Multiple sequence alignment - TraesCS2D01G256100

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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 TraesCS2D01G256100 chr2D 100.000 2635 0 0 1 2635 309165844 309168478 0.000000e+00 4867.0
1 TraesCS2D01G256100 chr2D 96.897 709 22 0 1927 2635 75666423 75665715 0.000000e+00 1188.0
2 TraesCS2D01G256100 chr2A 94.122 1361 67 10 497 1848 430482886 430481530 0.000000e+00 2058.0
3 TraesCS2D01G256100 chr2B 94.417 1236 45 12 667 1902 359038303 359037092 0.000000e+00 1879.0
4 TraesCS2D01G256100 chr2B 95.455 88 4 0 584 671 359039857 359039770 9.830000e-30 141.0
5 TraesCS2D01G256100 chr2B 74.658 292 57 13 133 417 518762649 518762930 2.140000e-21 113.0
6 TraesCS2D01G256100 chr2B 94.595 37 1 1 467 503 763844309 763844274 3.660000e-04 56.5
7 TraesCS2D01G256100 chr2B 100.000 29 0 0 530 558 359039883 359039855 1.000000e-03 54.7
8 TraesCS2D01G256100 chr5D 97.743 709 16 0 1927 2635 277645464 277644756 0.000000e+00 1221.0
9 TraesCS2D01G256100 chr5D 87.364 459 54 2 1 456 507868353 507868810 8.360000e-145 523.0
10 TraesCS2D01G256100 chr5D 87.640 445 52 1 1 442 507873912 507874356 5.030000e-142 514.0
11 TraesCS2D01G256100 chr5D 96.970 33 0 1 467 499 402189346 402189377 1.000000e-03 54.7
12 TraesCS2D01G256100 chr7D 97.038 709 21 0 1927 2635 596955523 596954815 0.000000e+00 1194.0
13 TraesCS2D01G256100 chr7D 94.930 710 35 1 1927 2635 402332401 402331692 0.000000e+00 1110.0
14 TraesCS2D01G256100 chr6D 97.167 706 20 0 1927 2632 52532466 52533171 0.000000e+00 1194.0
15 TraesCS2D01G256100 chr6D 94.093 711 40 2 1927 2635 438324414 438325124 0.000000e+00 1079.0
16 TraesCS2D01G256100 chr6D 87.104 442 56 1 1 442 156441096 156441536 1.410000e-137 499.0
17 TraesCS2D01G256100 chr6D 84.897 437 54 9 1 432 437961449 437961020 5.210000e-117 431.0
18 TraesCS2D01G256100 chr3D 97.853 559 12 0 1927 2485 520368114 520367556 0.000000e+00 966.0
19 TraesCS2D01G256100 chr6B 86.448 701 90 5 1931 2629 299956981 299956284 0.000000e+00 763.0
20 TraesCS2D01G256100 chr6B 86.087 460 58 4 1 456 695148207 695148664 8.480000e-135 490.0
21 TraesCS2D01G256100 chr6B 82.892 415 60 5 4 416 57005891 57005486 1.930000e-96 363.0
22 TraesCS2D01G256100 chr6B 72.995 374 84 16 54 416 98595796 98596163 5.960000e-22 115.0
23 TraesCS2D01G256100 chr6A 86.099 705 95 3 1927 2629 605861784 605862487 0.000000e+00 756.0
24 TraesCS2D01G256100 chr1D 88.063 444 48 3 1 442 418099517 418099957 3.010000e-144 521.0
25 TraesCS2D01G256100 chr1D 86.758 438 54 2 1 438 403231993 403232426 3.940000e-133 484.0
26 TraesCS2D01G256100 chr4D 86.623 456 61 0 1 456 432418374 432417919 3.030000e-139 505.0
27 TraesCS2D01G256100 chr7B 85.746 456 54 6 1 456 61629746 61629302 3.070000e-129 472.0
28 TraesCS2D01G256100 chr3B 84.728 478 60 8 9 475 739212823 739213298 1.430000e-127 466.0
29 TraesCS2D01G256100 chr3B 100.000 31 0 0 467 497 746988617 746988587 1.020000e-04 58.4
30 TraesCS2D01G256100 chr1A 76.327 245 53 5 177 418 458917364 458917122 2.750000e-25 126.0
31 TraesCS2D01G256100 chr5A 96.970 33 0 1 467 499 599374980 599375011 1.000000e-03 54.7


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 TraesCS2D01G256100 chr2D 309165844 309168478 2634 False 4867.000000 4867 100.000 1 2635 1 chr2D.!!$F1 2634
1 TraesCS2D01G256100 chr2D 75665715 75666423 708 True 1188.000000 1188 96.897 1927 2635 1 chr2D.!!$R1 708
2 TraesCS2D01G256100 chr2A 430481530 430482886 1356 True 2058.000000 2058 94.122 497 1848 1 chr2A.!!$R1 1351
3 TraesCS2D01G256100 chr2B 359037092 359039883 2791 True 691.566667 1879 96.624 530 1902 3 chr2B.!!$R2 1372
4 TraesCS2D01G256100 chr5D 277644756 277645464 708 True 1221.000000 1221 97.743 1927 2635 1 chr5D.!!$R1 708
5 TraesCS2D01G256100 chr7D 596954815 596955523 708 True 1194.000000 1194 97.038 1927 2635 1 chr7D.!!$R2 708
6 TraesCS2D01G256100 chr7D 402331692 402332401 709 True 1110.000000 1110 94.930 1927 2635 1 chr7D.!!$R1 708
7 TraesCS2D01G256100 chr6D 52532466 52533171 705 False 1194.000000 1194 97.167 1927 2632 1 chr6D.!!$F1 705
8 TraesCS2D01G256100 chr6D 438324414 438325124 710 False 1079.000000 1079 94.093 1927 2635 1 chr6D.!!$F3 708
9 TraesCS2D01G256100 chr3D 520367556 520368114 558 True 966.000000 966 97.853 1927 2485 1 chr3D.!!$R1 558
10 TraesCS2D01G256100 chr6B 299956284 299956981 697 True 763.000000 763 86.448 1931 2629 1 chr6B.!!$R2 698
11 TraesCS2D01G256100 chr6A 605861784 605862487 703 False 756.000000 756 86.099 1927 2629 1 chr6A.!!$F1 702

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
106 107 0.033228 TTTGTGGCGGCATGAAAAGG 59.967 50.0 17.19 0.0 0.0 3.11 F
388 389 0.036765 TTCGGACCGCATGCTAAACT 60.037 50.0 17.13 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1039 2514 0.035458 AGGAAGAACAGAGGCAACGG 59.965 55.0 0.00 0.0 46.39 4.44 R
2132 3617 0.530650 CGGGTGGAAGATGTCATCGG 60.531 60.0 7.18 0.0 0.00 4.18 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
24 25 3.443045 CGCCGCATTTGGGAGCTT 61.443 61.111 0.00 0.00 0.00 3.74
25 26 2.491621 GCCGCATTTGGGAGCTTC 59.508 61.111 0.00 0.00 0.00 3.86
26 27 2.793946 CCGCATTTGGGAGCTTCG 59.206 61.111 0.00 0.00 0.00 3.79
27 28 1.745115 CCGCATTTGGGAGCTTCGA 60.745 57.895 0.00 0.00 0.00 3.71
28 29 1.709147 CCGCATTTGGGAGCTTCGAG 61.709 60.000 0.00 0.00 0.00 4.04
29 30 0.740868 CGCATTTGGGAGCTTCGAGA 60.741 55.000 0.00 0.00 0.00 4.04
30 31 1.012841 GCATTTGGGAGCTTCGAGAG 58.987 55.000 0.00 0.00 0.00 3.20
31 32 1.661341 CATTTGGGAGCTTCGAGAGG 58.339 55.000 0.00 0.00 0.00 3.69
32 33 0.543749 ATTTGGGAGCTTCGAGAGGG 59.456 55.000 0.00 0.00 0.00 4.30
33 34 1.553690 TTTGGGAGCTTCGAGAGGGG 61.554 60.000 0.00 0.00 0.00 4.79
34 35 3.157949 GGGAGCTTCGAGAGGGGG 61.158 72.222 0.00 0.00 0.00 5.40
92 93 3.411351 CCGCCGAGGTCGTTTGTG 61.411 66.667 0.00 0.00 37.74 3.33
93 94 3.411351 CGCCGAGGTCGTTTGTGG 61.411 66.667 0.00 0.00 37.74 4.17
94 95 3.723348 GCCGAGGTCGTTTGTGGC 61.723 66.667 0.00 0.00 37.74 5.01
95 96 3.411351 CCGAGGTCGTTTGTGGCG 61.411 66.667 0.00 0.00 37.74 5.69
96 97 3.411351 CGAGGTCGTTTGTGGCGG 61.411 66.667 0.00 0.00 34.11 6.13
97 98 3.723348 GAGGTCGTTTGTGGCGGC 61.723 66.667 0.00 0.00 0.00 6.53
98 99 4.555709 AGGTCGTTTGTGGCGGCA 62.556 61.111 7.97 7.97 35.44 5.69
99 100 3.361977 GGTCGTTTGTGGCGGCAT 61.362 61.111 17.19 0.00 35.44 4.40
100 101 2.126888 GTCGTTTGTGGCGGCATG 60.127 61.111 17.19 3.30 33.75 4.06
101 102 2.281139 TCGTTTGTGGCGGCATGA 60.281 55.556 17.19 3.70 0.00 3.07
102 103 1.894282 TCGTTTGTGGCGGCATGAA 60.894 52.632 17.19 10.50 0.00 2.57
103 104 1.007964 CGTTTGTGGCGGCATGAAA 60.008 52.632 17.19 14.63 0.00 2.69
104 105 0.596083 CGTTTGTGGCGGCATGAAAA 60.596 50.000 17.19 13.67 0.00 2.29
105 106 1.139163 GTTTGTGGCGGCATGAAAAG 58.861 50.000 17.19 0.00 0.00 2.27
106 107 0.033228 TTTGTGGCGGCATGAAAAGG 59.967 50.000 17.19 0.00 0.00 3.11
107 108 2.125952 GTGGCGGCATGAAAAGGC 60.126 61.111 17.19 0.00 0.00 4.35
108 109 3.381136 TGGCGGCATGAAAAGGCC 61.381 61.111 7.97 0.00 46.80 5.19
131 132 3.197790 CGATGCCGGTGCTTGGAG 61.198 66.667 1.90 0.00 38.71 3.86
132 133 2.825836 GATGCCGGTGCTTGGAGG 60.826 66.667 1.90 0.00 38.71 4.30
133 134 3.329542 GATGCCGGTGCTTGGAGGA 62.330 63.158 1.90 0.00 38.71 3.71
134 135 3.335356 ATGCCGGTGCTTGGAGGAG 62.335 63.158 1.90 0.00 38.71 3.69
151 152 4.821589 GCACCGGCGGAGGAGAAG 62.822 72.222 35.78 13.30 34.73 2.85
152 153 4.821589 CACCGGCGGAGGAGAAGC 62.822 72.222 35.78 0.00 34.73 3.86
157 158 3.896479 GCGGAGGAGAAGCCAAAG 58.104 61.111 0.00 0.00 40.02 2.77
158 159 2.402572 GCGGAGGAGAAGCCAAAGC 61.403 63.158 0.00 0.00 40.02 3.51
169 170 4.467084 CCAAAGCTCCCCGCGCTA 62.467 66.667 5.56 0.00 45.59 4.26
170 171 2.892425 CAAAGCTCCCCGCGCTAG 60.892 66.667 5.56 0.00 45.59 3.42
171 172 4.162690 AAAGCTCCCCGCGCTAGG 62.163 66.667 5.56 5.96 45.59 3.02
208 209 3.834799 GAGGGGTCGCGGGTGTAG 61.835 72.222 6.13 0.00 0.00 2.74
211 212 3.384532 GGGTCGCGGGTGTAGGAA 61.385 66.667 6.13 0.00 0.00 3.36
212 213 2.183555 GGTCGCGGGTGTAGGAAG 59.816 66.667 6.13 0.00 0.00 3.46
213 214 2.183555 GTCGCGGGTGTAGGAAGG 59.816 66.667 6.13 0.00 0.00 3.46
214 215 3.072468 TCGCGGGTGTAGGAAGGG 61.072 66.667 6.13 0.00 0.00 3.95
215 216 4.157120 CGCGGGTGTAGGAAGGGG 62.157 72.222 0.00 0.00 0.00 4.79
216 217 3.007323 GCGGGTGTAGGAAGGGGT 61.007 66.667 0.00 0.00 0.00 4.95
217 218 2.987125 CGGGTGTAGGAAGGGGTG 59.013 66.667 0.00 0.00 0.00 4.61
218 219 1.611261 CGGGTGTAGGAAGGGGTGA 60.611 63.158 0.00 0.00 0.00 4.02
219 220 1.614241 CGGGTGTAGGAAGGGGTGAG 61.614 65.000 0.00 0.00 0.00 3.51
220 221 0.252558 GGGTGTAGGAAGGGGTGAGA 60.253 60.000 0.00 0.00 0.00 3.27
221 222 1.196012 GGTGTAGGAAGGGGTGAGAG 58.804 60.000 0.00 0.00 0.00 3.20
222 223 1.196012 GTGTAGGAAGGGGTGAGAGG 58.804 60.000 0.00 0.00 0.00 3.69
223 224 0.042731 TGTAGGAAGGGGTGAGAGGG 59.957 60.000 0.00 0.00 0.00 4.30
224 225 0.338814 GTAGGAAGGGGTGAGAGGGA 59.661 60.000 0.00 0.00 0.00 4.20
225 226 1.062044 GTAGGAAGGGGTGAGAGGGAT 60.062 57.143 0.00 0.00 0.00 3.85
226 227 0.327000 AGGAAGGGGTGAGAGGGATG 60.327 60.000 0.00 0.00 0.00 3.51
227 228 0.621862 GGAAGGGGTGAGAGGGATGT 60.622 60.000 0.00 0.00 0.00 3.06
228 229 0.833949 GAAGGGGTGAGAGGGATGTC 59.166 60.000 0.00 0.00 0.00 3.06
229 230 0.119155 AAGGGGTGAGAGGGATGTCA 59.881 55.000 0.00 0.00 0.00 3.58
230 231 0.326048 AGGGGTGAGAGGGATGTCAG 60.326 60.000 0.00 0.00 0.00 3.51
231 232 1.524482 GGGTGAGAGGGATGTCAGC 59.476 63.158 0.00 0.00 39.89 4.26
232 233 1.142748 GGTGAGAGGGATGTCAGCG 59.857 63.158 0.00 0.00 31.99 5.18
233 234 1.608717 GGTGAGAGGGATGTCAGCGT 61.609 60.000 0.00 0.00 31.99 5.07
234 235 0.459237 GTGAGAGGGATGTCAGCGTG 60.459 60.000 0.00 0.00 0.00 5.34
235 236 0.900182 TGAGAGGGATGTCAGCGTGT 60.900 55.000 0.00 0.00 0.00 4.49
236 237 0.179124 GAGAGGGATGTCAGCGTGTC 60.179 60.000 0.00 0.00 0.00 3.67
237 238 1.153549 GAGGGATGTCAGCGTGTCC 60.154 63.158 0.00 0.00 0.00 4.02
238 239 2.509336 GGGATGTCAGCGTGTCCG 60.509 66.667 0.00 0.00 37.07 4.79
239 240 2.261671 GGATGTCAGCGTGTCCGT 59.738 61.111 0.00 0.00 36.15 4.69
240 241 1.805945 GGATGTCAGCGTGTCCGTC 60.806 63.158 0.00 0.00 36.15 4.79
241 242 1.213013 GATGTCAGCGTGTCCGTCT 59.787 57.895 0.00 0.00 36.15 4.18
242 243 0.450583 GATGTCAGCGTGTCCGTCTA 59.549 55.000 0.00 0.00 36.15 2.59
243 244 1.065701 GATGTCAGCGTGTCCGTCTAT 59.934 52.381 0.00 0.00 36.15 1.98
244 245 0.450583 TGTCAGCGTGTCCGTCTATC 59.549 55.000 0.00 0.00 36.15 2.08
245 246 0.589229 GTCAGCGTGTCCGTCTATCG 60.589 60.000 0.00 0.00 39.52 2.92
294 295 3.798650 CGAAAGCGGCATGGCGAA 61.799 61.111 41.46 0.00 38.18 4.70
295 296 2.100991 GAAAGCGGCATGGCGAAG 59.899 61.111 41.46 16.70 38.18 3.79
296 297 2.359850 AAAGCGGCATGGCGAAGA 60.360 55.556 41.46 0.00 38.18 2.87
297 298 2.315038 GAAAGCGGCATGGCGAAGAG 62.315 60.000 41.46 15.93 38.18 2.85
298 299 4.845580 AGCGGCATGGCGAAGAGG 62.846 66.667 41.46 15.18 38.18 3.69
300 301 4.473520 CGGCATGGCGAAGAGGGT 62.474 66.667 35.61 0.00 0.00 4.34
301 302 2.825836 GGCATGGCGAAGAGGGTG 60.826 66.667 2.41 0.00 0.00 4.61
302 303 3.512516 GCATGGCGAAGAGGGTGC 61.513 66.667 0.00 0.00 0.00 5.01
303 304 3.197790 CATGGCGAAGAGGGTGCG 61.198 66.667 0.00 0.00 0.00 5.34
304 305 4.473520 ATGGCGAAGAGGGTGCGG 62.474 66.667 0.00 0.00 0.00 5.69
359 360 1.698984 CGTAGCAAATAAACGACGCG 58.301 50.000 3.53 3.53 38.89 6.01
360 361 1.588082 CGTAGCAAATAAACGACGCGG 60.588 52.381 12.47 0.00 38.89 6.46
361 362 1.000884 TAGCAAATAAACGACGCGGG 58.999 50.000 12.47 4.10 0.00 6.13
362 363 0.671163 AGCAAATAAACGACGCGGGA 60.671 50.000 12.47 0.00 0.00 5.14
363 364 0.375803 GCAAATAAACGACGCGGGAT 59.624 50.000 12.47 0.00 0.00 3.85
364 365 1.854434 GCAAATAAACGACGCGGGATG 60.854 52.381 12.47 0.00 0.00 3.51
365 366 1.011333 AAATAAACGACGCGGGATGG 58.989 50.000 12.47 0.00 0.00 3.51
366 367 1.433837 AATAAACGACGCGGGATGGC 61.434 55.000 12.47 0.00 0.00 4.40
375 376 3.192922 CGGGATGGCGTTTCGGAC 61.193 66.667 0.00 0.00 0.00 4.79
376 377 2.822701 GGGATGGCGTTTCGGACC 60.823 66.667 0.00 0.00 0.00 4.46
377 378 3.192922 GGATGGCGTTTCGGACCG 61.193 66.667 7.84 7.84 0.00 4.79
383 384 3.118454 CGTTTCGGACCGCATGCT 61.118 61.111 17.13 0.00 0.00 3.79
384 385 1.807981 CGTTTCGGACCGCATGCTA 60.808 57.895 17.13 0.00 0.00 3.49
385 386 1.355796 CGTTTCGGACCGCATGCTAA 61.356 55.000 17.13 0.00 0.00 3.09
386 387 0.800012 GTTTCGGACCGCATGCTAAA 59.200 50.000 17.13 0.00 0.00 1.85
387 388 0.800012 TTTCGGACCGCATGCTAAAC 59.200 50.000 17.13 4.41 0.00 2.01
388 389 0.036765 TTCGGACCGCATGCTAAACT 60.037 50.000 17.13 0.00 0.00 2.66
389 390 0.459585 TCGGACCGCATGCTAAACTC 60.460 55.000 17.13 2.50 0.00 3.01
390 391 0.460284 CGGACCGCATGCTAAACTCT 60.460 55.000 17.13 0.00 0.00 3.24
391 392 1.739067 GGACCGCATGCTAAACTCTT 58.261 50.000 17.13 0.00 0.00 2.85
392 393 2.084546 GGACCGCATGCTAAACTCTTT 58.915 47.619 17.13 0.00 0.00 2.52
393 394 3.267483 GGACCGCATGCTAAACTCTTTA 58.733 45.455 17.13 0.00 0.00 1.85
394 395 3.877508 GGACCGCATGCTAAACTCTTTAT 59.122 43.478 17.13 0.00 0.00 1.40
395 396 5.054477 GGACCGCATGCTAAACTCTTTATA 58.946 41.667 17.13 0.00 0.00 0.98
396 397 5.050295 GGACCGCATGCTAAACTCTTTATAC 60.050 44.000 17.13 0.00 0.00 1.47
397 398 4.814771 ACCGCATGCTAAACTCTTTATACC 59.185 41.667 17.13 0.00 0.00 2.73
398 399 4.084537 CCGCATGCTAAACTCTTTATACCG 60.085 45.833 17.13 0.00 0.00 4.02
399 400 4.506654 CGCATGCTAAACTCTTTATACCGT 59.493 41.667 17.13 0.00 0.00 4.83
400 401 5.556382 CGCATGCTAAACTCTTTATACCGTG 60.556 44.000 17.13 0.00 0.00 4.94
401 402 5.738370 CATGCTAAACTCTTTATACCGTGC 58.262 41.667 0.00 0.00 0.00 5.34
402 403 3.861113 TGCTAAACTCTTTATACCGTGCG 59.139 43.478 0.00 0.00 0.00 5.34
403 404 3.861689 GCTAAACTCTTTATACCGTGCGT 59.138 43.478 0.00 0.00 0.00 5.24
404 405 4.027050 GCTAAACTCTTTATACCGTGCGTC 60.027 45.833 0.00 0.00 0.00 5.19
405 406 2.573941 ACTCTTTATACCGTGCGTCC 57.426 50.000 0.00 0.00 0.00 4.79
406 407 1.202222 ACTCTTTATACCGTGCGTCCG 60.202 52.381 0.00 0.00 0.00 4.79
413 414 3.086309 CCGTGCGTCCGGTTATTG 58.914 61.111 0.00 0.00 43.07 1.90
414 415 2.398036 CGTGCGTCCGGTTATTGC 59.602 61.111 0.00 0.00 0.00 3.56
415 416 2.398036 GTGCGTCCGGTTATTGCG 59.602 61.111 0.00 0.00 0.00 4.85
416 417 3.492545 TGCGTCCGGTTATTGCGC 61.493 61.111 0.00 0.00 47.00 6.09
417 418 4.232248 GCGTCCGGTTATTGCGCC 62.232 66.667 4.18 0.00 41.93 6.53
418 419 2.510691 CGTCCGGTTATTGCGCCT 60.511 61.111 4.18 0.00 0.00 5.52
419 420 2.104253 CGTCCGGTTATTGCGCCTT 61.104 57.895 4.18 0.00 0.00 4.35
420 421 1.641123 CGTCCGGTTATTGCGCCTTT 61.641 55.000 4.18 0.00 0.00 3.11
421 422 0.179174 GTCCGGTTATTGCGCCTTTG 60.179 55.000 4.18 0.00 0.00 2.77
422 423 1.516169 CCGGTTATTGCGCCTTTGC 60.516 57.895 4.18 0.00 0.00 3.68
423 424 1.506262 CGGTTATTGCGCCTTTGCT 59.494 52.632 4.18 0.00 35.36 3.91
424 425 0.730265 CGGTTATTGCGCCTTTGCTA 59.270 50.000 4.18 0.00 35.36 3.49
425 426 1.268032 CGGTTATTGCGCCTTTGCTAG 60.268 52.381 4.18 0.00 35.36 3.42
426 427 2.014128 GGTTATTGCGCCTTTGCTAGA 58.986 47.619 4.18 0.00 35.36 2.43
427 428 2.032178 GGTTATTGCGCCTTTGCTAGAG 59.968 50.000 4.18 0.00 35.36 2.43
428 429 1.299541 TATTGCGCCTTTGCTAGAGC 58.700 50.000 4.18 0.00 42.50 4.09
429 430 0.393537 ATTGCGCCTTTGCTAGAGCT 60.394 50.000 4.18 0.00 42.66 4.09
430 431 1.021390 TTGCGCCTTTGCTAGAGCTC 61.021 55.000 5.27 5.27 42.66 4.09
431 432 2.176926 GCGCCTTTGCTAGAGCTCC 61.177 63.158 10.93 0.00 42.66 4.70
432 433 1.522580 CGCCTTTGCTAGAGCTCCC 60.523 63.158 10.93 0.00 42.66 4.30
433 434 1.522580 GCCTTTGCTAGAGCTCCCG 60.523 63.158 10.93 2.45 42.66 5.14
434 435 1.144936 CCTTTGCTAGAGCTCCCGG 59.855 63.158 10.93 0.00 42.66 5.73
435 436 1.330655 CCTTTGCTAGAGCTCCCGGA 61.331 60.000 10.93 0.00 42.66 5.14
436 437 0.103937 CTTTGCTAGAGCTCCCGGAG 59.896 60.000 10.93 10.41 42.66 4.63
444 445 4.867599 GCTCCCGGAGCGGTTACG 62.868 72.222 23.58 5.79 45.85 3.18
445 446 3.446570 CTCCCGGAGCGGTTACGT 61.447 66.667 0.73 0.00 46.80 3.57
446 447 2.045438 TCCCGGAGCGGTTACGTA 60.045 61.111 0.73 0.00 46.80 3.57
447 448 2.102946 CCCGGAGCGGTTACGTAC 59.897 66.667 0.73 0.00 46.80 3.67
448 449 2.277501 CCGGAGCGGTTACGTACG 60.278 66.667 15.01 15.01 42.73 3.67
461 462 7.985199 CGGTTACGTACGCTAAAAATTTAAA 57.015 32.000 16.72 0.00 34.81 1.52
462 463 8.415731 CGGTTACGTACGCTAAAAATTTAAAA 57.584 30.769 16.72 0.00 34.81 1.52
463 464 8.887052 CGGTTACGTACGCTAAAAATTTAAAAA 58.113 29.630 16.72 0.00 34.81 1.94
473 474 8.281807 GCTAAAAATTTAAAAATGTTAGCGCG 57.718 30.769 17.00 0.00 39.87 6.86
474 475 7.421331 GCTAAAAATTTAAAAATGTTAGCGCGG 59.579 33.333 17.00 0.00 39.87 6.46
475 476 4.833469 AATTTAAAAATGTTAGCGCGGC 57.167 36.364 8.83 0.00 0.00 6.53
476 477 3.562567 TTTAAAAATGTTAGCGCGGCT 57.437 38.095 8.83 8.38 43.41 5.52
477 478 2.535934 TAAAAATGTTAGCGCGGCTG 57.464 45.000 8.83 0.00 40.10 4.85
478 479 0.596082 AAAAATGTTAGCGCGGCTGT 59.404 45.000 8.83 0.00 40.10 4.40
479 480 0.596082 AAAATGTTAGCGCGGCTGTT 59.404 45.000 8.83 0.00 40.10 3.16
480 481 0.109781 AAATGTTAGCGCGGCTGTTG 60.110 50.000 8.83 0.00 40.10 3.33
481 482 1.922135 AATGTTAGCGCGGCTGTTGG 61.922 55.000 8.83 0.00 40.10 3.77
482 483 2.740826 GTTAGCGCGGCTGTTGGA 60.741 61.111 8.83 0.00 40.10 3.53
483 484 2.434185 TTAGCGCGGCTGTTGGAG 60.434 61.111 8.83 0.00 40.10 3.86
484 485 2.938086 TTAGCGCGGCTGTTGGAGA 61.938 57.895 8.83 0.00 40.10 3.71
485 486 2.238847 TTAGCGCGGCTGTTGGAGAT 62.239 55.000 8.83 0.00 40.10 2.75
486 487 2.906182 TAGCGCGGCTGTTGGAGATG 62.906 60.000 8.83 0.00 40.10 2.90
487 488 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
488 489 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
489 490 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
490 491 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
491 492 0.392193 CGGCTGTTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
492 493 1.134699 CGGCTGTTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
493 494 2.559440 GGCTGTTGGAGATGCTCTTAG 58.441 52.381 0.00 0.00 0.00 2.18
494 495 1.939255 GCTGTTGGAGATGCTCTTAGC 59.061 52.381 0.00 0.00 42.82 3.09
495 496 2.559440 CTGTTGGAGATGCTCTTAGCC 58.441 52.381 0.00 0.00 41.51 3.93
619 622 3.784511 AATGATATGCCCTCTGGACAG 57.215 47.619 0.00 0.00 0.00 3.51
746 2221 4.022242 GCACCCGAATCTGCTAGAACTATA 60.022 45.833 0.00 0.00 0.00 1.31
751 2226 8.211629 ACCCGAATCTGCTAGAACTATATTTTT 58.788 33.333 0.00 0.00 0.00 1.94
915 2390 2.004017 CCGATAGAGGTCTAGCTAGCG 58.996 57.143 16.35 10.54 43.70 4.26
935 2410 1.224965 GCTGGAAGATTCGGATCAGC 58.775 55.000 6.44 2.75 40.30 4.26
941 2416 0.531532 AGATTCGGATCAGCTTGCCG 60.532 55.000 6.44 11.38 46.08 5.69
1071 2546 0.705253 TCTTCCTCTCGGTCCTCCTT 59.295 55.000 0.00 0.00 0.00 3.36
1084 2559 1.456705 CTCCTTCTCCTCCCCTCCG 60.457 68.421 0.00 0.00 0.00 4.63
1119 2594 0.105039 CAGATGCCGGTAAGACCTCC 59.895 60.000 1.90 0.00 35.66 4.30
1228 2703 1.136329 ACAGGGAGGTTGCCACTGAT 61.136 55.000 0.00 0.00 33.29 2.90
1291 2766 3.282021 AGTTGTTGCTGTTGTCTGATGT 58.718 40.909 0.00 0.00 0.00 3.06
1385 2860 3.249752 AGGGGAGATGATGAAGATGGAG 58.750 50.000 0.00 0.00 0.00 3.86
1481 2956 1.304052 GGTGCCCATAGTGCCACAA 60.304 57.895 0.00 0.00 0.00 3.33
1614 3089 1.338200 GCTGGAAGTGTAGGTGTGGAG 60.338 57.143 0.00 0.00 35.30 3.86
1660 3135 7.151308 AGTATTCAACAGTCTCAACTTCTCAG 58.849 38.462 0.00 0.00 31.71 3.35
1711 3186 6.093219 GTGCAAATATGTATAGAGATGCCCTG 59.907 42.308 0.00 0.00 0.00 4.45
1820 3301 9.643693 CAAATTTCTTGTACATTTAGGAAGCAT 57.356 29.630 0.00 0.00 0.00 3.79
1873 3354 2.290896 CCATGACCTGGCCTGACTTTAA 60.291 50.000 11.88 0.00 38.47 1.52
1902 3383 8.821894 CAGTAGAGGCAAGTGAATTATTTAGTC 58.178 37.037 0.00 0.00 0.00 2.59
1903 3384 8.763601 AGTAGAGGCAAGTGAATTATTTAGTCT 58.236 33.333 0.00 0.00 0.00 3.24
1904 3385 7.856145 AGAGGCAAGTGAATTATTTAGTCTG 57.144 36.000 0.00 0.00 0.00 3.51
1905 3386 6.317391 AGAGGCAAGTGAATTATTTAGTCTGC 59.683 38.462 0.00 0.00 0.00 4.26
1906 3387 5.945784 AGGCAAGTGAATTATTTAGTCTGCA 59.054 36.000 10.88 0.00 0.00 4.41
1907 3388 6.604795 AGGCAAGTGAATTATTTAGTCTGCAT 59.395 34.615 0.00 4.72 0.00 3.96
1908 3389 7.123247 AGGCAAGTGAATTATTTAGTCTGCATT 59.877 33.333 0.00 0.00 0.00 3.56
1909 3390 7.761249 GGCAAGTGAATTATTTAGTCTGCATTT 59.239 33.333 0.00 0.00 0.00 2.32
1910 3391 9.787532 GCAAGTGAATTATTTAGTCTGCATTTA 57.212 29.630 0.00 0.00 0.00 1.40
2068 3553 5.738619 AATTTTCACTAATTGTGTCCCCC 57.261 39.130 7.57 0.00 46.27 5.40
2132 3617 2.232941 TCGATATTGGTCCTAATCGCCC 59.767 50.000 13.14 0.00 40.68 6.13
2405 3890 5.886609 TCAGATGGGTAGATGTTTCCAAAA 58.113 37.500 0.00 0.00 32.56 2.44
2417 3902 4.378774 TGTTTCCAAAATTCTGGTGCATG 58.621 39.130 0.00 0.00 37.74 4.06
2490 3975 1.107114 CACAGGCGGTCTCTGACTAT 58.893 55.000 0.00 0.00 36.22 2.12
2503 3988 4.652881 TCTCTGACTATGAGCCACATGAAT 59.347 41.667 0.00 0.00 39.77 2.57
2565 4050 0.935194 TTGTAAACTGGGTTGGGGGT 59.065 50.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.401243 GAAGCTCCCAAATGCGGCG 62.401 63.158 0.51 0.51 0.00 6.46
8 9 2.491621 GAAGCTCCCAAATGCGGC 59.508 61.111 0.00 0.00 0.00 6.53
9 10 1.709147 CTCGAAGCTCCCAAATGCGG 61.709 60.000 0.00 0.00 0.00 5.69
10 11 0.740868 TCTCGAAGCTCCCAAATGCG 60.741 55.000 0.00 0.00 0.00 4.73
11 12 1.012841 CTCTCGAAGCTCCCAAATGC 58.987 55.000 0.00 0.00 0.00 3.56
12 13 1.661341 CCTCTCGAAGCTCCCAAATG 58.339 55.000 0.00 0.00 0.00 2.32
13 14 0.543749 CCCTCTCGAAGCTCCCAAAT 59.456 55.000 0.00 0.00 0.00 2.32
14 15 1.553690 CCCCTCTCGAAGCTCCCAAA 61.554 60.000 0.00 0.00 0.00 3.28
15 16 1.990060 CCCCTCTCGAAGCTCCCAA 60.990 63.158 0.00 0.00 0.00 4.12
16 17 2.364317 CCCCTCTCGAAGCTCCCA 60.364 66.667 0.00 0.00 0.00 4.37
17 18 3.157949 CCCCCTCTCGAAGCTCCC 61.158 72.222 0.00 0.00 0.00 4.30
75 76 3.411351 CACAAACGACCTCGGCGG 61.411 66.667 7.21 0.00 44.95 6.13
76 77 3.411351 CCACAAACGACCTCGGCG 61.411 66.667 0.00 0.00 44.95 6.46
77 78 3.723348 GCCACAAACGACCTCGGC 61.723 66.667 0.00 0.00 44.95 5.54
78 79 3.411351 CGCCACAAACGACCTCGG 61.411 66.667 0.00 0.00 44.95 4.63
79 80 3.411351 CCGCCACAAACGACCTCG 61.411 66.667 0.00 0.00 46.33 4.63
80 81 3.723348 GCCGCCACAAACGACCTC 61.723 66.667 0.00 0.00 0.00 3.85
81 82 3.842925 ATGCCGCCACAAACGACCT 62.843 57.895 0.00 0.00 0.00 3.85
82 83 3.361977 ATGCCGCCACAAACGACC 61.362 61.111 0.00 0.00 0.00 4.79
83 84 2.123988 TTCATGCCGCCACAAACGAC 62.124 55.000 0.00 0.00 0.00 4.34
84 85 1.448119 TTTCATGCCGCCACAAACGA 61.448 50.000 0.00 0.00 0.00 3.85
85 86 0.596083 TTTTCATGCCGCCACAAACG 60.596 50.000 0.00 0.00 0.00 3.60
86 87 1.139163 CTTTTCATGCCGCCACAAAC 58.861 50.000 0.00 0.00 0.00 2.93
87 88 0.033228 CCTTTTCATGCCGCCACAAA 59.967 50.000 0.00 0.00 0.00 2.83
88 89 1.664873 CCTTTTCATGCCGCCACAA 59.335 52.632 0.00 0.00 0.00 3.33
89 90 2.929903 GCCTTTTCATGCCGCCACA 61.930 57.895 0.00 0.00 0.00 4.17
90 91 2.125952 GCCTTTTCATGCCGCCAC 60.126 61.111 0.00 0.00 0.00 5.01
91 92 3.381136 GGCCTTTTCATGCCGCCA 61.381 61.111 0.00 0.00 39.50 5.69
114 115 3.197790 CTCCAAGCACCGGCATCG 61.198 66.667 0.00 0.00 44.61 3.84
115 116 2.825836 CCTCCAAGCACCGGCATC 60.826 66.667 0.00 0.00 44.61 3.91
116 117 3.329889 TCCTCCAAGCACCGGCAT 61.330 61.111 0.00 0.00 44.61 4.40
117 118 4.020617 CTCCTCCAAGCACCGGCA 62.021 66.667 0.00 0.00 44.61 5.69
119 120 4.020617 TGCTCCTCCAAGCACCGG 62.021 66.667 0.00 0.00 47.00 5.28
134 135 4.821589 CTTCTCCTCCGCCGGTGC 62.822 72.222 10.27 0.00 0.00 5.01
135 136 4.821589 GCTTCTCCTCCGCCGGTG 62.822 72.222 8.42 8.42 0.00 4.94
138 139 3.605749 TTTGGCTTCTCCTCCGCCG 62.606 63.158 0.00 0.00 46.67 6.46
139 140 1.746991 CTTTGGCTTCTCCTCCGCC 60.747 63.158 0.00 0.00 44.02 6.13
140 141 2.402572 GCTTTGGCTTCTCCTCCGC 61.403 63.158 0.00 0.00 35.26 5.54
141 142 3.896479 GCTTTGGCTTCTCCTCCG 58.104 61.111 0.00 0.00 35.26 4.63
152 153 4.467084 TAGCGCGGGGAGCTTTGG 62.467 66.667 8.83 0.00 43.24 3.28
153 154 2.892425 CTAGCGCGGGGAGCTTTG 60.892 66.667 8.83 0.00 43.24 2.77
154 155 4.162690 CCTAGCGCGGGGAGCTTT 62.163 66.667 8.83 0.00 43.24 3.51
191 192 3.834799 CTACACCCGCGACCCCTC 61.835 72.222 8.23 0.00 0.00 4.30
194 195 3.366739 CTTCCTACACCCGCGACCC 62.367 68.421 8.23 0.00 0.00 4.46
195 196 2.183555 CTTCCTACACCCGCGACC 59.816 66.667 8.23 0.00 0.00 4.79
196 197 2.183555 CCTTCCTACACCCGCGAC 59.816 66.667 8.23 0.00 0.00 5.19
197 198 3.072468 CCCTTCCTACACCCGCGA 61.072 66.667 8.23 0.00 0.00 5.87
198 199 4.157120 CCCCTTCCTACACCCGCG 62.157 72.222 0.00 0.00 0.00 6.46
199 200 3.007323 ACCCCTTCCTACACCCGC 61.007 66.667 0.00 0.00 0.00 6.13
200 201 1.611261 TCACCCCTTCCTACACCCG 60.611 63.158 0.00 0.00 0.00 5.28
201 202 0.252558 TCTCACCCCTTCCTACACCC 60.253 60.000 0.00 0.00 0.00 4.61
202 203 1.196012 CTCTCACCCCTTCCTACACC 58.804 60.000 0.00 0.00 0.00 4.16
203 204 1.196012 CCTCTCACCCCTTCCTACAC 58.804 60.000 0.00 0.00 0.00 2.90
204 205 0.042731 CCCTCTCACCCCTTCCTACA 59.957 60.000 0.00 0.00 0.00 2.74
205 206 0.338814 TCCCTCTCACCCCTTCCTAC 59.661 60.000 0.00 0.00 0.00 3.18
206 207 1.062121 CATCCCTCTCACCCCTTCCTA 60.062 57.143 0.00 0.00 0.00 2.94
207 208 0.327000 CATCCCTCTCACCCCTTCCT 60.327 60.000 0.00 0.00 0.00 3.36
208 209 0.621862 ACATCCCTCTCACCCCTTCC 60.622 60.000 0.00 0.00 0.00 3.46
209 210 0.833949 GACATCCCTCTCACCCCTTC 59.166 60.000 0.00 0.00 0.00 3.46
210 211 0.119155 TGACATCCCTCTCACCCCTT 59.881 55.000 0.00 0.00 0.00 3.95
211 212 0.326048 CTGACATCCCTCTCACCCCT 60.326 60.000 0.00 0.00 0.00 4.79
212 213 1.977293 GCTGACATCCCTCTCACCCC 61.977 65.000 0.00 0.00 0.00 4.95
213 214 1.524482 GCTGACATCCCTCTCACCC 59.476 63.158 0.00 0.00 0.00 4.61
214 215 1.142748 CGCTGACATCCCTCTCACC 59.857 63.158 0.00 0.00 0.00 4.02
215 216 0.459237 CACGCTGACATCCCTCTCAC 60.459 60.000 0.00 0.00 0.00 3.51
216 217 0.900182 ACACGCTGACATCCCTCTCA 60.900 55.000 0.00 0.00 0.00 3.27
217 218 0.179124 GACACGCTGACATCCCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
218 219 1.608717 GGACACGCTGACATCCCTCT 61.609 60.000 0.00 0.00 0.00 3.69
219 220 1.153549 GGACACGCTGACATCCCTC 60.154 63.158 0.00 0.00 0.00 4.30
220 221 2.982130 GGACACGCTGACATCCCT 59.018 61.111 0.00 0.00 0.00 4.20
221 222 2.509336 CGGACACGCTGACATCCC 60.509 66.667 0.00 0.00 0.00 3.85
222 223 1.805945 GACGGACACGCTGACATCC 60.806 63.158 0.00 0.00 46.04 3.51
223 224 0.450583 TAGACGGACACGCTGACATC 59.549 55.000 0.00 0.00 46.04 3.06
224 225 1.065701 GATAGACGGACACGCTGACAT 59.934 52.381 0.00 0.00 46.04 3.06
225 226 0.450583 GATAGACGGACACGCTGACA 59.549 55.000 0.00 0.00 46.04 3.58
226 227 0.589229 CGATAGACGGACACGCTGAC 60.589 60.000 0.00 0.00 46.04 3.51
227 228 1.719709 CGATAGACGGACACGCTGA 59.280 57.895 0.00 0.00 46.04 4.26
228 229 4.286967 CGATAGACGGACACGCTG 57.713 61.111 0.00 0.00 46.04 5.18
237 238 2.421131 CGAATTCGCCCGATAGACG 58.579 57.895 15.93 0.00 42.18 4.18
277 278 3.723364 CTTCGCCATGCCGCTTTCG 62.723 63.158 0.00 0.00 0.00 3.46
278 279 2.100991 CTTCGCCATGCCGCTTTC 59.899 61.111 0.00 0.00 0.00 2.62
279 280 2.359850 TCTTCGCCATGCCGCTTT 60.360 55.556 0.00 0.00 0.00 3.51
280 281 2.821366 CTCTTCGCCATGCCGCTT 60.821 61.111 0.00 0.00 0.00 4.68
281 282 4.845580 CCTCTTCGCCATGCCGCT 62.846 66.667 0.00 0.00 0.00 5.52
283 284 4.473520 ACCCTCTTCGCCATGCCG 62.474 66.667 0.00 0.00 0.00 5.69
284 285 2.825836 CACCCTCTTCGCCATGCC 60.826 66.667 0.00 0.00 0.00 4.40
285 286 3.512516 GCACCCTCTTCGCCATGC 61.513 66.667 0.00 0.00 0.00 4.06
286 287 3.197790 CGCACCCTCTTCGCCATG 61.198 66.667 0.00 0.00 0.00 3.66
287 288 4.473520 CCGCACCCTCTTCGCCAT 62.474 66.667 0.00 0.00 0.00 4.40
330 331 1.369091 ATTTGCTACGCCCGCTTCTG 61.369 55.000 0.00 0.00 0.00 3.02
331 332 0.177141 TATTTGCTACGCCCGCTTCT 59.823 50.000 0.00 0.00 0.00 2.85
332 333 1.011333 TTATTTGCTACGCCCGCTTC 58.989 50.000 0.00 0.00 0.00 3.86
333 334 1.131693 GTTTATTTGCTACGCCCGCTT 59.868 47.619 0.00 0.00 0.00 4.68
334 335 0.730840 GTTTATTTGCTACGCCCGCT 59.269 50.000 0.00 0.00 0.00 5.52
335 336 0.587985 CGTTTATTTGCTACGCCCGC 60.588 55.000 0.00 0.00 0.00 6.13
336 337 1.000884 TCGTTTATTTGCTACGCCCG 58.999 50.000 0.00 0.00 35.40 6.13
337 338 1.267186 CGTCGTTTATTTGCTACGCCC 60.267 52.381 0.00 0.00 35.40 6.13
338 339 2.067459 CGTCGTTTATTTGCTACGCC 57.933 50.000 0.00 0.00 35.40 5.68
340 341 1.588082 CCGCGTCGTTTATTTGCTACG 60.588 52.381 4.92 0.00 36.67 3.51
341 342 1.267186 CCCGCGTCGTTTATTTGCTAC 60.267 52.381 4.92 0.00 0.00 3.58
342 343 1.000884 CCCGCGTCGTTTATTTGCTA 58.999 50.000 4.92 0.00 0.00 3.49
343 344 0.671163 TCCCGCGTCGTTTATTTGCT 60.671 50.000 4.92 0.00 0.00 3.91
344 345 0.375803 ATCCCGCGTCGTTTATTTGC 59.624 50.000 4.92 0.00 0.00 3.68
345 346 1.267832 CCATCCCGCGTCGTTTATTTG 60.268 52.381 4.92 0.00 0.00 2.32
346 347 1.011333 CCATCCCGCGTCGTTTATTT 58.989 50.000 4.92 0.00 0.00 1.40
347 348 1.433837 GCCATCCCGCGTCGTTTATT 61.434 55.000 4.92 0.00 0.00 1.40
348 349 1.885850 GCCATCCCGCGTCGTTTAT 60.886 57.895 4.92 0.00 0.00 1.40
349 350 2.509786 GCCATCCCGCGTCGTTTA 60.510 61.111 4.92 0.00 0.00 2.01
358 359 3.192922 GTCCGAAACGCCATCCCG 61.193 66.667 0.00 0.00 0.00 5.14
359 360 2.822701 GGTCCGAAACGCCATCCC 60.823 66.667 0.00 0.00 0.00 3.85
360 361 3.192922 CGGTCCGAAACGCCATCC 61.193 66.667 4.91 0.00 0.00 3.51
366 367 1.355796 TTAGCATGCGGTCCGAAACG 61.356 55.000 17.49 0.89 0.00 3.60
367 368 0.800012 TTTAGCATGCGGTCCGAAAC 59.200 50.000 17.49 0.73 0.00 2.78
368 369 0.800012 GTTTAGCATGCGGTCCGAAA 59.200 50.000 17.49 1.85 0.00 3.46
369 370 0.036765 AGTTTAGCATGCGGTCCGAA 60.037 50.000 17.49 4.27 0.00 4.30
370 371 0.459585 GAGTTTAGCATGCGGTCCGA 60.460 55.000 17.49 0.00 0.00 4.55
371 372 0.460284 AGAGTTTAGCATGCGGTCCG 60.460 55.000 13.01 6.99 0.00 4.79
372 373 1.739067 AAGAGTTTAGCATGCGGTCC 58.261 50.000 13.01 2.08 0.00 4.46
373 374 5.050295 GGTATAAAGAGTTTAGCATGCGGTC 60.050 44.000 13.01 5.91 0.00 4.79
374 375 4.814771 GGTATAAAGAGTTTAGCATGCGGT 59.185 41.667 13.01 0.00 0.00 5.68
375 376 4.084537 CGGTATAAAGAGTTTAGCATGCGG 60.085 45.833 13.01 0.00 0.00 5.69
376 377 4.506654 ACGGTATAAAGAGTTTAGCATGCG 59.493 41.667 13.01 0.00 0.00 4.73
377 378 5.738370 CACGGTATAAAGAGTTTAGCATGC 58.262 41.667 10.51 10.51 0.00 4.06
378 379 5.556382 CGCACGGTATAAAGAGTTTAGCATG 60.556 44.000 0.00 0.00 0.00 4.06
379 380 4.506654 CGCACGGTATAAAGAGTTTAGCAT 59.493 41.667 0.00 0.00 0.00 3.79
380 381 3.861113 CGCACGGTATAAAGAGTTTAGCA 59.139 43.478 0.00 0.00 0.00 3.49
381 382 3.861689 ACGCACGGTATAAAGAGTTTAGC 59.138 43.478 0.00 0.00 0.00 3.09
382 383 4.501921 GGACGCACGGTATAAAGAGTTTAG 59.498 45.833 0.00 0.00 0.00 1.85
383 384 4.423732 GGACGCACGGTATAAAGAGTTTA 58.576 43.478 0.00 0.00 0.00 2.01
384 385 3.256558 GGACGCACGGTATAAAGAGTTT 58.743 45.455 0.00 0.00 0.00 2.66
385 386 2.733227 CGGACGCACGGTATAAAGAGTT 60.733 50.000 0.00 0.00 0.00 3.01
386 387 1.202222 CGGACGCACGGTATAAAGAGT 60.202 52.381 0.00 0.00 0.00 3.24
387 388 1.474017 CGGACGCACGGTATAAAGAG 58.526 55.000 0.00 0.00 0.00 2.85
388 389 3.628005 CGGACGCACGGTATAAAGA 57.372 52.632 0.00 0.00 0.00 2.52
397 398 2.398036 GCAATAACCGGACGCACG 59.602 61.111 9.46 0.00 0.00 5.34
398 399 2.398036 CGCAATAACCGGACGCAC 59.602 61.111 9.46 0.00 0.00 5.34
401 402 1.641123 AAAGGCGCAATAACCGGACG 61.641 55.000 9.46 2.72 0.00 4.79
402 403 0.179174 CAAAGGCGCAATAACCGGAC 60.179 55.000 9.46 0.00 0.00 4.79
403 404 1.928706 GCAAAGGCGCAATAACCGGA 61.929 55.000 9.46 0.00 0.00 5.14
404 405 1.516169 GCAAAGGCGCAATAACCGG 60.516 57.895 10.83 0.00 0.00 5.28
405 406 4.071374 GCAAAGGCGCAATAACCG 57.929 55.556 10.83 0.00 0.00 4.44
415 416 1.522580 CGGGAGCTCTAGCAAAGGC 60.523 63.158 14.64 0.00 45.16 4.35
416 417 1.144936 CCGGGAGCTCTAGCAAAGG 59.855 63.158 14.64 3.26 45.16 3.11
417 418 0.103937 CTCCGGGAGCTCTAGCAAAG 59.896 60.000 14.64 0.63 45.16 2.77
418 419 2.202866 CTCCGGGAGCTCTAGCAAA 58.797 57.895 14.64 0.00 45.16 3.68
419 420 3.941081 CTCCGGGAGCTCTAGCAA 58.059 61.111 14.64 0.00 45.16 3.91
432 433 2.946086 GCGTACGTAACCGCTCCG 60.946 66.667 19.68 8.83 46.08 4.63
437 438 7.985199 TTTAAATTTTTAGCGTACGTAACCG 57.015 32.000 17.90 0.00 40.83 4.44
448 449 7.421331 CCGCGCTAACATTTTTAAATTTTTAGC 59.579 33.333 18.17 18.17 40.24 3.09
449 450 7.421331 GCCGCGCTAACATTTTTAAATTTTTAG 59.579 33.333 5.56 0.00 31.04 1.85
450 451 7.116519 AGCCGCGCTAACATTTTTAAATTTTTA 59.883 29.630 5.56 0.00 36.99 1.52
451 452 6.073494 AGCCGCGCTAACATTTTTAAATTTTT 60.073 30.769 5.56 0.00 36.99 1.94
452 453 5.407084 AGCCGCGCTAACATTTTTAAATTTT 59.593 32.000 5.56 0.00 36.99 1.82
453 454 4.926832 AGCCGCGCTAACATTTTTAAATTT 59.073 33.333 5.56 0.00 36.99 1.82
454 455 4.326009 CAGCCGCGCTAACATTTTTAAATT 59.674 37.500 5.56 0.00 36.40 1.82
455 456 3.857093 CAGCCGCGCTAACATTTTTAAAT 59.143 39.130 5.56 0.00 36.40 1.40
456 457 3.238441 CAGCCGCGCTAACATTTTTAAA 58.762 40.909 5.56 0.00 36.40 1.52
457 458 2.226912 ACAGCCGCGCTAACATTTTTAA 59.773 40.909 5.56 0.00 36.40 1.52
458 459 1.807742 ACAGCCGCGCTAACATTTTTA 59.192 42.857 5.56 0.00 36.40 1.52
459 460 0.596082 ACAGCCGCGCTAACATTTTT 59.404 45.000 5.56 0.00 36.40 1.94
460 461 0.596082 AACAGCCGCGCTAACATTTT 59.404 45.000 5.56 0.00 36.40 1.82
461 462 0.109781 CAACAGCCGCGCTAACATTT 60.110 50.000 5.56 0.00 36.40 2.32
462 463 1.501741 CAACAGCCGCGCTAACATT 59.498 52.632 5.56 0.00 36.40 2.71
463 464 2.398554 CCAACAGCCGCGCTAACAT 61.399 57.895 5.56 0.00 36.40 2.71
464 465 3.047280 CCAACAGCCGCGCTAACA 61.047 61.111 5.56 0.00 36.40 2.41
465 466 2.740714 CTCCAACAGCCGCGCTAAC 61.741 63.158 5.56 0.00 36.40 2.34
466 467 2.238847 ATCTCCAACAGCCGCGCTAA 62.239 55.000 5.56 0.00 36.40 3.09
467 468 2.721167 ATCTCCAACAGCCGCGCTA 61.721 57.895 5.56 0.00 36.40 4.26
468 469 4.087892 ATCTCCAACAGCCGCGCT 62.088 61.111 5.56 0.00 40.77 5.92
469 470 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
470 471 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
471 472 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
472 473 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
483 484 2.708386 ATACGTCGGCTAAGAGCATC 57.292 50.000 0.00 0.00 44.75 3.91
484 485 3.057456 CCTTATACGTCGGCTAAGAGCAT 60.057 47.826 14.25 0.00 44.75 3.79
485 486 2.292569 CCTTATACGTCGGCTAAGAGCA 59.707 50.000 14.25 0.00 44.75 4.26
486 487 2.292845 ACCTTATACGTCGGCTAAGAGC 59.707 50.000 14.25 0.00 41.46 4.09
487 488 4.036027 TCAACCTTATACGTCGGCTAAGAG 59.964 45.833 14.25 8.95 0.00 2.85
488 489 3.947196 TCAACCTTATACGTCGGCTAAGA 59.053 43.478 14.25 0.00 0.00 2.10
489 490 4.297299 TCAACCTTATACGTCGGCTAAG 57.703 45.455 0.00 3.37 0.00 2.18
490 491 4.717233 TTCAACCTTATACGTCGGCTAA 57.283 40.909 0.00 0.00 0.00 3.09
491 492 4.717233 TTTCAACCTTATACGTCGGCTA 57.283 40.909 0.00 0.00 0.00 3.93
492 493 3.598019 TTTCAACCTTATACGTCGGCT 57.402 42.857 0.00 0.00 0.00 5.52
493 494 4.870221 AATTTCAACCTTATACGTCGGC 57.130 40.909 0.00 0.00 0.00 5.54
494 495 8.605746 TGAAATAATTTCAACCTTATACGTCGG 58.394 33.333 0.00 0.00 45.94 4.79
524 525 2.866762 GGCTAAGAGCATTCTACAACCG 59.133 50.000 0.21 0.00 44.75 4.44
596 598 5.549228 TCTGTCCAGAGGGCATATCATTTAT 59.451 40.000 0.00 0.00 32.82 1.40
752 2227 9.793259 GATAGAATATTTGGTACTGGGATTGAA 57.207 33.333 0.00 0.00 0.00 2.69
915 2390 1.876322 CTGATCCGAATCTTCCAGCC 58.124 55.000 0.00 0.00 32.75 4.85
941 2416 2.044650 GGGTTTTCCGGCCCCTAC 60.045 66.667 3.52 0.00 41.82 3.18
956 2431 8.433421 TTCTTAATTAAACTAGCTCAATCGGG 57.567 34.615 0.00 0.00 0.00 5.14
995 2470 5.549742 TTGCAAAAGATGGACCATTCTTT 57.450 34.783 18.56 18.56 34.33 2.52
1039 2514 0.035458 AGGAAGAACAGAGGCAACGG 59.965 55.000 0.00 0.00 46.39 4.44
1071 2546 2.944954 TCCACGGAGGGGAGGAGA 60.945 66.667 0.00 0.00 38.24 3.71
1084 2559 2.462456 TCTGAATGTGCTGACTCCAC 57.538 50.000 0.00 0.00 0.00 4.02
1119 2594 5.873712 ACTAGAAACATTGAGATGAGCACTG 59.126 40.000 0.00 0.00 36.73 3.66
1228 2703 3.515502 ACTGCTGCCAATCTCTAGTAACA 59.484 43.478 0.00 0.00 0.00 2.41
1291 2766 1.616865 ACTGTAGCACGAGCAAAGGTA 59.383 47.619 7.77 0.00 45.49 3.08
1614 3089 5.068636 ACTTCATGGATCAAGTATCATGCC 58.931 41.667 0.00 0.00 36.20 4.40
1653 3128 3.935315 TCCTGATTGTTGAGCTGAGAAG 58.065 45.455 0.00 0.00 0.00 2.85
1660 3135 4.005650 TGAAGTGATCCTGATTGTTGAGC 58.994 43.478 0.00 0.00 0.00 4.26
1855 3336 1.351017 CCTTAAAGTCAGGCCAGGTCA 59.649 52.381 5.01 0.00 0.00 4.02
1873 3354 1.352083 TTCACTTGCCTCTACTGCCT 58.648 50.000 0.00 0.00 0.00 4.75
1921 3402 6.200854 GTGATTTGCCGAGTCTTTCAATTTTT 59.799 34.615 0.00 0.00 0.00 1.94
1922 3403 5.691754 GTGATTTGCCGAGTCTTTCAATTTT 59.308 36.000 0.00 0.00 0.00 1.82
1923 3404 5.222631 GTGATTTGCCGAGTCTTTCAATTT 58.777 37.500 0.00 0.00 0.00 1.82
1924 3405 4.321230 GGTGATTTGCCGAGTCTTTCAATT 60.321 41.667 0.00 0.00 0.00 2.32
1925 3406 3.191371 GGTGATTTGCCGAGTCTTTCAAT 59.809 43.478 0.00 0.00 0.00 2.57
2068 3553 3.887716 CCAAATTCATAGAGCCTCCCTTG 59.112 47.826 0.00 0.00 0.00 3.61
2132 3617 0.530650 CGGGTGGAAGATGTCATCGG 60.531 60.000 7.18 0.00 0.00 4.18
2405 3890 1.076485 GCCCTCCATGCACCAGAAT 60.076 57.895 0.00 0.00 0.00 2.40
2490 3975 4.951715 AGCTCAAAATATTCATGTGGCTCA 59.048 37.500 13.12 0.00 0.00 4.26
2503 3988 2.298729 GGCACCCAACAAGCTCAAAATA 59.701 45.455 0.00 0.00 0.00 1.40
2565 4050 1.003928 ACCAGATGCAATGTCAGCAGA 59.996 47.619 0.00 0.00 46.36 4.26


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

AutoCloner maintained by Alex Coulton.