Multiple sequence alignment - TraesCS6B01G154500

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 TraesCS6B01G154500 chr6B 100.000 2258 0 0 1 2258 157932461 157930204 0.000000e+00 4170.0
1 TraesCS6B01G154500 chr6B 87.633 1504 122 29 276 1758 157777241 157778701 0.000000e+00 1688.0
2 TraesCS6B01G154500 chr6B 79.844 898 171 10 867 1758 156652791 156653684 0.000000e+00 647.0
3 TraesCS6B01G154500 chr6B 95.307 277 13 0 1 277 430321593 430321317 7.400000e-120 440.0
4 TraesCS6B01G154500 chr6B 92.491 293 19 3 1 293 251059700 251059989 1.250000e-112 416.0
5 TraesCS6B01G154500 chr6B 91.864 295 19 4 1 293 243169334 243169625 7.510000e-110 407.0
6 TraesCS6B01G154500 chr6B 78.044 501 95 11 1770 2258 504069977 504069480 3.640000e-78 302.0
7 TraesCS6B01G154500 chr6B 86.408 206 27 1 1024 1229 157788347 157788551 8.120000e-55 224.0
8 TraesCS6B01G154500 chr6B 71.043 853 210 26 878 1714 158101912 158102743 2.980000e-39 172.0
9 TraesCS6B01G154500 chr6A 93.093 1332 75 6 430 1758 99784465 99785782 0.000000e+00 1934.0
10 TraesCS6B01G154500 chr6A 79.599 897 175 8 867 1758 98313921 98314814 8.800000e-179 636.0
11 TraesCS6B01G154500 chr6A 82.911 158 10 7 276 416 99784321 99784478 2.350000e-25 126.0
12 TraesCS6B01G154500 chr6D 90.998 1333 100 9 430 1758 82962179 82963495 0.000000e+00 1779.0
13 TraesCS6B01G154500 chr6D 80.045 897 171 8 867 1758 81924136 81925029 0.000000e+00 658.0
14 TraesCS6B01G154500 chr6D 71.612 856 206 26 883 1722 83055958 83056792 1.370000e-47 200.0
15 TraesCS6B01G154500 chr6D 78.931 318 41 17 760 1076 82972089 82972381 2.290000e-45 193.0
16 TraesCS6B01G154500 chr5D 88.336 1346 119 22 430 1758 372057876 372059200 0.000000e+00 1581.0
17 TraesCS6B01G154500 chr5D 80.303 990 176 12 757 1740 372061965 372062941 0.000000e+00 730.0
18 TraesCS6B01G154500 chr3B 92.491 293 19 3 1 293 304074480 304074769 1.250000e-112 416.0
19 TraesCS6B01G154500 chr5B 92.150 293 20 3 1 293 297437153 297437442 5.800000e-111 411.0
20 TraesCS6B01G154500 chr4B 92.150 293 20 3 1 293 102064854 102064565 5.800000e-111 411.0
21 TraesCS6B01G154500 chr4B 92.150 293 20 3 1 293 217565671 217565382 5.800000e-111 411.0
22 TraesCS6B01G154500 chr4B 92.150 293 20 3 1 293 290999284 290999573 5.800000e-111 411.0
23 TraesCS6B01G154500 chr4B 92.150 293 20 3 1 293 391603995 391603706 5.800000e-111 411.0
24 TraesCS6B01G154500 chr7D 82.392 301 49 3 1962 2258 10046651 10046351 2.220000e-65 259.0
25 TraesCS6B01G154500 chr2A 77.143 140 30 2 1922 2060 83605895 83606033 1.860000e-11 80.5


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 TraesCS6B01G154500 chr6B 157930204 157932461 2257 True 4170.0 4170 100.0000 1 2258 1 chr6B.!!$R1 2257
1 TraesCS6B01G154500 chr6B 157777241 157778701 1460 False 1688.0 1688 87.6330 276 1758 1 chr6B.!!$F2 1482
2 TraesCS6B01G154500 chr6B 156652791 156653684 893 False 647.0 647 79.8440 867 1758 1 chr6B.!!$F1 891
3 TraesCS6B01G154500 chr6A 99784321 99785782 1461 False 1030.0 1934 88.0020 276 1758 2 chr6A.!!$F2 1482
4 TraesCS6B01G154500 chr6A 98313921 98314814 893 False 636.0 636 79.5990 867 1758 1 chr6A.!!$F1 891
5 TraesCS6B01G154500 chr6D 82962179 82963495 1316 False 1779.0 1779 90.9980 430 1758 1 chr6D.!!$F2 1328
6 TraesCS6B01G154500 chr6D 81924136 81925029 893 False 658.0 658 80.0450 867 1758 1 chr6D.!!$F1 891
7 TraesCS6B01G154500 chr5D 372057876 372062941 5065 False 1155.5 1581 84.3195 430 1758 2 chr5D.!!$F1 1328

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
137 138 0.036732 TTCTCAATGTCGGCCAGCTT 59.963 50.0 2.24 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2040 0.59868 CAGCAGGGACGGATCGAATC 60.599 60.0 0.0 0.0 0.0 2.52 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
18 19 2.457080 GGCGGAAAGTTTCTCCTCG 58.543 57.895 15.05 10.85 0.00 4.63
19 20 1.636570 GGCGGAAAGTTTCTCCTCGC 61.637 60.000 21.39 21.39 40.77 5.03
20 21 1.956620 GCGGAAAGTTTCTCCTCGCG 61.957 60.000 17.17 0.00 32.72 5.87
21 22 1.788481 GGAAAGTTTCTCCTCGCGC 59.212 57.895 15.05 0.00 0.00 6.86
22 23 0.670854 GGAAAGTTTCTCCTCGCGCT 60.671 55.000 15.05 0.00 0.00 5.92
23 24 0.716666 GAAAGTTTCTCCTCGCGCTC 59.283 55.000 5.56 0.00 0.00 5.03
24 25 1.009389 AAAGTTTCTCCTCGCGCTCG 61.009 55.000 5.56 0.00 0.00 5.03
25 26 2.820767 AAGTTTCTCCTCGCGCTCGG 62.821 60.000 5.56 5.56 36.13 4.63
26 27 4.796231 TTTCTCCTCGCGCTCGGC 62.796 66.667 5.56 0.00 36.13 5.54
36 37 4.821589 CGCTCGGCAAGGTCCTCC 62.822 72.222 0.00 0.00 0.00 4.30
38 39 2.896443 CTCGGCAAGGTCCTCCTC 59.104 66.667 0.00 0.00 44.35 3.71
39 40 2.683933 TCGGCAAGGTCCTCCTCC 60.684 66.667 0.00 0.00 44.35 4.30
40 41 2.685380 CGGCAAGGTCCTCCTCCT 60.685 66.667 0.00 0.00 44.35 3.69
41 42 2.993853 GGCAAGGTCCTCCTCCTG 59.006 66.667 0.00 0.00 44.35 3.86
42 43 2.674220 GGCAAGGTCCTCCTCCTGG 61.674 68.421 0.00 0.00 44.35 4.45
43 44 2.674220 GCAAGGTCCTCCTCCTGGG 61.674 68.421 0.00 0.00 44.35 4.45
44 45 1.229658 CAAGGTCCTCCTCCTGGGT 60.230 63.158 0.00 0.00 44.35 4.51
45 46 1.081277 AAGGTCCTCCTCCTGGGTC 59.919 63.158 0.00 0.00 44.35 4.46
46 47 1.456518 AAGGTCCTCCTCCTGGGTCT 61.457 60.000 0.00 0.00 44.35 3.85
47 48 1.081277 GGTCCTCCTCCTGGGTCTT 59.919 63.158 0.00 0.00 36.25 3.01
48 49 0.978667 GGTCCTCCTCCTGGGTCTTC 60.979 65.000 0.00 0.00 36.25 2.87
49 50 0.252284 GTCCTCCTCCTGGGTCTTCA 60.252 60.000 0.00 0.00 36.25 3.02
50 51 0.041833 TCCTCCTCCTGGGTCTTCAG 59.958 60.000 0.00 0.00 36.25 3.02
56 57 4.785453 CTGGGTCTTCAGGGCGGC 62.785 72.222 0.00 0.00 0.00 6.53
59 60 4.475135 GGTCTTCAGGGCGGCCTC 62.475 72.222 30.43 16.66 0.00 4.70
60 61 4.821589 GTCTTCAGGGCGGCCTCG 62.822 72.222 30.43 22.69 39.81 4.63
74 75 4.436998 CTCGTGCTGGGACCGGAC 62.437 72.222 9.46 0.00 0.00 4.79
80 81 4.452733 CTGGGACCGGACGGCTTC 62.453 72.222 9.46 1.57 39.32 3.86
87 88 2.125832 CGGACGGCTTCGGCTTTA 60.126 61.111 0.00 0.00 42.59 1.85
88 89 1.520787 CGGACGGCTTCGGCTTTAT 60.521 57.895 0.00 0.00 42.59 1.40
89 90 1.087771 CGGACGGCTTCGGCTTTATT 61.088 55.000 0.00 0.00 42.59 1.40
90 91 0.377203 GGACGGCTTCGGCTTTATTG 59.623 55.000 0.00 0.00 42.59 1.90
91 92 0.377203 GACGGCTTCGGCTTTATTGG 59.623 55.000 0.00 0.00 39.21 3.16
92 93 1.064134 CGGCTTCGGCTTTATTGGC 59.936 57.895 0.00 0.00 41.44 4.52
93 94 1.437573 GGCTTCGGCTTTATTGGCC 59.562 57.895 0.00 0.00 45.57 5.36
102 103 3.961480 GCTTTATTGGCCAACCTCTTT 57.039 42.857 23.27 6.24 36.63 2.52
103 104 3.588955 GCTTTATTGGCCAACCTCTTTG 58.411 45.455 23.27 8.65 36.63 2.77
104 105 3.588955 CTTTATTGGCCAACCTCTTTGC 58.411 45.455 23.27 0.00 36.63 3.68
105 106 1.555967 TATTGGCCAACCTCTTTGCC 58.444 50.000 23.27 0.00 36.63 4.52
106 107 0.471591 ATTGGCCAACCTCTTTGCCA 60.472 50.000 23.27 0.00 38.71 4.92
107 108 0.471591 TTGGCCAACCTCTTTGCCAT 60.472 50.000 16.05 0.00 39.58 4.40
108 109 0.899717 TGGCCAACCTCTTTGCCATC 60.900 55.000 0.61 0.00 36.83 3.51
109 110 0.613012 GGCCAACCTCTTTGCCATCT 60.613 55.000 0.00 0.00 33.75 2.90
110 111 0.813821 GCCAACCTCTTTGCCATCTC 59.186 55.000 0.00 0.00 33.34 2.75
111 112 1.467920 CCAACCTCTTTGCCATCTCC 58.532 55.000 0.00 0.00 33.34 3.71
112 113 1.005215 CCAACCTCTTTGCCATCTCCT 59.995 52.381 0.00 0.00 33.34 3.69
113 114 2.089980 CAACCTCTTTGCCATCTCCTG 58.910 52.381 0.00 0.00 0.00 3.86
115 116 0.106819 CCTCTTTGCCATCTCCTGGG 60.107 60.000 0.00 0.00 46.06 4.45
120 121 2.194326 GCCATCTCCTGGGCCTTC 59.806 66.667 4.53 0.00 46.06 3.46
121 122 2.381941 GCCATCTCCTGGGCCTTCT 61.382 63.158 4.53 0.00 46.06 2.85
122 123 1.835693 CCATCTCCTGGGCCTTCTC 59.164 63.158 4.53 0.00 41.82 2.87
123 124 0.984961 CCATCTCCTGGGCCTTCTCA 60.985 60.000 4.53 0.00 41.82 3.27
124 125 0.914644 CATCTCCTGGGCCTTCTCAA 59.085 55.000 4.53 0.00 0.00 3.02
125 126 1.493871 CATCTCCTGGGCCTTCTCAAT 59.506 52.381 4.53 0.00 0.00 2.57
126 127 0.914644 TCTCCTGGGCCTTCTCAATG 59.085 55.000 4.53 0.00 0.00 2.82
127 128 0.622665 CTCCTGGGCCTTCTCAATGT 59.377 55.000 4.53 0.00 0.00 2.71
128 129 0.620556 TCCTGGGCCTTCTCAATGTC 59.379 55.000 4.53 0.00 0.00 3.06
129 130 0.745845 CCTGGGCCTTCTCAATGTCG 60.746 60.000 4.53 0.00 0.00 4.35
130 131 0.745845 CTGGGCCTTCTCAATGTCGG 60.746 60.000 4.53 0.00 0.00 4.79
131 132 2.115291 GGGCCTTCTCAATGTCGGC 61.115 63.158 0.84 0.00 39.98 5.54
132 133 3.502572 GCCTTCTCAATGTCGGCC 58.497 61.111 0.00 0.00 34.75 6.13
133 134 1.377202 GCCTTCTCAATGTCGGCCA 60.377 57.895 2.24 0.00 34.75 5.36
134 135 1.372087 GCCTTCTCAATGTCGGCCAG 61.372 60.000 2.24 0.00 34.75 4.85
135 136 1.372087 CCTTCTCAATGTCGGCCAGC 61.372 60.000 2.24 0.00 0.00 4.85
136 137 0.392193 CTTCTCAATGTCGGCCAGCT 60.392 55.000 2.24 0.00 0.00 4.24
137 138 0.036732 TTCTCAATGTCGGCCAGCTT 59.963 50.000 2.24 0.00 0.00 3.74
138 139 0.391661 TCTCAATGTCGGCCAGCTTC 60.392 55.000 2.24 0.00 0.00 3.86
139 140 0.674581 CTCAATGTCGGCCAGCTTCA 60.675 55.000 2.24 0.00 0.00 3.02
140 141 0.674581 TCAATGTCGGCCAGCTTCAG 60.675 55.000 2.24 0.00 0.00 3.02
141 142 1.377725 AATGTCGGCCAGCTTCAGG 60.378 57.895 2.24 0.00 0.00 3.86
142 143 2.826777 AATGTCGGCCAGCTTCAGGG 62.827 60.000 2.24 0.00 0.00 4.45
148 149 4.093291 CCAGCTTCAGGGCGAGCT 62.093 66.667 0.00 0.00 38.25 4.09
149 150 2.511145 CAGCTTCAGGGCGAGCTC 60.511 66.667 2.73 2.73 35.17 4.09
150 151 3.780173 AGCTTCAGGGCGAGCTCC 61.780 66.667 8.47 0.47 37.29 4.70
151 152 4.087892 GCTTCAGGGCGAGCTCCA 62.088 66.667 8.47 0.00 0.00 3.86
152 153 2.125350 CTTCAGGGCGAGCTCCAC 60.125 66.667 8.47 1.89 0.00 4.02
153 154 3.672295 CTTCAGGGCGAGCTCCACC 62.672 68.421 8.47 10.71 0.00 4.61
154 155 4.704103 TCAGGGCGAGCTCCACCT 62.704 66.667 16.10 16.10 0.00 4.00
155 156 4.154347 CAGGGCGAGCTCCACCTC 62.154 72.222 18.36 9.84 0.00 3.85
156 157 4.704103 AGGGCGAGCTCCACCTCA 62.704 66.667 16.10 0.00 0.00 3.86
157 158 4.459089 GGGCGAGCTCCACCTCAC 62.459 72.222 17.56 1.00 0.00 3.51
158 159 4.803426 GGCGAGCTCCACCTCACG 62.803 72.222 8.47 0.00 0.00 4.35
159 160 4.803426 GCGAGCTCCACCTCACGG 62.803 72.222 8.47 0.00 0.00 4.94
161 162 2.932234 CGAGCTCCACCTCACGGTT 61.932 63.158 8.47 0.00 42.13 4.44
162 163 1.374758 GAGCTCCACCTCACGGTTG 60.375 63.158 0.87 0.00 42.13 3.77
163 164 2.358737 GCTCCACCTCACGGTTGG 60.359 66.667 0.00 0.00 42.13 3.77
164 165 2.358737 CTCCACCTCACGGTTGGC 60.359 66.667 0.00 0.00 42.13 4.52
165 166 3.901797 CTCCACCTCACGGTTGGCC 62.902 68.421 0.00 0.00 42.13 5.36
166 167 4.263572 CCACCTCACGGTTGGCCA 62.264 66.667 0.00 0.00 42.13 5.36
167 168 2.669569 CACCTCACGGTTGGCCAG 60.670 66.667 5.11 0.00 42.13 4.85
168 169 4.643387 ACCTCACGGTTGGCCAGC 62.643 66.667 11.82 11.82 42.13 4.85
169 170 4.335647 CCTCACGGTTGGCCAGCT 62.336 66.667 19.84 0.00 34.09 4.24
170 171 2.743928 CTCACGGTTGGCCAGCTC 60.744 66.667 19.84 8.65 34.09 4.09
171 172 3.535629 CTCACGGTTGGCCAGCTCA 62.536 63.158 19.84 0.00 34.09 4.26
172 173 3.357079 CACGGTTGGCCAGCTCAC 61.357 66.667 19.84 8.23 34.09 3.51
173 174 4.643387 ACGGTTGGCCAGCTCACC 62.643 66.667 19.84 16.51 34.09 4.02
175 176 3.971702 GGTTGGCCAGCTCACCCT 61.972 66.667 19.84 0.00 34.09 4.34
176 177 2.674380 GTTGGCCAGCTCACCCTG 60.674 66.667 13.08 0.00 0.00 4.45
196 197 3.764466 CGGCCTTCAGCTCGTCCT 61.764 66.667 0.00 0.00 43.05 3.85
197 198 2.125350 GGCCTTCAGCTCGTCCTG 60.125 66.667 0.00 0.00 43.05 3.86
198 199 2.650116 GGCCTTCAGCTCGTCCTGA 61.650 63.158 0.00 4.14 43.05 3.86
206 207 4.504916 CTCGTCCTGAGCCTGGCG 62.505 72.222 13.96 0.00 38.03 5.69
209 210 3.706373 GTCCTGAGCCTGGCGGAA 61.706 66.667 13.96 1.76 0.00 4.30
210 211 3.706373 TCCTGAGCCTGGCGGAAC 61.706 66.667 13.96 7.11 0.00 3.62
211 212 4.785453 CCTGAGCCTGGCGGAACC 62.785 72.222 13.96 2.29 39.84 3.62
219 220 4.329545 TGGCGGAACCAGTCCTGC 62.330 66.667 0.00 0.00 46.36 4.85
223 224 4.021925 GGAACCAGTCCTGCGCCT 62.022 66.667 4.18 0.00 43.98 5.52
224 225 2.435059 GAACCAGTCCTGCGCCTC 60.435 66.667 4.18 0.00 0.00 4.70
225 226 4.379243 AACCAGTCCTGCGCCTCG 62.379 66.667 4.18 0.00 0.00 4.63
252 253 4.589569 CCCCCAAAGTCCTCCTCT 57.410 61.111 0.00 0.00 0.00 3.69
253 254 3.732159 CCCCCAAAGTCCTCCTCTA 57.268 57.895 0.00 0.00 0.00 2.43
254 255 2.198334 CCCCCAAAGTCCTCCTCTAT 57.802 55.000 0.00 0.00 0.00 1.98
255 256 2.050918 CCCCCAAAGTCCTCCTCTATC 58.949 57.143 0.00 0.00 0.00 2.08
256 257 2.360854 CCCCCAAAGTCCTCCTCTATCT 60.361 54.545 0.00 0.00 0.00 1.98
257 258 3.388913 CCCCAAAGTCCTCCTCTATCTT 58.611 50.000 0.00 0.00 0.00 2.40
258 259 3.389656 CCCCAAAGTCCTCCTCTATCTTC 59.610 52.174 0.00 0.00 0.00 2.87
259 260 4.294347 CCCAAAGTCCTCCTCTATCTTCT 58.706 47.826 0.00 0.00 0.00 2.85
260 261 4.343814 CCCAAAGTCCTCCTCTATCTTCTC 59.656 50.000 0.00 0.00 0.00 2.87
261 262 4.343814 CCAAAGTCCTCCTCTATCTTCTCC 59.656 50.000 0.00 0.00 0.00 3.71
262 263 4.890499 AAGTCCTCCTCTATCTTCTCCA 57.110 45.455 0.00 0.00 0.00 3.86
263 264 4.178956 AGTCCTCCTCTATCTTCTCCAC 57.821 50.000 0.00 0.00 0.00 4.02
264 265 3.117284 AGTCCTCCTCTATCTTCTCCACC 60.117 52.174 0.00 0.00 0.00 4.61
265 266 2.859404 TCCTCCTCTATCTTCTCCACCA 59.141 50.000 0.00 0.00 0.00 4.17
266 267 2.962421 CCTCCTCTATCTTCTCCACCAC 59.038 54.545 0.00 0.00 0.00 4.16
267 268 2.962421 CTCCTCTATCTTCTCCACCACC 59.038 54.545 0.00 0.00 0.00 4.61
268 269 1.683917 CCTCTATCTTCTCCACCACCG 59.316 57.143 0.00 0.00 0.00 4.94
269 270 1.067821 CTCTATCTTCTCCACCACCGC 59.932 57.143 0.00 0.00 0.00 5.68
270 271 0.105039 CTATCTTCTCCACCACCGCC 59.895 60.000 0.00 0.00 0.00 6.13
271 272 1.672854 TATCTTCTCCACCACCGCCG 61.673 60.000 0.00 0.00 0.00 6.46
272 273 4.003788 CTTCTCCACCACCGCCGT 62.004 66.667 0.00 0.00 0.00 5.68
273 274 3.934391 CTTCTCCACCACCGCCGTC 62.934 68.421 0.00 0.00 0.00 4.79
278 279 3.066190 CACCACCGCCGTCCTAGA 61.066 66.667 0.00 0.00 0.00 2.43
282 283 1.153823 CACCGCCGTCCTAGAACTG 60.154 63.158 0.00 0.00 0.00 3.16
287 288 1.711206 GCCGTCCTAGAACTGTTGTC 58.289 55.000 0.00 0.00 0.00 3.18
300 302 7.881775 AGAACTGTTGTCCTTGTTTAAGAAT 57.118 32.000 0.00 0.00 35.92 2.40
325 327 5.604758 TTTGTGATGGGTTTTTGACATGA 57.395 34.783 0.00 0.00 0.00 3.07
334 336 5.128499 TGGGTTTTTGACATGATGTTCTGTT 59.872 36.000 0.00 0.00 0.00 3.16
337 339 7.329226 GGGTTTTTGACATGATGTTCTGTTATG 59.671 37.037 0.00 0.00 0.00 1.90
343 345 4.637534 ACATGATGTTCTGTTATGGCAGTC 59.362 41.667 0.00 0.00 37.70 3.51
344 346 3.261580 TGATGTTCTGTTATGGCAGTCG 58.738 45.455 0.00 0.00 37.70 4.18
347 349 1.661112 GTTCTGTTATGGCAGTCGCTC 59.339 52.381 0.00 0.00 37.70 5.03
415 434 5.342433 CATGAAGCAAAGTGAACTGTGAAA 58.658 37.500 4.76 0.00 32.93 2.69
416 435 5.581126 TGAAGCAAAGTGAACTGTGAAAT 57.419 34.783 4.76 0.00 32.93 2.17
417 436 5.964758 TGAAGCAAAGTGAACTGTGAAATT 58.035 33.333 4.76 0.00 32.93 1.82
418 437 6.035843 TGAAGCAAAGTGAACTGTGAAATTC 58.964 36.000 4.76 5.95 32.93 2.17
419 438 4.936891 AGCAAAGTGAACTGTGAAATTCC 58.063 39.130 4.76 0.00 32.93 3.01
420 439 4.051237 GCAAAGTGAACTGTGAAATTCCC 58.949 43.478 4.76 0.00 32.93 3.97
421 440 4.202151 GCAAAGTGAACTGTGAAATTCCCT 60.202 41.667 4.76 0.00 32.93 4.20
422 441 5.009610 GCAAAGTGAACTGTGAAATTCCCTA 59.990 40.000 4.76 0.00 32.93 3.53
423 442 6.460953 GCAAAGTGAACTGTGAAATTCCCTAA 60.461 38.462 4.76 0.00 32.93 2.69
424 443 7.488322 CAAAGTGAACTGTGAAATTCCCTAAA 58.512 34.615 0.00 0.00 32.93 1.85
425 444 7.654022 AAGTGAACTGTGAAATTCCCTAAAA 57.346 32.000 0.00 0.00 0.00 1.52
426 445 7.654022 AGTGAACTGTGAAATTCCCTAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
461 480 9.352784 CTGTGAAAAATTGAAGTTTCAGTACAA 57.647 29.630 6.97 0.00 42.72 2.41
482 509 7.520119 ACAAAATTCGTTTTCCTGAAAGAAC 57.480 32.000 0.00 0.00 34.07 3.01
496 526 6.016276 TCCTGAAAGAACAAGAAAATACAGGC 60.016 38.462 0.00 0.00 40.31 4.85
506 536 4.215109 AGAAAATACAGGCAACACCAACT 58.785 39.130 0.00 0.00 43.14 3.16
565 596 7.663905 AGCCAACAATCTTACATTGTTACTACA 59.336 33.333 11.39 0.00 46.73 2.74
611 642 9.255304 GAATCACTCTTCACACTAGAATATTCC 57.745 37.037 11.92 0.00 0.00 3.01
654 686 7.406031 AAATAGTCATGACTCGAACCTTCTA 57.594 36.000 31.09 10.72 42.54 2.10
666 698 4.038763 TCGAACCTTCTAGAAGCTTGTTCA 59.961 41.667 31.01 22.52 37.16 3.18
667 699 4.387256 CGAACCTTCTAGAAGCTTGTTCAG 59.613 45.833 31.01 24.50 37.16 3.02
674 706 3.498774 AGAAGCTTGTTCAGTGGACAT 57.501 42.857 2.10 0.00 0.00 3.06
722 756 5.860941 ATCTCAAAGAAGCGGAGATAGAA 57.139 39.130 0.00 0.00 44.33 2.10
737 771 7.606349 CGGAGATAGAATGATATGGAAAGTGA 58.394 38.462 0.00 0.00 0.00 3.41
748 782 6.440647 TGATATGGAAAGTGAACAGTCCTAGT 59.559 38.462 4.62 0.00 0.00 2.57
755 789 4.130118 AGTGAACAGTCCTAGTGCAAAAG 58.870 43.478 0.00 0.00 0.00 2.27
786 820 6.537453 AAGACTAGCTGATCATACAACACT 57.463 37.500 0.00 0.00 0.00 3.55
911 950 2.683362 TGTGAGTGAGTATAGAGCCACG 59.317 50.000 0.00 0.00 34.93 4.94
1032 1071 3.620488 TGAAAGGAAGTGCAGTCTGTTT 58.380 40.909 0.93 0.00 0.00 2.83
1042 1081 3.673902 TGCAGTCTGTTTAATGCAGCTA 58.326 40.909 0.93 0.00 43.34 3.32
1256 1296 2.536761 GCAATGGGTATGCGGTACTA 57.463 50.000 0.00 0.00 33.57 1.82
1329 1369 4.249661 GGGCTTTAGTCTTCTCTGACTTG 58.750 47.826 2.44 0.00 44.01 3.16
1355 1395 5.796424 ATTTGCATATCCATCAGGTTTCC 57.204 39.130 0.00 0.00 35.89 3.13
1539 1579 6.575162 AACGAGCAATCATTTAAGGAAAGT 57.425 33.333 0.00 0.00 0.00 2.66
1597 1637 1.561542 CTGGCATTAACTCTCCCCTGT 59.438 52.381 0.00 0.00 0.00 4.00
1649 1689 2.637382 TGGTGCACCTCTGAAGAATGTA 59.363 45.455 34.75 8.56 36.82 2.29
1740 1781 1.073722 CTTGGTGAGAGCTGCCCAA 59.926 57.895 0.00 7.03 35.72 4.12
1749 1790 0.523519 GAGCTGCCCAAGTAAGTTGC 59.476 55.000 0.00 0.00 34.45 4.17
1754 1795 1.875963 CCCAAGTAAGTTGCTGCCG 59.124 57.895 0.00 0.00 34.45 5.69
1755 1796 0.605319 CCCAAGTAAGTTGCTGCCGA 60.605 55.000 0.00 0.00 34.45 5.54
1756 1797 1.453155 CCAAGTAAGTTGCTGCCGAT 58.547 50.000 0.00 0.00 34.45 4.18
1757 1798 2.627945 CCAAGTAAGTTGCTGCCGATA 58.372 47.619 0.00 0.00 34.45 2.92
1758 1799 2.351726 CCAAGTAAGTTGCTGCCGATAC 59.648 50.000 0.00 0.00 34.45 2.24
1760 1801 1.475280 AGTAAGTTGCTGCCGATACGA 59.525 47.619 0.00 0.00 0.00 3.43
1763 1804 0.530650 AGTTGCTGCCGATACGATGG 60.531 55.000 0.00 0.00 0.00 3.51
1765 1806 0.249447 TTGCTGCCGATACGATGGAG 60.249 55.000 0.00 0.00 0.00 3.86
1766 1807 2.024319 GCTGCCGATACGATGGAGC 61.024 63.158 0.00 0.00 0.00 4.70
1767 1808 1.373497 CTGCCGATACGATGGAGCC 60.373 63.158 0.00 0.00 0.00 4.70
1769 1810 2.657237 CCGATACGATGGAGCCCC 59.343 66.667 0.00 0.00 0.00 5.80
1770 1811 1.908793 CCGATACGATGGAGCCCCT 60.909 63.158 0.00 0.00 0.00 4.79
1771 1812 1.587054 CGATACGATGGAGCCCCTC 59.413 63.158 0.00 0.00 0.00 4.30
1785 1826 4.452733 CCTCCCGACCGTTGCCTC 62.453 72.222 0.00 0.00 0.00 4.70
1787 1828 3.649277 CTCCCGACCGTTGCCTCTG 62.649 68.421 0.00 0.00 0.00 3.35
1788 1829 4.760047 CCCGACCGTTGCCTCTGG 62.760 72.222 0.00 0.00 0.00 3.86
1899 1940 4.452733 CCCCTCCGTTGGCTCGAC 62.453 72.222 4.47 0.00 0.00 4.20
1900 1941 4.452733 CCCTCCGTTGGCTCGACC 62.453 72.222 4.47 0.00 39.84 4.79
1901 1942 3.382832 CCTCCGTTGGCTCGACCT 61.383 66.667 5.77 0.00 40.22 3.85
1902 1943 2.125912 CTCCGTTGGCTCGACCTG 60.126 66.667 5.77 0.00 40.22 4.00
1903 1944 4.373116 TCCGTTGGCTCGACCTGC 62.373 66.667 5.77 0.00 40.22 4.85
1922 1963 4.101448 CCTCCTGGGCCGACCTTG 62.101 72.222 0.00 0.00 41.11 3.61
1923 1964 4.785453 CTCCTGGGCCGACCTTGC 62.785 72.222 0.00 0.00 41.11 4.01
1963 2004 2.520260 GGGAGGCCCATCATGTGC 60.520 66.667 0.00 0.00 44.65 4.57
1964 2005 2.520260 GGAGGCCCATCATGTGCC 60.520 66.667 2.23 2.23 45.70 5.01
1970 2011 2.512286 CCATCATGTGCCGCGACT 60.512 61.111 8.23 0.00 0.00 4.18
1971 2012 2.705220 CATCATGTGCCGCGACTG 59.295 61.111 8.23 0.00 0.00 3.51
1972 2013 3.197790 ATCATGTGCCGCGACTGC 61.198 61.111 8.23 2.45 37.91 4.40
2007 2048 2.355956 GGTCCGGCCGATTCGATC 60.356 66.667 30.73 12.23 0.00 3.69
2008 2049 2.355956 GTCCGGCCGATTCGATCC 60.356 66.667 30.73 7.39 0.00 3.36
2009 2050 3.973516 TCCGGCCGATTCGATCCG 61.974 66.667 30.73 23.46 40.35 4.18
2013 2054 2.355956 GCCGATTCGATCCGTCCC 60.356 66.667 7.83 0.00 0.00 4.46
2014 2055 2.857744 GCCGATTCGATCCGTCCCT 61.858 63.158 7.83 0.00 0.00 4.20
2015 2056 1.007271 CCGATTCGATCCGTCCCTG 60.007 63.158 7.83 0.00 0.00 4.45
2016 2057 1.661821 CGATTCGATCCGTCCCTGC 60.662 63.158 0.00 0.00 0.00 4.85
2018 2059 0.598680 GATTCGATCCGTCCCTGCTG 60.599 60.000 0.00 0.00 0.00 4.41
2019 2060 2.032860 ATTCGATCCGTCCCTGCTGG 62.033 60.000 1.89 1.89 0.00 4.85
2020 2061 4.899239 CGATCCGTCCCTGCTGGC 62.899 72.222 3.63 0.00 0.00 4.85
2021 2062 4.899239 GATCCGTCCCTGCTGGCG 62.899 72.222 3.63 3.39 34.64 5.69
2073 2114 4.444838 CGGGACCGATCAACGCCA 62.445 66.667 4.40 0.00 42.83 5.69
2074 2115 2.818274 GGGACCGATCAACGCCAC 60.818 66.667 0.00 0.00 41.07 5.01
2075 2116 2.818274 GGACCGATCAACGCCACC 60.818 66.667 0.00 0.00 41.07 4.61
2076 2117 3.186047 GACCGATCAACGCCACCG 61.186 66.667 0.00 0.00 41.07 4.94
2131 2172 2.438434 GGTGATGCCTTGGGGTCG 60.438 66.667 0.00 0.00 34.45 4.79
2132 2173 3.134127 GTGATGCCTTGGGGTCGC 61.134 66.667 0.00 0.00 34.45 5.19
2133 2174 3.645660 TGATGCCTTGGGGTCGCA 61.646 61.111 0.00 0.00 36.84 5.10
2149 2704 4.900704 CATGCCCCATCCCGGTGG 62.901 72.222 0.00 1.56 39.05 4.61
2214 2769 3.393970 CGCTCTGGCCTCCTGGAA 61.394 66.667 3.32 0.00 34.57 3.53
2215 2770 2.588989 GCTCTGGCCTCCTGGAAG 59.411 66.667 3.32 0.00 34.57 3.46
2216 2771 2.297129 GCTCTGGCCTCCTGGAAGT 61.297 63.158 3.32 0.00 34.57 3.01
2217 2772 1.601171 CTCTGGCCTCCTGGAAGTG 59.399 63.158 3.32 0.00 34.57 3.16
2219 2774 3.635268 CTGGCCTCCTGGAAGTGCC 62.635 68.421 19.40 19.40 42.49 5.01
2221 2776 4.432741 GCCTCCTGGAAGTGCCCC 62.433 72.222 0.00 0.00 34.97 5.80
2222 2777 2.612115 CCTCCTGGAAGTGCCCCT 60.612 66.667 0.00 0.00 34.97 4.79
2223 2778 2.674220 CCTCCTGGAAGTGCCCCTC 61.674 68.421 0.00 0.00 34.97 4.30
2224 2779 3.003173 TCCTGGAAGTGCCCCTCG 61.003 66.667 0.00 0.00 34.97 4.63
2225 2780 3.322466 CCTGGAAGTGCCCCTCGT 61.322 66.667 0.00 0.00 34.97 4.18
2226 2781 2.266055 CTGGAAGTGCCCCTCGTC 59.734 66.667 0.00 0.00 34.97 4.20
2228 2783 4.452733 GGAAGTGCCCCTCGTCGG 62.453 72.222 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.636570 GCGAGGAGAAACTTTCCGCC 61.637 60.000 10.18 7.09 39.77 6.13
2 3 1.956620 GCGCGAGGAGAAACTTTCCG 61.957 60.000 12.10 0.00 39.77 4.30
3 4 0.670854 AGCGCGAGGAGAAACTTTCC 60.671 55.000 12.10 0.00 34.83 3.13
4 5 0.716666 GAGCGCGAGGAGAAACTTTC 59.283 55.000 12.10 0.00 0.00 2.62
5 6 1.009389 CGAGCGCGAGGAGAAACTTT 61.009 55.000 12.10 0.00 40.82 2.66
6 7 1.444553 CGAGCGCGAGGAGAAACTT 60.445 57.895 12.10 0.00 40.82 2.66
7 8 2.179517 CGAGCGCGAGGAGAAACT 59.820 61.111 12.10 0.00 40.82 2.66
8 9 2.881352 CCGAGCGCGAGGAGAAAC 60.881 66.667 12.10 0.00 40.82 2.78
9 10 4.796231 GCCGAGCGCGAGGAGAAA 62.796 66.667 24.74 0.00 40.82 2.52
19 20 4.821589 GGAGGACCTTGCCGAGCG 62.822 72.222 0.00 0.00 0.00 5.03
20 21 3.394836 AGGAGGACCTTGCCGAGC 61.395 66.667 0.00 0.00 45.36 5.03
29 30 0.978667 GAAGACCCAGGAGGAGGACC 60.979 65.000 0.00 0.00 39.89 4.46
30 31 0.252284 TGAAGACCCAGGAGGAGGAC 60.252 60.000 0.00 0.00 39.89 3.85
31 32 0.041833 CTGAAGACCCAGGAGGAGGA 59.958 60.000 0.00 0.00 39.89 3.71
32 33 2.601664 CTGAAGACCCAGGAGGAGG 58.398 63.158 0.00 0.00 39.89 4.30
39 40 4.785453 GCCGCCCTGAAGACCCAG 62.785 72.222 0.00 0.00 0.00 4.45
42 43 4.475135 GAGGCCGCCCTGAAGACC 62.475 72.222 5.55 0.00 43.12 3.85
43 44 4.821589 CGAGGCCGCCCTGAAGAC 62.822 72.222 5.55 0.00 43.12 3.01
57 58 4.436998 GTCCGGTCCCAGCACGAG 62.437 72.222 0.00 0.00 0.00 4.18
63 64 4.452733 GAAGCCGTCCGGTCCCAG 62.453 72.222 7.66 0.00 37.65 4.45
70 71 1.087771 AATAAAGCCGAAGCCGTCCG 61.088 55.000 0.00 0.00 41.25 4.79
71 72 0.377203 CAATAAAGCCGAAGCCGTCC 59.623 55.000 0.00 0.00 41.25 4.79
72 73 0.377203 CCAATAAAGCCGAAGCCGTC 59.623 55.000 0.00 0.00 41.25 4.79
73 74 1.654023 GCCAATAAAGCCGAAGCCGT 61.654 55.000 0.00 0.00 41.25 5.68
74 75 1.064134 GCCAATAAAGCCGAAGCCG 59.936 57.895 0.00 0.00 41.25 5.52
75 76 1.437573 GGCCAATAAAGCCGAAGCC 59.562 57.895 0.00 0.00 41.41 4.35
82 83 3.588955 CAAAGAGGTTGGCCAATAAAGC 58.411 45.455 23.66 9.09 37.19 3.51
83 84 3.588955 GCAAAGAGGTTGGCCAATAAAG 58.411 45.455 23.66 9.40 37.73 1.85
84 85 3.676291 GCAAAGAGGTTGGCCAATAAA 57.324 42.857 23.66 0.00 37.73 1.40
92 93 1.005215 AGGAGATGGCAAAGAGGTTGG 59.995 52.381 0.00 0.00 37.73 3.77
93 94 2.089980 CAGGAGATGGCAAAGAGGTTG 58.910 52.381 0.00 0.00 40.50 3.77
94 95 1.005215 CCAGGAGATGGCAAAGAGGTT 59.995 52.381 0.00 0.00 43.83 3.50
95 96 0.622665 CCAGGAGATGGCAAAGAGGT 59.377 55.000 0.00 0.00 43.83 3.85
96 97 3.491208 CCAGGAGATGGCAAAGAGG 57.509 57.895 0.00 0.00 43.83 3.69
105 106 0.914644 TTGAGAAGGCCCAGGAGATG 59.085 55.000 0.00 0.00 0.00 2.90
106 107 1.493871 CATTGAGAAGGCCCAGGAGAT 59.506 52.381 0.00 0.00 0.00 2.75
107 108 0.914644 CATTGAGAAGGCCCAGGAGA 59.085 55.000 0.00 0.00 0.00 3.71
108 109 0.622665 ACATTGAGAAGGCCCAGGAG 59.377 55.000 0.00 0.00 0.00 3.69
109 110 0.620556 GACATTGAGAAGGCCCAGGA 59.379 55.000 0.00 0.00 0.00 3.86
110 111 0.745845 CGACATTGAGAAGGCCCAGG 60.746 60.000 0.00 0.00 0.00 4.45
111 112 0.745845 CCGACATTGAGAAGGCCCAG 60.746 60.000 0.00 0.00 0.00 4.45
112 113 1.299648 CCGACATTGAGAAGGCCCA 59.700 57.895 0.00 0.00 0.00 5.36
113 114 2.115291 GCCGACATTGAGAAGGCCC 61.115 63.158 0.00 0.00 41.81 5.80
114 115 3.502572 GCCGACATTGAGAAGGCC 58.497 61.111 0.00 0.00 41.81 5.19
115 116 1.372087 CTGGCCGACATTGAGAAGGC 61.372 60.000 0.00 0.00 46.51 4.35
116 117 1.372087 GCTGGCCGACATTGAGAAGG 61.372 60.000 0.00 0.00 0.00 3.46
117 118 0.392193 AGCTGGCCGACATTGAGAAG 60.392 55.000 0.00 0.00 0.00 2.85
118 119 0.036732 AAGCTGGCCGACATTGAGAA 59.963 50.000 0.00 0.00 0.00 2.87
119 120 0.391661 GAAGCTGGCCGACATTGAGA 60.392 55.000 0.00 0.00 0.00 3.27
120 121 0.674581 TGAAGCTGGCCGACATTGAG 60.675 55.000 0.00 0.00 0.00 3.02
121 122 0.674581 CTGAAGCTGGCCGACATTGA 60.675 55.000 0.00 0.00 0.00 2.57
122 123 1.651240 CCTGAAGCTGGCCGACATTG 61.651 60.000 0.00 0.00 0.00 2.82
123 124 1.377725 CCTGAAGCTGGCCGACATT 60.378 57.895 0.00 0.00 0.00 2.71
124 125 2.270205 CCTGAAGCTGGCCGACAT 59.730 61.111 0.00 0.00 0.00 3.06
125 126 4.020617 CCCTGAAGCTGGCCGACA 62.021 66.667 0.00 0.00 0.00 4.35
131 132 4.093291 AGCTCGCCCTGAAGCTGG 62.093 66.667 0.00 0.00 36.15 4.85
132 133 2.511145 GAGCTCGCCCTGAAGCTG 60.511 66.667 0.00 0.00 37.79 4.24
133 134 3.780173 GGAGCTCGCCCTGAAGCT 61.780 66.667 7.83 0.00 40.68 3.74
134 135 4.087892 TGGAGCTCGCCCTGAAGC 62.088 66.667 7.83 0.00 0.00 3.86
135 136 2.125350 GTGGAGCTCGCCCTGAAG 60.125 66.667 7.83 0.00 0.00 3.02
136 137 3.706373 GGTGGAGCTCGCCCTGAA 61.706 66.667 7.83 0.00 40.09 3.02
141 142 4.803426 CGTGAGGTGGAGCTCGCC 62.803 72.222 15.69 15.69 46.19 5.54
153 154 2.743928 GAGCTGGCCAACCGTGAG 60.744 66.667 7.01 0.00 39.70 3.51
154 155 3.555324 TGAGCTGGCCAACCGTGA 61.555 61.111 7.01 0.00 39.70 4.35
155 156 3.357079 GTGAGCTGGCCAACCGTG 61.357 66.667 7.01 0.00 39.70 4.94
156 157 4.643387 GGTGAGCTGGCCAACCGT 62.643 66.667 7.01 0.00 39.70 4.83
158 159 3.971702 AGGGTGAGCTGGCCAACC 61.972 66.667 14.99 14.99 41.64 3.77
159 160 2.674380 CAGGGTGAGCTGGCCAAC 60.674 66.667 7.01 0.92 0.00 3.77
160 161 3.970410 CCAGGGTGAGCTGGCCAA 61.970 66.667 7.01 0.00 33.64 4.52
179 180 3.764466 AGGACGAGCTGAAGGCCG 61.764 66.667 0.00 0.00 43.05 6.13
180 181 2.125350 CAGGACGAGCTGAAGGCC 60.125 66.667 0.00 0.00 43.05 5.19
181 182 1.153667 CTCAGGACGAGCTGAAGGC 60.154 63.158 0.00 0.00 42.19 4.35
189 190 4.504916 CGCCAGGCTCAGGACGAG 62.505 72.222 10.54 0.00 45.37 4.18
192 193 3.706373 TTCCGCCAGGCTCAGGAC 61.706 66.667 10.54 0.00 37.47 3.85
193 194 3.706373 GTTCCGCCAGGCTCAGGA 61.706 66.667 10.54 6.12 37.47 3.86
194 195 4.785453 GGTTCCGCCAGGCTCAGG 62.785 72.222 10.54 3.35 37.47 3.86
195 196 4.020617 TGGTTCCGCCAGGCTCAG 62.021 66.667 10.54 0.00 43.61 3.35
206 207 3.959991 GAGGCGCAGGACTGGTTCC 62.960 68.421 10.83 0.00 46.33 3.62
207 208 2.435059 GAGGCGCAGGACTGGTTC 60.435 66.667 10.83 0.00 0.00 3.62
208 209 4.379243 CGAGGCGCAGGACTGGTT 62.379 66.667 10.83 0.00 0.00 3.67
235 236 2.050918 GATAGAGGAGGACTTTGGGGG 58.949 57.143 0.00 0.00 0.00 5.40
236 237 3.053359 AGATAGAGGAGGACTTTGGGG 57.947 52.381 0.00 0.00 0.00 4.96
237 238 4.294347 AGAAGATAGAGGAGGACTTTGGG 58.706 47.826 0.00 0.00 0.00 4.12
238 239 4.343814 GGAGAAGATAGAGGAGGACTTTGG 59.656 50.000 0.00 0.00 0.00 3.28
239 240 4.959210 TGGAGAAGATAGAGGAGGACTTTG 59.041 45.833 0.00 0.00 0.00 2.77
240 241 4.959839 GTGGAGAAGATAGAGGAGGACTTT 59.040 45.833 0.00 0.00 0.00 2.66
241 242 4.542697 GTGGAGAAGATAGAGGAGGACTT 58.457 47.826 0.00 0.00 0.00 3.01
242 243 3.117284 GGTGGAGAAGATAGAGGAGGACT 60.117 52.174 0.00 0.00 0.00 3.85
243 244 3.227614 GGTGGAGAAGATAGAGGAGGAC 58.772 54.545 0.00 0.00 0.00 3.85
244 245 2.859404 TGGTGGAGAAGATAGAGGAGGA 59.141 50.000 0.00 0.00 0.00 3.71
245 246 2.962421 GTGGTGGAGAAGATAGAGGAGG 59.038 54.545 0.00 0.00 0.00 4.30
246 247 2.962421 GGTGGTGGAGAAGATAGAGGAG 59.038 54.545 0.00 0.00 0.00 3.69
247 248 2.687014 CGGTGGTGGAGAAGATAGAGGA 60.687 54.545 0.00 0.00 0.00 3.71
248 249 1.683917 CGGTGGTGGAGAAGATAGAGG 59.316 57.143 0.00 0.00 0.00 3.69
249 250 1.067821 GCGGTGGTGGAGAAGATAGAG 59.932 57.143 0.00 0.00 0.00 2.43
250 251 1.112113 GCGGTGGTGGAGAAGATAGA 58.888 55.000 0.00 0.00 0.00 1.98
251 252 0.105039 GGCGGTGGTGGAGAAGATAG 59.895 60.000 0.00 0.00 0.00 2.08
252 253 1.672854 CGGCGGTGGTGGAGAAGATA 61.673 60.000 0.00 0.00 0.00 1.98
253 254 2.990479 GGCGGTGGTGGAGAAGAT 59.010 61.111 0.00 0.00 0.00 2.40
254 255 3.691342 CGGCGGTGGTGGAGAAGA 61.691 66.667 0.00 0.00 0.00 2.87
255 256 3.934391 GACGGCGGTGGTGGAGAAG 62.934 68.421 13.24 0.00 0.00 2.85
256 257 3.998672 GACGGCGGTGGTGGAGAA 61.999 66.667 13.24 0.00 0.00 2.87
259 260 4.682334 TAGGACGGCGGTGGTGGA 62.682 66.667 13.24 0.00 0.00 4.02
260 261 4.143333 CTAGGACGGCGGTGGTGG 62.143 72.222 13.24 0.00 0.00 4.61
261 262 2.642254 TTCTAGGACGGCGGTGGTG 61.642 63.158 13.24 0.00 0.00 4.17
262 263 2.283388 TTCTAGGACGGCGGTGGT 60.283 61.111 13.24 0.00 0.00 4.16
263 264 2.183555 GTTCTAGGACGGCGGTGG 59.816 66.667 13.24 0.00 0.00 4.61
264 265 1.153823 CAGTTCTAGGACGGCGGTG 60.154 63.158 13.24 0.00 0.00 4.94
265 266 1.183676 AACAGTTCTAGGACGGCGGT 61.184 55.000 13.24 0.00 0.00 5.68
266 267 0.736325 CAACAGTTCTAGGACGGCGG 60.736 60.000 13.24 0.00 0.00 6.13
267 268 0.038526 ACAACAGTTCTAGGACGGCG 60.039 55.000 4.80 4.80 0.00 6.46
268 269 1.672145 GGACAACAGTTCTAGGACGGC 60.672 57.143 0.59 0.00 0.00 5.68
269 270 1.893801 AGGACAACAGTTCTAGGACGG 59.106 52.381 0.00 0.00 0.00 4.79
270 271 3.243771 ACAAGGACAACAGTTCTAGGACG 60.244 47.826 0.00 0.00 0.00 4.79
271 272 4.338379 ACAAGGACAACAGTTCTAGGAC 57.662 45.455 0.00 0.00 0.00 3.85
272 273 5.367945 AAACAAGGACAACAGTTCTAGGA 57.632 39.130 0.00 0.00 0.00 2.94
273 274 6.990349 TCTTAAACAAGGACAACAGTTCTAGG 59.010 38.462 0.00 0.00 0.00 3.02
274 275 8.433421 TTCTTAAACAAGGACAACAGTTCTAG 57.567 34.615 0.00 0.00 0.00 2.43
287 288 9.369904 CCCATCACAAAATATTCTTAAACAAGG 57.630 33.333 0.00 0.00 0.00 3.61
300 302 7.730084 TCATGTCAAAAACCCATCACAAAATA 58.270 30.769 0.00 0.00 0.00 1.40
325 327 2.009774 GCGACTGCCATAACAGAACAT 58.990 47.619 0.00 0.00 40.25 2.71
334 336 1.613925 GATGTAGGAGCGACTGCCATA 59.386 52.381 0.00 0.00 44.31 2.74
337 339 0.249238 CTGATGTAGGAGCGACTGCC 60.249 60.000 0.00 0.00 44.31 4.85
343 345 3.637432 GAGATGAACTGATGTAGGAGCG 58.363 50.000 0.00 0.00 0.00 5.03
344 346 3.067461 ACGAGATGAACTGATGTAGGAGC 59.933 47.826 0.00 0.00 0.00 4.70
347 349 6.473778 CACTAAACGAGATGAACTGATGTAGG 59.526 42.308 0.00 0.00 0.00 3.18
461 480 7.543756 TCTTGTTCTTTCAGGAAAACGAATTT 58.456 30.769 0.00 0.00 0.00 1.82
482 509 4.582701 TGGTGTTGCCTGTATTTTCTTG 57.417 40.909 0.00 0.00 38.35 3.02
496 526 4.144297 CCCATCCCATATAGTTGGTGTTG 58.856 47.826 0.00 0.00 34.77 3.33
506 536 8.003564 TCTGTACTAGTAACCCATCCCATATA 57.996 38.462 3.61 0.00 0.00 0.86
623 654 7.308348 GGTTCGAGTCATGACTATTTCCAAAAA 60.308 37.037 27.95 9.15 42.66 1.94
624 655 6.148811 GGTTCGAGTCATGACTATTTCCAAAA 59.851 38.462 27.95 9.62 42.66 2.44
625 656 5.642063 GGTTCGAGTCATGACTATTTCCAAA 59.358 40.000 27.95 11.48 42.66 3.28
626 657 5.046591 AGGTTCGAGTCATGACTATTTCCAA 60.047 40.000 27.95 8.41 42.66 3.53
627 658 4.466370 AGGTTCGAGTCATGACTATTTCCA 59.534 41.667 27.95 6.92 42.66 3.53
628 659 5.012328 AGGTTCGAGTCATGACTATTTCC 57.988 43.478 27.95 24.07 42.66 3.13
629 660 6.334202 AGAAGGTTCGAGTCATGACTATTTC 58.666 40.000 27.95 21.01 42.66 2.17
630 661 6.287589 AGAAGGTTCGAGTCATGACTATTT 57.712 37.500 27.95 14.97 42.66 1.40
631 662 5.923733 AGAAGGTTCGAGTCATGACTATT 57.076 39.130 27.95 15.02 42.66 1.73
632 663 6.358178 TCTAGAAGGTTCGAGTCATGACTAT 58.642 40.000 27.95 7.92 42.66 2.12
637 668 4.109050 GCTTCTAGAAGGTTCGAGTCATG 58.891 47.826 29.22 5.09 38.80 3.07
654 686 3.498774 ATGTCCACTGAACAAGCTTCT 57.501 42.857 0.00 0.00 0.00 2.85
666 698 3.030291 TGGTTCAGCAAAAATGTCCACT 58.970 40.909 0.00 0.00 0.00 4.00
667 699 3.068024 TCTGGTTCAGCAAAAATGTCCAC 59.932 43.478 0.00 0.00 0.00 4.02
674 706 4.771590 CTGCTATCTGGTTCAGCAAAAA 57.228 40.909 0.00 0.00 44.21 1.94
722 756 6.319048 AGGACTGTTCACTTTCCATATCAT 57.681 37.500 0.00 0.00 0.00 2.45
748 782 4.396166 GCTAGTCTTATCAAGGCTTTTGCA 59.604 41.667 0.00 0.00 41.62 4.08
755 789 5.207110 TGATCAGCTAGTCTTATCAAGGC 57.793 43.478 0.00 0.00 33.70 4.35
786 820 0.947180 GCGCGTTCTTTGGTGTAGGA 60.947 55.000 8.43 0.00 0.00 2.94
831 865 3.380004 TGGCAACCAAACAAACTGACTAG 59.620 43.478 0.00 0.00 0.00 2.57
1009 1048 2.171448 ACAGACTGCACTTCCTTTCAGT 59.829 45.455 1.25 0.00 41.90 3.41
1042 1081 3.705051 ACAATCTCATTGGTGCAATCCT 58.295 40.909 0.00 0.00 44.42 3.24
1256 1296 5.340027 CCAGTTTATAGGGGTCCATCACTTT 60.340 44.000 0.00 0.00 0.00 2.66
1329 1369 8.031277 GGAAACCTGATGGATATGCAAATATTC 58.969 37.037 0.00 2.29 37.04 1.75
1355 1395 5.006386 ACAGCCTCACTAGAAAAATTCCAG 58.994 41.667 0.00 0.00 0.00 3.86
1364 1404 4.415881 TCAAACAACAGCCTCACTAGAA 57.584 40.909 0.00 0.00 0.00 2.10
1367 1407 5.804639 ACATATCAAACAACAGCCTCACTA 58.195 37.500 0.00 0.00 0.00 2.74
1515 1555 6.981722 ACTTTCCTTAAATGATTGCTCGTTT 58.018 32.000 0.00 0.00 42.08 3.60
1539 1579 5.250543 TGATGGTTTTGAGAATCTCCAGGTA 59.749 40.000 7.91 0.00 34.92 3.08
1597 1637 4.030913 ACACTACTTATGGGAAGCAGCTA 58.969 43.478 0.00 0.00 0.00 3.32
1649 1689 5.417811 TCACAAACATCACAAATGCACTTT 58.582 33.333 0.00 0.00 0.00 2.66
1740 1781 1.475280 TCGTATCGGCAGCAACTTACT 59.525 47.619 0.00 0.00 0.00 2.24
1749 1790 1.373497 GGCTCCATCGTATCGGCAG 60.373 63.158 0.00 0.00 0.00 4.85
1769 1810 3.382832 AGAGGCAACGGTCGGGAG 61.383 66.667 0.00 0.00 46.39 4.30
1770 1811 3.691342 CAGAGGCAACGGTCGGGA 61.691 66.667 0.00 0.00 46.39 5.14
1771 1812 4.760047 CCAGAGGCAACGGTCGGG 62.760 72.222 0.00 0.00 46.39 5.14
1882 1923 4.452733 GTCGAGCCAACGGAGGGG 62.453 72.222 0.00 0.00 0.00 4.79
1883 1924 4.452733 GGTCGAGCCAACGGAGGG 62.453 72.222 2.39 0.00 37.17 4.30
1885 1926 2.125912 CAGGTCGAGCCAACGGAG 60.126 66.667 11.73 0.00 40.61 4.63
1886 1927 4.373116 GCAGGTCGAGCCAACGGA 62.373 66.667 11.73 0.00 40.61 4.69
1894 1935 4.504916 CAGGAGGCGCAGGTCGAG 62.505 72.222 10.83 0.00 41.67 4.04
1905 1946 4.101448 CAAGGTCGGCCCAGGAGG 62.101 72.222 0.08 0.00 39.47 4.30
1906 1947 4.785453 GCAAGGTCGGCCCAGGAG 62.785 72.222 0.08 0.00 34.66 3.69
1923 1964 4.907034 CGATGTCGTCGGCCTCGG 62.907 72.222 15.47 0.00 46.47 4.63
1946 1987 2.520260 GCACATGATGGGCCTCCC 60.520 66.667 8.85 0.00 41.97 4.30
1954 1995 2.705220 CAGTCGCGGCACATGATG 59.295 61.111 15.58 0.00 0.00 3.07
1955 1996 3.197790 GCAGTCGCGGCACATGAT 61.198 61.111 15.58 0.00 0.00 2.45
1990 2031 2.355956 GATCGAATCGGCCGGACC 60.356 66.667 27.83 13.23 0.00 4.46
1991 2032 2.355956 GGATCGAATCGGCCGGAC 60.356 66.667 27.83 15.63 0.00 4.79
1994 2035 2.729862 GACGGATCGAATCGGCCG 60.730 66.667 26.67 26.67 45.13 6.13
1998 2039 1.661821 GCAGGGACGGATCGAATCG 60.662 63.158 0.00 0.00 0.00 3.34
1999 2040 0.598680 CAGCAGGGACGGATCGAATC 60.599 60.000 0.00 0.00 0.00 2.52
2001 2042 2.721167 CCAGCAGGGACGGATCGAA 61.721 63.158 0.00 0.00 40.01 3.71
2002 2043 3.147595 CCAGCAGGGACGGATCGA 61.148 66.667 0.00 0.00 40.01 3.59
2003 2044 4.899239 GCCAGCAGGGACGGATCG 62.899 72.222 0.00 0.00 40.01 3.69
2004 2045 4.899239 CGCCAGCAGGGACGGATC 62.899 72.222 0.00 0.00 40.01 3.36
2013 2054 4.537433 GAGTAGGGCCGCCAGCAG 62.537 72.222 12.58 0.00 46.50 4.24
2056 2097 4.444838 TGGCGTTGATCGGTCCCG 62.445 66.667 0.00 0.00 40.26 5.14
2057 2098 2.818274 GTGGCGTTGATCGGTCCC 60.818 66.667 0.00 0.00 40.26 4.46
2059 2100 3.186047 CGGTGGCGTTGATCGGTC 61.186 66.667 0.00 0.00 40.26 4.79
2060 2101 4.752879 CCGGTGGCGTTGATCGGT 62.753 66.667 0.00 0.00 40.26 4.69
2103 2144 2.106683 GCATCACCTTTCGGACCCG 61.107 63.158 1.31 1.31 41.35 5.28
2104 2145 1.749258 GGCATCACCTTTCGGACCC 60.749 63.158 0.00 0.00 34.51 4.46
2105 2146 3.905249 GGCATCACCTTTCGGACC 58.095 61.111 0.00 0.00 34.51 4.46
2115 2156 3.134127 GCGACCCCAAGGCATCAC 61.134 66.667 0.00 0.00 36.11 3.06
2116 2157 2.982643 ATGCGACCCCAAGGCATCA 61.983 57.895 0.00 0.00 43.46 3.07
2117 2158 2.124151 ATGCGACCCCAAGGCATC 60.124 61.111 0.00 0.00 43.46 3.91
2132 2173 4.900704 CCACCGGGATGGGGCATG 62.901 72.222 6.32 0.00 41.26 4.06
2197 2752 3.382803 CTTCCAGGAGGCCAGAGCG 62.383 68.421 5.01 0.00 41.24 5.03
2199 2754 1.601171 CACTTCCAGGAGGCCAGAG 59.399 63.158 5.01 0.00 33.74 3.35
2200 2755 2.596851 GCACTTCCAGGAGGCCAGA 61.597 63.158 5.01 0.00 33.74 3.86
2201 2756 2.045536 GCACTTCCAGGAGGCCAG 60.046 66.667 5.01 0.00 33.74 4.85
2202 2757 3.650950 GGCACTTCCAGGAGGCCA 61.651 66.667 19.16 0.00 44.01 5.36
2203 2758 4.432741 GGGCACTTCCAGGAGGCC 62.433 72.222 16.86 16.86 43.86 5.19
2205 2760 2.612115 AGGGGCACTTCCAGGAGG 60.612 66.667 0.00 0.00 36.21 4.30
2207 2762 3.003173 CGAGGGGCACTTCCAGGA 61.003 66.667 0.00 0.00 36.21 3.86
2208 2763 3.316573 GACGAGGGGCACTTCCAGG 62.317 68.421 0.00 0.00 36.21 4.45
2209 2764 2.266055 GACGAGGGGCACTTCCAG 59.734 66.667 0.00 0.00 36.21 3.86
2210 2765 3.691342 CGACGAGGGGCACTTCCA 61.691 66.667 0.00 0.00 36.21 3.53
2211 2766 4.452733 CCGACGAGGGGCACTTCC 62.453 72.222 0.00 0.00 35.97 3.46


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

AutoCloner maintained by Alex Coulton.