Multiple sequence alignment - TraesCS3B01G394700

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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 TraesCS3B01G394700 chr3B 100.000 3188 0 0 1 3188 621965503 621962316 0.000000e+00 5888
1 TraesCS3B01G394700 chr3B 84.525 1525 216 19 544 2057 772134547 772136062 0.000000e+00 1491
2 TraesCS3B01G394700 chr3B 96.013 301 11 1 44 343 621990074 621989774 3.700000e-134 488
3 TraesCS3B01G394700 chr6B 99.026 1540 14 1 1632 3170 27645352 27646891 0.000000e+00 2760
4 TraesCS3B01G394700 chr6B 97.685 864 9 2 666 1529 27635180 27636032 0.000000e+00 1474
5 TraesCS3B01G394700 chr6B 97.590 332 8 0 343 674 27632721 27633052 1.280000e-158 569
6 TraesCS3B01G394700 chr2A 86.851 1985 235 25 461 2434 35460996 35462965 0.000000e+00 2196
7 TraesCS3B01G394700 chr4A 81.305 1257 218 14 990 2236 536855157 536853908 0.000000e+00 1003
8 TraesCS3B01G394700 chr4A 80.876 1255 227 11 990 2236 521608584 521607335 0.000000e+00 976
9 TraesCS3B01G394700 chr4A 95.614 342 15 0 1 342 661960925 661960584 1.670000e-152 549
10 TraesCS3B01G394700 chr4A 96.000 300 12 0 44 343 661968451 661968152 3.700000e-134 488
11 TraesCS3B01G394700 chr1A 82.827 1054 166 14 544 1589 563280683 563279637 0.000000e+00 929
12 TraesCS3B01G394700 chr4B 92.733 344 21 4 1 342 72950947 72950606 7.940000e-136 494
13 TraesCS3B01G394700 chr6A 89.337 347 31 5 1 342 22907219 22907564 6.320000e-117 431
14 TraesCS3B01G394700 chr1B 89.306 346 33 4 1 342 515933718 515934063 6.320000e-117 431
15 TraesCS3B01G394700 chr1B 89.306 346 32 5 1 343 321116338 321115995 2.270000e-116 429
16 TraesCS3B01G394700 chr7A 89.112 349 32 6 1 346 714968854 714968509 2.270000e-116 429
17 TraesCS3B01G394700 chr5D 89.337 347 30 6 1 343 352831052 352830709 2.270000e-116 429


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 TraesCS3B01G394700 chr3B 621962316 621965503 3187 True 5888.0 5888 100.0000 1 3188 1 chr3B.!!$R1 3187
1 TraesCS3B01G394700 chr3B 772134547 772136062 1515 False 1491.0 1491 84.5250 544 2057 1 chr3B.!!$F1 1513
2 TraesCS3B01G394700 chr6B 27645352 27646891 1539 False 2760.0 2760 99.0260 1632 3170 1 chr6B.!!$F1 1538
3 TraesCS3B01G394700 chr6B 27632721 27636032 3311 False 1021.5 1474 97.6375 343 1529 2 chr6B.!!$F2 1186
4 TraesCS3B01G394700 chr2A 35460996 35462965 1969 False 2196.0 2196 86.8510 461 2434 1 chr2A.!!$F1 1973
5 TraesCS3B01G394700 chr4A 536853908 536855157 1249 True 1003.0 1003 81.3050 990 2236 1 chr4A.!!$R2 1246
6 TraesCS3B01G394700 chr4A 521607335 521608584 1249 True 976.0 976 80.8760 990 2236 1 chr4A.!!$R1 1246
7 TraesCS3B01G394700 chr1A 563279637 563280683 1046 True 929.0 929 82.8270 544 1589 1 chr1A.!!$R1 1045

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
274 275 0.039256 TTAACGACACGAGGGGAACG 60.039 55.0 0.00 0.0 0.0 3.95 F
1554 3702 0.035439 ACCCGGGTGCTTATTGTCTG 60.035 55.0 29.69 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 3725 0.957395 CACACTGACCCACCATCTGC 60.957 60.000 0.0 0.00 0.0 4.26 R
2716 4868 1.002900 CATTTTAACGGATGGCGCGAT 60.003 47.619 12.1 3.93 0.0 4.58 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
19 20 2.827800 CAGGCTTGACAGAGAGTTGA 57.172 50.000 0.00 0.00 0.00 3.18
20 21 3.331478 CAGGCTTGACAGAGAGTTGAT 57.669 47.619 0.00 0.00 0.00 2.57
21 22 3.001414 CAGGCTTGACAGAGAGTTGATG 58.999 50.000 0.00 0.00 0.00 3.07
22 23 2.027377 AGGCTTGACAGAGAGTTGATGG 60.027 50.000 0.00 0.00 0.00 3.51
23 24 2.027745 GGCTTGACAGAGAGTTGATGGA 60.028 50.000 0.00 0.00 0.00 3.41
24 25 3.260740 GCTTGACAGAGAGTTGATGGAG 58.739 50.000 0.00 0.00 0.00 3.86
25 26 3.260740 CTTGACAGAGAGTTGATGGAGC 58.739 50.000 0.00 0.00 0.00 4.70
26 27 1.203287 TGACAGAGAGTTGATGGAGCG 59.797 52.381 0.00 0.00 0.00 5.03
27 28 1.474478 GACAGAGAGTTGATGGAGCGA 59.526 52.381 0.00 0.00 0.00 4.93
28 29 1.895798 ACAGAGAGTTGATGGAGCGAA 59.104 47.619 0.00 0.00 0.00 4.70
29 30 2.094286 ACAGAGAGTTGATGGAGCGAAG 60.094 50.000 0.00 0.00 0.00 3.79
44 45 2.357954 CGAAGCGTGCTGATAACATG 57.642 50.000 0.00 0.00 0.00 3.21
45 46 1.660607 CGAAGCGTGCTGATAACATGT 59.339 47.619 0.00 0.00 0.00 3.21
46 47 2.094258 CGAAGCGTGCTGATAACATGTT 59.906 45.455 16.68 16.68 0.00 2.71
47 48 3.674423 GAAGCGTGCTGATAACATGTTC 58.326 45.455 15.85 1.96 0.00 3.18
48 49 2.009774 AGCGTGCTGATAACATGTTCC 58.990 47.619 15.85 9.06 0.00 3.62
49 50 1.267532 GCGTGCTGATAACATGTTCCG 60.268 52.381 15.85 8.16 0.00 4.30
50 51 1.267532 CGTGCTGATAACATGTTCCGC 60.268 52.381 15.85 10.51 0.00 5.54
51 52 1.737236 GTGCTGATAACATGTTCCGCA 59.263 47.619 15.85 13.10 0.00 5.69
52 53 2.161410 GTGCTGATAACATGTTCCGCAA 59.839 45.455 15.85 0.00 0.00 4.85
53 54 2.161410 TGCTGATAACATGTTCCGCAAC 59.839 45.455 15.85 7.86 0.00 4.17
54 55 2.420022 GCTGATAACATGTTCCGCAACT 59.580 45.455 15.85 0.00 33.17 3.16
55 56 3.485877 GCTGATAACATGTTCCGCAACTC 60.486 47.826 15.85 2.94 33.17 3.01
56 57 3.006940 TGATAACATGTTCCGCAACTCC 58.993 45.455 15.85 0.00 33.17 3.85
57 58 2.851263 TAACATGTTCCGCAACTCCT 57.149 45.000 15.85 0.00 33.17 3.69
58 59 1.238439 AACATGTTCCGCAACTCCTG 58.762 50.000 4.92 0.00 33.17 3.86
67 68 4.379243 CAACTCCTGCCGGCGAGT 62.379 66.667 25.78 25.78 41.10 4.18
68 69 4.070552 AACTCCTGCCGGCGAGTC 62.071 66.667 29.62 3.30 38.39 3.36
78 79 4.452733 GGCGAGTCCGGTCCAAGG 62.453 72.222 0.00 0.00 36.06 3.61
79 80 3.692406 GCGAGTCCGGTCCAAGGT 61.692 66.667 0.00 0.00 36.06 3.50
80 81 3.057337 CGAGTCCGGTCCAAGGTT 58.943 61.111 0.00 0.00 0.00 3.50
81 82 1.374252 CGAGTCCGGTCCAAGGTTG 60.374 63.158 0.00 0.00 0.00 3.77
82 83 1.671379 GAGTCCGGTCCAAGGTTGC 60.671 63.158 0.00 0.00 0.00 4.17
83 84 3.047877 GTCCGGTCCAAGGTTGCG 61.048 66.667 0.00 0.00 0.00 4.85
84 85 4.323477 TCCGGTCCAAGGTTGCGG 62.323 66.667 0.00 0.00 34.17 5.69
85 86 4.323477 CCGGTCCAAGGTTGCGGA 62.323 66.667 0.00 0.00 34.59 5.54
86 87 2.742372 CGGTCCAAGGTTGCGGAG 60.742 66.667 0.00 0.00 29.98 4.63
104 105 4.592936 CGGGAGCGAGCGTCGTAG 62.593 72.222 8.72 0.00 42.81 3.51
105 106 3.200593 GGGAGCGAGCGTCGTAGA 61.201 66.667 8.72 0.00 42.81 2.59
133 134 2.537013 CGAAGTAGTCGTACACGCG 58.463 57.895 3.53 3.53 45.09 6.01
134 135 0.093535 CGAAGTAGTCGTACACGCGA 59.906 55.000 15.93 0.00 45.09 5.87
135 136 1.462378 CGAAGTAGTCGTACACGCGAA 60.462 52.381 15.93 0.00 45.09 4.70
136 137 2.574322 GAAGTAGTCGTACACGCGAAA 58.426 47.619 15.93 0.00 42.82 3.46
137 138 2.238245 AGTAGTCGTACACGCGAAAG 57.762 50.000 15.93 4.52 42.82 2.62
138 139 1.532868 AGTAGTCGTACACGCGAAAGT 59.467 47.619 15.93 11.15 42.82 2.66
139 140 2.736721 AGTAGTCGTACACGCGAAAGTA 59.263 45.455 15.93 10.02 42.82 2.24
140 141 2.686558 AGTCGTACACGCGAAAGTAA 57.313 45.000 15.93 0.00 42.82 2.24
141 142 2.998772 AGTCGTACACGCGAAAGTAAA 58.001 42.857 15.93 2.06 42.82 2.01
142 143 3.568538 AGTCGTACACGCGAAAGTAAAT 58.431 40.909 15.93 0.00 42.82 1.40
143 144 3.362831 AGTCGTACACGCGAAAGTAAATG 59.637 43.478 15.93 0.00 42.82 2.32
144 145 3.361644 GTCGTACACGCGAAAGTAAATGA 59.638 43.478 15.93 8.62 42.82 2.57
145 146 3.361644 TCGTACACGCGAAAGTAAATGAC 59.638 43.478 15.93 2.20 37.99 3.06
146 147 3.119956 CGTACACGCGAAAGTAAATGACA 59.880 43.478 15.93 0.00 0.00 3.58
147 148 3.515071 ACACGCGAAAGTAAATGACAC 57.485 42.857 15.93 0.00 0.00 3.67
148 149 2.867368 ACACGCGAAAGTAAATGACACA 59.133 40.909 15.93 0.00 0.00 3.72
149 150 3.059868 ACACGCGAAAGTAAATGACACAG 60.060 43.478 15.93 0.00 0.00 3.66
150 151 3.183574 CACGCGAAAGTAAATGACACAGA 59.816 43.478 15.93 0.00 0.00 3.41
151 152 3.805422 ACGCGAAAGTAAATGACACAGAA 59.195 39.130 15.93 0.00 0.00 3.02
152 153 4.271533 ACGCGAAAGTAAATGACACAGAAA 59.728 37.500 15.93 0.00 0.00 2.52
153 154 4.840772 CGCGAAAGTAAATGACACAGAAAG 59.159 41.667 0.00 0.00 0.00 2.62
154 155 5.333035 CGCGAAAGTAAATGACACAGAAAGA 60.333 40.000 0.00 0.00 0.00 2.52
155 156 6.603095 GCGAAAGTAAATGACACAGAAAGAT 58.397 36.000 0.00 0.00 0.00 2.40
156 157 7.411480 CGCGAAAGTAAATGACACAGAAAGATA 60.411 37.037 0.00 0.00 0.00 1.98
157 158 8.391106 GCGAAAGTAAATGACACAGAAAGATAT 58.609 33.333 0.00 0.00 0.00 1.63
158 159 9.694520 CGAAAGTAAATGACACAGAAAGATATG 57.305 33.333 0.00 0.00 0.00 1.78
159 160 9.994432 GAAAGTAAATGACACAGAAAGATATGG 57.006 33.333 0.00 0.00 0.00 2.74
160 161 9.739276 AAAGTAAATGACACAGAAAGATATGGA 57.261 29.630 0.00 0.00 0.00 3.41
161 162 8.954950 AGTAAATGACACAGAAAGATATGGAG 57.045 34.615 0.00 0.00 0.00 3.86
162 163 8.762645 AGTAAATGACACAGAAAGATATGGAGA 58.237 33.333 0.00 0.00 0.00 3.71
163 164 9.383519 GTAAATGACACAGAAAGATATGGAGAA 57.616 33.333 0.00 0.00 0.00 2.87
164 165 8.503458 AAATGACACAGAAAGATATGGAGAAG 57.497 34.615 0.00 0.00 0.00 2.85
165 166 6.857437 TGACACAGAAAGATATGGAGAAGA 57.143 37.500 0.00 0.00 0.00 2.87
166 167 6.634805 TGACACAGAAAGATATGGAGAAGAC 58.365 40.000 0.00 0.00 0.00 3.01
167 168 5.983540 ACACAGAAAGATATGGAGAAGACC 58.016 41.667 0.00 0.00 0.00 3.85
168 169 5.485353 ACACAGAAAGATATGGAGAAGACCA 59.515 40.000 0.00 0.00 44.41 4.02
169 170 6.047870 CACAGAAAGATATGGAGAAGACCAG 58.952 44.000 0.00 0.00 43.49 4.00
170 171 5.055812 CAGAAAGATATGGAGAAGACCAGC 58.944 45.833 0.00 0.00 43.49 4.85
171 172 4.968080 AGAAAGATATGGAGAAGACCAGCT 59.032 41.667 0.00 0.00 43.49 4.24
172 173 5.428131 AGAAAGATATGGAGAAGACCAGCTT 59.572 40.000 0.00 0.00 43.49 3.74
173 174 5.707066 AAGATATGGAGAAGACCAGCTTT 57.293 39.130 0.00 0.00 43.49 3.51
174 175 6.814954 AAGATATGGAGAAGACCAGCTTTA 57.185 37.500 0.00 0.00 43.49 1.85
175 176 7.385894 AAGATATGGAGAAGACCAGCTTTAT 57.614 36.000 0.00 0.00 43.49 1.40
176 177 7.385894 AGATATGGAGAAGACCAGCTTTATT 57.614 36.000 0.00 0.00 43.49 1.40
177 178 8.497910 AGATATGGAGAAGACCAGCTTTATTA 57.502 34.615 0.00 0.00 43.49 0.98
178 179 8.938883 AGATATGGAGAAGACCAGCTTTATTAA 58.061 33.333 0.00 0.00 43.49 1.40
179 180 9.732130 GATATGGAGAAGACCAGCTTTATTAAT 57.268 33.333 0.00 0.00 43.49 1.40
180 181 9.732130 ATATGGAGAAGACCAGCTTTATTAATC 57.268 33.333 0.00 0.00 43.49 1.75
181 182 6.957631 TGGAGAAGACCAGCTTTATTAATCA 58.042 36.000 0.00 0.00 36.83 2.57
182 183 7.402054 TGGAGAAGACCAGCTTTATTAATCAA 58.598 34.615 0.00 0.00 36.83 2.57
183 184 8.055181 TGGAGAAGACCAGCTTTATTAATCAAT 58.945 33.333 0.00 0.00 36.83 2.57
184 185 8.348507 GGAGAAGACCAGCTTTATTAATCAATG 58.651 37.037 0.00 0.00 36.83 2.82
185 186 9.113838 GAGAAGACCAGCTTTATTAATCAATGA 57.886 33.333 0.00 0.00 36.83 2.57
186 187 9.638176 AGAAGACCAGCTTTATTAATCAATGAT 57.362 29.630 0.00 0.00 36.83 2.45
187 188 9.890352 GAAGACCAGCTTTATTAATCAATGATC 57.110 33.333 0.00 0.00 36.83 2.92
188 189 8.985315 AGACCAGCTTTATTAATCAATGATCA 57.015 30.769 0.00 0.00 0.00 2.92
189 190 9.064706 AGACCAGCTTTATTAATCAATGATCAG 57.935 33.333 0.09 0.00 0.00 2.90
190 191 8.174733 ACCAGCTTTATTAATCAATGATCAGG 57.825 34.615 0.09 0.00 0.00 3.86
191 192 7.232127 ACCAGCTTTATTAATCAATGATCAGGG 59.768 37.037 0.09 0.00 0.00 4.45
192 193 7.309621 CCAGCTTTATTAATCAATGATCAGGGG 60.310 40.741 0.09 0.00 0.00 4.79
193 194 7.232127 CAGCTTTATTAATCAATGATCAGGGGT 59.768 37.037 0.09 0.00 0.00 4.95
194 195 7.786464 AGCTTTATTAATCAATGATCAGGGGTT 59.214 33.333 0.09 0.73 0.00 4.11
195 196 9.077885 GCTTTATTAATCAATGATCAGGGGTTA 57.922 33.333 0.09 0.00 0.00 2.85
197 198 9.928618 TTTATTAATCAATGATCAGGGGTTACA 57.071 29.630 0.09 0.00 0.00 2.41
198 199 9.928618 TTATTAATCAATGATCAGGGGTTACAA 57.071 29.630 0.09 0.00 0.00 2.41
201 202 9.928618 TTAATCAATGATCAGGGGTTACAATAA 57.071 29.630 0.09 0.00 0.00 1.40
203 204 7.822161 TCAATGATCAGGGGTTACAATAATG 57.178 36.000 0.09 0.00 0.00 1.90
204 205 6.777091 TCAATGATCAGGGGTTACAATAATGG 59.223 38.462 0.09 0.00 0.00 3.16
205 206 4.469657 TGATCAGGGGTTACAATAATGGC 58.530 43.478 0.00 0.00 0.00 4.40
206 207 4.167892 TGATCAGGGGTTACAATAATGGCT 59.832 41.667 0.00 0.00 0.00 4.75
207 208 4.164843 TCAGGGGTTACAATAATGGCTC 57.835 45.455 0.00 0.00 0.00 4.70
208 209 3.117663 TCAGGGGTTACAATAATGGCTCC 60.118 47.826 0.00 0.00 0.00 4.70
209 210 3.117512 CAGGGGTTACAATAATGGCTCCT 60.118 47.826 0.00 0.00 30.95 3.69
210 211 3.138468 AGGGGTTACAATAATGGCTCCTC 59.862 47.826 0.00 0.00 0.00 3.71
211 212 3.139077 GGGTTACAATAATGGCTCCTCG 58.861 50.000 0.00 0.00 0.00 4.63
212 213 3.139077 GGTTACAATAATGGCTCCTCGG 58.861 50.000 0.00 0.00 0.00 4.63
213 214 3.433173 GGTTACAATAATGGCTCCTCGGT 60.433 47.826 0.00 0.00 0.00 4.69
214 215 2.332063 ACAATAATGGCTCCTCGGTG 57.668 50.000 0.00 0.00 0.00 4.94
215 216 0.947244 CAATAATGGCTCCTCGGTGC 59.053 55.000 1.50 1.50 0.00 5.01
216 217 0.839946 AATAATGGCTCCTCGGTGCT 59.160 50.000 9.56 0.00 35.28 4.40
217 218 0.839946 ATAATGGCTCCTCGGTGCTT 59.160 50.000 9.56 0.93 35.28 3.91
218 219 0.618458 TAATGGCTCCTCGGTGCTTT 59.382 50.000 9.56 6.87 35.28 3.51
219 220 0.618458 AATGGCTCCTCGGTGCTTTA 59.382 50.000 9.56 0.00 35.28 1.85
220 221 0.839946 ATGGCTCCTCGGTGCTTTAT 59.160 50.000 9.56 1.04 35.28 1.40
221 222 1.491668 TGGCTCCTCGGTGCTTTATA 58.508 50.000 9.56 0.00 35.28 0.98
222 223 2.047061 TGGCTCCTCGGTGCTTTATAT 58.953 47.619 9.56 0.00 35.28 0.86
223 224 3.236047 TGGCTCCTCGGTGCTTTATATA 58.764 45.455 9.56 0.00 35.28 0.86
224 225 3.258372 TGGCTCCTCGGTGCTTTATATAG 59.742 47.826 9.56 0.00 35.28 1.31
225 226 3.510360 GGCTCCTCGGTGCTTTATATAGA 59.490 47.826 9.56 0.00 35.28 1.98
226 227 4.381079 GGCTCCTCGGTGCTTTATATAGAG 60.381 50.000 9.56 0.00 35.28 2.43
227 228 4.459685 GCTCCTCGGTGCTTTATATAGAGA 59.540 45.833 4.50 0.00 0.00 3.10
228 229 5.047943 GCTCCTCGGTGCTTTATATAGAGAA 60.048 44.000 4.50 0.00 0.00 2.87
229 230 6.516860 GCTCCTCGGTGCTTTATATAGAGAAA 60.517 42.308 4.50 0.00 0.00 2.52
230 231 7.356089 TCCTCGGTGCTTTATATAGAGAAAA 57.644 36.000 4.50 0.00 0.00 2.29
231 232 7.434492 TCCTCGGTGCTTTATATAGAGAAAAG 58.566 38.462 4.50 0.00 34.14 2.27
232 233 6.647067 CCTCGGTGCTTTATATAGAGAAAAGG 59.353 42.308 4.50 0.00 32.14 3.11
233 234 6.522054 TCGGTGCTTTATATAGAGAAAAGGG 58.478 40.000 4.50 0.00 32.14 3.95
234 235 5.701290 CGGTGCTTTATATAGAGAAAAGGGG 59.299 44.000 4.50 0.00 32.14 4.79
235 236 6.004574 GGTGCTTTATATAGAGAAAAGGGGG 58.995 44.000 4.50 0.00 32.14 5.40
236 237 6.410504 GGTGCTTTATATAGAGAAAAGGGGGT 60.411 42.308 4.50 0.00 32.14 4.95
237 238 7.061054 GTGCTTTATATAGAGAAAAGGGGGTT 58.939 38.462 4.50 0.00 32.14 4.11
238 239 8.215736 GTGCTTTATATAGAGAAAAGGGGGTTA 58.784 37.037 4.50 0.00 32.14 2.85
239 240 8.783903 TGCTTTATATAGAGAAAAGGGGGTTAA 58.216 33.333 4.50 0.00 32.14 2.01
240 241 9.286170 GCTTTATATAGAGAAAAGGGGGTTAAG 57.714 37.037 4.50 0.00 32.14 1.85
241 242 9.794719 CTTTATATAGAGAAAAGGGGGTTAAGG 57.205 37.037 0.00 0.00 0.00 2.69
242 243 6.781857 ATATAGAGAAAAGGGGGTTAAGGG 57.218 41.667 0.00 0.00 0.00 3.95
243 244 3.013984 AGAGAAAAGGGGGTTAAGGGA 57.986 47.619 0.00 0.00 0.00 4.20
244 245 3.553235 AGAGAAAAGGGGGTTAAGGGAT 58.447 45.455 0.00 0.00 0.00 3.85
245 246 4.717755 AGAGAAAAGGGGGTTAAGGGATA 58.282 43.478 0.00 0.00 0.00 2.59
246 247 5.113125 AGAGAAAAGGGGGTTAAGGGATAA 58.887 41.667 0.00 0.00 0.00 1.75
247 248 5.558339 AGAGAAAAGGGGGTTAAGGGATAAA 59.442 40.000 0.00 0.00 0.00 1.40
248 249 6.221872 AGAGAAAAGGGGGTTAAGGGATAAAT 59.778 38.462 0.00 0.00 0.00 1.40
249 250 7.410885 AGAGAAAAGGGGGTTAAGGGATAAATA 59.589 37.037 0.00 0.00 0.00 1.40
250 251 7.359849 AGAAAAGGGGGTTAAGGGATAAATAC 58.640 38.462 0.00 0.00 0.00 1.89
251 252 5.674799 AAGGGGGTTAAGGGATAAATACC 57.325 43.478 0.00 0.00 0.00 2.73
263 264 5.673514 GGGATAAATACCCACTTAACGACA 58.326 41.667 0.00 0.00 46.05 4.35
264 265 5.525012 GGGATAAATACCCACTTAACGACAC 59.475 44.000 0.00 0.00 46.05 3.67
265 266 5.232838 GGATAAATACCCACTTAACGACACG 59.767 44.000 0.00 0.00 0.00 4.49
266 267 3.940209 AATACCCACTTAACGACACGA 57.060 42.857 0.00 0.00 0.00 4.35
267 268 2.995466 TACCCACTTAACGACACGAG 57.005 50.000 0.00 0.00 0.00 4.18
268 269 0.316204 ACCCACTTAACGACACGAGG 59.684 55.000 0.00 0.00 0.00 4.63
269 270 0.389426 CCCACTTAACGACACGAGGG 60.389 60.000 0.00 0.00 0.00 4.30
270 271 0.389426 CCACTTAACGACACGAGGGG 60.389 60.000 0.00 0.00 0.00 4.79
271 272 0.599558 CACTTAACGACACGAGGGGA 59.400 55.000 0.00 0.00 0.00 4.81
272 273 1.000060 CACTTAACGACACGAGGGGAA 60.000 52.381 0.00 0.00 0.00 3.97
273 274 1.000171 ACTTAACGACACGAGGGGAAC 60.000 52.381 0.00 0.00 0.00 3.62
274 275 0.039256 TTAACGACACGAGGGGAACG 60.039 55.000 0.00 0.00 0.00 3.95
275 276 1.865788 TAACGACACGAGGGGAACGG 61.866 60.000 0.00 0.00 34.93 4.44
276 277 4.430765 CGACACGAGGGGAACGGG 62.431 72.222 0.00 0.00 40.19 5.28
277 278 2.993264 GACACGAGGGGAACGGGA 60.993 66.667 0.00 0.00 37.60 5.14
278 279 2.995574 ACACGAGGGGAACGGGAG 60.996 66.667 0.00 0.00 37.60 4.30
279 280 3.771160 CACGAGGGGAACGGGAGG 61.771 72.222 0.00 0.00 36.15 4.30
284 285 4.810184 GGGGAACGGGAGGGGCTA 62.810 72.222 0.00 0.00 0.00 3.93
285 286 3.162154 GGGAACGGGAGGGGCTAG 61.162 72.222 0.00 0.00 0.00 3.42
286 287 3.862991 GGAACGGGAGGGGCTAGC 61.863 72.222 6.04 6.04 0.00 3.42
287 288 3.862991 GAACGGGAGGGGCTAGCC 61.863 72.222 26.55 26.55 0.00 3.93
297 298 2.125431 GGCTAGCCCGTGCGTTTA 60.125 61.111 24.19 0.00 44.33 2.01
298 299 2.171725 GGCTAGCCCGTGCGTTTAG 61.172 63.158 24.19 0.00 44.33 1.85
327 328 4.530857 CGCCACCCTCCGGATGAC 62.531 72.222 3.57 0.00 0.00 3.06
328 329 4.176752 GCCACCCTCCGGATGACC 62.177 72.222 3.57 0.00 0.00 4.02
329 330 3.480133 CCACCCTCCGGATGACCC 61.480 72.222 3.57 0.00 0.00 4.46
338 339 3.083386 GGATGACCCGGTTTCCCA 58.917 61.111 0.00 0.00 0.00 4.37
339 340 1.381076 GGATGACCCGGTTTCCCAA 59.619 57.895 0.00 0.00 0.00 4.12
340 341 0.963856 GGATGACCCGGTTTCCCAAC 60.964 60.000 0.00 0.00 0.00 3.77
341 342 0.250989 GATGACCCGGTTTCCCAACA 60.251 55.000 0.00 0.00 34.15 3.33
342 343 0.538746 ATGACCCGGTTTCCCAACAC 60.539 55.000 0.00 0.00 34.15 3.32
343 344 1.152922 GACCCGGTTTCCCAACACA 60.153 57.895 0.00 0.00 34.15 3.72
344 345 0.538746 GACCCGGTTTCCCAACACAT 60.539 55.000 0.00 0.00 34.15 3.21
416 417 2.968156 CAAAACCGCGTGTCCCGA 60.968 61.111 4.92 0.00 39.56 5.14
432 433 1.070134 CCCGAACTTGGACTGTCTGAA 59.930 52.381 7.85 0.65 0.00 3.02
440 441 4.098960 ACTTGGACTGTCTGAAGAACGTTA 59.901 41.667 19.92 0.00 0.00 3.18
780 2926 3.076621 CAAGCACATTTACTCCAGCTCA 58.923 45.455 0.00 0.00 0.00 4.26
897 3043 4.457466 GGTACACTTCCAGGACAGAAAAA 58.543 43.478 0.00 0.00 0.00 1.94
1477 3625 1.801913 GCGTGCTTCGTCGTCATCT 60.802 57.895 0.00 0.00 42.13 2.90
1490 3638 0.172803 GTCATCTACGGCGTGAAGGT 59.827 55.000 24.86 6.22 0.00 3.50
1539 3687 2.510691 GCACCGTACATCCACCCG 60.511 66.667 0.00 0.00 0.00 5.28
1554 3702 0.035439 ACCCGGGTGCTTATTGTCTG 60.035 55.000 29.69 0.00 0.00 3.51
1577 3725 1.915266 TCTGCACACTCCTGGAGGG 60.915 63.158 24.26 24.26 39.30 4.30
1592 3740 2.262774 GAGGGCAGATGGTGGGTCAG 62.263 65.000 0.00 0.00 0.00 3.51
1665 3813 1.623811 CGGGGTCTGGTTATAGATGGG 59.376 57.143 0.00 0.00 0.00 4.00
1910 4058 0.611200 AGTACATACAACCTGCGGCA 59.389 50.000 1.29 1.29 0.00 5.69
2255 4406 7.751348 CAGTAATACATAGATGTTCTAGCGGAC 59.249 40.741 0.00 0.00 41.97 4.79
2472 4624 2.363276 TCCTCCCCGCGTACATGT 60.363 61.111 4.92 2.69 0.00 3.21
2495 4647 6.036735 TGTGATAGAACACTAAATAAAGCGGC 59.963 38.462 0.00 0.00 40.87 6.53
2663 4815 2.802247 GCAAGCCATGTTTTCCAACTTC 59.198 45.455 0.00 0.00 33.58 3.01
2716 4868 0.242825 CTCACCGTTGAAGGCTCGTA 59.757 55.000 0.00 0.00 33.69 3.43
2720 4872 1.480219 CCGTTGAAGGCTCGTATCGC 61.480 60.000 0.00 0.00 0.00 4.58
2914 5066 5.532032 CCTTTTTCCATGCAAGAAAAACCAT 59.468 36.000 25.27 0.00 44.25 3.55
3148 5300 3.738481 CCATTTCCCGGGAGCCCA 61.738 66.667 25.26 5.74 35.37 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.027745 TCCATCAACTCTCTGTCAAGCC 60.028 50.000 0.00 0.00 0.00 4.35
5 6 2.353109 CGCTCCATCAACTCTCTGTCAA 60.353 50.000 0.00 0.00 0.00 3.18
6 7 1.203287 CGCTCCATCAACTCTCTGTCA 59.797 52.381 0.00 0.00 0.00 3.58
7 8 1.474478 TCGCTCCATCAACTCTCTGTC 59.526 52.381 0.00 0.00 0.00 3.51
8 9 1.550327 TCGCTCCATCAACTCTCTGT 58.450 50.000 0.00 0.00 0.00 3.41
9 10 2.538437 CTTCGCTCCATCAACTCTCTG 58.462 52.381 0.00 0.00 0.00 3.35
10 11 1.134848 GCTTCGCTCCATCAACTCTCT 60.135 52.381 0.00 0.00 0.00 3.10
11 12 1.285578 GCTTCGCTCCATCAACTCTC 58.714 55.000 0.00 0.00 0.00 3.20
12 13 0.459237 CGCTTCGCTCCATCAACTCT 60.459 55.000 0.00 0.00 0.00 3.24
13 14 0.737715 ACGCTTCGCTCCATCAACTC 60.738 55.000 0.00 0.00 0.00 3.01
14 15 1.016130 CACGCTTCGCTCCATCAACT 61.016 55.000 0.00 0.00 0.00 3.16
15 16 1.421485 CACGCTTCGCTCCATCAAC 59.579 57.895 0.00 0.00 0.00 3.18
16 17 2.390599 GCACGCTTCGCTCCATCAA 61.391 57.895 0.00 0.00 0.00 2.57
17 18 2.815211 GCACGCTTCGCTCCATCA 60.815 61.111 0.00 0.00 0.00 3.07
18 19 2.510238 AGCACGCTTCGCTCCATC 60.510 61.111 0.00 0.00 33.35 3.51
19 20 2.584261 ATCAGCACGCTTCGCTCCAT 62.584 55.000 0.00 0.00 37.72 3.41
20 21 1.944234 TATCAGCACGCTTCGCTCCA 61.944 55.000 0.00 0.00 37.72 3.86
21 22 0.806102 TTATCAGCACGCTTCGCTCC 60.806 55.000 0.00 0.00 37.72 4.70
22 23 0.299003 GTTATCAGCACGCTTCGCTC 59.701 55.000 0.00 0.00 37.72 5.03
23 24 0.389817 TGTTATCAGCACGCTTCGCT 60.390 50.000 0.00 0.00 41.47 4.93
24 25 0.652592 ATGTTATCAGCACGCTTCGC 59.347 50.000 0.00 0.00 0.00 4.70
25 26 1.660607 ACATGTTATCAGCACGCTTCG 59.339 47.619 0.00 0.00 0.00 3.79
26 27 3.485877 GGAACATGTTATCAGCACGCTTC 60.486 47.826 11.95 0.00 0.00 3.86
27 28 2.420022 GGAACATGTTATCAGCACGCTT 59.580 45.455 11.95 0.00 0.00 4.68
28 29 2.009774 GGAACATGTTATCAGCACGCT 58.990 47.619 11.95 0.00 0.00 5.07
29 30 1.267532 CGGAACATGTTATCAGCACGC 60.268 52.381 11.95 0.00 0.00 5.34
30 31 1.267532 GCGGAACATGTTATCAGCACG 60.268 52.381 11.95 8.70 36.85 5.34
31 32 1.737236 TGCGGAACATGTTATCAGCAC 59.263 47.619 17.79 2.56 40.87 4.40
32 33 2.106477 TGCGGAACATGTTATCAGCA 57.894 45.000 17.79 17.79 42.93 4.41
33 34 2.420022 AGTTGCGGAACATGTTATCAGC 59.580 45.455 22.29 13.00 37.29 4.26
34 35 3.063997 GGAGTTGCGGAACATGTTATCAG 59.936 47.826 22.29 1.99 34.17 2.90
35 36 3.006940 GGAGTTGCGGAACATGTTATCA 58.993 45.455 22.29 6.92 34.17 2.15
36 37 3.063997 CAGGAGTTGCGGAACATGTTATC 59.936 47.826 22.29 9.08 34.17 1.75
37 38 3.009723 CAGGAGTTGCGGAACATGTTAT 58.990 45.455 22.29 0.00 34.17 1.89
38 39 2.422597 CAGGAGTTGCGGAACATGTTA 58.577 47.619 22.29 0.00 34.17 2.41
39 40 1.238439 CAGGAGTTGCGGAACATGTT 58.762 50.000 22.29 11.78 34.17 2.71
40 41 1.237285 GCAGGAGTTGCGGAACATGT 61.237 55.000 22.29 0.55 44.09 3.21
41 42 1.503542 GCAGGAGTTGCGGAACATG 59.496 57.895 22.29 16.93 44.09 3.21
42 43 3.987404 GCAGGAGTTGCGGAACAT 58.013 55.556 22.29 7.01 44.09 2.71
50 51 4.379243 ACTCGCCGGCAGGAGTTG 62.379 66.667 25.78 9.78 40.47 3.16
51 52 4.070552 GACTCGCCGGCAGGAGTT 62.071 66.667 29.94 17.94 43.23 3.01
61 62 4.452733 CCTTGGACCGGACTCGCC 62.453 72.222 9.46 1.40 34.56 5.54
62 63 3.236003 AACCTTGGACCGGACTCGC 62.236 63.158 9.46 0.00 34.56 5.03
63 64 1.374252 CAACCTTGGACCGGACTCG 60.374 63.158 9.46 0.00 0.00 4.18
64 65 1.671379 GCAACCTTGGACCGGACTC 60.671 63.158 9.46 0.00 0.00 3.36
65 66 2.430367 GCAACCTTGGACCGGACT 59.570 61.111 9.46 0.00 0.00 3.85
66 67 3.047877 CGCAACCTTGGACCGGAC 61.048 66.667 9.46 0.00 0.00 4.79
67 68 4.323477 CCGCAACCTTGGACCGGA 62.323 66.667 9.46 0.00 41.34 5.14
68 69 4.323477 TCCGCAACCTTGGACCGG 62.323 66.667 0.00 0.00 40.25 5.28
69 70 2.742372 CTCCGCAACCTTGGACCG 60.742 66.667 0.00 0.00 0.00 4.79
70 71 3.056328 GCTCCGCAACCTTGGACC 61.056 66.667 0.00 0.00 0.00 4.46
71 72 3.423154 CGCTCCGCAACCTTGGAC 61.423 66.667 0.00 0.00 0.00 4.02
72 73 4.697756 CCGCTCCGCAACCTTGGA 62.698 66.667 0.00 0.00 0.00 3.53
74 75 4.697756 TCCCGCTCCGCAACCTTG 62.698 66.667 0.00 0.00 0.00 3.61
75 76 4.394712 CTCCCGCTCCGCAACCTT 62.395 66.667 0.00 0.00 0.00 3.50
87 88 4.592936 CTACGACGCTCGCTCCCG 62.593 72.222 0.00 0.00 45.12 5.14
88 89 3.200593 TCTACGACGCTCGCTCCC 61.201 66.667 0.00 0.00 45.12 4.30
89 90 2.023041 GTCTACGACGCTCGCTCC 59.977 66.667 0.00 0.00 45.12 4.70
116 117 2.232239 TTCGCGTGTACGACTACTTC 57.768 50.000 5.77 0.00 42.78 3.01
117 118 2.031682 ACTTTCGCGTGTACGACTACTT 60.032 45.455 5.77 0.00 42.78 2.24
118 119 1.532868 ACTTTCGCGTGTACGACTACT 59.467 47.619 5.77 0.00 42.78 2.57
119 120 1.955762 ACTTTCGCGTGTACGACTAC 58.044 50.000 5.77 0.00 42.78 2.73
120 121 3.804518 TTACTTTCGCGTGTACGACTA 57.195 42.857 5.77 0.00 42.78 2.59
121 122 2.686558 TTACTTTCGCGTGTACGACT 57.313 45.000 5.77 0.00 42.78 4.18
122 123 3.361644 TCATTTACTTTCGCGTGTACGAC 59.638 43.478 5.77 0.00 42.78 4.34
123 124 3.361644 GTCATTTACTTTCGCGTGTACGA 59.638 43.478 5.77 2.97 43.02 3.43
124 125 3.119956 TGTCATTTACTTTCGCGTGTACG 59.880 43.478 5.77 0.00 43.27 3.67
125 126 4.084952 TGTGTCATTTACTTTCGCGTGTAC 60.085 41.667 5.77 0.00 0.00 2.90
126 127 4.049869 TGTGTCATTTACTTTCGCGTGTA 58.950 39.130 5.77 5.65 0.00 2.90
127 128 2.867368 TGTGTCATTTACTTTCGCGTGT 59.133 40.909 5.77 6.70 0.00 4.49
128 129 3.183574 TCTGTGTCATTTACTTTCGCGTG 59.816 43.478 5.77 0.00 0.00 5.34
129 130 3.386486 TCTGTGTCATTTACTTTCGCGT 58.614 40.909 5.77 0.00 0.00 6.01
130 131 4.383774 TTCTGTGTCATTTACTTTCGCG 57.616 40.909 0.00 0.00 0.00 5.87
131 132 5.985781 TCTTTCTGTGTCATTTACTTTCGC 58.014 37.500 0.00 0.00 0.00 4.70
132 133 9.694520 CATATCTTTCTGTGTCATTTACTTTCG 57.305 33.333 0.00 0.00 0.00 3.46
133 134 9.994432 CCATATCTTTCTGTGTCATTTACTTTC 57.006 33.333 0.00 0.00 0.00 2.62
134 135 9.739276 TCCATATCTTTCTGTGTCATTTACTTT 57.261 29.630 0.00 0.00 0.00 2.66
135 136 9.388506 CTCCATATCTTTCTGTGTCATTTACTT 57.611 33.333 0.00 0.00 0.00 2.24
136 137 8.762645 TCTCCATATCTTTCTGTGTCATTTACT 58.237 33.333 0.00 0.00 0.00 2.24
137 138 8.948631 TCTCCATATCTTTCTGTGTCATTTAC 57.051 34.615 0.00 0.00 0.00 2.01
138 139 9.605275 CTTCTCCATATCTTTCTGTGTCATTTA 57.395 33.333 0.00 0.00 0.00 1.40
139 140 8.324306 TCTTCTCCATATCTTTCTGTGTCATTT 58.676 33.333 0.00 0.00 0.00 2.32
140 141 7.768120 GTCTTCTCCATATCTTTCTGTGTCATT 59.232 37.037 0.00 0.00 0.00 2.57
141 142 7.271511 GTCTTCTCCATATCTTTCTGTGTCAT 58.728 38.462 0.00 0.00 0.00 3.06
142 143 6.351371 GGTCTTCTCCATATCTTTCTGTGTCA 60.351 42.308 0.00 0.00 0.00 3.58
143 144 6.045955 GGTCTTCTCCATATCTTTCTGTGTC 58.954 44.000 0.00 0.00 0.00 3.67
144 145 5.485353 TGGTCTTCTCCATATCTTTCTGTGT 59.515 40.000 0.00 0.00 31.96 3.72
145 146 5.982356 TGGTCTTCTCCATATCTTTCTGTG 58.018 41.667 0.00 0.00 31.96 3.66
146 147 5.396213 GCTGGTCTTCTCCATATCTTTCTGT 60.396 44.000 0.00 0.00 36.84 3.41
147 148 5.055812 GCTGGTCTTCTCCATATCTTTCTG 58.944 45.833 0.00 0.00 36.84 3.02
148 149 4.968080 AGCTGGTCTTCTCCATATCTTTCT 59.032 41.667 0.00 0.00 36.84 2.52
149 150 5.289083 AGCTGGTCTTCTCCATATCTTTC 57.711 43.478 0.00 0.00 36.84 2.62
150 151 5.707066 AAGCTGGTCTTCTCCATATCTTT 57.293 39.130 0.00 0.00 36.84 2.52
151 152 5.707066 AAAGCTGGTCTTCTCCATATCTT 57.293 39.130 0.00 0.00 36.84 2.40
152 153 7.385894 AATAAAGCTGGTCTTCTCCATATCT 57.614 36.000 0.00 0.00 36.84 1.98
153 154 9.732130 ATTAATAAAGCTGGTCTTCTCCATATC 57.268 33.333 0.00 0.00 36.84 1.63
154 155 9.732130 GATTAATAAAGCTGGTCTTCTCCATAT 57.268 33.333 0.00 0.00 36.84 1.78
155 156 8.713971 TGATTAATAAAGCTGGTCTTCTCCATA 58.286 33.333 0.00 0.00 36.84 2.74
156 157 7.577303 TGATTAATAAAGCTGGTCTTCTCCAT 58.423 34.615 0.00 0.00 36.84 3.41
157 158 6.957631 TGATTAATAAAGCTGGTCTTCTCCA 58.042 36.000 0.00 0.00 32.88 3.86
158 159 7.865706 TTGATTAATAAAGCTGGTCTTCTCC 57.134 36.000 0.00 0.00 32.88 3.71
159 160 9.113838 TCATTGATTAATAAAGCTGGTCTTCTC 57.886 33.333 0.00 0.00 32.88 2.87
160 161 9.638176 ATCATTGATTAATAAAGCTGGTCTTCT 57.362 29.630 0.00 0.00 32.88 2.85
161 162 9.890352 GATCATTGATTAATAAAGCTGGTCTTC 57.110 33.333 0.00 0.00 32.88 2.87
162 163 9.412460 TGATCATTGATTAATAAAGCTGGTCTT 57.588 29.630 0.00 0.00 36.34 3.01
163 164 8.985315 TGATCATTGATTAATAAAGCTGGTCT 57.015 30.769 0.00 0.00 0.00 3.85
164 165 8.295288 CCTGATCATTGATTAATAAAGCTGGTC 58.705 37.037 0.00 0.00 0.00 4.02
165 166 7.232127 CCCTGATCATTGATTAATAAAGCTGGT 59.768 37.037 0.00 0.00 0.00 4.00
166 167 7.309621 CCCCTGATCATTGATTAATAAAGCTGG 60.310 40.741 0.00 0.00 0.00 4.85
167 168 7.232127 ACCCCTGATCATTGATTAATAAAGCTG 59.768 37.037 0.00 0.00 0.00 4.24
168 169 7.300658 ACCCCTGATCATTGATTAATAAAGCT 58.699 34.615 0.00 0.00 0.00 3.74
169 170 7.530426 ACCCCTGATCATTGATTAATAAAGC 57.470 36.000 0.00 0.00 0.00 3.51
171 172 9.928618 TGTAACCCCTGATCATTGATTAATAAA 57.071 29.630 0.00 0.00 0.00 1.40
172 173 9.928618 TTGTAACCCCTGATCATTGATTAATAA 57.071 29.630 0.00 0.00 0.00 1.40
175 176 9.928618 TTATTGTAACCCCTGATCATTGATTAA 57.071 29.630 0.00 0.00 0.00 1.40
177 178 8.863086 CATTATTGTAACCCCTGATCATTGATT 58.137 33.333 0.00 0.00 0.00 2.57
178 179 7.452501 CCATTATTGTAACCCCTGATCATTGAT 59.547 37.037 0.00 0.00 0.00 2.57
179 180 6.777091 CCATTATTGTAACCCCTGATCATTGA 59.223 38.462 0.00 0.00 0.00 2.57
180 181 6.517194 GCCATTATTGTAACCCCTGATCATTG 60.517 42.308 0.00 0.00 0.00 2.82
181 182 5.539955 GCCATTATTGTAACCCCTGATCATT 59.460 40.000 0.00 0.00 0.00 2.57
182 183 5.079643 GCCATTATTGTAACCCCTGATCAT 58.920 41.667 0.00 0.00 0.00 2.45
183 184 4.167892 AGCCATTATTGTAACCCCTGATCA 59.832 41.667 0.00 0.00 0.00 2.92
184 185 4.729868 AGCCATTATTGTAACCCCTGATC 58.270 43.478 0.00 0.00 0.00 2.92
185 186 4.447762 GGAGCCATTATTGTAACCCCTGAT 60.448 45.833 0.00 0.00 0.00 2.90
186 187 3.117663 GGAGCCATTATTGTAACCCCTGA 60.118 47.826 0.00 0.00 0.00 3.86
187 188 3.117512 AGGAGCCATTATTGTAACCCCTG 60.118 47.826 0.00 0.00 0.00 4.45
188 189 3.131252 AGGAGCCATTATTGTAACCCCT 58.869 45.455 0.00 0.00 0.00 4.79
189 190 3.487372 GAGGAGCCATTATTGTAACCCC 58.513 50.000 0.00 0.00 0.00 4.95
190 191 3.139077 CGAGGAGCCATTATTGTAACCC 58.861 50.000 0.00 0.00 0.00 4.11
191 192 3.139077 CCGAGGAGCCATTATTGTAACC 58.861 50.000 0.00 0.00 0.00 2.85
192 193 3.560068 CACCGAGGAGCCATTATTGTAAC 59.440 47.826 0.00 0.00 0.00 2.50
193 194 3.804036 CACCGAGGAGCCATTATTGTAA 58.196 45.455 0.00 0.00 0.00 2.41
194 195 2.484770 GCACCGAGGAGCCATTATTGTA 60.485 50.000 0.00 0.00 0.00 2.41
195 196 1.747206 GCACCGAGGAGCCATTATTGT 60.747 52.381 0.00 0.00 0.00 2.71
196 197 0.947244 GCACCGAGGAGCCATTATTG 59.053 55.000 0.00 0.00 0.00 1.90
197 198 0.839946 AGCACCGAGGAGCCATTATT 59.160 50.000 7.91 0.00 32.18 1.40
198 199 0.839946 AAGCACCGAGGAGCCATTAT 59.160 50.000 7.91 0.00 32.18 1.28
199 200 0.618458 AAAGCACCGAGGAGCCATTA 59.382 50.000 7.91 0.00 32.18 1.90
200 201 0.618458 TAAAGCACCGAGGAGCCATT 59.382 50.000 7.91 6.67 32.18 3.16
201 202 0.839946 ATAAAGCACCGAGGAGCCAT 59.160 50.000 7.91 0.60 32.18 4.40
202 203 1.491668 TATAAAGCACCGAGGAGCCA 58.508 50.000 7.91 0.00 32.18 4.75
203 204 2.841442 ATATAAAGCACCGAGGAGCC 57.159 50.000 7.91 0.00 32.18 4.70
204 205 4.459685 TCTCTATATAAAGCACCGAGGAGC 59.540 45.833 3.30 3.30 0.00 4.70
205 206 6.576662 TTCTCTATATAAAGCACCGAGGAG 57.423 41.667 0.00 0.00 0.00 3.69
206 207 6.971726 TTTCTCTATATAAAGCACCGAGGA 57.028 37.500 0.00 0.00 0.00 3.71
207 208 6.647067 CCTTTTCTCTATATAAAGCACCGAGG 59.353 42.308 0.00 0.00 0.00 4.63
208 209 6.647067 CCCTTTTCTCTATATAAAGCACCGAG 59.353 42.308 0.00 0.00 0.00 4.63
209 210 6.463897 CCCCTTTTCTCTATATAAAGCACCGA 60.464 42.308 0.00 0.00 0.00 4.69
210 211 5.701290 CCCCTTTTCTCTATATAAAGCACCG 59.299 44.000 0.00 0.00 0.00 4.94
211 212 6.004574 CCCCCTTTTCTCTATATAAAGCACC 58.995 44.000 0.00 0.00 0.00 5.01
212 213 6.602278 ACCCCCTTTTCTCTATATAAAGCAC 58.398 40.000 0.00 0.00 0.00 4.40
213 214 6.841781 ACCCCCTTTTCTCTATATAAAGCA 57.158 37.500 0.00 0.00 0.00 3.91
214 215 9.286170 CTTAACCCCCTTTTCTCTATATAAAGC 57.714 37.037 0.00 0.00 0.00 3.51
215 216 9.794719 CCTTAACCCCCTTTTCTCTATATAAAG 57.205 37.037 0.00 0.00 0.00 1.85
216 217 8.729997 CCCTTAACCCCCTTTTCTCTATATAAA 58.270 37.037 0.00 0.00 0.00 1.40
217 218 8.081948 TCCCTTAACCCCCTTTTCTCTATATAA 58.918 37.037 0.00 0.00 0.00 0.98
218 219 7.616871 TCCCTTAACCCCCTTTTCTCTATATA 58.383 38.462 0.00 0.00 0.00 0.86
219 220 6.467708 TCCCTTAACCCCCTTTTCTCTATAT 58.532 40.000 0.00 0.00 0.00 0.86
220 221 5.868662 TCCCTTAACCCCCTTTTCTCTATA 58.131 41.667 0.00 0.00 0.00 1.31
221 222 4.717755 TCCCTTAACCCCCTTTTCTCTAT 58.282 43.478 0.00 0.00 0.00 1.98
222 223 4.164865 TCCCTTAACCCCCTTTTCTCTA 57.835 45.455 0.00 0.00 0.00 2.43
223 224 3.013984 TCCCTTAACCCCCTTTTCTCT 57.986 47.619 0.00 0.00 0.00 3.10
224 225 5.461516 TTATCCCTTAACCCCCTTTTCTC 57.538 43.478 0.00 0.00 0.00 2.87
225 226 5.889286 TTTATCCCTTAACCCCCTTTTCT 57.111 39.130 0.00 0.00 0.00 2.52
226 227 6.552350 GGTATTTATCCCTTAACCCCCTTTTC 59.448 42.308 0.00 0.00 0.00 2.29
227 228 6.446451 GGTATTTATCCCTTAACCCCCTTTT 58.554 40.000 0.00 0.00 0.00 2.27
228 229 5.102956 GGGTATTTATCCCTTAACCCCCTTT 60.103 44.000 0.00 0.00 40.62 3.11
229 230 4.421231 GGGTATTTATCCCTTAACCCCCTT 59.579 45.833 0.00 0.00 40.62 3.95
230 231 3.992311 GGGTATTTATCCCTTAACCCCCT 59.008 47.826 0.00 0.00 40.62 4.79
231 232 3.728456 TGGGTATTTATCCCTTAACCCCC 59.272 47.826 5.91 0.00 44.97 5.40
232 233 4.417854 AGTGGGTATTTATCCCTTAACCCC 59.582 45.833 5.91 0.00 44.97 4.95
233 234 5.658198 AGTGGGTATTTATCCCTTAACCC 57.342 43.478 1.28 1.28 45.64 4.11
234 235 7.227314 CGTTAAGTGGGTATTTATCCCTTAACC 59.773 40.741 20.79 12.11 41.27 2.85
235 236 7.986889 TCGTTAAGTGGGTATTTATCCCTTAAC 59.013 37.037 18.96 18.96 44.84 2.01
236 237 7.986889 GTCGTTAAGTGGGTATTTATCCCTTAA 59.013 37.037 2.65 6.52 44.84 1.85
237 238 7.125507 TGTCGTTAAGTGGGTATTTATCCCTTA 59.874 37.037 2.65 0.00 44.84 2.69
238 239 6.070078 TGTCGTTAAGTGGGTATTTATCCCTT 60.070 38.462 2.65 0.00 44.84 3.95
239 240 5.426185 TGTCGTTAAGTGGGTATTTATCCCT 59.574 40.000 2.65 0.00 44.84 4.20
240 241 5.525012 GTGTCGTTAAGTGGGTATTTATCCC 59.475 44.000 0.00 0.00 44.81 3.85
241 242 5.232838 CGTGTCGTTAAGTGGGTATTTATCC 59.767 44.000 0.00 0.00 0.00 2.59
242 243 6.035843 TCGTGTCGTTAAGTGGGTATTTATC 58.964 40.000 0.00 0.00 0.00 1.75
243 244 5.964758 TCGTGTCGTTAAGTGGGTATTTAT 58.035 37.500 0.00 0.00 0.00 1.40
244 245 5.384063 TCGTGTCGTTAAGTGGGTATTTA 57.616 39.130 0.00 0.00 0.00 1.40
245 246 4.240096 CTCGTGTCGTTAAGTGGGTATTT 58.760 43.478 0.00 0.00 0.00 1.40
246 247 3.367703 CCTCGTGTCGTTAAGTGGGTATT 60.368 47.826 0.00 0.00 0.00 1.89
247 248 2.165030 CCTCGTGTCGTTAAGTGGGTAT 59.835 50.000 0.00 0.00 0.00 2.73
248 249 1.541147 CCTCGTGTCGTTAAGTGGGTA 59.459 52.381 0.00 0.00 0.00 3.69
249 250 0.316204 CCTCGTGTCGTTAAGTGGGT 59.684 55.000 0.00 0.00 0.00 4.51
250 251 0.389426 CCCTCGTGTCGTTAAGTGGG 60.389 60.000 0.00 0.00 0.00 4.61
251 252 0.389426 CCCCTCGTGTCGTTAAGTGG 60.389 60.000 0.00 0.00 0.00 4.00
252 253 0.599558 TCCCCTCGTGTCGTTAAGTG 59.400 55.000 0.00 0.00 0.00 3.16
253 254 1.000171 GTTCCCCTCGTGTCGTTAAGT 60.000 52.381 0.00 0.00 0.00 2.24
254 255 1.706443 GTTCCCCTCGTGTCGTTAAG 58.294 55.000 0.00 0.00 0.00 1.85
255 256 0.039256 CGTTCCCCTCGTGTCGTTAA 60.039 55.000 0.00 0.00 0.00 2.01
256 257 1.580942 CGTTCCCCTCGTGTCGTTA 59.419 57.895 0.00 0.00 0.00 3.18
257 258 2.337532 CGTTCCCCTCGTGTCGTT 59.662 61.111 0.00 0.00 0.00 3.85
258 259 3.677648 CCGTTCCCCTCGTGTCGT 61.678 66.667 0.00 0.00 0.00 4.34
259 260 4.430765 CCCGTTCCCCTCGTGTCG 62.431 72.222 0.00 0.00 0.00 4.35
260 261 2.993264 TCCCGTTCCCCTCGTGTC 60.993 66.667 0.00 0.00 0.00 3.67
261 262 2.995574 CTCCCGTTCCCCTCGTGT 60.996 66.667 0.00 0.00 0.00 4.49
262 263 3.771160 CCTCCCGTTCCCCTCGTG 61.771 72.222 0.00 0.00 0.00 4.35
267 268 4.810184 TAGCCCCTCCCGTTCCCC 62.810 72.222 0.00 0.00 0.00 4.81
268 269 3.162154 CTAGCCCCTCCCGTTCCC 61.162 72.222 0.00 0.00 0.00 3.97
269 270 3.862991 GCTAGCCCCTCCCGTTCC 61.863 72.222 2.29 0.00 0.00 3.62
270 271 3.862991 GGCTAGCCCCTCCCGTTC 61.863 72.222 24.19 0.00 0.00 3.95
280 281 2.125431 TAAACGCACGGGCTAGCC 60.125 61.111 26.55 26.55 38.10 3.93
281 282 2.810012 GCTAAACGCACGGGCTAGC 61.810 63.158 12.89 12.89 35.18 3.42
282 283 1.447140 TGCTAAACGCACGGGCTAG 60.447 57.895 8.62 3.72 45.47 3.42
283 284 2.657829 TGCTAAACGCACGGGCTA 59.342 55.556 8.62 0.00 45.47 3.93
330 331 2.959707 TGGTACAATGTGTTGGGAAACC 59.040 45.455 0.00 0.00 45.86 3.27
339 340 6.833027 CGGTCAGACCTTGGTACAATGTGT 62.833 50.000 17.95 0.00 36.21 3.72
340 341 4.413095 CGGTCAGACCTTGGTACAATGTG 61.413 52.174 17.95 0.00 36.21 3.21
341 342 2.289444 CGGTCAGACCTTGGTACAATGT 60.289 50.000 17.95 0.00 36.21 2.71
342 343 2.289444 ACGGTCAGACCTTGGTACAATG 60.289 50.000 17.95 0.31 36.21 2.82
343 344 1.975680 ACGGTCAGACCTTGGTACAAT 59.024 47.619 17.95 0.00 36.21 2.71
344 345 1.416243 ACGGTCAGACCTTGGTACAA 58.584 50.000 17.95 0.00 36.21 2.41
416 417 3.118738 ACGTTCTTCAGACAGTCCAAGTT 60.119 43.478 0.00 0.00 0.00 2.66
780 2926 1.296715 CGGTGCAGGGAAGTAAGCT 59.703 57.895 0.00 0.00 0.00 3.74
897 3043 1.604593 GTGGACATTGCTGGGCTGT 60.605 57.895 0.00 0.00 0.00 4.40
1076 3224 2.353803 GCCTTAGAGACGACACCACAAT 60.354 50.000 0.00 0.00 0.00 2.71
1490 3638 1.035139 GGGGTAGCCGTCGAAGAATA 58.965 55.000 4.56 0.00 39.69 1.75
1539 3687 1.429423 GCGCAGACAATAAGCACCC 59.571 57.895 0.30 0.00 0.00 4.61
1577 3725 0.957395 CACACTGACCCACCATCTGC 60.957 60.000 0.00 0.00 0.00 4.26
1592 3740 3.609853 TGCATGATAGGGAAAGACACAC 58.390 45.455 0.00 0.00 0.00 3.82
1623 3771 2.566724 GGGGTTTTCATGAGGAATGCAA 59.433 45.455 0.00 0.00 36.11 4.08
1665 3813 6.341316 CAGGGCATACATCATATACAGTACC 58.659 44.000 0.00 0.00 0.00 3.34
1910 4058 3.312421 CGGAATATGGCAATCGAACAACT 59.688 43.478 0.00 0.00 0.00 3.16
2472 4624 6.346096 AGCCGCTTTATTTAGTGTTCTATCA 58.654 36.000 0.00 0.00 0.00 2.15
2495 4647 9.787532 CACCATACATATACCAAAAACAGAAAG 57.212 33.333 0.00 0.00 0.00 2.62
2663 4815 3.897505 ACAGTTTTCCATCCCTCCAAAAG 59.102 43.478 0.00 0.00 0.00 2.27
2716 4868 1.002900 CATTTTAACGGATGGCGCGAT 60.003 47.619 12.10 3.93 0.00 4.58
2720 4872 2.085532 CGACATTTTAACGGATGGCG 57.914 50.000 6.53 6.53 46.83 5.69
2914 5066 3.433598 GGCAAGATACCCAATCAGTAGCA 60.434 47.826 0.00 0.00 37.03 3.49
3148 5300 1.622173 CCCCCTATGCCCACAAACATT 60.622 52.381 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.