0.00 0.00 0.00 2.45
56 57 6.554784 AGCATCATAATTATCACCCCAATCA 58.445 36.000 0.00 0.00 0.00 2.57
57 58 7.395489 AGAAGCATCATAATTATCACCCCAATC 59.605 37.037 0.00 0.00 0.00 2.67
58 59 7.243824 AGAAGCATCATAATTATCACCCCAAT 58.756 34.615 0.00 0.00 0.00 3.16
59 60 6.613699 AGAAGCATCATAATTATCACCCCAA 58.386 36.000 0.00 0.00 0.00 4.12
60 61 6.204852 AGAAGCATCATAATTATCACCCCA 57.795 37.500 0.00 0.00 0.00 4.96
61 62 8.680903 CATAAGAAGCATCATAATTATCACCCC 58.319 37.037 0.00 0.00 0.00 4.95
62 63 9.453572 TCATAAGAAGCATCATAATTATCACCC 57.546 33.333 0.00 0.00 0.00 4.61
69 70 9.074576 TGCAAGATCATAAGAAGCATCATAATT 57.925 29.630 0.00 0.00 0.00 1.40
70 71 8.631480 TGCAAGATCATAAGAAGCATCATAAT 57.369 30.769 0.00 0.00 0.00 1.28
71 72 8.454570 TTGCAAGATCATAAGAAGCATCATAA 57.545 30.769 0.00 0.00 0.00 1.90
72 73 8.454570 TTTGCAAGATCATAAGAAGCATCATA 57.545 30.769 0.00 0.00 0.00 2.15
73 74 6.954487 TTGCAAGATCATAAGAAGCATCAT 57.046 33.333 0.00 0.00 0.00 2.45
74 75 6.762702 TTTGCAAGATCATAAGAAGCATCA 57.237 33.333 0.00 0.00 0.00 3.07
75 76 8.644318 AAATTTGCAAGATCATAAGAAGCATC 57.356 30.769 0.00 0.00 0.00 3.91
135 136 9.590451 CTCACTTTCAATATAATTGCAACCATT 57.410 29.630 0.00 0.00 0.00 3.16
136 137 8.752187 ACTCACTTTCAATATAATTGCAACCAT 58.248 29.630 0.00 0.00 0.00 3.55
137 138 8.121305 ACTCACTTTCAATATAATTGCAACCA 57.879 30.769 0.00 0.00 0.00 3.67
138 139 8.986477 AACTCACTTTCAATATAATTGCAACC 57.014 30.769 0.00 0.00 0.00 3.77
140 141 9.421806 CCAAACTCACTTTCAATATAATTGCAA 57.578 29.630 0.00 0.00 0.00 4.08
141 142 8.801299 TCCAAACTCACTTTCAATATAATTGCA 58.199 29.630 0.00 0.00 0.00 4.08
142 143 9.638239 TTCCAAACTCACTTTCAATATAATTGC 57.362 29.630 0.00 0.00 0.00 3.56
146 147 8.730680 GCTCTTCCAAACTCACTTTCAATATAA 58.269 33.333 0.00 0.00 0.00 0.98
147 148 7.882791 TGCTCTTCCAAACTCACTTTCAATATA 59.117 33.333 0.00 0.00 0.00 0.86
148 149 6.716628 TGCTCTTCCAAACTCACTTTCAATAT 59.283 34.615 0.00 0.00 0.00 1.28
149 150 6.061441 TGCTCTTCCAAACTCACTTTCAATA 58.939 36.000 0.00 0.00 0.00 1.90
150 151 4.889409 TGCTCTTCCAAACTCACTTTCAAT 59.111 37.500 0.00 0.00 0.00 2.57
151 152 4.269183 TGCTCTTCCAAACTCACTTTCAA 58.731 39.130 0.00 0.00 0.00 2.69
152 153 3.884895 TGCTCTTCCAAACTCACTTTCA 58.115 40.909 0.00 0.00 0.00 2.69
153 154 4.516698 TGATGCTCTTCCAAACTCACTTTC 59.483 41.667 0.00 0.00 0.00 2.62
154 155 4.464008 TGATGCTCTTCCAAACTCACTTT 58.536 39.130 0.00 0.00 0.00 2.66
155 156 4.090761 TGATGCTCTTCCAAACTCACTT 57.909 40.909 0.00 0.00 0.00 3.16
156 157 3.777106 TGATGCTCTTCCAAACTCACT 57.223 42.857 0.00 0.00 0.00 3.41
157 158 3.817647 AGTTGATGCTCTTCCAAACTCAC 59.182 43.478 0.00 0.00 0.00 3.51
158 159 4.090761 AGTTGATGCTCTTCCAAACTCA 57.909 40.909 0.00 0.00 0.00 3.41
159 160 5.444663 AAAGTTGATGCTCTTCCAAACTC 57.555 39.130 0.00 0.00 0.00 3.01
160 161 5.474876 CCTAAAGTTGATGCTCTTCCAAACT 59.525 40.000 0.00 0.00 0.00 2.66
161 162 5.241728 ACCTAAAGTTGATGCTCTTCCAAAC 59.758 40.000 0.00 0.00 0.00 2.93
162 163 5.385198 ACCTAAAGTTGATGCTCTTCCAAA 58.615 37.500 0.00 0.00 0.00 3.28
163 164 4.985538 ACCTAAAGTTGATGCTCTTCCAA 58.014 39.130 0.00 0.00 0.00 3.53
164 165 4.640771 ACCTAAAGTTGATGCTCTTCCA 57.359 40.909 0.00 0.00 0.00 3.53
165 166 8.732746 TTATTACCTAAAGTTGATGCTCTTCC 57.267 34.615 0.00 0.00 0.00 3.46
167 168 9.905713 TCATTATTACCTAAAGTTGATGCTCTT 57.094 29.630 0.00 0.00 0.00 2.85
170 171 9.289782 GGATCATTATTACCTAAAGTTGATGCT 57.710 33.333 0.00 0.00 30.82 3.79
171 172 8.515414 GGGATCATTATTACCTAAAGTTGATGC 58.485 37.037 0.00 0.00 32.13 3.91
172 173 9.573166 TGGGATCATTATTACCTAAAGTTGATG 57.427 33.333 0.00 0.00 0.00 3.07
173 174 9.574516 GTGGGATCATTATTACCTAAAGTTGAT 57.425 33.333 0.00 0.00 0.00 2.57
174 175 8.778059 AGTGGGATCATTATTACCTAAAGTTGA 58.222 33.333 0.00 0.00 0.00 3.18
175 176 8.980481 AGTGGGATCATTATTACCTAAAGTTG 57.020 34.615 0.00 0.00 0.00 3.16
177 178 9.448587 AGTAGTGGGATCATTATTACCTAAAGT 57.551 33.333 0.00 0.00 0.00 2.66
181 182 8.656806 CCAAAGTAGTGGGATCATTATTACCTA 58.343 37.037 0.00 0.00 34.77 3.08
182 183 7.349859 TCCAAAGTAGTGGGATCATTATTACCT 59.650 37.037 0.00 0.00 39.34 3.08
183 184 7.514721 TCCAAAGTAGTGGGATCATTATTACC 58.485 38.462 0.00 0.00 39.34 2.85
184 185 8.429641 TCTCCAAAGTAGTGGGATCATTATTAC 58.570 37.037 0.00 0.00 39.34 1.89
185 186 8.561536 TCTCCAAAGTAGTGGGATCATTATTA 57.438 34.615 0.00 0.00 39.34 0.98
186 187 7.451731 TCTCCAAAGTAGTGGGATCATTATT 57.548 36.000 0.00 0.00 39.34 1.40
187 188 7.451731 TTCTCCAAAGTAGTGGGATCATTAT 57.548 36.000 0.00 0.00 39.34 1.28
188 189 6.884472 TTCTCCAAAGTAGTGGGATCATTA 57.116 37.500 0.00 0.00 39.34 1.90
189 190 5.779241 TTCTCCAAAGTAGTGGGATCATT 57.221 39.130 0.00 0.00 39.34 2.57
190 191 5.398353 CCATTCTCCAAAGTAGTGGGATCAT 60.398 44.000 0.00 0.00 39.34 2.45
191 192 4.080356 CCATTCTCCAAAGTAGTGGGATCA 60.080 45.833 0.00 0.00 39.34 2.92
192 193 4.080299 ACCATTCTCCAAAGTAGTGGGATC 60.080 45.833 0.00 0.00 39.34 3.36
193 194 3.852578 ACCATTCTCCAAAGTAGTGGGAT 59.147 43.478 0.00 0.00 39.34 3.85
194 195 3.256704 ACCATTCTCCAAAGTAGTGGGA 58.743 45.455 0.00 0.00 39.34 4.37
195 196 3.009033 TGACCATTCTCCAAAGTAGTGGG 59.991 47.826 0.00 0.00 39.34 4.61
196 197 4.286297 TGACCATTCTCCAAAGTAGTGG 57.714 45.455 0.00 0.00 40.33 4.00
197 198 6.176183 AGATTGACCATTCTCCAAAGTAGTG 58.824 40.000 0.00 0.00 0.00 2.74
198 199 6.380079 AGATTGACCATTCTCCAAAGTAGT 57.620 37.500 0.00 0.00 0.00 2.73
199 200 8.834465 CATAAGATTGACCATTCTCCAAAGTAG 58.166 37.037 0.00 0.00 0.00 2.57
200 201 8.548025 TCATAAGATTGACCATTCTCCAAAGTA 58.452 33.333 0.00 0.00 0.00 2.24
201 202 7.405292 TCATAAGATTGACCATTCTCCAAAGT 58.595 34.615 0.00 0.00 0.00 2.66
202 203 7.870509 TCATAAGATTGACCATTCTCCAAAG 57.129 36.000 0.00 0.00 0.00 2.77
203 204 8.648698 TTTCATAAGATTGACCATTCTCCAAA 57.351 30.769 0.00 0.00 0.00 3.28
204 205 8.827832 ATTTCATAAGATTGACCATTCTCCAA 57.172 30.769 0.00 0.00 0.00 3.53
205 206 8.827832 AATTTCATAAGATTGACCATTCTCCA 57.172 30.769 0.00 0.00 0.00 3.86
224 225 8.897752 CCAAACCCACTTTTATCAAAAATTTCA 58.102 29.630 0.00 0.00 34.18 2.69
225 226 9.114952 TCCAAACCCACTTTTATCAAAAATTTC 57.885 29.630 0.00 0.00 34.18 2.17
226 227 9.119418 CTCCAAACCCACTTTTATCAAAAATTT 57.881 29.630 0.00 0.00 34.18 1.82
227 228 8.490311 TCTCCAAACCCACTTTTATCAAAAATT 58.510 29.630 0.00 0.00 34.18 1.82
228 229 8.028652 TCTCCAAACCCACTTTTATCAAAAAT 57.971 30.769 0.00 0.00 34.18 1.82
229 230 7.418483 CCTCTCCAAACCCACTTTTATCAAAAA 60.418 37.037 0.00 0.00 33.58 1.94
230 231 6.041523 CCTCTCCAAACCCACTTTTATCAAAA 59.958 38.462 0.00 0.00 0.00 2.44
231 232 5.538433 CCTCTCCAAACCCACTTTTATCAAA 59.462 40.000 0.00 0.00 0.00 2.69
232 233 5.076873 CCTCTCCAAACCCACTTTTATCAA 58.923 41.667 0.00 0.00 0.00 2.57
233 234 4.105697 ACCTCTCCAAACCCACTTTTATCA 59.894 41.667 0.00 0.00 0.00 2.15
234 235 4.663334 ACCTCTCCAAACCCACTTTTATC 58.337 43.478 0.00 0.00 0.00 1.75
235 236 4.105697 TGACCTCTCCAAACCCACTTTTAT 59.894 41.667 0.00 0.00 0.00 1.40
236 237 3.460340 TGACCTCTCCAAACCCACTTTTA 59.540 43.478 0.00 0.00 0.00 1.52
237 238 2.243736 TGACCTCTCCAAACCCACTTTT 59.756 45.455 0.00 0.00 0.00 2.27
238 239 1.850345 TGACCTCTCCAAACCCACTTT 59.150 47.619 0.00 0.00 0.00 2.66
239 240 1.518367 TGACCTCTCCAAACCCACTT 58.482 50.000 0.00 0.00 0.00 3.16
240 241 1.352352 CATGACCTCTCCAAACCCACT 59.648 52.381 0.00 0.00 0.00 4.00
241 242 1.351017 TCATGACCTCTCCAAACCCAC 59.649 52.381 0.00 0.00 0.00 4.61
242 243 1.351017 GTCATGACCTCTCCAAACCCA 59.649 52.381 15.31 0.00 0.00 4.51
243 244 1.630878 AGTCATGACCTCTCCAAACCC 59.369 52.381 22.21 0.00 0.00 4.11
244 245 3.244561 TGAAGTCATGACCTCTCCAAACC 60.245 47.826 22.21 0.00 0.00 3.27
245 246 4.008074 TGAAGTCATGACCTCTCCAAAC 57.992 45.455 22.21 4.47 0.00 2.93
246 247 4.916041 ATGAAGTCATGACCTCTCCAAA 57.084 40.909 22.21 3.17 34.83 3.28
247 248 4.916041 AATGAAGTCATGACCTCTCCAA 57.084 40.909 22.21 3.54 36.56 3.53
248 249 4.286808 TCAAATGAAGTCATGACCTCTCCA 59.713 41.667 22.21 12.78 36.56 3.86
249 250 4.836825 TCAAATGAAGTCATGACCTCTCC 58.163 43.478 22.21 7.75 36.56 3.71
250 251 6.111382 TCATCAAATGAAGTCATGACCTCTC 58.889 40.000 22.21 16.00 36.11 3.20
251 252 6.058553 TCATCAAATGAAGTCATGACCTCT 57.941 37.500 22.21 7.31 36.11 3.69
252 253 6.939132 ATCATCAAATGAAGTCATGACCTC 57.061 37.500 22.21 19.02 43.50 3.85
253 254 8.991783 ATTATCATCAAATGAAGTCATGACCT 57.008 30.769 22.21 9.80 43.50 3.85
254 255 8.295288 GGATTATCATCAAATGAAGTCATGACC 58.705 37.037 22.21 8.64 43.50 4.02
255 256 8.295288 GGGATTATCATCAAATGAAGTCATGAC 58.705 37.037 18.47 18.47 43.50 3.06
256 257 8.000127 TGGGATTATCATCAAATGAAGTCATGA 59.000 33.333 0.00 0.00 43.50 3.07
257 258 8.080417 GTGGGATTATCATCAAATGAAGTCATG 58.920 37.037 0.00 0.00 43.50 3.07
258 259 8.003044 AGTGGGATTATCATCAAATGAAGTCAT 58.997 33.333 0.00 0.00 43.50 3.06
259 260 7.348815 AGTGGGATTATCATCAAATGAAGTCA 58.651 34.615 0.00 0.00 43.50 3.41
260 261 7.814264 AGTGGGATTATCATCAAATGAAGTC 57.186 36.000 0.00 0.00 43.50 3.01
261 262 9.872684 AATAGTGGGATTATCATCAAATGAAGT 57.127 29.630 0.00 0.00 43.50 3.01
269 270 9.919416 TCTTTCAAAATAGTGGGATTATCATCA 57.081 29.630 0.00 0.00 0.00 3.07
304 305 6.990798 TCTTTATGATCCACATGCACAAAAA 58.009 32.000 0.00 0.00 39.77 1.94
305 306 6.433716 TCTCTTTATGATCCACATGCACAAAA 59.566 34.615 0.00 0.00 39.77 2.44
306 307 5.945191 TCTCTTTATGATCCACATGCACAAA 59.055 36.000 0.00 0.00 39.77 2.83
307 308 5.499313 TCTCTTTATGATCCACATGCACAA 58.501 37.500 0.00 0.00 39.77 3.33
308 309 5.101648 TCTCTTTATGATCCACATGCACA 57.898 39.130 0.00 0.00 39.77 4.57
309 310 6.630444 ATTCTCTTTATGATCCACATGCAC 57.370 37.500 0.00 0.00 39.77 4.57
310 311 8.789762 CAATATTCTCTTTATGATCCACATGCA 58.210 33.333 0.00 0.00 39.77 3.96
311 312 8.790718 ACAATATTCTCTTTATGATCCACATGC 58.209 33.333 0.00 0.00 39.77 4.06
351 352 9.685276 TGTAGGATCATATTCAAGTTCAACAAT 57.315 29.630 0.00 0.00 0.00 2.71
352 353 9.685276 ATGTAGGATCATATTCAAGTTCAACAA 57.315 29.630 0.00 0.00 0.00 2.83
353 354 9.112725 CATGTAGGATCATATTCAAGTTCAACA 57.887 33.333 0.00 0.00 0.00 3.33
354 355 9.113838 ACATGTAGGATCATATTCAAGTTCAAC 57.886 33.333 0.00 0.00 0.00 3.18
388 389 9.284131 TCCTATAACCATATTTGCCTATCTCAT 57.716 33.333 0.00 0.00 0.00 2.90
422 423 7.907389 ACATCAAGAGAGGTAATTGAGTAACA 58.093 34.615 0.00 0.00 36.94 2.41
443 444 6.092748 ACGAAGCATTACCAATTTGAACATC 58.907 36.000 0.00 0.00 0.00 3.06
445 446 5.446143 ACGAAGCATTACCAATTTGAACA 57.554 34.783 0.00 0.00 0.00 3.18
456 457 3.863041 AGGAAGAAGGACGAAGCATTAC 58.137 45.455 0.00 0.00 0.00 1.89
462 463 2.169832 TGCAAGGAAGAAGGACGAAG 57.830 50.000 0.00 0.00 0.00 3.79
528 530 2.158798 TGACGGAGATCAGTCGATACCT 60.159 50.000 8.29 0.00 42.66 3.08
548 550 5.730296 AGACCCCTTTAGATACATCGATG 57.270 43.478 23.68 23.68 0.00 3.84
551 553 5.768662 TCAGTAGACCCCTTTAGATACATCG 59.231 44.000 0.00 0.00 0.00 3.84
574 576 9.085250 GCAGGTTAGTAATAACACTTCTACTTC 57.915 37.037 14.45 0.00 0.00 3.01
634 637 2.751806 GGGCTTGAGAAAGGAATGTCAG 59.248 50.000 0.00 0.00 0.00 3.51
639 642 1.680249 GCTCGGGCTTGAGAAAGGAAT 60.680 52.381 0.00 0.00 38.28 3.01
666 669 6.978080 TGAAAACAAAGTGTATTTCAGGCTTC 59.022 34.615 11.35 0.00 35.07 3.86
672 675 6.045955 GGGCTTGAAAACAAAGTGTATTTCA 58.954 36.000 11.35 11.35 36.54 2.69
697 700 1.620323 GCTTGATTTTGGGACAGGCTT 59.380 47.619 0.00 0.00 42.39 4.35
702 705 0.111446 TCGGGCTTGATTTTGGGACA 59.889 50.000 0.00 0.00 0.00 4.02
716 719 3.744719 GGTTTTCGGGCTTCGGGC 61.745 66.667 0.75 0.00 39.77 6.13
761 764 2.693762 CGGGCTGGTCTTGCACATG 61.694 63.158 0.00 0.00 32.55 3.21
904 915 4.454847 TCGACGTATTTATAGAGGGAGCAG 59.545 45.833 0.00 0.00 0.00 4.24
911 922 6.296365 TGTGGTCTCGACGTATTTATAGAG 57.704 41.667 0.00 0.00 0.00 2.43
992 1003 1.613836 CCCCATAGCCATTCTTCTGC 58.386 55.000 0.00 0.00 0.00 4.26
1076 1088 4.916041 TGACTCTGGATTGGAGATGTTT 57.084 40.909 0.00 0.00 35.10 2.83
1392 1450 4.944372 CGGGCGCGTAGATCACCC 62.944 72.222 15.94 6.83 37.19 4.61
1622 1695 7.058525 TCATCGTACCAGGTATAGAAGAAAGA 58.941 38.462 1.54 0.00 0.00 2.52
1942 2020 1.278127 CTGGTTCTTTCCTAGGGCGAA 59.722 52.381 9.46 6.58 0.00 4.70
2040 2118 9.837525 GTACGTGTCTCTTCTTTCTTATCTAAA 57.162 33.333 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.