Multiple sequence alignment - TraesCS2D01G166200

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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 TraesCS2D01G166200 chr2D 100.000 2751 0 0 1 2751 110066361 110063611 0.000000e+00 5081.0
1 TraesCS2D01G166200 chr2D 94.595 37 2 0 208 244 353966204 353966240 1.060000e-04 58.4
2 TraesCS2D01G166200 chr2B 87.223 1941 137 56 804 2698 159489902 159488027 0.000000e+00 2108.0
3 TraesCS2D01G166200 chr2B 87.551 490 58 3 282 770 159506401 159505914 5.140000e-157 564.0
4 TraesCS2D01G166200 chr2B 83.396 265 36 5 496 753 239414521 239414784 3.540000e-59 239.0
5 TraesCS2D01G166200 chr2B 87.121 132 16 1 1 131 486004513 486004644 6.140000e-32 148.0
6 TraesCS2D01G166200 chr2B 89.333 75 7 1 210 283 490909440 490909366 2.920000e-15 93.5
7 TraesCS2D01G166200 chr2A 92.354 994 48 15 773 1743 105639176 105638188 0.000000e+00 1389.0
8 TraesCS2D01G166200 chr2A 87.949 946 58 25 1808 2729 105638077 105637164 0.000000e+00 1064.0
9 TraesCS2D01G166200 chr2A 88.571 490 55 1 282 770 105639789 105639300 6.560000e-166 593.0
10 TraesCS2D01G166200 chr2A 88.789 223 23 1 1 221 135548195 135547973 3.490000e-69 272.0
11 TraesCS2D01G166200 chr2A 83.784 74 8 3 208 277 78721190 78721117 1.770000e-07 67.6
12 TraesCS2D01G166200 chr7B 89.324 281 29 1 3 283 279188090 279188369 4.360000e-93 351.0
13 TraesCS2D01G166200 chr7B 81.618 272 38 8 496 758 480682492 480682760 5.970000e-52 215.0
14 TraesCS2D01G166200 chr7A 85.000 280 38 4 1 277 255816132 255816410 5.800000e-72 281.0
15 TraesCS2D01G166200 chr1D 84.644 267 37 1 496 758 62440455 62440721 2.100000e-66 263.0
16 TraesCS2D01G166200 chr1D 82.432 222 38 1 279 500 449458402 449458622 2.800000e-45 193.0
17 TraesCS2D01G166200 chr3D 85.000 260 32 5 510 763 5414697 5414955 9.770000e-65 257.0
18 TraesCS2D01G166200 chr4D 86.878 221 27 2 282 502 39392903 39393121 2.120000e-61 246.0
19 TraesCS2D01G166200 chr4D 86.301 219 28 2 282 499 370304703 370304920 1.270000e-58 237.0
20 TraesCS2D01G166200 chr7D 85.973 221 31 0 282 502 619820637 619820857 1.270000e-58 237.0
21 TraesCS2D01G166200 chr5D 82.182 275 43 4 494 764 368820898 368821170 5.920000e-57 231.0
22 TraesCS2D01G166200 chr6D 82.288 271 42 3 496 761 407180459 407180728 2.130000e-56 230.0
23 TraesCS2D01G166200 chr6D 90.588 170 16 0 333 502 393927757 393927926 2.760000e-55 226.0
24 TraesCS2D01G166200 chr6D 94.595 37 2 0 208 244 187648018 187647982 1.060000e-04 58.4
25 TraesCS2D01G166200 chr3B 81.655 278 45 5 1 277 611484140 611484412 2.760000e-55 226.0
26 TraesCS2D01G166200 chr3B 89.941 169 17 0 334 502 523279336 523279168 4.610000e-53 219.0
27 TraesCS2D01G166200 chr4B 81.481 270 46 2 496 761 126591648 126591917 4.610000e-53 219.0
28 TraesCS2D01G166200 chr4B 84.422 199 29 2 52 248 391240328 391240130 7.770000e-46 195.0
29 TraesCS2D01G166200 chr4B 80.909 110 13 4 142 249 72213696 72213799 2.270000e-11 80.5
30 TraesCS2D01G166200 chrUn 82.192 219 39 0 282 500 86803542 86803760 3.620000e-44 189.0
31 TraesCS2D01G166200 chr5B 88.430 121 11 3 130 249 493322046 493322164 2.860000e-30 143.0
32 TraesCS2D01G166200 chr5B 91.026 78 7 0 1 78 248313601 248313524 3.750000e-19 106.0


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 TraesCS2D01G166200 chr2D 110063611 110066361 2750 True 5081.000000 5081 100.000000 1 2751 1 chr2D.!!$R1 2750
1 TraesCS2D01G166200 chr2B 159488027 159489902 1875 True 2108.000000 2108 87.223000 804 2698 1 chr2B.!!$R1 1894
2 TraesCS2D01G166200 chr2A 105637164 105639789 2625 True 1015.333333 1389 89.624667 282 2729 3 chr2A.!!$R3 2447

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
88 89 0.104620 AGCCAGTATAACCCGGGGAT 60.105 55.0 27.92 20.05 0.0 3.85 F
265 266 0.108207 GCCTAGCTCACATGCCTCAT 59.892 55.0 0.00 0.00 0.0 2.90 F
645 647 0.170561 CGACCGGACCAACACTCTAG 59.829 60.0 9.46 0.00 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1318 0.164002 GACGGCGACAGAAAGAAAGC 59.836 55.0 16.62 0.0 0.00 3.51 R
1184 1319 0.435008 CGACGGCGACAGAAAGAAAG 59.565 55.0 16.62 0.0 40.82 2.62 R
2397 2629 0.179000 ACTTCCGATCACCAGATGGC 59.821 55.0 0.00 0.0 39.32 4.40 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
19 20 2.642154 TGGCGACTTAAGGTCCAAAA 57.358 45.000 7.53 0.00 41.64 2.44
20 21 2.223745 TGGCGACTTAAGGTCCAAAAC 58.776 47.619 7.53 0.00 41.64 2.43
29 30 2.989253 GTCCAAAACCAGGGCGGG 60.989 66.667 0.00 0.00 40.22 6.13
30 31 3.503839 TCCAAAACCAGGGCGGGT 61.504 61.111 0.00 0.00 45.04 5.28
31 32 3.302344 CCAAAACCAGGGCGGGTG 61.302 66.667 0.00 0.00 41.32 4.61
32 33 2.203422 CAAAACCAGGGCGGGTGA 60.203 61.111 0.00 0.00 41.32 4.02
33 34 1.606313 CAAAACCAGGGCGGGTGAT 60.606 57.895 0.00 0.00 41.32 3.06
34 35 0.322997 CAAAACCAGGGCGGGTGATA 60.323 55.000 0.00 0.00 41.32 2.15
35 36 0.406361 AAAACCAGGGCGGGTGATAA 59.594 50.000 0.00 0.00 41.32 1.75
36 37 0.323087 AAACCAGGGCGGGTGATAAC 60.323 55.000 0.00 0.00 41.32 1.89
37 38 2.192175 CCAGGGCGGGTGATAACC 59.808 66.667 0.00 0.00 0.00 2.85
38 39 2.192175 CAGGGCGGGTGATAACCC 59.808 66.667 8.49 8.49 46.43 4.11
52 53 7.881775 GGTGATAACCCAAAGACTCAAATAT 57.118 36.000 0.00 0.00 0.00 1.28
53 54 7.707104 GGTGATAACCCAAAGACTCAAATATG 58.293 38.462 0.00 0.00 0.00 1.78
54 55 7.556275 GGTGATAACCCAAAGACTCAAATATGA 59.444 37.037 0.00 0.00 0.00 2.15
68 69 7.026631 CTCAAATATGAGCAAAATAACCCGA 57.973 36.000 0.00 0.00 46.11 5.14
69 70 7.397892 TCAAATATGAGCAAAATAACCCGAA 57.602 32.000 0.00 0.00 0.00 4.30
70 71 7.479980 TCAAATATGAGCAAAATAACCCGAAG 58.520 34.615 0.00 0.00 0.00 3.79
71 72 3.782889 ATGAGCAAAATAACCCGAAGC 57.217 42.857 0.00 0.00 0.00 3.86
72 73 1.816224 TGAGCAAAATAACCCGAAGCC 59.184 47.619 0.00 0.00 0.00 4.35
73 74 1.816224 GAGCAAAATAACCCGAAGCCA 59.184 47.619 0.00 0.00 0.00 4.75
74 75 1.818674 AGCAAAATAACCCGAAGCCAG 59.181 47.619 0.00 0.00 0.00 4.85
75 76 1.544246 GCAAAATAACCCGAAGCCAGT 59.456 47.619 0.00 0.00 0.00 4.00
76 77 2.750712 GCAAAATAACCCGAAGCCAGTA 59.249 45.455 0.00 0.00 0.00 2.74
77 78 3.380320 GCAAAATAACCCGAAGCCAGTAT 59.620 43.478 0.00 0.00 0.00 2.12
78 79 4.577283 GCAAAATAACCCGAAGCCAGTATA 59.423 41.667 0.00 0.00 0.00 1.47
79 80 5.066764 GCAAAATAACCCGAAGCCAGTATAA 59.933 40.000 0.00 0.00 0.00 0.98
80 81 6.492254 CAAAATAACCCGAAGCCAGTATAAC 58.508 40.000 0.00 0.00 0.00 1.89
81 82 2.704464 AACCCGAAGCCAGTATAACC 57.296 50.000 0.00 0.00 0.00 2.85
82 83 0.835276 ACCCGAAGCCAGTATAACCC 59.165 55.000 0.00 0.00 0.00 4.11
83 84 0.249741 CCCGAAGCCAGTATAACCCG 60.250 60.000 0.00 0.00 0.00 5.28
84 85 0.249741 CCGAAGCCAGTATAACCCGG 60.250 60.000 0.00 0.00 0.00 5.73
85 86 0.249741 CGAAGCCAGTATAACCCGGG 60.250 60.000 22.25 22.25 0.00 5.73
86 87 0.108019 GAAGCCAGTATAACCCGGGG 59.892 60.000 27.92 12.73 0.00 5.73
87 88 0.326808 AAGCCAGTATAACCCGGGGA 60.327 55.000 27.92 13.41 0.00 4.81
88 89 0.104620 AGCCAGTATAACCCGGGGAT 60.105 55.000 27.92 20.05 0.00 3.85
89 90 0.769247 GCCAGTATAACCCGGGGATT 59.231 55.000 27.92 14.03 0.00 3.01
90 91 1.271217 GCCAGTATAACCCGGGGATTC 60.271 57.143 27.92 15.29 0.00 2.52
91 92 2.051692 CCAGTATAACCCGGGGATTCA 58.948 52.381 27.92 4.67 0.00 2.57
92 93 2.642807 CCAGTATAACCCGGGGATTCAT 59.357 50.000 27.92 12.27 0.00 2.57
93 94 3.841845 CCAGTATAACCCGGGGATTCATA 59.158 47.826 27.92 11.24 0.00 2.15
94 95 4.287585 CCAGTATAACCCGGGGATTCATAA 59.712 45.833 27.92 0.00 0.00 1.90
95 96 5.045140 CCAGTATAACCCGGGGATTCATAAT 60.045 44.000 27.92 10.47 0.00 1.28
96 97 6.481643 CAGTATAACCCGGGGATTCATAATT 58.518 40.000 27.92 9.07 0.00 1.40
97 98 6.946009 CAGTATAACCCGGGGATTCATAATTT 59.054 38.462 27.92 8.25 0.00 1.82
98 99 6.946009 AGTATAACCCGGGGATTCATAATTTG 59.054 38.462 27.92 0.00 0.00 2.32
99 100 2.316108 ACCCGGGGATTCATAATTTGC 58.684 47.619 27.92 0.00 0.00 3.68
100 101 1.269448 CCCGGGGATTCATAATTTGCG 59.731 52.381 14.71 0.00 0.00 4.85
101 102 1.953686 CCGGGGATTCATAATTTGCGT 59.046 47.619 0.00 0.00 0.00 5.24
102 103 3.142951 CCGGGGATTCATAATTTGCGTA 58.857 45.455 0.00 0.00 0.00 4.42
103 104 3.566322 CCGGGGATTCATAATTTGCGTAA 59.434 43.478 0.00 0.00 0.00 3.18
104 105 4.036971 CCGGGGATTCATAATTTGCGTAAA 59.963 41.667 0.00 0.00 0.00 2.01
105 106 5.450688 CCGGGGATTCATAATTTGCGTAAAA 60.451 40.000 1.94 0.00 0.00 1.52
106 107 5.685511 CGGGGATTCATAATTTGCGTAAAAG 59.314 40.000 1.94 0.00 0.00 2.27
107 108 6.569780 GGGGATTCATAATTTGCGTAAAAGT 58.430 36.000 1.94 0.00 0.00 2.66
108 109 7.467539 CGGGGATTCATAATTTGCGTAAAAGTA 60.468 37.037 1.94 0.00 33.21 2.24
109 110 8.192110 GGGGATTCATAATTTGCGTAAAAGTAA 58.808 33.333 1.94 0.00 32.49 2.24
110 111 9.575783 GGGATTCATAATTTGCGTAAAAGTAAA 57.424 29.630 1.94 0.00 32.49 2.01
158 159 4.734398 AAACCAAAACAGAGAACATGCA 57.266 36.364 0.00 0.00 0.00 3.96
159 160 4.734398 AACCAAAACAGAGAACATGCAA 57.266 36.364 0.00 0.00 0.00 4.08
160 161 4.734398 ACCAAAACAGAGAACATGCAAA 57.266 36.364 0.00 0.00 0.00 3.68
161 162 5.280654 ACCAAAACAGAGAACATGCAAAT 57.719 34.783 0.00 0.00 0.00 2.32
162 163 5.291971 ACCAAAACAGAGAACATGCAAATC 58.708 37.500 0.00 0.00 0.00 2.17
163 164 5.069516 ACCAAAACAGAGAACATGCAAATCT 59.930 36.000 0.00 0.00 0.00 2.40
164 165 5.632347 CCAAAACAGAGAACATGCAAATCTC 59.368 40.000 15.26 15.26 39.88 2.75
165 166 6.210796 CAAAACAGAGAACATGCAAATCTCA 58.789 36.000 21.57 0.00 41.60 3.27
166 167 6.395426 AAACAGAGAACATGCAAATCTCAA 57.605 33.333 21.57 0.00 41.60 3.02
167 168 6.395426 AACAGAGAACATGCAAATCTCAAA 57.605 33.333 21.57 0.00 41.60 2.69
168 169 6.585695 ACAGAGAACATGCAAATCTCAAAT 57.414 33.333 21.57 9.23 41.60 2.32
169 170 7.692460 ACAGAGAACATGCAAATCTCAAATA 57.308 32.000 21.57 0.00 41.60 1.40
170 171 8.289939 ACAGAGAACATGCAAATCTCAAATAT 57.710 30.769 21.57 5.17 41.60 1.28
171 172 8.746530 ACAGAGAACATGCAAATCTCAAATATT 58.253 29.630 21.57 4.64 41.60 1.28
172 173 9.582431 CAGAGAACATGCAAATCTCAAATATTT 57.418 29.630 21.57 0.00 41.60 1.40
173 174 9.582431 AGAGAACATGCAAATCTCAAATATTTG 57.418 29.630 20.13 20.13 43.87 2.32
174 175 9.362539 GAGAACATGCAAATCTCAAATATTTGT 57.637 29.630 23.95 6.09 43.26 2.83
175 176 9.715121 AGAACATGCAAATCTCAAATATTTGTT 57.285 25.926 23.95 11.35 43.26 2.83
179 180 9.910511 CATGCAAATCTCAAATATTTGTTAAGC 57.089 29.630 23.95 20.15 43.26 3.09
180 181 8.477984 TGCAAATCTCAAATATTTGTTAAGCC 57.522 30.769 23.95 11.33 43.26 4.35
181 182 7.275341 TGCAAATCTCAAATATTTGTTAAGCCG 59.725 33.333 23.95 11.88 43.26 5.52
182 183 7.254084 GCAAATCTCAAATATTTGTTAAGCCGG 60.254 37.037 23.95 0.00 43.26 6.13
183 184 5.243426 TCTCAAATATTTGTTAAGCCGGC 57.757 39.130 21.89 21.89 39.18 6.13
184 185 4.947388 TCTCAAATATTTGTTAAGCCGGCT 59.053 37.500 27.08 27.08 39.18 5.52
185 186 5.417580 TCTCAAATATTTGTTAAGCCGGCTT 59.582 36.000 41.05 41.05 39.18 4.35
186 187 6.031751 TCAAATATTTGTTAAGCCGGCTTT 57.968 33.333 43.93 27.99 39.18 3.51
187 188 6.459923 TCAAATATTTGTTAAGCCGGCTTTT 58.540 32.000 43.93 27.05 39.18 2.27
188 189 7.603651 TCAAATATTTGTTAAGCCGGCTTTTA 58.396 30.769 43.93 29.47 39.18 1.52
189 190 8.088981 TCAAATATTTGTTAAGCCGGCTTTTAA 58.911 29.630 43.93 30.70 39.18 1.52
190 191 8.379902 CAAATATTTGTTAAGCCGGCTTTTAAG 58.620 33.333 43.93 21.26 34.39 1.85
191 192 3.926821 TTGTTAAGCCGGCTTTTAAGG 57.073 42.857 43.93 0.00 37.47 2.69
198 199 2.483745 GGCTTTTAAGGCGCGACC 59.516 61.111 9.25 10.36 41.93 4.79
199 200 2.097728 GCTTTTAAGGCGCGACCG 59.902 61.111 9.25 0.00 46.52 4.79
200 201 2.782615 CTTTTAAGGCGCGACCGG 59.217 61.111 9.25 0.00 46.52 5.28
201 202 1.738830 CTTTTAAGGCGCGACCGGA 60.739 57.895 9.25 0.00 46.52 5.14
202 203 1.293267 CTTTTAAGGCGCGACCGGAA 61.293 55.000 9.25 6.71 46.52 4.30
203 204 0.883814 TTTTAAGGCGCGACCGGAAA 60.884 50.000 9.25 12.31 46.52 3.13
204 205 0.883814 TTTAAGGCGCGACCGGAAAA 60.884 50.000 9.25 10.10 46.52 2.29
205 206 0.883814 TTAAGGCGCGACCGGAAAAA 60.884 50.000 9.25 0.14 46.52 1.94
229 230 2.927553 GCTCACAGGCCTTATGTTTG 57.072 50.000 0.00 0.00 0.00 2.93
230 231 1.135286 GCTCACAGGCCTTATGTTTGC 60.135 52.381 0.00 7.83 0.00 3.68
231 232 2.440409 CTCACAGGCCTTATGTTTGCT 58.560 47.619 0.00 0.00 0.00 3.91
232 233 2.821969 CTCACAGGCCTTATGTTTGCTT 59.178 45.455 0.00 0.00 0.00 3.91
233 234 3.230134 TCACAGGCCTTATGTTTGCTTT 58.770 40.909 0.00 0.00 0.00 3.51
234 235 3.255642 TCACAGGCCTTATGTTTGCTTTC 59.744 43.478 0.00 0.00 0.00 2.62
235 236 3.005684 CACAGGCCTTATGTTTGCTTTCA 59.994 43.478 0.00 0.00 0.00 2.69
236 237 3.640967 ACAGGCCTTATGTTTGCTTTCAA 59.359 39.130 0.00 0.00 0.00 2.69
237 238 4.240096 CAGGCCTTATGTTTGCTTTCAAG 58.760 43.478 0.00 0.00 33.12 3.02
238 239 3.259123 AGGCCTTATGTTTGCTTTCAAGG 59.741 43.478 0.00 0.00 36.45 3.61
240 241 3.588955 CCTTATGTTTGCTTTCAAGGCC 58.411 45.455 0.00 0.00 33.12 5.19
241 242 3.244976 CTTATGTTTGCTTTCAAGGCCG 58.755 45.455 0.00 0.00 33.12 6.13
242 243 0.319813 ATGTTTGCTTTCAAGGCCGC 60.320 50.000 0.00 0.00 33.12 6.53
243 244 1.067250 GTTTGCTTTCAAGGCCGCA 59.933 52.632 0.00 0.00 33.12 5.69
244 245 0.319813 GTTTGCTTTCAAGGCCGCAT 60.320 50.000 0.00 0.00 33.12 4.73
245 246 1.067915 GTTTGCTTTCAAGGCCGCATA 60.068 47.619 0.00 0.00 33.12 3.14
246 247 0.810648 TTGCTTTCAAGGCCGCATAG 59.189 50.000 0.00 0.00 31.77 2.23
247 248 1.064783 GCTTTCAAGGCCGCATAGC 59.935 57.895 0.00 0.11 0.00 2.97
255 256 2.737180 GCCGCATAGCCTAGCTCA 59.263 61.111 0.00 0.00 40.44 4.26
256 257 1.666234 GCCGCATAGCCTAGCTCAC 60.666 63.158 0.00 0.00 40.44 3.51
257 258 1.742146 CCGCATAGCCTAGCTCACA 59.258 57.895 0.00 0.00 40.44 3.58
258 259 0.319728 CCGCATAGCCTAGCTCACAT 59.680 55.000 0.00 0.00 40.44 3.21
259 260 1.426423 CGCATAGCCTAGCTCACATG 58.574 55.000 0.00 0.00 40.44 3.21
260 261 1.155042 GCATAGCCTAGCTCACATGC 58.845 55.000 6.97 6.97 39.71 4.06
261 262 1.805869 CATAGCCTAGCTCACATGCC 58.194 55.000 0.00 0.00 40.44 4.40
262 263 1.347050 CATAGCCTAGCTCACATGCCT 59.653 52.381 0.00 0.00 40.44 4.75
263 264 1.043816 TAGCCTAGCTCACATGCCTC 58.956 55.000 0.00 0.00 40.44 4.70
264 265 0.979709 AGCCTAGCTCACATGCCTCA 60.980 55.000 0.00 0.00 30.62 3.86
265 266 0.108207 GCCTAGCTCACATGCCTCAT 59.892 55.000 0.00 0.00 0.00 2.90
266 267 1.880271 CCTAGCTCACATGCCTCATG 58.120 55.000 5.35 5.35 46.18 3.07
276 277 3.306917 CATGCCTCATGTTTGCTTTCA 57.693 42.857 0.00 0.00 37.12 2.69
277 278 3.250744 CATGCCTCATGTTTGCTTTCAG 58.749 45.455 0.00 0.00 37.12 3.02
278 279 2.309613 TGCCTCATGTTTGCTTTCAGT 58.690 42.857 0.00 0.00 0.00 3.41
279 280 2.034939 TGCCTCATGTTTGCTTTCAGTG 59.965 45.455 0.00 0.00 0.00 3.66
280 281 2.608752 GCCTCATGTTTGCTTTCAGTGG 60.609 50.000 0.00 0.00 0.00 4.00
286 287 1.068264 GTTTGCTTTCAGTGGCCTAGC 60.068 52.381 3.32 4.03 0.00 3.42
312 313 2.044492 TCACTCCACTCCCCTTCACTAT 59.956 50.000 0.00 0.00 0.00 2.12
321 322 1.141858 CCCCTTCACTATCCAAGCTCC 59.858 57.143 0.00 0.00 0.00 4.70
327 328 2.092049 TCACTATCCAAGCTCCCGTCTA 60.092 50.000 0.00 0.00 0.00 2.59
335 336 2.047002 AGCTCCCGTCTAGTCTTCTC 57.953 55.000 0.00 0.00 0.00 2.87
358 359 3.411114 ATGGCAGGCAGTGGATCCG 62.411 63.158 7.39 0.00 0.00 4.18
360 361 2.268920 GCAGGCAGTGGATCCGAA 59.731 61.111 7.39 0.00 0.00 4.30
362 363 1.162800 GCAGGCAGTGGATCCGAATC 61.163 60.000 7.39 0.00 0.00 2.52
372 373 2.043227 GGATCCGAATCCTTCACCTCT 58.957 52.381 0.00 0.00 46.97 3.69
376 377 4.186077 TCCGAATCCTTCACCTCTAGAT 57.814 45.455 0.00 0.00 0.00 1.98
379 380 3.257127 CGAATCCTTCACCTCTAGATCCC 59.743 52.174 0.00 0.00 0.00 3.85
388 389 0.606944 CTCTAGATCCCTCGACCCCG 60.607 65.000 0.00 0.00 37.07 5.73
400 401 3.083997 ACCCCGAGCTGATCCCAC 61.084 66.667 0.00 0.00 0.00 4.61
423 424 1.834822 CCCCGAGGAGGAGATGGTC 60.835 68.421 0.00 0.00 45.00 4.02
493 494 2.927580 GCGGACTCCTTGTGTCGGA 61.928 63.158 0.00 0.00 37.06 4.55
501 502 3.244911 ACTCCTTGTGTCGGAAATCCATT 60.245 43.478 0.00 0.00 35.14 3.16
508 509 7.445402 CCTTGTGTCGGAAATCCATTATCTATT 59.555 37.037 0.00 0.00 35.14 1.73
512 513 9.003658 GTGTCGGAAATCCATTATCTATTTGAT 57.996 33.333 0.00 0.00 36.06 2.57
520 521 9.645128 AATCCATTATCTATTTGATGTCCACAA 57.355 29.630 0.00 0.00 36.65 3.33
521 522 8.681486 TCCATTATCTATTTGATGTCCACAAG 57.319 34.615 0.00 0.00 36.65 3.16
526 527 0.950836 TTTGATGTCCACAAGCACCG 59.049 50.000 0.00 0.00 0.00 4.94
530 531 1.227999 ATGTCCACAAGCACCGTTCG 61.228 55.000 0.00 0.00 0.00 3.95
531 532 2.280524 TCCACAAGCACCGTTCGG 60.281 61.111 9.81 9.81 0.00 4.30
575 576 2.849096 TAGGACATGGGAGACGGCGT 62.849 60.000 14.65 14.65 0.00 5.68
609 611 4.101448 GGCTCGTGTCCCATGCCT 62.101 66.667 0.00 0.00 40.36 4.75
621 623 2.771943 TCCCATGCCTTACTCTACCTTG 59.228 50.000 0.00 0.00 0.00 3.61
626 628 0.179081 CCTTACTCTACCTTGCCGGC 60.179 60.000 22.73 22.73 35.61 6.13
645 647 0.170561 CGACCGGACCAACACTCTAG 59.829 60.000 9.46 0.00 0.00 2.43
695 697 1.968540 GCAAAACTGGGCGAGCTCT 60.969 57.895 12.85 0.00 0.00 4.09
699 701 2.403132 AAACTGGGCGAGCTCTGCTT 62.403 55.000 23.23 11.64 39.88 3.91
701 703 1.219124 CTGGGCGAGCTCTGCTTAA 59.781 57.895 23.23 12.36 39.88 1.85
706 708 2.943033 GGGCGAGCTCTGCTTAAATTAA 59.057 45.455 23.23 0.00 39.88 1.40
1038 1173 2.203771 CCCTCCTTCCTCCCGATCG 61.204 68.421 8.51 8.51 0.00 3.69
1045 1180 0.822164 TTCCTCCCGATCGTTTCTCC 59.178 55.000 15.09 0.00 0.00 3.71
1048 1183 1.305465 TCCCGATCGTTTCTCCCCA 60.305 57.895 15.09 0.00 0.00 4.96
1070 1205 2.790791 CCACCACCAGCCGCAAAAA 61.791 57.895 0.00 0.00 0.00 1.94
1071 1206 1.300080 CACCACCAGCCGCAAAAAG 60.300 57.895 0.00 0.00 0.00 2.27
1194 1329 1.497722 GGTCGCCGCTTTCTTTCTG 59.502 57.895 0.00 0.00 0.00 3.02
1195 1330 1.228657 GGTCGCCGCTTTCTTTCTGT 61.229 55.000 0.00 0.00 0.00 3.41
1196 1331 0.164002 GTCGCCGCTTTCTTTCTGTC 59.836 55.000 0.00 0.00 0.00 3.51
1198 1333 1.154395 GCCGCTTTCTTTCTGTCGC 60.154 57.895 0.00 0.00 0.00 5.19
1201 1336 1.557443 CGCTTTCTTTCTGTCGCCGT 61.557 55.000 0.00 0.00 0.00 5.68
1239 1377 2.690510 GAGAAGCCCCCTGAGCCT 60.691 66.667 0.00 0.00 0.00 4.58
1346 1484 1.805945 CGCTCGAGCCAAGGTACAC 60.806 63.158 30.66 0.39 37.91 2.90
1370 1512 3.817084 TCGTGTTCTCTTCTTTCTCCGTA 59.183 43.478 0.00 0.00 0.00 4.02
1596 1738 0.323908 AGGTGAGGAGGAAGGTCTCG 60.324 60.000 0.00 0.00 34.74 4.04
1597 1742 1.324005 GGTGAGGAGGAAGGTCTCGG 61.324 65.000 0.00 0.00 34.74 4.63
1676 1824 0.581053 ACGCAAGCGCCAAAATTTTG 59.419 45.000 21.65 21.65 44.19 2.44
1693 1841 1.686325 TTGCGAGCTGTATCCCTCCC 61.686 60.000 0.00 0.00 0.00 4.30
1694 1842 1.834822 GCGAGCTGTATCCCTCCCT 60.835 63.158 0.00 0.00 0.00 4.20
1695 1843 1.811645 GCGAGCTGTATCCCTCCCTC 61.812 65.000 0.00 0.00 0.00 4.30
1696 1844 1.182385 CGAGCTGTATCCCTCCCTCC 61.182 65.000 0.00 0.00 0.00 4.30
1697 1845 0.834261 GAGCTGTATCCCTCCCTCCC 60.834 65.000 0.00 0.00 0.00 4.30
1699 1847 1.411651 GCTGTATCCCTCCCTCCCAC 61.412 65.000 0.00 0.00 0.00 4.61
1700 1848 0.266152 CTGTATCCCTCCCTCCCACT 59.734 60.000 0.00 0.00 0.00 4.00
1726 1878 7.957992 ATGTACCTGTAGCTTTCTACTAGTT 57.042 36.000 0.00 0.00 44.26 2.24
1727 1879 7.771927 TGTACCTGTAGCTTTCTACTAGTTT 57.228 36.000 0.00 0.00 44.26 2.66
1739 1891 9.047371 GCTTTCTACTAGTTTGAGAAGAAAAGT 57.953 33.333 14.22 0.00 33.82 2.66
1743 1895 8.483758 TCTACTAGTTTGAGAAGAAAAGTTGGT 58.516 33.333 0.00 0.00 0.00 3.67
1744 1896 7.321745 ACTAGTTTGAGAAGAAAAGTTGGTG 57.678 36.000 0.00 0.00 0.00 4.17
1745 1897 6.884836 ACTAGTTTGAGAAGAAAAGTTGGTGT 59.115 34.615 0.00 0.00 0.00 4.16
1746 1898 8.044908 ACTAGTTTGAGAAGAAAAGTTGGTGTA 58.955 33.333 0.00 0.00 0.00 2.90
1853 2059 0.603439 TTGCATTGACAGCGCTCTGA 60.603 50.000 7.13 0.00 42.95 3.27
1878 2095 1.053835 TGTCAGAGCCCAGGTGTTGA 61.054 55.000 0.00 0.00 0.00 3.18
1882 2099 2.237143 TCAGAGCCCAGGTGTTGATAAG 59.763 50.000 0.00 0.00 0.00 1.73
1959 2184 3.788775 GCAGCTCCTTGCAAAAGAG 57.211 52.632 17.79 17.79 45.94 2.85
1961 2186 1.339291 GCAGCTCCTTGCAAAAGAGTT 59.661 47.619 21.19 15.51 45.94 3.01
2001 2229 2.905996 AAATGGGTCAGCTGCCGGA 61.906 57.895 9.47 4.57 0.00 5.14
2003 2231 1.344953 AATGGGTCAGCTGCCGGATA 61.345 55.000 9.47 2.24 0.00 2.59
2004 2232 2.044806 ATGGGTCAGCTGCCGGATAC 62.045 60.000 9.47 0.00 0.00 2.24
2005 2233 2.435693 GGGTCAGCTGCCGGATACT 61.436 63.158 9.47 0.00 0.00 2.12
2006 2234 1.068250 GGTCAGCTGCCGGATACTC 59.932 63.158 9.47 0.00 0.00 2.59
2007 2235 1.299468 GTCAGCTGCCGGATACTCG 60.299 63.158 9.47 0.00 0.00 4.18
2008 2236 1.453197 TCAGCTGCCGGATACTCGA 60.453 57.895 9.47 0.00 0.00 4.04
2009 2237 1.299468 CAGCTGCCGGATACTCGAC 60.299 63.158 5.05 0.00 0.00 4.20
2010 2238 2.027751 GCTGCCGGATACTCGACC 59.972 66.667 5.05 0.00 0.00 4.79
2013 2241 2.836360 GCCGGATACTCGACCCCA 60.836 66.667 5.05 0.00 0.00 4.96
2025 2253 2.810274 CTCGACCCCAATAGCATGATTG 59.190 50.000 0.00 0.00 36.70 2.67
2086 2317 4.359434 AGGAAACAGTCTTCTTCCTTCC 57.641 45.455 6.45 0.00 45.37 3.46
2088 2319 3.244112 GGAAACAGTCTTCTTCCTTCCGA 60.244 47.826 3.35 0.00 36.48 4.55
2329 2561 3.108289 CTGCAGACGTCGCCTGTG 61.108 66.667 23.01 12.33 34.29 3.66
2397 2629 0.174845 TGTTTCCTAGGATGACGGCG 59.825 55.000 13.57 4.80 0.00 6.46
2439 2671 3.569701 TGGAAAATGTCTGCTTGAGTTCC 59.430 43.478 0.00 0.00 0.00 3.62
2486 2718 1.202336 GCCAGCCTATGCAACATGAAC 60.202 52.381 0.00 0.00 41.13 3.18
2488 2720 1.406539 CAGCCTATGCAACATGAACCC 59.593 52.381 0.00 0.00 41.13 4.11
2490 2722 1.134946 GCCTATGCAACATGAACCCAC 59.865 52.381 0.00 0.00 37.47 4.61
2496 2728 2.200899 GCAACATGAACCCACACAAAC 58.799 47.619 0.00 0.00 0.00 2.93
2497 2729 2.458951 CAACATGAACCCACACAAACG 58.541 47.619 0.00 0.00 0.00 3.60
2516 2748 7.222805 CACAAACGAGATGTTACTGCATATAGT 59.777 37.037 0.00 0.00 40.84 2.12
2543 2775 7.390718 ACACTGTAGATTTTGATGGTAAAGGAC 59.609 37.037 0.00 0.00 0.00 3.85
2544 2776 7.607991 CACTGTAGATTTTGATGGTAAAGGACT 59.392 37.037 0.00 0.00 0.00 3.85
2545 2777 7.607991 ACTGTAGATTTTGATGGTAAAGGACTG 59.392 37.037 0.00 0.00 0.00 3.51
2546 2778 7.458397 TGTAGATTTTGATGGTAAAGGACTGT 58.542 34.615 0.00 0.00 0.00 3.55
2547 2779 7.606456 TGTAGATTTTGATGGTAAAGGACTGTC 59.394 37.037 0.00 0.00 0.00 3.51
2548 2780 6.542821 AGATTTTGATGGTAAAGGACTGTCA 58.457 36.000 10.38 0.00 0.00 3.58
2549 2781 6.656693 AGATTTTGATGGTAAAGGACTGTCAG 59.343 38.462 10.38 0.00 0.00 3.51
2550 2782 4.974645 TTGATGGTAAAGGACTGTCAGT 57.025 40.909 4.81 4.81 0.00 3.41
2557 2789 3.460857 AAAGGACTGTCAGTCTGTCAC 57.539 47.619 27.82 13.89 44.46 3.67
2564 2796 1.230324 GTCAGTCTGTCACAAAGGGC 58.770 55.000 0.00 0.00 0.00 5.19
2573 2805 6.891908 AGTCTGTCACAAAGGGCAATATATTT 59.108 34.615 0.00 0.00 0.00 1.40
2576 2808 5.954752 TGTCACAAAGGGCAATATATTTGGA 59.045 36.000 0.00 0.00 37.04 3.53
2616 2848 9.825109 AGCTTAAGAGAATGATTCTACTAAACC 57.175 33.333 7.82 3.74 40.87 3.27
2645 2880 3.025262 GGTTGTGTTGGTTTACAGGGAA 58.975 45.455 0.00 0.00 0.00 3.97
2657 2892 0.957395 ACAGGGAAGCTGCATGAACG 60.957 55.000 1.02 0.00 0.00 3.95
2676 2911 5.237561 TGAACGTGCTAACAATTTCAGCTAA 59.762 36.000 0.00 0.00 36.26 3.09
2698 2933 7.171337 GCTAAAGGATGAAGAGAAGAATAGCAG 59.829 40.741 0.00 0.00 33.07 4.24
2708 2943 7.430760 AGAGAAGAATAGCAGGTAATGAGTT 57.569 36.000 0.00 0.00 0.00 3.01
2717 2952 5.675538 AGCAGGTAATGAGTTAATGGAGAC 58.324 41.667 0.00 0.00 0.00 3.36
2733 2968 4.717877 TGGAGACAATATACAGCATTGGG 58.282 43.478 0.00 0.00 37.64 4.12
2734 2969 4.165950 TGGAGACAATATACAGCATTGGGT 59.834 41.667 0.00 0.00 37.64 4.51
2735 2970 5.919721 TGGAGACAATATACAGCATTGGGTG 60.920 44.000 0.00 0.00 42.79 4.61
2748 2983 4.963318 CATTGGGTGCTTAGATAGAGGA 57.037 45.455 0.00 0.00 0.00 3.71
2749 2984 4.892433 CATTGGGTGCTTAGATAGAGGAG 58.108 47.826 0.00 0.00 0.00 3.69
2750 2985 3.973472 TGGGTGCTTAGATAGAGGAGA 57.027 47.619 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.989253 CCCGCCCTGGTTTTGGAC 60.989 66.667 0.00 0.00 35.15 4.02
13 14 3.503839 ACCCGCCCTGGTTTTGGA 61.504 61.111 0.00 0.00 33.91 3.53
14 15 3.302344 CACCCGCCCTGGTTTTGG 61.302 66.667 0.00 0.00 36.12 3.28
15 16 0.322997 TATCACCCGCCCTGGTTTTG 60.323 55.000 0.00 0.00 36.12 2.44
16 17 0.406361 TTATCACCCGCCCTGGTTTT 59.594 50.000 0.00 0.00 36.12 2.43
17 18 0.323087 GTTATCACCCGCCCTGGTTT 60.323 55.000 0.00 0.00 36.12 3.27
18 19 1.301954 GTTATCACCCGCCCTGGTT 59.698 57.895 0.00 0.00 36.12 3.67
19 20 2.676265 GGTTATCACCCGCCCTGGT 61.676 63.158 0.00 0.00 39.96 4.00
20 21 2.192175 GGTTATCACCCGCCCTGG 59.808 66.667 0.00 0.00 37.03 4.45
28 29 7.556275 TCATATTTGAGTCTTTGGGTTATCACC 59.444 37.037 0.00 0.00 43.37 4.02
29 30 8.506168 TCATATTTGAGTCTTTGGGTTATCAC 57.494 34.615 0.00 0.00 0.00 3.06
30 31 8.737168 CTCATATTTGAGTCTTTGGGTTATCA 57.263 34.615 5.10 0.00 43.73 2.15
45 46 7.397892 TTCGGGTTATTTTGCTCATATTTGA 57.602 32.000 0.00 0.00 0.00 2.69
46 47 6.198966 GCTTCGGGTTATTTTGCTCATATTTG 59.801 38.462 0.00 0.00 0.00 2.32
47 48 6.273071 GCTTCGGGTTATTTTGCTCATATTT 58.727 36.000 0.00 0.00 0.00 1.40
48 49 5.221244 GGCTTCGGGTTATTTTGCTCATATT 60.221 40.000 0.00 0.00 0.00 1.28
49 50 4.278419 GGCTTCGGGTTATTTTGCTCATAT 59.722 41.667 0.00 0.00 0.00 1.78
50 51 3.630312 GGCTTCGGGTTATTTTGCTCATA 59.370 43.478 0.00 0.00 0.00 2.15
51 52 2.427095 GGCTTCGGGTTATTTTGCTCAT 59.573 45.455 0.00 0.00 0.00 2.90
52 53 1.816224 GGCTTCGGGTTATTTTGCTCA 59.184 47.619 0.00 0.00 0.00 4.26
53 54 1.816224 TGGCTTCGGGTTATTTTGCTC 59.184 47.619 0.00 0.00 0.00 4.26
54 55 1.818674 CTGGCTTCGGGTTATTTTGCT 59.181 47.619 0.00 0.00 0.00 3.91
55 56 1.544246 ACTGGCTTCGGGTTATTTTGC 59.456 47.619 0.00 0.00 0.00 3.68
56 57 6.459161 GGTTATACTGGCTTCGGGTTATTTTG 60.459 42.308 0.00 0.00 0.00 2.44
57 58 5.591472 GGTTATACTGGCTTCGGGTTATTTT 59.409 40.000 0.00 0.00 0.00 1.82
58 59 5.128205 GGTTATACTGGCTTCGGGTTATTT 58.872 41.667 0.00 0.00 0.00 1.40
59 60 4.445305 GGGTTATACTGGCTTCGGGTTATT 60.445 45.833 0.00 0.00 0.00 1.40
60 61 3.072038 GGGTTATACTGGCTTCGGGTTAT 59.928 47.826 0.00 0.00 0.00 1.89
61 62 2.435437 GGGTTATACTGGCTTCGGGTTA 59.565 50.000 0.00 0.00 0.00 2.85
62 63 1.211212 GGGTTATACTGGCTTCGGGTT 59.789 52.381 0.00 0.00 0.00 4.11
63 64 0.835276 GGGTTATACTGGCTTCGGGT 59.165 55.000 0.00 0.00 0.00 5.28
64 65 0.249741 CGGGTTATACTGGCTTCGGG 60.250 60.000 0.00 0.00 0.00 5.14
65 66 0.249741 CCGGGTTATACTGGCTTCGG 60.250 60.000 0.00 0.00 0.00 4.30
66 67 0.249741 CCCGGGTTATACTGGCTTCG 60.250 60.000 14.18 0.00 35.47 3.79
67 68 0.108019 CCCCGGGTTATACTGGCTTC 59.892 60.000 21.85 0.00 35.47 3.86
68 69 0.326808 TCCCCGGGTTATACTGGCTT 60.327 55.000 21.85 0.00 35.47 4.35
69 70 0.104620 ATCCCCGGGTTATACTGGCT 60.105 55.000 21.85 0.00 35.47 4.75
70 71 0.769247 AATCCCCGGGTTATACTGGC 59.231 55.000 21.85 0.00 35.47 4.85
71 72 2.051692 TGAATCCCCGGGTTATACTGG 58.948 52.381 21.85 0.35 36.61 4.00
72 73 5.492855 TTATGAATCCCCGGGTTATACTG 57.507 43.478 21.85 1.24 0.00 2.74
73 74 6.713731 AATTATGAATCCCCGGGTTATACT 57.286 37.500 21.85 2.13 0.00 2.12
74 75 6.349860 GCAAATTATGAATCCCCGGGTTATAC 60.350 42.308 21.85 7.35 0.00 1.47
75 76 5.712917 GCAAATTATGAATCCCCGGGTTATA 59.287 40.000 21.85 4.77 0.00 0.98
76 77 4.526650 GCAAATTATGAATCCCCGGGTTAT 59.473 41.667 21.85 10.01 0.00 1.89
77 78 3.892588 GCAAATTATGAATCCCCGGGTTA 59.107 43.478 21.85 7.63 0.00 2.85
78 79 2.698274 GCAAATTATGAATCCCCGGGTT 59.302 45.455 21.85 8.14 0.00 4.11
79 80 2.316108 GCAAATTATGAATCCCCGGGT 58.684 47.619 21.85 0.00 0.00 5.28
80 81 1.269448 CGCAAATTATGAATCCCCGGG 59.731 52.381 15.80 15.80 0.00 5.73
81 82 1.953686 ACGCAAATTATGAATCCCCGG 59.046 47.619 0.00 0.00 0.00 5.73
82 83 4.822036 TTACGCAAATTATGAATCCCCG 57.178 40.909 0.00 0.00 0.00 5.73
83 84 6.569780 ACTTTTACGCAAATTATGAATCCCC 58.430 36.000 0.00 0.00 0.00 4.81
84 85 9.575783 TTTACTTTTACGCAAATTATGAATCCC 57.424 29.630 0.00 0.00 0.00 3.85
135 136 5.486526 TGCATGTTCTCTGTTTTGGTTTTT 58.513 33.333 0.00 0.00 0.00 1.94
136 137 5.083533 TGCATGTTCTCTGTTTTGGTTTT 57.916 34.783 0.00 0.00 0.00 2.43
137 138 4.734398 TGCATGTTCTCTGTTTTGGTTT 57.266 36.364 0.00 0.00 0.00 3.27
138 139 4.734398 TTGCATGTTCTCTGTTTTGGTT 57.266 36.364 0.00 0.00 0.00 3.67
139 140 4.734398 TTTGCATGTTCTCTGTTTTGGT 57.266 36.364 0.00 0.00 0.00 3.67
140 141 5.535333 AGATTTGCATGTTCTCTGTTTTGG 58.465 37.500 0.00 0.00 0.00 3.28
141 142 6.210796 TGAGATTTGCATGTTCTCTGTTTTG 58.789 36.000 17.08 0.00 37.40 2.44
142 143 6.395426 TGAGATTTGCATGTTCTCTGTTTT 57.605 33.333 17.08 0.00 37.40 2.43
143 144 6.395426 TTGAGATTTGCATGTTCTCTGTTT 57.605 33.333 17.08 0.00 37.40 2.83
144 145 6.395426 TTTGAGATTTGCATGTTCTCTGTT 57.605 33.333 17.08 0.00 37.40 3.16
145 146 6.585695 ATTTGAGATTTGCATGTTCTCTGT 57.414 33.333 17.08 5.64 37.40 3.41
146 147 9.582431 AAATATTTGAGATTTGCATGTTCTCTG 57.418 29.630 17.08 0.00 37.40 3.35
147 148 9.582431 CAAATATTTGAGATTTGCATGTTCTCT 57.418 29.630 21.35 3.97 40.55 3.10
148 149 9.362539 ACAAATATTTGAGATTTGCATGTTCTC 57.637 29.630 30.18 11.96 44.59 2.87
149 150 9.715121 AACAAATATTTGAGATTTGCATGTTCT 57.285 25.926 30.18 3.50 44.59 3.01
153 154 9.910511 GCTTAACAAATATTTGAGATTTGCATG 57.089 29.630 30.18 11.87 44.59 4.06
154 155 9.101655 GGCTTAACAAATATTTGAGATTTGCAT 57.898 29.630 30.18 5.85 44.59 3.96
155 156 7.275341 CGGCTTAACAAATATTTGAGATTTGCA 59.725 33.333 30.18 8.36 44.59 4.08
156 157 7.254084 CCGGCTTAACAAATATTTGAGATTTGC 60.254 37.037 30.18 22.75 44.59 3.68
157 158 7.254084 GCCGGCTTAACAAATATTTGAGATTTG 60.254 37.037 30.18 16.51 45.67 2.32
158 159 6.756542 GCCGGCTTAACAAATATTTGAGATTT 59.243 34.615 30.18 17.81 40.55 2.17
159 160 6.096846 AGCCGGCTTAACAAATATTTGAGATT 59.903 34.615 30.18 18.12 40.55 2.40
160 161 5.594317 AGCCGGCTTAACAAATATTTGAGAT 59.406 36.000 30.18 18.71 40.55 2.75
161 162 4.947388 AGCCGGCTTAACAAATATTTGAGA 59.053 37.500 30.18 16.39 40.55 3.27
162 163 5.248870 AGCCGGCTTAACAAATATTTGAG 57.751 39.130 30.18 19.39 40.55 3.02
163 164 5.652994 AAGCCGGCTTAACAAATATTTGA 57.347 34.783 39.65 9.97 36.76 2.69
164 165 6.720012 AAAAGCCGGCTTAACAAATATTTG 57.280 33.333 40.29 23.60 38.49 2.32
165 166 7.547722 CCTTAAAAGCCGGCTTAACAAATATTT 59.452 33.333 40.29 27.73 34.84 1.40
166 167 7.039270 CCTTAAAAGCCGGCTTAACAAATATT 58.961 34.615 40.29 28.41 34.84 1.28
167 168 6.569780 CCTTAAAAGCCGGCTTAACAAATAT 58.430 36.000 40.29 20.67 34.84 1.28
168 169 5.622687 GCCTTAAAAGCCGGCTTAACAAATA 60.623 40.000 40.29 22.22 40.62 1.40
169 170 4.816392 CCTTAAAAGCCGGCTTAACAAAT 58.184 39.130 40.29 22.24 34.84 2.32
170 171 3.553302 GCCTTAAAAGCCGGCTTAACAAA 60.553 43.478 40.29 27.37 40.62 2.83
171 172 2.029739 GCCTTAAAAGCCGGCTTAACAA 60.030 45.455 40.29 29.33 40.62 2.83
172 173 1.542472 GCCTTAAAAGCCGGCTTAACA 59.458 47.619 40.29 25.06 40.62 2.41
173 174 1.466866 CGCCTTAAAAGCCGGCTTAAC 60.467 52.381 40.29 23.36 41.61 2.01
174 175 0.806241 CGCCTTAAAAGCCGGCTTAA 59.194 50.000 40.29 29.43 41.61 1.85
175 176 1.650314 GCGCCTTAAAAGCCGGCTTA 61.650 55.000 40.29 24.63 41.61 3.09
176 177 2.989881 GCGCCTTAAAAGCCGGCTT 61.990 57.895 35.84 35.84 41.61 4.35
177 178 3.440415 GCGCCTTAAAAGCCGGCT 61.440 61.111 27.08 27.08 41.61 5.52
178 179 4.829518 CGCGCCTTAAAAGCCGGC 62.830 66.667 21.89 21.89 40.40 6.13
179 180 3.122323 TCGCGCCTTAAAAGCCGG 61.122 61.111 0.00 0.00 0.00 6.13
180 181 2.097728 GTCGCGCCTTAAAAGCCG 59.902 61.111 0.00 0.00 0.00 5.52
181 182 2.483745 GGTCGCGCCTTAAAAGCC 59.516 61.111 0.00 0.00 0.00 4.35
182 183 2.097728 CGGTCGCGCCTTAAAAGC 59.902 61.111 15.78 0.00 34.25 3.51
183 184 1.293267 TTCCGGTCGCGCCTTAAAAG 61.293 55.000 15.78 1.62 34.25 2.27
184 185 0.883814 TTTCCGGTCGCGCCTTAAAA 60.884 50.000 15.78 10.65 34.25 1.52
185 186 0.883814 TTTTCCGGTCGCGCCTTAAA 60.884 50.000 15.78 12.57 34.25 1.52
186 187 0.883814 TTTTTCCGGTCGCGCCTTAA 60.884 50.000 15.78 8.18 34.25 1.85
187 188 1.301558 TTTTTCCGGTCGCGCCTTA 60.302 52.632 15.78 3.10 34.25 2.69
188 189 2.592287 TTTTTCCGGTCGCGCCTT 60.592 55.556 15.78 0.00 34.25 4.35
210 211 1.135286 GCAAACATAAGGCCTGTGAGC 60.135 52.381 21.68 17.42 0.00 4.26
211 212 2.440409 AGCAAACATAAGGCCTGTGAG 58.560 47.619 21.68 12.98 0.00 3.51
212 213 2.584835 AGCAAACATAAGGCCTGTGA 57.415 45.000 21.68 5.14 0.00 3.58
213 214 3.005684 TGAAAGCAAACATAAGGCCTGTG 59.994 43.478 5.69 11.84 0.00 3.66
214 215 3.230134 TGAAAGCAAACATAAGGCCTGT 58.770 40.909 5.69 0.00 0.00 4.00
215 216 3.940209 TGAAAGCAAACATAAGGCCTG 57.060 42.857 5.69 0.00 0.00 4.85
216 217 3.259123 CCTTGAAAGCAAACATAAGGCCT 59.741 43.478 0.00 0.00 32.73 5.19
217 218 3.588955 CCTTGAAAGCAAACATAAGGCC 58.411 45.455 0.00 0.00 32.73 5.19
219 220 3.588955 GGCCTTGAAAGCAAACATAAGG 58.411 45.455 0.00 0.00 38.13 2.69
220 221 3.244976 CGGCCTTGAAAGCAAACATAAG 58.755 45.455 0.00 0.00 32.73 1.73
221 222 2.609244 GCGGCCTTGAAAGCAAACATAA 60.609 45.455 0.00 0.00 32.73 1.90
222 223 1.067915 GCGGCCTTGAAAGCAAACATA 60.068 47.619 0.00 0.00 32.73 2.29
223 224 0.319813 GCGGCCTTGAAAGCAAACAT 60.320 50.000 0.00 0.00 32.73 2.71
224 225 1.067250 GCGGCCTTGAAAGCAAACA 59.933 52.632 0.00 0.00 32.73 2.83
225 226 0.319813 ATGCGGCCTTGAAAGCAAAC 60.320 50.000 0.00 0.00 43.19 2.93
226 227 1.202114 CTATGCGGCCTTGAAAGCAAA 59.798 47.619 0.00 0.00 43.19 3.68
227 228 0.810648 CTATGCGGCCTTGAAAGCAA 59.189 50.000 0.00 0.00 43.19 3.91
228 229 1.656818 GCTATGCGGCCTTGAAAGCA 61.657 55.000 0.00 1.29 44.13 3.91
229 230 1.064783 GCTATGCGGCCTTGAAAGC 59.935 57.895 0.00 0.00 0.00 3.51
238 239 1.666234 GTGAGCTAGGCTATGCGGC 60.666 63.158 0.00 0.00 39.88 6.53
239 240 0.319728 ATGTGAGCTAGGCTATGCGG 59.680 55.000 0.00 0.00 39.88 5.69
240 241 1.426423 CATGTGAGCTAGGCTATGCG 58.574 55.000 0.00 0.00 39.88 4.73
241 242 1.155042 GCATGTGAGCTAGGCTATGC 58.845 55.000 9.11 9.11 39.71 3.14
242 243 1.347050 AGGCATGTGAGCTAGGCTATG 59.653 52.381 0.00 0.00 39.88 2.23
243 244 1.622811 GAGGCATGTGAGCTAGGCTAT 59.377 52.381 0.00 0.00 39.88 2.97
244 245 1.043816 GAGGCATGTGAGCTAGGCTA 58.956 55.000 0.00 0.00 39.88 3.93
245 246 0.979709 TGAGGCATGTGAGCTAGGCT 60.980 55.000 0.00 0.00 43.88 4.58
246 247 0.108207 ATGAGGCATGTGAGCTAGGC 59.892 55.000 0.00 0.00 34.17 3.93
247 248 1.880271 CATGAGGCATGTGAGCTAGG 58.120 55.000 0.00 0.00 37.12 3.02
254 255 7.738227 ACTGAAAGCAAACATGAGGCATGTG 62.738 44.000 13.19 4.16 46.37 3.21
256 257 3.250744 CTGAAAGCAAACATGAGGCATG 58.749 45.455 0.00 5.90 46.18 4.06
257 258 2.895404 ACTGAAAGCAAACATGAGGCAT 59.105 40.909 0.00 0.00 37.60 4.40
258 259 2.034939 CACTGAAAGCAAACATGAGGCA 59.965 45.455 0.00 0.00 37.60 4.75
259 260 2.608752 CCACTGAAAGCAAACATGAGGC 60.609 50.000 0.00 0.00 37.60 4.70
260 261 2.608752 GCCACTGAAAGCAAACATGAGG 60.609 50.000 0.00 0.00 37.60 3.86
261 262 2.608752 GGCCACTGAAAGCAAACATGAG 60.609 50.000 0.00 0.00 37.60 2.90
262 263 1.340889 GGCCACTGAAAGCAAACATGA 59.659 47.619 0.00 0.00 37.60 3.07
263 264 1.342174 AGGCCACTGAAAGCAAACATG 59.658 47.619 5.01 0.00 37.60 3.21
264 265 1.708341 AGGCCACTGAAAGCAAACAT 58.292 45.000 5.01 0.00 37.60 2.71
265 266 2.229792 CTAGGCCACTGAAAGCAAACA 58.770 47.619 5.01 0.00 37.60 2.83
266 267 1.068264 GCTAGGCCACTGAAAGCAAAC 60.068 52.381 5.01 0.00 37.60 2.93
267 268 1.247567 GCTAGGCCACTGAAAGCAAA 58.752 50.000 5.01 0.00 37.60 3.68
268 269 2.946947 GCTAGGCCACTGAAAGCAA 58.053 52.632 5.01 0.00 37.60 3.91
269 270 4.722193 GCTAGGCCACTGAAAGCA 57.278 55.556 5.01 0.00 37.60 3.91
280 281 0.176910 GTGGAGTGAAGAGGCTAGGC 59.823 60.000 8.55 8.55 0.00 3.93
286 287 0.252467 AGGGGAGTGGAGTGAAGAGG 60.252 60.000 0.00 0.00 0.00 3.69
294 295 2.043227 GGATAGTGAAGGGGAGTGGAG 58.957 57.143 0.00 0.00 0.00 3.86
312 313 0.331954 AGACTAGACGGGAGCTTGGA 59.668 55.000 0.00 0.00 0.00 3.53
321 322 1.030488 TGCCGGAGAAGACTAGACGG 61.030 60.000 5.05 0.00 39.37 4.79
327 328 2.249413 CTGCCATGCCGGAGAAGACT 62.249 60.000 5.05 0.00 36.56 3.24
360 361 3.499563 CGAGGGATCTAGAGGTGAAGGAT 60.500 52.174 0.00 0.00 0.00 3.24
362 363 2.158593 TCGAGGGATCTAGAGGTGAAGG 60.159 54.545 0.00 0.00 0.00 3.46
372 373 3.664769 TCGGGGTCGAGGGATCTA 58.335 61.111 0.00 0.00 40.88 1.98
409 410 1.448922 CGGACGACCATCTCCTCCTC 61.449 65.000 4.48 0.00 35.59 3.71
474 475 2.432628 CGACACAAGGAGTCCGCC 60.433 66.667 2.76 0.00 32.41 6.13
475 476 2.430382 TTCCGACACAAGGAGTCCGC 62.430 60.000 2.76 0.00 39.22 5.54
477 478 2.347731 GATTTCCGACACAAGGAGTCC 58.652 52.381 0.00 0.00 39.22 3.85
486 487 8.378172 TCAAATAGATAATGGATTTCCGACAC 57.622 34.615 0.00 0.00 39.43 3.67
488 489 9.003658 ACATCAAATAGATAATGGATTTCCGAC 57.996 33.333 0.00 0.00 35.12 4.79
493 494 9.645128 TGTGGACATCAAATAGATAATGGATTT 57.355 29.630 0.00 0.00 34.43 2.17
501 502 5.822519 GGTGCTTGTGGACATCAAATAGATA 59.177 40.000 0.00 0.00 36.16 1.98
508 509 0.179032 ACGGTGCTTGTGGACATCAA 60.179 50.000 0.00 0.00 36.16 2.57
512 513 1.885388 CGAACGGTGCTTGTGGACA 60.885 57.895 0.00 0.00 36.16 4.02
526 527 3.260931 GGAGCCCGAAAACCGAAC 58.739 61.111 0.00 0.00 41.76 3.95
550 551 2.359531 CGTCTCCCATGTCCTACTCTTC 59.640 54.545 0.00 0.00 0.00 2.87
609 611 0.966875 TCGCCGGCAAGGTAGAGTAA 60.967 55.000 28.98 0.00 43.70 2.24
626 628 0.170561 CTAGAGTGTTGGTCCGGTCG 59.829 60.000 0.00 0.00 0.00 4.79
659 661 2.896854 CATGTCCATGTCCGGCGG 60.897 66.667 22.51 22.51 34.23 6.13
695 697 8.963130 CATGAAACGTGAAACTTAATTTAAGCA 58.037 29.630 14.67 4.03 39.39 3.91
770 772 5.761234 TCAAAACGTTAGTACATCAGCCTTT 59.239 36.000 0.00 0.00 0.00 3.11
771 773 5.178809 GTCAAAACGTTAGTACATCAGCCTT 59.821 40.000 0.00 0.00 0.00 4.35
781 904 7.115805 GTCATGTCAGATGTCAAAACGTTAGTA 59.884 37.037 0.00 0.00 0.00 1.82
788 911 5.048504 ACCATGTCATGTCAGATGTCAAAAC 60.049 40.000 11.84 0.00 0.00 2.43
1027 1157 1.041447 GGGAGAAACGATCGGGAGGA 61.041 60.000 20.98 0.00 0.00 3.71
1038 1173 1.228459 GGTGGTGGTGGGGAGAAAC 60.228 63.158 0.00 0.00 0.00 2.78
1045 1180 4.974721 GCTGGTGGTGGTGGTGGG 62.975 72.222 0.00 0.00 0.00 4.61
1070 1205 0.603065 GCCCTTTCCGCACATTTTCT 59.397 50.000 0.00 0.00 0.00 2.52
1071 1206 0.389817 GGCCCTTTCCGCACATTTTC 60.390 55.000 0.00 0.00 0.00 2.29
1183 1318 0.164002 GACGGCGACAGAAAGAAAGC 59.836 55.000 16.62 0.00 0.00 3.51
1184 1319 0.435008 CGACGGCGACAGAAAGAAAG 59.565 55.000 16.62 0.00 40.82 2.62
1186 1321 2.019951 GCGACGGCGACAGAAAGAA 61.020 57.895 18.90 0.00 40.82 2.52
1239 1377 4.147449 CCGATGGCGAGCTCCACA 62.147 66.667 8.47 7.84 39.25 4.17
1302 1440 2.669569 TTGAGGCACGCCAGCTTC 60.670 61.111 11.35 0.00 40.63 3.86
1346 1484 3.610242 CGGAGAAAGAAGAGAACACGATG 59.390 47.826 0.00 0.00 0.00 3.84
1370 1512 2.280592 GCGTTCTTGGACCCGTGT 60.281 61.111 0.00 0.00 0.00 4.49
1383 1525 0.532573 ATGAGATGAGGACACGCGTT 59.467 50.000 10.22 0.17 0.00 4.84
1582 1724 2.756283 CGCCGAGACCTTCCTCCT 60.756 66.667 0.00 0.00 0.00 3.69
1676 1824 1.811645 GAGGGAGGGATACAGCTCGC 61.812 65.000 0.00 0.00 37.85 5.03
1693 1841 3.961408 AGCTACAGGTACATAAGTGGGAG 59.039 47.826 0.00 0.00 0.00 4.30
1694 1842 3.990369 AGCTACAGGTACATAAGTGGGA 58.010 45.455 0.00 0.00 0.00 4.37
1695 1843 4.755266 AAGCTACAGGTACATAAGTGGG 57.245 45.455 0.00 0.00 0.00 4.61
1696 1844 5.978814 AGAAAGCTACAGGTACATAAGTGG 58.021 41.667 0.00 0.00 0.00 4.00
1697 1845 7.988904 GTAGAAAGCTACAGGTACATAAGTG 57.011 40.000 0.00 0.00 45.10 3.16
1726 1878 5.522460 CGAGTACACCAACTTTTCTTCTCAA 59.478 40.000 0.00 0.00 0.00 3.02
1727 1879 5.047847 CGAGTACACCAACTTTTCTTCTCA 58.952 41.667 0.00 0.00 0.00 3.27
1765 1917 2.872245 GCAGGATACGCATACACATGTT 59.128 45.455 0.00 0.00 46.39 2.71
1767 1919 1.456923 CGCAGGATACGCATACACATG 59.543 52.381 0.00 0.00 46.39 3.21
1831 2037 1.078709 GAGCGCTGTCAATGCAACTA 58.921 50.000 18.48 0.00 0.00 2.24
1847 2053 3.849002 TCTGACATGGCTTCAGAGC 57.151 52.632 9.76 0.00 43.69 4.09
1853 2059 1.302285 CTGGGCTCTGACATGGCTT 59.698 57.895 0.00 0.00 0.00 4.35
1878 2095 9.331282 GATGGAACTGCTATTTCTGTTACTTAT 57.669 33.333 0.00 0.00 32.13 1.73
1882 2099 6.985188 TGATGGAACTGCTATTTCTGTTAC 57.015 37.500 0.00 0.00 31.69 2.50
1914 2136 2.050350 CCATTGTGCTGCAGGAGGG 61.050 63.158 17.12 8.25 0.00 4.30
1943 2165 4.050852 CAAAACTCTTTTGCAAGGAGCT 57.949 40.909 22.81 13.53 42.91 4.09
1958 2183 5.523552 GCTTGCCATTTGTTAAGTCAAAACT 59.476 36.000 0.00 0.00 40.05 2.66
1959 2184 5.293079 TGCTTGCCATTTGTTAAGTCAAAAC 59.707 36.000 0.00 0.00 40.05 2.43
1961 2186 5.016051 TGCTTGCCATTTGTTAAGTCAAA 57.984 34.783 0.00 0.00 40.74 2.69
1964 2189 5.106987 CCATTTGCTTGCCATTTGTTAAGTC 60.107 40.000 0.00 0.00 0.00 3.01
1975 2203 1.818959 GCTGACCCATTTGCTTGCCA 61.819 55.000 0.00 0.00 0.00 4.92
2001 2229 3.239449 TCATGCTATTGGGGTCGAGTAT 58.761 45.455 0.00 0.00 0.00 2.12
2003 2231 1.496060 TCATGCTATTGGGGTCGAGT 58.504 50.000 0.00 0.00 0.00 4.18
2004 2232 2.810274 CAATCATGCTATTGGGGTCGAG 59.190 50.000 0.00 0.00 33.95 4.04
2005 2233 2.172505 ACAATCATGCTATTGGGGTCGA 59.827 45.455 10.81 0.00 40.48 4.20
2006 2234 2.549754 GACAATCATGCTATTGGGGTCG 59.450 50.000 10.81 0.00 40.48 4.79
2007 2235 3.817647 GAGACAATCATGCTATTGGGGTC 59.182 47.826 10.81 1.73 40.48 4.46
2008 2236 3.202818 TGAGACAATCATGCTATTGGGGT 59.797 43.478 10.81 0.00 40.48 4.95
2009 2237 3.567164 GTGAGACAATCATGCTATTGGGG 59.433 47.826 10.81 0.00 40.92 4.96
2010 2238 3.567164 GGTGAGACAATCATGCTATTGGG 59.433 47.826 10.81 0.00 40.92 4.12
2013 2241 6.326064 ACTCTAGGTGAGACAATCATGCTATT 59.674 38.462 0.00 0.00 45.39 1.73
2086 2317 8.634475 TTGAGATCAGATGTTATGTTACTTCG 57.366 34.615 0.00 0.00 0.00 3.79
2328 2560 0.596600 GTTCGACGACACCTTCAGCA 60.597 55.000 0.00 0.00 0.00 4.41
2329 2561 1.282930 GGTTCGACGACACCTTCAGC 61.283 60.000 16.89 0.61 0.00 4.26
2397 2629 0.179000 ACTTCCGATCACCAGATGGC 59.821 55.000 0.00 0.00 39.32 4.40
2486 2718 3.186409 CAGTAACATCTCGTTTGTGTGGG 59.814 47.826 0.00 0.00 39.14 4.61
2488 2720 3.247411 TGCAGTAACATCTCGTTTGTGTG 59.753 43.478 0.00 0.00 39.14 3.82
2490 2722 4.668576 ATGCAGTAACATCTCGTTTGTG 57.331 40.909 0.00 0.00 39.14 3.33
2496 2728 7.535599 CAGTGTACTATATGCAGTAACATCTCG 59.464 40.741 0.00 0.00 32.92 4.04
2497 2729 8.353684 ACAGTGTACTATATGCAGTAACATCTC 58.646 37.037 0.00 0.00 32.92 2.75
2516 2748 8.598916 TCCTTTACCATCAAAATCTACAGTGTA 58.401 33.333 2.36 2.36 0.00 2.90
2535 2767 4.202121 TGTGACAGACTGACAGTCCTTTAC 60.202 45.833 28.08 21.37 46.18 2.01
2543 2775 2.487934 CCCTTTGTGACAGACTGACAG 58.512 52.381 10.08 0.00 0.00 3.51
2544 2776 1.475034 GCCCTTTGTGACAGACTGACA 60.475 52.381 10.08 6.48 0.00 3.58
2545 2777 1.230324 GCCCTTTGTGACAGACTGAC 58.770 55.000 10.08 3.32 0.00 3.51
2546 2778 0.836606 TGCCCTTTGTGACAGACTGA 59.163 50.000 10.08 0.00 0.00 3.41
2547 2779 1.679139 TTGCCCTTTGTGACAGACTG 58.321 50.000 0.00 0.00 0.00 3.51
2548 2780 2.664402 ATTGCCCTTTGTGACAGACT 57.336 45.000 0.00 0.00 0.00 3.24
2549 2781 6.699575 AATATATTGCCCTTTGTGACAGAC 57.300 37.500 0.00 0.00 0.00 3.51
2550 2782 6.096705 CCAAATATATTGCCCTTTGTGACAGA 59.903 38.462 0.00 0.00 0.00 3.41
2557 2789 8.299570 GTGACTATCCAAATATATTGCCCTTTG 58.700 37.037 0.00 0.00 0.00 2.77
2573 2805 6.439375 TCTTAAGCTAGTTTGGTGACTATCCA 59.561 38.462 1.54 0.00 32.07 3.41
2576 2808 7.719871 TCTCTTAAGCTAGTTTGGTGACTAT 57.280 36.000 1.54 0.00 32.07 2.12
2616 2848 4.320608 AAACCAACACAACCATAAGCTG 57.679 40.909 0.00 0.00 0.00 4.24
2618 2850 5.189659 TGTAAACCAACACAACCATAAGC 57.810 39.130 0.00 0.00 0.00 3.09
2657 2892 6.254281 TCCTTTAGCTGAAATTGTTAGCAC 57.746 37.500 0.00 0.00 39.84 4.40
2676 2911 5.428131 ACCTGCTATTCTTCTCTTCATCCTT 59.572 40.000 0.00 0.00 0.00 3.36
2708 2943 6.942005 CCCAATGCTGTATATTGTCTCCATTA 59.058 38.462 0.00 0.00 34.51 1.90
2729 2964 4.265856 TCTCCTCTATCTAAGCACCCAA 57.734 45.455 0.00 0.00 0.00 4.12
2730 2965 3.973472 TCTCCTCTATCTAAGCACCCA 57.027 47.619 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.