Multiple sequence alignment - TraesCS3A01G094800

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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 TraesCS3A01G094800 chr3A 100.000 4311 0 0 1 4311 60505018 60500708 0.000000e+00 7962
1 TraesCS3A01G094800 chr3A 90.909 198 17 1 319 515 60454238 60454041 9.190000e-67 265
2 TraesCS3A01G094800 chr3A 93.590 78 5 0 218 295 21358920 21358997 2.720000e-22 117
3 TraesCS3A01G094800 chr3D 92.983 2323 122 23 2019 4311 48355716 48353405 0.000000e+00 3349
4 TraesCS3A01G094800 chr3D 95.087 916 42 3 976 1889 48361316 48360402 0.000000e+00 1439
5 TraesCS3A01G094800 chr3D 90.411 438 26 5 511 934 48361760 48361325 2.910000e-156 562
6 TraesCS3A01G094800 chr3D 87.597 129 5 3 1 118 48364017 48363889 5.810000e-29 139
7 TraesCS3A01G094800 chr3B 93.333 1785 95 10 976 2738 76121574 76123356 0.000000e+00 2615
8 TraesCS3A01G094800 chr3B 92.669 1596 102 9 2724 4311 76124097 76125685 0.000000e+00 2285
9 TraesCS3A01G094800 chr3B 86.422 626 63 13 964 1570 39346262 39346884 0.000000e+00 665
10 TraesCS3A01G094800 chr3B 91.484 364 21 4 511 866 76121181 76121542 3.870000e-135 492
11 TraesCS3A01G094800 chr3B 84.897 437 57 7 2318 2754 39347637 39348064 2.380000e-117 433
12 TraesCS3A01G094800 chr3B 77.212 746 119 32 3584 4311 39356664 39357376 5.230000e-104 388
13 TraesCS3A01G094800 chr3B 88.000 225 10 9 1 214 76431205 76431423 2.570000e-62 250
14 TraesCS3A01G094800 chr3B 95.000 80 2 1 218 297 662917195 662917272 1.630000e-24 124
15 TraesCS3A01G094800 chr3B 92.647 68 5 0 305 372 76431432 76431499 9.870000e-17 99
16 TraesCS3A01G094800 chr6B 81.684 475 82 5 2404 2874 680165080 680164607 1.450000e-104 390
17 TraesCS3A01G094800 chr6B 85.976 164 23 0 991 1154 679766307 679766144 4.430000e-40 176
18 TraesCS3A01G094800 chr5B 82.000 250 43 2 2033 2281 625112940 625112692 1.210000e-50 211
19 TraesCS3A01G094800 chr5B 82.000 250 43 2 2033 2281 628692493 628692245 1.210000e-50 211
20 TraesCS3A01G094800 chr5B 79.920 249 44 4 2034 2281 629893697 629893454 1.230000e-40 178
21 TraesCS3A01G094800 chr5B 92.500 80 4 1 218 297 558062385 558062308 3.520000e-21 113
22 TraesCS3A01G094800 chr7A 80.297 269 46 7 2390 2655 715939522 715939786 3.400000e-46 196
23 TraesCS3A01G094800 chr7B 80.800 250 42 6 2409 2655 717175360 717175606 1.580000e-44 191
24 TraesCS3A01G094800 chr7B 80.800 250 42 6 2409 2655 717250013 717250259 1.580000e-44 191
25 TraesCS3A01G094800 chr7B 78.788 264 49 7 2397 2655 717337526 717337787 2.060000e-38 171
26 TraesCS3A01G094800 chr5D 80.435 230 34 9 1766 1990 24970919 24971142 9.590000e-37 165
27 TraesCS3A01G094800 chr6D 77.528 267 50 7 1243 1502 448690343 448690080 7.470000e-33 152
28 TraesCS3A01G094800 chr2B 95.000 80 3 1 215 294 580586434 580586512 1.630000e-24 124
29 TraesCS3A01G094800 chr2B 93.750 80 3 1 218 297 557174804 557174881 7.570000e-23 119
30 TraesCS3A01G094800 chr2A 93.750 80 5 0 218 297 341395607 341395686 2.110000e-23 121
31 TraesCS3A01G094800 chr7D 93.750 80 3 1 215 294 112833063 112833140 7.570000e-23 119
32 TraesCS3A01G094800 chr1B 93.750 80 3 1 218 297 114098566 114098643 7.570000e-23 119
33 TraesCS3A01G094800 chr1A 92.500 80 4 1 217 294 3384989 3385068 3.520000e-21 113
34 TraesCS3A01G094800 chr1D 86.813 91 9 3 1901 1990 20995320 20995232 9.870000e-17 99


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 TraesCS3A01G094800 chr3A 60500708 60505018 4310 True 7962.000000 7962 100.000000 1 4311 1 chr3A.!!$R2 4310
1 TraesCS3A01G094800 chr3D 48353405 48355716 2311 True 3349.000000 3349 92.983000 2019 4311 1 chr3D.!!$R1 2292
2 TraesCS3A01G094800 chr3D 48360402 48364017 3615 True 713.333333 1439 91.031667 1 1889 3 chr3D.!!$R2 1888
3 TraesCS3A01G094800 chr3B 76121181 76125685 4504 False 1797.333333 2615 92.495333 511 4311 3 chr3B.!!$F4 3800
4 TraesCS3A01G094800 chr3B 39346262 39348064 1802 False 549.000000 665 85.659500 964 2754 2 chr3B.!!$F3 1790
5 TraesCS3A01G094800 chr3B 39356664 39357376 712 False 388.000000 388 77.212000 3584 4311 1 chr3B.!!$F1 727

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
415 459 0.034896 GTCTCTTCGGCACTTTGGGA 59.965 55.0 0.00 0.0 0.00 4.37 F
435 479 0.179189 CGAAAAATGCCTCGCCACTC 60.179 55.0 0.00 0.0 0.00 3.51 F
497 541 0.252513 GCCACCCCTAAACCCCATTT 60.253 55.0 0.00 0.0 0.00 2.32 F
550 2355 0.601576 TAAGGCGCACGTTCATGTGT 60.602 50.0 10.83 0.0 41.94 3.72 F
870 2690 0.602905 ACTTTCGGGTGTACTGCTGC 60.603 55.0 0.00 0.0 0.00 5.25 F
2042 4091 0.899720 CCAGTAAACGCTAGGGACCA 59.100 55.0 14.59 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 4221 0.319641 GCGACAGGGTTTTCTCTCGT 60.320 55.000 0.00 0.0 0.00 4.18 R
2232 4295 1.219213 CACTCTACATCCCTCCCCTCT 59.781 57.143 0.00 0.0 0.00 3.69 R
2518 4659 4.436242 TTCAGGTCGAGATGAACAGTAC 57.564 45.455 7.89 0.0 36.45 2.73 R
2579 4720 7.284074 TCCTTGATAAACCAAAATCCGCTATA 58.716 34.615 0.00 0.0 0.00 1.31 R
2899 5796 0.742505 AGTGTTCGAAGGACGTGTCA 59.257 50.000 0.00 0.0 43.13 3.58 R
3371 6271 0.394938 TGCTCTCACCGGCTTTACAA 59.605 50.000 0.00 0.0 0.00 2.41 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
25 27 0.258774 ATTGGGATTTGGGACGGGAG 59.741 55.000 0.00 0.00 0.00 4.30
46 48 3.120385 TTCGCGGCTCACATGCTG 61.120 61.111 6.13 0.00 41.91 4.41
47 49 3.588057 TTCGCGGCTCACATGCTGA 62.588 57.895 6.13 0.00 41.56 4.26
58 60 0.179145 ACATGCTGACTACGTACCGC 60.179 55.000 0.00 0.00 0.00 5.68
61 63 0.109458 TGCTGACTACGTACCGCTTG 60.109 55.000 0.00 0.00 0.00 4.01
118 130 4.690748 CCGGACTAAATGTGTGGCATATAG 59.309 45.833 0.00 0.00 36.67 1.31
119 131 5.297547 CGGACTAAATGTGTGGCATATAGT 58.702 41.667 0.00 0.00 36.67 2.12
121 133 6.365247 CGGACTAAATGTGTGGCATATAGTAC 59.635 42.308 0.00 0.00 36.67 2.73
126 163 5.869649 ATGTGTGGCATATAGTACAGACA 57.130 39.130 0.00 0.00 40.61 3.41
133 170 5.838521 TGGCATATAGTACAGACATGAGGAA 59.161 40.000 0.00 0.00 0.00 3.36
140 177 5.571285 AGTACAGACATGAGGAACTAGACA 58.429 41.667 0.00 0.00 41.55 3.41
141 178 4.792521 ACAGACATGAGGAACTAGACAC 57.207 45.455 0.00 0.00 41.55 3.67
142 179 3.511934 ACAGACATGAGGAACTAGACACC 59.488 47.826 0.00 0.00 41.55 4.16
143 180 3.766591 CAGACATGAGGAACTAGACACCT 59.233 47.826 0.00 1.54 41.55 4.00
144 181 3.766591 AGACATGAGGAACTAGACACCTG 59.233 47.826 0.00 2.85 41.55 4.00
164 201 4.444876 CCTGACCGGAGATAATTCCATGTT 60.445 45.833 9.46 0.00 37.05 2.71
172 213 7.275560 CCGGAGATAATTCCATGTTTTTGTTTC 59.724 37.037 0.00 0.00 37.05 2.78
186 227 6.647067 TGTTTTTGTTTCGAAATGTTTCTGGT 59.353 30.769 14.69 0.00 35.07 4.00
198 239 3.030291 TGTTTCTGGTGCCACTGAAATT 58.970 40.909 15.41 0.00 39.42 1.82
209 250 2.624838 CCACTGAAATTTGACCAGCAGT 59.375 45.455 0.00 0.00 37.09 4.40
210 251 3.068590 CCACTGAAATTTGACCAGCAGTT 59.931 43.478 0.00 0.00 34.66 3.16
211 252 4.441913 CCACTGAAATTTGACCAGCAGTTT 60.442 41.667 0.00 0.00 34.66 2.66
212 253 4.741676 CACTGAAATTTGACCAGCAGTTTC 59.258 41.667 0.00 0.00 34.66 2.78
213 254 4.646492 ACTGAAATTTGACCAGCAGTTTCT 59.354 37.500 0.00 0.00 35.60 2.52
214 255 5.127682 ACTGAAATTTGACCAGCAGTTTCTT 59.872 36.000 0.00 0.00 35.60 2.52
216 257 6.042143 TGAAATTTGACCAGCAGTTTCTTTC 58.958 36.000 0.00 0.00 35.60 2.62
217 258 5.859205 AATTTGACCAGCAGTTTCTTTCT 57.141 34.783 0.00 0.00 0.00 2.52
218 259 6.959639 AATTTGACCAGCAGTTTCTTTCTA 57.040 33.333 0.00 0.00 0.00 2.10
219 260 5.751243 TTTGACCAGCAGTTTCTTTCTAC 57.249 39.130 0.00 0.00 0.00 2.59
220 261 4.689612 TGACCAGCAGTTTCTTTCTACT 57.310 40.909 0.00 0.00 0.00 2.57
221 262 4.632153 TGACCAGCAGTTTCTTTCTACTC 58.368 43.478 0.00 0.00 0.00 2.59
222 263 3.997681 GACCAGCAGTTTCTTTCTACTCC 59.002 47.826 0.00 0.00 0.00 3.85
223 264 3.244596 ACCAGCAGTTTCTTTCTACTCCC 60.245 47.826 0.00 0.00 0.00 4.30
224 265 3.008485 CCAGCAGTTTCTTTCTACTCCCT 59.992 47.826 0.00 0.00 0.00 4.20
226 267 3.262151 AGCAGTTTCTTTCTACTCCCTCC 59.738 47.826 0.00 0.00 0.00 4.30
227 268 3.851098 CAGTTTCTTTCTACTCCCTCCG 58.149 50.000 0.00 0.00 0.00 4.63
228 269 3.258622 CAGTTTCTTTCTACTCCCTCCGT 59.741 47.826 0.00 0.00 0.00 4.69
229 270 3.902467 AGTTTCTTTCTACTCCCTCCGTT 59.098 43.478 0.00 0.00 0.00 4.44
230 271 4.021280 AGTTTCTTTCTACTCCCTCCGTTC 60.021 45.833 0.00 0.00 0.00 3.95
234 275 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
236 277 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
238 279 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
239 280 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
241 282 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
242 283 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
243 284 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
244 285 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
246 287 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
247 288 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
250 291 4.196626 TCCAAATTACTCGTCGTGGAAT 57.803 40.909 0.00 0.00 32.31 3.01
251 292 4.571919 TCCAAATTACTCGTCGTGGAATT 58.428 39.130 10.90 10.90 32.31 2.17
252 293 4.998672 TCCAAATTACTCGTCGTGGAATTT 59.001 37.500 19.58 19.58 32.31 1.82
254 295 5.567534 CCAAATTACTCGTCGTGGAATTTTG 59.432 40.000 21.72 16.67 29.51 2.44
256 297 6.548441 AATTACTCGTCGTGGAATTTTGAA 57.452 33.333 10.90 0.00 0.00 2.69
257 298 3.872560 ACTCGTCGTGGAATTTTGAAC 57.127 42.857 0.00 0.00 0.00 3.18
259 300 4.624015 ACTCGTCGTGGAATTTTGAACTA 58.376 39.130 0.00 0.00 0.00 2.24
261 302 5.524646 ACTCGTCGTGGAATTTTGAACTAAA 59.475 36.000 0.00 0.00 0.00 1.85
262 303 6.037391 ACTCGTCGTGGAATTTTGAACTAAAA 59.963 34.615 0.00 0.00 42.10 1.52
263 304 6.193761 TCGTCGTGGAATTTTGAACTAAAAC 58.806 36.000 0.00 0.00 40.80 2.43
264 305 5.397240 CGTCGTGGAATTTTGAACTAAAACC 59.603 40.000 0.00 0.00 40.80 3.27
265 306 6.267070 GTCGTGGAATTTTGAACTAAAACCA 58.733 36.000 0.00 0.00 40.80 3.67
266 307 6.197655 GTCGTGGAATTTTGAACTAAAACCAC 59.802 38.462 19.08 19.08 44.24 4.16
268 309 6.267070 GTGGAATTTTGAACTAAAACCACGA 58.733 36.000 16.74 0.00 41.52 4.35
270 311 6.920758 TGGAATTTTGAACTAAAACCACGATG 59.079 34.615 0.00 0.00 40.80 3.84
271 312 7.142680 GGAATTTTGAACTAAAACCACGATGA 58.857 34.615 0.00 0.00 40.80 2.92
272 313 7.326063 GGAATTTTGAACTAAAACCACGATGAG 59.674 37.037 0.00 0.00 40.80 2.90
273 314 6.687081 TTTTGAACTAAAACCACGATGAGT 57.313 33.333 0.00 0.00 33.48 3.41
274 315 7.789273 TTTTGAACTAAAACCACGATGAGTA 57.211 32.000 0.00 0.00 33.48 2.59
275 316 7.789273 TTTGAACTAAAACCACGATGAGTAA 57.211 32.000 0.00 0.00 0.00 2.24
276 317 7.972832 TTGAACTAAAACCACGATGAGTAAT 57.027 32.000 0.00 0.00 0.00 1.89
277 318 7.972832 TGAACTAAAACCACGATGAGTAATT 57.027 32.000 0.00 0.00 0.00 1.40
278 319 8.385898 TGAACTAAAACCACGATGAGTAATTT 57.614 30.769 0.00 0.00 0.00 1.82
279 320 8.286800 TGAACTAAAACCACGATGAGTAATTTG 58.713 33.333 0.00 0.00 0.00 2.32
280 321 7.141100 ACTAAAACCACGATGAGTAATTTGG 57.859 36.000 0.00 0.00 0.00 3.28
281 322 6.938030 ACTAAAACCACGATGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
282 323 6.642707 AAAACCACGATGAGTAATTTGGAA 57.357 33.333 0.00 0.00 0.00 3.53
283 324 5.622770 AACCACGATGAGTAATTTGGAAC 57.377 39.130 0.00 0.00 0.00 3.62
284 325 4.647611 ACCACGATGAGTAATTTGGAACA 58.352 39.130 0.00 0.00 0.00 3.18
285 326 4.695455 ACCACGATGAGTAATTTGGAACAG 59.305 41.667 0.00 0.00 42.39 3.16
286 327 4.935205 CCACGATGAGTAATTTGGAACAGA 59.065 41.667 0.00 0.00 42.39 3.41
287 328 5.063944 CCACGATGAGTAATTTGGAACAGAG 59.936 44.000 0.00 0.00 42.39 3.35
288 329 5.869344 CACGATGAGTAATTTGGAACAGAGA 59.131 40.000 0.00 0.00 42.39 3.10
289 330 6.035435 CACGATGAGTAATTTGGAACAGAGAG 59.965 42.308 0.00 0.00 42.39 3.20
290 331 6.071334 ACGATGAGTAATTTGGAACAGAGAGA 60.071 38.462 0.00 0.00 42.39 3.10
291 332 6.475076 CGATGAGTAATTTGGAACAGAGAGAG 59.525 42.308 0.00 0.00 42.39 3.20
292 333 6.672266 TGAGTAATTTGGAACAGAGAGAGT 57.328 37.500 0.00 0.00 42.39 3.24
293 334 7.776618 TGAGTAATTTGGAACAGAGAGAGTA 57.223 36.000 0.00 0.00 42.39 2.59
294 335 7.603651 TGAGTAATTTGGAACAGAGAGAGTAC 58.396 38.462 0.00 0.00 42.39 2.73
295 336 6.622549 AGTAATTTGGAACAGAGAGAGTACG 58.377 40.000 0.00 0.00 42.39 3.67
296 337 5.470047 AATTTGGAACAGAGAGAGTACGT 57.530 39.130 0.00 0.00 42.39 3.57
297 338 4.500603 TTTGGAACAGAGAGAGTACGTC 57.499 45.455 0.00 0.00 42.39 4.34
298 339 2.074576 TGGAACAGAGAGAGTACGTCG 58.925 52.381 0.00 0.00 0.00 5.12
299 340 1.397692 GGAACAGAGAGAGTACGTCGG 59.602 57.143 0.00 0.00 0.00 4.79
300 341 2.075338 GAACAGAGAGAGTACGTCGGT 58.925 52.381 0.00 0.00 0.00 4.69
301 342 1.440708 ACAGAGAGAGTACGTCGGTG 58.559 55.000 0.00 0.00 0.00 4.94
302 343 0.727970 CAGAGAGAGTACGTCGGTGG 59.272 60.000 0.00 0.00 0.00 4.61
303 344 0.612229 AGAGAGAGTACGTCGGTGGA 59.388 55.000 0.00 0.00 0.00 4.02
304 345 1.008329 GAGAGAGTACGTCGGTGGAG 58.992 60.000 0.00 0.00 0.00 3.86
305 346 0.612229 AGAGAGTACGTCGGTGGAGA 59.388 55.000 0.00 0.00 0.00 3.71
306 347 0.726256 GAGAGTACGTCGGTGGAGAC 59.274 60.000 0.00 0.00 37.76 3.36
315 356 3.559238 GTCGGTGGAGACGTTAGTAAA 57.441 47.619 0.00 0.00 0.00 2.01
316 357 3.496155 GTCGGTGGAGACGTTAGTAAAG 58.504 50.000 0.00 0.00 0.00 1.85
317 358 2.489329 TCGGTGGAGACGTTAGTAAAGG 59.511 50.000 0.00 0.00 0.00 3.11
318 359 2.489329 CGGTGGAGACGTTAGTAAAGGA 59.511 50.000 0.00 0.00 0.00 3.36
319 360 3.427233 CGGTGGAGACGTTAGTAAAGGAG 60.427 52.174 0.00 0.00 0.00 3.69
320 361 3.119209 GGTGGAGACGTTAGTAAAGGAGG 60.119 52.174 0.00 0.00 0.00 4.30
321 362 3.760684 GTGGAGACGTTAGTAAAGGAGGA 59.239 47.826 0.00 0.00 0.00 3.71
322 363 4.015084 TGGAGACGTTAGTAAAGGAGGAG 58.985 47.826 0.00 0.00 0.00 3.69
323 364 4.263639 TGGAGACGTTAGTAAAGGAGGAGA 60.264 45.833 0.00 0.00 0.00 3.71
324 365 4.888823 GGAGACGTTAGTAAAGGAGGAGAT 59.111 45.833 0.00 0.00 0.00 2.75
325 366 5.008911 GGAGACGTTAGTAAAGGAGGAGATC 59.991 48.000 0.00 0.00 0.00 2.75
341 382 1.457831 ATCCCTAGACACCCGAGGC 60.458 63.158 0.00 0.00 36.46 4.70
364 405 1.510480 GGCTGCAGACTCCAACACAC 61.510 60.000 20.43 0.00 0.00 3.82
368 409 0.792640 GCAGACTCCAACACACGATG 59.207 55.000 0.00 0.00 0.00 3.84
372 415 3.185188 CAGACTCCAACACACGATGAAAG 59.815 47.826 0.00 0.00 0.00 2.62
375 418 2.131972 TCCAACACACGATGAAAGACG 58.868 47.619 0.00 0.00 0.00 4.18
415 459 0.034896 GTCTCTTCGGCACTTTGGGA 59.965 55.000 0.00 0.00 0.00 4.37
423 467 1.000717 CGGCACTTTGGGACGAAAAAT 60.001 47.619 0.00 0.00 0.00 1.82
430 474 1.136774 GGGACGAAAAATGCCTCGC 59.863 57.895 0.00 0.00 38.64 5.03
432 476 1.582610 GGACGAAAAATGCCTCGCCA 61.583 55.000 0.00 0.00 38.64 5.69
434 478 0.889186 ACGAAAAATGCCTCGCCACT 60.889 50.000 0.00 0.00 38.64 4.00
435 479 0.179189 CGAAAAATGCCTCGCCACTC 60.179 55.000 0.00 0.00 0.00 3.51
437 481 1.586154 AAAAATGCCTCGCCACTCGG 61.586 55.000 0.00 0.00 39.05 4.63
438 482 2.463589 AAAATGCCTCGCCACTCGGA 62.464 55.000 0.00 0.00 39.05 4.55
439 483 2.257409 AAATGCCTCGCCACTCGGAT 62.257 55.000 0.00 0.00 39.05 4.18
441 485 4.593864 GCCTCGCCACTCGGATCC 62.594 72.222 0.00 0.00 39.05 3.36
442 486 3.147595 CCTCGCCACTCGGATCCA 61.148 66.667 13.41 0.00 39.05 3.41
443 487 2.105128 CTCGCCACTCGGATCCAC 59.895 66.667 13.41 0.00 39.05 4.02
444 488 3.432051 CTCGCCACTCGGATCCACC 62.432 68.421 13.41 0.00 39.05 4.61
465 509 0.553333 CCCCCTTCCTCCTTCCATTC 59.447 60.000 0.00 0.00 0.00 2.67
472 516 3.680620 CTCCTTCCATTCGCCGCCA 62.681 63.158 0.00 0.00 0.00 5.69
488 532 2.598787 CCAGAACGGCCACCCCTAA 61.599 63.158 2.24 0.00 0.00 2.69
497 541 0.252513 GCCACCCCTAAACCCCATTT 60.253 55.000 0.00 0.00 0.00 2.32
508 552 1.379710 CCCCATTTGGTCGCCATCA 60.380 57.895 0.00 0.00 31.53 3.07
550 2355 0.601576 TAAGGCGCACGTTCATGTGT 60.602 50.000 10.83 0.00 41.94 3.72
594 2399 3.826157 CCAGCTCCCAAAAGTCAAATACA 59.174 43.478 0.00 0.00 0.00 2.29
622 2429 7.043458 GCACATGGATGTTTCGTTATTTATTGG 60.043 37.037 0.00 0.00 39.39 3.16
652 2464 2.465813 AGGGATCAGAGTCAGAACCTG 58.534 52.381 10.96 0.00 0.00 4.00
665 2477 2.097791 CAGAACCTGTCTACTAGGCGTC 59.902 54.545 0.00 0.00 38.96 5.19
675 2487 0.677842 ACTAGGCGTCGACCAAGTTT 59.322 50.000 10.58 0.00 0.00 2.66
687 2499 3.610242 CGACCAAGTTTCTTCTCATCTCG 59.390 47.826 0.00 0.00 0.00 4.04
704 2516 1.079127 CGACGCCCAAACTGGATCT 60.079 57.895 0.00 0.00 40.96 2.75
730 2542 3.181453 CCATTCTCATCAGTCAGCATCCT 60.181 47.826 0.00 0.00 0.00 3.24
823 2643 1.377333 GGCCCAGGTTAGTGTCAGC 60.377 63.158 0.00 0.00 0.00 4.26
826 2646 1.209504 GCCCAGGTTAGTGTCAGCATA 59.790 52.381 0.00 0.00 0.00 3.14
838 2658 0.880278 TCAGCATATTCTTCCGCGGC 60.880 55.000 23.51 4.97 0.00 6.53
851 2671 2.112198 CGCGGCATTGCTTCCCTAA 61.112 57.895 8.82 0.00 0.00 2.69
868 2688 2.028385 CCTAACTTTCGGGTGTACTGCT 60.028 50.000 0.00 0.00 0.00 4.24
869 2689 1.878953 AACTTTCGGGTGTACTGCTG 58.121 50.000 0.00 0.00 0.00 4.41
870 2690 0.602905 ACTTTCGGGTGTACTGCTGC 60.603 55.000 0.00 0.00 0.00 5.25
880 2700 2.863137 GTGTACTGCTGCAAGATCTAGC 59.137 50.000 8.75 8.75 34.07 3.42
902 2722 6.673154 GCCCTTCGCTTTTAAGACTATTTA 57.327 37.500 0.00 0.00 0.00 1.40
926 2746 4.637276 ACGATTTCACAATCAGGTGTACA 58.363 39.130 0.00 0.00 39.14 2.90
934 2754 8.492673 TTCACAATCAGGTGTACATAAAGATC 57.507 34.615 0.00 0.00 39.76 2.75
944 2764 8.043710 AGGTGTACATAAAGATCTCCTTTTCTG 58.956 37.037 0.00 0.00 42.13 3.02
958 2778 5.684704 TCCTTTTCTGCAGATTATAGTGGG 58.315 41.667 19.04 11.09 0.00 4.61
959 2779 5.428457 TCCTTTTCTGCAGATTATAGTGGGA 59.572 40.000 19.04 13.05 0.00 4.37
960 2780 6.069673 TCCTTTTCTGCAGATTATAGTGGGAA 60.070 38.462 19.04 1.26 0.00 3.97
961 2781 6.038714 CCTTTTCTGCAGATTATAGTGGGAAC 59.961 42.308 19.04 0.00 0.00 3.62
962 2782 5.957771 TTCTGCAGATTATAGTGGGAACT 57.042 39.130 19.04 0.00 0.00 3.01
1082 2904 4.677250 GCCTCTGCCATTTGAATTTCTGAG 60.677 45.833 0.00 0.00 0.00 3.35
1089 2911 5.589192 CCATTTGAATTTCTGAGAGCCATC 58.411 41.667 0.00 0.00 0.00 3.51
1170 2995 5.161943 AGGTATATACGGCCAATTCCTTC 57.838 43.478 2.24 0.00 0.00 3.46
1173 2998 2.348411 ATACGGCCAATTCCTTCCAG 57.652 50.000 2.24 0.00 0.00 3.86
1222 3055 3.072211 AGCCGTTAACTGTTTAGGAAGC 58.928 45.455 3.71 0.00 0.00 3.86
1236 3069 3.596310 AGGAAGCGAAGAGAGGTTTAC 57.404 47.619 0.00 0.00 0.00 2.01
1396 3230 2.749621 GCAGCTTATTGGTTACTGTGCT 59.250 45.455 0.00 0.00 0.00 4.40
1405 3239 2.357637 TGGTTACTGTGCTGAAACAAGC 59.642 45.455 0.00 0.00 43.82 4.01
1511 3349 4.851558 GCAACAAAAGCCTTCATTACTACG 59.148 41.667 0.00 0.00 0.00 3.51
1585 3423 5.638596 ACTCCTTTCGTTTGTGAAGTTTT 57.361 34.783 0.00 0.00 0.00 2.43
1733 3602 5.931441 ATAGCGCTAAATTTGGAGTCATC 57.069 39.130 22.98 0.00 0.00 2.92
1865 3734 1.523758 AGTGCTCGGGTTTTGATGTC 58.476 50.000 0.00 0.00 0.00 3.06
2042 4091 0.899720 CCAGTAAACGCTAGGGACCA 59.100 55.000 14.59 0.00 0.00 4.02
2059 4122 1.302383 CCACCGCAAACCGCATCTAA 61.302 55.000 0.00 0.00 42.60 2.10
2165 4228 4.373116 GGTTGCCGCCACGAGAGA 62.373 66.667 0.00 0.00 0.00 3.10
2183 4246 1.644786 GAAAACCCTGTCGCCATCGG 61.645 60.000 0.00 0.00 36.13 4.18
2447 4588 8.706322 ATTTAACAGATGGTACTTTTGACCTT 57.294 30.769 0.00 0.00 37.88 3.50
2518 4659 4.790766 GCATTACCTTCATGAGAAATGCCG 60.791 45.833 22.69 4.54 42.53 5.69
2579 4720 5.387113 TGGATGCTACTATGGTTCCAAAT 57.613 39.130 0.00 0.00 30.62 2.32
2684 4825 5.882557 AGTTTTGTCTCCCTGTTATAGCATG 59.117 40.000 0.00 0.00 0.00 4.06
2708 4849 4.101430 TCCTTTTCTTTCTTGCAATGCCTT 59.899 37.500 1.53 0.00 0.00 4.35
2711 4852 6.146673 CCTTTTCTTTCTTGCAATGCCTTAAG 59.853 38.462 1.53 0.00 0.00 1.85
2899 5796 1.272769 GACGGCAGTTTCCAGAGTACT 59.727 52.381 0.00 0.00 0.00 2.73
3161 6059 5.893512 TTACATTACATATTGTCGTCCGC 57.106 39.130 0.00 0.00 0.00 5.54
3165 6063 5.353123 ACATTACATATTGTCGTCCGCTTTT 59.647 36.000 0.00 0.00 0.00 2.27
3176 6074 3.810941 TCGTCCGCTTTTGTAACTCAAAT 59.189 39.130 0.00 0.00 44.15 2.32
3232 6130 3.034635 GAGGAATAGGCTGGAGAAGTCA 58.965 50.000 0.00 0.00 30.52 3.41
3285 6183 0.793861 GCGTGCGTTGAATTAGGACA 59.206 50.000 0.00 0.00 0.00 4.02
3389 6289 1.739067 ATTGTAAAGCCGGTGAGAGC 58.261 50.000 1.90 0.00 0.00 4.09
3391 6291 0.394938 TGTAAAGCCGGTGAGAGCAA 59.605 50.000 1.90 0.00 0.00 3.91
3393 6293 1.666189 GTAAAGCCGGTGAGAGCAATC 59.334 52.381 1.90 0.00 0.00 2.67
3396 6296 2.892425 CCGGTGAGAGCAATCCGC 60.892 66.667 0.00 0.00 41.38 5.54
3444 6344 1.335872 CGAAAAACATGGTCCCACTGC 60.336 52.381 0.00 0.00 0.00 4.40
3480 6380 8.621532 AGCTTTGTGAATTTGTGTATCTCTAA 57.378 30.769 0.00 0.00 0.00 2.10
3512 6413 5.543507 TTGTTGCTATGAATTGGTGGTTT 57.456 34.783 0.00 0.00 0.00 3.27
3514 6415 5.295950 TGTTGCTATGAATTGGTGGTTTTG 58.704 37.500 0.00 0.00 0.00 2.44
3563 6464 4.102210 TCAATAGGCAGGAGAATCTTCCAG 59.898 45.833 0.00 0.00 39.84 3.86
3566 6467 2.646798 AGGCAGGAGAATCTTCCAGTTT 59.353 45.455 0.00 0.00 39.84 2.66
3576 6477 6.008960 AGAATCTTCCAGTTTCAATGCTCTT 58.991 36.000 0.00 0.00 0.00 2.85
3645 6546 2.027469 ACTACCGGCAAAGGTTAAGGAG 60.027 50.000 0.00 0.00 43.00 3.69
3691 6592 2.095364 GTCAGCATTCCAGCAAGTGAAG 60.095 50.000 0.00 0.00 36.85 3.02
3706 6607 4.849813 AGTGAAGATGACATTCCCATCA 57.150 40.909 0.00 0.00 42.03 3.07
3717 6618 6.012113 TGACATTCCCATCACAAAGAAAGAT 58.988 36.000 0.00 0.00 0.00 2.40
3724 6625 6.884295 TCCCATCACAAAGAAAGATAAATCGT 59.116 34.615 0.00 0.00 0.00 3.73
3727 6628 7.907045 CCATCACAAAGAAAGATAAATCGTCAG 59.093 37.037 0.00 0.00 0.00 3.51
3738 6639 3.678056 AAATCGTCAGCTCCTGTTGTA 57.322 42.857 0.00 0.00 32.61 2.41
3814 6715 4.461119 CCACTGGGCAGGTCTCTA 57.539 61.111 0.00 0.00 0.00 2.43
3826 6727 4.040445 CAGGTCTCTACTTGCTTAGCTC 57.960 50.000 5.60 0.00 0.00 4.09
3862 6765 4.487714 TCTTATCATTCCACGGAGCTTT 57.512 40.909 0.00 0.00 0.00 3.51
3962 6876 1.007734 GCACGACACTTGTCCGAGA 60.008 57.895 3.77 0.00 41.86 4.04
4099 7013 2.422479 GCAGTGATGACAGTGATGCAAT 59.578 45.455 0.00 0.00 46.81 3.56
4112 7032 1.978080 TGCAATGCCGGCATCACTT 60.978 52.632 40.38 24.34 36.11 3.16
4180 7100 6.780457 ATCAGATTCCCAAAATGTTGTAGG 57.220 37.500 0.00 0.00 32.40 3.18
4257 7177 5.854010 TCAAGCGTGTATAGGAGATTCTT 57.146 39.130 0.00 0.00 0.00 2.52
4286 7206 1.134280 CCTATCCTGGTGAGCCTGTTG 60.134 57.143 0.00 0.00 35.27 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 60 1.908340 CTCTCCTGGCTCCCCACAAG 61.908 65.000 0.00 0.00 35.79 3.16
61 63 3.791586 GCTCTCCTGGCTCCCCAC 61.792 72.222 0.00 0.00 35.79 4.61
72 74 3.491792 CCTCTCAAACCTTATCGCTCTCC 60.492 52.174 0.00 0.00 0.00 3.71
118 130 5.393243 GGTGTCTAGTTCCTCATGTCTGTAC 60.393 48.000 0.00 0.00 0.00 2.90
119 131 4.705507 GGTGTCTAGTTCCTCATGTCTGTA 59.294 45.833 0.00 0.00 0.00 2.74
121 133 3.766591 AGGTGTCTAGTTCCTCATGTCTG 59.233 47.826 0.00 0.00 0.00 3.51
126 163 3.100671 GGTCAGGTGTCTAGTTCCTCAT 58.899 50.000 0.00 0.00 0.00 2.90
133 170 0.697079 TCTCCGGTCAGGTGTCTAGT 59.303 55.000 0.00 0.00 41.99 2.57
140 177 2.759355 TGGAATTATCTCCGGTCAGGT 58.241 47.619 0.00 0.00 41.99 4.00
141 178 3.071602 ACATGGAATTATCTCCGGTCAGG 59.928 47.826 0.00 0.00 38.44 3.86
142 179 4.342862 ACATGGAATTATCTCCGGTCAG 57.657 45.455 0.00 0.00 38.44 3.51
143 180 4.771114 AACATGGAATTATCTCCGGTCA 57.229 40.909 0.00 0.00 38.44 4.02
144 181 6.127730 ACAAAAACATGGAATTATCTCCGGTC 60.128 38.462 0.00 0.00 38.44 4.79
164 201 5.062809 GCACCAGAAACATTTCGAAACAAAA 59.937 36.000 13.81 0.00 41.92 2.44
172 213 1.608590 AGTGGCACCAGAAACATTTCG 59.391 47.619 15.27 0.00 41.92 3.46
186 227 1.340889 GCTGGTCAAATTTCAGTGGCA 59.659 47.619 7.09 0.00 0.00 4.92
198 239 5.036117 AGTAGAAAGAAACTGCTGGTCAA 57.964 39.130 0.00 0.00 0.00 3.18
209 250 3.260128 GGAACGGAGGGAGTAGAAAGAAA 59.740 47.826 0.00 0.00 0.00 2.52
210 251 2.830321 GGAACGGAGGGAGTAGAAAGAA 59.170 50.000 0.00 0.00 0.00 2.52
211 252 2.225192 TGGAACGGAGGGAGTAGAAAGA 60.225 50.000 0.00 0.00 0.00 2.52
212 253 2.176889 TGGAACGGAGGGAGTAGAAAG 58.823 52.381 0.00 0.00 0.00 2.62
213 254 2.314071 TGGAACGGAGGGAGTAGAAA 57.686 50.000 0.00 0.00 0.00 2.52
214 255 2.314071 TTGGAACGGAGGGAGTAGAA 57.686 50.000 0.00 0.00 0.00 2.10
216 257 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
217 258 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
218 259 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
219 260 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
220 261 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
221 262 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
222 263 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
223 264 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
224 265 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
226 267 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
227 268 3.319755 TCCACGACGAGTAATTTGGAAC 58.680 45.455 0.00 0.00 0.00 3.62
228 269 3.663995 TCCACGACGAGTAATTTGGAA 57.336 42.857 0.00 0.00 0.00 3.53
229 270 3.663995 TTCCACGACGAGTAATTTGGA 57.336 42.857 0.00 0.00 0.00 3.53
230 271 4.939509 AATTCCACGACGAGTAATTTGG 57.060 40.909 0.00 0.00 0.00 3.28
234 275 5.699458 AGTTCAAAATTCCACGACGAGTAAT 59.301 36.000 0.00 0.00 0.00 1.89
236 277 4.624015 AGTTCAAAATTCCACGACGAGTA 58.376 39.130 0.00 0.00 0.00 2.59
238 279 5.585500 TTAGTTCAAAATTCCACGACGAG 57.415 39.130 0.00 0.00 0.00 4.18
239 280 5.987777 TTTAGTTCAAAATTCCACGACGA 57.012 34.783 0.00 0.00 0.00 4.20
241 282 6.197655 GTGGTTTTAGTTCAAAATTCCACGAC 59.802 38.462 0.00 0.00 40.54 4.34
242 283 6.267070 GTGGTTTTAGTTCAAAATTCCACGA 58.733 36.000 0.00 0.00 40.54 4.35
243 284 6.505039 GTGGTTTTAGTTCAAAATTCCACG 57.495 37.500 0.00 0.00 40.54 4.94
244 285 6.267070 TCGTGGTTTTAGTTCAAAATTCCAC 58.733 36.000 10.15 10.15 43.40 4.02
246 287 7.142680 TCATCGTGGTTTTAGTTCAAAATTCC 58.857 34.615 0.00 0.00 38.36 3.01
247 288 7.860872 ACTCATCGTGGTTTTAGTTCAAAATTC 59.139 33.333 0.00 0.00 38.36 2.17
250 291 6.687081 ACTCATCGTGGTTTTAGTTCAAAA 57.313 33.333 0.00 0.00 33.66 2.44
251 292 7.789273 TTACTCATCGTGGTTTTAGTTCAAA 57.211 32.000 0.00 0.00 0.00 2.69
252 293 7.972832 ATTACTCATCGTGGTTTTAGTTCAA 57.027 32.000 0.00 0.00 0.00 2.69
254 295 7.749126 CCAAATTACTCATCGTGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
256 297 6.938030 TCCAAATTACTCATCGTGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
257 298 7.372451 TCCAAATTACTCATCGTGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
259 300 6.039941 TGTTCCAAATTACTCATCGTGGTTTT 59.960 34.615 0.00 0.00 0.00 2.43
261 302 5.067273 TGTTCCAAATTACTCATCGTGGTT 58.933 37.500 0.00 0.00 0.00 3.67
262 303 4.647611 TGTTCCAAATTACTCATCGTGGT 58.352 39.130 0.00 0.00 0.00 4.16
263 304 4.935205 TCTGTTCCAAATTACTCATCGTGG 59.065 41.667 0.00 0.00 0.00 4.94
264 305 5.869344 TCTCTGTTCCAAATTACTCATCGTG 59.131 40.000 0.00 0.00 0.00 4.35
265 306 6.037786 TCTCTGTTCCAAATTACTCATCGT 57.962 37.500 0.00 0.00 0.00 3.73
266 307 6.333416 TCTCTCTGTTCCAAATTACTCATCG 58.667 40.000 0.00 0.00 0.00 3.84
268 309 7.251321 ACTCTCTCTGTTCCAAATTACTCAT 57.749 36.000 0.00 0.00 0.00 2.90
270 311 6.748198 CGTACTCTCTCTGTTCCAAATTACTC 59.252 42.308 0.00 0.00 0.00 2.59
271 312 6.208994 ACGTACTCTCTCTGTTCCAAATTACT 59.791 38.462 0.00 0.00 0.00 2.24
272 313 6.388278 ACGTACTCTCTCTGTTCCAAATTAC 58.612 40.000 0.00 0.00 0.00 1.89
273 314 6.585695 ACGTACTCTCTCTGTTCCAAATTA 57.414 37.500 0.00 0.00 0.00 1.40
274 315 5.470047 ACGTACTCTCTCTGTTCCAAATT 57.530 39.130 0.00 0.00 0.00 1.82
275 316 4.379603 CGACGTACTCTCTCTGTTCCAAAT 60.380 45.833 0.00 0.00 0.00 2.32
276 317 3.058432 CGACGTACTCTCTCTGTTCCAAA 60.058 47.826 0.00 0.00 0.00 3.28
277 318 2.483106 CGACGTACTCTCTCTGTTCCAA 59.517 50.000 0.00 0.00 0.00 3.53
278 319 2.074576 CGACGTACTCTCTCTGTTCCA 58.925 52.381 0.00 0.00 0.00 3.53
279 320 1.397692 CCGACGTACTCTCTCTGTTCC 59.602 57.143 0.00 0.00 0.00 3.62
280 321 2.075338 ACCGACGTACTCTCTCTGTTC 58.925 52.381 0.00 0.00 0.00 3.18
281 322 1.805345 CACCGACGTACTCTCTCTGTT 59.195 52.381 0.00 0.00 0.00 3.16
282 323 1.440708 CACCGACGTACTCTCTCTGT 58.559 55.000 0.00 0.00 0.00 3.41
283 324 0.727970 CCACCGACGTACTCTCTCTG 59.272 60.000 0.00 0.00 0.00 3.35
284 325 0.612229 TCCACCGACGTACTCTCTCT 59.388 55.000 0.00 0.00 0.00 3.10
285 326 1.008329 CTCCACCGACGTACTCTCTC 58.992 60.000 0.00 0.00 0.00 3.20
286 327 0.612229 TCTCCACCGACGTACTCTCT 59.388 55.000 0.00 0.00 0.00 3.10
287 328 0.726256 GTCTCCACCGACGTACTCTC 59.274 60.000 0.00 0.00 0.00 3.20
288 329 2.851798 GTCTCCACCGACGTACTCT 58.148 57.895 0.00 0.00 0.00 3.24
295 336 3.496155 CTTTACTAACGTCTCCACCGAC 58.504 50.000 0.00 0.00 0.00 4.79
296 337 2.489329 CCTTTACTAACGTCTCCACCGA 59.511 50.000 0.00 0.00 0.00 4.69
297 338 2.489329 TCCTTTACTAACGTCTCCACCG 59.511 50.000 0.00 0.00 0.00 4.94
298 339 3.119209 CCTCCTTTACTAACGTCTCCACC 60.119 52.174 0.00 0.00 0.00 4.61
299 340 3.760684 TCCTCCTTTACTAACGTCTCCAC 59.239 47.826 0.00 0.00 0.00 4.02
300 341 4.015084 CTCCTCCTTTACTAACGTCTCCA 58.985 47.826 0.00 0.00 0.00 3.86
301 342 4.268359 TCTCCTCCTTTACTAACGTCTCC 58.732 47.826 0.00 0.00 0.00 3.71
302 343 5.008911 GGATCTCCTCCTTTACTAACGTCTC 59.991 48.000 0.00 0.00 41.29 3.36
303 344 4.888823 GGATCTCCTCCTTTACTAACGTCT 59.111 45.833 0.00 0.00 41.29 4.18
304 345 4.037803 GGGATCTCCTCCTTTACTAACGTC 59.962 50.000 0.00 0.00 44.28 4.34
305 346 3.959449 GGGATCTCCTCCTTTACTAACGT 59.041 47.826 0.00 0.00 44.28 3.99
306 347 4.216708 AGGGATCTCCTCCTTTACTAACG 58.783 47.826 0.00 0.00 44.06 3.18
307 348 6.491062 GTCTAGGGATCTCCTCCTTTACTAAC 59.509 46.154 6.07 0.00 44.06 2.34
308 349 6.161705 TGTCTAGGGATCTCCTCCTTTACTAA 59.838 42.308 6.07 0.00 44.06 2.24
309 350 5.675421 TGTCTAGGGATCTCCTCCTTTACTA 59.325 44.000 6.07 0.00 44.06 1.82
310 351 4.482772 TGTCTAGGGATCTCCTCCTTTACT 59.517 45.833 6.07 0.00 44.06 2.24
311 352 4.585581 GTGTCTAGGGATCTCCTCCTTTAC 59.414 50.000 6.07 1.11 44.06 2.01
312 353 4.387664 GGTGTCTAGGGATCTCCTCCTTTA 60.388 50.000 6.07 0.00 44.06 1.85
313 354 3.631346 GGTGTCTAGGGATCTCCTCCTTT 60.631 52.174 6.07 0.00 44.06 3.11
314 355 2.090999 GGTGTCTAGGGATCTCCTCCTT 60.091 54.545 6.07 0.00 44.06 3.36
315 356 1.501604 GGTGTCTAGGGATCTCCTCCT 59.498 57.143 6.07 0.10 44.06 3.69
316 357 1.481615 GGGTGTCTAGGGATCTCCTCC 60.482 61.905 6.07 2.26 44.06 4.30
317 358 1.820090 CGGGTGTCTAGGGATCTCCTC 60.820 61.905 6.07 0.00 44.06 3.71
319 360 0.185416 TCGGGTGTCTAGGGATCTCC 59.815 60.000 0.00 0.00 0.00 3.71
320 361 1.611519 CTCGGGTGTCTAGGGATCTC 58.388 60.000 0.00 0.00 0.00 2.75
321 362 0.186386 CCTCGGGTGTCTAGGGATCT 59.814 60.000 0.00 0.00 0.00 2.75
322 363 1.465200 GCCTCGGGTGTCTAGGGATC 61.465 65.000 0.00 0.00 0.00 3.36
323 364 1.457831 GCCTCGGGTGTCTAGGGAT 60.458 63.158 0.00 0.00 0.00 3.85
324 365 2.043248 GCCTCGGGTGTCTAGGGA 60.043 66.667 0.00 0.00 0.00 4.20
325 366 2.363795 TGCCTCGGGTGTCTAGGG 60.364 66.667 0.00 0.00 0.00 3.53
326 367 3.082579 GCTGCCTCGGGTGTCTAGG 62.083 68.421 0.00 0.00 0.00 3.02
341 382 3.889134 TTGGAGTCTGCAGCCGCTG 62.889 63.158 16.47 16.47 39.64 5.18
397 440 0.034896 GTCCCAAAGTGCCGAAGAGA 59.965 55.000 0.00 0.00 0.00 3.10
399 442 1.301401 CGTCCCAAAGTGCCGAAGA 60.301 57.895 0.00 0.00 0.00 2.87
415 459 0.889186 AGTGGCGAGGCATTTTTCGT 60.889 50.000 1.94 0.00 38.96 3.85
423 467 3.838271 GATCCGAGTGGCGAGGCA 61.838 66.667 0.00 0.00 44.57 4.75
437 481 4.191015 GGAAGGGGGCGGTGGATC 62.191 72.222 0.00 0.00 0.00 3.36
438 482 4.760220 AGGAAGGGGGCGGTGGAT 62.760 66.667 0.00 0.00 0.00 3.41
442 486 4.677151 AAGGAGGAAGGGGGCGGT 62.677 66.667 0.00 0.00 0.00 5.68
443 487 3.798511 GAAGGAGGAAGGGGGCGG 61.799 72.222 0.00 0.00 0.00 6.13
444 488 3.798511 GGAAGGAGGAAGGGGGCG 61.799 72.222 0.00 0.00 0.00 6.13
445 489 1.584717 AATGGAAGGAGGAAGGGGGC 61.585 60.000 0.00 0.00 0.00 5.80
472 516 1.377612 GTTTAGGGGTGGCCGTTCT 59.622 57.895 0.00 0.00 0.00 3.01
479 523 1.567357 CAAATGGGGTTTAGGGGTGG 58.433 55.000 0.00 0.00 0.00 4.61
484 528 0.815095 GCGACCAAATGGGGTTTAGG 59.185 55.000 4.17 0.00 42.53 2.69
488 532 0.970427 GATGGCGACCAAATGGGGTT 60.970 55.000 4.17 0.00 42.53 4.11
497 541 1.552799 ATCAGTGGTGATGGCGACCA 61.553 55.000 1.01 1.01 42.19 4.02
540 2345 2.872245 ACAAGAGGACAACACATGAACG 59.128 45.455 0.00 0.00 0.00 3.95
550 2355 3.557898 GGATTGAGCAGACAAGAGGACAA 60.558 47.826 0.00 0.00 33.22 3.18
594 2399 5.643379 AATAACGAAACATCCATGTGCTT 57.357 34.783 0.00 0.00 41.61 3.91
622 2429 2.290577 ACTCTGATCCCTTTGTTGCCTC 60.291 50.000 0.00 0.00 0.00 4.70
665 2477 3.610242 CGAGATGAGAAGAAACTTGGTCG 59.390 47.826 0.00 0.00 0.00 4.79
675 2487 0.679960 TGGGCGTCGAGATGAGAAGA 60.680 55.000 0.00 0.00 0.00 2.87
687 2499 1.087501 GAAGATCCAGTTTGGGCGTC 58.912 55.000 0.00 0.00 38.32 5.19
704 2516 2.092753 GCTGACTGATGAGAATGGGGAA 60.093 50.000 0.00 0.00 0.00 3.97
746 2563 1.064166 CCAGATGCAGGAAGGTGGATT 60.064 52.381 0.00 0.00 0.00 3.01
823 2643 1.664016 GCAATGCCGCGGAAGAATATG 60.664 52.381 33.48 17.23 0.00 1.78
826 2646 1.315257 AAGCAATGCCGCGGAAGAAT 61.315 50.000 33.48 13.48 36.85 2.40
838 2658 3.764885 CCGAAAGTTAGGGAAGCAATG 57.235 47.619 0.00 0.00 0.00 2.82
851 2671 0.602905 GCAGCAGTACACCCGAAAGT 60.603 55.000 0.00 0.00 0.00 2.66
868 2688 0.179073 GCGAAGGGCTAGATCTTGCA 60.179 55.000 26.66 0.00 39.11 4.08
869 2689 2.611012 GCGAAGGGCTAGATCTTGC 58.389 57.895 19.32 19.32 39.11 4.01
880 2700 8.485591 CGTATAAATAGTCTTAAAAGCGAAGGG 58.514 37.037 0.00 0.00 0.00 3.95
902 2722 6.403049 TGTACACCTGATTGTGAAATCGTAT 58.597 36.000 0.00 0.00 39.57 3.06
934 2754 5.762218 CCCACTATAATCTGCAGAAAAGGAG 59.238 44.000 22.50 16.00 0.00 3.69
944 2764 5.283457 ACTCAGTTCCCACTATAATCTGC 57.717 43.478 0.00 0.00 0.00 4.26
958 2778 4.882671 TGCTCTGTTTCAAACTCAGTTC 57.117 40.909 1.10 0.00 0.00 3.01
959 2779 5.402398 GTTTGCTCTGTTTCAAACTCAGTT 58.598 37.500 1.10 0.00 45.01 3.16
960 2780 4.986622 GTTTGCTCTGTTTCAAACTCAGT 58.013 39.130 1.10 0.00 45.01 3.41
1089 2911 3.495193 CTCGCTGGAAAAATCACATGTG 58.505 45.455 20.18 20.18 0.00 3.21
1122 2944 0.617413 CCACTCCATGCTCACCTCTT 59.383 55.000 0.00 0.00 0.00 2.85
1170 2995 7.962964 TGTTAAGATTTGACAAGTAGACTGG 57.037 36.000 0.00 0.00 0.00 4.00
1197 3022 6.674760 GCTTCCTAAACAGTTAACGGCTATTG 60.675 42.308 5.60 0.00 0.00 1.90
1236 3069 3.624777 ACTCCCTGTGATGCAATAAAGG 58.375 45.455 0.00 0.00 0.00 3.11
1396 3230 5.336150 TCACCATTTCAAAGCTTGTTTCA 57.664 34.783 0.00 0.00 0.00 2.69
1405 3239 4.262164 CCTTGGAGGTTCACCATTTCAAAG 60.262 45.833 0.00 0.00 37.26 2.77
1511 3349 6.931840 AGAGTTTCTGTGATTTTACCTGAGAC 59.068 38.462 0.00 0.00 0.00 3.36
1560 3398 6.937436 AACTTCACAAACGAAAGGAGTAAT 57.063 33.333 0.00 0.00 0.00 1.89
1598 3436 8.394121 GCATAGCTATAGCAGGCTATTTAAAAG 58.606 37.037 26.07 10.51 45.83 2.27
1891 3760 8.551682 TCAGGCATCATATATGGTATATCACA 57.448 34.615 12.78 0.00 0.00 3.58
1900 3769 9.842775 AAGTATACAATCAGGCATCATATATGG 57.157 33.333 12.78 0.00 0.00 2.74
2126 4189 1.690219 GATCTGGTGGGCACGGAGAT 61.690 60.000 0.00 0.00 35.30 2.75
2158 4221 0.319641 GCGACAGGGTTTTCTCTCGT 60.320 55.000 0.00 0.00 0.00 4.18
2232 4295 1.219213 CACTCTACATCCCTCCCCTCT 59.781 57.143 0.00 0.00 0.00 3.69
2518 4659 4.436242 TTCAGGTCGAGATGAACAGTAC 57.564 45.455 7.89 0.00 36.45 2.73
2579 4720 7.284074 TCCTTGATAAACCAAAATCCGCTATA 58.716 34.615 0.00 0.00 0.00 1.31
2684 4825 3.742882 GGCATTGCAAGAAAGAAAAGGAC 59.257 43.478 11.39 0.00 0.00 3.85
2708 4849 3.619419 TGCAGCACAATATGGAAGCTTA 58.381 40.909 0.00 0.00 32.35 3.09
2711 4852 1.535437 GCTGCAGCACAATATGGAAGC 60.535 52.381 33.36 0.81 41.59 3.86
2899 5796 0.742505 AGTGTTCGAAGGACGTGTCA 59.257 50.000 0.00 0.00 43.13 3.58
3058 5955 9.408648 ACTGGAAGATCAAAAGAACTAAAAGAA 57.591 29.630 0.00 0.00 37.43 2.52
3060 5957 9.455847 CAACTGGAAGATCAAAAGAACTAAAAG 57.544 33.333 0.00 0.00 37.43 2.27
3136 6034 6.790350 GCGGACGACAATATGTAATGTAAATG 59.210 38.462 0.00 0.00 0.00 2.32
3137 6035 6.704493 AGCGGACGACAATATGTAATGTAAAT 59.296 34.615 0.00 0.00 0.00 1.40
3206 6104 0.839946 TCCAGCCTATTCCTCCAAGC 59.160 55.000 0.00 0.00 0.00 4.01
3232 6130 3.891366 CCAATTTTTCTGTGACTCCCTGT 59.109 43.478 0.00 0.00 0.00 4.00
3285 6183 2.494870 GGGCTGATTTCAGTGCATTCTT 59.505 45.455 9.21 0.00 45.45 2.52
3306 6205 4.606457 GCTGTGTAGCTGGTCTTTTATG 57.394 45.455 0.00 0.00 46.57 1.90
3371 6271 0.394938 TGCTCTCACCGGCTTTACAA 59.605 50.000 0.00 0.00 0.00 2.41
3372 6272 0.394938 TTGCTCTCACCGGCTTTACA 59.605 50.000 0.00 0.00 0.00 2.41
3389 6289 1.091771 CCTGTGCTACTGGCGGATTG 61.092 60.000 0.00 0.00 45.43 2.67
3391 6291 0.686441 TACCTGTGCTACTGGCGGAT 60.686 55.000 0.00 0.00 45.43 4.18
3393 6293 0.530650 CATACCTGTGCTACTGGCGG 60.531 60.000 10.60 0.00 45.43 6.13
3396 6296 5.086104 AGTTTACATACCTGTGCTACTGG 57.914 43.478 9.55 9.55 42.22 4.00
3444 6344 3.126001 TCACAAAGCTTAGGTCACCAG 57.874 47.619 0.00 0.00 0.00 4.00
3480 6380 8.776470 CCAATTCATAGCAACAAAAGTGAAAAT 58.224 29.630 0.00 0.00 0.00 1.82
3499 6399 3.181467 CCAGAAGCAAAACCACCAATTCA 60.181 43.478 0.00 0.00 0.00 2.57
3563 6464 3.935203 TCCTCGATGAAGAGCATTGAAAC 59.065 43.478 0.00 0.00 44.76 2.78
3566 6467 3.026694 TCTCCTCGATGAAGAGCATTGA 58.973 45.455 0.00 0.00 43.58 2.57
3576 6477 3.137728 TGGTACCAGTATCTCCTCGATGA 59.862 47.826 11.60 0.00 33.48 2.92
3645 6546 4.787598 CAGATACTTGAACCTGCACAAAC 58.212 43.478 0.00 0.00 0.00 2.93
3691 6592 5.902613 TTCTTTGTGATGGGAATGTCATC 57.097 39.130 0.00 0.00 40.85 2.92
3706 6607 6.092807 GGAGCTGACGATTTATCTTTCTTTGT 59.907 38.462 0.00 0.00 0.00 2.83
3717 6618 3.678056 ACAACAGGAGCTGACGATTTA 57.322 42.857 0.00 0.00 35.18 1.40
3724 6625 0.541063 TCCGGTACAACAGGAGCTGA 60.541 55.000 0.00 0.00 37.55 4.26
3727 6628 1.090052 GCATCCGGTACAACAGGAGC 61.090 60.000 0.00 5.37 45.30 4.70
3738 6639 1.579429 GCAACGAAAAGCATCCGGT 59.421 52.632 0.00 0.00 0.00 5.28
3814 6715 8.415950 ACATATATAGAGTGAGCTAAGCAAGT 57.584 34.615 0.00 0.00 0.00 3.16
3899 6813 1.516603 GCCTCGGTCGTAAGTCTGC 60.517 63.158 0.00 0.00 39.48 4.26
4067 6981 2.675348 GTCATCACTGCTAACTTGAGCC 59.325 50.000 0.00 0.00 42.11 4.70
4112 7032 3.920231 ACATCTTGCTCAGAATAGGCA 57.080 42.857 0.00 0.00 34.16 4.75
4140 7060 2.428890 CTGATAGTCTCCGAACAAGGCT 59.571 50.000 0.00 0.00 32.41 4.58
4257 7177 1.344953 ACCAGGATAGGAATGCCGCA 61.345 55.000 0.00 0.00 39.96 5.69
4286 7206 4.223700 TGGGTGCTGATATCATCTATCCAC 59.776 45.833 5.72 6.96 0.00 4.02


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

AutoCloner maintained by Alex Coulton.