Multiple sequence alignment - TraesCS2D01G437500

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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 TraesCS2D01G437500 chr2D 100.000 3092 0 0 1 3092 547563154 547566245 0.000000e+00 5710
1 TraesCS2D01G437500 chr2D 94.826 2706 105 16 292 2976 182632456 182629765 0.000000e+00 4189
2 TraesCS2D01G437500 chr2D 97.659 299 5 2 1 299 547578280 547578576 2.130000e-141 512
3 TraesCS2D01G437500 chr2D 96.774 248 5 3 288 534 547570683 547570438 7.980000e-111 411
4 TraesCS2D01G437500 chr6D 97.339 2819 51 12 292 3092 472510963 472513775 0.000000e+00 4769
5 TraesCS2D01G437500 chr6D 96.884 2824 57 19 292 3092 51499464 51502279 0.000000e+00 4698
6 TraesCS2D01G437500 chr6D 96.448 2815 81 12 291 3092 367564538 367561730 0.000000e+00 4626
7 TraesCS2D01G437500 chr6D 96.432 2354 53 14 292 2619 7981042 7978694 0.000000e+00 3853
8 TraesCS2D01G437500 chr6D 95.853 1905 46 19 292 2168 29978789 29976890 0.000000e+00 3049
9 TraesCS2D01G437500 chr7D 97.203 2824 49 18 292 3092 245402431 245399615 0.000000e+00 4750
10 TraesCS2D01G437500 chr1D 97.219 2805 39 7 292 3092 12354514 12357283 0.000000e+00 4711
11 TraesCS2D01G437500 chr1D 96.671 2824 61 21 292 3092 22577395 22574582 0.000000e+00 4663
12 TraesCS2D01G437500 chr1D 94.980 2729 90 17 287 2976 420011146 420008426 0.000000e+00 4237
13 TraesCS2D01G437500 chr5D 96.955 2824 55 19 292 3092 565815802 565818617 0.000000e+00 4710
14 TraesCS2D01G437500 chr5D 96.565 2824 65 20 292 3092 75136832 75134018 0.000000e+00 4649
15 TraesCS2D01G437500 chr5D 96.371 248 7 2 288 534 408326949 408327195 1.030000e-109 407
16 TraesCS2D01G437500 chr4D 96.460 2825 70 16 292 3092 398986367 398983549 0.000000e+00 4636
17 TraesCS2D01G437500 chr4D 94.530 2724 105 18 291 2976 502867332 502870049 0.000000e+00 4165
18 TraesCS2D01G437500 chr4D 96.371 248 6 3 288 534 164904373 164904128 3.710000e-109 405
19 TraesCS2D01G437500 chr2B 88.667 300 11 5 1 299 653812892 653813169 8.210000e-91 344


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 TraesCS2D01G437500 chr2D 547563154 547566245 3091 False 5710 5710 100.000 1 3092 1 chr2D.!!$F1 3091
1 TraesCS2D01G437500 chr2D 182629765 182632456 2691 True 4189 4189 94.826 292 2976 1 chr2D.!!$R1 2684
2 TraesCS2D01G437500 chr6D 472510963 472513775 2812 False 4769 4769 97.339 292 3092 1 chr6D.!!$F2 2800
3 TraesCS2D01G437500 chr6D 51499464 51502279 2815 False 4698 4698 96.884 292 3092 1 chr6D.!!$F1 2800
4 TraesCS2D01G437500 chr6D 367561730 367564538 2808 True 4626 4626 96.448 291 3092 1 chr6D.!!$R3 2801
5 TraesCS2D01G437500 chr6D 7978694 7981042 2348 True 3853 3853 96.432 292 2619 1 chr6D.!!$R1 2327
6 TraesCS2D01G437500 chr6D 29976890 29978789 1899 True 3049 3049 95.853 292 2168 1 chr6D.!!$R2 1876
7 TraesCS2D01G437500 chr7D 245399615 245402431 2816 True 4750 4750 97.203 292 3092 1 chr7D.!!$R1 2800
8 TraesCS2D01G437500 chr1D 12354514 12357283 2769 False 4711 4711 97.219 292 3092 1 chr1D.!!$F1 2800
9 TraesCS2D01G437500 chr1D 22574582 22577395 2813 True 4663 4663 96.671 292 3092 1 chr1D.!!$R1 2800
10 TraesCS2D01G437500 chr1D 420008426 420011146 2720 True 4237 4237 94.980 287 2976 1 chr1D.!!$R2 2689
11 TraesCS2D01G437500 chr5D 565815802 565818617 2815 False 4710 4710 96.955 292 3092 1 chr5D.!!$F2 2800
12 TraesCS2D01G437500 chr5D 75134018 75136832 2814 True 4649 4649 96.565 292 3092 1 chr5D.!!$R1 2800
13 TraesCS2D01G437500 chr4D 398983549 398986367 2818 True 4636 4636 96.460 292 3092 1 chr4D.!!$R2 2800
14 TraesCS2D01G437500 chr4D 502867332 502870049 2717 False 4165 4165 94.530 291 2976 1 chr4D.!!$F1 2685

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
558 589 0.033894 AAGTCGTCTCCCTCCCTCTC 60.034 60.0 0.0 0.0 0.0 3.20 F
564 595 0.628522 TCTCCCTCCCTCTCACTCTG 59.371 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1640 0.467290 GGGCTTGTCAACCCACTCAA 60.467 55.000 14.79 0.00 46.22 3.02 R
2149 2240 5.001874 CACCCCATATCTTCACATCAGATG 58.998 45.833 9.03 9.03 32.94 2.90 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
33 34 6.827727 AGTTAGGTACTGAACTTTGATGTGT 58.172 36.000 7.01 0.00 41.52 3.72
34 35 6.706270 AGTTAGGTACTGAACTTTGATGTGTG 59.294 38.462 7.01 0.00 41.52 3.82
35 36 5.036117 AGGTACTGAACTTTGATGTGTGT 57.964 39.130 0.00 0.00 37.18 3.72
36 37 4.816385 AGGTACTGAACTTTGATGTGTGTG 59.184 41.667 0.00 0.00 37.18 3.82
37 38 4.814234 GGTACTGAACTTTGATGTGTGTGA 59.186 41.667 0.00 0.00 0.00 3.58
38 39 4.882671 ACTGAACTTTGATGTGTGTGAC 57.117 40.909 0.00 0.00 0.00 3.67
39 40 3.627577 ACTGAACTTTGATGTGTGTGACC 59.372 43.478 0.00 0.00 0.00 4.02
40 41 3.879295 CTGAACTTTGATGTGTGTGACCT 59.121 43.478 0.00 0.00 0.00 3.85
41 42 5.029807 TGAACTTTGATGTGTGTGACCTA 57.970 39.130 0.00 0.00 0.00 3.08
42 43 5.432645 TGAACTTTGATGTGTGTGACCTAA 58.567 37.500 0.00 0.00 0.00 2.69
43 44 5.883115 TGAACTTTGATGTGTGTGACCTAAA 59.117 36.000 0.00 0.00 0.00 1.85
44 45 6.038161 TGAACTTTGATGTGTGTGACCTAAAG 59.962 38.462 0.00 0.00 0.00 1.85
45 46 5.437060 ACTTTGATGTGTGTGACCTAAAGT 58.563 37.500 0.00 0.00 33.67 2.66
46 47 5.885912 ACTTTGATGTGTGTGACCTAAAGTT 59.114 36.000 0.00 0.00 34.53 2.66
47 48 6.377146 ACTTTGATGTGTGTGACCTAAAGTTT 59.623 34.615 0.00 0.00 34.53 2.66
48 49 6.767524 TTGATGTGTGTGACCTAAAGTTTT 57.232 33.333 0.00 0.00 0.00 2.43
49 50 6.371809 TGATGTGTGTGACCTAAAGTTTTC 57.628 37.500 0.00 0.00 0.00 2.29
50 51 5.883115 TGATGTGTGTGACCTAAAGTTTTCA 59.117 36.000 0.00 0.00 0.00 2.69
51 52 6.545666 TGATGTGTGTGACCTAAAGTTTTCAT 59.454 34.615 0.00 0.00 0.00 2.57
52 53 6.767524 TGTGTGTGACCTAAAGTTTTCATT 57.232 33.333 0.00 0.00 0.00 2.57
53 54 6.791303 TGTGTGTGACCTAAAGTTTTCATTC 58.209 36.000 0.00 0.00 0.00 2.67
54 55 6.601613 TGTGTGTGACCTAAAGTTTTCATTCT 59.398 34.615 0.00 0.00 0.00 2.40
55 56 6.912591 GTGTGTGACCTAAAGTTTTCATTCTG 59.087 38.462 0.00 0.00 0.00 3.02
56 57 5.915196 GTGTGACCTAAAGTTTTCATTCTGC 59.085 40.000 0.00 0.00 0.00 4.26
57 58 5.827797 TGTGACCTAAAGTTTTCATTCTGCT 59.172 36.000 0.00 0.00 0.00 4.24
58 59 6.321181 TGTGACCTAAAGTTTTCATTCTGCTT 59.679 34.615 0.00 0.00 0.00 3.91
59 60 6.638468 GTGACCTAAAGTTTTCATTCTGCTTG 59.362 38.462 0.00 0.00 0.00 4.01
60 61 6.321181 TGACCTAAAGTTTTCATTCTGCTTGT 59.679 34.615 0.00 0.00 0.00 3.16
61 62 6.739112 ACCTAAAGTTTTCATTCTGCTTGTC 58.261 36.000 0.00 0.00 0.00 3.18
62 63 5.853282 CCTAAAGTTTTCATTCTGCTTGTCG 59.147 40.000 0.00 0.00 0.00 4.35
63 64 3.273919 AGTTTTCATTCTGCTTGTCGC 57.726 42.857 0.00 0.00 39.77 5.19
75 76 2.797491 GCTTGTCGCAACTCTTTTTGT 58.203 42.857 0.00 0.00 38.92 2.83
76 77 2.531508 GCTTGTCGCAACTCTTTTTGTG 59.468 45.455 0.00 0.00 38.17 3.33
77 78 2.187351 TGTCGCAACTCTTTTTGTGC 57.813 45.000 0.00 0.00 36.99 4.57
78 79 1.742831 TGTCGCAACTCTTTTTGTGCT 59.257 42.857 0.00 0.00 36.99 4.40
79 80 2.223249 TGTCGCAACTCTTTTTGTGCTC 60.223 45.455 0.00 0.00 36.99 4.26
80 81 2.032178 GTCGCAACTCTTTTTGTGCTCT 59.968 45.455 0.00 0.00 36.99 4.09
81 82 2.032054 TCGCAACTCTTTTTGTGCTCTG 59.968 45.455 0.00 0.00 36.99 3.35
82 83 2.735823 GCAACTCTTTTTGTGCTCTGG 58.264 47.619 0.00 0.00 0.00 3.86
83 84 2.358898 GCAACTCTTTTTGTGCTCTGGA 59.641 45.455 0.00 0.00 0.00 3.86
84 85 3.005155 GCAACTCTTTTTGTGCTCTGGAT 59.995 43.478 0.00 0.00 0.00 3.41
85 86 4.216257 GCAACTCTTTTTGTGCTCTGGATA 59.784 41.667 0.00 0.00 0.00 2.59
86 87 5.105997 GCAACTCTTTTTGTGCTCTGGATAT 60.106 40.000 0.00 0.00 0.00 1.63
87 88 6.571150 GCAACTCTTTTTGTGCTCTGGATATT 60.571 38.462 0.00 0.00 0.00 1.28
88 89 7.373493 CAACTCTTTTTGTGCTCTGGATATTT 58.627 34.615 0.00 0.00 0.00 1.40
89 90 7.530426 ACTCTTTTTGTGCTCTGGATATTTT 57.470 32.000 0.00 0.00 0.00 1.82
90 91 7.597386 ACTCTTTTTGTGCTCTGGATATTTTC 58.403 34.615 0.00 0.00 0.00 2.29
91 92 7.449704 ACTCTTTTTGTGCTCTGGATATTTTCT 59.550 33.333 0.00 0.00 0.00 2.52
92 93 8.862325 TCTTTTTGTGCTCTGGATATTTTCTA 57.138 30.769 0.00 0.00 0.00 2.10
93 94 8.950210 TCTTTTTGTGCTCTGGATATTTTCTAG 58.050 33.333 0.00 0.00 34.37 2.43
94 95 8.862325 TTTTTGTGCTCTGGATATTTTCTAGA 57.138 30.769 0.00 0.00 39.43 2.43
95 96 8.862325 TTTTGTGCTCTGGATATTTTCTAGAA 57.138 30.769 0.00 0.00 40.97 2.10
96 97 8.862325 TTTGTGCTCTGGATATTTTCTAGAAA 57.138 30.769 13.99 13.99 40.97 2.52
97 98 8.862325 TTGTGCTCTGGATATTTTCTAGAAAA 57.138 30.769 28.07 28.07 40.97 2.29
98 99 8.862325 TGTGCTCTGGATATTTTCTAGAAAAA 57.138 30.769 29.22 19.84 40.97 1.94
147 148 9.135843 TGTAATATAAAATATGGAACGAGAGCG 57.864 33.333 0.00 0.00 44.79 5.03
148 149 4.992381 ATAAAATATGGAACGAGAGCGC 57.008 40.909 0.00 0.00 42.48 5.92
149 150 1.209128 AAATATGGAACGAGAGCGCG 58.791 50.000 0.00 0.00 42.48 6.86
150 151 1.215655 AATATGGAACGAGAGCGCGC 61.216 55.000 26.66 26.66 42.48 6.86
158 159 3.702555 GAGAGCGCGCGTGTTGTT 61.703 61.111 32.35 5.81 0.00 2.83
159 160 3.223435 GAGAGCGCGCGTGTTGTTT 62.223 57.895 32.35 4.88 0.00 2.83
160 161 2.351888 GAGCGCGCGTGTTGTTTT 60.352 55.556 32.35 3.96 0.00 2.43
161 162 1.937362 GAGCGCGCGTGTTGTTTTT 60.937 52.632 32.35 3.04 0.00 1.94
180 181 5.776519 TTTTTGTGTTTTGTCACTCATGC 57.223 34.783 0.00 0.00 38.90 4.06
181 182 4.717233 TTTGTGTTTTGTCACTCATGCT 57.283 36.364 0.00 0.00 38.90 3.79
182 183 3.969117 TGTGTTTTGTCACTCATGCTC 57.031 42.857 0.00 0.00 38.90 4.26
183 184 3.544684 TGTGTTTTGTCACTCATGCTCT 58.455 40.909 0.00 0.00 38.90 4.09
184 185 3.313249 TGTGTTTTGTCACTCATGCTCTG 59.687 43.478 0.00 0.00 38.90 3.35
185 186 3.561310 GTGTTTTGTCACTCATGCTCTGA 59.439 43.478 0.00 0.00 35.68 3.27
186 187 4.035558 GTGTTTTGTCACTCATGCTCTGAA 59.964 41.667 0.00 0.00 35.68 3.02
187 188 4.274214 TGTTTTGTCACTCATGCTCTGAAG 59.726 41.667 0.00 0.00 32.14 3.02
188 189 4.341366 TTTGTCACTCATGCTCTGAAGA 57.659 40.909 0.00 0.00 32.14 2.87
189 190 3.309961 TGTCACTCATGCTCTGAAGAC 57.690 47.619 11.62 11.62 38.51 3.01
190 191 2.896044 TGTCACTCATGCTCTGAAGACT 59.104 45.455 15.92 0.00 38.68 3.24
191 192 3.252400 GTCACTCATGCTCTGAAGACTG 58.748 50.000 11.42 0.00 36.64 3.51
192 193 3.056962 GTCACTCATGCTCTGAAGACTGA 60.057 47.826 11.42 0.00 36.64 3.41
193 194 3.768215 TCACTCATGCTCTGAAGACTGAT 59.232 43.478 0.00 0.00 32.14 2.90
194 195 4.114073 CACTCATGCTCTGAAGACTGATC 58.886 47.826 0.00 0.00 32.14 2.92
195 196 3.132646 ACTCATGCTCTGAAGACTGATCC 59.867 47.826 0.00 0.00 32.14 3.36
196 197 3.372897 TCATGCTCTGAAGACTGATCCT 58.627 45.455 0.00 0.00 0.00 3.24
197 198 3.773667 TCATGCTCTGAAGACTGATCCTT 59.226 43.478 0.00 0.00 0.00 3.36
198 199 4.958581 TCATGCTCTGAAGACTGATCCTTA 59.041 41.667 0.00 0.00 0.00 2.69
199 200 5.601729 TCATGCTCTGAAGACTGATCCTTAT 59.398 40.000 0.00 0.00 0.00 1.73
200 201 5.946942 TGCTCTGAAGACTGATCCTTATT 57.053 39.130 0.00 0.00 0.00 1.40
201 202 6.305272 TGCTCTGAAGACTGATCCTTATTT 57.695 37.500 0.00 0.00 0.00 1.40
202 203 6.111382 TGCTCTGAAGACTGATCCTTATTTG 58.889 40.000 0.00 0.00 0.00 2.32
203 204 6.112058 GCTCTGAAGACTGATCCTTATTTGT 58.888 40.000 0.00 0.00 0.00 2.83
204 205 6.597280 GCTCTGAAGACTGATCCTTATTTGTT 59.403 38.462 0.00 0.00 0.00 2.83
205 206 7.120432 GCTCTGAAGACTGATCCTTATTTGTTT 59.880 37.037 0.00 0.00 0.00 2.83
206 207 8.924511 TCTGAAGACTGATCCTTATTTGTTTT 57.075 30.769 0.00 0.00 0.00 2.43
207 208 9.003658 TCTGAAGACTGATCCTTATTTGTTTTC 57.996 33.333 0.00 0.00 0.00 2.29
208 209 8.924511 TGAAGACTGATCCTTATTTGTTTTCT 57.075 30.769 0.00 0.00 0.00 2.52
209 210 9.003658 TGAAGACTGATCCTTATTTGTTTTCTC 57.996 33.333 0.00 0.00 0.00 2.87
210 211 8.924511 AAGACTGATCCTTATTTGTTTTCTCA 57.075 30.769 0.00 0.00 0.00 3.27
211 212 9.525826 AAGACTGATCCTTATTTGTTTTCTCAT 57.474 29.630 0.00 0.00 0.00 2.90
212 213 8.954350 AGACTGATCCTTATTTGTTTTCTCATG 58.046 33.333 0.00 0.00 0.00 3.07
213 214 8.641498 ACTGATCCTTATTTGTTTTCTCATGT 57.359 30.769 0.00 0.00 0.00 3.21
214 215 9.082313 ACTGATCCTTATTTGTTTTCTCATGTT 57.918 29.630 0.00 0.00 0.00 2.71
215 216 9.918630 CTGATCCTTATTTGTTTTCTCATGTTT 57.081 29.630 0.00 0.00 0.00 2.83
216 217 9.912634 TGATCCTTATTTGTTTTCTCATGTTTC 57.087 29.630 0.00 0.00 0.00 2.78
217 218 9.912634 GATCCTTATTTGTTTTCTCATGTTTCA 57.087 29.630 0.00 0.00 0.00 2.69
218 219 9.918630 ATCCTTATTTGTTTTCTCATGTTTCAG 57.081 29.630 0.00 0.00 0.00 3.02
219 220 9.130661 TCCTTATTTGTTTTCTCATGTTTCAGA 57.869 29.630 0.00 0.00 0.00 3.27
220 221 9.918630 CCTTATTTGTTTTCTCATGTTTCAGAT 57.081 29.630 0.00 0.00 0.00 2.90
224 225 9.603921 ATTTGTTTTCTCATGTTTCAGATTGTT 57.396 25.926 0.00 0.00 0.00 2.83
225 226 7.990541 TGTTTTCTCATGTTTCAGATTGTTG 57.009 32.000 0.00 0.00 0.00 3.33
226 227 7.546358 TGTTTTCTCATGTTTCAGATTGTTGT 58.454 30.769 0.00 0.00 0.00 3.32
227 228 7.701924 TGTTTTCTCATGTTTCAGATTGTTGTC 59.298 33.333 0.00 0.00 0.00 3.18
228 229 5.947228 TCTCATGTTTCAGATTGTTGTCC 57.053 39.130 0.00 0.00 0.00 4.02
229 230 5.624159 TCTCATGTTTCAGATTGTTGTCCT 58.376 37.500 0.00 0.00 0.00 3.85
230 231 6.768483 TCTCATGTTTCAGATTGTTGTCCTA 58.232 36.000 0.00 0.00 0.00 2.94
231 232 7.223584 TCTCATGTTTCAGATTGTTGTCCTAA 58.776 34.615 0.00 0.00 0.00 2.69
232 233 7.884877 TCTCATGTTTCAGATTGTTGTCCTAAT 59.115 33.333 0.00 0.00 0.00 1.73
233 234 7.819644 TCATGTTTCAGATTGTTGTCCTAATG 58.180 34.615 0.00 0.00 0.00 1.90
234 235 7.448161 TCATGTTTCAGATTGTTGTCCTAATGT 59.552 33.333 0.00 0.00 0.00 2.71
235 236 6.969366 TGTTTCAGATTGTTGTCCTAATGTG 58.031 36.000 0.00 0.00 0.00 3.21
236 237 6.016360 TGTTTCAGATTGTTGTCCTAATGTGG 60.016 38.462 0.00 0.00 30.91 4.17
237 238 5.497464 TCAGATTGTTGTCCTAATGTGGA 57.503 39.130 0.00 0.00 30.91 4.02
249 250 5.989477 TCCTAATGTGGACCTAGAACAATG 58.011 41.667 0.00 0.00 0.00 2.82
250 251 5.487488 TCCTAATGTGGACCTAGAACAATGT 59.513 40.000 0.00 0.00 0.00 2.71
251 252 6.012858 TCCTAATGTGGACCTAGAACAATGTT 60.013 38.462 0.00 0.00 0.00 2.71
252 253 5.964958 AATGTGGACCTAGAACAATGTTG 57.035 39.130 2.20 0.00 0.00 3.33
253 254 4.431416 TGTGGACCTAGAACAATGTTGT 57.569 40.909 2.20 1.27 44.72 3.32
254 255 4.133820 TGTGGACCTAGAACAATGTTGTG 58.866 43.478 2.20 0.00 41.31 3.33
255 256 4.141597 TGTGGACCTAGAACAATGTTGTGA 60.142 41.667 2.20 0.00 41.31 3.58
256 257 5.003804 GTGGACCTAGAACAATGTTGTGAT 58.996 41.667 2.20 0.00 41.31 3.06
257 258 6.170506 GTGGACCTAGAACAATGTTGTGATA 58.829 40.000 2.20 0.00 41.31 2.15
258 259 6.092259 GTGGACCTAGAACAATGTTGTGATAC 59.908 42.308 2.20 0.00 41.31 2.24
259 260 6.170506 GGACCTAGAACAATGTTGTGATACA 58.829 40.000 2.20 0.00 41.31 2.29
260 261 6.653320 GGACCTAGAACAATGTTGTGATACAA 59.347 38.462 2.20 0.00 41.31 2.41
261 262 7.336931 GGACCTAGAACAATGTTGTGATACAAT 59.663 37.037 2.20 0.00 40.59 2.71
262 263 8.635765 ACCTAGAACAATGTTGTGATACAATT 57.364 30.769 2.20 0.00 40.59 2.32
263 264 8.514594 ACCTAGAACAATGTTGTGATACAATTG 58.485 33.333 2.20 3.24 40.59 2.32
264 265 7.485913 CCTAGAACAATGTTGTGATACAATTGC 59.514 37.037 2.20 0.00 40.59 3.56
265 266 6.747125 AGAACAATGTTGTGATACAATTGCA 58.253 32.000 2.20 0.00 40.59 4.08
266 267 7.380536 AGAACAATGTTGTGATACAATTGCAT 58.619 30.769 2.20 0.00 40.59 3.96
267 268 7.874016 AGAACAATGTTGTGATACAATTGCATT 59.126 29.630 2.20 1.80 40.59 3.56
268 269 7.966246 ACAATGTTGTGATACAATTGCATTT 57.034 28.000 5.05 0.00 40.59 2.32
269 270 7.798801 ACAATGTTGTGATACAATTGCATTTG 58.201 30.769 17.53 17.53 40.59 2.32
270 271 7.656542 ACAATGTTGTGATACAATTGCATTTGA 59.343 29.630 24.13 10.84 40.59 2.69
271 272 7.585286 ATGTTGTGATACAATTGCATTTGAC 57.415 32.000 24.13 13.80 40.59 3.18
272 273 5.925397 TGTTGTGATACAATTGCATTTGACC 59.075 36.000 24.13 13.82 40.59 4.02
273 274 5.981088 TGTGATACAATTGCATTTGACCT 57.019 34.783 24.13 10.37 0.00 3.85
274 275 6.343716 TGTGATACAATTGCATTTGACCTT 57.656 33.333 24.13 7.64 0.00 3.50
275 276 6.389091 TGTGATACAATTGCATTTGACCTTC 58.611 36.000 24.13 15.19 0.00 3.46
276 277 5.807011 GTGATACAATTGCATTTGACCTTCC 59.193 40.000 24.13 9.75 0.00 3.46
277 278 5.716228 TGATACAATTGCATTTGACCTTCCT 59.284 36.000 24.13 6.08 0.00 3.36
278 279 6.889177 TGATACAATTGCATTTGACCTTCCTA 59.111 34.615 24.13 7.85 0.00 2.94
279 280 7.560991 TGATACAATTGCATTTGACCTTCCTAT 59.439 33.333 24.13 11.55 0.00 2.57
280 281 8.995027 ATACAATTGCATTTGACCTTCCTATA 57.005 30.769 24.13 6.64 0.00 1.31
281 282 7.902920 ACAATTGCATTTGACCTTCCTATAT 57.097 32.000 24.13 0.00 0.00 0.86
282 283 8.310122 ACAATTGCATTTGACCTTCCTATATT 57.690 30.769 24.13 0.00 0.00 1.28
283 284 8.416329 ACAATTGCATTTGACCTTCCTATATTC 58.584 33.333 24.13 0.00 0.00 1.75
284 285 8.636213 CAATTGCATTTGACCTTCCTATATTCT 58.364 33.333 14.72 0.00 0.00 2.40
285 286 7.572523 TTGCATTTGACCTTCCTATATTCTG 57.427 36.000 0.00 0.00 0.00 3.02
286 287 6.064060 TGCATTTGACCTTCCTATATTCTGG 58.936 40.000 0.00 0.00 0.00 3.86
287 288 6.126507 TGCATTTGACCTTCCTATATTCTGGA 60.127 38.462 0.00 0.00 0.00 3.86
288 289 6.429385 GCATTTGACCTTCCTATATTCTGGAG 59.571 42.308 0.00 0.00 33.46 3.86
289 290 7.690301 GCATTTGACCTTCCTATATTCTGGAGA 60.690 40.741 0.00 0.00 33.46 3.71
373 374 5.147330 TGTTTGTGACTGATACCTACCAG 57.853 43.478 0.00 0.00 36.53 4.00
390 391 1.336517 CCAGTTTTCTCGTCGGCTGTA 60.337 52.381 0.00 0.00 0.00 2.74
557 588 1.296984 TAAGTCGTCTCCCTCCCTCT 58.703 55.000 0.00 0.00 0.00 3.69
558 589 0.033894 AAGTCGTCTCCCTCCCTCTC 60.034 60.000 0.00 0.00 0.00 3.20
559 590 1.208844 AGTCGTCTCCCTCCCTCTCA 61.209 60.000 0.00 0.00 0.00 3.27
560 591 1.033202 GTCGTCTCCCTCCCTCTCAC 61.033 65.000 0.00 0.00 0.00 3.51
561 592 1.208844 TCGTCTCCCTCCCTCTCACT 61.209 60.000 0.00 0.00 0.00 3.41
562 593 0.750182 CGTCTCCCTCCCTCTCACTC 60.750 65.000 0.00 0.00 0.00 3.51
563 594 0.629058 GTCTCCCTCCCTCTCACTCT 59.371 60.000 0.00 0.00 0.00 3.24
564 595 0.628522 TCTCCCTCCCTCTCACTCTG 59.371 60.000 0.00 0.00 0.00 3.35
565 596 1.000993 TCCCTCCCTCTCACTCTGC 59.999 63.158 0.00 0.00 0.00 4.26
566 597 1.001503 CCCTCCCTCTCACTCTGCT 59.998 63.158 0.00 0.00 0.00 4.24
567 598 1.042559 CCCTCCCTCTCACTCTGCTC 61.043 65.000 0.00 0.00 0.00 4.26
762 836 4.282496 TGGCTCTTTGGGTAAGTTTTTCA 58.718 39.130 0.00 0.00 35.28 2.69
943 1017 1.342374 GGTTCTTGCTGGATTGGGGAT 60.342 52.381 0.00 0.00 0.00 3.85
969 1043 8.506168 TTAATTTGTGATCTATGTCTGGTTCC 57.494 34.615 0.00 0.00 0.00 3.62
1028 1102 4.329545 CCCTGACACCACCGTGGG 62.330 72.222 21.77 12.64 44.86 4.61
1473 1551 5.870433 GCCTCACCTTTAGTTTCTTAGTCTC 59.130 44.000 0.00 0.00 0.00 3.36
1562 1640 5.529800 GTGAAGGTGTTAACTGTGGTGTTAT 59.470 40.000 7.22 0.00 33.16 1.89
1833 1912 7.167535 AGGAGGAAGAATTTGAGAAGAAGAAG 58.832 38.462 0.00 0.00 0.00 2.85
1834 1913 7.017056 AGGAGGAAGAATTTGAGAAGAAGAAGA 59.983 37.037 0.00 0.00 0.00 2.87
1835 1914 7.663493 GGAGGAAGAATTTGAGAAGAAGAAGAA 59.337 37.037 0.00 0.00 0.00 2.52
2149 2240 5.472478 GCCTTTATAAGTATGTGGCCTAACC 59.528 44.000 3.32 0.00 39.84 2.85
2197 2288 4.220602 ACATTTTGGGGAATGTGAAGCTAC 59.779 41.667 2.73 0.00 45.75 3.58
2241 2334 9.378551 CCAATGTTAAGAACTGTAGTTATGCTA 57.621 33.333 0.00 0.00 38.56 3.49
2990 3103 7.036996 TCAATTTTTGCATCAGTGTTGTCTA 57.963 32.000 3.24 0.00 0.00 2.59
3008 3121 7.038302 TGTTGTCTAAATCTACCCAGAAGTCAT 60.038 37.037 0.00 0.00 33.50 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.706270 CACACATCAAAGTTCAGTACCTAACT 59.294 38.462 4.94 4.94 39.81 2.24
10 11 6.482308 ACACACATCAAAGTTCAGTACCTAAC 59.518 38.462 0.00 0.00 0.00 2.34
11 12 6.481976 CACACACATCAAAGTTCAGTACCTAA 59.518 38.462 0.00 0.00 0.00 2.69
12 13 5.989168 CACACACATCAAAGTTCAGTACCTA 59.011 40.000 0.00 0.00 0.00 3.08
13 14 4.816385 CACACACATCAAAGTTCAGTACCT 59.184 41.667 0.00 0.00 0.00 3.08
14 15 4.814234 TCACACACATCAAAGTTCAGTACC 59.186 41.667 0.00 0.00 0.00 3.34
15 16 5.277345 GGTCACACACATCAAAGTTCAGTAC 60.277 44.000 0.00 0.00 0.00 2.73
16 17 4.814234 GGTCACACACATCAAAGTTCAGTA 59.186 41.667 0.00 0.00 0.00 2.74
17 18 3.627577 GGTCACACACATCAAAGTTCAGT 59.372 43.478 0.00 0.00 0.00 3.41
18 19 3.879295 AGGTCACACACATCAAAGTTCAG 59.121 43.478 0.00 0.00 0.00 3.02
19 20 3.884895 AGGTCACACACATCAAAGTTCA 58.115 40.909 0.00 0.00 0.00 3.18
20 21 6.038271 ACTTTAGGTCACACACATCAAAGTTC 59.962 38.462 0.00 0.00 32.60 3.01
21 22 5.885912 ACTTTAGGTCACACACATCAAAGTT 59.114 36.000 0.00 0.00 32.60 2.66
22 23 5.437060 ACTTTAGGTCACACACATCAAAGT 58.563 37.500 0.00 0.00 31.88 2.66
23 24 6.377327 AACTTTAGGTCACACACATCAAAG 57.623 37.500 0.00 0.00 0.00 2.77
24 25 6.767524 AAACTTTAGGTCACACACATCAAA 57.232 33.333 0.00 0.00 0.00 2.69
25 26 6.375736 TGAAAACTTTAGGTCACACACATCAA 59.624 34.615 0.00 0.00 0.00 2.57
26 27 5.883115 TGAAAACTTTAGGTCACACACATCA 59.117 36.000 0.00 0.00 0.00 3.07
27 28 6.371809 TGAAAACTTTAGGTCACACACATC 57.628 37.500 0.00 0.00 0.00 3.06
28 29 6.959639 ATGAAAACTTTAGGTCACACACAT 57.040 33.333 0.00 0.00 0.00 3.21
29 30 6.601613 AGAATGAAAACTTTAGGTCACACACA 59.398 34.615 0.00 0.00 0.00 3.72
30 31 6.912591 CAGAATGAAAACTTTAGGTCACACAC 59.087 38.462 0.00 0.00 39.69 3.82
31 32 6.459573 GCAGAATGAAAACTTTAGGTCACACA 60.460 38.462 0.00 0.00 39.69 3.72
32 33 5.915196 GCAGAATGAAAACTTTAGGTCACAC 59.085 40.000 0.00 0.00 39.69 3.82
33 34 5.827797 AGCAGAATGAAAACTTTAGGTCACA 59.172 36.000 0.00 0.00 39.69 3.58
34 35 6.319141 AGCAGAATGAAAACTTTAGGTCAC 57.681 37.500 0.00 0.00 39.69 3.67
35 36 6.321181 ACAAGCAGAATGAAAACTTTAGGTCA 59.679 34.615 0.00 0.00 39.69 4.02
36 37 6.739112 ACAAGCAGAATGAAAACTTTAGGTC 58.261 36.000 0.00 0.00 39.69 3.85
37 38 6.513393 CGACAAGCAGAATGAAAACTTTAGGT 60.513 38.462 0.00 0.00 39.69 3.08
38 39 5.853282 CGACAAGCAGAATGAAAACTTTAGG 59.147 40.000 0.00 0.00 39.69 2.69
39 40 6.901699 CGACAAGCAGAATGAAAACTTTAG 57.098 37.500 0.00 0.00 39.69 1.85
56 57 2.531508 GCACAAAAAGAGTTGCGACAAG 59.468 45.455 6.90 0.00 31.29 3.16
57 58 2.163412 AGCACAAAAAGAGTTGCGACAA 59.837 40.909 6.90 0.00 31.29 3.18
58 59 1.742831 AGCACAAAAAGAGTTGCGACA 59.257 42.857 6.90 0.00 31.29 4.35
59 60 2.032178 AGAGCACAAAAAGAGTTGCGAC 59.968 45.455 0.00 0.00 31.29 5.19
60 61 2.032054 CAGAGCACAAAAAGAGTTGCGA 59.968 45.455 0.00 0.00 31.29 5.10
61 62 2.378806 CAGAGCACAAAAAGAGTTGCG 58.621 47.619 0.00 0.00 31.29 4.85
62 63 2.358898 TCCAGAGCACAAAAAGAGTTGC 59.641 45.455 0.00 0.00 31.29 4.17
63 64 4.843220 ATCCAGAGCACAAAAAGAGTTG 57.157 40.909 0.00 0.00 34.52 3.16
64 65 7.530426 AAATATCCAGAGCACAAAAAGAGTT 57.470 32.000 0.00 0.00 0.00 3.01
65 66 7.449704 AGAAAATATCCAGAGCACAAAAAGAGT 59.550 33.333 0.00 0.00 0.00 3.24
66 67 7.824672 AGAAAATATCCAGAGCACAAAAAGAG 58.175 34.615 0.00 0.00 0.00 2.85
67 68 7.765695 AGAAAATATCCAGAGCACAAAAAGA 57.234 32.000 0.00 0.00 0.00 2.52
68 69 8.950210 TCTAGAAAATATCCAGAGCACAAAAAG 58.050 33.333 0.00 0.00 0.00 2.27
69 70 8.862325 TCTAGAAAATATCCAGAGCACAAAAA 57.138 30.769 0.00 0.00 0.00 1.94
70 71 8.862325 TTCTAGAAAATATCCAGAGCACAAAA 57.138 30.769 1.68 0.00 27.21 2.44
71 72 8.862325 TTTCTAGAAAATATCCAGAGCACAAA 57.138 30.769 15.57 0.00 27.21 2.83
72 73 8.862325 TTTTCTAGAAAATATCCAGAGCACAA 57.138 30.769 23.65 0.00 35.57 3.33
73 74 8.862325 TTTTTCTAGAAAATATCCAGAGCACA 57.138 30.769 26.90 8.39 39.69 4.57
121 122 9.135843 CGCTCTCGTTCCATATTTTATATTACA 57.864 33.333 0.00 0.00 0.00 2.41
122 123 8.108782 GCGCTCTCGTTCCATATTTTATATTAC 58.891 37.037 0.00 0.00 38.14 1.89
123 124 7.008901 CGCGCTCTCGTTCCATATTTTATATTA 59.991 37.037 5.56 0.00 38.14 0.98
124 125 6.183360 CGCGCTCTCGTTCCATATTTTATATT 60.183 38.462 5.56 0.00 38.14 1.28
125 126 5.288712 CGCGCTCTCGTTCCATATTTTATAT 59.711 40.000 5.56 0.00 38.14 0.86
126 127 4.619760 CGCGCTCTCGTTCCATATTTTATA 59.380 41.667 5.56 0.00 38.14 0.98
127 128 3.428870 CGCGCTCTCGTTCCATATTTTAT 59.571 43.478 5.56 0.00 38.14 1.40
128 129 2.792674 CGCGCTCTCGTTCCATATTTTA 59.207 45.455 5.56 0.00 38.14 1.52
129 130 1.593006 CGCGCTCTCGTTCCATATTTT 59.407 47.619 5.56 0.00 38.14 1.82
130 131 1.209128 CGCGCTCTCGTTCCATATTT 58.791 50.000 5.56 0.00 38.14 1.40
131 132 1.215655 GCGCGCTCTCGTTCCATATT 61.216 55.000 26.67 0.00 38.14 1.28
132 133 1.661821 GCGCGCTCTCGTTCCATAT 60.662 57.895 26.67 0.00 38.14 1.78
133 134 2.278596 GCGCGCTCTCGTTCCATA 60.279 61.111 26.67 0.00 38.14 2.74
141 142 2.695712 AAAACAACACGCGCGCTCTC 62.696 55.000 32.58 0.00 0.00 3.20
142 143 2.317685 AAAAACAACACGCGCGCTCT 62.318 50.000 32.58 11.50 0.00 4.09
143 144 1.937362 AAAAACAACACGCGCGCTC 60.937 52.632 32.58 0.59 0.00 5.03
144 145 2.101380 AAAAACAACACGCGCGCT 59.899 50.000 32.58 14.89 0.00 5.92
158 159 5.477510 AGCATGAGTGACAAAACACAAAAA 58.522 33.333 0.00 0.00 42.45 1.94
159 160 5.070770 AGCATGAGTGACAAAACACAAAA 57.929 34.783 0.00 0.00 42.45 2.44
160 161 4.398988 AGAGCATGAGTGACAAAACACAAA 59.601 37.500 0.00 0.00 42.45 2.83
161 162 3.947196 AGAGCATGAGTGACAAAACACAA 59.053 39.130 0.00 0.00 42.45 3.33
162 163 3.313249 CAGAGCATGAGTGACAAAACACA 59.687 43.478 0.00 0.00 42.45 3.72
163 164 3.561310 TCAGAGCATGAGTGACAAAACAC 59.439 43.478 0.00 0.00 40.60 3.32
164 165 3.807553 TCAGAGCATGAGTGACAAAACA 58.192 40.909 0.00 0.00 32.77 2.83
165 166 4.512944 TCTTCAGAGCATGAGTGACAAAAC 59.487 41.667 0.00 0.00 39.68 2.43
166 167 4.512944 GTCTTCAGAGCATGAGTGACAAAA 59.487 41.667 0.00 0.00 40.22 2.44
167 168 4.060900 GTCTTCAGAGCATGAGTGACAAA 58.939 43.478 0.00 0.00 40.22 2.83
168 169 3.323115 AGTCTTCAGAGCATGAGTGACAA 59.677 43.478 19.23 0.00 41.61 3.18
169 170 2.896044 AGTCTTCAGAGCATGAGTGACA 59.104 45.455 19.23 0.00 41.61 3.58
170 171 3.056962 TCAGTCTTCAGAGCATGAGTGAC 60.057 47.826 0.00 13.89 39.68 3.67
171 172 3.160269 TCAGTCTTCAGAGCATGAGTGA 58.840 45.455 0.00 0.00 39.68 3.41
172 173 3.589495 TCAGTCTTCAGAGCATGAGTG 57.411 47.619 0.00 0.00 39.68 3.51
173 174 3.132646 GGATCAGTCTTCAGAGCATGAGT 59.867 47.826 0.00 0.00 39.68 3.41
174 175 3.385433 AGGATCAGTCTTCAGAGCATGAG 59.615 47.826 0.00 0.00 39.68 2.90
175 176 3.372897 AGGATCAGTCTTCAGAGCATGA 58.627 45.455 0.00 0.00 35.62 3.07
176 177 3.823281 AGGATCAGTCTTCAGAGCATG 57.177 47.619 0.00 0.00 0.00 4.06
177 178 6.497624 AATAAGGATCAGTCTTCAGAGCAT 57.502 37.500 0.00 0.00 0.00 3.79
178 179 5.946942 AATAAGGATCAGTCTTCAGAGCA 57.053 39.130 0.00 0.00 0.00 4.26
179 180 6.112058 ACAAATAAGGATCAGTCTTCAGAGC 58.888 40.000 0.00 0.00 0.00 4.09
180 181 8.558973 AAACAAATAAGGATCAGTCTTCAGAG 57.441 34.615 0.00 0.00 0.00 3.35
181 182 8.924511 AAAACAAATAAGGATCAGTCTTCAGA 57.075 30.769 0.00 0.00 0.00 3.27
182 183 9.007901 AGAAAACAAATAAGGATCAGTCTTCAG 57.992 33.333 0.00 0.00 0.00 3.02
183 184 8.924511 AGAAAACAAATAAGGATCAGTCTTCA 57.075 30.769 0.00 0.00 0.00 3.02
184 185 9.003658 TGAGAAAACAAATAAGGATCAGTCTTC 57.996 33.333 0.00 0.00 0.00 2.87
185 186 8.924511 TGAGAAAACAAATAAGGATCAGTCTT 57.075 30.769 0.00 0.00 0.00 3.01
186 187 8.954350 CATGAGAAAACAAATAAGGATCAGTCT 58.046 33.333 0.00 0.00 0.00 3.24
187 188 8.734386 ACATGAGAAAACAAATAAGGATCAGTC 58.266 33.333 0.00 0.00 0.00 3.51
188 189 8.641498 ACATGAGAAAACAAATAAGGATCAGT 57.359 30.769 0.00 0.00 0.00 3.41
189 190 9.918630 AAACATGAGAAAACAAATAAGGATCAG 57.081 29.630 0.00 0.00 0.00 2.90
190 191 9.912634 GAAACATGAGAAAACAAATAAGGATCA 57.087 29.630 0.00 0.00 0.00 2.92
191 192 9.912634 TGAAACATGAGAAAACAAATAAGGATC 57.087 29.630 0.00 0.00 0.00 3.36
192 193 9.918630 CTGAAACATGAGAAAACAAATAAGGAT 57.081 29.630 0.00 0.00 0.00 3.24
193 194 9.130661 TCTGAAACATGAGAAAACAAATAAGGA 57.869 29.630 0.00 0.00 0.00 3.36
194 195 9.918630 ATCTGAAACATGAGAAAACAAATAAGG 57.081 29.630 0.00 0.00 0.00 2.69
198 199 9.603921 AACAATCTGAAACATGAGAAAACAAAT 57.396 25.926 0.00 0.00 0.00 2.32
199 200 8.871862 CAACAATCTGAAACATGAGAAAACAAA 58.128 29.630 0.00 0.00 0.00 2.83
200 201 8.034215 ACAACAATCTGAAACATGAGAAAACAA 58.966 29.630 0.00 0.00 0.00 2.83
201 202 7.546358 ACAACAATCTGAAACATGAGAAAACA 58.454 30.769 0.00 0.00 0.00 2.83
202 203 7.168135 GGACAACAATCTGAAACATGAGAAAAC 59.832 37.037 0.00 0.00 0.00 2.43
203 204 7.068593 AGGACAACAATCTGAAACATGAGAAAA 59.931 33.333 0.00 0.00 0.00 2.29
204 205 6.547141 AGGACAACAATCTGAAACATGAGAAA 59.453 34.615 0.00 0.00 0.00 2.52
205 206 6.064060 AGGACAACAATCTGAAACATGAGAA 58.936 36.000 0.00 0.00 0.00 2.87
206 207 5.624159 AGGACAACAATCTGAAACATGAGA 58.376 37.500 0.00 0.00 0.00 3.27
207 208 5.954296 AGGACAACAATCTGAAACATGAG 57.046 39.130 0.00 0.00 0.00 2.90
208 209 7.448161 ACATTAGGACAACAATCTGAAACATGA 59.552 33.333 0.00 0.00 0.00 3.07
209 210 7.539710 CACATTAGGACAACAATCTGAAACATG 59.460 37.037 0.00 0.00 0.00 3.21
210 211 7.309377 CCACATTAGGACAACAATCTGAAACAT 60.309 37.037 0.00 0.00 0.00 2.71
211 212 6.016360 CCACATTAGGACAACAATCTGAAACA 60.016 38.462 0.00 0.00 0.00 2.83
212 213 6.206634 TCCACATTAGGACAACAATCTGAAAC 59.793 38.462 0.00 0.00 31.23 2.78
213 214 6.303054 TCCACATTAGGACAACAATCTGAAA 58.697 36.000 0.00 0.00 31.23 2.69
214 215 5.875224 TCCACATTAGGACAACAATCTGAA 58.125 37.500 0.00 0.00 31.23 3.02
215 216 5.497464 TCCACATTAGGACAACAATCTGA 57.503 39.130 0.00 0.00 31.23 3.27
226 227 5.487488 ACATTGTTCTAGGTCCACATTAGGA 59.513 40.000 0.00 0.00 34.64 2.94
227 228 5.745227 ACATTGTTCTAGGTCCACATTAGG 58.255 41.667 0.00 0.00 0.00 2.69
228 229 6.655003 ACAACATTGTTCTAGGTCCACATTAG 59.345 38.462 0.00 0.00 38.47 1.73
229 230 6.429692 CACAACATTGTTCTAGGTCCACATTA 59.570 38.462 0.00 0.00 39.91 1.90
230 231 5.241506 CACAACATTGTTCTAGGTCCACATT 59.758 40.000 0.00 0.00 39.91 2.71
231 232 4.761739 CACAACATTGTTCTAGGTCCACAT 59.238 41.667 0.00 0.00 39.91 3.21
232 233 4.133820 CACAACATTGTTCTAGGTCCACA 58.866 43.478 0.00 0.00 39.91 4.17
233 234 4.385825 TCACAACATTGTTCTAGGTCCAC 58.614 43.478 0.00 0.00 39.91 4.02
234 235 4.698201 TCACAACATTGTTCTAGGTCCA 57.302 40.909 0.00 0.00 39.91 4.02
235 236 6.170506 TGTATCACAACATTGTTCTAGGTCC 58.829 40.000 0.00 0.00 39.91 4.46
236 237 7.667043 TTGTATCACAACATTGTTCTAGGTC 57.333 36.000 0.00 0.00 39.91 3.85
237 238 8.514594 CAATTGTATCACAACATTGTTCTAGGT 58.485 33.333 0.00 0.00 41.40 3.08
238 239 7.485913 GCAATTGTATCACAACATTGTTCTAGG 59.514 37.037 7.40 0.00 41.40 3.02
239 240 8.022550 TGCAATTGTATCACAACATTGTTCTAG 58.977 33.333 7.40 0.00 41.40 2.43
240 241 7.880105 TGCAATTGTATCACAACATTGTTCTA 58.120 30.769 7.40 0.00 41.40 2.10
241 242 6.747125 TGCAATTGTATCACAACATTGTTCT 58.253 32.000 7.40 0.00 41.40 3.01
242 243 7.585286 ATGCAATTGTATCACAACATTGTTC 57.415 32.000 7.40 0.00 41.40 3.18
243 244 7.966246 AATGCAATTGTATCACAACATTGTT 57.034 28.000 9.60 0.00 41.40 2.83
244 245 7.656542 TCAAATGCAATTGTATCACAACATTGT 59.343 29.630 14.00 0.00 41.40 2.71
245 246 7.953173 GTCAAATGCAATTGTATCACAACATTG 59.047 33.333 14.00 8.60 41.40 2.82
246 247 7.118101 GGTCAAATGCAATTGTATCACAACATT 59.882 33.333 14.00 3.98 41.40 2.71
247 248 6.591062 GGTCAAATGCAATTGTATCACAACAT 59.409 34.615 14.00 0.00 41.40 2.71
248 249 5.925397 GGTCAAATGCAATTGTATCACAACA 59.075 36.000 14.00 0.00 41.40 3.33
249 250 6.158598 AGGTCAAATGCAATTGTATCACAAC 58.841 36.000 14.00 3.43 41.40 3.32
250 251 6.343716 AGGTCAAATGCAATTGTATCACAA 57.656 33.333 14.00 0.00 42.95 3.33
251 252 5.981088 AGGTCAAATGCAATTGTATCACA 57.019 34.783 14.00 0.00 36.10 3.58
252 253 5.807011 GGAAGGTCAAATGCAATTGTATCAC 59.193 40.000 14.00 5.12 36.10 3.06
253 254 5.716228 AGGAAGGTCAAATGCAATTGTATCA 59.284 36.000 14.00 0.00 36.10 2.15
254 255 6.212888 AGGAAGGTCAAATGCAATTGTATC 57.787 37.500 14.00 8.24 36.10 2.24
255 256 7.902920 ATAGGAAGGTCAAATGCAATTGTAT 57.097 32.000 14.00 5.10 36.10 2.29
256 257 8.995027 ATATAGGAAGGTCAAATGCAATTGTA 57.005 30.769 14.00 2.30 36.10 2.41
257 258 7.902920 ATATAGGAAGGTCAAATGCAATTGT 57.097 32.000 14.00 0.00 36.10 2.71
258 259 8.636213 AGAATATAGGAAGGTCAAATGCAATTG 58.364 33.333 8.26 8.26 36.10 2.32
259 260 8.636213 CAGAATATAGGAAGGTCAAATGCAATT 58.364 33.333 0.00 0.00 38.98 2.32
260 261 7.232127 CCAGAATATAGGAAGGTCAAATGCAAT 59.768 37.037 0.00 0.00 0.00 3.56
261 262 6.547141 CCAGAATATAGGAAGGTCAAATGCAA 59.453 38.462 0.00 0.00 0.00 4.08
262 263 6.064060 CCAGAATATAGGAAGGTCAAATGCA 58.936 40.000 0.00 0.00 0.00 3.96
263 264 6.299141 TCCAGAATATAGGAAGGTCAAATGC 58.701 40.000 0.00 0.00 0.00 3.56
264 265 7.739825 TCTCCAGAATATAGGAAGGTCAAATG 58.260 38.462 0.00 0.00 32.57 2.32
265 266 7.937700 TCTCCAGAATATAGGAAGGTCAAAT 57.062 36.000 0.00 0.00 32.57 2.32
266 267 7.568738 TCATCTCCAGAATATAGGAAGGTCAAA 59.431 37.037 0.00 0.00 32.57 2.69
267 268 7.075797 TCATCTCCAGAATATAGGAAGGTCAA 58.924 38.462 0.00 0.00 32.57 3.18
268 269 6.624297 TCATCTCCAGAATATAGGAAGGTCA 58.376 40.000 0.00 0.00 32.57 4.02
269 270 6.723977 ACTCATCTCCAGAATATAGGAAGGTC 59.276 42.308 0.00 0.00 32.57 3.85
270 271 6.629156 ACTCATCTCCAGAATATAGGAAGGT 58.371 40.000 0.00 0.00 32.57 3.50
271 272 8.657387 TTACTCATCTCCAGAATATAGGAAGG 57.343 38.462 0.00 0.00 32.57 3.46
282 283 9.547753 GTTTTATGCTATTTACTCATCTCCAGA 57.452 33.333 0.00 0.00 0.00 3.86
283 284 9.553064 AGTTTTATGCTATTTACTCATCTCCAG 57.447 33.333 0.00 0.00 0.00 3.86
373 374 2.602878 TGATACAGCCGACGAGAAAAC 58.397 47.619 0.00 0.00 0.00 2.43
390 391 1.067213 CGGGCGATTTGGGTTTTTGAT 60.067 47.619 0.00 0.00 0.00 2.57
557 588 0.887247 GCAGAGTGAGAGCAGAGTGA 59.113 55.000 0.00 0.00 0.00 3.41
558 589 0.889994 AGCAGAGTGAGAGCAGAGTG 59.110 55.000 0.00 0.00 0.00 3.51
559 590 1.176527 GAGCAGAGTGAGAGCAGAGT 58.823 55.000 0.00 0.00 0.00 3.24
560 591 0.457035 GGAGCAGAGTGAGAGCAGAG 59.543 60.000 0.00 0.00 0.00 3.35
561 592 0.969917 GGGAGCAGAGTGAGAGCAGA 60.970 60.000 0.00 0.00 0.00 4.26
562 593 1.516892 GGGAGCAGAGTGAGAGCAG 59.483 63.158 0.00 0.00 0.00 4.24
563 594 1.986757 GGGGAGCAGAGTGAGAGCA 60.987 63.158 0.00 0.00 0.00 4.26
564 595 1.685421 AGGGGAGCAGAGTGAGAGC 60.685 63.158 0.00 0.00 0.00 4.09
565 596 1.958902 GCAGGGGAGCAGAGTGAGAG 61.959 65.000 0.00 0.00 0.00 3.20
566 597 1.986757 GCAGGGGAGCAGAGTGAGA 60.987 63.158 0.00 0.00 0.00 3.27
567 598 2.583520 GCAGGGGAGCAGAGTGAG 59.416 66.667 0.00 0.00 0.00 3.51
645 719 2.253758 GCTTCCACAGCGCAAGTCA 61.254 57.895 11.47 0.00 39.29 3.41
762 836 2.703007 CCTAACCCTAGCTCAGCAGATT 59.297 50.000 0.00 0.00 0.00 2.40
943 1017 8.956426 GGAACCAGACATAGATCACAAATTAAA 58.044 33.333 0.00 0.00 0.00 1.52
969 1043 4.213270 TGAACAAAATCACCTTAGCTCACG 59.787 41.667 0.00 0.00 0.00 4.35
1010 1084 3.238497 CCACGGTGGTGTCAGGGA 61.238 66.667 19.15 0.00 42.80 4.20
1425 1503 9.556030 GGCTTAAGTAAACTGAATATGTTGTTC 57.444 33.333 4.02 0.00 0.00 3.18
1490 1568 4.990543 TCACTAAGTGCACTCAAATTCG 57.009 40.909 21.95 2.43 32.98 3.34
1562 1640 0.467290 GGGCTTGTCAACCCACTCAA 60.467 55.000 14.79 0.00 46.22 3.02
1833 1912 5.652452 AGCTCTCTCTTCTACCTCTTTCTTC 59.348 44.000 0.00 0.00 0.00 2.87
1834 1913 5.580022 AGCTCTCTCTTCTACCTCTTTCTT 58.420 41.667 0.00 0.00 0.00 2.52
1835 1914 5.193099 AGCTCTCTCTTCTACCTCTTTCT 57.807 43.478 0.00 0.00 0.00 2.52
2149 2240 5.001874 CACCCCATATCTTCACATCAGATG 58.998 45.833 9.03 9.03 32.94 2.90
2197 2288 7.225784 ACATTGGCATAGACATAGACTAGAG 57.774 40.000 0.00 0.00 0.00 2.43
2971 3084 7.275888 AGATTTAGACAACACTGATGCAAAA 57.724 32.000 0.00 0.00 0.00 2.44
2990 3103 7.690256 AGTGTTTATGACTTCTGGGTAGATTT 58.310 34.615 0.00 0.00 31.81 2.17
3008 3121 7.367285 GTTGCATTATGAAACCTGAGTGTTTA 58.633 34.615 4.74 0.00 38.51 2.01


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

AutoCloner maintained by Alex Coulton.