Multiple sequence alignment - TraesCS3A01G329600

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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 TraesCS3A01G329600 chr3A 100.000 3381 0 0 1 3381 574510451 574513831 0.000000e+00 6244.0
1 TraesCS3A01G329600 chr3A 98.868 265 3 0 1 265 65018918 65019182 1.100000e-129 473.0
2 TraesCS3A01G329600 chr3B 91.336 2747 149 37 463 3158 571793965 571796673 0.000000e+00 3672.0
3 TraesCS3A01G329600 chr3B 80.952 273 11 16 3147 3381 571796884 571797153 9.640000e-41 178.0
4 TraesCS3A01G329600 chr3B 98.182 55 1 0 1 55 84457924 84457978 2.780000e-16 97.1
5 TraesCS3A01G329600 chr3B 86.585 82 8 2 363 443 422583676 422583755 1.670000e-13 87.9
6 TraesCS3A01G329600 chr3D 95.915 1738 66 4 463 2195 435699415 435701152 0.000000e+00 2811.0
7 TraesCS3A01G329600 chr3D 84.974 965 90 36 2220 3158 435701140 435702075 0.000000e+00 928.0
8 TraesCS3A01G329600 chr3D 96.241 266 9 1 1 265 54005322 54005587 5.180000e-118 435.0
9 TraesCS3A01G329600 chr3D 93.860 114 3 2 3175 3287 435702326 435702436 5.800000e-38 169.0
10 TraesCS3A01G329600 chr2B 80.645 124 15 7 347 464 744031598 744031478 1.670000e-13 87.9
11 TraesCS3A01G329600 chrUn 84.946 93 5 7 378 464 262619367 262619278 6.010000e-13 86.1
12 TraesCS3A01G329600 chr5D 84.946 93 5 7 378 464 492767179 492767090 6.010000e-13 86.1
13 TraesCS3A01G329600 chr6B 85.542 83 8 3 363 443 193989339 193989419 2.160000e-12 84.2
14 TraesCS3A01G329600 chr4D 82.653 98 14 2 347 443 457955874 457955779 2.160000e-12 84.2
15 TraesCS3A01G329600 chr7A 79.839 124 15 8 347 464 475465759 475465640 7.780000e-12 82.4
16 TraesCS3A01G329600 chr4B 79.839 124 16 7 347 464 542191852 542191732 7.780000e-12 82.4
17 TraesCS3A01G329600 chr7B 94.444 36 0 2 311 344 228276104 228276139 2.000000e-03 54.7


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 TraesCS3A01G329600 chr3A 574510451 574513831 3380 False 6244.000000 6244 100.000 1 3381 1 chr3A.!!$F2 3380
1 TraesCS3A01G329600 chr3B 571793965 571797153 3188 False 1925.000000 3672 86.144 463 3381 2 chr3B.!!$F3 2918
2 TraesCS3A01G329600 chr3D 435699415 435702436 3021 False 1302.666667 2811 91.583 463 3287 3 chr3D.!!$F2 2824

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
546 552 1.016130 CAGCCTGCTTCACTACGTGG 61.016 60.0 0.0 0.0 33.87 4.94 F
1335 1355 0.987294 AGGCAGTCAGTATGCACCTT 59.013 50.0 0.0 0.0 45.68 3.50 F
2153 2175 0.394216 TGTGGGAATCAGCGGAATGG 60.394 55.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 1967 0.034059 CCGCCTTAATGGAGCTCGAT 59.966 55.0 7.83 6.51 38.35 3.59 R
2254 2298 0.097674 GCATGTGAATCGCCTGTGTC 59.902 55.0 0.00 0.00 0.00 3.67 R
3290 3593 0.253327 GGAATGGAGGAGGACACACC 59.747 60.0 0.00 0.00 39.35 4.16 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
20 21 3.625649 TTAATCAATGGGGGCAAAAGC 57.374 42.857 0.00 0.00 0.00 3.51
21 22 1.360185 AATCAATGGGGGCAAAAGCA 58.640 45.000 0.00 0.00 0.00 3.91
22 23 1.587066 ATCAATGGGGGCAAAAGCAT 58.413 45.000 0.00 0.00 0.00 3.79
23 24 2.244486 TCAATGGGGGCAAAAGCATA 57.756 45.000 0.00 0.00 0.00 3.14
24 25 1.830477 TCAATGGGGGCAAAAGCATAC 59.170 47.619 0.00 0.00 0.00 2.39
25 26 1.832998 CAATGGGGGCAAAAGCATACT 59.167 47.619 0.00 0.00 0.00 2.12
26 27 3.030291 CAATGGGGGCAAAAGCATACTA 58.970 45.455 0.00 0.00 0.00 1.82
27 28 3.618120 ATGGGGGCAAAAGCATACTAT 57.382 42.857 0.00 0.00 0.00 2.12
28 29 2.665165 TGGGGGCAAAAGCATACTATG 58.335 47.619 0.00 0.00 0.00 2.23
154 155 4.771590 ACAATTGTGTGTATGCCTCTTG 57.228 40.909 11.07 0.00 36.31 3.02
155 156 4.144297 ACAATTGTGTGTATGCCTCTTGT 58.856 39.130 11.07 0.00 36.31 3.16
156 157 4.022935 ACAATTGTGTGTATGCCTCTTGTG 60.023 41.667 11.07 0.00 36.31 3.33
157 158 2.928801 TGTGTGTATGCCTCTTGTGT 57.071 45.000 0.00 0.00 0.00 3.72
158 159 4.344359 TTGTGTGTATGCCTCTTGTGTA 57.656 40.909 0.00 0.00 0.00 2.90
159 160 3.659786 TGTGTGTATGCCTCTTGTGTAC 58.340 45.455 0.00 0.00 0.00 2.90
160 161 3.000727 GTGTGTATGCCTCTTGTGTACC 58.999 50.000 0.00 0.00 0.00 3.34
161 162 2.635427 TGTGTATGCCTCTTGTGTACCA 59.365 45.455 0.00 0.00 0.00 3.25
162 163 3.263170 TGTGTATGCCTCTTGTGTACCAT 59.737 43.478 0.00 0.00 0.00 3.55
163 164 3.623060 GTGTATGCCTCTTGTGTACCATG 59.377 47.826 0.00 0.00 0.00 3.66
164 165 3.263170 TGTATGCCTCTTGTGTACCATGT 59.737 43.478 0.00 0.00 0.00 3.21
165 166 2.949177 TGCCTCTTGTGTACCATGTT 57.051 45.000 0.00 0.00 0.00 2.71
166 167 2.503331 TGCCTCTTGTGTACCATGTTG 58.497 47.619 0.00 0.00 0.00 3.33
167 168 2.105649 TGCCTCTTGTGTACCATGTTGA 59.894 45.455 0.00 0.00 0.00 3.18
168 169 2.484264 GCCTCTTGTGTACCATGTTGAC 59.516 50.000 0.00 0.00 0.00 3.18
169 170 3.738982 CCTCTTGTGTACCATGTTGACA 58.261 45.455 0.00 0.00 0.00 3.58
170 171 4.133820 CCTCTTGTGTACCATGTTGACAA 58.866 43.478 0.00 0.00 0.00 3.18
171 172 4.578516 CCTCTTGTGTACCATGTTGACAAA 59.421 41.667 0.00 0.00 0.00 2.83
172 173 5.493133 TCTTGTGTACCATGTTGACAAAC 57.507 39.130 0.00 0.00 36.78 2.93
173 174 5.189928 TCTTGTGTACCATGTTGACAAACT 58.810 37.500 0.00 0.00 37.19 2.66
174 175 6.350103 TCTTGTGTACCATGTTGACAAACTA 58.650 36.000 0.00 0.00 37.19 2.24
175 176 5.994887 TGTGTACCATGTTGACAAACTAC 57.005 39.130 0.00 0.00 37.19 2.73
176 177 5.429130 TGTGTACCATGTTGACAAACTACA 58.571 37.500 0.00 0.00 38.42 2.74
177 178 5.880887 TGTGTACCATGTTGACAAACTACAA 59.119 36.000 0.00 0.00 37.71 2.41
178 179 6.374613 TGTGTACCATGTTGACAAACTACAAA 59.625 34.615 0.00 0.00 37.71 2.83
179 180 6.689669 GTGTACCATGTTGACAAACTACAAAC 59.310 38.462 0.00 0.00 37.71 2.93
180 181 6.600032 TGTACCATGTTGACAAACTACAAACT 59.400 34.615 0.00 0.00 37.71 2.66
181 182 6.524101 ACCATGTTGACAAACTACAAACTT 57.476 33.333 0.00 0.00 37.71 2.66
182 183 6.930731 ACCATGTTGACAAACTACAAACTTT 58.069 32.000 0.00 0.00 37.71 2.66
183 184 7.033185 ACCATGTTGACAAACTACAAACTTTC 58.967 34.615 0.00 0.00 37.71 2.62
184 185 7.032580 CCATGTTGACAAACTACAAACTTTCA 58.967 34.615 0.00 0.00 37.71 2.69
185 186 7.220683 CCATGTTGACAAACTACAAACTTTCAG 59.779 37.037 0.00 0.00 37.71 3.02
186 187 7.209471 TGTTGACAAACTACAAACTTTCAGT 57.791 32.000 0.00 0.00 37.19 3.41
187 188 7.653647 TGTTGACAAACTACAAACTTTCAGTT 58.346 30.769 0.00 0.00 37.32 3.16
188 189 8.784994 TGTTGACAAACTACAAACTTTCAGTTA 58.215 29.630 0.00 0.00 35.88 2.24
189 190 9.783256 GTTGACAAACTACAAACTTTCAGTTAT 57.217 29.630 0.00 0.00 33.66 1.89
193 194 9.581099 ACAAACTACAAACTTTCAGTTATTTGG 57.419 29.630 0.00 0.00 37.47 3.28
194 195 9.796120 CAAACTACAAACTTTCAGTTATTTGGA 57.204 29.630 0.00 0.00 37.47 3.53
214 215 9.784531 ATTTGGAATCATATTATTCGTCAGAGT 57.215 29.630 4.03 0.00 36.84 3.24
227 228 9.976511 TTATTCGTCAGAGTAAAAGAAAAGAGA 57.023 29.630 0.00 0.00 0.00 3.10
229 230 8.888579 TTCGTCAGAGTAAAAGAAAAGAGATT 57.111 30.769 0.00 0.00 0.00 2.40
230 231 8.888579 TCGTCAGAGTAAAAGAAAAGAGATTT 57.111 30.769 0.00 0.00 0.00 2.17
231 232 8.979574 TCGTCAGAGTAAAAGAAAAGAGATTTC 58.020 33.333 0.00 0.00 46.45 2.17
248 249 7.769272 GAGATTTCTCTTCGTTCTCAATGAT 57.231 36.000 0.22 0.00 39.81 2.45
249 250 7.769272 AGATTTCTCTTCGTTCTCAATGATC 57.231 36.000 0.00 0.00 0.00 2.92
250 251 7.326454 AGATTTCTCTTCGTTCTCAATGATCA 58.674 34.615 0.00 0.00 0.00 2.92
251 252 7.821359 AGATTTCTCTTCGTTCTCAATGATCAA 59.179 33.333 0.00 0.00 0.00 2.57
252 253 7.912056 TTTCTCTTCGTTCTCAATGATCAAT 57.088 32.000 0.00 0.00 0.00 2.57
253 254 7.531280 TTCTCTTCGTTCTCAATGATCAATC 57.469 36.000 0.00 0.00 0.00 2.67
254 255 5.745769 TCTCTTCGTTCTCAATGATCAATCG 59.254 40.000 0.00 0.00 0.00 3.34
255 256 4.268644 TCTTCGTTCTCAATGATCAATCGC 59.731 41.667 0.00 0.00 0.00 4.58
256 257 3.785486 TCGTTCTCAATGATCAATCGCT 58.215 40.909 0.00 0.00 0.00 4.93
257 258 4.183865 TCGTTCTCAATGATCAATCGCTT 58.816 39.130 0.00 0.00 0.00 4.68
258 259 4.268644 TCGTTCTCAATGATCAATCGCTTC 59.731 41.667 0.00 0.00 0.00 3.86
259 260 4.033243 CGTTCTCAATGATCAATCGCTTCA 59.967 41.667 0.00 0.00 0.00 3.02
260 261 5.446340 CGTTCTCAATGATCAATCGCTTCAA 60.446 40.000 0.00 0.00 0.00 2.69
261 262 6.493116 GTTCTCAATGATCAATCGCTTCAAT 58.507 36.000 0.00 0.00 0.00 2.57
262 263 6.296365 TCTCAATGATCAATCGCTTCAATC 57.704 37.500 0.00 0.00 0.00 2.67
263 264 6.053650 TCTCAATGATCAATCGCTTCAATCT 58.946 36.000 0.00 0.00 0.00 2.40
264 265 7.212274 TCTCAATGATCAATCGCTTCAATCTA 58.788 34.615 0.00 0.00 0.00 1.98
265 266 7.170489 TCTCAATGATCAATCGCTTCAATCTAC 59.830 37.037 0.00 0.00 0.00 2.59
266 267 5.835911 ATGATCAATCGCTTCAATCTACG 57.164 39.130 0.00 0.00 0.00 3.51
267 268 4.932146 TGATCAATCGCTTCAATCTACGA 58.068 39.130 0.00 0.00 39.11 3.43
268 269 5.348164 TGATCAATCGCTTCAATCTACGAA 58.652 37.500 0.00 0.00 38.15 3.85
269 270 5.460091 TGATCAATCGCTTCAATCTACGAAG 59.540 40.000 0.00 0.00 42.31 3.79
270 271 4.993905 TCAATCGCTTCAATCTACGAAGA 58.006 39.130 4.16 0.00 42.05 2.87
271 272 5.037385 TCAATCGCTTCAATCTACGAAGAG 58.963 41.667 4.16 1.03 42.05 2.85
273 274 4.696899 TCGCTTCAATCTACGAAGAGAA 57.303 40.909 4.16 0.00 43.43 2.87
274 275 5.055642 TCGCTTCAATCTACGAAGAGAAA 57.944 39.130 4.16 0.00 43.43 2.52
275 276 5.651530 TCGCTTCAATCTACGAAGAGAAAT 58.348 37.500 4.16 0.00 43.43 2.17
276 277 5.744345 TCGCTTCAATCTACGAAGAGAAATC 59.256 40.000 4.16 0.00 43.43 2.17
277 278 5.746245 CGCTTCAATCTACGAAGAGAAATCT 59.254 40.000 4.16 0.00 41.24 2.40
278 279 6.075099 CGCTTCAATCTACGAAGAGAAATCTC 60.075 42.308 2.10 2.10 41.24 2.75
279 280 6.200097 GCTTCAATCTACGAAGAGAAATCTCC 59.800 42.308 6.81 0.00 43.88 3.71
280 281 6.150396 TCAATCTACGAAGAGAAATCTCCC 57.850 41.667 6.81 0.00 43.88 4.30
281 282 5.656859 TCAATCTACGAAGAGAAATCTCCCA 59.343 40.000 6.81 0.00 43.88 4.37
282 283 5.782893 ATCTACGAAGAGAAATCTCCCAG 57.217 43.478 6.81 1.76 43.88 4.45
283 284 3.954904 TCTACGAAGAGAAATCTCCCAGG 59.045 47.826 6.81 0.00 43.88 4.45
284 285 2.541466 ACGAAGAGAAATCTCCCAGGT 58.459 47.619 6.81 0.00 43.88 4.00
285 286 2.907042 ACGAAGAGAAATCTCCCAGGTT 59.093 45.455 6.81 0.00 43.88 3.50
286 287 3.055747 ACGAAGAGAAATCTCCCAGGTTC 60.056 47.826 6.81 3.65 43.88 3.62
287 288 3.526534 GAAGAGAAATCTCCCAGGTTCG 58.473 50.000 6.81 0.00 43.88 3.95
288 289 2.821437 AGAGAAATCTCCCAGGTTCGA 58.179 47.619 6.81 0.00 43.88 3.71
289 290 2.763448 AGAGAAATCTCCCAGGTTCGAG 59.237 50.000 6.81 0.00 43.88 4.04
290 291 2.761208 GAGAAATCTCCCAGGTTCGAGA 59.239 50.000 0.00 0.00 39.38 4.04
291 292 3.379452 AGAAATCTCCCAGGTTCGAGAT 58.621 45.455 1.72 1.72 45.64 2.75
296 297 4.467198 TCTCCCAGGTTCGAGATTTAAC 57.533 45.455 0.00 0.00 30.16 2.01
297 298 4.094476 TCTCCCAGGTTCGAGATTTAACT 58.906 43.478 0.00 0.00 30.16 2.24
298 299 5.266788 TCTCCCAGGTTCGAGATTTAACTA 58.733 41.667 0.00 0.00 30.16 2.24
299 300 5.360144 TCTCCCAGGTTCGAGATTTAACTAG 59.640 44.000 0.00 0.00 30.16 2.57
300 301 5.021458 TCCCAGGTTCGAGATTTAACTAGT 58.979 41.667 0.00 0.00 0.00 2.57
301 302 5.482878 TCCCAGGTTCGAGATTTAACTAGTT 59.517 40.000 13.68 13.68 0.00 2.24
302 303 6.013984 TCCCAGGTTCGAGATTTAACTAGTTT 60.014 38.462 14.49 0.00 0.00 2.66
303 304 6.653740 CCCAGGTTCGAGATTTAACTAGTTTT 59.346 38.462 14.49 0.00 0.00 2.43
304 305 7.174426 CCCAGGTTCGAGATTTAACTAGTTTTT 59.826 37.037 14.49 0.00 0.00 1.94
330 331 9.745880 TTTTAGACAAGTACTTCTCAACTAGTG 57.254 33.333 12.65 0.00 0.00 2.74
331 332 8.687292 TTAGACAAGTACTTCTCAACTAGTGA 57.313 34.615 12.65 0.00 34.17 3.41
332 333 7.768807 AGACAAGTACTTCTCAACTAGTGAT 57.231 36.000 12.65 0.00 35.07 3.06
333 334 8.184304 AGACAAGTACTTCTCAACTAGTGATT 57.816 34.615 12.65 0.00 35.07 2.57
334 335 8.643324 AGACAAGTACTTCTCAACTAGTGATTT 58.357 33.333 12.65 0.00 35.07 2.17
335 336 8.819643 ACAAGTACTTCTCAACTAGTGATTTC 57.180 34.615 4.77 0.00 35.07 2.17
336 337 7.595502 ACAAGTACTTCTCAACTAGTGATTTCG 59.404 37.037 4.77 0.00 35.07 3.46
337 338 6.622549 AGTACTTCTCAACTAGTGATTTCGG 58.377 40.000 0.00 0.00 35.07 4.30
338 339 5.723672 ACTTCTCAACTAGTGATTTCGGA 57.276 39.130 0.00 0.00 35.07 4.55
339 340 6.287589 ACTTCTCAACTAGTGATTTCGGAT 57.712 37.500 0.00 0.00 35.07 4.18
340 341 7.406031 ACTTCTCAACTAGTGATTTCGGATA 57.594 36.000 0.00 0.00 35.07 2.59
341 342 7.837863 ACTTCTCAACTAGTGATTTCGGATAA 58.162 34.615 0.00 0.00 35.07 1.75
342 343 8.311836 ACTTCTCAACTAGTGATTTCGGATAAA 58.688 33.333 0.00 0.00 35.07 1.40
343 344 9.319143 CTTCTCAACTAGTGATTTCGGATAAAT 57.681 33.333 0.00 0.00 35.07 1.40
345 346 9.967346 TCTCAACTAGTGATTTCGGATAAATAG 57.033 33.333 0.00 0.00 35.07 1.73
346 347 9.751542 CTCAACTAGTGATTTCGGATAAATAGT 57.248 33.333 0.00 0.00 35.07 2.12
351 352 9.843334 CTAGTGATTTCGGATAAATAGTACTCC 57.157 37.037 0.00 0.00 0.00 3.85
352 353 8.480133 AGTGATTTCGGATAAATAGTACTCCT 57.520 34.615 0.00 0.00 0.00 3.69
353 354 8.925338 AGTGATTTCGGATAAATAGTACTCCTT 58.075 33.333 0.00 0.00 0.00 3.36
354 355 9.194271 GTGATTTCGGATAAATAGTACTCCTTC 57.806 37.037 0.00 0.00 0.00 3.46
355 356 8.365647 TGATTTCGGATAAATAGTACTCCTTCC 58.634 37.037 0.00 0.00 0.00 3.46
356 357 5.954296 TCGGATAAATAGTACTCCTTCCG 57.046 43.478 18.87 18.87 44.64 4.30
357 358 5.380043 TCGGATAAATAGTACTCCTTCCGT 58.620 41.667 21.70 0.00 43.91 4.69
358 359 5.829924 TCGGATAAATAGTACTCCTTCCGTT 59.170 40.000 21.70 4.62 43.91 4.44
359 360 6.322201 TCGGATAAATAGTACTCCTTCCGTTT 59.678 38.462 21.70 8.82 43.91 3.60
360 361 6.640092 CGGATAAATAGTACTCCTTCCGTTTC 59.360 42.308 17.61 1.28 39.88 2.78
361 362 6.640092 GGATAAATAGTACTCCTTCCGTTTCG 59.360 42.308 0.00 0.00 0.00 3.46
362 363 5.649782 AAATAGTACTCCTTCCGTTTCGA 57.350 39.130 0.00 0.00 0.00 3.71
363 364 5.649782 AATAGTACTCCTTCCGTTTCGAA 57.350 39.130 0.00 0.00 0.00 3.71
364 365 5.649782 ATAGTACTCCTTCCGTTTCGAAA 57.350 39.130 6.47 6.47 0.00 3.46
365 366 4.532314 AGTACTCCTTCCGTTTCGAAAT 57.468 40.909 14.69 0.00 0.00 2.17
366 367 4.891260 AGTACTCCTTCCGTTTCGAAATT 58.109 39.130 14.69 0.00 0.00 1.82
367 368 4.928020 AGTACTCCTTCCGTTTCGAAATTC 59.072 41.667 14.69 0.87 0.00 2.17
368 369 4.004196 ACTCCTTCCGTTTCGAAATTCT 57.996 40.909 14.69 0.00 0.00 2.40
369 370 3.995048 ACTCCTTCCGTTTCGAAATTCTC 59.005 43.478 14.69 0.00 0.00 2.87
370 371 3.994392 CTCCTTCCGTTTCGAAATTCTCA 59.006 43.478 14.69 0.00 0.00 3.27
371 372 4.575885 TCCTTCCGTTTCGAAATTCTCAT 58.424 39.130 14.69 0.00 0.00 2.90
372 373 4.630069 TCCTTCCGTTTCGAAATTCTCATC 59.370 41.667 14.69 0.00 0.00 2.92
373 374 4.631813 CCTTCCGTTTCGAAATTCTCATCT 59.368 41.667 14.69 0.00 0.00 2.90
374 375 5.122396 CCTTCCGTTTCGAAATTCTCATCTT 59.878 40.000 14.69 0.00 0.00 2.40
375 376 5.779806 TCCGTTTCGAAATTCTCATCTTC 57.220 39.130 14.69 0.00 0.00 2.87
376 377 5.234752 TCCGTTTCGAAATTCTCATCTTCA 58.765 37.500 14.69 0.00 0.00 3.02
377 378 5.699001 TCCGTTTCGAAATTCTCATCTTCAA 59.301 36.000 14.69 0.00 0.00 2.69
378 379 6.371548 TCCGTTTCGAAATTCTCATCTTCAAT 59.628 34.615 14.69 0.00 0.00 2.57
379 380 7.023575 CCGTTTCGAAATTCTCATCTTCAATT 58.976 34.615 14.69 0.00 0.00 2.32
380 381 7.538678 CCGTTTCGAAATTCTCATCTTCAATTT 59.461 33.333 14.69 0.00 33.39 1.82
381 382 8.360855 CGTTTCGAAATTCTCATCTTCAATTTG 58.639 33.333 14.69 0.00 31.35 2.32
382 383 9.185192 GTTTCGAAATTCTCATCTTCAATTTGT 57.815 29.630 14.69 0.00 31.35 2.83
383 384 8.955061 TTCGAAATTCTCATCTTCAATTTGTC 57.045 30.769 0.00 0.00 31.35 3.18
384 385 8.327941 TCGAAATTCTCATCTTCAATTTGTCT 57.672 30.769 0.00 0.00 31.35 3.41
385 386 9.435688 TCGAAATTCTCATCTTCAATTTGTCTA 57.564 29.630 0.00 0.00 31.35 2.59
386 387 9.699985 CGAAATTCTCATCTTCAATTTGTCTAG 57.300 33.333 0.00 0.00 31.35 2.43
438 439 9.909644 ATGTTACTTGATACATCCGTATTAGAC 57.090 33.333 0.00 0.00 38.48 2.59
439 440 8.905850 TGTTACTTGATACATCCGTATTAGACA 58.094 33.333 0.00 0.00 38.48 3.41
440 441 9.740239 GTTACTTGATACATCCGTATTAGACAA 57.260 33.333 0.00 0.00 38.48 3.18
460 461 8.137210 AGACAAATACAAAAATTTTGGGAACG 57.863 30.769 20.79 9.77 35.23 3.95
461 462 7.225734 AGACAAATACAAAAATTTTGGGAACGG 59.774 33.333 20.79 9.27 35.23 4.44
478 479 1.442148 GGAGTAGCACCCCATCGAC 59.558 63.158 0.00 0.00 0.00 4.20
546 552 1.016130 CAGCCTGCTTCACTACGTGG 61.016 60.000 0.00 0.00 33.87 4.94
553 559 1.909376 CTTCACTACGTGGTCCGATG 58.091 55.000 0.00 0.00 40.70 3.84
791 808 1.944896 TACTCCCTCCTCCGCATCCA 61.945 60.000 0.00 0.00 0.00 3.41
815 832 2.456840 CCCCTCAGACCCCTCCTT 59.543 66.667 0.00 0.00 0.00 3.36
816 833 1.997874 CCCCTCAGACCCCTCCTTG 60.998 68.421 0.00 0.00 0.00 3.61
819 839 1.614824 CTCAGACCCCTCCTTGGCT 60.615 63.158 0.00 0.00 0.00 4.75
942 962 4.227134 CCCCAGGTCGCCTCATCG 62.227 72.222 0.00 0.00 0.00 3.84
948 968 2.496817 GTCGCCTCATCGCTCCTT 59.503 61.111 0.00 0.00 0.00 3.36
972 992 2.227703 TCCTATTCACTCCTCTCCCCT 58.772 52.381 0.00 0.00 0.00 4.79
977 997 3.999285 ACTCCTCTCCCCTGCGGT 61.999 66.667 0.00 0.00 0.00 5.68
1002 1022 2.162208 CCACCACCTGTTCGATCAAATG 59.838 50.000 0.00 0.00 0.00 2.32
1014 1034 2.172229 ATCAAATGCCCCCTGCCACT 62.172 55.000 0.00 0.00 40.16 4.00
1016 1036 1.610379 AAATGCCCCCTGCCACTTC 60.610 57.895 0.00 0.00 40.16 3.01
1233 1253 6.039047 CACTTGCTCCAGATTATGTAATGCTT 59.961 38.462 0.00 0.00 0.00 3.91
1251 1271 2.048127 GTCACCGTCCTCACAGGC 60.048 66.667 0.00 0.00 34.61 4.85
1335 1355 0.987294 AGGCAGTCAGTATGCACCTT 59.013 50.000 0.00 0.00 45.68 3.50
1393 1413 1.000506 GCCTCGATTATGCTTCCCGTA 59.999 52.381 0.00 0.00 0.00 4.02
1633 1653 4.721776 AGGAATATGACCTTGAGCCAACTA 59.278 41.667 0.00 0.00 33.55 2.24
1838 1858 6.807230 GCAATGGAGATATCTGATGAAAATGC 59.193 38.462 10.74 6.14 0.00 3.56
1938 1958 2.354821 GGAGGAACATAATGTGCGGAAC 59.645 50.000 0.00 0.00 0.00 3.62
1947 1967 0.396435 ATGTGCGGAACAACAGAGGA 59.604 50.000 0.00 0.00 43.61 3.71
1995 2015 0.529378 CTGGCTTGATTGTTCCTGCC 59.471 55.000 0.00 0.00 38.76 4.85
2013 2033 1.537202 GCCGTCAGTTGATCTTTTGCT 59.463 47.619 0.00 0.00 0.00 3.91
2015 2035 2.159787 CCGTCAGTTGATCTTTTGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
2023 2043 2.223144 TGATCTTTTGCTCGGTTCAACG 59.777 45.455 0.00 0.00 0.00 4.10
2066 2087 9.912634 TTGAATTGTTGGATGATACTCTTTTTC 57.087 29.630 0.00 0.00 0.00 2.29
2099 2120 4.262207 CCACAGATGTATTCAGCGGATAGT 60.262 45.833 0.00 0.00 34.90 2.12
2153 2175 0.394216 TGTGGGAATCAGCGGAATGG 60.394 55.000 0.00 0.00 0.00 3.16
2188 2210 5.300752 CGGTCTAATCTCCTGCAATATTGT 58.699 41.667 16.61 0.00 0.00 2.71
2189 2211 5.178252 CGGTCTAATCTCCTGCAATATTGTG 59.822 44.000 16.61 9.82 0.00 3.33
2199 2221 5.647658 TCCTGCAATATTGTGTTGAGGTAAG 59.352 40.000 16.61 0.83 31.56 2.34
2202 2224 5.121611 TGCAATATTGTGTTGAGGTAAGTCG 59.878 40.000 16.61 0.00 0.00 4.18
2203 2225 5.350365 GCAATATTGTGTTGAGGTAAGTCGA 59.650 40.000 16.61 0.00 0.00 4.20
2205 2227 7.621991 CAATATTGTGTTGAGGTAAGTCGATC 58.378 38.462 7.32 0.00 0.00 3.69
2206 2228 4.594123 TTGTGTTGAGGTAAGTCGATCA 57.406 40.909 0.00 0.00 0.00 2.92
2207 2229 3.909430 TGTGTTGAGGTAAGTCGATCAC 58.091 45.455 0.00 0.00 0.00 3.06
2208 2230 3.572682 TGTGTTGAGGTAAGTCGATCACT 59.427 43.478 0.00 0.00 36.64 3.41
2209 2231 3.921021 GTGTTGAGGTAAGTCGATCACTG 59.079 47.826 0.00 0.00 34.56 3.66
2210 2232 2.924290 GTTGAGGTAAGTCGATCACTGC 59.076 50.000 0.00 0.00 34.56 4.40
2211 2233 2.447443 TGAGGTAAGTCGATCACTGCT 58.553 47.619 0.00 0.00 34.56 4.24
2271 2317 1.806542 GTTGACACAGGCGATTCACAT 59.193 47.619 0.00 0.00 0.00 3.21
2280 2326 3.251487 CAGGCGATTCACATGCATATGAA 59.749 43.478 21.86 21.86 39.09 2.57
2282 2328 5.122711 CAGGCGATTCACATGCATATGAATA 59.877 40.000 28.40 7.47 43.85 1.75
2323 2369 2.457366 AACCGAACTCATGACTGGAC 57.543 50.000 0.00 0.00 0.00 4.02
2358 2407 7.041508 GGTCATGTACTGATTTCCATCTTCATC 60.042 40.741 0.00 0.00 35.97 2.92
2379 2428 1.071385 GTGCCCATAGGACTGGAGATG 59.929 57.143 0.00 0.00 38.69 2.90
2385 2434 3.573538 CCATAGGACTGGAGATGACAGAG 59.426 52.174 0.00 0.00 38.69 3.35
2414 2463 8.370182 AGATTTCTTTGAGTACATTGCCATTTT 58.630 29.630 0.00 0.00 0.00 1.82
2468 2518 4.008933 GGTGTCAGGTCAGCGGCT 62.009 66.667 0.00 0.00 0.00 5.52
2552 2602 7.063426 GCAGCCCTAAGTGTTTCAAATAAATTC 59.937 37.037 0.00 0.00 0.00 2.17
2553 2603 8.306761 CAGCCCTAAGTGTTTCAAATAAATTCT 58.693 33.333 0.00 0.00 0.00 2.40
2554 2604 9.528489 AGCCCTAAGTGTTTCAAATAAATTCTA 57.472 29.630 0.00 0.00 0.00 2.10
2630 2680 0.597568 TGGCAGGTGAAATCTTTGCG 59.402 50.000 0.00 0.00 35.68 4.85
2640 2690 2.919666 AATCTTTGCGGTGCATACAC 57.080 45.000 0.00 0.00 46.66 2.90
2671 2724 1.217882 GGTTCGTCCTGTCACAACTG 58.782 55.000 0.00 0.00 0.00 3.16
2725 2778 4.072131 TGTGCTCTGATGTAAAAAGACCC 58.928 43.478 0.00 0.00 0.00 4.46
2768 2821 3.703052 GCTGGGATCATGGAACTGATTTT 59.297 43.478 0.00 0.00 36.01 1.82
2785 2842 7.710896 ACTGATTTTCTGTGAAAAAGAAGAGG 58.289 34.615 9.13 1.06 42.14 3.69
2823 2888 1.188863 ACTTCTGATTGCCATTGCCC 58.811 50.000 0.00 0.00 36.33 5.36
2826 2891 0.040058 TCTGATTGCCATTGCCCTGT 59.960 50.000 0.00 0.00 36.33 4.00
2925 2993 8.464404 TGTTTACCTCATAGTACACACATAGAC 58.536 37.037 0.00 0.00 30.09 2.59
2927 2995 6.452494 ACCTCATAGTACACACATAGACAC 57.548 41.667 0.00 0.00 0.00 3.67
2962 3030 1.677966 TGACGCCCTAGTCTTCGCT 60.678 57.895 0.00 0.00 41.47 4.93
2968 3036 2.492090 CTAGTCTTCGCTGCGGCT 59.508 61.111 23.03 16.36 36.09 5.52
3027 3095 0.714439 GGAAGACGTTGACGCTAAGC 59.286 55.000 3.05 0.00 44.43 3.09
3070 3139 2.335712 GCCGCCTGAAAGTTCCCAG 61.336 63.158 0.00 0.00 0.00 4.45
3078 3147 0.804989 GAAAGTTCCCAGCATCACCG 59.195 55.000 0.00 0.00 0.00 4.94
3112 3181 1.137086 CTGTGCTACTGGCCGAAGTAT 59.863 52.381 3.54 0.00 40.92 2.12
3113 3182 1.553248 TGTGCTACTGGCCGAAGTATT 59.447 47.619 3.54 0.00 40.92 1.89
3114 3183 2.027561 TGTGCTACTGGCCGAAGTATTT 60.028 45.455 3.54 0.00 40.92 1.40
3131 3200 7.518052 CGAAGTATTTTCTTGGAGATCATCAGC 60.518 40.741 0.00 0.00 0.00 4.26
3199 3502 1.549037 CCGCTATAGCTTCCTCCTCCT 60.549 57.143 21.98 0.00 39.32 3.69
3200 3503 1.816224 CGCTATAGCTTCCTCCTCCTC 59.184 57.143 21.98 0.00 39.32 3.71
3203 3506 0.178947 ATAGCTTCCTCCTCCTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
3204 3507 2.930777 TAGCTTCCTCCTCCTCCCGC 62.931 65.000 0.00 0.00 0.00 6.13
3205 3508 3.157949 CTTCCTCCTCCTCCCGCC 61.158 72.222 0.00 0.00 0.00 6.13
3206 3509 4.798682 TTCCTCCTCCTCCCGCCC 62.799 72.222 0.00 0.00 0.00 6.13
3280 3583 2.430382 TTCGTTCTCGTCCCCACAGC 62.430 60.000 0.00 0.00 38.33 4.40
3289 3592 4.988598 CCCCACAGCGCTCGTGTT 62.989 66.667 26.88 0.00 32.26 3.32
3290 3593 3.716006 CCCACAGCGCTCGTGTTG 61.716 66.667 26.88 18.47 32.26 3.33
3291 3594 3.716006 CCACAGCGCTCGTGTTGG 61.716 66.667 26.88 17.16 32.26 3.77
3292 3595 2.967076 CACAGCGCTCGTGTTGGT 60.967 61.111 23.38 9.58 0.00 3.67
3293 3596 2.967076 ACAGCGCTCGTGTTGGTG 60.967 61.111 7.13 0.00 37.16 4.17
3294 3597 2.967076 CAGCGCTCGTGTTGGTGT 60.967 61.111 7.13 0.00 0.00 4.16
3295 3598 2.967076 AGCGCTCGTGTTGGTGTG 60.967 61.111 2.64 0.00 0.00 3.82
3296 3599 3.269347 GCGCTCGTGTTGGTGTGT 61.269 61.111 0.00 0.00 0.00 3.72
3297 3600 2.928361 CGCTCGTGTTGGTGTGTC 59.072 61.111 0.00 0.00 0.00 3.67
3299 3602 1.227556 GCTCGTGTTGGTGTGTCCT 60.228 57.895 0.00 0.00 37.07 3.85
3300 3603 1.222115 GCTCGTGTTGGTGTGTCCTC 61.222 60.000 0.00 0.00 37.07 3.71
3301 3604 0.600255 CTCGTGTTGGTGTGTCCTCC 60.600 60.000 0.00 0.00 37.07 4.30
3302 3605 1.046472 TCGTGTTGGTGTGTCCTCCT 61.046 55.000 0.00 0.00 37.07 3.69
3303 3606 0.600255 CGTGTTGGTGTGTCCTCCTC 60.600 60.000 0.00 0.00 37.07 3.71
3304 3607 0.250338 GTGTTGGTGTGTCCTCCTCC 60.250 60.000 0.00 0.00 37.07 4.30
3305 3608 0.692756 TGTTGGTGTGTCCTCCTCCA 60.693 55.000 0.00 0.00 37.07 3.86
3312 3642 0.914417 GTGTCCTCCTCCATTCCCCA 60.914 60.000 0.00 0.00 0.00 4.96
3320 3650 2.043046 CCATTCCCCACCGCCATT 60.043 61.111 0.00 0.00 0.00 3.16
3332 3662 2.798501 CGCCATTGTACGTCGCCAG 61.799 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.909006 TGCTTTTGCCCCCATTGATTAA 59.091 40.909 0.00 0.00 46.87 1.40
1 2 2.544721 TGCTTTTGCCCCCATTGATTA 58.455 42.857 0.00 0.00 46.87 1.75
2 3 1.360185 TGCTTTTGCCCCCATTGATT 58.640 45.000 0.00 0.00 46.87 2.57
3 4 1.587066 ATGCTTTTGCCCCCATTGAT 58.413 45.000 0.00 0.00 46.87 2.57
4 5 1.830477 GTATGCTTTTGCCCCCATTGA 59.170 47.619 0.00 0.00 46.87 2.57
5 6 1.832998 AGTATGCTTTTGCCCCCATTG 59.167 47.619 0.00 0.00 46.87 2.82
6 7 2.252535 AGTATGCTTTTGCCCCCATT 57.747 45.000 0.00 0.00 46.87 3.16
7 8 3.233507 CATAGTATGCTTTTGCCCCCAT 58.766 45.455 0.00 0.00 46.87 4.00
8 9 2.665165 CATAGTATGCTTTTGCCCCCA 58.335 47.619 0.00 0.00 46.87 4.96
133 134 4.022935 CACAAGAGGCATACACACAATTGT 60.023 41.667 4.92 4.92 35.84 2.71
134 135 4.022935 ACACAAGAGGCATACACACAATTG 60.023 41.667 3.24 3.24 0.00 2.32
135 136 4.144297 ACACAAGAGGCATACACACAATT 58.856 39.130 0.00 0.00 0.00 2.32
136 137 3.754965 ACACAAGAGGCATACACACAAT 58.245 40.909 0.00 0.00 0.00 2.71
137 138 3.207265 ACACAAGAGGCATACACACAA 57.793 42.857 0.00 0.00 0.00 3.33
138 139 2.928801 ACACAAGAGGCATACACACA 57.071 45.000 0.00 0.00 0.00 3.72
139 140 3.000727 GGTACACAAGAGGCATACACAC 58.999 50.000 0.00 0.00 0.00 3.82
140 141 2.635427 TGGTACACAAGAGGCATACACA 59.365 45.455 0.00 0.00 0.00 3.72
141 142 3.328382 TGGTACACAAGAGGCATACAC 57.672 47.619 0.00 0.00 0.00 2.90
156 157 7.023197 AGTTTGTAGTTTGTCAACATGGTAC 57.977 36.000 0.00 0.00 35.05 3.34
157 158 7.633193 AAGTTTGTAGTTTGTCAACATGGTA 57.367 32.000 0.00 0.00 35.05 3.25
158 159 6.524101 AAGTTTGTAGTTTGTCAACATGGT 57.476 33.333 0.00 0.00 35.05 3.55
159 160 7.032580 TGAAAGTTTGTAGTTTGTCAACATGG 58.967 34.615 0.00 0.00 35.05 3.66
160 161 8.107591 CTGAAAGTTTGTAGTTTGTCAACATG 57.892 34.615 0.00 0.00 35.05 3.21
188 189 9.784531 ACTCTGACGAATAATATGATTCCAAAT 57.215 29.630 7.16 0.00 33.04 2.32
201 202 9.976511 TCTCTTTTCTTTTACTCTGACGAATAA 57.023 29.630 0.00 0.00 0.00 1.40
203 204 9.495572 AATCTCTTTTCTTTTACTCTGACGAAT 57.504 29.630 0.00 0.00 0.00 3.34
204 205 8.888579 AATCTCTTTTCTTTTACTCTGACGAA 57.111 30.769 0.00 0.00 0.00 3.85
205 206 8.888579 AAATCTCTTTTCTTTTACTCTGACGA 57.111 30.769 0.00 0.00 0.00 4.20
224 225 7.490725 TGATCATTGAGAACGAAGAGAAATCTC 59.509 37.037 2.10 2.10 43.17 2.75
225 226 7.326454 TGATCATTGAGAACGAAGAGAAATCT 58.674 34.615 0.00 0.00 0.00 2.40
226 227 7.531280 TGATCATTGAGAACGAAGAGAAATC 57.469 36.000 0.00 0.00 0.00 2.17
227 228 7.912056 TTGATCATTGAGAACGAAGAGAAAT 57.088 32.000 0.00 0.00 0.00 2.17
228 229 7.201470 CGATTGATCATTGAGAACGAAGAGAAA 60.201 37.037 0.00 0.00 0.00 2.52
229 230 6.254373 CGATTGATCATTGAGAACGAAGAGAA 59.746 38.462 0.00 0.00 0.00 2.87
230 231 5.745769 CGATTGATCATTGAGAACGAAGAGA 59.254 40.000 0.00 0.00 0.00 3.10
231 232 5.556006 GCGATTGATCATTGAGAACGAAGAG 60.556 44.000 0.00 0.00 0.00 2.85
232 233 4.268644 GCGATTGATCATTGAGAACGAAGA 59.731 41.667 0.00 0.00 0.00 2.87
233 234 4.269603 AGCGATTGATCATTGAGAACGAAG 59.730 41.667 0.00 0.00 0.00 3.79
234 235 4.183865 AGCGATTGATCATTGAGAACGAA 58.816 39.130 0.00 0.00 0.00 3.85
235 236 3.785486 AGCGATTGATCATTGAGAACGA 58.215 40.909 0.00 0.00 0.00 3.85
236 237 4.033243 TGAAGCGATTGATCATTGAGAACG 59.967 41.667 0.00 0.00 0.00 3.95
237 238 5.475273 TGAAGCGATTGATCATTGAGAAC 57.525 39.130 0.00 0.00 0.00 3.01
238 239 6.541278 AGATTGAAGCGATTGATCATTGAGAA 59.459 34.615 0.00 0.00 0.00 2.87
239 240 6.053650 AGATTGAAGCGATTGATCATTGAGA 58.946 36.000 0.00 0.00 0.00 3.27
240 241 6.301687 AGATTGAAGCGATTGATCATTGAG 57.698 37.500 0.00 0.00 0.00 3.02
241 242 6.074142 CGTAGATTGAAGCGATTGATCATTGA 60.074 38.462 0.00 0.00 0.00 2.57
242 243 6.069563 CGTAGATTGAAGCGATTGATCATTG 58.930 40.000 0.00 0.00 0.00 2.82
243 244 5.985530 TCGTAGATTGAAGCGATTGATCATT 59.014 36.000 0.00 0.00 0.00 2.57
244 245 5.532557 TCGTAGATTGAAGCGATTGATCAT 58.467 37.500 0.00 0.00 0.00 2.45
245 246 4.932146 TCGTAGATTGAAGCGATTGATCA 58.068 39.130 0.00 0.00 0.00 2.92
246 247 5.687730 TCTTCGTAGATTGAAGCGATTGATC 59.312 40.000 0.00 0.00 42.02 2.92
247 248 5.592054 TCTTCGTAGATTGAAGCGATTGAT 58.408 37.500 0.00 0.00 42.02 2.57
248 249 4.993905 TCTTCGTAGATTGAAGCGATTGA 58.006 39.130 0.00 0.00 42.02 2.57
249 250 5.037385 TCTCTTCGTAGATTGAAGCGATTG 58.963 41.667 0.00 0.00 42.02 2.67
250 251 5.250235 TCTCTTCGTAGATTGAAGCGATT 57.750 39.130 0.00 0.00 42.02 3.34
251 252 4.902443 TCTCTTCGTAGATTGAAGCGAT 57.098 40.909 0.00 0.00 42.02 4.58
252 253 4.696899 TTCTCTTCGTAGATTGAAGCGA 57.303 40.909 0.00 0.00 42.02 4.93
253 254 5.746245 AGATTTCTCTTCGTAGATTGAAGCG 59.254 40.000 0.00 0.00 42.02 4.68
254 255 6.200097 GGAGATTTCTCTTCGTAGATTGAAGC 59.800 42.308 7.47 0.00 42.02 3.86
255 256 6.699642 GGGAGATTTCTCTTCGTAGATTGAAG 59.300 42.308 7.47 0.00 43.31 3.02
256 257 6.154534 TGGGAGATTTCTCTTCGTAGATTGAA 59.845 38.462 7.47 0.00 42.48 2.69
257 258 5.656859 TGGGAGATTTCTCTTCGTAGATTGA 59.343 40.000 7.47 0.00 42.48 2.57
258 259 5.907207 TGGGAGATTTCTCTTCGTAGATTG 58.093 41.667 7.47 0.00 42.48 2.67
259 260 5.069781 CCTGGGAGATTTCTCTTCGTAGATT 59.930 44.000 7.47 0.00 42.48 2.40
260 261 4.586841 CCTGGGAGATTTCTCTTCGTAGAT 59.413 45.833 7.47 0.00 42.48 1.98
261 262 3.954904 CCTGGGAGATTTCTCTTCGTAGA 59.045 47.826 7.47 0.00 42.48 2.59
262 263 3.702045 ACCTGGGAGATTTCTCTTCGTAG 59.298 47.826 7.47 0.00 42.48 3.51
263 264 3.709587 ACCTGGGAGATTTCTCTTCGTA 58.290 45.455 7.47 0.00 42.48 3.43
264 265 2.541466 ACCTGGGAGATTTCTCTTCGT 58.459 47.619 7.47 0.00 42.48 3.85
265 266 3.526534 GAACCTGGGAGATTTCTCTTCG 58.473 50.000 7.47 0.00 42.48 3.79
266 267 3.195825 TCGAACCTGGGAGATTTCTCTTC 59.804 47.826 7.47 2.85 42.48 2.87
267 268 3.173965 TCGAACCTGGGAGATTTCTCTT 58.826 45.455 7.47 0.00 42.48 2.85
268 269 2.763448 CTCGAACCTGGGAGATTTCTCT 59.237 50.000 7.47 0.00 42.48 3.10
269 270 2.761208 TCTCGAACCTGGGAGATTTCTC 59.239 50.000 0.00 0.00 42.14 2.87
270 271 2.821437 TCTCGAACCTGGGAGATTTCT 58.179 47.619 0.00 0.00 34.52 2.52
271 272 3.828875 ATCTCGAACCTGGGAGATTTC 57.171 47.619 7.80 0.00 45.29 2.17
275 276 4.094476 AGTTAAATCTCGAACCTGGGAGA 58.906 43.478 0.00 0.79 42.96 3.71
276 277 4.473477 AGTTAAATCTCGAACCTGGGAG 57.527 45.455 0.00 0.00 0.00 4.30
277 278 5.021458 ACTAGTTAAATCTCGAACCTGGGA 58.979 41.667 0.00 0.00 0.00 4.37
278 279 5.340439 ACTAGTTAAATCTCGAACCTGGG 57.660 43.478 0.00 0.00 0.00 4.45
279 280 7.668525 AAAACTAGTTAAATCTCGAACCTGG 57.331 36.000 8.92 0.00 0.00 4.45
304 305 9.745880 CACTAGTTGAGAAGTACTTGTCTAAAA 57.254 33.333 27.34 14.70 34.38 1.52
305 306 9.128404 TCACTAGTTGAGAAGTACTTGTCTAAA 57.872 33.333 27.34 15.31 34.38 1.85
306 307 8.687292 TCACTAGTTGAGAAGTACTTGTCTAA 57.313 34.615 27.34 18.67 34.38 2.10
307 308 8.865420 ATCACTAGTTGAGAAGTACTTGTCTA 57.135 34.615 27.34 20.05 37.77 2.59
308 309 7.768807 ATCACTAGTTGAGAAGTACTTGTCT 57.231 36.000 27.34 14.43 37.77 3.41
309 310 8.819643 AAATCACTAGTTGAGAAGTACTTGTC 57.180 34.615 22.49 22.49 37.77 3.18
310 311 7.595502 CGAAATCACTAGTTGAGAAGTACTTGT 59.404 37.037 14.14 9.35 37.77 3.16
311 312 7.062371 CCGAAATCACTAGTTGAGAAGTACTTG 59.938 40.741 14.14 0.00 37.77 3.16
312 313 7.039923 TCCGAAATCACTAGTTGAGAAGTACTT 60.040 37.037 8.13 8.13 37.77 2.24
313 314 6.433404 TCCGAAATCACTAGTTGAGAAGTACT 59.567 38.462 0.00 0.00 37.77 2.73
314 315 6.618811 TCCGAAATCACTAGTTGAGAAGTAC 58.381 40.000 0.00 0.00 37.77 2.73
315 316 6.829229 TCCGAAATCACTAGTTGAGAAGTA 57.171 37.500 0.00 0.00 37.77 2.24
316 317 5.723672 TCCGAAATCACTAGTTGAGAAGT 57.276 39.130 0.00 0.00 37.77 3.01
317 318 8.703604 TTTATCCGAAATCACTAGTTGAGAAG 57.296 34.615 0.00 0.00 37.77 2.85
319 320 9.967346 CTATTTATCCGAAATCACTAGTTGAGA 57.033 33.333 0.00 0.00 37.77 3.27
320 321 9.751542 ACTATTTATCCGAAATCACTAGTTGAG 57.248 33.333 0.00 0.00 37.77 3.02
325 326 9.843334 GGAGTACTATTTATCCGAAATCACTAG 57.157 37.037 0.00 0.00 0.00 2.57
326 327 9.584008 AGGAGTACTATTTATCCGAAATCACTA 57.416 33.333 0.00 0.00 36.91 2.74
327 328 8.480133 AGGAGTACTATTTATCCGAAATCACT 57.520 34.615 0.00 0.00 36.91 3.41
328 329 9.194271 GAAGGAGTACTATTTATCCGAAATCAC 57.806 37.037 0.00 0.00 36.91 3.06
329 330 8.365647 GGAAGGAGTACTATTTATCCGAAATCA 58.634 37.037 0.00 0.00 36.91 2.57
330 331 8.760103 GGAAGGAGTACTATTTATCCGAAATC 57.240 38.462 0.00 0.00 36.91 2.17
336 337 6.640092 CGAAACGGAAGGAGTACTATTTATCC 59.360 42.308 0.00 0.00 0.00 2.59
337 338 7.420800 TCGAAACGGAAGGAGTACTATTTATC 58.579 38.462 0.00 0.00 0.00 1.75
338 339 7.338800 TCGAAACGGAAGGAGTACTATTTAT 57.661 36.000 0.00 0.00 0.00 1.40
339 340 6.757897 TCGAAACGGAAGGAGTACTATTTA 57.242 37.500 0.00 0.00 0.00 1.40
340 341 5.649782 TCGAAACGGAAGGAGTACTATTT 57.350 39.130 0.00 0.00 0.00 1.40
341 342 5.649782 TTCGAAACGGAAGGAGTACTATT 57.350 39.130 0.00 0.00 0.00 1.73
342 343 5.649782 TTTCGAAACGGAAGGAGTACTAT 57.350 39.130 6.47 0.00 0.00 2.12
343 344 5.649782 ATTTCGAAACGGAAGGAGTACTA 57.350 39.130 13.81 0.00 0.00 1.82
344 345 4.532314 ATTTCGAAACGGAAGGAGTACT 57.468 40.909 13.81 0.00 0.00 2.73
345 346 4.928020 AGAATTTCGAAACGGAAGGAGTAC 59.072 41.667 13.81 0.00 0.00 2.73
346 347 5.143376 AGAATTTCGAAACGGAAGGAGTA 57.857 39.130 13.81 0.00 0.00 2.59
347 348 3.995048 GAGAATTTCGAAACGGAAGGAGT 59.005 43.478 13.81 0.00 0.00 3.85
348 349 3.994392 TGAGAATTTCGAAACGGAAGGAG 59.006 43.478 13.81 0.00 0.00 3.69
349 350 3.997762 TGAGAATTTCGAAACGGAAGGA 58.002 40.909 13.81 0.00 0.00 3.36
350 351 4.631813 AGATGAGAATTTCGAAACGGAAGG 59.368 41.667 13.81 0.00 0.00 3.46
351 352 5.786401 AGATGAGAATTTCGAAACGGAAG 57.214 39.130 13.81 0.00 0.00 3.46
352 353 5.699001 TGAAGATGAGAATTTCGAAACGGAA 59.301 36.000 13.81 0.00 0.00 4.30
353 354 5.234752 TGAAGATGAGAATTTCGAAACGGA 58.765 37.500 13.81 0.00 0.00 4.69
354 355 5.530519 TGAAGATGAGAATTTCGAAACGG 57.469 39.130 13.81 0.00 0.00 4.44
355 356 8.360855 CAAATTGAAGATGAGAATTTCGAAACG 58.639 33.333 13.81 0.00 28.93 3.60
356 357 9.185192 ACAAATTGAAGATGAGAATTTCGAAAC 57.815 29.630 13.81 1.12 28.93 2.78
357 358 9.398170 GACAAATTGAAGATGAGAATTTCGAAA 57.602 29.630 13.91 13.91 28.93 3.46
358 359 8.786898 AGACAAATTGAAGATGAGAATTTCGAA 58.213 29.630 0.00 0.00 28.93 3.71
359 360 8.327941 AGACAAATTGAAGATGAGAATTTCGA 57.672 30.769 0.00 0.00 28.93 3.71
360 361 9.699985 CTAGACAAATTGAAGATGAGAATTTCG 57.300 33.333 0.00 0.00 28.93 3.46
412 413 9.909644 GTCTAATACGGATGTATCAAGTAACAT 57.090 33.333 0.00 0.00 40.42 2.71
413 414 8.905850 TGTCTAATACGGATGTATCAAGTAACA 58.094 33.333 0.00 0.00 40.42 2.41
414 415 9.740239 TTGTCTAATACGGATGTATCAAGTAAC 57.260 33.333 0.00 0.97 40.42 2.50
434 435 9.250624 CGTTCCCAAAATTTTTGTATTTGTCTA 57.749 29.630 18.05 0.00 33.31 2.59
435 436 7.225734 CCGTTCCCAAAATTTTTGTATTTGTCT 59.774 33.333 18.05 0.00 33.31 3.41
436 437 7.224949 TCCGTTCCCAAAATTTTTGTATTTGTC 59.775 33.333 18.05 4.30 33.31 3.18
437 438 7.048512 TCCGTTCCCAAAATTTTTGTATTTGT 58.951 30.769 18.05 0.00 33.31 2.83
438 439 7.225734 ACTCCGTTCCCAAAATTTTTGTATTTG 59.774 33.333 18.05 5.02 34.60 2.32
439 440 7.276658 ACTCCGTTCCCAAAATTTTTGTATTT 58.723 30.769 18.05 0.00 0.00 1.40
440 441 6.822442 ACTCCGTTCCCAAAATTTTTGTATT 58.178 32.000 18.05 0.00 0.00 1.89
441 442 6.413783 ACTCCGTTCCCAAAATTTTTGTAT 57.586 33.333 18.05 0.00 0.00 2.29
442 443 5.855740 ACTCCGTTCCCAAAATTTTTGTA 57.144 34.783 18.05 5.79 0.00 2.41
443 444 4.746535 ACTCCGTTCCCAAAATTTTTGT 57.253 36.364 18.05 0.00 0.00 2.83
444 445 4.684242 GCTACTCCGTTCCCAAAATTTTTG 59.316 41.667 13.76 13.76 0.00 2.44
445 446 4.342665 TGCTACTCCGTTCCCAAAATTTTT 59.657 37.500 0.00 0.00 0.00 1.94
446 447 3.892588 TGCTACTCCGTTCCCAAAATTTT 59.107 39.130 0.00 0.00 0.00 1.82
447 448 3.254903 GTGCTACTCCGTTCCCAAAATTT 59.745 43.478 0.00 0.00 0.00 1.82
448 449 2.817844 GTGCTACTCCGTTCCCAAAATT 59.182 45.455 0.00 0.00 0.00 1.82
449 450 2.433436 GTGCTACTCCGTTCCCAAAAT 58.567 47.619 0.00 0.00 0.00 1.82
450 451 1.543871 GGTGCTACTCCGTTCCCAAAA 60.544 52.381 0.00 0.00 0.00 2.44
451 452 0.035739 GGTGCTACTCCGTTCCCAAA 59.964 55.000 0.00 0.00 0.00 3.28
452 453 1.675219 GGTGCTACTCCGTTCCCAA 59.325 57.895 0.00 0.00 0.00 4.12
453 454 2.288025 GGGTGCTACTCCGTTCCCA 61.288 63.158 0.00 0.00 35.43 4.37
454 455 2.582978 GGGTGCTACTCCGTTCCC 59.417 66.667 0.00 0.00 0.00 3.97
455 456 1.623542 ATGGGGTGCTACTCCGTTCC 61.624 60.000 1.49 0.00 43.44 3.62
456 457 0.179081 GATGGGGTGCTACTCCGTTC 60.179 60.000 2.03 0.00 43.44 3.95
457 458 1.905512 GATGGGGTGCTACTCCGTT 59.094 57.895 2.03 0.00 43.44 4.44
458 459 2.423898 CGATGGGGTGCTACTCCGT 61.424 63.158 0.12 0.12 43.44 4.69
459 460 2.125326 TCGATGGGGTGCTACTCCG 61.125 63.158 1.49 0.00 43.44 4.63
460 461 1.442148 GTCGATGGGGTGCTACTCC 59.558 63.158 0.00 0.00 39.92 3.85
461 462 1.065928 CGTCGATGGGGTGCTACTC 59.934 63.158 0.00 0.00 0.00 2.59
478 479 4.697514 TCATGGGCTCTTTAAGAAGATCG 58.302 43.478 0.00 0.00 40.93 3.69
546 552 1.675641 AAGTTGGGCTGCATCGGAC 60.676 57.895 0.50 0.00 0.00 4.79
553 559 2.669569 TCGAGCAAGTTGGGCTGC 60.670 61.111 4.75 0.00 42.78 5.25
685 702 1.077429 GGTGAGGAAGGGACATGGC 60.077 63.158 0.00 0.00 0.00 4.40
942 962 3.449632 GAGTGAATAGGAACGAAGGAGC 58.550 50.000 0.00 0.00 0.00 4.70
948 968 3.288964 GGAGAGGAGTGAATAGGAACGA 58.711 50.000 0.00 0.00 0.00 3.85
977 997 4.308458 CGAACAGGTGGTGGGCGA 62.308 66.667 0.00 0.00 0.00 5.54
1002 1022 4.299796 TTGGAAGTGGCAGGGGGC 62.300 66.667 0.00 0.00 43.74 5.80
1083 1103 3.181479 CGGGGATGTCGTCAAAGAATAGA 60.181 47.826 0.00 0.00 0.00 1.98
1233 1253 2.867855 GCCTGTGAGGACGGTGACA 61.868 63.158 0.00 0.00 37.67 3.58
1335 1355 2.618241 GCAATCAATAAGCGATGTCCCA 59.382 45.455 0.00 0.00 0.00 4.37
1938 1958 0.820226 TGGAGCTCGATCCTCTGTTG 59.180 55.000 7.83 0.00 40.29 3.33
1947 1967 0.034059 CCGCCTTAATGGAGCTCGAT 59.966 55.000 7.83 6.51 38.35 3.59
1995 2015 2.159787 CCGAGCAAAAGATCAACTGACG 60.160 50.000 0.00 0.00 0.00 4.35
2013 2033 0.934496 CTTTGCAGACGTTGAACCGA 59.066 50.000 0.00 0.00 0.00 4.69
2015 2035 2.844122 AACTTTGCAGACGTTGAACC 57.156 45.000 0.00 0.00 0.00 3.62
2023 2043 3.518634 TCAACCCAAAACTTTGCAGAC 57.481 42.857 0.00 0.00 36.86 3.51
2066 2087 6.108687 TGAATACATCTGTGGCAAGTCTAAG 58.891 40.000 0.00 0.00 0.00 2.18
2111 2132 1.135721 GCCCAGCTGGATTTCATCAAC 59.864 52.381 34.91 6.00 37.39 3.18
2153 2175 7.171678 CAGGAGATTAGACCGGAAATTTGTATC 59.828 40.741 9.46 0.00 0.00 2.24
2172 2194 4.885907 CCTCAACACAATATTGCAGGAGAT 59.114 41.667 15.48 0.00 31.40 2.75
2188 2210 3.614150 GCAGTGATCGACTTACCTCAACA 60.614 47.826 0.00 0.00 29.75 3.33
2189 2211 2.924290 GCAGTGATCGACTTACCTCAAC 59.076 50.000 0.00 0.00 29.75 3.18
2199 2221 1.412710 TCCCCAATAGCAGTGATCGAC 59.587 52.381 0.00 0.00 0.00 4.20
2202 2224 5.809001 TCATAATCCCCAATAGCAGTGATC 58.191 41.667 0.00 0.00 0.00 2.92
2203 2225 5.311649 ACTCATAATCCCCAATAGCAGTGAT 59.688 40.000 0.00 0.00 0.00 3.06
2205 2227 4.978099 ACTCATAATCCCCAATAGCAGTG 58.022 43.478 0.00 0.00 0.00 3.66
2206 2228 5.132648 TCAACTCATAATCCCCAATAGCAGT 59.867 40.000 0.00 0.00 0.00 4.40
2207 2229 5.624159 TCAACTCATAATCCCCAATAGCAG 58.376 41.667 0.00 0.00 0.00 4.24
2208 2230 5.369404 TCTCAACTCATAATCCCCAATAGCA 59.631 40.000 0.00 0.00 0.00 3.49
2209 2231 5.869579 TCTCAACTCATAATCCCCAATAGC 58.130 41.667 0.00 0.00 0.00 2.97
2254 2298 0.097674 GCATGTGAATCGCCTGTGTC 59.902 55.000 0.00 0.00 0.00 3.67
2271 2317 5.990996 ACACGTGATCACATATTCATATGCA 59.009 36.000 25.01 0.00 42.98 3.96
2280 2326 5.600696 TGCTCATAACACGTGATCACATAT 58.399 37.500 25.01 13.81 0.00 1.78
2282 2328 3.860641 TGCTCATAACACGTGATCACAT 58.139 40.909 25.01 7.78 0.00 3.21
2291 2337 2.478894 AGTTCGGTTTGCTCATAACACG 59.521 45.455 0.00 0.00 0.00 4.49
2316 2362 0.173708 GACCACGAGGATGTCCAGTC 59.826 60.000 5.68 0.00 38.89 3.51
2323 2369 2.427095 TCAGTACATGACCACGAGGATG 59.573 50.000 5.68 2.27 38.69 3.51
2358 2407 1.043116 TCTCCAGTCCTATGGGCACG 61.043 60.000 0.00 0.00 41.01 5.34
2379 2428 8.594881 TGTACTCAAAGAAATCTTTCTCTGTC 57.405 34.615 5.45 0.00 46.22 3.51
2385 2434 7.370383 TGGCAATGTACTCAAAGAAATCTTTC 58.630 34.615 5.45 0.00 43.72 2.62
2414 2463 1.266178 TCGTCATCTCTGAAAGGCCA 58.734 50.000 5.01 0.00 31.85 5.36
2428 2477 3.684305 CCATTGTTAGTCTGCATTCGTCA 59.316 43.478 0.00 0.00 0.00 4.35
2552 2602 4.020573 TGACAGGACCCAATGTTGTAGTAG 60.021 45.833 0.00 0.00 0.00 2.57
2553 2603 3.904965 TGACAGGACCCAATGTTGTAGTA 59.095 43.478 0.00 0.00 0.00 1.82
2554 2604 2.708861 TGACAGGACCCAATGTTGTAGT 59.291 45.455 0.00 0.00 0.00 2.73
2564 2614 2.025793 TCAACAAAGTTGACAGGACCCA 60.026 45.455 8.39 0.00 0.00 4.51
2630 2680 1.671054 ACTGCCGTGTGTATGCACC 60.671 57.895 11.66 2.20 44.65 5.01
2640 2690 3.716006 CGAACCAGCACTGCCGTG 61.716 66.667 3.57 3.57 44.07 4.94
2646 2696 1.367840 GACAGGACGAACCAGCACT 59.632 57.895 0.00 0.00 42.04 4.40
2671 2724 6.640907 CACTGGAATACAACAGGCTTTAAAAC 59.359 38.462 0.00 0.00 39.00 2.43
2725 2778 8.133627 CCCAGCAACAATATCTTTTGAATAGAG 58.866 37.037 0.00 0.00 0.00 2.43
2740 2793 2.762327 GTTCCATGATCCCAGCAACAAT 59.238 45.455 0.00 0.00 0.00 2.71
2741 2794 2.170166 GTTCCATGATCCCAGCAACAA 58.830 47.619 0.00 0.00 0.00 2.83
2768 2821 7.483307 CAAAACATCCTCTTCTTTTTCACAGA 58.517 34.615 0.00 0.00 0.00 3.41
2785 2842 0.814457 TACGGGCATGGCAAAACATC 59.186 50.000 22.06 0.21 0.00 3.06
2842 2907 5.643777 GCTAATTAATCACCGATATGCAGGT 59.356 40.000 0.00 0.00 42.34 4.00
2849 2914 6.869913 CCCGTAAAGCTAATTAATCACCGATA 59.130 38.462 0.00 0.00 0.00 2.92
2925 2993 2.793946 GCCATAGTGCAAGCCGTG 59.206 61.111 0.00 0.00 0.00 4.94
2927 2995 2.819595 ACGCCATAGTGCAAGCCG 60.820 61.111 0.00 0.00 0.00 5.52
2968 3036 2.734723 GCTCACGCGTCAAGCTGA 60.735 61.111 27.39 13.79 45.59 4.26
2973 3041 2.355837 GTCCTGCTCACGCGTCAA 60.356 61.111 9.86 0.00 39.65 3.18
2986 3054 1.760613 TCGGTTCTTGTCAACTGTCCT 59.239 47.619 0.00 0.00 34.66 3.85
3023 3091 5.730550 ACATCAAGATTAAGGTGTCGCTTA 58.269 37.500 0.00 0.00 0.00 3.09
3027 3095 5.872617 TGGTAACATCAAGATTAAGGTGTCG 59.127 40.000 0.00 0.00 46.17 4.35
3070 3139 3.963428 AGTATATCCTTCCGGTGATGC 57.037 47.619 0.00 0.00 0.00 3.91
3078 3147 6.071840 CCAGTAGCACAGTAGTATATCCTTCC 60.072 46.154 0.00 0.00 0.00 3.46
3091 3160 1.293498 CTTCGGCCAGTAGCACAGT 59.707 57.895 2.24 0.00 46.50 3.55
3092 3161 0.530744 TACTTCGGCCAGTAGCACAG 59.469 55.000 2.24 0.00 46.50 3.66
3093 3162 1.191535 ATACTTCGGCCAGTAGCACA 58.808 50.000 2.24 0.00 46.50 4.57
3112 3181 2.679837 GCGCTGATGATCTCCAAGAAAA 59.320 45.455 0.00 0.00 0.00 2.29
3113 3182 2.283298 GCGCTGATGATCTCCAAGAAA 58.717 47.619 0.00 0.00 0.00 2.52
3114 3183 1.207811 TGCGCTGATGATCTCCAAGAA 59.792 47.619 9.73 0.00 0.00 2.52
3234 3537 0.962356 GGGGCATTGGGATATCAGCG 60.962 60.000 4.83 0.00 0.00 5.18
3280 3583 2.594962 GGACACACCAACACGAGCG 61.595 63.158 0.00 0.00 38.79 5.03
3287 3590 0.693049 ATGGAGGAGGACACACCAAC 59.307 55.000 0.00 0.00 42.04 3.77
3288 3591 1.351017 GAATGGAGGAGGACACACCAA 59.649 52.381 0.00 0.00 42.04 3.67
3289 3592 0.984230 GAATGGAGGAGGACACACCA 59.016 55.000 0.00 0.00 42.04 4.17
3290 3593 0.253327 GGAATGGAGGAGGACACACC 59.747 60.000 0.00 0.00 39.35 4.16
3291 3594 0.253327 GGGAATGGAGGAGGACACAC 59.747 60.000 0.00 0.00 0.00 3.82
3292 3595 0.914417 GGGGAATGGAGGAGGACACA 60.914 60.000 0.00 0.00 0.00 3.72
3293 3596 0.914417 TGGGGAATGGAGGAGGACAC 60.914 60.000 0.00 0.00 0.00 3.67
3294 3597 0.914417 GTGGGGAATGGAGGAGGACA 60.914 60.000 0.00 0.00 0.00 4.02
3295 3598 1.636769 GGTGGGGAATGGAGGAGGAC 61.637 65.000 0.00 0.00 0.00 3.85
3296 3599 1.307866 GGTGGGGAATGGAGGAGGA 60.308 63.158 0.00 0.00 0.00 3.71
3297 3600 2.746375 CGGTGGGGAATGGAGGAGG 61.746 68.421 0.00 0.00 0.00 4.30
3299 3602 3.407967 GCGGTGGGGAATGGAGGA 61.408 66.667 0.00 0.00 0.00 3.71
3300 3603 4.506255 GGCGGTGGGGAATGGAGG 62.506 72.222 0.00 0.00 0.00 4.30
3301 3604 2.572333 AATGGCGGTGGGGAATGGAG 62.572 60.000 0.00 0.00 0.00 3.86
3302 3605 2.621445 AATGGCGGTGGGGAATGGA 61.621 57.895 0.00 0.00 0.00 3.41
3303 3606 2.043046 AATGGCGGTGGGGAATGG 60.043 61.111 0.00 0.00 0.00 3.16
3304 3607 0.395036 TACAATGGCGGTGGGGAATG 60.395 55.000 0.00 0.00 0.00 2.67
3305 3608 0.395173 GTACAATGGCGGTGGGGAAT 60.395 55.000 0.00 0.00 0.00 3.01
3312 3642 2.812178 GCGACGTACAATGGCGGT 60.812 61.111 0.00 0.00 0.00 5.68
3320 3650 2.019249 AGCTTATACTGGCGACGTACA 58.981 47.619 0.00 0.00 0.00 2.90
3348 3681 4.368808 CGCAAAGTGCACGGACGG 62.369 66.667 12.01 1.96 45.36 4.79


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

AutoCloner maintained by Alex Coulton.