Multiple sequence alignment - TraesCS7B01G308800

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 TraesCS7B01G308800 chr7B 100.000 3170 0 0 1 3170 552664406 552667575 0.000000e+00 5854
1 TraesCS7B01G308800 chr7B 87.125 800 101 2 1243 2041 552560863 552560065 0.000000e+00 905
2 TraesCS7B01G308800 chr7B 91.818 220 16 2 538 756 668921412 668921630 3.970000e-79 305
3 TraesCS7B01G308800 chr7B 78.674 347 39 21 2426 2769 552707052 552707366 6.940000e-47 198
4 TraesCS7B01G308800 chr7B 78.674 347 39 21 2426 2769 552754038 552754352 6.940000e-47 198
5 TraesCS7B01G308800 chr7B 83.432 169 19 6 2978 3146 552707757 552707916 7.080000e-32 148
6 TraesCS7B01G308800 chr7B 86.331 139 10 6 2978 3116 552754743 552754872 3.300000e-30 143
7 TraesCS7B01G308800 chr7D 94.608 2411 69 20 788 3170 519270783 519273160 0.000000e+00 3675
8 TraesCS7B01G308800 chr7D 86.733 799 106 0 1243 2041 519261821 519261023 0.000000e+00 889
9 TraesCS7B01G308800 chr7D 80.347 346 40 17 2427 2769 519406979 519407299 1.470000e-58 237
10 TraesCS7B01G308800 chr7D 84.141 227 28 3 1 219 519270384 519270610 2.480000e-51 213
11 TraesCS7B01G308800 chr7D 97.368 76 1 1 467 542 519270712 519270786 9.230000e-26 128
12 TraesCS7B01G308800 chr7A 94.140 2406 84 24 773 3152 595198368 595200742 0.000000e+00 3609
13 TraesCS7B01G308800 chr7A 87.985 799 96 0 1243 2041 595069695 595068897 0.000000e+00 944
14 TraesCS7B01G308800 chr7A 80.635 315 40 13 2458 2769 595281366 595281662 1.140000e-54 224
15 TraesCS7B01G308800 chr7A 87.097 124 6 4 426 549 595197830 595197943 7.130000e-27 132
16 TraesCS7B01G308800 chr5B 93.897 213 10 3 544 756 606309347 606309138 5.100000e-83 318
17 TraesCS7B01G308800 chr2B 92.627 217 15 1 540 756 247807315 247807530 8.540000e-81 311
18 TraesCS7B01G308800 chr2A 93.333 210 13 1 547 756 476402217 476402425 3.070000e-80 309
19 TraesCS7B01G308800 chr2A 91.556 225 15 3 539 763 22242233 22242013 1.100000e-79 307
20 TraesCS7B01G308800 chr2A 91.743 218 16 2 539 756 17808226 17808011 5.140000e-78 302
21 TraesCS7B01G308800 chr6D 92.202 218 15 2 539 756 26353978 26354193 1.100000e-79 307
22 TraesCS7B01G308800 chr4A 92.166 217 15 2 540 756 159363720 159363506 3.970000e-79 305
23 TraesCS7B01G308800 chr1D 88.417 259 20 7 539 791 475199873 475200127 1.430000e-78 303


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 TraesCS7B01G308800 chr7B 552664406 552667575 3169 False 5854.000000 5854 100.0000 1 3170 1 chr7B.!!$F1 3169
1 TraesCS7B01G308800 chr7B 552560065 552560863 798 True 905.000000 905 87.1250 1243 2041 1 chr7B.!!$R1 798
2 TraesCS7B01G308800 chr7D 519270384 519273160 2776 False 1338.666667 3675 92.0390 1 3170 3 chr7D.!!$F2 3169
3 TraesCS7B01G308800 chr7D 519261023 519261821 798 True 889.000000 889 86.7330 1243 2041 1 chr7D.!!$R1 798
4 TraesCS7B01G308800 chr7A 595197830 595200742 2912 False 1870.500000 3609 90.6185 426 3152 2 chr7A.!!$F2 2726
5 TraesCS7B01G308800 chr7A 595068897 595069695 798 True 944.000000 944 87.9850 1243 2041 1 chr7A.!!$R1 798

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
335 344 0.109597 GGCGATTTGTGACAGCCTTG 60.110 55.0 6.35 0.00 44.06 3.61 F
371 380 0.110554 GCATGCAAAGCGCCTTTTTG 60.111 50.0 14.21 14.35 41.33 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1968 1.020333 AGAGGACGTCGACGAAGAGG 61.020 60.000 41.52 14.53 43.02 3.69 R
2196 2673 1.078988 GAGCAGAGCAGAGCAAGCT 60.079 57.895 0.00 0.00 46.82 3.74 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 1.134491 CCTAAATGTCACCGGACCTCC 60.134 57.143 9.46 0.00 43.65 4.30
42 43 4.831307 GCTCGGTCGCGACGTGAT 62.831 66.667 30.99 0.00 0.00 3.06
54 61 2.214181 GACGTGATCGGCTGTGGAGT 62.214 60.000 0.00 0.00 42.52 3.85
61 68 2.743928 GGCTGTGGAGTTCCTGCG 60.744 66.667 0.00 0.00 36.82 5.18
70 77 2.202756 GTTCCTGCGACCGCTAGG 60.203 66.667 19.45 19.45 42.51 3.02
72 79 3.949885 TTCCTGCGACCGCTAGGGA 62.950 63.158 22.66 19.23 43.47 4.20
97 104 2.017049 AGTAGACGATGGCAAATTGGC 58.983 47.619 12.92 12.92 44.03 4.52
110 117 0.179200 AATTGGCAACGAATCGACGC 60.179 50.000 10.55 11.04 42.51 5.19
112 119 3.176578 GGCAACGAATCGACGCGA 61.177 61.111 15.93 4.51 41.13 5.87
119 126 4.508128 AATCGACGCGATGGCCGT 62.508 61.111 15.93 0.00 46.30 5.68
142 151 1.902556 CGGTCGGACTAAATGGGGT 59.097 57.895 8.23 0.00 0.00 4.95
150 159 1.680651 CTAAATGGGGTTGGCGGCA 60.681 57.895 7.97 7.97 0.00 5.69
204 213 2.789715 GGCGGGGTAGGGAAGTACG 61.790 68.421 0.00 0.00 0.00 3.67
207 216 1.718757 CGGGGTAGGGAAGTACGTCG 61.719 65.000 0.00 0.00 0.00 5.12
213 222 4.503314 GGAAGTACGTCGGGGCGG 62.503 72.222 0.00 0.00 35.98 6.13
242 251 2.434359 GCAGTGGTGGCCTACGAC 60.434 66.667 3.32 8.29 38.19 4.34
243 252 2.126071 CAGTGGTGGCCTACGACG 60.126 66.667 3.32 0.00 42.18 5.12
245 254 3.688159 GTGGTGGCCTACGACGGT 61.688 66.667 3.32 0.00 0.00 4.83
246 255 3.687102 TGGTGGCCTACGACGGTG 61.687 66.667 3.32 0.00 0.00 4.94
248 257 3.376078 GTGGCCTACGACGGTGGA 61.376 66.667 3.32 0.00 0.00 4.02
249 258 2.363276 TGGCCTACGACGGTGGAT 60.363 61.111 3.32 0.00 0.00 3.41
250 259 2.416260 GGCCTACGACGGTGGATC 59.584 66.667 11.71 0.00 0.00 3.36
251 260 2.125961 GGCCTACGACGGTGGATCT 61.126 63.158 11.71 0.00 0.00 2.75
252 261 0.820891 GGCCTACGACGGTGGATCTA 60.821 60.000 11.71 0.00 0.00 1.98
253 262 0.310232 GCCTACGACGGTGGATCTAC 59.690 60.000 11.71 0.00 0.00 2.59
254 263 1.964552 CCTACGACGGTGGATCTACT 58.035 55.000 9.27 0.00 0.00 2.57
255 264 2.808202 GCCTACGACGGTGGATCTACTA 60.808 54.545 9.27 0.00 0.00 1.82
256 265 3.672808 CCTACGACGGTGGATCTACTAT 58.327 50.000 9.27 0.00 0.00 2.12
257 266 3.436015 CCTACGACGGTGGATCTACTATG 59.564 52.174 9.27 2.56 0.00 2.23
258 267 2.228059 ACGACGGTGGATCTACTATGG 58.772 52.381 9.27 2.02 0.00 2.74
259 268 1.068472 CGACGGTGGATCTACTATGGC 60.068 57.143 9.27 1.20 0.00 4.40
260 269 1.961394 GACGGTGGATCTACTATGGCA 59.039 52.381 9.27 0.00 0.00 4.92
261 270 1.964223 ACGGTGGATCTACTATGGCAG 59.036 52.381 9.27 0.00 0.00 4.85
262 271 2.239400 CGGTGGATCTACTATGGCAGA 58.761 52.381 9.27 0.00 0.00 4.26
263 272 2.828520 CGGTGGATCTACTATGGCAGAT 59.171 50.000 9.27 0.00 34.19 2.90
264 273 3.367806 CGGTGGATCTACTATGGCAGATG 60.368 52.174 9.27 0.00 31.63 2.90
265 274 3.594134 GTGGATCTACTATGGCAGATGC 58.406 50.000 1.27 4.12 39.36 3.91
266 275 2.232208 TGGATCTACTATGGCAGATGCG 59.768 50.000 6.37 0.00 41.15 4.73
267 276 2.266554 GATCTACTATGGCAGATGCGC 58.733 52.381 0.00 0.00 43.26 6.09
268 277 1.039856 TCTACTATGGCAGATGCGCA 58.960 50.000 14.96 14.96 43.26 6.09
269 278 1.412343 TCTACTATGGCAGATGCGCAA 59.588 47.619 17.11 0.00 43.26 4.85
270 279 2.158971 TCTACTATGGCAGATGCGCAAA 60.159 45.455 17.11 0.00 43.26 3.68
271 280 1.683943 ACTATGGCAGATGCGCAAAT 58.316 45.000 17.11 2.11 43.26 2.32
272 281 2.026641 ACTATGGCAGATGCGCAAATT 58.973 42.857 17.11 0.00 43.26 1.82
273 282 3.213506 ACTATGGCAGATGCGCAAATTA 58.786 40.909 17.11 0.00 43.26 1.40
274 283 2.787601 ATGGCAGATGCGCAAATTAG 57.212 45.000 17.11 4.07 43.26 1.73
275 284 0.740149 TGGCAGATGCGCAAATTAGG 59.260 50.000 17.11 2.01 43.26 2.69
276 285 0.595825 GGCAGATGCGCAAATTAGGC 60.596 55.000 17.11 12.61 43.26 3.93
284 293 2.573920 GCAAATTAGGCGGGTTCCA 58.426 52.632 0.00 0.00 0.00 3.53
285 294 0.455815 GCAAATTAGGCGGGTTCCAG 59.544 55.000 0.00 0.00 0.00 3.86
286 295 0.455815 CAAATTAGGCGGGTTCCAGC 59.544 55.000 5.45 5.45 0.00 4.85
287 296 0.331616 AAATTAGGCGGGTTCCAGCT 59.668 50.000 12.96 3.34 0.00 4.24
288 297 0.394352 AATTAGGCGGGTTCCAGCTG 60.394 55.000 6.78 6.78 0.00 4.24
289 298 2.270874 ATTAGGCGGGTTCCAGCTGG 62.271 60.000 27.87 27.87 0.00 4.85
290 299 3.916438 TAGGCGGGTTCCAGCTGGA 62.916 63.158 32.00 32.00 43.73 3.86
291 300 4.785453 GGCGGGTTCCAGCTGGAG 62.785 72.222 33.16 23.17 46.36 3.86
292 301 4.785453 GCGGGTTCCAGCTGGAGG 62.785 72.222 33.16 23.63 46.36 4.30
293 302 4.785453 CGGGTTCCAGCTGGAGGC 62.785 72.222 33.16 27.66 46.36 4.70
294 303 4.785453 GGGTTCCAGCTGGAGGCG 62.785 72.222 33.16 8.11 46.36 5.52
295 304 4.785453 GGTTCCAGCTGGAGGCGG 62.785 72.222 33.16 7.42 46.36 6.13
302 311 2.282180 GCTGGAGGCGGGTGAAAA 60.282 61.111 0.00 0.00 0.00 2.29
303 312 1.901464 GCTGGAGGCGGGTGAAAAA 60.901 57.895 0.00 0.00 0.00 1.94
304 313 1.956802 CTGGAGGCGGGTGAAAAAC 59.043 57.895 0.00 0.00 0.00 2.43
305 314 1.852067 CTGGAGGCGGGTGAAAAACG 61.852 60.000 0.00 0.00 0.00 3.60
306 315 2.622962 GGAGGCGGGTGAAAAACGG 61.623 63.158 0.00 0.00 0.00 4.44
309 318 2.050442 GCGGGTGAAAAACGGCTG 60.050 61.111 0.00 0.00 0.00 4.85
310 319 2.050442 CGGGTGAAAAACGGCTGC 60.050 61.111 0.00 0.00 0.00 5.25
311 320 2.050442 GGGTGAAAAACGGCTGCG 60.050 61.111 0.00 0.00 0.00 5.18
312 321 2.729491 GGTGAAAAACGGCTGCGC 60.729 61.111 0.00 0.00 0.00 6.09
313 322 2.025441 GTGAAAAACGGCTGCGCA 59.975 55.556 10.98 10.98 0.00 6.09
314 323 2.025441 TGAAAAACGGCTGCGCAC 59.975 55.556 5.66 3.30 0.00 5.34
315 324 3.091022 GAAAAACGGCTGCGCACG 61.091 61.111 17.62 17.62 0.00 5.34
316 325 4.622456 AAAAACGGCTGCGCACGG 62.622 61.111 22.13 17.31 0.00 4.94
328 337 2.175811 GCACGGGCGATTTGTGAC 59.824 61.111 0.00 0.00 35.66 3.67
329 338 2.612567 GCACGGGCGATTTGTGACA 61.613 57.895 0.00 0.00 35.66 3.58
330 339 1.497278 CACGGGCGATTTGTGACAG 59.503 57.895 0.00 0.00 35.66 3.51
331 340 2.325082 ACGGGCGATTTGTGACAGC 61.325 57.895 0.00 0.00 0.00 4.40
332 341 2.877691 GGGCGATTTGTGACAGCC 59.122 61.111 5.11 5.11 46.51 4.85
333 342 1.675641 GGGCGATTTGTGACAGCCT 60.676 57.895 12.46 0.00 46.44 4.58
334 343 1.244019 GGGCGATTTGTGACAGCCTT 61.244 55.000 12.46 0.00 46.44 4.35
335 344 0.109597 GGCGATTTGTGACAGCCTTG 60.110 55.000 6.35 0.00 44.06 3.61
336 345 0.730494 GCGATTTGTGACAGCCTTGC 60.730 55.000 0.00 0.00 0.00 4.01
337 346 0.453282 CGATTTGTGACAGCCTTGCG 60.453 55.000 0.00 0.00 0.00 4.85
338 347 0.593128 GATTTGTGACAGCCTTGCGT 59.407 50.000 0.00 0.00 0.00 5.24
339 348 1.001378 GATTTGTGACAGCCTTGCGTT 60.001 47.619 0.00 0.00 0.00 4.84
340 349 0.814457 TTTGTGACAGCCTTGCGTTT 59.186 45.000 0.00 0.00 0.00 3.60
341 350 0.814457 TTGTGACAGCCTTGCGTTTT 59.186 45.000 0.00 0.00 0.00 2.43
342 351 0.814457 TGTGACAGCCTTGCGTTTTT 59.186 45.000 0.00 0.00 0.00 1.94
343 352 1.199624 GTGACAGCCTTGCGTTTTTG 58.800 50.000 0.00 0.00 0.00 2.44
344 353 0.527385 TGACAGCCTTGCGTTTTTGC 60.527 50.000 0.00 0.00 0.00 3.68
345 354 0.527385 GACAGCCTTGCGTTTTTGCA 60.527 50.000 0.00 0.00 44.61 4.08
351 360 4.100981 TGCGTTTTTGCAACAGCC 57.899 50.000 0.00 0.00 43.02 4.85
352 361 1.875813 TGCGTTTTTGCAACAGCCG 60.876 52.632 0.00 0.19 43.02 5.52
353 362 2.920126 CGTTTTTGCAACAGCCGC 59.080 55.556 0.00 0.00 0.00 6.53
354 363 1.875813 CGTTTTTGCAACAGCCGCA 60.876 52.632 0.00 0.00 37.68 5.69
371 380 0.110554 GCATGCAAAGCGCCTTTTTG 60.111 50.000 14.21 14.35 41.33 2.44
390 399 7.176515 CCTTTTTGGGCTAGCCAATTTTATTTT 59.823 33.333 34.09 0.00 37.98 1.82
391 400 9.225436 CTTTTTGGGCTAGCCAATTTTATTTTA 57.775 29.630 34.09 2.29 37.98 1.52
394 403 8.956533 TTGGGCTAGCCAATTTTATTTTATTC 57.043 30.769 34.09 11.89 37.98 1.75
397 406 9.045223 GGGCTAGCCAATTTTATTTTATTCTTG 57.955 33.333 34.09 0.00 37.98 3.02
398 407 8.551205 GGCTAGCCAATTTTATTTTATTCTTGC 58.449 33.333 29.33 0.00 35.81 4.01
399 408 9.097257 GCTAGCCAATTTTATTTTATTCTTGCA 57.903 29.630 2.29 0.00 0.00 4.08
418 427 9.850628 TTCTTGCAAGAAATTTCTATTGAGATG 57.149 29.630 34.01 13.94 41.75 2.90
419 428 9.017509 TCTTGCAAGAAATTTCTATTGAGATGT 57.982 29.630 26.61 0.00 36.28 3.06
420 429 9.635520 CTTGCAAGAAATTTCTATTGAGATGTT 57.364 29.630 22.31 0.00 36.28 2.71
421 430 8.975410 TGCAAGAAATTTCTATTGAGATGTTG 57.025 30.769 20.76 11.96 36.28 3.33
422 431 8.579006 TGCAAGAAATTTCTATTGAGATGTTGT 58.421 29.630 20.76 0.00 36.28 3.32
423 432 9.415544 GCAAGAAATTTCTATTGAGATGTTGTT 57.584 29.630 20.76 0.00 36.28 2.83
433 442 8.417106 TCTATTGAGATGTTGTTAGAGGATGTC 58.583 37.037 0.00 0.00 0.00 3.06
441 450 3.686016 TGTTAGAGGATGTCTTTTGCCC 58.314 45.455 0.00 0.00 36.64 5.36
456 465 0.324275 TGCCCCTTCATGCCCTAAAC 60.324 55.000 0.00 0.00 0.00 2.01
460 469 0.451783 CCTTCATGCCCTAAACACGC 59.548 55.000 0.00 0.00 0.00 5.34
464 473 1.378514 ATGCCCTAAACACGCCCTG 60.379 57.895 0.00 0.00 0.00 4.45
465 474 3.440415 GCCCTAAACACGCCCTGC 61.440 66.667 0.00 0.00 0.00 4.85
509 520 7.459234 AGATGCTCCAATTCATCATTATCTCA 58.541 34.615 7.40 0.00 41.02 3.27
542 1003 3.423539 TGCTTCACTTGCTTGGAGTAT 57.576 42.857 0.00 0.00 0.00 2.12
543 1004 3.754965 TGCTTCACTTGCTTGGAGTATT 58.245 40.909 0.00 0.00 0.00 1.89
544 1005 3.753272 TGCTTCACTTGCTTGGAGTATTC 59.247 43.478 0.00 0.00 0.00 1.75
545 1006 3.127721 GCTTCACTTGCTTGGAGTATTCC 59.872 47.826 0.00 0.00 44.31 3.01
546 1007 3.350219 TCACTTGCTTGGAGTATTCCC 57.650 47.619 1.20 0.00 43.33 3.97
547 1008 2.912956 TCACTTGCTTGGAGTATTCCCT 59.087 45.455 1.20 0.00 43.33 4.20
548 1009 3.055094 TCACTTGCTTGGAGTATTCCCTC 60.055 47.826 1.20 0.00 43.33 4.30
549 1010 3.054802 CACTTGCTTGGAGTATTCCCTCT 60.055 47.826 1.20 0.00 43.33 3.69
550 1011 3.054802 ACTTGCTTGGAGTATTCCCTCTG 60.055 47.826 1.20 0.00 43.33 3.35
551 1012 2.551270 TGCTTGGAGTATTCCCTCTGT 58.449 47.619 1.20 0.00 43.33 3.41
552 1013 2.912956 TGCTTGGAGTATTCCCTCTGTT 59.087 45.455 1.20 0.00 43.33 3.16
553 1014 3.330701 TGCTTGGAGTATTCCCTCTGTTT 59.669 43.478 1.20 0.00 43.33 2.83
554 1015 3.942115 GCTTGGAGTATTCCCTCTGTTTC 59.058 47.826 1.20 0.00 43.33 2.78
555 1016 4.323868 GCTTGGAGTATTCCCTCTGTTTCT 60.324 45.833 1.20 0.00 43.33 2.52
556 1017 5.804771 GCTTGGAGTATTCCCTCTGTTTCTT 60.805 44.000 1.20 0.00 43.33 2.52
557 1018 5.843019 TGGAGTATTCCCTCTGTTTCTTT 57.157 39.130 1.20 0.00 43.33 2.52
558 1019 6.200878 TGGAGTATTCCCTCTGTTTCTTTT 57.799 37.500 1.20 0.00 43.33 2.27
559 1020 6.610830 TGGAGTATTCCCTCTGTTTCTTTTT 58.389 36.000 1.20 0.00 43.33 1.94
582 1043 9.493206 TTTTTACTCCGCGTATAAAATTTGATC 57.507 29.630 15.68 0.00 29.78 2.92
583 1044 7.773864 TTACTCCGCGTATAAAATTTGATCA 57.226 32.000 4.92 0.00 0.00 2.92
584 1045 6.671614 ACTCCGCGTATAAAATTTGATCAA 57.328 33.333 3.38 3.38 0.00 2.57
585 1046 7.079182 ACTCCGCGTATAAAATTTGATCAAA 57.921 32.000 22.52 22.52 34.46 2.69
586 1047 7.186804 ACTCCGCGTATAAAATTTGATCAAAG 58.813 34.615 24.17 10.49 33.32 2.77
587 1048 7.079182 TCCGCGTATAAAATTTGATCAAAGT 57.921 32.000 24.17 19.88 33.32 2.66
588 1049 7.184106 TCCGCGTATAAAATTTGATCAAAGTC 58.816 34.615 24.17 9.96 33.32 3.01
589 1050 6.964370 CCGCGTATAAAATTTGATCAAAGTCA 59.036 34.615 24.17 14.37 33.32 3.41
590 1051 7.483375 CCGCGTATAAAATTTGATCAAAGTCAA 59.517 33.333 24.17 14.34 36.38 3.18
684 1145 7.459394 GAAAATACATTTCATGGTGCATCTG 57.541 36.000 0.00 0.00 45.58 2.90
685 1146 6.778834 AAATACATTTCATGGTGCATCTGA 57.221 33.333 0.00 0.00 33.60 3.27
686 1147 6.387041 AATACATTTCATGGTGCATCTGAG 57.613 37.500 0.00 0.00 33.60 3.35
687 1148 3.959293 ACATTTCATGGTGCATCTGAGA 58.041 40.909 0.00 0.00 33.60 3.27
688 1149 4.338012 ACATTTCATGGTGCATCTGAGAA 58.662 39.130 0.00 0.00 33.60 2.87
689 1150 4.954202 ACATTTCATGGTGCATCTGAGAAT 59.046 37.500 0.00 1.10 33.60 2.40
690 1151 6.124340 ACATTTCATGGTGCATCTGAGAATA 58.876 36.000 0.00 0.00 33.60 1.75
691 1152 6.776116 ACATTTCATGGTGCATCTGAGAATAT 59.224 34.615 0.00 0.00 33.60 1.28
692 1153 7.287005 ACATTTCATGGTGCATCTGAGAATATT 59.713 33.333 0.00 0.00 33.60 1.28
693 1154 6.628919 TTCATGGTGCATCTGAGAATATTG 57.371 37.500 0.00 0.00 0.00 1.90
694 1155 5.932455 TCATGGTGCATCTGAGAATATTGA 58.068 37.500 0.00 0.00 0.00 2.57
695 1156 6.540083 TCATGGTGCATCTGAGAATATTGAT 58.460 36.000 0.00 0.00 0.00 2.57
696 1157 7.002276 TCATGGTGCATCTGAGAATATTGATT 58.998 34.615 0.00 0.00 0.00 2.57
697 1158 7.504574 TCATGGTGCATCTGAGAATATTGATTT 59.495 33.333 0.00 0.00 0.00 2.17
698 1159 7.268199 TGGTGCATCTGAGAATATTGATTTC 57.732 36.000 0.00 0.00 0.00 2.17
699 1160 6.829811 TGGTGCATCTGAGAATATTGATTTCA 59.170 34.615 0.00 0.00 0.00 2.69
700 1161 7.504574 TGGTGCATCTGAGAATATTGATTTCAT 59.495 33.333 0.00 0.00 0.00 2.57
701 1162 9.006839 GGTGCATCTGAGAATATTGATTTCATA 57.993 33.333 0.00 0.00 0.00 2.15
752 1213 6.759497 AAGTGAGTCAAACTTTACAAAGCT 57.241 33.333 0.00 0.00 39.63 3.74
753 1214 6.759497 AGTGAGTCAAACTTTACAAAGCTT 57.241 33.333 0.00 0.00 39.63 3.74
754 1215 6.555315 AGTGAGTCAAACTTTACAAAGCTTG 58.445 36.000 0.00 10.28 41.23 4.01
755 1216 6.374333 AGTGAGTCAAACTTTACAAAGCTTGA 59.626 34.615 13.75 13.75 44.35 3.02
756 1217 7.027161 GTGAGTCAAACTTTACAAAGCTTGAA 58.973 34.615 17.58 4.98 46.50 2.69
757 1218 7.540745 GTGAGTCAAACTTTACAAAGCTTGAAA 59.459 33.333 17.58 0.38 46.50 2.69
758 1219 7.540745 TGAGTCAAACTTTACAAAGCTTGAAAC 59.459 33.333 17.58 14.94 46.50 2.78
759 1220 7.602753 AGTCAAACTTTACAAAGCTTGAAACT 58.397 30.769 17.58 11.69 46.50 2.66
760 1221 8.088365 AGTCAAACTTTACAAAGCTTGAAACTT 58.912 29.630 17.58 6.11 46.50 2.66
761 1222 8.708742 GTCAAACTTTACAAAGCTTGAAACTTT 58.291 29.630 17.58 1.03 46.50 2.66
762 1223 9.915629 TCAAACTTTACAAAGCTTGAAACTTTA 57.084 25.926 14.88 0.00 43.89 1.85
768 1229 9.973450 TTTACAAAGCTTGAAACTTTATATGCA 57.027 25.926 0.00 0.00 35.62 3.96
769 1230 9.624697 TTACAAAGCTTGAAACTTTATATGCAG 57.375 29.630 0.00 0.00 35.62 4.41
770 1231 7.885297 ACAAAGCTTGAAACTTTATATGCAGA 58.115 30.769 0.00 0.00 35.62 4.26
771 1232 7.809806 ACAAAGCTTGAAACTTTATATGCAGAC 59.190 33.333 0.00 0.00 35.62 3.51
772 1233 7.693969 AAGCTTGAAACTTTATATGCAGACT 57.306 32.000 0.00 0.00 0.00 3.24
773 1234 8.792830 AAGCTTGAAACTTTATATGCAGACTA 57.207 30.769 0.00 0.00 0.00 2.59
774 1235 8.792830 AGCTTGAAACTTTATATGCAGACTAA 57.207 30.769 0.00 0.00 0.00 2.24
775 1236 9.231297 AGCTTGAAACTTTATATGCAGACTAAA 57.769 29.630 0.00 0.00 0.00 1.85
776 1237 9.840427 GCTTGAAACTTTATATGCAGACTAAAA 57.160 29.630 0.00 0.00 0.00 1.52
827 1288 2.650322 TGGAGGGGTTGTGGCTAAATAA 59.350 45.455 0.00 0.00 0.00 1.40
834 1295 5.175127 GGGTTGTGGCTAAATAACATTTGG 58.825 41.667 0.00 0.00 0.00 3.28
993 1458 3.509757 CGGAAGCGAGCGAGAGGA 61.510 66.667 0.00 0.00 0.00 3.71
995 1460 2.115911 GGAAGCGAGCGAGAGGAGA 61.116 63.158 0.00 0.00 0.00 3.71
1050 1518 2.281484 CTCCACCACCACCAACCG 60.281 66.667 0.00 0.00 0.00 4.44
1989 2457 1.610624 GCCATGGACTCCGTCAAGAAA 60.611 52.381 18.40 0.00 33.68 2.52
2074 2542 4.497984 ACACCGCCAACACCAGCA 62.498 61.111 0.00 0.00 0.00 4.41
2075 2543 3.663176 CACCGCCAACACCAGCAG 61.663 66.667 0.00 0.00 0.00 4.24
2176 2644 1.265454 CGTCCCCAAGTAGCCTCCTT 61.265 60.000 0.00 0.00 0.00 3.36
2196 2673 3.381956 TCCCCTCCCCCATGCCTA 61.382 66.667 0.00 0.00 0.00 3.93
2227 2707 2.224475 GCTCTGCTCCATGGTGATGTAT 60.224 50.000 17.98 0.00 0.00 2.29
2228 2708 3.400255 CTCTGCTCCATGGTGATGTATG 58.600 50.000 17.98 0.90 0.00 2.39
2235 2715 5.942236 GCTCCATGGTGATGTATGTATGATT 59.058 40.000 17.98 0.00 0.00 2.57
2239 2719 9.671279 TCCATGGTGATGTATGTATGATTAATC 57.329 33.333 12.58 8.60 0.00 1.75
2351 2839 4.085357 AGCTTGCACCGAATTATGGATA 57.915 40.909 3.31 0.00 0.00 2.59
2352 2840 4.655963 AGCTTGCACCGAATTATGGATAT 58.344 39.130 3.31 0.00 0.00 1.63
2353 2841 5.804639 AGCTTGCACCGAATTATGGATATA 58.195 37.500 3.31 0.00 0.00 0.86
2535 3024 0.609131 AGTCCTTGTCGCCCCAAATG 60.609 55.000 0.00 0.00 0.00 2.32
2684 3175 2.741553 CGCCATTACTAGTGTGCCATCA 60.742 50.000 5.39 0.00 0.00 3.07
2708 3199 7.601130 TCAAACGAAACTGTGTGCTATAATACT 59.399 33.333 0.00 0.00 0.00 2.12
2771 3262 7.232300 CGTCATGTCATATAGCTTGCTTAATG 58.768 38.462 0.00 5.62 0.00 1.90
2812 3303 5.239359 TCATCATTAAGCAAGCATGACAC 57.761 39.130 0.00 0.00 29.74 3.67
2817 3314 0.250467 AAGCAAGCATGACACGGTCT 60.250 50.000 0.00 0.00 33.15 3.85
2819 3316 1.230635 GCAAGCATGACACGGTCTGT 61.231 55.000 0.00 0.00 34.96 3.41
2882 3380 3.988379 ATAACAGTGCAGTTTGTGTGG 57.012 42.857 0.00 0.00 33.07 4.17
2883 3381 1.832883 AACAGTGCAGTTTGTGTGGA 58.167 45.000 0.00 0.00 0.00 4.02
2884 3382 2.057137 ACAGTGCAGTTTGTGTGGAT 57.943 45.000 0.00 0.00 0.00 3.41
2885 3383 1.677576 ACAGTGCAGTTTGTGTGGATG 59.322 47.619 0.00 0.00 0.00 3.51
2886 3384 1.677576 CAGTGCAGTTTGTGTGGATGT 59.322 47.619 0.00 0.00 0.00 3.06
2887 3385 2.099592 CAGTGCAGTTTGTGTGGATGTT 59.900 45.455 0.00 0.00 0.00 2.71
2888 3386 2.358898 AGTGCAGTTTGTGTGGATGTTC 59.641 45.455 0.00 0.00 0.00 3.18
2889 3387 2.358898 GTGCAGTTTGTGTGGATGTTCT 59.641 45.455 0.00 0.00 0.00 3.01
2890 3388 3.023119 TGCAGTTTGTGTGGATGTTCTT 58.977 40.909 0.00 0.00 0.00 2.52
2891 3389 3.446873 TGCAGTTTGTGTGGATGTTCTTT 59.553 39.130 0.00 0.00 0.00 2.52
2892 3390 4.044426 GCAGTTTGTGTGGATGTTCTTTC 58.956 43.478 0.00 0.00 0.00 2.62
2893 3391 4.282068 CAGTTTGTGTGGATGTTCTTTCG 58.718 43.478 0.00 0.00 0.00 3.46
2894 3392 3.945285 AGTTTGTGTGGATGTTCTTTCGT 59.055 39.130 0.00 0.00 0.00 3.85
2895 3393 3.961477 TTGTGTGGATGTTCTTTCGTG 57.039 42.857 0.00 0.00 0.00 4.35
2947 3445 1.773856 TTGTGCTGGGGAATCCGTCA 61.774 55.000 0.00 0.00 38.76 4.35
2977 3475 3.314635 GCCAATACCAATCTGCTTCTCAG 59.685 47.826 0.00 0.00 44.21 3.35
3093 3599 4.532314 CCCTTTATATACGAGGGGTGAC 57.468 50.000 17.48 0.00 45.27 3.67
3118 3624 9.025041 ACACTATCATATTCTTATGGATCGACA 57.975 33.333 0.00 0.00 36.61 4.35
3139 3645 0.616395 TGTATCCGCTCCAACCTCCA 60.616 55.000 0.00 0.00 0.00 3.86
3146 3652 0.322008 GCTCCAACCTCCACTTCCAG 60.322 60.000 0.00 0.00 0.00 3.86
3147 3653 1.059913 CTCCAACCTCCACTTCCAGT 58.940 55.000 0.00 0.00 0.00 4.00
3155 3661 1.002544 CTCCACTTCCAGTCTTCCACC 59.997 57.143 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.816863 AACTCCACAGCCGATCACGT 61.817 55.000 0.00 0.00 37.88 4.49
39 40 0.904865 AGGAACTCCACAGCCGATCA 60.905 55.000 0.00 0.00 38.89 2.92
40 41 0.460987 CAGGAACTCCACAGCCGATC 60.461 60.000 0.00 0.00 34.60 3.69
41 42 1.599047 CAGGAACTCCACAGCCGAT 59.401 57.895 0.00 0.00 34.60 4.18
42 43 3.059982 CAGGAACTCCACAGCCGA 58.940 61.111 0.00 0.00 34.60 5.54
54 61 3.458163 CCCTAGCGGTCGCAGGAA 61.458 66.667 24.42 7.24 44.88 3.36
61 68 1.136500 CTACTTGGTTCCCTAGCGGTC 59.864 57.143 0.00 0.00 29.74 4.79
70 77 1.066430 TGCCATCGTCTACTTGGTTCC 60.066 52.381 0.00 0.00 32.90 3.62
72 79 2.851263 TTGCCATCGTCTACTTGGTT 57.149 45.000 0.00 0.00 32.90 3.67
86 93 1.668337 CGATTCGTTGCCAATTTGCCA 60.668 47.619 0.00 0.00 0.00 4.92
88 95 1.648681 GTCGATTCGTTGCCAATTTGC 59.351 47.619 5.89 0.00 0.00 3.68
97 104 1.269810 CCATCGCGTCGATTCGTTG 59.730 57.895 5.77 10.03 44.59 4.10
99 106 2.954868 GCCATCGCGTCGATTCGT 60.955 61.111 5.77 0.00 44.59 3.85
119 126 3.009192 ATTTAGTCCGACCGCGCCA 62.009 57.895 0.00 0.00 35.83 5.69
123 130 1.523032 CCCCATTTAGTCCGACCGC 60.523 63.158 0.00 0.00 0.00 5.68
124 131 0.251073 AACCCCATTTAGTCCGACCG 59.749 55.000 0.00 0.00 0.00 4.79
131 138 1.680989 GCCGCCAACCCCATTTAGT 60.681 57.895 0.00 0.00 0.00 2.24
167 176 2.442413 CCCCTTTTCCAGCTGCCT 59.558 61.111 8.66 0.00 0.00 4.75
225 234 2.434359 GTCGTAGGCCACCACTGC 60.434 66.667 5.01 0.00 0.00 4.40
226 235 2.126071 CGTCGTAGGCCACCACTG 60.126 66.667 5.01 0.00 0.00 3.66
227 236 3.379445 CCGTCGTAGGCCACCACT 61.379 66.667 5.01 0.00 0.00 4.00
228 237 3.688159 ACCGTCGTAGGCCACCAC 61.688 66.667 5.01 0.00 33.69 4.16
229 238 3.687102 CACCGTCGTAGGCCACCA 61.687 66.667 5.01 0.00 33.69 4.17
230 239 4.446413 CCACCGTCGTAGGCCACC 62.446 72.222 5.01 0.00 33.69 4.61
242 251 2.239400 TCTGCCATAGTAGATCCACCG 58.761 52.381 0.00 0.00 28.67 4.94
243 252 3.618507 GCATCTGCCATAGTAGATCCACC 60.619 52.174 0.00 0.00 42.85 4.61
245 254 2.232208 CGCATCTGCCATAGTAGATCCA 59.768 50.000 0.00 0.00 42.85 3.41
246 255 2.886081 CGCATCTGCCATAGTAGATCC 58.114 52.381 0.00 0.00 42.85 3.36
248 257 1.620323 TGCGCATCTGCCATAGTAGAT 59.380 47.619 5.66 0.00 45.27 1.98
249 258 1.039856 TGCGCATCTGCCATAGTAGA 58.960 50.000 5.66 0.00 39.22 2.59
250 259 1.869774 TTGCGCATCTGCCATAGTAG 58.130 50.000 12.75 0.00 37.91 2.57
251 260 2.323968 TTTGCGCATCTGCCATAGTA 57.676 45.000 12.75 0.00 37.91 1.82
252 261 1.683943 ATTTGCGCATCTGCCATAGT 58.316 45.000 12.75 0.00 37.91 2.12
253 262 2.787601 AATTTGCGCATCTGCCATAG 57.212 45.000 12.75 0.00 37.91 2.23
254 263 2.553602 CCTAATTTGCGCATCTGCCATA 59.446 45.455 12.75 0.00 37.91 2.74
255 264 1.338973 CCTAATTTGCGCATCTGCCAT 59.661 47.619 12.75 0.00 37.91 4.40
256 265 0.740149 CCTAATTTGCGCATCTGCCA 59.260 50.000 12.75 0.00 37.91 4.92
257 266 0.595825 GCCTAATTTGCGCATCTGCC 60.596 55.000 12.75 0.00 37.91 4.85
258 267 0.931662 CGCCTAATTTGCGCATCTGC 60.932 55.000 12.75 7.85 46.01 4.26
259 268 3.153364 CGCCTAATTTGCGCATCTG 57.847 52.632 12.75 0.00 46.01 2.90
266 275 0.455815 CTGGAACCCGCCTAATTTGC 59.544 55.000 0.00 0.00 0.00 3.68
267 276 0.455815 GCTGGAACCCGCCTAATTTG 59.544 55.000 0.00 0.00 0.00 2.32
268 277 0.331616 AGCTGGAACCCGCCTAATTT 59.668 50.000 3.77 0.00 0.00 1.82
269 278 0.394352 CAGCTGGAACCCGCCTAATT 60.394 55.000 5.57 0.00 0.00 1.40
270 279 1.224592 CAGCTGGAACCCGCCTAAT 59.775 57.895 5.57 0.00 0.00 1.73
271 280 2.668632 CAGCTGGAACCCGCCTAA 59.331 61.111 5.57 0.00 0.00 2.69
272 281 3.399181 CCAGCTGGAACCCGCCTA 61.399 66.667 29.88 0.00 37.39 3.93
274 283 4.785453 CTCCAGCTGGAACCCGCC 62.785 72.222 34.30 0.00 44.91 6.13
275 284 4.785453 CCTCCAGCTGGAACCCGC 62.785 72.222 34.30 0.00 44.91 6.13
276 285 4.785453 GCCTCCAGCTGGAACCCG 62.785 72.222 34.30 22.67 44.91 5.28
277 286 4.785453 CGCCTCCAGCTGGAACCC 62.785 72.222 34.30 23.01 44.91 4.11
278 287 4.785453 CCGCCTCCAGCTGGAACC 62.785 72.222 34.30 25.31 44.91 3.62
283 292 3.551496 TTTCACCCGCCTCCAGCTG 62.551 63.158 6.78 6.78 40.39 4.24
284 293 2.351924 TTTTTCACCCGCCTCCAGCT 62.352 55.000 0.00 0.00 40.39 4.24
285 294 1.901464 TTTTTCACCCGCCTCCAGC 60.901 57.895 0.00 0.00 38.52 4.85
286 295 1.852067 CGTTTTTCACCCGCCTCCAG 61.852 60.000 0.00 0.00 0.00 3.86
287 296 1.894756 CGTTTTTCACCCGCCTCCA 60.895 57.895 0.00 0.00 0.00 3.86
288 297 2.622962 CCGTTTTTCACCCGCCTCC 61.623 63.158 0.00 0.00 0.00 4.30
289 298 2.951458 CCGTTTTTCACCCGCCTC 59.049 61.111 0.00 0.00 0.00 4.70
290 299 3.292159 GCCGTTTTTCACCCGCCT 61.292 61.111 0.00 0.00 0.00 5.52
291 300 3.292159 AGCCGTTTTTCACCCGCC 61.292 61.111 0.00 0.00 0.00 6.13
292 301 2.050442 CAGCCGTTTTTCACCCGC 60.050 61.111 0.00 0.00 0.00 6.13
293 302 2.050442 GCAGCCGTTTTTCACCCG 60.050 61.111 0.00 0.00 0.00 5.28
294 303 2.050442 CGCAGCCGTTTTTCACCC 60.050 61.111 0.00 0.00 0.00 4.61
311 320 2.175811 GTCACAAATCGCCCGTGC 59.824 61.111 0.00 0.00 0.00 5.34
312 321 1.497278 CTGTCACAAATCGCCCGTG 59.503 57.895 0.00 0.00 0.00 4.94
313 322 2.325082 GCTGTCACAAATCGCCCGT 61.325 57.895 0.00 0.00 0.00 5.28
314 323 2.480555 GCTGTCACAAATCGCCCG 59.519 61.111 0.00 0.00 0.00 6.13
315 324 1.244019 AAGGCTGTCACAAATCGCCC 61.244 55.000 2.18 0.00 41.60 6.13
316 325 0.109597 CAAGGCTGTCACAAATCGCC 60.110 55.000 0.00 0.00 40.99 5.54
317 326 0.730494 GCAAGGCTGTCACAAATCGC 60.730 55.000 0.00 0.00 0.00 4.58
318 327 0.453282 CGCAAGGCTGTCACAAATCG 60.453 55.000 0.00 0.00 0.00 3.34
319 328 0.593128 ACGCAAGGCTGTCACAAATC 59.407 50.000 0.00 0.00 46.39 2.17
320 329 1.032014 AACGCAAGGCTGTCACAAAT 58.968 45.000 0.00 0.00 46.39 2.32
321 330 0.814457 AAACGCAAGGCTGTCACAAA 59.186 45.000 0.00 0.00 46.39 2.83
322 331 0.814457 AAAACGCAAGGCTGTCACAA 59.186 45.000 0.00 0.00 46.39 3.33
323 332 0.814457 AAAAACGCAAGGCTGTCACA 59.186 45.000 0.00 0.00 46.39 3.58
324 333 1.199624 CAAAAACGCAAGGCTGTCAC 58.800 50.000 0.00 0.00 46.39 3.67
325 334 0.527385 GCAAAAACGCAAGGCTGTCA 60.527 50.000 0.00 0.00 46.39 3.58
326 335 0.527385 TGCAAAAACGCAAGGCTGTC 60.527 50.000 0.00 0.00 46.39 3.51
327 336 0.108424 TTGCAAAAACGCAAGGCTGT 60.108 45.000 0.00 0.00 46.61 4.40
328 337 2.675519 TTGCAAAAACGCAAGGCTG 58.324 47.368 0.00 0.00 46.61 4.85
334 343 1.875813 CGGCTGTTGCAAAAACGCA 60.876 52.632 0.00 0.00 41.91 5.24
335 344 2.920126 CGGCTGTTGCAAAAACGC 59.080 55.556 0.00 0.00 41.91 4.84
336 345 1.214373 ATGCGGCTGTTGCAAAAACG 61.214 50.000 0.00 4.75 46.87 3.60
337 346 0.232816 CATGCGGCTGTTGCAAAAAC 59.767 50.000 0.00 0.00 46.87 2.43
338 347 1.497223 GCATGCGGCTGTTGCAAAAA 61.497 50.000 15.17 0.00 46.87 1.94
339 348 1.955157 GCATGCGGCTGTTGCAAAA 60.955 52.632 15.17 0.00 46.87 2.44
340 349 2.356075 GCATGCGGCTGTTGCAAA 60.356 55.556 15.17 0.00 46.87 3.68
341 350 3.603671 TGCATGCGGCTGTTGCAA 61.604 55.556 19.01 0.00 46.87 4.08
343 352 2.356075 TTTGCATGCGGCTGTTGC 60.356 55.556 14.09 13.70 45.15 4.17
344 353 2.377310 GCTTTGCATGCGGCTGTTG 61.377 57.895 14.09 0.00 45.15 3.33
345 354 2.048877 GCTTTGCATGCGGCTGTT 60.049 55.556 14.09 0.00 45.15 3.16
371 380 9.045223 CAAGAATAAAATAAAATTGGCTAGCCC 57.955 33.333 30.81 13.48 34.56 5.19
376 385 9.723601 TCTTGCAAGAATAAAATAAAATTGGCT 57.276 25.926 26.61 0.00 30.73 4.75
394 403 9.635520 AACATCTCAATAGAAATTTCTTGCAAG 57.364 29.630 25.02 20.81 38.70 4.01
397 406 8.976986 ACAACATCTCAATAGAAATTTCTTGC 57.023 30.769 25.02 0.00 38.70 4.01
405 414 9.605275 CATCCTCTAACAACATCTCAATAGAAA 57.395 33.333 0.00 0.00 34.73 2.52
406 415 8.762645 ACATCCTCTAACAACATCTCAATAGAA 58.237 33.333 0.00 0.00 34.73 2.10
416 425 5.183904 GGCAAAAGACATCCTCTAACAACAT 59.816 40.000 0.00 0.00 0.00 2.71
417 426 4.518970 GGCAAAAGACATCCTCTAACAACA 59.481 41.667 0.00 0.00 0.00 3.33
418 427 4.082733 GGGCAAAAGACATCCTCTAACAAC 60.083 45.833 0.00 0.00 0.00 3.32
419 428 4.079253 GGGCAAAAGACATCCTCTAACAA 58.921 43.478 0.00 0.00 0.00 2.83
420 429 3.561313 GGGGCAAAAGACATCCTCTAACA 60.561 47.826 0.00 0.00 0.00 2.41
421 430 3.017442 GGGGCAAAAGACATCCTCTAAC 58.983 50.000 0.00 0.00 0.00 2.34
422 431 2.919602 AGGGGCAAAAGACATCCTCTAA 59.080 45.455 0.00 0.00 0.00 2.10
423 432 2.562296 AGGGGCAAAAGACATCCTCTA 58.438 47.619 0.00 0.00 0.00 2.43
424 433 1.376649 AGGGGCAAAAGACATCCTCT 58.623 50.000 0.00 0.00 0.00 3.69
433 442 0.906282 AGGGCATGAAGGGGCAAAAG 60.906 55.000 0.00 0.00 0.00 2.27
441 450 0.451783 GCGTGTTTAGGGCATGAAGG 59.548 55.000 0.00 0.00 0.00 3.46
460 469 1.246056 CCATATCATTGGGCGCAGGG 61.246 60.000 10.83 0.20 32.80 4.45
509 520 5.564259 GCAAGTGAAGCAACATGATCTCTTT 60.564 40.000 0.00 0.00 0.00 2.52
556 1017 9.493206 GATCAAATTTTATACGCGGAGTAAAAA 57.507 29.630 21.01 16.23 39.04 1.94
557 1018 8.666573 TGATCAAATTTTATACGCGGAGTAAAA 58.333 29.630 20.07 20.07 39.04 1.52
558 1019 8.199176 TGATCAAATTTTATACGCGGAGTAAA 57.801 30.769 12.47 7.11 39.04 2.01
559 1020 7.773864 TGATCAAATTTTATACGCGGAGTAA 57.226 32.000 12.47 3.37 39.04 2.24
560 1021 7.773864 TTGATCAAATTTTATACGCGGAGTA 57.226 32.000 12.47 0.00 40.03 2.59
561 1022 6.671614 TTGATCAAATTTTATACGCGGAGT 57.328 33.333 12.47 0.00 0.00 3.85
562 1023 7.186804 ACTTTGATCAAATTTTATACGCGGAG 58.813 34.615 20.76 6.87 0.00 4.63
563 1024 7.079182 ACTTTGATCAAATTTTATACGCGGA 57.921 32.000 20.76 0.00 0.00 5.54
564 1025 6.964370 TGACTTTGATCAAATTTTATACGCGG 59.036 34.615 20.76 7.58 0.00 6.46
565 1026 7.946918 TGACTTTGATCAAATTTTATACGCG 57.053 32.000 20.76 3.53 0.00 6.01
660 1121 7.259882 TCAGATGCACCATGAAATGTATTTTC 58.740 34.615 0.00 0.00 44.81 2.29
661 1122 7.123098 TCTCAGATGCACCATGAAATGTATTTT 59.877 33.333 0.00 0.00 44.81 1.82
662 1123 6.604396 TCTCAGATGCACCATGAAATGTATTT 59.396 34.615 0.00 0.00 44.81 1.40
663 1124 6.124340 TCTCAGATGCACCATGAAATGTATT 58.876 36.000 0.00 0.00 44.81 1.89
664 1125 5.687780 TCTCAGATGCACCATGAAATGTAT 58.312 37.500 0.00 0.00 44.81 2.29
665 1126 5.101648 TCTCAGATGCACCATGAAATGTA 57.898 39.130 0.00 0.00 44.81 2.29
666 1127 3.959293 TCTCAGATGCACCATGAAATGT 58.041 40.909 0.00 0.00 44.81 2.71
667 1128 4.976224 TTCTCAGATGCACCATGAAATG 57.024 40.909 0.00 0.00 46.21 2.32
668 1129 7.504574 TCAATATTCTCAGATGCACCATGAAAT 59.495 33.333 0.00 0.41 0.00 2.17
669 1130 6.829811 TCAATATTCTCAGATGCACCATGAAA 59.170 34.615 0.00 0.00 0.00 2.69
670 1131 6.358991 TCAATATTCTCAGATGCACCATGAA 58.641 36.000 0.00 0.00 0.00 2.57
671 1132 5.932455 TCAATATTCTCAGATGCACCATGA 58.068 37.500 0.00 0.00 0.00 3.07
672 1133 6.819397 ATCAATATTCTCAGATGCACCATG 57.181 37.500 0.00 0.00 0.00 3.66
673 1134 7.504574 TGAAATCAATATTCTCAGATGCACCAT 59.495 33.333 0.00 0.00 0.00 3.55
674 1135 6.829811 TGAAATCAATATTCTCAGATGCACCA 59.170 34.615 0.00 0.00 0.00 4.17
675 1136 7.268199 TGAAATCAATATTCTCAGATGCACC 57.732 36.000 0.00 0.00 0.00 5.01
726 1187 8.903820 AGCTTTGTAAAGTTTGACTCACTTTAT 58.096 29.630 8.17 0.00 44.58 1.40
727 1188 8.276252 AGCTTTGTAAAGTTTGACTCACTTTA 57.724 30.769 0.00 1.91 41.68 1.85
728 1189 7.158099 AGCTTTGTAAAGTTTGACTCACTTT 57.842 32.000 0.00 3.70 44.78 2.66
729 1190 6.759497 AGCTTTGTAAAGTTTGACTCACTT 57.241 33.333 0.00 0.00 38.28 3.16
730 1191 6.759497 AAGCTTTGTAAAGTTTGACTCACT 57.241 33.333 5.78 0.00 37.92 3.41
742 1203 9.973450 TGCATATAAAGTTTCAAGCTTTGTAAA 57.027 25.926 9.35 0.00 36.88 2.01
743 1204 9.624697 CTGCATATAAAGTTTCAAGCTTTGTAA 57.375 29.630 9.35 0.00 36.88 2.41
744 1205 9.008965 TCTGCATATAAAGTTTCAAGCTTTGTA 57.991 29.630 9.35 7.47 36.88 2.41
745 1206 7.809806 GTCTGCATATAAAGTTTCAAGCTTTGT 59.190 33.333 9.35 5.45 36.88 2.83
746 1207 8.025445 AGTCTGCATATAAAGTTTCAAGCTTTG 58.975 33.333 9.35 0.00 36.88 2.77
747 1208 8.115490 AGTCTGCATATAAAGTTTCAAGCTTT 57.885 30.769 4.51 4.51 39.26 3.51
748 1209 7.693969 AGTCTGCATATAAAGTTTCAAGCTT 57.306 32.000 0.00 0.00 0.00 3.74
749 1210 8.792830 TTAGTCTGCATATAAAGTTTCAAGCT 57.207 30.769 0.00 0.00 0.00 3.74
750 1211 9.840427 TTTTAGTCTGCATATAAAGTTTCAAGC 57.160 29.630 0.00 0.00 0.00 4.01
786 1247 9.554395 CCCTCCAAACAAAAATGTTTATTACTT 57.446 29.630 6.62 0.00 39.68 2.24
787 1248 8.154203 CCCCTCCAAACAAAAATGTTTATTACT 58.846 33.333 6.62 0.00 39.68 2.24
788 1249 7.934665 ACCCCTCCAAACAAAAATGTTTATTAC 59.065 33.333 6.62 0.00 39.68 1.89
789 1250 8.035448 ACCCCTCCAAACAAAAATGTTTATTA 57.965 30.769 6.62 0.00 39.68 0.98
790 1251 6.905736 ACCCCTCCAAACAAAAATGTTTATT 58.094 32.000 6.62 0.00 39.68 1.40
827 1288 3.243359 ACATGTCCTCCAACCAAATGT 57.757 42.857 0.00 0.00 0.00 2.71
834 1295 2.286365 TTCCCAACATGTCCTCCAAC 57.714 50.000 0.00 0.00 0.00 3.77
918 1380 1.092921 TTGTGTGCTGTGTTCGGGTC 61.093 55.000 0.00 0.00 0.00 4.46
992 1457 3.434637 GAAGACGACAGCATCTTCTCTC 58.565 50.000 6.72 1.80 44.94 3.20
993 1458 2.165437 GGAAGACGACAGCATCTTCTCT 59.835 50.000 12.37 0.00 46.70 3.10
995 1460 1.895798 TGGAAGACGACAGCATCTTCT 59.104 47.619 12.37 3.79 46.70 2.85
1093 1561 2.044946 GGGCGACTGGAATTGGCT 60.045 61.111 0.00 0.00 0.00 4.75
1165 1633 2.513666 GATGGCGCGGATTGTGGA 60.514 61.111 8.83 0.00 0.00 4.02
1188 1656 4.124351 TAGTCGAACGGCTGGGCG 62.124 66.667 14.67 14.67 0.00 6.13
1428 1896 3.453070 GAGGATGGAGGTGGCGAGC 62.453 68.421 0.00 0.00 0.00 5.03
1500 1968 1.020333 AGAGGACGTCGACGAAGAGG 61.020 60.000 41.52 14.53 43.02 3.69
2176 2644 4.843331 GCATGGGGGAGGGGAGGA 62.843 72.222 0.00 0.00 0.00 3.71
2196 2673 1.078988 GAGCAGAGCAGAGCAAGCT 60.079 57.895 0.00 0.00 46.82 3.74
2227 2707 8.886719 CAGCAAAGAACTGAGATTAATCATACA 58.113 33.333 17.56 12.43 37.32 2.29
2228 2708 8.341173 CCAGCAAAGAACTGAGATTAATCATAC 58.659 37.037 17.56 8.83 37.32 2.39
2235 2715 5.489792 AGACCAGCAAAGAACTGAGATTA 57.510 39.130 0.00 0.00 37.32 1.75
2239 2719 6.166279 TGTATAAGACCAGCAAAGAACTGAG 58.834 40.000 0.00 0.00 37.32 3.35
2535 3024 0.680061 AGAGGGGTCACTGACGAAAC 59.320 55.000 3.04 0.00 32.65 2.78
2684 3175 7.900782 AGTATTATAGCACACAGTTTCGTTT 57.099 32.000 0.00 0.00 0.00 3.60
2708 3199 7.540400 CGCTTCCATGATGTGTAATTAAACAAA 59.460 33.333 12.46 4.98 0.00 2.83
2771 3262 5.237127 TGATGATCATCCGACTAAACATTGC 59.763 40.000 28.61 3.47 37.02 3.56
2812 3303 2.028476 TGGTTGGATGACTTACAGACCG 60.028 50.000 0.00 0.00 33.78 4.79
2817 3314 3.719268 ATGCTGGTTGGATGACTTACA 57.281 42.857 0.00 0.00 0.00 2.41
2873 3371 4.035017 CACGAAAGAACATCCACACAAAC 58.965 43.478 0.00 0.00 0.00 2.93
2882 3380 7.219917 TGAATTTTTCACACACGAAAGAACATC 59.780 33.333 0.00 0.00 36.31 3.06
2883 3381 7.032580 TGAATTTTTCACACACGAAAGAACAT 58.967 30.769 0.00 0.00 36.31 2.71
2884 3382 6.382608 TGAATTTTTCACACACGAAAGAACA 58.617 32.000 0.00 0.00 36.31 3.18
2885 3383 6.745450 TCTGAATTTTTCACACACGAAAGAAC 59.255 34.615 0.00 0.00 36.31 3.01
2886 3384 6.745450 GTCTGAATTTTTCACACACGAAAGAA 59.255 34.615 0.00 0.00 36.31 2.52
2887 3385 6.255215 GTCTGAATTTTTCACACACGAAAGA 58.745 36.000 0.00 0.00 36.31 2.52
2888 3386 5.169561 CGTCTGAATTTTTCACACACGAAAG 59.830 40.000 0.00 0.00 36.31 2.62
2889 3387 5.025190 CGTCTGAATTTTTCACACACGAAA 58.975 37.500 0.00 0.00 35.63 3.46
2890 3388 4.093703 ACGTCTGAATTTTTCACACACGAA 59.906 37.500 14.01 0.00 36.43 3.85
2891 3389 3.619483 ACGTCTGAATTTTTCACACACGA 59.381 39.130 14.01 0.00 36.43 4.35
2892 3390 3.935450 ACGTCTGAATTTTTCACACACG 58.065 40.909 0.00 0.00 37.77 4.49
2893 3391 6.626199 AAAACGTCTGAATTTTTCACACAC 57.374 33.333 0.00 0.00 35.46 3.82
2894 3392 7.753659 TCTAAAACGTCTGAATTTTTCACACA 58.246 30.769 6.30 0.00 35.46 3.72
2895 3393 7.376072 CCTCTAAAACGTCTGAATTTTTCACAC 59.624 37.037 6.30 0.00 35.46 3.82
2947 3445 5.129815 AGCAGATTGGTATTGGCAAATCATT 59.870 36.000 3.01 0.00 32.57 2.57
2977 3475 6.603599 AGACCTAAATTCTAAGGCATGGTTTC 59.396 38.462 0.00 0.00 36.24 2.78
3021 3527 7.995463 TTGCAAACATAGGTTCTACAAAAAC 57.005 32.000 0.00 0.00 35.82 2.43
3089 3595 9.295214 CGATCCATAAGAATATGATAGTGTCAC 57.705 37.037 0.00 0.00 41.25 3.67
3118 3624 1.141053 GGAGGTTGGAGCGGATACAAT 59.859 52.381 0.00 0.00 33.12 2.71
3122 3628 0.325296 AGTGGAGGTTGGAGCGGATA 60.325 55.000 0.00 0.00 0.00 2.59
3146 3652 2.224305 CCTATCCGAATGGGTGGAAGAC 60.224 54.545 0.00 0.00 37.90 3.01
3147 3653 2.047061 CCTATCCGAATGGGTGGAAGA 58.953 52.381 0.00 0.00 37.90 2.87


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

AutoCloner maintained by Alex Coulton.