Multiple sequence alignment - TraesCS2B01G052900

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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 TraesCS2B01G052900 chr2B 100.000 2548 0 0 1 2548 25860900 25863447 0 4706
1 TraesCS2B01G052900 chr2B 96.303 568 21 0 1 568 523004082 523004649 0 933
2 TraesCS2B01G052900 chr7A 98.393 1991 26 4 564 2548 701581932 701583922 0 3494
3 TraesCS2B01G052900 chr7A 98.335 1982 26 6 573 2548 696908898 696910878 0 3470
4 TraesCS2B01G052900 chr5A 98.437 1983 26 4 571 2548 459744879 459746861 0 3485
5 TraesCS2B01G052900 chr3A 98.390 1988 23 6 568 2548 722406051 722404066 0 3485
6 TraesCS2B01G052900 chr6B 98.436 1982 23 6 573 2548 660437743 660435764 0 3482
7 TraesCS2B01G052900 chr6B 98.044 1994 31 7 561 2548 116269134 116271125 0 3459
8 TraesCS2B01G052900 chr6B 96.831 568 18 0 1 568 170847863 170847296 0 950
9 TraesCS2B01G052900 chr6B 96.303 568 21 0 1 568 124612437 124611870 0 933
10 TraesCS2B01G052900 chr1A 98.384 1980 27 4 573 2548 22791529 22793507 0 3474
11 TraesCS2B01G052900 chr7B 98.193 1992 28 5 565 2548 552932152 552930161 0 3472
12 TraesCS2B01G052900 chr7B 98.092 1992 29 7 565 2548 337148370 337150360 0 3459
13 TraesCS2B01G052900 chr7B 96.991 565 17 0 4 568 730851899 730852463 0 950
14 TraesCS2B01G052900 chr7B 96.303 568 21 0 1 568 61717950 61718517 0 933
15 TraesCS2B01G052900 chr1B 96.831 568 18 0 1 568 458658386 458657819 0 950
16 TraesCS2B01G052900 chr1B 96.303 568 20 1 1 568 327811162 327810596 0 931
17 TraesCS2B01G052900 chr5B 96.655 568 19 0 1 568 55407045 55406478 0 944
18 TraesCS2B01G052900 chr5B 96.655 568 19 0 1 568 476865298 476865865 0 944


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 TraesCS2B01G052900 chr2B 25860900 25863447 2547 False 4706 4706 100.000 1 2548 1 chr2B.!!$F1 2547
1 TraesCS2B01G052900 chr2B 523004082 523004649 567 False 933 933 96.303 1 568 1 chr2B.!!$F2 567
2 TraesCS2B01G052900 chr7A 701581932 701583922 1990 False 3494 3494 98.393 564 2548 1 chr7A.!!$F2 1984
3 TraesCS2B01G052900 chr7A 696908898 696910878 1980 False 3470 3470 98.335 573 2548 1 chr7A.!!$F1 1975
4 TraesCS2B01G052900 chr5A 459744879 459746861 1982 False 3485 3485 98.437 571 2548 1 chr5A.!!$F1 1977
5 TraesCS2B01G052900 chr3A 722404066 722406051 1985 True 3485 3485 98.390 568 2548 1 chr3A.!!$R1 1980
6 TraesCS2B01G052900 chr6B 660435764 660437743 1979 True 3482 3482 98.436 573 2548 1 chr6B.!!$R3 1975
7 TraesCS2B01G052900 chr6B 116269134 116271125 1991 False 3459 3459 98.044 561 2548 1 chr6B.!!$F1 1987
8 TraesCS2B01G052900 chr6B 170847296 170847863 567 True 950 950 96.831 1 568 1 chr6B.!!$R2 567
9 TraesCS2B01G052900 chr6B 124611870 124612437 567 True 933 933 96.303 1 568 1 chr6B.!!$R1 567
10 TraesCS2B01G052900 chr1A 22791529 22793507 1978 False 3474 3474 98.384 573 2548 1 chr1A.!!$F1 1975
11 TraesCS2B01G052900 chr7B 552930161 552932152 1991 True 3472 3472 98.193 565 2548 1 chr7B.!!$R1 1983
12 TraesCS2B01G052900 chr7B 337148370 337150360 1990 False 3459 3459 98.092 565 2548 1 chr7B.!!$F2 1983
13 TraesCS2B01G052900 chr7B 730851899 730852463 564 False 950 950 96.991 4 568 1 chr7B.!!$F3 564
14 TraesCS2B01G052900 chr7B 61717950 61718517 567 False 933 933 96.303 1 568 1 chr7B.!!$F1 567
15 TraesCS2B01G052900 chr1B 458657819 458658386 567 True 950 950 96.831 1 568 1 chr1B.!!$R2 567
16 TraesCS2B01G052900 chr1B 327810596 327811162 566 True 931 931 96.303 1 568 1 chr1B.!!$R1 567
17 TraesCS2B01G052900 chr5B 55406478 55407045 567 True 944 944 96.655 1 568 1 chr5B.!!$R1 567
18 TraesCS2B01G052900 chr5B 476865298 476865865 567 False 944 944 96.655 1 568 1 chr5B.!!$F1 567

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
549 550 0.042131 AGATCCGGGTGTCCCAACTA 59.958 55.0 0.00 0.0 45.83 2.24 F
553 554 0.466963 CCGGGTGTCCCAACTATACC 59.533 60.0 5.64 0.0 45.83 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1365 1.139654 CGCCATCCATCTCTTCTTCCA 59.860 52.381 0.0 0.0 0.0 3.53 R
2122 2438 4.821260 GTGCATTTTCCACCCTTCATTTTT 59.179 37.500 0.0 0.0 0.0 1.94 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
43 44 6.435430 AAACGATAGAACATTGCATGCTTA 57.565 33.333 20.33 7.43 41.38 3.09
114 115 5.771153 TTCTGATGCTGAAACACAATCAA 57.229 34.783 0.00 0.00 29.11 2.57
150 151 8.862325 TGAACCTAGTGATAATGTTCATGTTT 57.138 30.769 4.87 0.00 40.06 2.83
151 152 9.952030 TGAACCTAGTGATAATGTTCATGTTTA 57.048 29.630 4.87 0.00 40.06 2.01
154 155 8.840321 ACCTAGTGATAATGTTCATGTTTATGC 58.160 33.333 0.00 0.00 34.21 3.14
155 156 9.060347 CCTAGTGATAATGTTCATGTTTATGCT 57.940 33.333 0.00 0.00 34.21 3.79
157 158 8.510243 AGTGATAATGTTCATGTTTATGCTCA 57.490 30.769 0.00 0.00 34.21 4.26
158 159 8.959548 AGTGATAATGTTCATGTTTATGCTCAA 58.040 29.630 0.00 0.00 34.21 3.02
159 160 9.013490 GTGATAATGTTCATGTTTATGCTCAAC 57.987 33.333 0.00 0.00 34.21 3.18
160 161 8.190122 TGATAATGTTCATGTTTATGCTCAACC 58.810 33.333 0.00 0.00 34.21 3.77
161 162 6.594788 AATGTTCATGTTTATGCTCAACCT 57.405 33.333 0.00 0.00 34.21 3.50
162 163 7.701539 AATGTTCATGTTTATGCTCAACCTA 57.298 32.000 0.00 0.00 34.21 3.08
163 164 6.741992 TGTTCATGTTTATGCTCAACCTAG 57.258 37.500 0.00 0.00 34.21 3.02
164 165 5.123820 TGTTCATGTTTATGCTCAACCTAGC 59.876 40.000 0.00 0.00 43.08 3.42
178 179 8.159344 GCTCAACCTAGCAAAGATAATAATGT 57.841 34.615 0.00 0.00 42.30 2.71
179 180 9.273016 GCTCAACCTAGCAAAGATAATAATGTA 57.727 33.333 0.00 0.00 42.30 2.29
193 194 9.434420 AGATAATAATGTAGAGATTGAAGCTGC 57.566 33.333 0.00 0.00 0.00 5.25
194 195 9.434420 GATAATAATGTAGAGATTGAAGCTGCT 57.566 33.333 0.00 0.00 0.00 4.24
195 196 7.493743 AATAATGTAGAGATTGAAGCTGCTG 57.506 36.000 1.35 0.00 0.00 4.41
196 197 3.969287 TGTAGAGATTGAAGCTGCTGT 57.031 42.857 1.35 0.00 0.00 4.40
197 198 4.277515 TGTAGAGATTGAAGCTGCTGTT 57.722 40.909 1.35 0.00 0.00 3.16
198 199 3.999001 TGTAGAGATTGAAGCTGCTGTTG 59.001 43.478 1.35 0.00 0.00 3.33
199 200 3.413846 AGAGATTGAAGCTGCTGTTGA 57.586 42.857 1.35 0.00 0.00 3.18
200 201 3.952931 AGAGATTGAAGCTGCTGTTGAT 58.047 40.909 1.35 0.00 0.00 2.57
201 202 3.940221 AGAGATTGAAGCTGCTGTTGATC 59.060 43.478 1.35 5.28 0.00 2.92
202 203 3.940221 GAGATTGAAGCTGCTGTTGATCT 59.060 43.478 1.35 10.03 0.00 2.75
203 204 4.333690 AGATTGAAGCTGCTGTTGATCTT 58.666 39.130 1.35 0.00 0.00 2.40
204 205 3.909776 TTGAAGCTGCTGTTGATCTTG 57.090 42.857 1.35 0.00 0.00 3.02
205 206 3.130280 TGAAGCTGCTGTTGATCTTGA 57.870 42.857 1.35 0.00 0.00 3.02
206 207 3.682696 TGAAGCTGCTGTTGATCTTGAT 58.317 40.909 1.35 0.00 0.00 2.57
207 208 4.835678 TGAAGCTGCTGTTGATCTTGATA 58.164 39.130 1.35 0.00 0.00 2.15
208 209 5.247862 TGAAGCTGCTGTTGATCTTGATAA 58.752 37.500 1.35 0.00 0.00 1.75
209 210 5.122869 TGAAGCTGCTGTTGATCTTGATAAC 59.877 40.000 1.35 0.00 0.00 1.89
210 211 3.944015 AGCTGCTGTTGATCTTGATAACC 59.056 43.478 0.00 0.00 0.00 2.85
211 212 3.065925 GCTGCTGTTGATCTTGATAACCC 59.934 47.826 0.00 0.00 0.00 4.11
212 213 4.264253 CTGCTGTTGATCTTGATAACCCA 58.736 43.478 0.00 0.00 0.00 4.51
213 214 4.009675 TGCTGTTGATCTTGATAACCCAC 58.990 43.478 0.00 0.00 0.00 4.61
214 215 4.009675 GCTGTTGATCTTGATAACCCACA 58.990 43.478 0.00 0.00 0.00 4.17
215 216 4.458989 GCTGTTGATCTTGATAACCCACAA 59.541 41.667 0.00 0.00 0.00 3.33
216 217 5.126061 GCTGTTGATCTTGATAACCCACAAT 59.874 40.000 0.00 0.00 0.00 2.71
217 218 6.678900 GCTGTTGATCTTGATAACCCACAATC 60.679 42.308 0.00 0.00 0.00 2.67
218 219 6.244654 TGTTGATCTTGATAACCCACAATCA 58.755 36.000 0.00 0.00 0.00 2.57
219 220 6.718912 TGTTGATCTTGATAACCCACAATCAA 59.281 34.615 0.00 0.00 39.24 2.57
220 221 7.232330 TGTTGATCTTGATAACCCACAATCAAA 59.768 33.333 0.00 0.00 40.56 2.69
221 222 7.395190 TGATCTTGATAACCCACAATCAAAG 57.605 36.000 0.00 0.00 40.56 2.77
222 223 7.174413 TGATCTTGATAACCCACAATCAAAGA 58.826 34.615 0.00 0.00 40.56 2.52
223 224 7.835682 TGATCTTGATAACCCACAATCAAAGAT 59.164 33.333 0.00 0.00 40.56 2.40
224 225 8.599624 ATCTTGATAACCCACAATCAAAGATT 57.400 30.769 0.00 0.00 40.56 2.40
225 226 8.055279 TCTTGATAACCCACAATCAAAGATTC 57.945 34.615 0.00 0.00 40.56 2.52
226 227 7.669304 TCTTGATAACCCACAATCAAAGATTCA 59.331 33.333 0.00 0.00 40.56 2.57
227 228 7.773489 TGATAACCCACAATCAAAGATTCAA 57.227 32.000 0.00 0.00 0.00 2.69
228 229 8.365060 TGATAACCCACAATCAAAGATTCAAT 57.635 30.769 0.00 0.00 0.00 2.57
229 230 8.252417 TGATAACCCACAATCAAAGATTCAATG 58.748 33.333 0.00 0.00 0.00 2.82
230 231 6.423776 AACCCACAATCAAAGATTCAATGT 57.576 33.333 0.00 0.00 0.00 2.71
231 232 6.423776 ACCCACAATCAAAGATTCAATGTT 57.576 33.333 0.00 0.00 0.00 2.71
232 233 7.537596 ACCCACAATCAAAGATTCAATGTTA 57.462 32.000 0.00 0.00 0.00 2.41
233 234 8.137745 ACCCACAATCAAAGATTCAATGTTAT 57.862 30.769 0.00 0.00 0.00 1.89
234 235 8.036575 ACCCACAATCAAAGATTCAATGTTATG 58.963 33.333 0.00 0.00 0.00 1.90
235 236 8.252417 CCCACAATCAAAGATTCAATGTTATGA 58.748 33.333 0.00 0.00 0.00 2.15
236 237 9.811995 CCACAATCAAAGATTCAATGTTATGAT 57.188 29.630 0.00 1.54 0.00 2.45
254 255 9.453572 TGTTATGATAAGAGAGATTTTGTTGCT 57.546 29.630 0.00 0.00 0.00 3.91
257 258 8.674263 ATGATAAGAGAGATTTTGTTGCTAGG 57.326 34.615 0.00 0.00 0.00 3.02
258 259 7.851228 TGATAAGAGAGATTTTGTTGCTAGGA 58.149 34.615 0.00 0.00 0.00 2.94
259 260 8.321353 TGATAAGAGAGATTTTGTTGCTAGGAA 58.679 33.333 0.00 0.00 0.00 3.36
260 261 8.729805 ATAAGAGAGATTTTGTTGCTAGGAAG 57.270 34.615 0.00 0.00 0.00 3.46
275 276 3.764237 AGGAAGCACGGTAAAGAAAGA 57.236 42.857 0.00 0.00 0.00 2.52
276 277 3.665190 AGGAAGCACGGTAAAGAAAGAG 58.335 45.455 0.00 0.00 0.00 2.85
277 278 3.323979 AGGAAGCACGGTAAAGAAAGAGA 59.676 43.478 0.00 0.00 0.00 3.10
278 279 4.062991 GGAAGCACGGTAAAGAAAGAGAA 58.937 43.478 0.00 0.00 0.00 2.87
279 280 4.083961 GGAAGCACGGTAAAGAAAGAGAAC 60.084 45.833 0.00 0.00 0.00 3.01
280 281 3.400255 AGCACGGTAAAGAAAGAGAACC 58.600 45.455 0.00 0.00 0.00 3.62
281 282 3.135994 GCACGGTAAAGAAAGAGAACCA 58.864 45.455 0.00 0.00 0.00 3.67
282 283 3.751698 GCACGGTAAAGAAAGAGAACCAT 59.248 43.478 0.00 0.00 0.00 3.55
283 284 4.378459 GCACGGTAAAGAAAGAGAACCATG 60.378 45.833 0.00 0.00 0.00 3.66
284 285 4.154195 CACGGTAAAGAAAGAGAACCATGG 59.846 45.833 11.19 11.19 0.00 3.66
285 286 3.689649 CGGTAAAGAAAGAGAACCATGGG 59.310 47.826 18.09 0.00 0.00 4.00
286 287 4.663334 GGTAAAGAAAGAGAACCATGGGT 58.337 43.478 18.09 10.33 37.65 4.51
303 304 3.363787 GTTCAGAAACCCATGCCCT 57.636 52.632 0.00 0.00 0.00 5.19
304 305 1.632589 GTTCAGAAACCCATGCCCTT 58.367 50.000 0.00 0.00 0.00 3.95
305 306 1.970640 GTTCAGAAACCCATGCCCTTT 59.029 47.619 0.00 0.00 0.00 3.11
306 307 1.923356 TCAGAAACCCATGCCCTTTC 58.077 50.000 0.00 0.00 0.00 2.62
307 308 0.897621 CAGAAACCCATGCCCTTTCC 59.102 55.000 0.00 0.00 0.00 3.13
308 309 0.786435 AGAAACCCATGCCCTTTCCT 59.214 50.000 0.00 0.00 0.00 3.36
309 310 1.186200 GAAACCCATGCCCTTTCCTC 58.814 55.000 0.00 0.00 0.00 3.71
310 311 0.252239 AAACCCATGCCCTTTCCTCC 60.252 55.000 0.00 0.00 0.00 4.30
311 312 1.149133 AACCCATGCCCTTTCCTCCT 61.149 55.000 0.00 0.00 0.00 3.69
312 313 0.253630 ACCCATGCCCTTTCCTCCTA 60.254 55.000 0.00 0.00 0.00 2.94
313 314 0.926293 CCCATGCCCTTTCCTCCTAA 59.074 55.000 0.00 0.00 0.00 2.69
314 315 1.287739 CCCATGCCCTTTCCTCCTAAA 59.712 52.381 0.00 0.00 0.00 1.85
315 316 2.379005 CCATGCCCTTTCCTCCTAAAC 58.621 52.381 0.00 0.00 0.00 2.01
316 317 2.379005 CATGCCCTTTCCTCCTAAACC 58.621 52.381 0.00 0.00 0.00 3.27
317 318 1.451449 TGCCCTTTCCTCCTAAACCA 58.549 50.000 0.00 0.00 0.00 3.67
318 319 2.000048 TGCCCTTTCCTCCTAAACCAT 59.000 47.619 0.00 0.00 0.00 3.55
319 320 2.025321 TGCCCTTTCCTCCTAAACCATC 60.025 50.000 0.00 0.00 0.00 3.51
320 321 2.687014 GCCCTTTCCTCCTAAACCATCC 60.687 54.545 0.00 0.00 0.00 3.51
321 322 2.580783 CCCTTTCCTCCTAAACCATCCA 59.419 50.000 0.00 0.00 0.00 3.41
322 323 3.011257 CCCTTTCCTCCTAAACCATCCAA 59.989 47.826 0.00 0.00 0.00 3.53
323 324 4.273318 CCTTTCCTCCTAAACCATCCAAG 58.727 47.826 0.00 0.00 0.00 3.61
324 325 4.263949 CCTTTCCTCCTAAACCATCCAAGT 60.264 45.833 0.00 0.00 0.00 3.16
325 326 4.569719 TTCCTCCTAAACCATCCAAGTC 57.430 45.455 0.00 0.00 0.00 3.01
326 327 3.526899 TCCTCCTAAACCATCCAAGTCA 58.473 45.455 0.00 0.00 0.00 3.41
327 328 3.913799 TCCTCCTAAACCATCCAAGTCAA 59.086 43.478 0.00 0.00 0.00 3.18
328 329 4.352595 TCCTCCTAAACCATCCAAGTCAAA 59.647 41.667 0.00 0.00 0.00 2.69
329 330 4.702131 CCTCCTAAACCATCCAAGTCAAAG 59.298 45.833 0.00 0.00 0.00 2.77
330 331 4.662278 TCCTAAACCATCCAAGTCAAAGG 58.338 43.478 0.00 0.00 0.00 3.11
331 332 4.352595 TCCTAAACCATCCAAGTCAAAGGA 59.647 41.667 0.00 0.00 38.50 3.36
332 333 5.015178 TCCTAAACCATCCAAGTCAAAGGAT 59.985 40.000 0.00 0.00 45.30 3.24
339 340 4.226427 TCCAAGTCAAAGGATGATGAGG 57.774 45.455 0.00 0.00 40.97 3.86
340 341 3.845992 TCCAAGTCAAAGGATGATGAGGA 59.154 43.478 0.00 0.00 40.97 3.71
341 342 4.476113 TCCAAGTCAAAGGATGATGAGGAT 59.524 41.667 0.00 0.00 40.97 3.24
342 343 5.044624 TCCAAGTCAAAGGATGATGAGGATT 60.045 40.000 0.00 0.00 40.97 3.01
343 344 5.655532 CCAAGTCAAAGGATGATGAGGATTT 59.344 40.000 0.00 0.00 40.97 2.17
344 345 6.154021 CCAAGTCAAAGGATGATGAGGATTTT 59.846 38.462 0.00 0.00 40.97 1.82
345 346 6.770746 AGTCAAAGGATGATGAGGATTTTG 57.229 37.500 0.00 0.00 40.97 2.44
346 347 6.487828 AGTCAAAGGATGATGAGGATTTTGA 58.512 36.000 0.00 0.00 40.97 2.69
347 348 6.602406 AGTCAAAGGATGATGAGGATTTTGAG 59.398 38.462 0.00 0.00 40.97 3.02
348 349 5.359009 TCAAAGGATGATGAGGATTTTGAGC 59.641 40.000 0.00 0.00 31.50 4.26
349 350 3.474600 AGGATGATGAGGATTTTGAGCG 58.525 45.455 0.00 0.00 0.00 5.03
350 351 2.031333 GGATGATGAGGATTTTGAGCGC 60.031 50.000 0.00 0.00 0.00 5.92
351 352 2.408271 TGATGAGGATTTTGAGCGCT 57.592 45.000 11.27 11.27 0.00 5.92
352 353 2.715046 TGATGAGGATTTTGAGCGCTT 58.285 42.857 13.26 0.00 0.00 4.68
353 354 3.084039 TGATGAGGATTTTGAGCGCTTT 58.916 40.909 13.26 0.00 0.00 3.51
354 355 2.995466 TGAGGATTTTGAGCGCTTTG 57.005 45.000 13.26 0.00 0.00 2.77
355 356 1.068333 TGAGGATTTTGAGCGCTTTGC 60.068 47.619 13.26 0.00 46.98 3.68
368 369 4.019919 GCGCTTTGCTGAAATGATTAGA 57.980 40.909 0.00 0.00 41.73 2.10
369 370 3.788163 GCGCTTTGCTGAAATGATTAGAC 59.212 43.478 0.00 0.00 41.73 2.59
370 371 4.346129 CGCTTTGCTGAAATGATTAGACC 58.654 43.478 0.00 0.00 0.00 3.85
371 372 4.095483 CGCTTTGCTGAAATGATTAGACCT 59.905 41.667 0.00 0.00 0.00 3.85
372 373 5.294306 CGCTTTGCTGAAATGATTAGACCTA 59.706 40.000 0.00 0.00 0.00 3.08
373 374 6.017605 CGCTTTGCTGAAATGATTAGACCTAT 60.018 38.462 0.00 0.00 0.00 2.57
374 375 7.467811 CGCTTTGCTGAAATGATTAGACCTATT 60.468 37.037 0.00 0.00 0.00 1.73
375 376 8.193438 GCTTTGCTGAAATGATTAGACCTATTT 58.807 33.333 0.00 0.00 0.00 1.40
378 379 9.466497 TTGCTGAAATGATTAGACCTATTTTCT 57.534 29.630 0.00 0.00 0.00 2.52
379 380 9.466497 TGCTGAAATGATTAGACCTATTTTCTT 57.534 29.630 0.00 0.00 0.00 2.52
387 388 9.472361 TGATTAGACCTATTTTCTTACGTATGC 57.528 33.333 0.00 0.00 0.00 3.14
388 389 7.919313 TTAGACCTATTTTCTTACGTATGCG 57.081 36.000 0.19 0.19 44.93 4.73
389 390 4.743644 AGACCTATTTTCTTACGTATGCGC 59.256 41.667 0.00 0.00 42.83 6.09
390 391 4.690122 ACCTATTTTCTTACGTATGCGCT 58.310 39.130 9.73 0.00 42.83 5.92
391 392 5.114081 ACCTATTTTCTTACGTATGCGCTT 58.886 37.500 9.73 4.59 42.83 4.68
392 393 6.275335 ACCTATTTTCTTACGTATGCGCTTA 58.725 36.000 9.73 3.30 42.83 3.09
393 394 6.757947 ACCTATTTTCTTACGTATGCGCTTAA 59.242 34.615 9.73 0.00 42.83 1.85
394 395 7.061634 CCTATTTTCTTACGTATGCGCTTAAC 58.938 38.462 9.73 2.89 42.83 2.01
395 396 6.657836 ATTTTCTTACGTATGCGCTTAACT 57.342 33.333 9.73 0.00 42.83 2.24
396 397 5.444586 TTTCTTACGTATGCGCTTAACTG 57.555 39.130 9.73 3.04 42.83 3.16
397 398 4.359971 TCTTACGTATGCGCTTAACTGA 57.640 40.909 9.73 0.00 42.83 3.41
398 399 4.928601 TCTTACGTATGCGCTTAACTGAT 58.071 39.130 9.73 0.00 42.83 2.90
399 400 6.063640 TCTTACGTATGCGCTTAACTGATA 57.936 37.500 9.73 0.00 42.83 2.15
400 401 6.675026 TCTTACGTATGCGCTTAACTGATAT 58.325 36.000 9.73 0.00 42.83 1.63
401 402 6.581166 TCTTACGTATGCGCTTAACTGATATG 59.419 38.462 9.73 4.13 42.83 1.78
402 403 3.428870 ACGTATGCGCTTAACTGATATGC 59.571 43.478 9.73 0.00 42.83 3.14
403 404 3.675225 CGTATGCGCTTAACTGATATGCT 59.325 43.478 9.73 0.00 33.61 3.79
404 405 4.150627 CGTATGCGCTTAACTGATATGCTT 59.849 41.667 9.73 0.00 33.61 3.91
405 406 5.344933 CGTATGCGCTTAACTGATATGCTTA 59.655 40.000 9.73 0.00 33.61 3.09
406 407 6.128929 CGTATGCGCTTAACTGATATGCTTAA 60.129 38.462 9.73 0.00 33.61 1.85
407 408 6.618287 ATGCGCTTAACTGATATGCTTAAA 57.382 33.333 9.73 0.00 33.61 1.52
408 409 6.048073 TGCGCTTAACTGATATGCTTAAAG 57.952 37.500 9.73 0.00 33.61 1.85
409 410 5.584649 TGCGCTTAACTGATATGCTTAAAGT 59.415 36.000 9.73 0.00 33.61 2.66
410 411 6.759356 TGCGCTTAACTGATATGCTTAAAGTA 59.241 34.615 9.73 0.00 33.61 2.24
411 412 7.279090 TGCGCTTAACTGATATGCTTAAAGTAA 59.721 33.333 9.73 0.00 33.61 2.24
412 413 8.120465 GCGCTTAACTGATATGCTTAAAGTAAA 58.880 33.333 0.00 0.00 33.61 2.01
421 422 9.231297 TGATATGCTTAAAGTAAATCCCTATGC 57.769 33.333 0.00 0.00 0.00 3.14
422 423 9.454859 GATATGCTTAAAGTAAATCCCTATGCT 57.545 33.333 0.00 0.00 0.00 3.79
425 426 8.677148 TGCTTAAAGTAAATCCCTATGCTAAG 57.323 34.615 0.00 0.00 0.00 2.18
426 427 8.272173 TGCTTAAAGTAAATCCCTATGCTAAGT 58.728 33.333 0.00 0.00 0.00 2.24
427 428 9.774413 GCTTAAAGTAAATCCCTATGCTAAGTA 57.226 33.333 0.00 0.00 0.00 2.24
436 437 8.917414 AATCCCTATGCTAAGTATATGAAGGA 57.083 34.615 0.00 0.00 0.00 3.36
437 438 9.512748 AATCCCTATGCTAAGTATATGAAGGAT 57.487 33.333 0.00 0.00 0.00 3.24
465 466 8.673711 TCATCACAAATAAAAGAAAGATACCGG 58.326 33.333 0.00 0.00 0.00 5.28
466 467 8.673711 CATCACAAATAAAAGAAAGATACCGGA 58.326 33.333 9.46 0.00 0.00 5.14
467 468 8.624367 TCACAAATAAAAGAAAGATACCGGAA 57.376 30.769 9.46 0.00 0.00 4.30
468 469 8.726988 TCACAAATAAAAGAAAGATACCGGAAG 58.273 33.333 9.46 0.00 0.00 3.46
469 470 7.484959 CACAAATAAAAGAAAGATACCGGAAGC 59.515 37.037 9.46 0.00 0.00 3.86
470 471 7.393515 ACAAATAAAAGAAAGATACCGGAAGCT 59.606 33.333 9.46 0.00 0.00 3.74
471 472 6.927294 ATAAAAGAAAGATACCGGAAGCTG 57.073 37.500 9.46 0.00 0.00 4.24
472 473 4.553330 AAAGAAAGATACCGGAAGCTGA 57.447 40.909 9.46 0.00 0.00 4.26
473 474 4.553330 AAGAAAGATACCGGAAGCTGAA 57.447 40.909 9.46 0.00 0.00 3.02
474 475 4.553330 AGAAAGATACCGGAAGCTGAAA 57.447 40.909 9.46 0.00 0.00 2.69
475 476 5.104259 AGAAAGATACCGGAAGCTGAAAT 57.896 39.130 9.46 0.00 0.00 2.17
476 477 5.501156 AGAAAGATACCGGAAGCTGAAATT 58.499 37.500 9.46 0.00 0.00 1.82
477 478 5.946377 AGAAAGATACCGGAAGCTGAAATTT 59.054 36.000 9.46 0.00 0.00 1.82
478 479 5.819825 AAGATACCGGAAGCTGAAATTTC 57.180 39.130 9.46 11.41 0.00 2.17
479 480 4.200092 AGATACCGGAAGCTGAAATTTCC 58.800 43.478 9.46 1.15 39.56 3.13
480 481 2.286365 ACCGGAAGCTGAAATTTCCA 57.714 45.000 9.46 3.32 42.39 3.53
481 482 1.886542 ACCGGAAGCTGAAATTTCCAC 59.113 47.619 9.46 7.50 42.39 4.02
482 483 1.202348 CCGGAAGCTGAAATTTCCACC 59.798 52.381 15.48 9.98 42.39 4.61
483 484 1.885887 CGGAAGCTGAAATTTCCACCA 59.114 47.619 15.48 0.00 42.39 4.17
484 485 2.493278 CGGAAGCTGAAATTTCCACCAT 59.507 45.455 15.48 0.00 42.39 3.55
485 486 3.674138 CGGAAGCTGAAATTTCCACCATG 60.674 47.826 15.48 0.00 42.39 3.66
486 487 3.256558 GAAGCTGAAATTTCCACCATGC 58.743 45.455 15.48 9.66 0.00 4.06
487 488 2.532843 AGCTGAAATTTCCACCATGCT 58.467 42.857 15.48 11.46 0.00 3.79
488 489 2.901839 AGCTGAAATTTCCACCATGCTT 59.098 40.909 15.48 0.00 0.00 3.91
489 490 2.997986 GCTGAAATTTCCACCATGCTTG 59.002 45.455 15.48 0.00 0.00 4.01
490 491 2.997986 CTGAAATTTCCACCATGCTTGC 59.002 45.455 15.48 0.00 0.00 4.01
491 492 2.633967 TGAAATTTCCACCATGCTTGCT 59.366 40.909 15.48 0.00 0.00 3.91
492 493 3.831333 TGAAATTTCCACCATGCTTGCTA 59.169 39.130 15.48 0.00 0.00 3.49
493 494 4.282957 TGAAATTTCCACCATGCTTGCTAA 59.717 37.500 15.48 0.00 0.00 3.09
494 495 5.046448 TGAAATTTCCACCATGCTTGCTAAT 60.046 36.000 15.48 0.00 0.00 1.73
495 496 5.425196 AATTTCCACCATGCTTGCTAATT 57.575 34.783 0.00 0.00 0.00 1.40
496 497 6.543430 AATTTCCACCATGCTTGCTAATTA 57.457 33.333 0.00 0.00 0.00 1.40
497 498 4.981806 TTCCACCATGCTTGCTAATTAC 57.018 40.909 0.00 0.00 0.00 1.89
498 499 3.961849 TCCACCATGCTTGCTAATTACA 58.038 40.909 0.00 0.00 0.00 2.41
499 500 3.694072 TCCACCATGCTTGCTAATTACAC 59.306 43.478 0.00 0.00 0.00 2.90
500 501 3.696051 CCACCATGCTTGCTAATTACACT 59.304 43.478 0.00 0.00 0.00 3.55
501 502 4.158394 CCACCATGCTTGCTAATTACACTT 59.842 41.667 0.00 0.00 0.00 3.16
502 503 5.336690 CCACCATGCTTGCTAATTACACTTT 60.337 40.000 0.00 0.00 0.00 2.66
503 504 6.158598 CACCATGCTTGCTAATTACACTTTT 58.841 36.000 0.00 0.00 0.00 2.27
504 505 7.312154 CACCATGCTTGCTAATTACACTTTTA 58.688 34.615 0.00 0.00 0.00 1.52
505 506 7.812191 CACCATGCTTGCTAATTACACTTTTAA 59.188 33.333 0.00 0.00 0.00 1.52
506 507 8.028938 ACCATGCTTGCTAATTACACTTTTAAG 58.971 33.333 0.00 0.00 0.00 1.85
507 508 7.489113 CCATGCTTGCTAATTACACTTTTAAGG 59.511 37.037 0.00 0.00 0.00 2.69
508 509 6.919721 TGCTTGCTAATTACACTTTTAAGGG 58.080 36.000 0.00 0.00 34.93 3.95
509 510 6.492087 TGCTTGCTAATTACACTTTTAAGGGT 59.508 34.615 2.56 2.56 46.27 4.34
510 511 6.806739 GCTTGCTAATTACACTTTTAAGGGTG 59.193 38.462 7.62 7.90 43.82 4.61
511 512 6.827586 TGCTAATTACACTTTTAAGGGTGG 57.172 37.500 7.62 0.00 43.82 4.61
512 513 6.544650 TGCTAATTACACTTTTAAGGGTGGA 58.455 36.000 7.62 3.59 43.82 4.02
513 514 7.005296 TGCTAATTACACTTTTAAGGGTGGAA 58.995 34.615 7.62 9.09 43.82 3.53
514 515 7.672239 TGCTAATTACACTTTTAAGGGTGGAAT 59.328 33.333 7.62 11.95 45.55 3.01
515 516 9.181061 GCTAATTACACTTTTAAGGGTGGAATA 57.819 33.333 15.84 7.89 43.63 1.75
517 518 7.949690 ATTACACTTTTAAGGGTGGAATACC 57.050 36.000 14.64 0.00 43.82 2.73
538 539 2.749621 CAAAGAAACTTGGAGATCCGGG 59.250 50.000 0.00 0.00 39.43 5.73
539 540 1.657804 AGAAACTTGGAGATCCGGGT 58.342 50.000 0.00 0.00 39.43 5.28
540 541 1.279271 AGAAACTTGGAGATCCGGGTG 59.721 52.381 0.00 0.00 39.43 4.61
541 542 1.003233 GAAACTTGGAGATCCGGGTGT 59.997 52.381 0.00 0.00 39.43 4.16
542 543 0.613777 AACTTGGAGATCCGGGTGTC 59.386 55.000 2.49 2.49 39.43 3.67
543 544 1.265454 ACTTGGAGATCCGGGTGTCC 61.265 60.000 23.98 23.98 39.43 4.02
544 545 1.972660 CTTGGAGATCCGGGTGTCCC 61.973 65.000 27.19 10.58 41.09 4.46
545 546 2.365105 GGAGATCCGGGTGTCCCA 60.365 66.667 20.41 0.00 45.83 4.37
546 547 1.993391 GGAGATCCGGGTGTCCCAA 60.993 63.158 20.41 0.00 45.83 4.12
547 548 1.221021 GAGATCCGGGTGTCCCAAC 59.779 63.158 0.00 0.00 45.83 3.77
548 549 1.229529 AGATCCGGGTGTCCCAACT 60.230 57.895 0.00 0.00 45.83 3.16
549 550 0.042131 AGATCCGGGTGTCCCAACTA 59.958 55.000 0.00 0.00 45.83 2.24
550 551 1.129058 GATCCGGGTGTCCCAACTAT 58.871 55.000 0.00 0.00 45.83 2.12
551 552 2.090943 AGATCCGGGTGTCCCAACTATA 60.091 50.000 0.00 0.00 45.83 1.31
552 553 1.488390 TCCGGGTGTCCCAACTATAC 58.512 55.000 0.00 0.00 45.83 1.47
553 554 0.466963 CCGGGTGTCCCAACTATACC 59.533 60.000 5.64 0.00 45.83 2.73
554 555 1.196911 CGGGTGTCCCAACTATACCA 58.803 55.000 5.64 0.00 45.83 3.25
555 556 1.766496 CGGGTGTCCCAACTATACCAT 59.234 52.381 5.64 0.00 45.83 3.55
556 557 2.484770 CGGGTGTCCCAACTATACCATG 60.485 54.545 5.64 0.00 45.83 3.66
557 558 2.572290 GGTGTCCCAACTATACCATGC 58.428 52.381 0.00 0.00 0.00 4.06
558 559 2.172717 GGTGTCCCAACTATACCATGCT 59.827 50.000 0.00 0.00 0.00 3.79
559 560 3.467803 GTGTCCCAACTATACCATGCTC 58.532 50.000 0.00 0.00 0.00 4.26
562 563 3.073062 GTCCCAACTATACCATGCTCCAT 59.927 47.826 0.00 0.00 0.00 3.41
565 566 5.371176 TCCCAACTATACCATGCTCCATTAA 59.629 40.000 0.00 0.00 0.00 1.40
618 620 1.537202 GGTGTCCATGTGCTCAGTTTC 59.463 52.381 0.00 0.00 0.00 2.78
878 880 1.109920 ACCACGGCGATAGAGAGCAT 61.110 55.000 16.62 0.00 39.76 3.79
909 913 2.109739 GGCGAGAGAGAGAGCACGA 61.110 63.158 0.00 0.00 0.00 4.35
1079 1083 1.285950 CTGTCTTCGTCTGTCCGCA 59.714 57.895 0.00 0.00 0.00 5.69
1360 1365 4.008933 GGCCACACCACGAGCTCT 62.009 66.667 12.85 0.00 38.86 4.09
1739 2052 1.480137 GCTCTCTGCTCTGCCTTTCTA 59.520 52.381 0.00 0.00 38.95 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.484643 CAGTAGGTTCACTATAAGCATGCAAT 59.515 38.462 21.98 15.14 33.43 3.56
43 44 5.418209 GGTGTGTCTACAGTAGGTTCACTAT 59.582 44.000 20.87 0.00 37.52 2.12
114 115 5.745312 TCACTAGGTTCATGTTCATCACT 57.255 39.130 0.00 0.00 0.00 3.41
153 154 8.159344 ACATTATTATCTTTGCTAGGTTGAGC 57.841 34.615 0.00 0.00 43.16 4.26
167 168 9.434420 GCAGCTTCAATCTCTACATTATTATCT 57.566 33.333 0.00 0.00 0.00 1.98
168 169 9.434420 AGCAGCTTCAATCTCTACATTATTATC 57.566 33.333 0.00 0.00 0.00 1.75
169 170 9.217278 CAGCAGCTTCAATCTCTACATTATTAT 57.783 33.333 0.00 0.00 0.00 1.28
170 171 8.206867 ACAGCAGCTTCAATCTCTACATTATTA 58.793 33.333 0.00 0.00 0.00 0.98
171 172 7.052873 ACAGCAGCTTCAATCTCTACATTATT 58.947 34.615 0.00 0.00 0.00 1.40
172 173 6.590068 ACAGCAGCTTCAATCTCTACATTAT 58.410 36.000 0.00 0.00 0.00 1.28
173 174 5.982356 ACAGCAGCTTCAATCTCTACATTA 58.018 37.500 0.00 0.00 0.00 1.90
174 175 4.841422 ACAGCAGCTTCAATCTCTACATT 58.159 39.130 0.00 0.00 0.00 2.71
175 176 4.484537 ACAGCAGCTTCAATCTCTACAT 57.515 40.909 0.00 0.00 0.00 2.29
176 177 3.969287 ACAGCAGCTTCAATCTCTACA 57.031 42.857 0.00 0.00 0.00 2.74
177 178 4.248859 TCAACAGCAGCTTCAATCTCTAC 58.751 43.478 0.00 0.00 0.00 2.59
178 179 4.541973 TCAACAGCAGCTTCAATCTCTA 57.458 40.909 0.00 0.00 0.00 2.43
179 180 3.413846 TCAACAGCAGCTTCAATCTCT 57.586 42.857 0.00 0.00 0.00 3.10
180 181 3.940221 AGATCAACAGCAGCTTCAATCTC 59.060 43.478 0.00 0.00 0.00 2.75
181 182 3.952931 AGATCAACAGCAGCTTCAATCT 58.047 40.909 0.00 0.00 0.00 2.40
182 183 4.155462 TCAAGATCAACAGCAGCTTCAATC 59.845 41.667 0.00 0.00 0.00 2.67
183 184 4.077108 TCAAGATCAACAGCAGCTTCAAT 58.923 39.130 0.00 0.00 0.00 2.57
184 185 3.479489 TCAAGATCAACAGCAGCTTCAA 58.521 40.909 0.00 0.00 0.00 2.69
185 186 3.130280 TCAAGATCAACAGCAGCTTCA 57.870 42.857 0.00 0.00 0.00 3.02
186 187 5.448360 GGTTATCAAGATCAACAGCAGCTTC 60.448 44.000 0.00 0.00 0.00 3.86
187 188 4.397417 GGTTATCAAGATCAACAGCAGCTT 59.603 41.667 0.00 0.00 0.00 3.74
188 189 3.944015 GGTTATCAAGATCAACAGCAGCT 59.056 43.478 0.00 0.00 0.00 4.24
189 190 3.065925 GGGTTATCAAGATCAACAGCAGC 59.934 47.826 0.00 0.00 0.00 5.25
190 191 4.095483 GTGGGTTATCAAGATCAACAGCAG 59.905 45.833 0.00 0.00 0.00 4.24
191 192 4.009675 GTGGGTTATCAAGATCAACAGCA 58.990 43.478 0.00 0.00 0.00 4.41
192 193 4.009675 TGTGGGTTATCAAGATCAACAGC 58.990 43.478 0.00 0.00 0.00 4.40
193 194 6.375174 TGATTGTGGGTTATCAAGATCAACAG 59.625 38.462 0.00 0.00 0.00 3.16
194 195 6.244654 TGATTGTGGGTTATCAAGATCAACA 58.755 36.000 0.00 0.00 0.00 3.33
195 196 6.757897 TGATTGTGGGTTATCAAGATCAAC 57.242 37.500 0.00 0.00 0.00 3.18
196 197 7.669304 TCTTTGATTGTGGGTTATCAAGATCAA 59.331 33.333 0.00 0.00 40.65 2.57
197 198 7.174413 TCTTTGATTGTGGGTTATCAAGATCA 58.826 34.615 0.00 0.00 40.65 2.92
198 199 7.630242 TCTTTGATTGTGGGTTATCAAGATC 57.370 36.000 0.00 0.00 40.65 2.75
199 200 8.599624 AATCTTTGATTGTGGGTTATCAAGAT 57.400 30.769 0.00 0.00 40.65 2.40
200 201 7.669304 TGAATCTTTGATTGTGGGTTATCAAGA 59.331 33.333 0.00 0.00 40.65 3.02
201 202 7.829725 TGAATCTTTGATTGTGGGTTATCAAG 58.170 34.615 0.00 0.00 40.65 3.02
202 203 7.773489 TGAATCTTTGATTGTGGGTTATCAA 57.227 32.000 0.00 0.00 38.59 2.57
203 204 7.773489 TTGAATCTTTGATTGTGGGTTATCA 57.227 32.000 0.00 0.00 0.00 2.15
204 205 8.253113 ACATTGAATCTTTGATTGTGGGTTATC 58.747 33.333 0.00 0.00 0.00 1.75
205 206 8.137745 ACATTGAATCTTTGATTGTGGGTTAT 57.862 30.769 0.00 0.00 0.00 1.89
206 207 7.537596 ACATTGAATCTTTGATTGTGGGTTA 57.462 32.000 0.00 0.00 0.00 2.85
207 208 6.423776 ACATTGAATCTTTGATTGTGGGTT 57.576 33.333 0.00 0.00 0.00 4.11
208 209 6.423776 AACATTGAATCTTTGATTGTGGGT 57.576 33.333 0.00 0.00 0.00 4.51
209 210 8.252417 TCATAACATTGAATCTTTGATTGTGGG 58.748 33.333 0.00 0.00 0.00 4.61
210 211 9.811995 ATCATAACATTGAATCTTTGATTGTGG 57.188 29.630 0.00 0.00 0.00 4.17
228 229 9.453572 AGCAACAAAATCTCTCTTATCATAACA 57.546 29.630 0.00 0.00 0.00 2.41
231 232 9.770097 CCTAGCAACAAAATCTCTCTTATCATA 57.230 33.333 0.00 0.00 0.00 2.15
232 233 8.489489 TCCTAGCAACAAAATCTCTCTTATCAT 58.511 33.333 0.00 0.00 0.00 2.45
233 234 7.851228 TCCTAGCAACAAAATCTCTCTTATCA 58.149 34.615 0.00 0.00 0.00 2.15
234 235 8.723942 TTCCTAGCAACAAAATCTCTCTTATC 57.276 34.615 0.00 0.00 0.00 1.75
235 236 7.281999 GCTTCCTAGCAACAAAATCTCTCTTAT 59.718 37.037 0.00 0.00 46.95 1.73
236 237 6.595716 GCTTCCTAGCAACAAAATCTCTCTTA 59.404 38.462 0.00 0.00 46.95 2.10
237 238 5.414144 GCTTCCTAGCAACAAAATCTCTCTT 59.586 40.000 0.00 0.00 46.95 2.85
238 239 4.940654 GCTTCCTAGCAACAAAATCTCTCT 59.059 41.667 0.00 0.00 46.95 3.10
239 240 5.228579 GCTTCCTAGCAACAAAATCTCTC 57.771 43.478 0.00 0.00 46.95 3.20
253 254 4.817517 TCTTTCTTTACCGTGCTTCCTAG 58.182 43.478 0.00 0.00 0.00 3.02
254 255 4.525487 TCTCTTTCTTTACCGTGCTTCCTA 59.475 41.667 0.00 0.00 0.00 2.94
255 256 3.323979 TCTCTTTCTTTACCGTGCTTCCT 59.676 43.478 0.00 0.00 0.00 3.36
256 257 3.660865 TCTCTTTCTTTACCGTGCTTCC 58.339 45.455 0.00 0.00 0.00 3.46
257 258 4.083961 GGTTCTCTTTCTTTACCGTGCTTC 60.084 45.833 0.00 0.00 0.00 3.86
258 259 3.813724 GGTTCTCTTTCTTTACCGTGCTT 59.186 43.478 0.00 0.00 0.00 3.91
259 260 3.181458 TGGTTCTCTTTCTTTACCGTGCT 60.181 43.478 0.00 0.00 0.00 4.40
260 261 3.135994 TGGTTCTCTTTCTTTACCGTGC 58.864 45.455 0.00 0.00 0.00 5.34
261 262 4.154195 CCATGGTTCTCTTTCTTTACCGTG 59.846 45.833 2.57 0.00 42.72 4.94
262 263 4.324267 CCATGGTTCTCTTTCTTTACCGT 58.676 43.478 2.57 0.00 0.00 4.83
263 264 3.689649 CCCATGGTTCTCTTTCTTTACCG 59.310 47.826 11.73 0.00 0.00 4.02
264 265 4.663334 ACCCATGGTTCTCTTTCTTTACC 58.337 43.478 11.73 0.00 27.29 2.85
285 286 1.632589 AAGGGCATGGGTTTCTGAAC 58.367 50.000 0.00 0.00 34.96 3.18
286 287 2.247358 GAAAGGGCATGGGTTTCTGAA 58.753 47.619 0.00 0.00 0.00 3.02
287 288 1.549950 GGAAAGGGCATGGGTTTCTGA 60.550 52.381 0.00 0.00 31.96 3.27
288 289 0.897621 GGAAAGGGCATGGGTTTCTG 59.102 55.000 0.00 0.00 31.96 3.02
289 290 0.786435 AGGAAAGGGCATGGGTTTCT 59.214 50.000 0.00 0.00 31.96 2.52
290 291 1.186200 GAGGAAAGGGCATGGGTTTC 58.814 55.000 0.00 0.00 0.00 2.78
291 292 0.252239 GGAGGAAAGGGCATGGGTTT 60.252 55.000 0.00 0.00 0.00 3.27
292 293 1.149133 AGGAGGAAAGGGCATGGGTT 61.149 55.000 0.00 0.00 0.00 4.11
293 294 0.253630 TAGGAGGAAAGGGCATGGGT 60.254 55.000 0.00 0.00 0.00 4.51
294 295 0.926293 TTAGGAGGAAAGGGCATGGG 59.074 55.000 0.00 0.00 0.00 4.00
295 296 2.379005 GTTTAGGAGGAAAGGGCATGG 58.621 52.381 0.00 0.00 0.00 3.66
296 297 2.291540 TGGTTTAGGAGGAAAGGGCATG 60.292 50.000 0.00 0.00 0.00 4.06
297 298 2.000048 TGGTTTAGGAGGAAAGGGCAT 59.000 47.619 0.00 0.00 0.00 4.40
298 299 1.451449 TGGTTTAGGAGGAAAGGGCA 58.549 50.000 0.00 0.00 0.00 5.36
299 300 2.656002 GATGGTTTAGGAGGAAAGGGC 58.344 52.381 0.00 0.00 0.00 5.19
300 301 2.580783 TGGATGGTTTAGGAGGAAAGGG 59.419 50.000 0.00 0.00 0.00 3.95
301 302 4.263949 ACTTGGATGGTTTAGGAGGAAAGG 60.264 45.833 0.00 0.00 0.00 3.11
302 303 4.923415 ACTTGGATGGTTTAGGAGGAAAG 58.077 43.478 0.00 0.00 0.00 2.62
303 304 4.352595 TGACTTGGATGGTTTAGGAGGAAA 59.647 41.667 0.00 0.00 0.00 3.13
304 305 3.913799 TGACTTGGATGGTTTAGGAGGAA 59.086 43.478 0.00 0.00 0.00 3.36
305 306 3.526899 TGACTTGGATGGTTTAGGAGGA 58.473 45.455 0.00 0.00 0.00 3.71
306 307 4.301072 TTGACTTGGATGGTTTAGGAGG 57.699 45.455 0.00 0.00 0.00 4.30
307 308 4.702131 CCTTTGACTTGGATGGTTTAGGAG 59.298 45.833 0.00 0.00 0.00 3.69
308 309 4.352595 TCCTTTGACTTGGATGGTTTAGGA 59.647 41.667 0.00 0.00 0.00 2.94
309 310 4.662278 TCCTTTGACTTGGATGGTTTAGG 58.338 43.478 0.00 0.00 0.00 2.69
317 318 4.476113 TCCTCATCATCCTTTGACTTGGAT 59.524 41.667 0.00 0.00 43.23 3.41
318 319 3.845992 TCCTCATCATCCTTTGACTTGGA 59.154 43.478 0.00 0.00 37.11 3.53
319 320 4.226427 TCCTCATCATCCTTTGACTTGG 57.774 45.455 0.00 0.00 37.11 3.61
320 321 6.770746 AAATCCTCATCATCCTTTGACTTG 57.229 37.500 0.00 0.00 37.11 3.16
321 322 6.950041 TCAAAATCCTCATCATCCTTTGACTT 59.050 34.615 0.00 0.00 37.11 3.01
322 323 6.487828 TCAAAATCCTCATCATCCTTTGACT 58.512 36.000 0.00 0.00 37.11 3.41
323 324 6.679884 GCTCAAAATCCTCATCATCCTTTGAC 60.680 42.308 0.00 0.00 37.11 3.18
324 325 5.359009 GCTCAAAATCCTCATCATCCTTTGA 59.641 40.000 0.00 0.00 39.12 2.69
325 326 5.589192 GCTCAAAATCCTCATCATCCTTTG 58.411 41.667 0.00 0.00 0.00 2.77
326 327 4.337555 CGCTCAAAATCCTCATCATCCTTT 59.662 41.667 0.00 0.00 0.00 3.11
327 328 3.881688 CGCTCAAAATCCTCATCATCCTT 59.118 43.478 0.00 0.00 0.00 3.36
328 329 3.474600 CGCTCAAAATCCTCATCATCCT 58.525 45.455 0.00 0.00 0.00 3.24
329 330 2.031333 GCGCTCAAAATCCTCATCATCC 60.031 50.000 0.00 0.00 0.00 3.51
330 331 2.877168 AGCGCTCAAAATCCTCATCATC 59.123 45.455 2.64 0.00 0.00 2.92
331 332 2.928334 AGCGCTCAAAATCCTCATCAT 58.072 42.857 2.64 0.00 0.00 2.45
332 333 2.408271 AGCGCTCAAAATCCTCATCA 57.592 45.000 2.64 0.00 0.00 3.07
333 334 3.432782 CAAAGCGCTCAAAATCCTCATC 58.567 45.455 12.06 0.00 0.00 2.92
334 335 2.416431 GCAAAGCGCTCAAAATCCTCAT 60.416 45.455 12.06 0.00 37.77 2.90
335 336 1.068333 GCAAAGCGCTCAAAATCCTCA 60.068 47.619 12.06 0.00 37.77 3.86
336 337 1.622232 GCAAAGCGCTCAAAATCCTC 58.378 50.000 12.06 0.00 37.77 3.71
337 338 3.800628 GCAAAGCGCTCAAAATCCT 57.199 47.368 12.06 0.00 37.77 3.24
347 348 3.788163 GTCTAATCATTTCAGCAAAGCGC 59.212 43.478 0.00 0.00 42.91 5.92
348 349 4.095483 AGGTCTAATCATTTCAGCAAAGCG 59.905 41.667 0.00 0.00 0.00 4.68
349 350 5.573337 AGGTCTAATCATTTCAGCAAAGC 57.427 39.130 0.00 0.00 0.00 3.51
352 353 9.466497 AGAAAATAGGTCTAATCATTTCAGCAA 57.534 29.630 0.00 0.00 0.00 3.91
353 354 9.466497 AAGAAAATAGGTCTAATCATTTCAGCA 57.534 29.630 0.00 0.00 0.00 4.41
361 362 9.472361 GCATACGTAAGAAAATAGGTCTAATCA 57.528 33.333 0.00 0.00 43.62 2.57
362 363 8.636843 CGCATACGTAAGAAAATAGGTCTAATC 58.363 37.037 0.00 0.00 43.62 1.75
363 364 7.115947 GCGCATACGTAAGAAAATAGGTCTAAT 59.884 37.037 0.30 0.00 42.83 1.73
364 365 6.418819 GCGCATACGTAAGAAAATAGGTCTAA 59.581 38.462 0.30 0.00 42.83 2.10
365 366 5.916883 GCGCATACGTAAGAAAATAGGTCTA 59.083 40.000 0.30 0.00 42.83 2.59
366 367 4.743644 GCGCATACGTAAGAAAATAGGTCT 59.256 41.667 0.30 0.00 42.83 3.85
367 368 4.743644 AGCGCATACGTAAGAAAATAGGTC 59.256 41.667 11.47 0.00 42.83 3.85
368 369 4.690122 AGCGCATACGTAAGAAAATAGGT 58.310 39.130 11.47 0.00 42.83 3.08
369 370 5.652744 AAGCGCATACGTAAGAAAATAGG 57.347 39.130 11.47 0.00 42.83 2.57
370 371 7.787935 CAGTTAAGCGCATACGTAAGAAAATAG 59.212 37.037 11.47 0.00 42.83 1.73
371 372 7.488792 TCAGTTAAGCGCATACGTAAGAAAATA 59.511 33.333 11.47 0.00 42.83 1.40
372 373 6.311935 TCAGTTAAGCGCATACGTAAGAAAAT 59.688 34.615 11.47 0.00 42.83 1.82
373 374 5.634439 TCAGTTAAGCGCATACGTAAGAAAA 59.366 36.000 11.47 0.00 42.83 2.29
374 375 5.162794 TCAGTTAAGCGCATACGTAAGAAA 58.837 37.500 11.47 0.00 42.83 2.52
375 376 4.735985 TCAGTTAAGCGCATACGTAAGAA 58.264 39.130 11.47 0.00 42.83 2.52
376 377 4.359971 TCAGTTAAGCGCATACGTAAGA 57.640 40.909 11.47 0.00 42.83 2.10
377 378 6.667621 GCATATCAGTTAAGCGCATACGTAAG 60.668 42.308 11.47 0.00 42.83 2.34
378 379 5.118050 GCATATCAGTTAAGCGCATACGTAA 59.882 40.000 11.47 0.00 42.83 3.18
379 380 4.619760 GCATATCAGTTAAGCGCATACGTA 59.380 41.667 11.47 0.00 42.83 3.57
380 381 3.428870 GCATATCAGTTAAGCGCATACGT 59.571 43.478 11.47 0.00 42.83 3.57
381 382 3.675225 AGCATATCAGTTAAGCGCATACG 59.325 43.478 11.47 1.53 44.07 3.06
382 383 5.597813 AAGCATATCAGTTAAGCGCATAC 57.402 39.130 11.47 4.07 29.85 2.39
383 384 7.441157 ACTTTAAGCATATCAGTTAAGCGCATA 59.559 33.333 11.47 0.00 29.85 3.14
384 385 6.260936 ACTTTAAGCATATCAGTTAAGCGCAT 59.739 34.615 11.47 0.00 29.85 4.73
385 386 5.584649 ACTTTAAGCATATCAGTTAAGCGCA 59.415 36.000 11.47 0.00 29.85 6.09
386 387 6.049263 ACTTTAAGCATATCAGTTAAGCGC 57.951 37.500 0.00 0.00 29.85 5.92
395 396 9.231297 GCATAGGGATTTACTTTAAGCATATCA 57.769 33.333 0.00 0.00 0.00 2.15
396 397 9.454859 AGCATAGGGATTTACTTTAAGCATATC 57.545 33.333 0.00 0.00 0.00 1.63
399 400 9.289782 CTTAGCATAGGGATTTACTTTAAGCAT 57.710 33.333 0.00 0.00 0.00 3.79
400 401 8.272173 ACTTAGCATAGGGATTTACTTTAAGCA 58.728 33.333 0.00 0.00 0.00 3.91
401 402 8.678593 ACTTAGCATAGGGATTTACTTTAAGC 57.321 34.615 0.00 0.00 0.00 3.09
410 411 9.338968 TCCTTCATATACTTAGCATAGGGATTT 57.661 33.333 0.00 0.00 0.00 2.17
411 412 8.917414 TCCTTCATATACTTAGCATAGGGATT 57.083 34.615 0.00 0.00 0.00 3.01
439 440 8.673711 CCGGTATCTTTCTTTTATTTGTGATGA 58.326 33.333 0.00 0.00 0.00 2.92
440 441 8.673711 TCCGGTATCTTTCTTTTATTTGTGATG 58.326 33.333 0.00 0.00 0.00 3.07
441 442 8.801882 TCCGGTATCTTTCTTTTATTTGTGAT 57.198 30.769 0.00 0.00 0.00 3.06
442 443 8.624367 TTCCGGTATCTTTCTTTTATTTGTGA 57.376 30.769 0.00 0.00 0.00 3.58
443 444 7.484959 GCTTCCGGTATCTTTCTTTTATTTGTG 59.515 37.037 0.00 0.00 0.00 3.33
444 445 7.393515 AGCTTCCGGTATCTTTCTTTTATTTGT 59.606 33.333 0.00 0.00 0.00 2.83
445 446 7.698130 CAGCTTCCGGTATCTTTCTTTTATTTG 59.302 37.037 0.00 0.00 0.00 2.32
446 447 7.610305 TCAGCTTCCGGTATCTTTCTTTTATTT 59.390 33.333 0.00 0.00 0.00 1.40
447 448 7.110155 TCAGCTTCCGGTATCTTTCTTTTATT 58.890 34.615 0.00 0.00 0.00 1.40
448 449 6.650120 TCAGCTTCCGGTATCTTTCTTTTAT 58.350 36.000 0.00 0.00 0.00 1.40
449 450 6.045072 TCAGCTTCCGGTATCTTTCTTTTA 57.955 37.500 0.00 0.00 0.00 1.52
450 451 4.906618 TCAGCTTCCGGTATCTTTCTTTT 58.093 39.130 0.00 0.00 0.00 2.27
451 452 4.553330 TCAGCTTCCGGTATCTTTCTTT 57.447 40.909 0.00 0.00 0.00 2.52
452 453 4.553330 TTCAGCTTCCGGTATCTTTCTT 57.447 40.909 0.00 0.00 0.00 2.52
453 454 4.553330 TTTCAGCTTCCGGTATCTTTCT 57.447 40.909 0.00 0.00 0.00 2.52
454 455 5.819825 AATTTCAGCTTCCGGTATCTTTC 57.180 39.130 0.00 0.00 0.00 2.62
455 456 5.125578 GGAAATTTCAGCTTCCGGTATCTTT 59.874 40.000 19.49 0.00 32.23 2.52
456 457 4.640647 GGAAATTTCAGCTTCCGGTATCTT 59.359 41.667 19.49 0.00 32.23 2.40
457 458 4.200092 GGAAATTTCAGCTTCCGGTATCT 58.800 43.478 19.49 0.00 32.23 1.98
458 459 3.945285 TGGAAATTTCAGCTTCCGGTATC 59.055 43.478 19.49 0.00 43.52 2.24
459 460 3.694566 GTGGAAATTTCAGCTTCCGGTAT 59.305 43.478 19.49 0.00 43.52 2.73
460 461 3.078837 GTGGAAATTTCAGCTTCCGGTA 58.921 45.455 19.49 0.00 43.52 4.02
461 462 1.886542 GTGGAAATTTCAGCTTCCGGT 59.113 47.619 19.49 0.00 43.52 5.28
462 463 1.202348 GGTGGAAATTTCAGCTTCCGG 59.798 52.381 19.49 0.00 43.52 5.14
463 464 1.885887 TGGTGGAAATTTCAGCTTCCG 59.114 47.619 19.49 0.00 43.52 4.30
464 465 3.853475 CATGGTGGAAATTTCAGCTTCC 58.147 45.455 19.49 12.95 41.37 3.46
465 466 3.056322 AGCATGGTGGAAATTTCAGCTTC 60.056 43.478 19.49 2.75 34.15 3.86
466 467 2.901839 AGCATGGTGGAAATTTCAGCTT 59.098 40.909 19.49 10.30 34.15 3.74
467 468 2.532843 AGCATGGTGGAAATTTCAGCT 58.467 42.857 19.49 13.88 34.15 4.24
468 469 2.997986 CAAGCATGGTGGAAATTTCAGC 59.002 45.455 19.49 14.45 0.00 4.26
469 470 2.997986 GCAAGCATGGTGGAAATTTCAG 59.002 45.455 19.49 3.65 0.00 3.02
470 471 2.633967 AGCAAGCATGGTGGAAATTTCA 59.366 40.909 19.49 3.64 35.55 2.69
471 472 3.323751 AGCAAGCATGGTGGAAATTTC 57.676 42.857 9.83 9.83 35.55 2.17
472 473 4.888326 TTAGCAAGCATGGTGGAAATTT 57.112 36.364 2.68 0.00 37.91 1.82
473 474 5.425196 AATTAGCAAGCATGGTGGAAATT 57.575 34.783 2.68 5.46 37.91 1.82
474 475 5.421693 TGTAATTAGCAAGCATGGTGGAAAT 59.578 36.000 2.68 0.00 37.91 2.17
475 476 4.769488 TGTAATTAGCAAGCATGGTGGAAA 59.231 37.500 2.68 0.00 37.91 3.13
476 477 4.157656 GTGTAATTAGCAAGCATGGTGGAA 59.842 41.667 2.68 0.00 37.91 3.53
477 478 3.694072 GTGTAATTAGCAAGCATGGTGGA 59.306 43.478 2.68 0.00 37.91 4.02
478 479 3.696051 AGTGTAATTAGCAAGCATGGTGG 59.304 43.478 3.49 0.00 37.91 4.61
479 480 4.970662 AGTGTAATTAGCAAGCATGGTG 57.029 40.909 3.49 0.00 37.91 4.17
480 481 5.982890 AAAGTGTAATTAGCAAGCATGGT 57.017 34.783 0.00 0.00 41.03 3.55
481 482 7.489113 CCTTAAAAGTGTAATTAGCAAGCATGG 59.511 37.037 0.00 0.00 0.00 3.66
482 483 7.489113 CCCTTAAAAGTGTAATTAGCAAGCATG 59.511 37.037 0.00 0.00 0.00 4.06
483 484 7.178451 ACCCTTAAAAGTGTAATTAGCAAGCAT 59.822 33.333 0.00 0.00 0.00 3.79
484 485 6.492087 ACCCTTAAAAGTGTAATTAGCAAGCA 59.508 34.615 0.00 0.00 0.00 3.91
485 486 6.806739 CACCCTTAAAAGTGTAATTAGCAAGC 59.193 38.462 0.00 0.00 0.00 4.01
486 487 7.175990 TCCACCCTTAAAAGTGTAATTAGCAAG 59.824 37.037 4.37 0.00 31.88 4.01
487 488 7.005296 TCCACCCTTAAAAGTGTAATTAGCAA 58.995 34.615 4.37 0.00 31.88 3.91
488 489 6.544650 TCCACCCTTAAAAGTGTAATTAGCA 58.455 36.000 4.37 0.00 31.88 3.49
489 490 7.457024 TTCCACCCTTAAAAGTGTAATTAGC 57.543 36.000 4.37 0.00 31.88 3.09
491 492 9.465199 GGTATTCCACCCTTAAAAGTGTAATTA 57.535 33.333 2.12 0.00 42.07 1.40
492 493 8.357290 GGTATTCCACCCTTAAAAGTGTAATT 57.643 34.615 2.12 0.00 42.07 1.40
493 494 7.949690 GGTATTCCACCCTTAAAAGTGTAAT 57.050 36.000 4.37 3.30 42.07 1.89
507 508 4.830600 TCCAAGTTTCTTTGGTATTCCACC 59.169 41.667 4.84 0.00 46.23 4.61
508 509 5.768164 TCTCCAAGTTTCTTTGGTATTCCAC 59.232 40.000 4.84 0.00 46.23 4.02
509 510 5.947663 TCTCCAAGTTTCTTTGGTATTCCA 58.052 37.500 4.84 0.00 46.23 3.53
510 511 6.095580 GGATCTCCAAGTTTCTTTGGTATTCC 59.904 42.308 4.84 6.00 46.23 3.01
511 512 6.183360 CGGATCTCCAAGTTTCTTTGGTATTC 60.183 42.308 4.84 1.49 46.23 1.75
512 513 5.648092 CGGATCTCCAAGTTTCTTTGGTATT 59.352 40.000 4.84 0.00 46.23 1.89
513 514 5.186198 CGGATCTCCAAGTTTCTTTGGTAT 58.814 41.667 4.84 1.13 46.23 2.73
514 515 4.564821 CCGGATCTCCAAGTTTCTTTGGTA 60.565 45.833 0.00 0.00 46.23 3.25
515 516 3.412386 CGGATCTCCAAGTTTCTTTGGT 58.588 45.455 4.84 0.00 46.23 3.67
517 518 2.749621 CCCGGATCTCCAAGTTTCTTTG 59.250 50.000 0.73 0.00 35.14 2.77
518 519 2.375509 ACCCGGATCTCCAAGTTTCTTT 59.624 45.455 0.73 0.00 35.14 2.52
519 520 1.985895 ACCCGGATCTCCAAGTTTCTT 59.014 47.619 0.73 0.00 35.14 2.52
520 521 1.279271 CACCCGGATCTCCAAGTTTCT 59.721 52.381 0.73 0.00 35.14 2.52
521 522 1.003233 ACACCCGGATCTCCAAGTTTC 59.997 52.381 0.73 0.00 35.14 2.78
522 523 1.003233 GACACCCGGATCTCCAAGTTT 59.997 52.381 0.73 0.00 35.14 2.66
523 524 0.613777 GACACCCGGATCTCCAAGTT 59.386 55.000 0.73 0.00 35.14 2.66
524 525 1.265454 GGACACCCGGATCTCCAAGT 61.265 60.000 0.73 0.00 35.14 3.16
525 526 1.522569 GGACACCCGGATCTCCAAG 59.477 63.158 0.73 0.00 35.14 3.61
526 527 1.993391 GGGACACCCGGATCTCCAA 60.993 63.158 0.73 0.00 32.13 3.53
527 528 2.365105 GGGACACCCGGATCTCCA 60.365 66.667 0.73 0.00 32.13 3.86
536 537 2.748465 GCATGGTATAGTTGGGACACCC 60.748 54.545 0.00 0.00 45.71 4.61
537 538 2.172717 AGCATGGTATAGTTGGGACACC 59.827 50.000 0.00 0.00 39.29 4.16
538 539 3.467803 GAGCATGGTATAGTTGGGACAC 58.532 50.000 0.00 0.00 39.29 3.67
539 540 2.438021 GGAGCATGGTATAGTTGGGACA 59.562 50.000 0.00 0.00 0.00 4.02
540 541 2.438021 TGGAGCATGGTATAGTTGGGAC 59.562 50.000 0.00 0.00 0.00 4.46
541 542 2.770447 TGGAGCATGGTATAGTTGGGA 58.230 47.619 0.00 0.00 0.00 4.37
542 543 3.795688 ATGGAGCATGGTATAGTTGGG 57.204 47.619 0.00 0.00 0.00 4.12
543 544 7.581213 TTTTAATGGAGCATGGTATAGTTGG 57.419 36.000 0.00 0.00 0.00 3.77
565 566 9.899661 GGCAAAAGGATAATTAACCCTATTTTT 57.100 29.630 8.09 6.04 0.00 1.94
909 913 4.148825 CAGCTAGCTTCCCGCCGT 62.149 66.667 16.46 0.00 40.39 5.68
1190 1195 0.249120 TGCTCAAACATCCCGACGAT 59.751 50.000 0.00 0.00 0.00 3.73
1360 1365 1.139654 CGCCATCCATCTCTTCTTCCA 59.860 52.381 0.00 0.00 0.00 3.53
2122 2438 4.821260 GTGCATTTTCCACCCTTCATTTTT 59.179 37.500 0.00 0.00 0.00 1.94
2293 2611 7.572353 GCAAACATTCACGGTCTCACTATTTTA 60.572 37.037 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.