Multiple sequence alignment - TraesCS3B01G558900

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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 TraesCS3B01G558900 chr3B 100.000 3434 0 0 1 3434 793031648 793028215 0.000000e+00 6342.0
1 TraesCS3B01G558900 chr3B 93.796 1773 92 7 780 2548 793017570 793015812 0.000000e+00 2649.0
2 TraesCS3B01G558900 chr3B 89.608 510 15 13 2567 3069 793015751 793015273 6.300000e-172 614.0
3 TraesCS3B01G558900 chr3B 93.023 215 9 1 3226 3434 793015256 793015042 3.330000e-80 309.0
4 TraesCS3B01G558900 chr3B 83.680 337 27 11 305 632 793018130 793017813 3.350000e-75 292.0
5 TraesCS3B01G558900 chr3B 91.558 154 12 1 70 223 793018329 793018177 9.660000e-51 211.0
6 TraesCS3B01G558900 chr3D 92.533 1741 113 3 821 2548 591616041 591617777 0.000000e+00 2479.0
7 TraesCS3B01G558900 chr3D 90.970 598 16 9 2868 3434 591618045 591618635 0.000000e+00 771.0
8 TraesCS3B01G558900 chr3D 81.740 701 71 22 1754 2434 591369552 591368889 1.810000e-147 532.0
9 TraesCS3B01G558900 chr3D 94.175 206 7 2 2567 2772 591617843 591618043 3.330000e-80 309.0
10 TraesCS3B01G558900 chr3D 89.815 108 10 1 166 272 566954390 566954283 1.660000e-28 137.0
11 TraesCS3B01G558900 chr3A 91.850 1681 114 10 825 2487 721663686 721665361 0.000000e+00 2324.0
12 TraesCS3B01G558900 chr3A 89.881 168 16 1 2 169 721672872 721673038 7.460000e-52 215.0
13 TraesCS3B01G558900 chr3A 78.824 170 11 10 1687 1848 721645219 721645067 1.310000e-14 91.6
14 TraesCS3B01G558900 chrUn 88.889 108 11 1 166 272 42480833 42480940 7.730000e-27 132.0
15 TraesCS3B01G558900 chrUn 78.788 165 27 4 1503 1667 137646098 137645942 1.690000e-18 104.0
16 TraesCS3B01G558900 chr5B 88.889 108 11 1 166 272 703539322 703539215 7.730000e-27 132.0
17 TraesCS3B01G558900 chr1B 88.889 108 11 1 166 272 577197262 577197155 7.730000e-27 132.0
18 TraesCS3B01G558900 chr1A 88.889 108 11 1 166 272 553964487 553964594 7.730000e-27 132.0
19 TraesCS3B01G558900 chr1A 85.039 127 18 1 2751 2876 506275158 506275284 1.000000e-25 128.0
20 TraesCS3B01G558900 chr4B 94.118 85 5 0 188 272 83028623 83028707 2.780000e-26 130.0
21 TraesCS3B01G558900 chr4B 89.320 103 10 1 166 267 522299520 522299622 1.000000e-25 128.0
22 TraesCS3B01G558900 chr5D 81.667 120 16 5 375 492 493809657 493809542 1.010000e-15 95.3
23 TraesCS3B01G558900 chr5D 84.058 69 10 1 426 493 493691453 493691385 7.950000e-07 65.8
24 TraesCS3B01G558900 chr5D 92.308 39 2 1 787 824 2503070 2503108 2.000000e-03 54.7
25 TraesCS3B01G558900 chr1D 80.992 121 21 2 2751 2870 77379253 77379372 1.010000e-15 95.3


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 TraesCS3B01G558900 chr3B 793028215 793031648 3433 True 6342.000000 6342 100.000000 1 3434 1 chr3B.!!$R1 3433
1 TraesCS3B01G558900 chr3B 793015042 793018329 3287 True 815.000000 2649 90.333000 70 3434 5 chr3B.!!$R2 3364
2 TraesCS3B01G558900 chr3D 591616041 591618635 2594 False 1186.333333 2479 92.559333 821 3434 3 chr3D.!!$F1 2613
3 TraesCS3B01G558900 chr3D 591368889 591369552 663 True 532.000000 532 81.740000 1754 2434 1 chr3D.!!$R2 680
4 TraesCS3B01G558900 chr3A 721663686 721665361 1675 False 2324.000000 2324 91.850000 825 2487 1 chr3A.!!$F1 1662

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
252 253 0.108186 TCTAAGAGCCACACATGCCG 60.108 55.000 0.0 0.0 0.00 5.69 F
271 272 0.468400 GCCCGGTAGAGAGAGTGGAT 60.468 60.000 0.0 0.0 0.00 3.41 F
1356 1529 1.006571 GTTCGTCTTCACCGAGCCA 60.007 57.895 0.0 0.0 35.49 4.75 F
2266 2464 1.598130 GCGGTGCTGGTCAAGAAGT 60.598 57.895 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2313 0.753848 TGATGATGGCGTCCGTCCTA 60.754 55.000 13.35 0.0 38.69 2.94 R
2121 2319 2.173669 CACGGTGATGATGGCGTCC 61.174 63.158 0.74 0.0 0.00 4.79 R
2388 2592 0.247460 CATCAAGCTCCACCTCGTCA 59.753 55.000 0.00 0.0 0.00 4.35 R
3083 3352 0.446222 GGCGCGCATTTCTAAGTCAA 59.554 50.000 34.42 0.0 0.00 3.18 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
34 35 8.029642 AGAATACACACAAGGTTCTAAAATCG 57.970 34.615 0.00 0.00 0.00 3.34
35 36 6.737254 ATACACACAAGGTTCTAAAATCGG 57.263 37.500 0.00 0.00 0.00 4.18
36 37 4.457466 ACACACAAGGTTCTAAAATCGGT 58.543 39.130 0.00 0.00 0.00 4.69
37 38 4.514066 ACACACAAGGTTCTAAAATCGGTC 59.486 41.667 0.00 0.00 0.00 4.79
38 39 4.070009 ACACAAGGTTCTAAAATCGGTCC 58.930 43.478 0.00 0.00 0.00 4.46
39 40 4.069304 CACAAGGTTCTAAAATCGGTCCA 58.931 43.478 0.00 0.00 0.00 4.02
40 41 4.517453 CACAAGGTTCTAAAATCGGTCCAA 59.483 41.667 0.00 0.00 0.00 3.53
41 42 5.009210 CACAAGGTTCTAAAATCGGTCCAAA 59.991 40.000 0.00 0.00 0.00 3.28
42 43 5.009310 ACAAGGTTCTAAAATCGGTCCAAAC 59.991 40.000 0.00 0.00 0.00 2.93
43 44 4.077108 AGGTTCTAAAATCGGTCCAAACC 58.923 43.478 0.00 0.00 42.66 3.27
54 55 2.786777 GGTCCAAACCGGTTCATAACT 58.213 47.619 22.53 0.00 35.36 2.24
55 56 3.151554 GGTCCAAACCGGTTCATAACTT 58.848 45.455 22.53 0.00 35.36 2.66
56 57 3.570975 GGTCCAAACCGGTTCATAACTTT 59.429 43.478 22.53 0.00 35.36 2.66
57 58 4.320714 GGTCCAAACCGGTTCATAACTTTC 60.321 45.833 22.53 4.66 35.36 2.62
58 59 3.822167 TCCAAACCGGTTCATAACTTTCC 59.178 43.478 22.53 0.00 35.57 3.13
59 60 3.824443 CCAAACCGGTTCATAACTTTCCT 59.176 43.478 22.53 0.00 0.00 3.36
60 61 5.005094 CCAAACCGGTTCATAACTTTCCTA 58.995 41.667 22.53 0.00 0.00 2.94
61 62 5.474189 CCAAACCGGTTCATAACTTTCCTAA 59.526 40.000 22.53 0.00 0.00 2.69
62 63 6.016108 CCAAACCGGTTCATAACTTTCCTAAA 60.016 38.462 22.53 0.00 0.00 1.85
63 64 7.427214 CAAACCGGTTCATAACTTTCCTAAAA 58.573 34.615 22.53 0.00 0.00 1.52
64 65 6.564709 ACCGGTTCATAACTTTCCTAAAAC 57.435 37.500 0.00 0.00 0.00 2.43
65 66 5.474532 ACCGGTTCATAACTTTCCTAAAACC 59.525 40.000 0.00 0.00 33.26 3.27
67 68 5.396484 GGTTCATAACTTTCCTAAAACCGC 58.604 41.667 0.00 0.00 0.00 5.68
68 69 5.182570 GGTTCATAACTTTCCTAAAACCGCT 59.817 40.000 0.00 0.00 0.00 5.52
95 96 2.928396 AGTGTTAGGCCAGCCCGT 60.928 61.111 5.01 0.00 39.21 5.28
106 107 3.141488 AGCCCGTCTAGTGGAGCG 61.141 66.667 5.49 0.00 0.00 5.03
142 143 7.127955 AGACCAAAGGACCTCTCACAATATTAT 59.872 37.037 0.00 0.00 0.00 1.28
164 165 4.998979 GCAAGAAATATTGCGCACTAAC 57.001 40.909 11.12 5.76 45.43 2.34
168 169 6.745450 GCAAGAAATATTGCGCACTAACTTTA 59.255 34.615 11.12 0.00 45.43 1.85
172 173 9.289303 AGAAATATTGCGCACTAACTTTATTTG 57.711 29.630 11.12 0.00 0.00 2.32
182 183 7.572353 CGCACTAACTTTATTTGAGTAAAGGCA 60.572 37.037 10.18 0.00 42.97 4.75
185 186 8.957466 ACTAACTTTATTTGAGTAAAGGCATCC 58.043 33.333 10.18 0.00 42.97 3.51
186 187 6.775594 ACTTTATTTGAGTAAAGGCATCCC 57.224 37.500 10.18 0.00 42.97 3.85
203 204 5.702209 GGCATCCCTTATTAATTGCAAATGG 59.298 40.000 1.71 0.00 0.00 3.16
226 227 8.208718 TGGTCAAAGGAATACAAATAATCTCG 57.791 34.615 0.00 0.00 0.00 4.04
227 228 7.282224 TGGTCAAAGGAATACAAATAATCTCGG 59.718 37.037 0.00 0.00 0.00 4.63
228 229 7.255139 GGTCAAAGGAATACAAATAATCTCGGG 60.255 40.741 0.00 0.00 0.00 5.14
229 230 6.262273 TCAAAGGAATACAAATAATCTCGGGC 59.738 38.462 0.00 0.00 0.00 6.13
232 233 6.126409 AGGAATACAAATAATCTCGGGCAAA 58.874 36.000 0.00 0.00 0.00 3.68
233 234 6.777580 AGGAATACAAATAATCTCGGGCAAAT 59.222 34.615 0.00 0.00 0.00 2.32
234 235 7.040409 AGGAATACAAATAATCTCGGGCAAATC 60.040 37.037 0.00 0.00 0.00 2.17
235 236 7.040409 GGAATACAAATAATCTCGGGCAAATCT 60.040 37.037 0.00 0.00 0.00 2.40
236 237 8.918202 AATACAAATAATCTCGGGCAAATCTA 57.082 30.769 0.00 0.00 0.00 1.98
237 238 8.918202 ATACAAATAATCTCGGGCAAATCTAA 57.082 30.769 0.00 0.00 0.00 2.10
238 239 7.264373 ACAAATAATCTCGGGCAAATCTAAG 57.736 36.000 0.00 0.00 0.00 2.18
239 240 7.054124 ACAAATAATCTCGGGCAAATCTAAGA 58.946 34.615 0.00 0.00 0.00 2.10
247 248 2.436417 GGCAAATCTAAGAGCCACACA 58.564 47.619 0.00 0.00 46.26 3.72
249 250 3.181493 GGCAAATCTAAGAGCCACACATG 60.181 47.826 0.00 0.00 46.26 3.21
250 251 3.733077 GCAAATCTAAGAGCCACACATGC 60.733 47.826 0.00 0.00 0.00 4.06
251 252 2.338577 ATCTAAGAGCCACACATGCC 57.661 50.000 0.00 0.00 0.00 4.40
252 253 0.108186 TCTAAGAGCCACACATGCCG 60.108 55.000 0.00 0.00 0.00 5.69
253 254 1.709147 CTAAGAGCCACACATGCCGC 61.709 60.000 0.00 0.00 0.00 6.53
259 260 4.769063 CACACATGCCGCCCGGTA 62.769 66.667 8.66 4.04 37.65 4.02
260 261 4.467084 ACACATGCCGCCCGGTAG 62.467 66.667 8.66 0.00 37.65 3.18
261 262 4.155733 CACATGCCGCCCGGTAGA 62.156 66.667 8.66 0.00 37.65 2.59
262 263 3.849951 ACATGCCGCCCGGTAGAG 61.850 66.667 8.66 3.82 37.65 2.43
263 264 3.536917 CATGCCGCCCGGTAGAGA 61.537 66.667 8.66 0.00 37.65 3.10
264 265 3.227276 ATGCCGCCCGGTAGAGAG 61.227 66.667 8.66 0.00 37.65 3.20
265 266 3.733507 ATGCCGCCCGGTAGAGAGA 62.734 63.158 8.66 0.00 37.65 3.10
266 267 3.597728 GCCGCCCGGTAGAGAGAG 61.598 72.222 8.66 0.00 37.65 3.20
268 269 2.482333 CCGCCCGGTAGAGAGAGTG 61.482 68.421 0.00 0.00 0.00 3.51
269 270 2.482333 CGCCCGGTAGAGAGAGTGG 61.482 68.421 0.00 0.00 0.00 4.00
270 271 1.076923 GCCCGGTAGAGAGAGTGGA 60.077 63.158 0.00 0.00 0.00 4.02
271 272 0.468400 GCCCGGTAGAGAGAGTGGAT 60.468 60.000 0.00 0.00 0.00 3.41
272 273 1.202903 GCCCGGTAGAGAGAGTGGATA 60.203 57.143 0.00 0.00 0.00 2.59
273 274 2.506444 CCCGGTAGAGAGAGTGGATAC 58.494 57.143 0.00 0.00 0.00 2.24
274 275 2.144730 CCGGTAGAGAGAGTGGATACG 58.855 57.143 0.00 0.00 42.51 3.06
288 289 3.788937 TGGATACGCACTAGCTTTAACC 58.211 45.455 0.00 0.00 39.10 2.85
289 290 3.129109 GGATACGCACTAGCTTTAACCC 58.871 50.000 0.00 0.00 39.10 4.11
290 291 3.431207 GGATACGCACTAGCTTTAACCCA 60.431 47.826 0.00 0.00 39.10 4.51
291 292 2.554370 ACGCACTAGCTTTAACCCAA 57.446 45.000 0.00 0.00 39.10 4.12
292 293 2.853705 ACGCACTAGCTTTAACCCAAA 58.146 42.857 0.00 0.00 39.10 3.28
293 294 3.418047 ACGCACTAGCTTTAACCCAAAT 58.582 40.909 0.00 0.00 39.10 2.32
294 295 3.439129 ACGCACTAGCTTTAACCCAAATC 59.561 43.478 0.00 0.00 39.10 2.17
295 296 3.181500 CGCACTAGCTTTAACCCAAATCC 60.181 47.826 0.00 0.00 39.10 3.01
296 297 3.130516 GCACTAGCTTTAACCCAAATCCC 59.869 47.826 0.00 0.00 37.91 3.85
297 298 4.600062 CACTAGCTTTAACCCAAATCCCT 58.400 43.478 0.00 0.00 0.00 4.20
298 299 4.640647 CACTAGCTTTAACCCAAATCCCTC 59.359 45.833 0.00 0.00 0.00 4.30
299 300 3.101643 AGCTTTAACCCAAATCCCTCC 57.898 47.619 0.00 0.00 0.00 4.30
300 301 2.108168 GCTTTAACCCAAATCCCTCCC 58.892 52.381 0.00 0.00 0.00 4.30
301 302 2.558800 GCTTTAACCCAAATCCCTCCCA 60.559 50.000 0.00 0.00 0.00 4.37
302 303 3.785364 CTTTAACCCAAATCCCTCCCAA 58.215 45.455 0.00 0.00 0.00 4.12
303 304 4.361783 CTTTAACCCAAATCCCTCCCAAT 58.638 43.478 0.00 0.00 0.00 3.16
310 311 3.346315 CAAATCCCTCCCAATTTTTGCC 58.654 45.455 0.00 0.00 0.00 4.52
317 318 1.548269 TCCCAATTTTTGCCGGTGATC 59.452 47.619 1.90 0.00 0.00 2.92
351 352 7.222224 GCAAAGAAAGCCTGATTTAATGAGATG 59.778 37.037 0.00 0.00 0.00 2.90
382 383 7.985589 AGAAGAGTCCAAAACTAGGGAAATAA 58.014 34.615 0.00 0.00 38.74 1.40
390 391 8.929487 TCCAAAACTAGGGAAATAACATTTTGT 58.071 29.630 0.00 0.00 35.18 2.83
400 401 9.419297 GGGAAATAACATTTTGTTTTCTAGGTC 57.581 33.333 0.00 0.00 41.45 3.85
493 494 9.160496 ACAATAAATTTGACTTTCTTTTGCACA 57.840 25.926 0.00 0.00 0.00 4.57
535 536 6.426633 TGAATAGAAAATCAGCGTTGACTTCA 59.573 34.615 20.69 11.93 35.83 3.02
538 539 4.999950 AGAAAATCAGCGTTGACTTCAGAT 59.000 37.500 20.69 0.00 35.83 2.90
539 540 5.471456 AGAAAATCAGCGTTGACTTCAGATT 59.529 36.000 20.69 3.26 35.83 2.40
540 541 5.695851 AAATCAGCGTTGACTTCAGATTT 57.304 34.783 3.33 0.00 35.83 2.17
541 542 5.695851 AATCAGCGTTGACTTCAGATTTT 57.304 34.783 3.33 0.00 35.83 1.82
542 543 5.695851 ATCAGCGTTGACTTCAGATTTTT 57.304 34.783 3.33 0.00 35.83 1.94
583 591 4.565166 CGCTATTCACACTATTTTGACCGA 59.435 41.667 0.00 0.00 0.00 4.69
588 596 9.840427 CTATTCACACTATTTTGACCGAAAATT 57.160 29.630 0.00 0.00 40.73 1.82
662 670 5.423704 TTTTATCCGTACATGGAAGGTGA 57.576 39.130 9.95 0.00 42.46 4.02
663 671 5.423704 TTTATCCGTACATGGAAGGTGAA 57.576 39.130 9.95 2.77 42.46 3.18
664 672 3.992943 ATCCGTACATGGAAGGTGAAA 57.007 42.857 9.95 0.00 42.46 2.69
665 673 3.992943 TCCGTACATGGAAGGTGAAAT 57.007 42.857 9.95 0.00 34.30 2.17
666 674 4.295141 TCCGTACATGGAAGGTGAAATT 57.705 40.909 9.95 0.00 34.30 1.82
667 675 4.658063 TCCGTACATGGAAGGTGAAATTT 58.342 39.130 9.95 0.00 34.30 1.82
668 676 4.457603 TCCGTACATGGAAGGTGAAATTTG 59.542 41.667 9.95 0.00 34.30 2.32
669 677 4.217550 CCGTACATGGAAGGTGAAATTTGT 59.782 41.667 0.94 0.00 28.09 2.83
670 678 5.278758 CCGTACATGGAAGGTGAAATTTGTT 60.279 40.000 0.94 0.00 28.09 2.83
671 679 6.212955 CGTACATGGAAGGTGAAATTTGTTT 58.787 36.000 0.00 0.00 28.09 2.83
672 680 6.362283 CGTACATGGAAGGTGAAATTTGTTTC 59.638 38.462 0.00 0.00 28.09 2.78
673 681 6.232581 ACATGGAAGGTGAAATTTGTTTCA 57.767 33.333 0.00 0.00 38.49 2.69
674 682 6.648192 ACATGGAAGGTGAAATTTGTTTCAA 58.352 32.000 0.00 0.00 41.95 2.69
675 683 7.281841 ACATGGAAGGTGAAATTTGTTTCAAT 58.718 30.769 0.00 0.00 41.95 2.57
893 1054 2.524569 ATTGCCAAACGAACCCAAAG 57.475 45.000 0.00 0.00 0.00 2.77
902 1063 1.770061 ACGAACCCAAAGTCCAACCTA 59.230 47.619 0.00 0.00 0.00 3.08
911 1072 4.765339 CCAAAGTCCAACCTAAAACCCTAG 59.235 45.833 0.00 0.00 0.00 3.02
936 1097 1.761198 GGGCAATCTCTACCCGTAACT 59.239 52.381 0.00 0.00 32.92 2.24
1206 1379 4.927782 GTGGTGCACTGCCCGTCA 62.928 66.667 17.98 0.67 0.00 4.35
1227 1400 1.379977 CTCCTCGTACCTGGAGCCA 60.380 63.158 13.69 0.00 42.62 4.75
1356 1529 1.006571 GTTCGTCTTCACCGAGCCA 60.007 57.895 0.00 0.00 35.49 4.75
1630 1803 4.403137 CCCGCGTCGACGTAACCA 62.403 66.667 35.48 0.00 42.22 3.67
1637 1810 4.764336 CGACGTAACCAGCGCCGA 62.764 66.667 2.29 0.00 37.40 5.54
1695 1868 2.044946 GGCCTTGTCGCCCTCATT 60.045 61.111 0.00 0.00 43.66 2.57
1767 1940 1.948834 CATGACACCAAGAGCAACACA 59.051 47.619 0.00 0.00 0.00 3.72
1848 2033 3.839432 CTTCCGAGGGAGGCGTCC 61.839 72.222 17.33 17.33 43.05 4.79
1981 2167 4.329545 GGCACAGGTTCGAGCCCA 62.330 66.667 15.45 0.00 41.25 5.36
2042 2240 4.552365 CGACCCATCGCTGGCCAT 62.552 66.667 5.51 0.00 42.43 4.40
2121 2319 1.828660 ATCGGAGCTGGGTAGGACG 60.829 63.158 0.00 0.00 0.00 4.79
2131 2329 2.420568 GGTAGGACGGACGCCATCA 61.421 63.158 7.65 0.00 0.00 3.07
2266 2464 1.598130 GCGGTGCTGGTCAAGAAGT 60.598 57.895 0.00 0.00 0.00 3.01
2349 2553 2.224606 GGTGATGTCGGCATTGATGAT 58.775 47.619 2.92 0.00 35.07 2.45
2388 2592 0.392998 GCATTGATCTGGACCCGTGT 60.393 55.000 0.00 0.00 0.00 4.49
2410 2614 1.338200 ACGAGGTGGAGCTTGATGAAC 60.338 52.381 0.00 0.00 0.00 3.18
2415 2619 1.467734 GTGGAGCTTGATGAACTGCTG 59.532 52.381 0.00 0.00 35.76 4.41
2453 2657 6.246163 TCTGAGAGTATGAGTTGTGACCTTA 58.754 40.000 0.00 0.00 0.00 2.69
2490 2698 3.415212 TGGTCTTGGAAGCTTCAGATTG 58.585 45.455 27.02 12.17 0.00 2.67
2500 2708 3.271729 AGCTTCAGATTGAGTGCATCTG 58.728 45.455 7.77 7.77 42.20 2.90
2501 2709 3.055312 AGCTTCAGATTGAGTGCATCTGA 60.055 43.478 11.95 11.95 46.18 3.27
2502 2710 3.878103 GCTTCAGATTGAGTGCATCTGAT 59.122 43.478 15.73 0.00 46.78 2.90
2503 2711 5.055144 GCTTCAGATTGAGTGCATCTGATA 58.945 41.667 15.73 7.87 46.78 2.15
2564 2806 7.279981 ACATTATCTGCTTGCGTTGTTATAGAA 59.720 33.333 0.00 0.00 0.00 2.10
2698 2957 2.242043 CTGTATGCCCCATGGATTTCC 58.758 52.381 15.22 0.00 0.00 3.13
2721 2980 3.779759 TGCCAAACACTCAAATGTTCAC 58.220 40.909 0.00 0.00 42.01 3.18
2820 3079 8.753497 GGATTAAATCCTCTACCAGTCAAAAT 57.247 34.615 0.00 0.00 46.19 1.82
2821 3080 8.841300 GGATTAAATCCTCTACCAGTCAAAATC 58.159 37.037 0.00 0.00 46.19 2.17
2822 3081 8.753497 ATTAAATCCTCTACCAGTCAAAATCC 57.247 34.615 0.00 0.00 0.00 3.01
2823 3082 4.779993 ATCCTCTACCAGTCAAAATCCC 57.220 45.455 0.00 0.00 0.00 3.85
2824 3083 2.844348 TCCTCTACCAGTCAAAATCCCC 59.156 50.000 0.00 0.00 0.00 4.81
2836 3095 4.642437 GTCAAAATCCCCTCAAATCCTCTC 59.358 45.833 0.00 0.00 0.00 3.20
2887 3146 5.841957 ACAAGGCCTAAATGATTCACATC 57.158 39.130 5.16 0.00 38.38 3.06
3010 3276 6.160576 ACAAAATACTGTGCTCCAACATTT 57.839 33.333 0.00 0.00 0.00 2.32
3011 3277 6.215845 ACAAAATACTGTGCTCCAACATTTC 58.784 36.000 0.00 0.00 0.00 2.17
3020 3289 5.538053 TGTGCTCCAACATTTCCTAAAATCA 59.462 36.000 0.00 0.00 32.69 2.57
3042 3311 6.903516 TCAGATTTCATCACCTGTTGGATAT 58.096 36.000 0.00 0.00 37.04 1.63
3081 3350 8.182361 TCGGGATCGTTGAGTTTTCTCACTTA 62.182 42.308 0.00 0.00 44.55 2.24
3082 3351 9.555303 TCGGGATCGTTGAGTTTTCTCACTTAA 62.555 40.741 0.00 0.00 44.55 1.85
3200 3469 3.448093 TCCCATTCCATAAACAGCACA 57.552 42.857 0.00 0.00 0.00 4.57
3201 3470 3.979911 TCCCATTCCATAAACAGCACAT 58.020 40.909 0.00 0.00 0.00 3.21
3202 3471 3.700539 TCCCATTCCATAAACAGCACATG 59.299 43.478 0.00 0.00 0.00 3.21
3205 3474 4.158209 CCATTCCATAAACAGCACATGACA 59.842 41.667 0.00 0.00 0.00 3.58
3206 3475 5.336610 CCATTCCATAAACAGCACATGACAA 60.337 40.000 0.00 0.00 0.00 3.18
3211 3480 1.242076 AACAGCACATGACAAGGCTC 58.758 50.000 0.00 0.00 33.60 4.70
3396 3691 4.780815 CAACACATACCCACCTCATGTAT 58.219 43.478 0.00 0.00 31.81 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 8.504005 CGATTTTAGAACCTTGTGTGTATTCTT 58.496 33.333 0.00 0.00 32.11 2.52
9 10 7.119262 CCGATTTTAGAACCTTGTGTGTATTCT 59.881 37.037 0.00 0.00 34.16 2.40
10 11 7.094933 ACCGATTTTAGAACCTTGTGTGTATTC 60.095 37.037 0.00 0.00 0.00 1.75
11 12 6.713450 ACCGATTTTAGAACCTTGTGTGTATT 59.287 34.615 0.00 0.00 0.00 1.89
12 13 6.235664 ACCGATTTTAGAACCTTGTGTGTAT 58.764 36.000 0.00 0.00 0.00 2.29
13 14 5.613329 ACCGATTTTAGAACCTTGTGTGTA 58.387 37.500 0.00 0.00 0.00 2.90
14 15 4.457466 ACCGATTTTAGAACCTTGTGTGT 58.543 39.130 0.00 0.00 0.00 3.72
15 16 4.083484 GGACCGATTTTAGAACCTTGTGTG 60.083 45.833 0.00 0.00 0.00 3.82
16 17 4.070009 GGACCGATTTTAGAACCTTGTGT 58.930 43.478 0.00 0.00 0.00 3.72
17 18 4.069304 TGGACCGATTTTAGAACCTTGTG 58.931 43.478 0.00 0.00 0.00 3.33
18 19 4.360951 TGGACCGATTTTAGAACCTTGT 57.639 40.909 0.00 0.00 0.00 3.16
19 20 5.458015 GTTTGGACCGATTTTAGAACCTTG 58.542 41.667 0.00 0.00 0.00 3.61
20 21 4.521639 GGTTTGGACCGATTTTAGAACCTT 59.478 41.667 0.00 0.00 35.91 3.50
21 22 4.077108 GGTTTGGACCGATTTTAGAACCT 58.923 43.478 0.00 0.00 35.91 3.50
22 23 4.430137 GGTTTGGACCGATTTTAGAACC 57.570 45.455 0.00 0.00 35.91 3.62
34 35 2.786777 AGTTATGAACCGGTTTGGACC 58.213 47.619 23.22 8.76 42.00 4.46
35 36 4.320714 GGAAAGTTATGAACCGGTTTGGAC 60.321 45.833 23.22 16.93 42.00 4.02
36 37 3.822167 GGAAAGTTATGAACCGGTTTGGA 59.178 43.478 23.22 9.23 42.00 3.53
37 38 3.824443 AGGAAAGTTATGAACCGGTTTGG 59.176 43.478 23.22 0.00 46.41 3.28
38 39 6.563222 TTAGGAAAGTTATGAACCGGTTTG 57.437 37.500 23.22 0.00 0.00 2.93
39 40 7.428020 GTTTTAGGAAAGTTATGAACCGGTTT 58.572 34.615 23.22 9.26 0.00 3.27
40 41 6.016024 GGTTTTAGGAAAGTTATGAACCGGTT 60.016 38.462 22.50 22.50 0.00 4.44
41 42 5.474532 GGTTTTAGGAAAGTTATGAACCGGT 59.525 40.000 0.00 0.00 0.00 5.28
42 43 5.946298 GGTTTTAGGAAAGTTATGAACCGG 58.054 41.667 0.00 0.00 0.00 5.28
44 45 5.182570 AGCGGTTTTAGGAAAGTTATGAACC 59.817 40.000 0.00 0.00 33.67 3.62
45 46 6.250344 AGCGGTTTTAGGAAAGTTATGAAC 57.750 37.500 0.00 0.00 0.00 3.18
46 47 6.294286 CCAAGCGGTTTTAGGAAAGTTATGAA 60.294 38.462 0.00 0.00 0.00 2.57
47 48 5.182380 CCAAGCGGTTTTAGGAAAGTTATGA 59.818 40.000 0.00 0.00 0.00 2.15
48 49 5.182380 TCCAAGCGGTTTTAGGAAAGTTATG 59.818 40.000 0.00 0.00 0.00 1.90
49 50 5.318630 TCCAAGCGGTTTTAGGAAAGTTAT 58.681 37.500 0.00 0.00 0.00 1.89
50 51 4.716794 TCCAAGCGGTTTTAGGAAAGTTA 58.283 39.130 0.00 0.00 0.00 2.24
51 52 3.558033 TCCAAGCGGTTTTAGGAAAGTT 58.442 40.909 0.00 0.00 0.00 2.66
52 53 3.217681 TCCAAGCGGTTTTAGGAAAGT 57.782 42.857 0.00 0.00 0.00 2.66
53 54 4.010349 AGATCCAAGCGGTTTTAGGAAAG 58.990 43.478 8.73 0.00 31.17 2.62
54 55 4.028993 AGATCCAAGCGGTTTTAGGAAA 57.971 40.909 8.73 0.00 31.17 3.13
55 56 3.713826 AGATCCAAGCGGTTTTAGGAA 57.286 42.857 8.73 0.00 31.17 3.36
56 57 4.028131 TCTAGATCCAAGCGGTTTTAGGA 58.972 43.478 7.28 7.28 0.00 2.94
57 58 4.141914 ACTCTAGATCCAAGCGGTTTTAGG 60.142 45.833 0.00 0.00 0.00 2.69
58 59 4.806247 CACTCTAGATCCAAGCGGTTTTAG 59.194 45.833 0.00 0.00 0.00 1.85
59 60 4.222145 ACACTCTAGATCCAAGCGGTTTTA 59.778 41.667 0.00 0.00 0.00 1.52
60 61 3.008049 ACACTCTAGATCCAAGCGGTTTT 59.992 43.478 0.00 0.00 0.00 2.43
61 62 2.567615 ACACTCTAGATCCAAGCGGTTT 59.432 45.455 0.00 0.00 0.00 3.27
62 63 2.180276 ACACTCTAGATCCAAGCGGTT 58.820 47.619 0.00 0.00 0.00 4.44
63 64 1.853963 ACACTCTAGATCCAAGCGGT 58.146 50.000 0.00 0.00 0.00 5.68
64 65 2.969628 AACACTCTAGATCCAAGCGG 57.030 50.000 0.00 0.00 0.00 5.52
65 66 3.797184 GCCTAACACTCTAGATCCAAGCG 60.797 52.174 0.00 0.00 0.00 4.68
66 67 3.493524 GGCCTAACACTCTAGATCCAAGC 60.494 52.174 0.00 0.00 0.00 4.01
67 68 3.706594 TGGCCTAACACTCTAGATCCAAG 59.293 47.826 3.32 0.00 0.00 3.61
68 69 3.706594 CTGGCCTAACACTCTAGATCCAA 59.293 47.826 3.32 0.00 0.00 3.53
95 96 1.754621 CCTCTGGCGCTCCACTAGA 60.755 63.158 7.64 1.33 37.47 2.43
106 107 2.119495 TCCTTTGGTCTATCCTCTGGC 58.881 52.381 0.00 0.00 37.07 4.85
113 114 3.769844 TGTGAGAGGTCCTTTGGTCTATC 59.230 47.826 0.00 0.00 0.00 2.08
153 154 5.682943 ACTCAAATAAAGTTAGTGCGCAA 57.317 34.783 14.00 0.00 0.00 4.85
163 164 6.494059 AGGGATGCCTTTACTCAAATAAAGT 58.506 36.000 0.00 0.00 39.53 2.66
164 165 7.410120 AAGGGATGCCTTTACTCAAATAAAG 57.590 36.000 13.61 0.00 40.44 1.85
168 169 9.660544 ATTAATAAGGGATGCCTTTACTCAAAT 57.339 29.630 24.73 12.04 28.05 2.32
172 173 7.014230 TGCAATTAATAAGGGATGCCTTTACTC 59.986 37.037 24.73 6.37 28.05 2.59
182 183 7.673641 TGACCATTTGCAATTAATAAGGGAT 57.326 32.000 0.00 0.00 0.00 3.85
185 186 8.040132 TCCTTTGACCATTTGCAATTAATAAGG 58.960 33.333 0.00 8.22 0.00 2.69
186 187 9.434420 TTCCTTTGACCATTTGCAATTAATAAG 57.566 29.630 0.00 0.00 0.00 1.73
203 204 7.639945 CCCGAGATTATTTGTATTCCTTTGAC 58.360 38.462 0.00 0.00 0.00 3.18
223 224 1.134401 TGGCTCTTAGATTTGCCCGAG 60.134 52.381 8.25 0.00 44.32 4.63
224 225 0.908910 TGGCTCTTAGATTTGCCCGA 59.091 50.000 8.25 0.00 44.32 5.14
225 226 1.017387 GTGGCTCTTAGATTTGCCCG 58.983 55.000 8.25 0.00 44.32 6.13
226 227 1.745653 GTGTGGCTCTTAGATTTGCCC 59.254 52.381 8.25 1.85 44.32 5.36
227 228 2.436417 TGTGTGGCTCTTAGATTTGCC 58.564 47.619 4.28 4.28 45.10 4.52
228 229 3.733077 GCATGTGTGGCTCTTAGATTTGC 60.733 47.826 0.00 0.00 0.00 3.68
229 230 3.181493 GGCATGTGTGGCTCTTAGATTTG 60.181 47.826 0.00 0.00 46.64 2.32
232 233 2.338577 GGCATGTGTGGCTCTTAGAT 57.661 50.000 0.00 0.00 46.64 1.98
233 234 3.861341 GGCATGTGTGGCTCTTAGA 57.139 52.632 0.00 0.00 46.64 2.10
243 244 4.467084 CTACCGGGCGGCATGTGT 62.467 66.667 12.47 4.19 39.32 3.72
244 245 4.155733 TCTACCGGGCGGCATGTG 62.156 66.667 12.47 0.00 39.32 3.21
245 246 3.849951 CTCTACCGGGCGGCATGT 61.850 66.667 12.47 9.69 39.32 3.21
246 247 3.506059 CTCTCTACCGGGCGGCATG 62.506 68.421 12.47 2.94 39.32 4.06
247 248 3.227276 CTCTCTACCGGGCGGCAT 61.227 66.667 12.47 0.00 39.32 4.40
249 250 3.597728 CTCTCTCTACCGGGCGGC 61.598 72.222 6.32 0.00 39.32 6.53
250 251 2.124236 ACTCTCTCTACCGGGCGG 60.124 66.667 6.32 0.00 42.03 6.13
251 252 2.482333 CCACTCTCTCTACCGGGCG 61.482 68.421 6.32 0.00 0.00 6.13
252 253 0.468400 ATCCACTCTCTCTACCGGGC 60.468 60.000 6.32 0.00 0.00 6.13
253 254 2.506444 GTATCCACTCTCTCTACCGGG 58.494 57.143 6.32 0.00 0.00 5.73
254 255 2.144730 CGTATCCACTCTCTCTACCGG 58.855 57.143 0.00 0.00 0.00 5.28
255 256 1.532007 GCGTATCCACTCTCTCTACCG 59.468 57.143 0.00 0.00 0.00 4.02
256 257 2.291190 GTGCGTATCCACTCTCTCTACC 59.709 54.545 0.00 0.00 33.02 3.18
257 258 3.207778 AGTGCGTATCCACTCTCTCTAC 58.792 50.000 0.00 0.00 42.10 2.59
258 259 3.562343 AGTGCGTATCCACTCTCTCTA 57.438 47.619 0.00 0.00 42.10 2.43
259 260 2.428544 AGTGCGTATCCACTCTCTCT 57.571 50.000 0.00 0.00 42.10 3.10
260 261 2.031508 GCTAGTGCGTATCCACTCTCTC 60.032 54.545 0.00 0.00 44.48 3.20
261 262 1.950909 GCTAGTGCGTATCCACTCTCT 59.049 52.381 0.00 0.00 44.48 3.10
262 263 1.950909 AGCTAGTGCGTATCCACTCTC 59.049 52.381 0.00 0.00 44.48 3.20
263 264 2.060050 AGCTAGTGCGTATCCACTCT 57.940 50.000 0.00 0.00 44.48 3.24
264 265 2.873133 AAGCTAGTGCGTATCCACTC 57.127 50.000 0.00 0.00 44.48 3.51
265 266 4.430908 GTTAAAGCTAGTGCGTATCCACT 58.569 43.478 0.00 0.23 46.98 4.00
266 267 3.554731 GGTTAAAGCTAGTGCGTATCCAC 59.445 47.826 0.00 0.00 45.42 4.02
268 269 3.129109 GGGTTAAAGCTAGTGCGTATCC 58.871 50.000 0.00 0.00 45.42 2.59
269 270 3.788937 TGGGTTAAAGCTAGTGCGTATC 58.211 45.455 0.00 0.00 45.42 2.24
270 271 3.899052 TGGGTTAAAGCTAGTGCGTAT 57.101 42.857 0.00 0.00 45.42 3.06
271 272 3.681593 TTGGGTTAAAGCTAGTGCGTA 57.318 42.857 0.00 0.00 45.42 4.42
272 273 2.554370 TTGGGTTAAAGCTAGTGCGT 57.446 45.000 0.00 0.00 45.42 5.24
273 274 3.181500 GGATTTGGGTTAAAGCTAGTGCG 60.181 47.826 0.00 0.00 45.42 5.34
274 275 3.130516 GGGATTTGGGTTAAAGCTAGTGC 59.869 47.826 0.00 0.00 35.10 4.40
275 276 4.600062 AGGGATTTGGGTTAAAGCTAGTG 58.400 43.478 0.00 0.00 35.10 2.74
276 277 4.325109 GGAGGGATTTGGGTTAAAGCTAGT 60.325 45.833 0.00 0.00 35.10 2.57
277 278 4.207955 GGAGGGATTTGGGTTAAAGCTAG 58.792 47.826 0.00 0.00 35.10 3.42
278 279 3.053170 GGGAGGGATTTGGGTTAAAGCTA 60.053 47.826 0.00 0.00 35.10 3.32
279 280 2.292257 GGGAGGGATTTGGGTTAAAGCT 60.292 50.000 0.00 0.00 35.10 3.74
280 281 2.108168 GGGAGGGATTTGGGTTAAAGC 58.892 52.381 0.00 0.00 33.99 3.51
281 282 3.466395 TGGGAGGGATTTGGGTTAAAG 57.534 47.619 0.00 0.00 0.00 1.85
282 283 3.925261 TTGGGAGGGATTTGGGTTAAA 57.075 42.857 0.00 0.00 0.00 1.52
283 284 4.427956 AATTGGGAGGGATTTGGGTTAA 57.572 40.909 0.00 0.00 0.00 2.01
284 285 4.427956 AAATTGGGAGGGATTTGGGTTA 57.572 40.909 0.00 0.00 0.00 2.85
285 286 3.290039 AAATTGGGAGGGATTTGGGTT 57.710 42.857 0.00 0.00 0.00 4.11
286 287 3.290039 AAAATTGGGAGGGATTTGGGT 57.710 42.857 0.00 0.00 0.00 4.51
287 288 3.873410 GCAAAAATTGGGAGGGATTTGGG 60.873 47.826 0.00 0.00 0.00 4.12
288 289 3.346315 GCAAAAATTGGGAGGGATTTGG 58.654 45.455 0.00 0.00 0.00 3.28
289 290 3.346315 GGCAAAAATTGGGAGGGATTTG 58.654 45.455 0.00 0.00 0.00 2.32
290 291 2.027285 CGGCAAAAATTGGGAGGGATTT 60.027 45.455 0.00 0.00 0.00 2.17
291 292 1.554617 CGGCAAAAATTGGGAGGGATT 59.445 47.619 0.00 0.00 0.00 3.01
292 293 1.194218 CGGCAAAAATTGGGAGGGAT 58.806 50.000 0.00 0.00 0.00 3.85
293 294 0.902516 CCGGCAAAAATTGGGAGGGA 60.903 55.000 0.00 0.00 0.00 4.20
294 295 1.191489 ACCGGCAAAAATTGGGAGGG 61.191 55.000 0.00 0.00 0.00 4.30
295 296 0.037419 CACCGGCAAAAATTGGGAGG 60.037 55.000 0.00 0.00 0.00 4.30
296 297 0.965439 TCACCGGCAAAAATTGGGAG 59.035 50.000 0.00 0.00 0.00 4.30
297 298 1.548269 GATCACCGGCAAAAATTGGGA 59.452 47.619 0.00 0.00 0.00 4.37
298 299 1.735369 CGATCACCGGCAAAAATTGGG 60.735 52.381 0.00 0.00 33.91 4.12
299 300 1.627879 CGATCACCGGCAAAAATTGG 58.372 50.000 0.00 0.00 33.91 3.16
310 311 1.511318 TTTGCCAACACCGATCACCG 61.511 55.000 0.00 0.00 38.18 4.94
317 318 2.885502 GCTTTCTTTGCCAACACCG 58.114 52.632 0.00 0.00 0.00 4.94
351 352 2.959030 AGTTTTGGACTCTTCTTTGCCC 59.041 45.455 0.00 0.00 31.20 5.36
472 473 9.328845 ACATATGTGCAAAAGAAAGTCAAATTT 57.671 25.926 7.78 0.00 0.00 1.82
510 511 6.426633 TGAAGTCAACGCTGATTTTCTATTCA 59.573 34.615 13.59 5.32 32.10 2.57
543 544 8.770828 GTGAATAGCGACCTATAATAGCAAAAA 58.229 33.333 0.00 0.00 33.14 1.94
544 545 7.929245 TGTGAATAGCGACCTATAATAGCAAAA 59.071 33.333 0.00 0.00 33.14 2.44
561 569 6.417191 TTCGGTCAAAATAGTGTGAATAGC 57.583 37.500 0.00 0.00 0.00 2.97
562 570 9.840427 AATTTTCGGTCAAAATAGTGTGAATAG 57.160 29.630 0.00 0.00 42.86 1.73
565 573 7.976734 ACAAATTTTCGGTCAAAATAGTGTGAA 59.023 29.630 8.21 0.00 42.86 3.18
639 647 5.806818 TCACCTTCCATGTACGGATAAAAA 58.193 37.500 0.00 0.00 34.19 1.94
641 649 5.423704 TTCACCTTCCATGTACGGATAAA 57.576 39.130 0.00 0.00 34.19 1.40
644 652 3.992943 TTTCACCTTCCATGTACGGAT 57.007 42.857 0.00 0.00 34.19 4.18
647 655 5.371115 ACAAATTTCACCTTCCATGTACG 57.629 39.130 0.00 0.00 0.00 3.67
648 656 7.637709 GAAACAAATTTCACCTTCCATGTAC 57.362 36.000 0.00 0.00 43.29 2.90
796 957 4.402474 GGACAGGAAATTTTGGTCTATGGG 59.598 45.833 13.81 0.00 0.00 4.00
883 1044 2.554370 TAGGTTGGACTTTGGGTTCG 57.446 50.000 0.00 0.00 0.00 3.95
893 1054 2.027837 TCGCTAGGGTTTTAGGTTGGAC 60.028 50.000 6.70 0.00 0.00 4.02
911 1072 2.993539 GGTAGAGATTGCCCTTCGC 58.006 57.895 0.00 0.00 38.31 4.70
1206 1379 2.814023 CTCCAGGTACGAGGAGCAT 58.186 57.895 16.42 0.00 45.29 3.79
1356 1529 1.376424 CCTGATGCGCTTGGAGTGT 60.376 57.895 9.73 0.00 0.00 3.55
1637 1810 1.132643 CGAAGAAGAAGTCGATCCCGT 59.867 52.381 0.00 0.00 39.64 5.28
1794 1972 4.007644 CACACCGGGCAGAGCTCA 62.008 66.667 17.77 0.00 0.00 4.26
2115 2313 0.753848 TGATGATGGCGTCCGTCCTA 60.754 55.000 13.35 0.00 38.69 2.94
2121 2319 2.173669 CACGGTGATGATGGCGTCC 61.174 63.158 0.74 0.00 0.00 4.79
2131 2329 2.261671 GTGCGTCCTCACGGTGAT 59.738 61.111 11.86 0.00 46.80 3.06
2214 2412 2.673200 GCTCTGCCCATCCAGGTCA 61.673 63.158 0.00 0.00 34.66 4.02
2266 2464 2.890371 GCCGCCCTTCTCGTAGAA 59.110 61.111 0.00 0.00 34.09 2.10
2349 2553 1.622449 CCTCCTATCCCCATGGCGATA 60.622 57.143 16.55 16.55 0.00 2.92
2364 2568 0.842635 GGTCCAGATCAATGCCTCCT 59.157 55.000 0.00 0.00 0.00 3.69
2388 2592 0.247460 CATCAAGCTCCACCTCGTCA 59.753 55.000 0.00 0.00 0.00 4.35
2410 2614 1.138661 GATTCTGAGGTCCTCCAGCAG 59.861 57.143 16.60 7.65 38.70 4.24
2490 2698 9.060347 TCCTCAATTTATTTATCAGATGCACTC 57.940 33.333 0.00 0.00 0.00 3.51
2604 2863 5.880332 GTGTGGGAGAATATTAGCAGTTCAA 59.120 40.000 0.00 0.00 0.00 2.69
2622 2881 5.641783 TGATCACAATAAACATGTGTGGG 57.358 39.130 12.03 4.71 46.42 4.61
2672 2931 1.340893 CCATGGGGCATACAGTTGTGA 60.341 52.381 2.85 0.00 0.00 3.58
2698 2957 4.268405 GTGAACATTTGAGTGTTTGGCAAG 59.732 41.667 0.00 0.00 42.08 4.01
2721 2980 2.696187 GCCTTAGGGAGACAGGAAGTAG 59.304 54.545 0.00 0.00 33.58 2.57
2806 3065 3.526899 TGAGGGGATTTTGACTGGTAGA 58.473 45.455 0.00 0.00 0.00 2.59
2807 3066 4.301072 TTGAGGGGATTTTGACTGGTAG 57.699 45.455 0.00 0.00 0.00 3.18
2808 3067 4.733077 TTTGAGGGGATTTTGACTGGTA 57.267 40.909 0.00 0.00 0.00 3.25
2809 3068 3.611025 TTTGAGGGGATTTTGACTGGT 57.389 42.857 0.00 0.00 0.00 4.00
2810 3069 3.448660 GGATTTGAGGGGATTTTGACTGG 59.551 47.826 0.00 0.00 0.00 4.00
2811 3070 4.347607 AGGATTTGAGGGGATTTTGACTG 58.652 43.478 0.00 0.00 0.00 3.51
2812 3071 4.293368 AGAGGATTTGAGGGGATTTTGACT 59.707 41.667 0.00 0.00 0.00 3.41
2813 3072 4.604156 AGAGGATTTGAGGGGATTTTGAC 58.396 43.478 0.00 0.00 0.00 3.18
2814 3073 4.325344 GGAGAGGATTTGAGGGGATTTTGA 60.325 45.833 0.00 0.00 0.00 2.69
2815 3074 3.956848 GGAGAGGATTTGAGGGGATTTTG 59.043 47.826 0.00 0.00 0.00 2.44
2816 3075 3.597868 TGGAGAGGATTTGAGGGGATTTT 59.402 43.478 0.00 0.00 0.00 1.82
2817 3076 3.201363 TGGAGAGGATTTGAGGGGATTT 58.799 45.455 0.00 0.00 0.00 2.17
2818 3077 2.863884 TGGAGAGGATTTGAGGGGATT 58.136 47.619 0.00 0.00 0.00 3.01
2819 3078 2.594536 TGGAGAGGATTTGAGGGGAT 57.405 50.000 0.00 0.00 0.00 3.85
2820 3079 2.359376 TTGGAGAGGATTTGAGGGGA 57.641 50.000 0.00 0.00 0.00 4.81
2821 3080 2.158549 GGATTGGAGAGGATTTGAGGGG 60.159 54.545 0.00 0.00 0.00 4.79
2822 3081 2.158549 GGGATTGGAGAGGATTTGAGGG 60.159 54.545 0.00 0.00 0.00 4.30
2823 3082 2.782341 AGGGATTGGAGAGGATTTGAGG 59.218 50.000 0.00 0.00 0.00 3.86
2824 3083 4.516652 AAGGGATTGGAGAGGATTTGAG 57.483 45.455 0.00 0.00 0.00 3.02
2836 3095 3.245052 ACACCTCTTCTCAAAGGGATTGG 60.245 47.826 0.00 0.00 39.62 3.16
2863 3122 6.351286 GGATGTGAATCATTTAGGCCTTGTTT 60.351 38.462 12.58 4.55 36.83 2.83
3010 3276 7.405292 ACAGGTGATGAAATCTGATTTTAGGA 58.595 34.615 16.14 1.69 45.81 2.94
3011 3277 7.636150 ACAGGTGATGAAATCTGATTTTAGG 57.364 36.000 16.14 4.65 45.81 2.69
3020 3289 6.903516 TCATATCCAACAGGTGATGAAATCT 58.096 36.000 0.00 0.00 45.81 2.40
3042 3311 5.914033 ACGATCCCGAGAATAAGAAATTCA 58.086 37.500 0.00 0.00 39.50 2.57
3081 3350 2.477863 GGCGCGCATTTCTAAGTCAATT 60.478 45.455 34.42 0.00 0.00 2.32
3082 3351 1.064060 GGCGCGCATTTCTAAGTCAAT 59.936 47.619 34.42 0.00 0.00 2.57
3083 3352 0.446222 GGCGCGCATTTCTAAGTCAA 59.554 50.000 34.42 0.00 0.00 3.18
3084 3353 1.366111 GGGCGCGCATTTCTAAGTCA 61.366 55.000 34.42 0.00 0.00 3.41
3156 3425 7.704047 GGAAAACCAGATAATGCAAATTCTCTC 59.296 37.037 0.00 0.00 0.00 3.20
3200 3469 3.569491 CCCATTATTGGAGCCTTGTCAT 58.431 45.455 5.18 0.00 46.92 3.06
3201 3470 2.949963 GCCCATTATTGGAGCCTTGTCA 60.950 50.000 5.18 0.00 46.92 3.58
3202 3471 1.683385 GCCCATTATTGGAGCCTTGTC 59.317 52.381 5.18 0.00 46.92 3.18
3205 3474 1.133356 GGAGCCCATTATTGGAGCCTT 60.133 52.381 5.18 0.00 46.92 4.35
3206 3475 0.480252 GGAGCCCATTATTGGAGCCT 59.520 55.000 5.18 0.00 46.92 4.58
3211 3480 2.077687 AAGCTGGAGCCCATTATTGG 57.922 50.000 0.00 0.00 43.38 3.16
3276 3567 4.660303 TGGATGTTATCTGCCCTGTAGAAT 59.340 41.667 0.00 0.00 0.00 2.40
3396 3691 8.614346 GTTACAACAGTATACTTGTTGGTGAAA 58.386 33.333 30.28 22.00 44.92 2.69


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

AutoCloner maintained by Alex Coulton.