Multiple sequence alignment - TraesCS6A01G226900

Loading Multiple Alignment...

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 TraesCS6A01G226900 chr6A 100.000 2454 0 0 1 2454 427195580 427193127 0.000000e+00 4532
1 TraesCS6A01G226900 chr6A 93.447 412 23 3 112 520 531028179 531027769 2.090000e-170 608
2 TraesCS6A01G226900 chr6D 89.074 1986 100 50 521 2454 293493576 293495496 0.000000e+00 2357
3 TraesCS6A01G226900 chr6D 93.478 414 23 4 109 520 178795927 178796338 1.610000e-171 612
4 TraesCS6A01G226900 chr6D 88.496 113 2 4 1 111 293493480 293493583 2.560000e-25 126
5 TraesCS6A01G226900 chr6B 89.266 1444 72 30 1049 2454 458007242 458008640 0.000000e+00 1731
6 TraesCS6A01G226900 chr6B 86.000 450 39 12 521 966 458006499 458006928 6.180000e-126 460
7 TraesCS6A01G226900 chr3D 94.712 416 18 4 107 520 43798013 43797600 0.000000e+00 643
8 TraesCS6A01G226900 chr3D 93.947 413 20 4 113 523 445107450 445107041 9.640000e-174 619
9 TraesCS6A01G226900 chr3D 93.917 411 21 4 112 520 570039119 570039527 3.470000e-173 617
10 TraesCS6A01G226900 chr1D 94.189 413 17 6 113 520 427487169 427487579 7.450000e-175 623
11 TraesCS6A01G226900 chr3A 94.146 410 19 5 113 520 86609511 86609105 9.640000e-174 619
12 TraesCS6A01G226900 chr3A 93.253 415 23 5 110 520 110335795 110335382 7.500000e-170 606
13 TraesCS6A01G226900 chr5D 93.705 413 22 3 112 520 332222411 332221999 1.250000e-172 616


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 TraesCS6A01G226900 chr6A 427193127 427195580 2453 True 4532.0 4532 100.000 1 2454 1 chr6A.!!$R1 2453
1 TraesCS6A01G226900 chr6D 293493480 293495496 2016 False 1241.5 2357 88.785 1 2454 2 chr6D.!!$F2 2453
2 TraesCS6A01G226900 chr6B 458006499 458008640 2141 False 1095.5 1731 87.633 521 2454 2 chr6B.!!$F1 1933

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
129 132 0.319469 TTGAGTGCGACGAATCTGCA 60.319 50.0 0.0 0.0 33.79 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1980 0.250467 ACGGATTTGCACTGCACTCT 60.25 50.0 2.26 0.0 38.71 3.24 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 69 8.262601 ACTTCCATGTTTTTCCTCCTTAATTT 57.737 30.769 0.00 0.00 0.00 1.82
73 76 8.533569 TGTTTTTCCTCCTTAATTTGAGAACT 57.466 30.769 0.00 0.00 0.00 3.01
74 77 9.635404 TGTTTTTCCTCCTTAATTTGAGAACTA 57.365 29.630 0.00 0.00 0.00 2.24
119 122 8.262715 TGTTAAGAAATTATCATTGAGTGCGA 57.737 30.769 0.00 0.00 0.00 5.10
120 123 8.175069 TGTTAAGAAATTATCATTGAGTGCGAC 58.825 33.333 0.00 0.00 0.00 5.19
121 124 5.395325 AGAAATTATCATTGAGTGCGACG 57.605 39.130 0.00 0.00 0.00 5.12
122 125 5.109210 AGAAATTATCATTGAGTGCGACGA 58.891 37.500 0.00 0.00 0.00 4.20
123 126 5.580691 AGAAATTATCATTGAGTGCGACGAA 59.419 36.000 0.00 0.00 0.00 3.85
124 127 5.991328 AATTATCATTGAGTGCGACGAAT 57.009 34.783 0.00 0.00 0.00 3.34
125 128 5.582439 ATTATCATTGAGTGCGACGAATC 57.418 39.130 0.00 0.00 0.00 2.52
126 129 2.654749 TCATTGAGTGCGACGAATCT 57.345 45.000 0.00 0.00 0.00 2.40
127 130 2.262211 TCATTGAGTGCGACGAATCTG 58.738 47.619 0.00 0.00 0.00 2.90
128 131 1.002366 ATTGAGTGCGACGAATCTGC 58.998 50.000 0.00 0.00 0.00 4.26
129 132 0.319469 TTGAGTGCGACGAATCTGCA 60.319 50.000 0.00 0.00 33.79 4.41
130 133 1.008875 TGAGTGCGACGAATCTGCAC 61.009 55.000 8.41 8.41 46.53 4.57
131 134 1.687494 GAGTGCGACGAATCTGCACC 61.687 60.000 12.43 1.86 46.96 5.01
132 135 2.434185 TGCGACGAATCTGCACCC 60.434 61.111 0.00 0.00 32.09 4.61
133 136 3.554692 GCGACGAATCTGCACCCG 61.555 66.667 0.00 0.00 0.00 5.28
134 137 2.885644 CGACGAATCTGCACCCGG 60.886 66.667 0.00 0.00 0.00 5.73
135 138 2.511600 GACGAATCTGCACCCGGG 60.512 66.667 22.25 22.25 0.00 5.73
136 139 4.778143 ACGAATCTGCACCCGGGC 62.778 66.667 24.08 8.36 0.00 6.13
137 140 4.473520 CGAATCTGCACCCGGGCT 62.474 66.667 24.08 4.79 34.04 5.19
138 141 2.514824 GAATCTGCACCCGGGCTC 60.515 66.667 24.08 13.62 34.04 4.70
139 142 3.329542 GAATCTGCACCCGGGCTCA 62.330 63.158 24.08 17.97 34.04 4.26
140 143 3.335356 AATCTGCACCCGGGCTCAG 62.335 63.158 27.84 27.84 34.04 3.35
169 172 2.697431 CGCTCACGGGAAAAATCAAA 57.303 45.000 0.00 0.00 34.97 2.69
170 173 3.006659 CGCTCACGGGAAAAATCAAAA 57.993 42.857 0.00 0.00 34.97 2.44
171 174 2.724174 CGCTCACGGGAAAAATCAAAAC 59.276 45.455 0.00 0.00 34.97 2.43
172 175 3.712187 GCTCACGGGAAAAATCAAAACA 58.288 40.909 0.00 0.00 0.00 2.83
173 176 4.116238 GCTCACGGGAAAAATCAAAACAA 58.884 39.130 0.00 0.00 0.00 2.83
174 177 4.568760 GCTCACGGGAAAAATCAAAACAAA 59.431 37.500 0.00 0.00 0.00 2.83
175 178 5.236263 GCTCACGGGAAAAATCAAAACAAAT 59.764 36.000 0.00 0.00 0.00 2.32
176 179 6.422400 GCTCACGGGAAAAATCAAAACAAATA 59.578 34.615 0.00 0.00 0.00 1.40
177 180 7.568679 GCTCACGGGAAAAATCAAAACAAATAC 60.569 37.037 0.00 0.00 0.00 1.89
178 181 7.265673 TCACGGGAAAAATCAAAACAAATACA 58.734 30.769 0.00 0.00 0.00 2.29
179 182 7.764443 TCACGGGAAAAATCAAAACAAATACAA 59.236 29.630 0.00 0.00 0.00 2.41
180 183 8.391106 CACGGGAAAAATCAAAACAAATACAAA 58.609 29.630 0.00 0.00 0.00 2.83
181 184 8.947115 ACGGGAAAAATCAAAACAAATACAAAA 58.053 25.926 0.00 0.00 0.00 2.44
182 185 9.774742 CGGGAAAAATCAAAACAAATACAAAAA 57.225 25.926 0.00 0.00 0.00 1.94
232 235 9.494271 AATTGTGTGATAGATAATTAGATGCGT 57.506 29.630 0.00 0.00 0.00 5.24
233 236 7.873739 TGTGTGATAGATAATTAGATGCGTG 57.126 36.000 0.00 0.00 0.00 5.34
234 237 7.657336 TGTGTGATAGATAATTAGATGCGTGA 58.343 34.615 0.00 0.00 0.00 4.35
235 238 7.809806 TGTGTGATAGATAATTAGATGCGTGAG 59.190 37.037 0.00 0.00 0.00 3.51
236 239 7.274468 GTGTGATAGATAATTAGATGCGTGAGG 59.726 40.741 0.00 0.00 0.00 3.86
237 240 7.039714 TGTGATAGATAATTAGATGCGTGAGGT 60.040 37.037 0.00 0.00 0.00 3.85
238 241 7.815068 GTGATAGATAATTAGATGCGTGAGGTT 59.185 37.037 0.00 0.00 0.00 3.50
239 242 8.029522 TGATAGATAATTAGATGCGTGAGGTTC 58.970 37.037 0.00 0.00 0.00 3.62
240 243 5.223382 AGATAATTAGATGCGTGAGGTTCG 58.777 41.667 0.00 0.00 0.00 3.95
249 252 2.969443 CGTGAGGTTCGCTGAAAAAT 57.031 45.000 0.00 0.00 0.00 1.82
250 253 3.268013 CGTGAGGTTCGCTGAAAAATT 57.732 42.857 0.00 0.00 0.00 1.82
251 254 3.226347 CGTGAGGTTCGCTGAAAAATTC 58.774 45.455 0.00 0.00 0.00 2.17
252 255 3.303725 CGTGAGGTTCGCTGAAAAATTCA 60.304 43.478 0.00 0.00 38.17 2.57
253 256 4.606961 GTGAGGTTCGCTGAAAAATTCAA 58.393 39.130 0.00 0.00 39.58 2.69
254 257 4.441087 GTGAGGTTCGCTGAAAAATTCAAC 59.559 41.667 0.00 0.00 39.58 3.18
255 258 4.338118 TGAGGTTCGCTGAAAAATTCAACT 59.662 37.500 0.00 0.00 39.58 3.16
256 259 4.860072 AGGTTCGCTGAAAAATTCAACTC 58.140 39.130 0.00 0.00 39.58 3.01
257 260 3.664025 GGTTCGCTGAAAAATTCAACTCG 59.336 43.478 0.00 0.00 39.58 4.18
258 261 4.279659 GTTCGCTGAAAAATTCAACTCGT 58.720 39.130 0.00 0.00 39.58 4.18
259 262 4.545823 TCGCTGAAAAATTCAACTCGTT 57.454 36.364 0.00 0.00 39.58 3.85
260 263 4.915704 TCGCTGAAAAATTCAACTCGTTT 58.084 34.783 0.00 0.00 39.58 3.60
261 264 4.732923 TCGCTGAAAAATTCAACTCGTTTG 59.267 37.500 0.00 0.00 39.58 2.93
262 265 4.085619 CGCTGAAAAATTCAACTCGTTTGG 60.086 41.667 0.00 0.00 39.58 3.28
263 266 5.040635 GCTGAAAAATTCAACTCGTTTGGA 58.959 37.500 0.00 0.00 39.58 3.53
264 267 5.051708 GCTGAAAAATTCAACTCGTTTGGAC 60.052 40.000 0.00 0.00 39.58 4.02
265 268 5.955488 TGAAAAATTCAACTCGTTTGGACA 58.045 33.333 0.00 0.00 36.59 4.02
266 269 6.568869 TGAAAAATTCAACTCGTTTGGACAT 58.431 32.000 0.00 0.00 36.59 3.06
267 270 7.038659 TGAAAAATTCAACTCGTTTGGACATT 58.961 30.769 0.00 0.00 36.59 2.71
268 271 7.547370 TGAAAAATTCAACTCGTTTGGACATTT 59.453 29.630 0.00 0.00 36.59 2.32
269 272 6.826893 AAATTCAACTCGTTTGGACATTTG 57.173 33.333 0.69 0.00 35.69 2.32
270 273 5.766150 ATTCAACTCGTTTGGACATTTGA 57.234 34.783 0.69 0.00 35.69 2.69
271 274 4.811555 TCAACTCGTTTGGACATTTGAG 57.188 40.909 0.69 0.00 35.69 3.02
272 275 3.003275 TCAACTCGTTTGGACATTTGAGC 59.997 43.478 0.69 0.00 35.69 4.26
273 276 2.571212 ACTCGTTTGGACATTTGAGCA 58.429 42.857 0.00 0.00 0.00 4.26
274 277 2.948979 ACTCGTTTGGACATTTGAGCAA 59.051 40.909 0.00 0.00 0.00 3.91
275 278 3.003689 ACTCGTTTGGACATTTGAGCAAG 59.996 43.478 0.00 0.00 0.00 4.01
276 279 2.948979 TCGTTTGGACATTTGAGCAAGT 59.051 40.909 0.00 0.00 0.00 3.16
277 280 3.003275 TCGTTTGGACATTTGAGCAAGTC 59.997 43.478 0.00 0.00 0.00 3.01
278 281 3.003689 CGTTTGGACATTTGAGCAAGTCT 59.996 43.478 0.00 0.00 0.00 3.24
279 282 4.293415 GTTTGGACATTTGAGCAAGTCTG 58.707 43.478 0.00 0.00 0.00 3.51
280 283 3.213206 TGGACATTTGAGCAAGTCTGT 57.787 42.857 0.00 0.00 0.00 3.41
281 284 2.880268 TGGACATTTGAGCAAGTCTGTG 59.120 45.455 0.00 0.00 0.00 3.66
282 285 2.351157 GGACATTTGAGCAAGTCTGTGC 60.351 50.000 0.00 0.00 45.28 4.57
305 308 4.584327 AAAAAGACAAAATCGGGGTCTG 57.416 40.909 0.00 0.00 40.80 3.51
306 309 2.951229 AAGACAAAATCGGGGTCTGT 57.049 45.000 0.00 0.00 40.80 3.41
307 310 4.360951 AAAGACAAAATCGGGGTCTGTA 57.639 40.909 0.00 0.00 40.80 2.74
308 311 4.360951 AAGACAAAATCGGGGTCTGTAA 57.639 40.909 0.00 0.00 40.80 2.41
309 312 4.360951 AGACAAAATCGGGGTCTGTAAA 57.639 40.909 0.00 0.00 40.21 2.01
310 313 4.721132 AGACAAAATCGGGGTCTGTAAAA 58.279 39.130 0.00 0.00 40.21 1.52
311 314 5.134661 AGACAAAATCGGGGTCTGTAAAAA 58.865 37.500 0.00 0.00 40.21 1.94
333 336 6.490566 AAAGTTTACTGTTCACGAACTGTT 57.509 33.333 22.23 10.63 46.58 3.16
334 337 6.490566 AAGTTTACTGTTCACGAACTGTTT 57.509 33.333 22.23 11.37 46.58 2.83
335 338 6.490566 AGTTTACTGTTCACGAACTGTTTT 57.509 33.333 22.23 5.92 46.58 2.43
336 339 6.311723 AGTTTACTGTTCACGAACTGTTTTG 58.688 36.000 22.23 0.00 46.58 2.44
337 340 6.148150 AGTTTACTGTTCACGAACTGTTTTGA 59.852 34.615 22.23 6.83 46.58 2.69
338 341 4.336532 ACTGTTCACGAACTGTTTTGAC 57.663 40.909 14.48 3.50 46.58 3.18
339 342 3.126343 ACTGTTCACGAACTGTTTTGACC 59.874 43.478 14.48 1.02 46.58 4.02
340 343 2.420722 TGTTCACGAACTGTTTTGACCC 59.579 45.455 11.01 2.06 41.67 4.46
341 344 1.292061 TCACGAACTGTTTTGACCCG 58.708 50.000 0.00 0.00 0.00 5.28
342 345 1.134759 TCACGAACTGTTTTGACCCGA 60.135 47.619 0.00 0.00 0.00 5.14
343 346 1.871039 CACGAACTGTTTTGACCCGAT 59.129 47.619 0.00 0.00 0.00 4.18
344 347 2.289547 CACGAACTGTTTTGACCCGATT 59.710 45.455 0.00 0.00 0.00 3.34
345 348 2.946990 ACGAACTGTTTTGACCCGATTT 59.053 40.909 0.00 0.00 0.00 2.17
346 349 3.242936 ACGAACTGTTTTGACCCGATTTG 60.243 43.478 0.00 0.00 0.00 2.32
347 350 3.242936 CGAACTGTTTTGACCCGATTTGT 60.243 43.478 0.00 0.00 0.00 2.83
348 351 3.982576 ACTGTTTTGACCCGATTTGTC 57.017 42.857 0.00 0.00 0.00 3.18
349 352 3.551846 ACTGTTTTGACCCGATTTGTCT 58.448 40.909 0.00 0.00 33.83 3.41
350 353 3.951680 ACTGTTTTGACCCGATTTGTCTT 59.048 39.130 0.00 0.00 33.83 3.01
351 354 4.401202 ACTGTTTTGACCCGATTTGTCTTT 59.599 37.500 0.00 0.00 33.83 2.52
352 355 5.105513 ACTGTTTTGACCCGATTTGTCTTTT 60.106 36.000 0.00 0.00 33.83 2.27
353 356 5.725362 TGTTTTGACCCGATTTGTCTTTTT 58.275 33.333 0.00 0.00 33.83 1.94
370 373 2.743636 TTTTGCCGAGACCTACTCAG 57.256 50.000 0.00 0.00 45.14 3.35
371 374 1.919240 TTTGCCGAGACCTACTCAGA 58.081 50.000 0.00 0.00 45.14 3.27
372 375 2.145397 TTGCCGAGACCTACTCAGAT 57.855 50.000 0.00 0.00 45.14 2.90
373 376 3.292492 TTGCCGAGACCTACTCAGATA 57.708 47.619 0.00 0.00 45.14 1.98
374 377 3.510531 TGCCGAGACCTACTCAGATAT 57.489 47.619 0.00 0.00 45.14 1.63
375 378 3.413327 TGCCGAGACCTACTCAGATATC 58.587 50.000 0.00 0.00 45.14 1.63
376 379 2.750712 GCCGAGACCTACTCAGATATCC 59.249 54.545 0.00 0.00 45.14 2.59
377 380 3.811098 GCCGAGACCTACTCAGATATCCA 60.811 52.174 0.00 0.00 45.14 3.41
378 381 4.399219 CCGAGACCTACTCAGATATCCAA 58.601 47.826 0.00 0.00 45.14 3.53
379 382 4.827835 CCGAGACCTACTCAGATATCCAAA 59.172 45.833 0.00 0.00 45.14 3.28
380 383 5.478679 CCGAGACCTACTCAGATATCCAAAT 59.521 44.000 0.00 0.00 45.14 2.32
381 384 6.385843 CGAGACCTACTCAGATATCCAAATG 58.614 44.000 0.00 0.00 45.14 2.32
382 385 6.207614 CGAGACCTACTCAGATATCCAAATGA 59.792 42.308 0.00 0.00 45.14 2.57
383 386 7.255625 CGAGACCTACTCAGATATCCAAATGAA 60.256 40.741 0.00 0.00 45.14 2.57
384 387 8.503428 AGACCTACTCAGATATCCAAATGAAT 57.497 34.615 0.00 0.00 0.00 2.57
385 388 8.943085 AGACCTACTCAGATATCCAAATGAATT 58.057 33.333 0.00 0.00 0.00 2.17
386 389 8.915057 ACCTACTCAGATATCCAAATGAATTG 57.085 34.615 0.00 0.00 38.84 2.32
387 390 8.717717 ACCTACTCAGATATCCAAATGAATTGA 58.282 33.333 0.00 0.00 41.85 2.57
388 391 9.565090 CCTACTCAGATATCCAAATGAATTGAA 57.435 33.333 0.00 0.00 41.85 2.69
398 401 7.119605 TCCAAATGAATTGAAATTTTGAGCG 57.880 32.000 0.00 0.00 41.85 5.03
399 402 6.147492 TCCAAATGAATTGAAATTTTGAGCGG 59.853 34.615 0.00 0.00 41.85 5.52
400 403 6.147492 CCAAATGAATTGAAATTTTGAGCGGA 59.853 34.615 0.00 0.00 41.85 5.54
401 404 7.148373 CCAAATGAATTGAAATTTTGAGCGGAT 60.148 33.333 0.00 0.00 41.85 4.18
402 405 7.529880 AATGAATTGAAATTTTGAGCGGATC 57.470 32.000 0.00 0.00 0.00 3.36
403 406 6.271488 TGAATTGAAATTTTGAGCGGATCT 57.729 33.333 0.00 0.00 0.00 2.75
404 407 6.324819 TGAATTGAAATTTTGAGCGGATCTC 58.675 36.000 0.00 0.00 42.23 2.75
418 421 4.997905 CGGATCTCACGCATCAAATTAT 57.002 40.909 0.00 0.00 0.00 1.28
419 422 4.950926 CGGATCTCACGCATCAAATTATC 58.049 43.478 0.00 0.00 0.00 1.75
420 423 4.687948 CGGATCTCACGCATCAAATTATCT 59.312 41.667 0.00 0.00 0.00 1.98
421 424 5.863935 CGGATCTCACGCATCAAATTATCTA 59.136 40.000 0.00 0.00 0.00 1.98
422 425 6.183360 CGGATCTCACGCATCAAATTATCTAC 60.183 42.308 0.00 0.00 0.00 2.59
423 426 6.091441 GGATCTCACGCATCAAATTATCTACC 59.909 42.308 0.00 0.00 0.00 3.18
424 427 5.912892 TCTCACGCATCAAATTATCTACCA 58.087 37.500 0.00 0.00 0.00 3.25
425 428 5.753438 TCTCACGCATCAAATTATCTACCAC 59.247 40.000 0.00 0.00 0.00 4.16
426 429 5.423886 TCACGCATCAAATTATCTACCACA 58.576 37.500 0.00 0.00 0.00 4.17
427 430 5.293324 TCACGCATCAAATTATCTACCACAC 59.707 40.000 0.00 0.00 0.00 3.82
428 431 5.064579 CACGCATCAAATTATCTACCACACA 59.935 40.000 0.00 0.00 0.00 3.72
429 432 5.645929 ACGCATCAAATTATCTACCACACAA 59.354 36.000 0.00 0.00 0.00 3.33
430 433 6.150307 ACGCATCAAATTATCTACCACACAAA 59.850 34.615 0.00 0.00 0.00 2.83
431 434 7.026562 CGCATCAAATTATCTACCACACAAAA 58.973 34.615 0.00 0.00 0.00 2.44
432 435 7.540400 CGCATCAAATTATCTACCACACAAAAA 59.460 33.333 0.00 0.00 0.00 1.94
488 491 3.758172 TTTTTGCTGACCGGGAGC 58.242 55.556 18.39 18.39 36.95 4.70
489 492 1.152860 TTTTTGCTGACCGGGAGCA 60.153 52.632 22.70 22.70 44.75 4.26
490 493 1.172180 TTTTTGCTGACCGGGAGCAG 61.172 55.000 24.44 19.65 46.81 4.24
494 497 3.385384 CTGACCGGGAGCAGCTGA 61.385 66.667 20.43 0.00 0.00 4.26
495 498 3.368190 CTGACCGGGAGCAGCTGAG 62.368 68.421 20.43 0.00 0.00 3.35
496 499 4.828925 GACCGGGAGCAGCTGAGC 62.829 72.222 20.43 7.89 0.00 4.26
513 516 3.089874 CCCGGGCTCCAGGATGAA 61.090 66.667 8.08 0.00 39.69 2.57
514 517 2.455565 CCCGGGCTCCAGGATGAAT 61.456 63.158 8.08 0.00 39.69 2.57
515 518 1.533711 CCGGGCTCCAGGATGAATT 59.466 57.895 0.00 0.00 39.69 2.17
516 519 0.764890 CCGGGCTCCAGGATGAATTA 59.235 55.000 0.00 0.00 39.69 1.40
517 520 1.352352 CCGGGCTCCAGGATGAATTAT 59.648 52.381 0.00 0.00 39.69 1.28
518 521 2.616510 CCGGGCTCCAGGATGAATTATC 60.617 54.545 0.00 0.00 39.69 1.75
519 522 2.704572 GGGCTCCAGGATGAATTATCG 58.295 52.381 0.00 0.00 39.69 2.92
528 531 9.610705 CTCCAGGATGAATTATCGATTATCATT 57.389 33.333 16.50 6.62 39.69 2.57
546 550 8.721019 TTATCATTGCCTTTTTGAATGGAATC 57.279 30.769 0.00 0.00 0.00 2.52
590 594 5.240623 TGGATCAAACAATATTATCGTGGGC 59.759 40.000 0.00 0.00 0.00 5.36
603 607 0.875908 CGTGGGCATACATCGTGAGG 60.876 60.000 0.00 0.00 0.00 3.86
664 668 8.687824 AAATTCATAGTCAAATTTAAGCACGG 57.312 30.769 0.00 0.00 34.25 4.94
669 673 9.168451 TCATAGTCAAATTTAAGCACGGATTAA 57.832 29.630 0.00 0.00 0.00 1.40
682 686 8.757164 AAGCACGGATTAAATTTTAGGAAAAG 57.243 30.769 0.00 0.00 33.22 2.27
683 687 7.320399 AGCACGGATTAAATTTTAGGAAAAGG 58.680 34.615 0.00 0.00 33.22 3.11
684 688 7.177744 AGCACGGATTAAATTTTAGGAAAAGGA 59.822 33.333 0.00 0.00 33.22 3.36
685 689 7.488150 GCACGGATTAAATTTTAGGAAAAGGAG 59.512 37.037 0.00 0.00 33.22 3.69
686 690 8.736244 CACGGATTAAATTTTAGGAAAAGGAGA 58.264 33.333 0.00 0.00 33.22 3.71
687 691 8.737175 ACGGATTAAATTTTAGGAAAAGGAGAC 58.263 33.333 0.00 0.00 33.22 3.36
689 693 9.031537 GGATTAAATTTTAGGAAAAGGAGACCA 57.968 33.333 0.00 0.00 33.22 4.02
691 695 9.601810 ATTAAATTTTAGGAAAAGGAGACCAGT 57.398 29.630 0.00 0.00 33.22 4.00
693 697 7.914427 AATTTTAGGAAAAGGAGACCAGTTT 57.086 32.000 0.00 0.00 33.22 2.66
696 700 2.175715 AGGAAAAGGAGACCAGTTTGCT 59.824 45.455 0.00 0.00 30.83 3.91
707 711 7.669722 AGGAGACCAGTTTGCTTATTTTCATAA 59.330 33.333 0.00 0.00 0.00 1.90
709 713 9.346725 GAGACCAGTTTGCTTATTTTCATAAAG 57.653 33.333 0.00 0.00 0.00 1.85
710 714 8.860088 AGACCAGTTTGCTTATTTTCATAAAGT 58.140 29.630 0.00 0.00 0.00 2.66
761 765 5.552195 CGACATATCGTCAACAGAATCAG 57.448 43.478 0.00 0.00 45.70 2.90
798 802 5.387113 ACACATGCTGGAGGGAAATAATA 57.613 39.130 0.00 0.00 0.00 0.98
839 844 3.058432 CACCACTAACGACGAGAAGAGAA 60.058 47.826 0.00 0.00 0.00 2.87
923 930 2.478292 CTTGCCCTTTCCCCTAGACTA 58.522 52.381 0.00 0.00 0.00 2.59
924 931 2.176247 TGCCCTTTCCCCTAGACTAG 57.824 55.000 2.18 2.18 0.00 2.57
925 932 1.649633 TGCCCTTTCCCCTAGACTAGA 59.350 52.381 11.27 0.00 0.00 2.43
926 933 2.040939 GCCCTTTCCCCTAGACTAGAC 58.959 57.143 11.27 0.00 0.00 2.59
927 934 2.359461 GCCCTTTCCCCTAGACTAGACT 60.359 54.545 11.27 0.00 0.00 3.24
928 935 3.568443 CCCTTTCCCCTAGACTAGACTC 58.432 54.545 11.27 0.00 0.00 3.36
972 1020 4.712337 CACCTACCAGACTAACATCTCCTT 59.288 45.833 0.00 0.00 0.00 3.36
983 1031 0.766288 CATCTCCTTCCTCCCCCTCC 60.766 65.000 0.00 0.00 0.00 4.30
1182 1421 2.653726 TCGTTCCATCATTTCCATGGG 58.346 47.619 13.02 0.00 41.25 4.00
1183 1422 1.682854 CGTTCCATCATTTCCATGGGG 59.317 52.381 13.02 2.96 41.25 4.96
1184 1423 2.041701 GTTCCATCATTTCCATGGGGG 58.958 52.381 13.02 2.87 41.25 5.40
1204 1443 3.771160 CGGGCGTCTAAGTGGGCT 61.771 66.667 0.00 0.00 0.00 5.19
1226 1465 3.561143 TGTGCAGTGGTTAAATCCTGTT 58.439 40.909 0.00 0.00 0.00 3.16
1319 1558 2.203480 TGGTGAAGGGCAAGGTGC 60.203 61.111 0.00 0.00 44.08 5.01
1450 1689 4.979388 AGTACTACAAGTTCGATTCGTCC 58.021 43.478 5.89 0.00 0.00 4.79
1457 1696 3.219052 AGTTCGATTCGTCCTGACTTC 57.781 47.619 5.89 0.00 0.00 3.01
1463 1702 4.052229 CGTCCTGACTTCGCCGGT 62.052 66.667 1.90 0.00 0.00 5.28
1464 1703 2.432628 GTCCTGACTTCGCCGGTG 60.433 66.667 9.28 9.28 0.00 4.94
1465 1704 2.599281 TCCTGACTTCGCCGGTGA 60.599 61.111 15.21 15.21 0.00 4.02
1466 1705 2.432628 CCTGACTTCGCCGGTGAC 60.433 66.667 19.40 7.23 0.00 3.67
1467 1706 2.651361 CTGACTTCGCCGGTGACT 59.349 61.111 19.40 5.52 0.00 3.41
1570 1809 1.404391 TCCGTCTCTATTGGCTTCGTC 59.596 52.381 0.00 0.00 0.00 4.20
1582 1821 1.198637 GGCTTCGTCGTGTGTAGTAGT 59.801 52.381 0.00 0.00 0.00 2.73
1583 1822 2.416547 GGCTTCGTCGTGTGTAGTAGTA 59.583 50.000 0.00 0.00 0.00 1.82
1584 1823 3.484886 GGCTTCGTCGTGTGTAGTAGTAG 60.485 52.174 0.00 0.00 0.00 2.57
1585 1824 3.124297 GCTTCGTCGTGTGTAGTAGTAGT 59.876 47.826 0.00 0.00 0.00 2.73
1586 1825 4.327357 GCTTCGTCGTGTGTAGTAGTAGTA 59.673 45.833 0.00 0.00 0.00 1.82
1589 1828 3.553511 CGTCGTGTGTAGTAGTAGTAGGG 59.446 52.174 0.00 0.00 0.00 3.53
1794 2051 1.672881 GTGGACTGCATTGTCTATGGC 59.327 52.381 6.11 0.00 37.16 4.40
1822 2083 6.127786 CCTTCCTTTTCTTCTTTATGAGCAGG 60.128 42.308 0.00 0.00 0.00 4.85
1848 2109 4.974721 GCCAGGGGTGTGTGTGGG 62.975 72.222 0.00 0.00 0.00 4.61
1849 2110 4.284550 CCAGGGGTGTGTGTGGGG 62.285 72.222 0.00 0.00 0.00 4.96
1850 2111 4.284550 CAGGGGTGTGTGTGGGGG 62.285 72.222 0.00 0.00 0.00 5.40
1921 2191 4.260170 GAGAGATGAGAATTGGCTTGTGT 58.740 43.478 0.00 0.00 0.00 3.72
1941 2211 4.736307 GTGTTTTATTTATAAAGCGGGGCG 59.264 41.667 3.94 0.00 36.59 6.13
1973 2243 6.533012 TGTTTGAGAGATGAGAATTGATCGAC 59.467 38.462 0.00 0.00 0.00 4.20
1981 2251 8.684386 AGATGAGAATTGATCGACTTCTAGTA 57.316 34.615 0.00 0.00 29.64 1.82
1983 2253 9.906660 GATGAGAATTGATCGACTTCTAGTATT 57.093 33.333 0.00 0.00 29.64 1.89
2011 2281 6.255670 TGATCTTATCTCGCATACAAACACAC 59.744 38.462 0.00 0.00 0.00 3.82
2012 2282 4.561213 TCTTATCTCGCATACAAACACACG 59.439 41.667 0.00 0.00 0.00 4.49
2013 2283 2.143008 TCTCGCATACAAACACACGT 57.857 45.000 0.00 0.00 0.00 4.49
2073 2343 8.668353 CAGCTACAATTAATGCTACTTTCTTCA 58.332 33.333 0.00 0.00 34.10 3.02
2097 2367 3.454812 TGTTTCTAACATCCTAGAGCCCC 59.545 47.826 0.00 0.00 36.25 5.80
2292 2573 1.457643 CACCCTAGATCCGCCTCCA 60.458 63.158 0.00 0.00 0.00 3.86
2294 2575 2.578714 CCCTAGATCCGCCTCCAGC 61.579 68.421 0.00 0.00 38.52 4.85
2295 2576 1.532794 CCTAGATCCGCCTCCAGCT 60.533 63.158 0.00 0.00 40.39 4.24
2296 2577 0.251386 CCTAGATCCGCCTCCAGCTA 60.251 60.000 0.00 0.00 40.39 3.32
2297 2578 1.173043 CTAGATCCGCCTCCAGCTAG 58.827 60.000 0.00 0.00 40.39 3.42
2298 2579 0.771755 TAGATCCGCCTCCAGCTAGA 59.228 55.000 0.00 0.00 40.39 2.43
2299 2580 0.105964 AGATCCGCCTCCAGCTAGAA 60.106 55.000 0.00 0.00 40.39 2.10
2300 2581 0.316841 GATCCGCCTCCAGCTAGAAG 59.683 60.000 0.00 0.00 40.39 2.85
2301 2582 1.753368 ATCCGCCTCCAGCTAGAAGC 61.753 60.000 0.00 0.00 42.84 3.86
2319 2600 1.306997 CCTAGAACCCCTGCCCTCA 60.307 63.158 0.00 0.00 0.00 3.86
2383 2664 6.827586 TTACCGAAAATGGCTAATGAAAGT 57.172 33.333 0.00 0.00 0.00 2.66
2390 2671 7.166473 CGAAAATGGCTAATGAAAGTTGCTATC 59.834 37.037 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.340232 ACATAATTCACTGCACTTTCATATGGT 59.660 33.333 2.13 0.00 0.00 3.55
111 114 1.288752 TGCAGATTCGTCGCACTCA 59.711 52.632 0.00 0.00 0.00 3.41
112 115 4.169102 TGCAGATTCGTCGCACTC 57.831 55.556 0.00 0.00 0.00 3.51
115 118 2.434185 GGGTGCAGATTCGTCGCA 60.434 61.111 0.00 0.00 0.00 5.10
116 119 3.554692 CGGGTGCAGATTCGTCGC 61.555 66.667 0.00 0.00 0.00 5.19
117 120 2.885644 CCGGGTGCAGATTCGTCG 60.886 66.667 0.00 0.00 0.00 5.12
118 121 2.511600 CCCGGGTGCAGATTCGTC 60.512 66.667 14.18 0.00 0.00 4.20
119 122 4.778143 GCCCGGGTGCAGATTCGT 62.778 66.667 24.63 0.00 0.00 3.85
120 123 4.473520 AGCCCGGGTGCAGATTCG 62.474 66.667 24.63 0.00 0.00 3.34
121 124 2.514824 GAGCCCGGGTGCAGATTC 60.515 66.667 24.63 1.65 0.00 2.52
122 125 3.329889 TGAGCCCGGGTGCAGATT 61.330 61.111 24.63 0.00 0.00 2.40
123 126 3.790437 CTGAGCCCGGGTGCAGAT 61.790 66.667 29.78 9.09 0.00 2.90
150 153 2.697431 TTTGATTTTTCCCGTGAGCG 57.303 45.000 0.00 0.00 37.95 5.03
151 154 3.712187 TGTTTTGATTTTTCCCGTGAGC 58.288 40.909 0.00 0.00 0.00 4.26
152 155 6.843069 ATTTGTTTTGATTTTTCCCGTGAG 57.157 33.333 0.00 0.00 0.00 3.51
153 156 7.265673 TGTATTTGTTTTGATTTTTCCCGTGA 58.734 30.769 0.00 0.00 0.00 4.35
154 157 7.470289 TGTATTTGTTTTGATTTTTCCCGTG 57.530 32.000 0.00 0.00 0.00 4.94
155 158 8.494016 TTTGTATTTGTTTTGATTTTTCCCGT 57.506 26.923 0.00 0.00 0.00 5.28
156 159 9.774742 TTTTTGTATTTGTTTTGATTTTTCCCG 57.225 25.926 0.00 0.00 0.00 5.14
206 209 9.494271 ACGCATCTAATTATCTATCACACAATT 57.506 29.630 0.00 0.00 0.00 2.32
207 210 8.929746 CACGCATCTAATTATCTATCACACAAT 58.070 33.333 0.00 0.00 0.00 2.71
208 211 8.141268 TCACGCATCTAATTATCTATCACACAA 58.859 33.333 0.00 0.00 0.00 3.33
209 212 7.657336 TCACGCATCTAATTATCTATCACACA 58.343 34.615 0.00 0.00 0.00 3.72
210 213 7.274468 CCTCACGCATCTAATTATCTATCACAC 59.726 40.741 0.00 0.00 0.00 3.82
211 214 7.039714 ACCTCACGCATCTAATTATCTATCACA 60.040 37.037 0.00 0.00 0.00 3.58
212 215 7.316640 ACCTCACGCATCTAATTATCTATCAC 58.683 38.462 0.00 0.00 0.00 3.06
213 216 7.468141 ACCTCACGCATCTAATTATCTATCA 57.532 36.000 0.00 0.00 0.00 2.15
214 217 7.219154 CGAACCTCACGCATCTAATTATCTATC 59.781 40.741 0.00 0.00 0.00 2.08
215 218 7.030165 CGAACCTCACGCATCTAATTATCTAT 58.970 38.462 0.00 0.00 0.00 1.98
216 219 6.379386 CGAACCTCACGCATCTAATTATCTA 58.621 40.000 0.00 0.00 0.00 1.98
217 220 5.223382 CGAACCTCACGCATCTAATTATCT 58.777 41.667 0.00 0.00 0.00 1.98
218 221 5.502214 CGAACCTCACGCATCTAATTATC 57.498 43.478 0.00 0.00 0.00 1.75
230 233 2.969443 ATTTTTCAGCGAACCTCACG 57.031 45.000 0.00 0.00 0.00 4.35
231 234 4.223320 TGAATTTTTCAGCGAACCTCAC 57.777 40.909 0.00 0.00 34.08 3.51
232 235 4.338118 AGTTGAATTTTTCAGCGAACCTCA 59.662 37.500 0.00 0.00 44.40 3.86
233 236 4.860072 AGTTGAATTTTTCAGCGAACCTC 58.140 39.130 0.00 0.00 44.40 3.85
234 237 4.554723 CGAGTTGAATTTTTCAGCGAACCT 60.555 41.667 0.00 0.00 44.40 3.50
235 238 3.664025 CGAGTTGAATTTTTCAGCGAACC 59.336 43.478 0.00 0.00 44.40 3.62
236 239 4.279659 ACGAGTTGAATTTTTCAGCGAAC 58.720 39.130 12.69 0.00 44.40 3.95
237 240 4.545823 ACGAGTTGAATTTTTCAGCGAA 57.454 36.364 12.69 0.00 44.40 4.70
238 241 4.545823 AACGAGTTGAATTTTTCAGCGA 57.454 36.364 12.69 0.00 44.40 4.93
239 242 4.085619 CCAAACGAGTTGAATTTTTCAGCG 60.086 41.667 5.36 0.00 44.40 5.18
240 243 5.040635 TCCAAACGAGTTGAATTTTTCAGC 58.959 37.500 5.36 0.00 41.38 4.26
241 244 6.033341 TGTCCAAACGAGTTGAATTTTTCAG 58.967 36.000 5.36 0.00 41.38 3.02
242 245 5.955488 TGTCCAAACGAGTTGAATTTTTCA 58.045 33.333 5.36 0.00 39.87 2.69
243 246 7.463469 AATGTCCAAACGAGTTGAATTTTTC 57.537 32.000 5.36 0.00 39.87 2.29
244 247 7.547370 TCAAATGTCCAAACGAGTTGAATTTTT 59.453 29.630 5.36 0.00 39.87 1.94
245 248 7.038659 TCAAATGTCCAAACGAGTTGAATTTT 58.961 30.769 5.36 0.00 39.87 1.82
246 249 6.568869 TCAAATGTCCAAACGAGTTGAATTT 58.431 32.000 5.36 5.93 39.87 1.82
247 250 6.142818 TCAAATGTCCAAACGAGTTGAATT 57.857 33.333 5.36 0.00 39.87 2.17
248 251 5.762045 CTCAAATGTCCAAACGAGTTGAAT 58.238 37.500 5.36 0.00 39.87 2.57
249 252 4.497340 GCTCAAATGTCCAAACGAGTTGAA 60.497 41.667 5.36 0.00 39.87 2.69
250 253 3.003275 GCTCAAATGTCCAAACGAGTTGA 59.997 43.478 5.36 0.00 39.87 3.18
251 254 3.243035 TGCTCAAATGTCCAAACGAGTTG 60.243 43.478 0.00 0.00 36.94 3.16
252 255 2.948979 TGCTCAAATGTCCAAACGAGTT 59.051 40.909 0.00 0.00 0.00 3.01
253 256 2.571212 TGCTCAAATGTCCAAACGAGT 58.429 42.857 0.00 0.00 0.00 4.18
254 257 3.003689 ACTTGCTCAAATGTCCAAACGAG 59.996 43.478 0.00 0.00 0.00 4.18
255 258 2.948979 ACTTGCTCAAATGTCCAAACGA 59.051 40.909 0.00 0.00 0.00 3.85
256 259 3.003689 AGACTTGCTCAAATGTCCAAACG 59.996 43.478 0.00 0.00 0.00 3.60
257 260 4.202050 ACAGACTTGCTCAAATGTCCAAAC 60.202 41.667 0.00 0.00 0.00 2.93
258 261 3.953612 ACAGACTTGCTCAAATGTCCAAA 59.046 39.130 0.00 0.00 0.00 3.28
259 262 3.316029 CACAGACTTGCTCAAATGTCCAA 59.684 43.478 0.00 0.00 0.00 3.53
260 263 2.880268 CACAGACTTGCTCAAATGTCCA 59.120 45.455 0.00 0.00 0.00 4.02
261 264 2.351157 GCACAGACTTGCTCAAATGTCC 60.351 50.000 0.00 0.00 39.59 4.02
262 265 2.291465 TGCACAGACTTGCTCAAATGTC 59.709 45.455 9.86 0.00 43.41 3.06
263 266 2.300433 TGCACAGACTTGCTCAAATGT 58.700 42.857 9.86 0.00 43.41 2.71
264 267 3.358707 TTGCACAGACTTGCTCAAATG 57.641 42.857 9.86 0.00 43.41 2.32
265 268 4.389890 TTTTGCACAGACTTGCTCAAAT 57.610 36.364 9.86 0.00 43.41 2.32
266 269 3.865011 TTTTGCACAGACTTGCTCAAA 57.135 38.095 9.86 7.06 43.41 2.69
267 270 3.865011 TTTTTGCACAGACTTGCTCAA 57.135 38.095 9.86 2.78 43.41 3.02
284 287 3.958147 ACAGACCCCGATTTTGTCTTTTT 59.042 39.130 0.00 0.00 37.25 1.94
285 288 3.562182 ACAGACCCCGATTTTGTCTTTT 58.438 40.909 0.00 0.00 37.25 2.27
286 289 3.223674 ACAGACCCCGATTTTGTCTTT 57.776 42.857 0.00 0.00 37.25 2.52
287 290 2.951229 ACAGACCCCGATTTTGTCTT 57.049 45.000 0.00 0.00 37.25 3.01
288 291 4.360951 TTTACAGACCCCGATTTTGTCT 57.639 40.909 0.00 0.00 39.86 3.41
289 292 5.441709 TTTTTACAGACCCCGATTTTGTC 57.558 39.130 0.00 0.00 0.00 3.18
308 311 6.905578 ACAGTTCGTGAACAGTAAACTTTTT 58.094 32.000 14.61 0.00 43.47 1.94
309 312 6.490566 ACAGTTCGTGAACAGTAAACTTTT 57.509 33.333 14.61 0.00 43.47 2.27
310 313 6.490566 AACAGTTCGTGAACAGTAAACTTT 57.509 33.333 14.61 0.00 43.47 2.66
311 314 6.490566 AAACAGTTCGTGAACAGTAAACTT 57.509 33.333 14.61 2.17 43.47 2.66
312 315 6.148150 TCAAAACAGTTCGTGAACAGTAAACT 59.852 34.615 14.61 0.00 43.47 2.66
313 316 6.247791 GTCAAAACAGTTCGTGAACAGTAAAC 59.752 38.462 14.61 6.17 43.47 2.01
314 317 6.308675 GTCAAAACAGTTCGTGAACAGTAAA 58.691 36.000 14.61 0.00 43.47 2.01
315 318 5.163834 GGTCAAAACAGTTCGTGAACAGTAA 60.164 40.000 14.61 0.00 43.47 2.24
316 319 4.330620 GGTCAAAACAGTTCGTGAACAGTA 59.669 41.667 14.61 0.00 43.47 2.74
317 320 3.126343 GGTCAAAACAGTTCGTGAACAGT 59.874 43.478 14.61 9.88 43.47 3.55
318 321 3.486875 GGGTCAAAACAGTTCGTGAACAG 60.487 47.826 14.61 9.26 43.47 3.16
319 322 2.420722 GGGTCAAAACAGTTCGTGAACA 59.579 45.455 14.61 0.00 43.47 3.18
320 323 2.538132 CGGGTCAAAACAGTTCGTGAAC 60.538 50.000 4.58 4.58 41.45 3.18
321 324 1.666700 CGGGTCAAAACAGTTCGTGAA 59.333 47.619 2.00 0.00 0.00 3.18
322 325 1.134759 TCGGGTCAAAACAGTTCGTGA 60.135 47.619 0.00 0.00 0.00 4.35
323 326 1.292061 TCGGGTCAAAACAGTTCGTG 58.708 50.000 0.00 0.00 0.00 4.35
324 327 2.249844 ATCGGGTCAAAACAGTTCGT 57.750 45.000 0.00 0.00 0.00 3.85
325 328 3.242936 ACAAATCGGGTCAAAACAGTTCG 60.243 43.478 0.00 0.00 0.00 3.95
326 329 4.036380 AGACAAATCGGGTCAAAACAGTTC 59.964 41.667 0.00 0.00 37.74 3.01
327 330 3.951680 AGACAAATCGGGTCAAAACAGTT 59.048 39.130 0.00 0.00 37.74 3.16
328 331 3.551846 AGACAAATCGGGTCAAAACAGT 58.448 40.909 0.00 0.00 37.74 3.55
329 332 4.568152 AAGACAAATCGGGTCAAAACAG 57.432 40.909 0.00 0.00 37.74 3.16
330 333 4.993029 AAAGACAAATCGGGTCAAAACA 57.007 36.364 0.00 0.00 37.74 2.83
350 353 2.631062 TCTGAGTAGGTCTCGGCAAAAA 59.369 45.455 0.00 0.00 46.16 1.94
351 354 2.244695 TCTGAGTAGGTCTCGGCAAAA 58.755 47.619 0.00 0.00 46.16 2.44
352 355 1.919240 TCTGAGTAGGTCTCGGCAAA 58.081 50.000 0.00 0.00 46.16 3.68
353 356 2.145397 ATCTGAGTAGGTCTCGGCAA 57.855 50.000 0.00 0.00 46.16 4.52
354 357 3.413327 GATATCTGAGTAGGTCTCGGCA 58.587 50.000 0.00 0.00 46.16 5.69
355 358 2.750712 GGATATCTGAGTAGGTCTCGGC 59.249 54.545 2.05 0.00 46.16 5.54
357 360 6.207614 TCATTTGGATATCTGAGTAGGTCTCG 59.792 42.308 2.05 0.00 45.46 4.04
358 361 7.531857 TCATTTGGATATCTGAGTAGGTCTC 57.468 40.000 2.05 0.00 43.03 3.36
359 362 7.921041 TTCATTTGGATATCTGAGTAGGTCT 57.079 36.000 2.05 0.00 0.00 3.85
360 363 8.997323 CAATTCATTTGGATATCTGAGTAGGTC 58.003 37.037 2.05 0.00 0.00 3.85
361 364 8.717717 TCAATTCATTTGGATATCTGAGTAGGT 58.282 33.333 2.05 0.00 35.92 3.08
362 365 9.565090 TTCAATTCATTTGGATATCTGAGTAGG 57.435 33.333 2.05 0.00 35.92 3.18
372 375 8.871862 CGCTCAAAATTTCAATTCATTTGGATA 58.128 29.630 0.00 0.00 35.92 2.59
373 376 7.148373 CCGCTCAAAATTTCAATTCATTTGGAT 60.148 33.333 0.00 0.00 35.92 3.41
374 377 6.147492 CCGCTCAAAATTTCAATTCATTTGGA 59.853 34.615 0.00 0.00 35.92 3.53
375 378 6.147492 TCCGCTCAAAATTTCAATTCATTTGG 59.853 34.615 0.00 0.00 35.92 3.28
376 379 7.119605 TCCGCTCAAAATTTCAATTCATTTG 57.880 32.000 0.00 0.00 36.61 2.32
377 380 7.820872 AGATCCGCTCAAAATTTCAATTCATTT 59.179 29.630 0.00 0.00 0.00 2.32
378 381 7.325694 AGATCCGCTCAAAATTTCAATTCATT 58.674 30.769 0.00 0.00 0.00 2.57
379 382 6.870769 AGATCCGCTCAAAATTTCAATTCAT 58.129 32.000 0.00 0.00 0.00 2.57
380 383 6.271488 AGATCCGCTCAAAATTTCAATTCA 57.729 33.333 0.00 0.00 0.00 2.57
381 384 6.802950 GAGATCCGCTCAAAATTTCAATTC 57.197 37.500 0.00 0.00 43.38 2.17
397 400 4.687948 AGATAATTTGATGCGTGAGATCCG 59.312 41.667 0.00 0.00 0.00 4.18
398 401 6.091441 GGTAGATAATTTGATGCGTGAGATCC 59.909 42.308 0.00 0.00 0.00 3.36
399 402 6.646653 TGGTAGATAATTTGATGCGTGAGATC 59.353 38.462 0.00 0.00 0.00 2.75
400 403 6.425114 GTGGTAGATAATTTGATGCGTGAGAT 59.575 38.462 0.00 0.00 0.00 2.75
401 404 5.753438 GTGGTAGATAATTTGATGCGTGAGA 59.247 40.000 0.00 0.00 0.00 3.27
402 405 5.523552 TGTGGTAGATAATTTGATGCGTGAG 59.476 40.000 0.00 0.00 0.00 3.51
403 406 5.293324 GTGTGGTAGATAATTTGATGCGTGA 59.707 40.000 0.00 0.00 0.00 4.35
404 407 5.064579 TGTGTGGTAGATAATTTGATGCGTG 59.935 40.000 0.00 0.00 0.00 5.34
405 408 5.182487 TGTGTGGTAGATAATTTGATGCGT 58.818 37.500 0.00 0.00 0.00 5.24
406 409 5.733226 TGTGTGGTAGATAATTTGATGCG 57.267 39.130 0.00 0.00 0.00 4.73
407 410 8.755696 TTTTTGTGTGGTAGATAATTTGATGC 57.244 30.769 0.00 0.00 0.00 3.91
471 474 1.152860 TGCTCCCGGTCAGCAAAAA 60.153 52.632 20.24 0.26 44.02 1.94
472 475 1.600636 CTGCTCCCGGTCAGCAAAA 60.601 57.895 22.10 4.37 46.22 2.44
473 476 2.032528 CTGCTCCCGGTCAGCAAA 59.967 61.111 22.10 4.99 46.22 3.68
477 480 3.368190 CTCAGCTGCTCCCGGTCAG 62.368 68.421 9.47 5.96 0.00 3.51
478 481 3.385384 CTCAGCTGCTCCCGGTCA 61.385 66.667 9.47 0.00 0.00 4.02
479 482 4.828925 GCTCAGCTGCTCCCGGTC 62.829 72.222 9.47 0.00 0.00 4.79
497 500 0.764890 TAATTCATCCTGGAGCCCGG 59.235 55.000 1.52 0.00 0.00 5.73
498 501 2.704572 GATAATTCATCCTGGAGCCCG 58.295 52.381 1.52 0.00 0.00 6.13
499 502 2.303022 TCGATAATTCATCCTGGAGCCC 59.697 50.000 1.52 0.00 0.00 5.19
500 503 3.685139 TCGATAATTCATCCTGGAGCC 57.315 47.619 1.52 0.00 0.00 4.70
501 504 7.044181 TGATAATCGATAATTCATCCTGGAGC 58.956 38.462 1.52 0.00 0.00 4.70
502 505 9.610705 AATGATAATCGATAATTCATCCTGGAG 57.389 33.333 14.43 0.00 0.00 3.86
503 506 9.387257 CAATGATAATCGATAATTCATCCTGGA 57.613 33.333 14.43 0.00 0.00 3.86
504 507 8.127327 GCAATGATAATCGATAATTCATCCTGG 58.873 37.037 14.43 0.00 0.00 4.45
505 508 8.127327 GGCAATGATAATCGATAATTCATCCTG 58.873 37.037 14.43 11.99 0.00 3.86
506 509 8.051535 AGGCAATGATAATCGATAATTCATCCT 58.948 33.333 14.43 14.10 0.00 3.24
507 510 8.218338 AGGCAATGATAATCGATAATTCATCC 57.782 34.615 14.43 12.71 0.00 3.51
515 518 9.681692 CATTCAAAAAGGCAATGATAATCGATA 57.318 29.630 0.00 0.00 30.31 2.92
516 519 7.654520 CCATTCAAAAAGGCAATGATAATCGAT 59.345 33.333 0.00 0.00 30.31 3.59
517 520 6.979817 CCATTCAAAAAGGCAATGATAATCGA 59.020 34.615 0.00 0.00 30.31 3.59
518 521 6.979817 TCCATTCAAAAAGGCAATGATAATCG 59.020 34.615 0.00 0.00 30.31 3.34
519 522 8.721019 TTCCATTCAAAAAGGCAATGATAATC 57.279 30.769 0.00 0.00 30.31 1.75
528 531 5.713792 TTACGATTCCATTCAAAAAGGCA 57.286 34.783 0.00 0.00 0.00 4.75
546 550 9.781834 TGATCCATAACTTTTGCTTATTTTACG 57.218 29.630 0.00 0.00 0.00 3.18
603 607 4.276926 GCCCCACAAGATAGTCAAATCATC 59.723 45.833 0.00 0.00 0.00 2.92
659 663 7.317390 TCCTTTTCCTAAAATTTAATCCGTGC 58.683 34.615 0.00 0.00 0.00 5.34
669 673 7.686859 GCAAACTGGTCTCCTTTTCCTAAAATT 60.687 37.037 0.00 0.00 0.00 1.82
678 682 6.731292 AAATAAGCAAACTGGTCTCCTTTT 57.269 33.333 0.00 0.00 0.00 2.27
680 684 5.833131 TGAAAATAAGCAAACTGGTCTCCTT 59.167 36.000 0.00 0.00 0.00 3.36
682 686 5.705609 TGAAAATAAGCAAACTGGTCTCC 57.294 39.130 0.00 0.00 0.00 3.71
683 687 9.346725 CTTTATGAAAATAAGCAAACTGGTCTC 57.653 33.333 0.00 0.00 0.00 3.36
684 688 8.860088 ACTTTATGAAAATAAGCAAACTGGTCT 58.140 29.630 0.00 0.00 0.00 3.85
693 697 9.855021 GCCTTTTCTACTTTATGAAAATAAGCA 57.145 29.630 0.00 0.00 40.11 3.91
707 711 3.933332 GACGCATAGTGCCTTTTCTACTT 59.067 43.478 0.00 0.00 41.12 2.24
709 713 2.281762 CGACGCATAGTGCCTTTTCTAC 59.718 50.000 0.00 0.00 41.12 2.59
710 714 2.164827 TCGACGCATAGTGCCTTTTCTA 59.835 45.455 0.00 0.00 41.12 2.10
712 716 1.355971 TCGACGCATAGTGCCTTTTC 58.644 50.000 0.00 0.00 41.12 2.29
713 717 2.024176 ATCGACGCATAGTGCCTTTT 57.976 45.000 0.00 0.00 41.12 2.27
714 718 2.882927 TATCGACGCATAGTGCCTTT 57.117 45.000 0.00 0.00 41.12 3.11
715 719 4.157840 TGATATATCGACGCATAGTGCCTT 59.842 41.667 8.19 0.00 41.12 4.35
716 720 3.694566 TGATATATCGACGCATAGTGCCT 59.305 43.478 8.19 0.00 41.12 4.75
717 721 3.791887 GTGATATATCGACGCATAGTGCC 59.208 47.826 8.19 0.00 41.12 5.01
749 753 1.699083 TGGGACAGCTGATTCTGTTGA 59.301 47.619 23.35 0.00 46.40 3.18
761 765 3.499918 GCATGTGTAGATATTGGGACAGC 59.500 47.826 0.00 0.00 42.39 4.40
839 844 1.051556 GCGGAGGGGAGGAATCTCTT 61.052 60.000 0.00 0.00 39.86 2.85
882 889 0.529378 CTCCAAAGGCAAGCATGACC 59.471 55.000 0.00 0.00 33.81 4.02
923 930 3.615811 TCTGGGGCTGGGGAGTCT 61.616 66.667 0.00 0.00 0.00 3.24
924 931 3.086600 CTCTGGGGCTGGGGAGTC 61.087 72.222 0.00 0.00 0.00 3.36
925 932 4.748798 CCTCTGGGGCTGGGGAGT 62.749 72.222 0.00 0.00 0.00 3.85
972 1020 3.752167 GGAGACGGAGGGGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
983 1031 0.179116 CATGAGCACCTCAGGAGACG 60.179 60.000 0.00 0.00 43.80 4.18
1183 1422 4.832608 CACTTAGACGCCCGCCCC 62.833 72.222 0.00 0.00 0.00 5.80
1184 1423 4.832608 CCACTTAGACGCCCGCCC 62.833 72.222 0.00 0.00 0.00 6.13
1185 1424 4.832608 CCCACTTAGACGCCCGCC 62.833 72.222 0.00 0.00 0.00 6.13
1204 1443 3.561143 ACAGGATTTAACCACTGCACAA 58.439 40.909 0.00 0.00 34.40 3.33
1450 1689 1.734477 CAGTCACCGGCGAAGTCAG 60.734 63.158 9.30 0.00 0.00 3.51
1463 1702 0.669619 TTAGTCACCGCGAACAGTCA 59.330 50.000 8.23 0.00 0.00 3.41
1464 1703 1.992170 ATTAGTCACCGCGAACAGTC 58.008 50.000 8.23 0.00 0.00 3.51
1465 1704 2.334838 GAATTAGTCACCGCGAACAGT 58.665 47.619 8.23 0.00 0.00 3.55
1466 1705 1.320555 CGAATTAGTCACCGCGAACAG 59.679 52.381 8.23 0.00 0.00 3.16
1467 1706 1.342555 CGAATTAGTCACCGCGAACA 58.657 50.000 8.23 0.00 0.00 3.18
1544 1783 6.153000 ACGAAGCCAATAGAGACGGATATTAT 59.847 38.462 0.00 0.00 0.00 1.28
1545 1784 5.475909 ACGAAGCCAATAGAGACGGATATTA 59.524 40.000 0.00 0.00 0.00 0.98
1546 1785 4.281182 ACGAAGCCAATAGAGACGGATATT 59.719 41.667 0.00 0.00 0.00 1.28
1570 1809 6.500684 TTTTCCCTACTACTACTACACACG 57.499 41.667 0.00 0.00 0.00 4.49
1601 1840 1.332195 CTCACCTCACCTCACTCACA 58.668 55.000 0.00 0.00 0.00 3.58
1606 1845 2.960688 GCCCCTCACCTCACCTCAC 61.961 68.421 0.00 0.00 0.00 3.51
1607 1846 2.607750 GCCCCTCACCTCACCTCA 60.608 66.667 0.00 0.00 0.00 3.86
1608 1847 1.977293 GATGCCCCTCACCTCACCTC 61.977 65.000 0.00 0.00 0.00 3.85
1609 1848 1.997874 GATGCCCCTCACCTCACCT 60.998 63.158 0.00 0.00 0.00 4.00
1610 1849 0.691078 TAGATGCCCCTCACCTCACC 60.691 60.000 0.00 0.00 0.00 4.02
1723 1980 0.250467 ACGGATTTGCACTGCACTCT 60.250 50.000 2.26 0.00 38.71 3.24
1794 2051 6.349694 GCTCATAAAGAAGAAAAGGAAGGTGG 60.350 42.308 0.00 0.00 0.00 4.61
1822 2083 1.227383 CACCCCTGGCCCTGTAATC 59.773 63.158 0.00 0.00 0.00 1.75
1849 2110 2.313427 TGGGTGGTCAATAGCCCCC 61.313 63.158 0.00 0.00 40.36 5.40
1850 2111 1.076995 GTGGGTGGTCAATAGCCCC 60.077 63.158 0.00 0.00 40.36 5.80
1851 2112 0.394352 CTGTGGGTGGTCAATAGCCC 60.394 60.000 0.00 0.00 41.42 5.19
1852 2113 1.032114 GCTGTGGGTGGTCAATAGCC 61.032 60.000 0.00 0.00 36.27 3.93
1853 2114 0.322456 TGCTGTGGGTGGTCAATAGC 60.322 55.000 0.00 0.00 32.90 2.97
1858 2119 0.840617 TAAAGTGCTGTGGGTGGTCA 59.159 50.000 0.00 0.00 0.00 4.02
1921 2191 5.124645 TCTCGCCCCGCTTTATAAATAAAA 58.875 37.500 0.00 0.00 32.39 1.52
1941 2211 3.119673 TCTCATCTCTCAAACACGCTCTC 60.120 47.826 0.00 0.00 0.00 3.20
1947 2217 6.533012 TCGATCAATTCTCATCTCTCAAACAC 59.467 38.462 0.00 0.00 0.00 3.32
1952 2222 6.320926 AGAAGTCGATCAATTCTCATCTCTCA 59.679 38.462 0.00 0.00 0.00 3.27
1983 2253 8.978539 GTGTTTGTATGCGAGATAAGATCATAA 58.021 33.333 0.00 0.00 0.00 1.90
1987 2257 6.560433 CGTGTGTTTGTATGCGAGATAAGATC 60.560 42.308 0.00 0.00 0.00 2.75
2073 2343 5.398012 GGGGCTCTAGGATGTTAGAAACAAT 60.398 44.000 0.00 0.00 45.86 2.71
2080 2350 1.974236 CAGGGGGCTCTAGGATGTTAG 59.026 57.143 0.00 0.00 0.00 2.34
2097 2367 2.143876 CCCCCACATTTTAGGTCAGG 57.856 55.000 0.00 0.00 0.00 3.86
2292 2573 1.292546 AGGGGTTCTAGGCTTCTAGCT 59.707 52.381 0.00 0.00 41.99 3.32
2294 2575 1.414550 GCAGGGGTTCTAGGCTTCTAG 59.585 57.143 0.00 0.00 41.32 2.43
2295 2576 1.497161 GCAGGGGTTCTAGGCTTCTA 58.503 55.000 0.00 0.00 0.00 2.10
2296 2577 1.275421 GGCAGGGGTTCTAGGCTTCT 61.275 60.000 0.00 0.00 0.00 2.85
2297 2578 1.224870 GGCAGGGGTTCTAGGCTTC 59.775 63.158 0.00 0.00 0.00 3.86
2298 2579 2.309504 GGGCAGGGGTTCTAGGCTT 61.310 63.158 0.00 0.00 0.00 4.35
2299 2580 2.692741 GGGCAGGGGTTCTAGGCT 60.693 66.667 0.00 0.00 0.00 4.58
2300 2581 2.692741 AGGGCAGGGGTTCTAGGC 60.693 66.667 0.00 0.00 0.00 3.93
2301 2582 0.914417 TTGAGGGCAGGGGTTCTAGG 60.914 60.000 0.00 0.00 0.00 3.02
2319 2600 5.579119 GGACGGTCATTCTTTTGTTTGTTTT 59.421 36.000 10.76 0.00 0.00 2.43
2383 2664 9.205513 TCTATGATGGCAATCTATAGATAGCAA 57.794 33.333 15.64 3.51 33.15 3.91
2390 2671 6.096141 ACGGTCTCTATGATGGCAATCTATAG 59.904 42.308 2.00 8.10 33.61 1.31


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

AutoCloner maintained by Alex Coulton.