Multiple sequence alignment - TraesCS3A01G293800

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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 TraesCS3A01G293800 chr3A 100.000 2531 0 0 1 2531 526515294 526512764 0.000000e+00 4674.0
1 TraesCS3A01G293800 chr3B 88.916 1227 93 20 469 1671 530243899 530242692 0.000000e+00 1472.0
2 TraesCS3A01G293800 chr3B 100.000 32 0 0 2372 2403 530239415 530239384 2.720000e-05 60.2
3 TraesCS3A01G293800 chr3D 90.463 1101 56 23 767 1843 403941740 403940665 0.000000e+00 1406.0
4 TraesCS3A01G293800 chr3D 91.238 719 40 14 1830 2531 403940121 403939409 0.000000e+00 957.0
5 TraesCS3A01G293800 chr3D 83.582 134 19 3 603 736 403941999 403941869 3.420000e-24 122.0
6 TraesCS3A01G293800 chr6A 94.010 384 19 4 4 385 34415370 34414989 1.690000e-161 579.0
7 TraesCS3A01G293800 chr6A 88.796 357 29 7 29 383 147931028 147931375 6.470000e-116 427.0
8 TraesCS3A01G293800 chr6A 86.550 171 21 2 469 639 235028249 235028081 1.200000e-43 187.0
9 TraesCS3A01G293800 chr6A 82.192 146 24 2 2045 2189 584142927 584142783 9.510000e-25 124.0
10 TraesCS3A01G293800 chr5A 94.010 384 19 4 4 385 439875242 439874861 1.690000e-161 579.0
11 TraesCS3A01G293800 chr2D 89.351 385 32 8 4 382 628185698 628185317 2.280000e-130 475.0
12 TraesCS3A01G293800 chr7A 89.444 360 26 7 28 384 690983582 690983232 6.420000e-121 444.0
13 TraesCS3A01G293800 chr1D 89.071 366 26 9 21 383 52289731 52290085 2.310000e-120 442.0
14 TraesCS3A01G293800 chr1D 88.144 194 19 4 451 643 28560007 28560197 7.040000e-56 228.0
15 TraesCS3A01G293800 chr1D 87.719 171 20 1 469 639 481697844 481698013 5.520000e-47 198.0
16 TraesCS3A01G293800 chr1D 84.500 200 29 2 450 649 26369904 26370101 1.990000e-46 196.0
17 TraesCS3A01G293800 chr1D 85.714 182 22 4 449 629 464249485 464249663 3.320000e-44 189.0
18 TraesCS3A01G293800 chr1B 87.371 388 40 8 1 383 612821089 612821472 1.080000e-118 436.0
19 TraesCS3A01G293800 chr2A 87.566 378 33 10 9 383 764865300 764864934 2.330000e-115 425.0
20 TraesCS3A01G293800 chr1A 88.202 356 29 7 30 383 90999825 91000169 1.810000e-111 412.0
21 TraesCS3A01G293800 chr1A 87.952 166 18 2 469 634 483863793 483863956 7.140000e-46 195.0
22 TraesCS3A01G293800 chr4A 81.724 290 45 6 1904 2189 632011430 632011715 4.210000e-58 235.0
23 TraesCS3A01G293800 chr4A 85.263 190 25 3 449 637 164521319 164521506 2.570000e-45 193.0
24 TraesCS3A01G293800 chr4A 84.422 199 25 3 446 639 80174585 80174388 9.240000e-45 191.0
25 TraesCS3A01G293800 chr4D 88.506 174 19 1 469 642 258893484 258893656 2.550000e-50 209.0
26 TraesCS3A01G293800 chr5B 86.857 175 19 4 472 644 503777988 503777816 2.570000e-45 193.0
27 TraesCS3A01G293800 chr7D 96.970 33 1 0 2259 2291 30408988 30409020 3.520000e-04 56.5


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 TraesCS3A01G293800 chr3A 526512764 526515294 2530 True 4674.000000 4674 100.000000 1 2531 1 chr3A.!!$R1 2530
1 TraesCS3A01G293800 chr3B 530239384 530243899 4515 True 766.100000 1472 94.458000 469 2403 2 chr3B.!!$R1 1934
2 TraesCS3A01G293800 chr3D 403939409 403941999 2590 True 828.333333 1406 88.427667 603 2531 3 chr3D.!!$R1 1928

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
398 399 0.036388 TTCCCTCGTGCAATCCAGTC 60.036 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2622 0.109597 CTCTGCACGCCATTGTTTCC 60.11 55.0 0.0 0.0 0.0 3.13 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
95 96 6.931243 TTTTGTAAAACCACGAACAAGTTC 57.069 33.333 2.89 2.89 33.70 3.01
96 97 5.883503 TTGTAAAACCACGAACAAGTTCT 57.116 34.783 10.83 0.00 37.44 3.01
97 98 5.224562 TGTAAAACCACGAACAAGTTCTG 57.775 39.130 10.83 7.97 37.44 3.02
98 99 4.936411 TGTAAAACCACGAACAAGTTCTGA 59.064 37.500 10.83 0.00 37.44 3.27
99 100 4.616181 AAAACCACGAACAAGTTCTGAG 57.384 40.909 10.83 4.08 37.44 3.35
100 101 3.536956 AACCACGAACAAGTTCTGAGA 57.463 42.857 10.83 0.00 37.44 3.27
101 102 3.536956 ACCACGAACAAGTTCTGAGAA 57.463 42.857 10.83 0.00 37.44 2.87
102 103 3.869065 ACCACGAACAAGTTCTGAGAAA 58.131 40.909 10.83 0.00 37.44 2.52
103 104 3.871594 ACCACGAACAAGTTCTGAGAAAG 59.128 43.478 10.83 0.00 37.44 2.62
104 105 4.119862 CCACGAACAAGTTCTGAGAAAGA 58.880 43.478 10.83 0.00 37.44 2.52
105 106 4.570772 CCACGAACAAGTTCTGAGAAAGAA 59.429 41.667 10.83 0.00 42.83 2.52
106 107 5.064707 CCACGAACAAGTTCTGAGAAAGAAA 59.935 40.000 10.83 0.00 46.51 2.52
107 108 6.403200 CCACGAACAAGTTCTGAGAAAGAAAA 60.403 38.462 10.83 0.00 46.51 2.29
108 109 7.021196 CACGAACAAGTTCTGAGAAAGAAAAA 58.979 34.615 10.83 0.00 46.51 1.94
109 110 7.698130 CACGAACAAGTTCTGAGAAAGAAAAAT 59.302 33.333 10.83 0.00 46.51 1.82
110 111 8.889717 ACGAACAAGTTCTGAGAAAGAAAAATA 58.110 29.630 10.83 0.00 46.51 1.40
111 112 9.716507 CGAACAAGTTCTGAGAAAGAAAAATAA 57.283 29.630 10.83 0.00 46.51 1.40
213 214 8.710835 AAAAACAATAGAAAGCCGAAAAAGAA 57.289 26.923 0.00 0.00 0.00 2.52
214 215 7.694388 AAACAATAGAAAGCCGAAAAAGAAC 57.306 32.000 0.00 0.00 0.00 3.01
215 216 5.769367 ACAATAGAAAGCCGAAAAAGAACC 58.231 37.500 0.00 0.00 0.00 3.62
216 217 5.300792 ACAATAGAAAGCCGAAAAAGAACCA 59.699 36.000 0.00 0.00 0.00 3.67
217 218 3.990318 AGAAAGCCGAAAAAGAACCAG 57.010 42.857 0.00 0.00 0.00 4.00
218 219 3.551846 AGAAAGCCGAAAAAGAACCAGA 58.448 40.909 0.00 0.00 0.00 3.86
219 220 3.951680 AGAAAGCCGAAAAAGAACCAGAA 59.048 39.130 0.00 0.00 0.00 3.02
220 221 3.990318 AAGCCGAAAAAGAACCAGAAG 57.010 42.857 0.00 0.00 0.00 2.85
221 222 3.208747 AGCCGAAAAAGAACCAGAAGA 57.791 42.857 0.00 0.00 0.00 2.87
222 223 3.551846 AGCCGAAAAAGAACCAGAAGAA 58.448 40.909 0.00 0.00 0.00 2.52
223 224 3.565902 AGCCGAAAAAGAACCAGAAGAAG 59.434 43.478 0.00 0.00 0.00 2.85
224 225 3.853676 GCCGAAAAAGAACCAGAAGAAGC 60.854 47.826 0.00 0.00 0.00 3.86
225 226 3.545633 CGAAAAAGAACCAGAAGAAGCG 58.454 45.455 0.00 0.00 0.00 4.68
226 227 3.247648 CGAAAAAGAACCAGAAGAAGCGA 59.752 43.478 0.00 0.00 0.00 4.93
227 228 4.083802 CGAAAAAGAACCAGAAGAAGCGAT 60.084 41.667 0.00 0.00 0.00 4.58
228 229 5.120208 CGAAAAAGAACCAGAAGAAGCGATA 59.880 40.000 0.00 0.00 0.00 2.92
229 230 5.864628 AAAAGAACCAGAAGAAGCGATAC 57.135 39.130 0.00 0.00 0.00 2.24
230 231 4.537135 AAGAACCAGAAGAAGCGATACA 57.463 40.909 0.00 0.00 0.00 2.29
231 232 4.116747 AGAACCAGAAGAAGCGATACAG 57.883 45.455 0.00 0.00 0.00 2.74
232 233 2.969628 ACCAGAAGAAGCGATACAGG 57.030 50.000 0.00 0.00 0.00 4.00
233 234 1.134670 ACCAGAAGAAGCGATACAGGC 60.135 52.381 0.00 0.00 0.00 4.85
234 235 1.134699 CCAGAAGAAGCGATACAGGCA 60.135 52.381 0.00 0.00 0.00 4.75
235 236 2.621338 CAGAAGAAGCGATACAGGCAA 58.379 47.619 0.00 0.00 0.00 4.52
236 237 3.002791 CAGAAGAAGCGATACAGGCAAA 58.997 45.455 0.00 0.00 0.00 3.68
237 238 3.436704 CAGAAGAAGCGATACAGGCAAAA 59.563 43.478 0.00 0.00 0.00 2.44
238 239 4.072131 AGAAGAAGCGATACAGGCAAAAA 58.928 39.130 0.00 0.00 0.00 1.94
267 268 7.192148 GTTCAAGGAACCTTCTAGAAAGTTC 57.808 40.000 27.98 27.98 39.69 3.01
273 274 6.954487 GAACCTTCTAGAAAGTTCCCAAAA 57.046 37.500 26.55 0.00 36.33 2.44
274 275 6.710597 AACCTTCTAGAAAGTTCCCAAAAC 57.289 37.500 12.76 0.00 0.00 2.43
275 276 6.014771 ACCTTCTAGAAAGTTCCCAAAACT 57.985 37.500 6.63 0.00 0.00 2.66
276 277 5.828328 ACCTTCTAGAAAGTTCCCAAAACTG 59.172 40.000 6.63 0.00 0.00 3.16
277 278 5.241728 CCTTCTAGAAAGTTCCCAAAACTGG 59.758 44.000 6.63 0.00 0.00 4.00
278 279 5.382664 TCTAGAAAGTTCCCAAAACTGGT 57.617 39.130 0.00 0.00 0.00 4.00
279 280 5.762279 TCTAGAAAGTTCCCAAAACTGGTT 58.238 37.500 0.00 0.00 0.00 3.67
280 281 4.736126 AGAAAGTTCCCAAAACTGGTTG 57.264 40.909 0.00 0.00 0.00 3.77
281 282 3.450817 AGAAAGTTCCCAAAACTGGTTGG 59.549 43.478 5.62 5.62 46.57 3.77
288 289 2.507339 CAAAACTGGTTGGACGCAAT 57.493 45.000 0.00 0.00 0.00 3.56
289 290 3.634568 CAAAACTGGTTGGACGCAATA 57.365 42.857 0.00 0.00 0.00 1.90
290 291 4.173036 CAAAACTGGTTGGACGCAATAT 57.827 40.909 0.00 0.00 0.00 1.28
291 292 3.848272 AAACTGGTTGGACGCAATATG 57.152 42.857 0.00 0.00 0.00 1.78
292 293 2.489938 ACTGGTTGGACGCAATATGT 57.510 45.000 0.00 0.00 0.00 2.29
293 294 3.620427 ACTGGTTGGACGCAATATGTA 57.380 42.857 0.00 0.00 0.00 2.29
294 295 4.150897 ACTGGTTGGACGCAATATGTAT 57.849 40.909 0.00 0.00 0.00 2.29
295 296 4.523083 ACTGGTTGGACGCAATATGTATT 58.477 39.130 0.00 0.00 0.00 1.89
296 297 5.676552 ACTGGTTGGACGCAATATGTATTA 58.323 37.500 0.00 0.00 0.00 0.98
297 298 5.758296 ACTGGTTGGACGCAATATGTATTAG 59.242 40.000 0.00 0.00 0.00 1.73
298 299 5.676552 TGGTTGGACGCAATATGTATTAGT 58.323 37.500 0.00 0.00 0.00 2.24
299 300 5.525745 TGGTTGGACGCAATATGTATTAGTG 59.474 40.000 0.00 0.00 0.00 2.74
300 301 5.049680 GGTTGGACGCAATATGTATTAGTGG 60.050 44.000 0.00 0.00 0.00 4.00
301 302 4.637276 TGGACGCAATATGTATTAGTGGG 58.363 43.478 0.00 0.00 42.54 4.61
302 303 3.435671 GGACGCAATATGTATTAGTGGGC 59.564 47.826 0.00 0.00 41.10 5.36
303 304 3.064207 ACGCAATATGTATTAGTGGGCG 58.936 45.455 0.00 0.00 41.10 6.13
304 305 2.415168 CGCAATATGTATTAGTGGGCGG 59.585 50.000 0.00 0.00 38.45 6.13
305 306 2.161609 GCAATATGTATTAGTGGGCGGC 59.838 50.000 0.00 0.00 0.00 6.53
306 307 2.747446 CAATATGTATTAGTGGGCGGCC 59.253 50.000 23.42 23.42 0.00 6.13
307 308 0.688487 TATGTATTAGTGGGCGGCCC 59.312 55.000 31.41 31.41 45.71 5.80
320 321 3.056328 GGCCCAGGTTTGTCGCTC 61.056 66.667 0.00 0.00 0.00 5.03
321 322 3.423154 GCCCAGGTTTGTCGCTCG 61.423 66.667 0.00 0.00 0.00 5.03
322 323 3.423154 CCCAGGTTTGTCGCTCGC 61.423 66.667 0.00 0.00 0.00 5.03
323 324 2.357517 CCAGGTTTGTCGCTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
324 325 2.671177 CCAGGTTTGTCGCTCGCTG 61.671 63.158 0.00 0.00 0.00 5.18
325 326 3.044305 AGGTTTGTCGCTCGCTGC 61.044 61.111 0.00 0.00 38.57 5.25
357 358 0.872388 GGTAGCCCGATATTTTGCCG 59.128 55.000 0.00 0.00 0.00 5.69
358 359 0.237498 GTAGCCCGATATTTTGCCGC 59.763 55.000 0.00 0.00 0.00 6.53
359 360 0.179043 TAGCCCGATATTTTGCCGCA 60.179 50.000 0.00 0.00 0.00 5.69
360 361 1.008538 GCCCGATATTTTGCCGCAG 60.009 57.895 0.00 0.00 0.00 5.18
361 362 1.008538 CCCGATATTTTGCCGCAGC 60.009 57.895 0.00 0.00 40.48 5.25
362 363 1.369209 CCGATATTTTGCCGCAGCG 60.369 57.895 8.18 8.18 44.31 5.18
363 364 1.641140 CGATATTTTGCCGCAGCGA 59.359 52.632 18.75 0.00 44.31 4.93
364 365 0.383491 CGATATTTTGCCGCAGCGAG 60.383 55.000 18.75 7.72 44.31 5.03
365 366 0.658536 GATATTTTGCCGCAGCGAGC 60.659 55.000 18.75 18.37 44.31 5.03
377 378 4.280494 GCGAGCGGCGAATAGGGA 62.280 66.667 12.98 0.00 44.57 4.20
378 379 2.651361 CGAGCGGCGAATAGGGAT 59.349 61.111 12.98 0.00 44.57 3.85
379 380 1.006102 CGAGCGGCGAATAGGGATT 60.006 57.895 12.98 0.00 44.57 3.01
380 381 0.600255 CGAGCGGCGAATAGGGATTT 60.600 55.000 12.98 0.00 44.57 2.17
381 382 1.149148 GAGCGGCGAATAGGGATTTC 58.851 55.000 12.98 0.00 0.00 2.17
382 383 0.250338 AGCGGCGAATAGGGATTTCC 60.250 55.000 12.98 0.00 0.00 3.13
394 395 1.025041 GGATTTCCCTCGTGCAATCC 58.975 55.000 0.00 0.00 38.36 3.01
395 396 1.681780 GGATTTCCCTCGTGCAATCCA 60.682 52.381 5.15 0.00 42.97 3.41
396 397 1.672881 GATTTCCCTCGTGCAATCCAG 59.327 52.381 0.00 0.00 0.00 3.86
397 398 0.400213 TTTCCCTCGTGCAATCCAGT 59.600 50.000 0.00 0.00 0.00 4.00
398 399 0.036388 TTCCCTCGTGCAATCCAGTC 60.036 55.000 0.00 0.00 0.00 3.51
399 400 0.904865 TCCCTCGTGCAATCCAGTCT 60.905 55.000 0.00 0.00 0.00 3.24
400 401 0.824109 CCCTCGTGCAATCCAGTCTA 59.176 55.000 0.00 0.00 0.00 2.59
401 402 1.414181 CCCTCGTGCAATCCAGTCTAT 59.586 52.381 0.00 0.00 0.00 1.98
402 403 2.628178 CCCTCGTGCAATCCAGTCTATA 59.372 50.000 0.00 0.00 0.00 1.31
403 404 3.305676 CCCTCGTGCAATCCAGTCTATAG 60.306 52.174 0.00 0.00 0.00 1.31
404 405 3.570125 CCTCGTGCAATCCAGTCTATAGA 59.430 47.826 0.00 0.00 0.00 1.98
405 406 4.038042 CCTCGTGCAATCCAGTCTATAGAA 59.962 45.833 3.40 0.00 0.00 2.10
406 407 5.451937 CCTCGTGCAATCCAGTCTATAGAAA 60.452 44.000 3.40 0.00 0.00 2.52
407 408 5.972935 TCGTGCAATCCAGTCTATAGAAAA 58.027 37.500 3.40 0.00 0.00 2.29
408 409 6.403049 TCGTGCAATCCAGTCTATAGAAAAA 58.597 36.000 3.40 0.00 0.00 1.94
437 438 2.922740 TTTTCTCAAGTACCTGCCGT 57.077 45.000 0.00 0.00 0.00 5.68
438 439 2.922740 TTTCTCAAGTACCTGCCGTT 57.077 45.000 0.00 0.00 0.00 4.44
439 440 2.163818 TTCTCAAGTACCTGCCGTTG 57.836 50.000 0.00 0.00 0.00 4.10
440 441 1.045407 TCTCAAGTACCTGCCGTTGT 58.955 50.000 0.00 0.00 0.00 3.32
441 442 2.241160 TCTCAAGTACCTGCCGTTGTA 58.759 47.619 0.00 0.00 0.00 2.41
442 443 2.029649 TCTCAAGTACCTGCCGTTGTAC 60.030 50.000 0.00 0.00 38.06 2.90
443 444 1.687660 TCAAGTACCTGCCGTTGTACA 59.312 47.619 0.00 0.00 39.79 2.90
444 445 2.066262 CAAGTACCTGCCGTTGTACAG 58.934 52.381 0.00 0.00 39.79 2.74
452 453 3.453559 CCGTTGTACAGGGCCTAAG 57.546 57.895 5.28 0.00 0.00 2.18
453 454 0.107848 CCGTTGTACAGGGCCTAAGG 60.108 60.000 5.28 2.24 0.00 2.69
465 466 1.739067 GCCTAAGGCCTTGTACAGTG 58.261 55.000 28.77 11.73 44.06 3.66
466 467 1.003233 GCCTAAGGCCTTGTACAGTGT 59.997 52.381 28.77 0.00 44.06 3.55
467 468 2.552373 GCCTAAGGCCTTGTACAGTGTT 60.552 50.000 28.77 0.00 44.06 3.32
472 473 2.038557 AGGCCTTGTACAGTGTTAGGTG 59.961 50.000 0.00 0.00 0.00 4.00
476 477 4.801581 GCCTTGTACAGTGTTAGGTGCTTA 60.802 45.833 0.00 0.00 0.00 3.09
477 478 4.929808 CCTTGTACAGTGTTAGGTGCTTAG 59.070 45.833 0.00 0.00 0.00 2.18
486 487 9.127277 ACAGTGTTAGGTGCTTAGAAAAATAAA 57.873 29.630 0.00 0.00 0.00 1.40
491 492 9.788960 GTTAGGTGCTTAGAAAAATAAATCAGG 57.211 33.333 0.00 0.00 0.00 3.86
524 525 2.550978 CACCGGTGCCTATTTCTACAG 58.449 52.381 24.02 0.00 0.00 2.74
525 526 2.167693 CACCGGTGCCTATTTCTACAGA 59.832 50.000 24.02 0.00 0.00 3.41
526 527 2.835764 ACCGGTGCCTATTTCTACAGAA 59.164 45.455 6.12 0.00 0.00 3.02
527 528 3.118738 ACCGGTGCCTATTTCTACAGAAG 60.119 47.826 6.12 0.00 35.21 2.85
534 535 4.612943 CCTATTTCTACAGAAGAGACGCC 58.387 47.826 5.12 0.00 35.05 5.68
538 539 5.717078 TTTCTACAGAAGAGACGCCTAAA 57.283 39.130 0.00 0.00 35.05 1.85
541 542 7.400599 TTCTACAGAAGAGACGCCTAAATAA 57.599 36.000 0.00 0.00 35.05 1.40
544 545 4.081642 ACAGAAGAGACGCCTAAATAAGCA 60.082 41.667 0.00 0.00 0.00 3.91
548 549 4.626042 AGAGACGCCTAAATAAGCATCTG 58.374 43.478 0.00 0.00 0.00 2.90
549 550 3.134458 AGACGCCTAAATAAGCATCTGC 58.866 45.455 0.00 0.00 42.49 4.26
567 576 5.371115 TCTGCTTTGTACAAATAAGCACC 57.629 39.130 23.26 8.23 46.59 5.01
569 578 3.057876 TGCTTTGTACAAATAAGCACCGG 60.058 43.478 23.26 0.00 46.59 5.28
571 580 4.472286 CTTTGTACAAATAAGCACCGGTG 58.528 43.478 30.66 30.66 0.00 4.94
620 629 3.577805 AACACCTGTCTTAAGCACCTT 57.422 42.857 0.00 0.00 0.00 3.50
759 849 2.359900 AGCAAATCGACCCTTGATCAC 58.640 47.619 0.00 0.00 0.00 3.06
801 907 1.081242 CAATGCCGTCAAGTGGTGC 60.081 57.895 0.00 0.00 0.00 5.01
831 945 2.198287 GCATGCCATCCTGCCGATT 61.198 57.895 6.36 0.00 32.15 3.34
1220 1349 0.176910 GGCCTACAGGAGCTGAACTC 59.823 60.000 0.00 0.00 45.45 3.01
1484 1613 1.741327 TTCTACCCATCCTACGGCGC 61.741 60.000 6.90 0.00 0.00 6.53
1533 1662 1.156736 GTCCATTGTGGGAGTGAACG 58.843 55.000 0.00 0.00 38.32 3.95
1534 1663 0.762418 TCCATTGTGGGAGTGAACGT 59.238 50.000 0.00 0.00 38.32 3.99
1584 1724 2.598565 AGTCTGGCTAGAAGTGTGTGA 58.401 47.619 0.00 0.00 34.01 3.58
1588 1728 2.822561 CTGGCTAGAAGTGTGTGAGAGA 59.177 50.000 0.00 0.00 0.00 3.10
1619 1759 6.650427 TTTTAGCTAGAAGTGTGTGAGAGA 57.350 37.500 0.00 0.00 0.00 3.10
1645 1785 4.725556 TTTTTAGCTAGAAGTGCGTGTG 57.274 40.909 0.00 0.00 35.28 3.82
1646 1786 3.653539 TTTAGCTAGAAGTGCGTGTGA 57.346 42.857 0.00 0.00 35.28 3.58
1647 1787 2.921634 TAGCTAGAAGTGCGTGTGAG 57.078 50.000 0.00 0.00 35.28 3.51
1648 1788 0.389166 AGCTAGAAGTGCGTGTGAGC 60.389 55.000 0.00 0.00 35.28 4.26
1649 1789 1.355066 GCTAGAAGTGCGTGTGAGCC 61.355 60.000 0.00 0.00 36.02 4.70
1650 1790 0.737715 CTAGAAGTGCGTGTGAGCCC 60.738 60.000 0.00 0.00 36.02 5.19
1651 1791 1.185618 TAGAAGTGCGTGTGAGCCCT 61.186 55.000 0.00 0.00 36.02 5.19
1652 1792 1.598130 GAAGTGCGTGTGAGCCCTT 60.598 57.895 0.00 0.00 37.53 3.95
1653 1793 1.152963 AAGTGCGTGTGAGCCCTTT 60.153 52.632 0.00 0.00 30.92 3.11
1654 1794 0.751643 AAGTGCGTGTGAGCCCTTTT 60.752 50.000 0.00 0.00 30.92 2.27
1655 1795 0.751643 AGTGCGTGTGAGCCCTTTTT 60.752 50.000 0.00 0.00 36.02 1.94
1680 1820 7.762588 TTTAGCTAGAAGAGTAGAAGTGTGT 57.237 36.000 0.00 0.00 0.00 3.72
1681 1821 5.637006 AGCTAGAAGAGTAGAAGTGTGTG 57.363 43.478 0.00 0.00 0.00 3.82
1682 1822 5.074115 AGCTAGAAGAGTAGAAGTGTGTGT 58.926 41.667 0.00 0.00 0.00 3.72
1683 1823 5.048364 AGCTAGAAGAGTAGAAGTGTGTGTG 60.048 44.000 0.00 0.00 0.00 3.82
1684 1824 5.048643 GCTAGAAGAGTAGAAGTGTGTGTGA 60.049 44.000 0.00 0.00 0.00 3.58
1685 1825 5.446143 AGAAGAGTAGAAGTGTGTGTGAG 57.554 43.478 0.00 0.00 0.00 3.51
1686 1826 3.651803 AGAGTAGAAGTGTGTGTGAGC 57.348 47.619 0.00 0.00 0.00 4.26
1687 1827 2.297597 AGAGTAGAAGTGTGTGTGAGCC 59.702 50.000 0.00 0.00 0.00 4.70
1688 1828 2.297597 GAGTAGAAGTGTGTGTGAGCCT 59.702 50.000 0.00 0.00 0.00 4.58
1689 1829 2.700897 AGTAGAAGTGTGTGTGAGCCTT 59.299 45.455 0.00 0.00 0.00 4.35
1690 1830 2.717639 AGAAGTGTGTGTGAGCCTTT 57.282 45.000 0.00 0.00 0.00 3.11
1691 1831 2.292267 AGAAGTGTGTGTGAGCCTTTG 58.708 47.619 0.00 0.00 0.00 2.77
1692 1832 2.017049 GAAGTGTGTGTGAGCCTTTGT 58.983 47.619 0.00 0.00 0.00 2.83
1693 1833 1.382522 AGTGTGTGTGAGCCTTTGTG 58.617 50.000 0.00 0.00 0.00 3.33
1694 1834 0.248621 GTGTGTGTGAGCCTTTGTGC 60.249 55.000 0.00 0.00 0.00 4.57
1695 1835 0.679321 TGTGTGTGAGCCTTTGTGCA 60.679 50.000 0.00 0.00 0.00 4.57
1696 1836 0.455410 GTGTGTGAGCCTTTGTGCAA 59.545 50.000 0.00 0.00 0.00 4.08
1782 1968 2.694616 ATACCCGTGGGCCATGGT 60.695 61.111 36.46 31.62 38.76 3.55
1870 2613 1.446791 GAGAGCATGAGGCCCTCAG 59.553 63.158 19.98 12.07 45.90 3.35
1879 2622 0.761802 GAGGCCCTCAGGTTATCTGG 59.238 60.000 5.69 0.00 43.53 3.86
1899 2642 0.109597 GAAACAATGGCGTGCAGAGG 60.110 55.000 0.00 0.00 0.00 3.69
1900 2643 1.526575 AAACAATGGCGTGCAGAGGG 61.527 55.000 0.00 0.00 0.00 4.30
1997 2740 3.056607 GGCAACTATGGAAAACATGCAGT 60.057 43.478 0.00 0.00 40.82 4.40
2011 2754 5.866159 ACATGCAGTCATCATTAGAGAGA 57.134 39.130 0.00 0.00 0.00 3.10
2083 2826 4.701765 AGGTAGCAATGTAGAAGCTCATG 58.298 43.478 0.00 0.00 39.68 3.07
2135 2878 1.259609 AGGCATCATGTGTGGTTTGG 58.740 50.000 0.00 0.00 0.00 3.28
2207 4188 4.808767 AAAATTAGGCCTTACCCCTAGG 57.191 45.455 12.58 0.06 40.58 3.02
2212 4193 2.651190 AGGCCTTACCCCTAGGAAAAA 58.349 47.619 11.48 0.00 40.58 1.94
2213 4194 2.581246 AGGCCTTACCCCTAGGAAAAAG 59.419 50.000 11.48 9.88 40.58 2.27
2240 5225 5.446073 GGACTAATTTAGTTCTGCTTGCGAC 60.446 44.000 10.32 0.00 39.59 5.19
2257 5242 3.057386 TGCGACCGTGTCAGAGTTATTTA 60.057 43.478 5.15 0.00 32.09 1.40
2308 5302 9.314501 GAGCGTTTAAACAAATAAAGTACAGAG 57.685 33.333 18.07 0.00 0.00 3.35
2351 5345 8.853077 TCTGAAATGAGTATGAAACTGTTGAT 57.147 30.769 0.00 0.00 39.07 2.57
2367 5361 6.581712 ACTGTTGATTGGTTGCTTATTTGTT 58.418 32.000 0.00 0.00 0.00 2.83
2370 5489 5.921004 TGATTGGTTGCTTATTTGTTTGC 57.079 34.783 0.00 0.00 0.00 3.68
2446 5566 7.716560 GCAAAAGATTTGCCCTATCCATTAAAT 59.283 33.333 15.12 0.00 39.38 1.40
2452 5572 9.088987 GATTTGCCCTATCCATTAAATAAGGAA 57.911 33.333 0.00 0.00 34.62 3.36
2492 5612 7.471657 GTGTTTTACAAACACCCATAAAAGG 57.528 36.000 17.95 0.00 43.39 3.11
2507 5629 6.096705 CCCATAAAAGGCATGACAATTACTCA 59.903 38.462 0.00 0.00 0.00 3.41
2508 5630 7.363705 CCCATAAAAGGCATGACAATTACTCAA 60.364 37.037 0.00 0.00 0.00 3.02
2526 5648 4.339247 ACTCAACTGACAACAAATTCCCTG 59.661 41.667 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 7.115095 CAGAACTTGTTCGTGGTTTTACAAAAA 59.885 33.333 7.71 0.00 30.87 1.94
72 73 6.583050 CAGAACTTGTTCGTGGTTTTACAAAA 59.417 34.615 7.71 0.00 30.87 2.44
73 74 6.072618 TCAGAACTTGTTCGTGGTTTTACAAA 60.073 34.615 7.71 0.00 30.87 2.83
74 75 5.411977 TCAGAACTTGTTCGTGGTTTTACAA 59.588 36.000 7.71 0.00 0.00 2.41
75 76 4.936411 TCAGAACTTGTTCGTGGTTTTACA 59.064 37.500 7.71 0.00 0.00 2.41
76 77 5.292589 TCTCAGAACTTGTTCGTGGTTTTAC 59.707 40.000 7.71 0.00 0.00 2.01
77 78 5.421277 TCTCAGAACTTGTTCGTGGTTTTA 58.579 37.500 7.71 0.00 0.00 1.52
78 79 4.258543 TCTCAGAACTTGTTCGTGGTTTT 58.741 39.130 7.71 0.00 0.00 2.43
79 80 3.869065 TCTCAGAACTTGTTCGTGGTTT 58.131 40.909 7.71 0.00 0.00 3.27
80 81 3.536956 TCTCAGAACTTGTTCGTGGTT 57.463 42.857 7.71 0.00 0.00 3.67
81 82 3.536956 TTCTCAGAACTTGTTCGTGGT 57.463 42.857 7.71 0.00 0.00 4.16
82 83 4.119862 TCTTTCTCAGAACTTGTTCGTGG 58.880 43.478 7.71 3.09 0.00 4.94
83 84 5.718649 TTCTTTCTCAGAACTTGTTCGTG 57.281 39.130 7.71 7.08 36.51 4.35
84 85 6.737254 TTTTCTTTCTCAGAACTTGTTCGT 57.263 33.333 7.71 0.00 41.56 3.85
85 86 9.716507 TTATTTTTCTTTCTCAGAACTTGTTCG 57.283 29.630 7.71 4.09 41.56 3.95
188 189 8.600625 GTTCTTTTTCGGCTTTCTATTGTTTTT 58.399 29.630 0.00 0.00 0.00 1.94
189 190 7.223971 GGTTCTTTTTCGGCTTTCTATTGTTTT 59.776 33.333 0.00 0.00 0.00 2.43
190 191 6.700081 GGTTCTTTTTCGGCTTTCTATTGTTT 59.300 34.615 0.00 0.00 0.00 2.83
191 192 6.183360 TGGTTCTTTTTCGGCTTTCTATTGTT 60.183 34.615 0.00 0.00 0.00 2.83
192 193 5.300792 TGGTTCTTTTTCGGCTTTCTATTGT 59.699 36.000 0.00 0.00 0.00 2.71
193 194 5.768317 TGGTTCTTTTTCGGCTTTCTATTG 58.232 37.500 0.00 0.00 0.00 1.90
194 195 5.768164 TCTGGTTCTTTTTCGGCTTTCTATT 59.232 36.000 0.00 0.00 0.00 1.73
195 196 5.313712 TCTGGTTCTTTTTCGGCTTTCTAT 58.686 37.500 0.00 0.00 0.00 1.98
196 197 4.710324 TCTGGTTCTTTTTCGGCTTTCTA 58.290 39.130 0.00 0.00 0.00 2.10
197 198 3.551846 TCTGGTTCTTTTTCGGCTTTCT 58.448 40.909 0.00 0.00 0.00 2.52
198 199 3.982576 TCTGGTTCTTTTTCGGCTTTC 57.017 42.857 0.00 0.00 0.00 2.62
199 200 3.951680 TCTTCTGGTTCTTTTTCGGCTTT 59.048 39.130 0.00 0.00 0.00 3.51
200 201 3.551846 TCTTCTGGTTCTTTTTCGGCTT 58.448 40.909 0.00 0.00 0.00 4.35
201 202 3.208747 TCTTCTGGTTCTTTTTCGGCT 57.791 42.857 0.00 0.00 0.00 5.52
202 203 3.853676 GCTTCTTCTGGTTCTTTTTCGGC 60.854 47.826 0.00 0.00 0.00 5.54
203 204 3.607078 CGCTTCTTCTGGTTCTTTTTCGG 60.607 47.826 0.00 0.00 0.00 4.30
204 205 3.247648 TCGCTTCTTCTGGTTCTTTTTCG 59.752 43.478 0.00 0.00 0.00 3.46
205 206 4.813296 TCGCTTCTTCTGGTTCTTTTTC 57.187 40.909 0.00 0.00 0.00 2.29
206 207 5.763204 TGTATCGCTTCTTCTGGTTCTTTTT 59.237 36.000 0.00 0.00 0.00 1.94
207 208 5.305585 TGTATCGCTTCTTCTGGTTCTTTT 58.694 37.500 0.00 0.00 0.00 2.27
208 209 4.894784 TGTATCGCTTCTTCTGGTTCTTT 58.105 39.130 0.00 0.00 0.00 2.52
209 210 4.499183 CTGTATCGCTTCTTCTGGTTCTT 58.501 43.478 0.00 0.00 0.00 2.52
210 211 3.118956 CCTGTATCGCTTCTTCTGGTTCT 60.119 47.826 0.00 0.00 0.00 3.01
211 212 3.190874 CCTGTATCGCTTCTTCTGGTTC 58.809 50.000 0.00 0.00 0.00 3.62
212 213 2.678190 GCCTGTATCGCTTCTTCTGGTT 60.678 50.000 0.00 0.00 0.00 3.67
213 214 1.134670 GCCTGTATCGCTTCTTCTGGT 60.135 52.381 0.00 0.00 0.00 4.00
214 215 1.134699 TGCCTGTATCGCTTCTTCTGG 60.135 52.381 0.00 0.00 0.00 3.86
215 216 2.299993 TGCCTGTATCGCTTCTTCTG 57.700 50.000 0.00 0.00 0.00 3.02
216 217 3.334583 TTTGCCTGTATCGCTTCTTCT 57.665 42.857 0.00 0.00 0.00 2.85
217 218 4.419522 TTTTTGCCTGTATCGCTTCTTC 57.580 40.909 0.00 0.00 0.00 2.87
243 244 7.192148 GAACTTTCTAGAAGGTTCCTTGAAC 57.808 40.000 34.04 18.11 45.76 3.18
251 252 6.321435 CAGTTTTGGGAACTTTCTAGAAGGTT 59.679 38.462 27.44 27.44 42.23 3.50
252 253 5.828328 CAGTTTTGGGAACTTTCTAGAAGGT 59.172 40.000 14.09 14.09 31.58 3.50
253 254 5.241728 CCAGTTTTGGGAACTTTCTAGAAGG 59.758 44.000 12.73 12.73 41.05 3.46
254 255 6.319141 CCAGTTTTGGGAACTTTCTAGAAG 57.681 41.667 5.12 3.14 41.05 2.85
269 270 2.507339 ATTGCGTCCAACCAGTTTTG 57.493 45.000 0.00 0.00 32.95 2.44
270 271 3.572255 ACATATTGCGTCCAACCAGTTTT 59.428 39.130 0.00 0.00 32.95 2.43
271 272 3.153919 ACATATTGCGTCCAACCAGTTT 58.846 40.909 0.00 0.00 32.95 2.66
272 273 2.790433 ACATATTGCGTCCAACCAGTT 58.210 42.857 0.00 0.00 32.95 3.16
273 274 2.489938 ACATATTGCGTCCAACCAGT 57.510 45.000 0.00 0.00 32.95 4.00
274 275 5.758296 ACTAATACATATTGCGTCCAACCAG 59.242 40.000 0.00 0.00 32.95 4.00
275 276 5.525745 CACTAATACATATTGCGTCCAACCA 59.474 40.000 0.00 0.00 32.95 3.67
276 277 5.049680 CCACTAATACATATTGCGTCCAACC 60.050 44.000 0.00 0.00 32.95 3.77
277 278 5.049680 CCCACTAATACATATTGCGTCCAAC 60.050 44.000 0.00 0.00 32.95 3.77
278 279 5.060506 CCCACTAATACATATTGCGTCCAA 58.939 41.667 0.00 0.00 35.01 3.53
279 280 4.637276 CCCACTAATACATATTGCGTCCA 58.363 43.478 0.00 0.00 0.00 4.02
280 281 3.435671 GCCCACTAATACATATTGCGTCC 59.564 47.826 0.00 0.00 0.00 4.79
281 282 3.122948 CGCCCACTAATACATATTGCGTC 59.877 47.826 0.00 0.00 32.18 5.19
282 283 3.064207 CGCCCACTAATACATATTGCGT 58.936 45.455 0.00 0.00 32.18 5.24
283 284 2.415168 CCGCCCACTAATACATATTGCG 59.585 50.000 0.00 0.00 34.75 4.85
284 285 2.161609 GCCGCCCACTAATACATATTGC 59.838 50.000 0.00 0.00 0.00 3.56
285 286 2.747446 GGCCGCCCACTAATACATATTG 59.253 50.000 0.00 0.00 0.00 1.90
286 287 2.290705 GGGCCGCCCACTAATACATATT 60.291 50.000 24.62 0.00 44.65 1.28
287 288 1.280998 GGGCCGCCCACTAATACATAT 59.719 52.381 24.62 0.00 44.65 1.78
288 289 0.688487 GGGCCGCCCACTAATACATA 59.312 55.000 24.62 0.00 44.65 2.29
289 290 1.454539 GGGCCGCCCACTAATACAT 59.545 57.895 24.62 0.00 44.65 2.29
290 291 2.912714 GGGCCGCCCACTAATACA 59.087 61.111 24.62 0.00 44.65 2.29
303 304 3.056328 GAGCGACAAACCTGGGCC 61.056 66.667 0.00 0.00 0.00 5.80
304 305 3.423154 CGAGCGACAAACCTGGGC 61.423 66.667 0.00 0.00 0.00 5.36
305 306 3.423154 GCGAGCGACAAACCTGGG 61.423 66.667 0.00 0.00 0.00 4.45
306 307 2.357517 AGCGAGCGACAAACCTGG 60.358 61.111 0.00 0.00 0.00 4.45
307 308 2.856032 CAGCGAGCGACAAACCTG 59.144 61.111 0.00 0.00 0.00 4.00
308 309 3.044305 GCAGCGAGCGACAAACCT 61.044 61.111 0.00 0.00 0.00 3.50
338 339 0.872388 CGGCAAAATATCGGGCTACC 59.128 55.000 0.00 0.00 0.00 3.18
339 340 0.237498 GCGGCAAAATATCGGGCTAC 59.763 55.000 0.00 0.00 0.00 3.58
340 341 0.179043 TGCGGCAAAATATCGGGCTA 60.179 50.000 0.00 0.00 0.00 3.93
341 342 1.447317 CTGCGGCAAAATATCGGGCT 61.447 55.000 3.44 0.00 0.00 5.19
342 343 1.008538 CTGCGGCAAAATATCGGGC 60.009 57.895 3.44 0.00 0.00 6.13
343 344 1.008538 GCTGCGGCAAAATATCGGG 60.009 57.895 14.08 0.00 38.54 5.14
344 345 1.369209 CGCTGCGGCAAAATATCGG 60.369 57.895 19.50 0.00 38.60 4.18
345 346 0.383491 CTCGCTGCGGCAAAATATCG 60.383 55.000 23.03 0.00 38.60 2.92
346 347 0.658536 GCTCGCTGCGGCAAAATATC 60.659 55.000 23.03 0.00 38.60 1.63
347 348 1.356624 GCTCGCTGCGGCAAAATAT 59.643 52.632 23.03 0.00 38.60 1.28
348 349 2.791256 GCTCGCTGCGGCAAAATA 59.209 55.556 23.03 0.00 38.60 1.40
357 358 3.696426 CTATTCGCCGCTCGCTGC 61.696 66.667 0.00 0.00 38.27 5.25
358 359 3.032609 CCTATTCGCCGCTCGCTG 61.033 66.667 0.00 0.00 38.27 5.18
359 360 4.286320 CCCTATTCGCCGCTCGCT 62.286 66.667 0.00 0.00 38.27 4.93
360 361 3.575351 ATCCCTATTCGCCGCTCGC 62.575 63.158 0.00 0.00 38.27 5.03
361 362 0.600255 AAATCCCTATTCGCCGCTCG 60.600 55.000 0.00 0.00 40.15 5.03
362 363 1.149148 GAAATCCCTATTCGCCGCTC 58.851 55.000 0.00 0.00 0.00 5.03
363 364 0.250338 GGAAATCCCTATTCGCCGCT 60.250 55.000 0.00 0.00 0.00 5.52
364 365 2.244946 GGAAATCCCTATTCGCCGC 58.755 57.895 0.00 0.00 0.00 6.53
375 376 1.025041 GGATTGCACGAGGGAAATCC 58.975 55.000 9.20 9.20 40.84 3.01
376 377 1.672881 CTGGATTGCACGAGGGAAATC 59.327 52.381 0.00 0.00 0.00 2.17
377 378 1.004745 ACTGGATTGCACGAGGGAAAT 59.995 47.619 0.00 0.00 0.00 2.17
378 379 0.400213 ACTGGATTGCACGAGGGAAA 59.600 50.000 0.00 0.00 0.00 3.13
379 380 0.036388 GACTGGATTGCACGAGGGAA 60.036 55.000 0.00 0.00 0.00 3.97
380 381 0.904865 AGACTGGATTGCACGAGGGA 60.905 55.000 0.00 0.00 0.00 4.20
381 382 0.824109 TAGACTGGATTGCACGAGGG 59.176 55.000 0.00 0.00 0.00 4.30
382 383 2.898729 ATAGACTGGATTGCACGAGG 57.101 50.000 0.00 0.00 0.00 4.63
383 384 4.837896 TCTATAGACTGGATTGCACGAG 57.162 45.455 0.00 0.00 0.00 4.18
384 385 5.592104 TTTCTATAGACTGGATTGCACGA 57.408 39.130 0.67 0.00 0.00 4.35
385 386 6.662414 TTTTTCTATAGACTGGATTGCACG 57.338 37.500 0.67 0.00 0.00 5.34
417 418 3.202829 ACGGCAGGTACTTGAGAAAAA 57.797 42.857 9.51 0.00 34.60 1.94
418 419 2.875933 CAACGGCAGGTACTTGAGAAAA 59.124 45.455 9.51 0.00 34.60 2.29
419 420 2.158871 ACAACGGCAGGTACTTGAGAAA 60.159 45.455 9.51 0.00 34.60 2.52
420 421 1.414919 ACAACGGCAGGTACTTGAGAA 59.585 47.619 9.51 0.00 34.60 2.87
421 422 1.045407 ACAACGGCAGGTACTTGAGA 58.955 50.000 9.51 0.00 34.60 3.27
422 423 2.288579 TGTACAACGGCAGGTACTTGAG 60.289 50.000 9.51 4.35 40.34 3.02
423 424 1.687660 TGTACAACGGCAGGTACTTGA 59.312 47.619 9.51 0.00 40.34 3.02
424 425 2.066262 CTGTACAACGGCAGGTACTTG 58.934 52.381 0.00 0.00 40.34 3.16
425 426 1.001633 CCTGTACAACGGCAGGTACTT 59.998 52.381 0.00 0.00 45.28 2.24
426 427 0.606604 CCTGTACAACGGCAGGTACT 59.393 55.000 0.00 0.00 45.28 2.73
427 428 3.132863 CCTGTACAACGGCAGGTAC 57.867 57.895 0.00 0.00 45.28 3.34
431 432 1.895020 TAGGCCCTGTACAACGGCAG 61.895 60.000 26.70 3.66 44.90 4.85
432 433 1.481901 TTAGGCCCTGTACAACGGCA 61.482 55.000 26.70 11.24 44.90 5.69
433 434 0.743345 CTTAGGCCCTGTACAACGGC 60.743 60.000 20.59 20.59 42.23 5.68
434 435 0.107848 CCTTAGGCCCTGTACAACGG 60.108 60.000 0.00 0.20 0.00 4.44
435 436 0.743345 GCCTTAGGCCCTGTACAACG 60.743 60.000 13.12 0.00 44.06 4.10
436 437 3.170360 GCCTTAGGCCCTGTACAAC 57.830 57.895 13.12 0.00 44.06 3.32
447 448 3.418684 AACACTGTACAAGGCCTTAGG 57.581 47.619 20.00 9.74 0.00 2.69
448 449 4.020485 ACCTAACACTGTACAAGGCCTTAG 60.020 45.833 20.00 14.70 0.00 2.18
449 450 3.905591 ACCTAACACTGTACAAGGCCTTA 59.094 43.478 20.00 0.00 0.00 2.69
450 451 2.709397 ACCTAACACTGTACAAGGCCTT 59.291 45.455 13.78 13.78 0.00 4.35
451 452 2.038557 CACCTAACACTGTACAAGGCCT 59.961 50.000 0.00 0.00 0.00 5.19
452 453 2.423577 CACCTAACACTGTACAAGGCC 58.576 52.381 9.96 0.00 0.00 5.19
453 454 1.804748 GCACCTAACACTGTACAAGGC 59.195 52.381 9.96 0.00 0.00 4.35
454 455 3.402628 AGCACCTAACACTGTACAAGG 57.597 47.619 8.69 8.69 0.00 3.61
455 456 5.779922 TCTAAGCACCTAACACTGTACAAG 58.220 41.667 0.00 0.00 0.00 3.16
456 457 5.794726 TCTAAGCACCTAACACTGTACAA 57.205 39.130 0.00 0.00 0.00 2.41
457 458 5.794726 TTCTAAGCACCTAACACTGTACA 57.205 39.130 0.00 0.00 0.00 2.90
458 459 7.486802 TTTTTCTAAGCACCTAACACTGTAC 57.513 36.000 0.00 0.00 0.00 2.90
459 460 9.781633 TTATTTTTCTAAGCACCTAACACTGTA 57.218 29.630 0.00 0.00 0.00 2.74
460 461 8.685838 TTATTTTTCTAAGCACCTAACACTGT 57.314 30.769 0.00 0.00 0.00 3.55
465 466 9.788960 CCTGATTTATTTTTCTAAGCACCTAAC 57.211 33.333 0.00 0.00 0.00 2.34
466 467 9.528489 ACCTGATTTATTTTTCTAAGCACCTAA 57.472 29.630 0.00 0.00 0.00 2.69
467 468 9.528489 AACCTGATTTATTTTTCTAAGCACCTA 57.472 29.630 0.00 0.00 0.00 3.08
513 514 5.508200 AGGCGTCTCTTCTGTAGAAATAG 57.492 43.478 0.00 0.00 33.07 1.73
519 520 5.688176 GCTTATTTAGGCGTCTCTTCTGTAG 59.312 44.000 0.00 0.00 0.00 2.74
522 523 4.433615 TGCTTATTTAGGCGTCTCTTCTG 58.566 43.478 0.00 0.00 0.00 3.02
524 525 5.583969 GATGCTTATTTAGGCGTCTCTTC 57.416 43.478 0.00 0.00 40.09 2.87
548 549 3.057806 ACCGGTGCTTATTTGTACAAAGC 60.058 43.478 24.22 21.65 44.63 3.51
549 550 4.472286 CACCGGTGCTTATTTGTACAAAG 58.528 43.478 24.02 13.29 33.32 2.77
550 551 4.491234 CACCGGTGCTTATTTGTACAAA 57.509 40.909 24.02 22.58 34.46 2.83
597 606 3.118038 AGGTGCTTAAGACAGGTGTTTGA 60.118 43.478 6.67 0.00 0.00 2.69
598 607 3.214328 AGGTGCTTAAGACAGGTGTTTG 58.786 45.455 6.67 0.00 0.00 2.93
607 616 3.923017 ACAATGCAAGGTGCTTAAGAC 57.077 42.857 6.67 1.68 45.31 3.01
610 619 5.163561 GCCTTATACAATGCAAGGTGCTTAA 60.164 40.000 9.61 0.00 45.31 1.85
620 629 5.299279 GCTTTCTTAGGCCTTATACAATGCA 59.701 40.000 12.58 0.00 0.00 3.96
714 724 6.698380 TCTAATGGGAGCGACCTAATTATTC 58.302 40.000 1.45 0.00 38.98 1.75
717 727 5.510861 GCTTCTAATGGGAGCGACCTAATTA 60.511 44.000 1.45 6.45 38.98 1.40
801 907 4.541482 GCATGCATGTGGACCGCG 62.541 66.667 26.79 0.00 0.00 6.46
831 945 0.958382 GCTGTGTGGGTGCCGAATTA 60.958 55.000 0.00 0.00 0.00 1.40
1081 1201 4.544689 CGCGTCCAGGAGCTCGAG 62.545 72.222 8.45 8.45 0.00 4.04
1112 1241 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1149 1278 4.785453 GGGAAGCCGAGCTGGTGG 62.785 72.222 0.00 0.00 39.62 4.61
1220 1349 4.838152 CCTGGTGCGGGTGGATCG 62.838 72.222 0.00 0.00 0.00 3.69
1376 1505 0.664466 GCCGTTGAAGAAGCCAAAGC 60.664 55.000 0.00 0.00 40.32 3.51
1432 1561 1.889530 CTCCCTTCGTCCCACTCCAC 61.890 65.000 0.00 0.00 0.00 4.02
1598 1738 5.317808 AGTCTCTCACACACTTCTAGCTAA 58.682 41.667 0.00 0.00 0.00 3.09
1599 1739 4.912586 AGTCTCTCACACACTTCTAGCTA 58.087 43.478 0.00 0.00 0.00 3.32
1637 1777 1.733526 AAAAAGGGCTCACACGCAC 59.266 52.632 0.00 0.00 0.00 5.34
1638 1778 4.251246 AAAAAGGGCTCACACGCA 57.749 50.000 0.00 0.00 0.00 5.24
1654 1794 8.639761 ACACACTTCTACTCTTCTAGCTAAAAA 58.360 33.333 0.00 0.00 0.00 1.94
1655 1795 8.082852 CACACACTTCTACTCTTCTAGCTAAAA 58.917 37.037 0.00 0.00 0.00 1.52
1656 1796 7.230913 ACACACACTTCTACTCTTCTAGCTAAA 59.769 37.037 0.00 0.00 0.00 1.85
1657 1797 6.715718 ACACACACTTCTACTCTTCTAGCTAA 59.284 38.462 0.00 0.00 0.00 3.09
1658 1798 6.149640 CACACACACTTCTACTCTTCTAGCTA 59.850 42.308 0.00 0.00 0.00 3.32
1659 1799 5.048364 CACACACACTTCTACTCTTCTAGCT 60.048 44.000 0.00 0.00 0.00 3.32
1660 1800 5.048643 TCACACACACTTCTACTCTTCTAGC 60.049 44.000 0.00 0.00 0.00 3.42
1661 1801 6.561737 TCACACACACTTCTACTCTTCTAG 57.438 41.667 0.00 0.00 0.00 2.43
1662 1802 5.048643 GCTCACACACACTTCTACTCTTCTA 60.049 44.000 0.00 0.00 0.00 2.10
1663 1803 4.261825 GCTCACACACACTTCTACTCTTCT 60.262 45.833 0.00 0.00 0.00 2.85
1664 1804 3.984633 GCTCACACACACTTCTACTCTTC 59.015 47.826 0.00 0.00 0.00 2.87
1665 1805 3.243907 GGCTCACACACACTTCTACTCTT 60.244 47.826 0.00 0.00 0.00 2.85
1666 1806 2.297597 GGCTCACACACACTTCTACTCT 59.702 50.000 0.00 0.00 0.00 3.24
1667 1807 2.297597 AGGCTCACACACACTTCTACTC 59.702 50.000 0.00 0.00 0.00 2.59
1668 1808 2.320781 AGGCTCACACACACTTCTACT 58.679 47.619 0.00 0.00 0.00 2.57
1669 1809 2.821991 AGGCTCACACACACTTCTAC 57.178 50.000 0.00 0.00 0.00 2.59
1670 1810 3.118408 ACAAAGGCTCACACACACTTCTA 60.118 43.478 0.00 0.00 0.00 2.10
1671 1811 2.292267 CAAAGGCTCACACACACTTCT 58.708 47.619 0.00 0.00 0.00 2.85
1672 1812 2.017049 ACAAAGGCTCACACACACTTC 58.983 47.619 0.00 0.00 0.00 3.01
1673 1813 1.745087 CACAAAGGCTCACACACACTT 59.255 47.619 0.00 0.00 0.00 3.16
1674 1814 1.382522 CACAAAGGCTCACACACACT 58.617 50.000 0.00 0.00 0.00 3.55
1675 1815 0.248621 GCACAAAGGCTCACACACAC 60.249 55.000 0.00 0.00 0.00 3.82
1676 1816 0.679321 TGCACAAAGGCTCACACACA 60.679 50.000 0.00 0.00 34.04 3.72
1677 1817 0.455410 TTGCACAAAGGCTCACACAC 59.545 50.000 0.00 0.00 34.04 3.82
1678 1818 1.180907 TTTGCACAAAGGCTCACACA 58.819 45.000 0.00 0.00 34.04 3.72
1679 1819 2.195922 CTTTTGCACAAAGGCTCACAC 58.804 47.619 11.34 0.00 34.04 3.82
1680 1820 1.824230 ACTTTTGCACAAAGGCTCACA 59.176 42.857 18.96 0.00 31.48 3.58
1681 1821 2.195922 CACTTTTGCACAAAGGCTCAC 58.804 47.619 18.96 0.00 31.48 3.51
1682 1822 1.824230 ACACTTTTGCACAAAGGCTCA 59.176 42.857 18.96 0.00 31.48 4.26
1683 1823 2.195922 CACACTTTTGCACAAAGGCTC 58.804 47.619 18.96 0.00 31.48 4.70
1684 1824 1.550072 ACACACTTTTGCACAAAGGCT 59.450 42.857 18.96 0.00 31.48 4.58
1685 1825 1.660104 CACACACTTTTGCACAAAGGC 59.340 47.619 18.96 0.00 31.48 4.35
1686 1826 3.181397 CTCACACACTTTTGCACAAAGG 58.819 45.455 18.96 3.92 34.11 3.11
1687 1827 2.599973 GCTCACACACTTTTGCACAAAG 59.400 45.455 15.42 15.42 0.00 2.77
1688 1828 2.605030 GCTCACACACTTTTGCACAAA 58.395 42.857 0.00 0.00 0.00 2.83
1689 1829 1.135141 GGCTCACACACTTTTGCACAA 60.135 47.619 0.00 0.00 0.00 3.33
1690 1830 0.455410 GGCTCACACACTTTTGCACA 59.545 50.000 0.00 0.00 0.00 4.57
1691 1831 0.740737 AGGCTCACACACTTTTGCAC 59.259 50.000 0.00 0.00 0.00 4.57
1692 1832 1.473258 AAGGCTCACACACTTTTGCA 58.527 45.000 0.00 0.00 0.00 4.08
1693 1833 2.584492 AAAGGCTCACACACTTTTGC 57.416 45.000 0.00 0.00 30.81 3.68
1716 1902 3.023119 TCACACACACTTTTGGCTCAAT 58.977 40.909 0.00 0.00 0.00 2.57
1792 1978 0.457166 CATGACATGCAAAGCCCACG 60.457 55.000 1.71 0.00 0.00 4.94
1826 2012 3.758554 AGCAAATTCAGGTCGTGCTAAAT 59.241 39.130 0.00 0.00 43.51 1.40
1863 2606 1.213296 TTCCCAGATAACCTGAGGGC 58.787 55.000 2.38 0.00 45.78 5.19
1870 2613 2.099098 CGCCATTGTTTCCCAGATAACC 59.901 50.000 0.00 0.00 0.00 2.85
1879 2622 0.109597 CTCTGCACGCCATTGTTTCC 60.110 55.000 0.00 0.00 0.00 3.13
1960 2703 0.610174 TTGCCTTGCTCGATGTCTCT 59.390 50.000 0.00 0.00 0.00 3.10
1961 2704 0.723981 GTTGCCTTGCTCGATGTCTC 59.276 55.000 0.00 0.00 0.00 3.36
2041 2784 9.140286 GCTACCTTGACCTTCAAAAATAAATTC 57.860 33.333 0.00 0.00 35.73 2.17
2060 2803 4.826274 TGAGCTTCTACATTGCTACCTT 57.174 40.909 0.00 0.00 37.16 3.50
2116 2859 1.259609 CCAAACCACACATGATGCCT 58.740 50.000 0.00 0.00 0.00 4.75
2135 2878 1.062002 CGTTATCGTCATGTGGTTGGC 59.938 52.381 0.00 0.00 0.00 4.52
2190 4171 3.512416 TTTCCTAGGGGTAAGGCCTAA 57.488 47.619 5.16 0.00 37.43 2.69
2206 4187 8.297426 CAGAACTAAATTAGTCCACCTTTTTCC 58.703 37.037 6.09 0.00 38.26 3.13
2207 4188 7.808381 GCAGAACTAAATTAGTCCACCTTTTTC 59.192 37.037 6.09 0.00 38.26 2.29
2212 4193 5.763876 AGCAGAACTAAATTAGTCCACCT 57.236 39.130 6.09 0.00 38.26 4.00
2213 4194 5.392057 GCAAGCAGAACTAAATTAGTCCACC 60.392 44.000 6.09 0.00 38.26 4.61
2240 5225 6.700520 GGGAGTATTAAATAACTCTGACACGG 59.299 42.308 12.84 0.00 41.53 4.94
2287 5273 9.856162 ACTCCCTCTGTACTTTATTTGTTTAAA 57.144 29.630 0.00 0.00 0.00 1.52
2291 5277 8.431910 TCTACTCCCTCTGTACTTTATTTGTT 57.568 34.615 0.00 0.00 0.00 2.83
2293 5279 9.319143 CAATCTACTCCCTCTGTACTTTATTTG 57.681 37.037 0.00 0.00 0.00 2.32
2294 5280 7.988028 GCAATCTACTCCCTCTGTACTTTATTT 59.012 37.037 0.00 0.00 0.00 1.40
2296 5282 6.841755 AGCAATCTACTCCCTCTGTACTTTAT 59.158 38.462 0.00 0.00 0.00 1.40
2299 5285 4.615513 AGCAATCTACTCCCTCTGTACTT 58.384 43.478 0.00 0.00 0.00 2.24
2301 5287 6.658188 ATAAGCAATCTACTCCCTCTGTAC 57.342 41.667 0.00 0.00 0.00 2.90
2308 5302 9.160496 CATTTCAGATATAAGCAATCTACTCCC 57.840 37.037 0.00 0.00 32.40 4.30
2351 5345 4.764172 ACTGCAAACAAATAAGCAACCAA 58.236 34.783 0.00 0.00 36.44 3.67
2367 5361 6.449635 AAATAACAGAACTGTCAACTGCAA 57.550 33.333 7.93 0.00 44.13 4.08
2370 5489 7.645340 CCAAGAAAATAACAGAACTGTCAACTG 59.355 37.037 7.93 0.00 44.13 3.16
2469 5589 6.049790 GCCTTTTATGGGTGTTTGTAAAACA 58.950 36.000 1.52 1.52 0.00 2.83
2476 5596 4.244862 GTCATGCCTTTTATGGGTGTTTG 58.755 43.478 0.00 0.00 0.00 2.93
2491 5611 4.455533 TGTCAGTTGAGTAATTGTCATGCC 59.544 41.667 0.00 0.00 0.00 4.40
2492 5612 5.611796 TGTCAGTTGAGTAATTGTCATGC 57.388 39.130 0.00 0.00 0.00 4.06
2507 5629 3.642141 ACCAGGGAATTTGTTGTCAGTT 58.358 40.909 0.00 0.00 0.00 3.16
2508 5630 3.312736 ACCAGGGAATTTGTTGTCAGT 57.687 42.857 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.