Multiple sequence alignment - TraesCS5D01G297400

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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 TraesCS5D01G297400 chr5D 100.000 2619 0 0 1 2619 394191619 394189001 0.000000e+00 4837.0
1 TraesCS5D01G297400 chr5D 79.043 606 60 28 1111 1692 394548800 394548238 1.150000e-93 353.0
2 TraesCS5D01G297400 chr5D 79.043 606 60 28 1111 1692 394550813 394550251 1.150000e-93 353.0
3 TraesCS5D01G297400 chr5D 85.032 314 29 6 24 327 261281656 261281351 1.180000e-78 303.0
4 TraesCS5D01G297400 chr5D 85.032 314 29 11 24 326 520897108 520896802 1.180000e-78 303.0
5 TraesCS5D01G297400 chr5D 85.185 108 11 3 848 954 394281123 394281020 3.560000e-19 106.0
6 TraesCS5D01G297400 chr5D 89.157 83 9 0 869 951 394559713 394559631 1.280000e-18 104.0
7 TraesCS5D01G297400 chr5D 89.157 83 9 0 869 951 394563128 394563046 1.280000e-18 104.0
8 TraesCS5D01G297400 chr5D 88.679 53 4 1 2537 2587 394279345 394279293 2.180000e-06 63.9
9 TraesCS5D01G297400 chr5A 84.142 2144 147 74 389 2440 496537170 496535128 0.000000e+00 1897.0
10 TraesCS5D01G297400 chr5A 86.047 903 57 26 749 1626 496175850 496174992 0.000000e+00 905.0
11 TraesCS5D01G297400 chr5A 79.575 612 69 25 1110 1697 496204805 496204226 1.140000e-103 387.0
12 TraesCS5D01G297400 chr5A 89.362 282 15 6 383 663 496176788 496176521 8.980000e-90 340.0
13 TraesCS5D01G297400 chr5A 94.152 171 4 3 2446 2613 496533661 496533494 3.340000e-64 255.0
14 TraesCS5D01G297400 chr5A 86.124 209 14 8 2423 2616 496174204 496173996 7.340000e-51 211.0
15 TraesCS5D01G297400 chr5A 89.286 84 7 2 869 951 496566638 496566556 1.280000e-18 104.0
16 TraesCS5D01G297400 chr5A 94.737 57 3 0 326 382 496177131 496177075 3.590000e-14 89.8
17 TraesCS5D01G297400 chr5B 85.069 2036 102 69 668 2613 474056799 474054876 0.000000e+00 1890.0
18 TraesCS5D01G297400 chr5B 80.414 531 44 25 1111 1607 474279006 474278502 1.490000e-92 350.0
19 TraesCS5D01G297400 chr5B 81.794 379 40 11 1113 1489 474453437 474453086 9.170000e-75 291.0
20 TraesCS5D01G297400 chr5B 97.794 136 3 0 450 585 474056987 474056852 4.360000e-58 235.0
21 TraesCS5D01G297400 chr5B 86.364 110 11 1 847 952 474279253 474279144 1.650000e-22 117.0
22 TraesCS5D01G297400 chr5B 96.667 60 2 0 325 384 474057169 474057110 1.660000e-17 100.0
23 TraesCS5D01G297400 chrUn 79.043 606 60 28 1111 1692 332176342 332175780 1.150000e-93 353.0
24 TraesCS5D01G297400 chrUn 84.639 319 28 9 24 330 83456282 83456591 5.480000e-77 298.0
25 TraesCS5D01G297400 chrUn 89.157 83 9 0 869 951 211147308 211147226 1.280000e-18 104.0
26 TraesCS5D01G297400 chrUn 89.157 83 7 2 869 950 332176560 332176479 4.610000e-18 102.0
27 TraesCS5D01G297400 chr6D 85.443 316 28 5 23 327 65276527 65276835 1.960000e-81 313.0
28 TraesCS5D01G297400 chr6D 84.179 335 31 10 24 347 131624674 131624351 3.270000e-79 305.0
29 TraesCS5D01G297400 chr6D 83.699 319 31 11 21 327 401772978 401773287 5.520000e-72 281.0
30 TraesCS5D01G297400 chr2D 85.350 314 29 5 24 327 42052870 42053176 2.530000e-80 309.0
31 TraesCS5D01G297400 chr2D 83.386 319 32 11 21 327 178401439 178401130 2.570000e-70 276.0
32 TraesCS5D01G297400 chr2B 85.161 310 33 9 24 327 14746457 14746759 3.270000e-79 305.0
33 TraesCS5D01G297400 chr2B 84.444 315 32 6 24 328 637570500 637570193 7.090000e-76 294.0
34 TraesCS5D01G297400 chr7D 84.520 323 32 9 21 332 637091220 637091535 1.180000e-78 303.0
35 TraesCS5D01G297400 chr7D 81.902 326 40 9 16 330 630765851 630765534 9.300000e-65 257.0
36 TraesCS5D01G297400 chr7A 84.858 317 31 8 24 330 700395500 700395191 1.180000e-78 303.0
37 TraesCS5D01G297400 chr3D 84.277 318 30 11 21 327 364434339 364434647 2.550000e-75 292.0
38 TraesCS5D01G297400 chr4B 83.333 318 37 8 19 327 460789260 460789570 1.980000e-71 279.0
39 TraesCS5D01G297400 chr4B 83.333 78 10 1 1565 1639 540726071 540725994 4.680000e-08 69.4
40 TraesCS5D01G297400 chr1A 82.143 336 41 10 3 327 336012062 336012389 1.190000e-68 270.0
41 TraesCS5D01G297400 chr1A 81.306 337 43 9 20 343 446650629 446650958 3.340000e-64 255.0
42 TraesCS5D01G297400 chr4D 82.759 319 34 11 21 327 236894714 236894405 5.560000e-67 265.0
43 TraesCS5D01G297400 chr4D 83.333 78 10 1 1565 1639 437818480 437818403 4.680000e-08 69.4
44 TraesCS5D01G297400 chr4A 90.566 53 5 0 1562 1614 30287265 30287317 1.300000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G297400 chr5D 394189001 394191619 2618 True 4837.000000 4837 100.000000 1 2619 1 chr5D.!!$R2 2618
1 TraesCS5D01G297400 chr5D 394548238 394550813 2575 True 353.000000 353 79.043000 1111 1692 2 chr5D.!!$R5 581
2 TraesCS5D01G297400 chr5A 496533494 496537170 3676 True 1076.000000 1897 89.147000 389 2613 2 chr5A.!!$R4 2224
3 TraesCS5D01G297400 chr5A 496204226 496204805 579 True 387.000000 387 79.575000 1110 1697 1 chr5A.!!$R1 587
4 TraesCS5D01G297400 chr5A 496173996 496177131 3135 True 386.450000 905 89.067500 326 2616 4 chr5A.!!$R3 2290
5 TraesCS5D01G297400 chr5B 474054876 474057169 2293 True 741.666667 1890 93.176667 325 2613 3 chr5B.!!$R2 2288
6 TraesCS5D01G297400 chr5B 474278502 474279253 751 True 233.500000 350 83.389000 847 1607 2 chr5B.!!$R3 760
7 TraesCS5D01G297400 chrUn 332175780 332176560 780 True 227.500000 353 84.100000 869 1692 2 chrUn.!!$R2 823

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
776 1661 0.319211 CTTCAACGCTACACACCGGA 60.319 55.0 9.46 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 4651 0.948623 TGATGAACACGAACGCAGGG 60.949 55.0 0.0 0.0 0.0 4.45 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
26 27 9.750783 TTTAGTGAGAGTAAACATCCTAGTACT 57.249 33.333 0.00 0.00 0.00 2.73
27 28 7.868906 AGTGAGAGTAAACATCCTAGTACTC 57.131 40.000 0.00 7.53 41.77 2.59
28 29 6.829811 AGTGAGAGTAAACATCCTAGTACTCC 59.170 42.308 0.00 5.50 42.20 3.85
29 30 6.039605 GTGAGAGTAAACATCCTAGTACTCCC 59.960 46.154 0.00 2.72 42.20 4.30
30 31 6.068971 TGAGAGTAAACATCCTAGTACTCCCT 60.069 42.308 0.00 0.00 42.20 4.20
31 32 6.367161 AGAGTAAACATCCTAGTACTCCCTC 58.633 44.000 0.00 0.00 42.20 4.30
32 33 5.456779 AGTAAACATCCTAGTACTCCCTCC 58.543 45.833 0.00 0.00 0.00 4.30
33 34 4.348020 AAACATCCTAGTACTCCCTCCA 57.652 45.455 0.00 0.00 0.00 3.86
34 35 4.561254 AACATCCTAGTACTCCCTCCAT 57.439 45.455 0.00 0.00 0.00 3.41
35 36 4.561254 ACATCCTAGTACTCCCTCCATT 57.439 45.455 0.00 0.00 0.00 3.16
36 37 4.484912 ACATCCTAGTACTCCCTCCATTC 58.515 47.826 0.00 0.00 0.00 2.67
37 38 3.614568 TCCTAGTACTCCCTCCATTCC 57.385 52.381 0.00 0.00 0.00 3.01
38 39 2.179424 TCCTAGTACTCCCTCCATTCCC 59.821 54.545 0.00 0.00 0.00 3.97
39 40 2.180308 CCTAGTACTCCCTCCATTCCCT 59.820 54.545 0.00 0.00 0.00 4.20
40 41 2.972153 AGTACTCCCTCCATTCCCTT 57.028 50.000 0.00 0.00 0.00 3.95
41 42 4.140758 CCTAGTACTCCCTCCATTCCCTTA 60.141 50.000 0.00 0.00 0.00 2.69
42 43 4.578149 AGTACTCCCTCCATTCCCTTAT 57.422 45.455 0.00 0.00 0.00 1.73
43 44 5.698369 AGTACTCCCTCCATTCCCTTATA 57.302 43.478 0.00 0.00 0.00 0.98
44 45 5.404395 AGTACTCCCTCCATTCCCTTATAC 58.596 45.833 0.00 0.00 0.00 1.47
45 46 4.295905 ACTCCCTCCATTCCCTTATACA 57.704 45.455 0.00 0.00 0.00 2.29
46 47 4.641868 ACTCCCTCCATTCCCTTATACAA 58.358 43.478 0.00 0.00 0.00 2.41
47 48 4.660771 ACTCCCTCCATTCCCTTATACAAG 59.339 45.833 0.00 0.00 0.00 3.16
69 70 9.819267 ACAAGGCTACTATGAAAAATACTCTAC 57.181 33.333 0.00 0.00 0.00 2.59
70 71 9.817809 CAAGGCTACTATGAAAAATACTCTACA 57.182 33.333 0.00 0.00 0.00 2.74
73 74 9.262358 GGCTACTATGAAAAATACTCTACAAGG 57.738 37.037 0.00 0.00 0.00 3.61
74 75 8.766151 GCTACTATGAAAAATACTCTACAAGGC 58.234 37.037 0.00 0.00 0.00 4.35
89 90 8.136165 ACTCTACAAGGCTAATAACAGTAATCG 58.864 37.037 0.00 0.00 0.00 3.34
90 91 8.229253 TCTACAAGGCTAATAACAGTAATCGA 57.771 34.615 0.00 0.00 0.00 3.59
91 92 8.350722 TCTACAAGGCTAATAACAGTAATCGAG 58.649 37.037 0.00 0.00 0.00 4.04
92 93 6.281405 ACAAGGCTAATAACAGTAATCGAGG 58.719 40.000 0.00 0.00 0.00 4.63
93 94 6.127140 ACAAGGCTAATAACAGTAATCGAGGT 60.127 38.462 0.00 0.00 0.00 3.85
94 95 7.069085 ACAAGGCTAATAACAGTAATCGAGGTA 59.931 37.037 0.00 0.00 0.00 3.08
95 96 7.592885 AGGCTAATAACAGTAATCGAGGTAA 57.407 36.000 0.00 0.00 0.00 2.85
96 97 8.015185 AGGCTAATAACAGTAATCGAGGTAAA 57.985 34.615 0.00 0.00 0.00 2.01
97 98 8.480501 AGGCTAATAACAGTAATCGAGGTAAAA 58.519 33.333 0.00 0.00 0.00 1.52
98 99 9.269453 GGCTAATAACAGTAATCGAGGTAAAAT 57.731 33.333 0.00 0.00 0.00 1.82
122 123 9.722056 AATTTAATGATGTTTTCTCGTGATAGC 57.278 29.630 0.00 0.00 0.00 2.97
123 124 7.841915 TTAATGATGTTTTCTCGTGATAGCA 57.158 32.000 0.00 0.00 0.00 3.49
124 125 6.741992 AATGATGTTTTCTCGTGATAGCAA 57.258 33.333 0.00 0.00 0.00 3.91
125 126 5.530519 TGATGTTTTCTCGTGATAGCAAC 57.469 39.130 0.00 0.00 0.00 4.17
126 127 5.237815 TGATGTTTTCTCGTGATAGCAACT 58.762 37.500 0.00 0.00 0.00 3.16
127 128 5.700832 TGATGTTTTCTCGTGATAGCAACTT 59.299 36.000 0.00 0.00 0.00 2.66
128 129 5.342806 TGTTTTCTCGTGATAGCAACTTG 57.657 39.130 0.00 0.00 0.00 3.16
129 130 4.814234 TGTTTTCTCGTGATAGCAACTTGT 59.186 37.500 0.00 0.00 0.00 3.16
130 131 5.295787 TGTTTTCTCGTGATAGCAACTTGTT 59.704 36.000 0.00 0.00 0.00 2.83
131 132 6.183360 TGTTTTCTCGTGATAGCAACTTGTTT 60.183 34.615 0.00 0.00 0.00 2.83
132 133 7.011576 TGTTTTCTCGTGATAGCAACTTGTTTA 59.988 33.333 0.00 0.00 0.00 2.01
133 134 7.485418 TTTCTCGTGATAGCAACTTGTTTAA 57.515 32.000 0.00 0.00 0.00 1.52
134 135 7.667043 TTCTCGTGATAGCAACTTGTTTAAT 57.333 32.000 0.00 0.00 0.00 1.40
135 136 8.766000 TTCTCGTGATAGCAACTTGTTTAATA 57.234 30.769 0.00 0.00 0.00 0.98
136 137 8.181487 TCTCGTGATAGCAACTTGTTTAATAC 57.819 34.615 0.00 0.00 0.00 1.89
137 138 8.033038 TCTCGTGATAGCAACTTGTTTAATACT 58.967 33.333 0.00 0.00 0.00 2.12
138 139 8.542497 TCGTGATAGCAACTTGTTTAATACTT 57.458 30.769 0.00 0.00 0.00 2.24
139 140 8.440059 TCGTGATAGCAACTTGTTTAATACTTG 58.560 33.333 0.00 0.00 0.00 3.16
140 141 7.216317 CGTGATAGCAACTTGTTTAATACTTGC 59.784 37.037 0.00 0.00 35.33 4.01
141 142 8.020819 GTGATAGCAACTTGTTTAATACTTGCA 58.979 33.333 0.00 0.00 37.14 4.08
142 143 8.739039 TGATAGCAACTTGTTTAATACTTGCAT 58.261 29.630 0.00 0.00 37.14 3.96
143 144 8.915871 ATAGCAACTTGTTTAATACTTGCATG 57.084 30.769 0.00 0.00 37.14 4.06
144 145 6.748132 AGCAACTTGTTTAATACTTGCATGT 58.252 32.000 10.40 10.40 37.14 3.21
145 146 7.881142 AGCAACTTGTTTAATACTTGCATGTA 58.119 30.769 14.16 14.16 37.14 2.29
146 147 8.522830 AGCAACTTGTTTAATACTTGCATGTAT 58.477 29.630 17.17 17.17 37.14 2.29
147 148 8.586273 GCAACTTGTTTAATACTTGCATGTATG 58.414 33.333 21.97 12.19 35.23 2.39
148 149 9.624697 CAACTTGTTTAATACTTGCATGTATGT 57.375 29.630 21.97 15.24 33.85 2.29
153 154 9.660180 TGTTTAATACTTGCATGTATGTAGTCA 57.340 29.630 21.97 15.32 33.85 3.41
173 174 6.663944 GTCATAATGACCTTGTACCACTTC 57.336 41.667 0.00 0.00 41.37 3.01
174 175 5.585047 GTCATAATGACCTTGTACCACTTCC 59.415 44.000 0.00 0.00 41.37 3.46
175 176 5.487488 TCATAATGACCTTGTACCACTTCCT 59.513 40.000 0.00 0.00 0.00 3.36
176 177 4.724279 AATGACCTTGTACCACTTCCTT 57.276 40.909 0.00 0.00 0.00 3.36
177 178 3.764237 TGACCTTGTACCACTTCCTTC 57.236 47.619 0.00 0.00 0.00 3.46
178 179 3.314693 TGACCTTGTACCACTTCCTTCT 58.685 45.455 0.00 0.00 0.00 2.85
179 180 3.714798 TGACCTTGTACCACTTCCTTCTT 59.285 43.478 0.00 0.00 0.00 2.52
180 181 4.903049 TGACCTTGTACCACTTCCTTCTTA 59.097 41.667 0.00 0.00 0.00 2.10
181 182 5.221581 TGACCTTGTACCACTTCCTTCTTAC 60.222 44.000 0.00 0.00 0.00 2.34
182 183 4.906060 ACCTTGTACCACTTCCTTCTTACT 59.094 41.667 0.00 0.00 0.00 2.24
183 184 5.011840 ACCTTGTACCACTTCCTTCTTACTC 59.988 44.000 0.00 0.00 0.00 2.59
184 185 5.479124 TTGTACCACTTCCTTCTTACTCC 57.521 43.478 0.00 0.00 0.00 3.85
185 186 4.748701 TGTACCACTTCCTTCTTACTCCT 58.251 43.478 0.00 0.00 0.00 3.69
186 187 5.895807 TGTACCACTTCCTTCTTACTCCTA 58.104 41.667 0.00 0.00 0.00 2.94
187 188 6.500336 TGTACCACTTCCTTCTTACTCCTAT 58.500 40.000 0.00 0.00 0.00 2.57
188 189 6.958192 TGTACCACTTCCTTCTTACTCCTATT 59.042 38.462 0.00 0.00 0.00 1.73
189 190 6.954352 ACCACTTCCTTCTTACTCCTATTT 57.046 37.500 0.00 0.00 0.00 1.40
190 191 6.948589 ACCACTTCCTTCTTACTCCTATTTC 58.051 40.000 0.00 0.00 0.00 2.17
191 192 6.731448 ACCACTTCCTTCTTACTCCTATTTCT 59.269 38.462 0.00 0.00 0.00 2.52
192 193 7.237887 ACCACTTCCTTCTTACTCCTATTTCTT 59.762 37.037 0.00 0.00 0.00 2.52
193 194 8.103935 CCACTTCCTTCTTACTCCTATTTCTTT 58.896 37.037 0.00 0.00 0.00 2.52
194 195 9.157104 CACTTCCTTCTTACTCCTATTTCTTTC 57.843 37.037 0.00 0.00 0.00 2.62
195 196 9.106977 ACTTCCTTCTTACTCCTATTTCTTTCT 57.893 33.333 0.00 0.00 0.00 2.52
196 197 9.952030 CTTCCTTCTTACTCCTATTTCTTTCTT 57.048 33.333 0.00 0.00 0.00 2.52
197 198 9.726438 TTCCTTCTTACTCCTATTTCTTTCTTG 57.274 33.333 0.00 0.00 0.00 3.02
198 199 7.824779 TCCTTCTTACTCCTATTTCTTTCTTGC 59.175 37.037 0.00 0.00 0.00 4.01
199 200 7.607991 CCTTCTTACTCCTATTTCTTTCTTGCA 59.392 37.037 0.00 0.00 0.00 4.08
200 201 9.171877 CTTCTTACTCCTATTTCTTTCTTGCAT 57.828 33.333 0.00 0.00 0.00 3.96
201 202 8.498054 TCTTACTCCTATTTCTTTCTTGCATG 57.502 34.615 0.00 0.00 0.00 4.06
202 203 5.573337 ACTCCTATTTCTTTCTTGCATGC 57.427 39.130 11.82 11.82 0.00 4.06
203 204 5.012239 ACTCCTATTTCTTTCTTGCATGCA 58.988 37.500 18.46 18.46 0.00 3.96
204 205 5.655532 ACTCCTATTTCTTTCTTGCATGCAT 59.344 36.000 23.37 5.47 0.00 3.96
205 206 5.898174 TCCTATTTCTTTCTTGCATGCATG 58.102 37.500 23.37 23.63 0.00 4.06
214 215 3.663176 GCATGCATGCGGGCGTAT 61.663 61.111 33.99 0.00 44.67 3.06
215 216 3.033184 CATGCATGCGGGCGTATT 58.967 55.556 14.93 0.00 36.28 1.89
216 217 1.851021 GCATGCATGCGGGCGTATTA 61.851 55.000 33.99 0.00 44.67 0.98
217 218 0.590682 CATGCATGCGGGCGTATTAA 59.409 50.000 14.93 0.00 36.28 1.40
218 219 1.199789 CATGCATGCGGGCGTATTAAT 59.800 47.619 14.93 0.00 36.28 1.40
219 220 2.171341 TGCATGCGGGCGTATTAATA 57.829 45.000 14.09 0.00 36.28 0.98
220 221 2.495084 TGCATGCGGGCGTATTAATAA 58.505 42.857 14.09 0.00 36.28 1.40
221 222 3.078097 TGCATGCGGGCGTATTAATAAT 58.922 40.909 14.09 0.00 36.28 1.28
222 223 3.126171 TGCATGCGGGCGTATTAATAATC 59.874 43.478 14.09 0.00 36.28 1.75
223 224 3.486875 GCATGCGGGCGTATTAATAATCC 60.487 47.826 0.00 1.63 0.00 3.01
224 225 2.702261 TGCGGGCGTATTAATAATCCC 58.298 47.619 17.45 17.45 0.00 3.85
227 228 3.339253 GGGCGTATTAATAATCCCGGT 57.661 47.619 14.24 0.00 0.00 5.28
228 229 3.678289 GGGCGTATTAATAATCCCGGTT 58.322 45.455 14.24 0.00 0.00 4.44
229 230 4.831107 GGGCGTATTAATAATCCCGGTTA 58.169 43.478 14.24 0.00 0.00 2.85
230 231 5.244755 GGGCGTATTAATAATCCCGGTTAA 58.755 41.667 14.24 0.00 0.00 2.01
231 232 5.122239 GGGCGTATTAATAATCCCGGTTAAC 59.878 44.000 14.24 0.00 0.00 2.01
232 233 5.700373 GGCGTATTAATAATCCCGGTTAACA 59.300 40.000 8.10 0.00 0.00 2.41
233 234 6.204495 GGCGTATTAATAATCCCGGTTAACAA 59.796 38.462 8.10 0.00 0.00 2.83
234 235 7.255070 GGCGTATTAATAATCCCGGTTAACAAA 60.255 37.037 8.10 0.00 0.00 2.83
235 236 8.127954 GCGTATTAATAATCCCGGTTAACAAAA 58.872 33.333 8.10 0.00 0.00 2.44
242 243 9.833917 AATAATCCCGGTTAACAAAAAGAAAAA 57.166 25.926 8.10 0.00 0.00 1.94
263 264 7.748691 AAAAATTAGCTTGCAAAATGGTCAT 57.251 28.000 0.00 0.00 0.00 3.06
264 265 7.748691 AAAATTAGCTTGCAAAATGGTCATT 57.251 28.000 0.00 0.00 0.00 2.57
265 266 8.845413 AAAATTAGCTTGCAAAATGGTCATTA 57.155 26.923 0.00 0.00 0.00 1.90
266 267 8.845413 AAATTAGCTTGCAAAATGGTCATTAA 57.155 26.923 0.00 0.00 0.00 1.40
267 268 8.845413 AATTAGCTTGCAAAATGGTCATTAAA 57.155 26.923 0.00 0.00 0.00 1.52
268 269 9.452287 AATTAGCTTGCAAAATGGTCATTAAAT 57.548 25.926 0.00 0.00 0.00 1.40
269 270 8.845413 TTAGCTTGCAAAATGGTCATTAAATT 57.155 26.923 0.00 0.00 0.00 1.82
270 271 7.748691 AGCTTGCAAAATGGTCATTAAATTT 57.251 28.000 0.00 0.00 0.00 1.82
271 272 8.168790 AGCTTGCAAAATGGTCATTAAATTTT 57.831 26.923 0.00 0.00 34.63 1.82
272 273 9.282569 AGCTTGCAAAATGGTCATTAAATTTTA 57.717 25.926 0.00 0.00 33.02 1.52
273 274 9.328721 GCTTGCAAAATGGTCATTAAATTTTAC 57.671 29.630 0.00 0.00 33.02 2.01
274 275 9.824534 CTTGCAAAATGGTCATTAAATTTTACC 57.175 29.630 0.00 0.63 33.02 2.85
275 276 9.566432 TTGCAAAATGGTCATTAAATTTTACCT 57.434 25.926 0.00 0.00 33.02 3.08
276 277 9.566432 TGCAAAATGGTCATTAAATTTTACCTT 57.434 25.926 0.00 0.00 33.02 3.50
301 302 9.632807 TTAATACATGTAATTTGAGTTTGTGGC 57.367 29.630 10.14 0.00 0.00 5.01
302 303 4.881920 ACATGTAATTTGAGTTTGTGGCC 58.118 39.130 0.00 0.00 0.00 5.36
303 304 4.588528 ACATGTAATTTGAGTTTGTGGCCT 59.411 37.500 3.32 0.00 0.00 5.19
304 305 5.070313 ACATGTAATTTGAGTTTGTGGCCTT 59.930 36.000 3.32 0.00 0.00 4.35
305 306 4.942852 TGTAATTTGAGTTTGTGGCCTTG 58.057 39.130 3.32 0.00 0.00 3.61
306 307 4.404073 TGTAATTTGAGTTTGTGGCCTTGT 59.596 37.500 3.32 0.00 0.00 3.16
307 308 5.594725 TGTAATTTGAGTTTGTGGCCTTGTA 59.405 36.000 3.32 0.00 0.00 2.41
308 309 5.806654 AATTTGAGTTTGTGGCCTTGTAT 57.193 34.783 3.32 0.00 0.00 2.29
309 310 6.909550 AATTTGAGTTTGTGGCCTTGTATA 57.090 33.333 3.32 0.00 0.00 1.47
310 311 6.909550 ATTTGAGTTTGTGGCCTTGTATAA 57.090 33.333 3.32 0.00 0.00 0.98
311 312 6.716934 TTTGAGTTTGTGGCCTTGTATAAA 57.283 33.333 3.32 0.00 0.00 1.40
312 313 5.957842 TGAGTTTGTGGCCTTGTATAAAG 57.042 39.130 3.32 0.00 0.00 1.85
313 314 4.764823 TGAGTTTGTGGCCTTGTATAAAGG 59.235 41.667 3.32 0.00 40.39 3.11
314 315 4.993028 AGTTTGTGGCCTTGTATAAAGGA 58.007 39.130 3.32 0.00 39.81 3.36
315 316 5.390387 AGTTTGTGGCCTTGTATAAAGGAA 58.610 37.500 3.32 0.00 39.81 3.36
316 317 6.016555 AGTTTGTGGCCTTGTATAAAGGAAT 58.983 36.000 3.32 0.00 39.81 3.01
317 318 5.913137 TTGTGGCCTTGTATAAAGGAATG 57.087 39.130 3.32 0.00 39.81 2.67
318 319 4.277476 TGTGGCCTTGTATAAAGGAATGG 58.723 43.478 3.32 0.00 39.81 3.16
319 320 4.017958 TGTGGCCTTGTATAAAGGAATGGA 60.018 41.667 3.32 0.00 39.81 3.41
320 321 4.580580 GTGGCCTTGTATAAAGGAATGGAG 59.419 45.833 3.32 0.00 39.81 3.86
321 322 4.476846 TGGCCTTGTATAAAGGAATGGAGA 59.523 41.667 3.32 0.00 39.81 3.71
322 323 5.066593 GGCCTTGTATAAAGGAATGGAGAG 58.933 45.833 8.31 0.00 39.81 3.20
323 324 5.163195 GGCCTTGTATAAAGGAATGGAGAGA 60.163 44.000 8.31 0.00 39.81 3.10
392 679 9.590451 TTACCATGGTTTATAGAGTAGAAAACG 57.410 33.333 25.38 0.00 33.61 3.60
448 743 1.639298 GGACATGCCAGCTTCACGAC 61.639 60.000 0.00 0.00 36.34 4.34
588 887 3.333189 CCGATGGATGCGTCGCAG 61.333 66.667 25.78 10.37 43.65 5.18
589 888 2.583319 CGATGGATGCGTCGCAGT 60.583 61.111 25.78 13.43 43.65 4.40
591 890 0.869880 CGATGGATGCGTCGCAGTAA 60.870 55.000 25.78 13.05 43.65 2.24
592 891 1.286501 GATGGATGCGTCGCAGTAAA 58.713 50.000 25.78 11.23 43.65 2.01
593 892 1.867233 GATGGATGCGTCGCAGTAAAT 59.133 47.619 25.78 15.37 43.65 1.40
594 893 1.006086 TGGATGCGTCGCAGTAAATG 58.994 50.000 25.78 0.00 43.65 2.32
609 908 3.629491 AATGCTCGCGCGTCAAACG 62.629 57.895 30.98 12.86 45.88 3.60
619 919 2.430367 GTCAAACGAGGGGCCACT 59.570 61.111 7.63 7.63 0.00 4.00
666 966 4.827087 GCTGGCTAGCTCGCTGCA 62.827 66.667 15.78 1.56 46.57 4.41
774 1659 1.491563 GCTTCAACGCTACACACCG 59.508 57.895 0.00 0.00 0.00 4.94
775 1660 1.897398 GCTTCAACGCTACACACCGG 61.897 60.000 0.00 0.00 0.00 5.28
776 1661 0.319211 CTTCAACGCTACACACCGGA 60.319 55.000 9.46 0.00 0.00 5.14
777 1662 0.598158 TTCAACGCTACACACCGGAC 60.598 55.000 9.46 0.00 0.00 4.79
778 1663 2.025418 CAACGCTACACACCGGACC 61.025 63.158 9.46 0.00 0.00 4.46
806 1691 4.697756 CCGGGCCGCTCTGACAAA 62.698 66.667 23.20 0.00 0.00 2.83
832 1717 1.290324 CGTGGCTAGTGCTGTGAGT 59.710 57.895 0.00 0.00 39.59 3.41
839 1724 2.231478 GCTAGTGCTGTGAGTTACTCCA 59.769 50.000 10.10 6.64 36.03 3.86
903 1792 1.135575 GCTTCCATTCCGTTCTGCTTG 60.136 52.381 0.00 0.00 0.00 4.01
977 1894 3.636679 CTCATTCTGTCTCCCCTGTCTA 58.363 50.000 0.00 0.00 0.00 2.59
995 1912 0.323302 TATGCCGTGCTGAACCAGAA 59.677 50.000 0.00 0.00 32.44 3.02
996 1913 1.237285 ATGCCGTGCTGAACCAGAAC 61.237 55.000 0.00 0.00 36.71 3.01
997 1914 2.617274 GCCGTGCTGAACCAGAACC 61.617 63.158 0.00 0.00 36.72 3.62
998 1915 1.227823 CCGTGCTGAACCAGAACCA 60.228 57.895 0.00 0.00 36.72 3.67
999 1916 1.230635 CCGTGCTGAACCAGAACCAG 61.231 60.000 0.00 0.00 36.72 4.00
1000 1917 0.249868 CGTGCTGAACCAGAACCAGA 60.250 55.000 0.00 0.00 36.72 3.86
1013 1930 2.840651 AGAACCAGATGGAGGTAAGTGG 59.159 50.000 5.72 0.00 38.76 4.00
1039 1956 4.100084 CCACCAGGCGAGCCATCA 62.100 66.667 17.18 0.00 38.92 3.07
1043 1960 1.227380 CCAGGCGAGCCATCAGTAC 60.227 63.158 17.18 0.00 38.92 2.73
1044 1961 1.680522 CCAGGCGAGCCATCAGTACT 61.681 60.000 17.18 0.00 38.92 2.73
1045 1962 0.249238 CAGGCGAGCCATCAGTACTC 60.249 60.000 17.18 0.00 38.92 2.59
1065 1982 1.880027 CCTAGCACAAACCTCACCAAC 59.120 52.381 0.00 0.00 0.00 3.77
1108 2032 4.833938 TCACCATGTACTACACTTGTGGTA 59.166 41.667 10.57 1.73 40.33 3.25
1175 2114 3.120199 TGGAACTACAACTACGACTACGC 60.120 47.826 0.00 0.00 43.96 4.42
1542 4517 1.078918 TCGTGATTGCTGGAGCTGG 60.079 57.895 0.00 0.00 42.66 4.85
1558 4533 2.049156 GGCCGCTCTTTGTTTGGC 60.049 61.111 0.00 0.00 44.98 4.52
1559 4534 2.049156 GCCGCTCTTTGTTTGGCC 60.049 61.111 0.00 0.00 39.83 5.36
1692 4705 5.296151 TGCCCTTTCTCTTGGATATACAG 57.704 43.478 0.00 0.00 0.00 2.74
1704 4717 8.265165 TCTTGGATATACAGTACTGCTATACG 57.735 38.462 22.90 9.10 0.00 3.06
1711 4724 3.626670 ACAGTACTGCTATACGTCTGTCC 59.373 47.826 22.90 0.00 30.43 4.02
1713 4726 3.626670 AGTACTGCTATACGTCTGTCCAC 59.373 47.826 0.00 0.00 0.00 4.02
1731 4744 2.094957 CCACTTCTCTCTCCGAGTGTTC 60.095 54.545 0.00 0.00 40.75 3.18
1766 4779 2.224161 TGGCTTGTGGCAAAATGGTTAC 60.224 45.455 0.00 0.00 46.03 2.50
1768 4781 3.257127 GGCTTGTGGCAAAATGGTTACTA 59.743 43.478 0.00 0.00 44.01 1.82
1832 4848 4.560128 TCTACTCTCTTGTGTGATGTTGC 58.440 43.478 0.00 0.00 0.00 4.17
1834 4850 3.397482 ACTCTCTTGTGTGATGTTGCTC 58.603 45.455 0.00 0.00 0.00 4.26
1884 4912 9.391006 AGTTTCTACTTCTTTTGTGTAATGTGA 57.609 29.630 0.00 0.00 0.00 3.58
1918 4950 1.896220 TGGGTGCAACATCTTGTCTC 58.104 50.000 3.06 0.00 39.98 3.36
1949 4981 5.032863 ACAAACACGTCGATATACAGTAGC 58.967 41.667 0.00 0.00 0.00 3.58
1979 5020 7.736447 ACTATCTGTCAACCTGAAAAGAAAG 57.264 36.000 0.00 0.00 28.92 2.62
1980 5021 7.509546 ACTATCTGTCAACCTGAAAAGAAAGA 58.490 34.615 0.00 0.00 28.92 2.52
1981 5022 6.874288 ATCTGTCAACCTGAAAAGAAAGAG 57.126 37.500 0.00 0.00 28.92 2.85
1982 5023 5.989477 TCTGTCAACCTGAAAAGAAAGAGA 58.011 37.500 0.00 0.00 0.00 3.10
1983 5024 6.595682 TCTGTCAACCTGAAAAGAAAGAGAT 58.404 36.000 0.00 0.00 0.00 2.75
1984 5025 6.708054 TCTGTCAACCTGAAAAGAAAGAGATC 59.292 38.462 0.00 0.00 0.00 2.75
1985 5026 6.595682 TGTCAACCTGAAAAGAAAGAGATCT 58.404 36.000 0.00 0.00 0.00 2.75
1986 5027 6.708054 TGTCAACCTGAAAAGAAAGAGATCTC 59.292 38.462 15.29 15.29 0.00 2.75
1987 5028 5.928839 TCAACCTGAAAAGAAAGAGATCTCG 59.071 40.000 16.97 1.02 34.09 4.04
1988 5029 5.730296 ACCTGAAAAGAAAGAGATCTCGA 57.270 39.130 16.97 0.00 34.09 4.04
1989 5030 6.102897 ACCTGAAAAGAAAGAGATCTCGAA 57.897 37.500 16.97 0.00 34.09 3.71
1990 5031 6.525629 ACCTGAAAAGAAAGAGATCTCGAAA 58.474 36.000 16.97 0.00 34.09 3.46
1991 5032 6.992715 ACCTGAAAAGAAAGAGATCTCGAAAA 59.007 34.615 16.97 0.00 34.09 2.29
1992 5033 7.172361 ACCTGAAAAGAAAGAGATCTCGAAAAG 59.828 37.037 16.97 6.60 34.09 2.27
1993 5034 7.386299 CCTGAAAAGAAAGAGATCTCGAAAAGA 59.614 37.037 16.97 0.00 38.72 2.52
1994 5035 8.662781 TGAAAAGAAAGAGATCTCGAAAAGAA 57.337 30.769 16.97 0.00 37.61 2.52
1995 5036 9.109393 TGAAAAGAAAGAGATCTCGAAAAGAAA 57.891 29.630 16.97 0.00 37.61 2.52
2013 5054 8.437360 AAAAGAAATCACTTTGGACCAATTTC 57.563 30.769 17.14 17.14 39.57 2.17
2029 5070 0.518636 TTTCTGATGTGCAAGCGAGC 59.481 50.000 0.00 0.00 0.00 5.03
2031 5072 1.017701 TCTGATGTGCAAGCGAGCTG 61.018 55.000 0.00 0.00 34.99 4.24
2054 5105 7.666063 TGGTCATCAGAGATTCAGAAAGATA 57.334 36.000 0.00 0.00 0.00 1.98
2056 5107 6.646240 GGTCATCAGAGATTCAGAAAGATAGC 59.354 42.308 0.00 0.00 0.00 2.97
2057 5108 7.208777 GTCATCAGAGATTCAGAAAGATAGCA 58.791 38.462 0.00 0.00 0.00 3.49
2058 5109 7.169645 GTCATCAGAGATTCAGAAAGATAGCAC 59.830 40.741 0.00 0.00 0.00 4.40
2059 5110 5.911752 TCAGAGATTCAGAAAGATAGCACC 58.088 41.667 0.00 0.00 0.00 5.01
2074 5125 5.650266 AGATAGCACCCAATAGATAGACGAG 59.350 44.000 0.00 0.00 0.00 4.18
2181 5371 2.474526 CGCATTGATTCCTGTCGTTGTC 60.475 50.000 0.00 0.00 0.00 3.18
2294 5506 1.743958 TGCCGCAGAGAGAGTAACTAC 59.256 52.381 0.00 0.00 0.00 2.73
2295 5507 2.018515 GCCGCAGAGAGAGTAACTACT 58.981 52.381 0.00 0.00 39.71 2.57
2296 5508 6.262433 CTGCCGCAGAGAGAGTAACTACTC 62.262 54.167 15.74 8.57 42.24 2.59
2330 5542 6.582636 TCGTGTCTTTTCTTGGCATAGATAT 58.417 36.000 0.00 0.00 0.00 1.63
2333 5545 7.412853 GTGTCTTTTCTTGGCATAGATATGTG 58.587 38.462 2.03 0.00 36.11 3.21
2499 7193 5.568825 CGAGTAGTGGAATTTCCCTTCTTGA 60.569 44.000 12.90 0.00 35.03 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.750783 AGTACTAGGATGTTTACTCTCACTAAA 57.249 33.333 0.00 0.00 0.00 1.85
1 2 9.393512 GAGTACTAGGATGTTTACTCTCACTAA 57.606 37.037 0.00 0.00 38.18 2.24
2 3 7.992033 GGAGTACTAGGATGTTTACTCTCACTA 59.008 40.741 12.91 0.00 40.17 2.74
3 4 6.829811 GGAGTACTAGGATGTTTACTCTCACT 59.170 42.308 12.91 0.00 40.17 3.41
4 5 6.039605 GGGAGTACTAGGATGTTTACTCTCAC 59.960 46.154 12.91 0.00 40.44 3.51
5 6 6.068971 AGGGAGTACTAGGATGTTTACTCTCA 60.069 42.308 14.79 0.00 42.34 3.27
6 7 6.367161 AGGGAGTACTAGGATGTTTACTCTC 58.633 44.000 12.91 10.32 40.85 3.20
7 8 6.344232 AGGGAGTACTAGGATGTTTACTCT 57.656 41.667 12.91 0.00 40.17 3.24
8 9 5.535783 GGAGGGAGTACTAGGATGTTTACTC 59.464 48.000 0.00 7.20 39.76 2.59
9 10 5.043582 TGGAGGGAGTACTAGGATGTTTACT 60.044 44.000 0.00 0.00 0.00 2.24
10 11 5.206587 TGGAGGGAGTACTAGGATGTTTAC 58.793 45.833 0.00 0.00 0.00 2.01
11 12 5.476950 TGGAGGGAGTACTAGGATGTTTA 57.523 43.478 0.00 0.00 0.00 2.01
12 13 4.348020 TGGAGGGAGTACTAGGATGTTT 57.652 45.455 0.00 0.00 0.00 2.83
13 14 4.561254 ATGGAGGGAGTACTAGGATGTT 57.439 45.455 0.00 0.00 0.00 2.71
14 15 4.484912 GAATGGAGGGAGTACTAGGATGT 58.515 47.826 0.00 0.00 0.00 3.06
15 16 3.835395 GGAATGGAGGGAGTACTAGGATG 59.165 52.174 0.00 0.00 0.00 3.51
16 17 3.181405 GGGAATGGAGGGAGTACTAGGAT 60.181 52.174 0.00 0.00 0.00 3.24
17 18 2.179424 GGGAATGGAGGGAGTACTAGGA 59.821 54.545 0.00 0.00 0.00 2.94
18 19 2.180308 AGGGAATGGAGGGAGTACTAGG 59.820 54.545 0.00 0.00 0.00 3.02
19 20 3.621682 AGGGAATGGAGGGAGTACTAG 57.378 52.381 0.00 0.00 0.00 2.57
20 21 5.698369 ATAAGGGAATGGAGGGAGTACTA 57.302 43.478 0.00 0.00 0.00 1.82
21 22 2.972153 AAGGGAATGGAGGGAGTACT 57.028 50.000 0.00 0.00 0.00 2.73
22 23 5.152934 TGTATAAGGGAATGGAGGGAGTAC 58.847 45.833 0.00 0.00 0.00 2.73
23 24 5.427857 TGTATAAGGGAATGGAGGGAGTA 57.572 43.478 0.00 0.00 0.00 2.59
24 25 4.295905 TGTATAAGGGAATGGAGGGAGT 57.704 45.455 0.00 0.00 0.00 3.85
25 26 5.234466 CTTGTATAAGGGAATGGAGGGAG 57.766 47.826 0.00 0.00 0.00 4.30
43 44 9.819267 GTAGAGTATTTTTCATAGTAGCCTTGT 57.181 33.333 0.00 0.00 0.00 3.16
44 45 9.817809 TGTAGAGTATTTTTCATAGTAGCCTTG 57.182 33.333 0.00 0.00 0.00 3.61
47 48 9.262358 CCTTGTAGAGTATTTTTCATAGTAGCC 57.738 37.037 0.00 0.00 0.00 3.93
48 49 8.766151 GCCTTGTAGAGTATTTTTCATAGTAGC 58.234 37.037 0.00 0.00 0.00 3.58
63 64 8.136165 CGATTACTGTTATTAGCCTTGTAGAGT 58.864 37.037 0.00 0.00 0.00 3.24
64 65 8.350722 TCGATTACTGTTATTAGCCTTGTAGAG 58.649 37.037 0.00 0.00 0.00 2.43
65 66 8.229253 TCGATTACTGTTATTAGCCTTGTAGA 57.771 34.615 0.00 0.00 0.00 2.59
66 67 7.595502 CCTCGATTACTGTTATTAGCCTTGTAG 59.404 40.741 0.00 0.00 0.00 2.74
67 68 7.069085 ACCTCGATTACTGTTATTAGCCTTGTA 59.931 37.037 0.00 0.00 0.00 2.41
68 69 6.127140 ACCTCGATTACTGTTATTAGCCTTGT 60.127 38.462 0.00 0.00 0.00 3.16
69 70 6.281405 ACCTCGATTACTGTTATTAGCCTTG 58.719 40.000 0.00 0.00 0.00 3.61
70 71 6.481434 ACCTCGATTACTGTTATTAGCCTT 57.519 37.500 0.00 0.00 0.00 4.35
71 72 7.592885 TTACCTCGATTACTGTTATTAGCCT 57.407 36.000 0.00 0.00 0.00 4.58
72 73 8.652810 TTTTACCTCGATTACTGTTATTAGCC 57.347 34.615 0.00 0.00 0.00 3.93
96 97 9.722056 GCTATCACGAGAAAACATCATTAAATT 57.278 29.630 0.00 0.00 0.00 1.82
97 98 8.892723 TGCTATCACGAGAAAACATCATTAAAT 58.107 29.630 0.00 0.00 0.00 1.40
98 99 8.262715 TGCTATCACGAGAAAACATCATTAAA 57.737 30.769 0.00 0.00 0.00 1.52
99 100 7.841915 TGCTATCACGAGAAAACATCATTAA 57.158 32.000 0.00 0.00 0.00 1.40
100 101 7.549134 AGTTGCTATCACGAGAAAACATCATTA 59.451 33.333 0.00 0.00 0.00 1.90
101 102 6.372659 AGTTGCTATCACGAGAAAACATCATT 59.627 34.615 0.00 0.00 0.00 2.57
102 103 5.877012 AGTTGCTATCACGAGAAAACATCAT 59.123 36.000 0.00 0.00 0.00 2.45
103 104 5.237815 AGTTGCTATCACGAGAAAACATCA 58.762 37.500 0.00 0.00 0.00 3.07
104 105 5.786401 AGTTGCTATCACGAGAAAACATC 57.214 39.130 0.00 0.00 0.00 3.06
105 106 5.470098 ACAAGTTGCTATCACGAGAAAACAT 59.530 36.000 1.81 0.00 0.00 2.71
106 107 4.814234 ACAAGTTGCTATCACGAGAAAACA 59.186 37.500 1.81 0.00 0.00 2.83
107 108 5.344207 ACAAGTTGCTATCACGAGAAAAC 57.656 39.130 1.81 0.00 0.00 2.43
108 109 6.371809 AAACAAGTTGCTATCACGAGAAAA 57.628 33.333 1.81 0.00 0.00 2.29
109 110 7.485418 TTAAACAAGTTGCTATCACGAGAAA 57.515 32.000 1.81 0.00 0.00 2.52
110 111 7.667043 ATTAAACAAGTTGCTATCACGAGAA 57.333 32.000 1.81 0.00 0.00 2.87
111 112 8.033038 AGTATTAAACAAGTTGCTATCACGAGA 58.967 33.333 1.81 0.00 0.00 4.04
112 113 8.186178 AGTATTAAACAAGTTGCTATCACGAG 57.814 34.615 1.81 0.00 0.00 4.18
113 114 8.440059 CAAGTATTAAACAAGTTGCTATCACGA 58.560 33.333 1.81 0.00 0.00 4.35
114 115 7.216317 GCAAGTATTAAACAAGTTGCTATCACG 59.784 37.037 15.67 0.00 44.79 4.35
115 116 8.382003 GCAAGTATTAAACAAGTTGCTATCAC 57.618 34.615 15.67 0.00 44.79 3.06
122 123 9.624697 ACATACATGCAAGTATTAAACAAGTTG 57.375 29.630 11.75 0.00 32.56 3.16
127 128 9.660180 TGACTACATACATGCAAGTATTAAACA 57.340 29.630 11.75 6.72 32.56 2.83
134 135 9.476202 GTCATTATGACTACATACATGCAAGTA 57.524 33.333 17.19 3.98 43.73 2.24
135 136 7.442364 GGTCATTATGACTACATACATGCAAGT 59.558 37.037 22.48 0.00 46.19 3.16
136 137 7.658982 AGGTCATTATGACTACATACATGCAAG 59.341 37.037 22.48 0.00 46.19 4.01
137 138 7.508687 AGGTCATTATGACTACATACATGCAA 58.491 34.615 22.48 0.00 46.19 4.08
138 139 7.066307 AGGTCATTATGACTACATACATGCA 57.934 36.000 22.48 0.00 46.19 3.96
139 140 7.442364 ACAAGGTCATTATGACTACATACATGC 59.558 37.037 22.48 4.43 46.19 4.06
140 141 8.893219 ACAAGGTCATTATGACTACATACATG 57.107 34.615 22.48 11.52 46.19 3.21
141 142 9.982651 GTACAAGGTCATTATGACTACATACAT 57.017 33.333 22.48 5.77 46.19 2.29
142 143 8.418662 GGTACAAGGTCATTATGACTACATACA 58.581 37.037 22.48 2.77 46.19 2.29
143 144 8.418662 TGGTACAAGGTCATTATGACTACATAC 58.581 37.037 22.48 18.15 41.07 2.39
144 145 8.418662 GTGGTACAAGGTCATTATGACTACATA 58.581 37.037 22.48 9.66 43.97 2.29
145 146 7.125811 AGTGGTACAAGGTCATTATGACTACAT 59.874 37.037 22.48 10.51 43.97 2.29
146 147 6.439375 AGTGGTACAAGGTCATTATGACTACA 59.561 38.462 22.48 9.97 43.97 2.74
147 148 6.875076 AGTGGTACAAGGTCATTATGACTAC 58.125 40.000 22.48 16.45 43.97 2.73
148 149 7.364408 GGAAGTGGTACAAGGTCATTATGACTA 60.364 40.741 22.48 6.62 43.97 2.59
149 150 6.374417 AAGTGGTACAAGGTCATTATGACT 57.626 37.500 22.48 7.55 43.97 3.41
150 151 5.585047 GGAAGTGGTACAAGGTCATTATGAC 59.415 44.000 16.30 16.30 43.84 3.06
151 152 5.487488 AGGAAGTGGTACAAGGTCATTATGA 59.513 40.000 0.00 0.00 44.16 2.15
152 153 5.745227 AGGAAGTGGTACAAGGTCATTATG 58.255 41.667 0.00 0.00 44.16 1.90
153 154 6.215636 AGAAGGAAGTGGTACAAGGTCATTAT 59.784 38.462 0.00 0.00 44.16 1.28
154 155 5.546499 AGAAGGAAGTGGTACAAGGTCATTA 59.454 40.000 0.00 0.00 44.16 1.90
155 156 4.351111 AGAAGGAAGTGGTACAAGGTCATT 59.649 41.667 0.00 0.00 44.16 2.57
156 157 3.910627 AGAAGGAAGTGGTACAAGGTCAT 59.089 43.478 0.00 0.00 44.16 3.06
157 158 3.314693 AGAAGGAAGTGGTACAAGGTCA 58.685 45.455 0.00 0.00 44.16 4.02
158 159 4.353383 AAGAAGGAAGTGGTACAAGGTC 57.647 45.455 0.00 0.00 44.16 3.85
159 160 4.906060 AGTAAGAAGGAAGTGGTACAAGGT 59.094 41.667 0.00 0.00 44.16 3.50
160 161 5.480205 GAGTAAGAAGGAAGTGGTACAAGG 58.520 45.833 0.00 0.00 44.16 3.61
161 162 5.246429 AGGAGTAAGAAGGAAGTGGTACAAG 59.754 44.000 0.00 0.00 44.16 3.16
162 163 5.152934 AGGAGTAAGAAGGAAGTGGTACAA 58.847 41.667 0.00 0.00 44.16 2.41
163 164 4.748701 AGGAGTAAGAAGGAAGTGGTACA 58.251 43.478 0.00 0.00 0.00 2.90
164 165 7.421087 AATAGGAGTAAGAAGGAAGTGGTAC 57.579 40.000 0.00 0.00 0.00 3.34
165 166 7.899709 AGAAATAGGAGTAAGAAGGAAGTGGTA 59.100 37.037 0.00 0.00 0.00 3.25
166 167 6.731448 AGAAATAGGAGTAAGAAGGAAGTGGT 59.269 38.462 0.00 0.00 0.00 4.16
167 168 7.189079 AGAAATAGGAGTAAGAAGGAAGTGG 57.811 40.000 0.00 0.00 0.00 4.00
168 169 9.157104 GAAAGAAATAGGAGTAAGAAGGAAGTG 57.843 37.037 0.00 0.00 0.00 3.16
169 170 9.106977 AGAAAGAAATAGGAGTAAGAAGGAAGT 57.893 33.333 0.00 0.00 0.00 3.01
170 171 9.952030 AAGAAAGAAATAGGAGTAAGAAGGAAG 57.048 33.333 0.00 0.00 0.00 3.46
171 172 9.726438 CAAGAAAGAAATAGGAGTAAGAAGGAA 57.274 33.333 0.00 0.00 0.00 3.36
172 173 7.824779 GCAAGAAAGAAATAGGAGTAAGAAGGA 59.175 37.037 0.00 0.00 0.00 3.36
173 174 7.607991 TGCAAGAAAGAAATAGGAGTAAGAAGG 59.392 37.037 0.00 0.00 0.00 3.46
174 175 8.553459 TGCAAGAAAGAAATAGGAGTAAGAAG 57.447 34.615 0.00 0.00 0.00 2.85
175 176 8.950210 CATGCAAGAAAGAAATAGGAGTAAGAA 58.050 33.333 0.00 0.00 0.00 2.52
176 177 7.066284 GCATGCAAGAAAGAAATAGGAGTAAGA 59.934 37.037 14.21 0.00 0.00 2.10
177 178 7.148188 TGCATGCAAGAAAGAAATAGGAGTAAG 60.148 37.037 20.30 0.00 0.00 2.34
178 179 6.658816 TGCATGCAAGAAAGAAATAGGAGTAA 59.341 34.615 20.30 0.00 0.00 2.24
179 180 6.179756 TGCATGCAAGAAAGAAATAGGAGTA 58.820 36.000 20.30 0.00 0.00 2.59
180 181 5.012239 TGCATGCAAGAAAGAAATAGGAGT 58.988 37.500 20.30 0.00 0.00 3.85
181 182 5.571784 TGCATGCAAGAAAGAAATAGGAG 57.428 39.130 20.30 0.00 0.00 3.69
182 183 5.898174 CATGCATGCAAGAAAGAAATAGGA 58.102 37.500 26.68 0.00 0.00 2.94
198 199 0.590682 TTAATACGCCCGCATGCATG 59.409 50.000 22.70 22.70 0.00 4.06
199 200 1.533625 ATTAATACGCCCGCATGCAT 58.466 45.000 19.57 0.00 0.00 3.96
200 201 2.171341 TATTAATACGCCCGCATGCA 57.829 45.000 19.57 0.00 0.00 3.96
201 202 3.486875 GGATTATTAATACGCCCGCATGC 60.487 47.826 7.91 7.91 0.00 4.06
202 203 3.064820 GGGATTATTAATACGCCCGCATG 59.935 47.826 13.42 0.00 0.00 4.06
203 204 3.275999 GGGATTATTAATACGCCCGCAT 58.724 45.455 13.42 0.00 0.00 4.73
204 205 2.702261 GGGATTATTAATACGCCCGCA 58.298 47.619 13.42 0.00 0.00 5.69
207 208 3.339253 ACCGGGATTATTAATACGCCC 57.661 47.619 16.77 16.77 0.00 6.13
208 209 5.700373 TGTTAACCGGGATTATTAATACGCC 59.300 40.000 6.32 0.00 0.00 5.68
209 210 6.783892 TGTTAACCGGGATTATTAATACGC 57.216 37.500 6.32 0.00 0.00 4.42
216 217 9.833917 TTTTTCTTTTTGTTAACCGGGATTATT 57.166 25.926 6.32 0.00 0.00 1.40
239 240 7.748691 ATGACCATTTTGCAAGCTAATTTTT 57.251 28.000 0.00 0.00 0.00 1.94
240 241 7.748691 AATGACCATTTTGCAAGCTAATTTT 57.251 28.000 0.00 0.00 0.00 1.82
241 242 8.845413 TTAATGACCATTTTGCAAGCTAATTT 57.155 26.923 0.00 0.00 32.50 1.82
242 243 8.845413 TTTAATGACCATTTTGCAAGCTAATT 57.155 26.923 0.00 0.00 32.50 1.40
243 244 9.452287 AATTTAATGACCATTTTGCAAGCTAAT 57.548 25.926 0.00 0.00 32.50 1.73
244 245 8.845413 AATTTAATGACCATTTTGCAAGCTAA 57.155 26.923 0.00 0.00 32.50 3.09
245 246 8.845413 AAATTTAATGACCATTTTGCAAGCTA 57.155 26.923 0.00 0.00 32.50 3.32
246 247 7.748691 AAATTTAATGACCATTTTGCAAGCT 57.251 28.000 0.00 0.00 32.50 3.74
247 248 9.328721 GTAAAATTTAATGACCATTTTGCAAGC 57.671 29.630 0.00 0.00 34.48 4.01
248 249 9.824534 GGTAAAATTTAATGACCATTTTGCAAG 57.175 29.630 0.00 0.00 35.42 4.01
249 250 9.566432 AGGTAAAATTTAATGACCATTTTGCAA 57.434 25.926 0.00 0.00 35.42 4.08
250 251 9.566432 AAGGTAAAATTTAATGACCATTTTGCA 57.434 25.926 11.77 0.00 35.42 4.08
275 276 9.632807 GCCACAAACTCAAATTACATGTATTAA 57.367 29.630 6.36 0.00 0.00 1.40
276 277 8.247562 GGCCACAAACTCAAATTACATGTATTA 58.752 33.333 6.36 0.00 0.00 0.98
277 278 7.039082 AGGCCACAAACTCAAATTACATGTATT 60.039 33.333 5.01 0.00 0.00 1.89
278 279 6.437162 AGGCCACAAACTCAAATTACATGTAT 59.563 34.615 5.01 0.00 0.00 2.29
279 280 5.772672 AGGCCACAAACTCAAATTACATGTA 59.227 36.000 5.01 0.08 0.00 2.29
280 281 4.588528 AGGCCACAAACTCAAATTACATGT 59.411 37.500 5.01 2.69 0.00 3.21
281 282 5.138125 AGGCCACAAACTCAAATTACATG 57.862 39.130 5.01 0.00 0.00 3.21
282 283 5.070313 ACAAGGCCACAAACTCAAATTACAT 59.930 36.000 5.01 0.00 0.00 2.29
283 284 4.404073 ACAAGGCCACAAACTCAAATTACA 59.596 37.500 5.01 0.00 0.00 2.41
284 285 4.944048 ACAAGGCCACAAACTCAAATTAC 58.056 39.130 5.01 0.00 0.00 1.89
285 286 6.909550 ATACAAGGCCACAAACTCAAATTA 57.090 33.333 5.01 0.00 0.00 1.40
286 287 5.806654 ATACAAGGCCACAAACTCAAATT 57.193 34.783 5.01 0.00 0.00 1.82
287 288 6.909550 TTATACAAGGCCACAAACTCAAAT 57.090 33.333 5.01 0.00 0.00 2.32
288 289 6.239176 CCTTTATACAAGGCCACAAACTCAAA 60.239 38.462 5.01 0.00 0.00 2.69
289 290 5.242838 CCTTTATACAAGGCCACAAACTCAA 59.757 40.000 5.01 0.00 0.00 3.02
290 291 4.764823 CCTTTATACAAGGCCACAAACTCA 59.235 41.667 5.01 0.00 0.00 3.41
291 292 5.007682 TCCTTTATACAAGGCCACAAACTC 58.992 41.667 5.01 0.00 37.34 3.01
292 293 4.993028 TCCTTTATACAAGGCCACAAACT 58.007 39.130 5.01 0.00 37.34 2.66
293 294 5.715434 TTCCTTTATACAAGGCCACAAAC 57.285 39.130 5.01 0.00 37.34 2.93
294 295 5.186797 CCATTCCTTTATACAAGGCCACAAA 59.813 40.000 5.01 0.00 37.34 2.83
295 296 4.709397 CCATTCCTTTATACAAGGCCACAA 59.291 41.667 5.01 0.00 37.34 3.33
296 297 4.017958 TCCATTCCTTTATACAAGGCCACA 60.018 41.667 5.01 0.00 37.34 4.17
297 298 4.532834 TCCATTCCTTTATACAAGGCCAC 58.467 43.478 5.01 0.00 37.34 5.01
298 299 4.476846 TCTCCATTCCTTTATACAAGGCCA 59.523 41.667 5.01 0.00 37.34 5.36
299 300 5.048846 TCTCCATTCCTTTATACAAGGCC 57.951 43.478 0.00 0.00 37.34 5.19
300 301 5.930135 TCTCTCCATTCCTTTATACAAGGC 58.070 41.667 8.17 0.00 37.34 4.35
301 302 7.130681 ACTCTCTCCATTCCTTTATACAAGG 57.869 40.000 7.15 7.15 38.78 3.61
302 303 8.696374 TGTACTCTCTCCATTCCTTTATACAAG 58.304 37.037 0.00 0.00 0.00 3.16
303 304 8.603898 TGTACTCTCTCCATTCCTTTATACAA 57.396 34.615 0.00 0.00 0.00 2.41
304 305 8.603898 TTGTACTCTCTCCATTCCTTTATACA 57.396 34.615 0.00 0.00 0.00 2.29
307 308 9.440761 AGTATTGTACTCTCTCCATTCCTTTAT 57.559 33.333 0.00 0.00 32.47 1.40
308 309 8.840200 AGTATTGTACTCTCTCCATTCCTTTA 57.160 34.615 0.00 0.00 32.47 1.85
309 310 7.741554 AGTATTGTACTCTCTCCATTCCTTT 57.258 36.000 0.00 0.00 32.47 3.11
310 311 8.062536 AGTAGTATTGTACTCTCTCCATTCCTT 58.937 37.037 0.00 0.00 40.14 3.36
311 312 7.588169 AGTAGTATTGTACTCTCTCCATTCCT 58.412 38.462 0.00 0.00 40.14 3.36
312 313 7.826918 AGTAGTATTGTACTCTCTCCATTCC 57.173 40.000 0.00 0.00 40.14 3.01
322 323 7.283580 ACATGGAGTGAGAGTAGTATTGTACTC 59.716 40.741 0.00 3.30 46.47 2.59
323 324 7.120051 ACATGGAGTGAGAGTAGTATTGTACT 58.880 38.462 0.00 0.00 42.68 2.73
373 374 6.870439 ACCACACGTTTTCTACTCTATAAACC 59.130 38.462 0.00 0.00 0.00 3.27
448 743 5.276773 GCTGATTAGAAAATCTGACTGAGCG 60.277 44.000 8.60 0.00 41.26 5.03
543 838 1.444119 TTCTTTTCTGGCTGCGCGTT 61.444 50.000 8.43 0.00 0.00 4.84
577 872 3.133814 GCATTTACTGCGACGCATC 57.866 52.632 24.71 3.17 41.97 3.91
619 919 2.352821 CGGTATGGTGTGTCCGGGA 61.353 63.158 0.00 0.00 39.41 5.14
663 963 0.667487 GCTTGTCAGTACGCTCTGCA 60.667 55.000 3.05 0.00 35.63 4.41
664 964 1.678269 CGCTTGTCAGTACGCTCTGC 61.678 60.000 3.05 0.00 35.63 4.26
666 966 0.109689 GACGCTTGTCAGTACGCTCT 60.110 55.000 0.00 0.00 42.41 4.09
797 1682 1.738099 CGCCCCGAGTTTGTCAGAG 60.738 63.158 0.00 0.00 0.00 3.35
832 1717 1.588082 GCGAGAACCGGTGGAGTAA 59.412 57.895 8.52 0.00 39.04 2.24
977 1894 1.073025 TTCTGGTTCAGCACGGCAT 59.927 52.632 0.00 0.00 0.00 4.40
995 1912 0.912486 GCCACTTACCTCCATCTGGT 59.088 55.000 0.00 0.00 41.28 4.00
996 1913 0.179073 CGCCACTTACCTCCATCTGG 60.179 60.000 0.00 0.00 0.00 3.86
997 1914 0.179073 CCGCCACTTACCTCCATCTG 60.179 60.000 0.00 0.00 0.00 2.90
998 1915 1.972660 GCCGCCACTTACCTCCATCT 61.973 60.000 0.00 0.00 0.00 2.90
999 1916 1.523938 GCCGCCACTTACCTCCATC 60.524 63.158 0.00 0.00 0.00 3.51
1000 1917 2.590092 GCCGCCACTTACCTCCAT 59.410 61.111 0.00 0.00 0.00 3.41
1039 1956 3.258622 GTGAGGTTTGTGCTAGGAGTACT 59.741 47.826 0.00 0.00 31.77 2.73
1043 1960 1.347707 TGGTGAGGTTTGTGCTAGGAG 59.652 52.381 0.00 0.00 0.00 3.69
1044 1961 1.429930 TGGTGAGGTTTGTGCTAGGA 58.570 50.000 0.00 0.00 0.00 2.94
1045 1962 1.880027 GTTGGTGAGGTTTGTGCTAGG 59.120 52.381 0.00 0.00 0.00 3.02
1065 1982 1.377202 CAGACCACGACCCCCATTG 60.377 63.158 0.00 0.00 0.00 2.82
1093 2017 5.479027 TCTGCAAGATACCACAAGTGTAGTA 59.521 40.000 0.00 0.00 38.67 1.82
1108 2032 0.177604 CTCCTCGCCTTCTGCAAGAT 59.822 55.000 0.00 0.00 46.36 2.40
1542 4517 2.049156 GGCCAAACAAAGAGCGGC 60.049 61.111 0.00 0.00 42.21 6.53
1558 4533 0.322277 ACATGCTCCACTTCTGCAGG 60.322 55.000 15.13 0.36 43.01 4.85
1559 4534 0.803117 CACATGCTCCACTTCTGCAG 59.197 55.000 7.63 7.63 40.18 4.41
1638 4651 0.948623 TGATGAACACGAACGCAGGG 60.949 55.000 0.00 0.00 0.00 4.45
1692 4705 3.626670 AGTGGACAGACGTATAGCAGTAC 59.373 47.826 0.00 0.00 0.00 2.73
1704 4717 1.470890 CGGAGAGAGAAGTGGACAGAC 59.529 57.143 0.00 0.00 0.00 3.51
1731 4744 1.129251 CAAGCCAAGACATACGCACAG 59.871 52.381 0.00 0.00 0.00 3.66
1766 4779 6.809196 CAGTCAGCTAGTTTTACTGGAGTTAG 59.191 42.308 9.72 0.00 35.12 2.34
1768 4781 5.542779 CAGTCAGCTAGTTTTACTGGAGTT 58.457 41.667 9.72 0.00 35.12 3.01
1884 4912 7.116075 TGTTGCACCCAATATGTTATCTTACT 58.884 34.615 0.00 0.00 32.75 2.24
1901 4933 1.195448 CACGAGACAAGATGTTGCACC 59.805 52.381 1.83 0.00 37.14 5.01
1949 4981 5.661056 TCAGGTTGACAGATAGTAACAGG 57.339 43.478 0.00 0.00 0.00 4.00
1979 5020 7.118390 TCCAAAGTGATTTCTTTTCGAGATCTC 59.882 37.037 13.05 13.05 35.77 2.75
1980 5021 6.936900 TCCAAAGTGATTTCTTTTCGAGATCT 59.063 34.615 0.00 0.00 35.77 2.75
1981 5022 7.018235 GTCCAAAGTGATTTCTTTTCGAGATC 58.982 38.462 0.00 0.00 35.77 2.75
1982 5023 6.072452 GGTCCAAAGTGATTTCTTTTCGAGAT 60.072 38.462 0.00 0.00 35.77 2.75
1983 5024 5.238650 GGTCCAAAGTGATTTCTTTTCGAGA 59.761 40.000 0.00 0.00 35.77 4.04
1984 5025 5.008613 TGGTCCAAAGTGATTTCTTTTCGAG 59.991 40.000 0.00 0.00 35.77 4.04
1985 5026 4.884744 TGGTCCAAAGTGATTTCTTTTCGA 59.115 37.500 0.00 0.00 35.77 3.71
1986 5027 5.181690 TGGTCCAAAGTGATTTCTTTTCG 57.818 39.130 0.00 0.00 35.77 3.46
1987 5028 8.437360 AAATTGGTCCAAAGTGATTTCTTTTC 57.563 30.769 8.75 0.00 35.77 2.29
1988 5029 8.267183 AGAAATTGGTCCAAAGTGATTTCTTTT 58.733 29.630 18.40 7.85 39.48 2.27
1989 5030 7.712205 CAGAAATTGGTCCAAAGTGATTTCTTT 59.288 33.333 20.36 9.58 40.12 2.52
1990 5031 7.069826 TCAGAAATTGGTCCAAAGTGATTTCTT 59.930 33.333 20.36 9.16 40.12 2.52
1991 5032 6.550854 TCAGAAATTGGTCCAAAGTGATTTCT 59.449 34.615 18.40 18.40 41.77 2.52
1992 5033 6.748132 TCAGAAATTGGTCCAAAGTGATTTC 58.252 36.000 8.75 13.01 35.05 2.17
1993 5034 6.729690 TCAGAAATTGGTCCAAAGTGATTT 57.270 33.333 8.75 4.08 0.00 2.17
1994 5035 6.268387 ACATCAGAAATTGGTCCAAAGTGATT 59.732 34.615 8.75 0.00 0.00 2.57
1995 5036 5.776716 ACATCAGAAATTGGTCCAAAGTGAT 59.223 36.000 8.75 11.10 0.00 3.06
2013 5054 1.424240 CAGCTCGCTTGCACATCAG 59.576 57.895 0.00 0.00 34.99 2.90
2029 5070 5.975282 TCTTTCTGAATCTCTGATGACCAG 58.025 41.667 0.00 0.00 44.27 4.00
2031 5072 6.646240 GCTATCTTTCTGAATCTCTGATGACC 59.354 42.308 0.00 0.00 0.00 4.02
2054 5105 2.297597 GCTCGTCTATCTATTGGGTGCT 59.702 50.000 0.00 0.00 0.00 4.40
2056 5107 3.643763 GTGCTCGTCTATCTATTGGGTG 58.356 50.000 0.00 0.00 0.00 4.61
2057 5108 2.293677 CGTGCTCGTCTATCTATTGGGT 59.706 50.000 0.00 0.00 0.00 4.51
2058 5109 2.922758 GCGTGCTCGTCTATCTATTGGG 60.923 54.545 10.18 0.00 39.49 4.12
2059 5110 2.287608 TGCGTGCTCGTCTATCTATTGG 60.288 50.000 10.18 0.00 39.49 3.16
2181 5371 2.174349 GCGCGAAGAAGCCAGTTG 59.826 61.111 12.10 0.00 0.00 3.16
2294 5506 5.591067 AGAAAAGACACGAGGTAGATAGGAG 59.409 44.000 0.00 0.00 0.00 3.69
2295 5507 5.507637 AGAAAAGACACGAGGTAGATAGGA 58.492 41.667 0.00 0.00 0.00 2.94
2296 5508 5.838531 AGAAAAGACACGAGGTAGATAGG 57.161 43.478 0.00 0.00 0.00 2.57
2297 5509 6.037098 CCAAGAAAAGACACGAGGTAGATAG 58.963 44.000 0.00 0.00 0.00 2.08
2298 5510 5.623824 GCCAAGAAAAGACACGAGGTAGATA 60.624 44.000 0.00 0.00 0.00 1.98
2299 5511 4.822026 CCAAGAAAAGACACGAGGTAGAT 58.178 43.478 0.00 0.00 0.00 1.98
2330 5542 3.405831 CATGCCAGTTCTCTTCTTCACA 58.594 45.455 0.00 0.00 0.00 3.58
2333 5545 3.064900 ACCATGCCAGTTCTCTTCTTC 57.935 47.619 0.00 0.00 0.00 2.87
2421 5636 2.412089 GACGATAGAGGTGTTGTTGCAC 59.588 50.000 0.00 0.00 41.38 4.57


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

AutoCloner maintained by Alex Coulton.