Multiple sequence alignment - TraesCS5D01G363900

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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 TraesCS5D01G363900 chr5D 100.000 3743 0 0 1 3743 441407004 441403262 0.000000e+00 6913.0
1 TraesCS5D01G363900 chr5D 90.943 265 21 2 109 373 418294035 418294296 1.650000e-93 353.0
2 TraesCS5D01G363900 chr5B 92.162 3177 150 30 594 3733 537785712 537782598 0.000000e+00 4396.0
3 TraesCS5D01G363900 chr5A 91.422 2553 128 34 565 3095 558177127 558174644 0.000000e+00 3417.0
4 TraesCS5D01G363900 chr5A 86.937 666 46 22 3093 3740 558174323 558173681 0.000000e+00 710.0
5 TraesCS5D01G363900 chr5A 95.798 119 5 0 1 119 558177364 558177246 3.820000e-45 193.0
6 TraesCS5D01G363900 chr1D 87.779 1391 111 25 1529 2914 239622529 239621193 0.000000e+00 1572.0
7 TraesCS5D01G363900 chr1D 86.384 661 59 14 2257 2914 212525835 212526467 0.000000e+00 693.0
8 TraesCS5D01G363900 chr1D 78.710 155 24 8 1308 1456 416627370 416627219 1.110000e-15 95.3
9 TraesCS5D01G363900 chr4B 87.563 1391 119 25 1529 2914 339264339 339262998 0.000000e+00 1561.0
10 TraesCS5D01G363900 chr4D 87.275 1391 119 24 1529 2914 93450115 93448778 0.000000e+00 1535.0
11 TraesCS5D01G363900 chr4D 91.473 258 20 1 110 367 488271084 488271339 1.650000e-93 353.0
12 TraesCS5D01G363900 chr2D 87.214 1400 115 22 1520 2914 118533048 118534388 0.000000e+00 1535.0
13 TraesCS5D01G363900 chr2D 92.308 260 18 1 118 377 541547288 541547545 5.910000e-98 368.0
14 TraesCS5D01G363900 chr3B 88.879 1079 84 14 1520 2595 809806224 809807269 0.000000e+00 1295.0
15 TraesCS5D01G363900 chr3A 87.918 1076 98 9 1591 2666 431134968 431136011 0.000000e+00 1238.0
16 TraesCS5D01G363900 chr4A 92.941 255 15 2 118 371 615435031 615435283 5.910000e-98 368.0
17 TraesCS5D01G363900 chr3D 92.578 256 17 1 118 373 563449184 563448931 2.120000e-97 366.0
18 TraesCS5D01G363900 chr7A 91.698 265 19 2 110 373 556161080 556161342 7.640000e-97 364.0
19 TraesCS5D01G363900 chr1B 92.549 255 15 4 114 368 671566520 671566770 2.750000e-96 363.0
20 TraesCS5D01G363900 chr6D 91.571 261 19 2 109 369 450269324 450269581 1.280000e-94 357.0
21 TraesCS5D01G363900 chr2A 92.742 248 15 2 118 365 452538961 452538717 4.600000e-94 355.0
22 TraesCS5D01G363900 chr7B 84.058 276 26 11 2642 2914 375392208 375392468 2.230000e-62 250.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G363900 chr5D 441403262 441407004 3742 True 6913 6913 100.000000 1 3743 1 chr5D.!!$R1 3742
1 TraesCS5D01G363900 chr5B 537782598 537785712 3114 True 4396 4396 92.162000 594 3733 1 chr5B.!!$R1 3139
2 TraesCS5D01G363900 chr5A 558173681 558177364 3683 True 1440 3417 91.385667 1 3740 3 chr5A.!!$R1 3739
3 TraesCS5D01G363900 chr1D 239621193 239622529 1336 True 1572 1572 87.779000 1529 2914 1 chr1D.!!$R1 1385
4 TraesCS5D01G363900 chr1D 212525835 212526467 632 False 693 693 86.384000 2257 2914 1 chr1D.!!$F1 657
5 TraesCS5D01G363900 chr4B 339262998 339264339 1341 True 1561 1561 87.563000 1529 2914 1 chr4B.!!$R1 1385
6 TraesCS5D01G363900 chr4D 93448778 93450115 1337 True 1535 1535 87.275000 1529 2914 1 chr4D.!!$R1 1385
7 TraesCS5D01G363900 chr2D 118533048 118534388 1340 False 1535 1535 87.214000 1520 2914 1 chr2D.!!$F1 1394
8 TraesCS5D01G363900 chr3B 809806224 809807269 1045 False 1295 1295 88.879000 1520 2595 1 chr3B.!!$F1 1075
9 TraesCS5D01G363900 chr3A 431134968 431136011 1043 False 1238 1238 87.918000 1591 2666 1 chr3A.!!$F1 1075

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
267 268 0.163146 GGTAAACGTGTTGAGCGCTC 59.837 55.0 30.42 30.42 0.00 5.03 F
296 297 0.175073 GCGGTCTAGGTCGTTGGATT 59.825 55.0 7.30 0.00 0.00 3.01 F
560 562 0.253044 AACCATGGTCACCTCCATCG 59.747 55.0 20.07 0.00 45.23 3.84 F
2289 2325 0.604511 TCTACTGCGAGTCCGACACA 60.605 55.0 0.40 0.00 38.22 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1745 0.852412 CGACAACGTAGAGCTCGTCG 60.852 60.000 24.07 24.07 40.69 5.12 R
2289 2325 0.456221 CGAGATGGTAGGCGACAAGT 59.544 55.000 0.00 0.00 0.00 3.16 R
2292 2328 4.649845 TCGAGATGGTAGGCGACA 57.350 55.556 0.00 0.00 0.00 4.35 R
3421 3818 0.449388 GCAATGGCTCTTCAGAACGG 59.551 55.000 0.00 0.00 36.96 4.44 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.868406 GAAGAGACTTGGTTGGTGCG 59.132 55.000 0.00 0.00 0.00 5.34
83 84 8.724153 CATTGTTCACGTATGAAATCATTAACG 58.276 33.333 14.10 14.10 46.40 3.18
107 108 6.516355 CGTGAACATAAACAAAATCGTCTGAG 59.484 38.462 0.00 0.00 0.00 3.35
125 126 9.387257 TCGTCTGAGTTTTGTATATACTAGTCA 57.613 33.333 13.89 14.24 0.00 3.41
126 127 9.999009 CGTCTGAGTTTTGTATATACTAGTCAA 57.001 33.333 13.89 0.00 0.00 3.18
143 144 8.936070 ACTAGTCAATTTATACGTGCAATACA 57.064 30.769 0.00 0.00 0.00 2.29
144 145 8.814235 ACTAGTCAATTTATACGTGCAATACAC 58.186 33.333 0.00 0.00 46.45 2.90
176 177 9.830975 TTTAGAAGTATATTAAGTGCATGCAGA 57.169 29.630 23.41 6.71 0.00 4.26
221 222 9.825972 ATTTGCGTGTTATTATATGATTAGCAC 57.174 29.630 0.00 0.00 0.00 4.40
222 223 8.601845 TTGCGTGTTATTATATGATTAGCACT 57.398 30.769 0.00 0.00 0.00 4.40
223 224 9.699703 TTGCGTGTTATTATATGATTAGCACTA 57.300 29.630 0.00 0.00 0.00 2.74
224 225 9.869757 TGCGTGTTATTATATGATTAGCACTAT 57.130 29.630 0.00 0.00 0.00 2.12
235 236 9.910267 ATATGATTAGCACTATATTTGGCATGA 57.090 29.630 0.00 0.00 0.00 3.07
236 237 8.640063 ATGATTAGCACTATATTTGGCATGAA 57.360 30.769 0.00 0.00 0.00 2.57
237 238 8.462589 TGATTAGCACTATATTTGGCATGAAA 57.537 30.769 0.00 0.00 0.00 2.69
238 239 9.081204 TGATTAGCACTATATTTGGCATGAAAT 57.919 29.630 0.00 0.00 0.00 2.17
239 240 9.918630 GATTAGCACTATATTTGGCATGAAATT 57.081 29.630 0.00 0.00 0.00 1.82
243 244 8.917088 AGCACTATATTTGGCATGAAATTAACT 58.083 29.630 0.00 0.00 0.00 2.24
244 245 8.971321 GCACTATATTTGGCATGAAATTAACTG 58.029 33.333 0.00 0.00 0.00 3.16
245 246 8.971321 CACTATATTTGGCATGAAATTAACTGC 58.029 33.333 0.00 0.00 0.00 4.40
246 247 8.694540 ACTATATTTGGCATGAAATTAACTGCA 58.305 29.630 0.00 0.00 36.34 4.41
247 248 7.775397 ATATTTGGCATGAAATTAACTGCAC 57.225 32.000 0.00 0.53 36.34 4.57
248 249 3.214697 TGGCATGAAATTAACTGCACG 57.785 42.857 0.00 0.00 36.34 5.34
249 250 2.094803 TGGCATGAAATTAACTGCACGG 60.095 45.455 0.00 0.00 36.34 4.94
250 251 2.094752 GGCATGAAATTAACTGCACGGT 60.095 45.455 0.00 0.00 36.34 4.83
251 252 3.127895 GGCATGAAATTAACTGCACGGTA 59.872 43.478 0.00 0.00 36.34 4.02
252 253 4.380023 GGCATGAAATTAACTGCACGGTAA 60.380 41.667 0.00 0.00 36.34 2.85
253 254 5.157781 GCATGAAATTAACTGCACGGTAAA 58.842 37.500 0.00 0.00 34.77 2.01
254 255 5.060446 GCATGAAATTAACTGCACGGTAAAC 59.940 40.000 0.00 0.00 34.77 2.01
265 266 1.154727 CGGTAAACGTGTTGAGCGC 60.155 57.895 8.58 0.00 37.98 5.92
266 267 1.554042 CGGTAAACGTGTTGAGCGCT 61.554 55.000 11.27 11.27 37.98 5.92
267 268 0.163146 GGTAAACGTGTTGAGCGCTC 59.837 55.000 30.42 30.42 0.00 5.03
268 269 0.179282 GTAAACGTGTTGAGCGCTCG 60.179 55.000 30.75 21.89 0.00 5.03
269 270 0.318022 TAAACGTGTTGAGCGCTCGA 60.318 50.000 30.75 27.40 0.00 4.04
270 271 1.818221 AAACGTGTTGAGCGCTCGAC 61.818 55.000 39.44 39.44 42.86 4.20
273 274 4.673403 TGTTGAGCGCTCGACATT 57.327 50.000 42.95 9.77 46.09 2.71
274 275 2.153039 TGTTGAGCGCTCGACATTG 58.847 52.632 42.95 0.00 46.09 2.82
275 276 0.319469 TGTTGAGCGCTCGACATTGA 60.319 50.000 42.95 27.81 46.09 2.57
276 277 0.790207 GTTGAGCGCTCGACATTGAA 59.210 50.000 40.41 22.88 42.27 2.69
277 278 1.070821 TTGAGCGCTCGACATTGAAG 58.929 50.000 30.75 0.00 0.00 3.02
278 279 1.346538 GAGCGCTCGACATTGAAGC 59.653 57.895 23.61 0.00 0.00 3.86
280 281 2.697425 CGCTCGACATTGAAGCGG 59.303 61.111 18.32 6.49 44.06 5.52
281 282 2.094659 CGCTCGACATTGAAGCGGT 61.095 57.895 18.32 0.00 44.06 5.68
282 283 1.710339 GCTCGACATTGAAGCGGTC 59.290 57.895 0.00 0.00 0.00 4.79
283 284 0.737715 GCTCGACATTGAAGCGGTCT 60.738 55.000 0.00 0.00 0.00 3.85
284 285 1.469251 GCTCGACATTGAAGCGGTCTA 60.469 52.381 0.00 0.00 0.00 2.59
285 286 2.455032 CTCGACATTGAAGCGGTCTAG 58.545 52.381 0.00 0.00 0.00 2.43
286 287 1.134367 TCGACATTGAAGCGGTCTAGG 59.866 52.381 0.00 0.00 0.00 3.02
287 288 1.135083 CGACATTGAAGCGGTCTAGGT 60.135 52.381 0.00 0.00 0.00 3.08
288 289 2.541556 GACATTGAAGCGGTCTAGGTC 58.458 52.381 4.60 4.60 36.05 3.85
289 290 1.135083 ACATTGAAGCGGTCTAGGTCG 60.135 52.381 0.00 0.00 0.00 4.79
290 291 1.135083 CATTGAAGCGGTCTAGGTCGT 60.135 52.381 0.00 0.00 0.00 4.34
291 292 0.963962 TTGAAGCGGTCTAGGTCGTT 59.036 50.000 0.00 0.00 0.00 3.85
292 293 0.242825 TGAAGCGGTCTAGGTCGTTG 59.757 55.000 0.00 0.00 0.00 4.10
293 294 0.458025 GAAGCGGTCTAGGTCGTTGG 60.458 60.000 0.00 0.00 0.00 3.77
294 295 0.896940 AAGCGGTCTAGGTCGTTGGA 60.897 55.000 0.00 0.00 0.00 3.53
295 296 0.683504 AGCGGTCTAGGTCGTTGGAT 60.684 55.000 7.30 0.00 0.00 3.41
296 297 0.175073 GCGGTCTAGGTCGTTGGATT 59.825 55.000 7.30 0.00 0.00 3.01
297 298 1.922570 CGGTCTAGGTCGTTGGATTG 58.077 55.000 0.00 0.00 0.00 2.67
298 299 1.475280 CGGTCTAGGTCGTTGGATTGA 59.525 52.381 0.00 0.00 0.00 2.57
299 300 2.734492 CGGTCTAGGTCGTTGGATTGAC 60.734 54.545 0.00 0.00 0.00 3.18
300 301 2.232941 GGTCTAGGTCGTTGGATTGACA 59.767 50.000 0.00 0.00 36.83 3.58
301 302 3.251571 GTCTAGGTCGTTGGATTGACAC 58.748 50.000 0.00 0.00 36.83 3.67
302 303 2.094906 TCTAGGTCGTTGGATTGACACG 60.095 50.000 0.00 0.00 36.83 4.49
303 304 0.677288 AGGTCGTTGGATTGACACGA 59.323 50.000 0.00 0.00 36.83 4.35
304 305 1.275291 AGGTCGTTGGATTGACACGAT 59.725 47.619 0.00 0.00 36.83 3.73
305 306 2.073816 GGTCGTTGGATTGACACGATT 58.926 47.619 0.00 0.00 36.83 3.34
306 307 2.482721 GGTCGTTGGATTGACACGATTT 59.517 45.455 0.00 0.00 36.83 2.17
307 308 3.479006 GTCGTTGGATTGACACGATTTG 58.521 45.455 0.00 0.00 35.28 2.32
308 309 3.185594 GTCGTTGGATTGACACGATTTGA 59.814 43.478 0.00 0.00 35.28 2.69
309 310 4.000325 TCGTTGGATTGACACGATTTGAT 59.000 39.130 0.00 0.00 0.00 2.57
310 311 4.090729 CGTTGGATTGACACGATTTGATG 58.909 43.478 0.00 0.00 0.00 3.07
311 312 4.142924 CGTTGGATTGACACGATTTGATGA 60.143 41.667 0.00 0.00 0.00 2.92
312 313 4.944962 TGGATTGACACGATTTGATGAC 57.055 40.909 0.00 0.00 0.00 3.06
313 314 3.689161 TGGATTGACACGATTTGATGACC 59.311 43.478 0.00 0.00 0.00 4.02
314 315 3.242413 GGATTGACACGATTTGATGACCG 60.242 47.826 0.00 0.00 0.00 4.79
315 316 2.734276 TGACACGATTTGATGACCGA 57.266 45.000 0.00 0.00 0.00 4.69
316 317 2.606108 TGACACGATTTGATGACCGAG 58.394 47.619 0.00 0.00 0.00 4.63
317 318 2.230266 TGACACGATTTGATGACCGAGA 59.770 45.455 0.00 0.00 0.00 4.04
318 319 3.119137 TGACACGATTTGATGACCGAGAT 60.119 43.478 0.00 0.00 0.00 2.75
319 320 3.861840 ACACGATTTGATGACCGAGATT 58.138 40.909 0.00 0.00 0.00 2.40
320 321 5.006153 ACACGATTTGATGACCGAGATTA 57.994 39.130 0.00 0.00 0.00 1.75
321 322 5.416083 ACACGATTTGATGACCGAGATTAA 58.584 37.500 0.00 0.00 0.00 1.40
322 323 6.049149 ACACGATTTGATGACCGAGATTAAT 58.951 36.000 0.00 0.00 0.00 1.40
323 324 6.538742 ACACGATTTGATGACCGAGATTAATT 59.461 34.615 0.00 0.00 0.00 1.40
324 325 7.709182 ACACGATTTGATGACCGAGATTAATTA 59.291 33.333 0.00 0.00 0.00 1.40
325 326 8.217115 CACGATTTGATGACCGAGATTAATTAG 58.783 37.037 0.00 0.00 0.00 1.73
326 327 8.141909 ACGATTTGATGACCGAGATTAATTAGA 58.858 33.333 0.00 0.00 0.00 2.10
327 328 9.144747 CGATTTGATGACCGAGATTAATTAGAT 57.855 33.333 0.00 0.00 0.00 1.98
330 331 9.481340 TTTGATGACCGAGATTAATTAGATCTG 57.519 33.333 5.18 5.07 34.13 2.90
331 332 7.093354 TGATGACCGAGATTAATTAGATCTGC 58.907 38.462 5.18 6.23 34.13 4.26
332 333 5.784177 TGACCGAGATTAATTAGATCTGCC 58.216 41.667 5.18 2.75 34.13 4.85
333 334 5.540337 TGACCGAGATTAATTAGATCTGCCT 59.460 40.000 5.18 0.00 34.13 4.75
334 335 6.031751 ACCGAGATTAATTAGATCTGCCTC 57.968 41.667 5.18 0.94 34.13 4.70
335 336 5.777732 ACCGAGATTAATTAGATCTGCCTCT 59.222 40.000 5.18 0.00 34.13 3.69
336 337 6.268847 ACCGAGATTAATTAGATCTGCCTCTT 59.731 38.462 5.18 0.00 34.13 2.85
337 338 7.158021 CCGAGATTAATTAGATCTGCCTCTTT 58.842 38.462 5.18 0.00 34.13 2.52
338 339 7.117523 CCGAGATTAATTAGATCTGCCTCTTTG 59.882 40.741 5.18 0.00 34.13 2.77
339 340 7.117523 CGAGATTAATTAGATCTGCCTCTTTGG 59.882 40.741 5.18 0.00 34.13 3.28
340 341 7.230027 AGATTAATTAGATCTGCCTCTTTGGG 58.770 38.462 5.18 0.00 32.79 4.12
341 342 4.870021 AATTAGATCTGCCTCTTTGGGT 57.130 40.909 5.18 0.00 36.00 4.51
342 343 3.914426 TTAGATCTGCCTCTTTGGGTC 57.086 47.619 5.18 0.00 36.00 4.46
343 344 1.963985 AGATCTGCCTCTTTGGGTCT 58.036 50.000 0.00 0.00 36.00 3.85
344 345 2.273619 AGATCTGCCTCTTTGGGTCTT 58.726 47.619 0.00 0.00 36.00 3.01
345 346 2.646798 AGATCTGCCTCTTTGGGTCTTT 59.353 45.455 0.00 0.00 36.00 2.52
346 347 3.075134 AGATCTGCCTCTTTGGGTCTTTT 59.925 43.478 0.00 0.00 36.00 2.27
347 348 3.312736 TCTGCCTCTTTGGGTCTTTTT 57.687 42.857 0.00 0.00 36.00 1.94
348 349 4.447138 TCTGCCTCTTTGGGTCTTTTTA 57.553 40.909 0.00 0.00 36.00 1.52
349 350 4.998051 TCTGCCTCTTTGGGTCTTTTTAT 58.002 39.130 0.00 0.00 36.00 1.40
350 351 6.134535 TCTGCCTCTTTGGGTCTTTTTATA 57.865 37.500 0.00 0.00 36.00 0.98
351 352 6.731467 TCTGCCTCTTTGGGTCTTTTTATAT 58.269 36.000 0.00 0.00 36.00 0.86
352 353 7.182060 TCTGCCTCTTTGGGTCTTTTTATATT 58.818 34.615 0.00 0.00 36.00 1.28
353 354 7.122650 TCTGCCTCTTTGGGTCTTTTTATATTG 59.877 37.037 0.00 0.00 36.00 1.90
354 355 6.154363 TGCCTCTTTGGGTCTTTTTATATTGG 59.846 38.462 0.00 0.00 36.00 3.16
355 356 6.154534 GCCTCTTTGGGTCTTTTTATATTGGT 59.845 38.462 0.00 0.00 36.00 3.67
356 357 7.340999 GCCTCTTTGGGTCTTTTTATATTGGTA 59.659 37.037 0.00 0.00 36.00 3.25
357 358 9.421399 CCTCTTTGGGTCTTTTTATATTGGTAT 57.579 33.333 0.00 0.00 0.00 2.73
414 415 8.798153 GTTTAAAAAGGCAATGAGATGTTATCG 58.202 33.333 0.00 0.00 0.00 2.92
416 417 7.624360 AAAAAGGCAATGAGATGTTATCGTA 57.376 32.000 0.00 0.00 0.00 3.43
419 420 6.161855 AGGCAATGAGATGTTATCGTAGAA 57.838 37.500 0.00 0.00 43.58 2.10
445 446 8.742554 AAAATATCAAAAGGATCGTTTGTGAC 57.257 30.769 13.77 0.00 37.28 3.67
446 447 7.687941 AATATCAAAAGGATCGTTTGTGACT 57.312 32.000 13.77 11.02 37.28 3.41
447 448 7.687941 ATATCAAAAGGATCGTTTGTGACTT 57.312 32.000 13.77 8.46 37.28 3.01
448 449 5.418310 TCAAAAGGATCGTTTGTGACTTC 57.582 39.130 13.77 0.00 37.28 3.01
449 450 4.878971 TCAAAAGGATCGTTTGTGACTTCA 59.121 37.500 13.77 0.00 37.28 3.02
450 451 5.530915 TCAAAAGGATCGTTTGTGACTTCAT 59.469 36.000 13.77 0.00 37.28 2.57
451 452 5.613358 AAAGGATCGTTTGTGACTTCATC 57.387 39.130 12.39 0.00 0.00 2.92
452 453 3.254060 AGGATCGTTTGTGACTTCATCG 58.746 45.455 0.00 0.00 0.00 3.84
453 454 2.993899 GGATCGTTTGTGACTTCATCGT 59.006 45.455 0.00 0.00 0.00 3.73
454 455 3.181530 GGATCGTTTGTGACTTCATCGTG 60.182 47.826 0.00 0.00 0.00 4.35
455 456 2.816689 TCGTTTGTGACTTCATCGTGT 58.183 42.857 0.00 0.00 0.00 4.49
456 457 2.538037 TCGTTTGTGACTTCATCGTGTG 59.462 45.455 0.00 0.00 0.00 3.82
457 458 2.639751 GTTTGTGACTTCATCGTGTGC 58.360 47.619 0.00 0.00 0.00 4.57
458 459 1.946745 TTGTGACTTCATCGTGTGCA 58.053 45.000 0.00 0.00 0.00 4.57
459 460 2.168326 TGTGACTTCATCGTGTGCAT 57.832 45.000 0.00 0.00 0.00 3.96
460 461 2.493035 TGTGACTTCATCGTGTGCATT 58.507 42.857 0.00 0.00 0.00 3.56
461 462 2.223845 TGTGACTTCATCGTGTGCATTG 59.776 45.455 0.00 0.00 0.00 2.82
462 463 1.197492 TGACTTCATCGTGTGCATTGC 59.803 47.619 0.46 0.46 0.00 3.56
463 464 1.197492 GACTTCATCGTGTGCATTGCA 59.803 47.619 7.38 7.38 35.60 4.08
480 481 7.751732 TGCATTGCACTACTACTAAAAAGATG 58.248 34.615 7.38 0.00 31.71 2.90
488 489 8.883731 CACTACTACTAAAAAGATGGGTTGATG 58.116 37.037 0.00 0.00 0.00 3.07
489 490 8.603304 ACTACTACTAAAAAGATGGGTTGATGT 58.397 33.333 0.00 0.00 0.00 3.06
502 504 9.449719 AGATGGGTTGATGTAAGTAAAAAGTAG 57.550 33.333 0.00 0.00 0.00 2.57
505 507 9.492973 TGGGTTGATGTAAGTAAAAAGTAGTAC 57.507 33.333 0.00 0.00 0.00 2.73
506 508 9.492973 GGGTTGATGTAAGTAAAAAGTAGTACA 57.507 33.333 2.52 0.00 0.00 2.90
510 512 9.616634 TGATGTAAGTAAAAAGTAGTACAGTCG 57.383 33.333 2.52 0.00 0.00 4.18
511 513 9.831737 GATGTAAGTAAAAAGTAGTACAGTCGA 57.168 33.333 2.52 0.00 0.00 4.20
513 515 9.450807 TGTAAGTAAAAAGTAGTACAGTCGAAC 57.549 33.333 2.52 0.00 0.00 3.95
514 516 7.936950 AAGTAAAAAGTAGTACAGTCGAACC 57.063 36.000 2.52 0.00 0.00 3.62
528 530 0.887247 CGAACCCCATGCATGTTTGA 59.113 50.000 24.58 0.00 0.00 2.69
532 534 0.458669 CCCCATGCATGTTTGAGCTC 59.541 55.000 24.58 6.82 0.00 4.09
533 535 1.179152 CCCATGCATGTTTGAGCTCA 58.821 50.000 24.58 13.74 0.00 4.26
534 536 1.754803 CCCATGCATGTTTGAGCTCAT 59.245 47.619 24.58 0.00 0.00 2.90
535 537 2.223735 CCCATGCATGTTTGAGCTCATC 60.224 50.000 24.58 14.22 0.00 2.92
536 538 2.540973 CCATGCATGTTTGAGCTCATCG 60.541 50.000 24.58 5.66 0.00 3.84
537 539 2.097680 TGCATGTTTGAGCTCATCGA 57.902 45.000 19.04 4.30 0.00 3.59
538 540 1.733912 TGCATGTTTGAGCTCATCGAC 59.266 47.619 19.04 16.44 0.00 4.20
539 541 1.733912 GCATGTTTGAGCTCATCGACA 59.266 47.619 19.04 21.18 32.99 4.35
540 542 2.160219 GCATGTTTGAGCTCATCGACAA 59.840 45.455 19.04 5.36 32.43 3.18
541 543 3.365264 GCATGTTTGAGCTCATCGACAAA 60.365 43.478 19.04 4.53 32.43 2.83
542 544 4.786507 CATGTTTGAGCTCATCGACAAAA 58.213 39.130 19.04 3.61 34.76 2.44
543 545 4.209452 TGTTTGAGCTCATCGACAAAAC 57.791 40.909 19.04 16.68 34.76 2.43
544 546 3.003275 TGTTTGAGCTCATCGACAAAACC 59.997 43.478 19.04 3.04 34.76 3.27
545 547 2.542020 TGAGCTCATCGACAAAACCA 57.458 45.000 13.74 0.00 0.00 3.67
546 548 3.057969 TGAGCTCATCGACAAAACCAT 57.942 42.857 13.74 0.00 0.00 3.55
547 549 2.743664 TGAGCTCATCGACAAAACCATG 59.256 45.455 13.74 0.00 0.00 3.66
548 550 2.086869 AGCTCATCGACAAAACCATGG 58.913 47.619 11.19 11.19 0.00 3.66
549 551 1.812571 GCTCATCGACAAAACCATGGT 59.187 47.619 13.00 13.00 0.00 3.55
550 552 2.159517 GCTCATCGACAAAACCATGGTC 60.160 50.000 20.07 3.89 0.00 4.02
551 553 3.073678 CTCATCGACAAAACCATGGTCA 58.926 45.455 20.07 0.00 0.00 4.02
552 554 2.811431 TCATCGACAAAACCATGGTCAC 59.189 45.455 20.07 7.20 0.00 3.67
553 555 1.600023 TCGACAAAACCATGGTCACC 58.400 50.000 20.07 5.31 0.00 4.02
554 556 1.142060 TCGACAAAACCATGGTCACCT 59.858 47.619 20.07 0.00 0.00 4.00
555 557 1.535462 CGACAAAACCATGGTCACCTC 59.465 52.381 20.07 9.91 0.00 3.85
556 558 1.886542 GACAAAACCATGGTCACCTCC 59.113 52.381 20.07 2.61 0.00 4.30
557 559 1.216678 ACAAAACCATGGTCACCTCCA 59.783 47.619 20.07 0.00 42.01 3.86
559 561 2.493278 CAAAACCATGGTCACCTCCATC 59.507 50.000 20.07 0.00 45.23 3.51
560 562 0.253044 AACCATGGTCACCTCCATCG 59.747 55.000 20.07 0.00 45.23 3.84
561 563 1.524621 CCATGGTCACCTCCATCGC 60.525 63.158 2.57 0.00 45.23 4.58
562 564 1.524621 CATGGTCACCTCCATCGCC 60.525 63.158 0.00 0.00 45.23 5.54
563 565 2.746375 ATGGTCACCTCCATCGCCC 61.746 63.158 0.00 0.00 43.85 6.13
590 592 2.341911 TGCAATCCACGCAGTCGA 59.658 55.556 0.00 0.00 41.61 4.20
591 593 2.027073 TGCAATCCACGCAGTCGAC 61.027 57.895 7.70 7.70 41.61 4.20
592 594 3.071459 GCAATCCACGCAGTCGACG 62.071 63.158 10.46 6.47 41.61 5.12
701 710 2.958576 GCGCGTTTCCATTCCCAA 59.041 55.556 8.43 0.00 0.00 4.12
702 711 1.510844 GCGCGTTTCCATTCCCAAT 59.489 52.632 8.43 0.00 0.00 3.16
731 740 2.507769 GGTAACCGAGCCGTTCCG 60.508 66.667 0.00 0.00 0.00 4.30
732 741 3.184003 GTAACCGAGCCGTTCCGC 61.184 66.667 0.00 0.00 0.00 5.54
733 742 3.376078 TAACCGAGCCGTTCCGCT 61.376 61.111 0.00 0.00 43.42 5.52
779 798 1.376812 CCCCACTCCAACTAACGGC 60.377 63.158 0.00 0.00 0.00 5.68
788 807 1.538135 AACTAACGGCCCCCACTCT 60.538 57.895 0.00 0.00 0.00 3.24
835 856 2.110578 CCAATCCAAGAACCAATCCCC 58.889 52.381 0.00 0.00 0.00 4.81
838 859 0.618458 TCCAAGAACCAATCCCCGAG 59.382 55.000 0.00 0.00 0.00 4.63
845 866 1.221840 CCAATCCCCGAGTCACCAG 59.778 63.158 0.00 0.00 0.00 4.00
991 1013 4.026744 TCTTCTTCTGATCCACCTACCTG 58.973 47.826 0.00 0.00 0.00 4.00
1260 1294 4.479993 GATGCGGAGGTGGCTGCT 62.480 66.667 0.00 0.00 40.79 4.24
1272 1306 4.459089 GCTGCTGACGGGGAGGAC 62.459 72.222 0.00 0.00 0.00 3.85
1698 1733 1.001633 GGCAGGTTCTTGTTCTCCGTA 59.998 52.381 0.00 0.00 0.00 4.02
1898 1934 3.057548 TGCCAGTCGCAGCATTGG 61.058 61.111 0.00 0.00 44.64 3.16
2061 2097 1.211457 GATTCCACTGTCCCAGCTCAT 59.789 52.381 0.00 0.00 34.37 2.90
2198 2234 3.274067 GGTGACCGACAAATGGGC 58.726 61.111 0.00 0.00 33.95 5.36
2268 2304 1.516386 CTGCGGCGACACGTTCTAT 60.516 57.895 12.98 0.00 35.98 1.98
2289 2325 0.604511 TCTACTGCGAGTCCGACACA 60.605 55.000 0.40 0.00 38.22 3.72
2292 2328 1.007271 CTGCGAGTCCGACACACTT 60.007 57.895 0.40 0.00 38.22 3.16
2457 2493 4.643387 AGGGACAAGGTGGTGCGC 62.643 66.667 0.00 0.00 0.00 6.09
2616 2652 0.970937 TCTTCGGCAAGGTCCTCGAT 60.971 55.000 2.29 0.00 0.00 3.59
2619 2655 0.323629 TCGGCAAGGTCCTCGATTTT 59.676 50.000 0.00 0.00 0.00 1.82
2622 2658 0.171231 GCAAGGTCCTCGATTTTGCC 59.829 55.000 0.00 0.00 38.48 4.52
2752 2800 1.299773 CTCCTCTGAAGATCGCCGC 60.300 63.158 0.00 0.00 0.00 6.53
2800 2848 8.084073 CCACTTACACTGATGATGATTTGTTTT 58.916 33.333 0.00 0.00 0.00 2.43
2860 2908 2.104111 CCATTCCATTGCATTGCCAGAT 59.896 45.455 6.12 0.00 0.00 2.90
2980 3035 5.046014 AGCCTCAATCAGACTCACTTTGTAT 60.046 40.000 0.00 0.00 0.00 2.29
2982 3037 6.402983 GCCTCAATCAGACTCACTTTGTATTG 60.403 42.308 0.00 0.00 0.00 1.90
2983 3038 6.652481 CCTCAATCAGACTCACTTTGTATTGT 59.348 38.462 0.00 0.00 0.00 2.71
2984 3039 7.819415 CCTCAATCAGACTCACTTTGTATTGTA 59.181 37.037 0.00 0.00 0.00 2.41
2986 3041 9.154847 TCAATCAGACTCACTTTGTATTGTATG 57.845 33.333 0.00 0.00 0.00 2.39
2988 3043 7.004555 TCAGACTCACTTTGTATTGTATGGT 57.995 36.000 0.00 0.00 0.00 3.55
2989 3044 8.129496 TCAGACTCACTTTGTATTGTATGGTA 57.871 34.615 0.00 0.00 0.00 3.25
2990 3045 8.251026 TCAGACTCACTTTGTATTGTATGGTAG 58.749 37.037 0.00 0.00 0.00 3.18
2991 3046 7.010552 CAGACTCACTTTGTATTGTATGGTAGC 59.989 40.741 0.00 0.00 0.00 3.58
2992 3047 6.707290 ACTCACTTTGTATTGTATGGTAGCA 58.293 36.000 0.00 0.00 0.00 3.49
2995 3050 6.093495 TCACTTTGTATTGTATGGTAGCAAGC 59.907 38.462 0.00 0.00 0.00 4.01
2996 3051 5.943416 ACTTTGTATTGTATGGTAGCAAGCA 59.057 36.000 0.00 0.00 37.55 3.91
2997 3052 6.603201 ACTTTGTATTGTATGGTAGCAAGCAT 59.397 34.615 0.00 0.00 45.54 3.79
2998 3053 6.375945 TTGTATTGTATGGTAGCAAGCATG 57.624 37.500 0.00 0.00 43.52 4.06
2999 3054 5.436175 TGTATTGTATGGTAGCAAGCATGT 58.564 37.500 0.00 0.00 43.52 3.21
3000 3055 6.587273 TGTATTGTATGGTAGCAAGCATGTA 58.413 36.000 0.00 0.00 43.52 2.29
3002 3057 7.554476 TGTATTGTATGGTAGCAAGCATGTAAA 59.446 33.333 0.00 0.00 43.52 2.01
3005 3060 7.403312 TGTATGGTAGCAAGCATGTAAATTT 57.597 32.000 0.00 0.00 43.52 1.82
3006 3061 7.257003 TGTATGGTAGCAAGCATGTAAATTTG 58.743 34.615 0.00 0.00 43.52 2.32
3007 3062 5.973899 TGGTAGCAAGCATGTAAATTTGA 57.026 34.783 0.00 0.00 0.00 2.69
3008 3063 5.708948 TGGTAGCAAGCATGTAAATTTGAC 58.291 37.500 0.00 0.00 0.00 3.18
3009 3064 5.242615 TGGTAGCAAGCATGTAAATTTGACA 59.757 36.000 0.00 2.26 0.00 3.58
3034 3089 7.502120 ACTTGGTCAATCTACATATGATTGC 57.498 36.000 10.38 5.80 46.01 3.56
3131 3523 5.487433 TATTGACAAATCACTGTCGATGGT 58.513 37.500 14.15 0.00 45.87 3.55
3147 3539 3.004839 CGATGGTAGTGGGACTATCACAG 59.995 52.174 0.00 0.00 43.84 3.66
3170 3562 2.620251 TCCTGCGTGGATGATTAAGG 57.380 50.000 0.00 0.00 40.56 2.69
3186 3581 9.941664 GATGATTAAGGTTTGTCATCATTAGTG 57.058 33.333 8.83 0.00 43.90 2.74
3282 3677 2.093869 GTGCAAGTGCCATGATCCAAAT 60.094 45.455 0.00 0.00 41.18 2.32
3283 3678 2.568062 TGCAAGTGCCATGATCCAAATT 59.432 40.909 0.00 0.00 41.18 1.82
3379 3776 8.887717 GCAAAATTGTACTCTATCACAGATCTT 58.112 33.333 0.00 0.00 31.13 2.40
3497 3894 5.110814 TCTTTATCATTCCGGTTGGTGAT 57.889 39.130 0.00 9.75 35.68 3.06
3526 3927 2.352960 CTCTTCCGCTTAACATCTTGCC 59.647 50.000 0.00 0.00 0.00 4.52
3631 4037 2.101582 AGAACTGACACTGACCACTCAC 59.898 50.000 0.00 0.00 0.00 3.51
3676 4085 6.897966 AGAGATAGAAATCACTAACAGGACCA 59.102 38.462 0.00 0.00 32.05 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.553922 CCCTTCATACGGCATCTTCTCTC 60.554 52.174 0.00 0.00 0.00 3.20
83 84 7.352739 ACTCAGACGATTTTGTTTATGTTCAC 58.647 34.615 0.00 0.00 0.00 3.18
85 86 8.782533 AAACTCAGACGATTTTGTTTATGTTC 57.217 30.769 0.00 0.00 0.00 3.18
86 87 9.019764 CAAAACTCAGACGATTTTGTTTATGTT 57.980 29.630 0.00 0.00 38.13 2.71
150 151 9.830975 TCTGCATGCACTTAATATACTTCTAAA 57.169 29.630 18.46 0.00 0.00 1.85
195 196 9.825972 GTGCTAATCATATAATAACACGCAAAT 57.174 29.630 0.00 0.00 0.00 2.32
196 197 9.051679 AGTGCTAATCATATAATAACACGCAAA 57.948 29.630 0.00 0.00 0.00 3.68
197 198 8.601845 AGTGCTAATCATATAATAACACGCAA 57.398 30.769 0.00 0.00 0.00 4.85
198 199 9.869757 ATAGTGCTAATCATATAATAACACGCA 57.130 29.630 0.00 0.00 0.00 5.24
209 210 9.910267 TCATGCCAAATATAGTGCTAATCATAT 57.090 29.630 0.00 0.00 0.00 1.78
210 211 9.737844 TTCATGCCAAATATAGTGCTAATCATA 57.262 29.630 0.00 0.00 0.00 2.15
211 212 8.640063 TTCATGCCAAATATAGTGCTAATCAT 57.360 30.769 0.00 0.00 0.00 2.45
212 213 8.462589 TTTCATGCCAAATATAGTGCTAATCA 57.537 30.769 0.00 0.00 0.00 2.57
213 214 9.918630 AATTTCATGCCAAATATAGTGCTAATC 57.081 29.630 0.00 0.00 0.00 1.75
217 218 8.917088 AGTTAATTTCATGCCAAATATAGTGCT 58.083 29.630 0.00 0.00 0.00 4.40
218 219 8.971321 CAGTTAATTTCATGCCAAATATAGTGC 58.029 33.333 0.00 0.00 0.00 4.40
219 220 8.971321 GCAGTTAATTTCATGCCAAATATAGTG 58.029 33.333 0.00 0.00 32.49 2.74
220 221 8.694540 TGCAGTTAATTTCATGCCAAATATAGT 58.305 29.630 6.13 0.00 37.89 2.12
221 222 8.971321 GTGCAGTTAATTTCATGCCAAATATAG 58.029 33.333 0.00 0.00 37.89 1.31
222 223 7.647318 CGTGCAGTTAATTTCATGCCAAATATA 59.353 33.333 0.00 0.00 37.89 0.86
223 224 6.476380 CGTGCAGTTAATTTCATGCCAAATAT 59.524 34.615 0.00 0.00 37.89 1.28
224 225 5.804473 CGTGCAGTTAATTTCATGCCAAATA 59.196 36.000 0.00 0.00 37.89 1.40
225 226 4.626604 CGTGCAGTTAATTTCATGCCAAAT 59.373 37.500 0.00 0.00 37.89 2.32
226 227 3.986572 CGTGCAGTTAATTTCATGCCAAA 59.013 39.130 0.00 0.00 37.89 3.28
227 228 3.573598 CGTGCAGTTAATTTCATGCCAA 58.426 40.909 0.00 0.00 37.89 4.52
228 229 2.094803 CCGTGCAGTTAATTTCATGCCA 60.095 45.455 0.00 0.00 37.89 4.92
229 230 2.094752 ACCGTGCAGTTAATTTCATGCC 60.095 45.455 0.00 0.00 37.89 4.40
230 231 3.216147 ACCGTGCAGTTAATTTCATGC 57.784 42.857 0.00 2.49 39.14 4.06
231 232 5.282778 CGTTTACCGTGCAGTTAATTTCATG 59.717 40.000 0.00 0.00 0.00 3.07
232 233 5.387279 CGTTTACCGTGCAGTTAATTTCAT 58.613 37.500 0.00 0.00 0.00 2.57
233 234 4.774586 CGTTTACCGTGCAGTTAATTTCA 58.225 39.130 0.00 0.00 0.00 2.69
247 248 1.154727 GCGCTCAACACGTTTACCG 60.155 57.895 0.00 0.00 44.03 4.02
248 249 0.163146 GAGCGCTCAACACGTTTACC 59.837 55.000 31.91 0.00 0.00 2.85
249 250 0.179282 CGAGCGCTCAACACGTTTAC 60.179 55.000 34.69 6.24 0.00 2.01
250 251 0.318022 TCGAGCGCTCAACACGTTTA 60.318 50.000 34.69 4.78 0.00 2.01
251 252 1.590525 TCGAGCGCTCAACACGTTT 60.591 52.632 34.69 0.00 0.00 3.60
252 253 2.027024 TCGAGCGCTCAACACGTT 59.973 55.556 34.69 0.00 0.00 3.99
253 254 2.729862 GTCGAGCGCTCAACACGT 60.730 61.111 34.69 0.00 0.00 4.49
254 255 1.617755 AATGTCGAGCGCTCAACACG 61.618 55.000 31.93 20.44 0.00 4.49
255 256 0.179240 CAATGTCGAGCGCTCAACAC 60.179 55.000 31.93 24.81 0.00 3.32
256 257 0.319469 TCAATGTCGAGCGCTCAACA 60.319 50.000 31.47 31.47 0.00 3.33
257 258 0.790207 TTCAATGTCGAGCGCTCAAC 59.210 50.000 34.69 28.50 0.00 3.18
258 259 1.070821 CTTCAATGTCGAGCGCTCAA 58.929 50.000 34.69 17.41 0.00 3.02
259 260 1.354337 GCTTCAATGTCGAGCGCTCA 61.354 55.000 34.69 18.66 0.00 4.26
260 261 1.346538 GCTTCAATGTCGAGCGCTC 59.653 57.895 27.64 27.64 0.00 5.03
261 262 3.479370 GCTTCAATGTCGAGCGCT 58.521 55.556 11.27 11.27 0.00 5.92
264 265 0.737715 AGACCGCTTCAATGTCGAGC 60.738 55.000 0.00 0.00 34.24 5.03
265 266 2.455032 CTAGACCGCTTCAATGTCGAG 58.545 52.381 0.00 0.00 34.24 4.04
266 267 1.134367 CCTAGACCGCTTCAATGTCGA 59.866 52.381 0.00 0.00 34.24 4.20
267 268 1.135083 ACCTAGACCGCTTCAATGTCG 60.135 52.381 0.00 0.00 34.24 4.35
268 269 2.541556 GACCTAGACCGCTTCAATGTC 58.458 52.381 0.00 0.00 0.00 3.06
269 270 1.135083 CGACCTAGACCGCTTCAATGT 60.135 52.381 0.00 0.00 0.00 2.71
270 271 1.135083 ACGACCTAGACCGCTTCAATG 60.135 52.381 0.00 0.00 0.00 2.82
271 272 1.183549 ACGACCTAGACCGCTTCAAT 58.816 50.000 0.00 0.00 0.00 2.57
272 273 0.963962 AACGACCTAGACCGCTTCAA 59.036 50.000 0.00 0.00 0.00 2.69
273 274 0.242825 CAACGACCTAGACCGCTTCA 59.757 55.000 0.00 0.00 0.00 3.02
274 275 0.458025 CCAACGACCTAGACCGCTTC 60.458 60.000 0.00 0.00 0.00 3.86
275 276 0.896940 TCCAACGACCTAGACCGCTT 60.897 55.000 0.00 0.00 0.00 4.68
276 277 0.683504 ATCCAACGACCTAGACCGCT 60.684 55.000 0.00 0.00 0.00 5.52
277 278 0.175073 AATCCAACGACCTAGACCGC 59.825 55.000 0.00 0.00 0.00 5.68
278 279 1.475280 TCAATCCAACGACCTAGACCG 59.525 52.381 0.00 0.00 0.00 4.79
279 280 2.232941 TGTCAATCCAACGACCTAGACC 59.767 50.000 0.00 0.00 0.00 3.85
280 281 3.251571 GTGTCAATCCAACGACCTAGAC 58.748 50.000 0.00 0.00 0.00 2.59
281 282 2.094906 CGTGTCAATCCAACGACCTAGA 60.095 50.000 0.00 0.00 39.64 2.43
282 283 2.094906 TCGTGTCAATCCAACGACCTAG 60.095 50.000 0.00 0.00 41.08 3.02
283 284 1.887854 TCGTGTCAATCCAACGACCTA 59.112 47.619 0.00 0.00 41.08 3.08
284 285 0.677288 TCGTGTCAATCCAACGACCT 59.323 50.000 0.00 0.00 41.08 3.85
285 286 3.204505 TCGTGTCAATCCAACGACC 57.795 52.632 0.00 0.00 41.08 4.79
288 289 3.804518 TCAAATCGTGTCAATCCAACG 57.195 42.857 0.00 0.00 38.64 4.10
289 290 5.088739 GTCATCAAATCGTGTCAATCCAAC 58.911 41.667 0.00 0.00 0.00 3.77
290 291 4.155826 GGTCATCAAATCGTGTCAATCCAA 59.844 41.667 0.00 0.00 0.00 3.53
291 292 3.689161 GGTCATCAAATCGTGTCAATCCA 59.311 43.478 0.00 0.00 0.00 3.41
292 293 3.242413 CGGTCATCAAATCGTGTCAATCC 60.242 47.826 0.00 0.00 0.00 3.01
293 294 3.616821 TCGGTCATCAAATCGTGTCAATC 59.383 43.478 0.00 0.00 0.00 2.67
294 295 3.595173 TCGGTCATCAAATCGTGTCAAT 58.405 40.909 0.00 0.00 0.00 2.57
295 296 2.993220 CTCGGTCATCAAATCGTGTCAA 59.007 45.455 0.00 0.00 0.00 3.18
296 297 2.230266 TCTCGGTCATCAAATCGTGTCA 59.770 45.455 0.00 0.00 0.00 3.58
297 298 2.876091 TCTCGGTCATCAAATCGTGTC 58.124 47.619 0.00 0.00 0.00 3.67
298 299 3.526931 ATCTCGGTCATCAAATCGTGT 57.473 42.857 0.00 0.00 0.00 4.49
299 300 5.966636 TTAATCTCGGTCATCAAATCGTG 57.033 39.130 0.00 0.00 0.00 4.35
300 301 8.141909 TCTAATTAATCTCGGTCATCAAATCGT 58.858 33.333 0.00 0.00 0.00 3.73
301 302 8.520835 TCTAATTAATCTCGGTCATCAAATCG 57.479 34.615 0.00 0.00 0.00 3.34
304 305 9.481340 CAGATCTAATTAATCTCGGTCATCAAA 57.519 33.333 0.00 0.00 31.05 2.69
305 306 7.600375 GCAGATCTAATTAATCTCGGTCATCAA 59.400 37.037 0.00 0.00 31.05 2.57
306 307 7.093354 GCAGATCTAATTAATCTCGGTCATCA 58.907 38.462 0.00 0.00 31.05 3.07
307 308 6.533367 GGCAGATCTAATTAATCTCGGTCATC 59.467 42.308 0.00 0.00 31.05 2.92
308 309 6.212388 AGGCAGATCTAATTAATCTCGGTCAT 59.788 38.462 0.00 0.00 31.05 3.06
309 310 5.540337 AGGCAGATCTAATTAATCTCGGTCA 59.460 40.000 0.00 0.00 31.05 4.02
310 311 6.031751 AGGCAGATCTAATTAATCTCGGTC 57.968 41.667 0.00 0.00 31.05 4.79
311 312 5.777732 AGAGGCAGATCTAATTAATCTCGGT 59.222 40.000 0.00 0.00 31.05 4.69
312 313 6.279513 AGAGGCAGATCTAATTAATCTCGG 57.720 41.667 0.00 0.00 31.05 4.63
313 314 7.117523 CCAAAGAGGCAGATCTAATTAATCTCG 59.882 40.741 0.00 5.63 31.05 4.04
314 315 7.390162 CCCAAAGAGGCAGATCTAATTAATCTC 59.610 40.741 0.00 0.00 35.39 2.75
315 316 7.147230 ACCCAAAGAGGCAGATCTAATTAATCT 60.147 37.037 0.00 5.04 35.39 2.40
316 317 7.001073 ACCCAAAGAGGCAGATCTAATTAATC 58.999 38.462 0.00 0.00 35.39 1.75
317 318 6.915786 ACCCAAAGAGGCAGATCTAATTAAT 58.084 36.000 0.00 0.00 35.39 1.40
318 319 6.158695 AGACCCAAAGAGGCAGATCTAATTAA 59.841 38.462 0.00 0.00 35.39 1.40
319 320 5.667626 AGACCCAAAGAGGCAGATCTAATTA 59.332 40.000 0.00 0.00 35.39 1.40
320 321 4.476479 AGACCCAAAGAGGCAGATCTAATT 59.524 41.667 0.00 0.00 35.39 1.40
321 322 4.043596 AGACCCAAAGAGGCAGATCTAAT 58.956 43.478 0.00 0.00 35.39 1.73
322 323 3.454858 AGACCCAAAGAGGCAGATCTAA 58.545 45.455 0.00 0.00 35.39 2.10
323 324 3.121929 AGACCCAAAGAGGCAGATCTA 57.878 47.619 0.00 0.00 35.39 1.98
324 325 1.963985 AGACCCAAAGAGGCAGATCT 58.036 50.000 0.00 0.00 35.39 2.75
325 326 2.797177 AAGACCCAAAGAGGCAGATC 57.203 50.000 0.00 0.00 35.39 2.75
326 327 3.532641 AAAAGACCCAAAGAGGCAGAT 57.467 42.857 0.00 0.00 35.39 2.90
327 328 3.312736 AAAAAGACCCAAAGAGGCAGA 57.687 42.857 0.00 0.00 35.39 4.26
328 329 7.260603 CAATATAAAAAGACCCAAAGAGGCAG 58.739 38.462 0.00 0.00 35.39 4.85
329 330 6.154363 CCAATATAAAAAGACCCAAAGAGGCA 59.846 38.462 0.00 0.00 35.39 4.75
330 331 6.154534 ACCAATATAAAAAGACCCAAAGAGGC 59.845 38.462 0.00 0.00 35.39 4.70
331 332 7.718334 ACCAATATAAAAAGACCCAAAGAGG 57.282 36.000 0.00 0.00 37.03 3.69
396 397 5.791336 TCTACGATAACATCTCATTGCCT 57.209 39.130 0.00 0.00 0.00 4.75
397 398 6.844696 TTTCTACGATAACATCTCATTGCC 57.155 37.500 0.00 0.00 0.00 4.52
419 420 9.191995 GTCACAAACGATCCTTTTGATATTTTT 57.808 29.630 17.35 0.00 37.39 1.94
424 425 6.708502 TGAAGTCACAAACGATCCTTTTGATA 59.291 34.615 17.35 5.79 37.39 2.15
433 434 3.428870 ACACGATGAAGTCACAAACGATC 59.571 43.478 0.00 0.00 0.00 3.69
434 435 3.184379 CACACGATGAAGTCACAAACGAT 59.816 43.478 0.00 0.00 0.00 3.73
436 437 2.891391 CACACGATGAAGTCACAAACG 58.109 47.619 0.00 0.00 0.00 3.60
438 439 2.284190 TGCACACGATGAAGTCACAAA 58.716 42.857 0.00 0.00 0.00 2.83
439 440 1.946745 TGCACACGATGAAGTCACAA 58.053 45.000 0.00 0.00 0.00 3.33
440 441 2.168326 ATGCACACGATGAAGTCACA 57.832 45.000 0.00 0.00 0.00 3.58
441 442 2.843077 CAATGCACACGATGAAGTCAC 58.157 47.619 0.00 0.00 0.00 3.67
442 443 1.197492 GCAATGCACACGATGAAGTCA 59.803 47.619 0.00 0.00 0.00 3.41
443 444 1.197492 TGCAATGCACACGATGAAGTC 59.803 47.619 2.72 0.00 31.71 3.01
444 445 1.237533 TGCAATGCACACGATGAAGT 58.762 45.000 2.72 0.00 31.71 3.01
455 456 7.148255 CCATCTTTTTAGTAGTAGTGCAATGCA 60.148 37.037 2.72 2.72 35.60 3.96
456 457 7.189512 CCATCTTTTTAGTAGTAGTGCAATGC 58.810 38.462 0.00 0.00 0.00 3.56
457 458 7.336931 ACCCATCTTTTTAGTAGTAGTGCAATG 59.663 37.037 0.00 0.00 0.00 2.82
458 459 7.402862 ACCCATCTTTTTAGTAGTAGTGCAAT 58.597 34.615 0.00 0.00 0.00 3.56
459 460 6.775708 ACCCATCTTTTTAGTAGTAGTGCAA 58.224 36.000 0.00 0.00 0.00 4.08
460 461 6.368779 ACCCATCTTTTTAGTAGTAGTGCA 57.631 37.500 0.00 0.00 0.00 4.57
461 462 6.877322 TCAACCCATCTTTTTAGTAGTAGTGC 59.123 38.462 0.00 0.00 0.00 4.40
462 463 8.883731 CATCAACCCATCTTTTTAGTAGTAGTG 58.116 37.037 0.00 0.00 0.00 2.74
463 464 8.603304 ACATCAACCCATCTTTTTAGTAGTAGT 58.397 33.333 0.00 0.00 0.00 2.73
466 467 9.449719 CTTACATCAACCCATCTTTTTAGTAGT 57.550 33.333 0.00 0.00 0.00 2.73
467 468 9.449719 ACTTACATCAACCCATCTTTTTAGTAG 57.550 33.333 0.00 0.00 0.00 2.57
469 470 9.802039 TTACTTACATCAACCCATCTTTTTAGT 57.198 29.630 0.00 0.00 0.00 2.24
473 474 9.981114 CTTTTTACTTACATCAACCCATCTTTT 57.019 29.630 0.00 0.00 0.00 2.27
480 481 9.492973 TGTACTACTTTTTACTTACATCAACCC 57.507 33.333 0.00 0.00 0.00 4.11
488 489 8.906693 GGTTCGACTGTACTACTTTTTACTTAC 58.093 37.037 0.00 0.00 0.00 2.34
489 490 8.082242 GGGTTCGACTGTACTACTTTTTACTTA 58.918 37.037 0.00 0.00 0.00 2.24
502 504 0.036765 TGCATGGGGTTCGACTGTAC 60.037 55.000 0.00 0.00 0.00 2.90
504 506 0.677731 CATGCATGGGGTTCGACTGT 60.678 55.000 19.40 0.00 0.00 3.55
505 507 0.677731 ACATGCATGGGGTTCGACTG 60.678 55.000 29.41 2.68 0.00 3.51
506 508 0.038166 AACATGCATGGGGTTCGACT 59.962 50.000 29.41 3.16 0.00 4.18
507 509 0.887933 AAACATGCATGGGGTTCGAC 59.112 50.000 29.41 0.00 0.00 4.20
508 510 0.887247 CAAACATGCATGGGGTTCGA 59.113 50.000 29.41 0.00 0.00 3.71
509 511 0.887247 TCAAACATGCATGGGGTTCG 59.113 50.000 29.41 12.07 0.00 3.95
510 512 1.404583 GCTCAAACATGCATGGGGTTC 60.405 52.381 29.41 10.83 0.00 3.62
511 513 0.609662 GCTCAAACATGCATGGGGTT 59.390 50.000 29.41 17.33 0.00 4.11
512 514 0.251922 AGCTCAAACATGCATGGGGT 60.252 50.000 29.41 15.77 0.00 4.95
513 515 0.458669 GAGCTCAAACATGCATGGGG 59.541 55.000 29.41 17.93 0.00 4.96
514 516 1.179152 TGAGCTCAAACATGCATGGG 58.821 50.000 29.41 18.27 0.00 4.00
528 530 2.086869 CCATGGTTTTGTCGATGAGCT 58.913 47.619 2.57 0.00 0.00 4.09
532 534 2.095263 GGTGACCATGGTTTTGTCGATG 60.095 50.000 20.85 0.00 0.00 3.84
533 535 2.159382 GGTGACCATGGTTTTGTCGAT 58.841 47.619 20.85 0.00 0.00 3.59
534 536 1.142060 AGGTGACCATGGTTTTGTCGA 59.858 47.619 20.85 0.00 0.00 4.20
535 537 1.535462 GAGGTGACCATGGTTTTGTCG 59.465 52.381 20.85 0.00 0.00 4.35
536 538 1.886542 GGAGGTGACCATGGTTTTGTC 59.113 52.381 20.85 13.52 0.00 3.18
537 539 1.216678 TGGAGGTGACCATGGTTTTGT 59.783 47.619 20.85 4.53 34.77 2.83
538 540 1.993956 TGGAGGTGACCATGGTTTTG 58.006 50.000 20.85 0.00 34.77 2.44
546 548 3.399181 GGGCGATGGAGGTGACCA 61.399 66.667 3.63 0.00 44.41 4.02
547 549 4.176752 GGGGCGATGGAGGTGACC 62.177 72.222 0.00 0.00 0.00 4.02
548 550 3.399181 TGGGGCGATGGAGGTGAC 61.399 66.667 0.00 0.00 0.00 3.67
549 551 3.399181 GTGGGGCGATGGAGGTGA 61.399 66.667 0.00 0.00 0.00 4.02
550 552 4.489771 GGTGGGGCGATGGAGGTG 62.490 72.222 0.00 0.00 0.00 4.00
551 553 4.741239 AGGTGGGGCGATGGAGGT 62.741 66.667 0.00 0.00 0.00 3.85
552 554 4.181010 CAGGTGGGGCGATGGAGG 62.181 72.222 0.00 0.00 0.00 4.30
553 555 4.864334 GCAGGTGGGGCGATGGAG 62.864 72.222 0.00 0.00 0.00 3.86
701 710 3.004354 TTACCGGTGGCGGTGGAT 61.004 61.111 19.93 0.00 42.89 3.41
702 711 4.006357 GTTACCGGTGGCGGTGGA 62.006 66.667 19.93 0.00 42.89 4.02
740 749 2.088096 TTGGGGAAAGTGGGCAGGA 61.088 57.895 0.00 0.00 0.00 3.86
741 750 1.908299 GTTGGGGAAAGTGGGCAGG 60.908 63.158 0.00 0.00 0.00 4.85
742 751 1.908299 GGTTGGGGAAAGTGGGCAG 60.908 63.158 0.00 0.00 0.00 4.85
743 752 2.200092 GGTTGGGGAAAGTGGGCA 59.800 61.111 0.00 0.00 0.00 5.36
744 753 2.603473 GGGTTGGGGAAAGTGGGC 60.603 66.667 0.00 0.00 0.00 5.36
764 783 1.376812 GGGGCCGTTAGTTGGAGTG 60.377 63.158 0.00 0.00 0.00 3.51
777 796 3.003763 ACGAGAAGAGTGGGGGCC 61.004 66.667 0.00 0.00 0.00 5.80
779 798 1.324005 GGAGACGAGAAGAGTGGGGG 61.324 65.000 0.00 0.00 0.00 5.40
835 856 4.436998 GCCCGGTCTGGTGACTCG 62.437 72.222 0.00 0.00 42.54 4.18
883 905 3.854669 CTGGCGAGCGAGGGGATT 61.855 66.667 0.00 0.00 0.00 3.01
1256 1290 3.775654 GGTCCTCCCCGTCAGCAG 61.776 72.222 0.00 0.00 0.00 4.24
1680 1715 2.338500 GCTACGGAGAACAAGAACCTG 58.662 52.381 0.00 0.00 0.00 4.00
1710 1745 0.852412 CGACAACGTAGAGCTCGTCG 60.852 60.000 24.07 24.07 40.69 5.12
1941 1977 4.659172 CCCAGCCGGAACTTGCCA 62.659 66.667 5.05 0.00 0.00 4.92
2157 2193 1.134226 CGTATATTTCGCCGGACACC 58.866 55.000 5.05 0.00 0.00 4.16
2198 2234 4.587189 GGAACCCGGCGATCTCGG 62.587 72.222 9.30 14.88 46.43 4.63
2268 2304 0.604511 TGTCGGACTCGCAGTAGACA 60.605 55.000 9.88 15.86 40.87 3.41
2289 2325 0.456221 CGAGATGGTAGGCGACAAGT 59.544 55.000 0.00 0.00 0.00 3.16
2292 2328 4.649845 TCGAGATGGTAGGCGACA 57.350 55.556 0.00 0.00 0.00 4.35
2752 2800 6.017852 GTGGAAAAGGAAAACAGAGTAGACAG 60.018 42.308 0.00 0.00 0.00 3.51
2800 2848 3.738982 TCAATCAGCTCGTGGAAGAAAA 58.261 40.909 0.00 0.00 0.00 2.29
2888 2940 4.863491 ACATGTTGAACAAACTCAGCATC 58.137 39.130 0.62 0.00 43.07 3.91
2957 3012 3.406764 ACAAAGTGAGTCTGATTGAGGC 58.593 45.455 8.63 0.00 0.00 4.70
2960 3015 9.154847 CATACAATACAAAGTGAGTCTGATTGA 57.845 33.333 8.63 0.00 0.00 2.57
2980 3035 7.403312 AATTTACATGCTTGCTACCATACAA 57.597 32.000 0.00 0.00 0.00 2.41
2982 3037 7.432252 GTCAAATTTACATGCTTGCTACCATAC 59.568 37.037 0.00 0.00 0.00 2.39
2983 3038 7.121907 TGTCAAATTTACATGCTTGCTACCATA 59.878 33.333 0.00 0.00 0.00 2.74
2984 3039 6.071447 TGTCAAATTTACATGCTTGCTACCAT 60.071 34.615 0.00 0.00 0.00 3.55
2986 3041 5.708948 TGTCAAATTTACATGCTTGCTACC 58.291 37.500 0.00 0.00 0.00 3.18
2988 3043 6.980593 AGTTGTCAAATTTACATGCTTGCTA 58.019 32.000 0.00 0.00 0.00 3.49
2989 3044 5.846203 AGTTGTCAAATTTACATGCTTGCT 58.154 33.333 0.00 0.00 0.00 3.91
2990 3045 6.357198 CAAGTTGTCAAATTTACATGCTTGC 58.643 36.000 18.40 0.00 35.48 4.01
2991 3046 6.479660 ACCAAGTTGTCAAATTTACATGCTTG 59.520 34.615 20.43 20.43 38.51 4.01
2992 3047 6.581712 ACCAAGTTGTCAAATTTACATGCTT 58.418 32.000 1.45 2.55 0.00 3.91
3005 3060 7.619965 TCATATGTAGATTGACCAAGTTGTCA 58.380 34.615 1.90 3.35 43.26 3.58
3006 3061 8.668510 ATCATATGTAGATTGACCAAGTTGTC 57.331 34.615 1.90 0.72 35.77 3.18
3034 3089 2.478134 CCGTTTCTCTTTGCTGTCTGAG 59.522 50.000 0.00 0.00 0.00 3.35
3053 3116 1.135939 CATGCACAGTCACATGCCG 59.864 57.895 1.84 0.00 41.33 5.69
3109 3501 4.326826 ACCATCGACAGTGATTTGTCAAT 58.673 39.130 0.00 0.00 46.11 2.57
3113 3505 4.245660 CACTACCATCGACAGTGATTTGT 58.754 43.478 11.04 0.00 41.80 2.83
3131 3523 3.388024 GGATTGCTGTGATAGTCCCACTA 59.612 47.826 0.00 0.00 34.82 2.74
3170 3562 9.546909 CATGAACTAACACTAATGATGACAAAC 57.453 33.333 0.00 0.00 0.00 2.93
3301 3696 9.627123 CTCACCCTTTCCTTCATAAAATATACA 57.373 33.333 0.00 0.00 0.00 2.29
3324 3721 4.248174 ACAGATCTGTCCTCATCTCTCA 57.752 45.455 22.89 0.00 40.24 3.27
3379 3776 6.014647 ACAATTGGGTAGACTAGTACTGTCA 58.985 40.000 20.38 9.30 36.94 3.58
3421 3818 0.449388 GCAATGGCTCTTCAGAACGG 59.551 55.000 0.00 0.00 36.96 4.44
3526 3927 4.494484 TCTCAACTGGTATGACATTCACG 58.506 43.478 0.00 0.00 0.00 4.35
3659 4065 4.373156 AAGCTGGTCCTGTTAGTGATTT 57.627 40.909 0.00 0.00 0.00 2.17
3668 4074 2.846532 CCCCAAAGCTGGTCCTGT 59.153 61.111 0.00 0.00 41.72 4.00
3676 4085 2.283460 GCTCTTGGCCCCAAAGCT 60.283 61.111 18.51 0.00 35.33 3.74
3700 4109 4.508124 GCTCTGGTTCATGATAAGGTAACG 59.492 45.833 0.00 0.00 46.39 3.18


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

AutoCloner maintained by Alex Coulton.