Multiple sequence alignment - TraesCS5B01G015600

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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 TraesCS5B01G015600 chr5B 100.000 1884 0 0 792 2675 15050409 15052292 0.000000e+00 3480.0
1 TraesCS5B01G015600 chr5B 89.429 1542 84 27 1159 2675 15128103 15129590 0.000000e+00 1871.0
2 TraesCS5B01G015600 chr5B 89.711 1419 75 20 1179 2575 15075223 15076592 0.000000e+00 1746.0
3 TraesCS5B01G015600 chr5B 91.965 1033 62 10 1158 2190 15094138 15095149 0.000000e+00 1428.0
4 TraesCS5B01G015600 chr5B 86.796 1030 98 12 874 1899 15192098 15191103 0.000000e+00 1114.0
5 TraesCS5B01G015600 chr5B 100.000 491 0 0 1 491 15049618 15050108 0.000000e+00 907.0
6 TraesCS5B01G015600 chr5B 85.579 846 90 10 1041 1884 15015055 15015870 0.000000e+00 857.0
7 TraesCS5B01G015600 chr5B 89.919 496 27 4 2182 2657 15114831 15115323 3.780000e-173 617.0
8 TraesCS5B01G015600 chr5B 79.386 684 131 7 998 1676 15197073 15197751 8.670000e-130 473.0
9 TraesCS5B01G015600 chr5B 85.938 128 11 2 874 1001 15014928 15015048 2.160000e-26 130.0
10 TraesCS5B01G015600 chr5B 90.909 88 5 3 405 491 326891034 326890949 6.050000e-22 115.0
11 TraesCS5B01G015600 chr5B 90.909 88 5 3 405 491 520230930 520230845 6.050000e-22 115.0
12 TraesCS5B01G015600 chr5B 90.909 77 7 0 1922 1998 15191022 15190946 1.310000e-18 104.0
13 TraesCS5B01G015600 chr5B 87.302 63 6 2 1899 1960 15038414 15038475 1.330000e-08 71.3
14 TraesCS5B01G015600 chr5B 83.117 77 5 3 1922 1998 15015966 15016034 2.220000e-06 63.9
15 TraesCS5B01G015600 chr5A 84.772 1031 109 27 874 1901 14255281 14254296 0.000000e+00 990.0
16 TraesCS5B01G015600 chr5A 88.089 403 38 9 1 395 51603530 51603930 1.120000e-128 470.0
17 TraesCS5B01G015600 chr7D 93.267 401 24 3 1 398 7872343 7871943 2.970000e-164 588.0
18 TraesCS5B01G015600 chr1D 92.786 402 25 3 1 398 11350371 11350772 1.790000e-161 579.0
19 TraesCS5B01G015600 chr2D 92.875 393 24 4 1 389 220705407 220705015 3.860000e-158 568.0
20 TraesCS5B01G015600 chr2D 90.909 88 5 3 405 491 532126266 532126181 6.050000e-22 115.0
21 TraesCS5B01G015600 chr4B 91.832 404 27 5 1 398 373235631 373236034 2.330000e-155 558.0
22 TraesCS5B01G015600 chr6A 88.395 405 37 8 2 398 11152847 11152445 1.860000e-131 479.0
23 TraesCS5B01G015600 chr4A 88.177 406 38 8 1 398 603104045 603103642 2.410000e-130 475.0
24 TraesCS5B01G015600 chr4A 90.909 88 5 3 405 491 94670726 94670641 6.050000e-22 115.0
25 TraesCS5B01G015600 chr2A 88.177 406 38 9 1 398 139909042 139909445 2.410000e-130 475.0
26 TraesCS5B01G015600 chr3A 88.413 397 36 9 1 389 34590589 34590195 1.120000e-128 470.0
27 TraesCS5B01G015600 chr6D 90.909 88 5 3 405 491 439951832 439951917 6.050000e-22 115.0
28 TraesCS5B01G015600 chr6B 90.909 88 5 3 405 491 504734818 504734733 6.050000e-22 115.0
29 TraesCS5B01G015600 chr6B 90.909 88 5 3 405 491 624472434 624472519 6.050000e-22 115.0
30 TraesCS5B01G015600 chr5D 90.909 88 5 3 405 491 108799951 108799866 6.050000e-22 115.0
31 TraesCS5B01G015600 chr3D 90.909 88 5 3 405 491 317705111 317705026 6.050000e-22 115.0


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 TraesCS5B01G015600 chr5B 15049618 15052292 2674 False 2193.5 3480 100.0000 1 2675 2 chr5B.!!$F8 2674
1 TraesCS5B01G015600 chr5B 15128103 15129590 1487 False 1871.0 1871 89.4290 1159 2675 1 chr5B.!!$F5 1516
2 TraesCS5B01G015600 chr5B 15075223 15076592 1369 False 1746.0 1746 89.7110 1179 2575 1 chr5B.!!$F2 1396
3 TraesCS5B01G015600 chr5B 15094138 15095149 1011 False 1428.0 1428 91.9650 1158 2190 1 chr5B.!!$F3 1032
4 TraesCS5B01G015600 chr5B 15190946 15192098 1152 True 609.0 1114 88.8525 874 1998 2 chr5B.!!$R3 1124
5 TraesCS5B01G015600 chr5B 15197073 15197751 678 False 473.0 473 79.3860 998 1676 1 chr5B.!!$F6 678
6 TraesCS5B01G015600 chr5B 15014928 15016034 1106 False 350.3 857 84.8780 874 1998 3 chr5B.!!$F7 1124
7 TraesCS5B01G015600 chr5A 14254296 14255281 985 True 990.0 990 84.7720 874 1901 1 chr5A.!!$R1 1027

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
962 963 0.179045 CCCGGTCCTCCATCATTCAC 60.179 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2474 1.451387 GCGTTGGGTATCACCAGGG 60.451 63.158 0.0 0.0 42.47 4.45 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
25 26 8.781067 CATTACGTCATGTTAATGGGTATTTG 57.219 34.615 1.42 0.00 34.30 2.32
26 27 8.616942 CATTACGTCATGTTAATGGGTATTTGA 58.383 33.333 1.42 0.00 34.30 2.69
27 28 8.563123 TTACGTCATGTTAATGGGTATTTGAA 57.437 30.769 0.00 0.00 34.30 2.69
28 29 7.639113 ACGTCATGTTAATGGGTATTTGAAT 57.361 32.000 0.00 0.00 34.30 2.57
29 30 8.740123 ACGTCATGTTAATGGGTATTTGAATA 57.260 30.769 0.00 0.00 34.30 1.75
30 31 9.349713 ACGTCATGTTAATGGGTATTTGAATAT 57.650 29.630 0.00 0.00 34.30 1.28
31 32 9.611284 CGTCATGTTAATGGGTATTTGAATATG 57.389 33.333 0.00 0.00 34.30 1.78
32 33 9.410556 GTCATGTTAATGGGTATTTGAATATGC 57.589 33.333 0.00 0.00 34.30 3.14
33 34 8.584157 TCATGTTAATGGGTATTTGAATATGCC 58.416 33.333 0.00 0.00 34.30 4.40
38 39 3.844640 GGGTATTTGAATATGCCCAGGT 58.155 45.455 5.08 0.00 46.43 4.00
39 40 4.993028 GGGTATTTGAATATGCCCAGGTA 58.007 43.478 5.08 0.00 46.43 3.08
40 41 5.580022 GGGTATTTGAATATGCCCAGGTAT 58.420 41.667 5.08 0.00 46.43 2.73
41 42 6.727394 GGGTATTTGAATATGCCCAGGTATA 58.273 40.000 5.08 0.00 46.43 1.47
42 43 7.354312 GGGTATTTGAATATGCCCAGGTATAT 58.646 38.462 5.08 1.77 46.43 0.86
43 44 7.502561 GGGTATTTGAATATGCCCAGGTATATC 59.497 40.741 7.62 3.53 46.43 1.63
44 45 7.502561 GGTATTTGAATATGCCCAGGTATATCC 59.497 40.741 7.62 0.00 33.41 2.59
45 46 6.461577 TTTGAATATGCCCAGGTATATCCA 57.538 37.500 7.62 0.00 39.02 3.41
46 47 6.656965 TTGAATATGCCCAGGTATATCCAT 57.343 37.500 7.62 0.00 39.02 3.41
47 48 7.763564 TTGAATATGCCCAGGTATATCCATA 57.236 36.000 7.62 0.00 39.02 2.74
48 49 7.952847 TGAATATGCCCAGGTATATCCATAT 57.047 36.000 7.62 0.00 39.02 1.78
49 50 7.748677 TGAATATGCCCAGGTATATCCATATG 58.251 38.462 7.62 0.00 39.02 1.78
50 51 7.350655 TGAATATGCCCAGGTATATCCATATGT 59.649 37.037 7.62 0.00 39.02 2.29
51 52 7.712142 ATATGCCCAGGTATATCCATATGTT 57.288 36.000 1.24 0.00 39.02 2.71
52 53 5.858876 TGCCCAGGTATATCCATATGTTT 57.141 39.130 1.24 0.00 39.02 2.83
53 54 6.212840 TGCCCAGGTATATCCATATGTTTT 57.787 37.500 1.24 0.00 39.02 2.43
54 55 6.619464 TGCCCAGGTATATCCATATGTTTTT 58.381 36.000 1.24 0.00 39.02 1.94
55 56 6.493115 TGCCCAGGTATATCCATATGTTTTTG 59.507 38.462 1.24 0.00 39.02 2.44
56 57 6.493458 GCCCAGGTATATCCATATGTTTTTGT 59.507 38.462 1.24 0.00 39.02 2.83
57 58 7.668052 GCCCAGGTATATCCATATGTTTTTGTA 59.332 37.037 1.24 0.00 39.02 2.41
58 59 9.753674 CCCAGGTATATCCATATGTTTTTGTAT 57.246 33.333 1.24 0.00 39.02 2.29
68 69 9.496873 TCCATATGTTTTTGTATATTACCTCCG 57.503 33.333 1.24 0.00 0.00 4.63
69 70 9.280174 CCATATGTTTTTGTATATTACCTCCGT 57.720 33.333 1.24 0.00 0.00 4.69
74 75 9.669887 TGTTTTTGTATATTACCTCCGTTATGT 57.330 29.630 0.00 0.00 0.00 2.29
75 76 9.925268 GTTTTTGTATATTACCTCCGTTATGTG 57.075 33.333 0.00 0.00 0.00 3.21
76 77 9.669887 TTTTTGTATATTACCTCCGTTATGTGT 57.330 29.630 0.00 0.00 0.00 3.72
198 199 8.081208 GCTATGTGTATAATAGCCTGCATATG 57.919 38.462 0.00 0.00 44.44 1.78
199 200 7.712639 GCTATGTGTATAATAGCCTGCATATGT 59.287 37.037 4.29 0.00 44.44 2.29
200 201 9.605275 CTATGTGTATAATAGCCTGCATATGTT 57.395 33.333 4.29 0.00 0.00 2.71
201 202 7.905604 TGTGTATAATAGCCTGCATATGTTC 57.094 36.000 4.29 0.00 0.00 3.18
202 203 7.449247 TGTGTATAATAGCCTGCATATGTTCA 58.551 34.615 4.29 0.00 0.00 3.18
203 204 8.102676 TGTGTATAATAGCCTGCATATGTTCAT 58.897 33.333 4.29 0.00 0.00 2.57
204 205 9.599866 GTGTATAATAGCCTGCATATGTTCATA 57.400 33.333 4.29 0.00 0.00 2.15
210 211 6.964807 AGCCTGCATATGTTCATATTTTCA 57.035 33.333 4.29 2.37 0.00 2.69
211 212 7.534723 AGCCTGCATATGTTCATATTTTCAT 57.465 32.000 4.29 0.00 0.00 2.57
212 213 7.959175 AGCCTGCATATGTTCATATTTTCATT 58.041 30.769 4.29 0.00 0.00 2.57
213 214 9.081204 AGCCTGCATATGTTCATATTTTCATTA 57.919 29.630 4.29 0.00 0.00 1.90
214 215 9.350357 GCCTGCATATGTTCATATTTTCATTAG 57.650 33.333 4.29 0.00 0.00 1.73
250 251 9.849166 TTGGAAACGAATTATTGTTAGGAAATC 57.151 29.630 0.00 0.00 32.66 2.17
251 252 9.015367 TGGAAACGAATTATTGTTAGGAAATCA 57.985 29.630 0.00 0.00 32.66 2.57
252 253 9.849166 GGAAACGAATTATTGTTAGGAAATCAA 57.151 29.630 0.00 0.00 32.66 2.57
254 255 9.634163 AAACGAATTATTGTTAGGAAATCAACC 57.366 29.630 0.00 0.00 32.66 3.77
255 256 8.575649 ACGAATTATTGTTAGGAAATCAACCT 57.424 30.769 0.00 0.00 41.05 3.50
256 257 9.675464 ACGAATTATTGTTAGGAAATCAACCTA 57.325 29.630 0.00 0.00 38.76 3.08
269 270 8.548025 AGGAAATCAACCTAATTATTTTTGGGG 58.452 33.333 0.00 0.00 35.84 4.96
270 271 8.544622 GGAAATCAACCTAATTATTTTTGGGGA 58.455 33.333 0.00 0.00 31.86 4.81
271 272 9.952030 GAAATCAACCTAATTATTTTTGGGGAA 57.048 29.630 0.00 0.00 31.86 3.97
272 273 9.958180 AAATCAACCTAATTATTTTTGGGGAAG 57.042 29.630 0.00 0.00 31.86 3.46
273 274 6.941857 TCAACCTAATTATTTTTGGGGAAGC 58.058 36.000 0.00 0.00 31.86 3.86
274 275 6.498651 TCAACCTAATTATTTTTGGGGAAGCA 59.501 34.615 0.00 0.00 31.86 3.91
275 276 6.943899 ACCTAATTATTTTTGGGGAAGCAA 57.056 33.333 0.00 0.00 31.86 3.91
276 277 7.509236 ACCTAATTATTTTTGGGGAAGCAAT 57.491 32.000 0.00 0.00 31.86 3.56
277 278 7.564793 ACCTAATTATTTTTGGGGAAGCAATC 58.435 34.615 0.00 0.00 31.86 2.67
278 279 7.181845 ACCTAATTATTTTTGGGGAAGCAATCA 59.818 33.333 0.00 0.00 31.86 2.57
279 280 8.212995 CCTAATTATTTTTGGGGAAGCAATCAT 58.787 33.333 0.00 0.00 0.00 2.45
280 281 9.617523 CTAATTATTTTTGGGGAAGCAATCATT 57.382 29.630 0.00 0.00 0.00 2.57
281 282 7.868906 ATTATTTTTGGGGAAGCAATCATTG 57.131 32.000 0.00 0.00 0.00 2.82
282 283 4.970860 TTTTTGGGGAAGCAATCATTGA 57.029 36.364 0.00 0.00 0.00 2.57
283 284 3.959535 TTTGGGGAAGCAATCATTGAC 57.040 42.857 0.00 0.00 0.00 3.18
284 285 1.851304 TGGGGAAGCAATCATTGACC 58.149 50.000 0.00 0.98 0.00 4.02
285 286 0.740737 GGGGAAGCAATCATTGACCG 59.259 55.000 0.00 0.00 0.00 4.79
286 287 1.463674 GGGAAGCAATCATTGACCGT 58.536 50.000 0.00 0.00 0.00 4.83
287 288 1.133025 GGGAAGCAATCATTGACCGTG 59.867 52.381 0.00 0.00 0.00 4.94
288 289 2.083774 GGAAGCAATCATTGACCGTGA 58.916 47.619 0.00 0.00 0.00 4.35
289 290 2.487762 GGAAGCAATCATTGACCGTGAA 59.512 45.455 0.00 0.00 0.00 3.18
290 291 3.426695 GGAAGCAATCATTGACCGTGAAG 60.427 47.826 0.00 0.00 0.00 3.02
292 293 1.133025 GCAATCATTGACCGTGAAGGG 59.867 52.381 0.00 0.00 46.96 3.95
293 294 2.436417 CAATCATTGACCGTGAAGGGT 58.564 47.619 0.00 0.00 46.96 4.34
294 295 3.605634 CAATCATTGACCGTGAAGGGTA 58.394 45.455 0.00 0.00 46.96 3.69
295 296 3.543680 ATCATTGACCGTGAAGGGTAG 57.456 47.619 0.00 0.00 46.96 3.18
296 297 2.253610 TCATTGACCGTGAAGGGTAGT 58.746 47.619 0.00 0.00 46.96 2.73
297 298 3.433343 TCATTGACCGTGAAGGGTAGTA 58.567 45.455 0.00 0.00 46.96 1.82
298 299 3.194116 TCATTGACCGTGAAGGGTAGTAC 59.806 47.826 0.00 0.00 46.96 2.73
299 300 2.592102 TGACCGTGAAGGGTAGTACT 57.408 50.000 0.00 0.00 46.96 2.73
300 301 2.165167 TGACCGTGAAGGGTAGTACTG 58.835 52.381 5.39 0.00 46.96 2.74
301 302 0.893447 ACCGTGAAGGGTAGTACTGC 59.107 55.000 5.39 3.50 46.96 4.40
302 303 0.892755 CCGTGAAGGGTAGTACTGCA 59.107 55.000 13.26 0.00 35.97 4.41
303 304 1.480954 CCGTGAAGGGTAGTACTGCAT 59.519 52.381 13.26 0.00 35.97 3.96
304 305 2.540515 CGTGAAGGGTAGTACTGCATG 58.459 52.381 13.26 0.00 0.00 4.06
305 306 2.280628 GTGAAGGGTAGTACTGCATGC 58.719 52.381 11.82 11.82 0.00 4.06
306 307 1.905894 TGAAGGGTAGTACTGCATGCA 59.094 47.619 21.29 21.29 0.00 3.96
307 308 2.304470 TGAAGGGTAGTACTGCATGCAA 59.696 45.455 22.88 4.63 0.00 4.08
308 309 3.244735 TGAAGGGTAGTACTGCATGCAAA 60.245 43.478 22.88 10.18 0.00 3.68
309 310 3.652057 AGGGTAGTACTGCATGCAAAT 57.348 42.857 22.88 15.21 0.00 2.32
310 311 3.282021 AGGGTAGTACTGCATGCAAATG 58.718 45.455 22.88 12.90 0.00 2.32
311 312 3.054434 AGGGTAGTACTGCATGCAAATGA 60.054 43.478 22.88 4.08 0.00 2.57
312 313 3.694072 GGGTAGTACTGCATGCAAATGAA 59.306 43.478 22.88 4.70 0.00 2.57
313 314 4.157656 GGGTAGTACTGCATGCAAATGAAA 59.842 41.667 22.88 3.00 0.00 2.69
314 315 5.336372 GGGTAGTACTGCATGCAAATGAAAA 60.336 40.000 22.88 1.29 0.00 2.29
315 316 6.332630 GGTAGTACTGCATGCAAATGAAAAT 58.667 36.000 22.88 6.33 0.00 1.82
316 317 6.254157 GGTAGTACTGCATGCAAATGAAAATG 59.746 38.462 22.88 9.02 0.00 2.32
317 318 5.172934 AGTACTGCATGCAAATGAAAATGG 58.827 37.500 22.88 8.25 0.00 3.16
318 319 4.274602 ACTGCATGCAAATGAAAATGGA 57.725 36.364 22.88 0.00 0.00 3.41
319 320 4.643463 ACTGCATGCAAATGAAAATGGAA 58.357 34.783 22.88 0.00 0.00 3.53
320 321 5.064558 ACTGCATGCAAATGAAAATGGAAA 58.935 33.333 22.88 0.00 0.00 3.13
321 322 5.180492 ACTGCATGCAAATGAAAATGGAAAG 59.820 36.000 22.88 6.37 0.00 2.62
322 323 4.083217 TGCATGCAAATGAAAATGGAAAGC 60.083 37.500 20.30 0.00 0.00 3.51
323 324 4.155280 GCATGCAAATGAAAATGGAAAGCT 59.845 37.500 14.21 0.00 0.00 3.74
324 325 5.352016 GCATGCAAATGAAAATGGAAAGCTA 59.648 36.000 14.21 0.00 0.00 3.32
325 326 6.037830 GCATGCAAATGAAAATGGAAAGCTAT 59.962 34.615 14.21 0.00 0.00 2.97
326 327 7.414762 GCATGCAAATGAAAATGGAAAGCTATT 60.415 33.333 14.21 0.00 0.00 1.73
327 328 9.100554 CATGCAAATGAAAATGGAAAGCTATTA 57.899 29.630 0.00 0.00 0.00 0.98
328 329 9.841295 ATGCAAATGAAAATGGAAAGCTATTAT 57.159 25.926 0.00 0.00 0.00 1.28
329 330 9.669887 TGCAAATGAAAATGGAAAGCTATTATT 57.330 25.926 0.00 0.00 0.00 1.40
345 346 8.767478 AGCTATTATTTCATAAATTGCATGCC 57.233 30.769 16.68 0.00 32.38 4.40
346 347 8.369424 AGCTATTATTTCATAAATTGCATGCCA 58.631 29.630 16.68 4.04 32.38 4.92
347 348 9.158233 GCTATTATTTCATAAATTGCATGCCAT 57.842 29.630 16.68 6.88 32.38 4.40
350 351 9.999660 ATTATTTCATAAATTGCATGCCATACA 57.000 25.926 16.68 1.36 32.38 2.29
351 352 7.718272 ATTTCATAAATTGCATGCCATACAC 57.282 32.000 16.68 0.00 0.00 2.90
352 353 6.468333 TTCATAAATTGCATGCCATACACT 57.532 33.333 16.68 0.00 0.00 3.55
353 354 7.579761 TTCATAAATTGCATGCCATACACTA 57.420 32.000 16.68 0.74 0.00 2.74
354 355 7.579761 TCATAAATTGCATGCCATACACTAA 57.420 32.000 16.68 0.00 0.00 2.24
355 356 8.180706 TCATAAATTGCATGCCATACACTAAT 57.819 30.769 16.68 2.30 0.00 1.73
356 357 9.294614 TCATAAATTGCATGCCATACACTAATA 57.705 29.630 16.68 0.00 0.00 0.98
357 358 9.911138 CATAAATTGCATGCCATACACTAATAA 57.089 29.630 16.68 0.00 0.00 1.40
360 361 9.664332 AAATTGCATGCCATACACTAATAAAAA 57.336 25.926 16.68 0.00 0.00 1.94
361 362 9.835389 AATTGCATGCCATACACTAATAAAAAT 57.165 25.926 16.68 0.00 0.00 1.82
362 363 8.870160 TTGCATGCCATACACTAATAAAAATC 57.130 30.769 16.68 0.00 0.00 2.17
363 364 8.005192 TGCATGCCATACACTAATAAAAATCA 57.995 30.769 16.68 0.00 0.00 2.57
364 365 7.920151 TGCATGCCATACACTAATAAAAATCAC 59.080 33.333 16.68 0.00 0.00 3.06
365 366 7.382218 GCATGCCATACACTAATAAAAATCACC 59.618 37.037 6.36 0.00 0.00 4.02
366 367 8.632679 CATGCCATACACTAATAAAAATCACCT 58.367 33.333 0.00 0.00 0.00 4.00
367 368 7.995289 TGCCATACACTAATAAAAATCACCTG 58.005 34.615 0.00 0.00 0.00 4.00
368 369 6.918022 GCCATACACTAATAAAAATCACCTGC 59.082 38.462 0.00 0.00 0.00 4.85
369 370 7.425606 CCATACACTAATAAAAATCACCTGCC 58.574 38.462 0.00 0.00 0.00 4.85
370 371 7.068103 CCATACACTAATAAAAATCACCTGCCA 59.932 37.037 0.00 0.00 0.00 4.92
371 372 8.632679 CATACACTAATAAAAATCACCTGCCAT 58.367 33.333 0.00 0.00 0.00 4.40
372 373 9.860650 ATACACTAATAAAAATCACCTGCCATA 57.139 29.630 0.00 0.00 0.00 2.74
373 374 8.588290 ACACTAATAAAAATCACCTGCCATAA 57.412 30.769 0.00 0.00 0.00 1.90
374 375 9.200817 ACACTAATAAAAATCACCTGCCATAAT 57.799 29.630 0.00 0.00 0.00 1.28
375 376 9.467258 CACTAATAAAAATCACCTGCCATAATG 57.533 33.333 0.00 0.00 0.00 1.90
376 377 8.641541 ACTAATAAAAATCACCTGCCATAATGG 58.358 33.333 0.00 0.00 41.55 3.16
386 387 3.346426 CCATAATGGCCCTAGGTGC 57.654 57.895 8.29 10.73 0.00 5.01
413 414 5.018539 GCACCTATTGCGGGTATATATGA 57.981 43.478 0.00 0.00 42.79 2.15
414 415 4.809426 GCACCTATTGCGGGTATATATGAC 59.191 45.833 0.00 0.00 42.79 3.06
415 416 5.395324 GCACCTATTGCGGGTATATATGACT 60.395 44.000 0.00 0.00 42.79 3.41
416 417 6.273825 CACCTATTGCGGGTATATATGACTC 58.726 44.000 0.00 0.00 35.00 3.36
417 418 5.955959 ACCTATTGCGGGTATATATGACTCA 59.044 40.000 0.00 0.00 35.00 3.41
418 419 6.611642 ACCTATTGCGGGTATATATGACTCAT 59.388 38.462 0.00 0.00 35.00 2.90
419 420 7.125811 ACCTATTGCGGGTATATATGACTCATT 59.874 37.037 0.00 0.00 35.00 2.57
420 421 8.638873 CCTATTGCGGGTATATATGACTCATTA 58.361 37.037 0.00 0.00 0.00 1.90
422 423 8.948631 ATTGCGGGTATATATGACTCATTAAG 57.051 34.615 0.00 0.00 0.00 1.85
423 424 7.712204 TGCGGGTATATATGACTCATTAAGA 57.288 36.000 0.00 0.00 0.00 2.10
445 446 5.674052 AGTGTAGATTCACTCATCTTGCT 57.326 39.130 0.00 0.00 44.07 3.91
446 447 5.659463 AGTGTAGATTCACTCATCTTGCTC 58.341 41.667 0.00 0.00 44.07 4.26
447 448 5.421693 AGTGTAGATTCACTCATCTTGCTCT 59.578 40.000 0.00 0.00 44.07 4.09
448 449 5.519566 GTGTAGATTCACTCATCTTGCTCTG 59.480 44.000 0.00 0.00 35.08 3.35
449 450 4.822685 AGATTCACTCATCTTGCTCTGT 57.177 40.909 0.00 0.00 28.19 3.41
450 451 5.929058 AGATTCACTCATCTTGCTCTGTA 57.071 39.130 0.00 0.00 28.19 2.74
451 452 6.482898 AGATTCACTCATCTTGCTCTGTAT 57.517 37.500 0.00 0.00 28.19 2.29
452 453 6.282167 AGATTCACTCATCTTGCTCTGTATG 58.718 40.000 0.00 0.00 28.19 2.39
453 454 5.411831 TTCACTCATCTTGCTCTGTATGT 57.588 39.130 0.00 0.00 0.00 2.29
454 455 6.530019 TTCACTCATCTTGCTCTGTATGTA 57.470 37.500 0.00 0.00 0.00 2.29
455 456 6.141560 TCACTCATCTTGCTCTGTATGTAG 57.858 41.667 0.00 0.00 0.00 2.74
456 457 5.654209 TCACTCATCTTGCTCTGTATGTAGT 59.346 40.000 0.00 0.00 0.00 2.73
457 458 5.976534 CACTCATCTTGCTCTGTATGTAGTC 59.023 44.000 0.00 0.00 0.00 2.59
458 459 5.654209 ACTCATCTTGCTCTGTATGTAGTCA 59.346 40.000 0.00 0.00 0.00 3.41
459 460 5.895928 TCATCTTGCTCTGTATGTAGTCAC 58.104 41.667 0.00 0.00 0.00 3.67
460 461 5.654209 TCATCTTGCTCTGTATGTAGTCACT 59.346 40.000 0.00 0.00 0.00 3.41
461 462 5.984695 TCTTGCTCTGTATGTAGTCACTT 57.015 39.130 0.00 0.00 0.00 3.16
462 463 5.714047 TCTTGCTCTGTATGTAGTCACTTG 58.286 41.667 0.00 0.00 0.00 3.16
463 464 5.243954 TCTTGCTCTGTATGTAGTCACTTGT 59.756 40.000 0.00 0.00 0.00 3.16
464 465 5.468540 TGCTCTGTATGTAGTCACTTGTT 57.531 39.130 0.00 0.00 0.00 2.83
465 466 5.230182 TGCTCTGTATGTAGTCACTTGTTG 58.770 41.667 0.00 0.00 0.00 3.33
466 467 5.010617 TGCTCTGTATGTAGTCACTTGTTGA 59.989 40.000 0.00 0.00 0.00 3.18
467 468 5.926542 GCTCTGTATGTAGTCACTTGTTGAA 59.073 40.000 0.00 0.00 35.39 2.69
468 469 6.423905 GCTCTGTATGTAGTCACTTGTTGAAA 59.576 38.462 0.00 0.00 35.39 2.69
469 470 7.118390 GCTCTGTATGTAGTCACTTGTTGAAAT 59.882 37.037 0.00 0.00 35.39 2.17
470 471 9.639601 CTCTGTATGTAGTCACTTGTTGAAATA 57.360 33.333 0.00 0.00 35.39 1.40
877 878 2.691409 TTCGGAGGTGGCTCATTAAG 57.309 50.000 0.00 0.00 0.00 1.85
884 885 3.887716 GAGGTGGCTCATTAAGATGCATT 59.112 43.478 0.00 0.00 33.14 3.56
901 902 5.581126 TGCATTTAAGAGGGCACATTTAG 57.419 39.130 0.00 0.00 0.00 1.85
902 903 4.402155 TGCATTTAAGAGGGCACATTTAGG 59.598 41.667 0.00 0.00 0.00 2.69
914 915 6.491403 AGGGCACATTTAGGCAGATATAAAAG 59.509 38.462 0.00 0.00 0.00 2.27
959 960 0.401979 ATCCCCGGTCCTCCATCATT 60.402 55.000 0.00 0.00 0.00 2.57
960 961 1.054406 TCCCCGGTCCTCCATCATTC 61.054 60.000 0.00 0.00 0.00 2.67
961 962 1.344953 CCCCGGTCCTCCATCATTCA 61.345 60.000 0.00 0.00 0.00 2.57
962 963 0.179045 CCCGGTCCTCCATCATTCAC 60.179 60.000 0.00 0.00 0.00 3.18
963 964 0.833287 CCGGTCCTCCATCATTCACT 59.167 55.000 0.00 0.00 0.00 3.41
964 965 2.039418 CCGGTCCTCCATCATTCACTA 58.961 52.381 0.00 0.00 0.00 2.74
965 966 2.434336 CCGGTCCTCCATCATTCACTAA 59.566 50.000 0.00 0.00 0.00 2.24
1014 1015 1.293924 CGACCATGGCATCTTCACTC 58.706 55.000 13.04 0.00 0.00 3.51
1120 1121 3.782443 CAGGCACCTACCCGGTCC 61.782 72.222 0.00 0.00 44.93 4.46
1150 1151 4.754667 GGCTCGACCCGGGTCAAC 62.755 72.222 44.16 33.28 44.77 3.18
1162 1163 2.568090 GTCAACTGGCCGCCATTG 59.432 61.111 13.86 18.01 30.82 2.82
1168 1169 1.377725 CTGGCCGCCATTGAAGTCT 60.378 57.895 13.86 0.00 30.82 3.24
1230 1231 2.034879 CAACTTCGATGCCAGCGGT 61.035 57.895 1.22 0.00 0.00 5.68
1287 1288 4.572571 TCCTGTGCCGCCGGTTTT 62.573 61.111 4.45 0.00 0.00 2.43
1302 1303 1.227883 TTTTAAGCCACCCGCGACA 60.228 52.632 8.23 0.00 44.76 4.35
1356 1357 3.386078 GCCCTGACTTCTATGACATCTCA 59.614 47.826 0.00 0.00 0.00 3.27
1357 1358 4.141846 GCCCTGACTTCTATGACATCTCAA 60.142 45.833 0.00 0.00 0.00 3.02
1361 1362 5.284864 TGACTTCTATGACATCTCAATCGC 58.715 41.667 0.00 0.00 0.00 4.58
1619 1623 1.400846 CAGCTACGCCTACGAGAAGAA 59.599 52.381 0.00 0.00 43.93 2.52
1636 1640 0.819259 GAACAGCACCTTCACCTGCA 60.819 55.000 0.00 0.00 35.73 4.41
1698 1702 4.580580 AGGCGATTGGGATTCAATTTACTC 59.419 41.667 0.00 0.00 45.36 2.59
1713 1720 8.070034 TCAATTTACTCCGATGGTTAAGTCTA 57.930 34.615 0.00 0.00 0.00 2.59
1770 1777 9.021807 GGAAATAATGATGACTGATGATTCCAT 57.978 33.333 0.00 0.00 33.40 3.41
1890 1899 5.244178 AGGACGAACATACTTCTCTCTTTGT 59.756 40.000 0.00 0.00 0.00 2.83
2047 2114 1.650314 TATGACGCTCGTTGCCTCGA 61.650 55.000 0.00 0.83 38.78 4.04
2103 2170 4.557205 GTGTCTAACAGGTGTCTAACAGG 58.443 47.826 0.00 0.00 0.00 4.00
2104 2171 4.038883 GTGTCTAACAGGTGTCTAACAGGT 59.961 45.833 0.00 0.00 0.00 4.00
2111 2178 1.014564 GTGTCTAACAGGTGCGAGCC 61.015 60.000 0.00 0.00 0.00 4.70
2112 2179 1.805945 GTCTAACAGGTGCGAGCCG 60.806 63.158 0.00 0.00 0.00 5.52
2113 2180 1.974875 TCTAACAGGTGCGAGCCGA 60.975 57.895 0.00 0.00 0.00 5.54
2114 2181 1.080093 CTAACAGGTGCGAGCCGAA 60.080 57.895 0.00 0.00 0.00 4.30
2115 2182 0.460284 CTAACAGGTGCGAGCCGAAT 60.460 55.000 0.00 0.00 0.00 3.34
2116 2183 0.818938 TAACAGGTGCGAGCCGAATA 59.181 50.000 0.00 0.00 0.00 1.75
2117 2184 0.460284 AACAGGTGCGAGCCGAATAG 60.460 55.000 0.00 0.00 0.00 1.73
2118 2185 1.592669 CAGGTGCGAGCCGAATAGG 60.593 63.158 0.00 0.00 44.97 2.57
2119 2186 1.756950 AGGTGCGAGCCGAATAGGA 60.757 57.895 0.00 0.00 45.00 2.94
2120 2187 1.300233 GGTGCGAGCCGAATAGGAG 60.300 63.158 0.00 0.00 45.00 3.69
2121 2188 1.951631 GTGCGAGCCGAATAGGAGC 60.952 63.158 0.00 0.00 45.00 4.70
2122 2189 2.417516 GCGAGCCGAATAGGAGCA 59.582 61.111 0.00 0.00 45.00 4.26
2123 2190 1.663074 GCGAGCCGAATAGGAGCAG 60.663 63.158 0.00 0.00 45.00 4.24
2124 2191 1.663074 CGAGCCGAATAGGAGCAGC 60.663 63.158 0.00 0.00 45.00 5.25
2125 2192 1.301322 GAGCCGAATAGGAGCAGCC 60.301 63.158 0.00 0.00 45.00 4.85
2126 2193 2.663188 GCCGAATAGGAGCAGCCG 60.663 66.667 0.00 0.00 45.00 5.52
2127 2194 2.663188 CCGAATAGGAGCAGCCGC 60.663 66.667 0.00 0.00 45.00 6.53
2128 2195 2.663188 CGAATAGGAGCAGCCGCC 60.663 66.667 0.00 0.00 43.43 6.13
2293 2360 6.786967 TGAGATGAGAGAATCACATGAAGA 57.213 37.500 0.00 0.00 46.43 2.87
2404 2474 9.678247 CCAAACGTTGTTTTGAGTTAATAAAAC 57.322 29.630 0.00 13.97 43.52 2.43
2420 2509 2.597578 AAACCCTGGTGATACCCAAC 57.402 50.000 0.00 0.00 37.50 3.77
2465 2554 6.919662 CGCTATAACCTTCTCCAATACGTTTA 59.080 38.462 0.00 0.00 0.00 2.01
2532 2621 8.753497 TGAGAAGAAGTAGTATTCTAGCATGA 57.247 34.615 0.00 0.00 38.59 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.616942 TCAAATACCCATTAACATGACGTAATG 58.383 33.333 11.60 11.60 31.07 1.90
1 2 8.740123 TCAAATACCCATTAACATGACGTAAT 57.260 30.769 0.00 0.00 31.07 1.89
2 3 8.563123 TTCAAATACCCATTAACATGACGTAA 57.437 30.769 0.00 0.00 31.07 3.18
3 4 8.740123 ATTCAAATACCCATTAACATGACGTA 57.260 30.769 0.00 0.00 31.07 3.57
4 5 7.639113 ATTCAAATACCCATTAACATGACGT 57.361 32.000 0.00 0.00 31.07 4.34
5 6 9.611284 CATATTCAAATACCCATTAACATGACG 57.389 33.333 0.00 0.00 31.07 4.35
6 7 9.410556 GCATATTCAAATACCCATTAACATGAC 57.589 33.333 0.00 0.00 31.07 3.06
7 8 8.584157 GGCATATTCAAATACCCATTAACATGA 58.416 33.333 0.00 0.00 31.07 3.07
8 9 7.818930 GGGCATATTCAAATACCCATTAACATG 59.181 37.037 0.00 0.00 37.30 3.21
9 10 7.512058 TGGGCATATTCAAATACCCATTAACAT 59.488 33.333 6.92 0.00 42.38 2.71
10 11 6.841229 TGGGCATATTCAAATACCCATTAACA 59.159 34.615 6.92 0.00 42.38 2.41
11 12 7.296628 TGGGCATATTCAAATACCCATTAAC 57.703 36.000 6.92 0.00 42.38 2.01
12 13 6.496565 CCTGGGCATATTCAAATACCCATTAA 59.503 38.462 10.13 0.00 45.96 1.40
13 14 6.015918 CCTGGGCATATTCAAATACCCATTA 58.984 40.000 10.13 0.00 45.96 1.90
14 15 4.840115 CCTGGGCATATTCAAATACCCATT 59.160 41.667 10.13 0.00 45.96 3.16
15 16 4.140710 ACCTGGGCATATTCAAATACCCAT 60.141 41.667 10.13 0.00 45.96 4.00
16 17 3.206412 ACCTGGGCATATTCAAATACCCA 59.794 43.478 9.56 9.56 45.00 4.51
17 18 3.844640 ACCTGGGCATATTCAAATACCC 58.155 45.455 0.00 0.00 37.88 3.69
18 19 7.502561 GGATATACCTGGGCATATTCAAATACC 59.497 40.741 0.00 0.00 35.41 2.73
19 20 8.052748 TGGATATACCTGGGCATATTCAAATAC 58.947 37.037 8.38 0.00 39.86 1.89
20 21 8.168905 TGGATATACCTGGGCATATTCAAATA 57.831 34.615 8.38 0.00 39.86 1.40
21 22 7.043300 TGGATATACCTGGGCATATTCAAAT 57.957 36.000 8.38 0.00 39.86 2.32
22 23 6.461577 TGGATATACCTGGGCATATTCAAA 57.538 37.500 8.38 0.00 39.86 2.69
23 24 6.656965 ATGGATATACCTGGGCATATTCAA 57.343 37.500 12.81 1.91 39.86 2.69
24 25 7.350655 ACATATGGATATACCTGGGCATATTCA 59.649 37.037 7.80 11.73 39.86 2.57
25 26 7.749666 ACATATGGATATACCTGGGCATATTC 58.250 38.462 7.80 0.54 39.86 1.75
26 27 7.712142 ACATATGGATATACCTGGGCATATT 57.288 36.000 7.80 0.00 39.86 1.28
27 28 7.712142 AACATATGGATATACCTGGGCATAT 57.288 36.000 7.80 0.60 39.86 1.78
28 29 7.523703 AAACATATGGATATACCTGGGCATA 57.476 36.000 7.80 0.00 39.86 3.14
29 30 6.407320 AAACATATGGATATACCTGGGCAT 57.593 37.500 7.80 0.00 39.86 4.40
30 31 5.858876 AAACATATGGATATACCTGGGCA 57.141 39.130 7.80 0.00 39.86 5.36
31 32 6.493458 ACAAAAACATATGGATATACCTGGGC 59.507 38.462 7.80 0.00 39.86 5.36
32 33 9.753674 ATACAAAAACATATGGATATACCTGGG 57.246 33.333 7.80 0.00 39.86 4.45
42 43 9.496873 CGGAGGTAATATACAAAAACATATGGA 57.503 33.333 7.80 0.00 0.00 3.41
43 44 9.280174 ACGGAGGTAATATACAAAAACATATGG 57.720 33.333 7.80 0.00 0.00 2.74
48 49 9.669887 ACATAACGGAGGTAATATACAAAAACA 57.330 29.630 0.00 0.00 0.00 2.83
49 50 9.925268 CACATAACGGAGGTAATATACAAAAAC 57.075 33.333 0.00 0.00 0.00 2.43
50 51 9.669887 ACACATAACGGAGGTAATATACAAAAA 57.330 29.630 0.00 0.00 0.00 1.94
163 164 9.988815 GCTATTATACACATAGCAGGCTATTAT 57.011 33.333 10.96 9.38 45.85 1.28
173 174 7.712639 ACATATGCAGGCTATTATACACATAGC 59.287 37.037 1.58 6.42 45.84 2.97
174 175 9.605275 AACATATGCAGGCTATTATACACATAG 57.395 33.333 1.58 0.00 0.00 2.23
175 176 9.599866 GAACATATGCAGGCTATTATACACATA 57.400 33.333 1.58 0.00 0.00 2.29
176 177 8.102676 TGAACATATGCAGGCTATTATACACAT 58.897 33.333 1.58 0.00 0.00 3.21
177 178 7.449247 TGAACATATGCAGGCTATTATACACA 58.551 34.615 1.58 0.00 0.00 3.72
178 179 7.905604 TGAACATATGCAGGCTATTATACAC 57.094 36.000 1.58 0.00 0.00 2.90
184 185 9.081204 TGAAAATATGAACATATGCAGGCTATT 57.919 29.630 1.58 0.00 34.45 1.73
185 186 8.640063 TGAAAATATGAACATATGCAGGCTAT 57.360 30.769 1.58 0.00 34.45 2.97
186 187 8.640063 ATGAAAATATGAACATATGCAGGCTA 57.360 30.769 1.58 0.00 34.45 3.93
187 188 6.964807 TGAAAATATGAACATATGCAGGCT 57.035 33.333 1.58 0.00 34.45 4.58
188 189 9.350357 CTAATGAAAATATGAACATATGCAGGC 57.650 33.333 1.58 0.00 34.45 4.85
224 225 9.849166 GATTTCCTAACAATAATTCGTTTCCAA 57.151 29.630 0.00 0.00 0.00 3.53
225 226 9.015367 TGATTTCCTAACAATAATTCGTTTCCA 57.985 29.630 0.00 0.00 0.00 3.53
226 227 9.849166 TTGATTTCCTAACAATAATTCGTTTCC 57.151 29.630 0.00 0.00 0.00 3.13
228 229 9.634163 GGTTGATTTCCTAACAATAATTCGTTT 57.366 29.630 0.00 0.00 0.00 3.60
229 230 9.020731 AGGTTGATTTCCTAACAATAATTCGTT 57.979 29.630 0.00 0.00 33.04 3.85
230 231 8.575649 AGGTTGATTTCCTAACAATAATTCGT 57.424 30.769 0.00 0.00 33.04 3.85
243 244 8.548025 CCCCAAAAATAATTAGGTTGATTTCCT 58.452 33.333 6.99 0.00 38.91 3.36
244 245 8.544622 TCCCCAAAAATAATTAGGTTGATTTCC 58.455 33.333 6.99 0.00 0.00 3.13
245 246 9.952030 TTCCCCAAAAATAATTAGGTTGATTTC 57.048 29.630 6.99 0.00 0.00 2.17
246 247 9.958180 CTTCCCCAAAAATAATTAGGTTGATTT 57.042 29.630 6.99 0.00 0.00 2.17
247 248 8.046708 GCTTCCCCAAAAATAATTAGGTTGATT 58.953 33.333 6.99 0.00 0.00 2.57
248 249 7.181845 TGCTTCCCCAAAAATAATTAGGTTGAT 59.818 33.333 6.99 0.00 0.00 2.57
249 250 6.498651 TGCTTCCCCAAAAATAATTAGGTTGA 59.501 34.615 6.99 0.00 0.00 3.18
250 251 6.706295 TGCTTCCCCAAAAATAATTAGGTTG 58.294 36.000 0.00 0.00 0.00 3.77
251 252 6.943899 TGCTTCCCCAAAAATAATTAGGTT 57.056 33.333 0.00 0.00 0.00 3.50
252 253 6.943899 TTGCTTCCCCAAAAATAATTAGGT 57.056 33.333 0.00 0.00 0.00 3.08
253 254 7.563906 TGATTGCTTCCCCAAAAATAATTAGG 58.436 34.615 0.00 0.00 0.00 2.69
254 255 9.617523 AATGATTGCTTCCCCAAAAATAATTAG 57.382 29.630 0.00 0.00 0.00 1.73
255 256 9.393512 CAATGATTGCTTCCCCAAAAATAATTA 57.606 29.630 0.00 0.00 0.00 1.40
256 257 8.108364 TCAATGATTGCTTCCCCAAAAATAATT 58.892 29.630 0.00 0.00 0.00 1.40
257 258 7.553760 GTCAATGATTGCTTCCCCAAAAATAAT 59.446 33.333 0.00 0.00 0.00 1.28
258 259 6.878389 GTCAATGATTGCTTCCCCAAAAATAA 59.122 34.615 0.00 0.00 0.00 1.40
259 260 6.405538 GTCAATGATTGCTTCCCCAAAAATA 58.594 36.000 0.00 0.00 0.00 1.40
260 261 5.247862 GTCAATGATTGCTTCCCCAAAAAT 58.752 37.500 0.00 0.00 0.00 1.82
261 262 4.504689 GGTCAATGATTGCTTCCCCAAAAA 60.505 41.667 0.00 0.00 0.00 1.94
262 263 3.007831 GGTCAATGATTGCTTCCCCAAAA 59.992 43.478 0.00 0.00 0.00 2.44
263 264 2.566724 GGTCAATGATTGCTTCCCCAAA 59.433 45.455 0.00 0.00 0.00 3.28
264 265 2.178580 GGTCAATGATTGCTTCCCCAA 58.821 47.619 0.00 0.00 0.00 4.12
265 266 1.851304 GGTCAATGATTGCTTCCCCA 58.149 50.000 0.00 0.00 0.00 4.96
266 267 0.740737 CGGTCAATGATTGCTTCCCC 59.259 55.000 0.00 0.00 0.00 4.81
267 268 1.133025 CACGGTCAATGATTGCTTCCC 59.867 52.381 0.00 0.00 0.00 3.97
268 269 2.083774 TCACGGTCAATGATTGCTTCC 58.916 47.619 0.00 2.54 0.00 3.46
269 270 3.426695 CCTTCACGGTCAATGATTGCTTC 60.427 47.826 0.00 0.00 0.00 3.86
270 271 2.489329 CCTTCACGGTCAATGATTGCTT 59.511 45.455 0.00 0.00 0.00 3.91
271 272 2.086869 CCTTCACGGTCAATGATTGCT 58.913 47.619 0.00 0.00 0.00 3.91
272 273 1.133025 CCCTTCACGGTCAATGATTGC 59.867 52.381 0.00 0.00 0.00 3.56
273 274 2.436417 ACCCTTCACGGTCAATGATTG 58.564 47.619 0.00 0.00 0.00 2.67
274 275 2.879103 ACCCTTCACGGTCAATGATT 57.121 45.000 0.00 0.00 0.00 2.57
275 276 2.838202 ACTACCCTTCACGGTCAATGAT 59.162 45.455 0.00 0.00 37.34 2.45
276 277 2.253610 ACTACCCTTCACGGTCAATGA 58.746 47.619 0.00 0.00 37.34 2.57
277 278 2.762535 ACTACCCTTCACGGTCAATG 57.237 50.000 0.00 0.00 37.34 2.82
278 279 3.194968 CAGTACTACCCTTCACGGTCAAT 59.805 47.826 0.00 0.00 37.34 2.57
279 280 2.559668 CAGTACTACCCTTCACGGTCAA 59.440 50.000 0.00 0.00 37.34 3.18
280 281 2.165167 CAGTACTACCCTTCACGGTCA 58.835 52.381 0.00 0.00 37.34 4.02
281 282 1.135170 GCAGTACTACCCTTCACGGTC 60.135 57.143 0.00 0.00 37.34 4.79
282 283 0.893447 GCAGTACTACCCTTCACGGT 59.107 55.000 0.00 0.00 40.13 4.83
283 284 0.892755 TGCAGTACTACCCTTCACGG 59.107 55.000 0.00 0.00 0.00 4.94
284 285 2.540515 CATGCAGTACTACCCTTCACG 58.459 52.381 0.00 0.00 0.00 4.35
285 286 2.280628 GCATGCAGTACTACCCTTCAC 58.719 52.381 14.21 0.00 0.00 3.18
286 287 1.905894 TGCATGCAGTACTACCCTTCA 59.094 47.619 18.46 0.00 0.00 3.02
287 288 2.691409 TGCATGCAGTACTACCCTTC 57.309 50.000 18.46 0.00 0.00 3.46
288 289 3.433306 TTTGCATGCAGTACTACCCTT 57.567 42.857 21.50 0.00 0.00 3.95
289 290 3.054434 TCATTTGCATGCAGTACTACCCT 60.054 43.478 21.50 0.00 0.00 4.34
290 291 3.278574 TCATTTGCATGCAGTACTACCC 58.721 45.455 21.50 0.00 0.00 3.69
291 292 4.963276 TTCATTTGCATGCAGTACTACC 57.037 40.909 21.50 0.00 0.00 3.18
292 293 6.254157 CCATTTTCATTTGCATGCAGTACTAC 59.746 38.462 21.50 0.00 0.00 2.73
293 294 6.152492 TCCATTTTCATTTGCATGCAGTACTA 59.848 34.615 21.50 2.08 0.00 1.82
294 295 5.047164 TCCATTTTCATTTGCATGCAGTACT 60.047 36.000 21.50 4.04 0.00 2.73
295 296 5.170021 TCCATTTTCATTTGCATGCAGTAC 58.830 37.500 21.50 0.00 0.00 2.73
296 297 5.402997 TCCATTTTCATTTGCATGCAGTA 57.597 34.783 21.50 13.54 0.00 2.74
297 298 4.274602 TCCATTTTCATTTGCATGCAGT 57.725 36.364 21.50 11.16 0.00 4.40
298 299 5.614923 TTTCCATTTTCATTTGCATGCAG 57.385 34.783 21.50 9.90 0.00 4.41
299 300 4.083217 GCTTTCCATTTTCATTTGCATGCA 60.083 37.500 18.46 18.46 0.00 3.96
300 301 4.155280 AGCTTTCCATTTTCATTTGCATGC 59.845 37.500 11.82 11.82 0.00 4.06
301 302 5.873179 AGCTTTCCATTTTCATTTGCATG 57.127 34.783 0.00 0.00 0.00 4.06
302 303 9.841295 ATAATAGCTTTCCATTTTCATTTGCAT 57.159 25.926 0.00 0.00 0.00 3.96
303 304 9.669887 AATAATAGCTTTCCATTTTCATTTGCA 57.330 25.926 0.00 0.00 0.00 4.08
319 320 9.211485 GGCATGCAATTTATGAAATAATAGCTT 57.789 29.630 21.36 0.00 38.83 3.74
320 321 8.369424 TGGCATGCAATTTATGAAATAATAGCT 58.631 29.630 21.36 0.00 38.83 3.32
321 322 8.537049 TGGCATGCAATTTATGAAATAATAGC 57.463 30.769 21.36 0.00 38.83 2.97
324 325 9.999660 TGTATGGCATGCAATTTATGAAATAAT 57.000 25.926 21.36 0.00 38.83 1.28
325 326 9.258826 GTGTATGGCATGCAATTTATGAAATAA 57.741 29.630 19.95 0.00 36.92 1.40
326 327 8.640651 AGTGTATGGCATGCAATTTATGAAATA 58.359 29.630 19.95 0.00 0.00 1.40
327 328 7.502696 AGTGTATGGCATGCAATTTATGAAAT 58.497 30.769 19.95 0.00 0.00 2.17
328 329 6.876155 AGTGTATGGCATGCAATTTATGAAA 58.124 32.000 19.95 0.00 0.00 2.69
329 330 6.468333 AGTGTATGGCATGCAATTTATGAA 57.532 33.333 19.95 0.00 0.00 2.57
330 331 7.579761 TTAGTGTATGGCATGCAATTTATGA 57.420 32.000 22.55 2.69 0.00 2.15
331 332 9.911138 TTATTAGTGTATGGCATGCAATTTATG 57.089 29.630 22.55 0.00 0.00 1.90
334 335 9.664332 TTTTTATTAGTGTATGGCATGCAATTT 57.336 25.926 22.55 13.46 0.00 1.82
335 336 9.835389 ATTTTTATTAGTGTATGGCATGCAATT 57.165 25.926 22.55 14.76 0.00 2.32
336 337 9.480053 GATTTTTATTAGTGTATGGCATGCAAT 57.520 29.630 21.28 21.28 0.00 3.56
337 338 8.473219 TGATTTTTATTAGTGTATGGCATGCAA 58.527 29.630 19.95 9.21 0.00 4.08
338 339 7.920151 GTGATTTTTATTAGTGTATGGCATGCA 59.080 33.333 21.36 14.53 0.00 3.96
339 340 7.382218 GGTGATTTTTATTAGTGTATGGCATGC 59.618 37.037 9.90 9.90 0.00 4.06
340 341 8.632679 AGGTGATTTTTATTAGTGTATGGCATG 58.367 33.333 10.98 0.00 0.00 4.06
341 342 8.632679 CAGGTGATTTTTATTAGTGTATGGCAT 58.367 33.333 4.88 4.88 0.00 4.40
342 343 7.416213 GCAGGTGATTTTTATTAGTGTATGGCA 60.416 37.037 0.00 0.00 0.00 4.92
343 344 6.918022 GCAGGTGATTTTTATTAGTGTATGGC 59.082 38.462 0.00 0.00 0.00 4.40
344 345 7.068103 TGGCAGGTGATTTTTATTAGTGTATGG 59.932 37.037 0.00 0.00 0.00 2.74
345 346 7.995289 TGGCAGGTGATTTTTATTAGTGTATG 58.005 34.615 0.00 0.00 0.00 2.39
346 347 8.766994 ATGGCAGGTGATTTTTATTAGTGTAT 57.233 30.769 0.00 0.00 0.00 2.29
347 348 9.688091 TTATGGCAGGTGATTTTTATTAGTGTA 57.312 29.630 0.00 0.00 0.00 2.90
348 349 8.588290 TTATGGCAGGTGATTTTTATTAGTGT 57.412 30.769 0.00 0.00 0.00 3.55
349 350 9.467258 CATTATGGCAGGTGATTTTTATTAGTG 57.533 33.333 0.00 0.00 0.00 2.74
350 351 8.641541 CCATTATGGCAGGTGATTTTTATTAGT 58.358 33.333 0.00 0.00 0.00 2.24
368 369 3.346426 GCACCTAGGGCCATTATGG 57.654 57.895 14.81 6.92 41.55 2.74
392 393 6.127451 TGAGTCATATATACCCGCAATAGGTG 60.127 42.308 0.00 0.00 38.36 4.00
393 394 5.955959 TGAGTCATATATACCCGCAATAGGT 59.044 40.000 0.00 0.00 41.64 3.08
394 395 6.465439 TGAGTCATATATACCCGCAATAGG 57.535 41.667 0.00 0.00 0.00 2.57
397 398 8.758829 TCTTAATGAGTCATATATACCCGCAAT 58.241 33.333 5.94 0.00 0.00 3.56
398 399 8.129496 TCTTAATGAGTCATATATACCCGCAA 57.871 34.615 5.94 0.00 0.00 4.85
399 400 7.712204 TCTTAATGAGTCATATATACCCGCA 57.288 36.000 5.94 0.00 0.00 5.69
424 425 5.519566 CAGAGCAAGATGAGTGAATCTACAC 59.480 44.000 0.00 0.00 35.83 2.90
425 426 5.186603 ACAGAGCAAGATGAGTGAATCTACA 59.813 40.000 0.00 0.00 35.83 2.74
426 427 5.659463 ACAGAGCAAGATGAGTGAATCTAC 58.341 41.667 0.00 0.00 35.83 2.59
427 428 5.929058 ACAGAGCAAGATGAGTGAATCTA 57.071 39.130 0.00 0.00 35.83 1.98
428 429 4.822685 ACAGAGCAAGATGAGTGAATCT 57.177 40.909 0.00 0.00 38.59 2.40
429 430 6.047870 ACATACAGAGCAAGATGAGTGAATC 58.952 40.000 0.00 0.00 0.00 2.52
430 431 5.987098 ACATACAGAGCAAGATGAGTGAAT 58.013 37.500 0.00 0.00 0.00 2.57
431 432 5.411831 ACATACAGAGCAAGATGAGTGAA 57.588 39.130 0.00 0.00 0.00 3.18
432 433 5.654209 ACTACATACAGAGCAAGATGAGTGA 59.346 40.000 0.00 0.00 0.00 3.41
433 434 5.900425 ACTACATACAGAGCAAGATGAGTG 58.100 41.667 0.00 0.00 0.00 3.51
434 435 5.654209 TGACTACATACAGAGCAAGATGAGT 59.346 40.000 0.00 0.00 0.00 3.41
435 436 5.976534 GTGACTACATACAGAGCAAGATGAG 59.023 44.000 0.00 0.00 0.00 2.90
436 437 5.654209 AGTGACTACATACAGAGCAAGATGA 59.346 40.000 0.00 0.00 0.00 2.92
437 438 5.900425 AGTGACTACATACAGAGCAAGATG 58.100 41.667 0.00 0.00 0.00 2.90
438 439 6.071108 ACAAGTGACTACATACAGAGCAAGAT 60.071 38.462 0.00 0.00 0.00 2.40
439 440 5.243954 ACAAGTGACTACATACAGAGCAAGA 59.756 40.000 0.00 0.00 0.00 3.02
440 441 5.473931 ACAAGTGACTACATACAGAGCAAG 58.526 41.667 0.00 0.00 0.00 4.01
441 442 5.468540 ACAAGTGACTACATACAGAGCAA 57.531 39.130 0.00 0.00 0.00 3.91
442 443 5.010617 TCAACAAGTGACTACATACAGAGCA 59.989 40.000 0.00 0.00 0.00 4.26
443 444 5.470368 TCAACAAGTGACTACATACAGAGC 58.530 41.667 0.00 0.00 0.00 4.09
444 445 7.946655 TTTCAACAAGTGACTACATACAGAG 57.053 36.000 0.00 0.00 35.39 3.35
847 848 9.775539 ATGAGCCACCTCCGAATATATATATAT 57.224 33.333 9.12 9.12 37.29 0.86
848 849 9.601810 AATGAGCCACCTCCGAATATATATATA 57.398 33.333 5.66 4.92 37.29 0.86
849 850 8.497910 AATGAGCCACCTCCGAATATATATAT 57.502 34.615 0.00 0.00 37.29 0.86
850 851 7.914427 AATGAGCCACCTCCGAATATATATA 57.086 36.000 0.00 0.00 37.29 0.86
851 852 6.814954 AATGAGCCACCTCCGAATATATAT 57.185 37.500 0.00 0.00 37.29 0.86
852 853 7.618117 TCTTAATGAGCCACCTCCGAATATATA 59.382 37.037 0.00 0.00 37.29 0.86
853 854 6.440647 TCTTAATGAGCCACCTCCGAATATAT 59.559 38.462 0.00 0.00 37.29 0.86
854 855 5.778241 TCTTAATGAGCCACCTCCGAATATA 59.222 40.000 0.00 0.00 37.29 0.86
855 856 4.593206 TCTTAATGAGCCACCTCCGAATAT 59.407 41.667 0.00 0.00 37.29 1.28
856 857 3.964688 TCTTAATGAGCCACCTCCGAATA 59.035 43.478 0.00 0.00 37.29 1.75
857 858 2.771943 TCTTAATGAGCCACCTCCGAAT 59.228 45.455 0.00 0.00 37.29 3.34
858 859 2.184533 TCTTAATGAGCCACCTCCGAA 58.815 47.619 0.00 0.00 37.29 4.30
859 860 1.860641 TCTTAATGAGCCACCTCCGA 58.139 50.000 0.00 0.00 37.29 4.55
860 861 2.487934 CATCTTAATGAGCCACCTCCG 58.512 52.381 0.00 0.00 37.29 4.63
861 862 2.225467 GCATCTTAATGAGCCACCTCC 58.775 52.381 0.00 0.00 37.29 4.30
862 863 2.923121 TGCATCTTAATGAGCCACCTC 58.077 47.619 0.00 0.00 38.62 3.85
863 864 3.589951 ATGCATCTTAATGAGCCACCT 57.410 42.857 0.00 0.00 34.61 4.00
864 865 4.660789 AAATGCATCTTAATGAGCCACC 57.339 40.909 0.00 0.00 34.61 4.61
865 866 7.031226 TCTTAAATGCATCTTAATGAGCCAC 57.969 36.000 0.00 0.00 34.61 5.01
866 867 6.263842 CCTCTTAAATGCATCTTAATGAGCCA 59.736 38.462 0.00 0.00 34.61 4.75
867 868 6.294397 CCCTCTTAAATGCATCTTAATGAGCC 60.294 42.308 0.00 0.00 34.61 4.70
868 869 6.675987 CCCTCTTAAATGCATCTTAATGAGC 58.324 40.000 0.00 0.00 34.61 4.26
869 870 6.263842 TGCCCTCTTAAATGCATCTTAATGAG 59.736 38.462 0.00 13.44 34.61 2.90
870 871 6.039717 GTGCCCTCTTAAATGCATCTTAATGA 59.960 38.462 0.00 6.53 35.96 2.57
871 872 6.183360 TGTGCCCTCTTAAATGCATCTTAATG 60.183 38.462 0.00 4.30 35.96 1.90
872 873 5.893255 TGTGCCCTCTTAAATGCATCTTAAT 59.107 36.000 0.00 0.00 35.96 1.40
877 878 4.660789 AATGTGCCCTCTTAAATGCATC 57.339 40.909 0.00 0.00 35.96 3.91
884 885 3.265737 TCTGCCTAAATGTGCCCTCTTAA 59.734 43.478 0.00 0.00 0.00 1.85
914 915 9.993454 TGCTCATGGATGCTAAATATAGATATC 57.007 33.333 0.00 0.00 0.00 1.63
935 936 2.764128 GAGGACCGGGGATGCTCA 60.764 66.667 6.32 0.00 34.84 4.26
959 960 4.039852 TGTTGCCTGTGTAGTGATTAGTGA 59.960 41.667 0.00 0.00 0.00 3.41
960 961 4.152402 GTGTTGCCTGTGTAGTGATTAGTG 59.848 45.833 0.00 0.00 0.00 2.74
961 962 4.202315 TGTGTTGCCTGTGTAGTGATTAGT 60.202 41.667 0.00 0.00 0.00 2.24
962 963 4.314961 TGTGTTGCCTGTGTAGTGATTAG 58.685 43.478 0.00 0.00 0.00 1.73
963 964 4.344359 TGTGTTGCCTGTGTAGTGATTA 57.656 40.909 0.00 0.00 0.00 1.75
964 965 3.207265 TGTGTTGCCTGTGTAGTGATT 57.793 42.857 0.00 0.00 0.00 2.57
965 966 2.878406 GTTGTGTTGCCTGTGTAGTGAT 59.122 45.455 0.00 0.00 0.00 3.06
1014 1015 2.937799 GAGAAGAGCAAGGATGAAGCTG 59.062 50.000 0.00 0.00 39.02 4.24
1060 1061 3.035363 TGTTGAGTAGGTGGACAGTGAA 58.965 45.455 0.00 0.00 0.00 3.18
1150 1151 1.372087 GAGACTTCAATGGCGGCCAG 61.372 60.000 27.62 14.79 36.75 4.85
1162 1163 2.190578 CATGCCCGGGGAGACTTC 59.809 66.667 25.28 3.41 0.00 3.01
1285 1286 1.962306 GTGTCGCGGGTGGCTTAAA 60.962 57.895 6.13 0.00 40.44 1.52
1286 1287 2.357760 GTGTCGCGGGTGGCTTAA 60.358 61.111 6.13 0.00 40.44 1.85
1287 1288 3.291101 GAGTGTCGCGGGTGGCTTA 62.291 63.158 6.13 0.00 40.44 3.09
1302 1303 3.054503 AGCGTGTACTCGGCGAGT 61.055 61.111 39.98 39.98 45.54 4.18
1356 1357 1.418342 CGTTGAATCCGTCGGCGATT 61.418 55.000 12.93 9.05 41.33 3.34
1357 1358 1.876714 CGTTGAATCCGTCGGCGAT 60.877 57.895 12.93 0.00 41.33 4.58
1413 1414 2.668212 GCGGCACAGCTTACCACA 60.668 61.111 0.00 0.00 0.00 4.17
1619 1623 1.526917 GTGCAGGTGAAGGTGCTGT 60.527 57.895 0.00 0.00 40.54 4.40
1636 1640 0.034767 TGGTAGTCTGATCGGACGGT 60.035 55.000 25.38 14.04 40.76 4.83
1713 1720 7.817418 ACATTGGGAAACGCTATTACATTAT 57.183 32.000 0.00 0.00 0.00 1.28
1890 1899 9.941325 ATTAATTGTTGCTGATTTAACATGGAA 57.059 25.926 0.00 0.00 36.75 3.53
1924 1991 4.721776 TGCCTTGTTTCATATACTCCCTCT 59.278 41.667 0.00 0.00 0.00 3.69
2103 2170 1.951631 GCTCCTATTCGGCTCGCAC 60.952 63.158 0.00 0.00 0.00 5.34
2104 2171 2.355445 CTGCTCCTATTCGGCTCGCA 62.355 60.000 0.00 0.00 0.00 5.10
2111 2178 2.663188 GGCGGCTGCTCCTATTCG 60.663 66.667 18.85 0.00 42.25 3.34
2112 2179 2.663188 CGGCGGCTGCTCCTATTC 60.663 66.667 18.85 0.00 42.25 1.75
2113 2180 4.241555 CCGGCGGCTGCTCCTATT 62.242 66.667 15.42 0.00 42.25 1.73
2136 2203 2.823154 GCAGTACTTTGTTTATGGGCCA 59.177 45.455 9.61 9.61 0.00 5.36
2176 2243 6.942532 TGGTCCTGCATTCAGATTATTAAC 57.057 37.500 0.00 0.00 42.95 2.01
2293 2360 2.157738 CTTTTGCTAGGCAGTGAGCTT 58.842 47.619 0.00 0.00 44.79 3.74
2404 2474 1.451387 GCGTTGGGTATCACCAGGG 60.451 63.158 0.00 0.00 42.47 4.45
2420 2509 1.933853 GGGAGTAGTTGCTACATTGCG 59.066 52.381 8.72 0.00 39.22 4.85
2465 2554 7.972832 TTTTTAACGTTGTCATGGACTCTAT 57.027 32.000 11.99 0.00 33.15 1.98
2519 2608 7.887381 ACCACTACAGTATCATGCTAGAATAC 58.113 38.462 0.00 0.00 0.00 1.89
2521 2610 6.551227 TGACCACTACAGTATCATGCTAGAAT 59.449 38.462 0.00 0.00 0.00 2.40
2532 2621 5.014755 TCCCCAAAAATGACCACTACAGTAT 59.985 40.000 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.