Multiple sequence alignment - TraesCS4D01G176500

Loading Multiple Alignment...

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 TraesCS4D01G176500 chr4D 100.000 4826 0 0 1 4826 306858870 306854045 0.000000e+00 8913
1 TraesCS4D01G176500 chr4D 98.802 167 2 0 90 256 42134167 42134001 1.020000e-76 298
2 TraesCS4D01G176500 chr4B 96.469 4021 91 25 252 4241 382825543 382821543 0.000000e+00 6591
3 TraesCS4D01G176500 chr4B 95.851 241 7 2 4347 4587 382820927 382820690 2.110000e-103 387
4 TraesCS4D01G176500 chr4B 100.000 91 0 0 1 91 382825632 382825542 8.310000e-38 169
5 TraesCS4D01G176500 chr4A 96.616 3989 99 19 254 4214 170625003 170628983 0.000000e+00 6586
6 TraesCS4D01G176500 chr4A 96.429 308 8 1 4269 4576 170629309 170629613 5.570000e-139 505
7 TraesCS4D01G176500 chr4A 97.753 89 2 0 1 89 170624914 170625002 2.330000e-33 154
8 TraesCS4D01G176500 chr5D 99.394 165 1 0 89 253 342716939 342716775 2.820000e-77 300
9 TraesCS4D01G176500 chr6D 95.808 167 6 1 88 253 41542484 41542650 7.960000e-68 268
10 TraesCS4D01G176500 chr6D 95.181 166 8 0 89 254 40409396 40409561 3.700000e-66 263
11 TraesCS4D01G176500 chr6D 93.182 176 9 3 81 254 346251373 346251547 6.200000e-64 255
12 TraesCS4D01G176500 chr2D 95.783 166 6 1 90 254 593801596 593801761 2.860000e-67 267
13 TraesCS4D01G176500 chr2D 94.737 171 7 2 88 257 420278155 420278324 1.030000e-66 265
14 TraesCS4D01G176500 chr1D 95.783 166 6 1 90 254 466603290 466603455 2.860000e-67 267
15 TraesCS4D01G176500 chr5A 91.803 183 12 3 82 263 367790249 367790069 8.020000e-63 252


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 TraesCS4D01G176500 chr4D 306854045 306858870 4825 True 8913.000000 8913 100.000000 1 4826 1 chr4D.!!$R2 4825
1 TraesCS4D01G176500 chr4B 382820690 382825632 4942 True 2382.333333 6591 97.440000 1 4587 3 chr4B.!!$R1 4586
2 TraesCS4D01G176500 chr4A 170624914 170629613 4699 False 2415.000000 6586 96.932667 1 4576 3 chr4A.!!$F1 4575

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
761 762 0.675522 TACAGCCACCGCCTAAAAGC 60.676 55.0 0.0 0.0 34.57 3.51 F
915 916 2.815589 GCAGGAGTGTTCTGGGAATTGT 60.816 50.0 0.0 0.0 33.16 2.71 F
2775 2786 0.824595 TGCTCCTTTGCACTGCATGT 60.825 50.0 4.1 0.0 38.76 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2053 0.616371 TGCGTATTAAGGTGGTGGCT 59.384 50.000 0.00 0.00 0.00 4.75 R
2810 2821 2.047061 AGCTGTGGTGAACTTCTACCA 58.953 47.619 8.28 8.28 44.31 3.25 R
4589 5191 0.030638 GGCGAGGGCGTATACGTTTA 59.969 55.000 25.04 0.00 42.22 2.01 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
89 90 7.112779 AGCTTACTTTATGTGCCTTATGAACT 58.887 34.615 0.00 0.00 0.00 3.01
90 91 8.265055 AGCTTACTTTATGTGCCTTATGAACTA 58.735 33.333 0.00 0.00 0.00 2.24
91 92 8.336080 GCTTACTTTATGTGCCTTATGAACTAC 58.664 37.037 0.00 0.00 0.00 2.73
92 93 9.601217 CTTACTTTATGTGCCTTATGAACTACT 57.399 33.333 0.00 0.00 0.00 2.57
93 94 9.595823 TTACTTTATGTGCCTTATGAACTACTC 57.404 33.333 0.00 0.00 0.00 2.59
94 95 7.048512 ACTTTATGTGCCTTATGAACTACTCC 58.951 38.462 0.00 0.00 0.00 3.85
95 96 3.906720 TGTGCCTTATGAACTACTCCC 57.093 47.619 0.00 0.00 0.00 4.30
96 97 3.450904 TGTGCCTTATGAACTACTCCCT 58.549 45.455 0.00 0.00 0.00 4.20
97 98 3.451178 TGTGCCTTATGAACTACTCCCTC 59.549 47.826 0.00 0.00 0.00 4.30
98 99 3.039011 TGCCTTATGAACTACTCCCTCC 58.961 50.000 0.00 0.00 0.00 4.30
99 100 2.036089 GCCTTATGAACTACTCCCTCCG 59.964 54.545 0.00 0.00 0.00 4.63
100 101 3.297736 CCTTATGAACTACTCCCTCCGT 58.702 50.000 0.00 0.00 0.00 4.69
101 102 3.705072 CCTTATGAACTACTCCCTCCGTT 59.295 47.826 0.00 0.00 0.00 4.44
102 103 4.202131 CCTTATGAACTACTCCCTCCGTTC 60.202 50.000 0.00 0.00 37.02 3.95
103 104 1.553706 TGAACTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 35.97 3.62
104 105 1.076677 TGAACTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 35.97 3.36
105 106 2.309755 TGAACTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 35.97 2.94
106 107 3.245371 TGAACTACTCCCTCCGTTCCTAA 60.245 47.826 0.00 0.00 35.97 2.69
107 108 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
108 109 3.095332 ACTACTCCCTCCGTTCCTAAAC 58.905 50.000 0.00 0.00 0.00 2.01
109 110 2.019807 ACTCCCTCCGTTCCTAAACA 57.980 50.000 0.00 0.00 34.93 2.83
110 111 2.547990 ACTCCCTCCGTTCCTAAACAT 58.452 47.619 0.00 0.00 34.93 2.71
111 112 3.716431 ACTCCCTCCGTTCCTAAACATA 58.284 45.455 0.00 0.00 34.93 2.29
112 113 4.098894 ACTCCCTCCGTTCCTAAACATAA 58.901 43.478 0.00 0.00 34.93 1.90
113 114 4.161754 ACTCCCTCCGTTCCTAAACATAAG 59.838 45.833 0.00 0.00 34.93 1.73
114 115 4.098894 TCCCTCCGTTCCTAAACATAAGT 58.901 43.478 0.00 0.00 34.93 2.24
115 116 4.161001 TCCCTCCGTTCCTAAACATAAGTC 59.839 45.833 0.00 0.00 34.93 3.01
116 117 4.161754 CCCTCCGTTCCTAAACATAAGTCT 59.838 45.833 0.00 0.00 34.93 3.24
117 118 5.338137 CCCTCCGTTCCTAAACATAAGTCTT 60.338 44.000 0.00 0.00 34.93 3.01
118 119 6.171213 CCTCCGTTCCTAAACATAAGTCTTT 58.829 40.000 0.00 0.00 34.93 2.52
119 120 6.653740 CCTCCGTTCCTAAACATAAGTCTTTT 59.346 38.462 0.00 0.00 34.93 2.27
120 121 7.174426 CCTCCGTTCCTAAACATAAGTCTTTTT 59.826 37.037 0.00 0.00 34.93 1.94
121 122 9.211485 CTCCGTTCCTAAACATAAGTCTTTTTA 57.789 33.333 0.00 0.00 34.93 1.52
122 123 9.211485 TCCGTTCCTAAACATAAGTCTTTTTAG 57.789 33.333 7.75 7.75 34.93 1.85
123 124 9.211485 CCGTTCCTAAACATAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 34.70 2.10
137 138 8.697507 AGTCTTTTTAGACATTCAAATGGACT 57.302 30.769 7.58 8.27 41.02 3.85
138 139 9.793259 AGTCTTTTTAGACATTCAAATGGACTA 57.207 29.630 7.58 7.47 41.02 2.59
139 140 9.827411 GTCTTTTTAGACATTCAAATGGACTAC 57.173 33.333 7.58 0.00 40.70 2.73
140 141 9.567776 TCTTTTTAGACATTCAAATGGACTACA 57.432 29.630 7.58 2.25 40.70 2.74
147 148 9.261180 AGACATTCAAATGGACTACAATATACG 57.739 33.333 7.58 0.00 40.70 3.06
148 149 8.378172 ACATTCAAATGGACTACAATATACGG 57.622 34.615 7.58 0.00 40.70 4.02
149 150 8.208224 ACATTCAAATGGACTACAATATACGGA 58.792 33.333 7.58 0.00 40.70 4.69
150 151 9.219603 CATTCAAATGGACTACAATATACGGAT 57.780 33.333 0.00 0.00 32.78 4.18
151 152 8.601845 TTCAAATGGACTACAATATACGGATG 57.398 34.615 0.00 0.00 0.00 3.51
152 153 6.649141 TCAAATGGACTACAATATACGGATGC 59.351 38.462 0.00 0.00 0.00 3.91
153 154 5.738619 ATGGACTACAATATACGGATGCA 57.261 39.130 0.00 0.00 0.00 3.96
154 155 5.738619 TGGACTACAATATACGGATGCAT 57.261 39.130 0.00 0.00 0.00 3.96
155 156 5.478407 TGGACTACAATATACGGATGCATG 58.522 41.667 2.46 0.00 0.00 4.06
156 157 5.011635 TGGACTACAATATACGGATGCATGT 59.988 40.000 2.46 0.00 0.00 3.21
157 158 6.209788 TGGACTACAATATACGGATGCATGTA 59.790 38.462 2.46 0.83 0.00 2.29
158 159 6.752351 GGACTACAATATACGGATGCATGTAG 59.248 42.308 19.56 19.56 42.61 2.74
159 160 7.362660 GGACTACAATATACGGATGCATGTAGA 60.363 40.741 24.44 9.03 40.56 2.59
160 161 7.313646 ACTACAATATACGGATGCATGTAGAC 58.686 38.462 24.44 0.24 40.56 2.59
161 162 6.096673 ACAATATACGGATGCATGTAGACA 57.903 37.500 2.46 0.00 0.00 3.41
162 163 6.701340 ACAATATACGGATGCATGTAGACAT 58.299 36.000 2.46 0.00 36.96 3.06
163 164 7.836842 ACAATATACGGATGCATGTAGACATA 58.163 34.615 2.46 0.00 34.26 2.29
164 165 7.759886 ACAATATACGGATGCATGTAGACATAC 59.240 37.037 2.46 0.00 34.26 2.39
165 166 5.984695 ATACGGATGCATGTAGACATACT 57.015 39.130 2.46 0.00 34.26 2.12
166 167 4.672587 ACGGATGCATGTAGACATACTT 57.327 40.909 2.46 0.00 34.26 2.24
167 168 5.023533 ACGGATGCATGTAGACATACTTT 57.976 39.130 2.46 0.00 34.26 2.66
168 169 6.156748 ACGGATGCATGTAGACATACTTTA 57.843 37.500 2.46 0.00 34.26 1.85
169 170 6.216569 ACGGATGCATGTAGACATACTTTAG 58.783 40.000 2.46 0.00 34.26 1.85
170 171 6.040504 ACGGATGCATGTAGACATACTTTAGA 59.959 38.462 2.46 0.00 34.26 2.10
171 172 6.584184 CGGATGCATGTAGACATACTTTAGAG 59.416 42.308 2.46 0.00 34.26 2.43
172 173 7.437748 GGATGCATGTAGACATACTTTAGAGT 58.562 38.462 2.46 0.00 39.97 3.24
173 174 7.383572 GGATGCATGTAGACATACTTTAGAGTG 59.616 40.741 2.46 0.00 36.60 3.51
174 175 7.170393 TGCATGTAGACATACTTTAGAGTGT 57.830 36.000 0.00 0.00 36.60 3.55
175 176 8.288689 TGCATGTAGACATACTTTAGAGTGTA 57.711 34.615 0.00 0.00 36.60 2.90
176 177 8.406297 TGCATGTAGACATACTTTAGAGTGTAG 58.594 37.037 0.00 0.00 36.60 2.74
177 178 8.622157 GCATGTAGACATACTTTAGAGTGTAGA 58.378 37.037 0.00 0.00 36.60 2.59
194 195 7.440523 AGTGTAGATTCACTCATTTTGTTCC 57.559 36.000 0.00 0.00 44.07 3.62
195 196 6.147821 AGTGTAGATTCACTCATTTTGTTCCG 59.852 38.462 0.00 0.00 44.07 4.30
196 197 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
197 198 7.117236 GTGTAGATTCACTCATTTTGTTCCGTA 59.883 37.037 0.00 0.00 35.68 4.02
198 199 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
199 200 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
200 201 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
201 202 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
202 203 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
203 204 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
204 205 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
205 206 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
206 207 6.367969 ACTCATTTTGTTCCGTATGTAGTCAC 59.632 38.462 0.00 0.00 0.00 3.67
207 208 6.460781 TCATTTTGTTCCGTATGTAGTCACT 58.539 36.000 0.00 0.00 0.00 3.41
208 209 6.932400 TCATTTTGTTCCGTATGTAGTCACTT 59.068 34.615 0.00 0.00 0.00 3.16
209 210 6.533819 TTTTGTTCCGTATGTAGTCACTTG 57.466 37.500 0.00 0.00 0.00 3.16
210 211 4.859304 TGTTCCGTATGTAGTCACTTGT 57.141 40.909 0.00 0.00 0.00 3.16
211 212 5.204409 TGTTCCGTATGTAGTCACTTGTT 57.796 39.130 0.00 0.00 0.00 2.83
212 213 4.986034 TGTTCCGTATGTAGTCACTTGTTG 59.014 41.667 0.00 0.00 0.00 3.33
213 214 5.221283 TGTTCCGTATGTAGTCACTTGTTGA 60.221 40.000 0.00 0.00 0.00 3.18
214 215 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
215 216 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
216 217 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
217 218 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
218 219 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
219 220 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
220 221 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
221 222 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
222 223 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
223 224 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
224 225 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
225 226 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
226 227 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
227 228 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
228 229 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
229 230 8.424918 TCACTTGTTGAAATCTCTAGAAAGACT 58.575 33.333 0.00 0.00 0.00 3.24
230 231 9.050601 CACTTGTTGAAATCTCTAGAAAGACTT 57.949 33.333 0.00 0.00 0.00 3.01
247 248 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
248 249 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
249 250 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
250 251 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
372 373 2.989571 ACCAGAGGAGACAAAAGGGAAT 59.010 45.455 0.00 0.00 0.00 3.01
761 762 0.675522 TACAGCCACCGCCTAAAAGC 60.676 55.000 0.00 0.00 34.57 3.51
802 803 3.716872 CCCTCCTTTTCCTATAAGGCTGA 59.283 47.826 0.00 0.00 41.59 4.26
915 916 2.815589 GCAGGAGTGTTCTGGGAATTGT 60.816 50.000 0.00 0.00 33.16 2.71
1088 1089 4.966168 TGGTGGTACCTGCATAAGATCTTA 59.034 41.667 17.32 17.32 39.58 2.10
1156 1157 6.162079 TCTCACTCTCAGCAAATAGAACTTG 58.838 40.000 0.00 0.00 0.00 3.16
1173 1174 6.564328 AGAACTTGAAGGTTTGATGAACAAC 58.436 36.000 0.00 0.00 40.13 3.32
1174 1175 5.262588 ACTTGAAGGTTTGATGAACAACC 57.737 39.130 0.00 0.00 40.13 3.77
1289 1291 5.477637 AGGAACTGAAGAGGTACAAGTCTAC 59.522 44.000 0.00 0.00 37.18 2.59
1291 1293 3.757493 ACTGAAGAGGTACAAGTCTACGG 59.243 47.826 0.00 0.00 0.00 4.02
1332 1334 4.379793 GCATGTGAAGTTTAGTTTTGCTCG 59.620 41.667 0.00 0.00 0.00 5.03
1344 1346 9.582223 GTTTAGTTTTGCTCGATATATTGCTAC 57.418 33.333 0.00 0.00 0.00 3.58
1367 1369 6.911308 ACCTATCCTAACCTGCAATATGTTT 58.089 36.000 0.00 0.00 0.00 2.83
1419 1421 4.488790 AGCCACAACCAGCTCTTG 57.511 55.556 0.00 0.00 32.71 3.02
1554 1556 3.535561 CCCTGAGCTACATGATCGTTTT 58.464 45.455 0.00 0.00 32.98 2.43
1603 1605 4.517285 ACCAGACAGTAAGTATGCATTGG 58.483 43.478 3.54 4.72 38.12 3.16
1868 1873 7.979444 TTTGTCTTTCACCTAGAAATACAGG 57.021 36.000 8.22 0.00 46.94 4.00
2126 2131 4.634883 TGCGTGTTTACAGAAGGTAACAAA 59.365 37.500 0.00 0.00 41.55 2.83
2221 2226 4.850680 TGAACAACTGGAGGTACAAAAGT 58.149 39.130 0.00 0.00 0.00 2.66
2365 2376 5.704354 TGGCTGACCATCCAATAAATGTAT 58.296 37.500 0.00 0.00 42.67 2.29
2413 2424 8.514330 AGACTATACACTAGAGACAGGAAAAG 57.486 38.462 0.00 0.00 0.00 2.27
2414 2425 8.330247 AGACTATACACTAGAGACAGGAAAAGA 58.670 37.037 0.00 0.00 0.00 2.52
2446 2457 4.833380 ACAAGAGCACCACGGATATATACT 59.167 41.667 0.00 0.00 0.00 2.12
2775 2786 0.824595 TGCTCCTTTGCACTGCATGT 60.825 50.000 4.10 0.00 38.76 3.21
2867 2878 9.567776 TGAAGAGAAGAAATAAATGGTGTGTTA 57.432 29.630 0.00 0.00 0.00 2.41
2903 2914 4.403113 TGGTCTGGTATCTAATGCGTAACA 59.597 41.667 0.00 0.00 0.00 2.41
2975 2986 1.549170 AGCACAAGGGAAGTACCTACG 59.451 52.381 0.00 0.00 40.87 3.51
3051 3062 5.488341 GGTGGTCTAGAAACTGCAAAGATA 58.512 41.667 0.00 0.00 0.00 1.98
3105 3116 5.899299 ACAGAATGCTTCCATAATGCTTTC 58.101 37.500 0.00 0.00 42.53 2.62
3354 3365 0.469144 GAAGGCCTCCAAACCACCAA 60.469 55.000 5.23 0.00 0.00 3.67
3363 3374 2.024846 TCCAAACCACCAAGAAGGACAA 60.025 45.455 0.00 0.00 41.22 3.18
3463 3474 7.475771 ACTCAGAATAGCAAGAAATTCGATC 57.524 36.000 0.00 0.00 37.22 3.69
3523 3534 5.355350 ACAAGAGTGCCAATTTCATAGTAGC 59.645 40.000 0.00 0.00 0.00 3.58
3598 3610 3.960102 ACCTGGAAAATCTTTGCTGTCAA 59.040 39.130 0.00 0.00 0.00 3.18
3630 3642 5.411669 AGTTCACCGAAATAAGTGATGGAAC 59.588 40.000 0.00 0.00 42.32 3.62
3712 3724 6.849502 AGTATTCGAGAACTATGTTCGTTCA 58.150 36.000 5.80 0.00 42.37 3.18
3767 3779 6.560711 ACCATAGAAATACCACGAATTTTGC 58.439 36.000 0.00 0.00 0.00 3.68
4148 4188 1.442017 GGCGACGCACAAATCCAAC 60.442 57.895 23.09 0.00 0.00 3.77
4221 4261 2.441410 TGAATAGCCCAACAAATCGCA 58.559 42.857 0.00 0.00 0.00 5.10
4241 4281 2.863740 CAATGCTTCATACGCGTAAGGA 59.136 45.455 24.55 19.36 38.28 3.36
4242 4282 2.203800 TGCTTCATACGCGTAAGGAG 57.796 50.000 24.55 23.33 38.28 3.69
4243 4283 1.746787 TGCTTCATACGCGTAAGGAGA 59.253 47.619 28.94 18.63 38.28 3.71
4244 4284 2.164827 TGCTTCATACGCGTAAGGAGAA 59.835 45.455 28.94 18.99 38.28 2.87
4245 4285 2.789893 GCTTCATACGCGTAAGGAGAAG 59.210 50.000 28.94 29.27 35.38 2.85
4246 4286 3.372954 CTTCATACGCGTAAGGAGAAGG 58.627 50.000 27.87 17.89 38.28 3.46
4247 4287 1.679680 TCATACGCGTAAGGAGAAGGG 59.320 52.381 24.55 4.74 38.28 3.95
4248 4288 1.038280 ATACGCGTAAGGAGAAGGGG 58.962 55.000 24.55 0.00 38.28 4.79
4249 4289 1.039233 TACGCGTAAGGAGAAGGGGG 61.039 60.000 18.22 0.00 38.28 5.40
4268 4308 3.489513 GGGAGGGCGGCCATAGTT 61.490 66.667 31.59 8.95 0.00 2.24
4269 4309 2.203209 GGAGGGCGGCCATAGTTG 60.203 66.667 31.59 0.00 0.00 3.16
4270 4310 2.203209 GAGGGCGGCCATAGTTGG 60.203 66.667 31.59 0.00 46.66 3.77
4337 4939 4.908601 TGGCAGAAATAACTGGAGAAGA 57.091 40.909 0.00 0.00 38.22 2.87
4345 4947 9.617975 CAGAAATAACTGGAGAAGATGAAAAAC 57.382 33.333 0.00 0.00 34.64 2.43
4455 5057 3.682292 ATCGCGGAGGAGGGTTTGC 62.682 63.158 6.13 0.00 0.00 3.68
4530 5132 4.168675 TCATCTCTTTCCCCTGGCAATAAT 59.831 41.667 0.00 0.00 0.00 1.28
4531 5133 5.372363 TCATCTCTTTCCCCTGGCAATAATA 59.628 40.000 0.00 0.00 0.00 0.98
4587 5189 0.322546 CCTGTAAGCCCACTTGACCC 60.323 60.000 0.00 0.00 36.57 4.46
4588 5190 0.400213 CTGTAAGCCCACTTGACCCA 59.600 55.000 0.00 0.00 36.57 4.51
4589 5191 1.004745 CTGTAAGCCCACTTGACCCAT 59.995 52.381 0.00 0.00 36.57 4.00
4590 5192 2.238646 CTGTAAGCCCACTTGACCCATA 59.761 50.000 0.00 0.00 36.57 2.74
4591 5193 2.645297 TGTAAGCCCACTTGACCCATAA 59.355 45.455 0.00 0.00 36.57 1.90
4592 5194 2.990740 AAGCCCACTTGACCCATAAA 57.009 45.000 0.00 0.00 33.84 1.40
4593 5195 2.215942 AGCCCACTTGACCCATAAAC 57.784 50.000 0.00 0.00 0.00 2.01
4594 5196 0.808755 GCCCACTTGACCCATAAACG 59.191 55.000 0.00 0.00 0.00 3.60
4595 5197 1.884928 GCCCACTTGACCCATAAACGT 60.885 52.381 0.00 0.00 0.00 3.99
4596 5198 2.616001 GCCCACTTGACCCATAAACGTA 60.616 50.000 0.00 0.00 0.00 3.57
4597 5199 3.881220 CCCACTTGACCCATAAACGTAT 58.119 45.455 0.00 0.00 0.00 3.06
4598 5200 4.683942 GCCCACTTGACCCATAAACGTATA 60.684 45.833 0.00 0.00 0.00 1.47
4599 5201 4.812626 CCCACTTGACCCATAAACGTATAC 59.187 45.833 0.00 0.00 0.00 1.47
4600 5202 4.505191 CCACTTGACCCATAAACGTATACG 59.495 45.833 23.24 23.24 46.33 3.06
4601 5203 4.026310 CACTTGACCCATAAACGTATACGC 60.026 45.833 24.64 6.03 44.43 4.42
4602 5204 3.096489 TGACCCATAAACGTATACGCC 57.904 47.619 24.64 4.22 44.43 5.68
4603 5205 2.224018 TGACCCATAAACGTATACGCCC 60.224 50.000 24.64 4.71 44.43 6.13
4604 5206 2.036346 GACCCATAAACGTATACGCCCT 59.964 50.000 24.64 11.76 44.43 5.19
4605 5207 2.036346 ACCCATAAACGTATACGCCCTC 59.964 50.000 24.64 0.00 44.43 4.30
4606 5208 2.322161 CCATAAACGTATACGCCCTCG 58.678 52.381 24.64 10.83 44.43 4.63
4607 5209 1.717645 CATAAACGTATACGCCCTCGC 59.282 52.381 24.64 0.00 44.43 5.03
4608 5210 0.030638 TAAACGTATACGCCCTCGCC 59.969 55.000 24.64 0.00 44.43 5.54
4609 5211 1.669999 AAACGTATACGCCCTCGCCT 61.670 55.000 24.64 0.00 44.43 5.52
4610 5212 2.050351 CGTATACGCCCTCGCCTG 60.050 66.667 13.08 0.00 39.84 4.85
4611 5213 2.549198 CGTATACGCCCTCGCCTGA 61.549 63.158 13.08 0.00 39.84 3.86
4612 5214 1.737816 GTATACGCCCTCGCCTGAA 59.262 57.895 0.00 0.00 39.84 3.02
4613 5215 0.318784 GTATACGCCCTCGCCTGAAG 60.319 60.000 0.00 0.00 39.84 3.02
4614 5216 2.083835 TATACGCCCTCGCCTGAAGC 62.084 60.000 0.00 0.00 39.84 3.86
4638 5240 4.864334 GAGATGGGCCGGCACAGG 62.864 72.222 37.68 0.00 30.39 4.00
4650 5252 3.730761 CACAGGTGCGCTGAAGGC 61.731 66.667 9.73 0.00 37.64 4.35
4655 5257 3.730761 GTGCGCTGAAGGCCACAG 61.731 66.667 20.77 20.77 39.86 3.66
4666 5268 4.633980 GCCACAGCCTCGTTTTTG 57.366 55.556 0.00 0.00 0.00 2.44
4667 5269 1.733526 GCCACAGCCTCGTTTTTGT 59.266 52.632 0.00 0.00 0.00 2.83
4668 5270 0.102300 GCCACAGCCTCGTTTTTGTT 59.898 50.000 0.00 0.00 0.00 2.83
4669 5271 1.470805 GCCACAGCCTCGTTTTTGTTT 60.471 47.619 0.00 0.00 0.00 2.83
4670 5272 2.887337 CCACAGCCTCGTTTTTGTTTT 58.113 42.857 0.00 0.00 0.00 2.43
4671 5273 2.857748 CCACAGCCTCGTTTTTGTTTTC 59.142 45.455 0.00 0.00 0.00 2.29
4672 5274 3.428862 CCACAGCCTCGTTTTTGTTTTCT 60.429 43.478 0.00 0.00 0.00 2.52
4673 5275 4.173256 CACAGCCTCGTTTTTGTTTTCTT 58.827 39.130 0.00 0.00 0.00 2.52
4674 5276 4.625311 CACAGCCTCGTTTTTGTTTTCTTT 59.375 37.500 0.00 0.00 0.00 2.52
4675 5277 5.120053 CACAGCCTCGTTTTTGTTTTCTTTT 59.880 36.000 0.00 0.00 0.00 2.27
4676 5278 5.699001 ACAGCCTCGTTTTTGTTTTCTTTTT 59.301 32.000 0.00 0.00 0.00 1.94
4700 5302 8.785329 TTTGCTTCCTTTTGATTTACTTTTGT 57.215 26.923 0.00 0.00 0.00 2.83
4701 5303 8.785329 TTGCTTCCTTTTGATTTACTTTTGTT 57.215 26.923 0.00 0.00 0.00 2.83
4702 5304 8.785329 TGCTTCCTTTTGATTTACTTTTGTTT 57.215 26.923 0.00 0.00 0.00 2.83
4703 5305 9.877178 TGCTTCCTTTTGATTTACTTTTGTTTA 57.123 25.926 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.173953 TGTTTAGGAACGGAGGGAGTA 57.826 47.619 0.00 0.00 38.65 2.59
90 91 2.019807 TGTTTAGGAACGGAGGGAGT 57.980 50.000 0.00 0.00 38.65 3.85
91 92 4.161754 ACTTATGTTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 38.65 4.30
92 93 4.098894 ACTTATGTTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 38.65 4.20
93 94 4.161754 AGACTTATGTTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 38.65 4.30
94 95 5.340439 AGACTTATGTTTAGGAACGGAGG 57.660 43.478 0.00 0.00 38.65 4.30
95 96 7.668525 AAAAGACTTATGTTTAGGAACGGAG 57.331 36.000 0.00 0.00 38.65 4.63
96 97 9.211485 CTAAAAAGACTTATGTTTAGGAACGGA 57.789 33.333 8.91 0.00 38.65 4.69
97 98 9.211485 TCTAAAAAGACTTATGTTTAGGAACGG 57.789 33.333 13.94 0.00 38.65 4.44
111 112 9.136323 AGTCCATTTGAATGTCTAAAAAGACTT 57.864 29.630 7.04 0.00 39.41 3.01
112 113 8.697507 AGTCCATTTGAATGTCTAAAAAGACT 57.302 30.769 7.04 3.51 39.41 3.24
113 114 9.827411 GTAGTCCATTTGAATGTCTAAAAAGAC 57.173 33.333 3.30 0.00 39.15 3.01
114 115 9.567776 TGTAGTCCATTTGAATGTCTAAAAAGA 57.432 29.630 3.30 0.00 34.60 2.52
121 122 9.261180 CGTATATTGTAGTCCATTTGAATGTCT 57.739 33.333 3.30 4.19 34.60 3.41
122 123 8.495949 CCGTATATTGTAGTCCATTTGAATGTC 58.504 37.037 3.30 0.00 34.60 3.06
123 124 8.208224 TCCGTATATTGTAGTCCATTTGAATGT 58.792 33.333 3.30 0.00 34.60 2.71
124 125 8.601845 TCCGTATATTGTAGTCCATTTGAATG 57.398 34.615 0.00 0.00 36.17 2.67
125 126 9.219603 CATCCGTATATTGTAGTCCATTTGAAT 57.780 33.333 0.00 0.00 0.00 2.57
126 127 7.172532 GCATCCGTATATTGTAGTCCATTTGAA 59.827 37.037 0.00 0.00 0.00 2.69
127 128 6.649141 GCATCCGTATATTGTAGTCCATTTGA 59.351 38.462 0.00 0.00 0.00 2.69
128 129 6.426633 TGCATCCGTATATTGTAGTCCATTTG 59.573 38.462 0.00 0.00 0.00 2.32
129 130 6.530120 TGCATCCGTATATTGTAGTCCATTT 58.470 36.000 0.00 0.00 0.00 2.32
130 131 6.109156 TGCATCCGTATATTGTAGTCCATT 57.891 37.500 0.00 0.00 0.00 3.16
131 132 5.738619 TGCATCCGTATATTGTAGTCCAT 57.261 39.130 0.00 0.00 0.00 3.41
132 133 5.011635 ACATGCATCCGTATATTGTAGTCCA 59.988 40.000 0.00 0.00 0.00 4.02
133 134 5.479306 ACATGCATCCGTATATTGTAGTCC 58.521 41.667 0.00 0.00 0.00 3.85
134 135 7.485277 GTCTACATGCATCCGTATATTGTAGTC 59.515 40.741 14.62 8.30 0.00 2.59
135 136 7.039993 TGTCTACATGCATCCGTATATTGTAGT 60.040 37.037 14.62 1.66 0.00 2.73
136 137 7.312899 TGTCTACATGCATCCGTATATTGTAG 58.687 38.462 10.63 10.63 0.00 2.74
137 138 7.222000 TGTCTACATGCATCCGTATATTGTA 57.778 36.000 0.00 0.00 0.00 2.41
138 139 6.096673 TGTCTACATGCATCCGTATATTGT 57.903 37.500 0.00 0.00 0.00 2.71
139 140 7.976175 AGTATGTCTACATGCATCCGTATATTG 59.024 37.037 12.71 0.00 40.71 1.90
140 141 8.067751 AGTATGTCTACATGCATCCGTATATT 57.932 34.615 12.71 0.00 40.71 1.28
141 142 7.646548 AGTATGTCTACATGCATCCGTATAT 57.353 36.000 12.71 0.00 40.71 0.86
142 143 7.462571 AAGTATGTCTACATGCATCCGTATA 57.537 36.000 12.71 0.00 40.71 1.47
143 144 5.984695 AGTATGTCTACATGCATCCGTAT 57.015 39.130 12.71 0.00 40.71 3.06
144 145 5.784578 AAGTATGTCTACATGCATCCGTA 57.215 39.130 12.71 0.00 40.71 4.02
145 146 4.672587 AAGTATGTCTACATGCATCCGT 57.327 40.909 12.71 0.00 40.71 4.69
146 147 6.447162 TCTAAAGTATGTCTACATGCATCCG 58.553 40.000 12.71 0.00 40.71 4.18
147 148 7.383572 CACTCTAAAGTATGTCTACATGCATCC 59.616 40.741 12.71 0.00 40.71 3.51
148 149 7.923344 ACACTCTAAAGTATGTCTACATGCATC 59.077 37.037 12.71 0.00 40.71 3.91
149 150 7.786030 ACACTCTAAAGTATGTCTACATGCAT 58.214 34.615 12.71 0.00 40.71 3.96
150 151 7.170393 ACACTCTAAAGTATGTCTACATGCA 57.830 36.000 12.71 0.00 40.71 3.96
151 152 8.622157 TCTACACTCTAAAGTATGTCTACATGC 58.378 37.037 5.85 4.53 38.92 4.06
157 158 9.469097 AGTGAATCTACACTCTAAAGTATGTCT 57.531 33.333 0.00 0.00 46.36 3.41
171 172 6.073222 ACGGAACAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
172 173 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
173 174 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
174 175 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
175 176 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
176 177 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
177 178 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
178 179 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
179 180 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
180 181 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
181 182 6.367969 GTGACTACATACGGAACAAAATGAGT 59.632 38.462 0.00 0.00 0.00 3.41
182 183 6.590292 AGTGACTACATACGGAACAAAATGAG 59.410 38.462 0.00 0.00 0.00 2.90
183 184 6.460781 AGTGACTACATACGGAACAAAATGA 58.539 36.000 0.00 0.00 0.00 2.57
184 185 6.721571 AGTGACTACATACGGAACAAAATG 57.278 37.500 0.00 0.00 0.00 2.32
185 186 6.708949 ACAAGTGACTACATACGGAACAAAAT 59.291 34.615 0.00 0.00 0.00 1.82
186 187 6.050432 ACAAGTGACTACATACGGAACAAAA 58.950 36.000 0.00 0.00 0.00 2.44
187 188 5.603596 ACAAGTGACTACATACGGAACAAA 58.396 37.500 0.00 0.00 0.00 2.83
188 189 5.204409 ACAAGTGACTACATACGGAACAA 57.796 39.130 0.00 0.00 0.00 2.83
189 190 4.859304 ACAAGTGACTACATACGGAACA 57.141 40.909 0.00 0.00 0.00 3.18
190 191 5.224888 TCAACAAGTGACTACATACGGAAC 58.775 41.667 0.00 0.00 0.00 3.62
191 192 5.456548 TCAACAAGTGACTACATACGGAA 57.543 39.130 0.00 0.00 0.00 4.30
192 193 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
193 194 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
194 195 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
195 196 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
197 198 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
198 199 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
199 200 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
200 201 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
201 202 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
202 203 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
203 204 8.424918 AGTCTTTCTAGAGATTTCAACAAGTGA 58.575 33.333 0.00 0.00 0.00 3.41
204 205 8.600449 AGTCTTTCTAGAGATTTCAACAAGTG 57.400 34.615 0.00 0.00 0.00 3.16
221 222 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
222 223 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
223 224 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
224 225 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
225 226 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
226 227 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
227 228 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
228 229 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
229 230 6.210185 GCTACTCCCTCCGTTCCTAAATATAA 59.790 42.308 0.00 0.00 0.00 0.98
230 231 5.713861 GCTACTCCCTCCGTTCCTAAATATA 59.286 44.000 0.00 0.00 0.00 0.86
231 232 4.527427 GCTACTCCCTCCGTTCCTAAATAT 59.473 45.833 0.00 0.00 0.00 1.28
232 233 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
233 234 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
234 235 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
235 236 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
236 237 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
237 238 0.252103 TTGCTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
238 239 0.831307 ATTGCTACTCCCTCCGTTCC 59.169 55.000 0.00 0.00 0.00 3.62
239 240 1.480954 TGATTGCTACTCCCTCCGTTC 59.519 52.381 0.00 0.00 0.00 3.95
240 241 1.568504 TGATTGCTACTCCCTCCGTT 58.431 50.000 0.00 0.00 0.00 4.44
241 242 1.568504 TTGATTGCTACTCCCTCCGT 58.431 50.000 0.00 0.00 0.00 4.69
242 243 2.691409 TTTGATTGCTACTCCCTCCG 57.309 50.000 0.00 0.00 0.00 4.63
243 244 4.526970 TGAATTTGATTGCTACTCCCTCC 58.473 43.478 0.00 0.00 0.00 4.30
244 245 5.431765 TCTGAATTTGATTGCTACTCCCTC 58.568 41.667 0.00 0.00 0.00 4.30
245 246 5.441718 TCTGAATTTGATTGCTACTCCCT 57.558 39.130 0.00 0.00 0.00 4.20
246 247 5.882557 TCTTCTGAATTTGATTGCTACTCCC 59.117 40.000 0.00 0.00 0.00 4.30
247 248 6.183360 GGTCTTCTGAATTTGATTGCTACTCC 60.183 42.308 0.00 0.00 0.00 3.85
248 249 6.456181 CGGTCTTCTGAATTTGATTGCTACTC 60.456 42.308 0.00 0.00 0.00 2.59
249 250 5.352569 CGGTCTTCTGAATTTGATTGCTACT 59.647 40.000 0.00 0.00 0.00 2.57
250 251 5.563842 CGGTCTTCTGAATTTGATTGCTAC 58.436 41.667 0.00 0.00 0.00 3.58
372 373 8.696043 AAGCAAAGTATGGAATAAGCATATGA 57.304 30.769 6.97 0.00 0.00 2.15
571 572 7.630026 TGCTTTATGTATTTTCAGCATACTCG 58.370 34.615 0.00 0.00 0.00 4.18
761 762 2.772287 GGAACCTTGTTCTCTGGACAG 58.228 52.381 6.89 0.00 0.00 3.51
802 803 6.827727 ACTAGAGGCGGTCATGTTATTTATT 58.172 36.000 0.00 0.00 0.00 1.40
915 916 7.275341 CCTATGCGCACAAATCTTTTTATTTGA 59.725 33.333 14.90 0.00 45.61 2.69
1088 1089 4.387598 ACGCCTCTACGACTACTCATATT 58.612 43.478 0.00 0.00 36.70 1.28
1174 1175 4.907875 TCTCTATTTCTGGTAATCAGGGGG 59.092 45.833 0.00 0.00 43.53 5.40
1289 1291 1.733912 CATGACACTTGACACATCCCG 59.266 52.381 0.00 0.00 0.00 5.14
1291 1293 2.153645 TGCATGACACTTGACACATCC 58.846 47.619 0.00 0.00 0.00 3.51
1332 1334 8.145122 GCAGGTTAGGATAGGTAGCAATATATC 58.855 40.741 0.00 0.00 0.00 1.63
1344 1346 8.950210 CATAAACATATTGCAGGTTAGGATAGG 58.050 37.037 0.00 0.00 29.22 2.57
1367 1369 9.264719 GTTGTTGATGATGATACATCTGACATA 57.735 33.333 11.98 0.00 44.61 2.29
1419 1421 2.026729 AGGAAAAGTCTGCCTAGAAGCC 60.027 50.000 0.00 0.00 34.01 4.35
1437 1439 3.176924 AGTAAGTGCCTCTCTGAAGGA 57.823 47.619 9.23 0.00 38.87 3.36
1554 1556 3.674997 GAGTTGATTTACTGCCTCCACA 58.325 45.455 0.00 0.00 0.00 4.17
1603 1605 4.503741 TGCTTCTATGGCAAAACTGTTC 57.496 40.909 0.00 0.00 36.71 3.18
1868 1873 5.713025 TGAACATGGAGATTTTTGCTTAGC 58.287 37.500 0.00 0.00 0.00 3.09
2048 2053 0.616371 TGCGTATTAAGGTGGTGGCT 59.384 50.000 0.00 0.00 0.00 4.75
2126 2131 7.664318 TGTGCATTGATCTGATAAGATAGCAAT 59.336 33.333 9.38 6.05 0.00 3.56
2163 2168 4.761227 TGCACTTCAATTTGCATCTGTAGA 59.239 37.500 0.00 0.00 43.79 2.59
2252 2257 4.326826 TGCAGAGGGATGTAAAAAGTGAG 58.673 43.478 0.00 0.00 0.00 3.51
2258 2263 9.288576 CTCATATTTATGCAGAGGGATGTAAAA 57.711 33.333 0.00 0.00 33.76 1.52
2259 2264 7.391554 GCTCATATTTATGCAGAGGGATGTAAA 59.608 37.037 0.00 0.00 33.76 2.01
2260 2265 6.881065 GCTCATATTTATGCAGAGGGATGTAA 59.119 38.462 0.00 0.00 33.76 2.41
2261 2266 6.214208 AGCTCATATTTATGCAGAGGGATGTA 59.786 38.462 0.00 0.00 33.76 2.29
2262 2267 5.013913 AGCTCATATTTATGCAGAGGGATGT 59.986 40.000 0.00 0.00 33.76 3.06
2263 2268 5.498393 AGCTCATATTTATGCAGAGGGATG 58.502 41.667 0.00 0.00 33.76 3.51
2264 2269 5.775813 AGCTCATATTTATGCAGAGGGAT 57.224 39.130 0.00 0.00 33.76 3.85
2708 2719 8.736244 GGAATATACAGAAAGTGTTGCCTTAAA 58.264 33.333 0.00 0.00 40.94 1.52
2810 2821 2.047061 AGCTGTGGTGAACTTCTACCA 58.953 47.619 8.28 8.28 44.31 3.25
2867 2878 8.554490 AGATACCAGACCATCACTATTTTAGT 57.446 34.615 0.00 0.00 40.28 2.24
2903 2914 5.981174 CCTGTTGAAGGGCATCATTAATTT 58.019 37.500 0.00 0.00 43.15 1.82
2975 2986 2.622942 TGTGCCTTTTCCAACACTGATC 59.377 45.455 0.00 0.00 34.14 2.92
3051 3062 7.721399 ACTTTTGAGACCAATTCTGATAGTTGT 59.279 33.333 0.00 0.00 33.22 3.32
3105 3116 4.082895 CCTTCAATCTCCTCAAAGCTTGTG 60.083 45.833 0.00 0.74 0.00 3.33
3354 3365 3.075283 TGTCTCTCCTCTCTTGTCCTTCT 59.925 47.826 0.00 0.00 0.00 2.85
3363 3374 2.041620 ACTCAAGCTGTCTCTCCTCTCT 59.958 50.000 0.00 0.00 0.00 3.10
3463 3474 2.019984 GCTCCAGCTGAACCCATTTAG 58.980 52.381 17.39 0.00 38.21 1.85
3598 3610 0.250124 TTTCGGTGAACTGCGATGGT 60.250 50.000 0.00 0.00 0.00 3.55
3712 3724 7.880160 TCACAGCAAAGCATATAATAAAGGT 57.120 32.000 0.00 0.00 0.00 3.50
3767 3779 3.072468 CTGGGCATGGGGTTGCAG 61.072 66.667 0.00 0.00 44.59 4.41
3852 3864 1.133025 GCCTTTGCATGACGTATTGCT 59.867 47.619 19.36 0.00 37.47 3.91
3953 3967 1.300963 GAGCAGGGTCAGGCAATGA 59.699 57.895 0.00 0.00 34.79 2.57
4221 4261 3.123804 CTCCTTACGCGTATGAAGCATT 58.876 45.455 27.93 0.00 34.19 3.56
4251 4291 3.489513 AACTATGGCCGCCCTCCC 61.490 66.667 7.03 0.00 0.00 4.30
4252 4292 2.203209 CAACTATGGCCGCCCTCC 60.203 66.667 7.03 0.00 0.00 4.30
4253 4293 2.203209 CCAACTATGGCCGCCCTC 60.203 66.667 7.03 0.00 40.58 4.30
4256 4296 2.895372 CGTCCAACTATGGCCGCC 60.895 66.667 1.04 1.04 41.66 6.13
4262 4302 0.460284 AGAAGCGGCGTCCAACTATG 60.460 55.000 12.30 0.00 0.00 2.23
4263 4303 0.249398 AAGAAGCGGCGTCCAACTAT 59.751 50.000 12.30 0.00 0.00 2.12
4264 4304 0.389426 GAAGAAGCGGCGTCCAACTA 60.389 55.000 12.30 0.00 0.00 2.24
4265 4305 1.668151 GAAGAAGCGGCGTCCAACT 60.668 57.895 12.30 0.00 0.00 3.16
4266 4306 2.677979 GGAAGAAGCGGCGTCCAAC 61.678 63.158 12.30 4.50 36.58 3.77
4267 4307 2.358247 GGAAGAAGCGGCGTCCAA 60.358 61.111 12.30 0.00 36.58 3.53
4268 4308 4.388499 GGGAAGAAGCGGCGTCCA 62.388 66.667 12.30 0.00 38.05 4.02
4270 4310 4.083862 AGGGGAAGAAGCGGCGTC 62.084 66.667 9.37 7.89 0.00 5.19
4315 4917 5.441718 TCTTCTCCAGTTATTTCTGCCAT 57.558 39.130 0.00 0.00 34.47 4.40
4318 4920 6.992063 TTCATCTTCTCCAGTTATTTCTGC 57.008 37.500 0.00 0.00 34.47 4.26
4337 4939 7.202139 GGAGATAGATAGGTCCCAGTTTTTCAT 60.202 40.741 0.00 0.00 0.00 2.57
4345 4947 4.955450 CAGATGGAGATAGATAGGTCCCAG 59.045 50.000 0.00 0.00 0.00 4.45
4530 5132 3.115390 AGGAGAAGCTATTGTGGGCTTA 58.885 45.455 0.00 0.00 46.91 3.09
4587 5189 1.717645 GCGAGGGCGTATACGTTTATG 59.282 52.381 25.04 14.11 42.22 1.90
4588 5190 1.336240 GGCGAGGGCGTATACGTTTAT 60.336 52.381 25.04 10.14 42.22 1.40
4589 5191 0.030638 GGCGAGGGCGTATACGTTTA 59.969 55.000 25.04 0.00 42.22 2.01
4590 5192 1.227060 GGCGAGGGCGTATACGTTT 60.227 57.895 25.04 11.83 42.22 3.60
4591 5193 2.123428 AGGCGAGGGCGTATACGTT 61.123 57.895 25.04 12.17 42.22 3.99
4592 5194 2.517875 AGGCGAGGGCGTATACGT 60.518 61.111 25.04 6.86 42.22 3.57
4593 5195 2.050351 CAGGCGAGGGCGTATACG 60.050 66.667 20.87 20.87 41.24 3.06
4594 5196 0.318784 CTTCAGGCGAGGGCGTATAC 60.319 60.000 0.00 0.00 41.24 1.47
4595 5197 2.038690 CTTCAGGCGAGGGCGTATA 58.961 57.895 0.00 0.00 41.24 1.47
4596 5198 2.815308 CTTCAGGCGAGGGCGTAT 59.185 61.111 0.00 0.00 41.24 3.06
4597 5199 4.143333 GCTTCAGGCGAGGGCGTA 62.143 66.667 0.00 0.00 41.24 4.42
4607 5209 3.376935 ATCTCGCCCGTGCTTCAGG 62.377 63.158 0.00 0.00 34.43 3.86
4608 5210 2.169789 CATCTCGCCCGTGCTTCAG 61.170 63.158 0.00 0.00 34.43 3.02
4609 5211 2.125552 CATCTCGCCCGTGCTTCA 60.126 61.111 0.00 0.00 34.43 3.02
4610 5212 2.892425 CCATCTCGCCCGTGCTTC 60.892 66.667 0.00 0.00 34.43 3.86
4611 5213 4.473520 CCCATCTCGCCCGTGCTT 62.474 66.667 0.00 0.00 34.43 3.91
4621 5223 4.864334 CCTGTGCCGGCCCATCTC 62.864 72.222 26.77 7.88 0.00 2.75
4633 5235 3.730761 GCCTTCAGCGCACCTGTG 61.731 66.667 11.47 0.00 42.38 3.66
4638 5240 3.730761 CTGTGGCCTTCAGCGCAC 61.731 66.667 11.47 0.00 45.17 5.34
4649 5251 0.102300 AACAAAAACGAGGCTGTGGC 59.898 50.000 0.00 0.00 37.82 5.01
4650 5252 2.577449 AAACAAAAACGAGGCTGTGG 57.423 45.000 0.00 0.00 0.00 4.17
4651 5253 3.769536 AGAAAACAAAAACGAGGCTGTG 58.230 40.909 0.00 0.00 0.00 3.66
4652 5254 4.450082 AAGAAAACAAAAACGAGGCTGT 57.550 36.364 0.00 0.00 0.00 4.40
4653 5255 5.778161 AAAAGAAAACAAAAACGAGGCTG 57.222 34.783 0.00 0.00 0.00 4.85
4674 5276 9.225436 ACAAAAGTAAATCAAAAGGAAGCAAAA 57.775 25.926 0.00 0.00 0.00 2.44
4675 5277 8.785329 ACAAAAGTAAATCAAAAGGAAGCAAA 57.215 26.923 0.00 0.00 0.00 3.68
4676 5278 8.785329 AACAAAAGTAAATCAAAAGGAAGCAA 57.215 26.923 0.00 0.00 0.00 3.91
4677 5279 8.785329 AAACAAAAGTAAATCAAAAGGAAGCA 57.215 26.923 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.