Multiple sequence alignment - TraesCS6B01G259500

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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 TraesCS6B01G259500 chr6B 100.000 5604 0 0 1 5604 469078172 469072569 0.000000e+00 10349.0
1 TraesCS6B01G259500 chr6A 94.572 5158 150 42 11 5110 411941445 411936360 0.000000e+00 7854.0
2 TraesCS6B01G259500 chr6A 89.623 106 10 1 5148 5252 411936361 411936256 3.520000e-27 134.0
3 TraesCS6B01G259500 chr6A 100.000 35 0 0 5281 5315 411936253 411936219 1.300000e-06 65.8
4 TraesCS6B01G259500 chr6D 94.079 5168 162 54 1 5110 303467287 303462206 0.000000e+00 7716.0
5 TraesCS6B01G259500 chr6D 80.828 459 49 11 5148 5601 303462207 303461783 1.950000e-84 324.0
6 TraesCS6B01G259500 chr1D 91.758 1007 74 5 663 1665 23445104 23446105 0.000000e+00 1391.0
7 TraesCS6B01G259500 chr1A 93.725 255 13 3 1412 1665 354536881 354536629 4.100000e-101 379.0
8 TraesCS6B01G259500 chr5A 93.333 255 14 3 1412 1665 565721036 565720784 1.910000e-99 374.0


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 TraesCS6B01G259500 chr6B 469072569 469078172 5603 True 10349.0 10349 100.000000 1 5604 1 chr6B.!!$R1 5603
1 TraesCS6B01G259500 chr6A 411936219 411941445 5226 True 2684.6 7854 94.731667 11 5315 3 chr6A.!!$R1 5304
2 TraesCS6B01G259500 chr6D 303461783 303467287 5504 True 4020.0 7716 87.453500 1 5601 2 chr6D.!!$R1 5600
3 TraesCS6B01G259500 chr1D 23445104 23446105 1001 False 1391.0 1391 91.758000 663 1665 1 chr1D.!!$F1 1002

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
191 195 1.001378 CTTCCCCTTCAAACAAGCGTG 60.001 52.381 0.00 0.0 0.00 5.34 F
759 786 1.276622 TTGTAGAGGAGTGGCCCTTC 58.723 55.000 0.00 0.0 36.49 3.46 F
945 972 2.029918 AGCAAAATCAAGCGTTCTTCCC 60.030 45.455 0.00 0.0 35.48 3.97 F
1907 1944 0.600255 CGGATCCACCTAATGTCGGC 60.600 60.000 13.41 0.0 36.31 5.54 F
1913 1950 1.138859 CCACCTAATGTCGGCAGATCA 59.861 52.381 0.00 0.0 0.00 2.92 F
2234 2272 1.610038 TGCTGTTGTCCTGCAGATTTG 59.390 47.619 17.39 0.0 42.34 2.32 F
3113 3165 2.217510 TCCAGTAGACACCAGAGGTC 57.782 55.000 0.00 0.0 31.02 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1074 0.240945 CCACATGTTGGCCGAAGAAC 59.759 55.000 0.00 0.0 39.07 3.01 R
1889 1926 0.468226 TGCCGACATTAGGTGGATCC 59.532 55.000 4.20 4.2 0.00 3.36 R
2602 2644 2.681848 CCCAATGCTCTGCTTCTGTTAG 59.318 50.000 0.00 0.0 0.00 2.34 R
3664 3717 0.034767 CAGAGGCTGCATTCCCAGAA 60.035 55.000 0.50 0.0 34.77 3.02 R
3970 4042 4.214119 GCATGCGTACCAATGACATATCTT 59.786 41.667 0.00 0.0 0.00 2.40 R
4157 4229 2.751166 ACAGCGCTAGAACACTGATT 57.249 45.000 10.99 0.0 34.25 2.57 R
5111 5213 0.390860 ATCTAGCGACACTGATGGCC 59.609 55.000 0.00 0.0 0.00 5.36 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
93 95 4.036734 TCGTTGCTTGATTTGCTTTCTTCT 59.963 37.500 0.00 0.00 0.00 2.85
94 96 4.741676 CGTTGCTTGATTTGCTTTCTTCTT 59.258 37.500 0.00 0.00 0.00 2.52
95 97 5.914635 CGTTGCTTGATTTGCTTTCTTCTTA 59.085 36.000 0.00 0.00 0.00 2.10
102 104 6.981722 TGATTTGCTTTCTTCTTACTTTCCC 58.018 36.000 0.00 0.00 0.00 3.97
166 170 7.944554 TCTTCTCTTCTCTTCTCTTCTCTTCTT 59.055 37.037 0.00 0.00 0.00 2.52
168 172 7.461749 TCTCTTCTCTTCTCTTCTCTTCTTCT 58.538 38.462 0.00 0.00 0.00 2.85
169 173 7.944554 TCTCTTCTCTTCTCTTCTCTTCTTCTT 59.055 37.037 0.00 0.00 0.00 2.52
170 174 9.231297 CTCTTCTCTTCTCTTCTCTTCTTCTTA 57.769 37.037 0.00 0.00 0.00 2.10
171 175 9.010029 TCTTCTCTTCTCTTCTCTTCTTCTTAC 57.990 37.037 0.00 0.00 0.00 2.34
172 176 8.934023 TTCTCTTCTCTTCTCTTCTTCTTACT 57.066 34.615 0.00 0.00 0.00 2.24
173 177 8.934023 TCTCTTCTCTTCTCTTCTTCTTACTT 57.066 34.615 0.00 0.00 0.00 2.24
174 178 9.010029 TCTCTTCTCTTCTCTTCTTCTTACTTC 57.990 37.037 0.00 0.00 0.00 3.01
175 179 8.117813 TCTTCTCTTCTCTTCTTCTTACTTCC 57.882 38.462 0.00 0.00 0.00 3.46
176 180 6.844097 TCTCTTCTCTTCTTCTTACTTCCC 57.156 41.667 0.00 0.00 0.00 3.97
177 181 5.717654 TCTCTTCTCTTCTTCTTACTTCCCC 59.282 44.000 0.00 0.00 0.00 4.81
178 182 5.656420 TCTTCTCTTCTTCTTACTTCCCCT 58.344 41.667 0.00 0.00 0.00 4.79
179 183 6.085416 TCTTCTCTTCTTCTTACTTCCCCTT 58.915 40.000 0.00 0.00 0.00 3.95
180 184 6.211785 TCTTCTCTTCTTCTTACTTCCCCTTC 59.788 42.308 0.00 0.00 0.00 3.46
182 186 5.844516 TCTCTTCTTCTTACTTCCCCTTCAA 59.155 40.000 0.00 0.00 0.00 2.69
183 187 6.329197 TCTCTTCTTCTTACTTCCCCTTCAAA 59.671 38.462 0.00 0.00 0.00 2.69
184 188 6.296803 TCTTCTTCTTACTTCCCCTTCAAAC 58.703 40.000 0.00 0.00 0.00 2.93
185 189 5.640158 TCTTCTTACTTCCCCTTCAAACA 57.360 39.130 0.00 0.00 0.00 2.83
191 195 1.001378 CTTCCCCTTCAAACAAGCGTG 60.001 52.381 0.00 0.00 0.00 5.34
295 300 4.651994 GCTGTACGGATTCAGTTTGATTG 58.348 43.478 5.68 0.00 34.57 2.67
318 323 4.334759 GGTATGTCTGCGTCTGAGTTAGTA 59.665 45.833 0.00 0.00 0.00 1.82
319 324 4.624336 ATGTCTGCGTCTGAGTTAGTAG 57.376 45.455 0.00 0.00 0.00 2.57
320 325 3.409570 TGTCTGCGTCTGAGTTAGTAGT 58.590 45.455 0.00 0.00 0.00 2.73
389 400 6.695713 ACCTCACGCTTTCTAACAAAAATTTC 59.304 34.615 0.00 0.00 0.00 2.17
426 445 3.401033 TCTTTGTCATCGTCACACCAT 57.599 42.857 0.00 0.00 0.00 3.55
759 786 1.276622 TTGTAGAGGAGTGGCCCTTC 58.723 55.000 0.00 0.00 36.49 3.46
844 871 3.731728 GTGGAGCCCTGGATGCCA 61.732 66.667 0.00 0.00 0.00 4.92
860 887 2.874014 TGCCAAGTTCACCATTGATGA 58.126 42.857 0.00 0.00 0.00 2.92
945 972 2.029918 AGCAAAATCAAGCGTTCTTCCC 60.030 45.455 0.00 0.00 35.48 3.97
1095 1122 3.064207 TCAGACGAGTGCAATTACCAAC 58.936 45.455 0.00 0.00 0.00 3.77
1156 1183 4.520492 GTGGGATAAATGGTAATCTGGCAG 59.480 45.833 8.58 8.58 0.00 4.85
1351 1383 4.253685 ACTGACTTTTATCACATCGGTGG 58.746 43.478 0.00 0.00 45.32 4.61
1545 1580 8.893219 TTTCATGATTAAGCTCGATACTTCAT 57.107 30.769 0.00 0.28 0.00 2.57
1889 1926 5.352569 AGCATCTATCACACTTTTTCCTTCG 59.647 40.000 0.00 0.00 0.00 3.79
1907 1944 0.600255 CGGATCCACCTAATGTCGGC 60.600 60.000 13.41 0.00 36.31 5.54
1911 1948 1.496060 TCCACCTAATGTCGGCAGAT 58.504 50.000 0.00 0.00 0.00 2.90
1913 1950 1.138859 CCACCTAATGTCGGCAGATCA 59.861 52.381 0.00 0.00 0.00 2.92
2225 2263 2.435372 TCCTTTTGTGCTGTTGTCCT 57.565 45.000 0.00 0.00 0.00 3.85
2234 2272 1.610038 TGCTGTTGTCCTGCAGATTTG 59.390 47.619 17.39 0.00 42.34 2.32
2400 2438 6.962686 TCATGACAAAAGCATGTATATCTGC 58.037 36.000 0.00 2.19 42.77 4.26
2720 2765 7.486407 AAAGCATATGATGTTTCCCTTTTCT 57.514 32.000 6.97 0.00 32.29 2.52
2800 2845 3.187227 CGGAAGACTGAAGAACACAATGG 59.813 47.826 0.00 0.00 0.00 3.16
2938 2983 7.122501 TCAGAAGCATGCACTAAATTTGGAATA 59.877 33.333 21.98 0.00 0.00 1.75
3003 3055 6.019318 CCTTGCAAAAATGAAGTTGAGAAGTG 60.019 38.462 0.00 0.00 0.00 3.16
3098 3150 3.125316 GGCTAACAATCGTTCTGTTCCAG 59.875 47.826 3.45 0.00 38.05 3.86
3099 3151 3.746492 GCTAACAATCGTTCTGTTCCAGT 59.254 43.478 3.45 0.00 38.05 4.00
3113 3165 2.217510 TCCAGTAGACACCAGAGGTC 57.782 55.000 0.00 0.00 31.02 3.85
3166 3218 8.141909 CGATAACTGATTTGTATCTGGAGGTTA 58.858 37.037 0.00 0.00 34.89 2.85
3239 3291 6.785191 TCCTTTTCTTGCGATTATCATGTTC 58.215 36.000 0.00 0.00 0.00 3.18
3247 3299 2.549754 CGATTATCATGTTCCACTGCCC 59.450 50.000 0.00 0.00 0.00 5.36
3339 3391 5.713389 TGCAAAGAATGAATGATTCAGGACT 59.287 36.000 13.79 9.29 43.98 3.85
3645 3698 7.241376 GTCCTATTTTCTAATGACCACGTTTG 58.759 38.462 0.00 0.00 0.00 2.93
3793 3865 9.398538 GTTGGTATTTTGTATGTATGGTAGGAA 57.601 33.333 0.00 0.00 0.00 3.36
4317 4389 3.057969 TGACACTGGCCTTGAATACAG 57.942 47.619 3.32 0.00 37.01 2.74
4321 4393 1.004745 ACTGGCCTTGAATACAGTGGG 59.995 52.381 3.32 0.00 42.14 4.61
4366 4456 2.102084 TGGCTGCTGATACTAGCTTCTG 59.898 50.000 0.00 0.00 44.01 3.02
4739 4835 3.900601 ACCTAATATCTGGAGAGCCACAG 59.099 47.826 1.50 0.00 39.92 3.66
4827 4925 6.437477 GTCATTGAAAATAGGGAGGGTTTTCT 59.563 38.462 10.11 0.00 40.62 2.52
4971 5069 1.941377 AGCAGGAAAATGAATGCCCA 58.059 45.000 0.00 0.00 39.51 5.36
5024 5122 5.005740 TGTAATGCAAAGCTCTCACTTCAT 58.994 37.500 0.00 0.00 0.00 2.57
5037 5135 6.697019 GCTCTCACTTCATTGTAATCTCTCTC 59.303 42.308 0.00 0.00 0.00 3.20
5067 5165 2.604914 GTGCCGAGTATGATCAACACAG 59.395 50.000 0.00 0.00 0.00 3.66
5095 5193 8.538701 ACAAATCTCATCAGATACTCAAGAACT 58.461 33.333 0.00 0.00 38.55 3.01
5097 5195 8.945481 AATCTCATCAGATACTCAAGAACTTG 57.055 34.615 8.09 8.09 38.55 3.16
5098 5196 7.709149 TCTCATCAGATACTCAAGAACTTGA 57.291 36.000 15.05 15.05 46.27 3.02
5112 5214 7.099764 TCAAGAACTTGAGTAGATAAAGCAGG 58.900 38.462 12.40 0.00 43.90 4.85
5113 5215 5.423886 AGAACTTGAGTAGATAAAGCAGGC 58.576 41.667 0.00 0.00 0.00 4.85
5114 5216 4.143986 ACTTGAGTAGATAAAGCAGGCC 57.856 45.455 0.00 0.00 0.00 5.19
5115 5217 3.519510 ACTTGAGTAGATAAAGCAGGCCA 59.480 43.478 5.01 0.00 0.00 5.36
5116 5218 4.164988 ACTTGAGTAGATAAAGCAGGCCAT 59.835 41.667 5.01 0.00 0.00 4.40
5117 5219 4.342862 TGAGTAGATAAAGCAGGCCATC 57.657 45.455 5.01 0.00 0.00 3.51
5118 5220 3.711190 TGAGTAGATAAAGCAGGCCATCA 59.289 43.478 5.01 0.00 0.00 3.07
5119 5221 4.202295 TGAGTAGATAAAGCAGGCCATCAG 60.202 45.833 5.01 0.00 0.00 2.90
5120 5222 3.713764 AGTAGATAAAGCAGGCCATCAGT 59.286 43.478 5.01 0.00 0.00 3.41
5121 5223 2.928334 AGATAAAGCAGGCCATCAGTG 58.072 47.619 5.01 0.00 0.00 3.66
5122 5224 2.240667 AGATAAAGCAGGCCATCAGTGT 59.759 45.455 5.01 0.00 0.00 3.55
5123 5225 2.113860 TAAAGCAGGCCATCAGTGTC 57.886 50.000 5.01 0.00 0.00 3.67
5124 5226 0.957395 AAAGCAGGCCATCAGTGTCG 60.957 55.000 5.01 0.00 0.00 4.35
5125 5227 3.503363 GCAGGCCATCAGTGTCGC 61.503 66.667 5.01 0.00 0.00 5.19
5126 5228 2.267006 CAGGCCATCAGTGTCGCT 59.733 61.111 5.01 0.00 0.00 4.93
5127 5229 1.517361 CAGGCCATCAGTGTCGCTA 59.483 57.895 5.01 0.00 0.00 4.26
5128 5230 0.529337 CAGGCCATCAGTGTCGCTAG 60.529 60.000 5.01 0.00 0.00 3.42
5129 5231 0.684479 AGGCCATCAGTGTCGCTAGA 60.684 55.000 5.01 0.00 0.00 2.43
5130 5232 0.390860 GGCCATCAGTGTCGCTAGAT 59.609 55.000 0.00 0.00 0.00 1.98
5131 5233 1.202580 GGCCATCAGTGTCGCTAGATT 60.203 52.381 0.00 0.00 0.00 2.40
5132 5234 2.555199 GCCATCAGTGTCGCTAGATTT 58.445 47.619 0.00 0.00 0.00 2.17
5133 5235 2.541762 GCCATCAGTGTCGCTAGATTTC 59.458 50.000 0.00 0.00 0.00 2.17
5134 5236 3.739519 GCCATCAGTGTCGCTAGATTTCT 60.740 47.826 0.00 0.00 0.00 2.52
5135 5237 3.801050 CCATCAGTGTCGCTAGATTTCTG 59.199 47.826 0.00 0.00 0.00 3.02
5136 5238 4.440663 CCATCAGTGTCGCTAGATTTCTGA 60.441 45.833 0.00 0.91 36.01 3.27
5137 5239 4.783764 TCAGTGTCGCTAGATTTCTGAA 57.216 40.909 0.00 0.00 32.21 3.02
5138 5240 5.134202 TCAGTGTCGCTAGATTTCTGAAA 57.866 39.130 5.15 5.15 32.21 2.69
5139 5241 5.724328 TCAGTGTCGCTAGATTTCTGAAAT 58.276 37.500 15.09 15.09 32.21 2.17
5140 5242 6.166279 TCAGTGTCGCTAGATTTCTGAAATT 58.834 36.000 16.14 9.28 32.21 1.82
5141 5243 6.311445 TCAGTGTCGCTAGATTTCTGAAATTC 59.689 38.462 16.14 9.86 32.21 2.17
5142 5244 6.312426 CAGTGTCGCTAGATTTCTGAAATTCT 59.688 38.462 16.14 15.34 0.00 2.40
5143 5245 6.533367 AGTGTCGCTAGATTTCTGAAATTCTC 59.467 38.462 16.14 5.71 0.00 2.87
5144 5246 5.812642 TGTCGCTAGATTTCTGAAATTCTCC 59.187 40.000 16.14 4.56 0.00 3.71
5145 5247 5.043903 TCGCTAGATTTCTGAAATTCTCCG 58.956 41.667 16.14 15.40 0.00 4.63
5146 5248 4.210120 CGCTAGATTTCTGAAATTCTCCGG 59.790 45.833 16.14 0.00 0.00 5.14
5152 5254 1.066143 TCTGAAATTCTCCGGGCTCAC 60.066 52.381 0.00 0.00 0.00 3.51
5159 5261 2.997315 TCCGGGCTCACTGAGTGG 60.997 66.667 13.33 4.77 33.87 4.00
5166 5268 0.035630 GCTCACTGAGTGGCCATTCT 60.036 55.000 26.57 12.74 33.87 2.40
5195 5297 8.190326 TGTTATGACTAGAAGAGGACTCAAAA 57.810 34.615 0.00 0.00 0.00 2.44
5222 5324 2.729882 AGTTTTTCATCGTCGGAGTTCG 59.270 45.455 0.00 0.00 40.90 3.95
5227 5330 2.632544 ATCGTCGGAGTTCGGCACA 61.633 57.895 0.00 0.00 44.96 4.57
5252 5355 6.377996 AGTTGCTATTTTATCATTGTGGCTCA 59.622 34.615 0.00 0.00 0.00 4.26
5253 5356 6.135290 TGCTATTTTATCATTGTGGCTCAC 57.865 37.500 0.00 0.00 34.56 3.51
5254 5357 5.887598 TGCTATTTTATCATTGTGGCTCACT 59.112 36.000 6.83 0.00 35.11 3.41
5255 5358 6.183360 TGCTATTTTATCATTGTGGCTCACTG 60.183 38.462 6.83 0.96 35.11 3.66
5256 5359 6.038603 GCTATTTTATCATTGTGGCTCACTGA 59.961 38.462 11.24 11.24 39.42 3.41
5257 5360 6.839124 ATTTTATCATTGTGGCTCACTGAA 57.161 33.333 12.58 0.00 38.77 3.02
5258 5361 6.647334 TTTTATCATTGTGGCTCACTGAAA 57.353 33.333 12.58 6.93 38.77 2.69
5259 5362 5.627499 TTATCATTGTGGCTCACTGAAAC 57.373 39.130 12.58 0.00 38.77 2.78
5260 5363 3.213206 TCATTGTGGCTCACTGAAACT 57.787 42.857 7.08 0.00 33.78 2.66
5261 5364 3.141398 TCATTGTGGCTCACTGAAACTC 58.859 45.455 7.08 0.00 33.78 3.01
5262 5365 3.144506 CATTGTGGCTCACTGAAACTCT 58.855 45.455 1.12 0.00 35.11 3.24
5263 5366 2.245159 TGTGGCTCACTGAAACTCTG 57.755 50.000 6.83 0.00 35.11 3.35
5264 5367 1.762370 TGTGGCTCACTGAAACTCTGA 59.238 47.619 6.83 0.00 35.11 3.27
5265 5368 2.170397 TGTGGCTCACTGAAACTCTGAA 59.830 45.455 6.83 0.00 35.11 3.02
5266 5369 3.206150 GTGGCTCACTGAAACTCTGAAA 58.794 45.455 0.00 0.00 0.00 2.69
5267 5370 3.249559 GTGGCTCACTGAAACTCTGAAAG 59.750 47.826 0.00 0.00 0.00 2.62
5268 5371 3.118261 TGGCTCACTGAAACTCTGAAAGT 60.118 43.478 0.00 0.00 41.10 2.66
5269 5372 3.249559 GGCTCACTGAAACTCTGAAAGTG 59.750 47.826 0.00 0.00 38.58 3.16
5270 5373 4.122776 GCTCACTGAAACTCTGAAAGTGA 58.877 43.478 3.99 3.99 43.64 3.41
5271 5374 4.572389 GCTCACTGAAACTCTGAAAGTGAA 59.428 41.667 5.44 0.00 44.75 3.18
5272 5375 5.238214 GCTCACTGAAACTCTGAAAGTGAAT 59.762 40.000 5.44 0.00 44.75 2.57
5273 5376 6.238593 GCTCACTGAAACTCTGAAAGTGAATT 60.239 38.462 5.44 0.00 44.75 2.17
5274 5377 7.630242 TCACTGAAACTCTGAAAGTGAATTT 57.370 32.000 1.52 0.00 43.08 1.82
5275 5378 8.731275 TCACTGAAACTCTGAAAGTGAATTTA 57.269 30.769 1.52 0.00 43.08 1.40
5276 5379 8.830580 TCACTGAAACTCTGAAAGTGAATTTAG 58.169 33.333 1.52 0.00 43.08 1.85
5277 5380 8.616076 CACTGAAACTCTGAAAGTGAATTTAGT 58.384 33.333 0.00 0.00 40.54 2.24
5278 5381 8.831550 ACTGAAACTCTGAAAGTGAATTTAGTC 58.168 33.333 0.00 0.00 38.58 2.59
5279 5382 7.851508 TGAAACTCTGAAAGTGAATTTAGTCG 58.148 34.615 0.00 0.00 38.58 4.18
5323 5427 7.441890 AAATTACATGACATGTTACAACCGA 57.558 32.000 25.34 2.90 41.63 4.69
5331 5435 0.941542 TGTTACAACCGAACTGCTGC 59.058 50.000 0.00 0.00 0.00 5.25
5351 5455 0.890683 GGTGCAGATCTGGGGTTTTG 59.109 55.000 23.89 0.00 0.00 2.44
5384 5488 6.493189 TTTTGGTCCTTATTTTGCTCCTTT 57.507 33.333 0.00 0.00 0.00 3.11
5385 5489 7.604657 TTTTGGTCCTTATTTTGCTCCTTTA 57.395 32.000 0.00 0.00 0.00 1.85
5386 5490 7.790782 TTTGGTCCTTATTTTGCTCCTTTAT 57.209 32.000 0.00 0.00 0.00 1.40
5398 5502 7.944729 TTTGCTCCTTTATCTAAGCTGATTT 57.055 32.000 0.00 0.00 35.76 2.17
5432 5536 6.459573 GCATACTGGCTTCCGAAAAATGAATA 60.460 38.462 0.00 0.00 0.00 1.75
5462 5569 8.814038 ATCTACAAGGCAAAATCTTGAAGTAT 57.186 30.769 10.30 0.00 42.94 2.12
5475 5582 9.793252 AAATCTTGAAGTATTTTGATTGATCGG 57.207 29.630 0.00 0.00 0.00 4.18
5487 5594 5.905480 TGATTGATCGGTCATATTGTTCG 57.095 39.130 0.00 0.00 33.56 3.95
5501 5608 8.709646 GTCATATTGTTCGTAGTGAGACTTTTT 58.290 33.333 0.00 0.00 0.00 1.94
5529 5636 6.683974 TTGAGAGAGAAAAGACACCAAAAG 57.316 37.500 0.00 0.00 0.00 2.27
5530 5637 5.126067 TGAGAGAGAAAAGACACCAAAAGG 58.874 41.667 0.00 0.00 0.00 3.11
5539 5646 2.158475 AGACACCAAAAGGGCATCTCAA 60.158 45.455 0.00 0.00 42.05 3.02
5543 5650 3.512724 CACCAAAAGGGCATCTCAAATCT 59.487 43.478 0.00 0.00 42.05 2.40
5547 5654 5.348986 CAAAAGGGCATCTCAAATCTGATG 58.651 41.667 0.00 0.00 41.96 3.07
5551 5658 3.003068 GGGCATCTCAAATCTGATGTTCG 59.997 47.826 0.00 0.00 41.33 3.95
5557 5664 4.931601 TCTCAAATCTGATGTTCGTCAAGG 59.068 41.667 0.00 0.00 0.00 3.61
5562 5669 6.633500 AATCTGATGTTCGTCAAGGAAAAA 57.367 33.333 0.00 0.00 0.00 1.94
5563 5670 5.418310 TCTGATGTTCGTCAAGGAAAAAC 57.582 39.130 0.00 0.00 0.00 2.43
5565 5672 5.007626 TCTGATGTTCGTCAAGGAAAAACAG 59.992 40.000 6.57 6.57 33.74 3.16
5566 5673 4.638421 TGATGTTCGTCAAGGAAAAACAGT 59.362 37.500 0.00 0.00 33.74 3.55
5571 5678 5.013568 TCGTCAAGGAAAAACAGTAGACA 57.986 39.130 0.00 0.00 0.00 3.41
5572 5679 5.421277 TCGTCAAGGAAAAACAGTAGACAA 58.579 37.500 0.00 0.00 0.00 3.18
5575 5682 7.876068 TCGTCAAGGAAAAACAGTAGACAATAT 59.124 33.333 0.00 0.00 0.00 1.28
5601 5708 7.524294 AATGAAAGACAACATGACACAAAAC 57.476 32.000 0.00 0.00 0.00 2.43
5602 5709 6.018589 TGAAAGACAACATGACACAAAACA 57.981 33.333 0.00 0.00 0.00 2.83
5603 5710 6.450545 TGAAAGACAACATGACACAAAACAA 58.549 32.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.299796 CCACCCACCCACCCAAGG 62.300 72.222 0.00 0.00 0.00 3.61
8 9 4.299796 CCCACCCACCCACCCAAG 62.300 72.222 0.00 0.00 0.00 3.61
93 95 7.614192 AGAAAGACTTGTTTGAAGGGAAAGTAA 59.386 33.333 0.00 0.00 31.45 2.24
94 96 7.116736 AGAAAGACTTGTTTGAAGGGAAAGTA 58.883 34.615 0.00 0.00 31.45 2.24
95 97 5.952347 AGAAAGACTTGTTTGAAGGGAAAGT 59.048 36.000 0.00 0.00 33.91 2.66
102 104 9.487790 AATAGAGAGAGAAAGACTTGTTTGAAG 57.512 33.333 0.00 0.00 0.00 3.02
166 170 4.142038 GCTTGTTTGAAGGGGAAGTAAGA 58.858 43.478 0.00 0.00 0.00 2.10
168 172 2.882137 CGCTTGTTTGAAGGGGAAGTAA 59.118 45.455 0.00 0.00 0.00 2.24
169 173 2.158726 ACGCTTGTTTGAAGGGGAAGTA 60.159 45.455 0.00 0.00 34.89 2.24
170 174 1.318576 CGCTTGTTTGAAGGGGAAGT 58.681 50.000 0.00 0.00 0.00 3.01
171 175 1.001378 CACGCTTGTTTGAAGGGGAAG 60.001 52.381 0.00 0.00 34.89 3.46
172 176 1.028905 CACGCTTGTTTGAAGGGGAA 58.971 50.000 0.00 0.00 34.89 3.97
173 177 1.452145 GCACGCTTGTTTGAAGGGGA 61.452 55.000 0.00 0.00 34.89 4.81
174 178 1.007387 GCACGCTTGTTTGAAGGGG 60.007 57.895 0.00 0.00 34.89 4.79
175 179 1.370414 CGCACGCTTGTTTGAAGGG 60.370 57.895 0.00 0.00 36.43 3.95
176 180 2.010817 GCGCACGCTTGTTTGAAGG 61.011 57.895 7.96 0.00 38.26 3.46
177 181 2.349376 CGCGCACGCTTGTTTGAAG 61.349 57.895 13.70 0.00 39.32 3.02
178 182 2.111932 ATCGCGCACGCTTGTTTGAA 62.112 50.000 13.70 0.00 39.84 2.69
179 183 2.111932 AATCGCGCACGCTTGTTTGA 62.112 50.000 13.70 2.00 39.84 2.69
180 184 1.655697 GAATCGCGCACGCTTGTTTG 61.656 55.000 13.70 0.00 39.84 2.93
182 186 1.011968 TAGAATCGCGCACGCTTGTT 61.012 50.000 13.70 4.91 39.84 2.83
183 187 0.806102 ATAGAATCGCGCACGCTTGT 60.806 50.000 13.70 2.85 39.84 3.16
184 188 0.111530 GATAGAATCGCGCACGCTTG 60.112 55.000 13.70 0.00 39.84 4.01
185 189 1.215655 GGATAGAATCGCGCACGCTT 61.216 55.000 13.70 1.01 39.84 4.68
191 195 1.271102 AGAGGAAGGATAGAATCGCGC 59.729 52.381 0.00 0.00 0.00 6.86
295 300 2.656560 AACTCAGACGCAGACATACC 57.343 50.000 0.00 0.00 0.00 2.73
318 323 3.387699 AGCAAACAAGTGGGCAATTTACT 59.612 39.130 0.00 0.00 0.00 2.24
319 324 3.727726 AGCAAACAAGTGGGCAATTTAC 58.272 40.909 0.00 0.00 0.00 2.01
320 325 4.414337 AAGCAAACAAGTGGGCAATTTA 57.586 36.364 0.00 0.00 0.00 1.40
389 400 2.754946 AGAATGCATGGCCAAAGTTG 57.245 45.000 10.96 4.15 0.00 3.16
480 501 6.927936 ACGATCAGTCATCTATTCTGAATTGG 59.072 38.462 8.38 2.86 40.73 3.16
515 536 0.328258 GAAGCTAACAGCCTGGGGAA 59.672 55.000 0.00 0.00 43.77 3.97
639 663 7.973388 TGCTTCTGCATAATAATACACAAAACC 59.027 33.333 0.00 0.00 45.31 3.27
759 786 8.273780 AGATAATGTCCAAAGCTTTACTGAAG 57.726 34.615 12.25 0.00 38.45 3.02
844 871 2.821969 GTGGCTCATCAATGGTGAACTT 59.178 45.455 0.00 0.00 37.30 2.66
860 887 2.260822 AGTTACATCTCCACAGTGGCT 58.739 47.619 15.64 0.23 37.47 4.75
945 972 3.876914 TCACAAACACTTGACCAAGCTAG 59.123 43.478 9.48 3.43 41.99 3.42
1047 1074 0.240945 CCACATGTTGGCCGAAGAAC 59.759 55.000 0.00 0.00 39.07 3.01
1347 1379 4.949856 TGATAAAATGCTCTCTTTCCCACC 59.050 41.667 0.00 0.00 0.00 4.61
1351 1383 7.093322 ACATGTGATAAAATGCTCTCTTTCC 57.907 36.000 0.00 0.00 0.00 3.13
1379 1411 8.757789 TGTTAAACTATATGAATTAACTCGGCG 58.242 33.333 0.00 0.00 38.46 6.46
1410 1442 6.095440 GTGTCAATTGCCAGGTGTATTCTATT 59.905 38.462 0.00 0.00 0.00 1.73
1533 1568 5.111989 TCCAGCAGAAAATGAAGTATCGAG 58.888 41.667 0.00 0.00 0.00 4.04
1535 1570 5.111989 TCTCCAGCAGAAAATGAAGTATCG 58.888 41.667 0.00 0.00 0.00 2.92
1545 1580 4.343231 TGCCATTATTCTCCAGCAGAAAA 58.657 39.130 0.00 0.00 44.66 2.29
1889 1926 0.468226 TGCCGACATTAGGTGGATCC 59.532 55.000 4.20 4.20 0.00 3.36
1940 1977 8.388484 AGAGAATGGATAAACATCTTGCATAC 57.612 34.615 0.00 0.00 0.00 2.39
2522 2560 5.514274 TTTTAGGAAAAGACAAGCCAGTG 57.486 39.130 0.00 0.00 0.00 3.66
2602 2644 2.681848 CCCAATGCTCTGCTTCTGTTAG 59.318 50.000 0.00 0.00 0.00 2.34
2938 2983 6.469782 ACAGAACCATGATTTTCACAAACT 57.530 33.333 0.00 0.00 0.00 2.66
2977 3026 5.850557 TCTCAACTTCATTTTTGCAAGGA 57.149 34.783 0.00 0.00 0.00 3.36
3098 3150 2.494073 CAGAAGGACCTCTGGTGTCTAC 59.506 54.545 11.21 0.00 39.39 2.59
3099 3151 2.110188 ACAGAAGGACCTCTGGTGTCTA 59.890 50.000 19.09 0.00 46.02 2.59
3166 3218 7.616150 ACAGATTATCTACACAAGTGACCTACT 59.384 37.037 7.28 0.00 42.89 2.57
3247 3299 6.991485 ATGCTTCAAACTTTTTATCACACG 57.009 33.333 0.00 0.00 0.00 4.49
3335 3387 7.940178 ATACGAAAAACCATTCAAAAAGTCC 57.060 32.000 0.00 0.00 0.00 3.85
3416 3468 6.230472 TGCATCAGAGCTTTAGTAAAAGACA 58.770 36.000 2.15 0.00 44.14 3.41
3664 3717 0.034767 CAGAGGCTGCATTCCCAGAA 60.035 55.000 0.50 0.00 34.77 3.02
3970 4042 4.214119 GCATGCGTACCAATGACATATCTT 59.786 41.667 0.00 0.00 0.00 2.40
3988 4060 4.617959 AGCATCACATTAGAATTGCATGC 58.382 39.130 11.82 11.82 36.47 4.06
4107 4179 6.909550 AGAGCATTTACCAAATTAACACCA 57.090 33.333 0.00 0.00 0.00 4.17
4157 4229 2.751166 ACAGCGCTAGAACACTGATT 57.249 45.000 10.99 0.00 34.25 2.57
4366 4456 3.615224 TTGGAGTACGGGATTGGTAAC 57.385 47.619 0.00 0.00 0.00 2.50
4739 4835 1.999071 TTTGAAGGCACACACCGCAC 61.999 55.000 0.00 0.00 33.69 5.34
4827 4925 5.302568 ACAAGATGAGGAAAACTGCAATTGA 59.697 36.000 10.34 0.00 0.00 2.57
4960 5058 4.571919 CAAGTGACAAATGGGCATTCATT 58.428 39.130 0.00 0.00 38.84 2.57
4961 5059 3.618019 GCAAGTGACAAATGGGCATTCAT 60.618 43.478 0.00 0.00 0.00 2.57
4962 5060 2.288948 GCAAGTGACAAATGGGCATTCA 60.289 45.455 0.00 0.00 0.00 2.57
4963 5061 2.288948 TGCAAGTGACAAATGGGCATTC 60.289 45.455 0.00 0.00 0.00 2.67
4971 5069 3.320826 GGGTTACCTTGCAAGTGACAAAT 59.679 43.478 24.35 4.24 0.00 2.32
5024 5122 3.444034 CGTCCAGTGGAGAGAGATTACAA 59.556 47.826 13.61 0.00 29.39 2.41
5067 5165 6.760298 TCTTGAGTATCTGATGAGATTTGTGC 59.240 38.462 0.00 0.00 39.76 4.57
5095 5193 4.164030 TGATGGCCTGCTTTATCTACTCAA 59.836 41.667 3.32 0.00 0.00 3.02
5097 5195 4.202305 ACTGATGGCCTGCTTTATCTACTC 60.202 45.833 3.32 0.00 0.00 2.59
5098 5196 3.713764 ACTGATGGCCTGCTTTATCTACT 59.286 43.478 3.32 0.00 0.00 2.57
5108 5210 2.578163 TAGCGACACTGATGGCCTGC 62.578 60.000 3.32 0.00 0.00 4.85
5109 5211 0.529337 CTAGCGACACTGATGGCCTG 60.529 60.000 3.32 0.00 0.00 4.85
5110 5212 0.684479 TCTAGCGACACTGATGGCCT 60.684 55.000 3.32 0.00 0.00 5.19
5111 5213 0.390860 ATCTAGCGACACTGATGGCC 59.609 55.000 0.00 0.00 0.00 5.36
5112 5214 2.231215 AATCTAGCGACACTGATGGC 57.769 50.000 0.00 0.00 0.00 4.40
5113 5215 3.801050 CAGAAATCTAGCGACACTGATGG 59.199 47.826 0.00 0.00 0.00 3.51
5114 5216 4.676546 TCAGAAATCTAGCGACACTGATG 58.323 43.478 0.00 0.00 0.00 3.07
5115 5217 4.991153 TCAGAAATCTAGCGACACTGAT 57.009 40.909 0.00 0.00 0.00 2.90
5116 5218 4.783764 TTCAGAAATCTAGCGACACTGA 57.216 40.909 0.00 0.00 0.00 3.41
5117 5219 6.312426 AGAATTTCAGAAATCTAGCGACACTG 59.688 38.462 8.90 0.00 0.00 3.66
5118 5220 6.402222 AGAATTTCAGAAATCTAGCGACACT 58.598 36.000 8.90 0.00 0.00 3.55
5119 5221 6.237969 GGAGAATTTCAGAAATCTAGCGACAC 60.238 42.308 8.90 0.00 0.00 3.67
5120 5222 5.812642 GGAGAATTTCAGAAATCTAGCGACA 59.187 40.000 8.90 0.00 0.00 4.35
5121 5223 5.051374 CGGAGAATTTCAGAAATCTAGCGAC 60.051 44.000 8.90 0.00 0.00 5.19
5122 5224 5.043903 CGGAGAATTTCAGAAATCTAGCGA 58.956 41.667 8.90 0.00 0.00 4.93
5123 5225 4.210120 CCGGAGAATTTCAGAAATCTAGCG 59.790 45.833 8.90 0.00 0.00 4.26
5124 5226 4.513318 CCCGGAGAATTTCAGAAATCTAGC 59.487 45.833 0.73 0.39 0.00 3.42
5125 5227 4.513318 GCCCGGAGAATTTCAGAAATCTAG 59.487 45.833 0.73 6.23 0.00 2.43
5126 5228 4.164221 AGCCCGGAGAATTTCAGAAATCTA 59.836 41.667 0.73 0.00 0.00 1.98
5127 5229 3.054065 AGCCCGGAGAATTTCAGAAATCT 60.054 43.478 0.73 7.94 0.00 2.40
5128 5230 3.282885 AGCCCGGAGAATTTCAGAAATC 58.717 45.455 0.73 3.55 0.00 2.17
5129 5231 3.282885 GAGCCCGGAGAATTTCAGAAAT 58.717 45.455 0.73 2.20 0.00 2.17
5130 5232 2.039746 TGAGCCCGGAGAATTTCAGAAA 59.960 45.455 0.73 0.00 0.00 2.52
5131 5233 1.628340 TGAGCCCGGAGAATTTCAGAA 59.372 47.619 0.73 0.00 0.00 3.02
5132 5234 1.066143 GTGAGCCCGGAGAATTTCAGA 60.066 52.381 0.73 0.00 0.00 3.27
5133 5235 1.065854 AGTGAGCCCGGAGAATTTCAG 60.066 52.381 0.73 0.00 0.00 3.02
5134 5236 0.984230 AGTGAGCCCGGAGAATTTCA 59.016 50.000 0.73 0.00 0.00 2.69
5135 5237 1.066143 TCAGTGAGCCCGGAGAATTTC 60.066 52.381 0.73 0.00 0.00 2.17
5136 5238 0.984230 TCAGTGAGCCCGGAGAATTT 59.016 50.000 0.73 0.00 0.00 1.82
5137 5239 0.539051 CTCAGTGAGCCCGGAGAATT 59.461 55.000 7.33 0.00 0.00 2.17
5138 5240 0.616111 ACTCAGTGAGCCCGGAGAAT 60.616 55.000 20.31 0.00 32.04 2.40
5139 5241 1.228894 ACTCAGTGAGCCCGGAGAA 60.229 57.895 20.31 0.00 32.04 2.87
5140 5242 1.979155 CACTCAGTGAGCCCGGAGA 60.979 63.158 20.31 0.00 35.23 3.71
5141 5243 2.575993 CACTCAGTGAGCCCGGAG 59.424 66.667 20.31 0.00 35.23 4.63
5142 5244 2.997315 CCACTCAGTGAGCCCGGA 60.997 66.667 20.31 0.00 35.23 5.14
5143 5245 4.767255 GCCACTCAGTGAGCCCGG 62.767 72.222 20.31 17.85 35.23 5.73
5144 5246 4.767255 GGCCACTCAGTGAGCCCG 62.767 72.222 20.99 8.78 41.00 6.13
5145 5247 2.490270 AATGGCCACTCAGTGAGCCC 62.490 60.000 25.84 17.10 43.84 5.19
5146 5248 1.001641 AATGGCCACTCAGTGAGCC 60.002 57.895 23.51 23.51 44.33 4.70
5152 5254 1.064906 ACATGGAGAATGGCCACTCAG 60.065 52.381 17.91 11.54 40.94 3.35
5159 5261 5.858381 TCTAGTCATAACATGGAGAATGGC 58.142 41.667 0.00 0.00 40.94 4.40
5166 5268 6.436027 AGTCCTCTTCTAGTCATAACATGGA 58.564 40.000 0.00 0.00 0.00 3.41
5195 5297 3.007182 TCCGACGATGAAAAACTAAGGGT 59.993 43.478 0.00 0.00 0.00 4.34
5211 5313 2.805353 CTGTGCCGAACTCCGACG 60.805 66.667 0.00 0.00 41.76 5.12
5212 5314 1.300697 AACTGTGCCGAACTCCGAC 60.301 57.895 0.00 0.00 41.76 4.79
5227 5330 6.377996 TGAGCCACAATGATAAAATAGCAACT 59.622 34.615 0.00 0.00 0.00 3.16
5252 5355 8.738645 ACTAAATTCACTTTCAGAGTTTCAGT 57.261 30.769 0.00 0.00 36.10 3.41
5253 5356 8.006590 CGACTAAATTCACTTTCAGAGTTTCAG 58.993 37.037 0.00 0.00 36.10 3.02
5254 5357 7.518370 GCGACTAAATTCACTTTCAGAGTTTCA 60.518 37.037 0.00 0.00 36.10 2.69
5255 5358 6.792726 GCGACTAAATTCACTTTCAGAGTTTC 59.207 38.462 0.00 0.00 36.10 2.78
5256 5359 6.260050 TGCGACTAAATTCACTTTCAGAGTTT 59.740 34.615 0.00 0.00 36.10 2.66
5257 5360 5.758296 TGCGACTAAATTCACTTTCAGAGTT 59.242 36.000 0.00 0.00 36.10 3.01
5258 5361 5.297547 TGCGACTAAATTCACTTTCAGAGT 58.702 37.500 0.00 0.00 39.89 3.24
5259 5362 5.845985 TGCGACTAAATTCACTTTCAGAG 57.154 39.130 0.00 0.00 0.00 3.35
5260 5363 5.390885 GCATGCGACTAAATTCACTTTCAGA 60.391 40.000 0.00 0.00 0.00 3.27
5261 5364 4.790140 GCATGCGACTAAATTCACTTTCAG 59.210 41.667 0.00 0.00 0.00 3.02
5262 5365 4.379394 GGCATGCGACTAAATTCACTTTCA 60.379 41.667 12.44 0.00 0.00 2.69
5263 5366 4.098416 GGCATGCGACTAAATTCACTTTC 58.902 43.478 12.44 0.00 0.00 2.62
5264 5367 3.505680 TGGCATGCGACTAAATTCACTTT 59.494 39.130 12.44 0.00 0.00 2.66
5265 5368 3.081061 TGGCATGCGACTAAATTCACTT 58.919 40.909 12.44 0.00 0.00 3.16
5266 5369 2.710377 TGGCATGCGACTAAATTCACT 58.290 42.857 12.44 0.00 0.00 3.41
5267 5370 3.698029 ATGGCATGCGACTAAATTCAC 57.302 42.857 12.44 0.00 0.00 3.18
5268 5371 4.157472 TGAAATGGCATGCGACTAAATTCA 59.843 37.500 12.44 11.64 0.00 2.57
5269 5372 4.671377 TGAAATGGCATGCGACTAAATTC 58.329 39.130 12.44 9.33 0.00 2.17
5270 5373 4.158394 ACTGAAATGGCATGCGACTAAATT 59.842 37.500 12.44 0.00 0.00 1.82
5271 5374 3.696051 ACTGAAATGGCATGCGACTAAAT 59.304 39.130 12.44 0.00 0.00 1.40
5272 5375 3.081061 ACTGAAATGGCATGCGACTAAA 58.919 40.909 12.44 0.00 0.00 1.85
5273 5376 2.710377 ACTGAAATGGCATGCGACTAA 58.290 42.857 12.44 0.00 0.00 2.24
5274 5377 2.401583 ACTGAAATGGCATGCGACTA 57.598 45.000 12.44 0.00 0.00 2.59
5275 5378 1.470098 GAACTGAAATGGCATGCGACT 59.530 47.619 12.44 0.00 0.00 4.18
5276 5379 1.199789 TGAACTGAAATGGCATGCGAC 59.800 47.619 12.44 0.00 0.00 5.19
5277 5380 1.532523 TGAACTGAAATGGCATGCGA 58.467 45.000 12.44 8.58 0.00 5.10
5278 5381 2.350899 TTGAACTGAAATGGCATGCG 57.649 45.000 12.44 0.00 0.00 4.73
5331 5435 0.609131 AAAACCCCAGATCTGCACCG 60.609 55.000 17.76 3.45 0.00 4.94
5343 5447 1.717032 AAAAGGAGAGGCAAAACCCC 58.283 50.000 0.00 0.00 40.58 4.95
5372 5476 8.530804 AATCAGCTTAGATAAAGGAGCAAAAT 57.469 30.769 0.00 0.00 37.59 1.82
5375 5479 9.113838 CTTAAATCAGCTTAGATAAAGGAGCAA 57.886 33.333 0.00 0.00 37.59 3.91
5377 5481 8.669946 ACTTAAATCAGCTTAGATAAAGGAGC 57.330 34.615 10.99 0.00 35.58 4.70
5384 5488 8.962884 TGCAATGACTTAAATCAGCTTAGATA 57.037 30.769 0.00 0.00 30.46 1.98
5385 5489 7.870509 TGCAATGACTTAAATCAGCTTAGAT 57.129 32.000 0.00 0.00 30.46 1.98
5386 5490 7.870509 ATGCAATGACTTAAATCAGCTTAGA 57.129 32.000 0.00 0.00 30.46 2.10
5398 5502 4.199310 GGAAGCCAGTATGCAATGACTTA 58.801 43.478 0.00 0.00 31.97 2.24
5408 5512 4.963276 TCATTTTTCGGAAGCCAGTATG 57.037 40.909 0.00 0.00 0.00 2.39
5432 5536 8.985315 TCAAGATTTTGCCTTGTAGATATCAT 57.015 30.769 5.32 0.00 41.18 2.45
5441 5545 8.203485 TCAAAATACTTCAAGATTTTGCCTTGT 58.797 29.630 19.75 0.00 45.97 3.16
5442 5546 8.592105 TCAAAATACTTCAAGATTTTGCCTTG 57.408 30.769 19.75 0.00 45.97 3.61
5453 5560 7.751732 TGACCGATCAATCAAAATACTTCAAG 58.248 34.615 0.00 0.00 0.00 3.02
5462 5569 7.148323 ACGAACAATATGACCGATCAATCAAAA 60.148 33.333 0.00 0.00 38.69 2.44
5474 5581 5.892568 AGTCTCACTACGAACAATATGACC 58.107 41.667 0.00 0.00 0.00 4.02
5475 5582 7.813852 AAAGTCTCACTACGAACAATATGAC 57.186 36.000 0.00 0.00 0.00 3.06
5503 5610 7.461182 TTTGGTGTCTTTTCTCTCTCAAAAA 57.539 32.000 0.00 0.00 0.00 1.94
5504 5611 7.362920 CCTTTTGGTGTCTTTTCTCTCTCAAAA 60.363 37.037 0.00 0.00 32.85 2.44
5505 5612 6.095440 CCTTTTGGTGTCTTTTCTCTCTCAAA 59.905 38.462 0.00 0.00 34.07 2.69
5506 5613 5.590259 CCTTTTGGTGTCTTTTCTCTCTCAA 59.410 40.000 0.00 0.00 34.07 3.02
5507 5614 5.126067 CCTTTTGGTGTCTTTTCTCTCTCA 58.874 41.667 0.00 0.00 34.07 3.27
5508 5615 4.517075 CCCTTTTGGTGTCTTTTCTCTCTC 59.483 45.833 0.00 0.00 38.10 3.20
5522 5629 3.512724 CAGATTTGAGATGCCCTTTTGGT 59.487 43.478 0.00 0.00 38.10 3.67
5523 5630 3.765511 TCAGATTTGAGATGCCCTTTTGG 59.234 43.478 0.00 0.00 39.97 3.28
5524 5631 5.105473 ACATCAGATTTGAGATGCCCTTTTG 60.105 40.000 0.00 0.00 44.16 2.44
5529 5636 3.003068 CGAACATCAGATTTGAGATGCCC 59.997 47.826 0.00 0.00 44.16 5.36
5530 5637 3.624861 ACGAACATCAGATTTGAGATGCC 59.375 43.478 0.00 0.00 44.16 4.40
5539 5646 6.039270 TGTTTTTCCTTGACGAACATCAGATT 59.961 34.615 0.00 0.00 0.00 2.40
5543 5650 4.638421 ACTGTTTTTCCTTGACGAACATCA 59.362 37.500 0.00 0.00 30.73 3.07
5547 5654 5.292589 TGTCTACTGTTTTTCCTTGACGAAC 59.707 40.000 0.00 0.00 0.00 3.95
5575 5682 9.081997 GTTTTGTGTCATGTTGTCTTTCATTTA 57.918 29.630 0.00 0.00 0.00 1.40
5579 5686 6.018589 TGTTTTGTGTCATGTTGTCTTTCA 57.981 33.333 0.00 0.00 0.00 2.69
5580 5687 6.942886 TTGTTTTGTGTCATGTTGTCTTTC 57.057 33.333 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.