Multiple sequence alignment - TraesCS5D01G244300

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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 TraesCS5D01G244300 chr5D 100.000 5626 0 0 1 5626 352823244 352828869 0.000000e+00 10390
1 TraesCS5D01G244300 chr5B 94.156 5185 189 42 128 5248 415794917 415800051 0.000000e+00 7792
2 TraesCS5D01G244300 chr5B 93.600 250 16 0 5377 5626 415800049 415800298 1.910000e-99 374
3 TraesCS5D01G244300 chr5A 90.745 4884 267 73 25 4797 453008024 453003215 0.000000e+00 6344
4 TraesCS5D01G244300 chr4A 87.578 161 20 0 4850 5010 453609484 453609324 2.680000e-43 187
5 TraesCS5D01G244300 chr2D 88.235 153 17 1 4858 5010 11394120 11393969 1.250000e-41 182
6 TraesCS5D01G244300 chr4B 86.875 160 21 0 4851 5010 184238147 184237988 4.480000e-41 180
7 TraesCS5D01G244300 chr2A 88.514 148 16 1 4863 5010 11998624 11998478 1.610000e-40 178
8 TraesCS5D01G244300 chr6B 86.624 157 18 3 4855 5010 625368128 625367974 2.700000e-38 171
9 TraesCS5D01G244300 chr6D 85.987 157 20 2 4855 5010 414781266 414781111 3.490000e-37 167
10 TraesCS5D01G244300 chr7B 84.848 165 23 2 4846 5010 89952171 89952333 1.250000e-36 165
11 TraesCS5D01G244300 chr7A 84.756 164 24 1 4846 5009 128783043 128783205 4.510000e-36 163


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 TraesCS5D01G244300 chr5D 352823244 352828869 5625 False 10390 10390 100.000 1 5626 1 chr5D.!!$F1 5625
1 TraesCS5D01G244300 chr5B 415794917 415800298 5381 False 4083 7792 93.878 128 5626 2 chr5B.!!$F1 5498
2 TraesCS5D01G244300 chr5A 453003215 453008024 4809 True 6344 6344 90.745 25 4797 1 chr5A.!!$R1 4772

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
121 122 0.179076 CCAGCATAGCATGTGACGGA 60.179 55.000 0.00 0.00 0.00 4.69 F
652 680 0.759346 GTGGAGTTGGTGAGGTGAGT 59.241 55.000 0.00 0.00 0.00 3.41 F
730 758 0.814010 CCGATCGGGGGCAAAACTAG 60.814 60.000 26.95 0.00 0.00 2.57 F
1725 1810 0.837691 ATCCTCCAGTGGTGAGCACA 60.838 55.000 17.69 0.00 0.00 4.57 F
2142 2241 1.004200 TCCGTTTTCTCCGGGCTTC 60.004 57.895 0.00 0.00 45.51 3.86 F
2283 2382 1.304464 CCAAAAGGGGTGGAGCTCC 60.304 63.158 26.78 26.78 38.54 4.70 F
3179 3286 1.473434 CGTAGAAGATTCAGCCCCCAC 60.473 57.143 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1899 0.036577 GCTGCAGAGGCTTCAGAGAA 60.037 55.000 20.43 0.0 41.91 2.87 R
1987 2086 0.316196 GTCGAACAGCACACAAGCAC 60.316 55.000 0.00 0.0 36.85 4.40 R
2250 2349 1.926489 TTGGTACCCCAAGGCCGAT 60.926 57.895 10.07 0.0 45.93 4.18 R
3327 3434 0.749049 TCTGCACATCCCTGATCTCG 59.251 55.000 0.00 0.0 0.00 4.04 R
3906 4030 0.035820 CCTTTGGCCCGTTGCTACTA 60.036 55.000 0.00 0.0 40.92 1.82 R
3987 4111 1.925255 TGGAGGAAGAGGATGCCAATT 59.075 47.619 0.00 0.0 0.00 2.32 R
5023 5169 0.613260 TCCAAATCGACTCCCACCTG 59.387 55.000 0.00 0.0 0.00 4.00 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 7.441890 TCTAAAAAGAACATGCACGGATTTA 57.558 32.000 0.00 0.00 0.00 1.40
39 40 5.895636 AAGAACATGCACGGATTTAATGA 57.104 34.783 0.00 0.00 0.00 2.57
44 45 5.762045 ACATGCACGGATTTAATGATTAGC 58.238 37.500 0.00 0.00 0.00 3.09
51 52 6.863126 CACGGATTTAATGATTAGCCCATTTC 59.137 38.462 0.00 0.00 35.94 2.17
52 53 6.015434 ACGGATTTAATGATTAGCCCATTTCC 60.015 38.462 0.00 0.00 35.94 3.13
59 60 2.710096 TTAGCCCATTTCCGGAGAAG 57.290 50.000 3.34 0.00 32.35 2.85
61 62 0.991920 AGCCCATTTCCGGAGAAGAA 59.008 50.000 3.34 0.00 32.35 2.52
62 63 1.354368 AGCCCATTTCCGGAGAAGAAA 59.646 47.619 3.34 0.00 32.35 2.52
63 64 2.167662 GCCCATTTCCGGAGAAGAAAA 58.832 47.619 3.34 0.00 32.35 2.29
88 89 7.734538 ATTCGCTAAATACGATTTGTTTTGG 57.265 32.000 0.00 0.00 39.65 3.28
90 91 4.264380 CGCTAAATACGATTTGTTTTGGCC 59.736 41.667 0.00 0.00 34.64 5.36
92 93 2.931512 ATACGATTTGTTTTGGCCGG 57.068 45.000 0.00 0.00 0.00 6.13
93 94 1.893544 TACGATTTGTTTTGGCCGGA 58.106 45.000 5.05 0.00 0.00 5.14
121 122 0.179076 CCAGCATAGCATGTGACGGA 60.179 55.000 0.00 0.00 0.00 4.69
123 124 1.114627 AGCATAGCATGTGACGGAGA 58.885 50.000 0.00 0.00 0.00 3.71
138 139 1.294659 GGAGAGAGCTTTGGTGCACG 61.295 60.000 11.45 0.00 34.99 5.34
151 152 1.372004 TGCACGGTAGGAACGTTCG 60.372 57.895 21.34 12.98 43.58 3.95
176 177 0.996462 CCGAACGACGCACACATTAT 59.004 50.000 0.00 0.00 41.07 1.28
178 179 2.792674 CCGAACGACGCACACATTATAT 59.207 45.455 0.00 0.00 41.07 0.86
179 180 3.361627 CCGAACGACGCACACATTATATG 60.362 47.826 0.00 0.00 41.07 1.78
188 196 2.892852 CACACATTATATGCCCCCAAGG 59.107 50.000 0.00 0.00 39.47 3.61
205 213 1.078426 GGCCTGTGCTATGTTCGGT 60.078 57.895 0.00 0.00 37.74 4.69
396 410 3.357079 CTGAAACTGCGCGCCCTT 61.357 61.111 30.77 18.77 0.00 3.95
581 596 2.103042 GTCACGAGACAGCCATGCC 61.103 63.158 8.20 0.00 44.34 4.40
652 680 0.759346 GTGGAGTTGGTGAGGTGAGT 59.241 55.000 0.00 0.00 0.00 3.41
728 756 2.045340 CCGATCGGGGGCAAAACT 60.045 61.111 26.95 0.00 0.00 2.66
729 757 1.222387 CCGATCGGGGGCAAAACTA 59.778 57.895 26.95 0.00 0.00 2.24
730 758 0.814010 CCGATCGGGGGCAAAACTAG 60.814 60.000 26.95 0.00 0.00 2.57
777 805 2.472049 GCGCACGTTCTTGAGCTC 59.528 61.111 6.82 6.82 39.06 4.09
843 875 4.096003 CCACGTCCCAATCCGCCT 62.096 66.667 0.00 0.00 0.00 5.52
845 877 3.000819 ACGTCCCAATCCGCCTGA 61.001 61.111 0.00 0.00 0.00 3.86
847 879 2.668632 GTCCCAATCCGCCTGACA 59.331 61.111 0.00 0.00 0.00 3.58
848 880 1.745489 GTCCCAATCCGCCTGACAC 60.745 63.158 0.00 0.00 0.00 3.67
849 881 2.819595 CCCAATCCGCCTGACACG 60.820 66.667 0.00 0.00 0.00 4.49
850 882 2.047274 CCAATCCGCCTGACACGT 60.047 61.111 0.00 0.00 0.00 4.49
852 884 1.079819 CAATCCGCCTGACACGTCT 60.080 57.895 0.00 0.00 0.00 4.18
1030 1080 1.078848 GGTGATTGCGAGCTGGAGT 60.079 57.895 0.00 0.00 0.00 3.85
1047 1097 3.799672 TTCCGGGGCGTAATGGGG 61.800 66.667 0.00 0.00 0.00 4.96
1294 1368 4.210120 GCACATAGAATCTCTTTACTGCCG 59.790 45.833 0.00 0.00 0.00 5.69
1367 1446 1.665916 CTGTCGCAGGTGACCACAG 60.666 63.158 3.63 4.80 38.11 3.66
1368 1447 2.369257 CTGTCGCAGGTGACCACAGT 62.369 60.000 3.63 0.00 38.11 3.55
1444 1523 4.276183 AGCGAGTGAATCTAGCGATCTAAA 59.724 41.667 0.00 0.00 46.70 1.85
1445 1524 4.976731 GCGAGTGAATCTAGCGATCTAAAA 59.023 41.667 0.00 0.00 35.34 1.52
1446 1525 5.108179 GCGAGTGAATCTAGCGATCTAAAAC 60.108 44.000 0.00 0.00 35.34 2.43
1447 1526 6.202937 CGAGTGAATCTAGCGATCTAAAACT 58.797 40.000 0.00 0.00 0.00 2.66
1509 1588 1.382522 TCGCCATCTTGATTCTTGCC 58.617 50.000 0.00 0.00 0.00 4.52
1725 1810 0.837691 ATCCTCCAGTGGTGAGCACA 60.838 55.000 17.69 0.00 0.00 4.57
1802 1895 2.152016 ACAGCCCTTTTAAGCGAGTTC 58.848 47.619 0.00 0.00 0.00 3.01
1957 2056 2.032030 AGATTTCCAAGTTTGCGACGTG 60.032 45.455 0.00 0.16 37.47 4.49
1987 2086 4.499696 GGTGTGAGGTTTTCCAATCTTGTG 60.500 45.833 0.00 0.00 43.73 3.33
2117 2216 3.283684 CAGCGCCGGGTTCAACAA 61.284 61.111 2.29 0.00 0.00 2.83
2142 2241 1.004200 TCCGTTTTCTCCGGGCTTC 60.004 57.895 0.00 0.00 45.51 3.86
2283 2382 1.304464 CCAAAAGGGGTGGAGCTCC 60.304 63.158 26.78 26.78 38.54 4.70
2526 2625 2.367567 TGGAAGACTTGGTGGACAGTAC 59.632 50.000 0.00 0.00 0.00 2.73
2604 2703 1.600413 GCAAACTCACCTTTCTTGGCG 60.600 52.381 0.00 0.00 0.00 5.69
2781 2880 2.496070 ACGGCTAGATACTGCAGTTGAA 59.504 45.455 27.06 7.61 34.22 2.69
3029 3136 9.034544 GCATTTGGTATCTTGGTAATTGATTTC 57.965 33.333 0.00 0.00 0.00 2.17
3089 3196 9.577003 GTTGATCTTACGTTTTTACTGTACTTG 57.423 33.333 0.00 0.00 0.00 3.16
3096 3203 9.919348 TTACGTTTTTACTGTACTTGATGAAAC 57.081 29.630 0.00 0.00 0.00 2.78
3179 3286 1.473434 CGTAGAAGATTCAGCCCCCAC 60.473 57.143 0.00 0.00 0.00 4.61
3493 3600 4.827304 TCATCTGAAACGAAATGCACAA 57.173 36.364 0.00 0.00 0.00 3.33
3655 3763 6.765512 TCTCGTATGATGTGCAAATATCCAAA 59.234 34.615 0.00 0.00 0.00 3.28
3657 3765 7.584108 TCGTATGATGTGCAAATATCCAAATC 58.416 34.615 0.00 0.00 0.00 2.17
3664 3772 9.585099 GATGTGCAAATATCCAAATCTTTTACA 57.415 29.630 0.00 0.00 0.00 2.41
3668 3776 9.638239 TGCAAATATCCAAATCTTTTACAGTTC 57.362 29.630 0.00 0.00 0.00 3.01
3837 3953 4.457834 AGTGGTATGTGCTTCAGACTAC 57.542 45.455 12.67 12.67 45.58 2.73
3956 4080 4.815269 AGTGAACTAAGCAAGTCTAGCTG 58.185 43.478 0.00 0.00 42.53 4.24
3962 4086 2.091852 AGCAAGTCTAGCTGCAGAAC 57.908 50.000 20.43 9.31 41.61 3.01
4012 4136 2.486907 GGCATCCTCTTCCTCCATCAAG 60.487 54.545 0.00 0.00 0.00 3.02
4033 4157 7.755591 TCAAGATAAGCATGTGAGAACATTTC 58.244 34.615 0.00 0.00 0.00 2.17
4039 4163 4.529377 AGCATGTGAGAACATTTCCCAAAT 59.471 37.500 0.00 0.00 0.00 2.32
4101 4230 4.103153 GGACATCAGTCATATTCTTGGGGA 59.897 45.833 0.00 0.00 46.80 4.81
4132 4261 3.819368 TCAGCCATTCTTTGTCAGACAA 58.181 40.909 12.24 12.24 36.11 3.18
4199 4328 1.289160 TCTCCAGCTGCCCAAGTATT 58.711 50.000 8.66 0.00 0.00 1.89
4200 4329 1.635487 TCTCCAGCTGCCCAAGTATTT 59.365 47.619 8.66 0.00 0.00 1.40
4201 4330 2.041620 TCTCCAGCTGCCCAAGTATTTT 59.958 45.455 8.66 0.00 0.00 1.82
4202 4331 2.827921 CTCCAGCTGCCCAAGTATTTTT 59.172 45.455 8.66 0.00 0.00 1.94
4481 4624 1.003233 GAACACCCTCAGGTCTGCC 60.003 63.158 0.00 0.00 46.45 4.85
4532 4675 1.402456 GCAACAGCAAGCCAAGATGAG 60.402 52.381 0.00 0.00 0.00 2.90
4628 4771 2.939103 CACCTGCCATGCTTTCTAGTAC 59.061 50.000 0.00 0.00 0.00 2.73
4633 4776 3.199727 TGCCATGCTTTCTAGTACCATGA 59.800 43.478 13.19 0.00 36.32 3.07
4634 4777 4.141413 TGCCATGCTTTCTAGTACCATGAT 60.141 41.667 13.19 0.00 36.32 2.45
4700 4845 5.308014 TGGGATCTCCGTTGATGAATATTG 58.692 41.667 0.00 0.00 38.76 1.90
4718 4863 7.387673 TGAATATTGTAGTGATTTAGATGCCCG 59.612 37.037 0.00 0.00 0.00 6.13
4747 4893 6.987386 AGTAAAGCCAGTAGCATCTATACTG 58.013 40.000 6.21 6.21 46.36 2.74
4748 4894 5.878406 AAAGCCAGTAGCATCTATACTGT 57.122 39.130 11.09 0.00 45.68 3.55
4816 4962 6.215121 TGCCAATGTTCACTTTTCAGTATTG 58.785 36.000 0.00 0.00 29.95 1.90
4913 5059 5.827666 AGTGGTTCAACGTAGGAAAATTTG 58.172 37.500 4.36 0.00 0.00 2.32
4925 5071 6.350949 CGTAGGAAAATTTGGATTGGGTTGAT 60.351 38.462 0.00 0.00 0.00 2.57
4927 5073 7.754091 AGGAAAATTTGGATTGGGTTGATAT 57.246 32.000 0.00 0.00 0.00 1.63
4985 5131 8.616076 CAAAGGTAAGGAAAGATATGATGTGAC 58.384 37.037 0.00 0.00 0.00 3.67
4995 5141 9.317936 GAAAGATATGATGTGACTGACATTGTA 57.682 33.333 0.00 0.00 45.90 2.41
4999 5145 9.696917 GATATGATGTGACTGACATTGTATACA 57.303 33.333 0.08 0.08 45.90 2.29
5023 5169 4.212716 ACAACTACAGGTTTTCTTTCCCC 58.787 43.478 0.00 0.00 35.74 4.81
5096 5254 1.621938 AAAAACGGTGGGAGGGGTT 59.378 52.632 0.00 0.00 0.00 4.11
5128 5286 2.714259 CGAAAGCAACCAACTCCCA 58.286 52.632 0.00 0.00 0.00 4.37
5149 5307 7.782049 TCCCATTTAATAGTAGAGATATGCCG 58.218 38.462 0.00 0.00 0.00 5.69
5160 5318 4.139786 AGAGATATGCCGCAATGATGTTT 58.860 39.130 0.00 0.00 0.00 2.83
5177 5335 7.990541 TGATGTTTGCAGTTCATAATTATGC 57.009 32.000 18.89 10.28 37.40 3.14
5186 5344 7.086376 GCAGTTCATAATTATGCCACCTAATG 58.914 38.462 18.89 12.60 33.76 1.90
5245 5403 9.880157 AAACATAATGAATTCCTCAATTTCCAG 57.120 29.630 2.27 0.00 37.67 3.86
5246 5404 8.015185 ACATAATGAATTCCTCAATTTCCAGG 57.985 34.615 2.27 0.00 37.67 4.45
5247 5405 7.840716 ACATAATGAATTCCTCAATTTCCAGGA 59.159 33.333 2.27 0.00 37.67 3.86
5248 5406 8.867097 CATAATGAATTCCTCAATTTCCAGGAT 58.133 33.333 2.27 0.00 38.66 3.24
5249 5407 7.744678 AATGAATTCCTCAATTTCCAGGATT 57.255 32.000 2.27 0.00 38.66 3.01
5250 5408 8.843308 AATGAATTCCTCAATTTCCAGGATTA 57.157 30.769 2.27 0.00 38.66 1.75
5251 5409 9.443365 AATGAATTCCTCAATTTCCAGGATTAT 57.557 29.630 2.27 0.00 38.66 1.28
5252 5410 8.241497 TGAATTCCTCAATTTCCAGGATTATG 57.759 34.615 2.27 0.00 38.66 1.90
5253 5411 7.288389 TGAATTCCTCAATTTCCAGGATTATGG 59.712 37.037 2.27 0.00 38.66 2.74
5266 5424 5.059833 CAGGATTATGGAACTTCCTGTAGC 58.940 45.833 9.31 0.00 46.64 3.58
5267 5425 4.721776 AGGATTATGGAACTTCCTGTAGCA 59.278 41.667 9.31 0.00 37.22 3.49
5268 5426 5.370880 AGGATTATGGAACTTCCTGTAGCAT 59.629 40.000 9.31 0.00 37.22 3.79
5269 5427 5.471456 GGATTATGGAACTTCCTGTAGCATG 59.529 44.000 9.31 0.00 37.46 4.06
5270 5428 5.435686 TTATGGAACTTCCTGTAGCATGT 57.564 39.130 9.31 0.00 37.46 3.21
5271 5429 3.788227 TGGAACTTCCTGTAGCATGTT 57.212 42.857 9.31 0.00 37.46 2.71
5272 5430 3.674997 TGGAACTTCCTGTAGCATGTTC 58.325 45.455 9.31 0.00 37.46 3.18
5273 5431 3.010420 GGAACTTCCTGTAGCATGTTCC 58.990 50.000 0.00 0.00 43.98 3.62
5274 5432 3.674997 GAACTTCCTGTAGCATGTTCCA 58.325 45.455 0.00 0.00 0.00 3.53
5275 5433 4.265073 GAACTTCCTGTAGCATGTTCCAT 58.735 43.478 0.00 0.00 0.00 3.41
5276 5434 5.428253 GAACTTCCTGTAGCATGTTCCATA 58.572 41.667 0.00 0.00 0.00 2.74
5277 5435 5.028549 ACTTCCTGTAGCATGTTCCATAG 57.971 43.478 0.00 0.00 0.00 2.23
5278 5436 4.141620 ACTTCCTGTAGCATGTTCCATAGG 60.142 45.833 0.00 0.00 0.00 2.57
5279 5437 2.705658 TCCTGTAGCATGTTCCATAGGG 59.294 50.000 0.00 0.00 0.00 3.53
5280 5438 2.439507 CCTGTAGCATGTTCCATAGGGT 59.560 50.000 0.00 0.00 34.93 4.34
5281 5439 3.117888 CCTGTAGCATGTTCCATAGGGTT 60.118 47.826 0.00 0.00 34.93 4.11
5282 5440 4.526970 CTGTAGCATGTTCCATAGGGTTT 58.473 43.478 0.00 0.00 34.93 3.27
5283 5441 4.929479 TGTAGCATGTTCCATAGGGTTTT 58.071 39.130 0.00 0.00 34.93 2.43
5284 5442 5.329399 TGTAGCATGTTCCATAGGGTTTTT 58.671 37.500 0.00 0.00 34.93 1.94
5311 5469 8.592105 TTTTGAAACAGAGGCATAAGATTTTG 57.408 30.769 0.00 0.00 0.00 2.44
5312 5470 5.713025 TGAAACAGAGGCATAAGATTTTGC 58.287 37.500 0.02 0.02 38.14 3.68
5322 5480 6.382869 GCATAAGATTTTGCCTCATGTACT 57.617 37.500 0.00 0.00 32.66 2.73
5323 5481 7.496529 GCATAAGATTTTGCCTCATGTACTA 57.503 36.000 0.00 0.00 32.66 1.82
5324 5482 7.930217 GCATAAGATTTTGCCTCATGTACTAA 58.070 34.615 0.00 0.00 32.66 2.24
5325 5483 8.571336 GCATAAGATTTTGCCTCATGTACTAAT 58.429 33.333 0.00 0.00 32.66 1.73
5327 5485 6.851222 AGATTTTGCCTCATGTACTAATCG 57.149 37.500 0.00 0.00 0.00 3.34
5328 5486 6.582636 AGATTTTGCCTCATGTACTAATCGA 58.417 36.000 0.00 0.00 0.00 3.59
5329 5487 6.703607 AGATTTTGCCTCATGTACTAATCGAG 59.296 38.462 0.00 0.00 0.00 4.04
5330 5488 5.592104 TTTGCCTCATGTACTAATCGAGA 57.408 39.130 0.00 0.00 0.00 4.04
5331 5489 4.837896 TGCCTCATGTACTAATCGAGAG 57.162 45.455 0.00 0.00 0.00 3.20
5348 5506 6.145338 TCGAGAGAACAGAGTTTTACAAGT 57.855 37.500 0.00 0.00 37.03 3.16
5349 5507 7.268199 TCGAGAGAACAGAGTTTTACAAGTA 57.732 36.000 0.00 0.00 37.03 2.24
5350 5508 7.137426 TCGAGAGAACAGAGTTTTACAAGTAC 58.863 38.462 0.00 0.00 37.03 2.73
5351 5509 6.362820 CGAGAGAACAGAGTTTTACAAGTACC 59.637 42.308 0.00 0.00 0.00 3.34
5352 5510 6.522946 AGAGAACAGAGTTTTACAAGTACCC 58.477 40.000 0.00 0.00 0.00 3.69
5353 5511 6.326843 AGAGAACAGAGTTTTACAAGTACCCT 59.673 38.462 0.00 0.00 0.00 4.34
5354 5512 6.522946 AGAACAGAGTTTTACAAGTACCCTC 58.477 40.000 0.00 0.00 0.00 4.30
5355 5513 5.881923 ACAGAGTTTTACAAGTACCCTCA 57.118 39.130 0.00 0.00 0.00 3.86
5356 5514 6.243216 ACAGAGTTTTACAAGTACCCTCAA 57.757 37.500 0.00 0.00 0.00 3.02
5357 5515 6.655930 ACAGAGTTTTACAAGTACCCTCAAA 58.344 36.000 0.00 0.00 0.00 2.69
5358 5516 7.114095 ACAGAGTTTTACAAGTACCCTCAAAA 58.886 34.615 0.00 0.00 0.00 2.44
5359 5517 7.066645 ACAGAGTTTTACAAGTACCCTCAAAAC 59.933 37.037 12.21 12.21 36.56 2.43
5360 5518 7.066525 CAGAGTTTTACAAGTACCCTCAAAACA 59.933 37.037 18.13 0.00 37.99 2.83
5361 5519 7.612633 AGAGTTTTACAAGTACCCTCAAAACAA 59.387 33.333 18.13 0.00 37.99 2.83
5362 5520 7.541162 AGTTTTACAAGTACCCTCAAAACAAC 58.459 34.615 18.13 2.54 37.99 3.32
5363 5521 5.738118 TTACAAGTACCCTCAAAACAACG 57.262 39.130 0.00 0.00 0.00 4.10
5364 5522 2.356695 ACAAGTACCCTCAAAACAACGC 59.643 45.455 0.00 0.00 0.00 4.84
5365 5523 2.335316 AGTACCCTCAAAACAACGCA 57.665 45.000 0.00 0.00 0.00 5.24
5366 5524 2.858745 AGTACCCTCAAAACAACGCAT 58.141 42.857 0.00 0.00 0.00 4.73
5367 5525 2.552315 AGTACCCTCAAAACAACGCATG 59.448 45.455 0.00 0.00 0.00 4.06
5368 5526 0.673437 ACCCTCAAAACAACGCATGG 59.327 50.000 0.00 0.00 0.00 3.66
5369 5527 0.667184 CCCTCAAAACAACGCATGGC 60.667 55.000 0.00 0.00 0.00 4.40
5370 5528 0.031857 CCTCAAAACAACGCATGGCA 59.968 50.000 0.00 0.00 0.00 4.92
5371 5529 1.537776 CCTCAAAACAACGCATGGCAA 60.538 47.619 0.00 0.00 0.00 4.52
5372 5530 1.788308 CTCAAAACAACGCATGGCAAG 59.212 47.619 0.00 0.00 0.00 4.01
5373 5531 0.232816 CAAAACAACGCATGGCAAGC 59.767 50.000 4.29 4.29 0.00 4.01
5398 5556 2.759114 CCCCATGGCAGTGTCACT 59.241 61.111 6.09 0.00 0.00 3.41
5455 5613 2.204090 TTGGGGAGGAGGGTGGTC 60.204 66.667 0.00 0.00 0.00 4.02
5504 5662 3.426568 GCTGTTGGTCGCAGGAGC 61.427 66.667 0.00 0.00 41.07 4.70
5555 5713 4.147219 ACACAGCGCATAAAGAAGAAAC 57.853 40.909 11.47 0.00 0.00 2.78
5586 5744 7.338196 TGACTGTGTTGATCCTTTAAGAACAAA 59.662 33.333 0.00 0.00 31.35 2.83
5618 5776 2.205022 TGATTTGAGGCAGGTTGAGG 57.795 50.000 0.00 0.00 0.00 3.86
5619 5777 0.813821 GATTTGAGGCAGGTTGAGGC 59.186 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.678218 GCATGTTCTTTTTAGAAGAGCGATGAT 60.678 37.037 11.97 0.00 31.26 2.45
1 2 6.402550 GCATGTTCTTTTTAGAAGAGCGATGA 60.403 38.462 11.97 0.00 31.26 2.92
2 3 5.736358 GCATGTTCTTTTTAGAAGAGCGATG 59.264 40.000 0.00 2.74 31.26 3.84
3 4 5.412594 TGCATGTTCTTTTTAGAAGAGCGAT 59.587 36.000 0.00 0.00 31.26 4.58
4 5 4.754618 TGCATGTTCTTTTTAGAAGAGCGA 59.245 37.500 0.00 0.00 31.26 4.93
5 6 4.848299 GTGCATGTTCTTTTTAGAAGAGCG 59.152 41.667 0.00 0.00 31.26 5.03
6 7 4.848299 CGTGCATGTTCTTTTTAGAAGAGC 59.152 41.667 0.00 0.00 0.00 4.09
7 8 5.179368 TCCGTGCATGTTCTTTTTAGAAGAG 59.821 40.000 4.96 0.00 0.00 2.85
8 9 5.060506 TCCGTGCATGTTCTTTTTAGAAGA 58.939 37.500 4.96 0.00 0.00 2.87
9 10 5.356882 TCCGTGCATGTTCTTTTTAGAAG 57.643 39.130 4.96 0.00 0.00 2.85
10 11 5.957842 ATCCGTGCATGTTCTTTTTAGAA 57.042 34.783 4.96 0.00 0.00 2.10
11 12 5.957842 AATCCGTGCATGTTCTTTTTAGA 57.042 34.783 4.96 0.00 0.00 2.10
12 13 8.586273 CATTAAATCCGTGCATGTTCTTTTTAG 58.414 33.333 4.96 0.00 0.00 1.85
13 14 8.300286 TCATTAAATCCGTGCATGTTCTTTTTA 58.700 29.630 4.96 0.00 0.00 1.52
14 15 7.151308 TCATTAAATCCGTGCATGTTCTTTTT 58.849 30.769 4.96 0.53 0.00 1.94
15 16 6.686630 TCATTAAATCCGTGCATGTTCTTTT 58.313 32.000 4.96 2.16 0.00 2.27
16 17 6.266168 TCATTAAATCCGTGCATGTTCTTT 57.734 33.333 4.96 4.31 0.00 2.52
17 18 5.895636 TCATTAAATCCGTGCATGTTCTT 57.104 34.783 4.96 0.00 0.00 2.52
18 19 6.455360 AATCATTAAATCCGTGCATGTTCT 57.545 33.333 4.96 0.00 0.00 3.01
19 20 6.360681 GCTAATCATTAAATCCGTGCATGTTC 59.639 38.462 4.96 0.00 0.00 3.18
20 21 6.208644 GCTAATCATTAAATCCGTGCATGTT 58.791 36.000 4.96 0.00 0.00 2.71
21 22 5.278463 GGCTAATCATTAAATCCGTGCATGT 60.278 40.000 4.96 0.00 0.00 3.21
22 23 5.156355 GGCTAATCATTAAATCCGTGCATG 58.844 41.667 0.00 0.00 0.00 4.06
23 24 4.218417 GGGCTAATCATTAAATCCGTGCAT 59.782 41.667 0.00 0.00 0.00 3.96
35 36 3.138283 TCTCCGGAAATGGGCTAATCATT 59.862 43.478 5.23 0.00 36.50 2.57
39 40 2.777692 TCTTCTCCGGAAATGGGCTAAT 59.222 45.455 5.23 0.00 0.00 1.73
44 45 5.405935 AATTTTTCTTCTCCGGAAATGGG 57.594 39.130 5.23 0.00 33.51 4.00
51 52 4.939509 TTAGCGAATTTTTCTTCTCCGG 57.060 40.909 0.00 0.00 0.00 5.14
52 53 6.623743 CGTATTTAGCGAATTTTTCTTCTCCG 59.376 38.462 0.00 0.00 0.00 4.63
62 63 8.643752 CCAAAACAAATCGTATTTAGCGAATTT 58.356 29.630 0.00 0.00 41.84 1.82
63 64 7.201401 GCCAAAACAAATCGTATTTAGCGAATT 60.201 33.333 0.00 0.00 41.84 2.17
86 87 2.682494 GGTCTAGTGGTCCGGCCA 60.682 66.667 12.86 12.86 46.95 5.36
88 89 2.893398 CTGGTCTAGTGGTCCGGC 59.107 66.667 0.00 0.00 0.00 6.13
90 91 1.338337 CTATGCTGGTCTAGTGGTCCG 59.662 57.143 0.00 0.00 0.00 4.79
92 93 1.757118 TGCTATGCTGGTCTAGTGGTC 59.243 52.381 0.00 0.00 0.00 4.02
93 94 1.866015 TGCTATGCTGGTCTAGTGGT 58.134 50.000 0.00 0.00 0.00 4.16
96 97 3.033909 TCACATGCTATGCTGGTCTAGT 58.966 45.455 0.00 0.00 0.00 2.57
97 98 3.388308 GTCACATGCTATGCTGGTCTAG 58.612 50.000 0.00 0.00 0.00 2.43
98 99 2.223805 CGTCACATGCTATGCTGGTCTA 60.224 50.000 0.00 0.00 0.00 2.59
99 100 1.472201 CGTCACATGCTATGCTGGTCT 60.472 52.381 0.00 0.00 0.00 3.85
100 101 0.933097 CGTCACATGCTATGCTGGTC 59.067 55.000 0.00 0.00 0.00 4.02
101 102 0.462581 CCGTCACATGCTATGCTGGT 60.463 55.000 0.00 0.00 0.00 4.00
102 103 0.179076 TCCGTCACATGCTATGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
121 122 1.302033 CCGTGCACCAAAGCTCTCT 60.302 57.895 12.15 0.00 34.99 3.10
123 124 0.320771 CTACCGTGCACCAAAGCTCT 60.321 55.000 12.15 0.00 34.99 4.09
138 139 1.005867 TGGCACGAACGTTCCTACC 60.006 57.895 22.07 19.18 32.65 3.18
188 196 0.391130 TCACCGAACATAGCACAGGC 60.391 55.000 0.00 0.00 41.61 4.85
189 197 1.732259 GTTCACCGAACATAGCACAGG 59.268 52.381 2.05 0.00 41.62 4.00
396 410 3.443925 CGGCGACCTCTCTGCTGA 61.444 66.667 0.00 0.00 37.16 4.26
626 654 2.446994 ACCAACTCCACCCACCGA 60.447 61.111 0.00 0.00 0.00 4.69
726 754 2.097825 ACGGACAGTTTATCGGCTAGT 58.902 47.619 0.00 0.00 0.00 2.57
727 755 2.858344 CAACGGACAGTTTATCGGCTAG 59.142 50.000 0.00 0.00 42.02 3.42
728 756 2.492881 TCAACGGACAGTTTATCGGCTA 59.507 45.455 0.00 0.00 42.02 3.93
729 757 1.274167 TCAACGGACAGTTTATCGGCT 59.726 47.619 0.00 0.00 42.02 5.52
730 758 1.717194 TCAACGGACAGTTTATCGGC 58.283 50.000 0.00 0.00 42.02 5.54
732 760 5.524511 TGAAATCAACGGACAGTTTATCG 57.475 39.130 0.00 0.00 42.02 2.92
733 761 5.324697 GCTGAAATCAACGGACAGTTTATC 58.675 41.667 0.00 0.00 42.02 1.75
734 762 4.142902 CGCTGAAATCAACGGACAGTTTAT 60.143 41.667 0.00 0.00 42.02 1.40
842 874 6.092122 TGGCATTTTAATAGAAGACGTGTCAG 59.908 38.462 0.00 0.00 0.00 3.51
843 875 5.935206 TGGCATTTTAATAGAAGACGTGTCA 59.065 36.000 0.00 0.00 0.00 3.58
845 877 5.354234 CCTGGCATTTTAATAGAAGACGTGT 59.646 40.000 0.00 0.00 0.00 4.49
847 879 5.585047 GTCCTGGCATTTTAATAGAAGACGT 59.415 40.000 0.00 0.00 0.00 4.34
848 880 5.817816 AGTCCTGGCATTTTAATAGAAGACG 59.182 40.000 0.00 0.00 0.00 4.18
849 881 7.554476 AGAAGTCCTGGCATTTTAATAGAAGAC 59.446 37.037 0.00 0.00 0.00 3.01
850 882 7.633789 AGAAGTCCTGGCATTTTAATAGAAGA 58.366 34.615 0.00 0.00 0.00 2.87
852 884 7.336931 GTGAGAAGTCCTGGCATTTTAATAGAA 59.663 37.037 0.00 0.00 0.00 2.10
1030 1080 3.799672 CCCCATTACGCCCCGGAA 61.800 66.667 0.73 0.00 32.91 4.30
1047 1097 4.890306 GCCCCCTCCTCCTCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
1048 1098 3.773154 AGCCCCCTCCTCCTCCTC 61.773 72.222 0.00 0.00 0.00 3.71
1049 1099 4.101077 CAGCCCCCTCCTCCTCCT 62.101 72.222 0.00 0.00 0.00 3.69
1315 1394 2.740055 GCTAGATCGGCATGGCGG 60.740 66.667 36.93 23.25 0.00 6.13
1367 1446 0.322008 CTGGAAAGGCTCCTGTGGAC 60.322 60.000 0.00 0.00 45.64 4.02
1368 1447 0.473694 TCTGGAAAGGCTCCTGTGGA 60.474 55.000 0.00 0.00 45.64 4.02
1444 1523 1.073199 CCCTCCGGCTTTGTCAGTT 59.927 57.895 0.00 0.00 0.00 3.16
1445 1524 2.750350 CCCTCCGGCTTTGTCAGT 59.250 61.111 0.00 0.00 0.00 3.41
1523 1602 1.211190 GCTCCTTTTCCGCTTGCTG 59.789 57.895 0.00 0.00 0.00 4.41
1532 1611 2.272471 CCCCCTCCGCTCCTTTTC 59.728 66.667 0.00 0.00 0.00 2.29
1802 1895 0.459934 CAGAGGCTTCAGAGAAGGCG 60.460 60.000 22.23 9.19 46.12 5.52
1805 1898 2.008045 GCTGCAGAGGCTTCAGAGAAG 61.008 57.143 20.43 2.48 41.91 2.85
1806 1899 0.036577 GCTGCAGAGGCTTCAGAGAA 60.037 55.000 20.43 0.00 41.91 2.87
1809 1902 2.104572 AACGCTGCAGAGGCTTCAGA 62.105 55.000 20.43 0.00 41.91 3.27
1853 1949 4.254709 TTCAGCCCACACTGCGCT 62.255 61.111 9.73 0.00 37.59 5.92
1866 1962 0.979665 TCTTGCCACTCTCCCTTCAG 59.020 55.000 0.00 0.00 0.00 3.02
1957 2056 2.152016 GAAAACCTCACACCACCTAGC 58.848 52.381 0.00 0.00 0.00 3.42
1987 2086 0.316196 GTCGAACAGCACACAAGCAC 60.316 55.000 0.00 0.00 36.85 4.40
2187 2286 3.071206 ACGCCGGAGCTGATCTGT 61.071 61.111 5.05 0.00 36.60 3.41
2250 2349 1.926489 TTGGTACCCCAAGGCCGAT 60.926 57.895 10.07 0.00 45.93 4.18
2526 2625 5.009510 AGACACGGATGAAGATACAGATGAG 59.990 44.000 0.00 0.00 0.00 2.90
2604 2703 5.615925 AATGTTCAGGTATCAGTACTCCC 57.384 43.478 0.00 0.00 0.00 4.30
2763 2862 6.145858 CAGATGATTCAACTGCAGTATCTAGC 59.854 42.308 22.01 12.34 28.40 3.42
2781 2880 2.763933 CTAGGCAATGACGCAGATGAT 58.236 47.619 0.00 0.00 0.00 2.45
3029 3136 8.494347 GTTATTCAGCTTAGAAGTGCTATGATG 58.506 37.037 3.39 3.39 40.21 3.07
3089 3196 9.766277 CAGCTGAAGATTTACTTAAGTTTCATC 57.234 33.333 14.49 12.06 38.88 2.92
3130 3237 4.160439 AGCCTCTTCGTCTGATATGAAACA 59.840 41.667 0.00 0.00 32.68 2.83
3179 3286 4.469945 TCCTTGAAGTTATAGGGGTGACAG 59.530 45.833 3.57 0.00 0.00 3.51
3210 3317 2.235891 TCTGGACTAGTTTGAGTCGCA 58.764 47.619 0.00 0.00 45.80 5.10
3327 3434 0.749049 TCTGCACATCCCTGATCTCG 59.251 55.000 0.00 0.00 0.00 4.04
3440 3547 3.447944 AGAAGATTTAGAGTCCACCGTCC 59.552 47.826 0.00 0.00 0.00 4.79
3493 3600 2.193993 AGCACCGGTCCCTTACTTTAT 58.806 47.619 2.59 0.00 0.00 1.40
3664 3772 7.399245 TTTACTTTGCACAGTTTTAGGAACT 57.601 32.000 11.39 0.00 46.37 3.01
3861 3977 6.824958 AATATTTCAGCAGGGGTCTTACTA 57.175 37.500 0.00 0.00 0.00 1.82
3906 4030 0.035820 CCTTTGGCCCGTTGCTACTA 60.036 55.000 0.00 0.00 40.92 1.82
3956 4080 8.485976 ACTAGTCAGATTTTATCTTGTTCTGC 57.514 34.615 0.00 0.00 37.58 4.26
3987 4111 1.925255 TGGAGGAAGAGGATGCCAATT 59.075 47.619 0.00 0.00 0.00 2.32
4012 4136 5.357878 TGGGAAATGTTCTCACATGCTTATC 59.642 40.000 0.00 0.00 43.34 1.75
4033 4157 4.549458 CACTAAGCAGTTGTTCATTTGGG 58.451 43.478 0.00 0.00 30.46 4.12
4101 4230 6.064717 ACAAAGAATGGCTGAAAGTAAGAGT 58.935 36.000 0.00 0.00 35.30 3.24
4481 4624 3.656559 CATCCCTTGTGCTTTTCTTTGG 58.343 45.455 0.00 0.00 0.00 3.28
4628 4771 6.495181 ACTTACTCAGTAGTGGGATATCATGG 59.505 42.308 3.89 0.00 36.36 3.66
4633 4776 5.661312 TGCAACTTACTCAGTAGTGGGATAT 59.339 40.000 3.89 0.00 36.36 1.63
4634 4777 5.020795 TGCAACTTACTCAGTAGTGGGATA 58.979 41.667 3.89 0.00 36.36 2.59
4700 4845 5.813080 AAAACGGGCATCTAAATCACTAC 57.187 39.130 0.00 0.00 0.00 2.73
4718 4863 6.986904 AGATGCTACTGGCTTTACTAAAAC 57.013 37.500 0.00 0.00 42.39 2.43
4747 4893 2.740981 CCTGATGTGACAGAAAGAGCAC 59.259 50.000 0.00 0.00 39.94 4.40
4748 4894 2.873245 GCCTGATGTGACAGAAAGAGCA 60.873 50.000 0.00 0.00 39.94 4.26
4839 4985 5.522097 CACGGGTTTTGAGCTTGTAATTTTT 59.478 36.000 0.00 0.00 0.00 1.94
4840 4986 5.047188 CACGGGTTTTGAGCTTGTAATTTT 58.953 37.500 0.00 0.00 0.00 1.82
4841 4987 4.616953 CACGGGTTTTGAGCTTGTAATTT 58.383 39.130 0.00 0.00 0.00 1.82
4927 5073 8.336235 GGATTCCCTTCCCACAATATATATCAA 58.664 37.037 0.00 0.00 0.00 2.57
4995 5141 9.227777 GGAAAGAAAACCTGTAGTTGTATGTAT 57.772 33.333 0.00 0.00 39.19 2.29
4999 5145 6.008331 GGGGAAAGAAAACCTGTAGTTGTAT 58.992 40.000 0.00 0.00 39.19 2.29
5009 5155 1.133167 CCACCTGGGGAAAGAAAACCT 60.133 52.381 0.00 0.00 0.00 3.50
5023 5169 0.613260 TCCAAATCGACTCCCACCTG 59.387 55.000 0.00 0.00 0.00 4.00
5082 5240 2.448931 TTCAACCCCTCCCACCGT 60.449 61.111 0.00 0.00 0.00 4.83
5096 5254 1.806542 GCTTTCGCTTCCATCACTTCA 59.193 47.619 0.00 0.00 0.00 3.02
5128 5286 9.102757 CATTGCGGCATATCTCTACTATTAAAT 57.897 33.333 2.28 0.00 0.00 1.40
5160 5318 4.535781 AGGTGGCATAATTATGAACTGCA 58.464 39.130 26.22 4.36 35.75 4.41
5169 5327 7.570132 ACACACTACATTAGGTGGCATAATTA 58.430 34.615 0.00 0.00 37.72 1.40
5177 5335 3.861276 TCGACACACTACATTAGGTGG 57.139 47.619 0.00 0.00 37.72 4.61
5186 5344 6.062434 ACATAAGAGCTATCGACACACTAC 57.938 41.667 0.00 0.00 0.00 2.73
5228 5386 7.506938 TCCATAATCCTGGAAATTGAGGAATTC 59.493 37.037 0.00 0.00 42.36 2.17
5229 5387 7.364627 TCCATAATCCTGGAAATTGAGGAATT 58.635 34.615 0.00 0.00 42.36 2.17
5230 5388 6.925934 TCCATAATCCTGGAAATTGAGGAAT 58.074 36.000 0.00 1.12 42.36 3.01
5232 5390 5.992564 TCCATAATCCTGGAAATTGAGGA 57.007 39.130 0.00 1.18 42.36 3.71
5244 5402 4.721776 TGCTACAGGAAGTTCCATAATCCT 59.278 41.667 23.87 0.00 43.00 3.24
5245 5403 5.036117 TGCTACAGGAAGTTCCATAATCC 57.964 43.478 23.87 7.90 39.61 3.01
5246 5404 6.058183 ACATGCTACAGGAAGTTCCATAATC 58.942 40.000 23.87 10.04 39.61 1.75
5247 5405 6.006275 ACATGCTACAGGAAGTTCCATAAT 57.994 37.500 23.87 8.36 39.61 1.28
5248 5406 5.435686 ACATGCTACAGGAAGTTCCATAA 57.564 39.130 23.87 7.24 39.61 1.90
5249 5407 5.428253 GAACATGCTACAGGAAGTTCCATA 58.572 41.667 23.87 13.99 39.61 2.74
5250 5408 4.265073 GAACATGCTACAGGAAGTTCCAT 58.735 43.478 23.87 13.59 39.61 3.41
5251 5409 3.674997 GAACATGCTACAGGAAGTTCCA 58.325 45.455 23.87 2.07 39.61 3.53
5253 5411 3.674997 TGGAACATGCTACAGGAAGTTC 58.325 45.455 9.51 9.51 41.28 3.01
5254 5412 3.788227 TGGAACATGCTACAGGAAGTT 57.212 42.857 0.00 0.00 30.29 2.66
5285 5443 9.044150 CAAAATCTTATGCCTCTGTTTCAAAAA 57.956 29.630 0.00 0.00 0.00 1.94
5286 5444 7.171337 GCAAAATCTTATGCCTCTGTTTCAAAA 59.829 33.333 0.00 0.00 36.56 2.44
5287 5445 6.646240 GCAAAATCTTATGCCTCTGTTTCAAA 59.354 34.615 0.00 0.00 36.56 2.69
5288 5446 6.158598 GCAAAATCTTATGCCTCTGTTTCAA 58.841 36.000 0.00 0.00 36.56 2.69
5289 5447 5.713025 GCAAAATCTTATGCCTCTGTTTCA 58.287 37.500 0.00 0.00 36.56 2.69
5299 5457 6.382869 AGTACATGAGGCAAAATCTTATGC 57.617 37.500 0.00 0.00 41.82 3.14
5301 5459 8.993121 CGATTAGTACATGAGGCAAAATCTTAT 58.007 33.333 0.00 0.00 0.00 1.73
5302 5460 8.201464 TCGATTAGTACATGAGGCAAAATCTTA 58.799 33.333 0.00 0.00 0.00 2.10
5303 5461 7.047891 TCGATTAGTACATGAGGCAAAATCTT 58.952 34.615 0.00 0.00 0.00 2.40
5304 5462 6.582636 TCGATTAGTACATGAGGCAAAATCT 58.417 36.000 0.00 0.00 0.00 2.40
5305 5463 6.701841 TCTCGATTAGTACATGAGGCAAAATC 59.298 38.462 0.00 0.48 0.00 2.17
5306 5464 6.582636 TCTCGATTAGTACATGAGGCAAAAT 58.417 36.000 0.00 0.00 0.00 1.82
5307 5465 5.972935 TCTCGATTAGTACATGAGGCAAAA 58.027 37.500 0.00 0.00 0.00 2.44
5308 5466 5.359860 TCTCTCGATTAGTACATGAGGCAAA 59.640 40.000 0.00 0.00 0.00 3.68
5309 5467 4.887655 TCTCTCGATTAGTACATGAGGCAA 59.112 41.667 0.00 0.00 0.00 4.52
5310 5468 4.461198 TCTCTCGATTAGTACATGAGGCA 58.539 43.478 0.00 0.00 0.00 4.75
5311 5469 5.216648 GTTCTCTCGATTAGTACATGAGGC 58.783 45.833 0.00 0.00 0.00 4.70
5312 5470 6.261158 TCTGTTCTCTCGATTAGTACATGAGG 59.739 42.308 0.00 0.00 0.00 3.86
5313 5471 7.011950 ACTCTGTTCTCTCGATTAGTACATGAG 59.988 40.741 18.54 18.54 0.00 2.90
5314 5472 6.824196 ACTCTGTTCTCTCGATTAGTACATGA 59.176 38.462 0.00 7.00 0.00 3.07
5315 5473 7.022055 ACTCTGTTCTCTCGATTAGTACATG 57.978 40.000 7.51 0.00 0.00 3.21
5316 5474 7.633193 AACTCTGTTCTCTCGATTAGTACAT 57.367 36.000 7.51 0.00 0.00 2.29
5317 5475 7.450124 AAACTCTGTTCTCTCGATTAGTACA 57.550 36.000 0.00 7.03 0.00 2.90
5318 5476 9.276397 GTAAAACTCTGTTCTCTCGATTAGTAC 57.724 37.037 0.00 0.00 0.00 2.73
5319 5477 9.006839 TGTAAAACTCTGTTCTCTCGATTAGTA 57.993 33.333 0.00 0.00 0.00 1.82
5320 5478 7.883217 TGTAAAACTCTGTTCTCTCGATTAGT 58.117 34.615 0.00 0.00 0.00 2.24
5321 5479 8.744008 TTGTAAAACTCTGTTCTCTCGATTAG 57.256 34.615 0.00 0.00 0.00 1.73
5322 5480 8.358148 ACTTGTAAAACTCTGTTCTCTCGATTA 58.642 33.333 0.00 0.00 0.00 1.75
5323 5481 7.210873 ACTTGTAAAACTCTGTTCTCTCGATT 58.789 34.615 0.00 0.00 0.00 3.34
5324 5482 6.750148 ACTTGTAAAACTCTGTTCTCTCGAT 58.250 36.000 0.00 0.00 0.00 3.59
5325 5483 6.145338 ACTTGTAAAACTCTGTTCTCTCGA 57.855 37.500 0.00 0.00 0.00 4.04
5326 5484 6.362820 GGTACTTGTAAAACTCTGTTCTCTCG 59.637 42.308 0.00 0.00 0.00 4.04
5327 5485 6.645827 GGGTACTTGTAAAACTCTGTTCTCTC 59.354 42.308 0.00 0.00 0.00 3.20
5328 5486 6.326843 AGGGTACTTGTAAAACTCTGTTCTCT 59.673 38.462 0.00 0.00 0.00 3.10
5329 5487 6.522946 AGGGTACTTGTAAAACTCTGTTCTC 58.477 40.000 0.00 0.00 0.00 2.87
5330 5488 6.099269 TGAGGGTACTTGTAAAACTCTGTTCT 59.901 38.462 0.00 0.00 0.00 3.01
5331 5489 6.285990 TGAGGGTACTTGTAAAACTCTGTTC 58.714 40.000 0.00 0.00 0.00 3.18
5332 5490 6.243216 TGAGGGTACTTGTAAAACTCTGTT 57.757 37.500 0.00 0.00 0.00 3.16
5333 5491 5.881923 TGAGGGTACTTGTAAAACTCTGT 57.118 39.130 0.00 0.00 0.00 3.41
5334 5492 7.066525 TGTTTTGAGGGTACTTGTAAAACTCTG 59.933 37.037 19.45 0.00 36.87 3.35
5335 5493 7.114095 TGTTTTGAGGGTACTTGTAAAACTCT 58.886 34.615 19.45 0.00 36.87 3.24
5336 5494 7.324354 TGTTTTGAGGGTACTTGTAAAACTC 57.676 36.000 19.45 0.00 36.87 3.01
5337 5495 7.541162 GTTGTTTTGAGGGTACTTGTAAAACT 58.459 34.615 19.45 0.00 36.87 2.66
5338 5496 6.469915 CGTTGTTTTGAGGGTACTTGTAAAAC 59.530 38.462 15.51 15.51 36.69 2.43
5339 5497 6.553524 CGTTGTTTTGAGGGTACTTGTAAAA 58.446 36.000 0.00 0.00 0.00 1.52
5340 5498 5.448904 GCGTTGTTTTGAGGGTACTTGTAAA 60.449 40.000 0.00 0.00 0.00 2.01
5341 5499 4.035441 GCGTTGTTTTGAGGGTACTTGTAA 59.965 41.667 0.00 0.00 0.00 2.41
5342 5500 3.560896 GCGTTGTTTTGAGGGTACTTGTA 59.439 43.478 0.00 0.00 0.00 2.41
5343 5501 2.356695 GCGTTGTTTTGAGGGTACTTGT 59.643 45.455 0.00 0.00 0.00 3.16
5344 5502 2.356382 TGCGTTGTTTTGAGGGTACTTG 59.644 45.455 0.00 0.00 0.00 3.16
5345 5503 2.645802 TGCGTTGTTTTGAGGGTACTT 58.354 42.857 0.00 0.00 0.00 2.24
5346 5504 2.335316 TGCGTTGTTTTGAGGGTACT 57.665 45.000 0.00 0.00 0.00 2.73
5347 5505 2.351350 CCATGCGTTGTTTTGAGGGTAC 60.351 50.000 0.00 0.00 0.00 3.34
5348 5506 1.883275 CCATGCGTTGTTTTGAGGGTA 59.117 47.619 0.00 0.00 0.00 3.69
5349 5507 0.673437 CCATGCGTTGTTTTGAGGGT 59.327 50.000 0.00 0.00 0.00 4.34
5350 5508 0.667184 GCCATGCGTTGTTTTGAGGG 60.667 55.000 0.00 0.00 0.00 4.30
5351 5509 0.031857 TGCCATGCGTTGTTTTGAGG 59.968 50.000 0.00 0.00 0.00 3.86
5352 5510 1.788308 CTTGCCATGCGTTGTTTTGAG 59.212 47.619 0.00 0.00 0.00 3.02
5353 5511 1.850377 CTTGCCATGCGTTGTTTTGA 58.150 45.000 0.00 0.00 0.00 2.69
5354 5512 0.232816 GCTTGCCATGCGTTGTTTTG 59.767 50.000 0.00 0.00 0.00 2.44
5355 5513 2.603915 GCTTGCCATGCGTTGTTTT 58.396 47.368 0.00 0.00 0.00 2.43
5356 5514 4.341827 GCTTGCCATGCGTTGTTT 57.658 50.000 0.00 0.00 0.00 2.83
5363 5521 3.830192 CTTCCCCGCTTGCCATGC 61.830 66.667 0.00 0.00 0.00 4.06
5364 5522 3.830192 GCTTCCCCGCTTGCCATG 61.830 66.667 0.00 0.00 0.00 3.66
5486 5644 3.114616 CTCCTGCGACCAACAGCG 61.115 66.667 0.00 0.00 35.87 5.18
5504 5662 3.622060 AAATGACACCCCGCTCCCG 62.622 63.158 0.00 0.00 0.00 5.14
5555 5713 5.362556 AAAGGATCAACACAGTCAAATCG 57.637 39.130 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.