Multiple sequence alignment - TraesCS2B01G187800

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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 TraesCS2B01G187800 chr2B 100.000 2609 0 0 1 2609 163230487 163233095 0.000000e+00 4819.0
1 TraesCS2B01G187800 chr2B 100.000 133 0 0 523 655 39373325 39373193 2.010000e-61 246.0
2 TraesCS2B01G187800 chr2B 98.020 101 0 2 214 314 39373416 39373318 9.600000e-40 174.0
3 TraesCS2B01G187800 chr2B 98.969 97 0 1 218 314 551636661 551636566 3.450000e-39 172.0
4 TraesCS2B01G187800 chr2D 95.374 1967 71 8 658 2609 112864943 112866904 0.000000e+00 3110.0
5 TraesCS2B01G187800 chr2D 90.708 226 6 3 1 221 112864723 112864938 1.180000e-73 287.0
6 TraesCS2B01G187800 chr2A 93.772 1959 90 16 661 2609 114300282 114302218 0.000000e+00 2913.0
7 TraesCS2B01G187800 chr2A 83.209 268 44 1 2261 2527 684904171 684904438 7.210000e-61 244.0
8 TraesCS2B01G187800 chr2A 81.301 246 10 7 2 221 114300039 114300274 1.610000e-37 167.0
9 TraesCS2B01G187800 chr2A 80.296 203 39 1 2286 2488 49503846 49503645 4.500000e-33 152.0
10 TraesCS2B01G187800 chr5A 97.521 242 4 2 304 543 328805513 328805272 1.870000e-111 412.0
11 TraesCS2B01G187800 chr5A 99.265 136 1 0 523 658 569457891 569458026 2.010000e-61 246.0
12 TraesCS2B01G187800 chr5A 74.588 425 72 24 2128 2521 647607953 647608372 1.250000e-33 154.0
13 TraesCS2B01G187800 chr6B 100.000 221 0 0 307 527 127754338 127754118 2.420000e-110 409.0
14 TraesCS2B01G187800 chr6B 99.270 137 1 0 523 659 26081678 26081814 5.580000e-62 248.0
15 TraesCS2B01G187800 chr6B 100.000 133 0 0 523 655 127754205 127754337 2.010000e-61 246.0
16 TraesCS2B01G187800 chr7B 99.550 222 1 0 306 527 23409670 23409449 3.130000e-109 405.0
17 TraesCS2B01G187800 chr3B 99.550 222 1 0 306 527 542749170 542749391 3.130000e-109 405.0
18 TraesCS2B01G187800 chr3B 98.000 100 1 1 215 314 69370468 69370370 3.450000e-39 172.0
19 TraesCS2B01G187800 chr3B 95.455 110 2 3 207 314 816483372 816483264 3.450000e-39 172.0
20 TraesCS2B01G187800 chr1A 99.550 222 1 0 305 526 532321507 532321286 3.130000e-109 405.0
21 TraesCS2B01G187800 chr1A 97.087 103 1 2 212 314 471731519 471731419 3.450000e-39 172.0
22 TraesCS2B01G187800 chr4D 98.261 230 4 0 306 535 3719612 3719841 1.120000e-108 403.0
23 TraesCS2B01G187800 chr4D 86.869 99 11 1 235 331 5141031 5141129 2.750000e-20 110.0
24 TraesCS2B01G187800 chr4A 99.107 224 2 0 305 528 584459867 584460090 1.120000e-108 403.0
25 TraesCS2B01G187800 chr1B 98.678 227 3 0 300 526 561755447 561755673 1.120000e-108 403.0
26 TraesCS2B01G187800 chr1B 97.872 141 2 1 523 662 561755587 561755447 2.590000e-60 243.0
27 TraesCS2B01G187800 chr5B 98.246 228 4 0 302 529 253187372 253187145 1.450000e-107 399.0
28 TraesCS2B01G187800 chr7A 99.270 137 1 0 523 659 545058367 545058231 5.580000e-62 248.0
29 TraesCS2B01G187800 chr7A 98.496 133 2 0 523 655 725204711 725204579 4.340000e-58 235.0
30 TraesCS2B01G187800 chr7A 96.262 107 1 3 208 314 88320823 88320720 3.450000e-39 172.0
31 TraesCS2B01G187800 chr7A 79.167 240 43 7 2275 2512 287210692 287210458 2.690000e-35 159.0
32 TraesCS2B01G187800 chr7D 100.000 133 0 0 523 655 593028703 593028571 2.010000e-61 246.0
33 TraesCS2B01G187800 chr7D 79.325 237 41 7 2272 2505 580762143 580761912 2.690000e-35 159.0
34 TraesCS2B01G187800 chr7D 81.579 152 26 2 2272 2422 608889470 608889620 9.800000e-25 124.0
35 TraesCS2B01G187800 chr6A 95.333 150 5 2 523 671 616878637 616878785 1.210000e-58 237.0
36 TraesCS2B01G187800 chr6A 97.087 103 1 2 213 314 552834760 552834659 3.450000e-39 172.0
37 TraesCS2B01G187800 chr6A 97.059 102 1 2 213 314 531399387 531399288 1.240000e-38 171.0
38 TraesCS2B01G187800 chr3A 98.980 98 0 1 217 314 149722741 149722645 9.600000e-40 174.0
39 TraesCS2B01G187800 chr3A 74.817 409 75 17 2130 2512 581620887 581621293 2.690000e-35 159.0
40 TraesCS2B01G187800 chr5D 78.008 241 51 2 2273 2512 487427288 487427049 1.620000e-32 150.0
41 TraesCS2B01G187800 chr5D 78.873 213 40 5 2283 2493 432945783 432945574 3.500000e-29 139.0
42 TraesCS2B01G187800 chr5D 76.587 252 51 8 2264 2511 185163027 185163274 5.860000e-27 132.0
43 TraesCS2B01G187800 chr5D 97.778 45 1 0 2483 2527 118221080 118221036 7.740000e-11 78.7
44 TraesCS2B01G187800 chr6D 77.143 245 48 8 2275 2515 61599056 61598816 4.530000e-28 135.0
45 TraesCS2B01G187800 chr1D 73.659 410 78 18 2130 2511 168330262 168330669 5.860000e-27 132.0
46 TraesCS2B01G187800 chr1D 78.341 217 34 12 2283 2493 6466807 6466598 7.580000e-26 128.0
47 TraesCS2B01G187800 chr1D 84.286 70 10 1 2275 2343 181944 181875 1.680000e-07 67.6
48 TraesCS2B01G187800 chr1D 87.719 57 6 1 2275 2330 165717 165661 6.030000e-07 65.8
49 TraesCS2B01G187800 chrUn 78.846 156 29 3 2280 2433 34295930 34296083 4.590000e-18 102.0


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 TraesCS2B01G187800 chr2B 163230487 163233095 2608 False 4819.0 4819 100.0000 1 2609 1 chr2B.!!$F1 2608
1 TraesCS2B01G187800 chr2D 112864723 112866904 2181 False 1698.5 3110 93.0410 1 2609 2 chr2D.!!$F1 2608
2 TraesCS2B01G187800 chr2A 114300039 114302218 2179 False 1540.0 2913 87.5365 2 2609 2 chr2A.!!$F2 2607

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
530 557 0.179009 CGGACGGAGGGAGTATACCA 60.179 60.0 0.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2101 0.106519 AAGCCAGCAGTCAACCTTGT 60.107 50.0 0.0 0.0 0.0 3.16 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
89 99 0.758123 ATGCCACCACCACCAAAAAG 59.242 50.000 0.00 0.00 0.00 2.27
132 148 2.837591 TCCACCAACAAGATGCTAGCTA 59.162 45.455 17.23 2.58 0.00 3.32
133 149 3.118629 TCCACCAACAAGATGCTAGCTAG 60.119 47.826 16.84 16.84 0.00 3.42
134 150 3.201290 CACCAACAAGATGCTAGCTAGG 58.799 50.000 22.10 6.87 0.00 3.02
135 151 3.107601 ACCAACAAGATGCTAGCTAGGA 58.892 45.455 22.10 20.14 0.00 2.94
136 152 3.118592 ACCAACAAGATGCTAGCTAGGAC 60.119 47.826 22.10 13.48 0.00 3.85
137 153 3.133721 CCAACAAGATGCTAGCTAGGACT 59.866 47.826 22.10 15.35 0.00 3.85
138 154 4.342378 CCAACAAGATGCTAGCTAGGACTA 59.658 45.833 22.10 0.00 0.00 2.59
139 155 5.508825 CCAACAAGATGCTAGCTAGGACTAG 60.509 48.000 22.10 12.41 42.20 2.57
207 234 9.176181 CAATAATAATGTATGTACCCGCAAAAC 57.824 33.333 0.00 0.00 0.00 2.43
221 248 6.096695 ACCCGCAAAACAATCAATAATGTAC 58.903 36.000 0.00 0.00 0.00 2.90
224 251 6.472163 CCGCAAAACAATCAATAATGTACTCC 59.528 38.462 0.00 0.00 0.00 3.85
225 252 6.472163 CGCAAAACAATCAATAATGTACTCCC 59.528 38.462 0.00 0.00 0.00 4.30
226 253 7.547227 GCAAAACAATCAATAATGTACTCCCT 58.453 34.615 0.00 0.00 0.00 4.20
227 254 7.702348 GCAAAACAATCAATAATGTACTCCCTC 59.298 37.037 0.00 0.00 0.00 4.30
228 255 7.881775 AAACAATCAATAATGTACTCCCTCC 57.118 36.000 0.00 0.00 0.00 4.30
229 256 5.611374 ACAATCAATAATGTACTCCCTCCG 58.389 41.667 0.00 0.00 0.00 4.63
230 257 5.130477 ACAATCAATAATGTACTCCCTCCGT 59.870 40.000 0.00 0.00 0.00 4.69
231 258 4.931661 TCAATAATGTACTCCCTCCGTC 57.068 45.455 0.00 0.00 0.00 4.79
232 259 3.640029 TCAATAATGTACTCCCTCCGTCC 59.360 47.826 0.00 0.00 0.00 4.79
233 260 1.683943 TAATGTACTCCCTCCGTCCG 58.316 55.000 0.00 0.00 0.00 4.79
234 261 1.041447 AATGTACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
235 262 2.832201 GTACTCCCTCCGTCCGGG 60.832 72.222 0.00 0.00 43.38 5.73
236 263 3.341629 TACTCCCTCCGTCCGGGT 61.342 66.667 0.00 0.00 42.56 5.28
237 264 3.650298 TACTCCCTCCGTCCGGGTG 62.650 68.421 0.00 0.00 42.56 4.61
239 266 3.650298 CTCCCTCCGTCCGGGTGTA 62.650 68.421 0.00 0.00 42.56 2.90
240 267 2.443390 CCCTCCGTCCGGGTGTAT 60.443 66.667 0.00 0.00 36.91 2.29
241 268 1.152694 CCCTCCGTCCGGGTGTATA 60.153 63.158 0.00 0.00 36.91 1.47
242 269 0.756442 CCCTCCGTCCGGGTGTATAA 60.756 60.000 0.00 0.00 36.91 0.98
243 270 0.672342 CCTCCGTCCGGGTGTATAAG 59.328 60.000 0.00 0.00 37.00 1.73
244 271 1.396653 CTCCGTCCGGGTGTATAAGT 58.603 55.000 0.00 0.00 37.00 2.24
245 272 1.336125 CTCCGTCCGGGTGTATAAGTC 59.664 57.143 0.00 0.00 37.00 3.01
246 273 1.105457 CCGTCCGGGTGTATAAGTCA 58.895 55.000 0.00 0.00 0.00 3.41
247 274 1.684983 CCGTCCGGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 0.00 3.06
248 275 2.101917 CCGTCCGGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 0.00 2.57
249 276 3.378339 CGTCCGGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
250 277 3.378339 GTCCGGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
251 278 2.132762 CCGGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
252 279 1.784856 CGGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
253 280 2.797087 CGGGTGTATAAGTCATTCGCGT 60.797 50.000 5.77 0.00 0.00 6.01
254 281 3.548616 CGGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
255 282 3.979495 GGGTGTATAAGTCATTCGCGTAG 59.021 47.826 5.77 0.00 0.00 3.51
256 283 4.498682 GGGTGTATAAGTCATTCGCGTAGT 60.499 45.833 5.77 0.00 0.00 2.73
257 284 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
258 285 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
259 286 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
260 287 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
261 288 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
262 289 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
263 290 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
264 291 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
265 292 3.011818 TCATTCGCGTAGTTCTAGGTCA 58.988 45.455 5.77 0.00 0.00 4.02
266 293 3.630769 TCATTCGCGTAGTTCTAGGTCAT 59.369 43.478 5.77 0.00 0.00 3.06
267 294 3.687572 TTCGCGTAGTTCTAGGTCATC 57.312 47.619 5.77 0.00 0.00 2.92
268 295 1.596260 TCGCGTAGTTCTAGGTCATCG 59.404 52.381 5.77 0.00 0.00 3.84
269 296 1.596260 CGCGTAGTTCTAGGTCATCGA 59.404 52.381 0.00 0.00 0.00 3.59
270 297 2.223611 CGCGTAGTTCTAGGTCATCGAT 59.776 50.000 0.00 0.00 0.00 3.59
271 298 3.303857 CGCGTAGTTCTAGGTCATCGATT 60.304 47.826 0.00 0.00 0.00 3.34
272 299 4.608951 GCGTAGTTCTAGGTCATCGATTT 58.391 43.478 0.00 0.00 0.00 2.17
273 300 4.441415 GCGTAGTTCTAGGTCATCGATTTG 59.559 45.833 0.00 0.00 0.00 2.32
274 301 5.732528 GCGTAGTTCTAGGTCATCGATTTGA 60.733 44.000 0.00 0.00 0.00 2.69
275 302 5.910166 CGTAGTTCTAGGTCATCGATTTGAG 59.090 44.000 0.00 0.00 0.00 3.02
276 303 5.269505 AGTTCTAGGTCATCGATTTGAGG 57.730 43.478 0.00 0.00 0.00 3.86
277 304 4.956700 AGTTCTAGGTCATCGATTTGAGGA 59.043 41.667 0.00 0.00 34.44 3.71
278 305 5.422331 AGTTCTAGGTCATCGATTTGAGGAA 59.578 40.000 0.00 0.00 39.46 3.36
279 306 6.098982 AGTTCTAGGTCATCGATTTGAGGAAT 59.901 38.462 0.00 0.00 39.46 3.01
280 307 6.485830 TCTAGGTCATCGATTTGAGGAATT 57.514 37.500 0.00 0.00 39.46 2.17
281 308 7.597288 TCTAGGTCATCGATTTGAGGAATTA 57.403 36.000 0.00 0.00 39.46 1.40
282 309 8.018537 TCTAGGTCATCGATTTGAGGAATTAA 57.981 34.615 0.00 0.00 39.46 1.40
283 310 8.482943 TCTAGGTCATCGATTTGAGGAATTAAA 58.517 33.333 0.00 0.00 39.46 1.52
284 311 9.277783 CTAGGTCATCGATTTGAGGAATTAAAT 57.722 33.333 0.00 0.00 39.46 1.40
286 313 9.799106 AGGTCATCGATTTGAGGAATTAAATAT 57.201 29.630 0.00 0.00 39.46 1.28
287 314 9.831737 GGTCATCGATTTGAGGAATTAAATATG 57.168 33.333 0.00 0.00 39.46 1.78
317 344 5.068234 TGTCATGAAAAGTACTACCTCCG 57.932 43.478 0.00 0.00 0.00 4.63
318 345 4.525487 TGTCATGAAAAGTACTACCTCCGT 59.475 41.667 0.00 0.00 0.00 4.69
319 346 5.100943 GTCATGAAAAGTACTACCTCCGTC 58.899 45.833 0.00 0.00 0.00 4.79
320 347 4.159135 TCATGAAAAGTACTACCTCCGTCC 59.841 45.833 0.00 0.00 0.00 4.79
321 348 2.827921 TGAAAAGTACTACCTCCGTCCC 59.172 50.000 0.00 0.00 0.00 4.46
322 349 1.467920 AAAGTACTACCTCCGTCCCG 58.532 55.000 0.00 0.00 0.00 5.14
333 360 3.953201 CCGTCCCGGTGTATAAGTC 57.047 57.895 0.00 0.00 42.73 3.01
334 361 1.105457 CCGTCCCGGTGTATAAGTCA 58.895 55.000 0.00 0.00 42.73 3.41
335 362 1.684983 CCGTCCCGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 42.73 3.06
336 363 2.101917 CCGTCCCGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 42.73 2.57
337 364 3.378339 CGTCCCGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
338 365 3.378339 GTCCCGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
339 366 2.132762 CCCGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
340 367 1.784856 CCGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
341 368 2.456989 CGGTGTATAAGTCATTCGCGT 58.543 47.619 5.77 0.00 0.00 6.01
342 369 3.548616 CCGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
343 370 3.662645 CGGTGTATAAGTCATTCGCGTAG 59.337 47.826 5.77 0.00 0.00 3.51
344 371 4.604976 GGTGTATAAGTCATTCGCGTAGT 58.395 43.478 5.77 0.00 0.00 2.73
345 372 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
346 373 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
347 374 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
348 375 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
349 376 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
350 377 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
351 378 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
352 379 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
353 380 2.031314 TCATTCGCGTAGTTCTAGGTCG 59.969 50.000 5.77 5.99 0.00 4.79
354 381 1.725641 TTCGCGTAGTTCTAGGTCGA 58.274 50.000 5.77 11.56 0.00 4.20
355 382 1.945387 TCGCGTAGTTCTAGGTCGAT 58.055 50.000 5.77 0.00 0.00 3.59
356 383 3.097877 TCGCGTAGTTCTAGGTCGATA 57.902 47.619 5.77 0.00 0.00 2.92
357 384 3.457234 TCGCGTAGTTCTAGGTCGATAA 58.543 45.455 5.77 0.00 0.00 1.75
358 385 4.060900 TCGCGTAGTTCTAGGTCGATAAT 58.939 43.478 5.77 0.00 0.00 1.28
359 386 4.512944 TCGCGTAGTTCTAGGTCGATAATT 59.487 41.667 5.77 0.00 0.00 1.40
360 387 5.008019 TCGCGTAGTTCTAGGTCGATAATTT 59.992 40.000 5.77 0.00 0.00 1.82
361 388 6.202762 TCGCGTAGTTCTAGGTCGATAATTTA 59.797 38.462 5.77 0.00 0.00 1.40
362 389 6.852853 CGCGTAGTTCTAGGTCGATAATTTAA 59.147 38.462 0.00 0.00 0.00 1.52
363 390 7.149224 CGCGTAGTTCTAGGTCGATAATTTAAC 60.149 40.741 0.00 0.00 0.00 2.01
364 391 7.859875 GCGTAGTTCTAGGTCGATAATTTAACT 59.140 37.037 0.00 0.00 0.00 2.24
422 449 9.706691 ATATATTTAGAAACTACATCCGTGTGG 57.293 33.333 0.00 0.00 42.04 4.17
438 465 6.985117 TCCGTGTGGAAATATAGTGGTATAC 58.015 40.000 0.00 0.00 42.85 1.47
439 466 6.779049 TCCGTGTGGAAATATAGTGGTATACT 59.221 38.462 2.25 0.00 42.85 2.12
440 467 7.288389 TCCGTGTGGAAATATAGTGGTATACTT 59.712 37.037 2.25 0.00 42.85 2.24
441 468 7.929785 CCGTGTGGAAATATAGTGGTATACTTT 59.070 37.037 2.25 0.00 37.99 2.66
442 469 9.321562 CGTGTGGAAATATAGTGGTATACTTTT 57.678 33.333 2.25 0.00 40.89 2.27
483 510 9.831737 CATATTTAATTCCTCAAATCGATGACC 57.168 33.333 0.00 0.00 0.00 4.02
484 511 9.799106 ATATTTAATTCCTCAAATCGATGACCT 57.201 29.630 0.00 0.00 0.00 3.85
486 513 8.662781 TTTAATTCCTCAAATCGATGACCTAG 57.337 34.615 0.00 0.00 0.00 3.02
487 514 6.485830 AATTCCTCAAATCGATGACCTAGA 57.514 37.500 0.00 0.00 0.00 2.43
488 515 5.932619 TTCCTCAAATCGATGACCTAGAA 57.067 39.130 0.00 0.00 0.00 2.10
489 516 5.263968 TCCTCAAATCGATGACCTAGAAC 57.736 43.478 0.00 0.00 0.00 3.01
490 517 4.956700 TCCTCAAATCGATGACCTAGAACT 59.043 41.667 0.00 0.00 0.00 3.01
491 518 6.127101 TCCTCAAATCGATGACCTAGAACTA 58.873 40.000 0.00 0.00 0.00 2.24
492 519 6.039493 TCCTCAAATCGATGACCTAGAACTAC 59.961 42.308 0.00 0.00 0.00 2.73
493 520 5.817988 TCAAATCGATGACCTAGAACTACG 58.182 41.667 0.00 0.00 0.00 3.51
494 521 3.900388 ATCGATGACCTAGAACTACGC 57.100 47.619 0.00 0.00 0.00 4.42
495 522 1.596260 TCGATGACCTAGAACTACGCG 59.404 52.381 3.53 3.53 0.00 6.01
496 523 1.596260 CGATGACCTAGAACTACGCGA 59.404 52.381 15.93 0.00 0.00 5.87
497 524 2.031314 CGATGACCTAGAACTACGCGAA 59.969 50.000 15.93 0.00 0.00 4.70
498 525 3.303857 CGATGACCTAGAACTACGCGAAT 60.304 47.826 15.93 0.00 0.00 3.34
499 526 3.416119 TGACCTAGAACTACGCGAATG 57.584 47.619 15.93 4.47 0.00 2.67
500 527 3.011818 TGACCTAGAACTACGCGAATGA 58.988 45.455 15.93 0.00 0.00 2.57
501 528 3.181503 TGACCTAGAACTACGCGAATGAC 60.182 47.826 15.93 0.66 0.00 3.06
502 529 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
503 530 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
504 531 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
505 532 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
506 533 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
507 534 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
508 535 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
509 536 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
510 537 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
511 538 2.817901 ACGCGAATGACTTATACACCC 58.182 47.619 15.93 0.00 0.00 4.61
512 539 1.784856 CGCGAATGACTTATACACCCG 59.215 52.381 0.00 0.00 0.00 5.28
513 540 2.132762 GCGAATGACTTATACACCCGG 58.867 52.381 0.00 0.00 0.00 5.73
514 541 2.223876 GCGAATGACTTATACACCCGGA 60.224 50.000 0.73 0.00 0.00 5.14
515 542 3.378339 CGAATGACTTATACACCCGGAC 58.622 50.000 0.73 0.00 0.00 4.79
516 543 3.378339 GAATGACTTATACACCCGGACG 58.622 50.000 0.73 0.00 0.00 4.79
517 544 1.105457 TGACTTATACACCCGGACGG 58.895 55.000 0.73 3.25 37.81 4.79
518 545 1.340893 TGACTTATACACCCGGACGGA 60.341 52.381 13.13 0.00 37.50 4.69
519 546 1.336125 GACTTATACACCCGGACGGAG 59.664 57.143 13.13 6.96 37.50 4.63
520 547 0.672342 CTTATACACCCGGACGGAGG 59.328 60.000 13.13 6.21 37.50 4.30
528 555 2.638744 CCGGACGGAGGGAGTATAC 58.361 63.158 4.40 0.00 37.50 1.47
529 556 0.892814 CCGGACGGAGGGAGTATACC 60.893 65.000 4.40 0.00 37.50 2.73
530 557 0.179009 CGGACGGAGGGAGTATACCA 60.179 60.000 0.00 0.00 0.00 3.25
531 558 1.326328 GGACGGAGGGAGTATACCAC 58.674 60.000 0.00 0.00 0.00 4.16
532 559 1.133544 GGACGGAGGGAGTATACCACT 60.134 57.143 0.00 0.00 41.47 4.00
533 560 2.107204 GGACGGAGGGAGTATACCACTA 59.893 54.545 0.00 0.00 37.72 2.74
534 561 3.245193 GGACGGAGGGAGTATACCACTAT 60.245 52.174 0.00 0.00 37.72 2.12
535 562 4.018960 GGACGGAGGGAGTATACCACTATA 60.019 50.000 0.00 0.00 37.72 1.31
536 563 5.339861 GGACGGAGGGAGTATACCACTATAT 60.340 48.000 0.00 0.00 37.72 0.86
537 564 6.150034 ACGGAGGGAGTATACCACTATATT 57.850 41.667 0.00 0.00 37.72 1.28
538 565 6.559429 ACGGAGGGAGTATACCACTATATTT 58.441 40.000 0.00 0.00 37.72 1.40
539 566 6.662663 ACGGAGGGAGTATACCACTATATTTC 59.337 42.308 0.00 0.00 37.72 2.17
540 567 6.096564 CGGAGGGAGTATACCACTATATTTCC 59.903 46.154 0.00 0.00 37.72 3.13
541 568 6.958192 GGAGGGAGTATACCACTATATTTCCA 59.042 42.308 0.00 0.00 37.72 3.53
542 569 7.093421 GGAGGGAGTATACCACTATATTTCCAC 60.093 44.444 0.00 0.00 37.72 4.02
543 570 7.310634 AGGGAGTATACCACTATATTTCCACA 58.689 38.462 0.00 0.00 37.72 4.17
544 571 7.234988 AGGGAGTATACCACTATATTTCCACAC 59.765 40.741 0.00 0.00 37.72 3.82
545 572 7.088905 GGAGTATACCACTATATTTCCACACG 58.911 42.308 0.00 0.00 37.72 4.49
546 573 6.989659 AGTATACCACTATATTTCCACACGG 58.010 40.000 0.00 0.00 34.98 4.94
547 574 6.779049 AGTATACCACTATATTTCCACACGGA 59.221 38.462 0.00 0.00 35.86 4.69
548 575 6.681729 ATACCACTATATTTCCACACGGAT 57.318 37.500 0.00 0.00 42.41 4.18
549 576 4.703897 ACCACTATATTTCCACACGGATG 58.296 43.478 0.00 0.00 42.41 3.51
550 577 4.163458 ACCACTATATTTCCACACGGATGT 59.837 41.667 0.00 0.00 42.41 3.06
551 578 5.364446 ACCACTATATTTCCACACGGATGTA 59.636 40.000 0.00 0.00 42.41 2.29
552 579 5.926542 CCACTATATTTCCACACGGATGTAG 59.073 44.000 0.00 0.00 42.41 2.74
553 580 6.462487 CCACTATATTTCCACACGGATGTAGT 60.462 42.308 0.00 0.00 42.41 2.73
554 581 6.984474 CACTATATTTCCACACGGATGTAGTT 59.016 38.462 0.00 0.00 42.41 2.24
555 582 7.494625 CACTATATTTCCACACGGATGTAGTTT 59.505 37.037 0.00 0.00 42.41 2.66
556 583 6.920569 ATATTTCCACACGGATGTAGTTTC 57.079 37.500 0.00 0.00 42.41 2.78
557 584 4.345859 TTTCCACACGGATGTAGTTTCT 57.654 40.909 0.00 0.00 42.41 2.52
558 585 5.471556 TTTCCACACGGATGTAGTTTCTA 57.528 39.130 0.00 0.00 42.41 2.10
559 586 5.471556 TTCCACACGGATGTAGTTTCTAA 57.528 39.130 0.00 0.00 42.41 2.10
560 587 5.471556 TCCACACGGATGTAGTTTCTAAA 57.528 39.130 0.00 0.00 36.72 1.85
561 588 6.045072 TCCACACGGATGTAGTTTCTAAAT 57.955 37.500 0.00 0.00 36.72 1.40
562 589 7.172868 TCCACACGGATGTAGTTTCTAAATA 57.827 36.000 0.00 0.00 36.72 1.40
563 590 7.788026 TCCACACGGATGTAGTTTCTAAATAT 58.212 34.615 0.00 0.00 36.72 1.28
564 591 8.916062 TCCACACGGATGTAGTTTCTAAATATA 58.084 33.333 0.00 0.00 36.72 0.86
565 592 9.706691 CCACACGGATGTAGTTTCTAAATATAT 57.293 33.333 0.00 0.00 36.72 0.86
623 650 7.859875 AGTTAAATTATCGACCTAGAACTACGC 59.140 37.037 0.00 0.00 0.00 4.42
624 651 3.867055 TTATCGACCTAGAACTACGCG 57.133 47.619 3.53 3.53 0.00 6.01
625 652 1.945387 ATCGACCTAGAACTACGCGA 58.055 50.000 15.93 0.00 0.00 5.87
626 653 1.725641 TCGACCTAGAACTACGCGAA 58.274 50.000 15.93 0.00 0.00 4.70
627 654 2.283298 TCGACCTAGAACTACGCGAAT 58.717 47.619 15.93 0.00 0.00 3.34
628 655 2.031314 TCGACCTAGAACTACGCGAATG 59.969 50.000 15.93 4.47 0.00 2.67
629 656 2.031314 CGACCTAGAACTACGCGAATGA 59.969 50.000 15.93 0.00 0.00 2.57
630 657 3.361414 GACCTAGAACTACGCGAATGAC 58.639 50.000 15.93 0.66 0.00 3.06
631 658 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
632 659 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
633 660 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
634 661 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
635 662 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
636 663 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
637 664 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
638 665 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
639 666 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
640 667 2.456989 ACGCGAATGACTTATACACCG 58.543 47.619 15.93 0.00 0.00 4.94
641 668 1.784856 CGCGAATGACTTATACACCGG 59.215 52.381 0.00 0.00 0.00 5.28
642 669 2.132762 GCGAATGACTTATACACCGGG 58.867 52.381 6.32 0.00 0.00 5.73
643 670 2.223876 GCGAATGACTTATACACCGGGA 60.224 50.000 6.32 0.00 0.00 5.14
644 671 3.378339 CGAATGACTTATACACCGGGAC 58.622 50.000 6.32 0.00 0.00 4.46
763 797 2.575532 GATGATTGAAATCTCCGCCCA 58.424 47.619 4.76 0.00 36.39 5.36
798 835 6.721208 ACCAAATGAATGATTTCCACTAGTGT 59.279 34.615 21.18 2.58 31.41 3.55
806 843 0.179043 TTCCACTAGTGTTGCGCCAA 60.179 50.000 21.18 0.00 0.00 4.52
987 1024 2.594592 GTGAAGTTGGCCAGCCGT 60.595 61.111 16.95 4.31 39.42 5.68
1104 1141 2.954684 CGTGCCCTGGAGCTGGTTA 61.955 63.158 0.00 0.00 0.00 2.85
1293 1330 1.112916 CGGGGGAGTTGCCAAAGTTT 61.113 55.000 0.00 0.00 38.95 2.66
1473 1510 2.544359 CGGTTGTTGCTGACGTCG 59.456 61.111 11.62 7.05 0.00 5.12
1929 1966 2.752903 GTGTCTTTCTTTGGGTGTGTGT 59.247 45.455 0.00 0.00 0.00 3.72
1930 1967 2.752354 TGTCTTTCTTTGGGTGTGTGTG 59.248 45.455 0.00 0.00 0.00 3.82
1931 1968 2.752903 GTCTTTCTTTGGGTGTGTGTGT 59.247 45.455 0.00 0.00 0.00 3.72
1932 1969 2.752354 TCTTTCTTTGGGTGTGTGTGTG 59.248 45.455 0.00 0.00 0.00 3.82
1992 2029 1.867363 ATATACAGGGGGAGGCGATC 58.133 55.000 0.00 0.00 0.00 3.69
2064 2101 7.030768 CGTTCTGGGTTTCTTGTTTTCTTTTA 58.969 34.615 0.00 0.00 0.00 1.52
2093 2130 0.829182 CTGCTGGCTTTCCCACCTTT 60.829 55.000 0.00 0.00 39.18 3.11
2126 2163 9.111613 TGTATTCTTGTTTTTCGAGGTTTTCTA 57.888 29.630 0.00 0.00 0.00 2.10
2135 2172 2.000447 CGAGGTTTTCTAGCTTTCCCG 59.000 52.381 0.00 0.00 33.94 5.14
2175 2215 4.255833 ACAACGGAATAAGGTACACGAA 57.744 40.909 0.00 0.00 0.00 3.85
2180 2220 4.107622 CGGAATAAGGTACACGAACGAAT 58.892 43.478 0.14 0.00 0.00 3.34
2187 2227 4.669318 AGGTACACGAACGAATGATACAG 58.331 43.478 0.14 0.00 0.00 2.74
2260 2300 3.368236 GCAAAACACTACGCAACCAAAAA 59.632 39.130 0.00 0.00 0.00 1.94
2332 2381 1.745489 GAGGGAGAACGGCGCAAAT 60.745 57.895 10.83 0.00 0.00 2.32
2391 2440 2.583441 CCGGAGCCCTGTCACAGAA 61.583 63.158 6.30 0.00 32.44 3.02
2433 2482 0.107703 CAAGAAGATAGCGGCACCCA 60.108 55.000 1.45 0.00 0.00 4.51
2450 2499 1.632046 CCACAAGCGTCGCCGTTATT 61.632 55.000 14.86 0.00 36.15 1.40
2528 2577 0.250513 GGACAAGCTCGGTGAGGAAT 59.749 55.000 0.00 0.00 0.00 3.01
2529 2578 1.480954 GGACAAGCTCGGTGAGGAATA 59.519 52.381 0.00 0.00 0.00 1.75
2598 2648 1.330655 CCGAGCCACCCACATCTAGT 61.331 60.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 99 9.262358 GTGGAGAGATTATTACTTGGTGTATTC 57.738 37.037 0.00 0.00 0.00 1.75
132 148 0.244994 CTTGTGCGACAGCTAGTCCT 59.755 55.000 9.71 0.00 44.66 3.85
133 149 0.243907 TCTTGTGCGACAGCTAGTCC 59.756 55.000 9.71 5.00 44.66 3.85
134 150 2.065993 TTCTTGTGCGACAGCTAGTC 57.934 50.000 6.31 6.31 45.42 2.59
135 151 2.035961 TCTTTCTTGTGCGACAGCTAGT 59.964 45.455 0.00 0.00 45.42 2.57
136 152 2.677199 TCTTTCTTGTGCGACAGCTAG 58.323 47.619 0.00 0.00 45.42 3.42
137 153 2.812358 TCTTTCTTGTGCGACAGCTA 57.188 45.000 0.00 0.00 45.42 3.32
138 154 1.953559 TTCTTTCTTGTGCGACAGCT 58.046 45.000 0.00 0.00 45.42 4.24
139 155 2.578495 CATTCTTTCTTGTGCGACAGC 58.422 47.619 0.00 0.00 45.41 4.40
140 156 2.807967 TCCATTCTTTCTTGTGCGACAG 59.192 45.455 0.00 0.00 0.00 3.51
141 157 2.844946 TCCATTCTTTCTTGTGCGACA 58.155 42.857 0.00 0.00 0.00 4.35
207 234 5.611374 ACGGAGGGAGTACATTATTGATTG 58.389 41.667 0.00 0.00 0.00 2.67
224 251 0.672342 CTTATACACCCGGACGGAGG 59.328 60.000 13.13 6.21 37.50 4.30
225 252 1.336125 GACTTATACACCCGGACGGAG 59.664 57.143 13.13 6.96 37.50 4.63
226 253 1.340893 TGACTTATACACCCGGACGGA 60.341 52.381 13.13 0.00 37.50 4.69
227 254 1.105457 TGACTTATACACCCGGACGG 58.895 55.000 0.73 3.25 37.81 4.79
228 255 3.378339 GAATGACTTATACACCCGGACG 58.622 50.000 0.73 0.00 0.00 4.79
229 256 3.378339 CGAATGACTTATACACCCGGAC 58.622 50.000 0.73 0.00 0.00 4.79
230 257 2.223876 GCGAATGACTTATACACCCGGA 60.224 50.000 0.73 0.00 0.00 5.14
231 258 2.132762 GCGAATGACTTATACACCCGG 58.867 52.381 0.00 0.00 0.00 5.73
232 259 1.784856 CGCGAATGACTTATACACCCG 59.215 52.381 0.00 0.00 0.00 5.28
233 260 2.817901 ACGCGAATGACTTATACACCC 58.182 47.619 15.93 0.00 0.00 4.61
234 261 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
235 262 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
236 263 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
237 264 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
238 265 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
239 266 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
240 267 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
241 268 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
242 269 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
243 270 3.181503 TGACCTAGAACTACGCGAATGAC 60.182 47.826 15.93 0.66 0.00 3.06
244 271 3.011818 TGACCTAGAACTACGCGAATGA 58.988 45.455 15.93 0.00 0.00 2.57
245 272 3.416119 TGACCTAGAACTACGCGAATG 57.584 47.619 15.93 4.47 0.00 2.67
246 273 3.303857 CGATGACCTAGAACTACGCGAAT 60.304 47.826 15.93 0.00 0.00 3.34
247 274 2.031314 CGATGACCTAGAACTACGCGAA 59.969 50.000 15.93 0.00 0.00 4.70
248 275 1.596260 CGATGACCTAGAACTACGCGA 59.404 52.381 15.93 0.00 0.00 5.87
249 276 1.596260 TCGATGACCTAGAACTACGCG 59.404 52.381 3.53 3.53 0.00 6.01
250 277 3.900388 ATCGATGACCTAGAACTACGC 57.100 47.619 0.00 0.00 0.00 4.42
251 278 5.817988 TCAAATCGATGACCTAGAACTACG 58.182 41.667 0.00 0.00 0.00 3.51
252 279 6.039493 TCCTCAAATCGATGACCTAGAACTAC 59.961 42.308 0.00 0.00 0.00 2.73
253 280 6.127101 TCCTCAAATCGATGACCTAGAACTA 58.873 40.000 0.00 0.00 0.00 2.24
254 281 4.956700 TCCTCAAATCGATGACCTAGAACT 59.043 41.667 0.00 0.00 0.00 3.01
255 282 5.263968 TCCTCAAATCGATGACCTAGAAC 57.736 43.478 0.00 0.00 0.00 3.01
256 283 5.932619 TTCCTCAAATCGATGACCTAGAA 57.067 39.130 0.00 0.00 0.00 2.10
257 284 6.485830 AATTCCTCAAATCGATGACCTAGA 57.514 37.500 0.00 0.00 0.00 2.43
258 285 8.662781 TTTAATTCCTCAAATCGATGACCTAG 57.337 34.615 0.00 0.00 0.00 3.02
260 287 9.799106 ATATTTAATTCCTCAAATCGATGACCT 57.201 29.630 0.00 0.00 0.00 3.85
261 288 9.831737 CATATTTAATTCCTCAAATCGATGACC 57.168 33.333 0.00 0.00 0.00 4.02
291 318 8.573885 CGGAGGTAGTACTTTTCATGACATATA 58.426 37.037 0.00 0.00 0.00 0.86
292 319 7.069578 ACGGAGGTAGTACTTTTCATGACATAT 59.930 37.037 0.00 0.00 0.00 1.78
293 320 6.379133 ACGGAGGTAGTACTTTTCATGACATA 59.621 38.462 0.00 0.00 0.00 2.29
294 321 5.187186 ACGGAGGTAGTACTTTTCATGACAT 59.813 40.000 0.00 0.00 0.00 3.06
295 322 4.525487 ACGGAGGTAGTACTTTTCATGACA 59.475 41.667 0.00 0.00 0.00 3.58
296 323 5.069501 ACGGAGGTAGTACTTTTCATGAC 57.930 43.478 0.00 0.00 0.00 3.06
297 324 4.159135 GGACGGAGGTAGTACTTTTCATGA 59.841 45.833 0.00 0.00 0.00 3.07
298 325 4.430908 GGACGGAGGTAGTACTTTTCATG 58.569 47.826 0.00 0.00 0.00 3.07
299 326 3.450096 GGGACGGAGGTAGTACTTTTCAT 59.550 47.826 0.00 0.00 0.00 2.57
300 327 2.827921 GGGACGGAGGTAGTACTTTTCA 59.172 50.000 0.00 0.00 0.00 2.69
301 328 3.516981 GGGACGGAGGTAGTACTTTTC 57.483 52.381 0.00 0.00 0.00 2.29
317 344 3.378339 CGAATGACTTATACACCGGGAC 58.622 50.000 6.32 0.00 0.00 4.46
318 345 2.223876 GCGAATGACTTATACACCGGGA 60.224 50.000 6.32 0.00 0.00 5.14
319 346 2.132762 GCGAATGACTTATACACCGGG 58.867 52.381 6.32 0.00 0.00 5.73
320 347 1.784856 CGCGAATGACTTATACACCGG 59.215 52.381 0.00 0.00 0.00 5.28
321 348 2.456989 ACGCGAATGACTTATACACCG 58.543 47.619 15.93 0.00 0.00 4.94
322 349 4.604976 ACTACGCGAATGACTTATACACC 58.395 43.478 15.93 0.00 0.00 4.16
323 350 5.970023 AGAACTACGCGAATGACTTATACAC 59.030 40.000 15.93 0.00 0.00 2.90
324 351 6.127810 AGAACTACGCGAATGACTTATACA 57.872 37.500 15.93 0.00 0.00 2.29
325 352 6.796072 CCTAGAACTACGCGAATGACTTATAC 59.204 42.308 15.93 0.00 0.00 1.47
326 353 6.484643 ACCTAGAACTACGCGAATGACTTATA 59.515 38.462 15.93 0.00 0.00 0.98
327 354 5.298777 ACCTAGAACTACGCGAATGACTTAT 59.701 40.000 15.93 0.00 0.00 1.73
328 355 4.637534 ACCTAGAACTACGCGAATGACTTA 59.362 41.667 15.93 0.00 0.00 2.24
329 356 3.442977 ACCTAGAACTACGCGAATGACTT 59.557 43.478 15.93 0.00 0.00 3.01
330 357 3.015327 ACCTAGAACTACGCGAATGACT 58.985 45.455 15.93 9.07 0.00 3.41
331 358 3.361414 GACCTAGAACTACGCGAATGAC 58.639 50.000 15.93 0.66 0.00 3.06
332 359 2.031314 CGACCTAGAACTACGCGAATGA 59.969 50.000 15.93 0.00 0.00 2.57
333 360 2.031314 TCGACCTAGAACTACGCGAATG 59.969 50.000 15.93 4.47 0.00 2.67
334 361 2.283298 TCGACCTAGAACTACGCGAAT 58.717 47.619 15.93 0.00 0.00 3.34
335 362 1.725641 TCGACCTAGAACTACGCGAA 58.274 50.000 15.93 0.00 0.00 4.70
336 363 1.945387 ATCGACCTAGAACTACGCGA 58.055 50.000 15.93 0.00 0.00 5.87
337 364 3.867055 TTATCGACCTAGAACTACGCG 57.133 47.619 3.53 3.53 0.00 6.01
338 365 7.859875 AGTTAAATTATCGACCTAGAACTACGC 59.140 37.037 0.00 0.00 0.00 4.42
396 423 9.706691 CCACACGGATGTAGTTTCTAAATATAT 57.293 33.333 0.00 0.00 36.72 0.86
397 424 8.916062 TCCACACGGATGTAGTTTCTAAATATA 58.084 33.333 0.00 0.00 36.72 0.86
398 425 7.788026 TCCACACGGATGTAGTTTCTAAATAT 58.212 34.615 0.00 0.00 36.72 1.28
399 426 7.172868 TCCACACGGATGTAGTTTCTAAATA 57.827 36.000 0.00 0.00 36.72 1.40
400 427 6.045072 TCCACACGGATGTAGTTTCTAAAT 57.955 37.500 0.00 0.00 36.72 1.40
401 428 5.471556 TCCACACGGATGTAGTTTCTAAA 57.528 39.130 0.00 0.00 36.72 1.85
402 429 5.471556 TTCCACACGGATGTAGTTTCTAA 57.528 39.130 0.00 0.00 42.41 2.10
403 430 5.471556 TTTCCACACGGATGTAGTTTCTA 57.528 39.130 0.00 0.00 42.41 2.10
404 431 4.345859 TTTCCACACGGATGTAGTTTCT 57.654 40.909 0.00 0.00 42.41 2.52
405 432 6.920569 ATATTTCCACACGGATGTAGTTTC 57.079 37.500 0.00 0.00 42.41 2.78
406 433 7.494625 CACTATATTTCCACACGGATGTAGTTT 59.505 37.037 0.00 0.00 42.41 2.66
407 434 6.984474 CACTATATTTCCACACGGATGTAGTT 59.016 38.462 0.00 0.00 42.41 2.24
408 435 6.462487 CCACTATATTTCCACACGGATGTAGT 60.462 42.308 0.00 0.00 42.41 2.73
409 436 5.926542 CCACTATATTTCCACACGGATGTAG 59.073 44.000 0.00 0.00 42.41 2.74
410 437 5.364446 ACCACTATATTTCCACACGGATGTA 59.636 40.000 0.00 0.00 42.41 2.29
411 438 4.163458 ACCACTATATTTCCACACGGATGT 59.837 41.667 0.00 0.00 42.41 3.06
412 439 4.703897 ACCACTATATTTCCACACGGATG 58.296 43.478 0.00 0.00 42.41 3.51
413 440 6.681729 ATACCACTATATTTCCACACGGAT 57.318 37.500 0.00 0.00 42.41 4.18
414 441 6.779049 AGTATACCACTATATTTCCACACGGA 59.221 38.462 0.00 0.00 35.86 4.69
415 442 6.989659 AGTATACCACTATATTTCCACACGG 58.010 40.000 0.00 0.00 34.98 4.94
416 443 8.882415 AAAGTATACCACTATATTTCCACACG 57.118 34.615 0.00 0.00 36.04 4.49
457 484 9.831737 GGTCATCGATTTGAGGAATTAAATATG 57.168 33.333 0.00 0.00 39.46 1.78
458 485 9.799106 AGGTCATCGATTTGAGGAATTAAATAT 57.201 29.630 0.00 0.00 39.46 1.28
460 487 9.277783 CTAGGTCATCGATTTGAGGAATTAAAT 57.722 33.333 0.00 0.00 39.46 1.40
461 488 8.482943 TCTAGGTCATCGATTTGAGGAATTAAA 58.517 33.333 0.00 0.00 39.46 1.52
462 489 8.018537 TCTAGGTCATCGATTTGAGGAATTAA 57.981 34.615 0.00 0.00 39.46 1.40
463 490 7.597288 TCTAGGTCATCGATTTGAGGAATTA 57.403 36.000 0.00 0.00 39.46 1.40
464 491 6.485830 TCTAGGTCATCGATTTGAGGAATT 57.514 37.500 0.00 0.00 39.46 2.17
465 492 6.098982 AGTTCTAGGTCATCGATTTGAGGAAT 59.901 38.462 0.00 0.00 39.46 3.01
466 493 5.422331 AGTTCTAGGTCATCGATTTGAGGAA 59.578 40.000 0.00 0.00 39.46 3.36
467 494 4.956700 AGTTCTAGGTCATCGATTTGAGGA 59.043 41.667 0.00 0.00 34.44 3.71
468 495 5.269505 AGTTCTAGGTCATCGATTTGAGG 57.730 43.478 0.00 0.00 0.00 3.86
469 496 5.910166 CGTAGTTCTAGGTCATCGATTTGAG 59.090 44.000 0.00 0.00 0.00 3.02
470 497 5.732528 GCGTAGTTCTAGGTCATCGATTTGA 60.733 44.000 0.00 0.00 0.00 2.69
471 498 4.441415 GCGTAGTTCTAGGTCATCGATTTG 59.559 45.833 0.00 0.00 0.00 2.32
472 499 4.608951 GCGTAGTTCTAGGTCATCGATTT 58.391 43.478 0.00 0.00 0.00 2.17
473 500 3.303857 CGCGTAGTTCTAGGTCATCGATT 60.304 47.826 0.00 0.00 0.00 3.34
474 501 2.223611 CGCGTAGTTCTAGGTCATCGAT 59.776 50.000 0.00 0.00 0.00 3.59
475 502 1.596260 CGCGTAGTTCTAGGTCATCGA 59.404 52.381 0.00 0.00 0.00 3.59
476 503 1.596260 TCGCGTAGTTCTAGGTCATCG 59.404 52.381 5.77 0.00 0.00 3.84
477 504 3.687572 TTCGCGTAGTTCTAGGTCATC 57.312 47.619 5.77 0.00 0.00 2.92
478 505 3.630769 TCATTCGCGTAGTTCTAGGTCAT 59.369 43.478 5.77 0.00 0.00 3.06
479 506 3.011818 TCATTCGCGTAGTTCTAGGTCA 58.988 45.455 5.77 0.00 0.00 4.02
480 507 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
481 508 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
482 509 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
483 510 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
484 511 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
485 512 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
486 513 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
487 514 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
488 515 4.498682 GGGTGTATAAGTCATTCGCGTAGT 60.499 45.833 5.77 0.00 0.00 2.73
489 516 3.979495 GGGTGTATAAGTCATTCGCGTAG 59.021 47.826 5.77 0.00 0.00 3.51
490 517 3.548616 CGGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
491 518 2.797087 CGGGTGTATAAGTCATTCGCGT 60.797 50.000 5.77 0.00 0.00 6.01
492 519 1.784856 CGGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
493 520 2.132762 CCGGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
494 521 3.378339 GTCCGGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
495 522 3.378339 CGTCCGGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
496 523 2.101917 CCGTCCGGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 0.00 2.57
497 524 1.684983 CCGTCCGGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 0.00 3.06
498 525 1.105457 CCGTCCGGGTGTATAAGTCA 58.895 55.000 0.00 0.00 0.00 3.41
499 526 1.336125 CTCCGTCCGGGTGTATAAGTC 59.664 57.143 0.00 0.00 37.00 3.01
500 527 1.396653 CTCCGTCCGGGTGTATAAGT 58.603 55.000 0.00 0.00 37.00 2.24
501 528 0.672342 CCTCCGTCCGGGTGTATAAG 59.328 60.000 0.00 0.00 37.00 1.73
502 529 0.756442 CCCTCCGTCCGGGTGTATAA 60.756 60.000 0.00 0.00 36.91 0.98
503 530 1.152694 CCCTCCGTCCGGGTGTATA 60.153 63.158 0.00 0.00 36.91 1.47
504 531 2.443390 CCCTCCGTCCGGGTGTAT 60.443 66.667 0.00 0.00 36.91 2.29
505 532 3.650298 CTCCCTCCGTCCGGGTGTA 62.650 68.421 0.00 0.00 42.56 2.90
507 534 2.923634 ATACTCCCTCCGTCCGGGTG 62.924 65.000 0.00 0.00 42.56 4.61
508 535 1.355718 TATACTCCCTCCGTCCGGGT 61.356 60.000 0.00 0.00 42.56 5.28
509 536 0.892814 GTATACTCCCTCCGTCCGGG 60.893 65.000 0.00 0.00 43.38 5.73
510 537 0.892814 GGTATACTCCCTCCGTCCGG 60.893 65.000 2.25 0.00 0.00 5.14
511 538 0.179009 TGGTATACTCCCTCCGTCCG 60.179 60.000 2.25 0.00 0.00 4.79
512 539 1.133544 AGTGGTATACTCCCTCCGTCC 60.134 57.143 2.25 0.00 33.17 4.79
513 540 2.361643 AGTGGTATACTCCCTCCGTC 57.638 55.000 2.25 0.00 33.17 4.79
514 541 5.793034 ATATAGTGGTATACTCCCTCCGT 57.207 43.478 2.25 0.00 40.89 4.69
515 542 6.096564 GGAAATATAGTGGTATACTCCCTCCG 59.903 46.154 2.25 0.00 40.89 4.63
516 543 6.958192 TGGAAATATAGTGGTATACTCCCTCC 59.042 42.308 2.25 0.00 40.89 4.30
517 544 7.453752 TGTGGAAATATAGTGGTATACTCCCTC 59.546 40.741 2.25 0.00 40.89 4.30
518 545 7.234988 GTGTGGAAATATAGTGGTATACTCCCT 59.765 40.741 2.25 0.00 40.89 4.20
519 546 7.384477 GTGTGGAAATATAGTGGTATACTCCC 58.616 42.308 2.25 0.00 40.89 4.30
520 547 7.088905 CGTGTGGAAATATAGTGGTATACTCC 58.911 42.308 2.25 0.00 40.89 3.85
521 548 7.040201 TCCGTGTGGAAATATAGTGGTATACTC 60.040 40.741 2.25 0.00 42.85 2.59
522 549 6.779049 TCCGTGTGGAAATATAGTGGTATACT 59.221 38.462 2.25 0.00 42.85 2.12
523 550 6.985117 TCCGTGTGGAAATATAGTGGTATAC 58.015 40.000 0.00 0.00 42.85 1.47
539 566 9.706691 ATATATTTAGAAACTACATCCGTGTGG 57.293 33.333 0.00 0.00 42.04 4.17
597 624 7.859875 GCGTAGTTCTAGGTCGATAATTTAACT 59.140 37.037 0.00 0.00 0.00 2.24
598 625 7.149224 CGCGTAGTTCTAGGTCGATAATTTAAC 60.149 40.741 0.00 0.00 0.00 2.01
599 626 6.852853 CGCGTAGTTCTAGGTCGATAATTTAA 59.147 38.462 0.00 0.00 0.00 1.52
600 627 6.202762 TCGCGTAGTTCTAGGTCGATAATTTA 59.797 38.462 5.77 0.00 0.00 1.40
601 628 5.008019 TCGCGTAGTTCTAGGTCGATAATTT 59.992 40.000 5.77 0.00 0.00 1.82
602 629 4.512944 TCGCGTAGTTCTAGGTCGATAATT 59.487 41.667 5.77 0.00 0.00 1.40
603 630 4.060900 TCGCGTAGTTCTAGGTCGATAAT 58.939 43.478 5.77 0.00 0.00 1.28
604 631 3.457234 TCGCGTAGTTCTAGGTCGATAA 58.543 45.455 5.77 0.00 0.00 1.75
605 632 3.097877 TCGCGTAGTTCTAGGTCGATA 57.902 47.619 5.77 0.00 0.00 2.92
606 633 1.945387 TCGCGTAGTTCTAGGTCGAT 58.055 50.000 5.77 0.00 0.00 3.59
607 634 1.725641 TTCGCGTAGTTCTAGGTCGA 58.274 50.000 5.77 11.56 0.00 4.20
608 635 2.031314 TCATTCGCGTAGTTCTAGGTCG 59.969 50.000 5.77 5.99 0.00 4.79
609 636 3.065095 AGTCATTCGCGTAGTTCTAGGTC 59.935 47.826 5.77 0.00 0.00 3.85
610 637 3.015327 AGTCATTCGCGTAGTTCTAGGT 58.985 45.455 5.77 0.00 0.00 3.08
611 638 3.694535 AGTCATTCGCGTAGTTCTAGG 57.305 47.619 5.77 0.00 0.00 3.02
612 639 7.320797 GTGTATAAGTCATTCGCGTAGTTCTAG 59.679 40.741 5.77 0.00 0.00 2.43
613 640 7.128331 GTGTATAAGTCATTCGCGTAGTTCTA 58.872 38.462 5.77 0.00 0.00 2.10
614 641 5.970023 GTGTATAAGTCATTCGCGTAGTTCT 59.030 40.000 5.77 0.00 0.00 3.01
615 642 5.172771 GGTGTATAAGTCATTCGCGTAGTTC 59.827 44.000 5.77 0.00 0.00 3.01
616 643 5.039333 GGTGTATAAGTCATTCGCGTAGTT 58.961 41.667 5.77 2.59 0.00 2.24
617 644 4.604976 GGTGTATAAGTCATTCGCGTAGT 58.395 43.478 5.77 0.00 0.00 2.73
618 645 3.662645 CGGTGTATAAGTCATTCGCGTAG 59.337 47.826 5.77 0.00 0.00 3.51
619 646 3.548616 CCGGTGTATAAGTCATTCGCGTA 60.549 47.826 5.77 0.00 0.00 4.42
620 647 2.456989 CGGTGTATAAGTCATTCGCGT 58.543 47.619 5.77 0.00 0.00 6.01
621 648 1.784856 CCGGTGTATAAGTCATTCGCG 59.215 52.381 0.00 0.00 0.00 5.87
622 649 2.132762 CCCGGTGTATAAGTCATTCGC 58.867 52.381 0.00 0.00 0.00 4.70
623 650 3.378339 GTCCCGGTGTATAAGTCATTCG 58.622 50.000 0.00 0.00 0.00 3.34
624 651 3.378339 CGTCCCGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
625 652 2.101917 CCGTCCCGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 42.73 2.57
626 653 1.684983 CCGTCCCGGTGTATAAGTCAT 59.315 52.381 0.00 0.00 42.73 3.06
627 654 1.105457 CCGTCCCGGTGTATAAGTCA 58.895 55.000 0.00 0.00 42.73 3.41
628 655 3.953201 CCGTCCCGGTGTATAAGTC 57.047 57.895 0.00 0.00 42.73 3.01
639 666 2.224378 TGATACTACTACCTCCGTCCCG 60.224 54.545 0.00 0.00 0.00 5.14
640 667 3.498774 TGATACTACTACCTCCGTCCC 57.501 52.381 0.00 0.00 0.00 4.46
641 668 4.396522 ACATGATACTACTACCTCCGTCC 58.603 47.826 0.00 0.00 0.00 4.79
642 669 6.654161 ACATACATGATACTACTACCTCCGTC 59.346 42.308 0.00 0.00 0.00 4.79
643 670 6.540995 ACATACATGATACTACTACCTCCGT 58.459 40.000 0.00 0.00 0.00 4.69
644 671 6.879993 AGACATACATGATACTACTACCTCCG 59.120 42.308 0.00 0.00 0.00 4.63
645 672 9.165035 GTAGACATACATGATACTACTACCTCC 57.835 40.741 0.00 0.00 34.03 4.30
646 673 9.722184 TGTAGACATACATGATACTACTACCTC 57.278 37.037 0.00 0.00 36.98 3.85
763 797 9.218440 GAAATCATTCATTTGGTGGTGTAAAAT 57.782 29.630 0.00 0.00 34.60 1.82
1104 1141 1.956170 CGTGCTGGACGTGAGCTTT 60.956 57.895 13.79 0.00 43.50 3.51
1293 1330 2.261671 GACTTCGAGCTGCCGGAA 59.738 61.111 5.05 0.00 0.00 4.30
1316 1353 1.792367 CGCTCTTCATCAACGACAACA 59.208 47.619 0.00 0.00 0.00 3.33
1456 1493 1.876453 CTCGACGTCAGCAACAACCG 61.876 60.000 17.16 0.00 0.00 4.44
1473 1510 2.043852 TCCCTCCTCCACGAGCTC 60.044 66.667 2.73 2.73 0.00 4.09
1709 1746 1.812686 CGACCCCAAGAACCTGACGA 61.813 60.000 0.00 0.00 0.00 4.20
1929 1966 1.397672 CCAATTCACACACACCCACA 58.602 50.000 0.00 0.00 0.00 4.17
1930 1967 0.673437 CCCAATTCACACACACCCAC 59.327 55.000 0.00 0.00 0.00 4.61
1931 1968 0.260230 ACCCAATTCACACACACCCA 59.740 50.000 0.00 0.00 0.00 4.51
1932 1969 1.068434 CAACCCAATTCACACACACCC 59.932 52.381 0.00 0.00 0.00 4.61
1992 2029 2.286772 CGAAAGGAAACCGTGTCAAAGG 60.287 50.000 0.00 0.00 0.00 3.11
2064 2101 0.106519 AAGCCAGCAGTCAACCTTGT 60.107 50.000 0.00 0.00 0.00 3.16
2126 2163 7.733402 TTTATATATAAAACGCGGGAAAGCT 57.267 32.000 12.47 0.00 30.48 3.74
2157 2197 2.487762 TCGTTCGTGTACCTTATTCCGT 59.512 45.455 0.00 0.00 0.00 4.69
2159 2199 5.104374 TCATTCGTTCGTGTACCTTATTCC 58.896 41.667 0.00 0.00 0.00 3.01
2163 2203 6.193514 TGTATCATTCGTTCGTGTACCTTA 57.806 37.500 0.00 0.00 0.00 2.69
2175 2215 5.141182 ACCTCAGTATCCTGTATCATTCGT 58.859 41.667 0.00 0.00 39.82 3.85
2180 2220 5.103215 AGGGTTACCTCAGTATCCTGTATCA 60.103 44.000 0.00 0.00 46.95 2.15
2199 2239 3.881089 CGGATCGGCTTTATAAAAGGGTT 59.119 43.478 0.00 0.00 0.00 4.11
2205 2245 4.884668 ATCCTCGGATCGGCTTTATAAA 57.115 40.909 0.00 0.00 0.00 1.40
2260 2300 1.937899 GGCGTAGTGTTGTGTTGTCTT 59.062 47.619 0.00 0.00 0.00 3.01
2395 2444 1.200716 TGAAGATGTCGTCGTGGGTAC 59.799 52.381 0.00 0.00 0.00 3.34
2481 2530 2.025155 CTCGTAGTAGCATGGGTGAGT 58.975 52.381 0.00 0.00 0.00 3.41
2540 2590 0.393944 ACTAGTGACGCTCCGATCCA 60.394 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.