Multiple sequence alignment - TraesCS1B01G056300

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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 TraesCS1B01G056300 chr1B 100.000 2411 0 0 1 2411 39310181 39312591 0.000000e+00 4453
1 TraesCS1B01G056300 chr1B 92.810 153 6 4 2122 2273 38915100 38914952 1.450000e-52 217
2 TraesCS1B01G056300 chr1B 88.961 154 11 5 2122 2271 38911889 38911738 4.090000e-43 185
3 TraesCS1B01G056300 chr1B 91.791 134 7 4 2134 2267 39386996 39387125 1.470000e-42 183
4 TraesCS1B01G056300 chr1A 82.539 2371 187 108 55 2278 24076431 24078721 0.000000e+00 1875
5 TraesCS1B01G056300 chr1A 88.961 154 12 4 2121 2272 24311635 24311785 4.090000e-43 185
6 TraesCS1B01G056300 chr1A 86.667 165 12 7 2122 2278 23965651 23965813 8.860000e-40 174
7 TraesCS1B01G056300 chr1D 85.180 1390 78 62 629 1925 22902802 22904156 0.000000e+00 1308
8 TraesCS1B01G056300 chr1D 82.947 475 27 20 1969 2411 22904155 22904607 1.750000e-101 379
9 TraesCS1B01G056300 chr1D 87.546 273 18 6 261 526 22902440 22902703 3.900000e-78 302
10 TraesCS1B01G056300 chr1D 91.852 135 5 6 2112 2240 22977766 22977900 1.470000e-42 183
11 TraesCS1B01G056300 chr1D 87.821 156 13 5 2122 2271 22883033 22883188 6.850000e-41 178


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 TraesCS1B01G056300 chr1B 39310181 39312591 2410 False 4453 4453 100.000000 1 2411 1 chr1B.!!$F1 2410
1 TraesCS1B01G056300 chr1B 38911738 38915100 3362 True 201 217 90.885500 2122 2273 2 chr1B.!!$R1 151
2 TraesCS1B01G056300 chr1A 24076431 24078721 2290 False 1875 1875 82.539000 55 2278 1 chr1A.!!$F2 2223
3 TraesCS1B01G056300 chr1D 22902440 22904607 2167 False 663 1308 85.224333 261 2411 3 chr1D.!!$F3 2150

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
177 191 0.038618 GGAAGCCGCGAAAATTGGTT 60.039 50.0 8.23 0.18 0.0 3.67 F
202 216 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.0 0.00 0.00 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1254 0.320050 GAAGAGAGGCCGGATGATCC 59.680 60.0 5.05 0.08 0.0 3.36 R
1956 2163 0.811281 GATTTTGCTCACTTCGGGGG 59.189 55.0 0.00 0.00 0.0 5.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.630242 TGACCTCCATTACTCAAATCAAATC 57.370 36.000 0.00 0.00 0.00 2.17
25 26 7.174413 TGACCTCCATTACTCAAATCAAATCA 58.826 34.615 0.00 0.00 0.00 2.57
26 27 7.669304 TGACCTCCATTACTCAAATCAAATCAA 59.331 33.333 0.00 0.00 0.00 2.57
27 28 8.421249 ACCTCCATTACTCAAATCAAATCAAA 57.579 30.769 0.00 0.00 0.00 2.69
28 29 8.526147 ACCTCCATTACTCAAATCAAATCAAAG 58.474 33.333 0.00 0.00 0.00 2.77
29 30 8.742777 CCTCCATTACTCAAATCAAATCAAAGA 58.257 33.333 0.00 0.00 0.00 2.52
35 36 9.630098 TTACTCAAATCAAATCAAAGATCAAGC 57.370 29.630 0.00 0.00 0.00 4.01
36 37 7.095270 ACTCAAATCAAATCAAAGATCAAGCC 58.905 34.615 0.00 0.00 0.00 4.35
37 38 7.039223 ACTCAAATCAAATCAAAGATCAAGCCT 60.039 33.333 0.00 0.00 0.00 4.58
38 39 7.318141 TCAAATCAAATCAAAGATCAAGCCTC 58.682 34.615 0.00 0.00 0.00 4.70
39 40 5.848833 ATCAAATCAAAGATCAAGCCTCC 57.151 39.130 0.00 0.00 0.00 4.30
40 41 3.691118 TCAAATCAAAGATCAAGCCTCCG 59.309 43.478 0.00 0.00 0.00 4.63
41 42 3.634397 AATCAAAGATCAAGCCTCCGA 57.366 42.857 0.00 0.00 0.00 4.55
42 43 3.853355 ATCAAAGATCAAGCCTCCGAT 57.147 42.857 0.00 0.00 0.00 4.18
43 44 3.185246 TCAAAGATCAAGCCTCCGATC 57.815 47.619 0.00 0.00 38.66 3.69
44 45 1.863454 CAAAGATCAAGCCTCCGATCG 59.137 52.381 8.51 8.51 42.36 3.69
45 46 1.403814 AAGATCAAGCCTCCGATCGA 58.596 50.000 18.66 1.60 42.36 3.59
46 47 0.958091 AGATCAAGCCTCCGATCGAG 59.042 55.000 18.66 11.81 42.36 4.04
47 48 0.665972 GATCAAGCCTCCGATCGAGC 60.666 60.000 18.66 16.10 37.27 5.03
48 49 1.395045 ATCAAGCCTCCGATCGAGCA 61.395 55.000 18.66 1.39 37.27 4.26
49 50 1.880340 CAAGCCTCCGATCGAGCAC 60.880 63.158 18.66 3.26 37.27 4.40
50 51 3.417275 AAGCCTCCGATCGAGCACG 62.417 63.158 18.66 0.00 37.27 5.34
51 52 4.194720 GCCTCCGATCGAGCACGT 62.195 66.667 18.66 0.00 40.69 4.49
52 53 2.831366 GCCTCCGATCGAGCACGTA 61.831 63.158 18.66 0.00 40.69 3.57
53 54 1.009900 CCTCCGATCGAGCACGTAC 60.010 63.158 18.66 0.00 40.69 3.67
65 66 3.306973 CGAGCACGTACATCAATCACAAT 59.693 43.478 0.00 0.00 34.56 2.71
66 67 4.548916 CGAGCACGTACATCAATCACAATC 60.549 45.833 0.00 0.00 34.56 2.67
67 68 4.507710 AGCACGTACATCAATCACAATCT 58.492 39.130 0.00 0.00 0.00 2.40
68 69 4.568359 AGCACGTACATCAATCACAATCTC 59.432 41.667 0.00 0.00 0.00 2.75
69 70 4.329801 GCACGTACATCAATCACAATCTCA 59.670 41.667 0.00 0.00 0.00 3.27
72 74 7.466805 CACGTACATCAATCACAATCTCAAAT 58.533 34.615 0.00 0.00 0.00 2.32
114 121 1.226717 GTTAGCTCCGCTCTGACCG 60.227 63.158 0.00 0.00 40.44 4.79
115 122 3.064987 TTAGCTCCGCTCTGACCGC 62.065 63.158 0.00 0.00 40.44 5.68
120 127 4.504916 CCGCTCTGACCGCTCCAG 62.505 72.222 0.00 0.00 0.00 3.86
128 141 2.597805 ACCGCTCCAGTGTCGTCT 60.598 61.111 0.00 0.00 0.00 4.18
144 157 0.306533 GTCTCGCAAAAGAAACCGCA 59.693 50.000 0.00 0.00 0.00 5.69
145 158 1.018148 TCTCGCAAAAGAAACCGCAA 58.982 45.000 0.00 0.00 0.00 4.85
148 161 2.123342 TCGCAAAAGAAACCGCAAATG 58.877 42.857 0.00 0.00 0.00 2.32
157 171 8.547069 CAAAAGAAACCGCAAATGATTAAGAAA 58.453 29.630 0.00 0.00 0.00 2.52
159 173 6.389906 AGAAACCGCAAATGATTAAGAAAGG 58.610 36.000 0.00 0.00 0.00 3.11
177 191 0.038618 GGAAGCCGCGAAAATTGGTT 60.039 50.000 8.23 0.18 0.00 3.67
186 200 1.399215 CGAAAATTGGTTCGGTCGGTG 60.399 52.381 4.66 0.00 45.21 4.94
187 201 1.605232 GAAAATTGGTTCGGTCGGTGT 59.395 47.619 0.00 0.00 0.00 4.16
188 202 0.948678 AAATTGGTTCGGTCGGTGTG 59.051 50.000 0.00 0.00 0.00 3.82
189 203 0.179040 AATTGGTTCGGTCGGTGTGT 60.179 50.000 0.00 0.00 0.00 3.72
190 204 0.882927 ATTGGTTCGGTCGGTGTGTG 60.883 55.000 0.00 0.00 0.00 3.82
191 205 2.107546 GGTTCGGTCGGTGTGTGT 59.892 61.111 0.00 0.00 0.00 3.72
192 206 2.241880 GGTTCGGTCGGTGTGTGTG 61.242 63.158 0.00 0.00 0.00 3.82
193 207 1.519898 GTTCGGTCGGTGTGTGTGT 60.520 57.895 0.00 0.00 0.00 3.72
194 208 1.519676 TTCGGTCGGTGTGTGTGTG 60.520 57.895 0.00 0.00 0.00 3.82
195 209 2.202824 CGGTCGGTGTGTGTGTGT 60.203 61.111 0.00 0.00 0.00 3.72
196 210 2.521771 CGGTCGGTGTGTGTGTGTG 61.522 63.158 0.00 0.00 0.00 3.82
197 211 1.448893 GGTCGGTGTGTGTGTGTGT 60.449 57.895 0.00 0.00 0.00 3.72
198 212 1.701545 GGTCGGTGTGTGTGTGTGTG 61.702 60.000 0.00 0.00 0.00 3.82
199 213 1.017177 GTCGGTGTGTGTGTGTGTGT 61.017 55.000 0.00 0.00 0.00 3.72
200 214 1.016653 TCGGTGTGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
201 215 1.295357 CGGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
202 216 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
203 217 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
207 221 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
217 231 1.742268 TGTGTGTGTGTGTGTGAATGG 59.258 47.619 0.00 0.00 0.00 3.16
218 232 0.737804 TGTGTGTGTGTGTGAATGGC 59.262 50.000 0.00 0.00 0.00 4.40
220 234 1.405105 GTGTGTGTGTGTGAATGGCTT 59.595 47.619 0.00 0.00 0.00 4.35
222 236 1.675483 GTGTGTGTGTGAATGGCTTGA 59.325 47.619 0.00 0.00 0.00 3.02
223 237 1.675483 TGTGTGTGTGAATGGCTTGAC 59.325 47.619 0.00 0.00 0.00 3.18
225 239 1.675483 TGTGTGTGAATGGCTTGACAC 59.325 47.619 10.65 10.65 46.05 3.67
228 242 3.435105 GTGTGAATGGCTTGACACAAA 57.565 42.857 11.99 0.00 45.43 2.83
231 245 3.635836 TGTGAATGGCTTGACACAAATGA 59.364 39.130 0.00 0.00 39.70 2.57
233 247 3.635836 TGAATGGCTTGACACAAATGACA 59.364 39.130 0.00 0.00 0.00 3.58
234 248 3.648339 ATGGCTTGACACAAATGACAC 57.352 42.857 0.00 0.00 29.93 3.67
235 249 2.373224 TGGCTTGACACAAATGACACA 58.627 42.857 0.00 0.00 29.93 3.72
236 250 2.957680 TGGCTTGACACAAATGACACAT 59.042 40.909 0.00 0.00 29.93 3.21
237 251 3.384146 TGGCTTGACACAAATGACACATT 59.616 39.130 0.00 0.00 29.93 2.71
238 252 3.737266 GGCTTGACACAAATGACACATTG 59.263 43.478 0.00 2.14 29.93 2.82
239 253 3.182972 GCTTGACACAAATGACACATTGC 59.817 43.478 0.00 0.00 29.93 3.56
240 254 4.613944 CTTGACACAAATGACACATTGCT 58.386 39.130 0.00 0.00 29.93 3.91
241 255 4.652421 TGACACAAATGACACATTGCTT 57.348 36.364 0.00 0.00 0.00 3.91
242 256 5.008619 TGACACAAATGACACATTGCTTT 57.991 34.783 0.00 0.00 0.00 3.51
243 257 4.804665 TGACACAAATGACACATTGCTTTG 59.195 37.500 0.00 0.25 33.98 2.77
244 258 5.008619 ACACAAATGACACATTGCTTTGA 57.991 34.783 4.41 0.00 32.54 2.69
245 259 5.045215 ACACAAATGACACATTGCTTTGAG 58.955 37.500 4.41 0.06 32.54 3.02
250 264 4.556942 TGACACATTGCTTTGAGTTGAG 57.443 40.909 0.00 0.00 0.00 3.02
267 292 1.598701 GAGCATGGCACCTCCCAAAC 61.599 60.000 5.86 0.00 38.61 2.93
288 313 4.025401 GCAACAAGTGGCGACGGG 62.025 66.667 0.00 0.00 0.00 5.28
289 314 4.025401 CAACAAGTGGCGACGGGC 62.025 66.667 0.00 0.00 42.51 6.13
323 356 2.515991 CCGGGGCGTACGTAGGTA 60.516 66.667 17.90 0.00 0.00 3.08
324 357 2.715624 CGGGGCGTACGTAGGTAC 59.284 66.667 17.90 14.38 44.50 3.34
333 366 4.845177 CGTAGGTACGTTGCGTGA 57.155 55.556 0.00 0.00 44.13 4.35
334 367 3.090598 CGTAGGTACGTTGCGTGAA 57.909 52.632 0.00 0.00 44.13 3.18
335 368 0.979811 CGTAGGTACGTTGCGTGAAG 59.020 55.000 0.00 0.00 44.13 3.02
336 369 2.887926 CGTAGGTACGTTGCGTGAAGC 61.888 57.143 0.00 0.00 44.13 3.86
412 447 4.392138 CACCTTTTTGTACTGCTACTAGCC 59.608 45.833 5.58 0.00 41.51 3.93
413 448 4.286291 ACCTTTTTGTACTGCTACTAGCCT 59.714 41.667 5.58 0.00 41.51 4.58
415 450 5.811100 CCTTTTTGTACTGCTACTAGCCTAC 59.189 44.000 5.58 5.97 41.51 3.18
416 451 6.351117 CCTTTTTGTACTGCTACTAGCCTACT 60.351 42.308 5.58 0.00 41.51 2.57
417 452 7.147949 CCTTTTTGTACTGCTACTAGCCTACTA 60.148 40.741 5.58 0.60 41.51 1.82
424 463 6.240145 ACTGCTACTAGCCTACTATACCTTC 58.760 44.000 5.58 0.00 41.51 3.46
427 466 6.489361 TGCTACTAGCCTACTATACCTTCAAC 59.511 42.308 5.58 0.00 41.51 3.18
434 473 6.098552 AGCCTACTATACCTTCAACTTCCTTC 59.901 42.308 0.00 0.00 0.00 3.46
446 485 2.941480 ACTTCCTTCCATGGATGCATC 58.059 47.619 17.06 18.81 35.83 3.91
460 503 3.790437 CATCGGGAGCAGGCAGGT 61.790 66.667 0.00 0.00 0.00 4.00
527 570 1.481056 AACAACCTGGAGGCTAGCGT 61.481 55.000 10.22 10.22 39.32 5.07
535 578 1.884926 GAGGCTAGCGTCCATGCAC 60.885 63.158 23.78 0.43 37.31 4.57
536 579 3.264897 GGCTAGCGTCCATGCACG 61.265 66.667 4.38 4.38 42.95 5.34
537 580 3.264897 GCTAGCGTCCATGCACGG 61.265 66.667 11.82 0.00 40.29 4.94
540 583 2.960957 CTAGCGTCCATGCACGGGAG 62.961 65.000 11.82 0.00 40.29 4.30
542 585 2.509336 CGTCCATGCACGGGAGAC 60.509 66.667 9.13 1.82 36.07 3.36
552 595 3.950397 TGCACGGGAGACTCAAAATAAT 58.050 40.909 4.53 0.00 0.00 1.28
555 598 4.513442 CACGGGAGACTCAAAATAATCCA 58.487 43.478 4.53 0.00 0.00 3.41
566 609 6.093495 ACTCAAAATAATCCACCATGTACGTG 59.907 38.462 8.18 8.18 0.00 4.49
602 645 6.953101 AGCCCCAATTTTTAACCGAATAATT 58.047 32.000 0.00 0.00 31.23 1.40
678 750 2.753296 CTAGCGCGTAGTAGTAGGAGT 58.247 52.381 8.43 0.00 0.00 3.85
690 762 9.810545 CGTAGTAGTAGGAGTAGTAGTAAAACT 57.189 37.037 0.00 0.00 0.00 2.66
744 816 0.462937 CACCGGCCCATTTCATACGA 60.463 55.000 0.00 0.00 0.00 3.43
748 820 1.156736 GGCCCATTTCATACGATCGG 58.843 55.000 20.98 1.30 0.00 4.18
749 821 0.517316 GCCCATTTCATACGATCGGC 59.483 55.000 20.98 4.96 0.00 5.54
844 929 2.786495 CGTCCGTCCCATCCTCCAG 61.786 68.421 0.00 0.00 0.00 3.86
845 930 1.686110 GTCCGTCCCATCCTCCAGT 60.686 63.158 0.00 0.00 0.00 4.00
846 931 1.381327 TCCGTCCCATCCTCCAGTC 60.381 63.158 0.00 0.00 0.00 3.51
847 932 2.435693 CCGTCCCATCCTCCAGTCC 61.436 68.421 0.00 0.00 0.00 3.85
848 933 1.381872 CGTCCCATCCTCCAGTCCT 60.382 63.158 0.00 0.00 0.00 3.85
849 934 1.395826 CGTCCCATCCTCCAGTCCTC 61.396 65.000 0.00 0.00 0.00 3.71
850 935 1.051556 GTCCCATCCTCCAGTCCTCC 61.052 65.000 0.00 0.00 0.00 4.30
851 936 1.231751 TCCCATCCTCCAGTCCTCCT 61.232 60.000 0.00 0.00 0.00 3.69
864 949 0.764369 TCCTCCTCGCCATAGCCAAT 60.764 55.000 0.00 0.00 34.57 3.16
878 983 1.876497 GCCAATCCCGCAAAGCTTCA 61.876 55.000 0.00 0.00 0.00 3.02
888 993 1.924524 GCAAAGCTTCATACGCTCGTA 59.075 47.619 0.00 4.53 36.56 3.43
889 994 2.285084 GCAAAGCTTCATACGCTCGTAC 60.285 50.000 0.00 0.00 36.56 3.67
890 995 1.823828 AAGCTTCATACGCTCGTACG 58.176 50.000 9.53 9.53 36.56 3.67
911 1016 4.406173 AGAGCCAGTGCGACGTCG 62.406 66.667 32.57 32.57 44.33 5.12
913 1018 4.702081 AGCCAGTGCGACGTCGAC 62.702 66.667 39.74 30.43 44.33 4.20
919 1024 2.981909 TGCGACGTCGACCTCCTT 60.982 61.111 39.74 0.00 43.02 3.36
946 1051 4.789173 TGGGCTAGGCTACCGGCA 62.789 66.667 16.80 1.18 44.01 5.69
1051 1177 1.000993 GTCCTCCTCCTCTGGCTCA 59.999 63.158 0.00 0.00 0.00 4.26
1130 1259 3.785859 GGCGGTCCAGCTGGATCA 61.786 66.667 38.48 17.28 45.67 2.92
1163 1301 0.539051 CCCAGGAAGATGCTTCTCGT 59.461 55.000 2.09 0.00 0.00 4.18
1221 1359 1.446907 GTGCTCCACAGGATCAACAG 58.553 55.000 0.00 0.00 29.28 3.16
1223 1361 1.364626 GCTCCACAGGATCAACAGCG 61.365 60.000 0.00 0.00 0.00 5.18
1224 1362 0.742281 CTCCACAGGATCAACAGCGG 60.742 60.000 0.00 0.00 0.00 5.52
1239 1377 2.045045 CGGCACCACCACCATCAT 60.045 61.111 0.00 0.00 39.03 2.45
1309 1453 1.200948 GCAAATGGAACTGGCAGAGAC 59.799 52.381 23.66 10.62 0.00 3.36
1311 1455 2.486472 AATGGAACTGGCAGAGACTG 57.514 50.000 23.66 0.00 34.12 3.51
1320 1464 3.371021 CAGAGACTGCCACCGTCT 58.629 61.111 0.00 0.00 43.97 4.18
1413 1557 1.296392 CCCGTTGCATCACTGAGGA 59.704 57.895 0.00 0.00 0.00 3.71
1415 1559 1.354337 CCGTTGCATCACTGAGGACG 61.354 60.000 0.00 0.00 0.00 4.79
1416 1560 1.354337 CGTTGCATCACTGAGGACGG 61.354 60.000 0.00 0.00 0.00 4.79
1417 1561 1.021390 GTTGCATCACTGAGGACGGG 61.021 60.000 0.00 0.00 0.00 5.28
1418 1562 2.512515 GCATCACTGAGGACGGGC 60.513 66.667 0.00 0.00 0.00 6.13
1419 1563 2.981302 CATCACTGAGGACGGGCA 59.019 61.111 0.00 0.00 0.00 5.36
1420 1564 1.153489 CATCACTGAGGACGGGCAG 60.153 63.158 0.00 0.00 38.10 4.85
1421 1565 2.362369 ATCACTGAGGACGGGCAGG 61.362 63.158 0.00 0.00 36.47 4.85
1422 1566 4.087892 CACTGAGGACGGGCAGGG 62.088 72.222 0.00 0.00 36.47 4.45
1423 1567 4.640690 ACTGAGGACGGGCAGGGT 62.641 66.667 0.00 0.00 36.47 4.34
1424 1568 3.775654 CTGAGGACGGGCAGGGTC 61.776 72.222 0.00 0.00 0.00 4.46
1425 1569 4.316823 TGAGGACGGGCAGGGTCT 62.317 66.667 3.23 0.00 34.82 3.85
1426 1570 3.003763 GAGGACGGGCAGGGTCTT 61.004 66.667 3.23 0.00 34.82 3.01
1427 1571 3.003763 AGGACGGGCAGGGTCTTC 61.004 66.667 3.23 0.00 34.82 2.87
1428 1572 3.319198 GGACGGGCAGGGTCTTCA 61.319 66.667 3.23 0.00 34.82 3.02
1429 1573 2.670148 GGACGGGCAGGGTCTTCAT 61.670 63.158 3.23 0.00 34.82 2.57
1430 1574 1.450312 GACGGGCAGGGTCTTCATG 60.450 63.158 0.00 0.00 0.00 3.07
1510 1663 2.881816 GCAAGGGAGAGGGAGAAAAAGG 60.882 54.545 0.00 0.00 0.00 3.11
1515 1668 2.375509 GGAGAGGGAGAAAAAGGAACCA 59.624 50.000 0.00 0.00 0.00 3.67
1523 1676 7.410174 AGGGAGAAAAAGGAACCAAAATTTTT 58.590 30.769 0.00 0.00 37.51 1.94
1540 1693 9.341899 CAAAATTTTTCTAGCTGTGGTACATAC 57.658 33.333 0.00 0.00 44.52 2.39
1541 1694 8.630054 AAATTTTTCTAGCTGTGGTACATACA 57.370 30.769 0.00 0.00 44.52 2.29
1543 1696 7.667043 TTTTTCTAGCTGTGGTACATACAAG 57.333 36.000 0.00 0.00 44.52 3.16
1551 1704 8.662781 AGCTGTGGTACATACAAGTTATTATG 57.337 34.615 0.00 3.23 44.52 1.90
1552 1705 7.226720 AGCTGTGGTACATACAAGTTATTATGC 59.773 37.037 0.00 0.00 44.52 3.14
1596 1762 3.842007 TTTCCGTTTCTAGGTTGTCCA 57.158 42.857 0.00 0.00 35.89 4.02
1597 1763 4.360951 TTTCCGTTTCTAGGTTGTCCAT 57.639 40.909 0.00 0.00 35.89 3.41
1598 1764 4.360951 TTCCGTTTCTAGGTTGTCCATT 57.639 40.909 0.00 0.00 35.89 3.16
1599 1765 3.934068 TCCGTTTCTAGGTTGTCCATTC 58.066 45.455 0.00 0.00 35.89 2.67
1600 1766 3.581332 TCCGTTTCTAGGTTGTCCATTCT 59.419 43.478 0.00 0.00 35.89 2.40
1626 1796 6.748333 TCTTTGATTTTCTCTGCTACATGG 57.252 37.500 0.00 0.00 0.00 3.66
1681 1854 3.503363 CAGGTGACATTTGCATGTACTGT 59.497 43.478 0.00 0.00 44.22 3.55
1689 1862 9.394767 TGACATTTGCATGTACTGTATAAGATT 57.605 29.630 0.00 0.00 44.22 2.40
1809 2012 8.175925 TCAAATCTCCAATTATGTGTTGAACA 57.824 30.769 0.00 0.00 44.79 3.18
1932 2139 0.758734 TAACATCCAGGCCAGGATCG 59.241 55.000 26.05 21.63 45.16 3.69
1941 2148 3.866582 CCAGGATCGGGCTCCACC 61.867 72.222 3.06 0.00 37.81 4.61
1954 2161 0.254747 CTCCACCTTTCCGCCCAATA 59.745 55.000 0.00 0.00 0.00 1.90
1955 2162 0.034863 TCCACCTTTCCGCCCAATAC 60.035 55.000 0.00 0.00 0.00 1.89
1956 2163 1.035385 CCACCTTTCCGCCCAATACC 61.035 60.000 0.00 0.00 0.00 2.73
1957 2164 1.035385 CACCTTTCCGCCCAATACCC 61.035 60.000 0.00 0.00 0.00 3.69
2028 2246 9.716556 ACATATTGTATTGTATACCCCCAAAAA 57.283 29.630 0.00 0.00 0.00 1.94
2096 2329 4.030306 CGAGTAGCAAAACATCTCACGTAC 59.970 45.833 0.00 0.00 0.00 3.67
2097 2330 4.243270 AGTAGCAAAACATCTCACGTACC 58.757 43.478 0.00 0.00 0.00 3.34
2098 2331 2.066262 AGCAAAACATCTCACGTACCG 58.934 47.619 0.00 0.00 0.00 4.02
2099 2332 1.127951 GCAAAACATCTCACGTACCGG 59.872 52.381 0.00 0.00 0.00 5.28
2100 2333 1.127951 CAAAACATCTCACGTACCGGC 59.872 52.381 0.00 0.00 0.00 6.13
2101 2334 0.390735 AAACATCTCACGTACCGGCC 60.391 55.000 0.00 0.00 0.00 6.13
2102 2335 2.106332 CATCTCACGTACCGGCCC 59.894 66.667 0.00 0.00 0.00 5.80
2103 2336 3.524606 ATCTCACGTACCGGCCCG 61.525 66.667 0.00 6.58 0.00 6.13
2117 2350 2.027007 CCGGCCCGGTTTGGATATATAA 60.027 50.000 15.86 0.00 42.73 0.98
2306 5547 5.471116 GGCAATGGAGCATTTCTTTTTCTTT 59.529 36.000 0.00 0.00 31.05 2.52
2307 5548 6.016860 GGCAATGGAGCATTTCTTTTTCTTTT 60.017 34.615 0.00 0.00 31.05 2.27
2308 5549 7.073883 GCAATGGAGCATTTCTTTTTCTTTTC 58.926 34.615 0.00 0.00 31.05 2.29
2313 5554 9.829507 TGGAGCATTTCTTTTTCTTTTCATAAA 57.170 25.926 0.00 0.00 0.00 1.40
2323 5564 7.698836 TTTTCTTTTCATAAACTTCTGCAGC 57.301 32.000 9.47 0.00 0.00 5.25
2338 5579 1.336440 TGCAGCGTGCTGTGTTTTATT 59.664 42.857 21.76 0.00 45.31 1.40
2339 5580 2.223688 TGCAGCGTGCTGTGTTTTATTT 60.224 40.909 21.76 0.00 45.31 1.40
2340 5581 2.794350 GCAGCGTGCTGTGTTTTATTTT 59.206 40.909 21.76 0.00 45.24 1.82
2341 5582 3.361917 GCAGCGTGCTGTGTTTTATTTTG 60.362 43.478 21.76 0.00 45.24 2.44
2342 5583 4.041049 CAGCGTGCTGTGTTTTATTTTGA 58.959 39.130 13.62 0.00 39.10 2.69
2343 5584 4.502282 CAGCGTGCTGTGTTTTATTTTGAA 59.498 37.500 13.62 0.00 39.10 2.69
2344 5585 5.175491 CAGCGTGCTGTGTTTTATTTTGAAT 59.825 36.000 13.62 0.00 39.10 2.57
2345 5586 5.175491 AGCGTGCTGTGTTTTATTTTGAATG 59.825 36.000 0.00 0.00 0.00 2.67
2347 5588 6.143118 GCGTGCTGTGTTTTATTTTGAATGTA 59.857 34.615 0.00 0.00 0.00 2.29
2348 5589 7.148820 GCGTGCTGTGTTTTATTTTGAATGTAT 60.149 33.333 0.00 0.00 0.00 2.29
2349 5590 9.335891 CGTGCTGTGTTTTATTTTGAATGTATA 57.664 29.630 0.00 0.00 0.00 1.47
2351 5592 9.632807 TGCTGTGTTTTATTTTGAATGTATACC 57.367 29.630 0.00 0.00 0.00 2.73
2352 5593 9.083080 GCTGTGTTTTATTTTGAATGTATACCC 57.917 33.333 0.00 0.00 0.00 3.69
2353 5594 9.284594 CTGTGTTTTATTTTGAATGTATACCCG 57.715 33.333 0.00 0.00 0.00 5.28
2354 5595 9.011095 TGTGTTTTATTTTGAATGTATACCCGA 57.989 29.630 0.00 0.00 0.00 5.14
2357 5598 9.673454 GTTTTATTTTGAATGTATACCCGATCC 57.327 33.333 0.00 0.00 0.00 3.36
2360 5601 4.617253 TTGAATGTATACCCGATCCTGG 57.383 45.455 0.00 0.00 0.00 4.45
2362 5603 2.024176 ATGTATACCCGATCCTGGCA 57.976 50.000 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.174413 TGATTTGATTTGAGTAATGGAGGTCA 58.826 34.615 0.00 0.00 0.00 4.02
1 2 7.630242 TGATTTGATTTGAGTAATGGAGGTC 57.370 36.000 0.00 0.00 0.00 3.85
2 3 8.421249 TTTGATTTGATTTGAGTAATGGAGGT 57.579 30.769 0.00 0.00 0.00 3.85
3 4 8.742777 TCTTTGATTTGATTTGAGTAATGGAGG 58.257 33.333 0.00 0.00 0.00 4.30
9 10 9.630098 GCTTGATCTTTGATTTGATTTGAGTAA 57.370 29.630 0.00 0.00 0.00 2.24
10 11 8.246180 GGCTTGATCTTTGATTTGATTTGAGTA 58.754 33.333 0.00 0.00 0.00 2.59
11 12 7.039223 AGGCTTGATCTTTGATTTGATTTGAGT 60.039 33.333 0.00 0.00 0.00 3.41
12 13 7.321153 AGGCTTGATCTTTGATTTGATTTGAG 58.679 34.615 0.00 0.00 0.00 3.02
13 14 7.235935 AGGCTTGATCTTTGATTTGATTTGA 57.764 32.000 0.00 0.00 0.00 2.69
14 15 6.534079 GGAGGCTTGATCTTTGATTTGATTTG 59.466 38.462 0.00 0.00 0.00 2.32
15 16 6.626623 CGGAGGCTTGATCTTTGATTTGATTT 60.627 38.462 0.00 0.00 0.00 2.17
16 17 5.163581 CGGAGGCTTGATCTTTGATTTGATT 60.164 40.000 0.00 0.00 0.00 2.57
17 18 4.337555 CGGAGGCTTGATCTTTGATTTGAT 59.662 41.667 0.00 0.00 0.00 2.57
18 19 3.691118 CGGAGGCTTGATCTTTGATTTGA 59.309 43.478 0.00 0.00 0.00 2.69
19 20 3.691118 TCGGAGGCTTGATCTTTGATTTG 59.309 43.478 0.00 0.00 0.00 2.32
20 21 3.955471 TCGGAGGCTTGATCTTTGATTT 58.045 40.909 0.00 0.00 0.00 2.17
21 22 3.634397 TCGGAGGCTTGATCTTTGATT 57.366 42.857 0.00 0.00 0.00 2.57
22 23 3.737850 GATCGGAGGCTTGATCTTTGAT 58.262 45.455 18.20 2.29 38.34 2.57
23 24 2.481969 CGATCGGAGGCTTGATCTTTGA 60.482 50.000 21.11 0.56 39.05 2.69
24 25 1.863454 CGATCGGAGGCTTGATCTTTG 59.137 52.381 21.11 8.49 39.05 2.77
25 26 1.757118 TCGATCGGAGGCTTGATCTTT 59.243 47.619 16.41 0.00 39.05 2.52
26 27 1.339610 CTCGATCGGAGGCTTGATCTT 59.660 52.381 16.41 0.00 39.05 2.40
27 28 0.958091 CTCGATCGGAGGCTTGATCT 59.042 55.000 16.41 0.00 39.05 2.75
28 29 0.665972 GCTCGATCGGAGGCTTGATC 60.666 60.000 16.41 16.44 43.36 2.92
29 30 1.365633 GCTCGATCGGAGGCTTGAT 59.634 57.895 16.41 3.19 43.36 2.57
30 31 2.052104 TGCTCGATCGGAGGCTTGA 61.052 57.895 16.41 0.00 43.36 3.02
31 32 1.880340 GTGCTCGATCGGAGGCTTG 60.880 63.158 16.41 0.00 43.36 4.01
32 33 2.496817 GTGCTCGATCGGAGGCTT 59.503 61.111 16.41 0.00 43.36 4.35
33 34 3.893763 CGTGCTCGATCGGAGGCT 61.894 66.667 16.41 0.00 43.36 4.58
34 35 2.831366 TACGTGCTCGATCGGAGGC 61.831 63.158 16.41 16.83 43.36 4.70
35 36 1.009900 GTACGTGCTCGATCGGAGG 60.010 63.158 16.41 7.92 43.36 4.30
36 37 0.308068 ATGTACGTGCTCGATCGGAG 59.692 55.000 16.41 12.22 46.06 4.63
37 38 0.306840 GATGTACGTGCTCGATCGGA 59.693 55.000 16.41 1.00 40.62 4.55
38 39 0.028902 TGATGTACGTGCTCGATCGG 59.971 55.000 16.41 7.26 40.62 4.18
39 40 1.822581 TTGATGTACGTGCTCGATCG 58.177 50.000 16.04 9.36 40.62 3.69
40 41 3.180584 GTGATTGATGTACGTGCTCGATC 59.819 47.826 16.04 17.97 40.62 3.69
41 42 3.116300 GTGATTGATGTACGTGCTCGAT 58.884 45.455 16.04 5.51 40.62 3.59
42 43 2.094957 TGTGATTGATGTACGTGCTCGA 60.095 45.455 16.04 0.69 40.62 4.04
43 44 2.258755 TGTGATTGATGTACGTGCTCG 58.741 47.619 6.63 6.63 43.34 5.03
44 45 4.568359 AGATTGTGATTGATGTACGTGCTC 59.432 41.667 4.97 0.90 0.00 4.26
45 46 4.507710 AGATTGTGATTGATGTACGTGCT 58.492 39.130 4.97 0.00 0.00 4.40
46 47 4.329801 TGAGATTGTGATTGATGTACGTGC 59.670 41.667 0.00 0.00 0.00 5.34
47 48 6.407475 TTGAGATTGTGATTGATGTACGTG 57.593 37.500 0.00 0.00 0.00 4.49
48 49 7.334171 TGATTTGAGATTGTGATTGATGTACGT 59.666 33.333 0.00 0.00 0.00 3.57
49 50 7.687445 TGATTTGAGATTGTGATTGATGTACG 58.313 34.615 0.00 0.00 0.00 3.67
50 51 9.282247 GTTGATTTGAGATTGTGATTGATGTAC 57.718 33.333 0.00 0.00 0.00 2.90
51 52 9.012161 TGTTGATTTGAGATTGTGATTGATGTA 57.988 29.630 0.00 0.00 0.00 2.29
52 53 7.888424 TGTTGATTTGAGATTGTGATTGATGT 58.112 30.769 0.00 0.00 0.00 3.06
53 54 8.751302 TTGTTGATTTGAGATTGTGATTGATG 57.249 30.769 0.00 0.00 0.00 3.07
65 66 6.547141 AGAACTTGTGGATTGTTGATTTGAGA 59.453 34.615 0.00 0.00 0.00 3.27
66 67 6.639686 CAGAACTTGTGGATTGTTGATTTGAG 59.360 38.462 0.00 0.00 0.00 3.02
67 68 6.320926 TCAGAACTTGTGGATTGTTGATTTGA 59.679 34.615 0.00 0.00 0.00 2.69
68 69 6.418819 GTCAGAACTTGTGGATTGTTGATTTG 59.581 38.462 0.00 0.00 0.00 2.32
69 70 6.322201 AGTCAGAACTTGTGGATTGTTGATTT 59.678 34.615 0.00 0.00 28.74 2.17
72 74 4.780815 AGTCAGAACTTGTGGATTGTTGA 58.219 39.130 0.00 0.00 28.74 3.18
114 121 2.505118 GCGAGACGACACTGGAGC 60.505 66.667 0.00 0.00 0.00 4.70
115 122 0.318699 TTTGCGAGACGACACTGGAG 60.319 55.000 0.00 0.00 0.00 3.86
120 127 2.599142 GGTTTCTTTTGCGAGACGACAC 60.599 50.000 0.00 0.00 0.00 3.67
128 141 2.123342 CATTTGCGGTTTCTTTTGCGA 58.877 42.857 0.00 0.00 0.00 5.10
144 157 4.438744 CGCGGCTTCCTTTCTTAATCATTT 60.439 41.667 0.00 0.00 0.00 2.32
145 158 3.065371 CGCGGCTTCCTTTCTTAATCATT 59.935 43.478 0.00 0.00 0.00 2.57
148 161 2.277084 TCGCGGCTTCCTTTCTTAATC 58.723 47.619 6.13 0.00 0.00 1.75
157 171 0.893727 ACCAATTTTCGCGGCTTCCT 60.894 50.000 6.13 0.00 0.00 3.36
159 173 1.336877 GAACCAATTTTCGCGGCTTC 58.663 50.000 6.13 0.00 0.00 3.86
177 191 2.105328 CACACACACACCGACCGA 59.895 61.111 0.00 0.00 0.00 4.69
180 194 1.017177 ACACACACACACACACCGAC 61.017 55.000 0.00 0.00 0.00 4.79
186 200 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
187 201 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
188 202 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
189 203 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
190 204 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
191 205 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
192 206 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
193 207 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
194 208 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
195 209 1.884235 TTCACACACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
196 210 2.477694 CCATTCACACACACACACACAC 60.478 50.000 0.00 0.00 0.00 3.82
197 211 1.742268 CCATTCACACACACACACACA 59.258 47.619 0.00 0.00 0.00 3.72
198 212 1.533756 GCCATTCACACACACACACAC 60.534 52.381 0.00 0.00 0.00 3.82
199 213 0.737804 GCCATTCACACACACACACA 59.262 50.000 0.00 0.00 0.00 3.72
200 214 1.024271 AGCCATTCACACACACACAC 58.976 50.000 0.00 0.00 0.00 3.82
201 215 1.404748 CAAGCCATTCACACACACACA 59.595 47.619 0.00 0.00 0.00 3.72
202 216 1.675483 TCAAGCCATTCACACACACAC 59.325 47.619 0.00 0.00 0.00 3.82
203 217 1.675483 GTCAAGCCATTCACACACACA 59.325 47.619 0.00 0.00 0.00 3.72
207 221 2.049888 TGTGTCAAGCCATTCACACA 57.950 45.000 0.00 0.00 45.31 3.72
217 231 3.182972 GCAATGTGTCATTTGTGTCAAGC 59.817 43.478 0.00 0.00 0.00 4.01
218 232 4.613944 AGCAATGTGTCATTTGTGTCAAG 58.386 39.130 0.00 0.00 0.00 3.02
220 234 4.652421 AAGCAATGTGTCATTTGTGTCA 57.348 36.364 0.00 0.00 0.00 3.58
222 236 5.008619 TCAAAGCAATGTGTCATTTGTGT 57.991 34.783 0.00 0.00 33.61 3.72
223 237 5.045215 ACTCAAAGCAATGTGTCATTTGTG 58.955 37.500 0.00 0.00 33.61 3.33
225 239 5.749588 TCAACTCAAAGCAATGTGTCATTTG 59.250 36.000 0.00 0.00 33.25 2.32
227 241 5.518848 TCAACTCAAAGCAATGTGTCATT 57.481 34.783 0.00 0.00 0.00 2.57
228 242 4.558095 GCTCAACTCAAAGCAATGTGTCAT 60.558 41.667 0.00 0.00 38.42 3.06
231 245 2.689471 TGCTCAACTCAAAGCAATGTGT 59.311 40.909 0.00 0.00 45.09 3.72
238 252 0.599558 TGCCATGCTCAACTCAAAGC 59.400 50.000 0.00 0.00 39.02 3.51
239 253 1.068055 GGTGCCATGCTCAACTCAAAG 60.068 52.381 0.00 0.00 0.00 2.77
240 254 0.961019 GGTGCCATGCTCAACTCAAA 59.039 50.000 0.00 0.00 0.00 2.69
241 255 0.111061 AGGTGCCATGCTCAACTCAA 59.889 50.000 0.00 0.00 0.00 3.02
242 256 0.321919 GAGGTGCCATGCTCAACTCA 60.322 55.000 19.93 0.00 45.19 3.41
243 257 1.028868 GGAGGTGCCATGCTCAACTC 61.029 60.000 17.82 17.82 45.14 3.01
244 258 1.001641 GGAGGTGCCATGCTCAACT 60.002 57.895 3.76 3.76 36.34 3.16
245 259 2.048603 GGGAGGTGCCATGCTCAAC 61.049 63.158 1.29 0.00 38.95 3.18
250 264 1.598701 GAGTTTGGGAGGTGCCATGC 61.599 60.000 0.00 0.00 38.95 4.06
286 311 2.788210 CTTTGACTTCCAGGGGGCCC 62.788 65.000 15.76 15.76 0.00 5.80
287 312 1.304464 CTTTGACTTCCAGGGGGCC 60.304 63.158 0.00 0.00 0.00 5.80
288 313 1.979155 GCTTTGACTTCCAGGGGGC 60.979 63.158 0.00 0.00 0.00 5.80
289 314 1.304464 GGCTTTGACTTCCAGGGGG 60.304 63.158 0.00 0.00 0.00 5.40
319 352 3.946907 GCTTCACGCAACGTACCT 58.053 55.556 0.00 0.00 38.32 3.08
328 361 2.253452 CTGTTGGCTGCTTCACGC 59.747 61.111 0.00 0.00 39.77 5.34
329 362 2.253452 GCTGTTGGCTGCTTCACG 59.747 61.111 0.00 0.00 38.06 4.35
330 363 1.008079 GTGCTGTTGGCTGCTTCAC 60.008 57.895 0.00 0.00 42.39 3.18
331 364 1.449726 CTGTGCTGTTGGCTGCTTCA 61.450 55.000 0.00 0.00 42.39 3.02
332 365 1.285023 CTGTGCTGTTGGCTGCTTC 59.715 57.895 0.00 0.00 42.39 3.86
333 366 2.853290 GCTGTGCTGTTGGCTGCTT 61.853 57.895 0.00 0.00 42.39 3.91
334 367 3.292936 GCTGTGCTGTTGGCTGCT 61.293 61.111 0.00 0.00 42.39 4.24
335 368 3.598715 TGCTGTGCTGTTGGCTGC 61.599 61.111 0.00 0.00 42.39 5.25
336 369 2.333938 GTGCTGTGCTGTTGGCTG 59.666 61.111 0.00 0.00 42.39 4.85
412 447 7.419711 TGGAAGGAAGTTGAAGGTATAGTAG 57.580 40.000 0.00 0.00 0.00 2.57
413 448 7.147549 CCATGGAAGGAAGTTGAAGGTATAGTA 60.148 40.741 5.56 0.00 0.00 1.82
415 450 6.058183 CCATGGAAGGAAGTTGAAGGTATAG 58.942 44.000 5.56 0.00 0.00 1.31
416 451 5.729229 TCCATGGAAGGAAGTTGAAGGTATA 59.271 40.000 13.46 0.00 33.93 1.47
417 452 4.540099 TCCATGGAAGGAAGTTGAAGGTAT 59.460 41.667 13.46 0.00 33.93 2.73
424 463 2.449464 TGCATCCATGGAAGGAAGTTG 58.551 47.619 20.67 11.74 41.92 3.16
427 466 1.878088 CGATGCATCCATGGAAGGAAG 59.122 52.381 20.67 10.51 41.92 3.46
434 473 1.970114 GCTCCCGATGCATCCATGG 60.970 63.158 20.87 17.64 0.00 3.66
446 485 3.854669 CCTACCTGCCTGCTCCCG 61.855 72.222 0.00 0.00 0.00 5.14
453 492 3.141488 CGAGACGCCTACCTGCCT 61.141 66.667 0.00 0.00 0.00 4.75
527 570 1.191489 TTGAGTCTCCCGTGCATGGA 61.191 55.000 27.13 16.54 0.00 3.41
530 573 2.496899 ATTTTGAGTCTCCCGTGCAT 57.503 45.000 0.00 0.00 0.00 3.96
531 574 3.410631 TTATTTTGAGTCTCCCGTGCA 57.589 42.857 0.00 0.00 0.00 4.57
535 578 3.877508 GGTGGATTATTTTGAGTCTCCCG 59.122 47.826 0.00 0.00 0.00 5.14
536 579 4.855340 TGGTGGATTATTTTGAGTCTCCC 58.145 43.478 0.00 0.00 0.00 4.30
537 580 5.888161 ACATGGTGGATTATTTTGAGTCTCC 59.112 40.000 0.00 0.00 0.00 3.71
540 583 6.315393 ACGTACATGGTGGATTATTTTGAGTC 59.685 38.462 0.00 0.00 0.00 3.36
542 585 6.486248 CACGTACATGGTGGATTATTTTGAG 58.514 40.000 0.00 0.00 0.00 3.02
555 598 1.202371 CGTATGAGCCACGTACATGGT 60.202 52.381 10.12 0.00 42.28 3.55
602 645 0.541863 GAAGCCGGGAAATGAGGAGA 59.458 55.000 2.18 0.00 0.00 3.71
669 737 9.236006 CACCAAGTTTTACTACTACTCCTACTA 57.764 37.037 0.00 0.00 0.00 1.82
678 750 4.309099 CGTGGCACCAAGTTTTACTACTA 58.691 43.478 12.86 0.00 0.00 1.82
690 762 4.555709 ACGGAAGCGTGGCACCAA 62.556 61.111 12.86 0.00 0.00 3.67
836 912 1.456705 GCGAGGAGGACTGGAGGAT 60.457 63.158 0.00 0.00 0.00 3.24
844 929 1.686325 TTGGCTATGGCGAGGAGGAC 61.686 60.000 0.00 0.00 39.81 3.85
845 930 0.764369 ATTGGCTATGGCGAGGAGGA 60.764 55.000 0.00 0.00 39.81 3.71
846 931 0.321122 GATTGGCTATGGCGAGGAGG 60.321 60.000 0.00 0.00 39.81 4.30
847 932 0.321122 GGATTGGCTATGGCGAGGAG 60.321 60.000 0.00 0.00 39.81 3.69
848 933 1.754745 GGATTGGCTATGGCGAGGA 59.245 57.895 0.00 0.00 39.81 3.71
849 934 1.302832 GGGATTGGCTATGGCGAGG 60.303 63.158 0.00 0.00 39.81 4.63
850 935 1.669115 CGGGATTGGCTATGGCGAG 60.669 63.158 0.00 0.00 39.81 5.03
851 936 2.425592 CGGGATTGGCTATGGCGA 59.574 61.111 0.00 0.00 39.81 5.54
864 949 1.366111 GCGTATGAAGCTTTGCGGGA 61.366 55.000 0.00 0.00 0.00 5.14
878 983 0.027716 CTCTGCACGTACGAGCGTAT 59.972 55.000 27.99 0.37 43.83 3.06
890 995 3.418068 GTCGCACTGGCTCTGCAC 61.418 66.667 7.57 2.28 38.10 4.57
911 1016 4.097361 GCCGGGTGGAAGGAGGTC 62.097 72.222 2.18 0.00 37.49 3.85
913 1018 4.101448 CAGCCGGGTGGAAGGAGG 62.101 72.222 26.09 0.00 37.49 4.30
938 1043 0.032267 GGTAGCTAGCTTGCCGGTAG 59.968 60.000 24.88 1.82 44.60 3.18
939 1044 0.396695 AGGTAGCTAGCTTGCCGGTA 60.397 55.000 24.88 0.00 0.00 4.02
940 1045 1.265454 AAGGTAGCTAGCTTGCCGGT 61.265 55.000 31.79 15.19 41.92 5.28
941 1046 1.522569 AAGGTAGCTAGCTTGCCGG 59.477 57.895 31.79 0.00 41.92 6.13
946 1051 0.833949 GAGGGCAAGGTAGCTAGCTT 59.166 55.000 28.22 28.22 44.08 3.74
961 1073 2.801631 GGGAGTCATGAGCCGAGGG 61.802 68.421 0.00 0.00 0.00 4.30
995 1121 4.873129 CGGGTCGTCTCATGGCCG 62.873 72.222 0.00 0.00 0.00 6.13
1120 1249 2.281345 GGCCGGATGATCCAGCTG 60.281 66.667 18.37 6.78 39.83 4.24
1121 1250 2.447379 AGGCCGGATGATCCAGCT 60.447 61.111 18.37 3.13 39.83 4.24
1123 1252 0.831288 AGAGAGGCCGGATGATCCAG 60.831 60.000 12.67 0.48 35.91 3.86
1125 1254 0.320050 GAAGAGAGGCCGGATGATCC 59.680 60.000 5.05 0.08 0.00 3.36
1128 1257 1.762460 GGGAAGAGAGGCCGGATGA 60.762 63.158 5.05 0.00 0.00 2.92
1130 1259 1.764054 CTGGGAAGAGAGGCCGGAT 60.764 63.158 5.05 0.00 0.00 4.18
1223 1361 1.001020 TGATGATGGTGGTGGTGCC 60.001 57.895 0.00 0.00 37.90 5.01
1224 1362 1.315257 GGTGATGATGGTGGTGGTGC 61.315 60.000 0.00 0.00 0.00 5.01
1256 1400 4.322385 GCCGTTGACGTTGGTGGC 62.322 66.667 7.00 7.00 37.74 5.01
1413 1557 2.671070 CATGAAGACCCTGCCCGT 59.329 61.111 0.00 0.00 0.00 5.28
1415 1559 2.440980 GCCATGAAGACCCTGCCC 60.441 66.667 0.00 0.00 0.00 5.36
1416 1560 2.440980 GGCCATGAAGACCCTGCC 60.441 66.667 0.00 0.00 0.00 4.85
1417 1561 2.825836 CGGCCATGAAGACCCTGC 60.826 66.667 2.24 0.00 0.00 4.85
1418 1562 2.124570 CCGGCCATGAAGACCCTG 60.125 66.667 2.24 0.00 0.00 4.45
1419 1563 3.411517 CCCGGCCATGAAGACCCT 61.412 66.667 2.24 0.00 0.00 4.34
1421 1565 3.645268 AAGCCCGGCCATGAAGACC 62.645 63.158 5.55 0.00 0.00 3.85
1422 1566 2.044946 AAGCCCGGCCATGAAGAC 60.045 61.111 5.55 0.00 0.00 3.01
1423 1567 2.272146 GAAGCCCGGCCATGAAGA 59.728 61.111 5.55 0.00 0.00 2.87
1424 1568 2.830370 GGAAGCCCGGCCATGAAG 60.830 66.667 5.55 0.00 0.00 3.02
1425 1569 2.995077 ATGGAAGCCCGGCCATGAA 61.995 57.895 10.22 0.00 43.04 2.57
1426 1570 3.419580 ATGGAAGCCCGGCCATGA 61.420 61.111 10.22 0.00 43.04 3.07
1428 1572 4.528039 CCATGGAAGCCCGGCCAT 62.528 66.667 5.56 5.56 45.47 4.40
1510 1663 6.280643 ACCACAGCTAGAAAAATTTTGGTTC 58.719 36.000 3.73 0.00 30.52 3.62
1515 1668 9.073475 TGTATGTACCACAGCTAGAAAAATTTT 57.927 29.630 0.00 0.00 0.00 1.82
1523 1676 5.995565 AACTTGTATGTACCACAGCTAGA 57.004 39.130 0.00 0.00 0.00 2.43
1540 1693 8.131455 ACGATACTCAACAGCATAATAACTTG 57.869 34.615 0.00 0.00 0.00 3.16
1541 1694 8.198109 AGACGATACTCAACAGCATAATAACTT 58.802 33.333 0.00 0.00 0.00 2.66
1543 1696 7.863375 AGAGACGATACTCAACAGCATAATAAC 59.137 37.037 0.00 0.00 39.14 1.89
1551 1704 3.129638 AGGAAGAGACGATACTCAACAGC 59.870 47.826 0.00 0.00 39.14 4.40
1552 1705 4.638421 AGAGGAAGAGACGATACTCAACAG 59.362 45.833 0.00 0.00 39.14 3.16
1597 1763 9.725019 TGTAGCAGAGAAAATCAAAGAATAGAA 57.275 29.630 0.00 0.00 0.00 2.10
1598 1764 9.896645 ATGTAGCAGAGAAAATCAAAGAATAGA 57.103 29.630 0.00 0.00 0.00 1.98
1599 1765 9.932699 CATGTAGCAGAGAAAATCAAAGAATAG 57.067 33.333 0.00 0.00 0.00 1.73
1600 1766 8.896744 CCATGTAGCAGAGAAAATCAAAGAATA 58.103 33.333 0.00 0.00 0.00 1.75
1626 1796 6.470235 CGTCTTATTCATGCCAAGATTTTGAC 59.530 38.462 0.00 0.00 36.36 3.18
1689 1862 8.830201 AAAGCACAAAGTGAAATGCAAATATA 57.170 26.923 0.58 0.00 40.63 0.86
1690 1863 7.733402 AAAGCACAAAGTGAAATGCAAATAT 57.267 28.000 0.58 0.00 40.63 1.28
1691 1864 7.925483 AGTAAAGCACAAAGTGAAATGCAAATA 59.075 29.630 0.58 0.00 40.63 1.40
1692 1865 6.762661 AGTAAAGCACAAAGTGAAATGCAAAT 59.237 30.769 0.58 0.00 40.63 2.32
1694 1867 5.519566 CAGTAAAGCACAAAGTGAAATGCAA 59.480 36.000 0.58 0.00 40.63 4.08
1696 1869 5.280945 TCAGTAAAGCACAAAGTGAAATGC 58.719 37.500 0.58 0.00 35.23 3.56
1697 1870 7.095940 CCAATCAGTAAAGCACAAAGTGAAATG 60.096 37.037 0.58 0.00 35.23 2.32
1785 1988 8.991243 ATGTTCAACACATAATTGGAGATTTG 57.009 30.769 0.00 0.00 45.00 2.32
1793 1996 8.592105 AGGTTCAAATGTTCAACACATAATTG 57.408 30.769 0.00 0.00 46.23 2.32
1825 2028 7.617723 TGTTTATAAGGTCCAATACATTTGCCT 59.382 33.333 0.00 0.00 33.36 4.75
1826 2029 7.704899 GTGTTTATAAGGTCCAATACATTTGCC 59.295 37.037 0.00 0.00 33.36 4.52
1828 2031 8.670135 TCGTGTTTATAAGGTCCAATACATTTG 58.330 33.333 0.00 0.00 33.36 2.32
1840 2046 6.105397 TCCTTCTGTTCGTGTTTATAAGGT 57.895 37.500 0.00 0.00 35.00 3.50
1939 2146 1.305287 GGGTATTGGGCGGAAAGGT 59.695 57.895 0.00 0.00 0.00 3.50
1941 2148 1.455032 GGGGGTATTGGGCGGAAAG 60.455 63.158 0.00 0.00 0.00 2.62
1956 2163 0.811281 GATTTTGCTCACTTCGGGGG 59.189 55.000 0.00 0.00 0.00 5.40
1957 2164 1.470098 CAGATTTTGCTCACTTCGGGG 59.530 52.381 0.00 0.00 0.00 5.73
2097 2330 3.337694 TTATATATCCAAACCGGGCCG 57.662 47.619 21.46 21.46 34.36 6.13
2098 2331 5.771165 TCTTTTTATATATCCAAACCGGGCC 59.229 40.000 6.32 0.00 34.36 5.80
2099 2332 6.887626 TCTTTTTATATATCCAAACCGGGC 57.112 37.500 6.32 0.00 34.36 6.13
2100 2333 9.297037 AGATTCTTTTTATATATCCAAACCGGG 57.703 33.333 6.32 0.00 34.36 5.73
2228 2465 4.511826 AGCACACCGAAGAAGTTAAAGAAG 59.488 41.667 0.00 0.00 0.00 2.85
2231 2468 3.607078 GCAGCACACCGAAGAAGTTAAAG 60.607 47.826 0.00 0.00 0.00 1.85
2232 2469 2.289547 GCAGCACACCGAAGAAGTTAAA 59.710 45.455 0.00 0.00 0.00 1.52
2234 2471 1.508632 GCAGCACACCGAAGAAGTTA 58.491 50.000 0.00 0.00 0.00 2.24
2242 2479 1.231221 AATAAAACGCAGCACACCGA 58.769 45.000 0.00 0.00 0.00 4.69
2280 2517 1.838112 AAGAAATGCTCCATTGCCGA 58.162 45.000 0.00 0.00 34.04 5.54
2306 5547 2.095768 GCACGCTGCAGAAGTTTATGAA 60.096 45.455 20.43 0.00 44.26 2.57
2307 5548 1.464608 GCACGCTGCAGAAGTTTATGA 59.535 47.619 20.43 0.00 44.26 2.15
2308 5549 1.887320 GCACGCTGCAGAAGTTTATG 58.113 50.000 20.43 5.81 44.26 1.90
2323 5564 6.509317 ACATTCAAAATAAAACACAGCACG 57.491 33.333 0.00 0.00 0.00 5.34
2338 5579 4.745478 GCCAGGATCGGGTATACATTCAAA 60.745 45.833 5.01 0.00 0.00 2.69
2339 5580 3.244422 GCCAGGATCGGGTATACATTCAA 60.244 47.826 5.01 0.00 0.00 2.69
2340 5581 2.301870 GCCAGGATCGGGTATACATTCA 59.698 50.000 5.01 0.00 0.00 2.57
2341 5582 2.301870 TGCCAGGATCGGGTATACATTC 59.698 50.000 5.01 0.00 0.00 2.67
2342 5583 2.334977 TGCCAGGATCGGGTATACATT 58.665 47.619 5.01 0.00 0.00 2.71
2343 5584 2.024176 TGCCAGGATCGGGTATACAT 57.976 50.000 5.01 0.00 0.00 2.29
2344 5585 1.796017 TTGCCAGGATCGGGTATACA 58.204 50.000 5.01 0.00 0.00 2.29
2345 5586 2.922740 TTTGCCAGGATCGGGTATAC 57.077 50.000 0.00 0.00 0.00 1.47
2347 5588 1.202927 CCATTTGCCAGGATCGGGTAT 60.203 52.381 0.00 0.00 0.00 2.73
2348 5589 0.182537 CCATTTGCCAGGATCGGGTA 59.817 55.000 0.00 0.00 0.00 3.69
2349 5590 1.076777 CCATTTGCCAGGATCGGGT 60.077 57.895 0.00 0.00 0.00 5.28
2350 5591 0.820891 CTCCATTTGCCAGGATCGGG 60.821 60.000 0.00 0.00 32.53 5.14
2351 5592 1.450531 GCTCCATTTGCCAGGATCGG 61.451 60.000 0.00 0.00 32.53 4.18
2352 5593 2.028130 GCTCCATTTGCCAGGATCG 58.972 57.895 0.00 0.00 32.53 3.69


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

AutoCloner maintained by Alex Coulton.