Multiple sequence alignment - TraesCS2A01G302500

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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 TraesCS2A01G302500 chr2A 100.000 4628 0 0 1 4628 519343589 519348216 0.000000e+00 8547
1 TraesCS2A01G302500 chr2A 95.359 474 22 0 4155 4628 643200468 643199995 0.000000e+00 754
2 TraesCS2A01G302500 chr2D 97.409 2547 63 3 857 3401 383845890 383848435 0.000000e+00 4335
3 TraesCS2A01G302500 chr2D 96.938 849 14 2 3287 4123 383848434 383849282 0.000000e+00 1413
4 TraesCS2A01G302500 chr2D 96.353 658 10 6 227 874 383845222 383845875 0.000000e+00 1070
5 TraesCS2A01G302500 chr2D 91.979 187 9 5 1 187 383845038 383845218 1.650000e-64 257
6 TraesCS2A01G302500 chr2B 94.226 2338 87 20 1821 4123 454326341 454328665 0.000000e+00 3526
7 TraesCS2A01G302500 chr2B 98.061 980 19 0 857 1836 454325347 454326326 0.000000e+00 1705
8 TraesCS2A01G302500 chr2B 95.570 632 18 4 244 874 454324710 454325332 0.000000e+00 1003
9 TraesCS2A01G302500 chr2B 91.617 334 22 2 4168 4495 450782155 450781822 1.520000e-124 457
10 TraesCS2A01G302500 chr2B 89.305 187 11 5 14 194 454324518 454324701 4.660000e-55 226
11 TraesCS2A01G302500 chr6A 94.433 467 20 2 4168 4628 49744555 49744089 0.000000e+00 713
12 TraesCS2A01G302500 chr4B 92.077 467 31 2 4168 4628 624403177 624403643 0.000000e+00 652
13 TraesCS2A01G302500 chr4A 91.863 467 32 2 4168 4628 677123268 677123734 0.000000e+00 647
14 TraesCS2A01G302500 chr4A 91.649 467 33 2 4168 4628 32411725 32411259 3.900000e-180 641
15 TraesCS2A01G302500 chr4A 95.325 385 18 0 4244 4628 640910583 640910967 3.060000e-171 612
16 TraesCS2A01G302500 chr7B 90.356 477 33 5 4164 4628 92061472 92060997 8.510000e-172 614
17 TraesCS2A01G302500 chr1B 89.507 467 34 5 4168 4628 363452918 363452461 1.120000e-160 577
18 TraesCS2A01G302500 chr1A 83.298 467 45 14 4168 4628 133202519 133202080 2.590000e-107 399


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 TraesCS2A01G302500 chr2A 519343589 519348216 4627 False 8547.00 8547 100.00000 1 4628 1 chr2A.!!$F1 4627
1 TraesCS2A01G302500 chr2D 383845038 383849282 4244 False 1768.75 4335 95.66975 1 4123 4 chr2D.!!$F1 4122
2 TraesCS2A01G302500 chr2B 454324518 454328665 4147 False 1615.00 3526 94.29050 14 4123 4 chr2B.!!$F1 4109

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
651 667 0.404040 TAACCAGCCCTCACCCTTTG 59.596 55.000 0.00 0.00 0.00 2.77 F
1107 1156 1.454847 CCTCGTCCTCCTCTCCCTG 60.455 68.421 0.00 0.00 0.00 4.45 F
2046 2126 2.957060 GGCAACCAAAGGTACCTCC 58.043 57.895 16.64 6.32 33.12 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1588 0.250234 CCTCGCCAATCACCTTCTCA 59.750 55.0 0.0 0.0 0.00 3.27 R
2343 2424 0.674895 CCTTTGGCTCAAGTCCCTCG 60.675 60.0 0.0 0.0 0.00 4.63 R
3882 4104 5.130477 TCAGCTTTACCCCTGAAAGTATAGG 59.870 44.0 0.0 0.0 36.47 2.57 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
35 36 3.967332 AGCCATTCCAAACCAATCAAG 57.033 42.857 0.00 0.00 0.00 3.02
37 38 4.098894 AGCCATTCCAAACCAATCAAGAT 58.901 39.130 0.00 0.00 0.00 2.40
187 195 3.438520 GCCCCCAAAATATCATCCTCCTT 60.439 47.826 0.00 0.00 0.00 3.36
189 197 5.218959 CCCCCAAAATATCATCCTCCTTTT 58.781 41.667 0.00 0.00 0.00 2.27
190 198 5.305386 CCCCCAAAATATCATCCTCCTTTTC 59.695 44.000 0.00 0.00 0.00 2.29
191 199 5.305386 CCCCAAAATATCATCCTCCTTTTCC 59.695 44.000 0.00 0.00 0.00 3.13
192 200 6.138967 CCCAAAATATCATCCTCCTTTTCCT 58.861 40.000 0.00 0.00 0.00 3.36
193 201 6.266330 CCCAAAATATCATCCTCCTTTTCCTC 59.734 42.308 0.00 0.00 0.00 3.71
194 202 6.835488 CCAAAATATCATCCTCCTTTTCCTCA 59.165 38.462 0.00 0.00 0.00 3.86
195 203 7.342799 CCAAAATATCATCCTCCTTTTCCTCAA 59.657 37.037 0.00 0.00 0.00 3.02
196 204 8.752187 CAAAATATCATCCTCCTTTTCCTCAAA 58.248 33.333 0.00 0.00 0.00 2.69
197 205 8.899887 AAATATCATCCTCCTTTTCCTCAAAA 57.100 30.769 0.00 0.00 0.00 2.44
198 206 8.899887 AATATCATCCTCCTTTTCCTCAAAAA 57.100 30.769 0.00 0.00 35.56 1.94
221 229 4.797912 AAAAATCATCCTCCTACCCTCC 57.202 45.455 0.00 0.00 0.00 4.30
222 230 3.438131 AAATCATCCTCCTACCCTCCA 57.562 47.619 0.00 0.00 0.00 3.86
223 231 3.663298 AATCATCCTCCTACCCTCCAT 57.337 47.619 0.00 0.00 0.00 3.41
224 232 2.405618 TCATCCTCCTACCCTCCATG 57.594 55.000 0.00 0.00 0.00 3.66
225 233 1.132721 TCATCCTCCTACCCTCCATGG 60.133 57.143 4.97 4.97 0.00 3.66
266 274 5.010617 ACTTCTCTTTCTCTTCTGACCTGAC 59.989 44.000 0.00 0.00 0.00 3.51
346 354 4.796618 GCAATTGCAATGGCCAAAACAAAT 60.797 37.500 25.78 4.51 41.59 2.32
387 401 1.841556 TCACCACTCACCACTCCCC 60.842 63.158 0.00 0.00 0.00 4.81
416 430 2.037136 CACTAGGCACTGGCACTGC 61.037 63.158 10.23 10.23 42.26 4.40
417 431 2.348620 CTAGGCACTGGCACTGCA 59.651 61.111 18.63 1.09 43.71 4.41
418 432 2.032528 TAGGCACTGGCACTGCAC 59.967 61.111 18.63 9.57 43.71 4.57
419 433 2.460662 CTAGGCACTGGCACTGCACT 62.461 60.000 18.63 14.99 43.71 4.40
420 434 2.736579 TAGGCACTGGCACTGCACTG 62.737 60.000 18.63 0.00 43.71 3.66
422 436 3.667282 CACTGGCACTGCACTGGC 61.667 66.667 12.13 12.13 41.68 4.85
651 667 0.404040 TAACCAGCCCTCACCCTTTG 59.596 55.000 0.00 0.00 0.00 2.77
682 698 5.420409 ACAATCGTCTAATCTTTGGTCTCC 58.580 41.667 0.00 0.00 0.00 3.71
778 795 2.103263 CTGTCCTAAATTCCCCTCCTCG 59.897 54.545 0.00 0.00 0.00 4.63
1107 1156 1.454847 CCTCGTCCTCCTCTCCCTG 60.455 68.421 0.00 0.00 0.00 4.45
2046 2126 2.957060 GGCAACCAAAGGTACCTCC 58.043 57.895 16.64 6.32 33.12 4.30
2138 2219 3.674997 TCTTTCCAGGATGCTTGTGTAC 58.325 45.455 0.00 0.00 31.97 2.90
2144 2225 3.067106 CAGGATGCTTGTGTACGAGTTT 58.933 45.455 0.00 0.00 0.00 2.66
2162 2243 7.138736 ACGAGTTTGTCAATAATGGAACTTTG 58.861 34.615 0.00 0.00 30.36 2.77
2168 2249 5.183713 TGTCAATAATGGAACTTTGGAGCAG 59.816 40.000 0.00 0.00 0.00 4.24
2277 2358 5.006455 GTGCATGTGAGTTACTGATGATCTG 59.994 44.000 0.00 0.00 0.00 2.90
2279 2360 5.814188 GCATGTGAGTTACTGATGATCTGAA 59.186 40.000 6.32 0.00 0.00 3.02
2282 2363 8.890718 CATGTGAGTTACTGATGATCTGAAAAT 58.109 33.333 6.32 0.00 0.00 1.82
2508 2589 2.635714 GGGACATTTGGGTTAGTACGG 58.364 52.381 0.00 0.00 0.00 4.02
2544 2626 5.931724 TCATCGTCACACAAGATAAACATGT 59.068 36.000 0.00 0.00 0.00 3.21
2545 2627 6.426633 TCATCGTCACACAAGATAAACATGTT 59.573 34.615 4.92 4.92 0.00 2.71
2836 2918 1.375908 GACAATGGTGAGCAGCCGA 60.376 57.895 0.00 0.00 0.00 5.54
3257 3347 4.657013 TGGTCATTGTAAGTTACATGGCA 58.343 39.130 16.26 2.18 38.68 4.92
3882 4104 8.184304 AGATATATCTCCGTATGATAAAGGCC 57.816 38.462 9.57 0.00 29.30 5.19
4057 4279 3.055094 GGTTCAGTTCTTCAGGCTGGATA 60.055 47.826 15.73 0.00 0.00 2.59
4060 4282 3.840666 TCAGTTCTTCAGGCTGGATACTT 59.159 43.478 15.73 0.00 37.61 2.24
4100 4329 2.158914 TGCATGGCATGGTACTCTACTG 60.159 50.000 27.48 0.60 31.71 2.74
4123 4352 7.389884 ACTGGTATCATATAATTGCTGCTTCAG 59.610 37.037 0.00 0.00 34.12 3.02
4134 4363 2.817396 GCTTCAGCACGAGCCTCC 60.817 66.667 0.00 0.00 43.56 4.30
4135 4364 2.659016 CTTCAGCACGAGCCTCCA 59.341 61.111 0.00 0.00 43.56 3.86
4136 4365 1.004560 CTTCAGCACGAGCCTCCAA 60.005 57.895 0.00 0.00 43.56 3.53
4137 4366 0.603707 CTTCAGCACGAGCCTCCAAA 60.604 55.000 0.00 0.00 43.56 3.28
4138 4367 0.603707 TTCAGCACGAGCCTCCAAAG 60.604 55.000 0.00 0.00 43.56 2.77
4139 4368 1.302033 CAGCACGAGCCTCCAAAGT 60.302 57.895 0.00 0.00 43.56 2.66
4140 4369 0.037326 CAGCACGAGCCTCCAAAGTA 60.037 55.000 0.00 0.00 43.56 2.24
4141 4370 0.685097 AGCACGAGCCTCCAAAGTAA 59.315 50.000 0.00 0.00 43.56 2.24
4142 4371 1.279271 AGCACGAGCCTCCAAAGTAAT 59.721 47.619 0.00 0.00 43.56 1.89
4143 4372 2.084546 GCACGAGCCTCCAAAGTAATT 58.915 47.619 0.00 0.00 33.58 1.40
4144 4373 2.096013 GCACGAGCCTCCAAAGTAATTC 59.904 50.000 0.00 0.00 33.58 2.17
4145 4374 2.348666 CACGAGCCTCCAAAGTAATTCG 59.651 50.000 0.00 0.00 0.00 3.34
4146 4375 2.028385 ACGAGCCTCCAAAGTAATTCGT 60.028 45.455 0.00 0.00 35.48 3.85
4147 4376 2.348666 CGAGCCTCCAAAGTAATTCGTG 59.651 50.000 0.00 0.00 0.00 4.35
4148 4377 2.084546 AGCCTCCAAAGTAATTCGTGC 58.915 47.619 0.00 0.00 0.00 5.34
4149 4378 1.202031 GCCTCCAAAGTAATTCGTGCG 60.202 52.381 0.00 0.00 0.00 5.34
4150 4379 2.343101 CCTCCAAAGTAATTCGTGCGA 58.657 47.619 0.00 0.00 0.00 5.10
4151 4380 2.936498 CCTCCAAAGTAATTCGTGCGAT 59.064 45.455 0.00 0.00 0.00 4.58
4152 4381 3.001330 CCTCCAAAGTAATTCGTGCGATC 59.999 47.826 0.00 0.00 0.00 3.69
4153 4382 2.933906 TCCAAAGTAATTCGTGCGATCC 59.066 45.455 0.00 0.00 0.00 3.36
4154 4383 2.675844 CCAAAGTAATTCGTGCGATCCA 59.324 45.455 0.00 0.00 0.00 3.41
4155 4384 3.126171 CCAAAGTAATTCGTGCGATCCAA 59.874 43.478 0.00 0.00 0.00 3.53
4156 4385 4.378978 CCAAAGTAATTCGTGCGATCCAAA 60.379 41.667 0.00 0.00 0.00 3.28
4157 4386 5.331902 CAAAGTAATTCGTGCGATCCAAAT 58.668 37.500 0.00 0.00 0.00 2.32
4158 4387 4.795970 AGTAATTCGTGCGATCCAAATC 57.204 40.909 0.00 0.00 0.00 2.17
4159 4388 4.442706 AGTAATTCGTGCGATCCAAATCT 58.557 39.130 0.00 0.00 0.00 2.40
4160 4389 5.597806 AGTAATTCGTGCGATCCAAATCTA 58.402 37.500 0.00 0.00 0.00 1.98
4161 4390 6.046593 AGTAATTCGTGCGATCCAAATCTAA 58.953 36.000 0.00 0.00 0.00 2.10
4162 4391 6.706270 AGTAATTCGTGCGATCCAAATCTAAT 59.294 34.615 0.00 0.00 0.00 1.73
4163 4392 5.597813 ATTCGTGCGATCCAAATCTAATC 57.402 39.130 0.00 0.00 0.00 1.75
4164 4393 3.390135 TCGTGCGATCCAAATCTAATCC 58.610 45.455 0.00 0.00 0.00 3.01
4165 4394 2.155732 CGTGCGATCCAAATCTAATCCG 59.844 50.000 0.00 0.00 0.00 4.18
4166 4395 3.131396 GTGCGATCCAAATCTAATCCGT 58.869 45.455 0.00 0.00 0.00 4.69
4167 4396 3.059597 GTGCGATCCAAATCTAATCCGTG 60.060 47.826 0.00 0.00 0.00 4.94
4168 4397 3.181470 TGCGATCCAAATCTAATCCGTGA 60.181 43.478 0.00 0.00 0.00 4.35
4169 4398 3.430218 GCGATCCAAATCTAATCCGTGAG 59.570 47.826 0.00 0.00 0.00 3.51
4170 4399 3.430218 CGATCCAAATCTAATCCGTGAGC 59.570 47.826 0.00 0.00 0.00 4.26
4171 4400 2.821546 TCCAAATCTAATCCGTGAGCG 58.178 47.619 0.00 0.00 37.95 5.03
4185 4414 4.521062 AGCGGACATGGCTCTCGC 62.521 66.667 12.15 12.15 45.72 5.03
4187 4416 4.193334 CGGACATGGCTCTCGCGA 62.193 66.667 9.26 9.26 36.88 5.87
4188 4417 2.279120 GGACATGGCTCTCGCGAG 60.279 66.667 30.03 30.03 40.35 5.03
4227 4456 3.483869 GCCGCCCTGATCTCCCTT 61.484 66.667 0.00 0.00 0.00 3.95
4228 4457 2.825264 CCGCCCTGATCTCCCTTC 59.175 66.667 0.00 0.00 0.00 3.46
4229 4458 1.764054 CCGCCCTGATCTCCCTTCT 60.764 63.158 0.00 0.00 0.00 2.85
4230 4459 1.745264 CGCCCTGATCTCCCTTCTC 59.255 63.158 0.00 0.00 0.00 2.87
4231 4460 1.753368 CGCCCTGATCTCCCTTCTCC 61.753 65.000 0.00 0.00 0.00 3.71
4232 4461 1.753368 GCCCTGATCTCCCTTCTCCG 61.753 65.000 0.00 0.00 0.00 4.63
4233 4462 1.118356 CCCTGATCTCCCTTCTCCGG 61.118 65.000 0.00 0.00 0.00 5.14
4234 4463 1.745264 CTGATCTCCCTTCTCCGGC 59.255 63.158 0.00 0.00 0.00 6.13
4235 4464 1.753368 CTGATCTCCCTTCTCCGGCC 61.753 65.000 0.00 0.00 0.00 6.13
4236 4465 1.458588 GATCTCCCTTCTCCGGCCT 60.459 63.158 0.00 0.00 0.00 5.19
4237 4466 1.458588 ATCTCCCTTCTCCGGCCTC 60.459 63.158 0.00 0.00 0.00 4.70
4238 4467 2.956077 ATCTCCCTTCTCCGGCCTCC 62.956 65.000 0.00 0.00 0.00 4.30
4239 4468 4.798682 TCCCTTCTCCGGCCTCCC 62.799 72.222 0.00 0.00 0.00 4.30
4241 4470 4.806339 CCTTCTCCGGCCTCCCCT 62.806 72.222 0.00 0.00 0.00 4.79
4242 4471 3.474570 CTTCTCCGGCCTCCCCTG 61.475 72.222 0.00 0.00 0.00 4.45
4251 4480 4.748144 CCTCCCCTGCAAGTGCCC 62.748 72.222 0.00 0.00 41.18 5.36
4257 4486 4.641645 CTGCAAGTGCCCGGTCCA 62.642 66.667 0.00 0.00 41.18 4.02
4258 4487 4.641645 TGCAAGTGCCCGGTCCAG 62.642 66.667 0.00 0.00 41.18 3.86
4259 4488 4.329545 GCAAGTGCCCGGTCCAGA 62.330 66.667 0.00 0.00 34.31 3.86
4260 4489 2.671070 CAAGTGCCCGGTCCAGAT 59.329 61.111 0.00 0.00 0.00 2.90
4261 4490 1.450312 CAAGTGCCCGGTCCAGATC 60.450 63.158 0.00 0.00 0.00 2.75
4262 4491 1.613630 AAGTGCCCGGTCCAGATCT 60.614 57.895 0.00 0.00 0.00 2.75
4263 4492 1.903877 AAGTGCCCGGTCCAGATCTG 61.904 60.000 16.24 16.24 0.00 2.90
4274 4503 0.317799 CCAGATCTGGCATCCTCTCG 59.682 60.000 28.45 1.31 44.73 4.04
4275 4504 1.326328 CAGATCTGGCATCCTCTCGA 58.674 55.000 15.38 0.00 0.00 4.04
4276 4505 1.000385 CAGATCTGGCATCCTCTCGAC 60.000 57.143 15.38 0.00 0.00 4.20
4277 4506 0.039617 GATCTGGCATCCTCTCGACG 60.040 60.000 0.00 0.00 0.00 5.12
4278 4507 2.081425 ATCTGGCATCCTCTCGACGC 62.081 60.000 0.00 0.00 0.00 5.19
4279 4508 3.781770 CTGGCATCCTCTCGACGCC 62.782 68.421 0.00 0.00 43.28 5.68
4280 4509 4.593864 GGCATCCTCTCGACGCCC 62.594 72.222 0.00 0.00 36.73 6.13
4281 4510 3.532155 GCATCCTCTCGACGCCCT 61.532 66.667 0.00 0.00 0.00 5.19
4282 4511 2.725008 CATCCTCTCGACGCCCTC 59.275 66.667 0.00 0.00 0.00 4.30
4283 4512 1.826054 CATCCTCTCGACGCCCTCT 60.826 63.158 0.00 0.00 0.00 3.69
4284 4513 1.076632 ATCCTCTCGACGCCCTCTT 60.077 57.895 0.00 0.00 0.00 2.85
4285 4514 1.388065 ATCCTCTCGACGCCCTCTTG 61.388 60.000 0.00 0.00 0.00 3.02
4286 4515 2.202676 CTCTCGACGCCCTCTTGC 60.203 66.667 0.00 0.00 0.00 4.01
4287 4516 2.989253 TCTCGACGCCCTCTTGCA 60.989 61.111 0.00 0.00 0.00 4.08
4288 4517 2.507992 CTCGACGCCCTCTTGCAG 60.508 66.667 0.00 0.00 0.00 4.41
4289 4518 4.742201 TCGACGCCCTCTTGCAGC 62.742 66.667 0.00 0.00 0.00 5.25
4291 4520 4.400961 GACGCCCTCTTGCAGCCT 62.401 66.667 0.00 0.00 0.00 4.58
4292 4521 3.003173 ACGCCCTCTTGCAGCCTA 61.003 61.111 0.00 0.00 0.00 3.93
4293 4522 2.317149 GACGCCCTCTTGCAGCCTAT 62.317 60.000 0.00 0.00 0.00 2.57
4294 4523 1.890979 CGCCCTCTTGCAGCCTATG 60.891 63.158 0.00 0.00 0.00 2.23
4295 4524 1.225704 GCCCTCTTGCAGCCTATGT 59.774 57.895 0.00 0.00 0.00 2.29
4296 4525 1.099879 GCCCTCTTGCAGCCTATGTG 61.100 60.000 0.00 0.00 0.00 3.21
4297 4526 1.099879 CCCTCTTGCAGCCTATGTGC 61.100 60.000 0.00 0.00 41.59 4.57
4298 4527 0.107312 CCTCTTGCAGCCTATGTGCT 60.107 55.000 0.00 0.00 44.00 4.40
4299 4528 1.681166 CCTCTTGCAGCCTATGTGCTT 60.681 52.381 0.00 0.00 40.32 3.91
4300 4529 1.669779 CTCTTGCAGCCTATGTGCTTC 59.330 52.381 0.00 0.00 40.32 3.86
4301 4530 1.280133 TCTTGCAGCCTATGTGCTTCT 59.720 47.619 0.00 0.00 40.32 2.85
4302 4531 1.669779 CTTGCAGCCTATGTGCTTCTC 59.330 52.381 0.00 0.00 40.32 2.87
4303 4532 0.107508 TGCAGCCTATGTGCTTCTCC 60.108 55.000 0.00 0.00 40.32 3.71
4304 4533 0.817229 GCAGCCTATGTGCTTCTCCC 60.817 60.000 0.00 0.00 40.32 4.30
4305 4534 0.179034 CAGCCTATGTGCTTCTCCCC 60.179 60.000 0.00 0.00 40.32 4.81
4306 4535 1.227674 GCCTATGTGCTTCTCCCCG 60.228 63.158 0.00 0.00 0.00 5.73
4307 4536 1.227674 CCTATGTGCTTCTCCCCGC 60.228 63.158 0.00 0.00 0.00 6.13
4308 4537 1.592669 CTATGTGCTTCTCCCCGCG 60.593 63.158 0.00 0.00 0.00 6.46
4309 4538 2.978452 CTATGTGCTTCTCCCCGCGG 62.978 65.000 21.04 21.04 0.00 6.46
4324 4553 3.702048 CGGGGTGACGTCATGGGT 61.702 66.667 23.12 0.00 0.00 4.51
4325 4554 2.046314 GGGGTGACGTCATGGGTG 60.046 66.667 23.12 0.00 0.00 4.61
4326 4555 2.746277 GGGTGACGTCATGGGTGC 60.746 66.667 23.12 7.31 0.00 5.01
4327 4556 2.347490 GGTGACGTCATGGGTGCT 59.653 61.111 23.12 0.00 0.00 4.40
4328 4557 1.741770 GGTGACGTCATGGGTGCTC 60.742 63.158 23.12 5.73 0.00 4.26
4329 4558 2.094659 GTGACGTCATGGGTGCTCG 61.095 63.158 23.12 0.00 0.00 5.03
4330 4559 2.261671 GACGTCATGGGTGCTCGT 59.738 61.111 11.55 0.00 37.93 4.18
4331 4560 1.805945 GACGTCATGGGTGCTCGTC 60.806 63.158 11.55 0.00 41.22 4.20
4332 4561 2.509336 CGTCATGGGTGCTCGTCC 60.509 66.667 0.00 0.00 0.00 4.79
4333 4562 2.662596 GTCATGGGTGCTCGTCCA 59.337 61.111 0.00 0.00 37.46 4.02
4334 4563 1.741770 GTCATGGGTGCTCGTCCAC 60.742 63.158 0.00 0.59 35.67 4.02
4335 4564 2.815211 CATGGGTGCTCGTCCACG 60.815 66.667 0.00 0.00 36.59 4.94
4337 4566 3.296709 ATGGGTGCTCGTCCACGAC 62.297 63.158 0.00 0.00 44.22 4.34
4338 4567 4.736896 GGGTGCTCGTCCACGACC 62.737 72.222 0.00 0.00 44.22 4.79
4339 4568 3.681835 GGTGCTCGTCCACGACCT 61.682 66.667 0.00 0.00 44.22 3.85
4340 4569 2.126424 GTGCTCGTCCACGACCTC 60.126 66.667 0.00 0.00 44.22 3.85
4341 4570 3.733960 TGCTCGTCCACGACCTCG 61.734 66.667 0.00 0.00 44.22 4.63
4342 4571 3.429141 GCTCGTCCACGACCTCGA 61.429 66.667 0.78 0.00 44.22 4.04
4343 4572 2.479650 CTCGTCCACGACCTCGAC 59.520 66.667 0.78 0.00 44.22 4.20
4344 4573 3.036783 CTCGTCCACGACCTCGACC 62.037 68.421 0.78 0.00 44.22 4.79
4345 4574 4.112341 CGTCCACGACCTCGACCC 62.112 72.222 0.78 0.00 43.02 4.46
4346 4575 4.112341 GTCCACGACCTCGACCCG 62.112 72.222 0.78 0.00 43.02 5.28
4420 4649 4.785453 CCCGCTGCTCCAGTTCCC 62.785 72.222 0.00 0.00 33.43 3.97
4421 4650 4.020617 CCGCTGCTCCAGTTCCCA 62.021 66.667 0.00 0.00 33.43 4.37
4422 4651 2.743928 CGCTGCTCCAGTTCCCAC 60.744 66.667 0.00 0.00 33.43 4.61
4423 4652 2.743928 GCTGCTCCAGTTCCCACG 60.744 66.667 0.00 0.00 33.43 4.94
4424 4653 3.059982 CTGCTCCAGTTCCCACGA 58.940 61.111 0.00 0.00 0.00 4.35
4425 4654 1.374758 CTGCTCCAGTTCCCACGAC 60.375 63.158 0.00 0.00 0.00 4.34
4426 4655 2.047179 GCTCCAGTTCCCACGACC 60.047 66.667 0.00 0.00 0.00 4.79
4427 4656 2.261671 CTCCAGTTCCCACGACCG 59.738 66.667 0.00 0.00 0.00 4.79
4428 4657 3.934391 CTCCAGTTCCCACGACCGC 62.934 68.421 0.00 0.00 0.00 5.68
4432 4661 4.754667 GTTCCCACGACCGCCCTC 62.755 72.222 0.00 0.00 0.00 4.30
4484 4713 4.470170 CATCCACGTCGGTCGCGA 62.470 66.667 3.71 3.71 44.19 5.87
4485 4714 3.515286 ATCCACGTCGGTCGCGAT 61.515 61.111 14.06 0.00 44.19 4.58
4486 4715 3.751401 ATCCACGTCGGTCGCGATG 62.751 63.158 14.06 8.75 44.19 3.84
4509 4738 4.643387 GGCCACTCCTGCCGTGTT 62.643 66.667 0.00 0.00 39.48 3.32
4510 4739 3.357079 GCCACTCCTGCCGTGTTG 61.357 66.667 0.00 0.00 0.00 3.33
4511 4740 2.425592 CCACTCCTGCCGTGTTGA 59.574 61.111 0.00 0.00 0.00 3.18
4512 4741 1.669115 CCACTCCTGCCGTGTTGAG 60.669 63.158 0.00 0.00 0.00 3.02
4513 4742 2.031163 ACTCCTGCCGTGTTGAGC 59.969 61.111 0.00 0.00 0.00 4.26
4514 4743 3.114616 CTCCTGCCGTGTTGAGCG 61.115 66.667 0.00 0.00 0.00 5.03
4515 4744 3.865929 CTCCTGCCGTGTTGAGCGT 62.866 63.158 0.00 0.00 0.00 5.07
4516 4745 3.414700 CCTGCCGTGTTGAGCGTC 61.415 66.667 0.00 0.00 0.00 5.19
4517 4746 3.767230 CTGCCGTGTTGAGCGTCG 61.767 66.667 0.00 0.00 0.00 5.12
4553 4782 4.069232 CTCCAGCTCCCGCGTCAA 62.069 66.667 4.92 0.00 42.32 3.18
4554 4783 4.373116 TCCAGCTCCCGCGTCAAC 62.373 66.667 4.92 0.00 42.32 3.18
4555 4784 4.379243 CCAGCTCCCGCGTCAACT 62.379 66.667 4.92 0.00 42.32 3.16
4556 4785 2.811317 CAGCTCCCGCGTCAACTC 60.811 66.667 4.92 0.00 42.32 3.01
4557 4786 2.992114 AGCTCCCGCGTCAACTCT 60.992 61.111 4.92 0.00 42.32 3.24
4558 4787 2.048127 GCTCCCGCGTCAACTCTT 60.048 61.111 4.92 0.00 0.00 2.85
4559 4788 2.383527 GCTCCCGCGTCAACTCTTG 61.384 63.158 4.92 0.00 0.00 3.02
4560 4789 2.357034 TCCCGCGTCAACTCTTGC 60.357 61.111 4.92 0.00 0.00 4.01
4561 4790 3.423154 CCCGCGTCAACTCTTGCC 61.423 66.667 4.92 0.00 0.00 4.52
4562 4791 3.777925 CCGCGTCAACTCTTGCCG 61.778 66.667 4.92 0.00 34.78 5.69
4565 4794 3.777925 CGTCAACTCTTGCCGCGG 61.778 66.667 24.05 24.05 0.00 6.46
4566 4795 4.090057 GTCAACTCTTGCCGCGGC 62.090 66.667 42.35 42.35 42.35 6.53
4604 4833 2.742372 CCGAACCAGCCGTCCAAG 60.742 66.667 0.00 0.00 0.00 3.61
4605 4834 2.742372 CGAACCAGCCGTCCAAGG 60.742 66.667 0.00 0.00 0.00 3.61
4606 4835 2.359975 GAACCAGCCGTCCAAGGG 60.360 66.667 0.00 0.00 0.00 3.95
4613 4842 4.778143 CCGTCCAAGGGCGAAGGG 62.778 72.222 15.66 0.00 0.00 3.95
4614 4843 4.016706 CGTCCAAGGGCGAAGGGT 62.017 66.667 7.44 0.00 0.00 4.34
4615 4844 2.359975 GTCCAAGGGCGAAGGGTG 60.360 66.667 0.00 0.00 0.00 4.61
4616 4845 3.646715 TCCAAGGGCGAAGGGTGG 61.647 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.321675 GGTTTGGAATGGCTTATCACGTTT 60.322 41.667 0.00 0.00 0.00 3.60
8 9 2.752354 TGGTTTGGAATGGCTTATCACG 59.248 45.455 0.00 0.00 0.00 4.35
64 65 1.507141 GCACGGTCTTGGGTCTGTTG 61.507 60.000 0.00 0.00 0.00 3.33
66 67 1.978455 TTGCACGGTCTTGGGTCTGT 61.978 55.000 0.00 0.00 0.00 3.41
71 73 1.178534 ATTGGTTGCACGGTCTTGGG 61.179 55.000 0.00 0.00 0.00 4.12
74 76 0.673437 CCAATTGGTTGCACGGTCTT 59.327 50.000 16.90 0.00 33.90 3.01
79 81 4.531708 CGTCCAATTGGTTGCACG 57.468 55.556 23.76 20.83 42.38 5.34
200 208 4.119155 TGGAGGGTAGGAGGATGATTTTT 58.881 43.478 0.00 0.00 0.00 1.94
201 209 3.747852 TGGAGGGTAGGAGGATGATTTT 58.252 45.455 0.00 0.00 0.00 1.82
202 210 3.438131 TGGAGGGTAGGAGGATGATTT 57.562 47.619 0.00 0.00 0.00 2.17
203 211 3.254960 CATGGAGGGTAGGAGGATGATT 58.745 50.000 0.00 0.00 0.00 2.57
204 212 2.496142 CCATGGAGGGTAGGAGGATGAT 60.496 54.545 5.56 0.00 0.00 2.45
205 213 1.132721 CCATGGAGGGTAGGAGGATGA 60.133 57.143 5.56 0.00 0.00 2.92
206 214 1.356124 CCATGGAGGGTAGGAGGATG 58.644 60.000 5.56 0.00 0.00 3.51
207 215 0.474660 GCCATGGAGGGTAGGAGGAT 60.475 60.000 18.40 0.00 38.09 3.24
208 216 1.074471 GCCATGGAGGGTAGGAGGA 60.074 63.158 18.40 0.00 38.09 3.71
209 217 3.568578 GCCATGGAGGGTAGGAGG 58.431 66.667 18.40 0.00 38.09 4.30
216 224 1.432852 ATGGATGGAGCCATGGAGGG 61.433 60.000 18.40 0.00 46.62 4.30
217 225 2.161581 ATGGATGGAGCCATGGAGG 58.838 57.895 18.40 0.00 46.62 4.30
225 233 1.073897 GTAGGGGCATGGATGGAGC 59.926 63.158 0.00 0.00 0.00 4.70
266 274 7.447545 GGGTCAAGGCCTAATAAAATAAGTAGG 59.552 40.741 5.16 0.00 36.89 3.18
341 349 3.131933 TGTGTGTGGCTGCTTTTATTTGT 59.868 39.130 0.00 0.00 0.00 2.83
346 354 1.028905 GGTGTGTGTGGCTGCTTTTA 58.971 50.000 0.00 0.00 0.00 1.52
387 401 1.260538 TGCCTAGTGGGAGCTGTGAG 61.261 60.000 0.00 0.00 37.23 3.51
416 430 4.154347 GGAGGAGGAGCGCCAGTG 62.154 72.222 9.88 0.00 36.29 3.66
422 436 4.150454 AGGAGGGGAGGAGGAGCG 62.150 72.222 0.00 0.00 0.00 5.03
423 437 2.445654 CAGGAGGGGAGGAGGAGC 60.446 72.222 0.00 0.00 0.00 4.70
424 438 2.445654 GCAGGAGGGGAGGAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
425 439 2.880612 TTGCAGGAGGGGAGGAGGA 61.881 63.158 0.00 0.00 0.00 3.71
426 440 2.285668 TTGCAGGAGGGGAGGAGG 60.286 66.667 0.00 0.00 0.00 4.30
651 667 3.694566 AGATTAGACGATTGTTTTGGGGC 59.305 43.478 0.00 0.00 0.00 5.80
682 698 2.825836 GGGAGCAATGTGGAGGCG 60.826 66.667 0.00 0.00 0.00 5.52
1320 1369 2.582052 GTCTCGATCTGGATGGACTCT 58.418 52.381 0.00 0.00 0.00 3.24
1458 1507 3.680786 TGTGAGACCTCGGGCACG 61.681 66.667 0.00 0.00 42.74 5.34
1539 1588 0.250234 CCTCGCCAATCACCTTCTCA 59.750 55.000 0.00 0.00 0.00 3.27
1581 1630 2.892640 CCGTCCTCGAGAATGCCA 59.107 61.111 15.71 0.00 39.71 4.92
1737 1786 0.392998 GATTCAGTGACCCGGTGCAT 60.393 55.000 0.00 0.00 0.00 3.96
2046 2126 5.468072 ACAGCAGTTCAACTTATCACTCAAG 59.532 40.000 0.00 0.00 0.00 3.02
2116 2197 3.228188 ACACAAGCATCCTGGAAAGAA 57.772 42.857 0.00 0.00 0.00 2.52
2122 2203 1.066858 ACTCGTACACAAGCATCCTGG 60.067 52.381 0.00 0.00 0.00 4.45
2138 2219 6.582295 CCAAAGTTCCATTATTGACAAACTCG 59.418 38.462 0.00 0.00 0.00 4.18
2144 2225 5.076182 TGCTCCAAAGTTCCATTATTGACA 58.924 37.500 0.00 0.00 0.00 3.58
2162 2243 1.065199 TCACCATGAATCCACTGCTCC 60.065 52.381 0.00 0.00 0.00 4.70
2168 2249 3.091545 ACCAACATCACCATGAATCCAC 58.908 45.455 0.00 0.00 33.72 4.02
2343 2424 0.674895 CCTTTGGCTCAAGTCCCTCG 60.675 60.000 0.00 0.00 0.00 4.63
2508 2589 7.520119 TGTGTGACGATGATTTTATGAGTAC 57.480 36.000 0.00 0.00 0.00 2.73
2544 2626 9.890629 AACAAGAGATACATAAGCAACTATGAA 57.109 29.630 7.30 0.00 34.07 2.57
2836 2918 3.628832 TCCAAAACCCCCTCTGAATTT 57.371 42.857 0.00 0.00 0.00 1.82
3190 3280 6.719370 ACAGGCAAAAGAGAAAATGTATGGTA 59.281 34.615 0.00 0.00 0.00 3.25
3257 3347 9.403583 TGTAACAAAGAGAAAAAGTATCAACCT 57.596 29.630 0.00 0.00 0.00 3.50
3576 3785 5.186996 TGTCTGCTTTTGATTGACCTTTC 57.813 39.130 0.00 0.00 0.00 2.62
3882 4104 5.130477 TCAGCTTTACCCCTGAAAGTATAGG 59.870 44.000 0.00 0.00 36.47 2.57
4007 4229 8.883731 TCAAATTTCTATGTGAAAGCTAGTAGC 58.116 33.333 14.62 14.62 46.39 3.58
4057 4279 2.551270 TCCCTGGCTGTCAATCTAAGT 58.449 47.619 0.00 0.00 0.00 2.24
4060 4282 2.421952 GCAATCCCTGGCTGTCAATCTA 60.422 50.000 0.00 0.00 0.00 1.98
4123 4352 1.739067 ATTACTTTGGAGGCTCGTGC 58.261 50.000 8.69 0.00 38.76 5.34
4124 4353 2.348666 CGAATTACTTTGGAGGCTCGTG 59.651 50.000 8.69 0.98 0.00 4.35
4125 4354 2.028385 ACGAATTACTTTGGAGGCTCGT 60.028 45.455 8.69 3.15 0.00 4.18
4126 4355 2.348666 CACGAATTACTTTGGAGGCTCG 59.651 50.000 8.69 0.00 0.00 5.03
4127 4356 2.096013 GCACGAATTACTTTGGAGGCTC 59.904 50.000 5.78 5.78 0.00 4.70
4128 4357 2.084546 GCACGAATTACTTTGGAGGCT 58.915 47.619 0.00 0.00 0.00 4.58
4129 4358 1.202031 CGCACGAATTACTTTGGAGGC 60.202 52.381 0.00 0.00 0.00 4.70
4130 4359 2.343101 TCGCACGAATTACTTTGGAGG 58.657 47.619 0.00 0.00 0.00 4.30
4131 4360 3.001330 GGATCGCACGAATTACTTTGGAG 59.999 47.826 0.00 0.00 0.00 3.86
4132 4361 2.933906 GGATCGCACGAATTACTTTGGA 59.066 45.455 0.00 0.00 0.00 3.53
4133 4362 2.675844 TGGATCGCACGAATTACTTTGG 59.324 45.455 0.00 0.00 0.00 3.28
4134 4363 4.335082 TTGGATCGCACGAATTACTTTG 57.665 40.909 0.00 0.00 0.00 2.77
4135 4364 5.354234 AGATTTGGATCGCACGAATTACTTT 59.646 36.000 0.00 0.00 37.37 2.66
4136 4365 4.876107 AGATTTGGATCGCACGAATTACTT 59.124 37.500 0.00 0.00 37.37 2.24
4137 4366 4.442706 AGATTTGGATCGCACGAATTACT 58.557 39.130 0.00 0.00 37.37 2.24
4138 4367 4.795970 AGATTTGGATCGCACGAATTAC 57.204 40.909 0.00 0.00 37.37 1.89
4139 4368 6.147164 GGATTAGATTTGGATCGCACGAATTA 59.853 38.462 0.00 0.00 37.37 1.40
4140 4369 5.049405 GGATTAGATTTGGATCGCACGAATT 60.049 40.000 0.00 0.00 37.37 2.17
4141 4370 4.452455 GGATTAGATTTGGATCGCACGAAT 59.548 41.667 0.00 0.00 37.37 3.34
4142 4371 3.807622 GGATTAGATTTGGATCGCACGAA 59.192 43.478 0.00 0.00 37.37 3.85
4143 4372 3.390135 GGATTAGATTTGGATCGCACGA 58.610 45.455 0.00 0.00 37.37 4.35
4144 4373 2.155732 CGGATTAGATTTGGATCGCACG 59.844 50.000 0.00 0.00 37.37 5.34
4145 4374 3.059597 CACGGATTAGATTTGGATCGCAC 60.060 47.826 0.00 0.00 37.37 5.34
4146 4375 3.130633 CACGGATTAGATTTGGATCGCA 58.869 45.455 0.00 0.00 37.37 5.10
4147 4376 3.390135 TCACGGATTAGATTTGGATCGC 58.610 45.455 0.00 0.00 37.37 4.58
4148 4377 3.430218 GCTCACGGATTAGATTTGGATCG 59.570 47.826 0.00 0.00 37.37 3.69
4149 4378 3.430218 CGCTCACGGATTAGATTTGGATC 59.570 47.826 0.00 0.00 34.97 3.36
4150 4379 3.393800 CGCTCACGGATTAGATTTGGAT 58.606 45.455 0.00 0.00 34.97 3.41
4151 4380 2.821546 CGCTCACGGATTAGATTTGGA 58.178 47.619 0.00 0.00 34.97 3.53
4210 4439 3.468326 GAAGGGAGATCAGGGCGGC 62.468 68.421 0.00 0.00 0.00 6.53
4211 4440 1.753368 GAGAAGGGAGATCAGGGCGG 61.753 65.000 0.00 0.00 0.00 6.13
4212 4441 1.745264 GAGAAGGGAGATCAGGGCG 59.255 63.158 0.00 0.00 0.00 6.13
4213 4442 1.753368 CGGAGAAGGGAGATCAGGGC 61.753 65.000 0.00 0.00 0.00 5.19
4214 4443 1.118356 CCGGAGAAGGGAGATCAGGG 61.118 65.000 0.00 0.00 0.00 4.45
4215 4444 1.753368 GCCGGAGAAGGGAGATCAGG 61.753 65.000 5.05 0.00 0.00 3.86
4216 4445 1.745264 GCCGGAGAAGGGAGATCAG 59.255 63.158 5.05 0.00 0.00 2.90
4217 4446 1.762460 GGCCGGAGAAGGGAGATCA 60.762 63.158 5.05 0.00 0.00 2.92
4218 4447 1.458588 AGGCCGGAGAAGGGAGATC 60.459 63.158 5.05 0.00 0.00 2.75
4219 4448 1.458588 GAGGCCGGAGAAGGGAGAT 60.459 63.158 5.05 0.00 0.00 2.75
4220 4449 2.042843 GAGGCCGGAGAAGGGAGA 60.043 66.667 5.05 0.00 0.00 3.71
4221 4450 3.157949 GGAGGCCGGAGAAGGGAG 61.158 72.222 5.05 0.00 0.00 4.30
4222 4451 4.798682 GGGAGGCCGGAGAAGGGA 62.799 72.222 5.05 0.00 0.00 4.20
4224 4453 4.806339 AGGGGAGGCCGGAGAAGG 62.806 72.222 5.05 0.00 0.00 3.46
4225 4454 3.474570 CAGGGGAGGCCGGAGAAG 61.475 72.222 5.05 0.00 0.00 2.85
4234 4463 4.748144 GGGCACTTGCAGGGGAGG 62.748 72.222 0.37 0.00 44.36 4.30
4240 4469 4.641645 TGGACCGGGCACTTGCAG 62.642 66.667 11.00 0.00 44.36 4.41
4241 4470 4.641645 CTGGACCGGGCACTTGCA 62.642 66.667 11.00 0.00 44.36 4.08
4242 4471 3.628646 ATCTGGACCGGGCACTTGC 62.629 63.158 11.00 0.00 41.14 4.01
4243 4472 1.450312 GATCTGGACCGGGCACTTG 60.450 63.158 11.00 0.00 0.00 3.16
4244 4473 1.613630 AGATCTGGACCGGGCACTT 60.614 57.895 11.00 0.00 0.00 3.16
4245 4474 2.039624 AGATCTGGACCGGGCACT 59.960 61.111 11.00 0.00 0.00 4.40
4246 4475 2.187946 CAGATCTGGACCGGGCAC 59.812 66.667 11.00 0.00 0.00 5.01
4256 4485 1.000385 GTCGAGAGGATGCCAGATCTG 60.000 57.143 16.24 16.24 0.00 2.90
4257 4486 1.327303 GTCGAGAGGATGCCAGATCT 58.673 55.000 0.00 0.00 0.00 2.75
4258 4487 0.039617 CGTCGAGAGGATGCCAGATC 60.040 60.000 0.00 0.00 0.00 2.75
4259 4488 2.037053 CGTCGAGAGGATGCCAGAT 58.963 57.895 0.00 0.00 0.00 2.90
4260 4489 3.514417 CGTCGAGAGGATGCCAGA 58.486 61.111 0.00 0.00 0.00 3.86
4265 4494 1.388065 AAGAGGGCGTCGAGAGGATG 61.388 60.000 0.00 0.00 34.62 3.51
4266 4495 1.076632 AAGAGGGCGTCGAGAGGAT 60.077 57.895 0.00 0.00 0.00 3.24
4267 4496 2.046864 CAAGAGGGCGTCGAGAGGA 61.047 63.158 0.00 0.00 0.00 3.71
4268 4497 2.492090 CAAGAGGGCGTCGAGAGG 59.508 66.667 0.00 0.00 0.00 3.69
4269 4498 2.202676 GCAAGAGGGCGTCGAGAG 60.203 66.667 0.00 0.00 0.00 3.20
4270 4499 2.989253 TGCAAGAGGGCGTCGAGA 60.989 61.111 0.00 0.00 36.28 4.04
4271 4500 2.507992 CTGCAAGAGGGCGTCGAG 60.508 66.667 0.00 0.00 34.07 4.04
4272 4501 4.742201 GCTGCAAGAGGGCGTCGA 62.742 66.667 0.00 0.00 34.07 4.20
4274 4503 2.317149 ATAGGCTGCAAGAGGGCGTC 62.317 60.000 0.50 0.00 34.07 5.19
4275 4504 2.370445 ATAGGCTGCAAGAGGGCGT 61.370 57.895 0.50 0.00 34.07 5.68
4276 4505 1.890979 CATAGGCTGCAAGAGGGCG 60.891 63.158 0.50 0.00 34.07 6.13
4277 4506 1.099879 CACATAGGCTGCAAGAGGGC 61.100 60.000 0.50 0.00 34.07 5.19
4278 4507 1.099879 GCACATAGGCTGCAAGAGGG 61.100 60.000 0.50 0.00 34.07 4.30
4279 4508 0.107312 AGCACATAGGCTGCAAGAGG 60.107 55.000 0.50 0.00 43.89 3.69
4280 4509 1.669779 GAAGCACATAGGCTGCAAGAG 59.330 52.381 0.50 0.00 45.07 2.85
4281 4510 1.280133 AGAAGCACATAGGCTGCAAGA 59.720 47.619 0.50 0.00 45.07 3.02
4282 4511 1.669779 GAGAAGCACATAGGCTGCAAG 59.330 52.381 0.50 0.00 45.07 4.01
4283 4512 1.679944 GGAGAAGCACATAGGCTGCAA 60.680 52.381 0.50 0.00 45.07 4.08
4284 4513 0.107508 GGAGAAGCACATAGGCTGCA 60.108 55.000 0.50 0.00 45.07 4.41
4285 4514 0.817229 GGGAGAAGCACATAGGCTGC 60.817 60.000 0.00 0.00 45.07 5.25
4286 4515 0.179034 GGGGAGAAGCACATAGGCTG 60.179 60.000 0.00 0.00 45.07 4.85
4288 4517 1.227674 CGGGGAGAAGCACATAGGC 60.228 63.158 0.00 0.00 0.00 3.93
4289 4518 1.227674 GCGGGGAGAAGCACATAGG 60.228 63.158 0.00 0.00 0.00 2.57
4290 4519 1.592669 CGCGGGGAGAAGCACATAG 60.593 63.158 0.00 0.00 0.00 2.23
4291 4520 2.499205 CGCGGGGAGAAGCACATA 59.501 61.111 0.00 0.00 0.00 2.29
4292 4521 4.473520 CCGCGGGGAGAAGCACAT 62.474 66.667 20.10 0.00 34.06 3.21
4307 4536 3.702048 ACCCATGACGTCACCCCG 61.702 66.667 22.71 11.08 0.00 5.73
4308 4537 2.046314 CACCCATGACGTCACCCC 60.046 66.667 22.71 0.00 0.00 4.95
4309 4538 2.746277 GCACCCATGACGTCACCC 60.746 66.667 22.71 1.86 0.00 4.61
4310 4539 1.741770 GAGCACCCATGACGTCACC 60.742 63.158 22.71 5.30 0.00 4.02
4311 4540 2.094659 CGAGCACCCATGACGTCAC 61.095 63.158 22.71 6.96 0.00 3.67
4312 4541 2.261361 CGAGCACCCATGACGTCA 59.739 61.111 22.48 22.48 0.00 4.35
4313 4542 1.805945 GACGAGCACCCATGACGTC 60.806 63.158 9.11 9.11 43.81 4.34
4314 4543 2.261671 GACGAGCACCCATGACGT 59.738 61.111 0.00 0.00 40.91 4.34
4315 4544 2.509336 GGACGAGCACCCATGACG 60.509 66.667 0.00 0.00 34.75 4.35
4316 4545 1.741770 GTGGACGAGCACCCATGAC 60.742 63.158 0.00 0.00 34.58 3.06
4317 4546 2.662596 GTGGACGAGCACCCATGA 59.337 61.111 0.00 0.00 34.58 3.07
4318 4547 2.815211 CGTGGACGAGCACCCATG 60.815 66.667 0.00 0.00 43.02 3.66
4319 4548 2.994995 TCGTGGACGAGCACCCAT 60.995 61.111 0.00 0.00 44.22 4.00
4328 4557 4.112341 GGGTCGAGGTCGTGGACG 62.112 72.222 0.00 0.00 40.80 4.79
4329 4558 4.112341 CGGGTCGAGGTCGTGGAC 62.112 72.222 0.00 0.00 40.80 4.02
4403 4632 4.785453 GGGAACTGGAGCAGCGGG 62.785 72.222 0.00 0.00 34.37 6.13
4404 4633 4.020617 TGGGAACTGGAGCAGCGG 62.021 66.667 0.00 0.00 34.37 5.52
4405 4634 2.743928 GTGGGAACTGGAGCAGCG 60.744 66.667 0.00 0.00 34.37 5.18
4406 4635 2.743928 CGTGGGAACTGGAGCAGC 60.744 66.667 0.00 0.00 34.37 5.25
4407 4636 1.374758 GTCGTGGGAACTGGAGCAG 60.375 63.158 0.00 0.00 37.52 4.24
4408 4637 2.741092 GTCGTGGGAACTGGAGCA 59.259 61.111 0.00 0.00 0.00 4.26
4409 4638 2.047179 GGTCGTGGGAACTGGAGC 60.047 66.667 0.00 0.00 0.00 4.70
4410 4639 2.261671 CGGTCGTGGGAACTGGAG 59.738 66.667 0.00 0.00 0.00 3.86
4411 4640 3.998672 GCGGTCGTGGGAACTGGA 61.999 66.667 0.00 0.00 0.00 3.86
4415 4644 4.754667 GAGGGCGGTCGTGGGAAC 62.755 72.222 0.00 0.00 0.00 3.62
4492 4721 4.643387 AACACGGCAGGAGTGGCC 62.643 66.667 0.00 0.00 46.64 5.36
4493 4722 3.357079 CAACACGGCAGGAGTGGC 61.357 66.667 1.39 0.00 45.87 5.01
4494 4723 1.669115 CTCAACACGGCAGGAGTGG 60.669 63.158 1.39 0.00 43.41 4.00
4495 4724 2.320587 GCTCAACACGGCAGGAGTG 61.321 63.158 0.00 0.00 44.57 3.51
4496 4725 2.031163 GCTCAACACGGCAGGAGT 59.969 61.111 0.00 0.00 0.00 3.85
4497 4726 3.114616 CGCTCAACACGGCAGGAG 61.115 66.667 0.00 0.00 0.00 3.69
4498 4727 3.858868 GACGCTCAACACGGCAGGA 62.859 63.158 0.00 0.00 38.80 3.86
4499 4728 3.414700 GACGCTCAACACGGCAGG 61.415 66.667 0.00 0.00 38.80 4.85
4500 4729 3.767230 CGACGCTCAACACGGCAG 61.767 66.667 0.00 0.00 38.93 4.85
4504 4733 3.767230 CAGCCGACGCTCAACACG 61.767 66.667 0.00 0.00 43.95 4.49
4505 4734 2.658707 GACAGCCGACGCTCAACAC 61.659 63.158 0.00 0.00 43.95 3.32
4506 4735 2.355837 GACAGCCGACGCTCAACA 60.356 61.111 0.00 0.00 43.95 3.33
4507 4736 3.112709 GGACAGCCGACGCTCAAC 61.113 66.667 0.00 0.00 43.95 3.18
4542 4771 2.383527 GCAAGAGTTGACGCGGGAG 61.384 63.158 12.47 0.00 0.00 4.30
4543 4772 2.357034 GCAAGAGTTGACGCGGGA 60.357 61.111 12.47 0.00 0.00 5.14
4544 4773 3.423154 GGCAAGAGTTGACGCGGG 61.423 66.667 12.47 0.00 0.00 6.13
4549 4778 4.090057 GCCGCGGCAAGAGTTGAC 62.090 66.667 43.55 11.09 41.49 3.18
4587 4816 2.742372 CTTGGACGGCTGGTTCGG 60.742 66.667 0.00 0.00 0.00 4.30
4588 4817 2.742372 CCTTGGACGGCTGGTTCG 60.742 66.667 0.00 0.00 0.00 3.95
4589 4818 2.359975 CCCTTGGACGGCTGGTTC 60.360 66.667 0.00 0.00 0.00 3.62
4590 4819 4.660938 GCCCTTGGACGGCTGGTT 62.661 66.667 0.00 0.00 43.48 3.67
4593 4822 4.697756 TTCGCCCTTGGACGGCTG 62.698 66.667 0.00 0.00 44.73 4.85
4594 4823 4.394712 CTTCGCCCTTGGACGGCT 62.395 66.667 0.00 0.00 44.73 5.52
4596 4825 4.778143 CCCTTCGCCCTTGGACGG 62.778 72.222 0.00 0.00 0.00 4.79
4597 4826 4.016706 ACCCTTCGCCCTTGGACG 62.017 66.667 0.00 0.00 0.00 4.79
4598 4827 2.359975 CACCCTTCGCCCTTGGAC 60.360 66.667 0.00 0.00 0.00 4.02
4599 4828 3.646715 CCACCCTTCGCCCTTGGA 61.647 66.667 0.00 0.00 0.00 3.53
4607 4836 4.807039 CGTACGGGCCACCCTTCG 62.807 72.222 7.57 0.00 42.67 3.79


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

AutoCloner maintained by Alex Coulton.