Multiple sequence alignment - TraesCS6A01G117500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G117500 chr6A 100.000 2285 0 0 1 2285 87924201 87926485 0.000000e+00 4220.0
1 TraesCS6A01G117500 chr6B 92.225 2058 108 28 256 2285 145892953 145894986 0.000000e+00 2867.0
2 TraesCS6A01G117500 chr6B 89.335 722 62 9 785 1495 145882861 145883578 0.000000e+00 893.0
3 TraesCS6A01G117500 chr6B 88.967 426 35 5 1865 2285 145886375 145886793 1.210000e-142 516.0
4 TraesCS6A01G117500 chr6B 82.833 233 17 13 1637 1854 145886113 145886337 1.080000e-43 187.0
5 TraesCS6A01G117500 chr6D 90.481 2059 104 28 256 2285 71137385 71139380 0.000000e+00 2632.0
6 TraesCS6A01G117500 chr6D 86.264 961 87 24 665 1605 71120061 71120996 0.000000e+00 1002.0
7 TraesCS6A01G117500 chr6D 89.930 427 32 3 1865 2285 71122878 71123299 7.180000e-150 540.0
8 TraesCS6A01G117500 chr6D 86.164 159 14 3 1637 1794 71122613 71122764 5.050000e-37 165.0
9 TraesCS6A01G117500 chr6D 76.786 168 35 4 128 294 289222524 289222688 8.690000e-15 91.6
10 TraesCS6A01G117500 chr3D 84.262 718 84 21 787 1497 360328993 360329688 0.000000e+00 673.0
11 TraesCS6A01G117500 chr3D 89.655 319 25 4 1968 2285 360330044 360330355 1.270000e-107 399.0
12 TraesCS6A01G117500 chr3D 85.209 311 33 7 1977 2285 360554121 360554420 7.930000e-80 307.0
13 TraesCS6A01G117500 chr3A 84.110 730 74 24 787 1504 479766806 479767505 0.000000e+00 667.0
14 TraesCS6A01G117500 chr3A 89.028 319 28 3 1968 2285 479768001 479768313 2.750000e-104 388.0
15 TraesCS6A01G117500 chr3B 83.239 710 79 22 793 1491 466256543 466257223 1.160000e-172 616.0
16 TraesCS6A01G117500 chr3B 89.899 297 24 2 1990 2285 466260095 466260386 5.960000e-101 377.0
17 TraesCS6A01G117500 chr3B 84.566 311 33 9 1977 2285 466606858 466607155 6.170000e-76 294.0
18 TraesCS6A01G117500 chr4A 83.696 92 15 0 148 239 515853199 515853290 1.120000e-13 87.9
19 TraesCS6A01G117500 chr4D 75.862 145 33 2 148 291 67162729 67162872 3.150000e-09 73.1


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 TraesCS6A01G117500 chr6A 87924201 87926485 2284 False 4220.0 4220 100.000000 1 2285 1 chr6A.!!$F1 2284
1 TraesCS6A01G117500 chr6B 145892953 145894986 2033 False 2867.0 2867 92.225000 256 2285 1 chr6B.!!$F1 2029
2 TraesCS6A01G117500 chr6B 145882861 145886793 3932 False 532.0 893 87.045000 785 2285 3 chr6B.!!$F2 1500
3 TraesCS6A01G117500 chr6D 71137385 71139380 1995 False 2632.0 2632 90.481000 256 2285 1 chr6D.!!$F1 2029
4 TraesCS6A01G117500 chr6D 71120061 71123299 3238 False 569.0 1002 87.452667 665 2285 3 chr6D.!!$F3 1620
5 TraesCS6A01G117500 chr3D 360328993 360330355 1362 False 536.0 673 86.958500 787 2285 2 chr3D.!!$F2 1498
6 TraesCS6A01G117500 chr3A 479766806 479768313 1507 False 527.5 667 86.569000 787 2285 2 chr3A.!!$F1 1498
7 TraesCS6A01G117500 chr3B 466256543 466260386 3843 False 496.5 616 86.569000 793 2285 2 chr3B.!!$F2 1492

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
158 159 0.102844 GCAAGCACAGCAAAACCTGA 59.897 50.0 0.0 0.0 36.67 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 5447 0.178967 TTGCATTCCTCACCCAAGCA 60.179 50.0 0.0 0.0 0.0 3.91 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.008021 ACACATATACTATCCATGCATGACA 57.992 36.000 28.31 14.17 0.00 3.58
25 26 7.452562 ACACATATACTATCCATGCATGACAA 58.547 34.615 28.31 13.04 0.00 3.18
26 27 7.388776 ACACATATACTATCCATGCATGACAAC 59.611 37.037 28.31 0.00 0.00 3.32
27 28 7.388500 CACATATACTATCCATGCATGACAACA 59.612 37.037 28.31 8.61 0.00 3.33
28 29 7.388776 ACATATACTATCCATGCATGACAACAC 59.611 37.037 28.31 0.00 0.00 3.32
29 30 3.954200 ACTATCCATGCATGACAACACA 58.046 40.909 28.31 4.81 0.00 3.72
30 31 4.334552 ACTATCCATGCATGACAACACAA 58.665 39.130 28.31 3.25 0.00 3.33
31 32 4.766373 ACTATCCATGCATGACAACACAAA 59.234 37.500 28.31 2.24 0.00 2.83
32 33 4.603989 ATCCATGCATGACAACACAAAA 57.396 36.364 28.31 0.75 0.00 2.44
33 34 4.397481 TCCATGCATGACAACACAAAAA 57.603 36.364 28.31 0.00 0.00 1.94
76 77 5.726980 AAATGATGTTAGCCTTTTGAGCA 57.273 34.783 0.00 0.00 0.00 4.26
77 78 5.927281 AATGATGTTAGCCTTTTGAGCAT 57.073 34.783 0.00 0.00 0.00 3.79
78 79 4.707030 TGATGTTAGCCTTTTGAGCATG 57.293 40.909 0.00 0.00 0.00 4.06
79 80 4.334552 TGATGTTAGCCTTTTGAGCATGA 58.665 39.130 0.00 0.00 0.00 3.07
80 81 4.397103 TGATGTTAGCCTTTTGAGCATGAG 59.603 41.667 0.00 0.00 0.00 2.90
81 82 2.489329 TGTTAGCCTTTTGAGCATGAGC 59.511 45.455 0.00 0.00 42.56 4.26
82 83 2.489329 GTTAGCCTTTTGAGCATGAGCA 59.511 45.455 0.00 0.00 45.49 4.26
83 84 1.848652 AGCCTTTTGAGCATGAGCAT 58.151 45.000 0.00 0.00 45.49 3.79
84 85 1.476891 AGCCTTTTGAGCATGAGCATG 59.523 47.619 6.11 6.11 45.49 4.06
85 86 1.470979 GCCTTTTGAGCATGAGCATGG 60.471 52.381 12.00 0.00 45.49 3.66
86 87 1.470979 CCTTTTGAGCATGAGCATGGC 60.471 52.381 12.00 5.02 45.49 4.40
87 88 1.203758 CTTTTGAGCATGAGCATGGCA 59.796 47.619 12.00 0.00 45.49 4.92
88 89 1.258676 TTTGAGCATGAGCATGGCAA 58.741 45.000 12.00 0.00 45.49 4.52
89 90 1.258676 TTGAGCATGAGCATGGCAAA 58.741 45.000 12.00 2.29 45.49 3.68
90 91 0.815095 TGAGCATGAGCATGGCAAAG 59.185 50.000 12.00 0.00 45.49 2.77
91 92 0.527817 GAGCATGAGCATGGCAAAGC 60.528 55.000 12.00 7.15 45.49 3.51
92 93 1.216977 GCATGAGCATGGCAAAGCA 59.783 52.632 16.10 2.11 41.58 3.91
93 94 0.390603 GCATGAGCATGGCAAAGCAA 60.391 50.000 16.10 5.79 41.58 3.91
94 95 1.942127 GCATGAGCATGGCAAAGCAAA 60.942 47.619 16.10 5.48 41.58 3.68
95 96 2.627945 CATGAGCATGGCAAAGCAAAT 58.372 42.857 16.10 7.29 35.24 2.32
96 97 2.087501 TGAGCATGGCAAAGCAAATG 57.912 45.000 16.10 0.00 0.00 2.32
97 98 1.345089 TGAGCATGGCAAAGCAAATGT 59.655 42.857 16.10 0.00 0.00 2.71
98 99 2.224329 TGAGCATGGCAAAGCAAATGTT 60.224 40.909 16.10 0.00 0.00 2.71
99 100 2.809696 GAGCATGGCAAAGCAAATGTTT 59.190 40.909 16.10 0.00 0.00 2.83
100 101 3.215975 AGCATGGCAAAGCAAATGTTTT 58.784 36.364 16.10 0.00 0.00 2.43
101 102 3.251487 AGCATGGCAAAGCAAATGTTTTC 59.749 39.130 16.10 0.00 0.00 2.29
102 103 3.003482 GCATGGCAAAGCAAATGTTTTCA 59.997 39.130 10.00 0.00 0.00 2.69
103 104 4.320641 GCATGGCAAAGCAAATGTTTTCAT 60.321 37.500 10.00 0.00 43.05 2.57
104 105 5.106634 GCATGGCAAAGCAAATGTTTTCATA 60.107 36.000 10.00 0.00 39.94 2.15
105 106 6.539324 CATGGCAAAGCAAATGTTTTCATAG 58.461 36.000 0.00 0.00 39.94 2.23
106 107 4.996122 TGGCAAAGCAAATGTTTTCATAGG 59.004 37.500 0.00 0.00 39.94 2.57
107 108 4.392754 GGCAAAGCAAATGTTTTCATAGGG 59.607 41.667 0.00 0.00 39.94 3.53
108 109 4.142838 GCAAAGCAAATGTTTTCATAGGGC 60.143 41.667 0.00 0.00 39.94 5.19
109 110 4.888326 AAGCAAATGTTTTCATAGGGCA 57.112 36.364 0.00 0.00 39.94 5.36
110 111 4.460948 AGCAAATGTTTTCATAGGGCAG 57.539 40.909 0.00 0.00 39.94 4.85
111 112 3.834231 AGCAAATGTTTTCATAGGGCAGT 59.166 39.130 0.00 0.00 39.94 4.40
112 113 4.284234 AGCAAATGTTTTCATAGGGCAGTT 59.716 37.500 0.00 0.00 39.94 3.16
113 114 4.996758 GCAAATGTTTTCATAGGGCAGTTT 59.003 37.500 0.00 0.00 39.94 2.66
114 115 6.014669 AGCAAATGTTTTCATAGGGCAGTTTA 60.015 34.615 0.00 0.00 39.94 2.01
115 116 6.818142 GCAAATGTTTTCATAGGGCAGTTTAT 59.182 34.615 0.00 0.00 39.94 1.40
116 117 7.978975 GCAAATGTTTTCATAGGGCAGTTTATA 59.021 33.333 0.00 0.00 39.94 0.98
119 120 7.490962 TGTTTTCATAGGGCAGTTTATATCG 57.509 36.000 0.00 0.00 0.00 2.92
120 121 7.276658 TGTTTTCATAGGGCAGTTTATATCGA 58.723 34.615 0.00 0.00 0.00 3.59
121 122 7.441157 TGTTTTCATAGGGCAGTTTATATCGAG 59.559 37.037 0.00 0.00 0.00 4.04
122 123 5.661056 TCATAGGGCAGTTTATATCGAGG 57.339 43.478 0.00 0.00 0.00 4.63
123 124 4.466370 TCATAGGGCAGTTTATATCGAGGG 59.534 45.833 0.00 0.00 0.00 4.30
124 125 2.690840 AGGGCAGTTTATATCGAGGGT 58.309 47.619 0.00 0.00 0.00 4.34
125 126 2.368875 AGGGCAGTTTATATCGAGGGTG 59.631 50.000 0.00 0.00 0.00 4.61
126 127 2.367567 GGGCAGTTTATATCGAGGGTGA 59.632 50.000 0.00 0.00 0.00 4.02
127 128 3.391049 GGCAGTTTATATCGAGGGTGAC 58.609 50.000 0.00 0.00 0.00 3.67
128 129 3.181469 GGCAGTTTATATCGAGGGTGACA 60.181 47.826 0.00 0.00 0.00 3.58
129 130 4.439057 GCAGTTTATATCGAGGGTGACAA 58.561 43.478 0.00 0.00 0.00 3.18
130 131 5.057149 GCAGTTTATATCGAGGGTGACAAT 58.943 41.667 0.00 0.00 0.00 2.71
131 132 5.527582 GCAGTTTATATCGAGGGTGACAATT 59.472 40.000 0.00 0.00 0.00 2.32
132 133 6.038271 GCAGTTTATATCGAGGGTGACAATTT 59.962 38.462 0.00 0.00 0.00 1.82
133 134 7.630924 CAGTTTATATCGAGGGTGACAATTTC 58.369 38.462 0.00 0.00 0.00 2.17
134 135 7.279981 CAGTTTATATCGAGGGTGACAATTTCA 59.720 37.037 0.00 0.00 0.00 2.69
135 136 7.495934 AGTTTATATCGAGGGTGACAATTTCAG 59.504 37.037 0.00 0.00 33.71 3.02
136 137 3.703001 ATCGAGGGTGACAATTTCAGT 57.297 42.857 0.00 0.00 33.71 3.41
137 138 3.485463 TCGAGGGTGACAATTTCAGTT 57.515 42.857 0.00 0.00 33.71 3.16
138 139 4.610605 TCGAGGGTGACAATTTCAGTTA 57.389 40.909 0.00 0.00 33.71 2.24
139 140 4.566004 TCGAGGGTGACAATTTCAGTTAG 58.434 43.478 0.00 0.00 33.71 2.34
140 141 3.125316 CGAGGGTGACAATTTCAGTTAGC 59.875 47.826 0.00 0.00 33.71 3.09
141 142 4.072131 GAGGGTGACAATTTCAGTTAGCA 58.928 43.478 0.00 0.00 33.71 3.49
142 143 4.469657 AGGGTGACAATTTCAGTTAGCAA 58.530 39.130 0.00 0.00 33.71 3.91
143 144 4.520492 AGGGTGACAATTTCAGTTAGCAAG 59.480 41.667 0.00 0.00 33.71 4.01
144 145 4.229876 GGTGACAATTTCAGTTAGCAAGC 58.770 43.478 0.00 0.00 33.71 4.01
145 146 4.261572 GGTGACAATTTCAGTTAGCAAGCA 60.262 41.667 0.00 0.00 33.71 3.91
146 147 4.676924 GTGACAATTTCAGTTAGCAAGCAC 59.323 41.667 0.00 0.00 33.71 4.40
147 148 4.337836 TGACAATTTCAGTTAGCAAGCACA 59.662 37.500 0.00 0.00 0.00 4.57
148 149 4.863491 ACAATTTCAGTTAGCAAGCACAG 58.137 39.130 0.00 0.00 0.00 3.66
149 150 3.565905 ATTTCAGTTAGCAAGCACAGC 57.434 42.857 0.00 0.00 0.00 4.40
150 151 1.965935 TTCAGTTAGCAAGCACAGCA 58.034 45.000 0.00 0.00 0.00 4.41
151 152 1.965935 TCAGTTAGCAAGCACAGCAA 58.034 45.000 0.00 0.00 0.00 3.91
152 153 2.296792 TCAGTTAGCAAGCACAGCAAA 58.703 42.857 0.00 0.00 0.00 3.68
153 154 2.687425 TCAGTTAGCAAGCACAGCAAAA 59.313 40.909 0.00 0.00 0.00 2.44
154 155 2.791004 CAGTTAGCAAGCACAGCAAAAC 59.209 45.455 0.00 0.00 33.18 2.43
155 156 2.127251 GTTAGCAAGCACAGCAAAACC 58.873 47.619 0.00 0.00 0.00 3.27
156 157 1.691196 TAGCAAGCACAGCAAAACCT 58.309 45.000 0.00 0.00 0.00 3.50
157 158 0.103572 AGCAAGCACAGCAAAACCTG 59.896 50.000 0.00 0.00 38.78 4.00
158 159 0.102844 GCAAGCACAGCAAAACCTGA 59.897 50.000 0.00 0.00 36.67 3.86
159 160 1.843992 CAAGCACAGCAAAACCTGAC 58.156 50.000 0.00 0.00 36.67 3.51
160 161 1.134753 CAAGCACAGCAAAACCTGACA 59.865 47.619 0.00 0.00 36.67 3.58
161 162 1.473258 AGCACAGCAAAACCTGACAA 58.527 45.000 0.00 0.00 36.67 3.18
162 163 1.824230 AGCACAGCAAAACCTGACAAA 59.176 42.857 0.00 0.00 36.67 2.83
163 164 2.233431 AGCACAGCAAAACCTGACAAAA 59.767 40.909 0.00 0.00 36.67 2.44
164 165 2.999355 GCACAGCAAAACCTGACAAAAA 59.001 40.909 0.00 0.00 36.67 1.94
182 183 4.335400 AAAAACTGAACATGGCGGATTT 57.665 36.364 0.00 0.00 0.00 2.17
183 184 4.335400 AAAACTGAACATGGCGGATTTT 57.665 36.364 0.00 0.00 0.00 1.82
184 185 3.575965 AACTGAACATGGCGGATTTTC 57.424 42.857 0.00 0.00 0.00 2.29
185 186 1.818674 ACTGAACATGGCGGATTTTCC 59.181 47.619 0.00 0.00 0.00 3.13
186 187 1.818060 CTGAACATGGCGGATTTTCCA 59.182 47.619 0.00 0.00 35.91 3.53
187 188 1.543802 TGAACATGGCGGATTTTCCAC 59.456 47.619 0.00 0.00 35.91 4.02
188 189 1.818674 GAACATGGCGGATTTTCCACT 59.181 47.619 0.00 0.00 35.91 4.00
189 190 1.463674 ACATGGCGGATTTTCCACTC 58.536 50.000 0.00 0.00 35.91 3.51
190 191 1.004745 ACATGGCGGATTTTCCACTCT 59.995 47.619 0.00 0.00 35.91 3.24
191 192 2.094675 CATGGCGGATTTTCCACTCTT 58.905 47.619 0.00 0.00 35.91 2.85
192 193 1.533625 TGGCGGATTTTCCACTCTTG 58.466 50.000 0.00 0.00 35.91 3.02
193 194 0.171231 GGCGGATTTTCCACTCTTGC 59.829 55.000 0.00 0.00 35.91 4.01
194 195 1.168714 GCGGATTTTCCACTCTTGCT 58.831 50.000 0.00 0.00 35.91 3.91
195 196 2.356135 GCGGATTTTCCACTCTTGCTA 58.644 47.619 0.00 0.00 35.91 3.49
196 197 2.747446 GCGGATTTTCCACTCTTGCTAA 59.253 45.455 0.00 0.00 35.91 3.09
197 198 3.190535 GCGGATTTTCCACTCTTGCTAAA 59.809 43.478 0.00 0.00 35.91 1.85
198 199 4.320935 GCGGATTTTCCACTCTTGCTAAAA 60.321 41.667 0.00 0.00 35.91 1.52
199 200 5.393962 CGGATTTTCCACTCTTGCTAAAAG 58.606 41.667 0.00 0.00 35.91 2.27
200 201 5.181245 CGGATTTTCCACTCTTGCTAAAAGA 59.819 40.000 0.00 0.00 35.91 2.52
201 202 6.293955 CGGATTTTCCACTCTTGCTAAAAGAA 60.294 38.462 0.00 0.00 35.91 2.52
202 203 7.433680 GGATTTTCCACTCTTGCTAAAAGAAA 58.566 34.615 0.00 0.00 36.28 2.52
203 204 8.090831 GGATTTTCCACTCTTGCTAAAAGAAAT 58.909 33.333 0.00 0.00 36.28 2.17
204 205 9.481340 GATTTTCCACTCTTGCTAAAAGAAATT 57.519 29.630 0.00 0.00 0.00 1.82
205 206 8.647143 TTTTCCACTCTTGCTAAAAGAAATTG 57.353 30.769 0.00 0.00 0.00 2.32
206 207 5.772521 TCCACTCTTGCTAAAAGAAATTGC 58.227 37.500 0.00 0.00 0.00 3.56
207 208 5.536161 TCCACTCTTGCTAAAAGAAATTGCT 59.464 36.000 0.00 0.00 0.00 3.91
208 209 6.714810 TCCACTCTTGCTAAAAGAAATTGCTA 59.285 34.615 0.00 0.00 0.00 3.49
209 210 7.394359 TCCACTCTTGCTAAAAGAAATTGCTAT 59.606 33.333 0.00 0.00 0.00 2.97
210 211 7.699812 CCACTCTTGCTAAAAGAAATTGCTATC 59.300 37.037 0.00 0.00 0.00 2.08
211 212 7.699812 CACTCTTGCTAAAAGAAATTGCTATCC 59.300 37.037 0.00 0.00 0.00 2.59
212 213 7.613411 ACTCTTGCTAAAAGAAATTGCTATCCT 59.387 33.333 0.00 0.00 0.00 3.24
213 214 7.989826 TCTTGCTAAAAGAAATTGCTATCCTC 58.010 34.615 0.00 0.00 0.00 3.71
214 215 7.611467 TCTTGCTAAAAGAAATTGCTATCCTCA 59.389 33.333 0.00 0.00 0.00 3.86
215 216 7.701539 TGCTAAAAGAAATTGCTATCCTCAA 57.298 32.000 0.00 0.00 0.00 3.02
216 217 7.765307 TGCTAAAAGAAATTGCTATCCTCAAG 58.235 34.615 0.00 0.00 0.00 3.02
217 218 7.611467 TGCTAAAAGAAATTGCTATCCTCAAGA 59.389 33.333 0.00 0.00 0.00 3.02
218 219 8.628280 GCTAAAAGAAATTGCTATCCTCAAGAT 58.372 33.333 0.00 0.00 39.15 2.40
222 223 9.466497 AAAGAAATTGCTATCCTCAAGATAACA 57.534 29.630 0.00 0.00 37.01 2.41
223 224 9.638176 AAGAAATTGCTATCCTCAAGATAACAT 57.362 29.630 0.00 0.00 37.01 2.71
230 231 8.786898 TGCTATCCTCAAGATAACATAATTTGC 58.213 33.333 0.00 0.00 37.01 3.68
231 232 8.239998 GCTATCCTCAAGATAACATAATTTGCC 58.760 37.037 0.00 0.00 37.01 4.52
232 233 9.288576 CTATCCTCAAGATAACATAATTTGCCA 57.711 33.333 0.00 0.00 37.01 4.92
233 234 8.716674 ATCCTCAAGATAACATAATTTGCCAT 57.283 30.769 0.00 0.00 31.60 4.40
234 235 9.812347 ATCCTCAAGATAACATAATTTGCCATA 57.188 29.630 0.00 0.00 31.60 2.74
235 236 9.639563 TCCTCAAGATAACATAATTTGCCATAA 57.360 29.630 0.00 0.00 0.00 1.90
481 493 6.875948 TTCCATGTTTATATCCACATTCCG 57.124 37.500 0.00 0.00 30.90 4.30
502 514 0.670162 GGCCGTACCAGCTTACGATA 59.330 55.000 17.45 0.00 46.37 2.92
507 519 3.562505 CGTACCAGCTTACGATATGTCC 58.437 50.000 11.69 0.00 46.37 4.02
582 595 3.936203 TGGCGGTGACCACTGACC 61.936 66.667 11.94 12.23 45.19 4.02
583 596 3.936203 GGCGGTGACCACTGACCA 61.936 66.667 12.77 0.00 39.85 4.02
584 597 2.665185 GCGGTGACCACTGACCAC 60.665 66.667 12.77 0.00 40.06 4.16
585 598 2.030562 CGGTGACCACTGACCACC 59.969 66.667 1.11 0.00 45.07 4.61
586 599 2.030562 GGTGACCACTGACCACCG 59.969 66.667 0.00 0.00 40.61 4.94
587 600 2.665185 GTGACCACTGACCACCGC 60.665 66.667 0.00 0.00 0.00 5.68
588 601 3.157949 TGACCACTGACCACCGCA 61.158 61.111 0.00 0.00 0.00 5.69
589 602 2.665185 GACCACTGACCACCGCAC 60.665 66.667 0.00 0.00 0.00 5.34
590 603 4.250305 ACCACTGACCACCGCACC 62.250 66.667 0.00 0.00 0.00 5.01
606 619 1.115467 CACCGGAGACCATCTTAGCT 58.885 55.000 9.46 0.00 0.00 3.32
612 625 2.364002 GGAGACCATCTTAGCTCACCTC 59.636 54.545 0.00 0.00 0.00 3.85
613 626 3.027412 GAGACCATCTTAGCTCACCTCA 58.973 50.000 0.00 0.00 0.00 3.86
614 627 3.030291 AGACCATCTTAGCTCACCTCAG 58.970 50.000 0.00 0.00 0.00 3.35
615 628 2.102252 GACCATCTTAGCTCACCTCAGG 59.898 54.545 0.00 0.00 0.00 3.86
631 655 4.223032 ACCTCAGGTTACAATACTGGTCAG 59.777 45.833 0.00 0.00 27.29 3.51
656 680 4.625742 CCATTTGACCAACTAGTGACTACG 59.374 45.833 0.00 0.00 0.00 3.51
657 681 3.293311 TTGACCAACTAGTGACTACGC 57.707 47.619 0.00 0.00 0.00 4.42
658 682 2.511659 TGACCAACTAGTGACTACGCT 58.488 47.619 0.00 0.00 40.21 5.07
659 683 2.228103 TGACCAACTAGTGACTACGCTG 59.772 50.000 0.00 0.00 37.97 5.18
660 684 2.486982 GACCAACTAGTGACTACGCTGA 59.513 50.000 0.00 0.00 37.97 4.26
661 685 2.488545 ACCAACTAGTGACTACGCTGAG 59.511 50.000 0.00 0.00 37.97 3.35
662 686 2.488545 CCAACTAGTGACTACGCTGAGT 59.511 50.000 0.00 0.00 37.97 3.41
663 687 3.426426 CCAACTAGTGACTACGCTGAGTC 60.426 52.174 0.00 7.70 45.19 3.36
668 692 1.226435 GACTACGCTGAGTCGCTGG 60.226 63.158 0.00 0.00 36.76 4.85
705 729 3.863142 AGGCTGTGAATCTTGAATTGC 57.137 42.857 0.00 0.00 0.00 3.56
739 763 3.627577 ACCACATGCCAACGATAAATCTC 59.372 43.478 0.00 0.00 0.00 2.75
753 777 3.559238 AAATCTCGTGCAAATCCACAC 57.441 42.857 0.00 0.00 35.47 3.82
755 779 1.960417 TCTCGTGCAAATCCACACAA 58.040 45.000 0.00 0.00 36.57 3.33
781 805 3.080300 AGTTGATAAATCCGTGGGCAA 57.920 42.857 0.00 0.00 0.00 4.52
860 884 3.011566 TCAGCCCAAGAACAGTCAAAA 57.988 42.857 0.00 0.00 0.00 2.44
866 890 2.100749 CCAAGAACAGTCAAAACACCCC 59.899 50.000 0.00 0.00 0.00 4.95
884 908 3.706373 GTCTTGGGCTCTGGGCGA 61.706 66.667 0.00 0.00 42.94 5.54
917 942 3.366476 GCGTATATACAGTGCTCCTCCAG 60.366 52.174 13.22 0.00 0.00 3.86
958 985 4.962836 GCACAGTGCAGGCTGGGT 62.963 66.667 21.22 0.00 44.26 4.51
1003 1033 1.065199 CCAGTAGCTGCCAGGAAATGA 60.065 52.381 5.12 0.00 0.00 2.57
1119 1149 1.288127 GTTCAGGTACGCCGACAGT 59.712 57.895 0.00 0.00 40.50 3.55
1292 1335 2.389059 CAGCTTACGGTGATCAGATCG 58.611 52.381 5.91 3.46 41.05 3.69
1324 1372 4.388378 AGATTGGCTAGACGAGTTAACC 57.612 45.455 0.88 0.00 0.00 2.85
1520 3120 7.187824 ACATTCAGTACATACCACTCTCAAT 57.812 36.000 0.00 0.00 0.00 2.57
1555 3155 6.479990 CCACAGAGGATTGTTTTTCTTTTTCC 59.520 38.462 0.00 0.00 41.22 3.13
1669 5039 0.678048 ATGGAAACCAGCTTCTCCGC 60.678 55.000 0.00 0.00 36.75 5.54
1869 5363 2.234908 CCTCCTTCTCGGTGTCATCTTT 59.765 50.000 0.00 0.00 0.00 2.52
1874 5368 5.932303 TCCTTCTCGGTGTCATCTTTTTAAG 59.068 40.000 0.00 0.00 0.00 1.85
1899 5393 5.163468 ACAAAATGATACACACTTTGGTGCA 60.163 36.000 0.00 0.00 45.92 4.57
2028 7825 6.327279 AGTACCAACTGCATTCCTAAAAAC 57.673 37.500 0.00 0.00 33.57 2.43
2079 7877 3.332485 TGGCAAAGAAGTTACCCCACTAT 59.668 43.478 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.008021 TGTCATGCATGGATAGTATATGTGT 57.992 36.000 25.97 0.00 0.00 3.72
1 2 7.388500 TGTTGTCATGCATGGATAGTATATGTG 59.612 37.037 25.97 0.00 0.00 3.21
2 3 7.388776 GTGTTGTCATGCATGGATAGTATATGT 59.611 37.037 25.97 0.00 0.00 2.29
3 4 7.388500 TGTGTTGTCATGCATGGATAGTATATG 59.612 37.037 25.97 0.00 0.00 1.78
4 5 7.452562 TGTGTTGTCATGCATGGATAGTATAT 58.547 34.615 25.97 0.00 0.00 0.86
5 6 6.825610 TGTGTTGTCATGCATGGATAGTATA 58.174 36.000 25.97 1.33 0.00 1.47
6 7 5.683681 TGTGTTGTCATGCATGGATAGTAT 58.316 37.500 25.97 0.00 0.00 2.12
7 8 5.096443 TGTGTTGTCATGCATGGATAGTA 57.904 39.130 25.97 2.92 0.00 1.82
8 9 3.954200 TGTGTTGTCATGCATGGATAGT 58.046 40.909 25.97 0.00 0.00 2.12
9 10 4.968812 TTGTGTTGTCATGCATGGATAG 57.031 40.909 25.97 0.21 0.00 2.08
10 11 5.718724 TTTTGTGTTGTCATGCATGGATA 57.281 34.783 25.97 10.25 0.00 2.59
11 12 4.603989 TTTTGTGTTGTCATGCATGGAT 57.396 36.364 25.97 0.00 0.00 3.41
12 13 4.397481 TTTTTGTGTTGTCATGCATGGA 57.603 36.364 25.97 10.82 0.00 3.41
52 53 6.523840 TGCTCAAAAGGCTAACATCATTTTT 58.476 32.000 0.00 0.00 0.00 1.94
53 54 6.100404 TGCTCAAAAGGCTAACATCATTTT 57.900 33.333 0.00 0.00 0.00 1.82
54 55 5.726980 TGCTCAAAAGGCTAACATCATTT 57.273 34.783 0.00 0.00 0.00 2.32
55 56 5.419788 TCATGCTCAAAAGGCTAACATCATT 59.580 36.000 0.00 0.00 0.00 2.57
56 57 4.951715 TCATGCTCAAAAGGCTAACATCAT 59.048 37.500 0.00 0.00 0.00 2.45
57 58 4.334552 TCATGCTCAAAAGGCTAACATCA 58.665 39.130 0.00 0.00 0.00 3.07
58 59 4.732938 GCTCATGCTCAAAAGGCTAACATC 60.733 45.833 0.00 0.00 36.03 3.06
59 60 3.129988 GCTCATGCTCAAAAGGCTAACAT 59.870 43.478 0.00 0.00 36.03 2.71
60 61 2.489329 GCTCATGCTCAAAAGGCTAACA 59.511 45.455 0.00 0.00 36.03 2.41
61 62 2.489329 TGCTCATGCTCAAAAGGCTAAC 59.511 45.455 0.00 0.00 40.48 2.34
62 63 2.794103 TGCTCATGCTCAAAAGGCTAA 58.206 42.857 0.00 0.00 40.48 3.09
63 64 2.495155 TGCTCATGCTCAAAAGGCTA 57.505 45.000 0.00 0.00 40.48 3.93
64 65 1.476891 CATGCTCATGCTCAAAAGGCT 59.523 47.619 0.00 0.00 40.48 4.58
65 66 1.470979 CCATGCTCATGCTCAAAAGGC 60.471 52.381 4.40 0.00 40.48 4.35
66 67 1.470979 GCCATGCTCATGCTCAAAAGG 60.471 52.381 4.40 0.00 40.48 3.11
67 68 1.203758 TGCCATGCTCATGCTCAAAAG 59.796 47.619 4.40 0.00 40.48 2.27
68 69 1.258676 TGCCATGCTCATGCTCAAAA 58.741 45.000 4.40 0.00 40.48 2.44
69 70 1.258676 TTGCCATGCTCATGCTCAAA 58.741 45.000 4.40 0.00 40.48 2.69
70 71 1.203758 CTTTGCCATGCTCATGCTCAA 59.796 47.619 4.40 7.69 40.48 3.02
71 72 0.815095 CTTTGCCATGCTCATGCTCA 59.185 50.000 4.40 2.45 40.48 4.26
72 73 0.527817 GCTTTGCCATGCTCATGCTC 60.528 55.000 4.40 0.07 40.48 4.26
73 74 1.254975 TGCTTTGCCATGCTCATGCT 61.255 50.000 4.40 0.00 40.48 3.79
74 75 0.390603 TTGCTTTGCCATGCTCATGC 60.391 50.000 4.40 1.77 37.49 4.06
75 76 2.087501 TTTGCTTTGCCATGCTCATG 57.912 45.000 2.97 2.97 38.51 3.07
76 77 2.027561 ACATTTGCTTTGCCATGCTCAT 60.028 40.909 0.00 0.00 0.00 2.90
77 78 1.345089 ACATTTGCTTTGCCATGCTCA 59.655 42.857 0.00 0.00 0.00 4.26
78 79 2.088950 ACATTTGCTTTGCCATGCTC 57.911 45.000 0.00 0.00 0.00 4.26
79 80 2.554370 AACATTTGCTTTGCCATGCT 57.446 40.000 0.00 0.00 0.00 3.79
80 81 3.003482 TGAAAACATTTGCTTTGCCATGC 59.997 39.130 0.00 0.00 0.00 4.06
81 82 4.815040 TGAAAACATTTGCTTTGCCATG 57.185 36.364 0.00 0.00 0.00 3.66
82 83 5.644636 CCTATGAAAACATTTGCTTTGCCAT 59.355 36.000 0.00 0.00 0.00 4.40
83 84 4.996122 CCTATGAAAACATTTGCTTTGCCA 59.004 37.500 0.00 0.00 0.00 4.92
84 85 4.392754 CCCTATGAAAACATTTGCTTTGCC 59.607 41.667 0.00 0.00 0.00 4.52
85 86 4.142838 GCCCTATGAAAACATTTGCTTTGC 60.143 41.667 0.00 0.00 0.00 3.68
86 87 4.996122 TGCCCTATGAAAACATTTGCTTTG 59.004 37.500 0.00 0.00 0.00 2.77
87 88 5.221702 ACTGCCCTATGAAAACATTTGCTTT 60.222 36.000 0.00 0.00 0.00 3.51
88 89 4.284234 ACTGCCCTATGAAAACATTTGCTT 59.716 37.500 0.00 0.00 0.00 3.91
89 90 3.834231 ACTGCCCTATGAAAACATTTGCT 59.166 39.130 0.00 0.00 0.00 3.91
90 91 4.192429 ACTGCCCTATGAAAACATTTGC 57.808 40.909 0.00 0.00 0.00 3.68
93 94 8.567948 CGATATAAACTGCCCTATGAAAACATT 58.432 33.333 0.00 0.00 0.00 2.71
94 95 7.936847 TCGATATAAACTGCCCTATGAAAACAT 59.063 33.333 0.00 0.00 0.00 2.71
95 96 7.276658 TCGATATAAACTGCCCTATGAAAACA 58.723 34.615 0.00 0.00 0.00 2.83
96 97 7.095187 CCTCGATATAAACTGCCCTATGAAAAC 60.095 40.741 0.00 0.00 0.00 2.43
97 98 6.934645 CCTCGATATAAACTGCCCTATGAAAA 59.065 38.462 0.00 0.00 0.00 2.29
98 99 6.464222 CCTCGATATAAACTGCCCTATGAAA 58.536 40.000 0.00 0.00 0.00 2.69
99 100 5.046591 CCCTCGATATAAACTGCCCTATGAA 60.047 44.000 0.00 0.00 0.00 2.57
100 101 4.466370 CCCTCGATATAAACTGCCCTATGA 59.534 45.833 0.00 0.00 0.00 2.15
101 102 4.223032 ACCCTCGATATAAACTGCCCTATG 59.777 45.833 0.00 0.00 0.00 2.23
102 103 4.223032 CACCCTCGATATAAACTGCCCTAT 59.777 45.833 0.00 0.00 0.00 2.57
103 104 3.576982 CACCCTCGATATAAACTGCCCTA 59.423 47.826 0.00 0.00 0.00 3.53
104 105 2.368875 CACCCTCGATATAAACTGCCCT 59.631 50.000 0.00 0.00 0.00 5.19
105 106 2.367567 TCACCCTCGATATAAACTGCCC 59.632 50.000 0.00 0.00 0.00 5.36
106 107 3.181469 TGTCACCCTCGATATAAACTGCC 60.181 47.826 0.00 0.00 0.00 4.85
107 108 4.054780 TGTCACCCTCGATATAAACTGC 57.945 45.455 0.00 0.00 0.00 4.40
108 109 7.279981 TGAAATTGTCACCCTCGATATAAACTG 59.720 37.037 0.00 0.00 0.00 3.16
109 110 7.335627 TGAAATTGTCACCCTCGATATAAACT 58.664 34.615 0.00 0.00 0.00 2.66
110 111 7.280205 ACTGAAATTGTCACCCTCGATATAAAC 59.720 37.037 0.00 0.00 31.13 2.01
111 112 7.335627 ACTGAAATTGTCACCCTCGATATAAA 58.664 34.615 0.00 0.00 31.13 1.40
112 113 6.884832 ACTGAAATTGTCACCCTCGATATAA 58.115 36.000 0.00 0.00 31.13 0.98
113 114 6.479972 ACTGAAATTGTCACCCTCGATATA 57.520 37.500 0.00 0.00 31.13 0.86
114 115 5.359194 ACTGAAATTGTCACCCTCGATAT 57.641 39.130 0.00 0.00 31.13 1.63
115 116 4.819105 ACTGAAATTGTCACCCTCGATA 57.181 40.909 0.00 0.00 31.13 2.92
116 117 3.703001 ACTGAAATTGTCACCCTCGAT 57.297 42.857 0.00 0.00 31.13 3.59
117 118 3.485463 AACTGAAATTGTCACCCTCGA 57.515 42.857 0.00 0.00 31.13 4.04
118 119 3.125316 GCTAACTGAAATTGTCACCCTCG 59.875 47.826 0.00 0.00 31.13 4.63
119 120 4.072131 TGCTAACTGAAATTGTCACCCTC 58.928 43.478 0.00 0.00 31.13 4.30
120 121 4.098914 TGCTAACTGAAATTGTCACCCT 57.901 40.909 0.00 0.00 31.13 4.34
121 122 4.798574 CTTGCTAACTGAAATTGTCACCC 58.201 43.478 0.00 0.00 31.13 4.61
122 123 4.229876 GCTTGCTAACTGAAATTGTCACC 58.770 43.478 0.00 0.00 31.13 4.02
123 124 4.676924 GTGCTTGCTAACTGAAATTGTCAC 59.323 41.667 0.00 0.00 31.13 3.67
124 125 4.337836 TGTGCTTGCTAACTGAAATTGTCA 59.662 37.500 0.00 0.00 34.17 3.58
125 126 4.858935 TGTGCTTGCTAACTGAAATTGTC 58.141 39.130 0.00 0.00 0.00 3.18
126 127 4.794003 GCTGTGCTTGCTAACTGAAATTGT 60.794 41.667 0.00 0.00 0.00 2.71
127 128 3.671928 GCTGTGCTTGCTAACTGAAATTG 59.328 43.478 0.00 0.00 0.00 2.32
128 129 3.318839 TGCTGTGCTTGCTAACTGAAATT 59.681 39.130 0.00 0.00 0.00 1.82
129 130 2.886523 TGCTGTGCTTGCTAACTGAAAT 59.113 40.909 0.00 0.00 0.00 2.17
130 131 2.296792 TGCTGTGCTTGCTAACTGAAA 58.703 42.857 0.00 0.00 0.00 2.69
131 132 1.965935 TGCTGTGCTTGCTAACTGAA 58.034 45.000 0.00 0.00 0.00 3.02
132 133 1.965935 TTGCTGTGCTTGCTAACTGA 58.034 45.000 0.00 0.00 0.00 3.41
133 134 2.780065 TTTGCTGTGCTTGCTAACTG 57.220 45.000 0.00 0.00 0.00 3.16
134 135 2.223805 GGTTTTGCTGTGCTTGCTAACT 60.224 45.455 0.00 0.00 0.00 2.24
135 136 2.127251 GGTTTTGCTGTGCTTGCTAAC 58.873 47.619 0.00 0.00 0.00 2.34
136 137 2.031120 AGGTTTTGCTGTGCTTGCTAA 58.969 42.857 0.00 0.00 0.00 3.09
137 138 1.337703 CAGGTTTTGCTGTGCTTGCTA 59.662 47.619 0.00 0.00 0.00 3.49
138 139 0.103572 CAGGTTTTGCTGTGCTTGCT 59.896 50.000 0.00 0.00 0.00 3.91
139 140 0.102844 TCAGGTTTTGCTGTGCTTGC 59.897 50.000 0.00 0.00 0.00 4.01
140 141 1.134753 TGTCAGGTTTTGCTGTGCTTG 59.865 47.619 0.00 0.00 0.00 4.01
141 142 1.473258 TGTCAGGTTTTGCTGTGCTT 58.527 45.000 0.00 0.00 0.00 3.91
142 143 1.473258 TTGTCAGGTTTTGCTGTGCT 58.527 45.000 0.00 0.00 0.00 4.40
143 144 2.292103 TTTGTCAGGTTTTGCTGTGC 57.708 45.000 0.00 0.00 0.00 4.57
161 162 4.335400 AAATCCGCCATGTTCAGTTTTT 57.665 36.364 0.00 0.00 0.00 1.94
162 163 4.306600 GAAAATCCGCCATGTTCAGTTTT 58.693 39.130 0.00 0.00 29.70 2.43
163 164 3.306019 GGAAAATCCGCCATGTTCAGTTT 60.306 43.478 0.00 0.00 30.77 2.66
164 165 2.231235 GGAAAATCCGCCATGTTCAGTT 59.769 45.455 0.00 0.00 30.77 3.16
165 166 1.818674 GGAAAATCCGCCATGTTCAGT 59.181 47.619 0.00 0.00 30.77 3.41
166 167 1.818060 TGGAAAATCCGCCATGTTCAG 59.182 47.619 0.00 0.00 40.17 3.02
167 168 1.543802 GTGGAAAATCCGCCATGTTCA 59.456 47.619 0.00 0.00 41.08 3.18
168 169 2.278026 GTGGAAAATCCGCCATGTTC 57.722 50.000 0.00 0.00 41.08 3.18
176 177 5.181245 TCTTTTAGCAAGAGTGGAAAATCCG 59.819 40.000 0.00 0.00 40.17 4.18
177 178 6.575162 TCTTTTAGCAAGAGTGGAAAATCC 57.425 37.500 0.00 0.00 36.96 3.01
178 179 9.481340 AATTTCTTTTAGCAAGAGTGGAAAATC 57.519 29.630 0.00 0.00 0.00 2.17
179 180 9.264719 CAATTTCTTTTAGCAAGAGTGGAAAAT 57.735 29.630 0.00 0.00 0.00 1.82
180 181 7.224557 GCAATTTCTTTTAGCAAGAGTGGAAAA 59.775 33.333 0.00 0.00 0.00 2.29
181 182 6.701400 GCAATTTCTTTTAGCAAGAGTGGAAA 59.299 34.615 0.00 0.00 0.00 3.13
182 183 6.040842 AGCAATTTCTTTTAGCAAGAGTGGAA 59.959 34.615 0.00 0.00 0.00 3.53
183 184 5.536161 AGCAATTTCTTTTAGCAAGAGTGGA 59.464 36.000 0.00 0.00 0.00 4.02
184 185 5.776744 AGCAATTTCTTTTAGCAAGAGTGG 58.223 37.500 0.00 0.00 0.00 4.00
185 186 7.699812 GGATAGCAATTTCTTTTAGCAAGAGTG 59.300 37.037 0.00 0.00 0.00 3.51
186 187 7.613411 AGGATAGCAATTTCTTTTAGCAAGAGT 59.387 33.333 0.00 0.00 0.00 3.24
187 188 7.994194 AGGATAGCAATTTCTTTTAGCAAGAG 58.006 34.615 0.00 0.00 0.00 2.85
188 189 7.611467 TGAGGATAGCAATTTCTTTTAGCAAGA 59.389 33.333 0.00 0.00 0.00 3.02
189 190 7.765307 TGAGGATAGCAATTTCTTTTAGCAAG 58.235 34.615 0.00 0.00 0.00 4.01
190 191 7.701539 TGAGGATAGCAATTTCTTTTAGCAA 57.298 32.000 0.00 0.00 0.00 3.91
191 192 7.611467 TCTTGAGGATAGCAATTTCTTTTAGCA 59.389 33.333 0.00 0.00 0.00 3.49
192 193 7.989826 TCTTGAGGATAGCAATTTCTTTTAGC 58.010 34.615 0.00 0.00 0.00 3.09
196 197 9.466497 TGTTATCTTGAGGATAGCAATTTCTTT 57.534 29.630 0.00 0.00 42.38 2.52
197 198 9.638176 ATGTTATCTTGAGGATAGCAATTTCTT 57.362 29.630 5.32 0.00 46.08 2.52
204 205 8.786898 GCAAATTATGTTATCTTGAGGATAGCA 58.213 33.333 3.80 3.80 46.66 3.49
205 206 8.239998 GGCAAATTATGTTATCTTGAGGATAGC 58.760 37.037 0.00 0.00 38.07 2.97
206 207 9.288576 TGGCAAATTATGTTATCTTGAGGATAG 57.711 33.333 0.00 0.00 38.07 2.08
207 208 9.812347 ATGGCAAATTATGTTATCTTGAGGATA 57.188 29.630 0.00 0.00 35.98 2.59
208 209 8.716674 ATGGCAAATTATGTTATCTTGAGGAT 57.283 30.769 0.00 0.00 38.38 3.24
209 210 9.639563 TTATGGCAAATTATGTTATCTTGAGGA 57.360 29.630 0.00 0.00 0.00 3.71
269 270 9.434420 TTTGGATTTTGATAACCAATGAATGTC 57.566 29.630 0.00 0.00 41.14 3.06
317 320 4.163552 CACATCAACAAGTCATGCATGTC 58.836 43.478 25.43 20.17 0.00 3.06
557 570 0.180642 TGGTCACCGCCACTTGTTTA 59.819 50.000 0.00 0.00 32.81 2.01
567 580 2.665185 GTGGTCAGTGGTCACCGC 60.665 66.667 0.00 0.00 35.15 5.68
585 598 0.249073 CTAAGATGGTCTCCGGTGCG 60.249 60.000 0.00 0.00 0.00 5.34
586 599 0.530870 GCTAAGATGGTCTCCGGTGC 60.531 60.000 0.00 0.00 0.00 5.01
587 600 1.067821 GAGCTAAGATGGTCTCCGGTG 59.932 57.143 0.00 0.00 0.00 4.94
588 601 1.342076 TGAGCTAAGATGGTCTCCGGT 60.342 52.381 0.00 0.00 35.68 5.28
589 602 1.067821 GTGAGCTAAGATGGTCTCCGG 59.932 57.143 0.00 0.00 35.68 5.14
590 603 1.067821 GGTGAGCTAAGATGGTCTCCG 59.932 57.143 0.00 0.00 38.01 4.63
591 604 2.364002 GAGGTGAGCTAAGATGGTCTCC 59.636 54.545 6.68 6.68 43.97 3.71
606 619 4.164981 ACCAGTATTGTAACCTGAGGTGA 58.835 43.478 4.15 0.00 35.34 4.02
612 625 4.020573 TGGACTGACCAGTATTGTAACCTG 60.021 45.833 2.23 0.00 44.64 4.00
613 626 4.164981 TGGACTGACCAGTATTGTAACCT 58.835 43.478 2.23 0.00 44.64 3.50
614 627 4.546829 TGGACTGACCAGTATTGTAACC 57.453 45.455 2.23 0.00 44.64 2.85
631 655 4.642429 AGTCACTAGTTGGTCAAATGGAC 58.358 43.478 0.00 0.00 46.20 4.02
668 692 0.452784 CCTACTTTTGTTCGCTGCGC 60.453 55.000 18.65 0.00 0.00 6.09
676 700 5.827797 TCAAGATTCACAGCCTACTTTTGTT 59.172 36.000 0.00 0.00 0.00 2.83
705 729 0.457166 CATGTGGTGATTTGCTGCCG 60.457 55.000 0.00 0.00 0.00 5.69
761 785 2.799126 TGCCCACGGATTTATCAACT 57.201 45.000 0.00 0.00 0.00 3.16
762 786 3.859411 TTTGCCCACGGATTTATCAAC 57.141 42.857 0.00 0.00 0.00 3.18
763 787 4.873746 TTTTTGCCCACGGATTTATCAA 57.126 36.364 0.00 0.00 0.00 2.57
781 805 8.560355 AAGTTTGCAATGGAAAAGTACTTTTT 57.440 26.923 29.26 14.84 42.26 1.94
798 822 1.529713 GGGACCGGGAAAGTTTGCA 60.530 57.895 6.32 0.00 0.00 4.08
884 908 2.288334 TGTATATACGCATTTCGCCGGT 60.288 45.455 1.90 0.00 43.23 5.28
931 956 3.022287 CACTGTGCCGTGTGGTTC 58.978 61.111 0.00 0.00 37.67 3.62
933 958 4.481617 TGCACTGTGCCGTGTGGT 62.482 61.111 28.17 0.00 44.23 4.16
958 985 2.355837 GCTGGTGTGCTCGACGAA 60.356 61.111 0.00 0.00 0.00 3.85
1119 1149 1.153958 CATGAGCAGCACGTCGAGA 60.154 57.895 0.00 0.00 0.00 4.04
1292 1335 4.572795 GTCTAGCCAATCTTCAGGTTAAGC 59.427 45.833 0.00 0.00 0.00 3.09
1324 1372 5.064452 CCTGGAGATCAAAAGAACATTCTCG 59.936 44.000 0.00 0.00 36.28 4.04
1515 3115 6.936279 TCCTCTGTGGTTAAGTCTAATTGAG 58.064 40.000 0.00 0.00 37.07 3.02
1520 3120 6.681729 ACAATCCTCTGTGGTTAAGTCTAA 57.318 37.500 0.00 0.00 37.07 2.10
1555 3155 5.763698 AGGGTTAAACTTCCTCTTCGAAAAG 59.236 40.000 0.00 2.38 0.00 2.27
1581 3181 2.131183 GTTAGCGATGATGCAGAGACC 58.869 52.381 0.00 0.00 37.31 3.85
1640 5010 7.753630 AGAAGCTGGTTTCCATCTGATATTAT 58.246 34.615 0.00 0.00 29.79 1.28
1669 5039 5.673337 TCTGATGGAGTTTTGAGTTTTCG 57.327 39.130 0.00 0.00 0.00 3.46
1721 5092 4.556942 TGAACTGCAGTTGAGTTTGATG 57.443 40.909 35.67 0.00 38.56 3.07
1798 5256 2.735134 GACTAAACGTCTGACCGCAAAT 59.265 45.455 1.55 0.00 39.61 2.32
1819 5279 4.460382 ACAACAAAGCTCACCCAATATCTG 59.540 41.667 0.00 0.00 0.00 2.90
1869 5363 9.743057 CCAAAGTGTGTATCATTTTGTCTTAAA 57.257 29.630 12.26 0.00 45.75 1.52
1874 5368 5.402270 GCACCAAAGTGTGTATCATTTTGTC 59.598 40.000 12.26 2.08 45.75 3.18
1943 5447 0.178967 TTGCATTCCTCACCCAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
1992 5513 4.637534 CAGTTGGTACTTCTCATGGAATGG 59.362 45.833 0.00 0.00 37.45 3.16
2079 7877 6.327386 AGATAATGAAGGGTGAGCCTTTTA 57.673 37.500 18.00 13.00 33.90 1.52
2126 7924 0.318441 TGACTGCCTTTCTCCTGACG 59.682 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.