Multiple sequence alignment - TraesCS2D01G110900

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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 TraesCS2D01G110900 chr2D 100.000 4196 0 0 1 4196 61795244 61799439 0.000000e+00 7749.0
1 TraesCS2D01G110900 chr2D 96.875 32 1 0 749 780 101985567 101985536 2.000000e-03 54.7
2 TraesCS2D01G110900 chr2D 100.000 29 0 0 748 776 536530862 536530890 2.000000e-03 54.7
3 TraesCS2D01G110900 chr2A 94.357 3048 116 18 778 3810 62265199 62268205 0.000000e+00 4625.0
4 TraesCS2D01G110900 chr2A 93.258 267 12 5 1 265 62242631 62242893 5.090000e-104 388.0
5 TraesCS2D01G110900 chr2A 89.270 233 24 1 440 671 62264924 62265156 1.480000e-74 291.0
6 TraesCS2D01G110900 chr2A 85.616 146 20 1 537 681 16619865 16619720 7.270000e-33 152.0
7 TraesCS2D01G110900 chr2A 84.247 146 21 2 537 681 16605414 16605270 1.570000e-29 141.0
8 TraesCS2D01G110900 chr2A 89.744 78 7 1 287 363 62242120 62242043 9.600000e-17 99.0
9 TraesCS2D01G110900 chr2B 95.908 2664 93 9 773 3422 96596252 96598913 0.000000e+00 4301.0
10 TraesCS2D01G110900 chr2B 94.588 388 17 3 3810 4194 96599540 96599926 7.760000e-167 597.0
11 TraesCS2D01G110900 chr2B 95.977 348 13 1 3404 3751 96599094 96599440 7.880000e-157 564.0
12 TraesCS2D01G110900 chr2B 84.423 520 71 8 266 779 96585493 96586008 1.740000e-138 503.0
13 TraesCS2D01G110900 chr2B 82.143 140 21 4 536 673 142450898 142450761 2.650000e-22 117.0
14 TraesCS2D01G110900 chr2B 100.000 30 0 0 750 779 431775484 431775455 5.860000e-04 56.5
15 TraesCS2D01G110900 chr5B 84.516 155 21 3 536 689 335201146 335201298 2.610000e-32 150.0
16 TraesCS2D01G110900 chr5A 83.871 155 22 3 536 689 386697482 386697634 1.220000e-30 145.0
17 TraesCS2D01G110900 chr5A 100.000 30 0 0 748 777 603340746 603340775 5.860000e-04 56.5
18 TraesCS2D01G110900 chr5D 83.099 142 23 1 536 677 251938102 251937962 1.220000e-25 128.0
19 TraesCS2D01G110900 chr3A 83.721 129 18 3 551 677 585013044 585012917 7.370000e-23 119.0
20 TraesCS2D01G110900 chr6A 87.037 54 6 1 121 173 595005342 595005289 4.530000e-05 60.2
21 TraesCS2D01G110900 chr3B 100.000 30 0 0 750 779 815158514 815158543 5.860000e-04 56.5


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 TraesCS2D01G110900 chr2D 61795244 61799439 4195 False 7749.000000 7749 100.0000 1 4196 1 chr2D.!!$F1 4195
1 TraesCS2D01G110900 chr2A 62264924 62268205 3281 False 2458.000000 4625 91.8135 440 3810 2 chr2A.!!$F2 3370
2 TraesCS2D01G110900 chr2B 96596252 96599926 3674 False 1820.666667 4301 95.4910 773 4194 3 chr2B.!!$F2 3421
3 TraesCS2D01G110900 chr2B 96585493 96586008 515 False 503.000000 503 84.4230 266 779 1 chr2B.!!$F1 513

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
442 443 0.030235 CGTCGCCACCATCGATCTAA 59.970 55.0 0.00 0.00 38.29 2.10 F
691 695 0.098200 GGTTATCTTCAAACGGCGCC 59.902 55.0 19.07 19.07 0.00 6.53 F
2416 2446 0.321919 TGACAGAGCAATGCAGGTCC 60.322 55.0 8.35 0.00 36.71 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2119 1.032014 AACATGGACACAAGCACACC 58.968 50.0 0.00 0.00 0.00 4.16 R
2508 2538 2.071778 TATCCCAGAATGCCTTTGCC 57.928 50.0 0.00 0.00 36.33 4.52 R
4173 4466 0.392193 AGCGAGCAATGCTAAGCTGT 60.392 50.0 28.24 12.27 45.75 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 9.744468 ATATTTTTCTACAAACACAGTCAAACC 57.256 29.630 0.00 0.00 0.00 3.27
115 116 6.827586 TTTTCTACAAACACAGTCAAACCT 57.172 33.333 0.00 0.00 0.00 3.50
116 117 5.811399 TTCTACAAACACAGTCAAACCTG 57.189 39.130 0.00 0.00 38.45 4.00
117 118 5.092554 TCTACAAACACAGTCAAACCTGA 57.907 39.130 0.00 0.00 36.30 3.86
118 119 5.492895 TCTACAAACACAGTCAAACCTGAA 58.507 37.500 0.00 0.00 36.30 3.02
119 120 4.701956 ACAAACACAGTCAAACCTGAAG 57.298 40.909 0.00 0.00 36.30 3.02
120 121 4.331968 ACAAACACAGTCAAACCTGAAGA 58.668 39.130 0.00 0.00 36.30 2.87
121 122 4.764823 ACAAACACAGTCAAACCTGAAGAA 59.235 37.500 0.00 0.00 36.30 2.52
122 123 5.106157 ACAAACACAGTCAAACCTGAAGAAG 60.106 40.000 0.00 0.00 36.30 2.85
123 124 4.222124 ACACAGTCAAACCTGAAGAAGT 57.778 40.909 0.00 0.00 36.30 3.01
124 125 4.589908 ACACAGTCAAACCTGAAGAAGTT 58.410 39.130 0.00 0.00 36.30 2.66
125 126 5.010282 ACACAGTCAAACCTGAAGAAGTTT 58.990 37.500 0.00 0.00 36.65 2.66
133 134 7.095695 CAAACCTGAAGAAGTTTGGTTTAGA 57.904 36.000 7.92 0.00 45.66 2.10
134 135 7.543756 CAAACCTGAAGAAGTTTGGTTTAGAA 58.456 34.615 7.92 0.00 45.66 2.10
135 136 7.712204 AACCTGAAGAAGTTTGGTTTAGAAA 57.288 32.000 0.00 0.00 37.71 2.52
136 137 7.712204 ACCTGAAGAAGTTTGGTTTAGAAAA 57.288 32.000 0.00 0.00 0.00 2.29
137 138 8.129496 ACCTGAAGAAGTTTGGTTTAGAAAAA 57.871 30.769 0.00 0.00 0.00 1.94
138 139 8.033038 ACCTGAAGAAGTTTGGTTTAGAAAAAC 58.967 33.333 0.00 0.00 43.58 2.43
168 169 8.675705 AACTTCAATTATTTTGAAACCAAGGG 57.324 30.769 2.77 0.00 37.89 3.95
169 170 8.028652 ACTTCAATTATTTTGAAACCAAGGGA 57.971 30.769 2.77 0.00 37.89 4.20
170 171 8.150296 ACTTCAATTATTTTGAAACCAAGGGAG 58.850 33.333 2.77 0.00 37.89 4.30
171 172 7.610580 TCAATTATTTTGAAACCAAGGGAGT 57.389 32.000 0.00 0.00 0.00 3.85
172 173 8.713708 TCAATTATTTTGAAACCAAGGGAGTA 57.286 30.769 0.00 0.00 0.00 2.59
173 174 8.802267 TCAATTATTTTGAAACCAAGGGAGTAG 58.198 33.333 0.00 0.00 0.00 2.57
174 175 8.585018 CAATTATTTTGAAACCAAGGGAGTAGT 58.415 33.333 0.00 0.00 0.00 2.73
175 176 9.816787 AATTATTTTGAAACCAAGGGAGTAGTA 57.183 29.630 0.00 0.00 0.00 1.82
176 177 9.990868 ATTATTTTGAAACCAAGGGAGTAGTAT 57.009 29.630 0.00 0.00 0.00 2.12
177 178 7.703058 ATTTTGAAACCAAGGGAGTAGTATG 57.297 36.000 0.00 0.00 0.00 2.39
178 179 6.442541 TTTGAAACCAAGGGAGTAGTATGA 57.557 37.500 0.00 0.00 0.00 2.15
179 180 6.636454 TTGAAACCAAGGGAGTAGTATGAT 57.364 37.500 0.00 0.00 0.00 2.45
180 181 5.989477 TGAAACCAAGGGAGTAGTATGATG 58.011 41.667 0.00 0.00 0.00 3.07
181 182 5.487488 TGAAACCAAGGGAGTAGTATGATGT 59.513 40.000 0.00 0.00 0.00 3.06
182 183 6.670464 TGAAACCAAGGGAGTAGTATGATGTA 59.330 38.462 0.00 0.00 0.00 2.29
183 184 6.481434 AACCAAGGGAGTAGTATGATGTAC 57.519 41.667 0.00 0.00 0.00 2.90
184 185 4.583489 ACCAAGGGAGTAGTATGATGTACG 59.417 45.833 0.00 0.00 0.00 3.67
185 186 4.547532 CAAGGGAGTAGTATGATGTACGC 58.452 47.826 0.00 0.00 0.00 4.42
186 187 3.828921 AGGGAGTAGTATGATGTACGCA 58.171 45.455 0.00 0.00 0.00 5.24
187 188 4.212716 AGGGAGTAGTATGATGTACGCAA 58.787 43.478 0.00 0.00 0.00 4.85
188 189 4.833380 AGGGAGTAGTATGATGTACGCAAT 59.167 41.667 0.00 0.00 0.00 3.56
189 190 5.047943 AGGGAGTAGTATGATGTACGCAATC 60.048 44.000 0.00 0.00 0.00 2.67
190 191 5.162075 GGAGTAGTATGATGTACGCAATCC 58.838 45.833 0.00 0.00 0.00 3.01
191 192 5.278808 GGAGTAGTATGATGTACGCAATCCA 60.279 44.000 0.00 0.00 0.00 3.41
192 193 6.156748 AGTAGTATGATGTACGCAATCCAA 57.843 37.500 0.00 0.00 0.00 3.53
193 194 6.578944 AGTAGTATGATGTACGCAATCCAAA 58.421 36.000 0.00 0.00 0.00 3.28
194 195 5.734855 AGTATGATGTACGCAATCCAAAC 57.265 39.130 0.00 0.00 0.00 2.93
195 196 5.428253 AGTATGATGTACGCAATCCAAACT 58.572 37.500 0.00 0.00 0.00 2.66
196 197 5.880332 AGTATGATGTACGCAATCCAAACTT 59.120 36.000 0.00 0.00 0.00 2.66
197 198 4.418013 TGATGTACGCAATCCAAACTTG 57.582 40.909 0.00 0.00 0.00 3.16
198 199 4.068599 TGATGTACGCAATCCAAACTTGA 58.931 39.130 0.00 0.00 0.00 3.02
199 200 4.699735 TGATGTACGCAATCCAAACTTGAT 59.300 37.500 0.00 0.00 0.00 2.57
200 201 4.418013 TGTACGCAATCCAAACTTGATG 57.582 40.909 0.00 0.00 0.00 3.07
201 202 4.068599 TGTACGCAATCCAAACTTGATGA 58.931 39.130 0.00 0.00 0.00 2.92
202 203 4.517075 TGTACGCAATCCAAACTTGATGAA 59.483 37.500 0.00 0.00 0.00 2.57
203 204 4.789012 ACGCAATCCAAACTTGATGAAT 57.211 36.364 0.00 0.00 0.00 2.57
204 205 5.895636 ACGCAATCCAAACTTGATGAATA 57.104 34.783 0.00 0.00 0.00 1.75
205 206 5.883661 ACGCAATCCAAACTTGATGAATAG 58.116 37.500 0.00 0.00 0.00 1.73
206 207 5.415701 ACGCAATCCAAACTTGATGAATAGT 59.584 36.000 0.00 0.00 0.00 2.12
207 208 6.597672 ACGCAATCCAAACTTGATGAATAGTA 59.402 34.615 0.00 0.00 0.00 1.82
208 209 7.283127 ACGCAATCCAAACTTGATGAATAGTAT 59.717 33.333 0.00 0.00 0.00 2.12
209 210 7.588854 CGCAATCCAAACTTGATGAATAGTATG 59.411 37.037 0.00 0.00 0.00 2.39
210 211 8.623903 GCAATCCAAACTTGATGAATAGTATGA 58.376 33.333 0.00 0.00 0.00 2.15
211 212 9.941664 CAATCCAAACTTGATGAATAGTATGAC 57.058 33.333 0.00 0.00 0.00 3.06
212 213 7.770801 TCCAAACTTGATGAATAGTATGACG 57.229 36.000 0.00 0.00 0.00 4.35
213 214 7.327975 TCCAAACTTGATGAATAGTATGACGT 58.672 34.615 0.00 0.00 0.00 4.34
214 215 8.471609 TCCAAACTTGATGAATAGTATGACGTA 58.528 33.333 0.00 0.00 0.00 3.57
215 216 8.755941 CCAAACTTGATGAATAGTATGACGTAG 58.244 37.037 0.00 0.00 0.00 3.51
230 231 2.910199 ACGTAGTAGTATGAGCGTCCA 58.090 47.619 3.73 0.00 41.94 4.02
231 232 2.871022 ACGTAGTAGTATGAGCGTCCAG 59.129 50.000 3.73 0.00 41.94 3.86
232 233 2.223611 CGTAGTAGTATGAGCGTCCAGG 59.776 54.545 0.00 0.00 0.00 4.45
233 234 1.693627 AGTAGTATGAGCGTCCAGGG 58.306 55.000 0.00 0.00 0.00 4.45
234 235 0.032267 GTAGTATGAGCGTCCAGGGC 59.968 60.000 0.00 0.00 0.00 5.19
235 236 0.106167 TAGTATGAGCGTCCAGGGCT 60.106 55.000 0.00 0.00 45.00 5.19
236 237 0.106167 AGTATGAGCGTCCAGGGCTA 60.106 55.000 0.00 0.00 41.72 3.93
237 238 0.750850 GTATGAGCGTCCAGGGCTAA 59.249 55.000 0.00 0.00 41.72 3.09
238 239 1.138266 GTATGAGCGTCCAGGGCTAAA 59.862 52.381 0.00 0.00 41.72 1.85
239 240 0.618458 ATGAGCGTCCAGGGCTAAAA 59.382 50.000 0.00 0.00 41.72 1.52
240 241 0.398696 TGAGCGTCCAGGGCTAAAAA 59.601 50.000 0.00 0.00 41.72 1.94
241 242 1.004277 TGAGCGTCCAGGGCTAAAAAT 59.996 47.619 0.00 0.00 41.72 1.82
242 243 1.401905 GAGCGTCCAGGGCTAAAAATG 59.598 52.381 0.00 0.00 41.72 2.32
243 244 1.004277 AGCGTCCAGGGCTAAAAATGA 59.996 47.619 0.00 0.00 39.39 2.57
244 245 1.816224 GCGTCCAGGGCTAAAAATGAA 59.184 47.619 0.00 0.00 0.00 2.57
245 246 2.230266 GCGTCCAGGGCTAAAAATGAAA 59.770 45.455 0.00 0.00 0.00 2.69
246 247 3.305744 GCGTCCAGGGCTAAAAATGAAAA 60.306 43.478 0.00 0.00 0.00 2.29
247 248 4.620567 GCGTCCAGGGCTAAAAATGAAAAT 60.621 41.667 0.00 0.00 0.00 1.82
248 249 4.864247 CGTCCAGGGCTAAAAATGAAAATG 59.136 41.667 0.00 0.00 0.00 2.32
249 250 5.336372 CGTCCAGGGCTAAAAATGAAAATGA 60.336 40.000 0.00 0.00 0.00 2.57
250 251 6.463360 GTCCAGGGCTAAAAATGAAAATGAA 58.537 36.000 0.00 0.00 0.00 2.57
251 252 7.105588 GTCCAGGGCTAAAAATGAAAATGAAT 58.894 34.615 0.00 0.00 0.00 2.57
252 253 8.257306 GTCCAGGGCTAAAAATGAAAATGAATA 58.743 33.333 0.00 0.00 0.00 1.75
253 254 8.820831 TCCAGGGCTAAAAATGAAAATGAATAA 58.179 29.630 0.00 0.00 0.00 1.40
254 255 9.617523 CCAGGGCTAAAAATGAAAATGAATAAT 57.382 29.630 0.00 0.00 0.00 1.28
256 257 9.617523 AGGGCTAAAAATGAAAATGAATAATGG 57.382 29.630 0.00 0.00 0.00 3.16
257 258 8.344831 GGGCTAAAAATGAAAATGAATAATGGC 58.655 33.333 0.00 0.00 0.00 4.40
258 259 8.891720 GGCTAAAAATGAAAATGAATAATGGCA 58.108 29.630 0.00 0.00 0.00 4.92
259 260 9.706846 GCTAAAAATGAAAATGAATAATGGCAC 57.293 29.630 0.00 0.00 0.00 5.01
300 301 1.653667 TGGCACACAAATCGCACAG 59.346 52.632 0.00 0.00 0.00 3.66
311 312 1.742761 ATCGCACAGATTCAACCTGG 58.257 50.000 0.00 0.00 35.73 4.45
312 313 0.321564 TCGCACAGATTCAACCTGGG 60.322 55.000 0.00 0.00 38.07 4.45
313 314 0.606401 CGCACAGATTCAACCTGGGT 60.606 55.000 0.00 0.00 37.38 4.51
352 353 7.928908 TCAAAAACATTGAACTTGTATCAGC 57.071 32.000 0.00 0.00 0.00 4.26
364 365 0.384309 GTATCAGCGTCGATCCCACA 59.616 55.000 0.00 0.00 0.00 4.17
365 366 1.000163 GTATCAGCGTCGATCCCACAT 60.000 52.381 0.00 0.00 0.00 3.21
366 367 1.328279 ATCAGCGTCGATCCCACATA 58.672 50.000 0.00 0.00 0.00 2.29
367 368 0.668535 TCAGCGTCGATCCCACATAG 59.331 55.000 0.00 0.00 0.00 2.23
373 374 0.467474 TCGATCCCACATAGGCTCGT 60.467 55.000 0.00 0.00 40.14 4.18
382 383 5.528902 CCCACATAGGCTCGTTAGAGATGA 61.529 50.000 0.00 0.00 45.98 2.92
390 391 3.953712 TCGTTAGAGATGAAAGCACCA 57.046 42.857 0.00 0.00 0.00 4.17
397 398 1.956477 AGATGAAAGCACCACAACCAC 59.044 47.619 0.00 0.00 0.00 4.16
405 406 0.905357 CACCACAACCACCCCAAAAA 59.095 50.000 0.00 0.00 0.00 1.94
416 417 3.132111 CCACCCCAAAAATATTTCCTCCG 59.868 47.826 0.10 0.00 0.00 4.63
424 425 2.436087 ATATTTCCTCCGCCTCGCCG 62.436 60.000 0.00 0.00 0.00 6.46
442 443 0.030235 CGTCGCCACCATCGATCTAA 59.970 55.000 0.00 0.00 38.29 2.10
468 470 1.002624 GGCGTGGATCAAAGGTCCA 60.003 57.895 0.00 0.00 43.26 4.02
475 477 2.168521 TGGATCAAAGGTCCATCTCGTC 59.831 50.000 0.00 0.00 40.72 4.20
479 481 3.371034 TCAAAGGTCCATCTCGTCCATA 58.629 45.455 0.00 0.00 0.00 2.74
506 508 0.661552 ATCGACATGTAGGACGACGG 59.338 55.000 9.25 0.00 37.58 4.79
600 602 6.899393 TTCAAGTATGAATGGATATTGCCC 57.101 37.500 0.00 0.00 40.59 5.36
603 605 3.587061 AGTATGAATGGATATTGCCCGGA 59.413 43.478 0.73 0.00 0.00 5.14
683 685 4.055360 CGGACATATGCGGTTATCTTCAA 58.945 43.478 1.58 0.00 35.75 2.69
685 687 5.558273 CGGACATATGCGGTTATCTTCAAAC 60.558 44.000 1.58 0.00 35.75 2.93
691 695 0.098200 GGTTATCTTCAAACGGCGCC 59.902 55.000 19.07 19.07 0.00 6.53
692 696 1.084289 GTTATCTTCAAACGGCGCCT 58.916 50.000 26.68 8.92 0.00 5.52
694 698 0.461339 TATCTTCAAACGGCGCCTCC 60.461 55.000 26.68 0.00 0.00 4.30
707 711 0.460284 CGCCTCCGCATAAGTGTCTT 60.460 55.000 0.00 0.00 34.03 3.01
709 713 1.134670 GCCTCCGCATAAGTGTCTTCT 60.135 52.381 0.00 0.00 34.03 2.85
716 720 3.615110 CGCATAAGTGTCTTCTGACTGGT 60.615 47.826 0.00 0.00 43.29 4.00
718 722 4.322349 GCATAAGTGTCTTCTGACTGGTCT 60.322 45.833 2.38 0.00 43.29 3.85
721 725 2.158385 AGTGTCTTCTGACTGGTCTCCT 60.158 50.000 2.38 0.00 43.29 3.69
728 734 1.304217 GACTGGTCTCCTCGGTCCA 60.304 63.158 0.00 0.00 0.00 4.02
729 735 3.609703 CTGGTCTCCTCGGTCCAG 58.390 66.667 0.00 0.00 40.83 3.86
766 772 1.229975 GGTTTACGGGTCGGTGTTGG 61.230 60.000 0.00 0.00 0.00 3.77
780 786 2.359900 GTGTTGGAGATGCCCTAAGTG 58.640 52.381 0.00 0.00 34.97 3.16
798 804 9.852091 CCCTAAGTGTAACAGTAAAAGTAGTAG 57.148 37.037 0.00 0.00 41.43 2.57
845 862 3.863142 AGGCAGCAATCTGAATTGAAC 57.137 42.857 0.00 0.00 44.25 3.18
847 864 3.192844 AGGCAGCAATCTGAATTGAACTG 59.807 43.478 0.00 2.79 44.25 3.16
880 897 4.624452 CAGTTAGTTACCCGCTAAGTTCAC 59.376 45.833 0.00 0.00 31.77 3.18
887 904 2.740826 GCTAAGTTCACGCCGGCA 60.741 61.111 28.98 3.37 0.00 5.69
981 1002 2.034532 TACCCTCTCGACCGTGCA 59.965 61.111 0.00 0.00 0.00 4.57
993 1014 3.777925 CGTGCACCTCCTTTCGCG 61.778 66.667 12.15 0.00 0.00 5.87
1241 1268 4.452733 GTTCGTGCCCTCCCTCCG 62.453 72.222 0.00 0.00 0.00 4.63
1881 1911 2.690778 GGTGATGGAAGGTGTGCGC 61.691 63.158 0.00 0.00 0.00 6.09
1948 1978 1.519719 CTCTGCCGGGAGAAAGAGG 59.480 63.158 26.78 10.93 36.31 3.69
1953 1983 1.679898 CCGGGAGAAAGAGGTTGCT 59.320 57.895 0.00 0.00 0.00 3.91
2262 2292 2.224281 TGTCACCTTCACCACACTCATC 60.224 50.000 0.00 0.00 0.00 2.92
2416 2446 0.321919 TGACAGAGCAATGCAGGTCC 60.322 55.000 8.35 0.00 36.71 4.46
2421 2451 1.078848 AGCAATGCAGGTCCTCGAC 60.079 57.895 8.35 0.00 0.00 4.20
2508 2538 3.130160 GCGGGGCAGCTTGAGAAG 61.130 66.667 0.00 0.00 0.00 2.85
2526 2556 0.337428 AGGCAAAGGCATTCTGGGAT 59.663 50.000 0.00 0.00 43.71 3.85
2817 2847 4.025360 TGCACCTTTATGGCAATGAAGAT 58.975 39.130 7.17 0.00 40.22 2.40
2832 2862 3.382278 TGAAGATCAAGAGGAGGAGCAT 58.618 45.455 0.00 0.00 0.00 3.79
2852 2882 0.890683 CAGGTCCCCAGTTTTCATGC 59.109 55.000 0.00 0.00 0.00 4.06
2941 2971 4.574599 TCATCGTCATCATCGTCAGAAT 57.425 40.909 0.00 0.00 0.00 2.40
2955 2985 6.908870 TCGTCAGAATATTTGGATGAAGTG 57.091 37.500 8.81 0.00 0.00 3.16
3114 3144 5.757320 GGACAAGGATCATACAATCAGTGAG 59.243 44.000 0.00 0.00 0.00 3.51
3216 3247 3.758554 AGAACAAGAACAAGTGTTGCTGT 59.241 39.130 0.42 2.09 38.07 4.40
3218 3249 4.096732 ACAAGAACAAGTGTTGCTGTTC 57.903 40.909 0.42 6.80 38.56 3.18
3332 3369 2.367567 AGAAGGCCGAGTTAGTGACAAA 59.632 45.455 0.00 0.00 0.00 2.83
3334 3371 1.968493 AGGCCGAGTTAGTGACAAAGA 59.032 47.619 0.00 0.00 0.00 2.52
3381 3418 5.435686 TTGGAGAATAAGGCTTGAGCTTA 57.564 39.130 10.69 1.03 41.70 3.09
3438 3674 5.551760 AAGCTTGTCGATAACAAATCTGG 57.448 39.130 0.00 0.00 46.95 3.86
3449 3685 8.465999 TCGATAACAAATCTGGCATGTTTTATT 58.534 29.630 9.25 3.82 38.22 1.40
3465 3701 7.987268 TGTTTTATTAGTGCATCTCTACTCG 57.013 36.000 0.00 0.00 0.00 4.18
3493 3729 4.764823 TCACCCAACAACTGAAATCCATAC 59.235 41.667 0.00 0.00 0.00 2.39
3546 3782 3.257393 CTGCATGTAGTGTCTTCAGGTC 58.743 50.000 2.12 0.00 0.00 3.85
3556 3792 0.603569 TCTTCAGGTCGCTCCAGTTC 59.396 55.000 0.00 0.00 39.02 3.01
3643 3879 7.041508 AGCATGCTCTACTTTATTCTACAATGC 60.042 37.037 16.30 0.00 0.00 3.56
3657 3893 1.073763 ACAATGCCTAAGTGCACCTGA 59.926 47.619 14.63 0.00 45.48 3.86
3684 3920 6.724351 TCTTTTGGATGAAGATCTCATGGAA 58.276 36.000 11.03 3.36 45.23 3.53
3705 3941 3.117589 GCTTGCAAGCCTGTGAATG 57.882 52.632 36.21 5.40 46.20 2.67
3800 4036 3.534357 TTCATGGGTGGTATTGTTGGT 57.466 42.857 0.00 0.00 0.00 3.67
3840 4130 4.718774 AGCCTGGAGTTCATCTATGAAGAA 59.281 41.667 5.64 0.00 46.44 2.52
3842 4132 5.046529 CCTGGAGTTCATCTATGAAGAACG 58.953 45.833 5.64 0.00 46.44 3.95
3843 4133 5.011090 TGGAGTTCATCTATGAAGAACGG 57.989 43.478 5.64 0.00 46.44 4.44
3846 4136 5.520649 GGAGTTCATCTATGAAGAACGGTTC 59.479 44.000 12.91 12.91 46.44 3.62
3952 4243 2.360483 CTGCTCTTCTCTGAGGCGATTA 59.640 50.000 4.59 0.00 34.82 1.75
3962 4253 1.835483 GAGGCGATTACATGGCAGCG 61.835 60.000 0.00 0.00 35.53 5.18
3994 4287 0.603707 CTGCGACCAAAAGAGCCTGA 60.604 55.000 0.00 0.00 0.00 3.86
4008 4301 9.342308 CAAAAGAGCCTGATATAATGGAAACTA 57.658 33.333 0.00 0.00 0.00 2.24
4017 4310 7.977818 TGATATAATGGAAACTATGGTGAGCT 58.022 34.615 0.00 0.00 0.00 4.09
4018 4311 8.097038 TGATATAATGGAAACTATGGTGAGCTC 58.903 37.037 6.82 6.82 0.00 4.09
4032 4325 3.426695 GGTGAGCTCCGATGTTTTGATTG 60.427 47.826 12.15 0.00 0.00 2.67
4066 4359 5.068198 GGCTTCAGATTGCTAATTCCATCAA 59.932 40.000 0.00 0.00 0.00 2.57
4092 4385 0.601558 TGTAGGAGACGAACAGGTGC 59.398 55.000 0.00 0.00 0.00 5.01
4096 4389 0.318762 GGAGACGAACAGGTGCTCTT 59.681 55.000 0.00 0.00 0.00 2.85
4105 4398 3.272574 ACAGGTGCTCTTACATGATGG 57.727 47.619 0.00 0.00 36.00 3.51
4143 4436 2.542907 CCGTGCACAGGTTGGACAC 61.543 63.158 18.64 0.00 46.70 3.67
4153 4446 0.533951 GGTTGGACACGGTAGGTAGG 59.466 60.000 0.00 0.00 0.00 3.18
4173 4466 2.311463 GGATACAGAGGTAGCAGCTCA 58.689 52.381 0.00 0.00 44.69 4.26
4194 4487 0.731417 AGCTTAGCATTGCTCGCTTG 59.269 50.000 22.46 9.57 40.73 4.01
4195 4488 0.449388 GCTTAGCATTGCTCGCTTGT 59.551 50.000 15.81 0.00 40.44 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 9.744468 GGTTTGACTGTGTTTGTAGAAAAATAT 57.256 29.630 0.00 0.00 0.00 1.28
89 90 8.962679 AGGTTTGACTGTGTTTGTAGAAAAATA 58.037 29.630 0.00 0.00 0.00 1.40
90 91 7.759433 CAGGTTTGACTGTGTTTGTAGAAAAAT 59.241 33.333 0.00 0.00 33.81 1.82
91 92 7.040340 TCAGGTTTGACTGTGTTTGTAGAAAAA 60.040 33.333 0.00 0.00 39.48 1.94
92 93 6.431543 TCAGGTTTGACTGTGTTTGTAGAAAA 59.568 34.615 0.00 0.00 39.48 2.29
93 94 5.941058 TCAGGTTTGACTGTGTTTGTAGAAA 59.059 36.000 0.00 0.00 39.48 2.52
94 95 5.492895 TCAGGTTTGACTGTGTTTGTAGAA 58.507 37.500 0.00 0.00 39.48 2.10
95 96 5.092554 TCAGGTTTGACTGTGTTTGTAGA 57.907 39.130 0.00 0.00 39.48 2.59
96 97 5.584649 TCTTCAGGTTTGACTGTGTTTGTAG 59.415 40.000 0.00 0.00 39.48 2.74
97 98 5.492895 TCTTCAGGTTTGACTGTGTTTGTA 58.507 37.500 0.00 0.00 39.48 2.41
98 99 4.331968 TCTTCAGGTTTGACTGTGTTTGT 58.668 39.130 0.00 0.00 39.48 2.83
99 100 4.963276 TCTTCAGGTTTGACTGTGTTTG 57.037 40.909 0.00 0.00 39.48 2.93
100 101 5.010282 ACTTCTTCAGGTTTGACTGTGTTT 58.990 37.500 0.00 0.00 39.48 2.83
101 102 4.589908 ACTTCTTCAGGTTTGACTGTGTT 58.410 39.130 0.00 0.00 39.48 3.32
102 103 4.222124 ACTTCTTCAGGTTTGACTGTGT 57.778 40.909 0.00 0.00 39.48 3.72
103 104 5.567138 AAACTTCTTCAGGTTTGACTGTG 57.433 39.130 0.00 0.00 39.48 3.66
111 112 7.712204 TTTCTAAACCAAACTTCTTCAGGTT 57.288 32.000 0.00 0.00 43.96 3.50
112 113 7.712204 TTTTCTAAACCAAACTTCTTCAGGT 57.288 32.000 0.00 0.00 0.00 4.00
113 114 8.407457 GTTTTTCTAAACCAAACTTCTTCAGG 57.593 34.615 0.00 0.00 38.13 3.86
142 143 9.119418 CCCTTGGTTTCAAAATAATTGAAGTTT 57.881 29.630 4.09 0.00 39.30 2.66
143 144 8.490311 TCCCTTGGTTTCAAAATAATTGAAGTT 58.510 29.630 4.09 0.00 39.30 2.66
144 145 8.028652 TCCCTTGGTTTCAAAATAATTGAAGT 57.971 30.769 4.09 0.00 39.30 3.01
145 146 8.150296 ACTCCCTTGGTTTCAAAATAATTGAAG 58.850 33.333 4.09 0.00 39.30 3.02
146 147 8.028652 ACTCCCTTGGTTTCAAAATAATTGAA 57.971 30.769 0.00 0.00 36.71 2.69
147 148 7.610580 ACTCCCTTGGTTTCAAAATAATTGA 57.389 32.000 0.00 0.00 31.77 2.57
148 149 8.585018 ACTACTCCCTTGGTTTCAAAATAATTG 58.415 33.333 0.00 0.00 31.77 2.32
149 150 8.721133 ACTACTCCCTTGGTTTCAAAATAATT 57.279 30.769 0.00 0.00 31.77 1.40
150 151 9.990868 ATACTACTCCCTTGGTTTCAAAATAAT 57.009 29.630 0.00 0.00 31.77 1.28
151 152 9.238368 CATACTACTCCCTTGGTTTCAAAATAA 57.762 33.333 0.00 0.00 31.77 1.40
152 153 8.607713 TCATACTACTCCCTTGGTTTCAAAATA 58.392 33.333 0.00 0.00 31.77 1.40
153 154 7.466804 TCATACTACTCCCTTGGTTTCAAAAT 58.533 34.615 0.00 0.00 31.77 1.82
154 155 6.843752 TCATACTACTCCCTTGGTTTCAAAA 58.156 36.000 0.00 0.00 31.77 2.44
155 156 6.442541 TCATACTACTCCCTTGGTTTCAAA 57.557 37.500 0.00 0.00 31.77 2.69
156 157 6.012858 ACATCATACTACTCCCTTGGTTTCAA 60.013 38.462 0.00 0.00 0.00 2.69
157 158 5.487488 ACATCATACTACTCCCTTGGTTTCA 59.513 40.000 0.00 0.00 0.00 2.69
158 159 5.990668 ACATCATACTACTCCCTTGGTTTC 58.009 41.667 0.00 0.00 0.00 2.78
159 160 6.406624 CGTACATCATACTACTCCCTTGGTTT 60.407 42.308 0.00 0.00 0.00 3.27
160 161 5.068723 CGTACATCATACTACTCCCTTGGTT 59.931 44.000 0.00 0.00 0.00 3.67
161 162 4.583489 CGTACATCATACTACTCCCTTGGT 59.417 45.833 0.00 0.00 0.00 3.67
162 163 4.558898 GCGTACATCATACTACTCCCTTGG 60.559 50.000 0.00 0.00 0.00 3.61
163 164 4.037565 TGCGTACATCATACTACTCCCTTG 59.962 45.833 0.00 0.00 0.00 3.61
164 165 4.212716 TGCGTACATCATACTACTCCCTT 58.787 43.478 0.00 0.00 0.00 3.95
165 166 3.828921 TGCGTACATCATACTACTCCCT 58.171 45.455 0.00 0.00 0.00 4.20
166 167 4.579454 TTGCGTACATCATACTACTCCC 57.421 45.455 0.00 0.00 0.00 4.30
167 168 5.162075 GGATTGCGTACATCATACTACTCC 58.838 45.833 0.00 0.00 0.00 3.85
168 169 5.769367 TGGATTGCGTACATCATACTACTC 58.231 41.667 0.00 0.00 0.00 2.59
169 170 5.784578 TGGATTGCGTACATCATACTACT 57.215 39.130 0.00 0.00 0.00 2.57
170 171 6.479001 AGTTTGGATTGCGTACATCATACTAC 59.521 38.462 0.00 0.00 0.00 2.73
171 172 6.578944 AGTTTGGATTGCGTACATCATACTA 58.421 36.000 0.00 0.00 0.00 1.82
172 173 5.428253 AGTTTGGATTGCGTACATCATACT 58.572 37.500 0.00 0.00 0.00 2.12
173 174 5.734855 AGTTTGGATTGCGTACATCATAC 57.265 39.130 0.00 0.00 0.00 2.39
174 175 5.877564 TCAAGTTTGGATTGCGTACATCATA 59.122 36.000 0.00 0.00 0.00 2.15
175 176 4.699735 TCAAGTTTGGATTGCGTACATCAT 59.300 37.500 0.00 0.00 0.00 2.45
176 177 4.068599 TCAAGTTTGGATTGCGTACATCA 58.931 39.130 0.00 0.00 0.00 3.07
177 178 4.678509 TCAAGTTTGGATTGCGTACATC 57.321 40.909 0.00 0.00 0.00 3.06
178 179 4.699735 TCATCAAGTTTGGATTGCGTACAT 59.300 37.500 0.00 0.00 0.00 2.29
179 180 4.068599 TCATCAAGTTTGGATTGCGTACA 58.931 39.130 0.00 0.00 0.00 2.90
180 181 4.678509 TCATCAAGTTTGGATTGCGTAC 57.321 40.909 0.00 0.00 0.00 3.67
181 182 5.895636 ATTCATCAAGTTTGGATTGCGTA 57.104 34.783 0.00 0.00 0.00 4.42
182 183 4.789012 ATTCATCAAGTTTGGATTGCGT 57.211 36.364 0.00 0.00 0.00 5.24
183 184 5.883661 ACTATTCATCAAGTTTGGATTGCG 58.116 37.500 0.00 0.00 0.00 4.85
184 185 8.623903 TCATACTATTCATCAAGTTTGGATTGC 58.376 33.333 0.00 0.00 0.00 3.56
185 186 9.941664 GTCATACTATTCATCAAGTTTGGATTG 57.058 33.333 0.00 0.00 0.00 2.67
186 187 8.830580 CGTCATACTATTCATCAAGTTTGGATT 58.169 33.333 0.00 0.00 0.00 3.01
187 188 7.987458 ACGTCATACTATTCATCAAGTTTGGAT 59.013 33.333 0.00 0.00 0.00 3.41
188 189 7.327975 ACGTCATACTATTCATCAAGTTTGGA 58.672 34.615 0.00 0.00 0.00 3.53
189 190 7.539712 ACGTCATACTATTCATCAAGTTTGG 57.460 36.000 0.00 0.00 0.00 3.28
190 191 9.302345 ACTACGTCATACTATTCATCAAGTTTG 57.698 33.333 0.00 0.00 0.00 2.93
193 194 9.339850 ACTACTACGTCATACTATTCATCAAGT 57.660 33.333 0.00 0.00 0.00 3.16
199 200 8.933807 GCTCATACTACTACGTCATACTATTCA 58.066 37.037 0.00 0.00 0.00 2.57
200 201 8.109391 CGCTCATACTACTACGTCATACTATTC 58.891 40.741 0.00 0.00 0.00 1.75
201 202 7.601886 ACGCTCATACTACTACGTCATACTATT 59.398 37.037 0.00 0.00 0.00 1.73
202 203 7.095910 ACGCTCATACTACTACGTCATACTAT 58.904 38.462 0.00 0.00 0.00 2.12
203 204 6.450545 ACGCTCATACTACTACGTCATACTA 58.549 40.000 0.00 0.00 0.00 1.82
204 205 5.295950 ACGCTCATACTACTACGTCATACT 58.704 41.667 0.00 0.00 0.00 2.12
205 206 5.588568 ACGCTCATACTACTACGTCATAC 57.411 43.478 0.00 0.00 0.00 2.39
206 207 5.835911 GACGCTCATACTACTACGTCATA 57.164 43.478 8.32 0.00 46.63 2.15
207 208 4.728917 GACGCTCATACTACTACGTCAT 57.271 45.455 8.32 0.00 46.63 3.06
209 210 2.868583 TGGACGCTCATACTACTACGTC 59.131 50.000 0.00 4.87 46.66 4.34
210 211 2.871022 CTGGACGCTCATACTACTACGT 59.129 50.000 0.00 0.00 36.30 3.57
211 212 2.223611 CCTGGACGCTCATACTACTACG 59.776 54.545 0.00 0.00 0.00 3.51
212 213 2.553172 CCCTGGACGCTCATACTACTAC 59.447 54.545 0.00 0.00 0.00 2.73
213 214 2.860009 CCCTGGACGCTCATACTACTA 58.140 52.381 0.00 0.00 0.00 1.82
214 215 1.693627 CCCTGGACGCTCATACTACT 58.306 55.000 0.00 0.00 0.00 2.57
215 216 0.032267 GCCCTGGACGCTCATACTAC 59.968 60.000 0.00 0.00 0.00 2.73
216 217 0.106167 AGCCCTGGACGCTCATACTA 60.106 55.000 0.00 0.00 0.00 1.82
217 218 0.106167 TAGCCCTGGACGCTCATACT 60.106 55.000 0.44 0.00 37.79 2.12
218 219 0.750850 TTAGCCCTGGACGCTCATAC 59.249 55.000 0.44 0.00 37.79 2.39
219 220 1.491668 TTTAGCCCTGGACGCTCATA 58.508 50.000 0.44 0.00 37.79 2.15
220 221 0.618458 TTTTAGCCCTGGACGCTCAT 59.382 50.000 0.44 0.00 37.79 2.90
221 222 0.398696 TTTTTAGCCCTGGACGCTCA 59.601 50.000 0.44 0.00 37.79 4.26
222 223 1.401905 CATTTTTAGCCCTGGACGCTC 59.598 52.381 0.44 0.00 37.79 5.03
223 224 1.004277 TCATTTTTAGCCCTGGACGCT 59.996 47.619 0.00 0.00 40.45 5.07
224 225 1.459450 TCATTTTTAGCCCTGGACGC 58.541 50.000 0.00 0.00 0.00 5.19
225 226 4.513198 TTTTCATTTTTAGCCCTGGACG 57.487 40.909 0.00 0.00 0.00 4.79
226 227 6.036577 TCATTTTCATTTTTAGCCCTGGAC 57.963 37.500 0.00 0.00 0.00 4.02
227 228 6.678568 TTCATTTTCATTTTTAGCCCTGGA 57.321 33.333 0.00 0.00 0.00 3.86
228 229 9.617523 ATTATTCATTTTCATTTTTAGCCCTGG 57.382 29.630 0.00 0.00 0.00 4.45
230 231 9.617523 CCATTATTCATTTTCATTTTTAGCCCT 57.382 29.630 0.00 0.00 0.00 5.19
231 232 8.344831 GCCATTATTCATTTTCATTTTTAGCCC 58.655 33.333 0.00 0.00 0.00 5.19
232 233 8.891720 TGCCATTATTCATTTTCATTTTTAGCC 58.108 29.630 0.00 0.00 0.00 3.93
233 234 9.706846 GTGCCATTATTCATTTTCATTTTTAGC 57.293 29.630 0.00 0.00 0.00 3.09
236 237 9.064706 TGTGTGCCATTATTCATTTTCATTTTT 57.935 25.926 0.00 0.00 0.00 1.94
237 238 8.618702 TGTGTGCCATTATTCATTTTCATTTT 57.381 26.923 0.00 0.00 0.00 1.82
238 239 8.618702 TTGTGTGCCATTATTCATTTTCATTT 57.381 26.923 0.00 0.00 0.00 2.32
239 240 8.618702 TTTGTGTGCCATTATTCATTTTCATT 57.381 26.923 0.00 0.00 0.00 2.57
240 241 8.618702 TTTTGTGTGCCATTATTCATTTTCAT 57.381 26.923 0.00 0.00 0.00 2.57
241 242 8.442632 TTTTTGTGTGCCATTATTCATTTTCA 57.557 26.923 0.00 0.00 0.00 2.69
264 265 7.664731 TGTGTGCCATTATTCATTTCCATTTTT 59.335 29.630 0.00 0.00 0.00 1.94
297 298 3.814504 ATTGACCCAGGTTGAATCTGT 57.185 42.857 4.56 0.00 0.00 3.41
300 301 7.453393 TCAGATATATTGACCCAGGTTGAATC 58.547 38.462 0.00 0.00 0.00 2.52
347 348 1.270826 CTATGTGGGATCGACGCTGAT 59.729 52.381 0.00 0.00 0.00 2.90
352 353 0.039074 GAGCCTATGTGGGATCGACG 60.039 60.000 0.00 0.00 31.96 5.12
364 365 4.342378 TGCTTTCATCTCTAACGAGCCTAT 59.658 41.667 0.00 0.00 37.19 2.57
365 366 3.699538 TGCTTTCATCTCTAACGAGCCTA 59.300 43.478 0.00 0.00 37.19 3.93
366 367 2.497675 TGCTTTCATCTCTAACGAGCCT 59.502 45.455 0.00 0.00 37.19 4.58
367 368 2.605366 GTGCTTTCATCTCTAACGAGCC 59.395 50.000 0.00 0.00 37.19 4.70
373 374 4.072131 GGTTGTGGTGCTTTCATCTCTAA 58.928 43.478 0.00 0.00 0.00 2.10
382 383 1.760480 GGGGTGGTTGTGGTGCTTT 60.760 57.895 0.00 0.00 0.00 3.51
390 391 4.910913 AGGAAATATTTTTGGGGTGGTTGT 59.089 37.500 1.43 0.00 0.00 3.32
397 398 2.102420 GGCGGAGGAAATATTTTTGGGG 59.898 50.000 1.43 0.00 0.00 4.96
405 406 1.371558 GGCGAGGCGGAGGAAATAT 59.628 57.895 0.00 0.00 0.00 1.28
424 425 2.288213 TGATTAGATCGATGGTGGCGAC 60.288 50.000 0.54 0.00 40.94 5.19
426 427 2.438868 TGATTAGATCGATGGTGGCG 57.561 50.000 0.54 0.00 0.00 5.69
442 443 2.281070 GATCCACGCCGCCATGAT 60.281 61.111 0.00 0.00 0.00 2.45
475 477 3.732212 ACATGTCGATGACCACATATGG 58.268 45.455 7.80 0.00 41.45 2.74
479 481 3.031013 TCCTACATGTCGATGACCACAT 58.969 45.455 0.00 0.00 39.67 3.21
506 508 2.948315 GAGAGAGAATGGAAACCATGGC 59.052 50.000 13.04 0.00 44.40 4.40
596 598 3.701542 TGCATATTTAAACAATCCGGGCA 59.298 39.130 0.00 0.00 0.00 5.36
599 601 8.592105 ATTTGATGCATATTTAAACAATCCGG 57.408 30.769 0.00 0.00 0.00 5.14
646 648 3.023946 TGTCCGGTTGCATTTTGATTG 57.976 42.857 0.00 0.00 0.00 2.67
647 649 3.959535 ATGTCCGGTTGCATTTTGATT 57.040 38.095 0.00 0.00 0.00 2.57
674 676 1.365699 GAGGCGCCGTTTGAAGATAA 58.634 50.000 23.20 0.00 0.00 1.75
677 679 2.358247 GGAGGCGCCGTTTGAAGA 60.358 61.111 23.20 0.00 0.00 2.87
691 695 3.182967 GTCAGAAGACACTTATGCGGAG 58.817 50.000 0.00 0.00 44.34 4.63
692 696 3.232213 GTCAGAAGACACTTATGCGGA 57.768 47.619 0.00 0.00 44.34 5.54
707 711 0.322636 GACCGAGGAGACCAGTCAGA 60.323 60.000 0.00 0.00 0.00 3.27
709 713 1.304217 GGACCGAGGAGACCAGTCA 60.304 63.158 0.00 0.00 0.00 3.41
716 720 2.359404 GTCCCTGGACCGAGGAGA 59.641 66.667 4.93 4.94 39.08 3.71
736 742 1.738830 CGTAAACCGGACACCGCAT 60.739 57.895 9.46 0.00 46.86 4.73
753 759 1.447838 CATCTCCAACACCGACCCG 60.448 63.158 0.00 0.00 0.00 5.28
758 764 0.251916 TTAGGGCATCTCCAACACCG 59.748 55.000 0.00 0.00 36.21 4.94
766 772 4.473477 ACTGTTACACTTAGGGCATCTC 57.527 45.455 0.00 0.00 0.00 2.75
831 848 3.367703 GGGTGGCAGTTCAATTCAGATTG 60.368 47.826 0.00 0.00 43.24 2.67
840 857 0.179020 CTGACTGGGTGGCAGTTCAA 60.179 55.000 0.00 0.00 46.57 2.69
847 864 2.614734 GGTAACTAACTGACTGGGTGGC 60.615 54.545 0.00 0.00 0.00 5.01
880 897 4.640855 ATCGTATCGGTGCCGGCG 62.641 66.667 23.90 7.87 40.25 6.46
968 989 2.179517 GAGGTGCACGGTCGAGAG 59.820 66.667 11.45 0.00 0.00 3.20
998 1019 3.274586 CTGCCGTCGCCATCATGG 61.275 66.667 0.00 0.00 41.55 3.66
1241 1268 1.003718 AGGAGGCGGTTGTAGTTGC 60.004 57.895 0.00 0.00 0.00 4.17
1617 1647 2.160417 GCGGAAGACAATGTGGAAGAAG 59.840 50.000 0.00 0.00 0.00 2.85
1948 1978 1.745653 GACATCCTTGGCCTTAGCAAC 59.254 52.381 3.32 0.00 42.56 4.17
2089 2119 1.032014 AACATGGACACAAGCACACC 58.968 50.000 0.00 0.00 0.00 4.16
2416 2446 5.062183 TGCTACTTGATTTCATTTCGTCGAG 59.938 40.000 0.00 0.00 0.00 4.04
2421 2451 6.685828 CAGTGATGCTACTTGATTTCATTTCG 59.314 38.462 0.00 0.00 0.00 3.46
2508 2538 2.071778 TATCCCAGAATGCCTTTGCC 57.928 50.000 0.00 0.00 36.33 4.52
2817 2847 1.273495 ACCTGATGCTCCTCCTCTTGA 60.273 52.381 0.00 0.00 0.00 3.02
2843 2873 4.618489 CAGAACTTTGATCGGCATGAAAAC 59.382 41.667 0.00 0.00 0.00 2.43
2852 2882 3.063180 GTCATCTGCAGAACTTTGATCGG 59.937 47.826 22.50 0.79 0.00 4.18
2919 2949 4.574599 TTCTGACGATGATGACGATGAT 57.425 40.909 0.00 0.00 34.70 2.45
2955 2985 7.117379 ACCTTAGCTTCGTTGTTATTCTTGTAC 59.883 37.037 0.00 0.00 0.00 2.90
3036 3066 2.645838 AGTTCTGCTCTTTTGCTGGA 57.354 45.000 0.00 0.00 33.58 3.86
3085 3115 6.661777 TGATTGTATGATCCTTGTCCATTGA 58.338 36.000 0.00 0.00 0.00 2.57
3216 3247 3.806949 AAAGTATGTGCCCCTTCTGAA 57.193 42.857 0.00 0.00 0.00 3.02
3218 3249 3.420893 TGAAAAGTATGTGCCCCTTCTG 58.579 45.455 0.00 0.00 0.00 3.02
3311 3348 1.629043 TGTCACTAACTCGGCCTTCT 58.371 50.000 0.00 0.00 0.00 2.85
3332 3369 2.224548 GGACAGGTTACCAGCTTTGTCT 60.225 50.000 16.61 0.00 0.00 3.41
3334 3371 1.493022 TGGACAGGTTACCAGCTTTGT 59.507 47.619 3.51 0.00 0.00 2.83
3381 3418 3.243068 GCCAAAAATCAGTCGTGTCAGTT 60.243 43.478 0.00 0.00 0.00 3.16
3438 3674 8.147642 AGTAGAGATGCACTAATAAAACATGC 57.852 34.615 0.00 0.00 36.81 4.06
3449 3685 4.141779 TGAGTACCGAGTAGAGATGCACTA 60.142 45.833 0.00 0.00 0.00 2.74
3465 3701 2.922740 TCAGTTGTTGGGTGAGTACC 57.077 50.000 0.00 0.00 46.76 3.34
3493 3729 2.813754 TCTCCATCGGTTTCTGCAAAAG 59.186 45.455 0.00 0.00 0.00 2.27
3546 3782 0.455633 GCAATTGCAGAACTGGAGCG 60.456 55.000 25.36 0.00 41.59 5.03
3556 3792 1.154093 CAGTGGCGAGCAATTGCAG 60.154 57.895 30.89 23.86 45.16 4.41
3643 3879 0.901124 AGAGCTCAGGTGCACTTAGG 59.099 55.000 17.77 6.40 30.02 2.69
3731 3967 6.054941 CCCTGTGACATGCTGTTACATATAA 58.945 40.000 12.06 0.00 44.18 0.98
3751 3987 2.046892 CTTGGCCGTCTCACCCTG 60.047 66.667 0.00 0.00 0.00 4.45
3753 3989 2.288025 TACCTTGGCCGTCTCACCC 61.288 63.158 0.00 0.00 0.00 4.61
3779 4015 3.576118 CACCAACAATACCACCCATGAAA 59.424 43.478 0.00 0.00 0.00 2.69
3840 4130 0.670546 CATCACCAGAAGCGAACCGT 60.671 55.000 0.00 0.00 0.00 4.83
3842 4132 1.648467 GCCATCACCAGAAGCGAACC 61.648 60.000 0.00 0.00 0.00 3.62
3843 4133 1.796796 GCCATCACCAGAAGCGAAC 59.203 57.895 0.00 0.00 0.00 3.95
3846 4136 3.197790 CCGCCATCACCAGAAGCG 61.198 66.667 0.00 0.00 45.04 4.68
3994 4287 7.398024 GGAGCTCACCATAGTTTCCATTATAT 58.602 38.462 17.19 0.00 0.00 0.86
4008 4301 2.086869 CAAAACATCGGAGCTCACCAT 58.913 47.619 17.19 0.42 0.00 3.55
4017 4310 6.317642 CACCCTAATACAATCAAAACATCGGA 59.682 38.462 0.00 0.00 0.00 4.55
4018 4311 6.459573 CCACCCTAATACAATCAAAACATCGG 60.460 42.308 0.00 0.00 0.00 4.18
4032 4325 3.565902 GCAATCTGAAGCCACCCTAATAC 59.434 47.826 0.00 0.00 0.00 1.89
4066 4359 4.369182 CTGTTCGTCTCCTACAAAGTTGT 58.631 43.478 1.75 1.75 44.86 3.32
4092 4385 5.757320 GTCTTGGATCACCATCATGTAAGAG 59.243 44.000 0.00 0.00 46.34 2.85
4096 4389 5.130809 TCATGTCTTGGATCACCATCATGTA 59.869 40.000 18.39 10.15 46.34 2.29
4105 4398 3.372206 CGGTTCTTCATGTCTTGGATCAC 59.628 47.826 0.00 0.00 0.00 3.06
4143 4436 2.107901 ACCTCTGTATCCCTACCTACCG 59.892 54.545 0.00 0.00 0.00 4.02
4153 4446 2.035321 GTGAGCTGCTACCTCTGTATCC 59.965 54.545 0.15 0.00 0.00 2.59
4173 4466 0.392193 AGCGAGCAATGCTAAGCTGT 60.392 50.000 28.24 12.27 45.75 4.40


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

AutoCloner maintained by Alex Coulton.