Multiple sequence alignment - TraesCS3A01G119500

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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 TraesCS3A01G119500 chr3A 100.000 3314 0 0 1 3314 93043873 93040560 0.000000e+00 6120
1 TraesCS3A01G119500 chr3A 91.314 1324 106 5 1001 2318 93263757 93265077 0.000000e+00 1799
2 TraesCS3A01G119500 chr3A 91.219 1321 110 4 1001 2318 93337359 93338676 0.000000e+00 1792
3 TraesCS3A01G119500 chr3A 93.208 265 18 0 2052 2316 93265663 93265927 1.120000e-104 390
4 TraesCS3A01G119500 chr3D 91.005 3113 174 52 267 3314 79422107 79419036 0.000000e+00 4100
5 TraesCS3A01G119500 chr3D 92.078 1338 91 7 1001 2323 79504251 79505588 0.000000e+00 1869
6 TraesCS3A01G119500 chr3D 90.712 1335 112 5 996 2318 79428062 79429396 0.000000e+00 1768
7 TraesCS3A01G119500 chr3D 86.957 138 16 1 19 154 79248058 79248195 1.590000e-33 154
8 TraesCS3A01G119500 chr3B 90.531 2672 141 51 268 2889 125525071 125522462 0.000000e+00 3430
9 TraesCS3A01G119500 chr3B 92.157 1326 98 3 996 2318 125551787 125553109 0.000000e+00 1868
10 TraesCS3A01G119500 chr3B 92.221 1324 91 6 1001 2318 125778975 125780292 0.000000e+00 1864
11 TraesCS3A01G119500 chr3B 86.747 332 44 0 2983 3314 194338630 194338299 1.450000e-98 370
12 TraesCS3A01G119500 chr3B 86.364 330 43 1 2987 3314 191120443 191120772 3.140000e-95 359
13 TraesCS3A01G119500 chr3B 88.060 134 14 1 13 144 723626613 723626480 1.230000e-34 158
14 TraesCS3A01G119500 chr3B 95.238 63 2 1 2923 2984 125522133 125522071 7.570000e-17 99
15 TraesCS3A01G119500 chr1D 82.105 855 124 17 1445 2292 117400295 117399463 0.000000e+00 704
16 TraesCS3A01G119500 chr1D 85.976 328 46 0 2987 3314 22745737 22746064 5.260000e-93 351
17 TraesCS3A01G119500 chr5D 87.009 331 39 3 2987 3314 429035713 429035384 1.450000e-98 370
18 TraesCS3A01G119500 chr4B 85.799 338 47 1 2978 3314 488151026 488151363 1.130000e-94 357
19 TraesCS3A01G119500 chr4B 92.500 120 7 1 18 135 626638173 626638054 1.580000e-38 171
20 TraesCS3A01G119500 chr1B 86.364 330 41 3 2987 3314 643276194 643276521 1.130000e-94 357
21 TraesCS3A01G119500 chr6B 86.280 328 44 1 2987 3314 184528891 184528565 4.070000e-94 355
22 TraesCS3A01G119500 chr2B 86.061 330 43 2 2987 3314 542670619 542670947 5.260000e-93 351
23 TraesCS3A01G119500 chr1A 76.650 394 65 21 1022 1409 129004987 129004615 3.370000e-45 193
24 TraesCS3A01G119500 chr1A 90.323 124 10 1 18 139 45829753 45829876 9.520000e-36 161
25 TraesCS3A01G119500 chrUn 89.630 135 12 1 18 150 117156483 117156349 1.580000e-38 171
26 TraesCS3A01G119500 chr7B 90.076 131 9 4 11 138 705656874 705657003 2.050000e-37 167
27 TraesCS3A01G119500 chr5A 91.057 123 9 1 15 135 377936805 377936927 7.360000e-37 165
28 TraesCS3A01G119500 chr2A 91.667 120 8 2 17 134 779662555 779662436 7.360000e-37 165
29 TraesCS3A01G119500 chr4A 87.681 138 14 2 18 153 736715943 736716079 1.230000e-34 158


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 TraesCS3A01G119500 chr3A 93040560 93043873 3313 True 6120.0 6120 100.0000 1 3314 1 chr3A.!!$R1 3313
1 TraesCS3A01G119500 chr3A 93337359 93338676 1317 False 1792.0 1792 91.2190 1001 2318 1 chr3A.!!$F1 1317
2 TraesCS3A01G119500 chr3A 93263757 93265927 2170 False 1094.5 1799 92.2610 1001 2318 2 chr3A.!!$F2 1317
3 TraesCS3A01G119500 chr3D 79419036 79422107 3071 True 4100.0 4100 91.0050 267 3314 1 chr3D.!!$R1 3047
4 TraesCS3A01G119500 chr3D 79504251 79505588 1337 False 1869.0 1869 92.0780 1001 2323 1 chr3D.!!$F3 1322
5 TraesCS3A01G119500 chr3D 79428062 79429396 1334 False 1768.0 1768 90.7120 996 2318 1 chr3D.!!$F2 1322
6 TraesCS3A01G119500 chr3B 125551787 125553109 1322 False 1868.0 1868 92.1570 996 2318 1 chr3B.!!$F1 1322
7 TraesCS3A01G119500 chr3B 125778975 125780292 1317 False 1864.0 1864 92.2210 1001 2318 1 chr3B.!!$F2 1317
8 TraesCS3A01G119500 chr3B 125522071 125525071 3000 True 1764.5 3430 92.8845 268 2984 2 chr3B.!!$R3 2716
9 TraesCS3A01G119500 chr1D 117399463 117400295 832 True 704.0 704 82.1050 1445 2292 1 chr1D.!!$R1 847

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
422 444 0.108585 AGTTCATGCCACTGTCGGTT 59.891 50.0 0.0 0.0 0.0 4.44 F
687 714 0.112412 TGTCCTTTGCCCTTTCTCCC 59.888 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1435 1.493950 GCTCGTCCTTGGCGATCATG 61.494 60.0 6.64 0.0 39.46 3.07 R
2678 2880 0.460459 TGACCGACACAAAACGCAGA 60.460 50.0 0.00 0.0 0.00 4.26 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 5.298347 GGATGTGCAAATACTAGTACTCCC 58.702 45.833 4.31 0.00 0.00 4.30
24 25 5.070580 GGATGTGCAAATACTAGTACTCCCT 59.929 44.000 4.31 0.00 0.00 4.20
25 26 5.593679 TGTGCAAATACTAGTACTCCCTC 57.406 43.478 4.31 0.00 0.00 4.30
26 27 4.404715 TGTGCAAATACTAGTACTCCCTCC 59.595 45.833 4.31 0.00 0.00 4.30
27 28 3.635373 TGCAAATACTAGTACTCCCTCCG 59.365 47.826 4.31 0.00 0.00 4.63
28 29 3.635836 GCAAATACTAGTACTCCCTCCGT 59.364 47.826 4.31 0.00 0.00 4.69
29 30 4.261530 GCAAATACTAGTACTCCCTCCGTC 60.262 50.000 4.31 0.00 0.00 4.79
30 31 5.131784 CAAATACTAGTACTCCCTCCGTCT 58.868 45.833 4.31 0.00 0.00 4.18
31 32 4.622260 ATACTAGTACTCCCTCCGTCTC 57.378 50.000 4.31 0.00 0.00 3.36
32 33 2.194859 ACTAGTACTCCCTCCGTCTCA 58.805 52.381 0.00 0.00 0.00 3.27
33 34 2.575279 ACTAGTACTCCCTCCGTCTCAA 59.425 50.000 0.00 0.00 0.00 3.02
34 35 2.599408 AGTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
35 36 2.885616 AGTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
36 37 3.442076 AGTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
37 38 3.838903 AGTACTCCCTCCGTCTCAAAATT 59.161 43.478 0.00 0.00 0.00 1.82
38 39 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
39 40 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
40 41 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
41 42 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
42 43 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
43 44 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
44 45 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
45 46 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
46 47 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
47 48 6.426937 CCTCCGTCTCAAAATTCTTGTCTTAA 59.573 38.462 0.00 0.00 0.00 1.85
48 49 7.041372 CCTCCGTCTCAAAATTCTTGTCTTAAA 60.041 37.037 0.00 0.00 0.00 1.52
49 50 8.391075 TCCGTCTCAAAATTCTTGTCTTAAAT 57.609 30.769 0.00 0.00 0.00 1.40
50 51 8.846211 TCCGTCTCAAAATTCTTGTCTTAAATT 58.154 29.630 0.00 0.00 0.00 1.82
51 52 9.463443 CCGTCTCAAAATTCTTGTCTTAAATTT 57.537 29.630 0.00 0.00 34.86 1.82
75 76 9.817809 TTTGTCTAAATACAGATGTATCAGGTC 57.182 33.333 5.97 5.42 40.10 3.85
76 77 8.533569 TGTCTAAATACAGATGTATCAGGTCA 57.466 34.615 5.97 7.27 40.10 4.02
77 78 8.414003 TGTCTAAATACAGATGTATCAGGTCAC 58.586 37.037 5.97 3.29 40.10 3.67
78 79 8.414003 GTCTAAATACAGATGTATCAGGTCACA 58.586 37.037 5.97 0.00 40.10 3.58
79 80 9.147732 TCTAAATACAGATGTATCAGGTCACAT 57.852 33.333 5.97 0.00 40.10 3.21
80 81 9.770097 CTAAATACAGATGTATCAGGTCACATT 57.230 33.333 5.97 0.00 40.10 2.71
82 83 9.466497 AAATACAGATGTATCAGGTCACATTTT 57.534 29.630 5.97 0.00 40.10 1.82
136 137 8.642908 AAAAGACAAAAATTTTAGGACGGAAG 57.357 30.769 3.34 0.00 0.00 3.46
137 138 7.576861 AAGACAAAAATTTTAGGACGGAAGA 57.423 32.000 3.34 0.00 0.00 2.87
138 139 7.576861 AGACAAAAATTTTAGGACGGAAGAA 57.423 32.000 3.34 0.00 0.00 2.52
139 140 8.002984 AGACAAAAATTTTAGGACGGAAGAAA 57.997 30.769 3.34 0.00 0.00 2.52
140 141 8.638873 AGACAAAAATTTTAGGACGGAAGAAAT 58.361 29.630 3.34 0.00 0.00 2.17
141 142 9.902196 GACAAAAATTTTAGGACGGAAGAAATA 57.098 29.630 3.34 0.00 0.00 1.40
142 143 9.687210 ACAAAAATTTTAGGACGGAAGAAATAC 57.313 29.630 3.34 0.00 0.00 1.89
143 144 9.685828 CAAAAATTTTAGGACGGAAGAAATACA 57.314 29.630 3.34 0.00 0.00 2.29
145 146 9.687210 AAAATTTTAGGACGGAAGAAATACAAC 57.313 29.630 0.37 0.00 0.00 3.32
146 147 7.989416 ATTTTAGGACGGAAGAAATACAACA 57.011 32.000 0.00 0.00 0.00 3.33
147 148 7.989416 TTTTAGGACGGAAGAAATACAACAT 57.011 32.000 0.00 0.00 0.00 2.71
148 149 9.675464 ATTTTAGGACGGAAGAAATACAACATA 57.325 29.630 0.00 0.00 0.00 2.29
149 150 9.675464 TTTTAGGACGGAAGAAATACAACATAT 57.325 29.630 0.00 0.00 0.00 1.78
151 152 9.754382 TTAGGACGGAAGAAATACAACATATAC 57.246 33.333 0.00 0.00 0.00 1.47
152 153 7.788026 AGGACGGAAGAAATACAACATATACA 58.212 34.615 0.00 0.00 0.00 2.29
153 154 8.429641 AGGACGGAAGAAATACAACATATACAT 58.570 33.333 0.00 0.00 0.00 2.29
154 155 8.709646 GGACGGAAGAAATACAACATATACATC 58.290 37.037 0.00 0.00 0.00 3.06
155 156 8.603242 ACGGAAGAAATACAACATATACATCC 57.397 34.615 0.00 0.00 0.00 3.51
156 157 7.660208 ACGGAAGAAATACAACATATACATCCC 59.340 37.037 0.00 0.00 0.00 3.85
157 158 7.659799 CGGAAGAAATACAACATATACATCCCA 59.340 37.037 0.00 0.00 0.00 4.37
158 159 9.003658 GGAAGAAATACAACATATACATCCCAG 57.996 37.037 0.00 0.00 0.00 4.45
159 160 7.986085 AGAAATACAACATATACATCCCAGC 57.014 36.000 0.00 0.00 0.00 4.85
160 161 7.749666 AGAAATACAACATATACATCCCAGCT 58.250 34.615 0.00 0.00 0.00 4.24
161 162 8.880244 AGAAATACAACATATACATCCCAGCTA 58.120 33.333 0.00 0.00 0.00 3.32
162 163 8.848474 AAATACAACATATACATCCCAGCTAC 57.152 34.615 0.00 0.00 0.00 3.58
163 164 7.798710 ATACAACATATACATCCCAGCTACT 57.201 36.000 0.00 0.00 0.00 2.57
164 165 6.500589 ACAACATATACATCCCAGCTACTT 57.499 37.500 0.00 0.00 0.00 2.24
165 166 6.525629 ACAACATATACATCCCAGCTACTTC 58.474 40.000 0.00 0.00 0.00 3.01
166 167 6.327626 ACAACATATACATCCCAGCTACTTCT 59.672 38.462 0.00 0.00 0.00 2.85
167 168 6.597832 ACATATACATCCCAGCTACTTCTC 57.402 41.667 0.00 0.00 0.00 2.87
168 169 5.482175 ACATATACATCCCAGCTACTTCTCC 59.518 44.000 0.00 0.00 0.00 3.71
169 170 1.501582 ACATCCCAGCTACTTCTCCC 58.498 55.000 0.00 0.00 0.00 4.30
170 171 0.761802 CATCCCAGCTACTTCTCCCC 59.238 60.000 0.00 0.00 0.00 4.81
171 172 0.644937 ATCCCAGCTACTTCTCCCCT 59.355 55.000 0.00 0.00 0.00 4.79
172 173 0.417841 TCCCAGCTACTTCTCCCCTT 59.582 55.000 0.00 0.00 0.00 3.95
173 174 0.833949 CCCAGCTACTTCTCCCCTTC 59.166 60.000 0.00 0.00 0.00 3.46
174 175 0.833949 CCAGCTACTTCTCCCCTTCC 59.166 60.000 0.00 0.00 0.00 3.46
175 176 1.573108 CAGCTACTTCTCCCCTTCCA 58.427 55.000 0.00 0.00 0.00 3.53
176 177 2.122768 CAGCTACTTCTCCCCTTCCAT 58.877 52.381 0.00 0.00 0.00 3.41
177 178 3.309296 CAGCTACTTCTCCCCTTCCATA 58.691 50.000 0.00 0.00 0.00 2.74
178 179 3.711704 CAGCTACTTCTCCCCTTCCATAA 59.288 47.826 0.00 0.00 0.00 1.90
179 180 4.349342 CAGCTACTTCTCCCCTTCCATAAT 59.651 45.833 0.00 0.00 0.00 1.28
180 181 5.544176 CAGCTACTTCTCCCCTTCCATAATA 59.456 44.000 0.00 0.00 0.00 0.98
181 182 6.214412 CAGCTACTTCTCCCCTTCCATAATAT 59.786 42.308 0.00 0.00 0.00 1.28
182 183 7.400339 CAGCTACTTCTCCCCTTCCATAATATA 59.600 40.741 0.00 0.00 0.00 0.86
183 184 7.962003 AGCTACTTCTCCCCTTCCATAATATAA 59.038 37.037 0.00 0.00 0.00 0.98
184 185 8.603304 GCTACTTCTCCCCTTCCATAATATAAA 58.397 37.037 0.00 0.00 0.00 1.40
187 188 9.015146 ACTTCTCCCCTTCCATAATATAAAAGT 57.985 33.333 0.00 0.00 0.00 2.66
242 243 9.774071 AAATTTATATTAATGGGATGGAGGGAG 57.226 33.333 0.00 0.00 0.00 4.30
243 244 7.905144 TTTATATTAATGGGATGGAGGGAGT 57.095 36.000 0.00 0.00 0.00 3.85
244 245 8.998957 TTTATATTAATGGGATGGAGGGAGTA 57.001 34.615 0.00 0.00 0.00 2.59
245 246 8.998957 TTATATTAATGGGATGGAGGGAGTAA 57.001 34.615 0.00 0.00 0.00 2.24
246 247 9.588432 TTATATTAATGGGATGGAGGGAGTAAT 57.412 33.333 0.00 0.00 0.00 1.89
248 249 9.764776 ATATTAATGGGATGGAGGGAGTAATAT 57.235 33.333 0.00 0.00 0.00 1.28
249 250 5.786121 AATGGGATGGAGGGAGTAATATG 57.214 43.478 0.00 0.00 0.00 1.78
250 251 2.912956 TGGGATGGAGGGAGTAATATGC 59.087 50.000 0.00 0.00 0.00 3.14
251 252 2.912956 GGGATGGAGGGAGTAATATGCA 59.087 50.000 0.00 0.00 0.00 3.96
252 253 3.054802 GGGATGGAGGGAGTAATATGCAG 60.055 52.174 0.00 0.00 0.00 4.41
253 254 3.584848 GGATGGAGGGAGTAATATGCAGT 59.415 47.826 0.00 0.00 0.00 4.40
254 255 4.042187 GGATGGAGGGAGTAATATGCAGTT 59.958 45.833 0.00 0.00 0.00 3.16
255 256 4.422073 TGGAGGGAGTAATATGCAGTTG 57.578 45.455 0.00 0.00 0.00 3.16
256 257 4.037222 TGGAGGGAGTAATATGCAGTTGA 58.963 43.478 0.00 0.00 0.00 3.18
257 258 4.473196 TGGAGGGAGTAATATGCAGTTGAA 59.527 41.667 0.00 0.00 0.00 2.69
258 259 5.059833 GGAGGGAGTAATATGCAGTTGAAG 58.940 45.833 0.00 0.00 0.00 3.02
259 260 5.163301 GGAGGGAGTAATATGCAGTTGAAGA 60.163 44.000 0.00 0.00 0.00 2.87
260 261 5.923204 AGGGAGTAATATGCAGTTGAAGAG 58.077 41.667 0.00 0.00 0.00 2.85
261 262 5.059833 GGGAGTAATATGCAGTTGAAGAGG 58.940 45.833 0.00 0.00 0.00 3.69
262 263 5.059833 GGAGTAATATGCAGTTGAAGAGGG 58.940 45.833 0.00 0.00 0.00 4.30
263 264 4.455606 AGTAATATGCAGTTGAAGAGGGC 58.544 43.478 0.00 0.00 0.00 5.19
264 265 1.959042 ATATGCAGTTGAAGAGGGCG 58.041 50.000 0.00 0.00 0.00 6.13
265 266 0.901827 TATGCAGTTGAAGAGGGCGA 59.098 50.000 0.00 0.00 0.00 5.54
281 282 1.011463 CGAGCTGATTGATGCGTGC 60.011 57.895 0.00 0.00 0.00 5.34
282 287 1.426816 CGAGCTGATTGATGCGTGCT 61.427 55.000 0.00 0.00 0.00 4.40
346 351 2.133641 GCTGCACCCACCACCTTTT 61.134 57.895 0.00 0.00 0.00 2.27
357 365 3.207778 CACCACCTTTTGTTTCTACCGA 58.792 45.455 0.00 0.00 0.00 4.69
358 366 3.818773 CACCACCTTTTGTTTCTACCGAT 59.181 43.478 0.00 0.00 0.00 4.18
402 410 6.608405 TGCCTGAATTAATGGACAGATCAATT 59.392 34.615 14.82 0.00 32.82 2.32
403 411 7.779326 TGCCTGAATTAATGGACAGATCAATTA 59.221 33.333 14.82 0.00 30.57 1.40
404 412 8.295288 GCCTGAATTAATGGACAGATCAATTAG 58.705 37.037 14.82 2.70 33.15 1.73
405 413 9.347240 CCTGAATTAATGGACAGATCAATTAGT 57.653 33.333 14.82 0.00 33.15 2.24
422 444 0.108585 AGTTCATGCCACTGTCGGTT 59.891 50.000 0.00 0.00 0.00 4.44
424 446 0.948623 TTCATGCCACTGTCGGTTCG 60.949 55.000 0.00 0.00 0.00 3.95
441 463 2.035530 TCGAATACACCATGCATGCA 57.964 45.000 25.04 25.04 0.00 3.96
446 468 2.323968 TACACCATGCATGCATACGT 57.676 45.000 31.73 27.04 34.91 3.57
450 472 1.939934 ACCATGCATGCATACGTGTAC 59.060 47.619 31.73 0.00 34.91 2.90
459 481 3.713288 TGCATACGTGTACCTGCTAATC 58.287 45.455 0.00 0.00 35.66 1.75
460 482 3.131400 TGCATACGTGTACCTGCTAATCA 59.869 43.478 0.00 0.00 35.66 2.57
461 483 3.736252 GCATACGTGTACCTGCTAATCAG 59.264 47.826 0.00 0.00 42.49 2.90
625 652 1.970917 GATTGGAACACGAGGCTGCG 61.971 60.000 0.00 0.00 39.29 5.18
679 706 0.759060 ACCACCTTTGTCCTTTGCCC 60.759 55.000 0.00 0.00 0.00 5.36
682 709 1.762370 CACCTTTGTCCTTTGCCCTTT 59.238 47.619 0.00 0.00 0.00 3.11
683 710 2.039418 ACCTTTGTCCTTTGCCCTTTC 58.961 47.619 0.00 0.00 0.00 2.62
684 711 2.319844 CCTTTGTCCTTTGCCCTTTCT 58.680 47.619 0.00 0.00 0.00 2.52
685 712 2.297315 CCTTTGTCCTTTGCCCTTTCTC 59.703 50.000 0.00 0.00 0.00 2.87
686 713 1.995376 TTGTCCTTTGCCCTTTCTCC 58.005 50.000 0.00 0.00 0.00 3.71
687 714 0.112412 TGTCCTTTGCCCTTTCTCCC 59.888 55.000 0.00 0.00 0.00 4.30
688 715 0.612174 GTCCTTTGCCCTTTCTCCCC 60.612 60.000 0.00 0.00 0.00 4.81
689 716 1.305297 CCTTTGCCCTTTCTCCCCC 60.305 63.158 0.00 0.00 0.00 5.40
690 717 1.464722 CTTTGCCCTTTCTCCCCCA 59.535 57.895 0.00 0.00 0.00 4.96
696 723 2.763902 CTTTCTCCCCCACCCCAC 59.236 66.667 0.00 0.00 0.00 4.61
768 809 1.280457 ACTCATCCCAGACACCTTCC 58.720 55.000 0.00 0.00 0.00 3.46
804 846 1.079127 CACCCATCCTCGTCACCAC 60.079 63.158 0.00 0.00 0.00 4.16
908 953 2.751436 GCCAGGCAGCCGATTGAA 60.751 61.111 6.55 0.00 0.00 2.69
910 955 0.819259 GCCAGGCAGCCGATTGAATA 60.819 55.000 6.55 0.00 0.00 1.75
911 956 0.947244 CCAGGCAGCCGATTGAATAC 59.053 55.000 5.55 0.00 0.00 1.89
912 957 0.583438 CAGGCAGCCGATTGAATACG 59.417 55.000 5.55 0.00 0.00 3.06
961 1013 1.977293 AATTCTCCCTCTCGCCAGCC 61.977 60.000 0.00 0.00 0.00 4.85
973 1025 3.958860 CCAGCCCCGATCCCCATC 61.959 72.222 0.00 0.00 0.00 3.51
1368 1435 0.983378 AGTACCTGGAGCACCCCATC 60.983 60.000 0.00 0.00 35.33 3.51
1401 1468 4.925861 GAGCTGCTCCCGCCCATC 62.926 72.222 18.80 0.00 34.43 3.51
1680 1750 1.381928 CCAAGCGGCTCGAGTACCTA 61.382 60.000 15.13 0.00 0.00 3.08
1749 1819 3.052620 CTCGTCGCACACCGGATCT 62.053 63.158 9.46 0.00 37.59 2.75
2441 2511 1.343142 GGGTTGGTTGTTTGGATGGAC 59.657 52.381 0.00 0.00 0.00 4.02
2451 2521 3.054434 TGTTTGGATGGACTGATGTAGGG 60.054 47.826 0.00 0.00 0.00 3.53
2461 2531 0.690192 TGATGTAGGGTGGTGGTGTG 59.310 55.000 0.00 0.00 0.00 3.82
2462 2532 0.676782 GATGTAGGGTGGTGGTGTGC 60.677 60.000 0.00 0.00 0.00 4.57
2463 2533 1.422977 ATGTAGGGTGGTGGTGTGCA 61.423 55.000 0.00 0.00 0.00 4.57
2591 2793 9.935241 ATCATTTGTGACATGATACTATACTCC 57.065 33.333 0.00 0.00 39.21 3.85
2592 2794 9.147732 TCATTTGTGACATGATACTATACTCCT 57.852 33.333 0.00 0.00 0.00 3.69
2595 2797 9.642343 TTTGTGACATGATACTATACTCCTACT 57.358 33.333 0.00 0.00 0.00 2.57
2655 2857 2.428187 CACGGTGGTGGTGGCTTA 59.572 61.111 0.00 0.00 40.58 3.09
2728 2935 2.202932 CGGCCGATTCAGTCCCAG 60.203 66.667 24.07 0.00 0.00 4.45
2737 2944 1.719063 TTCAGTCCCAGGCAAGCCTT 61.719 55.000 11.67 0.00 45.70 4.35
2739 2946 1.075659 AGTCCCAGGCAAGCCTTTC 59.924 57.895 11.67 2.48 45.70 2.62
2785 3019 2.298163 CCCTTTCTGCATTCACTTTGCT 59.702 45.455 0.00 0.00 40.77 3.91
2892 3131 8.370940 GGACATTGATAGGAATCTGACTTGATA 58.629 37.037 0.00 0.00 32.93 2.15
2893 3132 9.202273 GACATTGATAGGAATCTGACTTGATAC 57.798 37.037 0.00 0.00 32.93 2.24
2894 3133 8.708378 ACATTGATAGGAATCTGACTTGATACA 58.292 33.333 0.00 0.00 32.93 2.29
2895 3134 9.722184 CATTGATAGGAATCTGACTTGATACAT 57.278 33.333 0.00 0.00 32.93 2.29
2896 3135 9.941325 ATTGATAGGAATCTGACTTGATACATC 57.059 33.333 0.00 0.00 32.93 3.06
2897 3136 7.597386 TGATAGGAATCTGACTTGATACATCG 58.403 38.462 0.00 0.00 32.93 3.84
2915 3155 2.445427 TCGGGAACTGTCGGTTACATA 58.555 47.619 9.05 0.00 40.43 2.29
2985 3520 6.681777 ACAAATGATGAGCCTAAACAAAGAC 58.318 36.000 0.00 0.00 0.00 3.01
2990 3525 2.819608 TGAGCCTAAACAAAGACATGCC 59.180 45.455 0.00 0.00 0.00 4.40
3011 3546 9.096160 CATGCCTATGATATAGAGATGTGAAAC 57.904 37.037 0.00 0.00 36.36 2.78
3014 3549 8.317679 GCCTATGATATAGAGATGTGAAACCTT 58.682 37.037 0.00 0.00 34.36 3.50
3027 3562 7.607991 AGATGTGAAACCTTTACGAATGAAGAT 59.392 33.333 0.00 0.00 34.36 2.40
3029 3564 6.934645 TGTGAAACCTTTACGAATGAAGATCT 59.065 34.615 0.00 0.00 34.36 2.75
3032 3567 5.677319 ACCTTTACGAATGAAGATCTGGA 57.323 39.130 0.00 0.00 0.00 3.86
3097 3632 8.783093 TGTACTTCATTTTCGATGAACTTGATT 58.217 29.630 0.00 0.00 34.66 2.57
3159 3694 9.807921 AAAGAGAAATACCAGATAAGAACCAAA 57.192 29.630 0.00 0.00 0.00 3.28
3224 3759 4.024809 CGATACGATCAAGCTACTCACTCA 60.025 45.833 0.00 0.00 0.00 3.41
3278 3813 0.108329 CAACCCGGTCTCGCAACTAT 60.108 55.000 0.00 0.00 34.56 2.12
3299 3834 3.605634 TCACCATGAGACCGGTAAAATG 58.394 45.455 7.34 11.46 32.98 2.32
3306 3841 3.822167 TGAGACCGGTAAAATGGAAAACC 59.178 43.478 7.34 0.00 0.00 3.27
3307 3842 4.077108 GAGACCGGTAAAATGGAAAACCT 58.923 43.478 7.34 0.00 0.00 3.50
3308 3843 5.221884 TGAGACCGGTAAAATGGAAAACCTA 60.222 40.000 7.34 0.00 0.00 3.08
3309 3844 5.823312 AGACCGGTAAAATGGAAAACCTAT 58.177 37.500 7.34 0.00 0.00 2.57
3310 3845 5.884232 AGACCGGTAAAATGGAAAACCTATC 59.116 40.000 7.34 0.00 0.00 2.08
3313 3848 6.152154 ACCGGTAAAATGGAAAACCTATCAAG 59.848 38.462 4.49 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.070580 AGGGAGTACTAGTATTTGCACATCC 59.929 44.000 5.75 4.07 0.00 3.51
1 2 6.163135 AGGGAGTACTAGTATTTGCACATC 57.837 41.667 5.75 0.00 0.00 3.06
2 3 5.070580 GGAGGGAGTACTAGTATTTGCACAT 59.929 44.000 5.75 0.00 0.00 3.21
3 4 4.404715 GGAGGGAGTACTAGTATTTGCACA 59.595 45.833 5.75 0.00 0.00 4.57
4 5 4.499357 CGGAGGGAGTACTAGTATTTGCAC 60.499 50.000 5.75 0.00 0.00 4.57
5 6 3.635373 CGGAGGGAGTACTAGTATTTGCA 59.365 47.826 5.75 0.00 0.00 4.08
6 7 3.635836 ACGGAGGGAGTACTAGTATTTGC 59.364 47.826 5.75 3.35 0.00 3.68
7 8 5.131784 AGACGGAGGGAGTACTAGTATTTG 58.868 45.833 5.75 0.00 0.00 2.32
8 9 5.104193 TGAGACGGAGGGAGTACTAGTATTT 60.104 44.000 5.75 0.00 0.00 1.40
9 10 4.411540 TGAGACGGAGGGAGTACTAGTATT 59.588 45.833 5.75 0.94 0.00 1.89
10 11 3.972638 TGAGACGGAGGGAGTACTAGTAT 59.027 47.826 5.75 0.00 0.00 2.12
11 12 3.378512 TGAGACGGAGGGAGTACTAGTA 58.621 50.000 0.00 0.00 0.00 1.82
12 13 2.194859 TGAGACGGAGGGAGTACTAGT 58.805 52.381 0.00 0.00 0.00 2.57
13 14 3.278668 TTGAGACGGAGGGAGTACTAG 57.721 52.381 0.00 0.00 0.00 2.57
14 15 3.726557 TTTGAGACGGAGGGAGTACTA 57.273 47.619 0.00 0.00 0.00 1.82
15 16 2.599408 TTTGAGACGGAGGGAGTACT 57.401 50.000 0.00 0.00 0.00 2.73
16 17 3.889520 ATTTTGAGACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
17 18 4.094476 AGAATTTTGAGACGGAGGGAGTA 58.906 43.478 0.00 0.00 0.00 2.59
18 19 2.907042 AGAATTTTGAGACGGAGGGAGT 59.093 45.455 0.00 0.00 0.00 3.85
19 20 3.618690 AGAATTTTGAGACGGAGGGAG 57.381 47.619 0.00 0.00 0.00 4.30
20 21 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
21 22 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
22 23 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
23 24 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
24 25 7.795482 TTTAAGACAAGAATTTTGAGACGGA 57.205 32.000 7.18 0.00 0.00 4.69
25 26 9.463443 AAATTTAAGACAAGAATTTTGAGACGG 57.537 29.630 0.00 0.00 31.00 4.79
49 50 9.817809 GACCTGATACATCTGTATTTAGACAAA 57.182 33.333 4.44 0.00 40.99 2.83
50 51 8.977412 TGACCTGATACATCTGTATTTAGACAA 58.023 33.333 4.44 0.00 40.99 3.18
51 52 8.414003 GTGACCTGATACATCTGTATTTAGACA 58.586 37.037 4.44 7.37 40.99 3.41
52 53 8.414003 TGTGACCTGATACATCTGTATTTAGAC 58.586 37.037 4.44 3.17 40.99 2.59
53 54 8.533569 TGTGACCTGATACATCTGTATTTAGA 57.466 34.615 4.44 0.00 40.99 2.10
54 55 9.770097 AATGTGACCTGATACATCTGTATTTAG 57.230 33.333 4.44 6.48 40.99 1.85
56 57 9.466497 AAAATGTGACCTGATACATCTGTATTT 57.534 29.630 4.44 0.00 40.99 1.40
110 111 9.738832 CTTCCGTCCTAAAATTTTTGTCTTTTA 57.261 29.630 9.06 0.00 0.00 1.52
111 112 8.471609 TCTTCCGTCCTAAAATTTTTGTCTTTT 58.528 29.630 9.06 0.00 0.00 2.27
112 113 8.002984 TCTTCCGTCCTAAAATTTTTGTCTTT 57.997 30.769 9.06 0.00 0.00 2.52
113 114 7.576861 TCTTCCGTCCTAAAATTTTTGTCTT 57.423 32.000 9.06 0.00 0.00 3.01
114 115 7.576861 TTCTTCCGTCCTAAAATTTTTGTCT 57.423 32.000 9.06 0.00 0.00 3.41
115 116 8.812147 ATTTCTTCCGTCCTAAAATTTTTGTC 57.188 30.769 9.06 2.40 0.00 3.18
116 117 9.687210 GTATTTCTTCCGTCCTAAAATTTTTGT 57.313 29.630 9.06 0.00 0.00 2.83
117 118 9.685828 TGTATTTCTTCCGTCCTAAAATTTTTG 57.314 29.630 9.06 7.07 0.00 2.44
119 120 9.687210 GTTGTATTTCTTCCGTCCTAAAATTTT 57.313 29.630 8.75 8.75 0.00 1.82
120 121 8.852135 TGTTGTATTTCTTCCGTCCTAAAATTT 58.148 29.630 0.00 0.00 0.00 1.82
121 122 8.398878 TGTTGTATTTCTTCCGTCCTAAAATT 57.601 30.769 0.00 0.00 0.00 1.82
122 123 7.989416 TGTTGTATTTCTTCCGTCCTAAAAT 57.011 32.000 0.00 0.00 0.00 1.82
123 124 7.989416 ATGTTGTATTTCTTCCGTCCTAAAA 57.011 32.000 0.00 0.00 0.00 1.52
125 126 9.754382 GTATATGTTGTATTTCTTCCGTCCTAA 57.246 33.333 0.00 0.00 0.00 2.69
126 127 8.916062 TGTATATGTTGTATTTCTTCCGTCCTA 58.084 33.333 0.00 0.00 0.00 2.94
127 128 7.788026 TGTATATGTTGTATTTCTTCCGTCCT 58.212 34.615 0.00 0.00 0.00 3.85
128 129 8.603242 ATGTATATGTTGTATTTCTTCCGTCC 57.397 34.615 0.00 0.00 0.00 4.79
129 130 8.709646 GGATGTATATGTTGTATTTCTTCCGTC 58.290 37.037 0.00 0.00 0.00 4.79
130 131 7.660208 GGGATGTATATGTTGTATTTCTTCCGT 59.340 37.037 0.00 0.00 0.00 4.69
131 132 7.659799 TGGGATGTATATGTTGTATTTCTTCCG 59.340 37.037 0.00 0.00 0.00 4.30
132 133 8.918202 TGGGATGTATATGTTGTATTTCTTCC 57.082 34.615 0.00 0.00 0.00 3.46
133 134 8.507249 GCTGGGATGTATATGTTGTATTTCTTC 58.493 37.037 0.00 0.00 0.00 2.87
134 135 8.220559 AGCTGGGATGTATATGTTGTATTTCTT 58.779 33.333 0.00 0.00 0.00 2.52
135 136 7.749666 AGCTGGGATGTATATGTTGTATTTCT 58.250 34.615 0.00 0.00 0.00 2.52
136 137 7.986085 AGCTGGGATGTATATGTTGTATTTC 57.014 36.000 0.00 0.00 0.00 2.17
137 138 8.660435 AGTAGCTGGGATGTATATGTTGTATTT 58.340 33.333 0.00 0.00 0.00 1.40
138 139 8.207350 AGTAGCTGGGATGTATATGTTGTATT 57.793 34.615 0.00 0.00 0.00 1.89
139 140 7.798710 AGTAGCTGGGATGTATATGTTGTAT 57.201 36.000 0.00 0.00 0.00 2.29
140 141 7.509318 AGAAGTAGCTGGGATGTATATGTTGTA 59.491 37.037 0.00 0.00 0.00 2.41
141 142 6.327626 AGAAGTAGCTGGGATGTATATGTTGT 59.672 38.462 0.00 0.00 0.00 3.32
142 143 6.763355 AGAAGTAGCTGGGATGTATATGTTG 58.237 40.000 0.00 0.00 0.00 3.33
143 144 6.014156 GGAGAAGTAGCTGGGATGTATATGTT 60.014 42.308 0.00 0.00 0.00 2.71
144 145 5.482175 GGAGAAGTAGCTGGGATGTATATGT 59.518 44.000 0.00 0.00 0.00 2.29
145 146 5.105146 GGGAGAAGTAGCTGGGATGTATATG 60.105 48.000 0.00 0.00 0.00 1.78
146 147 5.026790 GGGAGAAGTAGCTGGGATGTATAT 58.973 45.833 0.00 0.00 0.00 0.86
147 148 4.417437 GGGAGAAGTAGCTGGGATGTATA 58.583 47.826 0.00 0.00 0.00 1.47
148 149 3.243724 GGGAGAAGTAGCTGGGATGTAT 58.756 50.000 0.00 0.00 0.00 2.29
149 150 2.679082 GGGAGAAGTAGCTGGGATGTA 58.321 52.381 0.00 0.00 0.00 2.29
150 151 1.501582 GGGAGAAGTAGCTGGGATGT 58.498 55.000 0.00 0.00 0.00 3.06
151 152 0.761802 GGGGAGAAGTAGCTGGGATG 59.238 60.000 0.00 0.00 0.00 3.51
152 153 0.644937 AGGGGAGAAGTAGCTGGGAT 59.355 55.000 0.00 0.00 0.00 3.85
153 154 0.417841 AAGGGGAGAAGTAGCTGGGA 59.582 55.000 0.00 0.00 0.00 4.37
154 155 0.833949 GAAGGGGAGAAGTAGCTGGG 59.166 60.000 0.00 0.00 0.00 4.45
155 156 0.833949 GGAAGGGGAGAAGTAGCTGG 59.166 60.000 0.00 0.00 0.00 4.85
156 157 1.573108 TGGAAGGGGAGAAGTAGCTG 58.427 55.000 0.00 0.00 0.00 4.24
157 158 2.577772 ATGGAAGGGGAGAAGTAGCT 57.422 50.000 0.00 0.00 0.00 3.32
158 159 4.984146 ATTATGGAAGGGGAGAAGTAGC 57.016 45.455 0.00 0.00 0.00 3.58
161 162 9.015146 ACTTTTATATTATGGAAGGGGAGAAGT 57.985 33.333 6.09 0.00 0.00 3.01
216 217 9.774071 CTCCCTCCATCCCATTAATATAAATTT 57.226 33.333 0.00 0.00 0.00 1.82
217 218 8.915438 ACTCCCTCCATCCCATTAATATAAATT 58.085 33.333 0.00 0.00 0.00 1.82
218 219 8.482378 ACTCCCTCCATCCCATTAATATAAAT 57.518 34.615 0.00 0.00 0.00 1.40
219 220 7.905144 ACTCCCTCCATCCCATTAATATAAA 57.095 36.000 0.00 0.00 0.00 1.40
220 221 8.998957 TTACTCCCTCCATCCCATTAATATAA 57.001 34.615 0.00 0.00 0.00 0.98
222 223 9.764776 ATATTACTCCCTCCATCCCATTAATAT 57.235 33.333 0.00 0.00 0.00 1.28
223 224 9.003145 CATATTACTCCCTCCATCCCATTAATA 57.997 37.037 0.00 0.00 0.00 0.98
224 225 7.586181 GCATATTACTCCCTCCATCCCATTAAT 60.586 40.741 0.00 0.00 0.00 1.40
225 226 6.297010 GCATATTACTCCCTCCATCCCATTAA 60.297 42.308 0.00 0.00 0.00 1.40
226 227 5.191722 GCATATTACTCCCTCCATCCCATTA 59.808 44.000 0.00 0.00 0.00 1.90
227 228 4.018050 GCATATTACTCCCTCCATCCCATT 60.018 45.833 0.00 0.00 0.00 3.16
228 229 3.525199 GCATATTACTCCCTCCATCCCAT 59.475 47.826 0.00 0.00 0.00 4.00
229 230 2.912956 GCATATTACTCCCTCCATCCCA 59.087 50.000 0.00 0.00 0.00 4.37
230 231 2.912956 TGCATATTACTCCCTCCATCCC 59.087 50.000 0.00 0.00 0.00 3.85
231 232 3.584848 ACTGCATATTACTCCCTCCATCC 59.415 47.826 0.00 0.00 0.00 3.51
232 233 4.899352 ACTGCATATTACTCCCTCCATC 57.101 45.455 0.00 0.00 0.00 3.51
233 234 4.660303 TCAACTGCATATTACTCCCTCCAT 59.340 41.667 0.00 0.00 0.00 3.41
234 235 4.037222 TCAACTGCATATTACTCCCTCCA 58.963 43.478 0.00 0.00 0.00 3.86
235 236 4.689612 TCAACTGCATATTACTCCCTCC 57.310 45.455 0.00 0.00 0.00 4.30
236 237 5.918608 TCTTCAACTGCATATTACTCCCTC 58.081 41.667 0.00 0.00 0.00 4.30
237 238 5.163258 CCTCTTCAACTGCATATTACTCCCT 60.163 44.000 0.00 0.00 0.00 4.20
238 239 5.059833 CCTCTTCAACTGCATATTACTCCC 58.940 45.833 0.00 0.00 0.00 4.30
239 240 5.059833 CCCTCTTCAACTGCATATTACTCC 58.940 45.833 0.00 0.00 0.00 3.85
240 241 4.513318 GCCCTCTTCAACTGCATATTACTC 59.487 45.833 0.00 0.00 0.00 2.59
241 242 4.455606 GCCCTCTTCAACTGCATATTACT 58.544 43.478 0.00 0.00 0.00 2.24
242 243 3.248602 CGCCCTCTTCAACTGCATATTAC 59.751 47.826 0.00 0.00 0.00 1.89
243 244 3.133901 TCGCCCTCTTCAACTGCATATTA 59.866 43.478 0.00 0.00 0.00 0.98
244 245 2.092968 TCGCCCTCTTCAACTGCATATT 60.093 45.455 0.00 0.00 0.00 1.28
245 246 1.486310 TCGCCCTCTTCAACTGCATAT 59.514 47.619 0.00 0.00 0.00 1.78
246 247 0.901827 TCGCCCTCTTCAACTGCATA 59.098 50.000 0.00 0.00 0.00 3.14
247 248 0.392193 CTCGCCCTCTTCAACTGCAT 60.392 55.000 0.00 0.00 0.00 3.96
248 249 1.004560 CTCGCCCTCTTCAACTGCA 60.005 57.895 0.00 0.00 0.00 4.41
249 250 2.394563 GCTCGCCCTCTTCAACTGC 61.395 63.158 0.00 0.00 0.00 4.40
250 251 1.018226 CAGCTCGCCCTCTTCAACTG 61.018 60.000 0.00 0.00 0.00 3.16
251 252 1.188219 TCAGCTCGCCCTCTTCAACT 61.188 55.000 0.00 0.00 0.00 3.16
252 253 0.107945 ATCAGCTCGCCCTCTTCAAC 60.108 55.000 0.00 0.00 0.00 3.18
253 254 0.615331 AATCAGCTCGCCCTCTTCAA 59.385 50.000 0.00 0.00 0.00 2.69
254 255 0.107993 CAATCAGCTCGCCCTCTTCA 60.108 55.000 0.00 0.00 0.00 3.02
255 256 0.176680 TCAATCAGCTCGCCCTCTTC 59.823 55.000 0.00 0.00 0.00 2.87
256 257 0.835941 ATCAATCAGCTCGCCCTCTT 59.164 50.000 0.00 0.00 0.00 2.85
257 258 0.106335 CATCAATCAGCTCGCCCTCT 59.894 55.000 0.00 0.00 0.00 3.69
258 259 1.505477 GCATCAATCAGCTCGCCCTC 61.505 60.000 0.00 0.00 0.00 4.30
259 260 1.525535 GCATCAATCAGCTCGCCCT 60.526 57.895 0.00 0.00 0.00 5.19
260 261 2.890109 CGCATCAATCAGCTCGCCC 61.890 63.158 0.00 0.00 0.00 6.13
261 262 2.176273 ACGCATCAATCAGCTCGCC 61.176 57.895 0.00 0.00 0.00 5.54
262 263 1.011463 CACGCATCAATCAGCTCGC 60.011 57.895 0.00 0.00 0.00 5.03
263 264 1.011463 GCACGCATCAATCAGCTCG 60.011 57.895 0.00 0.00 0.00 5.03
264 265 0.027716 CAGCACGCATCAATCAGCTC 59.972 55.000 0.00 0.00 0.00 4.09
265 266 1.374343 CCAGCACGCATCAATCAGCT 61.374 55.000 0.00 0.00 0.00 4.24
292 297 0.250124 CCACTTGCAGTCCCGTGTAA 60.250 55.000 0.00 0.00 0.00 2.41
333 338 2.543037 AGAAACAAAAGGTGGTGGGT 57.457 45.000 0.00 0.00 0.00 4.51
346 351 3.994392 GTCAGCAAAGATCGGTAGAAACA 59.006 43.478 0.00 0.00 0.00 2.83
357 365 1.912043 AGGGCTAGTGTCAGCAAAGAT 59.088 47.619 0.00 0.00 43.67 2.40
358 366 1.002430 CAGGGCTAGTGTCAGCAAAGA 59.998 52.381 0.00 0.00 43.67 2.52
402 410 0.973632 ACCGACAGTGGCATGAACTA 59.026 50.000 0.00 0.00 0.00 2.24
403 411 0.108585 AACCGACAGTGGCATGAACT 59.891 50.000 0.00 0.00 0.00 3.01
404 412 0.517316 GAACCGACAGTGGCATGAAC 59.483 55.000 0.00 0.00 0.00 3.18
405 413 0.948623 CGAACCGACAGTGGCATGAA 60.949 55.000 0.00 0.00 0.00 2.57
406 414 1.374125 CGAACCGACAGTGGCATGA 60.374 57.895 0.00 0.00 0.00 3.07
422 444 2.035530 TGCATGCATGGTGTATTCGA 57.964 45.000 27.34 0.00 0.00 3.71
424 446 3.250762 ACGTATGCATGCATGGTGTATTC 59.749 43.478 37.43 17.66 37.82 1.75
459 481 3.533606 AGTACAGGACTGCATTAGCTG 57.466 47.619 0.00 0.00 44.36 4.24
543 570 1.795170 AATTATCATGGCACGGGCGC 61.795 55.000 2.17 0.00 42.47 6.53
679 706 2.763902 GTGGGGTGGGGGAGAAAG 59.236 66.667 0.00 0.00 0.00 2.62
713 740 4.277476 TGACCGGGATGATATTTTTGCTT 58.723 39.130 6.32 0.00 0.00 3.91
714 741 3.897239 TGACCGGGATGATATTTTTGCT 58.103 40.909 6.32 0.00 0.00 3.91
768 809 2.158959 GTCGGACGAGTGAATGCCG 61.159 63.158 0.00 0.00 43.11 5.69
829 873 0.712222 GCGCGTCGTATTTATAGGGC 59.288 55.000 8.43 0.00 0.00 5.19
858 902 0.032540 GTTGCTTTGACTTGGCAGGG 59.967 55.000 0.44 0.00 37.28 4.45
961 1013 4.996434 GCTGCGATGGGGATCGGG 62.996 72.222 6.58 0.00 43.66 5.14
1368 1435 1.493950 GCTCGTCCTTGGCGATCATG 61.494 60.000 6.64 0.00 39.46 3.07
1572 1642 2.047179 GGCTCCACGGTCAAGTCC 60.047 66.667 0.00 0.00 0.00 3.85
1574 1644 4.681978 GCGGCTCCACGGTCAAGT 62.682 66.667 0.00 0.00 0.00 3.16
1680 1750 2.507944 GCGGAGATGTCCATGGCT 59.492 61.111 6.96 0.00 44.18 4.75
1749 1819 4.287781 TCGAACGCCGAGCACCAA 62.288 61.111 0.00 0.00 43.23 3.67
2359 2429 2.275318 CAAGTCAATTCCTCTCGCCTC 58.725 52.381 0.00 0.00 0.00 4.70
2441 2511 0.984230 ACACCACCACCCTACATCAG 59.016 55.000 0.00 0.00 0.00 2.90
2451 2521 1.675552 AAACTACTGCACACCACCAC 58.324 50.000 0.00 0.00 0.00 4.16
2461 2531 5.353400 AGCTTATTTCCGGTTAAACTACTGC 59.647 40.000 0.00 0.00 0.00 4.40
2462 2532 6.036844 GGAGCTTATTTCCGGTTAAACTACTG 59.963 42.308 0.00 0.00 0.00 2.74
2463 2533 6.111382 GGAGCTTATTTCCGGTTAAACTACT 58.889 40.000 0.00 0.00 0.00 2.57
2677 2879 0.865769 GACCGACACAAAACGCAGAT 59.134 50.000 0.00 0.00 0.00 2.90
2678 2880 0.460459 TGACCGACACAAAACGCAGA 60.460 50.000 0.00 0.00 0.00 4.26
2728 2935 3.752339 CGGGCAGAAAGGCTTGCC 61.752 66.667 18.40 18.40 45.99 4.52
2736 2943 0.457853 CGACGAGATTCGGGCAGAAA 60.458 55.000 3.74 0.00 45.59 2.52
2737 2944 1.138883 CGACGAGATTCGGGCAGAA 59.861 57.895 1.78 1.78 45.59 3.02
2739 2946 0.317103 CTACGACGAGATTCGGGCAG 60.317 60.000 0.00 0.00 45.59 4.85
2785 3019 0.940833 TTTTCTTGTCGACGCATGCA 59.059 45.000 19.57 0.00 0.00 3.96
2892 3131 1.067354 GTAACCGACAGTTCCCGATGT 60.067 52.381 0.00 0.00 40.05 3.06
2893 3132 1.067425 TGTAACCGACAGTTCCCGATG 60.067 52.381 0.00 0.00 40.05 3.84
2894 3133 1.259609 TGTAACCGACAGTTCCCGAT 58.740 50.000 0.00 0.00 40.05 4.18
2895 3134 1.259609 ATGTAACCGACAGTTCCCGA 58.740 50.000 0.00 0.00 42.79 5.14
2896 3135 2.945447 TATGTAACCGACAGTTCCCG 57.055 50.000 0.00 0.00 42.79 5.14
2897 3136 5.945466 TTTTTATGTAACCGACAGTTCCC 57.055 39.130 0.00 0.00 42.79 3.97
2985 3520 9.096160 GTTTCACATCTCTATATCATAGGCATG 57.904 37.037 0.00 0.00 0.00 4.06
3011 3546 7.559590 AATTCCAGATCTTCATTCGTAAAGG 57.440 36.000 0.00 0.00 0.00 3.11
3014 3549 9.314321 GAGTTAATTCCAGATCTTCATTCGTAA 57.686 33.333 0.00 0.00 0.00 3.18
3060 3595 8.551205 TCGAAAATGAAGTACATATGCATCTTC 58.449 33.333 19.32 19.32 38.38 2.87
3159 3694 2.927553 GCATCCTTGCGTCATCTTTT 57.072 45.000 0.00 0.00 39.49 2.27
3247 3782 5.667466 GAGACCGGGTTGTAAGATTGATTA 58.333 41.667 6.32 0.00 0.00 1.75
3278 3813 3.605634 CATTTTACCGGTCTCATGGTGA 58.394 45.455 12.40 0.00 39.30 4.02


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

AutoCloner maintained by Alex Coulton.