Multiple sequence alignment - TraesCS4D01G356000

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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 TraesCS4D01G356000 chr4D 100.000 1661 0 0 1 1661 505238851 505237191 0.000000e+00 3068.0
1 TraesCS4D01G356000 chr4D 100.000 470 0 0 1906 2375 505236946 505236477 0.000000e+00 869.0
2 TraesCS4D01G356000 chr4B 94.752 1372 51 5 295 1661 651903371 651904726 0.000000e+00 2115.0
3 TraesCS4D01G356000 chr4B 94.492 472 22 3 1906 2374 651904771 651905241 0.000000e+00 725.0
4 TraesCS4D01G356000 chr4B 96.358 302 7 1 1 298 651811935 651812236 5.900000e-136 494.0
5 TraesCS4D01G356000 chr4B 95.033 302 11 1 1 298 651874172 651874473 2.760000e-129 472.0
6 TraesCS4D01G356000 chr4B 90.873 252 22 1 2125 2375 25711702 25711451 1.050000e-88 337.0
7 TraesCS4D01G356000 chr4B 77.477 222 48 2 2020 2240 60548638 60548858 5.330000e-27 132.0
8 TraesCS4D01G356000 chr4B 79.255 188 36 3 2000 2185 421497457 421497271 6.890000e-26 128.0
9 TraesCS4D01G356000 chr5A 87.742 930 74 22 741 1639 689387365 689386445 0.000000e+00 1050.0
10 TraesCS4D01G356000 chr6D 88.564 376 39 4 2001 2374 304618659 304619032 1.000000e-123 453.0
11 TraesCS4D01G356000 chr2B 79.249 453 74 5 239 673 768806751 768806301 4.960000e-77 298.0
12 TraesCS4D01G356000 chr2D 79.369 412 64 9 239 632 19587259 19587667 1.080000e-68 270.0
13 TraesCS4D01G356000 chr2D 78.409 440 73 12 239 659 9604998 9605434 1.400000e-67 267.0
14 TraesCS4D01G356000 chr2D 77.650 434 76 7 243 658 9879502 9879072 6.560000e-61 244.0
15 TraesCS4D01G356000 chr2A 78.372 430 73 6 243 654 9847856 9848283 6.510000e-66 261.0
16 TraesCS4D01G356000 chr2A 77.907 430 75 6 243 654 9395379 9395806 1.410000e-62 250.0
17 TraesCS4D01G356000 chr2A 77.674 430 74 8 239 649 8707645 8708071 2.360000e-60 243.0
18 TraesCS4D01G356000 chr2A 78.421 190 33 7 2000 2185 618997356 618997171 1.490000e-22 117.0
19 TraesCS4D01G356000 chr2A 96.774 31 1 0 179 209 9118953 9118923 4.000000e-03 52.8
20 TraesCS4D01G356000 chr1B 79.360 344 57 8 303 632 44647025 44647368 1.840000e-56 230.0
21 TraesCS4D01G356000 chr1A 82.000 250 43 2 2127 2375 559930872 559930624 6.650000e-51 211.0
22 TraesCS4D01G356000 chr5D 76.640 381 80 9 2000 2375 356693953 356694329 4.000000e-48 202.0
23 TraesCS4D01G356000 chr5D 79.581 191 32 6 1999 2185 30547018 30546831 1.920000e-26 130.0
24 TraesCS4D01G356000 chr7D 79.255 188 36 3 2000 2185 419798962 419799148 6.890000e-26 128.0
25 TraesCS4D01G356000 chr7B 76.132 243 55 3 2000 2240 544417598 544417839 8.910000e-25 124.0


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 TraesCS4D01G356000 chr4D 505236477 505238851 2374 True 1968.5 3068 100.000 1 2375 2 chr4D.!!$R1 2374
1 TraesCS4D01G356000 chr4B 651903371 651905241 1870 False 1420.0 2115 94.622 295 2374 2 chr4B.!!$F4 2079
2 TraesCS4D01G356000 chr5A 689386445 689387365 920 True 1050.0 1050 87.742 741 1639 1 chr5A.!!$R1 898

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
272 273 0.032615 AAACCCTCCCAAACAGTGCA 60.033 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2182 0.036671 GGGTTCGTCGTTCTGGGAAT 60.037 55.0 0.0 0.0 0.0 3.01 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 2.542020 TTGTGTTGCTCGGAGATGAA 57.458 45.000 9.69 0.00 33.89 2.57
20 21 2.542020 TGTGTTGCTCGGAGATGAAA 57.458 45.000 9.69 0.00 33.89 2.69
21 22 3.057969 TGTGTTGCTCGGAGATGAAAT 57.942 42.857 9.69 0.00 33.89 2.17
22 23 4.200838 TGTGTTGCTCGGAGATGAAATA 57.799 40.909 9.69 0.00 33.89 1.40
23 24 4.574892 TGTGTTGCTCGGAGATGAAATAA 58.425 39.130 9.69 0.00 33.89 1.40
24 25 5.185454 TGTGTTGCTCGGAGATGAAATAAT 58.815 37.500 9.69 0.00 33.89 1.28
25 26 5.647658 TGTGTTGCTCGGAGATGAAATAATT 59.352 36.000 9.69 0.00 33.89 1.40
26 27 6.150976 TGTGTTGCTCGGAGATGAAATAATTT 59.849 34.615 9.69 0.00 33.89 1.82
27 28 7.029563 GTGTTGCTCGGAGATGAAATAATTTT 58.970 34.615 9.69 0.00 33.89 1.82
28 29 8.181573 GTGTTGCTCGGAGATGAAATAATTTTA 58.818 33.333 9.69 0.00 33.89 1.52
29 30 8.181573 TGTTGCTCGGAGATGAAATAATTTTAC 58.818 33.333 9.69 0.00 33.89 2.01
30 31 8.398665 GTTGCTCGGAGATGAAATAATTTTACT 58.601 33.333 9.69 0.00 33.89 2.24
31 32 8.142994 TGCTCGGAGATGAAATAATTTTACTC 57.857 34.615 9.69 0.00 33.89 2.59
32 33 7.987458 TGCTCGGAGATGAAATAATTTTACTCT 59.013 33.333 9.69 0.00 33.89 3.24
33 34 8.279103 GCTCGGAGATGAAATAATTTTACTCTG 58.721 37.037 9.69 0.00 33.89 3.35
34 35 9.534565 CTCGGAGATGAAATAATTTTACTCTGA 57.465 33.333 0.00 0.00 35.77 3.27
43 44 9.670719 GAAATAATTTTACTCTGATTAGCTGGC 57.329 33.333 0.00 0.00 0.00 4.85
44 45 8.752005 AATAATTTTACTCTGATTAGCTGGCA 57.248 30.769 0.00 0.00 0.00 4.92
45 46 8.752005 ATAATTTTACTCTGATTAGCTGGCAA 57.248 30.769 0.00 0.00 0.00 4.52
46 47 7.466746 AATTTTACTCTGATTAGCTGGCAAA 57.533 32.000 0.00 0.00 0.00 3.68
47 48 7.651027 ATTTTACTCTGATTAGCTGGCAAAT 57.349 32.000 0.00 0.00 0.00 2.32
48 49 6.683974 TTTACTCTGATTAGCTGGCAAATC 57.316 37.500 0.00 0.00 33.57 2.17
49 50 4.500499 ACTCTGATTAGCTGGCAAATCT 57.500 40.909 10.73 1.35 34.00 2.40
50 51 4.853007 ACTCTGATTAGCTGGCAAATCTT 58.147 39.130 10.73 0.00 34.00 2.40
51 52 5.259632 ACTCTGATTAGCTGGCAAATCTTT 58.740 37.500 10.73 0.00 34.00 2.52
52 53 5.713861 ACTCTGATTAGCTGGCAAATCTTTT 59.286 36.000 10.73 0.00 34.00 2.27
53 54 5.957798 TCTGATTAGCTGGCAAATCTTTTG 58.042 37.500 10.73 0.00 34.00 2.44
54 55 5.075858 TGATTAGCTGGCAAATCTTTTGG 57.924 39.130 10.73 0.00 34.00 3.28
55 56 4.771577 TGATTAGCTGGCAAATCTTTTGGA 59.228 37.500 10.73 0.00 34.00 3.53
56 57 5.245751 TGATTAGCTGGCAAATCTTTTGGAA 59.754 36.000 10.73 0.00 34.00 3.53
57 58 3.391506 AGCTGGCAAATCTTTTGGAAC 57.608 42.857 2.50 0.00 0.00 3.62
58 59 2.699846 AGCTGGCAAATCTTTTGGAACA 59.300 40.909 2.50 0.00 0.00 3.18
92 93 9.748708 TTGTTTCTGTTGAGAATTATCTTTTGG 57.251 29.630 1.19 0.00 38.05 3.28
93 94 8.359642 TGTTTCTGTTGAGAATTATCTTTTGGG 58.640 33.333 1.19 0.00 38.05 4.12
94 95 8.576442 GTTTCTGTTGAGAATTATCTTTTGGGA 58.424 33.333 1.19 0.00 38.05 4.37
95 96 8.704849 TTCTGTTGAGAATTATCTTTTGGGAA 57.295 30.769 1.19 0.00 35.54 3.97
96 97 8.110860 TCTGTTGAGAATTATCTTTTGGGAAC 57.889 34.615 1.19 0.00 35.54 3.62
97 98 7.723616 TCTGTTGAGAATTATCTTTTGGGAACA 59.276 33.333 1.19 1.40 35.54 3.18
98 99 8.243961 TGTTGAGAATTATCTTTTGGGAACAA 57.756 30.769 1.19 0.00 42.19 2.83
99 100 8.141268 TGTTGAGAATTATCTTTTGGGAACAAC 58.859 33.333 1.19 0.00 43.10 3.32
100 101 8.360390 GTTGAGAATTATCTTTTGGGAACAACT 58.640 33.333 1.19 0.00 43.10 3.16
101 102 7.885297 TGAGAATTATCTTTTGGGAACAACTG 58.115 34.615 1.19 0.00 43.10 3.16
102 103 7.039784 TGAGAATTATCTTTTGGGAACAACTGG 60.040 37.037 1.19 0.00 43.10 4.00
103 104 7.039714 GAGAATTATCTTTTGGGAACAACTGGT 60.040 37.037 0.00 0.00 43.10 4.00
110 111 3.374042 TGGGAACAACTGGTCTGAAAA 57.626 42.857 0.00 0.00 37.44 2.29
111 112 3.702792 TGGGAACAACTGGTCTGAAAAA 58.297 40.909 0.00 0.00 37.44 1.94
131 132 5.921962 AAAAGAAGTCCATAGGCCAATTC 57.078 39.130 5.01 0.00 0.00 2.17
132 133 3.584733 AGAAGTCCATAGGCCAATTCC 57.415 47.619 5.01 0.00 0.00 3.01
133 134 3.126453 AGAAGTCCATAGGCCAATTCCT 58.874 45.455 5.01 0.00 40.21 3.36
134 135 3.137360 AGAAGTCCATAGGCCAATTCCTC 59.863 47.826 5.01 0.00 37.66 3.71
135 136 1.417890 AGTCCATAGGCCAATTCCTCG 59.582 52.381 5.01 0.00 37.66 4.63
136 137 1.141053 GTCCATAGGCCAATTCCTCGT 59.859 52.381 5.01 0.00 37.66 4.18
137 138 1.416401 TCCATAGGCCAATTCCTCGTC 59.584 52.381 5.01 0.00 37.66 4.20
138 139 1.502231 CATAGGCCAATTCCTCGTCG 58.498 55.000 5.01 0.00 37.66 5.12
139 140 0.249911 ATAGGCCAATTCCTCGTCGC 60.250 55.000 5.01 0.00 37.66 5.19
140 141 1.609635 TAGGCCAATTCCTCGTCGCA 61.610 55.000 5.01 0.00 37.66 5.10
141 142 2.464459 GGCCAATTCCTCGTCGCAG 61.464 63.158 0.00 0.00 0.00 5.18
142 143 3.093278 CCAATTCCTCGTCGCAGC 58.907 61.111 0.00 0.00 0.00 5.25
143 144 1.448540 CCAATTCCTCGTCGCAGCT 60.449 57.895 0.00 0.00 0.00 4.24
144 145 1.699656 CCAATTCCTCGTCGCAGCTG 61.700 60.000 10.11 10.11 0.00 4.24
145 146 1.448540 AATTCCTCGTCGCAGCTGG 60.449 57.895 17.12 5.82 0.00 4.85
146 147 4.742201 TTCCTCGTCGCAGCTGGC 62.742 66.667 17.12 6.97 39.90 4.85
159 160 3.451665 CTGGCCAGCAGCTTGTTT 58.548 55.556 22.33 0.00 43.05 2.83
160 161 1.744014 CTGGCCAGCAGCTTGTTTT 59.256 52.632 22.33 0.00 43.05 2.43
161 162 0.319297 CTGGCCAGCAGCTTGTTTTC 60.319 55.000 22.33 0.00 43.05 2.29
162 163 1.042003 TGGCCAGCAGCTTGTTTTCA 61.042 50.000 0.00 0.00 43.05 2.69
163 164 0.104671 GGCCAGCAGCTTGTTTTCAA 59.895 50.000 0.00 0.00 43.05 2.69
178 179 7.487822 TTGTTTTCAAGATTATGGGCCATAA 57.512 32.000 34.45 34.45 36.58 1.90
179 180 7.673641 TGTTTTCAAGATTATGGGCCATAAT 57.326 32.000 39.16 39.16 45.94 1.28
180 181 7.499292 TGTTTTCAAGATTATGGGCCATAATG 58.501 34.615 42.02 32.42 44.11 1.90
181 182 7.125507 TGTTTTCAAGATTATGGGCCATAATGT 59.874 33.333 42.02 37.14 44.11 2.71
182 183 6.899393 TTCAAGATTATGGGCCATAATGTC 57.101 37.500 42.02 32.49 44.11 3.06
183 184 5.324409 TCAAGATTATGGGCCATAATGTCC 58.676 41.667 42.02 30.90 44.11 4.02
184 185 5.074929 TCAAGATTATGGGCCATAATGTCCT 59.925 40.000 42.02 32.18 44.11 3.85
185 186 5.184892 AGATTATGGGCCATAATGTCCTC 57.815 43.478 42.02 31.34 44.11 3.71
186 187 3.806949 TTATGGGCCATAATGTCCTCC 57.193 47.619 30.44 0.00 32.27 4.30
187 188 0.401738 ATGGGCCATAATGTCCTCCG 59.598 55.000 19.68 0.00 0.00 4.63
188 189 1.073199 GGGCCATAATGTCCTCCGG 59.927 63.158 4.39 0.00 0.00 5.14
189 190 1.415672 GGGCCATAATGTCCTCCGGA 61.416 60.000 4.39 2.93 0.00 5.14
190 191 0.472471 GGCCATAATGTCCTCCGGAA 59.528 55.000 5.23 0.00 31.38 4.30
191 192 1.543429 GGCCATAATGTCCTCCGGAAG 60.543 57.143 5.23 0.00 31.38 3.46
192 193 1.416401 GCCATAATGTCCTCCGGAAGA 59.584 52.381 5.23 0.63 31.38 2.87
193 194 2.039084 GCCATAATGTCCTCCGGAAGAT 59.961 50.000 5.94 0.00 31.38 2.40
194 195 3.496870 GCCATAATGTCCTCCGGAAGATT 60.497 47.826 5.94 4.91 31.38 2.40
195 196 4.262894 GCCATAATGTCCTCCGGAAGATTA 60.263 45.833 5.94 7.09 31.38 1.75
196 197 5.238583 CCATAATGTCCTCCGGAAGATTAC 58.761 45.833 5.94 0.41 31.38 1.89
197 198 5.012148 CCATAATGTCCTCCGGAAGATTACT 59.988 44.000 5.94 0.00 31.38 2.24
198 199 6.210784 CCATAATGTCCTCCGGAAGATTACTA 59.789 42.308 5.94 0.00 31.38 1.82
199 200 5.532664 AATGTCCTCCGGAAGATTACTAC 57.467 43.478 5.94 0.00 31.38 2.73
200 201 4.246712 TGTCCTCCGGAAGATTACTACT 57.753 45.455 5.94 0.00 31.38 2.57
201 202 5.378230 TGTCCTCCGGAAGATTACTACTA 57.622 43.478 5.94 0.00 31.38 1.82
202 203 5.759059 TGTCCTCCGGAAGATTACTACTAA 58.241 41.667 5.94 0.00 31.38 2.24
203 204 6.189859 TGTCCTCCGGAAGATTACTACTAAA 58.810 40.000 5.94 0.00 31.38 1.85
204 205 6.320672 TGTCCTCCGGAAGATTACTACTAAAG 59.679 42.308 5.94 0.00 31.38 1.85
205 206 6.320926 GTCCTCCGGAAGATTACTACTAAAGT 59.679 42.308 5.94 0.00 36.34 2.66
206 207 6.320672 TCCTCCGGAAGATTACTACTAAAGTG 59.679 42.308 5.23 0.00 39.39 3.16
207 208 6.096564 CCTCCGGAAGATTACTACTAAAGTGT 59.903 42.308 5.23 0.00 39.39 3.55
208 209 6.860080 TCCGGAAGATTACTACTAAAGTGTG 58.140 40.000 0.00 0.00 39.39 3.82
209 210 6.040878 CCGGAAGATTACTACTAAAGTGTGG 58.959 44.000 0.00 0.00 39.39 4.17
210 211 6.127535 CCGGAAGATTACTACTAAAGTGTGGA 60.128 42.308 0.00 0.00 39.39 4.02
211 212 7.318141 CGGAAGATTACTACTAAAGTGTGGAA 58.682 38.462 0.00 0.00 39.39 3.53
212 213 7.980099 CGGAAGATTACTACTAAAGTGTGGAAT 59.020 37.037 0.00 0.00 39.39 3.01
219 220 9.701098 TTACTACTAAAGTGTGGAATAGTTGTG 57.299 33.333 8.44 0.00 39.39 3.33
220 221 7.959175 ACTACTAAAGTGTGGAATAGTTGTGA 58.041 34.615 0.00 0.00 36.93 3.58
221 222 8.594550 ACTACTAAAGTGTGGAATAGTTGTGAT 58.405 33.333 0.00 0.00 36.93 3.06
222 223 9.436957 CTACTAAAGTGTGGAATAGTTGTGATT 57.563 33.333 0.00 0.00 31.46 2.57
223 224 8.324163 ACTAAAGTGTGGAATAGTTGTGATTC 57.676 34.615 0.00 0.00 33.34 2.52
224 225 8.157476 ACTAAAGTGTGGAATAGTTGTGATTCT 58.843 33.333 0.00 0.00 34.36 2.40
225 226 7.440523 AAAGTGTGGAATAGTTGTGATTCTC 57.559 36.000 0.00 0.00 34.36 2.87
226 227 6.114187 AGTGTGGAATAGTTGTGATTCTCA 57.886 37.500 0.00 0.00 34.36 3.27
227 228 6.715280 AGTGTGGAATAGTTGTGATTCTCAT 58.285 36.000 0.00 0.00 34.36 2.90
228 229 7.851228 AGTGTGGAATAGTTGTGATTCTCATA 58.149 34.615 0.00 0.00 34.36 2.15
229 230 8.489489 AGTGTGGAATAGTTGTGATTCTCATAT 58.511 33.333 0.00 0.00 34.36 1.78
230 231 9.113838 GTGTGGAATAGTTGTGATTCTCATATT 57.886 33.333 0.00 0.00 34.36 1.28
267 268 3.163616 GGTATCAAACCCTCCCAAACA 57.836 47.619 0.00 0.00 43.16 2.83
268 269 3.089284 GGTATCAAACCCTCCCAAACAG 58.911 50.000 0.00 0.00 43.16 3.16
269 270 3.499745 GGTATCAAACCCTCCCAAACAGT 60.500 47.826 0.00 0.00 43.16 3.55
270 271 2.065899 TCAAACCCTCCCAAACAGTG 57.934 50.000 0.00 0.00 0.00 3.66
271 272 0.389025 CAAACCCTCCCAAACAGTGC 59.611 55.000 0.00 0.00 0.00 4.40
272 273 0.032615 AAACCCTCCCAAACAGTGCA 60.033 50.000 0.00 0.00 0.00 4.57
273 274 0.188342 AACCCTCCCAAACAGTGCAT 59.812 50.000 0.00 0.00 0.00 3.96
274 275 0.540365 ACCCTCCCAAACAGTGCATG 60.540 55.000 0.00 0.00 0.00 4.06
275 276 1.252904 CCCTCCCAAACAGTGCATGG 61.253 60.000 7.64 7.64 0.00 3.66
276 277 0.540365 CCTCCCAAACAGTGCATGGT 60.540 55.000 12.42 0.00 32.13 3.55
277 278 1.331214 CTCCCAAACAGTGCATGGTT 58.669 50.000 12.42 1.65 40.37 3.67
278 279 1.688197 CTCCCAAACAGTGCATGGTTT 59.312 47.619 11.53 11.53 36.38 3.27
285 286 1.614903 ACAGTGCATGGTTTGACATGG 59.385 47.619 8.11 0.00 46.40 3.66
286 287 1.614903 CAGTGCATGGTTTGACATGGT 59.385 47.619 8.11 0.00 46.40 3.55
287 288 2.036217 CAGTGCATGGTTTGACATGGTT 59.964 45.455 8.11 0.00 46.40 3.67
288 289 3.255395 CAGTGCATGGTTTGACATGGTTA 59.745 43.478 8.11 0.00 46.40 2.85
289 290 3.507233 AGTGCATGGTTTGACATGGTTAG 59.493 43.478 8.11 0.00 46.40 2.34
290 291 2.230992 TGCATGGTTTGACATGGTTAGC 59.769 45.455 8.11 0.00 46.40 3.09
291 292 2.230992 GCATGGTTTGACATGGTTAGCA 59.769 45.455 8.11 0.00 46.40 3.49
292 293 3.119029 GCATGGTTTGACATGGTTAGCAT 60.119 43.478 8.11 0.00 46.40 3.79
293 294 4.675510 CATGGTTTGACATGGTTAGCATC 58.324 43.478 0.00 0.00 43.44 3.91
302 303 0.973632 TGGTTAGCATCGTGTGGACT 59.026 50.000 0.00 0.00 0.00 3.85
360 361 2.616842 AGCGTTCTCGAACAAAAACCAT 59.383 40.909 10.10 0.00 41.20 3.55
465 466 1.151668 GGTGGATGCGAGCATATGTC 58.848 55.000 10.85 0.00 36.70 3.06
538 539 2.554032 TGAAAAGGTAAAGCTGCTGAGC 59.446 45.455 1.35 0.00 46.64 4.26
564 565 2.440980 GGAGCACAATGGCCCTCC 60.441 66.667 7.61 7.61 37.33 4.30
565 566 2.679716 GAGCACAATGGCCCTCCT 59.320 61.111 0.00 0.00 0.00 3.69
566 567 1.751927 GAGCACAATGGCCCTCCTG 60.752 63.158 0.00 0.00 0.00 3.86
567 568 2.757099 GCACAATGGCCCTCCTGG 60.757 66.667 0.00 0.00 37.09 4.45
568 569 2.765969 CACAATGGCCCTCCTGGT 59.234 61.111 0.00 0.00 36.04 4.00
569 570 1.679977 CACAATGGCCCTCCTGGTG 60.680 63.158 0.00 0.00 36.04 4.17
570 571 2.043652 CAATGGCCCTCCTGGTGG 60.044 66.667 7.84 7.84 36.04 4.61
601 602 5.824624 ACTGCCAATTCTTTCGATCATATGT 59.175 36.000 1.90 0.00 0.00 2.29
673 674 1.005340 CTCACATGCGCTTCTTCTCC 58.995 55.000 9.73 0.00 0.00 3.71
693 694 2.611518 CAGGTGACGAAGACTGGAATC 58.388 52.381 0.00 0.00 0.00 2.52
842 843 1.632948 CCACACATGAGCACGAGCAG 61.633 60.000 7.77 0.00 45.49 4.24
924 925 6.083630 CGCCCATATATAAATTCCACAAACG 58.916 40.000 0.00 0.00 0.00 3.60
957 958 2.029666 ACACACGGCTCACAGCTC 59.970 61.111 0.00 0.00 41.99 4.09
977 978 0.663568 ACACGTGCGTAGTTCAGCTC 60.664 55.000 17.22 0.00 0.00 4.09
979 980 1.080772 CGTGCGTAGTTCAGCTCCA 60.081 57.895 0.00 0.00 0.00 3.86
1167 1173 2.124570 ATGCCAGGCGACACCATC 60.125 61.111 7.03 0.00 43.14 3.51
1182 1188 1.047002 CCATCTCGGAGCTGGAGATT 58.953 55.000 20.58 7.11 46.37 2.40
1386 1392 3.766691 GGGTAGCGCGTCCTTCCA 61.767 66.667 19.72 0.00 0.00 3.53
1388 1394 1.153429 GGTAGCGCGTCCTTCCATT 60.153 57.895 8.43 0.00 0.00 3.16
1498 1504 1.286260 GTCGACGCCACTCTTGACT 59.714 57.895 0.00 0.00 0.00 3.41
1537 1560 1.480954 CTGTGTCGGTGCTAGGGTTAT 59.519 52.381 0.00 0.00 0.00 1.89
1541 1564 1.068741 GTCGGTGCTAGGGTTATGGAG 59.931 57.143 0.00 0.00 0.00 3.86
1542 1565 1.120530 CGGTGCTAGGGTTATGGAGT 58.879 55.000 0.00 0.00 0.00 3.85
1929 1961 4.454161 TCAATCGGTACAACATCTGGTTTG 59.546 41.667 0.00 0.00 37.72 2.93
1994 2026 7.037873 TCCTATAAAAGTGTGACTGGGTTATGT 60.038 37.037 0.00 0.00 0.00 2.29
1997 2029 3.418684 AGTGTGACTGGGTTATGTTCC 57.581 47.619 0.00 0.00 0.00 3.62
1998 2030 2.039879 AGTGTGACTGGGTTATGTTCCC 59.960 50.000 0.00 0.00 44.81 3.97
2043 2075 7.086230 TCGCTTTACTTAAACAAAGTTTGGA 57.914 32.000 19.45 2.08 46.61 3.53
2083 2115 6.245408 ACATCTAAAATAAAGTCTGGTGGCA 58.755 36.000 0.00 0.00 0.00 4.92
2087 2119 5.869649 AAAATAAAGTCTGGTGGCAAGTT 57.130 34.783 0.00 0.00 0.00 2.66
2096 2128 0.755327 GGTGGCAAGTTCACCCAAGT 60.755 55.000 2.89 0.00 46.58 3.16
2112 2144 1.135083 CAAGTATCACGGCGTTCCTCT 60.135 52.381 11.19 4.14 0.00 3.69
2143 2177 4.928661 AATCTAGCTAATTTATGCGCGG 57.071 40.909 8.83 0.00 0.00 6.46
2148 2182 1.532921 GCTAATTTATGCGCGGCAACA 60.533 47.619 8.83 0.00 43.62 3.33
2155 2189 4.481112 GCGCGGCAACATTCCCAG 62.481 66.667 8.83 0.00 0.00 4.45
2176 2210 0.466963 ACGACGAACCCAAGAAACCT 59.533 50.000 0.00 0.00 0.00 3.50
2193 2227 1.269621 ACCTTGAACTCCGTCAACGAG 60.270 52.381 3.71 2.70 43.02 4.18
2214 2248 4.032310 AGTTGAGCATCTCCTTGATCTCT 58.968 43.478 0.00 0.00 33.25 3.10
2342 2377 0.837272 GCCAACTGATAGCCCACCTA 59.163 55.000 0.00 0.00 0.00 3.08
2367 2402 2.266055 GGACCTCCACTGCTTCCG 59.734 66.667 0.00 0.00 35.64 4.30
2374 2409 0.036388 TCCACTGCTTCCGGATCAAC 60.036 55.000 4.15 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.542020 TTCATCTCCGAGCAACACAA 57.458 45.000 0.00 0.00 0.00 3.33
1 2 2.542020 TTTCATCTCCGAGCAACACA 57.458 45.000 0.00 0.00 0.00 3.72
2 3 5.741388 ATTATTTCATCTCCGAGCAACAC 57.259 39.130 0.00 0.00 0.00 3.32
3 4 6.757897 AAATTATTTCATCTCCGAGCAACA 57.242 33.333 0.00 0.00 0.00 3.33
4 5 8.398665 AGTAAAATTATTTCATCTCCGAGCAAC 58.601 33.333 0.00 0.00 0.00 4.17
5 6 8.506168 AGTAAAATTATTTCATCTCCGAGCAA 57.494 30.769 0.00 0.00 0.00 3.91
6 7 7.987458 AGAGTAAAATTATTTCATCTCCGAGCA 59.013 33.333 10.56 0.00 0.00 4.26
7 8 8.279103 CAGAGTAAAATTATTTCATCTCCGAGC 58.721 37.037 10.56 0.00 0.00 5.03
8 9 9.534565 TCAGAGTAAAATTATTTCATCTCCGAG 57.465 33.333 10.56 0.00 0.00 4.63
17 18 9.670719 GCCAGCTAATCAGAGTAAAATTATTTC 57.329 33.333 0.00 0.00 0.00 2.17
18 19 9.189156 TGCCAGCTAATCAGAGTAAAATTATTT 57.811 29.630 0.00 0.00 0.00 1.40
19 20 8.752005 TGCCAGCTAATCAGAGTAAAATTATT 57.248 30.769 0.00 0.00 0.00 1.40
20 21 8.752005 TTGCCAGCTAATCAGAGTAAAATTAT 57.248 30.769 0.00 0.00 0.00 1.28
21 22 8.574251 TTTGCCAGCTAATCAGAGTAAAATTA 57.426 30.769 0.00 0.00 0.00 1.40
22 23 7.466746 TTTGCCAGCTAATCAGAGTAAAATT 57.533 32.000 0.00 0.00 0.00 1.82
23 24 7.559170 AGATTTGCCAGCTAATCAGAGTAAAAT 59.441 33.333 22.61 3.52 39.44 1.82
24 25 6.886459 AGATTTGCCAGCTAATCAGAGTAAAA 59.114 34.615 22.61 0.00 39.44 1.52
25 26 6.418101 AGATTTGCCAGCTAATCAGAGTAAA 58.582 36.000 22.61 0.00 39.44 2.01
26 27 5.994250 AGATTTGCCAGCTAATCAGAGTAA 58.006 37.500 22.61 0.00 39.44 2.24
27 28 5.620738 AGATTTGCCAGCTAATCAGAGTA 57.379 39.130 22.61 0.00 39.44 2.59
28 29 4.500499 AGATTTGCCAGCTAATCAGAGT 57.500 40.909 22.61 5.40 39.44 3.24
29 30 5.831702 AAAGATTTGCCAGCTAATCAGAG 57.168 39.130 22.61 0.00 39.44 3.35
30 31 5.105635 CCAAAAGATTTGCCAGCTAATCAGA 60.106 40.000 22.61 0.00 39.44 3.27
31 32 5.105635 TCCAAAAGATTTGCCAGCTAATCAG 60.106 40.000 22.61 12.45 39.44 2.90
32 33 4.771577 TCCAAAAGATTTGCCAGCTAATCA 59.228 37.500 22.61 4.53 39.44 2.57
33 34 5.329035 TCCAAAAGATTTGCCAGCTAATC 57.671 39.130 15.94 15.94 38.05 1.75
34 35 5.011943 TGTTCCAAAAGATTTGCCAGCTAAT 59.988 36.000 0.00 0.00 0.00 1.73
35 36 4.343526 TGTTCCAAAAGATTTGCCAGCTAA 59.656 37.500 0.00 0.00 0.00 3.09
36 37 3.894427 TGTTCCAAAAGATTTGCCAGCTA 59.106 39.130 0.00 0.00 0.00 3.32
37 38 2.699846 TGTTCCAAAAGATTTGCCAGCT 59.300 40.909 0.00 0.00 0.00 4.24
38 39 3.110447 TGTTCCAAAAGATTTGCCAGC 57.890 42.857 0.00 0.00 0.00 4.85
39 40 4.696455 AGTTGTTCCAAAAGATTTGCCAG 58.304 39.130 0.00 0.00 0.00 4.85
40 41 4.751767 AGTTGTTCCAAAAGATTTGCCA 57.248 36.364 0.00 0.00 0.00 4.92
41 42 6.435430 AAAAGTTGTTCCAAAAGATTTGCC 57.565 33.333 0.00 0.00 0.00 4.52
66 67 9.748708 CCAAAAGATAATTCTCAACAGAAACAA 57.251 29.630 0.00 0.00 42.14 2.83
67 68 8.359642 CCCAAAAGATAATTCTCAACAGAAACA 58.640 33.333 0.00 0.00 42.14 2.83
68 69 8.576442 TCCCAAAAGATAATTCTCAACAGAAAC 58.424 33.333 0.00 0.00 42.14 2.78
69 70 8.704849 TCCCAAAAGATAATTCTCAACAGAAA 57.295 30.769 0.00 0.00 42.14 2.52
70 71 8.576442 GTTCCCAAAAGATAATTCTCAACAGAA 58.424 33.333 0.00 0.00 43.06 3.02
71 72 7.723616 TGTTCCCAAAAGATAATTCTCAACAGA 59.276 33.333 0.00 0.00 0.00 3.41
72 73 7.885297 TGTTCCCAAAAGATAATTCTCAACAG 58.115 34.615 0.00 0.00 0.00 3.16
73 74 7.831691 TGTTCCCAAAAGATAATTCTCAACA 57.168 32.000 0.00 0.00 0.00 3.33
74 75 8.360390 AGTTGTTCCCAAAAGATAATTCTCAAC 58.640 33.333 0.00 0.00 30.94 3.18
75 76 8.359642 CAGTTGTTCCCAAAAGATAATTCTCAA 58.640 33.333 0.00 0.00 30.94 3.02
76 77 7.039784 CCAGTTGTTCCCAAAAGATAATTCTCA 60.040 37.037 0.00 0.00 30.94 3.27
77 78 7.039714 ACCAGTTGTTCCCAAAAGATAATTCTC 60.040 37.037 0.00 0.00 30.94 2.87
78 79 6.782494 ACCAGTTGTTCCCAAAAGATAATTCT 59.218 34.615 0.00 0.00 30.94 2.40
79 80 6.993079 ACCAGTTGTTCCCAAAAGATAATTC 58.007 36.000 0.00 0.00 30.94 2.17
80 81 6.782494 AGACCAGTTGTTCCCAAAAGATAATT 59.218 34.615 0.00 0.00 30.94 1.40
81 82 6.209391 CAGACCAGTTGTTCCCAAAAGATAAT 59.791 38.462 0.00 0.00 30.94 1.28
82 83 5.534654 CAGACCAGTTGTTCCCAAAAGATAA 59.465 40.000 0.00 0.00 30.94 1.75
83 84 5.070001 CAGACCAGTTGTTCCCAAAAGATA 58.930 41.667 0.00 0.00 30.94 1.98
84 85 3.891366 CAGACCAGTTGTTCCCAAAAGAT 59.109 43.478 0.00 0.00 30.94 2.40
85 86 3.053991 TCAGACCAGTTGTTCCCAAAAGA 60.054 43.478 0.00 0.00 30.94 2.52
86 87 3.287222 TCAGACCAGTTGTTCCCAAAAG 58.713 45.455 0.00 0.00 30.94 2.27
87 88 3.374042 TCAGACCAGTTGTTCCCAAAA 57.626 42.857 0.00 0.00 30.94 2.44
88 89 3.374042 TTCAGACCAGTTGTTCCCAAA 57.626 42.857 0.00 0.00 30.94 3.28
89 90 3.374042 TTTCAGACCAGTTGTTCCCAA 57.626 42.857 0.00 0.00 0.00 4.12
90 91 3.374042 TTTTCAGACCAGTTGTTCCCA 57.626 42.857 0.00 0.00 0.00 4.37
108 109 5.187772 GGAATTGGCCTATGGACTTCTTTTT 59.812 40.000 3.32 0.00 0.00 1.94
109 110 4.711846 GGAATTGGCCTATGGACTTCTTTT 59.288 41.667 3.32 0.00 0.00 2.27
110 111 4.017130 AGGAATTGGCCTATGGACTTCTTT 60.017 41.667 3.32 0.00 36.22 2.52
111 112 3.529319 AGGAATTGGCCTATGGACTTCTT 59.471 43.478 3.32 0.00 36.22 2.52
112 113 3.126453 AGGAATTGGCCTATGGACTTCT 58.874 45.455 3.32 0.00 36.22 2.85
113 114 3.481453 GAGGAATTGGCCTATGGACTTC 58.519 50.000 3.32 0.00 38.73 3.01
114 115 2.158755 CGAGGAATTGGCCTATGGACTT 60.159 50.000 3.32 0.00 38.73 3.01
115 116 1.417890 CGAGGAATTGGCCTATGGACT 59.582 52.381 3.32 0.98 38.73 3.85
116 117 1.141053 ACGAGGAATTGGCCTATGGAC 59.859 52.381 3.32 0.00 38.73 4.02
117 118 1.416401 GACGAGGAATTGGCCTATGGA 59.584 52.381 3.32 0.00 38.73 3.41
118 119 1.873903 CGACGAGGAATTGGCCTATGG 60.874 57.143 3.32 0.00 38.73 2.74
119 120 1.502231 CGACGAGGAATTGGCCTATG 58.498 55.000 3.32 0.00 38.73 2.23
120 121 0.249911 GCGACGAGGAATTGGCCTAT 60.250 55.000 3.32 0.00 38.73 2.57
121 122 1.143183 GCGACGAGGAATTGGCCTA 59.857 57.895 3.32 0.00 38.73 3.93
122 123 2.125106 GCGACGAGGAATTGGCCT 60.125 61.111 3.32 0.00 42.17 5.19
123 124 2.435938 TGCGACGAGGAATTGGCC 60.436 61.111 0.00 0.00 0.00 5.36
124 125 3.093278 CTGCGACGAGGAATTGGC 58.907 61.111 0.00 0.00 0.00 4.52
125 126 1.448540 AGCTGCGACGAGGAATTGG 60.449 57.895 0.00 0.00 0.00 3.16
126 127 1.699656 CCAGCTGCGACGAGGAATTG 61.700 60.000 8.66 0.00 0.00 2.32
127 128 1.448540 CCAGCTGCGACGAGGAATT 60.449 57.895 8.66 0.00 0.00 2.17
128 129 2.185350 CCAGCTGCGACGAGGAAT 59.815 61.111 8.66 0.00 0.00 3.01
129 130 4.742201 GCCAGCTGCGACGAGGAA 62.742 66.667 8.66 0.00 0.00 3.36
142 143 0.319297 GAAAACAAGCTGCTGGCCAG 60.319 55.000 29.34 29.34 44.67 4.85
143 144 1.042003 TGAAAACAAGCTGCTGGCCA 61.042 50.000 4.71 4.71 43.05 5.36
144 145 0.104671 TTGAAAACAAGCTGCTGGCC 59.895 50.000 1.35 0.00 43.05 5.36
145 146 1.067516 TCTTGAAAACAAGCTGCTGGC 59.932 47.619 1.35 0.00 42.19 4.85
146 147 3.655276 ATCTTGAAAACAAGCTGCTGG 57.345 42.857 1.35 1.47 32.52 4.85
147 148 5.575606 CCATAATCTTGAAAACAAGCTGCTG 59.424 40.000 1.35 0.00 32.52 4.41
148 149 5.337009 CCCATAATCTTGAAAACAAGCTGCT 60.337 40.000 0.00 0.00 32.52 4.24
149 150 4.866486 CCCATAATCTTGAAAACAAGCTGC 59.134 41.667 0.00 0.00 32.52 5.25
150 151 4.866486 GCCCATAATCTTGAAAACAAGCTG 59.134 41.667 0.00 0.00 32.52 4.24
151 152 4.081476 GGCCCATAATCTTGAAAACAAGCT 60.081 41.667 0.00 0.00 32.52 3.74
152 153 4.183865 GGCCCATAATCTTGAAAACAAGC 58.816 43.478 0.00 0.00 32.52 4.01
153 154 5.404466 TGGCCCATAATCTTGAAAACAAG 57.596 39.130 0.00 0.00 0.00 3.16
154 155 7.487822 TTATGGCCCATAATCTTGAAAACAA 57.512 32.000 12.21 0.00 32.27 2.83
155 156 7.125507 ACATTATGGCCCATAATCTTGAAAACA 59.874 33.333 23.24 0.00 42.80 2.83
156 157 7.500141 ACATTATGGCCCATAATCTTGAAAAC 58.500 34.615 23.24 0.00 42.80 2.43
157 158 7.201992 GGACATTATGGCCCATAATCTTGAAAA 60.202 37.037 23.24 0.00 40.64 2.29
158 159 6.267471 GGACATTATGGCCCATAATCTTGAAA 59.733 38.462 23.24 0.00 40.64 2.69
159 160 5.774690 GGACATTATGGCCCATAATCTTGAA 59.225 40.000 23.24 0.68 40.64 2.69
160 161 5.324409 GGACATTATGGCCCATAATCTTGA 58.676 41.667 23.24 0.00 40.64 3.02
161 162 5.649782 GGACATTATGGCCCATAATCTTG 57.350 43.478 23.24 17.25 40.64 3.02
182 183 6.096564 ACACTTTAGTAGTAATCTTCCGGAGG 59.903 42.308 7.38 7.38 42.95 4.30
183 184 6.973474 CACACTTTAGTAGTAATCTTCCGGAG 59.027 42.308 3.34 0.00 34.56 4.63
184 185 6.127535 CCACACTTTAGTAGTAATCTTCCGGA 60.128 42.308 0.00 0.00 34.56 5.14
185 186 6.040878 CCACACTTTAGTAGTAATCTTCCGG 58.959 44.000 0.00 0.00 34.56 5.14
186 187 6.860080 TCCACACTTTAGTAGTAATCTTCCG 58.140 40.000 0.00 0.00 34.56 4.30
193 194 9.701098 CACAACTATTCCACACTTTAGTAGTAA 57.299 33.333 0.00 0.00 34.56 2.24
194 195 9.081204 TCACAACTATTCCACACTTTAGTAGTA 57.919 33.333 0.00 0.00 34.56 1.82
195 196 7.959175 TCACAACTATTCCACACTTTAGTAGT 58.041 34.615 0.00 0.00 37.68 2.73
196 197 9.436957 AATCACAACTATTCCACACTTTAGTAG 57.563 33.333 0.00 0.00 0.00 2.57
197 198 9.431887 GAATCACAACTATTCCACACTTTAGTA 57.568 33.333 0.00 0.00 0.00 1.82
198 199 8.157476 AGAATCACAACTATTCCACACTTTAGT 58.843 33.333 0.00 0.00 34.50 2.24
199 200 8.553459 AGAATCACAACTATTCCACACTTTAG 57.447 34.615 0.00 0.00 34.50 1.85
200 201 8.154203 TGAGAATCACAACTATTCCACACTTTA 58.846 33.333 0.00 0.00 42.56 1.85
201 202 6.998074 TGAGAATCACAACTATTCCACACTTT 59.002 34.615 0.00 0.00 42.56 2.66
202 203 6.533730 TGAGAATCACAACTATTCCACACTT 58.466 36.000 0.00 0.00 42.56 3.16
203 204 6.114187 TGAGAATCACAACTATTCCACACT 57.886 37.500 0.00 0.00 42.56 3.55
246 247 2.719705 TGTTTGGGAGGGTTTGATACCT 59.280 45.455 0.00 0.00 46.86 3.08
247 248 3.089284 CTGTTTGGGAGGGTTTGATACC 58.911 50.000 0.00 0.00 46.99 2.73
248 249 3.506067 CACTGTTTGGGAGGGTTTGATAC 59.494 47.826 0.00 0.00 0.00 2.24
249 250 3.761897 CACTGTTTGGGAGGGTTTGATA 58.238 45.455 0.00 0.00 0.00 2.15
250 251 2.597455 CACTGTTTGGGAGGGTTTGAT 58.403 47.619 0.00 0.00 0.00 2.57
251 252 2.026905 GCACTGTTTGGGAGGGTTTGA 61.027 52.381 0.00 0.00 0.00 2.69
252 253 0.389025 GCACTGTTTGGGAGGGTTTG 59.611 55.000 0.00 0.00 0.00 2.93
253 254 0.032615 TGCACTGTTTGGGAGGGTTT 60.033 50.000 0.00 0.00 0.00 3.27
254 255 0.188342 ATGCACTGTTTGGGAGGGTT 59.812 50.000 0.00 0.00 0.00 4.11
255 256 0.540365 CATGCACTGTTTGGGAGGGT 60.540 55.000 0.00 0.00 0.00 4.34
256 257 1.252904 CCATGCACTGTTTGGGAGGG 61.253 60.000 0.00 0.00 0.00 4.30
257 258 0.540365 ACCATGCACTGTTTGGGAGG 60.540 55.000 8.12 0.00 34.72 4.30
258 259 1.331214 AACCATGCACTGTTTGGGAG 58.669 50.000 8.12 0.00 34.72 4.30
259 260 1.411977 CAAACCATGCACTGTTTGGGA 59.588 47.619 24.80 0.00 44.68 4.37
260 261 1.868469 CAAACCATGCACTGTTTGGG 58.132 50.000 24.80 9.29 44.68 4.12
263 264 3.493002 CCATGTCAAACCATGCACTGTTT 60.493 43.478 9.08 9.08 40.72 2.83
264 265 2.036217 CCATGTCAAACCATGCACTGTT 59.964 45.455 0.00 0.00 40.72 3.16
265 266 1.614903 CCATGTCAAACCATGCACTGT 59.385 47.619 0.00 0.00 40.72 3.55
266 267 1.614903 ACCATGTCAAACCATGCACTG 59.385 47.619 0.00 0.00 40.72 3.66
267 268 1.999648 ACCATGTCAAACCATGCACT 58.000 45.000 0.00 0.00 40.72 4.40
268 269 2.818130 AACCATGTCAAACCATGCAC 57.182 45.000 0.00 0.00 40.72 4.57
269 270 2.230992 GCTAACCATGTCAAACCATGCA 59.769 45.455 0.00 0.00 40.72 3.96
270 271 2.230992 TGCTAACCATGTCAAACCATGC 59.769 45.455 0.00 0.00 40.72 4.06
271 272 4.675510 GATGCTAACCATGTCAAACCATG 58.324 43.478 0.00 0.00 41.52 3.66
272 273 3.378112 CGATGCTAACCATGTCAAACCAT 59.622 43.478 0.00 0.00 33.29 3.55
273 274 2.746904 CGATGCTAACCATGTCAAACCA 59.253 45.455 0.00 0.00 33.29 3.67
274 275 2.747446 ACGATGCTAACCATGTCAAACC 59.253 45.455 0.00 0.00 33.29 3.27
275 276 3.188460 ACACGATGCTAACCATGTCAAAC 59.812 43.478 0.00 0.00 33.29 2.93
276 277 3.188254 CACACGATGCTAACCATGTCAAA 59.812 43.478 0.00 0.00 33.29 2.69
277 278 2.741517 CACACGATGCTAACCATGTCAA 59.258 45.455 0.00 0.00 33.29 3.18
278 279 2.345876 CACACGATGCTAACCATGTCA 58.654 47.619 0.00 0.00 33.29 3.58
279 280 1.665679 CCACACGATGCTAACCATGTC 59.334 52.381 0.00 0.00 33.29 3.06
280 281 1.277842 TCCACACGATGCTAACCATGT 59.722 47.619 0.00 0.00 33.29 3.21
281 282 1.665679 GTCCACACGATGCTAACCATG 59.334 52.381 0.00 0.00 33.29 3.66
282 283 1.555075 AGTCCACACGATGCTAACCAT 59.445 47.619 0.00 0.00 36.70 3.55
283 284 0.973632 AGTCCACACGATGCTAACCA 59.026 50.000 0.00 0.00 0.00 3.67
284 285 1.067142 TGAGTCCACACGATGCTAACC 60.067 52.381 0.00 0.00 0.00 2.85
285 286 2.363788 TGAGTCCACACGATGCTAAC 57.636 50.000 0.00 0.00 0.00 2.34
286 287 2.760650 AGATGAGTCCACACGATGCTAA 59.239 45.455 0.00 0.00 0.00 3.09
287 288 2.379005 AGATGAGTCCACACGATGCTA 58.621 47.619 0.00 0.00 0.00 3.49
288 289 1.189752 AGATGAGTCCACACGATGCT 58.810 50.000 0.00 0.00 0.00 3.79
289 290 2.736978 CTAGATGAGTCCACACGATGC 58.263 52.381 0.00 0.00 0.00 3.91
290 291 2.099756 TGCTAGATGAGTCCACACGATG 59.900 50.000 0.00 0.00 0.00 3.84
291 292 2.379005 TGCTAGATGAGTCCACACGAT 58.621 47.619 0.00 0.00 0.00 3.73
292 293 1.834188 TGCTAGATGAGTCCACACGA 58.166 50.000 0.00 0.00 0.00 4.35
293 294 2.654749 TTGCTAGATGAGTCCACACG 57.345 50.000 0.00 0.00 0.00 4.49
319 320 5.163652 ACGCTTGAAAGGAATGGCTAAATAC 60.164 40.000 0.00 0.00 0.00 1.89
325 326 1.541588 GAACGCTTGAAAGGAATGGCT 59.458 47.619 0.00 0.00 0.00 4.75
360 361 1.956636 GCATGGCCTTGTCATCCTTCA 60.957 52.381 19.05 0.00 0.00 3.02
389 390 1.407979 GCTTCCCAAGGCATCATCTTG 59.592 52.381 0.00 0.00 40.75 3.02
390 391 1.287146 AGCTTCCCAAGGCATCATCTT 59.713 47.619 0.00 0.00 0.00 2.40
465 466 6.715280 AGGTAAACATGATATGGCCTATGAG 58.285 40.000 3.32 0.00 33.60 2.90
538 539 2.608752 GCCATTGTGCTCCAACAAGAAG 60.609 50.000 0.00 0.00 42.99 2.85
564 565 2.260434 GCAGTGCATTGCCACCAG 59.740 61.111 22.56 2.40 38.13 4.00
570 571 2.088950 AAGAATTGGCAGTGCATTGC 57.911 45.000 24.69 24.69 43.34 3.56
571 572 2.664568 CGAAAGAATTGGCAGTGCATTG 59.335 45.455 18.61 4.57 0.00 2.82
572 573 2.557924 TCGAAAGAATTGGCAGTGCATT 59.442 40.909 18.61 9.00 37.03 3.56
573 574 2.161855 TCGAAAGAATTGGCAGTGCAT 58.838 42.857 18.61 0.00 37.03 3.96
574 575 1.603456 TCGAAAGAATTGGCAGTGCA 58.397 45.000 18.61 0.00 37.03 4.57
587 588 4.875536 TCCAACACCACATATGATCGAAAG 59.124 41.667 10.38 0.00 0.00 2.62
601 602 5.011125 TGTTTTCTTTGAAACTCCAACACCA 59.989 36.000 2.68 0.00 39.62 4.17
673 674 2.611518 GATTCCAGTCTTCGTCACCTG 58.388 52.381 0.00 0.00 0.00 4.00
924 925 3.798878 CGTGTGTGTGGATGATGATCTAC 59.201 47.826 1.63 1.63 39.84 2.59
957 958 0.939577 AGCTGAACTACGCACGTGTG 60.940 55.000 26.70 26.70 0.00 3.82
977 978 6.255596 TCTCGAAGATAGATTATCGGTTGG 57.744 41.667 0.00 0.00 40.12 3.77
979 980 6.626181 GCCATCTCGAAGATAGATTATCGGTT 60.626 42.308 0.00 0.00 40.12 4.44
1111 1117 1.290009 CCAGCTTTTTCTTGCCCGG 59.710 57.895 0.00 0.00 0.00 5.73
1122 1128 4.586235 ACCAGCACCGCCAGCTTT 62.586 61.111 0.00 0.00 41.14 3.51
1167 1173 1.342496 TGCATAATCTCCAGCTCCGAG 59.658 52.381 1.47 1.47 0.00 4.63
1236 1242 2.496817 GCGCTCTCGAAGGTCCAT 59.503 61.111 0.00 0.00 38.10 3.41
1386 1392 3.596214 ACTTTTGCGGATCTACGTCAAT 58.404 40.909 0.00 0.00 35.98 2.57
1388 1394 2.736144 ACTTTTGCGGATCTACGTCA 57.264 45.000 0.00 0.00 35.98 4.35
1498 1504 7.095565 CGACACAGTTACATACATAAACAACCA 60.096 37.037 0.00 0.00 0.00 3.67
1537 1560 2.617788 GCCCATATCAACACACACTCCA 60.618 50.000 0.00 0.00 0.00 3.86
1541 1564 3.623060 CACTAGCCCATATCAACACACAC 59.377 47.826 0.00 0.00 0.00 3.82
1542 1565 3.263170 ACACTAGCCCATATCAACACACA 59.737 43.478 0.00 0.00 0.00 3.72
1630 1662 8.729756 CACAATCAAGTTACCACATATTTCTCA 58.270 33.333 0.00 0.00 0.00 3.27
1632 1664 7.176515 TGCACAATCAAGTTACCACATATTTCT 59.823 33.333 0.00 0.00 0.00 2.52
1960 1992 5.005779 GTCACACTTTTATAGGAGCACGATG 59.994 44.000 0.00 0.00 0.00 3.84
1969 2001 7.110155 ACATAACCCAGTCACACTTTTATAGG 58.890 38.462 0.00 0.00 0.00 2.57
2019 2051 7.086230 TCCAAACTTTGTTTAAGTAAAGCGA 57.914 32.000 11.32 3.19 46.34 4.93
2081 2113 2.159627 CGTGATACTTGGGTGAACTTGC 59.840 50.000 0.00 0.00 0.00 4.01
2083 2115 2.874457 GCCGTGATACTTGGGTGAACTT 60.874 50.000 0.00 0.00 0.00 2.66
2087 2119 1.216977 CGCCGTGATACTTGGGTGA 59.783 57.895 0.00 0.00 31.77 4.02
2096 2128 0.395311 AGGAGAGGAACGCCGTGATA 60.395 55.000 0.00 0.00 43.25 2.15
2123 2157 2.673368 GCCGCGCATAAATTAGCTAGAT 59.327 45.455 8.75 0.00 0.00 1.98
2143 2177 0.165944 CGTCGTTCTGGGAATGTTGC 59.834 55.000 0.00 0.00 0.00 4.17
2148 2182 0.036671 GGGTTCGTCGTTCTGGGAAT 60.037 55.000 0.00 0.00 0.00 3.01
2155 2189 1.262417 GGTTTCTTGGGTTCGTCGTTC 59.738 52.381 0.00 0.00 0.00 3.95
2193 2227 4.405116 AGAGATCAAGGAGATGCTCAAC 57.595 45.455 0.00 0.00 37.00 3.18
2214 2248 2.303175 GCTGTTGGACCCTGTTTACAA 58.697 47.619 0.00 0.00 0.00 2.41
2342 2377 1.539869 AGTGGAGGTCCTGGCATGT 60.540 57.895 0.00 0.00 36.82 3.21


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

AutoCloner maintained by Alex Coulton.