Multiple sequence alignment - TraesCS4A01G255400

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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 TraesCS4A01G255400 chr4A 100.000 4499 0 0 1 4499 567483101 567478603 0.000000e+00 8309.0
1 TraesCS4A01G255400 chr4A 73.723 274 55 10 2939 3199 61616183 61615914 1.720000e-14 91.6
2 TraesCS4A01G255400 chr4D 93.010 4077 152 55 484 4499 35163260 35167264 0.000000e+00 5827.0
3 TraesCS4A01G255400 chr4D 89.256 121 8 2 1 121 35162948 35163063 3.630000e-31 147.0
4 TraesCS4A01G255400 chr4D 74.013 304 60 12 2913 3202 404111587 404111289 6.160000e-19 106.0
5 TraesCS4A01G255400 chr4D 90.789 76 3 2 4211 4286 35166904 35166975 1.030000e-16 99.0
6 TraesCS4A01G255400 chr4D 97.674 43 1 0 287 329 494875988 494876030 1.740000e-09 75.0
7 TraesCS4A01G255400 chr4B 90.698 4053 197 82 551 4499 50838813 50834837 0.000000e+00 5230.0
8 TraesCS4A01G255400 chr4B 74.426 305 59 12 2913 3203 500869014 500868715 3.680000e-21 113.0
9 TraesCS4A01G255400 chr5D 90.850 153 13 1 122 273 269296592 269296440 2.120000e-48 204.0
10 TraesCS4A01G255400 chr5D 77.778 225 35 9 2972 3184 1802004 1802225 1.700000e-24 124.0
11 TraesCS4A01G255400 chr5D 97.727 44 1 0 287 330 254343038 254342995 4.830000e-10 76.8
12 TraesCS4A01G255400 chr5D 76.577 111 23 2 3083 3193 351807026 351806919 1.750000e-04 58.4
13 TraesCS4A01G255400 chr3B 90.728 151 13 1 121 270 25486025 25486175 2.740000e-47 200.0
14 TraesCS4A01G255400 chr3B 76.744 301 49 14 2904 3189 673170524 673170230 1.010000e-31 148.0
15 TraesCS4A01G255400 chr5B 89.262 149 15 1 122 269 513797920 513798068 7.690000e-43 185.0
16 TraesCS4A01G255400 chr5B 76.923 221 36 8 2972 3180 656497 656280 1.320000e-20 111.0
17 TraesCS4A01G255400 chr5B 74.286 315 50 23 2926 3217 682819627 682819933 2.210000e-18 104.0
18 TraesCS4A01G255400 chr5B 77.451 102 20 2 3077 3178 417153600 417153698 1.750000e-04 58.4
19 TraesCS4A01G255400 chrUn 88.591 149 16 1 122 269 291208354 291208206 3.580000e-41 180.0
20 TraesCS4A01G255400 chrUn 77.333 225 36 8 2972 3184 122077474 122077695 7.910000e-23 119.0
21 TraesCS4A01G255400 chr2A 94.048 84 5 0 187 270 276054471 276054554 1.310000e-25 128.0
22 TraesCS4A01G255400 chr3A 74.419 301 56 15 2904 3189 647613453 647613747 4.760000e-20 110.0
23 TraesCS4A01G255400 chr3A 97.500 40 1 0 233 272 439298263 439298302 8.080000e-08 69.4
24 TraesCS4A01G255400 chr2B 97.917 48 0 1 281 328 667821776 667821822 1.040000e-11 82.4
25 TraesCS4A01G255400 chr7D 100.000 42 0 0 287 328 20938811 20938852 1.340000e-10 78.7
26 TraesCS4A01G255400 chr7D 73.663 243 47 10 2942 3171 566015852 566016090 1.340000e-10 78.7
27 TraesCS4A01G255400 chr6A 97.727 44 1 0 287 330 277889725 277889682 4.830000e-10 76.8
28 TraesCS4A01G255400 chr5A 97.727 44 1 0 287 330 677754298 677754255 4.830000e-10 76.8
29 TraesCS4A01G255400 chr5A 78.431 102 19 2 3077 3178 454271772 454271870 3.760000e-06 63.9
30 TraesCS4A01G255400 chr1D 97.727 44 1 0 287 330 307346547 307346504 4.830000e-10 76.8
31 TraesCS4A01G255400 chr1D 97.727 44 1 0 287 330 449490208 449490165 4.830000e-10 76.8
32 TraesCS4A01G255400 chr1D 97.674 43 1 0 287 329 268535541 268535583 1.740000e-09 75.0
33 TraesCS4A01G255400 chr7A 76.056 142 32 2 2902 3042 652288278 652288418 6.240000e-09 73.1
34 TraesCS4A01G255400 chr3D 97.500 40 1 0 233 272 325967929 325967890 8.080000e-08 69.4
35 TraesCS4A01G255400 chr3D 97.500 40 1 0 233 272 550743290 550743329 8.080000e-08 69.4
36 TraesCS4A01G255400 chr1B 94.444 36 0 2 2742 2776 626687946 626687980 2.000000e-03 54.7
37 TraesCS4A01G255400 chr1A 94.444 36 0 2 2742 2776 549712110 549712144 2.000000e-03 54.7


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 TraesCS4A01G255400 chr4A 567478603 567483101 4498 True 8309.000000 8309 100.000000 1 4499 1 chr4A.!!$R2 4498
1 TraesCS4A01G255400 chr4D 35162948 35167264 4316 False 2024.333333 5827 91.018333 1 4499 3 chr4D.!!$F2 4498
2 TraesCS4A01G255400 chr4B 50834837 50838813 3976 True 5230.000000 5230 90.698000 551 4499 1 chr4B.!!$R1 3948

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
169 170 0.099259 CATGATTTGCGCACGATGGT 59.901 50.0 11.12 0.0 0.00 3.55 F
197 198 0.107214 GCCATCGGATGAAGGAACCA 60.107 55.0 19.30 0.0 34.86 3.67 F
691 738 0.176680 ACAGGCTGCTATCTTGTCCG 59.823 55.0 15.89 0.0 0.00 4.79 F
1588 1670 0.248539 GGCGCTCAAGTACTACTCGG 60.249 60.0 7.64 0.0 0.00 4.63 F
1591 1673 0.248539 GCTCAAGTACTACTCGGGCG 60.249 60.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2178 0.378257 GCACATATTCCTGCACACCG 59.622 55.000 0.00 0.0 33.31 4.94 R
2109 2191 3.463585 GGGTCGTCCCGGCACATA 61.464 66.667 0.76 0.0 44.74 2.29 R
2688 2770 1.246056 CCAGGTTGAGGTGGTGCATG 61.246 60.000 0.00 0.0 0.00 4.06 R
3471 3574 0.824109 CCTGGACGCAGAAGATGGTA 59.176 55.000 0.00 0.0 0.00 3.25 R
3535 3638 8.866093 ACCACTTGGCTTTGTTTTTATATTACT 58.134 29.630 0.00 0.0 39.32 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.600375 TCAAACTTCAAGACATAGCTGAACTAG 59.400 37.037 0.00 0.00 33.29 2.57
62 63 7.934120 ACTTCAAGACATAGCTGAACTAGTTTT 59.066 33.333 10.02 0.00 33.29 2.43
91 92 4.084888 GTAGCAACGCACGGGCAC 62.085 66.667 11.77 0.00 41.24 5.01
122 123 9.444600 CCTTACTAGCAAGGTATTAAGTTTTCA 57.555 33.333 13.03 0.00 40.29 2.69
125 126 7.803724 ACTAGCAAGGTATTAAGTTTTCAACG 58.196 34.615 0.00 0.00 36.23 4.10
126 127 5.458015 AGCAAGGTATTAAGTTTTCAACGC 58.542 37.500 0.00 0.00 36.23 4.84
127 128 5.240844 AGCAAGGTATTAAGTTTTCAACGCT 59.759 36.000 0.00 0.00 36.23 5.07
128 129 5.342259 GCAAGGTATTAAGTTTTCAACGCTG 59.658 40.000 0.00 0.00 36.23 5.18
129 130 5.043189 AGGTATTAAGTTTTCAACGCTGC 57.957 39.130 0.00 0.00 36.23 5.25
130 131 4.760204 AGGTATTAAGTTTTCAACGCTGCT 59.240 37.500 0.00 0.00 36.23 4.24
131 132 5.935789 AGGTATTAAGTTTTCAACGCTGCTA 59.064 36.000 0.00 0.00 36.23 3.49
132 133 6.598064 AGGTATTAAGTTTTCAACGCTGCTAT 59.402 34.615 0.00 0.00 36.23 2.97
133 134 7.767198 AGGTATTAAGTTTTCAACGCTGCTATA 59.233 33.333 0.00 0.00 36.23 1.31
134 135 7.849515 GGTATTAAGTTTTCAACGCTGCTATAC 59.150 37.037 0.00 0.00 36.23 1.47
135 136 6.788684 TTAAGTTTTCAACGCTGCTATACA 57.211 33.333 0.00 0.00 36.23 2.29
136 137 4.663636 AGTTTTCAACGCTGCTATACAC 57.336 40.909 0.00 0.00 36.23 2.90
137 138 4.062293 AGTTTTCAACGCTGCTATACACA 58.938 39.130 0.00 0.00 36.23 3.72
138 139 4.695455 AGTTTTCAACGCTGCTATACACAT 59.305 37.500 0.00 0.00 36.23 3.21
139 140 4.598406 TTTCAACGCTGCTATACACATG 57.402 40.909 0.00 0.00 0.00 3.21
140 141 3.518634 TCAACGCTGCTATACACATGA 57.481 42.857 0.00 0.00 0.00 3.07
141 142 4.058721 TCAACGCTGCTATACACATGAT 57.941 40.909 0.00 0.00 0.00 2.45
142 143 5.195001 TCAACGCTGCTATACACATGATA 57.805 39.130 0.00 0.00 0.00 2.15
143 144 4.982295 TCAACGCTGCTATACACATGATAC 59.018 41.667 0.00 0.00 0.00 2.24
144 145 4.855715 ACGCTGCTATACACATGATACT 57.144 40.909 0.00 0.00 0.00 2.12
145 146 5.201713 ACGCTGCTATACACATGATACTT 57.798 39.130 0.00 0.00 0.00 2.24
146 147 6.327279 ACGCTGCTATACACATGATACTTA 57.673 37.500 0.00 0.00 0.00 2.24
147 148 6.745116 ACGCTGCTATACACATGATACTTAA 58.255 36.000 0.00 0.00 0.00 1.85
148 149 7.378966 ACGCTGCTATACACATGATACTTAAT 58.621 34.615 0.00 0.00 0.00 1.40
149 150 7.329471 ACGCTGCTATACACATGATACTTAATG 59.671 37.037 0.00 0.00 0.00 1.90
150 151 7.459486 GCTGCTATACACATGATACTTAATGC 58.541 38.462 0.00 0.00 0.00 3.56
151 152 7.118245 GCTGCTATACACATGATACTTAATGCA 59.882 37.037 0.00 0.00 0.00 3.96
152 153 9.159364 CTGCTATACACATGATACTTAATGCAT 57.841 33.333 0.00 0.00 0.00 3.96
153 154 8.938906 TGCTATACACATGATACTTAATGCATG 58.061 33.333 0.00 0.00 42.75 4.06
154 155 9.154847 GCTATACACATGATACTTAATGCATGA 57.845 33.333 0.00 0.00 40.29 3.07
166 167 4.696078 GCATGATTTGCGCACGAT 57.304 50.000 11.12 7.51 42.54 3.73
167 168 2.200927 GCATGATTTGCGCACGATG 58.799 52.632 11.12 11.08 42.54 3.84
168 169 1.204228 GCATGATTTGCGCACGATGG 61.204 55.000 11.12 0.00 42.54 3.51
169 170 0.099259 CATGATTTGCGCACGATGGT 59.901 50.000 11.12 0.00 0.00 3.55
170 171 0.378257 ATGATTTGCGCACGATGGTC 59.622 50.000 11.12 2.64 0.00 4.02
171 172 0.952984 TGATTTGCGCACGATGGTCA 60.953 50.000 11.12 5.51 0.00 4.02
172 173 0.521242 GATTTGCGCACGATGGTCAC 60.521 55.000 11.12 0.00 0.00 3.67
173 174 1.233950 ATTTGCGCACGATGGTCACA 61.234 50.000 11.12 0.00 0.00 3.58
174 175 1.233950 TTTGCGCACGATGGTCACAT 61.234 50.000 11.12 0.00 40.85 3.21
182 183 3.815133 GATGGTCACATCCAGCCAT 57.185 52.632 0.00 0.00 46.23 4.40
183 184 1.602311 GATGGTCACATCCAGCCATC 58.398 55.000 6.66 6.66 46.23 3.51
184 185 0.179037 ATGGTCACATCCAGCCATCG 60.179 55.000 0.00 0.00 41.05 3.84
185 186 1.524621 GGTCACATCCAGCCATCGG 60.525 63.158 0.00 0.00 0.00 4.18
186 187 1.522092 GTCACATCCAGCCATCGGA 59.478 57.895 0.00 0.00 36.84 4.55
187 188 0.107456 GTCACATCCAGCCATCGGAT 59.893 55.000 0.00 0.00 44.35 4.18
192 193 0.399454 ATCCAGCCATCGGATGAAGG 59.601 55.000 19.30 15.95 42.34 3.46
193 194 0.690744 TCCAGCCATCGGATGAAGGA 60.691 55.000 19.30 17.73 42.34 3.36
194 195 0.181114 CCAGCCATCGGATGAAGGAA 59.819 55.000 19.30 0.00 42.34 3.36
195 196 1.303309 CAGCCATCGGATGAAGGAAC 58.697 55.000 19.30 2.03 42.34 3.62
196 197 0.181350 AGCCATCGGATGAAGGAACC 59.819 55.000 19.30 0.00 34.86 3.62
197 198 0.107214 GCCATCGGATGAAGGAACCA 60.107 55.000 19.30 0.00 34.86 3.67
198 199 1.681780 GCCATCGGATGAAGGAACCAA 60.682 52.381 19.30 0.00 34.86 3.67
199 200 2.292267 CCATCGGATGAAGGAACCAAG 58.708 52.381 19.30 0.00 34.86 3.61
200 201 2.356125 CCATCGGATGAAGGAACCAAGT 60.356 50.000 19.30 0.00 34.86 3.16
201 202 2.472695 TCGGATGAAGGAACCAAGTG 57.527 50.000 0.00 0.00 0.00 3.16
202 203 0.804989 CGGATGAAGGAACCAAGTGC 59.195 55.000 0.00 0.00 0.00 4.40
203 204 1.881925 CGGATGAAGGAACCAAGTGCA 60.882 52.381 0.00 0.00 0.00 4.57
204 205 2.450476 GGATGAAGGAACCAAGTGCAT 58.550 47.619 0.00 0.00 0.00 3.96
205 206 2.424956 GGATGAAGGAACCAAGTGCATC 59.575 50.000 0.00 0.00 0.00 3.91
206 207 2.655090 TGAAGGAACCAAGTGCATCA 57.345 45.000 0.00 0.00 0.00 3.07
207 208 2.229792 TGAAGGAACCAAGTGCATCAC 58.770 47.619 0.00 0.00 34.10 3.06
208 209 2.229792 GAAGGAACCAAGTGCATCACA 58.770 47.619 0.00 0.00 36.74 3.58
217 218 3.556817 GTGCATCACACCCATCAGA 57.443 52.632 0.00 0.00 44.02 3.27
218 219 2.048444 GTGCATCACACCCATCAGAT 57.952 50.000 0.00 0.00 44.02 2.90
219 220 1.674441 GTGCATCACACCCATCAGATG 59.326 52.381 3.04 3.04 44.02 2.90
220 221 3.583840 GTGCATCACACCCATCAGATGG 61.584 54.545 21.47 21.47 44.02 3.51
230 231 2.487934 CCATCAGATGGTCAATCGTCC 58.512 52.381 20.30 0.00 45.54 4.79
231 232 2.158914 CCATCAGATGGTCAATCGTCCA 60.159 50.000 20.30 0.00 45.54 4.02
232 233 3.495629 CCATCAGATGGTCAATCGTCCAT 60.496 47.826 20.30 0.00 45.54 3.41
233 234 3.183793 TCAGATGGTCAATCGTCCATG 57.816 47.619 1.27 0.00 43.45 3.66
234 235 1.600957 CAGATGGTCAATCGTCCATGC 59.399 52.381 1.27 0.00 43.45 4.06
235 236 1.210234 AGATGGTCAATCGTCCATGCA 59.790 47.619 1.27 0.00 43.45 3.96
236 237 2.158711 AGATGGTCAATCGTCCATGCAT 60.159 45.455 0.00 0.00 43.45 3.96
237 238 1.667236 TGGTCAATCGTCCATGCATC 58.333 50.000 0.00 0.00 0.00 3.91
238 239 0.583438 GGTCAATCGTCCATGCATCG 59.417 55.000 0.00 0.00 0.00 3.84
239 240 1.290203 GTCAATCGTCCATGCATCGT 58.710 50.000 0.00 0.00 0.00 3.73
240 241 1.004610 GTCAATCGTCCATGCATCGTG 60.005 52.381 0.00 0.00 0.00 4.35
241 242 0.316442 CAATCGTCCATGCATCGTGC 60.316 55.000 0.00 3.44 45.29 5.34
250 251 2.751436 GCATCGTGCATGGTGGGT 60.751 61.111 20.53 0.00 44.26 4.51
251 252 2.764314 GCATCGTGCATGGTGGGTC 61.764 63.158 20.53 0.38 44.26 4.46
252 253 2.125147 ATCGTGCATGGTGGGTCG 60.125 61.111 5.98 0.00 0.00 4.79
253 254 3.680620 ATCGTGCATGGTGGGTCGG 62.681 63.158 5.98 0.00 0.00 4.79
255 256 4.722700 GTGCATGGTGGGTCGGCT 62.723 66.667 0.00 0.00 0.00 5.52
256 257 4.720902 TGCATGGTGGGTCGGCTG 62.721 66.667 0.00 0.00 0.00 4.85
257 258 4.722700 GCATGGTGGGTCGGCTGT 62.723 66.667 0.00 0.00 0.00 4.40
258 259 2.747460 CATGGTGGGTCGGCTGTG 60.747 66.667 0.00 0.00 0.00 3.66
259 260 2.927856 ATGGTGGGTCGGCTGTGA 60.928 61.111 0.00 0.00 0.00 3.58
260 261 2.525124 ATGGTGGGTCGGCTGTGAA 61.525 57.895 0.00 0.00 0.00 3.18
261 262 2.358737 GGTGGGTCGGCTGTGAAG 60.359 66.667 0.00 0.00 0.00 3.02
262 263 2.426023 GTGGGTCGGCTGTGAAGT 59.574 61.111 0.00 0.00 0.00 3.01
263 264 1.669440 GTGGGTCGGCTGTGAAGTA 59.331 57.895 0.00 0.00 0.00 2.24
264 265 0.389948 GTGGGTCGGCTGTGAAGTAG 60.390 60.000 0.00 0.00 0.00 2.57
265 266 0.830444 TGGGTCGGCTGTGAAGTAGT 60.830 55.000 0.00 0.00 0.00 2.73
266 267 0.320697 GGGTCGGCTGTGAAGTAGTT 59.679 55.000 0.00 0.00 0.00 2.24
267 268 1.270678 GGGTCGGCTGTGAAGTAGTTT 60.271 52.381 0.00 0.00 0.00 2.66
268 269 2.067013 GGTCGGCTGTGAAGTAGTTTC 58.933 52.381 0.00 0.00 36.29 2.78
269 270 1.719780 GTCGGCTGTGAAGTAGTTTCG 59.280 52.381 0.00 0.00 38.71 3.46
270 271 1.338973 TCGGCTGTGAAGTAGTTTCGT 59.661 47.619 0.00 0.00 38.71 3.85
271 272 2.132762 CGGCTGTGAAGTAGTTTCGTT 58.867 47.619 0.00 0.00 38.71 3.85
272 273 3.004629 TCGGCTGTGAAGTAGTTTCGTTA 59.995 43.478 0.00 0.00 38.71 3.18
273 274 3.737266 CGGCTGTGAAGTAGTTTCGTTAA 59.263 43.478 0.00 0.00 38.71 2.01
274 275 4.143389 CGGCTGTGAAGTAGTTTCGTTAAG 60.143 45.833 0.00 0.00 38.71 1.85
275 276 4.748600 GGCTGTGAAGTAGTTTCGTTAAGT 59.251 41.667 0.00 0.00 38.71 2.24
276 277 5.235831 GGCTGTGAAGTAGTTTCGTTAAGTT 59.764 40.000 0.00 0.00 38.71 2.66
277 278 6.238293 GGCTGTGAAGTAGTTTCGTTAAGTTT 60.238 38.462 0.00 0.00 38.71 2.66
278 279 7.184779 GCTGTGAAGTAGTTTCGTTAAGTTTT 58.815 34.615 0.00 0.00 38.71 2.43
279 280 8.330302 GCTGTGAAGTAGTTTCGTTAAGTTTTA 58.670 33.333 0.00 0.00 38.71 1.52
280 281 9.628983 CTGTGAAGTAGTTTCGTTAAGTTTTAC 57.371 33.333 0.00 0.00 38.71 2.01
281 282 9.369904 TGTGAAGTAGTTTCGTTAAGTTTTACT 57.630 29.630 0.00 0.00 38.71 2.24
282 283 9.841016 GTGAAGTAGTTTCGTTAAGTTTTACTC 57.159 33.333 0.00 0.00 38.71 2.59
283 284 9.034544 TGAAGTAGTTTCGTTAAGTTTTACTCC 57.965 33.333 0.00 0.00 38.71 3.85
284 285 7.953158 AGTAGTTTCGTTAAGTTTTACTCCC 57.047 36.000 0.00 0.00 0.00 4.30
285 286 7.730084 AGTAGTTTCGTTAAGTTTTACTCCCT 58.270 34.615 0.00 0.00 0.00 4.20
286 287 8.206867 AGTAGTTTCGTTAAGTTTTACTCCCTT 58.793 33.333 0.00 0.00 0.00 3.95
287 288 9.476202 GTAGTTTCGTTAAGTTTTACTCCCTTA 57.524 33.333 0.00 0.00 0.00 2.69
288 289 8.370493 AGTTTCGTTAAGTTTTACTCCCTTAC 57.630 34.615 0.00 0.00 0.00 2.34
289 290 7.986889 AGTTTCGTTAAGTTTTACTCCCTTACA 59.013 33.333 0.00 0.00 0.00 2.41
290 291 8.777413 GTTTCGTTAAGTTTTACTCCCTTACAT 58.223 33.333 0.00 0.00 0.00 2.29
291 292 8.538409 TTCGTTAAGTTTTACTCCCTTACATC 57.462 34.615 0.00 0.00 0.00 3.06
292 293 7.099120 TCGTTAAGTTTTACTCCCTTACATCC 58.901 38.462 0.00 0.00 0.00 3.51
293 294 6.875195 CGTTAAGTTTTACTCCCTTACATCCA 59.125 38.462 0.00 0.00 0.00 3.41
294 295 7.551617 CGTTAAGTTTTACTCCCTTACATCCAT 59.448 37.037 0.00 0.00 0.00 3.41
295 296 9.239551 GTTAAGTTTTACTCCCTTACATCCATT 57.760 33.333 0.00 0.00 0.00 3.16
296 297 9.816787 TTAAGTTTTACTCCCTTACATCCATTT 57.183 29.630 0.00 0.00 0.00 2.32
297 298 7.703058 AGTTTTACTCCCTTACATCCATTTG 57.297 36.000 0.00 0.00 0.00 2.32
298 299 7.466804 AGTTTTACTCCCTTACATCCATTTGA 58.533 34.615 0.00 0.00 0.00 2.69
299 300 7.947890 AGTTTTACTCCCTTACATCCATTTGAA 59.052 33.333 0.00 0.00 0.00 2.69
300 301 7.938140 TTTACTCCCTTACATCCATTTGAAG 57.062 36.000 0.00 0.00 0.00 3.02
301 302 4.860022 ACTCCCTTACATCCATTTGAAGG 58.140 43.478 0.00 0.00 37.09 3.46
302 303 4.540099 ACTCCCTTACATCCATTTGAAGGA 59.460 41.667 0.51 0.00 39.26 3.36
303 304 4.855340 TCCCTTACATCCATTTGAAGGAC 58.145 43.478 0.51 0.00 39.26 3.85
304 305 4.290985 TCCCTTACATCCATTTGAAGGACA 59.709 41.667 0.51 0.00 39.26 4.02
305 306 5.016173 CCCTTACATCCATTTGAAGGACAA 58.984 41.667 0.51 0.00 39.26 3.18
306 307 5.126061 CCCTTACATCCATTTGAAGGACAAG 59.874 44.000 0.51 0.00 39.26 3.16
307 308 5.711976 CCTTACATCCATTTGAAGGACAAGT 59.288 40.000 0.00 0.00 39.26 3.16
308 309 6.209391 CCTTACATCCATTTGAAGGACAAGTT 59.791 38.462 0.00 0.00 39.26 2.66
309 310 7.255942 CCTTACATCCATTTGAAGGACAAGTTT 60.256 37.037 0.00 0.00 39.26 2.66
310 311 6.484364 ACATCCATTTGAAGGACAAGTTTT 57.516 33.333 0.00 0.00 39.77 2.43
311 312 6.888105 ACATCCATTTGAAGGACAAGTTTTT 58.112 32.000 0.00 0.00 39.77 1.94
343 344 4.831710 AGGGAGTACTCGGTAATTATGGAC 59.168 45.833 16.56 0.00 0.00 4.02
377 378 2.738846 ACTAGTTTTCTGTGCATCAGCG 59.261 45.455 10.36 0.00 46.23 5.18
379 380 1.532868 AGTTTTCTGTGCATCAGCGAC 59.467 47.619 10.36 8.78 46.23 5.19
385 387 1.223417 TGTGCATCAGCGACACACTG 61.223 55.000 0.00 0.00 46.23 3.66
389 391 4.868195 TCAGCGACACACTGATCG 57.132 55.556 0.00 3.88 39.21 3.69
425 428 2.550830 TTCACAGAGAGGCTTTGGTC 57.449 50.000 0.00 0.00 0.00 4.02
464 467 1.371558 GCACGGTTCAAGGGACTCT 59.628 57.895 0.00 0.00 38.49 3.24
467 470 0.317479 ACGGTTCAAGGGACTCTTCG 59.683 55.000 0.00 0.00 38.49 3.79
487 493 7.320399 TCTTCGTTATAGCTCATTCACTTTCA 58.680 34.615 0.00 0.00 0.00 2.69
488 494 7.489435 TCTTCGTTATAGCTCATTCACTTTCAG 59.511 37.037 0.00 0.00 0.00 3.02
496 537 3.084039 TCATTCACTTTCAGGGCATCAC 58.916 45.455 0.00 0.00 0.00 3.06
558 603 5.180117 CCCATATCTGATCAATTTCCGTCAC 59.820 44.000 0.00 0.00 0.00 3.67
569 614 2.031258 TTCCGTCACTTTTCACAGCA 57.969 45.000 0.00 0.00 0.00 4.41
572 617 1.603802 CCGTCACTTTTCACAGCACAT 59.396 47.619 0.00 0.00 0.00 3.21
586 633 1.535462 AGCACATTTTCGTCCCTTTCG 59.465 47.619 0.00 0.00 0.00 3.46
597 644 1.810755 GTCCCTTTCGACAACCCATTC 59.189 52.381 0.00 0.00 32.74 2.67
602 649 1.790755 TTCGACAACCCATTCTCGTG 58.209 50.000 0.00 0.00 29.36 4.35
610 657 4.158764 ACAACCCATTCTCGTGTTCAAAAA 59.841 37.500 0.00 0.00 0.00 1.94
615 662 6.149474 ACCCATTCTCGTGTTCAAAAATCTAG 59.851 38.462 0.00 0.00 0.00 2.43
616 663 6.024049 CCATTCTCGTGTTCAAAAATCTAGC 58.976 40.000 0.00 0.00 0.00 3.42
617 664 6.348458 CCATTCTCGTGTTCAAAAATCTAGCA 60.348 38.462 0.00 0.00 0.00 3.49
618 665 5.591643 TCTCGTGTTCAAAAATCTAGCAC 57.408 39.130 0.00 0.00 0.00 4.40
639 686 1.683365 CCCATTTCCTGCCCCAGTG 60.683 63.158 0.00 0.00 0.00 3.66
640 687 1.383799 CCATTTCCTGCCCCAGTGA 59.616 57.895 0.00 0.00 0.00 3.41
645 692 0.401738 TTCCTGCCCCAGTGAAGAAG 59.598 55.000 0.00 0.00 0.00 2.85
657 704 5.188434 CCAGTGAAGAAGAATGAATAGCCA 58.812 41.667 0.00 0.00 0.00 4.75
658 705 5.649395 CCAGTGAAGAAGAATGAATAGCCAA 59.351 40.000 0.00 0.00 0.00 4.52
691 738 0.176680 ACAGGCTGCTATCTTGTCCG 59.823 55.000 15.89 0.00 0.00 4.79
696 743 1.202973 CTGCTATCTTGTCCGACGCG 61.203 60.000 3.53 3.53 0.00 6.01
702 749 1.225745 CTTGTCCGACGCGAATTGC 60.226 57.895 15.93 0.00 41.47 3.56
780 832 2.031870 CTCCCGGGGAATCAATTTTCC 58.968 52.381 23.50 0.84 43.78 3.13
878 935 3.390639 TCCAAATTGGACAATTGGTGCTT 59.609 39.130 11.23 0.00 42.67 3.91
882 942 6.222389 CAAATTGGACAATTGGTGCTTCTAA 58.778 36.000 10.83 2.48 40.57 2.10
912 975 5.128827 TGTTGGGGATTAGCACTAGAAGTAG 59.871 44.000 0.00 0.00 0.00 2.57
913 976 3.641906 TGGGGATTAGCACTAGAAGTAGC 59.358 47.826 0.00 0.00 0.00 3.58
917 980 4.320641 GGATTAGCACTAGAAGTAGCCGAG 60.321 50.000 0.00 0.00 0.00 4.63
942 1005 4.079038 TCCACCAGATTCATCCATCCATTT 60.079 41.667 0.00 0.00 0.00 2.32
943 1006 4.280174 CCACCAGATTCATCCATCCATTTC 59.720 45.833 0.00 0.00 0.00 2.17
944 1007 4.280174 CACCAGATTCATCCATCCATTTCC 59.720 45.833 0.00 0.00 0.00 3.13
945 1008 4.079038 ACCAGATTCATCCATCCATTTCCA 60.079 41.667 0.00 0.00 0.00 3.53
946 1009 5.084519 CCAGATTCATCCATCCATTTCCAT 58.915 41.667 0.00 0.00 0.00 3.41
947 1010 5.542635 CCAGATTCATCCATCCATTTCCATT 59.457 40.000 0.00 0.00 0.00 3.16
982 1049 2.344129 GCTCCGATCGAATCCCCC 59.656 66.667 18.66 0.00 0.00 5.40
1000 1067 3.531961 CCCCCAATTCCTTCCCCA 58.468 61.111 0.00 0.00 0.00 4.96
1001 1068 2.026945 CCCCCAATTCCTTCCCCAT 58.973 57.895 0.00 0.00 0.00 4.00
1002 1069 0.398948 CCCCCAATTCCTTCCCCATG 60.399 60.000 0.00 0.00 0.00 3.66
1003 1070 0.398948 CCCCAATTCCTTCCCCATGG 60.399 60.000 4.14 4.14 0.00 3.66
1021 1088 2.780040 CCATGGCCCTCCTCCCAT 60.780 66.667 0.00 0.00 42.41 4.00
1318 1391 4.477975 GCTCCACCCTCGTCGTCG 62.478 72.222 0.00 0.00 38.55 5.12
1378 1457 1.852157 ATCTGGACCCTGCCCAACA 60.852 57.895 0.00 0.00 32.53 3.33
1379 1458 2.142292 ATCTGGACCCTGCCCAACAC 62.142 60.000 0.00 0.00 32.53 3.32
1446 1525 2.047179 GTGTTCGGCTCCTGGTCC 60.047 66.667 0.00 0.00 0.00 4.46
1583 1665 1.409064 CTCCATGGCGCTCAAGTACTA 59.591 52.381 6.96 0.00 0.00 1.82
1587 1669 0.450583 TGGCGCTCAAGTACTACTCG 59.549 55.000 7.64 0.00 0.00 4.18
1588 1670 0.248539 GGCGCTCAAGTACTACTCGG 60.249 60.000 7.64 0.00 0.00 4.63
1589 1671 0.248539 GCGCTCAAGTACTACTCGGG 60.249 60.000 0.00 0.00 0.00 5.14
1590 1672 0.248539 CGCTCAAGTACTACTCGGGC 60.249 60.000 0.00 0.00 0.00 6.13
1591 1673 0.248539 GCTCAAGTACTACTCGGGCG 60.249 60.000 0.00 0.00 0.00 6.13
1592 1674 1.376543 CTCAAGTACTACTCGGGCGA 58.623 55.000 0.00 0.00 0.00 5.54
1593 1675 1.331138 CTCAAGTACTACTCGGGCGAG 59.669 57.143 0.00 0.00 46.91 5.03
1594 1676 0.248539 CAAGTACTACTCGGGCGAGC 60.249 60.000 0.00 0.00 45.54 5.03
1595 1677 1.712977 AAGTACTACTCGGGCGAGCG 61.713 60.000 0.00 0.00 45.54 5.03
1665 1747 2.320587 GCTGCTGAACCTCACCACG 61.321 63.158 0.00 0.00 0.00 4.94
2073 2155 0.691078 ATCCTGGCCCGTACATGTCT 60.691 55.000 0.00 0.00 0.00 3.41
2075 2157 1.048601 CCTGGCCCGTACATGTCTAT 58.951 55.000 0.00 0.00 0.00 1.98
2076 2158 1.000955 CCTGGCCCGTACATGTCTATC 59.999 57.143 0.00 0.00 0.00 2.08
2185 2267 0.600255 GACGTGCCTGCTGTACAAGT 60.600 55.000 0.00 3.09 0.00 3.16
2232 2314 2.408022 GGGACGGAGATGTCGACG 59.592 66.667 11.62 0.00 39.83 5.12
2264 2346 3.775654 GGAGGCGGACAGGGACAG 61.776 72.222 0.00 0.00 0.00 3.51
2265 2347 4.459089 GAGGCGGACAGGGACAGC 62.459 72.222 0.00 0.00 0.00 4.40
2688 2770 4.285149 GTGACCATCATCGCGCGC 62.285 66.667 27.95 23.91 0.00 6.86
2867 2949 3.819920 CGAGGAGAGCTCGCAGCA 61.820 66.667 19.55 0.00 45.56 4.41
2868 2950 2.575993 GAGGAGAGCTCGCAGCAA 59.424 61.111 19.55 0.00 45.56 3.91
2870 2952 2.511145 GGAGAGCTCGCAGCAAGG 60.511 66.667 19.55 0.00 45.56 3.61
3051 3142 4.792087 GACTTCGGGCTGTCCAAA 57.208 55.556 0.00 0.00 34.36 3.28
3512 3615 5.769162 AGGACGACTAACTAACAAGTCTTCT 59.231 40.000 8.32 0.00 39.61 2.85
3513 3616 6.264970 AGGACGACTAACTAACAAGTCTTCTT 59.735 38.462 8.32 0.00 39.61 2.52
3514 3617 6.581919 GGACGACTAACTAACAAGTCTTCTTC 59.418 42.308 8.32 0.00 39.61 2.87
3624 3747 5.163652 TGACTGACTGATTGGACTACGTATG 60.164 44.000 0.00 0.00 0.00 2.39
3727 3850 0.514691 GAGTTTCTTGGTGCTGAGCG 59.485 55.000 0.00 0.00 0.00 5.03
3799 3922 2.586079 CGTAGCCTGCATGGACCG 60.586 66.667 6.40 1.69 38.35 4.79
3960 4089 2.604914 CGACCTCTGGAATCGACAAATG 59.395 50.000 0.00 0.00 38.10 2.32
3972 4101 4.074627 TCGACAAATGGGTGAACTACAA 57.925 40.909 0.00 0.00 0.00 2.41
4005 4137 9.624373 AATTCTATGATCTTGCTACTGTTCATT 57.376 29.630 0.00 0.00 0.00 2.57
4016 4148 6.658849 TGCTACTGTTCATTATATGTGGGTT 58.341 36.000 0.00 0.00 0.00 4.11
4031 4163 3.119173 TGTGGGTTGCTATTTTGCATAGC 60.119 43.478 10.29 10.29 45.28 2.97
4065 4197 1.068954 GTTCAGCAAGTGCAAGTAGCC 60.069 52.381 6.00 0.00 44.83 3.93
4082 4214 7.420800 CAAGTAGCCCATATCAGATGAAAAAC 58.579 38.462 0.00 0.00 0.00 2.43
4083 4215 6.662755 AGTAGCCCATATCAGATGAAAAACA 58.337 36.000 0.00 0.00 0.00 2.83
4084 4216 7.293073 AGTAGCCCATATCAGATGAAAAACAT 58.707 34.615 0.00 0.00 42.47 2.71
4088 4222 7.781693 AGCCCATATCAGATGAAAAACATAAGT 59.218 33.333 0.00 0.00 39.56 2.24
4092 4226 5.940192 TCAGATGAAAAACATAAGTGCGT 57.060 34.783 0.00 0.00 39.56 5.24
4093 4227 5.688823 TCAGATGAAAAACATAAGTGCGTG 58.311 37.500 0.00 0.00 39.56 5.34
4158 4324 4.999950 GCTAGTATGCTAATGCTGACCAAT 59.000 41.667 0.00 0.00 40.48 3.16
4323 4489 2.223479 CGGTCCAATGATTAAAAGCCCG 60.223 50.000 0.00 0.00 0.00 6.13
4427 4593 4.323417 TGCGACACCTGATAACAGAAAAT 58.677 39.130 0.79 0.00 46.03 1.82
4429 4595 5.106712 TGCGACACCTGATAACAGAAAATTC 60.107 40.000 0.79 0.00 46.03 2.17
4431 4597 5.411361 CGACACCTGATAACAGAAAATTCCA 59.589 40.000 0.79 0.00 46.03 3.53
4433 4599 7.219484 ACACCTGATAACAGAAAATTCCAAG 57.781 36.000 0.79 0.00 46.03 3.61
4434 4600 6.095377 CACCTGATAACAGAAAATTCCAAGC 58.905 40.000 0.79 0.00 46.03 4.01
4435 4601 5.774690 ACCTGATAACAGAAAATTCCAAGCA 59.225 36.000 0.79 0.00 46.03 3.91
4436 4602 6.095377 CCTGATAACAGAAAATTCCAAGCAC 58.905 40.000 0.79 0.00 46.03 4.40
4437 4603 6.071728 CCTGATAACAGAAAATTCCAAGCACT 60.072 38.462 0.79 0.00 46.03 4.40
4473 4640 0.869730 GATTGGTTGCGGTGTTACGT 59.130 50.000 0.00 0.00 35.98 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.752661 TGCTACGGAACCACAATAAAAC 57.247 40.909 0.00 0.00 0.00 2.43
62 63 2.339418 CGTTGCTACGGAACCACAATA 58.661 47.619 13.04 0.00 43.94 1.90
86 87 1.835531 TGCTAGTAAGGTAAGGTGCCC 59.164 52.381 0.00 0.00 0.00 5.36
87 88 3.532542 CTTGCTAGTAAGGTAAGGTGCC 58.467 50.000 12.39 0.00 0.00 5.01
88 89 3.532542 CCTTGCTAGTAAGGTAAGGTGC 58.467 50.000 26.63 0.00 41.85 5.01
100 101 7.572539 GCGTTGAAAACTTAATACCTTGCTAGT 60.573 37.037 0.00 0.00 46.99 2.57
105 106 5.342259 GCAGCGTTGAAAACTTAATACCTTG 59.658 40.000 2.38 0.00 46.99 3.61
111 112 7.094975 TGTGTATAGCAGCGTTGAAAACTTAAT 60.095 33.333 2.38 0.00 46.99 1.40
116 117 4.398549 TGTGTATAGCAGCGTTGAAAAC 57.601 40.909 2.38 0.00 45.31 2.43
120 121 3.518634 TCATGTGTATAGCAGCGTTGA 57.481 42.857 2.38 0.00 0.00 3.18
121 122 4.984785 AGTATCATGTGTATAGCAGCGTTG 59.015 41.667 0.00 0.00 0.00 4.10
122 123 5.201713 AGTATCATGTGTATAGCAGCGTT 57.798 39.130 0.00 0.00 0.00 4.84
123 124 4.855715 AGTATCATGTGTATAGCAGCGT 57.144 40.909 0.00 0.00 0.00 5.07
124 125 7.670007 CATTAAGTATCATGTGTATAGCAGCG 58.330 38.462 0.00 0.00 0.00 5.18
125 126 7.118245 TGCATTAAGTATCATGTGTATAGCAGC 59.882 37.037 0.00 0.00 0.00 5.25
126 127 8.538409 TGCATTAAGTATCATGTGTATAGCAG 57.462 34.615 0.00 0.00 0.00 4.24
127 128 8.938906 CATGCATTAAGTATCATGTGTATAGCA 58.061 33.333 0.00 0.00 33.55 3.49
128 129 9.154847 TCATGCATTAAGTATCATGTGTATAGC 57.845 33.333 0.00 0.00 37.95 2.97
150 151 0.099259 ACCATCGTGCGCAAATCATG 59.901 50.000 14.00 11.74 0.00 3.07
151 152 0.378257 GACCATCGTGCGCAAATCAT 59.622 50.000 14.00 0.00 0.00 2.45
152 153 0.952984 TGACCATCGTGCGCAAATCA 60.953 50.000 14.00 7.04 0.00 2.57
153 154 0.521242 GTGACCATCGTGCGCAAATC 60.521 55.000 14.00 0.00 0.00 2.17
154 155 1.233950 TGTGACCATCGTGCGCAAAT 61.234 50.000 14.00 6.12 0.00 2.32
155 156 1.233950 ATGTGACCATCGTGCGCAAA 61.234 50.000 14.00 3.25 0.00 3.68
156 157 1.634757 GATGTGACCATCGTGCGCAA 61.635 55.000 14.00 0.00 38.28 4.85
157 158 2.047370 ATGTGACCATCGTGCGCA 60.047 55.556 5.66 5.66 0.00 6.09
158 159 2.703409 GATGTGACCATCGTGCGC 59.297 61.111 0.00 0.00 38.28 6.09
162 163 4.698898 GATGGCTGGATGTGACCATCGT 62.699 54.545 5.21 0.00 46.54 3.73
163 164 2.143873 GATGGCTGGATGTGACCATCG 61.144 57.143 5.21 0.00 46.54 3.84
164 165 3.815133 ATGGCTGGATGTGACCATC 57.185 52.632 0.00 0.00 45.65 3.51
165 166 0.179037 CGATGGCTGGATGTGACCAT 60.179 55.000 0.00 0.00 45.52 3.55
166 167 1.221566 CGATGGCTGGATGTGACCA 59.778 57.895 0.00 0.00 38.33 4.02
167 168 1.524621 CCGATGGCTGGATGTGACC 60.525 63.158 0.00 0.00 0.00 4.02
168 169 0.107456 ATCCGATGGCTGGATGTGAC 59.893 55.000 5.83 0.00 44.51 3.67
169 170 2.531672 ATCCGATGGCTGGATGTGA 58.468 52.632 5.83 0.00 44.51 3.58
174 175 0.690744 TCCTTCATCCGATGGCTGGA 60.691 55.000 8.54 10.23 40.46 3.86
175 176 0.181114 TTCCTTCATCCGATGGCTGG 59.819 55.000 8.54 8.30 36.59 4.85
176 177 1.303309 GTTCCTTCATCCGATGGCTG 58.697 55.000 8.54 0.00 36.59 4.85
177 178 0.181350 GGTTCCTTCATCCGATGGCT 59.819 55.000 8.54 0.00 36.59 4.75
178 179 0.107214 TGGTTCCTTCATCCGATGGC 60.107 55.000 8.54 0.00 36.59 4.40
179 180 2.292267 CTTGGTTCCTTCATCCGATGG 58.708 52.381 8.54 0.00 37.72 3.51
180 181 2.679837 CACTTGGTTCCTTCATCCGATG 59.320 50.000 1.55 1.55 0.00 3.84
181 182 2.941415 GCACTTGGTTCCTTCATCCGAT 60.941 50.000 0.00 0.00 0.00 4.18
182 183 1.610624 GCACTTGGTTCCTTCATCCGA 60.611 52.381 0.00 0.00 0.00 4.55
183 184 0.804989 GCACTTGGTTCCTTCATCCG 59.195 55.000 0.00 0.00 0.00 4.18
184 185 1.909700 TGCACTTGGTTCCTTCATCC 58.090 50.000 0.00 0.00 0.00 3.51
185 186 3.084039 TGATGCACTTGGTTCCTTCATC 58.916 45.455 0.00 0.00 0.00 2.92
186 187 2.821969 GTGATGCACTTGGTTCCTTCAT 59.178 45.455 0.00 0.00 0.00 2.57
187 188 2.229792 GTGATGCACTTGGTTCCTTCA 58.770 47.619 0.00 0.00 0.00 3.02
188 189 2.030805 GTGTGATGCACTTGGTTCCTTC 60.031 50.000 0.00 0.00 44.41 3.46
189 190 1.956477 GTGTGATGCACTTGGTTCCTT 59.044 47.619 0.00 0.00 44.41 3.36
190 191 1.609208 GTGTGATGCACTTGGTTCCT 58.391 50.000 0.00 0.00 44.41 3.36
191 192 0.598065 GGTGTGATGCACTTGGTTCC 59.402 55.000 0.00 0.00 46.86 3.62
192 193 0.598065 GGGTGTGATGCACTTGGTTC 59.402 55.000 0.00 0.00 46.86 3.62
193 194 0.106268 TGGGTGTGATGCACTTGGTT 60.106 50.000 0.00 0.00 46.86 3.67
194 195 0.112995 ATGGGTGTGATGCACTTGGT 59.887 50.000 0.00 0.00 46.86 3.67
195 196 0.813184 GATGGGTGTGATGCACTTGG 59.187 55.000 0.00 0.00 46.86 3.61
196 197 1.471287 CTGATGGGTGTGATGCACTTG 59.529 52.381 0.00 0.00 46.86 3.16
197 198 1.352017 TCTGATGGGTGTGATGCACTT 59.648 47.619 0.00 0.00 46.86 3.16
198 199 0.986527 TCTGATGGGTGTGATGCACT 59.013 50.000 0.00 0.00 46.86 4.40
199 200 1.674441 CATCTGATGGGTGTGATGCAC 59.326 52.381 9.82 0.00 46.97 4.57
200 201 1.409101 CCATCTGATGGGTGTGATGCA 60.409 52.381 25.84 0.00 46.86 3.96
201 202 1.315690 CCATCTGATGGGTGTGATGC 58.684 55.000 25.84 0.00 46.86 3.91
211 212 3.183793 TGGACGATTGACCATCTGATG 57.816 47.619 10.71 10.71 34.93 3.07
212 213 3.736720 CATGGACGATTGACCATCTGAT 58.263 45.455 13.36 0.00 45.68 2.90
213 214 2.742856 GCATGGACGATTGACCATCTGA 60.743 50.000 13.36 0.00 45.68 3.27
214 215 1.600957 GCATGGACGATTGACCATCTG 59.399 52.381 13.36 7.23 45.68 2.90
215 216 1.210234 TGCATGGACGATTGACCATCT 59.790 47.619 13.36 0.00 45.68 2.90
216 217 1.667236 TGCATGGACGATTGACCATC 58.333 50.000 13.36 9.51 45.68 3.51
218 219 1.667236 GATGCATGGACGATTGACCA 58.333 50.000 2.46 6.61 43.97 4.02
219 220 0.583438 CGATGCATGGACGATTGACC 59.417 55.000 2.46 0.00 0.00 4.02
220 221 1.004610 CACGATGCATGGACGATTGAC 60.005 52.381 16.26 0.00 0.00 3.18
221 222 1.289276 CACGATGCATGGACGATTGA 58.711 50.000 16.26 0.00 0.00 2.57
222 223 0.316442 GCACGATGCATGGACGATTG 60.316 55.000 16.26 3.88 44.26 2.67
223 224 2.016961 GCACGATGCATGGACGATT 58.983 52.632 16.26 0.00 44.26 3.34
224 225 3.723172 GCACGATGCATGGACGAT 58.277 55.556 16.26 0.00 44.26 3.73
233 234 2.751436 ACCCACCATGCACGATGC 60.751 61.111 0.00 0.00 45.29 3.91
234 235 2.463620 CGACCCACCATGCACGATG 61.464 63.158 0.00 0.00 0.00 3.84
235 236 2.125147 CGACCCACCATGCACGAT 60.125 61.111 0.00 0.00 0.00 3.73
236 237 4.386951 CCGACCCACCATGCACGA 62.387 66.667 0.00 0.00 0.00 4.35
238 239 4.722700 AGCCGACCCACCATGCAC 62.723 66.667 0.00 0.00 0.00 4.57
239 240 4.720902 CAGCCGACCCACCATGCA 62.721 66.667 0.00 0.00 0.00 3.96
240 241 4.722700 ACAGCCGACCCACCATGC 62.723 66.667 0.00 0.00 0.00 4.06
241 242 2.746412 TTCACAGCCGACCCACCATG 62.746 60.000 0.00 0.00 0.00 3.66
242 243 2.469465 CTTCACAGCCGACCCACCAT 62.469 60.000 0.00 0.00 0.00 3.55
243 244 3.164977 TTCACAGCCGACCCACCA 61.165 61.111 0.00 0.00 0.00 4.17
244 245 1.823169 TACTTCACAGCCGACCCACC 61.823 60.000 0.00 0.00 0.00 4.61
245 246 0.389948 CTACTTCACAGCCGACCCAC 60.390 60.000 0.00 0.00 0.00 4.61
246 247 0.830444 ACTACTTCACAGCCGACCCA 60.830 55.000 0.00 0.00 0.00 4.51
247 248 0.320697 AACTACTTCACAGCCGACCC 59.679 55.000 0.00 0.00 0.00 4.46
248 249 2.067013 GAAACTACTTCACAGCCGACC 58.933 52.381 0.00 0.00 33.86 4.79
249 250 1.719780 CGAAACTACTTCACAGCCGAC 59.280 52.381 0.00 0.00 33.17 4.79
250 251 1.338973 ACGAAACTACTTCACAGCCGA 59.661 47.619 0.00 0.00 33.17 5.54
251 252 1.779569 ACGAAACTACTTCACAGCCG 58.220 50.000 0.00 0.00 33.17 5.52
252 253 4.748600 ACTTAACGAAACTACTTCACAGCC 59.251 41.667 0.00 0.00 33.17 4.85
253 254 5.902051 ACTTAACGAAACTACTTCACAGC 57.098 39.130 0.00 0.00 33.17 4.40
254 255 9.628983 GTAAAACTTAACGAAACTACTTCACAG 57.371 33.333 0.00 0.00 33.17 3.66
255 256 9.369904 AGTAAAACTTAACGAAACTACTTCACA 57.630 29.630 0.00 0.00 33.17 3.58
256 257 9.841016 GAGTAAAACTTAACGAAACTACTTCAC 57.159 33.333 0.00 0.00 33.17 3.18
257 258 9.034544 GGAGTAAAACTTAACGAAACTACTTCA 57.965 33.333 0.00 0.00 33.17 3.02
258 259 8.491152 GGGAGTAAAACTTAACGAAACTACTTC 58.509 37.037 0.00 0.00 0.00 3.01
259 260 8.206867 AGGGAGTAAAACTTAACGAAACTACTT 58.793 33.333 0.00 0.00 0.00 2.24
260 261 7.730084 AGGGAGTAAAACTTAACGAAACTACT 58.270 34.615 0.00 0.00 0.00 2.57
261 262 7.953158 AGGGAGTAAAACTTAACGAAACTAC 57.047 36.000 0.00 0.00 0.00 2.73
262 263 9.476202 GTAAGGGAGTAAAACTTAACGAAACTA 57.524 33.333 0.00 0.00 0.00 2.24
263 264 7.986889 TGTAAGGGAGTAAAACTTAACGAAACT 59.013 33.333 0.00 0.00 0.00 2.66
264 265 8.141835 TGTAAGGGAGTAAAACTTAACGAAAC 57.858 34.615 0.00 0.00 0.00 2.78
265 266 8.907222 ATGTAAGGGAGTAAAACTTAACGAAA 57.093 30.769 0.00 0.00 0.00 3.46
266 267 7.603784 GGATGTAAGGGAGTAAAACTTAACGAA 59.396 37.037 0.00 0.00 0.00 3.85
267 268 7.099120 GGATGTAAGGGAGTAAAACTTAACGA 58.901 38.462 0.00 0.00 0.00 3.85
268 269 6.875195 TGGATGTAAGGGAGTAAAACTTAACG 59.125 38.462 0.00 0.00 0.00 3.18
269 270 8.803397 ATGGATGTAAGGGAGTAAAACTTAAC 57.197 34.615 0.00 0.00 0.00 2.01
270 271 9.816787 AAATGGATGTAAGGGAGTAAAACTTAA 57.183 29.630 0.00 0.00 0.00 1.85
271 272 9.238368 CAAATGGATGTAAGGGAGTAAAACTTA 57.762 33.333 0.00 0.00 0.00 2.24
272 273 7.947890 TCAAATGGATGTAAGGGAGTAAAACTT 59.052 33.333 0.00 0.00 0.00 2.66
273 274 7.466804 TCAAATGGATGTAAGGGAGTAAAACT 58.533 34.615 0.00 0.00 0.00 2.66
274 275 7.696992 TCAAATGGATGTAAGGGAGTAAAAC 57.303 36.000 0.00 0.00 0.00 2.43
275 276 7.396055 CCTTCAAATGGATGTAAGGGAGTAAAA 59.604 37.037 0.00 0.00 34.35 1.52
276 277 6.889722 CCTTCAAATGGATGTAAGGGAGTAAA 59.110 38.462 0.00 0.00 34.35 2.01
277 278 6.216662 TCCTTCAAATGGATGTAAGGGAGTAA 59.783 38.462 0.00 0.00 37.81 2.24
278 279 5.729229 TCCTTCAAATGGATGTAAGGGAGTA 59.271 40.000 0.00 0.00 37.81 2.59
279 280 4.540099 TCCTTCAAATGGATGTAAGGGAGT 59.460 41.667 0.00 0.00 37.81 3.85
280 281 4.884164 GTCCTTCAAATGGATGTAAGGGAG 59.116 45.833 0.00 0.00 37.81 4.30
281 282 4.290985 TGTCCTTCAAATGGATGTAAGGGA 59.709 41.667 0.00 0.00 37.81 4.20
282 283 4.599041 TGTCCTTCAAATGGATGTAAGGG 58.401 43.478 0.00 0.00 37.81 3.95
283 284 5.711976 ACTTGTCCTTCAAATGGATGTAAGG 59.288 40.000 0.00 0.00 38.44 2.69
284 285 6.824305 ACTTGTCCTTCAAATGGATGTAAG 57.176 37.500 0.00 0.00 35.87 2.34
285 286 7.595819 AAACTTGTCCTTCAAATGGATGTAA 57.404 32.000 0.00 0.00 35.87 2.41
286 287 7.595819 AAAACTTGTCCTTCAAATGGATGTA 57.404 32.000 0.00 0.00 35.87 2.29
287 288 6.484364 AAAACTTGTCCTTCAAATGGATGT 57.516 33.333 0.00 0.00 35.87 3.06
308 309 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
309 310 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
310 311 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
311 312 0.393537 GAGTACTCCCTCCGTCCGAA 60.394 60.000 12.13 0.00 0.00 4.30
312 313 1.222936 GAGTACTCCCTCCGTCCGA 59.777 63.158 12.13 0.00 0.00 4.55
313 314 2.178890 CGAGTACTCCCTCCGTCCG 61.179 68.421 17.23 0.00 0.00 4.79
314 315 1.823041 CCGAGTACTCCCTCCGTCC 60.823 68.421 17.23 0.00 0.00 4.79
315 316 0.179000 TACCGAGTACTCCCTCCGTC 59.821 60.000 17.23 0.00 0.00 4.79
316 317 0.620556 TTACCGAGTACTCCCTCCGT 59.379 55.000 17.23 8.08 0.00 4.69
317 318 1.978454 ATTACCGAGTACTCCCTCCG 58.022 55.000 17.23 5.64 0.00 4.63
318 319 4.220163 CCATAATTACCGAGTACTCCCTCC 59.780 50.000 17.23 0.00 0.00 4.30
319 320 5.048154 GTCCATAATTACCGAGTACTCCCTC 60.048 48.000 17.23 0.00 0.00 4.30
320 321 4.831710 GTCCATAATTACCGAGTACTCCCT 59.168 45.833 17.23 4.84 0.00 4.20
321 322 4.586001 TGTCCATAATTACCGAGTACTCCC 59.414 45.833 17.23 0.00 0.00 4.30
322 323 5.779529 TGTCCATAATTACCGAGTACTCC 57.220 43.478 17.23 0.00 0.00 3.85
323 324 8.658499 AAAATGTCCATAATTACCGAGTACTC 57.342 34.615 13.18 13.18 0.00 2.59
324 325 8.483758 AGAAAATGTCCATAATTACCGAGTACT 58.516 33.333 0.00 0.00 0.00 2.73
325 326 8.658499 AGAAAATGTCCATAATTACCGAGTAC 57.342 34.615 0.00 0.00 0.00 2.73
365 366 3.107194 CAGTGTGTCGCTGATGCACAG 62.107 57.143 10.75 10.75 43.78 3.66
385 387 9.678941 TGTGAATACTATAATGTTCTCACGATC 57.321 33.333 0.00 0.00 35.20 3.69
386 388 9.684448 CTGTGAATACTATAATGTTCTCACGAT 57.316 33.333 0.00 0.00 35.20 3.73
410 413 0.324285 AGCTGACCAAAGCCTCTCTG 59.676 55.000 0.00 0.00 44.68 3.35
425 428 3.155167 GGGTCCCCGGTCTAGCTG 61.155 72.222 0.00 0.00 0.00 4.24
444 447 3.047877 GTCCCTTGAACCGTGCCG 61.048 66.667 0.00 0.00 0.00 5.69
451 454 4.804665 GCTATAACGAAGAGTCCCTTGAAC 59.195 45.833 0.00 0.00 34.68 3.18
457 460 4.857509 ATGAGCTATAACGAAGAGTCCC 57.142 45.455 0.00 0.00 0.00 4.46
464 467 6.535150 CCTGAAAGTGAATGAGCTATAACGAA 59.465 38.462 0.00 0.00 0.00 3.85
467 470 5.008118 GCCCTGAAAGTGAATGAGCTATAAC 59.992 44.000 0.00 0.00 0.00 1.89
505 546 5.006261 GCTGCCAGTTTGTTTTCGTATTTTT 59.994 36.000 0.00 0.00 0.00 1.94
526 568 2.302157 TGATCAGATATGGGCAGAGCTG 59.698 50.000 0.00 0.00 37.39 4.24
534 579 5.180117 GTGACGGAAATTGATCAGATATGGG 59.820 44.000 0.00 0.00 0.00 4.00
535 580 5.994054 AGTGACGGAAATTGATCAGATATGG 59.006 40.000 0.00 0.00 0.00 2.74
538 583 7.606073 TGAAAAGTGACGGAAATTGATCAGATA 59.394 33.333 0.00 0.00 0.00 1.98
558 603 3.730715 GGACGAAAATGTGCTGTGAAAAG 59.269 43.478 0.00 0.00 0.00 2.27
569 614 2.841215 TGTCGAAAGGGACGAAAATGT 58.159 42.857 0.00 0.00 41.31 2.71
572 617 1.941975 GGTTGTCGAAAGGGACGAAAA 59.058 47.619 0.00 0.00 41.31 2.29
586 633 2.489971 TGAACACGAGAATGGGTTGTC 58.510 47.619 0.00 0.00 0.00 3.18
597 644 5.342806 TGTGCTAGATTTTTGAACACGAG 57.657 39.130 0.00 0.00 0.00 4.18
602 649 5.195001 TGGGTTGTGCTAGATTTTTGAAC 57.805 39.130 0.00 0.00 0.00 3.18
610 657 3.624777 CAGGAAATGGGTTGTGCTAGAT 58.375 45.455 0.00 0.00 0.00 1.98
615 662 1.293179 GGCAGGAAATGGGTTGTGC 59.707 57.895 0.00 0.00 0.00 4.57
616 663 1.543944 GGGGCAGGAAATGGGTTGTG 61.544 60.000 0.00 0.00 0.00 3.33
617 664 1.229177 GGGGCAGGAAATGGGTTGT 60.229 57.895 0.00 0.00 0.00 3.32
618 665 1.229145 TGGGGCAGGAAATGGGTTG 60.229 57.895 0.00 0.00 0.00 3.77
639 686 6.982724 CCCATTTTGGCTATTCATTCTTCTTC 59.017 38.462 0.00 0.00 35.79 2.87
640 687 6.441604 ACCCATTTTGGCTATTCATTCTTCTT 59.558 34.615 0.00 0.00 35.79 2.52
645 692 5.105392 TGTGACCCATTTTGGCTATTCATTC 60.105 40.000 0.00 0.00 35.79 2.67
657 704 1.895131 GCCTGTGATGTGACCCATTTT 59.105 47.619 0.00 0.00 32.56 1.82
658 705 1.076024 AGCCTGTGATGTGACCCATTT 59.924 47.619 0.00 0.00 32.56 2.32
691 738 2.339400 CACTGATTTTGCAATTCGCGTC 59.661 45.455 5.77 0.00 46.97 5.19
696 743 3.367025 GCTGCTCACTGATTTTGCAATTC 59.633 43.478 0.00 1.10 33.07 2.17
702 749 2.876091 CATGGCTGCTCACTGATTTTG 58.124 47.619 0.00 0.00 0.00 2.44
878 935 6.826741 GTGCTAATCCCCAACAGTTAATTAGA 59.173 38.462 14.90 0.00 31.43 2.10
882 942 5.193099 AGTGCTAATCCCCAACAGTTAAT 57.807 39.130 0.00 0.00 0.00 1.40
912 975 0.036388 TGAATCTGGTGGAACTCGGC 60.036 55.000 0.00 0.00 36.74 5.54
913 976 2.555199 GATGAATCTGGTGGAACTCGG 58.445 52.381 0.00 0.00 36.74 4.63
917 980 3.217626 GGATGGATGAATCTGGTGGAAC 58.782 50.000 0.00 0.00 0.00 3.62
942 1005 2.268920 GACTGCGGCTGGAATGGA 59.731 61.111 11.64 0.00 0.00 3.41
943 1006 3.197790 CGACTGCGGCTGGAATGG 61.198 66.667 11.64 0.00 0.00 3.16
983 1050 0.398948 CATGGGGAAGGAATTGGGGG 60.399 60.000 0.00 0.00 0.00 5.40
984 1051 0.398948 CCATGGGGAAGGAATTGGGG 60.399 60.000 2.85 0.00 35.59 4.96
985 1052 1.050421 GCCATGGGGAAGGAATTGGG 61.050 60.000 15.13 0.00 35.59 4.12
988 1055 0.643822 ATGGCCATGGGGAAGGAATT 59.356 50.000 20.04 0.00 35.59 2.17
989 1056 0.105349 CATGGCCATGGGGAAGGAAT 60.105 55.000 34.31 0.00 35.24 3.01
990 1057 1.310715 CATGGCCATGGGGAAGGAA 59.689 57.895 34.31 0.00 35.24 3.36
991 1058 3.018019 CATGGCCATGGGGAAGGA 58.982 61.111 34.31 0.00 35.24 3.36
1019 1086 1.074623 AGGAGGAGGAGGAGGCATG 60.075 63.158 0.00 0.00 0.00 4.06
1020 1087 1.074623 CAGGAGGAGGAGGAGGCAT 60.075 63.158 0.00 0.00 0.00 4.40
1021 1088 2.366167 CAGGAGGAGGAGGAGGCA 59.634 66.667 0.00 0.00 0.00 4.75
1260 1330 2.280524 CCGTTGGAGGCGTTGTGA 60.281 61.111 0.00 0.00 0.00 3.58
1351 1424 2.673523 GGTCCAGATGGTGCTGCT 59.326 61.111 0.00 0.00 34.56 4.24
1398 1477 2.049156 TCGTTGAGCGTCAGCCTG 60.049 61.111 0.00 0.00 46.67 4.85
1431 1510 2.266055 CTGGACCAGGAGCCGAAC 59.734 66.667 14.26 0.00 0.00 3.95
1458 1537 4.760047 ATGAGCGTGTCCGTGGGC 62.760 66.667 0.00 0.00 36.15 5.36
1839 1921 2.439156 GTGCCCTGGATCCTGCAC 60.439 66.667 27.13 27.13 46.09 4.57
2073 2155 1.692173 GGTTACTGGGCGGCTGGATA 61.692 60.000 9.56 0.00 0.00 2.59
2075 2157 3.712907 GGTTACTGGGCGGCTGGA 61.713 66.667 9.56 0.00 0.00 3.86
2076 2158 3.717294 AGGTTACTGGGCGGCTGG 61.717 66.667 9.56 4.48 0.00 4.85
2096 2178 0.378257 GCACATATTCCTGCACACCG 59.622 55.000 0.00 0.00 33.31 4.94
2109 2191 3.463585 GGGTCGTCCCGGCACATA 61.464 66.667 0.76 0.00 44.74 2.29
2258 2340 2.112297 TGAACGGGTTGCTGTCCC 59.888 61.111 0.00 2.16 41.41 4.46
2259 2341 2.604174 CGTGAACGGGTTGCTGTCC 61.604 63.158 0.00 0.00 35.37 4.02
2530 2612 3.119096 GAAGTCCTTGGTCGCCGC 61.119 66.667 0.00 0.00 0.00 6.53
2688 2770 1.246056 CCAGGTTGAGGTGGTGCATG 61.246 60.000 0.00 0.00 0.00 4.06
3051 3142 1.621992 TCTCCTTCTTGCTCGTCAGT 58.378 50.000 0.00 0.00 0.00 3.41
3471 3574 0.824109 CCTGGACGCAGAAGATGGTA 59.176 55.000 0.00 0.00 0.00 3.25
3535 3638 8.866093 ACCACTTGGCTTTGTTTTTATATTACT 58.134 29.630 0.00 0.00 39.32 2.24
3557 3665 9.185192 GATGGTATAATACACGTAACTAACCAC 57.815 37.037 6.54 0.40 36.21 4.16
3559 3667 9.617975 GAGATGGTATAATACACGTAACTAACC 57.382 37.037 0.00 0.00 0.00 2.85
3607 3728 3.185188 GCATGCATACGTAGTCCAATCAG 59.815 47.826 14.21 0.00 43.93 2.90
3624 3747 2.353406 ACTTTTCCAAGAGCATGCATGC 60.353 45.455 38.60 38.60 42.56 4.06
3675 3798 5.909054 CGCGGATAGTTCGTACTAATTTGTA 59.091 40.000 5.98 0.00 40.14 2.41
3684 3807 0.569349 GCAACGCGGATAGTTCGTAC 59.431 55.000 12.47 0.00 35.18 3.67
3687 3810 3.003478 GGCAACGCGGATAGTTCG 58.997 61.111 12.47 0.00 0.00 3.95
3709 3832 0.886490 CCGCTCAGCACCAAGAAACT 60.886 55.000 0.00 0.00 0.00 2.66
3711 3834 2.260869 GCCGCTCAGCACCAAGAAA 61.261 57.895 0.00 0.00 0.00 2.52
3727 3850 2.046892 ATGCTGTGGTCAGACGCC 60.047 61.111 0.00 0.00 43.76 5.68
3799 3922 2.047179 GCGGTCCCTGTTGGTCTC 60.047 66.667 0.00 0.00 34.77 3.36
3878 4001 7.375053 TGAACTTGGTTAGTTTCAAATATGGC 58.625 34.615 0.00 0.00 47.00 4.40
3922 4050 2.284417 GGTCGAGAACAGTTGAACACAC 59.716 50.000 0.00 0.00 0.00 3.82
3977 4106 9.453572 TGAACAGTAGCAAGATCATAGAATTTT 57.546 29.630 0.00 0.00 0.00 1.82
3978 4107 9.624373 ATGAACAGTAGCAAGATCATAGAATTT 57.376 29.630 0.00 0.00 0.00 1.82
3979 4108 9.624373 AATGAACAGTAGCAAGATCATAGAATT 57.376 29.630 0.00 0.00 0.00 2.17
3993 4125 6.513393 GCAACCCACATATAATGAACAGTAGC 60.513 42.308 0.00 0.00 0.00 3.58
3997 4129 7.750229 ATAGCAACCCACATATAATGAACAG 57.250 36.000 0.00 0.00 0.00 3.16
4031 4163 7.346695 CACTTGCTGAACAAAATGGTTTTATG 58.653 34.615 0.00 0.00 37.96 1.90
4065 4197 7.588854 CGCACTTATGTTTTTCATCTGATATGG 59.411 37.037 0.00 0.00 37.91 2.74
4082 4214 4.730613 GCTTATCCCAAACACGCACTTATG 60.731 45.833 0.00 0.00 0.00 1.90
4083 4215 3.377172 GCTTATCCCAAACACGCACTTAT 59.623 43.478 0.00 0.00 0.00 1.73
4084 4216 2.745281 GCTTATCCCAAACACGCACTTA 59.255 45.455 0.00 0.00 0.00 2.24
4088 4222 1.539388 CTTGCTTATCCCAAACACGCA 59.461 47.619 0.00 0.00 0.00 5.24
4092 4226 6.909550 ATTACAACTTGCTTATCCCAAACA 57.090 33.333 0.00 0.00 0.00 2.83
4093 4227 9.353999 CTTAATTACAACTTGCTTATCCCAAAC 57.646 33.333 0.00 0.00 0.00 2.93
4201 4367 7.053498 TGGTCAGTATTAGCATAAATCTTGCA 58.947 34.615 0.00 0.00 42.62 4.08
4236 4402 6.708502 TCCATCTATCAAAGTGTTTCAACGAA 59.291 34.615 0.00 0.00 0.00 3.85
4323 4489 2.105466 CAGCAGCGAGGAGGAAAGC 61.105 63.158 0.00 0.00 0.00 3.51
4401 4567 3.056179 TCTGTTATCAGGTGTCGCAATCA 60.056 43.478 1.00 0.00 41.59 2.57
4437 4603 5.687780 ACCAATCAGATACTCATGCATTGA 58.312 37.500 0.00 0.00 0.00 2.57
4473 4640 2.942804 TCCATTCTTTGTGACCTTGCA 58.057 42.857 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.