Multiple sequence alignment - TraesCS3B01G273300

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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 TraesCS3B01G273300 chr3B 100.000 4529 0 0 1 4529 440251255 440246727 0.000000e+00 8364
1 TraesCS3B01G273300 chr1A 98.501 4204 56 7 1 4202 576125723 576121525 0.000000e+00 7408
2 TraesCS3B01G273300 chr1B 96.968 4387 124 6 1 4384 135945171 135949551 0.000000e+00 7356
3 TraesCS3B01G273300 chr1B 94.954 4479 206 15 1 4469 590050776 590055244 0.000000e+00 7014
4 TraesCS3B01G273300 chr2B 95.883 4542 167 16 1 4529 533470893 533475427 0.000000e+00 7334
5 TraesCS3B01G273300 chr5A 96.049 4480 155 18 1 4469 502103648 502099180 0.000000e+00 7273
6 TraesCS3B01G273300 chr5A 94.825 4541 218 14 1 4529 316934074 316938609 0.000000e+00 7068
7 TraesCS3B01G273300 chr5A 95.939 4334 161 13 1 4324 211479243 211483571 0.000000e+00 7014
8 TraesCS3B01G273300 chr4B 95.438 4537 186 12 1 4529 582604146 582599623 0.000000e+00 7212
9 TraesCS3B01G273300 chr6A 95.399 4542 186 18 1 4529 420970592 420966061 0.000000e+00 7208
10 TraesCS3B01G273300 chr2A 94.459 379 16 5 4154 4529 245752421 245752797 3.040000e-161 579


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 TraesCS3B01G273300 chr3B 440246727 440251255 4528 True 8364 8364 100.000 1 4529 1 chr3B.!!$R1 4528
1 TraesCS3B01G273300 chr1A 576121525 576125723 4198 True 7408 7408 98.501 1 4202 1 chr1A.!!$R1 4201
2 TraesCS3B01G273300 chr1B 135945171 135949551 4380 False 7356 7356 96.968 1 4384 1 chr1B.!!$F1 4383
3 TraesCS3B01G273300 chr1B 590050776 590055244 4468 False 7014 7014 94.954 1 4469 1 chr1B.!!$F2 4468
4 TraesCS3B01G273300 chr2B 533470893 533475427 4534 False 7334 7334 95.883 1 4529 1 chr2B.!!$F1 4528
5 TraesCS3B01G273300 chr5A 502099180 502103648 4468 True 7273 7273 96.049 1 4469 1 chr5A.!!$R1 4468
6 TraesCS3B01G273300 chr5A 316934074 316938609 4535 False 7068 7068 94.825 1 4529 1 chr5A.!!$F2 4528
7 TraesCS3B01G273300 chr5A 211479243 211483571 4328 False 7014 7014 95.939 1 4324 1 chr5A.!!$F1 4323
8 TraesCS3B01G273300 chr4B 582599623 582604146 4523 True 7212 7212 95.438 1 4529 1 chr4B.!!$R1 4528
9 TraesCS3B01G273300 chr6A 420966061 420970592 4531 True 7208 7208 95.399 1 4529 1 chr6A.!!$R1 4528

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
468 469 0.250234 CATGAGCTTTCCCGAGTCCA 59.750 55.000 0.00 0.0 0.00 4.02 F
1316 1323 3.050275 GCCGACTGAAAAGGCGCT 61.050 61.111 7.64 0.0 41.53 5.92 F
1540 1549 0.749049 CACGAGATGGAGGATGCAGA 59.251 55.000 0.00 0.0 42.42 4.26 F
2364 2378 1.063717 CAACAGGATTAGTGGGGGCAT 60.064 52.381 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1360 0.539051 CCTTCATCTTCGGCAGGAGT 59.461 55.000 0.00 0.0 0.00 3.85 R
3150 3164 1.153939 GACAGCTGCGACACGAGAT 60.154 57.895 15.27 0.0 0.00 2.75 R
3351 3365 1.800805 CATCTTTGCAGTGGACTCGT 58.199 50.000 0.00 0.0 0.00 4.18 R
4317 5309 0.036952 TAGCTGCAGTCCAAGCACTC 60.037 55.000 16.64 0.0 37.02 3.51 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
305 306 1.971695 GGGTTTCTTGGGCTGTCGG 60.972 63.158 0.00 0.00 0.00 4.79
468 469 0.250234 CATGAGCTTTCCCGAGTCCA 59.750 55.000 0.00 0.00 0.00 4.02
1316 1323 3.050275 GCCGACTGAAAAGGCGCT 61.050 61.111 7.64 0.00 41.53 5.92
1353 1360 1.301401 CTCACCGAAGCCGACCAAA 60.301 57.895 0.00 0.00 38.22 3.28
1540 1549 0.749049 CACGAGATGGAGGATGCAGA 59.251 55.000 0.00 0.00 42.42 4.26
1756 1765 3.149196 GCCTGAAATTCTGACTGTGGAA 58.851 45.455 1.26 0.00 0.00 3.53
2279 2288 1.736126 CGACTGCTTGCAGTTGATCAT 59.264 47.619 29.32 8.03 38.54 2.45
2364 2378 1.063717 CAACAGGATTAGTGGGGGCAT 60.064 52.381 0.00 0.00 0.00 4.40
2872 2886 1.133976 ACTGACAAAGCTGCCTTGACT 60.134 47.619 17.27 0.00 0.00 3.41
2908 2922 6.636044 GCAAATTGACTGAGAAGAAAACTGAG 59.364 38.462 0.00 0.00 0.00 3.35
3351 3365 1.820010 ATGTCGCTCTGTGTCTGGCA 61.820 55.000 0.00 0.00 0.00 4.92
3481 3495 4.120085 GGATCGCCGACGGAATTT 57.880 55.556 20.50 0.00 40.63 1.82
4163 5155 6.057321 ACCACTCGGTAGGATTTTGATAAA 57.943 37.500 0.00 0.00 46.71 1.40
4164 5156 5.878669 ACCACTCGGTAGGATTTTGATAAAC 59.121 40.000 0.00 0.00 46.71 2.01
4165 5157 6.113411 CCACTCGGTAGGATTTTGATAAACT 58.887 40.000 0.00 0.00 0.00 2.66
4166 5158 6.598064 CCACTCGGTAGGATTTTGATAAACTT 59.402 38.462 0.00 0.00 0.00 2.66
4167 5159 7.767198 CCACTCGGTAGGATTTTGATAAACTTA 59.233 37.037 0.00 0.00 0.00 2.24
4168 5160 8.818057 CACTCGGTAGGATTTTGATAAACTTAG 58.182 37.037 0.00 0.00 0.00 2.18
4169 5161 7.985752 ACTCGGTAGGATTTTGATAAACTTAGG 59.014 37.037 0.00 0.00 0.00 2.69
4170 5162 6.764560 TCGGTAGGATTTTGATAAACTTAGGC 59.235 38.462 0.00 0.00 0.00 3.93
4171 5163 6.292703 CGGTAGGATTTTGATAAACTTAGGCG 60.293 42.308 0.00 0.00 0.00 5.52
4172 5164 6.764560 GGTAGGATTTTGATAAACTTAGGCGA 59.235 38.462 0.00 0.00 0.00 5.54
4173 5165 7.281549 GGTAGGATTTTGATAAACTTAGGCGAA 59.718 37.037 0.00 0.00 0.00 4.70
4174 5166 7.085052 AGGATTTTGATAAACTTAGGCGAAC 57.915 36.000 0.00 0.00 0.00 3.95
4175 5167 6.657541 AGGATTTTGATAAACTTAGGCGAACA 59.342 34.615 0.00 0.00 0.00 3.18
4176 5168 6.745907 GGATTTTGATAAACTTAGGCGAACAC 59.254 38.462 0.00 0.00 0.00 3.32
4177 5169 4.914312 TTGATAAACTTAGGCGAACACG 57.086 40.909 0.00 0.00 0.00 4.49
4178 5170 4.177165 TGATAAACTTAGGCGAACACGA 57.823 40.909 0.00 0.00 0.00 4.35
4179 5171 4.558178 TGATAAACTTAGGCGAACACGAA 58.442 39.130 0.00 0.00 0.00 3.85
4180 5172 4.624024 TGATAAACTTAGGCGAACACGAAG 59.376 41.667 0.00 0.00 0.00 3.79
4181 5173 1.145803 AACTTAGGCGAACACGAAGC 58.854 50.000 0.00 0.00 0.00 3.86
4182 5174 0.317479 ACTTAGGCGAACACGAAGCT 59.683 50.000 0.00 0.00 0.00 3.74
4183 5175 0.716108 CTTAGGCGAACACGAAGCTG 59.284 55.000 0.00 0.00 0.00 4.24
4184 5176 1.289109 TTAGGCGAACACGAAGCTGC 61.289 55.000 0.00 0.00 0.00 5.25
4185 5177 2.428960 TAGGCGAACACGAAGCTGCA 62.429 55.000 1.02 0.00 0.00 4.41
4186 5178 2.171940 GCGAACACGAAGCTGCAG 59.828 61.111 10.11 10.11 0.00 4.41
4187 5179 2.171940 CGAACACGAAGCTGCAGC 59.828 61.111 31.53 31.53 42.49 5.25
4198 5190 3.785859 CTGCAGCTAAGCCCCCGA 61.786 66.667 0.00 0.00 0.00 5.14
4199 5191 3.746949 CTGCAGCTAAGCCCCCGAG 62.747 68.421 0.00 0.00 0.00 4.63
4200 5192 3.787001 GCAGCTAAGCCCCCGAGT 61.787 66.667 0.00 0.00 0.00 4.18
4201 5193 2.187946 CAGCTAAGCCCCCGAGTG 59.812 66.667 0.00 0.00 0.00 3.51
4202 5194 2.038975 AGCTAAGCCCCCGAGTGA 59.961 61.111 0.00 0.00 0.00 3.41
4203 5195 2.060980 AGCTAAGCCCCCGAGTGAG 61.061 63.158 0.00 0.00 0.00 3.51
4204 5196 2.058595 GCTAAGCCCCCGAGTGAGA 61.059 63.158 0.00 0.00 0.00 3.27
4205 5197 2.022240 GCTAAGCCCCCGAGTGAGAG 62.022 65.000 0.00 0.00 0.00 3.20
4206 5198 1.381327 TAAGCCCCCGAGTGAGAGG 60.381 63.158 0.00 0.00 0.00 3.69
4207 5199 1.870941 TAAGCCCCCGAGTGAGAGGA 61.871 60.000 0.00 0.00 0.00 3.71
4208 5200 2.444895 GCCCCCGAGTGAGAGGAT 60.445 66.667 0.00 0.00 0.00 3.24
4209 5201 2.066999 GCCCCCGAGTGAGAGGATT 61.067 63.158 0.00 0.00 0.00 3.01
4210 5202 1.826024 CCCCCGAGTGAGAGGATTG 59.174 63.158 0.00 0.00 0.00 2.67
4211 5203 1.144936 CCCCGAGTGAGAGGATTGC 59.855 63.158 0.00 0.00 0.00 3.56
4212 5204 1.333636 CCCCGAGTGAGAGGATTGCT 61.334 60.000 0.00 0.00 0.00 3.91
4213 5205 0.103937 CCCGAGTGAGAGGATTGCTC 59.896 60.000 0.00 0.00 0.00 4.26
4214 5206 1.110442 CCGAGTGAGAGGATTGCTCT 58.890 55.000 7.50 7.50 33.57 4.09
4215 5207 1.480137 CCGAGTGAGAGGATTGCTCTT 59.520 52.381 9.24 0.00 33.57 2.85
4216 5208 2.481104 CCGAGTGAGAGGATTGCTCTTC 60.481 54.545 9.24 6.25 33.57 2.87
4217 5209 2.165234 CGAGTGAGAGGATTGCTCTTCA 59.835 50.000 9.24 6.26 33.57 3.02
4218 5210 3.520569 GAGTGAGAGGATTGCTCTTCAC 58.479 50.000 19.99 19.99 33.44 3.18
4219 5211 3.172339 AGTGAGAGGATTGCTCTTCACT 58.828 45.455 22.41 22.41 36.02 3.41
4220 5212 3.195396 AGTGAGAGGATTGCTCTTCACTC 59.805 47.826 22.41 8.59 36.02 3.51
4221 5213 2.165234 TGAGAGGATTGCTCTTCACTCG 59.835 50.000 9.24 0.00 33.57 4.18
4222 5214 1.480137 AGAGGATTGCTCTTCACTCGG 59.520 52.381 1.25 0.00 30.11 4.63
4223 5215 1.205893 GAGGATTGCTCTTCACTCGGT 59.794 52.381 0.00 0.00 0.00 4.69
4224 5216 2.427453 GAGGATTGCTCTTCACTCGGTA 59.573 50.000 0.00 0.00 0.00 4.02
4225 5217 2.428890 AGGATTGCTCTTCACTCGGTAG 59.571 50.000 0.00 0.00 0.00 3.18
4226 5218 2.482142 GGATTGCTCTTCACTCGGTAGG 60.482 54.545 0.00 0.00 0.00 3.18
4227 5219 1.919240 TTGCTCTTCACTCGGTAGGA 58.081 50.000 0.00 0.00 0.00 2.94
4228 5220 2.145397 TGCTCTTCACTCGGTAGGAT 57.855 50.000 0.00 0.00 0.00 3.24
4229 5221 2.457598 TGCTCTTCACTCGGTAGGATT 58.542 47.619 0.00 0.00 0.00 3.01
4230 5222 2.832129 TGCTCTTCACTCGGTAGGATTT 59.168 45.455 0.00 0.00 0.00 2.17
4231 5223 3.260884 TGCTCTTCACTCGGTAGGATTTT 59.739 43.478 0.00 0.00 0.00 1.82
4232 5224 4.254492 GCTCTTCACTCGGTAGGATTTTT 58.746 43.478 0.00 0.00 0.00 1.94
4233 5225 5.046878 TGCTCTTCACTCGGTAGGATTTTTA 60.047 40.000 0.00 0.00 0.00 1.52
4234 5226 6.049790 GCTCTTCACTCGGTAGGATTTTTAT 58.950 40.000 0.00 0.00 0.00 1.40
4235 5227 7.147794 TGCTCTTCACTCGGTAGGATTTTTATA 60.148 37.037 0.00 0.00 0.00 0.98
4236 5228 7.709613 GCTCTTCACTCGGTAGGATTTTTATAA 59.290 37.037 0.00 0.00 0.00 0.98
4237 5229 8.937634 TCTTCACTCGGTAGGATTTTTATAAC 57.062 34.615 0.00 0.00 0.00 1.89
4238 5230 8.755977 TCTTCACTCGGTAGGATTTTTATAACT 58.244 33.333 0.00 0.00 0.00 2.24
4239 5231 9.379791 CTTCACTCGGTAGGATTTTTATAACTT 57.620 33.333 0.00 0.00 0.00 2.66
4242 5234 9.257651 CACTCGGTAGGATTTTTATAACTTAGG 57.742 37.037 0.00 0.00 0.00 2.69
4243 5235 7.930325 ACTCGGTAGGATTTTTATAACTTAGGC 59.070 37.037 0.00 0.00 0.00 3.93
4244 5236 6.925165 TCGGTAGGATTTTTATAACTTAGGCG 59.075 38.462 0.00 0.00 0.00 5.52
4245 5237 6.925165 CGGTAGGATTTTTATAACTTAGGCGA 59.075 38.462 0.00 0.00 0.00 5.54
4246 5238 7.115947 CGGTAGGATTTTTATAACTTAGGCGAG 59.884 40.741 0.00 0.00 0.00 5.03
4247 5239 6.862711 AGGATTTTTATAACTTAGGCGAGC 57.137 37.500 0.00 0.00 0.00 5.03
4248 5240 6.354130 AGGATTTTTATAACTTAGGCGAGCA 58.646 36.000 0.00 0.00 0.00 4.26
4249 5241 6.260271 AGGATTTTTATAACTTAGGCGAGCAC 59.740 38.462 0.00 0.00 0.00 4.40
4250 5242 5.459110 TTTTTATAACTTAGGCGAGCACG 57.541 39.130 0.00 0.00 42.93 5.34
4251 5243 4.374843 TTTATAACTTAGGCGAGCACGA 57.625 40.909 8.01 0.00 42.66 4.35
4252 5244 2.493713 ATAACTTAGGCGAGCACGAG 57.506 50.000 8.01 0.00 42.66 4.18
4253 5245 0.454600 TAACTTAGGCGAGCACGAGG 59.545 55.000 8.01 0.00 42.66 4.63
4254 5246 1.533469 AACTTAGGCGAGCACGAGGT 61.533 55.000 8.01 0.00 42.66 3.85
4255 5247 1.226717 CTTAGGCGAGCACGAGGTC 60.227 63.158 8.01 1.65 42.66 3.85
4262 5254 3.062466 AGCACGAGGTCGCAGCTA 61.062 61.111 15.66 0.00 46.86 3.32
4263 5255 2.126071 GCACGAGGTCGCAGCTAA 60.126 61.111 9.41 0.00 44.43 3.09
4264 5256 2.161486 GCACGAGGTCGCAGCTAAG 61.161 63.158 9.41 0.00 44.43 2.18
4265 5257 2.161486 CACGAGGTCGCAGCTAAGC 61.161 63.158 0.00 0.00 44.43 3.09
4266 5258 2.583593 CGAGGTCGCAGCTAAGCC 60.584 66.667 0.00 0.00 0.00 4.35
4267 5259 2.896443 GAGGTCGCAGCTAAGCCT 59.104 61.111 0.00 0.00 0.00 4.58
4268 5260 1.227118 GAGGTCGCAGCTAAGCCTC 60.227 63.158 9.16 9.16 38.89 4.70
4269 5261 2.202946 GGTCGCAGCTAAGCCTCC 60.203 66.667 0.00 0.00 0.00 4.30
4270 5262 2.583593 GTCGCAGCTAAGCCTCCG 60.584 66.667 0.00 0.00 0.00 4.63
4271 5263 2.754254 TCGCAGCTAAGCCTCCGA 60.754 61.111 0.00 0.00 0.00 4.55
4272 5264 2.279120 CGCAGCTAAGCCTCCGAG 60.279 66.667 0.00 0.00 0.00 4.63
4273 5265 2.896443 GCAGCTAAGCCTCCGAGT 59.104 61.111 0.00 0.00 0.00 4.18
4274 5266 1.520342 GCAGCTAAGCCTCCGAGTG 60.520 63.158 0.00 0.00 0.00 3.51
4275 5267 1.142748 CAGCTAAGCCTCCGAGTGG 59.857 63.158 0.00 0.00 0.00 4.00
4276 5268 1.000486 AGCTAAGCCTCCGAGTGGA 60.000 57.895 0.00 0.00 43.88 4.02
4277 5269 0.614979 AGCTAAGCCTCCGAGTGGAA 60.615 55.000 0.00 0.00 45.87 3.53
4278 5270 0.179097 GCTAAGCCTCCGAGTGGAAG 60.179 60.000 0.00 0.00 45.87 3.46
4279 5271 0.461961 CTAAGCCTCCGAGTGGAAGG 59.538 60.000 0.00 0.00 45.87 3.46
4281 5273 3.394836 GCCTCCGAGTGGAAGGCT 61.395 66.667 13.91 0.00 46.55 4.58
4282 5274 2.581354 CCTCCGAGTGGAAGGCTG 59.419 66.667 0.00 0.00 45.87 4.85
4283 5275 2.581354 CTCCGAGTGGAAGGCTGG 59.419 66.667 0.00 0.00 45.87 4.85
4284 5276 3.672295 CTCCGAGTGGAAGGCTGGC 62.672 68.421 0.00 0.00 45.87 4.85
4285 5277 3.710722 CCGAGTGGAAGGCTGGCT 61.711 66.667 0.00 0.00 37.49 4.75
4286 5278 2.348998 CGAGTGGAAGGCTGGCTT 59.651 61.111 17.01 17.01 0.00 4.35
4287 5279 1.596934 CGAGTGGAAGGCTGGCTTA 59.403 57.895 17.01 0.00 0.00 3.09
4288 5280 0.741221 CGAGTGGAAGGCTGGCTTAC 60.741 60.000 18.59 18.59 0.00 2.34
4289 5281 0.393132 GAGTGGAAGGCTGGCTTACC 60.393 60.000 21.93 20.07 0.00 2.85
4290 5282 1.133809 AGTGGAAGGCTGGCTTACCA 61.134 55.000 21.93 22.01 46.51 3.25
4291 5283 0.960861 GTGGAAGGCTGGCTTACCAC 60.961 60.000 30.16 30.16 42.67 4.16
4292 5284 1.133809 TGGAAGGCTGGCTTACCACT 61.134 55.000 21.93 0.00 42.67 4.00
4293 5285 0.393132 GGAAGGCTGGCTTACCACTC 60.393 60.000 17.01 3.10 42.67 3.51
4294 5286 0.741221 GAAGGCTGGCTTACCACTCG 60.741 60.000 17.01 0.00 42.67 4.18
4295 5287 2.125106 GGCTGGCTTACCACTCGG 60.125 66.667 0.00 0.00 42.67 4.63
4297 5289 1.610554 GGCTGGCTTACCACTCGGTA 61.611 60.000 0.00 0.00 46.71 4.02
4307 5299 3.329929 ACCACTCGGTAGGATTTTCAC 57.670 47.619 0.00 0.00 46.71 3.18
4308 5300 2.635915 ACCACTCGGTAGGATTTTCACA 59.364 45.455 0.00 0.00 46.71 3.58
4309 5301 3.071892 ACCACTCGGTAGGATTTTCACAA 59.928 43.478 0.00 0.00 46.71 3.33
4310 5302 3.435671 CCACTCGGTAGGATTTTCACAAC 59.564 47.826 0.00 0.00 0.00 3.32
4311 5303 4.315803 CACTCGGTAGGATTTTCACAACT 58.684 43.478 0.00 0.00 0.00 3.16
4312 5304 4.755123 CACTCGGTAGGATTTTCACAACTT 59.245 41.667 0.00 0.00 0.00 2.66
4313 5305 5.929992 CACTCGGTAGGATTTTCACAACTTA 59.070 40.000 0.00 0.00 0.00 2.24
4314 5306 6.090898 CACTCGGTAGGATTTTCACAACTTAG 59.909 42.308 0.00 0.00 0.00 2.18
4315 5307 5.484715 TCGGTAGGATTTTCACAACTTAGG 58.515 41.667 0.00 0.00 0.00 2.69
4316 5308 5.012354 TCGGTAGGATTTTCACAACTTAGGT 59.988 40.000 0.00 0.00 0.00 3.08
4317 5309 5.121768 CGGTAGGATTTTCACAACTTAGGTG 59.878 44.000 0.00 0.00 37.60 4.00
4318 5310 6.235664 GGTAGGATTTTCACAACTTAGGTGA 58.764 40.000 3.50 0.00 43.12 4.02
4319 5311 6.371825 GGTAGGATTTTCACAACTTAGGTGAG 59.628 42.308 3.50 0.00 45.20 3.51
4320 5312 5.941788 AGGATTTTCACAACTTAGGTGAGT 58.058 37.500 3.50 0.00 45.20 3.41
4321 5313 5.765182 AGGATTTTCACAACTTAGGTGAGTG 59.235 40.000 3.50 4.93 45.20 3.51
4322 5314 4.893424 TTTTCACAACTTAGGTGAGTGC 57.107 40.909 3.50 0.00 45.20 4.40
4323 5315 3.838244 TTCACAACTTAGGTGAGTGCT 57.162 42.857 3.50 0.00 45.20 4.40
4324 5316 3.838244 TCACAACTTAGGTGAGTGCTT 57.162 42.857 3.50 0.00 40.16 3.91
4325 5317 3.466836 TCACAACTTAGGTGAGTGCTTG 58.533 45.455 3.50 0.00 40.16 4.01
4326 5318 2.549754 CACAACTTAGGTGAGTGCTTGG 59.450 50.000 3.50 0.00 38.54 3.61
4327 5319 2.438021 ACAACTTAGGTGAGTGCTTGGA 59.562 45.455 3.50 0.00 0.00 3.53
4328 5320 2.808543 CAACTTAGGTGAGTGCTTGGAC 59.191 50.000 0.00 0.00 0.00 4.02
4329 5321 2.330216 ACTTAGGTGAGTGCTTGGACT 58.670 47.619 0.00 0.00 0.00 3.85
4330 5322 2.037772 ACTTAGGTGAGTGCTTGGACTG 59.962 50.000 0.00 0.00 0.00 3.51
4331 5323 0.321671 TAGGTGAGTGCTTGGACTGC 59.678 55.000 0.00 0.00 0.00 4.40
4332 5324 1.227943 GGTGAGTGCTTGGACTGCA 60.228 57.895 0.00 0.00 38.19 4.41
4333 5325 1.233285 GGTGAGTGCTTGGACTGCAG 61.233 60.000 13.48 13.48 41.41 4.41
4334 5326 1.598962 TGAGTGCTTGGACTGCAGC 60.599 57.895 15.27 6.61 41.41 5.25
4335 5327 1.302351 GAGTGCTTGGACTGCAGCT 60.302 57.895 15.27 0.23 41.41 4.24
4336 5328 0.036952 GAGTGCTTGGACTGCAGCTA 60.037 55.000 15.27 1.42 41.41 3.32
4337 5329 0.397941 AGTGCTTGGACTGCAGCTAA 59.602 50.000 15.27 9.98 41.41 3.09
4338 5330 0.801251 GTGCTTGGACTGCAGCTAAG 59.199 55.000 21.43 21.43 41.41 2.18
4339 5331 0.957395 TGCTTGGACTGCAGCTAAGC 60.957 55.000 32.25 32.25 42.92 3.09
4340 5332 1.652167 GCTTGGACTGCAGCTAAGCC 61.652 60.000 30.56 19.28 38.17 4.35
4341 5333 1.002134 TTGGACTGCAGCTAAGCCC 60.002 57.895 15.27 6.29 0.00 5.19
4342 5334 2.124529 GGACTGCAGCTAAGCCCC 60.125 66.667 15.27 0.00 0.00 5.80
4343 5335 2.124529 GACTGCAGCTAAGCCCCC 60.125 66.667 15.27 0.00 0.00 5.40
4344 5336 4.101448 ACTGCAGCTAAGCCCCCG 62.101 66.667 15.27 0.00 0.00 5.73
4345 5337 3.785859 CTGCAGCTAAGCCCCCGA 61.786 66.667 0.00 0.00 0.00 5.14
4346 5338 3.326578 TGCAGCTAAGCCCCCGAA 61.327 61.111 0.00 0.00 0.00 4.30
4347 5339 2.193248 GCAGCTAAGCCCCCGAAT 59.807 61.111 0.00 0.00 0.00 3.34
4348 5340 2.189499 GCAGCTAAGCCCCCGAATG 61.189 63.158 0.00 0.00 0.00 2.67
4349 5341 1.526917 CAGCTAAGCCCCCGAATGG 60.527 63.158 0.00 0.00 0.00 3.16
4350 5342 1.692749 AGCTAAGCCCCCGAATGGA 60.693 57.895 0.00 0.00 37.49 3.41
4351 5343 1.226262 GCTAAGCCCCCGAATGGAA 59.774 57.895 0.00 0.00 37.49 3.53
4352 5344 0.819666 GCTAAGCCCCCGAATGGAAG 60.820 60.000 0.00 0.00 37.49 3.46
4353 5345 0.179018 CTAAGCCCCCGAATGGAAGG 60.179 60.000 0.00 0.00 37.49 3.46
4355 5347 4.129148 GCCCCCGAATGGAAGGCT 62.129 66.667 7.76 0.00 45.87 4.58
4356 5348 2.124151 CCCCCGAATGGAAGGCTG 60.124 66.667 0.00 0.00 37.49 4.85
4357 5349 2.124151 CCCCGAATGGAAGGCTGG 60.124 66.667 0.00 0.00 37.49 4.85
4358 5350 2.830370 CCCGAATGGAAGGCTGGC 60.830 66.667 0.00 0.00 37.49 4.85
4359 5351 2.273449 CCGAATGGAAGGCTGGCT 59.727 61.111 0.00 0.00 37.49 4.75
4360 5352 1.379044 CCGAATGGAAGGCTGGCTT 60.379 57.895 17.01 17.01 37.49 4.35
4361 5353 0.107214 CCGAATGGAAGGCTGGCTTA 60.107 55.000 17.01 2.43 37.49 3.09
4362 5354 1.017387 CGAATGGAAGGCTGGCTTAC 58.983 55.000 18.59 18.59 0.00 2.34
4363 5355 1.393603 GAATGGAAGGCTGGCTTACC 58.606 55.000 21.93 20.07 0.00 2.85
4364 5356 0.704076 AATGGAAGGCTGGCTTACCA 59.296 50.000 25.44 25.44 46.51 3.25
4365 5357 0.034089 ATGGAAGGCTGGCTTACCAC 60.034 55.000 25.62 14.87 42.67 4.16
4366 5358 1.133809 TGGAAGGCTGGCTTACCACT 61.134 55.000 21.93 0.00 42.67 4.00
4367 5359 0.393132 GGAAGGCTGGCTTACCACTC 60.393 60.000 17.01 3.10 42.67 3.51
4368 5360 0.741221 GAAGGCTGGCTTACCACTCG 60.741 60.000 17.01 0.00 42.67 4.18
4369 5361 2.125106 GGCTGGCTTACCACTCGG 60.125 66.667 0.00 0.00 42.67 4.63
4371 5363 1.610554 GGCTGGCTTACCACTCGGTA 61.611 60.000 0.00 0.00 46.71 4.02
4383 5375 5.687166 ACCACTCGGTAGGATTTTGATAA 57.313 39.130 0.00 0.00 46.71 1.75
4384 5376 6.057321 ACCACTCGGTAGGATTTTGATAAA 57.943 37.500 0.00 0.00 46.71 1.40
4385 5377 5.878669 ACCACTCGGTAGGATTTTGATAAAC 59.121 40.000 0.00 0.00 46.71 2.01
4386 5378 6.113411 CCACTCGGTAGGATTTTGATAAACT 58.887 40.000 0.00 0.00 0.00 2.66
4387 5379 6.598064 CCACTCGGTAGGATTTTGATAAACTT 59.402 38.462 0.00 0.00 0.00 2.66
4388 5380 7.767198 CCACTCGGTAGGATTTTGATAAACTTA 59.233 37.037 0.00 0.00 0.00 2.24
4389 5381 8.818057 CACTCGGTAGGATTTTGATAAACTTAG 58.182 37.037 0.00 0.00 0.00 2.18
4390 5382 7.985752 ACTCGGTAGGATTTTGATAAACTTAGG 59.014 37.037 0.00 0.00 0.00 2.69
4391 5383 6.764560 TCGGTAGGATTTTGATAAACTTAGGC 59.235 38.462 0.00 0.00 0.00 3.93
4392 5384 6.292703 CGGTAGGATTTTGATAAACTTAGGCG 60.293 42.308 0.00 0.00 0.00 5.52
4393 5385 6.764560 GGTAGGATTTTGATAAACTTAGGCGA 59.235 38.462 0.00 0.00 0.00 5.54
4394 5386 6.927294 AGGATTTTGATAAACTTAGGCGAG 57.073 37.500 0.00 0.00 0.00 5.03
4395 5387 6.415573 AGGATTTTGATAAACTTAGGCGAGT 58.584 36.000 0.00 0.00 0.00 4.18
4396 5388 6.539103 AGGATTTTGATAAACTTAGGCGAGTC 59.461 38.462 0.00 0.00 0.00 3.36
4397 5389 6.238402 GGATTTTGATAAACTTAGGCGAGTCC 60.238 42.308 0.00 0.00 0.00 3.85
4399 5391 5.416271 TTGATAAACTTAGGCGAGTCCTT 57.584 39.130 0.00 0.00 44.75 3.36
4400 5392 6.534475 TTGATAAACTTAGGCGAGTCCTTA 57.466 37.500 0.00 0.00 44.75 2.69
4401 5393 6.145338 TGATAAACTTAGGCGAGTCCTTAG 57.855 41.667 0.00 0.00 44.75 2.18
4402 5394 5.889853 TGATAAACTTAGGCGAGTCCTTAGA 59.110 40.000 4.24 0.00 44.75 2.10
4403 5395 4.453177 AAACTTAGGCGAGTCCTTAGAC 57.547 45.455 4.24 0.00 44.75 2.59
4414 5406 2.545731 GTCCTTAGACTGCAGCTAAGC 58.454 52.381 31.48 22.72 42.08 3.09
4415 5407 1.482593 TCCTTAGACTGCAGCTAAGCC 59.517 52.381 31.48 12.70 42.08 4.35
4416 5408 1.484240 CCTTAGACTGCAGCTAAGCCT 59.516 52.381 31.48 17.32 42.08 4.58
4417 5409 2.482839 CCTTAGACTGCAGCTAAGCCTC 60.483 54.545 31.48 16.96 42.08 4.70
4418 5410 1.115467 TAGACTGCAGCTAAGCCTCC 58.885 55.000 15.27 0.00 0.00 4.30
4419 5411 1.520342 GACTGCAGCTAAGCCTCCG 60.520 63.158 15.27 0.00 0.00 4.63
4420 5412 1.949847 GACTGCAGCTAAGCCTCCGA 61.950 60.000 15.27 0.00 0.00 4.55
4421 5413 1.227205 CTGCAGCTAAGCCTCCGAG 60.227 63.158 0.00 0.00 0.00 4.63
4422 5414 1.954362 CTGCAGCTAAGCCTCCGAGT 61.954 60.000 0.00 0.00 0.00 4.18
4423 5415 1.520342 GCAGCTAAGCCTCCGAGTG 60.520 63.158 0.00 0.00 0.00 3.51
4424 5416 1.142748 CAGCTAAGCCTCCGAGTGG 59.857 63.158 0.00 0.00 0.00 4.00
4425 5417 1.000486 AGCTAAGCCTCCGAGTGGA 60.000 57.895 0.00 0.00 43.88 4.02
4426 5418 0.614979 AGCTAAGCCTCCGAGTGGAA 60.615 55.000 0.00 0.00 45.87 3.53
4427 5419 0.179097 GCTAAGCCTCCGAGTGGAAG 60.179 60.000 0.00 0.00 45.87 3.46
4428 5420 0.461961 CTAAGCCTCCGAGTGGAAGG 59.538 60.000 0.00 0.00 45.87 3.46
4430 5422 3.394836 GCCTCCGAGTGGAAGGCT 61.395 66.667 13.91 0.00 46.55 4.58
4431 5423 2.581354 CCTCCGAGTGGAAGGCTG 59.419 66.667 0.00 0.00 45.87 4.85
4432 5424 2.581354 CTCCGAGTGGAAGGCTGG 59.419 66.667 0.00 0.00 45.87 4.85
4433 5425 3.672295 CTCCGAGTGGAAGGCTGGC 62.672 68.421 0.00 0.00 45.87 4.85
4434 5426 3.710722 CCGAGTGGAAGGCTGGCT 61.711 66.667 0.00 0.00 37.49 4.75
4435 5427 2.348998 CGAGTGGAAGGCTGGCTT 59.651 61.111 17.01 17.01 0.00 4.35
4436 5428 1.596934 CGAGTGGAAGGCTGGCTTA 59.403 57.895 17.01 0.00 0.00 3.09
4437 5429 0.741221 CGAGTGGAAGGCTGGCTTAC 60.741 60.000 18.59 18.59 0.00 2.34
4438 5430 0.393132 GAGTGGAAGGCTGGCTTACC 60.393 60.000 21.93 20.07 0.00 2.85
4439 5431 1.133809 AGTGGAAGGCTGGCTTACCA 61.134 55.000 21.93 22.01 46.51 3.25
4440 5432 0.960861 GTGGAAGGCTGGCTTACCAC 60.961 60.000 30.16 30.16 42.67 4.16
4441 5433 1.133809 TGGAAGGCTGGCTTACCACT 61.134 55.000 21.93 0.00 42.67 4.00
4442 5434 0.393132 GGAAGGCTGGCTTACCACTC 60.393 60.000 17.01 3.10 42.67 3.51
4443 5435 0.741221 GAAGGCTGGCTTACCACTCG 60.741 60.000 17.01 0.00 42.67 4.18
4444 5436 2.125106 GGCTGGCTTACCACTCGG 60.125 66.667 0.00 0.00 42.67 4.63
4446 5438 1.610554 GGCTGGCTTACCACTCGGTA 61.611 60.000 0.00 0.00 46.71 4.02
4458 5450 5.687166 ACCACTCGGTAGGATTTTGATAA 57.313 39.130 0.00 0.00 46.71 1.75
4499 5564 2.284699 AGCTAAGCCCCCGAGTGT 60.285 61.111 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 306 3.207547 GAACAAACCCCAGTGCGGC 62.208 63.158 0.00 0.00 0.00 6.53
468 469 1.683707 TCGACTGCCAGCCTCTGAT 60.684 57.895 0.00 0.00 32.44 2.90
895 896 4.154347 GACTCAGCGGAGGGCAGG 62.154 72.222 18.37 0.00 45.81 4.85
905 906 3.232213 TGAATACGACAAGGACTCAGC 57.768 47.619 0.00 0.00 0.00 4.26
1339 1346 2.033194 GGAGTTTGGTCGGCTTCGG 61.033 63.158 0.00 0.00 34.13 4.30
1353 1360 0.539051 CCTTCATCTTCGGCAGGAGT 59.461 55.000 0.00 0.00 0.00 3.85
1490 1499 1.216710 GGCCGAGGTCTCAGAAGTG 59.783 63.158 0.00 0.00 0.00 3.16
1540 1549 4.202326 ACACAGTACCTGGATTCGAAGTTT 60.202 41.667 3.35 0.00 35.51 2.66
1756 1765 2.034812 GTGTCGAGTGGTGTTCTCTTCT 59.965 50.000 0.00 0.00 0.00 2.85
2872 2886 3.988379 GTCAATTTGCTGACTTGGTCA 57.012 42.857 0.43 0.43 42.11 4.02
2971 2985 5.757808 ACAGTTGGAAATATTTGCCAAACAC 59.242 36.000 22.68 15.98 42.77 3.32
3150 3164 1.153939 GACAGCTGCGACACGAGAT 60.154 57.895 15.27 0.00 0.00 2.75
3351 3365 1.800805 CATCTTTGCAGTGGACTCGT 58.199 50.000 0.00 0.00 0.00 4.18
3481 3495 3.438781 GGTGCAACGAATTCATCAAGGTA 59.561 43.478 6.22 0.00 38.12 3.08
3544 3558 5.063880 ACTGAGGCAAATTTAAAGAGTCGT 58.936 37.500 0.00 0.00 0.00 4.34
4163 5155 0.317479 AGCTTCGTGTTCGCCTAAGT 59.683 50.000 0.00 0.00 36.96 2.24
4164 5156 0.716108 CAGCTTCGTGTTCGCCTAAG 59.284 55.000 0.00 0.00 36.96 2.18
4165 5157 1.289109 GCAGCTTCGTGTTCGCCTAA 61.289 55.000 0.00 0.00 36.96 2.69
4166 5158 1.736645 GCAGCTTCGTGTTCGCCTA 60.737 57.895 0.00 0.00 36.96 3.93
4167 5159 3.044305 GCAGCTTCGTGTTCGCCT 61.044 61.111 0.00 0.00 36.96 5.52
4168 5160 3.300667 CTGCAGCTTCGTGTTCGCC 62.301 63.158 0.00 0.00 36.96 5.54
4169 5161 2.171940 CTGCAGCTTCGTGTTCGC 59.828 61.111 0.00 0.00 36.96 4.70
4170 5162 2.171940 GCTGCAGCTTCGTGTTCG 59.828 61.111 31.33 0.00 38.21 3.95
4181 5173 3.746949 CTCGGGGGCTTAGCTGCAG 62.747 68.421 10.11 10.11 34.04 4.41
4182 5174 3.785859 CTCGGGGGCTTAGCTGCA 61.786 66.667 3.59 0.00 34.04 4.41
4183 5175 3.787001 ACTCGGGGGCTTAGCTGC 61.787 66.667 3.59 0.00 0.00 5.25
4184 5176 2.187946 CACTCGGGGGCTTAGCTG 59.812 66.667 3.59 0.00 0.00 4.24
4185 5177 2.038975 TCACTCGGGGGCTTAGCT 59.961 61.111 3.59 0.00 0.00 3.32
4186 5178 2.022240 CTCTCACTCGGGGGCTTAGC 62.022 65.000 0.00 0.00 0.00 3.09
4187 5179 1.395826 CCTCTCACTCGGGGGCTTAG 61.396 65.000 0.00 0.00 0.00 2.18
4188 5180 1.381327 CCTCTCACTCGGGGGCTTA 60.381 63.158 0.00 0.00 0.00 3.09
4189 5181 2.537714 ATCCTCTCACTCGGGGGCTT 62.538 60.000 0.00 0.00 0.00 4.35
4190 5182 2.537714 AATCCTCTCACTCGGGGGCT 62.538 60.000 0.00 0.00 0.00 5.19
4191 5183 2.066999 AATCCTCTCACTCGGGGGC 61.067 63.158 0.00 0.00 0.00 5.80
4192 5184 1.826024 CAATCCTCTCACTCGGGGG 59.174 63.158 0.00 0.00 0.00 5.40
4193 5185 1.144936 GCAATCCTCTCACTCGGGG 59.855 63.158 0.00 0.00 0.00 5.73
4194 5186 0.103937 GAGCAATCCTCTCACTCGGG 59.896 60.000 0.00 0.00 37.60 5.14
4195 5187 3.657956 GAGCAATCCTCTCACTCGG 57.342 57.895 0.00 0.00 37.60 4.63
4203 5195 1.205893 ACCGAGTGAAGAGCAATCCTC 59.794 52.381 0.00 0.00 38.32 3.71
4204 5196 1.270907 ACCGAGTGAAGAGCAATCCT 58.729 50.000 0.00 0.00 38.32 3.24
4205 5197 2.482142 CCTACCGAGTGAAGAGCAATCC 60.482 54.545 0.00 0.00 38.32 3.01
4206 5198 2.427453 TCCTACCGAGTGAAGAGCAATC 59.573 50.000 0.00 0.00 38.20 2.67
4207 5199 2.457598 TCCTACCGAGTGAAGAGCAAT 58.542 47.619 0.00 0.00 0.00 3.56
4208 5200 1.919240 TCCTACCGAGTGAAGAGCAA 58.081 50.000 0.00 0.00 0.00 3.91
4209 5201 2.145397 ATCCTACCGAGTGAAGAGCA 57.855 50.000 0.00 0.00 0.00 4.26
4210 5202 3.528597 AAATCCTACCGAGTGAAGAGC 57.471 47.619 0.00 0.00 0.00 4.09
4211 5203 9.032420 GTTATAAAAATCCTACCGAGTGAAGAG 57.968 37.037 0.00 0.00 0.00 2.85
4212 5204 8.755977 AGTTATAAAAATCCTACCGAGTGAAGA 58.244 33.333 0.00 0.00 0.00 2.87
4213 5205 8.943909 AGTTATAAAAATCCTACCGAGTGAAG 57.056 34.615 0.00 0.00 0.00 3.02
4216 5208 9.257651 CCTAAGTTATAAAAATCCTACCGAGTG 57.742 37.037 0.00 0.00 0.00 3.51
4217 5209 7.930325 GCCTAAGTTATAAAAATCCTACCGAGT 59.070 37.037 0.00 0.00 0.00 4.18
4218 5210 7.115947 CGCCTAAGTTATAAAAATCCTACCGAG 59.884 40.741 0.00 0.00 0.00 4.63
4219 5211 6.925165 CGCCTAAGTTATAAAAATCCTACCGA 59.075 38.462 0.00 0.00 0.00 4.69
4220 5212 6.925165 TCGCCTAAGTTATAAAAATCCTACCG 59.075 38.462 0.00 0.00 0.00 4.02
4221 5213 7.095313 GCTCGCCTAAGTTATAAAAATCCTACC 60.095 40.741 0.00 0.00 0.00 3.18
4222 5214 7.440255 TGCTCGCCTAAGTTATAAAAATCCTAC 59.560 37.037 0.00 0.00 0.00 3.18
4223 5215 7.440255 GTGCTCGCCTAAGTTATAAAAATCCTA 59.560 37.037 0.00 0.00 0.00 2.94
4224 5216 6.260271 GTGCTCGCCTAAGTTATAAAAATCCT 59.740 38.462 0.00 0.00 0.00 3.24
4225 5217 6.427974 GTGCTCGCCTAAGTTATAAAAATCC 58.572 40.000 0.00 0.00 0.00 3.01
4226 5218 6.019318 TCGTGCTCGCCTAAGTTATAAAAATC 60.019 38.462 2.69 0.00 36.96 2.17
4227 5219 5.813672 TCGTGCTCGCCTAAGTTATAAAAAT 59.186 36.000 2.69 0.00 36.96 1.82
4228 5220 5.170021 TCGTGCTCGCCTAAGTTATAAAAA 58.830 37.500 2.69 0.00 36.96 1.94
4229 5221 4.746729 TCGTGCTCGCCTAAGTTATAAAA 58.253 39.130 2.69 0.00 36.96 1.52
4230 5222 4.357142 CTCGTGCTCGCCTAAGTTATAAA 58.643 43.478 2.69 0.00 36.96 1.40
4231 5223 3.243301 CCTCGTGCTCGCCTAAGTTATAA 60.243 47.826 2.69 0.00 36.96 0.98
4232 5224 2.292569 CCTCGTGCTCGCCTAAGTTATA 59.707 50.000 2.69 0.00 36.96 0.98
4233 5225 1.067212 CCTCGTGCTCGCCTAAGTTAT 59.933 52.381 2.69 0.00 36.96 1.89
4234 5226 0.454600 CCTCGTGCTCGCCTAAGTTA 59.545 55.000 2.69 0.00 36.96 2.24
4235 5227 1.215647 CCTCGTGCTCGCCTAAGTT 59.784 57.895 2.69 0.00 36.96 2.66
4236 5228 1.935327 GACCTCGTGCTCGCCTAAGT 61.935 60.000 2.69 0.00 36.96 2.24
4237 5229 1.226717 GACCTCGTGCTCGCCTAAG 60.227 63.158 2.69 0.00 36.96 2.18
4238 5230 2.882876 GACCTCGTGCTCGCCTAA 59.117 61.111 2.69 0.00 36.96 2.69
4239 5231 3.506096 CGACCTCGTGCTCGCCTA 61.506 66.667 2.69 0.00 36.96 3.93
4244 5236 2.543687 TTAGCTGCGACCTCGTGCTC 62.544 60.000 16.44 0.00 44.65 4.26
4245 5237 2.549611 CTTAGCTGCGACCTCGTGCT 62.550 60.000 16.90 16.90 46.26 4.40
4246 5238 2.126071 TTAGCTGCGACCTCGTGC 60.126 61.111 0.00 6.69 42.22 5.34
4247 5239 2.161486 GCTTAGCTGCGACCTCGTG 61.161 63.158 0.00 0.00 42.22 4.35
4248 5240 2.182030 GCTTAGCTGCGACCTCGT 59.818 61.111 0.00 0.00 42.22 4.18
4249 5241 2.583593 GGCTTAGCTGCGACCTCG 60.584 66.667 3.59 0.00 43.27 4.63
4250 5242 1.227118 GAGGCTTAGCTGCGACCTC 60.227 63.158 14.35 14.35 40.14 3.85
4251 5243 2.726351 GGAGGCTTAGCTGCGACCT 61.726 63.158 3.59 5.67 0.00 3.85
4252 5244 2.202946 GGAGGCTTAGCTGCGACC 60.203 66.667 3.59 0.00 0.00 4.79
4253 5245 2.583593 CGGAGGCTTAGCTGCGAC 60.584 66.667 3.59 0.00 36.54 5.19
4254 5246 2.754254 TCGGAGGCTTAGCTGCGA 60.754 61.111 13.63 13.63 40.84 5.10
4255 5247 2.279120 CTCGGAGGCTTAGCTGCG 60.279 66.667 3.59 7.64 35.78 5.18
4256 5248 1.520342 CACTCGGAGGCTTAGCTGC 60.520 63.158 10.23 0.00 0.00 5.25
4257 5249 1.142748 CCACTCGGAGGCTTAGCTG 59.857 63.158 10.23 0.00 0.00 4.24
4258 5250 0.614979 TTCCACTCGGAGGCTTAGCT 60.615 55.000 10.23 0.00 44.10 3.32
4259 5251 0.179097 CTTCCACTCGGAGGCTTAGC 60.179 60.000 10.23 0.00 44.10 3.09
4260 5252 0.461961 CCTTCCACTCGGAGGCTTAG 59.538 60.000 10.23 1.74 44.10 2.18
4261 5253 1.614241 GCCTTCCACTCGGAGGCTTA 61.614 60.000 10.23 0.00 45.21 3.09
4262 5254 2.960688 GCCTTCCACTCGGAGGCTT 61.961 63.158 10.23 0.00 45.21 4.35
4263 5255 3.394836 GCCTTCCACTCGGAGGCT 61.395 66.667 10.23 0.00 45.21 4.58
4265 5257 2.581354 CAGCCTTCCACTCGGAGG 59.419 66.667 10.23 0.00 44.10 4.30
4266 5258 2.581354 CCAGCCTTCCACTCGGAG 59.419 66.667 2.83 2.83 44.10 4.63
4267 5259 3.706373 GCCAGCCTTCCACTCGGA 61.706 66.667 0.00 0.00 40.60 4.55
4268 5260 1.899437 TAAGCCAGCCTTCCACTCGG 61.899 60.000 0.00 0.00 34.95 4.63
4269 5261 0.741221 GTAAGCCAGCCTTCCACTCG 60.741 60.000 0.00 0.00 34.95 4.18
4270 5262 0.393132 GGTAAGCCAGCCTTCCACTC 60.393 60.000 0.00 0.00 34.95 3.51
4271 5263 1.133809 TGGTAAGCCAGCCTTCCACT 61.134 55.000 0.00 0.00 40.46 4.00
4272 5264 1.378762 TGGTAAGCCAGCCTTCCAC 59.621 57.895 0.00 0.00 40.46 4.02
4273 5265 3.914645 TGGTAAGCCAGCCTTCCA 58.085 55.556 0.00 0.00 40.46 3.53
4288 5280 3.328382 TGTGAAAATCCTACCGAGTGG 57.672 47.619 0.00 0.00 42.84 4.00
4289 5281 4.315803 AGTTGTGAAAATCCTACCGAGTG 58.684 43.478 0.00 0.00 0.00 3.51
4290 5282 4.618920 AGTTGTGAAAATCCTACCGAGT 57.381 40.909 0.00 0.00 0.00 4.18
4291 5283 5.581085 CCTAAGTTGTGAAAATCCTACCGAG 59.419 44.000 0.00 0.00 0.00 4.63
4292 5284 5.012354 ACCTAAGTTGTGAAAATCCTACCGA 59.988 40.000 0.00 0.00 0.00 4.69
4293 5285 5.121768 CACCTAAGTTGTGAAAATCCTACCG 59.878 44.000 0.00 0.00 35.74 4.02
4294 5286 6.235664 TCACCTAAGTTGTGAAAATCCTACC 58.764 40.000 0.00 0.00 39.66 3.18
4295 5287 6.935208 ACTCACCTAAGTTGTGAAAATCCTAC 59.065 38.462 0.00 0.00 41.85 3.18
4296 5288 6.934645 CACTCACCTAAGTTGTGAAAATCCTA 59.065 38.462 0.00 0.00 41.85 2.94
4297 5289 5.765182 CACTCACCTAAGTTGTGAAAATCCT 59.235 40.000 0.00 0.00 41.85 3.24
4298 5290 5.562890 GCACTCACCTAAGTTGTGAAAATCC 60.563 44.000 0.00 0.00 41.85 3.01
4299 5291 5.239525 AGCACTCACCTAAGTTGTGAAAATC 59.760 40.000 0.00 0.00 41.85 2.17
4300 5292 5.133221 AGCACTCACCTAAGTTGTGAAAAT 58.867 37.500 0.00 0.00 41.85 1.82
4301 5293 4.523083 AGCACTCACCTAAGTTGTGAAAA 58.477 39.130 0.00 0.00 41.85 2.29
4302 5294 4.150897 AGCACTCACCTAAGTTGTGAAA 57.849 40.909 0.00 0.00 41.85 2.69
4303 5295 3.838244 AGCACTCACCTAAGTTGTGAA 57.162 42.857 0.00 0.00 41.85 3.18
4304 5296 3.466836 CAAGCACTCACCTAAGTTGTGA 58.533 45.455 0.00 0.00 40.28 3.58
4305 5297 2.549754 CCAAGCACTCACCTAAGTTGTG 59.450 50.000 0.00 0.00 33.41 3.33
4306 5298 2.438021 TCCAAGCACTCACCTAAGTTGT 59.562 45.455 0.00 0.00 0.00 3.32
4307 5299 2.808543 GTCCAAGCACTCACCTAAGTTG 59.191 50.000 0.00 0.00 0.00 3.16
4308 5300 2.706190 AGTCCAAGCACTCACCTAAGTT 59.294 45.455 0.00 0.00 0.00 2.66
4309 5301 2.037772 CAGTCCAAGCACTCACCTAAGT 59.962 50.000 0.00 0.00 0.00 2.24
4310 5302 2.693069 CAGTCCAAGCACTCACCTAAG 58.307 52.381 0.00 0.00 0.00 2.18
4311 5303 1.270839 GCAGTCCAAGCACTCACCTAA 60.271 52.381 0.00 0.00 0.00 2.69
4312 5304 0.321671 GCAGTCCAAGCACTCACCTA 59.678 55.000 0.00 0.00 0.00 3.08
4313 5305 1.072159 GCAGTCCAAGCACTCACCT 59.928 57.895 0.00 0.00 0.00 4.00
4314 5306 1.227943 TGCAGTCCAAGCACTCACC 60.228 57.895 0.00 0.00 37.02 4.02
4315 5307 1.849976 GCTGCAGTCCAAGCACTCAC 61.850 60.000 16.64 0.00 37.02 3.51
4316 5308 1.598962 GCTGCAGTCCAAGCACTCA 60.599 57.895 16.64 0.00 37.02 3.41
4317 5309 0.036952 TAGCTGCAGTCCAAGCACTC 60.037 55.000 16.64 0.00 37.02 3.51
4318 5310 0.397941 TTAGCTGCAGTCCAAGCACT 59.602 50.000 16.64 3.46 37.02 4.40
4319 5311 0.801251 CTTAGCTGCAGTCCAAGCAC 59.199 55.000 16.64 0.00 37.02 4.40
4320 5312 0.957395 GCTTAGCTGCAGTCCAAGCA 60.957 55.000 28.67 6.13 40.96 3.91
4321 5313 1.652167 GGCTTAGCTGCAGTCCAAGC 61.652 60.000 27.08 27.08 40.65 4.01
4322 5314 1.028868 GGGCTTAGCTGCAGTCCAAG 61.029 60.000 16.64 15.95 35.91 3.61
4323 5315 1.002134 GGGCTTAGCTGCAGTCCAA 60.002 57.895 16.64 6.12 35.91 3.53
4324 5316 2.671070 GGGCTTAGCTGCAGTCCA 59.329 61.111 16.64 0.00 35.91 4.02
4325 5317 2.124529 GGGGCTTAGCTGCAGTCC 60.125 66.667 16.64 9.44 35.00 3.85
4326 5318 2.124529 GGGGGCTTAGCTGCAGTC 60.125 66.667 16.64 7.83 34.04 3.51
4327 5319 4.101448 CGGGGGCTTAGCTGCAGT 62.101 66.667 16.64 4.79 34.04 4.40
4328 5320 2.615227 ATTCGGGGGCTTAGCTGCAG 62.615 60.000 10.11 10.11 34.04 4.41
4329 5321 2.679342 ATTCGGGGGCTTAGCTGCA 61.679 57.895 3.59 0.00 34.04 4.41
4330 5322 2.189499 CATTCGGGGGCTTAGCTGC 61.189 63.158 3.59 0.00 0.00 5.25
4331 5323 1.526917 CCATTCGGGGGCTTAGCTG 60.527 63.158 3.59 0.00 0.00 4.24
4332 5324 1.279025 TTCCATTCGGGGGCTTAGCT 61.279 55.000 3.59 0.00 37.22 3.32
4333 5325 0.819666 CTTCCATTCGGGGGCTTAGC 60.820 60.000 0.00 0.00 37.22 3.09
4334 5326 0.179018 CCTTCCATTCGGGGGCTTAG 60.179 60.000 0.00 0.00 37.22 2.18
4335 5327 1.919771 CCTTCCATTCGGGGGCTTA 59.080 57.895 0.00 0.00 37.22 3.09
4336 5328 2.683475 CCTTCCATTCGGGGGCTT 59.317 61.111 0.00 0.00 37.22 4.35
4337 5329 4.129148 GCCTTCCATTCGGGGGCT 62.129 66.667 8.46 0.00 43.58 5.19
4338 5330 4.129148 AGCCTTCCATTCGGGGGC 62.129 66.667 7.87 7.87 45.69 5.80
4339 5331 2.124151 CAGCCTTCCATTCGGGGG 60.124 66.667 0.00 0.00 37.22 5.40
4340 5332 2.124151 CCAGCCTTCCATTCGGGG 60.124 66.667 0.00 0.00 37.22 5.73
4341 5333 2.830370 GCCAGCCTTCCATTCGGG 60.830 66.667 0.00 0.00 38.37 5.14
4342 5334 0.107214 TAAGCCAGCCTTCCATTCGG 60.107 55.000 0.00 0.00 34.95 4.30
4343 5335 1.017387 GTAAGCCAGCCTTCCATTCG 58.983 55.000 0.00 0.00 34.95 3.34
4344 5336 1.340991 TGGTAAGCCAGCCTTCCATTC 60.341 52.381 0.00 0.00 40.46 2.67
4345 5337 0.704076 TGGTAAGCCAGCCTTCCATT 59.296 50.000 0.00 0.00 40.46 3.16
4346 5338 2.397815 TGGTAAGCCAGCCTTCCAT 58.602 52.632 0.00 0.00 40.46 3.41
4347 5339 3.914645 TGGTAAGCCAGCCTTCCA 58.085 55.556 0.00 0.00 40.46 3.53
4362 5354 6.113411 AGTTTATCAAAATCCTACCGAGTGG 58.887 40.000 0.00 0.00 42.84 4.00
4363 5355 7.611213 AAGTTTATCAAAATCCTACCGAGTG 57.389 36.000 0.00 0.00 0.00 3.51
4364 5356 7.985752 CCTAAGTTTATCAAAATCCTACCGAGT 59.014 37.037 0.00 0.00 0.00 4.18
4365 5357 7.041984 GCCTAAGTTTATCAAAATCCTACCGAG 60.042 40.741 0.00 0.00 0.00 4.63
4366 5358 6.764560 GCCTAAGTTTATCAAAATCCTACCGA 59.235 38.462 0.00 0.00 0.00 4.69
4367 5359 6.292703 CGCCTAAGTTTATCAAAATCCTACCG 60.293 42.308 0.00 0.00 0.00 4.02
4368 5360 6.764560 TCGCCTAAGTTTATCAAAATCCTACC 59.235 38.462 0.00 0.00 0.00 3.18
4369 5361 7.494952 ACTCGCCTAAGTTTATCAAAATCCTAC 59.505 37.037 0.00 0.00 0.00 3.18
4370 5362 7.562135 ACTCGCCTAAGTTTATCAAAATCCTA 58.438 34.615 0.00 0.00 0.00 2.94
4371 5363 6.415573 ACTCGCCTAAGTTTATCAAAATCCT 58.584 36.000 0.00 0.00 0.00 3.24
4372 5364 6.238402 GGACTCGCCTAAGTTTATCAAAATCC 60.238 42.308 0.00 0.00 0.00 3.01
4373 5365 6.716438 GGACTCGCCTAAGTTTATCAAAATC 58.284 40.000 0.00 0.00 0.00 2.17
4374 5366 6.679327 GGACTCGCCTAAGTTTATCAAAAT 57.321 37.500 0.00 0.00 0.00 1.82
4394 5386 2.545731 GCTTAGCTGCAGTCTAAGGAC 58.454 52.381 34.06 24.30 41.86 3.85
4395 5387 1.482593 GGCTTAGCTGCAGTCTAAGGA 59.517 52.381 34.06 17.04 41.86 3.36
4396 5388 1.484240 AGGCTTAGCTGCAGTCTAAGG 59.516 52.381 34.06 24.48 41.86 2.69
4397 5389 2.482839 GGAGGCTTAGCTGCAGTCTAAG 60.483 54.545 31.95 31.95 43.49 2.18
4398 5390 1.482593 GGAGGCTTAGCTGCAGTCTAA 59.517 52.381 21.48 21.48 34.04 2.10
4399 5391 1.115467 GGAGGCTTAGCTGCAGTCTA 58.885 55.000 16.64 13.97 34.04 2.59
4400 5392 1.904032 GGAGGCTTAGCTGCAGTCT 59.096 57.895 16.64 15.00 34.04 3.24
4401 5393 1.520342 CGGAGGCTTAGCTGCAGTC 60.520 63.158 16.64 7.83 34.04 3.51
4402 5394 1.954362 CTCGGAGGCTTAGCTGCAGT 61.954 60.000 16.64 4.79 34.04 4.40
4403 5395 1.227205 CTCGGAGGCTTAGCTGCAG 60.227 63.158 10.11 10.11 34.04 4.41
4404 5396 1.984570 ACTCGGAGGCTTAGCTGCA 60.985 57.895 10.23 0.00 34.04 4.41
4405 5397 1.520342 CACTCGGAGGCTTAGCTGC 60.520 63.158 10.23 0.00 0.00 5.25
4406 5398 1.142748 CCACTCGGAGGCTTAGCTG 59.857 63.158 10.23 0.00 0.00 4.24
4407 5399 0.614979 TTCCACTCGGAGGCTTAGCT 60.615 55.000 10.23 0.00 44.10 3.32
4408 5400 0.179097 CTTCCACTCGGAGGCTTAGC 60.179 60.000 10.23 0.00 44.10 3.09
4409 5401 0.461961 CCTTCCACTCGGAGGCTTAG 59.538 60.000 10.23 1.74 44.10 2.18
4410 5402 1.614241 GCCTTCCACTCGGAGGCTTA 61.614 60.000 10.23 0.00 45.21 3.09
4411 5403 2.960688 GCCTTCCACTCGGAGGCTT 61.961 63.158 10.23 0.00 45.21 4.35
4412 5404 3.394836 GCCTTCCACTCGGAGGCT 61.395 66.667 10.23 0.00 45.21 4.58
4414 5406 2.581354 CAGCCTTCCACTCGGAGG 59.419 66.667 10.23 0.00 44.10 4.30
4415 5407 2.581354 CCAGCCTTCCACTCGGAG 59.419 66.667 2.83 2.83 44.10 4.63
4416 5408 3.706373 GCCAGCCTTCCACTCGGA 61.706 66.667 0.00 0.00 40.60 4.55
4417 5409 1.899437 TAAGCCAGCCTTCCACTCGG 61.899 60.000 0.00 0.00 34.95 4.63
4418 5410 0.741221 GTAAGCCAGCCTTCCACTCG 60.741 60.000 0.00 0.00 34.95 4.18
4419 5411 0.393132 GGTAAGCCAGCCTTCCACTC 60.393 60.000 0.00 0.00 34.95 3.51
4420 5412 1.133809 TGGTAAGCCAGCCTTCCACT 61.134 55.000 0.00 0.00 40.46 4.00
4421 5413 1.378762 TGGTAAGCCAGCCTTCCAC 59.621 57.895 0.00 0.00 40.46 4.02
4422 5414 3.914645 TGGTAAGCCAGCCTTCCA 58.085 55.556 0.00 0.00 40.46 3.53
4437 5429 6.113411 AGTTTATCAAAATCCTACCGAGTGG 58.887 40.000 0.00 0.00 42.84 4.00
4438 5430 7.611213 AAGTTTATCAAAATCCTACCGAGTG 57.389 36.000 0.00 0.00 0.00 3.51
4439 5431 7.985752 CCTAAGTTTATCAAAATCCTACCGAGT 59.014 37.037 0.00 0.00 0.00 4.18
4440 5432 7.041984 GCCTAAGTTTATCAAAATCCTACCGAG 60.042 40.741 0.00 0.00 0.00 4.63
4441 5433 6.764560 GCCTAAGTTTATCAAAATCCTACCGA 59.235 38.462 0.00 0.00 0.00 4.69
4442 5434 6.292703 CGCCTAAGTTTATCAAAATCCTACCG 60.293 42.308 0.00 0.00 0.00 4.02
4443 5435 6.764560 TCGCCTAAGTTTATCAAAATCCTACC 59.235 38.462 0.00 0.00 0.00 3.18
4444 5436 7.494952 ACTCGCCTAAGTTTATCAAAATCCTAC 59.505 37.037 0.00 0.00 0.00 3.18
4445 5437 7.562135 ACTCGCCTAAGTTTATCAAAATCCTA 58.438 34.615 0.00 0.00 0.00 2.94
4446 5438 6.415573 ACTCGCCTAAGTTTATCAAAATCCT 58.584 36.000 0.00 0.00 0.00 3.24
4447 5439 6.238402 GGACTCGCCTAAGTTTATCAAAATCC 60.238 42.308 0.00 0.00 0.00 3.01
4448 5440 6.716438 GGACTCGCCTAAGTTTATCAAAATC 58.284 40.000 0.00 0.00 0.00 2.17
4449 5441 6.679327 GGACTCGCCTAAGTTTATCAAAAT 57.321 37.500 0.00 0.00 0.00 1.82
4499 5564 0.735471 CGAGTGAAGAGCGATCCTCA 59.265 55.000 0.00 0.00 43.31 3.86


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

AutoCloner maintained by Alex Coulton.