Multiple sequence alignment - TraesCS5A01G296800

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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 TraesCS5A01G296800 chr5A 100.000 4502 0 0 1 4502 504868240 504863739 0.000000e+00 8314
1 TraesCS5A01G296800 chr5B 96.252 3922 136 10 227 4144 479630377 479626463 0.000000e+00 6418
2 TraesCS5A01G296800 chr5B 92.958 213 11 3 4145 4353 479626339 479626127 1.570000e-79 307
3 TraesCS5A01G296800 chr5B 90.043 231 23 0 1 231 9593319 9593089 2.630000e-77 300
4 TraesCS5A01G296800 chr5D 96.712 3589 105 7 918 4501 399221049 399217469 0.000000e+00 5962
5 TraesCS5A01G296800 chr5D 85.377 636 68 18 227 844 399221796 399221168 1.770000e-178 636
6 TraesCS5A01G296800 chr3D 89.693 456 32 7 2917 3367 480417187 480417632 6.540000e-158 568
7 TraesCS5A01G296800 chr3D 89.976 409 35 4 3763 4171 543810589 543810991 1.430000e-144 523
8 TraesCS5A01G296800 chr3D 81.275 251 22 9 3681 3929 480417663 480417890 3.580000e-41 180
9 TraesCS5A01G296800 chr3D 92.308 78 6 0 3639 3716 543810512 543810589 1.320000e-20 111
10 TraesCS5A01G296800 chr3B 86.780 469 37 9 2912 3377 640973160 640973606 2.420000e-137 499
11 TraesCS5A01G296800 chr3B 88.646 229 25 1 1 228 6194077 6194305 1.230000e-70 278
12 TraesCS5A01G296800 chr3B 80.488 369 40 17 3842 4206 640973786 640974126 2.080000e-63 254
13 TraesCS5A01G296800 chr3A 86.333 439 31 17 2912 3346 623529803 623530216 6.870000e-123 451
14 TraesCS5A01G296800 chr3A 80.708 565 63 18 3653 4206 623530317 623530846 9.070000e-107 398
15 TraesCS5A01G296800 chr6D 96.930 228 7 0 1 228 32912020 32911793 2.540000e-102 383
16 TraesCS5A01G296800 chr6D 95.349 215 9 1 1 215 468177512 468177725 1.550000e-89 340
17 TraesCS5A01G296800 chr6D 77.289 273 47 10 238 496 16140736 16141007 3.630000e-31 147
18 TraesCS5A01G296800 chr2A 96.137 233 7 2 1 231 195108322 195108554 3.290000e-101 379
19 TraesCS5A01G296800 chr7D 92.982 228 16 0 1 228 60460040 60460267 2.600000e-87 333
20 TraesCS5A01G296800 chr7D 77.039 331 49 15 227 538 561709808 561709486 1.000000e-36 165
21 TraesCS5A01G296800 chr1D 92.982 228 16 0 1 228 269810728 269810501 2.600000e-87 333
22 TraesCS5A01G296800 chr7B 91.111 225 20 0 2 226 586635439 586635215 5.660000e-79 305
23 TraesCS5A01G296800 chr7B 90.393 229 21 1 1 228 117634379 117634151 2.630000e-77 300
24 TraesCS5A01G296800 chr7A 76.364 330 52 17 227 538 646548590 646548269 2.170000e-33 154
25 TraesCS5A01G296800 chr6A 77.206 272 47 10 238 495 16440481 16440751 1.310000e-30 145


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 TraesCS5A01G296800 chr5A 504863739 504868240 4501 True 8314.0 8314 100.0000 1 4502 1 chr5A.!!$R1 4501
1 TraesCS5A01G296800 chr5B 479626127 479630377 4250 True 3362.5 6418 94.6050 227 4353 2 chr5B.!!$R2 4126
2 TraesCS5A01G296800 chr5D 399217469 399221796 4327 True 3299.0 5962 91.0445 227 4501 2 chr5D.!!$R1 4274
3 TraesCS5A01G296800 chr3D 480417187 480417890 703 False 374.0 568 85.4840 2917 3929 2 chr3D.!!$F1 1012
4 TraesCS5A01G296800 chr3B 640973160 640974126 966 False 376.5 499 83.6340 2912 4206 2 chr3B.!!$F2 1294
5 TraesCS5A01G296800 chr3A 623529803 623530846 1043 False 424.5 451 83.5205 2912 4206 2 chr3A.!!$F1 1294

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
102 103 0.037697 ATGTCGAGGCGCACAAACTA 60.038 50.0 10.83 0.0 0.00 2.24 F
188 189 0.038892 TTCGTCCCTGTAAGCGTGAC 60.039 55.0 0.00 0.0 0.00 3.67 F
549 563 0.315886 AACGAAAAATCCCGGTTGGC 59.684 50.0 0.00 0.0 0.00 4.52 F
1833 1908 0.467384 AGCAGGGATCGGTCAGATTG 59.533 55.0 0.00 0.0 40.26 2.67 F
1870 1945 0.921896 TCTAGTACTACGGCTGGGGT 59.078 55.0 0.00 0.0 0.00 4.95 F
3000 3075 0.387878 CGCGAGATCCAGCTCCATAC 60.388 60.0 0.00 0.0 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1689 1.004918 CACCAGGTGTCCGTTCCTC 60.005 63.158 11.99 0.00 30.91 3.71 R
1824 1899 1.304381 TTGCTGCCCCAATCTGACC 60.304 57.895 0.00 0.00 0.00 4.02 R
2249 2324 0.249398 GAACGCCTTTCTAGCCTCCA 59.751 55.000 0.00 0.00 0.00 3.86 R
2907 2982 0.037232 AAGTCCTACAAGCACCGAGC 60.037 55.000 0.00 0.00 46.19 5.03 R
3247 3322 2.742856 GCTCATCCGACATGTCATGGAA 60.743 50.000 24.93 9.68 33.48 3.53 R
4022 4136 1.974265 TCAAACGGTTGATGCTTCCA 58.026 45.000 12.93 0.00 38.88 3.53 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
28 29 3.176552 CAGTAGTGCAGGAGATCAAGG 57.823 52.381 0.00 0.00 0.00 3.61
29 30 2.762887 CAGTAGTGCAGGAGATCAAGGA 59.237 50.000 0.00 0.00 0.00 3.36
30 31 3.030291 AGTAGTGCAGGAGATCAAGGAG 58.970 50.000 0.00 0.00 0.00 3.69
31 32 0.540923 AGTGCAGGAGATCAAGGAGC 59.459 55.000 0.00 0.00 0.00 4.70
32 33 0.251354 GTGCAGGAGATCAAGGAGCA 59.749 55.000 0.00 0.00 0.00 4.26
33 34 1.134159 GTGCAGGAGATCAAGGAGCAT 60.134 52.381 0.00 0.00 32.75 3.79
34 35 1.562942 TGCAGGAGATCAAGGAGCATT 59.437 47.619 0.00 0.00 0.00 3.56
35 36 2.220313 GCAGGAGATCAAGGAGCATTC 58.780 52.381 0.00 0.00 0.00 2.67
36 37 2.158784 GCAGGAGATCAAGGAGCATTCT 60.159 50.000 0.00 0.00 0.00 2.40
37 38 3.070734 GCAGGAGATCAAGGAGCATTCTA 59.929 47.826 0.00 0.00 0.00 2.10
38 39 4.800249 GCAGGAGATCAAGGAGCATTCTAG 60.800 50.000 0.00 0.00 0.00 2.43
39 40 4.344679 CAGGAGATCAAGGAGCATTCTAGT 59.655 45.833 0.00 0.00 0.00 2.57
40 41 5.538053 CAGGAGATCAAGGAGCATTCTAGTA 59.462 44.000 0.00 0.00 0.00 1.82
41 42 5.774690 AGGAGATCAAGGAGCATTCTAGTAG 59.225 44.000 0.00 0.00 0.00 2.57
42 43 5.538433 GGAGATCAAGGAGCATTCTAGTAGT 59.462 44.000 0.00 0.00 0.00 2.73
43 44 6.041523 GGAGATCAAGGAGCATTCTAGTAGTT 59.958 42.308 0.00 0.00 0.00 2.24
44 45 7.418483 GGAGATCAAGGAGCATTCTAGTAGTTT 60.418 40.741 0.00 0.00 0.00 2.66
45 46 7.856415 AGATCAAGGAGCATTCTAGTAGTTTT 58.144 34.615 0.00 0.00 0.00 2.43
46 47 8.982723 AGATCAAGGAGCATTCTAGTAGTTTTA 58.017 33.333 0.00 0.00 0.00 1.52
47 48 9.771534 GATCAAGGAGCATTCTAGTAGTTTTAT 57.228 33.333 0.00 0.00 0.00 1.40
49 50 9.959721 TCAAGGAGCATTCTAGTAGTTTTATTT 57.040 29.630 0.00 0.00 0.00 1.40
51 52 8.966069 AGGAGCATTCTAGTAGTTTTATTTCC 57.034 34.615 0.00 0.00 0.00 3.13
52 53 8.773216 AGGAGCATTCTAGTAGTTTTATTTCCT 58.227 33.333 0.00 0.89 0.00 3.36
53 54 8.831550 GGAGCATTCTAGTAGTTTTATTTCCTG 58.168 37.037 0.00 0.00 0.00 3.86
54 55 9.384764 GAGCATTCTAGTAGTTTTATTTCCTGT 57.615 33.333 0.00 0.00 0.00 4.00
55 56 9.740710 AGCATTCTAGTAGTTTTATTTCCTGTT 57.259 29.630 0.00 0.00 0.00 3.16
70 71 9.715121 TTATTTCCTGTTTATTTAGACACGAGT 57.285 29.630 0.00 0.00 0.00 4.18
71 72 8.617290 ATTTCCTGTTTATTTAGACACGAGTT 57.383 30.769 0.00 0.00 0.00 3.01
72 73 8.441312 TTTCCTGTTTATTTAGACACGAGTTT 57.559 30.769 0.00 0.00 0.00 2.66
73 74 9.545105 TTTCCTGTTTATTTAGACACGAGTTTA 57.455 29.630 0.00 0.00 0.00 2.01
74 75 8.752766 TCCTGTTTATTTAGACACGAGTTTAG 57.247 34.615 0.00 0.00 0.00 1.85
75 76 8.579006 TCCTGTTTATTTAGACACGAGTTTAGA 58.421 33.333 0.00 0.00 0.00 2.10
76 77 9.199982 CCTGTTTATTTAGACACGAGTTTAGAA 57.800 33.333 0.00 0.00 0.00 2.10
78 79 8.981647 TGTTTATTTAGACACGAGTTTAGAACC 58.018 33.333 0.00 0.00 0.00 3.62
79 80 9.201127 GTTTATTTAGACACGAGTTTAGAACCT 57.799 33.333 0.00 0.00 0.00 3.50
80 81 8.976986 TTATTTAGACACGAGTTTAGAACCTC 57.023 34.615 0.00 0.00 0.00 3.85
81 82 3.555917 AGACACGAGTTTAGAACCTCG 57.444 47.619 7.57 7.57 43.89 4.63
82 83 3.144506 AGACACGAGTTTAGAACCTCGA 58.855 45.455 15.01 0.00 41.24 4.04
83 84 3.567164 AGACACGAGTTTAGAACCTCGAA 59.433 43.478 15.01 0.00 41.24 3.71
84 85 4.217983 AGACACGAGTTTAGAACCTCGAAT 59.782 41.667 15.01 3.56 41.24 3.34
85 86 4.235360 ACACGAGTTTAGAACCTCGAATG 58.765 43.478 15.01 7.13 41.24 2.67
86 87 4.235360 CACGAGTTTAGAACCTCGAATGT 58.765 43.478 15.01 0.00 41.24 2.71
87 88 4.323868 CACGAGTTTAGAACCTCGAATGTC 59.676 45.833 15.01 0.00 41.24 3.06
88 89 3.542704 CGAGTTTAGAACCTCGAATGTCG 59.457 47.826 3.37 0.00 41.24 4.35
96 97 2.506217 TCGAATGTCGAGGCGCAC 60.506 61.111 10.83 0.00 44.82 5.34
97 98 2.809174 CGAATGTCGAGGCGCACA 60.809 61.111 10.83 4.98 43.74 4.57
98 99 2.379634 CGAATGTCGAGGCGCACAA 61.380 57.895 10.83 0.00 43.74 3.33
99 100 1.866237 GAATGTCGAGGCGCACAAA 59.134 52.632 10.83 0.00 0.00 2.83
100 101 0.452784 GAATGTCGAGGCGCACAAAC 60.453 55.000 10.83 2.14 0.00 2.93
101 102 0.884704 AATGTCGAGGCGCACAAACT 60.885 50.000 10.83 0.00 0.00 2.66
102 103 0.037697 ATGTCGAGGCGCACAAACTA 60.038 50.000 10.83 0.00 0.00 2.24
103 104 0.666274 TGTCGAGGCGCACAAACTAG 60.666 55.000 10.83 0.00 0.00 2.57
104 105 1.736645 TCGAGGCGCACAAACTAGC 60.737 57.895 10.83 0.00 0.00 3.42
105 106 2.027073 CGAGGCGCACAAACTAGCA 61.027 57.895 10.83 0.00 0.00 3.49
106 107 1.565156 CGAGGCGCACAAACTAGCAA 61.565 55.000 10.83 0.00 0.00 3.91
107 108 0.591170 GAGGCGCACAAACTAGCAAA 59.409 50.000 10.83 0.00 0.00 3.68
108 109 0.593128 AGGCGCACAAACTAGCAAAG 59.407 50.000 10.83 0.00 0.00 2.77
109 110 1.003769 GGCGCACAAACTAGCAAAGC 61.004 55.000 10.83 0.00 0.00 3.51
110 111 0.317770 GCGCACAAACTAGCAAAGCA 60.318 50.000 0.30 0.00 0.00 3.91
111 112 1.666888 GCGCACAAACTAGCAAAGCAT 60.667 47.619 0.30 0.00 0.00 3.79
112 113 1.980844 CGCACAAACTAGCAAAGCATG 59.019 47.619 0.00 0.00 0.00 4.06
126 127 4.240096 CAAAGCATGCTTTAACTCTTGGG 58.760 43.478 37.87 21.97 43.56 4.12
127 128 3.439857 AGCATGCTTTAACTCTTGGGA 57.560 42.857 16.30 0.00 0.00 4.37
128 129 3.084786 AGCATGCTTTAACTCTTGGGAC 58.915 45.455 16.30 0.00 0.00 4.46
129 130 2.164422 GCATGCTTTAACTCTTGGGACC 59.836 50.000 11.37 0.00 0.00 4.46
130 131 2.178912 TGCTTTAACTCTTGGGACCG 57.821 50.000 0.00 0.00 0.00 4.79
131 132 1.271163 TGCTTTAACTCTTGGGACCGG 60.271 52.381 0.00 0.00 0.00 5.28
132 133 1.271217 GCTTTAACTCTTGGGACCGGT 60.271 52.381 6.92 6.92 0.00 5.28
133 134 2.696506 CTTTAACTCTTGGGACCGGTC 58.303 52.381 27.04 27.04 0.00 4.79
134 135 0.604578 TTAACTCTTGGGACCGGTCG 59.395 55.000 27.68 15.31 0.00 4.79
135 136 1.880819 TAACTCTTGGGACCGGTCGC 61.881 60.000 37.21 37.21 42.16 5.19
136 137 4.452733 CTCTTGGGACCGGTCGCC 62.453 72.222 39.17 32.56 41.25 5.54
138 139 4.096003 CTTGGGACCGGTCGCCAT 62.096 66.667 39.17 4.17 41.25 4.40
139 140 4.402528 TTGGGACCGGTCGCCATG 62.403 66.667 39.17 0.00 41.25 3.66
141 142 4.404098 GGGACCGGTCGCCATGTT 62.404 66.667 34.98 0.00 36.65 2.71
142 143 2.359478 GGACCGGTCGCCATGTTT 60.359 61.111 27.68 0.00 0.00 2.83
143 144 2.686816 GGACCGGTCGCCATGTTTG 61.687 63.158 27.68 0.00 0.00 2.93
144 145 2.671619 ACCGGTCGCCATGTTTGG 60.672 61.111 0.00 0.00 46.66 3.28
145 146 2.671619 CCGGTCGCCATGTTTGGT 60.672 61.111 0.00 0.00 45.57 3.67
146 147 2.265182 CCGGTCGCCATGTTTGGTT 61.265 57.895 0.00 0.00 45.57 3.67
147 148 0.956410 CCGGTCGCCATGTTTGGTTA 60.956 55.000 0.00 0.00 45.57 2.85
148 149 0.446222 CGGTCGCCATGTTTGGTTAG 59.554 55.000 0.00 0.00 45.57 2.34
149 150 0.808755 GGTCGCCATGTTTGGTTAGG 59.191 55.000 0.00 0.00 45.57 2.69
150 151 0.170339 GTCGCCATGTTTGGTTAGGC 59.830 55.000 0.00 0.00 45.57 3.93
151 152 0.963355 TCGCCATGTTTGGTTAGGCC 60.963 55.000 0.00 0.00 45.57 5.19
152 153 1.247419 CGCCATGTTTGGTTAGGCCA 61.247 55.000 5.01 0.00 45.57 5.36
159 160 4.660611 TGGTTAGGCCACCCGGGA 62.661 66.667 32.02 0.00 43.61 5.14
160 161 3.793888 GGTTAGGCCACCCGGGAG 61.794 72.222 32.02 21.47 40.01 4.30
161 162 2.686106 GTTAGGCCACCCGGGAGA 60.686 66.667 32.02 0.00 40.01 3.71
162 163 2.123180 TTAGGCCACCCGGGAGAA 59.877 61.111 32.02 6.58 40.01 2.87
163 164 2.295602 TTAGGCCACCCGGGAGAAC 61.296 63.158 32.02 15.64 40.01 3.01
164 165 2.758852 TTAGGCCACCCGGGAGAACT 62.759 60.000 32.02 21.98 40.01 3.01
165 166 2.758852 TAGGCCACCCGGGAGAACTT 62.759 60.000 32.02 13.97 40.01 2.66
166 167 2.434774 GCCACCCGGGAGAACTTT 59.565 61.111 32.02 0.00 40.01 2.66
167 168 1.674651 GCCACCCGGGAGAACTTTC 60.675 63.158 32.02 2.90 40.01 2.62
168 169 2.067197 CCACCCGGGAGAACTTTCT 58.933 57.895 32.02 0.00 40.01 2.52
169 170 0.400594 CCACCCGGGAGAACTTTCTT 59.599 55.000 32.02 0.00 40.01 2.52
170 171 1.202891 CCACCCGGGAGAACTTTCTTT 60.203 52.381 32.02 0.00 40.01 2.52
171 172 2.152016 CACCCGGGAGAACTTTCTTTC 58.848 52.381 32.02 0.00 37.73 2.62
172 173 1.270678 ACCCGGGAGAACTTTCTTTCG 60.271 52.381 32.02 0.00 37.73 3.46
173 174 1.270678 CCCGGGAGAACTTTCTTTCGT 60.271 52.381 18.48 0.00 37.73 3.85
174 175 2.067013 CCGGGAGAACTTTCTTTCGTC 58.933 52.381 0.00 0.00 37.73 4.20
175 176 2.067013 CGGGAGAACTTTCTTTCGTCC 58.933 52.381 0.00 0.00 37.73 4.79
176 177 2.424557 GGGAGAACTTTCTTTCGTCCC 58.575 52.381 0.00 0.00 37.73 4.46
177 178 2.038689 GGGAGAACTTTCTTTCGTCCCT 59.961 50.000 6.14 0.00 38.57 4.20
178 179 3.067833 GGAGAACTTTCTTTCGTCCCTG 58.932 50.000 0.00 0.00 37.73 4.45
179 180 3.494573 GGAGAACTTTCTTTCGTCCCTGT 60.495 47.826 0.00 0.00 37.73 4.00
180 181 4.262335 GGAGAACTTTCTTTCGTCCCTGTA 60.262 45.833 0.00 0.00 37.73 2.74
181 182 5.286267 AGAACTTTCTTTCGTCCCTGTAA 57.714 39.130 0.00 0.00 32.55 2.41
182 183 5.298347 AGAACTTTCTTTCGTCCCTGTAAG 58.702 41.667 0.00 0.00 32.55 2.34
183 184 3.400255 ACTTTCTTTCGTCCCTGTAAGC 58.600 45.455 0.00 0.00 0.00 3.09
184 185 2.074547 TTCTTTCGTCCCTGTAAGCG 57.925 50.000 0.00 0.00 0.00 4.68
185 186 0.963962 TCTTTCGTCCCTGTAAGCGT 59.036 50.000 0.00 0.00 0.00 5.07
186 187 1.068474 CTTTCGTCCCTGTAAGCGTG 58.932 55.000 0.00 0.00 0.00 5.34
187 188 0.675083 TTTCGTCCCTGTAAGCGTGA 59.325 50.000 0.00 0.00 0.00 4.35
188 189 0.038892 TTCGTCCCTGTAAGCGTGAC 60.039 55.000 0.00 0.00 0.00 3.67
189 190 1.174078 TCGTCCCTGTAAGCGTGACA 61.174 55.000 0.00 0.00 0.00 3.58
190 191 0.732880 CGTCCCTGTAAGCGTGACAG 60.733 60.000 8.28 8.28 43.32 3.51
191 192 0.601558 GTCCCTGTAAGCGTGACAGA 59.398 55.000 14.84 0.00 46.01 3.41
192 193 1.204941 GTCCCTGTAAGCGTGACAGAT 59.795 52.381 14.84 0.00 46.01 2.90
193 194 1.476891 TCCCTGTAAGCGTGACAGATC 59.523 52.381 14.84 0.00 46.01 2.75
194 195 1.204704 CCCTGTAAGCGTGACAGATCA 59.795 52.381 14.84 0.00 46.01 2.92
195 196 2.159043 CCCTGTAAGCGTGACAGATCAT 60.159 50.000 14.84 0.00 46.01 2.45
196 197 3.525537 CCTGTAAGCGTGACAGATCATT 58.474 45.455 14.84 0.00 46.01 2.57
197 198 4.441495 CCCTGTAAGCGTGACAGATCATTA 60.441 45.833 14.84 0.00 46.01 1.90
198 199 5.109210 CCTGTAAGCGTGACAGATCATTAA 58.891 41.667 14.84 0.00 46.01 1.40
199 200 5.755375 CCTGTAAGCGTGACAGATCATTAAT 59.245 40.000 14.84 0.00 46.01 1.40
200 201 6.923508 CCTGTAAGCGTGACAGATCATTAATA 59.076 38.462 14.84 0.00 46.01 0.98
201 202 7.438160 CCTGTAAGCGTGACAGATCATTAATAA 59.562 37.037 14.84 0.00 46.01 1.40
202 203 8.710835 TGTAAGCGTGACAGATCATTAATAAA 57.289 30.769 0.00 0.00 37.14 1.40
203 204 8.817100 TGTAAGCGTGACAGATCATTAATAAAG 58.183 33.333 0.00 0.00 37.14 1.85
204 205 6.292389 AGCGTGACAGATCATTAATAAAGC 57.708 37.500 0.00 0.00 37.14 3.51
205 206 6.051717 AGCGTGACAGATCATTAATAAAGCT 58.948 36.000 0.00 0.00 37.14 3.74
206 207 6.540189 AGCGTGACAGATCATTAATAAAGCTT 59.460 34.615 0.00 0.00 37.14 3.74
207 208 7.066284 AGCGTGACAGATCATTAATAAAGCTTT 59.934 33.333 17.30 17.30 37.14 3.51
208 209 7.164826 GCGTGACAGATCATTAATAAAGCTTTG 59.835 37.037 22.02 4.52 37.14 2.77
209 210 7.164826 CGTGACAGATCATTAATAAAGCTTTGC 59.835 37.037 22.02 0.36 37.14 3.68
210 211 7.164826 GTGACAGATCATTAATAAAGCTTTGCG 59.835 37.037 22.02 3.83 37.14 4.85
211 212 7.065683 TGACAGATCATTAATAAAGCTTTGCGA 59.934 33.333 22.02 1.88 0.00 5.10
212 213 7.412853 ACAGATCATTAATAAAGCTTTGCGAG 58.587 34.615 22.02 6.87 0.00 5.03
213 214 7.066284 ACAGATCATTAATAAAGCTTTGCGAGT 59.934 33.333 22.02 3.77 0.00 4.18
214 215 7.912250 CAGATCATTAATAAAGCTTTGCGAGTT 59.088 33.333 22.02 10.47 0.00 3.01
215 216 8.125448 AGATCATTAATAAAGCTTTGCGAGTTC 58.875 33.333 22.02 10.36 0.00 3.01
216 217 6.247903 TCATTAATAAAGCTTTGCGAGTTCG 58.752 36.000 22.02 3.82 43.27 3.95
217 218 5.600908 TTAATAAAGCTTTGCGAGTTCGT 57.399 34.783 22.02 0.00 42.22 3.85
218 219 3.724295 ATAAAGCTTTGCGAGTTCGTC 57.276 42.857 22.02 0.00 42.22 4.20
219 220 1.583054 AAAGCTTTGCGAGTTCGTCT 58.417 45.000 11.80 0.00 42.22 4.18
220 221 2.433868 AAGCTTTGCGAGTTCGTCTA 57.566 45.000 0.00 0.00 42.22 2.59
221 222 2.433868 AGCTTTGCGAGTTCGTCTAA 57.566 45.000 3.27 0.00 42.22 2.10
222 223 2.750948 AGCTTTGCGAGTTCGTCTAAA 58.249 42.857 3.27 2.88 42.22 1.85
223 224 3.128349 AGCTTTGCGAGTTCGTCTAAAA 58.872 40.909 3.27 0.04 42.22 1.52
224 225 3.558418 AGCTTTGCGAGTTCGTCTAAAAA 59.442 39.130 3.27 0.00 42.22 1.94
432 446 2.758130 ACAAAAGGGATTGTGGGTTGT 58.242 42.857 0.00 0.00 41.78 3.32
452 466 3.891977 TGTGAAATGAAAAATCCCGGTCA 59.108 39.130 0.00 0.00 0.00 4.02
461 475 5.888724 TGAAAAATCCCGGTCAGCATAAATA 59.111 36.000 0.00 0.00 0.00 1.40
486 500 1.606668 GGAATTGTGGACTGCGAAACA 59.393 47.619 0.00 0.00 0.00 2.83
542 556 2.055838 GGTTGCGAAACGAAAAATCCC 58.944 47.619 0.00 0.00 0.00 3.85
548 562 2.668250 GAAACGAAAAATCCCGGTTGG 58.332 47.619 0.00 0.00 35.67 3.77
549 563 0.315886 AACGAAAAATCCCGGTTGGC 59.684 50.000 0.00 0.00 0.00 4.52
559 573 4.305011 CGGTTGGCAACGGGATTA 57.695 55.556 25.18 0.00 42.51 1.75
581 595 3.547649 AGTATGCGAAACGAAAAACCC 57.452 42.857 0.00 0.00 0.00 4.11
586 600 1.464219 GCGAAACGAAAAACCCCGATA 59.536 47.619 0.00 0.00 0.00 2.92
643 659 7.547722 ACAAAAAGTAAACAAATGTCTTCCCAC 59.452 33.333 0.00 0.00 0.00 4.61
652 668 3.959495 ATGTCTTCCCACTGGCATAAT 57.041 42.857 0.00 0.00 0.00 1.28
654 670 3.355378 TGTCTTCCCACTGGCATAATTG 58.645 45.455 0.00 0.00 0.00 2.32
666 683 5.358160 ACTGGCATAATTGAAAAGAGGCTAC 59.642 40.000 0.00 0.00 0.00 3.58
700 717 0.471591 AAAAGGGATTGTGGGCTGCA 60.472 50.000 0.50 0.00 0.00 4.41
701 718 0.471591 AAAGGGATTGTGGGCTGCAA 60.472 50.000 0.50 0.00 0.00 4.08
707 727 2.550639 GGATTGTGGGCTGCAAAACAAT 60.551 45.455 19.88 19.88 43.91 2.71
745 765 3.640967 TCTTGGCTGGCATAAACAAAAGT 59.359 39.130 4.22 0.00 0.00 2.66
792 812 4.230745 AGTAAACAACACTGGGTGAACT 57.769 40.909 4.62 0.00 36.96 3.01
795 815 7.069877 AGTAAACAACACTGGGTGAACTATA 57.930 36.000 4.62 0.00 36.96 1.31
846 866 6.035650 TCGTTTAAAGGCTGAATTATGTCGAG 59.964 38.462 2.98 0.00 0.00 4.04
854 874 6.769822 AGGCTGAATTATGTCGAGAATTTCAT 59.230 34.615 0.00 0.00 0.00 2.57
943 1018 2.746277 ACGCCGCAGTCCATTTCC 60.746 61.111 0.00 0.00 0.00 3.13
1020 1095 2.787866 CCCTCTCCCTCCCTTCCA 59.212 66.667 0.00 0.00 0.00 3.53
1047 1122 4.864334 GCCATGGCCTCGACCCTG 62.864 72.222 27.24 0.00 34.56 4.45
1112 1187 1.153289 CCCCTCATCGCCACTTCAG 60.153 63.158 0.00 0.00 0.00 3.02
1121 1196 2.358737 CCACTTCAGCCCACGGAC 60.359 66.667 0.00 0.00 0.00 4.79
1380 1455 4.778415 CTCGTGTCCTGGACGGCG 62.778 72.222 26.79 26.79 37.43 6.46
1550 1625 2.561037 CCGTGGTCCTTGGGTTTGC 61.561 63.158 0.00 0.00 0.00 3.68
1611 1686 4.046462 GCTGCGCATTGATTGATATGTTT 58.954 39.130 12.24 0.00 0.00 2.83
1614 1689 4.602507 CGCATTGATTGATATGTTTGCG 57.397 40.909 0.00 0.00 44.39 4.85
1624 1699 1.717194 TATGTTTGCGAGGAACGGAC 58.283 50.000 0.00 0.00 42.85 4.79
1833 1908 0.467384 AGCAGGGATCGGTCAGATTG 59.533 55.000 0.00 0.00 40.26 2.67
1870 1945 0.921896 TCTAGTACTACGGCTGGGGT 59.078 55.000 0.00 0.00 0.00 4.95
1895 1970 4.390297 GGTTTCTGATACTTGTGTGAGCTC 59.610 45.833 6.82 6.82 0.00 4.09
1902 1977 2.598565 ACTTGTGTGAGCTCTGGACTA 58.401 47.619 16.19 5.00 0.00 2.59
1986 2061 1.466950 CGAATGCCCACACATAACGTT 59.533 47.619 5.88 5.88 0.00 3.99
2249 2324 1.180029 GCTGAATCTGGTTGCATGGT 58.820 50.000 0.00 0.00 0.00 3.55
2573 2648 3.683989 CATTTGATGAAATGGACGACCG 58.316 45.455 9.53 0.00 43.30 4.79
2775 2850 5.306114 TCAGATCAATGCAGAAGGATCAT 57.694 39.130 16.86 0.00 38.84 2.45
2782 2857 2.190538 TGCAGAAGGATCATGGACTCA 58.809 47.619 0.00 0.00 0.00 3.41
2907 2982 5.450137 GGATGCATTGATTTGGAAGACTCTG 60.450 44.000 0.00 0.00 0.00 3.35
2933 3008 4.608951 GGTGCTTGTAGGACTTACGATAG 58.391 47.826 0.00 0.00 36.73 2.08
2958 3033 5.726980 TTGAGATTGGTAAAATTGCAGCT 57.273 34.783 0.00 0.00 0.00 4.24
3000 3075 0.387878 CGCGAGATCCAGCTCCATAC 60.388 60.000 0.00 0.00 0.00 2.39
3194 3269 3.944015 GAGATCTATGCAAAGTTGGCTGT 59.056 43.478 3.39 0.00 0.00 4.40
3417 3519 9.631452 TCTGCAATCAAGTATATCTCTAAATCG 57.369 33.333 0.00 0.00 0.00 3.34
3515 3617 2.401766 GGTGAGCTGTGAATGGCGG 61.402 63.158 0.00 0.00 0.00 6.13
3655 3758 7.894708 TGATTTTGCAAAGGATTAGATGTTGA 58.105 30.769 12.41 0.00 0.00 3.18
3767 3874 5.450818 TTGGGCATACTTGGATTACTTCT 57.549 39.130 0.00 0.00 0.00 2.85
3853 3960 6.040504 GGGAATGAACTTAGTTGTTTTCCACT 59.959 38.462 21.39 0.00 38.01 4.00
4005 4118 6.677920 GCAAATACATACACATGGTGAAGACC 60.678 42.308 2.98 0.00 43.48 3.85
4022 4136 7.278875 GTGAAGACCAAAATCATCCTAGATCT 58.721 38.462 0.00 0.00 0.00 2.75
4050 4164 1.133761 TCAACCGTTTGAACCCATGGA 60.134 47.619 15.22 0.00 38.87 3.41
4051 4165 1.000717 CAACCGTTTGAACCCATGGAC 60.001 52.381 15.22 0.36 34.24 4.02
4276 4517 6.373495 ACGAGAAAAGTAAACCAGAACTTGTT 59.627 34.615 0.00 0.00 36.12 2.83
4323 4564 1.573829 AAGCCGCACACCATGTAACG 61.574 55.000 0.00 0.00 0.00 3.18
4344 4585 3.681034 CGCTGAAGTCTTGGATCTCCATT 60.681 47.826 0.00 0.00 46.97 3.16
4363 4604 4.452455 CCATTAATTCGTCCCTGCTGTATC 59.548 45.833 0.00 0.00 0.00 2.24
4430 4675 6.549364 ACTGAGATTATACTCCTTCTGACTGG 59.451 42.308 0.00 0.00 36.22 4.00
4435 4680 7.841729 AGATTATACTCCTTCTGACTGGAAGAA 59.158 37.037 5.89 0.00 43.70 2.52
4446 4691 6.533730 TCTGACTGGAAGAAAATAAAGCAGA 58.466 36.000 0.00 0.00 37.43 4.26
4469 4714 5.091261 GTGAAGTCACATCATCCTTACCT 57.909 43.478 6.57 0.00 45.75 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.548875 CTTGATCTCCTGCACTACTGC 58.451 52.381 0.00 0.00 44.52 4.40
8 9 2.762887 TCCTTGATCTCCTGCACTACTG 59.237 50.000 0.00 0.00 0.00 2.74
9 10 3.030291 CTCCTTGATCTCCTGCACTACT 58.970 50.000 0.00 0.00 0.00 2.57
10 11 2.482839 GCTCCTTGATCTCCTGCACTAC 60.483 54.545 0.00 0.00 0.00 2.73
11 12 1.759445 GCTCCTTGATCTCCTGCACTA 59.241 52.381 0.00 0.00 0.00 2.74
12 13 0.540923 GCTCCTTGATCTCCTGCACT 59.459 55.000 0.00 0.00 0.00 4.40
13 14 0.251354 TGCTCCTTGATCTCCTGCAC 59.749 55.000 0.00 0.00 0.00 4.57
14 15 1.210538 ATGCTCCTTGATCTCCTGCA 58.789 50.000 0.00 0.00 0.00 4.41
15 16 2.158784 AGAATGCTCCTTGATCTCCTGC 60.159 50.000 0.00 0.00 0.00 4.85
16 17 3.842007 AGAATGCTCCTTGATCTCCTG 57.158 47.619 0.00 0.00 0.00 3.86
17 18 4.555689 ACTAGAATGCTCCTTGATCTCCT 58.444 43.478 0.00 0.00 0.00 3.69
18 19 4.953940 ACTAGAATGCTCCTTGATCTCC 57.046 45.455 0.00 0.00 0.00 3.71
19 20 6.648879 ACTACTAGAATGCTCCTTGATCTC 57.351 41.667 0.00 0.00 0.00 2.75
20 21 7.430760 AAACTACTAGAATGCTCCTTGATCT 57.569 36.000 0.00 0.00 0.00 2.75
21 22 9.771534 ATAAAACTACTAGAATGCTCCTTGATC 57.228 33.333 0.00 0.00 0.00 2.92
23 24 9.959721 AAATAAAACTACTAGAATGCTCCTTGA 57.040 29.630 0.00 0.00 0.00 3.02
25 26 9.397280 GGAAATAAAACTACTAGAATGCTCCTT 57.603 33.333 0.00 0.00 0.00 3.36
26 27 8.773216 AGGAAATAAAACTACTAGAATGCTCCT 58.227 33.333 0.00 0.00 0.00 3.69
27 28 8.831550 CAGGAAATAAAACTACTAGAATGCTCC 58.168 37.037 0.00 0.00 0.00 4.70
28 29 9.384764 ACAGGAAATAAAACTACTAGAATGCTC 57.615 33.333 0.00 0.00 0.00 4.26
29 30 9.740710 AACAGGAAATAAAACTACTAGAATGCT 57.259 29.630 0.00 0.00 0.00 3.79
44 45 9.715121 ACTCGTGTCTAAATAAACAGGAAATAA 57.285 29.630 0.00 0.00 39.12 1.40
45 46 9.715121 AACTCGTGTCTAAATAAACAGGAAATA 57.285 29.630 0.00 0.00 39.12 1.40
46 47 8.617290 AACTCGTGTCTAAATAAACAGGAAAT 57.383 30.769 0.00 0.00 39.12 2.17
47 48 8.441312 AAACTCGTGTCTAAATAAACAGGAAA 57.559 30.769 0.00 0.00 39.12 3.13
48 49 9.199982 CTAAACTCGTGTCTAAATAAACAGGAA 57.800 33.333 0.00 0.00 39.12 3.36
49 50 8.579006 TCTAAACTCGTGTCTAAATAAACAGGA 58.421 33.333 0.00 0.00 37.80 3.86
50 51 8.752766 TCTAAACTCGTGTCTAAATAAACAGG 57.247 34.615 0.00 0.00 33.67 4.00
52 53 8.981647 GGTTCTAAACTCGTGTCTAAATAAACA 58.018 33.333 0.00 0.00 0.00 2.83
53 54 9.201127 AGGTTCTAAACTCGTGTCTAAATAAAC 57.799 33.333 0.00 0.00 0.00 2.01
54 55 9.415544 GAGGTTCTAAACTCGTGTCTAAATAAA 57.584 33.333 0.00 0.00 0.00 1.40
55 56 8.976986 GAGGTTCTAAACTCGTGTCTAAATAA 57.023 34.615 0.00 0.00 0.00 1.40
67 68 4.730657 TCGACATTCGAGGTTCTAAACTC 58.269 43.478 0.00 0.00 44.82 3.01
68 69 4.778534 TCGACATTCGAGGTTCTAAACT 57.221 40.909 0.00 0.00 44.82 2.66
80 81 1.896339 TTTGTGCGCCTCGACATTCG 61.896 55.000 4.18 0.00 42.10 3.34
81 82 0.452784 GTTTGTGCGCCTCGACATTC 60.453 55.000 4.18 0.00 0.00 2.67
82 83 0.884704 AGTTTGTGCGCCTCGACATT 60.885 50.000 4.18 0.00 0.00 2.71
83 84 0.037697 TAGTTTGTGCGCCTCGACAT 60.038 50.000 4.18 0.00 0.00 3.06
84 85 0.666274 CTAGTTTGTGCGCCTCGACA 60.666 55.000 4.18 0.00 0.00 4.35
85 86 1.956620 GCTAGTTTGTGCGCCTCGAC 61.957 60.000 4.18 0.00 0.00 4.20
86 87 1.736645 GCTAGTTTGTGCGCCTCGA 60.737 57.895 4.18 0.00 0.00 4.04
87 88 1.565156 TTGCTAGTTTGTGCGCCTCG 61.565 55.000 4.18 0.00 0.00 4.63
88 89 0.591170 TTTGCTAGTTTGTGCGCCTC 59.409 50.000 4.18 0.00 0.00 4.70
89 90 0.593128 CTTTGCTAGTTTGTGCGCCT 59.407 50.000 4.18 0.00 0.00 5.52
90 91 1.003769 GCTTTGCTAGTTTGTGCGCC 61.004 55.000 4.18 0.00 0.00 6.53
91 92 0.317770 TGCTTTGCTAGTTTGTGCGC 60.318 50.000 0.00 0.00 0.00 6.09
92 93 1.980844 CATGCTTTGCTAGTTTGTGCG 59.019 47.619 0.00 0.00 0.00 5.34
104 105 4.022068 TCCCAAGAGTTAAAGCATGCTTTG 60.022 41.667 42.11 29.17 44.84 2.77
105 106 4.021981 GTCCCAAGAGTTAAAGCATGCTTT 60.022 41.667 39.21 39.21 46.56 3.51
106 107 3.507622 GTCCCAAGAGTTAAAGCATGCTT 59.492 43.478 27.21 27.21 37.98 3.91
107 108 3.084786 GTCCCAAGAGTTAAAGCATGCT 58.915 45.455 16.30 16.30 0.00 3.79
108 109 2.164422 GGTCCCAAGAGTTAAAGCATGC 59.836 50.000 10.51 10.51 0.00 4.06
109 110 2.420022 CGGTCCCAAGAGTTAAAGCATG 59.580 50.000 0.00 0.00 0.00 4.06
110 111 2.618045 CCGGTCCCAAGAGTTAAAGCAT 60.618 50.000 0.00 0.00 0.00 3.79
111 112 1.271163 CCGGTCCCAAGAGTTAAAGCA 60.271 52.381 0.00 0.00 0.00 3.91
112 113 1.271217 ACCGGTCCCAAGAGTTAAAGC 60.271 52.381 0.00 0.00 0.00 3.51
113 114 2.696506 GACCGGTCCCAAGAGTTAAAG 58.303 52.381 24.75 0.00 0.00 1.85
114 115 1.001181 CGACCGGTCCCAAGAGTTAAA 59.999 52.381 28.52 0.00 0.00 1.52
115 116 0.604578 CGACCGGTCCCAAGAGTTAA 59.395 55.000 28.52 0.00 0.00 2.01
116 117 1.880819 GCGACCGGTCCCAAGAGTTA 61.881 60.000 28.52 0.00 0.00 2.24
117 118 3.057337 CGACCGGTCCCAAGAGTT 58.943 61.111 28.52 0.00 0.00 3.01
118 119 3.692406 GCGACCGGTCCCAAGAGT 61.692 66.667 28.52 0.00 0.00 3.24
119 120 4.452733 GGCGACCGGTCCCAAGAG 62.453 72.222 28.52 14.39 0.00 2.85
121 122 4.096003 ATGGCGACCGGTCCCAAG 62.096 66.667 34.25 21.42 34.94 3.61
122 123 4.402528 CATGGCGACCGGTCCCAA 62.403 66.667 34.25 21.29 34.94 4.12
124 125 3.912745 AAACATGGCGACCGGTCCC 62.913 63.158 28.52 27.36 0.00 4.46
125 126 2.359478 AAACATGGCGACCGGTCC 60.359 61.111 28.52 20.04 0.00 4.46
126 127 2.686816 CCAAACATGGCGACCGGTC 61.687 63.158 25.28 25.28 0.00 4.79
127 128 2.671619 CCAAACATGGCGACCGGT 60.672 61.111 6.92 6.92 0.00 5.28
128 129 0.956410 TAACCAAACATGGCGACCGG 60.956 55.000 0.00 0.00 0.00 5.28
129 130 0.446222 CTAACCAAACATGGCGACCG 59.554 55.000 0.00 0.00 0.00 4.79
130 131 0.808755 CCTAACCAAACATGGCGACC 59.191 55.000 0.00 0.00 0.00 4.79
131 132 0.170339 GCCTAACCAAACATGGCGAC 59.830 55.000 0.00 0.00 33.96 5.19
132 133 0.963355 GGCCTAACCAAACATGGCGA 60.963 55.000 0.00 0.00 44.07 5.54
133 134 1.510844 GGCCTAACCAAACATGGCG 59.489 57.895 0.00 0.00 44.07 5.69
143 144 3.793888 CTCCCGGGTGGCCTAACC 61.794 72.222 22.86 3.45 39.71 2.85
144 145 2.295602 TTCTCCCGGGTGGCCTAAC 61.296 63.158 22.86 0.00 0.00 2.34
145 146 2.123180 TTCTCCCGGGTGGCCTAA 59.877 61.111 22.86 5.26 0.00 2.69
146 147 2.686106 GTTCTCCCGGGTGGCCTA 60.686 66.667 22.86 0.00 0.00 3.93
147 148 4.658786 AGTTCTCCCGGGTGGCCT 62.659 66.667 22.86 14.23 0.00 5.19
148 149 3.205851 AAAGTTCTCCCGGGTGGCC 62.206 63.158 22.86 12.08 0.00 5.36
149 150 1.674651 GAAAGTTCTCCCGGGTGGC 60.675 63.158 22.86 14.53 0.00 5.01
150 151 0.400594 AAGAAAGTTCTCCCGGGTGG 59.599 55.000 22.86 15.04 36.28 4.61
151 152 2.152016 GAAAGAAAGTTCTCCCGGGTG 58.848 52.381 22.86 19.64 36.28 4.61
152 153 1.270678 CGAAAGAAAGTTCTCCCGGGT 60.271 52.381 22.86 0.00 36.28 5.28
153 154 1.270678 ACGAAAGAAAGTTCTCCCGGG 60.271 52.381 16.85 16.85 36.28 5.73
154 155 2.067013 GACGAAAGAAAGTTCTCCCGG 58.933 52.381 15.01 0.00 36.28 5.73
155 156 2.067013 GGACGAAAGAAAGTTCTCCCG 58.933 52.381 11.20 11.20 36.28 5.14
156 157 2.038689 AGGGACGAAAGAAAGTTCTCCC 59.961 50.000 7.06 7.06 41.05 4.30
157 158 3.067833 CAGGGACGAAAGAAAGTTCTCC 58.932 50.000 0.00 0.00 36.28 3.71
158 159 3.729966 ACAGGGACGAAAGAAAGTTCTC 58.270 45.455 0.00 0.00 36.28 2.87
159 160 3.840124 ACAGGGACGAAAGAAAGTTCT 57.160 42.857 0.00 0.00 39.74 3.01
160 161 4.083961 GCTTACAGGGACGAAAGAAAGTTC 60.084 45.833 0.00 0.00 0.00 3.01
161 162 3.813724 GCTTACAGGGACGAAAGAAAGTT 59.186 43.478 0.00 0.00 0.00 2.66
162 163 3.400255 GCTTACAGGGACGAAAGAAAGT 58.600 45.455 0.00 0.00 0.00 2.66
163 164 2.412089 CGCTTACAGGGACGAAAGAAAG 59.588 50.000 0.00 0.00 0.00 2.62
164 165 2.224113 ACGCTTACAGGGACGAAAGAAA 60.224 45.455 0.00 0.00 31.91 2.52
165 166 1.342174 ACGCTTACAGGGACGAAAGAA 59.658 47.619 0.00 0.00 31.91 2.52
166 167 0.963962 ACGCTTACAGGGACGAAAGA 59.036 50.000 0.00 0.00 31.91 2.52
167 168 1.068474 CACGCTTACAGGGACGAAAG 58.932 55.000 0.00 0.00 31.91 2.62
168 169 0.675083 TCACGCTTACAGGGACGAAA 59.325 50.000 0.00 0.00 31.91 3.46
169 170 0.038892 GTCACGCTTACAGGGACGAA 60.039 55.000 0.00 0.00 31.92 3.85
170 171 1.174078 TGTCACGCTTACAGGGACGA 61.174 55.000 0.00 0.00 44.51 4.20
171 172 0.732880 CTGTCACGCTTACAGGGACG 60.733 60.000 4.85 0.00 44.51 4.79
172 173 0.601558 TCTGTCACGCTTACAGGGAC 59.398 55.000 11.19 0.00 43.69 4.46
173 174 1.476891 GATCTGTCACGCTTACAGGGA 59.523 52.381 11.19 0.00 43.69 4.20
174 175 1.204704 TGATCTGTCACGCTTACAGGG 59.795 52.381 11.19 0.00 43.69 4.45
175 176 2.654749 TGATCTGTCACGCTTACAGG 57.345 50.000 11.19 0.00 43.69 4.00
176 177 6.834959 ATTAATGATCTGTCACGCTTACAG 57.165 37.500 6.15 6.15 44.66 2.74
177 178 8.710835 TTTATTAATGATCTGTCACGCTTACA 57.289 30.769 0.00 0.00 37.14 2.41
178 179 7.794349 GCTTTATTAATGATCTGTCACGCTTAC 59.206 37.037 0.00 0.00 37.14 2.34
179 180 7.710907 AGCTTTATTAATGATCTGTCACGCTTA 59.289 33.333 0.00 0.00 37.14 3.09
180 181 6.540189 AGCTTTATTAATGATCTGTCACGCTT 59.460 34.615 0.00 0.00 37.14 4.68
181 182 6.051717 AGCTTTATTAATGATCTGTCACGCT 58.948 36.000 0.00 0.00 37.14 5.07
182 183 6.292389 AGCTTTATTAATGATCTGTCACGC 57.708 37.500 0.00 0.00 37.14 5.34
183 184 7.164826 GCAAAGCTTTATTAATGATCTGTCACG 59.835 37.037 12.25 0.00 37.14 4.35
184 185 7.164826 CGCAAAGCTTTATTAATGATCTGTCAC 59.835 37.037 12.25 0.00 37.14 3.67
185 186 7.065683 TCGCAAAGCTTTATTAATGATCTGTCA 59.934 33.333 12.25 0.00 39.04 3.58
186 187 7.409697 TCGCAAAGCTTTATTAATGATCTGTC 58.590 34.615 12.25 0.00 0.00 3.51
187 188 7.066284 ACTCGCAAAGCTTTATTAATGATCTGT 59.934 33.333 12.25 0.00 0.00 3.41
188 189 7.412853 ACTCGCAAAGCTTTATTAATGATCTG 58.587 34.615 12.25 0.00 0.00 2.90
189 190 7.559590 ACTCGCAAAGCTTTATTAATGATCT 57.440 32.000 12.25 0.00 0.00 2.75
190 191 7.110765 CGAACTCGCAAAGCTTTATTAATGATC 59.889 37.037 12.25 3.60 0.00 2.92
191 192 6.907212 CGAACTCGCAAAGCTTTATTAATGAT 59.093 34.615 12.25 0.00 0.00 2.45
192 193 6.128391 ACGAACTCGCAAAGCTTTATTAATGA 60.128 34.615 12.25 3.12 44.43 2.57
193 194 6.021596 ACGAACTCGCAAAGCTTTATTAATG 58.978 36.000 12.25 0.00 44.43 1.90
194 195 6.092259 AGACGAACTCGCAAAGCTTTATTAAT 59.908 34.615 12.25 0.00 44.43 1.40
195 196 5.407387 AGACGAACTCGCAAAGCTTTATTAA 59.593 36.000 12.25 0.00 44.43 1.40
196 197 4.927425 AGACGAACTCGCAAAGCTTTATTA 59.073 37.500 12.25 0.00 44.43 0.98
197 198 3.746492 AGACGAACTCGCAAAGCTTTATT 59.254 39.130 12.25 1.68 44.43 1.40
198 199 3.326747 AGACGAACTCGCAAAGCTTTAT 58.673 40.909 12.25 0.00 44.43 1.40
199 200 2.750948 AGACGAACTCGCAAAGCTTTA 58.249 42.857 12.25 0.00 44.43 1.85
200 201 1.583054 AGACGAACTCGCAAAGCTTT 58.417 45.000 5.69 5.69 44.43 3.51
201 202 2.433868 TAGACGAACTCGCAAAGCTT 57.566 45.000 0.00 0.00 44.43 3.74
202 203 2.433868 TTAGACGAACTCGCAAAGCT 57.566 45.000 0.00 0.00 44.43 3.74
203 204 3.515071 TTTTAGACGAACTCGCAAAGC 57.485 42.857 0.00 0.00 44.43 3.51
223 224 3.702548 GGTGGGACTTGTAACCTGTTTTT 59.297 43.478 0.00 0.00 0.00 1.94
224 225 3.053170 AGGTGGGACTTGTAACCTGTTTT 60.053 43.478 0.00 0.00 41.52 2.43
225 226 2.512476 AGGTGGGACTTGTAACCTGTTT 59.488 45.455 0.00 0.00 41.52 2.83
311 312 5.044919 TCACCCTCCATTAGTTGATTCACAT 60.045 40.000 0.00 0.00 0.00 3.21
314 315 4.536090 ACTCACCCTCCATTAGTTGATTCA 59.464 41.667 0.00 0.00 0.00 2.57
432 446 3.056891 GCTGACCGGGATTTTTCATTTCA 60.057 43.478 6.32 0.00 0.00 2.69
452 466 7.400052 AGTCCACAATTCCCTTTTATTTATGCT 59.600 33.333 0.00 0.00 0.00 3.79
461 475 1.613437 CGCAGTCCACAATTCCCTTTT 59.387 47.619 0.00 0.00 0.00 2.27
542 556 1.871039 CTATAATCCCGTTGCCAACCG 59.129 52.381 1.21 0.00 0.00 4.44
548 562 3.581755 TCGCATACTATAATCCCGTTGC 58.418 45.455 0.00 0.00 0.00 4.17
549 563 5.388061 CGTTTCGCATACTATAATCCCGTTG 60.388 44.000 0.00 0.00 0.00 4.10
559 573 4.095334 GGGGTTTTTCGTTTCGCATACTAT 59.905 41.667 0.00 0.00 0.00 2.12
613 628 9.670180 GAAGACATTTGTTTACTTTTTGTTTCG 57.330 29.630 0.00 0.00 0.00 3.46
643 659 4.996788 AGCCTCTTTTCAATTATGCCAG 57.003 40.909 0.00 0.00 0.00 4.85
652 668 1.529438 CGCAACGTAGCCTCTTTTCAA 59.471 47.619 0.00 0.00 0.00 2.69
654 670 0.442699 CCGCAACGTAGCCTCTTTTC 59.557 55.000 0.00 0.00 0.00 2.29
666 683 5.738118 TCCCTTTTATTTATACCGCAACG 57.262 39.130 0.00 0.00 0.00 4.10
719 739 4.502105 TGTTTATGCCAGCCAAGAGATA 57.498 40.909 0.00 0.00 0.00 1.98
729 749 6.393720 GCATAACACTTTTGTTTATGCCAG 57.606 37.500 12.49 0.00 43.89 4.85
745 765 1.621317 TCTTCACTCCACGGCATAACA 59.379 47.619 0.00 0.00 0.00 2.41
749 769 2.270352 TTTTCTTCACTCCACGGCAT 57.730 45.000 0.00 0.00 0.00 4.40
753 773 7.857569 TGTTTACTTATTTTCTTCACTCCACG 58.142 34.615 0.00 0.00 0.00 4.94
795 815 9.762933 AAAATAATATTGGCGTAAAATGCTGAT 57.237 25.926 0.00 0.00 0.00 2.90
846 866 7.073265 CCAGTGTTGCAAAAATGATGAAATTC 58.927 34.615 18.40 0.00 0.00 2.17
854 874 2.741228 GCACCCAGTGTTGCAAAAATGA 60.741 45.455 18.40 0.00 35.75 2.57
943 1018 4.524305 CGCTCTCGGATAAGCTCG 57.476 61.111 9.85 0.00 36.35 5.03
1112 1187 3.292159 GGTTTGGTGTCCGTGGGC 61.292 66.667 0.00 0.00 0.00 5.36
1121 1196 4.347453 GCGCCTGCAGGTTTGGTG 62.347 66.667 32.81 15.95 42.15 4.17
1535 1610 2.909965 GCGCAAACCCAAGGACCA 60.910 61.111 0.30 0.00 0.00 4.02
1550 1625 1.738099 CAGAACCCCGTCTTGAGCG 60.738 63.158 0.00 0.00 0.00 5.03
1596 1671 6.498304 GTTCCTCGCAAACATATCAATCAAT 58.502 36.000 0.00 0.00 0.00 2.57
1611 1686 2.915659 AGGTGTCCGTTCCTCGCA 60.916 61.111 0.00 0.00 38.35 5.10
1614 1689 1.004918 CACCAGGTGTCCGTTCCTC 60.005 63.158 11.99 0.00 30.91 3.71
1824 1899 1.304381 TTGCTGCCCCAATCTGACC 60.304 57.895 0.00 0.00 0.00 4.02
1870 1945 4.515191 GCTCACACAAGTATCAGAAACCAA 59.485 41.667 0.00 0.00 0.00 3.67
1895 1970 2.479730 GCGTACATGTCCACTAGTCCAG 60.480 54.545 0.00 0.00 0.00 3.86
1902 1977 3.611530 GCAATTTTGCGTACATGTCCACT 60.612 43.478 0.00 0.00 45.11 4.00
1986 2061 5.305128 TGATATCAGTGCTGTCCATGACATA 59.695 40.000 0.00 0.00 41.94 2.29
2249 2324 0.249398 GAACGCCTTTCTAGCCTCCA 59.751 55.000 0.00 0.00 0.00 3.86
2573 2648 7.383102 ACTGAAGTCCATGAAATCACATTAC 57.617 36.000 0.00 0.00 0.00 1.89
2775 2850 1.216930 TCCATCCTCGGTATGAGTCCA 59.783 52.381 0.00 0.00 43.64 4.02
2782 2857 4.287067 AGCATAATGTTCCATCCTCGGTAT 59.713 41.667 0.00 0.00 0.00 2.73
2907 2982 0.037232 AAGTCCTACAAGCACCGAGC 60.037 55.000 0.00 0.00 46.19 5.03
2933 3008 7.260603 AGCTGCAATTTTACCAATCTCAATAC 58.739 34.615 1.02 0.00 0.00 1.89
2958 3033 5.163713 CGGCTCGAGATCTATGACATGATTA 60.164 44.000 18.75 0.00 0.00 1.75
3000 3075 4.092091 GCATACAAGTTTGAGAGAAGGACG 59.908 45.833 0.00 0.00 0.00 4.79
3194 3269 8.456471 CAATGTCTTTAATTTCTCTGATCAGCA 58.544 33.333 18.36 3.93 0.00 4.41
3247 3322 2.742856 GCTCATCCGACATGTCATGGAA 60.743 50.000 24.93 9.68 33.48 3.53
3417 3519 5.602978 TCTCAATATTACCTCCCTTCCAGTC 59.397 44.000 0.00 0.00 0.00 3.51
3515 3617 3.733443 AAACCAAACCTGCTCATCAAC 57.267 42.857 0.00 0.00 0.00 3.18
3853 3960 4.996793 TGGATCATTTTGTTCCTTCCTGA 58.003 39.130 0.00 0.00 37.20 3.86
4005 4118 6.060136 TGCTTCCAGATCTAGGATGATTTTG 58.940 40.000 21.10 0.00 34.56 2.44
4022 4136 1.974265 TCAAACGGTTGATGCTTCCA 58.026 45.000 12.93 0.00 38.88 3.53
4050 4164 8.846943 TTTGTATTATGTTGTCAGATGTGAGT 57.153 30.769 0.00 0.00 31.53 3.41
4051 4165 9.764870 CTTTTGTATTATGTTGTCAGATGTGAG 57.235 33.333 0.00 0.00 31.53 3.51
4193 4431 4.092675 GCTATTTTGACTCTCTCACTGCAC 59.907 45.833 0.00 0.00 0.00 4.57
4276 4517 2.787473 ACTGCGAAGGATGGAATGAA 57.213 45.000 0.00 0.00 0.00 2.57
4344 4585 6.295123 GGATAAGATACAGCAGGGACGAATTA 60.295 42.308 0.00 0.00 0.00 1.40
4430 4675 7.800847 GTGACTTCACTCTGCTTTATTTTCTTC 59.199 37.037 1.92 0.00 43.25 2.87
4435 4680 6.712095 TGATGTGACTTCACTCTGCTTTATTT 59.288 34.615 10.63 0.00 46.55 1.40
4446 4691 4.780021 AGGTAAGGATGATGTGACTTCACT 59.220 41.667 10.63 0.00 46.55 3.41
4458 4703 7.288560 AGTATCTTCTTCGTAGGTAAGGATGA 58.711 38.462 0.00 0.00 0.00 2.92
4469 4714 6.207025 GGCATCCTTCTAGTATCTTCTTCGTA 59.793 42.308 0.00 0.00 0.00 3.43


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

AutoCloner maintained by Alex Coulton.