Multiple sequence alignment - TraesCS3A01G348400

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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 TraesCS3A01G348400 chr3A 100.000 1890 0 0 732 2621 597183965 597185854 0.000000e+00 3491
1 TraesCS3A01G348400 chr3A 100.000 462 0 0 1 462 597183234 597183695 0.000000e+00 854
2 TraesCS3A01G348400 chr3D 94.891 1918 59 15 733 2621 454903716 454905623 0.000000e+00 2963
3 TraesCS3A01G348400 chr3B 93.216 1931 71 18 733 2621 597815886 597817798 0.000000e+00 2785
4 TraesCS3A01G348400 chr1D 87.109 512 48 8 1085 1596 392697009 392697502 4.900000e-157 564
5 TraesCS3A01G348400 chr1D 91.066 347 27 2 119 462 62694445 62694100 1.420000e-127 466
6 TraesCS3A01G348400 chr1A 86.731 520 51 8 1085 1604 492652784 492652283 1.760000e-156 562
7 TraesCS3A01G348400 chr1A 88.333 360 39 1 106 462 547386514 547386155 1.860000e-116 429
8 TraesCS3A01G348400 chr1A 85.833 120 17 0 1477 1596 492654809 492654690 7.610000e-26 128
9 TraesCS3A01G348400 chr1B 86.719 512 50 8 1085 1596 529998583 529998090 1.060000e-153 553
10 TraesCS3A01G348400 chr1B 90.588 340 29 1 126 462 618195582 618195921 5.150000e-122 448
11 TraesCS3A01G348400 chr1B 89.136 359 34 2 109 462 668070779 668070421 2.390000e-120 442
12 TraesCS3A01G348400 chr4B 87.629 388 43 3 79 461 517443107 517442720 1.850000e-121 446
13 TraesCS3A01G348400 chr4B 89.655 348 32 2 119 462 94793921 94794268 8.610000e-120 440
14 TraesCS3A01G348400 chr4B 78.672 497 81 15 1087 1575 412590781 412591260 9.110000e-80 307
15 TraesCS3A01G348400 chr6A 88.889 360 36 2 106 462 539622247 539622605 8.610000e-120 440
16 TraesCS3A01G348400 chr5A 88.611 360 38 1 106 462 680855854 680856213 4.010000e-118 435
17 TraesCS3A01G348400 chr5B 88.333 360 39 1 106 462 456197261 456196902 1.860000e-116 429
18 TraesCS3A01G348400 chr4A 78.427 496 84 14 1087 1575 138833010 138832531 4.240000e-78 302
19 TraesCS3A01G348400 chr4D 77.980 495 88 12 1087 1575 334632293 334632772 9.180000e-75 291


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 TraesCS3A01G348400 chr3A 597183234 597185854 2620 False 2172.5 3491 100.000 1 2621 2 chr3A.!!$F1 2620
1 TraesCS3A01G348400 chr3D 454903716 454905623 1907 False 2963.0 2963 94.891 733 2621 1 chr3D.!!$F1 1888
2 TraesCS3A01G348400 chr3B 597815886 597817798 1912 False 2785.0 2785 93.216 733 2621 1 chr3B.!!$F1 1888
3 TraesCS3A01G348400 chr1A 492652283 492654809 2526 True 345.0 562 86.282 1085 1604 2 chr1A.!!$R2 519

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
149 150 0.036022 TCATCATGTGGGCACGAACA 59.964 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 2697 2.563702 CAGGTGCACAAAGCCAAAAAT 58.436 42.857 20.43 0.0 44.83 1.82 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
17 18 2.501610 GTGATCCAGAGACCCGGC 59.498 66.667 0.00 0.00 0.00 6.13
18 19 2.060980 GTGATCCAGAGACCCGGCT 61.061 63.158 0.00 0.00 0.00 5.52
20 21 3.453070 GATCCAGAGACCCGGCTGC 62.453 68.421 0.00 0.00 0.00 5.25
21 22 3.991924 ATCCAGAGACCCGGCTGCT 62.992 63.158 0.00 0.00 0.00 4.24
66 67 2.032528 CGCTCCTGTTCCAGCCAA 59.967 61.111 0.00 0.00 31.37 4.52
67 68 2.328099 CGCTCCTGTTCCAGCCAAC 61.328 63.158 0.00 0.00 31.37 3.77
68 69 1.228245 GCTCCTGTTCCAGCCAACA 60.228 57.895 0.00 0.00 34.99 3.33
70 71 0.890996 CTCCTGTTCCAGCCAACACC 60.891 60.000 0.00 0.00 32.70 4.16
71 72 2.260869 CCTGTTCCAGCCAACACCG 61.261 63.158 0.00 0.00 32.70 4.94
72 73 2.203280 TGTTCCAGCCAACACCGG 60.203 61.111 0.00 0.00 31.08 5.28
94 95 4.629523 GTGGTTCCCCGCCAACGA 62.630 66.667 0.00 0.00 43.93 3.85
95 96 4.323477 TGGTTCCCCGCCAACGAG 62.323 66.667 0.00 0.00 43.93 4.18
98 99 3.006728 TTCCCCGCCAACGAGGAT 61.007 61.111 2.86 0.00 46.46 3.24
101 102 4.776322 CCCGCCAACGAGGATGCA 62.776 66.667 2.86 0.00 43.93 3.96
102 103 3.197790 CCGCCAACGAGGATGCAG 61.198 66.667 0.00 0.00 43.93 4.41
104 105 2.169789 CGCCAACGAGGATGCAGAG 61.170 63.158 0.00 0.00 43.93 3.35
106 107 1.220206 CCAACGAGGATGCAGAGCT 59.780 57.895 0.00 0.00 41.22 4.09
108 109 1.140589 AACGAGGATGCAGAGCTCG 59.859 57.895 8.37 0.00 42.41 5.03
109 110 1.315981 AACGAGGATGCAGAGCTCGA 61.316 55.000 8.37 0.00 40.29 4.04
110 111 1.299014 CGAGGATGCAGAGCTCGAC 60.299 63.158 8.37 5.00 39.56 4.20
112 113 0.248990 GAGGATGCAGAGCTCGACAG 60.249 60.000 8.37 1.04 0.00 3.51
131 132 3.670377 GTGCCCGTGCCCTGTTTC 61.670 66.667 0.00 0.00 36.33 2.78
132 133 4.196778 TGCCCGTGCCCTGTTTCA 62.197 61.111 0.00 0.00 36.33 2.69
133 134 2.676471 GCCCGTGCCCTGTTTCAT 60.676 61.111 0.00 0.00 0.00 2.57
134 135 2.700773 GCCCGTGCCCTGTTTCATC 61.701 63.158 0.00 0.00 0.00 2.92
135 136 1.303236 CCCGTGCCCTGTTTCATCA 60.303 57.895 0.00 0.00 0.00 3.07
136 137 0.680921 CCCGTGCCCTGTTTCATCAT 60.681 55.000 0.00 0.00 0.00 2.45
137 138 0.452987 CCGTGCCCTGTTTCATCATG 59.547 55.000 0.00 0.00 0.00 3.07
138 139 1.167851 CGTGCCCTGTTTCATCATGT 58.832 50.000 0.00 0.00 0.00 3.21
140 141 1.203052 GTGCCCTGTTTCATCATGTGG 59.797 52.381 0.00 0.00 0.00 4.17
141 142 0.819582 GCCCTGTTTCATCATGTGGG 59.180 55.000 0.00 0.00 36.41 4.61
142 143 0.819582 CCCTGTTTCATCATGTGGGC 59.180 55.000 0.00 0.00 0.00 5.36
143 144 1.548081 CCTGTTTCATCATGTGGGCA 58.452 50.000 0.00 0.00 0.00 5.36
144 145 1.203052 CCTGTTTCATCATGTGGGCAC 59.797 52.381 0.00 0.00 0.00 5.01
145 146 0.880441 TGTTTCATCATGTGGGCACG 59.120 50.000 0.00 0.00 0.00 5.34
146 147 1.164411 GTTTCATCATGTGGGCACGA 58.836 50.000 0.00 0.00 0.00 4.35
147 148 1.539388 GTTTCATCATGTGGGCACGAA 59.461 47.619 0.00 0.00 0.00 3.85
148 149 1.164411 TTCATCATGTGGGCACGAAC 58.836 50.000 0.00 0.00 0.00 3.95
149 150 0.036022 TCATCATGTGGGCACGAACA 59.964 50.000 0.00 0.00 0.00 3.18
151 152 0.036732 ATCATGTGGGCACGAACACT 59.963 50.000 0.00 0.00 38.39 3.55
152 153 0.682292 TCATGTGGGCACGAACACTA 59.318 50.000 0.00 0.00 38.39 2.74
153 154 1.078709 CATGTGGGCACGAACACTAG 58.921 55.000 0.00 0.00 38.39 2.57
154 155 0.036388 ATGTGGGCACGAACACTAGG 60.036 55.000 0.00 0.00 38.39 3.02
155 156 1.370064 GTGGGCACGAACACTAGGT 59.630 57.895 0.00 0.00 34.84 3.08
169 170 3.250040 ACACTAGGTGTTCGTTGAAATGC 59.750 43.478 0.00 0.00 45.08 3.56
170 171 2.812011 ACTAGGTGTTCGTTGAAATGCC 59.188 45.455 0.00 0.00 0.00 4.40
171 172 1.981256 AGGTGTTCGTTGAAATGCCT 58.019 45.000 0.00 0.00 0.00 4.75
173 174 3.482436 AGGTGTTCGTTGAAATGCCTAA 58.518 40.909 0.00 0.00 0.00 2.69
174 175 3.502211 AGGTGTTCGTTGAAATGCCTAAG 59.498 43.478 0.00 0.00 0.00 2.18
175 176 3.500680 GGTGTTCGTTGAAATGCCTAAGA 59.499 43.478 0.00 0.00 0.00 2.10
178 179 4.690748 TGTTCGTTGAAATGCCTAAGAGAG 59.309 41.667 0.00 0.00 0.00 3.20
179 180 4.801330 TCGTTGAAATGCCTAAGAGAGA 57.199 40.909 0.00 0.00 0.00 3.10
180 181 5.147330 TCGTTGAAATGCCTAAGAGAGAA 57.853 39.130 0.00 0.00 0.00 2.87
181 182 5.547465 TCGTTGAAATGCCTAAGAGAGAAA 58.453 37.500 0.00 0.00 0.00 2.52
182 183 5.639506 TCGTTGAAATGCCTAAGAGAGAAAG 59.360 40.000 0.00 0.00 0.00 2.62
183 184 5.639506 CGTTGAAATGCCTAAGAGAGAAAGA 59.360 40.000 0.00 0.00 0.00 2.52
184 185 6.183360 CGTTGAAATGCCTAAGAGAGAAAGAG 60.183 42.308 0.00 0.00 0.00 2.85
185 186 5.738909 TGAAATGCCTAAGAGAGAAAGAGG 58.261 41.667 0.00 0.00 0.00 3.69
186 187 5.485353 TGAAATGCCTAAGAGAGAAAGAGGA 59.515 40.000 0.00 0.00 0.00 3.71
187 188 6.157645 TGAAATGCCTAAGAGAGAAAGAGGAT 59.842 38.462 0.00 0.00 0.00 3.24
188 189 5.549742 ATGCCTAAGAGAGAAAGAGGATG 57.450 43.478 0.00 0.00 0.00 3.51
189 190 4.614475 TGCCTAAGAGAGAAAGAGGATGA 58.386 43.478 0.00 0.00 0.00 2.92
190 191 4.648762 TGCCTAAGAGAGAAAGAGGATGAG 59.351 45.833 0.00 0.00 0.00 2.90
191 192 4.039124 GCCTAAGAGAGAAAGAGGATGAGG 59.961 50.000 0.00 0.00 0.00 3.86
192 193 5.454062 CCTAAGAGAGAAAGAGGATGAGGA 58.546 45.833 0.00 0.00 0.00 3.71
193 194 5.896678 CCTAAGAGAGAAAGAGGATGAGGAA 59.103 44.000 0.00 0.00 0.00 3.36
195 196 5.205517 AGAGAGAAAGAGGATGAGGAAGA 57.794 43.478 0.00 0.00 0.00 2.87
196 197 5.588845 AGAGAGAAAGAGGATGAGGAAGAA 58.411 41.667 0.00 0.00 0.00 2.52
197 198 5.658190 AGAGAGAAAGAGGATGAGGAAGAAG 59.342 44.000 0.00 0.00 0.00 2.85
198 199 4.716287 AGAGAAAGAGGATGAGGAAGAAGG 59.284 45.833 0.00 0.00 0.00 3.46
199 200 4.434195 AGAAAGAGGATGAGGAAGAAGGT 58.566 43.478 0.00 0.00 0.00 3.50
200 201 5.594777 AGAAAGAGGATGAGGAAGAAGGTA 58.405 41.667 0.00 0.00 0.00 3.08
201 202 5.660864 AGAAAGAGGATGAGGAAGAAGGTAG 59.339 44.000 0.00 0.00 0.00 3.18
202 203 4.890499 AGAGGATGAGGAAGAAGGTAGA 57.110 45.455 0.00 0.00 0.00 2.59
203 204 5.417170 AGAGGATGAGGAAGAAGGTAGAT 57.583 43.478 0.00 0.00 0.00 1.98
204 205 5.147032 AGAGGATGAGGAAGAAGGTAGATG 58.853 45.833 0.00 0.00 0.00 2.90
205 206 3.645687 AGGATGAGGAAGAAGGTAGATGC 59.354 47.826 0.00 0.00 0.00 3.91
207 208 4.502950 GGATGAGGAAGAAGGTAGATGCTG 60.503 50.000 0.00 0.00 0.00 4.41
208 209 3.713003 TGAGGAAGAAGGTAGATGCTGA 58.287 45.455 0.00 0.00 0.00 4.26
209 210 3.449018 TGAGGAAGAAGGTAGATGCTGAC 59.551 47.826 0.00 0.00 0.00 3.51
210 211 3.445008 AGGAAGAAGGTAGATGCTGACA 58.555 45.455 0.00 0.00 0.00 3.58
211 212 4.036518 AGGAAGAAGGTAGATGCTGACAT 58.963 43.478 0.00 0.00 39.98 3.06
213 214 4.383552 GGAAGAAGGTAGATGCTGACATGT 60.384 45.833 0.00 0.00 36.35 3.21
215 216 2.996249 AGGTAGATGCTGACATGTGG 57.004 50.000 1.15 0.00 36.35 4.17
216 217 1.487976 AGGTAGATGCTGACATGTGGG 59.512 52.381 1.15 0.00 36.35 4.61
219 220 0.254178 AGATGCTGACATGTGGGACC 59.746 55.000 1.15 0.00 36.35 4.46
220 221 0.749454 GATGCTGACATGTGGGACCC 60.749 60.000 1.15 2.45 36.35 4.46
221 222 1.499913 ATGCTGACATGTGGGACCCA 61.500 55.000 9.95 9.95 34.35 4.51
233 234 1.555992 TGGGACCCACCTGTAATAACG 59.444 52.381 9.95 0.00 38.98 3.18
235 236 1.556451 GGACCCACCTGTAATAACGGT 59.444 52.381 0.00 0.00 34.29 4.83
236 237 2.419159 GGACCCACCTGTAATAACGGTC 60.419 54.545 0.00 0.00 38.04 4.79
237 238 2.234414 GACCCACCTGTAATAACGGTCA 59.766 50.000 0.00 0.00 38.52 4.02
238 239 2.638855 ACCCACCTGTAATAACGGTCAA 59.361 45.455 0.00 0.00 32.51 3.18
239 240 3.264964 ACCCACCTGTAATAACGGTCAAT 59.735 43.478 0.00 0.00 32.51 2.57
240 241 3.625764 CCCACCTGTAATAACGGTCAATG 59.374 47.826 0.00 0.00 32.51 2.82
241 242 4.258543 CCACCTGTAATAACGGTCAATGT 58.741 43.478 0.00 0.00 32.51 2.71
242 243 5.421277 CCACCTGTAATAACGGTCAATGTA 58.579 41.667 0.00 0.00 32.51 2.29
243 244 5.875910 CCACCTGTAATAACGGTCAATGTAA 59.124 40.000 0.00 0.00 32.51 2.41
244 245 6.183360 CCACCTGTAATAACGGTCAATGTAAC 60.183 42.308 0.00 0.00 32.51 2.50
245 246 6.592607 CACCTGTAATAACGGTCAATGTAACT 59.407 38.462 0.00 0.00 32.51 2.24
247 248 6.592607 CCTGTAATAACGGTCAATGTAACTGT 59.407 38.462 0.00 0.00 0.00 3.55
248 249 7.201496 CCTGTAATAACGGTCAATGTAACTGTC 60.201 40.741 0.00 0.00 0.00 3.51
251 252 7.499321 AATAACGGTCAATGTAACTGTCAAA 57.501 32.000 0.00 0.00 0.00 2.69
252 253 5.821516 AACGGTCAATGTAACTGTCAAAA 57.178 34.783 0.00 0.00 0.00 2.44
253 254 6.385649 AACGGTCAATGTAACTGTCAAAAT 57.614 33.333 0.00 0.00 0.00 1.82
255 256 7.499321 ACGGTCAATGTAACTGTCAAAATAA 57.501 32.000 0.00 0.00 0.00 1.40
256 257 7.932335 ACGGTCAATGTAACTGTCAAAATAAA 58.068 30.769 0.00 0.00 0.00 1.40
258 259 7.059033 CGGTCAATGTAACTGTCAAAATAAACG 59.941 37.037 0.00 0.00 0.00 3.60
259 260 7.325097 GGTCAATGTAACTGTCAAAATAAACGG 59.675 37.037 0.00 0.00 0.00 4.44
275 276 0.942252 ACGGAGTTGACTTTTTCGCC 59.058 50.000 0.00 0.00 37.78 5.54
276 277 0.941542 CGGAGTTGACTTTTTCGCCA 59.058 50.000 0.00 0.00 0.00 5.69
277 278 1.333791 CGGAGTTGACTTTTTCGCCAC 60.334 52.381 0.00 0.00 0.00 5.01
278 279 1.333791 GGAGTTGACTTTTTCGCCACG 60.334 52.381 0.00 0.00 0.00 4.94
279 280 1.329599 GAGTTGACTTTTTCGCCACGT 59.670 47.619 0.00 0.00 0.00 4.49
280 281 1.329599 AGTTGACTTTTTCGCCACGTC 59.670 47.619 0.00 0.00 0.00 4.34
281 282 1.062880 GTTGACTTTTTCGCCACGTCA 59.937 47.619 0.00 0.00 33.25 4.35
282 283 0.934496 TGACTTTTTCGCCACGTCAG 59.066 50.000 0.00 0.00 31.62 3.51
283 284 0.384353 GACTTTTTCGCCACGTCAGC 60.384 55.000 0.00 0.00 0.00 4.26
284 285 0.814010 ACTTTTTCGCCACGTCAGCT 60.814 50.000 5.62 0.00 0.00 4.24
285 286 0.110644 CTTTTTCGCCACGTCAGCTC 60.111 55.000 5.62 0.00 0.00 4.09
287 288 1.221466 TTTTCGCCACGTCAGCTCTG 61.221 55.000 5.62 0.00 0.00 3.35
288 289 2.082629 TTTCGCCACGTCAGCTCTGA 62.083 55.000 5.62 0.00 37.24 3.27
296 297 3.051210 TCAGCTCTGACACACGGG 58.949 61.111 0.00 0.00 34.14 5.28
297 298 2.740055 CAGCTCTGACACACGGGC 60.740 66.667 0.00 0.00 0.00 6.13
298 299 4.008933 AGCTCTGACACACGGGCC 62.009 66.667 0.00 0.00 0.00 5.80
300 301 4.394712 CTCTGACACACGGGCCCC 62.395 72.222 18.66 0.23 0.00 5.80
310 311 4.248842 CGGGCCCCGCATGTCATA 62.249 66.667 18.66 0.00 41.17 2.15
311 312 2.194597 GGGCCCCGCATGTCATAA 59.805 61.111 12.23 0.00 0.00 1.90
312 313 1.454847 GGGCCCCGCATGTCATAAA 60.455 57.895 12.23 0.00 0.00 1.40
313 314 0.827507 GGGCCCCGCATGTCATAAAT 60.828 55.000 12.23 0.00 0.00 1.40
314 315 1.546773 GGGCCCCGCATGTCATAAATA 60.547 52.381 12.23 0.00 0.00 1.40
315 316 1.812571 GGCCCCGCATGTCATAAATAG 59.187 52.381 0.00 0.00 0.00 1.73
316 317 1.812571 GCCCCGCATGTCATAAATAGG 59.187 52.381 0.00 0.00 0.00 2.57
317 318 2.814097 GCCCCGCATGTCATAAATAGGT 60.814 50.000 0.00 0.00 0.00 3.08
318 319 3.486383 CCCCGCATGTCATAAATAGGTT 58.514 45.455 0.00 0.00 0.00 3.50
321 322 5.533154 CCCCGCATGTCATAAATAGGTTTAA 59.467 40.000 0.00 0.00 33.76 1.52
323 324 7.416890 CCCCGCATGTCATAAATAGGTTTAAAA 60.417 37.037 0.00 0.00 33.76 1.52
324 325 8.141268 CCCGCATGTCATAAATAGGTTTAAAAT 58.859 33.333 0.00 0.00 33.76 1.82
325 326 9.180678 CCGCATGTCATAAATAGGTTTAAAATC 57.819 33.333 0.00 0.00 33.76 2.17
326 327 9.729023 CGCATGTCATAAATAGGTTTAAAATCA 57.271 29.630 0.00 0.00 33.76 2.57
340 341 9.634163 AGGTTTAAAATCATAAAAACGGTCATC 57.366 29.630 0.00 0.00 33.61 2.92
341 342 9.413048 GGTTTAAAATCATAAAAACGGTCATCA 57.587 29.630 0.00 0.00 33.61 3.07
346 347 9.703892 AAAATCATAAAAACGGTCATCAATTCA 57.296 25.926 0.00 0.00 0.00 2.57
347 348 9.703892 AAATCATAAAAACGGTCATCAATTCAA 57.296 25.926 0.00 0.00 0.00 2.69
349 350 9.874205 ATCATAAAAACGGTCATCAATTCAATT 57.126 25.926 0.00 0.00 0.00 2.32
351 352 9.743937 CATAAAAACGGTCATCAATTCAATTTG 57.256 29.630 0.00 0.00 0.00 2.32
352 353 6.783892 AAAACGGTCATCAATTCAATTTGG 57.216 33.333 0.00 0.00 0.00 3.28
354 355 6.582677 AACGGTCATCAATTCAATTTGGTA 57.417 33.333 0.00 0.00 0.00 3.25
355 356 6.194796 ACGGTCATCAATTCAATTTGGTAG 57.805 37.500 0.00 0.00 0.00 3.18
356 357 5.710099 ACGGTCATCAATTCAATTTGGTAGT 59.290 36.000 0.00 0.00 0.00 2.73
357 358 6.208599 ACGGTCATCAATTCAATTTGGTAGTT 59.791 34.615 0.00 0.00 0.00 2.24
358 359 7.090173 CGGTCATCAATTCAATTTGGTAGTTT 58.910 34.615 0.00 0.00 0.00 2.66
359 360 7.598493 CGGTCATCAATTCAATTTGGTAGTTTT 59.402 33.333 0.00 0.00 0.00 2.43
360 361 9.271828 GGTCATCAATTCAATTTGGTAGTTTTT 57.728 29.630 0.00 0.00 0.00 1.94
395 396 9.939802 AATTAGTACTAATCTGAAGTTTTCGGT 57.060 29.630 24.80 5.02 34.90 4.69
397 398 6.989659 AGTACTAATCTGAAGTTTTCGGTCA 58.010 36.000 0.00 0.00 37.33 4.02
399 400 5.855045 ACTAATCTGAAGTTTTCGGTCACT 58.145 37.500 0.00 0.00 37.33 3.41
400 401 6.289064 ACTAATCTGAAGTTTTCGGTCACTT 58.711 36.000 0.00 0.00 37.33 3.16
401 402 6.766467 ACTAATCTGAAGTTTTCGGTCACTTT 59.234 34.615 0.00 0.00 37.33 2.66
402 403 6.451064 AATCTGAAGTTTTCGGTCACTTTT 57.549 33.333 0.00 0.00 37.33 2.27
403 404 5.890424 TCTGAAGTTTTCGGTCACTTTTT 57.110 34.783 0.00 0.00 37.33 1.94
405 406 7.011828 TCTGAAGTTTTCGGTCACTTTTTAG 57.988 36.000 0.00 0.00 37.33 1.85
407 408 7.334921 TCTGAAGTTTTCGGTCACTTTTTAGAA 59.665 33.333 0.00 0.00 37.33 2.10
408 409 7.992008 TGAAGTTTTCGGTCACTTTTTAGAAT 58.008 30.769 0.00 0.00 33.22 2.40
411 412 9.893305 AAGTTTTCGGTCACTTTTTAGAATATG 57.107 29.630 0.00 0.00 28.27 1.78
412 413 8.512138 AGTTTTCGGTCACTTTTTAGAATATGG 58.488 33.333 0.00 0.00 0.00 2.74
414 415 9.504708 TTTTCGGTCACTTTTTAGAATATGGTA 57.495 29.630 0.00 0.00 0.00 3.25
415 416 8.712285 TTCGGTCACTTTTTAGAATATGGTAG 57.288 34.615 0.00 0.00 0.00 3.18
416 417 7.844009 TCGGTCACTTTTTAGAATATGGTAGT 58.156 34.615 0.00 0.00 0.00 2.73
417 418 8.316214 TCGGTCACTTTTTAGAATATGGTAGTT 58.684 33.333 0.00 0.00 0.00 2.24
418 419 8.601476 CGGTCACTTTTTAGAATATGGTAGTTC 58.399 37.037 0.00 0.00 0.00 3.01
419 420 9.668497 GGTCACTTTTTAGAATATGGTAGTTCT 57.332 33.333 0.00 0.00 38.22 3.01
423 424 9.449719 ACTTTTTAGAATATGGTAGTTCTGTGG 57.550 33.333 0.00 0.00 36.23 4.17
424 425 8.801882 TTTTTAGAATATGGTAGTTCTGTGGG 57.198 34.615 0.00 0.00 36.23 4.61
426 427 5.615925 AGAATATGGTAGTTCTGTGGGAC 57.384 43.478 0.00 0.00 33.64 4.46
427 428 4.099573 AGAATATGGTAGTTCTGTGGGACG 59.900 45.833 0.00 0.00 33.64 4.79
428 429 0.902531 ATGGTAGTTCTGTGGGACGG 59.097 55.000 0.00 0.00 0.00 4.79
429 430 0.470456 TGGTAGTTCTGTGGGACGGT 60.470 55.000 0.00 0.00 0.00 4.83
431 432 0.963962 GTAGTTCTGTGGGACGGTGA 59.036 55.000 0.00 0.00 0.00 4.02
432 433 1.342174 GTAGTTCTGTGGGACGGTGAA 59.658 52.381 0.00 0.00 0.00 3.18
433 434 0.834612 AGTTCTGTGGGACGGTGAAA 59.165 50.000 0.00 0.00 0.00 2.69
434 435 1.420138 AGTTCTGTGGGACGGTGAAAT 59.580 47.619 0.00 0.00 0.00 2.17
435 436 1.535462 GTTCTGTGGGACGGTGAAATG 59.465 52.381 0.00 0.00 0.00 2.32
438 439 2.158740 TCTGTGGGACGGTGAAATGAAA 60.159 45.455 0.00 0.00 0.00 2.69
439 440 2.819608 CTGTGGGACGGTGAAATGAAAT 59.180 45.455 0.00 0.00 0.00 2.17
440 441 2.556189 TGTGGGACGGTGAAATGAAATG 59.444 45.455 0.00 0.00 0.00 2.32
442 443 2.556189 TGGGACGGTGAAATGAAATGTG 59.444 45.455 0.00 0.00 0.00 3.21
443 444 2.817258 GGGACGGTGAAATGAAATGTGA 59.183 45.455 0.00 0.00 0.00 3.58
444 445 3.443681 GGGACGGTGAAATGAAATGTGAT 59.556 43.478 0.00 0.00 0.00 3.06
445 446 4.638421 GGGACGGTGAAATGAAATGTGATA 59.362 41.667 0.00 0.00 0.00 2.15
446 447 5.220854 GGGACGGTGAAATGAAATGTGATAG 60.221 44.000 0.00 0.00 0.00 2.08
447 448 5.354234 GGACGGTGAAATGAAATGTGATAGT 59.646 40.000 0.00 0.00 0.00 2.12
449 450 7.214467 ACGGTGAAATGAAATGTGATAGTTT 57.786 32.000 0.00 0.00 0.00 2.66
450 451 7.657336 ACGGTGAAATGAAATGTGATAGTTTT 58.343 30.769 0.00 0.00 0.00 2.43
451 452 8.141268 ACGGTGAAATGAAATGTGATAGTTTTT 58.859 29.630 0.00 0.00 0.00 1.94
1249 2191 1.003476 TTCATCAAGAGCTGCCGCA 60.003 52.632 2.05 0.00 39.10 5.69
1752 2697 5.208890 ACTAGCCCTAGTGTCATGTGATTA 58.791 41.667 7.15 0.00 44.11 1.75
1859 2807 7.798801 ACTGATTCGACTACATATTACTCGAG 58.201 38.462 11.84 11.84 35.01 4.04
1937 2887 9.263538 ACAACAAACTAAATGATGAAGTACGTA 57.736 29.630 0.00 0.00 0.00 3.57
2051 3016 2.127383 CCGACGCGAAGTTTTGCC 60.127 61.111 15.93 0.00 33.96 4.52
2056 3021 2.008697 CGCGAAGTTTTGCCCAACG 61.009 57.895 0.00 0.00 33.96 4.10
2149 3116 9.250624 CTATTAAACAGATCACAACTAGTAGCC 57.749 37.037 0.00 0.00 0.00 3.93
2302 3270 5.350633 TCCAAGCTCAATTCAACAAAGTTG 58.649 37.500 3.58 3.58 0.00 3.16
2378 3346 5.290386 GCCTGCAATCGAGTAATTAGTAGT 58.710 41.667 0.00 0.00 0.00 2.73
2417 3385 2.168728 GGGACTAGTCTTAGGGCAAGTG 59.831 54.545 21.88 0.00 35.58 3.16
2517 3485 0.098200 TGCGTAGAATCTGGTCGACG 59.902 55.000 9.92 3.87 45.76 5.12
2522 3490 2.060050 AGAATCTGGTCGACGGATCT 57.940 50.000 18.42 14.73 44.47 2.75
2523 3491 3.210232 AGAATCTGGTCGACGGATCTA 57.790 47.619 18.42 0.00 44.47 1.98
2533 3501 4.271533 GGTCGACGGATCTATAGATAGCTG 59.728 50.000 15.31 11.19 34.37 4.24
2535 3503 5.581479 GTCGACGGATCTATAGATAGCTGAA 59.419 44.000 15.31 0.00 34.37 3.02
2536 3504 6.259167 GTCGACGGATCTATAGATAGCTGAAT 59.741 42.308 15.31 0.00 34.37 2.57
2537 3505 7.438757 GTCGACGGATCTATAGATAGCTGAATA 59.561 40.741 15.31 0.00 34.37 1.75
2538 3506 7.654116 TCGACGGATCTATAGATAGCTGAATAG 59.346 40.741 15.31 0.00 34.37 1.73
2539 3507 7.504924 ACGGATCTATAGATAGCTGAATAGC 57.495 40.000 15.31 0.00 41.68 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.060383 CAGCCGGGTCTCTGGATCA 61.060 63.158 1.27 0.00 42.08 2.92
2 3 2.818132 CAGCCGGGTCTCTGGATC 59.182 66.667 1.27 0.00 42.08 3.36
3 4 3.474570 GCAGCCGGGTCTCTGGAT 61.475 66.667 1.27 0.00 42.08 3.41
4 5 4.704103 AGCAGCCGGGTCTCTGGA 62.704 66.667 1.27 0.00 42.08 3.86
5 6 4.463879 CAGCAGCCGGGTCTCTGG 62.464 72.222 19.48 4.32 42.40 3.86
55 56 2.203280 CCGGTGTTGGCTGGAACA 60.203 61.111 0.00 0.00 37.06 3.18
56 57 2.983592 CCCGGTGTTGGCTGGAAC 60.984 66.667 0.00 0.00 37.06 3.62
57 58 4.966787 GCCCGGTGTTGGCTGGAA 62.967 66.667 0.00 0.00 45.70 3.53
86 87 2.125552 TCTGCATCCTCGTTGGCG 60.126 61.111 0.00 0.00 39.92 5.69
87 88 2.467826 GCTCTGCATCCTCGTTGGC 61.468 63.158 0.00 0.00 35.26 4.52
89 90 1.144565 CGAGCTCTGCATCCTCGTTG 61.145 60.000 12.85 0.00 42.41 4.10
90 91 1.140589 CGAGCTCTGCATCCTCGTT 59.859 57.895 12.85 0.00 42.41 3.85
91 92 1.750780 TCGAGCTCTGCATCCTCGT 60.751 57.895 22.00 0.00 46.15 4.18
94 95 1.815196 CTGTCGAGCTCTGCATCCT 59.185 57.895 12.85 0.00 0.00 3.24
95 96 1.882167 GCTGTCGAGCTCTGCATCC 60.882 63.158 12.85 1.60 42.52 3.51
98 99 3.674523 ACGCTGTCGAGCTCTGCA 61.675 61.111 12.85 9.36 43.77 4.41
114 115 3.670377 GAAACAGGGCACGGGCAC 61.670 66.667 13.89 8.54 46.58 5.01
115 116 3.505790 ATGAAACAGGGCACGGGCA 62.506 57.895 13.89 0.00 43.71 5.36
116 117 2.676471 ATGAAACAGGGCACGGGC 60.676 61.111 0.00 0.00 40.13 6.13
118 119 0.452987 CATGATGAAACAGGGCACGG 59.547 55.000 0.00 0.00 0.00 4.94
120 121 1.203052 CCACATGATGAAACAGGGCAC 59.797 52.381 0.00 0.00 0.00 5.01
121 122 1.548081 CCACATGATGAAACAGGGCA 58.452 50.000 0.00 0.00 0.00 5.36
122 123 0.819582 CCCACATGATGAAACAGGGC 59.180 55.000 0.00 0.00 0.00 5.19
124 125 1.203052 GTGCCCACATGATGAAACAGG 59.797 52.381 0.00 0.00 0.00 4.00
126 127 0.880441 CGTGCCCACATGATGAAACA 59.120 50.000 0.00 0.00 34.49 2.83
128 129 1.539388 GTTCGTGCCCACATGATGAAA 59.461 47.619 0.00 0.00 41.42 2.69
131 132 0.168788 GTGTTCGTGCCCACATGATG 59.831 55.000 0.00 0.00 41.42 3.07
132 133 0.036732 AGTGTTCGTGCCCACATGAT 59.963 50.000 0.00 0.00 41.42 2.45
133 134 0.682292 TAGTGTTCGTGCCCACATGA 59.318 50.000 0.00 0.00 40.10 3.07
134 135 1.078709 CTAGTGTTCGTGCCCACATG 58.921 55.000 0.00 0.00 33.99 3.21
135 136 0.036388 CCTAGTGTTCGTGCCCACAT 60.036 55.000 0.00 0.00 33.99 3.21
136 137 1.369692 CCTAGTGTTCGTGCCCACA 59.630 57.895 0.00 0.00 33.99 4.17
137 138 0.949105 CACCTAGTGTTCGTGCCCAC 60.949 60.000 0.00 0.00 0.00 4.61
138 139 1.369692 CACCTAGTGTTCGTGCCCA 59.630 57.895 0.00 0.00 0.00 5.36
148 149 3.364964 GGCATTTCAACGAACACCTAGTG 60.365 47.826 0.00 0.00 39.75 2.74
149 150 2.812011 GGCATTTCAACGAACACCTAGT 59.188 45.455 0.00 0.00 0.00 2.57
151 152 3.134574 AGGCATTTCAACGAACACCTA 57.865 42.857 0.00 0.00 0.00 3.08
152 153 1.981256 AGGCATTTCAACGAACACCT 58.019 45.000 0.00 0.00 0.00 4.00
153 154 3.500680 TCTTAGGCATTTCAACGAACACC 59.499 43.478 0.00 0.00 0.00 4.16
154 155 4.451096 TCTCTTAGGCATTTCAACGAACAC 59.549 41.667 0.00 0.00 0.00 3.32
155 156 4.637276 TCTCTTAGGCATTTCAACGAACA 58.363 39.130 0.00 0.00 0.00 3.18
157 158 5.147330 TCTCTCTTAGGCATTTCAACGAA 57.853 39.130 0.00 0.00 0.00 3.85
158 159 4.801330 TCTCTCTTAGGCATTTCAACGA 57.199 40.909 0.00 0.00 0.00 3.85
159 160 5.639506 TCTTTCTCTCTTAGGCATTTCAACG 59.360 40.000 0.00 0.00 0.00 4.10
160 161 6.093357 CCTCTTTCTCTCTTAGGCATTTCAAC 59.907 42.308 0.00 0.00 0.00 3.18
161 162 6.013379 TCCTCTTTCTCTCTTAGGCATTTCAA 60.013 38.462 0.00 0.00 0.00 2.69
163 164 5.983540 TCCTCTTTCTCTCTTAGGCATTTC 58.016 41.667 0.00 0.00 0.00 2.17
164 165 6.157645 TCATCCTCTTTCTCTCTTAGGCATTT 59.842 38.462 0.00 0.00 0.00 2.32
166 167 5.215069 TCATCCTCTTTCTCTCTTAGGCAT 58.785 41.667 0.00 0.00 0.00 4.40
167 168 4.614475 TCATCCTCTTTCTCTCTTAGGCA 58.386 43.478 0.00 0.00 0.00 4.75
168 169 4.039124 CCTCATCCTCTTTCTCTCTTAGGC 59.961 50.000 0.00 0.00 0.00 3.93
169 170 5.454062 TCCTCATCCTCTTTCTCTCTTAGG 58.546 45.833 0.00 0.00 0.00 2.69
170 171 6.833416 TCTTCCTCATCCTCTTTCTCTCTTAG 59.167 42.308 0.00 0.00 0.00 2.18
171 172 6.736581 TCTTCCTCATCCTCTTTCTCTCTTA 58.263 40.000 0.00 0.00 0.00 2.10
173 174 5.205517 TCTTCCTCATCCTCTTTCTCTCT 57.794 43.478 0.00 0.00 0.00 3.10
174 175 5.163416 CCTTCTTCCTCATCCTCTTTCTCTC 60.163 48.000 0.00 0.00 0.00 3.20
175 176 4.716287 CCTTCTTCCTCATCCTCTTTCTCT 59.284 45.833 0.00 0.00 0.00 3.10
178 179 4.835284 ACCTTCTTCCTCATCCTCTTTC 57.165 45.455 0.00 0.00 0.00 2.62
179 180 5.594777 TCTACCTTCTTCCTCATCCTCTTT 58.405 41.667 0.00 0.00 0.00 2.52
180 181 5.213868 TCTACCTTCTTCCTCATCCTCTT 57.786 43.478 0.00 0.00 0.00 2.85
181 182 4.890499 TCTACCTTCTTCCTCATCCTCT 57.110 45.455 0.00 0.00 0.00 3.69
182 183 4.262420 GCATCTACCTTCTTCCTCATCCTC 60.262 50.000 0.00 0.00 0.00 3.71
183 184 3.645687 GCATCTACCTTCTTCCTCATCCT 59.354 47.826 0.00 0.00 0.00 3.24
184 185 3.645687 AGCATCTACCTTCTTCCTCATCC 59.354 47.826 0.00 0.00 0.00 3.51
185 186 4.343526 TCAGCATCTACCTTCTTCCTCATC 59.656 45.833 0.00 0.00 0.00 2.92
186 187 4.100808 GTCAGCATCTACCTTCTTCCTCAT 59.899 45.833 0.00 0.00 0.00 2.90
187 188 3.449018 GTCAGCATCTACCTTCTTCCTCA 59.551 47.826 0.00 0.00 0.00 3.86
188 189 3.449018 TGTCAGCATCTACCTTCTTCCTC 59.551 47.826 0.00 0.00 0.00 3.71
189 190 3.445008 TGTCAGCATCTACCTTCTTCCT 58.555 45.455 0.00 0.00 0.00 3.36
190 191 3.895232 TGTCAGCATCTACCTTCTTCC 57.105 47.619 0.00 0.00 0.00 3.46
191 192 4.569966 CACATGTCAGCATCTACCTTCTTC 59.430 45.833 0.00 0.00 31.99 2.87
192 193 4.511527 CACATGTCAGCATCTACCTTCTT 58.488 43.478 0.00 0.00 31.99 2.52
193 194 3.118482 CCACATGTCAGCATCTACCTTCT 60.118 47.826 0.00 0.00 31.99 2.85
195 196 2.092753 CCCACATGTCAGCATCTACCTT 60.093 50.000 0.00 0.00 31.99 3.50
196 197 1.487976 CCCACATGTCAGCATCTACCT 59.512 52.381 0.00 0.00 31.99 3.08
197 198 1.486310 TCCCACATGTCAGCATCTACC 59.514 52.381 0.00 0.00 31.99 3.18
198 199 2.555199 GTCCCACATGTCAGCATCTAC 58.445 52.381 0.00 0.00 31.99 2.59
199 200 1.486310 GGTCCCACATGTCAGCATCTA 59.514 52.381 0.00 0.00 31.99 1.98
200 201 0.254178 GGTCCCACATGTCAGCATCT 59.746 55.000 0.00 0.00 31.99 2.90
201 202 0.749454 GGGTCCCACATGTCAGCATC 60.749 60.000 1.78 0.00 31.99 3.91
202 203 1.304282 GGGTCCCACATGTCAGCAT 59.696 57.895 1.78 0.00 35.32 3.79
203 204 2.152729 TGGGTCCCACATGTCAGCA 61.153 57.895 6.47 0.00 0.00 4.41
204 205 2.756400 TGGGTCCCACATGTCAGC 59.244 61.111 6.47 0.00 0.00 4.26
213 214 1.555992 CGTTATTACAGGTGGGTCCCA 59.444 52.381 6.47 6.47 36.75 4.37
215 216 1.556451 ACCGTTATTACAGGTGGGTCC 59.444 52.381 0.00 0.00 36.81 4.46
216 217 2.234414 TGACCGTTATTACAGGTGGGTC 59.766 50.000 3.68 0.53 42.10 4.46
219 220 4.258543 ACATTGACCGTTATTACAGGTGG 58.741 43.478 3.68 0.00 38.57 4.61
220 221 6.592607 AGTTACATTGACCGTTATTACAGGTG 59.407 38.462 3.68 0.00 38.57 4.00
221 222 6.592607 CAGTTACATTGACCGTTATTACAGGT 59.407 38.462 0.00 0.00 41.63 4.00
222 223 6.592607 ACAGTTACATTGACCGTTATTACAGG 59.407 38.462 0.00 0.00 0.00 4.00
223 224 7.329962 TGACAGTTACATTGACCGTTATTACAG 59.670 37.037 0.00 0.00 0.00 2.74
224 225 7.153315 TGACAGTTACATTGACCGTTATTACA 58.847 34.615 0.00 0.00 0.00 2.41
225 226 7.585286 TGACAGTTACATTGACCGTTATTAC 57.415 36.000 0.00 0.00 0.00 1.89
226 227 8.604640 TTTGACAGTTACATTGACCGTTATTA 57.395 30.769 0.00 0.00 0.00 0.98
227 228 7.499321 TTTGACAGTTACATTGACCGTTATT 57.501 32.000 0.00 0.00 0.00 1.40
228 229 7.499321 TTTTGACAGTTACATTGACCGTTAT 57.501 32.000 0.00 0.00 0.00 1.89
229 230 6.922247 TTTTGACAGTTACATTGACCGTTA 57.078 33.333 0.00 0.00 0.00 3.18
230 231 5.821516 TTTTGACAGTTACATTGACCGTT 57.178 34.783 0.00 0.00 0.00 4.44
232 233 7.059033 CGTTTATTTTGACAGTTACATTGACCG 59.941 37.037 0.00 0.00 0.00 4.79
233 234 7.325097 CCGTTTATTTTGACAGTTACATTGACC 59.675 37.037 0.00 0.00 0.00 4.02
235 236 8.155821 TCCGTTTATTTTGACAGTTACATTGA 57.844 30.769 0.00 0.00 0.00 2.57
236 237 8.073768 ACTCCGTTTATTTTGACAGTTACATTG 58.926 33.333 0.00 0.00 0.00 2.82
237 238 8.161699 ACTCCGTTTATTTTGACAGTTACATT 57.838 30.769 0.00 0.00 0.00 2.71
238 239 7.739498 ACTCCGTTTATTTTGACAGTTACAT 57.261 32.000 0.00 0.00 0.00 2.29
239 240 7.280428 TCAACTCCGTTTATTTTGACAGTTACA 59.720 33.333 0.00 0.00 0.00 2.41
240 241 7.585210 GTCAACTCCGTTTATTTTGACAGTTAC 59.415 37.037 7.68 0.00 43.60 2.50
241 242 7.496591 AGTCAACTCCGTTTATTTTGACAGTTA 59.503 33.333 13.57 0.00 45.57 2.24
242 243 6.317893 AGTCAACTCCGTTTATTTTGACAGTT 59.682 34.615 13.57 0.00 45.57 3.16
243 244 5.820947 AGTCAACTCCGTTTATTTTGACAGT 59.179 36.000 13.57 0.00 45.57 3.55
244 245 6.300354 AGTCAACTCCGTTTATTTTGACAG 57.700 37.500 13.57 0.00 45.57 3.51
245 246 6.687081 AAGTCAACTCCGTTTATTTTGACA 57.313 33.333 13.57 0.00 45.57 3.58
247 248 7.429920 CGAAAAAGTCAACTCCGTTTATTTTGA 59.570 33.333 0.00 0.00 0.00 2.69
248 249 7.543756 CGAAAAAGTCAACTCCGTTTATTTTG 58.456 34.615 0.00 0.00 0.00 2.44
251 252 5.209977 GCGAAAAAGTCAACTCCGTTTATT 58.790 37.500 0.00 0.00 0.00 1.40
252 253 4.319984 GGCGAAAAAGTCAACTCCGTTTAT 60.320 41.667 0.00 0.00 0.00 1.40
253 254 3.002553 GGCGAAAAAGTCAACTCCGTTTA 59.997 43.478 0.00 0.00 0.00 2.01
255 256 1.332686 GGCGAAAAAGTCAACTCCGTT 59.667 47.619 0.00 0.00 0.00 4.44
256 257 0.942252 GGCGAAAAAGTCAACTCCGT 59.058 50.000 0.00 0.00 0.00 4.69
258 259 1.333791 CGTGGCGAAAAAGTCAACTCC 60.334 52.381 0.00 0.00 0.00 3.85
259 260 1.329599 ACGTGGCGAAAAAGTCAACTC 59.670 47.619 0.00 0.00 0.00 3.01
262 263 1.329292 CTGACGTGGCGAAAAAGTCAA 59.671 47.619 0.00 0.00 40.68 3.18
263 264 0.934496 CTGACGTGGCGAAAAAGTCA 59.066 50.000 0.00 0.00 39.21 3.41
264 265 0.384353 GCTGACGTGGCGAAAAAGTC 60.384 55.000 0.00 0.00 0.00 3.01
266 267 0.110644 GAGCTGACGTGGCGAAAAAG 60.111 55.000 0.00 0.00 34.52 2.27
267 268 0.531974 AGAGCTGACGTGGCGAAAAA 60.532 50.000 0.00 0.00 34.52 1.94
268 269 1.069090 AGAGCTGACGTGGCGAAAA 59.931 52.632 0.00 0.00 34.52 2.29
269 270 1.664649 CAGAGCTGACGTGGCGAAA 60.665 57.895 0.00 0.00 34.52 3.46
270 271 2.049156 CAGAGCTGACGTGGCGAA 60.049 61.111 0.00 0.00 34.52 4.70
271 272 2.983592 TCAGAGCTGACGTGGCGA 60.984 61.111 0.00 0.00 34.14 5.54
279 280 3.051210 CCCGTGTGTCAGAGCTGA 58.949 61.111 0.00 0.00 37.24 4.26
280 281 2.740055 GCCCGTGTGTCAGAGCTG 60.740 66.667 0.00 0.00 0.00 4.24
281 282 4.008933 GGCCCGTGTGTCAGAGCT 62.009 66.667 0.00 0.00 0.00 4.09
283 284 4.394712 GGGGCCCGTGTGTCAGAG 62.395 72.222 17.79 0.00 0.00 3.35
294 295 0.827507 ATTTATGACATGCGGGGCCC 60.828 55.000 15.76 15.76 0.00 5.80
295 296 1.812571 CTATTTATGACATGCGGGGCC 59.187 52.381 0.00 0.00 0.00 5.80
296 297 1.812571 CCTATTTATGACATGCGGGGC 59.187 52.381 0.00 0.00 0.00 5.80
297 298 3.140325 ACCTATTTATGACATGCGGGG 57.860 47.619 0.00 0.00 0.00 5.73
298 299 6.627395 TTAAACCTATTTATGACATGCGGG 57.373 37.500 0.00 0.00 30.33 6.13
299 300 9.180678 GATTTTAAACCTATTTATGACATGCGG 57.819 33.333 0.00 0.00 30.33 5.69
300 301 9.729023 TGATTTTAAACCTATTTATGACATGCG 57.271 29.630 0.00 0.00 30.33 4.73
314 315 9.634163 GATGACCGTTTTTATGATTTTAAACCT 57.366 29.630 0.00 0.00 0.00 3.50
315 316 9.413048 TGATGACCGTTTTTATGATTTTAAACC 57.587 29.630 0.00 0.00 0.00 3.27
321 322 9.703892 TTGAATTGATGACCGTTTTTATGATTT 57.296 25.926 0.00 0.00 0.00 2.17
323 324 9.874205 AATTGAATTGATGACCGTTTTTATGAT 57.126 25.926 0.00 0.00 0.00 2.45
324 325 9.703892 AAATTGAATTGATGACCGTTTTTATGA 57.296 25.926 0.00 0.00 0.00 2.15
325 326 9.743937 CAAATTGAATTGATGACCGTTTTTATG 57.256 29.630 0.00 0.00 31.84 1.90
326 327 8.934825 CCAAATTGAATTGATGACCGTTTTTAT 58.065 29.630 0.00 0.00 31.84 1.40
327 328 7.928706 ACCAAATTGAATTGATGACCGTTTTTA 59.071 29.630 0.00 0.00 31.84 1.52
328 329 6.765512 ACCAAATTGAATTGATGACCGTTTTT 59.234 30.769 0.00 0.00 31.84 1.94
331 332 5.467035 ACCAAATTGAATTGATGACCGTT 57.533 34.783 0.00 0.00 31.84 4.44
333 334 6.194796 ACTACCAAATTGAATTGATGACCG 57.805 37.500 0.00 0.00 31.84 4.79
334 335 8.831715 AAAACTACCAAATTGAATTGATGACC 57.168 30.769 0.00 0.00 31.84 4.02
369 370 9.939802 ACCGAAAACTTCAGATTAGTACTAATT 57.060 29.630 25.25 14.38 36.02 1.40
370 371 9.583765 GACCGAAAACTTCAGATTAGTACTAAT 57.416 33.333 24.86 24.86 38.38 1.73
371 372 8.579006 TGACCGAAAACTTCAGATTAGTACTAA 58.421 33.333 17.41 17.41 0.00 2.24
372 373 8.025445 GTGACCGAAAACTTCAGATTAGTACTA 58.975 37.037 0.00 0.00 0.00 1.82
373 374 6.867293 GTGACCGAAAACTTCAGATTAGTACT 59.133 38.462 0.00 0.00 0.00 2.73
374 375 6.867293 AGTGACCGAAAACTTCAGATTAGTAC 59.133 38.462 0.00 0.00 0.00 2.73
375 376 6.989659 AGTGACCGAAAACTTCAGATTAGTA 58.010 36.000 0.00 0.00 0.00 1.82
376 377 5.855045 AGTGACCGAAAACTTCAGATTAGT 58.145 37.500 0.00 0.00 0.00 2.24
377 378 6.787085 AAGTGACCGAAAACTTCAGATTAG 57.213 37.500 0.00 0.00 30.87 1.73
378 379 7.562454 AAAAGTGACCGAAAACTTCAGATTA 57.438 32.000 0.00 0.00 35.60 1.75
380 381 6.451064 AAAAAGTGACCGAAAACTTCAGAT 57.549 33.333 0.00 0.00 35.60 2.90
381 382 5.890424 AAAAAGTGACCGAAAACTTCAGA 57.110 34.783 0.00 0.00 35.60 3.27
382 383 7.011828 TCTAAAAAGTGACCGAAAACTTCAG 57.988 36.000 0.00 0.00 35.60 3.02
383 384 6.988622 TCTAAAAAGTGACCGAAAACTTCA 57.011 33.333 0.00 0.00 35.60 3.02
386 387 8.512138 CCATATTCTAAAAAGTGACCGAAAACT 58.488 33.333 0.00 0.00 0.00 2.66
388 389 8.398878 ACCATATTCTAAAAAGTGACCGAAAA 57.601 30.769 0.00 0.00 0.00 2.29
389 390 7.989416 ACCATATTCTAAAAAGTGACCGAAA 57.011 32.000 0.00 0.00 0.00 3.46
390 391 8.316214 ACTACCATATTCTAAAAAGTGACCGAA 58.684 33.333 0.00 0.00 0.00 4.30
391 392 7.844009 ACTACCATATTCTAAAAAGTGACCGA 58.156 34.615 0.00 0.00 0.00 4.69
392 393 8.488651 AACTACCATATTCTAAAAAGTGACCG 57.511 34.615 0.00 0.00 0.00 4.79
393 394 9.668497 AGAACTACCATATTCTAAAAAGTGACC 57.332 33.333 0.00 0.00 33.35 4.02
397 398 9.449719 CCACAGAACTACCATATTCTAAAAAGT 57.550 33.333 0.00 0.00 33.35 2.66
399 400 8.607713 TCCCACAGAACTACCATATTCTAAAAA 58.392 33.333 0.00 0.00 33.35 1.94
400 401 8.044908 GTCCCACAGAACTACCATATTCTAAAA 58.955 37.037 0.00 0.00 33.35 1.52
401 402 7.562135 GTCCCACAGAACTACCATATTCTAAA 58.438 38.462 0.00 0.00 33.35 1.85
402 403 6.183360 CGTCCCACAGAACTACCATATTCTAA 60.183 42.308 0.00 0.00 33.35 2.10
403 404 5.301045 CGTCCCACAGAACTACCATATTCTA 59.699 44.000 0.00 0.00 33.35 2.10
405 406 4.369182 CGTCCCACAGAACTACCATATTC 58.631 47.826 0.00 0.00 0.00 1.75
407 408 2.698797 CCGTCCCACAGAACTACCATAT 59.301 50.000 0.00 0.00 0.00 1.78
408 409 2.104967 CCGTCCCACAGAACTACCATA 58.895 52.381 0.00 0.00 0.00 2.74
410 411 0.470456 ACCGTCCCACAGAACTACCA 60.470 55.000 0.00 0.00 0.00 3.25
411 412 0.037605 CACCGTCCCACAGAACTACC 60.038 60.000 0.00 0.00 0.00 3.18
412 413 0.963962 TCACCGTCCCACAGAACTAC 59.036 55.000 0.00 0.00 0.00 2.73
414 415 0.834612 TTTCACCGTCCCACAGAACT 59.165 50.000 0.00 0.00 0.00 3.01
415 416 1.535462 CATTTCACCGTCCCACAGAAC 59.465 52.381 0.00 0.00 0.00 3.01
416 417 1.418264 TCATTTCACCGTCCCACAGAA 59.582 47.619 0.00 0.00 0.00 3.02
417 418 1.052617 TCATTTCACCGTCCCACAGA 58.947 50.000 0.00 0.00 0.00 3.41
418 419 1.890876 TTCATTTCACCGTCCCACAG 58.109 50.000 0.00 0.00 0.00 3.66
419 420 2.350057 TTTCATTTCACCGTCCCACA 57.650 45.000 0.00 0.00 0.00 4.17
422 423 2.817258 TCACATTTCATTTCACCGTCCC 59.183 45.455 0.00 0.00 0.00 4.46
423 424 4.701956 ATCACATTTCATTTCACCGTCC 57.298 40.909 0.00 0.00 0.00 4.79
424 425 6.422776 ACTATCACATTTCATTTCACCGTC 57.577 37.500 0.00 0.00 0.00 4.79
426 427 8.519492 AAAAACTATCACATTTCATTTCACCG 57.481 30.769 0.00 0.00 0.00 4.94
731 732 6.980577 AGGGATTGTTTCTAATGAATGGGTA 58.019 36.000 0.00 0.00 31.56 3.69
752 753 4.260784 GCAAGTTGATGCGATAGTTTAGGG 60.261 45.833 7.16 0.00 36.45 3.53
871 872 7.611467 GGATGTGCTATATATGTCAAATGGGAA 59.389 37.037 0.00 0.00 0.00 3.97
1694 2639 3.450096 TCATGTCACTCCAGATTCCAGAG 59.550 47.826 0.00 0.24 0.00 3.35
1752 2697 2.563702 CAGGTGCACAAAGCCAAAAAT 58.436 42.857 20.43 0.00 44.83 1.82
1859 2807 7.549842 AGATCTCACTGATATCATATGCAAAGC 59.450 37.037 5.72 0.96 35.14 3.51
1910 2860 9.263538 ACGTACTTCATCATTTAGTTTGTTGTA 57.736 29.630 0.00 0.00 0.00 2.41
1911 2861 8.149973 ACGTACTTCATCATTTAGTTTGTTGT 57.850 30.769 0.00 0.00 0.00 3.32
1953 2903 3.252974 AGGATTAAGCACACGAGGAAG 57.747 47.619 0.00 0.00 0.00 3.46
1956 2906 4.693283 TGATTAGGATTAAGCACACGAGG 58.307 43.478 0.00 0.00 30.69 4.63
1960 2910 7.702348 GGTTCATTTGATTAGGATTAAGCACAC 59.298 37.037 0.00 0.00 35.10 3.82
2149 3116 2.483745 CAAGTGAGGCGCATGCAG 59.516 61.111 19.57 11.69 45.35 4.41
2302 3270 0.881796 CCCGCTCTGGTTTTTCTTCC 59.118 55.000 0.00 0.00 35.15 3.46
2342 3310 0.255890 TGCAGGCCAGGGAAAGATAC 59.744 55.000 5.01 0.00 0.00 2.24
2378 3346 0.107897 CCATACGCTGCAAGGTGGTA 60.108 55.000 0.00 0.00 0.00 3.25
2417 3385 3.067320 GCATCATGGAGTTTCTTTAGGCC 59.933 47.826 0.00 0.00 0.00 5.19
2449 3417 3.243226 GCAACTTGCACAATCAAAAGC 57.757 42.857 8.97 0.00 44.26 3.51
2533 3501 4.323537 CATCGACATGCATCAGCTATTC 57.676 45.455 0.00 0.00 42.74 1.75


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

AutoCloner maintained by Alex Coulton.