Multiple sequence alignment - TraesCS3A01G127000

Loading Multiple Alignment...

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 TraesCS3A01G127000 chr3A 100.000 2834 0 0 1 2834 102434978 102437811 0.000000e+00 5234
1 TraesCS3A01G127000 chr3A 99.727 1464 4 0 1371 2834 102491298 102492761 0.000000e+00 2682
2 TraesCS3A01G127000 chr3A 95.578 1176 28 10 809 1975 102388516 102389676 0.000000e+00 1862
3 TraesCS3A01G127000 chr3A 99.537 648 3 0 1 648 102489747 102490394 0.000000e+00 1181
4 TraesCS3A01G127000 chr3A 94.940 672 30 3 2167 2834 102389664 102390335 0.000000e+00 1050
5 TraesCS3A01G127000 chr3A 87.160 405 25 10 11 403 102522575 102522964 4.340000e-118 435
6 TraesCS3A01G127000 chr3A 86.064 409 30 13 7 403 102471736 102472129 5.650000e-112 414
7 TraesCS3A01G127000 chr3A 82.184 174 13 10 527 689 102388350 102388516 1.770000e-27 134
8 TraesCS3A01G127000 chr3B 94.475 905 28 8 864 1747 135711283 135712186 0.000000e+00 1375
9 TraesCS3A01G127000 chr3B 94.918 669 30 2 2167 2834 135770029 135770694 0.000000e+00 1044
10 TraesCS3A01G127000 chr3B 94.768 669 31 2 2167 2834 135815014 135815679 0.000000e+00 1038
11 TraesCS3A01G127000 chr3B 87.841 403 35 10 2 403 135701707 135702096 7.150000e-126 460
12 TraesCS3A01G127000 chr3B 92.045 264 12 6 405 659 135710997 135711260 2.080000e-96 363
13 TraesCS3A01G127000 chr3B 92.045 264 12 6 405 659 135768413 135768676 2.080000e-96 363
14 TraesCS3A01G127000 chr3B 92.045 264 12 6 405 659 135807937 135808200 2.080000e-96 363
15 TraesCS3A01G127000 chr3B 93.534 232 12 2 2167 2397 135712606 135712835 2.700000e-90 342
16 TraesCS3A01G127000 chr2D 91.971 959 61 6 931 1878 393204780 393205733 0.000000e+00 1330
17 TraesCS3A01G127000 chr2D 92.522 896 63 1 992 1887 393069617 393070508 0.000000e+00 1280
18 TraesCS3A01G127000 chr1D 91.219 968 67 6 931 1887 113994941 113993981 0.000000e+00 1301
19 TraesCS3A01G127000 chr1B 90.909 968 73 5 931 1887 174252478 174251515 0.000000e+00 1286
20 TraesCS3A01G127000 chr2B 92.522 896 60 2 992 1887 464878518 464879406 0.000000e+00 1277
21 TraesCS3A01G127000 chr2B 91.964 896 65 2 992 1887 464898108 464898996 0.000000e+00 1249
22 TraesCS3A01G127000 chr3D 91.494 917 33 12 863 1747 85826893 85827796 0.000000e+00 1219
23 TraesCS3A01G127000 chr3D 96.319 652 19 2 2167 2817 85828220 85828867 0.000000e+00 1066
24 TraesCS3A01G127000 chr3D 84.627 644 62 14 2193 2830 2398745 2398133 8.680000e-170 606
25 TraesCS3A01G127000 chr3D 90.544 349 17 3 64 403 85585631 85585972 5.570000e-122 448
26 TraesCS3A01G127000 chr3D 89.272 261 16 10 405 659 85826617 85826871 1.640000e-82 316
27 TraesCS3A01G127000 chr2A 89.955 896 60 12 992 1887 531151386 531152251 0.000000e+00 1129
28 TraesCS3A01G127000 chr2A 93.301 209 12 2 1976 2183 496256961 496257168 9.860000e-80 307
29 TraesCS3A01G127000 chr1A 86.687 661 70 9 2175 2830 247806283 247805636 0.000000e+00 717
30 TraesCS3A01G127000 chr5A 79.675 615 81 21 2213 2797 19985743 19985143 1.220000e-108 403
31 TraesCS3A01G127000 chr5A 96.410 195 7 0 1976 2170 223549937 223549743 3.520000e-84 322
32 TraesCS3A01G127000 chr5A 93.119 218 12 3 1976 2191 166733709 166733925 1.640000e-82 316
33 TraesCS3A01G127000 chr5D 79.479 614 78 23 2213 2797 29171350 29170756 2.650000e-105 392
34 TraesCS3A01G127000 chr7A 95.897 195 8 0 1976 2170 402003258 402003064 1.640000e-82 316
35 TraesCS3A01G127000 chr7A 90.909 231 15 5 1976 2203 523513612 523513385 3.550000e-79 305
36 TraesCS3A01G127000 chr4A 95.897 195 8 0 1976 2170 47842205 47842011 1.640000e-82 316
37 TraesCS3A01G127000 chr4A 84.848 330 28 13 482 797 255587222 255587543 2.120000e-81 313
38 TraesCS3A01G127000 chr6B 92.857 210 14 1 1963 2172 587545058 587544850 1.280000e-78 303
39 TraesCS3A01G127000 chr6A 92.417 211 15 1 1976 2185 327338901 327338691 1.650000e-77 300


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 TraesCS3A01G127000 chr3A 102434978 102437811 2833 False 5234.000000 5234 100.000000 1 2834 1 chr3A.!!$F1 2833
1 TraesCS3A01G127000 chr3A 102489747 102492761 3014 False 1931.500000 2682 99.632000 1 2834 2 chr3A.!!$F5 2833
2 TraesCS3A01G127000 chr3A 102388350 102390335 1985 False 1015.333333 1862 90.900667 527 2834 3 chr3A.!!$F4 2307
3 TraesCS3A01G127000 chr3B 135815014 135815679 665 False 1038.000000 1038 94.768000 2167 2834 1 chr3B.!!$F3 667
4 TraesCS3A01G127000 chr3B 135768413 135770694 2281 False 703.500000 1044 93.481500 405 2834 2 chr3B.!!$F5 2429
5 TraesCS3A01G127000 chr3B 135710997 135712835 1838 False 693.333333 1375 93.351333 405 2397 3 chr3B.!!$F4 1992
6 TraesCS3A01G127000 chr2D 393204780 393205733 953 False 1330.000000 1330 91.971000 931 1878 1 chr2D.!!$F2 947
7 TraesCS3A01G127000 chr2D 393069617 393070508 891 False 1280.000000 1280 92.522000 992 1887 1 chr2D.!!$F1 895
8 TraesCS3A01G127000 chr1D 113993981 113994941 960 True 1301.000000 1301 91.219000 931 1887 1 chr1D.!!$R1 956
9 TraesCS3A01G127000 chr1B 174251515 174252478 963 True 1286.000000 1286 90.909000 931 1887 1 chr1B.!!$R1 956
10 TraesCS3A01G127000 chr2B 464878518 464879406 888 False 1277.000000 1277 92.522000 992 1887 1 chr2B.!!$F1 895
11 TraesCS3A01G127000 chr2B 464898108 464898996 888 False 1249.000000 1249 91.964000 992 1887 1 chr2B.!!$F2 895
12 TraesCS3A01G127000 chr3D 85826617 85828867 2250 False 867.000000 1219 92.361667 405 2817 3 chr3D.!!$F2 2412
13 TraesCS3A01G127000 chr3D 2398133 2398745 612 True 606.000000 606 84.627000 2193 2830 1 chr3D.!!$R1 637
14 TraesCS3A01G127000 chr2A 531151386 531152251 865 False 1129.000000 1129 89.955000 992 1887 1 chr2A.!!$F2 895
15 TraesCS3A01G127000 chr1A 247805636 247806283 647 True 717.000000 717 86.687000 2175 2830 1 chr1A.!!$R1 655
16 TraesCS3A01G127000 chr5A 19985143 19985743 600 True 403.000000 403 79.675000 2213 2797 1 chr5A.!!$R1 584
17 TraesCS3A01G127000 chr5D 29170756 29171350 594 True 392.000000 392 79.479000 2213 2797 1 chr5D.!!$R1 584

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
728 751 0.031449 GAGGAGATCGCCGGAAGAAG 59.969 60.0 5.05 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 3570 0.035152 CAGCACATGGCCACCTTAGA 60.035 55.0 8.16 0.0 46.5 2.1 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
87 88 1.068748 TCGCTCGTCCTTGTTCTACAC 60.069 52.381 0.00 0.00 0.00 2.90
191 192 1.674221 CCTTCTCCCGAGAACAAGCAG 60.674 57.143 2.98 0.00 42.06 4.24
192 193 1.001406 CTTCTCCCGAGAACAAGCAGT 59.999 52.381 2.98 0.00 42.06 4.40
193 194 0.603569 TCTCCCGAGAACAAGCAGTC 59.396 55.000 0.00 0.00 33.91 3.51
194 195 0.605589 CTCCCGAGAACAAGCAGTCT 59.394 55.000 0.00 0.00 0.00 3.24
195 196 0.318441 TCCCGAGAACAAGCAGTCTG 59.682 55.000 0.00 0.00 0.00 3.51
196 197 0.034059 CCCGAGAACAAGCAGTCTGT 59.966 55.000 0.93 0.00 0.00 3.41
197 198 1.143305 CCGAGAACAAGCAGTCTGTG 58.857 55.000 0.93 0.00 0.00 3.66
198 199 1.539065 CCGAGAACAAGCAGTCTGTGT 60.539 52.381 0.93 0.00 0.00 3.72
199 200 1.524355 CGAGAACAAGCAGTCTGTGTG 59.476 52.381 0.93 2.76 0.00 3.82
200 201 1.869767 GAGAACAAGCAGTCTGTGTGG 59.130 52.381 0.93 0.00 0.00 4.17
201 202 1.486310 AGAACAAGCAGTCTGTGTGGA 59.514 47.619 0.93 0.00 0.00 4.02
202 203 1.599542 GAACAAGCAGTCTGTGTGGAC 59.400 52.381 0.93 0.00 36.56 4.02
203 204 0.179045 ACAAGCAGTCTGTGTGGACC 60.179 55.000 0.93 0.00 36.95 4.46
204 205 0.179048 CAAGCAGTCTGTGTGGACCA 60.179 55.000 0.93 0.00 36.95 4.02
205 206 0.107456 AAGCAGTCTGTGTGGACCAG 59.893 55.000 0.00 0.00 36.95 4.00
206 207 1.302033 GCAGTCTGTGTGGACCAGG 60.302 63.158 0.00 0.00 36.95 4.45
207 208 2.044806 GCAGTCTGTGTGGACCAGGT 62.045 60.000 0.00 0.00 36.95 4.00
208 209 0.034059 CAGTCTGTGTGGACCAGGTC 59.966 60.000 11.70 11.70 36.95 3.85
209 210 0.105453 AGTCTGTGTGGACCAGGTCT 60.105 55.000 19.57 0.00 36.95 3.85
210 211 0.759346 GTCTGTGTGGACCAGGTCTT 59.241 55.000 19.57 0.00 32.47 3.01
211 212 1.141053 GTCTGTGTGGACCAGGTCTTT 59.859 52.381 19.57 0.00 32.47 2.52
212 213 1.140852 TCTGTGTGGACCAGGTCTTTG 59.859 52.381 19.57 4.71 32.47 2.77
213 214 0.465460 TGTGTGGACCAGGTCTTTGC 60.465 55.000 19.57 8.39 32.47 3.68
214 215 1.150536 TGTGGACCAGGTCTTTGCC 59.849 57.895 19.57 3.29 32.47 4.52
215 216 1.603739 GTGGACCAGGTCTTTGCCC 60.604 63.158 19.57 2.51 32.47 5.36
216 217 2.359975 GGACCAGGTCTTTGCCCG 60.360 66.667 19.57 0.00 32.47 6.13
217 218 2.747686 GACCAGGTCTTTGCCCGA 59.252 61.111 12.94 0.00 0.00 5.14
218 219 1.376037 GACCAGGTCTTTGCCCGAG 60.376 63.158 12.94 0.00 0.00 4.63
219 220 2.747855 CCAGGTCTTTGCCCGAGC 60.748 66.667 0.00 0.00 40.48 5.03
230 231 4.379243 CCCGAGCAACTGAGCGGT 62.379 66.667 0.00 0.00 42.08 5.68
231 232 3.114616 CCGAGCAACTGAGCGGTG 61.115 66.667 0.00 0.00 38.99 4.94
232 233 3.114616 CGAGCAACTGAGCGGTGG 61.115 66.667 0.00 0.00 40.15 4.61
233 234 2.031163 GAGCAACTGAGCGGTGGT 59.969 61.111 0.00 0.00 40.15 4.16
234 235 2.281070 AGCAACTGAGCGGTGGTG 60.281 61.111 0.00 0.00 40.15 4.17
235 236 4.030452 GCAACTGAGCGGTGGTGC 62.030 66.667 0.00 0.00 0.00 5.01
236 237 3.716006 CAACTGAGCGGTGGTGCG 61.716 66.667 0.00 0.00 40.67 5.34
255 256 4.643387 GCGGGGCCACAAGTCACT 62.643 66.667 5.46 0.00 0.00 3.41
256 257 2.669569 CGGGGCCACAAGTCACTG 60.670 66.667 5.46 0.00 0.00 3.66
257 258 2.282462 GGGGCCACAAGTCACTGG 60.282 66.667 4.39 0.00 0.00 4.00
258 259 2.829384 GGGGCCACAAGTCACTGGA 61.829 63.158 4.39 0.00 0.00 3.86
259 260 1.380302 GGGCCACAAGTCACTGGAT 59.620 57.895 4.39 0.00 0.00 3.41
260 261 0.962356 GGGCCACAAGTCACTGGATG 60.962 60.000 4.39 0.00 0.00 3.51
261 262 0.962356 GGCCACAAGTCACTGGATGG 60.962 60.000 0.00 0.00 0.00 3.51
262 263 1.589716 GCCACAAGTCACTGGATGGC 61.590 60.000 10.63 10.63 45.26 4.40
263 264 1.300971 CCACAAGTCACTGGATGGCG 61.301 60.000 0.00 0.00 38.28 5.69
264 265 1.672356 ACAAGTCACTGGATGGCGC 60.672 57.895 0.00 0.00 38.28 6.53
265 266 1.376424 CAAGTCACTGGATGGCGCT 60.376 57.895 7.64 0.00 38.28 5.92
266 267 1.376424 AAGTCACTGGATGGCGCTG 60.376 57.895 7.64 0.00 38.28 5.18
267 268 2.809861 AAGTCACTGGATGGCGCTGG 62.810 60.000 7.64 0.00 38.28 4.85
268 269 3.321648 TCACTGGATGGCGCTGGT 61.322 61.111 7.64 0.00 0.00 4.00
269 270 2.360350 CACTGGATGGCGCTGGTT 60.360 61.111 7.64 0.00 0.00 3.67
270 271 2.045926 ACTGGATGGCGCTGGTTC 60.046 61.111 7.64 0.00 0.00 3.62
271 272 2.825836 CTGGATGGCGCTGGTTCC 60.826 66.667 7.64 9.33 0.00 3.62
272 273 4.776322 TGGATGGCGCTGGTTCCG 62.776 66.667 7.64 0.00 0.00 4.30
274 275 4.778143 GATGGCGCTGGTTCCGGT 62.778 66.667 7.64 0.00 0.00 5.28
296 297 2.264480 CGACACCGGGCTCATTCA 59.736 61.111 6.32 0.00 0.00 2.57
297 298 1.811266 CGACACCGGGCTCATTCAG 60.811 63.158 6.32 0.00 0.00 3.02
305 306 3.595819 GCTCATTCAGCCCACCAC 58.404 61.111 0.00 0.00 43.17 4.16
306 307 2.401766 GCTCATTCAGCCCACCACG 61.402 63.158 0.00 0.00 43.17 4.94
307 308 2.359850 TCATTCAGCCCACCACGC 60.360 61.111 0.00 0.00 0.00 5.34
308 309 3.443045 CATTCAGCCCACCACGCC 61.443 66.667 0.00 0.00 0.00 5.68
316 317 4.082523 CCACCACGCCGTCTCCAT 62.083 66.667 0.00 0.00 0.00 3.41
317 318 2.509336 CACCACGCCGTCTCCATC 60.509 66.667 0.00 0.00 0.00 3.51
318 319 2.994995 ACCACGCCGTCTCCATCA 60.995 61.111 0.00 0.00 0.00 3.07
319 320 2.359169 ACCACGCCGTCTCCATCAT 61.359 57.895 0.00 0.00 0.00 2.45
320 321 1.592669 CCACGCCGTCTCCATCATC 60.593 63.158 0.00 0.00 0.00 2.92
321 322 1.946156 CACGCCGTCTCCATCATCG 60.946 63.158 0.00 0.00 0.00 3.84
322 323 3.032609 CGCCGTCTCCATCATCGC 61.033 66.667 0.00 0.00 0.00 4.58
323 324 2.663188 GCCGTCTCCATCATCGCC 60.663 66.667 0.00 0.00 0.00 5.54
324 325 2.814604 CCGTCTCCATCATCGCCA 59.185 61.111 0.00 0.00 0.00 5.69
325 326 1.143838 CCGTCTCCATCATCGCCAA 59.856 57.895 0.00 0.00 0.00 4.52
326 327 0.877649 CCGTCTCCATCATCGCCAAG 60.878 60.000 0.00 0.00 0.00 3.61
327 328 0.179100 CGTCTCCATCATCGCCAAGT 60.179 55.000 0.00 0.00 0.00 3.16
328 329 1.740380 CGTCTCCATCATCGCCAAGTT 60.740 52.381 0.00 0.00 0.00 2.66
329 330 2.481276 CGTCTCCATCATCGCCAAGTTA 60.481 50.000 0.00 0.00 0.00 2.24
330 331 3.531538 GTCTCCATCATCGCCAAGTTAA 58.468 45.455 0.00 0.00 0.00 2.01
331 332 3.309954 GTCTCCATCATCGCCAAGTTAAC 59.690 47.826 0.00 0.00 0.00 2.01
332 333 2.276201 TCCATCATCGCCAAGTTAACG 58.724 47.619 0.00 0.00 0.00 3.18
333 334 2.093921 TCCATCATCGCCAAGTTAACGA 60.094 45.455 0.00 2.31 40.53 3.85
334 335 2.285220 CCATCATCGCCAAGTTAACGAG 59.715 50.000 0.00 0.00 39.48 4.18
335 336 2.004583 TCATCGCCAAGTTAACGAGG 57.995 50.000 13.18 13.18 39.48 4.63
336 337 0.373716 CATCGCCAAGTTAACGAGGC 59.626 55.000 25.40 25.40 43.61 4.70
340 341 2.046283 GCCAAGTTAACGAGGCAAAC 57.954 50.000 28.35 8.50 46.26 2.93
341 342 1.335597 GCCAAGTTAACGAGGCAAACC 60.336 52.381 28.35 8.21 46.26 3.27
342 343 1.069500 CCAAGTTAACGAGGCAAACCG 60.069 52.381 6.46 0.00 42.76 4.44
343 344 1.868498 CAAGTTAACGAGGCAAACCGA 59.132 47.619 0.00 0.00 42.76 4.69
344 345 2.243602 AGTTAACGAGGCAAACCGAA 57.756 45.000 0.00 0.00 42.76 4.30
345 346 2.140717 AGTTAACGAGGCAAACCGAAG 58.859 47.619 0.00 0.00 42.76 3.79
346 347 0.869730 TTAACGAGGCAAACCGAAGC 59.130 50.000 0.00 0.00 42.76 3.86
347 348 1.286354 TAACGAGGCAAACCGAAGCG 61.286 55.000 0.00 0.00 42.76 4.68
364 365 2.987125 GGCAGGCCGAAACTAGGA 59.013 61.111 0.00 0.00 0.00 2.94
365 366 1.153349 GGCAGGCCGAAACTAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
366 367 1.815840 GCAGGCCGAAACTAGGAGC 60.816 63.158 0.00 0.00 0.00 4.70
367 368 1.153349 CAGGCCGAAACTAGGAGCC 60.153 63.158 0.00 0.00 44.20 4.70
368 369 2.189784 GGCCGAAACTAGGAGCCC 59.810 66.667 0.00 0.00 37.66 5.19
369 370 2.189784 GCCGAAACTAGGAGCCCC 59.810 66.667 0.00 0.00 0.00 5.80
370 371 2.908796 CCGAAACTAGGAGCCCCC 59.091 66.667 0.00 0.00 0.00 5.40
371 372 1.993391 CCGAAACTAGGAGCCCCCA 60.993 63.158 0.00 0.00 37.41 4.96
372 373 1.559065 CCGAAACTAGGAGCCCCCAA 61.559 60.000 0.00 0.00 37.41 4.12
373 374 0.326927 CGAAACTAGGAGCCCCCAAA 59.673 55.000 0.00 0.00 37.41 3.28
374 375 1.835494 GAAACTAGGAGCCCCCAAAC 58.165 55.000 0.00 0.00 37.41 2.93
375 376 0.408309 AAACTAGGAGCCCCCAAACC 59.592 55.000 0.00 0.00 37.41 3.27
376 377 0.477795 AACTAGGAGCCCCCAAACCT 60.478 55.000 0.00 0.00 37.41 3.50
377 378 1.208165 ACTAGGAGCCCCCAAACCTG 61.208 60.000 0.00 0.00 37.41 4.00
378 379 0.914417 CTAGGAGCCCCCAAACCTGA 60.914 60.000 0.00 0.00 37.41 3.86
379 380 0.476808 TAGGAGCCCCCAAACCTGAA 60.477 55.000 0.00 0.00 37.41 3.02
380 381 1.155155 GGAGCCCCCAAACCTGAAA 59.845 57.895 0.00 0.00 34.14 2.69
381 382 1.185618 GGAGCCCCCAAACCTGAAAC 61.186 60.000 0.00 0.00 34.14 2.78
382 383 1.152333 AGCCCCCAAACCTGAAACC 60.152 57.895 0.00 0.00 0.00 3.27
383 384 2.214216 GCCCCCAAACCTGAAACCC 61.214 63.158 0.00 0.00 0.00 4.11
384 385 1.535444 CCCCCAAACCTGAAACCCC 60.535 63.158 0.00 0.00 0.00 4.95
385 386 1.546738 CCCCAAACCTGAAACCCCT 59.453 57.895 0.00 0.00 0.00 4.79
386 387 0.541998 CCCCAAACCTGAAACCCCTC 60.542 60.000 0.00 0.00 0.00 4.30
387 388 0.541998 CCCAAACCTGAAACCCCTCC 60.542 60.000 0.00 0.00 0.00 4.30
388 389 0.541998 CCAAACCTGAAACCCCTCCC 60.542 60.000 0.00 0.00 0.00 4.30
389 390 0.541998 CAAACCTGAAACCCCTCCCC 60.542 60.000 0.00 0.00 0.00 4.81
390 391 1.002242 AAACCTGAAACCCCTCCCCA 61.002 55.000 0.00 0.00 0.00 4.96
391 392 1.726192 AACCTGAAACCCCTCCCCAC 61.726 60.000 0.00 0.00 0.00 4.61
392 393 2.763902 CTGAAACCCCTCCCCACC 59.236 66.667 0.00 0.00 0.00 4.61
393 394 3.253838 TGAAACCCCTCCCCACCG 61.254 66.667 0.00 0.00 0.00 4.94
394 395 4.735358 GAAACCCCTCCCCACCGC 62.735 72.222 0.00 0.00 0.00 5.68
477 478 0.833287 AGGGATGGAGATGGTTGACG 59.167 55.000 0.00 0.00 0.00 4.35
519 520 1.022735 GGATGAACAGCAGCAGATGG 58.977 55.000 0.00 0.00 34.87 3.51
520 521 0.381089 GATGAACAGCAGCAGATGGC 59.619 55.000 0.00 0.00 45.30 4.40
521 522 1.035932 ATGAACAGCAGCAGATGGCC 61.036 55.000 0.00 0.00 46.50 5.36
522 523 1.676635 GAACAGCAGCAGATGGCCA 60.677 57.895 8.56 8.56 46.50 5.36
523 524 1.654954 GAACAGCAGCAGATGGCCAG 61.655 60.000 13.05 0.00 46.50 4.85
524 525 2.829003 CAGCAGCAGATGGCCAGG 60.829 66.667 13.05 4.30 46.50 4.45
525 526 3.013327 AGCAGCAGATGGCCAGGA 61.013 61.111 13.05 0.00 46.50 3.86
526 527 2.044650 GCAGCAGATGGCCAGGAA 60.045 61.111 13.05 0.00 46.50 3.36
527 528 2.119655 GCAGCAGATGGCCAGGAAG 61.120 63.158 13.05 1.83 46.50 3.46
528 529 1.605992 CAGCAGATGGCCAGGAAGA 59.394 57.895 13.05 0.00 46.50 2.87
529 530 0.183014 CAGCAGATGGCCAGGAAGAT 59.817 55.000 13.05 0.00 46.50 2.40
530 531 0.183014 AGCAGATGGCCAGGAAGATG 59.817 55.000 13.05 4.44 46.50 2.90
531 532 0.182061 GCAGATGGCCAGGAAGATGA 59.818 55.000 13.05 0.00 36.11 2.92
564 574 4.409718 ACGTAGATCAGAGCAGAGACTA 57.590 45.455 0.00 0.00 0.00 2.59
568 578 5.177511 CGTAGATCAGAGCAGAGACTAGAAG 59.822 48.000 0.00 0.00 0.00 2.85
569 579 5.372343 AGATCAGAGCAGAGACTAGAAGA 57.628 43.478 0.00 0.00 0.00 2.87
570 580 5.754782 AGATCAGAGCAGAGACTAGAAGAA 58.245 41.667 0.00 0.00 0.00 2.52
571 581 5.590259 AGATCAGAGCAGAGACTAGAAGAAC 59.410 44.000 0.00 0.00 0.00 3.01
572 582 4.013728 TCAGAGCAGAGACTAGAAGAACC 58.986 47.826 0.00 0.00 0.00 3.62
576 599 5.305644 AGAGCAGAGACTAGAAGAACCAAAA 59.694 40.000 0.00 0.00 0.00 2.44
612 635 1.134936 GGCGGAGAAGAGAGGAAGAAC 60.135 57.143 0.00 0.00 0.00 3.01
616 639 1.478916 GAGAAGAGAGGAAGAACGGGG 59.521 57.143 0.00 0.00 0.00 5.73
668 691 1.135859 GCACGATCCAACAAGCAGAAG 60.136 52.381 0.00 0.00 0.00 2.85
674 697 3.423539 TCCAACAAGCAGAAGCAGTAT 57.576 42.857 0.00 0.00 45.49 2.12
684 707 3.870419 GCAGAAGCAGTATGAGAGAAAGG 59.130 47.826 0.00 0.00 39.69 3.11
688 711 4.751767 AGCAGTATGAGAGAAAGGGAAG 57.248 45.455 0.00 0.00 39.69 3.46
689 712 4.357325 AGCAGTATGAGAGAAAGGGAAGA 58.643 43.478 0.00 0.00 39.69 2.87
690 713 4.780021 AGCAGTATGAGAGAAAGGGAAGAA 59.220 41.667 0.00 0.00 39.69 2.52
691 714 5.104982 AGCAGTATGAGAGAAAGGGAAGAAG 60.105 44.000 0.00 0.00 39.69 2.85
692 715 5.105146 GCAGTATGAGAGAAAGGGAAGAAGA 60.105 44.000 0.00 0.00 39.69 2.87
693 716 6.575254 GCAGTATGAGAGAAAGGGAAGAAGAA 60.575 42.308 0.00 0.00 39.69 2.52
694 717 7.390027 CAGTATGAGAGAAAGGGAAGAAGAAA 58.610 38.462 0.00 0.00 39.69 2.52
695 718 7.880195 CAGTATGAGAGAAAGGGAAGAAGAAAA 59.120 37.037 0.00 0.00 39.69 2.29
696 719 7.880713 AGTATGAGAGAAAGGGAAGAAGAAAAC 59.119 37.037 0.00 0.00 0.00 2.43
697 720 6.001449 TGAGAGAAAGGGAAGAAGAAAACA 57.999 37.500 0.00 0.00 0.00 2.83
698 721 6.423182 TGAGAGAAAGGGAAGAAGAAAACAA 58.577 36.000 0.00 0.00 0.00 2.83
699 722 6.543831 TGAGAGAAAGGGAAGAAGAAAACAAG 59.456 38.462 0.00 0.00 0.00 3.16
700 723 5.830457 AGAGAAAGGGAAGAAGAAAACAAGG 59.170 40.000 0.00 0.00 0.00 3.61
701 724 4.895889 AGAAAGGGAAGAAGAAAACAAGGG 59.104 41.667 0.00 0.00 0.00 3.95
702 725 4.536295 AAGGGAAGAAGAAAACAAGGGA 57.464 40.909 0.00 0.00 0.00 4.20
703 726 3.833732 AGGGAAGAAGAAAACAAGGGAC 58.166 45.455 0.00 0.00 0.00 4.46
704 727 3.204382 AGGGAAGAAGAAAACAAGGGACA 59.796 43.478 0.00 0.00 0.00 4.02
705 728 3.570125 GGGAAGAAGAAAACAAGGGACAG 59.430 47.826 0.00 0.00 0.00 3.51
706 729 3.570125 GGAAGAAGAAAACAAGGGACAGG 59.430 47.826 0.00 0.00 0.00 4.00
707 730 3.229697 AGAAGAAAACAAGGGACAGGG 57.770 47.619 0.00 0.00 0.00 4.45
708 731 2.158460 AGAAGAAAACAAGGGACAGGGG 60.158 50.000 0.00 0.00 0.00 4.79
709 732 0.482887 AGAAAACAAGGGACAGGGGG 59.517 55.000 0.00 0.00 0.00 5.40
710 733 0.481128 GAAAACAAGGGACAGGGGGA 59.519 55.000 0.00 0.00 0.00 4.81
711 734 0.482887 AAAACAAGGGACAGGGGGAG 59.517 55.000 0.00 0.00 0.00 4.30
712 735 1.435346 AAACAAGGGACAGGGGGAGG 61.435 60.000 0.00 0.00 0.00 4.30
713 736 2.124996 CAAGGGACAGGGGGAGGA 59.875 66.667 0.00 0.00 0.00 3.71
714 737 1.997874 CAAGGGACAGGGGGAGGAG 60.998 68.421 0.00 0.00 0.00 3.69
715 738 2.184631 AAGGGACAGGGGGAGGAGA 61.185 63.158 0.00 0.00 0.00 3.71
716 739 1.541168 AAGGGACAGGGGGAGGAGAT 61.541 60.000 0.00 0.00 0.00 2.75
717 740 1.460497 GGGACAGGGGGAGGAGATC 60.460 68.421 0.00 0.00 0.00 2.75
718 741 1.834822 GGACAGGGGGAGGAGATCG 60.835 68.421 0.00 0.00 0.00 3.69
719 742 2.444895 ACAGGGGGAGGAGATCGC 60.445 66.667 0.00 0.00 40.10 4.58
724 747 2.838225 GGGAGGAGATCGCCGGAA 60.838 66.667 5.05 0.00 36.06 4.30
725 748 2.731374 GGAGGAGATCGCCGGAAG 59.269 66.667 5.05 0.00 0.00 3.46
726 749 1.828660 GGAGGAGATCGCCGGAAGA 60.829 63.158 5.05 3.48 0.00 2.87
727 750 1.392710 GGAGGAGATCGCCGGAAGAA 61.393 60.000 5.05 0.00 0.00 2.52
728 751 0.031449 GAGGAGATCGCCGGAAGAAG 59.969 60.000 5.05 0.00 0.00 2.85
729 752 1.068250 GGAGATCGCCGGAAGAAGG 59.932 63.158 5.05 0.00 0.00 3.46
730 753 1.068250 GAGATCGCCGGAAGAAGGG 59.932 63.158 5.05 0.00 0.00 3.95
731 754 1.381327 AGATCGCCGGAAGAAGGGA 60.381 57.895 5.05 0.00 0.00 4.20
732 755 1.068250 GATCGCCGGAAGAAGGGAG 59.932 63.158 5.05 0.00 0.00 4.30
733 756 1.381327 ATCGCCGGAAGAAGGGAGA 60.381 57.895 5.05 0.00 36.55 3.71
734 757 1.395826 ATCGCCGGAAGAAGGGAGAG 61.396 60.000 5.05 0.00 35.56 3.20
735 758 2.904131 GCCGGAAGAAGGGAGAGG 59.096 66.667 5.05 0.00 0.00 3.69
736 759 2.736826 GCCGGAAGAAGGGAGAGGG 61.737 68.421 5.05 0.00 0.00 4.30
737 760 1.001760 CCGGAAGAAGGGAGAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
738 761 1.045911 CCGGAAGAAGGGAGAGGGAG 61.046 65.000 0.00 0.00 0.00 4.30
739 762 0.033011 CGGAAGAAGGGAGAGGGAGA 60.033 60.000 0.00 0.00 0.00 3.71
740 763 1.788229 GGAAGAAGGGAGAGGGAGAG 58.212 60.000 0.00 0.00 0.00 3.20
741 764 1.691163 GGAAGAAGGGAGAGGGAGAGG 60.691 61.905 0.00 0.00 0.00 3.69
742 765 1.289530 GAAGAAGGGAGAGGGAGAGGA 59.710 57.143 0.00 0.00 0.00 3.71
743 766 0.634465 AGAAGGGAGAGGGAGAGGAC 59.366 60.000 0.00 0.00 0.00 3.85
744 767 0.753848 GAAGGGAGAGGGAGAGGACG 60.754 65.000 0.00 0.00 0.00 4.79
745 768 2.123640 GGGAGAGGGAGAGGACGG 60.124 72.222 0.00 0.00 0.00 4.79
746 769 2.835895 GGAGAGGGAGAGGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
747 770 2.043852 GAGAGGGAGAGGACGGCA 60.044 66.667 0.00 0.00 0.00 5.69
748 771 1.456705 GAGAGGGAGAGGACGGCAT 60.457 63.158 0.00 0.00 0.00 4.40
749 772 1.456705 AGAGGGAGAGGACGGCATC 60.457 63.158 0.00 0.00 0.00 3.91
750 773 1.758514 GAGGGAGAGGACGGCATCA 60.759 63.158 5.38 0.00 0.00 3.07
751 774 2.022240 GAGGGAGAGGACGGCATCAC 62.022 65.000 5.38 0.00 0.00 3.06
752 775 2.105128 GGAGAGGACGGCATCACG 59.895 66.667 5.38 0.00 40.31 4.35
753 776 2.583593 GAGAGGACGGCATCACGC 60.584 66.667 5.38 0.00 41.28 5.34
762 785 4.907946 GCATCACGCCAATCATCG 57.092 55.556 0.00 0.00 32.94 3.84
763 786 1.280746 GCATCACGCCAATCATCGG 59.719 57.895 0.00 0.00 32.94 4.18
764 787 1.159713 GCATCACGCCAATCATCGGA 61.160 55.000 0.00 0.00 32.94 4.55
765 788 0.583438 CATCACGCCAATCATCGGAC 59.417 55.000 0.00 0.00 0.00 4.79
766 789 0.532862 ATCACGCCAATCATCGGACC 60.533 55.000 0.00 0.00 0.00 4.46
767 790 1.153369 CACGCCAATCATCGGACCT 60.153 57.895 0.00 0.00 0.00 3.85
768 791 1.153369 ACGCCAATCATCGGACCTG 60.153 57.895 0.00 0.00 0.00 4.00
769 792 1.143838 CGCCAATCATCGGACCTGA 59.856 57.895 0.00 0.00 0.00 3.86
770 793 0.461870 CGCCAATCATCGGACCTGAA 60.462 55.000 0.00 0.00 0.00 3.02
771 794 1.303309 GCCAATCATCGGACCTGAAG 58.697 55.000 0.00 0.00 0.00 3.02
772 795 1.407437 GCCAATCATCGGACCTGAAGT 60.407 52.381 0.00 0.00 0.00 3.01
773 796 2.555199 CCAATCATCGGACCTGAAGTC 58.445 52.381 0.00 0.00 45.51 3.01
780 803 4.094684 GACCTGAAGTCATCGCCG 57.905 61.111 0.00 0.00 45.55 6.46
781 804 1.519455 GACCTGAAGTCATCGCCGG 60.519 63.158 0.00 0.00 45.55 6.13
782 805 1.945354 GACCTGAAGTCATCGCCGGA 61.945 60.000 5.05 0.00 45.55 5.14
783 806 1.218047 CCTGAAGTCATCGCCGGAA 59.782 57.895 5.05 0.00 0.00 4.30
784 807 0.807667 CCTGAAGTCATCGCCGGAAG 60.808 60.000 5.05 0.00 0.00 3.46
785 808 0.108615 CTGAAGTCATCGCCGGAAGT 60.109 55.000 5.05 0.00 0.00 3.01
786 809 0.108804 TGAAGTCATCGCCGGAAGTC 60.109 55.000 5.05 0.00 0.00 3.01
787 810 1.140407 GAAGTCATCGCCGGAAGTCG 61.140 60.000 5.05 0.00 38.88 4.18
788 811 3.255379 GTCATCGCCGGAAGTCGC 61.255 66.667 5.05 0.00 37.59 5.19
789 812 4.508128 TCATCGCCGGAAGTCGCC 62.508 66.667 5.05 0.00 37.59 5.54
790 813 4.812476 CATCGCCGGAAGTCGCCA 62.812 66.667 5.05 0.00 37.59 5.69
791 814 4.814294 ATCGCCGGAAGTCGCCAC 62.814 66.667 5.05 0.00 37.59 5.01
797 820 2.668550 GGAAGTCGCCACCGCTTT 60.669 61.111 0.00 0.00 33.31 3.51
798 821 2.677979 GGAAGTCGCCACCGCTTTC 61.678 63.158 0.00 0.00 33.31 2.62
799 822 3.011760 GAAGTCGCCACCGCTTTCG 62.012 63.158 0.00 0.00 33.31 3.46
803 826 4.520846 CGCCACCGCTTTCGCATC 62.521 66.667 0.00 0.00 35.30 3.91
804 827 4.520846 GCCACCGCTTTCGCATCG 62.521 66.667 0.00 0.00 35.30 3.84
806 829 3.864686 CACCGCTTTCGCATCGGG 61.865 66.667 4.89 0.00 46.78 5.14
826 849 1.375326 GGGCCTTCCTCGTTCTGTT 59.625 57.895 0.84 0.00 0.00 3.16
827 850 0.673956 GGGCCTTCCTCGTTCTGTTC 60.674 60.000 0.84 0.00 0.00 3.18
828 851 0.321996 GGCCTTCCTCGTTCTGTTCT 59.678 55.000 0.00 0.00 0.00 3.01
829 852 1.433534 GCCTTCCTCGTTCTGTTCTG 58.566 55.000 0.00 0.00 0.00 3.02
830 853 1.270358 GCCTTCCTCGTTCTGTTCTGT 60.270 52.381 0.00 0.00 0.00 3.41
831 854 2.678324 CCTTCCTCGTTCTGTTCTGTC 58.322 52.381 0.00 0.00 0.00 3.51
832 855 2.610727 CCTTCCTCGTTCTGTTCTGTCC 60.611 54.545 0.00 0.00 0.00 4.02
909 932 1.671054 CTCGCTCGAAGGGGCAAAA 60.671 57.895 0.00 0.00 0.00 2.44
1185 1244 2.585876 GGGCTTCTCCGACTTCTCT 58.414 57.895 0.00 0.00 34.94 3.10
1832 3567 2.824936 TCCTCGTACCCGTGTTCAATTA 59.175 45.455 0.00 0.00 35.01 1.40
1833 3568 3.257873 TCCTCGTACCCGTGTTCAATTAA 59.742 43.478 0.00 0.00 35.01 1.40
1834 3569 4.081531 TCCTCGTACCCGTGTTCAATTAAT 60.082 41.667 0.00 0.00 35.01 1.40
1835 3570 4.632688 CCTCGTACCCGTGTTCAATTAATT 59.367 41.667 0.00 0.00 35.01 1.40
2076 3817 4.250464 GGCCGATAAATCAACCGATATGA 58.750 43.478 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.916392 GAGGTGAGCGGGTGACACG 62.916 68.421 1.25 1.25 35.68 4.49
128 129 2.047179 GAAGGTGAGACGGGTGCC 60.047 66.667 0.00 0.00 0.00 5.01
191 192 0.759346 AAGACCTGGTCCACACAGAC 59.241 55.000 22.81 0.00 38.20 3.51
192 193 1.140852 CAAAGACCTGGTCCACACAGA 59.859 52.381 22.81 0.00 38.20 3.41
193 194 1.597742 CAAAGACCTGGTCCACACAG 58.402 55.000 22.81 4.31 32.18 3.66
194 195 0.465460 GCAAAGACCTGGTCCACACA 60.465 55.000 22.81 0.00 32.18 3.72
195 196 1.172812 GGCAAAGACCTGGTCCACAC 61.173 60.000 22.81 10.61 32.18 3.82
196 197 1.150536 GGCAAAGACCTGGTCCACA 59.849 57.895 22.81 0.00 32.18 4.17
197 198 1.603739 GGGCAAAGACCTGGTCCAC 60.604 63.158 22.81 9.92 32.18 4.02
198 199 2.843545 GGGCAAAGACCTGGTCCA 59.156 61.111 22.81 0.00 32.18 4.02
199 200 2.359975 CGGGCAAAGACCTGGTCC 60.360 66.667 22.81 8.08 32.18 4.46
200 201 1.376037 CTCGGGCAAAGACCTGGTC 60.376 63.158 19.20 19.20 36.66 4.02
201 202 2.750350 CTCGGGCAAAGACCTGGT 59.250 61.111 0.00 0.00 36.66 4.00
202 203 2.747855 GCTCGGGCAAAGACCTGG 60.748 66.667 0.00 0.00 36.66 4.45
203 204 2.032528 TGCTCGGGCAAAGACCTG 59.967 61.111 8.00 0.00 46.36 4.00
213 214 4.379243 ACCGCTCAGTTGCTCGGG 62.379 66.667 13.50 0.00 45.58 5.14
214 215 3.114616 CACCGCTCAGTTGCTCGG 61.115 66.667 9.29 9.29 46.61 4.63
215 216 3.114616 CCACCGCTCAGTTGCTCG 61.115 66.667 0.00 0.00 0.00 5.03
216 217 2.031163 ACCACCGCTCAGTTGCTC 59.969 61.111 0.00 0.00 0.00 4.26
217 218 2.281070 CACCACCGCTCAGTTGCT 60.281 61.111 0.00 0.00 0.00 3.91
218 219 4.030452 GCACCACCGCTCAGTTGC 62.030 66.667 0.00 0.00 0.00 4.17
219 220 3.716006 CGCACCACCGCTCAGTTG 61.716 66.667 0.00 0.00 0.00 3.16
238 239 4.643387 AGTGACTTGTGGCCCCGC 62.643 66.667 0.00 0.00 0.00 6.13
239 240 2.669569 CAGTGACTTGTGGCCCCG 60.670 66.667 0.00 0.00 0.00 5.73
240 241 2.142292 ATCCAGTGACTTGTGGCCCC 62.142 60.000 0.00 0.00 33.43 5.80
241 242 0.962356 CATCCAGTGACTTGTGGCCC 60.962 60.000 0.00 0.00 33.43 5.80
242 243 0.962356 CCATCCAGTGACTTGTGGCC 60.962 60.000 0.00 0.00 33.43 5.36
243 244 1.589716 GCCATCCAGTGACTTGTGGC 61.590 60.000 14.36 14.36 44.37 5.01
244 245 1.300971 CGCCATCCAGTGACTTGTGG 61.301 60.000 0.00 3.92 34.87 4.17
245 246 1.915614 GCGCCATCCAGTGACTTGTG 61.916 60.000 0.00 0.00 0.00 3.33
246 247 1.672356 GCGCCATCCAGTGACTTGT 60.672 57.895 0.00 0.00 0.00 3.16
247 248 1.376424 AGCGCCATCCAGTGACTTG 60.376 57.895 2.29 0.00 0.00 3.16
248 249 1.376424 CAGCGCCATCCAGTGACTT 60.376 57.895 2.29 0.00 0.00 3.01
249 250 2.267006 CAGCGCCATCCAGTGACT 59.733 61.111 2.29 0.00 0.00 3.41
250 251 2.821366 CCAGCGCCATCCAGTGAC 60.821 66.667 2.29 0.00 0.00 3.67
251 252 2.803155 GAACCAGCGCCATCCAGTGA 62.803 60.000 2.29 0.00 0.00 3.41
252 253 2.360350 AACCAGCGCCATCCAGTG 60.360 61.111 2.29 0.00 0.00 3.66
253 254 2.045926 GAACCAGCGCCATCCAGT 60.046 61.111 2.29 0.00 0.00 4.00
254 255 2.825836 GGAACCAGCGCCATCCAG 60.826 66.667 2.29 0.00 32.08 3.86
255 256 4.776322 CGGAACCAGCGCCATCCA 62.776 66.667 2.29 0.00 32.08 3.41
257 258 4.778143 ACCGGAACCAGCGCCATC 62.778 66.667 9.46 0.00 0.00 3.51
279 280 1.811266 CTGAATGAGCCCGGTGTCG 60.811 63.158 0.00 0.00 0.00 4.35
280 281 2.109126 GCTGAATGAGCCCGGTGTC 61.109 63.158 0.00 0.00 42.54 3.67
281 282 2.045926 GCTGAATGAGCCCGGTGT 60.046 61.111 0.00 0.00 42.54 4.16
289 290 2.401766 GCGTGGTGGGCTGAATGAG 61.402 63.158 0.00 0.00 0.00 2.90
290 291 2.359850 GCGTGGTGGGCTGAATGA 60.360 61.111 0.00 0.00 0.00 2.57
291 292 3.443045 GGCGTGGTGGGCTGAATG 61.443 66.667 0.00 0.00 0.00 2.67
299 300 4.082523 ATGGAGACGGCGTGGTGG 62.083 66.667 21.19 0.00 0.00 4.61
300 301 2.509336 GATGGAGACGGCGTGGTG 60.509 66.667 21.19 0.00 0.00 4.17
301 302 2.298158 GATGATGGAGACGGCGTGGT 62.298 60.000 21.19 3.59 0.00 4.16
302 303 1.592669 GATGATGGAGACGGCGTGG 60.593 63.158 21.19 0.00 0.00 4.94
303 304 1.946156 CGATGATGGAGACGGCGTG 60.946 63.158 21.19 0.00 0.00 5.34
304 305 2.413351 CGATGATGGAGACGGCGT 59.587 61.111 14.65 14.65 0.00 5.68
305 306 3.032609 GCGATGATGGAGACGGCG 61.033 66.667 4.80 4.80 0.00 6.46
306 307 2.663188 GGCGATGATGGAGACGGC 60.663 66.667 0.00 0.00 42.98 5.68
307 308 0.877649 CTTGGCGATGATGGAGACGG 60.878 60.000 0.00 0.00 0.00 4.79
308 309 0.179100 ACTTGGCGATGATGGAGACG 60.179 55.000 0.00 0.00 0.00 4.18
309 310 2.029838 AACTTGGCGATGATGGAGAC 57.970 50.000 0.00 0.00 0.00 3.36
310 311 3.531538 GTTAACTTGGCGATGATGGAGA 58.468 45.455 0.00 0.00 0.00 3.71
311 312 2.285220 CGTTAACTTGGCGATGATGGAG 59.715 50.000 3.71 0.00 0.00 3.86
312 313 2.093921 TCGTTAACTTGGCGATGATGGA 60.094 45.455 3.71 0.00 0.00 3.41
313 314 2.276201 TCGTTAACTTGGCGATGATGG 58.724 47.619 3.71 0.00 0.00 3.51
314 315 2.285220 CCTCGTTAACTTGGCGATGATG 59.715 50.000 3.71 0.00 34.04 3.07
315 316 2.550978 CCTCGTTAACTTGGCGATGAT 58.449 47.619 3.71 0.00 34.04 2.45
316 317 2.004583 CCTCGTTAACTTGGCGATGA 57.995 50.000 3.71 0.00 34.04 2.92
317 318 0.373716 GCCTCGTTAACTTGGCGATG 59.626 55.000 18.44 3.88 35.79 3.84
318 319 2.763651 GCCTCGTTAACTTGGCGAT 58.236 52.632 18.44 0.00 35.79 4.58
319 320 4.272100 GCCTCGTTAACTTGGCGA 57.728 55.556 18.44 4.37 35.79 5.54
321 322 1.335597 GGTTTGCCTCGTTAACTTGGC 60.336 52.381 23.39 23.39 45.10 4.52
322 323 1.069500 CGGTTTGCCTCGTTAACTTGG 60.069 52.381 3.71 6.70 0.00 3.61
323 324 1.868498 TCGGTTTGCCTCGTTAACTTG 59.132 47.619 3.71 0.00 0.00 3.16
324 325 2.243602 TCGGTTTGCCTCGTTAACTT 57.756 45.000 3.71 0.00 0.00 2.66
325 326 2.140717 CTTCGGTTTGCCTCGTTAACT 58.859 47.619 3.71 0.00 0.00 2.24
326 327 1.399343 GCTTCGGTTTGCCTCGTTAAC 60.399 52.381 0.00 0.00 0.00 2.01
327 328 0.869730 GCTTCGGTTTGCCTCGTTAA 59.130 50.000 0.00 0.00 0.00 2.01
328 329 1.286354 CGCTTCGGTTTGCCTCGTTA 61.286 55.000 0.00 0.00 0.00 3.18
329 330 2.604174 CGCTTCGGTTTGCCTCGTT 61.604 57.895 0.00 0.00 0.00 3.85
330 331 3.041940 CGCTTCGGTTTGCCTCGT 61.042 61.111 0.00 0.00 0.00 4.18
331 332 3.788766 CCGCTTCGGTTTGCCTCG 61.789 66.667 0.00 0.00 42.73 4.63
347 348 1.153349 CTCCTAGTTTCGGCCTGCC 60.153 63.158 0.00 0.00 0.00 4.85
348 349 1.815840 GCTCCTAGTTTCGGCCTGC 60.816 63.158 0.00 0.00 0.00 4.85
349 350 1.153349 GGCTCCTAGTTTCGGCCTG 60.153 63.158 0.00 0.00 39.68 4.85
350 351 2.368011 GGGCTCCTAGTTTCGGCCT 61.368 63.158 0.00 0.00 42.14 5.19
351 352 2.189784 GGGCTCCTAGTTTCGGCC 59.810 66.667 0.00 0.00 41.80 6.13
352 353 2.189784 GGGGCTCCTAGTTTCGGC 59.810 66.667 0.00 0.00 0.00 5.54
353 354 1.559065 TTGGGGGCTCCTAGTTTCGG 61.559 60.000 4.32 0.00 36.20 4.30
354 355 0.326927 TTTGGGGGCTCCTAGTTTCG 59.673 55.000 4.32 0.00 36.20 3.46
355 356 1.616187 GGTTTGGGGGCTCCTAGTTTC 60.616 57.143 4.32 0.00 36.20 2.78
356 357 0.408309 GGTTTGGGGGCTCCTAGTTT 59.592 55.000 4.32 0.00 36.20 2.66
357 358 0.477795 AGGTTTGGGGGCTCCTAGTT 60.478 55.000 4.32 0.00 36.20 2.24
358 359 1.163555 AGGTTTGGGGGCTCCTAGT 59.836 57.895 4.32 0.00 36.20 2.57
359 360 0.914417 TCAGGTTTGGGGGCTCCTAG 60.914 60.000 4.32 0.00 36.20 3.02
360 361 0.476808 TTCAGGTTTGGGGGCTCCTA 60.477 55.000 4.32 0.00 36.20 2.94
361 362 1.368268 TTTCAGGTTTGGGGGCTCCT 61.368 55.000 4.32 0.00 36.20 3.69
362 363 1.155155 TTTCAGGTTTGGGGGCTCC 59.845 57.895 0.00 0.00 0.00 4.70
363 364 1.185618 GGTTTCAGGTTTGGGGGCTC 61.186 60.000 0.00 0.00 0.00 4.70
364 365 1.152333 GGTTTCAGGTTTGGGGGCT 60.152 57.895 0.00 0.00 0.00 5.19
365 366 2.214216 GGGTTTCAGGTTTGGGGGC 61.214 63.158 0.00 0.00 0.00 5.80
366 367 1.535444 GGGGTTTCAGGTTTGGGGG 60.535 63.158 0.00 0.00 0.00 5.40
367 368 0.541998 GAGGGGTTTCAGGTTTGGGG 60.542 60.000 0.00 0.00 0.00 4.96
368 369 0.541998 GGAGGGGTTTCAGGTTTGGG 60.542 60.000 0.00 0.00 0.00 4.12
369 370 0.541998 GGGAGGGGTTTCAGGTTTGG 60.542 60.000 0.00 0.00 0.00 3.28
370 371 0.541998 GGGGAGGGGTTTCAGGTTTG 60.542 60.000 0.00 0.00 0.00 2.93
371 372 1.002242 TGGGGAGGGGTTTCAGGTTT 61.002 55.000 0.00 0.00 0.00 3.27
372 373 1.388217 TGGGGAGGGGTTTCAGGTT 60.388 57.895 0.00 0.00 0.00 3.50
373 374 2.160853 GTGGGGAGGGGTTTCAGGT 61.161 63.158 0.00 0.00 0.00 4.00
374 375 2.763902 GTGGGGAGGGGTTTCAGG 59.236 66.667 0.00 0.00 0.00 3.86
375 376 2.763902 GGTGGGGAGGGGTTTCAG 59.236 66.667 0.00 0.00 0.00 3.02
376 377 3.253838 CGGTGGGGAGGGGTTTCA 61.254 66.667 0.00 0.00 0.00 2.69
377 378 4.735358 GCGGTGGGGAGGGGTTTC 62.735 72.222 0.00 0.00 0.00 2.78
392 393 4.569023 TGATACTCCTGCGCCGCG 62.569 66.667 8.83 8.83 0.00 6.46
393 394 1.595382 ATTGATACTCCTGCGCCGC 60.595 57.895 4.18 0.00 0.00 6.53
394 395 0.249447 TCATTGATACTCCTGCGCCG 60.249 55.000 4.18 0.00 0.00 6.46
395 396 1.953559 TTCATTGATACTCCTGCGCC 58.046 50.000 4.18 0.00 0.00 6.53
396 397 2.289002 CCTTTCATTGATACTCCTGCGC 59.711 50.000 0.00 0.00 0.00 6.09
397 398 2.289002 GCCTTTCATTGATACTCCTGCG 59.711 50.000 0.00 0.00 0.00 5.18
398 399 3.549794 AGCCTTTCATTGATACTCCTGC 58.450 45.455 0.00 0.00 0.00 4.85
399 400 5.188434 TGAAGCCTTTCATTGATACTCCTG 58.812 41.667 0.00 0.00 38.37 3.86
400 401 5.435291 CTGAAGCCTTTCATTGATACTCCT 58.565 41.667 0.00 0.00 42.19 3.69
401 402 4.036144 GCTGAAGCCTTTCATTGATACTCC 59.964 45.833 0.00 0.00 42.19 3.85
402 403 4.260538 CGCTGAAGCCTTTCATTGATACTC 60.261 45.833 0.00 0.00 42.19 2.59
403 404 3.624861 CGCTGAAGCCTTTCATTGATACT 59.375 43.478 0.00 0.00 42.19 2.12
477 478 1.817099 CCGCTGCTGTTCCATCTCC 60.817 63.158 0.00 0.00 0.00 3.71
519 520 1.153005 CCTGGCTCATCTTCCTGGC 60.153 63.158 0.00 0.00 35.21 4.85
520 521 0.984961 TCCCTGGCTCATCTTCCTGG 60.985 60.000 0.00 0.00 40.10 4.45
521 522 0.469070 CTCCCTGGCTCATCTTCCTG 59.531 60.000 0.00 0.00 0.00 3.86
522 523 0.693767 CCTCCCTGGCTCATCTTCCT 60.694 60.000 0.00 0.00 0.00 3.36
523 524 0.985490 ACCTCCCTGGCTCATCTTCC 60.985 60.000 0.00 0.00 40.22 3.46
524 525 1.414550 GTACCTCCCTGGCTCATCTTC 59.585 57.143 0.00 0.00 40.22 2.87
525 526 1.501582 GTACCTCCCTGGCTCATCTT 58.498 55.000 0.00 0.00 40.22 2.40
526 527 0.757188 CGTACCTCCCTGGCTCATCT 60.757 60.000 0.00 0.00 40.22 2.90
527 528 1.043673 ACGTACCTCCCTGGCTCATC 61.044 60.000 0.00 0.00 40.22 2.92
528 529 0.260816 TACGTACCTCCCTGGCTCAT 59.739 55.000 0.00 0.00 40.22 2.90
529 530 0.395311 CTACGTACCTCCCTGGCTCA 60.395 60.000 0.00 0.00 40.22 4.26
530 531 0.106819 TCTACGTACCTCCCTGGCTC 60.107 60.000 0.00 0.00 40.22 4.70
531 532 0.556747 ATCTACGTACCTCCCTGGCT 59.443 55.000 0.00 0.00 40.22 4.75
564 574 3.960755 CCCCTGTTTCTTTTGGTTCTTCT 59.039 43.478 0.00 0.00 0.00 2.85
568 578 2.628178 CCTCCCCTGTTTCTTTTGGTTC 59.372 50.000 0.00 0.00 0.00 3.62
569 579 2.246327 TCCTCCCCTGTTTCTTTTGGTT 59.754 45.455 0.00 0.00 0.00 3.67
570 580 1.856920 TCCTCCCCTGTTTCTTTTGGT 59.143 47.619 0.00 0.00 0.00 3.67
571 581 2.519013 CTCCTCCCCTGTTTCTTTTGG 58.481 52.381 0.00 0.00 0.00 3.28
572 582 2.519013 CCTCCTCCCCTGTTTCTTTTG 58.481 52.381 0.00 0.00 0.00 2.44
576 599 1.925972 GCCCTCCTCCCCTGTTTCT 60.926 63.158 0.00 0.00 0.00 2.52
668 691 4.744795 TCTTCCCTTTCTCTCATACTGC 57.255 45.455 0.00 0.00 0.00 4.40
674 697 6.001449 TGTTTTCTTCTTCCCTTTCTCTCA 57.999 37.500 0.00 0.00 0.00 3.27
684 707 3.570125 CCTGTCCCTTGTTTTCTTCTTCC 59.430 47.826 0.00 0.00 0.00 3.46
688 711 2.239400 CCCCTGTCCCTTGTTTTCTTC 58.761 52.381 0.00 0.00 0.00 2.87
689 712 1.133167 CCCCCTGTCCCTTGTTTTCTT 60.133 52.381 0.00 0.00 0.00 2.52
690 713 0.482887 CCCCCTGTCCCTTGTTTTCT 59.517 55.000 0.00 0.00 0.00 2.52
691 714 0.481128 TCCCCCTGTCCCTTGTTTTC 59.519 55.000 0.00 0.00 0.00 2.29
692 715 0.482887 CTCCCCCTGTCCCTTGTTTT 59.517 55.000 0.00 0.00 0.00 2.43
693 716 1.435346 CCTCCCCCTGTCCCTTGTTT 61.435 60.000 0.00 0.00 0.00 2.83
694 717 1.852626 CCTCCCCCTGTCCCTTGTT 60.853 63.158 0.00 0.00 0.00 2.83
695 718 2.204151 CCTCCCCCTGTCCCTTGT 60.204 66.667 0.00 0.00 0.00 3.16
696 719 1.997874 CTCCTCCCCCTGTCCCTTG 60.998 68.421 0.00 0.00 0.00 3.61
697 720 1.541168 ATCTCCTCCCCCTGTCCCTT 61.541 60.000 0.00 0.00 0.00 3.95
698 721 1.949449 ATCTCCTCCCCCTGTCCCT 60.949 63.158 0.00 0.00 0.00 4.20
699 722 1.460497 GATCTCCTCCCCCTGTCCC 60.460 68.421 0.00 0.00 0.00 4.46
700 723 1.834822 CGATCTCCTCCCCCTGTCC 60.835 68.421 0.00 0.00 0.00 4.02
701 724 2.503382 GCGATCTCCTCCCCCTGTC 61.503 68.421 0.00 0.00 0.00 3.51
702 725 2.444895 GCGATCTCCTCCCCCTGT 60.445 66.667 0.00 0.00 0.00 4.00
703 726 3.237741 GGCGATCTCCTCCCCCTG 61.238 72.222 0.00 0.00 0.00 4.45
704 727 4.924187 CGGCGATCTCCTCCCCCT 62.924 72.222 0.00 0.00 0.00 4.79
706 729 4.916314 TCCGGCGATCTCCTCCCC 62.916 72.222 9.30 0.00 0.00 4.81
707 730 2.838225 TTCCGGCGATCTCCTCCC 60.838 66.667 9.30 0.00 0.00 4.30
708 731 1.392710 TTCTTCCGGCGATCTCCTCC 61.393 60.000 9.30 0.00 0.00 4.30
709 732 0.031449 CTTCTTCCGGCGATCTCCTC 59.969 60.000 9.30 0.00 0.00 3.71
710 733 1.395826 CCTTCTTCCGGCGATCTCCT 61.396 60.000 9.30 0.00 0.00 3.69
711 734 1.068250 CCTTCTTCCGGCGATCTCC 59.932 63.158 9.30 0.00 0.00 3.71
712 735 1.068250 CCCTTCTTCCGGCGATCTC 59.932 63.158 9.30 0.00 0.00 2.75
713 736 1.381327 TCCCTTCTTCCGGCGATCT 60.381 57.895 9.30 0.00 0.00 2.75
714 737 1.068250 CTCCCTTCTTCCGGCGATC 59.932 63.158 9.30 0.00 0.00 3.69
715 738 1.381327 TCTCCCTTCTTCCGGCGAT 60.381 57.895 9.30 0.00 0.00 4.58
716 739 2.036731 TCTCCCTTCTTCCGGCGA 59.963 61.111 9.30 0.00 0.00 5.54
717 740 2.496817 CTCTCCCTTCTTCCGGCG 59.503 66.667 0.00 0.00 0.00 6.46
718 741 2.736826 CCCTCTCCCTTCTTCCGGC 61.737 68.421 0.00 0.00 0.00 6.13
719 742 1.001760 TCCCTCTCCCTTCTTCCGG 59.998 63.158 0.00 0.00 0.00 5.14
720 743 0.033011 TCTCCCTCTCCCTTCTTCCG 60.033 60.000 0.00 0.00 0.00 4.30
721 744 1.691163 CCTCTCCCTCTCCCTTCTTCC 60.691 61.905 0.00 0.00 0.00 3.46
722 745 1.289530 TCCTCTCCCTCTCCCTTCTTC 59.710 57.143 0.00 0.00 0.00 2.87
723 746 1.007842 GTCCTCTCCCTCTCCCTTCTT 59.992 57.143 0.00 0.00 0.00 2.52
724 747 0.634465 GTCCTCTCCCTCTCCCTTCT 59.366 60.000 0.00 0.00 0.00 2.85
725 748 0.753848 CGTCCTCTCCCTCTCCCTTC 60.754 65.000 0.00 0.00 0.00 3.46
726 749 1.308326 CGTCCTCTCCCTCTCCCTT 59.692 63.158 0.00 0.00 0.00 3.95
727 750 2.695970 CCGTCCTCTCCCTCTCCCT 61.696 68.421 0.00 0.00 0.00 4.20
728 751 2.123640 CCGTCCTCTCCCTCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
729 752 2.835895 GCCGTCCTCTCCCTCTCC 60.836 72.222 0.00 0.00 0.00 3.71
730 753 1.456705 ATGCCGTCCTCTCCCTCTC 60.457 63.158 0.00 0.00 0.00 3.20
731 754 1.456705 GATGCCGTCCTCTCCCTCT 60.457 63.158 0.00 0.00 0.00 3.69
732 755 1.758514 TGATGCCGTCCTCTCCCTC 60.759 63.158 0.00 0.00 0.00 4.30
733 756 2.060980 GTGATGCCGTCCTCTCCCT 61.061 63.158 0.00 0.00 0.00 4.20
734 757 2.501610 GTGATGCCGTCCTCTCCC 59.498 66.667 0.00 0.00 0.00 4.30
735 758 2.105128 CGTGATGCCGTCCTCTCC 59.895 66.667 0.00 0.00 0.00 3.71
736 759 2.583593 GCGTGATGCCGTCCTCTC 60.584 66.667 0.00 0.00 37.76 3.20
745 768 1.159713 TCCGATGATTGGCGTGATGC 61.160 55.000 0.00 0.00 45.38 3.91
746 769 0.583438 GTCCGATGATTGGCGTGATG 59.417 55.000 0.00 0.00 0.00 3.07
747 770 0.532862 GGTCCGATGATTGGCGTGAT 60.533 55.000 0.00 0.00 0.00 3.06
748 771 1.153449 GGTCCGATGATTGGCGTGA 60.153 57.895 0.00 0.00 0.00 4.35
749 772 1.153369 AGGTCCGATGATTGGCGTG 60.153 57.895 0.00 0.00 0.00 5.34
750 773 1.153369 CAGGTCCGATGATTGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
751 774 0.461870 TTCAGGTCCGATGATTGGCG 60.462 55.000 0.00 0.00 0.00 5.69
752 775 1.303309 CTTCAGGTCCGATGATTGGC 58.697 55.000 0.00 0.00 0.00 4.52
753 776 2.093500 TGACTTCAGGTCCGATGATTGG 60.093 50.000 0.00 0.00 43.89 3.16
754 777 3.251479 TGACTTCAGGTCCGATGATTG 57.749 47.619 0.00 0.00 43.89 2.67
755 778 3.491619 CGATGACTTCAGGTCCGATGATT 60.492 47.826 0.00 0.00 43.89 2.57
756 779 2.035193 CGATGACTTCAGGTCCGATGAT 59.965 50.000 0.00 0.00 43.89 2.45
757 780 1.405463 CGATGACTTCAGGTCCGATGA 59.595 52.381 0.00 0.00 43.89 2.92
758 781 1.845266 CGATGACTTCAGGTCCGATG 58.155 55.000 0.00 0.00 43.89 3.84
759 782 0.103208 GCGATGACTTCAGGTCCGAT 59.897 55.000 0.00 0.00 43.89 4.18
760 783 1.511305 GCGATGACTTCAGGTCCGA 59.489 57.895 0.00 0.00 43.89 4.55
761 784 1.519455 GGCGATGACTTCAGGTCCG 60.519 63.158 0.00 0.00 43.89 4.79
762 785 1.519455 CGGCGATGACTTCAGGTCC 60.519 63.158 0.00 0.00 43.89 4.46
763 786 1.519455 CCGGCGATGACTTCAGGTC 60.519 63.158 9.30 0.00 44.70 3.85
764 787 1.541310 TTCCGGCGATGACTTCAGGT 61.541 55.000 9.30 0.00 0.00 4.00
765 788 0.807667 CTTCCGGCGATGACTTCAGG 60.808 60.000 9.30 0.00 0.00 3.86
766 789 0.108615 ACTTCCGGCGATGACTTCAG 60.109 55.000 9.30 0.00 0.00 3.02
767 790 0.108804 GACTTCCGGCGATGACTTCA 60.109 55.000 9.30 0.00 0.00 3.02
768 791 1.140407 CGACTTCCGGCGATGACTTC 61.140 60.000 9.30 0.00 33.91 3.01
769 792 1.153823 CGACTTCCGGCGATGACTT 60.154 57.895 9.30 0.00 33.91 3.01
770 793 2.490217 CGACTTCCGGCGATGACT 59.510 61.111 9.30 0.00 33.91 3.41
771 794 3.255379 GCGACTTCCGGCGATGAC 61.255 66.667 9.30 0.00 39.04 3.06
780 803 2.668550 AAAGCGGTGGCGACTTCC 60.669 61.111 0.00 0.00 46.35 3.46
781 804 2.861006 GAAAGCGGTGGCGACTTC 59.139 61.111 0.00 0.00 46.35 3.01
782 805 3.041940 CGAAAGCGGTGGCGACTT 61.042 61.111 0.00 0.00 46.35 3.01
806 829 4.083862 AGAACGAGGAAGGCCCGC 62.084 66.667 0.00 0.00 40.87 6.13
807 830 2.125512 CAGAACGAGGAAGGCCCG 60.126 66.667 0.00 0.00 40.87 6.13
831 854 7.442666 GCAATAGGATAGTTTTCCTCAACTAGG 59.557 40.741 0.00 0.00 42.71 3.02
832 855 7.442666 GGCAATAGGATAGTTTTCCTCAACTAG 59.557 40.741 0.00 0.00 42.71 2.57
895 918 0.250727 TCACCTTTTGCCCCTTCGAG 60.251 55.000 0.00 0.00 0.00 4.04
909 932 5.123344 GCGTCAAACTTATATTGGTTCACCT 59.877 40.000 0.00 0.00 36.82 4.00
1185 1244 1.816835 CCGGAGTAGCAGTACTTGACA 59.183 52.381 0.00 0.00 39.78 3.58
1832 3567 2.102578 GCACATGGCCACCTTAGAATT 58.897 47.619 8.16 0.00 36.11 2.17
1833 3568 1.285962 AGCACATGGCCACCTTAGAAT 59.714 47.619 8.16 0.00 46.50 2.40
1834 3569 0.698238 AGCACATGGCCACCTTAGAA 59.302 50.000 8.16 0.00 46.50 2.10
1835 3570 0.035152 CAGCACATGGCCACCTTAGA 60.035 55.000 8.16 0.00 46.50 2.10
2076 3817 2.268298 GCATATCGGCGGATTTATCGT 58.732 47.619 12.41 0.00 34.00 3.73
2580 4339 3.075882 ACATTTTTGGATGAGGGAGTGGA 59.924 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.