Multiple sequence alignment - TraesCS3D01G099000

Loading Multiple Alignment...

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 TraesCS3D01G099000 chr3D 100.000 2411 0 0 1 2411 50659446 50657036 0.000000e+00 4453.0
1 TraesCS3D01G099000 chr3D 85.980 1776 146 36 697 2411 36822111 36823844 0.000000e+00 1805.0
2 TraesCS3D01G099000 chr3D 91.829 257 10 3 347 593 83428535 83428790 4.930000e-92 348.0
3 TraesCS3D01G099000 chr3D 90.530 264 13 4 340 593 295392466 295392205 2.970000e-89 339.0
4 TraesCS3D01G099000 chr3D 88.235 153 18 0 170 322 110409610 110409458 1.470000e-42 183.0
5 TraesCS3D01G099000 chr3B 90.031 973 46 13 592 1519 80659343 80658377 0.000000e+00 1212.0
6 TraesCS3D01G099000 chr3B 87.846 831 54 27 987 1783 59323797 59324614 0.000000e+00 931.0
7 TraesCS3D01G099000 chr3B 86.916 749 67 18 889 1615 80201469 80200730 0.000000e+00 811.0
8 TraesCS3D01G099000 chr3B 93.432 472 26 2 1938 2409 59324630 59325096 0.000000e+00 695.0
9 TraesCS3D01G099000 chr3B 95.122 205 10 0 668 872 80201758 80201554 8.310000e-85 324.0
10 TraesCS3D01G099000 chr3B 92.771 166 12 0 1 166 80202614 80202449 8.610000e-60 241.0
11 TraesCS3D01G099000 chr3B 91.620 179 8 2 1936 2111 80658140 80657966 8.610000e-60 241.0
12 TraesCS3D01G099000 chr3B 92.169 166 12 1 1 166 80659523 80659359 1.440000e-57 233.0
13 TraesCS3D01G099000 chr3B 80.800 125 18 4 1533 1652 80200632 80200509 2.550000e-15 93.5
14 TraesCS3D01G099000 chr3B 100.000 28 0 0 592 619 80202433 80202406 4.000000e-03 52.8
15 TraesCS3D01G099000 chr3A 85.621 1071 92 30 693 1702 47046102 47047171 0.000000e+00 1068.0
16 TraesCS3D01G099000 chr3A 95.567 203 9 0 2209 2411 47047233 47047435 2.310000e-85 326.0
17 TraesCS3D01G099000 chr3A 86.219 283 21 10 347 612 673474487 673474206 8.430000e-75 291.0
18 TraesCS3D01G099000 chr3A 80.597 201 25 5 1419 1615 303562597 303562407 2.500000e-30 143.0
19 TraesCS3D01G099000 chr6B 95.238 420 20 0 990 1409 35629113 35629532 0.000000e+00 665.0
20 TraesCS3D01G099000 chr6B 94.601 426 23 0 984 1409 35818873 35818448 0.000000e+00 660.0
21 TraesCS3D01G099000 chr6B 93.807 436 24 1 969 1404 101325635 101325203 0.000000e+00 652.0
22 TraesCS3D01G099000 chr6B 88.679 159 18 0 170 328 708939546 708939704 6.800000e-46 195.0
23 TraesCS3D01G099000 chrUn 94.787 422 19 1 980 1401 69362330 69362748 0.000000e+00 654.0
24 TraesCS3D01G099000 chr7A 91.571 261 10 4 343 593 5906410 5906668 1.370000e-92 350.0
25 TraesCS3D01G099000 chr7A 88.281 256 17 5 348 593 65157803 65158055 6.520000e-76 294.0
26 TraesCS3D01G099000 chr7A 86.782 174 20 3 169 340 732053483 732053311 8.800000e-45 191.0
27 TraesCS3D01G099000 chr6A 91.829 257 10 3 347 593 76520939 76520684 4.930000e-92 348.0
28 TraesCS3D01G099000 chr2D 91.538 260 10 5 344 593 204112947 204112690 4.930000e-92 348.0
29 TraesCS3D01G099000 chr2D 89.091 165 18 0 169 333 73402884 73403048 3.140000e-49 206.0
30 TraesCS3D01G099000 chr2D 86.364 176 15 7 160 333 532176545 532176713 1.470000e-42 183.0
31 TraesCS3D01G099000 chr2D 85.976 164 22 1 170 333 9646117 9646279 8.860000e-40 174.0
32 TraesCS3D01G099000 chr6D 90.943 265 11 5 340 593 388990613 388990875 6.380000e-91 344.0
33 TraesCS3D01G099000 chr6D 90.840 262 12 4 342 593 26354245 26353986 8.250000e-90 340.0
34 TraesCS3D01G099000 chr6D 87.662 154 17 2 170 322 176827546 176827698 6.850000e-41 178.0
35 TraesCS3D01G099000 chr6D 82.587 201 21 5 1419 1615 110865157 110864967 5.330000e-37 165.0
36 TraesCS3D01G099000 chr6D 77.224 281 42 18 1516 1778 27757880 27758156 6.950000e-31 145.0
37 TraesCS3D01G099000 chr7B 91.440 257 11 3 347 593 598955038 598954783 2.300000e-90 342.0
38 TraesCS3D01G099000 chr4A 90.875 263 12 4 341 593 111436100 111436360 2.300000e-90 342.0
39 TraesCS3D01G099000 chr5A 86.691 278 23 6 340 606 484883521 484883795 1.810000e-76 296.0
40 TraesCS3D01G099000 chr5A 84.791 263 19 8 348 602 466612737 466612986 6.660000e-61 244.0
41 TraesCS3D01G099000 chr1A 87.730 163 16 2 160 322 32274690 32274848 1.140000e-43 187.0
42 TraesCS3D01G099000 chr7D 86.061 165 21 2 170 333 593923594 593923431 2.460000e-40 176.0


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 TraesCS3D01G099000 chr3D 50657036 50659446 2410 True 4453.00 4453 100.000000 1 2411 1 chr3D.!!$R1 2410
1 TraesCS3D01G099000 chr3D 36822111 36823844 1733 False 1805.00 1805 85.980000 697 2411 1 chr3D.!!$F1 1714
2 TraesCS3D01G099000 chr3B 59323797 59325096 1299 False 813.00 931 90.639000 987 2409 2 chr3B.!!$F1 1422
3 TraesCS3D01G099000 chr3B 80657966 80659523 1557 True 562.00 1212 91.273333 1 2111 3 chr3B.!!$R2 2110
4 TraesCS3D01G099000 chr3B 80200509 80202614 2105 True 304.46 811 91.121800 1 1652 5 chr3B.!!$R1 1651
5 TraesCS3D01G099000 chr3A 47046102 47047435 1333 False 697.00 1068 90.594000 693 2411 2 chr3A.!!$F1 1718

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
935 1605 1.265454 ATCACCGTTCCTCCCACCTC 61.265 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2761 0.02877 ACGGACAAATTGTGCACACG 59.971 50.0 21.56 19.74 38.73 4.49 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
23 24 6.414408 CGGTGAATATTTCTCTATGATGCC 57.586 41.667 0.00 0.00 0.00 4.40
103 104 7.858382 TCGAATAAAGTTGCGAATTTTTCTTCA 59.142 29.630 4.45 0.00 0.00 3.02
110 111 3.006752 TGCGAATTTTTCTTCAATGGCCT 59.993 39.130 3.32 0.00 0.00 5.19
127 128 2.166870 GGCCTTGCATGTCATGAAATCA 59.833 45.455 17.24 1.97 0.00 2.57
136 137 6.773685 TGCATGTCATGAAATCAAGGATGATA 59.226 34.615 17.24 0.00 45.60 2.15
139 140 9.010029 CATGTCATGAAATCAAGGATGATATCA 57.990 33.333 8.10 8.10 45.60 2.15
166 167 3.845781 AAGAGCGAATCCCACATGTAT 57.154 42.857 0.00 0.00 0.00 2.29
167 168 3.393089 AGAGCGAATCCCACATGTATC 57.607 47.619 0.00 0.00 0.00 2.24
168 169 2.061773 GAGCGAATCCCACATGTATCG 58.938 52.381 0.00 5.49 0.00 2.92
169 170 1.412710 AGCGAATCCCACATGTATCGT 59.587 47.619 0.00 0.00 33.18 3.73
170 171 2.626266 AGCGAATCCCACATGTATCGTA 59.374 45.455 0.00 0.00 33.18 3.43
171 172 2.729882 GCGAATCCCACATGTATCGTAC 59.270 50.000 0.00 0.00 33.18 3.67
172 173 3.552273 GCGAATCCCACATGTATCGTACT 60.552 47.826 0.00 0.00 33.18 2.73
173 174 4.227538 CGAATCCCACATGTATCGTACTC 58.772 47.826 0.00 0.00 0.00 2.59
174 175 4.557205 GAATCCCACATGTATCGTACTCC 58.443 47.826 0.00 0.00 0.00 3.85
175 176 2.313317 TCCCACATGTATCGTACTCCC 58.687 52.381 0.00 0.00 0.00 4.30
176 177 2.091499 TCCCACATGTATCGTACTCCCT 60.091 50.000 0.00 0.00 0.00 4.20
177 178 2.296471 CCCACATGTATCGTACTCCCTC 59.704 54.545 0.00 0.00 0.00 4.30
178 179 3.223435 CCACATGTATCGTACTCCCTCT 58.777 50.000 0.00 0.00 0.00 3.69
179 180 3.004839 CCACATGTATCGTACTCCCTCTG 59.995 52.174 0.00 0.00 0.00 3.35
180 181 3.632604 CACATGTATCGTACTCCCTCTGT 59.367 47.826 0.00 0.00 0.00 3.41
181 182 4.098044 CACATGTATCGTACTCCCTCTGTT 59.902 45.833 0.00 0.00 0.00 3.16
182 183 4.338682 ACATGTATCGTACTCCCTCTGTTC 59.661 45.833 0.00 0.00 0.00 3.18
183 184 3.285484 TGTATCGTACTCCCTCTGTTCC 58.715 50.000 0.00 0.00 0.00 3.62
184 185 2.830651 ATCGTACTCCCTCTGTTCCT 57.169 50.000 0.00 0.00 0.00 3.36
185 186 3.947612 ATCGTACTCCCTCTGTTCCTA 57.052 47.619 0.00 0.00 0.00 2.94
186 187 3.726557 TCGTACTCCCTCTGTTCCTAA 57.273 47.619 0.00 0.00 0.00 2.69
187 188 4.038271 TCGTACTCCCTCTGTTCCTAAA 57.962 45.455 0.00 0.00 0.00 1.85
188 189 4.607239 TCGTACTCCCTCTGTTCCTAAAT 58.393 43.478 0.00 0.00 0.00 1.40
189 190 5.759059 TCGTACTCCCTCTGTTCCTAAATA 58.241 41.667 0.00 0.00 0.00 1.40
190 191 6.371278 TCGTACTCCCTCTGTTCCTAAATAT 58.629 40.000 0.00 0.00 0.00 1.28
191 192 7.520798 TCGTACTCCCTCTGTTCCTAAATATA 58.479 38.462 0.00 0.00 0.00 0.86
192 193 8.168725 TCGTACTCCCTCTGTTCCTAAATATAT 58.831 37.037 0.00 0.00 0.00 0.86
193 194 8.244802 CGTACTCCCTCTGTTCCTAAATATATG 58.755 40.741 0.00 0.00 0.00 1.78
194 195 9.091220 GTACTCCCTCTGTTCCTAAATATATGT 57.909 37.037 0.00 0.00 0.00 2.29
195 196 8.196378 ACTCCCTCTGTTCCTAAATATATGTC 57.804 38.462 0.00 0.00 0.00 3.06
196 197 8.013667 ACTCCCTCTGTTCCTAAATATATGTCT 58.986 37.037 0.00 0.00 0.00 3.41
197 198 8.798975 TCCCTCTGTTCCTAAATATATGTCTT 57.201 34.615 0.00 0.00 0.00 3.01
198 199 9.225682 TCCCTCTGTTCCTAAATATATGTCTTT 57.774 33.333 0.00 0.00 0.00 2.52
227 228 9.221933 AGAGATTTCACTGTAGACTATATACGG 57.778 37.037 0.00 0.00 35.92 4.02
228 229 9.217278 GAGATTTCACTGTAGACTATATACGGA 57.783 37.037 0.00 0.00 34.29 4.69
229 230 9.221933 AGATTTCACTGTAGACTATATACGGAG 57.778 37.037 0.00 0.00 34.29 4.63
230 231 6.798315 TTCACTGTAGACTATATACGGAGC 57.202 41.667 0.00 0.00 34.29 4.70
231 232 5.861727 TCACTGTAGACTATATACGGAGCA 58.138 41.667 0.00 0.00 34.29 4.26
232 233 6.293698 TCACTGTAGACTATATACGGAGCAA 58.706 40.000 0.00 0.00 34.29 3.91
233 234 6.769341 TCACTGTAGACTATATACGGAGCAAA 59.231 38.462 0.00 0.00 34.29 3.68
234 235 7.283807 TCACTGTAGACTATATACGGAGCAAAA 59.716 37.037 0.00 0.00 34.29 2.44
235 236 8.082852 CACTGTAGACTATATACGGAGCAAAAT 58.917 37.037 0.00 0.00 34.29 1.82
236 237 8.082852 ACTGTAGACTATATACGGAGCAAAATG 58.917 37.037 0.00 0.00 34.29 2.32
237 238 8.173542 TGTAGACTATATACGGAGCAAAATGA 57.826 34.615 0.00 0.00 0.00 2.57
238 239 8.297426 TGTAGACTATATACGGAGCAAAATGAG 58.703 37.037 0.00 0.00 0.00 2.90
239 240 7.291411 AGACTATATACGGAGCAAAATGAGT 57.709 36.000 0.00 0.00 0.00 3.41
240 241 8.405418 AGACTATATACGGAGCAAAATGAGTA 57.595 34.615 0.00 0.00 0.00 2.59
241 242 8.857098 AGACTATATACGGAGCAAAATGAGTAA 58.143 33.333 0.00 0.00 0.00 2.24
242 243 9.472361 GACTATATACGGAGCAAAATGAGTAAA 57.528 33.333 0.00 0.00 0.00 2.01
243 244 9.257651 ACTATATACGGAGCAAAATGAGTAAAC 57.742 33.333 0.00 0.00 0.00 2.01
244 245 5.813080 ATACGGAGCAAAATGAGTAAACC 57.187 39.130 0.00 0.00 0.00 3.27
245 246 3.751518 ACGGAGCAAAATGAGTAAACCT 58.248 40.909 0.00 0.00 0.00 3.50
246 247 4.901868 ACGGAGCAAAATGAGTAAACCTA 58.098 39.130 0.00 0.00 0.00 3.08
247 248 5.497474 ACGGAGCAAAATGAGTAAACCTAT 58.503 37.500 0.00 0.00 0.00 2.57
248 249 5.944007 ACGGAGCAAAATGAGTAAACCTATT 59.056 36.000 0.00 0.00 0.00 1.73
249 250 6.433093 ACGGAGCAAAATGAGTAAACCTATTT 59.567 34.615 0.00 0.00 0.00 1.40
250 251 7.039993 ACGGAGCAAAATGAGTAAACCTATTTT 60.040 33.333 0.00 0.00 34.17 1.82
251 252 7.484959 CGGAGCAAAATGAGTAAACCTATTTTC 59.515 37.037 0.00 0.00 32.21 2.29
252 253 8.523658 GGAGCAAAATGAGTAAACCTATTTTCT 58.476 33.333 0.00 0.00 32.21 2.52
261 262 9.768662 TGAGTAAACCTATTTTCTAAAAGACGT 57.231 29.630 0.00 0.00 0.00 4.34
263 264 9.993454 AGTAAACCTATTTTCTAAAAGACGTCT 57.007 29.630 13.58 13.58 0.00 4.18
347 348 8.840200 TGAAGGAAGTAGATTAACTCCATAGT 57.160 34.615 0.00 0.00 37.65 2.12
348 349 9.931698 TGAAGGAAGTAGATTAACTCCATAGTA 57.068 33.333 0.00 0.00 33.75 1.82
350 351 9.939424 AAGGAAGTAGATTAACTCCATAGTACT 57.061 33.333 0.00 0.00 33.75 2.73
351 352 9.577222 AGGAAGTAGATTAACTCCATAGTACTC 57.423 37.037 0.00 0.00 33.75 2.59
352 353 8.795513 GGAAGTAGATTAACTCCATAGTACTCC 58.204 40.741 0.00 0.00 33.75 3.85
353 354 8.709272 AAGTAGATTAACTCCATAGTACTCCC 57.291 38.462 0.00 0.00 33.75 4.30
354 355 8.059565 AGTAGATTAACTCCATAGTACTCCCT 57.940 38.462 0.00 0.00 33.75 4.20
355 356 9.180282 AGTAGATTAACTCCATAGTACTCCCTA 57.820 37.037 0.00 0.00 33.75 3.53
356 357 9.230122 GTAGATTAACTCCATAGTACTCCCTAC 57.770 40.741 0.00 0.00 33.75 3.18
357 358 6.941436 AGATTAACTCCATAGTACTCCCTACG 59.059 42.308 0.00 0.00 33.75 3.51
358 359 4.516652 AACTCCATAGTACTCCCTACGT 57.483 45.455 0.00 0.00 33.75 3.57
359 360 4.516652 ACTCCATAGTACTCCCTACGTT 57.483 45.455 0.00 0.00 32.84 3.99
360 361 4.864726 ACTCCATAGTACTCCCTACGTTT 58.135 43.478 0.00 0.00 32.84 3.60
361 362 4.886489 ACTCCATAGTACTCCCTACGTTTC 59.114 45.833 0.00 0.00 32.84 2.78
362 363 5.121380 TCCATAGTACTCCCTACGTTTCT 57.879 43.478 0.00 0.00 0.00 2.52
363 364 5.513233 TCCATAGTACTCCCTACGTTTCTT 58.487 41.667 0.00 0.00 0.00 2.52
364 365 5.954150 TCCATAGTACTCCCTACGTTTCTTT 59.046 40.000 0.00 0.00 0.00 2.52
365 366 6.438425 TCCATAGTACTCCCTACGTTTCTTTT 59.562 38.462 0.00 0.00 0.00 2.27
366 367 7.038799 TCCATAGTACTCCCTACGTTTCTTTTT 60.039 37.037 0.00 0.00 0.00 1.94
367 368 8.253113 CCATAGTACTCCCTACGTTTCTTTTTA 58.747 37.037 0.00 0.00 0.00 1.52
368 369 9.298774 CATAGTACTCCCTACGTTTCTTTTTAG 57.701 37.037 0.00 0.00 0.00 1.85
369 370 7.295322 AGTACTCCCTACGTTTCTTTTTAGT 57.705 36.000 0.00 0.00 0.00 2.24
370 371 7.374272 AGTACTCCCTACGTTTCTTTTTAGTC 58.626 38.462 0.00 0.00 0.00 2.59
371 372 5.545588 ACTCCCTACGTTTCTTTTTAGTCC 58.454 41.667 0.00 0.00 0.00 3.85
372 373 4.559153 TCCCTACGTTTCTTTTTAGTCCG 58.441 43.478 0.00 0.00 0.00 4.79
373 374 3.124128 CCCTACGTTTCTTTTTAGTCCGC 59.876 47.826 0.00 0.00 0.00 5.54
374 375 3.742369 CCTACGTTTCTTTTTAGTCCGCA 59.258 43.478 0.00 0.00 0.00 5.69
375 376 4.390909 CCTACGTTTCTTTTTAGTCCGCAT 59.609 41.667 0.00 0.00 0.00 4.73
376 377 5.577945 CCTACGTTTCTTTTTAGTCCGCATA 59.422 40.000 0.00 0.00 0.00 3.14
377 378 6.257193 CCTACGTTTCTTTTTAGTCCGCATAT 59.743 38.462 0.00 0.00 0.00 1.78
378 379 7.436080 CCTACGTTTCTTTTTAGTCCGCATATA 59.564 37.037 0.00 0.00 0.00 0.86
379 380 7.599630 ACGTTTCTTTTTAGTCCGCATATAA 57.400 32.000 0.00 0.00 0.00 0.98
380 381 7.681903 ACGTTTCTTTTTAGTCCGCATATAAG 58.318 34.615 0.00 0.00 0.00 1.73
381 382 7.123830 CGTTTCTTTTTAGTCCGCATATAAGG 58.876 38.462 0.00 0.00 0.00 2.69
382 383 7.201582 CGTTTCTTTTTAGTCCGCATATAAGGT 60.202 37.037 0.00 0.00 0.00 3.50
383 384 8.456471 GTTTCTTTTTAGTCCGCATATAAGGTT 58.544 33.333 0.00 0.00 0.00 3.50
384 385 8.570068 TTCTTTTTAGTCCGCATATAAGGTTT 57.430 30.769 0.00 0.00 0.00 3.27
385 386 7.981142 TCTTTTTAGTCCGCATATAAGGTTTG 58.019 34.615 0.00 0.00 0.00 2.93
386 387 6.687081 TTTTAGTCCGCATATAAGGTTTGG 57.313 37.500 0.00 0.00 0.00 3.28
387 388 3.926058 AGTCCGCATATAAGGTTTGGT 57.074 42.857 0.00 0.00 0.00 3.67
388 389 3.805207 AGTCCGCATATAAGGTTTGGTC 58.195 45.455 0.00 0.00 0.00 4.02
389 390 3.199071 AGTCCGCATATAAGGTTTGGTCA 59.801 43.478 0.00 0.00 0.00 4.02
390 391 3.942748 GTCCGCATATAAGGTTTGGTCAA 59.057 43.478 0.00 0.00 0.00 3.18
391 392 4.396790 GTCCGCATATAAGGTTTGGTCAAA 59.603 41.667 0.00 0.00 0.00 2.69
392 393 4.638421 TCCGCATATAAGGTTTGGTCAAAG 59.362 41.667 0.00 0.00 0.00 2.77
393 394 4.398044 CCGCATATAAGGTTTGGTCAAAGT 59.602 41.667 0.00 0.00 0.00 2.66
394 395 5.448632 CCGCATATAAGGTTTGGTCAAAGTC 60.449 44.000 0.00 0.00 0.00 3.01
395 396 5.123186 CGCATATAAGGTTTGGTCAAAGTCA 59.877 40.000 0.00 0.00 0.00 3.41
396 397 6.348950 CGCATATAAGGTTTGGTCAAAGTCAA 60.349 38.462 0.00 0.00 0.00 3.18
397 398 7.029563 GCATATAAGGTTTGGTCAAAGTCAAG 58.970 38.462 0.00 0.00 0.00 3.02
398 399 3.801114 AAGGTTTGGTCAAAGTCAAGC 57.199 42.857 0.00 0.00 0.00 4.01
399 400 3.018423 AGGTTTGGTCAAAGTCAAGCT 57.982 42.857 0.00 0.00 0.00 3.74
400 401 3.365472 AGGTTTGGTCAAAGTCAAGCTT 58.635 40.909 0.00 0.00 39.52 3.74
402 403 4.953579 AGGTTTGGTCAAAGTCAAGCTTTA 59.046 37.500 0.00 0.00 44.95 1.85
403 404 5.598417 AGGTTTGGTCAAAGTCAAGCTTTAT 59.402 36.000 0.00 0.00 44.95 1.40
404 405 6.775629 AGGTTTGGTCAAAGTCAAGCTTTATA 59.224 34.615 0.00 0.00 44.95 0.98
405 406 7.040409 AGGTTTGGTCAAAGTCAAGCTTTATAG 60.040 37.037 0.00 0.00 44.95 1.31
406 407 7.040686 GGTTTGGTCAAAGTCAAGCTTTATAGA 60.041 37.037 0.00 0.00 44.95 1.98
407 408 7.672983 TTGGTCAAAGTCAAGCTTTATAGAG 57.327 36.000 0.00 0.00 44.95 2.43
408 409 6.769512 TGGTCAAAGTCAAGCTTTATAGAGT 58.230 36.000 0.00 0.00 44.95 3.24
409 410 7.224297 TGGTCAAAGTCAAGCTTTATAGAGTT 58.776 34.615 0.00 0.00 44.95 3.01
410 411 7.719633 TGGTCAAAGTCAAGCTTTATAGAGTTT 59.280 33.333 10.15 10.15 44.95 2.66
411 412 8.017946 GGTCAAAGTCAAGCTTTATAGAGTTTG 58.982 37.037 24.99 24.99 44.95 2.93
482 483 9.878667 TTATCAGATGCATCATGAAACATTTTT 57.121 25.926 27.81 12.52 0.00 1.94
556 557 8.840833 AAATTTGGTTTGTGTAGTTTGACTTT 57.159 26.923 0.00 0.00 0.00 2.66
557 558 7.826260 ATTTGGTTTGTGTAGTTTGACTTTG 57.174 32.000 0.00 0.00 0.00 2.77
558 559 6.576662 TTGGTTTGTGTAGTTTGACTTTGA 57.423 33.333 0.00 0.00 0.00 2.69
559 560 6.767524 TGGTTTGTGTAGTTTGACTTTGAT 57.232 33.333 0.00 0.00 0.00 2.57
560 561 6.791303 TGGTTTGTGTAGTTTGACTTTGATC 58.209 36.000 0.00 0.00 0.00 2.92
561 562 6.375736 TGGTTTGTGTAGTTTGACTTTGATCA 59.624 34.615 0.00 0.00 0.00 2.92
562 563 7.094162 TGGTTTGTGTAGTTTGACTTTGATCAA 60.094 33.333 3.38 3.38 36.80 2.57
563 564 7.757624 GGTTTGTGTAGTTTGACTTTGATCAAA 59.242 33.333 19.45 19.45 44.40 2.69
574 575 9.720667 TTTGACTTTGATCAAATCTTATATGCG 57.279 29.630 20.76 8.05 42.32 4.73
575 576 7.864686 TGACTTTGATCAAATCTTATATGCGG 58.135 34.615 20.76 7.58 0.00 5.69
576 577 7.714813 TGACTTTGATCAAATCTTATATGCGGA 59.285 33.333 20.76 0.00 0.00 5.54
577 578 8.092521 ACTTTGATCAAATCTTATATGCGGAG 57.907 34.615 20.76 6.87 0.00 4.63
578 579 7.716998 ACTTTGATCAAATCTTATATGCGGAGT 59.283 33.333 20.76 7.49 0.00 3.85
579 580 8.450578 TTTGATCAAATCTTATATGCGGAGTT 57.549 30.769 16.91 0.00 0.00 3.01
580 581 9.554395 TTTGATCAAATCTTATATGCGGAGTTA 57.446 29.630 16.91 0.00 0.00 2.24
581 582 9.554395 TTGATCAAATCTTATATGCGGAGTTAA 57.446 29.630 5.45 0.00 0.00 2.01
582 583 9.554395 TGATCAAATCTTATATGCGGAGTTAAA 57.446 29.630 0.00 0.00 0.00 1.52
585 586 9.607988 TCAAATCTTATATGCGGAGTTAAAAGA 57.392 29.630 0.00 0.00 0.00 2.52
589 590 7.902032 TCTTATATGCGGAGTTAAAAGAAACG 58.098 34.615 0.00 0.00 34.46 3.60
590 591 3.824414 ATGCGGAGTTAAAAGAAACGG 57.176 42.857 0.00 0.00 34.46 4.44
619 620 5.499139 TTGTTGACTCATGAAGTTGAACC 57.501 39.130 0.00 0.00 38.74 3.62
622 623 6.295249 TGTTGACTCATGAAGTTGAACCATA 58.705 36.000 0.00 0.00 38.74 2.74
625 626 6.475504 TGACTCATGAAGTTGAACCATACAT 58.524 36.000 0.00 0.00 38.74 2.29
642 643 7.083875 CCATACATTGATGGTTCGTTACTTT 57.916 36.000 0.00 0.00 41.42 2.66
643 644 6.966632 CCATACATTGATGGTTCGTTACTTTG 59.033 38.462 0.00 0.00 41.42 2.77
650 651 3.834938 TGGTTCGTTACTTTGGGGAAAT 58.165 40.909 0.00 0.00 0.00 2.17
651 652 4.983053 TGGTTCGTTACTTTGGGGAAATA 58.017 39.130 0.00 0.00 0.00 1.40
660 661 8.287503 CGTTACTTTGGGGAAATATATACAAGC 58.712 37.037 0.00 0.00 0.00 4.01
719 1319 1.674322 CTCAAATTCCCGCCACGGT 60.674 57.895 5.17 0.00 46.80 4.83
917 1587 3.148084 CCCTCGCCGGTTATCCAT 58.852 61.111 1.90 0.00 0.00 3.41
935 1605 1.265454 ATCACCGTTCCTCCCACCTC 61.265 60.000 0.00 0.00 0.00 3.85
1401 2083 1.227853 GGCCGTCACCAAGTTCACT 60.228 57.895 0.00 0.00 0.00 3.41
1475 2199 3.991121 GCTCTGTCCTCTTGTAACTTGTC 59.009 47.826 0.00 0.00 0.00 3.18
1592 2506 0.671472 CGATCTGTGGTGCAAGCTCA 60.671 55.000 0.00 0.00 36.33 4.26
1606 2520 3.434984 GCAAGCTCACCTTTTCTCTGTAG 59.565 47.826 0.00 0.00 0.00 2.74
1667 2582 9.535270 GTCTCTCTGTTTCAATTCTTAATTTCG 57.465 33.333 0.00 0.00 0.00 3.46
1676 2592 6.386654 TCAATTCTTAATTTCGGTTTCAGCC 58.613 36.000 0.00 0.00 0.00 4.85
1688 2604 2.360801 GGTTTCAGCCAACTGTTTAGCA 59.639 45.455 13.11 0.00 44.77 3.49
1707 2623 2.287608 GCACCCTGTTTCAGTTAACTGC 60.288 50.000 27.49 15.88 43.46 4.40
1755 2687 1.740025 CAATTTCAGCTCCCGACCTTC 59.260 52.381 0.00 0.00 0.00 3.46
1757 2689 0.608640 TTTCAGCTCCCGACCTTCTC 59.391 55.000 0.00 0.00 0.00 2.87
1758 2690 0.541998 TTCAGCTCCCGACCTTCTCA 60.542 55.000 0.00 0.00 0.00 3.27
1759 2691 0.541998 TCAGCTCCCGACCTTCTCAA 60.542 55.000 0.00 0.00 0.00 3.02
1760 2692 0.539051 CAGCTCCCGACCTTCTCAAT 59.461 55.000 0.00 0.00 0.00 2.57
1818 2761 4.962693 CAGATGTTGCTGTTACTGCTTAC 58.037 43.478 14.81 12.58 0.00 2.34
1819 2762 3.679980 AGATGTTGCTGTTACTGCTTACG 59.320 43.478 14.81 0.00 0.00 3.18
1820 2763 2.828877 TGTTGCTGTTACTGCTTACGT 58.171 42.857 14.81 0.00 0.00 3.57
1821 2764 2.542178 TGTTGCTGTTACTGCTTACGTG 59.458 45.455 14.81 0.00 0.00 4.49
1822 2765 2.519377 TGCTGTTACTGCTTACGTGT 57.481 45.000 14.81 0.00 0.00 4.49
1823 2766 2.131972 TGCTGTTACTGCTTACGTGTG 58.868 47.619 14.81 0.00 0.00 3.82
1834 2777 2.719046 GCTTACGTGTGCACAATTTGTC 59.281 45.455 23.59 6.98 0.00 3.18
1835 2778 3.296628 CTTACGTGTGCACAATTTGTCC 58.703 45.455 23.59 6.17 0.00 4.02
1840 2783 0.665835 GTGCACAATTTGTCCGTCCA 59.334 50.000 13.17 0.00 0.00 4.02
1854 2797 1.732259 CCGTCCATTTTTCTCTCGTGG 59.268 52.381 0.00 0.00 0.00 4.94
1862 2805 6.488683 TCCATTTTTCTCTCGTGGTGTTTATT 59.511 34.615 0.00 0.00 0.00 1.40
1878 2821 7.812191 TGGTGTTTATTTGTTGTATCATTGCTC 59.188 33.333 0.00 0.00 0.00 4.26
1896 2839 7.911727 TCATTGCTCGAACATAAGATGAAAATG 59.088 33.333 0.00 0.00 0.00 2.32
1897 2840 6.741992 TGCTCGAACATAAGATGAAAATGT 57.258 33.333 0.00 0.00 35.40 2.71
1933 2876 1.066002 GCAGCACGTTACGGTAGGATA 59.934 52.381 10.20 0.00 0.00 2.59
1934 2877 2.288030 GCAGCACGTTACGGTAGGATAT 60.288 50.000 10.20 0.00 0.00 1.63
1990 2933 5.542779 CCGAGGAGAGGATGTTTATTTAGG 58.457 45.833 0.00 0.00 0.00 2.69
2045 2988 9.019764 GAAATGCATATTTTGTACCATGTGTAC 57.980 33.333 0.00 14.19 41.84 2.90
2061 3004 6.073003 CCATGTGTACTTTCTTTCTCCACTTC 60.073 42.308 0.00 0.00 0.00 3.01
2107 3053 3.716353 TCTTGGGAGTACATGGTATGCAT 59.284 43.478 3.79 3.79 0.00 3.96
2113 3059 5.479306 GGAGTACATGGTATGCATATCGTT 58.521 41.667 10.16 4.68 0.00 3.85
2116 3062 5.926542 AGTACATGGTATGCATATCGTTCAC 59.073 40.000 10.16 10.18 0.00 3.18
2144 3090 4.063967 TGGAACAGCCGCGATCGT 62.064 61.111 17.81 0.00 40.66 3.73
2145 3091 2.813908 GGAACAGCCGCGATCGTT 60.814 61.111 17.81 7.25 0.00 3.85
2146 3092 2.388232 GGAACAGCCGCGATCGTTT 61.388 57.895 17.81 0.73 0.00 3.60
2176 3122 4.859798 GTCTCGTCATCAGAAGTGTAAAGG 59.140 45.833 0.00 0.00 0.00 3.11
2294 3241 1.677217 GGTCTGGAGTCAACATCTGGC 60.677 57.143 0.00 0.00 0.00 4.85
2296 3243 0.742281 CTGGAGTCAACATCTGGCGG 60.742 60.000 0.00 0.00 33.60 6.13
2297 3244 1.296715 GGAGTCAACATCTGGCGGT 59.703 57.895 0.00 0.00 33.60 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.218635 GGTATTCAGTCTCGGCATCATAGA 59.781 45.833 0.00 0.00 0.00 1.98
23 24 1.334243 GGGTCTCGGTATTCAGTCTCG 59.666 57.143 0.00 0.00 0.00 4.04
72 73 6.436843 AATTCGCAACTTTATTCGATTCCT 57.563 33.333 0.00 0.00 0.00 3.36
74 75 8.850452 AGAAAAATTCGCAACTTTATTCGATTC 58.150 29.630 0.00 0.00 34.02 2.52
103 104 1.855295 TCATGACATGCAAGGCCATT 58.145 45.000 10.76 0.00 0.00 3.16
105 106 1.630223 TTTCATGACATGCAAGGCCA 58.370 45.000 10.76 0.00 0.00 5.36
110 111 5.419471 TCATCCTTGATTTCATGACATGCAA 59.581 36.000 10.76 6.77 0.00 4.08
127 128 8.316946 TCGCTCTTAATTCATGATATCATCCTT 58.683 33.333 15.49 11.11 33.61 3.36
136 137 5.471456 GTGGGATTCGCTCTTAATTCATGAT 59.529 40.000 0.00 0.00 0.00 2.45
139 140 4.780815 TGTGGGATTCGCTCTTAATTCAT 58.219 39.130 2.19 0.00 0.00 2.57
166 167 3.726557 TTAGGAACAGAGGGAGTACGA 57.273 47.619 0.00 0.00 0.00 3.43
167 168 6.651975 ATATTTAGGAACAGAGGGAGTACG 57.348 41.667 0.00 0.00 0.00 3.67
168 169 9.091220 ACATATATTTAGGAACAGAGGGAGTAC 57.909 37.037 0.00 0.00 0.00 2.73
169 170 9.310449 GACATATATTTAGGAACAGAGGGAGTA 57.690 37.037 0.00 0.00 0.00 2.59
170 171 8.013667 AGACATATATTTAGGAACAGAGGGAGT 58.986 37.037 0.00 0.00 0.00 3.85
171 172 8.429237 AGACATATATTTAGGAACAGAGGGAG 57.571 38.462 0.00 0.00 0.00 4.30
172 173 8.798975 AAGACATATATTTAGGAACAGAGGGA 57.201 34.615 0.00 0.00 0.00 4.20
201 202 9.221933 CCGTATATAGTCTACAGTGAAATCTCT 57.778 37.037 0.00 0.00 0.00 3.10
202 203 9.217278 TCCGTATATAGTCTACAGTGAAATCTC 57.783 37.037 0.00 0.00 0.00 2.75
203 204 9.221933 CTCCGTATATAGTCTACAGTGAAATCT 57.778 37.037 0.00 0.00 0.00 2.40
204 205 7.964011 GCTCCGTATATAGTCTACAGTGAAATC 59.036 40.741 0.00 0.00 0.00 2.17
205 206 7.447545 TGCTCCGTATATAGTCTACAGTGAAAT 59.552 37.037 0.00 0.00 0.00 2.17
206 207 6.769341 TGCTCCGTATATAGTCTACAGTGAAA 59.231 38.462 0.00 0.00 0.00 2.69
207 208 6.293698 TGCTCCGTATATAGTCTACAGTGAA 58.706 40.000 0.00 0.00 0.00 3.18
208 209 5.861727 TGCTCCGTATATAGTCTACAGTGA 58.138 41.667 0.00 0.00 0.00 3.41
209 210 6.555812 TTGCTCCGTATATAGTCTACAGTG 57.444 41.667 0.00 0.00 0.00 3.66
210 211 7.578310 TTTTGCTCCGTATATAGTCTACAGT 57.422 36.000 0.00 0.00 0.00 3.55
211 212 8.297426 TCATTTTGCTCCGTATATAGTCTACAG 58.703 37.037 0.00 0.00 0.00 2.74
212 213 8.173542 TCATTTTGCTCCGTATATAGTCTACA 57.826 34.615 0.00 0.00 0.00 2.74
213 214 8.298140 ACTCATTTTGCTCCGTATATAGTCTAC 58.702 37.037 0.00 0.00 0.00 2.59
214 215 8.405418 ACTCATTTTGCTCCGTATATAGTCTA 57.595 34.615 0.00 0.00 0.00 2.59
215 216 7.291411 ACTCATTTTGCTCCGTATATAGTCT 57.709 36.000 0.00 0.00 0.00 3.24
216 217 9.472361 TTTACTCATTTTGCTCCGTATATAGTC 57.528 33.333 0.00 0.00 0.00 2.59
217 218 9.257651 GTTTACTCATTTTGCTCCGTATATAGT 57.742 33.333 0.00 0.00 0.00 2.12
218 219 8.709646 GGTTTACTCATTTTGCTCCGTATATAG 58.290 37.037 0.00 0.00 0.00 1.31
219 220 8.426489 AGGTTTACTCATTTTGCTCCGTATATA 58.574 33.333 0.00 0.00 0.00 0.86
220 221 7.280356 AGGTTTACTCATTTTGCTCCGTATAT 58.720 34.615 0.00 0.00 0.00 0.86
221 222 6.646267 AGGTTTACTCATTTTGCTCCGTATA 58.354 36.000 0.00 0.00 0.00 1.47
222 223 5.497474 AGGTTTACTCATTTTGCTCCGTAT 58.503 37.500 0.00 0.00 0.00 3.06
223 224 4.901868 AGGTTTACTCATTTTGCTCCGTA 58.098 39.130 0.00 0.00 0.00 4.02
224 225 3.751518 AGGTTTACTCATTTTGCTCCGT 58.248 40.909 0.00 0.00 0.00 4.69
225 226 6.436843 AATAGGTTTACTCATTTTGCTCCG 57.563 37.500 0.00 0.00 0.00 4.63
226 227 8.523658 AGAAAATAGGTTTACTCATTTTGCTCC 58.476 33.333 8.59 0.00 32.29 4.70
235 236 9.768662 ACGTCTTTTAGAAAATAGGTTTACTCA 57.231 29.630 0.00 0.00 0.00 3.41
237 238 9.993454 AGACGTCTTTTAGAAAATAGGTTTACT 57.007 29.630 13.58 0.00 0.00 2.24
256 257 9.727859 ACTACATTCTGATGTATATAGACGTCT 57.272 33.333 23.66 23.66 45.20 4.18
257 258 9.976255 GACTACATTCTGATGTATATAGACGTC 57.024 37.037 7.70 7.70 45.20 4.34
258 259 9.727859 AGACTACATTCTGATGTATATAGACGT 57.272 33.333 0.00 0.00 45.20 4.34
316 317 8.925338 GGAGTTAATCTACTTCCTTCATTCCTA 58.075 37.037 0.00 0.00 0.00 2.94
317 318 7.403231 TGGAGTTAATCTACTTCCTTCATTCCT 59.597 37.037 0.00 0.00 0.00 3.36
318 319 7.565680 TGGAGTTAATCTACTTCCTTCATTCC 58.434 38.462 0.00 0.00 0.00 3.01
321 322 9.440761 ACTATGGAGTTAATCTACTTCCTTCAT 57.559 33.333 0.00 0.00 28.61 2.57
322 323 8.840200 ACTATGGAGTTAATCTACTTCCTTCA 57.160 34.615 0.00 0.00 28.61 3.02
324 325 9.939424 AGTACTATGGAGTTAATCTACTTCCTT 57.061 33.333 0.00 0.00 37.10 3.36
325 326 9.577222 GAGTACTATGGAGTTAATCTACTTCCT 57.423 37.037 0.00 0.00 37.10 3.36
326 327 8.795513 GGAGTACTATGGAGTTAATCTACTTCC 58.204 40.741 0.00 0.00 37.10 3.46
327 328 8.795513 GGGAGTACTATGGAGTTAATCTACTTC 58.204 40.741 0.00 0.00 37.10 3.01
328 329 8.512813 AGGGAGTACTATGGAGTTAATCTACTT 58.487 37.037 0.00 0.00 37.10 2.24
329 330 8.059565 AGGGAGTACTATGGAGTTAATCTACT 57.940 38.462 0.00 0.00 37.10 2.57
345 346 7.295322 ACTAAAAAGAAACGTAGGGAGTACT 57.705 36.000 0.00 0.00 0.00 2.73
346 347 6.587990 GGACTAAAAAGAAACGTAGGGAGTAC 59.412 42.308 0.00 0.00 0.00 2.73
347 348 6.570378 CGGACTAAAAAGAAACGTAGGGAGTA 60.570 42.308 0.00 0.00 0.00 2.59
348 349 5.545588 GGACTAAAAAGAAACGTAGGGAGT 58.454 41.667 0.00 0.00 0.00 3.85
349 350 4.624452 CGGACTAAAAAGAAACGTAGGGAG 59.376 45.833 0.00 0.00 0.00 4.30
350 351 4.559153 CGGACTAAAAAGAAACGTAGGGA 58.441 43.478 0.00 0.00 0.00 4.20
351 352 3.124128 GCGGACTAAAAAGAAACGTAGGG 59.876 47.826 0.00 0.00 0.00 3.53
352 353 3.742369 TGCGGACTAAAAAGAAACGTAGG 59.258 43.478 0.00 0.00 0.00 3.18
353 354 4.977741 TGCGGACTAAAAAGAAACGTAG 57.022 40.909 0.00 0.00 0.00 3.51
354 355 8.700722 TTATATGCGGACTAAAAAGAAACGTA 57.299 30.769 0.00 0.00 0.00 3.57
355 356 7.201582 CCTTATATGCGGACTAAAAAGAAACGT 60.202 37.037 0.00 0.00 0.00 3.99
356 357 7.123830 CCTTATATGCGGACTAAAAAGAAACG 58.876 38.462 0.00 0.00 0.00 3.60
357 358 7.982224 ACCTTATATGCGGACTAAAAAGAAAC 58.018 34.615 0.00 0.00 0.00 2.78
358 359 8.570068 AACCTTATATGCGGACTAAAAAGAAA 57.430 30.769 0.00 0.00 0.00 2.52
359 360 8.455682 CAAACCTTATATGCGGACTAAAAAGAA 58.544 33.333 0.00 0.00 0.00 2.52
360 361 7.066525 CCAAACCTTATATGCGGACTAAAAAGA 59.933 37.037 0.00 0.00 0.00 2.52
361 362 7.148137 ACCAAACCTTATATGCGGACTAAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
362 363 6.660094 ACCAAACCTTATATGCGGACTAAAAA 59.340 34.615 0.00 0.00 0.00 1.94
363 364 6.181908 ACCAAACCTTATATGCGGACTAAAA 58.818 36.000 0.00 0.00 0.00 1.52
364 365 5.747342 ACCAAACCTTATATGCGGACTAAA 58.253 37.500 0.00 0.00 0.00 1.85
365 366 5.104859 TGACCAAACCTTATATGCGGACTAA 60.105 40.000 0.00 0.00 0.00 2.24
366 367 4.406326 TGACCAAACCTTATATGCGGACTA 59.594 41.667 0.00 0.00 0.00 2.59
367 368 3.199071 TGACCAAACCTTATATGCGGACT 59.801 43.478 0.00 0.00 0.00 3.85
368 369 3.537580 TGACCAAACCTTATATGCGGAC 58.462 45.455 0.00 0.00 0.00 4.79
369 370 3.916359 TGACCAAACCTTATATGCGGA 57.084 42.857 0.00 0.00 0.00 5.54
370 371 4.398044 ACTTTGACCAAACCTTATATGCGG 59.602 41.667 0.00 0.00 0.00 5.69
371 372 5.123186 TGACTTTGACCAAACCTTATATGCG 59.877 40.000 0.00 0.00 0.00 4.73
372 373 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
373 374 7.029563 GCTTGACTTTGACCAAACCTTATATG 58.970 38.462 0.00 0.00 0.00 1.78
374 375 6.948309 AGCTTGACTTTGACCAAACCTTATAT 59.052 34.615 0.00 0.00 0.00 0.86
375 376 6.303839 AGCTTGACTTTGACCAAACCTTATA 58.696 36.000 0.00 0.00 0.00 0.98
376 377 5.140454 AGCTTGACTTTGACCAAACCTTAT 58.860 37.500 0.00 0.00 0.00 1.73
377 378 4.532834 AGCTTGACTTTGACCAAACCTTA 58.467 39.130 0.00 0.00 0.00 2.69
378 379 3.365472 AGCTTGACTTTGACCAAACCTT 58.635 40.909 0.00 0.00 0.00 3.50
379 380 3.018423 AGCTTGACTTTGACCAAACCT 57.982 42.857 0.00 0.00 0.00 3.50
380 381 3.801114 AAGCTTGACTTTGACCAAACC 57.199 42.857 0.00 0.00 33.71 3.27
390 391 9.998106 TTAGTCAAACTCTATAAAGCTTGACTT 57.002 29.630 23.23 12.05 41.70 3.01
391 392 9.998106 TTTAGTCAAACTCTATAAAGCTTGACT 57.002 29.630 22.20 22.20 36.89 3.41
456 457 9.878667 AAAAATGTTTCATGATGCATCTGATAA 57.121 25.926 26.32 17.90 0.00 1.75
530 531 9.930693 AAAGTCAAACTACACAAACCAAATTTA 57.069 25.926 0.00 0.00 0.00 1.40
531 532 8.716909 CAAAGTCAAACTACACAAACCAAATTT 58.283 29.630 0.00 0.00 0.00 1.82
532 533 8.091449 TCAAAGTCAAACTACACAAACCAAATT 58.909 29.630 0.00 0.00 0.00 1.82
533 534 7.607250 TCAAAGTCAAACTACACAAACCAAAT 58.393 30.769 0.00 0.00 0.00 2.32
534 535 6.982852 TCAAAGTCAAACTACACAAACCAAA 58.017 32.000 0.00 0.00 0.00 3.28
535 536 6.576662 TCAAAGTCAAACTACACAAACCAA 57.423 33.333 0.00 0.00 0.00 3.67
536 537 6.375736 TGATCAAAGTCAAACTACACAAACCA 59.624 34.615 0.00 0.00 0.00 3.67
537 538 6.791303 TGATCAAAGTCAAACTACACAAACC 58.209 36.000 0.00 0.00 0.00 3.27
538 539 8.682128 TTTGATCAAAGTCAAACTACACAAAC 57.318 30.769 16.91 0.00 41.70 2.93
549 550 8.344831 CCGCATATAAGATTTGATCAAAGTCAA 58.655 33.333 24.17 11.64 36.38 3.18
550 551 7.714813 TCCGCATATAAGATTTGATCAAAGTCA 59.285 33.333 24.17 11.02 33.32 3.41
551 552 8.087982 TCCGCATATAAGATTTGATCAAAGTC 57.912 34.615 24.17 19.70 33.32 3.01
552 553 7.716998 ACTCCGCATATAAGATTTGATCAAAGT 59.283 33.333 24.17 14.86 33.32 2.66
553 554 8.092521 ACTCCGCATATAAGATTTGATCAAAG 57.907 34.615 24.17 10.49 33.32 2.77
554 555 8.450578 AACTCCGCATATAAGATTTGATCAAA 57.549 30.769 22.52 22.52 34.46 2.69
555 556 9.554395 TTAACTCCGCATATAAGATTTGATCAA 57.446 29.630 3.38 3.38 0.00 2.57
556 557 9.554395 TTTAACTCCGCATATAAGATTTGATCA 57.446 29.630 0.00 0.00 0.00 2.92
559 560 9.607988 TCTTTTAACTCCGCATATAAGATTTGA 57.392 29.630 0.00 0.00 0.00 2.69
563 564 8.548721 CGTTTCTTTTAACTCCGCATATAAGAT 58.451 33.333 0.00 0.00 0.00 2.40
564 565 7.010738 CCGTTTCTTTTAACTCCGCATATAAGA 59.989 37.037 0.00 0.00 0.00 2.10
565 566 7.010738 TCCGTTTCTTTTAACTCCGCATATAAG 59.989 37.037 0.00 0.00 0.00 1.73
566 567 6.817641 TCCGTTTCTTTTAACTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
567 568 6.339730 TCCGTTTCTTTTAACTCCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
568 569 5.180271 TCCGTTTCTTTTAACTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
569 570 4.567971 TCCGTTTCTTTTAACTCCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
570 571 3.404899 TCCGTTTCTTTTAACTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
571 572 2.803956 CTCCGTTTCTTTTAACTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
572 573 2.804527 ACTCCGTTTCTTTTAACTCCGC 59.195 45.455 0.00 0.00 0.00 5.54
573 574 7.998753 ATATACTCCGTTTCTTTTAACTCCG 57.001 36.000 0.00 0.00 0.00 4.63
574 575 9.159364 ACAATATACTCCGTTTCTTTTAACTCC 57.841 33.333 0.00 0.00 0.00 3.85
579 580 9.715121 AGTCAACAATATACTCCGTTTCTTTTA 57.285 29.630 0.00 0.00 0.00 1.52
580 581 8.617290 AGTCAACAATATACTCCGTTTCTTTT 57.383 30.769 0.00 0.00 0.00 2.27
581 582 7.876068 TGAGTCAACAATATACTCCGTTTCTTT 59.124 33.333 0.00 0.00 39.10 2.52
582 583 7.383687 TGAGTCAACAATATACTCCGTTTCTT 58.616 34.615 0.00 0.00 39.10 2.52
583 584 6.931838 TGAGTCAACAATATACTCCGTTTCT 58.068 36.000 0.00 0.00 39.10 2.52
584 585 7.491372 TCATGAGTCAACAATATACTCCGTTTC 59.509 37.037 0.00 0.00 39.10 2.78
585 586 7.327975 TCATGAGTCAACAATATACTCCGTTT 58.672 34.615 0.00 0.00 39.10 3.60
586 587 6.873997 TCATGAGTCAACAATATACTCCGTT 58.126 36.000 0.00 0.00 39.10 4.44
587 588 6.465439 TCATGAGTCAACAATATACTCCGT 57.535 37.500 0.00 0.00 39.10 4.69
588 589 6.980978 ACTTCATGAGTCAACAATATACTCCG 59.019 38.462 0.00 0.00 39.10 4.63
589 590 8.607459 CAACTTCATGAGTCAACAATATACTCC 58.393 37.037 0.00 0.00 39.10 3.85
590 591 9.371136 TCAACTTCATGAGTCAACAATATACTC 57.629 33.333 0.00 0.00 37.72 2.59
619 620 6.966632 CCAAAGTAACGAACCATCAATGTATG 59.033 38.462 0.00 0.00 0.00 2.39
622 623 4.217550 CCCAAAGTAACGAACCATCAATGT 59.782 41.667 0.00 0.00 0.00 2.71
625 626 3.150767 CCCCAAAGTAACGAACCATCAA 58.849 45.455 0.00 0.00 0.00 2.57
642 643 5.534654 GCACTTGCTTGTATATATTTCCCCA 59.465 40.000 0.00 0.00 38.21 4.96
643 644 6.013842 GCACTTGCTTGTATATATTTCCCC 57.986 41.667 0.00 0.00 38.21 4.81
660 661 2.212869 TTTCTGCTGCAAAGCACTTG 57.787 45.000 3.02 0.00 40.23 3.16
719 1319 2.560861 GCGCGCATTGGAGTTTCA 59.439 55.556 29.10 0.00 0.00 2.69
917 1587 1.911766 GAGGTGGGAGGAACGGTGA 60.912 63.158 0.00 0.00 0.00 4.02
922 1592 2.972819 GCTGGGAGGTGGGAGGAAC 61.973 68.421 0.00 0.00 0.00 3.62
1031 1710 4.148825 CCGCGGGGGTCTTCTCTG 62.149 72.222 20.10 0.00 0.00 3.35
1056 1735 1.679898 CTTCTTCTCCGCCTTGGGT 59.320 57.895 0.00 0.00 38.76 4.51
1097 1776 2.258748 CTTCCCCTTCTTCTCGCCCC 62.259 65.000 0.00 0.00 0.00 5.80
1098 1777 1.222113 CTTCCCCTTCTTCTCGCCC 59.778 63.158 0.00 0.00 0.00 6.13
1099 1778 0.613777 TTCTTCCCCTTCTTCTCGCC 59.386 55.000 0.00 0.00 0.00 5.54
1417 2099 1.413812 CAGGGTGACATCGATCCATCA 59.586 52.381 0.00 0.00 0.00 3.07
1475 2199 2.946947 GTGATCCCACACAACCAGG 58.053 57.895 0.00 0.00 42.72 4.45
1496 2227 6.749139 TGTTACTATTTCTCCGGATCATGAG 58.251 40.000 3.57 2.71 0.00 2.90
1592 2506 4.142271 CGCAGAGATCTACAGAGAAAAGGT 60.142 45.833 0.00 0.00 34.61 3.50
1606 2520 2.167861 GGTCGTTGCCGCAGAGATC 61.168 63.158 0.00 0.00 0.00 2.75
1667 2582 2.360801 TGCTAAACAGTTGGCTGAAACC 59.639 45.455 11.32 0.00 45.28 3.27
1676 2592 3.380004 TGAAACAGGGTGCTAAACAGTTG 59.620 43.478 0.00 0.00 0.00 3.16
1688 2604 3.118038 TCAGCAGTTAACTGAAACAGGGT 60.118 43.478 34.43 12.09 46.59 4.34
1755 2687 0.942962 GGCCATTCAGCGAGATTGAG 59.057 55.000 0.00 0.00 30.89 3.02
1757 2689 1.001706 CATGGCCATTCAGCGAGATTG 60.002 52.381 17.92 0.00 0.00 2.67
1758 2690 1.134007 TCATGGCCATTCAGCGAGATT 60.134 47.619 17.92 0.00 0.00 2.40
1759 2691 0.471191 TCATGGCCATTCAGCGAGAT 59.529 50.000 17.92 0.00 0.00 2.75
1760 2692 0.471191 ATCATGGCCATTCAGCGAGA 59.529 50.000 17.92 8.97 0.00 4.04
1812 2755 2.098280 ACAAATTGTGCACACGTAAGCA 59.902 40.909 21.56 9.72 45.62 3.91
1813 2756 2.719046 GACAAATTGTGCACACGTAAGC 59.281 45.455 21.56 4.55 45.62 3.09
1814 2757 3.296628 GGACAAATTGTGCACACGTAAG 58.703 45.455 21.56 11.25 38.66 2.34
1815 2758 2.286477 CGGACAAATTGTGCACACGTAA 60.286 45.455 21.56 4.97 38.73 3.18
1816 2759 1.261885 CGGACAAATTGTGCACACGTA 59.738 47.619 21.56 5.41 38.73 3.57
1818 2761 0.028770 ACGGACAAATTGTGCACACG 59.971 50.000 21.56 19.74 38.73 4.49
1819 2762 1.599419 GGACGGACAAATTGTGCACAC 60.599 52.381 21.56 6.69 38.73 3.82
1820 2763 0.665835 GGACGGACAAATTGTGCACA 59.334 50.000 17.42 17.42 38.73 4.57
1821 2764 0.665835 TGGACGGACAAATTGTGCAC 59.334 50.000 17.34 10.75 38.73 4.57
1822 2765 1.614996 ATGGACGGACAAATTGTGCA 58.385 45.000 17.34 0.00 38.73 4.57
1823 2766 2.723124 AATGGACGGACAAATTGTGC 57.277 45.000 2.20 5.25 35.21 4.57
1834 2777 1.732259 CCACGAGAGAAAAATGGACGG 59.268 52.381 0.00 0.00 31.69 4.79
1835 2778 2.157668 CACCACGAGAGAAAAATGGACG 59.842 50.000 0.00 0.00 34.38 4.79
1840 2783 7.712797 ACAAATAAACACCACGAGAGAAAAAT 58.287 30.769 0.00 0.00 0.00 1.82
1854 2797 7.748683 TCGAGCAATGATACAACAAATAAACAC 59.251 33.333 0.00 0.00 0.00 3.32
1862 2805 5.878332 ATGTTCGAGCAATGATACAACAA 57.122 34.783 5.91 0.00 0.00 2.83
1878 2821 7.090173 ACCCAAACATTTTCATCTTATGTTCG 58.910 34.615 0.00 0.00 40.54 3.95
1896 2839 1.282875 GCGCTGACTGAACCCAAAC 59.717 57.895 0.00 0.00 0.00 2.93
1897 2840 1.153066 TGCGCTGACTGAACCCAAA 60.153 52.632 9.73 0.00 0.00 3.28
1933 2876 4.524802 TGCCTGATCCATTAACCTCAAT 57.475 40.909 0.00 0.00 0.00 2.57
1934 2877 4.272489 CTTGCCTGATCCATTAACCTCAA 58.728 43.478 0.00 0.00 0.00 3.02
1990 2933 7.115378 CACAAGAAAAGTTTATGTGCATCTTCC 59.885 37.037 13.07 0.00 33.92 3.46
2054 2997 9.952030 TGTCATTACATTATTACAAGAAGTGGA 57.048 29.630 0.00 0.00 0.00 4.02
2107 3053 7.604545 TGTTCCATCAAACTAATGTGAACGATA 59.395 33.333 0.00 0.00 37.25 2.92
2113 3059 4.458989 GGCTGTTCCATCAAACTAATGTGA 59.541 41.667 0.00 0.00 34.01 3.58
2116 3062 3.731867 GCGGCTGTTCCATCAAACTAATG 60.732 47.826 0.00 0.00 34.01 1.90
2142 3088 1.114842 TGACGAGACGAAACGAAACG 58.885 50.000 0.00 0.00 0.00 3.60
2143 3089 2.722629 TGATGACGAGACGAAACGAAAC 59.277 45.455 0.00 0.00 0.00 2.78
2144 3090 2.977829 CTGATGACGAGACGAAACGAAA 59.022 45.455 0.00 0.00 0.00 3.46
2145 3091 2.224784 TCTGATGACGAGACGAAACGAA 59.775 45.455 0.00 0.00 0.00 3.85
2146 3092 1.802365 TCTGATGACGAGACGAAACGA 59.198 47.619 0.00 0.00 0.00 3.85
2176 3122 1.884926 CTCGCCGCCCATTCTCTTC 60.885 63.158 0.00 0.00 0.00 2.87
2294 3241 3.190327 TGGAACATCAGCACAATTTACCG 59.810 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.