Multiple sequence alignment - TraesCS1A01G248700

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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 TraesCS1A01G248700 chr1A 100.000 2800 0 0 1 2800 440802965 440800166 0.000000e+00 5171
1 TraesCS1A01G248700 chr1D 85.439 1923 160 53 637 2489 341177169 341175297 0.000000e+00 1890
2 TraesCS1A01G248700 chr1D 87.345 403 21 9 238 633 341177690 341177311 4.280000e-118 435
3 TraesCS1A01G248700 chr1D 85.583 326 29 6 2478 2800 341175252 341174942 2.690000e-85 326
4 TraesCS1A01G248700 chr1D 96.386 83 3 0 42 124 341177859 341177777 1.350000e-28 137
5 TraesCS1A01G248700 chr1B 85.888 1318 127 36 1201 2489 456840133 456838846 0.000000e+00 1349
6 TraesCS1A01G248700 chr1B 83.488 539 55 16 644 1156 456840664 456840134 3.260000e-129 472
7 TraesCS1A01G248700 chr1B 85.401 274 29 6 2537 2800 456838714 456838442 9.880000e-70 274
8 TraesCS1A01G248700 chr1B 88.344 163 18 1 417 579 456841236 456841075 7.910000e-46 195


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 TraesCS1A01G248700 chr1A 440800166 440802965 2799 True 5171.0 5171 100.00000 1 2800 1 chr1A.!!$R1 2799
1 TraesCS1A01G248700 chr1D 341174942 341177859 2917 True 697.0 1890 88.68825 42 2800 4 chr1D.!!$R1 2758
2 TraesCS1A01G248700 chr1B 456838442 456841236 2794 True 572.5 1349 85.78025 417 2800 4 chr1B.!!$R1 2383

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
215 248 0.034756 ACCGTGCTAACATGCTGACA 59.965 50.0 0.0 0.0 0.00 3.58 F
810 1347 0.240945 GCAGCCTGCGTGTAAACAAT 59.759 50.0 0.0 0.0 31.71 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1843 0.029300 TATACGCACCGTTCCTACGC 59.971 55.0 0.00 0.00 46.27 4.42 R
2415 3030 0.105862 ACATGGGCCCATCATCAAGG 60.106 55.0 35.42 23.04 33.90 3.61 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
20 21 2.298411 CCGAATTGGGCCTGAAATTG 57.702 50.000 4.53 8.11 0.00 2.32
21 22 1.550072 CCGAATTGGGCCTGAAATTGT 59.450 47.619 4.53 0.00 0.00 2.71
22 23 2.028203 CCGAATTGGGCCTGAAATTGTT 60.028 45.455 4.53 0.00 0.00 2.83
23 24 3.556843 CCGAATTGGGCCTGAAATTGTTT 60.557 43.478 4.53 0.00 0.00 2.83
24 25 4.064388 CGAATTGGGCCTGAAATTGTTTT 58.936 39.130 4.53 0.00 0.00 2.43
25 26 4.514816 CGAATTGGGCCTGAAATTGTTTTT 59.485 37.500 4.53 0.00 0.00 1.94
26 27 5.698545 CGAATTGGGCCTGAAATTGTTTTTA 59.301 36.000 4.53 0.00 0.00 1.52
27 28 6.347321 CGAATTGGGCCTGAAATTGTTTTTAC 60.347 38.462 4.53 1.23 0.00 2.01
28 29 5.359194 TTGGGCCTGAAATTGTTTTTACA 57.641 34.783 4.53 0.00 0.00 2.41
29 30 5.359194 TGGGCCTGAAATTGTTTTTACAA 57.641 34.783 4.53 0.00 0.00 2.41
30 31 5.363939 TGGGCCTGAAATTGTTTTTACAAG 58.636 37.500 4.53 0.00 32.69 3.16
31 32 5.104735 TGGGCCTGAAATTGTTTTTACAAGT 60.105 36.000 4.53 0.00 32.69 3.16
32 33 6.098409 TGGGCCTGAAATTGTTTTTACAAGTA 59.902 34.615 4.53 0.00 32.69 2.24
33 34 7.158697 GGGCCTGAAATTGTTTTTACAAGTAT 58.841 34.615 0.84 0.00 32.69 2.12
34 35 8.308207 GGGCCTGAAATTGTTTTTACAAGTATA 58.692 33.333 0.84 0.00 32.69 1.47
35 36 9.699703 GGCCTGAAATTGTTTTTACAAGTATAA 57.300 29.630 0.00 0.00 32.69 0.98
63 64 2.163818 TCCTTTGTTTCACGCTCGAT 57.836 45.000 0.00 0.00 0.00 3.59
124 125 1.227118 GTTGCTCTAGGCGCTCTCC 60.227 63.158 7.64 0.00 45.43 3.71
125 126 1.682344 TTGCTCTAGGCGCTCTCCA 60.682 57.895 7.64 0.00 45.43 3.86
126 127 1.670949 TTGCTCTAGGCGCTCTCCAG 61.671 60.000 7.64 3.75 45.43 3.86
127 128 2.124693 GCTCTAGGCGCTCTCCAGT 61.125 63.158 7.64 0.00 0.00 4.00
132 160 1.595993 TAGGCGCTCTCCAGTGTCAC 61.596 60.000 7.64 0.00 37.20 3.67
136 164 1.278172 CGCTCTCCAGTGTCACGTTG 61.278 60.000 0.00 0.00 0.00 4.10
139 167 0.249447 TCTCCAGTGTCACGTTGCTG 60.249 55.000 0.00 0.00 0.00 4.41
150 183 4.021807 TGTCACGTTGCTGAGGATTTACTA 60.022 41.667 0.00 0.00 0.00 1.82
182 215 5.513233 ACTAAGGTGATGCTTTGATGGATT 58.487 37.500 0.00 0.00 0.00 3.01
184 217 5.841957 AAGGTGATGCTTTGATGGATTAC 57.158 39.130 0.00 0.00 0.00 1.89
185 218 4.210331 AGGTGATGCTTTGATGGATTACC 58.790 43.478 0.00 0.00 42.08 2.85
186 219 4.079558 AGGTGATGCTTTGATGGATTACCT 60.080 41.667 6.64 6.64 45.16 3.08
187 220 4.276926 GGTGATGCTTTGATGGATTACCTC 59.723 45.833 0.00 0.00 39.88 3.85
189 222 2.288666 TGCTTTGATGGATTACCTCGC 58.711 47.619 0.00 0.00 37.04 5.03
191 224 2.682856 GCTTTGATGGATTACCTCGCAA 59.317 45.455 0.00 0.00 37.04 4.85
193 226 4.555511 GCTTTGATGGATTACCTCGCAATC 60.556 45.833 0.00 0.00 37.04 2.67
194 227 4.422073 TTGATGGATTACCTCGCAATCT 57.578 40.909 0.00 0.00 37.04 2.40
195 228 4.422073 TGATGGATTACCTCGCAATCTT 57.578 40.909 0.00 0.00 37.04 2.40
196 229 5.545063 TGATGGATTACCTCGCAATCTTA 57.455 39.130 0.00 0.00 37.04 2.10
197 230 5.297547 TGATGGATTACCTCGCAATCTTAC 58.702 41.667 0.00 0.00 37.04 2.34
198 231 4.067972 TGGATTACCTCGCAATCTTACC 57.932 45.455 0.00 0.00 37.04 2.85
199 232 3.057734 GGATTACCTCGCAATCTTACCG 58.942 50.000 0.00 0.00 33.70 4.02
200 233 3.492137 GGATTACCTCGCAATCTTACCGT 60.492 47.826 0.00 0.00 33.70 4.83
201 234 2.572191 TACCTCGCAATCTTACCGTG 57.428 50.000 0.00 0.00 0.00 4.94
202 235 0.739813 ACCTCGCAATCTTACCGTGC 60.740 55.000 0.00 0.00 34.87 5.34
203 236 0.460284 CCTCGCAATCTTACCGTGCT 60.460 55.000 0.00 0.00 36.10 4.40
204 237 1.202371 CCTCGCAATCTTACCGTGCTA 60.202 52.381 0.00 0.00 36.10 3.49
205 238 2.536365 CTCGCAATCTTACCGTGCTAA 58.464 47.619 0.00 0.00 36.10 3.09
206 239 2.264813 TCGCAATCTTACCGTGCTAAC 58.735 47.619 0.00 0.00 36.10 2.34
207 240 1.996898 CGCAATCTTACCGTGCTAACA 59.003 47.619 0.00 0.00 36.10 2.41
208 241 2.607635 CGCAATCTTACCGTGCTAACAT 59.392 45.455 0.00 0.00 36.10 2.71
209 242 3.544048 CGCAATCTTACCGTGCTAACATG 60.544 47.826 0.00 0.00 36.10 3.21
210 243 3.788797 GCAATCTTACCGTGCTAACATGC 60.789 47.826 0.00 0.00 35.36 4.06
211 244 3.543680 ATCTTACCGTGCTAACATGCT 57.456 42.857 0.00 0.00 0.00 3.79
212 245 2.616960 TCTTACCGTGCTAACATGCTG 58.383 47.619 0.00 0.00 0.00 4.41
213 246 2.232696 TCTTACCGTGCTAACATGCTGA 59.767 45.455 0.00 0.00 0.00 4.26
214 247 2.004583 TACCGTGCTAACATGCTGAC 57.995 50.000 0.00 0.00 0.00 3.51
215 248 0.034756 ACCGTGCTAACATGCTGACA 59.965 50.000 0.00 0.00 0.00 3.58
216 249 1.339055 ACCGTGCTAACATGCTGACAT 60.339 47.619 0.00 0.00 36.79 3.06
217 250 1.739466 CCGTGCTAACATGCTGACATT 59.261 47.619 0.00 0.00 32.87 2.71
218 251 2.476686 CCGTGCTAACATGCTGACATTG 60.477 50.000 0.00 0.00 32.87 2.82
219 252 2.160219 CGTGCTAACATGCTGACATTGT 59.840 45.455 0.00 0.00 32.87 2.71
220 253 3.495193 GTGCTAACATGCTGACATTGTG 58.505 45.455 0.00 0.00 32.87 3.33
221 254 3.058016 GTGCTAACATGCTGACATTGTGT 60.058 43.478 0.00 0.00 32.87 3.72
222 255 3.058085 TGCTAACATGCTGACATTGTGTG 60.058 43.478 0.00 0.00 32.87 3.82
223 256 3.058016 GCTAACATGCTGACATTGTGTGT 60.058 43.478 0.00 0.00 45.83 3.72
232 265 2.260844 ACATTGTGTGTCTGTGGGAG 57.739 50.000 0.00 0.00 35.77 4.30
233 266 1.202806 ACATTGTGTGTCTGTGGGAGG 60.203 52.381 0.00 0.00 35.77 4.30
234 267 1.140312 ATTGTGTGTCTGTGGGAGGT 58.860 50.000 0.00 0.00 0.00 3.85
235 268 0.916086 TTGTGTGTCTGTGGGAGGTT 59.084 50.000 0.00 0.00 0.00 3.50
236 269 1.796017 TGTGTGTCTGTGGGAGGTTA 58.204 50.000 0.00 0.00 0.00 2.85
237 270 1.691976 TGTGTGTCTGTGGGAGGTTAG 59.308 52.381 0.00 0.00 0.00 2.34
238 271 1.002087 GTGTGTCTGTGGGAGGTTAGG 59.998 57.143 0.00 0.00 0.00 2.69
239 272 1.132977 TGTGTCTGTGGGAGGTTAGGA 60.133 52.381 0.00 0.00 0.00 2.94
240 273 2.188817 GTGTCTGTGGGAGGTTAGGAT 58.811 52.381 0.00 0.00 0.00 3.24
241 274 3.245839 TGTGTCTGTGGGAGGTTAGGATA 60.246 47.826 0.00 0.00 0.00 2.59
242 275 3.773119 GTGTCTGTGGGAGGTTAGGATAA 59.227 47.826 0.00 0.00 0.00 1.75
243 276 4.409247 GTGTCTGTGGGAGGTTAGGATAAT 59.591 45.833 0.00 0.00 0.00 1.28
244 277 5.601313 GTGTCTGTGGGAGGTTAGGATAATA 59.399 44.000 0.00 0.00 0.00 0.98
245 278 6.270231 GTGTCTGTGGGAGGTTAGGATAATAT 59.730 42.308 0.00 0.00 0.00 1.28
246 279 7.453752 GTGTCTGTGGGAGGTTAGGATAATATA 59.546 40.741 0.00 0.00 0.00 0.86
247 280 8.184249 TGTCTGTGGGAGGTTAGGATAATATAT 58.816 37.037 0.00 0.00 0.00 0.86
248 281 8.478877 GTCTGTGGGAGGTTAGGATAATATATG 58.521 40.741 0.00 0.00 0.00 1.78
249 282 8.184249 TCTGTGGGAGGTTAGGATAATATATGT 58.816 37.037 0.00 0.00 0.00 2.29
250 283 9.488762 CTGTGGGAGGTTAGGATAATATATGTA 57.511 37.037 0.00 0.00 0.00 2.29
253 286 8.934697 TGGGAGGTTAGGATAATATATGTATGC 58.065 37.037 0.00 0.00 0.00 3.14
254 287 8.088981 GGGAGGTTAGGATAATATATGTATGCG 58.911 40.741 0.00 0.00 0.00 4.73
285 318 2.928801 TGTAGCATGACCAGTTGTGT 57.071 45.000 0.00 0.00 0.00 3.72
334 367 4.316446 CGTAATCTTGTACACGATCAAGCG 60.316 45.833 14.58 12.23 40.27 4.68
342 375 4.657077 CGATCAAGCGTCGTCGTA 57.343 55.556 3.66 0.00 39.49 3.43
343 376 3.144300 CGATCAAGCGTCGTCGTAT 57.856 52.632 3.66 0.00 39.49 3.06
344 377 1.463805 CGATCAAGCGTCGTCGTATT 58.536 50.000 3.66 0.00 39.49 1.89
345 378 1.185121 CGATCAAGCGTCGTCGTATTG 59.815 52.381 12.95 12.95 39.49 1.90
346 379 1.517276 GATCAAGCGTCGTCGTATTGG 59.483 52.381 16.76 4.79 36.91 3.16
347 380 0.241749 TCAAGCGTCGTCGTATTGGT 59.758 50.000 16.76 0.00 36.91 3.67
348 381 1.468127 TCAAGCGTCGTCGTATTGGTA 59.532 47.619 16.76 2.62 36.91 3.25
372 405 6.939622 AGTATTAGTAATACCAATACGGCCC 58.060 40.000 23.53 1.36 43.78 5.80
377 410 1.344065 ATACCAATACGGCCCGATGA 58.656 50.000 11.71 0.00 39.03 2.92
386 419 1.821061 CGGCCCGATGAGATAGGCTT 61.821 60.000 0.00 0.00 45.07 4.35
404 437 6.663944 AGGCTTCTCGAAACATAAACATAC 57.336 37.500 0.00 0.00 0.00 2.39
405 438 6.170506 AGGCTTCTCGAAACATAAACATACA 58.829 36.000 0.00 0.00 0.00 2.29
406 439 6.653320 AGGCTTCTCGAAACATAAACATACAA 59.347 34.615 0.00 0.00 0.00 2.41
407 440 7.336931 AGGCTTCTCGAAACATAAACATACAAT 59.663 33.333 0.00 0.00 0.00 2.71
408 441 7.640240 GGCTTCTCGAAACATAAACATACAATC 59.360 37.037 0.00 0.00 0.00 2.67
409 442 7.640240 GCTTCTCGAAACATAAACATACAATCC 59.360 37.037 0.00 0.00 0.00 3.01
410 443 7.229228 TCTCGAAACATAAACATACAATCCG 57.771 36.000 0.00 0.00 0.00 4.18
474 507 3.206150 CAACCCCTAACGAGAATCATGG 58.794 50.000 0.00 0.00 33.17 3.66
584 623 9.010029 ACTGGTGTACAACTTCCATTTTATTAG 57.990 33.333 13.07 0.00 0.00 1.73
588 680 8.456471 GTGTACAACTTCCATTTTATTAGGGTC 58.544 37.037 0.00 0.00 0.00 4.46
589 681 6.753107 ACAACTTCCATTTTATTAGGGTCG 57.247 37.500 0.00 0.00 0.00 4.79
590 682 5.650703 ACAACTTCCATTTTATTAGGGTCGG 59.349 40.000 0.00 0.00 0.00 4.79
591 683 5.446260 ACTTCCATTTTATTAGGGTCGGT 57.554 39.130 0.00 0.00 0.00 4.69
592 684 6.564557 ACTTCCATTTTATTAGGGTCGGTA 57.435 37.500 0.00 0.00 0.00 4.02
593 685 7.145474 ACTTCCATTTTATTAGGGTCGGTAT 57.855 36.000 0.00 0.00 0.00 2.73
612 704 5.091552 GGTATATGGATGTCACCTTCCCTA 58.908 45.833 0.00 0.00 34.69 3.53
633 725 3.857052 ACCGGTATCACACACAATGTAG 58.143 45.455 4.49 0.00 40.64 2.74
643 873 4.035558 CACACACAATGTAGAAGCACAAGT 59.964 41.667 0.00 0.00 40.64 3.16
698 1220 4.039730 CACACCCAAACCCAAACATATTCA 59.960 41.667 0.00 0.00 0.00 2.57
712 1234 2.979814 TATTCACGGTGTGGATGAGG 57.020 50.000 8.17 0.00 32.20 3.86
727 1258 0.678950 TGAGGCTGTCAACACGATCA 59.321 50.000 0.00 0.00 29.64 2.92
757 1290 0.719465 CGTACAAAGCGGGCTACTTG 59.281 55.000 0.00 0.00 0.00 3.16
773 1306 4.273480 GCTACTTGCAAGTCAAAGTCAGAA 59.727 41.667 34.29 12.81 40.37 3.02
774 1307 4.889832 ACTTGCAAGTCAAAGTCAGAAG 57.110 40.909 26.36 0.00 32.86 2.85
810 1347 0.240945 GCAGCCTGCGTGTAAACAAT 59.759 50.000 0.00 0.00 31.71 2.71
821 1372 4.484236 CGTGTAAACAATGGCAATGACAT 58.516 39.130 10.01 0.00 29.26 3.06
822 1373 4.922692 CGTGTAAACAATGGCAATGACATT 59.077 37.500 8.80 8.80 42.67 2.71
834 1385 3.611113 GCAATGACATTGTGCATTCTCAC 59.389 43.478 25.18 5.02 42.20 3.51
836 1387 2.493035 TGACATTGTGCATTCTCACGT 58.507 42.857 0.00 0.00 39.73 4.49
945 1499 4.744137 CCATTGAATCTCTTCTAGTGCTCG 59.256 45.833 0.00 0.00 32.29 5.03
1029 1588 2.027625 CGTTGAGGACAGCGGGAAC 61.028 63.158 0.00 0.00 44.55 3.62
1086 1645 3.655211 CTGGCCCTGAGGGTGCTT 61.655 66.667 20.64 0.00 46.51 3.91
1102 1661 1.081376 CTTCTGTTCGCCGTCTCGT 60.081 57.895 0.00 0.00 0.00 4.18
1188 1747 2.106683 GTTCAGATTCGGGCCGGTG 61.107 63.158 27.98 17.90 0.00 4.94
1231 1790 0.243907 AGCGCTCATGTACGTGAGTT 59.756 50.000 34.51 22.56 46.40 3.01
1271 1833 2.625790 CTCTCCTCTCCTACGGGAATTG 59.374 54.545 0.00 0.00 41.69 2.32
1276 1838 4.587684 TCCTCTCCTACGGGAATTGATAAC 59.412 45.833 0.00 0.00 41.69 1.89
1277 1839 4.589374 CCTCTCCTACGGGAATTGATAACT 59.411 45.833 0.00 0.00 41.69 2.24
1279 1841 6.158023 TCTCCTACGGGAATTGATAACTTC 57.842 41.667 0.00 0.00 41.69 3.01
1281 1843 4.056050 CCTACGGGAATTGATAACTTCCG 58.944 47.826 0.00 0.00 41.57 4.30
1282 1844 2.285977 ACGGGAATTGATAACTTCCGC 58.714 47.619 0.00 0.00 41.57 5.54
1283 1845 1.260561 CGGGAATTGATAACTTCCGCG 59.739 52.381 0.00 0.00 41.57 6.46
1284 1846 2.285977 GGGAATTGATAACTTCCGCGT 58.714 47.619 4.92 0.00 41.57 6.01
1285 1847 3.460103 GGGAATTGATAACTTCCGCGTA 58.540 45.455 4.92 0.00 41.57 4.42
1311 1878 4.890088 ACGGTGCGTATAATAACATGGAT 58.110 39.130 0.00 0.00 38.73 3.41
1324 1891 7.534723 AATAACATGGATTGCTGATGCTTAT 57.465 32.000 0.00 0.00 40.48 1.73
1330 1897 4.142337 TGGATTGCTGATGCTTATTGTGTG 60.142 41.667 0.00 0.00 40.48 3.82
1483 2051 2.681848 CCTCATTCTGCTTGATGTGGTC 59.318 50.000 0.00 0.00 0.00 4.02
1494 2074 4.569966 GCTTGATGTGGTCAGTATCTTCTG 59.430 45.833 0.00 0.00 38.29 3.02
1505 2085 6.054295 GTCAGTATCTTCTGCCTTGAATGAT 58.946 40.000 0.00 0.00 35.63 2.45
1520 2100 7.575532 GCCTTGAATGATTTGTTCTCACATGTA 60.576 37.037 0.00 0.00 31.06 2.29
1522 2102 7.984422 TGAATGATTTGTTCTCACATGTACT 57.016 32.000 0.00 0.00 31.06 2.73
1523 2103 7.809665 TGAATGATTTGTTCTCACATGTACTG 58.190 34.615 0.00 0.00 31.06 2.74
1524 2104 7.445096 TGAATGATTTGTTCTCACATGTACTGT 59.555 33.333 0.00 0.00 39.20 3.55
1538 2118 0.037697 TACTGTAGTTGCACGCAGGG 60.038 55.000 9.72 0.00 32.92 4.45
1542 2122 3.468326 TAGTTGCACGCAGGGCACA 62.468 57.895 4.97 0.00 41.75 4.57
1563 2143 6.512415 GCACAGCTTGATGTAACAATCCTATC 60.512 42.308 0.00 0.00 0.00 2.08
1687 2274 3.525537 ACAAGATCTGCAACATCTACGG 58.474 45.455 8.00 4.82 29.97 4.02
1806 2393 0.179124 GAGAAGCCGCTGATCGAACT 60.179 55.000 0.00 0.00 41.67 3.01
1859 2446 1.994916 GGGACAAATTTCATGTGCCG 58.005 50.000 3.85 0.00 47.00 5.69
1889 2476 2.383527 CGTCGGCTTTGGTGAGCTC 61.384 63.158 6.82 6.82 42.32 4.09
1951 2538 0.831711 TGTGGCTGTGGAGTGCTCTA 60.832 55.000 0.00 0.00 0.00 2.43
1955 2542 0.456995 GCTGTGGAGTGCTCTACGAC 60.457 60.000 10.35 2.61 43.00 4.34
1957 2544 1.474478 CTGTGGAGTGCTCTACGACAT 59.526 52.381 10.35 0.00 43.00 3.06
1958 2545 1.202348 TGTGGAGTGCTCTACGACATG 59.798 52.381 10.35 0.00 43.00 3.21
1959 2546 0.173481 TGGAGTGCTCTACGACATGC 59.827 55.000 0.00 0.00 0.00 4.06
1969 2556 3.701530 CGACATGCGTGTGTGCGT 61.702 61.111 18.17 0.00 39.09 5.24
1976 2563 3.323903 CGTGTGTGCGTGCGTGTA 61.324 61.111 0.00 0.00 0.00 2.90
1989 2576 0.450482 GCGTGTACATGTGCGTTGAC 60.450 55.000 16.28 0.06 0.00 3.18
1994 2581 3.060406 GTGTACATGTGCGTTGACGTTTA 60.060 43.478 9.11 0.00 42.22 2.01
1995 2582 3.741856 TGTACATGTGCGTTGACGTTTAT 59.258 39.130 9.11 0.00 42.22 1.40
1996 2583 3.449322 ACATGTGCGTTGACGTTTATC 57.551 42.857 0.00 0.00 42.22 1.75
2051 2639 2.928116 AGTAAGCACGACTTTTATCGGC 59.072 45.455 0.00 1.01 46.56 5.54
2061 2649 4.142687 CGACTTTTATCGGCCAAAATCACT 60.143 41.667 2.24 0.00 38.47 3.41
2065 2653 4.433186 TTATCGGCCAAAATCACTGTTG 57.567 40.909 2.24 0.00 0.00 3.33
2067 2655 2.852449 TCGGCCAAAATCACTGTTGTA 58.148 42.857 2.24 0.00 0.00 2.41
2086 2674 6.546403 TGTTGTAACCTTTGTGGCATAGTTTA 59.454 34.615 0.00 0.00 40.22 2.01
2088 2676 4.783764 AACCTTTGTGGCATAGTTTAGC 57.216 40.909 0.00 0.00 40.22 3.09
2090 2678 4.344104 ACCTTTGTGGCATAGTTTAGCAT 58.656 39.130 0.00 0.00 40.22 3.79
2095 2683 6.528537 TTGTGGCATAGTTTAGCATGATTT 57.471 33.333 0.00 0.00 0.00 2.17
2096 2684 7.637631 TTGTGGCATAGTTTAGCATGATTTA 57.362 32.000 0.00 0.00 0.00 1.40
2098 2686 8.236585 TGTGGCATAGTTTAGCATGATTTAAT 57.763 30.769 0.00 0.00 0.00 1.40
2099 2687 8.694540 TGTGGCATAGTTTAGCATGATTTAATT 58.305 29.630 0.00 0.00 0.00 1.40
2107 2695 9.255029 AGTTTAGCATGATTTAATTAACCCTGT 57.745 29.630 0.00 0.00 0.00 4.00
2108 2696 9.869757 GTTTAGCATGATTTAATTAACCCTGTT 57.130 29.630 0.00 0.00 0.00 3.16
2111 2699 8.776376 AGCATGATTTAATTAACCCTGTTTTG 57.224 30.769 0.00 0.00 0.00 2.44
2113 2701 8.872845 GCATGATTTAATTAACCCTGTTTTGAG 58.127 33.333 0.00 0.00 0.00 3.02
2123 2711 6.499106 AACCCTGTTTTGAGAAAAATGGAT 57.501 33.333 0.00 0.00 30.99 3.41
2126 2714 8.028652 ACCCTGTTTTGAGAAAAATGGATTTA 57.971 30.769 0.00 0.00 30.99 1.40
2127 2715 8.490311 ACCCTGTTTTGAGAAAAATGGATTTAA 58.510 29.630 0.00 0.00 30.99 1.52
2128 2716 8.773645 CCCTGTTTTGAGAAAAATGGATTTAAC 58.226 33.333 0.00 0.00 30.99 2.01
2130 2718 9.546428 CTGTTTTGAGAAAAATGGATTTAACCT 57.454 29.630 0.00 0.00 31.13 3.50
2131 2719 9.898152 TGTTTTGAGAAAAATGGATTTAACCTT 57.102 25.926 0.00 0.00 31.13 3.50
2145 2733 5.455056 TTTAACCTTTTTGCTATCGCCAA 57.545 34.783 0.00 0.00 34.43 4.52
2148 2736 1.467374 CCTTTTTGCTATCGCCAACGG 60.467 52.381 0.00 0.00 40.63 4.44
2149 2737 1.199097 CTTTTTGCTATCGCCAACGGT 59.801 47.619 0.00 0.00 40.63 4.83
2174 2771 2.237893 AGGATTTAACGTACCACCAGGG 59.762 50.000 0.00 0.00 44.81 4.45
2183 2780 3.739922 CCACCAGGGTCTATGGCA 58.260 61.111 0.00 0.00 41.87 4.92
2184 2781 1.224592 CCACCAGGGTCTATGGCAC 59.775 63.158 0.00 0.00 41.87 5.01
2185 2782 1.224592 CACCAGGGTCTATGGCACC 59.775 63.158 0.00 0.00 41.87 5.01
2191 2788 1.282157 AGGGTCTATGGCACCAGAAAC 59.718 52.381 2.43 0.00 35.35 2.78
2194 2791 2.504175 GGTCTATGGCACCAGAAACCTA 59.496 50.000 0.00 0.00 33.63 3.08
2200 2797 1.672145 GGCACCAGAAACCTAGTCGTC 60.672 57.143 0.00 0.00 0.00 4.20
2207 2804 0.386478 AAACCTAGTCGTCGTCACGC 60.386 55.000 0.00 0.00 46.28 5.34
2208 2805 1.233285 AACCTAGTCGTCGTCACGCT 61.233 55.000 0.00 0.00 46.28 5.07
2209 2806 1.060622 CCTAGTCGTCGTCACGCTC 59.939 63.158 0.00 0.00 46.28 5.03
2210 2807 1.632948 CCTAGTCGTCGTCACGCTCA 61.633 60.000 0.00 0.00 46.28 4.26
2212 2809 0.096454 TAGTCGTCGTCACGCTCATG 59.904 55.000 0.00 0.00 46.28 3.07
2213 2810 2.504026 TCGTCGTCACGCTCATGC 60.504 61.111 0.00 0.00 46.28 4.06
2224 2828 2.360350 CTCATGCGGGCAAGTGGT 60.360 61.111 0.00 0.00 0.00 4.16
2237 2841 4.234574 GGCAAGTGGTTAGCACATTAAAC 58.765 43.478 17.00 0.18 0.00 2.01
2242 2846 5.497474 AGTGGTTAGCACATTAAACCCTAG 58.503 41.667 17.00 0.00 41.66 3.02
2246 2850 1.021968 GCACATTAAACCCTAGGCCG 58.978 55.000 2.05 0.00 0.00 6.13
2249 2853 0.106918 CATTAAACCCTAGGCCGGCA 60.107 55.000 30.85 7.71 0.00 5.69
2264 2873 1.457823 CGGCATACGGTAGGCACCTA 61.458 60.000 23.99 0.00 43.33 3.08
2268 2877 1.887198 CATACGGTAGGCACCTAGAGG 59.113 57.143 0.00 0.00 43.33 3.69
2276 2885 0.326332 GGCACCTAGAGGGGGTAAGT 60.326 60.000 0.00 0.00 41.58 2.24
2279 2888 2.829023 CACCTAGAGGGGGTAAGTGAA 58.171 52.381 0.00 0.00 40.27 3.18
2285 2894 0.122435 AGGGGGTAAGTGAATGGGGA 59.878 55.000 0.00 0.00 0.00 4.81
2286 2895 1.004436 GGGGGTAAGTGAATGGGGAA 58.996 55.000 0.00 0.00 0.00 3.97
2288 2897 2.666317 GGGGTAAGTGAATGGGGAATG 58.334 52.381 0.00 0.00 0.00 2.67
2331 2946 0.037605 CACCAAGGTCCTCACGGTAC 60.038 60.000 7.16 0.00 0.00 3.34
2353 2968 7.067372 GGTACGGTAGTAAATTTAGCCCAAAAT 59.933 37.037 0.00 0.00 34.16 1.82
2367 2982 4.653801 AGCCCAAAATGGTACTGAAAGTTT 59.346 37.500 0.00 0.00 39.53 2.66
2368 2983 4.988540 GCCCAAAATGGTACTGAAAGTTTC 59.011 41.667 8.75 8.75 39.53 2.78
2380 2995 4.758561 CTGAAAGTTTCCGTACGTTTCTG 58.241 43.478 21.46 18.46 0.00 3.02
2381 2996 3.001533 TGAAAGTTTCCGTACGTTTCTGC 59.998 43.478 21.46 6.73 0.00 4.26
2388 3003 1.373748 GTACGTTTCTGCAGGCGGA 60.374 57.895 22.66 15.76 0.00 5.54
2392 3007 1.302511 GTTTCTGCAGGCGGAAGGA 60.303 57.895 15.13 0.00 41.64 3.36
2404 3019 2.012051 GCGGAAGGACATGTAACCCTG 61.012 57.143 5.39 0.00 0.00 4.45
2405 3020 1.751437 GGAAGGACATGTAACCCTGC 58.249 55.000 5.39 3.62 0.00 4.85
2407 3022 1.004277 GAAGGACATGTAACCCTGCCA 59.996 52.381 5.39 0.00 0.00 4.92
2411 3026 0.480690 ACATGTAACCCTGCCACCAA 59.519 50.000 0.00 0.00 0.00 3.67
2415 3030 1.244816 GTAACCCTGCCACCAAGAAC 58.755 55.000 0.00 0.00 0.00 3.01
2416 3031 0.111639 TAACCCTGCCACCAAGAACC 59.888 55.000 0.00 0.00 0.00 3.62
2418 3033 1.153756 CCCTGCCACCAAGAACCTT 59.846 57.895 0.00 0.00 0.00 3.50
2420 3035 0.178992 CCTGCCACCAAGAACCTTGA 60.179 55.000 8.16 0.00 0.00 3.02
2421 3036 1.548582 CCTGCCACCAAGAACCTTGAT 60.549 52.381 8.16 0.00 0.00 2.57
2423 3038 1.144708 TGCCACCAAGAACCTTGATGA 59.855 47.619 8.16 0.00 0.00 2.92
2424 3039 2.225091 TGCCACCAAGAACCTTGATGAT 60.225 45.455 8.16 0.00 0.00 2.45
2425 3040 2.165030 GCCACCAAGAACCTTGATGATG 59.835 50.000 8.16 2.10 0.00 3.07
2436 3051 2.511659 CTTGATGATGGGCCCATGTAG 58.488 52.381 42.21 24.06 36.70 2.74
2437 3052 1.521764 TGATGATGGGCCCATGTAGT 58.478 50.000 42.21 23.08 36.70 2.73
2461 3076 4.946157 CACTCCAGAGCTCATTTACCATTT 59.054 41.667 17.77 0.00 0.00 2.32
2464 3079 5.324409 TCCAGAGCTCATTTACCATTTTGT 58.676 37.500 17.77 0.00 0.00 2.83
2490 3160 9.979578 TCTAGCACACAATTAACATTCAAATTT 57.020 25.926 0.00 0.00 0.00 1.82
2516 3186 4.043750 CACACAACAATTGTCCATCACAC 58.956 43.478 12.39 0.00 43.23 3.82
2519 3189 4.503734 CACAACAATTGTCCATCACACAAC 59.496 41.667 12.39 0.00 43.23 3.32
2561 3259 6.494893 TCAACATACCAAGTTCAACATAGC 57.505 37.500 0.00 0.00 0.00 2.97
2575 3273 6.565060 GTTCAACATAGCGTGTTCAACATACA 60.565 38.462 15.84 0.00 46.99 2.29
2581 3279 4.597079 AGCGTGTTCAACATACAAAGTTG 58.403 39.130 0.00 0.00 45.82 3.16
2582 3280 3.728718 GCGTGTTCAACATACAAAGTTGG 59.271 43.478 0.00 0.00 44.84 3.77
2587 3285 4.804608 TCAACATACAAAGTTGGACACG 57.195 40.909 6.26 0.00 44.84 4.49
2645 3343 8.299570 CAAGCAAGTGTCCATATTACTTTCTTT 58.700 33.333 0.00 0.00 36.33 2.52
2661 3359 4.974645 TTCTTTCCCTCTTGCTTAGACA 57.025 40.909 0.00 0.00 0.00 3.41
2668 3366 3.198635 CCCTCTTGCTTAGACAATCCTCA 59.801 47.826 0.00 0.00 0.00 3.86
2669 3367 4.323792 CCCTCTTGCTTAGACAATCCTCAA 60.324 45.833 0.00 0.00 0.00 3.02
2682 3380 3.777106 ATCCTCAACTCTCTTTGTGCA 57.223 42.857 0.00 0.00 0.00 4.57
2683 3381 3.558931 TCCTCAACTCTCTTTGTGCAA 57.441 42.857 0.00 0.00 0.00 4.08
2684 3382 3.206150 TCCTCAACTCTCTTTGTGCAAC 58.794 45.455 0.00 0.00 37.35 4.17
2698 3396 2.503356 TGTGCAACCCTCATTTGGTTTT 59.497 40.909 0.00 0.00 43.52 2.43
2701 3399 3.323403 TGCAACCCTCATTTGGTTTTAGG 59.677 43.478 0.00 0.00 43.52 2.69
2728 3426 0.244994 GAGCACGCTCTCTCTGGAAA 59.755 55.000 11.81 0.00 39.80 3.13
2740 3438 0.537188 TCTGGAAAGGCGATGGACTC 59.463 55.000 0.00 0.00 0.00 3.36
2741 3439 0.539051 CTGGAAAGGCGATGGACTCT 59.461 55.000 0.00 0.00 0.00 3.24
2755 3453 5.182380 CGATGGACTCTTAAGGATCCTCTAC 59.818 48.000 16.52 2.89 32.06 2.59
2757 3455 6.031964 TGGACTCTTAAGGATCCTCTACAT 57.968 41.667 16.52 0.61 32.06 2.29
2766 3474 0.833834 ATCCTCTACATGCCCCCTCG 60.834 60.000 0.00 0.00 0.00 4.63
2788 3496 1.728323 TGGGATGGTTGAGTGAGTGA 58.272 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.550072 ACAATTTCAGGCCCAATTCGG 59.450 47.619 0.00 0.00 0.00 4.30
2 3 3.317603 AACAATTTCAGGCCCAATTCG 57.682 42.857 0.00 0.62 0.00 3.34
3 4 6.484977 TGTAAAAACAATTTCAGGCCCAATTC 59.515 34.615 0.00 0.00 0.00 2.17
4 5 6.360618 TGTAAAAACAATTTCAGGCCCAATT 58.639 32.000 0.00 0.00 0.00 2.32
5 6 5.934781 TGTAAAAACAATTTCAGGCCCAAT 58.065 33.333 0.00 0.00 0.00 3.16
6 7 5.359194 TGTAAAAACAATTTCAGGCCCAA 57.641 34.783 0.00 0.00 0.00 4.12
7 8 5.104735 ACTTGTAAAAACAATTTCAGGCCCA 60.105 36.000 0.00 0.00 0.00 5.36
8 9 5.364778 ACTTGTAAAAACAATTTCAGGCCC 58.635 37.500 0.00 0.00 0.00 5.80
9 10 9.699703 TTATACTTGTAAAAACAATTTCAGGCC 57.300 29.630 0.00 0.00 0.00 5.19
32 33 7.920682 GCGTGAAACAAAGGATTATTCCATTAT 59.079 33.333 6.44 0.00 40.29 1.28
33 34 7.122055 AGCGTGAAACAAAGGATTATTCCATTA 59.878 33.333 6.44 0.00 40.29 1.90
34 35 6.071391 AGCGTGAAACAAAGGATTATTCCATT 60.071 34.615 6.44 0.00 40.29 3.16
35 36 5.418840 AGCGTGAAACAAAGGATTATTCCAT 59.581 36.000 6.44 0.00 40.29 3.41
36 37 4.764823 AGCGTGAAACAAAGGATTATTCCA 59.235 37.500 6.44 0.00 40.29 3.53
37 38 5.310720 AGCGTGAAACAAAGGATTATTCC 57.689 39.130 0.00 0.00 38.64 3.01
38 39 5.022021 CGAGCGTGAAACAAAGGATTATTC 58.978 41.667 0.00 0.00 35.74 1.75
39 40 4.693566 TCGAGCGTGAAACAAAGGATTATT 59.306 37.500 0.00 0.00 35.74 1.40
40 41 4.250464 TCGAGCGTGAAACAAAGGATTAT 58.750 39.130 0.00 0.00 35.74 1.28
48 49 2.349438 GCTTTGATCGAGCGTGAAACAA 60.349 45.455 5.29 0.00 35.74 2.83
63 64 2.613026 TCAACTTCGGTGAGCTTTGA 57.387 45.000 0.00 0.00 0.00 2.69
101 102 1.815840 GCGCCTAGAGCAACCTTCC 60.816 63.158 0.00 0.00 44.04 3.46
124 125 0.249447 TCCTCAGCAACGTGACACTG 60.249 55.000 3.68 0.00 0.00 3.66
125 126 0.681733 ATCCTCAGCAACGTGACACT 59.318 50.000 3.68 0.00 0.00 3.55
126 127 1.512926 AATCCTCAGCAACGTGACAC 58.487 50.000 0.00 0.00 0.00 3.67
127 128 2.254546 AAATCCTCAGCAACGTGACA 57.745 45.000 0.00 0.00 0.00 3.58
132 160 4.624024 TCGTTTAGTAAATCCTCAGCAACG 59.376 41.667 0.00 0.00 36.65 4.10
136 164 4.181578 TGCTCGTTTAGTAAATCCTCAGC 58.818 43.478 0.00 3.62 0.00 4.26
139 167 7.010275 CCTTAGTTGCTCGTTTAGTAAATCCTC 59.990 40.741 0.00 0.00 31.05 3.71
150 183 2.484264 GCATCACCTTAGTTGCTCGTTT 59.516 45.455 0.00 0.00 32.78 3.60
174 207 4.422073 AAGATTGCGAGGTAATCCATCA 57.578 40.909 3.33 0.00 35.73 3.07
182 215 1.470285 GCACGGTAAGATTGCGAGGTA 60.470 52.381 0.00 0.00 0.00 3.08
184 217 0.460284 AGCACGGTAAGATTGCGAGG 60.460 55.000 0.00 0.00 41.33 4.63
185 218 2.203800 TAGCACGGTAAGATTGCGAG 57.796 50.000 0.00 0.00 41.33 5.03
186 219 2.264813 GTTAGCACGGTAAGATTGCGA 58.735 47.619 0.00 0.00 41.33 5.10
187 220 1.996898 TGTTAGCACGGTAAGATTGCG 59.003 47.619 0.00 0.00 41.33 4.85
189 222 3.623060 AGCATGTTAGCACGGTAAGATTG 59.377 43.478 0.00 0.00 36.85 2.67
191 224 3.118775 TCAGCATGTTAGCACGGTAAGAT 60.119 43.478 0.00 0.00 37.40 2.40
193 226 2.348666 GTCAGCATGTTAGCACGGTAAG 59.651 50.000 0.00 0.00 37.40 2.34
194 227 2.289133 TGTCAGCATGTTAGCACGGTAA 60.289 45.455 0.00 0.00 37.40 2.85
195 228 1.273886 TGTCAGCATGTTAGCACGGTA 59.726 47.619 0.00 0.00 37.40 4.02
196 229 0.034756 TGTCAGCATGTTAGCACGGT 59.965 50.000 0.00 0.00 37.40 4.83
197 230 1.372582 ATGTCAGCATGTTAGCACGG 58.627 50.000 0.00 0.00 37.40 4.94
198 231 2.160219 ACAATGTCAGCATGTTAGCACG 59.840 45.455 0.00 0.00 37.40 5.34
199 232 3.058016 ACACAATGTCAGCATGTTAGCAC 60.058 43.478 0.00 0.00 37.40 4.40
200 233 3.058085 CACACAATGTCAGCATGTTAGCA 60.058 43.478 0.00 0.00 37.40 3.49
201 234 3.058016 ACACACAATGTCAGCATGTTAGC 60.058 43.478 0.00 0.00 36.54 3.09
202 235 4.754372 ACACACAATGTCAGCATGTTAG 57.246 40.909 0.00 0.00 36.54 2.34
214 247 1.202806 ACCTCCCACAGACACACAATG 60.203 52.381 0.00 0.00 0.00 2.82
215 248 1.140312 ACCTCCCACAGACACACAAT 58.860 50.000 0.00 0.00 0.00 2.71
216 249 0.916086 AACCTCCCACAGACACACAA 59.084 50.000 0.00 0.00 0.00 3.33
217 250 1.691976 CTAACCTCCCACAGACACACA 59.308 52.381 0.00 0.00 0.00 3.72
218 251 1.002087 CCTAACCTCCCACAGACACAC 59.998 57.143 0.00 0.00 0.00 3.82
219 252 1.132977 TCCTAACCTCCCACAGACACA 60.133 52.381 0.00 0.00 0.00 3.72
220 253 1.640917 TCCTAACCTCCCACAGACAC 58.359 55.000 0.00 0.00 0.00 3.67
221 254 2.642171 ATCCTAACCTCCCACAGACA 57.358 50.000 0.00 0.00 0.00 3.41
222 255 6.936968 ATATTATCCTAACCTCCCACAGAC 57.063 41.667 0.00 0.00 0.00 3.51
223 256 8.184249 ACATATATTATCCTAACCTCCCACAGA 58.816 37.037 0.00 0.00 0.00 3.41
224 257 8.380742 ACATATATTATCCTAACCTCCCACAG 57.619 38.462 0.00 0.00 0.00 3.66
227 260 8.934697 GCATACATATATTATCCTAACCTCCCA 58.065 37.037 0.00 0.00 0.00 4.37
228 261 8.088981 CGCATACATATATTATCCTAACCTCCC 58.911 40.741 0.00 0.00 0.00 4.30
229 262 8.857098 TCGCATACATATATTATCCTAACCTCC 58.143 37.037 0.00 0.00 0.00 4.30
246 279 8.998377 TGCTACAATATGTTAATTCGCATACAT 58.002 29.630 4.61 0.00 35.55 2.29
247 280 8.371770 TGCTACAATATGTTAATTCGCATACA 57.628 30.769 4.61 0.00 31.38 2.29
248 281 9.265938 CATGCTACAATATGTTAATTCGCATAC 57.734 33.333 0.00 0.00 33.58 2.39
249 282 9.213799 TCATGCTACAATATGTTAATTCGCATA 57.786 29.630 0.00 4.89 33.58 3.14
250 283 8.017373 GTCATGCTACAATATGTTAATTCGCAT 58.983 33.333 0.00 0.00 35.04 4.73
251 284 7.351981 GTCATGCTACAATATGTTAATTCGCA 58.648 34.615 0.00 0.00 0.00 5.10
252 285 6.797033 GGTCATGCTACAATATGTTAATTCGC 59.203 38.462 0.00 0.00 0.00 4.70
253 286 7.860613 TGGTCATGCTACAATATGTTAATTCG 58.139 34.615 0.00 0.00 0.00 3.34
254 287 8.840321 ACTGGTCATGCTACAATATGTTAATTC 58.160 33.333 0.00 0.00 0.00 2.17
285 318 1.276705 TCGTGGGGATCAAATCGTGAA 59.723 47.619 0.00 0.00 40.50 3.18
318 351 1.333115 CGACGCTTGATCGTGTACAA 58.667 50.000 0.00 0.00 43.42 2.41
344 377 8.522830 GCCGTATTGGTATTACTAATACTACCA 58.477 37.037 26.86 7.94 44.96 3.25
345 378 7.976175 GGCCGTATTGGTATTACTAATACTACC 59.024 40.741 26.86 24.10 44.96 3.18
346 379 7.976175 GGGCCGTATTGGTATTACTAATACTAC 59.024 40.741 26.86 21.18 44.96 2.73
347 380 7.148086 CGGGCCGTATTGGTATTACTAATACTA 60.148 40.741 26.86 9.18 44.96 1.82
348 381 6.350445 CGGGCCGTATTGGTATTACTAATACT 60.350 42.308 26.86 5.89 44.96 2.12
367 400 1.821061 AAGCCTATCTCATCGGGCCG 61.821 60.000 22.51 22.51 45.07 6.13
372 405 3.906014 TTCGAGAAGCCTATCTCATCG 57.094 47.619 11.09 0.00 44.98 3.84
377 410 6.640518 TGTTTATGTTTCGAGAAGCCTATCT 58.359 36.000 0.00 0.00 0.00 1.98
386 419 6.814644 ACGGATTGTATGTTTATGTTTCGAGA 59.185 34.615 0.00 0.00 0.00 4.04
404 437 6.318628 GTGCTCTATCTGATAGTACGGATTG 58.681 44.000 20.88 0.00 37.17 2.67
405 438 5.122554 CGTGCTCTATCTGATAGTACGGATT 59.877 44.000 25.57 0.00 37.17 3.01
406 439 4.632251 CGTGCTCTATCTGATAGTACGGAT 59.368 45.833 25.57 0.00 39.01 4.18
407 440 3.995048 CGTGCTCTATCTGATAGTACGGA 59.005 47.826 25.57 15.92 34.97 4.69
408 441 3.747010 ACGTGCTCTATCTGATAGTACGG 59.253 47.826 30.34 21.54 38.60 4.02
409 442 4.994220 ACGTGCTCTATCTGATAGTACG 57.006 45.455 28.24 28.24 39.32 3.67
410 443 6.017770 AGTCAACGTGCTCTATCTGATAGTAC 60.018 42.308 20.88 16.87 34.47 2.73
487 520 0.659427 ATGCATCCATCGCTTTCACG 59.341 50.000 0.00 0.00 0.00 4.35
584 623 2.028385 GGTGACATCCATATACCGACCC 60.028 54.545 0.00 0.00 0.00 4.46
612 704 2.851263 ACATTGTGTGTGATACCGGT 57.149 45.000 13.98 13.98 40.28 5.28
633 725 2.294233 TGGAATTCAGCACTTGTGCTTC 59.706 45.455 23.59 18.01 43.52 3.86
643 873 4.584874 TCTCCGTTAATTGGAATTCAGCA 58.415 39.130 7.93 0.00 34.44 4.41
657 887 0.669619 TGTTCACGTGCTCTCCGTTA 59.330 50.000 11.67 0.00 36.17 3.18
698 1220 2.172483 GACAGCCTCATCCACACCGT 62.172 60.000 0.00 0.00 0.00 4.83
712 1234 5.103000 ACTTAGTATGATCGTGTTGACAGC 58.897 41.667 0.00 0.00 0.00 4.40
727 1258 3.615496 CCGCTTTGTACGCAACTTAGTAT 59.385 43.478 0.00 0.00 33.82 2.12
757 1290 2.355756 TGCACTTCTGACTTTGACTTGC 59.644 45.455 0.00 0.00 0.00 4.01
773 1306 1.915614 GCTGCAAGTACGCATGCACT 61.916 55.000 19.57 11.83 46.87 4.40
774 1307 1.512734 GCTGCAAGTACGCATGCAC 60.513 57.895 19.57 9.42 46.87 4.57
810 1347 2.563620 AGAATGCACAATGTCATTGCCA 59.436 40.909 22.79 19.57 43.98 4.92
821 1372 2.143008 ACGTACGTGAGAATGCACAA 57.857 45.000 22.14 0.00 38.69 3.33
822 1373 3.877874 ACGTACGTGAGAATGCACA 57.122 47.368 22.14 0.00 38.69 4.57
945 1499 2.046217 GGGGAGTCTGCGGTTTCC 60.046 66.667 8.90 8.90 0.00 3.13
1011 1570 2.027625 GTTCCCGCTGTCCTCAACG 61.028 63.158 0.00 0.00 33.62 4.10
1014 1573 2.741092 GTGTTCCCGCTGTCCTCA 59.259 61.111 0.00 0.00 0.00 3.86
1086 1645 1.371267 CAACGAGACGGCGAACAGA 60.371 57.895 16.62 0.00 34.83 3.41
1102 1661 4.351938 CACGACGAGCCCCGACAA 62.352 66.667 0.00 0.00 41.76 3.18
1188 1747 2.282180 TCTTTGAACTGGGCGGGC 60.282 61.111 0.00 0.00 0.00 6.13
1231 1790 3.877508 AGAGACGTATGACATGACGATCA 59.122 43.478 18.16 0.00 41.60 2.92
1281 1843 0.029300 TATACGCACCGTTCCTACGC 59.971 55.000 0.00 0.00 46.27 4.42
1283 1845 5.280945 TGTTATTATACGCACCGTTCCTAC 58.719 41.667 0.00 0.00 41.54 3.18
1284 1846 5.512753 TGTTATTATACGCACCGTTCCTA 57.487 39.130 0.00 0.00 41.54 2.94
1285 1847 4.389890 TGTTATTATACGCACCGTTCCT 57.610 40.909 0.00 0.00 41.54 3.36
1288 1851 4.695396 TCCATGTTATTATACGCACCGTT 58.305 39.130 0.00 0.00 41.54 4.44
1296 1863 8.048534 AGCATCAGCAATCCATGTTATTATAC 57.951 34.615 0.00 0.00 45.49 1.47
1311 1878 2.094597 GGCACACAATAAGCATCAGCAA 60.095 45.455 0.00 0.00 45.49 3.91
1324 1891 0.249699 CACGTAGACAGGGCACACAA 60.250 55.000 0.00 0.00 0.00 3.33
1330 1897 0.250166 AAACCACACGTAGACAGGGC 60.250 55.000 0.00 0.00 0.00 5.19
1410 1978 0.608130 TGACATGGACTTGACCGAGG 59.392 55.000 0.00 0.00 0.00 4.63
1414 1982 2.079925 GAGCTTGACATGGACTTGACC 58.920 52.381 0.00 0.00 0.00 4.02
1483 2051 6.939132 AATCATTCAAGGCAGAAGATACTG 57.061 37.500 0.00 0.00 40.43 2.74
1494 2074 5.125100 TGTGAGAACAAATCATTCAAGGC 57.875 39.130 0.00 0.00 0.00 4.35
1505 2085 6.018262 GCAACTACAGTACATGTGAGAACAAA 60.018 38.462 9.11 0.00 43.80 2.83
1520 2100 1.301716 CCCTGCGTGCAACTACAGT 60.302 57.895 0.00 0.00 37.08 3.55
1522 2102 2.668212 GCCCTGCGTGCAACTACA 60.668 61.111 0.00 0.00 31.75 2.74
1523 2103 2.668212 TGCCCTGCGTGCAACTAC 60.668 61.111 0.00 0.00 35.40 2.73
1524 2104 2.668212 GTGCCCTGCGTGCAACTA 60.668 61.111 0.00 0.00 41.06 2.24
1538 2118 3.441572 AGGATTGTTACATCAAGCTGTGC 59.558 43.478 0.00 0.00 34.66 4.57
1859 2446 2.813179 GCCGACGGATGACATGCAC 61.813 63.158 20.50 0.00 0.00 4.57
1959 2546 3.323903 TACACGCACGCACACACG 61.324 61.111 0.00 0.00 39.50 4.49
1960 2547 1.827315 ATGTACACGCACGCACACAC 61.827 55.000 0.00 0.00 0.00 3.82
1961 2548 1.592939 ATGTACACGCACGCACACA 60.593 52.632 0.00 0.00 0.00 3.72
1962 2549 1.154672 CATGTACACGCACGCACAC 60.155 57.895 0.00 0.00 0.00 3.82
1963 2550 1.592939 ACATGTACACGCACGCACA 60.593 52.632 0.00 0.00 0.00 4.57
1964 2551 1.154672 CACATGTACACGCACGCAC 60.155 57.895 0.00 0.00 0.00 5.34
1965 2552 2.949030 GCACATGTACACGCACGCA 61.949 57.895 0.00 0.00 0.00 5.24
1966 2553 2.202171 GCACATGTACACGCACGC 60.202 61.111 0.00 0.00 0.00 5.34
1967 2554 2.093799 CGCACATGTACACGCACG 59.906 61.111 0.00 0.00 0.00 5.34
1968 2555 0.721155 CAACGCACATGTACACGCAC 60.721 55.000 13.21 0.00 0.00 5.34
1969 2556 0.876342 TCAACGCACATGTACACGCA 60.876 50.000 13.21 0.00 0.00 5.24
1970 2557 0.450482 GTCAACGCACATGTACACGC 60.450 55.000 13.21 0.10 0.00 5.34
1971 2558 0.179285 CGTCAACGCACATGTACACG 60.179 55.000 12.07 12.07 0.00 4.49
1972 2559 0.856641 ACGTCAACGCACATGTACAC 59.143 50.000 0.00 0.00 44.43 2.90
1976 2563 2.158841 GGATAAACGTCAACGCACATGT 59.841 45.455 1.81 0.00 44.43 3.21
1989 2576 7.911205 TGTTGTAGAAACAAACAAGGATAAACG 59.089 33.333 0.00 0.00 46.84 3.60
1994 2581 5.355910 ACGTGTTGTAGAAACAAACAAGGAT 59.644 36.000 0.00 0.00 46.84 3.24
1995 2582 4.696402 ACGTGTTGTAGAAACAAACAAGGA 59.304 37.500 0.00 0.00 46.84 3.36
1996 2583 4.976987 ACGTGTTGTAGAAACAAACAAGG 58.023 39.130 0.00 0.00 46.84 3.61
2051 2639 6.255453 CACAAAGGTTACAACAGTGATTTTGG 59.745 38.462 0.00 0.00 0.00 3.28
2061 2649 4.465886 ACTATGCCACAAAGGTTACAACA 58.534 39.130 0.00 0.00 40.61 3.33
2065 2653 5.182380 TGCTAAACTATGCCACAAAGGTTAC 59.818 40.000 0.00 0.00 40.61 2.50
2067 2655 4.148838 TGCTAAACTATGCCACAAAGGTT 58.851 39.130 0.00 0.00 40.61 3.50
2086 2674 8.592809 TCAAAACAGGGTTAATTAAATCATGCT 58.407 29.630 0.00 0.00 33.18 3.79
2095 2683 9.771534 CCATTTTTCTCAAAACAGGGTTAATTA 57.228 29.630 0.00 0.00 34.63 1.40
2096 2684 8.490311 TCCATTTTTCTCAAAACAGGGTTAATT 58.510 29.630 0.00 0.00 34.63 1.40
2098 2686 7.425224 TCCATTTTTCTCAAAACAGGGTTAA 57.575 32.000 0.00 0.00 34.63 2.01
2099 2687 7.610580 ATCCATTTTTCTCAAAACAGGGTTA 57.389 32.000 0.00 0.00 34.63 2.85
2100 2688 5.948742 TCCATTTTTCTCAAAACAGGGTT 57.051 34.783 0.00 0.00 34.63 4.11
2102 2690 8.773645 GTTAAATCCATTTTTCTCAAAACAGGG 58.226 33.333 0.00 0.00 34.63 4.45
2103 2691 8.773645 GGTTAAATCCATTTTTCTCAAAACAGG 58.226 33.333 0.00 0.00 34.63 4.00
2110 2698 8.835439 GCAAAAAGGTTAAATCCATTTTTCTCA 58.165 29.630 0.00 0.00 36.61 3.27
2111 2699 9.056005 AGCAAAAAGGTTAAATCCATTTTTCTC 57.944 29.630 0.00 0.00 36.61 2.87
2145 2733 3.119137 GGTACGTTAAATCCTACCACCGT 60.119 47.826 0.00 0.00 30.67 4.83
2149 2737 3.837146 TGGTGGTACGTTAAATCCTACCA 59.163 43.478 0.00 0.00 37.00 3.25
2174 2771 2.789409 AGGTTTCTGGTGCCATAGAC 57.211 50.000 0.00 0.00 0.00 2.59
2183 2780 1.538950 GACGACGACTAGGTTTCTGGT 59.461 52.381 0.00 0.00 37.42 4.00
2184 2781 1.538512 TGACGACGACTAGGTTTCTGG 59.461 52.381 0.00 0.00 0.00 3.86
2185 2782 2.582687 GTGACGACGACTAGGTTTCTG 58.417 52.381 0.00 0.00 0.00 3.02
2206 2803 3.818787 CCACTTGCCCGCATGAGC 61.819 66.667 9.33 0.00 37.42 4.26
2207 2804 0.676466 TAACCACTTGCCCGCATGAG 60.676 55.000 9.33 0.00 0.00 2.90
2208 2805 0.676466 CTAACCACTTGCCCGCATGA 60.676 55.000 9.33 0.00 0.00 3.07
2209 2806 1.802636 CTAACCACTTGCCCGCATG 59.197 57.895 1.34 1.34 0.00 4.06
2210 2807 2.046285 GCTAACCACTTGCCCGCAT 61.046 57.895 0.00 0.00 0.00 4.73
2212 2809 2.671619 TGCTAACCACTTGCCCGC 60.672 61.111 0.00 0.00 0.00 6.13
2213 2810 0.960364 ATGTGCTAACCACTTGCCCG 60.960 55.000 0.00 0.00 44.92 6.13
2216 2820 4.234574 GGTTTAATGTGCTAACCACTTGC 58.765 43.478 0.00 0.00 44.92 4.01
2224 2828 3.683281 CGGCCTAGGGTTTAATGTGCTAA 60.683 47.826 11.72 0.00 0.00 3.09
2258 2867 0.831307 CACTTACCCCCTCTAGGTGC 59.169 60.000 0.00 0.00 38.36 5.01
2264 2873 1.596496 CCCATTCACTTACCCCCTCT 58.404 55.000 0.00 0.00 0.00 3.69
2268 2877 2.666317 CATTCCCCATTCACTTACCCC 58.334 52.381 0.00 0.00 0.00 4.95
2276 2885 1.702840 CCCACCCATTCCCCATTCA 59.297 57.895 0.00 0.00 0.00 2.57
2279 2888 4.141876 CGCCCACCCATTCCCCAT 62.142 66.667 0.00 0.00 0.00 4.00
2285 2894 3.416880 CCCTACCGCCCACCCATT 61.417 66.667 0.00 0.00 0.00 3.16
2322 2936 5.456822 GCTAAATTTACTACCGTACCGTGAG 59.543 44.000 0.00 0.00 0.00 3.51
2323 2937 5.339990 GCTAAATTTACTACCGTACCGTGA 58.660 41.667 0.00 0.00 0.00 4.35
2324 2938 4.504097 GGCTAAATTTACTACCGTACCGTG 59.496 45.833 0.00 0.00 0.00 4.94
2325 2939 4.441495 GGGCTAAATTTACTACCGTACCGT 60.441 45.833 0.00 0.00 0.00 4.83
2331 2946 6.127563 ACCATTTTGGGCTAAATTTACTACCG 60.128 38.462 0.00 0.00 43.37 4.02
2336 2951 7.832769 TCAGTACCATTTTGGGCTAAATTTAC 58.167 34.615 0.00 2.63 43.37 2.01
2367 2982 1.373748 GCCTGCAGAAACGTACGGA 60.374 57.895 21.06 0.00 0.00 4.69
2368 2983 2.726691 CGCCTGCAGAAACGTACGG 61.727 63.158 21.06 1.82 0.00 4.02
2380 2995 0.392461 TTACATGTCCTTCCGCCTGC 60.392 55.000 0.00 0.00 0.00 4.85
2381 2996 1.369625 GTTACATGTCCTTCCGCCTG 58.630 55.000 0.00 0.00 0.00 4.85
2388 3003 1.072266 TGGCAGGGTTACATGTCCTT 58.928 50.000 0.00 0.00 0.00 3.36
2392 3007 0.480690 TTGGTGGCAGGGTTACATGT 59.519 50.000 2.69 2.69 0.00 3.21
2404 3019 1.909700 TCATCAAGGTTCTTGGTGGC 58.090 50.000 17.54 0.00 31.71 5.01
2405 3020 2.756760 CCATCATCAAGGTTCTTGGTGG 59.243 50.000 17.54 11.86 31.71 4.61
2407 3022 2.885554 GCCCATCATCAAGGTTCTTGGT 60.886 50.000 7.67 0.00 0.00 3.67
2411 3026 0.259938 GGGCCCATCATCAAGGTTCT 59.740 55.000 19.95 0.00 0.00 3.01
2415 3030 0.105862 ACATGGGCCCATCATCAAGG 60.106 55.000 35.42 23.04 33.90 3.61
2416 3031 2.158564 ACTACATGGGCCCATCATCAAG 60.159 50.000 35.42 25.62 33.90 3.02
2418 3033 1.421268 GACTACATGGGCCCATCATCA 59.579 52.381 35.42 17.86 33.90 3.07
2420 3035 1.143684 GTGACTACATGGGCCCATCAT 59.856 52.381 35.42 26.55 33.90 2.45
2421 3036 0.546122 GTGACTACATGGGCCCATCA 59.454 55.000 35.42 26.58 33.90 3.07
2423 3038 0.839946 GAGTGACTACATGGGCCCAT 59.160 55.000 32.75 32.75 37.08 4.00
2424 3039 1.271840 GGAGTGACTACATGGGCCCA 61.272 60.000 30.92 30.92 0.00 5.36
2425 3040 1.271840 TGGAGTGACTACATGGGCCC 61.272 60.000 17.59 17.59 0.00 5.80
2436 3051 3.055819 TGGTAAATGAGCTCTGGAGTGAC 60.056 47.826 16.19 0.00 0.00 3.67
2437 3052 3.173151 TGGTAAATGAGCTCTGGAGTGA 58.827 45.455 16.19 0.00 0.00 3.41
2461 3076 7.503521 TGAATGTTAATTGTGTGCTAGACAA 57.496 32.000 0.00 0.00 35.91 3.18
2464 3079 9.979578 AAATTTGAATGTTAATTGTGTGCTAGA 57.020 25.926 0.00 0.00 0.00 2.43
2490 3160 2.728007 TGGACAATTGTTGTGTGGTGA 58.272 42.857 13.36 0.00 45.52 4.02
2561 3259 4.967575 GTCCAACTTTGTATGTTGAACACG 59.032 41.667 0.00 0.00 45.27 4.49
2575 3273 4.710324 TCTATTTGGTCGTGTCCAACTTT 58.290 39.130 8.44 2.21 45.60 2.66
2581 3279 3.329929 ACCTTCTATTTGGTCGTGTCC 57.670 47.619 0.00 0.00 29.18 4.02
2582 3280 4.566987 AGAACCTTCTATTTGGTCGTGTC 58.433 43.478 0.00 0.00 35.34 3.67
2585 3283 4.884668 TGAGAACCTTCTATTTGGTCGT 57.115 40.909 0.00 0.00 37.73 4.34
2587 3285 8.794335 AGTATTTGAGAACCTTCTATTTGGTC 57.206 34.615 0.00 0.00 37.73 4.02
2645 3343 3.452627 GAGGATTGTCTAAGCAAGAGGGA 59.547 47.826 0.00 0.00 33.88 4.20
2661 3359 4.090761 TGCACAAAGAGAGTTGAGGATT 57.909 40.909 0.00 0.00 32.59 3.01
2668 3366 2.092429 TGAGGGTTGCACAAAGAGAGTT 60.092 45.455 0.00 0.00 0.00 3.01
2669 3367 1.490490 TGAGGGTTGCACAAAGAGAGT 59.510 47.619 0.00 0.00 0.00 3.24
2683 3381 2.536066 GGCCTAAAACCAAATGAGGGT 58.464 47.619 0.00 0.00 41.41 4.34
2684 3382 1.476488 CGGCCTAAAACCAAATGAGGG 59.524 52.381 0.00 0.00 0.00 4.30
2728 3426 2.160721 TCCTTAAGAGTCCATCGCCT 57.839 50.000 3.36 0.00 0.00 5.52
2740 3438 3.008485 GGGGCATGTAGAGGATCCTTAAG 59.992 52.174 17.42 4.58 33.66 1.85
2741 3439 2.979678 GGGGCATGTAGAGGATCCTTAA 59.020 50.000 17.42 4.11 33.66 1.85
2755 3453 2.755469 CCCAAACGAGGGGGCATG 60.755 66.667 4.72 0.00 45.60 4.06
2766 3474 2.554032 CACTCACTCAACCATCCCAAAC 59.446 50.000 0.00 0.00 0.00 2.93
2777 3485 3.007290 CAGATGGACCTTCACTCACTCAA 59.993 47.826 9.87 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.