Multiple sequence alignment - TraesCS3B01G284300

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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 TraesCS3B01G284300 chr3B 100.000 3069 0 0 1 3069 455067856 455064788 0.000000e+00 5668
1 TraesCS3B01G284300 chr3B 93.382 272 17 1 88 359 455125876 455125606 4.770000e-108 401
2 TraesCS3B01G284300 chr3B 86.726 226 26 4 139 362 733879252 733879475 6.570000e-62 248
3 TraesCS3B01G284300 chr3D 89.111 2250 131 36 358 2557 354622405 354620220 0.000000e+00 2693
4 TraesCS3B01G284300 chr3D 95.155 516 23 1 2556 3069 354620178 354619663 0.000000e+00 813
5 TraesCS3B01G284300 chr3D 78.947 399 64 16 1019 1404 588696316 588696707 1.410000e-63 254
6 TraesCS3B01G284300 chr3A 88.210 2061 125 54 360 2337 473218164 473216139 0.000000e+00 2351
7 TraesCS3B01G284300 chr3A 93.529 680 42 2 2341 3019 473213393 473212715 0.000000e+00 1011
8 TraesCS3B01G284300 chr4D 92.244 361 23 5 1 359 446993423 446993780 9.820000e-140 507
9 TraesCS3B01G284300 chr1D 83.483 333 43 11 1 326 25216902 25217229 1.790000e-77 300
10 TraesCS3B01G284300 chr1D 78.199 422 72 13 999 1404 447925417 447925000 5.080000e-63 252
11 TraesCS3B01G284300 chr2D 92.195 205 14 2 10 213 87168101 87167898 3.870000e-74 289
12 TraesCS3B01G284300 chr2D 79.000 400 62 18 1019 1404 586831126 586831517 1.410000e-63 254
13 TraesCS3B01G284300 chr1B 79.858 422 61 16 999 1402 613415580 613415165 1.390000e-73 287
14 TraesCS3B01G284300 chr4B 90.187 214 18 3 1 213 105663781 105663992 3.010000e-70 276
15 TraesCS3B01G284300 chr4B 85.586 222 30 2 139 359 626634771 626634991 6.620000e-57 231
16 TraesCS3B01G284300 chr1A 78.960 423 67 13 999 1404 544048745 544048328 5.040000e-68 268
17 TraesCS3B01G284300 chr1A 88.479 217 16 8 1 211 354540641 354540854 1.410000e-63 254
18 TraesCS3B01G284300 chr1A 79.921 254 32 13 122 361 22604729 22604977 5.260000e-38 169
19 TraesCS3B01G284300 chr5A 81.459 329 47 13 4 323 565724694 565725017 1.090000e-64 257
20 TraesCS3B01G284300 chr7B 78.803 401 61 18 1019 1404 97120331 97119940 6.570000e-62 248
21 TraesCS3B01G284300 chr7B 77.556 401 64 19 1019 1404 89870217 89869828 5.150000e-53 219
22 TraesCS3B01G284300 chr7B 79.545 220 37 7 119 334 44937877 44938092 1.910000e-32 150
23 TraesCS3B01G284300 chr5D 78.000 400 66 17 1019 1404 556578548 556578157 6.620000e-57 231
24 TraesCS3B01G284300 chr5D 83.041 171 21 6 193 359 350700734 350700900 6.860000e-32 148
25 TraesCS3B01G284300 chr5B 79.817 327 53 12 38 359 17842861 17842543 3.080000e-55 226
26 TraesCS3B01G284300 chr5B 76.794 418 79 17 999 1404 527733241 527733652 5.150000e-53 219
27 TraesCS3B01G284300 chr5B 77.000 400 70 18 1019 1404 581253261 581252870 3.100000e-50 209
28 TraesCS3B01G284300 chr6B 80.935 278 43 10 83 356 45756425 45756696 8.620000e-51 211


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 TraesCS3B01G284300 chr3B 455064788 455067856 3068 True 5668 5668 100.0000 1 3069 1 chr3B.!!$R1 3068
1 TraesCS3B01G284300 chr3D 354619663 354622405 2742 True 1753 2693 92.1330 358 3069 2 chr3D.!!$R1 2711
2 TraesCS3B01G284300 chr3A 473212715 473218164 5449 True 1681 2351 90.8695 360 3019 2 chr3A.!!$R1 2659

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 0.037512 TCGACGGGGCAACGAATTTA 60.038 50.0 7.82 0.0 37.61 1.40 F
176 177 0.095762 CGACGGGGCAACGAATTTAC 59.904 55.0 7.82 0.0 37.61 2.01 F
320 321 0.101759 CCAGGAATGCCAAATCGCTG 59.898 55.0 0.00 0.0 36.29 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 1977 2.056577 GTCGACACGGTTTAACAGGAG 58.943 52.381 11.55 0.0 0.0 3.69 R
1933 2025 4.473444 TGACCTGGAAAGCAAGAAGAATT 58.527 39.130 0.00 0.0 0.0 2.17 R
2310 2402 0.311790 AAAACACGCATCACCAGCAG 59.688 50.000 0.00 0.0 0.0 4.24 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
17 18 2.360980 ACTGACGGAGGGAGAGGG 59.639 66.667 0.00 0.00 0.00 4.30
18 19 2.239439 ACTGACGGAGGGAGAGGGA 61.239 63.158 0.00 0.00 0.00 4.20
19 20 1.454847 CTGACGGAGGGAGAGGGAG 60.455 68.421 0.00 0.00 0.00 4.30
20 21 1.927569 CTGACGGAGGGAGAGGGAGA 61.928 65.000 0.00 0.00 0.00 3.71
21 22 1.152839 GACGGAGGGAGAGGGAGAG 60.153 68.421 0.00 0.00 0.00 3.20
22 23 2.197324 CGGAGGGAGAGGGAGAGG 59.803 72.222 0.00 0.00 0.00 3.69
23 24 2.387772 CGGAGGGAGAGGGAGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
24 25 1.541672 GGAGGGAGAGGGAGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
25 26 0.996762 GGAGGGAGAGGGAGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
26 27 0.478507 GAGGGAGAGGGAGAGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
27 28 0.998945 AGGGAGAGGGAGAGGAGAGG 60.999 65.000 0.00 0.00 0.00 3.69
28 29 1.541672 GGAGAGGGAGAGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
29 30 1.152546 GAGAGGGAGAGGAGAGGGC 60.153 68.421 0.00 0.00 0.00 5.19
30 31 2.520741 GAGGGAGAGGAGAGGGCG 60.521 72.222 0.00 0.00 0.00 6.13
31 32 4.150454 AGGGAGAGGAGAGGGCGG 62.150 72.222 0.00 0.00 0.00 6.13
97 98 3.541713 CTGGGGAGCGGCTAGGTC 61.542 72.222 0.60 3.87 46.08 3.85
102 103 2.737830 GAGCGGCTAGGTCATCCC 59.262 66.667 0.60 0.00 46.08 3.85
103 104 2.844839 AGCGGCTAGGTCATCCCC 60.845 66.667 0.00 0.00 0.00 4.81
104 105 3.161450 GCGGCTAGGTCATCCCCA 61.161 66.667 0.00 0.00 0.00 4.96
105 106 2.742116 GCGGCTAGGTCATCCCCAA 61.742 63.158 0.00 0.00 0.00 4.12
106 107 1.447643 CGGCTAGGTCATCCCCAAG 59.552 63.158 0.00 0.00 0.00 3.61
107 108 1.149401 GGCTAGGTCATCCCCAAGC 59.851 63.158 0.00 0.00 35.25 4.01
108 109 1.227674 GCTAGGTCATCCCCAAGCG 60.228 63.158 0.00 0.00 0.00 4.68
109 110 1.447643 CTAGGTCATCCCCAAGCGG 59.552 63.158 0.00 0.00 0.00 5.52
110 111 1.002403 TAGGTCATCCCCAAGCGGA 59.998 57.895 0.00 0.00 36.02 5.54
111 112 1.048724 TAGGTCATCCCCAAGCGGAG 61.049 60.000 0.00 0.00 34.69 4.63
128 129 2.614829 GAGCGGCCTCCTTTTATACA 57.385 50.000 0.00 0.00 31.68 2.29
129 130 2.210961 GAGCGGCCTCCTTTTATACAC 58.789 52.381 0.00 0.00 31.68 2.90
130 131 1.134189 AGCGGCCTCCTTTTATACACC 60.134 52.381 0.00 0.00 0.00 4.16
131 132 1.134189 GCGGCCTCCTTTTATACACCT 60.134 52.381 0.00 0.00 0.00 4.00
132 133 2.561569 CGGCCTCCTTTTATACACCTG 58.438 52.381 0.00 0.00 0.00 4.00
133 134 2.093128 CGGCCTCCTTTTATACACCTGT 60.093 50.000 0.00 0.00 0.00 4.00
134 135 3.133362 CGGCCTCCTTTTATACACCTGTA 59.867 47.826 0.00 0.00 34.67 2.74
135 136 4.704965 GGCCTCCTTTTATACACCTGTAG 58.295 47.826 0.00 0.00 33.52 2.74
136 137 4.444449 GGCCTCCTTTTATACACCTGTAGG 60.444 50.000 0.00 0.00 42.17 3.18
137 138 4.704965 CCTCCTTTTATACACCTGTAGGC 58.295 47.826 0.00 0.00 39.32 3.93
138 139 4.369182 CTCCTTTTATACACCTGTAGGCG 58.631 47.826 0.00 0.00 39.32 5.52
139 140 4.025360 TCCTTTTATACACCTGTAGGCGA 58.975 43.478 0.00 0.00 39.32 5.54
140 141 4.467082 TCCTTTTATACACCTGTAGGCGAA 59.533 41.667 0.00 0.00 39.32 4.70
141 142 5.046448 TCCTTTTATACACCTGTAGGCGAAA 60.046 40.000 0.00 0.00 39.32 3.46
142 143 5.820947 CCTTTTATACACCTGTAGGCGAAAT 59.179 40.000 0.00 0.00 39.32 2.17
143 144 6.238374 CCTTTTATACACCTGTAGGCGAAATG 60.238 42.308 0.00 0.00 39.32 2.32
144 145 5.601583 TTATACACCTGTAGGCGAAATGA 57.398 39.130 0.00 0.00 39.32 2.57
145 146 2.094762 ACACCTGTAGGCGAAATGAC 57.905 50.000 0.00 0.00 39.32 3.06
146 147 0.999406 CACCTGTAGGCGAAATGACG 59.001 55.000 0.00 0.00 39.32 4.35
147 148 0.892755 ACCTGTAGGCGAAATGACGA 59.107 50.000 0.00 0.00 39.32 4.20
148 149 1.274167 ACCTGTAGGCGAAATGACGAA 59.726 47.619 0.00 0.00 39.32 3.85
149 150 2.289195 ACCTGTAGGCGAAATGACGAAA 60.289 45.455 0.00 0.00 39.32 3.46
150 151 2.739913 CCTGTAGGCGAAATGACGAAAA 59.260 45.455 0.00 0.00 35.09 2.29
151 152 3.374058 CCTGTAGGCGAAATGACGAAAAT 59.626 43.478 0.00 0.00 35.09 1.82
152 153 4.334443 CTGTAGGCGAAATGACGAAAATG 58.666 43.478 0.00 0.00 35.09 2.32
153 154 2.262572 AGGCGAAATGACGAAAATGC 57.737 45.000 0.00 0.00 35.09 3.56
154 155 1.135402 AGGCGAAATGACGAAAATGCC 60.135 47.619 0.00 0.00 41.50 4.40
155 156 1.268265 GCGAAATGACGAAAATGCCC 58.732 50.000 0.00 0.00 35.09 5.36
156 157 1.135402 GCGAAATGACGAAAATGCCCT 60.135 47.619 0.00 0.00 35.09 5.19
157 158 2.785679 CGAAATGACGAAAATGCCCTC 58.214 47.619 0.00 0.00 35.09 4.30
158 159 2.785679 GAAATGACGAAAATGCCCTCG 58.214 47.619 0.00 0.00 40.87 4.63
159 160 2.107950 AATGACGAAAATGCCCTCGA 57.892 45.000 0.00 0.00 38.43 4.04
160 161 1.369625 ATGACGAAAATGCCCTCGAC 58.630 50.000 0.00 0.00 38.43 4.20
161 162 1.011968 TGACGAAAATGCCCTCGACG 61.012 55.000 0.00 0.00 38.43 5.12
162 163 1.693083 GACGAAAATGCCCTCGACGG 61.693 60.000 0.00 0.00 38.43 4.79
171 172 4.367023 CCTCGACGGGGCAACGAA 62.367 66.667 0.00 0.00 35.70 3.85
172 173 2.125673 CTCGACGGGGCAACGAAT 60.126 61.111 7.82 0.00 35.70 3.34
173 174 1.740296 CTCGACGGGGCAACGAATT 60.740 57.895 7.82 0.00 35.70 2.17
174 175 1.296056 CTCGACGGGGCAACGAATTT 61.296 55.000 7.82 0.00 35.70 1.82
175 176 0.037512 TCGACGGGGCAACGAATTTA 60.038 50.000 7.82 0.00 37.61 1.40
176 177 0.095762 CGACGGGGCAACGAATTTAC 59.904 55.000 7.82 0.00 37.61 2.01
177 178 1.158434 GACGGGGCAACGAATTTACA 58.842 50.000 7.82 0.00 37.61 2.41
178 179 0.876399 ACGGGGCAACGAATTTACAC 59.124 50.000 7.82 0.00 37.61 2.90
179 180 0.179210 CGGGGCAACGAATTTACACG 60.179 55.000 0.00 0.00 35.47 4.49
180 181 0.455464 GGGGCAACGAATTTACACGC 60.455 55.000 0.00 0.00 37.60 5.34
181 182 0.791610 GGGCAACGAATTTACACGCG 60.792 55.000 3.53 3.53 37.60 6.01
182 183 0.791610 GGCAACGAATTTACACGCGG 60.792 55.000 12.47 1.27 0.00 6.46
183 184 0.110554 GCAACGAATTTACACGCGGT 60.111 50.000 12.47 8.38 0.00 5.68
184 185 1.586908 CAACGAATTTACACGCGGTG 58.413 50.000 12.47 9.20 39.75 4.94
185 186 0.513820 AACGAATTTACACGCGGTGG 59.486 50.000 12.47 1.38 37.94 4.61
186 187 1.225908 CGAATTTACACGCGGTGGC 60.226 57.895 12.47 0.00 37.94 5.01
187 188 1.870383 GAATTTACACGCGGTGGCA 59.130 52.632 12.47 0.00 37.94 4.92
188 189 0.179200 GAATTTACACGCGGTGGCAG 60.179 55.000 12.47 0.00 37.94 4.85
189 190 1.582610 AATTTACACGCGGTGGCAGG 61.583 55.000 12.47 0.00 37.94 4.85
190 191 2.457743 ATTTACACGCGGTGGCAGGA 62.458 55.000 12.47 0.00 37.94 3.86
191 192 2.661840 TTTACACGCGGTGGCAGGAA 62.662 55.000 12.47 0.00 37.94 3.36
192 193 3.869473 TACACGCGGTGGCAGGAAC 62.869 63.158 12.47 0.00 37.94 3.62
196 197 4.373116 GCGGTGGCAGGAACGAGA 62.373 66.667 5.21 0.00 39.62 4.04
197 198 2.125912 CGGTGGCAGGAACGAGAG 60.126 66.667 0.00 0.00 0.00 3.20
198 199 2.266055 GGTGGCAGGAACGAGAGG 59.734 66.667 0.00 0.00 0.00 3.69
199 200 2.584391 GGTGGCAGGAACGAGAGGT 61.584 63.158 0.00 0.00 0.00 3.85
200 201 1.255667 GGTGGCAGGAACGAGAGGTA 61.256 60.000 0.00 0.00 0.00 3.08
201 202 0.606604 GTGGCAGGAACGAGAGGTAA 59.393 55.000 0.00 0.00 0.00 2.85
202 203 0.606604 TGGCAGGAACGAGAGGTAAC 59.393 55.000 0.00 0.00 0.00 2.50
223 224 9.614792 GGTAACTATTCATTCCATCAGTAACTT 57.385 33.333 0.00 0.00 0.00 2.66
245 246 3.405823 TTTTTATCCAACGGACGAGGT 57.594 42.857 0.00 0.00 32.98 3.85
246 247 2.660189 TTTATCCAACGGACGAGGTC 57.340 50.000 0.00 0.00 32.98 3.85
260 261 2.492451 AGGTCCTCTCACCTCTGGA 58.508 57.895 0.00 0.00 44.08 3.86
261 262 1.014804 AGGTCCTCTCACCTCTGGAT 58.985 55.000 0.00 0.00 44.08 3.41
262 263 1.063266 AGGTCCTCTCACCTCTGGATC 60.063 57.143 0.00 0.00 44.08 3.36
263 264 1.408969 GTCCTCTCACCTCTGGATCC 58.591 60.000 4.20 4.20 0.00 3.36
264 265 1.010795 TCCTCTCACCTCTGGATCCA 58.989 55.000 15.27 15.27 0.00 3.41
265 266 1.362584 TCCTCTCACCTCTGGATCCAA 59.637 52.381 17.00 6.19 0.00 3.53
266 267 1.484240 CCTCTCACCTCTGGATCCAAC 59.516 57.143 17.00 0.00 0.00 3.77
267 268 1.135915 CTCTCACCTCTGGATCCAACG 59.864 57.143 17.00 9.35 0.00 4.10
268 269 0.176680 CTCACCTCTGGATCCAACGG 59.823 60.000 21.70 21.70 0.00 4.44
269 270 1.450312 CACCTCTGGATCCAACGGC 60.450 63.158 22.75 0.00 0.00 5.68
270 271 2.190578 CCTCTGGATCCAACGGCC 59.809 66.667 17.00 0.00 0.00 6.13
271 272 2.202932 CTCTGGATCCAACGGCCG 60.203 66.667 26.86 26.86 0.00 6.13
272 273 2.682136 TCTGGATCCAACGGCCGA 60.682 61.111 35.90 10.13 0.00 5.54
273 274 2.238847 CTCTGGATCCAACGGCCGAA 62.239 60.000 35.90 14.60 0.00 4.30
274 275 1.376683 CTGGATCCAACGGCCGAAA 60.377 57.895 35.90 14.20 0.00 3.46
275 276 0.958382 CTGGATCCAACGGCCGAAAA 60.958 55.000 35.90 14.60 0.00 2.29
276 277 0.322997 TGGATCCAACGGCCGAAAAT 60.323 50.000 35.90 18.92 0.00 1.82
277 278 1.065345 TGGATCCAACGGCCGAAAATA 60.065 47.619 35.90 13.41 0.00 1.40
278 279 1.332686 GGATCCAACGGCCGAAAATAC 59.667 52.381 35.90 16.09 0.00 1.89
279 280 2.011222 GATCCAACGGCCGAAAATACA 58.989 47.619 35.90 8.80 0.00 2.29
280 281 2.116827 TCCAACGGCCGAAAATACAT 57.883 45.000 35.90 2.60 0.00 2.29
281 282 2.011222 TCCAACGGCCGAAAATACATC 58.989 47.619 35.90 0.00 0.00 3.06
282 283 1.740585 CCAACGGCCGAAAATACATCA 59.259 47.619 35.90 0.00 0.00 3.07
283 284 2.162608 CCAACGGCCGAAAATACATCAA 59.837 45.455 35.90 0.00 0.00 2.57
284 285 3.425404 CAACGGCCGAAAATACATCAAG 58.575 45.455 35.90 0.00 0.00 3.02
285 286 1.400494 ACGGCCGAAAATACATCAAGC 59.600 47.619 35.90 0.00 0.00 4.01
286 287 1.594518 CGGCCGAAAATACATCAAGCG 60.595 52.381 24.07 0.00 0.00 4.68
287 288 1.268539 GGCCGAAAATACATCAAGCGG 60.269 52.381 0.00 0.00 40.17 5.52
288 289 2.105323 CCGAAAATACATCAAGCGGC 57.895 50.000 0.00 0.00 0.00 6.53
289 290 1.268539 CCGAAAATACATCAAGCGGCC 60.269 52.381 0.00 0.00 0.00 6.13
290 291 1.400142 CGAAAATACATCAAGCGGCCA 59.600 47.619 2.24 0.00 0.00 5.36
291 292 2.539547 CGAAAATACATCAAGCGGCCAG 60.540 50.000 2.24 0.00 0.00 4.85
292 293 2.418368 AAATACATCAAGCGGCCAGA 57.582 45.000 2.24 0.00 0.00 3.86
293 294 2.645838 AATACATCAAGCGGCCAGAT 57.354 45.000 2.24 0.00 0.00 2.90
294 295 2.175878 ATACATCAAGCGGCCAGATC 57.824 50.000 2.24 0.00 0.00 2.75
295 296 0.106708 TACATCAAGCGGCCAGATCC 59.893 55.000 2.24 0.00 0.00 3.36
296 297 1.153107 CATCAAGCGGCCAGATCCA 60.153 57.895 2.24 0.00 0.00 3.41
297 298 0.749091 CATCAAGCGGCCAGATCCAA 60.749 55.000 2.24 0.00 0.00 3.53
298 299 0.749454 ATCAAGCGGCCAGATCCAAC 60.749 55.000 2.24 0.00 0.00 3.77
299 300 2.436646 AAGCGGCCAGATCCAACG 60.437 61.111 2.24 0.00 0.00 4.10
300 301 3.976701 AAGCGGCCAGATCCAACGG 62.977 63.158 2.24 0.00 0.00 4.44
304 305 2.825836 GCCAGATCCAACGGCCAG 60.826 66.667 2.24 0.00 40.07 4.85
305 306 2.124570 CCAGATCCAACGGCCAGG 60.125 66.667 2.24 0.60 0.00 4.45
306 307 2.669133 CCAGATCCAACGGCCAGGA 61.669 63.158 10.66 10.66 38.50 3.86
307 308 1.299648 CAGATCCAACGGCCAGGAA 59.700 57.895 12.10 0.00 37.48 3.36
308 309 0.107017 CAGATCCAACGGCCAGGAAT 60.107 55.000 12.10 2.60 37.48 3.01
309 310 0.107017 AGATCCAACGGCCAGGAATG 60.107 55.000 12.10 0.00 37.48 2.67
310 311 1.728490 GATCCAACGGCCAGGAATGC 61.728 60.000 12.10 2.74 37.48 3.56
311 312 3.451894 CCAACGGCCAGGAATGCC 61.452 66.667 2.24 0.00 45.70 4.40
318 319 1.227060 GCCAGGAATGCCAAATCGC 60.227 57.895 0.00 0.00 36.29 4.58
319 320 1.669999 GCCAGGAATGCCAAATCGCT 61.670 55.000 0.00 0.00 36.29 4.93
320 321 0.101759 CCAGGAATGCCAAATCGCTG 59.898 55.000 0.00 0.00 36.29 5.18
321 322 1.097232 CAGGAATGCCAAATCGCTGA 58.903 50.000 0.00 0.00 36.29 4.26
322 323 1.065102 CAGGAATGCCAAATCGCTGAG 59.935 52.381 0.00 0.00 36.29 3.35
323 324 0.383231 GGAATGCCAAATCGCTGAGG 59.617 55.000 0.00 0.00 0.00 3.86
324 325 1.382522 GAATGCCAAATCGCTGAGGA 58.617 50.000 0.00 0.00 0.00 3.71
325 326 1.332997 GAATGCCAAATCGCTGAGGAG 59.667 52.381 0.00 0.00 0.00 3.69
326 327 0.254178 ATGCCAAATCGCTGAGGAGT 59.746 50.000 0.00 0.00 0.00 3.85
327 328 0.391661 TGCCAAATCGCTGAGGAGTC 60.392 55.000 0.00 0.00 0.00 3.36
328 329 1.424493 GCCAAATCGCTGAGGAGTCG 61.424 60.000 0.00 0.00 0.00 4.18
329 330 0.807667 CCAAATCGCTGAGGAGTCGG 60.808 60.000 0.00 0.00 0.00 4.79
330 331 0.807667 CAAATCGCTGAGGAGTCGGG 60.808 60.000 0.00 0.00 0.00 5.14
331 332 0.970937 AAATCGCTGAGGAGTCGGGA 60.971 55.000 0.00 0.00 0.00 5.14
332 333 1.388065 AATCGCTGAGGAGTCGGGAG 61.388 60.000 0.00 0.00 0.00 4.30
333 334 3.522731 CGCTGAGGAGTCGGGAGG 61.523 72.222 0.00 0.00 0.00 4.30
334 335 2.043852 GCTGAGGAGTCGGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
335 336 2.124693 GCTGAGGAGTCGGGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
336 337 1.610327 CTGAGGAGTCGGGAGGAGA 59.390 63.158 0.00 0.00 0.00 3.71
337 338 0.465460 CTGAGGAGTCGGGAGGAGAG 60.465 65.000 0.00 0.00 0.00 3.20
338 339 1.826487 GAGGAGTCGGGAGGAGAGC 60.826 68.421 0.00 0.00 0.00 4.09
339 340 2.277404 GGAGTCGGGAGGAGAGCT 59.723 66.667 0.00 0.00 0.00 4.09
340 341 1.826487 GGAGTCGGGAGGAGAGCTC 60.826 68.421 5.27 5.27 0.00 4.09
356 357 6.463360 GGAGAGCTCCTATTCTTATTTCTGG 58.537 44.000 10.93 0.00 46.16 3.86
378 381 9.466497 TCTGGATATAGAATCAGCTTTTTGTTT 57.534 29.630 0.00 0.00 0.00 2.83
379 382 9.512435 CTGGATATAGAATCAGCTTTTTGTTTG 57.488 33.333 0.00 0.00 0.00 2.93
381 384 9.727627 GGATATAGAATCAGCTTTTTGTTTGAG 57.272 33.333 0.00 0.00 0.00 3.02
385 388 6.268566 AGAATCAGCTTTTTGTTTGAGACAC 58.731 36.000 0.00 0.00 38.18 3.67
386 389 5.841957 ATCAGCTTTTTGTTTGAGACACT 57.158 34.783 0.00 0.00 38.18 3.55
497 500 1.189446 CGCCGCAGTACTATAAAAGCG 59.811 52.381 14.17 14.17 44.24 4.68
541 544 4.012895 CAGCCGCCACACACGAAC 62.013 66.667 0.00 0.00 0.00 3.95
594 600 2.028112 TCCAATCACCGGTGAGAAGAAG 60.028 50.000 37.98 23.50 43.61 2.85
615 621 0.960861 CTTTCCCTCCTTTCCACGGC 60.961 60.000 0.00 0.00 0.00 5.68
643 649 2.307768 CCTACGAGGCCACTCTATCAA 58.692 52.381 5.01 0.00 41.71 2.57
668 674 3.244491 CCCAATTGTTCAATTTGCTCCCA 60.244 43.478 4.43 0.00 0.00 4.37
702 708 1.040893 TCGGGATTTGAGGCGCTAGA 61.041 55.000 7.64 0.00 0.00 2.43
713 720 3.451178 TGAGGCGCTAGAGATTTAGGTTT 59.549 43.478 7.64 0.00 0.00 3.27
738 745 4.401519 CGGGTGAAATCTCTAGTGTTCCTA 59.598 45.833 0.00 0.00 0.00 2.94
772 779 4.388773 CGCATCGTATATGCCATACTGTTT 59.611 41.667 4.50 0.00 41.71 2.83
779 786 5.947228 ATATGCCATACTGTTTGAATCGG 57.053 39.130 0.00 0.00 0.00 4.18
786 793 5.410132 CCATACTGTTTGAATCGGTTGTACA 59.590 40.000 0.00 0.00 0.00 2.90
795 802 2.798976 TCGGTTGTACAGCGTAGTTT 57.201 45.000 13.72 0.00 46.86 2.66
803 810 6.793680 GGTTGTACAGCGTAGTTTATTTGTTC 59.206 38.462 3.46 0.00 0.00 3.18
816 823 6.540914 AGTTTATTTGTTCGAAACCAGTCAGA 59.459 34.615 0.00 0.00 0.00 3.27
924 932 2.604174 CGTCTGTTGGGGTCGTTGC 61.604 63.158 0.00 0.00 0.00 4.17
961 970 5.468072 ACTTAGATTTATGCTCGGCTTCATG 59.532 40.000 0.00 0.00 0.00 3.07
964 973 3.763097 TTTATGCTCGGCTTCATGTTG 57.237 42.857 0.00 0.00 0.00 3.33
974 983 2.030805 GGCTTCATGTTGAGTGGTTGAC 60.031 50.000 0.00 0.00 0.00 3.18
980 989 2.997980 TGTTGAGTGGTTGACATGTGT 58.002 42.857 1.15 0.00 0.00 3.72
1035 1045 1.836802 GATTCTCTGGTCTGGGAGCTT 59.163 52.381 0.00 0.00 0.00 3.74
1181 1191 2.649312 TGACCTCCCCTGATTGTTTGAT 59.351 45.455 0.00 0.00 0.00 2.57
1256 1283 2.286418 GGCAAACAAGAAGACTGTGACG 60.286 50.000 0.00 0.00 0.00 4.35
1410 1437 5.880332 GTCAAGAACCAGGTATTAGCATCAA 59.120 40.000 0.00 0.00 0.00 2.57
1486 1514 9.372369 AGATTAAGTACTCTAAATGACAACTGC 57.628 33.333 0.00 0.00 0.00 4.40
1571 1624 7.583625 TGTACAGTCCCATCTCTAATCTTCTA 58.416 38.462 0.00 0.00 0.00 2.10
1572 1625 8.059461 TGTACAGTCCCATCTCTAATCTTCTAA 58.941 37.037 0.00 0.00 0.00 2.10
1593 1646 7.110155 TCTAAAGGGACTGTGTTATGAAATCC 58.890 38.462 0.00 0.00 40.86 3.01
1638 1691 9.614792 ATCAACCTGGAACATTACTCTATAAAC 57.385 33.333 0.00 0.00 38.20 2.01
1639 1692 8.822805 TCAACCTGGAACATTACTCTATAAACT 58.177 33.333 0.00 0.00 38.20 2.66
1640 1693 9.449719 CAACCTGGAACATTACTCTATAAACTT 57.550 33.333 0.00 0.00 38.20 2.66
1641 1694 9.449719 AACCTGGAACATTACTCTATAAACTTG 57.550 33.333 0.00 0.00 38.20 3.16
1642 1695 7.553044 ACCTGGAACATTACTCTATAAACTTGC 59.447 37.037 0.00 0.00 38.20 4.01
1643 1696 7.770897 CCTGGAACATTACTCTATAAACTTGCT 59.229 37.037 0.00 0.00 38.20 3.91
1644 1697 8.718102 TGGAACATTACTCTATAAACTTGCTC 57.282 34.615 0.00 0.00 0.00 4.26
1645 1698 8.540388 TGGAACATTACTCTATAAACTTGCTCT 58.460 33.333 0.00 0.00 0.00 4.09
1765 1822 9.877178 TGTGGAAAAAGCTTTAATTCAGTAAAA 57.123 25.926 20.02 1.78 0.00 1.52
1789 1860 3.153919 TGGAATGCCTGTCTTGTAAACC 58.846 45.455 0.00 0.00 34.31 3.27
1817 1888 2.676463 GCCTGTTTGTGCTTGGTTTTCA 60.676 45.455 0.00 0.00 0.00 2.69
1828 1899 4.217550 TGCTTGGTTTTCAATGGTACTAGC 59.782 41.667 0.00 0.00 34.45 3.42
1885 1977 4.036144 GGAGAAATGCTGCTTAAGATGTCC 59.964 45.833 6.67 0.00 31.32 4.02
1898 1990 3.611766 AGATGTCCTCCTGTTAAACCG 57.388 47.619 0.00 0.00 0.00 4.44
1903 1995 1.000060 TCCTCCTGTTAAACCGTGTCG 60.000 52.381 0.00 0.00 0.00 4.35
1904 1996 1.000060 CCTCCTGTTAAACCGTGTCGA 60.000 52.381 0.00 0.00 0.00 4.20
1906 1998 1.142474 CCTGTTAAACCGTGTCGACC 58.858 55.000 14.12 3.43 0.00 4.79
2187 2279 1.078214 TGTGCTCTGCATACTGGCC 60.078 57.895 0.00 0.00 41.91 5.36
2268 2360 6.822676 TGAAATCATTTCCACAATTATTGGCC 59.177 34.615 7.68 0.00 38.90 5.36
2278 2370 5.490159 CACAATTATTGGCCTTCCACATTT 58.510 37.500 3.32 0.00 43.33 2.32
2308 2400 1.242076 CTGAGTTGCTTGGAGTTGGG 58.758 55.000 0.00 0.00 0.00 4.12
2309 2401 0.843309 TGAGTTGCTTGGAGTTGGGA 59.157 50.000 0.00 0.00 0.00 4.37
2310 2402 1.239347 GAGTTGCTTGGAGTTGGGAC 58.761 55.000 0.00 0.00 0.00 4.46
2316 2408 0.607489 CTTGGAGTTGGGACTGCTGG 60.607 60.000 0.00 0.00 43.87 4.85
2337 2429 4.277174 TGGTGATGCGTGTTTTTCTGTTAT 59.723 37.500 0.00 0.00 0.00 1.89
2338 2430 4.616802 GGTGATGCGTGTTTTTCTGTTATG 59.383 41.667 0.00 0.00 0.00 1.90
2351 5185 3.073678 TCTGTTATGCATGTGCTCGTTT 58.926 40.909 10.16 0.00 42.66 3.60
2391 5226 3.161866 ACTTGGTATTTTGCGTGGGAAT 58.838 40.909 0.00 0.00 0.00 3.01
2503 5356 3.627395 AGTATTCCGTGAGCATCCAAA 57.373 42.857 0.00 0.00 0.00 3.28
2526 5379 3.712091 AATTTAACGCCACGGAACAAA 57.288 38.095 0.00 0.00 0.00 2.83
2549 5402 6.811253 ATTTAACAGTCAAAATCTACGCCA 57.189 33.333 0.00 0.00 0.00 5.69
2623 5519 0.178992 TGGAGCCAAACCCACTCTTG 60.179 55.000 0.00 0.00 0.00 3.02
2628 5524 1.754226 GCCAAACCCACTCTTGACAAA 59.246 47.619 0.00 0.00 0.00 2.83
2677 5573 2.413310 ACCGGTATAAAACCCAGCTG 57.587 50.000 4.49 6.78 46.62 4.24
2720 5618 1.574702 CGAAGAAACCAAGACCCCGC 61.575 60.000 0.00 0.00 0.00 6.13
2721 5619 0.250770 GAAGAAACCAAGACCCCGCT 60.251 55.000 0.00 0.00 0.00 5.52
2743 5641 2.362369 ATGTCAGTCGGCCAGAGGG 61.362 63.158 2.24 0.00 37.18 4.30
2754 5652 3.003173 CAGAGGGCCACCGAGGAA 61.003 66.667 6.18 0.00 43.47 3.36
2820 5718 2.359169 CCGCCTCTTGTCTGGCCTA 61.359 63.158 3.32 0.00 45.90 3.93
2823 5721 1.903877 GCCTCTTGTCTGGCCTAGCA 61.904 60.000 3.32 0.00 43.11 3.49
3001 5899 0.400213 ATTCGGCTTGGACTGGACAA 59.600 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.218115 CTCCCTCTCCCTCCGTCAGT 62.218 65.000 0.00 0.00 0.00 3.41
1 2 1.454847 CTCCCTCTCCCTCCGTCAG 60.455 68.421 0.00 0.00 0.00 3.51
2 3 1.927569 CTCTCCCTCTCCCTCCGTCA 61.928 65.000 0.00 0.00 0.00 4.35
3 4 1.152839 CTCTCCCTCTCCCTCCGTC 60.153 68.421 0.00 0.00 0.00 4.79
4 5 2.695970 CCTCTCCCTCTCCCTCCGT 61.696 68.421 0.00 0.00 0.00 4.69
5 6 2.197324 CCTCTCCCTCTCCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
6 7 0.996762 TCTCCTCTCCCTCTCCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
7 8 0.478507 CTCTCCTCTCCCTCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
8 9 0.998945 CCTCTCCTCTCCCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
9 10 1.541672 CCTCTCCTCTCCCTCTCCC 59.458 68.421 0.00 0.00 0.00 4.30
10 11 1.541672 CCCTCTCCTCTCCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
11 12 1.152546 GCCCTCTCCTCTCCCTCTC 60.153 68.421 0.00 0.00 0.00 3.20
12 13 3.024217 GCCCTCTCCTCTCCCTCT 58.976 66.667 0.00 0.00 0.00 3.69
13 14 2.520741 CGCCCTCTCCTCTCCCTC 60.521 72.222 0.00 0.00 0.00 4.30
14 15 4.150454 CCGCCCTCTCCTCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
80 81 3.541713 GACCTAGCCGCTCCCCAG 61.542 72.222 0.00 0.00 0.00 4.45
81 82 3.696518 ATGACCTAGCCGCTCCCCA 62.697 63.158 0.00 0.00 0.00 4.96
82 83 2.844839 ATGACCTAGCCGCTCCCC 60.845 66.667 0.00 0.00 0.00 4.81
83 84 2.737830 GATGACCTAGCCGCTCCC 59.262 66.667 0.00 0.00 0.00 4.30
84 85 2.737830 GGATGACCTAGCCGCTCC 59.262 66.667 0.00 0.00 0.00 4.70
85 86 2.737830 GGGATGACCTAGCCGCTC 59.262 66.667 0.00 0.00 34.98 5.03
86 87 2.844839 GGGGATGACCTAGCCGCT 60.845 66.667 0.00 0.00 43.82 5.52
88 89 1.447643 CTTGGGGATGACCTAGCCG 59.552 63.158 0.00 0.00 40.03 5.52
91 92 1.048724 TCCGCTTGGGGATGACCTAG 61.049 60.000 2.10 0.00 40.03 3.02
92 93 1.002403 TCCGCTTGGGGATGACCTA 59.998 57.895 2.10 0.00 40.03 3.08
93 94 2.285368 TCCGCTTGGGGATGACCT 60.285 61.111 2.10 0.00 40.03 3.85
94 95 2.190578 CTCCGCTTGGGGATGACC 59.809 66.667 6.87 0.00 33.75 4.02
95 96 2.514824 GCTCCGCTTGGGGATGAC 60.515 66.667 6.87 0.00 33.75 3.06
96 97 4.161295 CGCTCCGCTTGGGGATGA 62.161 66.667 6.87 0.00 33.75 2.92
108 109 1.140252 TGTATAAAAGGAGGCCGCTCC 59.860 52.381 6.40 4.40 43.65 4.70
109 110 2.210961 GTGTATAAAAGGAGGCCGCTC 58.789 52.381 6.40 0.00 0.00 5.03
110 111 1.134189 GGTGTATAAAAGGAGGCCGCT 60.134 52.381 6.40 0.00 0.00 5.52
111 112 1.134189 AGGTGTATAAAAGGAGGCCGC 60.134 52.381 0.00 0.00 0.00 6.53
112 113 2.093128 ACAGGTGTATAAAAGGAGGCCG 60.093 50.000 0.00 0.00 0.00 6.13
113 114 3.646736 ACAGGTGTATAAAAGGAGGCC 57.353 47.619 0.00 0.00 0.00 5.19
114 115 4.704965 CCTACAGGTGTATAAAAGGAGGC 58.295 47.826 0.00 0.00 0.00 4.70
115 116 4.704965 GCCTACAGGTGTATAAAAGGAGG 58.295 47.826 0.81 0.00 37.57 4.30
116 117 4.098960 TCGCCTACAGGTGTATAAAAGGAG 59.901 45.833 8.62 0.00 45.57 3.69
117 118 4.025360 TCGCCTACAGGTGTATAAAAGGA 58.975 43.478 8.62 0.00 45.57 3.36
118 119 4.395959 TCGCCTACAGGTGTATAAAAGG 57.604 45.455 8.62 0.00 45.57 3.11
119 120 6.537301 TCATTTCGCCTACAGGTGTATAAAAG 59.463 38.462 8.62 0.80 45.57 2.27
120 121 6.314400 GTCATTTCGCCTACAGGTGTATAAAA 59.686 38.462 8.62 2.90 45.57 1.52
121 122 5.813672 GTCATTTCGCCTACAGGTGTATAAA 59.186 40.000 8.62 3.22 45.57 1.40
122 123 5.353938 GTCATTTCGCCTACAGGTGTATAA 58.646 41.667 8.62 3.27 45.57 0.98
123 124 4.498513 CGTCATTTCGCCTACAGGTGTATA 60.499 45.833 8.62 0.00 45.57 1.47
124 125 3.737047 CGTCATTTCGCCTACAGGTGTAT 60.737 47.826 8.62 1.92 45.57 2.29
125 126 2.416296 CGTCATTTCGCCTACAGGTGTA 60.416 50.000 8.62 0.00 45.57 2.90
126 127 1.671850 CGTCATTTCGCCTACAGGTGT 60.672 52.381 8.62 0.00 45.57 4.16
127 128 0.999406 CGTCATTTCGCCTACAGGTG 59.001 55.000 2.22 2.22 46.72 4.00
128 129 0.892755 TCGTCATTTCGCCTACAGGT 59.107 50.000 0.00 0.00 37.57 4.00
129 130 2.004583 TTCGTCATTTCGCCTACAGG 57.995 50.000 0.00 0.00 38.53 4.00
130 131 4.334443 CATTTTCGTCATTTCGCCTACAG 58.666 43.478 0.00 0.00 0.00 2.74
131 132 3.425625 GCATTTTCGTCATTTCGCCTACA 60.426 43.478 0.00 0.00 0.00 2.74
132 133 3.098636 GCATTTTCGTCATTTCGCCTAC 58.901 45.455 0.00 0.00 0.00 3.18
133 134 2.096819 GGCATTTTCGTCATTTCGCCTA 59.903 45.455 0.00 0.00 35.39 3.93
134 135 1.135402 GGCATTTTCGTCATTTCGCCT 60.135 47.619 0.00 0.00 35.39 5.52
135 136 1.268265 GGCATTTTCGTCATTTCGCC 58.732 50.000 0.00 0.00 0.00 5.54
136 137 1.135402 AGGGCATTTTCGTCATTTCGC 60.135 47.619 0.00 0.00 0.00 4.70
137 138 2.785679 GAGGGCATTTTCGTCATTTCG 58.214 47.619 0.00 0.00 0.00 3.46
138 139 2.418628 TCGAGGGCATTTTCGTCATTTC 59.581 45.455 0.00 0.00 37.99 2.17
139 140 2.161609 GTCGAGGGCATTTTCGTCATTT 59.838 45.455 0.00 0.00 37.99 2.32
140 141 1.737793 GTCGAGGGCATTTTCGTCATT 59.262 47.619 0.00 0.00 37.99 2.57
141 142 1.369625 GTCGAGGGCATTTTCGTCAT 58.630 50.000 0.00 0.00 37.99 3.06
142 143 1.011968 CGTCGAGGGCATTTTCGTCA 61.012 55.000 0.00 0.00 37.99 4.35
143 144 1.693083 CCGTCGAGGGCATTTTCGTC 61.693 60.000 11.85 0.00 37.99 4.20
144 145 1.740296 CCGTCGAGGGCATTTTCGT 60.740 57.895 11.85 0.00 37.99 3.85
145 146 3.089784 CCGTCGAGGGCATTTTCG 58.910 61.111 11.85 0.00 38.13 3.46
154 155 3.659089 ATTCGTTGCCCCGTCGAGG 62.659 63.158 0.00 0.00 40.63 4.63
155 156 1.296056 AAATTCGTTGCCCCGTCGAG 61.296 55.000 0.00 0.00 35.13 4.04
156 157 0.037512 TAAATTCGTTGCCCCGTCGA 60.038 50.000 0.00 0.00 0.00 4.20
157 158 0.095762 GTAAATTCGTTGCCCCGTCG 59.904 55.000 0.00 0.00 0.00 5.12
158 159 1.135888 GTGTAAATTCGTTGCCCCGTC 60.136 52.381 0.00 0.00 0.00 4.79
159 160 0.876399 GTGTAAATTCGTTGCCCCGT 59.124 50.000 0.00 0.00 0.00 5.28
160 161 0.179210 CGTGTAAATTCGTTGCCCCG 60.179 55.000 0.00 0.00 0.00 5.73
161 162 0.455464 GCGTGTAAATTCGTTGCCCC 60.455 55.000 0.00 0.00 0.00 5.80
162 163 0.791610 CGCGTGTAAATTCGTTGCCC 60.792 55.000 0.00 0.00 0.00 5.36
163 164 0.791610 CCGCGTGTAAATTCGTTGCC 60.792 55.000 4.92 0.00 0.00 4.52
164 165 0.110554 ACCGCGTGTAAATTCGTTGC 60.111 50.000 4.92 0.00 0.00 4.17
165 166 1.586908 CACCGCGTGTAAATTCGTTG 58.413 50.000 4.92 0.00 0.00 4.10
166 167 0.513820 CCACCGCGTGTAAATTCGTT 59.486 50.000 4.92 0.00 0.00 3.85
167 168 1.903783 GCCACCGCGTGTAAATTCGT 61.904 55.000 4.92 0.00 0.00 3.85
168 169 1.225908 GCCACCGCGTGTAAATTCG 60.226 57.895 4.92 0.00 0.00 3.34
169 170 0.179200 CTGCCACCGCGTGTAAATTC 60.179 55.000 4.92 0.00 38.08 2.17
170 171 1.582610 CCTGCCACCGCGTGTAAATT 61.583 55.000 4.92 0.00 38.08 1.82
171 172 2.038269 CCTGCCACCGCGTGTAAAT 61.038 57.895 4.92 0.00 38.08 1.40
172 173 2.661840 TTCCTGCCACCGCGTGTAAA 62.662 55.000 4.92 0.00 38.08 2.01
173 174 3.166490 TTCCTGCCACCGCGTGTAA 62.166 57.895 4.92 0.00 38.08 2.41
174 175 3.617735 TTCCTGCCACCGCGTGTA 61.618 61.111 4.92 0.00 38.08 2.90
179 180 4.373116 TCTCGTTCCTGCCACCGC 62.373 66.667 0.00 0.00 0.00 5.68
180 181 2.125912 CTCTCGTTCCTGCCACCG 60.126 66.667 0.00 0.00 0.00 4.94
181 182 1.255667 TACCTCTCGTTCCTGCCACC 61.256 60.000 0.00 0.00 0.00 4.61
182 183 0.606604 TTACCTCTCGTTCCTGCCAC 59.393 55.000 0.00 0.00 0.00 5.01
183 184 0.606604 GTTACCTCTCGTTCCTGCCA 59.393 55.000 0.00 0.00 0.00 4.92
184 185 0.896226 AGTTACCTCTCGTTCCTGCC 59.104 55.000 0.00 0.00 0.00 4.85
185 186 4.142227 TGAATAGTTACCTCTCGTTCCTGC 60.142 45.833 0.00 0.00 0.00 4.85
186 187 5.578005 TGAATAGTTACCTCTCGTTCCTG 57.422 43.478 0.00 0.00 0.00 3.86
187 188 6.183360 GGAATGAATAGTTACCTCTCGTTCCT 60.183 42.308 15.85 0.00 40.99 3.36
188 189 5.984323 GGAATGAATAGTTACCTCTCGTTCC 59.016 44.000 11.06 11.06 39.37 3.62
189 190 6.570692 TGGAATGAATAGTTACCTCTCGTTC 58.429 40.000 0.00 0.00 32.72 3.95
190 191 6.540438 TGGAATGAATAGTTACCTCTCGTT 57.460 37.500 0.00 0.00 0.00 3.85
191 192 6.323996 TGATGGAATGAATAGTTACCTCTCGT 59.676 38.462 0.00 0.00 0.00 4.18
192 193 6.749139 TGATGGAATGAATAGTTACCTCTCG 58.251 40.000 0.00 0.00 0.00 4.04
193 194 7.731054 ACTGATGGAATGAATAGTTACCTCTC 58.269 38.462 0.00 0.00 0.00 3.20
194 195 7.682787 ACTGATGGAATGAATAGTTACCTCT 57.317 36.000 0.00 0.00 0.00 3.69
195 196 9.262358 GTTACTGATGGAATGAATAGTTACCTC 57.738 37.037 0.00 0.00 0.00 3.85
196 197 8.993424 AGTTACTGATGGAATGAATAGTTACCT 58.007 33.333 0.00 0.00 0.00 3.08
197 198 9.614792 AAGTTACTGATGGAATGAATAGTTACC 57.385 33.333 0.00 0.00 0.00 2.85
225 226 3.328505 GACCTCGTCCGTTGGATAAAAA 58.671 45.455 8.05 0.00 32.73 1.94
226 227 2.354003 GGACCTCGTCCGTTGGATAAAA 60.354 50.000 0.00 0.00 43.14 1.52
227 228 1.205417 GGACCTCGTCCGTTGGATAAA 59.795 52.381 0.00 0.00 43.14 1.40
228 229 0.819582 GGACCTCGTCCGTTGGATAA 59.180 55.000 0.00 0.00 43.14 1.75
229 230 2.496942 GGACCTCGTCCGTTGGATA 58.503 57.895 0.00 0.00 43.14 2.59
230 231 3.295800 GGACCTCGTCCGTTGGAT 58.704 61.111 0.00 0.00 43.14 3.41
238 239 4.747218 AGGTGAGAGGACCTCGTC 57.253 61.111 15.97 13.53 43.33 4.20
243 244 1.408969 GATCCAGAGGTGAGAGGACC 58.591 60.000 0.00 0.00 36.09 4.46
244 245 1.342474 TGGATCCAGAGGTGAGAGGAC 60.342 57.143 11.44 0.00 32.04 3.85
245 246 1.010795 TGGATCCAGAGGTGAGAGGA 58.989 55.000 11.44 0.00 34.12 3.71
246 247 1.484240 GTTGGATCCAGAGGTGAGAGG 59.516 57.143 15.53 0.00 0.00 3.69
247 248 1.135915 CGTTGGATCCAGAGGTGAGAG 59.864 57.143 15.53 0.00 0.00 3.20
248 249 1.186200 CGTTGGATCCAGAGGTGAGA 58.814 55.000 15.53 0.00 0.00 3.27
249 250 0.176680 CCGTTGGATCCAGAGGTGAG 59.823 60.000 22.59 8.92 0.00 3.51
250 251 1.899437 GCCGTTGGATCCAGAGGTGA 61.899 60.000 27.85 8.20 0.00 4.02
251 252 1.450312 GCCGTTGGATCCAGAGGTG 60.450 63.158 27.85 14.02 0.00 4.00
252 253 2.670148 GGCCGTTGGATCCAGAGGT 61.670 63.158 27.85 0.00 0.00 3.85
253 254 2.190578 GGCCGTTGGATCCAGAGG 59.809 66.667 25.15 25.15 0.00 3.69
254 255 2.202932 CGGCCGTTGGATCCAGAG 60.203 66.667 19.50 12.64 0.00 3.35
255 256 1.832719 TTTCGGCCGTTGGATCCAGA 61.833 55.000 27.15 4.69 0.00 3.86
256 257 0.958382 TTTTCGGCCGTTGGATCCAG 60.958 55.000 27.15 4.71 0.00 3.86
257 258 0.322997 ATTTTCGGCCGTTGGATCCA 60.323 50.000 27.15 11.44 0.00 3.41
258 259 1.332686 GTATTTTCGGCCGTTGGATCC 59.667 52.381 27.15 4.20 0.00 3.36
259 260 2.011222 TGTATTTTCGGCCGTTGGATC 58.989 47.619 27.15 13.37 0.00 3.36
260 261 2.116827 TGTATTTTCGGCCGTTGGAT 57.883 45.000 27.15 16.73 0.00 3.41
261 262 2.011222 GATGTATTTTCGGCCGTTGGA 58.989 47.619 27.15 10.38 0.00 3.53
262 263 1.740585 TGATGTATTTTCGGCCGTTGG 59.259 47.619 27.15 0.00 0.00 3.77
263 264 3.425404 CTTGATGTATTTTCGGCCGTTG 58.575 45.455 27.15 0.00 0.00 4.10
264 265 2.159435 GCTTGATGTATTTTCGGCCGTT 60.159 45.455 27.15 11.28 0.00 4.44
265 266 1.400494 GCTTGATGTATTTTCGGCCGT 59.600 47.619 27.15 8.36 0.00 5.68
266 267 1.594518 CGCTTGATGTATTTTCGGCCG 60.595 52.381 22.12 22.12 0.00 6.13
267 268 1.268539 CCGCTTGATGTATTTTCGGCC 60.269 52.381 0.00 0.00 0.00 6.13
268 269 2.105323 CCGCTTGATGTATTTTCGGC 57.895 50.000 0.00 0.00 0.00 5.54
269 270 1.268539 GGCCGCTTGATGTATTTTCGG 60.269 52.381 0.00 0.00 38.51 4.30
270 271 1.400142 TGGCCGCTTGATGTATTTTCG 59.600 47.619 0.00 0.00 0.00 3.46
271 272 2.682856 TCTGGCCGCTTGATGTATTTTC 59.317 45.455 0.00 0.00 0.00 2.29
272 273 2.722094 TCTGGCCGCTTGATGTATTTT 58.278 42.857 0.00 0.00 0.00 1.82
273 274 2.418368 TCTGGCCGCTTGATGTATTT 57.582 45.000 0.00 0.00 0.00 1.40
274 275 2.498167 GATCTGGCCGCTTGATGTATT 58.502 47.619 0.00 0.00 0.00 1.89
275 276 1.271054 GGATCTGGCCGCTTGATGTAT 60.271 52.381 0.00 0.00 0.00 2.29
276 277 0.106708 GGATCTGGCCGCTTGATGTA 59.893 55.000 0.00 0.00 0.00 2.29
277 278 1.153086 GGATCTGGCCGCTTGATGT 60.153 57.895 0.00 0.00 0.00 3.06
278 279 0.749091 TTGGATCTGGCCGCTTGATG 60.749 55.000 0.00 0.00 0.00 3.07
279 280 0.749454 GTTGGATCTGGCCGCTTGAT 60.749 55.000 0.00 0.00 0.00 2.57
280 281 1.377202 GTTGGATCTGGCCGCTTGA 60.377 57.895 0.00 0.00 0.00 3.02
281 282 2.753966 CGTTGGATCTGGCCGCTTG 61.754 63.158 0.00 0.00 0.00 4.01
282 283 2.436646 CGTTGGATCTGGCCGCTT 60.437 61.111 0.00 0.00 0.00 4.68
283 284 4.473520 CCGTTGGATCTGGCCGCT 62.474 66.667 0.00 0.00 0.00 5.52
288 289 2.124570 CCTGGCCGTTGGATCTGG 60.125 66.667 0.00 0.00 0.00 3.86
289 290 0.107017 ATTCCTGGCCGTTGGATCTG 60.107 55.000 11.92 0.00 31.76 2.90
290 291 0.107017 CATTCCTGGCCGTTGGATCT 60.107 55.000 11.92 2.00 31.76 2.75
291 292 1.728490 GCATTCCTGGCCGTTGGATC 61.728 60.000 11.92 2.97 31.76 3.36
292 293 1.754234 GCATTCCTGGCCGTTGGAT 60.754 57.895 11.92 0.00 31.76 3.41
293 294 2.361104 GCATTCCTGGCCGTTGGA 60.361 61.111 7.73 7.73 0.00 3.53
294 295 3.451894 GGCATTCCTGGCCGTTGG 61.452 66.667 0.00 0.00 42.39 3.77
301 302 0.101759 CAGCGATTTGGCATTCCTGG 59.898 55.000 0.00 0.00 34.64 4.45
302 303 1.065102 CTCAGCGATTTGGCATTCCTG 59.935 52.381 0.00 0.00 34.64 3.86
303 304 1.386533 CTCAGCGATTTGGCATTCCT 58.613 50.000 0.00 0.00 34.64 3.36
304 305 0.383231 CCTCAGCGATTTGGCATTCC 59.617 55.000 0.00 0.00 34.64 3.01
305 306 1.332997 CTCCTCAGCGATTTGGCATTC 59.667 52.381 0.00 0.00 34.64 2.67
306 307 1.340405 ACTCCTCAGCGATTTGGCATT 60.340 47.619 0.00 0.00 34.64 3.56
307 308 0.254178 ACTCCTCAGCGATTTGGCAT 59.746 50.000 0.00 0.00 34.64 4.40
308 309 0.391661 GACTCCTCAGCGATTTGGCA 60.392 55.000 0.00 0.00 34.64 4.92
309 310 1.424493 CGACTCCTCAGCGATTTGGC 61.424 60.000 0.00 0.00 0.00 4.52
310 311 0.807667 CCGACTCCTCAGCGATTTGG 60.808 60.000 0.00 0.00 0.00 3.28
311 312 0.807667 CCCGACTCCTCAGCGATTTG 60.808 60.000 0.00 0.00 0.00 2.32
312 313 0.970937 TCCCGACTCCTCAGCGATTT 60.971 55.000 0.00 0.00 0.00 2.17
313 314 1.379977 TCCCGACTCCTCAGCGATT 60.380 57.895 0.00 0.00 0.00 3.34
314 315 1.826054 CTCCCGACTCCTCAGCGAT 60.826 63.158 0.00 0.00 0.00 4.58
315 316 2.438614 CTCCCGACTCCTCAGCGA 60.439 66.667 0.00 0.00 0.00 4.93
316 317 3.522731 CCTCCCGACTCCTCAGCG 61.523 72.222 0.00 0.00 0.00 5.18
317 318 2.043852 TCCTCCCGACTCCTCAGC 60.044 66.667 0.00 0.00 0.00 4.26
318 319 0.465460 CTCTCCTCCCGACTCCTCAG 60.465 65.000 0.00 0.00 0.00 3.35
319 320 1.610327 CTCTCCTCCCGACTCCTCA 59.390 63.158 0.00 0.00 0.00 3.86
320 321 1.826487 GCTCTCCTCCCGACTCCTC 60.826 68.421 0.00 0.00 0.00 3.71
321 322 2.277404 GCTCTCCTCCCGACTCCT 59.723 66.667 0.00 0.00 0.00 3.69
322 323 1.826487 GAGCTCTCCTCCCGACTCC 60.826 68.421 6.43 0.00 34.35 3.85
323 324 3.836151 GAGCTCTCCTCCCGACTC 58.164 66.667 6.43 0.00 34.35 3.36
333 334 7.296628 TCCAGAAATAAGAATAGGAGCTCTC 57.703 40.000 14.64 2.86 0.00 3.20
334 335 7.870426 ATCCAGAAATAAGAATAGGAGCTCT 57.130 36.000 14.64 2.18 0.00 4.09
350 351 9.466497 ACAAAAAGCTGATTCTATATCCAGAAA 57.534 29.630 0.00 0.00 38.03 2.52
351 352 9.466497 AACAAAAAGCTGATTCTATATCCAGAA 57.534 29.630 0.00 0.00 38.84 3.02
352 353 9.466497 AAACAAAAAGCTGATTCTATATCCAGA 57.534 29.630 0.00 0.00 0.00 3.86
353 354 9.512435 CAAACAAAAAGCTGATTCTATATCCAG 57.488 33.333 0.00 0.00 0.00 3.86
354 355 9.241919 TCAAACAAAAAGCTGATTCTATATCCA 57.758 29.630 0.00 0.00 0.00 3.41
355 356 9.727627 CTCAAACAAAAAGCTGATTCTATATCC 57.272 33.333 0.00 0.00 0.00 2.59
378 381 8.363390 CCAGCTGATTCTATATTTAGTGTCTCA 58.637 37.037 17.39 0.00 0.00 3.27
379 382 8.580720 TCCAGCTGATTCTATATTTAGTGTCTC 58.419 37.037 17.39 0.00 0.00 3.36
381 384 9.149225 CATCCAGCTGATTCTATATTTAGTGTC 57.851 37.037 17.39 0.00 0.00 3.67
382 385 7.605691 GCATCCAGCTGATTCTATATTTAGTGT 59.394 37.037 17.39 0.00 41.15 3.55
383 386 7.065563 GGCATCCAGCTGATTCTATATTTAGTG 59.934 40.741 17.39 0.00 44.79 2.74
385 388 6.541641 GGGCATCCAGCTGATTCTATATTTAG 59.458 42.308 17.39 0.00 44.79 1.85
386 389 6.012596 TGGGCATCCAGCTGATTCTATATTTA 60.013 38.462 17.39 0.00 44.79 1.40
497 500 3.062466 GGCGAGTTTTGGGGCCTC 61.062 66.667 0.84 0.00 42.29 4.70
498 501 4.678743 GGGCGAGTTTTGGGGCCT 62.679 66.667 0.84 0.00 44.91 5.19
541 544 3.447025 GATCTGCTTCGTCCCGGGG 62.447 68.421 23.50 6.77 0.00 5.73
542 545 2.107141 GATCTGCTTCGTCCCGGG 59.893 66.667 16.85 16.85 0.00 5.73
594 600 0.960861 CGTGGAAAGGAGGGAAAGGC 60.961 60.000 0.00 0.00 0.00 4.35
622 628 1.249407 GATAGAGTGGCCTCGTAGGG 58.751 60.000 3.32 0.00 42.86 3.53
643 649 4.262592 GGAGCAAATTGAACAATTGGGAGT 60.263 41.667 10.83 0.00 40.57 3.85
668 674 2.978824 CGAATGGGTCGGGACTGT 59.021 61.111 0.00 0.00 46.45 3.55
686 692 2.829741 ATCTCTAGCGCCTCAAATCC 57.170 50.000 2.29 0.00 0.00 3.01
702 708 6.718294 AGATTTCACCCGTAAACCTAAATCT 58.282 36.000 0.00 0.00 37.37 2.40
713 720 4.159135 GGAACACTAGAGATTTCACCCGTA 59.841 45.833 0.00 0.00 0.00 4.02
772 779 2.229543 ACTACGCTGTACAACCGATTCA 59.770 45.455 18.88 4.21 0.00 2.57
779 786 6.513991 CGAACAAATAAACTACGCTGTACAAC 59.486 38.462 0.00 0.00 0.00 3.32
786 793 5.236911 TGGTTTCGAACAAATAAACTACGCT 59.763 36.000 0.00 0.00 34.34 5.07
795 802 6.227522 TCATCTGACTGGTTTCGAACAAATA 58.772 36.000 0.00 0.00 0.00 1.40
803 810 8.236586 TGAAAATAAATCATCTGACTGGTTTCG 58.763 33.333 2.91 0.00 31.99 3.46
830 837 4.398044 TGAGCAGACGAACACATACTGATA 59.602 41.667 0.00 0.00 0.00 2.15
839 846 0.598680 ACAGCTGAGCAGACGAACAC 60.599 55.000 23.35 0.00 0.00 3.32
924 932 9.239002 GCATAAATCTAAGTACTATCGCCATAG 57.761 37.037 0.00 0.00 38.45 2.23
961 970 4.370364 AAACACATGTCAACCACTCAAC 57.630 40.909 0.00 0.00 0.00 3.18
1035 1045 3.206150 GAAGCAGTTGTTCTTCCTGACA 58.794 45.455 0.00 0.00 34.22 3.58
1181 1191 4.160439 AGAGACACTCATAGCATCCGAAAA 59.840 41.667 0.00 0.00 32.06 2.29
1447 1474 8.908903 AGAGTACTTAATCTAGAACATCCAGTG 58.091 37.037 0.00 0.00 0.00 3.66
1486 1514 8.784043 GGTTGCTACAGGTTATATTTCCAATAG 58.216 37.037 0.00 0.00 0.00 1.73
1571 1624 4.700213 CGGATTTCATAACACAGTCCCTTT 59.300 41.667 0.00 0.00 0.00 3.11
1572 1625 4.261801 CGGATTTCATAACACAGTCCCTT 58.738 43.478 0.00 0.00 0.00 3.95
1593 1646 6.197096 GGTTGATTAAAAGCATTACATCTGCG 59.803 38.462 0.00 0.00 44.38 5.18
1671 1724 6.651643 ACAACCATACAGCGTTACAAATAGAA 59.348 34.615 0.00 0.00 0.00 2.10
1674 1727 7.982919 AGATACAACCATACAGCGTTACAAATA 59.017 33.333 0.00 0.00 0.00 1.40
1684 1737 7.595502 GTCACATACTAGATACAACCATACAGC 59.404 40.741 0.00 0.00 0.00 4.40
1685 1738 8.630037 TGTCACATACTAGATACAACCATACAG 58.370 37.037 0.00 0.00 0.00 2.74
1765 1822 5.279456 GGTTTACAAGACAGGCATTCCATTT 60.279 40.000 0.00 0.00 33.74 2.32
1767 1824 3.763897 GGTTTACAAGACAGGCATTCCAT 59.236 43.478 0.00 0.00 33.74 3.41
1789 1860 3.673484 CACAAACAGGCAGGGGCG 61.673 66.667 0.00 0.00 42.47 6.13
1817 1888 4.385310 GGACCATTTCCAGCTAGTACCATT 60.385 45.833 0.00 0.00 45.10 3.16
1885 1977 2.056577 GTCGACACGGTTTAACAGGAG 58.943 52.381 11.55 0.00 0.00 3.69
1898 1990 4.813296 AGAAAACAAATGAGGTCGACAC 57.187 40.909 18.91 11.25 0.00 3.67
1903 1995 9.565213 CATTAGATCAAGAAAACAAATGAGGTC 57.435 33.333 0.00 0.00 0.00 3.85
1904 1996 8.526147 CCATTAGATCAAGAAAACAAATGAGGT 58.474 33.333 0.00 0.00 0.00 3.85
1906 1998 9.918630 AACCATTAGATCAAGAAAACAAATGAG 57.081 29.630 0.00 0.00 0.00 2.90
1933 2025 4.473444 TGACCTGGAAAGCAAGAAGAATT 58.527 39.130 0.00 0.00 0.00 2.17
2187 2279 9.535878 GATATAGAACCTACTGAGAAAACTTGG 57.464 37.037 0.00 0.00 0.00 3.61
2268 2360 7.439056 ACTCAGCAAAAACAATAAATGTGGAAG 59.561 33.333 0.00 0.00 42.99 3.46
2278 2370 5.049167 CCAAGCAACTCAGCAAAAACAATA 58.951 37.500 0.00 0.00 36.85 1.90
2308 2400 1.230635 AACACGCATCACCAGCAGTC 61.231 55.000 0.00 0.00 0.00 3.51
2309 2401 0.819259 AAACACGCATCACCAGCAGT 60.819 50.000 0.00 0.00 0.00 4.40
2310 2402 0.311790 AAAACACGCATCACCAGCAG 59.688 50.000 0.00 0.00 0.00 4.24
2316 2408 4.088496 GCATAACAGAAAAACACGCATCAC 59.912 41.667 0.00 0.00 0.00 3.06
2337 2429 1.069296 GCACTTAAACGAGCACATGCA 60.069 47.619 6.64 0.00 45.16 3.96
2338 2430 1.197721 AGCACTTAAACGAGCACATGC 59.802 47.619 0.00 0.00 42.49 4.06
2373 5208 5.244178 ACTTAAATTCCCACGCAAAATACCA 59.756 36.000 0.00 0.00 0.00 3.25
2380 5215 3.759086 TGCATACTTAAATTCCCACGCAA 59.241 39.130 0.00 0.00 0.00 4.85
2503 5356 2.879646 TGTTCCGTGGCGTTAAATTTCT 59.120 40.909 0.00 0.00 0.00 2.52
2526 5379 6.811253 TGGCGTAGATTTTGACTGTTAAAT 57.189 33.333 0.00 0.78 0.00 1.40
2549 5402 5.368989 GTCCAAGGAATCGACTTTCCATAT 58.631 41.667 17.84 3.50 46.40 1.78
2623 5519 2.589442 TGTCCCGCACGGTTTGTC 60.589 61.111 8.49 0.00 0.00 3.18
2677 5573 5.221244 GGTGAAATTGTGGATTATAGGTGGC 60.221 44.000 0.00 0.00 0.00 5.01
2720 5618 2.821366 GGCCGACTGACATGCCAG 60.821 66.667 7.56 7.56 43.46 4.85
2794 5692 0.824759 GACAAGAGGCGGTCATACCT 59.175 55.000 0.00 0.00 39.65 3.08
3001 5899 2.938354 GCTGTGAAGTGCCATCAGT 58.062 52.632 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.