Multiple sequence alignment - TraesCS1A01G370700

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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 TraesCS1A01G370700 chr1A 100.000 2798 0 0 1 2798 547909459 547906662 0.000000e+00 5168.0
1 TraesCS1A01G370700 chr1A 82.564 780 67 40 992 1767 547886724 547887438 8.510000e-175 623.0
2 TraesCS1A01G370700 chr1A 81.981 727 57 41 1048 1767 547863952 547864611 1.470000e-152 549.0
3 TraesCS1A01G370700 chr1A 96.721 61 1 1 130 189 549034805 549034745 1.770000e-17 100.0
4 TraesCS1A01G370700 chr1D 89.147 2414 99 68 427 2741 453211711 453209362 0.000000e+00 2856.0
5 TraesCS1A01G370700 chr1D 85.337 682 55 26 983 1656 453199602 453200246 0.000000e+00 664.0
6 TraesCS1A01G370700 chr1D 82.902 772 68 36 1001 1767 453181698 453182410 1.090000e-178 636.0
7 TraesCS1A01G370700 chr1D 83.104 728 63 30 1043 1764 453134695 453135368 2.380000e-170 608.0
8 TraesCS1A01G370700 chr1D 89.888 89 7 2 1 87 21845110 21845198 2.280000e-21 113.0
9 TraesCS1A01G370700 chr1B 88.037 1956 125 48 427 2347 623689988 623688107 0.000000e+00 2215.0
10 TraesCS1A01G370700 chr1B 86.183 579 54 12 1088 1656 623679655 623680217 1.110000e-168 603.0
11 TraesCS1A01G370700 chr1B 85.179 614 52 21 1046 1656 623672602 623673179 6.670000e-166 593.0
12 TraesCS1A01G370700 chr1B 86.076 158 21 1 259 415 684895994 684896151 4.790000e-38 169.0
13 TraesCS1A01G370700 chr5D 88.535 157 17 1 259 414 58404200 58404356 3.680000e-44 189.0
14 TraesCS1A01G370700 chr5D 90.000 90 7 2 1 88 426161688 426161777 6.330000e-22 115.0
15 TraesCS1A01G370700 chr5D 90.000 90 6 3 1 87 135058440 135058351 2.280000e-21 113.0
16 TraesCS1A01G370700 chr5D 86.139 101 12 2 1 99 3756028 3755928 1.060000e-19 108.0
17 TraesCS1A01G370700 chr7D 89.796 147 14 1 269 414 575402175 575402029 1.320000e-43 187.0
18 TraesCS1A01G370700 chr7D 87.179 156 19 1 259 414 312187049 312186895 2.860000e-40 176.0
19 TraesCS1A01G370700 chr7D 96.721 61 1 1 125 184 529385682 529385622 1.770000e-17 100.0
20 TraesCS1A01G370700 chr7D 96.667 60 1 1 125 183 591077424 591077483 6.380000e-17 99.0
21 TraesCS1A01G370700 chr7B 87.261 157 19 1 259 414 138877097 138877253 7.960000e-41 178.0
22 TraesCS1A01G370700 chr7B 90.110 91 5 4 1 87 383873356 383873446 6.330000e-22 115.0
23 TraesCS1A01G370700 chr4A 87.179 156 19 1 260 414 659211075 659211230 2.860000e-40 176.0
24 TraesCS1A01G370700 chr4A 90.909 88 7 1 1 87 668444439 668444526 1.760000e-22 117.0
25 TraesCS1A01G370700 chr2A 87.755 147 18 0 260 406 57529829 57529975 3.710000e-39 172.0
26 TraesCS1A01G370700 chr6B 86.538 156 20 1 260 414 290212470 290212315 1.330000e-38 171.0
27 TraesCS1A01G370700 chr6B 93.846 65 3 1 125 188 120659402 120659466 2.290000e-16 97.1
28 TraesCS1A01G370700 chr7A 86.452 155 20 1 261 414 182714735 182714581 4.790000e-38 169.0
29 TraesCS1A01G370700 chrUn 90.000 90 6 3 1 87 317389881 317389970 2.280000e-21 113.0
30 TraesCS1A01G370700 chrUn 96.667 60 1 1 125 183 459698321 459698380 6.380000e-17 99.0
31 TraesCS1A01G370700 chr3D 89.888 89 7 2 1 87 585095983 585096071 2.280000e-21 113.0
32 TraesCS1A01G370700 chr2D 90.000 90 6 3 1 87 184131606 184131695 2.280000e-21 113.0
33 TraesCS1A01G370700 chr2D 96.721 61 1 1 125 184 7798517 7798457 1.770000e-17 100.0
34 TraesCS1A01G370700 chr5A 95.312 64 2 1 125 187 362736514 362736451 1.770000e-17 100.0
35 TraesCS1A01G370700 chr5A 90.789 76 3 4 125 198 130259764 130259691 6.380000e-17 99.0
36 TraesCS1A01G370700 chr4B 96.721 61 1 1 125 184 661136844 661136784 1.770000e-17 100.0


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 TraesCS1A01G370700 chr1A 547906662 547909459 2797 True 5168 5168 100.000 1 2798 1 chr1A.!!$R1 2797
1 TraesCS1A01G370700 chr1A 547886724 547887438 714 False 623 623 82.564 992 1767 1 chr1A.!!$F2 775
2 TraesCS1A01G370700 chr1A 547863952 547864611 659 False 549 549 81.981 1048 1767 1 chr1A.!!$F1 719
3 TraesCS1A01G370700 chr1D 453209362 453211711 2349 True 2856 2856 89.147 427 2741 1 chr1D.!!$R1 2314
4 TraesCS1A01G370700 chr1D 453199602 453200246 644 False 664 664 85.337 983 1656 1 chr1D.!!$F4 673
5 TraesCS1A01G370700 chr1D 453181698 453182410 712 False 636 636 82.902 1001 1767 1 chr1D.!!$F3 766
6 TraesCS1A01G370700 chr1D 453134695 453135368 673 False 608 608 83.104 1043 1764 1 chr1D.!!$F2 721
7 TraesCS1A01G370700 chr1B 623688107 623689988 1881 True 2215 2215 88.037 427 2347 1 chr1B.!!$R1 1920
8 TraesCS1A01G370700 chr1B 623679655 623680217 562 False 603 603 86.183 1088 1656 1 chr1B.!!$F2 568
9 TraesCS1A01G370700 chr1B 623672602 623673179 577 False 593 593 85.179 1046 1656 1 chr1B.!!$F1 610

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
665 666 1.067425 GGGCAACACCGGAAATAAACC 60.067 52.381 9.46 0.0 40.62 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 2622 0.036952 CGAGAGGAGGAAAGCAAGCA 60.037 55.0 0.0 0.0 0.0 3.91 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
19 20 2.093306 CACGCCTTACAGGAATGTGA 57.907 50.000 0.00 0.00 37.67 3.58
20 21 2.632377 CACGCCTTACAGGAATGTGAT 58.368 47.619 0.00 0.00 37.67 3.06
21 22 3.009723 CACGCCTTACAGGAATGTGATT 58.990 45.455 0.00 0.00 37.67 2.57
22 23 3.440173 CACGCCTTACAGGAATGTGATTT 59.560 43.478 0.00 0.00 37.67 2.17
23 24 3.689649 ACGCCTTACAGGAATGTGATTTC 59.310 43.478 0.00 0.00 37.67 2.17
24 25 3.689161 CGCCTTACAGGAATGTGATTTCA 59.311 43.478 0.00 0.00 37.67 2.69
25 26 4.336433 CGCCTTACAGGAATGTGATTTCAT 59.664 41.667 0.00 0.00 37.67 2.57
26 27 5.585390 GCCTTACAGGAATGTGATTTCATG 58.415 41.667 0.00 0.00 41.77 3.07
27 28 5.357878 GCCTTACAGGAATGTGATTTCATGA 59.642 40.000 5.92 0.00 39.18 3.07
28 29 6.127647 GCCTTACAGGAATGTGATTTCATGAA 60.128 38.462 3.38 3.38 39.18 2.57
29 30 7.577426 GCCTTACAGGAATGTGATTTCATGAAA 60.577 37.037 22.52 22.52 39.18 2.69
30 31 8.306038 CCTTACAGGAATGTGATTTCATGAAAA 58.694 33.333 23.91 8.76 39.18 2.29
31 32 9.695526 CTTACAGGAATGTGATTTCATGAAAAA 57.304 29.630 23.91 13.05 39.18 1.94
54 55 7.848223 AAAAATTGCAAGCACTTAGAACTTT 57.152 28.000 4.94 0.00 0.00 2.66
55 56 7.848223 AAAATTGCAAGCACTTAGAACTTTT 57.152 28.000 4.94 0.00 0.00 2.27
56 57 6.833342 AATTGCAAGCACTTAGAACTTTTG 57.167 33.333 4.94 0.00 0.00 2.44
57 58 4.981806 TGCAAGCACTTAGAACTTTTGT 57.018 36.364 0.00 0.00 0.00 2.83
58 59 4.920376 TGCAAGCACTTAGAACTTTTGTC 58.080 39.130 0.00 0.00 0.00 3.18
59 60 4.397730 TGCAAGCACTTAGAACTTTTGTCA 59.602 37.500 0.00 0.00 0.00 3.58
60 61 5.105957 TGCAAGCACTTAGAACTTTTGTCAA 60.106 36.000 0.00 0.00 0.00 3.18
61 62 5.979517 GCAAGCACTTAGAACTTTTGTCAAT 59.020 36.000 0.00 0.00 0.00 2.57
62 63 6.074676 GCAAGCACTTAGAACTTTTGTCAATG 60.075 38.462 0.00 0.00 0.00 2.82
63 64 6.699575 AGCACTTAGAACTTTTGTCAATGT 57.300 33.333 0.00 0.00 0.00 2.71
64 65 7.100458 AGCACTTAGAACTTTTGTCAATGTT 57.900 32.000 4.72 4.72 33.94 2.71
65 66 7.547227 AGCACTTAGAACTTTTGTCAATGTTT 58.453 30.769 6.10 0.00 31.96 2.83
66 67 7.702348 AGCACTTAGAACTTTTGTCAATGTTTC 59.298 33.333 6.10 1.04 31.96 2.78
67 68 7.702348 GCACTTAGAACTTTTGTCAATGTTTCT 59.298 33.333 6.10 6.96 31.96 2.52
68 69 9.226345 CACTTAGAACTTTTGTCAATGTTTCTC 57.774 33.333 6.42 0.00 31.96 2.87
69 70 8.406297 ACTTAGAACTTTTGTCAATGTTTCTCC 58.594 33.333 6.42 0.00 31.96 3.71
70 71 6.773976 AGAACTTTTGTCAATGTTTCTCCA 57.226 33.333 6.10 0.00 31.96 3.86
71 72 7.169158 AGAACTTTTGTCAATGTTTCTCCAA 57.831 32.000 6.10 0.00 31.96 3.53
72 73 7.610865 AGAACTTTTGTCAATGTTTCTCCAAA 58.389 30.769 6.10 0.00 31.96 3.28
73 74 8.093927 AGAACTTTTGTCAATGTTTCTCCAAAA 58.906 29.630 6.10 0.00 31.96 2.44
74 75 8.614469 AACTTTTGTCAATGTTTCTCCAAAAA 57.386 26.923 0.00 0.00 33.09 1.94
103 104 2.060326 TTTACTGTTCACCGAGCTCG 57.940 50.000 29.06 29.06 39.44 5.03
120 121 2.588620 CTCGGGAGCATAGAGGTACTT 58.411 52.381 0.00 0.00 41.55 2.24
121 122 2.554893 CTCGGGAGCATAGAGGTACTTC 59.445 54.545 0.00 0.00 41.55 3.01
122 123 1.614413 CGGGAGCATAGAGGTACTTCC 59.386 57.143 0.61 0.00 41.55 3.46
123 124 2.679082 GGGAGCATAGAGGTACTTCCA 58.321 52.381 0.61 0.00 41.55 3.53
124 125 3.039011 GGGAGCATAGAGGTACTTCCAA 58.961 50.000 0.61 0.00 41.55 3.53
125 126 3.648545 GGGAGCATAGAGGTACTTCCAAT 59.351 47.826 0.61 0.00 41.55 3.16
126 127 4.503991 GGGAGCATAGAGGTACTTCCAATG 60.504 50.000 11.49 11.49 41.55 2.82
127 128 4.101741 GGAGCATAGAGGTACTTCCAATGT 59.898 45.833 15.19 6.38 41.55 2.71
128 129 5.396884 GGAGCATAGAGGTACTTCCAATGTT 60.397 44.000 15.19 11.28 41.55 2.71
129 130 6.067217 AGCATAGAGGTACTTCCAATGTTT 57.933 37.500 15.19 5.91 41.55 2.83
130 131 6.485171 AGCATAGAGGTACTTCCAATGTTTT 58.515 36.000 15.19 4.20 41.55 2.43
131 132 7.630082 AGCATAGAGGTACTTCCAATGTTTTA 58.370 34.615 15.19 0.00 41.55 1.52
132 133 8.275040 AGCATAGAGGTACTTCCAATGTTTTAT 58.725 33.333 15.19 0.00 41.55 1.40
133 134 8.560374 GCATAGAGGTACTTCCAATGTTTTATC 58.440 37.037 15.19 0.43 41.55 1.75
134 135 9.838339 CATAGAGGTACTTCCAATGTTTTATCT 57.162 33.333 0.61 0.00 41.55 1.98
137 138 9.047947 AGAGGTACTTCCAATGTTTTATCTAGT 57.952 33.333 0.61 0.00 41.55 2.57
199 200 6.845758 TCCAACATATACTATTACCTCCGG 57.154 41.667 0.00 0.00 0.00 5.14
200 201 6.317312 TCCAACATATACTATTACCTCCGGT 58.683 40.000 0.00 0.00 40.16 5.28
201 202 6.435277 TCCAACATATACTATTACCTCCGGTC 59.565 42.308 0.00 0.00 37.09 4.79
202 203 6.209986 CCAACATATACTATTACCTCCGGTCA 59.790 42.308 0.00 0.00 37.09 4.02
203 204 7.313646 CAACATATACTATTACCTCCGGTCAG 58.686 42.308 0.00 0.00 37.09 3.51
204 205 6.787170 ACATATACTATTACCTCCGGTCAGA 58.213 40.000 0.00 0.00 37.09 3.27
205 206 7.236529 ACATATACTATTACCTCCGGTCAGAA 58.763 38.462 0.00 0.00 37.09 3.02
206 207 7.176340 ACATATACTATTACCTCCGGTCAGAAC 59.824 40.741 0.00 0.00 37.09 3.01
207 208 3.978610 ACTATTACCTCCGGTCAGAACT 58.021 45.455 0.00 0.00 37.09 3.01
208 209 5.121380 ACTATTACCTCCGGTCAGAACTA 57.879 43.478 0.00 0.00 37.09 2.24
209 210 5.513233 ACTATTACCTCCGGTCAGAACTAA 58.487 41.667 0.00 0.00 37.09 2.24
210 211 5.954150 ACTATTACCTCCGGTCAGAACTAAA 59.046 40.000 0.00 0.00 37.09 1.85
211 212 5.952347 ATTACCTCCGGTCAGAACTAAAT 57.048 39.130 0.00 0.00 37.09 1.40
212 213 3.611766 ACCTCCGGTCAGAACTAAATG 57.388 47.619 0.00 0.00 0.00 2.32
213 214 2.904434 ACCTCCGGTCAGAACTAAATGT 59.096 45.455 0.00 0.00 0.00 2.71
214 215 3.056035 ACCTCCGGTCAGAACTAAATGTC 60.056 47.826 0.00 0.00 0.00 3.06
215 216 3.522553 CTCCGGTCAGAACTAAATGTCC 58.477 50.000 0.00 0.00 0.00 4.02
216 217 2.094390 TCCGGTCAGAACTAAATGTCCG 60.094 50.000 0.00 4.28 44.32 4.79
217 218 1.659098 CGGTCAGAACTAAATGTCCGC 59.341 52.381 0.00 0.00 40.26 5.54
218 219 2.674177 CGGTCAGAACTAAATGTCCGCT 60.674 50.000 0.00 0.00 40.26 5.52
219 220 2.673368 GGTCAGAACTAAATGTCCGCTG 59.327 50.000 0.00 0.00 0.00 5.18
220 221 3.585862 GTCAGAACTAAATGTCCGCTGA 58.414 45.455 0.00 0.00 32.64 4.26
221 222 3.994392 GTCAGAACTAAATGTCCGCTGAA 59.006 43.478 0.00 0.00 35.00 3.02
222 223 4.451096 GTCAGAACTAAATGTCCGCTGAAA 59.549 41.667 0.00 0.00 35.00 2.69
223 224 5.122396 GTCAGAACTAAATGTCCGCTGAAAT 59.878 40.000 0.00 0.00 35.00 2.17
224 225 5.122239 TCAGAACTAAATGTCCGCTGAAATG 59.878 40.000 0.00 0.00 32.36 2.32
225 226 3.764885 ACTAAATGTCCGCTGAAATGC 57.235 42.857 0.00 0.00 0.00 3.56
226 227 3.347216 ACTAAATGTCCGCTGAAATGCT 58.653 40.909 0.00 0.00 0.00 3.79
227 228 4.513442 ACTAAATGTCCGCTGAAATGCTA 58.487 39.130 0.00 0.00 0.00 3.49
228 229 4.572389 ACTAAATGTCCGCTGAAATGCTAG 59.428 41.667 0.00 0.00 0.00 3.42
229 230 2.988010 ATGTCCGCTGAAATGCTAGA 57.012 45.000 0.00 0.00 0.00 2.43
230 231 2.760634 TGTCCGCTGAAATGCTAGAA 57.239 45.000 0.00 0.00 0.00 2.10
231 232 2.621338 TGTCCGCTGAAATGCTAGAAG 58.379 47.619 0.00 0.00 0.00 2.85
232 233 2.028112 TGTCCGCTGAAATGCTAGAAGT 60.028 45.455 0.00 0.00 0.00 3.01
233 234 2.605366 GTCCGCTGAAATGCTAGAAGTC 59.395 50.000 0.00 0.00 0.00 3.01
234 235 2.233676 TCCGCTGAAATGCTAGAAGTCA 59.766 45.455 0.00 0.00 0.00 3.41
235 236 3.002791 CCGCTGAAATGCTAGAAGTCAA 58.997 45.455 0.00 0.00 0.00 3.18
236 237 3.181516 CCGCTGAAATGCTAGAAGTCAAC 60.182 47.826 0.00 0.00 0.00 3.18
237 238 3.681897 CGCTGAAATGCTAGAAGTCAACT 59.318 43.478 0.00 0.00 0.00 3.16
238 239 4.201666 CGCTGAAATGCTAGAAGTCAACTC 60.202 45.833 0.00 0.00 0.00 3.01
239 240 4.692625 GCTGAAATGCTAGAAGTCAACTCA 59.307 41.667 0.00 0.00 0.00 3.41
240 241 5.353678 GCTGAAATGCTAGAAGTCAACTCAT 59.646 40.000 0.00 0.00 0.00 2.90
241 242 6.128063 GCTGAAATGCTAGAAGTCAACTCATT 60.128 38.462 0.00 0.00 0.00 2.57
242 243 7.574592 GCTGAAATGCTAGAAGTCAACTCATTT 60.575 37.037 0.00 6.51 35.97 2.32
243 244 8.169977 TGAAATGCTAGAAGTCAACTCATTTT 57.830 30.769 0.00 0.00 34.17 1.82
244 245 8.077991 TGAAATGCTAGAAGTCAACTCATTTTG 58.922 33.333 0.00 0.00 34.17 2.44
245 246 7.750229 AATGCTAGAAGTCAACTCATTTTGA 57.250 32.000 0.00 0.00 32.94 2.69
255 256 1.755179 CTCATTTTGAGCGATGGGGT 58.245 50.000 0.00 0.00 37.72 4.95
256 257 2.917933 CTCATTTTGAGCGATGGGGTA 58.082 47.619 0.00 0.00 37.72 3.69
257 258 2.874701 CTCATTTTGAGCGATGGGGTAG 59.125 50.000 0.00 0.00 37.72 3.18
258 259 2.503765 TCATTTTGAGCGATGGGGTAGA 59.496 45.455 0.00 0.00 0.00 2.59
259 260 2.691409 TTTTGAGCGATGGGGTAGAG 57.309 50.000 0.00 0.00 0.00 2.43
260 261 1.568504 TTTGAGCGATGGGGTAGAGT 58.431 50.000 0.00 0.00 0.00 3.24
261 262 1.568504 TTGAGCGATGGGGTAGAGTT 58.431 50.000 0.00 0.00 0.00 3.01
262 263 1.568504 TGAGCGATGGGGTAGAGTTT 58.431 50.000 0.00 0.00 0.00 2.66
263 264 1.207089 TGAGCGATGGGGTAGAGTTTG 59.793 52.381 0.00 0.00 0.00 2.93
264 265 1.480954 GAGCGATGGGGTAGAGTTTGA 59.519 52.381 0.00 0.00 0.00 2.69
265 266 1.207329 AGCGATGGGGTAGAGTTTGAC 59.793 52.381 0.00 0.00 0.00 3.18
266 267 1.742750 GCGATGGGGTAGAGTTTGACC 60.743 57.143 0.00 0.00 34.75 4.02
267 268 1.553248 CGATGGGGTAGAGTTTGACCA 59.447 52.381 0.00 0.00 37.47 4.02
268 269 2.027561 CGATGGGGTAGAGTTTGACCAA 60.028 50.000 0.00 0.00 37.47 3.67
269 270 3.610911 GATGGGGTAGAGTTTGACCAAG 58.389 50.000 0.00 0.00 37.47 3.61
270 271 2.414612 TGGGGTAGAGTTTGACCAAGT 58.585 47.619 0.00 0.00 37.47 3.16
271 272 2.781174 TGGGGTAGAGTTTGACCAAGTT 59.219 45.455 0.00 0.00 37.47 2.66
272 273 3.203487 TGGGGTAGAGTTTGACCAAGTTT 59.797 43.478 0.00 0.00 37.47 2.66
273 274 3.568430 GGGGTAGAGTTTGACCAAGTTTG 59.432 47.826 0.00 0.00 37.47 2.93
274 275 4.204799 GGGTAGAGTTTGACCAAGTTTGT 58.795 43.478 0.00 0.00 37.47 2.83
275 276 4.036380 GGGTAGAGTTTGACCAAGTTTGTG 59.964 45.833 0.00 0.00 37.47 3.33
276 277 3.782889 AGAGTTTGACCAAGTTTGTGC 57.217 42.857 0.00 0.00 0.00 4.57
277 278 3.088532 AGAGTTTGACCAAGTTTGTGCA 58.911 40.909 0.00 0.00 0.00 4.57
278 279 3.509575 AGAGTTTGACCAAGTTTGTGCAA 59.490 39.130 0.00 0.00 0.00 4.08
279 280 4.021544 AGAGTTTGACCAAGTTTGTGCAAA 60.022 37.500 0.00 0.00 31.45 3.68
280 281 4.636249 AGTTTGACCAAGTTTGTGCAAAA 58.364 34.783 0.00 0.00 33.89 2.44
281 282 5.059833 AGTTTGACCAAGTTTGTGCAAAAA 58.940 33.333 0.00 0.00 33.89 1.94
282 283 4.999751 TTGACCAAGTTTGTGCAAAAAC 57.000 36.364 22.60 22.60 39.80 2.43
283 284 3.995199 TGACCAAGTTTGTGCAAAAACA 58.005 36.364 29.51 9.27 41.56 2.83
284 285 4.380531 TGACCAAGTTTGTGCAAAAACAA 58.619 34.783 29.51 9.19 41.56 2.83
285 286 4.816385 TGACCAAGTTTGTGCAAAAACAAA 59.184 33.333 29.51 14.52 41.56 2.83
286 287 5.471456 TGACCAAGTTTGTGCAAAAACAAAT 59.529 32.000 29.51 15.29 41.56 2.32
287 288 5.937187 ACCAAGTTTGTGCAAAAACAAATC 58.063 33.333 29.51 6.99 41.56 2.17
288 289 5.471456 ACCAAGTTTGTGCAAAAACAAATCA 59.529 32.000 29.51 0.00 41.56 2.57
289 290 6.016777 ACCAAGTTTGTGCAAAAACAAATCAA 60.017 30.769 29.51 5.92 41.56 2.57
290 291 7.028361 CCAAGTTTGTGCAAAAACAAATCAAT 58.972 30.769 29.51 8.54 41.56 2.57
291 292 7.008447 CCAAGTTTGTGCAAAAACAAATCAATG 59.992 33.333 29.51 16.75 41.56 2.82
292 293 6.028987 AGTTTGTGCAAAAACAAATCAATGC 58.971 32.000 29.51 3.57 41.56 3.56
293 294 5.814764 TTGTGCAAAAACAAATCAATGCT 57.185 30.435 0.00 0.00 34.99 3.79
294 295 5.814764 TGTGCAAAAACAAATCAATGCTT 57.185 30.435 0.00 0.00 34.97 3.91
295 296 5.570344 TGTGCAAAAACAAATCAATGCTTG 58.430 33.333 0.00 0.00 34.97 4.01
296 297 5.123502 TGTGCAAAAACAAATCAATGCTTGT 59.876 32.000 0.00 0.00 37.36 3.16
297 298 5.452944 GTGCAAAAACAAATCAATGCTTGTG 59.547 36.000 0.00 0.00 35.95 3.33
298 299 5.353400 TGCAAAAACAAATCAATGCTTGTGA 59.647 32.000 2.16 0.00 35.95 3.58
299 300 6.128090 TGCAAAAACAAATCAATGCTTGTGAA 60.128 30.769 2.16 0.00 35.95 3.18
300 301 6.746364 GCAAAAACAAATCAATGCTTGTGAAA 59.254 30.769 2.16 0.00 35.95 2.69
301 302 7.253387 GCAAAAACAAATCAATGCTTGTGAAAC 60.253 33.333 2.16 0.00 35.95 2.78
302 303 5.989551 AACAAATCAATGCTTGTGAAACC 57.010 34.783 2.16 0.00 35.95 3.27
303 304 5.021033 ACAAATCAATGCTTGTGAAACCA 57.979 34.783 0.75 0.00 34.52 3.67
304 305 5.426504 ACAAATCAATGCTTGTGAAACCAA 58.573 33.333 0.75 0.00 34.52 3.67
305 306 5.879223 ACAAATCAATGCTTGTGAAACCAAA 59.121 32.000 0.75 0.00 34.52 3.28
306 307 5.989551 AATCAATGCTTGTGAAACCAAAC 57.010 34.783 0.00 0.00 34.36 2.93
307 308 3.443037 TCAATGCTTGTGAAACCAAACG 58.557 40.909 0.00 0.00 34.36 3.60
308 309 2.507339 ATGCTTGTGAAACCAAACGG 57.493 45.000 0.00 0.00 34.36 4.44
309 310 1.178276 TGCTTGTGAAACCAAACGGT 58.822 45.000 0.00 0.00 38.95 4.83
311 312 2.753452 TGCTTGTGAAACCAAACGGTTA 59.247 40.909 0.00 0.00 46.41 2.85
312 313 3.381908 TGCTTGTGAAACCAAACGGTTAT 59.618 39.130 0.00 0.00 46.41 1.89
313 314 4.579340 TGCTTGTGAAACCAAACGGTTATA 59.421 37.500 0.00 0.00 46.41 0.98
314 315 5.241949 TGCTTGTGAAACCAAACGGTTATAT 59.758 36.000 0.00 0.00 46.41 0.86
315 316 5.571357 GCTTGTGAAACCAAACGGTTATATG 59.429 40.000 0.00 0.00 46.41 1.78
316 317 6.568844 GCTTGTGAAACCAAACGGTTATATGA 60.569 38.462 0.00 0.00 46.41 2.15
317 318 6.243811 TGTGAAACCAAACGGTTATATGAC 57.756 37.500 0.00 0.00 46.41 3.06
318 319 5.107026 TGTGAAACCAAACGGTTATATGACG 60.107 40.000 0.00 0.00 46.41 4.35
319 320 5.120519 GTGAAACCAAACGGTTATATGACGA 59.879 40.000 0.00 0.00 46.41 4.20
320 321 5.699915 TGAAACCAAACGGTTATATGACGAA 59.300 36.000 0.00 0.00 46.41 3.85
321 322 6.204301 TGAAACCAAACGGTTATATGACGAAA 59.796 34.615 0.00 0.00 46.41 3.46
322 323 6.557291 AACCAAACGGTTATATGACGAAAA 57.443 33.333 0.00 0.00 45.24 2.29
323 324 6.746745 ACCAAACGGTTATATGACGAAAAT 57.253 33.333 0.00 0.00 30.22 1.82
324 325 7.846644 ACCAAACGGTTATATGACGAAAATA 57.153 32.000 0.00 0.00 30.22 1.40
325 326 8.441312 ACCAAACGGTTATATGACGAAAATAT 57.559 30.769 0.00 0.00 30.22 1.28
326 327 9.545105 ACCAAACGGTTATATGACGAAAATATA 57.455 29.630 0.00 0.00 30.22 0.86
362 363 8.752005 AATCTAATGCTACTTATTTGAAGGCA 57.248 30.769 0.00 0.00 0.00 4.75
363 364 8.930846 ATCTAATGCTACTTATTTGAAGGCAT 57.069 30.769 0.00 0.00 40.04 4.40
365 366 9.845740 TCTAATGCTACTTATTTGAAGGCATAA 57.154 29.630 0.00 0.00 37.85 1.90
368 369 9.754382 AATGCTACTTATTTGAAGGCATAAATG 57.246 29.630 0.00 0.00 37.85 2.32
369 370 8.292444 TGCTACTTATTTGAAGGCATAAATGT 57.708 30.769 0.00 0.00 0.00 2.71
370 371 8.748412 TGCTACTTATTTGAAGGCATAAATGTT 58.252 29.630 0.00 0.00 0.00 2.71
371 372 9.023967 GCTACTTATTTGAAGGCATAAATGTTG 57.976 33.333 0.00 0.00 0.00 3.33
374 375 9.807649 ACTTATTTGAAGGCATAAATGTTGATC 57.192 29.630 0.00 0.00 0.00 2.92
379 380 9.806203 TTTGAAGGCATAAATGTTGATCTATTG 57.194 29.630 0.00 0.00 0.00 1.90
380 381 8.523915 TGAAGGCATAAATGTTGATCTATTGT 57.476 30.769 0.00 0.00 0.00 2.71
381 382 8.970020 TGAAGGCATAAATGTTGATCTATTGTT 58.030 29.630 0.00 0.00 0.00 2.83
382 383 9.241317 GAAGGCATAAATGTTGATCTATTGTTG 57.759 33.333 0.00 0.00 0.00 3.33
383 384 8.297470 AGGCATAAATGTTGATCTATTGTTGT 57.703 30.769 0.00 0.00 0.00 3.32
384 385 9.407380 AGGCATAAATGTTGATCTATTGTTGTA 57.593 29.630 0.00 0.00 0.00 2.41
416 417 8.832521 ACGATCTAACATAAAAAGTTTGACACA 58.167 29.630 0.00 0.00 34.53 3.72
417 418 9.825972 CGATCTAACATAAAAAGTTTGACACAT 57.174 29.630 0.00 0.00 34.53 3.21
423 424 7.651808 ACATAAAAAGTTTGACACATCAGAGG 58.348 34.615 0.00 0.00 35.83 3.69
424 425 7.502226 ACATAAAAAGTTTGACACATCAGAGGA 59.498 33.333 0.00 0.00 35.83 3.71
425 426 6.382869 AAAAAGTTTGACACATCAGAGGAG 57.617 37.500 0.00 0.00 35.83 3.69
451 452 1.151450 ACCTGAACCAACCAGCCAG 59.849 57.895 0.00 0.00 0.00 4.85
506 507 2.263852 GGAAAGACCGACGGACCC 59.736 66.667 23.38 7.65 0.00 4.46
551 552 1.992277 CCCACTCCCAGTCTCCCAG 60.992 68.421 0.00 0.00 0.00 4.45
561 562 1.484240 CAGTCTCCCAGGATTCCACTC 59.516 57.143 5.29 0.00 0.00 3.51
591 592 4.699522 GCGTCACCCTCACCCCAC 62.700 72.222 0.00 0.00 0.00 4.61
592 593 4.016706 CGTCACCCTCACCCCACC 62.017 72.222 0.00 0.00 0.00 4.61
593 594 4.016706 GTCACCCTCACCCCACCG 62.017 72.222 0.00 0.00 0.00 4.94
665 666 1.067425 GGGCAACACCGGAAATAAACC 60.067 52.381 9.46 0.00 40.62 3.27
669 670 3.491104 GCAACACCGGAAATAAACCAACA 60.491 43.478 9.46 0.00 0.00 3.33
801 806 2.926586 GCGATCCAACAAAAAGGGAAGC 60.927 50.000 0.00 0.00 33.73 3.86
808 813 4.574421 CCAACAAAAAGGGAAGCGAATTTT 59.426 37.500 0.00 0.00 0.00 1.82
827 832 1.303643 CCACAGGCAGAAAGGGGAC 60.304 63.158 0.00 0.00 0.00 4.46
834 839 2.997897 AGAAAGGGGACGAGCGCT 60.998 61.111 11.27 11.27 0.00 5.92
836 841 2.997897 AAAGGGGACGAGCGCTCT 60.998 61.111 32.88 20.73 0.00 4.09
849 862 3.126225 GCTCTGGCTGCTCTGCAC 61.126 66.667 0.00 0.00 33.79 4.57
880 893 3.898627 CTGCGACGTCAGCCTCGTT 62.899 63.158 23.01 0.00 41.64 3.85
898 911 1.698067 TTTATAACCCTCGCCCCCGG 61.698 60.000 0.00 0.00 34.56 5.73
919 932 2.750350 CCCTGTTCCCGCTCACTT 59.250 61.111 0.00 0.00 0.00 3.16
934 947 2.618709 CTCACTTCAAACCACCTGAACC 59.381 50.000 0.00 0.00 0.00 3.62
941 954 2.281484 CCACCTGAACCCACCACG 60.281 66.667 0.00 0.00 0.00 4.94
944 957 2.358737 CCTGAACCCACCACGCTC 60.359 66.667 0.00 0.00 0.00 5.03
990 1003 1.431440 CACCACCAACAACACCACG 59.569 57.895 0.00 0.00 0.00 4.94
1063 1104 1.067212 ACGAGTACATGATCCGCTTCC 59.933 52.381 0.00 0.00 0.00 3.46
1066 1107 1.831106 AGTACATGATCCGCTTCCACA 59.169 47.619 0.00 0.00 0.00 4.17
1227 1295 1.078356 GGACTTCTTCTTCCCGGCC 60.078 63.158 0.00 0.00 0.00 6.13
1342 1419 3.118454 CATTGGACGCGCCGAAGT 61.118 61.111 5.73 0.00 40.66 3.01
1343 1420 2.813908 ATTGGACGCGCCGAAGTC 60.814 61.111 5.73 2.74 40.66 3.01
1392 1475 3.854669 CAGCGGAGGCGGAGGAAT 61.855 66.667 0.00 0.00 46.35 3.01
2239 2380 2.457598 TCTCCTGTGGTACATCACTCC 58.542 52.381 0.00 0.00 44.52 3.85
2263 2406 6.381801 CCTATCACTTGGCTAACACTTTTTG 58.618 40.000 0.00 0.00 0.00 2.44
2353 2497 6.120220 ACATTGGTCATTTACTAGTAAGCCC 58.880 40.000 14.73 13.02 0.00 5.19
2374 2519 1.275291 CCCGTAGCCGTTGATATGGAT 59.725 52.381 0.00 0.00 41.21 3.41
2388 2533 7.984422 TTGATATGGATCAACAAAGCGATAT 57.016 32.000 0.00 0.00 45.26 1.63
2391 2536 4.880886 TGGATCAACAAAGCGATATGTG 57.119 40.909 0.00 0.00 0.00 3.21
2424 2569 4.202274 TGGTCGAAGTGTTGTTCTATTCCA 60.202 41.667 0.00 0.00 0.00 3.53
2446 2591 3.211803 TGTATATGCCGAGCACGATAC 57.788 47.619 4.70 17.05 43.04 2.24
2457 2602 3.262420 GAGCACGATACCACAAGTTCAT 58.738 45.455 0.00 0.00 0.00 2.57
2542 2687 5.471556 TCGTCCATTAGGTGTGTCTTTTA 57.528 39.130 0.00 0.00 35.89 1.52
2561 2706 0.179084 ACATCTACGTTCATGCGGGG 60.179 55.000 0.00 0.00 35.98 5.73
2585 2730 1.775934 AAAGTGTTCCCGACCCCCTC 61.776 60.000 0.00 0.00 0.00 4.30
2588 2733 3.459063 GTTCCCGACCCCCTCTCG 61.459 72.222 0.00 0.00 0.00 4.04
2633 2778 0.755698 TCCATCCGCTGTCTCCCTAC 60.756 60.000 0.00 0.00 0.00 3.18
2646 2791 1.992277 CCCTACCCTGCTCAGCACT 60.992 63.158 0.00 0.00 33.79 4.40
2690 2835 6.375455 GCAATCTTCTTCCTGATGGTCTAAAA 59.625 38.462 0.00 0.00 34.23 1.52
2752 2898 7.910304 ACTCAAAATTTGTATCGTCTCTATGC 58.090 34.615 5.56 0.00 0.00 3.14
2753 2899 7.011482 ACTCAAAATTTGTATCGTCTCTATGCC 59.989 37.037 5.56 0.00 0.00 4.40
2754 2900 7.047891 TCAAAATTTGTATCGTCTCTATGCCT 58.952 34.615 5.56 0.00 0.00 4.75
2755 2901 6.851222 AAATTTGTATCGTCTCTATGCCTG 57.149 37.500 0.00 0.00 0.00 4.85
2756 2902 5.791336 ATTTGTATCGTCTCTATGCCTGA 57.209 39.130 0.00 0.00 0.00 3.86
2757 2903 5.592104 TTTGTATCGTCTCTATGCCTGAA 57.408 39.130 0.00 0.00 0.00 3.02
2758 2904 5.592104 TTGTATCGTCTCTATGCCTGAAA 57.408 39.130 0.00 0.00 0.00 2.69
2759 2905 5.592104 TGTATCGTCTCTATGCCTGAAAA 57.408 39.130 0.00 0.00 0.00 2.29
2760 2906 5.348986 TGTATCGTCTCTATGCCTGAAAAC 58.651 41.667 0.00 0.00 0.00 2.43
2761 2907 3.953712 TCGTCTCTATGCCTGAAAACA 57.046 42.857 0.00 0.00 0.00 2.83
2762 2908 4.265904 TCGTCTCTATGCCTGAAAACAA 57.734 40.909 0.00 0.00 0.00 2.83
2763 2909 4.637276 TCGTCTCTATGCCTGAAAACAAA 58.363 39.130 0.00 0.00 0.00 2.83
2764 2910 4.451096 TCGTCTCTATGCCTGAAAACAAAC 59.549 41.667 0.00 0.00 0.00 2.93
2765 2911 4.666655 CGTCTCTATGCCTGAAAACAAACG 60.667 45.833 0.00 0.00 0.00 3.60
2766 2912 4.213482 GTCTCTATGCCTGAAAACAAACGT 59.787 41.667 0.00 0.00 0.00 3.99
2767 2913 4.213270 TCTCTATGCCTGAAAACAAACGTG 59.787 41.667 0.00 0.00 0.00 4.49
2768 2914 2.507339 ATGCCTGAAAACAAACGTGG 57.493 45.000 0.00 0.00 0.00 4.94
2769 2915 0.179124 TGCCTGAAAACAAACGTGGC 60.179 50.000 0.00 0.00 39.33 5.01
2770 2916 0.102300 GCCTGAAAACAAACGTGGCT 59.898 50.000 0.00 0.00 36.32 4.75
2771 2917 1.470805 GCCTGAAAACAAACGTGGCTT 60.471 47.619 0.00 0.00 36.32 4.35
2772 2918 2.223618 GCCTGAAAACAAACGTGGCTTA 60.224 45.455 0.00 0.00 36.32 3.09
2773 2919 3.735514 GCCTGAAAACAAACGTGGCTTAA 60.736 43.478 0.00 0.00 36.32 1.85
2774 2920 4.425520 CCTGAAAACAAACGTGGCTTAAA 58.574 39.130 0.00 0.00 0.00 1.52
2775 2921 4.865365 CCTGAAAACAAACGTGGCTTAAAA 59.135 37.500 0.00 0.00 0.00 1.52
2776 2922 5.348997 CCTGAAAACAAACGTGGCTTAAAAA 59.651 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.695526 TTTTTCATGAAATCACATTCCTGTAAG 57.304 29.630 21.10 0.00 33.14 2.34
30 31 7.848223 AAAGTTCTAAGTGCTTGCAATTTTT 57.152 28.000 13.31 5.33 0.00 1.94
31 32 7.334171 ACAAAAGTTCTAAGTGCTTGCAATTTT 59.666 29.630 13.31 0.00 0.00 1.82
32 33 6.818142 ACAAAAGTTCTAAGTGCTTGCAATTT 59.182 30.769 13.31 6.28 0.00 1.82
33 34 6.340522 ACAAAAGTTCTAAGTGCTTGCAATT 58.659 32.000 12.72 12.72 0.00 2.32
34 35 5.906073 ACAAAAGTTCTAAGTGCTTGCAAT 58.094 33.333 0.00 0.00 0.00 3.56
35 36 5.105957 TGACAAAAGTTCTAAGTGCTTGCAA 60.106 36.000 0.00 0.00 0.00 4.08
36 37 4.397730 TGACAAAAGTTCTAAGTGCTTGCA 59.602 37.500 0.00 0.00 0.00 4.08
37 38 4.920376 TGACAAAAGTTCTAAGTGCTTGC 58.080 39.130 0.00 0.00 0.00 4.01
38 39 6.974622 ACATTGACAAAAGTTCTAAGTGCTTG 59.025 34.615 0.00 0.00 0.00 4.01
39 40 7.100458 ACATTGACAAAAGTTCTAAGTGCTT 57.900 32.000 0.00 0.00 0.00 3.91
40 41 6.699575 ACATTGACAAAAGTTCTAAGTGCT 57.300 33.333 0.00 0.00 0.00 4.40
41 42 7.702348 AGAAACATTGACAAAAGTTCTAAGTGC 59.298 33.333 9.09 0.00 0.00 4.40
42 43 9.226345 GAGAAACATTGACAAAAGTTCTAAGTG 57.774 33.333 9.09 0.00 0.00 3.16
43 44 8.406297 GGAGAAACATTGACAAAAGTTCTAAGT 58.594 33.333 9.09 0.00 0.00 2.24
44 45 8.405531 TGGAGAAACATTGACAAAAGTTCTAAG 58.594 33.333 9.09 0.00 0.00 2.18
45 46 8.287439 TGGAGAAACATTGACAAAAGTTCTAA 57.713 30.769 9.09 1.59 0.00 2.10
46 47 7.873719 TGGAGAAACATTGACAAAAGTTCTA 57.126 32.000 9.09 0.00 0.00 2.10
47 48 6.773976 TGGAGAAACATTGACAAAAGTTCT 57.226 33.333 9.09 9.17 0.00 3.01
48 49 7.826260 TTTGGAGAAACATTGACAAAAGTTC 57.174 32.000 9.09 5.33 0.00 3.01
49 50 8.614469 TTTTTGGAGAAACATTGACAAAAGTT 57.386 26.923 0.00 0.00 38.52 2.66
82 83 2.798283 CGAGCTCGGTGAACAGTAAAAA 59.202 45.455 28.40 0.00 35.37 1.94
83 84 2.400399 CGAGCTCGGTGAACAGTAAAA 58.600 47.619 28.40 0.00 35.37 1.52
84 85 2.060326 CGAGCTCGGTGAACAGTAAA 57.940 50.000 28.40 0.00 35.37 2.01
85 86 3.786809 CGAGCTCGGTGAACAGTAA 57.213 52.632 28.40 0.00 35.37 2.24
100 101 2.279935 AGTACCTCTATGCTCCCGAG 57.720 55.000 0.00 0.00 0.00 4.63
101 102 2.584236 GAAGTACCTCTATGCTCCCGA 58.416 52.381 0.00 0.00 0.00 5.14
102 103 1.614413 GGAAGTACCTCTATGCTCCCG 59.386 57.143 0.00 0.00 35.41 5.14
103 104 2.679082 TGGAAGTACCTCTATGCTCCC 58.321 52.381 0.00 0.00 39.86 4.30
104 105 4.101741 ACATTGGAAGTACCTCTATGCTCC 59.898 45.833 0.00 0.00 39.86 4.70
105 106 5.283457 ACATTGGAAGTACCTCTATGCTC 57.717 43.478 0.00 0.00 39.86 4.26
106 107 5.700402 AACATTGGAAGTACCTCTATGCT 57.300 39.130 0.00 0.00 39.86 3.79
107 108 6.759497 AAAACATTGGAAGTACCTCTATGC 57.241 37.500 0.00 0.00 39.86 3.14
108 109 9.838339 AGATAAAACATTGGAAGTACCTCTATG 57.162 33.333 0.00 0.00 39.86 2.23
111 112 9.047947 ACTAGATAAAACATTGGAAGTACCTCT 57.952 33.333 0.00 0.00 39.86 3.69
194 195 3.522553 GGACATTTAGTTCTGACCGGAG 58.477 50.000 9.46 0.00 0.00 4.63
195 196 2.094390 CGGACATTTAGTTCTGACCGGA 60.094 50.000 9.46 0.00 43.65 5.14
196 197 2.268298 CGGACATTTAGTTCTGACCGG 58.732 52.381 0.00 0.00 43.65 5.28
198 199 2.673368 CAGCGGACATTTAGTTCTGACC 59.327 50.000 0.00 0.00 0.00 4.02
199 200 3.585862 TCAGCGGACATTTAGTTCTGAC 58.414 45.455 0.00 0.00 31.25 3.51
200 201 3.953712 TCAGCGGACATTTAGTTCTGA 57.046 42.857 0.00 0.00 32.68 3.27
201 202 5.327091 CATTTCAGCGGACATTTAGTTCTG 58.673 41.667 0.00 0.00 0.00 3.02
202 203 4.142600 GCATTTCAGCGGACATTTAGTTCT 60.143 41.667 0.00 0.00 0.00 3.01
203 204 4.098416 GCATTTCAGCGGACATTTAGTTC 58.902 43.478 0.00 0.00 0.00 3.01
204 205 3.758554 AGCATTTCAGCGGACATTTAGTT 59.241 39.130 0.00 0.00 40.15 2.24
205 206 3.347216 AGCATTTCAGCGGACATTTAGT 58.653 40.909 0.00 0.00 40.15 2.24
206 207 4.811024 TCTAGCATTTCAGCGGACATTTAG 59.189 41.667 0.00 0.00 40.15 1.85
207 208 4.765273 TCTAGCATTTCAGCGGACATTTA 58.235 39.130 0.00 0.00 40.15 1.40
208 209 3.609853 TCTAGCATTTCAGCGGACATTT 58.390 40.909 0.00 0.00 40.15 2.32
209 210 3.266510 TCTAGCATTTCAGCGGACATT 57.733 42.857 0.00 0.00 40.15 2.71
210 211 2.988010 TCTAGCATTTCAGCGGACAT 57.012 45.000 0.00 0.00 40.15 3.06
211 212 2.028112 ACTTCTAGCATTTCAGCGGACA 60.028 45.455 0.00 0.00 40.15 4.02
212 213 2.605366 GACTTCTAGCATTTCAGCGGAC 59.395 50.000 0.00 0.00 40.15 4.79
213 214 2.233676 TGACTTCTAGCATTTCAGCGGA 59.766 45.455 0.00 0.00 40.15 5.54
214 215 2.621338 TGACTTCTAGCATTTCAGCGG 58.379 47.619 0.00 0.00 40.15 5.52
215 216 3.681897 AGTTGACTTCTAGCATTTCAGCG 59.318 43.478 0.00 0.00 40.15 5.18
216 217 4.692625 TGAGTTGACTTCTAGCATTTCAGC 59.307 41.667 0.00 0.00 0.00 4.26
217 218 6.981762 ATGAGTTGACTTCTAGCATTTCAG 57.018 37.500 0.00 0.00 0.00 3.02
218 219 7.750229 AAATGAGTTGACTTCTAGCATTTCA 57.250 32.000 0.00 0.00 31.14 2.69
219 220 8.292448 TCAAAATGAGTTGACTTCTAGCATTTC 58.708 33.333 0.00 0.00 34.51 2.17
220 221 8.169977 TCAAAATGAGTTGACTTCTAGCATTT 57.830 30.769 0.00 0.00 36.40 2.32
221 222 7.574592 GCTCAAAATGAGTTGACTTCTAGCATT 60.575 37.037 8.97 0.00 45.94 3.56
222 223 6.128063 GCTCAAAATGAGTTGACTTCTAGCAT 60.128 38.462 8.97 0.00 45.94 3.79
223 224 5.180117 GCTCAAAATGAGTTGACTTCTAGCA 59.820 40.000 8.97 0.00 45.94 3.49
224 225 5.626211 GCTCAAAATGAGTTGACTTCTAGC 58.374 41.667 8.97 0.00 45.94 3.42
225 226 5.635280 TCGCTCAAAATGAGTTGACTTCTAG 59.365 40.000 8.97 0.00 45.94 2.43
226 227 5.538118 TCGCTCAAAATGAGTTGACTTCTA 58.462 37.500 8.97 0.00 45.94 2.10
227 228 4.380531 TCGCTCAAAATGAGTTGACTTCT 58.619 39.130 8.97 0.00 45.94 2.85
228 229 4.732285 TCGCTCAAAATGAGTTGACTTC 57.268 40.909 8.97 0.00 45.94 3.01
229 230 4.083110 CCATCGCTCAAAATGAGTTGACTT 60.083 41.667 8.97 0.00 45.94 3.01
230 231 3.438087 CCATCGCTCAAAATGAGTTGACT 59.562 43.478 8.97 0.00 45.94 3.41
231 232 3.426695 CCCATCGCTCAAAATGAGTTGAC 60.427 47.826 8.97 0.00 45.94 3.18
232 233 2.749076 CCCATCGCTCAAAATGAGTTGA 59.251 45.455 8.97 7.77 45.94 3.18
233 234 2.159338 CCCCATCGCTCAAAATGAGTTG 60.159 50.000 8.97 5.13 45.94 3.16
234 235 2.094675 CCCCATCGCTCAAAATGAGTT 58.905 47.619 8.97 0.00 45.94 3.01
235 236 1.004745 ACCCCATCGCTCAAAATGAGT 59.995 47.619 8.97 0.00 45.94 3.41
236 237 1.755179 ACCCCATCGCTCAAAATGAG 58.245 50.000 3.00 3.00 46.90 2.90
237 238 2.503765 TCTACCCCATCGCTCAAAATGA 59.496 45.455 0.00 0.00 0.00 2.57
238 239 2.874701 CTCTACCCCATCGCTCAAAATG 59.125 50.000 0.00 0.00 0.00 2.32
239 240 2.505819 ACTCTACCCCATCGCTCAAAAT 59.494 45.455 0.00 0.00 0.00 1.82
240 241 1.906574 ACTCTACCCCATCGCTCAAAA 59.093 47.619 0.00 0.00 0.00 2.44
241 242 1.568504 ACTCTACCCCATCGCTCAAA 58.431 50.000 0.00 0.00 0.00 2.69
242 243 1.568504 AACTCTACCCCATCGCTCAA 58.431 50.000 0.00 0.00 0.00 3.02
243 244 1.207089 CAAACTCTACCCCATCGCTCA 59.793 52.381 0.00 0.00 0.00 4.26
244 245 1.480954 TCAAACTCTACCCCATCGCTC 59.519 52.381 0.00 0.00 0.00 5.03
245 246 1.207329 GTCAAACTCTACCCCATCGCT 59.793 52.381 0.00 0.00 0.00 4.93
246 247 1.653151 GTCAAACTCTACCCCATCGC 58.347 55.000 0.00 0.00 0.00 4.58
247 248 1.553248 TGGTCAAACTCTACCCCATCG 59.447 52.381 0.00 0.00 34.69 3.84
248 249 3.009143 ACTTGGTCAAACTCTACCCCATC 59.991 47.826 0.00 0.00 34.69 3.51
249 250 2.986728 ACTTGGTCAAACTCTACCCCAT 59.013 45.455 0.00 0.00 34.69 4.00
250 251 2.414612 ACTTGGTCAAACTCTACCCCA 58.585 47.619 0.00 0.00 34.69 4.96
251 252 3.503800 AACTTGGTCAAACTCTACCCC 57.496 47.619 0.00 0.00 34.69 4.95
252 253 4.036380 CACAAACTTGGTCAAACTCTACCC 59.964 45.833 0.00 0.00 34.69 3.69
253 254 4.497507 GCACAAACTTGGTCAAACTCTACC 60.498 45.833 0.00 0.00 36.24 3.18
254 255 4.095782 TGCACAAACTTGGTCAAACTCTAC 59.904 41.667 0.00 0.00 0.00 2.59
255 256 4.265893 TGCACAAACTTGGTCAAACTCTA 58.734 39.130 0.00 0.00 0.00 2.43
256 257 3.088532 TGCACAAACTTGGTCAAACTCT 58.911 40.909 0.00 0.00 0.00 3.24
257 258 3.502191 TGCACAAACTTGGTCAAACTC 57.498 42.857 0.00 0.00 0.00 3.01
258 259 3.951775 TTGCACAAACTTGGTCAAACT 57.048 38.095 0.00 0.00 0.00 2.66
259 260 4.999751 TTTTGCACAAACTTGGTCAAAC 57.000 36.364 9.43 0.00 35.14 2.93
260 261 4.816385 TGTTTTTGCACAAACTTGGTCAAA 59.184 33.333 24.53 3.89 37.51 2.69
261 262 4.380531 TGTTTTTGCACAAACTTGGTCAA 58.619 34.783 24.53 4.54 37.51 3.18
262 263 3.995199 TGTTTTTGCACAAACTTGGTCA 58.005 36.364 24.53 5.24 37.51 4.02
263 264 4.999751 TTGTTTTTGCACAAACTTGGTC 57.000 36.364 24.53 2.85 37.51 4.02
264 265 5.471456 TGATTTGTTTTTGCACAAACTTGGT 59.529 32.000 24.53 11.35 46.76 3.67
265 266 5.936054 TGATTTGTTTTTGCACAAACTTGG 58.064 33.333 24.53 0.00 46.76 3.61
266 267 7.461677 GCATTGATTTGTTTTTGCACAAACTTG 60.462 33.333 24.53 13.36 46.76 3.16
267 268 6.527372 GCATTGATTTGTTTTTGCACAAACTT 59.473 30.769 24.53 12.53 46.76 2.66
268 269 6.028987 GCATTGATTTGTTTTTGCACAAACT 58.971 32.000 24.53 8.82 46.76 2.66
269 270 6.028987 AGCATTGATTTGTTTTTGCACAAAC 58.971 32.000 19.25 19.25 46.76 2.93
271 272 5.814764 AGCATTGATTTGTTTTTGCACAA 57.185 30.435 0.00 0.00 34.76 3.33
272 273 5.814764 AAGCATTGATTTGTTTTTGCACA 57.185 30.435 0.00 0.00 32.66 4.57
288 289 2.820330 CCGTTTGGTTTCACAAGCATT 58.180 42.857 0.00 0.00 40.10 3.56
289 290 2.507339 CCGTTTGGTTTCACAAGCAT 57.493 45.000 0.00 0.00 40.10 3.79
336 337 9.189156 TGCCTTCAAATAAGTAGCATTAGATTT 57.811 29.630 0.00 0.00 0.00 2.17
337 338 8.752005 TGCCTTCAAATAAGTAGCATTAGATT 57.248 30.769 0.00 0.00 0.00 2.40
338 339 8.930846 ATGCCTTCAAATAAGTAGCATTAGAT 57.069 30.769 0.00 0.00 36.10 1.98
339 340 9.845740 TTATGCCTTCAAATAAGTAGCATTAGA 57.154 29.630 0.00 0.00 39.89 2.10
342 343 9.754382 CATTTATGCCTTCAAATAAGTAGCATT 57.246 29.630 0.00 0.00 39.89 3.56
343 344 8.917088 ACATTTATGCCTTCAAATAAGTAGCAT 58.083 29.630 0.00 0.00 41.89 3.79
344 345 8.292444 ACATTTATGCCTTCAAATAAGTAGCA 57.708 30.769 0.00 0.00 0.00 3.49
345 346 9.023967 CAACATTTATGCCTTCAAATAAGTAGC 57.976 33.333 0.00 0.00 0.00 3.58
348 349 9.807649 GATCAACATTTATGCCTTCAAATAAGT 57.192 29.630 0.00 0.00 0.00 2.24
353 354 9.806203 CAATAGATCAACATTTATGCCTTCAAA 57.194 29.630 0.00 0.00 0.00 2.69
354 355 8.970020 ACAATAGATCAACATTTATGCCTTCAA 58.030 29.630 0.00 0.00 0.00 2.69
355 356 8.523915 ACAATAGATCAACATTTATGCCTTCA 57.476 30.769 0.00 0.00 0.00 3.02
356 357 9.241317 CAACAATAGATCAACATTTATGCCTTC 57.759 33.333 0.00 0.00 0.00 3.46
357 358 8.752187 ACAACAATAGATCAACATTTATGCCTT 58.248 29.630 0.00 0.00 0.00 4.35
358 359 8.297470 ACAACAATAGATCAACATTTATGCCT 57.703 30.769 0.00 0.00 0.00 4.75
390 391 8.832521 TGTGTCAAACTTTTTATGTTAGATCGT 58.167 29.630 0.00 0.00 0.00 3.73
391 392 9.825972 ATGTGTCAAACTTTTTATGTTAGATCG 57.174 29.630 0.00 0.00 0.00 3.69
397 398 8.137437 CCTCTGATGTGTCAAACTTTTTATGTT 58.863 33.333 0.00 0.00 33.05 2.71
398 399 7.502226 TCCTCTGATGTGTCAAACTTTTTATGT 59.498 33.333 0.00 0.00 33.05 2.29
399 400 7.874940 TCCTCTGATGTGTCAAACTTTTTATG 58.125 34.615 0.00 0.00 33.05 1.90
400 401 7.308830 GCTCCTCTGATGTGTCAAACTTTTTAT 60.309 37.037 0.00 0.00 33.05 1.40
401 402 6.017109 GCTCCTCTGATGTGTCAAACTTTTTA 60.017 38.462 0.00 0.00 33.05 1.52
402 403 5.221126 GCTCCTCTGATGTGTCAAACTTTTT 60.221 40.000 0.00 0.00 33.05 1.94
403 404 4.276926 GCTCCTCTGATGTGTCAAACTTTT 59.723 41.667 0.00 0.00 33.05 2.27
404 405 3.817647 GCTCCTCTGATGTGTCAAACTTT 59.182 43.478 0.00 0.00 33.05 2.66
405 406 3.181451 TGCTCCTCTGATGTGTCAAACTT 60.181 43.478 0.00 0.00 33.05 2.66
406 407 2.369860 TGCTCCTCTGATGTGTCAAACT 59.630 45.455 0.00 0.00 33.05 2.66
407 408 2.771089 TGCTCCTCTGATGTGTCAAAC 58.229 47.619 0.00 0.00 33.05 2.93
408 409 3.490439 TTGCTCCTCTGATGTGTCAAA 57.510 42.857 0.00 0.00 33.05 2.69
409 410 3.490439 TTTGCTCCTCTGATGTGTCAA 57.510 42.857 0.00 0.00 33.05 3.18
410 411 3.141398 GTTTTGCTCCTCTGATGTGTCA 58.859 45.455 0.00 0.00 0.00 3.58
411 412 2.485814 GGTTTTGCTCCTCTGATGTGTC 59.514 50.000 0.00 0.00 0.00 3.67
412 413 2.158623 TGGTTTTGCTCCTCTGATGTGT 60.159 45.455 0.00 0.00 0.00 3.72
413 414 2.227388 GTGGTTTTGCTCCTCTGATGTG 59.773 50.000 0.00 0.00 0.00 3.21
414 415 2.508526 GTGGTTTTGCTCCTCTGATGT 58.491 47.619 0.00 0.00 0.00 3.06
415 416 1.815003 GGTGGTTTTGCTCCTCTGATG 59.185 52.381 0.00 0.00 0.00 3.07
416 417 1.707427 AGGTGGTTTTGCTCCTCTGAT 59.293 47.619 0.00 0.00 0.00 2.90
417 418 1.140312 AGGTGGTTTTGCTCCTCTGA 58.860 50.000 0.00 0.00 0.00 3.27
418 419 1.202806 TCAGGTGGTTTTGCTCCTCTG 60.203 52.381 0.00 0.00 0.00 3.35
419 420 1.140312 TCAGGTGGTTTTGCTCCTCT 58.860 50.000 0.00 0.00 0.00 3.69
420 421 1.609072 GTTCAGGTGGTTTTGCTCCTC 59.391 52.381 0.00 0.00 0.00 3.71
421 422 1.692411 GTTCAGGTGGTTTTGCTCCT 58.308 50.000 0.00 0.00 0.00 3.69
422 423 0.673985 GGTTCAGGTGGTTTTGCTCC 59.326 55.000 0.00 0.00 0.00 4.70
423 424 1.398692 TGGTTCAGGTGGTTTTGCTC 58.601 50.000 0.00 0.00 0.00 4.26
424 425 1.480545 GTTGGTTCAGGTGGTTTTGCT 59.519 47.619 0.00 0.00 0.00 3.91
425 426 1.472552 GGTTGGTTCAGGTGGTTTTGC 60.473 52.381 0.00 0.00 0.00 3.68
506 507 2.430921 GGACAGCAGACGACGGTG 60.431 66.667 0.00 0.00 37.86 4.94
510 511 2.433318 GCCTGGACAGCAGACGAC 60.433 66.667 0.00 0.00 0.00 4.34
511 512 2.917227 TGCCTGGACAGCAGACGA 60.917 61.111 0.00 0.00 34.69 4.20
665 666 1.406205 GGGTTTGGGTTGGTTGTGTTG 60.406 52.381 0.00 0.00 0.00 3.33
669 670 0.753848 CTCGGGTTTGGGTTGGTTGT 60.754 55.000 0.00 0.00 0.00 3.32
801 806 3.568538 CTTTCTGCCTGTGGAAAATTCG 58.431 45.455 0.00 0.00 32.17 3.34
808 813 1.463214 TCCCCTTTCTGCCTGTGGA 60.463 57.895 0.00 0.00 0.00 4.02
880 893 2.142104 CCGGGGGCGAGGGTTATAA 61.142 63.158 0.00 0.00 0.00 0.98
898 911 4.475135 GAGCGGGAACAGGGGAGC 62.475 72.222 0.00 0.00 0.00 4.70
919 932 0.106419 GGTGGGTTCAGGTGGTTTGA 60.106 55.000 0.00 0.00 0.00 2.69
941 954 1.376553 GGTTGAGAGGTGCTGGAGC 60.377 63.158 0.00 0.00 42.50 4.70
944 957 0.397941 TTGAGGTTGAGAGGTGCTGG 59.602 55.000 0.00 0.00 0.00 4.85
950 963 1.671261 CGCTGACTTGAGGTTGAGAGG 60.671 57.143 0.00 0.00 0.00 3.69
990 1003 2.481952 GCTGAAGGTCATGTGTGTTCTC 59.518 50.000 0.00 0.00 0.00 2.87
1035 1070 1.815421 CATGTACTCGTGCCCCTGC 60.815 63.158 0.00 0.00 38.26 4.85
1036 1071 0.465705 ATCATGTACTCGTGCCCCTG 59.534 55.000 0.00 0.00 0.00 4.45
1037 1072 0.753262 GATCATGTACTCGTGCCCCT 59.247 55.000 0.00 0.00 0.00 4.79
1038 1073 0.249911 GGATCATGTACTCGTGCCCC 60.250 60.000 0.00 0.00 0.00 5.80
1039 1074 0.597637 CGGATCATGTACTCGTGCCC 60.598 60.000 0.00 0.00 0.00 5.36
1040 1075 1.215655 GCGGATCATGTACTCGTGCC 61.216 60.000 0.00 0.00 0.00 5.01
1041 1076 0.249073 AGCGGATCATGTACTCGTGC 60.249 55.000 0.00 0.00 0.00 5.34
1063 1104 2.022129 GGTCGTCGAAGTGGCTGTG 61.022 63.158 0.00 0.00 0.00 3.66
1066 1107 4.052229 CGGGTCGTCGAAGTGGCT 62.052 66.667 0.00 0.00 0.00 4.75
1378 1461 0.750850 TTCTTATTCCTCCGCCTCCG 59.249 55.000 0.00 0.00 0.00 4.63
1392 1475 2.027837 GCCCCGGTACTTGTTCTTCTTA 60.028 50.000 0.00 0.00 0.00 2.10
2152 2291 8.142994 TGTCAAGTCACAAAACTTATTCTCTC 57.857 34.615 0.00 0.00 37.38 3.20
2153 2292 8.682936 ATGTCAAGTCACAAAACTTATTCTCT 57.317 30.769 0.00 0.00 37.38 3.10
2154 2293 8.017946 GGATGTCAAGTCACAAAACTTATTCTC 58.982 37.037 0.00 0.00 37.38 2.87
2239 2380 6.016276 ACAAAAAGTGTTAGCCAAGTGATAGG 60.016 38.462 0.00 0.00 37.01 2.57
2263 2406 3.691118 TGCAATCTGTTATCCAGCAAGAC 59.309 43.478 0.00 0.00 41.25 3.01
2353 2497 0.320421 CCATATCAACGGCTACGGGG 60.320 60.000 0.00 0.00 46.48 5.73
2356 2500 3.297830 TGATCCATATCAACGGCTACG 57.702 47.619 0.00 0.00 39.20 3.51
2374 2519 5.805486 GTCTCTACACATATCGCTTTGTTGA 59.195 40.000 0.00 0.00 0.00 3.18
2383 2528 4.280461 GACCAACGTCTCTACACATATCG 58.720 47.826 0.00 0.00 35.99 2.92
2388 2533 1.596603 TCGACCAACGTCTCTACACA 58.403 50.000 0.00 0.00 43.13 3.72
2391 2536 2.031333 ACACTTCGACCAACGTCTCTAC 60.031 50.000 0.00 0.00 43.13 2.59
2424 2569 2.812358 TCGTGCTCGGCATATACAAT 57.188 45.000 8.49 0.00 41.91 2.71
2446 2591 5.437289 TTGCTTCTGTTATGAACTTGTGG 57.563 39.130 0.00 0.00 0.00 4.17
2477 2622 0.036952 CGAGAGGAGGAAAGCAAGCA 60.037 55.000 0.00 0.00 0.00 3.91
2542 2687 0.179084 CCCCGCATGAACGTAGATGT 60.179 55.000 0.00 0.00 0.00 3.06
2561 2706 1.335810 GGGTCGGGAACACTTTGTTTC 59.664 52.381 0.00 0.00 41.28 2.78
2585 2730 1.807573 GCGCAGAGAAAGGACCGAG 60.808 63.158 0.30 0.00 0.00 4.63
2588 2733 0.460459 GGTAGCGCAGAGAAAGGACC 60.460 60.000 11.47 0.00 0.00 4.46
2633 2778 0.814410 CATAGCAGTGCTGAGCAGGG 60.814 60.000 27.97 3.82 40.08 4.45
2646 2791 0.744057 CCATGTGGCACGACATAGCA 60.744 55.000 13.77 0.00 34.69 3.49
2658 2803 2.426024 CAGGAAGAAGATTGCCATGTGG 59.574 50.000 0.00 0.00 38.53 4.17
2690 2835 8.942338 TCTGTCTAATGCGAGTATGTTATTTT 57.058 30.769 0.00 0.00 0.00 1.82
2694 2839 6.972901 CACTTCTGTCTAATGCGAGTATGTTA 59.027 38.462 0.00 0.00 0.00 2.41
2695 2840 5.807520 CACTTCTGTCTAATGCGAGTATGTT 59.192 40.000 0.00 0.00 0.00 2.71
2697 2842 5.344066 ACACTTCTGTCTAATGCGAGTATG 58.656 41.667 0.00 0.00 0.00 2.39
2703 2849 8.129840 AGTAGTAATACACTTCTGTCTAATGCG 58.870 37.037 2.81 0.00 38.80 4.73
2741 2887 3.953712 TGTTTTCAGGCATAGAGACGA 57.046 42.857 0.00 0.00 0.00 4.20
2742 2888 4.666655 CGTTTGTTTTCAGGCATAGAGACG 60.667 45.833 0.00 0.00 0.00 4.18
2743 2889 4.213482 ACGTTTGTTTTCAGGCATAGAGAC 59.787 41.667 0.00 0.00 0.00 3.36
2744 2890 4.213270 CACGTTTGTTTTCAGGCATAGAGA 59.787 41.667 0.00 0.00 0.00 3.10
2745 2891 4.466828 CACGTTTGTTTTCAGGCATAGAG 58.533 43.478 0.00 0.00 0.00 2.43
2746 2892 3.252215 CCACGTTTGTTTTCAGGCATAGA 59.748 43.478 0.00 0.00 0.00 1.98
2747 2893 3.564511 CCACGTTTGTTTTCAGGCATAG 58.435 45.455 0.00 0.00 0.00 2.23
2748 2894 2.287909 GCCACGTTTGTTTTCAGGCATA 60.288 45.455 3.15 0.00 36.53 3.14
2749 2895 1.537990 GCCACGTTTGTTTTCAGGCAT 60.538 47.619 3.15 0.00 36.53 4.40
2750 2896 0.179124 GCCACGTTTGTTTTCAGGCA 60.179 50.000 3.15 0.00 36.53 4.75
2751 2897 0.102300 AGCCACGTTTGTTTTCAGGC 59.898 50.000 0.00 0.00 36.70 4.85
2752 2898 2.577449 AAGCCACGTTTGTTTTCAGG 57.423 45.000 0.00 0.00 0.00 3.86
2753 2899 6.396459 TTTTTAAGCCACGTTTGTTTTCAG 57.604 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.