Multiple sequence alignment - TraesCS3B01G302800

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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 TraesCS3B01G302800 chr3B 100.000 1994 0 0 619 2612 486817560 486819553 0.000000e+00 3683.0
1 TraesCS3B01G302800 chr3B 100.000 361 0 0 1 361 486816942 486817302 0.000000e+00 667.0
2 TraesCS3B01G302800 chr3A 92.012 1978 92 20 653 2609 494045154 494047086 0.000000e+00 2717.0
3 TraesCS3B01G302800 chr3A 91.379 174 15 0 2163 2336 744921119 744920946 3.360000e-59 239.0
4 TraesCS3B01G302800 chr3A 80.645 93 16 2 2336 2427 417920436 417920345 1.300000e-08 71.3
5 TraesCS3B01G302800 chr3D 91.291 1309 58 18 880 2172 372632513 372633781 0.000000e+00 1735.0
6 TraesCS3B01G302800 chr3D 94.298 228 10 3 653 878 372632258 372632484 1.920000e-91 346.0
7 TraesCS3B01G302800 chr3D 87.709 179 17 4 185 361 452374806 452374981 1.230000e-48 204.0
8 TraesCS3B01G302800 chr7B 91.038 212 15 4 2343 2554 716287171 716286964 1.530000e-72 283.0
9 TraesCS3B01G302800 chr7B 92.727 165 12 0 2171 2335 619322496 619322660 3.360000e-59 239.0
10 TraesCS3B01G302800 chr7B 87.692 65 7 1 2341 2404 693047404 693047340 1.000000e-09 75.0
11 TraesCS3B01G302800 chr2B 84.982 273 25 8 2340 2609 462292053 462292312 1.990000e-66 263.0
12 TraesCS3B01G302800 chr2B 81.503 173 28 4 192 361 510346175 510346346 3.510000e-29 139.0
13 TraesCS3B01G302800 chr2B 77.056 231 42 11 2340 2565 183263393 183263617 3.530000e-24 122.0
14 TraesCS3B01G302800 chr2B 86.486 74 9 1 2337 2409 108689074 108689001 2.150000e-11 80.5
15 TraesCS3B01G302800 chr7D 85.317 252 32 4 2339 2588 46129882 46130130 3.340000e-64 255.0
16 TraesCS3B01G302800 chr7D 92.727 165 12 0 2171 2335 611236443 611236607 3.360000e-59 239.0
17 TraesCS3B01G302800 chr7D 90.857 175 16 0 2171 2345 102575541 102575715 4.350000e-58 235.0
18 TraesCS3B01G302800 chr7A 91.489 188 13 3 6 190 115739332 115739519 3.340000e-64 255.0
19 TraesCS3B01G302800 chr5D 89.796 196 16 3 1 192 94050736 94050931 5.580000e-62 248.0
20 TraesCS3B01G302800 chr5D 92.727 165 12 0 2171 2335 464930195 464930359 3.360000e-59 239.0
21 TraesCS3B01G302800 chr5D 89.385 179 15 2 185 361 94050955 94051131 3.380000e-54 222.0
22 TraesCS3B01G302800 chrUn 92.727 165 12 0 2171 2335 358753915 358754079 3.360000e-59 239.0
23 TraesCS3B01G302800 chr4D 88.119 202 23 1 2406 2606 353046605 353046806 3.360000e-59 239.0
24 TraesCS3B01G302800 chr4D 90.503 179 13 2 185 361 233150827 233151003 1.560000e-57 233.0
25 TraesCS3B01G302800 chr4D 81.818 242 38 6 2341 2580 478036106 478035869 5.700000e-47 198.0
26 TraesCS3B01G302800 chr4D 88.660 97 7 3 2515 2610 478233558 478233651 5.910000e-22 115.0
27 TraesCS3B01G302800 chr2D 91.329 173 15 0 2171 2343 580013767 580013939 1.210000e-58 237.0
28 TraesCS3B01G302800 chr2D 89.503 181 17 2 2156 2335 89441267 89441446 7.270000e-56 228.0
29 TraesCS3B01G302800 chr2D 87.582 153 17 2 2461 2612 33564453 33564302 2.670000e-40 176.0
30 TraesCS3B01G302800 chr6D 88.136 177 15 4 191 361 82097107 82096931 3.410000e-49 206.0
31 TraesCS3B01G302800 chr6D 82.184 174 20 6 199 361 447913392 447913565 3.510000e-29 139.0
32 TraesCS3B01G302800 chr6D 86.486 74 5 4 2343 2413 413509893 413509822 2.790000e-10 76.8
33 TraesCS3B01G302800 chr5A 88.889 153 13 2 197 347 374914990 374914840 4.440000e-43 185.0
34 TraesCS3B01G302800 chr1D 82.759 174 19 5 199 361 490039042 490039215 7.530000e-31 145.0
35 TraesCS3B01G302800 chr4A 91.346 104 7 1 260 361 709690852 709690955 9.750000e-30 141.0
36 TraesCS3B01G302800 chr4B 74.909 275 51 9 2341 2612 80958189 80957930 2.750000e-20 110.0


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 TraesCS3B01G302800 chr3B 486816942 486819553 2611 False 2175.0 3683 100.0000 1 2612 2 chr3B.!!$F1 2611
1 TraesCS3B01G302800 chr3A 494045154 494047086 1932 False 2717.0 2717 92.0120 653 2609 1 chr3A.!!$F1 1956
2 TraesCS3B01G302800 chr3D 372632258 372633781 1523 False 1040.5 1735 92.7945 653 2172 2 chr3D.!!$F2 1519

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
273 274 0.525761 TAAAAAGCGCATGTGAGGGC 59.474 50.0 11.47 0.00 46.61 5.19 F
651 652 0.676782 GGGTGTACCGAAGCATTGCT 60.677 55.0 5.03 5.03 37.42 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1226 0.248702 GAGGAGGACGAGCGAATCAC 60.249 60.0 0.00 0.0 0.0 3.06 R
2451 2514 0.251787 AAAGGACATCTGGGGCCAAC 60.252 55.0 4.39 0.0 0.0 3.77 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
71 72 8.926715 ATGAACAAAACAGGAAAACTAGAAAC 57.073 30.769 0.00 0.00 0.00 2.78
72 73 7.317390 TGAACAAAACAGGAAAACTAGAAACC 58.683 34.615 0.00 0.00 0.00 3.27
73 74 6.216801 ACAAAACAGGAAAACTAGAAACCC 57.783 37.500 0.00 0.00 0.00 4.11
74 75 5.955959 ACAAAACAGGAAAACTAGAAACCCT 59.044 36.000 0.00 0.00 0.00 4.34
75 76 7.120716 ACAAAACAGGAAAACTAGAAACCCTA 58.879 34.615 0.00 0.00 0.00 3.53
76 77 7.616542 ACAAAACAGGAAAACTAGAAACCCTAA 59.383 33.333 0.00 0.00 0.00 2.69
77 78 7.578310 AAACAGGAAAACTAGAAACCCTAAC 57.422 36.000 0.00 0.00 0.00 2.34
78 79 6.511017 ACAGGAAAACTAGAAACCCTAACT 57.489 37.500 0.00 0.00 0.00 2.24
79 80 7.622502 ACAGGAAAACTAGAAACCCTAACTA 57.377 36.000 0.00 0.00 0.00 2.24
80 81 8.037723 ACAGGAAAACTAGAAACCCTAACTAA 57.962 34.615 0.00 0.00 0.00 2.24
81 82 8.496916 ACAGGAAAACTAGAAACCCTAACTAAA 58.503 33.333 0.00 0.00 0.00 1.85
82 83 9.346005 CAGGAAAACTAGAAACCCTAACTAAAA 57.654 33.333 0.00 0.00 0.00 1.52
83 84 9.347240 AGGAAAACTAGAAACCCTAACTAAAAC 57.653 33.333 0.00 0.00 0.00 2.43
84 85 8.571336 GGAAAACTAGAAACCCTAACTAAAACC 58.429 37.037 0.00 0.00 0.00 3.27
85 86 7.734924 AAACTAGAAACCCTAACTAAAACCG 57.265 36.000 0.00 0.00 0.00 4.44
86 87 6.425210 ACTAGAAACCCTAACTAAAACCGT 57.575 37.500 0.00 0.00 0.00 4.83
87 88 6.226052 ACTAGAAACCCTAACTAAAACCGTG 58.774 40.000 0.00 0.00 0.00 4.94
88 89 3.817084 AGAAACCCTAACTAAAACCGTGC 59.183 43.478 0.00 0.00 0.00 5.34
89 90 2.934886 ACCCTAACTAAAACCGTGCA 57.065 45.000 0.00 0.00 0.00 4.57
90 91 3.211718 ACCCTAACTAAAACCGTGCAA 57.788 42.857 0.00 0.00 0.00 4.08
91 92 3.553904 ACCCTAACTAAAACCGTGCAAA 58.446 40.909 0.00 0.00 0.00 3.68
92 93 3.952967 ACCCTAACTAAAACCGTGCAAAA 59.047 39.130 0.00 0.00 0.00 2.44
93 94 4.401837 ACCCTAACTAAAACCGTGCAAAAA 59.598 37.500 0.00 0.00 0.00 1.94
117 118 9.936759 AAAAAGAAACATAAACCAAAGAGTGAA 57.063 25.926 0.00 0.00 0.00 3.18
118 119 9.586435 AAAAGAAACATAAACCAAAGAGTGAAG 57.414 29.630 0.00 0.00 0.00 3.02
119 120 7.277174 AGAAACATAAACCAAAGAGTGAAGG 57.723 36.000 0.00 0.00 0.00 3.46
120 121 6.833933 AGAAACATAAACCAAAGAGTGAAGGT 59.166 34.615 0.00 0.00 35.47 3.50
121 122 6.391227 AACATAAACCAAAGAGTGAAGGTG 57.609 37.500 0.00 0.00 33.93 4.00
122 123 4.278419 ACATAAACCAAAGAGTGAAGGTGC 59.722 41.667 0.00 0.00 33.93 5.01
123 124 2.736670 AACCAAAGAGTGAAGGTGCT 57.263 45.000 0.00 0.00 33.93 4.40
124 125 2.736670 ACCAAAGAGTGAAGGTGCTT 57.263 45.000 0.00 0.00 32.04 3.91
125 126 3.018423 ACCAAAGAGTGAAGGTGCTTT 57.982 42.857 0.00 0.00 32.04 3.51
126 127 3.365472 ACCAAAGAGTGAAGGTGCTTTT 58.635 40.909 0.00 0.00 32.04 2.27
127 128 3.769300 ACCAAAGAGTGAAGGTGCTTTTT 59.231 39.130 0.00 0.00 32.04 1.94
148 149 4.553330 TTTTCCTTGGCGTTATCTCTCT 57.447 40.909 0.00 0.00 0.00 3.10
149 150 5.670792 TTTTCCTTGGCGTTATCTCTCTA 57.329 39.130 0.00 0.00 0.00 2.43
150 151 4.920640 TTCCTTGGCGTTATCTCTCTAG 57.079 45.455 0.00 0.00 0.00 2.43
151 152 4.166246 TCCTTGGCGTTATCTCTCTAGA 57.834 45.455 0.00 0.00 35.80 2.43
152 153 4.533815 TCCTTGGCGTTATCTCTCTAGAA 58.466 43.478 0.00 0.00 34.73 2.10
153 154 4.338682 TCCTTGGCGTTATCTCTCTAGAAC 59.661 45.833 0.00 0.00 34.73 3.01
154 155 4.098044 CCTTGGCGTTATCTCTCTAGAACA 59.902 45.833 0.00 0.00 34.73 3.18
155 156 5.394224 CCTTGGCGTTATCTCTCTAGAACAA 60.394 44.000 0.00 0.00 34.73 2.83
156 157 5.250235 TGGCGTTATCTCTCTAGAACAAG 57.750 43.478 0.00 0.00 34.73 3.16
157 158 4.948004 TGGCGTTATCTCTCTAGAACAAGA 59.052 41.667 0.00 0.00 34.73 3.02
158 159 5.417894 TGGCGTTATCTCTCTAGAACAAGAA 59.582 40.000 0.00 0.00 34.73 2.52
159 160 5.974751 GGCGTTATCTCTCTAGAACAAGAAG 59.025 44.000 0.00 0.00 34.73 2.85
160 161 6.183360 GGCGTTATCTCTCTAGAACAAGAAGA 60.183 42.308 0.00 0.00 34.73 2.87
161 162 7.251994 GCGTTATCTCTCTAGAACAAGAAGAA 58.748 38.462 0.00 0.00 34.73 2.52
162 163 7.431084 GCGTTATCTCTCTAGAACAAGAAGAAG 59.569 40.741 0.00 0.00 34.73 2.85
163 164 8.670135 CGTTATCTCTCTAGAACAAGAAGAAGA 58.330 37.037 0.00 0.00 34.73 2.87
167 168 9.705290 ATCTCTCTAGAACAAGAAGAAGAAAAC 57.295 33.333 0.00 0.00 34.73 2.43
168 169 8.696374 TCTCTCTAGAACAAGAAGAAGAAAACA 58.304 33.333 0.00 0.00 0.00 2.83
169 170 9.487790 CTCTCTAGAACAAGAAGAAGAAAACAT 57.512 33.333 0.00 0.00 0.00 2.71
170 171 9.265901 TCTCTAGAACAAGAAGAAGAAAACATG 57.734 33.333 0.00 0.00 0.00 3.21
171 172 7.865707 TCTAGAACAAGAAGAAGAAAACATGC 58.134 34.615 0.00 0.00 0.00 4.06
172 173 5.514279 AGAACAAGAAGAAGAAAACATGCG 58.486 37.500 0.00 0.00 0.00 4.73
173 174 4.900635 ACAAGAAGAAGAAAACATGCGT 57.099 36.364 0.00 0.00 0.00 5.24
174 175 6.260050 AGAACAAGAAGAAGAAAACATGCGTA 59.740 34.615 0.00 0.00 0.00 4.42
175 176 5.990408 ACAAGAAGAAGAAAACATGCGTAG 58.010 37.500 0.00 0.00 0.00 3.51
176 177 5.527582 ACAAGAAGAAGAAAACATGCGTAGT 59.472 36.000 0.00 0.00 0.00 2.73
177 178 6.704493 ACAAGAAGAAGAAAACATGCGTAGTA 59.296 34.615 0.00 0.00 0.00 1.82
178 179 6.952935 AGAAGAAGAAAACATGCGTAGTAG 57.047 37.500 0.00 0.00 0.00 2.57
179 180 6.456501 AGAAGAAGAAAACATGCGTAGTAGT 58.543 36.000 0.00 0.00 0.00 2.73
180 181 7.600065 AGAAGAAGAAAACATGCGTAGTAGTA 58.400 34.615 0.00 0.00 0.00 1.82
181 182 8.086522 AGAAGAAGAAAACATGCGTAGTAGTAA 58.913 33.333 0.00 0.00 0.00 2.24
182 183 8.597662 AAGAAGAAAACATGCGTAGTAGTAAA 57.402 30.769 0.00 0.00 0.00 2.01
183 184 8.597662 AGAAGAAAACATGCGTAGTAGTAAAA 57.402 30.769 0.00 0.00 0.00 1.52
184 185 9.216117 AGAAGAAAACATGCGTAGTAGTAAAAT 57.784 29.630 0.00 0.00 0.00 1.82
185 186 9.474249 GAAGAAAACATGCGTAGTAGTAAAATC 57.526 33.333 0.00 0.00 0.00 2.17
186 187 8.542497 AGAAAACATGCGTAGTAGTAAAATCA 57.458 30.769 0.00 0.00 0.00 2.57
187 188 8.656849 AGAAAACATGCGTAGTAGTAAAATCAG 58.343 33.333 0.00 0.00 0.00 2.90
188 189 8.542497 AAAACATGCGTAGTAGTAAAATCAGA 57.458 30.769 0.00 0.00 0.00 3.27
189 190 8.718102 AAACATGCGTAGTAGTAAAATCAGAT 57.282 30.769 0.00 0.00 0.00 2.90
190 191 7.700322 ACATGCGTAGTAGTAAAATCAGATG 57.300 36.000 0.00 0.00 0.00 2.90
191 192 7.265673 ACATGCGTAGTAGTAAAATCAGATGT 58.734 34.615 0.00 0.00 0.00 3.06
192 193 8.410912 ACATGCGTAGTAGTAAAATCAGATGTA 58.589 33.333 0.00 0.00 0.00 2.29
193 194 8.906693 CATGCGTAGTAGTAAAATCAGATGTAG 58.093 37.037 0.00 0.00 0.00 2.74
194 195 7.993101 TGCGTAGTAGTAAAATCAGATGTAGT 58.007 34.615 0.00 0.00 0.00 2.73
195 196 8.464404 TGCGTAGTAGTAAAATCAGATGTAGTT 58.536 33.333 0.00 0.00 0.00 2.24
196 197 8.956014 GCGTAGTAGTAAAATCAGATGTAGTTC 58.044 37.037 0.00 0.00 0.00 3.01
203 204 8.043710 AGTAAAATCAGATGTAGTTCTTGAGGG 58.956 37.037 0.00 0.00 0.00 4.30
204 205 3.895232 TCAGATGTAGTTCTTGAGGGC 57.105 47.619 0.00 0.00 0.00 5.19
205 206 3.445008 TCAGATGTAGTTCTTGAGGGCT 58.555 45.455 0.00 0.00 0.00 5.19
206 207 3.196469 TCAGATGTAGTTCTTGAGGGCTG 59.804 47.826 0.00 0.00 0.00 4.85
207 208 3.055530 CAGATGTAGTTCTTGAGGGCTGT 60.056 47.826 0.00 0.00 0.00 4.40
208 209 4.160439 CAGATGTAGTTCTTGAGGGCTGTA 59.840 45.833 0.00 0.00 0.00 2.74
209 210 4.404073 AGATGTAGTTCTTGAGGGCTGTAG 59.596 45.833 0.00 0.00 0.00 2.74
210 211 3.507411 TGTAGTTCTTGAGGGCTGTAGT 58.493 45.455 0.00 0.00 0.00 2.73
211 212 3.901844 TGTAGTTCTTGAGGGCTGTAGTT 59.098 43.478 0.00 0.00 0.00 2.24
212 213 3.686916 AGTTCTTGAGGGCTGTAGTTC 57.313 47.619 0.00 0.00 0.00 3.01
213 214 2.028930 AGTTCTTGAGGGCTGTAGTTCG 60.029 50.000 0.00 0.00 0.00 3.95
214 215 1.919240 TCTTGAGGGCTGTAGTTCGA 58.081 50.000 0.00 0.00 0.00 3.71
215 216 2.244695 TCTTGAGGGCTGTAGTTCGAA 58.755 47.619 0.00 0.00 0.00 3.71
216 217 2.832129 TCTTGAGGGCTGTAGTTCGAAT 59.168 45.455 0.00 0.00 0.00 3.34
217 218 2.961526 TGAGGGCTGTAGTTCGAATC 57.038 50.000 0.00 0.00 0.00 2.52
218 219 2.457598 TGAGGGCTGTAGTTCGAATCT 58.542 47.619 0.00 3.29 0.00 2.40
219 220 2.166459 TGAGGGCTGTAGTTCGAATCTG 59.834 50.000 0.00 1.23 0.00 2.90
220 221 1.482593 AGGGCTGTAGTTCGAATCTGG 59.517 52.381 0.00 0.00 0.00 3.86
221 222 1.480954 GGGCTGTAGTTCGAATCTGGA 59.519 52.381 0.00 0.00 0.00 3.86
222 223 2.093658 GGGCTGTAGTTCGAATCTGGAA 60.094 50.000 0.00 0.00 0.00 3.53
223 224 3.190874 GGCTGTAGTTCGAATCTGGAAG 58.809 50.000 0.00 0.00 0.00 3.46
270 271 8.667987 TTATAAAACTAAAAAGCGCATGTGAG 57.332 30.769 11.47 0.00 0.00 3.51
271 272 3.559238 AACTAAAAAGCGCATGTGAGG 57.441 42.857 11.47 0.00 0.00 3.86
272 273 1.812571 ACTAAAAAGCGCATGTGAGGG 59.187 47.619 11.47 0.00 0.00 4.30
273 274 0.525761 TAAAAAGCGCATGTGAGGGC 59.474 50.000 11.47 0.00 46.61 5.19
277 278 3.058160 GCGCATGTGAGGGCTGTT 61.058 61.111 11.26 0.00 43.34 3.16
278 279 3.044059 GCGCATGTGAGGGCTGTTC 62.044 63.158 11.26 0.00 43.34 3.18
279 280 2.743752 CGCATGTGAGGGCTGTTCG 61.744 63.158 0.00 0.00 0.00 3.95
280 281 3.044059 GCATGTGAGGGCTGTTCGC 62.044 63.158 0.00 0.00 38.13 4.70
289 290 4.840168 GCTGTTCGCCGGGTATTA 57.160 55.556 2.18 0.00 0.00 0.98
290 291 3.300711 GCTGTTCGCCGGGTATTAT 57.699 52.632 2.18 0.00 0.00 1.28
291 292 2.443887 GCTGTTCGCCGGGTATTATA 57.556 50.000 2.18 0.00 0.00 0.98
292 293 2.064014 GCTGTTCGCCGGGTATTATAC 58.936 52.381 2.18 0.00 0.00 1.47
293 294 2.322161 CTGTTCGCCGGGTATTATACG 58.678 52.381 2.18 0.00 0.00 3.06
294 295 1.952990 TGTTCGCCGGGTATTATACGA 59.047 47.619 2.18 0.00 0.00 3.43
295 296 2.360483 TGTTCGCCGGGTATTATACGAA 59.640 45.455 2.18 4.18 37.21 3.85
296 297 2.704725 TCGCCGGGTATTATACGAAC 57.295 50.000 2.18 0.00 0.00 3.95
297 298 1.269448 TCGCCGGGTATTATACGAACC 59.731 52.381 2.18 0.00 0.00 3.62
298 299 1.270550 CGCCGGGTATTATACGAACCT 59.729 52.381 2.18 0.00 33.59 3.50
299 300 2.487762 CGCCGGGTATTATACGAACCTA 59.512 50.000 2.18 0.00 33.59 3.08
300 301 3.670627 CGCCGGGTATTATACGAACCTAC 60.671 52.174 2.18 0.00 33.59 3.18
301 302 3.255642 GCCGGGTATTATACGAACCTACA 59.744 47.826 2.18 0.00 33.59 2.74
302 303 4.616835 GCCGGGTATTATACGAACCTACAG 60.617 50.000 2.18 0.00 33.59 2.74
303 304 4.520492 CCGGGTATTATACGAACCTACAGT 59.480 45.833 0.00 0.00 33.59 3.55
304 305 5.455392 CGGGTATTATACGAACCTACAGTG 58.545 45.833 0.00 0.00 33.59 3.66
305 306 5.009010 CGGGTATTATACGAACCTACAGTGT 59.991 44.000 0.00 0.00 33.59 3.55
306 307 6.204688 CGGGTATTATACGAACCTACAGTGTA 59.795 42.308 2.36 2.36 33.59 2.90
307 308 7.094634 CGGGTATTATACGAACCTACAGTGTAT 60.095 40.741 2.82 0.00 33.59 2.29
308 309 9.231297 GGGTATTATACGAACCTACAGTGTATA 57.769 37.037 2.82 0.00 33.59 1.47
323 324 8.272545 TACAGTGTATATGTAGAAACGTGAGT 57.727 34.615 0.00 0.00 37.84 3.41
324 325 9.382275 TACAGTGTATATGTAGAAACGTGAGTA 57.618 33.333 0.00 0.00 36.12 2.59
358 359 9.590451 TGAAAAGTTCATACTACCCTTTATACG 57.410 33.333 0.00 0.00 34.08 3.06
359 360 9.591792 GAAAAGTTCATACTACCCTTTATACGT 57.408 33.333 0.00 0.00 33.17 3.57
360 361 9.948964 AAAAGTTCATACTACCCTTTATACGTT 57.051 29.630 0.00 0.00 33.17 3.99
638 639 3.702623 GGAGGGGGAGGGGGTGTA 61.703 72.222 0.00 0.00 0.00 2.90
639 640 2.366569 GAGGGGGAGGGGGTGTAC 60.367 72.222 0.00 0.00 0.00 2.90
640 641 4.034636 AGGGGGAGGGGGTGTACC 62.035 72.222 0.00 0.00 39.11 3.34
642 643 4.403502 GGGGAGGGGGTGTACCGA 62.404 72.222 0.00 0.00 41.60 4.69
643 644 2.284847 GGGAGGGGGTGTACCGAA 60.285 66.667 0.00 0.00 41.60 4.30
644 645 2.364780 GGGAGGGGGTGTACCGAAG 61.365 68.421 0.00 0.00 41.60 3.79
645 646 2.582978 GAGGGGGTGTACCGAAGC 59.417 66.667 0.00 0.00 41.60 3.86
646 647 2.203877 AGGGGGTGTACCGAAGCA 60.204 61.111 0.00 0.00 41.60 3.91
647 648 1.615424 AGGGGGTGTACCGAAGCAT 60.615 57.895 0.00 0.00 41.60 3.79
648 649 1.205460 AGGGGGTGTACCGAAGCATT 61.205 55.000 0.00 0.00 41.60 3.56
649 650 1.029947 GGGGGTGTACCGAAGCATTG 61.030 60.000 0.00 0.00 41.60 2.82
650 651 1.654023 GGGGTGTACCGAAGCATTGC 61.654 60.000 0.00 0.00 41.60 3.56
651 652 0.676782 GGGTGTACCGAAGCATTGCT 60.677 55.000 5.03 5.03 37.42 3.91
663 664 3.738830 AGCATTGCTCTTCTTTTTGCA 57.261 38.095 5.03 0.00 30.62 4.08
671 672 4.036734 TGCTCTTCTTTTTGCAGGTGTTAG 59.963 41.667 0.00 0.00 0.00 2.34
747 748 4.774124 TGCACACCTACTACTACGACTAT 58.226 43.478 0.00 0.00 0.00 2.12
749 750 5.065602 TGCACACCTACTACTACGACTATTG 59.934 44.000 0.00 0.00 0.00 1.90
750 751 5.065731 GCACACCTACTACTACGACTATTGT 59.934 44.000 0.00 0.00 0.00 2.71
751 752 6.258727 GCACACCTACTACTACGACTATTGTA 59.741 42.308 0.00 0.00 0.00 2.41
752 753 7.625553 CACACCTACTACTACGACTATTGTAC 58.374 42.308 0.00 0.00 0.00 2.90
753 754 7.493971 CACACCTACTACTACGACTATTGTACT 59.506 40.741 0.00 0.00 0.00 2.73
754 755 7.493971 ACACCTACTACTACGACTATTGTACTG 59.506 40.741 0.00 0.00 0.00 2.74
755 756 7.708322 CACCTACTACTACGACTATTGTACTGA 59.292 40.741 0.00 0.00 0.00 3.41
756 757 7.708752 ACCTACTACTACGACTATTGTACTGAC 59.291 40.741 0.00 0.00 0.00 3.51
828 830 2.476241 GCATAAGTTGGTTTTGCACTGC 59.524 45.455 0.00 0.00 41.38 4.40
855 857 3.391965 TGATTGTTGCAATTGACCAAGC 58.608 40.909 10.34 10.92 0.00 4.01
865 867 2.111999 TTGACCAAGCCCAGAGTCCG 62.112 60.000 0.00 0.00 0.00 4.79
890 919 3.279434 CACCAAGGGAGTATAAAGCCAC 58.721 50.000 0.00 0.00 0.00 5.01
940 969 1.270785 TGCATCCAGGCACATATACCG 60.271 52.381 0.00 0.00 39.25 4.02
1014 1043 1.396301 GCGAAGATGAAGGTTCTGCAG 59.604 52.381 7.63 7.63 0.00 4.41
1028 1057 3.719268 TCTGCAGGCTCTTAATTTCCA 57.281 42.857 15.13 0.00 0.00 3.53
1065 1094 6.464222 TGTTTCTGAGATTTTATCGGTCACT 58.536 36.000 0.00 0.00 0.00 3.41
1066 1095 6.590292 TGTTTCTGAGATTTTATCGGTCACTC 59.410 38.462 0.00 0.00 0.00 3.51
1067 1096 5.914898 TCTGAGATTTTATCGGTCACTCA 57.085 39.130 0.00 0.00 0.00 3.41
1068 1097 5.651530 TCTGAGATTTTATCGGTCACTCAC 58.348 41.667 0.00 0.00 0.00 3.51
1069 1098 5.185056 TCTGAGATTTTATCGGTCACTCACA 59.815 40.000 0.00 0.00 0.00 3.58
1070 1099 5.410924 TGAGATTTTATCGGTCACTCACAG 58.589 41.667 0.00 0.00 0.00 3.66
1177 1206 3.456644 TGTCCAAGGTCAAAGGTCTGTAA 59.543 43.478 0.00 0.00 0.00 2.41
1178 1207 4.104102 TGTCCAAGGTCAAAGGTCTGTAAT 59.896 41.667 0.00 0.00 0.00 1.89
1179 1208 5.308497 TGTCCAAGGTCAAAGGTCTGTAATA 59.692 40.000 0.00 0.00 0.00 0.98
1183 1215 7.037586 TCCAAGGTCAAAGGTCTGTAATATTCT 60.038 37.037 0.00 0.00 0.00 2.40
1192 1224 8.429237 AAGGTCTGTAATATTCTCTCTATGGG 57.571 38.462 0.00 0.00 0.00 4.00
1194 1226 6.326375 GTCTGTAATATTCTCTCTATGGGCG 58.674 44.000 0.00 0.00 0.00 6.13
1210 1242 3.984241 CGTGATTCGCTCGTCCTC 58.016 61.111 0.00 0.00 0.00 3.71
1228 1260 5.048224 CGTCCTCCTCTGTAACTTACTTGAA 60.048 44.000 0.71 0.00 0.00 2.69
1229 1261 6.391537 GTCCTCCTCTGTAACTTACTTGAAG 58.608 44.000 0.71 0.00 41.37 3.02
1621 1680 0.879400 CATCATGTGAGCGAGAGGGC 60.879 60.000 0.00 0.00 0.00 5.19
1769 1831 3.284617 TCAGAGCTTGCATGCACATTAT 58.715 40.909 22.58 4.71 34.99 1.28
1850 1912 6.869388 GGAGACCTTCTTTTACTACTCACAAG 59.131 42.308 0.00 0.00 0.00 3.16
1851 1913 7.362802 AGACCTTCTTTTACTACTCACAAGT 57.637 36.000 0.00 0.00 39.66 3.16
1852 1914 7.435305 AGACCTTCTTTTACTACTCACAAGTC 58.565 38.462 0.00 0.00 36.92 3.01
1853 1915 7.069578 AGACCTTCTTTTACTACTCACAAGTCA 59.930 37.037 0.00 0.00 36.92 3.41
1854 1916 6.985059 ACCTTCTTTTACTACTCACAAGTCAC 59.015 38.462 0.00 0.00 36.92 3.67
1855 1917 6.984474 CCTTCTTTTACTACTCACAAGTCACA 59.016 38.462 0.00 0.00 36.92 3.58
1856 1918 7.494625 CCTTCTTTTACTACTCACAAGTCACAA 59.505 37.037 0.00 0.00 36.92 3.33
1898 1960 3.947910 AATGAGCTGTTTGGTTCATGG 57.052 42.857 0.00 0.00 37.27 3.66
1971 2033 9.988350 CACCTAATAATGTGACAAGTTGATTAC 57.012 33.333 10.54 5.98 34.37 1.89
2024 2086 6.482973 CAGTTTATTGCAACAATTTGTCCCTT 59.517 34.615 0.00 0.00 34.90 3.95
2051 2113 2.032178 GCTGGAACTTTCATATGCCGTC 59.968 50.000 0.00 0.00 0.00 4.79
2176 2238 5.390387 AGAACACTCTTGAGACTTACTCCT 58.610 41.667 4.49 0.00 44.34 3.69
2218 2280 6.038603 TGTCTTTCCAGAGATTTCAACAAGTG 59.961 38.462 0.00 0.00 0.00 3.16
2227 2289 9.376075 CAGAGATTTCAACAAGTGACTACATAT 57.624 33.333 0.00 0.00 35.39 1.78
2229 2291 7.978982 AGATTTCAACAAGTGACTACATATGC 58.021 34.615 1.58 0.00 35.39 3.14
2231 2293 6.726258 TTCAACAAGTGACTACATATGCAG 57.274 37.500 1.58 1.32 35.39 4.41
2249 2311 6.710597 ATGCAGCAAAATGAGTGAATCTAT 57.289 33.333 0.00 0.00 0.00 1.98
2250 2312 7.812690 ATGCAGCAAAATGAGTGAATCTATA 57.187 32.000 0.00 0.00 0.00 1.31
2253 2315 7.337689 TGCAGCAAAATGAGTGAATCTATACTT 59.662 33.333 0.00 0.00 0.00 2.24
2328 2390 6.927294 AAAGACAAATATTTAGGAGCGGAG 57.073 37.500 0.00 0.00 0.00 4.63
2344 2406 1.143277 CGGAGGGAGTAGGAGCTAAGA 59.857 57.143 0.00 0.00 0.00 2.10
2388 2451 0.249911 AGGGACTGAAATATCGCCGC 60.250 55.000 0.00 0.00 37.18 6.53
2425 2488 2.204865 CTATTTCCACCGTGGGGGCA 62.205 60.000 17.76 0.00 40.62 5.36
2463 2526 2.677228 CCGAAGTTGGCCCCAGAT 59.323 61.111 0.00 0.00 0.00 2.90
2465 2528 1.002134 CGAAGTTGGCCCCAGATGT 60.002 57.895 0.00 0.00 0.00 3.06
2467 2530 0.681243 GAAGTTGGCCCCAGATGTCC 60.681 60.000 0.00 0.00 0.00 4.02
2496 2559 8.614469 TTTGAAATCCAAATTCGGCTAAATTT 57.386 26.923 0.00 0.00 39.65 1.82
2497 2560 8.614469 TTGAAATCCAAATTCGGCTAAATTTT 57.386 26.923 0.00 0.00 36.86 1.82
2498 2561 8.027440 TGAAATCCAAATTCGGCTAAATTTTG 57.973 30.769 0.00 0.00 36.86 2.44
2520 2583 7.545362 TTGTACAAAATGACACAAATTTGGG 57.455 32.000 18.95 18.95 37.15 4.12
2533 2596 3.971245 AATTTGGGCGAAATTTAGGCA 57.029 38.095 22.80 9.29 40.73 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.979537 GGTTTCTAGTTTTCCTGTTTTGTTCAT 59.020 33.333 0.00 0.00 0.00 2.57
47 48 7.317390 GGTTTCTAGTTTTCCTGTTTTGTTCA 58.683 34.615 0.00 0.00 0.00 3.18
48 49 6.755141 GGGTTTCTAGTTTTCCTGTTTTGTTC 59.245 38.462 0.00 0.00 0.00 3.18
49 50 6.439375 AGGGTTTCTAGTTTTCCTGTTTTGTT 59.561 34.615 0.00 0.00 0.00 2.83
50 51 5.955959 AGGGTTTCTAGTTTTCCTGTTTTGT 59.044 36.000 0.00 0.00 0.00 2.83
51 52 6.465439 AGGGTTTCTAGTTTTCCTGTTTTG 57.535 37.500 0.00 0.00 0.00 2.44
52 53 7.837689 AGTTAGGGTTTCTAGTTTTCCTGTTTT 59.162 33.333 0.00 0.00 0.00 2.43
53 54 7.351952 AGTTAGGGTTTCTAGTTTTCCTGTTT 58.648 34.615 0.00 0.00 0.00 2.83
54 55 6.907961 AGTTAGGGTTTCTAGTTTTCCTGTT 58.092 36.000 0.00 0.00 0.00 3.16
55 56 6.511017 AGTTAGGGTTTCTAGTTTTCCTGT 57.489 37.500 0.00 0.00 0.00 4.00
56 57 8.913487 TTTAGTTAGGGTTTCTAGTTTTCCTG 57.087 34.615 0.00 0.00 0.00 3.86
57 58 9.347240 GTTTTAGTTAGGGTTTCTAGTTTTCCT 57.653 33.333 0.00 0.00 0.00 3.36
58 59 8.571336 GGTTTTAGTTAGGGTTTCTAGTTTTCC 58.429 37.037 0.00 0.00 0.00 3.13
59 60 8.285394 CGGTTTTAGTTAGGGTTTCTAGTTTTC 58.715 37.037 0.00 0.00 0.00 2.29
60 61 7.775093 ACGGTTTTAGTTAGGGTTTCTAGTTTT 59.225 33.333 0.00 0.00 0.00 2.43
61 62 7.227314 CACGGTTTTAGTTAGGGTTTCTAGTTT 59.773 37.037 0.00 0.00 0.00 2.66
62 63 6.707608 CACGGTTTTAGTTAGGGTTTCTAGTT 59.292 38.462 0.00 0.00 0.00 2.24
63 64 6.226052 CACGGTTTTAGTTAGGGTTTCTAGT 58.774 40.000 0.00 0.00 0.00 2.57
64 65 5.121298 GCACGGTTTTAGTTAGGGTTTCTAG 59.879 44.000 0.00 0.00 0.00 2.43
65 66 4.996758 GCACGGTTTTAGTTAGGGTTTCTA 59.003 41.667 0.00 0.00 0.00 2.10
66 67 3.817084 GCACGGTTTTAGTTAGGGTTTCT 59.183 43.478 0.00 0.00 0.00 2.52
67 68 3.565063 TGCACGGTTTTAGTTAGGGTTTC 59.435 43.478 0.00 0.00 0.00 2.78
68 69 3.553904 TGCACGGTTTTAGTTAGGGTTT 58.446 40.909 0.00 0.00 0.00 3.27
69 70 3.211718 TGCACGGTTTTAGTTAGGGTT 57.788 42.857 0.00 0.00 0.00 4.11
70 71 2.934886 TGCACGGTTTTAGTTAGGGT 57.065 45.000 0.00 0.00 0.00 4.34
71 72 4.571372 TTTTGCACGGTTTTAGTTAGGG 57.429 40.909 0.00 0.00 0.00 3.53
91 92 9.936759 TTCACTCTTTGGTTTATGTTTCTTTTT 57.063 25.926 0.00 0.00 0.00 1.94
92 93 9.586435 CTTCACTCTTTGGTTTATGTTTCTTTT 57.414 29.630 0.00 0.00 0.00 2.27
93 94 8.197439 CCTTCACTCTTTGGTTTATGTTTCTTT 58.803 33.333 0.00 0.00 0.00 2.52
94 95 7.342026 ACCTTCACTCTTTGGTTTATGTTTCTT 59.658 33.333 0.00 0.00 0.00 2.52
95 96 6.833933 ACCTTCACTCTTTGGTTTATGTTTCT 59.166 34.615 0.00 0.00 0.00 2.52
96 97 6.918022 CACCTTCACTCTTTGGTTTATGTTTC 59.082 38.462 0.00 0.00 0.00 2.78
97 98 6.682861 GCACCTTCACTCTTTGGTTTATGTTT 60.683 38.462 0.00 0.00 0.00 2.83
98 99 5.221244 GCACCTTCACTCTTTGGTTTATGTT 60.221 40.000 0.00 0.00 0.00 2.71
99 100 4.278419 GCACCTTCACTCTTTGGTTTATGT 59.722 41.667 0.00 0.00 0.00 2.29
100 101 4.520492 AGCACCTTCACTCTTTGGTTTATG 59.480 41.667 0.00 0.00 0.00 1.90
101 102 4.729868 AGCACCTTCACTCTTTGGTTTAT 58.270 39.130 0.00 0.00 0.00 1.40
102 103 4.164843 AGCACCTTCACTCTTTGGTTTA 57.835 40.909 0.00 0.00 0.00 2.01
103 104 3.018423 AGCACCTTCACTCTTTGGTTT 57.982 42.857 0.00 0.00 0.00 3.27
104 105 2.736670 AGCACCTTCACTCTTTGGTT 57.263 45.000 0.00 0.00 0.00 3.67
105 106 2.736670 AAGCACCTTCACTCTTTGGT 57.263 45.000 0.00 0.00 0.00 3.67
106 107 4.391405 AAAAAGCACCTTCACTCTTTGG 57.609 40.909 0.00 0.00 0.00 3.28
126 127 4.906618 AGAGAGATAACGCCAAGGAAAAA 58.093 39.130 0.00 0.00 0.00 1.94
127 128 4.553330 AGAGAGATAACGCCAAGGAAAA 57.447 40.909 0.00 0.00 0.00 2.29
128 129 4.954202 TCTAGAGAGATAACGCCAAGGAAA 59.046 41.667 0.00 0.00 0.00 3.13
129 130 4.533815 TCTAGAGAGATAACGCCAAGGAA 58.466 43.478 0.00 0.00 0.00 3.36
130 131 4.166246 TCTAGAGAGATAACGCCAAGGA 57.834 45.455 0.00 0.00 0.00 3.36
131 132 4.098044 TGTTCTAGAGAGATAACGCCAAGG 59.902 45.833 0.00 0.00 0.00 3.61
132 133 5.250235 TGTTCTAGAGAGATAACGCCAAG 57.750 43.478 0.00 0.00 0.00 3.61
133 134 5.417894 TCTTGTTCTAGAGAGATAACGCCAA 59.582 40.000 0.00 0.00 0.00 4.52
134 135 4.948004 TCTTGTTCTAGAGAGATAACGCCA 59.052 41.667 0.00 0.00 0.00 5.69
135 136 5.502153 TCTTGTTCTAGAGAGATAACGCC 57.498 43.478 0.00 0.00 0.00 5.68
136 137 6.787225 TCTTCTTGTTCTAGAGAGATAACGC 58.213 40.000 0.00 0.00 0.00 4.84
137 138 8.670135 TCTTCTTCTTGTTCTAGAGAGATAACG 58.330 37.037 0.00 0.00 0.00 3.18
141 142 9.705290 GTTTTCTTCTTCTTGTTCTAGAGAGAT 57.295 33.333 0.00 0.00 0.00 2.75
142 143 8.696374 TGTTTTCTTCTTCTTGTTCTAGAGAGA 58.304 33.333 0.00 0.00 0.00 3.10
143 144 8.879342 TGTTTTCTTCTTCTTGTTCTAGAGAG 57.121 34.615 0.00 0.00 0.00 3.20
144 145 9.265901 CATGTTTTCTTCTTCTTGTTCTAGAGA 57.734 33.333 0.00 0.00 0.00 3.10
145 146 8.014517 GCATGTTTTCTTCTTCTTGTTCTAGAG 58.985 37.037 0.00 0.00 0.00 2.43
146 147 7.307396 CGCATGTTTTCTTCTTCTTGTTCTAGA 60.307 37.037 0.00 0.00 0.00 2.43
147 148 6.794158 CGCATGTTTTCTTCTTCTTGTTCTAG 59.206 38.462 0.00 0.00 0.00 2.43
148 149 6.260050 ACGCATGTTTTCTTCTTCTTGTTCTA 59.740 34.615 0.00 0.00 0.00 2.10
149 150 5.066505 ACGCATGTTTTCTTCTTCTTGTTCT 59.933 36.000 0.00 0.00 0.00 3.01
150 151 5.273944 ACGCATGTTTTCTTCTTCTTGTTC 58.726 37.500 0.00 0.00 0.00 3.18
151 152 5.248870 ACGCATGTTTTCTTCTTCTTGTT 57.751 34.783 0.00 0.00 0.00 2.83
152 153 4.900635 ACGCATGTTTTCTTCTTCTTGT 57.099 36.364 0.00 0.00 0.00 3.16
153 154 5.990408 ACTACGCATGTTTTCTTCTTCTTG 58.010 37.500 0.00 0.00 0.00 3.02
154 155 6.929606 ACTACTACGCATGTTTTCTTCTTCTT 59.070 34.615 0.00 0.00 0.00 2.52
155 156 6.456501 ACTACTACGCATGTTTTCTTCTTCT 58.543 36.000 0.00 0.00 0.00 2.85
156 157 6.707599 ACTACTACGCATGTTTTCTTCTTC 57.292 37.500 0.00 0.00 0.00 2.87
157 158 8.597662 TTTACTACTACGCATGTTTTCTTCTT 57.402 30.769 0.00 0.00 0.00 2.52
158 159 8.597662 TTTTACTACTACGCATGTTTTCTTCT 57.402 30.769 0.00 0.00 0.00 2.85
159 160 9.474249 GATTTTACTACTACGCATGTTTTCTTC 57.526 33.333 0.00 0.00 0.00 2.87
160 161 8.995220 TGATTTTACTACTACGCATGTTTTCTT 58.005 29.630 0.00 0.00 0.00 2.52
161 162 8.542497 TGATTTTACTACTACGCATGTTTTCT 57.458 30.769 0.00 0.00 0.00 2.52
162 163 8.653338 TCTGATTTTACTACTACGCATGTTTTC 58.347 33.333 0.00 0.00 0.00 2.29
163 164 8.542497 TCTGATTTTACTACTACGCATGTTTT 57.458 30.769 0.00 0.00 0.00 2.43
164 165 8.604035 CATCTGATTTTACTACTACGCATGTTT 58.396 33.333 0.00 0.00 0.00 2.83
165 166 7.764443 ACATCTGATTTTACTACTACGCATGTT 59.236 33.333 0.00 0.00 0.00 2.71
166 167 7.265673 ACATCTGATTTTACTACTACGCATGT 58.734 34.615 0.00 0.00 0.00 3.21
167 168 7.700322 ACATCTGATTTTACTACTACGCATG 57.300 36.000 0.00 0.00 0.00 4.06
168 169 8.630917 ACTACATCTGATTTTACTACTACGCAT 58.369 33.333 0.00 0.00 0.00 4.73
169 170 7.993101 ACTACATCTGATTTTACTACTACGCA 58.007 34.615 0.00 0.00 0.00 5.24
170 171 8.853469 AACTACATCTGATTTTACTACTACGC 57.147 34.615 0.00 0.00 0.00 4.42
177 178 8.043710 CCCTCAAGAACTACATCTGATTTTACT 58.956 37.037 0.00 0.00 0.00 2.24
178 179 7.201652 GCCCTCAAGAACTACATCTGATTTTAC 60.202 40.741 0.00 0.00 0.00 2.01
179 180 6.823689 GCCCTCAAGAACTACATCTGATTTTA 59.176 38.462 0.00 0.00 0.00 1.52
180 181 5.649831 GCCCTCAAGAACTACATCTGATTTT 59.350 40.000 0.00 0.00 0.00 1.82
181 182 5.045286 AGCCCTCAAGAACTACATCTGATTT 60.045 40.000 0.00 0.00 0.00 2.17
182 183 4.472833 AGCCCTCAAGAACTACATCTGATT 59.527 41.667 0.00 0.00 0.00 2.57
183 184 4.036518 AGCCCTCAAGAACTACATCTGAT 58.963 43.478 0.00 0.00 0.00 2.90
184 185 3.196469 CAGCCCTCAAGAACTACATCTGA 59.804 47.826 0.00 0.00 0.00 3.27
185 186 3.055530 ACAGCCCTCAAGAACTACATCTG 60.056 47.826 0.00 0.00 0.00 2.90
186 187 3.177228 ACAGCCCTCAAGAACTACATCT 58.823 45.455 0.00 0.00 0.00 2.90
187 188 3.618690 ACAGCCCTCAAGAACTACATC 57.381 47.619 0.00 0.00 0.00 3.06
188 189 4.097418 ACTACAGCCCTCAAGAACTACAT 58.903 43.478 0.00 0.00 0.00 2.29
189 190 3.507411 ACTACAGCCCTCAAGAACTACA 58.493 45.455 0.00 0.00 0.00 2.74
190 191 4.496360 GAACTACAGCCCTCAAGAACTAC 58.504 47.826 0.00 0.00 0.00 2.73
191 192 3.192844 CGAACTACAGCCCTCAAGAACTA 59.807 47.826 0.00 0.00 0.00 2.24
192 193 2.028930 CGAACTACAGCCCTCAAGAACT 60.029 50.000 0.00 0.00 0.00 3.01
193 194 2.029290 TCGAACTACAGCCCTCAAGAAC 60.029 50.000 0.00 0.00 0.00 3.01
194 195 2.244695 TCGAACTACAGCCCTCAAGAA 58.755 47.619 0.00 0.00 0.00 2.52
195 196 1.919240 TCGAACTACAGCCCTCAAGA 58.081 50.000 0.00 0.00 0.00 3.02
196 197 2.743636 TTCGAACTACAGCCCTCAAG 57.256 50.000 0.00 0.00 0.00 3.02
197 198 2.832129 AGATTCGAACTACAGCCCTCAA 59.168 45.455 0.00 0.00 0.00 3.02
198 199 2.166459 CAGATTCGAACTACAGCCCTCA 59.834 50.000 0.00 0.00 0.00 3.86
199 200 2.482142 CCAGATTCGAACTACAGCCCTC 60.482 54.545 0.00 0.00 0.00 4.30
200 201 1.482593 CCAGATTCGAACTACAGCCCT 59.517 52.381 0.00 0.00 0.00 5.19
201 202 1.480954 TCCAGATTCGAACTACAGCCC 59.519 52.381 0.00 0.00 0.00 5.19
202 203 2.961526 TCCAGATTCGAACTACAGCC 57.038 50.000 0.00 0.00 0.00 4.85
203 204 4.109050 CTCTTCCAGATTCGAACTACAGC 58.891 47.826 0.00 0.00 0.00 4.40
204 205 4.399618 TCCTCTTCCAGATTCGAACTACAG 59.600 45.833 0.00 0.00 0.00 2.74
205 206 4.158025 GTCCTCTTCCAGATTCGAACTACA 59.842 45.833 0.00 0.00 0.00 2.74
206 207 4.158025 TGTCCTCTTCCAGATTCGAACTAC 59.842 45.833 0.00 0.00 0.00 2.73
207 208 4.341487 TGTCCTCTTCCAGATTCGAACTA 58.659 43.478 0.00 0.00 0.00 2.24
208 209 3.165875 TGTCCTCTTCCAGATTCGAACT 58.834 45.455 0.00 0.00 0.00 3.01
209 210 3.594603 TGTCCTCTTCCAGATTCGAAC 57.405 47.619 0.00 0.00 0.00 3.95
210 211 4.467795 AGAATGTCCTCTTCCAGATTCGAA 59.532 41.667 0.00 0.00 0.00 3.71
211 212 4.026744 AGAATGTCCTCTTCCAGATTCGA 58.973 43.478 0.00 0.00 0.00 3.71
212 213 4.399004 AGAATGTCCTCTTCCAGATTCG 57.601 45.455 0.00 0.00 0.00 3.34
213 214 7.459795 AAAAAGAATGTCCTCTTCCAGATTC 57.540 36.000 0.00 0.00 34.49 2.52
244 245 9.289303 CTCACATGCGCTTTTTAGTTTTATAAT 57.711 29.630 9.73 0.00 0.00 1.28
245 246 7.753132 CCTCACATGCGCTTTTTAGTTTTATAA 59.247 33.333 9.73 0.00 0.00 0.98
246 247 7.247728 CCTCACATGCGCTTTTTAGTTTTATA 58.752 34.615 9.73 0.00 0.00 0.98
247 248 6.092748 CCTCACATGCGCTTTTTAGTTTTAT 58.907 36.000 9.73 0.00 0.00 1.40
248 249 5.457140 CCTCACATGCGCTTTTTAGTTTTA 58.543 37.500 9.73 0.00 0.00 1.52
249 250 4.298332 CCTCACATGCGCTTTTTAGTTTT 58.702 39.130 9.73 0.00 0.00 2.43
250 251 3.305335 CCCTCACATGCGCTTTTTAGTTT 60.305 43.478 9.73 0.00 0.00 2.66
251 252 2.228822 CCCTCACATGCGCTTTTTAGTT 59.771 45.455 9.73 0.00 0.00 2.24
252 253 1.812571 CCCTCACATGCGCTTTTTAGT 59.187 47.619 9.73 0.00 0.00 2.24
253 254 1.468054 GCCCTCACATGCGCTTTTTAG 60.468 52.381 9.73 0.46 0.00 1.85
254 255 0.525761 GCCCTCACATGCGCTTTTTA 59.474 50.000 9.73 0.00 0.00 1.52
255 256 1.181098 AGCCCTCACATGCGCTTTTT 61.181 50.000 9.73 0.00 0.00 1.94
256 257 1.604593 AGCCCTCACATGCGCTTTT 60.605 52.632 9.73 0.00 0.00 2.27
257 258 2.034687 AGCCCTCACATGCGCTTT 59.965 55.556 9.73 0.00 0.00 3.51
258 259 2.749044 CAGCCCTCACATGCGCTT 60.749 61.111 9.73 0.00 0.00 4.68
259 260 3.557903 AACAGCCCTCACATGCGCT 62.558 57.895 9.73 0.00 0.00 5.92
260 261 3.044059 GAACAGCCCTCACATGCGC 62.044 63.158 0.00 0.00 0.00 6.09
261 262 2.743752 CGAACAGCCCTCACATGCG 61.744 63.158 0.00 0.00 0.00 4.73
262 263 3.044059 GCGAACAGCCCTCACATGC 62.044 63.158 0.00 0.00 40.81 4.06
263 264 3.181367 GCGAACAGCCCTCACATG 58.819 61.111 0.00 0.00 40.81 3.21
273 274 2.030893 TCGTATAATACCCGGCGAACAG 60.031 50.000 9.30 0.00 0.00 3.16
274 275 1.952990 TCGTATAATACCCGGCGAACA 59.047 47.619 9.30 0.00 0.00 3.18
275 276 2.704725 TCGTATAATACCCGGCGAAC 57.295 50.000 9.30 0.00 0.00 3.95
276 277 2.288152 GGTTCGTATAATACCCGGCGAA 60.288 50.000 9.30 0.00 36.26 4.70
277 278 1.269448 GGTTCGTATAATACCCGGCGA 59.731 52.381 9.30 0.00 0.00 5.54
278 279 1.270550 AGGTTCGTATAATACCCGGCG 59.729 52.381 0.00 0.00 32.20 6.46
279 280 3.255642 TGTAGGTTCGTATAATACCCGGC 59.744 47.826 0.00 0.00 32.20 6.13
280 281 4.520492 ACTGTAGGTTCGTATAATACCCGG 59.480 45.833 0.00 0.00 32.20 5.73
281 282 5.009010 ACACTGTAGGTTCGTATAATACCCG 59.991 44.000 0.00 0.00 32.20 5.28
282 283 6.396829 ACACTGTAGGTTCGTATAATACCC 57.603 41.667 0.00 0.00 32.20 3.69
289 290 9.565090 TTCTACATATACACTGTAGGTTCGTAT 57.435 33.333 10.63 0.00 44.01 3.06
290 291 8.962884 TTCTACATATACACTGTAGGTTCGTA 57.037 34.615 10.63 0.00 44.01 3.43
291 292 7.870509 TTCTACATATACACTGTAGGTTCGT 57.129 36.000 10.63 0.00 44.01 3.85
292 293 7.375280 CGTTTCTACATATACACTGTAGGTTCG 59.625 40.741 10.63 9.12 44.01 3.95
293 294 8.186821 ACGTTTCTACATATACACTGTAGGTTC 58.813 37.037 10.63 3.41 44.01 3.62
294 295 7.972277 CACGTTTCTACATATACACTGTAGGTT 59.028 37.037 10.63 0.00 44.01 3.50
295 296 7.337689 TCACGTTTCTACATATACACTGTAGGT 59.662 37.037 10.63 1.14 44.01 3.08
296 297 7.700505 TCACGTTTCTACATATACACTGTAGG 58.299 38.462 10.63 0.67 44.01 3.18
297 298 8.396390 ACTCACGTTTCTACATATACACTGTAG 58.604 37.037 5.86 5.86 44.82 2.74
298 299 8.272545 ACTCACGTTTCTACATATACACTGTA 57.727 34.615 0.00 0.00 0.00 2.74
299 300 7.154435 ACTCACGTTTCTACATATACACTGT 57.846 36.000 0.00 0.00 0.00 3.55
332 333 9.590451 CGTATAAAGGGTAGTATGAACTTTTCA 57.410 33.333 0.00 0.00 45.01 2.69
333 334 9.591792 ACGTATAAAGGGTAGTATGAACTTTTC 57.408 33.333 0.00 0.00 37.15 2.29
334 335 9.948964 AACGTATAAAGGGTAGTATGAACTTTT 57.051 29.630 0.00 0.00 37.15 2.27
621 622 3.702623 TACACCCCCTCCCCCTCC 61.703 72.222 0.00 0.00 0.00 4.30
622 623 2.366569 GTACACCCCCTCCCCCTC 60.367 72.222 0.00 0.00 0.00 4.30
623 624 4.034636 GGTACACCCCCTCCCCCT 62.035 72.222 0.00 0.00 0.00 4.79
625 626 3.929723 TTCGGTACACCCCCTCCCC 62.930 68.421 0.00 0.00 0.00 4.81
626 627 2.284847 TTCGGTACACCCCCTCCC 60.285 66.667 0.00 0.00 0.00 4.30
627 628 3.027675 GCTTCGGTACACCCCCTCC 62.028 68.421 0.00 0.00 0.00 4.30
628 629 1.623542 ATGCTTCGGTACACCCCCTC 61.624 60.000 0.00 0.00 0.00 4.30
629 630 1.205460 AATGCTTCGGTACACCCCCT 61.205 55.000 0.00 0.00 0.00 4.79
630 631 1.029947 CAATGCTTCGGTACACCCCC 61.030 60.000 0.00 0.00 0.00 5.40
631 632 1.654023 GCAATGCTTCGGTACACCCC 61.654 60.000 0.00 0.00 0.00 4.95
632 633 0.676782 AGCAATGCTTCGGTACACCC 60.677 55.000 0.00 0.00 33.89 4.61
633 634 0.727398 GAGCAATGCTTCGGTACACC 59.273 55.000 9.91 0.00 39.88 4.16
634 635 1.726853 AGAGCAATGCTTCGGTACAC 58.273 50.000 9.91 0.00 39.88 2.90
635 636 2.028112 AGAAGAGCAATGCTTCGGTACA 60.028 45.455 9.91 0.00 44.88 2.90
636 637 2.622436 AGAAGAGCAATGCTTCGGTAC 58.378 47.619 9.91 0.00 44.88 3.34
637 638 3.334583 AAGAAGAGCAATGCTTCGGTA 57.665 42.857 9.91 0.00 44.88 4.02
638 639 2.191128 AAGAAGAGCAATGCTTCGGT 57.809 45.000 9.91 0.00 44.88 4.69
639 640 3.565905 AAAAGAAGAGCAATGCTTCGG 57.434 42.857 9.91 0.00 44.88 4.30
640 641 3.120782 GCAAAAAGAAGAGCAATGCTTCG 59.879 43.478 9.91 0.00 44.88 3.79
641 642 4.053295 TGCAAAAAGAAGAGCAATGCTTC 58.947 39.130 9.91 3.70 39.88 3.86
642 643 4.056050 CTGCAAAAAGAAGAGCAATGCTT 58.944 39.130 9.91 0.00 39.88 3.91
643 644 3.554337 CCTGCAAAAAGAAGAGCAATGCT 60.554 43.478 7.79 7.79 43.88 3.79
644 645 2.735134 CCTGCAAAAAGAAGAGCAATGC 59.265 45.455 0.00 0.00 36.44 3.56
645 646 3.739300 CACCTGCAAAAAGAAGAGCAATG 59.261 43.478 0.00 0.00 36.44 2.82
646 647 3.385755 ACACCTGCAAAAAGAAGAGCAAT 59.614 39.130 0.00 0.00 36.44 3.56
647 648 2.760092 ACACCTGCAAAAAGAAGAGCAA 59.240 40.909 0.00 0.00 36.44 3.91
648 649 2.378038 ACACCTGCAAAAAGAAGAGCA 58.622 42.857 0.00 0.00 35.43 4.26
649 650 3.443099 AACACCTGCAAAAAGAAGAGC 57.557 42.857 0.00 0.00 0.00 4.09
650 651 6.566197 ATCTAACACCTGCAAAAAGAAGAG 57.434 37.500 0.00 0.00 0.00 2.85
651 652 8.635765 ATTATCTAACACCTGCAAAAAGAAGA 57.364 30.769 0.00 0.00 0.00 2.87
663 664 7.869937 CGACATGATGAGAATTATCTAACACCT 59.130 37.037 0.00 0.00 35.54 4.00
671 672 6.034363 CGGATGTCGACATGATGAGAATTATC 59.966 42.308 34.48 16.02 42.43 1.75
701 702 2.307929 CGTATGTATTCAGCCGACTCG 58.692 52.381 0.00 0.00 0.00 4.18
855 857 1.764571 TTGGTGGTTCGGACTCTGGG 61.765 60.000 0.00 0.00 0.00 4.45
865 867 3.945921 GCTTTATACTCCCTTGGTGGTTC 59.054 47.826 0.00 0.00 0.00 3.62
890 919 0.627986 AAAGCCTCCTCTCCAATGGG 59.372 55.000 0.00 0.00 0.00 4.00
940 969 3.059352 AGGTTGCTGATTGGTGTACTC 57.941 47.619 0.00 0.00 0.00 2.59
1014 1043 3.139211 AGGGAGGATGGAAATTAAGAGCC 59.861 47.826 0.00 0.00 0.00 4.70
1028 1057 1.005215 CAGAAACAAGCCAGGGAGGAT 59.995 52.381 0.00 0.00 41.22 3.24
1065 1094 2.684001 AACAGAAACGGTGACTGTGA 57.316 45.000 16.94 0.00 42.81 3.58
1066 1095 4.750098 AGAATAACAGAAACGGTGACTGTG 59.250 41.667 16.94 2.15 42.81 3.66
1067 1096 4.750098 CAGAATAACAGAAACGGTGACTGT 59.250 41.667 12.49 12.49 45.02 3.55
1068 1097 4.988540 TCAGAATAACAGAAACGGTGACTG 59.011 41.667 11.46 11.46 37.62 3.51
1069 1098 5.209818 TCAGAATAACAGAAACGGTGACT 57.790 39.130 0.00 0.00 0.00 3.41
1070 1099 5.333875 GGTTCAGAATAACAGAAACGGTGAC 60.334 44.000 0.00 0.00 0.00 3.67
1177 1206 5.393569 CGAATCACGCCCATAGAGAGAATAT 60.394 44.000 0.00 0.00 34.51 1.28
1178 1207 4.082733 CGAATCACGCCCATAGAGAGAATA 60.083 45.833 0.00 0.00 34.51 1.75
1179 1208 3.305676 CGAATCACGCCCATAGAGAGAAT 60.306 47.826 0.00 0.00 34.51 2.40
1194 1226 0.248702 GAGGAGGACGAGCGAATCAC 60.249 60.000 0.00 0.00 0.00 3.06
1207 1239 5.246429 ACCTTCAAGTAAGTTACAGAGGAGG 59.754 44.000 21.07 19.66 32.89 4.30
1208 1240 6.347859 ACCTTCAAGTAAGTTACAGAGGAG 57.652 41.667 21.07 12.61 32.89 3.69
1209 1241 5.048224 CGACCTTCAAGTAAGTTACAGAGGA 60.048 44.000 21.07 9.85 32.89 3.71
1210 1242 5.162075 CGACCTTCAAGTAAGTTACAGAGG 58.838 45.833 15.28 15.83 32.89 3.69
1228 1260 1.371183 CCATGGACACACACGACCT 59.629 57.895 5.56 0.00 0.00 3.85
1229 1261 2.325082 GCCATGGACACACACGACC 61.325 63.158 18.40 0.00 0.00 4.79
1492 1545 4.129737 GCAGTAGAGTGGCGGCGA 62.130 66.667 12.98 0.00 0.00 5.54
1606 1665 1.047596 ATCTGCCCTCTCGCTCACAT 61.048 55.000 0.00 0.00 0.00 3.21
1621 1680 2.355126 CGCCGGGTCGATGATCTG 60.355 66.667 2.18 0.00 0.00 2.90
1769 1831 7.068962 ACCGGAAAAGATACAGGAAAAGAAAAA 59.931 33.333 9.46 0.00 0.00 1.94
1853 1915 3.494626 CAGATTGCAAGTACACGAGTTGT 59.505 43.478 4.94 0.00 40.19 3.32
1854 1916 3.665323 GCAGATTGCAAGTACACGAGTTG 60.665 47.826 4.94 0.00 44.26 3.16
1855 1917 2.480419 GCAGATTGCAAGTACACGAGTT 59.520 45.455 4.94 0.00 44.26 3.01
1856 1918 2.069273 GCAGATTGCAAGTACACGAGT 58.931 47.619 4.94 0.00 44.26 4.18
1898 1960 1.286501 TATCCAAGTCGTCGCATTGC 58.713 50.000 0.00 0.00 0.00 3.56
1971 2033 1.883084 GCAATGCCGACCGGTAGAG 60.883 63.158 17.16 6.75 37.65 2.43
2024 2086 4.379394 GCATATGAAAGTTCCAGCGTCAAA 60.379 41.667 6.97 0.00 0.00 2.69
2051 2113 1.299165 CGGAGAGTACCAATCGGCG 60.299 63.158 0.00 0.00 34.57 6.46
2154 2216 5.715434 AGGAGTAAGTCTCAAGAGTGTTC 57.285 43.478 0.00 0.00 44.40 3.18
2196 2258 6.261826 AGTCACTTGTTGAAATCTCTGGAAAG 59.738 38.462 0.00 0.00 35.39 2.62
2201 2263 7.664082 ATGTAGTCACTTGTTGAAATCTCTG 57.336 36.000 0.00 0.00 35.39 3.35
2218 2280 6.037500 TCACTCATTTTGCTGCATATGTAGTC 59.962 38.462 20.18 13.50 0.00 2.59
2227 2289 6.825213 AGTATAGATTCACTCATTTTGCTGCA 59.175 34.615 0.00 0.00 0.00 4.41
2300 2362 7.644157 CCGCTCCTAAATATTTGTCTTTTTAGC 59.356 37.037 11.05 7.27 32.72 3.09
2308 2370 4.065789 CCCTCCGCTCCTAAATATTTGTC 58.934 47.826 11.05 0.00 0.00 3.18
2310 2372 4.202367 ACTCCCTCCGCTCCTAAATATTTG 60.202 45.833 11.05 1.40 0.00 2.32
2321 2383 2.197605 GCTCCTACTCCCTCCGCTC 61.198 68.421 0.00 0.00 0.00 5.03
2328 2390 2.074729 TGCTCTTAGCTCCTACTCCC 57.925 55.000 0.00 0.00 42.97 4.30
2344 2406 2.185350 CGAACGGCTGGAGATGCT 59.815 61.111 0.00 0.00 0.00 3.79
2363 2425 0.474184 ATATTTCAGTCCCTGGGGCG 59.526 55.000 12.53 7.27 34.68 6.13
2403 2466 2.469516 CCCACGGTGGAAATAGCGC 61.470 63.158 28.36 0.00 44.68 5.92
2404 2467 1.817941 CCCCACGGTGGAAATAGCG 60.818 63.158 28.36 9.40 40.96 4.26
2445 2508 2.983879 ATCTGGGGCCAACTTCGGG 61.984 63.158 4.39 0.00 0.00 5.14
2448 2511 0.681243 GGACATCTGGGGCCAACTTC 60.681 60.000 4.39 0.00 0.00 3.01
2451 2514 0.251787 AAAGGACATCTGGGGCCAAC 60.252 55.000 4.39 0.00 0.00 3.77
2496 2559 6.037610 GCCCAAATTTGTGTCATTTTGTACAA 59.962 34.615 16.73 3.59 0.00 2.41
2497 2560 5.525378 GCCCAAATTTGTGTCATTTTGTACA 59.475 36.000 16.73 0.00 0.00 2.90
2498 2561 5.332959 CGCCCAAATTTGTGTCATTTTGTAC 60.333 40.000 16.73 0.00 0.00 2.90
2520 2583 5.633182 TCAATGAAAACTGCCTAAATTTCGC 59.367 36.000 0.00 0.00 35.15 4.70
2528 2591 9.237187 TGTACAAATATCAATGAAAACTGCCTA 57.763 29.630 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.