Multiple sequence alignment - TraesCS4A01G084200

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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 TraesCS4A01G084200 chr4A 100.000 2700 0 0 1 2700 88706142 88703443 0.000000e+00 4987.0
1 TraesCS4A01G084200 chr4A 77.257 576 89 29 1130 1671 88541338 88540771 1.570000e-77 300.0
2 TraesCS4A01G084200 chr4D 93.775 1237 44 10 330 1558 375444563 375445774 0.000000e+00 1827.0
3 TraesCS4A01G084200 chr4D 94.461 343 16 3 1 341 426600636 426600295 2.380000e-145 525.0
4 TraesCS4A01G084200 chr4D 84.413 494 44 17 1980 2444 375446360 375446849 3.170000e-124 455.0
5 TraesCS4A01G084200 chr4D 94.203 276 8 4 1597 1864 375445771 375446046 5.380000e-112 414.0
6 TraesCS4A01G084200 chr4D 91.760 267 17 3 2435 2699 375447148 375447411 1.530000e-97 366.0
7 TraesCS4A01G084200 chr4D 76.619 556 98 22 1130 1657 375508845 375509396 7.360000e-71 278.0
8 TraesCS4A01G084200 chr4B 94.759 935 29 8 938 1872 462592099 462593013 0.000000e+00 1437.0
9 TraesCS4A01G084200 chr4B 91.841 527 32 4 331 853 462591552 462592071 0.000000e+00 725.0
10 TraesCS4A01G084200 chr4B 82.867 572 65 17 1902 2444 462593080 462593647 1.450000e-132 483.0
11 TraesCS4A01G084200 chr4B 92.623 244 15 3 2455 2697 462593961 462594202 5.530000e-92 348.0
12 TraesCS4A01G084200 chr4B 76.512 562 94 28 1130 1657 462696856 462697413 3.430000e-69 272.0
13 TraesCS4A01G084200 chr2D 95.858 338 14 0 1 338 555391230 555391567 5.080000e-152 547.0
14 TraesCS4A01G084200 chr2D 94.118 340 18 2 1 338 314360445 314360784 1.430000e-142 516.0
15 TraesCS4A01G084200 chr5D 95.280 339 15 1 1 338 318818890 318818552 1.100000e-148 536.0
16 TraesCS4A01G084200 chr5D 94.940 336 15 2 1 335 539720716 539721050 2.380000e-145 525.0
17 TraesCS4A01G084200 chr5D 94.659 337 16 1 1 335 387602384 387602720 3.080000e-144 521.0
18 TraesCS4A01G084200 chr6D 94.186 344 17 2 1 341 68859201 68859544 3.080000e-144 521.0
19 TraesCS4A01G084200 chr7A 94.169 343 17 3 1 341 221207481 221207822 1.110000e-143 520.0
20 TraesCS4A01G084200 chr7A 89.668 271 21 6 2435 2699 668992284 668992553 3.330000e-89 339.0
21 TraesCS4A01G084200 chr7A 87.919 149 15 3 1991 2136 668991524 668991672 3.570000e-39 172.0
22 TraesCS4A01G084200 chr7D 94.152 342 17 2 1 340 456718870 456718530 3.980000e-143 518.0
23 TraesCS4A01G084200 chr1D 86.667 75 6 4 1991 2061 394948016 394947942 2.230000e-11 80.5


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 TraesCS4A01G084200 chr4A 88703443 88706142 2699 True 4987.00 4987 100.00000 1 2700 1 chr4A.!!$R2 2699
1 TraesCS4A01G084200 chr4A 88540771 88541338 567 True 300.00 300 77.25700 1130 1671 1 chr4A.!!$R1 541
2 TraesCS4A01G084200 chr4D 375444563 375447411 2848 False 765.50 1827 91.03775 330 2699 4 chr4D.!!$F2 2369
3 TraesCS4A01G084200 chr4D 375508845 375509396 551 False 278.00 278 76.61900 1130 1657 1 chr4D.!!$F1 527
4 TraesCS4A01G084200 chr4B 462591552 462594202 2650 False 748.25 1437 90.52250 331 2697 4 chr4B.!!$F2 2366
5 TraesCS4A01G084200 chr4B 462696856 462697413 557 False 272.00 272 76.51200 1130 1657 1 chr4B.!!$F1 527
6 TraesCS4A01G084200 chr7A 668991524 668992553 1029 False 255.50 339 88.79350 1991 2699 2 chr7A.!!$F2 708

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
868 874 0.033011 GCTCCTCCACCTCCACTCTA 60.033 60.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2625 0.397941 TTGCAGTTCAGGTCTGGGAG 59.602 55.0 0.0 0.0 33.98 4.3 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
23 24 2.675767 GCATATGCGGACTCATGTTG 57.324 50.000 12.82 0.00 0.00 3.33
24 25 1.265095 GCATATGCGGACTCATGTTGG 59.735 52.381 12.82 0.00 0.00 3.77
25 26 1.265095 CATATGCGGACTCATGTTGGC 59.735 52.381 0.00 0.00 0.00 4.52
26 27 0.251634 TATGCGGACTCATGTTGGCA 59.748 50.000 0.00 0.00 38.41 4.92
27 28 0.608856 ATGCGGACTCATGTTGGCAA 60.609 50.000 0.00 0.00 37.88 4.52
28 29 1.210155 GCGGACTCATGTTGGCAAC 59.790 57.895 23.12 23.12 0.00 4.17
29 30 1.875963 CGGACTCATGTTGGCAACC 59.124 57.895 26.31 10.38 0.00 3.77
30 31 0.888736 CGGACTCATGTTGGCAACCA 60.889 55.000 26.31 15.17 0.00 3.67
31 32 1.327303 GGACTCATGTTGGCAACCAA 58.673 50.000 26.31 10.36 41.69 3.67
32 33 1.895131 GGACTCATGTTGGCAACCAAT 59.105 47.619 26.31 12.28 45.80 3.16
33 34 3.088532 GGACTCATGTTGGCAACCAATA 58.911 45.455 26.31 9.22 45.80 1.90
34 35 3.129287 GGACTCATGTTGGCAACCAATAG 59.871 47.826 26.31 19.15 45.80 1.73
35 36 4.009675 GACTCATGTTGGCAACCAATAGA 58.990 43.478 26.31 15.20 45.80 1.98
36 37 4.603131 ACTCATGTTGGCAACCAATAGAT 58.397 39.130 26.31 10.10 45.80 1.98
37 38 4.400251 ACTCATGTTGGCAACCAATAGATG 59.600 41.667 26.31 20.43 45.80 2.90
38 39 4.343231 TCATGTTGGCAACCAATAGATGT 58.657 39.130 26.31 0.10 45.80 3.06
39 40 5.504853 TCATGTTGGCAACCAATAGATGTA 58.495 37.500 26.31 5.08 45.80 2.29
40 41 6.128486 TCATGTTGGCAACCAATAGATGTAT 58.872 36.000 26.31 7.24 45.80 2.29
41 42 6.262944 TCATGTTGGCAACCAATAGATGTATC 59.737 38.462 26.31 0.00 45.80 2.24
42 43 5.754782 TGTTGGCAACCAATAGATGTATCT 58.245 37.500 26.31 0.00 45.80 1.98
43 44 6.186957 TGTTGGCAACCAATAGATGTATCTT 58.813 36.000 26.31 0.00 45.80 2.40
44 45 6.318648 TGTTGGCAACCAATAGATGTATCTTC 59.681 38.462 26.31 0.00 45.80 2.87
45 46 6.252599 TGGCAACCAATAGATGTATCTTCT 57.747 37.500 0.00 0.00 38.32 2.85
46 47 6.662755 TGGCAACCAATAGATGTATCTTCTT 58.337 36.000 0.00 0.00 38.32 2.52
47 48 7.118723 TGGCAACCAATAGATGTATCTTCTTT 58.881 34.615 0.00 0.00 38.32 2.52
48 49 7.615365 TGGCAACCAATAGATGTATCTTCTTTT 59.385 33.333 0.00 0.00 38.32 2.27
49 50 9.120538 GGCAACCAATAGATGTATCTTCTTTTA 57.879 33.333 0.00 0.00 38.32 1.52
115 116 9.787435 TGGCCTGTAACTATACTATTTATTTGG 57.213 33.333 3.32 0.00 32.98 3.28
116 117 9.227777 GGCCTGTAACTATACTATTTATTTGGG 57.772 37.037 0.00 0.00 32.98 4.12
117 118 8.727910 GCCTGTAACTATACTATTTATTTGGGC 58.272 37.037 0.00 0.00 32.98 5.36
118 119 8.932791 CCTGTAACTATACTATTTATTTGGGCG 58.067 37.037 0.00 0.00 32.98 6.13
119 120 8.836268 TGTAACTATACTATTTATTTGGGCGG 57.164 34.615 0.00 0.00 32.98 6.13
120 121 8.649591 TGTAACTATACTATTTATTTGGGCGGA 58.350 33.333 0.00 0.00 32.98 5.54
121 122 7.974482 AACTATACTATTTATTTGGGCGGAC 57.026 36.000 0.00 0.00 0.00 4.79
122 123 7.312415 ACTATACTATTTATTTGGGCGGACT 57.688 36.000 0.00 0.00 0.00 3.85
123 124 8.426569 ACTATACTATTTATTTGGGCGGACTA 57.573 34.615 0.00 0.00 0.00 2.59
124 125 9.043548 ACTATACTATTTATTTGGGCGGACTAT 57.956 33.333 0.00 0.00 0.00 2.12
125 126 9.886132 CTATACTATTTATTTGGGCGGACTATT 57.114 33.333 0.00 0.00 0.00 1.73
127 128 7.891498 ACTATTTATTTGGGCGGACTATTTT 57.109 32.000 0.00 0.00 0.00 1.82
128 129 7.712797 ACTATTTATTTGGGCGGACTATTTTG 58.287 34.615 0.00 0.00 0.00 2.44
129 130 5.986501 TTTATTTGGGCGGACTATTTTGT 57.013 34.783 0.00 0.00 0.00 2.83
130 131 5.986501 TTATTTGGGCGGACTATTTTGTT 57.013 34.783 0.00 0.00 0.00 2.83
131 132 4.882842 ATTTGGGCGGACTATTTTGTTT 57.117 36.364 0.00 0.00 0.00 2.83
132 133 3.651803 TTGGGCGGACTATTTTGTTTG 57.348 42.857 0.00 0.00 0.00 2.93
133 134 2.588620 TGGGCGGACTATTTTGTTTGT 58.411 42.857 0.00 0.00 0.00 2.83
134 135 2.959707 TGGGCGGACTATTTTGTTTGTT 59.040 40.909 0.00 0.00 0.00 2.83
135 136 4.142790 TGGGCGGACTATTTTGTTTGTTA 58.857 39.130 0.00 0.00 0.00 2.41
136 137 4.583489 TGGGCGGACTATTTTGTTTGTTAA 59.417 37.500 0.00 0.00 0.00 2.01
137 138 5.068723 TGGGCGGACTATTTTGTTTGTTAAA 59.931 36.000 0.00 0.00 0.00 1.52
138 139 6.160684 GGGCGGACTATTTTGTTTGTTAAAT 58.839 36.000 0.00 0.00 0.00 1.40
139 140 6.647481 GGGCGGACTATTTTGTTTGTTAAATT 59.353 34.615 0.00 0.00 0.00 1.82
140 141 7.171848 GGGCGGACTATTTTGTTTGTTAAATTT 59.828 33.333 0.00 0.00 0.00 1.82
141 142 8.552865 GGCGGACTATTTTGTTTGTTAAATTTT 58.447 29.630 0.00 0.00 0.00 1.82
142 143 9.923786 GCGGACTATTTTGTTTGTTAAATTTTT 57.076 25.926 0.00 0.00 0.00 1.94
168 169 6.650239 TTCACAATATGTTGAATGCAATGC 57.350 33.333 9.40 0.00 38.71 3.56
169 170 5.721232 TCACAATATGTTGAATGCAATGCA 58.279 33.333 11.44 11.44 39.82 3.96
170 171 6.164176 TCACAATATGTTGAATGCAATGCAA 58.836 32.000 13.45 0.00 40.33 4.08
171 172 6.649557 TCACAATATGTTGAATGCAATGCAAA 59.350 30.769 13.45 0.00 45.25 3.68
172 173 7.172703 TCACAATATGTTGAATGCAATGCAAAA 59.827 29.630 13.45 4.57 45.25 2.44
173 174 7.965655 CACAATATGTTGAATGCAATGCAAAAT 59.034 29.630 13.45 0.98 45.25 1.82
174 175 8.516234 ACAATATGTTGAATGCAATGCAAAATT 58.484 25.926 13.45 1.30 45.25 1.82
175 176 8.793472 CAATATGTTGAATGCAATGCAAAATTG 58.207 29.630 13.45 5.92 45.25 2.32
176 177 5.109662 TGTTGAATGCAATGCAAAATTGG 57.890 34.783 13.45 0.00 45.25 3.16
177 178 4.023107 TGTTGAATGCAATGCAAAATTGGG 60.023 37.500 13.45 0.00 45.25 4.12
178 179 2.488545 TGAATGCAATGCAAAATTGGGC 59.511 40.909 13.45 0.00 43.62 5.36
179 180 1.088306 ATGCAATGCAAAATTGGGCG 58.912 45.000 13.45 0.00 43.62 6.13
180 181 0.954449 TGCAATGCAAAATTGGGCGG 60.954 50.000 5.01 0.00 34.76 6.13
181 182 1.795507 CAATGCAAAATTGGGCGGC 59.204 52.632 0.00 0.00 0.00 6.53
182 183 1.377072 AATGCAAAATTGGGCGGCC 60.377 52.632 23.42 23.42 0.00 6.13
183 184 2.121992 AATGCAAAATTGGGCGGCCA 62.122 50.000 29.27 29.27 0.00 5.36
184 185 2.434709 GCAAAATTGGGCGGCCAG 60.435 61.111 30.86 19.70 0.00 4.85
204 205 2.516930 GGCCACGCCTGCACATAT 60.517 61.111 0.00 0.00 46.69 1.78
205 206 2.717485 GCCACGCCTGCACATATG 59.283 61.111 0.00 0.00 0.00 1.78
206 207 2.837883 GCCACGCCTGCACATATGG 61.838 63.158 7.80 0.00 0.00 2.74
207 208 2.188829 CCACGCCTGCACATATGGG 61.189 63.158 7.80 3.61 0.00 4.00
208 209 1.451927 CACGCCTGCACATATGGGT 60.452 57.895 6.86 0.00 0.00 4.51
209 210 1.153168 ACGCCTGCACATATGGGTC 60.153 57.895 6.86 0.00 0.00 4.46
210 211 2.246739 CGCCTGCACATATGGGTCG 61.247 63.158 6.86 2.08 0.00 4.79
211 212 1.893808 GCCTGCACATATGGGTCGG 60.894 63.158 6.86 8.44 0.00 4.79
212 213 1.893808 CCTGCACATATGGGTCGGC 60.894 63.158 6.86 3.06 0.00 5.54
213 214 2.203001 TGCACATATGGGTCGGCG 60.203 61.111 6.86 0.00 0.00 6.46
214 215 2.203015 GCACATATGGGTCGGCGT 60.203 61.111 6.85 0.00 0.00 5.68
215 216 2.534019 GCACATATGGGTCGGCGTG 61.534 63.158 6.85 0.00 0.00 5.34
216 217 1.153449 CACATATGGGTCGGCGTGT 60.153 57.895 6.85 0.00 0.00 4.49
217 218 0.742990 CACATATGGGTCGGCGTGTT 60.743 55.000 6.85 0.00 0.00 3.32
218 219 0.742990 ACATATGGGTCGGCGTGTTG 60.743 55.000 6.85 0.00 0.00 3.33
219 220 1.153249 ATATGGGTCGGCGTGTTGG 60.153 57.895 6.85 0.00 0.00 3.77
220 221 1.618876 ATATGGGTCGGCGTGTTGGA 61.619 55.000 6.85 0.00 0.00 3.53
221 222 1.618876 TATGGGTCGGCGTGTTGGAT 61.619 55.000 6.85 0.00 0.00 3.41
222 223 3.124921 GGGTCGGCGTGTTGGATG 61.125 66.667 6.85 0.00 0.00 3.51
223 224 2.358247 GGTCGGCGTGTTGGATGT 60.358 61.111 6.85 0.00 0.00 3.06
224 225 2.677003 GGTCGGCGTGTTGGATGTG 61.677 63.158 6.85 0.00 0.00 3.21
225 226 3.047280 TCGGCGTGTTGGATGTGC 61.047 61.111 6.85 0.00 0.00 4.57
226 227 3.049674 CGGCGTGTTGGATGTGCT 61.050 61.111 0.00 0.00 0.00 4.40
227 228 2.562912 GGCGTGTTGGATGTGCTG 59.437 61.111 0.00 0.00 0.00 4.41
228 229 2.260869 GGCGTGTTGGATGTGCTGT 61.261 57.895 0.00 0.00 0.00 4.40
229 230 1.207593 GCGTGTTGGATGTGCTGTC 59.792 57.895 0.00 0.00 0.00 3.51
230 231 1.492873 CGTGTTGGATGTGCTGTCG 59.507 57.895 0.00 0.00 0.00 4.35
231 232 0.943835 CGTGTTGGATGTGCTGTCGA 60.944 55.000 0.00 0.00 0.00 4.20
232 233 0.512952 GTGTTGGATGTGCTGTCGAC 59.487 55.000 9.11 9.11 0.00 4.20
233 234 0.602638 TGTTGGATGTGCTGTCGACC 60.603 55.000 14.12 0.00 0.00 4.79
234 235 1.003839 TTGGATGTGCTGTCGACCC 60.004 57.895 14.12 5.42 0.00 4.46
235 236 1.763546 TTGGATGTGCTGTCGACCCA 61.764 55.000 14.12 8.25 0.00 4.51
236 237 1.221840 GGATGTGCTGTCGACCCAT 59.778 57.895 14.12 9.72 0.00 4.00
237 238 0.464036 GGATGTGCTGTCGACCCATA 59.536 55.000 14.12 9.03 0.00 2.74
238 239 1.070758 GGATGTGCTGTCGACCCATAT 59.929 52.381 14.12 13.40 0.00 1.78
239 240 2.138320 GATGTGCTGTCGACCCATATG 58.862 52.381 14.12 0.00 0.00 1.78
240 241 1.190643 TGTGCTGTCGACCCATATGA 58.809 50.000 14.12 0.00 0.00 2.15
241 242 1.552792 TGTGCTGTCGACCCATATGAA 59.447 47.619 14.12 0.00 0.00 2.57
242 243 2.027653 TGTGCTGTCGACCCATATGAAA 60.028 45.455 14.12 0.00 0.00 2.69
243 244 3.006940 GTGCTGTCGACCCATATGAAAA 58.993 45.455 14.12 0.00 0.00 2.29
244 245 3.438781 GTGCTGTCGACCCATATGAAAAA 59.561 43.478 14.12 0.00 0.00 1.94
245 246 3.438781 TGCTGTCGACCCATATGAAAAAC 59.561 43.478 14.12 0.00 0.00 2.43
246 247 3.438781 GCTGTCGACCCATATGAAAAACA 59.561 43.478 14.12 1.52 0.00 2.83
247 248 4.437390 GCTGTCGACCCATATGAAAAACAG 60.437 45.833 14.12 11.47 35.78 3.16
248 249 4.006989 TGTCGACCCATATGAAAAACAGG 58.993 43.478 14.12 0.00 0.00 4.00
249 250 4.258543 GTCGACCCATATGAAAAACAGGA 58.741 43.478 3.51 0.00 0.00 3.86
250 251 4.094442 GTCGACCCATATGAAAAACAGGAC 59.906 45.833 3.51 0.00 0.00 3.85
251 252 3.063452 CGACCCATATGAAAAACAGGACG 59.937 47.826 3.65 3.53 0.00 4.79
252 253 3.352648 ACCCATATGAAAAACAGGACGG 58.647 45.455 3.65 0.00 0.00 4.79
253 254 3.009695 ACCCATATGAAAAACAGGACGGA 59.990 43.478 3.65 0.00 0.00 4.69
254 255 3.377172 CCCATATGAAAAACAGGACGGAC 59.623 47.826 3.65 0.00 0.00 4.79
255 256 3.063452 CCATATGAAAAACAGGACGGACG 59.937 47.826 3.65 0.00 0.00 4.79
256 257 0.872388 ATGAAAAACAGGACGGACGC 59.128 50.000 0.00 0.00 0.00 5.19
257 258 1.161563 TGAAAAACAGGACGGACGCC 61.162 55.000 0.00 0.00 0.00 5.68
302 303 3.759550 AAAAACGGACGAAATCGCC 57.240 47.368 2.15 4.66 44.43 5.54
306 307 2.693285 CGGACGAAATCGCCGTTC 59.307 61.111 21.85 6.57 46.11 3.95
311 312 2.609404 CGAAATCGCCGTTCGTTTG 58.391 52.632 2.15 0.00 42.23 2.93
312 313 0.787908 CGAAATCGCCGTTCGTTTGG 60.788 55.000 2.15 0.00 42.23 3.28
313 314 0.453782 GAAATCGCCGTTCGTTTGGG 60.454 55.000 0.00 0.00 39.67 4.12
314 315 1.167781 AAATCGCCGTTCGTTTGGGT 61.168 50.000 0.00 0.00 39.67 4.51
315 316 1.571215 AATCGCCGTTCGTTTGGGTC 61.571 55.000 0.00 0.00 39.67 4.46
316 317 4.067016 CGCCGTTCGTTTGGGTCG 62.067 66.667 0.00 0.00 0.00 4.79
317 318 3.719144 GCCGTTCGTTTGGGTCGG 61.719 66.667 0.00 0.00 43.37 4.79
318 319 3.719144 CCGTTCGTTTGGGTCGGC 61.719 66.667 0.00 0.00 35.01 5.54
319 320 3.719144 CGTTCGTTTGGGTCGGCC 61.719 66.667 0.00 0.00 0.00 6.13
347 348 4.141846 GGAGTTGCTCTTATGTCATCCTCA 60.142 45.833 0.00 0.00 0.00 3.86
367 368 6.097554 TCCTCAGTGATCTCAACCTTATCTTC 59.902 42.308 0.00 0.00 0.00 2.87
395 396 2.494918 GATGTCCCCGTCCGTCAG 59.505 66.667 0.00 0.00 0.00 3.51
471 472 7.394359 AGTTAGAATTTGTTATGCTCACATGGT 59.606 33.333 0.00 0.00 37.04 3.55
489 490 6.863126 CACATGGTTACCAAGAATTTTGAGTC 59.137 38.462 13.88 0.00 36.95 3.36
531 533 2.030274 ACCGCAGCTTGGTTAATGTTTC 60.030 45.455 1.40 0.00 35.82 2.78
545 547 4.871933 AATGTTTCCCACAAAGTCATCC 57.128 40.909 0.00 0.00 39.50 3.51
602 604 1.356624 GTGGCGCAACATAGATGCC 59.643 57.895 10.88 0.00 45.91 4.40
605 607 1.134250 TGGCGCAACATAGATGCCTAA 60.134 47.619 10.83 0.00 45.90 2.69
625 627 1.115930 AGGTGTTGGAGAGAGCACGT 61.116 55.000 0.00 0.00 33.09 4.49
626 628 0.601558 GGTGTTGGAGAGAGCACGTA 59.398 55.000 0.00 0.00 33.09 3.57
627 629 1.402984 GGTGTTGGAGAGAGCACGTAG 60.403 57.143 0.00 0.00 33.09 3.51
685 687 1.299926 AACGCAGACGACACAGGTC 60.300 57.895 0.00 0.00 43.93 3.85
697 699 1.006102 ACAGGTCGCCAAAGACTCG 60.006 57.895 0.00 0.00 40.76 4.18
815 821 1.533731 ACGGGATAACAAAACACTGCG 59.466 47.619 0.00 0.00 0.00 5.18
859 865 2.267324 GCACAGAGCTCCTCCACC 59.733 66.667 10.93 0.00 41.15 4.61
860 866 2.289532 GCACAGAGCTCCTCCACCT 61.290 63.158 10.93 0.00 41.15 4.00
861 867 1.896694 CACAGAGCTCCTCCACCTC 59.103 63.158 10.93 0.00 0.00 3.85
862 868 1.305718 ACAGAGCTCCTCCACCTCC 60.306 63.158 10.93 0.00 0.00 4.30
863 869 1.305633 CAGAGCTCCTCCACCTCCA 60.306 63.158 10.93 0.00 0.00 3.86
864 870 1.305718 AGAGCTCCTCCACCTCCAC 60.306 63.158 10.93 0.00 0.00 4.02
865 871 1.305718 GAGCTCCTCCACCTCCACT 60.306 63.158 0.87 0.00 0.00 4.00
868 874 0.033011 GCTCCTCCACCTCCACTCTA 60.033 60.000 0.00 0.00 0.00 2.43
874 880 6.485388 TCCTCCACCTCCACTCTATATATT 57.515 41.667 0.00 0.00 0.00 1.28
885 891 6.071560 TCCACTCTATATATTTGCCCTACACG 60.072 42.308 0.00 0.00 0.00 4.49
890 896 7.600065 TCTATATATTTGCCCTACACGACTTC 58.400 38.462 0.00 0.00 0.00 3.01
915 921 3.545481 CACTCACATCGTCCGCGC 61.545 66.667 0.00 0.00 38.14 6.86
948 956 0.736325 CGATCGAGGTGACCACAACC 60.736 60.000 10.26 0.00 33.63 3.77
985 994 2.486203 CTCCGATTCGAGATCCCTACTG 59.514 54.545 7.83 0.00 30.97 2.74
1377 1392 3.309675 CGATCGGTCGTTCATGCC 58.690 61.111 10.62 0.00 42.78 4.40
1558 1597 1.734477 CCTCGTGCTCACCTTCGTG 60.734 63.158 0.00 0.00 41.72 4.35
1576 1615 4.008933 GTGTCGCAGCCCAGGACT 62.009 66.667 0.00 0.00 0.00 3.85
1717 1756 2.358737 GAGTTGACTGGCGGGTGG 60.359 66.667 0.00 0.00 0.00 4.61
1769 1808 0.250338 GGCCAGGGAATTAGCGGTAG 60.250 60.000 0.00 0.00 0.00 3.18
1813 1860 6.920758 GGAGTATGCTCAGTGAACTAGTTATG 59.079 42.308 8.42 8.22 43.37 1.90
1848 1895 6.566564 CGTTTTCTTCAAGCTGTGTGACATAT 60.567 38.462 0.00 0.00 0.00 1.78
1872 1953 3.720818 GCTGATGTTAATGAATTGACGCG 59.279 43.478 3.53 3.53 0.00 6.01
1895 1976 2.350804 GCTGTGTGACATACTGCTGATG 59.649 50.000 21.57 0.00 39.15 3.07
1906 2024 5.819379 ACATACTGCTGATGTTAGTGAATGG 59.181 40.000 0.00 0.00 33.70 3.16
1954 2073 3.886505 ACGGCAAAAATAACAGTGAAGGA 59.113 39.130 0.00 0.00 0.00 3.36
1955 2074 4.023193 ACGGCAAAAATAACAGTGAAGGAG 60.023 41.667 0.00 0.00 0.00 3.69
1956 2075 4.215399 CGGCAAAAATAACAGTGAAGGAGA 59.785 41.667 0.00 0.00 0.00 3.71
1957 2076 5.106157 CGGCAAAAATAACAGTGAAGGAGAT 60.106 40.000 0.00 0.00 0.00 2.75
1958 2077 6.570378 CGGCAAAAATAACAGTGAAGGAGATT 60.570 38.462 0.00 0.00 0.00 2.40
1959 2078 7.154656 GGCAAAAATAACAGTGAAGGAGATTT 58.845 34.615 0.00 0.00 0.00 2.17
2114 2397 1.164041 CCAAGACACGACAACCACCC 61.164 60.000 0.00 0.00 0.00 4.61
2124 2407 2.747446 CGACAACCACCCTTTTATGAGG 59.253 50.000 0.00 0.00 36.52 3.86
2145 2454 3.623510 GGGAATCTAAGGTTTCAGAAGCG 59.376 47.826 0.00 0.00 38.28 4.68
2150 2459 5.464030 TCTAAGGTTTCAGAAGCGTAGTT 57.536 39.130 9.77 0.00 42.27 2.24
2156 2465 4.321824 GGTTTCAGAAGCGTAGTTCTAGGT 60.322 45.833 0.00 0.00 34.90 3.08
2193 2503 3.303526 GCGAAAAACAGAAGCGTTCCTAA 60.304 43.478 0.00 0.00 0.00 2.69
2196 2506 3.898517 AAACAGAAGCGTTCCTAAAGC 57.101 42.857 0.00 0.00 0.00 3.51
2199 2509 0.984995 AGAAGCGTTCCTAAAGCCCT 59.015 50.000 0.00 0.00 0.00 5.19
2208 2518 5.105877 GCGTTCCTAAAGCCCTAAATTTTCT 60.106 40.000 0.00 0.00 0.00 2.52
2210 2520 7.201794 GCGTTCCTAAAGCCCTAAATTTTCTAT 60.202 37.037 0.00 0.00 0.00 1.98
2243 2553 1.133869 GACCGACGGCCAAATTTCG 59.866 57.895 15.39 1.94 0.00 3.46
2255 2565 1.323534 CAAATTTCGTAGTCGAGCCCG 59.676 52.381 0.00 0.00 46.81 6.13
2258 2568 1.526575 TTTCGTAGTCGAGCCCGGTT 61.527 55.000 0.00 0.00 46.81 4.44
2262 2572 1.001020 TAGTCGAGCCCGGTTGGTA 60.001 57.895 0.00 0.00 36.04 3.25
2266 2576 1.004200 CGAGCCCGGTTGGTAAAGT 60.004 57.895 0.00 0.00 36.04 2.66
2280 2590 9.122779 CGGTTGGTAAAGTTATATCCCAAATTA 57.877 33.333 0.00 0.00 34.05 1.40
2342 2652 1.008538 CTGAACTGCAAACGGGCAC 60.009 57.895 0.00 0.00 39.25 5.01
2400 2710 1.014352 ACATCGCGGGCAAATAGAAC 58.986 50.000 6.13 0.00 0.00 3.01
2416 2726 7.306866 GCAAATAGAACCATTAGTGATCGTCTC 60.307 40.741 0.00 0.00 0.00 3.36
2462 3081 4.087182 TGAGTAGAGGTGAGGGTAAACAG 58.913 47.826 0.00 0.00 0.00 3.16
2489 3108 6.465035 GGCTAGAGGTTTATGAGTGATCCAAT 60.465 42.308 0.00 0.00 0.00 3.16
2527 3153 4.000988 AGTAGTAAGGCCATTGTTTGTCG 58.999 43.478 5.01 0.00 0.00 4.35
2632 3259 6.546403 GCGATGGAGTGGGAGTATCTATTATA 59.454 42.308 0.00 0.00 33.73 0.98
2655 3282 1.353358 ACCAGTTTACCCAAGGTAGGC 59.647 52.381 0.00 0.00 39.52 3.93
2665 3292 2.359994 CCCAAGGTAGGCTCTTACCCTA 60.360 54.545 1.25 0.00 43.42 3.53
2699 3326 7.711846 TGAAAGCAAACTTCATTAGTAAGCAA 58.288 30.769 0.00 0.00 38.52 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.160822 ACATGAGTCCGCATATGCTC 57.839 50.000 24.56 15.61 39.32 4.26
3 4 2.216046 CAACATGAGTCCGCATATGCT 58.784 47.619 24.56 6.50 39.32 3.79
5 6 1.265095 GCCAACATGAGTCCGCATATG 59.735 52.381 0.00 0.00 0.00 1.78
7 8 0.251634 TGCCAACATGAGTCCGCATA 59.748 50.000 0.00 0.00 29.71 3.14
8 9 0.608856 TTGCCAACATGAGTCCGCAT 60.609 50.000 0.00 0.00 33.38 4.73
9 10 1.228094 TTGCCAACATGAGTCCGCA 60.228 52.632 0.00 0.00 31.97 5.69
10 11 1.210155 GTTGCCAACATGAGTCCGC 59.790 57.895 1.91 0.00 0.00 5.54
11 12 0.888736 TGGTTGCCAACATGAGTCCG 60.889 55.000 10.18 0.00 0.00 4.79
12 13 1.327303 TTGGTTGCCAACATGAGTCC 58.673 50.000 10.18 0.00 38.75 3.85
13 14 4.009675 TCTATTGGTTGCCAACATGAGTC 58.990 43.478 10.18 0.00 46.95 3.36
14 15 4.032960 TCTATTGGTTGCCAACATGAGT 57.967 40.909 10.18 0.00 46.95 3.41
15 16 4.400251 ACATCTATTGGTTGCCAACATGAG 59.600 41.667 10.18 1.21 46.95 2.90
16 17 4.343231 ACATCTATTGGTTGCCAACATGA 58.657 39.130 10.18 10.44 46.95 3.07
17 18 4.724074 ACATCTATTGGTTGCCAACATG 57.276 40.909 10.18 5.90 46.95 3.21
18 19 6.367983 AGATACATCTATTGGTTGCCAACAT 58.632 36.000 10.18 0.00 46.95 2.71
19 20 5.754782 AGATACATCTATTGGTTGCCAACA 58.245 37.500 10.18 0.00 46.95 3.33
20 21 6.543831 AGAAGATACATCTATTGGTTGCCAAC 59.456 38.462 0.00 0.00 40.42 3.77
21 22 6.662755 AGAAGATACATCTATTGGTTGCCAA 58.337 36.000 2.86 2.86 41.26 4.52
22 23 6.252599 AGAAGATACATCTATTGGTTGCCA 57.747 37.500 0.00 0.00 35.76 4.92
23 24 7.573968 AAAGAAGATACATCTATTGGTTGCC 57.426 36.000 0.00 0.00 35.76 4.52
49 50 9.959749 ATGTTTCACATAGTTTTACAAACGAAT 57.040 25.926 0.00 0.00 36.99 3.34
50 51 9.790389 AATGTTTCACATAGTTTTACAAACGAA 57.210 25.926 0.00 0.00 37.97 3.85
51 52 9.790389 AAATGTTTCACATAGTTTTACAAACGA 57.210 25.926 0.00 0.00 37.97 3.85
89 90 9.787435 CCAAATAAATAGTATAGTTACAGGCCA 57.213 33.333 5.01 0.00 33.63 5.36
90 91 9.227777 CCCAAATAAATAGTATAGTTACAGGCC 57.772 37.037 0.00 0.00 33.63 5.19
91 92 8.727910 GCCCAAATAAATAGTATAGTTACAGGC 58.272 37.037 0.00 0.00 33.63 4.85
92 93 8.932791 CGCCCAAATAAATAGTATAGTTACAGG 58.067 37.037 0.00 0.00 33.63 4.00
93 94 8.932791 CCGCCCAAATAAATAGTATAGTTACAG 58.067 37.037 0.00 0.00 33.63 2.74
94 95 8.649591 TCCGCCCAAATAAATAGTATAGTTACA 58.350 33.333 0.00 0.00 33.63 2.41
95 96 8.929746 GTCCGCCCAAATAAATAGTATAGTTAC 58.070 37.037 0.00 0.00 33.63 2.50
96 97 8.873144 AGTCCGCCCAAATAAATAGTATAGTTA 58.127 33.333 0.00 0.00 35.44 2.24
97 98 7.742767 AGTCCGCCCAAATAAATAGTATAGTT 58.257 34.615 0.00 0.00 31.73 2.24
98 99 7.312415 AGTCCGCCCAAATAAATAGTATAGT 57.688 36.000 0.00 0.00 0.00 2.12
99 100 9.886132 AATAGTCCGCCCAAATAAATAGTATAG 57.114 33.333 0.00 0.00 0.00 1.31
101 102 9.582648 AAAATAGTCCGCCCAAATAAATAGTAT 57.417 29.630 0.00 0.00 0.00 2.12
102 103 8.842280 CAAAATAGTCCGCCCAAATAAATAGTA 58.158 33.333 0.00 0.00 0.00 1.82
103 104 7.340999 ACAAAATAGTCCGCCCAAATAAATAGT 59.659 33.333 0.00 0.00 0.00 2.12
104 105 7.712797 ACAAAATAGTCCGCCCAAATAAATAG 58.287 34.615 0.00 0.00 0.00 1.73
105 106 7.648039 ACAAAATAGTCCGCCCAAATAAATA 57.352 32.000 0.00 0.00 0.00 1.40
106 107 6.538945 ACAAAATAGTCCGCCCAAATAAAT 57.461 33.333 0.00 0.00 0.00 1.40
107 108 5.986501 ACAAAATAGTCCGCCCAAATAAA 57.013 34.783 0.00 0.00 0.00 1.40
108 109 5.986501 AACAAAATAGTCCGCCCAAATAA 57.013 34.783 0.00 0.00 0.00 1.40
109 110 5.244178 ACAAACAAAATAGTCCGCCCAAATA 59.756 36.000 0.00 0.00 0.00 1.40
110 111 4.039852 ACAAACAAAATAGTCCGCCCAAAT 59.960 37.500 0.00 0.00 0.00 2.32
111 112 3.385111 ACAAACAAAATAGTCCGCCCAAA 59.615 39.130 0.00 0.00 0.00 3.28
112 113 2.959707 ACAAACAAAATAGTCCGCCCAA 59.040 40.909 0.00 0.00 0.00 4.12
113 114 2.588620 ACAAACAAAATAGTCCGCCCA 58.411 42.857 0.00 0.00 0.00 5.36
114 115 3.653539 AACAAACAAAATAGTCCGCCC 57.346 42.857 0.00 0.00 0.00 6.13
115 116 7.646446 AATTTAACAAACAAAATAGTCCGCC 57.354 32.000 0.00 0.00 0.00 6.13
116 117 9.923786 AAAAATTTAACAAACAAAATAGTCCGC 57.076 25.926 0.00 0.00 0.00 5.54
142 143 8.819015 GCATTGCATTCAACATATTGTGAAATA 58.181 29.630 3.15 0.00 37.11 1.40
143 144 7.334671 TGCATTGCATTCAACATATTGTGAAAT 59.665 29.630 7.38 0.00 33.49 2.17
144 145 6.649557 TGCATTGCATTCAACATATTGTGAAA 59.350 30.769 7.38 0.00 33.49 2.69
145 146 6.164176 TGCATTGCATTCAACATATTGTGAA 58.836 32.000 7.38 1.31 33.49 3.18
146 147 5.721232 TGCATTGCATTCAACATATTGTGA 58.279 33.333 7.38 0.00 33.49 3.58
147 148 6.410243 TTGCATTGCATTCAACATATTGTG 57.590 33.333 12.95 0.00 38.76 3.33
148 149 7.436430 TTTTGCATTGCATTCAACATATTGT 57.564 28.000 12.95 0.00 38.76 2.71
149 150 8.793472 CAATTTTGCATTGCATTCAACATATTG 58.207 29.630 12.95 9.28 38.76 1.90
150 151 7.971168 CCAATTTTGCATTGCATTCAACATATT 59.029 29.630 12.95 0.86 38.76 1.28
151 152 7.415765 CCCAATTTTGCATTGCATTCAACATAT 60.416 33.333 12.95 0.00 38.76 1.78
152 153 6.127980 CCCAATTTTGCATTGCATTCAACATA 60.128 34.615 12.95 0.00 38.76 2.29
153 154 5.336055 CCCAATTTTGCATTGCATTCAACAT 60.336 36.000 12.95 0.00 38.76 2.71
154 155 4.023107 CCCAATTTTGCATTGCATTCAACA 60.023 37.500 12.95 0.00 38.76 3.33
155 156 4.477780 CCCAATTTTGCATTGCATTCAAC 58.522 39.130 12.95 0.00 38.76 3.18
156 157 3.057456 GCCCAATTTTGCATTGCATTCAA 60.057 39.130 12.95 6.53 38.76 2.69
157 158 2.488545 GCCCAATTTTGCATTGCATTCA 59.511 40.909 12.95 0.00 38.76 2.57
158 159 2.476519 CGCCCAATTTTGCATTGCATTC 60.477 45.455 12.95 0.00 38.76 2.67
159 160 1.469308 CGCCCAATTTTGCATTGCATT 59.531 42.857 12.95 0.76 38.76 3.56
160 161 1.088306 CGCCCAATTTTGCATTGCAT 58.912 45.000 12.95 0.00 38.76 3.96
161 162 0.954449 CCGCCCAATTTTGCATTGCA 60.954 50.000 7.38 7.38 36.47 4.08
162 163 1.795507 CCGCCCAATTTTGCATTGC 59.204 52.632 0.46 0.46 0.00 3.56
163 164 1.646624 GGCCGCCCAATTTTGCATTG 61.647 55.000 0.00 0.00 0.00 2.82
164 165 1.377072 GGCCGCCCAATTTTGCATT 60.377 52.632 0.00 0.00 0.00 3.56
165 166 2.268600 GGCCGCCCAATTTTGCAT 59.731 55.556 0.00 0.00 0.00 3.96
166 167 3.236987 TGGCCGCCCAATTTTGCA 61.237 55.556 7.03 0.00 38.46 4.08
167 168 2.434709 CTGGCCGCCCAATTTTGC 60.435 61.111 7.03 0.00 41.58 3.68
168 169 2.434709 GCTGGCCGCCCAATTTTG 60.435 61.111 7.03 0.00 41.58 2.44
188 189 2.717485 CATATGTGCAGGCGTGGC 59.283 61.111 8.72 1.33 0.00 5.01
189 190 2.188829 CCCATATGTGCAGGCGTGG 61.189 63.158 8.72 0.00 0.00 4.94
190 191 1.439353 GACCCATATGTGCAGGCGTG 61.439 60.000 1.01 1.01 0.00 5.34
191 192 1.153168 GACCCATATGTGCAGGCGT 60.153 57.895 1.24 0.00 0.00 5.68
192 193 2.246739 CGACCCATATGTGCAGGCG 61.247 63.158 1.24 0.00 0.00 5.52
193 194 1.893808 CCGACCCATATGTGCAGGC 60.894 63.158 1.24 0.00 0.00 4.85
194 195 1.893808 GCCGACCCATATGTGCAGG 60.894 63.158 1.24 0.00 0.00 4.85
195 196 2.246739 CGCCGACCCATATGTGCAG 61.247 63.158 1.24 0.00 0.00 4.41
196 197 2.203001 CGCCGACCCATATGTGCA 60.203 61.111 1.24 0.00 0.00 4.57
197 198 2.203015 ACGCCGACCCATATGTGC 60.203 61.111 1.24 0.00 0.00 4.57
198 199 0.742990 AACACGCCGACCCATATGTG 60.743 55.000 1.24 0.00 0.00 3.21
199 200 0.742990 CAACACGCCGACCCATATGT 60.743 55.000 1.24 0.00 0.00 2.29
200 201 1.436195 CCAACACGCCGACCCATATG 61.436 60.000 0.00 0.00 0.00 1.78
201 202 1.153249 CCAACACGCCGACCCATAT 60.153 57.895 0.00 0.00 0.00 1.78
202 203 1.618876 ATCCAACACGCCGACCCATA 61.619 55.000 0.00 0.00 0.00 2.74
203 204 2.966732 ATCCAACACGCCGACCCAT 61.967 57.895 0.00 0.00 0.00 4.00
204 205 3.632080 ATCCAACACGCCGACCCA 61.632 61.111 0.00 0.00 0.00 4.51
205 206 3.124921 CATCCAACACGCCGACCC 61.125 66.667 0.00 0.00 0.00 4.46
206 207 2.358247 ACATCCAACACGCCGACC 60.358 61.111 0.00 0.00 0.00 4.79
207 208 2.860293 CACATCCAACACGCCGAC 59.140 61.111 0.00 0.00 0.00 4.79
208 209 3.047280 GCACATCCAACACGCCGA 61.047 61.111 0.00 0.00 0.00 5.54
209 210 3.049674 AGCACATCCAACACGCCG 61.050 61.111 0.00 0.00 0.00 6.46
210 211 2.187599 GACAGCACATCCAACACGCC 62.188 60.000 0.00 0.00 0.00 5.68
211 212 1.207593 GACAGCACATCCAACACGC 59.792 57.895 0.00 0.00 0.00 5.34
212 213 0.943835 TCGACAGCACATCCAACACG 60.944 55.000 0.00 0.00 0.00 4.49
213 214 0.512952 GTCGACAGCACATCCAACAC 59.487 55.000 11.55 0.00 0.00 3.32
214 215 0.602638 GGTCGACAGCACATCCAACA 60.603 55.000 18.91 0.00 0.00 3.33
215 216 1.298859 GGGTCGACAGCACATCCAAC 61.299 60.000 18.91 0.00 0.00 3.77
216 217 1.003839 GGGTCGACAGCACATCCAA 60.004 57.895 18.91 0.00 0.00 3.53
217 218 1.552799 ATGGGTCGACAGCACATCCA 61.553 55.000 18.91 13.60 0.00 3.41
218 219 0.464036 TATGGGTCGACAGCACATCC 59.536 55.000 18.91 7.85 0.00 3.51
219 220 2.138320 CATATGGGTCGACAGCACATC 58.862 52.381 18.91 0.00 0.00 3.06
220 221 1.762370 TCATATGGGTCGACAGCACAT 59.238 47.619 18.91 16.66 0.00 3.21
221 222 1.190643 TCATATGGGTCGACAGCACA 58.809 50.000 18.91 10.67 0.00 4.57
222 223 2.309528 TTCATATGGGTCGACAGCAC 57.690 50.000 18.91 4.90 0.00 4.40
223 224 3.342377 TTTTCATATGGGTCGACAGCA 57.658 42.857 18.91 0.00 0.00 4.41
224 225 3.438781 TGTTTTTCATATGGGTCGACAGC 59.561 43.478 18.91 0.00 0.00 4.40
225 226 4.094887 CCTGTTTTTCATATGGGTCGACAG 59.905 45.833 18.91 10.50 33.60 3.51
226 227 4.006989 CCTGTTTTTCATATGGGTCGACA 58.993 43.478 18.91 0.00 0.00 4.35
227 228 4.094442 GTCCTGTTTTTCATATGGGTCGAC 59.906 45.833 7.13 7.13 0.00 4.20
228 229 4.258543 GTCCTGTTTTTCATATGGGTCGA 58.741 43.478 2.13 0.00 0.00 4.20
229 230 3.063452 CGTCCTGTTTTTCATATGGGTCG 59.937 47.826 2.13 0.47 0.00 4.79
230 231 3.377172 CCGTCCTGTTTTTCATATGGGTC 59.623 47.826 2.13 0.00 0.00 4.46
231 232 3.009695 TCCGTCCTGTTTTTCATATGGGT 59.990 43.478 2.13 0.00 0.00 4.51
232 233 3.377172 GTCCGTCCTGTTTTTCATATGGG 59.623 47.826 2.13 0.00 0.00 4.00
233 234 3.063452 CGTCCGTCCTGTTTTTCATATGG 59.937 47.826 2.13 0.00 0.00 2.74
234 235 3.485216 GCGTCCGTCCTGTTTTTCATATG 60.485 47.826 0.00 0.00 0.00 1.78
235 236 2.676342 GCGTCCGTCCTGTTTTTCATAT 59.324 45.455 0.00 0.00 0.00 1.78
236 237 2.070783 GCGTCCGTCCTGTTTTTCATA 58.929 47.619 0.00 0.00 0.00 2.15
237 238 0.872388 GCGTCCGTCCTGTTTTTCAT 59.128 50.000 0.00 0.00 0.00 2.57
238 239 1.161563 GGCGTCCGTCCTGTTTTTCA 61.162 55.000 0.00 0.00 0.00 2.69
239 240 1.572941 GGCGTCCGTCCTGTTTTTC 59.427 57.895 0.00 0.00 0.00 2.29
240 241 2.248835 CGGCGTCCGTCCTGTTTTT 61.249 57.895 9.69 0.00 42.73 1.94
241 242 2.663852 CGGCGTCCGTCCTGTTTT 60.664 61.111 9.69 0.00 42.73 2.43
242 243 4.675029 CCGGCGTCCGTCCTGTTT 62.675 66.667 15.38 0.00 46.80 2.83
265 266 3.047877 GTCCGTTTGGGTCGGCTG 61.048 66.667 0.00 0.00 46.49 4.85
266 267 2.612095 TTTGTCCGTTTGGGTCGGCT 62.612 55.000 0.00 0.00 46.49 5.52
267 268 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
284 285 0.110554 CGGCGATTTCGTCCGTTTTT 60.111 50.000 20.13 0.00 46.11 1.94
285 286 1.494189 CGGCGATTTCGTCCGTTTT 59.506 52.632 20.13 0.00 46.11 2.43
286 287 3.161817 CGGCGATTTCGTCCGTTT 58.838 55.556 20.13 0.00 46.11 3.60
290 291 2.693285 CGAACGGCGATTTCGTCC 59.307 61.111 16.62 1.69 44.57 4.79
294 295 0.453782 CCCAAACGAACGGCGATTTC 60.454 55.000 16.62 7.09 44.57 2.17
295 296 1.167781 ACCCAAACGAACGGCGATTT 61.168 50.000 16.62 5.62 44.57 2.17
296 297 1.571215 GACCCAAACGAACGGCGATT 61.571 55.000 16.62 3.78 44.57 3.34
297 298 2.030958 GACCCAAACGAACGGCGAT 61.031 57.895 16.62 0.00 44.57 4.58
298 299 2.662527 GACCCAAACGAACGGCGA 60.663 61.111 16.62 0.00 44.57 5.54
300 301 3.719144 CCGACCCAAACGAACGGC 61.719 66.667 0.00 0.00 37.32 5.68
301 302 3.719144 GCCGACCCAAACGAACGG 61.719 66.667 0.00 0.00 45.26 4.44
302 303 3.719144 GGCCGACCCAAACGAACG 61.719 66.667 0.00 0.00 0.00 3.95
312 313 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
313 314 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
316 317 3.056328 GAGCAACTCCAACGGGCC 61.056 66.667 0.00 0.00 0.00 5.80
317 318 0.321298 TAAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
318 319 2.009774 CATAAGAGCAACTCCAACGGG 58.990 52.381 0.00 0.00 0.00 5.28
319 320 2.673368 GACATAAGAGCAACTCCAACGG 59.327 50.000 0.00 0.00 0.00 4.44
320 321 3.325870 TGACATAAGAGCAACTCCAACG 58.674 45.455 0.00 0.00 0.00 4.10
321 322 4.333926 GGATGACATAAGAGCAACTCCAAC 59.666 45.833 0.00 0.00 0.00 3.77
322 323 4.225942 AGGATGACATAAGAGCAACTCCAA 59.774 41.667 0.00 0.00 0.00 3.53
323 324 3.776969 AGGATGACATAAGAGCAACTCCA 59.223 43.478 0.00 0.00 0.00 3.86
324 325 4.141846 TGAGGATGACATAAGAGCAACTCC 60.142 45.833 0.00 0.00 0.00 3.85
325 326 5.016051 TGAGGATGACATAAGAGCAACTC 57.984 43.478 0.00 0.00 0.00 3.01
326 327 4.469227 ACTGAGGATGACATAAGAGCAACT 59.531 41.667 0.00 0.00 0.00 3.16
327 328 4.569966 CACTGAGGATGACATAAGAGCAAC 59.430 45.833 0.00 0.00 0.00 4.17
328 329 4.467438 TCACTGAGGATGACATAAGAGCAA 59.533 41.667 0.00 0.00 0.00 3.91
347 348 4.712337 ACGGAAGATAAGGTTGAGATCACT 59.288 41.667 0.00 0.00 0.00 3.41
367 368 1.153628 GGGACATCGGTCAGAACGG 60.154 63.158 8.31 0.00 46.17 4.44
395 396 4.569943 TCCTGCTTGTTGTCTTGATAGTC 58.430 43.478 0.00 0.00 0.00 2.59
489 490 7.700234 TGCGGTGCATTATTAAGTGAAAAATAG 59.300 33.333 0.00 0.00 31.71 1.73
531 533 3.260475 TCGTATGGATGACTTTGTGGG 57.740 47.619 0.00 0.00 0.00 4.61
545 547 5.538118 TGGTTGCCATATAGTCTTCGTATG 58.462 41.667 0.00 0.00 0.00 2.39
602 604 3.330267 GTGCTCTCTCCAACACCTTTAG 58.670 50.000 0.00 0.00 0.00 1.85
605 607 0.034059 CGTGCTCTCTCCAACACCTT 59.966 55.000 0.00 0.00 0.00 3.50
625 627 1.001181 GTTGGGCACTTGGACGTACTA 59.999 52.381 0.00 0.00 0.00 1.82
626 628 0.250166 GTTGGGCACTTGGACGTACT 60.250 55.000 0.00 0.00 0.00 2.73
627 629 0.533308 TGTTGGGCACTTGGACGTAC 60.533 55.000 0.00 0.00 0.00 3.67
685 687 2.383527 GCTGACCGAGTCTTTGGCG 61.384 63.158 5.77 0.00 33.15 5.69
697 699 0.610232 ACCCTGCATTTCAGCTGACC 60.610 55.000 18.03 5.92 41.50 4.02
749 755 4.128643 CCCGTATCTTCTACGAACTCTCT 58.871 47.826 6.37 0.00 42.94 3.10
788 794 7.021196 CAGTGTTTTGTTATCCCGTAGAAATG 58.979 38.462 0.00 0.00 0.00 2.32
815 821 2.667724 CGGGTCAAGTGAAGTCTACGAC 60.668 54.545 0.00 0.00 0.00 4.34
858 864 6.440647 TGTAGGGCAAATATATAGAGTGGAGG 59.559 42.308 0.00 0.00 0.00 4.30
859 865 7.324178 GTGTAGGGCAAATATATAGAGTGGAG 58.676 42.308 0.00 0.00 0.00 3.86
860 866 6.071560 CGTGTAGGGCAAATATATAGAGTGGA 60.072 42.308 0.00 0.00 0.00 4.02
861 867 6.071560 TCGTGTAGGGCAAATATATAGAGTGG 60.072 42.308 0.00 0.00 0.00 4.00
862 868 6.807230 GTCGTGTAGGGCAAATATATAGAGTG 59.193 42.308 0.00 0.00 0.00 3.51
863 869 6.720288 AGTCGTGTAGGGCAAATATATAGAGT 59.280 38.462 0.00 0.00 0.00 3.24
864 870 7.159322 AGTCGTGTAGGGCAAATATATAGAG 57.841 40.000 0.00 0.00 0.00 2.43
865 871 7.231925 TGAAGTCGTGTAGGGCAAATATATAGA 59.768 37.037 0.00 0.00 0.00 1.98
868 874 5.989777 GTGAAGTCGTGTAGGGCAAATATAT 59.010 40.000 0.00 0.00 0.00 0.86
874 880 1.045407 AGTGAAGTCGTGTAGGGCAA 58.955 50.000 0.00 0.00 0.00 4.52
885 891 1.069204 TGTGAGTGGCTCAGTGAAGTC 59.931 52.381 0.00 0.00 41.46 3.01
890 896 0.037882 ACGATGTGAGTGGCTCAGTG 60.038 55.000 0.00 0.00 41.46 3.66
915 921 1.151777 CGATCGATCGGGGTTGGTTG 61.152 60.000 34.54 7.49 45.93 3.77
948 956 0.955919 GGAGGAAGGTTCGGTGCTTG 60.956 60.000 0.00 0.00 0.00 4.01
985 994 1.227380 CCATGCTCGCTCACTACCC 60.227 63.158 0.00 0.00 0.00 3.69
1375 1390 0.463654 TCAACCGATACTGGCATGGC 60.464 55.000 13.29 13.29 0.00 4.40
1376 1391 1.299541 GTCAACCGATACTGGCATGG 58.700 55.000 0.00 0.00 0.00 3.66
1377 1392 2.022764 TGTCAACCGATACTGGCATG 57.977 50.000 0.00 0.00 0.00 4.06
1440 1479 3.417275 ATCGAGCTCGCGAACCCAG 62.417 63.158 30.97 1.91 44.22 4.45
1585 1624 0.105593 CCCAGACGAGGATGTCCATG 59.894 60.000 1.30 0.00 39.77 3.66
1717 1756 2.194212 TCCGGCTGGACGATAGAGC 61.194 63.158 11.27 0.00 40.17 4.09
1784 1824 1.393603 TCACTGAGCATACTCCCTCG 58.606 55.000 0.00 0.00 42.74 4.63
1813 1860 5.123979 AGCTTGAAGAAAACGGTAATCATCC 59.876 40.000 0.00 0.00 0.00 3.51
1848 1895 5.094812 GCGTCAATTCATTAACATCAGCAA 58.905 37.500 0.00 0.00 0.00 3.91
1872 1953 1.998315 CAGCAGTATGTCACACAGCTC 59.002 52.381 0.00 0.00 39.31 4.09
1895 1976 3.428870 CACGTGACTGTCCATTCACTAAC 59.571 47.826 10.90 0.00 38.41 2.34
1906 2024 2.795175 TCTCCTTTCACGTGACTGTC 57.205 50.000 19.90 0.00 0.00 3.51
1988 2242 2.230266 CCCCACGGTGATTGTTAAAAGG 59.770 50.000 10.28 0.00 0.00 3.11
1989 2243 3.150767 TCCCCACGGTGATTGTTAAAAG 58.849 45.455 10.28 0.00 0.00 2.27
2052 2334 1.751924 CTAGCGCTCTCTTGTAACCCT 59.248 52.381 16.34 0.00 0.00 4.34
2053 2335 1.803252 GCTAGCGCTCTCTTGTAACCC 60.803 57.143 16.34 0.00 0.00 4.11
2114 2397 8.807948 TGAAACCTTAGATTCCCTCATAAAAG 57.192 34.615 0.00 0.00 0.00 2.27
2124 2407 4.254492 ACGCTTCTGAAACCTTAGATTCC 58.746 43.478 0.00 0.00 0.00 3.01
2133 2416 4.174762 CCTAGAACTACGCTTCTGAAACC 58.825 47.826 0.00 0.00 32.54 3.27
2135 2418 4.280174 ACACCTAGAACTACGCTTCTGAAA 59.720 41.667 0.00 0.00 32.54 2.69
2145 2454 7.907214 ATGAAAATCACACACCTAGAACTAC 57.093 36.000 0.00 0.00 0.00 2.73
2150 2459 4.154015 CGCAATGAAAATCACACACCTAGA 59.846 41.667 0.00 0.00 0.00 2.43
2181 2491 2.685850 TAGGGCTTTAGGAACGCTTC 57.314 50.000 0.00 0.00 0.00 3.86
2208 2518 5.276270 GTCGGTCGTGCTCACTATTTTATA 58.724 41.667 0.00 0.00 0.00 0.98
2210 2520 3.504863 GTCGGTCGTGCTCACTATTTTA 58.495 45.455 0.00 0.00 0.00 1.52
2225 2535 1.133869 CGAAATTTGGCCGTCGGTC 59.866 57.895 9.51 9.51 0.00 4.79
2243 2553 1.315257 TACCAACCGGGCTCGACTAC 61.315 60.000 8.08 0.00 42.05 2.73
2262 2572 9.869757 GCTTGTTGTAATTTGGGATATAACTTT 57.130 29.630 0.00 0.00 0.00 2.66
2266 2576 7.771361 TCTCGCTTGTTGTAATTTGGGATATAA 59.229 33.333 0.00 0.00 0.00 0.98
2280 2590 1.160329 GCACCACTCTCGCTTGTTGT 61.160 55.000 0.00 0.00 0.00 3.32
2283 2593 2.356313 CGCACCACTCTCGCTTGT 60.356 61.111 0.00 0.00 0.00 3.16
2315 2625 0.397941 TTGCAGTTCAGGTCTGGGAG 59.602 55.000 0.00 0.00 33.98 4.30
2342 2652 3.466836 TGCTACTCACTTGTTTGTCCAG 58.533 45.455 0.00 0.00 0.00 3.86
2387 2697 4.196193 TCACTAATGGTTCTATTTGCCCG 58.804 43.478 0.00 0.00 0.00 6.13
2400 2710 4.500545 CCTCAAGGAGACGATCACTAATGG 60.501 50.000 0.00 0.00 37.39 3.16
2416 2726 4.256920 CACCAAGTACAATCTCCTCAAGG 58.743 47.826 0.00 0.00 0.00 3.61
2431 2741 3.305720 TCACCTCTACTCAACACCAAGT 58.694 45.455 0.00 0.00 0.00 3.16
2462 3081 4.737855 TCACTCATAAACCTCTAGCCAC 57.262 45.455 0.00 0.00 0.00 5.01
2519 3145 1.686355 ATCCTTTGTGCCGACAAACA 58.314 45.000 0.00 0.00 45.26 2.83
2520 3146 5.751243 ATATATCCTTTGTGCCGACAAAC 57.249 39.130 0.00 0.00 45.26 2.93
2527 3153 7.547227 ACACTTCAAAATATATCCTTTGTGCC 58.453 34.615 8.89 0.00 34.74 5.01
2632 3259 3.842436 CCTACCTTGGGTAAACTGGTACT 59.158 47.826 0.00 0.00 37.76 2.73
2655 3282 7.660208 TGCTTTCAAACTACTTTAGGGTAAGAG 59.340 37.037 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.