Multiple sequence alignment - TraesCS6D01G222200

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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 TraesCS6D01G222200 chr6D 100.000 2552 0 0 1 2552 313027708 313025157 0.000000e+00 4713.0
1 TraesCS6D01G222200 chr6D 87.908 306 32 1 1087 1392 470390417 470390717 3.120000e-94 355.0
2 TraesCS6D01G222200 chr6D 90.741 54 5 0 886 939 410110904 410110851 3.520000e-09 73.1
3 TraesCS6D01G222200 chr6D 97.368 38 1 0 890 927 451106383 451106420 5.890000e-07 65.8
4 TraesCS6D01G222200 chr6A 94.995 959 34 6 1608 2552 449965206 449964248 0.000000e+00 1493.0
5 TraesCS6D01G222200 chr6A 96.610 59 2 0 966 1024 449965262 449965204 5.810000e-17 99.0
6 TraesCS6D01G222200 chr6B 94.253 957 37 3 1614 2552 513332983 513332027 0.000000e+00 1447.0
7 TraesCS6D01G222200 chr6B 88.235 476 49 5 423 892 513333491 513333017 1.710000e-156 562.0
8 TraesCS6D01G222200 chr6B 89.383 405 40 3 423 825 513340231 513339828 8.150000e-140 507.0
9 TraesCS6D01G222200 chr6B 88.416 423 43 4 405 825 513342494 513342076 2.930000e-139 505.0
10 TraesCS6D01G222200 chr6B 89.136 405 41 3 423 825 513337421 513337018 3.790000e-138 501.0
11 TraesCS6D01G222200 chr6B 88.642 405 43 3 423 825 513335739 513335336 8.210000e-135 490.0
12 TraesCS6D01G222200 chr6B 89.059 393 41 2 423 813 513334053 513333661 1.060000e-133 486.0
13 TraesCS6D01G222200 chr6B 87.470 423 47 4 405 825 513334630 513334212 1.370000e-132 483.0
14 TraesCS6D01G222200 chr6B 87.893 413 45 3 405 815 513336316 513335907 4.940000e-132 481.0
15 TraesCS6D01G222200 chr6B 86.761 423 50 4 405 825 513336878 513336460 1.380000e-127 466.0
16 TraesCS6D01G222200 chr6B 97.222 36 1 0 956 991 513333017 513332982 7.620000e-06 62.1
17 TraesCS6D01G222200 chr1A 97.227 577 11 3 1026 1602 452052171 452052742 0.000000e+00 972.0
18 TraesCS6D01G222200 chr7B 97.059 578 13 2 1026 1602 14900397 14900971 0.000000e+00 970.0
19 TraesCS6D01G222200 chr7B 97.727 44 1 0 887 930 252686031 252685988 2.720000e-10 76.8
20 TraesCS6D01G222200 chr3B 97.059 578 13 2 1026 1602 229461008 229461582 0.000000e+00 970.0
21 TraesCS6D01G222200 chr3B 92.794 569 37 2 1029 1597 358899127 358898563 0.000000e+00 821.0
22 TraesCS6D01G222200 chr3B 100.000 41 0 0 890 930 40772033 40772073 2.720000e-10 76.8
23 TraesCS6D01G222200 chr3B 93.878 49 3 0 886 934 602475731 602475779 9.790000e-10 75.0
24 TraesCS6D01G222200 chr5A 96.880 577 13 3 1026 1602 579411876 579412447 0.000000e+00 961.0
25 TraesCS6D01G222200 chr3D 78.403 551 102 14 1053 1597 191561671 191562210 2.430000e-90 342.0
26 TraesCS6D01G222200 chr7D 89.706 68 2 1 887 954 627318460 627318522 5.850000e-12 82.4
27 TraesCS6D01G222200 chr7D 92.500 40 0 3 932 971 187081942 187081906 1.000000e-03 54.7
28 TraesCS6D01G222200 chr4A 95.556 45 2 0 891 935 543333344 543333388 3.520000e-09 73.1
29 TraesCS6D01G222200 chr2D 95.349 43 2 0 897 939 533671656 533671614 4.560000e-08 69.4
30 TraesCS6D01G222200 chr5B 83.582 67 9 2 889 955 533569881 533569817 7.620000e-06 62.1


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 TraesCS6D01G222200 chr6D 313025157 313027708 2551 True 4713.000000 4713 100.000000 1 2552 1 chr6D.!!$R1 2551
1 TraesCS6D01G222200 chr6A 449964248 449965262 1014 True 796.000000 1493 95.802500 966 2552 2 chr6A.!!$R1 1586
2 TraesCS6D01G222200 chr6B 513332027 513342494 10467 True 544.554545 1447 89.679091 405 2552 11 chr6B.!!$R1 2147
3 TraesCS6D01G222200 chr1A 452052171 452052742 571 False 972.000000 972 97.227000 1026 1602 1 chr1A.!!$F1 576
4 TraesCS6D01G222200 chr7B 14900397 14900971 574 False 970.000000 970 97.059000 1026 1602 1 chr7B.!!$F1 576
5 TraesCS6D01G222200 chr3B 229461008 229461582 574 False 970.000000 970 97.059000 1026 1602 1 chr3B.!!$F2 576
6 TraesCS6D01G222200 chr3B 358898563 358899127 564 True 821.000000 821 92.794000 1029 1597 1 chr3B.!!$R1 568
7 TraesCS6D01G222200 chr5A 579411876 579412447 571 False 961.000000 961 96.880000 1026 1602 1 chr5A.!!$F1 576
8 TraesCS6D01G222200 chr3D 191561671 191562210 539 False 342.000000 342 78.403000 1053 1597 1 chr3D.!!$F1 544

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
573 3943 0.034059 AGGCCGAGTGAACTGAACAG 59.966 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 10605 0.452784 GTAGCTTTGCTTGAACGCGG 60.453 55.0 12.47 0.0 40.44 6.46 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
32 33 9.445786 TTTCTTGATTTTACTGAATTCGTGAAC 57.554 29.630 11.54 2.72 0.00 3.18
33 34 8.378172 TCTTGATTTTACTGAATTCGTGAACT 57.622 30.769 11.54 5.71 0.00 3.01
34 35 8.836413 TCTTGATTTTACTGAATTCGTGAACTT 58.164 29.630 11.54 2.93 0.00 2.66
35 36 9.450807 CTTGATTTTACTGAATTCGTGAACTTT 57.549 29.630 11.54 1.13 0.00 2.66
36 37 9.796120 TTGATTTTACTGAATTCGTGAACTTTT 57.204 25.926 11.54 0.00 0.00 2.27
37 38 9.796120 TGATTTTACTGAATTCGTGAACTTTTT 57.204 25.926 11.54 0.00 0.00 1.94
65 66 8.601845 ACTTTGCAAAGTTTTTCTAAAGTTGT 57.398 26.923 33.85 10.80 46.52 3.32
66 67 8.495148 ACTTTGCAAAGTTTTTCTAAAGTTGTG 58.505 29.630 33.85 9.51 46.52 3.33
67 68 8.594881 TTTGCAAAGTTTTTCTAAAGTTGTGA 57.405 26.923 8.05 0.00 37.07 3.58
68 69 8.594881 TTGCAAAGTTTTTCTAAAGTTGTGAA 57.405 26.923 0.00 0.00 37.07 3.18
69 70 8.770438 TGCAAAGTTTTTCTAAAGTTGTGAAT 57.230 26.923 0.00 0.00 37.07 2.57
70 71 9.213799 TGCAAAGTTTTTCTAAAGTTGTGAATT 57.786 25.926 0.00 0.00 37.07 2.17
71 72 9.476761 GCAAAGTTTTTCTAAAGTTGTGAATTG 57.523 29.630 0.00 0.00 37.07 2.32
77 78 8.795786 TTTTCTAAAGTTGTGAATTGAATCCG 57.204 30.769 0.00 0.00 0.00 4.18
78 79 7.737972 TTCTAAAGTTGTGAATTGAATCCGA 57.262 32.000 0.00 0.00 0.00 4.55
79 80 7.921786 TCTAAAGTTGTGAATTGAATCCGAT 57.078 32.000 0.00 0.00 0.00 4.18
80 81 7.751732 TCTAAAGTTGTGAATTGAATCCGATG 58.248 34.615 0.00 0.00 0.00 3.84
81 82 6.573664 AAAGTTGTGAATTGAATCCGATGA 57.426 33.333 0.00 0.00 0.00 2.92
82 83 6.573664 AAGTTGTGAATTGAATCCGATGAA 57.426 33.333 0.00 0.00 0.00 2.57
83 84 5.942872 AGTTGTGAATTGAATCCGATGAAC 58.057 37.500 0.00 0.00 0.00 3.18
84 85 5.707298 AGTTGTGAATTGAATCCGATGAACT 59.293 36.000 0.00 0.00 0.00 3.01
85 86 6.207417 AGTTGTGAATTGAATCCGATGAACTT 59.793 34.615 0.00 0.00 0.00 2.66
86 87 6.573664 TGTGAATTGAATCCGATGAACTTT 57.426 33.333 0.00 0.00 0.00 2.66
87 88 6.980593 TGTGAATTGAATCCGATGAACTTTT 58.019 32.000 0.00 0.00 0.00 2.27
88 89 7.432869 TGTGAATTGAATCCGATGAACTTTTT 58.567 30.769 0.00 0.00 0.00 1.94
89 90 7.594758 TGTGAATTGAATCCGATGAACTTTTTC 59.405 33.333 0.00 0.00 0.00 2.29
90 91 7.062255 GTGAATTGAATCCGATGAACTTTTTCC 59.938 37.037 0.00 0.00 0.00 3.13
91 92 6.588719 ATTGAATCCGATGAACTTTTTCCA 57.411 33.333 0.00 0.00 0.00 3.53
92 93 6.398234 TTGAATCCGATGAACTTTTTCCAA 57.602 33.333 0.00 0.00 0.00 3.53
93 94 6.398234 TGAATCCGATGAACTTTTTCCAAA 57.602 33.333 0.00 0.00 0.00 3.28
94 95 6.991938 TGAATCCGATGAACTTTTTCCAAAT 58.008 32.000 0.00 0.00 0.00 2.32
95 96 7.090173 TGAATCCGATGAACTTTTTCCAAATC 58.910 34.615 0.00 0.00 0.00 2.17
96 97 5.385509 TCCGATGAACTTTTTCCAAATCC 57.614 39.130 0.00 0.00 0.00 3.01
97 98 5.076873 TCCGATGAACTTTTTCCAAATCCT 58.923 37.500 0.00 0.00 0.00 3.24
98 99 5.538433 TCCGATGAACTTTTTCCAAATCCTT 59.462 36.000 0.00 0.00 0.00 3.36
99 100 5.634859 CCGATGAACTTTTTCCAAATCCTTG 59.365 40.000 0.00 0.00 0.00 3.61
100 101 6.215845 CGATGAACTTTTTCCAAATCCTTGT 58.784 36.000 0.00 0.00 0.00 3.16
101 102 6.701400 CGATGAACTTTTTCCAAATCCTTGTT 59.299 34.615 0.00 0.00 0.00 2.83
102 103 7.224557 CGATGAACTTTTTCCAAATCCTTGTTT 59.775 33.333 0.00 0.00 0.00 2.83
103 104 8.806429 ATGAACTTTTTCCAAATCCTTGTTTT 57.194 26.923 0.00 0.00 0.00 2.43
104 105 8.628630 TGAACTTTTTCCAAATCCTTGTTTTT 57.371 26.923 0.00 0.00 0.00 1.94
175 176 7.967890 AATGAACTTTTTCAAATCCATGGAC 57.032 32.000 18.99 0.00 45.01 4.02
176 177 5.852827 TGAACTTTTTCAAATCCATGGACC 58.147 37.500 18.99 0.00 38.87 4.46
177 178 5.602145 TGAACTTTTTCAAATCCATGGACCT 59.398 36.000 18.99 4.16 38.87 3.85
178 179 6.099557 TGAACTTTTTCAAATCCATGGACCTT 59.900 34.615 18.99 10.97 38.87 3.50
179 180 6.499106 ACTTTTTCAAATCCATGGACCTTT 57.501 33.333 18.99 12.23 0.00 3.11
180 181 6.899089 ACTTTTTCAAATCCATGGACCTTTT 58.101 32.000 18.99 11.43 0.00 2.27
181 182 6.992123 ACTTTTTCAAATCCATGGACCTTTTC 59.008 34.615 18.99 0.00 0.00 2.29
182 183 6.745794 TTTTCAAATCCATGGACCTTTTCT 57.254 33.333 18.99 0.00 0.00 2.52
183 184 6.745794 TTTCAAATCCATGGACCTTTTCTT 57.254 33.333 18.99 2.10 0.00 2.52
184 185 6.745794 TTCAAATCCATGGACCTTTTCTTT 57.254 33.333 18.99 9.05 0.00 2.52
185 186 6.745794 TCAAATCCATGGACCTTTTCTTTT 57.254 33.333 18.99 8.26 0.00 2.27
186 187 7.135591 TCAAATCCATGGACCTTTTCTTTTT 57.864 32.000 18.99 7.49 0.00 1.94
187 188 8.256356 TCAAATCCATGGACCTTTTCTTTTTA 57.744 30.769 18.99 0.00 0.00 1.52
188 189 8.709308 TCAAATCCATGGACCTTTTCTTTTTAA 58.291 29.630 18.99 0.00 0.00 1.52
189 190 9.336171 CAAATCCATGGACCTTTTCTTTTTAAA 57.664 29.630 18.99 0.00 0.00 1.52
190 191 9.913310 AAATCCATGGACCTTTTCTTTTTAAAA 57.087 25.926 18.99 0.00 0.00 1.52
192 193 9.725019 ATCCATGGACCTTTTCTTTTTAAAATC 57.275 29.630 18.99 0.00 0.00 2.17
193 194 8.154203 TCCATGGACCTTTTCTTTTTAAAATCC 58.846 33.333 11.44 3.97 32.04 3.01
194 195 7.117667 CCATGGACCTTTTCTTTTTAAAATCCG 59.882 37.037 5.56 0.00 33.23 4.18
195 196 6.517605 TGGACCTTTTCTTTTTAAAATCCGG 58.482 36.000 0.55 0.00 33.23 5.14
196 197 5.929992 GGACCTTTTCTTTTTAAAATCCGGG 59.070 40.000 0.00 3.21 0.00 5.73
197 198 6.239373 GGACCTTTTCTTTTTAAAATCCGGGA 60.239 38.462 0.00 0.00 0.00 5.14
198 199 7.127012 ACCTTTTCTTTTTAAAATCCGGGAA 57.873 32.000 0.00 0.35 0.00 3.97
199 200 6.987992 ACCTTTTCTTTTTAAAATCCGGGAAC 59.012 34.615 0.00 0.00 0.00 3.62
200 201 6.987404 CCTTTTCTTTTTAAAATCCGGGAACA 59.013 34.615 0.00 0.00 0.00 3.18
201 202 7.659799 CCTTTTCTTTTTAAAATCCGGGAACAT 59.340 33.333 0.00 0.00 0.00 2.71
202 203 7.954788 TTTCTTTTTAAAATCCGGGAACATG 57.045 32.000 0.00 0.00 0.00 3.21
203 204 6.658188 TCTTTTTAAAATCCGGGAACATGT 57.342 33.333 0.00 0.00 0.00 3.21
204 205 7.056844 TCTTTTTAAAATCCGGGAACATGTT 57.943 32.000 11.78 11.78 0.00 2.71
205 206 7.501844 TCTTTTTAAAATCCGGGAACATGTTT 58.498 30.769 13.36 0.00 0.00 2.83
206 207 7.654116 TCTTTTTAAAATCCGGGAACATGTTTC 59.346 33.333 13.36 10.89 0.00 2.78
207 208 6.406692 TTTAAAATCCGGGAACATGTTTCA 57.593 33.333 18.62 0.00 0.00 2.69
208 209 4.946478 AAAATCCGGGAACATGTTTCAA 57.054 36.364 18.62 3.93 0.00 2.69
209 210 4.946478 AAATCCGGGAACATGTTTCAAA 57.054 36.364 18.62 3.57 0.00 2.69
210 211 5.482163 AAATCCGGGAACATGTTTCAAAT 57.518 34.783 18.62 5.74 0.00 2.32
211 212 4.718940 ATCCGGGAACATGTTTCAAATC 57.281 40.909 18.62 1.76 0.00 2.17
212 213 2.486203 TCCGGGAACATGTTTCAAATCG 59.514 45.455 18.62 11.94 0.00 3.34
213 214 2.415357 CCGGGAACATGTTTCAAATCGG 60.415 50.000 18.62 16.69 0.00 4.18
214 215 2.606108 GGGAACATGTTTCAAATCGGC 58.394 47.619 18.62 0.00 0.00 5.54
215 216 2.029470 GGGAACATGTTTCAAATCGGCA 60.029 45.455 18.62 0.00 0.00 5.69
216 217 3.553922 GGGAACATGTTTCAAATCGGCAA 60.554 43.478 18.62 0.00 0.00 4.52
217 218 4.244862 GGAACATGTTTCAAATCGGCAAT 58.755 39.130 13.36 0.00 0.00 3.56
218 219 4.690280 GGAACATGTTTCAAATCGGCAATT 59.310 37.500 13.36 0.00 0.00 2.32
219 220 5.179182 GGAACATGTTTCAAATCGGCAATTT 59.821 36.000 13.36 0.00 38.11 1.82
220 221 6.293353 GGAACATGTTTCAAATCGGCAATTTT 60.293 34.615 13.36 0.00 35.32 1.82
221 222 6.616774 ACATGTTTCAAATCGGCAATTTTT 57.383 29.167 0.00 0.00 35.32 1.94
251 252 9.953565 AATCTGATGATTTTTCCACAAATTGAT 57.046 25.926 0.00 0.00 39.68 2.57
252 253 8.766000 TCTGATGATTTTTCCACAAATTGATG 57.234 30.769 0.00 0.00 0.00 3.07
253 254 8.586744 TCTGATGATTTTTCCACAAATTGATGA 58.413 29.630 0.00 0.00 0.00 2.92
254 255 9.210329 CTGATGATTTTTCCACAAATTGATGAA 57.790 29.630 0.00 0.00 0.00 2.57
255 256 8.991026 TGATGATTTTTCCACAAATTGATGAAC 58.009 29.630 0.00 0.00 0.00 3.18
256 257 7.727331 TGATTTTTCCACAAATTGATGAACC 57.273 32.000 0.00 0.00 0.00 3.62
257 258 7.507829 TGATTTTTCCACAAATTGATGAACCT 58.492 30.769 0.00 0.00 0.00 3.50
258 259 7.992033 TGATTTTTCCACAAATTGATGAACCTT 59.008 29.630 0.00 0.00 0.00 3.50
259 260 8.750515 ATTTTTCCACAAATTGATGAACCTTT 57.249 26.923 0.00 0.00 0.00 3.11
260 261 8.572855 TTTTTCCACAAATTGATGAACCTTTT 57.427 26.923 0.00 0.00 0.00 2.27
261 262 8.572855 TTTTCCACAAATTGATGAACCTTTTT 57.427 26.923 0.00 0.00 0.00 1.94
279 280 3.810310 TTTTTCAAACCCATGAGCGTT 57.190 38.095 0.00 0.00 0.00 4.84
280 281 3.810310 TTTTCAAACCCATGAGCGTTT 57.190 38.095 0.00 0.00 32.48 3.60
281 282 3.363341 TTTCAAACCCATGAGCGTTTC 57.637 42.857 0.00 0.00 29.85 2.78
282 283 2.270352 TCAAACCCATGAGCGTTTCT 57.730 45.000 0.00 0.00 29.85 2.52
283 284 2.151202 TCAAACCCATGAGCGTTTCTC 58.849 47.619 0.00 0.00 42.23 2.87
320 321 6.890663 TTTTGAACGACTAACTTCTTTCGA 57.109 33.333 0.00 0.00 35.45 3.71
321 322 6.890663 TTTGAACGACTAACTTCTTTCGAA 57.109 33.333 0.00 0.00 35.45 3.71
322 323 7.473027 TTTGAACGACTAACTTCTTTCGAAT 57.527 32.000 0.00 0.00 35.45 3.34
323 324 7.473027 TTGAACGACTAACTTCTTTCGAATT 57.527 32.000 0.00 0.00 35.45 2.17
324 325 7.473027 TGAACGACTAACTTCTTTCGAATTT 57.527 32.000 0.00 0.00 35.45 1.82
325 326 8.578308 TGAACGACTAACTTCTTTCGAATTTA 57.422 30.769 0.00 0.00 35.45 1.40
326 327 8.697067 TGAACGACTAACTTCTTTCGAATTTAG 58.303 33.333 0.00 4.40 42.99 1.85
328 329 8.004585 ACGACTAACTTCTTTCGAATTTAGTG 57.995 34.615 17.08 13.03 46.64 2.74
329 330 7.115947 ACGACTAACTTCTTTCGAATTTAGTGG 59.884 37.037 17.08 17.22 46.64 4.00
330 331 7.327761 CGACTAACTTCTTTCGAATTTAGTGGA 59.672 37.037 17.08 5.65 46.64 4.02
331 332 8.897872 ACTAACTTCTTTCGAATTTAGTGGAA 57.102 30.769 13.51 0.00 45.77 3.53
332 333 9.503399 ACTAACTTCTTTCGAATTTAGTGGAAT 57.497 29.630 13.51 0.00 45.77 3.01
401 402 5.652518 CTTTTCCCAAAAAGTAAACGGTCA 58.347 37.500 3.11 0.00 44.17 4.02
402 403 5.656213 TTTCCCAAAAAGTAAACGGTCAA 57.344 34.783 0.00 0.00 0.00 3.18
403 404 4.904253 TCCCAAAAAGTAAACGGTCAAG 57.096 40.909 0.00 0.00 0.00 3.02
408 409 4.625972 AAAAGTAAACGGTCAAGTGGTG 57.374 40.909 0.00 0.00 0.00 4.17
420 421 3.041940 GTGGTGAACCGCGACCAG 61.042 66.667 16.81 0.00 43.01 4.00
421 422 4.308458 TGGTGAACCGCGACCAGG 62.308 66.667 12.90 0.00 37.32 4.45
428 2112 1.833787 AACCGCGACCAGGTAACCAT 61.834 55.000 8.23 0.00 41.95 3.55
434 2118 2.944094 GCGACCAGGTAACCATGGAAAT 60.944 50.000 21.47 6.72 39.02 2.17
472 2718 1.220749 GTCGCTCTATGTTGGGCCA 59.779 57.895 0.00 0.00 0.00 5.36
486 2732 4.816984 GCCAGCCCATGAGCAGCT 62.817 66.667 0.76 0.00 37.32 4.24
497 2743 3.989838 GAGCAGCTGGGCATGAGCA 62.990 63.158 17.12 0.00 44.61 4.26
505 2751 1.337384 TGGGCATGAGCACCGTCTAT 61.337 55.000 0.00 0.00 46.13 1.98
511 2757 3.739519 GCATGAGCACCGTCTATTCTTCT 60.740 47.826 0.00 0.00 41.58 2.85
513 2759 2.166459 TGAGCACCGTCTATTCTTCTGG 59.834 50.000 0.00 0.00 0.00 3.86
515 2761 2.166664 AGCACCGTCTATTCTTCTGGAC 59.833 50.000 0.00 0.00 0.00 4.02
557 3927 2.124695 CCCTCCGGTTTGCTAGGC 60.125 66.667 0.00 0.00 0.00 3.93
571 3941 1.997669 CTAGGCCGAGTGAACTGAAC 58.002 55.000 4.41 0.00 0.00 3.18
573 3943 0.034059 AGGCCGAGTGAACTGAACAG 59.966 55.000 0.00 0.00 0.00 3.16
576 3946 1.795286 GCCGAGTGAACTGAACAGAAG 59.205 52.381 8.87 0.00 0.00 2.85
579 3949 4.310769 CCGAGTGAACTGAACAGAAGAAT 58.689 43.478 8.87 0.00 0.00 2.40
603 3973 9.935682 AATGACACATAATTTTAGACGCTATTG 57.064 29.630 0.00 0.00 0.00 1.90
606 3976 8.500753 ACACATAATTTTAGACGCTATTGGAA 57.499 30.769 0.00 0.00 0.00 3.53
631 4001 4.540715 GGAATCAGACCCAATTCCTGAAT 58.459 43.478 6.83 0.00 44.97 2.57
722 9147 1.812571 AGTCGCAAATCACAACATCCC 59.187 47.619 0.00 0.00 0.00 3.85
817 9805 6.667007 ATTTGGATTCAAAATTCATTCGGC 57.333 33.333 2.57 0.00 44.83 5.54
824 9812 3.058450 CAAAATTCATTCGGCAACTGCA 58.942 40.909 3.76 0.00 44.36 4.41
841 9832 4.769688 ACTGCATGATATCTTTCGACCAA 58.230 39.130 3.98 0.00 0.00 3.67
849 9840 5.188163 TGATATCTTTCGACCAAGGTAACCA 59.812 40.000 3.98 0.00 37.17 3.67
853 9844 5.134661 TCTTTCGACCAAGGTAACCAAAAT 58.865 37.500 0.00 0.00 37.17 1.82
859 9850 6.043411 CGACCAAGGTAACCAAAATTTTTGA 58.957 36.000 20.74 1.13 37.17 2.69
873 9864 2.214376 TTTTGATGCCCCACGAGATT 57.786 45.000 0.00 0.00 0.00 2.40
898 9889 6.732896 TTTATCATCTGAACTACTCCCTCC 57.267 41.667 0.00 0.00 0.00 4.30
899 9890 2.656002 TCATCTGAACTACTCCCTCCG 58.344 52.381 0.00 0.00 0.00 4.63
900 9891 2.025226 TCATCTGAACTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
901 9892 2.125773 TCTGAACTACTCCCTCCGTC 57.874 55.000 0.00 0.00 0.00 4.79
902 9893 1.104630 CTGAACTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
903 9894 0.324091 TGAACTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
904 9895 0.324091 GAACTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
905 9896 0.614134 AACTACTCCCTCCGTCCCAC 60.614 60.000 0.00 0.00 0.00 4.61
906 9897 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
907 9898 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
908 9899 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
909 9900 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
910 9901 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
911 9902 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
912 9903 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
913 9904 3.386063 TCCCTCCGTCCCACAATATAAA 58.614 45.455 0.00 0.00 0.00 1.40
914 9905 3.781407 TCCCTCCGTCCCACAATATAAAA 59.219 43.478 0.00 0.00 0.00 1.52
915 9906 4.134563 CCCTCCGTCCCACAATATAAAAG 58.865 47.826 0.00 0.00 0.00 2.27
916 9907 3.564225 CCTCCGTCCCACAATATAAAAGC 59.436 47.826 0.00 0.00 0.00 3.51
917 9908 3.199677 TCCGTCCCACAATATAAAAGCG 58.800 45.455 0.00 0.00 0.00 4.68
918 9909 2.940410 CCGTCCCACAATATAAAAGCGT 59.060 45.455 0.00 0.00 0.00 5.07
919 9910 3.375922 CCGTCCCACAATATAAAAGCGTT 59.624 43.478 0.00 0.00 0.00 4.84
920 9911 4.142556 CCGTCCCACAATATAAAAGCGTTT 60.143 41.667 2.53 2.53 0.00 3.60
921 9912 5.395642 CGTCCCACAATATAAAAGCGTTTT 58.604 37.500 2.19 1.29 36.67 2.43
922 9913 5.859648 CGTCCCACAATATAAAAGCGTTTTT 59.140 36.000 14.50 14.50 39.69 1.94
923 9914 6.183359 CGTCCCACAATATAAAAGCGTTTTTG 60.183 38.462 18.77 6.09 37.12 2.44
924 9915 6.864165 GTCCCACAATATAAAAGCGTTTTTGA 59.136 34.615 18.77 8.06 37.12 2.69
925 9916 6.864165 TCCCACAATATAAAAGCGTTTTTGAC 59.136 34.615 18.77 0.00 37.12 3.18
926 9917 6.642950 CCCACAATATAAAAGCGTTTTTGACA 59.357 34.615 18.77 5.33 37.12 3.58
927 9918 7.358848 CCCACAATATAAAAGCGTTTTTGACAC 60.359 37.037 18.77 0.00 37.12 3.67
928 9919 7.381139 CCACAATATAAAAGCGTTTTTGACACT 59.619 33.333 18.77 2.86 37.12 3.55
929 9920 9.388346 CACAATATAAAAGCGTTTTTGACACTA 57.612 29.630 18.77 0.00 37.12 2.74
930 9921 9.607285 ACAATATAAAAGCGTTTTTGACACTAG 57.393 29.630 18.77 6.47 37.12 2.57
931 9922 9.607285 CAATATAAAAGCGTTTTTGACACTAGT 57.393 29.630 18.77 0.00 37.12 2.57
937 9928 9.607285 AAAAGCGTTTTTGACACTAGTATATTG 57.393 29.630 9.31 0.00 35.26 1.90
938 9929 7.900782 AGCGTTTTTGACACTAGTATATTGT 57.099 32.000 0.00 0.00 37.15 2.71
939 9930 7.739295 AGCGTTTTTGACACTAGTATATTGTG 58.261 34.615 0.00 0.00 34.37 3.33
940 9931 6.959311 GCGTTTTTGACACTAGTATATTGTGG 59.041 38.462 0.00 0.00 34.37 4.17
941 9932 7.461107 CGTTTTTGACACTAGTATATTGTGGG 58.539 38.462 0.00 0.00 34.37 4.61
942 9933 7.332430 CGTTTTTGACACTAGTATATTGTGGGA 59.668 37.037 0.00 0.00 34.37 4.37
943 9934 8.448615 GTTTTTGACACTAGTATATTGTGGGAC 58.551 37.037 0.00 0.00 34.37 4.46
944 9935 5.509716 TGACACTAGTATATTGTGGGACG 57.490 43.478 0.00 0.00 34.37 4.79
945 9936 4.340097 TGACACTAGTATATTGTGGGACGG 59.660 45.833 0.00 0.00 34.37 4.79
946 9937 4.539726 ACACTAGTATATTGTGGGACGGA 58.460 43.478 0.00 0.00 38.75 4.69
947 9938 4.583489 ACACTAGTATATTGTGGGACGGAG 59.417 45.833 0.00 0.00 38.75 4.63
948 9939 4.022242 CACTAGTATATTGTGGGACGGAGG 60.022 50.000 0.00 0.00 31.83 4.30
949 9940 2.326428 AGTATATTGTGGGACGGAGGG 58.674 52.381 0.00 0.00 0.00 4.30
950 9941 2.090943 AGTATATTGTGGGACGGAGGGA 60.091 50.000 0.00 0.00 0.00 4.20
951 9942 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
952 9943 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
953 9944 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
954 9945 0.613853 TTGTGGGACGGAGGGAGTAG 60.614 60.000 0.00 0.00 0.00 2.57
988 9979 3.993920 ACAATCCACTTTTGGCATGTTC 58.006 40.909 0.00 0.00 43.56 3.18
992 9983 2.361757 TCCACTTTTGGCATGTTCACTG 59.638 45.455 0.00 0.00 43.56 3.66
1024 10015 7.720957 ACATGCATAGCCTGTTTGAATCTTATA 59.279 33.333 0.00 0.00 33.97 0.98
1113 10104 2.018515 GCTACTTCTCTAGCTCGTGGT 58.981 52.381 0.00 0.00 36.88 4.16
1469 10460 3.499745 GGTTGTTGGGGTCCTCTTTGTAT 60.500 47.826 0.00 0.00 0.00 2.29
1541 10532 8.194104 TGTAAAATGCTGTGTACTTCATGTTTT 58.806 29.630 0.00 4.86 0.00 2.43
1542 10533 9.030301 GTAAAATGCTGTGTACTTCATGTTTTT 57.970 29.630 0.00 3.67 0.00 1.94
1543 10534 7.698836 AAATGCTGTGTACTTCATGTTTTTC 57.301 32.000 0.00 0.00 0.00 2.29
1544 10535 5.826601 TGCTGTGTACTTCATGTTTTTCA 57.173 34.783 0.00 0.00 0.00 2.69
1545 10536 5.577835 TGCTGTGTACTTCATGTTTTTCAC 58.422 37.500 0.00 0.00 0.00 3.18
1564 10555 1.065491 ACTGTTAATGCAGCATCGGGA 60.065 47.619 8.77 0.00 39.96 5.14
1588 10579 3.495453 CCTTCTGGACCCGTCTTTTGTTA 60.495 47.826 0.00 0.00 34.57 2.41
1592 10583 5.134661 TCTGGACCCGTCTTTTGTTAAAAT 58.865 37.500 0.00 0.00 0.00 1.82
1597 10588 8.422566 TGGACCCGTCTTTTGTTAAAATAAAAT 58.577 29.630 0.00 0.00 30.40 1.82
1731 10743 7.427214 GTTATCTACAGTATGGAACCTCTCAC 58.573 42.308 0.00 0.00 43.62 3.51
1815 10827 1.785041 GCGGACACTTCAGCAAGCAA 61.785 55.000 0.00 0.00 42.10 3.91
1868 10880 0.616964 TCCATCTGCCTCAGCTCACT 60.617 55.000 0.00 0.00 40.80 3.41
1869 10881 0.462225 CCATCTGCCTCAGCTCACTG 60.462 60.000 0.00 0.00 45.95 3.66
1896 10908 0.684805 CTCCGCAGAGGTAGTTCCCT 60.685 60.000 0.00 0.00 41.99 4.20
1990 11002 4.719369 GCACGCCTCCGACGAACT 62.719 66.667 0.00 0.00 38.29 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.445786 GTTCACGAATTCAGTAAAATCAAGAAA 57.554 29.630 6.22 0.00 0.00 2.52
7 8 8.836413 AGTTCACGAATTCAGTAAAATCAAGAA 58.164 29.630 6.22 0.34 0.00 2.52
8 9 8.378172 AGTTCACGAATTCAGTAAAATCAAGA 57.622 30.769 6.22 0.00 0.00 3.02
9 10 9.450807 AAAGTTCACGAATTCAGTAAAATCAAG 57.549 29.630 6.22 0.00 0.00 3.02
10 11 9.796120 AAAAGTTCACGAATTCAGTAAAATCAA 57.204 25.926 6.22 0.00 0.00 2.57
11 12 9.796120 AAAAAGTTCACGAATTCAGTAAAATCA 57.204 25.926 6.22 0.00 0.00 2.57
41 42 8.707839 TCACAACTTTAGAAAAACTTTGCAAAG 58.292 29.630 32.53 32.53 41.73 2.77
42 43 8.594881 TCACAACTTTAGAAAAACTTTGCAAA 57.405 26.923 12.14 12.14 0.00 3.68
43 44 8.594881 TTCACAACTTTAGAAAAACTTTGCAA 57.405 26.923 0.00 0.00 0.00 4.08
44 45 8.770438 ATTCACAACTTTAGAAAAACTTTGCA 57.230 26.923 0.00 0.00 0.00 4.08
45 46 9.476761 CAATTCACAACTTTAGAAAAACTTTGC 57.523 29.630 0.00 0.00 0.00 3.68
51 52 9.243637 CGGATTCAATTCACAACTTTAGAAAAA 57.756 29.630 0.00 0.00 0.00 1.94
52 53 8.625651 TCGGATTCAATTCACAACTTTAGAAAA 58.374 29.630 0.00 0.00 0.00 2.29
53 54 8.160521 TCGGATTCAATTCACAACTTTAGAAA 57.839 30.769 0.00 0.00 0.00 2.52
54 55 7.737972 TCGGATTCAATTCACAACTTTAGAA 57.262 32.000 0.00 0.00 0.00 2.10
55 56 7.606073 TCATCGGATTCAATTCACAACTTTAGA 59.394 33.333 0.00 0.00 0.00 2.10
56 57 7.751732 TCATCGGATTCAATTCACAACTTTAG 58.248 34.615 0.00 0.00 0.00 1.85
57 58 7.680442 TCATCGGATTCAATTCACAACTTTA 57.320 32.000 0.00 0.00 0.00 1.85
58 59 6.573664 TCATCGGATTCAATTCACAACTTT 57.426 33.333 0.00 0.00 0.00 2.66
59 60 6.207417 AGTTCATCGGATTCAATTCACAACTT 59.793 34.615 0.00 0.00 0.00 2.66
60 61 5.707298 AGTTCATCGGATTCAATTCACAACT 59.293 36.000 0.00 0.00 0.00 3.16
61 62 5.942872 AGTTCATCGGATTCAATTCACAAC 58.057 37.500 0.00 0.00 0.00 3.32
62 63 6.573664 AAGTTCATCGGATTCAATTCACAA 57.426 33.333 0.00 0.00 0.00 3.33
63 64 6.573664 AAAGTTCATCGGATTCAATTCACA 57.426 33.333 0.00 0.00 0.00 3.58
64 65 7.062255 GGAAAAAGTTCATCGGATTCAATTCAC 59.938 37.037 0.00 0.00 35.25 3.18
65 66 7.090173 GGAAAAAGTTCATCGGATTCAATTCA 58.910 34.615 0.00 0.00 35.25 2.57
66 67 7.090173 TGGAAAAAGTTCATCGGATTCAATTC 58.910 34.615 0.00 0.00 35.25 2.17
67 68 6.991938 TGGAAAAAGTTCATCGGATTCAATT 58.008 32.000 0.00 0.00 35.25 2.32
68 69 6.588719 TGGAAAAAGTTCATCGGATTCAAT 57.411 33.333 0.00 0.00 35.25 2.57
69 70 6.398234 TTGGAAAAAGTTCATCGGATTCAA 57.602 33.333 0.00 0.00 35.25 2.69
70 71 6.398234 TTTGGAAAAAGTTCATCGGATTCA 57.602 33.333 0.00 0.00 35.25 2.57
71 72 6.531594 GGATTTGGAAAAAGTTCATCGGATTC 59.468 38.462 0.00 0.00 35.25 2.52
72 73 6.211384 AGGATTTGGAAAAAGTTCATCGGATT 59.789 34.615 0.00 0.00 35.25 3.01
73 74 5.716703 AGGATTTGGAAAAAGTTCATCGGAT 59.283 36.000 0.00 0.00 35.25 4.18
74 75 5.076873 AGGATTTGGAAAAAGTTCATCGGA 58.923 37.500 0.00 0.00 35.25 4.55
75 76 5.391312 AGGATTTGGAAAAAGTTCATCGG 57.609 39.130 0.00 0.00 35.25 4.18
76 77 6.215845 ACAAGGATTTGGAAAAAGTTCATCG 58.784 36.000 0.00 0.00 38.66 3.84
77 78 8.437360 AAACAAGGATTTGGAAAAAGTTCATC 57.563 30.769 0.00 0.00 38.66 2.92
78 79 8.806429 AAAACAAGGATTTGGAAAAAGTTCAT 57.194 26.923 0.00 0.00 38.66 2.57
79 80 8.628630 AAAAACAAGGATTTGGAAAAAGTTCA 57.371 26.923 0.00 0.00 38.66 3.18
149 150 9.487790 GTCCATGGATTTGAAAAAGTTCATTAA 57.512 29.630 19.62 0.00 43.29 1.40
150 151 8.093927 GGTCCATGGATTTGAAAAAGTTCATTA 58.906 33.333 19.62 0.00 43.29 1.90
151 152 6.936335 GGTCCATGGATTTGAAAAAGTTCATT 59.064 34.615 19.62 0.00 43.29 2.57
152 153 6.270695 AGGTCCATGGATTTGAAAAAGTTCAT 59.729 34.615 19.62 0.00 43.29 2.57
153 154 5.602145 AGGTCCATGGATTTGAAAAAGTTCA 59.398 36.000 19.62 0.00 42.12 3.18
154 155 6.101650 AGGTCCATGGATTTGAAAAAGTTC 57.898 37.500 19.62 0.00 0.00 3.01
155 156 6.499106 AAGGTCCATGGATTTGAAAAAGTT 57.501 33.333 19.62 0.00 0.00 2.66
156 157 6.499106 AAAGGTCCATGGATTTGAAAAAGT 57.501 33.333 19.62 0.00 0.00 2.66
157 158 7.219322 AGAAAAGGTCCATGGATTTGAAAAAG 58.781 34.615 19.62 0.00 0.00 2.27
158 159 7.135591 AGAAAAGGTCCATGGATTTGAAAAA 57.864 32.000 19.62 0.00 0.00 1.94
159 160 6.745794 AGAAAAGGTCCATGGATTTGAAAA 57.254 33.333 19.62 0.00 0.00 2.29
160 161 6.745794 AAGAAAAGGTCCATGGATTTGAAA 57.254 33.333 19.62 0.00 0.00 2.69
161 162 6.745794 AAAGAAAAGGTCCATGGATTTGAA 57.254 33.333 19.62 0.00 0.00 2.69
162 163 6.745794 AAAAGAAAAGGTCCATGGATTTGA 57.254 33.333 19.62 0.00 0.00 2.69
163 164 8.900983 TTAAAAAGAAAAGGTCCATGGATTTG 57.099 30.769 19.62 0.00 0.00 2.32
164 165 9.913310 TTTTAAAAAGAAAAGGTCCATGGATTT 57.087 25.926 19.62 14.61 0.00 2.17
166 167 9.725019 GATTTTAAAAAGAAAAGGTCCATGGAT 57.275 29.630 19.62 0.00 32.06 3.41
167 168 8.154203 GGATTTTAAAAAGAAAAGGTCCATGGA 58.846 33.333 11.44 11.44 31.77 3.41
168 169 7.117667 CGGATTTTAAAAAGAAAAGGTCCATGG 59.882 37.037 4.97 4.97 31.25 3.66
169 170 7.117667 CCGGATTTTAAAAAGAAAAGGTCCATG 59.882 37.037 4.44 0.00 31.25 3.66
170 171 7.158697 CCGGATTTTAAAAAGAAAAGGTCCAT 58.841 34.615 4.44 0.00 31.25 3.41
171 172 6.463190 CCCGGATTTTAAAAAGAAAAGGTCCA 60.463 38.462 0.73 0.00 31.25 4.02
172 173 5.929992 CCCGGATTTTAAAAAGAAAAGGTCC 59.070 40.000 0.73 4.04 32.06 4.46
173 174 6.751157 TCCCGGATTTTAAAAAGAAAAGGTC 58.249 36.000 0.73 0.00 32.06 3.85
174 175 6.734502 TCCCGGATTTTAAAAAGAAAAGGT 57.265 33.333 0.73 0.00 32.06 3.50
175 176 6.987404 TGTTCCCGGATTTTAAAAAGAAAAGG 59.013 34.615 0.73 2.30 32.06 3.11
176 177 8.495148 CATGTTCCCGGATTTTAAAAAGAAAAG 58.505 33.333 0.73 0.00 32.06 2.27
177 178 7.988028 ACATGTTCCCGGATTTTAAAAAGAAAA 59.012 29.630 0.73 0.17 33.04 2.29
178 179 7.501844 ACATGTTCCCGGATTTTAAAAAGAAA 58.498 30.769 0.73 0.00 0.00 2.52
179 180 7.056844 ACATGTTCCCGGATTTTAAAAAGAA 57.943 32.000 0.73 1.50 0.00 2.52
180 181 6.658188 ACATGTTCCCGGATTTTAAAAAGA 57.342 33.333 0.73 0.00 0.00 2.52
181 182 7.439655 TGAAACATGTTCCCGGATTTTAAAAAG 59.560 33.333 12.39 0.06 0.00 2.27
182 183 7.272978 TGAAACATGTTCCCGGATTTTAAAAA 58.727 30.769 12.39 0.00 0.00 1.94
183 184 6.817184 TGAAACATGTTCCCGGATTTTAAAA 58.183 32.000 12.39 2.51 0.00 1.52
184 185 6.406692 TGAAACATGTTCCCGGATTTTAAA 57.593 33.333 12.39 0.00 0.00 1.52
185 186 6.406692 TTGAAACATGTTCCCGGATTTTAA 57.593 33.333 12.39 0.00 0.00 1.52
186 187 6.406692 TTTGAAACATGTTCCCGGATTTTA 57.593 33.333 12.39 0.00 0.00 1.52
187 188 4.946478 TTGAAACATGTTCCCGGATTTT 57.054 36.364 12.39 0.00 0.00 1.82
188 189 4.946478 TTTGAAACATGTTCCCGGATTT 57.054 36.364 12.39 0.00 0.00 2.17
189 190 4.380444 CGATTTGAAACATGTTCCCGGATT 60.380 41.667 12.39 0.00 0.00 3.01
190 191 3.128589 CGATTTGAAACATGTTCCCGGAT 59.871 43.478 12.39 3.07 0.00 4.18
191 192 2.486203 CGATTTGAAACATGTTCCCGGA 59.514 45.455 12.39 0.00 0.00 5.14
192 193 2.415357 CCGATTTGAAACATGTTCCCGG 60.415 50.000 12.39 13.59 0.00 5.73
193 194 2.862512 CCGATTTGAAACATGTTCCCG 58.137 47.619 12.39 8.94 0.00 5.14
194 195 2.029470 TGCCGATTTGAAACATGTTCCC 60.029 45.455 12.39 7.71 0.00 3.97
195 196 3.296322 TGCCGATTTGAAACATGTTCC 57.704 42.857 12.39 0.00 0.00 3.62
196 197 5.844301 AATTGCCGATTTGAAACATGTTC 57.156 34.783 12.39 6.33 0.00 3.18
197 198 6.616774 AAAATTGCCGATTTGAAACATGTT 57.383 29.167 4.92 4.92 37.98 2.71
198 199 6.616774 AAAAATTGCCGATTTGAAACATGT 57.383 29.167 0.00 0.00 37.98 3.21
225 226 9.953565 ATCAATTTGTGGAAAAATCATCAGATT 57.046 25.926 0.00 0.00 46.20 2.40
226 227 9.378551 CATCAATTTGTGGAAAAATCATCAGAT 57.621 29.630 0.00 0.00 35.53 2.90
227 228 8.586744 TCATCAATTTGTGGAAAAATCATCAGA 58.413 29.630 0.00 0.00 0.00 3.27
228 229 8.766000 TCATCAATTTGTGGAAAAATCATCAG 57.234 30.769 0.00 0.00 0.00 2.90
229 230 8.991026 GTTCATCAATTTGTGGAAAAATCATCA 58.009 29.630 0.00 0.00 0.00 3.07
230 231 8.445493 GGTTCATCAATTTGTGGAAAAATCATC 58.555 33.333 0.00 0.00 0.00 2.92
231 232 8.158789 AGGTTCATCAATTTGTGGAAAAATCAT 58.841 29.630 0.00 0.00 0.00 2.45
232 233 7.507829 AGGTTCATCAATTTGTGGAAAAATCA 58.492 30.769 0.00 0.00 0.00 2.57
233 234 7.967890 AGGTTCATCAATTTGTGGAAAAATC 57.032 32.000 0.00 0.00 0.00 2.17
234 235 8.750515 AAAGGTTCATCAATTTGTGGAAAAAT 57.249 26.923 0.00 0.00 0.00 1.82
235 236 8.572855 AAAAGGTTCATCAATTTGTGGAAAAA 57.427 26.923 0.00 0.00 0.00 1.94
236 237 8.572855 AAAAAGGTTCATCAATTTGTGGAAAA 57.427 26.923 0.00 0.00 0.00 2.29
259 260 3.810310 AACGCTCATGGGTTTGAAAAA 57.190 38.095 0.00 0.00 45.22 1.94
296 297 7.293402 TCGAAAGAAGTTAGTCGTTCAAAAA 57.707 32.000 0.00 0.00 36.24 1.94
297 298 6.890663 TCGAAAGAAGTTAGTCGTTCAAAA 57.109 33.333 0.00 0.00 36.24 2.44
298 299 6.890663 TTCGAAAGAAGTTAGTCGTTCAAA 57.109 33.333 0.00 0.00 46.92 2.69
379 380 5.656213 TGACCGTTTACTTTTTGGGAAAA 57.344 34.783 0.00 0.00 33.86 2.29
380 381 5.185442 ACTTGACCGTTTACTTTTTGGGAAA 59.815 36.000 0.00 0.00 0.00 3.13
381 382 4.705991 ACTTGACCGTTTACTTTTTGGGAA 59.294 37.500 0.00 0.00 0.00 3.97
382 383 4.096682 CACTTGACCGTTTACTTTTTGGGA 59.903 41.667 0.00 0.00 0.00 4.37
383 384 4.356289 CACTTGACCGTTTACTTTTTGGG 58.644 43.478 0.00 0.00 0.00 4.12
384 385 4.142337 ACCACTTGACCGTTTACTTTTTGG 60.142 41.667 0.00 0.00 0.00 3.28
385 386 4.796312 CACCACTTGACCGTTTACTTTTTG 59.204 41.667 0.00 0.00 0.00 2.44
386 387 4.701171 TCACCACTTGACCGTTTACTTTTT 59.299 37.500 0.00 0.00 0.00 1.94
387 388 4.263435 TCACCACTTGACCGTTTACTTTT 58.737 39.130 0.00 0.00 0.00 2.27
388 389 3.876341 TCACCACTTGACCGTTTACTTT 58.124 40.909 0.00 0.00 0.00 2.66
389 390 3.547054 TCACCACTTGACCGTTTACTT 57.453 42.857 0.00 0.00 0.00 2.24
390 391 3.200483 GTTCACCACTTGACCGTTTACT 58.800 45.455 0.00 0.00 32.26 2.24
391 392 2.288729 GGTTCACCACTTGACCGTTTAC 59.711 50.000 0.00 0.00 32.26 2.01
392 393 2.563702 GGTTCACCACTTGACCGTTTA 58.436 47.619 0.00 0.00 32.26 2.01
393 394 1.385528 GGTTCACCACTTGACCGTTT 58.614 50.000 0.00 0.00 32.26 3.60
394 395 0.812412 CGGTTCACCACTTGACCGTT 60.812 55.000 5.67 0.00 40.84 4.44
395 396 1.227438 CGGTTCACCACTTGACCGT 60.227 57.895 5.67 0.00 40.84 4.83
396 397 2.604174 GCGGTTCACCACTTGACCG 61.604 63.158 9.23 9.23 44.84 4.79
397 398 2.604174 CGCGGTTCACCACTTGACC 61.604 63.158 0.00 0.00 32.26 4.02
398 399 1.593209 TCGCGGTTCACCACTTGAC 60.593 57.895 6.13 0.00 32.26 3.18
399 400 1.593209 GTCGCGGTTCACCACTTGA 60.593 57.895 6.13 0.00 35.14 3.02
400 401 2.604174 GGTCGCGGTTCACCACTTG 61.604 63.158 6.13 0.00 35.14 3.16
401 402 2.280592 GGTCGCGGTTCACCACTT 60.281 61.111 6.13 0.00 35.14 3.16
402 403 3.515316 CTGGTCGCGGTTCACCACT 62.515 63.158 12.90 0.00 37.78 4.00
403 404 3.041940 CTGGTCGCGGTTCACCAC 61.042 66.667 12.90 0.00 37.78 4.16
408 409 1.739196 GGTTACCTGGTCGCGGTTC 60.739 63.158 6.13 0.00 35.98 3.62
418 419 2.689983 GCCAGATTTCCATGGTTACCTG 59.310 50.000 12.58 14.27 38.91 4.00
419 420 2.683742 CGCCAGATTTCCATGGTTACCT 60.684 50.000 12.58 2.72 38.91 3.08
420 421 1.676006 CGCCAGATTTCCATGGTTACC 59.324 52.381 12.58 0.00 38.91 2.85
421 422 2.614057 CTCGCCAGATTTCCATGGTTAC 59.386 50.000 12.58 2.41 38.91 2.50
428 2112 1.153568 CTCGCTCGCCAGATTTCCA 60.154 57.895 0.00 0.00 0.00 3.53
434 2118 3.758088 GATTCGCTCGCTCGCCAGA 62.758 63.158 0.00 0.00 0.00 3.86
485 2731 1.960040 TAGACGGTGCTCATGCCCAG 61.960 60.000 0.00 0.00 38.71 4.45
486 2732 1.337384 ATAGACGGTGCTCATGCCCA 61.337 55.000 0.00 0.00 38.71 5.36
501 2747 4.441634 GCCTTAAGCGTCCAGAAGAATAGA 60.442 45.833 0.00 0.00 0.00 1.98
505 2751 2.094762 GCCTTAAGCGTCCAGAAGAA 57.905 50.000 0.00 0.00 0.00 2.52
557 3927 3.371102 TCTTCTGTTCAGTTCACTCGG 57.629 47.619 0.00 0.00 0.00 4.63
571 3941 9.694520 CGTCTAAAATTATGTGTCATTCTTCTG 57.305 33.333 0.00 0.00 0.00 3.02
573 3943 8.391106 AGCGTCTAAAATTATGTGTCATTCTTC 58.609 33.333 0.00 0.00 0.00 2.87
579 3949 7.766738 TCCAATAGCGTCTAAAATTATGTGTCA 59.233 33.333 0.00 0.00 0.00 3.58
603 3973 3.941704 ATTGGGTCTGATTCCTCTTCC 57.058 47.619 2.55 0.00 0.00 3.46
606 3976 3.941704 GGAATTGGGTCTGATTCCTCT 57.058 47.619 7.65 0.00 45.05 3.69
646 4578 5.917462 CCAAAACCTTGGTTCAAAGAATCT 58.083 37.500 5.43 0.00 46.25 2.40
703 5760 1.539388 TGGGATGTTGTGATTTGCGAC 59.461 47.619 0.00 0.00 0.00 5.19
716 5773 1.637553 AGGTGCTTTCTCATGGGATGT 59.362 47.619 0.00 0.00 0.00 3.06
722 9147 2.932614 CTCGGTAAGGTGCTTTCTCATG 59.067 50.000 0.00 0.00 0.00 3.07
815 9803 3.561310 TCGAAAGATATCATGCAGTTGCC 59.439 43.478 5.32 0.00 35.93 4.52
817 9805 4.571984 TGGTCGAAAGATATCATGCAGTTG 59.428 41.667 5.32 0.00 45.19 3.16
824 9812 6.126883 TGGTTACCTTGGTCGAAAGATATCAT 60.127 38.462 5.32 0.00 45.19 2.45
841 9832 5.312895 GGGCATCAAAAATTTTGGTTACCT 58.687 37.500 17.21 0.00 0.00 3.08
849 9840 3.323403 TCTCGTGGGGCATCAAAAATTTT 59.677 39.130 0.00 0.00 0.00 1.82
853 9844 2.214376 ATCTCGTGGGGCATCAAAAA 57.786 45.000 0.00 0.00 0.00 1.94
873 9864 7.565680 GGAGGGAGTAGTTCAGATGATAAAAA 58.434 38.462 0.00 0.00 0.00 1.94
891 9882 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
892 9883 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
893 9884 3.849563 TTTATATTGTGGGACGGAGGG 57.150 47.619 0.00 0.00 0.00 4.30
894 9885 3.564225 GCTTTTATATTGTGGGACGGAGG 59.436 47.826 0.00 0.00 0.00 4.30
895 9886 3.247648 CGCTTTTATATTGTGGGACGGAG 59.752 47.826 0.00 0.00 0.00 4.63
896 9887 3.199677 CGCTTTTATATTGTGGGACGGA 58.800 45.455 0.00 0.00 0.00 4.69
897 9888 2.940410 ACGCTTTTATATTGTGGGACGG 59.060 45.455 0.00 0.00 0.00 4.79
898 9889 4.609691 AACGCTTTTATATTGTGGGACG 57.390 40.909 0.00 0.00 0.00 4.79
899 9890 6.864165 TCAAAAACGCTTTTATATTGTGGGAC 59.136 34.615 0.00 0.00 32.85 4.46
900 9891 6.864165 GTCAAAAACGCTTTTATATTGTGGGA 59.136 34.615 0.00 0.00 32.85 4.37
901 9892 6.642950 TGTCAAAAACGCTTTTATATTGTGGG 59.357 34.615 0.00 0.00 32.85 4.61
902 9893 7.381139 AGTGTCAAAAACGCTTTTATATTGTGG 59.619 33.333 0.00 0.00 46.62 4.17
903 9894 8.280909 AGTGTCAAAAACGCTTTTATATTGTG 57.719 30.769 0.00 0.00 46.62 3.33
904 9895 9.607285 CTAGTGTCAAAAACGCTTTTATATTGT 57.393 29.630 0.00 0.00 46.62 2.71
905 9896 9.607285 ACTAGTGTCAAAAACGCTTTTATATTG 57.393 29.630 0.00 0.00 46.62 1.90
911 9902 9.607285 CAATATACTAGTGTCAAAAACGCTTTT 57.393 29.630 5.39 0.00 46.62 2.27
912 9903 8.780249 ACAATATACTAGTGTCAAAAACGCTTT 58.220 29.630 5.39 0.00 46.62 3.51
913 9904 8.227791 CACAATATACTAGTGTCAAAAACGCTT 58.772 33.333 5.39 0.00 46.62 4.68
915 9906 6.959311 CCACAATATACTAGTGTCAAAAACGC 59.041 38.462 5.39 0.00 34.37 4.84
916 9907 7.332430 TCCCACAATATACTAGTGTCAAAAACG 59.668 37.037 5.39 0.00 34.37 3.60
917 9908 8.448615 GTCCCACAATATACTAGTGTCAAAAAC 58.551 37.037 5.39 0.00 34.37 2.43
918 9909 7.332430 CGTCCCACAATATACTAGTGTCAAAAA 59.668 37.037 5.39 0.00 34.37 1.94
919 9910 6.814644 CGTCCCACAATATACTAGTGTCAAAA 59.185 38.462 5.39 0.00 34.37 2.44
920 9911 6.334989 CGTCCCACAATATACTAGTGTCAAA 58.665 40.000 5.39 0.00 34.37 2.69
921 9912 5.163488 CCGTCCCACAATATACTAGTGTCAA 60.163 44.000 5.39 0.00 34.37 3.18
922 9913 4.340097 CCGTCCCACAATATACTAGTGTCA 59.660 45.833 5.39 0.00 34.37 3.58
923 9914 4.581824 TCCGTCCCACAATATACTAGTGTC 59.418 45.833 5.39 0.00 34.37 3.67
924 9915 4.539726 TCCGTCCCACAATATACTAGTGT 58.460 43.478 5.39 0.39 37.49 3.55
925 9916 4.022242 CCTCCGTCCCACAATATACTAGTG 60.022 50.000 5.39 0.00 0.00 2.74
926 9917 4.150359 CCTCCGTCCCACAATATACTAGT 58.850 47.826 0.00 0.00 0.00 2.57
927 9918 3.510360 CCCTCCGTCCCACAATATACTAG 59.490 52.174 0.00 0.00 0.00 2.57
928 9919 3.140707 TCCCTCCGTCCCACAATATACTA 59.859 47.826 0.00 0.00 0.00 1.82
929 9920 2.090943 TCCCTCCGTCCCACAATATACT 60.091 50.000 0.00 0.00 0.00 2.12
930 9921 2.299297 CTCCCTCCGTCCCACAATATAC 59.701 54.545 0.00 0.00 0.00 1.47
931 9922 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
932 9923 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
933 9924 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
934 9925 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
935 9926 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
936 9927 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
937 9928 2.424733 GCTACTCCCTCCGTCCCAC 61.425 68.421 0.00 0.00 0.00 4.61
938 9929 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
939 9930 2.043248 TGCTACTCCCTCCGTCCC 60.043 66.667 0.00 0.00 0.00 4.46
940 9931 1.668101 CTGTGCTACTCCCTCCGTCC 61.668 65.000 0.00 0.00 0.00 4.79
941 9932 0.966370 ACTGTGCTACTCCCTCCGTC 60.966 60.000 0.00 0.00 0.00 4.79
942 9933 0.330604 TACTGTGCTACTCCCTCCGT 59.669 55.000 0.00 0.00 0.00 4.69
943 9934 0.739561 GTACTGTGCTACTCCCTCCG 59.260 60.000 0.00 0.00 0.00 4.63
944 9935 2.146920 AGTACTGTGCTACTCCCTCC 57.853 55.000 0.00 0.00 0.00 4.30
945 9936 3.090037 TGAAGTACTGTGCTACTCCCTC 58.910 50.000 0.00 0.00 0.00 4.30
946 9937 3.170991 TGAAGTACTGTGCTACTCCCT 57.829 47.619 0.00 0.00 0.00 4.20
947 9938 3.006537 TGTTGAAGTACTGTGCTACTCCC 59.993 47.826 0.00 0.00 0.00 4.30
948 9939 4.252971 TGTTGAAGTACTGTGCTACTCC 57.747 45.455 0.00 0.00 0.00 3.85
949 9940 5.348997 GGATTGTTGAAGTACTGTGCTACTC 59.651 44.000 0.00 0.00 0.00 2.59
950 9941 5.221641 TGGATTGTTGAAGTACTGTGCTACT 60.222 40.000 0.00 0.00 0.00 2.57
951 9942 4.994852 TGGATTGTTGAAGTACTGTGCTAC 59.005 41.667 0.00 0.00 0.00 3.58
952 9943 4.994852 GTGGATTGTTGAAGTACTGTGCTA 59.005 41.667 0.00 0.00 0.00 3.49
953 9944 3.815401 GTGGATTGTTGAAGTACTGTGCT 59.185 43.478 0.00 0.00 0.00 4.40
954 9945 3.815401 AGTGGATTGTTGAAGTACTGTGC 59.185 43.478 0.00 0.00 0.00 4.57
988 9979 2.292569 GGCTATGCATGTGAATCCAGTG 59.707 50.000 10.16 0.00 0.00 3.66
1113 10104 3.800685 CTTCACCACCACGGCGACA 62.801 63.158 16.62 0.00 39.03 4.35
1469 10460 2.097110 ACACACTGGTCCCTGTCTTA 57.903 50.000 0.00 0.00 0.00 2.10
1541 10532 2.419673 CCGATGCTGCATTAACAGTGAA 59.580 45.455 17.36 0.00 39.96 3.18
1542 10533 2.009051 CCGATGCTGCATTAACAGTGA 58.991 47.619 17.36 0.00 39.96 3.41
1543 10534 1.064505 CCCGATGCTGCATTAACAGTG 59.935 52.381 17.36 1.57 39.96 3.66
1544 10535 1.065491 TCCCGATGCTGCATTAACAGT 60.065 47.619 17.36 0.00 39.96 3.55
1545 10536 1.667236 TCCCGATGCTGCATTAACAG 58.333 50.000 17.36 6.34 40.80 3.16
1592 10583 8.018520 CGCGGTGGCATATAAGATTTTATTTTA 58.981 33.333 0.00 0.00 39.92 1.52
1597 10588 4.382291 ACGCGGTGGCATATAAGATTTTA 58.618 39.130 12.47 0.00 39.92 1.52
1602 10593 1.137282 TGAACGCGGTGGCATATAAGA 59.863 47.619 12.47 0.00 39.92 2.10
1603 10594 1.577468 TGAACGCGGTGGCATATAAG 58.423 50.000 12.47 0.00 39.92 1.73
1604 10595 1.937223 CTTGAACGCGGTGGCATATAA 59.063 47.619 12.47 0.00 39.92 0.98
1605 10596 1.577468 CTTGAACGCGGTGGCATATA 58.423 50.000 12.47 0.00 39.92 0.86
1606 10597 1.714899 GCTTGAACGCGGTGGCATAT 61.715 55.000 12.47 0.00 39.92 1.78
1607 10598 2.395360 GCTTGAACGCGGTGGCATA 61.395 57.895 12.47 0.00 39.92 3.14
1608 10599 3.737172 GCTTGAACGCGGTGGCAT 61.737 61.111 12.47 0.00 39.92 4.40
1610 10601 3.477224 TTTGCTTGAACGCGGTGGC 62.477 57.895 12.47 8.83 0.00 5.01
1611 10602 1.370414 CTTTGCTTGAACGCGGTGG 60.370 57.895 12.47 0.00 0.00 4.61
1612 10603 2.010817 GCTTTGCTTGAACGCGGTG 61.011 57.895 12.47 0.00 0.00 4.94
1613 10604 0.882927 TAGCTTTGCTTGAACGCGGT 60.883 50.000 12.47 1.91 40.44 5.68
1614 10605 0.452784 GTAGCTTTGCTTGAACGCGG 60.453 55.000 12.47 0.00 40.44 6.46
1684 10693 9.731819 ATAACGCATTCATATCGTATACCTTAG 57.268 33.333 0.00 0.00 35.18 2.18
1731 10743 1.671054 ATGTCCCAAGTGCGAACCG 60.671 57.895 0.00 0.00 0.00 4.44
1806 10818 1.444895 GGCGGACAATTGCTTGCTG 60.445 57.895 5.05 0.00 35.69 4.41
1815 10827 2.045926 GTGAGCCTGGCGGACAAT 60.046 61.111 13.96 0.00 0.00 2.71
1850 10862 0.462225 CAGTGAGCTGAGGCAGATGG 60.462 60.000 0.00 0.00 45.28 3.51


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

AutoCloner maintained by Alex Coulton.