Multiple sequence alignment - TraesCS3D01G387400

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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 TraesCS3D01G387400 chr3D 100.000 3137 0 0 1 3137 502157416 502160552 0.000000e+00 5794.0
1 TraesCS3D01G387400 chr3B 96.531 2133 45 14 241 2349 663572980 663575107 0.000000e+00 3502.0
2 TraesCS3D01G387400 chr3B 85.697 839 63 31 2342 3137 663575293 663576117 0.000000e+00 832.0
3 TraesCS3D01G387400 chr3B 91.204 216 18 1 1 216 663557490 663557704 3.060000e-75 292.0
4 TraesCS3D01G387400 chr6B 90.648 1636 101 28 614 2233 659808627 659810226 0.000000e+00 2126.0
5 TraesCS3D01G387400 chr6B 92.338 509 39 0 1633 2141 659653863 659653355 0.000000e+00 725.0
6 TraesCS3D01G387400 chr6A 92.123 1498 76 16 666 2138 584757879 584759359 0.000000e+00 2074.0
7 TraesCS3D01G387400 chr6A 92.496 1426 85 9 748 2155 584695520 584694099 0.000000e+00 2021.0
8 TraesCS3D01G387400 chr6A 90.106 1506 110 17 745 2227 584593390 584594879 0.000000e+00 1919.0
9 TraesCS3D01G387400 chr6A 94.452 757 36 1 1391 2141 584717354 584716598 0.000000e+00 1160.0
10 TraesCS3D01G387400 chr6A 87.960 598 34 16 668 1244 584717945 584717365 0.000000e+00 671.0
11 TraesCS3D01G387400 chr6A 79.730 148 21 8 2091 2234 584761581 584761723 7.160000e-17 99.0
12 TraesCS3D01G387400 chr6D 91.299 1517 89 19 668 2155 436637995 436639497 0.000000e+00 2030.0
13 TraesCS3D01G387400 chr6D 89.253 1526 101 21 745 2231 436420916 436422417 0.000000e+00 1851.0
14 TraesCS3D01G387400 chr6D 89.501 581 32 17 749 1312 436474437 436473869 0.000000e+00 708.0
15 TraesCS3D01G387400 chr5A 79.200 125 15 9 2873 2996 316656901 316656787 3.350000e-10 76.8
16 TraesCS3D01G387400 chr2A 79.310 116 16 6 2881 2996 488917207 488917314 1.210000e-09 75.0
17 TraesCS3D01G387400 chrUn 89.796 49 3 2 2881 2928 21557928 21557975 9.390000e-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 TraesCS3D01G387400 chr3D 502157416 502160552 3136 False 5794.0 5794 100.0000 1 3137 1 chr3D.!!$F1 3136
1 TraesCS3D01G387400 chr3B 663572980 663576117 3137 False 2167.0 3502 91.1140 241 3137 2 chr3B.!!$F2 2896
2 TraesCS3D01G387400 chr6B 659808627 659810226 1599 False 2126.0 2126 90.6480 614 2233 1 chr6B.!!$F1 1619
3 TraesCS3D01G387400 chr6B 659653355 659653863 508 True 725.0 725 92.3380 1633 2141 1 chr6B.!!$R1 508
4 TraesCS3D01G387400 chr6A 584694099 584695520 1421 True 2021.0 2021 92.4960 748 2155 1 chr6A.!!$R1 1407
5 TraesCS3D01G387400 chr6A 584593390 584594879 1489 False 1919.0 1919 90.1060 745 2227 1 chr6A.!!$F1 1482
6 TraesCS3D01G387400 chr6A 584757879 584761723 3844 False 1086.5 2074 85.9265 666 2234 2 chr6A.!!$F2 1568
7 TraesCS3D01G387400 chr6A 584716598 584717945 1347 True 915.5 1160 91.2060 668 2141 2 chr6A.!!$R2 1473
8 TraesCS3D01G387400 chr6D 436637995 436639497 1502 False 2030.0 2030 91.2990 668 2155 1 chr6D.!!$F2 1487
9 TraesCS3D01G387400 chr6D 436420916 436422417 1501 False 1851.0 1851 89.2530 745 2231 1 chr6D.!!$F1 1486
10 TraesCS3D01G387400 chr6D 436473869 436474437 568 True 708.0 708 89.5010 749 1312 1 chr6D.!!$R1 563

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
39 40 0.249120 ACGATGAACATTGAGGGCGA 59.751 50.000 8.77 0.0 0.0 5.54 F
41 42 1.062587 CGATGAACATTGAGGGCGAAC 59.937 52.381 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1500 3.003763 GGAAGAGGTGGGCGAGGT 61.004 66.667 0.0 0.0 0.0 3.85 R
2151 4500 5.813717 AGTAAAACACGCTACAAAGGAAAC 58.186 37.500 0.0 0.0 0.0 2.78 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
35 36 7.770801 TTTAGATACACGATGAACATTGAGG 57.229 36.000 8.77 3.81 0.00 3.86
36 37 4.697514 AGATACACGATGAACATTGAGGG 58.302 43.478 8.77 0.00 0.00 4.30
37 38 1.453155 ACACGATGAACATTGAGGGC 58.547 50.000 8.77 0.00 0.00 5.19
38 39 0.374758 CACGATGAACATTGAGGGCG 59.625 55.000 8.77 0.00 0.00 6.13
39 40 0.249120 ACGATGAACATTGAGGGCGA 59.751 50.000 8.77 0.00 0.00 5.54
40 41 1.338674 ACGATGAACATTGAGGGCGAA 60.339 47.619 8.77 0.00 0.00 4.70
41 42 1.062587 CGATGAACATTGAGGGCGAAC 59.937 52.381 0.00 0.00 0.00 3.95
42 43 2.083774 GATGAACATTGAGGGCGAACA 58.916 47.619 0.00 0.00 0.00 3.18
43 44 2.198827 TGAACATTGAGGGCGAACAT 57.801 45.000 0.00 0.00 0.00 2.71
44 45 2.513753 TGAACATTGAGGGCGAACATT 58.486 42.857 0.00 0.00 0.00 2.71
45 46 2.890311 TGAACATTGAGGGCGAACATTT 59.110 40.909 0.00 0.00 0.00 2.32
46 47 3.320541 TGAACATTGAGGGCGAACATTTT 59.679 39.130 0.00 0.00 0.00 1.82
47 48 3.575965 ACATTGAGGGCGAACATTTTC 57.424 42.857 0.00 0.00 0.00 2.29
48 49 3.157087 ACATTGAGGGCGAACATTTTCT 58.843 40.909 0.00 0.00 0.00 2.52
49 50 3.573967 ACATTGAGGGCGAACATTTTCTT 59.426 39.130 0.00 0.00 0.00 2.52
50 51 4.039124 ACATTGAGGGCGAACATTTTCTTT 59.961 37.500 0.00 0.00 0.00 2.52
51 52 4.664150 TTGAGGGCGAACATTTTCTTTT 57.336 36.364 0.00 0.00 0.00 2.27
52 53 5.776173 TTGAGGGCGAACATTTTCTTTTA 57.224 34.783 0.00 0.00 0.00 1.52
53 54 5.776173 TGAGGGCGAACATTTTCTTTTAA 57.224 34.783 0.00 0.00 0.00 1.52
54 55 6.150396 TGAGGGCGAACATTTTCTTTTAAA 57.850 33.333 0.00 0.00 0.00 1.52
55 56 5.980715 TGAGGGCGAACATTTTCTTTTAAAC 59.019 36.000 0.00 0.00 0.00 2.01
56 57 5.908341 AGGGCGAACATTTTCTTTTAAACA 58.092 33.333 0.00 0.00 0.00 2.83
57 58 6.521162 AGGGCGAACATTTTCTTTTAAACAT 58.479 32.000 0.00 0.00 0.00 2.71
58 59 6.423604 AGGGCGAACATTTTCTTTTAAACATG 59.576 34.615 0.00 0.00 0.00 3.21
59 60 6.347321 GGGCGAACATTTTCTTTTAAACATGG 60.347 38.462 0.00 0.00 0.00 3.66
60 61 6.201997 GGCGAACATTTTCTTTTAAACATGGT 59.798 34.615 0.00 0.00 0.00 3.55
61 62 7.062848 GCGAACATTTTCTTTTAAACATGGTG 58.937 34.615 0.00 0.00 0.00 4.17
62 63 7.043059 GCGAACATTTTCTTTTAAACATGGTGA 60.043 33.333 0.00 0.00 0.00 4.02
63 64 8.812329 CGAACATTTTCTTTTAAACATGGTGAA 58.188 29.630 0.00 0.00 0.00 3.18
76 77 7.798596 AAACATGGTGAAATTTTAATGTGCA 57.201 28.000 0.00 0.00 0.00 4.57
77 78 7.982761 AACATGGTGAAATTTTAATGTGCAT 57.017 28.000 0.00 0.00 0.00 3.96
78 79 7.367159 ACATGGTGAAATTTTAATGTGCATG 57.633 32.000 0.00 0.00 0.00 4.06
79 80 7.160049 ACATGGTGAAATTTTAATGTGCATGA 58.840 30.769 0.00 0.00 0.00 3.07
80 81 7.825270 ACATGGTGAAATTTTAATGTGCATGAT 59.175 29.630 0.00 0.00 0.00 2.45
81 82 8.670135 CATGGTGAAATTTTAATGTGCATGATT 58.330 29.630 0.00 0.00 0.00 2.57
82 83 8.030744 TGGTGAAATTTTAATGTGCATGATTG 57.969 30.769 0.00 0.00 0.00 2.67
83 84 7.876582 TGGTGAAATTTTAATGTGCATGATTGA 59.123 29.630 0.00 0.00 0.00 2.57
84 85 8.719648 GGTGAAATTTTAATGTGCATGATTGAA 58.280 29.630 0.00 0.00 0.00 2.69
89 90 9.451002 AATTTTAATGTGCATGATTGAAATGGA 57.549 25.926 17.51 0.63 32.39 3.41
90 91 9.621629 ATTTTAATGTGCATGATTGAAATGGAT 57.378 25.926 16.70 2.34 31.42 3.41
91 92 8.651391 TTTAATGTGCATGATTGAAATGGATC 57.349 30.769 0.00 0.00 0.00 3.36
92 93 6.479972 AATGTGCATGATTGAAATGGATCT 57.520 33.333 0.00 0.00 0.00 2.75
93 94 7.591421 AATGTGCATGATTGAAATGGATCTA 57.409 32.000 0.00 0.00 0.00 1.98
94 95 7.591421 ATGTGCATGATTGAAATGGATCTAA 57.409 32.000 0.00 0.00 0.00 2.10
95 96 7.407393 TGTGCATGATTGAAATGGATCTAAA 57.593 32.000 0.00 0.00 0.00 1.85
96 97 7.259882 TGTGCATGATTGAAATGGATCTAAAC 58.740 34.615 0.00 0.00 0.00 2.01
97 98 7.093858 TGTGCATGATTGAAATGGATCTAAACA 60.094 33.333 0.00 0.00 0.00 2.83
98 99 7.924412 GTGCATGATTGAAATGGATCTAAACAT 59.076 33.333 0.00 0.00 0.00 2.71
99 100 7.923878 TGCATGATTGAAATGGATCTAAACATG 59.076 33.333 0.00 0.00 32.43 3.21
100 101 7.384115 GCATGATTGAAATGGATCTAAACATGG 59.616 37.037 0.00 0.00 31.33 3.66
101 102 8.635328 CATGATTGAAATGGATCTAAACATGGA 58.365 33.333 0.00 0.00 0.00 3.41
102 103 8.592529 TGATTGAAATGGATCTAAACATGGAA 57.407 30.769 0.00 0.00 0.00 3.53
103 104 9.204337 TGATTGAAATGGATCTAAACATGGAAT 57.796 29.630 0.00 0.00 0.00 3.01
156 157 8.575649 AAAAATATGTGAACTCTTTATCGGGT 57.424 30.769 0.00 0.00 0.00 5.28
157 158 8.575649 AAAATATGTGAACTCTTTATCGGGTT 57.424 30.769 0.00 0.00 0.00 4.11
158 159 8.575649 AAATATGTGAACTCTTTATCGGGTTT 57.424 30.769 0.00 0.00 0.00 3.27
159 160 5.880054 ATGTGAACTCTTTATCGGGTTTG 57.120 39.130 0.00 0.00 0.00 2.93
160 161 4.710324 TGTGAACTCTTTATCGGGTTTGT 58.290 39.130 0.00 0.00 0.00 2.83
161 162 5.856156 TGTGAACTCTTTATCGGGTTTGTA 58.144 37.500 0.00 0.00 0.00 2.41
162 163 6.469410 TGTGAACTCTTTATCGGGTTTGTAT 58.531 36.000 0.00 0.00 0.00 2.29
163 164 6.938030 TGTGAACTCTTTATCGGGTTTGTATT 59.062 34.615 0.00 0.00 0.00 1.89
164 165 7.094975 TGTGAACTCTTTATCGGGTTTGTATTG 60.095 37.037 0.00 0.00 0.00 1.90
165 166 5.813080 ACTCTTTATCGGGTTTGTATTGC 57.187 39.130 0.00 0.00 0.00 3.56
166 167 5.250200 ACTCTTTATCGGGTTTGTATTGCA 58.750 37.500 0.00 0.00 0.00 4.08
167 168 5.123344 ACTCTTTATCGGGTTTGTATTGCAC 59.877 40.000 0.00 0.00 0.00 4.57
168 169 4.093703 TCTTTATCGGGTTTGTATTGCACG 59.906 41.667 0.00 0.00 0.00 5.34
169 170 1.816074 ATCGGGTTTGTATTGCACGT 58.184 45.000 0.00 0.00 0.00 4.49
170 171 1.595466 TCGGGTTTGTATTGCACGTT 58.405 45.000 0.00 0.00 0.00 3.99
171 172 1.948145 TCGGGTTTGTATTGCACGTTT 59.052 42.857 0.00 0.00 0.00 3.60
172 173 2.358267 TCGGGTTTGTATTGCACGTTTT 59.642 40.909 0.00 0.00 0.00 2.43
173 174 2.722116 CGGGTTTGTATTGCACGTTTTC 59.278 45.455 0.00 0.00 0.00 2.29
174 175 3.054166 GGGTTTGTATTGCACGTTTTCC 58.946 45.455 0.00 0.00 0.00 3.13
175 176 3.243602 GGGTTTGTATTGCACGTTTTCCT 60.244 43.478 0.00 0.00 0.00 3.36
176 177 4.364860 GGTTTGTATTGCACGTTTTCCTT 58.635 39.130 0.00 0.00 0.00 3.36
177 178 4.806775 GGTTTGTATTGCACGTTTTCCTTT 59.193 37.500 0.00 0.00 0.00 3.11
178 179 5.292345 GGTTTGTATTGCACGTTTTCCTTTT 59.708 36.000 0.00 0.00 0.00 2.27
179 180 6.407623 GTTTGTATTGCACGTTTTCCTTTTC 58.592 36.000 0.00 0.00 0.00 2.29
180 181 4.612943 TGTATTGCACGTTTTCCTTTTCC 58.387 39.130 0.00 0.00 0.00 3.13
181 182 2.588027 TTGCACGTTTTCCTTTTCCC 57.412 45.000 0.00 0.00 0.00 3.97
182 183 1.475403 TGCACGTTTTCCTTTTCCCA 58.525 45.000 0.00 0.00 0.00 4.37
183 184 2.035632 TGCACGTTTTCCTTTTCCCAT 58.964 42.857 0.00 0.00 0.00 4.00
184 185 2.432510 TGCACGTTTTCCTTTTCCCATT 59.567 40.909 0.00 0.00 0.00 3.16
185 186 3.118592 TGCACGTTTTCCTTTTCCCATTT 60.119 39.130 0.00 0.00 0.00 2.32
186 187 3.493129 GCACGTTTTCCTTTTCCCATTTC 59.507 43.478 0.00 0.00 0.00 2.17
187 188 4.739436 GCACGTTTTCCTTTTCCCATTTCT 60.739 41.667 0.00 0.00 0.00 2.52
188 189 5.356426 CACGTTTTCCTTTTCCCATTTCTT 58.644 37.500 0.00 0.00 0.00 2.52
189 190 5.815222 CACGTTTTCCTTTTCCCATTTCTTT 59.185 36.000 0.00 0.00 0.00 2.52
190 191 6.315144 CACGTTTTCCTTTTCCCATTTCTTTT 59.685 34.615 0.00 0.00 0.00 2.27
191 192 6.882140 ACGTTTTCCTTTTCCCATTTCTTTTT 59.118 30.769 0.00 0.00 0.00 1.94
192 193 7.065324 ACGTTTTCCTTTTCCCATTTCTTTTTC 59.935 33.333 0.00 0.00 0.00 2.29
193 194 7.279981 CGTTTTCCTTTTCCCATTTCTTTTTCT 59.720 33.333 0.00 0.00 0.00 2.52
194 195 9.607988 GTTTTCCTTTTCCCATTTCTTTTTCTA 57.392 29.630 0.00 0.00 0.00 2.10
195 196 9.607988 TTTTCCTTTTCCCATTTCTTTTTCTAC 57.392 29.630 0.00 0.00 0.00 2.59
196 197 7.906199 TCCTTTTCCCATTTCTTTTTCTACA 57.094 32.000 0.00 0.00 0.00 2.74
197 198 8.491045 TCCTTTTCCCATTTCTTTTTCTACAT 57.509 30.769 0.00 0.00 0.00 2.29
198 199 8.367156 TCCTTTTCCCATTTCTTTTTCTACATG 58.633 33.333 0.00 0.00 0.00 3.21
199 200 8.367156 CCTTTTCCCATTTCTTTTTCTACATGA 58.633 33.333 0.00 0.00 0.00 3.07
200 201 9.762933 CTTTTCCCATTTCTTTTTCTACATGAA 57.237 29.630 0.00 0.00 0.00 2.57
217 218 8.783093 TCTACATGAAAAACTTGTAAGTCATGG 58.217 33.333 19.54 9.53 39.71 3.66
218 219 6.748132 ACATGAAAAACTTGTAAGTCATGGG 58.252 36.000 19.54 5.32 39.71 4.00
219 220 5.195001 TGAAAAACTTGTAAGTCATGGGC 57.805 39.130 0.00 0.00 38.57 5.36
220 221 4.646945 TGAAAAACTTGTAAGTCATGGGCA 59.353 37.500 0.00 0.00 38.57 5.36
221 222 5.127845 TGAAAAACTTGTAAGTCATGGGCAA 59.872 36.000 0.00 0.00 38.57 4.52
222 223 5.606348 AAAACTTGTAAGTCATGGGCAAA 57.394 34.783 0.00 0.00 38.57 3.68
223 224 4.584327 AACTTGTAAGTCATGGGCAAAC 57.416 40.909 0.00 0.00 38.57 2.93
224 225 2.890945 ACTTGTAAGTCATGGGCAAACC 59.109 45.455 0.00 0.00 32.86 3.27
225 226 2.969821 TGTAAGTCATGGGCAAACCT 57.030 45.000 0.00 0.00 41.11 3.50
226 227 3.237268 TGTAAGTCATGGGCAAACCTT 57.763 42.857 0.00 0.00 41.11 3.50
227 228 3.571590 TGTAAGTCATGGGCAAACCTTT 58.428 40.909 0.00 0.00 41.11 3.11
228 229 3.572255 TGTAAGTCATGGGCAAACCTTTC 59.428 43.478 0.00 0.00 41.11 2.62
229 230 2.683211 AGTCATGGGCAAACCTTTCT 57.317 45.000 0.00 0.00 41.11 2.52
230 231 3.806949 AGTCATGGGCAAACCTTTCTA 57.193 42.857 0.00 0.00 41.11 2.10
231 232 4.112634 AGTCATGGGCAAACCTTTCTAA 57.887 40.909 0.00 0.00 41.11 2.10
232 233 4.479158 AGTCATGGGCAAACCTTTCTAAA 58.521 39.130 0.00 0.00 41.11 1.85
233 234 5.086621 AGTCATGGGCAAACCTTTCTAAAT 58.913 37.500 0.00 0.00 41.11 1.40
234 235 6.252995 AGTCATGGGCAAACCTTTCTAAATA 58.747 36.000 0.00 0.00 41.11 1.40
235 236 6.152831 AGTCATGGGCAAACCTTTCTAAATAC 59.847 38.462 0.00 0.00 41.11 1.89
236 237 5.420739 TCATGGGCAAACCTTTCTAAATACC 59.579 40.000 0.00 0.00 41.11 2.73
237 238 4.090819 TGGGCAAACCTTTCTAAATACCC 58.909 43.478 0.00 0.00 41.11 3.69
238 239 3.129813 GGGCAAACCTTTCTAAATACCCG 59.870 47.826 0.00 0.00 35.85 5.28
239 240 4.011698 GGCAAACCTTTCTAAATACCCGA 58.988 43.478 0.00 0.00 0.00 5.14
240 241 4.643334 GGCAAACCTTTCTAAATACCCGAT 59.357 41.667 0.00 0.00 0.00 4.18
241 242 5.449999 GGCAAACCTTTCTAAATACCCGATG 60.450 44.000 0.00 0.00 0.00 3.84
242 243 5.355910 GCAAACCTTTCTAAATACCCGATGA 59.644 40.000 0.00 0.00 0.00 2.92
243 244 6.127842 GCAAACCTTTCTAAATACCCGATGAA 60.128 38.462 0.00 0.00 0.00 2.57
244 245 6.997239 AACCTTTCTAAATACCCGATGAAC 57.003 37.500 0.00 0.00 0.00 3.18
245 246 6.057321 ACCTTTCTAAATACCCGATGAACA 57.943 37.500 0.00 0.00 0.00 3.18
246 247 6.659824 ACCTTTCTAAATACCCGATGAACAT 58.340 36.000 0.00 0.00 0.00 2.71
606 619 2.352519 GGAGTCTCAACGGACTTGTACC 60.353 54.545 1.47 0.00 45.32 3.34
625 638 2.025037 ACCAGAGGCAAATTGCTATGGA 60.025 45.455 29.03 0.00 44.28 3.41
745 768 4.511527 ACGAACTCTGTCTACGGATCTAA 58.488 43.478 0.00 0.00 0.00 2.10
746 769 4.940046 ACGAACTCTGTCTACGGATCTAAA 59.060 41.667 0.00 0.00 0.00 1.85
1805 1884 4.122776 GTCATGTCGCTGATAAAGGACAT 58.877 43.478 0.01 0.01 42.62 3.06
2121 2200 4.339247 CGTTTTCCCATGCCTGATTTAGAT 59.661 41.667 0.00 0.00 0.00 1.98
2151 4500 5.220172 CGAGATGTGATAATCGCTATGCTTG 60.220 44.000 0.00 0.00 0.00 4.01
2263 4618 8.225603 AGCAAAGTTTATATATTGTGGAGGTG 57.774 34.615 0.00 0.00 0.00 4.00
2265 4620 8.850156 GCAAAGTTTATATATTGTGGAGGTGAT 58.150 33.333 0.00 0.00 0.00 3.06
2364 4913 3.565764 TGATGATGCCTAGTTGGAAGG 57.434 47.619 0.00 0.00 38.35 3.46
2373 4922 2.463589 TAGTTGGAAGGGTGCGGCTG 62.464 60.000 0.00 0.00 0.00 4.85
2387 4936 2.184579 GCTGCCTGACGAGGGTAC 59.815 66.667 0.00 0.00 40.19 3.34
2388 4937 2.352032 GCTGCCTGACGAGGGTACT 61.352 63.158 0.00 0.00 40.19 2.73
2389 4938 1.035932 GCTGCCTGACGAGGGTACTA 61.036 60.000 0.00 0.00 40.19 1.82
2390 4939 1.693627 CTGCCTGACGAGGGTACTAT 58.306 55.000 0.00 0.00 40.19 2.12
2391 4940 2.860009 CTGCCTGACGAGGGTACTATA 58.140 52.381 0.00 0.00 40.19 1.31
2402 4958 2.891580 AGGGTACTATATCAGTGTGGCG 59.108 50.000 0.00 0.00 38.24 5.69
2411 4967 5.899120 ATATCAGTGTGGCGGTAGTATAG 57.101 43.478 0.00 0.00 0.00 1.31
2440 4996 3.135994 TCCTTTAAACCAAGCGACTCAC 58.864 45.455 0.00 0.00 0.00 3.51
2455 5011 2.174107 CACGCAACGGCACATGAG 59.826 61.111 0.00 0.00 41.24 2.90
2462 5018 1.135859 CAACGGCACATGAGAGAAAGC 60.136 52.381 0.00 0.00 0.00 3.51
2492 5048 0.521242 CTACAAAGGAATGTGCGCGC 60.521 55.000 27.26 27.26 34.75 6.86
2493 5049 1.917782 TACAAAGGAATGTGCGCGCC 61.918 55.000 30.77 20.33 34.75 6.53
2518 5074 3.426695 CCATTGATCGGCAACAAAGAGAC 60.427 47.826 0.00 0.00 39.78 3.36
2519 5075 1.428448 TGATCGGCAACAAAGAGACG 58.572 50.000 0.00 0.00 0.00 4.18
2556 5112 5.598830 ACCATAGGGATACACAGAGTAACTG 59.401 44.000 0.00 0.00 44.03 3.16
2571 5127 0.534877 AACTGCACCGCATCAACTGA 60.535 50.000 0.00 0.00 38.13 3.41
2593 5149 7.023197 TGACGAGTCAGAACGATCATAAATA 57.977 36.000 1.24 0.00 34.14 1.40
2615 5171 1.064979 AGGAAAACACAGGTCAACCGT 60.065 47.619 0.00 0.00 42.08 4.83
2649 5231 0.104120 AGGCAAAACCAAAACGAGCC 59.896 50.000 0.00 0.00 43.14 4.70
2670 5252 3.884693 CCAGCCAATCATAATAGCACACA 59.115 43.478 0.00 0.00 0.00 3.72
2671 5253 4.261322 CCAGCCAATCATAATAGCACACAC 60.261 45.833 0.00 0.00 0.00 3.82
2685 5268 3.122297 GCACACACAAAAATGCTAAGCA 58.878 40.909 0.00 0.00 44.86 3.91
2695 5278 8.710551 CACAAAAATGCTAAGCAACAAATGATA 58.289 29.630 0.00 0.00 43.62 2.15
2726 5309 2.003672 CGAACCGCCGTTTATCCTG 58.996 57.895 0.00 0.00 30.30 3.86
2727 5310 0.738412 CGAACCGCCGTTTATCCTGT 60.738 55.000 0.00 0.00 30.30 4.00
2728 5311 1.469595 CGAACCGCCGTTTATCCTGTA 60.470 52.381 0.00 0.00 30.30 2.74
2729 5312 1.929169 GAACCGCCGTTTATCCTGTAC 59.071 52.381 0.00 0.00 30.30 2.90
2732 5315 0.176219 CGCCGTTTATCCTGTACCCA 59.824 55.000 0.00 0.00 0.00 4.51
2733 5316 1.405797 CGCCGTTTATCCTGTACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
2734 5317 2.713877 GCCGTTTATCCTGTACCCAAA 58.286 47.619 0.00 0.00 0.00 3.28
2735 5318 2.421073 GCCGTTTATCCTGTACCCAAAC 59.579 50.000 0.00 0.00 0.00 2.93
2736 5319 3.871074 GCCGTTTATCCTGTACCCAAACT 60.871 47.826 0.00 0.00 0.00 2.66
2737 5320 4.623647 GCCGTTTATCCTGTACCCAAACTA 60.624 45.833 0.00 0.00 0.00 2.24
2738 5321 4.872124 CCGTTTATCCTGTACCCAAACTAC 59.128 45.833 0.00 0.00 0.00 2.73
2739 5322 5.337813 CCGTTTATCCTGTACCCAAACTACT 60.338 44.000 0.00 0.00 0.00 2.57
2751 5334 7.714813 TGTACCCAAACTACTAGTAAAACCAAC 59.285 37.037 3.76 0.00 0.00 3.77
2777 5361 3.963383 AAGAACGCAACCACAAACTAG 57.037 42.857 0.00 0.00 0.00 2.57
2786 5370 3.418684 ACCACAAACTAGACATGGGTC 57.581 47.619 0.00 0.00 44.66 4.46
2795 5379 3.080647 GACATGGGTCGGCTTAAGG 57.919 57.895 4.29 0.00 33.68 2.69
2827 5411 7.810282 TGGTGGTATTGTTAATTGAAATTGTCG 59.190 33.333 0.00 0.00 0.00 4.35
2859 5443 2.044252 TCCTAGGACCGCTCGCTT 60.044 61.111 7.62 0.00 0.00 4.68
2927 5511 5.237236 TCCTCGAACCAGGTTTTCTATTT 57.763 39.130 6.21 0.00 34.76 1.40
2928 5512 5.001232 TCCTCGAACCAGGTTTTCTATTTG 58.999 41.667 6.21 0.00 34.76 2.32
2929 5513 4.156008 CCTCGAACCAGGTTTTCTATTTGG 59.844 45.833 6.21 0.00 35.07 3.28
2932 5516 5.702209 TCGAACCAGGTTTTCTATTTGGTAC 59.298 40.000 6.21 0.00 41.08 3.34
2937 5521 5.704053 CCAGGTTTTCTATTTGGTACGTTCT 59.296 40.000 0.00 0.00 0.00 3.01
2991 5575 9.729023 CTTTCTTCTTCTTCTTTTCTCTTTTCC 57.271 33.333 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.830580 CCTCAATGTTCATCGTGTATCTAAAAT 58.169 33.333 0.00 0.00 0.00 1.82
10 11 7.279981 CCCTCAATGTTCATCGTGTATCTAAAA 59.720 37.037 0.00 0.00 0.00 1.52
11 12 6.761242 CCCTCAATGTTCATCGTGTATCTAAA 59.239 38.462 0.00 0.00 0.00 1.85
12 13 6.280643 CCCTCAATGTTCATCGTGTATCTAA 58.719 40.000 0.00 0.00 0.00 2.10
13 14 5.739070 GCCCTCAATGTTCATCGTGTATCTA 60.739 44.000 0.00 0.00 0.00 1.98
14 15 4.697514 CCCTCAATGTTCATCGTGTATCT 58.302 43.478 0.00 0.00 0.00 1.98
15 16 3.248602 GCCCTCAATGTTCATCGTGTATC 59.751 47.826 0.00 0.00 0.00 2.24
16 17 3.206150 GCCCTCAATGTTCATCGTGTAT 58.794 45.455 0.00 0.00 0.00 2.29
17 18 2.627945 GCCCTCAATGTTCATCGTGTA 58.372 47.619 0.00 0.00 0.00 2.90
18 19 1.453155 GCCCTCAATGTTCATCGTGT 58.547 50.000 0.00 0.00 0.00 4.49
19 20 0.374758 CGCCCTCAATGTTCATCGTG 59.625 55.000 0.00 0.00 0.00 4.35
20 21 0.249120 TCGCCCTCAATGTTCATCGT 59.751 50.000 0.00 0.00 0.00 3.73
21 22 1.062587 GTTCGCCCTCAATGTTCATCG 59.937 52.381 0.00 0.00 0.00 3.84
22 23 2.083774 TGTTCGCCCTCAATGTTCATC 58.916 47.619 0.00 0.00 0.00 2.92
23 24 2.198827 TGTTCGCCCTCAATGTTCAT 57.801 45.000 0.00 0.00 0.00 2.57
24 25 2.198827 ATGTTCGCCCTCAATGTTCA 57.801 45.000 0.00 0.00 0.00 3.18
25 26 3.575965 AAATGTTCGCCCTCAATGTTC 57.424 42.857 0.00 0.00 0.00 3.18
26 27 3.573967 AGAAAATGTTCGCCCTCAATGTT 59.426 39.130 0.00 0.00 38.90 2.71
27 28 3.157087 AGAAAATGTTCGCCCTCAATGT 58.843 40.909 0.00 0.00 38.90 2.71
28 29 3.855689 AGAAAATGTTCGCCCTCAATG 57.144 42.857 0.00 0.00 38.90 2.82
29 30 4.871933 AAAGAAAATGTTCGCCCTCAAT 57.128 36.364 0.00 0.00 38.90 2.57
30 31 4.664150 AAAAGAAAATGTTCGCCCTCAA 57.336 36.364 0.00 0.00 38.90 3.02
31 32 5.776173 TTAAAAGAAAATGTTCGCCCTCA 57.224 34.783 0.00 0.00 38.90 3.86
32 33 5.980715 TGTTTAAAAGAAAATGTTCGCCCTC 59.019 36.000 0.00 0.00 38.90 4.30
33 34 5.908341 TGTTTAAAAGAAAATGTTCGCCCT 58.092 33.333 0.00 0.00 38.90 5.19
34 35 6.347321 CCATGTTTAAAAGAAAATGTTCGCCC 60.347 38.462 0.00 0.00 38.90 6.13
35 36 6.201997 ACCATGTTTAAAAGAAAATGTTCGCC 59.798 34.615 0.00 0.00 38.90 5.54
36 37 7.043059 TCACCATGTTTAAAAGAAAATGTTCGC 60.043 33.333 0.00 0.00 38.90 4.70
37 38 8.346476 TCACCATGTTTAAAAGAAAATGTTCG 57.654 30.769 0.00 0.00 38.90 3.95
50 51 9.330063 TGCACATTAAAATTTCACCATGTTTAA 57.670 25.926 0.00 0.00 0.00 1.52
51 52 8.893219 TGCACATTAAAATTTCACCATGTTTA 57.107 26.923 0.00 0.00 0.00 2.01
52 53 7.798596 TGCACATTAAAATTTCACCATGTTT 57.201 28.000 0.00 0.00 0.00 2.83
53 54 7.660617 TCATGCACATTAAAATTTCACCATGTT 59.339 29.630 0.00 0.00 0.00 2.71
54 55 7.160049 TCATGCACATTAAAATTTCACCATGT 58.840 30.769 0.00 0.00 0.00 3.21
55 56 7.598189 TCATGCACATTAAAATTTCACCATG 57.402 32.000 0.00 0.00 0.00 3.66
56 57 8.670135 CAATCATGCACATTAAAATTTCACCAT 58.330 29.630 0.00 0.00 0.00 3.55
57 58 7.876582 TCAATCATGCACATTAAAATTTCACCA 59.123 29.630 0.00 0.00 0.00 4.17
58 59 8.254178 TCAATCATGCACATTAAAATTTCACC 57.746 30.769 0.00 0.00 0.00 4.02
63 64 9.451002 TCCATTTCAATCATGCACATTAAAATT 57.549 25.926 0.00 0.00 0.00 1.82
64 65 9.621629 ATCCATTTCAATCATGCACATTAAAAT 57.378 25.926 0.00 0.00 0.00 1.82
65 66 9.100554 GATCCATTTCAATCATGCACATTAAAA 57.899 29.630 0.00 0.00 0.00 1.52
66 67 8.479689 AGATCCATTTCAATCATGCACATTAAA 58.520 29.630 0.00 0.00 0.00 1.52
67 68 8.014070 AGATCCATTTCAATCATGCACATTAA 57.986 30.769 0.00 0.00 0.00 1.40
68 69 7.591421 AGATCCATTTCAATCATGCACATTA 57.409 32.000 0.00 0.00 0.00 1.90
69 70 6.479972 AGATCCATTTCAATCATGCACATT 57.520 33.333 0.00 0.00 0.00 2.71
70 71 7.591421 TTAGATCCATTTCAATCATGCACAT 57.409 32.000 0.00 0.00 0.00 3.21
71 72 7.093858 TGTTTAGATCCATTTCAATCATGCACA 60.094 33.333 0.00 0.00 0.00 4.57
72 73 7.259882 TGTTTAGATCCATTTCAATCATGCAC 58.740 34.615 0.00 0.00 0.00 4.57
73 74 7.407393 TGTTTAGATCCATTTCAATCATGCA 57.593 32.000 0.00 0.00 0.00 3.96
74 75 7.384115 CCATGTTTAGATCCATTTCAATCATGC 59.616 37.037 0.00 0.00 0.00 4.06
75 76 8.635328 TCCATGTTTAGATCCATTTCAATCATG 58.365 33.333 0.00 0.00 0.00 3.07
76 77 8.771521 TCCATGTTTAGATCCATTTCAATCAT 57.228 30.769 0.00 0.00 0.00 2.45
77 78 8.592529 TTCCATGTTTAGATCCATTTCAATCA 57.407 30.769 0.00 0.00 0.00 2.57
78 79 9.472361 CATTCCATGTTTAGATCCATTTCAATC 57.528 33.333 0.00 0.00 0.00 2.67
79 80 7.929785 GCATTCCATGTTTAGATCCATTTCAAT 59.070 33.333 0.00 0.00 0.00 2.57
80 81 7.124599 AGCATTCCATGTTTAGATCCATTTCAA 59.875 33.333 0.00 0.00 0.00 2.69
81 82 6.608405 AGCATTCCATGTTTAGATCCATTTCA 59.392 34.615 0.00 0.00 0.00 2.69
82 83 7.047460 AGCATTCCATGTTTAGATCCATTTC 57.953 36.000 0.00 0.00 0.00 2.17
83 84 7.427989 AAGCATTCCATGTTTAGATCCATTT 57.572 32.000 0.00 0.00 31.68 2.32
84 85 7.427989 AAAGCATTCCATGTTTAGATCCATT 57.572 32.000 0.00 0.00 32.29 3.16
85 86 7.427989 AAAAGCATTCCATGTTTAGATCCAT 57.572 32.000 0.00 0.00 32.29 3.41
86 87 6.855763 AAAAGCATTCCATGTTTAGATCCA 57.144 33.333 0.00 0.00 32.29 3.41
87 88 9.651913 TTTTAAAAGCATTCCATGTTTAGATCC 57.348 29.630 0.00 0.00 32.29 3.36
130 131 9.675464 ACCCGATAAAGAGTTCACATATTTTTA 57.325 29.630 0.00 0.00 0.00 1.52
131 132 8.575649 ACCCGATAAAGAGTTCACATATTTTT 57.424 30.769 0.00 0.00 0.00 1.94
132 133 8.575649 AACCCGATAAAGAGTTCACATATTTT 57.424 30.769 0.00 0.00 0.00 1.82
133 134 8.458843 CAAACCCGATAAAGAGTTCACATATTT 58.541 33.333 0.00 0.00 0.00 1.40
134 135 7.610305 ACAAACCCGATAAAGAGTTCACATATT 59.390 33.333 0.00 0.00 0.00 1.28
135 136 7.110155 ACAAACCCGATAAAGAGTTCACATAT 58.890 34.615 0.00 0.00 0.00 1.78
136 137 6.469410 ACAAACCCGATAAAGAGTTCACATA 58.531 36.000 0.00 0.00 0.00 2.29
137 138 5.313712 ACAAACCCGATAAAGAGTTCACAT 58.686 37.500 0.00 0.00 0.00 3.21
138 139 4.710324 ACAAACCCGATAAAGAGTTCACA 58.290 39.130 0.00 0.00 0.00 3.58
139 140 6.980051 ATACAAACCCGATAAAGAGTTCAC 57.020 37.500 0.00 0.00 0.00 3.18
140 141 6.128117 GCAATACAAACCCGATAAAGAGTTCA 60.128 38.462 0.00 0.00 0.00 3.18
141 142 6.128117 TGCAATACAAACCCGATAAAGAGTTC 60.128 38.462 0.00 0.00 0.00 3.01
142 143 5.708230 TGCAATACAAACCCGATAAAGAGTT 59.292 36.000 0.00 0.00 0.00 3.01
143 144 5.123344 GTGCAATACAAACCCGATAAAGAGT 59.877 40.000 0.00 0.00 0.00 3.24
144 145 5.569413 GTGCAATACAAACCCGATAAAGAG 58.431 41.667 0.00 0.00 0.00 2.85
145 146 4.093703 CGTGCAATACAAACCCGATAAAGA 59.906 41.667 0.00 0.00 0.00 2.52
146 147 4.142773 ACGTGCAATACAAACCCGATAAAG 60.143 41.667 0.00 0.00 0.00 1.85
147 148 3.752222 ACGTGCAATACAAACCCGATAAA 59.248 39.130 0.00 0.00 0.00 1.40
148 149 3.336468 ACGTGCAATACAAACCCGATAA 58.664 40.909 0.00 0.00 0.00 1.75
149 150 2.975266 ACGTGCAATACAAACCCGATA 58.025 42.857 0.00 0.00 0.00 2.92
150 151 1.816074 ACGTGCAATACAAACCCGAT 58.184 45.000 0.00 0.00 0.00 4.18
151 152 1.595466 AACGTGCAATACAAACCCGA 58.405 45.000 0.00 0.00 0.00 5.14
152 153 2.409152 AAACGTGCAATACAAACCCG 57.591 45.000 0.00 0.00 0.00 5.28
153 154 3.054166 GGAAAACGTGCAATACAAACCC 58.946 45.455 0.00 0.00 0.00 4.11
154 155 3.972403 AGGAAAACGTGCAATACAAACC 58.028 40.909 0.00 0.00 0.00 3.27
155 156 5.959652 AAAGGAAAACGTGCAATACAAAC 57.040 34.783 0.00 0.00 0.00 2.93
156 157 5.520649 GGAAAAGGAAAACGTGCAATACAAA 59.479 36.000 0.00 0.00 0.00 2.83
157 158 5.044558 GGAAAAGGAAAACGTGCAATACAA 58.955 37.500 0.00 0.00 0.00 2.41
158 159 4.500035 GGGAAAAGGAAAACGTGCAATACA 60.500 41.667 0.00 0.00 0.00 2.29
159 160 3.985279 GGGAAAAGGAAAACGTGCAATAC 59.015 43.478 0.00 0.00 0.00 1.89
160 161 3.637229 TGGGAAAAGGAAAACGTGCAATA 59.363 39.130 0.00 0.00 0.00 1.90
161 162 2.432510 TGGGAAAAGGAAAACGTGCAAT 59.567 40.909 0.00 0.00 0.00 3.56
162 163 1.825474 TGGGAAAAGGAAAACGTGCAA 59.175 42.857 0.00 0.00 0.00 4.08
163 164 1.475403 TGGGAAAAGGAAAACGTGCA 58.525 45.000 0.00 0.00 0.00 4.57
164 165 2.812358 ATGGGAAAAGGAAAACGTGC 57.188 45.000 0.00 0.00 0.00 5.34
165 166 4.944048 AGAAATGGGAAAAGGAAAACGTG 58.056 39.130 0.00 0.00 0.00 4.49
166 167 5.607939 AAGAAATGGGAAAAGGAAAACGT 57.392 34.783 0.00 0.00 0.00 3.99
167 168 6.918892 AAAAGAAATGGGAAAAGGAAAACG 57.081 33.333 0.00 0.00 0.00 3.60
168 169 8.506168 AGAAAAAGAAATGGGAAAAGGAAAAC 57.494 30.769 0.00 0.00 0.00 2.43
169 170 9.607988 GTAGAAAAAGAAATGGGAAAAGGAAAA 57.392 29.630 0.00 0.00 0.00 2.29
170 171 8.763601 TGTAGAAAAAGAAATGGGAAAAGGAAA 58.236 29.630 0.00 0.00 0.00 3.13
171 172 8.312669 TGTAGAAAAAGAAATGGGAAAAGGAA 57.687 30.769 0.00 0.00 0.00 3.36
172 173 7.906199 TGTAGAAAAAGAAATGGGAAAAGGA 57.094 32.000 0.00 0.00 0.00 3.36
173 174 8.367156 TCATGTAGAAAAAGAAATGGGAAAAGG 58.633 33.333 0.00 0.00 0.00 3.11
174 175 9.762933 TTCATGTAGAAAAAGAAATGGGAAAAG 57.237 29.630 0.00 0.00 32.05 2.27
191 192 8.783093 CCATGACTTACAAGTTTTTCATGTAGA 58.217 33.333 15.04 0.00 39.88 2.59
192 193 8.023128 CCCATGACTTACAAGTTTTTCATGTAG 58.977 37.037 15.04 7.19 39.88 2.74
193 194 7.523052 GCCCATGACTTACAAGTTTTTCATGTA 60.523 37.037 15.04 0.00 39.88 2.29
194 195 6.738453 GCCCATGACTTACAAGTTTTTCATGT 60.738 38.462 15.04 0.00 39.88 3.21
195 196 5.634859 GCCCATGACTTACAAGTTTTTCATG 59.365 40.000 11.66 11.66 39.88 3.07
196 197 5.304101 TGCCCATGACTTACAAGTTTTTCAT 59.696 36.000 0.00 0.00 39.88 2.57
197 198 4.646945 TGCCCATGACTTACAAGTTTTTCA 59.353 37.500 0.00 0.00 39.88 2.69
198 199 5.195001 TGCCCATGACTTACAAGTTTTTC 57.805 39.130 0.00 0.00 39.88 2.29
199 200 5.606348 TTGCCCATGACTTACAAGTTTTT 57.394 34.783 0.00 0.00 39.88 1.94
200 201 5.356426 GTTTGCCCATGACTTACAAGTTTT 58.644 37.500 0.00 0.00 39.88 2.43
201 202 4.202212 GGTTTGCCCATGACTTACAAGTTT 60.202 41.667 0.00 0.00 39.88 2.66
202 203 3.320826 GGTTTGCCCATGACTTACAAGTT 59.679 43.478 0.00 0.00 39.88 2.66
203 204 2.890945 GGTTTGCCCATGACTTACAAGT 59.109 45.455 0.00 0.00 43.16 3.16
204 205 3.157087 AGGTTTGCCCATGACTTACAAG 58.843 45.455 0.00 0.00 34.66 3.16
205 206 3.237268 AGGTTTGCCCATGACTTACAA 57.763 42.857 0.00 0.00 34.66 2.41
206 207 2.969821 AGGTTTGCCCATGACTTACA 57.030 45.000 0.00 0.00 34.66 2.41
207 208 3.826729 AGAAAGGTTTGCCCATGACTTAC 59.173 43.478 0.00 0.00 34.66 2.34
208 209 4.112634 AGAAAGGTTTGCCCATGACTTA 57.887 40.909 0.00 0.00 34.66 2.24
209 210 2.962859 AGAAAGGTTTGCCCATGACTT 58.037 42.857 0.00 0.00 34.66 3.01
210 211 2.683211 AGAAAGGTTTGCCCATGACT 57.317 45.000 0.00 0.00 34.66 3.41
211 212 4.864704 TTTAGAAAGGTTTGCCCATGAC 57.135 40.909 0.00 0.00 34.66 3.06
212 213 5.420739 GGTATTTAGAAAGGTTTGCCCATGA 59.579 40.000 0.00 0.00 34.66 3.07
213 214 5.395214 GGGTATTTAGAAAGGTTTGCCCATG 60.395 44.000 0.00 0.00 34.66 3.66
214 215 4.714802 GGGTATTTAGAAAGGTTTGCCCAT 59.285 41.667 0.00 0.00 34.66 4.00
215 216 4.090819 GGGTATTTAGAAAGGTTTGCCCA 58.909 43.478 0.00 0.00 34.66 5.36
216 217 3.129813 CGGGTATTTAGAAAGGTTTGCCC 59.870 47.826 0.00 0.00 34.57 5.36
217 218 4.011698 TCGGGTATTTAGAAAGGTTTGCC 58.988 43.478 0.00 0.00 0.00 4.52
218 219 5.355910 TCATCGGGTATTTAGAAAGGTTTGC 59.644 40.000 0.00 0.00 0.00 3.68
219 220 6.995511 TCATCGGGTATTTAGAAAGGTTTG 57.004 37.500 0.00 0.00 0.00 2.93
220 221 6.943718 TGTTCATCGGGTATTTAGAAAGGTTT 59.056 34.615 0.00 0.00 0.00 3.27
221 222 6.478129 TGTTCATCGGGTATTTAGAAAGGTT 58.522 36.000 0.00 0.00 0.00 3.50
222 223 6.057321 TGTTCATCGGGTATTTAGAAAGGT 57.943 37.500 0.00 0.00 0.00 3.50
223 224 7.568199 AATGTTCATCGGGTATTTAGAAAGG 57.432 36.000 0.00 0.00 0.00 3.11
224 225 9.855021 AAAAATGTTCATCGGGTATTTAGAAAG 57.145 29.630 0.00 0.00 0.00 2.62
346 347 4.949238 TGGCATGCATTACAGTTGTCTTAT 59.051 37.500 21.36 0.00 0.00 1.73
606 619 3.018856 TGTCCATAGCAATTTGCCTCTG 58.981 45.455 17.51 11.96 46.52 3.35
625 638 3.953775 CCAACGAGCCTGGGGTGT 61.954 66.667 0.00 0.00 0.00 4.16
745 768 1.066573 CGAGTTCAGATGGAGCAGGTT 60.067 52.381 0.00 0.00 0.00 3.50
746 769 0.534412 CGAGTTCAGATGGAGCAGGT 59.466 55.000 0.00 0.00 0.00 4.00
854 903 1.487452 TTGCTGTTGTCGTCGTGAGC 61.487 55.000 0.00 0.00 0.00 4.26
1427 1500 3.003763 GGAAGAGGTGGGCGAGGT 61.004 66.667 0.00 0.00 0.00 3.85
2151 4500 5.813717 AGTAAAACACGCTACAAAGGAAAC 58.186 37.500 0.00 0.00 0.00 2.78
2298 4653 4.063689 CCACATGCTAGCAATTCTAGGAG 58.936 47.826 23.54 5.82 46.68 3.69
2349 4898 0.034089 GCACCCTTCCAACTAGGCAT 60.034 55.000 0.00 0.00 37.29 4.40
2373 4922 3.418995 TGATATAGTACCCTCGTCAGGC 58.581 50.000 0.00 0.00 38.72 4.85
2382 4931 2.029290 CCGCCACACTGATATAGTACCC 60.029 54.545 0.00 0.00 37.60 3.69
2387 4936 5.899120 ATACTACCGCCACACTGATATAG 57.101 43.478 0.00 0.00 0.00 1.31
2388 4937 5.884232 CCTATACTACCGCCACACTGATATA 59.116 44.000 0.00 0.00 0.00 0.86
2389 4938 4.705507 CCTATACTACCGCCACACTGATAT 59.294 45.833 0.00 0.00 0.00 1.63
2390 4939 4.077108 CCTATACTACCGCCACACTGATA 58.923 47.826 0.00 0.00 0.00 2.15
2391 4940 2.891580 CCTATACTACCGCCACACTGAT 59.108 50.000 0.00 0.00 0.00 2.90
2402 4958 5.588958 AAAGGAACACGACCTATACTACC 57.411 43.478 0.00 0.00 36.67 3.18
2411 4967 3.549423 GCTTGGTTTAAAGGAACACGACC 60.549 47.826 0.00 0.00 0.00 4.79
2440 4996 1.291184 TTCTCTCATGTGCCGTTGCG 61.291 55.000 0.00 0.00 41.78 4.85
2447 5003 1.875514 TGTGTGCTTTCTCTCATGTGC 59.124 47.619 0.00 0.00 0.00 4.57
2455 5011 1.242076 AGGCATGTGTGTGCTTTCTC 58.758 50.000 0.00 0.00 44.45 2.87
2462 5018 2.503331 TCCTTTGTAGGCATGTGTGTG 58.497 47.619 0.00 0.00 41.69 3.82
2476 5032 2.504681 GGCGCGCACATTCCTTTG 60.505 61.111 34.42 0.00 0.00 2.77
2500 5056 1.000394 TCGTCTCTTTGTTGCCGATCA 60.000 47.619 0.00 0.00 0.00 2.92
2501 5057 1.710013 TCGTCTCTTTGTTGCCGATC 58.290 50.000 0.00 0.00 0.00 3.69
2502 5058 2.002586 CATCGTCTCTTTGTTGCCGAT 58.997 47.619 0.00 0.00 35.63 4.18
2518 5074 3.312421 CCCTATGGTGCTTTTACACATCG 59.688 47.826 0.00 0.00 42.55 3.84
2519 5075 4.523083 TCCCTATGGTGCTTTTACACATC 58.477 43.478 0.00 0.00 42.55 3.06
2556 5112 1.959899 CTCGTCAGTTGATGCGGTGC 61.960 60.000 0.00 0.00 0.00 5.01
2571 5127 7.435488 CCTTTATTTATGATCGTTCTGACTCGT 59.565 37.037 0.00 0.00 0.00 4.18
2583 5139 9.788960 GACCTGTGTTTTCCTTTATTTATGATC 57.211 33.333 0.00 0.00 0.00 2.92
2588 5144 7.468906 CGGTTGACCTGTGTTTTCCTTTATTTA 60.469 37.037 0.00 0.00 0.00 1.40
2593 5149 2.425668 CGGTTGACCTGTGTTTTCCTTT 59.574 45.455 0.00 0.00 0.00 3.11
2615 5171 0.252239 TGCCTAGCCAGTTCAGGAGA 60.252 55.000 0.00 0.00 0.00 3.71
2649 5231 4.336153 TGTGTGTGCTATTATGATTGGCTG 59.664 41.667 0.00 0.00 0.00 4.85
2670 5252 7.733402 ATCATTTGTTGCTTAGCATTTTTGT 57.267 28.000 8.05 0.00 38.76 2.83
2683 5266 5.332959 CCACACCGTTTTTATCATTTGTTGC 60.333 40.000 0.00 0.00 0.00 4.17
2685 5268 4.747605 GCCACACCGTTTTTATCATTTGTT 59.252 37.500 0.00 0.00 0.00 2.83
2695 5278 1.434287 GGTTCGCCACACCGTTTTT 59.566 52.632 0.00 0.00 37.19 1.94
2716 5299 5.727434 AGTAGTTTGGGTACAGGATAAACG 58.273 41.667 0.00 0.00 36.61 3.60
2726 5309 7.714813 TGTTGGTTTTACTAGTAGTTTGGGTAC 59.285 37.037 8.40 0.95 0.00 3.34
2727 5310 7.800092 TGTTGGTTTTACTAGTAGTTTGGGTA 58.200 34.615 8.40 0.00 0.00 3.69
2728 5311 6.661777 TGTTGGTTTTACTAGTAGTTTGGGT 58.338 36.000 8.40 0.00 0.00 4.51
2729 5312 7.499895 TCTTGTTGGTTTTACTAGTAGTTTGGG 59.500 37.037 8.40 0.00 0.00 4.12
2734 5317 9.895138 TCTTTTCTTGTTGGTTTTACTAGTAGT 57.105 29.630 8.14 8.14 0.00 2.73
2737 5320 8.179615 CGTTCTTTTCTTGTTGGTTTTACTAGT 58.820 33.333 0.00 0.00 0.00 2.57
2738 5321 7.165318 GCGTTCTTTTCTTGTTGGTTTTACTAG 59.835 37.037 0.00 0.00 0.00 2.57
2739 5322 6.968335 GCGTTCTTTTCTTGTTGGTTTTACTA 59.032 34.615 0.00 0.00 0.00 1.82
2751 5334 3.143807 TGTGGTTGCGTTCTTTTCTTG 57.856 42.857 0.00 0.00 0.00 3.02
2777 5361 1.095807 GCCTTAAGCCGACCCATGTC 61.096 60.000 0.00 0.00 38.18 3.06
2786 5370 1.449601 ACCACATCGCCTTAAGCCG 60.450 57.895 0.00 0.00 38.78 5.52
2789 5373 2.684001 TACCACCACATCGCCTTAAG 57.316 50.000 0.00 0.00 0.00 1.85
2795 5379 4.893424 ATTAACAATACCACCACATCGC 57.107 40.909 0.00 0.00 0.00 4.58
2827 5411 6.367161 GGTCCTAGGAGGGTGTATATCTATC 58.633 48.000 13.15 0.00 35.59 2.08
2838 5422 2.279408 GAGCGGTCCTAGGAGGGT 59.721 66.667 13.15 13.02 35.59 4.34
2845 5429 3.305813 CCATATTTAAGCGAGCGGTCCTA 60.306 47.826 9.39 0.00 0.00 2.94
2846 5430 2.548067 CCATATTTAAGCGAGCGGTCCT 60.548 50.000 9.39 4.40 0.00 3.85
2859 5443 2.295349 GACGCGAGAGGTCCCATATTTA 59.705 50.000 15.93 0.00 0.00 1.40
2906 5490 4.156008 CCAAATAGAAAACCTGGTTCGAGG 59.844 45.833 13.36 3.37 39.28 4.63
2910 5494 5.471116 ACGTACCAAATAGAAAACCTGGTTC 59.529 40.000 13.36 0.94 40.77 3.62
2965 5549 9.729023 GGAAAAGAGAAAAGAAGAAGAAGAAAG 57.271 33.333 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.