Multiple sequence alignment - TraesCS4B01G288000

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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 TraesCS4B01G288000 chr4B 100.000 2462 0 0 1 2462 573090561 573093022 0.000000e+00 4547.0
1 TraesCS4B01G288000 chr4B 93.772 289 17 1 93 381 114866986 114867273 1.350000e-117 433.0
2 TraesCS4B01G288000 chr4B 93.772 289 17 1 93 381 130977034 130977321 1.350000e-117 433.0
3 TraesCS4B01G288000 chr4A 92.402 1803 77 27 382 2149 10165686 10163909 0.000000e+00 2516.0
4 TraesCS4B01G288000 chr4A 85.124 121 7 5 1 111 10165801 10165682 2.000000e-21 113.0
5 TraesCS4B01G288000 chr4D 91.272 1478 56 31 644 2063 458993339 458994801 0.000000e+00 1947.0
6 TraesCS4B01G288000 chr4D 92.763 304 14 5 2059 2360 458995081 458995378 1.350000e-117 433.0
7 TraesCS4B01G288000 chr4D 93.162 117 8 0 2346 2462 458995393 458995509 3.260000e-39 172.0
8 TraesCS4B01G288000 chr4D 80.992 121 12 5 1 111 458992654 458992773 4.360000e-13 86.1
9 TraesCS4B01G288000 chr2B 95.357 280 13 0 102 381 511849944 511849665 1.740000e-121 446.0
10 TraesCS4B01G288000 chr2B 94.718 284 14 1 102 384 417420607 417420890 8.080000e-120 440.0
11 TraesCS4B01G288000 chr2B 88.406 69 8 0 1 69 9142087 9142019 1.570000e-12 84.2
12 TraesCS4B01G288000 chr7B 95.000 280 14 0 102 381 426204185 426203906 8.080000e-120 440.0
13 TraesCS4B01G288000 chr5B 95.000 280 14 0 102 381 269926144 269926423 8.080000e-120 440.0
14 TraesCS4B01G288000 chr5B 97.059 34 1 0 71 104 246149954 246149987 9.510000e-05 58.4
15 TraesCS4B01G288000 chr3B 95.000 280 14 0 102 381 667303417 667303138 8.080000e-120 440.0
16 TraesCS4B01G288000 chr3B 93.493 292 18 1 90 381 6690808 6691098 1.350000e-117 433.0
17 TraesCS4B01G288000 chr3B 93.772 289 17 1 93 381 7782669 7782382 1.350000e-117 433.0
18 TraesCS4B01G288000 chr2D 82.456 114 8 3 1 103 561212856 561212744 3.370000e-14 89.8


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 TraesCS4B01G288000 chr4B 573090561 573093022 2461 False 4547.000 4547 100.00000 1 2462 1 chr4B.!!$F3 2461
1 TraesCS4B01G288000 chr4A 10163909 10165801 1892 True 1314.500 2516 88.76300 1 2149 2 chr4A.!!$R1 2148
2 TraesCS4B01G288000 chr4D 458992654 458995509 2855 False 659.525 1947 89.54725 1 2462 4 chr4D.!!$F1 2461

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
547 561 0.038251 TTACTCTGGCTGACTGCACG 60.038 55.0 6.65 0.0 45.15 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 3117 0.254178 ACGGATCTCATGCTTTGGCT 59.746 50.0 0.0 0.0 39.59 4.75 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
29 30 5.595952 GCCTCCTTGGTGAATGAAATAAGAT 59.404 40.000 0.00 0.00 38.35 2.40
41 42 8.190122 TGAATGAAATAAGATTGCTATTGCGTT 58.810 29.630 0.00 0.00 43.34 4.84
59 60 5.216648 TGCGTTTTAGGCAAACTTGTATTC 58.783 37.500 0.00 0.00 42.51 1.75
64 65 7.574967 CGTTTTAGGCAAACTTGTATTCCTCAT 60.575 37.037 0.00 0.00 42.51 2.90
77 88 8.877864 TTGTATTCCTCATGTTTGAATAAGGT 57.122 30.769 12.54 0.00 33.94 3.50
83 94 7.685481 TCCTCATGTTTGAATAAGGTTAGTGA 58.315 34.615 0.00 0.00 0.00 3.41
101 112 8.766151 GGTTAGTGATAGTTTAGCTAGATTTGC 58.234 37.037 0.00 0.00 32.45 3.68
102 113 9.535878 GTTAGTGATAGTTTAGCTAGATTTGCT 57.464 33.333 0.00 0.00 43.79 3.91
120 131 3.268023 GCTAAGAGTAGCCACAATGGT 57.732 47.619 0.00 0.00 46.10 3.55
121 132 2.939103 GCTAAGAGTAGCCACAATGGTG 59.061 50.000 0.00 0.00 46.10 4.17
122 133 3.369471 GCTAAGAGTAGCCACAATGGTGA 60.369 47.826 0.30 0.00 46.10 4.02
123 134 5.213045 GCTAAGAGTAGCCACAATGGTGAG 61.213 50.000 0.30 0.00 46.10 3.51
124 135 7.591391 GCTAAGAGTAGCCACAATGGTGAGT 62.591 48.000 0.30 0.00 46.10 3.41
125 136 8.299409 GCTAAGAGTAGCCACAATGGTGAGTA 62.299 46.154 0.30 0.00 46.10 2.59
126 137 9.669065 GCTAAGAGTAGCCACAATGGTGAGTAA 62.669 44.444 0.30 0.00 46.10 2.24
163 174 7.689446 ACATACACATATCGCTAGACTATGT 57.311 36.000 0.00 0.29 34.50 2.29
164 175 8.112016 ACATACACATATCGCTAGACTATGTT 57.888 34.615 0.00 0.00 33.24 2.71
165 176 9.227777 ACATACACATATCGCTAGACTATGTTA 57.772 33.333 0.00 0.74 33.24 2.41
166 177 9.491934 CATACACATATCGCTAGACTATGTTAC 57.508 37.037 0.00 0.00 33.24 2.50
167 178 7.747155 ACACATATCGCTAGACTATGTTACT 57.253 36.000 0.00 0.00 33.24 2.24
168 179 7.585867 ACACATATCGCTAGACTATGTTACTG 58.414 38.462 0.00 0.00 33.24 2.74
169 180 6.524933 CACATATCGCTAGACTATGTTACTGC 59.475 42.308 0.00 0.00 33.24 4.40
170 181 3.984508 TCGCTAGACTATGTTACTGCC 57.015 47.619 0.00 0.00 0.00 4.85
171 182 3.552875 TCGCTAGACTATGTTACTGCCT 58.447 45.455 0.00 0.00 0.00 4.75
172 183 3.952323 TCGCTAGACTATGTTACTGCCTT 59.048 43.478 0.00 0.00 0.00 4.35
173 184 4.036498 TCGCTAGACTATGTTACTGCCTTC 59.964 45.833 0.00 0.00 0.00 3.46
174 185 4.202020 CGCTAGACTATGTTACTGCCTTCA 60.202 45.833 0.00 0.00 0.00 3.02
175 186 5.508153 CGCTAGACTATGTTACTGCCTTCAT 60.508 44.000 0.00 0.00 0.00 2.57
176 187 6.294010 CGCTAGACTATGTTACTGCCTTCATA 60.294 42.308 0.00 0.00 0.00 2.15
177 188 7.087639 GCTAGACTATGTTACTGCCTTCATAG 58.912 42.308 0.00 8.77 42.80 2.23
179 190 6.810911 AGACTATGTTACTGCCTTCATAGTG 58.189 40.000 17.43 0.00 46.89 2.74
180 191 5.918608 ACTATGTTACTGCCTTCATAGTGG 58.081 41.667 13.45 0.00 45.91 4.00
181 192 3.627395 TGTTACTGCCTTCATAGTGGG 57.373 47.619 0.00 0.00 0.00 4.61
182 193 2.910319 TGTTACTGCCTTCATAGTGGGT 59.090 45.455 0.00 0.00 0.00 4.51
183 194 4.098155 TGTTACTGCCTTCATAGTGGGTA 58.902 43.478 0.00 0.00 0.00 3.69
184 195 4.161565 TGTTACTGCCTTCATAGTGGGTAG 59.838 45.833 0.00 0.00 38.50 3.18
185 196 2.834113 ACTGCCTTCATAGTGGGTAGT 58.166 47.619 0.00 0.00 40.31 2.73
186 197 3.990369 ACTGCCTTCATAGTGGGTAGTA 58.010 45.455 0.00 0.00 42.55 1.82
187 198 4.359105 ACTGCCTTCATAGTGGGTAGTAA 58.641 43.478 0.00 0.00 42.55 2.24
188 199 4.161754 ACTGCCTTCATAGTGGGTAGTAAC 59.838 45.833 0.00 0.00 42.55 2.50
189 200 4.098155 TGCCTTCATAGTGGGTAGTAACA 58.902 43.478 0.00 0.00 0.00 2.41
190 201 4.719773 TGCCTTCATAGTGGGTAGTAACAT 59.280 41.667 0.00 0.00 0.00 2.71
191 202 5.900699 TGCCTTCATAGTGGGTAGTAACATA 59.099 40.000 0.00 0.00 0.00 2.29
192 203 6.384595 TGCCTTCATAGTGGGTAGTAACATAA 59.615 38.462 0.00 0.00 0.00 1.90
193 204 7.092802 TGCCTTCATAGTGGGTAGTAACATAAA 60.093 37.037 0.00 0.00 0.00 1.40
194 205 7.937394 GCCTTCATAGTGGGTAGTAACATAAAT 59.063 37.037 0.00 0.00 0.00 1.40
195 206 9.273016 CCTTCATAGTGGGTAGTAACATAAATG 57.727 37.037 0.00 0.00 0.00 2.32
196 207 9.832445 CTTCATAGTGGGTAGTAACATAAATGT 57.168 33.333 0.00 0.00 44.20 2.71
197 208 9.607988 TTCATAGTGGGTAGTAACATAAATGTG 57.392 33.333 0.00 0.00 41.61 3.21
198 209 8.208224 TCATAGTGGGTAGTAACATAAATGTGG 58.792 37.037 0.00 0.00 41.61 4.17
199 210 6.382919 AGTGGGTAGTAACATAAATGTGGT 57.617 37.500 0.00 0.00 41.61 4.16
200 211 7.499200 AGTGGGTAGTAACATAAATGTGGTA 57.501 36.000 0.00 0.00 41.61 3.25
201 212 7.920227 AGTGGGTAGTAACATAAATGTGGTAA 58.080 34.615 0.00 0.00 41.61 2.85
202 213 7.825761 AGTGGGTAGTAACATAAATGTGGTAAC 59.174 37.037 0.00 0.00 41.61 2.50
246 257 9.725019 TTAGGTTATAGACTCATATTGCATTGG 57.275 33.333 0.00 0.00 0.00 3.16
247 258 7.170965 AGGTTATAGACTCATATTGCATTGGG 58.829 38.462 0.00 0.00 0.00 4.12
248 259 7.017551 AGGTTATAGACTCATATTGCATTGGGA 59.982 37.037 0.00 0.00 0.00 4.37
249 260 7.119846 GGTTATAGACTCATATTGCATTGGGAC 59.880 40.741 0.00 0.00 0.00 4.46
250 261 4.508551 AGACTCATATTGCATTGGGACA 57.491 40.909 0.00 0.00 0.00 4.02
251 262 5.057843 AGACTCATATTGCATTGGGACAT 57.942 39.130 0.00 0.00 39.30 3.06
252 263 4.825634 AGACTCATATTGCATTGGGACATG 59.174 41.667 0.00 0.00 39.30 3.21
253 264 4.539726 ACTCATATTGCATTGGGACATGT 58.460 39.130 0.00 0.00 39.30 3.21
254 265 4.340097 ACTCATATTGCATTGGGACATGTG 59.660 41.667 1.15 0.00 39.30 3.21
255 266 4.534797 TCATATTGCATTGGGACATGTGA 58.465 39.130 1.15 0.00 39.30 3.58
256 267 5.141910 TCATATTGCATTGGGACATGTGAT 58.858 37.500 1.15 0.00 39.30 3.06
257 268 3.812156 ATTGCATTGGGACATGTGATG 57.188 42.857 1.15 3.48 39.30 3.07
259 270 2.527497 TGCATTGGGACATGTGATGTT 58.473 42.857 1.15 0.00 45.03 2.71
260 271 3.694926 TGCATTGGGACATGTGATGTTA 58.305 40.909 1.15 0.00 45.03 2.41
261 272 3.443329 TGCATTGGGACATGTGATGTTAC 59.557 43.478 1.15 0.00 45.03 2.50
262 273 3.443329 GCATTGGGACATGTGATGTTACA 59.557 43.478 1.15 0.00 45.03 2.41
263 274 4.439153 GCATTGGGACATGTGATGTTACAG 60.439 45.833 1.15 0.00 45.03 2.74
264 275 4.365514 TTGGGACATGTGATGTTACAGT 57.634 40.909 1.15 0.00 45.03 3.55
265 276 5.491323 TTGGGACATGTGATGTTACAGTA 57.509 39.130 1.15 0.00 45.03 2.74
266 277 5.491323 TGGGACATGTGATGTTACAGTAA 57.509 39.130 1.15 0.00 45.03 2.24
267 278 5.242434 TGGGACATGTGATGTTACAGTAAC 58.758 41.667 15.58 15.58 45.03 2.50
268 279 5.012664 TGGGACATGTGATGTTACAGTAACT 59.987 40.000 21.56 9.41 45.03 2.24
269 280 6.211785 TGGGACATGTGATGTTACAGTAACTA 59.788 38.462 21.56 10.50 45.03 2.24
270 281 6.757010 GGGACATGTGATGTTACAGTAACTAG 59.243 42.308 21.56 8.25 45.03 2.57
271 282 6.255887 GGACATGTGATGTTACAGTAACTAGC 59.744 42.308 21.56 12.59 45.03 3.42
272 283 6.936279 ACATGTGATGTTACAGTAACTAGCT 58.064 36.000 21.56 6.57 41.63 3.32
273 284 8.063200 ACATGTGATGTTACAGTAACTAGCTA 57.937 34.615 21.56 4.25 41.63 3.32
274 285 8.528643 ACATGTGATGTTACAGTAACTAGCTAA 58.471 33.333 21.56 3.59 41.63 3.09
275 286 9.025020 CATGTGATGTTACAGTAACTAGCTAAG 57.975 37.037 21.56 6.36 39.38 2.18
276 287 8.118976 TGTGATGTTACAGTAACTAGCTAAGT 57.881 34.615 21.56 0.00 41.49 2.24
295 306 9.783081 AGCTAAGTTACTATAACTACCTCTCTC 57.217 37.037 1.79 0.00 0.00 3.20
296 307 9.002600 GCTAAGTTACTATAACTACCTCTCTCC 57.997 40.741 1.79 0.00 0.00 3.71
299 310 8.334522 AGTTACTATAACTACCTCTCTCCTCA 57.665 38.462 0.00 0.00 0.00 3.86
300 311 8.951541 AGTTACTATAACTACCTCTCTCCTCAT 58.048 37.037 0.00 0.00 0.00 2.90
301 312 9.577222 GTTACTATAACTACCTCTCTCCTCATT 57.423 37.037 0.00 0.00 0.00 2.57
304 315 9.577222 ACTATAACTACCTCTCTCCTCATTAAC 57.423 37.037 0.00 0.00 0.00 2.01
305 316 9.802039 CTATAACTACCTCTCTCCTCATTAACT 57.198 37.037 0.00 0.00 0.00 2.24
306 317 8.700439 ATAACTACCTCTCTCCTCATTAACTC 57.300 38.462 0.00 0.00 0.00 3.01
307 318 6.080969 ACTACCTCTCTCCTCATTAACTCA 57.919 41.667 0.00 0.00 0.00 3.41
308 319 5.889289 ACTACCTCTCTCCTCATTAACTCAC 59.111 44.000 0.00 0.00 0.00 3.51
309 320 4.941713 ACCTCTCTCCTCATTAACTCACT 58.058 43.478 0.00 0.00 0.00 3.41
310 321 4.709397 ACCTCTCTCCTCATTAACTCACTG 59.291 45.833 0.00 0.00 0.00 3.66
311 322 4.441356 CCTCTCTCCTCATTAACTCACTGC 60.441 50.000 0.00 0.00 0.00 4.40
312 323 3.449018 TCTCTCCTCATTAACTCACTGCC 59.551 47.826 0.00 0.00 0.00 4.85
313 324 3.173151 TCTCCTCATTAACTCACTGCCA 58.827 45.455 0.00 0.00 0.00 4.92
314 325 3.055819 TCTCCTCATTAACTCACTGCCAC 60.056 47.826 0.00 0.00 0.00 5.01
315 326 2.637382 TCCTCATTAACTCACTGCCACA 59.363 45.455 0.00 0.00 0.00 4.17
316 327 3.264193 TCCTCATTAACTCACTGCCACAT 59.736 43.478 0.00 0.00 0.00 3.21
317 328 4.469586 TCCTCATTAACTCACTGCCACATA 59.530 41.667 0.00 0.00 0.00 2.29
318 329 5.045942 TCCTCATTAACTCACTGCCACATAA 60.046 40.000 0.00 0.00 0.00 1.90
319 330 5.647658 CCTCATTAACTCACTGCCACATAAA 59.352 40.000 0.00 0.00 0.00 1.40
320 331 6.403636 CCTCATTAACTCACTGCCACATAAAC 60.404 42.308 0.00 0.00 0.00 2.01
321 332 6.000840 TCATTAACTCACTGCCACATAAACA 58.999 36.000 0.00 0.00 0.00 2.83
322 333 6.488344 TCATTAACTCACTGCCACATAAACAA 59.512 34.615 0.00 0.00 0.00 2.83
323 334 6.701145 TTAACTCACTGCCACATAAACAAA 57.299 33.333 0.00 0.00 0.00 2.83
324 335 5.789643 AACTCACTGCCACATAAACAAAT 57.210 34.783 0.00 0.00 0.00 2.32
325 336 5.789643 ACTCACTGCCACATAAACAAATT 57.210 34.783 0.00 0.00 0.00 1.82
326 337 6.160576 ACTCACTGCCACATAAACAAATTT 57.839 33.333 0.00 0.00 0.00 1.82
327 338 7.283625 ACTCACTGCCACATAAACAAATTTA 57.716 32.000 0.00 0.00 34.78 1.40
328 339 7.145323 ACTCACTGCCACATAAACAAATTTAC 58.855 34.615 0.00 0.00 33.09 2.01
329 340 7.014230 ACTCACTGCCACATAAACAAATTTACT 59.986 33.333 0.00 0.00 33.09 2.24
330 341 7.144661 TCACTGCCACATAAACAAATTTACTG 58.855 34.615 0.00 0.00 33.09 2.74
331 342 7.013750 TCACTGCCACATAAACAAATTTACTGA 59.986 33.333 0.00 0.00 33.09 3.41
332 343 7.326789 CACTGCCACATAAACAAATTTACTGAG 59.673 37.037 0.00 0.00 33.09 3.35
333 344 7.014230 ACTGCCACATAAACAAATTTACTGAGT 59.986 33.333 0.00 0.00 33.09 3.41
334 345 7.721402 TGCCACATAAACAAATTTACTGAGTT 58.279 30.769 0.00 0.00 33.09 3.01
335 346 7.651304 TGCCACATAAACAAATTTACTGAGTTG 59.349 33.333 0.00 0.00 33.09 3.16
336 347 7.116233 GCCACATAAACAAATTTACTGAGTTGG 59.884 37.037 0.00 0.00 33.09 3.77
337 348 8.356657 CCACATAAACAAATTTACTGAGTTGGA 58.643 33.333 0.00 0.00 33.09 3.53
338 349 9.180678 CACATAAACAAATTTACTGAGTTGGAC 57.819 33.333 0.00 0.00 33.09 4.02
339 350 9.131791 ACATAAACAAATTTACTGAGTTGGACT 57.868 29.630 0.00 0.00 33.09 3.85
340 351 9.612620 CATAAACAAATTTACTGAGTTGGACTC 57.387 33.333 0.00 1.21 38.11 3.36
341 352 8.504005 ATAAACAAATTTACTGAGTTGGACTCG 58.496 33.333 0.00 2.09 39.27 4.18
351 362 2.924290 GAGTTGGACTCGATGTTACTGC 59.076 50.000 0.00 0.00 35.28 4.40
352 363 2.563179 AGTTGGACTCGATGTTACTGCT 59.437 45.455 0.00 0.00 0.00 4.24
353 364 2.654749 TGGACTCGATGTTACTGCTG 57.345 50.000 0.00 0.00 0.00 4.41
354 365 2.167662 TGGACTCGATGTTACTGCTGA 58.832 47.619 0.00 0.00 0.00 4.26
355 366 2.560981 TGGACTCGATGTTACTGCTGAA 59.439 45.455 0.00 0.00 0.00 3.02
356 367 3.182967 GGACTCGATGTTACTGCTGAAG 58.817 50.000 0.00 0.00 0.00 3.02
357 368 3.367498 GGACTCGATGTTACTGCTGAAGT 60.367 47.826 0.00 0.00 43.40 3.01
358 369 4.238514 GACTCGATGTTACTGCTGAAGTT 58.761 43.478 0.00 0.00 40.56 2.66
359 370 5.386958 ACTCGATGTTACTGCTGAAGTTA 57.613 39.130 0.00 0.00 40.56 2.24
360 371 5.162075 ACTCGATGTTACTGCTGAAGTTAC 58.838 41.667 0.00 0.00 40.56 2.50
361 372 5.047943 ACTCGATGTTACTGCTGAAGTTACT 60.048 40.000 6.50 0.00 38.87 2.24
362 373 5.399858 TCGATGTTACTGCTGAAGTTACTC 58.600 41.667 6.50 1.79 38.87 2.59
363 374 4.563184 CGATGTTACTGCTGAAGTTACTCC 59.437 45.833 6.50 0.00 38.87 3.85
364 375 4.267349 TGTTACTGCTGAAGTTACTCCC 57.733 45.455 6.50 0.00 38.87 4.30
365 376 3.644265 TGTTACTGCTGAAGTTACTCCCA 59.356 43.478 6.50 0.00 38.87 4.37
366 377 2.841442 ACTGCTGAAGTTACTCCCAC 57.159 50.000 0.00 0.00 34.57 4.61
367 378 2.330216 ACTGCTGAAGTTACTCCCACT 58.670 47.619 0.00 0.00 34.57 4.00
368 379 2.037772 ACTGCTGAAGTTACTCCCACTG 59.962 50.000 0.00 0.00 34.57 3.66
369 380 2.037772 CTGCTGAAGTTACTCCCACTGT 59.962 50.000 0.00 0.00 0.00 3.55
370 381 2.224281 TGCTGAAGTTACTCCCACTGTG 60.224 50.000 0.00 0.00 0.00 3.66
371 382 2.037251 GCTGAAGTTACTCCCACTGTGA 59.963 50.000 9.86 0.00 0.00 3.58
372 383 3.654414 CTGAAGTTACTCCCACTGTGAC 58.346 50.000 9.86 0.00 0.00 3.67
373 384 3.305720 TGAAGTTACTCCCACTGTGACT 58.694 45.455 9.86 0.30 36.11 3.41
374 385 4.476297 TGAAGTTACTCCCACTGTGACTA 58.524 43.478 9.86 0.00 33.98 2.59
375 386 4.523173 TGAAGTTACTCCCACTGTGACTAG 59.477 45.833 9.86 5.97 33.98 2.57
376 387 4.115398 AGTTACTCCCACTGTGACTAGT 57.885 45.455 9.86 11.33 33.46 2.57
377 388 4.080687 AGTTACTCCCACTGTGACTAGTC 58.919 47.826 16.32 16.32 33.46 2.59
380 391 4.383931 ACTCCCACTGTGACTAGTCTAA 57.616 45.455 23.01 10.61 0.00 2.10
390 401 6.151480 ACTGTGACTAGTCTAAAGTAGAAGGC 59.849 42.308 23.01 0.00 36.40 4.35
407 418 1.485066 AGGCCGGACTATAACTTGGTG 59.515 52.381 9.02 0.00 0.00 4.17
423 434 2.037367 TGAGGGTCCGGTCCTGAG 59.963 66.667 20.64 0.00 34.21 3.35
442 453 4.541705 TGAGGAAGTTTTGGGAATTGTCA 58.458 39.130 0.00 0.00 0.00 3.58
443 454 4.340950 TGAGGAAGTTTTGGGAATTGTCAC 59.659 41.667 0.00 0.00 0.00 3.67
445 456 5.701224 AGGAAGTTTTGGGAATTGTCACTA 58.299 37.500 0.00 0.00 0.00 2.74
473 487 7.041848 TGACTGTAAAGACATTGTGATTGAGTG 60.042 37.037 0.00 0.00 34.24 3.51
489 503 9.593134 GTGATTGAGTGATACAAGTATTTCTCT 57.407 33.333 17.61 6.30 32.38 3.10
492 506 8.988064 TTGAGTGATACAAGTATTTCTCTCAC 57.012 34.615 17.61 11.33 32.38 3.51
494 508 8.029522 TGAGTGATACAAGTATTTCTCTCACAC 58.970 37.037 17.61 10.70 32.38 3.82
496 510 7.815068 AGTGATACAAGTATTTCTCTCACACAC 59.185 37.037 10.32 0.00 0.00 3.82
544 558 4.260948 GCAATATTTACTCTGGCTGACTGC 60.261 45.833 0.00 0.00 41.94 4.40
545 559 4.760530 ATATTTACTCTGGCTGACTGCA 57.239 40.909 6.65 0.00 45.15 4.41
546 560 2.169832 TTTACTCTGGCTGACTGCAC 57.830 50.000 6.65 0.00 45.15 4.57
547 561 0.038251 TTACTCTGGCTGACTGCACG 60.038 55.000 6.65 0.00 45.15 5.34
548 562 2.492449 TACTCTGGCTGACTGCACGC 62.492 60.000 6.65 0.00 45.15 5.34
588 603 1.701847 ACAGAGGACAGTGGAGCAATT 59.298 47.619 0.00 0.00 0.00 2.32
667 998 1.839994 TCATCATTCTGGGTCCTCCAC 59.160 52.381 0.00 0.00 41.46 4.02
773 1105 0.578683 CGCCATCAATGTGCTAGACG 59.421 55.000 0.00 0.00 0.00 4.18
776 1108 2.478134 GCCATCAATGTGCTAGACGATC 59.522 50.000 0.00 0.00 0.00 3.69
777 1109 3.801638 GCCATCAATGTGCTAGACGATCT 60.802 47.826 0.00 0.00 0.00 2.75
778 1110 3.986572 CCATCAATGTGCTAGACGATCTC 59.013 47.826 0.00 0.00 0.00 2.75
996 1340 3.137459 CGGCCGCAGAGAGAGAGT 61.137 66.667 14.67 0.00 0.00 3.24
1153 1500 1.343142 TCTCCTGCGAGTTGCTTGTTA 59.657 47.619 3.50 0.00 46.63 2.41
1344 1695 2.209064 TACTGAAGGAGACGTGCGGC 62.209 60.000 0.00 0.00 0.00 6.53
1395 1746 2.378038 GATCTGTCTGACAGGCTCTCT 58.622 52.381 31.26 13.48 45.94 3.10
1421 1772 0.811915 ATGTCGACCTTGGACGAGAG 59.188 55.000 14.12 0.00 39.16 3.20
1479 1830 2.170012 AGCCGGACTTTATCCTACCA 57.830 50.000 5.05 0.00 46.69 3.25
1480 1831 1.761198 AGCCGGACTTTATCCTACCAC 59.239 52.381 5.05 0.00 46.69 4.16
1527 1882 8.723942 ATATATTAGCTTCAATTCATCGACCC 57.276 34.615 0.00 0.00 0.00 4.46
1816 2218 1.740718 GCTGTTGTAGGCCTGTAGCTC 60.741 57.143 17.99 1.44 43.05 4.09
1901 2309 6.739331 ACTATCTATTGCTAGCTTTGTCCT 57.261 37.500 17.23 0.00 0.00 3.85
1964 2376 5.048507 ACTACGGAGAACTGTCTGTTTTTC 58.951 41.667 0.00 0.00 39.30 2.29
2010 2422 6.257411 CCATGTCTTCTCTGCATAACTTACTG 59.743 42.308 0.00 0.00 0.00 2.74
2013 2425 6.152831 TGTCTTCTCTGCATAACTTACTGCTA 59.847 38.462 0.00 0.00 39.16 3.49
2018 2430 6.829298 TCTCTGCATAACTTACTGCTACTACT 59.171 38.462 0.00 0.00 39.16 2.57
2045 2457 3.252458 ACGGTCAAGTTATTTGGAGCAAC 59.748 43.478 0.00 0.00 37.39 4.17
2051 2463 5.368005 CAAGTTATTTGGAGCAACGTGCAG 61.368 45.833 11.58 0.00 38.31 4.41
2123 2820 2.875633 CGCATGTAACGTCGAAATAGC 58.124 47.619 0.00 0.00 0.00 2.97
2144 2841 5.307204 AGCCGGTGTACTTGTAAATGTAAA 58.693 37.500 1.90 0.00 0.00 2.01
2178 2875 0.179100 ATGAGCGAGACGTTCCATGG 60.179 55.000 4.97 4.97 36.32 3.66
2188 2885 2.028130 ACGTTCCATGGTGCAAAAGAA 58.972 42.857 12.58 0.00 0.00 2.52
2239 2936 0.468214 TCTCGAGTGATAGGCCCCAG 60.468 60.000 13.13 0.00 0.00 4.45
2243 2940 0.470341 GAGTGATAGGCCCCAGGAAC 59.530 60.000 0.00 0.00 0.00 3.62
2246 2943 0.988145 TGATAGGCCCCAGGAACAGG 60.988 60.000 0.00 0.00 33.40 4.00
2283 2980 0.890683 GTGAACTTGGCCCCATGAAG 59.109 55.000 0.00 0.00 0.00 3.02
2298 2995 3.300009 CATGAAGTGTCAACTTTTCGCC 58.700 45.455 0.00 0.00 46.84 5.54
2299 2996 2.639065 TGAAGTGTCAACTTTTCGCCT 58.361 42.857 0.00 0.00 46.84 5.52
2343 3040 1.153429 CGTCGGATCCCTCCAAACC 60.153 63.158 6.06 0.00 42.19 3.27
2345 3042 0.326927 GTCGGATCCCTCCAAACCAA 59.673 55.000 6.06 0.00 42.19 3.67
2346 3043 0.326927 TCGGATCCCTCCAAACCAAC 59.673 55.000 6.06 0.00 42.19 3.77
2347 3044 0.328258 CGGATCCCTCCAAACCAACT 59.672 55.000 6.06 0.00 42.19 3.16
2367 3091 0.101399 AGTCGATCGACATGGCAGTC 59.899 55.000 40.51 17.82 46.76 3.51
2369 3093 1.946156 CGATCGACATGGCAGTCCG 60.946 63.158 10.26 5.46 35.07 4.79
2370 3094 2.202932 ATCGACATGGCAGTCCGC 60.203 61.111 0.00 0.00 41.28 5.54
2372 3096 4.794439 CGACATGGCAGTCCGCGA 62.794 66.667 8.23 0.00 43.84 5.87
2393 3117 2.755876 AGAGCCGTCCGATCAGCA 60.756 61.111 0.00 0.00 0.00 4.41
2427 3151 5.243060 TGAGATCCGTAGTGTTTTCTTCTGA 59.757 40.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.924918 TTGCCTAAAACGCAATAGCAA 57.075 38.095 0.00 0.00 41.17 3.91
41 42 6.719370 ACATGAGGAATACAAGTTTGCCTAAA 59.281 34.615 0.00 0.00 0.00 1.85
59 60 7.921786 TCACTAACCTTATTCAAACATGAGG 57.078 36.000 0.00 0.00 36.25 3.86
101 112 4.081420 ACTCACCATTGTGGCTACTCTTAG 60.081 45.833 0.64 0.00 42.67 2.18
102 113 3.838317 ACTCACCATTGTGGCTACTCTTA 59.162 43.478 0.64 0.00 42.67 2.10
103 114 2.639839 ACTCACCATTGTGGCTACTCTT 59.360 45.455 0.64 0.00 42.67 2.85
104 115 2.260822 ACTCACCATTGTGGCTACTCT 58.739 47.619 0.64 0.00 42.67 3.24
105 116 2.770164 ACTCACCATTGTGGCTACTC 57.230 50.000 0.64 0.00 42.67 2.59
106 117 3.326588 TGTTACTCACCATTGTGGCTACT 59.673 43.478 0.64 0.00 42.67 2.57
107 118 3.670625 TGTTACTCACCATTGTGGCTAC 58.329 45.455 0.00 0.00 42.67 3.58
108 119 4.568072 ATGTTACTCACCATTGTGGCTA 57.432 40.909 0.00 0.00 42.67 3.93
109 120 2.949177 TGTTACTCACCATTGTGGCT 57.051 45.000 0.00 0.00 42.67 4.75
110 121 5.183140 AGTTTATGTTACTCACCATTGTGGC 59.817 40.000 0.00 0.00 42.67 5.01
111 122 6.817765 AGTTTATGTTACTCACCATTGTGG 57.182 37.500 0.00 0.00 45.02 4.17
137 148 9.227777 ACATAGTCTAGCGATATGTGTATGTAA 57.772 33.333 11.31 0.00 38.40 2.41
138 149 8.788325 ACATAGTCTAGCGATATGTGTATGTA 57.212 34.615 11.31 0.00 38.40 2.29
139 150 7.689446 ACATAGTCTAGCGATATGTGTATGT 57.311 36.000 11.31 0.00 38.40 2.29
140 151 9.491934 GTAACATAGTCTAGCGATATGTGTATG 57.508 37.037 12.30 0.00 39.46 2.39
141 152 9.451002 AGTAACATAGTCTAGCGATATGTGTAT 57.549 33.333 12.30 3.87 39.46 2.29
142 153 8.718734 CAGTAACATAGTCTAGCGATATGTGTA 58.281 37.037 12.30 7.04 39.46 2.90
143 154 7.585867 CAGTAACATAGTCTAGCGATATGTGT 58.414 38.462 12.30 7.67 39.46 3.72
144 155 6.524933 GCAGTAACATAGTCTAGCGATATGTG 59.475 42.308 12.30 4.86 39.46 3.21
145 156 6.349445 GGCAGTAACATAGTCTAGCGATATGT 60.349 42.308 7.92 7.92 40.86 2.29
146 157 6.030849 GGCAGTAACATAGTCTAGCGATATG 58.969 44.000 0.00 6.97 33.93 1.78
147 158 5.946972 AGGCAGTAACATAGTCTAGCGATAT 59.053 40.000 0.00 0.00 0.00 1.63
148 159 5.314529 AGGCAGTAACATAGTCTAGCGATA 58.685 41.667 0.00 0.00 0.00 2.92
149 160 4.145807 AGGCAGTAACATAGTCTAGCGAT 58.854 43.478 0.00 0.00 0.00 4.58
150 161 3.552875 AGGCAGTAACATAGTCTAGCGA 58.447 45.455 0.00 0.00 0.00 4.93
151 162 3.992260 AGGCAGTAACATAGTCTAGCG 57.008 47.619 0.00 0.00 0.00 4.26
152 163 5.263968 TGAAGGCAGTAACATAGTCTAGC 57.736 43.478 0.00 0.00 0.00 3.42
153 164 8.079203 CACTATGAAGGCAGTAACATAGTCTAG 58.921 40.741 13.37 3.03 46.61 2.43
154 165 7.014326 CCACTATGAAGGCAGTAACATAGTCTA 59.986 40.741 13.37 0.00 46.61 2.59
155 166 6.183360 CCACTATGAAGGCAGTAACATAGTCT 60.183 42.308 13.37 0.00 46.61 3.24
156 167 5.986135 CCACTATGAAGGCAGTAACATAGTC 59.014 44.000 13.37 0.00 46.61 2.59
158 169 5.163301 ACCCACTATGAAGGCAGTAACATAG 60.163 44.000 0.00 0.00 44.14 2.23
159 170 4.719773 ACCCACTATGAAGGCAGTAACATA 59.280 41.667 0.00 0.00 0.00 2.29
160 171 3.523564 ACCCACTATGAAGGCAGTAACAT 59.476 43.478 0.00 0.00 0.00 2.71
161 172 2.910319 ACCCACTATGAAGGCAGTAACA 59.090 45.455 0.00 0.00 0.00 2.41
162 173 3.629142 ACCCACTATGAAGGCAGTAAC 57.371 47.619 0.00 0.00 0.00 2.50
163 174 4.359105 ACTACCCACTATGAAGGCAGTAA 58.641 43.478 0.00 0.00 0.00 2.24
164 175 3.990369 ACTACCCACTATGAAGGCAGTA 58.010 45.455 0.00 0.00 0.00 2.74
165 176 2.834113 ACTACCCACTATGAAGGCAGT 58.166 47.619 0.00 0.00 0.00 4.40
166 177 4.161565 TGTTACTACCCACTATGAAGGCAG 59.838 45.833 0.00 0.00 0.00 4.85
167 178 4.098155 TGTTACTACCCACTATGAAGGCA 58.902 43.478 0.00 0.00 0.00 4.75
168 179 4.748277 TGTTACTACCCACTATGAAGGC 57.252 45.455 0.00 0.00 0.00 4.35
169 180 9.273016 CATTTATGTTACTACCCACTATGAAGG 57.727 37.037 0.00 0.00 0.00 3.46
170 181 9.832445 ACATTTATGTTACTACCCACTATGAAG 57.168 33.333 0.00 0.00 37.90 3.02
171 182 9.607988 CACATTTATGTTACTACCCACTATGAA 57.392 33.333 0.00 0.00 39.39 2.57
172 183 8.208224 CCACATTTATGTTACTACCCACTATGA 58.792 37.037 0.00 0.00 39.39 2.15
173 184 7.990886 ACCACATTTATGTTACTACCCACTATG 59.009 37.037 0.00 0.00 39.39 2.23
174 185 8.097791 ACCACATTTATGTTACTACCCACTAT 57.902 34.615 0.00 0.00 39.39 2.12
175 186 7.499200 ACCACATTTATGTTACTACCCACTA 57.501 36.000 0.00 0.00 39.39 2.74
176 187 6.382919 ACCACATTTATGTTACTACCCACT 57.617 37.500 0.00 0.00 39.39 4.00
177 188 7.607223 TGTTACCACATTTATGTTACTACCCAC 59.393 37.037 0.00 0.00 39.39 4.61
178 189 7.687388 TGTTACCACATTTATGTTACTACCCA 58.313 34.615 0.00 0.00 39.39 4.51
179 190 8.617809 CATGTTACCACATTTATGTTACTACCC 58.382 37.037 0.00 0.00 41.16 3.69
180 191 8.126700 GCATGTTACCACATTTATGTTACTACC 58.873 37.037 0.00 0.00 41.16 3.18
181 192 8.670135 TGCATGTTACCACATTTATGTTACTAC 58.330 33.333 0.00 0.00 41.16 2.73
182 193 8.794335 TGCATGTTACCACATTTATGTTACTA 57.206 30.769 0.00 0.00 41.16 1.82
183 194 7.695480 TGCATGTTACCACATTTATGTTACT 57.305 32.000 0.00 0.00 41.16 2.24
184 195 8.749841 TTTGCATGTTACCACATTTATGTTAC 57.250 30.769 0.00 0.00 41.16 2.50
185 196 9.197694 GTTTTGCATGTTACCACATTTATGTTA 57.802 29.630 0.00 0.00 41.16 2.41
186 197 7.930865 AGTTTTGCATGTTACCACATTTATGTT 59.069 29.630 0.00 0.00 41.16 2.71
187 198 7.441017 AGTTTTGCATGTTACCACATTTATGT 58.559 30.769 0.00 0.00 41.16 2.29
188 199 7.887996 AGTTTTGCATGTTACCACATTTATG 57.112 32.000 0.00 0.00 41.16 1.90
189 200 8.900983 AAAGTTTTGCATGTTACCACATTTAT 57.099 26.923 0.00 0.00 41.16 1.40
190 201 9.988815 ATAAAGTTTTGCATGTTACCACATTTA 57.011 25.926 0.00 0.00 41.16 1.40
191 202 8.900983 ATAAAGTTTTGCATGTTACCACATTT 57.099 26.923 0.00 0.00 41.16 2.32
192 203 8.900983 AATAAAGTTTTGCATGTTACCACATT 57.099 26.923 0.00 0.00 41.16 2.71
193 204 8.900983 AAATAAAGTTTTGCATGTTACCACAT 57.099 26.923 0.00 0.00 45.18 3.21
194 205 9.988815 ATAAATAAAGTTTTGCATGTTACCACA 57.011 25.926 0.00 0.00 37.31 4.17
220 231 9.725019 CCAATGCAATATGAGTCTATAACCTAA 57.275 33.333 0.00 0.00 0.00 2.69
221 232 8.321353 CCCAATGCAATATGAGTCTATAACCTA 58.679 37.037 0.00 0.00 0.00 3.08
222 233 7.017551 TCCCAATGCAATATGAGTCTATAACCT 59.982 37.037 0.00 0.00 0.00 3.50
223 234 7.119846 GTCCCAATGCAATATGAGTCTATAACC 59.880 40.741 0.00 0.00 0.00 2.85
224 235 7.661437 TGTCCCAATGCAATATGAGTCTATAAC 59.339 37.037 0.00 0.00 0.00 1.89
225 236 7.744733 TGTCCCAATGCAATATGAGTCTATAA 58.255 34.615 0.00 0.00 0.00 0.98
226 237 7.315066 TGTCCCAATGCAATATGAGTCTATA 57.685 36.000 0.00 0.00 0.00 1.31
227 238 6.191657 TGTCCCAATGCAATATGAGTCTAT 57.808 37.500 0.00 0.00 0.00 1.98
228 239 5.628797 TGTCCCAATGCAATATGAGTCTA 57.371 39.130 0.00 0.00 0.00 2.59
229 240 4.508551 TGTCCCAATGCAATATGAGTCT 57.491 40.909 0.00 0.00 0.00 3.24
230 241 4.581824 ACATGTCCCAATGCAATATGAGTC 59.418 41.667 0.00 0.00 0.00 3.36
231 242 4.340097 CACATGTCCCAATGCAATATGAGT 59.660 41.667 0.00 0.00 0.00 3.41
232 243 4.581409 TCACATGTCCCAATGCAATATGAG 59.419 41.667 0.00 0.00 0.00 2.90
233 244 4.534797 TCACATGTCCCAATGCAATATGA 58.465 39.130 0.00 0.00 0.00 2.15
234 245 4.922471 TCACATGTCCCAATGCAATATG 57.078 40.909 0.00 0.00 0.00 1.78
235 246 4.897076 ACATCACATGTCCCAATGCAATAT 59.103 37.500 0.00 0.00 39.92 1.28
236 247 4.279982 ACATCACATGTCCCAATGCAATA 58.720 39.130 0.00 0.00 39.92 1.90
237 248 3.101437 ACATCACATGTCCCAATGCAAT 58.899 40.909 0.00 0.00 39.92 3.56
238 249 2.527497 ACATCACATGTCCCAATGCAA 58.473 42.857 0.00 0.00 39.92 4.08
239 250 2.219080 ACATCACATGTCCCAATGCA 57.781 45.000 0.00 0.00 39.92 3.96
240 251 3.443329 TGTAACATCACATGTCCCAATGC 59.557 43.478 0.00 0.00 44.07 3.56
241 252 4.701651 ACTGTAACATCACATGTCCCAATG 59.298 41.667 0.00 0.45 44.07 2.82
242 253 4.922206 ACTGTAACATCACATGTCCCAAT 58.078 39.130 0.00 0.00 44.07 3.16
243 254 4.365514 ACTGTAACATCACATGTCCCAA 57.634 40.909 0.00 0.00 44.07 4.12
244 255 5.012664 AGTTACTGTAACATCACATGTCCCA 59.987 40.000 27.12 0.00 44.07 4.37
245 256 5.488341 AGTTACTGTAACATCACATGTCCC 58.512 41.667 27.12 1.55 44.07 4.46
246 257 6.255887 GCTAGTTACTGTAACATCACATGTCC 59.744 42.308 27.12 1.73 44.07 4.02
247 258 7.036220 AGCTAGTTACTGTAACATCACATGTC 58.964 38.462 27.12 9.51 44.07 3.06
249 260 8.926715 TTAGCTAGTTACTGTAACATCACATG 57.073 34.615 27.12 12.57 41.07 3.21
250 261 8.750298 ACTTAGCTAGTTACTGTAACATCACAT 58.250 33.333 27.12 11.85 41.07 3.21
251 262 8.118976 ACTTAGCTAGTTACTGTAACATCACA 57.881 34.615 27.12 10.61 41.07 3.58
252 263 8.983307 AACTTAGCTAGTTACTGTAACATCAC 57.017 34.615 27.12 15.70 45.22 3.06
269 280 9.783081 GAGAGAGGTAGTTATAGTAACTTAGCT 57.217 37.037 7.58 8.45 0.00 3.32
270 281 9.002600 GGAGAGAGGTAGTTATAGTAACTTAGC 57.997 40.741 7.58 4.77 0.00 3.09
273 284 8.780003 TGAGGAGAGAGGTAGTTATAGTAACTT 58.220 37.037 7.58 0.00 0.00 2.66
274 285 8.334522 TGAGGAGAGAGGTAGTTATAGTAACT 57.665 38.462 7.44 7.44 0.00 2.24
275 286 9.577222 AATGAGGAGAGAGGTAGTTATAGTAAC 57.423 37.037 0.00 0.00 0.00 2.50
278 289 9.577222 GTTAATGAGGAGAGAGGTAGTTATAGT 57.423 37.037 0.00 0.00 0.00 2.12
279 290 9.802039 AGTTAATGAGGAGAGAGGTAGTTATAG 57.198 37.037 0.00 0.00 0.00 1.31
280 291 9.796180 GAGTTAATGAGGAGAGAGGTAGTTATA 57.204 37.037 0.00 0.00 0.00 0.98
281 292 8.282982 TGAGTTAATGAGGAGAGAGGTAGTTAT 58.717 37.037 0.00 0.00 0.00 1.89
282 293 7.556996 GTGAGTTAATGAGGAGAGAGGTAGTTA 59.443 40.741 0.00 0.00 0.00 2.24
283 294 6.378848 GTGAGTTAATGAGGAGAGAGGTAGTT 59.621 42.308 0.00 0.00 0.00 2.24
284 295 5.889289 GTGAGTTAATGAGGAGAGAGGTAGT 59.111 44.000 0.00 0.00 0.00 2.73
285 296 6.039270 CAGTGAGTTAATGAGGAGAGAGGTAG 59.961 46.154 0.00 0.00 0.00 3.18
286 297 5.888724 CAGTGAGTTAATGAGGAGAGAGGTA 59.111 44.000 0.00 0.00 0.00 3.08
287 298 4.709397 CAGTGAGTTAATGAGGAGAGAGGT 59.291 45.833 0.00 0.00 0.00 3.85
288 299 4.441356 GCAGTGAGTTAATGAGGAGAGAGG 60.441 50.000 0.00 0.00 0.00 3.69
289 300 4.441356 GGCAGTGAGTTAATGAGGAGAGAG 60.441 50.000 0.00 0.00 0.00 3.20
290 301 3.449018 GGCAGTGAGTTAATGAGGAGAGA 59.551 47.826 0.00 0.00 0.00 3.10
291 302 3.196469 TGGCAGTGAGTTAATGAGGAGAG 59.804 47.826 0.00 0.00 0.00 3.20
292 303 3.055819 GTGGCAGTGAGTTAATGAGGAGA 60.056 47.826 0.00 0.00 0.00 3.71
293 304 3.265791 GTGGCAGTGAGTTAATGAGGAG 58.734 50.000 0.00 0.00 0.00 3.69
294 305 2.637382 TGTGGCAGTGAGTTAATGAGGA 59.363 45.455 0.00 0.00 0.00 3.71
295 306 3.057969 TGTGGCAGTGAGTTAATGAGG 57.942 47.619 0.00 0.00 0.00 3.86
296 307 6.149308 TGTTTATGTGGCAGTGAGTTAATGAG 59.851 38.462 0.00 0.00 0.00 2.90
297 308 6.000840 TGTTTATGTGGCAGTGAGTTAATGA 58.999 36.000 0.00 0.00 0.00 2.57
298 309 6.252967 TGTTTATGTGGCAGTGAGTTAATG 57.747 37.500 0.00 0.00 0.00 1.90
299 310 6.892658 TTGTTTATGTGGCAGTGAGTTAAT 57.107 33.333 0.00 0.00 0.00 1.40
300 311 6.701145 TTTGTTTATGTGGCAGTGAGTTAA 57.299 33.333 0.00 0.00 0.00 2.01
301 312 6.892658 ATTTGTTTATGTGGCAGTGAGTTA 57.107 33.333 0.00 0.00 0.00 2.24
302 313 5.789643 ATTTGTTTATGTGGCAGTGAGTT 57.210 34.783 0.00 0.00 0.00 3.01
303 314 5.789643 AATTTGTTTATGTGGCAGTGAGT 57.210 34.783 0.00 0.00 0.00 3.41
304 315 7.326789 CAGTAAATTTGTTTATGTGGCAGTGAG 59.673 37.037 0.00 0.00 0.00 3.51
305 316 7.013750 TCAGTAAATTTGTTTATGTGGCAGTGA 59.986 33.333 0.00 0.00 0.00 3.41
306 317 7.144661 TCAGTAAATTTGTTTATGTGGCAGTG 58.855 34.615 0.00 0.00 0.00 3.66
307 318 7.014230 ACTCAGTAAATTTGTTTATGTGGCAGT 59.986 33.333 0.00 0.00 0.00 4.40
308 319 7.370383 ACTCAGTAAATTTGTTTATGTGGCAG 58.630 34.615 0.00 0.00 0.00 4.85
309 320 7.283625 ACTCAGTAAATTTGTTTATGTGGCA 57.716 32.000 0.00 0.00 0.00 4.92
310 321 7.116233 CCAACTCAGTAAATTTGTTTATGTGGC 59.884 37.037 0.00 0.00 0.00 5.01
311 322 8.356657 TCCAACTCAGTAAATTTGTTTATGTGG 58.643 33.333 0.00 1.86 0.00 4.17
312 323 9.180678 GTCCAACTCAGTAAATTTGTTTATGTG 57.819 33.333 0.00 0.00 0.00 3.21
313 324 9.131791 AGTCCAACTCAGTAAATTTGTTTATGT 57.868 29.630 0.00 0.00 0.00 2.29
314 325 9.612620 GAGTCCAACTCAGTAAATTTGTTTATG 57.387 33.333 0.00 0.00 44.45 1.90
315 326 8.504005 CGAGTCCAACTCAGTAAATTTGTTTAT 58.496 33.333 0.00 0.00 45.30 1.40
316 327 7.711772 TCGAGTCCAACTCAGTAAATTTGTTTA 59.288 33.333 0.00 0.00 45.30 2.01
317 328 6.540914 TCGAGTCCAACTCAGTAAATTTGTTT 59.459 34.615 0.00 0.00 45.30 2.83
318 329 6.053005 TCGAGTCCAACTCAGTAAATTTGTT 58.947 36.000 0.00 0.00 45.30 2.83
319 330 5.607477 TCGAGTCCAACTCAGTAAATTTGT 58.393 37.500 0.00 0.00 45.30 2.83
320 331 6.147821 ACATCGAGTCCAACTCAGTAAATTTG 59.852 38.462 0.00 0.00 45.30 2.32
321 332 6.231211 ACATCGAGTCCAACTCAGTAAATTT 58.769 36.000 7.78 0.00 45.30 1.82
322 333 5.794894 ACATCGAGTCCAACTCAGTAAATT 58.205 37.500 7.78 0.00 45.30 1.82
323 334 5.407407 ACATCGAGTCCAACTCAGTAAAT 57.593 39.130 7.78 0.00 45.30 1.40
324 335 4.866508 ACATCGAGTCCAACTCAGTAAA 57.133 40.909 7.78 0.00 45.30 2.01
325 336 4.866508 AACATCGAGTCCAACTCAGTAA 57.133 40.909 7.78 0.00 45.30 2.24
326 337 5.008331 AGTAACATCGAGTCCAACTCAGTA 58.992 41.667 7.78 0.00 45.30 2.74
327 338 3.827302 AGTAACATCGAGTCCAACTCAGT 59.173 43.478 7.78 0.61 45.30 3.41
328 339 4.169508 CAGTAACATCGAGTCCAACTCAG 58.830 47.826 7.78 1.37 45.30 3.35
329 340 3.614150 GCAGTAACATCGAGTCCAACTCA 60.614 47.826 7.78 0.00 45.30 3.41
330 341 2.924290 GCAGTAACATCGAGTCCAACTC 59.076 50.000 0.00 0.00 41.71 3.01
331 342 2.563179 AGCAGTAACATCGAGTCCAACT 59.437 45.455 0.00 0.00 0.00 3.16
332 343 2.668457 CAGCAGTAACATCGAGTCCAAC 59.332 50.000 0.00 0.00 0.00 3.77
333 344 2.560981 TCAGCAGTAACATCGAGTCCAA 59.439 45.455 0.00 0.00 0.00 3.53
334 345 2.167662 TCAGCAGTAACATCGAGTCCA 58.832 47.619 0.00 0.00 0.00 4.02
335 346 2.941453 TCAGCAGTAACATCGAGTCC 57.059 50.000 0.00 0.00 0.00 3.85
336 347 3.839293 ACTTCAGCAGTAACATCGAGTC 58.161 45.455 0.00 0.00 31.97 3.36
337 348 3.944055 ACTTCAGCAGTAACATCGAGT 57.056 42.857 0.00 0.00 31.97 4.18
338 349 5.403246 AGTAACTTCAGCAGTAACATCGAG 58.597 41.667 0.00 0.00 32.94 4.04
339 350 5.386958 AGTAACTTCAGCAGTAACATCGA 57.613 39.130 0.00 0.00 32.94 3.59
340 351 4.563184 GGAGTAACTTCAGCAGTAACATCG 59.437 45.833 0.00 0.00 32.94 3.84
341 352 4.870991 GGGAGTAACTTCAGCAGTAACATC 59.129 45.833 0.00 0.00 32.94 3.06
342 353 4.286032 TGGGAGTAACTTCAGCAGTAACAT 59.714 41.667 0.00 0.00 32.94 2.71
343 354 3.644265 TGGGAGTAACTTCAGCAGTAACA 59.356 43.478 0.00 0.00 32.94 2.41
344 355 3.995048 GTGGGAGTAACTTCAGCAGTAAC 59.005 47.826 0.00 0.00 32.94 2.50
345 356 3.901844 AGTGGGAGTAACTTCAGCAGTAA 59.098 43.478 0.00 0.00 32.94 2.24
346 357 3.258372 CAGTGGGAGTAACTTCAGCAGTA 59.742 47.826 0.00 0.00 32.94 2.74
347 358 2.037772 CAGTGGGAGTAACTTCAGCAGT 59.962 50.000 0.00 0.00 37.30 4.40
348 359 2.037772 ACAGTGGGAGTAACTTCAGCAG 59.962 50.000 0.00 0.00 0.00 4.24
349 360 2.047061 ACAGTGGGAGTAACTTCAGCA 58.953 47.619 0.00 0.00 0.00 4.41
350 361 2.037251 TCACAGTGGGAGTAACTTCAGC 59.963 50.000 0.00 0.00 0.00 4.26
351 362 3.322254 AGTCACAGTGGGAGTAACTTCAG 59.678 47.826 0.00 0.00 0.00 3.02
352 363 3.305720 AGTCACAGTGGGAGTAACTTCA 58.694 45.455 0.00 0.00 0.00 3.02
353 364 4.523558 ACTAGTCACAGTGGGAGTAACTTC 59.476 45.833 11.10 0.00 0.00 3.01
354 365 4.481072 ACTAGTCACAGTGGGAGTAACTT 58.519 43.478 11.10 0.00 0.00 2.66
355 366 4.080687 GACTAGTCACAGTGGGAGTAACT 58.919 47.826 18.20 0.68 0.00 2.24
356 367 4.080687 AGACTAGTCACAGTGGGAGTAAC 58.919 47.826 24.44 8.29 0.00 2.50
357 368 4.383931 AGACTAGTCACAGTGGGAGTAA 57.616 45.455 24.44 0.00 0.00 2.24
358 369 5.509832 TTAGACTAGTCACAGTGGGAGTA 57.490 43.478 24.44 9.60 0.00 2.59
359 370 2.982339 AGACTAGTCACAGTGGGAGT 57.018 50.000 24.44 8.06 0.00 3.85
360 371 4.767928 ACTTTAGACTAGTCACAGTGGGAG 59.232 45.833 24.44 11.96 0.00 4.30
361 372 4.737578 ACTTTAGACTAGTCACAGTGGGA 58.262 43.478 24.44 0.00 0.00 4.37
362 373 5.944599 TCTACTTTAGACTAGTCACAGTGGG 59.055 44.000 24.44 16.77 0.00 4.61
363 374 7.362229 CCTTCTACTTTAGACTAGTCACAGTGG 60.362 44.444 24.44 20.93 33.84 4.00
364 375 7.531716 CCTTCTACTTTAGACTAGTCACAGTG 58.468 42.308 24.44 15.07 33.84 3.66
365 376 6.151480 GCCTTCTACTTTAGACTAGTCACAGT 59.849 42.308 24.44 21.58 33.84 3.55
366 377 6.404954 GGCCTTCTACTTTAGACTAGTCACAG 60.405 46.154 24.44 17.52 33.84 3.66
367 378 5.418209 GGCCTTCTACTTTAGACTAGTCACA 59.582 44.000 24.44 9.25 33.84 3.58
368 379 5.448904 CGGCCTTCTACTTTAGACTAGTCAC 60.449 48.000 24.44 0.00 33.84 3.67
369 380 4.639310 CGGCCTTCTACTTTAGACTAGTCA 59.361 45.833 24.44 8.16 33.84 3.41
370 381 4.036616 CCGGCCTTCTACTTTAGACTAGTC 59.963 50.000 15.41 15.41 33.84 2.59
371 382 3.952967 CCGGCCTTCTACTTTAGACTAGT 59.047 47.826 0.00 0.00 33.84 2.57
372 383 4.036616 GTCCGGCCTTCTACTTTAGACTAG 59.963 50.000 0.00 0.00 33.84 2.57
373 384 3.950395 GTCCGGCCTTCTACTTTAGACTA 59.050 47.826 0.00 0.00 33.84 2.59
374 385 2.759535 GTCCGGCCTTCTACTTTAGACT 59.240 50.000 0.00 0.00 33.84 3.24
375 386 2.759535 AGTCCGGCCTTCTACTTTAGAC 59.240 50.000 0.00 0.00 33.84 2.59
376 387 3.097342 AGTCCGGCCTTCTACTTTAGA 57.903 47.619 0.00 0.00 0.00 2.10
377 388 6.264970 AGTTATAGTCCGGCCTTCTACTTTAG 59.735 42.308 0.00 0.00 0.00 1.85
380 391 4.544683 AGTTATAGTCCGGCCTTCTACTT 58.455 43.478 0.00 0.00 0.00 2.24
390 401 2.102588 CCCTCACCAAGTTATAGTCCGG 59.897 54.545 0.00 0.00 0.00 5.14
407 418 2.760385 CCTCAGGACCGGACCCTC 60.760 72.222 19.83 0.00 0.00 4.30
423 434 4.937201 AGTGACAATTCCCAAAACTTCC 57.063 40.909 0.00 0.00 0.00 3.46
442 453 9.507329 AATCACAATGTCTTTACAGTCATTAGT 57.493 29.630 1.82 1.54 36.85 2.24
443 454 9.764870 CAATCACAATGTCTTTACAGTCATTAG 57.235 33.333 1.82 0.00 36.85 1.73
445 456 8.394971 TCAATCACAATGTCTTTACAGTCATT 57.605 30.769 0.00 0.00 38.76 2.57
473 487 8.534333 TTGTGTGTGAGAGAAATACTTGTATC 57.466 34.615 0.00 0.00 0.00 2.24
517 531 6.604795 AGTCAGCCAGAGTAAATATTGCAAAT 59.395 34.615 1.71 0.00 0.00 2.32
518 532 5.945784 AGTCAGCCAGAGTAAATATTGCAAA 59.054 36.000 1.71 0.00 0.00 3.68
519 533 5.355071 CAGTCAGCCAGAGTAAATATTGCAA 59.645 40.000 0.00 0.00 0.00 4.08
520 534 4.877823 CAGTCAGCCAGAGTAAATATTGCA 59.122 41.667 0.00 0.00 0.00 4.08
524 538 4.446371 GTGCAGTCAGCCAGAGTAAATAT 58.554 43.478 0.00 0.00 44.83 1.28
544 558 2.226262 ATGATTTCGAACAACGCGTG 57.774 45.000 14.98 10.05 42.26 5.34
545 559 4.092237 TGATTATGATTTCGAACAACGCGT 59.908 37.500 5.58 5.58 42.26 6.01
546 560 4.430118 GTGATTATGATTTCGAACAACGCG 59.570 41.667 3.53 3.53 42.26 6.01
547 561 5.320723 TGTGATTATGATTTCGAACAACGC 58.679 37.500 0.00 0.00 42.26 4.84
548 562 6.761117 TCTGTGATTATGATTTCGAACAACG 58.239 36.000 0.00 0.00 44.09 4.10
549 563 7.064609 TCCTCTGTGATTATGATTTCGAACAAC 59.935 37.037 0.00 0.00 0.00 3.32
667 998 3.866582 GGCCCGGGATCCAGACAG 61.867 72.222 29.31 3.20 0.00 3.51
676 1008 2.543797 AAAATGACCAGGCCCGGGA 61.544 57.895 29.31 0.00 0.00 5.14
773 1105 1.045911 AGGAGAACGGGGCAGAGATC 61.046 60.000 0.00 0.00 0.00 2.75
776 1108 1.219393 GAAGGAGAACGGGGCAGAG 59.781 63.158 0.00 0.00 0.00 3.35
777 1109 1.125093 TTGAAGGAGAACGGGGCAGA 61.125 55.000 0.00 0.00 0.00 4.26
778 1110 0.250727 TTTGAAGGAGAACGGGGCAG 60.251 55.000 0.00 0.00 0.00 4.85
996 1340 4.193334 CGGCGGCTCGACATCTCA 62.193 66.667 7.61 0.00 32.52 3.27
1133 1477 0.106708 AACAAGCAACTCGCAGGAGA 59.893 50.000 0.00 0.00 46.13 3.71
1344 1695 1.833630 TGGTGGAGGCTCTTGATGTAG 59.166 52.381 15.23 0.00 0.00 2.74
1395 1746 2.094182 GTCCAAGGTCGACATTAGCTCA 60.094 50.000 15.94 0.00 0.00 4.26
1467 1818 2.981859 ACTGGCGTGGTAGGATAAAG 57.018 50.000 0.00 0.00 0.00 1.85
1527 1882 1.671901 GCCTCCTCGTCTCCCTCTTG 61.672 65.000 0.00 0.00 0.00 3.02
1755 2131 9.393512 CTACAACCTAGTAGTAATACACTCAGT 57.606 37.037 2.81 0.00 38.80 3.41
1775 2151 3.666001 CACAAACACACACGTCTACAAC 58.334 45.455 0.00 0.00 0.00 3.32
1901 2309 2.096248 AGCTTGTCCGTTGGAAAACAA 58.904 42.857 0.00 0.00 36.54 2.83
1964 2376 9.547753 ACATGGCAGTAATTAAACAGATAGTAG 57.452 33.333 0.00 0.00 0.00 2.57
1988 2400 5.047021 AGCAGTAAGTTATGCAGAGAAGACA 60.047 40.000 15.22 0.00 45.01 3.41
2013 2425 7.023575 CAAATAACTTGACCGTACGTAGTAGT 58.976 38.462 15.21 9.23 39.81 2.73
2018 2430 5.384063 TCCAAATAACTTGACCGTACGTA 57.616 39.130 15.21 0.00 37.17 3.57
2045 2457 0.673333 TTCTATGTGGCACCTGCACG 60.673 55.000 16.26 0.00 44.36 5.34
2051 2463 4.072131 TCTTCACTTTTCTATGTGGCACC 58.928 43.478 16.26 0.00 35.15 5.01
2123 2820 7.863666 TCTTTTTACATTTACAAGTACACCGG 58.136 34.615 0.00 0.00 0.00 5.28
2144 2841 8.543774 CGTCTCGCTCATTTTTATATCTTCTTT 58.456 33.333 0.00 0.00 0.00 2.52
2178 2875 6.412214 TCTAGGTAATAGGGTTCTTTTGCAC 58.588 40.000 0.00 0.00 31.83 4.57
2210 2907 2.839486 TCACTCGAGAAGCCAAATGT 57.161 45.000 21.68 0.00 0.00 2.71
2211 2908 3.806521 CCTATCACTCGAGAAGCCAAATG 59.193 47.826 21.68 4.08 0.00 2.32
2212 2909 3.742640 GCCTATCACTCGAGAAGCCAAAT 60.743 47.826 21.68 3.47 0.00 2.32
2239 2936 2.569404 AGATGAAGACACCTCCTGTTCC 59.431 50.000 0.00 0.00 31.03 3.62
2243 2940 4.214971 CACAAAAGATGAAGACACCTCCTG 59.785 45.833 0.00 0.00 0.00 3.86
2246 2943 5.529060 AGTTCACAAAAGATGAAGACACCTC 59.471 40.000 0.00 0.00 36.76 3.85
2283 2980 3.558418 TCTTGTAGGCGAAAAGTTGACAC 59.442 43.478 0.00 0.00 0.00 3.67
2298 2995 3.247173 GCTTGATTGCGGAGATCTTGTAG 59.753 47.826 0.00 0.00 0.00 2.74
2299 2996 3.198068 GCTTGATTGCGGAGATCTTGTA 58.802 45.455 0.00 0.00 0.00 2.41
2343 3040 2.120232 GCCATGTCGATCGACTAGTTG 58.880 52.381 39.10 29.72 44.80 3.16
2345 3042 1.335182 CTGCCATGTCGATCGACTAGT 59.665 52.381 39.10 25.92 44.80 2.57
2346 3043 1.335182 ACTGCCATGTCGATCGACTAG 59.665 52.381 39.10 31.13 44.80 2.57
2347 3044 1.333931 GACTGCCATGTCGATCGACTA 59.666 52.381 39.10 28.39 44.80 2.59
2393 3117 0.254178 ACGGATCTCATGCTTTGGCT 59.746 50.000 0.00 0.00 39.59 4.75
2427 3151 9.661563 TGACACGTCTCTATAAACCAAAATAAT 57.338 29.630 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.