Multiple sequence alignment - TraesCS6D01G189500

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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 TraesCS6D01G189500 chr6D 100.000 2318 0 0 1 2318 262290935 262288618 0.000000e+00 4281
1 TraesCS6D01G189500 chr6D 97.054 645 19 0 1673 2317 2078541 2077897 0.000000e+00 1086
2 TraesCS6D01G189500 chr6A 89.444 1260 54 36 455 1679 322984638 322985853 0.000000e+00 1517
3 TraesCS6D01G189500 chr6B 89.286 1260 45 31 454 1679 348687683 348688886 0.000000e+00 1496
4 TraesCS6D01G189500 chr6B 89.127 1260 47 31 454 1679 348658876 348657673 0.000000e+00 1485
5 TraesCS6D01G189500 chr3D 97.523 646 16 0 1673 2318 592538582 592539227 0.000000e+00 1105
6 TraesCS6D01G189500 chr3D 97.218 647 16 2 1673 2318 79185470 79186115 0.000000e+00 1094
7 TraesCS6D01G189500 chr3D 97.214 646 18 0 1673 2318 442800489 442801134 0.000000e+00 1094
8 TraesCS6D01G189500 chr4D 97.806 638 12 2 1681 2318 36542170 36541535 0.000000e+00 1099
9 TraesCS6D01G189500 chr1D 97.214 646 18 0 1673 2318 6903094 6902449 0.000000e+00 1094
10 TraesCS6D01G189500 chr1D 97.059 646 19 0 1673 2318 452747827 452747182 0.000000e+00 1088
11 TraesCS6D01G189500 chr7D 97.214 646 14 2 1673 2318 557925835 557925194 0.000000e+00 1090
12 TraesCS6D01G189500 chr7D 97.209 645 17 1 1674 2318 586402250 586402893 0.000000e+00 1090
13 TraesCS6D01G189500 chr7D 90.244 410 29 7 47 449 616459960 616459555 2.040000e-145 525
14 TraesCS6D01G189500 chr7D 88.915 424 31 8 40 449 596942558 596942979 2.050000e-140 508
15 TraesCS6D01G189500 chr2D 89.706 408 31 7 49 447 196003096 196003501 5.710000e-141 510
16 TraesCS6D01G189500 chr2D 88.998 409 27 14 47 449 7656713 7656317 7.440000e-135 490
17 TraesCS6D01G189500 chr7B 89.630 405 33 8 53 448 172368940 172368536 7.390000e-140 507
18 TraesCS6D01G189500 chrUn 88.783 419 30 9 46 449 434310253 434309837 4.450000e-137 497
19 TraesCS6D01G189500 chrUn 88.443 424 32 9 40 449 390768099 390768519 1.600000e-136 496
20 TraesCS6D01G189500 chr2B 87.931 406 43 6 48 448 720628731 720629135 7.500000e-130 473
21 TraesCS6D01G189500 chr1B 87.681 414 37 10 47 449 408654090 408653680 9.700000e-129 470


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 TraesCS6D01G189500 chr6D 262288618 262290935 2317 True 4281 4281 100.000 1 2318 1 chr6D.!!$R2 2317
1 TraesCS6D01G189500 chr6D 2077897 2078541 644 True 1086 1086 97.054 1673 2317 1 chr6D.!!$R1 644
2 TraesCS6D01G189500 chr6A 322984638 322985853 1215 False 1517 1517 89.444 455 1679 1 chr6A.!!$F1 1224
3 TraesCS6D01G189500 chr6B 348687683 348688886 1203 False 1496 1496 89.286 454 1679 1 chr6B.!!$F1 1225
4 TraesCS6D01G189500 chr6B 348657673 348658876 1203 True 1485 1485 89.127 454 1679 1 chr6B.!!$R1 1225
5 TraesCS6D01G189500 chr3D 592538582 592539227 645 False 1105 1105 97.523 1673 2318 1 chr3D.!!$F3 645
6 TraesCS6D01G189500 chr3D 79185470 79186115 645 False 1094 1094 97.218 1673 2318 1 chr3D.!!$F1 645
7 TraesCS6D01G189500 chr3D 442800489 442801134 645 False 1094 1094 97.214 1673 2318 1 chr3D.!!$F2 645
8 TraesCS6D01G189500 chr4D 36541535 36542170 635 True 1099 1099 97.806 1681 2318 1 chr4D.!!$R1 637
9 TraesCS6D01G189500 chr1D 6902449 6903094 645 True 1094 1094 97.214 1673 2318 1 chr1D.!!$R1 645
10 TraesCS6D01G189500 chr1D 452747182 452747827 645 True 1088 1088 97.059 1673 2318 1 chr1D.!!$R2 645
11 TraesCS6D01G189500 chr7D 557925194 557925835 641 True 1090 1090 97.214 1673 2318 1 chr7D.!!$R1 645
12 TraesCS6D01G189500 chr7D 586402250 586402893 643 False 1090 1090 97.209 1674 2318 1 chr7D.!!$F1 644

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
84 85 0.035317 TCGAGCTCACATGCACCTTT 59.965 50.0 15.4 0.0 34.99 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2003 0.108138 GCCACACTACCGCAAGAGAT 60.108 55.0 0.0 0.0 43.02 2.75 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
24 25 5.471116 AGAAAAGGAAAAATTGCTTCCATGC 59.529 36.000 17.61 8.11 44.19 4.06
25 26 4.354893 AAGGAAAAATTGCTTCCATGCA 57.645 36.364 17.61 0.00 44.19 3.96
26 27 3.667360 AGGAAAAATTGCTTCCATGCAC 58.333 40.909 17.61 0.00 44.19 4.57
27 28 3.071312 AGGAAAAATTGCTTCCATGCACA 59.929 39.130 17.61 0.00 44.19 4.57
28 29 3.814283 GGAAAAATTGCTTCCATGCACAA 59.186 39.130 12.62 0.00 43.20 3.33
29 30 4.275443 GGAAAAATTGCTTCCATGCACAAA 59.725 37.500 12.62 0.00 43.20 2.83
30 31 5.427036 AAAAATTGCTTCCATGCACAAAG 57.573 34.783 0.00 0.00 43.20 2.77
31 32 2.088950 ATTGCTTCCATGCACAAAGC 57.911 45.000 18.00 18.00 43.20 3.51
43 44 3.565905 GCACAAAGCAGAGCATTAGTT 57.434 42.857 0.00 0.00 44.79 2.24
44 45 3.905784 GCACAAAGCAGAGCATTAGTTT 58.094 40.909 0.00 0.00 44.79 2.66
45 46 3.671928 GCACAAAGCAGAGCATTAGTTTG 59.328 43.478 0.00 0.00 44.79 2.93
46 47 3.671928 CACAAAGCAGAGCATTAGTTTGC 59.328 43.478 0.00 0.00 43.09 3.68
55 56 2.933769 GCATTAGTTTGCGAAAGTGCT 58.066 42.857 0.00 0.00 35.36 4.40
56 57 2.911102 GCATTAGTTTGCGAAAGTGCTC 59.089 45.455 0.00 0.00 35.36 4.26
57 58 3.365364 GCATTAGTTTGCGAAAGTGCTCT 60.365 43.478 0.00 0.00 35.36 4.09
58 59 4.787598 CATTAGTTTGCGAAAGTGCTCTT 58.212 39.130 0.00 0.00 35.36 2.85
59 60 2.763249 AGTTTGCGAAAGTGCTCTTG 57.237 45.000 1.02 0.00 33.79 3.02
60 61 2.017049 AGTTTGCGAAAGTGCTCTTGT 58.983 42.857 1.02 0.00 33.79 3.16
61 62 2.111756 GTTTGCGAAAGTGCTCTTGTG 58.888 47.619 1.02 0.00 33.79 3.33
62 63 1.662517 TTGCGAAAGTGCTCTTGTGA 58.337 45.000 1.02 0.00 33.79 3.58
63 64 1.220529 TGCGAAAGTGCTCTTGTGAG 58.779 50.000 1.02 0.00 42.96 3.51
80 81 3.088044 GCTCGAGCTCACATGCAC 58.912 61.111 29.88 0.00 38.21 4.57
81 82 2.459442 GCTCGAGCTCACATGCACC 61.459 63.158 29.88 0.00 38.21 5.01
82 83 1.217511 CTCGAGCTCACATGCACCT 59.782 57.895 15.40 0.00 34.99 4.00
83 84 0.390866 CTCGAGCTCACATGCACCTT 60.391 55.000 15.40 0.00 34.99 3.50
84 85 0.035317 TCGAGCTCACATGCACCTTT 59.965 50.000 15.40 0.00 34.99 3.11
85 86 0.877071 CGAGCTCACATGCACCTTTT 59.123 50.000 15.40 0.00 34.99 2.27
86 87 1.400629 CGAGCTCACATGCACCTTTTG 60.401 52.381 15.40 0.00 34.99 2.44
103 104 8.641499 CACCTTTTGCTACAGTAAAATCAAAA 57.359 30.769 5.82 0.00 38.55 2.44
104 105 9.092876 CACCTTTTGCTACAGTAAAATCAAAAA 57.907 29.630 5.82 0.00 38.55 1.94
161 162 8.467402 TTTTTCACAACAAACGTTGATGTATT 57.533 26.923 12.00 0.00 43.60 1.89
162 163 8.467402 TTTTCACAACAAACGTTGATGTATTT 57.533 26.923 12.00 0.00 43.60 1.40
163 164 8.467402 TTTCACAACAAACGTTGATGTATTTT 57.533 26.923 12.00 0.00 43.60 1.82
164 165 8.467402 TTCACAACAAACGTTGATGTATTTTT 57.533 26.923 12.00 0.00 43.60 1.94
165 166 8.109843 TCACAACAAACGTTGATGTATTTTTC 57.890 30.769 12.00 0.00 43.60 2.29
166 167 7.755373 TCACAACAAACGTTGATGTATTTTTCA 59.245 29.630 12.00 0.00 43.60 2.69
167 168 7.838879 CACAACAAACGTTGATGTATTTTTCAC 59.161 33.333 12.00 0.00 43.60 3.18
168 169 7.542477 ACAACAAACGTTGATGTATTTTTCACA 59.458 29.630 12.00 0.00 45.52 3.58
169 170 8.538856 CAACAAACGTTGATGTATTTTTCACAT 58.461 29.630 0.00 0.00 45.52 3.21
170 171 8.060020 ACAAACGTTGATGTATTTTTCACATG 57.940 30.769 0.00 0.00 36.76 3.21
171 172 7.704472 ACAAACGTTGATGTATTTTTCACATGT 59.296 29.630 0.00 0.00 36.76 3.21
172 173 7.621832 AACGTTGATGTATTTTTCACATGTG 57.378 32.000 20.18 20.18 36.76 3.21
173 174 6.734137 ACGTTGATGTATTTTTCACATGTGT 58.266 32.000 24.63 8.38 36.76 3.72
174 175 6.636447 ACGTTGATGTATTTTTCACATGTGTG 59.364 34.615 24.63 6.81 46.91 3.82
175 176 6.398830 CGTTGATGTATTTTTCACATGTGTGC 60.399 38.462 24.63 9.82 45.25 4.57
176 177 6.081872 TGATGTATTTTTCACATGTGTGCA 57.918 33.333 24.63 14.99 45.25 4.57
177 178 6.510536 TGATGTATTTTTCACATGTGTGCAA 58.489 32.000 24.63 15.37 45.25 4.08
178 179 6.982724 TGATGTATTTTTCACATGTGTGCAAA 59.017 30.769 24.63 19.87 45.25 3.68
183 184 5.731599 TTTTCACATGTGTGCAAAATTCC 57.268 34.783 24.63 0.00 45.25 3.01
184 185 4.397481 TTCACATGTGTGCAAAATTCCA 57.603 36.364 24.63 0.00 45.25 3.53
185 186 4.603989 TCACATGTGTGCAAAATTCCAT 57.396 36.364 24.63 0.00 45.25 3.41
186 187 4.308265 TCACATGTGTGCAAAATTCCATG 58.692 39.130 24.63 4.14 45.25 3.66
187 188 4.038883 TCACATGTGTGCAAAATTCCATGA 59.961 37.500 24.63 0.00 45.25 3.07
188 189 4.150980 CACATGTGTGCAAAATTCCATGAC 59.849 41.667 18.03 0.00 39.39 3.06
189 190 4.202233 ACATGTGTGCAAAATTCCATGACA 60.202 37.500 11.15 0.00 35.04 3.58
190 191 4.397481 TGTGTGCAAAATTCCATGACAA 57.603 36.364 0.00 0.00 0.00 3.18
191 192 4.763073 TGTGTGCAAAATTCCATGACAAA 58.237 34.783 0.00 0.00 0.00 2.83
192 193 5.181009 TGTGTGCAAAATTCCATGACAAAA 58.819 33.333 0.00 0.00 0.00 2.44
193 194 5.821470 TGTGTGCAAAATTCCATGACAAAAT 59.179 32.000 0.00 0.00 0.00 1.82
194 195 6.137415 GTGTGCAAAATTCCATGACAAAATG 58.863 36.000 0.00 0.00 0.00 2.32
195 196 6.018098 GTGTGCAAAATTCCATGACAAAATGA 60.018 34.615 0.00 0.00 0.00 2.57
196 197 6.018098 TGTGCAAAATTCCATGACAAAATGAC 60.018 34.615 0.00 0.00 0.00 3.06
197 198 6.018098 GTGCAAAATTCCATGACAAAATGACA 60.018 34.615 0.00 0.00 0.00 3.58
198 199 6.711194 TGCAAAATTCCATGACAAAATGACAT 59.289 30.769 0.00 0.00 33.31 3.06
199 200 7.228906 TGCAAAATTCCATGACAAAATGACATT 59.771 29.630 0.00 0.00 30.83 2.71
200 201 7.747357 GCAAAATTCCATGACAAAATGACATTC 59.253 33.333 0.05 0.00 30.83 2.67
201 202 8.775527 CAAAATTCCATGACAAAATGACATTCA 58.224 29.630 0.05 0.00 30.83 2.57
202 203 9.509956 AAAATTCCATGACAAAATGACATTCAT 57.490 25.926 0.05 0.00 39.09 2.57
203 204 8.487313 AATTCCATGACAAAATGACATTCATG 57.513 30.769 16.16 16.16 42.10 3.07
204 205 5.412640 TCCATGACAAAATGACATTCATGC 58.587 37.500 17.14 9.90 41.43 4.06
205 206 5.047235 TCCATGACAAAATGACATTCATGCA 60.047 36.000 17.14 13.51 41.43 3.96
206 207 5.290885 CCATGACAAAATGACATTCATGCAG 59.709 40.000 17.14 6.20 41.43 4.41
207 208 4.811908 TGACAAAATGACATTCATGCAGG 58.188 39.130 0.05 0.00 37.15 4.85
208 209 4.281435 TGACAAAATGACATTCATGCAGGT 59.719 37.500 0.05 0.00 37.15 4.00
209 210 4.813027 ACAAAATGACATTCATGCAGGTC 58.187 39.130 3.09 3.09 37.15 3.85
210 211 4.525487 ACAAAATGACATTCATGCAGGTCT 59.475 37.500 11.26 0.00 37.15 3.85
211 212 4.978083 AAATGACATTCATGCAGGTCTC 57.022 40.909 11.26 0.00 37.15 3.36
212 213 2.014335 TGACATTCATGCAGGTCTCG 57.986 50.000 11.26 0.00 0.00 4.04
213 214 1.293924 GACATTCATGCAGGTCTCGG 58.706 55.000 2.82 0.00 0.00 4.63
214 215 0.615331 ACATTCATGCAGGTCTCGGT 59.385 50.000 0.00 0.00 0.00 4.69
215 216 1.012086 CATTCATGCAGGTCTCGGTG 58.988 55.000 0.00 0.00 0.00 4.94
216 217 0.904649 ATTCATGCAGGTCTCGGTGA 59.095 50.000 0.00 0.00 0.00 4.02
217 218 0.684535 TTCATGCAGGTCTCGGTGAA 59.315 50.000 0.00 0.00 0.00 3.18
218 219 0.684535 TCATGCAGGTCTCGGTGAAA 59.315 50.000 0.00 0.00 0.00 2.69
219 220 1.071542 TCATGCAGGTCTCGGTGAAAA 59.928 47.619 0.00 0.00 0.00 2.29
220 221 1.879380 CATGCAGGTCTCGGTGAAAAA 59.121 47.619 0.00 0.00 0.00 1.94
243 244 8.859517 AAAAACAAAATCAATGCTCCAAAATG 57.140 26.923 0.00 0.00 0.00 2.32
244 245 5.616488 ACAAAATCAATGCTCCAAAATGC 57.384 34.783 0.00 0.00 0.00 3.56
245 246 5.310451 ACAAAATCAATGCTCCAAAATGCT 58.690 33.333 0.00 0.00 0.00 3.79
246 247 5.766174 ACAAAATCAATGCTCCAAAATGCTT 59.234 32.000 0.00 0.00 0.00 3.91
247 248 6.072893 ACAAAATCAATGCTCCAAAATGCTTC 60.073 34.615 0.00 0.00 0.00 3.86
248 249 4.811969 ATCAATGCTCCAAAATGCTTCA 57.188 36.364 0.00 0.00 0.00 3.02
249 250 4.603989 TCAATGCTCCAAAATGCTTCAA 57.396 36.364 0.00 0.00 0.00 2.69
250 251 4.958509 TCAATGCTCCAAAATGCTTCAAA 58.041 34.783 0.00 0.00 0.00 2.69
251 252 5.366460 TCAATGCTCCAAAATGCTTCAAAA 58.634 33.333 0.00 0.00 0.00 2.44
252 253 5.821470 TCAATGCTCCAAAATGCTTCAAAAA 59.179 32.000 0.00 0.00 0.00 1.94
253 254 5.678132 ATGCTCCAAAATGCTTCAAAAAC 57.322 34.783 0.00 0.00 0.00 2.43
254 255 4.511527 TGCTCCAAAATGCTTCAAAAACA 58.488 34.783 0.00 0.00 0.00 2.83
255 256 4.940046 TGCTCCAAAATGCTTCAAAAACAA 59.060 33.333 0.00 0.00 0.00 2.83
256 257 5.413833 TGCTCCAAAATGCTTCAAAAACAAA 59.586 32.000 0.00 0.00 0.00 2.83
257 258 6.095160 TGCTCCAAAATGCTTCAAAAACAAAT 59.905 30.769 0.00 0.00 0.00 2.32
258 259 6.974048 GCTCCAAAATGCTTCAAAAACAAATT 59.026 30.769 0.00 0.00 0.00 1.82
259 260 7.488792 GCTCCAAAATGCTTCAAAAACAAATTT 59.511 29.630 0.00 0.00 0.00 1.82
260 261 9.356433 CTCCAAAATGCTTCAAAAACAAATTTT 57.644 25.926 0.00 0.00 41.93 1.82
261 262 9.702494 TCCAAAATGCTTCAAAAACAAATTTTT 57.298 22.222 0.00 0.00 46.68 1.94
262 263 9.955310 CCAAAATGCTTCAAAAACAAATTTTTC 57.045 25.926 0.00 0.00 44.47 2.29
263 264 9.659493 CAAAATGCTTCAAAAACAAATTTTTCG 57.341 25.926 0.00 0.00 44.47 3.46
264 265 9.617975 AAAATGCTTCAAAAACAAATTTTTCGA 57.382 22.222 0.00 0.00 44.47 3.71
265 266 8.825064 AATGCTTCAAAAACAAATTTTTCGAG 57.175 26.923 0.00 0.00 44.47 4.04
266 267 6.247176 TGCTTCAAAAACAAATTTTTCGAGC 58.753 32.000 15.57 15.57 44.47 5.03
267 268 6.128445 TGCTTCAAAAACAAATTTTTCGAGCA 60.128 30.769 18.56 18.56 46.95 4.26
268 269 6.906678 GCTTCAAAAACAAATTTTTCGAGCAT 59.093 30.769 16.62 0.00 44.47 3.79
269 270 7.097329 GCTTCAAAAACAAATTTTTCGAGCATG 60.097 33.333 16.62 0.00 44.47 4.06
270 271 7.531280 TCAAAAACAAATTTTTCGAGCATGA 57.469 28.000 0.00 0.00 44.47 3.07
271 272 8.140677 TCAAAAACAAATTTTTCGAGCATGAT 57.859 26.923 0.00 0.00 44.47 2.45
272 273 8.610896 TCAAAAACAAATTTTTCGAGCATGATT 58.389 25.926 0.00 0.00 44.47 2.57
273 274 9.224058 CAAAAACAAATTTTTCGAGCATGATTT 57.776 25.926 0.00 0.00 44.47 2.17
274 275 9.786105 AAAAACAAATTTTTCGAGCATGATTTT 57.214 22.222 0.00 0.00 43.10 1.82
275 276 8.770850 AAACAAATTTTTCGAGCATGATTTTG 57.229 26.923 0.00 0.00 0.00 2.44
276 277 7.481275 ACAAATTTTTCGAGCATGATTTTGT 57.519 28.000 0.00 0.00 0.00 2.83
277 278 7.566709 ACAAATTTTTCGAGCATGATTTTGTC 58.433 30.769 0.00 0.00 0.00 3.18
278 279 7.439056 ACAAATTTTTCGAGCATGATTTTGTCT 59.561 29.630 0.00 0.00 0.00 3.41
279 280 7.951530 AATTTTTCGAGCATGATTTTGTCTT 57.048 28.000 0.00 0.00 0.00 3.01
280 281 7.951530 ATTTTTCGAGCATGATTTTGTCTTT 57.048 28.000 0.00 0.00 0.00 2.52
281 282 7.769272 TTTTTCGAGCATGATTTTGTCTTTT 57.231 28.000 0.00 0.00 0.00 2.27
282 283 7.769272 TTTTCGAGCATGATTTTGTCTTTTT 57.231 28.000 0.00 0.00 0.00 1.94
296 297 4.716025 TTTTTGCCAAGGCCTCCA 57.284 50.000 5.23 0.18 41.09 3.86
297 298 2.132300 TTTTTGCCAAGGCCTCCAC 58.868 52.632 5.23 0.00 41.09 4.02
298 299 0.689080 TTTTTGCCAAGGCCTCCACA 60.689 50.000 5.23 0.59 41.09 4.17
299 300 0.689080 TTTTGCCAAGGCCTCCACAA 60.689 50.000 5.23 8.06 41.09 3.33
300 301 0.689080 TTTGCCAAGGCCTCCACAAA 60.689 50.000 18.15 18.15 41.09 2.83
301 302 0.471591 TTGCCAAGGCCTCCACAAAT 60.472 50.000 5.23 0.00 41.09 2.32
302 303 1.186917 TGCCAAGGCCTCCACAAATG 61.187 55.000 5.23 0.00 41.09 2.32
303 304 1.187567 GCCAAGGCCTCCACAAATGT 61.188 55.000 5.23 0.00 34.56 2.71
304 305 0.890683 CCAAGGCCTCCACAAATGTC 59.109 55.000 5.23 0.00 0.00 3.06
305 306 1.619654 CAAGGCCTCCACAAATGTCA 58.380 50.000 5.23 0.00 0.00 3.58
306 307 2.173519 CAAGGCCTCCACAAATGTCAT 58.826 47.619 5.23 0.00 0.00 3.06
307 308 2.564062 CAAGGCCTCCACAAATGTCATT 59.436 45.455 5.23 0.00 0.00 2.57
308 309 2.893424 AGGCCTCCACAAATGTCATTT 58.107 42.857 0.00 4.91 0.00 2.32
309 310 2.827921 AGGCCTCCACAAATGTCATTTC 59.172 45.455 7.87 0.00 0.00 2.17
310 311 2.562298 GGCCTCCACAAATGTCATTTCA 59.438 45.455 7.87 0.00 0.00 2.69
311 312 3.196254 GGCCTCCACAAATGTCATTTCAT 59.804 43.478 7.87 0.00 0.00 2.57
312 313 4.427312 GCCTCCACAAATGTCATTTCATC 58.573 43.478 7.87 0.00 0.00 2.92
313 314 4.082081 GCCTCCACAAATGTCATTTCATCA 60.082 41.667 7.87 0.00 0.00 3.07
314 315 5.404946 CCTCCACAAATGTCATTTCATCAC 58.595 41.667 7.87 0.00 0.00 3.06
315 316 5.045668 TCCACAAATGTCATTTCATCACG 57.954 39.130 7.87 0.00 0.00 4.35
316 317 4.759183 TCCACAAATGTCATTTCATCACGA 59.241 37.500 7.87 0.00 0.00 4.35
317 318 5.240403 TCCACAAATGTCATTTCATCACGAA 59.760 36.000 7.87 0.00 0.00 3.85
319 320 6.420306 CCACAAATGTCATTTCATCACGAAAA 59.580 34.615 7.87 0.00 46.48 2.29
320 321 7.116662 CCACAAATGTCATTTCATCACGAAAAT 59.883 33.333 7.87 0.00 46.48 1.82
321 322 8.489559 CACAAATGTCATTTCATCACGAAAATT 58.510 29.630 7.87 0.00 46.48 1.82
322 323 8.489559 ACAAATGTCATTTCATCACGAAAATTG 58.510 29.630 7.87 0.00 46.48 2.32
323 324 8.701540 CAAATGTCATTTCATCACGAAAATTGA 58.298 29.630 7.87 0.00 46.48 2.57
324 325 7.801547 ATGTCATTTCATCACGAAAATTGAC 57.198 32.000 11.60 11.60 46.48 3.18
326 327 6.636447 TGTCATTTCATCACGAAAATTGACAC 59.364 34.615 15.05 0.00 46.63 3.67
327 328 5.850653 TCATTTCATCACGAAAATTGACACG 59.149 36.000 0.00 0.00 46.48 4.49
328 329 3.181826 TCATCACGAAAATTGACACGC 57.818 42.857 0.00 0.00 0.00 5.34
329 330 2.545946 TCATCACGAAAATTGACACGCA 59.454 40.909 0.00 0.00 0.00 5.24
330 331 3.188254 TCATCACGAAAATTGACACGCAT 59.812 39.130 0.00 0.00 0.00 4.73
331 332 2.914861 TCACGAAAATTGACACGCATG 58.085 42.857 0.00 0.00 0.00 4.06
332 333 2.289274 TCACGAAAATTGACACGCATGT 59.711 40.909 0.00 0.00 43.71 3.21
357 358 3.456280 ACACACATCAATGTTTGTTGCC 58.544 40.909 8.69 0.00 46.18 4.52
358 359 3.118847 ACACACATCAATGTTTGTTGCCA 60.119 39.130 8.69 0.00 46.18 4.92
359 360 3.869832 CACACATCAATGTTTGTTGCCAA 59.130 39.130 1.90 0.00 39.39 4.52
360 361 4.331992 CACACATCAATGTTTGTTGCCAAA 59.668 37.500 1.90 0.00 39.39 3.28
361 362 4.940046 ACACATCAATGTTTGTTGCCAAAA 59.060 33.333 0.00 0.00 41.99 2.44
362 363 5.413833 ACACATCAATGTTTGTTGCCAAAAA 59.586 32.000 0.00 0.00 41.99 1.94
417 418 6.569179 TTGATTTTACTGTAGAAAGGGTGC 57.431 37.500 0.00 0.00 0.00 5.01
418 419 5.626142 TGATTTTACTGTAGAAAGGGTGCA 58.374 37.500 0.00 0.00 0.00 4.57
419 420 6.245408 TGATTTTACTGTAGAAAGGGTGCAT 58.755 36.000 0.00 0.00 0.00 3.96
420 421 5.957842 TTTTACTGTAGAAAGGGTGCATG 57.042 39.130 0.00 0.00 0.00 4.06
421 422 4.634012 TTACTGTAGAAAGGGTGCATGT 57.366 40.909 0.00 0.00 0.00 3.21
422 423 2.783135 ACTGTAGAAAGGGTGCATGTG 58.217 47.619 0.00 0.00 0.00 3.21
423 424 2.371841 ACTGTAGAAAGGGTGCATGTGA 59.628 45.455 0.00 0.00 0.00 3.58
424 425 3.005554 CTGTAGAAAGGGTGCATGTGAG 58.994 50.000 0.00 0.00 0.00 3.51
425 426 1.740025 GTAGAAAGGGTGCATGTGAGC 59.260 52.381 0.00 0.00 0.00 4.26
426 427 0.403271 AGAAAGGGTGCATGTGAGCT 59.597 50.000 0.00 0.00 34.99 4.09
427 428 0.807496 GAAAGGGTGCATGTGAGCTC 59.193 55.000 6.82 6.82 34.99 4.09
428 429 0.957395 AAAGGGTGCATGTGAGCTCG 60.957 55.000 9.64 0.00 34.99 5.03
429 430 1.830587 AAGGGTGCATGTGAGCTCGA 61.831 55.000 9.64 0.00 34.99 4.04
430 431 1.812922 GGGTGCATGTGAGCTCGAG 60.813 63.158 8.45 8.45 34.99 4.04
431 432 2.459442 GGTGCATGTGAGCTCGAGC 61.459 63.158 30.01 30.01 42.49 5.03
442 443 3.560826 GCTCGAGCTCACATACTCC 57.439 57.895 29.88 0.00 38.21 3.85
443 444 0.741326 GCTCGAGCTCACATACTCCA 59.259 55.000 29.88 0.00 38.21 3.86
444 445 1.339610 GCTCGAGCTCACATACTCCAT 59.660 52.381 29.88 0.00 38.21 3.41
445 446 2.861750 GCTCGAGCTCACATACTCCATG 60.862 54.545 29.88 0.00 38.15 3.66
446 447 5.348794 GCTCGAGCTCACATACTCCATGT 62.349 52.174 29.88 0.00 42.53 3.21
447 448 2.359214 TCGAGCTCACATACTCCATGTC 59.641 50.000 15.40 0.00 44.99 3.06
448 449 2.544694 CGAGCTCACATACTCCATGTCC 60.545 54.545 15.40 0.00 44.99 4.02
449 450 1.410517 AGCTCACATACTCCATGTCCG 59.589 52.381 0.00 0.00 44.99 4.79
450 451 1.137086 GCTCACATACTCCATGTCCGT 59.863 52.381 0.00 0.00 44.99 4.69
451 452 2.418746 GCTCACATACTCCATGTCCGTT 60.419 50.000 0.00 0.00 44.99 4.44
452 453 3.861840 CTCACATACTCCATGTCCGTTT 58.138 45.455 0.00 0.00 44.99 3.60
456 457 4.215399 CACATACTCCATGTCCGTTTGTTT 59.785 41.667 0.00 0.00 44.99 2.83
521 522 3.766591 TGAAGGAAAGAAACAAGCACCAA 59.233 39.130 0.00 0.00 0.00 3.67
532 533 1.386525 AAGCACCAACAGCACCACAG 61.387 55.000 0.00 0.00 0.00 3.66
533 534 2.723746 CACCAACAGCACCACAGC 59.276 61.111 0.00 0.00 0.00 4.40
534 535 2.901840 ACCAACAGCACCACAGCG 60.902 61.111 0.00 0.00 40.15 5.18
535 536 4.332637 CCAACAGCACCACAGCGC 62.333 66.667 0.00 0.00 40.15 5.92
536 537 3.585020 CAACAGCACCACAGCGCA 61.585 61.111 11.47 0.00 40.15 6.09
537 538 3.585990 AACAGCACCACAGCGCAC 61.586 61.111 11.47 0.00 40.15 5.34
538 539 4.854924 ACAGCACCACAGCGCACA 62.855 61.111 11.47 0.00 40.15 4.57
567 568 2.372074 GCGGAATCCCACCCCACTA 61.372 63.158 0.00 0.00 0.00 2.74
568 569 1.830145 CGGAATCCCACCCCACTAG 59.170 63.158 0.00 0.00 0.00 2.57
569 570 1.532238 GGAATCCCACCCCACTAGC 59.468 63.158 0.00 0.00 0.00 3.42
570 571 0.988678 GGAATCCCACCCCACTAGCT 60.989 60.000 0.00 0.00 0.00 3.32
571 572 0.470341 GAATCCCACCCCACTAGCTC 59.530 60.000 0.00 0.00 0.00 4.09
572 573 1.338136 AATCCCACCCCACTAGCTCG 61.338 60.000 0.00 0.00 0.00 5.03
573 574 2.531483 ATCCCACCCCACTAGCTCGT 62.531 60.000 0.00 0.00 0.00 4.18
574 575 1.380785 CCCACCCCACTAGCTCGTA 60.381 63.158 0.00 0.00 0.00 3.43
575 576 1.392710 CCCACCCCACTAGCTCGTAG 61.393 65.000 0.00 0.00 34.52 3.51
576 577 1.392710 CCACCCCACTAGCTCGTAGG 61.393 65.000 0.00 0.00 32.29 3.18
601 602 2.747855 GCCTTTGAGTGCTCCCCG 60.748 66.667 0.00 0.00 0.00 5.73
648 649 1.484038 CTGTCTCCTCTTCCTCCCTG 58.516 60.000 0.00 0.00 0.00 4.45
655 656 4.046489 TCTCCTCTTCCTCCCTGCATATAT 59.954 45.833 0.00 0.00 0.00 0.86
670 671 3.196901 GCATATATACCACCGTGATCCCA 59.803 47.826 0.00 0.00 0.00 4.37
674 675 3.770040 CCACCGTGATCCCAGCGA 61.770 66.667 0.00 0.00 0.00 4.93
803 809 2.437359 GCTGGTCGCTCCAAGCAT 60.437 61.111 0.00 0.00 46.59 3.79
845 851 0.948623 CGAGCCGTGTGATCCACAAA 60.949 55.000 12.80 0.00 46.28 2.83
874 880 3.871775 CACGCAAGGATGTGCTTTT 57.128 47.368 0.00 0.00 42.62 2.27
875 881 1.689959 CACGCAAGGATGTGCTTTTC 58.310 50.000 0.00 0.00 42.62 2.29
910 916 0.972134 CAAGCTCTGGTGGTGAGAGA 59.028 55.000 0.00 0.00 39.58 3.10
911 917 0.972883 AAGCTCTGGTGGTGAGAGAC 59.027 55.000 0.00 0.00 39.58 3.36
991 997 0.388649 CGTGTCTAGCTTCTTGCCGT 60.389 55.000 0.00 0.00 44.23 5.68
992 998 1.797025 GTGTCTAGCTTCTTGCCGTT 58.203 50.000 0.00 0.00 44.23 4.44
993 999 2.143925 GTGTCTAGCTTCTTGCCGTTT 58.856 47.619 0.00 0.00 44.23 3.60
1065 1071 3.430497 CGGAGGAGGGGGAGGAGA 61.430 72.222 0.00 0.00 0.00 3.71
1068 1074 1.228737 GAGGAGGGGGAGGAGATCG 60.229 68.421 0.00 0.00 0.00 3.69
1363 1374 3.891422 ACGTACGATTGATTGGGGTTA 57.109 42.857 24.41 0.00 0.00 2.85
1456 1471 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1458 1473 1.384783 ACCACCACCACCACCACTA 60.385 57.895 0.00 0.00 0.00 2.74
1576 1616 6.537355 TGTCAACAAAGATTCATCTCTTCCT 58.463 36.000 0.00 0.00 35.76 3.36
1577 1617 6.652481 TGTCAACAAAGATTCATCTCTTCCTC 59.348 38.462 0.00 0.00 35.76 3.71
1579 1619 7.390162 GTCAACAAAGATTCATCTCTTCCTCTT 59.610 37.037 0.00 0.00 35.76 2.85
1580 1620 7.941238 TCAACAAAGATTCATCTCTTCCTCTTT 59.059 33.333 0.00 0.00 35.76 2.52
1581 1621 9.224267 CAACAAAGATTCATCTCTTCCTCTTTA 57.776 33.333 0.00 0.00 35.76 1.85
1582 1622 9.972106 AACAAAGATTCATCTCTTCCTCTTTAT 57.028 29.630 0.00 0.00 35.76 1.40
1583 1623 9.612066 ACAAAGATTCATCTCTTCCTCTTTATC 57.388 33.333 0.00 0.00 35.76 1.75
1584 1624 9.835389 CAAAGATTCATCTCTTCCTCTTTATCT 57.165 33.333 0.00 0.00 35.76 1.98
1587 1627 6.739331 TTCATCTCTTCCTCTTTATCTCCC 57.261 41.667 0.00 0.00 0.00 4.30
1588 1628 4.830046 TCATCTCTTCCTCTTTATCTCCCG 59.170 45.833 0.00 0.00 0.00 5.14
1617 1670 3.878699 TGTACCCTTTGGTTTCGTTCTTC 59.121 43.478 0.00 0.00 44.75 2.87
1792 1845 1.267574 ATGGAGTGGTCGTCCTGCAT 61.268 55.000 0.00 0.00 35.26 3.96
1933 1987 2.933260 GTTTTCACAAAAATGGTGCCGT 59.067 40.909 0.00 0.00 36.77 5.68
1949 2003 1.206371 GCCGTTGGGTAGAGAGCTTTA 59.794 52.381 0.00 0.00 34.97 1.85
2075 2129 1.093972 CATTGTGGCCGACATGCTAA 58.906 50.000 8.55 0.00 33.40 3.09
2099 2153 3.391665 CTAGTGGAGCGGGCCAAGG 62.392 68.421 4.39 0.00 40.20 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.239087 TGCATGGAAGCAATTTTTCCTTTTC 59.761 36.000 15.87 7.62 43.63 2.29
23 24 3.565905 AACTAATGCTCTGCTTTGTGC 57.434 42.857 0.00 0.00 43.25 4.57
24 25 3.671928 GCAAACTAATGCTCTGCTTTGTG 59.328 43.478 0.00 0.00 43.06 3.33
25 26 3.610114 CGCAAACTAATGCTCTGCTTTGT 60.610 43.478 0.00 0.00 44.21 2.83
26 27 2.912967 CGCAAACTAATGCTCTGCTTTG 59.087 45.455 0.00 0.00 44.21 2.77
27 28 2.813754 TCGCAAACTAATGCTCTGCTTT 59.186 40.909 0.00 0.00 44.21 3.51
28 29 2.426522 TCGCAAACTAATGCTCTGCTT 58.573 42.857 0.00 0.00 44.21 3.91
29 30 2.099141 TCGCAAACTAATGCTCTGCT 57.901 45.000 0.00 0.00 44.21 4.24
30 31 2.900122 TTCGCAAACTAATGCTCTGC 57.100 45.000 0.00 0.00 44.21 4.26
31 32 4.153986 CACTTTCGCAAACTAATGCTCTG 58.846 43.478 0.00 0.00 44.21 3.35
32 33 3.365364 GCACTTTCGCAAACTAATGCTCT 60.365 43.478 0.00 0.00 44.21 4.09
33 34 2.911102 GCACTTTCGCAAACTAATGCTC 59.089 45.455 0.00 0.00 44.21 4.26
34 35 2.554032 AGCACTTTCGCAAACTAATGCT 59.446 40.909 0.00 0.00 44.21 3.79
35 36 2.911102 GAGCACTTTCGCAAACTAATGC 59.089 45.455 0.00 0.00 42.94 3.56
36 37 4.410492 AGAGCACTTTCGCAAACTAATG 57.590 40.909 0.00 0.00 0.00 1.90
37 38 4.275936 ACAAGAGCACTTTCGCAAACTAAT 59.724 37.500 0.00 0.00 33.70 1.73
38 39 3.625764 ACAAGAGCACTTTCGCAAACTAA 59.374 39.130 0.00 0.00 33.70 2.24
39 40 3.002246 CACAAGAGCACTTTCGCAAACTA 59.998 43.478 0.00 0.00 33.70 2.24
40 41 2.017049 ACAAGAGCACTTTCGCAAACT 58.983 42.857 0.00 0.00 33.70 2.66
41 42 2.111756 CACAAGAGCACTTTCGCAAAC 58.888 47.619 0.00 0.00 33.70 2.93
42 43 2.013400 TCACAAGAGCACTTTCGCAAA 58.987 42.857 0.00 0.00 33.70 3.68
43 44 1.599071 CTCACAAGAGCACTTTCGCAA 59.401 47.619 0.00 0.00 34.61 4.85
44 45 1.220529 CTCACAAGAGCACTTTCGCA 58.779 50.000 0.00 0.00 34.61 5.10
63 64 2.459442 GGTGCATGTGAGCTCGAGC 61.459 63.158 30.01 30.01 42.49 5.03
64 65 0.390866 AAGGTGCATGTGAGCTCGAG 60.391 55.000 8.45 8.45 34.99 4.04
65 66 0.035317 AAAGGTGCATGTGAGCTCGA 59.965 50.000 9.64 0.00 34.99 4.04
66 67 0.877071 AAAAGGTGCATGTGAGCTCG 59.123 50.000 9.64 0.00 34.99 5.03
67 68 2.342910 CAAAAGGTGCATGTGAGCTC 57.657 50.000 6.82 6.82 34.99 4.09
78 79 8.641499 TTTTGATTTTACTGTAGCAAAAGGTG 57.359 30.769 2.17 0.00 33.11 4.00
144 145 8.538856 CATGTGAAAAATACATCAACGTTTGTT 58.461 29.630 10.66 0.00 33.95 2.83
145 146 7.704472 ACATGTGAAAAATACATCAACGTTTGT 59.296 29.630 10.28 10.28 32.66 2.83
146 147 7.997658 CACATGTGAAAAATACATCAACGTTTG 59.002 33.333 21.64 0.00 32.66 2.93
147 148 7.704472 ACACATGTGAAAAATACATCAACGTTT 59.296 29.630 31.94 0.00 32.66 3.60
148 149 7.199766 ACACATGTGAAAAATACATCAACGTT 58.800 30.769 31.94 0.00 32.66 3.99
149 150 6.734137 ACACATGTGAAAAATACATCAACGT 58.266 32.000 31.94 0.06 32.66 3.99
166 167 4.202233 TGTCATGGAATTTTGCACACATGT 60.202 37.500 0.00 0.00 37.53 3.21
167 168 4.308265 TGTCATGGAATTTTGCACACATG 58.692 39.130 0.00 0.00 37.60 3.21
168 169 4.603989 TGTCATGGAATTTTGCACACAT 57.396 36.364 0.00 0.00 0.00 3.21
169 170 4.397481 TTGTCATGGAATTTTGCACACA 57.603 36.364 0.00 0.00 0.00 3.72
170 171 5.731599 TTTTGTCATGGAATTTTGCACAC 57.268 34.783 0.00 0.00 0.00 3.82
171 172 6.018098 GTCATTTTGTCATGGAATTTTGCACA 60.018 34.615 0.00 0.00 0.00 4.57
172 173 6.018098 TGTCATTTTGTCATGGAATTTTGCAC 60.018 34.615 0.00 0.00 0.00 4.57
173 174 6.053650 TGTCATTTTGTCATGGAATTTTGCA 58.946 32.000 0.00 0.00 0.00 4.08
174 175 6.542574 TGTCATTTTGTCATGGAATTTTGC 57.457 33.333 0.00 0.00 0.00 3.68
175 176 8.775527 TGAATGTCATTTTGTCATGGAATTTTG 58.224 29.630 0.00 0.00 0.00 2.44
176 177 8.905660 TGAATGTCATTTTGTCATGGAATTTT 57.094 26.923 0.00 0.00 0.00 1.82
177 178 8.941977 CATGAATGTCATTTTGTCATGGAATTT 58.058 29.630 13.91 0.00 41.12 1.82
178 179 7.065324 GCATGAATGTCATTTTGTCATGGAATT 59.935 33.333 19.69 0.00 43.69 2.17
179 180 6.537301 GCATGAATGTCATTTTGTCATGGAAT 59.463 34.615 19.69 0.00 43.69 3.01
180 181 5.870433 GCATGAATGTCATTTTGTCATGGAA 59.130 36.000 19.69 0.00 43.69 3.53
181 182 5.047235 TGCATGAATGTCATTTTGTCATGGA 60.047 36.000 19.69 16.40 43.69 3.41
182 183 5.172205 TGCATGAATGTCATTTTGTCATGG 58.828 37.500 19.69 8.00 43.69 3.66
183 184 5.290885 CCTGCATGAATGTCATTTTGTCATG 59.709 40.000 16.16 16.16 45.40 3.07
184 185 5.046878 ACCTGCATGAATGTCATTTTGTCAT 60.047 36.000 0.00 0.00 34.28 3.06
185 186 4.281435 ACCTGCATGAATGTCATTTTGTCA 59.719 37.500 0.00 0.00 34.28 3.58
186 187 4.813027 ACCTGCATGAATGTCATTTTGTC 58.187 39.130 0.00 0.01 34.28 3.18
187 188 4.525487 AGACCTGCATGAATGTCATTTTGT 59.475 37.500 11.29 0.00 34.28 2.83
188 189 5.068234 AGACCTGCATGAATGTCATTTTG 57.932 39.130 11.29 2.73 34.28 2.44
189 190 4.142534 CGAGACCTGCATGAATGTCATTTT 60.143 41.667 11.29 0.00 34.28 1.82
190 191 3.376234 CGAGACCTGCATGAATGTCATTT 59.624 43.478 11.29 0.00 34.28 2.32
191 192 2.941064 CGAGACCTGCATGAATGTCATT 59.059 45.455 11.29 0.00 34.28 2.57
192 193 2.558378 CGAGACCTGCATGAATGTCAT 58.442 47.619 11.29 0.00 37.65 3.06
193 194 1.405933 CCGAGACCTGCATGAATGTCA 60.406 52.381 11.29 0.00 0.00 3.58
194 195 1.293924 CCGAGACCTGCATGAATGTC 58.706 55.000 0.00 0.00 0.00 3.06
195 196 0.615331 ACCGAGACCTGCATGAATGT 59.385 50.000 0.00 0.00 0.00 2.71
196 197 1.012086 CACCGAGACCTGCATGAATG 58.988 55.000 0.00 0.00 0.00 2.67
197 198 0.904649 TCACCGAGACCTGCATGAAT 59.095 50.000 0.00 0.00 0.00 2.57
198 199 0.684535 TTCACCGAGACCTGCATGAA 59.315 50.000 0.00 0.00 0.00 2.57
199 200 0.684535 TTTCACCGAGACCTGCATGA 59.315 50.000 0.00 0.00 0.00 3.07
200 201 1.522668 TTTTCACCGAGACCTGCATG 58.477 50.000 0.00 0.00 0.00 4.06
201 202 2.270352 TTTTTCACCGAGACCTGCAT 57.730 45.000 0.00 0.00 0.00 3.96
202 203 3.790691 TTTTTCACCGAGACCTGCA 57.209 47.368 0.00 0.00 0.00 4.41
218 219 7.435784 GCATTTTGGAGCATTGATTTTGTTTTT 59.564 29.630 0.00 0.00 0.00 1.94
219 220 6.919115 GCATTTTGGAGCATTGATTTTGTTTT 59.081 30.769 0.00 0.00 0.00 2.43
220 221 6.263617 AGCATTTTGGAGCATTGATTTTGTTT 59.736 30.769 0.00 0.00 0.00 2.83
221 222 5.766174 AGCATTTTGGAGCATTGATTTTGTT 59.234 32.000 0.00 0.00 0.00 2.83
222 223 5.310451 AGCATTTTGGAGCATTGATTTTGT 58.690 33.333 0.00 0.00 0.00 2.83
223 224 5.873179 AGCATTTTGGAGCATTGATTTTG 57.127 34.783 0.00 0.00 0.00 2.44
224 225 5.998981 TGAAGCATTTTGGAGCATTGATTTT 59.001 32.000 0.00 0.00 0.00 1.82
225 226 5.553123 TGAAGCATTTTGGAGCATTGATTT 58.447 33.333 0.00 0.00 0.00 2.17
226 227 5.155278 TGAAGCATTTTGGAGCATTGATT 57.845 34.783 0.00 0.00 0.00 2.57
227 228 4.811969 TGAAGCATTTTGGAGCATTGAT 57.188 36.364 0.00 0.00 0.00 2.57
228 229 4.603989 TTGAAGCATTTTGGAGCATTGA 57.396 36.364 0.00 0.00 0.00 2.57
229 230 5.676532 TTTTGAAGCATTTTGGAGCATTG 57.323 34.783 0.00 0.00 0.00 2.82
230 231 5.589452 TGTTTTTGAAGCATTTTGGAGCATT 59.411 32.000 0.00 0.00 0.00 3.56
231 232 5.124645 TGTTTTTGAAGCATTTTGGAGCAT 58.875 33.333 0.00 0.00 0.00 3.79
232 233 4.511527 TGTTTTTGAAGCATTTTGGAGCA 58.488 34.783 0.00 0.00 0.00 4.26
233 234 5.482686 TTGTTTTTGAAGCATTTTGGAGC 57.517 34.783 0.00 0.00 0.00 4.70
234 235 8.914328 AAATTTGTTTTTGAAGCATTTTGGAG 57.086 26.923 0.00 0.00 0.00 3.86
235 236 9.702494 AAAAATTTGTTTTTGAAGCATTTTGGA 57.298 22.222 0.00 0.00 37.59 3.53
236 237 9.955310 GAAAAATTTGTTTTTGAAGCATTTTGG 57.045 25.926 3.84 0.00 37.59 3.28
237 238 9.659493 CGAAAAATTTGTTTTTGAAGCATTTTG 57.341 25.926 3.84 0.00 37.59 2.44
238 239 9.617975 TCGAAAAATTTGTTTTTGAAGCATTTT 57.382 22.222 3.84 0.00 37.59 1.82
239 240 9.276397 CTCGAAAAATTTGTTTTTGAAGCATTT 57.724 25.926 3.84 0.00 37.59 2.32
240 241 7.429051 GCTCGAAAAATTTGTTTTTGAAGCATT 59.571 29.630 16.54 0.00 37.59 3.56
241 242 6.906678 GCTCGAAAAATTTGTTTTTGAAGCAT 59.093 30.769 16.54 0.00 37.59 3.79
242 243 6.128445 TGCTCGAAAAATTTGTTTTTGAAGCA 60.128 30.769 18.45 18.45 41.08 3.91
243 244 6.247176 TGCTCGAAAAATTTGTTTTTGAAGC 58.753 32.000 15.51 15.51 37.59 3.86
244 245 8.115520 TCATGCTCGAAAAATTTGTTTTTGAAG 58.884 29.630 3.84 3.10 37.59 3.02
245 246 7.968246 TCATGCTCGAAAAATTTGTTTTTGAA 58.032 26.923 3.84 0.00 37.59 2.69
246 247 7.531280 TCATGCTCGAAAAATTTGTTTTTGA 57.469 28.000 3.84 1.95 37.59 2.69
247 248 8.770850 AATCATGCTCGAAAAATTTGTTTTTG 57.229 26.923 3.84 0.00 37.59 2.44
248 249 9.786105 AAAATCATGCTCGAAAAATTTGTTTTT 57.214 22.222 0.00 0.00 39.22 1.94
249 250 9.224058 CAAAATCATGCTCGAAAAATTTGTTTT 57.776 25.926 0.00 0.00 0.00 2.43
250 251 8.397148 ACAAAATCATGCTCGAAAAATTTGTTT 58.603 25.926 0.00 0.00 35.60 2.83
251 252 7.918643 ACAAAATCATGCTCGAAAAATTTGTT 58.081 26.923 0.00 0.00 35.60 2.83
252 253 7.439056 AGACAAAATCATGCTCGAAAAATTTGT 59.561 29.630 0.00 0.00 40.12 2.83
253 254 7.790000 AGACAAAATCATGCTCGAAAAATTTG 58.210 30.769 0.00 0.00 0.00 2.32
254 255 7.951530 AGACAAAATCATGCTCGAAAAATTT 57.048 28.000 0.00 0.00 0.00 1.82
255 256 7.951530 AAGACAAAATCATGCTCGAAAAATT 57.048 28.000 0.00 0.00 0.00 1.82
256 257 7.951530 AAAGACAAAATCATGCTCGAAAAAT 57.048 28.000 0.00 0.00 0.00 1.82
257 258 7.769272 AAAAGACAAAATCATGCTCGAAAAA 57.231 28.000 0.00 0.00 0.00 1.94
258 259 7.769272 AAAAAGACAAAATCATGCTCGAAAA 57.231 28.000 0.00 0.00 0.00 2.29
279 280 0.689080 TGTGGAGGCCTTGGCAAAAA 60.689 50.000 6.77 0.00 0.00 1.94
280 281 0.689080 TTGTGGAGGCCTTGGCAAAA 60.689 50.000 6.77 0.00 0.00 2.44
281 282 0.689080 TTTGTGGAGGCCTTGGCAAA 60.689 50.000 6.77 15.30 0.00 3.68
282 283 0.471591 ATTTGTGGAGGCCTTGGCAA 60.472 50.000 6.77 9.74 0.00 4.52
283 284 1.155859 ATTTGTGGAGGCCTTGGCA 59.844 52.632 6.77 2.97 0.00 4.92
284 285 1.187567 ACATTTGTGGAGGCCTTGGC 61.188 55.000 6.77 2.49 0.00 4.52
285 286 0.890683 GACATTTGTGGAGGCCTTGG 59.109 55.000 6.77 0.00 0.00 3.61
286 287 1.619654 TGACATTTGTGGAGGCCTTG 58.380 50.000 6.77 0.69 0.00 3.61
287 288 2.610438 ATGACATTTGTGGAGGCCTT 57.390 45.000 6.77 0.00 0.00 4.35
288 289 2.610438 AATGACATTTGTGGAGGCCT 57.390 45.000 3.86 3.86 0.00 5.19
289 290 2.562298 TGAAATGACATTTGTGGAGGCC 59.438 45.455 18.00 0.00 31.47 5.19
290 291 3.940209 TGAAATGACATTTGTGGAGGC 57.060 42.857 18.00 2.75 31.47 4.70
291 292 5.404946 GTGATGAAATGACATTTGTGGAGG 58.595 41.667 18.00 0.00 27.82 4.30
292 293 5.090757 CGTGATGAAATGACATTTGTGGAG 58.909 41.667 18.00 2.09 25.53 3.86
293 294 4.759183 TCGTGATGAAATGACATTTGTGGA 59.241 37.500 18.00 4.36 25.53 4.02
294 295 5.045668 TCGTGATGAAATGACATTTGTGG 57.954 39.130 18.00 2.26 25.53 4.17
295 296 6.989796 TTTCGTGATGAAATGACATTTGTG 57.010 33.333 18.00 2.12 41.59 3.33
296 297 8.489559 CAATTTTCGTGATGAAATGACATTTGT 58.510 29.630 18.00 6.62 45.62 2.83
297 298 8.701540 TCAATTTTCGTGATGAAATGACATTTG 58.298 29.630 18.00 3.05 45.62 2.32
298 299 8.702438 GTCAATTTTCGTGATGAAATGACATTT 58.298 29.630 20.60 13.24 46.38 2.32
299 300 8.231304 GTCAATTTTCGTGATGAAATGACATT 57.769 30.769 20.60 8.30 46.38 2.71
300 301 7.801547 GTCAATTTTCGTGATGAAATGACAT 57.198 32.000 20.60 3.54 46.38 3.06
302 303 6.183359 CGTGTCAATTTTCGTGATGAAATGAC 60.183 38.462 19.48 19.48 46.83 3.06
303 304 5.850653 CGTGTCAATTTTCGTGATGAAATGA 59.149 36.000 0.02 0.34 45.62 2.57
304 305 5.441872 GCGTGTCAATTTTCGTGATGAAATG 60.442 40.000 0.02 0.00 45.62 2.32
305 306 4.616802 GCGTGTCAATTTTCGTGATGAAAT 59.383 37.500 0.02 0.00 45.62 2.17
306 307 3.971871 GCGTGTCAATTTTCGTGATGAAA 59.028 39.130 0.00 0.00 44.70 2.69
307 308 3.002759 TGCGTGTCAATTTTCGTGATGAA 59.997 39.130 0.00 0.00 33.85 2.57
308 309 2.545946 TGCGTGTCAATTTTCGTGATGA 59.454 40.909 0.00 0.00 0.00 2.92
309 310 2.914861 TGCGTGTCAATTTTCGTGATG 58.085 42.857 0.00 0.00 0.00 3.07
310 311 3.058293 ACATGCGTGTCAATTTTCGTGAT 60.058 39.130 5.51 0.00 31.41 3.06
311 312 2.289274 ACATGCGTGTCAATTTTCGTGA 59.711 40.909 5.51 0.00 31.41 4.35
312 313 2.401391 CACATGCGTGTCAATTTTCGTG 59.599 45.455 9.07 0.00 38.41 4.35
313 314 2.649516 CACATGCGTGTCAATTTTCGT 58.350 42.857 9.07 0.00 38.41 3.85
391 392 8.088365 GCACCCTTTCTACAGTAAAATCAATTT 58.912 33.333 0.00 0.00 34.92 1.82
392 393 7.232534 TGCACCCTTTCTACAGTAAAATCAATT 59.767 33.333 0.00 0.00 0.00 2.32
393 394 6.719370 TGCACCCTTTCTACAGTAAAATCAAT 59.281 34.615 0.00 0.00 0.00 2.57
394 395 6.065374 TGCACCCTTTCTACAGTAAAATCAA 58.935 36.000 0.00 0.00 0.00 2.57
395 396 5.626142 TGCACCCTTTCTACAGTAAAATCA 58.374 37.500 0.00 0.00 0.00 2.57
396 397 6.151144 ACATGCACCCTTTCTACAGTAAAATC 59.849 38.462 0.00 0.00 0.00 2.17
397 398 6.010219 ACATGCACCCTTTCTACAGTAAAAT 58.990 36.000 0.00 0.00 0.00 1.82
398 399 5.240623 CACATGCACCCTTTCTACAGTAAAA 59.759 40.000 0.00 0.00 0.00 1.52
399 400 4.759693 CACATGCACCCTTTCTACAGTAAA 59.240 41.667 0.00 0.00 0.00 2.01
400 401 4.041075 TCACATGCACCCTTTCTACAGTAA 59.959 41.667 0.00 0.00 0.00 2.24
401 402 3.580895 TCACATGCACCCTTTCTACAGTA 59.419 43.478 0.00 0.00 0.00 2.74
402 403 2.371841 TCACATGCACCCTTTCTACAGT 59.628 45.455 0.00 0.00 0.00 3.55
403 404 3.005554 CTCACATGCACCCTTTCTACAG 58.994 50.000 0.00 0.00 0.00 2.74
404 405 2.875672 GCTCACATGCACCCTTTCTACA 60.876 50.000 0.00 0.00 0.00 2.74
405 406 1.740025 GCTCACATGCACCCTTTCTAC 59.260 52.381 0.00 0.00 0.00 2.59
406 407 1.630369 AGCTCACATGCACCCTTTCTA 59.370 47.619 0.00 0.00 34.99 2.10
407 408 0.403271 AGCTCACATGCACCCTTTCT 59.597 50.000 0.00 0.00 34.99 2.52
408 409 0.807496 GAGCTCACATGCACCCTTTC 59.193 55.000 9.40 0.00 34.99 2.62
409 410 0.957395 CGAGCTCACATGCACCCTTT 60.957 55.000 15.40 0.00 34.99 3.11
410 411 1.376424 CGAGCTCACATGCACCCTT 60.376 57.895 15.40 0.00 34.99 3.95
411 412 2.236223 CTCGAGCTCACATGCACCCT 62.236 60.000 15.40 0.00 34.99 4.34
412 413 1.812922 CTCGAGCTCACATGCACCC 60.813 63.158 15.40 0.00 34.99 4.61
413 414 2.459442 GCTCGAGCTCACATGCACC 61.459 63.158 29.88 0.00 38.21 5.01
414 415 3.088044 GCTCGAGCTCACATGCAC 58.912 61.111 29.88 0.00 38.21 4.57
423 424 5.106103 CATGGAGTATGTGAGCTCGAGCT 62.106 52.174 38.87 38.87 42.14 4.09
424 425 0.741326 TGGAGTATGTGAGCTCGAGC 59.259 55.000 30.01 30.01 42.49 5.03
425 426 3.010624 CATGGAGTATGTGAGCTCGAG 57.989 52.381 8.45 8.45 32.83 4.04
435 436 4.215399 ACAAACAAACGGACATGGAGTATG 59.785 41.667 0.00 0.00 42.68 2.39
436 437 4.394729 ACAAACAAACGGACATGGAGTAT 58.605 39.130 0.00 0.00 0.00 2.12
437 438 3.811083 ACAAACAAACGGACATGGAGTA 58.189 40.909 0.00 0.00 0.00 2.59
438 439 2.650322 ACAAACAAACGGACATGGAGT 58.350 42.857 0.00 0.00 0.00 3.85
439 440 3.708563 AACAAACAAACGGACATGGAG 57.291 42.857 0.00 0.00 0.00 3.86
440 441 3.429547 CCAAACAAACAAACGGACATGGA 60.430 43.478 0.00 0.00 0.00 3.41
441 442 2.863137 CCAAACAAACAAACGGACATGG 59.137 45.455 0.00 0.00 0.00 3.66
442 443 2.863137 CCCAAACAAACAAACGGACATG 59.137 45.455 0.00 0.00 0.00 3.21
443 444 2.498078 ACCCAAACAAACAAACGGACAT 59.502 40.909 0.00 0.00 0.00 3.06
444 445 1.893801 ACCCAAACAAACAAACGGACA 59.106 42.857 0.00 0.00 0.00 4.02
445 446 2.658373 ACCCAAACAAACAAACGGAC 57.342 45.000 0.00 0.00 0.00 4.79
446 447 3.326747 CAAACCCAAACAAACAAACGGA 58.673 40.909 0.00 0.00 0.00 4.69
447 448 2.416893 CCAAACCCAAACAAACAAACGG 59.583 45.455 0.00 0.00 0.00 4.44
448 449 2.159639 GCCAAACCCAAACAAACAAACG 60.160 45.455 0.00 0.00 0.00 3.60
449 450 3.078097 AGCCAAACCCAAACAAACAAAC 58.922 40.909 0.00 0.00 0.00 2.93
450 451 3.425162 AGCCAAACCCAAACAAACAAA 57.575 38.095 0.00 0.00 0.00 2.83
451 452 3.077359 CAAGCCAAACCCAAACAAACAA 58.923 40.909 0.00 0.00 0.00 2.83
452 453 2.704572 CAAGCCAAACCCAAACAAACA 58.295 42.857 0.00 0.00 0.00 2.83
456 457 1.142748 CGCAAGCCAAACCCAAACA 59.857 52.632 0.00 0.00 0.00 2.83
572 573 2.230750 ACTCAAAGGCACGTACTCCTAC 59.769 50.000 3.96 0.00 31.24 3.18
573 574 2.230508 CACTCAAAGGCACGTACTCCTA 59.769 50.000 3.96 0.00 31.24 2.94
574 575 1.000955 CACTCAAAGGCACGTACTCCT 59.999 52.381 0.00 0.00 0.00 3.69
575 576 1.429463 CACTCAAAGGCACGTACTCC 58.571 55.000 0.00 0.00 0.00 3.85
576 577 0.790814 GCACTCAAAGGCACGTACTC 59.209 55.000 0.00 0.00 0.00 2.59
601 602 1.152881 GATGATGGTGGTGGGGAGC 60.153 63.158 0.00 0.00 0.00 4.70
648 649 3.196901 TGGGATCACGGTGGTATATATGC 59.803 47.826 8.50 0.00 0.00 3.14
655 656 2.717044 CGCTGGGATCACGGTGGTA 61.717 63.158 9.65 0.00 0.00 3.25
670 671 2.586792 GGATGGTGGAAGCTCGCT 59.413 61.111 0.00 0.00 33.76 4.93
674 675 2.204291 TGGGGGATGGTGGAAGCT 60.204 61.111 0.00 0.00 33.76 3.74
803 809 3.170672 CGCCCATGGATCCTCCCA 61.171 66.667 15.22 0.00 41.05 4.37
860 866 1.067354 GGCAGGAAAAGCACATCCTTG 60.067 52.381 1.80 0.87 43.59 3.61
947 953 1.945394 GCACAGCAGTATGGAATGGAG 59.055 52.381 0.00 0.00 35.86 3.86
991 997 1.963855 CGCCCCACATGTCGACAAA 60.964 57.895 24.13 0.00 0.00 2.83
992 998 2.358125 CGCCCCACATGTCGACAA 60.358 61.111 24.13 6.23 0.00 3.18
993 999 3.307108 TCGCCCCACATGTCGACA 61.307 61.111 22.48 22.48 0.00 4.35
1051 1057 1.701757 TCGATCTCCTCCCCCTCCT 60.702 63.158 0.00 0.00 0.00 3.69
1053 1059 1.899534 CGTCGATCTCCTCCCCCTC 60.900 68.421 0.00 0.00 0.00 4.30
1278 1287 2.587194 ATGCTCTCGCGCACCATC 60.587 61.111 8.75 0.00 43.61 3.51
1341 1352 3.891422 ACCCCAATCAATCGTACGTAA 57.109 42.857 16.05 0.00 0.00 3.18
1363 1374 5.359009 ACACCATACACAGCTAGTTATACGT 59.641 40.000 0.00 0.00 0.00 3.57
1456 1471 3.119673 CGCCATGGCATCTCTAGTAGTAG 60.120 52.174 34.93 10.67 42.06 2.57
1458 1473 1.615883 CGCCATGGCATCTCTAGTAGT 59.384 52.381 34.93 0.00 42.06 2.73
1617 1670 1.656652 ATCGGAGCGTCAAAAGGATG 58.343 50.000 0.00 0.00 35.52 3.51
1679 1732 4.209870 CGATTAGTCGCTACCTTCGTAAG 58.790 47.826 0.00 0.00 41.49 2.34
1792 1845 3.563808 GGTGCAGTTCATGTACAGTTTCA 59.436 43.478 0.33 0.00 45.52 2.69
1898 1952 3.907894 TGAAAACCCTTTCATGCGTAC 57.092 42.857 0.00 0.00 44.76 3.67
1949 2003 0.108138 GCCACACTACCGCAAGAGAT 60.108 55.000 0.00 0.00 43.02 2.75
1955 2009 0.325272 TTTATGGCCACACTACCGCA 59.675 50.000 8.16 0.00 0.00 5.69
2075 2129 1.076192 CCCGCTCCACTAGGGTAGT 60.076 63.158 0.00 0.00 40.27 2.73
2099 2153 1.676006 CCCGCTAATTTGACCATCCAC 59.324 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.