Multiple sequence alignment - TraesCS6B01G288000

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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 TraesCS6B01G288000 chr6B 100.000 2312 0 0 1 2312 518680231 518677920 0.000000e+00 4270
1 TraesCS6B01G288000 chr6B 97.849 279 6 0 179 457 41757182 41757460 1.240000e-132 483
2 TraesCS6B01G288000 chr6D 91.563 1529 87 23 454 1963 343677356 343675851 0.000000e+00 2071
3 TraesCS6B01G288000 chr6D 90.191 367 32 4 1584 1947 195978862 195979227 2.080000e-130 475
4 TraesCS6B01G288000 chr6D 86.513 304 21 12 2017 2312 343675851 343675560 1.330000e-82 316
5 TraesCS6B01G288000 chr6D 91.758 182 15 0 1 182 343677534 343677353 1.060000e-63 254
6 TraesCS6B01G288000 chr6D 88.623 167 18 1 1385 1551 195978698 195978863 3.900000e-48 202
7 TraesCS6B01G288000 chr6A 91.758 910 54 10 454 1356 484079981 484079086 0.000000e+00 1245
8 TraesCS6B01G288000 chr6A 89.247 930 67 16 1393 2310 484078743 484077835 0.000000e+00 1133
9 TraesCS6B01G288000 chr6A 97.133 279 8 0 179 457 50270112 50269834 2.690000e-129 472
10 TraesCS6B01G288000 chr6A 87.059 255 22 5 1574 1819 413097465 413097213 6.290000e-71 278
11 TraesCS6B01G288000 chr2D 96.508 315 11 0 996 1310 498766983 498767297 2.630000e-144 521
12 TraesCS6B01G288000 chr2D 87.597 258 20 6 1571 1819 166479609 166479863 2.910000e-74 289
13 TraesCS6B01G288000 chr2A 96.190 315 12 0 996 1310 643438489 643438803 1.220000e-142 516
14 TraesCS6B01G288000 chr1A 95.899 317 11 2 1001 1317 485012905 485012591 1.580000e-141 512
15 TraesCS6B01G288000 chr1A 99.640 278 1 0 180 457 436890473 436890196 2.050000e-140 508
16 TraesCS6B01G288000 chr1A 94.479 326 17 1 998 1322 543928362 543928687 3.430000e-138 501
17 TraesCS6B01G288000 chr7D 95.873 315 13 0 996 1310 134467044 134466730 5.700000e-141 510
18 TraesCS6B01G288000 chr7D 88.391 379 35 5 1574 1947 103192321 103191947 4.530000e-122 448
19 TraesCS6B01G288000 chr7D 87.795 254 25 3 1571 1819 638018207 638018459 2.250000e-75 292
20 TraesCS6B01G288000 chr7D 87.597 258 21 5 1571 1819 538580156 538580411 2.910000e-74 289
21 TraesCS6B01G288000 chr3D 93.294 343 19 3 998 1339 459878583 459878922 9.530000e-139 503
22 TraesCS6B01G288000 chr3A 93.294 343 19 3 998 1339 602012323 602012662 9.530000e-139 503
23 TraesCS6B01G288000 chr3A 87.206 383 40 5 1571 1947 502782104 502782483 5.900000e-116 427
24 TraesCS6B01G288000 chr7A 99.635 274 1 0 182 455 681096716 681096443 3.430000e-138 501
25 TraesCS6B01G288000 chr7A 97.203 286 6 2 180 464 625740995 625741279 1.240000e-132 483
26 TraesCS6B01G288000 chr7A 97.810 274 6 0 182 455 696639108 696639381 7.480000e-130 473
27 TraesCS6B01G288000 chrUn 97.491 279 7 0 179 457 40187666 40187388 5.780000e-131 477
28 TraesCS6B01G288000 chr5B 96.820 283 8 1 175 457 451177106 451177387 2.690000e-129 472
29 TraesCS6B01G288000 chr2B 96.809 282 8 1 176 457 620862419 620862139 9.670000e-129 470
30 TraesCS6B01G288000 chr5D 88.327 257 20 4 1574 1822 300555096 300554842 1.340000e-77 300
31 TraesCS6B01G288000 chr4D 87.402 254 22 4 1574 1819 242981811 242981560 1.350000e-72 283


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 TraesCS6B01G288000 chr6B 518677920 518680231 2311 True 4270.000000 4270 100.000000 1 2312 1 chr6B.!!$R1 2311
1 TraesCS6B01G288000 chr6D 343675560 343677534 1974 True 880.333333 2071 89.944667 1 2312 3 chr6D.!!$R1 2311
2 TraesCS6B01G288000 chr6D 195978698 195979227 529 False 338.500000 475 89.407000 1385 1947 2 chr6D.!!$F1 562
3 TraesCS6B01G288000 chr6A 484077835 484079981 2146 True 1189.000000 1245 90.502500 454 2310 2 chr6A.!!$R3 1856

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
969 988 0.035458 CAGCGACTCCCATTATCCCC 59.965 60.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2483 0.81361 CAGGAACCAGTCAACACGCA 60.814 55.0 0.0 0.0 0.0 5.24 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
41 42 8.591072 CCAATCAGAAAGCCCAAAATATCATAT 58.409 33.333 0.00 0.00 0.00 1.78
72 73 4.686191 ATTTTGACAAGGGTGCATTTGA 57.314 36.364 13.37 0.00 0.00 2.69
88 89 3.290948 TTTGAGTACCAACCAAGCACT 57.709 42.857 0.00 0.00 33.85 4.40
89 90 4.425180 TTTGAGTACCAACCAAGCACTA 57.575 40.909 0.00 0.00 33.85 2.74
93 94 6.116711 TGAGTACCAACCAAGCACTATAAA 57.883 37.500 0.00 0.00 0.00 1.40
97 98 8.086143 AGTACCAACCAAGCACTATAAATCTA 57.914 34.615 0.00 0.00 0.00 1.98
129 130 2.356695 ACCGAAAAACTGAGTTTTCCCG 59.643 45.455 22.06 23.90 43.67 5.14
149 150 3.366883 CCGGAAAGAGAAGTCTCAGTGAG 60.367 52.174 14.36 14.36 45.21 3.51
171 172 0.958091 TTTTGTTGATGGCTGACCCG 59.042 50.000 0.00 0.00 35.87 5.28
173 174 0.321564 TTGTTGATGGCTGACCCGAG 60.322 55.000 0.00 0.00 35.87 4.63
180 181 3.518998 GCTGACCCGAGCGAGCTA 61.519 66.667 0.00 0.00 0.00 3.32
181 182 3.064987 GCTGACCCGAGCGAGCTAA 62.065 63.158 0.00 0.00 0.00 3.09
182 183 1.064946 CTGACCCGAGCGAGCTAAG 59.935 63.158 0.00 0.00 0.00 2.18
183 184 2.343163 CTGACCCGAGCGAGCTAAGG 62.343 65.000 10.32 10.32 0.00 2.69
184 185 3.140225 GACCCGAGCGAGCTAAGGG 62.140 68.421 26.29 26.29 44.56 3.95
185 186 4.593864 CCCGAGCGAGCTAAGGGC 62.594 72.222 20.08 0.00 37.31 5.19
186 187 3.838271 CCGAGCGAGCTAAGGGCA 61.838 66.667 10.13 0.00 44.79 5.36
187 188 2.419198 CGAGCGAGCTAAGGGCAT 59.581 61.111 0.00 0.00 44.79 4.40
188 189 1.953138 CGAGCGAGCTAAGGGCATG 60.953 63.158 0.00 0.00 44.79 4.06
189 190 1.144936 GAGCGAGCTAAGGGCATGT 59.855 57.895 0.00 0.00 44.79 3.21
190 191 0.389391 GAGCGAGCTAAGGGCATGTA 59.611 55.000 0.00 0.00 44.79 2.29
191 192 0.105039 AGCGAGCTAAGGGCATGTAC 59.895 55.000 0.00 0.00 44.79 2.90
192 193 0.179084 GCGAGCTAAGGGCATGTACA 60.179 55.000 0.00 0.00 44.79 2.90
193 194 1.742411 GCGAGCTAAGGGCATGTACAA 60.742 52.381 0.00 0.00 44.79 2.41
194 195 2.838736 CGAGCTAAGGGCATGTACAAT 58.161 47.619 0.00 0.00 44.79 2.71
195 196 2.545526 CGAGCTAAGGGCATGTACAATG 59.454 50.000 0.00 0.12 44.79 2.82
196 197 2.880890 GAGCTAAGGGCATGTACAATGG 59.119 50.000 0.00 0.00 44.79 3.16
197 198 2.242196 AGCTAAGGGCATGTACAATGGT 59.758 45.455 0.00 0.00 44.79 3.55
198 199 3.023832 GCTAAGGGCATGTACAATGGTT 58.976 45.455 0.00 0.00 41.35 3.67
199 200 3.181487 GCTAAGGGCATGTACAATGGTTG 60.181 47.826 0.00 0.00 41.35 3.77
200 201 2.897271 AGGGCATGTACAATGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
201 202 3.386932 AGGGCATGTACAATGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
202 203 4.518278 AGGGCATGTACAATGGTTGATA 57.482 40.909 0.00 0.00 0.00 2.15
203 204 4.865905 AGGGCATGTACAATGGTTGATAA 58.134 39.130 0.00 0.00 0.00 1.75
204 205 4.889409 AGGGCATGTACAATGGTTGATAAG 59.111 41.667 0.00 0.00 0.00 1.73
205 206 4.887071 GGGCATGTACAATGGTTGATAAGA 59.113 41.667 0.00 0.00 0.00 2.10
206 207 5.221048 GGGCATGTACAATGGTTGATAAGAC 60.221 44.000 0.00 0.00 0.00 3.01
207 208 5.356751 GGCATGTACAATGGTTGATAAGACA 59.643 40.000 0.00 0.00 0.00 3.41
208 209 6.458751 GGCATGTACAATGGTTGATAAGACAG 60.459 42.308 0.00 0.00 0.00 3.51
209 210 6.094048 GCATGTACAATGGTTGATAAGACAGT 59.906 38.462 0.00 0.00 0.00 3.55
210 211 7.677276 GCATGTACAATGGTTGATAAGACAGTC 60.677 40.741 0.00 0.00 0.00 3.51
211 212 7.004555 TGTACAATGGTTGATAAGACAGTCT 57.995 36.000 0.00 0.00 0.00 3.24
212 213 7.450074 TGTACAATGGTTGATAAGACAGTCTT 58.550 34.615 19.81 19.81 40.35 3.01
213 214 8.590204 TGTACAATGGTTGATAAGACAGTCTTA 58.410 33.333 22.68 22.68 42.49 2.10
228 229 9.678260 AAGACAGTCTTATCTTAAATCTTGCAT 57.322 29.630 14.58 0.00 34.42 3.96
229 230 9.107177 AGACAGTCTTATCTTAAATCTTGCATG 57.893 33.333 0.00 0.00 0.00 4.06
230 231 8.798859 ACAGTCTTATCTTAAATCTTGCATGT 57.201 30.769 0.00 0.00 0.00 3.21
231 232 9.890629 ACAGTCTTATCTTAAATCTTGCATGTA 57.109 29.630 0.00 0.00 0.00 2.29
245 246 8.969260 ATCTTGCATGTAATTTAGAGATGACA 57.031 30.769 0.00 0.00 0.00 3.58
246 247 8.791327 TCTTGCATGTAATTTAGAGATGACAA 57.209 30.769 0.00 0.00 0.00 3.18
247 248 9.230122 TCTTGCATGTAATTTAGAGATGACAAA 57.770 29.630 0.00 0.00 0.00 2.83
248 249 9.844790 CTTGCATGTAATTTAGAGATGACAAAA 57.155 29.630 0.00 0.00 0.00 2.44
279 280 7.676947 TGTCTACAATGGGTTATATCTTAGCC 58.323 38.462 0.00 0.00 0.00 3.93
280 281 7.512746 TGTCTACAATGGGTTATATCTTAGCCT 59.487 37.037 0.00 0.00 33.15 4.58
281 282 8.376270 GTCTACAATGGGTTATATCTTAGCCTT 58.624 37.037 0.00 0.00 33.15 4.35
282 283 9.610104 TCTACAATGGGTTATATCTTAGCCTTA 57.390 33.333 0.00 0.00 33.15 2.69
285 286 9.117223 ACAATGGGTTATATCTTAGCCTTATCT 57.883 33.333 0.00 0.00 33.15 1.98
286 287 9.965902 CAATGGGTTATATCTTAGCCTTATCTT 57.034 33.333 0.00 0.00 33.15 2.40
288 289 8.736097 TGGGTTATATCTTAGCCTTATCTTCA 57.264 34.615 0.00 0.00 33.15 3.02
289 290 9.166222 TGGGTTATATCTTAGCCTTATCTTCAA 57.834 33.333 0.00 0.00 33.15 2.69
297 298 9.936759 ATCTTAGCCTTATCTTCAATAACTAGC 57.063 33.333 0.00 0.00 0.00 3.42
298 299 8.924303 TCTTAGCCTTATCTTCAATAACTAGCA 58.076 33.333 0.00 0.00 0.00 3.49
299 300 9.547753 CTTAGCCTTATCTTCAATAACTAGCAA 57.452 33.333 0.00 0.00 0.00 3.91
301 302 8.986929 AGCCTTATCTTCAATAACTAGCAATT 57.013 30.769 0.00 0.00 0.00 2.32
302 303 9.061435 AGCCTTATCTTCAATAACTAGCAATTC 57.939 33.333 0.00 0.00 0.00 2.17
303 304 8.293157 GCCTTATCTTCAATAACTAGCAATTCC 58.707 37.037 0.00 0.00 0.00 3.01
304 305 9.566432 CCTTATCTTCAATAACTAGCAATTCCT 57.434 33.333 0.00 0.00 0.00 3.36
315 316 7.539034 AACTAGCAATTCCTTAAAACATGGT 57.461 32.000 0.00 0.00 0.00 3.55
316 317 6.924111 ACTAGCAATTCCTTAAAACATGGTG 58.076 36.000 0.00 0.00 0.00 4.17
317 318 6.719370 ACTAGCAATTCCTTAAAACATGGTGA 59.281 34.615 0.00 0.00 0.00 4.02
318 319 6.029346 AGCAATTCCTTAAAACATGGTGAG 57.971 37.500 0.00 0.00 0.00 3.51
319 320 5.774690 AGCAATTCCTTAAAACATGGTGAGA 59.225 36.000 0.00 0.00 0.00 3.27
320 321 5.863935 GCAATTCCTTAAAACATGGTGAGAC 59.136 40.000 0.00 0.00 0.00 3.36
321 322 6.516527 GCAATTCCTTAAAACATGGTGAGACA 60.517 38.462 0.00 0.00 0.00 3.41
322 323 7.432869 CAATTCCTTAAAACATGGTGAGACAA 58.567 34.615 0.00 0.00 0.00 3.18
323 324 7.595819 ATTCCTTAAAACATGGTGAGACAAA 57.404 32.000 0.00 0.00 0.00 2.83
324 325 7.595819 TTCCTTAAAACATGGTGAGACAAAT 57.404 32.000 0.00 0.00 0.00 2.32
325 326 7.595819 TCCTTAAAACATGGTGAGACAAATT 57.404 32.000 0.00 0.00 0.00 1.82
326 327 7.432869 TCCTTAAAACATGGTGAGACAAATTG 58.567 34.615 0.00 0.00 0.00 2.32
327 328 7.069331 TCCTTAAAACATGGTGAGACAAATTGT 59.931 33.333 0.00 0.00 0.00 2.71
328 329 7.169645 CCTTAAAACATGGTGAGACAAATTGTG 59.830 37.037 2.20 0.00 0.00 3.33
329 330 3.648339 ACATGGTGAGACAAATTGTGC 57.352 42.857 2.20 0.00 0.00 4.57
330 331 3.225104 ACATGGTGAGACAAATTGTGCT 58.775 40.909 2.20 0.36 0.00 4.40
331 332 4.397420 ACATGGTGAGACAAATTGTGCTA 58.603 39.130 2.20 0.00 0.00 3.49
332 333 4.826733 ACATGGTGAGACAAATTGTGCTAA 59.173 37.500 2.20 0.00 0.00 3.09
333 334 5.048504 ACATGGTGAGACAAATTGTGCTAAG 60.049 40.000 2.20 0.00 0.00 2.18
334 335 4.713553 TGGTGAGACAAATTGTGCTAAGA 58.286 39.130 2.20 0.00 0.00 2.10
335 336 4.756642 TGGTGAGACAAATTGTGCTAAGAG 59.243 41.667 2.20 0.00 0.00 2.85
336 337 4.997395 GGTGAGACAAATTGTGCTAAGAGA 59.003 41.667 2.20 0.00 0.00 3.10
337 338 5.645497 GGTGAGACAAATTGTGCTAAGAGAT 59.355 40.000 2.20 0.00 0.00 2.75
338 339 6.183360 GGTGAGACAAATTGTGCTAAGAGATC 60.183 42.308 2.20 0.00 0.00 2.75
339 340 6.369890 GTGAGACAAATTGTGCTAAGAGATCA 59.630 38.462 2.20 0.00 0.00 2.92
340 341 7.065563 GTGAGACAAATTGTGCTAAGAGATCAT 59.934 37.037 2.20 0.00 0.00 2.45
341 342 7.279536 TGAGACAAATTGTGCTAAGAGATCATC 59.720 37.037 2.20 0.00 0.00 2.92
342 343 7.337167 AGACAAATTGTGCTAAGAGATCATCT 58.663 34.615 2.20 0.00 41.27 2.90
343 344 7.495279 AGACAAATTGTGCTAAGAGATCATCTC 59.505 37.037 6.55 6.55 43.70 2.75
377 378 9.746457 ATCTTAAATAAGAGAAGACAAGGCTTT 57.254 29.630 0.00 0.00 44.67 3.51
378 379 9.574516 TCTTAAATAAGAGAAGACAAGGCTTTT 57.425 29.630 0.00 0.00 37.40 2.27
379 380 9.833182 CTTAAATAAGAGAAGACAAGGCTTTTC 57.167 33.333 5.24 5.24 35.33 2.29
380 381 9.574516 TTAAATAAGAGAAGACAAGGCTTTTCT 57.425 29.630 10.06 10.06 40.01 2.52
381 382 8.470657 AAATAAGAGAAGACAAGGCTTTTCTT 57.529 30.769 24.50 24.50 45.59 2.52
382 383 9.574516 AAATAAGAGAAGACAAGGCTTTTCTTA 57.425 29.630 24.34 23.06 46.51 2.10
384 385 7.446001 AAGAGAAGACAAGGCTTTTCTTATG 57.554 36.000 23.52 3.43 43.42 1.90
385 386 6.773638 AGAGAAGACAAGGCTTTTCTTATGA 58.226 36.000 23.52 0.00 36.32 2.15
386 387 6.878389 AGAGAAGACAAGGCTTTTCTTATGAG 59.122 38.462 23.52 1.37 36.32 2.90
387 388 6.538263 AGAAGACAAGGCTTTTCTTATGAGT 58.462 36.000 24.34 5.78 29.54 3.41
388 389 7.001073 AGAAGACAAGGCTTTTCTTATGAGTT 58.999 34.615 24.34 5.11 29.54 3.01
389 390 6.809630 AGACAAGGCTTTTCTTATGAGTTC 57.190 37.500 10.06 0.00 0.00 3.01
390 391 6.538263 AGACAAGGCTTTTCTTATGAGTTCT 58.462 36.000 10.06 0.00 0.00 3.01
391 392 6.652900 AGACAAGGCTTTTCTTATGAGTTCTC 59.347 38.462 10.06 0.00 0.00 2.87
392 393 6.538263 ACAAGGCTTTTCTTATGAGTTCTCT 58.462 36.000 0.00 0.00 0.00 3.10
393 394 6.652900 ACAAGGCTTTTCTTATGAGTTCTCTC 59.347 38.462 0.00 0.00 40.79 3.20
394 395 6.619329 AGGCTTTTCTTATGAGTTCTCTCT 57.381 37.500 1.53 0.00 40.98 3.10
395 396 6.639563 AGGCTTTTCTTATGAGTTCTCTCTC 58.360 40.000 1.53 0.00 40.98 3.20
396 397 5.815222 GGCTTTTCTTATGAGTTCTCTCTCC 59.185 44.000 1.53 0.00 40.98 3.71
397 398 6.351796 GGCTTTTCTTATGAGTTCTCTCTCCT 60.352 42.308 1.53 0.00 40.98 3.69
398 399 6.756542 GCTTTTCTTATGAGTTCTCTCTCCTC 59.243 42.308 1.53 0.00 40.98 3.71
399 400 6.783708 TTTCTTATGAGTTCTCTCTCCTCC 57.216 41.667 1.53 0.00 40.98 4.30
400 401 5.458451 TCTTATGAGTTCTCTCTCCTCCA 57.542 43.478 1.53 0.00 40.98 3.86
401 402 5.197451 TCTTATGAGTTCTCTCTCCTCCAC 58.803 45.833 1.53 0.00 40.98 4.02
402 403 2.223803 TGAGTTCTCTCTCCTCCACC 57.776 55.000 1.53 0.00 40.98 4.61
403 404 1.713647 TGAGTTCTCTCTCCTCCACCT 59.286 52.381 1.53 0.00 40.98 4.00
404 405 2.291282 TGAGTTCTCTCTCCTCCACCTC 60.291 54.545 1.53 0.00 40.98 3.85
405 406 1.713647 AGTTCTCTCTCCTCCACCTCA 59.286 52.381 0.00 0.00 0.00 3.86
406 407 2.314549 AGTTCTCTCTCCTCCACCTCAT 59.685 50.000 0.00 0.00 0.00 2.90
407 408 2.693074 GTTCTCTCTCCTCCACCTCATC 59.307 54.545 0.00 0.00 0.00 2.92
408 409 1.925959 TCTCTCTCCTCCACCTCATCA 59.074 52.381 0.00 0.00 0.00 3.07
409 410 2.517553 TCTCTCTCCTCCACCTCATCAT 59.482 50.000 0.00 0.00 0.00 2.45
410 411 3.052262 TCTCTCTCCTCCACCTCATCATT 60.052 47.826 0.00 0.00 0.00 2.57
411 412 3.710677 CTCTCTCCTCCACCTCATCATTT 59.289 47.826 0.00 0.00 0.00 2.32
412 413 4.883759 TCTCTCCTCCACCTCATCATTTA 58.116 43.478 0.00 0.00 0.00 1.40
413 414 5.471424 TCTCTCCTCCACCTCATCATTTAT 58.529 41.667 0.00 0.00 0.00 1.40
414 415 5.541868 TCTCTCCTCCACCTCATCATTTATC 59.458 44.000 0.00 0.00 0.00 1.75
415 416 4.594920 TCTCCTCCACCTCATCATTTATCC 59.405 45.833 0.00 0.00 0.00 2.59
416 417 4.570926 TCCTCCACCTCATCATTTATCCT 58.429 43.478 0.00 0.00 0.00 3.24
417 418 5.726560 TCCTCCACCTCATCATTTATCCTA 58.273 41.667 0.00 0.00 0.00 2.94
418 419 5.544176 TCCTCCACCTCATCATTTATCCTAC 59.456 44.000 0.00 0.00 0.00 3.18
419 420 5.468540 TCCACCTCATCATTTATCCTACG 57.531 43.478 0.00 0.00 0.00 3.51
420 421 4.899457 TCCACCTCATCATTTATCCTACGT 59.101 41.667 0.00 0.00 0.00 3.57
421 422 4.991056 CCACCTCATCATTTATCCTACGTG 59.009 45.833 0.00 0.00 0.00 4.49
422 423 4.991056 CACCTCATCATTTATCCTACGTGG 59.009 45.833 0.00 0.00 37.10 4.94
423 424 3.997021 CCTCATCATTTATCCTACGTGGC 59.003 47.826 0.00 0.00 35.26 5.01
424 425 4.503123 CCTCATCATTTATCCTACGTGGCA 60.503 45.833 0.00 0.00 35.26 4.92
425 426 4.377021 TCATCATTTATCCTACGTGGCAC 58.623 43.478 7.79 7.79 35.26 5.01
426 427 4.100963 TCATCATTTATCCTACGTGGCACT 59.899 41.667 16.72 5.47 35.26 4.40
427 428 4.054780 TCATTTATCCTACGTGGCACTC 57.945 45.455 16.72 0.00 35.26 3.51
428 429 2.973694 TTTATCCTACGTGGCACTCC 57.026 50.000 16.72 0.00 35.26 3.85
429 430 2.154567 TTATCCTACGTGGCACTCCT 57.845 50.000 16.72 0.21 35.26 3.69
430 431 3.301794 TTATCCTACGTGGCACTCCTA 57.698 47.619 16.72 1.46 35.26 2.94
431 432 2.154567 ATCCTACGTGGCACTCCTAA 57.845 50.000 16.72 0.00 35.26 2.69
432 433 1.471119 TCCTACGTGGCACTCCTAAG 58.529 55.000 16.72 0.92 35.26 2.18
433 434 1.005097 TCCTACGTGGCACTCCTAAGA 59.995 52.381 16.72 2.12 35.26 2.10
434 435 2.032620 CCTACGTGGCACTCCTAAGAT 58.967 52.381 16.72 0.00 0.00 2.40
435 436 3.117776 TCCTACGTGGCACTCCTAAGATA 60.118 47.826 16.72 0.00 35.26 1.98
436 437 3.253677 CCTACGTGGCACTCCTAAGATAG 59.746 52.174 16.72 0.00 0.00 2.08
437 438 1.409427 ACGTGGCACTCCTAAGATAGC 59.591 52.381 16.72 0.00 0.00 2.97
438 439 1.409064 CGTGGCACTCCTAAGATAGCA 59.591 52.381 16.72 0.00 0.00 3.49
439 440 2.799917 CGTGGCACTCCTAAGATAGCAC 60.800 54.545 16.72 0.00 0.00 4.40
440 441 1.762957 TGGCACTCCTAAGATAGCACC 59.237 52.381 0.00 0.00 0.00 5.01
441 442 1.762957 GGCACTCCTAAGATAGCACCA 59.237 52.381 0.00 0.00 0.00 4.17
442 443 2.370189 GGCACTCCTAAGATAGCACCAT 59.630 50.000 0.00 0.00 0.00 3.55
443 444 3.181450 GGCACTCCTAAGATAGCACCATT 60.181 47.826 0.00 0.00 0.00 3.16
444 445 3.812053 GCACTCCTAAGATAGCACCATTG 59.188 47.826 0.00 0.00 0.00 2.82
445 446 4.684485 GCACTCCTAAGATAGCACCATTGT 60.684 45.833 0.00 0.00 0.00 2.71
446 447 5.453339 GCACTCCTAAGATAGCACCATTGTA 60.453 44.000 0.00 0.00 0.00 2.41
447 448 5.986135 CACTCCTAAGATAGCACCATTGTAC 59.014 44.000 0.00 0.00 0.00 2.90
448 449 5.661312 ACTCCTAAGATAGCACCATTGTACA 59.339 40.000 0.00 0.00 0.00 2.90
449 450 6.327626 ACTCCTAAGATAGCACCATTGTACAT 59.672 38.462 0.00 0.00 0.00 2.29
450 451 6.524734 TCCTAAGATAGCACCATTGTACATG 58.475 40.000 0.00 0.00 0.00 3.21
451 452 5.180117 CCTAAGATAGCACCATTGTACATGC 59.820 44.000 10.53 10.53 38.39 4.06
452 453 3.480470 AGATAGCACCATTGTACATGCC 58.520 45.455 14.08 1.71 38.92 4.40
465 466 4.188462 TGTACATGCCCTAATGAGTTTCG 58.812 43.478 0.00 0.00 0.00 3.46
467 468 1.003545 CATGCCCTAATGAGTTTCGCG 60.004 52.381 0.00 0.00 0.00 5.87
520 522 7.601508 AGCAAGCAATTTGGAAGATAGAAAAAG 59.398 33.333 0.00 0.00 37.26 2.27
521 523 7.599998 GCAAGCAATTTGGAAGATAGAAAAAGA 59.400 33.333 0.00 0.00 37.26 2.52
548 550 4.675146 GCAGTACCATCATTTTTGCATCGT 60.675 41.667 0.00 0.00 0.00 3.73
589 591 3.072468 AGCGCGCCCCTGTTACTA 61.072 61.111 30.33 0.00 0.00 1.82
618 623 3.273080 GAAAAGCAGCGTGCCCCAG 62.273 63.158 6.39 0.00 46.52 4.45
693 705 1.698506 CCAGCTCCGAATCTACCTCT 58.301 55.000 0.00 0.00 0.00 3.69
766 778 1.911293 GCGCCAGCGATCAACAGAAA 61.911 55.000 17.53 0.00 42.83 2.52
767 779 0.729116 CGCCAGCGATCAACAGAAAT 59.271 50.000 6.06 0.00 42.83 2.17
769 781 2.285834 CGCCAGCGATCAACAGAAATAC 60.286 50.000 6.06 0.00 42.83 1.89
771 783 3.270027 CCAGCGATCAACAGAAATACCA 58.730 45.455 0.00 0.00 0.00 3.25
778 792 2.983192 TCAACAGAAATACCACCCCTCA 59.017 45.455 0.00 0.00 0.00 3.86
849 863 0.963856 AAAACCGAAATCCTCCCGCC 60.964 55.000 0.00 0.00 0.00 6.13
850 864 2.831894 AAACCGAAATCCTCCCGCCC 62.832 60.000 0.00 0.00 0.00 6.13
944 963 0.742281 CGCATCACCTCCTCACCAAG 60.742 60.000 0.00 0.00 0.00 3.61
948 967 0.471780 TCACCTCCTCACCAAGCTCA 60.472 55.000 0.00 0.00 0.00 4.26
962 981 1.078848 GCTCAACAGCGACTCCCAT 60.079 57.895 0.00 0.00 35.39 4.00
964 983 1.405526 GCTCAACAGCGACTCCCATTA 60.406 52.381 0.00 0.00 35.39 1.90
969 988 0.035458 CAGCGACTCCCATTATCCCC 59.965 60.000 0.00 0.00 0.00 4.81
972 991 1.424638 CGACTCCCATTATCCCCTGT 58.575 55.000 0.00 0.00 0.00 4.00
978 997 4.235372 CTCCCATTATCCCCTGTTAGACT 58.765 47.826 0.00 0.00 0.00 3.24
1302 1321 2.264794 CGCACCCTCTACGGCTTT 59.735 61.111 0.00 0.00 0.00 3.51
1364 1389 1.073216 CCTGCGTTGCTCTGTAGTCG 61.073 60.000 0.00 0.00 0.00 4.18
1426 1757 7.011109 GCTTGTTTCTGTAGTTTGTCTAGTGAA 59.989 37.037 0.00 0.00 0.00 3.18
1459 1790 7.093322 TCTAGTTGTAACTCCTATCGTTTCC 57.907 40.000 0.00 0.00 40.37 3.13
1465 1796 4.532314 AACTCCTATCGTTTCCTTTCGT 57.468 40.909 0.00 0.00 0.00 3.85
1491 1822 7.315142 TGCAATGACAAGTTAATTCCAATCTC 58.685 34.615 0.00 0.00 0.00 2.75
1500 1831 9.196552 CAAGTTAATTCCAATCTCAGAAAAACC 57.803 33.333 0.00 0.00 0.00 3.27
1511 1842 5.868454 TCTCAGAAAAACCATCATGTCTGA 58.132 37.500 5.14 5.14 39.24 3.27
1514 1845 7.120285 TCTCAGAAAAACCATCATGTCTGATTC 59.880 37.037 5.59 0.50 40.20 2.52
1517 1849 4.978083 AAACCATCATGTCTGATTCTGC 57.022 40.909 0.00 0.00 40.20 4.26
1555 1887 5.692654 GCTTCTAGTATCGGAGGAATTGAAC 59.307 44.000 0.00 0.00 0.00 3.18
1561 1893 6.653989 AGTATCGGAGGAATTGAACAAATCT 58.346 36.000 3.24 0.00 0.00 2.40
1567 1899 6.540189 CGGAGGAATTGAACAAATCTAGTGAT 59.460 38.462 3.24 0.00 33.70 3.06
1623 1957 1.228124 CCCTGCAGTTTGGTTCCGA 60.228 57.895 13.81 0.00 0.00 4.55
1639 1973 4.392138 GGTTCCGAAGAGTGGTAAATTCAG 59.608 45.833 0.00 0.00 0.00 3.02
1708 2042 1.542915 TCCGTACTGTCAGTTGGCTAC 59.457 52.381 11.54 1.67 0.00 3.58
1716 2050 2.158827 TGTCAGTTGGCTACTTCTGCAA 60.159 45.455 0.00 0.00 33.85 4.08
1766 2107 6.657541 TGGTAGAAAATATGGAACTGGAACAC 59.342 38.462 0.00 0.00 0.00 3.32
1776 2117 4.141367 TGGAACTGGAACACCATCAACTTA 60.141 41.667 0.00 0.00 32.90 2.24
1778 2119 6.177610 GGAACTGGAACACCATCAACTTATA 58.822 40.000 0.00 0.00 32.90 0.98
1793 2134 8.737175 CATCAACTTATATGGGAAATCCTGATG 58.263 37.037 0.00 4.22 32.90 3.07
1871 2215 7.652524 AAAAACTTGGCCCAATTTATTTGTT 57.347 28.000 0.00 0.00 33.15 2.83
1877 2221 4.518211 TGGCCCAATTTATTTGTTTGCAAG 59.482 37.500 0.00 0.00 35.82 4.01
1885 2229 5.446143 TTATTTGTTTGCAAGTCATCGGT 57.554 34.783 0.00 0.00 35.82 4.69
1894 2238 0.036306 AAGTCATCGGTTGTGACCCC 59.964 55.000 2.90 0.00 45.47 4.95
1921 2265 7.544804 AAGAATTGCTCTGGTTCCTTAATTT 57.455 32.000 0.00 0.00 33.37 1.82
1922 2266 7.544804 AGAATTGCTCTGGTTCCTTAATTTT 57.455 32.000 0.00 0.00 31.12 1.82
2066 2411 4.243007 GCCACAAGCTTACAAATCTGTT 57.757 40.909 0.00 0.00 38.99 3.16
2090 2435 9.517609 GTTACTACAGTTTGATATGTGACTAGG 57.482 37.037 0.00 0.00 0.00 3.02
2135 2483 6.105333 GTCAGTGTTCAGAAGCAGATTAGAT 58.895 40.000 0.00 0.00 0.00 1.98
2177 2525 7.810282 CCTGTGGATAAGAGTAATCGATTAGTG 59.190 40.741 26.30 10.35 0.00 2.74
2208 2556 1.218316 CCGGTCTCCAGCTGTAACC 59.782 63.158 13.81 15.03 0.00 2.85
2214 2570 2.168521 GTCTCCAGCTGTAACCATAGCA 59.831 50.000 13.81 0.00 41.12 3.49
2246 2602 1.815817 TAAGCAGACGAGCAGCCACA 61.816 55.000 0.00 0.00 36.85 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 6.958767 AGATTTATAGTGCTTGGTTGGTACT 58.041 36.000 0.00 0.00 34.33 2.73
105 106 3.310501 GGAAAACTCAGTTTTTCGGTCGA 59.689 43.478 16.71 0.00 44.33 4.20
110 111 2.614983 TCCGGGAAAACTCAGTTTTTCG 59.385 45.455 16.71 20.18 44.33 3.46
129 130 4.864704 ACTCACTGAGACTTCTCTTTCC 57.135 45.455 13.25 0.00 43.25 3.13
163 164 2.945398 CTTAGCTCGCTCGGGTCAGC 62.945 65.000 0.00 0.00 35.90 4.26
171 172 0.389391 TACATGCCCTTAGCTCGCTC 59.611 55.000 0.00 0.00 44.23 5.03
173 174 0.179084 TGTACATGCCCTTAGCTCGC 60.179 55.000 0.00 0.00 44.23 5.03
178 179 4.269183 TCAACCATTGTACATGCCCTTAG 58.731 43.478 0.00 0.00 0.00 2.18
179 180 4.308526 TCAACCATTGTACATGCCCTTA 57.691 40.909 0.00 0.00 0.00 2.69
180 181 3.168035 TCAACCATTGTACATGCCCTT 57.832 42.857 0.00 0.00 0.00 3.95
181 182 2.897271 TCAACCATTGTACATGCCCT 57.103 45.000 0.00 0.00 0.00 5.19
182 183 4.887071 TCTTATCAACCATTGTACATGCCC 59.113 41.667 0.00 0.00 0.00 5.36
183 184 5.356751 TGTCTTATCAACCATTGTACATGCC 59.643 40.000 0.00 0.00 0.00 4.40
184 185 6.094048 ACTGTCTTATCAACCATTGTACATGC 59.906 38.462 0.00 0.00 0.00 4.06
185 186 7.550551 AGACTGTCTTATCAACCATTGTACATG 59.449 37.037 4.06 0.00 0.00 3.21
186 187 7.624549 AGACTGTCTTATCAACCATTGTACAT 58.375 34.615 4.06 0.00 0.00 2.29
187 188 7.004555 AGACTGTCTTATCAACCATTGTACA 57.995 36.000 4.06 0.00 0.00 2.90
188 189 7.907214 AAGACTGTCTTATCAACCATTGTAC 57.093 36.000 20.85 0.00 34.42 2.90
202 203 9.678260 ATGCAAGATTTAAGATAAGACTGTCTT 57.322 29.630 24.80 24.80 40.35 3.01
203 204 9.107177 CATGCAAGATTTAAGATAAGACTGTCT 57.893 33.333 4.06 4.06 0.00 3.41
204 205 8.887717 ACATGCAAGATTTAAGATAAGACTGTC 58.112 33.333 0.00 0.00 0.00 3.51
205 206 8.798859 ACATGCAAGATTTAAGATAAGACTGT 57.201 30.769 0.00 0.00 0.00 3.55
219 220 9.399797 TGTCATCTCTAAATTACATGCAAGATT 57.600 29.630 0.00 0.00 0.00 2.40
220 221 8.969260 TGTCATCTCTAAATTACATGCAAGAT 57.031 30.769 0.00 0.00 0.00 2.40
221 222 8.791327 TTGTCATCTCTAAATTACATGCAAGA 57.209 30.769 0.00 0.00 0.00 3.02
222 223 9.844790 TTTTGTCATCTCTAAATTACATGCAAG 57.155 29.630 0.00 0.00 0.00 4.01
253 254 8.322091 GGCTAAGATATAACCCATTGTAGACAT 58.678 37.037 0.00 0.00 0.00 3.06
254 255 7.512746 AGGCTAAGATATAACCCATTGTAGACA 59.487 37.037 0.00 0.00 0.00 3.41
255 256 7.908453 AGGCTAAGATATAACCCATTGTAGAC 58.092 38.462 0.00 0.00 0.00 2.59
256 257 8.506196 AAGGCTAAGATATAACCCATTGTAGA 57.494 34.615 0.00 0.00 0.00 2.59
259 260 9.117223 AGATAAGGCTAAGATATAACCCATTGT 57.883 33.333 0.00 0.00 0.00 2.71
260 261 9.965902 AAGATAAGGCTAAGATATAACCCATTG 57.034 33.333 0.00 0.00 0.00 2.82
262 263 9.338968 TGAAGATAAGGCTAAGATATAACCCAT 57.661 33.333 0.00 0.00 0.00 4.00
263 264 8.736097 TGAAGATAAGGCTAAGATATAACCCA 57.264 34.615 0.00 0.00 0.00 4.51
271 272 9.936759 GCTAGTTATTGAAGATAAGGCTAAGAT 57.063 33.333 0.00 0.00 0.00 2.40
272 273 8.924303 TGCTAGTTATTGAAGATAAGGCTAAGA 58.076 33.333 0.00 0.00 0.00 2.10
273 274 9.547753 TTGCTAGTTATTGAAGATAAGGCTAAG 57.452 33.333 0.00 0.00 0.00 2.18
276 277 8.986929 AATTGCTAGTTATTGAAGATAAGGCT 57.013 30.769 0.00 0.00 0.00 4.58
277 278 8.293157 GGAATTGCTAGTTATTGAAGATAAGGC 58.707 37.037 0.00 0.00 0.00 4.35
278 279 9.566432 AGGAATTGCTAGTTATTGAAGATAAGG 57.434 33.333 0.00 0.00 0.00 2.69
289 290 9.255029 ACCATGTTTTAAGGAATTGCTAGTTAT 57.745 29.630 0.00 0.00 0.00 1.89
290 291 8.519526 CACCATGTTTTAAGGAATTGCTAGTTA 58.480 33.333 0.00 0.00 0.00 2.24
291 292 7.232534 TCACCATGTTTTAAGGAATTGCTAGTT 59.767 33.333 0.00 0.00 0.00 2.24
292 293 6.719370 TCACCATGTTTTAAGGAATTGCTAGT 59.281 34.615 0.00 0.00 0.00 2.57
293 294 7.121168 TCTCACCATGTTTTAAGGAATTGCTAG 59.879 37.037 0.00 0.00 0.00 3.42
294 295 6.945435 TCTCACCATGTTTTAAGGAATTGCTA 59.055 34.615 0.00 0.00 0.00 3.49
295 296 5.774690 TCTCACCATGTTTTAAGGAATTGCT 59.225 36.000 0.00 0.00 0.00 3.91
296 297 5.863935 GTCTCACCATGTTTTAAGGAATTGC 59.136 40.000 0.00 0.00 0.00 3.56
297 298 6.980593 TGTCTCACCATGTTTTAAGGAATTG 58.019 36.000 0.00 0.00 0.00 2.32
298 299 7.595819 TTGTCTCACCATGTTTTAAGGAATT 57.404 32.000 0.00 0.00 0.00 2.17
299 300 7.595819 TTTGTCTCACCATGTTTTAAGGAAT 57.404 32.000 0.00 0.00 0.00 3.01
300 301 7.595819 ATTTGTCTCACCATGTTTTAAGGAA 57.404 32.000 0.00 0.00 0.00 3.36
301 302 7.069331 ACAATTTGTCTCACCATGTTTTAAGGA 59.931 33.333 0.00 0.00 0.00 3.36
302 303 7.169645 CACAATTTGTCTCACCATGTTTTAAGG 59.830 37.037 0.00 0.00 0.00 2.69
303 304 7.306749 GCACAATTTGTCTCACCATGTTTTAAG 60.307 37.037 0.00 0.00 0.00 1.85
304 305 6.478344 GCACAATTTGTCTCACCATGTTTTAA 59.522 34.615 0.00 0.00 0.00 1.52
305 306 5.982516 GCACAATTTGTCTCACCATGTTTTA 59.017 36.000 0.00 0.00 0.00 1.52
306 307 4.810491 GCACAATTTGTCTCACCATGTTTT 59.190 37.500 0.00 0.00 0.00 2.43
307 308 4.099881 AGCACAATTTGTCTCACCATGTTT 59.900 37.500 0.00 0.00 0.00 2.83
308 309 3.638160 AGCACAATTTGTCTCACCATGTT 59.362 39.130 0.00 0.00 0.00 2.71
309 310 3.225104 AGCACAATTTGTCTCACCATGT 58.775 40.909 0.00 0.00 0.00 3.21
310 311 3.928727 AGCACAATTTGTCTCACCATG 57.071 42.857 0.00 0.00 0.00 3.66
311 312 5.316167 TCTTAGCACAATTTGTCTCACCAT 58.684 37.500 0.00 0.00 0.00 3.55
312 313 4.713553 TCTTAGCACAATTTGTCTCACCA 58.286 39.130 0.00 0.00 0.00 4.17
313 314 4.997395 TCTCTTAGCACAATTTGTCTCACC 59.003 41.667 0.00 0.00 0.00 4.02
314 315 6.369890 TGATCTCTTAGCACAATTTGTCTCAC 59.630 38.462 0.00 0.00 0.00 3.51
315 316 6.466812 TGATCTCTTAGCACAATTTGTCTCA 58.533 36.000 0.00 0.00 0.00 3.27
316 317 6.974932 TGATCTCTTAGCACAATTTGTCTC 57.025 37.500 0.00 0.00 0.00 3.36
317 318 7.337167 AGATGATCTCTTAGCACAATTTGTCT 58.663 34.615 0.00 3.34 0.00 3.41
318 319 7.551035 AGATGATCTCTTAGCACAATTTGTC 57.449 36.000 0.00 0.00 0.00 3.18
319 320 7.551035 GAGATGATCTCTTAGCACAATTTGT 57.449 36.000 14.98 0.00 40.30 2.83
351 352 9.746457 AAAGCCTTGTCTTCTCTTATTTAAGAT 57.254 29.630 0.71 0.00 41.12 2.40
352 353 9.574516 AAAAGCCTTGTCTTCTCTTATTTAAGA 57.425 29.630 0.44 0.44 39.82 2.10
353 354 9.833182 GAAAAGCCTTGTCTTCTCTTATTTAAG 57.167 33.333 0.00 0.00 34.65 1.85
354 355 9.574516 AGAAAAGCCTTGTCTTCTCTTATTTAA 57.425 29.630 0.00 0.00 0.00 1.52
355 356 9.574516 AAGAAAAGCCTTGTCTTCTCTTATTTA 57.425 29.630 3.94 0.00 33.09 1.40
356 357 8.470657 AAGAAAAGCCTTGTCTTCTCTTATTT 57.529 30.769 3.94 0.00 33.09 1.40
357 358 9.746457 ATAAGAAAAGCCTTGTCTTCTCTTATT 57.254 29.630 13.15 0.00 40.61 1.40
358 359 9.171877 CATAAGAAAAGCCTTGTCTTCTCTTAT 57.828 33.333 13.15 0.00 42.53 1.73
359 360 8.375506 TCATAAGAAAAGCCTTGTCTTCTCTTA 58.624 33.333 13.15 0.00 38.93 2.10
360 361 7.227156 TCATAAGAAAAGCCTTGTCTTCTCTT 58.773 34.615 13.15 1.38 37.23 2.85
361 362 6.773638 TCATAAGAAAAGCCTTGTCTTCTCT 58.226 36.000 13.15 0.00 33.70 3.10
362 363 6.652900 ACTCATAAGAAAAGCCTTGTCTTCTC 59.347 38.462 13.15 0.00 33.70 2.87
363 364 6.538263 ACTCATAAGAAAAGCCTTGTCTTCT 58.462 36.000 13.15 1.32 33.70 2.85
364 365 6.809630 ACTCATAAGAAAAGCCTTGTCTTC 57.190 37.500 13.15 0.00 33.70 2.87
365 366 7.001073 AGAACTCATAAGAAAAGCCTTGTCTT 58.999 34.615 14.16 14.16 35.77 3.01
366 367 6.538263 AGAACTCATAAGAAAAGCCTTGTCT 58.462 36.000 0.00 0.00 0.00 3.41
367 368 6.652900 AGAGAACTCATAAGAAAAGCCTTGTC 59.347 38.462 4.64 0.00 0.00 3.18
368 369 6.538263 AGAGAACTCATAAGAAAAGCCTTGT 58.462 36.000 4.64 0.00 0.00 3.16
369 370 6.878389 AGAGAGAACTCATAAGAAAAGCCTTG 59.122 38.462 4.64 0.00 44.79 3.61
370 371 7.014988 AGAGAGAACTCATAAGAAAAGCCTT 57.985 36.000 4.64 0.00 44.79 4.35
371 372 6.351796 GGAGAGAGAACTCATAAGAAAAGCCT 60.352 42.308 4.64 0.00 44.79 4.58
372 373 5.815222 GGAGAGAGAACTCATAAGAAAAGCC 59.185 44.000 4.64 0.00 44.79 4.35
373 374 6.639563 AGGAGAGAGAACTCATAAGAAAAGC 58.360 40.000 4.64 0.00 44.79 3.51
374 375 7.093552 TGGAGGAGAGAGAACTCATAAGAAAAG 60.094 40.741 4.64 0.00 44.79 2.27
375 376 6.726299 TGGAGGAGAGAGAACTCATAAGAAAA 59.274 38.462 4.64 0.00 44.79 2.29
376 377 6.153680 GTGGAGGAGAGAGAACTCATAAGAAA 59.846 42.308 4.64 0.00 44.79 2.52
377 378 5.654650 GTGGAGGAGAGAGAACTCATAAGAA 59.345 44.000 4.64 0.00 44.79 2.52
378 379 5.197451 GTGGAGGAGAGAGAACTCATAAGA 58.803 45.833 4.64 0.00 44.79 2.10
379 380 4.340950 GGTGGAGGAGAGAGAACTCATAAG 59.659 50.000 4.64 0.00 44.79 1.73
380 381 4.017037 AGGTGGAGGAGAGAGAACTCATAA 60.017 45.833 4.64 0.00 44.79 1.90
381 382 3.529734 AGGTGGAGGAGAGAGAACTCATA 59.470 47.826 4.64 0.00 44.79 2.15
382 383 2.314549 AGGTGGAGGAGAGAGAACTCAT 59.685 50.000 4.64 0.00 44.79 2.90
383 384 1.713647 AGGTGGAGGAGAGAGAACTCA 59.286 52.381 4.64 0.00 44.79 3.41
384 385 2.291282 TGAGGTGGAGGAGAGAGAACTC 60.291 54.545 0.00 0.00 42.90 3.01
385 386 1.713647 TGAGGTGGAGGAGAGAGAACT 59.286 52.381 0.00 0.00 0.00 3.01
386 387 2.223803 TGAGGTGGAGGAGAGAGAAC 57.776 55.000 0.00 0.00 0.00 3.01
387 388 2.313041 TGATGAGGTGGAGGAGAGAGAA 59.687 50.000 0.00 0.00 0.00 2.87
388 389 1.925959 TGATGAGGTGGAGGAGAGAGA 59.074 52.381 0.00 0.00 0.00 3.10
389 390 2.450867 TGATGAGGTGGAGGAGAGAG 57.549 55.000 0.00 0.00 0.00 3.20
390 391 3.411454 AATGATGAGGTGGAGGAGAGA 57.589 47.619 0.00 0.00 0.00 3.10
391 392 5.279910 GGATAAATGATGAGGTGGAGGAGAG 60.280 48.000 0.00 0.00 0.00 3.20
392 393 4.594920 GGATAAATGATGAGGTGGAGGAGA 59.405 45.833 0.00 0.00 0.00 3.71
393 394 4.596643 AGGATAAATGATGAGGTGGAGGAG 59.403 45.833 0.00 0.00 0.00 3.69
394 395 4.570926 AGGATAAATGATGAGGTGGAGGA 58.429 43.478 0.00 0.00 0.00 3.71
395 396 4.989875 AGGATAAATGATGAGGTGGAGG 57.010 45.455 0.00 0.00 0.00 4.30
396 397 5.011125 ACGTAGGATAAATGATGAGGTGGAG 59.989 44.000 0.00 0.00 0.00 3.86
397 398 4.899457 ACGTAGGATAAATGATGAGGTGGA 59.101 41.667 0.00 0.00 0.00 4.02
398 399 4.991056 CACGTAGGATAAATGATGAGGTGG 59.009 45.833 0.00 0.00 0.00 4.61
399 400 4.991056 CCACGTAGGATAAATGATGAGGTG 59.009 45.833 0.00 0.00 41.22 4.00
400 401 4.503296 GCCACGTAGGATAAATGATGAGGT 60.503 45.833 8.04 0.00 41.22 3.85
401 402 3.997021 GCCACGTAGGATAAATGATGAGG 59.003 47.826 8.04 0.00 41.22 3.86
402 403 4.449068 GTGCCACGTAGGATAAATGATGAG 59.551 45.833 8.04 0.00 41.22 2.90
403 404 4.100963 AGTGCCACGTAGGATAAATGATGA 59.899 41.667 8.04 0.00 41.22 2.92
404 405 4.380531 AGTGCCACGTAGGATAAATGATG 58.619 43.478 8.04 0.00 41.22 3.07
405 406 4.503296 GGAGTGCCACGTAGGATAAATGAT 60.503 45.833 8.04 0.00 41.22 2.45
406 407 3.181469 GGAGTGCCACGTAGGATAAATGA 60.181 47.826 8.04 0.00 41.22 2.57
407 408 3.131396 GGAGTGCCACGTAGGATAAATG 58.869 50.000 8.04 0.00 41.22 2.32
408 409 3.039011 AGGAGTGCCACGTAGGATAAAT 58.961 45.455 8.04 0.00 41.22 1.40
409 410 2.463752 AGGAGTGCCACGTAGGATAAA 58.536 47.619 8.04 0.00 41.22 1.40
410 411 2.154567 AGGAGTGCCACGTAGGATAA 57.845 50.000 8.04 0.00 41.22 1.75
411 412 3.117776 TCTTAGGAGTGCCACGTAGGATA 60.118 47.826 8.04 0.00 41.22 2.59
412 413 2.032620 CTTAGGAGTGCCACGTAGGAT 58.967 52.381 8.04 0.00 41.22 3.24
413 414 1.005097 TCTTAGGAGTGCCACGTAGGA 59.995 52.381 8.04 0.00 41.22 2.94
414 415 1.471119 TCTTAGGAGTGCCACGTAGG 58.529 55.000 0.00 0.00 41.84 3.18
415 416 3.304794 GCTATCTTAGGAGTGCCACGTAG 60.305 52.174 0.00 0.00 36.29 3.51
416 417 2.621998 GCTATCTTAGGAGTGCCACGTA 59.378 50.000 0.00 0.00 36.29 3.57
417 418 1.409427 GCTATCTTAGGAGTGCCACGT 59.591 52.381 0.00 0.00 36.29 4.49
418 419 1.409064 TGCTATCTTAGGAGTGCCACG 59.591 52.381 0.00 0.00 36.29 4.94
419 420 2.483889 GGTGCTATCTTAGGAGTGCCAC 60.484 54.545 0.00 0.00 36.29 5.01
420 421 1.762957 GGTGCTATCTTAGGAGTGCCA 59.237 52.381 0.00 0.00 36.29 4.92
421 422 1.762957 TGGTGCTATCTTAGGAGTGCC 59.237 52.381 0.70 0.00 0.00 5.01
422 423 3.760580 ATGGTGCTATCTTAGGAGTGC 57.239 47.619 0.00 0.00 0.00 4.40
423 424 5.028549 ACAATGGTGCTATCTTAGGAGTG 57.971 43.478 0.00 0.00 0.00 3.51
424 425 5.661312 TGTACAATGGTGCTATCTTAGGAGT 59.339 40.000 0.00 0.00 0.00 3.85
425 426 6.161855 TGTACAATGGTGCTATCTTAGGAG 57.838 41.667 0.00 0.00 0.00 3.69
426 427 6.524734 CATGTACAATGGTGCTATCTTAGGA 58.475 40.000 0.00 0.00 0.00 2.94
427 428 5.180117 GCATGTACAATGGTGCTATCTTAGG 59.820 44.000 11.12 0.00 34.85 2.69
428 429 5.180117 GGCATGTACAATGGTGCTATCTTAG 59.820 44.000 16.47 0.00 37.70 2.18
429 430 5.063204 GGCATGTACAATGGTGCTATCTTA 58.937 41.667 16.47 0.00 37.70 2.10
430 431 3.885297 GGCATGTACAATGGTGCTATCTT 59.115 43.478 16.47 0.00 37.70 2.40
431 432 3.480470 GGCATGTACAATGGTGCTATCT 58.520 45.455 16.47 0.00 37.70 1.98
432 433 2.554032 GGGCATGTACAATGGTGCTATC 59.446 50.000 16.47 3.12 37.70 2.08
433 434 2.175499 AGGGCATGTACAATGGTGCTAT 59.825 45.455 16.47 5.35 37.70 2.97
434 435 1.563879 AGGGCATGTACAATGGTGCTA 59.436 47.619 16.47 0.00 37.70 3.49
435 436 0.332632 AGGGCATGTACAATGGTGCT 59.667 50.000 16.47 0.00 37.70 4.40
436 437 2.051334 TAGGGCATGTACAATGGTGC 57.949 50.000 10.12 10.12 36.88 5.01
437 438 4.206375 TCATTAGGGCATGTACAATGGTG 58.794 43.478 0.00 0.00 0.00 4.17
438 439 4.079787 ACTCATTAGGGCATGTACAATGGT 60.080 41.667 0.00 0.00 0.00 3.55
439 440 4.464008 ACTCATTAGGGCATGTACAATGG 58.536 43.478 0.00 0.00 0.00 3.16
440 441 6.455360 AAACTCATTAGGGCATGTACAATG 57.545 37.500 0.00 0.00 0.00 2.82
441 442 5.296780 CGAAACTCATTAGGGCATGTACAAT 59.703 40.000 0.00 0.00 0.00 2.71
442 443 4.634004 CGAAACTCATTAGGGCATGTACAA 59.366 41.667 0.00 0.00 0.00 2.41
443 444 4.188462 CGAAACTCATTAGGGCATGTACA 58.812 43.478 0.00 0.00 0.00 2.90
444 445 3.002348 GCGAAACTCATTAGGGCATGTAC 59.998 47.826 0.00 0.00 0.00 2.90
445 446 3.202906 GCGAAACTCATTAGGGCATGTA 58.797 45.455 0.00 0.00 0.00 2.29
446 447 2.017049 GCGAAACTCATTAGGGCATGT 58.983 47.619 0.00 0.00 0.00 3.21
447 448 1.003545 CGCGAAACTCATTAGGGCATG 60.004 52.381 0.00 0.00 0.00 4.06
448 449 1.299541 CGCGAAACTCATTAGGGCAT 58.700 50.000 0.00 0.00 0.00 4.40
449 450 1.366111 GCGCGAAACTCATTAGGGCA 61.366 55.000 12.10 0.00 46.87 5.36
450 451 1.352056 GCGCGAAACTCATTAGGGC 59.648 57.895 12.10 0.00 43.20 5.19
451 452 0.804544 TCGCGCGAAACTCATTAGGG 60.805 55.000 32.97 0.00 0.00 3.53
452 453 0.996462 TTCGCGCGAAACTCATTAGG 59.004 50.000 40.02 2.91 0.00 2.69
478 479 4.635765 TGCTTGCTAAAATCATTAGCTCGT 59.364 37.500 17.97 0.00 45.57 4.18
479 480 5.160699 TGCTTGCTAAAATCATTAGCTCG 57.839 39.130 17.97 11.29 45.57 5.03
520 522 5.695816 TGCAAAAATGATGGTACTGCTTTTC 59.304 36.000 0.00 0.00 0.00 2.29
521 523 5.609423 TGCAAAAATGATGGTACTGCTTTT 58.391 33.333 0.00 0.00 0.00 2.27
596 601 1.081175 GGCACGCTGCTTTTCCTTC 60.081 57.895 9.31 0.00 44.28 3.46
597 602 2.564721 GGGCACGCTGCTTTTCCTT 61.565 57.895 9.31 0.00 44.28 3.36
598 603 2.985847 GGGCACGCTGCTTTTCCT 60.986 61.111 9.31 0.00 44.28 3.36
599 604 4.056125 GGGGCACGCTGCTTTTCC 62.056 66.667 9.31 3.21 44.28 3.13
600 605 3.273080 CTGGGGCACGCTGCTTTTC 62.273 63.158 9.31 0.00 44.28 2.29
618 623 2.203294 AGTGGCCAACAACGTCCC 60.203 61.111 7.24 0.00 0.00 4.46
625 630 1.488812 AGTTGTGTAGAGTGGCCAACA 59.511 47.619 7.24 5.16 38.24 3.33
678 690 5.505780 AGATGGATAGAGGTAGATTCGGAG 58.494 45.833 0.00 0.00 0.00 4.63
693 705 0.521735 CGTCGGATGCGAGATGGATA 59.478 55.000 10.47 0.00 0.00 2.59
753 765 2.354821 GGGTGGTATTTCTGTTGATCGC 59.645 50.000 0.00 0.00 0.00 4.58
766 778 0.647738 TGGGATCTGAGGGGTGGTAT 59.352 55.000 0.00 0.00 0.00 2.73
767 779 0.419865 TTGGGATCTGAGGGGTGGTA 59.580 55.000 0.00 0.00 0.00 3.25
769 781 0.475906 GATTGGGATCTGAGGGGTGG 59.524 60.000 0.00 0.00 0.00 4.61
771 783 1.056700 CGGATTGGGATCTGAGGGGT 61.057 60.000 0.00 0.00 40.48 4.95
778 792 1.033574 GAGACGTCGGATTGGGATCT 58.966 55.000 10.46 0.00 32.66 2.75
803 817 3.371166 GGATGGGTTTCGTTGGAAGGATA 60.371 47.826 0.00 0.00 32.80 2.59
849 863 0.758685 TGCTGGTTTGGGGTTTGAGG 60.759 55.000 0.00 0.00 0.00 3.86
850 864 0.389025 GTGCTGGTTTGGGGTTTGAG 59.611 55.000 0.00 0.00 0.00 3.02
944 963 0.674895 AATGGGAGTCGCTGTTGAGC 60.675 55.000 8.82 0.00 42.37 4.26
948 967 1.141053 GGGATAATGGGAGTCGCTGTT 59.859 52.381 8.82 6.25 0.00 3.16
960 979 4.696479 AGCAGTCTAACAGGGGATAATG 57.304 45.455 0.00 0.00 0.00 1.90
962 981 3.454812 GGAAGCAGTCTAACAGGGGATAA 59.545 47.826 0.00 0.00 0.00 1.75
964 983 1.840635 GGAAGCAGTCTAACAGGGGAT 59.159 52.381 0.00 0.00 0.00 3.85
969 988 4.462508 TGAGATGGAAGCAGTCTAACAG 57.537 45.455 0.00 0.00 0.00 3.16
972 991 4.343526 GGAGATGAGATGGAAGCAGTCTAA 59.656 45.833 0.00 0.00 0.00 2.10
978 997 0.755079 CCGGAGATGAGATGGAAGCA 59.245 55.000 0.00 0.00 0.00 3.91
1374 1400 0.526211 AGCGCACTAGATTCACGACA 59.474 50.000 11.47 0.00 0.00 4.35
1385 1411 0.811219 CAAGCATAGCCAGCGCACTA 60.811 55.000 11.47 8.86 37.52 2.74
1459 1790 6.991485 ATTAACTTGTCATTGCAACGAAAG 57.009 33.333 0.00 8.42 0.00 2.62
1465 1796 7.669427 AGATTGGAATTAACTTGTCATTGCAA 58.331 30.769 0.00 0.00 40.92 4.08
1491 1822 7.027760 CAGAATCAGACATGATGGTTTTTCTG 58.972 38.462 0.00 10.50 45.67 3.02
1599 1933 1.402787 ACCAAACTGCAGGGTTCTTG 58.597 50.000 19.93 12.22 0.00 3.02
1623 1957 5.471257 GTCGAGACTGAATTTACCACTCTT 58.529 41.667 0.00 0.00 0.00 2.85
1639 1973 2.005971 AACCCATAAAGCGTCGAGAC 57.994 50.000 0.00 0.00 0.00 3.36
1766 2107 7.233632 TCAGGATTTCCCATATAAGTTGATGG 58.766 38.462 10.36 10.36 42.06 3.51
1776 2117 6.017211 TGTCAACATCAGGATTTCCCATAT 57.983 37.500 0.00 0.00 37.41 1.78
1778 2119 4.320546 TGTCAACATCAGGATTTCCCAT 57.679 40.909 0.00 0.00 37.41 4.00
1793 2134 5.860182 CAGGATGAATTGTCACAATGTCAAC 59.140 40.000 3.07 8.63 39.69 3.18
1871 2215 1.601903 GTCACAACCGATGACTTGCAA 59.398 47.619 0.00 0.00 42.68 4.08
1885 2229 1.691434 GCAATTCTTTGGGGGTCACAA 59.309 47.619 0.00 0.00 33.22 3.33
1921 2265 3.492337 ACAAGAGGAACCGCCATAAAAA 58.508 40.909 0.00 0.00 40.02 1.94
1922 2266 3.149005 ACAAGAGGAACCGCCATAAAA 57.851 42.857 0.00 0.00 40.02 1.52
1969 2314 3.880047 TGGTAAAGACGGATCAACGAT 57.120 42.857 0.00 0.00 37.61 3.73
1986 2331 2.604614 GCGCAAACGAGATTTCTTTGGT 60.605 45.455 0.30 0.00 43.93 3.67
1997 2342 2.159720 TGTTCATACATGCGCAAACGAG 60.160 45.455 17.11 5.03 43.93 4.18
1998 2343 1.801178 TGTTCATACATGCGCAAACGA 59.199 42.857 17.11 4.00 43.93 3.85
2003 2348 2.097304 GTGGAATGTTCATACATGCGCA 59.903 45.455 14.96 14.96 44.14 6.09
2066 2411 9.642343 ATCCTAGTCACATATCAAACTGTAGTA 57.358 33.333 0.00 0.00 0.00 1.82
2097 2442 5.868258 TGAACACTGACAAACGTACTGTTAA 59.132 36.000 4.83 0.00 40.84 2.01
2102 2447 4.380841 TCTGAACACTGACAAACGTACT 57.619 40.909 0.00 0.00 0.00 2.73
2103 2448 4.550255 GCTTCTGAACACTGACAAACGTAC 60.550 45.833 0.00 0.00 0.00 3.67
2135 2483 0.813610 CAGGAACCAGTCAACACGCA 60.814 55.000 0.00 0.00 0.00 5.24
2177 2525 2.045926 ACCGGCTTCATCAGTGCC 60.046 61.111 0.00 0.00 42.94 5.01
2208 2556 6.749139 TGCTTAGGAGTACTACATTGCTATG 58.251 40.000 8.10 6.59 37.79 2.23
2214 2570 5.191426 TCGTCTGCTTAGGAGTACTACATT 58.809 41.667 8.10 0.00 0.00 2.71
2246 2602 6.038936 GGTTTACGATCTCTTCTAGAGCTCTT 59.961 42.308 23.84 6.22 42.04 2.85


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

AutoCloner maintained by Alex Coulton.