Multiple sequence alignment - TraesCS6A01G255500

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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 TraesCS6A01G255500 chr6A 100.000 4108 0 0 1 4108 473577711 473573604 0.000000e+00 7587.0
1 TraesCS6A01G255500 chr6A 85.859 198 26 2 2139 2334 500083818 500083621 4.160000e-50 209.0
2 TraesCS6A01G255500 chr6D 94.090 3841 104 44 309 4063 334229529 334225726 0.000000e+00 5722.0
3 TraesCS6A01G255500 chr6D 89.441 161 17 0 2174 2334 358326162 358326002 1.940000e-48 204.0
4 TraesCS6A01G255500 chr6D 82.381 210 31 6 2144 2350 378379475 378379269 1.170000e-40 178.0
5 TraesCS6A01G255500 chr6B 92.929 3861 130 50 318 4101 486222845 486226639 0.000000e+00 5485.0
6 TraesCS6A01G255500 chr6B 85.354 198 27 2 2139 2334 539727743 539727546 1.940000e-48 204.0
7 TraesCS6A01G255500 chr5D 91.649 467 20 8 708 1160 344617661 344618122 2.700000e-176 628.0
8 TraesCS6A01G255500 chr5D 91.919 297 12 5 872 1160 344616580 344616872 4.940000e-109 405.0
9 TraesCS6A01G255500 chr5D 88.591 298 34 0 5 302 510829562 510829265 3.020000e-96 363.0
10 TraesCS6A01G255500 chr2D 79.328 595 91 23 2145 2724 512686870 512687447 4.980000e-104 388.0
11 TraesCS6A01G255500 chr2D 88.255 298 35 0 5 302 552138306 552138009 1.400000e-94 357.0
12 TraesCS6A01G255500 chr2D 86.913 298 39 0 5 302 487936915 487937212 6.580000e-88 335.0
13 TraesCS6A01G255500 chr2D 86.667 300 39 1 5 304 543289443 543289145 8.510000e-87 331.0
14 TraesCS6A01G255500 chr2D 81.915 94 12 3 3954 4043 512688661 512688753 1.580000e-09 75.0
15 TraesCS6A01G255500 chr2A 79.362 596 89 24 2145 2724 656240947 656241524 4.980000e-104 388.0
16 TraesCS6A01G255500 chr2A 84.043 94 10 3 3954 4043 656242730 656242822 7.320000e-13 86.1
17 TraesCS6A01G255500 chr2B 78.583 593 93 24 2145 2724 602763481 602764052 1.090000e-95 361.0
18 TraesCS6A01G255500 chr2B 83.333 102 12 3 3954 4051 602765264 602765364 5.660000e-14 89.8
19 TraesCS6A01G255500 chr7D 87.960 299 34 2 5 302 373242530 373242233 6.530000e-93 351.0
20 TraesCS6A01G255500 chr7D 87.333 300 37 1 5 304 159701102 159700804 3.930000e-90 342.0
21 TraesCS6A01G255500 chr7D 87.375 301 35 3 5 304 402317606 402317904 3.930000e-90 342.0
22 TraesCS6A01G255500 chr5B 86.379 301 41 0 5 305 80271111 80270811 3.060000e-86 329.0
23 TraesCS6A01G255500 chr5B 86.047 301 42 0 5 305 80675900 80675600 1.420000e-84 324.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G255500 chr6A 473573604 473577711 4107 True 7587.00 7587 100.0000 1 4108 1 chr6A.!!$R1 4107
1 TraesCS6A01G255500 chr6D 334225726 334229529 3803 True 5722.00 5722 94.0900 309 4063 1 chr6D.!!$R1 3754
2 TraesCS6A01G255500 chr6B 486222845 486226639 3794 False 5485.00 5485 92.9290 318 4101 1 chr6B.!!$F1 3783
3 TraesCS6A01G255500 chr5D 344616580 344618122 1542 False 516.50 628 91.7840 708 1160 2 chr5D.!!$F1 452
4 TraesCS6A01G255500 chr2D 512686870 512688753 1883 False 231.50 388 80.6215 2145 4043 2 chr2D.!!$F2 1898
5 TraesCS6A01G255500 chr2A 656240947 656242822 1875 False 237.05 388 81.7025 2145 4043 2 chr2A.!!$F1 1898
6 TraesCS6A01G255500 chr2B 602763481 602765364 1883 False 225.40 361 80.9580 2145 4051 2 chr2B.!!$F1 1906

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
253 254 0.093026 CACTTTTGTCCGCGTCGATC 59.907 55.0 4.92 0.0 0.00 3.69 F
282 283 0.107848 ACGAACGGATGGAATGGGTC 60.108 55.0 0.00 0.0 0.00 4.46 F
743 1118 0.556380 TCTTCCTCCTCCTCCTCCCT 60.556 60.0 0.00 0.0 0.00 4.20 F
750 1125 0.620121 CCTCCTCCTCCCTTGCTCTT 60.620 60.0 0.00 0.0 0.00 2.85 F
1902 2331 0.625849 ACTTGCCCTAACATCTGGGG 59.374 55.0 0.00 0.0 43.53 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1793 0.106669 AATTAAAGGCCCCGAGCTCC 60.107 55.000 8.47 0.00 43.05 4.70 R
1394 1798 0.549469 GGGAGAATTAAAGGCCCCGA 59.451 55.000 0.00 0.00 32.50 5.14 R
1598 2026 1.375652 CAGTACTGCTGCTGCTGCT 60.376 57.895 27.67 14.24 41.07 4.24 R
2744 3209 1.211969 CTGCTGCTGTTGATGGTGC 59.788 57.895 0.00 0.00 0.00 5.01 R
3744 4496 2.000447 GAAAACACGCCTGCTACTAGG 59.000 52.381 0.00 0.00 40.95 3.02 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
44 45 2.359850 GCTGATGCGTGGGTCCAA 60.360 61.111 0.00 0.00 0.00 3.53
45 46 2.401766 GCTGATGCGTGGGTCCAAG 61.402 63.158 0.00 0.00 0.00 3.61
46 47 1.746615 CTGATGCGTGGGTCCAAGG 60.747 63.158 5.19 0.00 0.00 3.61
47 48 2.351276 GATGCGTGGGTCCAAGGT 59.649 61.111 5.19 0.00 0.00 3.50
48 49 2.034066 ATGCGTGGGTCCAAGGTG 59.966 61.111 5.19 0.00 0.00 4.00
49 50 3.567579 ATGCGTGGGTCCAAGGTGG 62.568 63.158 5.19 0.00 39.43 4.61
59 60 4.308458 CAAGGTGGGCGGTCGTCA 62.308 66.667 0.00 0.00 0.00 4.35
60 61 3.319198 AAGGTGGGCGGTCGTCAT 61.319 61.111 0.00 0.00 0.00 3.06
61 62 1.985662 AAGGTGGGCGGTCGTCATA 60.986 57.895 0.00 0.00 0.00 2.15
62 63 1.546589 AAGGTGGGCGGTCGTCATAA 61.547 55.000 0.00 0.00 0.00 1.90
63 64 1.078988 GGTGGGCGGTCGTCATAAA 60.079 57.895 0.00 0.00 0.00 1.40
64 65 0.463116 GGTGGGCGGTCGTCATAAAT 60.463 55.000 0.00 0.00 0.00 1.40
65 66 1.202557 GGTGGGCGGTCGTCATAAATA 60.203 52.381 0.00 0.00 0.00 1.40
66 67 2.553086 GTGGGCGGTCGTCATAAATAA 58.447 47.619 0.00 0.00 0.00 1.40
68 69 3.059188 GTGGGCGGTCGTCATAAATAATG 60.059 47.826 0.00 0.00 36.88 1.90
70 71 3.562557 GGGCGGTCGTCATAAATAATGTT 59.437 43.478 0.00 0.00 36.89 2.71
71 72 4.523813 GGCGGTCGTCATAAATAATGTTG 58.476 43.478 0.00 0.00 36.89 3.33
72 73 4.271533 GGCGGTCGTCATAAATAATGTTGA 59.728 41.667 0.00 0.00 36.89 3.18
75 76 5.734311 GGTCGTCATAAATAATGTTGACCG 58.266 41.667 12.26 0.00 43.87 4.79
76 77 5.292589 GGTCGTCATAAATAATGTTGACCGT 59.707 40.000 12.26 0.00 43.87 4.83
77 78 6.182634 GTCGTCATAAATAATGTTGACCGTG 58.817 40.000 0.00 0.00 36.07 4.94
78 79 6.035220 GTCGTCATAAATAATGTTGACCGTGA 59.965 38.462 0.00 0.00 36.07 4.35
79 80 6.759356 TCGTCATAAATAATGTTGACCGTGAT 59.241 34.615 0.00 0.00 36.06 3.06
80 81 7.921745 TCGTCATAAATAATGTTGACCGTGATA 59.078 33.333 0.00 0.00 36.06 2.15
82 83 9.042008 GTCATAAATAATGTTGACCGTGATAGT 57.958 33.333 0.00 0.00 36.89 2.12
83 84 9.607988 TCATAAATAATGTTGACCGTGATAGTT 57.392 29.630 0.00 0.00 36.89 2.24
84 85 9.650371 CATAAATAATGTTGACCGTGATAGTTG 57.350 33.333 0.00 0.00 0.00 3.16
86 87 3.973206 ATGTTGACCGTGATAGTTGGA 57.027 42.857 0.00 0.00 0.00 3.53
87 88 3.034721 TGTTGACCGTGATAGTTGGAC 57.965 47.619 0.00 0.00 0.00 4.02
88 89 2.365941 TGTTGACCGTGATAGTTGGACA 59.634 45.455 0.00 0.00 0.00 4.02
89 90 2.993899 GTTGACCGTGATAGTTGGACAG 59.006 50.000 0.00 0.00 0.00 3.51
90 91 1.067142 TGACCGTGATAGTTGGACAGC 60.067 52.381 0.00 0.00 0.00 4.40
91 92 0.249398 ACCGTGATAGTTGGACAGCC 59.751 55.000 0.00 0.00 0.00 4.85
92 93 0.806102 CCGTGATAGTTGGACAGCCG 60.806 60.000 0.00 0.00 36.79 5.52
93 94 1.421410 CGTGATAGTTGGACAGCCGC 61.421 60.000 0.00 0.00 36.79 6.53
94 95 1.090052 GTGATAGTTGGACAGCCGCC 61.090 60.000 0.00 0.00 36.79 6.13
95 96 1.220749 GATAGTTGGACAGCCGCCA 59.779 57.895 0.00 0.00 36.79 5.69
96 97 0.811616 GATAGTTGGACAGCCGCCAG 60.812 60.000 0.00 0.00 36.64 4.85
97 98 2.257409 ATAGTTGGACAGCCGCCAGG 62.257 60.000 0.00 0.00 36.64 4.45
98 99 4.643387 GTTGGACAGCCGCCAGGT 62.643 66.667 0.00 0.00 40.50 4.00
149 150 4.842091 GTGTCCGCGCCGACGTAT 62.842 66.667 21.08 0.00 42.83 3.06
151 152 3.317795 GTCCGCGCCGACGTATTC 61.318 66.667 12.97 0.00 42.83 1.75
152 153 4.557605 TCCGCGCCGACGTATTCC 62.558 66.667 0.00 0.00 42.83 3.01
153 154 4.858433 CCGCGCCGACGTATTCCA 62.858 66.667 0.00 0.00 42.83 3.53
154 155 3.320078 CGCGCCGACGTATTCCAG 61.320 66.667 0.00 0.00 42.83 3.86
155 156 2.960129 GCGCCGACGTATTCCAGG 60.960 66.667 0.00 0.00 42.83 4.45
156 157 2.960129 CGCCGACGTATTCCAGGC 60.960 66.667 0.00 0.00 44.00 4.85
157 158 2.960129 GCCGACGTATTCCAGGCG 60.960 66.667 0.00 0.00 38.28 5.52
158 159 2.960129 CCGACGTATTCCAGGCGC 60.960 66.667 0.00 0.00 0.00 6.53
160 161 1.807981 CGACGTATTCCAGGCGCAA 60.808 57.895 10.83 0.00 0.00 4.85
161 162 1.151777 CGACGTATTCCAGGCGCAAT 61.152 55.000 10.83 2.33 0.00 3.56
162 163 1.014352 GACGTATTCCAGGCGCAATT 58.986 50.000 10.83 0.00 0.00 2.32
163 164 1.400494 GACGTATTCCAGGCGCAATTT 59.600 47.619 10.83 0.00 0.00 1.82
166 167 3.440872 ACGTATTCCAGGCGCAATTTTAA 59.559 39.130 10.83 0.00 0.00 1.52
167 168 4.035017 CGTATTCCAGGCGCAATTTTAAG 58.965 43.478 10.83 0.00 0.00 1.85
171 172 4.086860 GGCGCAATTTTAAGCCGG 57.913 55.556 10.83 0.00 40.17 6.13
172 173 1.509004 GGCGCAATTTTAAGCCGGA 59.491 52.632 10.83 0.00 40.17 5.14
173 174 0.109039 GGCGCAATTTTAAGCCGGAA 60.109 50.000 10.83 0.00 40.17 4.30
175 176 2.267426 GCGCAATTTTAAGCCGGAAAT 58.733 42.857 5.05 0.00 0.00 2.17
176 177 2.029124 GCGCAATTTTAAGCCGGAAATG 59.971 45.455 5.05 0.00 0.00 2.32
177 178 2.602660 CGCAATTTTAAGCCGGAAATGG 59.397 45.455 5.05 0.28 0.00 3.16
178 179 3.674682 CGCAATTTTAAGCCGGAAATGGA 60.675 43.478 5.05 0.00 0.00 3.41
179 180 4.441792 GCAATTTTAAGCCGGAAATGGAT 58.558 39.130 5.05 0.00 0.00 3.41
180 181 4.507756 GCAATTTTAAGCCGGAAATGGATC 59.492 41.667 5.05 0.00 0.00 3.36
181 182 4.568152 ATTTTAAGCCGGAAATGGATCG 57.432 40.909 5.05 0.00 0.00 3.69
182 183 1.961793 TTAAGCCGGAAATGGATCGG 58.038 50.000 5.05 0.00 45.84 4.18
185 186 3.649986 CCGGAAATGGATCGGCGC 61.650 66.667 0.00 0.00 37.25 6.53
186 187 4.000557 CGGAAATGGATCGGCGCG 62.001 66.667 0.00 0.00 0.00 6.86
187 188 3.649986 GGAAATGGATCGGCGCGG 61.650 66.667 8.83 8.94 0.00 6.46
189 190 2.882366 GAAATGGATCGGCGCGGAC 61.882 63.158 20.65 13.38 0.00 4.79
190 191 3.673956 AAATGGATCGGCGCGGACA 62.674 57.895 20.65 14.71 0.00 4.02
191 192 4.891727 ATGGATCGGCGCGGACAC 62.892 66.667 20.65 15.64 0.00 3.67
202 203 2.126965 CGGACACGAGACGGACAC 60.127 66.667 0.00 0.00 44.60 3.67
203 204 3.923356 CGGACACGAGACGGACACG 62.923 68.421 0.00 0.00 44.60 4.49
204 205 2.610694 GGACACGAGACGGACACGA 61.611 63.158 4.35 0.00 44.60 4.35
205 206 1.500844 GACACGAGACGGACACGAT 59.499 57.895 4.35 0.00 44.60 3.73
207 208 0.313043 ACACGAGACGGACACGATTT 59.687 50.000 4.35 0.00 44.60 2.17
208 209 0.708370 CACGAGACGGACACGATTTG 59.292 55.000 4.35 0.00 44.60 2.32
210 211 1.260206 CGAGACGGACACGATTTGAG 58.740 55.000 0.00 0.00 44.60 3.02
211 212 1.401148 CGAGACGGACACGATTTGAGT 60.401 52.381 0.00 0.00 44.60 3.41
213 214 3.057734 GAGACGGACACGATTTGAGTTT 58.942 45.455 0.00 0.00 44.60 2.66
214 215 2.800544 AGACGGACACGATTTGAGTTTG 59.199 45.455 0.00 0.00 44.60 2.93
215 216 1.871039 ACGGACACGATTTGAGTTTGG 59.129 47.619 0.00 0.00 44.60 3.28
217 218 2.227194 GGACACGATTTGAGTTTGGGT 58.773 47.619 0.00 0.00 0.00 4.51
218 219 2.621526 GGACACGATTTGAGTTTGGGTT 59.378 45.455 0.00 0.00 0.00 4.11
219 220 3.550030 GGACACGATTTGAGTTTGGGTTG 60.550 47.826 0.00 0.00 0.00 3.77
220 221 2.360801 ACACGATTTGAGTTTGGGTTGG 59.639 45.455 0.00 0.00 0.00 3.77
221 222 1.339929 ACGATTTGAGTTTGGGTTGGC 59.660 47.619 0.00 0.00 0.00 4.52
222 223 1.665735 CGATTTGAGTTTGGGTTGGCG 60.666 52.381 0.00 0.00 0.00 5.69
223 224 1.339929 GATTTGAGTTTGGGTTGGCGT 59.660 47.619 0.00 0.00 0.00 5.68
224 225 0.457851 TTTGAGTTTGGGTTGGCGTG 59.542 50.000 0.00 0.00 0.00 5.34
226 227 0.681564 TGAGTTTGGGTTGGCGTGTT 60.682 50.000 0.00 0.00 0.00 3.32
227 228 0.248866 GAGTTTGGGTTGGCGTGTTG 60.249 55.000 0.00 0.00 0.00 3.33
229 230 2.427245 TTTGGGTTGGCGTGTTGGG 61.427 57.895 0.00 0.00 0.00 4.12
237 238 2.594592 GCGTGTTGGGCCTTCACT 60.595 61.111 21.90 0.00 0.00 3.41
239 240 1.734388 GCGTGTTGGGCCTTCACTTT 61.734 55.000 21.90 0.00 0.00 2.66
241 242 1.535860 CGTGTTGGGCCTTCACTTTTG 60.536 52.381 21.90 8.91 0.00 2.44
244 245 1.068588 GTTGGGCCTTCACTTTTGTCC 59.931 52.381 4.53 0.00 0.00 4.02
247 248 1.082104 GCCTTCACTTTTGTCCGCG 60.082 57.895 0.00 0.00 0.00 6.46
248 249 1.782028 GCCTTCACTTTTGTCCGCGT 61.782 55.000 4.92 0.00 0.00 6.01
249 250 0.234884 CCTTCACTTTTGTCCGCGTC 59.765 55.000 4.92 0.00 0.00 5.19
251 252 0.528033 TTCACTTTTGTCCGCGTCGA 60.528 50.000 4.92 0.00 0.00 4.20
252 253 0.319211 TCACTTTTGTCCGCGTCGAT 60.319 50.000 4.92 0.00 0.00 3.59
253 254 0.093026 CACTTTTGTCCGCGTCGATC 59.907 55.000 4.92 0.00 0.00 3.69
254 255 1.012486 ACTTTTGTCCGCGTCGATCC 61.012 55.000 4.92 0.00 0.00 3.36
255 256 1.005984 TTTTGTCCGCGTCGATCCA 60.006 52.632 4.92 0.00 0.00 3.41
256 257 0.600518 TTTTGTCCGCGTCGATCCAA 60.601 50.000 4.92 0.00 0.00 3.53
257 258 0.600518 TTTGTCCGCGTCGATCCAAA 60.601 50.000 4.92 1.44 0.00 3.28
258 259 1.286354 TTGTCCGCGTCGATCCAAAC 61.286 55.000 4.92 0.00 0.00 2.93
259 260 1.735198 GTCCGCGTCGATCCAAACA 60.735 57.895 4.92 0.00 0.00 2.83
260 261 1.445410 TCCGCGTCGATCCAAACAG 60.445 57.895 4.92 0.00 0.00 3.16
261 262 1.445410 CCGCGTCGATCCAAACAGA 60.445 57.895 4.92 0.00 0.00 3.41
262 263 1.011968 CCGCGTCGATCCAAACAGAA 61.012 55.000 4.92 0.00 0.00 3.02
263 264 0.787787 CGCGTCGATCCAAACAGAAA 59.212 50.000 0.00 0.00 0.00 2.52
265 266 1.461888 GCGTCGATCCAAACAGAAACG 60.462 52.381 0.00 0.00 0.00 3.60
266 267 2.055838 CGTCGATCCAAACAGAAACGA 58.944 47.619 0.00 0.00 0.00 3.85
267 268 2.473609 CGTCGATCCAAACAGAAACGAA 59.526 45.455 0.00 0.00 33.13 3.85
268 269 3.660904 CGTCGATCCAAACAGAAACGAAC 60.661 47.826 0.00 0.00 33.13 3.95
270 271 2.411031 CGATCCAAACAGAAACGAACGG 60.411 50.000 0.00 0.00 0.00 4.44
271 272 2.312722 TCCAAACAGAAACGAACGGA 57.687 45.000 0.00 0.00 0.00 4.69
272 273 2.841215 TCCAAACAGAAACGAACGGAT 58.159 42.857 0.00 0.00 0.00 4.18
273 274 2.546368 TCCAAACAGAAACGAACGGATG 59.454 45.455 0.00 0.00 0.00 3.51
274 275 2.350388 CCAAACAGAAACGAACGGATGG 60.350 50.000 0.00 0.00 0.00 3.51
275 276 2.536761 AACAGAAACGAACGGATGGA 57.463 45.000 0.00 0.00 0.00 3.41
276 277 2.536761 ACAGAAACGAACGGATGGAA 57.463 45.000 0.00 0.00 0.00 3.53
277 278 3.053831 ACAGAAACGAACGGATGGAAT 57.946 42.857 0.00 0.00 0.00 3.01
279 280 2.095853 CAGAAACGAACGGATGGAATGG 59.904 50.000 0.00 0.00 0.00 3.16
280 281 1.400494 GAAACGAACGGATGGAATGGG 59.600 52.381 0.00 0.00 0.00 4.00
281 282 0.326927 AACGAACGGATGGAATGGGT 59.673 50.000 0.00 0.00 0.00 4.51
282 283 0.107848 ACGAACGGATGGAATGGGTC 60.108 55.000 0.00 0.00 0.00 4.46
283 284 1.151777 CGAACGGATGGAATGGGTCG 61.152 60.000 0.00 0.00 31.62 4.79
284 285 0.107848 GAACGGATGGAATGGGTCGT 60.108 55.000 0.00 0.00 0.00 4.34
286 287 1.227556 CGGATGGAATGGGTCGTCC 60.228 63.158 0.00 0.00 0.00 4.79
300 301 2.418976 GGTCGTCCCATTAAAGTTGCTC 59.581 50.000 0.00 0.00 0.00 4.26
301 302 3.335579 GTCGTCCCATTAAAGTTGCTCT 58.664 45.455 0.00 0.00 0.00 4.09
302 303 4.501071 GTCGTCCCATTAAAGTTGCTCTA 58.499 43.478 0.00 0.00 0.00 2.43
303 304 4.933400 GTCGTCCCATTAAAGTTGCTCTAA 59.067 41.667 0.00 0.00 0.00 2.10
304 305 4.933400 TCGTCCCATTAAAGTTGCTCTAAC 59.067 41.667 0.00 0.00 39.65 2.34
317 318 6.283161 GTTGCTCTAACTTTTACGAACACT 57.717 37.500 0.00 0.00 36.34 3.55
318 319 5.900339 TGCTCTAACTTTTACGAACACTG 57.100 39.130 0.00 0.00 0.00 3.66
320 321 4.210537 GCTCTAACTTTTACGAACACTGCA 59.789 41.667 0.00 0.00 0.00 4.41
322 323 5.353938 TCTAACTTTTACGAACACTGCACT 58.646 37.500 0.00 0.00 0.00 4.40
325 326 6.425577 AACTTTTACGAACACTGCACTTAA 57.574 33.333 0.00 0.00 0.00 1.85
327 328 6.844254 ACTTTTACGAACACTGCACTTAAAA 58.156 32.000 0.00 0.00 0.00 1.52
328 329 7.477494 ACTTTTACGAACACTGCACTTAAAAT 58.523 30.769 0.00 0.00 0.00 1.82
329 330 7.971722 ACTTTTACGAACACTGCACTTAAAATT 59.028 29.630 0.00 0.00 0.00 1.82
331 332 7.672351 TTACGAACACTGCACTTAAAATTTG 57.328 32.000 0.00 0.00 0.00 2.32
332 333 5.646606 ACGAACACTGCACTTAAAATTTGT 58.353 33.333 0.00 0.00 0.00 2.83
334 335 7.251994 ACGAACACTGCACTTAAAATTTGTTA 58.748 30.769 0.00 0.00 0.00 2.41
335 336 7.755822 ACGAACACTGCACTTAAAATTTGTTAA 59.244 29.630 0.00 0.00 0.00 2.01
336 337 8.751335 CGAACACTGCACTTAAAATTTGTTAAT 58.249 29.630 0.00 0.00 0.00 1.40
367 368 3.009723 GCATTCGAAATGAAGGAGGTGA 58.990 45.455 0.00 0.00 40.79 4.02
559 567 2.483106 TGACTAGTTTCTCACCGACTCG 59.517 50.000 0.00 0.00 0.00 4.18
653 663 3.869473 TTCCGCGACCAACGAAGGG 62.869 63.158 8.23 0.00 45.77 3.95
656 666 3.423154 GCGACCAACGAAGGGCAG 61.423 66.667 4.71 0.00 45.77 4.85
743 1118 0.556380 TCTTCCTCCTCCTCCTCCCT 60.556 60.000 0.00 0.00 0.00 4.20
746 1121 2.069430 CCTCCTCCTCCTCCCTTGC 61.069 68.421 0.00 0.00 0.00 4.01
747 1122 1.002792 CTCCTCCTCCTCCCTTGCT 59.997 63.158 0.00 0.00 0.00 3.91
748 1123 1.002274 TCCTCCTCCTCCCTTGCTC 59.998 63.158 0.00 0.00 0.00 4.26
749 1124 1.002792 CCTCCTCCTCCCTTGCTCT 59.997 63.158 0.00 0.00 0.00 4.09
750 1125 0.620121 CCTCCTCCTCCCTTGCTCTT 60.620 60.000 0.00 0.00 0.00 2.85
757 1132 1.412343 CCTCCCTTGCTCTTCTCTAGC 59.588 57.143 0.00 0.00 40.50 3.42
1035 1430 1.209504 TGGCACCAGGTAAGCTGATAC 59.790 52.381 0.00 0.00 0.00 2.24
1037 1432 2.555199 GCACCAGGTAAGCTGATACAG 58.445 52.381 0.00 0.00 34.12 2.74
1039 1434 3.786635 CACCAGGTAAGCTGATACAGAC 58.213 50.000 0.00 0.00 32.44 3.51
1053 1456 2.550830 ACAGACGAGCACCTCAAATT 57.449 45.000 0.00 0.00 0.00 1.82
1183 1586 2.961526 TGCCTTCTTGGTCGACTATC 57.038 50.000 16.46 0.00 38.35 2.08
1187 1591 4.254492 GCCTTCTTGGTCGACTATCTTTT 58.746 43.478 16.46 0.00 38.35 2.27
1417 1821 1.403814 GGCCTTTAATTCTCCCCTGC 58.596 55.000 0.00 0.00 0.00 4.85
1493 1921 5.892348 TGCCTTTCTTTCTTATCCTTTCCT 58.108 37.500 0.00 0.00 0.00 3.36
1499 1927 9.460019 CTTTCTTTCTTATCCTTTCCTCTCATT 57.540 33.333 0.00 0.00 0.00 2.57
1704 2132 1.142060 TTTCGTCTCCTTTTCCCCCA 58.858 50.000 0.00 0.00 0.00 4.96
1806 2235 3.533606 AAGAATCATCCTCACACCTCG 57.466 47.619 0.00 0.00 0.00 4.63
1898 2327 5.763876 AGTTCTTACTTGCCCTAACATCT 57.236 39.130 0.00 0.00 0.00 2.90
1899 2328 5.491982 AGTTCTTACTTGCCCTAACATCTG 58.508 41.667 0.00 0.00 0.00 2.90
1902 2331 0.625849 ACTTGCCCTAACATCTGGGG 59.374 55.000 0.00 0.00 43.53 4.96
1907 2336 1.474330 CCCTAACATCTGGGGTTTGC 58.526 55.000 0.00 0.00 39.76 3.68
2171 2600 2.124942 CCGCAGAAGGAGAAGGCC 60.125 66.667 0.00 0.00 0.00 5.19
2339 2768 3.615110 GCTCACGGAAGAACAAGAGATCA 60.615 47.826 0.00 0.00 0.00 2.92
2751 3216 1.728069 CAGCATCAGCAGCACCATC 59.272 57.895 0.00 0.00 45.49 3.51
2752 3217 1.029947 CAGCATCAGCAGCACCATCA 61.030 55.000 0.00 0.00 45.49 3.07
2753 3218 0.323087 AGCATCAGCAGCACCATCAA 60.323 50.000 0.00 0.00 45.49 2.57
2997 3510 1.283793 CACAGCAAAGACCAAGGCG 59.716 57.895 0.00 0.00 0.00 5.52
2998 3511 1.898574 ACAGCAAAGACCAAGGCGG 60.899 57.895 0.00 0.00 42.50 6.13
2999 3512 2.985847 AGCAAAGACCAAGGCGGC 60.986 61.111 0.00 0.00 39.03 6.53
3238 3786 7.502696 GGTGGTGGTGATTAGTGTTACATATA 58.497 38.462 0.00 0.00 0.00 0.86
3508 4084 4.325472 CGTTCGGGTTGAATACAAGTAGAC 59.675 45.833 0.00 0.00 39.21 2.59
3744 4496 0.166814 GATCGGTTTGCTGTGCTGAC 59.833 55.000 0.00 0.00 0.00 3.51
3779 4548 6.347110 GCGTGTTTTCTTGATTTGTTCATTC 58.653 36.000 0.00 0.00 33.34 2.67
4101 4879 7.875041 AGAGAATATGTATGTATGACAAGCACC 59.125 37.037 0.00 0.00 0.00 5.01
4102 4880 7.739825 AGAATATGTATGTATGACAAGCACCT 58.260 34.615 0.00 0.00 0.00 4.00
4103 4881 8.213679 AGAATATGTATGTATGACAAGCACCTT 58.786 33.333 0.00 0.00 0.00 3.50
4104 4882 7.969536 ATATGTATGTATGACAAGCACCTTC 57.030 36.000 0.00 0.00 0.00 3.46
4105 4883 5.159273 TGTATGTATGACAAGCACCTTCA 57.841 39.130 0.00 0.00 0.00 3.02
4106 4884 4.935205 TGTATGTATGACAAGCACCTTCAC 59.065 41.667 0.00 0.00 0.00 3.18
4107 4885 3.483808 TGTATGACAAGCACCTTCACA 57.516 42.857 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.359850 TTGGACCCACGCATCAGC 60.360 61.111 0.00 0.00 37.42 4.26
30 31 2.040544 CACCTTGGACCCACGCATC 61.041 63.158 0.00 0.00 0.00 3.91
38 39 4.717313 GACCGCCCACCTTGGACC 62.717 72.222 0.00 0.00 40.96 4.46
42 43 2.233605 TATGACGACCGCCCACCTTG 62.234 60.000 0.00 0.00 0.00 3.61
43 44 1.546589 TTATGACGACCGCCCACCTT 61.547 55.000 0.00 0.00 0.00 3.50
44 45 1.546589 TTTATGACGACCGCCCACCT 61.547 55.000 0.00 0.00 0.00 4.00
45 46 0.463116 ATTTATGACGACCGCCCACC 60.463 55.000 0.00 0.00 0.00 4.61
46 47 2.228138 TATTTATGACGACCGCCCAC 57.772 50.000 0.00 0.00 0.00 4.61
47 48 2.983907 TTATTTATGACGACCGCCCA 57.016 45.000 0.00 0.00 0.00 5.36
48 49 3.135994 ACATTATTTATGACGACCGCCC 58.864 45.455 0.00 0.00 37.69 6.13
49 50 4.271533 TCAACATTATTTATGACGACCGCC 59.728 41.667 0.00 0.00 37.69 6.13
50 51 5.195379 GTCAACATTATTTATGACGACCGC 58.805 41.667 0.00 0.00 37.69 5.68
51 52 5.734311 GGTCAACATTATTTATGACGACCG 58.266 41.667 10.32 0.00 42.98 4.79
52 53 5.292589 ACGGTCAACATTATTTATGACGACC 59.707 40.000 13.46 13.46 45.44 4.79
53 54 6.035220 TCACGGTCAACATTATTTATGACGAC 59.965 38.462 0.00 0.00 42.35 4.34
54 55 6.100668 TCACGGTCAACATTATTTATGACGA 58.899 36.000 0.00 0.00 42.35 4.20
57 58 9.607988 AACTATCACGGTCAACATTATTTATGA 57.392 29.630 0.00 0.00 37.69 2.15
58 59 9.650371 CAACTATCACGGTCAACATTATTTATG 57.350 33.333 0.00 0.00 40.26 1.90
59 60 8.836413 CCAACTATCACGGTCAACATTATTTAT 58.164 33.333 0.00 0.00 0.00 1.40
60 61 8.041919 TCCAACTATCACGGTCAACATTATTTA 58.958 33.333 0.00 0.00 0.00 1.40
61 62 6.882140 TCCAACTATCACGGTCAACATTATTT 59.118 34.615 0.00 0.00 0.00 1.40
62 63 6.315393 GTCCAACTATCACGGTCAACATTATT 59.685 38.462 0.00 0.00 0.00 1.40
63 64 5.815740 GTCCAACTATCACGGTCAACATTAT 59.184 40.000 0.00 0.00 0.00 1.28
64 65 5.172934 GTCCAACTATCACGGTCAACATTA 58.827 41.667 0.00 0.00 0.00 1.90
65 66 4.000988 GTCCAACTATCACGGTCAACATT 58.999 43.478 0.00 0.00 0.00 2.71
66 67 3.007506 TGTCCAACTATCACGGTCAACAT 59.992 43.478 0.00 0.00 0.00 2.71
68 69 2.993899 CTGTCCAACTATCACGGTCAAC 59.006 50.000 0.00 0.00 0.00 3.18
70 71 1.067142 GCTGTCCAACTATCACGGTCA 60.067 52.381 0.00 0.00 0.00 4.02
71 72 1.641577 GCTGTCCAACTATCACGGTC 58.358 55.000 0.00 0.00 0.00 4.79
72 73 0.249398 GGCTGTCCAACTATCACGGT 59.751 55.000 0.00 0.00 0.00 4.83
75 76 1.090052 GGCGGCTGTCCAACTATCAC 61.090 60.000 0.00 0.00 0.00 3.06
76 77 1.220749 GGCGGCTGTCCAACTATCA 59.779 57.895 0.00 0.00 0.00 2.15
77 78 0.811616 CTGGCGGCTGTCCAACTATC 60.812 60.000 11.43 0.00 32.41 2.08
78 79 1.221840 CTGGCGGCTGTCCAACTAT 59.778 57.895 11.43 0.00 32.41 2.12
79 80 2.662596 CTGGCGGCTGTCCAACTA 59.337 61.111 11.43 0.00 32.41 2.24
80 81 4.335647 CCTGGCGGCTGTCCAACT 62.336 66.667 11.43 0.00 32.41 3.16
82 83 4.641645 CACCTGGCGGCTGTCCAA 62.642 66.667 11.43 0.00 32.41 3.53
132 133 4.842091 ATACGTCGGCGCGGACAC 62.842 66.667 36.77 19.59 42.83 3.67
133 134 4.118995 AATACGTCGGCGCGGACA 62.119 61.111 36.77 24.43 42.83 4.02
135 136 4.557605 GGAATACGTCGGCGCGGA 62.558 66.667 22.98 14.27 42.83 5.54
138 139 2.960129 CCTGGAATACGTCGGCGC 60.960 66.667 10.50 0.00 42.83 6.53
139 140 2.960129 GCCTGGAATACGTCGGCG 60.960 66.667 8.42 8.42 44.93 6.46
140 141 2.960129 CGCCTGGAATACGTCGGC 60.960 66.667 0.00 0.00 37.40 5.54
141 142 2.960129 GCGCCTGGAATACGTCGG 60.960 66.667 0.00 0.00 0.00 4.79
142 143 1.151777 ATTGCGCCTGGAATACGTCG 61.152 55.000 4.18 0.00 33.99 5.12
143 144 1.014352 AATTGCGCCTGGAATACGTC 58.986 50.000 4.18 0.00 34.76 4.34
146 147 3.796717 GCTTAAAATTGCGCCTGGAATAC 59.203 43.478 4.18 0.00 34.76 1.89
147 148 3.181480 GGCTTAAAATTGCGCCTGGAATA 60.181 43.478 4.18 0.00 39.42 1.75
148 149 2.418609 GGCTTAAAATTGCGCCTGGAAT 60.419 45.455 4.18 0.00 39.42 3.01
149 150 1.067213 GGCTTAAAATTGCGCCTGGAA 60.067 47.619 4.18 0.00 39.42 3.53
151 152 0.801836 CGGCTTAAAATTGCGCCTGG 60.802 55.000 4.18 0.00 40.34 4.45
152 153 0.801836 CCGGCTTAAAATTGCGCCTG 60.802 55.000 4.18 0.00 40.34 4.85
153 154 0.963355 TCCGGCTTAAAATTGCGCCT 60.963 50.000 4.18 0.00 40.34 5.52
154 155 0.109039 TTCCGGCTTAAAATTGCGCC 60.109 50.000 4.18 0.00 39.14 6.53
155 156 1.704070 TTTCCGGCTTAAAATTGCGC 58.296 45.000 0.00 0.00 0.00 6.09
156 157 2.602660 CCATTTCCGGCTTAAAATTGCG 59.397 45.455 0.00 0.00 0.00 4.85
157 158 3.855858 TCCATTTCCGGCTTAAAATTGC 58.144 40.909 0.00 0.00 0.00 3.56
158 159 4.739716 CGATCCATTTCCGGCTTAAAATTG 59.260 41.667 0.00 0.00 0.00 2.32
160 161 3.317993 CCGATCCATTTCCGGCTTAAAAT 59.682 43.478 0.00 0.00 36.62 1.82
161 162 2.685897 CCGATCCATTTCCGGCTTAAAA 59.314 45.455 0.00 0.00 36.62 1.52
162 163 2.294074 CCGATCCATTTCCGGCTTAAA 58.706 47.619 0.00 0.00 36.62 1.52
163 164 1.961793 CCGATCCATTTCCGGCTTAA 58.038 50.000 0.00 0.00 36.62 1.85
169 170 4.000557 CGCGCCGATCCATTTCCG 62.001 66.667 0.00 0.00 0.00 4.30
171 172 2.587753 TCCGCGCCGATCCATTTC 60.588 61.111 0.00 0.00 0.00 2.17
172 173 2.895372 GTCCGCGCCGATCCATTT 60.895 61.111 0.00 0.00 0.00 2.32
173 174 4.155733 TGTCCGCGCCGATCCATT 62.156 61.111 0.00 0.00 0.00 3.16
184 185 4.034258 TGTCCGTCTCGTGTCCGC 62.034 66.667 0.00 0.00 0.00 5.54
185 186 2.126965 GTGTCCGTCTCGTGTCCG 60.127 66.667 0.00 0.00 0.00 4.79
186 187 1.919956 ATCGTGTCCGTCTCGTGTCC 61.920 60.000 0.00 0.00 35.06 4.02
187 188 0.109873 AATCGTGTCCGTCTCGTGTC 60.110 55.000 0.00 0.00 35.06 3.67
189 190 0.708370 CAAATCGTGTCCGTCTCGTG 59.292 55.000 0.00 0.00 35.06 4.35
190 191 0.594602 TCAAATCGTGTCCGTCTCGT 59.405 50.000 0.00 0.00 35.06 4.18
191 192 1.260206 CTCAAATCGTGTCCGTCTCG 58.740 55.000 0.00 0.00 35.01 4.04
192 193 2.349297 ACTCAAATCGTGTCCGTCTC 57.651 50.000 0.00 0.00 35.01 3.36
194 195 2.096417 CCAAACTCAAATCGTGTCCGTC 60.096 50.000 0.00 0.00 35.01 4.79
195 196 1.871039 CCAAACTCAAATCGTGTCCGT 59.129 47.619 0.00 0.00 35.01 4.69
196 197 1.196808 CCCAAACTCAAATCGTGTCCG 59.803 52.381 0.00 0.00 0.00 4.79
197 198 2.227194 ACCCAAACTCAAATCGTGTCC 58.773 47.619 0.00 0.00 0.00 4.02
198 199 3.550030 CCAACCCAAACTCAAATCGTGTC 60.550 47.826 0.00 0.00 0.00 3.67
202 203 1.665735 CGCCAACCCAAACTCAAATCG 60.666 52.381 0.00 0.00 0.00 3.34
203 204 1.339929 ACGCCAACCCAAACTCAAATC 59.660 47.619 0.00 0.00 0.00 2.17
204 205 1.068434 CACGCCAACCCAAACTCAAAT 59.932 47.619 0.00 0.00 0.00 2.32
205 206 0.457851 CACGCCAACCCAAACTCAAA 59.542 50.000 0.00 0.00 0.00 2.69
207 208 0.681564 AACACGCCAACCCAAACTCA 60.682 50.000 0.00 0.00 0.00 3.41
208 209 0.248866 CAACACGCCAACCCAAACTC 60.249 55.000 0.00 0.00 0.00 3.01
210 211 1.227118 CCAACACGCCAACCCAAAC 60.227 57.895 0.00 0.00 0.00 2.93
211 212 2.427245 CCCAACACGCCAACCCAAA 61.427 57.895 0.00 0.00 0.00 3.28
220 221 1.734388 AAAGTGAAGGCCCAACACGC 61.734 55.000 15.47 4.00 39.19 5.34
221 222 0.744281 AAAAGTGAAGGCCCAACACG 59.256 50.000 15.47 0.00 39.19 4.49
222 223 1.480545 ACAAAAGTGAAGGCCCAACAC 59.519 47.619 14.18 14.18 35.15 3.32
223 224 1.754226 GACAAAAGTGAAGGCCCAACA 59.246 47.619 0.00 0.00 0.00 3.33
224 225 1.068588 GGACAAAAGTGAAGGCCCAAC 59.931 52.381 0.00 0.00 0.00 3.77
226 227 0.821711 CGGACAAAAGTGAAGGCCCA 60.822 55.000 0.00 0.00 0.00 5.36
227 228 1.956802 CGGACAAAAGTGAAGGCCC 59.043 57.895 0.00 0.00 0.00 5.80
229 230 1.082104 CGCGGACAAAAGTGAAGGC 60.082 57.895 0.00 0.00 0.00 4.35
230 231 0.234884 GACGCGGACAAAAGTGAAGG 59.765 55.000 12.47 0.00 0.00 3.46
231 232 0.111266 CGACGCGGACAAAAGTGAAG 60.111 55.000 12.47 0.00 0.00 3.02
232 233 0.528033 TCGACGCGGACAAAAGTGAA 60.528 50.000 12.47 0.00 0.00 3.18
233 234 0.319211 ATCGACGCGGACAAAAGTGA 60.319 50.000 12.47 0.00 0.00 3.41
234 235 0.093026 GATCGACGCGGACAAAAGTG 59.907 55.000 12.47 0.00 0.00 3.16
236 237 1.011968 TGGATCGACGCGGACAAAAG 61.012 55.000 12.47 0.00 0.00 2.27
237 238 0.600518 TTGGATCGACGCGGACAAAA 60.601 50.000 12.47 0.00 0.00 2.44
239 240 1.005984 TTTGGATCGACGCGGACAA 60.006 52.632 12.47 3.13 0.00 3.18
241 242 1.683790 CTGTTTGGATCGACGCGGAC 61.684 60.000 12.47 2.84 0.00 4.79
244 245 0.787787 TTTCTGTTTGGATCGACGCG 59.212 50.000 3.53 3.53 0.00 6.01
247 248 3.660904 CGTTCGTTTCTGTTTGGATCGAC 60.661 47.826 0.00 0.00 0.00 4.20
248 249 2.473609 CGTTCGTTTCTGTTTGGATCGA 59.526 45.455 0.00 0.00 0.00 3.59
249 250 2.411031 CCGTTCGTTTCTGTTTGGATCG 60.411 50.000 0.00 0.00 0.00 3.69
251 252 2.841215 TCCGTTCGTTTCTGTTTGGAT 58.159 42.857 0.00 0.00 0.00 3.41
252 253 2.312722 TCCGTTCGTTTCTGTTTGGA 57.687 45.000 0.00 0.00 0.00 3.53
253 254 2.350388 CCATCCGTTCGTTTCTGTTTGG 60.350 50.000 0.00 0.00 0.00 3.28
254 255 2.546368 TCCATCCGTTCGTTTCTGTTTG 59.454 45.455 0.00 0.00 0.00 2.93
255 256 2.841215 TCCATCCGTTCGTTTCTGTTT 58.159 42.857 0.00 0.00 0.00 2.83
256 257 2.536761 TCCATCCGTTCGTTTCTGTT 57.463 45.000 0.00 0.00 0.00 3.16
257 258 2.536761 TTCCATCCGTTCGTTTCTGT 57.463 45.000 0.00 0.00 0.00 3.41
258 259 2.095853 CCATTCCATCCGTTCGTTTCTG 59.904 50.000 0.00 0.00 0.00 3.02
259 260 2.356135 CCATTCCATCCGTTCGTTTCT 58.644 47.619 0.00 0.00 0.00 2.52
260 261 1.400494 CCCATTCCATCCGTTCGTTTC 59.600 52.381 0.00 0.00 0.00 2.78
261 262 1.271707 ACCCATTCCATCCGTTCGTTT 60.272 47.619 0.00 0.00 0.00 3.60
262 263 0.326927 ACCCATTCCATCCGTTCGTT 59.673 50.000 0.00 0.00 0.00 3.85
263 264 0.107848 GACCCATTCCATCCGTTCGT 60.108 55.000 0.00 0.00 0.00 3.85
265 266 0.107848 ACGACCCATTCCATCCGTTC 60.108 55.000 0.00 0.00 0.00 3.95
266 267 0.107848 GACGACCCATTCCATCCGTT 60.108 55.000 0.00 0.00 0.00 4.44
267 268 1.520666 GACGACCCATTCCATCCGT 59.479 57.895 0.00 0.00 0.00 4.69
268 269 1.227556 GGACGACCCATTCCATCCG 60.228 63.158 0.00 0.00 34.14 4.18
279 280 2.418976 GAGCAACTTTAATGGGACGACC 59.581 50.000 0.00 0.00 40.81 4.79
280 281 3.335579 AGAGCAACTTTAATGGGACGAC 58.664 45.455 0.00 0.00 0.00 4.34
281 282 3.695830 AGAGCAACTTTAATGGGACGA 57.304 42.857 0.00 0.00 0.00 4.20
282 283 4.935808 AGTTAGAGCAACTTTAATGGGACG 59.064 41.667 0.00 0.00 45.54 4.79
294 295 6.127403 CAGTGTTCGTAAAAGTTAGAGCAAC 58.873 40.000 0.00 0.00 37.41 4.17
295 296 5.277154 GCAGTGTTCGTAAAAGTTAGAGCAA 60.277 40.000 0.00 0.00 0.00 3.91
296 297 4.210537 GCAGTGTTCGTAAAAGTTAGAGCA 59.789 41.667 0.00 0.00 0.00 4.26
297 298 4.210537 TGCAGTGTTCGTAAAAGTTAGAGC 59.789 41.667 0.00 0.00 0.00 4.09
300 301 5.652744 AGTGCAGTGTTCGTAAAAGTTAG 57.347 39.130 0.00 0.00 0.00 2.34
301 302 7.536895 TTAAGTGCAGTGTTCGTAAAAGTTA 57.463 32.000 0.00 0.00 0.00 2.24
302 303 4.957759 AAGTGCAGTGTTCGTAAAAGTT 57.042 36.364 0.00 0.00 0.00 2.66
303 304 6.425577 TTTAAGTGCAGTGTTCGTAAAAGT 57.574 33.333 0.00 0.00 0.00 2.66
304 305 7.908193 ATTTTAAGTGCAGTGTTCGTAAAAG 57.092 32.000 17.19 0.00 32.31 2.27
305 306 8.587950 CAAATTTTAAGTGCAGTGTTCGTAAAA 58.412 29.630 15.78 15.78 32.90 1.52
306 307 7.755822 ACAAATTTTAAGTGCAGTGTTCGTAAA 59.244 29.630 0.00 0.00 0.00 2.01
308 309 6.787225 ACAAATTTTAAGTGCAGTGTTCGTA 58.213 32.000 0.00 0.00 0.00 3.43
309 310 5.646606 ACAAATTTTAAGTGCAGTGTTCGT 58.353 33.333 0.00 0.00 0.00 3.85
310 311 6.567769 AACAAATTTTAAGTGCAGTGTTCG 57.432 33.333 0.00 0.00 0.00 3.95
367 368 1.371558 GACTGACCGGCTTGGACTT 59.628 57.895 0.00 0.00 42.00 3.01
559 567 0.733223 GTTCGCAGAGGACTTCGGAC 60.733 60.000 0.00 0.00 38.43 4.79
704 718 2.100991 GAGGGAAATTGCTGCGCG 59.899 61.111 0.00 0.00 0.00 6.86
743 1118 0.324368 TCCGGGCTAGAGAAGAGCAA 60.324 55.000 0.00 0.00 41.98 3.91
746 1121 1.314730 GTCTCCGGGCTAGAGAAGAG 58.685 60.000 0.00 0.00 41.88 2.85
747 1122 0.624254 TGTCTCCGGGCTAGAGAAGA 59.376 55.000 0.00 0.00 41.88 2.87
748 1123 1.698506 ATGTCTCCGGGCTAGAGAAG 58.301 55.000 0.00 0.00 41.88 2.85
749 1124 3.308035 TTATGTCTCCGGGCTAGAGAA 57.692 47.619 0.00 0.00 41.88 2.87
750 1125 3.308035 TTTATGTCTCCGGGCTAGAGA 57.692 47.619 0.00 0.00 38.05 3.10
936 1320 1.514678 CGCCGATCAGGAGGAGAGAG 61.515 65.000 7.64 0.00 45.00 3.20
996 1391 4.193893 TGGGCCGCATCCATCCAG 62.194 66.667 0.00 0.00 0.00 3.86
1035 1430 2.414481 CTGAATTTGAGGTGCTCGTCTG 59.586 50.000 9.59 0.00 32.35 3.51
1037 1432 1.734465 CCTGAATTTGAGGTGCTCGTC 59.266 52.381 1.63 1.63 32.35 4.20
1039 1434 1.813513 ACCTGAATTTGAGGTGCTCG 58.186 50.000 6.76 0.00 42.56 5.03
1053 1456 4.142622 CGTACCGATGTTGTAGTAACCTGA 60.143 45.833 0.00 0.00 0.00 3.86
1092 1495 0.873054 CGGGAGATCTTGCATGCATC 59.127 55.000 23.37 16.45 0.00 3.91
1183 1586 3.081804 AGATCAAGGGCACGGTAAAAAG 58.918 45.455 0.00 0.00 0.00 2.27
1187 1591 1.626321 TGAAGATCAAGGGCACGGTAA 59.374 47.619 0.00 0.00 0.00 2.85
1388 1792 2.325393 ATTAAAGGCCCCGAGCTCCG 62.325 60.000 8.47 0.80 43.05 4.63
1389 1793 0.106669 AATTAAAGGCCCCGAGCTCC 60.107 55.000 8.47 0.00 43.05 4.70
1390 1794 1.134068 AGAATTAAAGGCCCCGAGCTC 60.134 52.381 2.73 2.73 43.05 4.09
1391 1795 0.919710 AGAATTAAAGGCCCCGAGCT 59.080 50.000 0.00 0.00 43.05 4.09
1392 1796 1.309950 GAGAATTAAAGGCCCCGAGC 58.690 55.000 0.00 0.00 42.60 5.03
1393 1797 1.477014 GGGAGAATTAAAGGCCCCGAG 60.477 57.143 0.00 0.00 32.50 4.63
1394 1798 0.549469 GGGAGAATTAAAGGCCCCGA 59.451 55.000 0.00 0.00 32.50 5.14
1417 1821 2.596904 TCGAGGATTAAAAGCGGAGG 57.403 50.000 0.00 0.00 0.00 4.30
1493 1921 9.736414 AGAGATGAAAAGATGAAAAGAATGAGA 57.264 29.630 0.00 0.00 0.00 3.27
1598 2026 1.375652 CAGTACTGCTGCTGCTGCT 60.376 57.895 27.67 14.24 41.07 4.24
1599 2027 3.175724 CAGTACTGCTGCTGCTGC 58.824 61.111 22.51 22.51 41.07 5.25
1704 2132 6.409234 GGGGAAAAGGAGAATGAAAAAGGTTT 60.409 38.462 0.00 0.00 0.00 3.27
1806 2235 4.322349 GGTATGACATGACTATGAGAGCCC 60.322 50.000 0.00 0.00 37.73 5.19
1898 2327 2.685106 TATCACAAAGGCAAACCCCA 57.315 45.000 0.00 0.00 36.11 4.96
1899 2328 3.365472 AGATATCACAAAGGCAAACCCC 58.635 45.455 5.32 0.00 36.11 4.95
1902 2331 9.109393 TCATTAGTAGATATCACAAAGGCAAAC 57.891 33.333 5.32 0.00 0.00 2.93
1907 2336 7.386299 GCACCTCATTAGTAGATATCACAAAGG 59.614 40.741 5.32 3.51 0.00 3.11
2171 2600 2.401766 GCACCTCGGGCAGTTGATG 61.402 63.158 0.00 0.00 0.00 3.07
2339 2768 2.697761 CGACACCACCGAGGACGAT 61.698 63.158 0.00 0.00 42.66 3.73
2422 2851 3.062466 GCTTCGGGTTCTTGGCCC 61.062 66.667 0.00 0.00 42.68 5.80
2744 3209 1.211969 CTGCTGCTGTTGATGGTGC 59.788 57.895 0.00 0.00 0.00 5.01
2751 3216 2.255554 CTGCTGCTGCTGCTGTTG 59.744 61.111 27.67 13.98 39.81 3.33
2813 3278 2.047179 GTGTCCAGCGAGAACCCC 60.047 66.667 0.00 0.00 0.00 4.95
3238 3786 3.744660 ACCAAAAGAGAGATCAAACGCT 58.255 40.909 0.00 0.00 0.00 5.07
3380 3956 6.232581 ACGAGAGATTCAATTGGAGAAGAT 57.767 37.500 5.42 0.00 0.00 2.40
3744 4496 2.000447 GAAAACACGCCTGCTACTAGG 59.000 52.381 0.00 0.00 40.95 3.02
3779 4548 5.759763 TGGATTAATCAGGAATCACGATGTG 59.240 40.000 17.07 0.00 35.40 3.21


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

AutoCloner maintained by Alex Coulton.