Multiple sequence alignment - TraesCS7A01G345000

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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 TraesCS7A01G345000 chr7A 100.000 2720 0 0 1 2720 507015225 507012506 0.000000e+00 5024
1 TraesCS7A01G345000 chr7A 89.799 1794 116 37 332 2113 507023366 507021628 0.000000e+00 2237
2 TraesCS7A01G345000 chr7A 92.487 945 69 1 1089 2031 506854997 506854053 0.000000e+00 1351
3 TraesCS7A01G345000 chr7A 91.523 696 52 5 2027 2720 506853573 506852883 0.000000e+00 952
4 TraesCS7A01G345000 chr7A 90.476 294 27 1 2427 2720 507021339 507021047 1.180000e-103 387
5 TraesCS7A01G345000 chr7B 92.173 1776 95 17 450 2207 443689814 443691563 0.000000e+00 2470
6 TraesCS7A01G345000 chr7B 85.180 1336 124 41 851 2178 443696517 443697786 0.000000e+00 1303
7 TraesCS7A01G345000 chr7B 83.018 1478 171 43 549 2005 443731916 443733334 0.000000e+00 1266
8 TraesCS7A01G345000 chr7B 87.193 937 102 10 787 1720 443702212 443703133 0.000000e+00 1050
9 TraesCS7A01G345000 chr7B 81.941 742 95 20 1727 2453 443703501 443704218 2.330000e-165 592
10 TraesCS7A01G345000 chr7B 85.091 275 32 5 2449 2718 443704460 443704730 3.450000e-69 272
11 TraesCS7A01G345000 chr7B 87.500 144 14 4 92 233 700904686 700904827 2.170000e-36 163
12 TraesCS7A01G345000 chr7D 89.529 1910 129 37 323 2208 426449914 426451776 0.000000e+00 2353
13 TraesCS7A01G345000 chr7D 84.473 1945 229 40 801 2718 426496436 426498334 0.000000e+00 1851
14 TraesCS7A01G345000 chr7D 83.649 1951 246 32 787 2718 426632543 426634439 0.000000e+00 1768
15 TraesCS7A01G345000 chr7D 88.097 1319 97 32 851 2164 426517894 426519157 0.000000e+00 1511
16 TraesCS7A01G345000 chr7D 81.756 1469 181 49 1145 2582 426553866 426555278 0.000000e+00 1147
17 TraesCS7A01G345000 chr7D 85.976 328 37 5 801 1127 426547791 426548110 2.590000e-90 342
18 TraesCS7A01G345000 chr7D 75.292 599 96 24 2098 2672 426491913 426492483 3.500000e-59 239
19 TraesCS7A01G345000 chr2B 83.798 2333 233 76 450 2718 753834366 753836617 0.000000e+00 2080
20 TraesCS7A01G345000 chr2D 81.768 181 15 4 96 275 627929930 627929767 4.720000e-28 135
21 TraesCS7A01G345000 chr5D 78.610 187 27 4 95 275 524327599 524327420 7.960000e-21 111
22 TraesCS7A01G345000 chr6B 79.235 183 17 10 95 275 613310656 613310493 1.030000e-19 108


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 TraesCS7A01G345000 chr7A 507012506 507015225 2719 True 5024.0 5024 100.000000 1 2720 1 chr7A.!!$R1 2719
1 TraesCS7A01G345000 chr7A 507021047 507023366 2319 True 1312.0 2237 90.137500 332 2720 2 chr7A.!!$R3 2388
2 TraesCS7A01G345000 chr7A 506852883 506854997 2114 True 1151.5 1351 92.005000 1089 2720 2 chr7A.!!$R2 1631
3 TraesCS7A01G345000 chr7B 443689814 443691563 1749 False 2470.0 2470 92.173000 450 2207 1 chr7B.!!$F1 1757
4 TraesCS7A01G345000 chr7B 443696517 443697786 1269 False 1303.0 1303 85.180000 851 2178 1 chr7B.!!$F2 1327
5 TraesCS7A01G345000 chr7B 443731916 443733334 1418 False 1266.0 1266 83.018000 549 2005 1 chr7B.!!$F3 1456
6 TraesCS7A01G345000 chr7B 443702212 443704730 2518 False 638.0 1050 84.741667 787 2718 3 chr7B.!!$F5 1931
7 TraesCS7A01G345000 chr7D 426449914 426451776 1862 False 2353.0 2353 89.529000 323 2208 1 chr7D.!!$F1 1885
8 TraesCS7A01G345000 chr7D 426632543 426634439 1896 False 1768.0 1768 83.649000 787 2718 1 chr7D.!!$F5 1931
9 TraesCS7A01G345000 chr7D 426517894 426519157 1263 False 1511.0 1511 88.097000 851 2164 1 chr7D.!!$F2 1313
10 TraesCS7A01G345000 chr7D 426553866 426555278 1412 False 1147.0 1147 81.756000 1145 2582 1 chr7D.!!$F4 1437
11 TraesCS7A01G345000 chr7D 426491913 426498334 6421 False 1045.0 1851 79.882500 801 2718 2 chr7D.!!$F6 1917
12 TraesCS7A01G345000 chr2B 753834366 753836617 2251 False 2080.0 2080 83.798000 450 2718 1 chr2B.!!$F1 2268

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
243 244 0.035343 GAGGGGGAAAGGAAAGTCCG 60.035 60.0 0.0 0.0 42.75 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 5994 0.380733 CGGCGCTGTACATCTCTACA 59.619 55.0 8.45 0.0 0.0 2.74 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
22 23 1.799933 ATCCAAGGGCTCTAGGTGAG 58.200 55.000 0.00 0.00 45.33 3.51
33 34 3.096092 CTCTAGGTGAGCTTTGTCCTCT 58.904 50.000 0.00 0.00 35.84 3.69
34 35 3.093057 TCTAGGTGAGCTTTGTCCTCTC 58.907 50.000 0.00 0.00 0.00 3.20
35 36 0.980423 AGGTGAGCTTTGTCCTCTCC 59.020 55.000 0.00 0.00 41.18 3.71
37 38 2.180276 GGTGAGCTTTGTCCTCTCCTA 58.820 52.381 0.00 0.00 39.00 2.94
38 39 2.567615 GGTGAGCTTTGTCCTCTCCTAA 59.432 50.000 0.00 0.00 39.00 2.69
40 41 4.505039 GGTGAGCTTTGTCCTCTCCTAAAA 60.505 45.833 0.00 0.00 39.00 1.52
41 42 4.452795 GTGAGCTTTGTCCTCTCCTAAAAC 59.547 45.833 0.00 0.00 0.00 2.43
42 43 4.102524 TGAGCTTTGTCCTCTCCTAAAACA 59.897 41.667 0.00 0.00 0.00 2.83
44 45 5.249420 AGCTTTGTCCTCTCCTAAAACATC 58.751 41.667 0.00 0.00 0.00 3.06
45 46 4.396478 GCTTTGTCCTCTCCTAAAACATCC 59.604 45.833 0.00 0.00 0.00 3.51
46 47 5.804771 GCTTTGTCCTCTCCTAAAACATCCT 60.805 44.000 0.00 0.00 0.00 3.24
47 48 5.843019 TTGTCCTCTCCTAAAACATCCTT 57.157 39.130 0.00 0.00 0.00 3.36
49 50 4.844085 TGTCCTCTCCTAAAACATCCTTGA 59.156 41.667 0.00 0.00 0.00 3.02
50 51 5.046304 TGTCCTCTCCTAAAACATCCTTGAG 60.046 44.000 0.00 0.00 0.00 3.02
51 52 4.471386 TCCTCTCCTAAAACATCCTTGAGG 59.529 45.833 0.00 0.00 39.69 3.86
72 73 7.732025 TGAGGATCAAGAAAGTTGTAGTAACA 58.268 34.615 0.00 0.00 45.97 2.41
73 74 8.208224 TGAGGATCAAGAAAGTTGTAGTAACAA 58.792 33.333 0.00 0.00 45.97 2.83
75 76 8.837389 AGGATCAAGAAAGTTGTAGTAACAAAC 58.163 33.333 0.00 0.00 46.84 2.93
76 77 7.797123 GGATCAAGAAAGTTGTAGTAACAAACG 59.203 37.037 0.00 0.00 46.84 3.60
78 79 6.817641 TCAAGAAAGTTGTAGTAACAAACGGA 59.182 34.615 0.00 0.00 46.84 4.69
79 80 6.839820 AGAAAGTTGTAGTAACAAACGGAG 57.160 37.500 0.00 0.00 46.84 4.63
81 82 6.478016 AGAAAGTTGTAGTAACAAACGGAGAC 59.522 38.462 0.00 0.00 46.84 3.36
84 85 4.566545 TGTAGTAACAAACGGAGACGAA 57.433 40.909 0.00 0.00 45.41 3.85
85 86 4.539870 TGTAGTAACAAACGGAGACGAAG 58.460 43.478 0.00 0.00 45.41 3.79
88 89 8.647628 TGTAGTAACAAACGGAGACGAAGTCC 62.648 46.154 0.00 0.00 46.29 3.85
104 105 3.675995 TCCACAATGGAGCAATGCT 57.324 47.368 7.79 7.79 42.67 3.79
106 107 2.368439 TCCACAATGGAGCAATGCTAC 58.632 47.619 11.21 11.21 42.67 3.58
113 114 2.549926 TGGAGCAATGCTACATACACG 58.450 47.619 17.45 0.00 45.48 4.49
114 115 1.867233 GGAGCAATGCTACATACACGG 59.133 52.381 13.46 0.00 39.71 4.94
115 116 1.867233 GAGCAATGCTACATACACGGG 59.133 52.381 8.12 0.00 39.88 5.28
117 118 1.662517 CAATGCTACATACACGGGCA 58.337 50.000 0.00 0.00 37.32 5.36
121 122 1.002659 TGCTACATACACGGGCACTTT 59.997 47.619 0.00 0.00 0.00 2.66
122 123 2.234168 TGCTACATACACGGGCACTTTA 59.766 45.455 0.00 0.00 0.00 1.85
124 125 1.717194 ACATACACGGGCACTTTACG 58.283 50.000 0.00 0.00 0.00 3.18
125 126 1.003851 CATACACGGGCACTTTACGG 58.996 55.000 0.00 0.00 0.00 4.02
127 128 0.038343 TACACGGGCACTTTACGGAC 60.038 55.000 0.00 0.00 0.00 4.79
128 129 2.048877 ACGGGCACTTTACGGACG 60.049 61.111 0.00 0.00 0.00 4.79
129 130 2.048877 CGGGCACTTTACGGACGT 60.049 61.111 1.98 1.98 0.00 4.34
130 131 1.665599 CGGGCACTTTACGGACGTT 60.666 57.895 1.57 0.00 0.00 3.99
131 132 1.223417 CGGGCACTTTACGGACGTTT 61.223 55.000 1.57 0.00 0.00 3.60
135 136 3.425227 GGGCACTTTACGGACGTTTTATG 60.425 47.826 1.57 0.00 0.00 1.90
136 137 3.425227 GGCACTTTACGGACGTTTTATGG 60.425 47.826 1.57 0.00 0.00 2.74
137 138 3.425227 GCACTTTACGGACGTTTTATGGG 60.425 47.826 1.57 0.00 0.00 4.00
138 139 3.747529 CACTTTACGGACGTTTTATGGGT 59.252 43.478 1.57 0.00 0.00 4.51
139 140 3.996363 ACTTTACGGACGTTTTATGGGTC 59.004 43.478 1.57 0.00 0.00 4.46
140 141 3.959535 TTACGGACGTTTTATGGGTCT 57.040 42.857 1.57 0.00 0.00 3.85
142 143 3.515330 ACGGACGTTTTATGGGTCTAG 57.485 47.619 0.00 0.00 0.00 2.43
143 144 2.167075 ACGGACGTTTTATGGGTCTAGG 59.833 50.000 0.00 0.00 0.00 3.02
144 145 2.558378 GGACGTTTTATGGGTCTAGGC 58.442 52.381 0.00 0.00 0.00 3.93
145 146 2.169978 GGACGTTTTATGGGTCTAGGCT 59.830 50.000 0.00 0.00 0.00 4.58
146 147 3.195661 GACGTTTTATGGGTCTAGGCTG 58.804 50.000 0.00 0.00 0.00 4.85
147 148 2.835764 ACGTTTTATGGGTCTAGGCTGA 59.164 45.455 0.00 0.00 0.00 4.26
149 150 4.080526 ACGTTTTATGGGTCTAGGCTGAAT 60.081 41.667 0.00 0.00 0.00 2.57
150 151 4.273480 CGTTTTATGGGTCTAGGCTGAATG 59.727 45.833 0.00 0.00 0.00 2.67
151 152 5.193679 GTTTTATGGGTCTAGGCTGAATGT 58.806 41.667 0.00 0.00 0.00 2.71
152 153 4.422073 TTATGGGTCTAGGCTGAATGTG 57.578 45.455 0.00 0.00 0.00 3.21
153 154 0.911769 TGGGTCTAGGCTGAATGTGG 59.088 55.000 0.00 0.00 0.00 4.17
154 155 0.181350 GGGTCTAGGCTGAATGTGGG 59.819 60.000 0.00 0.00 0.00 4.61
156 157 1.282157 GGTCTAGGCTGAATGTGGGTT 59.718 52.381 0.00 0.00 0.00 4.11
157 158 2.290960 GGTCTAGGCTGAATGTGGGTTT 60.291 50.000 0.00 0.00 0.00 3.27
158 159 3.010420 GTCTAGGCTGAATGTGGGTTTC 58.990 50.000 0.00 0.00 0.00 2.78
159 160 2.009774 CTAGGCTGAATGTGGGTTTCG 58.990 52.381 0.00 0.00 0.00 3.46
160 161 0.110486 AGGCTGAATGTGGGTTTCGT 59.890 50.000 0.00 0.00 0.00 3.85
161 162 0.958822 GGCTGAATGTGGGTTTCGTT 59.041 50.000 0.00 0.00 0.00 3.85
165 166 4.321675 GGCTGAATGTGGGTTTCGTTAATT 60.322 41.667 0.00 0.00 0.00 1.40
166 167 5.106078 GGCTGAATGTGGGTTTCGTTAATTA 60.106 40.000 0.00 0.00 0.00 1.40
167 168 6.027749 GCTGAATGTGGGTTTCGTTAATTAG 58.972 40.000 0.00 0.00 0.00 1.73
169 170 7.136289 TGAATGTGGGTTTCGTTAATTAGAC 57.864 36.000 0.00 0.00 0.00 2.59
170 171 6.711194 TGAATGTGGGTTTCGTTAATTAGACA 59.289 34.615 0.00 0.00 0.00 3.41
171 172 7.392113 TGAATGTGGGTTTCGTTAATTAGACAT 59.608 33.333 0.00 0.00 0.00 3.06
172 173 7.696992 ATGTGGGTTTCGTTAATTAGACATT 57.303 32.000 0.00 0.00 0.00 2.71
173 174 8.795842 ATGTGGGTTTCGTTAATTAGACATTA 57.204 30.769 0.00 0.00 0.00 1.90
174 175 8.259049 TGTGGGTTTCGTTAATTAGACATTAG 57.741 34.615 0.00 0.00 0.00 1.73
175 176 7.334921 TGTGGGTTTCGTTAATTAGACATTAGG 59.665 37.037 0.00 0.00 0.00 2.69
176 177 7.550196 GTGGGTTTCGTTAATTAGACATTAGGA 59.450 37.037 0.00 0.00 0.00 2.94
177 178 7.767198 TGGGTTTCGTTAATTAGACATTAGGAG 59.233 37.037 0.00 0.00 0.00 3.69
178 179 7.983484 GGGTTTCGTTAATTAGACATTAGGAGA 59.017 37.037 0.00 0.00 0.00 3.71
179 180 8.815189 GGTTTCGTTAATTAGACATTAGGAGAC 58.185 37.037 0.00 0.00 0.00 3.36
180 181 9.362539 GTTTCGTTAATTAGACATTAGGAGACA 57.637 33.333 0.00 0.00 0.00 3.41
181 182 8.922058 TTCGTTAATTAGACATTAGGAGACAC 57.078 34.615 0.00 0.00 0.00 3.67
182 183 7.486647 TCGTTAATTAGACATTAGGAGACACC 58.513 38.462 0.00 0.00 39.35 4.16
183 184 6.700520 CGTTAATTAGACATTAGGAGACACCC 59.299 42.308 0.00 0.00 40.05 4.61
184 185 5.632034 AATTAGACATTAGGAGACACCCC 57.368 43.478 0.00 0.00 40.05 4.95
226 227 0.676736 GGGGGCGAGATTAGTGAGAG 59.323 60.000 0.00 0.00 0.00 3.20
229 230 0.676736 GGCGAGATTAGTGAGAGGGG 59.323 60.000 0.00 0.00 0.00 4.79
230 231 0.676736 GCGAGATTAGTGAGAGGGGG 59.323 60.000 0.00 0.00 0.00 5.40
232 233 2.667470 CGAGATTAGTGAGAGGGGGAA 58.333 52.381 0.00 0.00 0.00 3.97
233 234 3.031736 CGAGATTAGTGAGAGGGGGAAA 58.968 50.000 0.00 0.00 0.00 3.13
235 236 3.388913 AGATTAGTGAGAGGGGGAAAGG 58.611 50.000 0.00 0.00 0.00 3.11
236 237 3.014110 AGATTAGTGAGAGGGGGAAAGGA 59.986 47.826 0.00 0.00 0.00 3.36
238 239 2.133858 AGTGAGAGGGGGAAAGGAAA 57.866 50.000 0.00 0.00 0.00 3.13
239 240 1.988846 AGTGAGAGGGGGAAAGGAAAG 59.011 52.381 0.00 0.00 0.00 2.62
241 242 1.985895 TGAGAGGGGGAAAGGAAAGTC 59.014 52.381 0.00 0.00 0.00 3.01
242 243 1.282447 GAGAGGGGGAAAGGAAAGTCC 59.718 57.143 0.00 0.00 36.58 3.85
243 244 0.035343 GAGGGGGAAAGGAAAGTCCG 60.035 60.000 0.00 0.00 42.75 4.79
245 246 0.111832 GGGGGAAAGGAAAGTCCGTT 59.888 55.000 0.00 0.00 42.75 4.44
247 248 1.202842 GGGGAAAGGAAAGTCCGTTGA 60.203 52.381 0.00 0.00 42.75 3.18
248 249 2.554564 GGGGAAAGGAAAGTCCGTTGAT 60.555 50.000 0.00 0.00 42.75 2.57
250 251 4.329392 GGGAAAGGAAAGTCCGTTGATTA 58.671 43.478 0.00 0.00 42.75 1.75
252 253 5.106277 GGGAAAGGAAAGTCCGTTGATTAAG 60.106 44.000 0.00 0.00 42.75 1.85
254 255 6.652062 GGAAAGGAAAGTCCGTTGATTAAGTA 59.348 38.462 0.00 0.00 42.75 2.24
255 256 7.173735 GGAAAGGAAAGTCCGTTGATTAAGTAA 59.826 37.037 0.00 0.00 42.75 2.24
257 258 8.454570 AAGGAAAGTCCGTTGATTAAGTAAAA 57.545 30.769 0.00 0.00 42.75 1.52
258 259 8.631480 AGGAAAGTCCGTTGATTAAGTAAAAT 57.369 30.769 0.00 0.00 42.75 1.82
259 260 8.512138 AGGAAAGTCCGTTGATTAAGTAAAATG 58.488 33.333 0.00 0.00 42.75 2.32
260 261 8.508875 GGAAAGTCCGTTGATTAAGTAAAATGA 58.491 33.333 0.00 0.00 0.00 2.57
262 263 8.617290 AAGTCCGTTGATTAAGTAAAATGAGT 57.383 30.769 0.00 0.00 0.00 3.41
263 264 8.252964 AGTCCGTTGATTAAGTAAAATGAGTC 57.747 34.615 0.00 0.00 0.00 3.36
265 266 6.311935 TCCGTTGATTAAGTAAAATGAGTCCG 59.688 38.462 0.00 0.00 0.00 4.79
266 267 6.091713 CCGTTGATTAAGTAAAATGAGTCCGT 59.908 38.462 0.00 0.00 0.00 4.69
267 268 6.953743 CGTTGATTAAGTAAAATGAGTCCGTG 59.046 38.462 0.00 0.00 0.00 4.94
268 269 7.148705 CGTTGATTAAGTAAAATGAGTCCGTGA 60.149 37.037 0.00 0.00 0.00 4.35
270 271 7.383687 TGATTAAGTAAAATGAGTCCGTGAGT 58.616 34.615 0.00 0.00 0.00 3.41
271 272 7.330946 TGATTAAGTAAAATGAGTCCGTGAGTG 59.669 37.037 0.00 0.00 0.00 3.51
272 273 4.602340 AGTAAAATGAGTCCGTGAGTGT 57.398 40.909 0.00 0.00 0.00 3.55
274 275 5.710984 AGTAAAATGAGTCCGTGAGTGTAG 58.289 41.667 0.00 0.00 0.00 2.74
275 276 3.594603 AAATGAGTCCGTGAGTGTAGG 57.405 47.619 0.00 0.00 0.00 3.18
276 277 0.818296 ATGAGTCCGTGAGTGTAGGC 59.182 55.000 0.00 0.00 0.00 3.93
277 278 0.538746 TGAGTCCGTGAGTGTAGGCA 60.539 55.000 0.00 0.00 0.00 4.75
278 279 0.601558 GAGTCCGTGAGTGTAGGCAA 59.398 55.000 0.00 0.00 0.00 4.52
279 280 1.000506 GAGTCCGTGAGTGTAGGCAAA 59.999 52.381 0.00 0.00 0.00 3.68
281 282 2.038557 AGTCCGTGAGTGTAGGCAAAAT 59.961 45.455 0.00 0.00 0.00 1.82
282 283 2.812011 GTCCGTGAGTGTAGGCAAAATT 59.188 45.455 0.00 0.00 0.00 1.82
283 284 3.998341 GTCCGTGAGTGTAGGCAAAATTA 59.002 43.478 0.00 0.00 0.00 1.40
285 286 4.000988 CCGTGAGTGTAGGCAAAATTAGT 58.999 43.478 0.00 0.00 0.00 2.24
287 288 4.669197 CGTGAGTGTAGGCAAAATTAGTGC 60.669 45.833 5.64 5.64 41.45 4.40
288 289 4.455877 GTGAGTGTAGGCAAAATTAGTGCT 59.544 41.667 12.37 3.70 41.88 4.40
290 291 5.534654 TGAGTGTAGGCAAAATTAGTGCTTT 59.465 36.000 12.37 5.75 41.88 3.51
291 292 5.772521 AGTGTAGGCAAAATTAGTGCTTTG 58.227 37.500 12.37 0.00 41.88 2.77
292 293 5.534654 AGTGTAGGCAAAATTAGTGCTTTGA 59.465 36.000 12.37 0.00 41.88 2.69
293 294 5.858581 GTGTAGGCAAAATTAGTGCTTTGAG 59.141 40.000 12.37 0.00 41.88 3.02
295 296 3.259123 AGGCAAAATTAGTGCTTTGAGGG 59.741 43.478 12.37 0.00 41.88 4.30
296 297 3.006859 GGCAAAATTAGTGCTTTGAGGGT 59.993 43.478 12.37 0.00 41.88 4.34
297 298 3.989817 GCAAAATTAGTGCTTTGAGGGTG 59.010 43.478 6.76 0.00 39.00 4.61
298 299 4.501400 GCAAAATTAGTGCTTTGAGGGTGT 60.501 41.667 6.76 0.00 39.00 4.16
299 300 5.600696 CAAAATTAGTGCTTTGAGGGTGTT 58.399 37.500 0.00 0.00 35.03 3.32
300 301 5.869649 AAATTAGTGCTTTGAGGGTGTTT 57.130 34.783 0.00 0.00 0.00 2.83
301 302 5.869649 AATTAGTGCTTTGAGGGTGTTTT 57.130 34.783 0.00 0.00 0.00 2.43
302 303 6.969993 AATTAGTGCTTTGAGGGTGTTTTA 57.030 33.333 0.00 0.00 0.00 1.52
303 304 7.539034 AATTAGTGCTTTGAGGGTGTTTTAT 57.461 32.000 0.00 0.00 0.00 1.40
304 305 6.569179 TTAGTGCTTTGAGGGTGTTTTATC 57.431 37.500 0.00 0.00 0.00 1.75
306 307 2.817258 TGCTTTGAGGGTGTTTTATCGG 59.183 45.455 0.00 0.00 0.00 4.18
307 308 3.078837 GCTTTGAGGGTGTTTTATCGGA 58.921 45.455 0.00 0.00 0.00 4.55
308 309 3.119955 GCTTTGAGGGTGTTTTATCGGAC 60.120 47.826 0.00 0.00 0.00 4.79
310 311 1.066716 TGAGGGTGTTTTATCGGACCG 60.067 52.381 7.84 7.84 0.00 4.79
311 312 0.978907 AGGGTGTTTTATCGGACCGT 59.021 50.000 14.79 3.95 0.00 4.83
312 313 1.081094 GGGTGTTTTATCGGACCGTG 58.919 55.000 14.79 0.00 0.00 4.94
315 316 1.532007 GTGTTTTATCGGACCGTGCAA 59.468 47.619 14.79 3.68 0.00 4.08
319 320 4.231439 GTTTTATCGGACCGTGCAAAAAT 58.769 39.130 14.79 0.14 0.00 1.82
320 321 3.479505 TTATCGGACCGTGCAAAAATG 57.520 42.857 14.79 0.00 0.00 2.32
322 323 0.535328 TCGGACCGTGCAAAAATGGA 60.535 50.000 14.79 0.00 0.00 3.41
326 327 0.387565 ACCGTGCAAAAATGGACCAC 59.612 50.000 0.00 0.00 0.00 4.16
327 328 0.673437 CCGTGCAAAAATGGACCACT 59.327 50.000 0.00 0.00 0.00 4.00
328 329 1.335872 CCGTGCAAAAATGGACCACTC 60.336 52.381 0.00 0.00 0.00 3.51
330 331 2.030007 CGTGCAAAAATGGACCACTCAT 60.030 45.455 0.00 0.00 0.00 2.90
343 344 4.938226 GGACCACTCATCTTTTGAACTAGG 59.062 45.833 0.00 0.00 32.78 3.02
348 350 6.239008 CCACTCATCTTTTGAACTAGGCAAAA 60.239 38.462 18.65 18.65 41.42 2.44
351 353 7.068716 ACTCATCTTTTGAACTAGGCAAAAAGT 59.931 33.333 19.61 17.27 42.59 2.66
352 354 7.781056 TCATCTTTTGAACTAGGCAAAAAGTT 58.219 30.769 19.61 12.19 42.59 2.66
369 371 1.603802 AGTTCAAGTGGACAACATGCG 59.396 47.619 0.00 0.00 0.00 4.73
371 373 0.943673 TCAAGTGGACAACATGCGTG 59.056 50.000 3.82 3.82 0.00 5.34
376 378 0.248825 TGGACAACATGCGTGTTTGC 60.249 50.000 21.60 17.06 46.07 3.68
384 397 2.252747 CATGCGTGTTTGCGATTCAAT 58.747 42.857 0.00 0.00 37.81 2.57
396 409 2.415893 GCGATTCAATGGTTTGTCCCAG 60.416 50.000 0.00 0.00 38.07 4.45
399 412 0.541764 TCAATGGTTTGTCCCAGCCC 60.542 55.000 0.00 0.00 38.07 5.19
400 413 1.606313 AATGGTTTGTCCCAGCCCG 60.606 57.895 0.00 0.00 38.07 6.13
402 415 2.203437 GGTTTGTCCCAGCCCGTT 60.203 61.111 0.00 0.00 0.00 4.44
403 416 2.265904 GGTTTGTCCCAGCCCGTTC 61.266 63.158 0.00 0.00 0.00 3.95
404 417 1.228154 GTTTGTCCCAGCCCGTTCT 60.228 57.895 0.00 0.00 0.00 3.01
405 418 1.072505 TTTGTCCCAGCCCGTTCTC 59.927 57.895 0.00 0.00 0.00 2.87
406 419 2.406002 TTTGTCCCAGCCCGTTCTCC 62.406 60.000 0.00 0.00 0.00 3.71
409 422 2.359975 CCCAGCCCGTTCTCCAAC 60.360 66.667 0.00 0.00 0.00 3.77
411 424 1.966451 CCAGCCCGTTCTCCAACAC 60.966 63.158 0.00 0.00 32.14 3.32
413 426 2.280592 GCCCGTTCTCCAACACGT 60.281 61.111 0.00 0.00 34.47 4.49
422 435 2.040939 TCTCCAACACGTACCCTTTGA 58.959 47.619 0.00 0.00 0.00 2.69
433 446 2.514458 ACCCTTTGATTCCAGCGAAT 57.486 45.000 0.00 0.00 41.57 3.34
434 447 2.094675 ACCCTTTGATTCCAGCGAATG 58.905 47.619 0.00 0.00 38.88 2.67
438 451 4.498682 CCCTTTGATTCCAGCGAATGATTC 60.499 45.833 0.00 0.00 38.88 2.52
464 477 5.007034 TCAATTAAGATTCTTGGCGTGGAA 58.993 37.500 9.22 0.00 0.00 3.53
509 522 1.836383 GTGTCGACGGGATCACATAC 58.164 55.000 11.62 0.00 31.31 2.39
510 523 1.133598 GTGTCGACGGGATCACATACA 59.866 52.381 11.62 0.00 31.31 2.29
546 559 7.409697 TGTAATTTAAGCTAGGTACGTACTCG 58.590 38.462 24.07 13.75 43.34 4.18
547 560 6.683974 AATTTAAGCTAGGTACGTACTCGA 57.316 37.500 24.07 10.46 40.62 4.04
548 561 6.874288 ATTTAAGCTAGGTACGTACTCGAT 57.126 37.500 24.07 9.57 40.62 3.59
549 562 5.914085 TTAAGCTAGGTACGTACTCGATC 57.086 43.478 24.07 8.13 40.62 3.69
572 585 5.975344 TCGTATTAGTTAGCCTGTCAATTCG 59.025 40.000 0.00 0.00 0.00 3.34
598 611 3.968724 CGCTTTTGTTTTCTCTTCTTCCG 59.031 43.478 0.00 0.00 0.00 4.30
599 612 4.260620 CGCTTTTGTTTTCTCTTCTTCCGA 60.261 41.667 0.00 0.00 0.00 4.55
602 615 3.121738 TGTTTTCTCTTCTTCCGACCC 57.878 47.619 0.00 0.00 0.00 4.46
649 662 1.597854 CACAAGGCGGCAGACAGAA 60.598 57.895 13.08 0.00 0.00 3.02
651 664 2.357517 AAGGCGGCAGACAGAACG 60.358 61.111 13.08 0.00 0.00 3.95
790 818 5.199024 AGCTGATAGTAAGCATCTCACTG 57.801 43.478 0.00 0.00 43.37 3.66
795 823 6.125719 TGATAGTAAGCATCTCACTGTCTCT 58.874 40.000 0.00 0.00 33.18 3.10
799 827 4.613925 AAGCATCTCACTGTCTCTTTGA 57.386 40.909 0.00 0.00 0.00 2.69
829 4628 2.125952 CACCGTGCAGCGATCTCA 60.126 61.111 9.75 0.00 44.77 3.27
1159 4980 6.222389 TGGTTTCACTTTCATTTGCTAATGG 58.778 36.000 18.70 7.38 41.23 3.16
1458 5291 0.112412 AATCCACCAAGAACGGCCTT 59.888 50.000 0.00 0.00 0.00 4.35
1533 5366 0.313987 TTGACGCTCGTGACATGACT 59.686 50.000 0.00 0.00 0.00 3.41
1584 5417 0.610174 CCAGCTGCAAGACCTACAGA 59.390 55.000 8.66 0.00 34.07 3.41
1719 5913 2.060326 TGAGGTTCGACAACGCTTAG 57.940 50.000 0.00 0.00 39.58 2.18
1739 5933 2.094390 AGTACAAGAACCTTATCGCGCA 60.094 45.455 8.75 0.00 0.00 6.09
1755 5949 2.262915 CAGCGCGGTCTCCTTTCT 59.737 61.111 8.38 0.00 0.00 2.52
1778 5972 1.339824 GGACCAGACTCTCTACGGTGA 60.340 57.143 0.00 0.00 0.00 4.02
1788 5982 2.775960 TCTCTACGGTGATGGAGGTCTA 59.224 50.000 0.00 0.00 0.00 2.59
1800 5994 5.485353 TGATGGAGGTCTACAAGACAATCTT 59.515 40.000 9.15 0.00 46.79 2.40
1932 6126 1.412079 AGTGCTCCATGGCAAACAAA 58.588 45.000 6.96 0.00 44.18 2.83
1972 6167 2.371306 TGATCCCAAGTGCATCATGTG 58.629 47.619 0.00 0.00 0.00 3.21
1988 6183 1.524621 GTGACCCGGCCTGATCATG 60.525 63.158 0.00 0.00 0.00 3.07
2038 6252 5.772825 TGTAACAGTCCTAGTACGTGTTT 57.227 39.130 0.00 0.00 33.50 2.83
2069 6781 3.859411 TTTTTCCCCATACAATGTCGC 57.141 42.857 0.00 0.00 0.00 5.19
2146 6889 6.802834 GTGTTTCTCAAGTTTGTTTTAACGGA 59.197 34.615 0.00 0.00 33.26 4.69
2225 6969 3.644966 TTTCTGCACTCGGGGATTATT 57.355 42.857 0.00 0.00 0.00 1.40
2239 6985 4.505039 GGGGATTATTAGTGATGCTTCCGT 60.505 45.833 0.00 0.00 0.00 4.69
2416 7198 5.885352 TGAATATCTTCAAAAGGCCGATCAA 59.115 36.000 0.00 0.00 38.43 2.57
2505 7539 2.268730 GCCGATGAAAGAGGCTTTTG 57.731 50.000 0.00 0.00 46.83 2.44
2564 7604 5.565509 TGGGAGTGTTCACTTTATGCATTA 58.434 37.500 3.54 0.00 0.00 1.90
2651 7691 3.857157 TCTTGTAAGTTGTTGCCTCCT 57.143 42.857 0.00 0.00 0.00 3.69
2654 7694 4.591498 TCTTGTAAGTTGTTGCCTCCTAGA 59.409 41.667 0.00 0.00 0.00 2.43
2659 7699 5.966742 AAGTTGTTGCCTCCTAGAATTTC 57.033 39.130 0.00 0.00 0.00 2.17
2681 7721 6.061022 TCTGGATTTGACATGGCTACTTTA 57.939 37.500 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.309296 CTCACCTAGAGCCCTTGGATTA 58.691 50.000 2.10 0.00 38.44 1.75
14 15 2.167487 GGAGAGGACAAAGCTCACCTAG 59.833 54.545 0.00 0.00 32.53 3.02
17 18 0.980423 AGGAGAGGACAAAGCTCACC 59.020 55.000 0.00 0.00 0.00 4.02
18 19 3.963428 TTAGGAGAGGACAAAGCTCAC 57.037 47.619 0.00 0.00 0.00 3.51
19 20 4.102524 TGTTTTAGGAGAGGACAAAGCTCA 59.897 41.667 0.00 0.00 0.00 4.26
20 21 4.642429 TGTTTTAGGAGAGGACAAAGCTC 58.358 43.478 0.00 0.00 0.00 4.09
22 23 4.396478 GGATGTTTTAGGAGAGGACAAAGC 59.604 45.833 0.00 0.00 0.00 3.51
23 24 5.810095 AGGATGTTTTAGGAGAGGACAAAG 58.190 41.667 0.00 0.00 0.00 2.77
24 25 5.843019 AGGATGTTTTAGGAGAGGACAAA 57.157 39.130 0.00 0.00 0.00 2.83
26 27 4.844085 TCAAGGATGTTTTAGGAGAGGACA 59.156 41.667 0.00 0.00 0.00 4.02
27 28 5.422214 TCAAGGATGTTTTAGGAGAGGAC 57.578 43.478 0.00 0.00 0.00 3.85
29 30 4.471386 TCCTCAAGGATGTTTTAGGAGAGG 59.529 45.833 0.00 0.00 39.78 3.69
46 47 8.208224 TGTTACTACAACTTTCTTGATCCTCAA 58.792 33.333 0.00 0.00 34.79 3.02
47 48 7.732025 TGTTACTACAACTTTCTTGATCCTCA 58.268 34.615 0.00 0.00 0.00 3.86
49 50 8.837389 GTTTGTTACTACAACTTTCTTGATCCT 58.163 33.333 0.00 0.00 43.66 3.24
50 51 7.797123 CGTTTGTTACTACAACTTTCTTGATCC 59.203 37.037 0.00 0.00 43.66 3.36
51 52 7.797123 CCGTTTGTTACTACAACTTTCTTGATC 59.203 37.037 0.00 0.00 43.66 2.92
54 55 7.007313 TCCGTTTGTTACTACAACTTTCTTG 57.993 36.000 0.00 0.00 43.66 3.02
55 56 7.010830 GTCTCCGTTTGTTACTACAACTTTCTT 59.989 37.037 0.00 0.00 43.66 2.52
57 58 6.560983 CGTCTCCGTTTGTTACTACAACTTTC 60.561 42.308 0.00 0.00 43.66 2.62
60 61 4.036734 TCGTCTCCGTTTGTTACTACAACT 59.963 41.667 0.00 0.00 43.66 3.16
62 63 4.566545 TCGTCTCCGTTTGTTACTACAA 57.433 40.909 0.00 0.00 42.34 2.41
63 64 4.036734 ACTTCGTCTCCGTTTGTTACTACA 59.963 41.667 0.00 0.00 35.01 2.74
64 65 4.540824 ACTTCGTCTCCGTTTGTTACTAC 58.459 43.478 0.00 0.00 35.01 2.73
68 69 2.361757 TGGACTTCGTCTCCGTTTGTTA 59.638 45.455 0.00 0.00 35.01 2.41
70 71 0.748450 TGGACTTCGTCTCCGTTTGT 59.252 50.000 0.00 0.00 35.01 2.83
71 72 1.137513 GTGGACTTCGTCTCCGTTTG 58.862 55.000 0.00 0.00 35.01 2.93
72 73 0.748450 TGTGGACTTCGTCTCCGTTT 59.252 50.000 0.00 0.00 35.01 3.60
73 74 0.748450 TTGTGGACTTCGTCTCCGTT 59.252 50.000 0.00 0.00 35.01 4.44
75 76 1.350193 CATTGTGGACTTCGTCTCCG 58.650 55.000 0.00 0.00 32.47 4.63
76 77 1.275291 TCCATTGTGGACTTCGTCTCC 59.725 52.381 0.00 0.00 42.67 3.71
78 79 1.338200 GCTCCATTGTGGACTTCGTCT 60.338 52.381 0.00 0.00 42.67 4.18
79 80 1.079503 GCTCCATTGTGGACTTCGTC 58.920 55.000 0.00 0.00 42.67 4.20
81 82 1.522668 TTGCTCCATTGTGGACTTCG 58.477 50.000 0.00 0.00 42.67 3.79
82 83 2.416431 GCATTGCTCCATTGTGGACTTC 60.416 50.000 0.16 0.00 42.67 3.01
83 84 1.547372 GCATTGCTCCATTGTGGACTT 59.453 47.619 0.16 0.00 42.67 3.01
84 85 1.180029 GCATTGCTCCATTGTGGACT 58.820 50.000 0.16 0.00 42.67 3.85
85 86 1.180029 AGCATTGCTCCATTGTGGAC 58.820 50.000 5.03 0.00 42.67 4.02
88 89 4.336153 TGTATGTAGCATTGCTCCATTGTG 59.664 41.667 20.02 0.00 36.63 3.33
92 93 3.133691 CGTGTATGTAGCATTGCTCCAT 58.866 45.455 19.00 19.00 38.66 3.41
94 95 1.867233 CCGTGTATGTAGCATTGCTCC 59.133 52.381 15.81 3.99 40.44 4.70
96 97 1.953559 CCCGTGTATGTAGCATTGCT 58.046 50.000 16.63 16.63 43.41 3.91
98 99 1.330521 GTGCCCGTGTATGTAGCATTG 59.669 52.381 0.00 0.00 35.62 2.82
100 101 0.830648 AGTGCCCGTGTATGTAGCAT 59.169 50.000 0.00 0.00 35.62 3.79
102 103 1.734163 AAAGTGCCCGTGTATGTAGC 58.266 50.000 0.00 0.00 0.00 3.58
103 104 2.855963 CGTAAAGTGCCCGTGTATGTAG 59.144 50.000 0.00 0.00 0.00 2.74
104 105 2.417107 CCGTAAAGTGCCCGTGTATGTA 60.417 50.000 0.00 0.00 0.00 2.29
106 107 1.003851 CCGTAAAGTGCCCGTGTATG 58.996 55.000 0.00 0.00 0.00 2.39
107 108 0.896923 TCCGTAAAGTGCCCGTGTAT 59.103 50.000 0.00 0.00 0.00 2.29
108 109 0.038343 GTCCGTAAAGTGCCCGTGTA 60.038 55.000 0.00 0.00 0.00 2.90
110 111 2.377310 CGTCCGTAAAGTGCCCGTG 61.377 63.158 0.00 0.00 0.00 4.94
111 112 2.048877 CGTCCGTAAAGTGCCCGT 60.049 61.111 0.00 0.00 0.00 5.28
113 114 0.946528 AAAACGTCCGTAAAGTGCCC 59.053 50.000 0.00 0.00 0.00 5.36
114 115 3.425227 CCATAAAACGTCCGTAAAGTGCC 60.425 47.826 0.00 0.00 0.00 5.01
115 116 3.425227 CCCATAAAACGTCCGTAAAGTGC 60.425 47.826 0.00 0.00 0.00 4.40
117 118 3.996363 GACCCATAAAACGTCCGTAAAGT 59.004 43.478 0.00 0.00 0.00 2.66
121 122 3.381272 CCTAGACCCATAAAACGTCCGTA 59.619 47.826 0.00 0.00 0.00 4.02
122 123 2.167075 CCTAGACCCATAAAACGTCCGT 59.833 50.000 0.00 0.00 0.00 4.69
124 125 2.169978 AGCCTAGACCCATAAAACGTCC 59.830 50.000 0.00 0.00 0.00 4.79
125 126 3.118884 TCAGCCTAGACCCATAAAACGTC 60.119 47.826 0.00 0.00 0.00 4.34
127 128 3.536956 TCAGCCTAGACCCATAAAACG 57.463 47.619 0.00 0.00 0.00 3.60
128 129 5.066505 CACATTCAGCCTAGACCCATAAAAC 59.933 44.000 0.00 0.00 0.00 2.43
129 130 5.192927 CACATTCAGCCTAGACCCATAAAA 58.807 41.667 0.00 0.00 0.00 1.52
130 131 4.385199 CCACATTCAGCCTAGACCCATAAA 60.385 45.833 0.00 0.00 0.00 1.40
131 132 3.136443 CCACATTCAGCCTAGACCCATAA 59.864 47.826 0.00 0.00 0.00 1.90
135 136 0.181350 CCCACATTCAGCCTAGACCC 59.819 60.000 0.00 0.00 0.00 4.46
136 137 0.912486 ACCCACATTCAGCCTAGACC 59.088 55.000 0.00 0.00 0.00 3.85
137 138 2.789409 AACCCACATTCAGCCTAGAC 57.211 50.000 0.00 0.00 0.00 2.59
138 139 2.354704 CGAAACCCACATTCAGCCTAGA 60.355 50.000 0.00 0.00 0.00 2.43
139 140 2.009774 CGAAACCCACATTCAGCCTAG 58.990 52.381 0.00 0.00 0.00 3.02
140 141 1.349688 ACGAAACCCACATTCAGCCTA 59.650 47.619 0.00 0.00 0.00 3.93
142 143 0.958822 AACGAAACCCACATTCAGCC 59.041 50.000 0.00 0.00 0.00 4.85
143 144 3.907894 TTAACGAAACCCACATTCAGC 57.092 42.857 0.00 0.00 0.00 4.26
144 145 7.094975 TGTCTAATTAACGAAACCCACATTCAG 60.095 37.037 0.00 0.00 0.00 3.02
145 146 6.711194 TGTCTAATTAACGAAACCCACATTCA 59.289 34.615 0.00 0.00 0.00 2.57
146 147 7.136289 TGTCTAATTAACGAAACCCACATTC 57.864 36.000 0.00 0.00 0.00 2.67
147 148 7.696992 ATGTCTAATTAACGAAACCCACATT 57.303 32.000 0.00 0.00 0.00 2.71
149 150 7.334921 CCTAATGTCTAATTAACGAAACCCACA 59.665 37.037 0.00 0.00 0.00 4.17
150 151 7.550196 TCCTAATGTCTAATTAACGAAACCCAC 59.450 37.037 0.00 0.00 0.00 4.61
151 152 7.622713 TCCTAATGTCTAATTAACGAAACCCA 58.377 34.615 0.00 0.00 0.00 4.51
152 153 7.983484 TCTCCTAATGTCTAATTAACGAAACCC 59.017 37.037 0.00 0.00 0.00 4.11
153 154 8.815189 GTCTCCTAATGTCTAATTAACGAAACC 58.185 37.037 0.00 0.00 0.00 3.27
154 155 9.362539 TGTCTCCTAATGTCTAATTAACGAAAC 57.637 33.333 0.00 0.00 0.00 2.78
156 157 7.977853 GGTGTCTCCTAATGTCTAATTAACGAA 59.022 37.037 0.00 0.00 0.00 3.85
157 158 7.417116 GGGTGTCTCCTAATGTCTAATTAACGA 60.417 40.741 0.00 0.00 36.25 3.85
158 159 6.700520 GGGTGTCTCCTAATGTCTAATTAACG 59.299 42.308 0.00 0.00 36.25 3.18
159 160 6.990939 GGGGTGTCTCCTAATGTCTAATTAAC 59.009 42.308 0.00 0.00 36.25 2.01
160 161 6.100714 GGGGGTGTCTCCTAATGTCTAATTAA 59.899 42.308 0.00 0.00 36.25 1.40
161 162 5.605488 GGGGGTGTCTCCTAATGTCTAATTA 59.395 44.000 0.00 0.00 36.25 1.40
165 166 3.042059 GGGGGTGTCTCCTAATGTCTA 57.958 52.381 0.00 0.00 36.25 2.59
166 167 1.880941 GGGGGTGTCTCCTAATGTCT 58.119 55.000 0.00 0.00 36.25 3.41
208 209 0.676736 CCTCTCACTAATCTCGCCCC 59.323 60.000 0.00 0.00 0.00 5.80
210 211 0.676736 CCCCTCTCACTAATCTCGCC 59.323 60.000 0.00 0.00 0.00 5.54
211 212 0.676736 CCCCCTCTCACTAATCTCGC 59.323 60.000 0.00 0.00 0.00 5.03
212 213 2.366640 TCCCCCTCTCACTAATCTCG 57.633 55.000 0.00 0.00 0.00 4.04
214 215 3.014110 TCCTTTCCCCCTCTCACTAATCT 59.986 47.826 0.00 0.00 0.00 2.40
215 216 3.385115 TCCTTTCCCCCTCTCACTAATC 58.615 50.000 0.00 0.00 0.00 1.75
216 217 3.508952 TCCTTTCCCCCTCTCACTAAT 57.491 47.619 0.00 0.00 0.00 1.73
219 220 1.988846 CTTTCCTTTCCCCCTCTCACT 59.011 52.381 0.00 0.00 0.00 3.41
220 221 1.705745 ACTTTCCTTTCCCCCTCTCAC 59.294 52.381 0.00 0.00 0.00 3.51
221 222 1.985895 GACTTTCCTTTCCCCCTCTCA 59.014 52.381 0.00 0.00 0.00 3.27
222 223 1.282447 GGACTTTCCTTTCCCCCTCTC 59.718 57.143 0.00 0.00 32.53 3.20
223 224 1.373536 GGACTTTCCTTTCCCCCTCT 58.626 55.000 0.00 0.00 32.53 3.69
226 227 0.111832 AACGGACTTTCCTTTCCCCC 59.888 55.000 0.00 0.00 33.30 5.40
229 230 5.472478 ACTTAATCAACGGACTTTCCTTTCC 59.528 40.000 0.00 0.00 33.30 3.13
230 231 6.555812 ACTTAATCAACGGACTTTCCTTTC 57.444 37.500 0.00 0.00 33.30 2.62
232 233 8.454570 TTTTACTTAATCAACGGACTTTCCTT 57.545 30.769 0.00 0.00 33.30 3.36
233 234 8.512138 CATTTTACTTAATCAACGGACTTTCCT 58.488 33.333 0.00 0.00 33.30 3.36
235 236 9.543018 CTCATTTTACTTAATCAACGGACTTTC 57.457 33.333 0.00 0.00 0.00 2.62
236 237 9.063615 ACTCATTTTACTTAATCAACGGACTTT 57.936 29.630 0.00 0.00 0.00 2.66
238 239 7.333672 GGACTCATTTTACTTAATCAACGGACT 59.666 37.037 0.00 0.00 0.00 3.85
239 240 7.461918 GGACTCATTTTACTTAATCAACGGAC 58.538 38.462 0.00 0.00 0.00 4.79
241 242 6.091713 ACGGACTCATTTTACTTAATCAACGG 59.908 38.462 0.00 0.00 0.00 4.44
242 243 6.953743 CACGGACTCATTTTACTTAATCAACG 59.046 38.462 0.00 0.00 0.00 4.10
243 244 8.025243 TCACGGACTCATTTTACTTAATCAAC 57.975 34.615 0.00 0.00 0.00 3.18
245 246 7.330946 CACTCACGGACTCATTTTACTTAATCA 59.669 37.037 0.00 0.00 0.00 2.57
247 248 7.159372 ACACTCACGGACTCATTTTACTTAAT 58.841 34.615 0.00 0.00 0.00 1.40
248 249 6.518493 ACACTCACGGACTCATTTTACTTAA 58.482 36.000 0.00 0.00 0.00 1.85
250 251 4.957296 ACACTCACGGACTCATTTTACTT 58.043 39.130 0.00 0.00 0.00 2.24
252 253 4.863131 CCTACACTCACGGACTCATTTTAC 59.137 45.833 0.00 0.00 0.00 2.01
254 255 3.864921 GCCTACACTCACGGACTCATTTT 60.865 47.826 0.00 0.00 0.00 1.82
255 256 2.353803 GCCTACACTCACGGACTCATTT 60.354 50.000 0.00 0.00 0.00 2.32
257 258 0.818296 GCCTACACTCACGGACTCAT 59.182 55.000 0.00 0.00 0.00 2.90
258 259 0.538746 TGCCTACACTCACGGACTCA 60.539 55.000 0.00 0.00 0.00 3.41
259 260 0.601558 TTGCCTACACTCACGGACTC 59.398 55.000 0.00 0.00 0.00 3.36
260 261 1.045407 TTTGCCTACACTCACGGACT 58.955 50.000 0.00 0.00 0.00 3.85
262 263 2.851263 ATTTTGCCTACACTCACGGA 57.149 45.000 0.00 0.00 0.00 4.69
263 264 4.000988 ACTAATTTTGCCTACACTCACGG 58.999 43.478 0.00 0.00 0.00 4.94
265 266 4.455877 AGCACTAATTTTGCCTACACTCAC 59.544 41.667 7.85 0.00 41.18 3.51
266 267 4.651778 AGCACTAATTTTGCCTACACTCA 58.348 39.130 7.85 0.00 41.18 3.41
267 268 5.629079 AAGCACTAATTTTGCCTACACTC 57.371 39.130 7.85 0.00 41.18 3.51
268 269 5.534654 TCAAAGCACTAATTTTGCCTACACT 59.465 36.000 7.85 0.00 41.18 3.55
270 271 5.048083 CCTCAAAGCACTAATTTTGCCTACA 60.048 40.000 7.85 0.00 41.18 2.74
271 272 5.402398 CCTCAAAGCACTAATTTTGCCTAC 58.598 41.667 7.85 0.00 41.18 3.18
272 273 4.462483 CCCTCAAAGCACTAATTTTGCCTA 59.538 41.667 7.85 0.00 41.18 3.93
274 275 3.006859 ACCCTCAAAGCACTAATTTTGCC 59.993 43.478 7.85 0.00 41.18 4.52
275 276 3.989817 CACCCTCAAAGCACTAATTTTGC 59.010 43.478 4.00 4.00 40.52 3.68
276 277 5.200368 ACACCCTCAAAGCACTAATTTTG 57.800 39.130 0.00 0.00 36.00 2.44
277 278 5.869649 AACACCCTCAAAGCACTAATTTT 57.130 34.783 0.00 0.00 0.00 1.82
278 279 5.869649 AAACACCCTCAAAGCACTAATTT 57.130 34.783 0.00 0.00 0.00 1.82
279 280 5.869649 AAAACACCCTCAAAGCACTAATT 57.130 34.783 0.00 0.00 0.00 1.40
281 282 5.180492 CGATAAAACACCCTCAAAGCACTAA 59.820 40.000 0.00 0.00 0.00 2.24
282 283 4.693566 CGATAAAACACCCTCAAAGCACTA 59.306 41.667 0.00 0.00 0.00 2.74
283 284 3.502211 CGATAAAACACCCTCAAAGCACT 59.498 43.478 0.00 0.00 0.00 4.40
285 286 2.817258 CCGATAAAACACCCTCAAAGCA 59.183 45.455 0.00 0.00 0.00 3.91
287 288 3.439129 GGTCCGATAAAACACCCTCAAAG 59.561 47.826 0.00 0.00 0.00 2.77
288 289 3.414269 GGTCCGATAAAACACCCTCAAA 58.586 45.455 0.00 0.00 0.00 2.69
290 291 1.066716 CGGTCCGATAAAACACCCTCA 60.067 52.381 4.91 0.00 0.00 3.86
291 292 1.066645 ACGGTCCGATAAAACACCCTC 60.067 52.381 20.51 0.00 0.00 4.30
292 293 0.978907 ACGGTCCGATAAAACACCCT 59.021 50.000 20.51 0.00 0.00 4.34
293 294 1.081094 CACGGTCCGATAAAACACCC 58.919 55.000 20.51 0.00 0.00 4.61
295 296 1.149987 TGCACGGTCCGATAAAACAC 58.850 50.000 20.51 0.00 0.00 3.32
296 297 1.880271 TTGCACGGTCCGATAAAACA 58.120 45.000 20.51 3.51 0.00 2.83
297 298 2.973419 TTTGCACGGTCCGATAAAAC 57.027 45.000 20.51 0.75 0.00 2.43
298 299 3.984508 TTTTTGCACGGTCCGATAAAA 57.015 38.095 20.51 17.34 0.00 1.52
299 300 3.366476 CCATTTTTGCACGGTCCGATAAA 60.366 43.478 20.51 12.57 0.00 1.40
300 301 2.162608 CCATTTTTGCACGGTCCGATAA 59.837 45.455 20.51 6.89 0.00 1.75
301 302 1.740585 CCATTTTTGCACGGTCCGATA 59.259 47.619 20.51 0.02 0.00 2.92
302 303 0.525761 CCATTTTTGCACGGTCCGAT 59.474 50.000 20.51 0.00 0.00 4.18
303 304 0.535328 TCCATTTTTGCACGGTCCGA 60.535 50.000 20.51 0.00 0.00 4.55
304 305 0.386731 GTCCATTTTTGCACGGTCCG 60.387 55.000 10.48 10.48 0.00 4.79
306 307 0.671251 TGGTCCATTTTTGCACGGTC 59.329 50.000 0.00 0.00 0.00 4.79
307 308 0.387565 GTGGTCCATTTTTGCACGGT 59.612 50.000 0.00 0.00 0.00 4.83
308 309 0.673437 AGTGGTCCATTTTTGCACGG 59.327 50.000 0.00 0.00 0.00 4.94
310 311 3.256631 AGATGAGTGGTCCATTTTTGCAC 59.743 43.478 0.00 0.00 0.00 4.57
311 312 3.499338 AGATGAGTGGTCCATTTTTGCA 58.501 40.909 0.00 0.00 0.00 4.08
312 313 4.525912 AAGATGAGTGGTCCATTTTTGC 57.474 40.909 0.00 0.00 0.00 3.68
315 316 6.324770 AGTTCAAAAGATGAGTGGTCCATTTT 59.675 34.615 0.00 0.00 39.77 1.82
319 320 4.437682 AGTTCAAAAGATGAGTGGTCCA 57.562 40.909 0.00 0.00 39.77 4.02
320 321 4.938226 CCTAGTTCAAAAGATGAGTGGTCC 59.062 45.833 0.00 0.00 39.77 4.46
322 323 4.202461 TGCCTAGTTCAAAAGATGAGTGGT 60.202 41.667 0.00 0.00 39.77 4.16
326 327 7.428826 ACTTTTTGCCTAGTTCAAAAGATGAG 58.571 34.615 17.81 14.40 42.24 2.90
327 328 7.346751 ACTTTTTGCCTAGTTCAAAAGATGA 57.653 32.000 17.81 6.82 42.24 2.92
328 329 8.065557 GAACTTTTTGCCTAGTTCAAAAGATG 57.934 34.615 17.81 14.10 45.99 2.90
343 344 4.241681 TGTTGTCCACTTGAACTTTTTGC 58.758 39.130 0.00 0.00 0.00 3.68
348 350 2.033299 CGCATGTTGTCCACTTGAACTT 59.967 45.455 0.00 0.00 33.21 2.66
351 353 1.333308 CACGCATGTTGTCCACTTGAA 59.667 47.619 0.00 0.00 33.21 2.69
352 354 0.943673 CACGCATGTTGTCCACTTGA 59.056 50.000 0.00 0.00 33.21 3.02
369 371 3.801594 ACAAACCATTGAATCGCAAACAC 59.198 39.130 0.00 0.00 40.48 3.32
371 373 3.428534 GGACAAACCATTGAATCGCAAAC 59.571 43.478 0.00 0.00 40.48 2.93
376 378 2.415893 GCTGGGACAAACCATTGAATCG 60.416 50.000 0.00 0.00 40.36 3.34
384 397 2.969300 GAACGGGCTGGGACAAACCA 62.969 60.000 0.00 0.00 38.70 3.67
396 409 1.005867 TACGTGTTGGAGAACGGGC 60.006 57.895 0.00 0.00 43.96 6.13
399 412 0.316204 AGGGTACGTGTTGGAGAACG 59.684 55.000 0.00 0.00 45.15 3.95
400 413 2.538512 AAGGGTACGTGTTGGAGAAC 57.461 50.000 0.00 0.00 0.00 3.01
402 415 2.040939 TCAAAGGGTACGTGTTGGAGA 58.959 47.619 0.00 0.00 0.00 3.71
403 416 2.536761 TCAAAGGGTACGTGTTGGAG 57.463 50.000 0.00 0.00 0.00 3.86
404 417 3.404899 GAATCAAAGGGTACGTGTTGGA 58.595 45.455 0.00 0.00 0.00 3.53
405 418 2.486592 GGAATCAAAGGGTACGTGTTGG 59.513 50.000 0.00 0.00 0.00 3.77
406 419 3.142951 TGGAATCAAAGGGTACGTGTTG 58.857 45.455 0.00 0.00 0.00 3.33
409 422 1.737793 GCTGGAATCAAAGGGTACGTG 59.262 52.381 0.00 0.00 0.00 4.49
411 424 1.006832 CGCTGGAATCAAAGGGTACG 58.993 55.000 0.00 0.00 0.00 3.67
413 426 3.054728 TCATTCGCTGGAATCAAAGGGTA 60.055 43.478 0.62 0.00 40.90 3.69
433 446 7.518848 CGCCAAGAATCTTAATTGATCGAATCA 60.519 37.037 0.00 0.00 37.55 2.57
434 447 6.794158 CGCCAAGAATCTTAATTGATCGAATC 59.206 38.462 0.00 0.00 0.00 2.52
438 451 5.200454 CACGCCAAGAATCTTAATTGATCG 58.800 41.667 0.00 0.00 0.00 3.69
440 453 5.192927 TCCACGCCAAGAATCTTAATTGAT 58.807 37.500 0.00 0.00 0.00 2.57
442 455 4.963276 TCCACGCCAAGAATCTTAATTG 57.037 40.909 0.00 0.00 0.00 2.32
443 456 5.975693 TTTCCACGCCAAGAATCTTAATT 57.024 34.783 0.00 0.00 0.00 1.40
446 459 5.708948 CAATTTTCCACGCCAAGAATCTTA 58.291 37.500 0.00 0.00 0.00 2.10
447 460 4.559153 CAATTTTCCACGCCAAGAATCTT 58.441 39.130 0.00 0.00 0.00 2.40
455 468 1.365633 GGTGCAATTTTCCACGCCA 59.634 52.632 0.00 0.00 32.85 5.69
464 477 2.872842 GCTTGCTTGGATGGTGCAATTT 60.873 45.455 0.00 0.00 44.20 1.82
528 541 3.983988 CGATCGAGTACGTACCTAGCTTA 59.016 47.826 21.80 1.94 40.69 3.09
543 556 5.049612 TGACAGGCTAACTAATACGATCGAG 60.050 44.000 24.34 11.21 0.00 4.04
545 558 5.104562 TGACAGGCTAACTAATACGATCG 57.895 43.478 14.88 14.88 0.00 3.69
546 559 7.148950 CGAATTGACAGGCTAACTAATACGATC 60.149 40.741 0.00 0.00 0.00 3.69
547 560 6.641314 CGAATTGACAGGCTAACTAATACGAT 59.359 38.462 0.00 0.00 0.00 3.73
548 561 5.975344 CGAATTGACAGGCTAACTAATACGA 59.025 40.000 0.00 0.00 0.00 3.43
549 562 5.332355 GCGAATTGACAGGCTAACTAATACG 60.332 44.000 0.00 0.00 0.00 3.06
620 633 2.277591 GCCTTGTGCATCTTGGCCA 61.278 57.895 0.00 0.00 40.77 5.36
649 662 0.536687 TCGACTGACAAGGTCTCCGT 60.537 55.000 0.00 0.00 33.15 4.69
651 664 0.109039 GCTCGACTGACAAGGTCTCC 60.109 60.000 0.00 0.00 33.15 3.71
699 712 0.394938 TTTGTGCTGCCGTCTTCCTA 59.605 50.000 0.00 0.00 0.00 2.94
790 818 6.313252 GTGCAGAAGAATCAATCAAAGAGAC 58.687 40.000 0.00 0.00 0.00 3.36
795 823 3.820467 ACGGTGCAGAAGAATCAATCAAA 59.180 39.130 0.00 0.00 0.00 2.69
799 827 1.470098 GCACGGTGCAGAAGAATCAAT 59.530 47.619 27.10 0.00 44.26 2.57
827 4626 0.461548 GGCCGACTGATGATGAGTGA 59.538 55.000 0.00 0.00 0.00 3.41
829 4628 1.683917 GTAGGCCGACTGATGATGAGT 59.316 52.381 9.01 0.00 0.00 3.41
992 4806 1.079612 CTGCTCGCCATCACTGACA 60.080 57.895 0.00 0.00 0.00 3.58
1129 4949 5.695816 GCAAATGAAAGTGAAACCATAGCAA 59.304 36.000 0.00 0.00 37.80 3.91
1159 4980 8.046294 TGTCACACCATATTTGTAAACCATAC 57.954 34.615 0.00 0.00 0.00 2.39
1698 5531 1.148310 AAGCGTTGTCGAACCTCATG 58.852 50.000 0.00 0.00 39.71 3.07
1719 5913 2.264813 TGCGCGATAAGGTTCTTGTAC 58.735 47.619 12.10 0.00 0.00 2.90
1739 5933 1.079750 GAAGAAAGGAGACCGCGCT 60.080 57.895 5.56 0.00 0.00 5.92
1755 5949 1.678123 CCGTAGAGAGTCTGGTCCGAA 60.678 57.143 0.00 0.00 0.00 4.30
1778 5972 5.738909 CAAGATTGTCTTGTAGACCTCCAT 58.261 41.667 10.72 0.00 46.50 3.41
1800 5994 0.380733 CGGCGCTGTACATCTCTACA 59.619 55.000 8.45 0.00 0.00 2.74
1803 5997 1.433879 GTCGGCGCTGTACATCTCT 59.566 57.895 17.37 0.00 0.00 3.10
1972 6167 1.097547 CAACATGATCAGGCCGGGTC 61.098 60.000 9.51 9.51 0.00 4.46
2069 6781 4.898829 TGTGTCAAACATTCTGTTGAGG 57.101 40.909 0.00 0.00 40.14 3.86
2093 6806 1.725641 ACACACACATGTATGGAGCG 58.274 50.000 9.31 0.00 36.72 5.03
2095 6808 8.344831 CCATTTATTACACACACATGTATGGAG 58.655 37.037 9.31 3.21 37.24 3.86
2146 6889 7.652300 TCAACGCGAGCTCATTATATATTTT 57.348 32.000 15.93 0.00 0.00 1.82
2195 6939 6.878923 TCCCCGAGTGCAGAAATATAATAATG 59.121 38.462 0.00 0.00 0.00 1.90
2199 6943 4.974645 TCCCCGAGTGCAGAAATATAAT 57.025 40.909 0.00 0.00 0.00 1.28
2215 6959 4.003648 GGAAGCATCACTAATAATCCCCG 58.996 47.826 0.00 0.00 0.00 5.73
2225 6969 2.034179 CGGACATACGGAAGCATCACTA 59.966 50.000 0.00 0.00 0.00 2.74
2239 6985 5.242171 TCAATAGAATAGCCGTTCGGACATA 59.758 40.000 15.69 4.80 33.36 2.29
2333 7099 2.028130 TGAAGTGCCGTGGTCATTTTT 58.972 42.857 0.00 0.00 0.00 1.94
2336 7102 1.686355 TTTGAAGTGCCGTGGTCATT 58.314 45.000 0.00 0.00 0.00 2.57
2416 7198 7.301068 TCGAAGAACAATTTTGTGCATTTTT 57.699 28.000 4.30 0.00 41.31 1.94
2505 7539 6.258947 GTCATCCTCTTACTTTACTCATTGCC 59.741 42.308 0.00 0.00 0.00 4.52
2534 7572 0.798776 GTGAACACTCCCAAGCATCG 59.201 55.000 0.00 0.00 0.00 3.84
2564 7604 3.245586 TGTTGGGCAATTATTCCACCTCT 60.246 43.478 0.00 0.00 0.00 3.69
2651 7691 6.189859 AGCCATGTCAAATCCAGAAATTCTA 58.810 36.000 0.00 0.00 0.00 2.10
2654 7694 5.954150 AGTAGCCATGTCAAATCCAGAAATT 59.046 36.000 0.00 0.00 0.00 1.82
2659 7699 5.220931 GCTAAAGTAGCCATGTCAAATCCAG 60.221 44.000 0.00 0.00 45.95 3.86
2681 7721 2.502142 TTGTGAGATTCATGCAGGCT 57.498 45.000 0.00 0.00 0.00 4.58
2688 7729 6.321435 AGCATTGATGTCATTGTGAGATTCAT 59.679 34.615 6.72 0.00 29.83 2.57


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

AutoCloner maintained by Alex Coulton.