Multiple sequence alignment - TraesCS5D01G211400

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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 TraesCS5D01G211400 chr5D 100.000 2704 0 0 1 2704 319735119 319732416 0.000000e+00 4994
1 TraesCS5D01G211400 chr5D 93.158 190 11 2 175 364 438062136 438062323 7.370000e-71 278
2 TraesCS5D01G211400 chr5D 92.982 171 11 1 9 178 355673756 355673586 5.780000e-62 248
3 TraesCS5D01G211400 chr5B 95.211 2318 100 10 376 2688 370451806 370449495 0.000000e+00 3655
4 TraesCS5D01G211400 chr5A 95.140 1893 73 14 353 2227 414299698 414297807 0.000000e+00 2968
5 TraesCS5D01G211400 chr5A 91.614 477 30 6 2231 2699 414297733 414297259 0.000000e+00 651
6 TraesCS5D01G211400 chr4B 94.571 571 22 4 1702 2272 351298224 351298785 0.000000e+00 874
7 TraesCS5D01G211400 chr4B 93.892 573 28 5 1705 2277 257299752 257299187 0.000000e+00 857
8 TraesCS5D01G211400 chr4B 91.456 316 22 1 1962 2277 257273080 257272770 1.920000e-116 429
9 TraesCS5D01G211400 chr2B 93.651 567 27 5 1705 2271 574921234 574920677 0.000000e+00 839
10 TraesCS5D01G211400 chr2D 94.272 419 3 7 1201 1619 321172353 321171956 2.960000e-174 621
11 TraesCS5D01G211400 chr2D 91.667 192 13 3 175 365 380692236 380692425 2.060000e-66 263
12 TraesCS5D01G211400 chr2D 92.982 171 11 1 9 178 34361889 34361719 5.780000e-62 248
13 TraesCS5D01G211400 chr2D 92.982 171 11 1 9 178 620188282 620188112 5.780000e-62 248
14 TraesCS5D01G211400 chr2D 90.217 184 15 3 9 190 472144718 472144536 1.250000e-58 237
15 TraesCS5D01G211400 chr7D 94.681 188 8 2 175 362 477407708 477407893 9.470000e-75 291
16 TraesCS5D01G211400 chr7D 93.229 192 12 1 175 366 152355835 152356025 5.700000e-72 281
17 TraesCS5D01G211400 chr7D 89.604 202 16 4 175 376 35545716 35545520 4.470000e-63 252
18 TraesCS5D01G211400 chr6D 91.710 193 14 2 175 367 331252202 331252392 1.600000e-67 267
19 TraesCS5D01G211400 chr7A 91.099 191 14 3 175 365 109077802 109077989 3.450000e-64 255
20 TraesCS5D01G211400 chr1D 91.444 187 14 2 175 361 479208466 479208650 3.450000e-64 255
21 TraesCS5D01G211400 chr1D 92.982 171 11 1 9 178 352189112 352188942 5.780000e-62 248
22 TraesCS5D01G211400 chr4A 90.155 193 17 2 175 366 599346898 599347089 1.610000e-62 250
23 TraesCS5D01G211400 chr7B 92.982 171 11 1 9 178 446648465 446648295 5.780000e-62 248
24 TraesCS5D01G211400 chr4D 92.398 171 12 1 9 178 508493433 508493263 2.690000e-60 243
25 TraesCS5D01G211400 chr1A 92.398 171 12 1 9 178 557121204 557121034 2.690000e-60 243
26 TraesCS5D01G211400 chr1A 92.398 171 12 1 9 178 585992773 585992943 2.690000e-60 243


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 TraesCS5D01G211400 chr5D 319732416 319735119 2703 True 4994.0 4994 100.000 1 2704 1 chr5D.!!$R1 2703
1 TraesCS5D01G211400 chr5B 370449495 370451806 2311 True 3655.0 3655 95.211 376 2688 1 chr5B.!!$R1 2312
2 TraesCS5D01G211400 chr5A 414297259 414299698 2439 True 1809.5 2968 93.377 353 2699 2 chr5A.!!$R1 2346
3 TraesCS5D01G211400 chr4B 351298224 351298785 561 False 874.0 874 94.571 1702 2272 1 chr4B.!!$F1 570
4 TraesCS5D01G211400 chr4B 257299187 257299752 565 True 857.0 857 93.892 1705 2277 1 chr4B.!!$R2 572
5 TraesCS5D01G211400 chr2B 574920677 574921234 557 True 839.0 839 93.651 1705 2271 1 chr2B.!!$R1 566

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
175 176 0.03601 AGGTCGCCTCATTGGAGTTG 60.036 55.0 0.0 0.0 39.64 3.16 F
235 236 0.45339 GGGCTCCGCAGATTTTCTTG 59.547 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1247 0.665670 CGATGTAGCTGGAGATGGCG 60.666 60.000 0.0 0.0 0.0 5.69 R
1984 1997 2.289547 GCGACCAAGTACACAACAACAT 59.710 45.455 0.0 0.0 0.0 2.71 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 4.520846 CGCCGACGCAAATCAGGC 62.521 66.667 0.00 0.00 44.00 4.85
36 37 3.127533 GCCGACGCAAATCAGGCT 61.128 61.111 0.00 0.00 44.06 4.58
37 38 1.813753 GCCGACGCAAATCAGGCTA 60.814 57.895 0.00 0.00 44.06 3.93
38 39 1.366111 GCCGACGCAAATCAGGCTAA 61.366 55.000 0.00 0.00 44.06 3.09
39 40 1.083489 CCGACGCAAATCAGGCTAAA 58.917 50.000 0.00 0.00 0.00 1.85
40 41 1.466950 CCGACGCAAATCAGGCTAAAA 59.533 47.619 0.00 0.00 0.00 1.52
41 42 2.095466 CCGACGCAAATCAGGCTAAAAA 60.095 45.455 0.00 0.00 0.00 1.94
57 58 0.617935 AAAAATGGGCCGGAAATGGG 59.382 50.000 5.05 0.00 0.00 4.00
58 59 0.546507 AAAATGGGCCGGAAATGGGT 60.547 50.000 5.05 0.00 0.00 4.51
59 60 0.975556 AAATGGGCCGGAAATGGGTC 60.976 55.000 5.05 0.00 0.00 4.46
60 61 3.714487 ATGGGCCGGAAATGGGTCG 62.714 63.158 5.05 0.00 0.00 4.79
61 62 4.419921 GGGCCGGAAATGGGTCGT 62.420 66.667 5.05 0.00 0.00 4.34
62 63 2.360726 GGCCGGAAATGGGTCGTT 60.361 61.111 5.05 0.00 0.00 3.85
63 64 2.404186 GGCCGGAAATGGGTCGTTC 61.404 63.158 5.05 0.00 0.00 3.95
64 65 2.746803 GCCGGAAATGGGTCGTTCG 61.747 63.158 5.05 0.00 0.00 3.95
65 66 2.746803 CCGGAAATGGGTCGTTCGC 61.747 63.158 0.00 0.00 0.00 4.70
66 67 2.782615 GGAAATGGGTCGTTCGCG 59.217 61.111 0.00 0.00 42.98 5.87
67 68 2.746803 GGAAATGGGTCGTTCGCGG 61.747 63.158 6.13 0.00 41.70 6.46
68 69 1.738830 GAAATGGGTCGTTCGCGGA 60.739 57.895 6.13 0.00 41.70 5.54
69 70 1.078708 AAATGGGTCGTTCGCGGAT 60.079 52.632 6.13 0.00 41.70 4.18
70 71 1.366111 AAATGGGTCGTTCGCGGATG 61.366 55.000 6.13 2.03 41.70 3.51
71 72 2.233605 AATGGGTCGTTCGCGGATGA 62.234 55.000 4.85 4.85 41.70 2.92
72 73 2.125832 GGGTCGTTCGCGGATGAA 60.126 61.111 11.76 0.00 41.70 2.57
73 74 1.738830 GGGTCGTTCGCGGATGAAA 60.739 57.895 11.76 0.00 41.70 2.69
74 75 1.293267 GGGTCGTTCGCGGATGAAAA 61.293 55.000 11.76 0.00 41.70 2.29
75 76 0.513820 GGTCGTTCGCGGATGAAAAA 59.486 50.000 11.76 0.00 41.70 1.94
76 77 1.587991 GTCGTTCGCGGATGAAAAAC 58.412 50.000 11.76 2.47 41.70 2.43
77 78 0.162082 TCGTTCGCGGATGAAAAACG 59.838 50.000 17.53 17.53 42.87 3.60
78 79 0.787908 CGTTCGCGGATGAAAAACGG 60.788 55.000 16.30 1.94 39.10 4.44
79 80 0.513820 GTTCGCGGATGAAAAACGGA 59.486 50.000 6.13 0.00 0.00 4.69
80 81 0.513820 TTCGCGGATGAAAAACGGAC 59.486 50.000 6.13 0.00 0.00 4.79
81 82 1.225637 CGCGGATGAAAAACGGACG 60.226 57.895 0.00 0.00 0.00 4.79
82 83 1.511254 GCGGATGAAAAACGGACGC 60.511 57.895 0.00 0.00 38.70 5.19
83 84 1.225637 CGGATGAAAAACGGACGCG 60.226 57.895 3.53 3.53 0.00 6.01
84 85 1.511254 GGATGAAAAACGGACGCGC 60.511 57.895 5.73 0.00 0.00 6.86
85 86 1.857426 GATGAAAAACGGACGCGCG 60.857 57.895 30.96 30.96 0.00 6.86
86 87 2.488852 GATGAAAAACGGACGCGCGT 62.489 55.000 38.52 38.52 0.00 6.01
87 88 2.488852 ATGAAAAACGGACGCGCGTC 62.489 55.000 45.60 45.60 43.87 5.19
106 107 4.676586 GTTTGGGTCGGCGCGTTG 62.677 66.667 8.43 0.00 0.00 4.10
119 120 2.046700 CGTTGGGCCGCCTTTCTA 60.047 61.111 9.86 0.00 0.00 2.10
120 121 1.451387 CGTTGGGCCGCCTTTCTAT 60.451 57.895 9.86 0.00 0.00 1.98
121 122 1.436983 CGTTGGGCCGCCTTTCTATC 61.437 60.000 9.86 0.00 0.00 2.08
122 123 0.107165 GTTGGGCCGCCTTTCTATCT 60.107 55.000 9.86 0.00 0.00 1.98
123 124 0.107214 TTGGGCCGCCTTTCTATCTG 60.107 55.000 9.86 0.00 0.00 2.90
124 125 1.894282 GGGCCGCCTTTCTATCTGC 60.894 63.158 9.86 0.00 0.00 4.26
125 126 2.247437 GGCCGCCTTTCTATCTGCG 61.247 63.158 0.71 0.00 46.14 5.18
126 127 2.886782 GCCGCCTTTCTATCTGCGC 61.887 63.158 0.00 0.00 45.28 6.09
127 128 1.521457 CCGCCTTTCTATCTGCGCA 60.521 57.895 10.98 10.98 45.28 6.09
128 129 1.493950 CCGCCTTTCTATCTGCGCAG 61.494 60.000 31.53 31.53 45.28 5.18
129 130 0.528466 CGCCTTTCTATCTGCGCAGA 60.528 55.000 39.63 39.63 40.58 4.26
130 131 0.933796 GCCTTTCTATCTGCGCAGAC 59.066 55.000 40.34 21.96 40.75 3.51
131 132 1.576356 CCTTTCTATCTGCGCAGACC 58.424 55.000 40.34 0.00 40.75 3.85
132 133 1.576356 CTTTCTATCTGCGCAGACCC 58.424 55.000 40.34 0.00 40.75 4.46
133 134 0.901827 TTTCTATCTGCGCAGACCCA 59.098 50.000 40.34 26.26 40.75 4.51
134 135 0.901827 TTCTATCTGCGCAGACCCAA 59.098 50.000 40.34 27.75 40.75 4.12
135 136 0.901827 TCTATCTGCGCAGACCCAAA 59.098 50.000 40.34 21.54 40.75 3.28
136 137 1.009829 CTATCTGCGCAGACCCAAAC 58.990 55.000 40.34 0.00 40.75 2.93
137 138 0.739462 TATCTGCGCAGACCCAAACG 60.739 55.000 40.34 11.94 40.75 3.60
138 139 2.449031 ATCTGCGCAGACCCAAACGA 62.449 55.000 40.34 17.34 40.75 3.85
139 140 2.203084 TGCGCAGACCCAAACGAA 60.203 55.556 5.66 0.00 0.00 3.85
140 141 2.251371 GCGCAGACCCAAACGAAC 59.749 61.111 0.30 0.00 0.00 3.95
141 142 2.549282 CGCAGACCCAAACGAACG 59.451 61.111 0.00 0.00 0.00 3.95
142 143 2.943653 GCAGACCCAAACGAACGG 59.056 61.111 0.00 0.00 0.00 4.44
143 144 2.943653 CAGACCCAAACGAACGGC 59.056 61.111 0.00 0.00 0.00 5.68
144 145 2.281276 AGACCCAAACGAACGGCC 60.281 61.111 0.00 0.00 0.00 6.13
145 146 3.719144 GACCCAAACGAACGGCCG 61.719 66.667 26.86 26.86 0.00 6.13
158 159 2.965462 GGCCGCGGACGAAATAGG 60.965 66.667 33.48 0.00 43.93 2.57
159 160 2.202837 GCCGCGGACGAAATAGGT 60.203 61.111 33.48 0.00 43.93 3.08
160 161 2.235699 GCCGCGGACGAAATAGGTC 61.236 63.158 33.48 1.41 43.93 3.85
161 162 1.942712 CCGCGGACGAAATAGGTCG 60.943 63.158 24.07 0.00 46.54 4.79
162 163 2.574222 CGCGGACGAAATAGGTCGC 61.574 63.158 0.00 0.00 45.00 5.19
163 164 2.235699 GCGGACGAAATAGGTCGCC 61.236 63.158 0.00 0.00 45.00 5.54
164 165 1.436336 CGGACGAAATAGGTCGCCT 59.564 57.895 3.87 3.87 45.00 5.52
165 166 0.594284 CGGACGAAATAGGTCGCCTC 60.594 60.000 1.46 0.00 45.00 4.70
166 167 0.458669 GGACGAAATAGGTCGCCTCA 59.541 55.000 1.46 0.00 45.00 3.86
167 168 1.068741 GGACGAAATAGGTCGCCTCAT 59.931 52.381 1.46 0.00 45.00 2.90
168 169 2.483188 GGACGAAATAGGTCGCCTCATT 60.483 50.000 1.46 0.00 45.00 2.57
169 170 2.540101 GACGAAATAGGTCGCCTCATTG 59.460 50.000 1.46 0.00 45.00 2.82
170 171 1.867233 CGAAATAGGTCGCCTCATTGG 59.133 52.381 1.46 0.00 34.61 3.16
171 172 2.483013 CGAAATAGGTCGCCTCATTGGA 60.483 50.000 1.46 0.00 37.63 3.53
172 173 2.918712 AATAGGTCGCCTCATTGGAG 57.081 50.000 1.46 0.00 41.02 3.86
173 174 1.794714 ATAGGTCGCCTCATTGGAGT 58.205 50.000 1.46 0.00 39.64 3.85
174 175 1.568504 TAGGTCGCCTCATTGGAGTT 58.431 50.000 1.46 0.00 39.64 3.01
175 176 0.036010 AGGTCGCCTCATTGGAGTTG 60.036 55.000 0.00 0.00 39.64 3.16
176 177 1.648467 GGTCGCCTCATTGGAGTTGC 61.648 60.000 0.00 0.00 39.64 4.17
177 178 0.674895 GTCGCCTCATTGGAGTTGCT 60.675 55.000 0.00 0.00 39.64 3.91
178 179 0.901827 TCGCCTCATTGGAGTTGCTA 59.098 50.000 0.00 0.00 39.64 3.49
179 180 1.009829 CGCCTCATTGGAGTTGCTAC 58.990 55.000 0.00 0.00 39.64 3.58
180 181 1.675714 CGCCTCATTGGAGTTGCTACA 60.676 52.381 0.13 0.00 39.64 2.74
181 182 2.012673 GCCTCATTGGAGTTGCTACAG 58.987 52.381 0.13 0.00 39.64 2.74
182 183 2.616510 GCCTCATTGGAGTTGCTACAGT 60.617 50.000 0.13 0.00 39.64 3.55
183 184 3.005554 CCTCATTGGAGTTGCTACAGTG 58.994 50.000 0.13 0.00 39.64 3.66
184 185 3.005554 CTCATTGGAGTTGCTACAGTGG 58.994 50.000 0.13 0.00 33.60 4.00
185 186 2.371841 TCATTGGAGTTGCTACAGTGGT 59.628 45.455 0.13 0.00 33.60 4.16
186 187 2.543777 TTGGAGTTGCTACAGTGGTC 57.456 50.000 0.13 0.00 0.00 4.02
187 188 1.717032 TGGAGTTGCTACAGTGGTCT 58.283 50.000 0.13 0.00 0.00 3.85
188 189 2.047061 TGGAGTTGCTACAGTGGTCTT 58.953 47.619 0.13 0.00 0.00 3.01
189 190 2.037251 TGGAGTTGCTACAGTGGTCTTC 59.963 50.000 0.13 0.00 0.00 2.87
190 191 2.300437 GGAGTTGCTACAGTGGTCTTCT 59.700 50.000 0.13 0.00 0.00 2.85
191 192 3.580731 GAGTTGCTACAGTGGTCTTCTC 58.419 50.000 0.13 0.00 0.00 2.87
192 193 3.235200 AGTTGCTACAGTGGTCTTCTCT 58.765 45.455 0.13 0.00 0.00 3.10
193 194 3.257127 AGTTGCTACAGTGGTCTTCTCTC 59.743 47.826 0.13 0.00 0.00 3.20
194 195 2.876581 TGCTACAGTGGTCTTCTCTCA 58.123 47.619 0.00 0.00 0.00 3.27
195 196 3.230976 TGCTACAGTGGTCTTCTCTCAA 58.769 45.455 0.00 0.00 0.00 3.02
196 197 3.256879 TGCTACAGTGGTCTTCTCTCAAG 59.743 47.826 0.00 0.00 0.00 3.02
197 198 3.508012 GCTACAGTGGTCTTCTCTCAAGA 59.492 47.826 0.00 0.00 0.00 3.02
198 199 4.159506 GCTACAGTGGTCTTCTCTCAAGAT 59.840 45.833 0.00 0.00 0.00 2.40
199 200 5.337169 GCTACAGTGGTCTTCTCTCAAGATT 60.337 44.000 0.00 0.00 0.00 2.40
200 201 5.146010 ACAGTGGTCTTCTCTCAAGATTC 57.854 43.478 0.00 0.00 0.00 2.52
201 202 4.590647 ACAGTGGTCTTCTCTCAAGATTCA 59.409 41.667 0.00 0.00 0.00 2.57
202 203 5.170021 CAGTGGTCTTCTCTCAAGATTCAG 58.830 45.833 0.00 0.00 0.00 3.02
203 204 4.222588 AGTGGTCTTCTCTCAAGATTCAGG 59.777 45.833 0.00 0.00 0.00 3.86
204 205 3.517100 TGGTCTTCTCTCAAGATTCAGGG 59.483 47.826 0.00 0.00 0.00 4.45
205 206 3.772025 GGTCTTCTCTCAAGATTCAGGGA 59.228 47.826 0.00 0.00 0.00 4.20
206 207 4.408596 GGTCTTCTCTCAAGATTCAGGGAT 59.591 45.833 0.00 0.00 0.00 3.85
207 208 5.358922 GTCTTCTCTCAAGATTCAGGGATG 58.641 45.833 0.00 0.00 0.00 3.51
208 209 5.128499 GTCTTCTCTCAAGATTCAGGGATGA 59.872 44.000 0.00 0.00 0.00 2.92
209 210 5.723405 TCTTCTCTCAAGATTCAGGGATGAA 59.277 40.000 0.00 0.00 0.00 2.57
210 211 5.611128 TCTCTCAAGATTCAGGGATGAAG 57.389 43.478 0.00 0.00 0.00 3.02
211 212 5.275630 TCTCTCAAGATTCAGGGATGAAGA 58.724 41.667 0.00 0.00 0.00 2.87
212 213 5.128499 TCTCTCAAGATTCAGGGATGAAGAC 59.872 44.000 0.00 0.00 0.00 3.01
213 214 4.779489 TCTCAAGATTCAGGGATGAAGACA 59.221 41.667 0.00 0.00 0.00 3.41
214 215 4.836825 TCAAGATTCAGGGATGAAGACAC 58.163 43.478 0.00 0.00 0.00 3.67
215 216 3.533606 AGATTCAGGGATGAAGACACG 57.466 47.619 0.00 0.00 0.00 4.49
216 217 2.169352 AGATTCAGGGATGAAGACACGG 59.831 50.000 0.00 0.00 0.00 4.94
217 218 0.613260 TTCAGGGATGAAGACACGGG 59.387 55.000 0.00 0.00 0.00 5.28
218 219 1.221840 CAGGGATGAAGACACGGGG 59.778 63.158 0.00 0.00 0.00 5.73
219 220 2.124695 GGGATGAAGACACGGGGC 60.125 66.667 0.00 0.00 0.00 5.80
220 221 2.670148 GGGATGAAGACACGGGGCT 61.670 63.158 0.00 0.00 0.00 5.19
221 222 1.153349 GGATGAAGACACGGGGCTC 60.153 63.158 0.00 0.00 0.00 4.70
222 223 1.153349 GATGAAGACACGGGGCTCC 60.153 63.158 0.00 0.00 0.00 4.70
232 233 3.514417 GGGGCTCCGCAGATTTTC 58.486 61.111 0.00 0.00 0.00 2.29
233 234 1.077429 GGGGCTCCGCAGATTTTCT 60.077 57.895 0.00 0.00 0.00 2.52
234 235 0.681243 GGGGCTCCGCAGATTTTCTT 60.681 55.000 0.00 0.00 0.00 2.52
235 236 0.453390 GGGCTCCGCAGATTTTCTTG 59.547 55.000 0.00 0.00 0.00 3.02
236 237 1.168714 GGCTCCGCAGATTTTCTTGT 58.831 50.000 0.00 0.00 0.00 3.16
237 238 1.135575 GGCTCCGCAGATTTTCTTGTG 60.136 52.381 0.00 0.00 0.00 3.33
238 239 1.537202 GCTCCGCAGATTTTCTTGTGT 59.463 47.619 0.00 0.00 0.00 3.72
239 240 2.030805 GCTCCGCAGATTTTCTTGTGTT 60.031 45.455 0.00 0.00 0.00 3.32
240 241 3.188460 GCTCCGCAGATTTTCTTGTGTTA 59.812 43.478 0.00 0.00 0.00 2.41
241 242 4.142600 GCTCCGCAGATTTTCTTGTGTTAT 60.143 41.667 0.00 0.00 0.00 1.89
242 243 5.295431 TCCGCAGATTTTCTTGTGTTATG 57.705 39.130 0.00 0.00 0.00 1.90
243 244 4.155826 TCCGCAGATTTTCTTGTGTTATGG 59.844 41.667 0.00 0.00 0.00 2.74
244 245 4.082787 CCGCAGATTTTCTTGTGTTATGGT 60.083 41.667 0.00 0.00 0.00 3.55
245 246 5.460646 CGCAGATTTTCTTGTGTTATGGTT 58.539 37.500 0.00 0.00 0.00 3.67
246 247 5.343058 CGCAGATTTTCTTGTGTTATGGTTG 59.657 40.000 0.00 0.00 0.00 3.77
247 248 6.215845 GCAGATTTTCTTGTGTTATGGTTGT 58.784 36.000 0.00 0.00 0.00 3.32
248 249 6.363357 GCAGATTTTCTTGTGTTATGGTTGTC 59.637 38.462 0.00 0.00 0.00 3.18
249 250 7.651808 CAGATTTTCTTGTGTTATGGTTGTCT 58.348 34.615 0.00 0.00 0.00 3.41
250 251 8.137437 CAGATTTTCTTGTGTTATGGTTGTCTT 58.863 33.333 0.00 0.00 0.00 3.01
251 252 9.349713 AGATTTTCTTGTGTTATGGTTGTCTTA 57.650 29.630 0.00 0.00 0.00 2.10
252 253 9.612620 GATTTTCTTGTGTTATGGTTGTCTTAG 57.387 33.333 0.00 0.00 0.00 2.18
253 254 7.504924 TTTCTTGTGTTATGGTTGTCTTAGG 57.495 36.000 0.00 0.00 0.00 2.69
254 255 5.556915 TCTTGTGTTATGGTTGTCTTAGGG 58.443 41.667 0.00 0.00 0.00 3.53
255 256 4.986054 TGTGTTATGGTTGTCTTAGGGT 57.014 40.909 0.00 0.00 0.00 4.34
256 257 6.270463 TCTTGTGTTATGGTTGTCTTAGGGTA 59.730 38.462 0.00 0.00 0.00 3.69
257 258 6.630203 TGTGTTATGGTTGTCTTAGGGTAT 57.370 37.500 0.00 0.00 0.00 2.73
258 259 7.023171 TGTGTTATGGTTGTCTTAGGGTATT 57.977 36.000 0.00 0.00 0.00 1.89
259 260 7.107542 TGTGTTATGGTTGTCTTAGGGTATTC 58.892 38.462 0.00 0.00 0.00 1.75
260 261 7.037873 TGTGTTATGGTTGTCTTAGGGTATTCT 60.038 37.037 0.00 0.00 0.00 2.40
261 262 8.480501 GTGTTATGGTTGTCTTAGGGTATTCTA 58.519 37.037 0.00 0.00 0.00 2.10
262 263 8.701895 TGTTATGGTTGTCTTAGGGTATTCTAG 58.298 37.037 0.00 0.00 0.00 2.43
263 264 6.749036 ATGGTTGTCTTAGGGTATTCTAGG 57.251 41.667 0.00 0.00 0.00 3.02
264 265 5.596763 TGGTTGTCTTAGGGTATTCTAGGT 58.403 41.667 0.00 0.00 0.00 3.08
265 266 5.424252 TGGTTGTCTTAGGGTATTCTAGGTG 59.576 44.000 0.00 0.00 0.00 4.00
266 267 5.424573 GGTTGTCTTAGGGTATTCTAGGTGT 59.575 44.000 0.00 0.00 0.00 4.16
267 268 6.070366 GGTTGTCTTAGGGTATTCTAGGTGTT 60.070 42.308 0.00 0.00 0.00 3.32
268 269 6.786967 TGTCTTAGGGTATTCTAGGTGTTC 57.213 41.667 0.00 0.00 0.00 3.18
269 270 6.258354 TGTCTTAGGGTATTCTAGGTGTTCA 58.742 40.000 0.00 0.00 0.00 3.18
270 271 6.901300 TGTCTTAGGGTATTCTAGGTGTTCAT 59.099 38.462 0.00 0.00 0.00 2.57
271 272 7.147724 TGTCTTAGGGTATTCTAGGTGTTCATG 60.148 40.741 0.00 0.00 0.00 3.07
272 273 6.326583 TCTTAGGGTATTCTAGGTGTTCATGG 59.673 42.308 0.00 0.00 0.00 3.66
273 274 4.371681 AGGGTATTCTAGGTGTTCATGGT 58.628 43.478 0.00 0.00 0.00 3.55
274 275 4.409247 AGGGTATTCTAGGTGTTCATGGTC 59.591 45.833 0.00 0.00 0.00 4.02
275 276 4.444449 GGGTATTCTAGGTGTTCATGGTCC 60.444 50.000 0.00 0.00 0.00 4.46
276 277 4.409247 GGTATTCTAGGTGTTCATGGTCCT 59.591 45.833 0.00 0.00 0.00 3.85
277 278 5.104485 GGTATTCTAGGTGTTCATGGTCCTT 60.104 44.000 0.00 0.00 0.00 3.36
278 279 4.993705 TTCTAGGTGTTCATGGTCCTTT 57.006 40.909 0.00 0.00 0.00 3.11
279 280 4.286297 TCTAGGTGTTCATGGTCCTTTG 57.714 45.455 0.00 0.00 0.00 2.77
280 281 3.650942 TCTAGGTGTTCATGGTCCTTTGT 59.349 43.478 0.00 0.00 0.00 2.83
281 282 2.586425 AGGTGTTCATGGTCCTTTGTG 58.414 47.619 0.00 0.00 0.00 3.33
282 283 2.091885 AGGTGTTCATGGTCCTTTGTGT 60.092 45.455 0.00 0.00 0.00 3.72
283 284 2.693074 GGTGTTCATGGTCCTTTGTGTT 59.307 45.455 0.00 0.00 0.00 3.32
284 285 3.132111 GGTGTTCATGGTCCTTTGTGTTT 59.868 43.478 0.00 0.00 0.00 2.83
285 286 4.111916 GTGTTCATGGTCCTTTGTGTTTG 58.888 43.478 0.00 0.00 0.00 2.93
286 287 3.123050 GTTCATGGTCCTTTGTGTTTGC 58.877 45.455 0.00 0.00 0.00 3.68
287 288 1.336440 TCATGGTCCTTTGTGTTTGCG 59.664 47.619 0.00 0.00 0.00 4.85
288 289 1.066908 CATGGTCCTTTGTGTTTGCGT 59.933 47.619 0.00 0.00 0.00 5.24
289 290 1.178276 TGGTCCTTTGTGTTTGCGTT 58.822 45.000 0.00 0.00 0.00 4.84
290 291 1.546476 TGGTCCTTTGTGTTTGCGTTT 59.454 42.857 0.00 0.00 0.00 3.60
291 292 2.190161 GGTCCTTTGTGTTTGCGTTTC 58.810 47.619 0.00 0.00 0.00 2.78
292 293 2.416162 GGTCCTTTGTGTTTGCGTTTCA 60.416 45.455 0.00 0.00 0.00 2.69
293 294 2.851824 GTCCTTTGTGTTTGCGTTTCAG 59.148 45.455 0.00 0.00 0.00 3.02
294 295 2.490115 TCCTTTGTGTTTGCGTTTCAGT 59.510 40.909 0.00 0.00 0.00 3.41
295 296 2.598192 CCTTTGTGTTTGCGTTTCAGTG 59.402 45.455 0.00 0.00 0.00 3.66
296 297 2.999507 TTGTGTTTGCGTTTCAGTGT 57.000 40.000 0.00 0.00 0.00 3.55
297 298 2.254918 TGTGTTTGCGTTTCAGTGTG 57.745 45.000 0.00 0.00 0.00 3.82
298 299 0.913876 GTGTTTGCGTTTCAGTGTGC 59.086 50.000 0.00 0.00 0.00 4.57
299 300 0.808125 TGTTTGCGTTTCAGTGTGCT 59.192 45.000 0.00 0.00 0.00 4.40
300 301 1.201181 TGTTTGCGTTTCAGTGTGCTT 59.799 42.857 0.00 0.00 0.00 3.91
301 302 1.583404 GTTTGCGTTTCAGTGTGCTTG 59.417 47.619 0.00 0.00 0.00 4.01
302 303 0.808125 TTGCGTTTCAGTGTGCTTGT 59.192 45.000 0.00 0.00 0.00 3.16
303 304 1.657822 TGCGTTTCAGTGTGCTTGTA 58.342 45.000 0.00 0.00 0.00 2.41
304 305 2.010497 TGCGTTTCAGTGTGCTTGTAA 58.990 42.857 0.00 0.00 0.00 2.41
305 306 2.031560 TGCGTTTCAGTGTGCTTGTAAG 59.968 45.455 0.00 0.00 0.00 2.34
306 307 2.602217 GCGTTTCAGTGTGCTTGTAAGG 60.602 50.000 0.00 0.00 0.00 2.69
307 308 2.032030 CGTTTCAGTGTGCTTGTAAGGG 60.032 50.000 0.00 0.00 0.00 3.95
308 309 2.949644 GTTTCAGTGTGCTTGTAAGGGT 59.050 45.455 0.00 0.00 0.00 4.34
309 310 2.543777 TCAGTGTGCTTGTAAGGGTC 57.456 50.000 0.00 0.00 0.00 4.46
310 311 1.148310 CAGTGTGCTTGTAAGGGTCG 58.852 55.000 0.00 0.00 0.00 4.79
311 312 1.045407 AGTGTGCTTGTAAGGGTCGA 58.955 50.000 0.00 0.00 0.00 4.20
312 313 1.414919 AGTGTGCTTGTAAGGGTCGAA 59.585 47.619 0.00 0.00 0.00 3.71
313 314 1.529865 GTGTGCTTGTAAGGGTCGAAC 59.470 52.381 0.00 0.00 0.00 3.95
314 315 1.414919 TGTGCTTGTAAGGGTCGAACT 59.585 47.619 0.00 0.00 0.00 3.01
315 316 2.629137 TGTGCTTGTAAGGGTCGAACTA 59.371 45.455 0.00 0.00 0.00 2.24
316 317 2.991866 GTGCTTGTAAGGGTCGAACTAC 59.008 50.000 0.00 0.00 0.00 2.73
317 318 2.895404 TGCTTGTAAGGGTCGAACTACT 59.105 45.455 0.00 0.00 0.00 2.57
318 319 3.322828 TGCTTGTAAGGGTCGAACTACTT 59.677 43.478 0.00 0.00 0.00 2.24
319 320 4.202284 TGCTTGTAAGGGTCGAACTACTTT 60.202 41.667 0.00 0.00 0.00 2.66
320 321 4.151867 GCTTGTAAGGGTCGAACTACTTTG 59.848 45.833 0.00 0.00 0.00 2.77
321 322 4.942761 TGTAAGGGTCGAACTACTTTGT 57.057 40.909 0.00 0.00 0.00 2.83
322 323 6.403866 TTGTAAGGGTCGAACTACTTTGTA 57.596 37.500 0.00 0.00 0.00 2.41
323 324 5.772521 TGTAAGGGTCGAACTACTTTGTAC 58.227 41.667 0.00 0.00 0.00 2.90
324 325 5.536161 TGTAAGGGTCGAACTACTTTGTACT 59.464 40.000 0.00 0.00 0.00 2.73
325 326 6.714810 TGTAAGGGTCGAACTACTTTGTACTA 59.285 38.462 0.00 0.00 0.00 1.82
326 327 6.655078 AAGGGTCGAACTACTTTGTACTAA 57.345 37.500 0.00 0.00 0.00 2.24
327 328 6.847421 AGGGTCGAACTACTTTGTACTAAT 57.153 37.500 0.00 0.00 0.00 1.73
328 329 7.237209 AGGGTCGAACTACTTTGTACTAATT 57.763 36.000 0.00 0.00 0.00 1.40
329 330 7.318893 AGGGTCGAACTACTTTGTACTAATTC 58.681 38.462 0.00 0.00 0.00 2.17
330 331 7.039504 AGGGTCGAACTACTTTGTACTAATTCA 60.040 37.037 0.00 0.00 0.00 2.57
331 332 7.763071 GGGTCGAACTACTTTGTACTAATTCAT 59.237 37.037 0.00 0.00 0.00 2.57
332 333 8.592998 GGTCGAACTACTTTGTACTAATTCATG 58.407 37.037 0.00 0.00 0.00 3.07
333 334 9.350357 GTCGAACTACTTTGTACTAATTCATGA 57.650 33.333 0.00 0.00 0.00 3.07
425 430 2.124277 GGTACCACAGTCATTTCCCC 57.876 55.000 7.15 0.00 0.00 4.81
501 506 1.270550 CCAGCAAAAGCGTTTCAGGAT 59.729 47.619 0.00 0.00 0.00 3.24
512 517 1.067071 GTTTCAGGATCGTTCCCTCGT 60.067 52.381 8.95 0.00 43.76 4.18
582 588 2.299727 CTTCTCCCCTCTCCGCCCTA 62.300 65.000 0.00 0.00 0.00 3.53
904 910 1.478654 CCCCCGATCCAAATCCGAAAT 60.479 52.381 0.00 0.00 0.00 2.17
1064 1070 1.215647 CCGAGGTGAGTTTCTCCCG 59.784 63.158 0.00 0.00 30.62 5.14
1103 1109 0.743345 GTGCCTTCCGCCGTAGATTT 60.743 55.000 0.00 0.00 36.24 2.17
1129 1135 2.538939 GCGGCGTATCATTTCCTTGTTC 60.539 50.000 9.37 0.00 0.00 3.18
1131 1137 2.676342 GGCGTATCATTTCCTTGTTCGT 59.324 45.455 0.00 0.00 0.00 3.85
1238 1247 2.048127 AACGGCTCGAGCAAGTCC 60.048 61.111 36.27 18.92 44.36 3.85
1370 1379 3.391296 TCAAGAACAACTACCTCAAGGCT 59.609 43.478 0.00 0.00 39.32 4.58
1535 1544 4.814294 GCCGACGCCGTCAAGGAT 62.814 66.667 18.40 0.00 45.00 3.24
1984 1997 6.458615 CCGCATTATGATGAAGATGTTTGTCA 60.459 38.462 0.85 0.00 35.16 3.58
2067 2080 6.804677 TGCATTGTCACTTAGTGTTGAATTT 58.195 32.000 12.41 0.00 34.79 1.82
2185 2198 7.038088 TCACTTCCAGGTATACATGCATCATAT 60.038 37.037 12.01 0.39 0.00 1.78
2417 2517 7.890515 TGTCAATCTACTTCTGCATATAGGAG 58.109 38.462 0.00 0.00 36.96 3.69
2430 2530 8.297426 TCTGCATATAGGAGTAACGTTCATAAG 58.703 37.037 2.82 0.00 36.95 1.73
2454 2554 4.963276 TTGTCGCTTTGGAATTATCTGG 57.037 40.909 0.00 0.00 0.00 3.86
2484 2584 6.639632 ACTTTGCCTACATAGCATAATTGG 57.360 37.500 0.00 0.00 40.59 3.16
2498 2598 2.723124 AATTGGTCACCATGTTTCGC 57.277 45.000 0.00 0.00 31.53 4.70
2537 2640 2.475187 GCACTGATCGTTGCAAGCTAAG 60.475 50.000 12.31 0.00 0.00 2.18
2538 2641 2.738846 CACTGATCGTTGCAAGCTAAGT 59.261 45.455 0.00 0.00 0.00 2.24
2690 2793 0.251165 TTGCTTGCCTAGTGTTCCCC 60.251 55.000 0.00 0.00 0.00 4.81
2699 2802 1.541310 TAGTGTTCCCCTGCTGTCGG 61.541 60.000 0.00 0.00 0.00 4.79
2700 2803 3.636231 TGTTCCCCTGCTGTCGGG 61.636 66.667 0.00 0.00 41.59 5.14
2703 2806 3.083349 TCCCCTGCTGTCGGGATG 61.083 66.667 3.87 0.00 43.72 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.520846 GCCTGATTTGCGTCGGCG 62.521 66.667 4.29 4.29 44.10 6.46
19 20 1.366111 TTAGCCTGATTTGCGTCGGC 61.366 55.000 0.00 0.00 37.76 5.54
20 21 1.083489 TTTAGCCTGATTTGCGTCGG 58.917 50.000 0.00 0.00 0.00 4.79
21 22 2.892373 TTTTAGCCTGATTTGCGTCG 57.108 45.000 0.00 0.00 0.00 5.12
38 39 0.617935 CCCATTTCCGGCCCATTTTT 59.382 50.000 0.00 0.00 0.00 1.94
39 40 0.546507 ACCCATTTCCGGCCCATTTT 60.547 50.000 0.00 0.00 0.00 1.82
40 41 0.975556 GACCCATTTCCGGCCCATTT 60.976 55.000 0.00 0.00 0.00 2.32
41 42 1.381191 GACCCATTTCCGGCCCATT 60.381 57.895 0.00 0.00 0.00 3.16
42 43 2.278738 GACCCATTTCCGGCCCAT 59.721 61.111 0.00 0.00 0.00 4.00
43 44 4.418328 CGACCCATTTCCGGCCCA 62.418 66.667 0.00 0.00 0.00 5.36
44 45 3.931190 AACGACCCATTTCCGGCCC 62.931 63.158 0.00 0.00 0.00 5.80
45 46 2.360726 AACGACCCATTTCCGGCC 60.361 61.111 0.00 0.00 0.00 6.13
46 47 2.746803 CGAACGACCCATTTCCGGC 61.747 63.158 0.00 0.00 0.00 6.13
47 48 2.746803 GCGAACGACCCATTTCCGG 61.747 63.158 0.00 0.00 0.00 5.14
48 49 2.782615 GCGAACGACCCATTTCCG 59.217 61.111 0.00 0.00 0.00 4.30
49 50 2.746803 CCGCGAACGACCCATTTCC 61.747 63.158 8.23 0.00 43.93 3.13
50 51 1.087771 ATCCGCGAACGACCCATTTC 61.088 55.000 8.23 0.00 43.93 2.17
51 52 1.078708 ATCCGCGAACGACCCATTT 60.079 52.632 8.23 0.00 43.93 2.32
52 53 1.813753 CATCCGCGAACGACCCATT 60.814 57.895 8.23 0.00 43.93 3.16
53 54 2.202878 CATCCGCGAACGACCCAT 60.203 61.111 8.23 0.00 43.93 4.00
54 55 2.437518 TTTCATCCGCGAACGACCCA 62.438 55.000 8.23 0.00 43.93 4.51
55 56 1.293267 TTTTCATCCGCGAACGACCC 61.293 55.000 8.23 0.00 43.93 4.46
56 57 0.513820 TTTTTCATCCGCGAACGACC 59.486 50.000 8.23 0.00 43.93 4.79
57 58 1.587991 GTTTTTCATCCGCGAACGAC 58.412 50.000 8.23 0.00 43.93 4.34
58 59 0.162082 CGTTTTTCATCCGCGAACGA 59.838 50.000 18.46 3.63 44.01 3.85
59 60 0.787908 CCGTTTTTCATCCGCGAACG 60.788 55.000 8.23 14.00 41.77 3.95
60 61 0.513820 TCCGTTTTTCATCCGCGAAC 59.486 50.000 8.23 0.19 0.00 3.95
61 62 0.513820 GTCCGTTTTTCATCCGCGAA 59.486 50.000 8.23 0.00 0.00 4.70
62 63 1.619526 CGTCCGTTTTTCATCCGCGA 61.620 55.000 8.23 0.00 0.00 5.87
63 64 1.225637 CGTCCGTTTTTCATCCGCG 60.226 57.895 0.00 0.00 0.00 6.46
64 65 1.511254 GCGTCCGTTTTTCATCCGC 60.511 57.895 0.00 0.00 0.00 5.54
65 66 1.225637 CGCGTCCGTTTTTCATCCG 60.226 57.895 0.00 0.00 0.00 4.18
66 67 1.511254 GCGCGTCCGTTTTTCATCC 60.511 57.895 8.43 0.00 36.67 3.51
67 68 1.857426 CGCGCGTCCGTTTTTCATC 60.857 57.895 24.19 0.00 36.67 2.92
68 69 2.172419 CGCGCGTCCGTTTTTCAT 59.828 55.556 24.19 0.00 36.67 2.57
69 70 3.213009 GACGCGCGTCCGTTTTTCA 62.213 57.895 44.30 0.00 42.24 2.69
70 71 2.496171 GACGCGCGTCCGTTTTTC 60.496 61.111 44.30 23.38 42.24 2.29
89 90 4.676586 CAACGCGCCGACCCAAAC 62.677 66.667 5.73 0.00 0.00 2.93
102 103 1.436983 GATAGAAAGGCGGCCCAACG 61.437 60.000 17.02 0.00 0.00 4.10
103 104 0.107165 AGATAGAAAGGCGGCCCAAC 60.107 55.000 17.02 7.11 0.00 3.77
104 105 0.107214 CAGATAGAAAGGCGGCCCAA 60.107 55.000 17.02 0.00 0.00 4.12
105 106 1.526887 CAGATAGAAAGGCGGCCCA 59.473 57.895 17.02 0.00 0.00 5.36
106 107 1.894282 GCAGATAGAAAGGCGGCCC 60.894 63.158 17.02 0.00 0.00 5.80
107 108 2.247437 CGCAGATAGAAAGGCGGCC 61.247 63.158 12.11 12.11 45.27 6.13
108 109 3.324035 CGCAGATAGAAAGGCGGC 58.676 61.111 0.00 0.00 45.27 6.53
111 112 0.933796 GTCTGCGCAGATAGAAAGGC 59.066 55.000 39.91 22.14 39.97 4.35
112 113 1.576356 GGTCTGCGCAGATAGAAAGG 58.424 55.000 39.91 12.38 39.97 3.11
113 114 1.134699 TGGGTCTGCGCAGATAGAAAG 60.135 52.381 39.91 13.17 39.97 2.62
114 115 0.901827 TGGGTCTGCGCAGATAGAAA 59.098 50.000 39.91 22.08 39.97 2.52
115 116 0.901827 TTGGGTCTGCGCAGATAGAA 59.098 50.000 39.91 27.78 39.97 2.10
116 117 0.901827 TTTGGGTCTGCGCAGATAGA 59.098 50.000 39.91 24.12 39.97 1.98
117 118 1.009829 GTTTGGGTCTGCGCAGATAG 58.990 55.000 39.91 16.00 39.97 2.08
118 119 0.739462 CGTTTGGGTCTGCGCAGATA 60.739 55.000 39.91 26.48 39.97 1.98
119 120 2.034879 CGTTTGGGTCTGCGCAGAT 61.035 57.895 39.91 0.00 39.97 2.90
120 121 2.652382 TTCGTTTGGGTCTGCGCAGA 62.652 55.000 35.30 35.30 38.79 4.26
121 122 2.250939 TTCGTTTGGGTCTGCGCAG 61.251 57.895 31.53 31.53 38.79 5.18
122 123 2.203084 TTCGTTTGGGTCTGCGCA 60.203 55.556 10.98 10.98 35.68 6.09
123 124 2.251371 GTTCGTTTGGGTCTGCGC 59.749 61.111 0.00 0.00 0.00 6.09
124 125 2.549282 CGTTCGTTTGGGTCTGCG 59.451 61.111 0.00 0.00 0.00 5.18
125 126 2.943653 CCGTTCGTTTGGGTCTGC 59.056 61.111 0.00 0.00 0.00 4.26
126 127 2.613506 GGCCGTTCGTTTGGGTCTG 61.614 63.158 0.00 0.00 0.00 3.51
127 128 2.281276 GGCCGTTCGTTTGGGTCT 60.281 61.111 0.00 0.00 0.00 3.85
128 129 3.719144 CGGCCGTTCGTTTGGGTC 61.719 66.667 19.50 0.00 0.00 4.46
138 139 3.646023 TATTTCGTCCGCGGCCGTT 62.646 57.895 28.95 16.49 38.89 4.44
139 140 4.132441 TATTTCGTCCGCGGCCGT 62.132 61.111 28.95 12.23 38.89 5.68
140 141 3.327754 CTATTTCGTCCGCGGCCG 61.328 66.667 24.62 24.62 38.89 6.13
141 142 2.965462 CCTATTTCGTCCGCGGCC 60.965 66.667 23.51 8.79 38.89 6.13
142 143 2.202837 ACCTATTTCGTCCGCGGC 60.203 61.111 23.51 15.21 38.89 6.53
143 144 1.942712 CGACCTATTTCGTCCGCGG 60.943 63.158 22.12 22.12 38.89 6.46
144 145 2.574222 GCGACCTATTTCGTCCGCG 61.574 63.158 0.00 0.00 41.26 6.46
145 146 2.235699 GGCGACCTATTTCGTCCGC 61.236 63.158 0.00 0.00 41.26 5.54
146 147 0.594284 GAGGCGACCTATTTCGTCCG 60.594 60.000 0.00 0.00 44.90 4.79
147 148 0.458669 TGAGGCGACCTATTTCGTCC 59.541 55.000 0.00 0.00 44.90 4.79
148 149 2.510768 ATGAGGCGACCTATTTCGTC 57.489 50.000 0.00 0.00 44.12 4.20
149 150 2.550978 CAATGAGGCGACCTATTTCGT 58.449 47.619 0.00 0.00 41.26 3.85
150 151 1.867233 CCAATGAGGCGACCTATTTCG 59.133 52.381 0.00 0.00 42.15 3.46
151 152 3.134458 CTCCAATGAGGCGACCTATTTC 58.866 50.000 0.00 0.00 37.29 2.17
152 153 2.505819 ACTCCAATGAGGCGACCTATTT 59.494 45.455 0.00 0.00 43.29 1.40
153 154 2.119495 ACTCCAATGAGGCGACCTATT 58.881 47.619 0.00 0.00 43.29 1.73
154 155 1.794714 ACTCCAATGAGGCGACCTAT 58.205 50.000 0.00 0.00 43.29 2.57
155 156 1.207089 CAACTCCAATGAGGCGACCTA 59.793 52.381 0.00 0.00 43.29 3.08
156 157 0.036010 CAACTCCAATGAGGCGACCT 60.036 55.000 0.00 0.00 43.29 3.85
157 158 1.648467 GCAACTCCAATGAGGCGACC 61.648 60.000 0.00 0.00 43.29 4.79
158 159 0.674895 AGCAACTCCAATGAGGCGAC 60.675 55.000 0.00 0.00 43.29 5.19
159 160 0.901827 TAGCAACTCCAATGAGGCGA 59.098 50.000 0.00 0.00 43.29 5.54
160 161 1.009829 GTAGCAACTCCAATGAGGCG 58.990 55.000 0.00 0.00 43.29 5.52
161 162 2.012673 CTGTAGCAACTCCAATGAGGC 58.987 52.381 0.00 0.00 43.29 4.70
162 163 3.005554 CACTGTAGCAACTCCAATGAGG 58.994 50.000 0.00 0.00 43.29 3.86
163 164 3.005554 CCACTGTAGCAACTCCAATGAG 58.994 50.000 0.00 0.00 44.62 2.90
164 165 2.371841 ACCACTGTAGCAACTCCAATGA 59.628 45.455 0.00 0.00 0.00 2.57
165 166 2.744202 GACCACTGTAGCAACTCCAATG 59.256 50.000 0.00 0.00 0.00 2.82
166 167 2.639839 AGACCACTGTAGCAACTCCAAT 59.360 45.455 0.00 0.00 0.00 3.16
167 168 2.047061 AGACCACTGTAGCAACTCCAA 58.953 47.619 0.00 0.00 0.00 3.53
168 169 1.717032 AGACCACTGTAGCAACTCCA 58.283 50.000 0.00 0.00 0.00 3.86
169 170 2.300437 AGAAGACCACTGTAGCAACTCC 59.700 50.000 0.00 0.00 0.00 3.85
170 171 3.257127 AGAGAAGACCACTGTAGCAACTC 59.743 47.826 0.00 0.00 0.00 3.01
171 172 3.235200 AGAGAAGACCACTGTAGCAACT 58.765 45.455 0.00 0.00 0.00 3.16
172 173 3.005897 TGAGAGAAGACCACTGTAGCAAC 59.994 47.826 0.00 0.00 0.00 4.17
173 174 3.230976 TGAGAGAAGACCACTGTAGCAA 58.769 45.455 0.00 0.00 0.00 3.91
174 175 2.876581 TGAGAGAAGACCACTGTAGCA 58.123 47.619 0.00 0.00 0.00 3.49
175 176 3.508012 TCTTGAGAGAAGACCACTGTAGC 59.492 47.826 0.00 0.00 0.00 3.58
176 177 5.913137 ATCTTGAGAGAAGACCACTGTAG 57.087 43.478 0.00 0.00 35.07 2.74
177 178 5.775195 TGAATCTTGAGAGAAGACCACTGTA 59.225 40.000 0.00 0.00 35.07 2.74
178 179 4.590647 TGAATCTTGAGAGAAGACCACTGT 59.409 41.667 0.00 0.00 35.07 3.55
179 180 5.144692 TGAATCTTGAGAGAAGACCACTG 57.855 43.478 0.00 0.00 35.07 3.66
180 181 4.222588 CCTGAATCTTGAGAGAAGACCACT 59.777 45.833 0.00 0.00 35.07 4.00
181 182 4.502962 CCTGAATCTTGAGAGAAGACCAC 58.497 47.826 0.00 0.00 35.07 4.16
182 183 3.517100 CCCTGAATCTTGAGAGAAGACCA 59.483 47.826 0.00 0.00 35.07 4.02
183 184 3.772025 TCCCTGAATCTTGAGAGAAGACC 59.228 47.826 0.00 0.00 35.07 3.85
184 185 5.128499 TCATCCCTGAATCTTGAGAGAAGAC 59.872 44.000 0.00 0.00 35.07 3.01
185 186 5.275630 TCATCCCTGAATCTTGAGAGAAGA 58.724 41.667 0.00 0.00 35.07 2.87
186 187 5.611128 TCATCCCTGAATCTTGAGAGAAG 57.389 43.478 0.00 0.00 35.07 2.85
187 188 5.723405 TCTTCATCCCTGAATCTTGAGAGAA 59.277 40.000 0.00 0.00 40.52 2.87
188 189 5.128499 GTCTTCATCCCTGAATCTTGAGAGA 59.872 44.000 0.00 0.00 40.52 3.10
189 190 5.105023 TGTCTTCATCCCTGAATCTTGAGAG 60.105 44.000 0.00 0.00 40.52 3.20
190 191 4.779489 TGTCTTCATCCCTGAATCTTGAGA 59.221 41.667 0.00 0.00 40.52 3.27
191 192 4.874966 GTGTCTTCATCCCTGAATCTTGAG 59.125 45.833 0.00 0.00 40.52 3.02
192 193 4.621510 CGTGTCTTCATCCCTGAATCTTGA 60.622 45.833 0.00 0.00 40.52 3.02
193 194 3.620374 CGTGTCTTCATCCCTGAATCTTG 59.380 47.826 0.00 0.00 40.52 3.02
194 195 3.369892 CCGTGTCTTCATCCCTGAATCTT 60.370 47.826 0.00 0.00 40.52 2.40
195 196 2.169352 CCGTGTCTTCATCCCTGAATCT 59.831 50.000 0.00 0.00 40.52 2.40
196 197 2.555199 CCGTGTCTTCATCCCTGAATC 58.445 52.381 0.00 0.00 40.52 2.52
197 198 1.210478 CCCGTGTCTTCATCCCTGAAT 59.790 52.381 0.00 0.00 40.52 2.57
198 199 0.613260 CCCGTGTCTTCATCCCTGAA 59.387 55.000 0.00 0.00 39.07 3.02
199 200 1.264749 CCCCGTGTCTTCATCCCTGA 61.265 60.000 0.00 0.00 0.00 3.86
200 201 1.221840 CCCCGTGTCTTCATCCCTG 59.778 63.158 0.00 0.00 0.00 4.45
201 202 2.670148 GCCCCGTGTCTTCATCCCT 61.670 63.158 0.00 0.00 0.00 4.20
202 203 2.124695 GCCCCGTGTCTTCATCCC 60.125 66.667 0.00 0.00 0.00 3.85
203 204 1.153349 GAGCCCCGTGTCTTCATCC 60.153 63.158 0.00 0.00 0.00 3.51
204 205 1.153349 GGAGCCCCGTGTCTTCATC 60.153 63.158 0.00 0.00 0.00 2.92
205 206 2.990479 GGAGCCCCGTGTCTTCAT 59.010 61.111 0.00 0.00 0.00 2.57
219 220 3.904136 AACACAAGAAAATCTGCGGAG 57.096 42.857 0.00 0.00 0.00 4.63
220 221 4.155826 CCATAACACAAGAAAATCTGCGGA 59.844 41.667 0.00 0.00 0.00 5.54
221 222 4.082787 ACCATAACACAAGAAAATCTGCGG 60.083 41.667 0.00 0.00 0.00 5.69
222 223 5.046910 ACCATAACACAAGAAAATCTGCG 57.953 39.130 0.00 0.00 0.00 5.18
223 224 6.215845 ACAACCATAACACAAGAAAATCTGC 58.784 36.000 0.00 0.00 0.00 4.26
224 225 7.651808 AGACAACCATAACACAAGAAAATCTG 58.348 34.615 0.00 0.00 0.00 2.90
225 226 7.823745 AGACAACCATAACACAAGAAAATCT 57.176 32.000 0.00 0.00 0.00 2.40
226 227 9.612620 CTAAGACAACCATAACACAAGAAAATC 57.387 33.333 0.00 0.00 0.00 2.17
227 228 8.576442 CCTAAGACAACCATAACACAAGAAAAT 58.424 33.333 0.00 0.00 0.00 1.82
228 229 7.013846 CCCTAAGACAACCATAACACAAGAAAA 59.986 37.037 0.00 0.00 0.00 2.29
229 230 6.488683 CCCTAAGACAACCATAACACAAGAAA 59.511 38.462 0.00 0.00 0.00 2.52
230 231 6.001460 CCCTAAGACAACCATAACACAAGAA 58.999 40.000 0.00 0.00 0.00 2.52
231 232 5.072600 ACCCTAAGACAACCATAACACAAGA 59.927 40.000 0.00 0.00 0.00 3.02
232 233 5.313712 ACCCTAAGACAACCATAACACAAG 58.686 41.667 0.00 0.00 0.00 3.16
233 234 5.313280 ACCCTAAGACAACCATAACACAA 57.687 39.130 0.00 0.00 0.00 3.33
234 235 4.986054 ACCCTAAGACAACCATAACACA 57.014 40.909 0.00 0.00 0.00 3.72
235 236 7.336396 AGAATACCCTAAGACAACCATAACAC 58.664 38.462 0.00 0.00 0.00 3.32
236 237 7.504926 AGAATACCCTAAGACAACCATAACA 57.495 36.000 0.00 0.00 0.00 2.41
237 238 8.148999 CCTAGAATACCCTAAGACAACCATAAC 58.851 40.741 0.00 0.00 0.00 1.89
238 239 7.847848 ACCTAGAATACCCTAAGACAACCATAA 59.152 37.037 0.00 0.00 0.00 1.90
239 240 7.289317 CACCTAGAATACCCTAAGACAACCATA 59.711 40.741 0.00 0.00 0.00 2.74
240 241 6.099845 CACCTAGAATACCCTAAGACAACCAT 59.900 42.308 0.00 0.00 0.00 3.55
241 242 5.424252 CACCTAGAATACCCTAAGACAACCA 59.576 44.000 0.00 0.00 0.00 3.67
242 243 5.424573 ACACCTAGAATACCCTAAGACAACC 59.575 44.000 0.00 0.00 0.00 3.77
243 244 6.541934 ACACCTAGAATACCCTAAGACAAC 57.458 41.667 0.00 0.00 0.00 3.32
244 245 6.727231 TGAACACCTAGAATACCCTAAGACAA 59.273 38.462 0.00 0.00 0.00 3.18
245 246 6.258354 TGAACACCTAGAATACCCTAAGACA 58.742 40.000 0.00 0.00 0.00 3.41
246 247 6.786967 TGAACACCTAGAATACCCTAAGAC 57.213 41.667 0.00 0.00 0.00 3.01
247 248 6.326583 CCATGAACACCTAGAATACCCTAAGA 59.673 42.308 0.00 0.00 0.00 2.10
248 249 6.099845 ACCATGAACACCTAGAATACCCTAAG 59.900 42.308 0.00 0.00 0.00 2.18
249 250 5.968167 ACCATGAACACCTAGAATACCCTAA 59.032 40.000 0.00 0.00 0.00 2.69
250 251 5.535029 ACCATGAACACCTAGAATACCCTA 58.465 41.667 0.00 0.00 0.00 3.53
251 252 4.371681 ACCATGAACACCTAGAATACCCT 58.628 43.478 0.00 0.00 0.00 4.34
252 253 4.444449 GGACCATGAACACCTAGAATACCC 60.444 50.000 0.00 0.00 0.00 3.69
253 254 4.409247 AGGACCATGAACACCTAGAATACC 59.591 45.833 0.00 0.00 0.00 2.73
254 255 5.615925 AGGACCATGAACACCTAGAATAC 57.384 43.478 0.00 0.00 0.00 1.89
255 256 6.012858 ACAAAGGACCATGAACACCTAGAATA 60.013 38.462 0.00 0.00 32.06 1.75
256 257 5.222130 ACAAAGGACCATGAACACCTAGAAT 60.222 40.000 0.00 0.00 32.06 2.40
257 258 4.104102 ACAAAGGACCATGAACACCTAGAA 59.896 41.667 0.00 0.00 32.06 2.10
258 259 3.650942 ACAAAGGACCATGAACACCTAGA 59.349 43.478 0.00 0.00 32.06 2.43
259 260 3.753272 CACAAAGGACCATGAACACCTAG 59.247 47.826 0.00 0.00 32.06 3.02
260 261 3.137544 ACACAAAGGACCATGAACACCTA 59.862 43.478 0.00 0.00 32.06 3.08
261 262 2.091885 ACACAAAGGACCATGAACACCT 60.092 45.455 0.00 0.00 0.00 4.00
262 263 2.306847 ACACAAAGGACCATGAACACC 58.693 47.619 0.00 0.00 0.00 4.16
263 264 4.111916 CAAACACAAAGGACCATGAACAC 58.888 43.478 0.00 0.00 0.00 3.32
264 265 3.430098 GCAAACACAAAGGACCATGAACA 60.430 43.478 0.00 0.00 0.00 3.18
265 266 3.123050 GCAAACACAAAGGACCATGAAC 58.877 45.455 0.00 0.00 0.00 3.18
266 267 2.223688 CGCAAACACAAAGGACCATGAA 60.224 45.455 0.00 0.00 0.00 2.57
267 268 1.336440 CGCAAACACAAAGGACCATGA 59.664 47.619 0.00 0.00 0.00 3.07
268 269 1.066908 ACGCAAACACAAAGGACCATG 59.933 47.619 0.00 0.00 0.00 3.66
269 270 1.398692 ACGCAAACACAAAGGACCAT 58.601 45.000 0.00 0.00 0.00 3.55
270 271 1.178276 AACGCAAACACAAAGGACCA 58.822 45.000 0.00 0.00 0.00 4.02
271 272 2.190161 GAAACGCAAACACAAAGGACC 58.810 47.619 0.00 0.00 0.00 4.46
272 273 2.851824 CTGAAACGCAAACACAAAGGAC 59.148 45.455 0.00 0.00 0.00 3.85
273 274 2.490115 ACTGAAACGCAAACACAAAGGA 59.510 40.909 0.00 0.00 0.00 3.36
274 275 2.598192 CACTGAAACGCAAACACAAAGG 59.402 45.455 0.00 0.00 0.00 3.11
275 276 3.059306 CACACTGAAACGCAAACACAAAG 59.941 43.478 0.00 0.00 0.00 2.77
276 277 2.983136 CACACTGAAACGCAAACACAAA 59.017 40.909 0.00 0.00 0.00 2.83
277 278 2.590073 CACACTGAAACGCAAACACAA 58.410 42.857 0.00 0.00 0.00 3.33
278 279 1.730772 GCACACTGAAACGCAAACACA 60.731 47.619 0.00 0.00 0.00 3.72
279 280 0.913876 GCACACTGAAACGCAAACAC 59.086 50.000 0.00 0.00 0.00 3.32
280 281 0.808125 AGCACACTGAAACGCAAACA 59.192 45.000 0.00 0.00 0.00 2.83
281 282 1.583404 CAAGCACACTGAAACGCAAAC 59.417 47.619 0.00 0.00 0.00 2.93
282 283 1.201181 ACAAGCACACTGAAACGCAAA 59.799 42.857 0.00 0.00 0.00 3.68
283 284 0.808125 ACAAGCACACTGAAACGCAA 59.192 45.000 0.00 0.00 0.00 4.85
284 285 1.657822 TACAAGCACACTGAAACGCA 58.342 45.000 0.00 0.00 0.00 5.24
285 286 2.602217 CCTTACAAGCACACTGAAACGC 60.602 50.000 0.00 0.00 0.00 4.84
286 287 2.032030 CCCTTACAAGCACACTGAAACG 60.032 50.000 0.00 0.00 0.00 3.60
287 288 2.949644 ACCCTTACAAGCACACTGAAAC 59.050 45.455 0.00 0.00 0.00 2.78
288 289 3.211045 GACCCTTACAAGCACACTGAAA 58.789 45.455 0.00 0.00 0.00 2.69
289 290 2.805295 CGACCCTTACAAGCACACTGAA 60.805 50.000 0.00 0.00 0.00 3.02
290 291 1.270094 CGACCCTTACAAGCACACTGA 60.270 52.381 0.00 0.00 0.00 3.41
291 292 1.148310 CGACCCTTACAAGCACACTG 58.852 55.000 0.00 0.00 0.00 3.66
292 293 1.045407 TCGACCCTTACAAGCACACT 58.955 50.000 0.00 0.00 0.00 3.55
293 294 1.529865 GTTCGACCCTTACAAGCACAC 59.470 52.381 0.00 0.00 0.00 3.82
294 295 1.414919 AGTTCGACCCTTACAAGCACA 59.585 47.619 0.00 0.00 0.00 4.57
295 296 2.165319 AGTTCGACCCTTACAAGCAC 57.835 50.000 0.00 0.00 0.00 4.40
296 297 2.895404 AGTAGTTCGACCCTTACAAGCA 59.105 45.455 0.00 0.00 0.00 3.91
297 298 3.589495 AGTAGTTCGACCCTTACAAGC 57.411 47.619 0.00 0.00 0.00 4.01
298 299 5.295152 ACAAAGTAGTTCGACCCTTACAAG 58.705 41.667 0.00 0.00 0.00 3.16
299 300 5.280654 ACAAAGTAGTTCGACCCTTACAA 57.719 39.130 0.00 0.00 0.00 2.41
300 301 4.942761 ACAAAGTAGTTCGACCCTTACA 57.057 40.909 0.00 0.00 0.00 2.41
301 302 6.018589 AGTACAAAGTAGTTCGACCCTTAC 57.981 41.667 0.00 0.00 0.00 2.34
302 303 7.759489 TTAGTACAAAGTAGTTCGACCCTTA 57.241 36.000 0.00 0.00 0.00 2.69
303 304 6.655078 TTAGTACAAAGTAGTTCGACCCTT 57.345 37.500 0.00 0.00 0.00 3.95
304 305 6.847421 ATTAGTACAAAGTAGTTCGACCCT 57.153 37.500 0.00 0.00 0.00 4.34
305 306 7.092716 TGAATTAGTACAAAGTAGTTCGACCC 58.907 38.462 0.00 0.00 32.57 4.46
306 307 8.592998 CATGAATTAGTACAAAGTAGTTCGACC 58.407 37.037 0.00 0.00 32.57 4.79
307 308 9.350357 TCATGAATTAGTACAAAGTAGTTCGAC 57.650 33.333 0.00 0.00 32.57 4.20
365 366 8.208224 TGTCCATATAAACAATAGGGTACAGTG 58.792 37.037 0.00 0.00 41.80 3.66
372 373 4.154195 GCGCTGTCCATATAAACAATAGGG 59.846 45.833 0.00 0.00 42.35 3.53
402 405 0.326927 AAATGACTGTGGTACCCCCG 59.673 55.000 10.07 0.00 35.15 5.73
408 411 1.276989 GTCGGGGAAATGACTGTGGTA 59.723 52.381 0.00 0.00 32.37 3.25
409 412 0.036306 GTCGGGGAAATGACTGTGGT 59.964 55.000 0.00 0.00 32.37 4.16
410 413 0.676782 GGTCGGGGAAATGACTGTGG 60.677 60.000 0.00 0.00 35.45 4.17
411 414 0.676782 GGGTCGGGGAAATGACTGTG 60.677 60.000 0.00 0.00 35.45 3.66
412 415 1.131303 TGGGTCGGGGAAATGACTGT 61.131 55.000 0.00 0.00 35.45 3.55
413 416 0.037590 TTGGGTCGGGGAAATGACTG 59.962 55.000 0.00 0.00 35.45 3.51
414 417 0.774908 TTTGGGTCGGGGAAATGACT 59.225 50.000 0.00 0.00 35.45 3.41
425 430 4.084888 GCCTCGCGTTTTGGGTCG 62.085 66.667 5.77 0.00 0.00 4.79
501 506 2.993264 GGTGGGACGAGGGAACGA 60.993 66.667 0.00 0.00 37.03 3.85
641 647 2.585869 CGCCTTTATCGATGCGCGT 61.586 57.895 13.82 0.00 40.58 6.01
645 651 3.398954 TTTGAACGCCTTTATCGATGC 57.601 42.857 8.54 1.31 0.00 3.91
748 754 1.961919 GCGTAGGTTAGTACCCTGGGT 60.962 57.143 24.15 24.15 46.28 4.51
790 796 1.262640 ATGACCTAGGGTTTCCGCGT 61.263 55.000 14.81 0.00 35.25 6.01
904 910 2.438795 CTGCGGGGAGGGGAAAAA 59.561 61.111 0.00 0.00 0.00 1.94
1064 1070 1.081175 GAAGCAGAGCGCCAAAACC 60.081 57.895 2.29 0.00 44.04 3.27
1103 1109 1.149361 GAAATGATACGCCGCCGACA 61.149 55.000 0.00 0.00 38.29 4.35
1129 1135 2.799917 CGGCAAGGAGAAGGATCTAACG 60.800 54.545 0.00 0.00 35.54 3.18
1131 1137 1.762957 CCGGCAAGGAGAAGGATCTAA 59.237 52.381 0.00 0.00 45.00 2.10
1238 1247 0.665670 CGATGTAGCTGGAGATGGCG 60.666 60.000 0.00 0.00 0.00 5.69
1418 1427 2.894919 GGCGCGTTAGGGTCCTTA 59.105 61.111 8.43 0.00 0.00 2.69
1984 1997 2.289547 GCGACCAAGTACACAACAACAT 59.710 45.455 0.00 0.00 0.00 2.71
2212 2231 4.855715 TGTACTACTAGGATGCATCTGC 57.144 45.455 25.28 10.56 42.50 4.26
2223 2242 4.524714 AGCCACCATGCTATGTACTACTAG 59.475 45.833 0.00 0.00 40.56 2.57
2224 2243 4.480115 AGCCACCATGCTATGTACTACTA 58.520 43.478 0.00 0.00 40.56 1.82
2225 2244 3.309296 AGCCACCATGCTATGTACTACT 58.691 45.455 0.00 0.00 40.56 2.57
2226 2245 3.753294 AGCCACCATGCTATGTACTAC 57.247 47.619 0.00 0.00 40.56 2.73
2339 2436 4.142447 TGAAGCACGACCTAATAGTGAGAC 60.142 45.833 0.00 0.00 36.07 3.36
2417 2517 6.091123 AGCGACAATTCTTATGAACGTTAC 57.909 37.500 0.00 0.00 34.71 2.50
2430 2530 5.973565 CCAGATAATTCCAAAGCGACAATTC 59.026 40.000 0.00 0.00 0.00 2.17
2471 2571 6.395426 AACATGGTGACCAATTATGCTATG 57.605 37.500 9.06 0.87 36.95 2.23
2484 2584 1.601903 TGAAGTGCGAAACATGGTGAC 59.398 47.619 0.00 0.00 0.00 3.67
2498 2598 4.012374 AGTGCAATCCCAAGTATGAAGTG 58.988 43.478 0.00 0.00 0.00 3.16
2537 2640 6.747280 CAGCTATATGCAAACTTGTAACCAAC 59.253 38.462 0.00 0.00 45.94 3.77
2538 2641 6.432783 ACAGCTATATGCAAACTTGTAACCAA 59.567 34.615 0.00 0.00 45.94 3.67
2578 2681 4.669206 TCAACTGCAACATTTCACCATT 57.331 36.364 0.00 0.00 0.00 3.16
2626 2729 4.294523 TCGCCATCGAAACCAAGG 57.705 55.556 0.00 0.00 42.44 3.61
2649 2752 6.034256 GCAATCAGCAAGCAACAAAATACTAG 59.966 38.462 0.00 0.00 44.79 2.57


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

AutoCloner maintained by Alex Coulton.