Multiple sequence alignment - TraesCS4D01G209600

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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 TraesCS4D01G209600 chr4D 100.000 2578 0 0 1 2578 360953831 360951254 0.000000e+00 4761.0
1 TraesCS4D01G209600 chr4D 98.707 232 3 0 2077 2308 360951523 360951292 1.850000e-111 412.0
2 TraesCS4D01G209600 chr4D 98.707 232 3 0 2309 2540 360951755 360951524 1.850000e-111 412.0
3 TraesCS4D01G209600 chr4B 90.153 1767 92 36 18 1758 446334416 446336126 0.000000e+00 2224.0
4 TraesCS4D01G209600 chr4B 88.148 270 29 2 2309 2578 446336670 446336936 4.140000e-83 318.0
5 TraesCS4D01G209600 chr4B 89.516 248 23 2 2061 2308 446336654 446336898 6.930000e-81 311.0
6 TraesCS4D01G209600 chr4B 82.555 321 29 5 1742 2056 446336272 446336571 9.150000e-65 257.0
7 TraesCS4D01G209600 chr4B 100.000 29 0 0 1 29 446334142 446334170 1.000000e-03 54.7
8 TraesCS4D01G209600 chr4A 91.456 1346 53 27 18 1348 103726373 103727671 0.000000e+00 1792.0
9 TraesCS4D01G209600 chr4A 96.178 968 34 3 1343 2308 103729651 103730617 0.000000e+00 1580.0
10 TraesCS4D01G209600 chr4A 96.296 270 10 0 2309 2578 103730386 103730655 6.550000e-121 444.0


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 TraesCS4D01G209600 chr4D 360951254 360953831 2577 True 1861.666667 4761 99.138000 1 2578 3 chr4D.!!$R1 2577
1 TraesCS4D01G209600 chr4B 446334142 446336936 2794 False 632.940000 2224 90.074400 1 2578 5 chr4B.!!$F1 2577
2 TraesCS4D01G209600 chr4A 103726373 103730655 4282 False 1272.000000 1792 94.643333 18 2578 3 chr4A.!!$F1 2560

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
225 488 0.032952 ATGATCGCCATTTGCATGCC 59.967 50.0 16.68 0.0 41.33 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 3871 0.598562 TGAGTTCTCACAGCGAGGTC 59.401 55.0 0.0 0.0 42.55 3.85 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
36 295 7.786178 TGGGTGAATTACGAATATTCAGAAG 57.214 36.000 15.57 1.76 41.31 2.85
45 304 3.561725 CGAATATTCAGAAGGCTGGGAAC 59.438 47.826 15.57 0.00 42.53 3.62
50 309 1.004745 TCAGAAGGCTGGGAACATTCC 59.995 52.381 1.70 1.70 46.82 3.01
51 310 1.005215 CAGAAGGCTGGGAACATTCCT 59.995 52.381 10.45 0.00 46.72 3.36
54 313 2.808906 AGGCTGGGAACATTCCTAAC 57.191 50.000 10.45 0.00 46.72 2.34
55 314 2.279173 AGGCTGGGAACATTCCTAACT 58.721 47.619 10.45 3.35 46.72 2.24
58 317 2.369394 CTGGGAACATTCCTAACTGCC 58.631 52.381 10.45 0.00 46.72 4.85
59 318 1.339631 TGGGAACATTCCTAACTGCCG 60.340 52.381 10.45 0.00 46.72 5.69
60 319 0.733150 GGAACATTCCTAACTGCCGC 59.267 55.000 3.24 0.00 44.11 6.53
61 320 1.448985 GAACATTCCTAACTGCCGCA 58.551 50.000 0.00 0.00 0.00 5.69
62 321 2.017049 GAACATTCCTAACTGCCGCAT 58.983 47.619 0.00 0.00 0.00 4.73
80 339 6.095580 TGCCGCATTATGTTTCACCTAAATTA 59.904 34.615 0.00 0.00 0.00 1.40
102 361 9.659135 AATTATTCAGAACCATCCATATTCCAA 57.341 29.630 0.00 0.00 0.00 3.53
115 374 5.363580 TCCATATTCCAATCTTTTCAAGGGC 59.636 40.000 0.00 0.00 0.00 5.19
126 385 2.434709 CAAGGGCGGGCAAATTGC 60.435 61.111 9.87 9.87 44.08 3.56
129 388 1.604147 AAGGGCGGGCAAATTGCTAC 61.604 55.000 18.04 10.15 44.28 3.58
132 391 1.589113 GCGGGCAAATTGCTACCAA 59.411 52.632 18.04 0.00 44.28 3.67
133 392 0.458370 GCGGGCAAATTGCTACCAAG 60.458 55.000 18.04 1.43 44.28 3.61
140 402 4.427312 GCAAATTGCTACCAAGATTCCAG 58.573 43.478 11.19 0.00 40.96 3.86
146 408 3.776969 TGCTACCAAGATTCCAGACATCT 59.223 43.478 0.00 0.00 31.94 2.90
159 422 5.766590 TCCAGACATCTACATCCTTACTCA 58.233 41.667 0.00 0.00 0.00 3.41
161 424 6.096987 TCCAGACATCTACATCCTTACTCAAC 59.903 42.308 0.00 0.00 0.00 3.18
174 437 6.231211 TCCTTACTCAACCATCAAAACTCTC 58.769 40.000 0.00 0.00 0.00 3.20
184 447 4.379813 CCATCAAAACTCTCAAATCCACGG 60.380 45.833 0.00 0.00 0.00 4.94
206 469 4.099881 GGTAATACTACCAATCGACCACCA 59.900 45.833 0.00 0.00 46.23 4.17
208 471 2.691409 ACTACCAATCGACCACCATG 57.309 50.000 0.00 0.00 0.00 3.66
209 472 2.184533 ACTACCAATCGACCACCATGA 58.815 47.619 0.00 0.00 0.00 3.07
210 473 2.771943 ACTACCAATCGACCACCATGAT 59.228 45.455 0.00 0.00 0.00 2.45
211 474 2.332063 ACCAATCGACCACCATGATC 57.668 50.000 0.00 0.00 0.00 2.92
212 475 1.220529 CCAATCGACCACCATGATCG 58.779 55.000 0.00 0.00 33.90 3.69
214 477 0.532862 AATCGACCACCATGATCGCC 60.533 55.000 0.00 0.00 32.29 5.54
215 478 1.685355 ATCGACCACCATGATCGCCA 61.685 55.000 0.00 0.00 32.29 5.69
216 479 1.227645 CGACCACCATGATCGCCAT 60.228 57.895 0.00 0.00 35.44 4.40
217 480 0.815213 CGACCACCATGATCGCCATT 60.815 55.000 0.00 0.00 31.94 3.16
218 481 1.392589 GACCACCATGATCGCCATTT 58.607 50.000 0.00 0.00 31.94 2.32
220 483 0.249155 CCACCATGATCGCCATTTGC 60.249 55.000 0.00 0.00 31.94 3.68
221 484 0.456628 CACCATGATCGCCATTTGCA 59.543 50.000 0.00 0.00 41.33 4.08
222 485 1.067974 CACCATGATCGCCATTTGCAT 59.932 47.619 0.00 0.00 41.33 3.96
223 486 1.067974 ACCATGATCGCCATTTGCATG 59.932 47.619 0.00 0.00 41.33 4.06
224 487 1.136690 CATGATCGCCATTTGCATGC 58.863 50.000 11.82 11.82 41.33 4.06
225 488 0.032952 ATGATCGCCATTTGCATGCC 59.967 50.000 16.68 0.00 41.33 4.40
226 489 1.321074 TGATCGCCATTTGCATGCCA 61.321 50.000 16.68 0.00 41.33 4.92
227 490 0.179105 GATCGCCATTTGCATGCCAA 60.179 50.000 16.68 11.51 41.33 4.52
228 491 0.460635 ATCGCCATTTGCATGCCAAC 60.461 50.000 16.68 0.00 41.33 3.77
229 492 2.101835 CGCCATTTGCATGCCAACC 61.102 57.895 16.68 2.15 41.33 3.77
230 493 2.101835 GCCATTTGCATGCCAACCG 61.102 57.895 16.68 5.54 40.77 4.44
231 494 1.448189 CCATTTGCATGCCAACCGG 60.448 57.895 16.68 11.05 31.97 5.28
232 495 1.292860 CATTTGCATGCCAACCGGT 59.707 52.632 16.68 0.00 31.97 5.28
233 496 0.529833 CATTTGCATGCCAACCGGTA 59.470 50.000 16.68 0.00 31.97 4.02
234 497 1.067283 CATTTGCATGCCAACCGGTAA 60.067 47.619 16.68 0.00 31.97 2.85
235 498 0.315568 TTTGCATGCCAACCGGTAAC 59.684 50.000 16.68 0.00 31.97 2.50
236 499 0.538516 TTGCATGCCAACCGGTAACT 60.539 50.000 16.68 0.00 33.28 2.24
237 500 1.240641 TGCATGCCAACCGGTAACTG 61.241 55.000 16.68 1.67 33.28 3.16
238 501 1.241315 GCATGCCAACCGGTAACTGT 61.241 55.000 8.00 0.00 34.41 3.55
239 502 0.521291 CATGCCAACCGGTAACTGTG 59.479 55.000 8.00 0.73 32.69 3.66
240 503 0.608035 ATGCCAACCGGTAACTGTGG 60.608 55.000 16.55 16.55 32.69 4.17
241 504 4.390048 CCAACCGGTAACTGTGGG 57.610 61.111 8.00 0.00 38.67 4.61
242 505 1.969589 CCAACCGGTAACTGTGGGC 60.970 63.158 8.00 0.00 38.14 5.36
243 506 1.228003 CAACCGGTAACTGTGGGCA 60.228 57.895 8.00 0.00 32.69 5.36
424 687 0.525311 CACAACACAGCACACCACAA 59.475 50.000 0.00 0.00 0.00 3.33
441 704 4.648626 AGCTTGCCTCAGCCGCAA 62.649 61.111 0.00 0.00 43.71 4.85
468 731 7.309377 CCCAAATGAAAACAGCAGAAGAGATAA 60.309 37.037 0.00 0.00 0.00 1.75
469 732 7.540055 CCAAATGAAAACAGCAGAAGAGATAAC 59.460 37.037 0.00 0.00 0.00 1.89
606 870 2.838225 TCTCCCGCTCCCGAATCC 60.838 66.667 0.00 0.00 36.29 3.01
748 1031 1.135915 ACAAACAAACTGGCGAATGCA 59.864 42.857 0.00 0.00 45.35 3.96
752 1035 0.592637 CAAACTGGCGAATGCAGACA 59.407 50.000 0.00 0.00 45.35 3.41
814 1097 0.315568 CCTTCGTCTCGATGGGGATC 59.684 60.000 13.70 0.00 44.09 3.36
841 1124 2.589159 GGAATTCTCTCGGCCGCC 60.589 66.667 23.51 9.67 0.00 6.13
1025 1311 4.390556 AGCGTGCTCTCTCCCCCT 62.391 66.667 0.00 0.00 0.00 4.79
1182 1468 3.840831 CATCGAAGAGGTGGAGCAA 57.159 52.632 0.00 0.00 43.63 3.91
1329 1615 5.352846 TGTTCTTTGTTGTCTGTCGAATCAA 59.647 36.000 0.00 0.00 0.00 2.57
1348 1634 4.697514 TCAATTCGCTCCTCCTTGAATAG 58.302 43.478 0.00 0.00 31.20 1.73
1373 3644 2.670905 CGAATTGCGTTGATGGACAGTA 59.329 45.455 0.00 0.00 34.64 2.74
1391 3671 7.612244 TGGACAGTATTATTTTTGGATTTCGGA 59.388 33.333 0.00 0.00 0.00 4.55
1402 3682 2.093711 TGGATTTCGGAGCTGATTTCGA 60.094 45.455 0.00 0.00 0.00 3.71
1418 3698 5.238650 TGATTTCGAAGGTCTTTTCTGGTTC 59.761 40.000 12.12 0.00 0.00 3.62
1419 3699 4.417426 TTCGAAGGTCTTTTCTGGTTCT 57.583 40.909 0.00 0.00 0.00 3.01
1422 3702 3.304057 CGAAGGTCTTTTCTGGTTCTTGC 60.304 47.826 0.00 0.00 0.00 4.01
1591 3871 2.665537 GACGATGACTGCTTCTTCAGTG 59.334 50.000 0.72 0.00 46.40 3.66
1597 3877 1.000283 ACTGCTTCTTCAGTGACCTCG 60.000 52.381 0.00 0.00 44.88 4.63
1598 3878 0.319900 TGCTTCTTCAGTGACCTCGC 60.320 55.000 0.00 0.00 0.00 5.03
1617 3897 1.085091 CTGTGAGAACTCATGGCTGC 58.915 55.000 7.77 0.00 42.18 5.25
1669 3949 3.133542 AGCTTTTCTGCCTTTGCTTCTTT 59.866 39.130 0.00 0.00 38.71 2.52
1842 4287 1.994916 TTGTACTTTAGCGCGGGTAC 58.005 50.000 8.83 19.89 36.19 3.34
1951 4396 8.170553 CACTCACATTTGGAAGTTTTTCTTTTG 58.829 33.333 0.00 0.00 36.40 2.44
2116 4643 8.522178 AAAACTCTAGACAGAAGACAAATACG 57.478 34.615 0.00 0.00 0.00 3.06
2308 4835 2.292267 CATGGTTCAGCTGGTCCATAC 58.708 52.381 29.16 13.87 38.43 2.39
2309 4836 1.357137 TGGTTCAGCTGGTCCATACA 58.643 50.000 20.98 7.20 0.00 2.29
2310 4837 1.915489 TGGTTCAGCTGGTCCATACAT 59.085 47.619 20.98 0.00 0.00 2.29
2311 4838 2.092968 TGGTTCAGCTGGTCCATACATC 60.093 50.000 20.98 0.00 0.00 3.06
2312 4839 2.092968 GGTTCAGCTGGTCCATACATCA 60.093 50.000 15.13 0.00 0.00 3.07
2313 4840 3.434167 GGTTCAGCTGGTCCATACATCAT 60.434 47.826 15.13 0.00 0.00 2.45
2314 4841 4.202441 GTTCAGCTGGTCCATACATCATT 58.798 43.478 15.13 0.00 0.00 2.57
2315 4842 4.508551 TCAGCTGGTCCATACATCATTT 57.491 40.909 15.13 0.00 0.00 2.32
2316 4843 4.858850 TCAGCTGGTCCATACATCATTTT 58.141 39.130 15.13 0.00 0.00 1.82
2317 4844 5.263599 TCAGCTGGTCCATACATCATTTTT 58.736 37.500 15.13 0.00 0.00 1.94
2318 4845 6.422333 TCAGCTGGTCCATACATCATTTTTA 58.578 36.000 15.13 0.00 0.00 1.52
2319 4846 6.318648 TCAGCTGGTCCATACATCATTTTTAC 59.681 38.462 15.13 0.00 0.00 2.01
2320 4847 6.095300 CAGCTGGTCCATACATCATTTTTACA 59.905 38.462 5.57 0.00 0.00 2.41
2321 4848 6.663093 AGCTGGTCCATACATCATTTTTACAA 59.337 34.615 0.00 0.00 0.00 2.41
2322 4849 6.974622 GCTGGTCCATACATCATTTTTACAAG 59.025 38.462 0.00 0.00 0.00 3.16
2323 4850 7.148086 GCTGGTCCATACATCATTTTTACAAGA 60.148 37.037 0.00 0.00 0.00 3.02
2324 4851 8.642935 TGGTCCATACATCATTTTTACAAGAA 57.357 30.769 0.00 0.00 0.00 2.52
2325 4852 9.083422 TGGTCCATACATCATTTTTACAAGAAA 57.917 29.630 0.00 0.00 0.00 2.52
2326 4853 9.921637 GGTCCATACATCATTTTTACAAGAAAA 57.078 29.630 0.00 0.00 33.46 2.29
2341 4868 9.530633 TTTACAAGAAAACTCTAGACAGAAGAC 57.469 33.333 0.00 0.00 0.00 3.01
2342 4869 7.113658 ACAAGAAAACTCTAGACAGAAGACA 57.886 36.000 0.00 0.00 0.00 3.41
2343 4870 7.556844 ACAAGAAAACTCTAGACAGAAGACAA 58.443 34.615 0.00 0.00 0.00 3.18
2344 4871 8.041323 ACAAGAAAACTCTAGACAGAAGACAAA 58.959 33.333 0.00 0.00 0.00 2.83
2345 4872 9.050601 CAAGAAAACTCTAGACAGAAGACAAAT 57.949 33.333 0.00 0.00 0.00 2.32
2347 4874 9.699703 AGAAAACTCTAGACAGAAGACAAATAC 57.300 33.333 0.00 0.00 0.00 1.89
2348 4875 9.477484 GAAAACTCTAGACAGAAGACAAATACA 57.523 33.333 0.00 0.00 0.00 2.29
2349 4876 9.832445 AAAACTCTAGACAGAAGACAAATACAA 57.168 29.630 0.00 0.00 0.00 2.41
2350 4877 9.832445 AAACTCTAGACAGAAGACAAATACAAA 57.168 29.630 0.00 0.00 0.00 2.83
2351 4878 9.832445 AACTCTAGACAGAAGACAAATACAAAA 57.168 29.630 0.00 0.00 0.00 2.44
2352 4879 9.482627 ACTCTAGACAGAAGACAAATACAAAAG 57.517 33.333 0.00 0.00 0.00 2.27
2353 4880 9.698309 CTCTAGACAGAAGACAAATACAAAAGA 57.302 33.333 0.00 0.00 0.00 2.52
2356 4883 7.931275 AGACAGAAGACAAATACAAAAGAACC 58.069 34.615 0.00 0.00 0.00 3.62
2357 4884 7.556275 AGACAGAAGACAAATACAAAAGAACCA 59.444 33.333 0.00 0.00 0.00 3.67
2358 4885 8.062065 ACAGAAGACAAATACAAAAGAACCAA 57.938 30.769 0.00 0.00 0.00 3.67
2359 4886 7.973944 ACAGAAGACAAATACAAAAGAACCAAC 59.026 33.333 0.00 0.00 0.00 3.77
2360 4887 7.973388 CAGAAGACAAATACAAAAGAACCAACA 59.027 33.333 0.00 0.00 0.00 3.33
2361 4888 7.973944 AGAAGACAAATACAAAAGAACCAACAC 59.026 33.333 0.00 0.00 0.00 3.32
2362 4889 7.164230 AGACAAATACAAAAGAACCAACACA 57.836 32.000 0.00 0.00 0.00 3.72
2363 4890 7.781056 AGACAAATACAAAAGAACCAACACAT 58.219 30.769 0.00 0.00 0.00 3.21
2364 4891 7.920682 AGACAAATACAAAAGAACCAACACATC 59.079 33.333 0.00 0.00 0.00 3.06
2365 4892 6.695278 ACAAATACAAAAGAACCAACACATCG 59.305 34.615 0.00 0.00 0.00 3.84
2366 4893 6.627395 AATACAAAAGAACCAACACATCGA 57.373 33.333 0.00 0.00 0.00 3.59
2367 4894 4.974368 ACAAAAGAACCAACACATCGAA 57.026 36.364 0.00 0.00 0.00 3.71
2368 4895 5.514274 ACAAAAGAACCAACACATCGAAT 57.486 34.783 0.00 0.00 0.00 3.34
2369 4896 5.901552 ACAAAAGAACCAACACATCGAATT 58.098 33.333 0.00 0.00 0.00 2.17
2370 4897 6.337356 ACAAAAGAACCAACACATCGAATTT 58.663 32.000 0.00 0.00 0.00 1.82
2371 4898 6.816140 ACAAAAGAACCAACACATCGAATTTT 59.184 30.769 0.00 0.00 0.00 1.82
2372 4899 6.826893 AAAGAACCAACACATCGAATTTTG 57.173 33.333 0.00 0.00 0.00 2.44
2373 4900 5.514274 AGAACCAACACATCGAATTTTGT 57.486 34.783 0.00 0.00 0.00 2.83
2374 4901 6.627395 AGAACCAACACATCGAATTTTGTA 57.373 33.333 0.00 0.00 0.00 2.41
2375 4902 6.435428 AGAACCAACACATCGAATTTTGTAC 58.565 36.000 0.00 0.00 0.00 2.90
2376 4903 6.262273 AGAACCAACACATCGAATTTTGTACT 59.738 34.615 0.00 0.00 0.00 2.73
2377 4904 7.442969 AGAACCAACACATCGAATTTTGTACTA 59.557 33.333 0.00 0.00 0.00 1.82
2378 4905 7.681939 ACCAACACATCGAATTTTGTACTAT 57.318 32.000 0.00 0.00 0.00 2.12
2379 4906 7.526608 ACCAACACATCGAATTTTGTACTATG 58.473 34.615 0.00 0.00 0.00 2.23
2380 4907 6.966632 CCAACACATCGAATTTTGTACTATGG 59.033 38.462 0.00 0.00 0.00 2.74
2381 4908 7.148323 CCAACACATCGAATTTTGTACTATGGA 60.148 37.037 0.00 0.00 0.00 3.41
2382 4909 8.397906 CAACACATCGAATTTTGTACTATGGAT 58.602 33.333 0.00 0.00 0.00 3.41
2383 4910 9.607988 AACACATCGAATTTTGTACTATGGATA 57.392 29.630 0.00 0.00 0.00 2.59
2384 4911 9.042008 ACACATCGAATTTTGTACTATGGATAC 57.958 33.333 0.00 0.00 0.00 2.24
2402 4929 6.242508 GGATACAAAAGAACCAAGACACTC 57.757 41.667 0.00 0.00 0.00 3.51
2403 4930 5.107065 GGATACAAAAGAACCAAGACACTCG 60.107 44.000 0.00 0.00 0.00 4.18
2404 4931 2.354821 ACAAAAGAACCAAGACACTCGC 59.645 45.455 0.00 0.00 0.00 5.03
2405 4932 2.325583 AAAGAACCAAGACACTCGCA 57.674 45.000 0.00 0.00 0.00 5.10
2406 4933 2.550830 AAGAACCAAGACACTCGCAT 57.449 45.000 0.00 0.00 0.00 4.73
2407 4934 3.678056 AAGAACCAAGACACTCGCATA 57.322 42.857 0.00 0.00 0.00 3.14
2408 4935 3.895232 AGAACCAAGACACTCGCATAT 57.105 42.857 0.00 0.00 0.00 1.78
2409 4936 3.525537 AGAACCAAGACACTCGCATATG 58.474 45.455 0.00 0.00 0.00 1.78
2410 4937 2.315925 ACCAAGACACTCGCATATGG 57.684 50.000 4.56 0.00 0.00 2.74
2411 4938 1.831106 ACCAAGACACTCGCATATGGA 59.169 47.619 4.56 0.00 0.00 3.41
2412 4939 2.236146 ACCAAGACACTCGCATATGGAA 59.764 45.455 4.56 0.00 0.00 3.53
2413 4940 2.868583 CCAAGACACTCGCATATGGAAG 59.131 50.000 4.56 0.00 0.00 3.46
2414 4941 3.525537 CAAGACACTCGCATATGGAAGT 58.474 45.455 4.56 2.49 0.00 3.01
2415 4942 4.441495 CCAAGACACTCGCATATGGAAGTA 60.441 45.833 4.56 0.00 0.00 2.24
2416 4943 5.292765 CAAGACACTCGCATATGGAAGTAT 58.707 41.667 4.56 0.00 0.00 2.12
2417 4944 5.537300 AGACACTCGCATATGGAAGTATT 57.463 39.130 4.56 0.00 0.00 1.89
2418 4945 5.533482 AGACACTCGCATATGGAAGTATTC 58.467 41.667 4.56 2.53 46.67 1.75
2458 4985 7.900782 AATAGTATTCAACCACCGTATATGC 57.099 36.000 0.00 0.00 0.00 3.14
2459 4986 5.546621 AGTATTCAACCACCGTATATGCT 57.453 39.130 0.00 0.00 0.00 3.79
2460 4987 6.659745 AGTATTCAACCACCGTATATGCTA 57.340 37.500 0.00 0.00 0.00 3.49
2461 4988 6.453092 AGTATTCAACCACCGTATATGCTAC 58.547 40.000 0.00 0.00 0.00 3.58
2462 4989 5.546621 ATTCAACCACCGTATATGCTACT 57.453 39.130 0.00 0.00 0.00 2.57
2463 4990 6.659745 ATTCAACCACCGTATATGCTACTA 57.340 37.500 0.00 0.00 0.00 1.82
2464 4991 6.659745 TTCAACCACCGTATATGCTACTAT 57.340 37.500 0.00 0.00 0.00 2.12
2465 4992 6.263516 TCAACCACCGTATATGCTACTATC 57.736 41.667 0.00 0.00 0.00 2.08
2466 4993 5.771165 TCAACCACCGTATATGCTACTATCA 59.229 40.000 0.00 0.00 0.00 2.15
2467 4994 5.899120 ACCACCGTATATGCTACTATCAG 57.101 43.478 0.00 0.00 0.00 2.90
2468 4995 5.567430 ACCACCGTATATGCTACTATCAGA 58.433 41.667 0.00 0.00 0.00 3.27
2469 4996 6.008331 ACCACCGTATATGCTACTATCAGAA 58.992 40.000 0.00 0.00 0.00 3.02
2470 4997 6.492429 ACCACCGTATATGCTACTATCAGAAA 59.508 38.462 0.00 0.00 0.00 2.52
2471 4998 7.178628 ACCACCGTATATGCTACTATCAGAAAT 59.821 37.037 0.00 0.00 0.00 2.17
2472 4999 8.035394 CCACCGTATATGCTACTATCAGAAATT 58.965 37.037 0.00 0.00 0.00 1.82
2473 5000 9.424319 CACCGTATATGCTACTATCAGAAATTT 57.576 33.333 0.00 0.00 0.00 1.82
2474 5001 9.424319 ACCGTATATGCTACTATCAGAAATTTG 57.576 33.333 0.00 0.00 0.00 2.32
2475 5002 9.424319 CCGTATATGCTACTATCAGAAATTTGT 57.576 33.333 0.00 0.00 0.00 2.83
2481 5008 9.890629 ATGCTACTATCAGAAATTTGTACTTCA 57.109 29.630 0.00 0.00 0.00 3.02
2482 5009 9.371136 TGCTACTATCAGAAATTTGTACTTCAG 57.629 33.333 0.00 0.00 0.00 3.02
2483 5010 8.331742 GCTACTATCAGAAATTTGTACTTCAGC 58.668 37.037 0.00 0.00 0.00 4.26
2484 5011 7.617041 ACTATCAGAAATTTGTACTTCAGCC 57.383 36.000 0.00 0.00 0.00 4.85
2485 5012 7.168219 ACTATCAGAAATTTGTACTTCAGCCA 58.832 34.615 0.00 0.00 0.00 4.75
2486 5013 5.947228 TCAGAAATTTGTACTTCAGCCAG 57.053 39.130 0.00 0.00 0.00 4.85
2487 5014 5.620206 TCAGAAATTTGTACTTCAGCCAGA 58.380 37.500 0.00 0.00 0.00 3.86
2488 5015 5.702670 TCAGAAATTTGTACTTCAGCCAGAG 59.297 40.000 0.00 0.00 0.00 3.35
2489 5016 5.702670 CAGAAATTTGTACTTCAGCCAGAGA 59.297 40.000 0.00 0.00 0.00 3.10
2490 5017 5.936956 AGAAATTTGTACTTCAGCCAGAGAG 59.063 40.000 0.00 0.00 0.00 3.20
2491 5018 2.751166 TTGTACTTCAGCCAGAGAGC 57.249 50.000 0.00 0.00 0.00 4.09
2492 5019 1.632589 TGTACTTCAGCCAGAGAGCA 58.367 50.000 0.00 0.00 34.23 4.26
2493 5020 1.547820 TGTACTTCAGCCAGAGAGCAG 59.452 52.381 0.00 0.00 34.23 4.24
2494 5021 1.821753 GTACTTCAGCCAGAGAGCAGA 59.178 52.381 0.00 0.00 34.23 4.26
2495 5022 1.346062 ACTTCAGCCAGAGAGCAGAA 58.654 50.000 0.00 0.00 36.10 3.02
2496 5023 1.696336 ACTTCAGCCAGAGAGCAGAAA 59.304 47.619 0.00 0.00 37.74 2.52
2497 5024 2.289569 ACTTCAGCCAGAGAGCAGAAAG 60.290 50.000 0.00 0.00 37.74 2.62
2498 5025 1.637338 TCAGCCAGAGAGCAGAAAGA 58.363 50.000 0.00 0.00 34.23 2.52
2499 5026 2.186243 TCAGCCAGAGAGCAGAAAGAT 58.814 47.619 0.00 0.00 34.23 2.40
2500 5027 2.093606 TCAGCCAGAGAGCAGAAAGATG 60.094 50.000 0.00 0.00 34.23 2.90
2501 5028 1.209990 AGCCAGAGAGCAGAAAGATGG 59.790 52.381 0.00 0.00 34.23 3.51
2502 5029 1.209019 GCCAGAGAGCAGAAAGATGGA 59.791 52.381 0.00 0.00 0.00 3.41
2503 5030 2.742530 GCCAGAGAGCAGAAAGATGGAG 60.743 54.545 0.00 0.00 0.00 3.86
2504 5031 2.765135 CCAGAGAGCAGAAAGATGGAGA 59.235 50.000 0.00 0.00 0.00 3.71
2505 5032 3.181473 CCAGAGAGCAGAAAGATGGAGAG 60.181 52.174 0.00 0.00 0.00 3.20
2506 5033 3.700539 CAGAGAGCAGAAAGATGGAGAGA 59.299 47.826 0.00 0.00 0.00 3.10
2507 5034 3.956199 AGAGAGCAGAAAGATGGAGAGAG 59.044 47.826 0.00 0.00 0.00 3.20
2508 5035 3.033184 AGAGCAGAAAGATGGAGAGAGG 58.967 50.000 0.00 0.00 0.00 3.69
2509 5036 3.030291 GAGCAGAAAGATGGAGAGAGGA 58.970 50.000 0.00 0.00 0.00 3.71
2510 5037 3.642848 GAGCAGAAAGATGGAGAGAGGAT 59.357 47.826 0.00 0.00 0.00 3.24
2511 5038 4.039339 AGCAGAAAGATGGAGAGAGGATT 58.961 43.478 0.00 0.00 0.00 3.01
2512 5039 4.474287 AGCAGAAAGATGGAGAGAGGATTT 59.526 41.667 0.00 0.00 0.00 2.17
2513 5040 4.575645 GCAGAAAGATGGAGAGAGGATTTG 59.424 45.833 0.00 0.00 0.00 2.32
2514 5041 4.575645 CAGAAAGATGGAGAGAGGATTTGC 59.424 45.833 0.00 0.00 0.00 3.68
2515 5042 4.474287 AGAAAGATGGAGAGAGGATTTGCT 59.526 41.667 0.00 0.00 0.00 3.91
2516 5043 5.664908 AGAAAGATGGAGAGAGGATTTGCTA 59.335 40.000 0.00 0.00 0.00 3.49
2517 5044 5.965033 AAGATGGAGAGAGGATTTGCTAA 57.035 39.130 0.00 0.00 0.00 3.09
2518 5045 5.289083 AGATGGAGAGAGGATTTGCTAAC 57.711 43.478 0.00 0.00 0.00 2.34
2519 5046 3.914426 TGGAGAGAGGATTTGCTAACC 57.086 47.619 0.00 0.00 0.00 2.85
2520 5047 2.505819 TGGAGAGAGGATTTGCTAACCC 59.494 50.000 0.00 0.00 0.00 4.11
2521 5048 2.505819 GGAGAGAGGATTTGCTAACCCA 59.494 50.000 0.00 0.00 0.00 4.51
2522 5049 3.137360 GGAGAGAGGATTTGCTAACCCAT 59.863 47.826 0.00 0.00 0.00 4.00
2523 5050 4.133078 GAGAGAGGATTTGCTAACCCATG 58.867 47.826 0.00 0.00 0.00 3.66
2524 5051 3.117738 AGAGAGGATTTGCTAACCCATGG 60.118 47.826 4.14 4.14 0.00 3.66
2525 5052 2.582636 AGAGGATTTGCTAACCCATGGT 59.417 45.455 11.73 0.00 37.65 3.55
2527 5054 3.365472 AGGATTTGCTAACCCATGGTTC 58.635 45.455 11.73 0.00 43.05 3.62
2528 5055 3.096092 GGATTTGCTAACCCATGGTTCA 58.904 45.455 11.73 0.00 43.05 3.18
2529 5056 3.131046 GGATTTGCTAACCCATGGTTCAG 59.869 47.826 11.73 5.20 43.05 3.02
2530 5057 1.544724 TTGCTAACCCATGGTTCAGC 58.455 50.000 11.73 15.29 43.05 4.26
2531 5058 0.698238 TGCTAACCCATGGTTCAGCT 59.302 50.000 22.16 0.00 43.05 4.24
2532 5059 1.098050 GCTAACCCATGGTTCAGCTG 58.902 55.000 11.73 7.63 43.05 4.24
2533 5060 1.755179 CTAACCCATGGTTCAGCTGG 58.245 55.000 15.13 0.00 43.05 4.85
2534 5061 1.004745 CTAACCCATGGTTCAGCTGGT 59.995 52.381 15.13 0.00 43.05 4.00
2535 5062 0.251341 AACCCATGGTTCAGCTGGTC 60.251 55.000 15.13 7.19 43.05 4.02
2536 5063 1.379044 CCCATGGTTCAGCTGGTCC 60.379 63.158 15.13 16.40 0.00 4.46
2537 5064 1.379916 CCATGGTTCAGCTGGTCCA 59.620 57.895 24.83 24.83 0.00 4.02
2538 5065 0.033796 CCATGGTTCAGCTGGTCCAT 60.034 55.000 26.38 26.38 40.73 3.41
2539 5066 1.212688 CCATGGTTCAGCTGGTCCATA 59.787 52.381 29.16 13.69 38.43 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 304 3.565482 ACATAATGCGGCAGTTAGGAATG 59.435 43.478 8.69 8.37 0.00 2.67
50 309 4.342772 GTGAAACATAATGCGGCAGTTAG 58.657 43.478 8.69 4.21 36.32 2.34
51 310 3.127895 GGTGAAACATAATGCGGCAGTTA 59.872 43.478 8.69 7.69 39.98 2.24
54 313 1.745087 AGGTGAAACATAATGCGGCAG 59.255 47.619 9.25 0.00 39.98 4.85
55 314 1.832883 AGGTGAAACATAATGCGGCA 58.167 45.000 4.58 4.58 39.98 5.69
58 317 9.729023 TGAATAATTTAGGTGAAACATAATGCG 57.271 29.630 0.00 0.00 43.15 4.73
80 339 7.533083 AGATTGGAATATGGATGGTTCTGAAT 58.467 34.615 0.00 0.00 0.00 2.57
115 374 1.173043 TCTTGGTAGCAATTTGCCCG 58.827 50.000 17.51 2.23 46.52 6.13
126 385 6.471233 TGTAGATGTCTGGAATCTTGGTAG 57.529 41.667 0.00 0.00 35.92 3.18
129 388 5.071519 AGGATGTAGATGTCTGGAATCTTGG 59.928 44.000 0.00 0.00 35.92 3.61
132 391 7.072562 AGTAAGGATGTAGATGTCTGGAATCT 58.927 38.462 0.00 0.00 38.03 2.40
133 392 7.014711 TGAGTAAGGATGTAGATGTCTGGAATC 59.985 40.741 0.00 0.00 0.00 2.52
140 402 6.222038 TGGTTGAGTAAGGATGTAGATGTC 57.778 41.667 0.00 0.00 0.00 3.06
146 408 7.458397 AGTTTTGATGGTTGAGTAAGGATGTA 58.542 34.615 0.00 0.00 0.00 2.29
159 422 5.278463 CGTGGATTTGAGAGTTTTGATGGTT 60.278 40.000 0.00 0.00 0.00 3.67
161 424 4.379813 CCGTGGATTTGAGAGTTTTGATGG 60.380 45.833 0.00 0.00 0.00 3.51
184 447 5.266733 TGGTGGTCGATTGGTAGTATTAC 57.733 43.478 0.00 0.00 0.00 1.89
212 475 2.101835 CGGTTGGCATGCAAATGGC 61.102 57.895 21.36 6.90 45.99 4.40
214 477 0.529833 TACCGGTTGGCATGCAAATG 59.470 50.000 21.36 11.28 39.70 2.32
215 478 1.067213 GTTACCGGTTGGCATGCAAAT 60.067 47.619 21.36 1.52 39.70 2.32
216 479 0.315568 GTTACCGGTTGGCATGCAAA 59.684 50.000 21.36 12.68 39.70 3.68
217 480 0.538516 AGTTACCGGTTGGCATGCAA 60.539 50.000 21.36 4.92 39.70 4.08
218 481 1.074072 AGTTACCGGTTGGCATGCA 59.926 52.632 21.36 2.54 39.70 3.96
220 483 0.521291 CACAGTTACCGGTTGGCATG 59.479 55.000 15.04 7.93 39.70 4.06
221 484 0.608035 CCACAGTTACCGGTTGGCAT 60.608 55.000 15.04 0.00 39.70 4.40
222 485 1.228003 CCACAGTTACCGGTTGGCA 60.228 57.895 15.04 0.00 39.70 4.92
223 486 1.969589 CCCACAGTTACCGGTTGGC 60.970 63.158 15.04 3.12 39.70 4.52
224 487 1.969589 GCCCACAGTTACCGGTTGG 60.970 63.158 15.04 14.60 42.84 3.77
225 488 0.820074 TTGCCCACAGTTACCGGTTG 60.820 55.000 15.04 8.05 0.00 3.77
226 489 0.820482 GTTGCCCACAGTTACCGGTT 60.820 55.000 15.04 0.00 0.00 4.44
227 490 1.228033 GTTGCCCACAGTTACCGGT 60.228 57.895 13.98 13.98 0.00 5.28
228 491 1.072505 AGTTGCCCACAGTTACCGG 59.927 57.895 0.00 0.00 0.00 5.28
229 492 0.250124 TCAGTTGCCCACAGTTACCG 60.250 55.000 0.00 0.00 0.00 4.02
230 493 2.084546 GATCAGTTGCCCACAGTTACC 58.915 52.381 0.00 0.00 0.00 2.85
231 494 2.084546 GGATCAGTTGCCCACAGTTAC 58.915 52.381 0.00 0.00 0.00 2.50
232 495 1.338674 CGGATCAGTTGCCCACAGTTA 60.339 52.381 0.00 0.00 0.00 2.24
233 496 0.606401 CGGATCAGTTGCCCACAGTT 60.606 55.000 0.00 0.00 0.00 3.16
234 497 1.003355 CGGATCAGTTGCCCACAGT 60.003 57.895 0.00 0.00 0.00 3.55
235 498 0.249120 TACGGATCAGTTGCCCACAG 59.751 55.000 3.18 0.00 0.00 3.66
236 499 0.036765 GTACGGATCAGTTGCCCACA 60.037 55.000 3.18 0.00 0.00 4.17
237 500 0.743345 GGTACGGATCAGTTGCCCAC 60.743 60.000 3.18 0.00 0.00 4.61
238 501 0.907704 AGGTACGGATCAGTTGCCCA 60.908 55.000 3.18 0.00 0.00 5.36
239 502 0.252197 AAGGTACGGATCAGTTGCCC 59.748 55.000 3.18 2.63 0.00 5.36
240 503 1.653151 GAAGGTACGGATCAGTTGCC 58.347 55.000 3.18 7.42 0.00 4.52
241 504 1.135199 TCGAAGGTACGGATCAGTTGC 60.135 52.381 3.18 0.00 0.00 4.17
242 505 2.933495 TCGAAGGTACGGATCAGTTG 57.067 50.000 3.18 0.00 0.00 3.16
243 506 2.758979 ACATCGAAGGTACGGATCAGTT 59.241 45.455 3.18 0.00 0.00 3.16
424 687 4.648626 TTGCGGCTGAGGCAAGCT 62.649 61.111 6.86 0.00 44.79 3.74
441 704 3.960102 TCTTCTGCTGTTTTCATTTGGGT 59.040 39.130 0.00 0.00 0.00 4.51
468 731 1.614317 CGAAGGGAAATGGAGGCTTGT 60.614 52.381 0.00 0.00 0.00 3.16
469 732 1.098050 CGAAGGGAAATGGAGGCTTG 58.902 55.000 0.00 0.00 0.00 4.01
731 1009 1.001378 GTCTGCATTCGCCAGTTTGTT 60.001 47.619 0.00 0.00 37.32 2.83
814 1097 4.047822 CCGAGAGAATTCCAGAGAAATCG 58.952 47.826 0.65 1.28 37.06 3.34
1017 1303 2.015726 GAGAGGGAGGAGGGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
1045 1331 3.849951 CGCTGGCCTGGGTATCGT 61.850 66.667 17.33 0.00 0.00 3.73
1182 1468 1.528824 CCTCATCATGGCCTCGGTT 59.471 57.895 3.32 0.00 0.00 4.44
1302 1588 5.216566 TCGACAGACAACAAAGAACAAAG 57.783 39.130 0.00 0.00 0.00 2.77
1329 1615 4.262249 GCTACTATTCAAGGAGGAGCGAAT 60.262 45.833 0.00 0.00 36.55 3.34
1338 1624 3.802139 CGCAATTCGCTACTATTCAAGGA 59.198 43.478 0.00 0.00 39.08 3.36
1348 1634 1.663643 TCCATCAACGCAATTCGCTAC 59.336 47.619 0.00 0.00 43.23 3.58
1373 3644 6.773976 TCAGCTCCGAAATCCAAAAATAAT 57.226 33.333 0.00 0.00 0.00 1.28
1391 3671 4.453819 CAGAAAAGACCTTCGAAATCAGCT 59.546 41.667 10.74 0.00 0.00 4.24
1402 3682 3.903467 AGCAAGAACCAGAAAAGACCTT 58.097 40.909 0.00 0.00 0.00 3.50
1418 3698 2.478894 CTGCATTTCCAGCAAAAGCAAG 59.521 45.455 0.00 0.00 45.55 4.01
1419 3699 2.485903 CTGCATTTCCAGCAAAAGCAA 58.514 42.857 0.00 0.00 45.55 3.91
1422 3702 2.036217 TCACCTGCATTTCCAGCAAAAG 59.964 45.455 0.00 0.00 42.17 2.27
1591 3871 0.598562 TGAGTTCTCACAGCGAGGTC 59.401 55.000 0.00 0.00 42.55 3.85
1597 3877 1.085091 CAGCCATGAGTTCTCACAGC 58.915 55.000 14.23 14.23 0.00 4.40
1598 3878 1.085091 GCAGCCATGAGTTCTCACAG 58.915 55.000 4.58 1.27 0.00 3.66
1617 3897 3.839293 CTCACCGAGGTTACAGAAGAAG 58.161 50.000 0.00 0.00 0.00 2.85
1669 3949 7.328404 TGGATCTAATATTACTGCCATTCCA 57.672 36.000 0.00 0.00 0.00 3.53
1789 4231 4.826274 AGCATATACGGTGGCTGAATAT 57.174 40.909 0.00 0.00 34.83 1.28
1842 4287 1.135972 GCTGTCACACCGTAAGCATTG 60.136 52.381 0.00 0.00 34.01 2.82
1965 4410 6.640907 GCGTCTTCCATCTAAAAACATGTTTT 59.359 34.615 27.01 27.01 43.88 2.43
2116 4643 6.475402 ACAAAATTCGATGTGTTGGTTCTTTC 59.525 34.615 6.29 0.00 0.00 2.62
2315 4842 9.530633 GTCTTCTGTCTAGAGTTTTCTTGTAAA 57.469 33.333 0.00 0.00 34.79 2.01
2316 4843 8.692710 TGTCTTCTGTCTAGAGTTTTCTTGTAA 58.307 33.333 0.00 0.00 34.79 2.41
2317 4844 8.234136 TGTCTTCTGTCTAGAGTTTTCTTGTA 57.766 34.615 0.00 0.00 34.79 2.41
2318 4845 7.113658 TGTCTTCTGTCTAGAGTTTTCTTGT 57.886 36.000 0.00 0.00 34.79 3.16
2319 4846 8.425577 TTTGTCTTCTGTCTAGAGTTTTCTTG 57.574 34.615 0.00 0.00 34.79 3.02
2321 4848 9.699703 GTATTTGTCTTCTGTCTAGAGTTTTCT 57.300 33.333 0.00 0.00 37.46 2.52
2322 4849 9.477484 TGTATTTGTCTTCTGTCTAGAGTTTTC 57.523 33.333 0.00 0.00 33.70 2.29
2323 4850 9.832445 TTGTATTTGTCTTCTGTCTAGAGTTTT 57.168 29.630 0.00 0.00 33.70 2.43
2324 4851 9.832445 TTTGTATTTGTCTTCTGTCTAGAGTTT 57.168 29.630 0.00 0.00 33.70 2.66
2325 4852 9.832445 TTTTGTATTTGTCTTCTGTCTAGAGTT 57.168 29.630 0.00 0.00 33.70 3.01
2326 4853 9.482627 CTTTTGTATTTGTCTTCTGTCTAGAGT 57.517 33.333 0.00 0.00 33.70 3.24
2327 4854 9.698309 TCTTTTGTATTTGTCTTCTGTCTAGAG 57.302 33.333 0.00 0.00 33.70 2.43
2330 4857 9.052759 GGTTCTTTTGTATTTGTCTTCTGTCTA 57.947 33.333 0.00 0.00 0.00 2.59
2331 4858 7.556275 TGGTTCTTTTGTATTTGTCTTCTGTCT 59.444 33.333 0.00 0.00 0.00 3.41
2332 4859 7.703328 TGGTTCTTTTGTATTTGTCTTCTGTC 58.297 34.615 0.00 0.00 0.00 3.51
2333 4860 7.639113 TGGTTCTTTTGTATTTGTCTTCTGT 57.361 32.000 0.00 0.00 0.00 3.41
2334 4861 7.973388 TGTTGGTTCTTTTGTATTTGTCTTCTG 59.027 33.333 0.00 0.00 0.00 3.02
2335 4862 7.973944 GTGTTGGTTCTTTTGTATTTGTCTTCT 59.026 33.333 0.00 0.00 0.00 2.85
2336 4863 7.757624 TGTGTTGGTTCTTTTGTATTTGTCTTC 59.242 33.333 0.00 0.00 0.00 2.87
2337 4864 7.607250 TGTGTTGGTTCTTTTGTATTTGTCTT 58.393 30.769 0.00 0.00 0.00 3.01
2338 4865 7.164230 TGTGTTGGTTCTTTTGTATTTGTCT 57.836 32.000 0.00 0.00 0.00 3.41
2339 4866 7.096640 CGATGTGTTGGTTCTTTTGTATTTGTC 60.097 37.037 0.00 0.00 0.00 3.18
2340 4867 6.695278 CGATGTGTTGGTTCTTTTGTATTTGT 59.305 34.615 0.00 0.00 0.00 2.83
2341 4868 6.915300 TCGATGTGTTGGTTCTTTTGTATTTG 59.085 34.615 0.00 0.00 0.00 2.32
2342 4869 7.033530 TCGATGTGTTGGTTCTTTTGTATTT 57.966 32.000 0.00 0.00 0.00 1.40
2343 4870 6.627395 TCGATGTGTTGGTTCTTTTGTATT 57.373 33.333 0.00 0.00 0.00 1.89
2344 4871 6.627395 TTCGATGTGTTGGTTCTTTTGTAT 57.373 33.333 0.00 0.00 0.00 2.29
2345 4872 6.627395 ATTCGATGTGTTGGTTCTTTTGTA 57.373 33.333 0.00 0.00 0.00 2.41
2346 4873 4.974368 TTCGATGTGTTGGTTCTTTTGT 57.026 36.364 0.00 0.00 0.00 2.83
2347 4874 6.826893 AAATTCGATGTGTTGGTTCTTTTG 57.173 33.333 0.00 0.00 0.00 2.44
2348 4875 6.816140 ACAAAATTCGATGTGTTGGTTCTTTT 59.184 30.769 6.29 0.00 0.00 2.27
2349 4876 6.337356 ACAAAATTCGATGTGTTGGTTCTTT 58.663 32.000 6.29 0.00 0.00 2.52
2350 4877 5.901552 ACAAAATTCGATGTGTTGGTTCTT 58.098 33.333 6.29 0.00 0.00 2.52
2351 4878 5.514274 ACAAAATTCGATGTGTTGGTTCT 57.486 34.783 6.29 0.00 0.00 3.01
2352 4879 6.435428 AGTACAAAATTCGATGTGTTGGTTC 58.565 36.000 0.00 0.00 0.00 3.62
2353 4880 6.385649 AGTACAAAATTCGATGTGTTGGTT 57.614 33.333 0.00 0.00 0.00 3.67
2354 4881 7.361713 CCATAGTACAAAATTCGATGTGTTGGT 60.362 37.037 0.00 0.00 0.00 3.67
2355 4882 6.966632 CCATAGTACAAAATTCGATGTGTTGG 59.033 38.462 0.00 0.00 0.00 3.77
2356 4883 7.747888 TCCATAGTACAAAATTCGATGTGTTG 58.252 34.615 0.00 0.37 0.00 3.33
2357 4884 7.915293 TCCATAGTACAAAATTCGATGTGTT 57.085 32.000 0.00 0.00 0.00 3.32
2358 4885 9.042008 GTATCCATAGTACAAAATTCGATGTGT 57.958 33.333 0.00 0.00 0.00 3.72
2359 4886 9.040939 TGTATCCATAGTACAAAATTCGATGTG 57.959 33.333 0.00 0.00 0.00 3.21
2360 4887 9.607988 TTGTATCCATAGTACAAAATTCGATGT 57.392 29.630 0.00 0.00 38.65 3.06
2369 4896 9.575868 TTGGTTCTTTTGTATCCATAGTACAAA 57.424 29.630 7.21 7.21 45.31 2.83
2370 4897 9.226606 CTTGGTTCTTTTGTATCCATAGTACAA 57.773 33.333 0.00 0.00 39.53 2.41
2371 4898 8.598916 TCTTGGTTCTTTTGTATCCATAGTACA 58.401 33.333 0.00 0.00 0.00 2.90
2372 4899 8.880750 GTCTTGGTTCTTTTGTATCCATAGTAC 58.119 37.037 0.00 0.00 0.00 2.73
2373 4900 8.598916 TGTCTTGGTTCTTTTGTATCCATAGTA 58.401 33.333 0.00 0.00 0.00 1.82
2374 4901 7.390718 GTGTCTTGGTTCTTTTGTATCCATAGT 59.609 37.037 0.00 0.00 0.00 2.12
2375 4902 7.607991 AGTGTCTTGGTTCTTTTGTATCCATAG 59.392 37.037 0.00 0.00 0.00 2.23
2376 4903 7.458397 AGTGTCTTGGTTCTTTTGTATCCATA 58.542 34.615 0.00 0.00 0.00 2.74
2377 4904 6.306987 AGTGTCTTGGTTCTTTTGTATCCAT 58.693 36.000 0.00 0.00 0.00 3.41
2378 4905 5.690865 AGTGTCTTGGTTCTTTTGTATCCA 58.309 37.500 0.00 0.00 0.00 3.41
2379 4906 5.107065 CGAGTGTCTTGGTTCTTTTGTATCC 60.107 44.000 0.00 0.00 0.00 2.59
2380 4907 5.614887 GCGAGTGTCTTGGTTCTTTTGTATC 60.615 44.000 0.00 0.00 0.00 2.24
2381 4908 4.213482 GCGAGTGTCTTGGTTCTTTTGTAT 59.787 41.667 0.00 0.00 0.00 2.29
2382 4909 3.558418 GCGAGTGTCTTGGTTCTTTTGTA 59.442 43.478 0.00 0.00 0.00 2.41
2383 4910 2.354821 GCGAGTGTCTTGGTTCTTTTGT 59.645 45.455 0.00 0.00 0.00 2.83
2384 4911 2.354510 TGCGAGTGTCTTGGTTCTTTTG 59.645 45.455 0.00 0.00 0.00 2.44
2385 4912 2.639065 TGCGAGTGTCTTGGTTCTTTT 58.361 42.857 0.00 0.00 0.00 2.27
2386 4913 2.325583 TGCGAGTGTCTTGGTTCTTT 57.674 45.000 0.00 0.00 0.00 2.52
2387 4914 2.550830 ATGCGAGTGTCTTGGTTCTT 57.449 45.000 0.00 0.00 0.00 2.52
2388 4915 3.525537 CATATGCGAGTGTCTTGGTTCT 58.474 45.455 0.00 0.00 0.00 3.01
2389 4916 2.609459 CCATATGCGAGTGTCTTGGTTC 59.391 50.000 0.00 0.00 0.00 3.62
2390 4917 2.236146 TCCATATGCGAGTGTCTTGGTT 59.764 45.455 0.00 0.00 0.00 3.67
2391 4918 1.831106 TCCATATGCGAGTGTCTTGGT 59.169 47.619 0.00 0.00 0.00 3.67
2392 4919 2.602257 TCCATATGCGAGTGTCTTGG 57.398 50.000 0.00 0.00 0.00 3.61
2393 4920 3.525537 ACTTCCATATGCGAGTGTCTTG 58.474 45.455 8.02 0.00 0.00 3.02
2394 4921 3.895232 ACTTCCATATGCGAGTGTCTT 57.105 42.857 8.02 0.00 0.00 3.01
2395 4922 5.069119 TGAATACTTCCATATGCGAGTGTCT 59.931 40.000 15.51 4.22 0.00 3.41
2396 4923 5.289595 TGAATACTTCCATATGCGAGTGTC 58.710 41.667 15.51 13.16 0.00 3.67
2397 4924 5.276461 TGAATACTTCCATATGCGAGTGT 57.724 39.130 15.51 8.91 0.00 3.55
2398 4925 5.390251 GCATGAATACTTCCATATGCGAGTG 60.390 44.000 15.51 6.93 30.36 3.51
2399 4926 4.692625 GCATGAATACTTCCATATGCGAGT 59.307 41.667 12.15 12.15 30.36 4.18
2400 4927 4.692155 TGCATGAATACTTCCATATGCGAG 59.308 41.667 0.00 0.00 38.63 5.03
2401 4928 4.452114 GTGCATGAATACTTCCATATGCGA 59.548 41.667 0.00 0.00 38.63 5.10
2402 4929 4.213906 TGTGCATGAATACTTCCATATGCG 59.786 41.667 0.00 0.00 38.63 4.73
2403 4930 5.455392 GTGTGCATGAATACTTCCATATGC 58.545 41.667 0.00 0.00 37.21 3.14
2404 4931 5.766670 AGGTGTGCATGAATACTTCCATATG 59.233 40.000 0.00 0.00 0.00 1.78
2405 4932 5.945310 AGGTGTGCATGAATACTTCCATAT 58.055 37.500 0.00 0.00 0.00 1.78
2406 4933 5.372343 AGGTGTGCATGAATACTTCCATA 57.628 39.130 0.00 0.00 0.00 2.74
2407 4934 4.240881 AGGTGTGCATGAATACTTCCAT 57.759 40.909 0.00 0.00 0.00 3.41
2408 4935 3.719268 AGGTGTGCATGAATACTTCCA 57.281 42.857 0.00 0.00 0.00 3.53
2409 4936 6.509418 TTTAAGGTGTGCATGAATACTTCC 57.491 37.500 0.00 0.22 0.00 3.46
2432 4959 8.780249 GCATATACGGTGGTTGAATACTATTTT 58.220 33.333 0.00 0.00 0.00 1.82
2433 4960 8.154856 AGCATATACGGTGGTTGAATACTATTT 58.845 33.333 0.00 0.00 0.00 1.40
2434 4961 7.676947 AGCATATACGGTGGTTGAATACTATT 58.323 34.615 0.00 0.00 0.00 1.73
2435 4962 7.241042 AGCATATACGGTGGTTGAATACTAT 57.759 36.000 0.00 0.00 0.00 2.12
2436 4963 6.659745 AGCATATACGGTGGTTGAATACTA 57.340 37.500 0.00 0.00 0.00 1.82
2437 4964 5.546621 AGCATATACGGTGGTTGAATACT 57.453 39.130 0.00 0.00 0.00 2.12
2438 4965 6.453092 AGTAGCATATACGGTGGTTGAATAC 58.547 40.000 0.00 0.00 0.00 1.89
2439 4966 6.659745 AGTAGCATATACGGTGGTTGAATA 57.340 37.500 0.00 0.00 0.00 1.75
2440 4967 5.546621 AGTAGCATATACGGTGGTTGAAT 57.453 39.130 0.00 0.00 0.00 2.57
2441 4968 6.265876 TGATAGTAGCATATACGGTGGTTGAA 59.734 38.462 0.00 0.00 0.00 2.69
2442 4969 5.771165 TGATAGTAGCATATACGGTGGTTGA 59.229 40.000 0.00 0.00 0.00 3.18
2443 4970 6.020971 TGATAGTAGCATATACGGTGGTTG 57.979 41.667 0.00 0.00 0.00 3.77
2444 4971 6.008331 TCTGATAGTAGCATATACGGTGGTT 58.992 40.000 0.00 0.00 0.00 3.67
2445 4972 5.567430 TCTGATAGTAGCATATACGGTGGT 58.433 41.667 0.00 0.00 0.00 4.16
2446 4973 6.510879 TTCTGATAGTAGCATATACGGTGG 57.489 41.667 0.00 0.00 0.00 4.61
2447 4974 8.988064 AATTTCTGATAGTAGCATATACGGTG 57.012 34.615 0.00 0.00 0.00 4.94
2448 4975 9.424319 CAAATTTCTGATAGTAGCATATACGGT 57.576 33.333 0.00 0.00 0.00 4.83
2449 4976 9.424319 ACAAATTTCTGATAGTAGCATATACGG 57.576 33.333 0.00 0.00 0.00 4.02
2455 4982 9.890629 TGAAGTACAAATTTCTGATAGTAGCAT 57.109 29.630 0.00 0.00 0.00 3.79
2456 4983 9.371136 CTGAAGTACAAATTTCTGATAGTAGCA 57.629 33.333 0.00 0.00 0.00 3.49
2457 4984 8.331742 GCTGAAGTACAAATTTCTGATAGTAGC 58.668 37.037 0.00 0.00 0.00 3.58
2458 4985 8.821894 GGCTGAAGTACAAATTTCTGATAGTAG 58.178 37.037 0.00 0.00 0.00 2.57
2459 4986 8.318412 TGGCTGAAGTACAAATTTCTGATAGTA 58.682 33.333 0.00 0.00 0.00 1.82
2460 4987 7.168219 TGGCTGAAGTACAAATTTCTGATAGT 58.832 34.615 0.00 0.00 0.00 2.12
2461 4988 7.550551 TCTGGCTGAAGTACAAATTTCTGATAG 59.449 37.037 0.00 0.00 0.00 2.08
2462 4989 7.394016 TCTGGCTGAAGTACAAATTTCTGATA 58.606 34.615 0.00 0.00 0.00 2.15
2463 4990 6.240894 TCTGGCTGAAGTACAAATTTCTGAT 58.759 36.000 0.00 0.00 0.00 2.90
2464 4991 5.620206 TCTGGCTGAAGTACAAATTTCTGA 58.380 37.500 0.00 0.00 0.00 3.27
2465 4992 5.702670 TCTCTGGCTGAAGTACAAATTTCTG 59.297 40.000 0.00 0.00 0.00 3.02
2466 4993 5.869579 TCTCTGGCTGAAGTACAAATTTCT 58.130 37.500 0.00 0.00 0.00 2.52
2467 4994 5.391416 GCTCTCTGGCTGAAGTACAAATTTC 60.391 44.000 0.00 0.00 0.00 2.17
2468 4995 4.457257 GCTCTCTGGCTGAAGTACAAATTT 59.543 41.667 0.00 0.00 0.00 1.82
2469 4996 4.006319 GCTCTCTGGCTGAAGTACAAATT 58.994 43.478 0.00 0.00 0.00 1.82
2470 4997 3.008375 TGCTCTCTGGCTGAAGTACAAAT 59.992 43.478 0.00 0.00 0.00 2.32
2471 4998 2.368548 TGCTCTCTGGCTGAAGTACAAA 59.631 45.455 0.00 0.00 0.00 2.83
2472 4999 1.970640 TGCTCTCTGGCTGAAGTACAA 59.029 47.619 0.00 0.00 0.00 2.41
2473 5000 1.547820 CTGCTCTCTGGCTGAAGTACA 59.452 52.381 0.00 0.00 33.89 2.90
2474 5001 1.821753 TCTGCTCTCTGGCTGAAGTAC 59.178 52.381 0.00 0.00 37.27 2.73
2475 5002 2.222227 TCTGCTCTCTGGCTGAAGTA 57.778 50.000 0.00 0.00 37.27 2.24
2476 5003 1.346062 TTCTGCTCTCTGGCTGAAGT 58.654 50.000 5.04 0.00 42.30 3.01
2477 5004 2.028294 TCTTTCTGCTCTCTGGCTGAAG 60.028 50.000 8.31 0.00 45.64 3.02
2478 5005 1.973515 TCTTTCTGCTCTCTGGCTGAA 59.026 47.619 5.04 5.04 44.28 3.02
2479 5006 1.637338 TCTTTCTGCTCTCTGGCTGA 58.363 50.000 0.00 0.00 38.15 4.26
2480 5007 2.281517 CATCTTTCTGCTCTCTGGCTG 58.718 52.381 0.00 0.00 0.00 4.85
2481 5008 1.209990 CCATCTTTCTGCTCTCTGGCT 59.790 52.381 0.00 0.00 0.00 4.75
2482 5009 1.209019 TCCATCTTTCTGCTCTCTGGC 59.791 52.381 0.00 0.00 0.00 4.85
2483 5010 2.765135 TCTCCATCTTTCTGCTCTCTGG 59.235 50.000 0.00 0.00 0.00 3.86
2484 5011 3.700539 TCTCTCCATCTTTCTGCTCTCTG 59.299 47.826 0.00 0.00 0.00 3.35
2485 5012 3.956199 CTCTCTCCATCTTTCTGCTCTCT 59.044 47.826 0.00 0.00 0.00 3.10
2486 5013 3.068590 CCTCTCTCCATCTTTCTGCTCTC 59.931 52.174 0.00 0.00 0.00 3.20
2487 5014 3.033184 CCTCTCTCCATCTTTCTGCTCT 58.967 50.000 0.00 0.00 0.00 4.09
2488 5015 3.030291 TCCTCTCTCCATCTTTCTGCTC 58.970 50.000 0.00 0.00 0.00 4.26
2489 5016 3.113191 TCCTCTCTCCATCTTTCTGCT 57.887 47.619 0.00 0.00 0.00 4.24
2490 5017 4.420522 AATCCTCTCTCCATCTTTCTGC 57.579 45.455 0.00 0.00 0.00 4.26
2491 5018 4.575645 GCAAATCCTCTCTCCATCTTTCTG 59.424 45.833 0.00 0.00 0.00 3.02
2492 5019 4.474287 AGCAAATCCTCTCTCCATCTTTCT 59.526 41.667 0.00 0.00 0.00 2.52
2493 5020 4.779696 AGCAAATCCTCTCTCCATCTTTC 58.220 43.478 0.00 0.00 0.00 2.62
2494 5021 4.858965 AGCAAATCCTCTCTCCATCTTT 57.141 40.909 0.00 0.00 0.00 2.52
2495 5022 5.397334 GGTTAGCAAATCCTCTCTCCATCTT 60.397 44.000 0.00 0.00 0.00 2.40
2496 5023 4.102367 GGTTAGCAAATCCTCTCTCCATCT 59.898 45.833 0.00 0.00 0.00 2.90
2497 5024 4.384940 GGTTAGCAAATCCTCTCTCCATC 58.615 47.826 0.00 0.00 0.00 3.51
2498 5025 3.137360 GGGTTAGCAAATCCTCTCTCCAT 59.863 47.826 0.00 0.00 32.57 3.41
2499 5026 2.505819 GGGTTAGCAAATCCTCTCTCCA 59.494 50.000 0.00 0.00 32.57 3.86
2500 5027 2.505819 TGGGTTAGCAAATCCTCTCTCC 59.494 50.000 0.00 0.00 36.75 3.71
2501 5028 3.914426 TGGGTTAGCAAATCCTCTCTC 57.086 47.619 0.00 0.00 36.75 3.20
2502 5029 3.117738 CCATGGGTTAGCAAATCCTCTCT 60.118 47.826 2.85 0.00 36.75 3.10
2503 5030 3.217626 CCATGGGTTAGCAAATCCTCTC 58.782 50.000 2.85 0.00 36.75 3.20
2504 5031 2.582636 ACCATGGGTTAGCAAATCCTCT 59.417 45.455 18.09 0.00 36.75 3.69
2505 5032 3.018423 ACCATGGGTTAGCAAATCCTC 57.982 47.619 18.09 0.00 36.75 3.71
2506 5033 3.245586 TGAACCATGGGTTAGCAAATCCT 60.246 43.478 18.09 0.00 46.95 3.24
2507 5034 3.096092 TGAACCATGGGTTAGCAAATCC 58.904 45.455 18.09 0.00 46.95 3.01
2508 5035 3.429410 GCTGAACCATGGGTTAGCAAATC 60.429 47.826 34.95 10.59 46.95 2.17
2509 5036 2.497273 GCTGAACCATGGGTTAGCAAAT 59.503 45.455 34.95 0.40 46.95 2.32
2510 5037 1.892474 GCTGAACCATGGGTTAGCAAA 59.108 47.619 34.95 4.15 46.95 3.68
2511 5038 1.075374 AGCTGAACCATGGGTTAGCAA 59.925 47.619 38.91 9.22 46.95 3.91
2512 5039 0.698238 AGCTGAACCATGGGTTAGCA 59.302 50.000 38.91 18.03 46.95 3.49
2513 5040 1.098050 CAGCTGAACCATGGGTTAGC 58.902 55.000 33.53 33.53 46.95 3.09
2514 5041 1.004745 ACCAGCTGAACCATGGGTTAG 59.995 52.381 17.16 17.16 46.95 2.34
2515 5042 1.004277 GACCAGCTGAACCATGGGTTA 59.996 52.381 17.39 5.12 46.95 2.85
2517 5044 1.380302 GACCAGCTGAACCATGGGT 59.620 57.895 17.39 10.33 38.48 4.51
2518 5045 1.379044 GGACCAGCTGAACCATGGG 60.379 63.158 17.39 0.00 38.48 4.00
2519 5046 0.033796 ATGGACCAGCTGAACCATGG 60.034 55.000 29.88 11.19 40.91 3.66
2520 5047 2.715749 TATGGACCAGCTGAACCATG 57.284 50.000 33.90 16.13 42.16 3.66
2521 5048 3.051581 AGATATGGACCAGCTGAACCAT 58.948 45.455 31.49 31.49 44.03 3.55
2522 5049 2.435805 GAGATATGGACCAGCTGAACCA 59.564 50.000 25.64 25.64 36.83 3.67
2523 5050 2.703007 AGAGATATGGACCAGCTGAACC 59.297 50.000 17.39 17.78 0.00 3.62
2524 5051 5.537300 TTAGAGATATGGACCAGCTGAAC 57.463 43.478 17.39 8.45 0.00 3.18
2525 5052 5.163301 GGTTTAGAGATATGGACCAGCTGAA 60.163 44.000 17.39 0.00 0.00 3.02
2526 5053 4.345257 GGTTTAGAGATATGGACCAGCTGA 59.655 45.833 17.39 0.00 0.00 4.26
2527 5054 4.636249 GGTTTAGAGATATGGACCAGCTG 58.364 47.826 6.78 6.78 0.00 4.24
2528 5055 3.322254 CGGTTTAGAGATATGGACCAGCT 59.678 47.826 0.00 0.00 0.00 4.24
2529 5056 3.069729 ACGGTTTAGAGATATGGACCAGC 59.930 47.826 0.00 0.00 0.00 4.85
2530 5057 4.939052 ACGGTTTAGAGATATGGACCAG 57.061 45.455 0.00 0.00 0.00 4.00
2531 5058 4.831155 CCTACGGTTTAGAGATATGGACCA 59.169 45.833 0.00 0.00 0.00 4.02
2532 5059 5.075493 TCCTACGGTTTAGAGATATGGACC 58.925 45.833 0.00 0.00 0.00 4.46
2533 5060 6.622549 CATCCTACGGTTTAGAGATATGGAC 58.377 44.000 0.00 0.00 0.00 4.02
2534 5061 5.185249 GCATCCTACGGTTTAGAGATATGGA 59.815 44.000 0.00 0.00 0.00 3.41
2535 5062 5.047306 TGCATCCTACGGTTTAGAGATATGG 60.047 44.000 0.00 0.00 0.00 2.74
2536 5063 6.025749 TGCATCCTACGGTTTAGAGATATG 57.974 41.667 0.00 0.00 0.00 1.78
2537 5064 6.010850 TCTGCATCCTACGGTTTAGAGATAT 58.989 40.000 0.00 0.00 0.00 1.63
2538 5065 5.382616 TCTGCATCCTACGGTTTAGAGATA 58.617 41.667 0.00 0.00 0.00 1.98
2539 5066 4.215908 TCTGCATCCTACGGTTTAGAGAT 58.784 43.478 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.