Multiple sequence alignment - TraesCS3A01G370100

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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 TraesCS3A01G370100 chr3A 100.000 3156 0 0 1 3156 620990687 620987532 0.000000e+00 5829
1 TraesCS3A01G370100 chr3D 89.392 2074 110 44 352 2361 477410609 477408582 0.000000e+00 2510
2 TraesCS3A01G370100 chr3D 87.640 801 74 15 2375 3156 477402878 477402084 0.000000e+00 907
3 TraesCS3A01G370100 chr3D 86.441 236 28 3 1 233 477410869 477410635 4.040000e-64 255
4 TraesCS3A01G370100 chr3B 91.997 1412 70 24 813 2204 636734678 636733290 0.000000e+00 1941
5 TraesCS3A01G370100 chr3B 89.251 614 55 8 2205 2815 636733078 636732473 0.000000e+00 758
6 TraesCS3A01G370100 chr3B 91.266 229 18 2 2808 3035 636732012 636731785 8.500000e-81 311
7 TraesCS3A01G370100 chr3B 84.663 163 18 5 366 525 636734899 636734741 4.210000e-34 156
8 TraesCS3A01G370100 chr4B 82.727 440 63 8 1703 2140 660703714 660704142 2.300000e-101 379
9 TraesCS3A01G370100 chr4B 81.560 423 67 6 1719 2140 660495206 660494794 3.900000e-89 339
10 TraesCS3A01G370100 chr4B 79.048 420 64 20 1095 1495 660703109 660703523 1.870000e-67 267
11 TraesCS3A01G370100 chr4B 85.043 234 35 0 1095 1328 660495898 660495665 4.070000e-59 239
12 TraesCS3A01G370100 chrUn 80.952 441 73 6 1701 2140 273156650 273157080 3.900000e-89 339
13 TraesCS3A01G370100 chrUn 84.937 239 33 3 1092 1328 110764521 110764758 4.070000e-59 239
14 TraesCS3A01G370100 chrUn 85.043 234 35 0 1095 1328 273155976 273156209 4.070000e-59 239
15 TraesCS3A01G370100 chr7D 82.540 252 39 5 554 802 269717135 269717384 1.910000e-52 217
16 TraesCS3A01G370100 chr4A 81.395 258 41 6 560 812 650052366 650052111 1.480000e-48 204
17 TraesCS3A01G370100 chr4A 81.500 200 31 6 560 758 703329496 703329690 3.260000e-35 159
18 TraesCS3A01G370100 chr4A 81.500 200 31 6 560 758 703329978 703330172 3.260000e-35 159
19 TraesCS3A01G370100 chr7A 81.154 260 41 7 560 812 42265822 42265564 5.340000e-48 202
20 TraesCS3A01G370100 chr7B 80.556 252 44 5 554 802 271315934 271316183 4.160000e-44 189
21 TraesCS3A01G370100 chr1B 79.216 255 47 5 560 810 464138022 464137770 4.190000e-39 172
22 TraesCS3A01G370100 chr4D 89.313 131 14 0 560 690 399957225 399957355 7.000000e-37 165
23 TraesCS3A01G370100 chr6D 80.102 196 36 3 562 755 470299150 470299344 3.280000e-30 143


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 TraesCS3A01G370100 chr3A 620987532 620990687 3155 True 5829.0 5829 100.00000 1 3156 1 chr3A.!!$R1 3155
1 TraesCS3A01G370100 chr3D 477408582 477410869 2287 True 1382.5 2510 87.91650 1 2361 2 chr3D.!!$R2 2360
2 TraesCS3A01G370100 chr3D 477402084 477402878 794 True 907.0 907 87.64000 2375 3156 1 chr3D.!!$R1 781
3 TraesCS3A01G370100 chr3B 636731785 636734899 3114 True 791.5 1941 89.29425 366 3035 4 chr3B.!!$R1 2669
4 TraesCS3A01G370100 chr4B 660703109 660704142 1033 False 323.0 379 80.88750 1095 2140 2 chr4B.!!$F1 1045
5 TraesCS3A01G370100 chr4B 660494794 660495898 1104 True 289.0 339 83.30150 1095 2140 2 chr4B.!!$R1 1045
6 TraesCS3A01G370100 chrUn 273155976 273157080 1104 False 289.0 339 82.99750 1095 2140 2 chrUn.!!$F2 1045

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
292 296 0.247185 AATGCCAATCTTGTTGCGGG 59.753 50.0 0.0 0.0 0.0 6.13 F
1348 1430 0.035881 AGCACATCACACCTGACCTG 59.964 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1965 0.953471 CGAATTCCGTCCCTGCACAA 60.953 55.0 0.0 0.0 0.0 3.33 R
3016 3982 0.175760 TCGGCTCTTTTCTCCCATCG 59.824 55.0 0.0 0.0 0.0 3.84 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
24 25 5.901853 TGGAGTCTCAATCATGGATCTAAGT 59.098 40.000 1.47 0.00 0.00 2.24
30 31 5.359756 TCAATCATGGATCTAAGTGAACCG 58.640 41.667 0.00 0.00 40.14 4.44
66 67 5.939764 TCTAAGTCCATCAAGCTACACAT 57.060 39.130 0.00 0.00 0.00 3.21
83 84 8.526147 AGCTACACATGATTTCTAAAATTTGCT 58.474 29.630 0.00 0.00 0.00 3.91
120 121 5.913137 TGTTGGACAAAGAATCAACAAGT 57.087 34.783 5.43 0.00 44.05 3.16
121 122 5.649557 TGTTGGACAAAGAATCAACAAGTG 58.350 37.500 5.43 0.00 44.05 3.16
122 123 5.184864 TGTTGGACAAAGAATCAACAAGTGT 59.815 36.000 5.43 0.00 44.05 3.55
123 124 5.247507 TGGACAAAGAATCAACAAGTGTG 57.752 39.130 0.00 0.00 0.00 3.82
124 125 4.946772 TGGACAAAGAATCAACAAGTGTGA 59.053 37.500 0.00 0.00 0.00 3.58
125 126 5.593909 TGGACAAAGAATCAACAAGTGTGAT 59.406 36.000 0.00 0.00 0.00 3.06
126 127 6.145535 GGACAAAGAATCAACAAGTGTGATC 58.854 40.000 0.00 0.00 0.00 2.92
127 128 6.238731 GGACAAAGAATCAACAAGTGTGATCA 60.239 38.462 0.00 0.00 0.00 2.92
128 129 6.498304 ACAAAGAATCAACAAGTGTGATCAC 58.502 36.000 19.27 19.27 44.15 3.06
142 144 8.783093 CAAGTGTGATCACCAACTTAGAAATAA 58.217 33.333 23.67 0.85 44.83 1.40
144 146 8.784043 AGTGTGATCACCAACTTAGAAATAAAC 58.216 33.333 22.85 8.33 44.83 2.01
146 148 9.295825 TGTGATCACCAACTTAGAAATAAACAT 57.704 29.630 22.85 0.00 0.00 2.71
148 150 8.664798 TGATCACCAACTTAGAAATAAACATCG 58.335 33.333 0.00 0.00 0.00 3.84
166 168 2.426522 TCGTCTCCTGAGCATTTTTGG 58.573 47.619 0.00 0.00 0.00 3.28
172 176 5.693555 GTCTCCTGAGCATTTTTGGAAAAAG 59.306 40.000 3.83 0.00 40.78 2.27
173 177 4.959723 TCCTGAGCATTTTTGGAAAAAGG 58.040 39.130 5.16 5.16 40.78 3.11
177 181 5.600696 TGAGCATTTTTGGAAAAAGGTCTC 58.399 37.500 16.38 17.27 40.60 3.36
181 185 6.707608 AGCATTTTTGGAAAAAGGTCTCAATC 59.292 34.615 10.07 0.00 40.60 2.67
203 207 7.787725 ATCGACCAATACTTAAGGATTTCAC 57.212 36.000 10.41 4.24 0.00 3.18
205 209 5.006358 CGACCAATACTTAAGGATTTCACGG 59.994 44.000 10.41 10.95 0.00 4.94
212 216 4.630069 ACTTAAGGATTTCACGGTTGATCG 59.370 41.667 7.53 0.00 0.00 3.69
220 224 2.876091 TCACGGTTGATCGATCTTGTC 58.124 47.619 25.02 12.51 0.00 3.18
229 233 2.677971 CGATCTTGTCGCGGGATTT 58.322 52.632 6.13 0.00 44.33 2.17
233 237 3.362986 CGATCTTGTCGCGGGATTTAATG 60.363 47.826 6.13 0.00 44.33 1.90
234 238 1.668751 TCTTGTCGCGGGATTTAATGC 59.331 47.619 6.13 0.00 0.00 3.56
235 239 0.736053 TTGTCGCGGGATTTAATGCC 59.264 50.000 6.13 5.36 37.42 4.40
236 240 0.393132 TGTCGCGGGATTTAATGCCA 60.393 50.000 15.51 0.00 41.46 4.92
237 241 0.736053 GTCGCGGGATTTAATGCCAA 59.264 50.000 15.51 0.00 41.46 4.52
239 243 1.336440 TCGCGGGATTTAATGCCAATG 59.664 47.619 15.51 4.57 41.46 2.82
240 244 1.066908 CGCGGGATTTAATGCCAATGT 59.933 47.619 15.51 0.00 41.46 2.71
241 245 2.472816 GCGGGATTTAATGCCAATGTG 58.527 47.619 15.51 0.12 41.46 3.21
243 247 3.796504 GCGGGATTTAATGCCAATGTGAG 60.797 47.826 15.51 0.00 41.46 3.51
244 248 3.243501 CGGGATTTAATGCCAATGTGAGG 60.244 47.826 15.51 0.00 41.46 3.86
245 249 3.960102 GGGATTTAATGCCAATGTGAGGA 59.040 43.478 10.66 0.00 40.99 3.71
246 250 4.405358 GGGATTTAATGCCAATGTGAGGAA 59.595 41.667 10.66 0.00 40.99 3.36
247 251 5.452356 GGGATTTAATGCCAATGTGAGGAAG 60.452 44.000 10.66 0.00 40.99 3.46
248 252 5.360714 GGATTTAATGCCAATGTGAGGAAGA 59.639 40.000 0.00 0.00 0.00 2.87
250 254 6.855763 TTTAATGCCAATGTGAGGAAGATT 57.144 33.333 0.00 0.00 0.00 2.40
251 255 4.996788 AATGCCAATGTGAGGAAGATTC 57.003 40.909 0.00 0.00 0.00 2.52
252 256 2.358957 TGCCAATGTGAGGAAGATTCG 58.641 47.619 0.00 0.00 0.00 3.34
253 257 2.027285 TGCCAATGTGAGGAAGATTCGA 60.027 45.455 0.00 0.00 0.00 3.71
254 258 3.009723 GCCAATGTGAGGAAGATTCGAA 58.990 45.455 0.00 0.00 0.00 3.71
256 260 4.256920 CCAATGTGAGGAAGATTCGAACT 58.743 43.478 0.00 0.00 0.00 3.01
257 261 4.331168 CCAATGTGAGGAAGATTCGAACTC 59.669 45.833 0.00 2.63 0.00 3.01
258 262 3.217599 TGTGAGGAAGATTCGAACTCG 57.782 47.619 0.00 0.00 41.45 4.18
269 273 2.427232 TCGAACTCGATTTCACGGTT 57.573 45.000 14.88 0.17 44.22 4.44
270 274 2.746269 TCGAACTCGATTTCACGGTTT 58.254 42.857 14.88 0.00 44.22 3.27
271 275 3.125316 TCGAACTCGATTTCACGGTTTT 58.875 40.909 14.88 0.00 44.22 2.43
272 276 3.556775 TCGAACTCGATTTCACGGTTTTT 59.443 39.130 14.88 0.00 44.22 1.94
273 277 4.744137 TCGAACTCGATTTCACGGTTTTTA 59.256 37.500 14.88 0.00 44.22 1.52
274 278 5.233902 TCGAACTCGATTTCACGGTTTTTAA 59.766 36.000 14.88 0.00 44.22 1.52
275 279 6.073657 TCGAACTCGATTTCACGGTTTTTAAT 60.074 34.615 14.88 0.00 44.22 1.40
276 280 6.031003 CGAACTCGATTTCACGGTTTTTAATG 59.969 38.462 14.88 0.00 43.02 1.90
277 281 5.151389 ACTCGATTTCACGGTTTTTAATGC 58.849 37.500 0.00 0.00 0.00 3.56
278 282 4.477780 TCGATTTCACGGTTTTTAATGCC 58.522 39.130 0.00 0.00 0.00 4.40
279 283 4.023107 TCGATTTCACGGTTTTTAATGCCA 60.023 37.500 0.00 0.00 0.00 4.92
280 284 4.681942 CGATTTCACGGTTTTTAATGCCAA 59.318 37.500 0.00 0.00 0.00 4.52
281 285 5.347364 CGATTTCACGGTTTTTAATGCCAAT 59.653 36.000 0.00 0.00 0.00 3.16
282 286 6.453659 CGATTTCACGGTTTTTAATGCCAATC 60.454 38.462 0.00 0.00 0.00 2.67
283 287 5.461032 TTCACGGTTTTTAATGCCAATCT 57.539 34.783 0.00 0.00 0.00 2.40
284 288 5.461032 TCACGGTTTTTAATGCCAATCTT 57.539 34.783 0.00 0.00 0.00 2.40
285 289 5.226396 TCACGGTTTTTAATGCCAATCTTG 58.774 37.500 0.00 0.00 0.00 3.02
286 290 4.987912 CACGGTTTTTAATGCCAATCTTGT 59.012 37.500 0.00 0.00 0.00 3.16
287 291 5.465056 CACGGTTTTTAATGCCAATCTTGTT 59.535 36.000 0.00 0.00 0.00 2.83
288 292 5.465056 ACGGTTTTTAATGCCAATCTTGTTG 59.535 36.000 0.00 0.00 0.00 3.33
289 293 5.614449 CGGTTTTTAATGCCAATCTTGTTGC 60.614 40.000 0.00 0.00 0.00 4.17
290 294 5.373262 GTTTTTAATGCCAATCTTGTTGCG 58.627 37.500 0.00 0.00 0.00 4.85
291 295 2.937469 TAATGCCAATCTTGTTGCGG 57.063 45.000 0.00 0.00 0.00 5.69
292 296 0.247185 AATGCCAATCTTGTTGCGGG 59.753 50.000 0.00 0.00 0.00 6.13
293 297 0.611618 ATGCCAATCTTGTTGCGGGA 60.612 50.000 0.00 0.00 0.00 5.14
294 298 0.611618 TGCCAATCTTGTTGCGGGAT 60.612 50.000 0.00 0.00 0.00 3.85
295 299 0.532115 GCCAATCTTGTTGCGGGATT 59.468 50.000 0.00 0.00 0.00 3.01
296 300 1.469767 GCCAATCTTGTTGCGGGATTC 60.470 52.381 0.00 0.00 0.00 2.52
297 301 1.818060 CCAATCTTGTTGCGGGATTCA 59.182 47.619 0.00 0.00 0.00 2.57
298 302 2.230992 CCAATCTTGTTGCGGGATTCAA 59.769 45.455 0.00 0.00 0.00 2.69
299 303 3.305950 CCAATCTTGTTGCGGGATTCAAA 60.306 43.478 0.00 0.00 0.00 2.69
300 304 3.575965 ATCTTGTTGCGGGATTCAAAC 57.424 42.857 0.00 0.00 0.00 2.93
301 305 2.582052 TCTTGTTGCGGGATTCAAACT 58.418 42.857 0.00 0.00 0.00 2.66
302 306 2.955660 TCTTGTTGCGGGATTCAAACTT 59.044 40.909 0.00 0.00 0.00 2.66
303 307 2.791383 TGTTGCGGGATTCAAACTTG 57.209 45.000 0.00 0.00 0.00 3.16
304 308 2.302260 TGTTGCGGGATTCAAACTTGA 58.698 42.857 0.00 0.00 34.92 3.02
305 309 2.890311 TGTTGCGGGATTCAAACTTGAT 59.110 40.909 0.00 0.00 37.00 2.57
306 310 3.320541 TGTTGCGGGATTCAAACTTGATT 59.679 39.130 0.00 0.00 37.00 2.57
307 311 4.202202 TGTTGCGGGATTCAAACTTGATTT 60.202 37.500 0.00 0.00 37.00 2.17
308 312 4.173036 TGCGGGATTCAAACTTGATTTC 57.827 40.909 0.00 0.00 37.00 2.17
309 313 3.571828 TGCGGGATTCAAACTTGATTTCA 59.428 39.130 0.00 0.00 37.00 2.69
310 314 3.920412 GCGGGATTCAAACTTGATTTCAC 59.080 43.478 0.00 0.00 37.00 3.18
311 315 4.485163 CGGGATTCAAACTTGATTTCACC 58.515 43.478 0.00 0.00 37.00 4.02
312 316 4.485163 GGGATTCAAACTTGATTTCACCG 58.515 43.478 0.00 0.00 37.00 4.94
313 317 4.022329 GGGATTCAAACTTGATTTCACCGT 60.022 41.667 0.00 0.00 37.00 4.83
314 318 4.917415 GGATTCAAACTTGATTTCACCGTG 59.083 41.667 0.00 0.00 37.00 4.94
315 319 5.278266 GGATTCAAACTTGATTTCACCGTGA 60.278 40.000 0.00 0.00 37.00 4.35
316 320 5.568685 TTCAAACTTGATTTCACCGTGAA 57.431 34.783 9.99 9.99 37.00 3.18
329 333 7.989416 TTTCACCGTGAAATCCTTAAGTATT 57.011 32.000 20.42 0.00 41.02 1.89
330 334 6.978343 TCACCGTGAAATCCTTAAGTATTG 57.022 37.500 0.00 0.00 0.00 1.90
331 335 5.878116 TCACCGTGAAATCCTTAAGTATTGG 59.122 40.000 0.00 0.00 0.00 3.16
332 336 5.646360 CACCGTGAAATCCTTAAGTATTGGT 59.354 40.000 0.97 0.00 0.00 3.67
333 337 5.878669 ACCGTGAAATCCTTAAGTATTGGTC 59.121 40.000 0.97 0.00 0.00 4.02
334 338 5.878116 CCGTGAAATCCTTAAGTATTGGTCA 59.122 40.000 0.97 0.00 0.00 4.02
335 339 6.373216 CCGTGAAATCCTTAAGTATTGGTCAA 59.627 38.462 0.97 0.00 0.00 3.18
336 340 7.414098 CCGTGAAATCCTTAAGTATTGGTCAAG 60.414 40.741 0.97 2.37 0.00 3.02
337 341 7.251281 GTGAAATCCTTAAGTATTGGTCAAGC 58.749 38.462 0.97 0.00 0.00 4.01
338 342 6.093495 TGAAATCCTTAAGTATTGGTCAAGCG 59.907 38.462 0.97 0.00 0.00 4.68
339 343 4.546829 TCCTTAAGTATTGGTCAAGCGT 57.453 40.909 0.97 0.00 0.00 5.07
340 344 4.250464 TCCTTAAGTATTGGTCAAGCGTG 58.750 43.478 0.97 0.00 0.00 5.34
341 345 4.020928 TCCTTAAGTATTGGTCAAGCGTGA 60.021 41.667 0.00 0.00 0.00 4.35
342 346 4.693566 CCTTAAGTATTGGTCAAGCGTGAA 59.306 41.667 3.20 0.00 34.87 3.18
343 347 5.180492 CCTTAAGTATTGGTCAAGCGTGAAA 59.820 40.000 3.20 0.00 34.87 2.69
344 348 6.128007 CCTTAAGTATTGGTCAAGCGTGAAAT 60.128 38.462 3.20 4.41 34.87 2.17
345 349 4.946784 AGTATTGGTCAAGCGTGAAATC 57.053 40.909 3.20 0.00 34.87 2.17
346 350 3.689649 AGTATTGGTCAAGCGTGAAATCC 59.310 43.478 3.20 2.20 34.87 3.01
347 351 2.270352 TTGGTCAAGCGTGAAATCCT 57.730 45.000 3.20 0.00 34.87 3.24
348 352 2.270352 TGGTCAAGCGTGAAATCCTT 57.730 45.000 3.20 0.00 34.87 3.36
349 353 3.410631 TGGTCAAGCGTGAAATCCTTA 57.589 42.857 3.20 0.00 34.87 2.69
350 354 3.745799 TGGTCAAGCGTGAAATCCTTAA 58.254 40.909 3.20 0.00 34.87 1.85
357 361 4.546570 AGCGTGAAATCCTTAAGTTTTGC 58.453 39.130 0.97 3.33 0.00 3.68
364 368 3.726291 TCCTTAAGTTTTGCTTGTGGC 57.274 42.857 0.97 0.00 38.05 5.01
370 374 2.041701 AGTTTTGCTTGTGGCTTCCAT 58.958 42.857 0.00 0.00 42.39 3.41
394 398 5.714333 TGCCATTTGACTTTGATTTAGGCTA 59.286 36.000 0.00 0.00 39.10 3.93
434 438 5.242838 TGAATTCACTTAATCCCGTTTGCTT 59.757 36.000 3.38 0.00 0.00 3.91
470 477 7.672240 TCCCTATTTTAATGTTTGTTTGACCC 58.328 34.615 0.00 0.00 0.00 4.46
564 599 2.156098 TCAACAAGCATAAACGGACCC 58.844 47.619 0.00 0.00 0.00 4.46
610 645 1.514678 GCACATGGCAACTCCGAACA 61.515 55.000 0.00 0.00 43.97 3.18
611 646 1.167851 CACATGGCAACTCCGAACAT 58.832 50.000 0.00 0.00 37.80 2.71
612 647 1.541147 CACATGGCAACTCCGAACATT 59.459 47.619 0.00 0.00 37.80 2.71
613 648 2.030007 CACATGGCAACTCCGAACATTT 60.030 45.455 0.00 0.00 37.80 2.32
614 649 2.627699 ACATGGCAACTCCGAACATTTT 59.372 40.909 0.00 0.00 37.80 1.82
615 650 3.069443 ACATGGCAACTCCGAACATTTTT 59.931 39.130 0.00 0.00 37.80 1.94
652 687 4.264253 TGACATGAGGATGGCAACTTTAG 58.736 43.478 0.00 0.00 45.22 1.85
701 736 9.160496 TGCTTCAATTTATTTTTGACACAAACT 57.840 25.926 0.00 0.00 33.03 2.66
712 747 9.691362 ATTTTTGACACAAACTTACCATATGTC 57.309 29.630 1.24 0.00 36.40 3.06
715 750 6.530120 TGACACAAACTTACCATATGTCACT 58.470 36.000 1.24 0.00 39.87 3.41
716 751 6.426633 TGACACAAACTTACCATATGTCACTG 59.573 38.462 1.24 0.00 39.87 3.66
725 776 4.847198 ACCATATGTCACTGAATTCTGCA 58.153 39.130 11.86 3.39 0.00 4.41
751 802 1.612950 TGCGTGACTGAAATTGCCATT 59.387 42.857 0.00 0.00 0.00 3.16
758 809 6.562640 CGTGACTGAAATTGCCATTGAAAAAG 60.563 38.462 0.00 0.00 0.00 2.27
759 810 6.479660 GTGACTGAAATTGCCATTGAAAAAGA 59.520 34.615 0.00 0.00 0.00 2.52
765 816 7.932491 TGAAATTGCCATTGAAAAAGATCAAGA 59.068 29.630 0.00 0.00 42.21 3.02
767 818 5.138125 TGCCATTGAAAAAGATCAAGACC 57.862 39.130 0.00 0.00 42.21 3.85
774 825 4.516698 TGAAAAAGATCAAGACCAGAGTGC 59.483 41.667 0.00 0.00 0.00 4.40
787 838 1.218047 GAGTGCCACGCATCTGGTA 59.782 57.895 0.00 0.00 41.91 3.25
793 844 1.290203 CCACGCATCTGGTATGACAC 58.710 55.000 0.00 0.00 0.00 3.67
805 856 6.356556 TCTGGTATGACACTTATCATTTGGG 58.643 40.000 0.00 0.00 39.97 4.12
806 857 6.069673 TCTGGTATGACACTTATCATTTGGGT 60.070 38.462 0.00 0.00 39.97 4.51
809 860 8.110271 TGGTATGACACTTATCATTTGGGTAAA 58.890 33.333 0.00 0.00 39.97 2.01
825 876 8.927411 ATTTGGGTAAATAAATCCTTGATGAGG 58.073 33.333 0.00 0.00 39.57 3.86
837 888 4.139859 CTTGATGAGGATCTTGCACTCT 57.860 45.455 3.29 0.00 34.92 3.24
854 905 5.178797 GCACTCTAAGACTAGCAATTCCAA 58.821 41.667 0.00 0.00 0.00 3.53
855 906 5.064071 GCACTCTAAGACTAGCAATTCCAAC 59.936 44.000 0.00 0.00 0.00 3.77
859 910 7.389053 ACTCTAAGACTAGCAATTCCAACAAAG 59.611 37.037 0.00 0.00 0.00 2.77
883 935 2.443887 TACTTAGCCGAACGTGCTTT 57.556 45.000 4.04 0.00 40.23 3.51
884 936 1.589803 ACTTAGCCGAACGTGCTTTT 58.410 45.000 4.04 0.00 40.23 2.27
885 937 2.758009 ACTTAGCCGAACGTGCTTTTA 58.242 42.857 4.04 0.00 40.23 1.52
886 938 2.735134 ACTTAGCCGAACGTGCTTTTAG 59.265 45.455 4.04 3.46 40.23 1.85
887 939 1.717194 TAGCCGAACGTGCTTTTAGG 58.283 50.000 4.04 0.00 40.23 2.69
889 941 0.442699 GCCGAACGTGCTTTTAGGAG 59.557 55.000 0.00 0.00 0.00 3.69
890 942 1.792006 CCGAACGTGCTTTTAGGAGT 58.208 50.000 0.00 0.00 0.00 3.85
893 945 3.311106 CGAACGTGCTTTTAGGAGTGTA 58.689 45.455 0.00 0.00 0.00 2.90
1347 1429 1.276421 GTAGCACATCACACCTGACCT 59.724 52.381 0.00 0.00 0.00 3.85
1348 1430 0.035881 AGCACATCACACCTGACCTG 59.964 55.000 0.00 0.00 0.00 4.00
1350 1432 0.957395 CACATCACACCTGACCTGGC 60.957 60.000 0.00 0.00 0.00 4.85
1546 1642 2.354704 CCTCACATTTTGGCCGTCTCTA 60.355 50.000 0.00 0.00 0.00 2.43
1547 1643 3.535561 CTCACATTTTGGCCGTCTCTAT 58.464 45.455 0.00 0.00 0.00 1.98
1548 1644 3.941483 CTCACATTTTGGCCGTCTCTATT 59.059 43.478 0.00 0.00 0.00 1.73
1549 1645 3.689161 TCACATTTTGGCCGTCTCTATTG 59.311 43.478 0.00 0.00 0.00 1.90
1550 1646 2.423538 ACATTTTGGCCGTCTCTATTGC 59.576 45.455 0.00 0.00 0.00 3.56
1590 1686 3.503363 GCACTCCGCTCCATGTGC 61.503 66.667 0.00 0.00 46.66 4.57
1592 1688 4.457496 ACTCCGCTCCATGTGCCG 62.457 66.667 0.00 0.00 0.00 5.69
1622 1718 2.863740 CGGCAGATGAATTAACGCACTA 59.136 45.455 0.00 0.00 0.00 2.74
1627 1723 6.423905 GGCAGATGAATTAACGCACTAATCTA 59.576 38.462 0.00 0.00 0.00 1.98
1651 1757 5.902051 GTGATAACCACTAAGATTACGGC 57.098 43.478 0.00 0.00 42.44 5.68
1652 1758 5.598769 GTGATAACCACTAAGATTACGGCT 58.401 41.667 0.00 0.00 42.44 5.52
1677 1783 4.279145 AGAACAGCCCGATTTCTACTCTA 58.721 43.478 0.00 0.00 0.00 2.43
1679 1785 2.362717 ACAGCCCGATTTCTACTCTAGC 59.637 50.000 0.00 0.00 0.00 3.42
1681 1787 2.362717 AGCCCGATTTCTACTCTAGCAC 59.637 50.000 0.00 0.00 0.00 4.40
1683 1789 3.797184 GCCCGATTTCTACTCTAGCACTG 60.797 52.174 0.00 0.00 0.00 3.66
1688 1797 5.537188 GATTTCTACTCTAGCACTGATGGG 58.463 45.833 0.00 0.00 0.00 4.00
1691 1959 5.125367 TCTACTCTAGCACTGATGGGTTA 57.875 43.478 0.00 0.00 0.00 2.85
1697 1965 3.508845 AGCACTGATGGGTTACTGTTT 57.491 42.857 0.00 0.00 0.00 2.83
1717 1985 2.435938 TGCAGGGACGGAATTCGC 60.436 61.111 0.00 0.00 43.89 4.70
1803 2071 0.250338 GAGGCAACGAGGGACAACTT 60.250 55.000 0.00 0.00 46.39 2.66
2161 2429 0.876342 GGAGGAATCCGTAGCGCAAG 60.876 60.000 11.47 0.00 43.44 4.01
2162 2430 0.876342 GAGGAATCCGTAGCGCAAGG 60.876 60.000 11.47 10.08 38.28 3.61
2163 2431 2.534903 GGAATCCGTAGCGCAAGGC 61.535 63.158 11.47 0.00 44.05 4.35
2172 2440 1.801309 TAGCGCAAGGCCACCAAAAC 61.801 55.000 11.47 0.00 45.17 2.43
2213 2696 3.690475 AGTGCATGACTCACTTGATCA 57.310 42.857 0.00 0.00 41.61 2.92
2257 2740 4.064388 GGGCATTTCTAGCAGATCTCTTC 58.936 47.826 0.00 0.00 0.00 2.87
2284 2769 5.529800 GGTAAACTGTCAAAAGTGCTCCTTA 59.470 40.000 0.00 0.00 31.48 2.69
2442 2930 9.862371 ATAGCATAATTCCATAACTTCTAGACG 57.138 33.333 0.00 0.00 0.00 4.18
2451 2939 9.888878 TTCCATAACTTCTAGACGTTAATATCG 57.111 33.333 21.53 10.53 0.00 2.92
2489 2984 6.303054 TCATCACCTAAACCAAGAACATCAA 58.697 36.000 0.00 0.00 0.00 2.57
2490 2985 6.206634 TCATCACCTAAACCAAGAACATCAAC 59.793 38.462 0.00 0.00 0.00 3.18
2536 3031 1.065926 AGAGCTGCAAATGATCCGTCA 60.066 47.619 1.02 0.00 39.04 4.35
2586 3081 4.434483 GGAATGCCCGGTTCCTTT 57.566 55.556 13.72 0.86 41.52 3.11
2610 3106 0.389025 CCGTTGCCTTGGAAGCTTTT 59.611 50.000 0.00 0.00 0.00 2.27
2616 3112 2.225242 TGCCTTGGAAGCTTTTATCCCA 60.225 45.455 0.00 0.00 34.68 4.37
2624 3120 5.072741 GGAAGCTTTTATCCCATATGCTCA 58.927 41.667 0.00 0.00 0.00 4.26
2646 3142 1.227527 CACGTCTGCTCCAACCACA 60.228 57.895 0.00 0.00 0.00 4.17
2669 3165 0.593518 CGAAGATCAGCTCGTCGCAT 60.594 55.000 0.00 0.00 46.13 4.73
2742 3240 9.760660 GAGTGTATTTTGTATGAACTTGATGAC 57.239 33.333 0.00 0.00 0.00 3.06
2757 3255 6.162079 ACTTGATGACAGTGAGAGTGTATTG 58.838 40.000 0.00 0.00 30.64 1.90
2769 3267 7.815068 AGTGAGAGTGTATTGTGTATGAACTTC 59.185 37.037 0.00 0.00 0.00 3.01
2778 3276 9.760660 GTATTGTGTATGAACTTCATGAAAGAC 57.239 33.333 13.66 2.78 37.70 3.01
2804 3302 3.536158 GCAGTTGCAATGACGAGTTTA 57.464 42.857 0.59 0.00 41.59 2.01
2816 3781 7.949962 GCAATGACGAGTTTAAAAATAAAAGGC 59.050 33.333 0.00 0.00 0.00 4.35
2874 3839 2.092646 TGAGTGGTGGTTTGTAGCAACT 60.093 45.455 0.00 0.00 40.16 3.16
2891 3857 2.942376 CAACTGTGGTATGTGTGTGTGT 59.058 45.455 0.00 0.00 0.00 3.72
2904 3870 2.432874 TGTGTGTGTGTTGTAGGTAGCT 59.567 45.455 0.00 0.00 0.00 3.32
2914 3880 1.697432 TGTAGGTAGCTGGTTGCAACT 59.303 47.619 27.64 11.65 45.94 3.16
3010 3976 2.264794 GTGCCCCGATCTCACGTT 59.735 61.111 0.00 0.00 0.00 3.99
3027 3993 1.667756 CGTTGACGTCGATGGGAGAAA 60.668 52.381 16.12 0.00 34.11 2.52
3046 4012 3.703001 AAAGAGCCGAGATGGAAGAAA 57.297 42.857 0.00 0.00 42.00 2.52
3073 4039 1.139095 GGGTAGAGTCGGTCAAGCG 59.861 63.158 0.00 0.00 0.00 4.68
3079 4045 2.811317 GTCGGTCAAGCGGCTGAG 60.811 66.667 1.81 0.00 0.00 3.35
3083 4049 4.785453 GTCAAGCGGCTGAGGGGG 62.785 72.222 1.81 0.00 0.00 5.40
3101 4067 3.319137 GGGGGAAAGAAAAAGATGTGC 57.681 47.619 0.00 0.00 0.00 4.57
3102 4068 2.632512 GGGGGAAAGAAAAAGATGTGCA 59.367 45.455 0.00 0.00 0.00 4.57
3105 4071 3.069443 GGGAAAGAAAAAGATGTGCACCA 59.931 43.478 15.69 2.61 0.00 4.17
3107 4073 4.301628 GAAAGAAAAAGATGTGCACCAGG 58.698 43.478 15.69 0.00 0.00 4.45
3108 4074 2.242043 AGAAAAAGATGTGCACCAGGG 58.758 47.619 15.69 0.00 0.00 4.45
3130 4104 4.348168 GGAGGGATAAGGAAAGACTATGCA 59.652 45.833 0.00 0.00 0.00 3.96
3136 4110 4.322057 AAGGAAAGACTATGCATGGGTT 57.678 40.909 15.11 4.64 0.00 4.11
3141 4115 1.212935 AGACTATGCATGGGTTCCACC 59.787 52.381 15.11 0.00 35.80 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.481644 GGTTCACTTAGATCCATGATTGAGAC 59.518 42.308 0.00 0.00 36.33 3.36
11 12 4.278310 TCTCGGTTCACTTAGATCCATGA 58.722 43.478 0.00 0.00 36.12 3.07
51 52 7.558161 TTAGAAATCATGTGTAGCTTGATGG 57.442 36.000 0.00 0.00 40.49 3.51
117 118 8.918202 TTATTTCTAAGTTGGTGATCACACTT 57.082 30.769 25.92 25.92 45.32 3.16
118 119 8.784043 GTTTATTTCTAAGTTGGTGATCACACT 58.216 33.333 26.47 18.84 45.32 3.55
119 120 8.564574 TGTTTATTTCTAAGTTGGTGATCACAC 58.435 33.333 26.47 16.93 45.27 3.82
120 121 8.684386 TGTTTATTTCTAAGTTGGTGATCACA 57.316 30.769 26.47 10.65 0.00 3.58
121 122 9.774742 GATGTTTATTTCTAAGTTGGTGATCAC 57.225 33.333 17.91 17.91 0.00 3.06
122 123 8.664798 CGATGTTTATTTCTAAGTTGGTGATCA 58.335 33.333 0.00 0.00 0.00 2.92
123 124 8.665685 ACGATGTTTATTTCTAAGTTGGTGATC 58.334 33.333 0.00 0.00 0.00 2.92
124 125 8.561738 ACGATGTTTATTTCTAAGTTGGTGAT 57.438 30.769 0.00 0.00 0.00 3.06
125 126 7.876068 AGACGATGTTTATTTCTAAGTTGGTGA 59.124 33.333 0.00 0.00 0.00 4.02
126 127 8.029642 AGACGATGTTTATTTCTAAGTTGGTG 57.970 34.615 0.00 0.00 0.00 4.17
127 128 7.333672 GGAGACGATGTTTATTTCTAAGTTGGT 59.666 37.037 0.00 0.00 0.00 3.67
128 129 7.549488 AGGAGACGATGTTTATTTCTAAGTTGG 59.451 37.037 0.00 0.00 0.00 3.77
142 144 3.340814 AAATGCTCAGGAGACGATGTT 57.659 42.857 0.00 0.00 0.00 2.71
144 146 3.181503 CCAAAAATGCTCAGGAGACGATG 60.182 47.826 0.00 0.00 0.00 3.84
146 148 2.038426 TCCAAAAATGCTCAGGAGACGA 59.962 45.455 0.00 0.00 0.00 4.20
148 150 4.853924 TTTCCAAAAATGCTCAGGAGAC 57.146 40.909 0.00 0.00 0.00 3.36
173 177 6.570692 TCCTTAAGTATTGGTCGATTGAGAC 58.429 40.000 0.97 0.00 40.25 3.36
177 181 8.122952 GTGAAATCCTTAAGTATTGGTCGATTG 58.877 37.037 0.97 0.00 0.00 2.67
181 185 5.006358 CCGTGAAATCCTTAAGTATTGGTCG 59.994 44.000 0.97 3.89 0.00 4.79
188 192 5.808540 CGATCAACCGTGAAATCCTTAAGTA 59.191 40.000 0.97 0.00 37.30 2.24
193 197 3.328382 TCGATCAACCGTGAAATCCTT 57.672 42.857 0.00 0.00 37.30 3.36
212 216 3.607078 GCATTAAATCCCGCGACAAGATC 60.607 47.826 8.23 0.00 0.00 2.75
220 224 1.066908 ACATTGGCATTAAATCCCGCG 59.933 47.619 0.00 0.00 0.00 6.46
223 227 3.960102 TCCTCACATTGGCATTAAATCCC 59.040 43.478 0.00 0.00 0.00 3.85
229 233 4.576053 CGAATCTTCCTCACATTGGCATTA 59.424 41.667 0.00 0.00 0.00 1.90
233 237 2.632377 TCGAATCTTCCTCACATTGGC 58.368 47.619 0.00 0.00 0.00 4.52
234 238 4.256920 AGTTCGAATCTTCCTCACATTGG 58.743 43.478 0.00 0.00 0.00 3.16
235 239 4.032217 CGAGTTCGAATCTTCCTCACATTG 59.968 45.833 0.00 0.00 43.02 2.82
236 240 4.082190 TCGAGTTCGAATCTTCCTCACATT 60.082 41.667 0.00 0.00 46.30 2.71
237 241 3.444034 TCGAGTTCGAATCTTCCTCACAT 59.556 43.478 0.00 0.00 46.30 3.21
239 243 3.489180 TCGAGTTCGAATCTTCCTCAC 57.511 47.619 0.00 0.00 46.30 3.51
251 255 3.515071 AAAACCGTGAAATCGAGTTCG 57.485 42.857 19.49 10.04 41.45 3.95
252 256 6.183359 GCATTAAAAACCGTGAAATCGAGTTC 60.183 38.462 18.22 18.22 0.00 3.01
253 257 5.627780 GCATTAAAAACCGTGAAATCGAGTT 59.372 36.000 0.00 0.00 0.00 3.01
254 258 5.151389 GCATTAAAAACCGTGAAATCGAGT 58.849 37.500 0.00 0.00 0.00 4.18
256 260 4.023107 TGGCATTAAAAACCGTGAAATCGA 60.023 37.500 0.00 0.00 0.00 3.59
257 261 4.230657 TGGCATTAAAAACCGTGAAATCG 58.769 39.130 0.00 0.00 0.00 3.34
258 262 6.589907 AGATTGGCATTAAAAACCGTGAAATC 59.410 34.615 0.00 0.00 0.00 2.17
259 263 6.463360 AGATTGGCATTAAAAACCGTGAAAT 58.537 32.000 0.00 0.00 0.00 2.17
260 264 5.848406 AGATTGGCATTAAAAACCGTGAAA 58.152 33.333 0.00 0.00 0.00 2.69
261 265 5.461032 AGATTGGCATTAAAAACCGTGAA 57.539 34.783 0.00 0.00 0.00 3.18
262 266 5.221342 ACAAGATTGGCATTAAAAACCGTGA 60.221 36.000 0.00 0.00 0.00 4.35
263 267 4.987912 ACAAGATTGGCATTAAAAACCGTG 59.012 37.500 0.00 0.00 0.00 4.94
264 268 5.208463 ACAAGATTGGCATTAAAAACCGT 57.792 34.783 0.00 0.00 0.00 4.83
265 269 5.614449 GCAACAAGATTGGCATTAAAAACCG 60.614 40.000 0.00 0.00 0.00 4.44
266 270 5.614449 CGCAACAAGATTGGCATTAAAAACC 60.614 40.000 0.00 0.00 0.00 3.27
267 271 5.373262 CGCAACAAGATTGGCATTAAAAAC 58.627 37.500 0.00 0.00 0.00 2.43
268 272 4.450419 CCGCAACAAGATTGGCATTAAAAA 59.550 37.500 0.00 0.00 0.00 1.94
269 273 3.993081 CCGCAACAAGATTGGCATTAAAA 59.007 39.130 0.00 0.00 0.00 1.52
270 274 3.583806 CCGCAACAAGATTGGCATTAAA 58.416 40.909 0.00 0.00 0.00 1.52
271 275 2.094286 CCCGCAACAAGATTGGCATTAA 60.094 45.455 0.00 0.00 0.00 1.40
272 276 1.476085 CCCGCAACAAGATTGGCATTA 59.524 47.619 0.00 0.00 0.00 1.90
273 277 0.247185 CCCGCAACAAGATTGGCATT 59.753 50.000 0.00 0.00 0.00 3.56
274 278 0.611618 TCCCGCAACAAGATTGGCAT 60.612 50.000 0.00 0.00 0.00 4.40
275 279 0.611618 ATCCCGCAACAAGATTGGCA 60.612 50.000 0.00 0.00 0.00 4.92
276 280 0.532115 AATCCCGCAACAAGATTGGC 59.468 50.000 0.00 0.00 0.00 4.52
277 281 1.818060 TGAATCCCGCAACAAGATTGG 59.182 47.619 0.00 0.00 30.52 3.16
278 282 3.574284 TTGAATCCCGCAACAAGATTG 57.426 42.857 0.00 0.00 30.52 2.67
279 283 3.573967 AGTTTGAATCCCGCAACAAGATT 59.426 39.130 0.00 0.00 33.01 2.40
280 284 3.157087 AGTTTGAATCCCGCAACAAGAT 58.843 40.909 0.00 0.00 0.00 2.40
281 285 2.582052 AGTTTGAATCCCGCAACAAGA 58.418 42.857 0.00 0.00 0.00 3.02
282 286 3.052036 CAAGTTTGAATCCCGCAACAAG 58.948 45.455 0.00 0.00 0.00 3.16
283 287 2.690497 TCAAGTTTGAATCCCGCAACAA 59.310 40.909 0.00 0.00 33.55 2.83
284 288 2.302260 TCAAGTTTGAATCCCGCAACA 58.698 42.857 0.00 0.00 33.55 3.33
285 289 3.575965 ATCAAGTTTGAATCCCGCAAC 57.424 42.857 0.00 0.00 41.13 4.17
286 290 4.038522 TGAAATCAAGTTTGAATCCCGCAA 59.961 37.500 0.00 0.00 41.13 4.85
287 291 3.571828 TGAAATCAAGTTTGAATCCCGCA 59.428 39.130 0.00 0.00 41.13 5.69
288 292 3.920412 GTGAAATCAAGTTTGAATCCCGC 59.080 43.478 0.00 0.00 41.13 6.13
289 293 4.485163 GGTGAAATCAAGTTTGAATCCCG 58.515 43.478 0.00 0.00 41.13 5.14
290 294 4.022329 ACGGTGAAATCAAGTTTGAATCCC 60.022 41.667 0.00 4.41 41.13 3.85
291 295 4.917415 CACGGTGAAATCAAGTTTGAATCC 59.083 41.667 0.74 0.00 41.13 3.01
292 296 5.757886 TCACGGTGAAATCAAGTTTGAATC 58.242 37.500 8.68 2.12 41.13 2.52
293 297 5.766150 TCACGGTGAAATCAAGTTTGAAT 57.234 34.783 8.68 0.00 41.13 2.57
294 298 5.568685 TTCACGGTGAAATCAAGTTTGAA 57.431 34.783 20.52 0.00 34.42 2.69
295 299 5.568685 TTTCACGGTGAAATCAAGTTTGA 57.431 34.783 27.49 6.37 41.02 2.69
306 310 6.373216 CCAATACTTAAGGATTTCACGGTGAA 59.627 38.462 19.07 19.07 34.03 3.18
307 311 5.878116 CCAATACTTAAGGATTTCACGGTGA 59.122 40.000 10.41 6.76 0.00 4.02
308 312 5.646360 ACCAATACTTAAGGATTTCACGGTG 59.354 40.000 15.93 0.56 0.00 4.94
309 313 5.812286 ACCAATACTTAAGGATTTCACGGT 58.188 37.500 10.41 11.57 0.00 4.83
310 314 5.878116 TGACCAATACTTAAGGATTTCACGG 59.122 40.000 10.41 10.95 0.00 4.94
311 315 6.978343 TGACCAATACTTAAGGATTTCACG 57.022 37.500 10.41 0.00 0.00 4.35
312 316 7.251281 GCTTGACCAATACTTAAGGATTTCAC 58.749 38.462 10.41 5.57 0.00 3.18
313 317 6.093495 CGCTTGACCAATACTTAAGGATTTCA 59.907 38.462 10.41 10.04 0.00 2.69
314 318 6.093633 ACGCTTGACCAATACTTAAGGATTTC 59.906 38.462 10.41 7.58 0.00 2.17
315 319 5.944007 ACGCTTGACCAATACTTAAGGATTT 59.056 36.000 10.41 0.00 0.00 2.17
316 320 5.354234 CACGCTTGACCAATACTTAAGGATT 59.646 40.000 7.14 7.14 0.00 3.01
317 321 4.876107 CACGCTTGACCAATACTTAAGGAT 59.124 41.667 7.53 0.00 0.00 3.24
318 322 4.020928 TCACGCTTGACCAATACTTAAGGA 60.021 41.667 7.53 0.00 0.00 3.36
319 323 4.250464 TCACGCTTGACCAATACTTAAGG 58.750 43.478 7.53 0.00 0.00 2.69
320 324 5.856126 TTCACGCTTGACCAATACTTAAG 57.144 39.130 0.00 0.00 0.00 1.85
321 325 6.128117 GGATTTCACGCTTGACCAATACTTAA 60.128 38.462 0.00 0.00 0.00 1.85
322 326 5.353123 GGATTTCACGCTTGACCAATACTTA 59.647 40.000 0.00 0.00 0.00 2.24
323 327 4.156008 GGATTTCACGCTTGACCAATACTT 59.844 41.667 0.00 0.00 0.00 2.24
324 328 3.689649 GGATTTCACGCTTGACCAATACT 59.310 43.478 0.00 0.00 0.00 2.12
325 329 3.689649 AGGATTTCACGCTTGACCAATAC 59.310 43.478 0.00 0.00 0.00 1.89
326 330 3.950397 AGGATTTCACGCTTGACCAATA 58.050 40.909 0.00 0.00 0.00 1.90
327 331 2.795329 AGGATTTCACGCTTGACCAAT 58.205 42.857 0.00 0.00 0.00 3.16
328 332 2.270352 AGGATTTCACGCTTGACCAA 57.730 45.000 0.00 0.00 0.00 3.67
329 333 2.270352 AAGGATTTCACGCTTGACCA 57.730 45.000 0.00 0.00 0.00 4.02
330 334 3.751698 ACTTAAGGATTTCACGCTTGACC 59.248 43.478 7.53 0.00 0.00 4.02
331 335 5.358298 AACTTAAGGATTTCACGCTTGAC 57.642 39.130 7.53 0.00 0.00 3.18
332 336 6.205784 CAAAACTTAAGGATTTCACGCTTGA 58.794 36.000 7.53 0.00 0.00 3.02
333 337 5.107875 GCAAAACTTAAGGATTTCACGCTTG 60.108 40.000 7.53 0.00 0.00 4.01
334 338 4.982295 GCAAAACTTAAGGATTTCACGCTT 59.018 37.500 7.53 0.00 0.00 4.68
335 339 4.278419 AGCAAAACTTAAGGATTTCACGCT 59.722 37.500 7.53 9.63 0.00 5.07
336 340 4.546570 AGCAAAACTTAAGGATTTCACGC 58.453 39.130 7.53 7.77 0.00 5.34
337 341 5.977129 ACAAGCAAAACTTAAGGATTTCACG 59.023 36.000 7.53 0.00 36.04 4.35
338 342 6.200854 CCACAAGCAAAACTTAAGGATTTCAC 59.799 38.462 7.53 3.19 36.04 3.18
339 343 6.279882 CCACAAGCAAAACTTAAGGATTTCA 58.720 36.000 7.53 0.00 36.04 2.69
340 344 5.177511 GCCACAAGCAAAACTTAAGGATTTC 59.822 40.000 7.53 0.00 42.97 2.17
341 345 5.056480 GCCACAAGCAAAACTTAAGGATTT 58.944 37.500 7.53 5.15 42.97 2.17
342 346 4.631131 GCCACAAGCAAAACTTAAGGATT 58.369 39.130 7.53 0.00 42.97 3.01
343 347 4.257267 GCCACAAGCAAAACTTAAGGAT 57.743 40.909 7.53 0.00 42.97 3.24
344 348 3.726291 GCCACAAGCAAAACTTAAGGA 57.274 42.857 7.53 0.00 42.97 3.36
364 368 4.524316 TCAAAGTCAAATGGCATGGAAG 57.476 40.909 0.00 0.00 0.00 3.46
370 374 4.527816 AGCCTAAATCAAAGTCAAATGGCA 59.472 37.500 0.00 0.00 39.10 4.92
376 380 6.208599 CCAAAGGTAGCCTAAATCAAAGTCAA 59.791 38.462 0.00 0.00 31.13 3.18
377 381 5.710099 CCAAAGGTAGCCTAAATCAAAGTCA 59.290 40.000 0.00 0.00 31.13 3.41
394 398 1.112315 TTCACCGCAATGCCAAAGGT 61.112 50.000 0.00 0.00 35.24 3.50
434 438 7.466804 ACATTAAAATAGGGAGAAACAGGTGA 58.533 34.615 0.00 0.00 0.00 4.02
524 533 3.888323 TGAACCATTGTGTTGTGCATACT 59.112 39.130 0.00 0.00 0.00 2.12
559 594 2.361438 CGTCAGGTACTTATCAGGGTCC 59.639 54.545 0.00 0.00 34.60 4.46
564 599 3.770666 CCACACGTCAGGTACTTATCAG 58.229 50.000 0.00 0.00 34.60 2.90
612 647 7.946207 TCATGTCACTAAACTTGCCATAAAAA 58.054 30.769 0.00 0.00 0.00 1.94
613 648 7.309133 CCTCATGTCACTAAACTTGCCATAAAA 60.309 37.037 0.00 0.00 0.00 1.52
614 649 6.150976 CCTCATGTCACTAAACTTGCCATAAA 59.849 38.462 0.00 0.00 0.00 1.40
615 650 5.647658 CCTCATGTCACTAAACTTGCCATAA 59.352 40.000 0.00 0.00 0.00 1.90
616 651 5.045942 TCCTCATGTCACTAAACTTGCCATA 60.046 40.000 0.00 0.00 0.00 2.74
617 652 4.012374 CCTCATGTCACTAAACTTGCCAT 58.988 43.478 0.00 0.00 0.00 4.40
618 653 3.072330 TCCTCATGTCACTAAACTTGCCA 59.928 43.478 0.00 0.00 0.00 4.92
619 654 3.674997 TCCTCATGTCACTAAACTTGCC 58.325 45.455 0.00 0.00 0.00 4.52
620 655 4.095483 CCATCCTCATGTCACTAAACTTGC 59.905 45.833 0.00 0.00 0.00 4.01
621 656 4.095483 GCCATCCTCATGTCACTAAACTTG 59.905 45.833 0.00 0.00 0.00 3.16
622 657 4.263462 TGCCATCCTCATGTCACTAAACTT 60.263 41.667 0.00 0.00 0.00 2.66
623 658 3.264193 TGCCATCCTCATGTCACTAAACT 59.736 43.478 0.00 0.00 0.00 2.66
688 723 8.132362 GTGACATATGGTAAGTTTGTGTCAAAA 58.868 33.333 7.80 0.00 43.92 2.44
689 724 7.500892 AGTGACATATGGTAAGTTTGTGTCAAA 59.499 33.333 7.80 0.00 43.92 2.69
690 725 6.995686 AGTGACATATGGTAAGTTTGTGTCAA 59.004 34.615 7.80 0.00 43.92 3.18
691 726 6.426633 CAGTGACATATGGTAAGTTTGTGTCA 59.573 38.462 7.80 0.00 41.27 3.58
692 727 6.649141 TCAGTGACATATGGTAAGTTTGTGTC 59.351 38.462 7.80 0.00 36.09 3.67
693 728 6.530120 TCAGTGACATATGGTAAGTTTGTGT 58.470 36.000 7.80 0.00 0.00 3.72
694 729 7.433708 TTCAGTGACATATGGTAAGTTTGTG 57.566 36.000 7.80 0.00 0.00 3.33
695 730 8.635765 AATTCAGTGACATATGGTAAGTTTGT 57.364 30.769 7.80 0.00 0.00 2.83
696 731 8.950210 AGAATTCAGTGACATATGGTAAGTTTG 58.050 33.333 8.44 0.00 0.00 2.93
698 733 7.066284 GCAGAATTCAGTGACATATGGTAAGTT 59.934 37.037 8.44 0.00 0.00 2.66
699 734 6.540189 GCAGAATTCAGTGACATATGGTAAGT 59.460 38.462 8.44 0.00 0.00 2.24
701 736 6.413892 TGCAGAATTCAGTGACATATGGTAA 58.586 36.000 8.44 0.00 0.00 2.85
703 738 4.847198 TGCAGAATTCAGTGACATATGGT 58.153 39.130 8.44 0.00 0.00 3.55
704 739 5.823209 TTGCAGAATTCAGTGACATATGG 57.177 39.130 8.44 0.00 0.00 2.74
705 740 6.262496 AGGATTGCAGAATTCAGTGACATATG 59.738 38.462 8.44 0.00 0.00 1.78
706 741 6.363065 AGGATTGCAGAATTCAGTGACATAT 58.637 36.000 8.44 0.00 0.00 1.78
708 743 4.597004 AGGATTGCAGAATTCAGTGACAT 58.403 39.130 8.44 0.00 0.00 3.06
725 776 3.612479 GCAATTTCAGTCACGCAAGGATT 60.612 43.478 0.00 0.00 46.39 3.01
742 793 6.652062 GGTCTTGATCTTTTTCAATGGCAATT 59.348 34.615 0.00 0.00 35.20 2.32
751 802 4.516698 GCACTCTGGTCTTGATCTTTTTCA 59.483 41.667 0.00 0.00 0.00 2.69
758 809 1.731720 GTGGCACTCTGGTCTTGATC 58.268 55.000 11.13 0.00 0.00 2.92
759 810 0.036952 CGTGGCACTCTGGTCTTGAT 60.037 55.000 16.72 0.00 0.00 2.57
765 816 2.046892 GATGCGTGGCACTCTGGT 60.047 61.111 16.72 0.00 43.04 4.00
767 818 2.104859 CCAGATGCGTGGCACTCTG 61.105 63.158 21.94 21.94 43.04 3.35
774 825 1.134699 AGTGTCATACCAGATGCGTGG 60.135 52.381 0.00 0.00 44.01 4.94
825 876 5.255710 TGCTAGTCTTAGAGTGCAAGATC 57.744 43.478 10.24 0.00 34.67 2.75
834 885 7.604164 TCTTTGTTGGAATTGCTAGTCTTAGAG 59.396 37.037 0.00 0.00 0.00 2.43
836 887 7.672983 TCTTTGTTGGAATTGCTAGTCTTAG 57.327 36.000 0.00 0.00 0.00 2.18
837 888 8.458573 TTTCTTTGTTGGAATTGCTAGTCTTA 57.541 30.769 0.00 0.00 0.00 2.10
854 905 5.467735 ACGTTCGGCTAAGTAATTTCTTTGT 59.532 36.000 2.43 0.00 0.00 2.83
855 906 5.788531 CACGTTCGGCTAAGTAATTTCTTTG 59.211 40.000 2.43 2.57 0.00 2.77
859 910 3.370061 AGCACGTTCGGCTAAGTAATTTC 59.630 43.478 0.00 0.00 40.47 2.17
885 937 9.601217 GTAGTTTTGATGAACATATACACTCCT 57.399 33.333 0.00 0.00 31.94 3.69
886 938 9.378551 TGTAGTTTTGATGAACATATACACTCC 57.621 33.333 0.00 0.00 31.94 3.85
889 941 8.653338 ACGTGTAGTTTTGATGAACATATACAC 58.347 33.333 0.00 0.00 31.94 2.90
890 942 8.766000 ACGTGTAGTTTTGATGAACATATACA 57.234 30.769 0.00 0.00 31.94 2.29
1364 1448 2.636412 GGAGGGAGCCGGCAAAAAC 61.636 63.158 31.54 16.31 0.00 2.43
1365 1449 2.282887 GGAGGGAGCCGGCAAAAA 60.283 61.111 31.54 0.00 0.00 1.94
1546 1642 4.280174 GGTGCATCTTATCAGAATGGCAAT 59.720 41.667 0.00 0.00 36.79 3.56
1547 1643 3.633525 GGTGCATCTTATCAGAATGGCAA 59.366 43.478 0.00 0.00 36.79 4.52
1548 1644 3.216800 GGTGCATCTTATCAGAATGGCA 58.783 45.455 0.00 0.00 36.16 4.92
1549 1645 2.555757 GGGTGCATCTTATCAGAATGGC 59.444 50.000 0.00 0.00 36.16 4.40
1550 1646 2.810274 CGGGTGCATCTTATCAGAATGG 59.190 50.000 0.00 0.00 36.16 3.16
1604 1700 9.035607 ACTTAGATTAGTGCGTTAATTCATCTG 57.964 33.333 0.00 0.00 0.00 2.90
1651 1757 2.704572 AGAAATCGGGCTGTTCTTCAG 58.295 47.619 0.00 0.00 46.12 3.02
1652 1758 2.859165 AGAAATCGGGCTGTTCTTCA 57.141 45.000 0.00 0.00 0.00 3.02
1663 1769 4.902443 TCAGTGCTAGAGTAGAAATCGG 57.098 45.455 0.00 0.00 0.00 4.18
1670 1776 4.890581 AGTAACCCATCAGTGCTAGAGTAG 59.109 45.833 0.00 0.00 0.00 2.57
1677 1783 3.508845 AAACAGTAACCCATCAGTGCT 57.491 42.857 0.00 0.00 0.00 4.40
1679 1785 4.792704 GCACAAAACAGTAACCCATCAGTG 60.793 45.833 0.00 0.00 0.00 3.66
1681 1787 3.317711 TGCACAAAACAGTAACCCATCAG 59.682 43.478 0.00 0.00 0.00 2.90
1683 1789 3.305335 CCTGCACAAAACAGTAACCCATC 60.305 47.826 0.00 0.00 33.09 3.51
1688 1797 2.286772 CGTCCCTGCACAAAACAGTAAC 60.287 50.000 0.00 0.00 33.09 2.50
1691 1959 1.101049 CCGTCCCTGCACAAAACAGT 61.101 55.000 0.00 0.00 33.09 3.55
1697 1965 0.953471 CGAATTCCGTCCCTGCACAA 60.953 55.000 0.00 0.00 0.00 3.33
1717 1985 1.585521 GTCGCCGATCACACGTAGG 60.586 63.158 0.00 0.00 0.00 3.18
1803 2071 4.724602 GCGTCAGGTCGAGCTGCA 62.725 66.667 34.11 22.04 0.00 4.41
2172 2440 6.417930 GCACTAAAGCTTCTAAAAACACCAAG 59.582 38.462 0.00 0.00 0.00 3.61
2213 2696 4.348168 CCTTATCTGCCCAATGTACCTACT 59.652 45.833 0.00 0.00 0.00 2.57
2257 2740 3.632145 AGCACTTTTGACAGTTTACCCAG 59.368 43.478 0.00 0.00 0.00 4.45
2259 2742 3.004419 GGAGCACTTTTGACAGTTTACCC 59.996 47.826 0.00 0.00 0.00 3.69
2451 2939 9.680315 GTTTAGGTGATGATGAGTAGTATGTAC 57.320 37.037 0.00 0.00 0.00 2.90
2489 2984 1.625315 TGGTGAGAGCTATTGCACTGT 59.375 47.619 3.59 0.00 40.10 3.55
2490 2985 2.391616 TGGTGAGAGCTATTGCACTG 57.608 50.000 3.59 0.00 40.10 3.66
2585 3080 0.395862 TTCCAAGGCAACGGGAACAA 60.396 50.000 0.00 0.00 45.86 2.83
2586 3081 0.821711 CTTCCAAGGCAACGGGAACA 60.822 55.000 0.00 0.00 45.86 3.18
2610 3106 2.562738 CGTGGTCTGAGCATATGGGATA 59.437 50.000 13.18 0.00 0.00 2.59
2646 3142 1.565305 GACGAGCTGATCTTCGCAAT 58.435 50.000 12.54 0.00 0.00 3.56
2669 3165 1.562942 AGATCCTGCTCTTCATTGCCA 59.437 47.619 0.00 0.00 0.00 4.92
2742 3240 7.093354 AGTTCATACACAATACACTCTCACTG 58.907 38.462 0.00 0.00 0.00 3.66
2757 3255 6.467723 ACGTCTTTCATGAAGTTCATACAC 57.532 37.500 17.86 9.18 34.28 2.90
2769 3267 3.665323 GCAACTGCACTACGTCTTTCATG 60.665 47.826 0.00 0.00 41.59 3.07
2794 3292 6.639279 GCTGCCTTTTATTTTTAAACTCGTCA 59.361 34.615 0.00 0.00 0.00 4.35
2804 3302 4.880696 TGCAAGTTGCTGCCTTTTATTTTT 59.119 33.333 27.17 0.00 45.31 1.94
2816 3781 1.202440 ACACATGGTTGCAAGTTGCTG 60.202 47.619 27.17 18.79 45.31 4.41
2853 3818 2.092646 AGTTGCTACAAACCACCACTCA 60.093 45.455 0.13 0.00 0.00 3.41
2874 3839 2.680339 CAACACACACACACATACCACA 59.320 45.455 0.00 0.00 0.00 4.17
2891 3857 1.418264 TGCAACCAGCTACCTACAACA 59.582 47.619 0.00 0.00 45.94 3.33
2904 3870 0.392336 GGCCAATGAAGTTGCAACCA 59.608 50.000 25.62 17.51 36.46 3.67
2914 3880 0.762082 TGCAACCCTTGGCCAATGAA 60.762 50.000 20.85 5.93 0.00 2.57
3010 3976 1.890489 TCTTTTCTCCCATCGACGTCA 59.110 47.619 17.16 3.13 0.00 4.35
3016 3982 0.175760 TCGGCTCTTTTCTCCCATCG 59.824 55.000 0.00 0.00 0.00 3.84
3027 3993 3.922171 ATTTCTTCCATCTCGGCTCTT 57.078 42.857 0.00 0.00 33.14 2.85
3046 4012 2.244252 ACCGACTCTACCCCAACTCTAT 59.756 50.000 0.00 0.00 0.00 1.98
3083 4049 3.069443 TGGTGCACATCTTTTTCTTTCCC 59.931 43.478 20.43 0.00 0.00 3.97
3093 4059 1.687612 CCTCCCTGGTGCACATCTT 59.312 57.895 20.43 0.00 0.00 2.40
3101 4067 1.893315 TTCCTTATCCCTCCCTGGTG 58.107 55.000 0.00 0.00 0.00 4.17
3102 4068 2.047296 TCTTTCCTTATCCCTCCCTGGT 59.953 50.000 0.00 0.00 0.00 4.00
3105 4071 3.805360 AGTCTTTCCTTATCCCTCCCT 57.195 47.619 0.00 0.00 0.00 4.20
3107 4073 4.348168 TGCATAGTCTTTCCTTATCCCTCC 59.652 45.833 0.00 0.00 0.00 4.30
3108 4074 5.552870 TGCATAGTCTTTCCTTATCCCTC 57.447 43.478 0.00 0.00 0.00 4.30
3136 4110 3.260297 ACCATGTGCCTTGGTGGA 58.740 55.556 10.61 0.00 45.71 4.02


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

AutoCloner maintained by Alex Coulton.