Multiple sequence alignment - TraesCS2A01G018000

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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 TraesCS2A01G018000 chr2A 100.000 2944 0 0 1 2944 8542322 8545265 0.000000e+00 5437
1 TraesCS2A01G018000 chr2A 100.000 66 0 0 179 244 8542435 8542500 3.980000e-24 122
2 TraesCS2A01G018000 chr2A 100.000 66 0 0 114 179 8542500 8542565 3.980000e-24 122
3 TraesCS2A01G018000 chr2B 93.219 2389 106 26 591 2944 11838021 11835654 0.000000e+00 3463
4 TraesCS2A01G018000 chr2B 89.444 180 16 2 1 179 11838391 11838214 1.060000e-54 224
5 TraesCS2A01G018000 chr2B 93.056 144 9 1 448 591 784509195 784509337 2.970000e-50 209
6 TraesCS2A01G018000 chr2B 86.705 173 12 5 179 349 11838280 11838117 6.480000e-42 182
7 TraesCS2A01G018000 chr2D 94.589 1774 66 14 591 2345 9079341 9081103 0.000000e+00 2717
8 TraesCS2A01G018000 chr2D 93.513 632 17 10 2328 2944 9081117 9081739 0.000000e+00 918
9 TraesCS2A01G018000 chr2D 88.462 182 16 3 1 179 9078954 9079133 6.390000e-52 215
10 TraesCS2A01G018000 chr2D 94.245 139 8 0 445 583 622315647 622315785 2.300000e-51 213
11 TraesCS2A01G018000 chr2D 85.955 178 15 5 179 349 9079065 9079239 6.480000e-42 182
12 TraesCS2A01G018000 chr5D 88.021 192 23 0 1220 1411 322577507 322577698 8.210000e-56 228
13 TraesCS2A01G018000 chr5B 88.021 192 23 0 1220 1411 374191437 374191628 8.210000e-56 228
14 TraesCS2A01G018000 chr5B 94.326 141 6 2 443 583 660144573 660144711 6.390000e-52 215
15 TraesCS2A01G018000 chr3A 97.656 128 3 0 456 583 52198982 52198855 1.370000e-53 220
16 TraesCS2A01G018000 chrUn 94.928 138 7 0 447 584 108296183 108296320 1.780000e-52 217
17 TraesCS2A01G018000 chr3B 96.212 132 5 0 452 583 140988014 140987883 1.780000e-52 217
18 TraesCS2A01G018000 chr1D 96.241 133 4 1 452 583 178459643 178459511 1.780000e-52 217
19 TraesCS2A01G018000 chr1A 94.891 137 7 0 451 587 486045904 486045768 6.390000e-52 215
20 TraesCS2A01G018000 chr6D 93.662 142 8 1 456 596 119147666 119147807 8.270000e-51 211
21 TraesCS2A01G018000 chr4A 86.806 144 15 3 1245 1386 582840662 582840521 1.090000e-34 158
22 TraesCS2A01G018000 chr4D 86.713 143 15 3 1245 1385 18464582 18464722 3.930000e-34 156
23 TraesCS2A01G018000 chr4B 86.111 144 16 3 1245 1386 30362610 30362751 5.080000e-33 152


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 TraesCS2A01G018000 chr2A 8542322 8545265 2943 False 1893.666667 5437 100.000000 1 2944 3 chr2A.!!$F1 2943
1 TraesCS2A01G018000 chr2B 11835654 11838391 2737 True 1289.666667 3463 89.789333 1 2944 3 chr2B.!!$R1 2943
2 TraesCS2A01G018000 chr2D 9078954 9081739 2785 False 1008.000000 2717 90.629750 1 2944 4 chr2D.!!$F2 2943

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
470 477 0.033796 AATGTACTCCCTCCGTCCGA 60.034 55.0 0.0 0.0 0.0 4.55 F
583 590 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.0 0.0 0.0 0.0 2.73 F
587 594 0.106116 GGACGGAGGGAGTACTGGAT 60.106 60.0 0.0 0.0 0.0 3.41 F
1087 1103 0.108329 CCGAGATGTACCACCACCAC 60.108 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1809 0.108186 TAGAACGCACCCAGCATGAG 60.108 55.000 0.0 0.0 46.13 2.90 R
1848 1883 1.064758 AGCACTGGAAACACAGGACAA 60.065 47.619 0.0 0.0 42.75 3.18 R
1852 1887 2.254546 TGTAGCACTGGAAACACAGG 57.745 50.000 0.0 0.0 42.75 4.00 R
2729 2817 0.391263 AACGAAATGGAGAGACCGGC 60.391 55.000 0.0 0.0 42.61 6.13 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
30 31 5.992829 TGTGTACAAATACGTGACCATTCTT 59.007 36.000 0.00 0.00 33.60 2.52
32 33 7.329962 TGTGTACAAATACGTGACCATTCTTAG 59.670 37.037 0.00 0.00 33.60 2.18
47 48 5.964477 CCATTCTTAGATGGGTATAGGCCTA 59.036 44.000 16.60 16.60 42.36 3.93
48 49 6.127026 CCATTCTTAGATGGGTATAGGCCTAC 60.127 46.154 16.61 5.74 42.36 3.18
90 91 2.739292 CAGTAGTAACTGCACACACGT 58.261 47.619 0.00 0.00 46.28 4.49
96 97 4.982999 AGTAACTGCACACACGTATAGAG 58.017 43.478 0.00 0.00 0.00 2.43
116 117 4.036027 AGAGATTTGCCTCACAATAATGCG 59.964 41.667 0.00 0.00 38.31 4.73
162 165 1.338484 CCAGCAGAAGCAGACAAGCTA 60.338 52.381 0.00 0.00 45.89 3.32
171 174 2.165437 AGCAGACAAGCTAGCTAGACAC 59.835 50.000 25.15 6.84 44.50 3.67
172 175 2.737039 GCAGACAAGCTAGCTAGACACC 60.737 54.545 25.15 6.46 0.00 4.16
173 176 2.757868 CAGACAAGCTAGCTAGACACCT 59.242 50.000 25.15 8.82 0.00 4.00
174 177 3.194542 CAGACAAGCTAGCTAGACACCTT 59.805 47.826 25.15 14.32 0.00 3.50
175 178 4.399618 CAGACAAGCTAGCTAGACACCTTA 59.600 45.833 25.15 0.00 0.00 2.69
176 179 4.399934 AGACAAGCTAGCTAGACACCTTAC 59.600 45.833 25.15 13.52 0.00 2.34
177 180 3.447944 ACAAGCTAGCTAGACACCTTACC 59.552 47.826 25.15 3.08 0.00 2.85
178 181 3.673543 AGCTAGCTAGACACCTTACCT 57.326 47.619 25.15 5.47 0.00 3.08
179 182 3.292460 AGCTAGCTAGACACCTTACCTG 58.708 50.000 25.15 0.00 0.00 4.00
180 183 2.223852 GCTAGCTAGACACCTTACCTGC 60.224 54.545 25.15 0.75 0.00 4.85
181 184 0.818296 AGCTAGACACCTTACCTGCG 59.182 55.000 0.00 0.00 0.00 5.18
182 185 0.531200 GCTAGACACCTTACCTGCGT 59.469 55.000 0.00 0.00 0.00 5.24
183 186 1.067071 GCTAGACACCTTACCTGCGTT 60.067 52.381 0.00 0.00 0.00 4.84
184 187 2.877335 CTAGACACCTTACCTGCGTTC 58.123 52.381 0.00 0.00 0.00 3.95
185 188 1.045407 AGACACCTTACCTGCGTTCA 58.955 50.000 0.00 0.00 0.00 3.18
186 189 1.623811 AGACACCTTACCTGCGTTCAT 59.376 47.619 0.00 0.00 0.00 2.57
187 190 2.000447 GACACCTTACCTGCGTTCATC 59.000 52.381 0.00 0.00 0.00 2.92
188 191 1.346395 ACACCTTACCTGCGTTCATCA 59.654 47.619 0.00 0.00 0.00 3.07
189 192 2.027192 ACACCTTACCTGCGTTCATCAT 60.027 45.455 0.00 0.00 0.00 2.45
190 193 3.009723 CACCTTACCTGCGTTCATCATT 58.990 45.455 0.00 0.00 0.00 2.57
191 194 3.063997 CACCTTACCTGCGTTCATCATTC 59.936 47.826 0.00 0.00 0.00 2.67
192 195 2.285220 CCTTACCTGCGTTCATCATTCG 59.715 50.000 0.00 0.00 0.00 3.34
196 199 3.496711 GCGTTCATCATTCGCCCA 58.503 55.556 0.00 0.00 43.41 5.36
197 200 1.062525 GCGTTCATCATTCGCCCAC 59.937 57.895 0.00 0.00 43.41 4.61
198 201 1.643868 GCGTTCATCATTCGCCCACA 61.644 55.000 0.00 0.00 43.41 4.17
199 202 0.096976 CGTTCATCATTCGCCCACAC 59.903 55.000 0.00 0.00 0.00 3.82
200 203 1.164411 GTTCATCATTCGCCCACACA 58.836 50.000 0.00 0.00 0.00 3.72
201 204 1.135689 GTTCATCATTCGCCCACACAC 60.136 52.381 0.00 0.00 0.00 3.82
202 205 0.036022 TCATCATTCGCCCACACACA 59.964 50.000 0.00 0.00 0.00 3.72
203 206 0.168788 CATCATTCGCCCACACACAC 59.831 55.000 0.00 0.00 0.00 3.82
204 207 0.960364 ATCATTCGCCCACACACACC 60.960 55.000 0.00 0.00 0.00 4.16
205 208 2.282180 ATTCGCCCACACACACCC 60.282 61.111 0.00 0.00 0.00 4.61
206 209 3.126703 ATTCGCCCACACACACCCA 62.127 57.895 0.00 0.00 0.00 4.51
207 210 4.555709 TCGCCCACACACACCCAC 62.556 66.667 0.00 0.00 0.00 4.61
209 212 4.514585 GCCCACACACACCCACCA 62.515 66.667 0.00 0.00 0.00 4.17
210 213 2.203337 CCCACACACACCCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
211 214 2.906897 CCACACACACCCACCAGC 60.907 66.667 0.00 0.00 0.00 4.85
212 215 2.124362 CACACACACCCACCAGCA 60.124 61.111 0.00 0.00 0.00 4.41
213 216 2.188829 CACACACACCCACCAGCAG 61.189 63.158 0.00 0.00 0.00 4.24
214 217 2.374525 ACACACACCCACCAGCAGA 61.375 57.895 0.00 0.00 0.00 4.26
215 218 1.152984 CACACACCCACCAGCAGAA 60.153 57.895 0.00 0.00 0.00 3.02
216 219 1.149174 ACACACCCACCAGCAGAAG 59.851 57.895 0.00 0.00 0.00 2.85
217 220 2.113986 ACACCCACCAGCAGAAGC 59.886 61.111 0.00 0.00 42.56 3.86
218 221 2.113774 CACCCACCAGCAGAAGCA 59.886 61.111 0.00 0.00 45.49 3.91
219 222 1.970114 CACCCACCAGCAGAAGCAG 60.970 63.158 0.00 0.00 45.49 4.24
220 223 2.149383 ACCCACCAGCAGAAGCAGA 61.149 57.895 0.00 0.00 45.49 4.26
221 224 1.673665 CCCACCAGCAGAAGCAGAC 60.674 63.158 0.00 0.00 45.49 3.51
222 225 1.071987 CCACCAGCAGAAGCAGACA 59.928 57.895 0.00 0.00 45.49 3.41
223 226 0.535780 CCACCAGCAGAAGCAGACAA 60.536 55.000 0.00 0.00 45.49 3.18
224 227 0.873054 CACCAGCAGAAGCAGACAAG 59.127 55.000 0.00 0.00 45.49 3.16
225 228 0.888285 ACCAGCAGAAGCAGACAAGC 60.888 55.000 0.00 0.00 45.49 4.01
227 230 1.338484 CCAGCAGAAGCAGACAAGCTA 60.338 52.381 0.00 0.00 45.89 3.32
228 231 2.001159 CAGCAGAAGCAGACAAGCTAG 58.999 52.381 0.00 0.00 45.89 3.42
229 232 0.726256 GCAGAAGCAGACAAGCTAGC 59.274 55.000 6.62 6.62 45.89 3.42
230 233 1.675415 GCAGAAGCAGACAAGCTAGCT 60.675 52.381 12.68 12.68 45.89 3.32
231 234 2.417924 GCAGAAGCAGACAAGCTAGCTA 60.418 50.000 19.70 0.00 45.89 3.32
232 235 3.446799 CAGAAGCAGACAAGCTAGCTAG 58.553 50.000 19.70 16.84 45.89 3.42
233 236 3.130164 CAGAAGCAGACAAGCTAGCTAGA 59.870 47.826 25.15 0.00 45.89 2.43
234 237 3.130340 AGAAGCAGACAAGCTAGCTAGAC 59.870 47.826 25.15 15.03 45.89 2.59
235 238 2.451490 AGCAGACAAGCTAGCTAGACA 58.549 47.619 25.15 0.00 44.50 3.41
257 260 0.490017 TTACCTCTCCTGACCCCACA 59.510 55.000 0.00 0.00 0.00 4.17
265 268 1.676635 CTGACCCCACATGCCAGTG 60.677 63.158 0.00 0.00 39.21 3.66
285 291 5.682862 CAGTGCACATTAACAGTTTTGAGAC 59.317 40.000 21.04 0.00 0.00 3.36
293 299 7.819900 ACATTAACAGTTTTGAGACCTAGCTAG 59.180 37.037 14.20 14.20 0.00 3.42
294 300 4.195225 ACAGTTTTGAGACCTAGCTAGC 57.805 45.455 15.74 6.62 0.00 3.42
296 302 3.055819 CAGTTTTGAGACCTAGCTAGCCA 60.056 47.826 15.74 7.18 0.00 4.75
297 303 3.196685 AGTTTTGAGACCTAGCTAGCCAG 59.803 47.826 15.74 7.24 0.00 4.85
313 319 3.813443 AGCCAGCTACTACATCAAATGG 58.187 45.455 0.00 0.00 33.60 3.16
336 342 1.838112 TGCCATCCAACCATGAAGAC 58.162 50.000 0.00 0.00 0.00 3.01
339 345 2.618816 GCCATCCAACCATGAAGACAGA 60.619 50.000 0.00 0.00 0.00 3.41
342 348 1.003580 TCCAACCATGAAGACAGAGCC 59.996 52.381 0.00 0.00 0.00 4.70
345 351 1.220206 CCATGAAGACAGAGCCGCT 59.780 57.895 0.00 0.00 0.00 5.52
349 355 2.359230 AAGACAGAGCCGCTTGCC 60.359 61.111 0.00 0.00 42.71 4.52
350 356 2.794820 GAAGACAGAGCCGCTTGCCT 62.795 60.000 0.00 0.00 42.71 4.75
351 357 3.123620 GACAGAGCCGCTTGCCTG 61.124 66.667 6.12 6.12 42.71 4.85
359 365 3.800863 CGCTTGCCTGCAGAGCTG 61.801 66.667 17.39 14.08 34.33 4.24
386 392 3.116079 CCAGCACAGGCAAAAAGAAAT 57.884 42.857 0.00 0.00 44.61 2.17
392 398 7.387397 CCAGCACAGGCAAAAAGAAATAAATTA 59.613 33.333 0.00 0.00 44.61 1.40
445 452 4.771114 AATGCAAGCTGGGTATAGTACA 57.229 40.909 0.00 0.00 0.00 2.90
447 454 3.104512 TGCAAGCTGGGTATAGTACACT 58.895 45.455 0.00 0.00 31.94 3.55
464 471 2.290323 ACACTTGCAATGTACTCCCTCC 60.290 50.000 0.00 0.00 0.00 4.30
465 472 1.066143 ACTTGCAATGTACTCCCTCCG 60.066 52.381 0.00 0.00 0.00 4.63
466 473 0.981183 TTGCAATGTACTCCCTCCGT 59.019 50.000 0.00 0.00 0.00 4.69
467 474 0.535335 TGCAATGTACTCCCTCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
468 475 0.179081 GCAATGTACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
469 476 0.102481 CAATGTACTCCCTCCGTCCG 59.898 60.000 0.00 0.00 0.00 4.79
470 477 0.033796 AATGTACTCCCTCCGTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
472 479 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
473 480 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
475 482 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
476 483 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
477 484 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
478 485 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
479 486 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
480 487 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
481 488 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
482 489 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
483 490 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
484 491 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
485 492 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
486 493 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
487 494 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
488 495 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
489 496 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
490 497 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
491 498 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
492 499 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
493 500 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
501 508 9.439500 ACTTGTCATCAAAATGGATAAAAATGG 57.561 29.630 0.00 0.00 33.42 3.16
502 509 9.656040 CTTGTCATCAAAATGGATAAAAATGGA 57.344 29.630 0.00 0.00 33.42 3.41
504 511 9.602568 TGTCATCAAAATGGATAAAAATGGATG 57.397 29.630 0.00 0.00 33.42 3.51
505 512 9.603921 GTCATCAAAATGGATAAAAATGGATGT 57.396 29.630 0.00 0.00 33.42 3.06
547 554 9.607333 ACATCTAGATACATCTCCTTTTATCCA 57.393 33.333 4.54 0.00 38.32 3.41
569 576 9.801873 ATCCATTTTAATGACAAGTATTTTCGG 57.198 29.630 4.07 0.00 38.70 4.30
570 577 9.015367 TCCATTTTAATGACAAGTATTTTCGGA 57.985 29.630 4.07 0.00 38.70 4.55
571 578 9.072294 CCATTTTAATGACAAGTATTTTCGGAC 57.928 33.333 4.07 0.00 38.70 4.79
572 579 8.785101 CATTTTAATGACAAGTATTTTCGGACG 58.215 33.333 0.00 0.00 38.70 4.79
573 580 4.939509 AATGACAAGTATTTTCGGACGG 57.060 40.909 0.00 0.00 0.00 4.79
574 581 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
575 582 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
576 583 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
577 584 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
578 585 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
579 586 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
580 587 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
581 588 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
582 589 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
583 590 0.038744 TTTCGGACGGAGGGAGTACT 59.961 55.000 0.00 0.00 0.00 2.73
584 591 0.679002 TTCGGACGGAGGGAGTACTG 60.679 60.000 0.00 0.00 0.00 2.74
585 592 2.119655 CGGACGGAGGGAGTACTGG 61.120 68.421 0.00 0.00 0.00 4.00
586 593 1.305623 GGACGGAGGGAGTACTGGA 59.694 63.158 0.00 0.00 0.00 3.86
587 594 0.106116 GGACGGAGGGAGTACTGGAT 60.106 60.000 0.00 0.00 0.00 3.41
588 595 1.144503 GGACGGAGGGAGTACTGGATA 59.855 57.143 0.00 0.00 0.00 2.59
589 596 2.228925 GACGGAGGGAGTACTGGATAC 58.771 57.143 0.00 0.00 0.00 2.24
621 628 6.240002 CCATATCTTAATACTCAAGTGGGCCT 60.240 42.308 4.53 0.00 0.00 5.19
630 637 0.607489 CAAGTGGGCCTGAAGGAGTG 60.607 60.000 4.53 0.00 37.39 3.51
652 659 2.672098 CCTATCTAGATGCCGGCCTAT 58.328 52.381 26.77 15.00 0.00 2.57
654 661 3.570550 CCTATCTAGATGCCGGCCTATAC 59.429 52.174 26.77 10.56 0.00 1.47
655 662 1.848652 TCTAGATGCCGGCCTATACC 58.151 55.000 26.77 6.34 0.00 2.73
803 817 7.721286 AGAAGTAAGATTTAGATCCGCATTG 57.279 36.000 0.00 0.00 32.44 2.82
818 832 3.046390 CGCATTGACACTAGCTAGTAGC 58.954 50.000 25.63 19.45 42.84 3.58
831 845 1.389609 TAGTAGCGCAGGCCACTACC 61.390 60.000 11.47 0.00 39.42 3.18
835 849 2.662596 CGCAGGCCACTACCAGAA 59.337 61.111 5.01 0.00 0.00 3.02
842 856 0.250513 GCCACTACCAGAACAGGGAG 59.749 60.000 0.00 0.00 45.75 4.30
872 886 3.383223 TGTCCATCCACTGATCCACATA 58.617 45.455 0.00 0.00 0.00 2.29
882 896 5.065218 CCACTGATCCACATAAGTTTACTGC 59.935 44.000 0.00 0.00 0.00 4.40
886 900 5.123820 TGATCCACATAAGTTTACTGCTTGC 59.876 40.000 0.00 0.00 0.00 4.01
988 1002 2.764637 ATCCCACCAAGAACCGCCAC 62.765 60.000 0.00 0.00 0.00 5.01
1030 1046 2.827190 CGCCACATGCATCCAGCT 60.827 61.111 0.00 0.00 45.94 4.24
1031 1047 2.831366 CGCCACATGCATCCAGCTC 61.831 63.158 0.00 0.00 45.94 4.09
1085 1101 1.153429 GCCGAGATGTACCACCACC 60.153 63.158 0.00 0.00 0.00 4.61
1086 1102 1.895020 GCCGAGATGTACCACCACCA 61.895 60.000 0.00 0.00 0.00 4.17
1087 1103 0.108329 CCGAGATGTACCACCACCAC 60.108 60.000 0.00 0.00 0.00 4.16
1095 1111 4.584518 CCACCACCACCAGCAGCA 62.585 66.667 0.00 0.00 0.00 4.41
1418 1440 4.776322 CCATCGACCGGCTTGCCA 62.776 66.667 12.45 0.00 0.00 4.92
1465 1487 2.250939 CGCTGCAGGACCGTTGAAA 61.251 57.895 17.12 0.00 0.00 2.69
1645 1667 7.141758 AGGATTGGACTAATTAATGAGAGCA 57.858 36.000 6.84 0.00 0.00 4.26
1742 1774 6.343716 TGATATGCAAACTTTGTGTCCAAT 57.656 33.333 3.48 0.00 0.00 3.16
1758 1791 6.891361 TGTGTCCAATGGTGAGATTAATTGAT 59.109 34.615 0.00 0.00 32.86 2.57
1789 1822 0.666913 CTTATGCTCATGCTGGGTGC 59.333 55.000 0.00 0.00 40.48 5.01
1794 1827 1.376424 CTCATGCTGGGTGCGTTCT 60.376 57.895 0.00 0.00 46.63 3.01
1805 1838 3.754323 TGGGTGCGTTCTACTAATTTTGG 59.246 43.478 0.00 0.00 0.00 3.28
1848 1883 5.241728 GTGCTAATTTTGAGGTTCTTGGAGT 59.758 40.000 0.00 0.00 0.00 3.85
1852 1887 5.774498 ATTTTGAGGTTCTTGGAGTTGTC 57.226 39.130 0.00 0.00 0.00 3.18
1997 2034 7.382218 AGTGCAAACTAAATGTACTCAATTTGC 59.618 33.333 17.89 17.89 46.76 3.68
2011 2048 9.045223 GTACTCAATTTGCTCACATCACATATA 57.955 33.333 0.00 0.00 0.00 0.86
2147 2189 3.584733 AAGCAGGTTTCAGGTCTTCTT 57.415 42.857 0.00 0.00 0.00 2.52
2190 2232 5.756195 TTCTTATCAAATTCGGATGGCAG 57.244 39.130 0.00 0.00 0.00 4.85
2368 2445 4.920340 CCTGTATCGCATGTATCTGAGAAC 59.080 45.833 0.00 0.00 0.00 3.01
2563 2651 5.894298 AAGTATTCTCTGGATGTATGGCA 57.106 39.130 0.00 0.00 0.00 4.92
2729 2817 5.412640 TCATTAAATGCTTCATGTGCCTTG 58.587 37.500 10.03 0.00 0.00 3.61
2730 2818 2.088950 AAATGCTTCATGTGCCTTGC 57.911 45.000 10.03 0.00 0.00 4.01
2731 2819 0.248289 AATGCTTCATGTGCCTTGCC 59.752 50.000 10.03 0.00 0.00 4.52
2732 2820 1.940883 ATGCTTCATGTGCCTTGCCG 61.941 55.000 10.03 0.00 0.00 5.69
2818 2909 5.777802 ACTGACTTGAGTAGTGAGATGTTG 58.222 41.667 0.00 0.00 40.17 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.702329 CCTATACCCATCTAAGAATGGTCAC 58.298 44.000 2.49 0.00 44.05 3.67
30 31 3.709587 GCTGTAGGCCTATACCCATCTA 58.290 50.000 17.38 0.00 34.27 1.98
47 48 1.002868 GACATGTGCTGAGGGCTGT 60.003 57.895 1.15 0.00 42.39 4.40
48 49 1.748122 GGACATGTGCTGAGGGCTG 60.748 63.158 10.51 0.00 42.39 4.85
52 53 0.904649 TGTAGGGACATGTGCTGAGG 59.095 55.000 17.44 0.00 0.00 3.86
55 56 2.497675 ACTACTGTAGGGACATGTGCTG 59.502 50.000 17.44 5.51 34.24 4.41
56 57 2.821437 ACTACTGTAGGGACATGTGCT 58.179 47.619 17.44 5.98 34.24 4.40
59 60 5.916661 CAGTTACTACTGTAGGGACATGT 57.083 43.478 18.38 0.00 45.46 3.21
89 90 8.233190 GCATTATTGTGAGGCAAATCTCTATAC 58.767 37.037 0.00 0.00 40.91 1.47
90 91 7.118245 CGCATTATTGTGAGGCAAATCTCTATA 59.882 37.037 0.00 0.00 40.91 1.31
96 97 4.032703 ACGCATTATTGTGAGGCAAATC 57.967 40.909 5.23 0.00 40.91 2.17
116 117 1.135689 GTGTGTGGGCGAATGATGAAC 60.136 52.381 0.00 0.00 0.00 3.18
162 165 0.818296 CGCAGGTAAGGTGTCTAGCT 59.182 55.000 0.00 0.00 35.86 3.32
171 174 2.285220 CGAATGATGAACGCAGGTAAGG 59.715 50.000 0.00 0.00 0.00 2.69
172 175 3.575858 CGAATGATGAACGCAGGTAAG 57.424 47.619 0.00 0.00 0.00 2.34
180 183 0.096976 GTGTGGGCGAATGATGAACG 59.903 55.000 0.00 0.00 0.00 3.95
181 184 1.135689 GTGTGTGGGCGAATGATGAAC 60.136 52.381 0.00 0.00 0.00 3.18
182 185 1.164411 GTGTGTGGGCGAATGATGAA 58.836 50.000 0.00 0.00 0.00 2.57
183 186 0.036022 TGTGTGTGGGCGAATGATGA 59.964 50.000 0.00 0.00 0.00 2.92
184 187 0.168788 GTGTGTGTGGGCGAATGATG 59.831 55.000 0.00 0.00 0.00 3.07
185 188 0.960364 GGTGTGTGTGGGCGAATGAT 60.960 55.000 0.00 0.00 0.00 2.45
186 189 1.599518 GGTGTGTGTGGGCGAATGA 60.600 57.895 0.00 0.00 0.00 2.57
187 190 2.625823 GGGTGTGTGTGGGCGAATG 61.626 63.158 0.00 0.00 0.00 2.67
188 191 2.282180 GGGTGTGTGTGGGCGAAT 60.282 61.111 0.00 0.00 0.00 3.34
189 192 3.798511 TGGGTGTGTGTGGGCGAA 61.799 61.111 0.00 0.00 0.00 4.70
190 193 4.555709 GTGGGTGTGTGTGGGCGA 62.556 66.667 0.00 0.00 0.00 5.54
192 195 4.514585 TGGTGGGTGTGTGTGGGC 62.515 66.667 0.00 0.00 0.00 5.36
193 196 2.203337 CTGGTGGGTGTGTGTGGG 60.203 66.667 0.00 0.00 0.00 4.61
194 197 2.906897 GCTGGTGGGTGTGTGTGG 60.907 66.667 0.00 0.00 0.00 4.17
195 198 2.124362 TGCTGGTGGGTGTGTGTG 60.124 61.111 0.00 0.00 0.00 3.82
196 199 1.920734 TTCTGCTGGTGGGTGTGTGT 61.921 55.000 0.00 0.00 0.00 3.72
197 200 1.152984 TTCTGCTGGTGGGTGTGTG 60.153 57.895 0.00 0.00 0.00 3.82
198 201 1.149174 CTTCTGCTGGTGGGTGTGT 59.851 57.895 0.00 0.00 0.00 3.72
199 202 2.263741 GCTTCTGCTGGTGGGTGTG 61.264 63.158 0.00 0.00 36.03 3.82
200 203 2.113986 GCTTCTGCTGGTGGGTGT 59.886 61.111 0.00 0.00 36.03 4.16
201 204 1.970114 CTGCTTCTGCTGGTGGGTG 60.970 63.158 0.00 0.00 40.48 4.61
202 205 2.149383 TCTGCTTCTGCTGGTGGGT 61.149 57.895 0.00 0.00 40.48 4.51
203 206 1.673665 GTCTGCTTCTGCTGGTGGG 60.674 63.158 0.00 0.00 40.48 4.61
204 207 0.535780 TTGTCTGCTTCTGCTGGTGG 60.536 55.000 0.00 0.00 40.48 4.61
205 208 0.873054 CTTGTCTGCTTCTGCTGGTG 59.127 55.000 0.00 0.00 40.48 4.17
206 209 0.888285 GCTTGTCTGCTTCTGCTGGT 60.888 55.000 0.00 0.00 40.48 4.00
207 210 0.605860 AGCTTGTCTGCTTCTGCTGG 60.606 55.000 0.00 0.00 40.93 4.85
208 211 2.001159 CTAGCTTGTCTGCTTCTGCTG 58.999 52.381 0.00 0.00 43.74 4.41
209 212 1.675415 GCTAGCTTGTCTGCTTCTGCT 60.675 52.381 7.70 0.00 43.74 4.24
210 213 0.726256 GCTAGCTTGTCTGCTTCTGC 59.274 55.000 7.70 0.00 43.74 4.26
211 214 2.383368 AGCTAGCTTGTCTGCTTCTG 57.617 50.000 12.68 0.00 43.74 3.02
212 215 3.130340 GTCTAGCTAGCTTGTCTGCTTCT 59.870 47.826 24.88 0.00 43.74 2.85
213 216 3.119316 TGTCTAGCTAGCTTGTCTGCTTC 60.119 47.826 24.88 7.72 43.74 3.86
214 217 2.828520 TGTCTAGCTAGCTTGTCTGCTT 59.171 45.455 24.88 0.00 43.74 3.91
215 218 2.165437 GTGTCTAGCTAGCTTGTCTGCT 59.835 50.000 24.88 0.00 46.11 4.24
216 219 2.535331 GTGTCTAGCTAGCTTGTCTGC 58.465 52.381 24.88 11.66 0.00 4.26
217 220 2.757868 AGGTGTCTAGCTAGCTTGTCTG 59.242 50.000 24.88 8.60 31.69 3.51
218 221 3.094484 AGGTGTCTAGCTAGCTTGTCT 57.906 47.619 24.88 13.79 31.69 3.41
219 222 3.878160 AAGGTGTCTAGCTAGCTTGTC 57.122 47.619 24.88 18.67 33.76 3.18
220 223 3.447944 GGTAAGGTGTCTAGCTAGCTTGT 59.552 47.826 24.88 6.26 36.23 3.16
221 224 3.702045 AGGTAAGGTGTCTAGCTAGCTTG 59.298 47.826 24.88 21.44 36.23 4.01
222 225 3.955551 GAGGTAAGGTGTCTAGCTAGCTT 59.044 47.826 24.88 14.73 38.15 3.74
223 226 3.203487 AGAGGTAAGGTGTCTAGCTAGCT 59.797 47.826 23.12 23.12 33.49 3.32
224 227 3.558033 AGAGGTAAGGTGTCTAGCTAGC 58.442 50.000 16.35 6.62 33.49 3.42
225 228 4.139038 GGAGAGGTAAGGTGTCTAGCTAG 58.861 52.174 15.01 15.01 33.49 3.42
226 229 3.787013 AGGAGAGGTAAGGTGTCTAGCTA 59.213 47.826 0.00 0.00 33.49 3.32
227 230 2.583566 AGGAGAGGTAAGGTGTCTAGCT 59.416 50.000 0.00 0.00 35.86 3.32
228 231 2.691011 CAGGAGAGGTAAGGTGTCTAGC 59.309 54.545 0.00 0.00 0.00 3.42
229 232 3.949113 GTCAGGAGAGGTAAGGTGTCTAG 59.051 52.174 0.00 0.00 0.00 2.43
230 233 3.308976 GGTCAGGAGAGGTAAGGTGTCTA 60.309 52.174 0.00 0.00 0.00 2.59
231 234 2.557901 GGTCAGGAGAGGTAAGGTGTCT 60.558 54.545 0.00 0.00 0.00 3.41
232 235 1.826096 GGTCAGGAGAGGTAAGGTGTC 59.174 57.143 0.00 0.00 0.00 3.67
233 236 1.552719 GGGTCAGGAGAGGTAAGGTGT 60.553 57.143 0.00 0.00 0.00 4.16
234 237 1.196012 GGGTCAGGAGAGGTAAGGTG 58.804 60.000 0.00 0.00 0.00 4.00
235 238 0.042881 GGGGTCAGGAGAGGTAAGGT 59.957 60.000 0.00 0.00 0.00 3.50
265 268 5.438761 AGGTCTCAAAACTGTTAATGTGC 57.561 39.130 0.00 0.00 0.00 4.57
293 299 2.291741 GCCATTTGATGTAGTAGCTGGC 59.708 50.000 0.00 0.00 40.89 4.85
294 300 3.544684 TGCCATTTGATGTAGTAGCTGG 58.455 45.455 0.00 0.00 0.00 4.85
296 302 4.037208 GCAATGCCATTTGATGTAGTAGCT 59.963 41.667 0.00 0.00 0.00 3.32
297 303 4.293415 GCAATGCCATTTGATGTAGTAGC 58.707 43.478 0.00 0.00 0.00 3.58
313 319 0.825410 TCATGGTTGGATGGCAATGC 59.175 50.000 0.00 0.00 0.00 3.56
325 331 0.674895 GCGGCTCTGTCTTCATGGTT 60.675 55.000 0.00 0.00 0.00 3.67
326 332 1.078848 GCGGCTCTGTCTTCATGGT 60.079 57.895 0.00 0.00 0.00 3.55
342 348 3.800863 CAGCTCTGCAGGCAAGCG 61.801 66.667 23.46 13.72 40.95 4.68
366 372 2.600470 TTTCTTTTTGCCTGTGCTGG 57.400 45.000 0.00 0.00 38.71 4.85
367 373 6.790285 ATTTATTTCTTTTTGCCTGTGCTG 57.210 33.333 0.00 0.00 38.71 4.41
368 374 8.150296 AGTAATTTATTTCTTTTTGCCTGTGCT 58.850 29.630 0.00 0.00 38.71 4.40
369 375 8.310406 AGTAATTTATTTCTTTTTGCCTGTGC 57.690 30.769 0.00 0.00 38.26 4.57
431 437 3.536956 TGCAAGTGTACTATACCCAGC 57.463 47.619 0.00 0.00 0.00 4.85
434 440 6.839820 GTACATTGCAAGTGTACTATACCC 57.160 41.667 27.15 12.25 45.24 3.69
445 452 1.066143 CGGAGGGAGTACATTGCAAGT 60.066 52.381 4.94 6.05 0.00 3.16
447 454 0.981183 ACGGAGGGAGTACATTGCAA 59.019 50.000 0.00 0.00 0.00 4.08
459 466 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
460 467 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
464 471 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
465 472 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
466 473 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
467 474 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
468 475 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
475 482 9.439500 CCATTTTTATCCATTTTGATGACAAGT 57.561 29.630 0.00 0.00 37.32 3.16
476 483 9.656040 TCCATTTTTATCCATTTTGATGACAAG 57.344 29.630 0.00 0.00 37.32 3.16
478 485 9.602568 CATCCATTTTTATCCATTTTGATGACA 57.397 29.630 0.00 0.00 0.00 3.58
479 486 9.603921 ACATCCATTTTTATCCATTTTGATGAC 57.396 29.630 0.00 0.00 32.39 3.06
521 528 9.607333 TGGATAAAAGGAGATGTATCTAGATGT 57.393 33.333 15.79 1.25 37.25 3.06
543 550 9.801873 CCGAAAATACTTGTCATTAAAATGGAT 57.198 29.630 3.00 0.00 37.03 3.41
544 551 9.015367 TCCGAAAATACTTGTCATTAAAATGGA 57.985 29.630 3.00 0.00 37.03 3.41
545 552 9.072294 GTCCGAAAATACTTGTCATTAAAATGG 57.928 33.333 3.00 0.00 37.03 3.16
546 553 8.785101 CGTCCGAAAATACTTGTCATTAAAATG 58.215 33.333 0.00 0.00 37.75 2.32
547 554 7.966204 CCGTCCGAAAATACTTGTCATTAAAAT 59.034 33.333 0.00 0.00 0.00 1.82
548 555 7.172875 TCCGTCCGAAAATACTTGTCATTAAAA 59.827 33.333 0.00 0.00 0.00 1.52
549 556 6.649973 TCCGTCCGAAAATACTTGTCATTAAA 59.350 34.615 0.00 0.00 0.00 1.52
550 557 6.164876 TCCGTCCGAAAATACTTGTCATTAA 58.835 36.000 0.00 0.00 0.00 1.40
551 558 5.722263 TCCGTCCGAAAATACTTGTCATTA 58.278 37.500 0.00 0.00 0.00 1.90
552 559 4.571919 TCCGTCCGAAAATACTTGTCATT 58.428 39.130 0.00 0.00 0.00 2.57
553 560 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
554 561 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
555 562 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
556 563 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
557 564 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
558 565 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
559 566 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
560 567 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
561 568 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
562 569 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
563 570 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
564 571 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
565 572 0.679002 CAGTACTCCCTCCGTCCGAA 60.679 60.000 0.00 0.00 0.00 4.30
566 573 1.077930 CAGTACTCCCTCCGTCCGA 60.078 63.158 0.00 0.00 0.00 4.55
567 574 2.119655 CCAGTACTCCCTCCGTCCG 61.120 68.421 0.00 0.00 0.00 4.79
568 575 0.106116 ATCCAGTACTCCCTCCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
569 576 2.228925 GTATCCAGTACTCCCTCCGTC 58.771 57.143 0.00 0.00 0.00 4.79
570 577 1.567649 TGTATCCAGTACTCCCTCCGT 59.432 52.381 0.00 0.00 34.27 4.69
571 578 1.955080 GTGTATCCAGTACTCCCTCCG 59.045 57.143 0.00 0.00 34.27 4.63
572 579 3.315880 AGTGTATCCAGTACTCCCTCC 57.684 52.381 0.00 0.00 34.27 4.30
573 580 4.024670 ACAAGTGTATCCAGTACTCCCTC 58.975 47.826 0.00 0.00 34.27 4.30
574 581 4.024670 GACAAGTGTATCCAGTACTCCCT 58.975 47.826 0.00 0.00 34.27 4.20
575 582 3.132467 GGACAAGTGTATCCAGTACTCCC 59.868 52.174 0.00 0.00 34.87 4.30
576 583 3.767673 TGGACAAGTGTATCCAGTACTCC 59.232 47.826 0.00 0.00 40.17 3.85
588 595 9.823647 CTTGAGTATTAAGATATGGACAAGTGT 57.176 33.333 0.00 0.00 0.00 3.55
589 596 9.823647 ACTTGAGTATTAAGATATGGACAAGTG 57.176 33.333 0.00 0.00 41.21 3.16
621 628 3.973472 TCTAGATAGGGCACTCCTTCA 57.027 47.619 0.00 0.00 45.47 3.02
630 637 1.219393 GCCGGCATCTAGATAGGGC 59.781 63.158 24.80 19.23 0.00 5.19
652 659 3.042871 GCTAGCTAGCTAGAGACGGTA 57.957 52.381 42.59 15.67 46.56 4.02
759 773 7.156000 ACTTCTACTTTTACTGCTCCTTTCTC 58.844 38.462 0.00 0.00 0.00 2.87
803 817 1.002251 CCTGCGCTACTAGCTAGTGTC 60.002 57.143 32.21 22.13 39.60 3.67
818 832 1.741770 GTTCTGGTAGTGGCCTGCG 60.742 63.158 3.32 0.00 0.00 5.18
821 835 1.201429 CCCTGTTCTGGTAGTGGCCT 61.201 60.000 3.32 0.00 0.00 5.19
831 845 2.307934 GCTAGAAGCTCCCTGTTCTG 57.692 55.000 0.00 0.00 38.45 3.02
842 856 1.484240 AGTGGATGGACAGCTAGAAGC 59.516 52.381 0.00 0.00 42.84 3.86
872 886 4.736126 AACCAAAGCAAGCAGTAAACTT 57.264 36.364 0.00 0.00 0.00 2.66
882 896 3.988379 TCAGTAGCAAACCAAAGCAAG 57.012 42.857 0.00 0.00 0.00 4.01
988 1002 3.069158 CGGTGGGTAGTAGGGTTTGATAG 59.931 52.174 0.00 0.00 0.00 2.08
1030 1046 1.372499 CTCGCCAAAAGACGACGGA 60.372 57.895 0.00 0.00 34.08 4.69
1031 1047 1.663702 ACTCGCCAAAAGACGACGG 60.664 57.895 0.00 0.00 34.08 4.79
1050 1066 2.041115 GCGGGGAAGAACTGGAAGC 61.041 63.158 0.00 0.00 37.60 3.86
1461 1483 1.372501 CCCCTCCCCTTTCTCTTTCA 58.627 55.000 0.00 0.00 0.00 2.69
1465 1487 2.286502 GCCCCCTCCCCTTTCTCT 60.287 66.667 0.00 0.00 0.00 3.10
1645 1667 1.666872 GTACTCCGCCGTTGTTGCT 60.667 57.895 0.00 0.00 0.00 3.91
1700 1722 6.569610 CATATCAATATGTCATGCAGCTGCAA 60.570 38.462 42.25 27.80 43.21 4.08
1701 1723 5.106317 CATATCAATATGTCATGCAGCTGCA 60.106 40.000 41.05 41.05 43.62 4.41
1742 1774 7.465353 TGCAAGAAATCAATTAATCTCACCA 57.535 32.000 0.00 0.00 0.00 4.17
1758 1791 5.808540 GCATGAGCATAAGATTTGCAAGAAA 59.191 36.000 0.00 0.00 42.62 2.52
1776 1809 0.108186 TAGAACGCACCCAGCATGAG 60.108 55.000 0.00 0.00 46.13 2.90
1848 1883 1.064758 AGCACTGGAAACACAGGACAA 60.065 47.619 0.00 0.00 42.75 3.18
1852 1887 2.254546 TGTAGCACTGGAAACACAGG 57.745 50.000 0.00 0.00 42.75 4.00
2170 2212 6.808008 ATACTGCCATCCGAATTTGATAAG 57.192 37.500 0.00 0.00 0.00 1.73
2368 2445 5.858581 CAGGCACCTTTTTCTTTTCTAATCG 59.141 40.000 0.00 0.00 0.00 3.34
2608 2696 6.293081 CCAGTGTACATGCATATTGCTAGTTC 60.293 42.308 0.00 0.00 45.31 3.01
2729 2817 0.391263 AACGAAATGGAGAGACCGGC 60.391 55.000 0.00 0.00 42.61 6.13
2730 2818 2.953466 TAACGAAATGGAGAGACCGG 57.047 50.000 0.00 0.00 42.61 5.28
2731 2819 5.796350 AAATTAACGAAATGGAGAGACCG 57.204 39.130 0.00 0.00 42.61 4.79
2732 2820 7.333672 ACAGTAAATTAACGAAATGGAGAGACC 59.666 37.037 0.00 0.00 39.54 3.85
2790 2881 6.465439 TCTCACTACTCAAGTCAGTTGAAA 57.535 37.500 0.00 0.00 44.83 2.69
2844 2935 7.333423 CGAGAGGAAAATCTGGTGTGTTAATAA 59.667 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.